Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007967.1 Hibiscus syriacus cultivar Beakdansim tig00110402_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: 2476418
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 11
Found at i:2040580 original size:74 final size:74
Alignment explanation
Indices: 2040410--2040583 Score: 180
Period size: 74 Copynumber: 2.4 Consensus size: 74
2040400 AGGTCATGGG
* * *
2040410 ATCCT-CTTCAGAGGGTACAT-CTCATC-ATGTTTCCTAATTTCTATTGATATTCTCTTCAGAAG
1 ATCCTCCTTGAGAGGGTACATCCCCATCTA-GTTTCCTAATTTCTATTGATATCCTCTTCAGAAG
2040472 TTAATTTGGT
65 TTAATTTGGT
* * * * * *
2040482 ATCTTCTTTGAGTGGGTACATCCCCATCTAGTTTCCTAATTTTTGTTGAGT-TCCTCTTCAGAGG
1 ATCCTCCTTGAGAGGGTACATCCCCATCTAGTTTCCTAATTTCTATTGA-TATCCTCTTCAGAAG
2040546 TTAATTTGGGT
65 TTAATTT-GGT
*
2040557 -TCCTCCTTG-GAGGGTAACGTCCCCATC
1 ATCCTCCTTGAGAGGGT-ACATCCCCATC
2040584 CTAATCTATG
Statistics
Matches: 83, Mismatches: 13, Indels: 10
0.78 0.12 0.09
Matches are distributed among these distances:
72 4 0.05
73 17 0.20
74 57 0.69
75 5 0.06
ACGTcount: A:0.20, C:0.22, G:0.18, T:0.41
Consensus pattern (74 bp):
ATCCTCCTTGAGAGGGTACATCCCCATCTAGTTTCCTAATTTCTATTGATATCCTCTTCAGAAGT
TAATTTGGT
Found at i:2041507 original size:2 final size:2
Alignment explanation
Indices: 2041500--2041531 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2041490 TCCTGAATCA
2041500 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
2041532 TATTGGCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2049901 original size:13 final size:12
Alignment explanation
Indices: 2049851--2049903 Score: 54
Period size: 13 Copynumber: 4.3 Consensus size: 12
2049841 GTATCTGGAA
2049851 GAAAAT-AATAT
1 GAAAATAAATAT
*
2049862 GAAAATGAATAT
1 GAAAATAAATAT
* *
2049874 GAAAGTGAAAGAT
1 GAAAAT-AAATAT
2049887 GAAAATAAAATAT
1 GAAAAT-AAATAT
2049900 GAAA
1 GAAA
2049904 TGTTCAGAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
11 6 0.18
12 10 0.29
13 18 0.53
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.21
Consensus pattern (12 bp):
GAAAATAAATAT
Found at i:2053934 original size:20 final size:20
Alignment explanation
Indices: 2053906--2053957 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
2053896 GACCGTTTTT
2053906 AGTTATTGGGGACATTTTGG
1 AGTTATTGGGGACATTTTGG
*
2053926 AGTTGTTGGGGACATTTTGG
1 AGTTATTGGGGACATTTTGG
**
2053946 AGCAATTGGGGA
1 AGTTATTGGGGA
2053958 TTAATTTTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.21, C:0.06, G:0.38, T:0.35
Consensus pattern (20 bp):
AGTTATTGGGGACATTTTGG
Found at i:2056220 original size:2 final size:2
Alignment explanation
Indices: 2056213--2056278 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
2056203 TACCTTTTAC
2056213 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
2056255 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
2056279 TAAACTATAT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2059052 original size:2 final size:2
Alignment explanation
Indices: 2059045--2059089 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
2059035 AAATTCCTCT
2059045 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
2059087 TA T
1 TA T
2059090 TAGAAAATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2062310 original size:20 final size:20
Alignment explanation
Indices: 2062287--2062352 Score: 105
Period size: 20 Copynumber: 3.3 Consensus size: 20
2062277 AATTTGTAAA
*
2062287 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
2062307 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
* *
2062327 TCGTAACACATAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
2062347 TCGCAA
1 TCGCAA
2062353 AGCGCGTTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.45, C:0.24, G:0.12, T:0.18
Consensus pattern (20 bp):
TCGCAACACAAAAGTCAAAT
Found at i:2062531 original size:22 final size:22
Alignment explanation
Indices: 2062481--2062538 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
2062471 TCGGTCTCTA
*
2062481 CGGCGACATCCGTCCCCATCTT
1 CGGCGAAATCCGTCCCCATCTT
* *
2062503 CGACGAAATCTGTCCCCATC-T
1 CGGCGAAATCCGTCCCCATCTT
2062524 CAGGCGAAATCCGTC
1 C-GGCGAAATCCGTC
2062539 TATCTCCATC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 2 0.07
22 28 0.93
ACGTcount: A:0.21, C:0.40, G:0.19, T:0.21
Consensus pattern (22 bp):
CGGCGAAATCCGTCCCCATCTT
Found at i:2062906 original size:20 final size:20
Alignment explanation
Indices: 2062891--2062932 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
2062881 ATTCGCAAGA
2062891 CGAAAATGAAAATCGCAACG
1 CGAAAATGAAAATCGCAACG
2062911 CGAAAATGAAAATCGCAACG
1 CGAAAATGAAAATCGCAACG
2062931 CG
1 CG
2062933 GTTTTAGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.48, C:0.21, G:0.21, T:0.10
Consensus pattern (20 bp):
CGAAAATGAAAATCGCAACG
Found at i:2065138 original size:21 final size:21
Alignment explanation
Indices: 2065114--2065229 Score: 94
Period size: 21 Copynumber: 5.6 Consensus size: 21
2065104 TTCACCTGTC
* *
2065114 ATCGTTCAAGTGGCACCTCCT
1 ATCGTTCAAGAGGCCCCTCCT
2065135 ATCGTTCAAGAGGCCCCT-CT
1 ATCGTTCAAGAGGCCCCTCCT
* *
2065155 CATCATTCAAGAGGCCCCTCCC
1 -ATCGTTCAAGAGGCCCCTCCT
* * *
2065177 ACCGTTCAAGA-GACCCT-GT
1 ATCGTTCAAGAGGCCCCTCCT
* * *
2065196 CATCGTTCAAGAGGTCTCTCCC
1 -ATCGTTCAAGAGGCCCCTCCT
*
2065218 ACCGTTCAAGAG
1 ATCGTTCAAGAG
2065230 CCCGATTCAC
Statistics
Matches: 75, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
20 17 0.23
21 57 0.76
22 1 0.01
ACGTcount: A:0.22, C:0.35, G:0.19, T:0.23
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCCCTCCT
Found at i:2065217 original size:41 final size:40
Alignment explanation
Indices: 2065108--2065229 Score: 145
Period size: 41 Copynumber: 3.0 Consensus size: 40
2065098 GCCCGATTCA
* * * *
2065108 CCTGTCATCGTTCAAGTGGCACCTCCTATCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGC-CCTCCCACCGTTCAAGA-GAC
* *
2065150 CCTCTCATCATTCAAGAGGCCCCTCCCACCGTTCAAGAGAC
1 CCTGTCATCGTTCAAGAGG-CCCTCCCACCGTTCAAGAGAC
*
2065191 CCTGTCATCGTTCAAGAGGTCTCTCCCACCGTTCAAGAG
1 CCTGTCATCGTTCAAGAGG-CCCTCCCACCGTTCAAGAG
2065230 CCCGATTCAC
Statistics
Matches: 69, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
41 37 0.54
42 31 0.45
43 1 0.01
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (40 bp):
CCTGTCATCGTTCAAGAGGCCCTCCCACCGTTCAAGAGAC
Found at i:2066700 original size:64 final size:64
Alignment explanation
Indices: 2066590--2066747 Score: 255
Period size: 64 Copynumber: 2.5 Consensus size: 64
2066580 TTAATTGAAT
2066590 TTTACATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTG
1 TTTA-ATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTG
* * *
2066655 TTTAATTGATTTGTAAAAGTTGATTTGTTTAATTTATGTGTAAATAAGAATTATTTTTTGCTTG
1 TTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTG
*
2066719 TTTAATTAATTT-TCAAAAGTTGATTTGTT
1 TTTAATTGATTTGT-AAAAGTTGATTTGTT
2066748 GTTTTAAATT
Statistics
Matches: 88, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
63 1 0.01
64 83 0.94
65 4 0.05
ACGTcount: A:0.30, C:0.03, G:0.16, T:0.51
Consensus pattern (64 bp):
TTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTG
Found at i:2066866 original size:20 final size:20
Alignment explanation
Indices: 2066839--2066887 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
2066829 GCGTTGAGAT
* *
2066839 AGTCAAATTCGTAACGTGAA
1 AGTCAAATTCGCAACGCGAA
*
2066859 AGTTAAATTCGCAACGCGAA
1 AGTCAAATTCGCAACGCGAA
2066879 AGTCAAATT
1 AGTCAAATT
2066888 GGCGTTGCGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.24
Consensus pattern (20 bp):
AGTCAAATTCGCAACGCGAA
Found at i:2066944 original size:29 final size:29
Alignment explanation
Indices: 2066911--2066992 Score: 146
Period size: 29 Copynumber: 2.8 Consensus size: 29
2066901 CGCGTTTCTT
2066911 ATTTGACTTTCGCAATAATCGCAATGCGA
1 ATTTGACTTTCGCAATAATCGCAATGCGA
*
2066940 ATTTGACTTTCGCAATAATCACAATGCGA
1 ATTTGACTTTCGCAATAATCGCAATGCGA
*
2066969 ATTTGACTTTCGCAACAATCGCAA
1 ATTTGACTTTCGCAATAATCGCAA
2066993 CAAAAAATCT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (29 bp):
ATTTGACTTTCGCAATAATCGCAATGCGA
Found at i:2068118 original size:18 final size:18
Alignment explanation
Indices: 2068095--2068131 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2068085 ATTTATATAT
2068095 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
2068113 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
2068131 A
1 A
2068132 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:2068545 original size:25 final size:25
Alignment explanation
Indices: 2068517--2068566 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
2068507 CATTATTTTC
*
2068517 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
*
2068542 CAAATAATGTACTCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
2068567 TAATTGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.44, C:0.20, G:0.08, T:0.28
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:2068760 original size:20 final size:20
Alignment explanation
Indices: 2068714--2068760 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
2068704 CGTTGCGATT
*
2068714 GTTGCGAAAGTCAAATTCGT
1 GTTGCGAAAGTCAAATTCGC
***
2068734 AACGCGAAAGTCAAATTCGC
1 GTTGCGAAAGTCAAATTCGC
2068754 GTTGCGA
1 GTTGCGA
2068761 TTTTTGCGTT
Statistics
Matches: 20, Mismatches: 7, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (20 bp):
GTTGCGAAAGTCAAATTCGC
Found at i:2071503 original size:12 final size:12
Alignment explanation
Indices: 2071482--2071515 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2071472 GGTTATGGGT
*
2071482 TTTGAGATTGTG
1 TTTGATATTGTG
2071494 TTTGATATTGTG
1 TTTGATATTGTG
*
2071506 TTTGGTATTG
1 TTTGATATTG
2071516 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:2072331 original size:19 final size:20
Alignment explanation
Indices: 2072307--2072451 Score: 75
Period size: 20 Copynumber: 7.3 Consensus size: 20
2072297 CTAAAACCTA
*
2072307 TTGCGAAATT-AAATTCGTG
1 TTGCGAAATTGAAATTCGAG
*
2072326 TTGCG-AATTCGAAAATCGAG
1 TTGCGAAATT-GAAATTCGAG
*
2072346 TTGCGAATTTGAAATTC-AG
1 TTGCGAAATTGAAATTCGAG
* ** * *
2072365 TTGCGAATTTGACTTTTGTG
1 TTGCGAAATTGAAATTCGAG
* * *
2072385 TTGCG-ATTTACAAATTCGCG
1 TTGCGAAATT-GAAATTCGAG
* * *
2072405 TTGCGAATTTGGAAACT-GGG
1 TTGCGAAATT-GAAATTCGAG
* * *
2072425 TTGCGAAATTGGAGTTCGCG
1 TTGCGAAATTGAAATTCGAG
2072445 TTGCGAA
1 TTGCGAA
2072452 TTTGTTGGTC
Statistics
Matches: 97, Mismatches: 22, Indels: 13
0.73 0.17 0.10
Matches are distributed among these distances:
18 4 0.04
19 28 0.29
20 54 0.56
21 11 0.11
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.34
Consensus pattern (20 bp):
TTGCGAAATTGAAATTCGAG
Found at i:2073257 original size:80 final size:80
Alignment explanation
Indices: 2073124--2073281 Score: 282
Period size: 80 Copynumber: 2.0 Consensus size: 80
2073114 AAAATACTCC
*
2073124 AAAAAAGAATATAAGTTAAAATGACAATTCTAATAAAGGTTGAAAACCAATTTTAGCATTATG-G
1 AAAAAAGAATATAAGTTAAAATAACAATTCTAATAAAGGTTGAAAACCAATTTTAGCATTATGTG
2073188 TTTTTTTAATCGAACA
66 -TTTTTTAATCGAACA
*
2073204 AAAAAAGAATATAAGTTAAAATAACAATTCTAATAAATGTTGAAAACCAATTTTAGCATTATGTG
1 AAAAAAGAATATAAGTTAAAATAACAATTCTAATAAAGGTTGAAAACCAATTTTAGCATTATGTG
2073269 TTTTTTAATCGAA
66 TTTTTTAATCGAA
2073282 GAGTAGATCC
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
80 74 0.99
81 1 0.01
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.34
Consensus pattern (80 bp):
AAAAAAGAATATAAGTTAAAATAACAATTCTAATAAAGGTTGAAAACCAATTTTAGCATTATGTG
TTTTTTAATCGAACA
Found at i:2074169 original size:31 final size:31
Alignment explanation
Indices: 2074131--2074213 Score: 103
Period size: 31 Copynumber: 2.7 Consensus size: 31
2074121 ATACGTGGTA
* * *
2074131 ATGTCACATCGTTACTTTGGACACATGATAT
1 ATGTCACATCATTACTTTGAACACATAATAT
*
2074162 ATGTCACATCATTACTTTGAACATATAATAT
1 ATGTCACATCATTACTTTGAACACATAATAT
* * *
2074193 ATGCCATATCATCACTTTGAA
1 ATGTCACATCATTACTTTGAA
2074214 AATATGGTAA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (31 bp):
ATGTCACATCATTACTTTGAACACATAATAT
Found at i:2078941 original size:42 final size:42
Alignment explanation
Indices: 2078862--2078942 Score: 101
Period size: 42 Copynumber: 1.9 Consensus size: 42
2078852 ATTCTTACGT
* * ** *
2078862 TTAAATATGTAAATATATTTTTATTTGTTTATTTAAATACAC
1 TTAAATATATAAATATATTTTTATTAGTAAATATAAATACAC
2078904 TTAAATATATAAATATATTTTTATTCAG-AAATATAAATA
1 TTAAATATATAAATATATTTTTATT-AGTAAATATAAATA
2078943 TATTTTAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
42 32 0.97
43 1 0.03
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (42 bp):
TTAAATATATAAATATATTTTTATTAGTAAATATAAATACAC
Found at i:2079099 original size:23 final size:20
Alignment explanation
Indices: 2079073--2079122 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 20
2079063 TTATTAATTA
2079073 TATAAATATATTCAATTTAAAAT
1 TATAAATATATTC--TTT-AAAT
*
2079096 TATATATATATTCTTTAAAT
1 TATAAATATATTCTTTAAAT
2079116 TATAAAT
1 TATAAAT
2079123 GTAAAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 10 0.40
21 3 0.12
23 12 0.48
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (20 bp):
TATAAATATATTCTTTAAAT
Found at i:2079122 original size:27 final size:26
Alignment explanation
Indices: 2079060--2079122 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
2079050 TAATAAAATA
*
2079060 AAATTATTAATTATATAAATATATTC
1 AAATTATAAATTATATAAATATATTC
* * * *
2079086 AATTTA-AAATTATATATATATTCTTT
1 AAATTATAAATTATATAAATA-TATTC
2079112 AAATTATAAAT
1 AAATTATAAAT
2079123 GTAAAAAATA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
25 12 0.41
26 13 0.45
27 4 0.14
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (26 bp):
AAATTATAAATTATATAAATATATTC
Found at i:2079151 original size:23 final size:24
Alignment explanation
Indices: 2079125--2079170 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
2079115 TTATAAATGT
2079125 AAAAAATATTAAAT-TT-AATTTAC
1 AAAAAATA-TAAATCTTAAATTTAC
*
2079148 AAAATATATAAATCTTAAATTTA
1 AAAAAATATAAATCTTAAATTTA
2079171 ATTTTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 5 0.25
23 9 0.45
24 6 0.30
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (24 bp):
AAAAAATATAAATCTTAAATTTAC
Found at i:2079728 original size:21 final size:22
Alignment explanation
Indices: 2079704--2079748 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
2079694 ATACGTTGAC
* *
2079704 AAATTAAAA-GATAAATGATTA
1 AAATGAAAAGGATAAATAATTA
*
2079725 AAATGAAAAGGCTAAATAATTA
1 AAATGAAAAGGATAAATAATTA
2079747 AA
1 AA
2079749 TGGTTACTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.62, C:0.02, G:0.11, T:0.24
Consensus pattern (22 bp):
AAATGAAAAGGATAAATAATTA
Found at i:2080530 original size:21 final size:21
Alignment explanation
Indices: 2080504--2080550 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
2080494 ACCTATGTCA
2080504 GTCGTTGTCTATGTTGCCTTG
1 GTCGTTGTCTATGTTGCCTTG
2080525 GTCGTTGTCTATGTTGCCTTG
1 GTCGTTGTCTATGTTGCCTTG
2080546 GTCGT
1 GTCGT
2080551 CGTCCTTACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.04, C:0.19, G:0.30, T:0.47
Consensus pattern (21 bp):
GTCGTTGTCTATGTTGCCTTG
Found at i:2083149 original size:2 final size:2
Alignment explanation
Indices: 2083144--2083170 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2083134 TGGATGCCTT
2083144 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2083171 TGGTTGCCTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2090977 original size:20 final size:19
Alignment explanation
Indices: 2090933--2090979 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
2090923 GAAAATGAAA
* *
2090933 ATAAAAAATAACAAAAGAT
1 ATAAAAAATAAAAAAAAAT
2090952 AGTAAAAAATAAAAAAAAAT
1 A-TAAAAAATAAAAAAAAAT
2090972 CATAAAAA
1 -ATAAAAA
2090980 TAACAGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 1 0.04
20 22 0.92
21 1 0.04
ACGTcount: A:0.77, C:0.04, G:0.04, T:0.15
Consensus pattern (19 bp):
ATAAAAAATAAAAAAAAAT
Found at i:2090978 original size:10 final size:10
Alignment explanation
Indices: 2090932--2090979 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
2090922 AGAAAATGAA
2090932 AATAAAAAAT
1 AATAAAAAAT
* *
2090942 AACAAAAGAT
1 AATAAAAAAT
*
2090952 AGTAAAAAAT
1 AATAAAAAAT
*
2090962 AAAAAAAAAT
1 AATAAAAAAT
*
2090972 CATAAAAA
1 AATAAAAA
2090980 TAACAGAAAA
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.77, C:0.04, G:0.04, T:0.15
Consensus pattern (10 bp):
AATAAAAAAT
Found at i:2093088 original size:35 final size:35
Alignment explanation
Indices: 2093049--2093158 Score: 159
Period size: 35 Copynumber: 3.1 Consensus size: 35
2093039 ATGGGAAGCT
* *
2093049 AGCAATTCAATCTAGCCTTCACAAAAGAGTAGTGA
1 AGCAATGCAATCAAGCCTTCACAAAAGAGTAGTGA
*
2093084 AGCAATGCAATCAAGCTTTCACAAAAGAGTAGTGA
1 AGCAATGCAATCAAGCCTTCACAAAAGAGTAGTGA
* *
2093119 AACAATGCAATCCAGCCTTCACAAAAAGAGTAGTG-
1 AGCAATGCAATCAAGCCTTCAC-AAAAGAGTAGTGA
2093154 AGCAA
1 AGCAA
2093159 GATTAGATCA
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
35 55 0.82
36 12 0.18
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.19
Consensus pattern (35 bp):
AGCAATGCAATCAAGCCTTCACAAAAGAGTAGTGA
Found at i:2104584 original size:18 final size:18
Alignment explanation
Indices: 2104554--2104591 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2104544 AATGTCACAA
2104554 TTTTTTTATAATAGAATT
1 TTTTTTTATAATAGAATT
*
2104572 TTTTATTTA-AATATAATT
1 TTTT-TTTATAATAGAATT
2104590 TT
1 TT
2104592 ATTTATAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (18 bp):
TTTTTTTATAATAGAATT
Found at i:2112214 original size:70 final size:70
Alignment explanation
Indices: 2112091--2112221 Score: 217
Period size: 70 Copynumber: 1.9 Consensus size: 70
2112081 ACCTCAAATA
* * *
2112091 AATTATGAATGTTGGGAATCATATTGGAGTCAATAGAGACGTTGTGGTGTGAAATCCACTTGGAA
1 AATTATGAACGTTGGGAATCATATTGGAGTCAATAAAGACGTTGTGGTGTGAAATACACTTGGAA
2112156 AAGCT
66 AAGCT
* *
2112161 AATTCTGAACGTTGGGAATCATATTGGAGTCAATAAAGCCGTTGTGGTGTGAAATACACTT
1 AATTATGAACGTTGGGAATCATATTGGAGTCAATAAAGACGTTGTGGTGTGAAATACACTT
2112222 AAAAAAACTG
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
70 56 1.00
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.31
Consensus pattern (70 bp):
AATTATGAACGTTGGGAATCATATTGGAGTCAATAAAGACGTTGTGGTGTGAAATACACTTGGAA
AAGCT
Found at i:2117314 original size:20 final size:20
Alignment explanation
Indices: 2117291--2117334 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2117281 ATTCAACCTT
*
2117291 AAATGCAAATTAATC-AAACC
1 AAATGCAAA-CAATCAAAACC
*
2117311 AAATTCAAACAATCAAAACC
1 AAATGCAAACAATCAAAACC
2117331 AAAT
1 AAAT
2117335 ATAAACATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.59, C:0.20, G:0.02, T:0.18
Consensus pattern (20 bp):
AAATGCAAACAATCAAAACC
Found at i:2119314 original size:44 final size:44
Alignment explanation
Indices: 2119247--2119349 Score: 134
Period size: 44 Copynumber: 2.3 Consensus size: 44
2119237 TACACTGCAG
* * * *
2119247 AGTGTAACGATGCACATTTAAGGAATGCATAGGTGCACCTTCAT
1 AGTGTATCGATGCACATTCAAGGAATGCATAGATACACCTTCAT
* * *
2119291 AGTGTATCGATGCATATTCAAGGAATGCATCGATACACTTTCAT
1 AGTGTATCGATGCACATTCAAGGAATGCATAGATACACCTTCAT
*
2119335 AGTGTATCAATGCAC
1 AGTGTATCGATGCAC
2119350 TGTGCACAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 50 1.00
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.29
Consensus pattern (44 bp):
AGTGTATCGATGCACATTCAAGGAATGCATAGATACACCTTCAT
Found at i:2123286 original size:117 final size:117
Alignment explanation
Indices: 2123078--2123303 Score: 298
Period size: 117 Copynumber: 1.9 Consensus size: 117
2123068 AACTTTCAAA
* * * *
2123078 TTGAAATTTTCTTTTTCAAAGCTTTCTCATTTCATTTTTAAGAGCTCTAAATCCTTCTTCAATAT
1 TTGAAAATTTCTTTTTCAAAGCTTTCACATTTCATTTTTAAGAGCTCTAAATCATTCTTCAACAT
*
2123143 TTCATTTTGATTTTCAATATCCATTTTAG-TTTCTAGAAGAAGATTGTTTAAT
66 TTCATTTTGATTTTCAATATCCATTTTAGCTTTCAAG-AGAAGATTGTTTAAT
* * * *
2123195 TTGAAAATTTCTTTTTCAAAG-TTTACAGATTTCATTTTT-GGAAGCTCTAACTCATTTTTCAAC
1 TTGAAAATTTCTTTTTCAAAGCTTT-CACATTTCATTTTTAAG-AGCTCTAAATCATTCTTCAAC
*
2123258 ATTTCATTTTGATTTTCCAAT-TCTATTTTAGCTTTCAAGAGAAGAT
64 ATTTCATTTTGATTTT-CAATATCCATTTTAGCTTTCAAGAGAAGAT
2123304 CATTTTTTGC
Statistics
Matches: 95, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
116 4 0.04
117 81 0.85
118 10 0.11
ACGTcount: A:0.28, C:0.15, G:0.09, T:0.48
Consensus pattern (117 bp):
TTGAAAATTTCTTTTTCAAAGCTTTCACATTTCATTTTTAAGAGCTCTAAATCATTCTTCAACAT
TTCATTTTGATTTTCAATATCCATTTTAGCTTTCAAGAGAAGATTGTTTAAT
Found at i:2127999 original size:24 final size:24
Alignment explanation
Indices: 2127927--2128013 Score: 97
Period size: 23 Copynumber: 3.7 Consensus size: 24
2127917 AGAGTTGAGG
*
2127927 ATTCTACGCGGTCCTTCGGGAT-A
1 ATTCTACGTGGTCCTTCGGGATAA
* *
2127950 ATTCTACGTGGTCATTCGGGACAA
1 ATTCTACGTGGTCCTTCGGGATAA
* *
2127974 ATTCTACGTGGTCCTTTGGAATAA
1 ATTCTACGTGGTCCTTCGGGATAA
* *
2127998 A-TCTATGTGGTGCTTC
1 ATTCTACGTGGTCCTTC
2128014 AGTGCATATT
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
23 31 0.58
24 22 0.42
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (24 bp):
ATTCTACGTGGTCCTTCGGGATAA
Found at i:2145382 original size:44 final size:43
Alignment explanation
Indices: 2145318--2145662 Score: 348
Period size: 44 Copynumber: 7.9 Consensus size: 43
2145308 TAAAACATAT
* * ** * *
2145318 TTACCCTGTGCACAAAGCAAAGGGGCCTGCAAAAATGGTAAGGTC
1 TTACCCT-TGCACATAGCAAAGGAGCCTG-GGAAACGGTAAGGAC
* ** * **
2145363 TTACCTTTGCACATAGCAAAAAAGCCTGGGAAACGGTAATGTT
1 TTACCCTTGCACATAGCAAAGGAGCCTGGGAAACGGTAAGGAC
* *
2145406 TTATCCTTGCACATAGCAAAGGAGCCTGGGAAACGGTAAGGTC
1 TTACCCTTGCACATAGCAAAGGAGCCTGGGAAACGGTAAGGAC
* *
2145449 TTATCCTTGCACATAGCAAAGGAGCTTGGGAAACGGTAAGGAC
1 TTACCCTTGCACATAGCAAAGGAGCCTGGGAAACGGTAAGGAC
* * *
2145492 TTTCCCTTGCACATAGCAGAGGAGCCTGCGGTAACGGTAAGGAC
1 TTACCCTTGCACATAGCAAAGGAGCCTG-GGAAACGGTAAGGAC
* * * * * *
2145536 TTACCCTTACATATAGCAGAGGAGCCTGAGAAAATGGTAAGGAA
1 TTACCCTTGCACATAGCAAAGGAGCCTG-GGAAACGGTAAGGAC
* * * * *
2145580 TTACCCTTGCACATAGCAGAGGATCCTAGGAAAATGGTAAAGAC
1 TTACCCTTGCACATAGCAAAGGAGCCT-GGGAAACGGTAAGGAC
* * *
2145624 TTACCCTTGCACATAGCAGAGGAGCCTAGGAAATGGTAA
1 TTACCCTTGCACATAGCAAAGGAGCCTGGGAAACGGTAA
2145663 TTAATCCATT
Statistics
Matches: 259, Mismatches: 39, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
43 122 0.47
44 130 0.50
45 7 0.03
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.21
Consensus pattern (43 bp):
TTACCCTTGCACATAGCAAAGGAGCCTGGGAAACGGTAAGGAC
Found at i:2148035 original size:30 final size:30
Alignment explanation
Indices: 2147991--2148057 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
2147981 AAAAGACAAT
*
2147991 GTCAACGGTCAACGGGTTGACTCGGTCAAA
1 GTCAACGGTCAACGGGTTGACTCGATCAAA
* *
2148021 GTCAATGGTTAACGGGTTGACTCGATCAAA
1 GTCAACGGTCAACGGGTTGACTCGATCAAA
2148051 GTCAACG
1 GTCAACG
2148058 AAATGACCAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.22
Consensus pattern (30 bp):
GTCAACGGTCAACGGGTTGACTCGATCAAA
Found at i:2150264 original size:44 final size:42
Alignment explanation
Indices: 2150077--2150434 Score: 353
Period size: 44 Copynumber: 8.2 Consensus size: 42
2150067 GGGCCTGTAA
** * *
2150077 AAACGGTAAGGTTTTACCCTTGCACATAGTAAAAGAGA-CTGAG
1 AAACGGTAAGGACTTACCCTTGCACATAGCAAAGGA-ACCTG-G
* * *
2150120 AAGCGGTAAGGTCTTATCCTTGCACATAGCAAAGGAACCTGGG
1 AAACGGTAAGGACTTACCCTTGCACATAGCAAAGGAACCT-GG
** * *
2150163 AAACGGTAAGCTCTTATCCTTGCACATAGCAAAGG-ACATTGAG
1 AAACGGTAAGGACTTACCCTTGCACATAGCAAAGGAAC-CTG-G
*
2150206 AAACGGTAAGGACTTACCCTTGCACATAGCAGAGGAACCTACGG
1 AAACGGTAAGGACTTACCCTTGCACATAGCAAAGGAACCT--GG
* * * *
2150250 TAACGGTAAGGACTTACTCTTGCACATAGCAGAGGAGCCTGAG
1 AAACGGTAAGGACTTACCCTTGCACATAGCAAAGGAACCTG-G
*
2150293 AAAACGGTAAGGACTTACCCTTGCACATAGCAAAGGATCCTGAG
1 -AAACGGTAAGGACTTACCCTTGCACATAGCAAAGGAACCTG-G
* * * *
2150337 AAAACGGTAAGGACTTACCCATGTACATAGCATAGGAGCCTGGG
1 -AAACGGTAAGGACTTACCCTTGCACATAGCAAAGGAACCT-GG
*
2150381 AAAACGGTAAGGACTTACCCTTGCACATAGCAGAA-GAGCCTAGG
1 -AAACGGTAAGGACTTACCCTTGCACATAGCA-AAGGAACCT-GG
2150425 AAAACGGTAA
1 -AAACGGTAA
2150435 TTAATCCATT
Statistics
Matches: 276, Mismatches: 28, Indels: 21
0.85 0.09 0.06
Matches are distributed among these distances:
42 5 0.02
43 102 0.37
44 166 0.60
45 3 0.01
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.19
Consensus pattern (42 bp):
AAACGGTAAGGACTTACCCTTGCACATAGCAAAGGAACCTGG
Found at i:2150322 original size:88 final size:86
Alignment explanation
Indices: 2150077--2150434 Score: 423
Period size: 88 Copynumber: 4.1 Consensus size: 86
2150067 GGGCCTGTAA
** * * * * * *
2150077 AAACGGTAAGGTTTTACCCTTGCACATAGTAAAAGAGACTGAGAAGCGGTAAGGTCTTATCCTTG
1 AAACGGTAAGGACTTACCCTTGCACATAGCAAAGGAGCCTGAGAAACGGTAAGGACTTACCCTTG
*
2150142 CACATAGCAAAGGAACCTGGG
66 CACATAGCAAAGGAACCTAGG
** * *
2150163 AAACGGTAAGCTCTTATCCTTGCACATAGCAAAGGA-CATTGAGAAACGGTAAGGACTTACCCTT
1 AAACGGTAAGGACTTACCCTTGCACATAGCAAAGGAGC-CTGAGAAACGGTAAGGACTTACCCTT
*
2150227 GCACATAGCAGAGGAACCTACGG
65 GCACATAGCAAAGGAACCTA-GG
* * *
2150250 TAACGGTAAGGACTTACTCTTGCACATAGCAGAGGAGCCTGAGAAAACGGTAAGGACTTACCCTT
1 AAACGGTAAGGACTTACCCTTGCACATAGCAAAGGAGCCTGAG-AAACGGTAAGGACTTACCCTT
* *
2150315 GCACATAGCAAAGGATCCTGAGA
65 GCACATAGCAAAGGAACCT-AGG
* * * *
2150338 AAACGGTAAGGACTTACCCATGTACATAGCATAGGAGCCTGGGAAAACGGTAAGGACTTACCCTT
1 AAACGGTAAGGACTTACCCTTGCACATAGCAAAGGAGCCTGAG-AAACGGTAAGGACTTACCCTT
*
2150403 GCACATAGCAGAA-GAGCCTAGG
65 GCACATAGCA-AAGGAACCTAGG
2150425 AAAACGGTAA
1 -AAACGGTAA
2150435 TTAATCCATT
Statistics
Matches: 235, Mismatches: 30, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
86 71 0.30
87 38 0.16
88 123 0.52
89 3 0.01
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.19
Consensus pattern (86 bp):
AAACGGTAAGGACTTACCCTTGCACATAGCAAAGGAGCCTGAGAAACGGTAAGGACTTACCCTTG
CACATAGCAAAGGAACCTAGG
Found at i:2150391 original size:132 final size:131
Alignment explanation
Indices: 2150123--2150434 Score: 400
Period size: 132 Copynumber: 2.4 Consensus size: 131
2150113 GACTGAGAAG
* * * * * *
2150123 CGGTAAGGTCTTA-TCCTTGCACATAGCAAAGGAACCTG-GGAAACGGTAAGCTCTTATCCTTGC
1 CGGTAAGGACTTACT-CTTGCACATAGCAGAGGAGCCTGAGAAAACGGTAAGCACTTACCCTTGC
* * *
2150186 ACATAGCAAAGGACATTGAGAAACGGTAAGGACTTACCCTTGCACATAGCAGAGGAACCTACGGT
65 ACATAGCAAAGGACACTGAGAAACGGTAAGGACTTACCCATGCACATAGCAGAGGAACCTACGGA
2150251 AA
130 AA
*
2150253 CGGTAAGGACTTACTCTTGCACATAGCAGAGGAGCCTGAGAAAACGGTAAGGACTTACCCTTGCA
1 CGGTAAGGACTTACTCTTGCACATAGCAGAGGAGCCTGAGAAAACGGTAAGCACTTACCCTTGCA
* * * *
2150318 CATAGCAAAGGATC-CTGAGAAAACGGTAAGGACTTACCCATGTACATAGCATAGGAGCCT-GGG
66 CATAGCAAAGGA-CACTGAG-AAACGGTAAGGACTTACCCATGCACATAGCAGAGGAACCTACGG
2150381 AAAA
129 -AAA
* *
2150385 CGGTAAGGACTTACCCTTGCACATAGCAGAAGAGCCT-AGGAAAACGGTAA
1 CGGTAAGGACTTACTCTTGCACATAGCAGAGGAGCCTGA-GAAAACGGTAA
2150435 TTAATCCATT
Statistics
Matches: 160, Mismatches: 16, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
130 33 0.21
131 42 0.26
132 85 0.53
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.19
Consensus pattern (131 bp):
CGGTAAGGACTTACTCTTGCACATAGCAGAGGAGCCTGAGAAAACGGTAAGCACTTACCCTTGCA
CATAGCAAAGGACACTGAGAAACGGTAAGGACTTACCCATGCACATAGCAGAGGAACCTACGGAA
A
Found at i:2152874 original size:30 final size:30
Alignment explanation
Indices: 2152838--2152909 Score: 110
Period size: 30 Copynumber: 2.4 Consensus size: 30
2152828 TTGGTAAAAG
*
2152838 TCAAAGTCAATGGTCAAC-AGGTTGACTCGA
1 TCAAAGTCAACGGTCAACGA-GTTGACTCGA
*
2152868 TCAAAGTCAACGGTCAACGAGTTGACTCGG
1 TCAAAGTCAACGGTCAACGAGTTGACTCGA
2152898 TCAAAGTCAACG
1 TCAAAGTCAACG
2152910 AGTTGACCCA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
30 38 0.97
31 1 0.03
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.21
Consensus pattern (30 bp):
TCAAAGTCAACGGTCAACGAGTTGACTCGA
Found at i:2155119 original size:44 final size:43
Alignment explanation
Indices: 2154930--2155276 Score: 365
Period size: 44 Copynumber: 8.0 Consensus size: 43
2154920 CCTACAAAAT
** * * * *
2154930 CGGTAAGGTTTTACCCTTGCACATAGCAAAAGATCCTAGGAAA
1 CGGTAAGGACTTACCCTTGCACATAGCAGAGGAGCCTGGGAAA
* * * * *
2154973 TGGTAAGGTCTTATCCTTGCACATAGCAAAGGAGTCTGGG-AA
1 CGGTAAGGACTTACCCTTGCACATAGCAGAGGAGCCTGGGAAA
* * * *
2155015 TGGTAAGGTCTTATCCC-TGTACATAGCAAAGGAGCCTGGGAAA
1 CGGTAAGGACTTA-CCCTTGCACATAGCAGAGGAGCCTGGGAAA
* * * * *
2155058 CAGTAAGGACTTTCCCTTGTACATAGCAGAGGAACCTGCGGTAA
1 CGGTAAGGACTTACCCTTGCACATAGCAGAGGAGCCTG-GGAAA
* * *
2155102 CGGTAAGGACTTACCCTTGCACATAGCAGAGAAGCTTGAGAAAA
1 CGGTAAGGACTTACCCTTGCACATAGCAGAGGAGCCTG-GGAAA
*
2155146 CGGTAAGGACTTACCCTTGCACATAGCAGAGGAGCCTGAGTAAA
1 CGGTAAGGACTTACCCTTGCACATAGCAGAGGAGCCTG-GGAAA
* * * *
2155190 CGATAAGGACTTACCCTTGTACATAGCAGAGGAGCATAGGAAAA
1 CGGTAAGGACTTACCCTTGCACATAGCAGAGGAGCCT-GGGAAA
* *
2155234 CGGTAAGGACTTACCTTTGCACATAGCAGAGGAGCCTAGGAAA
1 CGGTAAGGACTTACCCTTGCACATAGCAGAGGAGCCTGGGAAA
2155277 ACGCTAATTA
Statistics
Matches: 260, Mismatches: 39, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
42 39 0.15
43 69 0.27
44 151 0.58
45 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.21
Consensus pattern (43 bp):
CGGTAAGGACTTACCCTTGCACATAGCAGAGGAGCCTGGGAAA
Found at i:2160857 original size:24 final size:24
Alignment explanation
Indices: 2160830--2160881 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
2160820 AACGAATATA
*
2160830 TCAAAAATCAAAACATAATCCAGG
1 TCAAAAATCAAAACAAAATCCAGG
** * *
2160854 TCAAGTATCATATCAAAATCCAGG
1 TCAAAAATCAAAACAAAATCCAGG
2160878 TCAA
1 TCAA
2160882 GTATTCGATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.48, C:0.21, G:0.10, T:0.21
Consensus pattern (24 bp):
TCAAAAATCAAAACAAAATCCAGG
Found at i:2160882 original size:24 final size:24
Alignment explanation
Indices: 2160846--2160935 Score: 119
Period size: 24 Copynumber: 3.8 Consensus size: 24
2160836 ATCAAAACAT
*
2160846 AATCCAGGTCAAGTATCATATCAA
1 AATCCAGGTCAAGTATCATATCAG
*
2160870 AATCCAGGTCAAGTATTC-GATCAG
1 AATCCAGGTCAAGTA-TCATATCAG
* *
2160894 AATTCAAGTCAAGTATCATATCAG
1 AATCCAGGTCAAGTATCATATCAG
*
2160918 AATCCATGTCAAGTATCA
1 AATCCAGGTCAAGTATCA
2160936 GATTAGAAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
23 2 0.04
24 53 0.93
25 2 0.04
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (24 bp):
AATCCAGGTCAAGTATCATATCAG
Found at i:2165425 original size:32 final size:32
Alignment explanation
Indices: 2165232--2165423 Score: 188
Period size: 32 Copynumber: 6.0 Consensus size: 32
2165222 TTATGCATAA
* * * **
2165232 CAGTGTCACATTTAGATATTGCATAATTGTGT
1 CAGTGTCACATTCAGATAATGCACAACAGTGT
*
2165264 TAGTGTC-CTATTCAGATAATGCACAACAGTGT
1 CAGTGTCAC-ATTCAGATAATGCACAACAGTGT
* * * *
2165296 CAGTGTTACATTCAAATAATGCACAACAATGC
1 CAGTGTCACATTCAGATAATGCACAACAGTGT
* * * *
2165328 CAATGTCACATTTAGATAATGTACTACAGTGT
1 CAGTGTCACATTCAGATAATGCACAACAGTGT
* * * * *
2165360 CAGTATCCCATTTAGATAATACACAGCAGTGT
1 CAGTGTCACATTCAGATAATGCACAACAGTGT
*
2165392 TAGTGTCACATTCAGATAATGCACAACAGTGT
1 CAGTGTCACATTCAGATAATGCACAACAGTGT
2165424 TAATGTTGCA
Statistics
Matches: 126, Mismatches: 32, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
31 1 0.01
32 124 0.98
33 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (32 bp):
CAGTGTCACATTCAGATAATGCACAACAGTGT
Found at i:2167643 original size:10 final size:10
Alignment explanation
Indices: 2167628--2167721 Score: 59
Period size: 10 Copynumber: 9.3 Consensus size: 10
2167618 GTTCTATTTC
2167628 TTTTTTTCTT
1 TTTTTTTCTT
*
2167638 TTTTTTTCCAT
1 TTTTTTT-CTT
* *
2167649 TTATTTT-TG
1 TTTTTTTCTT
*
2167658 TTGTTTTC--
1 TTTTTTTCTT
*
2167666 TTTTTTCCTT
1 TTTTTTTCTT
*
2167676 CTATTTTTCTT
1 -TTTTTTTCTT
*
2167687 TTTTTCTCTT
1 TTTTTTTCTT
2167697 TTTTTATCTCTT
1 TTTTT-T-TCTT
*
2167709 TTTTCTTCTT
1 TTTTTTTCTT
2167719 TTT
1 TTT
2167722 CTCCTTTTTT
Statistics
Matches: 64, Mismatches: 13, Indels: 14
0.70 0.14 0.15
Matches are distributed among these distances:
8 6 0.09
9 6 0.09
10 27 0.42
11 17 0.27
12 8 0.12
ACGTcount: A:0.04, C:0.15, G:0.02, T:0.79
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:2167680 original size:27 final size:27
Alignment explanation
Indices: 2167639--2167699 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 27
2167629 TTTTTTCTTT
*
2167639 TTTTTTCCATTTATTTTTGTTGTTTTC
1 TTTTTTCCATTTATTTTTCTTGTTTTC
*
2167666 TTTTTTCC-TTCTATTTTTCTTTTTTTC
1 TTTTTTCCATT-TATTTTTCTTGTTTTC
2167693 TCTTTTT
1 T-TTTTT
2167700 TTATCTCTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
26 2 0.07
27 23 0.77
28 5 0.17
ACGTcount: A:0.05, C:0.15, G:0.03, T:0.77
Consensus pattern (27 bp):
TTTTTTCCATTTATTTTTCTTGTTTTC
Found at i:2167700 original size:30 final size:30
Alignment explanation
Indices: 2167624--2167731 Score: 102
Period size: 30 Copynumber: 3.7 Consensus size: 30
2167614 ATTTGTTCTA
*
2167624 TTTCTTTTTTTCTTTTTTTTTCCATT-TATT
1 TTTCTTTTTTTCTCTTTTTTTCC-TTCTATT
* *
2167654 TTT-GTTGTTT-TC-TTTTTTCCTTCTATT
1 TTTCTTTTTTTCTCTTTTTTTCCTTCTATT
*
2167681 TTTCTTTTTTTCTCTTTTTTT-ATCTCT-TT
1 TTTCTTTTTTTCTCTTTTTTTCCT-TCTATT
*
2167710 TTTCTTCTTTTTCTCCTTTTTT
1 TTTCTT-TTTTTCTCTTTTTTT
2167732 ATCTCTCTTT
Statistics
Matches: 65, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
26 2 0.03
27 15 0.23
28 6 0.09
29 16 0.25
30 26 0.40
ACGTcount: A:0.04, C:0.17, G:0.02, T:0.78
Consensus pattern (30 bp):
TTTCTTTTTTTCTCTTTTTTTCCTTCTATT
Found at i:2167732 original size:30 final size:29
Alignment explanation
Indices: 2167679--2167742 Score: 101
Period size: 30 Copynumber: 2.2 Consensus size: 29
2167669 TTTCCTTCTA
*
2167679 TTTTTCTTTTTTTCTCTTTTTTTATCTCT
1 TTTTTCTTTTTTTCTCCTTTTTTATCTCT
2167708 TTTTTCTTCTTTTTCTCCTTTTTTATCTCT
1 TTTTTCTT-TTTTTCTCCTTTTTTATCTCT
*
2167738 CTTTT
1 TTTTT
2167743 ATGGGTTCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 8 0.25
30 24 0.75
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (29 bp):
TTTTTCTTTTTTTCTCCTTTTTTATCTCT
Found at i:2167742 original size:12 final size:11
Alignment explanation
Indices: 2167664--2167742 Score: 64
Period size: 10 Copynumber: 7.6 Consensus size: 11
2167654 TTTGTTGTTT
2167664 TCTTTTTTC-C
1 TCTTTTTTCTC
*
2167674 TTCTATTTT-TC
1 -TCTTTTTTCTC
2167685 T-TTTTTTCTC
1 TCTTTTTTCTC
*
2167695 T-TTTTTTATC
1 TCTTTTTTCTC
2167705 TCTTTTTTCT-
1 TCTTTTTTCTC
2167715 TC-TTTTTCTC
1 TCTTTTTTCTC
*
2167725 -CTTTTTTATC
1 TCTTTTTTCTC
2167735 TCTCTTTT
1 TCT-TTTT
2167743 ATGGGTTCGA
Statistics
Matches: 56, Mismatches: 5, Indels: 13
0.76 0.07 0.18
Matches are distributed among these distances:
9 13 0.23
10 22 0.39
11 17 0.30
12 4 0.07
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.75
Consensus pattern (11 bp):
TCTTTTTTCTC
Found at i:2168986 original size:26 final size:26
Alignment explanation
Indices: 2168956--2169008 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
2168946 ACTAGCAATA
2168956 TCACATTCAGATAATGCACAATAGTG
1 TCACATTCAGATAATGCACAATAGTG
* * * *
2168982 TCACATTTATATAATGCATAATTGTG
1 TCACATTCAGATAATGCACAATAGTG
2169008 T
1 T
2169009 TGGTTTCATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (26 bp):
TCACATTCAGATAATGCACAATAGTG
Found at i:2169156 original size:64 final size:64
Alignment explanation
Indices: 2169018--2169182 Score: 181
Period size: 64 Copynumber: 2.6 Consensus size: 64
2169008 TTGGTTTCAT
* * * *
2169018 ATTCAGATAATGCATAGTAGTATCAGTGTCAT-ATTCAGATAATACACAACAGTGTCAGTGTCAC
1 ATTCAGATAATGCACAGTAGTGTCAGTGTC-TCATTTAGATAATACACAACAGTGTCAGTATCAC
* * * *
2169082 ATTTAGATAATGTACAGTAGTGTCAGTGTCTCATTTAGATAATACA-AAGTAGTGTCAGTATCGC
1 ATTCAGATAATGCACAGTAGTGTCAGTGTCTCATTTAGATAATACACAA-CAGTGTCAGTATCAC
* * * * *
2169146 ATTCATATAATGCACAATAGTGTTAATGTCGCATTTA
1 ATTCAGATAATGCACAGTAGTGTCAGTGTCTCATTTA
2169183 AAAAATGCAA
Statistics
Matches: 84, Mismatches: 15, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
63 3 0.04
64 81 0.96
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.33
Consensus pattern (64 bp):
ATTCAGATAATGCACAGTAGTGTCAGTGTCTCATTTAGATAATACACAACAGTGTCAGTATCAC
Found at i:2169167 original size:32 final size:32
Alignment explanation
Indices: 2168956--2169168 Score: 161
Period size: 32 Copynumber: 6.8 Consensus size: 32
2168946 ACTAGCAATA
2168956 TCACATTCAGATAATGCAC-A-A---T-AGTG
1 TCACATTCAGATAATGCACAATAGTGTCAGTG
* * * * ** *
2168982 TCACATTTATATAATGCATAATTGTGTTGGTT
1 TCACATTCAGATAATGCACAATAGTGTCAGTG
* * * *
2169014 TCATATTCAGATAATGCATAGTAGTATCAGTG
1 TCACATTCAGATAATGCACAATAGTGTCAGTG
* * *
2169046 TCATATTCAGATAATACACAACAGTGTCAGTG
1 TCACATTCAGATAATGCACAATAGTGTCAGTG
* * *
2169078 TCACATTTAGATAATGTACAGTAGTGTCAGTG
1 TCACATTCAGATAATGCACAATAGTGTCAGTG
* * * *
2169110 TCTCATTTAGATAATACA-AAGTAGTGTCAGTA
1 TCACATTCAGATAATGCACAA-TAGTGTCAGTG
* *
2169142 TCGCATTCATATAATGCACAATAGTGT
1 TCACATTCAGATAATGCACAATAGTGT
2169169 TAATGTCGCA
Statistics
Matches: 144, Mismatches: 35, Indels: 10
0.76 0.19 0.05
Matches are distributed among these distances:
26 16 0.11
27 1 0.01
31 2 0.01
32 123 0.85
33 2 0.01
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (32 bp):
TCACATTCAGATAATGCACAATAGTGTCAGTG
Found at i:2171504 original size:32 final size:32
Alignment explanation
Indices: 2171463--2171627 Score: 138
Period size: 32 Copynumber: 5.2 Consensus size: 32
2171453 CCATTTTGTT
*
2171463 AGTGTCACATTCATATAATGCACAAAAGTGTC
1 AGTGTCACATTCAGATAATGCACAAAAGTGTC
* *
2171495 AGTGTCACATTCAGATAAGGCATAACAA-TGTC
1 AGTGTCACATTCAGATAATGCACAA-AAGTGTC
* * ** * *
2171527 AGTGTCATATTCAAATAATATACAACAGTGTT
1 AGTGTCACATTCAGATAATGCACAAAAGTGTC
* * * * *
2171559 AGTATCGCATTCAGATAATGTACAACAGTGTT
1 AGTGTCACATTCAGATAATGCACAAAAGTGTC
* *
2171591 AGTGTCATATTCCA-ATAATGCATAACAA-TGTC
1 AGTGTCACATT-CAGATAATGCACAA-AAGTGTC
2171623 AGTGT
1 AGTGT
2171628 TGTATTTAGA
Statistics
Matches: 106, Mismatches: 23, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
31 1 0.01
32 100 0.94
33 5 0.05
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.30
Consensus pattern (32 bp):
AGTGTCACATTCAGATAATGCACAAAAGTGTC
Found at i:2171639 original size:64 final size:64
Alignment explanation
Indices: 2171459--2171627 Score: 180
Period size: 64 Copynumber: 2.6 Consensus size: 64
2171449 AAAACCATTT
* * *
2171459 TGTTAGTGTCACATT-CATATAATGCACAA-AAGTGTCAGTGTCACATTCAGATAAGGCATAACA
1 TGTTAGTGTCATATTCCA-ATAATGCACAACAA-TGTCAGTGTCGCATTCAGATAAGGCACAACA
2171522 A
64 A
* * ** * * * * * *
2171523 TGTCAGTGTCATATTCAAATAATATACAACAGTGTTAGTATCGCATTCAGATAATGTACAACAG
1 TGTTAGTGTCATATTCCAATAATGCACAACAATGTCAGTGTCGCATTCAGATAAGGCACAACAA
*
2171587 TGTTAGTGTCATATTCCAATAATGCATAACAATGTCAGTGT
1 TGTTAGTGTCATATTCCAATAATGCACAACAATGTCAGTGT
2171628 TGTATTTAGA
Statistics
Matches: 82, Mismatches: 21, Indels: 4
0.77 0.20 0.04
Matches are distributed among these distances:
64 80 0.98
65 2 0.02
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (64 bp):
TGTTAGTGTCATATTCCAATAATGCACAACAATGTCAGTGTCGCATTCAGATAAGGCACAACAA
Found at i:2172248 original size:17 final size:17
Alignment explanation
Indices: 2172226--2172267 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
2172216 CTTGTGTTCT
*
2172226 ATATTTATATGTTTTAA
1 ATATTTATATGTTTCAA
*
2172243 ATATTTATTTGTTTCAA
1 ATATTTATATGTTTCAA
2172260 ATATTTAT
1 ATATTTAT
2172268 CTGAACTACC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (17 bp):
ATATTTATATGTTTCAA
Found at i:2172615 original size:60 final size:60
Alignment explanation
Indices: 2172550--2172704 Score: 240
Period size: 60 Copynumber: 2.6 Consensus size: 60
2172540 ATTGGATGCT
* *
2172550 TAGATCTTAGTGGTCTACGGTAAGTCCTTATGGATGTC-TTTATCTTCAATATTGGACTCC
1 TAGATCTTAGTGGTCTACGGTAAGTCCTTATGGATG-CATGTATCTTCAATAATGGACTCC
* *
2172610 TAGATCTTAGTGGTCTAGGGTAAGTCCTTATGGATGCATGTATCTTCCATAATGGACTCC
1 TAGATCTTAGTGGTCTACGGTAAGTCCTTATGGATGCATGTATCTTCAATAATGGACTCC
* *
2172670 TAGATCTTAGTGGTCTATGGTATGTCCTTATGGAT
1 TAGATCTTAGTGGTCTACGGTAAGTCCTTATGGAT
2172705 ACCTGTTTTA
Statistics
Matches: 88, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
59 1 0.01
60 87 0.99
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.39
Consensus pattern (60 bp):
TAGATCTTAGTGGTCTACGGTAAGTCCTTATGGATGCATGTATCTTCAATAATGGACTCC
Found at i:2177860 original size:3 final size:3
Alignment explanation
Indices: 2177852--2177909 Score: 73
Period size: 3 Copynumber: 19.7 Consensus size: 3
2177842 TGTAACAATA
* * *
2177852 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ACT AAT TAT TA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
2177899 ATT AAT AAT AA
1 AAT AAT AAT AA
2177910 CAAATATTAA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
2 1 0.02
3 47 0.98
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:2177941 original size:23 final size:23
Alignment explanation
Indices: 2177850--2177926 Score: 79
Period size: 23 Copynumber: 3.4 Consensus size: 23
2177840 TTTGTAACAA
* * *
2177850 TAAATAATAATAATAA-TAATAA
1 TAAATATTAATAATAACAAATAT
* *
2177872 T-AATAATAATAAT-ACTAATTAT
1 TAAATATTAATAATAAC-AAATAT
2177894 TAAATATTAATAATAACAAATAT
1 TAAATATTAATAATAACAAATAT
2177917 TAAATATTAA
1 TAAATATTAA
2177927 ACATTAATAA
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
20 1 0.02
21 12 0.26
22 5 0.11
23 26 0.57
24 2 0.04
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (23 bp):
TAAATATTAATAATAACAAATAT
Found at i:2178553 original size:258 final size:258
Alignment explanation
Indices: 2178079--2179543 Score: 1806
Period size: 258 Copynumber: 5.7 Consensus size: 258
2178069 TGAGATTGAT
* * * * * *
2178079 AGATAACCCGAAGGATTTAGTCATCATGCTTGAAAGATTTACTGATGGCCCGAAGGACTTACCAA
1 AGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCTGAAGGACTTACTAA
* *
2178144 TTTTGGAAATAGTTTACTAGGTAAGAAACTTTGG-AATCGCTTTCTTACTTTTCAAAAATTTCAT
66 TTTTGGAAATAGTTTACTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAAATTCAT
* * ** *
2178208 TTTCCT-AAAATACTAAATGAGAAACTTTGAAGATTTCTTTTCTCATTTTTCAAAAATCATGTGA
131 TTT-CTGAAAATATTAAATGAGAAACTTTGAAAATCGC-TTTCTCATTTTTCGAAAATCATGTGA
* * * * * *** * * *
2178272 GAACATATTGCTCGAATGTCTTATAGACGGTTTGAAGGACTTAACATCTTGCTCGAAAAAATGAT
194 AAACATCTTGCCCTAAGGTCTTATAGACGGCCCGAAGGACTTAACATCTTGCTCGAAAGACTGAC
* *
2178337 AGATGGCTCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCTGAAGGACTTACTAA
1 AGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCTGAAGGACTTACTAA
* * *
2178402 TTTTGAAAATAGTTTACTAGATACGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAAATTCA-
66 TTTTGGAAATAGTTTACTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAAATTCAT
* *
2178466 TTTCTGAAAAATATTAAATGAGAAACTTTGAAAATCGCTTCCACATTTTTCGAAAATCATGTGAA
131 TTTCTG-AAAATATTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTTCGAAAATCATGTGAA
* * *
2178531 AACATCTTGCCCTAAGGTCTTATAGATGGTCCGAAGGACTTAACATCTTAG-TCGAAAGACTGAA
195 AACATCTTGCCCTAAGGTCTTATAGACGGCCCGAAGGACTTAACATCTT-GCTCGAAAGACTGAC
* * * *
2178595 AGAT-AGCCTGAAGGATTTAATCATCATGCTTGAAAGACATACTGATGG-CTCGAAGGACATACT
1 AGATGA-CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCT-GAAGGACTTACT
* * *
2178658 AATTTTGGAAATAATTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAAATTC
64 AATTTTGGAAATAGTTTACTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAAATTC
*
2178723 ATTTTCTGAAAATATTAAATGAGAAACTTTGAAAATCGCTTTCT-ATTTTTTCGAAAATCATATG
129 ATTTTCTGAAAATATTAAATGAGAAACTTTGAAAATCGCTTTCTCA-TTTTTCGAAAATCATGTG
* *** * *
2178787 AAAACATCCTGCTAGAAGGTCTTATAGACGGCTCGAAGGATTTAACATCTTGCTCGAAAGACTGA
193 AAAACATCTTGCCCTAAGGTCTTATAGACGGCCCGAAGGACTTAACATCTTGCTCGAAAGACTGA
2178852 C
258 C
* * * * * *
2178853 AGATAACCCAAAGGATTTAATCATCATGCTCAAAAGACTTACAGATGGCCCGAAGAACTTACTAA
1 AGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCTGAAGGACTTACTAA
* * * *
2178918 TTTAGGAAATAGTATACTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAGAAATTTCAT
66 TTTTGGAAATAGTTTACTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAAATTCAT
* *
2178983 TTTTTGAAAATATTAAATGAGAAACTTTGATAATCGCTTTCTCATTTTTCGAAAATCATGTGAAA
131 TTTCTGAAAATATTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTTCGAAAATCATGTGAAA
* ** * *
2179048 ACATCCTG-AATGATGGTCTTATAGATGGCCCGAAGGACTTAACATCTTGCTCGAAAGACTGAC
196 ACATCTTGCCCT-AAGGTCTTATAGACGGCCCGAAGGACTTAACATCTTGCTCGAAAGACTGAC
* * * * * * *
2179111 ATATGACCCAAAGGATTTAGTCATCATGCTTGAAAGCCTTACTGATGG-CTCGAATGACTTATTA
1 AGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCT-GAAGGACTTACTA
* * * * * * ** *
2179175 ATTTTGGTAATAGTTTAGTATGTAAGAAAATTTGCAAATCGCTTTCTTACTTAACAAAAATTTCA
65 ATTTTGGAAATAGTTTACTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAAATTCA
* * * * *
2179240 TTTTTTTTTGAAAATATTAAATGAGAAACTTTGAAAATTGATTTCTTAGTTTTTC-AAAATTATG
130 ---TTTTCTGAAAATATTAAATGAGAAACTTTGAAAATCGCTTTCTCA-TTTTTCGAAAATCATG
* * **
2179304 TGAAAATATCCTT--CCTGAAGGTCTTATAGACGGCACGAAGGACTTAACATCTTGCTCGAACTA
191 TGAAAACAT-CTTGCCCT-AAGGTCTTATAGACGGCCCGAAGGACTTAACATCTTGCTCGAAAGA
*
2179367 CTTAC
254 CTGAC
* *
2179372 AGATGACAC-AGAGGATTTAATCATAATGCTCGAAAGACTTACTGATAGGCC-GAAGGACTTACT
1 AGATGACCCGA-AGGATTTAATCATCATGCTCGAAAGACTTACTGAT-GGCCTGAAGGACTTACT
* *
2179435 AATTTTGGAAATAGATTACTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTTAAAAAATTC
64 AATTTTGGAAATAGTTTACTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAAATTC
* *
2179500 ATTTTCTAAAAATATTAAATGTGAAACTTTGAAAATCGCTTTCT
129 ATTTTCTGAAAATATTAAATGAGAAACTTTGAAAATCGCTTTCT
2179544 GTGGATTTGG
Statistics
Matches: 1044, Mismatches: 141, Indels: 44
0.85 0.11 0.04
Matches are distributed among these distances:
257 8 0.01
258 753 0.72
259 64 0.06
260 1 0.00
261 207 0.20
262 10 0.01
263 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.33
Consensus pattern (258 bp):
AGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCTGAAGGACTTACTAA
TTTTGGAAATAGTTTACTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAAATTCAT
TTTCTGAAAATATTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTTCGAAAATCATGTGAAA
ACATCTTGCCCTAAGGTCTTATAGACGGCCCGAAGGACTTAACATCTTGCTCGAAAGACTGAC
Found at i:2179068 original size:516 final size:513
Alignment explanation
Indices: 2178079--2179543 Score: 1992
Period size: 516 Copynumber: 2.8 Consensus size: 513
2178069 TGAGATTGAT
* * * *
2178079 AGATAACCCGAAGGATTTAGTCATCATGCTTGAAAGATTTACTGATGGCCCGAAGGACTTACCAA
1 AGATAGCCCGAAGGATTTAGTCATCATGCTTGAAAGACTTACTGATGGCTCGAAGGACTTACTAA
2178144 TTTTGGAAATAGTTTACTAGGTAAGAAACTTTGG-AATCGCTTTCTTACTTTTCAAAAATTTCAT
66 TTTTGGAAATAGTTTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCAT
* * *
2178208 TTTCCT-AAAATACTAAATGAGAAACTTTGAAGATTTCTTTTCTCATTTTTCAAAAATCATGTGA
131 TTT-CTGAAAATATTAAATGAGAAACTTTGAAAATTGC-TTTCT-ATTTTTC-AAAATCATGTGA
* ** * * * * *
2178272 GAACATATTGCTCGAATGTCTTATAGACGGTTTGAAGGACTTAACATCTTGCTCGAAAAAATGAT
192 AAACATCCTGCT-GAAGGTCTTATAGACGGCTCGAAGGACTTAACATCTTGCTCGAAAAACTGAC
* * * *
2178337 AGATGGCTCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCTGAAGGACTTACTAA
256 AGATGACACAAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTAA
* * * *
2178402 TTTTGAAAATAGTTTACTAGATACGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAAATTCA-
321 TTTTGGAAATAGTATACTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAAATTCAT
* *
2178466 TTTCTGAAAAATATTAAATGAGAAACTTTGAAAATCGCTTCCACATTTTTCGAAAATCATGTGAA
386 TTTCTG-AAAATATTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTTCGAAAATCATGTGAA
* ** *
2178531 AACATCTTGCCCTAAGGTCTTATAGATGGTCCGAAGGACTTAACATCTTAG-TCGAAAGACTGAA
450 AACATCCTGCAATAAGGTCTTATAGATGGCCCGAAGGACTTAACATCTT-GCTCGAAAGACTGAA
* * * *
2178595 AGATAGCCTGAAGGATTTAATCATCATGCTTGAAAGACATACTGATGGCTCGAAGGACATACTAA
1 AGATAGCCCGAAGGATTTAGTCATCATGCTTGAAAGACTTACTGATGGCTCGAAGGACTTACTAA
* * *
2178660 TTTTGGAAATAATTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAAATTCAT
66 TTTTGGAAATAGTTTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCAT
* *
2178725 TTTCTGAAAATATTAAATGAGAAACTTTGAAAATCGCTTTCTATTTTTTCGAAAATCATATGAAA
131 TTTCTGAAAATATTAAATGAGAAACTTTGAAAATTGCTTTCTA-TTTTTC-AAAATCATGTGAAA
* *
2178790 ACATCCTGCTAGAAGGTCTTATAGACGGCTCGAAGGATTTAACATCTTGCTCGAAAGACTGACAG
194 ACATCCTGCT-GAAGGTCTTATAGACGGCTCGAAGGACTTAACATCTTGCTCGAAAAACTGACAG
* * * * *
2178855 ATAACCCAAAGGATTTAATCATCATGCTCAAAAGACTTACAGATGGCCCGAAGAACTTACTAATT
258 ATGACACAAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTAATT
* * *
2178920 TAGGAAATAGTATACTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAGAAATTTCATTT
323 TTGGAAATAGTATACTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAAATTCATTT
* *
2178985 TTTGAAAATATTAAATGAGAAACTTTGATAATCGCTTTCTCATTTTTCGAAAATCATGTGAAAAC
388 TCTGAAAATATTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTTCGAAAATCATGTGAAAAC
* *
2179050 ATCCTG-AATGATGGTCTTATAGATGGCCCGAAGGACTTAACATCTTGCTCGAAAGACTGAC
453 ATCCTGCAAT-AAGGTCTTATAGATGGCCCGAAGGACTTAACATCTTGCTCGAAAGACTGAA
* * * * *
2179111 ATAT-GACCCAAAGGATTTAGTCATCATGCTTGAAAGCCTTACTGATGGCTCGAATGACTTATTA
1 AGATAG-CCCGAAGGATTTAGTCATCATGCTTGAAAGACTTACTGATGGCTCGAAGGACTTACTA
* * * * * **
2179175 ATTTTGGTAATAGTTTAGTATGTAAGAAAATTTGCAAATCGCTTTCTTACTTAACAAAAATTTCA
65 ATTTTGGAAATAGTTTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCA
* * *
2179240 TTTTTTTTTGAAAATATTAAATGAGAAACTTTGAAAATTGATTTCTTAGTTTTTCAAAATTATGT
130 ---TTTTCTGAAAATATTAAATGAGAAACTTTGAAAATTGCTTTC-TA-TTTTTCAAAATCATGT
* * * ** *
2179305 GAAAATATCCTTCCTGAAGGTCTTATAGACGGCACGAAGGACTTAACATCTTGCTCGAACTACTT
190 GAAAACATCC-TGCTGAAGGTCTTATAGACGGCTCGAAGGACTTAACATCTTGCTCGAAAAACTG
* *
2179370 ACAGATGACACAGAGGATTTAATCATAATGCTCGAAAGACTTACTGATAGG-CCGAAGGACTTAC
254 ACAGATGACACAAAGGATTTAATCATCATGCTCGAAAGACTTACTGAT-GGCCCGAAGGACTTAC
*
2179434 TAATTTTGGAAATAG-ATTACTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTTAAAAAAT
318 TAATTTTGGAAATAGTA-TACTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAAAT
* *
2179498 TCATTTTCTAAAAATATTAAATGTGAAACTTTGAAAATCGCTTTCT
382 TCATTTTCTGAAAATATTAAATGAGAAACTTTGAAAATCGCTTTCT
2179544 GTGGATTTGG
Statistics
Matches: 835, Mismatches: 100, Indels: 25
0.87 0.10 0.03
Matches are distributed among these distances:
515 4 0.00
516 498 0.60
517 64 0.08
518 1 0.00
519 255 0.31
520 13 0.02
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.33
Consensus pattern (513 bp):
AGATAGCCCGAAGGATTTAGTCATCATGCTTGAAAGACTTACTGATGGCTCGAAGGACTTACTAA
TTTTGGAAATAGTTTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCAT
TTTCTGAAAATATTAAATGAGAAACTTTGAAAATTGCTTTCTATTTTTCAAAATCATGTGAAAAC
ATCCTGCTGAAGGTCTTATAGACGGCTCGAAGGACTTAACATCTTGCTCGAAAAACTGACAGATG
ACACAAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTAATTTTG
GAAATAGTATACTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAAATTCATTTTCT
GAAAATATTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTTCGAAAATCATGTGAAAACATC
CTGCAATAAGGTCTTATAGATGGCCCGAAGGACTTAACATCTTGCTCGAAAGACTGAA
Found at i:2180438 original size:20 final size:20
Alignment explanation
Indices: 2180385--2180432 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
2180375 AAAACGAATA
2180385 ATGTTTACATTTCTCATATG
1 ATGTTTACATTTCTCATATG
2180405 ATGTTTACATTTCTCATATG
1 ATGTTTACATTTCTCATATG
2180425 ATGTTTAC
1 ATGTTTAC
2180433 TCTTCTTGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.25, C:0.15, G:0.10, T:0.50
Consensus pattern (20 bp):
ATGTTTACATTTCTCATATG
Found at i:2187516 original size:31 final size:31
Alignment explanation
Indices: 2187478--2187538 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
2187468 CCGAAGGACC
*
2187478 AGTCCATA-GATCCCCAAGAACCTAGGTAAAT
1 AGTCCATATG-TCCCCAAGAACATAGGTAAAT
* *
2187509 AGTCCATATGTTCCGAAGAACATAGGTAAA
1 AGTCCATATGTCCCCAAGAACATAGGTAAA
2187539 CCCTCGACCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 25 0.96
32 1 0.04
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.21
Consensus pattern (31 bp):
AGTCCATATGTCCCCAAGAACATAGGTAAAT
Found at i:2188304 original size:64 final size:64
Alignment explanation
Indices: 2188204--2188372 Score: 241
Period size: 64 Copynumber: 2.6 Consensus size: 64
2188194 GTATGCATTG
* * ** * * *
2188204 ATGCACTACTGATGCATCGGTGCATAAAATGTATTCGATGTTGT-ATTATTACTGGGATGCATCA
1 ATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTT-TCATTATTAATGGGATGCATCA
* *
2188268 ATGTACTACTTATGCATCGATGCACGAATTGCATTCGATGTTTCATTATTAATGGGATGCATCG
1 ATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTTTCATTATTAATGGGATGCATCA
2188332 ATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGT
1 ATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGT
2188373 ATTTATTTTA
Statistics
Matches: 94, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
63 1 0.01
64 93 0.99
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (64 bp):
ATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTTTCATTATTAATGGGATGCATCA
Found at i:2188393 original size:64 final size:64
Alignment explanation
Indices: 2188196--2188416 Score: 232
Period size: 64 Copynumber: 3.5 Consensus size: 64
2188186 TAATGAAGGT
* * * ** * * ** *
2188196 ATGCATTGATGCACTACTGATGCATCGGTGCATAAAATGTATTCGATGTTGT-ATTATTACTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTT-TCATTATTAAAGAG
* * * *
2188260 ATGCATCAATGTACTACTTATGCATCGATGCACGAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTTTCATTATTAAAGAG
*
2188324 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTATTTATT-TTAAA-AG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGT-TTCATTATTAAAGAG
* * *
2188387 AGTGCATCGATGCACTTCCTGTGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
2188417 ACACCTTCAA
Statistics
Matches: 136, Mismatches: 18, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
63 3 0.02
64 128 0.94
65 5 0.04
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTTTCATTATTAAAGAG
Found at i:2191648 original size:31 final size:31
Alignment explanation
Indices: 2191610--2191672 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
2191600 CCCGAAGGAC
*
2191610 CAGTCCATA-GATCCCCAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCCAAGAACATAGGTAAA
* *
2191641 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCCAAGAACATAGGTAAA
2191672 C
1 C
2191673 CCTCGACCCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 27 0.96
32 1 0.04
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.19
Consensus pattern (31 bp):
CAGTCCATATGTCCCCAAGAACATAGGTAAA
Found at i:2192385 original size:64 final size:64
Alignment explanation
Indices: 2192277--2192497 Score: 259
Period size: 64 Copynumber: 3.5 Consensus size: 64
2192267 TAATGAAGGT
* * * * * *
2192277 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGTATTCGATGTTGT-ATTATTACTAGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTT-TCATTATTAATAGG
* *
2192341 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTTTCATTATTAATAGG
* * *
2192405 ATGCATTGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTATTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGT-TTCATTATTAATAGG
* * * *
2192468 AGTACATCGATGCACTTCATGTGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
2192498 ACACCTTCAA
Statistics
Matches: 136, Mismatches: 18, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
63 3 0.02
64 128 0.94
65 5 0.04
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTTTCATTATTAATAGG
Found at i:2196738 original size:3 final size:3
Alignment explanation
Indices: 2196730--2196785 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
2196720 ATTATAAGTT
2196730 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2196778 TTA TTA TT
1 TTA TTA TT
2196786 TTCCGTCTCA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2198178 original size:22 final size:22
Alignment explanation
Indices: 2198135--2198183 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
2198125 TTGGGTAAGA
**
2198135 AGAGTATTAGTACTCATGAAGG
1 AGAGTATTAGTACTCACCAAGG
2198157 AGAGTATCT-GTACTCACCAAGG
1 AGAGTAT-TAGTACTCACCAAGG
2198179 -GAGTA
1 AGAGTA
2198184 CCAATACTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 5 0.21
22 18 0.75
23 1 0.04
ACGTcount: A:0.35, C:0.14, G:0.27, T:0.24
Consensus pattern (22 bp):
AGAGTATTAGTACTCACCAAGG
Found at i:2201248 original size:30 final size:30
Alignment explanation
Indices: 2201212--2201273 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
2201202 TGAGGTTAGA
*
2201212 AGTTTCTTGAGATTAGTAGACTATTATCGT
1 AGTTTCTTGAGATTAGCAGACTATTATCGT
*
2201242 AGTTTCTTGAGATTAGCAGGCTATTATCGT
1 AGTTTCTTGAGATTAGCAGACTATTATCGT
2201272 AG
1 AG
2201274 ATTCATGAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.26, C:0.11, G:0.23, T:0.40
Consensus pattern (30 bp):
AGTTTCTTGAGATTAGCAGACTATTATCGT
Found at i:2203676 original size:3 final size:3
Alignment explanation
Indices: 2203661--2203768 Score: 175
Period size: 3 Copynumber: 36.7 Consensus size: 3
2203651 AGTTAAAAAA
* * *
2203661 TAT TAT TA- AAT TAT TAT TAT TAT TGT TGT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2203708 TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2203755 TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TA
2203769 AGTGTGTTTA
Statistics
Matches: 99, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
2 3 0.03
3 96 0.97
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:2206024 original size:19 final size:19
Alignment explanation
Indices: 2205985--2206024 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
2205975 TCCTCTTTTT
*
2205985 AAATAATTAATTTGAAGTA
1 AAATAATTAATTTCAAGTA
2206004 AAATAATTAAATTTCAA-TA
1 AAATAATT-AATTTCAAGTA
2206023 AA
1 AA
2206025 TGGATCATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (19 bp):
AAATAATTAATTTCAAGTA
Found at i:2217108 original size:7 final size:7
Alignment explanation
Indices: 2217096--2217145 Score: 52
Period size: 7 Copynumber: 7.4 Consensus size: 7
2217086 AGAAAAGAAC
2217096 AAATGAA
1 AAATGAA
2217103 AAATGAA
1 AAATGAA
2217110 AAATG-A
1 AAATGAA
2217116 AAA-GAAA
1 AAATG-AA
2217123 AAATGAA
1 AAATGAA
*
2217130 AAA-AAA
1 AAATGAA
*
2217136 AAAGGAA
1 AAATGAA
2217143 AAA
1 AAA
2217146 AAAGAGAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
5 1 0.03
6 9 0.24
7 26 0.70
8 1 0.03
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (7 bp):
AAATGAA
Found at i:2217118 original size:13 final size:12
Alignment explanation
Indices: 2217087--2217179 Score: 64
Period size: 13 Copynumber: 7.2 Consensus size: 12
2217077 TTGAAGGAAA
2217087 GAAAAGAACAAAT
1 GAAAAGAA-AAAT
2217100 GAAAAATGAAAAAT
1 G-AAAA-GAAAAAT
2217114 GAAAAGAAAAAAT
1 GAAAAG-AAAAAT
* *
2217127 GAAAAAAAAAAAG
1 G-AAAAGAAAAAT
2217140 GAAAA-AAAAGA-
1 GAAAAGAAAA-AT
*
2217151 GAAATGAAAAAAT
1 GAAAAG-AAAAAT
2217164 GAAGAGAGAAAAAT
1 GAA-A-AGAAAAAT
2217178 GA
1 GA
2217180 GGGTTTGAGA
Statistics
Matches: 66, Mismatches: 4, Indels: 19
0.74 0.04 0.21
Matches are distributed among these distances:
11 8 0.12
12 7 0.11
13 25 0.38
14 22 0.33
15 4 0.06
ACGTcount: A:0.73, C:0.01, G:0.18, T:0.08
Consensus pattern (12 bp):
GAAAAGAAAAAT
Found at i:2218619 original size:105 final size:105
Alignment explanation
Indices: 2218405--2218653 Score: 311
Period size: 105 Copynumber: 2.4 Consensus size: 105
2218395 TGAGGGATTG
2218405 ACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCATAAAGGAGAAAGTTCATAATGAGAA
1 ACATTTCC-A-GAAGAGTTCATAATGAGAAGAACTCATCATAAAGGAGAAAGTTCATAATGAGAA
* * * * *
2218470 GAACTTGTTCCTTTCAAATTCACCACAGATAGAGGTGAACCA
64 AAACATGTTCCTTTCAAATCCACCACAAAGAGAGGTGAACCA
* *
2218512 ACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATGAGAAAA
1 ACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCATAAAGGAGAAAGTTCATAATGAGAAAA
* * * ** * *
2218577 ACATGTT-CTTTCTAAGTCCACCGCAAAGGGATTTGGATCA
66 ACATGTTCCTTTC-AAATCCACCACAAAGAGAGGTGAACCA
* * *
2218617 ACATTTCCAAAAGAGTTCATAATGATAATAACTCATC
1 ACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATC
2218654 CACGAGAAAA
Statistics
Matches: 123, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
104 5 0.04
105 109 0.89
106 1 0.01
107 8 0.07
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.25
Consensus pattern (105 bp):
ACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCATAAAGGAGAAAGTTCATAATGAGAAAA
ACATGTTCCTTTCAAATCCACCACAAAGAGAGGTGAACCA
Found at i:2218835 original size:3 final size:3
Alignment explanation
Indices: 2218820--2218916 Score: 160
Period size: 3 Copynumber: 32.7 Consensus size: 3
2218810 AGTTAAAAAA
* * *
2218820 TAT TAT TA- AAT TAT TAT TAT TGT TGT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2218867 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2218915 TA
1 TA
2218917 AGTGTGTTTA
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
2 1 0.01
3 88 0.99
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:2221176 original size:19 final size:19
Alignment explanation
Indices: 2221137--2221176 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
2221127 TCCTCTTTTT
*
2221137 AAATAATTAATTTGAAGTA
1 AAATAATTAATTTCAAGTA
2221156 AAATAATTAAATTTCAA-TA
1 AAATAATT-AATTTCAAGTA
2221175 AA
1 AA
2221177 TGGATCATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (19 bp):
AAATAATTAATTTCAAGTA
Found at i:2221934 original size:23 final size:23
Alignment explanation
Indices: 2221892--2221940 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
2221882 TATTCGAATG
*
2221892 ATTGAATAGAATATAATCTTGAAA
1 ATTGAATAGAAAATAATCTT-AAA
2221916 ATTGAATA-AAAATAATCTTAAA
1 ATTGAATAGAAAATAATCTTAAA
2221938 ATT
1 ATT
2221941 TCTTTAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 6 0.25
23 10 0.42
24 8 0.33
ACGTcount: A:0.53, C:0.04, G:0.08, T:0.35
Consensus pattern (23 bp):
ATTGAATAGAAAATAATCTTAAA
Found at i:2222825 original size:182 final size:188
Alignment explanation
Indices: 2222510--2222881 Score: 684
Period size: 182 Copynumber: 2.0 Consensus size: 188
2222500 CACTTCCCTA
2222510 CTTTCTCCATTAGGTACAGTGAATCTCCACCTTTTGTAACTCTCCCACCAACCAAACCAAATAAA
1 CTTTCTCCATTAGGTACAGTGAATCTCCACCTTTTGTAACTCT-CCACCAACCAAACC-AATAAA
2222575 AAGAGGATCATTATGATGTTTGAAAAAGTTTCATGTTAAATTTATTTTAGGGTAAAGTACACGAA
64 AAGAGGATCATTATGATGTTTGAAAAAGTTTCATGTTAAATTTATTTTAGGGTAAAGTACACGAA
2222640 TGATCTCAGATTATAGGATGTTACTTTGTTGGGTTCTCCGATTATTAAAAGATATAAAAT
129 TGATCTCAGATTATAGGATGTTACTTTGTTGGGTTCTCCGATTATTAAAAGATATAAAAT
2222700 CTTTCTCCATTAGGTACAGTGAATCTCCACCTTTTGTAACTCT-C-CC-ACC-AACC-A-AAAAA
1 CTTTCTCCATTAGGTACAGTGAATCTCCACCTTTTGTAACTCTCCACCAACCAAACCAATAAAAA
2222759 GAGGATCATTATGATGTTTGAAAAAGTTTCATGTTAAATTTATTTTAGGGTAAAGTACACGAATG
66 GAGGATCATTATGATGTTTGAAAAAGTTTCATGTTAAATTTATTTTAGGGTAAAGTACACGAATG
2222824 ATCTCAGATTATAGGATGTTACTTTGTTGGGTTCTCCGATTATTAAAAGATATAAAAT
131 ATCTCAGATTATAGGATGTTACTTTGTTGGGTTCTCCGATTATTAAAAGATATAAAAT
2222882 GGTCTCCTGA
Statistics
Matches: 182, Mismatches: 0, Indels: 8
0.96 0.00 0.04
Matches are distributed among these distances:
182 128 0.70
183 1 0.01
185 4 0.02
186 3 0.02
187 2 0.01
188 1 0.01
190 43 0.24
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Consensus pattern (188 bp):
CTTTCTCCATTAGGTACAGTGAATCTCCACCTTTTGTAACTCTCCACCAACCAAACCAATAAAAA
GAGGATCATTATGATGTTTGAAAAAGTTTCATGTTAAATTTATTTTAGGGTAAAGTACACGAATG
ATCTCAGATTATAGGATGTTACTTTGTTGGGTTCTCCGATTATTAAAAGATATAAAAT
Found at i:2224410 original size:4 final size:4
Alignment explanation
Indices: 2224401--2224426 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2224391 ATACTATTCA
2224401 ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT AT
2224427 ATGGGATATG
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:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:2224651 original size:2 final size:2
Alignment explanation
Indices: 2224644--2224669 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2224634 TTAAGTAGAT
2224644 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
2224670 ACAATTAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2231429 original size:27 final size:26
Alignment explanation
Indices: 2231383--2231447 Score: 78
Period size: 27 Copynumber: 2.5 Consensus size: 26
2231373 AATTTTAGCA
* *
2231383 GTGAAACTTAAC-ATAGACTTATACTG
1 GTGAAA-TTAACAATAGACTTACACCG
2231409 GTGAAATTAACATATAGACTTACACCG
1 GTGAAATTAACA-ATAGACTTACACCG
*
2231436 GTGAAATGAACA
1 GTGAAATTAACA
2231448 CCTAACTCCA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
25 5 0.15
26 6 0.18
27 23 0.68
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.26
Consensus pattern (26 bp):
GTGAAATTAACAATAGACTTACACCG
Found at i:2231565 original size:25 final size:25
Alignment explanation
Indices: 2231537--2231623 Score: 77
Period size: 25 Copynumber: 3.4 Consensus size: 25
2231527 CCTACACCGG
*
2231537 TGAAATTAGCACTTAATTCCAACAT
1 TGAAATTAACACTTAATTCCAACAT
* * *
2231562 TGAAACTTAACA-TAAACTTACACCAT
1 TGAAA-TTAACACTTAA-TTCCAACAT
* * *
2231588 TTAAATTAACACTTAATTCCAGCAG
1 TGAAATTAACACTTAATTCCAACAT
*
2231613 TGAACTTAACA
1 TGAAATTAACA
2231624 TAAACTTACA
Statistics
Matches: 48, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
25 29 0.60
26 19 0.40
ACGTcount: A:0.43, C:0.21, G:0.07, T:0.30
Consensus pattern (25 bp):
TGAAATTAACACTTAATTCCAACAT
Found at i:2231594 original size:51 final size:51
Alignment explanation
Indices: 2231409--2231705 Score: 271
Period size: 50 Copynumber: 5.9 Consensus size: 51
2231399 ACTTATACTG
* * * * ***
2231409 GTGAAA-TTAACATATAGACTTACACCGGTGAAATGAACACCTAACTCCAGTT
1 GTGAAACTTAACATA-A-ACTTACACCAGTGAAATTAACACTTAATTCCAACA
* * * * * ** *
2231461 GTGAAACTTACCATAGA-TTACATCGGTGAAATTAACAGTTAATTTTAGCA
1 GTGAAACTTAACATAAACTTACACCAGTGAAATTAACACTTAATTCCAACA
* * * *
2231511 GTGAAACTTAA-TTAAACCTACACCGGTGAAATTAGCACTTAATTCCAACA
1 GTGAAACTTAACATAAACTTACACCAGTGAAATTAACACTTAATTCCAACA
* * * *
2231561 TTGAAACTTAACATAAACTTACACCATTTAAATTAACACTTAATTCCAGCA
1 GTGAAACTTAACATAAACTTACACCAGTGAAATTAACACTTAATTCCAACA
* * * *
2231612 GTG-AACTTAACATAAACTTACACAAGTGAAACTAACGCTTAATTCCAATA
1 GTGAAACTTAACATAAACTTACACCAGTGAAATTAACACTTAATTCCAACA
* *
2231662 GTGTAACTTAACATAGACTTACACC-GTTGAAATTAACACTTAAT
1 GTGAAACTTAACATAAACTTACACCAG-TGAAATTAACACTTAAT
2231706 ATGTTCATGA
Statistics
Matches: 199, Mismatches: 41, Indels: 11
0.79 0.16 0.04
Matches are distributed among these distances:
49 3 0.02
50 114 0.57
51 69 0.35
52 6 0.03
53 7 0.04
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (51 bp):
GTGAAACTTAACATAAACTTACACCAGTGAAATTAACACTTAATTCCAACA
Found at i:2231612 original size:101 final size:101
Alignment explanation
Indices: 2231461--2231705 Score: 278
Period size: 101 Copynumber: 2.4 Consensus size: 101
2231451 AACTCCAGTT
* * * ** * ** *
2231461 GTGAAACTTACCATAGA-TTACATCGGTGAAATTAACAGTTAATTTTAGCAGTGAAACTTAA-TT
1 GTGAAACTTAACATAAACTTACACCATTGAAATTAACACTTAATTCCAGCAGTG-AACTTAACAT
** * *
2231524 AAACCTACACCGGTGAAATTAGCACTTAATTCCAACA
65 AAACCTACACAAGTGAAACTAACACTTAATTCCAACA
* *
2231561 TTGAAACTTAACATAAACTTACACCATTTAAATTAACACTTAATTCCAGCAGTGAACTTAACATA
1 GTGAAACTTAACATAAACTTACACCATTGAAATTAACACTTAATTCCAGCAGTGAACTTAACATA
* * *
2231626 AACTTACACAAGTGAAACTAACGCTTAATTCCAATA
66 AACCTACACAAGTGAAACTAACACTTAATTCCAACA
* * *
2231662 GTGTAACTTAACATAGACTTACACCGTTGAAATTAACACTTAAT
1 GTGAAACTTAACATAAACTTACACCATTGAAATTAACACTTAAT
2231706 ATGTTCATGA
Statistics
Matches: 120, Mismatches: 23, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
100 21 0.17
101 99 0.82
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.29
Consensus pattern (101 bp):
GTGAAACTTAACATAAACTTACACCATTGAAATTAACACTTAATTCCAGCAGTGAACTTAACATA
AACCTACACAAGTGAAACTAACACTTAATTCCAACA
Found at i:2231647 original size:25 final size:25
Alignment explanation
Indices: 2231562--2231644 Score: 73
Period size: 25 Copynumber: 3.3 Consensus size: 25
2231552 ATTCCAACAT
*
2231562 TGAAACTTAACATAAACTTACACCAT
1 TGAAACTTAACATAAACTTACA-CAG
* * *
2231588 TTAAA-TTAACACTTAA-TTCCAGCAG
1 TGAAACTTAACA-TAAACTTACA-CAG
2231613 TG-AACTTAACATAAACTTACACAAG
1 TGAAACTTAACATAAACTTACAC-AG
2231638 TGAAACT
1 TGAAACT
2231645 AACGCTTAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
24 6 0.14
25 27 0.61
26 11 0.25
ACGTcount: A:0.45, C:0.20, G:0.07, T:0.28
Consensus pattern (25 bp):
TGAAACTTAACATAAACTTACACAG
Found at i:2243464 original size:14 final size:14
Alignment explanation
Indices: 2243436--2243468 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2243426 ATGCATAGAT
2243436 ACTAATAAAACTAA
1 ACTAATAAAACTAA
2243450 ACTAAGTAAAA-TAA
1 ACTAA-TAAAACTAA
2243464 ACTAA
1 ACTAA
2243469 AATAGTTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.64, C:0.12, G:0.03, T:0.21
Consensus pattern (14 bp):
ACTAATAAAACTAA
Found at i:2244679 original size:22 final size:22
Alignment explanation
Indices: 2244651--2244708 Score: 107
Period size: 22 Copynumber: 2.6 Consensus size: 22
2244641 CAAACCATTC
2244651 AGGGGGGAATCGGTACCCCCTT
1 AGGGGGGAATCGGTACCCCCTT
2244673 AGGGGGGAATCGGTACCCCCTT
1 AGGGGGGAATCGGTACCCCCTT
*
2244695 AGGGGGAAATCGGT
1 AGGGGGGAATCGGT
2244709 TCCCTCTGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.21, C:0.22, G:0.40, T:0.17
Consensus pattern (22 bp):
AGGGGGGAATCGGTACCCCCTT
Found at i:2245368 original size:18 final size:17
Alignment explanation
Indices: 2245345--2245391 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
2245335 ATAAATCCTA
2245345 AAAAATTCAAAGCAATCC
1 AAAAATTCAAA-CAATCC
* *
2245363 ACAAATTCAAACATTCC
1 AAAAATTCAAACAATCC
2245380 AAAATATTCAAA
1 AAAA-ATTCAAA
2245392 ATGTTAAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.55, C:0.21, G:0.02, T:0.21
Consensus pattern (17 bp):
AAAAATTCAAACAATCC
Found at i:2247353 original size:21 final size:21
Alignment explanation
Indices: 2247327--2247366 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2247317 CAGAACCCCA
*
2247327 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
2247348 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
2247367 TCAAAGGGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:2247398 original size:23 final size:24
Alignment explanation
Indices: 2247348--2247396 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 24
2247338 ATTCCCCTGT
2247348 GGGGG-GAATCGGTTCCCCTTCAA
1 GGGGGAGAATCGGTTCCCCTTCAA
*
2247371 -AGGGAGAATCGGTT-CCC-TCAA
1 GGGGGAGAATCGGTTCCCCTTCAA
2247392 GGGGG
1 GGGGG
2247397 GATCTATTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
21 4 0.18
22 9 0.41
23 9 0.41
ACGTcount: A:0.20, C:0.22, G:0.39, T:0.18
Consensus pattern (24 bp):
GGGGGAGAATCGGTTCCCCTTCAA
Found at i:2250140 original size:14 final size:15
Alignment explanation
Indices: 2250114--2250166 Score: 72
Period size: 15 Copynumber: 3.6 Consensus size: 15
2250104 TTTGAGACCT
2250114 CACCCGCCCCGCATC
1 CACCCGCCCCGCATC
2250129 CACCCG-CCCGCATC
1 CACCCGCCCCGCATC
* *
2250143 CGCCCGCCCCACATC
1 CACCCGCCCCGCATC
*
2250158 CGCCCGCCC
1 CACCCGCCC
2250167 AACTAAATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.37
15 22 0.63
ACGTcount: A:0.11, C:0.68, G:0.15, T:0.06
Consensus pattern (15 bp):
CACCCGCCCCGCATC
Found at i:2250167 original size:14 final size:14
Alignment explanation
Indices: 2250125--2250167 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
2250115 ACCCGCCCCG
* *
2250125 CATCCACCCGCCCG
1 CATCCGCCCGCCCA
2250139 CATCCGCCCGCCCCA
1 CATCCGCCCG-CCCA
2250154 CATCCGCCCGCCCA
1 CATCCGCCCGCCCA
2250168 ACTAAATATC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 13 0.50
15 13 0.50
ACGTcount: A:0.14, C:0.65, G:0.14, T:0.07
Consensus pattern (14 bp):
CATCCGCCCGCCCA
Found at i:2257187 original size:28 final size:29
Alignment explanation
Indices: 2257123--2257196 Score: 96
Period size: 28 Copynumber: 2.5 Consensus size: 29
2257113 AAATTACCAT
* * *
2257123 TTTGGTCCCTAAACTTTTTCAAAGTTTATAC
1 TTTGGTCACTAAAC--TTTCAAAATTTATAA
2257154 TTTGGTCACTAAACTTT-AAAATTTATAA
1 TTTGGTCACTAAACTTTCAAAATTTATAA
2257182 TTTGGTCACTAAACT
1 TTTGGTCACTAAACT
2257197 AAATCCATTA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
28 24 0.60
29 3 0.08
31 13 0.32
ACGTcount: A:0.31, C:0.16, G:0.09, T:0.43
Consensus pattern (29 bp):
TTTGGTCACTAAACTTTCAAAATTTATAA
Found at i:2258494 original size:21 final size:21
Alignment explanation
Indices: 2258474--2258512 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2258464 CACTGTAAGA
* *
2258474 ATTT-ATGGCTTCGACAAAAG
1 ATTTCATGGATTCAACAAAAG
2258494 ATTTCATGGATTCAACAAA
1 ATTTCATGGATTCAACAAA
2258513 GGCCTTGATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (21 bp):
ATTTCATGGATTCAACAAAAG
Found at i:2259560 original size:146 final size:146
Alignment explanation
Indices: 2259319--2259833 Score: 816
Period size: 146 Copynumber: 3.5 Consensus size: 146
2259309 ATCTCCGATT
*
2259319 AATATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAGGACGA
1 AATATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACAAACAACATATTGAAAAATCAGGACGA
* ** *
2259384 TCGGACGGTGGACGGTGACGAATCGGAGAAAACAAATCCGGGTGGTTTTTAGCCTCTTGCCGGTG
66 TCGGACGGTGGACGGTGACGGATCGGAGAAAACAAATCCGGACGATTTTTAGCCTCTTGCCGGTG
2259449 ATCGGAATATTTGATC
131 ATCGGAATATTTGATC
* **
2259465 AATATTCTGAATAGTCAAAAGTTGCGGAAGGCCATCACAAACAACATATTGAAAAATCAGGACGA
1 AATATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACAAACAACATATTGAAAAATCAGGACGA
* *
2259530 TCTGACGGTGGACGGTGACGGATCGGAGAAAACAAATCCGGCCGATTTTTAGCCTCTTGCCGGTG
66 TCGGACGGTGGACGGTGACGGATCGGAGAAAACAAATCCGGACGATTTTTAGCCTCTTGCCGGTG
2259595 ATCGGAATATTTGATC
131 ATCGGAATATTTGATC
* *
2259611 AATATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAGGATGA
1 AATATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACAAACAACATATTGAAAAATCAGGACGA
*
2259676 TCGGACGGTGGACGGTGACGGATCGGAGAAAATAAATCCGGACGATTTTTAGCCTCTTGCCGGTG
66 TCGGACGGTGGACGGTGACGGATCGGAGAAAACAAATCCGGACGATTTTTAGCCTCTTGCCGGTG
* **
2259741 ATCGGAATCTGCGATC
131 ATCGGAATATTTGATC
* * * * * *
2259757 AATATTCCGAACGGTGAAAAGTTGCGCG-ATGCCAACACAAACAACCTATTGAAAAATAAGGACA
1 AATATTCCGAACGGTCAAAAGTTGCG-GAAGGCCATCACAAACAACATATTGAAAAATCAGGACG
2259821 ATCGGACGGTGGA
65 ATCGGACGGTGGA
2259834 TGACGGCAGA
Statistics
Matches: 340, Mismatches: 28, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
146 339 1.00
147 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.21
Consensus pattern (146 bp):
AATATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACAAACAACATATTGAAAAATCAGGACGA
TCGGACGGTGGACGGTGACGGATCGGAGAAAACAAATCCGGACGATTTTTAGCCTCTTGCCGGTG
ATCGGAATATTTGATC
Found at i:2265271 original size:15 final size:14
Alignment explanation
Indices: 2265240--2265287 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
2265230 AAGAAAAGAT
* *
2265240 AAAAAAAGAAAAAG
1 AAAAAATGAAAATG
*
2265254 AAAAAATTGTAAATG
1 AAAAAA-TGAAAATG
2265269 AAAAAATGAAAAT-
1 AAAAAATGAAAATG
2265282 AAAAAA
1 AAAAAA
2265288 AAAGAGAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 6 0.21
14 12 0.41
15 11 0.38
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.12
Consensus pattern (14 bp):
AAAAAATGAAAATG
Found at i:2265288 original size:15 final size:15
Alignment explanation
Indices: 2265227--2265305 Score: 56
Period size: 15 Copynumber: 5.3 Consensus size: 15
2265217 GTTAAAAGAG
* *
2265227 AAAAAGAAAAGATAA
1 AAAAAGAAAATAGAA
2265242 AAAAAGAAAA-AGAA
1 AAAAAGAAAATAGAA
* *
2265256 AAAATTGTAAAT-GAA
1 AAAA-AGAAAATAGAA
* *
2265271 AAAATGAAAATAAAA
1 AAAAAGAAAATAGAA
*
2265286 AAAAAGAGAAT-GAA
1 AAAAAGAAAATAGAA
2265300 AGAAAA
1 A-AAAA
2265306 CTCACCCAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
14 16 0.31
15 36 0.69
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (15 bp):
AAAAAGAAAATAGAA
Found at i:2266763 original size:125 final size:126
Alignment explanation
Indices: 2266535--2266843 Score: 399
Period size: 125 Copynumber: 2.5 Consensus size: 126
2266525 TTAGGATATG
* **
2266535 TTGGGGCACGACTGAACCCACATCAGGTTGAGATGACAAGATTCAGACCAATGAGGCATGAAGAA
1 TTGGGGCACGACTGAACCCACATCATGTTGAGATGACAAGATTCAGACCAAAAAGGCATGAAGAA
* **
2266600 TGAGCCTTAGAATTTGAGGTGATGAGGCATTTTAAAGGCCTGTACCAGTATAAGACAAT-A
66 GGAGCCTTAGAATTTGAGGTGATGAGGCATTTTAAAGGCCCATACCAGTATAAGACAATGA
* * * *
2266660 TTGGGGCACGACTGAACCTACGTCATGTTGAGATGACAAGATTTAAACCAAAAAGGCATGAAGAA
1 TTGGGGCACGACTGAACCCACATCATGTTGAGATGACAAGATTCAGACCAAAAAGGCATGAAGAA
* * ** * * *
2266725 GGAGCCTTATAATTTGAGGTGATGGGGTTTTTTGAAGGCCCATACCGGTATAAGACACTGA
66 GGAGCCTTAGAATTTGAGGTGATGAGGCATTTTAAAGGCCCATACCAGTATAAGACAATGA
* * * *
2266786 -TGGGGCATGACTGCACCCACATCGTG-TGAAGATGACAAGATTCAGACCAAGAAGGCAT
1 TTGGGGCACGACTGAACCCACATCATGTTG-AGATGACAAGATTCAGACCAAAAAGGCAT
2266844 TGAGAGCAAG
Statistics
Matches: 157, Mismatches: 25, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
124 2 0.01
125 154 0.98
126 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.27, T:0.22
Consensus pattern (126 bp):
TTGGGGCACGACTGAACCCACATCATGTTGAGATGACAAGATTCAGACCAAAAAGGCATGAAGAA
GGAGCCTTAGAATTTGAGGTGATGAGGCATTTTAAAGGCCCATACCAGTATAAGACAATGA
Found at i:2266904 original size:125 final size:123
Alignment explanation
Indices: 2266535--2266912 Score: 388
Period size: 125 Copynumber: 3.0 Consensus size: 123
2266525 TTAGGATATG
2266535 TTGGGGCACGACTGAACCCACATCAG-GTTGAGATGACAAGATTCAGACCAATG-AGGCATGA-A
1 TTGGGGCACGACTGAACCCACATC-GTGTTGAGATGACAAGATTCAGACCAA-GAAGGCATGAGA
* * * *
2266597 GAATGAGCCTTAGAATTTGAGGTGATGAGGCATTTTAAAGGCCTGTACCAGTATAAGACAATA
64 G-A--AGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGACAATA
* * * * * *
2266660 TTGGGGCACGACTGAACCTACGTCATGTTGAGATGACAAGATTTAAACCAAAAAGGCATGAAGAA
1 TTGGGGCACGACTGAACCCACATCGTGTTGAGATGACAAGATTCAGACCAAGAAGGCATG-AG-A
* * ** * * *
2266725 GGAGCCTTATAATTTGAGGTGATGGGGTTTTTTGAAGGCCCATACCGGTATAAGACACTGA
64 GAAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGACAAT-A
* *
2266786 -TGGGGCATGACTGCACCCACATCGTG-TGAAGATGACAAGATTCAGACCAAGAAGGCATTGAGA
1 TTGGGGCACGACTGAACCCACATCGTGTTG-AGATGACAAGATTCAGACCAAGAAGGCA-TGAGA
* * * * * * *
2266849 GCAAGCCTTACAATCTGAGATGTTGGGGCATTTTGAAGGCCCGTACTAATGTAAGATAATA
64 G-AAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGACAATA
2266910 TTG
1 TTG
2266913 CGACACTAGG
Statistics
Matches: 205, Mismatches: 38, Indels: 20
0.78 0.14 0.08
Matches are distributed among these distances:
124 5 0.02
125 194 0.95
126 4 0.02
128 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.27, T:0.24
Consensus pattern (123 bp):
TTGGGGCACGACTGAACCCACATCGTGTTGAGATGACAAGATTCAGACCAAGAAGGCATGAGAGA
AGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGACAATA
Found at i:2268180 original size:36 final size:36
Alignment explanation
Indices: 2268017--2268210 Score: 140
Period size: 36 Copynumber: 5.4 Consensus size: 36
2268007 AGCAAAGTCA
* * * ** * *
2268017 ATCTAAAGCCTTCACCGAAGAGGAGTGAAGCAGATCA
1 ATCTTAAGTCTTCACCAAAGAATAGTGAAGCA-AACC
* *
2268054 ATCTGAAGTCTTCACCAAATAATAGTGAAGC-AACC
1 ATCTTAAGTCTTCACCAAAGAATAGTGAAGCAAACC
* * *
2268089 ATCTTAAGCCTTCACTAAAGAGTAGTGAAGCAAACC
1 ATCTTAAGTCTTCACCAAAGAATAGTGAAGCAAACC
* * *
2268125 GTCTTAAG-CATGCACCAAAGAATAATGAAGCAAACC
1 ATCTTAAGTC-TTCACCAAAGAATAGTGAAGCAAACC
** * * * *
2268161 ATCTTGTGTCTTCATCAAAGAGTCGTGAAGGAAATCC
1 ATCTTAAGTCTTCACCAAAGAATAGTGAAGCAAA-CC
* *
2268198 ATTTTAAGCCTTC
1 ATCTTAAGTCTTC
2268211 TCATAAGAGT
Statistics
Matches: 122, Mismatches: 31, Indels: 8
0.76 0.19 0.05
Matches are distributed among these distances:
35 29 0.24
36 56 0.46
37 37 0.30
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.23
Consensus pattern (36 bp):
ATCTTAAGTCTTCACCAAAGAATAGTGAAGCAAACC
Found at i:2268660 original size:54 final size:54
Alignment explanation
Indices: 2268579--2269422 Score: 1108
Period size: 54 Copynumber: 15.5 Consensus size: 54
2268569 AGTGAAGCAA
* *
2268579 AAGAAGATTTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
*
2268633 AAGAAGATGTACGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
*
2268687 AAGAAGATGTACGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
*
2268741 AAGAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
2268795 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
2268849 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
*
2268903 AAGAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
2268957 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* *
2269011 AAGAAGATTTCCGAGTTCCATACTTCCTAGAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* * * * *
2269065 AAG-AGATATCCGAGTTCCATACTCCTTAAAGAAAGAAGGAGTGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* * **
2269118 AAG-AGATGTCTGAGTTCCATACTCCCTAGAGAAAGAGGGAGTGAACCCCGTAAG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAA-CCCGTTTG
* *
2269172 AAGAAGATGTTCGAGTTCCATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTTTG
** * * * * * *
2269227 TTGAAGATGGTTCGAG-TCTTATACTCTCT-GCAAGAAATAGAGAGC-AGACACGATTT-
1 AAGAAGAT-GTCCGAGTTC-CATACTCCCTAG--AGAAAGAGGGAGCGA-ACCCG-TTTG
** * ** * * *
2269283 TTGAAGATTGTTCGAGTTTTATACTCCCTGAAAGAAAGATGGAGCGAACCCGTTTT
1 AAGAAGA-TGTCCGAGTTCCATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTTTG
* * * * * * *
2269339 CAGAAGATTATTCGAGTTCTATACTCCCTAAAGCAATAGGGAGCGAACCCGGTTT-
1 AAGAAGA-TGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCC-GTTTG
* * * *
2269394 CAGAAGGTTGTTCGAGTTCTATACTCCCT
1 AAGAA-GATGTCCGAGTTCCATACTCCCT
2269423 GAAAGAATAG
Statistics
Matches: 721, Mismatches: 52, Indels: 33
0.89 0.06 0.04
Matches are distributed among these distances:
53 84 0.12
54 435 0.60
55 83 0.12
56 113 0.16
57 6 0.01
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (54 bp):
AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
Found at i:2269298 original size:112 final size:109
Alignment explanation
Indices: 2268634--2269512 Score: 479
Period size: 108 Copynumber: 8.1 Consensus size: 109
2268624 ACCCGTTTGA
* * * *
2268634 AGAAGA-TGTACGAGTTCCATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGA-TG
1 AGAAGATTGTTCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTTTGTAGAAGATTG
* * * * * *
2268696 TACGAGT-TCCATACTCCCT-AGAGAA-AGAGGGAGCGAACCCGTTTGA
66 TTCGAGTCT-TATACTCTCTGAAAGAATAGA--GAGCG-ACACGTTT-T
* * *
2268742 AGAAGA-TGTCCGAGTTCTATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGA-TG
1 AGAAGATTGTTCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTTTGTAGAAGATTG
* * * * * *
2268804 TCCGAGT-TCCATACTCCCT-AGAGAA-AGAGGGAGCGAACCCGTTTGA
66 TTCGAGTCT-TATACTCTCTGAAAGAATAGA--GAGCG-ACACGTTT-T
* * * *
2268850 AGAAGA-TGTCCGAGTTCCATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGA-TG
1 AGAAGATTGTTCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTTTGTAGAAGATTG
* * * * *
2268912 TCCGAGT-TCTATACTCCCT-AGAGAA-AGAGGGAGCGAACCCGTTTGA
66 TTCGAGTCT-TATACTCTCTGAAAGAATAGA--GAGCG-ACACGTTT-T
* * * *
2268958 AGAAGA-TGTCCGAGTTCCATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATT-
1 AGAAGATTGTTCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTTTGTAGAAGATTG
* * * *
2269020 TCCGAGT-TCCATACT-TCCT-AGAGAA-AGAGGGAGCGAACCCG-TTT
66 TTCGAGTCT-TATACTCT-CTGAAAGAATAGA--GAGCG-ACACGTTTT
* * * * * * * *
2269064 -GAAGAGATATCCGAGTTCCATACT-CCTTAAAGAAAGAAGGAGTGAACCCGTTTGAAG-AGA-T
1 AGAAGA-TTGTTCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTTTGTAGAAGATT
* * * * * ***
2269125 G-TCTGAGT-TCCATACTCCCT-AGAGAA-AGAGGGAGTGAACCCCGTAAGA
65 GTTC-GAGTCT-TATACTCTCTGAAAGAATAGA--GAGCG-A-CACGT-TTT
* * *
2269173 AGAAGA-TGTTCGAGTTCCATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTTTGTTGAAGATGG
1 AGAAGATTGTTCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTTTGTAGAAGATTG
*
2269237 TTCGAGTCTTATACTCTCTGCAAGAAATAGAGAGCAGACACGATTTT
66 TTCGAGTCTTATACTCTCTGAAAG-AATAGAGAGC-GACACG-TTTT
* * *
2269284 TGAAGATTGTTCGAGTTTTATACTCCCTGAAAGAAAGATGGAGCGAACCCGTTT-TCAGAAGATT
1 AGAAGATTGTTCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTTTGT-AGAAGATT
* * * * *
2269348 ATTCGAGT-TCTATACTCCCT-AAAGCAATAGGGAGCGAACCCGGTTTC
65 GTTCGAGTCT-TATACTCTCTGAAAG-AATAGAGAGCG-ACAC-GTTTT
* * * * * *
2269395 AGAAGGTTGTTCGAGTTCTATACTCCCTGAAAG-AATAGGAAGC-AGACACGTTGGTCGAAGATT
1 AGAAGATTGTTCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGA-ACCCGTTTGTAGAAGATT
*
2269458 GTTCAAGTCTTATACTCTCTGAAAGAATAGAGAGCGGACACGTTTT
65 GTTCGAGTCTTATACTCTCTGAAAGAATAGAGAGC-GACACGTTTT
*
2269504 CCGAAGATT
1 -AGAAGATT
2269513 TTTCAAGTCT
Statistics
Matches: 673, Mismatches: 65, Indels: 64
0.84 0.08 0.08
Matches are distributed among these distances:
105 7 0.01
106 37 0.05
107 48 0.07
108 324 0.48
109 34 0.05
110 62 0.09
111 78 0.12
112 77 0.11
113 3 0.00
114 3 0.00
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (109 bp):
AGAAGATTGTTCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTTTGTAGAAGATTG
TTCGAGTCTTATACTCTCTGAAAGAATAGAGAGCGACACGTTTT
Found at i:2269498 original size:55 final size:54
Alignment explanation
Indices: 2269174--2269522 Score: 286
Period size: 55 Copynumber: 6.3 Consensus size: 54
2269164 CCCGTAAGAA
* * *
2269174 GAAGA-TGTTCGAGT-TCCATACTCCCTGAAAGAA-AGAGGGAGCGAACCCGTTTGTT
1 GAAGATTGTTCGAGTCT-TATACTCCCTGAAAGAATAGA--GAGCGAACACGTTT-TC
* * * *
2269229 GAAGATGGTTCGAGTCTTATACTCTCTGCAAGAAATAGAGAGC-AGACACGATTTTT
1 GAAGATTGTTCGAGTCTTATACTCCCTGAAAG-AATAGAGAGCGA-ACACG-TTTTC
* *
2269285 GAAGATTGTTCGAGTTTTATACTCCCTGAAAGAA-AGATGGAGCGAACCCGTTTTC
1 GAAGATTGTTCGAGTCTTATACTCCCTGAAAGAATAGA--GAGCGAACACGTTTTC
* * * *
2269340 AGAAGATTATTCGAGT-TCTATACTCCCT-AAAGCAATAGGGAGCGAACCCGGTTTC
1 -GAAGATTGTTCGAGTCT-TATACTCCCTGAAAG-AATAGAGAGCGAACACGTTTTC
* *
2269395 AGAAGGTTGTTCGAGT-TCTATACTCCCTGAAAGAATAG-GAAGC-AGACACGTTGGTC
1 -GAAGATTGTTCGAGTCT-TATACTCCCTGAAAGAATAGAG-AGCGA-ACACGTT-TTC
* * *
2269451 GAAGATTGTTCAAGTCTTATACTCTCTGAAAGAATAGAGAGCGGACACGTTTTCC
1 GAAGATTGTTCGAGTCTTATACTCCCTGAAAGAATAGAGAGCGAACACGTTTT-C
* *
2269506 GAAGATTTTTCAAGTCT
1 GAAGATTGTTCGAGTCT
2269523 CATTTAGTTA
Statistics
Matches: 248, Mismatches: 25, Indels: 42
0.79 0.08 0.13
Matches are distributed among these distances:
54 6 0.02
55 130 0.52
56 100 0.40
57 9 0.04
58 3 0.01
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (54 bp):
GAAGATTGTTCGAGTCTTATACTCCCTGAAAGAATAGAGAGCGAACACGTTTTC
Found at i:2270344 original size:146 final size:146
Alignment explanation
Indices: 2270103--2270616 Score: 816
Period size: 146 Copynumber: 3.5 Consensus size: 146
2270093 ATCTCCGATT
2270103 AATATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAGGACGA
1 AATATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAGGACGA
* **
2270168 TCGGACGGTGGACGGTGACGAATCGGAGAAAACAAATCCGGGTGGTTTTTAGCCTCTTGCCGGTG
66 TCGGACGGTGGACGGTGACGGATCGGAGAAAACAAATCCGGACGGTTTTTAGCCTCTTGCCGGTG
2270233 ATCGGAATATTTGATC
131 ATCGGAATATTTGATC
* **
2270249 AATATTCTGAATAGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAGGACGA
1 AATATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAGGACGA
* * *
2270314 TCTGACGGTGGACGGTGACGGATCGGAGAAAACAAATCCGGCCGGTTTTTAGCCTCTTTCCGGTG
66 TCGGACGGTGGACGGTGACGGATCGGAGAAAACAAATCCGGACGGTTTTTAGCCTCTTGCCGGTG
2270379 ATCGGAATATTTGATC
131 ATCGGAATATTTGATC
*
2270395 AATATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAGGATGA
1 AATATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAGGACGA
* *
2270460 TCGGACGGTGGACGGTGACGGATCGGAGAAAATAAATCCGGACGATTTTTAGCCTCTTGCCGGTG
66 TCGGACGGTGGACGGTGACGGATCGGAGAAAACAAATCCGGACGGTTTTTAGCCTCTTGCCGGTG
* **
2270525 ATCGGAATCTGCGATC
131 ATCGGAATATTTGATC
* * * * * *
2270541 AATATTCCGAACGGTGAAAAGTTGCGCG-ATGCCAACACAAACAACCTATTG-AAAATCAGGACA
1 AATATTCCGAACGGTCAAAAGTTGCG-GAAGGCCATCACGAACAACATATTGAAAAATCAGGACG
2270604 ATCGGACGGTGGA
65 ATCGGACGGTGGA
2270617 TGACGGCAGA
Statistics
Matches: 340, Mismatches: 27, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
145 23 0.07
146 316 0.93
147 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (146 bp):
AATATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAGGACGA
TCGGACGGTGGACGGTGACGGATCGGAGAAAACAAATCCGGACGGTTTTTAGCCTCTTGCCGGTG
ATCGGAATATTTGATC
Found at i:2273704 original size:151 final size:149
Alignment explanation
Indices: 2273426--2273712 Score: 371
Period size: 150 Copynumber: 1.9 Consensus size: 149
2273416 TGTAAAAATG
* * * *
2273426 GAACATTTATAAATTTAGACTTTAGCATTAACCAACTTATTTTAGTGGTTAAAGAAATCATTGTT
1 GAACATTTATAAATTTAGACTTTAGCATGAACCAACTTACTTCAGTGATTAAAG-AATCATTGTT
2273491 GTTCATATAAGTCACGACTTCGAACACCAGCAACTGCAGCAAGGTGATTGAGCGTTCATTTTTTT
65 GTTCATATAAGTCACGACTTCGAACACCAGCAACTGCAGCAAGGTGATTGAGCGTTCATTTTTTT
2273556 TATAAAAGAAAAGCTGGTGTT
130 TA-AAAAGAAAAGCTGGTGTT
* *
2273577 GAACATTTATAAATTTAGATTTTAGCATGAACCAACTTACTTCAGTGATTAAATG-ATCGTTGTT
1 GAACATTTATAAATTTAGACTTTAGCATGAACCAACTTACTTCAGTGATTAAA-GAATCATTGTT
* * ** * * * * * *
2273641 GTTCCTATAGGTCACGGGTTTGAGCACTAGCAGCTGCATC-AGAGTGATTGAGCGTTTATTTTTT
65 GTTCATATAAGTCACGACTTCGAACACCAGCAACTGCAGCAAG-GTGATTGAGCGTTCA-TTTTT
2273705 TTTAAAAA
128 TTTAAAAA
2273713 TAAATTGTGT
Statistics
Matches: 117, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
149 2 0.02
150 57 0.49
151 57 0.49
152 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (149 bp):
GAACATTTATAAATTTAGACTTTAGCATGAACCAACTTACTTCAGTGATTAAAGAATCATTGTTG
TTCATATAAGTCACGACTTCGAACACCAGCAACTGCAGCAAGGTGATTGAGCGTTCATTTTTTTT
AAAAAGAAAAGCTGGTGTT
Found at i:2277212 original size:2 final size:2
Alignment explanation
Indices: 2277207--2277244 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2277197 CGGTATAAAC
2277207 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
2277245 GCACTATGCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2279581 original size:111 final size:111
Alignment explanation
Indices: 2279387--2279671 Score: 446
Period size: 111 Copynumber: 2.6 Consensus size: 111
2279377 TGTCACTCAC
* * * *
2279387 GGAATATCAGATCT-GGAGATGTTGATTCATTGAATCAGAGTAGACTTGTTCCGCTGTTACTCAG
1 GGAATATCAGATCTGGGAGA-GTTGATCCATTGAATCAGGGTAGACTTGTTCCACTGTCACTCAG
*
2279451 GGAATATCAAATCTTGAAAGAGAGAGATATGTTCCGCTTCCTCTGAG
65 GGAATATCAAATCTTGAAAGAAAGAGATATGTTCCGCTTCCTCTGAG
* * * *
2279498 GGAATATCAGATATGGGAGAGTTGATCCATTGAATCGGGGCAGATTTGTTCCACTGTCACTCAGG
1 GGAATATCAGATCTGGGAGAGTTGATCCATTGAATCAGGGTAGACTTGTTCCACTGTCACTCAGG
* *
2279563 GAATATCAAATCTTGAAAGAAAGAGATCTGTTCTGCTTCCTCTGAG
66 GAATATCAAATCTTGAAAGAAAGAGATATGTTCCGCTTCCTCTGAG
*
2279609 GGAATATCAGATCTGGGAGAGTTGATCCATTAAATCAGGGTAGACTTGTTCCACTGTCACTCA
1 GGAATATCAGATCTGGGAGAGTTGATCCATTGAATCAGGGTAGACTTGTTCCACTGTCACTCA
2279672 AATCTTGGAT
Statistics
Matches: 157, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
111 152 0.97
112 5 0.03
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (111 bp):
GGAATATCAGATCTGGGAGAGTTGATCCATTGAATCAGGGTAGACTTGTTCCACTGTCACTCAGG
GAATATCAAATCTTGAAAGAAAGAGATATGTTCCGCTTCCTCTGAG
Found at i:2279744 original size:48 final size:48
Alignment explanation
Indices: 2279669--2279772 Score: 163
Period size: 48 Copynumber: 2.2 Consensus size: 48
2279659 CCACTGTCAC
* ** *
2279669 TCAAATCTTGGATAAGAGAGACTTGTTCCGCTTATTCTGAAGGGAATA
1 TCAAATCTTGGATAAGAGAGACCTGTTCCAATTACTCTGAAGGGAATA
2279717 TCAAATCTTGGATAAGAGAGACCTGTTCCAATTACTCTGAAGGGAATA
1 TCAAATCTTGGATAAGAGAGACCTGTTCCAATTACTCTGAAGGGAATA
*
2279765 TCAGATCT
1 TCAAATCT
2279773 GGGGGATTTG
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (48 bp):
TCAAATCTTGGATAAGAGAGACCTGTTCCAATTACTCTGAAGGGAATA
Found at i:2279885 original size:113 final size:113
Alignment explanation
Indices: 2279687--2279908 Score: 390
Period size: 113 Copynumber: 2.0 Consensus size: 113
2279677 TGGATAAGAG
* * *
2279687 AGACTTGTTCCGCTTATTCTGAAGGGAATATCAAATCTTGGATAAGAGAGACCTGTTCCAATTAC
1 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAAACTTGGATAAGAGAGACCTGTTCCAATTAC
*
2279752 TCTGAAGGGAATATCAGATCTGGGGGATTTGATCCATTGAATCAGGAT
66 TCTGAAGGAAATATCAGATCTGGGGGATTTGATCCATTGAATCAGGAT
**
2279800 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAAACTTGGATAAGAGAGACCTGTTCCGCTTAC
1 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAAACTTGGATAAGAGAGACCTGTTCCAATTAC
2279865 TCTGAAGGAAATATCAGATCTGGGGGATTTGATCCATTGAATCA
66 TCTGAAGGAAATATCAGATCTGGGGGATTTGATCCATTGAATCA
2279909 AGATCGAACC
Statistics
Matches: 103, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
113 103 1.00
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (113 bp):
AGACTTGTTCCACTTACTCTGAAGGGAATATCAAAACTTGGATAAGAGAGACCTGTTCCAATTAC
TCTGAAGGAAATATCAGATCTGGGGGATTTGATCCATTGAATCAGGAT
Found at i:2290691 original size:2 final size:2
Alignment explanation
Indices: 2290681--2290745 Score: 121
Period size: 2 Copynumber: 32.5 Consensus size: 2
2290671 ATATATACGG
*
2290681 TA TA AA 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
2290723 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
2290746 GCACTATGCA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2292710 original size:3 final size:3
Alignment explanation
Indices: 2292698--2292745 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
2292688 TAACAACAAC
*
2292698 AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2292745 A
1 A
2292746 TTAAAAGACG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:2292750 original size:8 final size:8
Alignment explanation
Indices: 2292707--2292751 Score: 54
Period size: 9 Copynumber: 5.2 Consensus size: 8
2292697 CAATAACAAT
2292707 AATAATAA
1 AATAATAA
2292715 TAATAATAA
1 -AATAATAA
2292724 TAATAATAA
1 -AATAATAA
2292733 TAATAATAA
1 -AATAATAA
*
2292742 AATATTAA
1 AATAATAA
2292750 AA
1 AA
2292752 GACGAGATGA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
8 9 0.26
9 26 0.74
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (8 bp):
AATAATAA
Found at i:2299652 original size:14 final size:14
Alignment explanation
Indices: 2299633--2299663 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
2299623 ATCTTATTGA
2299633 CTGGAGCCCCACGT
1 CTGGAGCCCCACGT
2299647 CTGGAGCCCCACGT
1 CTGGAGCCCCACGT
2299661 CTG
1 CTG
2299664 CAGGAGTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.13, C:0.42, G:0.29, T:0.16
Consensus pattern (14 bp):
CTGGAGCCCCACGT
Found at i:2303074 original size:34 final size:34
Alignment explanation
Indices: 2303031--2303098 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
2303021 ATATATACAT
2303031 GATTACAAGAGATCAATTAGGCTACAATTAAGGA
1 GATTACAAGAGATCAATTAGGCTACAATTAAGGA
2303065 GATTACAAGAGATCAATTAGGCTACAATTAAGGA
1 GATTACAAGAGATCAATTAGGCTACAATTAAGGA
2303099 AACAAAGATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.24
Consensus pattern (34 bp):
GATTACAAGAGATCAATTAGGCTACAATTAAGGA
Found at i:2307693 original size:34 final size:34
Alignment explanation
Indices: 2307650--2307717 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
2307640 ATATATACAT
2307650 GATTACAAGAGATCAATTAGGCTACAATTAAGGA
1 GATTACAAGAGATCAATTAGGCTACAATTAAGGA
*
2307684 GATTACAAGATATCAATTAGGCTACAATTAAGGA
1 GATTACAAGAGATCAATTAGGCTACAATTAAGGA
2307718 AACAAAGATA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (34 bp):
GATTACAAGAGATCAATTAGGCTACAATTAAGGA
Found at i:2309522 original size:3 final size:3
Alignment explanation
Indices: 2309514--2309539 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2309504 TATTTTTAAA
2309514 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
2309540 CATATATATA
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:2310791 original size:15 final size:15
Alignment explanation
Indices: 2310771--2310800 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2310761 GGATTTCTTA
2310771 ATTTTAATAATTGAT
1 ATTTTAATAATTGAT
*
2310786 ATTTTAATCATTGAT
1 ATTTTAATAATTGAT
2310801 TAATAATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.03, G:0.07, T:0.53
Consensus pattern (15 bp):
ATTTTAATAATTGAT
Done.