Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009572.1 Hibiscus syriacus cultivar Beakdansim tig00116937_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: 2529503
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 13
Found at i:2156856 original size:33 final size:32
Alignment explanation
Indices: 2156809--2156925 Score: 164
Period size: 33 Copynumber: 3.6 Consensus size: 32
2156799 CGCATTTCGA
2156809 TTTCATTTCGCGTTGCGATTCCCTCGTTGCAAT
1 TTTCATTTCGCGTTGCGATT-CCTCGTTGCAAT
* *
2156842 TTTCATTTCACGTTGCGATT-CTCGTTGCGAT
1 TTTCATTTCGCGTTGCGATTCCTCGTTGCAAT
2156873 TTTCATTTCGCGTTGCGATTCTCTCGTTGCAAT
1 TTTCATTTCGCGTTGCGATTC-CTCGTTGCAAT
**
2156906 AGTCATTTCTGCGTTGCGAT
1 TTTCATTTC-GCGTTGCGAT
2156926 AGTCATTCTC
Statistics
Matches: 75, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
31 29 0.39
33 36 0.48
34 10 0.13
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.44
Consensus pattern (32 bp):
TTTCATTTCGCGTTGCGATTCCTCGTTGCAAT
Found at i:2156952 original size:20 final size:20
Alignment explanation
Indices: 2156890--2156945 Score: 87
Period size: 20 Copynumber: 2.8 Consensus size: 20
2156880 TCGCGTTGCG
*
2156890 ATTCTCTCGTTGCAATAGTC
1 ATTCTCTCGTTGCGATAGTC
2156910 ATT-TCTGCGTTGCGATAGTC
1 ATTCTCT-CGTTGCGATAGTC
2156930 ATTCTCTCGTTGCGAT
1 ATTCTCTCGTTGCGAT
2156946 TTTCATTTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
19 3 0.09
20 27 0.82
21 3 0.09
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.41
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATAGTC
Found at i:2158491 original size:123 final size:123
Alignment explanation
Indices: 2158272--2158514 Score: 470
Period size: 123 Copynumber: 2.0 Consensus size: 123
2158262 TCGAGCTCTT
2158272 CTTCACCATCACCTCATGATAGGCGACCAGCAAAGATGCCACGATTCTATCTCCCTGTTCTCCAC
1 CTTCACCATCACCTCATGATAGGCGACCAGCAAAGATGCCACGATTCTATCTCCCTGTTCTCCAC
2158337 CTCCACCTCCACGGGATGAGTCAAGGGAGTTACGTGATGAGGTCAATGCCTTGCGTGA
66 CTCCACCTCCACGGGATGAGTCAAGGGAGTTACGTGATGAGGTCAATGCCTTGCGTGA
2158395 CTTCACCATCACCTCATGATAGGCGACCAGCAAAGATGCCACGACTTCTATCTCCCTGTTCTCCA
1 CTTCACCATCACCTCATGATAGGCGACCAGCAAAGATGCCACGA-TTCTATCTCCCTGTTCTCCA
2158460 CCT-CACCTCCACGGGATGAGTCAAGGGAGTTACGTGATGAGGTCAATGCCTTGCG
65 CCTCCACCTCCACGGGATGAGTCAAGGGAGTTACGTGATGAGGTCAATGCCTTGCG
2158515 AGGAGATCGG
Statistics
Matches: 119, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
123 96 0.81
124 23 0.19
ACGTcount: A:0.23, C:0.31, G:0.22, T:0.23
Consensus pattern (123 bp):
CTTCACCATCACCTCATGATAGGCGACCAGCAAAGATGCCACGATTCTATCTCCCTGTTCTCCAC
CTCCACCTCCACGGGATGAGTCAAGGGAGTTACGTGATGAGGTCAATGCCTTGCGTGA
Found at i:2158889 original size:94 final size:93
Alignment explanation
Indices: 2158727--2159091 Score: 536
Period size: 94 Copynumber: 4.0 Consensus size: 93
2158717 GATTGCTTAG
* *
2158727 AAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTA-TCTTTAACACTGTGAAGTTAGTATT
1 AAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATT
2158791 TGTCTTTTGTTTTGTCTTTTGATTGAAGT
66 TGTC-TTTGTTTTGTCTTTTGATTGAAGT
2158820 AAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATT
1 AAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATT
*
2158885 TGTC--T-TTTAG----TTGA---AAGT
66 TGTCTTTGTTTTGTCTTTTGATTGAAGT
* * * *
2158903 AAATTTGTTTGGTTGCTGCCAATTCTGCTAAATTGTGTATTCTTTAACATTGTGAAGTTAGTATT
1 AAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATT
*
2158968 TGTCTTTGTTTTGTCTTTTGGTTGAAAGT
66 TGTCTTTGTTTTGTCTTTTGATTG-AAGT
* *
2158997 AAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGTATT
1 AAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATT
*
2159062 TGTCTTTGTTTTGTCTTTTGGTTGAAGT
66 TGTCTTTGTTTTGTCTTTTGATTGAAGT
2159090 AA
1 AA
2159092 TACAATCCAT
Statistics
Matches: 245, Mismatches: 15, Indels: 24
0.86 0.05 0.08
Matches are distributed among these distances:
83 69 0.28
85 1 0.00
86 8 0.03
90 7 0.03
91 1 0.00
93 43 0.18
94 116 0.47
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.47
Consensus pattern (93 bp):
AAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATT
TGTCTTTGTTTTGTCTTTTGATTGAAGT
Found at i:2159032 original size:177 final size:176
Alignment explanation
Indices: 2158727--2159068 Score: 578
Period size: 177 Copynumber: 1.9 Consensus size: 176
2158717 GATTGCTTAG
*
2158727 AAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATCTTTAACACTGTGAAGTTAGTATTT
1 AAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTGTATCTTTAACACTGTGAAGTTAGTATTT
2158792 GTCTTTTGTTTTGTCTTTTGATTGAAGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTG
66 GTCTTTTGTTTTGTCTTTTGATTGAAGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTG
*
2158857 TATTCTTTAACACTGTGAAGTTAGTATTTGTCTTTTAGTTGAAAGT
131 TATTCTTTAACACTCTGAAGTTAGTATTTGTCTTTTAGTTGAAAGT
* * * * *
2158903 AAATTTGTTTGGTTGCTGCCAATTCTGCTAAATTGTGTATTCTTTAACATTGTGAAGTTAGTATT
1 AAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTGTA-TCTTTAACACTGTGAAGTTAGTATT
*
2158968 TGTC-TTTGTTTTGTCTTTTGGTTGAAAGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTG
65 TGTCTTTTGTTTTGTCTTTTGATTG-AAGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTG
*
2159032 TGTATTCTTTAATACTCTGAAGTTAGTATTTGTCTTT
129 TGTATTCTTTAACACTCTGAAGTTAGTATTTGTCTTT
2159069 GTTTTGTCTT
Statistics
Matches: 155, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
176 53 0.34
177 102 0.66
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.47
Consensus pattern (176 bp):
AAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTGTATCTTTAACACTGTGAAGTTAGTATTT
GTCTTTTGTTTTGTCTTTTGATTGAAGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTG
TATTCTTTAACACTCTGAAGTTAGTATTTGTCTTTTAGTTGAAAGT
Found at i:2159309 original size:19 final size:19
Alignment explanation
Indices: 2159139--2159299 Score: 138
Period size: 19 Copynumber: 8.7 Consensus size: 19
2159129 TAGTTTACTT
* *
2159139 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
* **
2159159 TCGCAACGTGAAAAATGACTA
1 TCGCAACGCG--AAATGAAAA
2159180 TCGCAACGCGAAATG--AA
1 TCGCAACGCGAAATGAAAA
*
2159197 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
* *
2159211 TCACAACGAGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
2159230 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
2159249 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
* **
2159268 TCGCAACGTGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
*
2159287 TCGCAATGCGAAA
1 TCGCAACGCGAAA
2159300 CTATAATCGC
Statistics
Matches: 115, Mismatches: 17, Indels: 19
0.76 0.11 0.13
Matches are distributed among these distances:
12 1 0.01
13 1 0.01
14 7 0.06
15 2 0.02
16 1 0.01
17 7 0.06
18 1 0.01
19 72 0.63
20 8 0.07
21 12 0.10
22 3 0.03
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:2159369 original size:20 final size:20
Alignment explanation
Indices: 2159344--2159430 Score: 129
Period size: 20 Copynumber: 4.3 Consensus size: 20
2159334 GATTCTCTCG
**
2159344 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
* *
2159364 TTGCGATAGTCATTTTTGTA
1 TTGCGATAGTCATTTTCGCA
2159384 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
2159404 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
2159424 TTGCGAT
1 TTGCGAT
2159431 TTTAAGTTTC
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.40
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:2159953 original size:18 final size:19
Alignment explanation
Indices: 2159914--2159955 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
2159904 CTCACCTGTC
2159914 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
2159935 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
2159953 ATC
1 ATC
2159956 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:2160009 original size:42 final size:42
Alignment explanation
Indices: 2159939--2160030 Score: 98
Period size: 42 Copynumber: 2.2 Consensus size: 42
2159929 TCCCCTATCG
*
2159939 TTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCC-CTCCAACCA
1 TTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTC-CCAA-CA
* ** *
2159981 TTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCAACA
1 TTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCAACA
*
2160023 TTCTAGAG
1 TTCAAGAG
2160031 CTCGATTCAC
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
42 32 0.76
43 9 0.21
44 1 0.02
ACGTcount: A:0.26, C:0.35, G:0.17, T:0.22
Consensus pattern (42 bp):
TTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCAACA
Found at i:2161389 original size:14 final size:14
Alignment explanation
Indices: 2161370--2161405 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2161360 ATTGTTTAAT
2161370 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
2161384 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
2161398 TGATTTGT
1 TGATTTGT
2161406 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2161999 original size:20 final size:20
Alignment explanation
Indices: 2161968--2162297 Score: 303
Period size: 20 Copynumber: 16.5 Consensus size: 20
2161958 GTCAGAATCT
* *
2161968 CGTTGTGATTTACATATTCG
1 CGTTGCGATTTACGTATTCG
*
2161988 CATTGCGATTTACGTATTCG
1 CGTTGCGATTTACGTATTCG
*
2162008 CATTGCGATTTACGTATTCG
1 CGTTGCGATTTACGTATTCG
* *
2162028 CATTGCGATTTACGTAATCG
1 CGTTGCGATTTACGTATTCG
* *
2162048 CATTGCGATTTACGTAAT--
1 CGTTGCGATTTACGTATTCG
* *
2162066 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGTATTCG
* *
2162086 CATTGCGATTTACGTATTCT
1 CGTTGCGATTTACGTATTCG
*
2162106 CGTTGCGATTTACAG-ATACG
1 CGTTGCGATTTAC-GTATTCG
*
2162126 CGTTGCGATTTACGTATTCT
1 CGTTGCGATTTACGTATTCG
* *
2162146 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGTATTCG
2162166 CGTTGCGATTTTACGTATT-G
1 CGTTGCGA-TTTACGTATTCG
* * *
2162186 TCGTTGCAATTTACGGATACG
1 -CGTTGCGATTTACGTATTCG
* * *
2162207 CGTTGCGATTTTACGGATACT
1 CGTTGCGA-TTTACGTATTCG
* *
2162228 CGTTGCGATAGT-CAG-AATCG
1 CGTTGCGAT-TTAC-GTATTCG
** *
2162248 CGTTGCGATTTATATGTTCG
1 CGTTGCGATTTACGTATTCG
* *
2162268 CGTTGCGATTTTCATATTCG
1 CGTTGCGATTTACGTATTCG
2162288 CGTTGCGATT
1 CGTTGCGATT
2162298 CTGAAAAATC
Statistics
Matches: 259, Mismatches: 39, Indels: 24
0.80 0.12 0.07
Matches are distributed among these distances:
18 14 0.05
19 2 0.01
20 205 0.79
21 38 0.15
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (20 bp):
CGTTGCGATTTACGTATTCG
Found at i:2162077 original size:98 final size:100
Alignment explanation
Indices: 2161967--2162236 Score: 296
Period size: 98 Copynumber: 2.7 Consensus size: 100
2161957 AGTCAGAATC
* * * *
2161967 TCGTTGTGATTTACATATTCGCATTGCGATTTACGTATTCGCATTGCGATTTAC-GTATTCGCAT
1 TCGTTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCGTTGCGATTTACAG-ATACGCAT
2162031 TGCGATTTACGTAATCGCATTGCGATTTAC-G-TAA
65 TGCGATTTACGTAATCGCATTGCGATTTACGGATAA
* * * *
2162065 TCGTTGCGATTTACGGATACGCATTGCGATTTACGTATTCTCGTTGCGATTTACAGATACGCGTT
1 TCGTTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCGTTGCGATTTACAGATACGCATT
* * * *
2162130 GCGATTTACGTATTCTCGTTGCGATTTACGGATAC
66 GCGATTTACGTAATCGCATTGCGATTTACGGATAA
* * * * * * *
2162165 GCGTTGCGATTTTACGTATT-GTCGTTGCAATTTACGGATACGCGTTGCGATTTTACGGATACTC
1 TCGTTGCGA-TTTACGTATTCG-CATTGCGATTTACGTATTCGCGTTGCGA-TTTACAGATACGC
*
2162229 GTTGCGAT
63 ATTGCGAT
2162237 AGTCAGAATC
Statistics
Matches: 144, Mismatches: 22, Indels: 8
0.83 0.13 0.05
Matches are distributed among these distances:
98 81 0.56
99 2 0.01
100 11 0.08
101 31 0.22
102 19 0.13
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (100 bp):
TCGTTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCGTTGCGATTTACAGATACGCATT
GCGATTTACGTAATCGCATTGCGATTTACGGATAA
Found at i:2162088 original size:78 final size:78
Alignment explanation
Indices: 2161990--2162297 Score: 313
Period size: 81 Copynumber: 3.9 Consensus size: 78
2161980 CATATTCGCA
* * * *
2161990 TTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTAAT-CGCATTGC
1 TTGCGATTTACGGATACGCATTGCGATTTACGTATTCGCGTTGCGATTTACG-AATACGCGTTGC
*
2162054 GATTTACGTAATCG
65 GATTTACGTACTCG
*
2162068 TTGCGATTTACGGATACGCATTGCGATTTACGTATTCTCGTTGCGATTTAC-AGATACGCGTTGC
1 TTGCGATTTACGGATACGCATTGCGATTTACGTATTCGCGTTGCGATTTACGA-ATACGCGTTGC
2162132 GATTTACGTATTCTCG
65 GATTTACGTA--CTCG
* * *
2162148 TTGCGATTTACGGATACGCGTTGCGATTTTACGTATT-GTCGTTGCAATTTACGGATACGCGTTG
1 TTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCG-CGTTGCGATTTACGAATACGCGTTG
2162212 CGATTTTACGGATACTCG
64 CGA-TTTAC-G-TACTCG
* * * ** * * *
2162230 TTGCGATAGT-CAGA-ATCGCGTTGCGATTTATATGTTCGCGTTGCGATTTTC-ATATTCGCGTT
1 TTGCGAT-TTACGGATA-CGCATTGCGATTTACGTATTCGCGTTGCGATTTACGA-ATACGCGTT
2162292 GCGATT
63 GCGATT
2162298 CTGAAAAATC
Statistics
Matches: 197, Mismatches: 19, Indels: 26
0.81 0.08 0.11
Matches are distributed among these distances:
76 1 0.01
77 2 0.01
78 64 0.32
80 30 0.15
81 66 0.34
82 30 0.15
83 2 0.01
84 2 0.01
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (78 bp):
TTGCGATTTACGGATACGCATTGCGATTTACGTATTCGCGTTGCGATTTACGAATACGCGTTGCG
ATTTACGTACTCG
Found at i:2162358 original size:42 final size:42
Alignment explanation
Indices: 2162265--2162358 Score: 95
Period size: 42 Copynumber: 2.3 Consensus size: 42
2162255 ATTTATATGT
*
2162265 TCGCGTTGCG-ATTTTCATATTCGCGTTGCGATTCTGAAAAA
1 TCGCGTTGCGAATTTTCATATTCGCATTGCGATTCTGAAAAA
** ** *
2162306 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTCTTCATAA
1 TCGCGTTGCGAATTT-TCA-TATTCGCATTGCGATTCTGAAAAA
2162348 TCGCGTTGCGA
1 TCGCGTTGCGA
2162359 TTCTGGGAAC
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
41 8 0.19
42 31 0.74
43 3 0.07
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.35
Consensus pattern (42 bp):
TCGCGTTGCGAATTTTCATATTCGCATTGCGATTCTGAAAAA
Found at i:2162396 original size:20 final size:19
Alignment explanation
Indices: 2162347--2162400 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
2162337 ATTCTTCATA
2162347 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
2162366 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
2162387 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
2162401 TTTATTTCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:2164704 original size:17 final size:19
Alignment explanation
Indices: 2164682--2164717 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
2164672 TCTCAAAGTG
2164682 TGATCCTT-A-TTTTAAAT
1 TGATCCTTAACTTTTAAAT
2164699 TGATCCTTAACTTTTAAAT
1 TGATCCTTAACTTTTAAAT
2164718 GTTTCAATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 1 0.06
19 8 0.47
ACGTcount: A:0.31, C:0.14, G:0.06, T:0.50
Consensus pattern (19 bp):
TGATCCTTAACTTTTAAAT
Found at i:2164980 original size:59 final size:58
Alignment explanation
Indices: 2164917--2165073 Score: 194
Period size: 59 Copynumber: 2.7 Consensus size: 58
2164907 GATGAATTTG
* ** *
2164917 GGGATGAAATTTGAATATTCAAAAGGTTGGAGACTAATTTAGAAAG-AGGTCATAGTTT
1 GGGATGAAATTAGAATATTCAAAA-GTTTAAGACTAATTTAGAAAGAAAGTCATAGTTT
* * *
2164975 AGGGATGAAATTAGAATGTTCAATAGTTTAAGGACTAATTTAGAATGAAAGTCATAGTTT
1 -GGGATGAAATTAGAATATTCAAAAGTTTAA-GACTAATTTAGAAAGAAAGTCATAGTTT
2165035 GTGGATG--ATTAGAATATTCAAAAGTTTAAGACTAATTTA
1 G-GGATGAAATTAGAATATTCAAAAGTTTAAGACTAATTTA
2165074 AAATGAGAGT
Statistics
Matches: 86, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
57 10 0.12
58 24 0.28
59 36 0.42
60 16 0.19
ACGTcount: A:0.39, C:0.05, G:0.22, T:0.33
Consensus pattern (58 bp):
GGGATGAAATTAGAATATTCAAAAGTTTAAGACTAATTTAGAAAGAAAGTCATAGTTT
Found at i:2165420 original size:20 final size:21
Alignment explanation
Indices: 2165395--2165436 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2165385 ACCTTTTCAA
2165395 AATTTTGA-AATATTAAAACT
1 AATTTTGATAATATTAAAACT
* *
2165415 AATTTTGATACTCTTAAAACT
1 AATTTTGATAATATTAAAACT
2165436 A
1 A
2165437 TTAGCATTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (21 bp):
AATTTTGATAATATTAAAACT
Found at i:2166495 original size:2 final size:2
Alignment explanation
Indices: 2166488--2166529 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
2166478 ATTCAATTTG
2166488 AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2166529 A
1 A
2166530 ATTAGATAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2167929 original size:27 final size:28
Alignment explanation
Indices: 2167881--2167938 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
2167871 ACGTAAAATA
2167881 TATGGTTTTAAAAACATTTTTGAAAACG
1 TATGGTTTTAAAAACATTTTTGAAAACG
2167909 TATGGTTTTAAAAACA-TTTTGAAAACG
1 TATGGTTTTAAAAACATTTTTGAAAACG
2167936 TAT
1 TAT
2167939 ATATATGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 14 0.47
28 16 0.53
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.40
Consensus pattern (28 bp):
TATGGTTTTAAAAACATTTTTGAAAACG
Found at i:2167962 original size:33 final size:33
Alignment explanation
Indices: 2167801--2168048 Score: 136
Period size: 33 Copynumber: 7.4 Consensus size: 33
2167791 TTAAAAATAT
* *
2167801 ATATATATAGTTCTTGGAAACTCATTTTTGAAAAC
1 ATATATATAGTT-TTTGAAA-ACATTTTTGAAAAC
* * *
2167836 ATATATATATAATTTTTTTAAAA-ACTGTTTCGAAAAC
1 --ATATATAT-AGTTTTTGAAAACA-T-TTTTGAAAAC
* * * *
2167873 GTAAAATATATGGTTTTAAAAACATTTTTGAAAAC
1 AT-ATATATA-GTTTTTGAAAACATTTTTGAAAAC
* * *
2167908 ----GTAT-GGTTTTAAAAACA-TTTTGAAAAC
1 ATATATATAGTTTTTGAAAACATTTTTGAAAAC
* ***
2167935 GTATATATATGTTTTTGATTTC-TTTTTGAAAAC
1 ATATATATA-GTTTTTGAAAACATTTTTGAAAAC
* *
2167968 ATA-ATATATGATTTTAAAAACATTTTTGAAAAC
1 ATATATATA-GTTTTTGAAAACATTTTTGAAAAC
* *
2168001 ATATATATAATTTTTGAAAACATATTTCGAAAAC
1 ATATATATAGTTTTTGAAAACAT-TTTTGAAAAC
*
2168035 GTATATATAGTTTT
1 ATATATATAGTTTT
2168049 AAATATTATT
Statistics
Matches: 165, Mismatches: 30, Indels: 35
0.72 0.13 0.15
Matches are distributed among these distances:
27 10 0.06
28 13 0.08
30 3 0.02
31 3 0.02
32 13 0.08
33 44 0.27
34 26 0.16
35 12 0.07
36 15 0.09
37 23 0.14
38 3 0.02
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (33 bp):
ATATATATAGTTTTTGAAAACATTTTTGAAAAC
Found at i:2168112 original size:18 final size:20
Alignment explanation
Indices: 2168069--2168114 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 20
2168059 GGAAGAATAT
2168069 ATAATATATAATTTTCGAAA
1 ATAATATATAATTTTCGAAA
* *
2168089 A-CATAT-T-ATTTTTGAAA
1 ATAATATATAATTTTCGAAA
2168106 ATAATATAT
1 ATAATATAT
2168115 TATATAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 5
0.72 0.10 0.17
Matches are distributed among these distances:
17 10 0.48
18 5 0.24
19 5 0.24
20 1 0.05
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.43
Consensus pattern (20 bp):
ATAATATATAATTTTCGAAA
Found at i:2177868 original size:3 final size:3
Alignment explanation
Indices: 2177862--2177902 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
2177852 GTAATAATTT
* *
2177862 ATA ATA ATA ATA ATA ATA ATA CATA TTA TTA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA A
2177903 AAGATAAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:2177881 original size:22 final size:22
Alignment explanation
Indices: 2177853--2177902 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
2177843 GCATACTTTG
**
2177853 TAATAATTTATAATAATAATAA
1 TAATAATACATAATAATAATAA
* *
2177875 TAATAATACATATTATTAATAA
1 TAATAATACATAATAATAATAA
2177897 TAATAA
1 TAATAA
2177903 AAGATAAAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
TAATAATACATAATAATAATAA
Found at i:2178291 original size:45 final size:45
Alignment explanation
Indices: 2178243--2178854 Score: 878
Period size: 45 Copynumber: 13.7 Consensus size: 45
2178233 CACTTTAGGT
* *
2178243 CTTACAGATGACCCGAAGGCTTTAAAAACATCATGCACTGAAGGT
1 CTTACAGATGACCCGAAGGCTTTGAAAACATCATGCACTGAAGGG
* * *
2178288 CTTACAGATGACCCAAAGGTTTTGAAAACATCATGCACTGAAAGG
1 CTTACAGATGACCCGAAGGCTTTGAAAACATCATGCACTGAAGGG
2178333 CTTACAGAT------AAGGCTTT-AAACACATCATGCACTGAAGGG
1 CTTACAGATGACCCGAAGGCTTTGAAA-ACATCATGCACTGAAGGG
* *
2178372 CTTACAGATGACCCGAAGGCTTTCAAAACATCATGCACTGAAGGT
1 CTTACAGATGACCCGAAGGCTTTGAAAACATCATGCACTGAAGGG
* * * *
2178417 CTTACAAATGACTCGAAGGCTTTAAAAACATCATGCACTGAAGGT
1 CTTACAGATGACCCGAAGGCTTTGAAAACATCATGCACTGAAGGG
* * *
2178462 TTTACAGATGACTCGAAGGCTTTGAAAACATCATGCACTAAAGGG
1 CTTACAGATGACCCGAAGGCTTTGAAAACATCATGCACTGAAGGG
*
2178507 CTTACAGATGACCCAAAGGCTTTGAAAACATCATGCACTGAAGGG
1 CTTACAGATGACCCGAAGGCTTTGAAAACATCATGCACTGAAGGG
* * * * * *
2178552 CTTACAGATTAACCGAAGGTTTTGAAAATATCATACACTGAAGGA
1 CTTACAGATGACCCGAAGGCTTTGAAAACATCATGCACTGAAGGG
*
2178597 CTTACAGATGACCCGAAGGCTTTGAAAACATCATACACTGAAGGG
1 CTTACAGATGACCCGAAGGCTTTGAAAACATCATGCACTGAAGGG
* * *
2178642 CTTATAGATAACCCGAAGGATTTGAAAACATCATGCACTGAAGGG
1 CTTACAGATGACCCGAAGGCTTTGAAAACATCATGCACTGAAGGG
* * * *
2178687 CTTACATATGATCCGAAGGCTTTAAAAACGTCATGCACTGAAGGG
1 CTTACAGATGACCCGAAGGCTTTGAAAACATCATGCACTGAAGGG
* *
2178732 CTTACATATGACCTGAAGGCTTTGAAAACATCATGCACTGAAGGG
1 CTTACAGATGACCCGAAGGCTTTGAAAACATCATGCACTGAAGGG
2178777 CTTACAGATGACCCGAAGGCTTTGAAAACATCATGCACTGAAGGG
1 CTTACAGATGACCCGAAGGCTTTGAAAACATCATGCACTGAAGGG
*
2178822 CTTACAGATGACCCGAAGGTTTTGAAAACATCA
1 CTTACAGATGACCCGAAGGCTTTGAAAACATCA
2178855 AAAAGCTCCC
Statistics
Matches: 509, Mismatches: 50, Indels: 16
0.89 0.09 0.03
Matches are distributed among these distances:
38 3 0.01
39 33 0.06
45 470 0.92
46 3 0.01
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (45 bp):
CTTACAGATGACCCGAAGGCTTTGAAAACATCATGCACTGAAGGG
Found at i:2178465 original size:25 final size:25
Alignment explanation
Indices: 2178386--2178505 Score: 68
Period size: 25 Copynumber: 5.2 Consensus size: 25
2178376 CAGATGACCC
*
2178386 GAAGGCTTTCAAAACATCATGCACT
1 GAAGGCTTTAAAAACATCATGCACT
*
2178411 GAAGG-TCTT----ACA-AATG-ACT
1 GAAGGCT-TTAAAAACATCATGCACT
2178430 CGAAGGCTTTAAAAACATCATGCACT
1 -GAAGGCTTTAAAAACATCATGCACT
* *
2178456 GAAGG-TTT---TACA-GATG-ACT
1 GAAGGCTTTAAAAACATCATGCACT
*
2178475 CGAAGGCTTTGAAAACATCATGCACT
1 -GAAGGCTTTAAAAACATCATGCACT
*
2178501 AAAGG
1 GAAGG
2178506 GCTTACAGAT
Statistics
Matches: 72, Mismatches: 7, Indels: 32
0.65 0.06 0.29
Matches are distributed among these distances:
19 6 0.08
20 18 0.25
21 10 0.14
24 10 0.14
25 22 0.31
26 6 0.08
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (25 bp):
GAAGGCTTTAAAAACATCATGCACT
Found at i:2179614 original size:22 final size:22
Alignment explanation
Indices: 2179577--2179655 Score: 131
Period size: 22 Copynumber: 3.6 Consensus size: 22
2179567 AATAAAGTTT
* *
2179577 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
*
2179599 TTATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
2179621 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
2179643 TCATCTTTGAAGA
1 TCATCTTTGAAGA
2179656 ATGTAGATGT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:2180228 original size:108 final size:108
Alignment explanation
Indices: 2180021--2180239 Score: 305
Period size: 108 Copynumber: 2.0 Consensus size: 108
2180011 AGAATAACTG
*** *
2180021 GTTCGTAAAACATTTGACAACACATTCATCATCTCATATGGATTTTACTTAGATGCTCGTAAAAT
1 GTTCGTAAAACATTTGACAACACATTCATCATCTCATATGGATTTTAAACAAATGCTCGTAAAAT
* * *
2180086 ATTTGACAACATATTCATTCTTTCCCGTGGCTTCTGCCCAGAT
66 ATTTGACAACATATTCATTCTTTCCCGTGCCTTCTGCACAAAT
* * * *
2180129 GTTCGTAAAGCATTTGATAACACATTCATCATCTCATATGGTTTTTAAACAAATGTTCGTAAAAT
1 GTTCGTAAAACATTTGACAACACATTCATCATCTCATATGGATTTTAAACAAATGCTCGTAAAAT
**
2180194 ATTTGACAACATATTCA-TCATTTCTTGTGCCTTCTGCACAAAT
66 ATTTGACAACATATTCATTC-TTTCCCGTGCCTTCTGCACAAAT
2180237 GTT
1 GTT
2180240 TTCCAGTGAA
Statistics
Matches: 97, Mismatches: 13, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
107 2 0.02
108 95 0.98
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.37
Consensus pattern (108 bp):
GTTCGTAAAACATTTGACAACACATTCATCATCTCATATGGATTTTAAACAAATGCTCGTAAAAT
ATTTGACAACATATTCATTCTTTCCCGTGCCTTCTGCACAAAT
Found at i:2180235 original size:54 final size:54
Alignment explanation
Indices: 2180021--2180239 Score: 179
Period size: 54 Copynumber: 4.1 Consensus size: 54
2180011 AGAATAACTG
* * * * * * * ** *
2180021 GTTCGTAAAACATTTGACAACACATTCATCATCTCATATGGATTTTACTTAGAT
1 GTTCGTAAAATATTTGACAACATATTCATCATTTCATGTGGCTTCTGCACAAAT
* ** * *
2180075 GCTCGTAAAATATTTGACAACATATTCATTC-TTTCCCGTGGCTTCTGCCCAGAT
1 GTTCGTAAAATATTTGACAACATATTCA-TCATTTCATGTGGCTTCTGCACAAAT
** * * * * * * **
2180129 GTTCGTAAAGCATTTGATAACACATTCATCATCTCATATGGTTTTTAAACAAAT
1 GTTCGTAAAATATTTGACAACATATTCATCATTTCATGTGGCTTCTGCACAAAT
* *
2180183 GTTCGTAAAATATTTGACAACATATTCATCATTTCTTGTGCCTTCTGCACAAAT
1 GTTCGTAAAATATTTGACAACATATTCATCATTTCATGTGGCTTCTGCACAAAT
2180237 GTT
1 GTT
2180240 TTCCAGTGAA
Statistics
Matches: 124, Mismatches: 39, Indels: 4
0.74 0.23 0.02
Matches are distributed among these distances:
53 2 0.02
54 120 0.97
55 2 0.02
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.37
Consensus pattern (54 bp):
GTTCGTAAAATATTTGACAACATATTCATCATTTCATGTGGCTTCTGCACAAAT
Found at i:2180585 original size:27 final size:27
Alignment explanation
Indices: 2180546--2180604 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
2180536 CCTGCTGCTG
2180546 TAGATGAAACGCACATGATAAACAAAA
1 TAGATGAAACGCACATGATAAACAAAA
*
2180573 TAGATGAATCGCACATGATAAACAAAA
1 TAGATGAAACGCACATGATAAACAAAA
2180600 TAGAT
1 TAGAT
2180605 AAAAACTCAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.53, C:0.14, G:0.15, T:0.19
Consensus pattern (27 bp):
TAGATGAAACGCACATGATAAACAAAA
Found at i:2181266 original size:75 final size:75
Alignment explanation
Indices: 2181174--2181383 Score: 339
Period size: 75 Copynumber: 2.8 Consensus size: 75
2181164 ATGAACATTC
* *
2181174 AAAATGTGCCAATATTCCAATTTCTGATTGAAATGGGCTTTTAGCATGCCCCAACATTTGCTAAT
1 AAAATGCGCCAATATTCCAATTTCTGATTGAAATGGGCTTTCAGCATGCCCCAACATTTGCTAAT
*
2181239 GCATACGTTA
66 ACATACGTTA
* *
2181249 AAAATGCGCCAATATTCCAATTTCTGATTGAAATGGGCTTTCACCATGCCCCAGCATTTGCTAAT
1 AAAATGCGCCAATATTCCAATTTCTGATTGAAATGGGCTTTCAGCATGCCCCAACATTTGCTAAT
*
2181314 ACATACGTTC
66 ACATACGTTA
* * *
2181324 AAAATGCTCCAAAATTCCAATTTCTGATTGAAATGGGCTTTCAGCATGCCTCAACATTTG
1 AAAATGCGCCAATATTCCAATTTCTGATTGAAATGGGCTTTCAGCATGCCCCAACATTTG
2181384 TTGATATAAA
Statistics
Matches: 124, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
75 124 1.00
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.32
Consensus pattern (75 bp):
AAAATGCGCCAATATTCCAATTTCTGATTGAAATGGGCTTTCAGCATGCCCCAACATTTGCTAAT
ACATACGTTA
Found at i:2181399 original size:75 final size:75
Alignment explanation
Indices: 2181138--2181404 Score: 329
Period size: 75 Copynumber: 3.6 Consensus size: 75
2181128 GATTTAGGCC
* * * * ** *
2181138 TTCATCATGCCCAAACATTTGATGATATGAACATTCAAAATG-TGCCAATATTCCAATTTCTGAT
1 TTCAGCATGCCCCAACATTTGCTAATACAAACGTTCAAAATGCT-CCAATATTCCAATTTCTGAT
2181202 TGAAATGGGCT
65 TGAAATGGGCT
* * * * *
2181213 TTTAGCATGCCCCAACATTTGCTAATGCATACGTTAAAAATGCGCCAATATTCCAATTTCTGATT
1 TTCAGCATGCCCCAACATTTGCTAATACAAACGTTCAAAATGCTCCAATATTCCAATTTCTGATT
2181278 GAAATGGGCT
66 GAAATGGGCT
* * * *
2181288 TTCACCATGCCCCAGCATTTGCTAATACATACGTTCAAAATGCTCCAAAATTCCAATTTCTGATT
1 TTCAGCATGCCCCAACATTTGCTAATACAAACGTTCAAAATGCTCCAATATTCCAATTTCTGATT
2181353 GAAATGGGCT
66 GAAATGGGCT
* * * * *
2181363 TTCAGCATGCCTCAACATTTGTTGATATAAATGTTCAAAATG
1 TTCAGCATGCCCCAACATTTGCTAATACAAACGTTCAAAATG
2181405 TATTCAAAAT
Statistics
Matches: 164, Mismatches: 27, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
75 164 1.00
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.33
Consensus pattern (75 bp):
TTCAGCATGCCCCAACATTTGCTAATACAAACGTTCAAAATGCTCCAATATTCCAATTTCTGATT
GAAATGGGCT
Found at i:2183671 original size:135 final size:135
Alignment explanation
Indices: 2183429--2183697 Score: 470
Period size: 135 Copynumber: 2.0 Consensus size: 135
2183419 GTTTTATTGG
*
2183429 CATTAGCCTTCATTGGACTAATTAAACGGTTCAACTCATCACAATGTCTTTGACTTGACAATCAC
1 CATTAGCCTTCATTGGACTAATTAAACGGTTCAACTCATCACAATATCTTTGACTTGACAATCAC
2183494 AGTGGAGCAAACACCGAACTGCCAAATACCCGATCAAGGTCATGT-TTTGAATATATGACTCTTT
66 AGTGGAGCAAACACCGAACTGCCAAATACCCGATCAAGGTCAT-TCTTTGAATATATGACTCTTT
2183558 TTTTTA
130 TTTTTA
2183564 CATTAGCCTTCATTGGACTAATTAAA-GGATTCAACTCATCACAATATCTTTGACTTGACAATCA
1 CATTAGCCTTCATTGGACTAATTAAACGG-TTCAACTCATCACAATATCTTTGACTTGACAATCA
* * *
2183628 CAGTGGGGCAAACACCGAACTGCCAAATATCCGATCAATGTCATTCTTTGAATATATGACTCTTT
65 CAGTGGAGCAAACACCGAACTGCCAAATACCCGATCAAGGTCATTCTTTGAATATATGACTCTTT
2183693 TTTTT
130 TTTTT
2183698 GAAAAACCTG
Statistics
Matches: 128, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
134 3 0.02
135 125 0.98
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (135 bp):
CATTAGCCTTCATTGGACTAATTAAACGGTTCAACTCATCACAATATCTTTGACTTGACAATCAC
AGTGGAGCAAACACCGAACTGCCAAATACCCGATCAAGGTCATTCTTTGAATATATGACTCTTTT
TTTTA
Found at i:2186286 original size:43 final size:43
Alignment explanation
Indices: 2186204--2186288 Score: 134
Period size: 43 Copynumber: 2.0 Consensus size: 43
2186194 CGGTGCATCA
* *
2186204 AACAAAACTTTACATATAGGGGATAACTTTTACTCCTAACTTT
1 AACAAAACTTTACATATAGGAGATAACTTTCACTCCTAACTTT
* *
2186247 AACAAAACTTTACATATAGGAGATAACTTTCCCTTCTAACTT
1 AACAAAACTTTACATATAGGAGATAACTTTCACTCCTAACTT
2186289 CTCTAAAGCC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.38, C:0.20, G:0.08, T:0.34
Consensus pattern (43 bp):
AACAAAACTTTACATATAGGAGATAACTTTCACTCCTAACTTT
Found at i:2189512 original size:29 final size:29
Alignment explanation
Indices: 2189478--2189534 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
2189468 TGGAGGGCGT
* *
2189478 CGTGGCAGCCGCTTGAATCTTTGACGAGA
1 CGTGGCAGCCGCTGGAATCTTCGACGAGA
2189507 CGTGGCAGCCGCTGGAATCTTCGACGAG
1 CGTGGCAGCCGCTGGAATCTTCGACGAG
2189535 GCATGGCAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.19, C:0.26, G:0.33, T:0.21
Consensus pattern (29 bp):
CGTGGCAGCCGCTGGAATCTTCGACGAGA
Found at i:2189541 original size:29 final size:29
Alignment explanation
Indices: 2189480--2189542 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
2189470 GAGGGCGTCG
* * *
2189480 TGGCAGCCGCTTGAATCTTTGACGAGACG
1 TGGCAGCCGCTGGAATCTTCGACGAGACA
*
2189509 TGGCAGCCGCTGGAATCTTCGACGAGGCA
1 TGGCAGCCGCTGGAATCTTCGACGAGACA
2189538 TGGCA
1 TGGCA
2189543 ACAGCTTCCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.21, C:0.25, G:0.33, T:0.21
Consensus pattern (29 bp):
TGGCAGCCGCTGGAATCTTCGACGAGACA
Found at i:2189794 original size:3 final size:3
Alignment explanation
Indices: 2189788--2189831 Score: 61
Period size: 3 Copynumber: 14.3 Consensus size: 3
2189778 GTAATAATTT
* *
2189788 ATA ATA ATA ATA ATA ATA ATA ATA CATA TTA TTA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA A
2189832 AGAAAAAGGA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:2189810 original size:25 final size:25
Alignment explanation
Indices: 2189779--2189831 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
2189769 GCCTGCTTTG
**
2189779 TAATAATTTATAATAATAATAATAA
1 TAATAATACATAATAATAATAATAA
* *
2189804 TAATAATACATATTATTAATAATAA
1 TAATAATACATAATAATAATAATAA
2189829 TAA
1 TAA
2189832 AGAAAAAGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (25 bp):
TAATAATACATAATAATAATAATAA
Found at i:2198047 original size:21 final size:19
Alignment explanation
Indices: 2198019--2198064 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
2198009 TCATTAAATC
2198019 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
2198039 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
2198058 ACTTAGT
1 A-TTAGT
2198065 AGGATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Found at i:2205109 original size:48 final size:48
Alignment explanation
Indices: 2205027--2205146 Score: 131
Period size: 47 Copynumber: 2.5 Consensus size: 48
2205017 AGAAATATTT
* * *
2205027 CGCTTAGGGGAAAACCT-AAAAGG-GCACCTAAGTTGAAGCCAAAAAAA
1 CGCTTAAGGGAAAAACTGAAAGGGTGCACCTAAGTTGAAG-CAAAAAAA
*
2205074 TGCTTAAGGGAAAAACTGAAAGGGTGC-CCTAAGTTGAAGCAAAAAAA
1 CGCTTAAGGGAAAAACTGAAAGGGTGCACCTAAGTTGAAGCAAAAAAA
* *
2205121 CG-TTTAGGGTGAAAACTCGAAAGGGT
1 CGCTTAAGGG-AAAAACT-GAAAGGGT
2205147 AATCTAAATT
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
46 6 0.10
47 29 0.47
48 25 0.40
49 2 0.03
ACGTcount: A:0.42, C:0.15, G:0.27, T:0.17
Consensus pattern (48 bp):
CGCTTAAGGGAAAAACTGAAAGGGTGCACCTAAGTTGAAGCAAAAAAA
Found at i:2205136 original size:47 final size:49
Alignment explanation
Indices: 2205053--2205146 Score: 131
Period size: 48 Copynumber: 2.0 Consensus size: 49
2205043 TAAAAGGGCA
*
2205053 CCTAAGTTGAAGCCAAAAAAATGCTTAAGGGAAAAACT-GAAAGGGTGC
1 CCTAAGTTGAAGCCAAAAAAACGCTTAAGGGAAAAACTCGAAAGGGTGC
* *
2205101 CCTAAGTTGAAG-CAAAAAAACG-TTTAGGGTGAAAACTCGAAAGGGT
1 CCTAAGTTGAAGCCAAAAAAACGCTTAAGGG-AAAAACTCGAAAGGGT
2205147 AATCTAAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
46 6 0.15
47 15 0.37
48 20 0.49
ACGTcount: A:0.43, C:0.14, G:0.26, T:0.18
Consensus pattern (49 bp):
CCTAAGTTGAAGCCAAAAAAACGCTTAAGGGAAAAACTCGAAAGGGTGC
Found at i:2207008 original size:35 final size:36
Alignment explanation
Indices: 2206942--2207016 Score: 98
Period size: 35 Copynumber: 2.1 Consensus size: 36
2206932 TTTCGAAATG
* * *
2206942 TATAATATGGTTTTAAAAACATTTTTGAAAAACATA
1 TATAATATAGTTTTAAAAACATATTTCAAAAACATA
* *
2206978 TATAATATAG-TTTGAAAACATATTTCAAAAACGTA
1 TATAATATAGTTTTAAAAACATATTTCAAAAACATA
2207013 TATA
1 TATA
2207017 TAGTTTTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 25 0.74
36 9 0.26
ACGTcount: A:0.48, C:0.07, G:0.08, T:0.37
Consensus pattern (36 bp):
TATAATATAGTTTTAAAAACATATTTCAAAAACATA
Found at i:2207269 original size:27 final size:27
Alignment explanation
Indices: 2207227--2207292 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 27
2207217 TAACCCGGTA
2207227 GCCTGACCCAGCAAACCTTGTTAGGGG
1 GCCTGACCCAGCAAACCTTGTTAGGGG
*
2207254 GCCTGACCCAGGAAACCTTGTTAGGGG
1 GCCTGACCCAGCAAACCTTGTTAGGGG
*
2207281 GCCTAACCCAGC
1 GCCTGACCCAGC
2207293 CCAAGATCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.23, C:0.32, G:0.29, T:0.17
Consensus pattern (27 bp):
GCCTGACCCAGCAAACCTTGTTAGGGG
Found at i:2208282 original size:18 final size:17
Alignment explanation
Indices: 2208259--2208318 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 17
2208249 CATTTAAACC
2208259 CTTTTAATTTAAAGTTTT
1 CTTTTAATTTAAA-TTTT
* *
2208277 CTTTTACTTTATATTTT
1 CTTTTAATTTAAATTTT
2208294 C--TTAATTT-AATTTT
1 CTTTTAATTTAAATTTT
*
2208308 -TTTTACTTTAA
1 CTTTTAATTTAA
2208319 TAATTAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
14 5 0.15
15 12 0.35
16 1 0.03
17 5 0.15
18 11 0.32
ACGTcount: A:0.25, C:0.08, G:0.02, T:0.65
Consensus pattern (17 bp):
CTTTTAATTTAAATTTT
Found at i:2209313 original size:251 final size:250
Alignment explanation
Indices: 2208871--2209369 Score: 811
Period size: 251 Copynumber: 2.0 Consensus size: 250
2208861 GTATCGGTCA
* *
2208871 AAGATGCAGTGAACTAAAATTTTCAACAAGAAATAATTTAAACTTCTCGAACCTGGTACGAAGAG
1 AAGATGCAGTGAACTAAAATTTTCAACAAGAAATAATTTAAACTTCTCGAACCAGGTACGAAGAA
* *
2208936 CTTGTTTAAGACCATATAATGAATTTTTTAACTGAGAAACCAGTTGATTTCCATTATCATCCACT
66 CTTGTTTAAAACCATATAATGAATTTTTTAACTGAGAAACCAATTGATTTCCATTATCATCCACT
2209001 TGCTCAAATCCATATGGTTGTTTCATATAAACTTCTTCAACTAAATCACCATTCAAGAAGGCATT
131 TGCTCAAATCCATATGGTTGTTTCATATAAACTTCTTCAACTAAATCACCATTCAAGAAGGCATT
2209066 ATCTACATCAATCTGCCTAAGTACCAATTATTTGCTAAGAGCTATACTAAGTACC
196 ATCTACATCAATCTGCCTAAGTACCAATTATTTGCTAAGAGCTATACTAAGTACC
*
2209121 AAGATGCAGTGAACTAAAGATTTTCAA-AAGAAATGATTTAAACTTCTCGAACCAGGTACGAAGA
1 AAGATGCAGTGAACTAAA-ATTTTCAACAAGAAATAATTTAAACTTCTCGAACCAGGTACGAAGA
* * * * *
2209185 ATTTGTTTAAAACCATATAATGATTTTTTTTATCTGGGAAACCAATTGATTTCCATTCTCATCCA
65 ACTTGTTTAAAACCATATAATGA-ATTTTTTAACTGAGAAACCAATTGATTTCCATTATCATCCA
* * * * *
2209250 CTTTCTCAAATTCATATGGTTGTTTCATATAAATTTCTTCAACTAAATCATCATTTAAGAAGGCA
129 CTTGCTCAAATCCATATGGTTGTTTCATATAAACTTCTTCAACTAAATCACCATTCAAGAAGGCA
* * *
2209315 TTGTCTACATCAATCTGTCTAAGTACCAATTCTTTGCTAAGAGCTATACTAAGTA
194 TTATCTACATCAATCTGCCTAAGTACCAATTATTTGCTAAGAGCTATACTAAGTA
2209370 AACTCTTATT
Statistics
Matches: 229, Mismatches: 18, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
250 73 0.32
251 156 0.68
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.34
Consensus pattern (250 bp):
AAGATGCAGTGAACTAAAATTTTCAACAAGAAATAATTTAAACTTCTCGAACCAGGTACGAAGAA
CTTGTTTAAAACCATATAATGAATTTTTTAACTGAGAAACCAATTGATTTCCATTATCATCCACT
TGCTCAAATCCATATGGTTGTTTCATATAAACTTCTTCAACTAAATCACCATTCAAGAAGGCATT
ATCTACATCAATCTGCCTAAGTACCAATTATTTGCTAAGAGCTATACTAAGTACC
Found at i:2213310 original size:27 final size:27
Alignment explanation
Indices: 2213239--2213303 Score: 130
Period size: 27 Copynumber: 2.4 Consensus size: 27
2213229 CTTGAGGGCG
2213239 AAAGCCTTGATTATGAAGTCTTAACGA
1 AAAGCCTTGATTATGAAGTCTTAACGA
2213266 AAAGCCTTGATTATGAAGTCTTAACGA
1 AAAGCCTTGATTATGAAGTCTTAACGA
2213293 AAAGCCTTGAT
1 AAAGCCTTGAT
2213304 CTTGAAGAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.29
Consensus pattern (27 bp):
AAAGCCTTGATTATGAAGTCTTAACGA
Found at i:2214284 original size:21 final size:21
Alignment explanation
Indices: 2214258--2214301 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
2214248 CGTGAACAAC
2214258 AAACTTAGTAACCGAATAACT
1 AAACTTAGTAACCGAATAACT
* *
2214279 AAACTTTGTAACTGAATAACT
1 AAACTTAGTAACCGAATAACT
2214300 AA
1 AA
2214302 TCTTGAACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.16, G:0.09, T:0.27
Consensus pattern (21 bp):
AAACTTAGTAACCGAATAACT
Found at i:2219131 original size:33 final size:33
Alignment explanation
Indices: 2219089--2219153 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
2219079 CATAGACATC
2219089 GACATCGAAACCGTCGATTGTTGCTTTTTCATA
1 GACATCGAAACCGTCGATTGTTGCTTTTTCATA
2219122 GACATCGAAACCGTCGATTGTTGCTTTTTCAT
1 GACATCGAAACCGTCGATTGTTGCTTTTTCAT
2219154 TTTCGAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (33 bp):
GACATCGAAACCGTCGATTGTTGCTTTTTCATA
Found at i:2227479 original size:22 final size:23
Alignment explanation
Indices: 2227439--2227482 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
2227429 TTTGTTTAGT
*
2227439 GTTCGTGAACATGTTCGTTTAAC
1 GTTCGTGAACATGTACGTTTAAC
2227462 GTTCGTG-ACATGTACGTTTAA
1 GTTCGTGAACATGTACGTTTAA
2227483 TATTCGTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.39
Consensus pattern (23 bp):
GTTCGTGAACATGTACGTTTAAC
Found at i:2227488 original size:22 final size:23
Alignment explanation
Indices: 2227440--2227489 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
2227430 TTGTTTAGTG
* *
2227440 TTCGTGAACATGTTCGTTTAACG
1 TTCGTGAACATGTACGTTTAACA
*
2227463 TTCGTG-ACATGTACGTTTAATA
1 TTCGTGAACATGTACGTTTAACA
2227485 TTCGT
1 TTCGT
2227490 TTAGTGTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.42
Consensus pattern (23 bp):
TTCGTGAACATGTACGTTTAACA
Found at i:2227690 original size:38 final size:38
Alignment explanation
Indices: 2227643--2227717 Score: 96
Period size: 38 Copynumber: 2.0 Consensus size: 38
2227633 AAAGTAAATG
* *
2227643 AGTTTATAAACAAGCTTGTTCATTAACATAAACGAACA
1 AGTTGATAAACAAGCTTGTTCATGAACATAAACGAACA
* * * *
2227681 AGTTGATAAATAATCTTGTTCGTGGACATAAACGAAC
1 AGTTGATAAACAAGCTTGTTCATGAACATAAACGAAC
2227718 TAAACACACA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (38 bp):
AGTTGATAAACAAGCTTGTTCATGAACATAAACGAACA
Found at i:2232961 original size:36 final size:36
Alignment explanation
Indices: 2232911--2232986 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
2232901 TTATAGCAAA
*
2232911 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
2232947 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
2232983 AAAA
1 AAAA
2232987 TCCCGAAAAT
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:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:2241509 original size:14 final size:14
Alignment explanation
Indices: 2241466--2241510 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 14
2241456 TTAGGAACCA
2241466 AAATTTTGTCTTCT
1 AAATTTTGTCTTCT
2241480 AACATATTCGTGTCTTCT
1 AA-AT-TT--TGTCTTCT
2241498 AAATTTTGTCTTC
1 AAATTTTGTCTTC
2241511 GCATCTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
14 9 0.33
15 2 0.07
16 4 0.15
17 2 0.07
18 10 0.37
ACGTcount: A:0.22, C:0.18, G:0.09, T:0.51
Consensus pattern (14 bp):
AAATTTTGTCTTCT
Found at i:2242288 original size:24 final size:24
Alignment explanation
Indices: 2242256--2242303 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
2242246 GAAAACTTGG
2242256 CTTTGAAAATATTACTAATATGTC
1 CTTTGAAAATATTACTAATATGTC
2242280 CTTTGAAAATATTACTAATATGTC
1 CTTTGAAAATATTACTAATATGTC
2242304 ATTATTGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (24 bp):
CTTTGAAAATATTACTAATATGTC
Found at i:2252425 original size:20 final size:20
Alignment explanation
Indices: 2252400--2252452 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
2252390 TTTGATTTTC
*
2252400 TATTATATATATTTTTATTT
1 TATTATATATATTATTATTT
2252420 TATTAT-TATTATTATTATTT
1 TATTATATA-TATTATTATTT
2252440 TACTTATATATAT
1 TA-TTATATATAT
2252453 ATACTTTTAC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 2 0.07
20 18 0.62
21 7 0.24
22 2 0.07
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (20 bp):
TATTATATATATTATTATTT
Found at i:2252478 original size:16 final size:18
Alignment explanation
Indices: 2252437--2252486 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
2252427 ATTATTATTA
*
2252437 TTTTACTTATATATATATAC
1 TTTTACTTAT-T-TTTATAC
2252457 TTTTACTT-TTTTTATA-
1 TTTTACTTATTTTTATAC
2252473 TTTTACTTATTTTT
1 TTTTACTTATTTTT
2252487 TTATCTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 8 0.29
17 10 0.36
18 1 0.04
19 1 0.04
20 8 0.29
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTACTTATTTTTATAC
Found at i:2252551 original size:17 final size:17
Alignment explanation
Indices: 2252530--2252571 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
2252520 TTTATCTTCC
*
2252530 TTTTATTTGCTTTATTCA
1 TTTTATTTGCATTA-TCA
2252548 -TTTATTTGCATTATCA
1 TTTTATTTGCATTATCA
2252564 TTTTATTT
1 TTTTATTT
2252572 TTATTTGGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 3 0.14
17 19 0.86
ACGTcount: A:0.19, C:0.10, G:0.05, T:0.67
Consensus pattern (17 bp):
TTTTATTTGCATTATCA
Found at i:2253807 original size:15 final size:16
Alignment explanation
Indices: 2253780--2253809 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2253770 CCTCACTAAC
2253780 TCTTTTCATTTTATTA
1 TCTTTTCATTTTATTA
2253796 TCTTTT-ATTTTATT
1 TCTTTTCATTTTATT
2253810 TTCATCTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.73
Consensus pattern (16 bp):
TCTTTTCATTTTATTA
Found at i:2256754 original size:94 final size:95
Alignment explanation
Indices: 2256635--2256815 Score: 285
Period size: 94 Copynumber: 1.9 Consensus size: 95
2256625 ATATTATTTA
* *
2256635 TATACAATAAAGCTTGAGTTATCCCTCT-AGAGCAATTGGTTAAACGCCCCGGCTTTATGGATAA
1 TATACAATAAAGCCTGAGCTATCCCTCTAAG-GCAATTGGTTAAACGCCCCGGCTTTATGGATAA
* *
2256699 TATTCAGCTAGCCTGATAAAGGTGATTATAC
65 GATTCAGCTAACCTGATAAAGGTGATTATAC
* *
2256730 TATAC-ATAAAGCCTGAGCTGTCCCTCTAAGGCAATTGGTTAAACGCCCTGGCTTTATGGATAAG
1 TATACAATAAAGCCTGAGCTATCCCTCTAAGGCAATTGGTTAAACGCCCCGGCTTTATGGATAAG
2256794 ATTCAGCTAACCTGATAAAGGT
66 ATTCAGCTAACCTGATAAAGGT
2256816 ATTTACATAT
Statistics
Matches: 79, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
94 72 0.91
95 7 0.09
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (95 bp):
TATACAATAAAGCCTGAGCTATCCCTCTAAGGCAATTGGTTAAACGCCCCGGCTTTATGGATAAG
ATTCAGCTAACCTGATAAAGGTGATTATAC
Found at i:2258385 original size:110 final size:110
Alignment explanation
Indices: 2258183--2258440 Score: 319
Period size: 110 Copynumber: 2.4 Consensus size: 110
2258173 GCTTCTCAAT
* * *
2258183 TTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGGACTCAAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCA
* * * *
2258248 CAACGAAGGGGTGGCTGATTGTCAACAAACAACTTTTCAGTTTCA
66 CAACGAAGGGGCGACTGACTGTAAACAAACAACTTTTCAGTTTCA
*
2258293 TTCAGAGTCAATTTCAACTTCACAACGAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCA
* * * *
2258358 CAGCGAAGGGGCGACTTACTGTAAACAAGCAA-TTTCCCAG-TTC-
66 CAACGAAGGGGCGACTGACTGTAAACAAACAACTTT-TCAGTTTCA
* ** * *
2258401 --CAGAACCAATTTCAACTTCACGGCGGAGGATATTGGACTC
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAGACTC
2258441 GGTGCAATAC
Statistics
Matches: 129, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
106 34 0.26
109 6 0.05
110 89 0.69
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (110 bp):
TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCA
CAACGAAGGGGCGACTGACTGTAAACAAACAACTTTTCAGTTTCA
Found at i:2258856 original size:37 final size:37
Alignment explanation
Indices: 2258806--2258888 Score: 139
Period size: 37 Copynumber: 2.2 Consensus size: 37
2258796 ATTGACCCAA
*
2258806 CTTGAAACAAAATCTTGTCTCTCTTGAGATAGTTTCC
1 CTTGAAACAAAATCTTGTCTCTCTTGAGACAGTTTCC
*
2258843 CTTGAAACAAAATCTTGTTTCTCTTGAGACAGTTTCC
1 CTTGAAACAAAATCTTGTCTCTCTTGAGACAGTTTCC
*
2258880 ATTGAAACA
1 CTTGAAACA
2258889 TCCAACTCAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.36
Consensus pattern (37 bp):
CTTGAAACAAAATCTTGTCTCTCTTGAGACAGTTTCC
Found at i:2259140 original size:37 final size:37
Alignment explanation
Indices: 2259090--2259245 Score: 260
Period size: 37 Copynumber: 4.2 Consensus size: 37
2259080 ATTGACCCAA
*
2259090 CTTGAAACAAAATCTTGTCTCTCTTGAGATAGTTTCC
1 CTTGAAACAAAATCTTGTCTCTCTTGAGACAGTTTCC
*
2259127 CTTGAAACAAAATCTTGTTTCTCTTGAGACAGTTTCC
1 CTTGAAACAAAATCTTGTCTCTCTTGAGACAGTTTCC
*
2259164 ATTGAAACAAAATCTTGTCTCTCTTGAGACAGTTTCC
1 CTTGAAACAAAATCTTGTCTCTCTTGAGACAGTTTCC
* *
2259201 CTTGAAACAAAATATTGTCTCTTTTGAGACAG-TTCC
1 CTTGAAACAAAATCTTGTCTCTCTTGAGACAGTTTCC
2259237 CTTGAAACA
1 CTTGAAACA
2259246 CAACCTCTGA
Statistics
Matches: 112, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
36 13 0.12
37 99 0.88
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.36
Consensus pattern (37 bp):
CTTGAAACAAAATCTTGTCTCTCTTGAGACAGTTTCC
Found at i:2259144 original size:284 final size:284
Alignment explanation
Indices: 2258629--2259172 Score: 971
Period size: 284 Copynumber: 1.9 Consensus size: 284
2258619 GGAGTGTATG
* * **
2258629 TTAACAAACTTCCCAGTTTTAGAGTCAATTTCAACTTCACAGTGAAGGATATTGGCCTCAAAACA
1 TTAACAAACTTCCCAGTTTCAGACTCAATTTCAACTTCACAACGAAGGATATTGGCCTCAAAACA
* *
2258694 ACACAACTTACATTAGATTTCAACTTCACGACGAAGGATATCCAATTTCAAGGCTTAACTTCACG
66 ACACAACTTACATTAGATTTCAACTTAACGACGAAAGATATCCAATTTCAAGGCTTAACTTCACG
*
2258759 ACGGAGGGGCCATACACGATTCTAACTTCACAAACAGATTGACCCAACTTGAAACAAAATCTTGT
131 ACAGAGGGGCCATACACGATTCTAACTTCACAAACAGATTGACCCAACTTGAAACAAAATCTTGT
2258824 CTCTCTTGAGATAGTTTCCCTTGAAACAAAATCTTGTTTCTCTTGAGACAGTTTCCATTGAAACA
196 CTCTCTTGAGATAGTTTCCCTTGAAACAAAATCTTGTTTCTCTTGAGACAGTTTCCATTGAAACA
2258889 TCCAACTCAAAGAATGAGTGCCTA
261 TCCAACTCAAAGAATGAGTGCCTA
* * *
2258913 TTAATAAACTTCCCAGTTTCAGACTCAATTTCAACTTCACAACGAAGGATATTGGCCTCGAAATA
1 TTAACAAACTTCCCAGTTTCAGACTCAATTTCAACTTCACAACGAAGGATATTGGCCTCAAAACA
** *
2258978 ATGCAACTTACATTGGATTTCAACTTAACGACGAAAGATATCCAATTTCAAGGCTTAACTTCACG
66 ACACAACTTACATTAGATTTCAACTTAACGACGAAAGATATCCAATTTCAAGGCTTAACTTCACG
2259043 ACAGAGGGGCCATACACGATTCTAACTTCACAAACAGATTGACCCAACTTGAAACAAAATCTTGT
131 ACAGAGGGGCCATACACGATTCTAACTTCACAAACAGATTGACCCAACTTGAAACAAAATCTTGT
2259108 CTCTCTTGAGATAGTTTCCCTTGAAACAAAATCTTGTTTCTCTTGAGACAGTTTCCATTGAAACA
196 CTCTCTTGAGATAGTTTCCCTTGAAACAAAATCTTGTTTCTCTTGAGACAGTTTCCATTGAAACA
2259173 AAATCTTGTC
Statistics
Matches: 247, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
284 247 1.00
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (284 bp):
TTAACAAACTTCCCAGTTTCAGACTCAATTTCAACTTCACAACGAAGGATATTGGCCTCAAAACA
ACACAACTTACATTAGATTTCAACTTAACGACGAAAGATATCCAATTTCAAGGCTTAACTTCACG
ACAGAGGGGCCATACACGATTCTAACTTCACAAACAGATTGACCCAACTTGAAACAAAATCTTGT
CTCTCTTGAGATAGTTTCCCTTGAAACAAAATCTTGTTTCTCTTGAGACAGTTTCCATTGAAACA
TCCAACTCAAAGAATGAGTGCCTA
Found at i:2259291 original size:34 final size:32
Alignment explanation
Indices: 2259247--2259311 Score: 85
Period size: 34 Copynumber: 2.0 Consensus size: 32
2259237 CTTGAAACAC
*
2259247 AACCTCTGAAATTATTTCTCTTGAAACACAAAAA
1 AACCTCTGAAAATATTTCTCTT-AAA-ACAAAAA
* *
2259281 AACCTTTGAAAATGTTTCTCTTAAAACAAAA
1 AACCTCTGAAAATATTTCTCTTAAAACAAAA
2259312 GACCTTCAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 6 0.21
33 3 0.11
34 19 0.68
ACGTcount: A:0.45, C:0.18, G:0.06, T:0.31
Consensus pattern (32 bp):
AACCTCTGAAAATATTTCTCTTAAAACAAAAA
Found at i:2259671 original size:15 final size:15
Alignment explanation
Indices: 2259651--2259680 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2259641 TGATCTCATT
2259651 CAGCTCGATGTCACA
1 CAGCTCGATGTCACA
2259666 CAGCTCGATGTCACA
1 CAGCTCGATGTCACA
2259681 TCAAGAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.33, G:0.20, T:0.20
Consensus pattern (15 bp):
CAGCTCGATGTCACA
Found at i:2260124 original size:22 final size:22
Alignment explanation
Indices: 2260072--2260119 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
2260062 CATGGCATTT
*
2260072 ATATTTATGTGTTATTACTTATA
1 ATATATATGTGTTATTAC-TATA
2260095 ATATATATGTG-TATTA-TATA
1 ATATATATGTGTTATTACTATA
2260115 ATATA
1 ATATA
2260120 CATATCATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 9 0.38
22 5 0.21
23 10 0.42
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (22 bp):
ATATATATGTGTTATTACTATA
Found at i:2261539 original size:20 final size:20
Alignment explanation
Indices: 2261493--2261566 Score: 66
Period size: 20 Copynumber: 3.8 Consensus size: 20
2261483 GATTTTCTAT
*
2261493 TATATATATT-TTTTA-TTT
1 TATATATATTATTTTACTTA
2261511 TAT-TAATATTATTTTACTTA
1 TATAT-ATATTATTTTACTTA
2261531 TATATATA-TACTTTTACTTA
1 TATATATATTA-TTTTACTTA
* *
2261551 TTTATTTATCTATTTT
1 TATATATAT-TATTTT
2261567 CTTTCTATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
17 1 0.02
18 8 0.17
19 7 0.15
20 23 0.50
21 5 0.11
22 2 0.04
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (20 bp):
TATATATATTATTTTACTTA
Found at i:2261630 original size:17 final size:17
Alignment explanation
Indices: 2261607--2261648 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
2261597 TTTATCTTCC
*
2261607 TTTTATTTGCTTTATTCA
1 TTTTATTTGCATTA-TCA
2261625 -TTTATTTGCATTATCA
1 TTTTATTTGCATTATCA
2261641 TTTTATTT
1 TTTTATTT
2261649 TTATTTGGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 3 0.14
17 19 0.86
ACGTcount: A:0.19, C:0.10, G:0.05, T:0.67
Consensus pattern (17 bp):
TTTTATTTGCATTATCA
Found at i:2261732 original size:17 final size:16
Alignment explanation
Indices: 2261684--2261733 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
2261674 GTATGCGTTA
*
2261684 TTATTT-TTCTTCATT
1 TTATTTATTCTTTATT
2261699 TTATTTATT-TATGTATT
1 TTATTTATTCT-T-TATT
2261716 TTATTTATTCTTATATT
1 TTATTTATTCTT-TATT
2261733 T
1 T
2261734 ACTTTATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
15 7 0.24
16 3 0.10
17 18 0.62
18 1 0.03
ACGTcount: A:0.20, C:0.06, G:0.02, T:0.72
Consensus pattern (16 bp):
TTATTTATTCTTTATT
Found at i:2263487 original size:25 final size:25
Alignment explanation
Indices: 2263455--2263512 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
2263445 TATAGAGAAA
2263455 GAAG-AAAAGATATAGCAAAAAAAG
1 GAAGAAAAAGATATAGCAAAAAAAG
2263479 GAAGAAAAAGATATAGCAAAAAAAG
1 GAAGAAAAAGATATAGCAAAAAAAG
2263504 GAAGAAAAA
1 GAAGAAAAA
2263513 AAGAAAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 4 0.12
25 29 0.88
ACGTcount: A:0.69, C:0.03, G:0.21, T:0.07
Consensus pattern (25 bp):
GAAGAAAAAGATATAGCAAAAAAAG
Found at i:2263518 original size:8 final size:8
Alignment explanation
Indices: 2263505--2263604 Score: 87
Period size: 8 Copynumber: 11.9 Consensus size: 8
2263495 CAAAAAAAGG
2263505 AAGAAAAA
1 AAGAAAAA
2263513 AAGAAAAA
1 AAGAAAAA
2263521 ATAGAGAAAA
1 A-AGA-AAAA
*
2263531 AAGGAAAA
1 AAGAAAAA
*
2263539 AAGGAAAA
1 AAGAAAAA
2263547 AAGAAAAA
1 AAGAAAAA
2263555 AAG-AAAA
1 AAGAAAAA
*
2263562 AAGAAAGAG
1 AAGAAA-AA
*
2263571 AA-AAGAA
1 AAGAAAAA
2263578 AAGAAAAGA
1 AAGAAAA-A
2263587 AAGGAAGAAGA
1 AA-GAA-AA-A
2263598 AAGAAAA
1 AAGAAAA
2263605 CTGATCAAAT
Statistics
Matches: 78, Mismatches: 6, Indels: 15
0.79 0.06 0.15
Matches are distributed among these distances:
7 10 0.13
8 38 0.49
9 13 0.17
10 11 0.14
11 6 0.08
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.01
Consensus pattern (8 bp):
AAGAAAAA
Found at i:2263519 original size:19 final size:19
Alignment explanation
Indices: 2263497--2263579 Score: 71
Period size: 19 Copynumber: 4.2 Consensus size: 19
2263487 AGATATAGCA
2263497 AAAAAAGGAAGAAAAAAAG
1 AAAAAAGGAAGAAAAAAAG
* *
2263516 AAAAAA-TAGAGAAAAAAGG
1 AAAAAAGGA-AGAAAAAAAG
2263535 AAAAAAGGAAAAAAGAAAAAAAG
1 AAAAAAGG----AAGAAAAAAAG
* *
2263558 AAAAAAGAAAG-AGAAAAG
1 AAAAAAGGAAGAAAAAAAG
2263576 AAAA
1 AAAA
2263580 GAAAAGAAAG
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
18 11 0.21
19 24 0.46
23 16 0.31
24 1 0.02
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (19 bp):
AAAAAAGGAAGAAAAAAAG
Found at i:2263561 original size:5 final size:5
Alignment explanation
Indices: 2263545--2263604 Score: 61
Period size: 5 Copynumber: 11.8 Consensus size: 5
2263535 AAAAAAGGAA
* *
2263545 AAAAG AAAA- AAAGAA AAAAG AAAGAG AAAAG AAAAG AAAAG AAAGG AAGAAG
1 AAAAG AAAAG AAA-AG AAAAG AAA-AG AAAAG AAAAG AAAAG AAAAG AA-AAG
2263597 -AAAG AAAA
1 AAAAG AAAA
2263605 CTGATCAAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
4 6 0.13
5 31 0.66
6 10 0.21
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:2263574 original size:26 final size:24
Alignment explanation
Indices: 2263509--2263588 Score: 81
Period size: 23 Copynumber: 3.1 Consensus size: 24
2263499 AAAAGGAAGA
*
2263509 AAAAAAGAAAAAATAGAGAAAAAAGG
1 AAAAAAGAAAAAA-A-AGAAAAAAAG
*
2263535 AAAAAAG-GAAAAAAGAAAAAAAG
1 AAAAAAGAAAAAAAAGAAAAAAAG
2263558 AAAAAAGAAAGAGAAAAGAAAAGAAAAG
1 AAAAAAGAAA-A-AAAAG-AAA-AAAAG
2263586 AAA
1 AAA
2263589 GGAAGAAGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
23 16 0.35
24 2 0.04
25 5 0.11
26 12 0.26
27 3 0.07
28 8 0.17
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (24 bp):
AAAAAAGAAAAAAAAGAAAAAAAG
Found at i:2263585 original size:21 final size:21
Alignment explanation
Indices: 2263499--2263604 Score: 64
Period size: 21 Copynumber: 5.2 Consensus size: 21
2263489 ATATAGCAAA
*
2263499 AAAAGGAAGAAAAAAAGAAAA-
1 AAAAGAAAG-AAAAAAGAAAAG
* *
2263520 AATAG--AGAAAAAAGGAAA-
1 AAAAGAAAGAAAAAAGAAAAG
*
2263538 AAAGGAAA-AAAGAAA-AAAAG
1 AAAAGAAAGAAA-AAAGAAAAG
*
2263558 AAAAAAGAAAGAGAAAAGAAAAG
1 --AAAAGAAAGAAAAAAGAAAAG
* *
2263581 AAAAGAAAGGAAGAAG-AAAG
1 AAAAGAAAGAAAAAAGAAAAG
2263601 AAAA
1 AAAA
2263605 CTGATCAAAT
Statistics
Matches: 67, Mismatches: 10, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
18 13 0.19
19 8 0.12
20 12 0.18
21 17 0.25
22 10 0.15
23 7 0.10
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.01
Consensus pattern (21 bp):
AAAAGAAAGAAAAAAGAAAAG
Found at i:2265633 original size:42 final size:42
Alignment explanation
Indices: 2265567--2265648 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
2265557 TCTTTATGAG
*
2265567 TAAGGCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCT
1 TAAGGCCTTCGGGCCATCAGTAAGTCTTTCGAGCAAGATGCT
* *
2265609 TAAGTCCTTCGGGCCATTTA-TAAGTCTTTCGAGCAAGATG
1 TAAGGCCTTCGGGCCA-TCAGTAAGTCTTTCGAGCAAGATG
2265649 ATAAGACCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 34 0.94
43 2 0.06
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.30
Consensus pattern (42 bp):
TAAGGCCTTCGGGCCATCAGTAAGTCTTTCGAGCAAGATGCT
Found at i:2266136 original size:42 final size:42
Alignment explanation
Indices: 2266063--2266156 Score: 111
Period size: 42 Copynumber: 2.3 Consensus size: 42
2266053 AAGGGTTTCT
* * *
2266063 TGATGAGTAAGTCATTCGGGCCATCAGTAAGTCTTTTGAGCA
1 TGATGAGTAAGTCATTCAGACCATCAGTAAGTCTTTCGAGCA
* *
2266105 TGATGCGTAAGTCATTCAGACCATTTA-TAAGTCTTTCGAGCA
1 TGATGAGTAAGTCATTCAGACCA-TCAGTAAGTCTTTCGAGCA
*
2266147 AGATGA-TAAG
1 TGATGAGTAAG
2266157 ACCTTCAGGA
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
41 4 0.09
42 38 0.86
43 2 0.05
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (42 bp):
TGATGAGTAAGTCATTCAGACCATCAGTAAGTCTTTCGAGCA
Found at i:2269797 original size:18 final size:19
Alignment explanation
Indices: 2269765--2269800 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2269755 TTTCAGTTAG
*
2269765 TTAAACATTTTTATTTTAA
1 TTAAACATTTATATTTTAA
2269784 TTAAA-ATTTATATTTTA
1 TTAAACATTTATATTTTA
2269801 TATCCAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (19 bp):
TTAAACATTTATATTTTAA
Found at i:2270543 original size:17 final size:18
Alignment explanation
Indices: 2270521--2270556 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2270511 AGAACTTTTT
2270521 AAAAAC-TTTTTAAATGA
1 AAAAACATTTTTAAATGA
*
2270538 AAAAACATTTTTAACTGA
1 AAAAACATTTTTAAATGA
2270556 A
1 A
2270557 CCAAACTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.53, C:0.08, G:0.06, T:0.33
Consensus pattern (18 bp):
AAAAACATTTTTAAATGA
Found at i:2271968 original size:25 final size:25
Alignment explanation
Indices: 2271934--2271982 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
2271924 GTTATAGGTG
*
2271934 AATTTTTAAAATTTTAAAAAGGATT
1 AATTTCTAAAATTTTAAAAAGGATT
*
2271959 AATTTCTAAAATTTTAAAAGGGAT
1 AATTTCTAAAATTTTAAAAAGGAT
2271983 GAAAATAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.47, C:0.02, G:0.10, T:0.41
Consensus pattern (25 bp):
AATTTCTAAAATTTTAAAAAGGATT
Found at i:2273484 original size:44 final size:44
Alignment explanation
Indices: 2273418--2273618 Score: 152
Period size: 44 Copynumber: 4.6 Consensus size: 44
2273408 TTTAGCGGCT
* * * *
2273418 TTTTTTGGATACAAACGTCGCAAAAGGTCTGGTATATAGC-AGTG
1 TTTTTTGGATACAAATGCCGCAAAAGGTCTTGTATATAGCGA-CG
* *
2273462 TTTTTTAGATACAAATGCCGCAAAAGTTCTTGTATATAGCGACG
1 TTTTTTGGATACAAATGCCGCAAAAGGTCTTGTATATAGCGACG
* * * * * *
2273506 TTTTTCGGATATAAATGCTGCTAAAGGTCTTGTATATAACGATG
1 TTTTTTGGATACAAATGCCGCAAAAGGTCTTGTATATAGCGACG
* * * * * * * * * * * *
2273550 TTTGTCGTATATAAACGTCGCTAAAGGTATGGGATATAGTGGCG
1 TTTTTTGGATACAAATGCCGCAAAAGGTCTTGTATATAGCGACG
* *
2273594 TTTTTGGGATACAAACGCCGCAAAA
1 TTTTTTGGATACAAATGCCGCAAAA
2273619 TATCTAAACT
Statistics
Matches: 124, Mismatches: 32, Indels: 2
0.78 0.20 0.01
Matches are distributed among these distances:
44 123 0.99
45 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (44 bp):
TTTTTTGGATACAAATGCCGCAAAAGGTCTTGTATATAGCGACG
Found at i:2274075 original size:21 final size:21
Alignment explanation
Indices: 2274021--2274075 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
2274011 CTTCTATATG
* *
2274021 TGCTTCCATTGCTGCTCTTTA
1 TGCTTCCCTTGCTGCTCTCTA
* *
2274042 TGTTTCCGC-TGCTGCTCTCTC
1 TGCTTCC-CTTGCTGCTCTCTA
2274063 TGCTTCCCTTGCT
1 TGCTTCCCTTGCT
2274076 TCATTTTCGA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
20 1 0.04
21 26 0.96
ACGTcount: A:0.04, C:0.35, G:0.16, T:0.45
Consensus pattern (21 bp):
TGCTTCCCTTGCTGCTCTCTA
Found at i:2282380 original size:41 final size:42
Alignment explanation
Indices: 2282329--2282496 Score: 135
Period size: 42 Copynumber: 4.0 Consensus size: 42
2282319 TATAAATATG
*
2282329 TTGCGGCATTTGTTG-AAAAACGCCACTATAGATTACACCTA
1 TTGCGACATTTGTTGAAAAAACGCCACTATAGATTACACCTA
* * * * * * ** *
2282370 TTGTGACATTTG-T-ATAAAAATGCCGCTAAAGTTTAAATATG
1 TTGCGACATTTGTTGA-AAAAACGCCACTATAGATTACACCTA
* * * * *
2282411 TTACGACATTTGTTGAAAAAACGCTACAATAGATTACACTTC
1 TTGCGACATTTGTTGAAAAAACGCCACTATAGATTACACCTA
* * * *
2282453 TTGCGGCGTTTGTTGAAAAAACACCAATATAGATTACACCTA
1 TTGCGACATTTGTTGAAAAAACGCCACTATAGATTACACCTA
2282495 TT
1 TT
2282497 ACGGCGTTTG
Statistics
Matches: 92, Mismatches: 31, Indels: 7
0.71 0.24 0.05
Matches are distributed among these distances:
40 1 0.01
41 38 0.41
42 52 0.57
43 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.32
Consensus pattern (42 bp):
TTGCGACATTTGTTGAAAAAACGCCACTATAGATTACACCTA
Found at i:2282465 original size:42 final size:42
Alignment explanation
Indices: 2282419--2282507 Score: 117
Period size: 42 Copynumber: 2.1 Consensus size: 42
2282409 TGTTACGACA
* * * * *
2282419 TTTGTTGAAAAAACGCTACA-ATAGATTACACTTCTTGCGGCG
1 TTTGTTGAAAAAACACCA-ATATAGATTACACCTATTACGGCG
2282461 TTTGTTGAAAAAACACCAATATAGATTACACCTATTACGGCG
1 TTTGTTGAAAAAACACCAATATAGATTACACCTATTACGGCG
2282503 TTTGT
1 TTTGT
2282508 ATAAGAACGC
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
41 1 0.02
42 40 0.98
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Consensus pattern (42 bp):
TTTGTTGAAAAAACACCAATATAGATTACACCTATTACGGCG
Found at i:2282488 original size:125 final size:125
Alignment explanation
Indices: 2282329--2282597 Score: 324
Period size: 125 Copynumber: 2.2 Consensus size: 125
2282319 TATAAATATG
* * * ** *
2282329 TTGCGGCATTTGTTG-AAAAACGCCACTATAGATTACACCTATTGTGACATTTGTATAAAAATGC
1 TTGCGGCGTTTGTTGAAAAAACACCAATATAGATTACACCTATTACGACATTTGTATAAAAACGC
* ** * * * * *
2282393 CGCTAAAGTTTAAATATGTTACGACATTTGTTGAAAAAACGCTACAATAGATTACACTTC
66 CCCTAAAGTACAAATATGTTACGACATTTGTTGAAAAAACGCCACAATAGATCAAACCTA
* * *
2282453 TTGCGGCGTTTGTTGAAAAAACACCAATATAGATTACACCTATTACGGCGTTTGTATAAGAACGC
1 TTGCGGCGTTTGTTGAAAAAACACCAATATAGATTACACCTATTACGACATTTGTATAAAAACGC
* * ** *
2282518 CCCTAAAGTACAAATATTTTACGACGTTTGTTGAAAAATTGCCACTATAGATCAAACCTA
66 CCCTAAAGTACAAATATGTTACGACATTTGTTGAAAAAACGCCACAATAGATCAAACCTA
*
2282578 TTGCGGCGTTTGTAGAAAAA
1 TTGCGGCGTTTGTTGAAAAA
2282598 TGCCGCTAAC
Statistics
Matches: 121, Mismatches: 23, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
124 14 0.12
125 107 0.88
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (125 bp):
TTGCGGCGTTTGTTGAAAAAACACCAATATAGATTACACCTATTACGACATTTGTATAAAAACGC
CCCTAAAGTACAAATATGTTACGACATTTGTTGAAAAAACGCCACAATAGATCAAACCTA
Found at i:2282612 original size:83 final size:83
Alignment explanation
Indices: 2282459--2282613 Score: 202
Period size: 83 Copynumber: 1.9 Consensus size: 83
2282449 CTTCTTGCGG
* * * *
2282459 CGTTTGTTGAAAAAACACCAATATAGATTACACCTATTACGGCGTTTGTATAAGAACGCCCCTAA
1 CGTTTGTTGAAAAAACACCAATATAGATCAAACCTATTACGGCGTTTGTAGAAAAACGCCCCTAA
2282524 AGTACAAATATTTTACGA
66 AGTACAAATATTTTACGA
*** * * * *
2282542 CGTTTGTTGAAAAATTGCCACTATAGATCAAACCTATTGCGGCGTTTGTAGAAAAATGCCGCTAA
1 CGTTTGTTGAAAAAACACCAATATAGATCAAACCTATTACGGCGTTTGTAGAAAAACGCCCCTAA
*
2282607 CGTACAA
66 AGTACAA
2282614 TTCTATGTCG
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
83 60 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.28
Consensus pattern (83 bp):
CGTTTGTTGAAAAAACACCAATATAGATCAAACCTATTACGGCGTTTGTAGAAAAACGCCCCTAA
AGTACAAATATTTTACGA
Found at i:2282629 original size:83 final size:83
Alignment explanation
Indices: 2282456--2282632 Score: 194
Period size: 83 Copynumber: 2.1 Consensus size: 83
2282446 ACACTTCTTG
* * * *
2282456 CGGCGTTTGTTGAAAAAACACCAATATAGATTACACCTATTACGGCGTTTGTATAAGAACGCCCC
1 CGGCGTTTGTTGAAAAAACACCAATATAGATCAAACCTATTACGGCGTTTGTAGAAAAACGCCCC
*
2282521 TAAAGTACAAATATTTTA
66 TAAAGTACAAATATTGTA
* *** * * * *
2282539 CGACGTTTGTTGAAAAATTGCCACTATAGATCAAACCTATTGCGGCGTTTGTAGAAAAATGCCGC
1 CGGCGTTTGTTGAAAAAACACCAATATAGATCAAACCTATTACGGCGTTTGTAGAAAAACGCCCC
* * *
2282604 TAACGTACAATTCTATGT-
66 TAAAGTACAAATAT-TGTA
2282622 CGGCGTTTGTT
1 CGGCGTTTGTT
2282633 TTAAACGCCA
Statistics
Matches: 76, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
83 74 0.97
84 2 0.03
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Consensus pattern (83 bp):
CGGCGTTTGTTGAAAAAACACCAATATAGATCAAACCTATTACGGCGTTTGTAGAAAAACGCCCC
TAAAGTACAAATATTGTA
Found at i:2284087 original size:23 final size:23
Alignment explanation
Indices: 2284061--2284117 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
2284051 CTCGTATAAA
2284061 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
2284084 TGCACCGAAGTTCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
2284107 TGCACCTAAGT
1 TGCACCGAAGT
2284118 ACCATATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.28, C:0.26, G:0.25, T:0.21
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:2290219 original size:82 final size:82
Alignment explanation
Indices: 2290011--2290219 Score: 256
Period size: 82 Copynumber: 2.5 Consensus size: 82
2290001 ATTTTTCTAA
* * * * * *
2290011 AAACGCCACTATAAACAACCATATTGCGGCGTTTGAAGGGCAAACGCCGCTAAATTACTACTTTA
1 AAACGCCACTATAAACAACCCTATTGCGGCGTTTGTA-TGAAAACGCCGCTAAATTAATACTCTA
* *
2290076 TAGTGGCATTTTTTGCAG
65 TAGTGGCATTTGTTGCAC
* * * *
2290094 AAACGCCACTATAAACAACCCTATTGTGGCATTTGTTTGAAAACGCTGCTAAATTAATACTCTAT
1 AAACGCCACTATAAACAACCCTATTGCGGCGTTTGTATGAAAACGCCGCTAAATTAATACTCTAT
* * *
2290159 AGTGTCGTTTGTTGGAC
66 AGTGGCATTTGTTGCAC
* *
2290176 AAATGCCACTATAAACAACCCTATTGCGGCGTTTGTATAAAAAC
1 AAACGCCACTATAAACAACCCTATTGCGGCGTTTGTATGAAAAC
2290220 ATCGCTAATT
Statistics
Matches: 106, Mismatches: 20, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
82 74 0.70
83 32 0.30
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (82 bp):
AAACGCCACTATAAACAACCCTATTGCGGCGTTTGTATGAAAACGCCGCTAAATTAATACTCTAT
AGTGGCATTTGTTGCAC
Found at i:2290250 original size:82 final size:80
Alignment explanation
Indices: 2290009--2290282 Score: 224
Period size: 82 Copynumber: 3.3 Consensus size: 80
2289999 GCATTTTTCT
* * * * * *
2290009 AAAAACGCCACTATAAACAACCATATTGCGGCGTTTGAAGGGCAAACGCCGCTAAATTACTACTT
1 AAAAAAGCCACTATAAACAACCCTATTGCGGCGTTTGTA-TGAAAAC-CCGCTAAATTACTACTA
* * * *
2290074 TATAGTGGCATTTTTTGC
64 TATAG-AGCGTTTGTTGA
* * * * * * * *
2290092 AGAAACGCCACTATAAACAACCCTATTGTGGCATTTGTTTGAAAACGCTGCTAAATTAATACTCT
1 AAAAAAGCCACTATAAACAACCCTATTGCGGCGTTTGTATGAAAAC-CCGCTAAATTACTACTAT
* *
2290157 ATAGTGTCGTTTGTTGG
65 ATAGAG-CGTTTGTTGA
* * * * *
2290174 ACAAATGCCACTATAAACAACCCTATTGCGGCGTTTGTATAAAAACATCGCTAATTTACTACTAT
1 AAAAAAGCCACTATAAACAACCCTATTGCGGCGTTTGTATGAAAAC-CCGCTAAATTACTACTAT
* *
2290239 ATTGCAGCGTTTGTTAA
65 ATAG-AGCGTTTGTTGA
* *
2290256 AAAAAAGCTACTATAAACAACTCTATT
1 AAAAAAGCCACTATAAACAACCCTATT
2290283 TATGCGTTTG
Statistics
Matches: 154, Mismatches: 35, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
81 1 0.01
82 119 0.77
83 34 0.22
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.30
Consensus pattern (80 bp):
AAAAAAGCCACTATAAACAACCCTATTGCGGCGTTTGTATGAAAACCCGCTAAATTACTACTATA
TAGAGCGTTTGTTGA
Found at i:2293091 original size:21 final size:17
Alignment explanation
Indices: 2293043--2293077 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
2293033 TAGTAGAATA
*
2293043 TTTTCTAAAATATTAAT
1 TTTTTTAAAATATTAAT
2293060 TTTTTT-AAATATTAAT
1 TTTTTTAAAATATTAAT
2293076 TT
1 TT
2293078 CGTTACTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTTTTAAAATATTAAT
Found at i:2294223 original size:22 final size:22
Alignment explanation
Indices: 2294181--2294223 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
2294171 GTCCATATAA
*
2294181 TTATTTTAAAATATAAGTTTAT
1 TTATTTTAAAATATAAATTTAT
*
2294203 TTATTATTCAAAT-TAAATTTA
1 TTATT-TTAAAATATAAATTTA
2294224 AAATATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
TTATTTTAAAATATAAATTTAT
Found at i:2295315 original size:22 final size:21
Alignment explanation
Indices: 2295271--2295315 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
2295261 AGTATATATG
*
2295271 ATATATATAGTTTTTGAAGAT
1 ATATATATAGTTTTAGAAGAT
2295292 ATATAGTATAGTTTTCAGAA-AT
1 ATATA-TATAGTTTT-AGAAGAT
2295314 AT
1 AT
2295316 TTTTGATAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 5 0.24
22 13 0.62
23 3 0.14
ACGTcount: A:0.40, C:0.02, G:0.13, T:0.44
Consensus pattern (21 bp):
ATATATATAGTTTTAGAAGAT
Found at i:2295401 original size:38 final size:37
Alignment explanation
Indices: 2295315--2295439 Score: 154
Period size: 34 Copynumber: 3.4 Consensus size: 37
2295305 TTCAGAAATA
*
2295315 TTTTTGATAA-CATATAATATATA-ATTTTTAAATA--G
1 TTTTTGA-AAGCATATAATATATAGA-TTTTAAAAACGG
*
2295350 -TTTTGAAAACATATAATATATAGATTTTAAAAGACGG
1 TTTTTGAAAGCATATAATATATAGATTTTAAAA-ACGG
2295387 TTTTTGAAAGCATATAATATATAG-TTTTAAAAACGG
1 TTTTTGAAAGCATATAATATATAGATTTTAAAAACGG
2295423 TTTTTTGAAAGCATATA
1 -TTTTTGAAAGCATATA
2295440 TAATATAATT
Statistics
Matches: 81, Mismatches: 2, Indels: 12
0.85 0.02 0.13
Matches are distributed among these distances:
33 2 0.02
34 26 0.32
35 2 0.02
36 4 0.05
37 25 0.31
38 22 0.27
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.42
Consensus pattern (37 bp):
TTTTTGAAAGCATATAATATATAGATTTTAAAAACGG
Found at i:2295446 original size:37 final size:38
Alignment explanation
Indices: 2295315--2295439 Score: 156
Period size: 37 Copynumber: 3.4 Consensus size: 38
2295305 TTCAGAAATA
* *
2295315 TTTTTGATAA-CATATAATATATA-ATTTTTAAATA--G
1 TTTTTGA-AAGCATATAATATATAGATTTTAAAAGACGG
*
2295350 -TTTTGAAAACATATAATATATAGATTTTAAAAGACGG
1 TTTTTGAAAGCATATAATATATAGATTTTAAAAGACGG
2295387 TTTTTGAAAGCATATAATATATAG-TTTTAAAA-ACGG
1 TTTTTGAAAGCATATAATATATAGATTTTAAAAGACGG
2295423 TTTTTTGAAAGCATATA
1 -TTTTTGAAAGCATATA
2295440 TAATATAATT
Statistics
Matches: 81, Mismatches: 3, Indels: 10
0.86 0.03 0.11
Matches are distributed among these distances:
33 2 0.02
34 19 0.23
35 9 0.11
36 4 0.05
37 25 0.31
38 22 0.27
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.42
Consensus pattern (38 bp):
TTTTTGAAAGCATATAATATATAGATTTTAAAAGACGG
Found at i:2295475 original size:21 final size:23
Alignment explanation
Indices: 2295424--2295478 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 23
2295414 TAAAAACGGT
*
2295424 TTTTTGAAAGCATATATAATATAA
1 TTTTTGAAAACATATAT-ATATAA
* *
2295448 TTGTTGAAAACATAT-T-TATAG
1 TTTTTGAAAACATATATATATAA
2295469 TTTTTGAAAA
1 TTTTTGAAAA
2295479 TATAGAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 13 0.48
23 1 0.04
24 13 0.48
ACGTcount: A:0.42, C:0.04, G:0.11, T:0.44
Consensus pattern (23 bp):
TTTTTGAAAACATATATATATAA
Found at i:2295499 original size:2 final size:2
Alignment explanation
Indices: 2295485--2295550 Score: 56
Period size: 2 Copynumber: 35.5 Consensus size: 2
2295475 AAAATATAGA
*
2295485 AT AT AT GAT -T AT AT AT -T AT AT -T GT AT AT AT AT -T 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
2295524 AT -T AT AT AGT AT -T AT AT -T AT AT AT AT A
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT A
2295551 AATTATTTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 18
0.74 0.01 0.25
Matches are distributed among these distances:
1 7 0.13
2 43 0.80
3 4 0.07
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (2 bp):
AT
Found at i:2295502 original size:7 final size:7
Alignment explanation
Indices: 2295486--2295584 Score: 77
Period size: 7 Copynumber: 14.7 Consensus size: 7
2295476 AAATATAGAA
2295486 TATATGAT
1 TATAT-AT
2295494 TATATAT
1 TATATAT
2295501 TATAT-T
1 TATATAT
2295507 GTATATA-
1 -TATATAT
2295514 TAT-TA-
1 TATATAT
2295519 TATATAT
1 TATATAT
*
2295526 TATATAG
1 TATATAT
2295533 TATTATAT
1 TA-TATAT
2295541 TATATA-
1 TATATAT
*
2295547 TATAAAT
1 TATATAT
*
2295554 TATTTA-
1 TATATAT
2295560 T-TATAT
1 TATATAT
*
2295566 TGTATAT
1 TATATAT
*
2295573 TATTTAT
1 TATATAT
2295580 TATAT
1 TATAT
2295585 TTTTATTTAA
Statistics
Matches: 74, Mismatches: 9, Indels: 17
0.74 0.09 0.17
Matches are distributed among these distances:
5 8 0.11
6 13 0.18
7 42 0.57
8 11 0.15
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (7 bp):
TATATAT
Found at i:2295566 original size:9 final size:9
Alignment explanation
Indices: 2295498--2295590 Score: 50
Period size: 9 Copynumber: 9.7 Consensus size: 9
2295488 TATGATTATA
2295498 TATTATATT
1 TATTATATT
2295507 GTA-TATATAT
1 -TATTATAT-T
2295517 TA-TATATAT
1 TATTATAT-T
2295526 TATATAGTATT
1 TAT-TA-TATT
*
2295537 ATATTATATA
1 -TATTATATT
*
2295547 TATAAATTATT
1 TAT-TA-TATT
2295558 TATTATATT
1 TATTATATT
2295567 GTA-TATTATT
1 -TATTA-TATT
2295577 TATTATATT
1 TATTATATT
2295586 T-TTAT
1 TATTAT
2295591 TTAACTTTTT
Statistics
Matches: 69, Mismatches: 4, Indels: 22
0.73 0.04 0.23
Matches are distributed among these distances:
8 4 0.06
9 32 0.46
10 16 0.23
11 11 0.16
12 6 0.09
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (9 bp):
TATTATATT
Found at i:2297007 original size:20 final size:20
Alignment explanation
Indices: 2296978--2297016 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2296968 ATTCAATTAA
*
2296978 TTTAAAATTTCTTTTATTTC
1 TTTAAAATTTATTTTATTTC
*
2296998 TTTAATATTTATTTTATTT
1 TTTAAAATTTATTTTATTT
2297017 TAATTATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTAAAATTTATTTTATTTC
Found at i:2298170 original size:23 final size:23
Alignment explanation
Indices: 2298140--2298192 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
2298130 TGAATATCTT
*
2298140 ATCATCTTCTACTGTTAATCTCA
1 ATCATCTTCTACTGTTAATCCCA
*
2298163 ATCATCTTCTATTGTTAATCCCA
1 ATCATCTTCTACTGTTAATCCCA
2298186 ATCATCT
1 ATCATCT
2298193 ATTTTCATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.26, C:0.26, G:0.04, T:0.43
Consensus pattern (23 bp):
ATCATCTTCTACTGTTAATCCCA
Found at i:2298553 original size:2 final size:2
Alignment explanation
Indices: 2298548--2298595 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
2298538 TCTCTCCCTC
2298548 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
2298590 TA TA TA
1 TA TA TA
2298596 AATTTTTACC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2299200 original size:22 final size:22
Alignment explanation
Indices: 2299173--2299214 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2299163 CATTTTTTCG
2299173 TTTTATATATATATTATTATAT
1 TTTTATATATATATTATTATAT
* * *
2299195 TTTTATTTATTTGTTATTAT
1 TTTTATATATATATTATTAT
2299215 TACTTAAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTTATATATATATTATTATAT
Found at i:2299268 original size:21 final size:22
Alignment explanation
Indices: 2299251--2299315 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
2299241 TTGCAAATCG
*
2299251 GTCCAAACCAAACCCAAACCGA
1 GTCCAAACAAAACCCAAACCGA
* *
2299273 GTCCAAACAAAACCCAAACTGG
1 GTCCAAACAAAACCCAAACCGA
* *
2299295 GCCCAAATCAAAACCTAAACC
1 GTCCAAA-CAAAACCCAAACC
2299316 TAGCTTTAGC
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 25 0.69
23 11 0.31
ACGTcount: A:0.46, C:0.37, G:0.09, T:0.08
Consensus pattern (22 bp):
GTCCAAACAAAACCCAAACCGA
Found at i:2300231 original size:106 final size:107
Alignment explanation
Indices: 2300026--2300235 Score: 298
Period size: 109 Copynumber: 2.0 Consensus size: 107
2300016 GTTTAGCGTT
* * * * *
2300026 TTTTTCATTTTGGTTACCTATAAGGACCAAAATTGGTATTTACCCTTTTTCATGCGTGTTATACA
1 TTTTGCATTCTGGTCACATATAAGAACCAAAATTGGTATTTACCCTTTTTCATGCG-GTTATA-A
* * *
2300091 TTTATTGGGTTATTTTTTATTTAGTCCCTCTAAGTTTAGGGCGC
64 TTTATTGGGTTATTTTCTATTTAGACCCTATAAGTTTAGGGCGC
*
2300135 TTTTGCATTCTGGTCACATATAAGAACCGAAATTGGTATTTACCCTTTTTTCATGC-GTTAT-AT
1 TTTTGCATTCTGGTCACATATAAGAACCAAAATTGGTATTTACCC-TTTTTCATGCGGTTATAAT
2300198 TTATTGGGTTATTTTCTATTTAGACCCTATAAGTTTAG
65 TTATTGGGTTATTTTCTATTTAGACCCTATAAGTTTAG
2300236 CATATTTTTG
Statistics
Matches: 91, Mismatches: 9, Indels: 5
0.87 0.09 0.05
Matches are distributed among these distances:
106 37 0.41
108 5 0.05
109 39 0.43
110 10 0.11
ACGTcount: A:0.23, C:0.15, G:0.16, T:0.46
Consensus pattern (107 bp):
TTTTGCATTCTGGTCACATATAAGAACCAAAATTGGTATTTACCCTTTTTCATGCGGTTATAATT
TATTGGGTTATTTTCTATTTAGACCCTATAAGTTTAGGGCGC
Found at i:2300245 original size:106 final size:106
Alignment explanation
Indices: 2300016--2300256 Score: 308
Period size: 106 Copynumber: 2.2 Consensus size: 106
2300006 AGTCCCCTAG
* * * * *
2300016 GTTTAGCGTTTTTTTCATTTTGGTTACCTATAAGGACCAAAATTGGTATTTACCCTTTTTCATGC
1 GTTTAGCGTTTTTTGCATTCTGGTCACATATAAGAACCAAAATTGGTATTTACCCTTTTTCATGC
* * *
2300081 GTGTTATACATTTATTGGGTTATTTTTTATTTAGTCCCTCTAA
66 G-GTTATA-ATTTATTGGGTTATTTTCTATTTAGACCCTATAA
* *
2300124 GTTTAGGGCG-CTTTTGCATTCTGGTCACATATAAGAACCGAAATTGGTATTTACCCTTTTTTCA
1 GTTTA--GCGTTTTTTGCATTCTGGTCACATATAAGAACCAAAATTGGTATTTACCC-TTTTTCA
2300188 TGC-GTTAT-ATTTATTGGGTTATTTTCTATTTAGACCCTATAA
63 TGCGGTTATAATTTATTGGGTTATTTTCTATTTAGACCCTATAA
*
2300230 GTTTAGCATATTTTTGCATTCTGGTCA
1 GTTTAGCGT-TTTTTGCATTCTGGTCA
2300257 TCTGTGAGGA
Statistics
Matches: 116, Mismatches: 12, Indels: 12
0.83 0.09 0.09
Matches are distributed among these distances:
104 2 0.02
106 52 0.45
108 10 0.09
109 39 0.34
110 13 0.11
ACGTcount: A:0.22, C:0.15, G:0.16, T:0.46
Consensus pattern (106 bp):
GTTTAGCGTTTTTTGCATTCTGGTCACATATAAGAACCAAAATTGGTATTTACCCTTTTTCATGC
GGTTATAATTTATTGGGTTATTTTCTATTTAGACCCTATAA
Found at i:2300513 original size:22 final size:21
Alignment explanation
Indices: 2300479--2300519 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
2300469 CCCCTAAACT
2300479 TTTGTGTTTATTTTATTTTAG
1 TTTGTGTTTATTTTATTTTAG
*
2300500 TTTGTTTTGTATTTTATTTT
1 TTTGTGTT-TATTTTATTTT
2300520 GATTTAGTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (21 bp):
TTTGTGTTTATTTTATTTTAG
Found at i:2300547 original size:30 final size:32
Alignment explanation
Indices: 2300512--2300582 Score: 83
Period size: 30 Copynumber: 2.2 Consensus size: 32
2300502 TGTTTTGTAT
* * *
2300512 TTTATTTTGATTTAGTC-TCTTA-ATTTTTAA
1 TTTATTTTAATTTAGTCTTCTAACATGTTTAA
*
2300542 TTTATTTTAATTTGGTCTTTCTAACATGTTTAA
1 TTTATTTTAATTTAGTC-TTCTAACATGTTTAA
2300575 TTTATTTT
1 TTTATTTT
2300583 TAATCGCTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 15 0.44
32 4 0.12
33 15 0.44
ACGTcount: A:0.23, C:0.07, G:0.07, T:0.63
Consensus pattern (32 bp):
TTTATTTTAATTTAGTCTTCTAACATGTTTAA
Found at i:2300900 original size:45 final size:46
Alignment explanation
Indices: 2300827--2300919 Score: 179
Period size: 45 Copynumber: 2.0 Consensus size: 46
2300817 TTGTTGATTG
2300827 TTCGAACTCTTAATTTGTCAATCATCGACTAATTTTAAAAACTATT
1 TTCGAACTCTTAATTTGTCAATCATCGACTAATTTTAAAAACTATT
2300873 TTCGAACTCTTAA-TTGTCAATCATCGACTAATTTTAAAAACTATT
1 TTCGAACTCTTAATTTGTCAATCATCGACTAATTTTAAAAACTATT
2300918 TT
1 TT
2300920 AATTTAATCC
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 34 0.72
46 13 0.28
ACGTcount: A:0.34, C:0.17, G:0.06, T:0.42
Consensus pattern (46 bp):
TTCGAACTCTTAATTTGTCAATCATCGACTAATTTTAAAAACTATT
Found at i:2301601 original size:49 final size:49
Alignment explanation
Indices: 2301527--2301624 Score: 160
Period size: 49 Copynumber: 2.0 Consensus size: 49
2301517 AAGGTAATAT
*
2301527 CCAGTTATTAGGTGCAATAGCTGATCTCCCGCATTCATACTAGGGGTGA
1 CCAGTTATTAGGCGCAATAGCTGATCTCCCGCATTCATACTAGGGGTGA
* * *
2301576 CCAGTTATTGGGCGCAATAGTTGATCTCCCTCATTCATACTAGGGGTGA
1 CCAGTTATTAGGCGCAATAGCTGATCTCCCGCATTCATACTAGGGGTGA
2301625 ATGCTATGGG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.30
Consensus pattern (49 bp):
CCAGTTATTAGGCGCAATAGCTGATCTCCCGCATTCATACTAGGGGTGA
Found at i:2306081 original size:22 final size:22
Alignment explanation
Indices: 2306053--2306103 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
2306043 ATTTTGGGGG
2306053 TAGTACCGCCACGTTACTGATT
1 TAGTACCGCCACGTTACTGATT
2306075 TAGTACCGCCACGTTACTGATT
1 TAGTACCGCCACGTTACTGATT
2306097 TAGTACC
1 TAGTACC
2306104 TGATAGATGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (22 bp):
TAGTACCGCCACGTTACTGATT
Found at i:2313306 original size:18 final size:18
Alignment explanation
Indices: 2313274--2313312 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2313264 CCATTTTTTA
*
2313274 TATATTTATTATTATTCT
1 TATATTTATTATTATTAT
2313292 TATATTT-TTATTTATTAT
1 TATATTTATTA-TTATTAT
2313310 TAT
1 TAT
2313313 TACTTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (18 bp):
TATATTTATTATTATTAT
Found at i:2313327 original size:24 final size:24
Alignment explanation
Indices: 2313273--2313327 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
2313263 TCCATTTTTT
*
2313273 ATATATTTATTATTATTCTTATAT
1 ATATATTTATTATTATTCTTATAA
* *
2313297 TTTTATTTATTATTATTACTTA-AA
1 ATATATTTATTATTATT-CTTATAA
2313321 ATATATT
1 ATATATT
2313328 ACAAACCCCA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
24 21 0.84
25 4 0.16
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (24 bp):
ATATATTTATTATTATTCTTATAA
Found at i:2315435 original size:43 final size:43
Alignment explanation
Indices: 2315374--2315462 Score: 178
Period size: 43 Copynumber: 2.1 Consensus size: 43
2315364 CATAGGACGG
2315374 TTCATATCTCAGTTAACCGACAAGTGTGACCCAATCTTTCGTC
1 TTCATATCTCAGTTAACCGACAAGTGTGACCCAATCTTTCGTC
2315417 TTCATATCTCAGTTAACCGACAAGTGTGACCCAATCTTTCGTC
1 TTCATATCTCAGTTAACCGACAAGTGTGACCCAATCTTTCGTC
2315460 TTC
1 TTC
2315463 TTCAAAAGAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.25, C:0.28, G:0.13, T:0.34
Consensus pattern (43 bp):
TTCATATCTCAGTTAACCGACAAGTGTGACCCAATCTTTCGTC
Found at i:2317782 original size:1 final size:1
Alignment explanation
Indices: 2317776--2317844 Score: 75
Period size: 1 Copynumber: 69.0 Consensus size: 1
2317766 TCGAAGAAAG
* * * * * * *
2317776 AAAAAAAAGAAAAAAAAAAAAAAAAAAAAAAGAAAAGAAAAAAGAAAAAGAAAAAAAAGAAAAGA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2317841 AAAA
1 AAAA
2317845 GAGGAAAATG
Statistics
Matches: 54, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 54 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (1 bp):
A
Found at i:2317787 original size:13 final size:13
Alignment explanation
Indices: 2317769--2317844 Score: 97
Period size: 13 Copynumber: 5.9 Consensus size: 13
2317759 GTCCAAGTCG
2317769 AAGAAAGAAAAAA
1 AAGAAAGAAAAAA
2317782 AAGAAA-AAAAAA
1 AAGAAAGAAAAAA
2317794 AA-AAA-AAAAAA
1 AAGAAAGAAAAAA
2317805 AAGAAAAGAAAAAA
1 AAG-AAAGAAAAAA
2317819 GAA-AAAGAAAAAA
1 -AAGAAAGAAAAAA
2317832 AAGAAAAGAAAAA
1 AAG-AAAGAAAAA
2317845 GAGGAAAATG
Statistics
Matches: 57, Mismatches: 0, Indels: 11
0.84 0.00 0.16
Matches are distributed among these distances:
11 11 0.19
12 10 0.18
13 19 0.33
14 15 0.26
15 2 0.04
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAGAAAGAAAAAA
Found at i:2317816 original size:27 final size:27
Alignment explanation
Indices: 2317776--2317844 Score: 104
Period size: 27 Copynumber: 2.6 Consensus size: 27
2317766 TCGAAGAAAG
2317776 AAAA-AAAAGAAAAAAAAAAAAAAAAAA
1 AAAAGAAAAG-AAAAAAAAAAAAAAAAA
* *
2317803 AAAAGAAAAGAAAAAAGAAAAAGAAAA
1 AAAAGAAAAGAAAAAAAAAAAAAAAAA
2317830 AAAAGAAAAGAAAAA
1 AAAAGAAAAGAAAAA
2317845 GAGGAAAATG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
27 34 0.87
28 5 0.13
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (27 bp):
AAAAGAAAAGAAAAAAAAAAAAAAAAA
Found at i:2317922 original size:17 final size:17
Alignment explanation
Indices: 2317902--2317934 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2317892 AAAAAATATG
2317902 AAAAAGAGAAAA-AAGGA
1 AAAAAGA-AAAATAAGGA
2317919 AAAAAGAAAAATAAGG
1 AAAAAGAAAAATAAGG
2317935 TGGGTTCAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (17 bp):
AAAAAGAAAAATAAGGA
Found at i:2321048 original size:13 final size:12
Alignment explanation
Indices: 2321000--2321067 Score: 50
Period size: 12 Copynumber: 5.6 Consensus size: 12
2320990 TTTCTTTTAG
2321000 TTTTTATTATTTA
1 TTTTTATTA-TTA
2321013 TTTTTAATT-TT-
1 TTTTT-ATTATTA
*
2321024 TTTTCATTATTA
1 TTTTTATTATTA
2321036 TGTTTTATTATTA
1 T-TTTTATTATTA
** *
2321049 CATATATTATTA
1 TTTTTATTATTA
*
2321061 TTATTAT
1 TTTTTAT
2321068 ATGTATATAT
Statistics
Matches: 42, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
10 3 0.07
11 6 0.14
12 15 0.36
13 15 0.36
14 3 0.07
ACGTcount: A:0.26, C:0.03, G:0.01, T:0.69
Consensus pattern (12 bp):
TTTTTATTATTA
Found at i:2321078 original size:2 final size:2
Alignment explanation
Indices: 2321050--2321097 Score: 59
Period size: 2 Copynumber: 26.0 Consensus size: 2
2321040 TTATTATTAC
*
2321050 AT AT AT -T AT -T AT -T AT -T AT AT GT 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
2321088 AT AT AT AT AT
1 AT AT AT AT AT
2321098 TTTATTCAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
1 4 0.10
2 36 0.90
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (2 bp):
AT
Done.