Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009634.1 Hibiscus syriacus cultivar Beakdansim tig00117034_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: 17174986
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 78
Found at i:1871123 original size:9 final size:9
Alignment explanation
Indices: 1871109--1871137 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1871099 ATAGGCATTA
1871109 AAATAAAAT
1 AAATAAAAT
1871118 AAATAAAAT
1 AAATAAAAT
1871127 AAAT-AAAT
1 AAATAAAAT
1871135 AAA
1 AAA
1871138 CATATTTTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 7 0.35
9 13 0.65
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AAATAAAAT
Found at i:1872514 original size:3 final size:3
Alignment explanation
Indices: 1872501--1872556 Score: 94
Period size: 3 Copynumber: 18.0 Consensus size: 3
1872491 CAAATGTAAG
1872501 ATA ATTA ATA ATA ATA ATA ATAA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA A-TA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA
1872548 ATA ATA ATA
1 ATA ATA ATA
1872557 TTTTTTCGAC
Statistics
Matches: 51, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
3 45 0.88
4 6 0.12
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1872616 original size:36 final size:36
Alignment explanation
Indices: 1872576--1872672 Score: 104
Period size: 36 Copynumber: 2.7 Consensus size: 36
1872566 CCCGCTCCGT
** *
1872576 TAATTCCAAATCTTTTTCAACTTCCACCAGCTCCAC
1 TAATTCCAAATCCCTTTCAACCTCCACCAGCTCCAC
* * * *
1872612 TAATTCCAAACCCCTTTCAGCCTCCATCAGCTCCTC
1 TAATTCCAAATCCCTTTCAACCTCCACCAGCTCCAC
* * *
1872648 TTATTCCAAATCCATTTCAGCCTCC
1 TAATTCCAAATCCCTTTCAACCTCC
1872673 TCATACACCT
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.25, C:0.39, G:0.04, T:0.32
Consensus pattern (36 bp):
TAATTCCAAATCCCTTTCAACCTCCACCAGCTCCAC
Found at i:1872765 original size:45 final size:46
Alignment explanation
Indices: 1872650--1872766 Score: 168
Period size: 45 Copynumber: 2.6 Consensus size: 46
1872640 AGCTCCTCTT
* *
1872650 ATTCCAAATCCATTT-CAGCCTCCT-CATACACCTCCAGCTCCACTA
1 ATTCCAAA-CCCTTTCCAGCCTCCTCCATACACCTCCAGCACCACTA
*
1872695 ATTCCAAACCCCTTCCAGCCTCCTCCA-ACACCTCCAGCACCACTA
1 ATTCCAAACCCTTTCCAGCCTCCTCCATACACCTCCAGCACCACTA
*
1872740 TTTCCAAACCCTTTCCAGCCTCCTCCA
1 ATTCCAAACCCTTTCCAGCCTCCTCCA
1872767 GTACCTTTTA
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
44 4 0.06
45 59 0.91
46 2 0.03
ACGTcount: A:0.25, C:0.47, G:0.04, T:0.24
Consensus pattern (46 bp):
ATTCCAAACCCTTTCCAGCCTCCTCCATACACCTCCAGCACCACTA
Found at i:1880510 original size:34 final size:34
Alignment explanation
Indices: 1880443--1880511 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 34
1880433 ACCAGCGGTC
* *
1880443 GAAAACCTCCTCCACTCACCGAAACTCGTCGCTG
1 GAAAACCTCCTCCACTCACCGAAACCCGCCGCTG
*
1880477 GAAAACCTCCTCCACTCATC-ATAACCCGCCGCTG
1 GAAAACCTCCTCCACTCACCGA-AACCCGCCGCTG
1880511 G
1 G
1880512 CCGACACCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
33 1 0.03
34 30 0.97
ACGTcount: A:0.26, C:0.42, G:0.14, T:0.17
Consensus pattern (34 bp):
GAAAACCTCCTCCACTCACCGAAACCCGCCGCTG
Found at i:1882414 original size:21 final size:23
Alignment explanation
Indices: 1882376--1882419 Score: 74
Period size: 21 Copynumber: 2.0 Consensus size: 23
1882366 CTGGTATTAA
1882376 TACCTTCCTTATGGTATCGATAC
1 TACCTTCCTTATGGTATCGATAC
1882399 TACCTTCC-TA-GGTATCGATAC
1 TACCTTCCTTATGGTATCGATAC
1882420 CTTTTAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 11 0.52
22 2 0.10
23 8 0.38
ACGTcount: A:0.23, C:0.27, G:0.14, T:0.36
Consensus pattern (23 bp):
TACCTTCCTTATGGTATCGATAC
Found at i:1883864 original size:20 final size:21
Alignment explanation
Indices: 1883798--1883870 Score: 80
Period size: 20 Copynumber: 3.6 Consensus size: 21
1883788 AATCTAATTT
*
1883798 GGGTATCGATACC-TAGA-GG
1 GGGTATCGATACCATAGATGA
* * *
1883817 GGGTATCAATACCATAGCTTA
1 GGGTATCGATACCATAGATGA
1883838 GGGGTATCGATACCAT-GATGA
1 -GGGTATCGATACCATAGATGA
1883859 GGGTATCGATAC
1 GGGTATCGATAC
1883871 AGGTTACTTC
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
19 12 0.27
20 15 0.34
21 3 0.07
22 14 0.32
ACGTcount: A:0.29, C:0.16, G:0.30, T:0.25
Consensus pattern (21 bp):
GGGTATCGATACCATAGATGA
Found at i:1883867 original size:95 final size:93
Alignment explanation
Indices: 1883745--1883966 Score: 220
Period size: 94 Copynumber: 2.3 Consensus size: 93
1883735 CGAGCAATGA
* * * * * *
1883745 GGTATAGATACCATGGTAAGTGTATCGATACCA-GTAAATTTCGAATCTAATTTGGGTATCGATA
1 GGTATCGATACCATGATGAGGGTATCGATACCAGGT-AACTTCGAAGCTAATTTGGGTATCGATA
*
1883809 CCTA-G-AGGGGGTATCAATACCATAGCTTAGG
65 --TATGAAGGGGGTATCAATACCATA--ATAGG
* * *
1883840 GGTATCGATACCATGATGAGGGTATCGATA-CAGGTTACTTCGAAGCTAATTTTGGTATTGATAT
1 GGTATCGATACCATGATGAGGGTATCGATACCAGGTAACTTCGAAGCTAATTTGGGTATCGATAT
*
1883904 ATGAAGGGGGTATCAATACCCTAATAGG
66 ATGAAGGGGGTATCAATACCATAATAGG
*
1883932 GTAGTATCGATACCAT-AAGCAGGGGTATCGATACC
1 G--GTATCGATACCATGATG-A-GGGTATCGATACC
1883967 TAAGGGCTAG
Statistics
Matches: 107, Mismatches: 12, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
92 7 0.07
93 3 0.03
94 57 0.53
95 39 0.36
96 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (93 bp):
GGTATCGATACCATGATGAGGGTATCGATACCAGGTAACTTCGAAGCTAATTTGGGTATCGATAT
ATGAAGGGGGTATCAATACCATAATAGG
Found at i:1884873 original size:59 final size:59
Alignment explanation
Indices: 1884265--1884854 Score: 885
Period size: 59 Copynumber: 10.0 Consensus size: 59
1884255 TTTATTGATG
* * *
1884265 TATGTATAGTGAATTTCTAGATAGGGCACTTTGTGTGTTAAAATGGTAAGGAAATCATAC
1 TATGTGTA-TGAATTTCCAGATAGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATAC
* **
1884325 TATGTGTATGAATTTCCAAATAGGATACTTTGTGTGCTAAAATGGTAAGGAAATCATAC
1 TATGTGTATGAATTTCCAGATAGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATAC
* * *
1884384 TATGTGTATAAATTTCCTGATAGGGCACTTTGTGTGCTAAAATGGTAAGGAAATTATAC
1 TATGTGTATGAATTTCCAGATAGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATAC
* * * *
1884443 CATGTGTATGAATTTTCTGATAGGGCACTTTGTGTGTTAAAATGGTAAGGAAATCATAC
1 TATGTGTATGAATTTCCAGATAGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATAC
* *
1884502 TATGTGAATGAATTTCCATATAGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATAC
1 TATGTGTATGAATTTCCAGATAGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATAC
* * * * * * * *
1884561 TATGTTTATGAATTTCCAGATAGAGCACTTTATGAGTTAAAACGGTGAGGAAAACATAC
1 TATGTGTATGAATTTCCAGATAGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATAC
1884620 TATGTGTATGAATTTCCAGATAGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATAC
1 TATGTGTATGAATTTCCAGATAGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATAC
1884679 TATGTGTATGAATTTCCAGATAGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATAC
1 TATGTGTATGAATTTCCAGATAGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATAC
* * * *
1884738 AAAGGGTATGAATTTCCAGATAGGGCACTTTGTGTGCTAAAA-GAGTAAGAAAATCATAC
1 TATGTGTATGAATTTCCAGATAGGGCACTTTGTGTGCTAAAATG-GTAAGGAAATCATAC
* * *
1884797 TAAGTGTATGAATTTCCAGATAGGGCACTCTGTGTGCTAAAATGATAAGGAAATCATA
1 TATGTGTATGAATTTCCAGATAGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATA
1884855 TTGCTTGTAT
Statistics
Matches: 478, Mismatches: 50, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
58 1 0.00
59 469 0.98
60 8 0.02
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (59 bp):
TATGTGTATGAATTTCCAGATAGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATAC
Found at i:1888494 original size:18 final size:18
Alignment explanation
Indices: 1888471--1888545 Score: 96
Period size: 18 Copynumber: 4.1 Consensus size: 18
1888461 ACTGAATATT
1888471 TGTCCCGAAGAACCACTG
1 TGTCCCGAAGAACCACTG
*
1888489 TGTCCCGAAGGACCACTGG
1 TGTCCCGAAGAACCACT-G
* *
1888508 TTGTTCCGAAGAACCACTA
1 -TGTCCCGAAGAACCACTG
*
1888527 TGTCCCGAAGGACCACTG
1 TGTCCCGAAGAACCACTG
1888545 T
1 T
1888546 TAATCCCTCG
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
18 32 0.67
19 1 0.02
20 15 0.31
ACGTcount: A:0.25, C:0.31, G:0.24, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGAACCACTG
Found at i:1888517 original size:38 final size:38
Alignment explanation
Indices: 1888470--1888544 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
1888460 CACTGAATAT
*
1888470 TTGTCCCGAAGAACCACTGTGTCCCGAAGGACCACTGG
1 TTGTCCCGAAGAACCACTATGTCCCGAAGGACCACTGG
*
1888508 TTGTTCCGAAGAACCACTATGTCCCGAAGGACCACTG
1 TTGTCCCGAAGAACCACTATGTCCCGAAGGACCACTG
1888545 TTAATCCCTC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.25, C:0.31, G:0.24, T:0.20
Consensus pattern (38 bp):
TTGTCCCGAAGAACCACTATGTCCCGAAGGACCACTGG
Found at i:1889821 original size:20 final size:22
Alignment explanation
Indices: 1889796--1889853 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
1889786 TTCCCCTTGA
1889796 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
1889816 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
1889839 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
1889854 CTACTCATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.50
22 1 0.03
23 3 0.09
24 13 0.38
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:1889919 original size:64 final size:63
Alignment explanation
Indices: 1889841--1889981 Score: 176
Period size: 64 Copynumber: 2.2 Consensus size: 63
1889831 TCTTTAACAT
* * *
1889841 GTGCATCGATGCACTACTCATGCATCGATACACAAATTACCTTCGATGTTTTCAT-TTTAAGGG
1 GTGCATCGATGCACTACTCATGCATCGATACACAAATTACATTCGATG-TTTCATCTTTAAAGA
* * * * * *
1889904 GATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTACTCATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
1889968 GTGCATCGATGCAC
1 GTGCATCGATGCAC
1889982 ATTGAATGTG
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
63 19 0.28
64 48 0.72
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTACTCATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
Found at i:1891254 original size:20 final size:19
Alignment explanation
Indices: 1891229--1891268 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
1891219 TTCAATCCCT
*
1891229 TTCATTTCTTTATTCCATTA
1 TTCATTTATTTATTCC-TTA
1891249 TTCATTTATTTATTCCTTA
1 TTCATTTATTTATTCCTTA
1891268 T
1 T
1891269 ACACAAATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.20, C:0.17, G:0.00, T:0.62
Consensus pattern (19 bp):
TTCATTTATTTATTCCTTA
Found at i:1893238 original size:20 final size:20
Alignment explanation
Indices: 1893210--1893247 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1893200 CACTGAATAT
*
1893210 TTGTCCCGAAGGACCACTGG
1 TTGTCCCGAAGAACCACTGG
*
1893230 TTGTTCCGAAGAACCACT
1 TTGTCCCGAAGAACCACT
1893248 ATATCCCGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.24
Consensus pattern (20 bp):
TTGTCCCGAAGAACCACTGG
Found at i:1894543 original size:20 final size:20
Alignment explanation
Indices: 1894518--1894555 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1894508 TTCCCCTTGA
*
1894518 AGTGCATTGAAGCATTCTAC
1 AGTGCATCGAAGCATTCTAC
*
1894538 AGTGCATCGATGCATTCT
1 AGTGCATCGAAGCATTCT
1894556 TTAACATGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (20 bp):
AGTGCATCGAAGCATTCTAC
Found at i:1894640 original size:64 final size:63
Alignment explanation
Indices: 1894567--1894703 Score: 168
Period size: 64 Copynumber: 2.2 Consensus size: 63
1894557 TAACATGTGT
* * *
1894567 ATCGATGCACTACATATGCATCGATACACAAATTACCTTCGATGTTT-TCATTTTAAGGGGATGC
1 ATCGATGCACTACATATGCATCGATACACAAATTACATTCGATGTTTCT-ATTTTAAAGAG-TGC
* * * * * *
1894631 ATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCTTTTTTAAAGAGTGC
1 ATCGATGCACTACATATGCATCGATACACAAATTACATTCGATGTTTCTATTTTAAAGAGTGC
1894694 ATCGATGCAC
1 ATCGATGCAC
1894704 ATTGAATGTG
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
63 13 0.21
64 49 0.78
65 1 0.02
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.34
Consensus pattern (63 bp):
ATCGATGCACTACATATGCATCGATACACAAATTACATTCGATGTTTCTATTTTAAAGAGTGC
Found at i:1916487 original size:23 final size:23
Alignment explanation
Indices: 1916456--1916499 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1916446 TTGTTAAGGA
1916456 TAAAAAATTA-AACAAATTATTTT
1 TAAAAAATTATAA-AAATTATTTT
*
1916479 TAAATAATTATAAAAATTATT
1 TAAAAAATTATAAAAATTATT
1916500 AAATTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
TAAAAAATTATAAAAATTATTTT
Found at i:1917238 original size:20 final size:20
Alignment explanation
Indices: 1917213--1917253 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1917203 ATTAGTCATG
1917213 AATAATTTATTTAATTTTTT
1 AATAATTTATTTAATTTTTT
*
1917233 AATAATTTGTTTAATTTTTT
1 AATAATTTATTTAATTTTTT
1917253 A
1 A
1917254 TCCTTAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (20 bp):
AATAATTTATTTAATTTTTT
Found at i:1918081 original size:11 final size:11
Alignment explanation
Indices: 1918048--1918098 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
1918038 TTACAAATAT
*
1918048 AAAAAAATCTA
1 AAAAAAATCCA
*
1918059 AAAAATAT--A
1 AAAAAAATCCA
1918068 AAAAAAATCCA
1 AAAAAAATCCA
*
1918079 AAATAAATCCA
1 AAAAAAATCCA
1918090 AAATAAAAT
1 AAA-AAAAT
1918099 TAATATGATT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
9 8 0.24
11 21 0.64
12 4 0.12
ACGTcount: A:0.73, C:0.10, G:0.00, T:0.18
Consensus pattern (11 bp):
AAAAAAATCCA
Found at i:1918134 original size:21 final size:22
Alignment explanation
Indices: 1918098--1918143 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 22
1918088 CAAAATAAAA
1918098 TTAATATGATTATTTATCTAATT
1 TTAATATGATTATTTATCT-ATT
1918121 TTAATAT-ATT-TTTATCTATT
1 TTAATATGATTATTTATCTATT
1918141 TTA
1 TTA
1918144 TAATTTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.26
21 7 0.30
22 3 0.13
23 7 0.30
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (22 bp):
TTAATATGATTATTTATCTATT
Found at i:1920847 original size:2 final size:2
Alignment explanation
Indices: 1920842--1920875 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1920832 TCTATATAGC
1920842 AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1920876 GGTACATGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1920856 original size:17 final size:17
Alignment explanation
Indices: 1920834--1920873 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
1920824 CACTACATTC
1920834 TATATAGCATATATATA
1 TATATAGCATATATATA
**
1920851 TATATATTATATATATA
1 TATATAGCATATATATA
1920868 TATATA
1 TATATA
1920874 TAGGTACATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (17 bp):
TATATAGCATATATATA
Found at i:1920870 original size:15 final size:15
Alignment explanation
Indices: 1920843--1920872 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1920833 CTATATAGCA
1920843 TATATATATATATAT
1 TATATATATATATAT
1920858 TATATATATATATAT
1 TATATATATATATAT
1920873 ATAGGTACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATATATATATATAT
Found at i:1920874 original size:17 final size:17
Alignment explanation
Indices: 1920842--1920874 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1920832 TCTATATAGC
1920842 ATATATATATATATATT
1 ATATATATATATATATT
1920859 ATATATATATATATAT
1 ATATATATATATATAT
1920875 AGGTACATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATATATATATATATATT
Found at i:1921813 original size:214 final size:214
Alignment explanation
Indices: 1921565--1922654 Score: 1537
Period size: 214 Copynumber: 5.3 Consensus size: 214
1921555 ATTTAAGAAT
*
1921565 TAAATTGAACAAATATGAAATTAAAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
*
1921630 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTATTACAAAAAAGTACTAAAGTATAC
66 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAAGTATAC
*
1921695 CCATTTAAAAATTTATGGGCCAATTAAAAAATAGAATTAA-AAAAAGTATGGATCAATTTCAGAT
131 CCATTTAAAAAGTTATGGGCCAATT-AAAAATAGAATTAAGAAAAAGTATGGATCAATTTCAGAT
1921759 GCAAATAAAATTTGGAGGAC
195 GCAAATAAAATTTGGAGGAC
1921779 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
1921844 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATAC-AAAAA-TACTAAAGTATAC
66 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAAGTATAC
*
1921907 CCATTTAAAAATTTATGGGCCAATTAAAAAATAGAATTAAGGAAAAAGTATGGATCAATTTCAGA
131 CCATTTAAAAAGTTATGGGCCAATT-AAAAATAGAATTAA-GAAAAAGTATGGATCAATTTCAGA
1921972 TGCAAATAAAATTTGGAGGAC
194 TGCAAATAAAATTTGGAGGAC
*
1921993 TAAATTGAGCAAATATGAAATT--AAATAAAAAATTTAAATAAATTAAACAACACA-A---A--A
1 TAAATTGAACAAATATGAAATTACAAAT-AAAAATTTAAATAAATTAAACAACACACATTGATGA
* * *
1922050 GGGATGAAATCAAAATAATTTTAAATTGTGATGTTGAAATTAATAC-AAAAAGTACTAAA-T-TA
65 GGGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAAGTATA
* *
1922112 -CCATTTAAAAAGTTATGGGCCAATTAAAAATAGAATTAAGTAAAAAGTATGTATCAATTTCATA
130 CCCATTTAAAAAGTTATGGGCCAATTAAAAATAGAATTAAG-AAAAAGTATGGATCAATTTCAGA
1922176 TGCAAATAAAATTTGGAGGAC
194 TGCAAATAAAATTTGGAGGAC
* *
1922197 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATTAATTAAACAACACACGTTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
* * *
1922262 GGATCAAATCGAAATAAATTTAAATTGTGATGTTGAAATTAATACAAAAAAGTACTAAATTATA-
66 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAAGTATAC
* * * * *
1922326 CCATTTAAAAAGTTATGAGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCACA
131 CCATTTAAAAAGTTATGGGCCAA-TTAAAAATAGAATTAAG-AAAAAGTATGGATCAATTTCAGA
*
1922391 TGCAAATAAAATTTAGAGGAC
194 TGCAAATAAAATTTGGAGGAC
*
1922412 TAAATTGAACAAATA--AAATTACAAAATAAAAATTTAAATAAACTAAACAACACA-A---A--A
1 TAAATTGAACAAATATGAAATTAC-AAATAAAAATTTAAATAAATTAAACAACACACATTGATGA
* * * *
1922469 GGGATCAAATCTAAATAATTTTAAATTTTGAGGTTGAAATTAATACAAAAATGTACTAAATTATA
65 GGGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAAGTATA
* *
1922534 CTCATTTAAAAAGTTATGGGCCAATT---AATA-AA-T-AG----A--A---AT-AA-GT-A-AT
130 CCCATTTAAAAAGTTATGGGCCAATTAAAAATAGAATTAAGAAAAAGTATGGATCAATTTCAGAT
*
1922580 GCAAATAAAATGTGGAGGAC
195 GCAAATAAAATTTGGAGGAC
*
1922600 TAAATTGAACAAATATGAAATTACAAGTAAAAATTTAAATAAATTAAACAACACA
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACA
1922655 AAAGGGATCA
Statistics
Matches: 817, Mismatches: 38, Indels: 67
0.89 0.04 0.07
Matches are distributed among these distances:
188 35 0.04
189 30 0.04
190 8 0.01
191 2 0.00
192 1 0.00
195 1 0.00
197 1 0.00
202 2 0.00
203 2 0.00
204 79 0.10
205 54 0.07
206 6 0.01
207 50 0.06
208 70 0.09
209 23 0.03
210 1 0.00
211 44 0.05
212 71 0.09
213 40 0.05
214 226 0.28
215 71 0.09
ACGTcount: A:0.51, C:0.08, G:0.12, T:0.28
Consensus pattern (214 bp):
TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAAGTATAC
CCATTTAAAAAGTTATGGGCCAATTAAAAATAGAATTAAGAAAAAGTATGGATCAATTTCAGATG
CAAATAAAATTTGGAGGAC
Found at i:1922774 original size:19 final size:19
Alignment explanation
Indices: 1922750--1922936 Score: 82
Period size: 19 Copynumber: 9.6 Consensus size: 19
1922740 TATATATATA
*
1922750 ATATAAACTATATAGTTTT
1 ATATAAACTATATAGTTAT
*
1922769 ATATAAAGTATAT-GTATAT
1 ATATAAACTATATAGT-TAT
*
1922788 ATATAAACTATGTAGTTAT
1 ATATAAACTATATAGTTAT
* *
1922807 ATATATA-T-TAT-GTATAA
1 ATATAAACTATATAGT-TAT
* * * *
1922824 ACTATATACCATGTA--TAA
1 A-TATAAACTATATAGTTAT
1922842 ACTATAATACTATATAGTTTAT
1 A-TATAA-ACTATATAG-TTAT
* **
1922864 ATATGAACTAT-TGAACTAT
1 ATATAAACTATAT-AGTTAT
* * *
1922883 ATAGAACCTACATAGTTTAT
1 ATATAAACTATATAG-TTAT
*
1922903 ATATAAATTATATATGAATTAT
1 ATATAAACTATATA-G--TTAT
1922925 ATATAAACTATA
1 ATATAAACTATA
1922937 CAATTTATAT
Statistics
Matches: 124, Mismatches: 28, Indels: 29
0.69 0.15 0.16
Matches are distributed among these distances:
16 2 0.02
17 5 0.04
18 18 0.15
19 52 0.42
20 24 0.19
21 5 0.04
22 18 0.15
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (19 bp):
ATATAAACTATATAGTTAT
Found at i:1922780 original size:17 final size:19
Alignment explanation
Indices: 1922738--1922813 Score: 64
Period size: 19 Copynumber: 3.8 Consensus size: 19
1922728 AAACAACTAA
* *
1922738 TATATATATATAATATAAAC
1 TATATGTATAT-ATATAAAG
*
1922758 TATATAGT-TTTATATAAAG
1 TATAT-GTATATATATAAAG
*
1922777 TATATGTATATATATAAAC
1 TATATGTATATATATAAAG
*
1922796 TATGTAGTTATATATATA
1 TATAT-G-TATATATATA
1922814 TTATGTATAA
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
18 2 0.04
19 25 0.54
20 8 0.17
21 11 0.24
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.45
Consensus pattern (19 bp):
TATATGTATATATATAAAG
Found at i:1922798 original size:38 final size:39
Alignment explanation
Indices: 1922738--1922811 Score: 114
Period size: 38 Copynumber: 1.9 Consensus size: 39
1922728 AAACAACTAA
*
1922738 TATATATATATAATATAAACTATATAGTTTTATATAAAG
1 TATATATATATAATATAAACTATATAGTTATATATAAAG
* *
1922777 TATATGTATAT-ATATAAACTATGTAGTTATATATA
1 TATATATATATAATATAAACTATATAGTTATATATA
1922812 TATTATGTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 22 0.69
39 10 0.31
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.45
Consensus pattern (39 bp):
TATATATATATAATATAAACTATATAGTTATATATAAAG
Found at i:1922913 original size:11 final size:11
Alignment explanation
Indices: 1922899--1922936 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
1922889 CCTACATAGT
1922899 TTATATATAAA
1 TTATATATAAA
*
1922910 TTATATATGAA
1 TTATATATAAA
1922921 TTATATATAAA
1 TTATATATAAA
*
1922932 CTATA
1 TTATA
1922937 CAATTTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (11 bp):
TTATATATAAA
Found at i:1922962 original size:17 final size:17
Alignment explanation
Indices: 1922942--1922995 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
1922932 CTATACAATT
* *
1922942 TATATTTATATATTATG
1 TATATTTATAAATTATA
* *
1922959 TATAATTATAAATAATA
1 TATATTTATAAATTATA
1922976 TATATTGTATAAATTATA
1 TATATT-TATAAATTATA
1922994 TA
1 TA
1922996 GTTTATTAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 18 0.60
18 12 0.40
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (17 bp):
TATATTTATAAATTATA
Found at i:1923015 original size:22 final size:24
Alignment explanation
Indices: 1922974--1923032 Score: 77
Period size: 22 Copynumber: 2.5 Consensus size: 24
1922964 TTATAAATAA
* *
1922974 TATATATTGTATAAATTATATAGTT
1 TATATA-TATATAAACTATATAGTT
1922999 TAT-TA-ATATAAACTATATAGTT
1 TATATATATATAAACTATATAGTT
1923021 TATATATATATA
1 TATATATATATA
1923033 GTATATATGG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
22 18 0.60
23 2 0.07
24 7 0.23
25 3 0.10
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (24 bp):
TATATATATATAAACTATATAGTT
Found at i:1923142 original size:29 final size:28
Alignment explanation
Indices: 1923080--1923136 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
1923070 GTTTATGGTG
1923080 TATATTTATATTTATATTTATATAAACTA
1 TATATTTATATTTATATTTATAT-AACTA
*
1923109 CATA-TTATAATTTATATTTATAT-ACTA
1 TATATTTAT-ATTTATATTTATATAACTA
1923136 T
1 T
1923137 TTATATAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
27 4 0.16
28 4 0.16
29 17 0.68
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.54
Consensus pattern (28 bp):
TATATTTATATTTATATTTATATAACTA
Found at i:1923157 original size:40 final size:39
Alignment explanation
Indices: 1923080--1923174 Score: 113
Period size: 40 Copynumber: 2.4 Consensus size: 39
1923070 GTTTATGGTG
1923080 TATATTTATATTTATATTTATATAAACTACATATTATAATT-
1 TATATTTATA--TATATTTATATAAACTACATATTAT-ATTA
*
1923121 TATATTTATATACTATTTATATAAACTATAGT-TTATATTA
1 TATATTTATATA-TATTTATATAAACTACA-TATTATATTA
*
1923161 TATATATATATATA
1 TATATTTATATATA
1923175 CATATACATA
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
39 7 0.14
40 31 0.63
41 11 0.22
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.53
Consensus pattern (39 bp):
TATATTTATATATATTTATATAAACTACATATTATATTA
Found at i:1923193 original size:29 final size:28
Alignment explanation
Indices: 1923161--1923228 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 28
1923151 GTTTATATTA
1923161 TATATATATATATACATAT-ACATATGAAC
1 TATATATATATATA-AT-TGACATATGAAC
* * *
1923190 TATATATAAAATATAGTTGACATATGAAT
1 TATATAT-ATATATAATTGACATATGAAC
1923219 TATATATATA
1 TATATATATA
1923229 CTAAAGTTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
28 3 0.09
29 24 0.73
30 6 0.18
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.40
Consensus pattern (28 bp):
TATATATATATATAATTGACATATGAAC
Found at i:1923236 original size:29 final size:29
Alignment explanation
Indices: 1923180--1923238 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
1923170 ATATACATAT
*
1923180 ACATATGAACTATATATAAAATATAGTTG
1 ACATATGAACTATATATAAAATAAAGTTG
* * *
1923209 ACATATGAATTATATATATACTAAAGTTG
1 ACATATGAACTATATATAAAATAAAGTTG
1923238 A
1 A
1923239 TATTTATATG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.47, C:0.07, G:0.10, T:0.36
Consensus pattern (29 bp):
ACATATGAACTATATATAAAATAAAGTTG
Found at i:1923265 original size:18 final size:18
Alignment explanation
Indices: 1923244--1923311 Score: 75
Period size: 18 Copynumber: 3.7 Consensus size: 18
1923234 GTTGATATTT
1923244 ATATGAACTATAGTTTAC
1 ATATGAACTATAGTTTAC
* *
1923262 ATATAAACTATATAGTTTAT
1 ATATGAAC--TATAGTTTAC
1923282 ATACT-AACTATAGTTTAC
1 ATA-TGAACTATAGTTTAC
*
1923300 ATATGACCTATA
1 ATATGAACTATA
1923312 TATATATACT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
17 1 0.02
18 25 0.60
20 15 0.36
21 1 0.02
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.40
Consensus pattern (18 bp):
ATATGAACTATAGTTTAC
Found at i:1923266 original size:20 final size:19
Alignment explanation
Indices: 1923243--1923303 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 19
1923233 AGTTGATATT
1923243 TATATGAACTATAGTTTACA
1 TATAT-AACTATAGTTTACA
1923263 TATA-AACTATATAGTTT--A
1 TATATAAC--TATAGTTTACA
1923281 TATACTAACTATAGTTTACA
1 TATA-TAACTATAGTTTACA
1923301 TAT
1 TAT
1923304 GACCTATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
18 16 0.46
20 19 0.54
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.43
Consensus pattern (19 bp):
TATATAACTATAGTTTACA
Found at i:1923313 original size:20 final size:18
Alignment explanation
Indices: 1923252--1923366 Score: 57
Period size: 20 Copynumber: 6.2 Consensus size: 18
1923242 TTATATGAAC
1923252 TATAGTTTACATATAAACTA
1 TATAGTTTACATAT--ACTA
1923272 TATAGTTT--ATATACTAA
1 TATAGTTTACATATACT-A
1923289 CTATAGTTTACATATGACCTA
1 -TATAGTTTACATAT-A-CTA
*
1923310 TATA-TATATAC-TATAGT-
1 TATAGT-T-TACATATACTA
*
1923327 TGATA-TTT--ATATATTA
1 T-ATAGTTTACATATACTA
1923343 TATAGTTTACATATGACCTA
1 TATAGTTTACATAT-A-CTA
1923363 TATA
1 TATA
1923367 TATACTATAG
Statistics
Matches: 76, Mismatches: 3, Indels: 32
0.68 0.03 0.29
Matches are distributed among these distances:
15 8 0.11
16 8 0.11
17 3 0.04
18 21 0.28
19 3 0.04
20 26 0.34
21 5 0.07
22 2 0.03
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (18 bp):
TATAGTTTACATATACTA
Found at i:1923323 original size:31 final size:30
Alignment explanation
Indices: 1923278--1923380 Score: 109
Period size: 29 Copynumber: 3.7 Consensus size: 30
1923268 ACTATATAGT
1923278 TTATATACTA-ACTATAGTTTACATATGACC
1 TTATATA-TATACTATAGTTTACATATGACC
*
1923308 TATATATATATACTATAG-TT-GATAT----
1 T-TATATATATACTATAGTTTACATATGACC
1923333 TTATATAT-TA-TATAGTTTACATATGACC
1 TTATATATATACTATAGTTTACATATGACC
1923361 -TATATATATACTATAGTTTA
1 TTATATATATACTATAGTTTA
1923381 TTTATATACT
Statistics
Matches: 61, Mismatches: 2, Indels: 21
0.73 0.02 0.25
Matches are distributed among these distances:
22 5 0.08
23 4 0.07
24 11 0.18
25 1 0.02
27 7 0.11
28 2 0.03
29 13 0.21
30 5 0.08
31 13 0.21
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.46
Consensus pattern (30 bp):
TTATATATATACTATAGTTTACATATGACC
Found at i:1923323 original size:51 final size:49
Alignment explanation
Indices: 1923262--1923396 Score: 139
Period size: 53 Copynumber: 2.6 Consensus size: 49
1923252 TATAGTTTAC
*
1923262 ATATAAACTATATAGTTTATATACTAACTATAGTTTACATATGACCTATAT
1 ATATATACTATATA-TTTATATACTAA-TATAGTTTACATATGACCTATAT
*
1923313 ATATATACTATAGTTGATATTTATATA-TTATATAGTTTACATATGACCTATAT
1 ATATATAC--TA--T-ATATTTATATACTAATATAGTTTACATATGACCTATAT
*
1923366 ATATACTA-TAGTTTATTTATATACTATATAT
1 ATATA-TACTA-TATATTTATATACTA-ATAT
1923397 TATATATAAA
Statistics
Matches: 71, Mismatches: 5, Indels: 16
0.77 0.05 0.17
Matches are distributed among these distances:
49 10 0.14
50 2 0.03
51 13 0.18
53 30 0.42
54 4 0.06
55 9 0.13
56 3 0.04
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.46
Consensus pattern (49 bp):
ATATATACTATATATTTATATACTAATATAGTTTACATATGACCTATAT
Found at i:1923347 original size:91 final size:87
Alignment explanation
Indices: 1923128--1923375 Score: 251
Period size: 91 Copynumber: 2.9 Consensus size: 87
1923118 ATTTATATTT
* * * * *
1923128 ATAT-ACTATTTATATAAACTATAGTTTATA-TTATATATATATA-TATACATATACA-TATGA-
1 ATATGACTATATATATATACTATAGTTGATATTTATATATATATAGTTTACATATAAACTAT-AT
1923188 ACTATATATAAAATATAGTTGAC
65 ACTATATATAAAATATAGTTGAC
* *
1923211 ATATGAAT-TATATATATACTAAAGTTGATATTTATATGA-ACTATAGTTTACATATAAACTATA
1 ATATGACTATATATATATACTATAGTTGATATTTATAT-ATA-TATAGTTTACATATAAACTATA
* * * *
1923274 TAGTTTATATACTAACTATAGTTTAC
64 TACTATATATA--AAATATAGTTGAC
* *
1923300 ATATGACCTATATATATATACTATAGTTGATATTTATATATTATATAGTTTACATATGACCTATA
1 ATATGA-CTATATATATATACTATAGTTGATATTTATATA-TATATAGTTTACATATAAACTATA
1923365 TA-TATACTATA
64 TACTATA-TATA
1923376 GTTTATTTAT
Statistics
Matches: 135, Mismatches: 16, Indels: 20
0.79 0.09 0.12
Matches are distributed among these distances:
83 22 0.16
84 9 0.07
85 5 0.04
86 11 0.08
87 11 0.08
89 17 0.13
90 5 0.04
91 54 0.40
92 1 0.01
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.43
Consensus pattern (87 bp):
ATATGACTATATATATATACTATAGTTGATATTTATATATATATAGTTTACATATAAACTATATA
CTATATATAAAATATAGTTGAC
Found at i:1923349 original size:53 final size:49
Alignment explanation
Indices: 1923277--1923395 Score: 175
Period size: 51 Copynumber: 2.3 Consensus size: 49
1923267 AACTATATAG
1923277 TTTATATACTAACTATAGTTTACATATGACCTATATATATATACTATAGTTGATA
1 TTTATATACT-A-TATAGTTTACATATGACC--TATATATATACTATAGTT--TA
*
1923332 TTTATATATTATATAGTTTACATATGACCTATATATATACTATAGTTTA
1 TTTATATACTATATAGTTTACATATGACCTATATATATACTATAGTTTA
1923381 TTTATATACTATATA
1 TTTATATACTATATA
1923396 TTATATATAA
Statistics
Matches: 62, Mismatches: 2, Indels: 6
0.89 0.03 0.09
Matches are distributed among these distances:
49 16 0.26
51 18 0.29
53 18 0.29
54 1 0.02
55 9 0.15
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (49 bp):
TTTATATACTATATAGTTTACATATGACCTATATATATACTATAGTTTA
Found at i:1923388 original size:18 final size:18
Alignment explanation
Indices: 1923334--1923423 Score: 76
Period size: 18 Copynumber: 4.8 Consensus size: 18
1923324 AGTTGATATT
*
1923334 TATATATTATATAGTTTAC
1 TATATATTATATA-TATAC
*
1923353 -ATATGACCTATATATATAC
1 TATAT-A-TTATATATATAC
*
1923372 TATAGT-TTATTTATATAC
1 TATA-TATTATATATATAC
*
1923390 TATATATTATATATAAAC
1 TATATATTATATATATAC
*
1923408 TATATACTATAGTATA
1 TATATATTATA-TATA
1923424 ATTTACATAT
Statistics
Matches: 58, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
17 1 0.02
18 38 0.66
19 9 0.16
20 9 0.16
21 1 0.02
ACGTcount: A:0.41, C:0.08, G:0.04, T:0.47
Consensus pattern (18 bp):
TATATATTATATATATAC
Found at i:1924104 original size:64 final size:65
Alignment explanation
Indices: 1923988--1924130 Score: 175
Period size: 64 Copynumber: 2.2 Consensus size: 65
1923978 TTTCATAGTG
* * *
1923988 ATGCACCGATGCACCAATCCAGGCATCGATGCACCATGGAATAAATTGAACATCGAATGCATTTC
1 ATGCATCGATGCACCAAGCCAGGCATCGATGCACCATGGAATAAATTGAACATCGAATGCACTTC
* * **
1924053 ATGCATCGATGCACC-AGCCATGCATCGATGCACTC-TGG-CTATTTTGAAACATCGAATGCACT
1 ATGCATCGATGCACCAAGCCAGGCATCGATGCAC-CATGGAATAAATTG-AACATCGAATGCACT
*
1924115 TG
64 TC
1924117 ATGCATCGATGCAC
1 ATGCATCGATGCAC
1924131 TCTTAGTGCA
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
63 5 0.07
64 48 0.71
65 15 0.22
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.24
Consensus pattern (65 bp):
ATGCATCGATGCACCAAGCCAGGCATCGATGCACCATGGAATAAATTGAACATCGAATGCACTTC
Found at i:1924130 original size:17 final size:19
Alignment explanation
Indices: 1924102--1924150 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1924092 TATTTTGAAA
1924102 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
1924120 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
1924139 CACCGATGCACT
1 CATCGATGCACT
1924151 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:1926144 original size:20 final size:21
Alignment explanation
Indices: 1926119--1926174 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
1926109 GACCAACAAT
1926119 GATTTGAAAGTAAAA-TCA-AA
1 GATTTGAAAGTAAAACT-AGAA
*
1926139 GATTTGCAAA-TCAAACTAGAA
1 GATTTG-AAAGTAAAACTAGAA
*
1926160 GATTTGAAAGGAAAA
1 GATTTGAAAGTAAAA
1926175 ATTCAGATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.52, C:0.07, G:0.18, T:0.23
Consensus pattern (21 bp):
GATTTGAAAGTAAAACTAGAA
Found at i:1931934 original size:14 final size:15
Alignment explanation
Indices: 1931909--1931937 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1931899 TTATTTTTGA
1931909 TGTTTCTGGATTGTT
1 TGTTTCTGGATTGTT
1931924 TGTTT-TGGATTGTT
1 TGTTTCTGGATTGTT
1931938 AAATGCTTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.07, C:0.03, G:0.28, T:0.62
Consensus pattern (15 bp):
TGTTTCTGGATTGTT
Found at i:1934155 original size:12 final size:12
Alignment explanation
Indices: 1934138--1934166 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
1934128 TTGTTGTGCT
1934138 TGCTCCTCGGGC
1 TGCTCCTCGGGC
1934150 TGCTCCTCGGGC
1 TGCTCCTCGGGC
1934162 TGCTC
1 TGCTC
1934167 AGGCTCATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.41, G:0.31, T:0.28
Consensus pattern (12 bp):
TGCTCCTCGGGC
Found at i:1935410 original size:24 final size:23
Alignment explanation
Indices: 1935377--1935423 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
1935367 AAACACAATA
1935377 ATTTGAAAA-TCAACATTTTTTTT
1 ATTTGAAAATTCAA-ATTTTTTTT
*
1935400 ATTTCGAAAATTTAAATTTTTTTT
1 ATTT-GAAAATTCAAATTTTTTTT
1935424 GGAAAATTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 14 0.67
25 3 0.14
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.55
Consensus pattern (23 bp):
ATTTGAAAATTCAAATTTTTTTT
Found at i:1935821 original size:21 final size:21
Alignment explanation
Indices: 1935795--1935834 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1935785 CAGAACCCCA
*
1935795 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
1935816 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
1935835 TCAAAGGGGG
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:1944008 original size:51 final size:49
Alignment explanation
Indices: 1943953--1944083 Score: 142
Period size: 51 Copynumber: 2.6 Consensus size: 49
1943943 TAATATAAAA
1943953 ATAAATTTCAAAAAAGTAATTATATTAATTTGAA-TATCATAATAATTTATG
1 ATAAATTTCAAAAAAGTAATTATATTAATTT-AATTATCAT-A-AATTTATG
* * * *
1944004 ATAAAATTTC-AAATAGTAATCATATTAATTTAATTATCATAAGTTTATT
1 AT-AAATTTCAAAAAAGTAATTATATTAATTTAATTATCATAAATTTATG
*
1944053 ATAAATTT-AAAATAACATAATTATATTAATT
1 ATAAATTTCAAAA-AA-GTAATTATATTAATT
1944084 GTAACTTTAC
Statistics
Matches: 68, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
48 9 0.13
49 9 0.13
50 16 0.24
51 27 0.40
52 7 0.10
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.43
Consensus pattern (49 bp):
ATAAATTTCAAAAAAGTAATTATATTAATTTAATTATCATAAATTTATG
Found at i:1944179 original size:16 final size:16
Alignment explanation
Indices: 1944160--1944198 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1944150 TGAGTAAATT
*
1944160 ACAGGTCAGGTTCATA
1 ACAGGTCAGGTTCAAA
*
1944176 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTCAAA
1944192 ACAGGTC
1 ACAGGTC
1944199 GGGTAATACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.21
Consensus pattern (16 bp):
ACAGGTCAGGTTCAAA
Found at i:1948452 original size:37 final size:36
Alignment explanation
Indices: 1948371--1948498 Score: 177
Period size: 37 Copynumber: 3.4 Consensus size: 36
1948361 ATGAAAGACA
1948371 CATTGCACTCCATGCGTCTCTCCCTTTCCCTCGAAGAAG
1 CATTGCACTCCATGCGTCTC-CCCTTTCCCT-GAAG-AG
* *
1948410 TATTGCACTCCATGCGTCTCCACTTTCCCCTGAAGAG
1 CATTGCACTCCATGCGTCTCCCCTTT-CCCTGAAGAG
1948447 CATTGCACTCCATGCGTCTCCCCCTTTCCCT-AAGACG
1 CATTGCACTCCATGCGTCT-CCCCTTTCCCTGAAGA-G
1948484 CATTGCACTCCATGC
1 CATTGCACTCCATGC
1948499 ATCGCTCCCC
Statistics
Matches: 82, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
36 4 0.05
37 40 0.49
38 15 0.18
39 23 0.28
ACGTcount: A:0.18, C:0.39, G:0.15, T:0.28
Consensus pattern (36 bp):
CATTGCACTCCATGCGTCTCCCCTTTCCCTGAAGAG
Found at i:1948701 original size:3 final size:3
Alignment explanation
Indices: 1948693--1948799 Score: 62
Period size: 3 Copynumber: 35.3 Consensus size: 3
1948683 GAAAGAAAGA
* *
1948693 AAG AAG AAGG AAG CAATG AAG AAG -AG AA- AAG AGG AAG AAT AAG AA-
1 AAG AAG AA-G AAG -AA-G AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
* * *
1948738 AA- AAG AGG AAG AGAG AAG AAG AAG AGG AAAG AAG AAG AA- AAA AAG
1 AAG AAG AAG AAG A-AG AAG AAG AAG AAG -AAG AAG AAG AAG AAG AAG
* *
1948783 AGG GAG AAAG AAG AAG A
1 AAG AAG -AAG AAG AAG A
1948800 GGAAAATAAG
Statistics
Matches: 81, Mismatches: 13, Indels: 20
0.71 0.11 0.18
Matches are distributed among these distances:
2 10 0.12
3 56 0.69
4 14 0.17
5 1 0.01
ACGTcount: A:0.64, C:0.01, G:0.34, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:1948714 original size:26 final size:25
Alignment explanation
Indices: 1948685--1948774 Score: 77
Period size: 23 Copynumber: 3.7 Consensus size: 25
1948675 TGAATGAAGA
1948685 AAGAAAGAAAGAAGAAGGAAGCAATG
1 AAGAAAGAAAGAAGAAGGAAG-AATG
1948711 AAG-AAGAGAA-AAG-AGGAAGAAT-
1 AAGAAAGA-AAGAAGAAGGAAGAATG
*
1948733 AAGAAA-AAAGAGGAA-GAGAGAA-G
1 AAGAAAGAAAGAAGAAGGA-AGAATG
1948756 AAGAAGAGGAAAGAAGAAG
1 AAGAA-A-GAAAGAAGAAG
1948775 AAAAAAAGAG
Statistics
Matches: 52, Mismatches: 2, Indels: 19
0.71 0.03 0.26
Matches are distributed among these distances:
21 2 0.04
22 8 0.15
23 15 0.29
24 7 0.13
25 7 0.13
26 13 0.25
ACGTcount: A:0.63, C:0.01, G:0.33, T:0.02
Consensus pattern (25 bp):
AAGAAAGAAAGAAGAAGGAAGAATG
Found at i:1948741 original size:19 final size:19
Alignment explanation
Indices: 1948710--1948797 Score: 97
Period size: 19 Copynumber: 4.5 Consensus size: 19
1948700 AGGAAGCAAT
*
1948710 GAAGAAGAGAAAAGAGGAA
1 GAAGAAGAAAAAAGAGGAA
*
1948729 GAATAAGAAAAAAGAGGAA
1 GAAGAAGAAAAAAGAGGAA
*
1948748 GAGAGAAG-AAGAAGAGGAAA
1 GA-AGAAGAAAAAAGAGG-AA
*
1948768 GAAGAAGAAAAAAAGAGGGA
1 GAAGAAG-AAAAAAGAGGAA
1948788 GAAAGAAGAA
1 G-AAGAAGAA
1948798 GAGGAAAATA
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
19 32 0.55
20 12 0.21
21 14 0.24
ACGTcount: A:0.65, C:0.00, G:0.34, T:0.01
Consensus pattern (19 bp):
GAAGAAGAAAAAAGAGGAA
Found at i:1948743 original size:13 final size:13
Alignment explanation
Indices: 1948727--1948811 Score: 62
Period size: 13 Copynumber: 6.4 Consensus size: 13
1948717 AGAAAAGAGG
*
1948727 AAGAATAAGAAAA
1 AAGAAGAAGAAAA
* * *
1948740 AAGAGGAAGAGAG
1 AAGAAGAAGAAAA
**
1948753 AAGAAGAAGAGGA
1 AAGAAGAAGAAAA
1948766 AAGAAGAAGAAAAA
1 AAGAAGAAG-AAAA
* * *
1948780 AAGAGGGAGAAAG
1 AAGAAGAAGAAAA
*
1948793 AAGAAGAGGAAAA
1 AAGAAGAAGAAAA
1948806 TAAGAA
1 -AAGAA
1948812 AGTTAGAGTC
Statistics
Matches: 54, Mismatches: 16, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
13 40 0.74
14 14 0.26
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (13 bp):
AAGAAGAAGAAAA
Found at i:1952536 original size:20 final size:20
Alignment explanation
Indices: 1952493--1952552 Score: 84
Period size: 20 Copynumber: 2.9 Consensus size: 20
1952483 GATTCTCTGT
1952493 GGGGGAATCGGTTCCCCTTCAA
1 GGGGGAATCGGTT-CCC-TCAA
1952515 GGGGGAATCGGTTCCCTCAA
1 GGGGGAATCGGTTCCCTCAA
* *
1952535 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
1952553 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 20 0.56
21 3 0.08
22 13 0.36
ACGTcount: A:0.17, C:0.27, G:0.35, T:0.22
Consensus pattern (20 bp):
GGGGGAATCGGTTCCCTCAA
Found at i:1956595 original size:19 final size:20
Alignment explanation
Indices: 1956563--1956610 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
1956553 TTTCAACATT
* *
1956563 TCATTTTTA-TTTTCCAAG-
1 TCATTTTTAGCTTTCAAAGA
*
1956581 TCCTTTTTAGCTTTCAAAGA
1 TCATTTTTAGCTTTCAAAGA
1956601 TCATTTTTAG
1 TCATTTTTAG
1956611 TAATAAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 8 0.33
19 7 0.29
20 9 0.38
ACGTcount: A:0.23, C:0.17, G:0.08, T:0.52
Consensus pattern (20 bp):
TCATTTTTAGCTTTCAAAGA
Found at i:1958969 original size:56 final size:56
Alignment explanation
Indices: 1958883--1958994 Score: 190
Period size: 56 Copynumber: 2.0 Consensus size: 56
1958873 CGTATGGTCC
*
1958883 AAGTAGATGGTACGTGGTTGTATGGTCAATATAAACATA-TATTGTTGATGGCATTT
1 AAGTAGATGGTACATGGTTGTATGGTCAATATAAACA-AGTATTGTTGATGGCATTT
*
1958939 AAGTAGATGGTACATGGTTGTATGGTCAATATAAACAAGTATTGTTGATGGTATTT
1 AAGTAGATGGTACATGGTTGTATGGTCAATATAAACAAGTATTGTTGATGGCATTT
1958995 GCACAAGATG
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
55 1 0.02
56 52 0.98
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.38
Consensus pattern (56 bp):
AAGTAGATGGTACATGGTTGTATGGTCAATATAAACAAGTATTGTTGATGGCATTT
Found at i:1959865 original size:21 final size:21
Alignment explanation
Indices: 1959826--1959865 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1959816 TTAAAAACCC
*
1959826 AACCCGATCGGGTCGGGTCAG
1 AACCCGATCGGGTCAGGTCAG
1959847 AACCCG-TCGGGTTCAGGTC
1 AACCCGATCGGG-TCAGGTC
1959866 CCATGCCCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.17, C:0.30, G:0.35, T:0.17
Consensus pattern (21 bp):
AACCCGATCGGGTCAGGTCAG
Found at i:1961559 original size:43 final size:41
Alignment explanation
Indices: 1961275--1961660 Score: 370
Period size: 40 Copynumber: 9.4 Consensus size: 41
1961265 AACCTAACTT
* * * *
1961275 TGGCGTTTGTATACAAACGCCGCAAAAGA-TCTTACTTTAG
1 TGGCGTTTTTATACAAACGCCGCTATAGACTCGTACTTTAG
* * * * * * *
1961315 TGGCATTTGTATAC-AACGCTGCTAAAGATTAGTATTTTAG
1 TGGCGTTTTTATACAAACGCCGCTATAGACTCGTACTTTAG
* * * *
1961355 TGGCG-TTTTACACAAACGCCGGTATAGAATCGTTCTTTAG
1 TGGCGTTTTTATACAAACGCCGCTATAGACTCGTACTTTAG
* *
1961395 TGGCGTTTTTATACAAACGCCGCTAAAGACTCATACTTTAG
1 TGGCGTTTTTATACAAACGCCGCTATAGACTCGTACTTTAG
* *
1961436 TGGCGTTTTTATA-AAAGCGCTGCTATA-ACTCATACTTTAG
1 TGGCGTTTTTATACAAA-CGCCGCTATAGACTCGTACTTTAG
* * * * *
1961476 TGGCATTTTTATAAAAACACTGCTATA-ACTCATACTTTAG
1 TGGCGTTTTTATACAAACGCCGCTATAGACTCGTACTTTAG
* *
1961516 TGGCGTTTTTGTTTACAAACGCCGCTATAGACTTGTACTTTAG
1 TGGCG-TTTT-TATACAAACGCCGCTATAGACTCGTACTTTAG
* * *
1961559 TGGCGTTTTTGTTTACAAACGTCGCTATAGACTTGTACTTTAG
1 TGGCG-TTTT-TATACAAACGCCGCTATAGACTCGTACTTTAG
* * * *
1961602 TGGCGTTTTTATAAAAATGCCGCAAAAGACTCGTACTTTAG
1 TGGCGTTTTTATACAAACGCCGCTATAGACTCGTACTTTAG
*
1961643 TGGCGTTTGTATCACAAA
1 TGGCGTTTTTAT-ACAAA
1961661 TTTATAGTTT
Statistics
Matches: 294, Mismatches: 43, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
39 18 0.06
40 103 0.35
41 93 0.32
42 22 0.07
43 58 0.20
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (41 bp):
TGGCGTTTTTATACAAACGCCGCTATAGACTCGTACTTTAG
Found at i:1964298 original size:43 final size:42
Alignment explanation
Indices: 1964250--1964560 Score: 297
Period size: 43 Copynumber: 7.2 Consensus size: 42
1964240 ATGGTAATTA
*
1964250 GCGGCGTTTGTATCAAAAAACGCCGCTATATATCCGACCTTTT
1 GCGGCGTTTGT-TCAAAAAACGCCGCTATATATCTGACCTTTT
* * *
1964293 ACGGCGTTTGTGTCCAAAAACGCCGCTATAGATCTGACCTTTT
1 GCGGCGTTTGT-TCAAAAAACGCCGCTATATATCTGACCTTTT
*
1964336 GCGGCGTTTGTATCAAAAAACGCCACTATATATCTGACCTTTT
1 GCGGCGTTTGT-TCAAAAAACGCCGCTATATATCTGACCTTTT
** *
1964379 GCGGCGTTTGTGTGC-AAAAACGCCGCTATAGGTCTGACATTTT
1 GCGGCGTTTGT-T-CAAAAAACGCCGCTATATATCTGACCTTTT
* * * * * *
1964422 GCAGCGTTTTTTTCTAGAAACGCCGCTATATATCATAACTTTTT
1 GCGGCG-TTTGTTCAAAAAACGCCGCTATATATC-TGACCTTTT
* * * *
1964466 GCGGCGTTTATTCCAAAAATGCCGCTATAGATATC-AACCTTTT
1 GCGGCGTTTGTTCAAAAAACGCCGCTAT--ATATCTGACCTTTT
* * *
1964509 GCGGCGTTTGTTTAAAAAATGCCG-TAATAGATAT-TGACCTATT
1 GCGGCGTTTGTTCAAAAAACGCCGCT-AT--ATATCTGACCTTTT
1964552 GCGGCGTTT
1 GCGGCGTTT
1964561 TTTGTTCTCA
Statistics
Matches: 227, Mismatches: 33, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
42 2 0.01
43 203 0.89
44 17 0.07
45 5 0.02
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (42 bp):
GCGGCGTTTGTTCAAAAAACGCCGCTATATATCTGACCTTTT
Found at i:1964397 original size:86 final size:86
Alignment explanation
Indices: 1964250--1964560 Score: 358
Period size: 86 Copynumber: 3.6 Consensus size: 86
1964240 ATGGTAATTA
* * *
1964250 GCGGCGTTTGTATCAAAAAACGCCGCTATATATCCGACCTTTTACGGCGTTTGTGTCCAAAAACG
1 GCGGCGTTTGTATCAAAAAACGCCACTATATATCTGACCTTTTGCGGCGTTTGTGTCCAAAAACG
1964315 CCGCTATAGATCTGACCTTTT
66 CCGCTATAGATCTGACCTTTT
*
1964336 GCGGCGTTTGTATCAAAAAACGCCACTATATATCTGACCTTTTGCGGCGTTTGTGTGCAAAAACG
1 GCGGCGTTTGTATCAAAAAACGCCACTATATATCTGACCTTTTGCGGCGTTTGTGTCCAAAAACG
* *
1964401 CCGCTATAGGTCTGACATTTT
66 CCGCTATAGATCTGACCTTTT
* * * * * * * * * *
1964422 GCAGCGTTTTTTTCTAGAAACGCCGCTATATATCATAACTTTTTGCGGCGTTTAT-TCCAAAAAT
1 GCGGCGTTTGTATCAAAAAACGCCACTATATATC-TGACCTTTTGCGGCGTTTGTGTCCAAAAAC
* *
1964486 GCCGCTATAGATATCAACCTTTT
65 GCCGCTATAGATCT-GACCTTTT
* * * * *
1964509 GCGGCGTTTGT-TTAAAAAATGCCGTAATAGATAT-TGACCTATTGCGGCGTTT
1 GCGGCGTTTGTATCAAAAAACGCC--ACTATATATCTGACCTTTTGCGGCGTTT
1964561 TTTGTTCTCA
Statistics
Matches: 188, Mismatches: 33, Indels: 8
0.82 0.14 0.03
Matches are distributed among these distances:
86 150 0.80
87 32 0.17
88 6 0.03
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (86 bp):
GCGGCGTTTGTATCAAAAAACGCCACTATATATCTGACCTTTTGCGGCGTTTGTGTCCAAAAACG
CCGCTATAGATCTGACCTTTT
Found at i:1967116 original size:29 final size:29
Alignment explanation
Indices: 1967072--1967164 Score: 87
Period size: 29 Copynumber: 3.0 Consensus size: 29
1967062 TTACTTTATA
* *
1967072 TTTTTTTTTTTTTTCCTTTCTTCTTCTTC
1 TTTTTTTTCTTCTTCCTTTCTTCTTCTTC
* *
1967101 TTTTTTTTCTTCTTCCTTTGTTCATTTTTC
1 TTTTTTTTCTTCTTCCTTTCTTC-TTCTTC
**
1967131 TTTTCTTCTTCTTCCCCCTTTCTTTCTTCATTC
1 TTTT-TT-TTCTTCTTCCTTTC-TTCTTC-TTC
1967164 T
1 T
1967165 CATATTTTTC
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
29 20 0.39
30 9 0.18
31 2 0.04
32 13 0.25
33 7 0.14
ACGTcount: A:0.02, C:0.26, G:0.01, T:0.71
Consensus pattern (29 bp):
TTTTTTTTCTTCTTCCTTTCTTCTTCTTC
Found at i:1974926 original size:154 final size:153
Alignment explanation
Indices: 1974674--1974980 Score: 589
Period size: 154 Copynumber: 2.0 Consensus size: 153
1974664 TCCGTCTTCC
1974674 GATTATTGAGAAAGCAAACCCGGAGAATGGGATGATAGTTGCCAAGAATGTTTTGATAAAATTAA
1 GATTATTGAGAAAGCAAACCCGGAGAATGGGATGATAGTTGCCAAGAATGTTTTGATAAAATTAA
1974739 GAATTACTTGACTAACGCTCCAGTCCTAATGCCACCAACCCCACCAAATAAACCATTGATCTT-A
66 GAATTACTTGACTAACGCTCCAGTCCTAATGCCACCAACCCCACCAAATAAACCATTGATCTTAA
1974803 ACTTGACTGTATTTGAGAAGTCA
131 ACTTGACTGTATTTGAGAAGTCA
1974826 GATTATTGAGAAAGCAAAACCCAGGAGAATGGGATGATAGTTGCCAAGAATGTTTTGATAAAATT
1 GATTATTGAGAAAGC-AAACCC-GGAGAATGGGATGATAGTTGCCAAGAATGTTTTGATAAAATT
1974891 AAGAATTACTTGACTAACGCTCCAGTCCTAATGCCACCAACCCCACCAAATAAACCATTGATCTT
64 AAGAATTACTTGACTAACGCTCCAGTCCTAATGCCACCAACCCCACCAAATAAACCATTGATCTT
1974956 AAACTTGACTGTATTTGAGAAGTCA
129 AAACTTGACTGTATTTGAGAAGTCA
1974981 ATGGGATGTG
Statistics
Matches: 152, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
152 15 0.10
153 6 0.04
154 107 0.70
155 24 0.16
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.26
Consensus pattern (153 bp):
GATTATTGAGAAAGCAAACCCGGAGAATGGGATGATAGTTGCCAAGAATGTTTTGATAAAATTAA
GAATTACTTGACTAACGCTCCAGTCCTAATGCCACCAACCCCACCAAATAAACCATTGATCTTAA
ACTTGACTGTATTTGAGAAGTCA
Found at i:1977134 original size:3 final size:3
Alignment explanation
Indices: 1977126--1977172 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
1977116 TATTACACTT
* *
1977126 GAA GAA GAA GAA GAA GAA AAA G-A GAA GAA GAA GAA GAA GAA AAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1977173 ATGAGGGTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1977153 original size:17 final size:17
Alignment explanation
Indices: 1977131--1977165 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1977121 CACTTGAAGA
1977131 AGAAGAAGAAGAAAAAG
1 AGAAGAAGAAGAAAAAG
*
1977148 AGAAGAAGAAGAAGAAG
1 AGAAGAAGAAGAAAAAG
1977165 A
1 A
1977166 AAAAGAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (17 bp):
AGAAGAAGAAGAAAAAG
Found at i:1977156 original size:23 final size:23
Alignment explanation
Indices: 1977126--1977171 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1977116 TATTACACTT
1977126 GAAGAAGAAGAAGAAGAAAAAGA
1 GAAGAAGAAGAAGAAGAAAAAGA
1977149 GAAGAAGAAGAAGAAGAAAAAGA
1 GAAGAAGAAGAAGAAGAAAAAGA
1977172 AATGAGGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (23 bp):
GAAGAAGAAGAAGAAGAAAAAGA
Found at i:1978628 original size:126 final size:127
Alignment explanation
Indices: 1978188--1978687 Score: 745
Period size: 127 Copynumber: 4.0 Consensus size: 127
1978178 TATGAGCATT
* *
1978188 GATAACCAACTGTCCTCATCACATAGGAACTGTGTTATCACCCTTAGATGGCCAAGACTCATGAA
1 GATAACCAACCGTCCTCATCACATAGGAACCGTGTTATCACCCTTAGATGGCCAAGACTCATGAA
*
1978253 CAAATGAGCAGTGTTATCACATGACCAGATCTCCTCATTATGTAAGGAGCTGTGTCAACTCA
66 CAAATGAGCAGTGTCATCACATGACCAGATCTCCTCATTATGTAAGGAGCTGTGTCAACTCA
* ** * *
1978315 AATAACCGGCCGTCCTCATCACGTAGGAACCGTGTTATCACCCTTAGATGGCCAAGACTCGTGAA
1 GATAACCAACCGTCCTCATCACATAGGAACCGTGTTATCACCCTTAGATGGCCAAGACTCATGAA
*
1978380 CAAATGAGCAGTGTCATCACATGACCAGATCTCCTCATTATGTAAGGAGTTGTGTCAACTCA
66 CAAATGAGCAGTGTCATCACATGACCAGATCTCCTCATTATGTAAGGAGCTGTGTCAACTCA
* *
1978442 GATAACCAACAGTCCTCATCACATATGAACCGTGTTATCACCCTTAGATGGCCAAGACTCATGAA
1 GATAACCAACCGTCCTCATCACATAGGAACCGTGTTATCACCCTTAGATGGCCAAGACTCATGAA
* * * *
1978507 CATATGAGCAGTGTCATCACCTG-CCTAGATCTCTTCATTATGT-ATGAGCTGTGTCAACTCA
66 CAAATGAGCAGTGTCATCACATGACC-AGATCTCCTCATTATGTAAGGAGCTGTGTCAACTCA
* * *
1978568 GATAACCAGCCGTCCTCATCATATAGGAACTGTGTTATCACCCTTAGATGGCCAAGACTCATGAA
1 GATAACCAACCGTCCTCATCACATAGGAACCGTGTTATCACCCTTAGATGGCCAAGACTCATGAA
* * * * * * *
1978633 CAGATGAGCAGTGTCATCACTTTACCAGATCTCTTCATCACGT-ACGAGCTGTGTC
66 CAAATGAGCAGTGTCATCACATGACCAGATCTCCTCATTATGTAAGGAGCTGTGTC
1978688 GTCTCCCAAA
Statistics
Matches: 339, Mismatches: 32, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
126 124 0.37
127 215 0.63
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (127 bp):
GATAACCAACCGTCCTCATCACATAGGAACCGTGTTATCACCCTTAGATGGCCAAGACTCATGAA
CAAATGAGCAGTGTCATCACATGACCAGATCTCCTCATTATGTAAGGAGCTGTGTCAACTCA
Found at i:1978662 original size:253 final size:254
Alignment explanation
Indices: 1978188--1978670 Score: 781
Period size: 253 Copynumber: 1.9 Consensus size: 254
1978178 TATGAGCATT
* *
1978188 GATAACCAACTGTCCTCATCACATAGGAACTGTGTTATCACCCTTAGATGGCCAAGACTCATGAA
1 GATAACCAACAGTCCTCATCACATAGGAACCGTGTTATCACCCTTAGATGGCCAAGACTCATGAA
*
1978253 CAAATGAGCAGTGTTATCACATGACCAGATCTCCTCATTATGTAAGGAGCTGTGTCAACTCAAAT
66 CAAATGAGCAGTGTCATCACATGACCAGATCTCCTCATTATGTAAGGAGCTGTGTCAACTCAAAT
* * *
1978318 AACCGGCCGTCCTCATCACGTAGGAACCGTGTTATCACCCTTAGATGGCCAAGACTCGTGAACAA
131 AACCAGCCGTCCTCATCACATAGGAACCGTGTTATCACCCTTAGATGGCCAAGACTCATGAACAA
1978383 ATGAGCAGTGTCATCACATGACCAGATCTCCTCATTATGTAAGGAGTTGTGTCAACTCA
196 ATGAGCAGTGTCATCACATGACCAGATCTCCTCATTATGTAAGGAGTTGTGTCAACTCA
*
1978442 GATAACCAACAGTCCTCATCACATATGAACCGTGTTATCACCCTTAGATGGCCAAGACTCATGAA
1 GATAACCAACAGTCCTCATCACATAGGAACCGTGTTATCACCCTTAGATGGCCAAGACTCATGAA
* * * * *
1978507 CATATGAGCAGTGTCATCACCTG-CCTAGATCTCTTCATTATGT-ATGAGCTGTGTCAACTCAGA
66 CAAATGAGCAGTGTCATCACATGACC-AGATCTCCTCATTATGTAAGGAGCTGTGTCAACTCAAA
* *
1978570 TAACCAGCCGTCCTCATCATATAGGAACTGTGTTATCACCCTTAGATGGCCAAGACTCATGAACA
130 TAACCAGCCGTCCTCATCACATAGGAACCGTGTTATCACCCTTAGATGGCCAAGACTCATGAACA
* * * *
1978635 GATGAGCAGTGTCATCACTTTACCAGATCTCTTCAT
195 AATGAGCAGTGTCATCACATGACCAGATCTCCTCAT
1978671 CACGTACGAG
Statistics
Matches: 210, Mismatches: 18, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
253 112 0.53
254 98 0.47
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (254 bp):
GATAACCAACAGTCCTCATCACATAGGAACCGTGTTATCACCCTTAGATGGCCAAGACTCATGAA
CAAATGAGCAGTGTCATCACATGACCAGATCTCCTCATTATGTAAGGAGCTGTGTCAACTCAAAT
AACCAGCCGTCCTCATCACATAGGAACCGTGTTATCACCCTTAGATGGCCAAGACTCATGAACAA
ATGAGCAGTGTCATCACATGACCAGATCTCCTCATTATGTAAGGAGTTGTGTCAACTCA
Found at i:1994450 original size:2 final size:2
Alignment explanation
Indices: 1994445--1994493 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1994435 ATTAATCCTT
1994445 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
1994487 TA TA TA T
1 TA TA TA T
1994494 GTCTTTTCTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1994571 original size:19 final size:18
Alignment explanation
Indices: 1994549--1994588 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
1994539 TTGTTCACCC
*
1994549 ATTTATTATTTAATTTATT
1 ATTTAGTATTTAA-TTATT
1994568 ATTTAGTATTTAATTATT
1 ATTTAGTATTTAATTATT
1994586 ATT
1 ATT
1994589 GAACAATCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (18 bp):
ATTTAGTATTTAATTATT
Found at i:1997664 original size:81 final size:83
Alignment explanation
Indices: 1997510--1997668 Score: 227
Period size: 81 Copynumber: 1.9 Consensus size: 83
1997500 GTTATGTTAT
*
1997510 ATCATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTTGAACTTATATAATGTAATAG
1 ATCATTTAACCGGAAATATTATCAAGTACAATAACA-ATCAGGTTGAACTTATATAATGTAATAG
*
1997575 GTAACGCTTATATAATAAA
65 ATAACGCTTATATAATAAA
*
1997594 ATCATTTAATCGGAAATATTA-CAAGTACAATAAC-ATCAGG-T-AACGCTTATATAATGTAATA
1 ATCATTTAACCGGAAATATTATCAAGTACAATAACAATCAGGTTGAA--CTTATATAATGTAATA
*
1997655 GATAGCGCTTATAT
64 GATAACGCTTATAT
1997669 TGACCTATTT
Statistics
Matches: 69, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
79 2 0.03
80 1 0.01
81 33 0.48
83 13 0.19
84 20 0.29
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.33
Consensus pattern (83 bp):
ATCATTTAACCGGAAATATTATCAAGTACAATAACAATCAGGTTGAACTTATATAATGTAATAGA
TAACGCTTATATAATAAA
Found at i:1998106 original size:197 final size:199
Alignment explanation
Indices: 1997692--1998184 Score: 630
Period size: 197 Copynumber: 2.5 Consensus size: 199
1997682 AGTAAACTGA
* * * *
1997692 TATATTTATACCGGTAACATTGCAAATTTACCTATTACATTATATTATCGGTTTCGATGTTTTTT
1 TATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATATTATCGGTTTCGATGTTTATG
*
1997757 GGATCGATACAATTT--TAAATGTATCGACAC-TTATGCATGCACCTCGTTGGGCATTCATTATG
66 GGATCGATACATTTTAATAAATGTATCGACACTTTATGCATGCACCTCGTTGGGCATTCATTATG
* * *
1997819 GAAAAAGGTATCGACACAAACTTAAAAAGTGTCGATACATTATTTAGACTTATTTTCTCATAAAA
131 GAAAAAAGTATCGACACAAACTTAAAAAGTGTCGATACATTATCTAGACCTATTTTCTCATAAAA
1997884 CCGG
196 CCGG
* * * * ** * *
1997888 TATATTTCTATCGGGTACATTGTAATTTTACCTATCGCATTGTAATTATCGGTTTCGATGTTTGT
1 TATATTTATACCGGTTACATTGTAAATTTACCTATTACATTAT-ATTATCGGTTTCGATGTTTAT
* *
1997953 GGGATC-ATAC-TTTTAATAAATGTATCGACACTTTATGCGTGCACC-CTGTTTGGCATTCATTA
65 GGGATCGATACATTTTAATAAATGTATCGACACTTTATGCATGCACCTC-GTTGGGCATTCATTA
* * ** * *
1998015 TGGACAAAAAGTATCGATACAAATTTAAATGGTGTCGATACTTTATGCT-GACCTATTTTCTTAT
129 TGGA-AAAAAGTATCGACACAAACTTAAAAAGTGTCGATACATTAT-CTAGACCTATTTTCTCAT
1998079 AAAACC-G
192 AAAACCGG
*
1998086 -ATATTTATACCAGTTACATTGTAAATTTACCTATTACATTATATTATCGGTTTCGATG-TTATG
1 TATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATATTATCGGTTTCGATGTTTATG
* *
1998149 GGATCGATACTTTTTAATAAATGT-TCGGCACTTTAT
66 GGATCGATACATTTTAATAAATGTATCGACACTTTAT
1998185 ATTATGGACA
Statistics
Matches: 255, Mismatches: 33, Indels: 18
0.83 0.11 0.06
Matches are distributed among these distances:
195 12 0.05
196 69 0.27
197 88 0.35
198 31 0.12
199 54 0.21
200 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (199 bp):
TATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATATTATCGGTTTCGATGTTTATG
GGATCGATACATTTTAATAAATGTATCGACACTTTATGCATGCACCTCGTTGGGCATTCATTATG
GAAAAAAGTATCGACACAAACTTAAAAAGTGTCGATACATTATCTAGACCTATTTTCTCATAAAA
CCGG
Found at i:1998308 original size:168 final size:172
Alignment explanation
Indices: 1998011--1998330 Score: 407
Period size: 168 Copynumber: 1.9 Consensus size: 172
1998001 TTTGGCATTC
* * ** * *
1998011 ATTATGGACAAAAAGTATCGATACAAATTTAAATGGTGTCGATACTTTATGCTGACCTATTTTCT
1 ATTATGGACAAAAAGTATAGATACAAATTCAAAAAGTGTCGATACATTATGCTGACATATTTTCT
* *
1998076 TATAAAACCGATATTTATACCAGTTACATTGTAAATTTACCTATTACATTATATTATCGGTTTCG
66 AATAAAACCGATATTTAT--CAGTTACATTGTAAATTTACCTATTACATTAAATTATCGGTTTCG
1998141 ATG-TTATGGGATCGATACTTTTTAATAAATGTTCGGCACTTTAT
129 ATGTTTATGGG-TCGATACTTTTTAATAAATGTTCGGCACTTTAT
* * * *
1998185 ATTATGGACAATAAGTATAGA-ACAAATTCAAAAATTGTCGATACATTATGTTGACATGTTTTCT
1 ATTATGGACAAAAAGTATAGATACAAATTCAAAAAGTGTCGATACATTATGCTGACATATTTTCT
* * * * * *
1998249 AAT-TAACCGGTATTT-T-AGTTATATTGTTAATTTACCTATTATATTAAATTATTGGTTTCGAT
66 AATAAAACCGATATTTATCAGTTACATTGTAAATTTACCTATTACATTAAATTATCGGTTTCGAT
*
1998311 GTTTTTGGGTCGATACTTTT
131 GTTTATGGGTCGATACTTTT
1998331 AGAAAATGTA
Statistics
Matches: 126, Mismatches: 19, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
168 53 0.42
169 6 0.05
171 1 0.01
172 10 0.08
173 37 0.29
174 19 0.15
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (172 bp):
ATTATGGACAAAAAGTATAGATACAAATTCAAAAAGTGTCGATACATTATGCTGACATATTTTCT
AATAAAACCGATATTTATCAGTTACATTGTAAATTTACCTATTACATTAAATTATCGGTTTCGAT
GTTTATGGGTCGATACTTTTTAATAAATGTTCGGCACTTTAT
Found at i:2000824 original size:18 final size:19
Alignment explanation
Indices: 2000785--2000832 Score: 71
Period size: 18 Copynumber: 2.6 Consensus size: 19
2000775 TTACATTCAC
2000785 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
* *
2000804 ATACAACATTAT-AATCTT
1 ATACAAAATTATAAATCGT
2000822 ATACAAAATTA
1 ATACAAAATTA
2000833 ACCCTACATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 15 0.58
19 11 0.42
ACGTcount: A:0.52, C:0.12, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:2002490 original size:200 final size:194
Alignment explanation
Indices: 2002126--2002695 Score: 822
Period size: 200 Copynumber: 2.9 Consensus size: 194
2002116 GCGTAATTTA
* * *
2002126 AAAACGTATCGACACAAATT-TAAAGTGTCGATACATTATGTTAACATATTTTCTCATAAAACCG
1 AAAATGTATCGACACAAATTAAAAAGTGTCGATACATTATGTT-ACCTATTTTCTCATAAAACCG
* * * *
2002190 GTATATTTATATCGGTTACATTGTAAATTTACCTATTACATTATAAGTTTTGGTTTCAATATTTT
65 GTATA-TTATACCGGTTACATTGTAAATTTACCTATTACATTATAA-TTTCGGTTTCGAT-GTTT
* * *
2002255 TTGGATCGATGCTTTTTATAAATGTATCGACACTTTATGCGTGCACCCCGTTTTGCATTCATTCT
127 TTGGATCGATACTTTTTA-AAATGTATCGACACTTTATGCGTGCACCCCGTTTGGCATTCATTAT
2002320 GGAC
191 GGAC
* *
2002324 AAAATGTATCGACACAAATCTAAAAAGTGTCGATATATTATGTTCACCTATTTTCTCATAAAACT
1 AAAATGTATCGACACAAAT-TAAAAAGTGTCGATACATTATGTT-ACCTATTTTCTCATAAAACC
2002389 GGTATACTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
64 GGTATA-TTATACCGGTTACATTGTAAATTTACCTATTACATTATAATT-TCGGTTTCGATGTTT
*
2002454 TTGAGATCGATACTTTTTAAAAATTTATCGACACTTTATGCGTGCACCCCGTTTGGCATTCATTA
127 TTG-GATCGATACTTTTT-AAAATGTATCGACACTTTATGCGTGCACCCCGTTTGGCATTCATTA
2002519 TGGAC
190 TGGAC
2002524 AAAATGTATCGACACAAATTTAAACAA-TGTCGATACATTATGTATACCTATTTTCTCATAAAAC
1 AAAATGTATCGACACAAA-TTAAA-AAGTGTCGATACATTATGT-TACCTATTTTCTCATAAAAC
*
2002588 CGGTATATTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTTCAGTTTCGATGTTTT
63 CGGTATATTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTTCGGTTTCGATG-TTT
* *
2002653 TTGGATTGATACAATTTT-AAATGTATCGACACTTTTATGCGTG
127 TTGGATCGATAC-TTTTTAAAATGTATCGACAC-TTTATGCGTG
2002696 AAGCTCGTTG
Statistics
Matches: 340, Mismatches: 21, Indels: 22
0.89 0.05 0.06
Matches are distributed among these distances:
197 13 0.04
198 47 0.14
199 61 0.18
200 214 0.63
201 5 0.01
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (194 bp):
AAAATGTATCGACACAAATTAAAAAGTGTCGATACATTATGTTACCTATTTTCTCATAAAACCGG
TATATTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTTCGGTTTCGATGTTTTTGG
ATCGATACTTTTTAAAATGTATCGACACTTTATGCGTGCACCCCGTTTGGCATTCATTATGGAC
Found at i:2004888 original size:21 final size:21
Alignment explanation
Indices: 2004864--2004914 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
2004854 TCTGGACAAA
*
2004864 AAGTATTGACACAAATTCAAC
1 AAGTATCGACACAAATTCAAC
2004885 AAGTATCGACACAAATTCAAC
1 AAGTATCGACACAAATTCAAC
*
2004906 AAGTGTCGA
1 AAGTATCGA
2004915 TACATTTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.45, C:0.20, G:0.14, T:0.22
Consensus pattern (21 bp):
AAGTATCGACACAAATTCAAC
Found at i:2005048 original size:221 final size:224
Alignment explanation
Indices: 2004663--2005101 Score: 645
Period size: 223 Copynumber: 2.0 Consensus size: 224
2004653 TATTGAAAAT
* * * *
2004663 AGTATCGACACAAATTTAACAATTGTTGATACTTTATGCTGACCTATTTTCTCATAAAACCGGTA
1 AGTATCGACACAAATTCAACAAGTGTCGATACTTTATGCTGACCTATTCTCTCATAAAACCGGTA
* * *
2004728 TATTTATACTGGTTACATTTGGAAATTTTCCTATTACATTATAATTATCTGTTTCGATGTTTTTA
66 TATTTATACCGATTACATTTGGAAATTTACCTATTACATTATAATTATCTGTTTCGATGTTTTTA
* *
2004793 GGATCGACACATTTTAAAAATGTATCGACACTTTATGAGTGCACC-CCTTTTGGGCATTCCTTCT
131 GGATCGACACATTTTAAAAATGTATCAACACTTTATGAGTGCACCACCTTTTGGGCATTCATTCT
*
2004857 GGACAAAAAGTATTGACACAAATTCAACA
196 GGACAAAAAGTATCGACACAAATTCAACA
*
2004886 AGTATCGACACAAATTCAACAAGTGTCGATACATTT-TG-TAGAGCTATTCTCTCATAAAACCGG
1 AGTATCGACACAAATTCAACAAGTGTCGATAC-TTTATGCT-GACCTATTCTCTCATAAAACCGG
*
2004949 TATATTTATACCGATTATA-TT-GAAATTTACCTATTACATTATAATTATCTGTTTCGATGTTTT
64 TATATTTATACCGATTACATTTGGAAATTTACCTATTACATTATAATTATCTGTTTCGATGTTTT
* ** * **
2005012 TGGGATCGACATTTTTTAAAAATGTATCAACACTTTATGCGTGCACCATTTTTTTGGGCATTCAT
129 TAGGATCGACACATTTTAAAAATGTATCAACACTTTATGAGTGCACCA-CCTTTTGGGCATTCAT
*
2005077 TCTGGACAAAATGTATCGACACAAA
193 TCTGGACAAAAAGTATCGACACAAA
2005102 ATTAAAAAGT
Statistics
Matches: 193, Mismatches: 19, Indels: 8
0.88 0.09 0.04
Matches are distributed among these distances:
221 83 0.43
222 3 0.02
223 104 0.54
224 3 0.02
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.38
Consensus pattern (224 bp):
AGTATCGACACAAATTCAACAAGTGTCGATACTTTATGCTGACCTATTCTCTCATAAAACCGGTA
TATTTATACCGATTACATTTGGAAATTTACCTATTACATTATAATTATCTGTTTCGATGTTTTTA
GGATCGACACATTTTAAAAATGTATCAACACTTTATGAGTGCACCACCTTTTGGGCATTCATTCT
GGACAAAAAGTATCGACACAAATTCAACA
Found at i:2005389 original size:200 final size:198
Alignment explanation
Indices: 2004885--2005644 Score: 979
Period size: 200 Copynumber: 3.8 Consensus size: 198
2004875 CAAATTCAAC
* * * *
2004885 AAGTATCGACACAAATTCAACAAGTGTCGATACATTTTGTAGAGCTATTCTCTCATAAAACCGGT
1 AAGTATCGACACAAATTCAAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGT
* * * ** *
2004950 ATATTTATACCGATTATATTGAAATTTACCTATTACATTATAATTATCTGTTTCGATGTTTTTGG
66 ATATTTATACCGGTTACATTGAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGG
* *
2005015 GATCGACATTTTTTAAAAATGTATCAACACTTTATGCGTGCACCATTTTTTTGGGCATTCATTCT
131 GATCGACACTTTTTAAAAATGTATCGACACTTTATGCGTGCACC---TTTTTGGGCATTCATTCT
2005080 GGACAA
193 GGACAA
*
2005086 AATGTATCGACACAAAATT-AAAAAGTGTCGATACATTATGTTGACCTATTCTCACATAAAACCG
1 AA-GTATCGACAC-AAATTCAAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCG
* * * * *
2005150 ATATATTTATACCGGTTACCTTACAAAATTACTTATTACATTATAATTATGGGTTTCGATGTCTC
64 GTATATTTATACCGGTTACATT-GAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTC
*
2005215 TGGGATCGACACTTTTTAAAAATGTATCGACACTTTATTG-GTGCACCTTTTTGGGCATTCCTTC
128 TGGGATCGACACTTTTTAAAAATGTATCGACACTTTA-TGCGTGCACCTTTTTGGGCATTCATTC
2005279 TGGACAA
192 TGGACAA
* * * * * *
2005286 ACAGTATCGACACAAATTCCAGAAGTATCGATATATTATGTAGACATATTCTCTCATAAAACCGG
1 A-AGTATCGACACAAATTCAAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGG
* * *
2005351 TATAGTTATATCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTCT
65 TATATTTATACCGGTTACATTG-AAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCT
* * ** * * *
2005416 GGGATCAATACTTTTTGTAAATGTATCGACACTTTATGCGTTCACCATTTTGGGCATTCATTATG
129 GGGATCGACACTTTTTAAAAATGTATCGACACTTTATGCGTGCACCTTTTTGGGCATTCATTCTG
2005481 GACAAA
194 GAC-AA
* *
2005487 AAGTATCGACACCAATTTC-AAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACTGG
1 AAGTATCGACA-CAAATTCAAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGG
* * * * *
2005551 TATATTTATACCGGTTATATTACAAAAATTGCATATTACATTATAATTATGGGTTTCGATGTTTT
65 TATATTTATACCGGTTACATT--GAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTC
* *
2005616 TGGGATCGATAC-TTTTATAAATGTATCGA
128 TGGGATCGACACTTTTTAAAAATGTATCGA
2005645 TACATCTGCT
Statistics
Matches: 488, Mismatches: 59, Indels: 25
0.85 0.10 0.04
Matches are distributed among these distances:
199 7 0.01
200 269 0.55
201 60 0.12
202 68 0.14
203 82 0.17
204 2 0.00
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (198 bp):
AAGTATCGACACAAATTCAAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGT
ATATTTATACCGGTTACATTGAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGG
GATCGACACTTTTTAAAAATGTATCGACACTTTATGCGTGCACCTTTTTGGGCATTCATTCTGGA
CAA
Found at i:2005562 original size:400 final size:400
Alignment explanation
Indices: 2004886--2005644 Score: 1137
Period size: 400 Copynumber: 1.9 Consensus size: 400
2004876 AAATTCAACA
* *
2004886 AGTATCGACACAAATTCAACAAGTGTCGATACATTTTGTAGAGCTATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAATTCAACAAGTATCGATACATTATGTAGAGCTATTCTCTCATAAAACCGGTA
* * * *
2004951 TATTTATACCGATTATATTGAAATTTACCTATTACATTATAATTATCTGTTTCGATGTTTTTGGG
66 TAGTTATACCGATTACATTGAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTCTGGG
* * *
2005016 ATCGACATTTTTTAAAAATGTATCAACACTTTATGCGTGCACCATTTTTTTGGGCATTCATTCTG
131 ATCAACACTTTTTAAAAATGTATCAACACTTTATGCGTGCACCA--TTTTTGGGCATTCATTATG
* *
2005081 GACAAAATGTATCGACACAAAATTAAAAAGTGTCGATACATTATGTTGACCTATTCTCACATAAA
194 GACAAAAAGTATCGACACAAAATTAAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAA
* *
2005146 ACCGATATATTTATACCGGTTACCTTAC-AAAATTACTTATTACATTATAATTATGGGTTTCGAT
259 ACCGATATATTTATACCGGTTACATTACAAAAATTACATATTACATTATAATTATGGGTTTCGAT
2005210 GTCTCTGGGATCGACACTTTTTAAAAATGTATCGACACTTTATTGGTGCACCTTTTTGGGCATTC
324 GTCTCTGGGATCGACAC-TTTTAAAAATGTATCGACACTTTATTGGTGCACCTTTTTGGGCATTC
2005275 CTTCTGGACAAAC
388 CTTCTGGACAAAC
* * *
2005288 AGTATCGACACAAATTCCAGAAGTATCGATATATTATGTAGA-CATATTCTCTCATAAAACCGGT
1 AGTATCGACACAAATTCAACAAGTATCGATACATTATGTAGAGC-TATTCTCTCATAAAACCGGT
* * *
2005352 ATAGTTATATCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTCTG
65 ATAGTTATACCGATTACATTG-AAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTCTG
* ** * *
2005417 GGATCAATACTTTTTGTAAATGTATCGACACTTTATGCGTTCACCA-TTTTGGGCATTCATTATG
129 GGATCAACACTTTTTAAAAATGTATCAACACTTTATGCGTGCACCATTTTTGGGCATTCATTATG
* * *
2005481 GACAAAAAGTATCGACACCAATTTCAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAA
194 GACAAAAAGTATCGACACAAAATTAAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAA
* * * *
2005546 ACTGGTATATTTATACCGGTTATATTACAAAAATTGCATATTACATTATAATTATGGGTTTCGAT
259 ACCGATATATTTATACCGGTTACATTACAAAAATTACATATTACATTATAATTATGGGTTTCGAT
* * * *
2005611 GTTTTTGGGATCGATACTTTTATAAATGTATCGA
324 GTCTCTGGGATCGACACTTTTAAAAATGTATCGA
2005645 TACATCTGCT
Statistics
Matches: 319, Mismatches: 35, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
400 117 0.37
401 49 0.15
402 74 0.23
403 79 0.25
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (400 bp):
AGTATCGACACAAATTCAACAAGTATCGATACATTATGTAGAGCTATTCTCTCATAAAACCGGTA
TAGTTATACCGATTACATTGAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTCTGGG
ATCAACACTTTTTAAAAATGTATCAACACTTTATGCGTGCACCATTTTTGGGCATTCATTATGGA
CAAAAAGTATCGACACAAAATTAAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAAC
CGATATATTTATACCGGTTACATTACAAAAATTACATATTACATTATAATTATGGGTTTCGATGT
CTCTGGGATCGACACTTTTAAAAATGTATCGACACTTTATTGGTGCACCTTTTTGGGCATTCCTT
CTGGACAAAC
Found at i:2006026 original size:19 final size:19
Alignment explanation
Indices: 2006002--2006046 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
2005992 ATTCACATAC
*
2006002 AAAATTATAAATCGTATAA
1 AAAATTATAAATAGTATAA
* *
2006021 AAAATTATAAATATTATAC
1 AAAATTATAAATAGTATAA
2006040 AAAATTA
1 AAAATTA
2006047 ACCCTACATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (19 bp):
AAAATTATAAATAGTATAA
Found at i:2007824 original size:33 final size:33
Alignment explanation
Indices: 2007787--2007853 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
2007777 CCATCTTAAG
*
2007787 TTCACCTCTCAACACCTCAACTTCTTTCACCAC
1 TTCACCCCTCAACACCTCAACTTCTTTCACCAC
2007820 TTCACCCCTCAACACCTCAACTTCTTTCACCAC
1 TTCACCCCTCAACACCTCAACTTCTTTCACCAC
2007853 T
1 T
2007854 CCATCTAGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.24, C:0.46, G:0.00, T:0.30
Consensus pattern (33 bp):
TTCACCCCTCAACACCTCAACTTCTTTCACCAC
Found at i:2010584 original size:176 final size:181
Alignment explanation
Indices: 2010271--2010759 Score: 706
Period size: 176 Copynumber: 2.7 Consensus size: 181
2010261 TTATTATGCG
* *
2010271 TACTTAT-TAAAGTATCGACACTTTCAATATATTCGGTAGCTCTTTACCGGTTTTGTCATTTCGA
1 TACTTATATTAAGTATCGACACTTTCAATATATCCGGTAGCTCTTTACCGGTTTTGTCATTTCGA
* *
2010335 GACCGGTTTTGTCATATTTTTACCTGTTATATCGTTATGGATCAATATATTTTTATAAAGTATCG
66 GACCGGTTTTGTCATATTTTTACCTGTTATATCGTTATGGATCGATACATTTTTATAAAGTATCG
* * * ** *
2010400 ATACTTTATAGGCGCTAAAACTGCTTATCTTTTAAA-TTACAAAGTGTTGA
131 ACACTTTATAGGCGCTAAAAATACTTATCTTTTAAACACACAAAGTGTCGA
* *
2010450 TACTTATATTAAGTATCGACACTTTC-A-ATATCCGGTAGCTCTATA-C-GTTTTGTCATTTAGA
1 TACTTATATTAAGTATCGACACTTTCAATATATCCGGTAGCTCTTTACCGGTTTTGTCATTTCGA
* *
2010511 GACCGGTTTTGTCATATTTTTACTTGTTATATCGTTGTGGA-CTGATACATTTTTATAAAGTATC
66 GACCGGTTTTGTCATATTTTTACCTGTTATATCGTTATGGATC-GATACATTTTTATAAAGTATC
*
2010575 GACACTTTATAGGCGCTAAAAATACTTCTCTTTTAAACACACAAAGTGTCGA
130 GACACTTTATAGGCGCTAAAAATACTTATCTTTTAAACACACAAAGTGTCGA
* * *
2010627 TACTTATATTAAAGTATCGACACTTTCAATATATCCGATAGCGCTTTACCGGTTTTGTCTTTTCG
1 TACTTATATT-AAGTATCGACACTTTCAATATATCCGGTAGCTCTTTACCGGTTTTGTCATTTCG
* * * *
2010692 AGATCGG-TTTGTCATATTTTTACCTATTATATTGATATGGATCGATACATTTTTATAAAGTATC
65 AGACCGGTTTTGTCATATTTTTACCTGTTATATCGTTATGGATCGATACATTTTTATAAAGTATC
2010756 GACA
130 GACA
2010760 TAAACCGATA
Statistics
Matches: 275, Mismatches: 26, Indels: 16
0.87 0.08 0.05
Matches are distributed among these distances:
175 1 0.00
176 105 0.38
177 22 0.08
178 32 0.12
179 9 0.03
180 32 0.12
181 55 0.20
182 19 0.07
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (181 bp):
TACTTATATTAAGTATCGACACTTTCAATATATCCGGTAGCTCTTTACCGGTTTTGTCATTTCGA
GACCGGTTTTGTCATATTTTTACCTGTTATATCGTTATGGATCGATACATTTTTATAAAGTATCG
ACACTTTATAGGCGCTAAAAATACTTATCTTTTAAACACACAAAGTGTCGA
Found at i:2011319 original size:12 final size:12
Alignment explanation
Indices: 2011280--2011321 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
2011270 TATGTATATT
2011280 ATATATA-TATA
1 ATATATACTATA
* *
2011291 ATACATACTATG
1 ATATATACTATA
*
2011303 TTATATACTATA
1 ATATATACTATA
2011315 ATATATA
1 ATATATA
2011322 GAATATATTT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
11 6 0.25
12 18 0.75
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (12 bp):
ATATATACTATA
Found at i:2012400 original size:19 final size:19
Alignment explanation
Indices: 2012376--2012412 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2012366 CTCTTTGATT
2012376 TTTATTATGTT-ATTATTTA
1 TTTATTAT-TTGATTATTTA
2012395 TTTATTATTTGATTATTT
1 TTTATTATTTGATTATTT
2012413 TTTTCTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.70
Consensus pattern (19 bp):
TTTATTATTTGATTATTTA
Found at i:2012447 original size:25 final size:24
Alignment explanation
Indices: 2012418--2012493 Score: 75
Period size: 25 Copynumber: 3.1 Consensus size: 24
2012408 TATTTTTTTC
2012418 TTTATCTTTTTTCCTTTTAATTTAT
1 TTTATCTTTTTT-CTTTTAATTTAT
* *
2012443 TTTATCATTTTTAT-TTTTTATTTTT
1 TTTATC-TTTTT-TCTTTTAATTTAT
*
2012468 TTTA-CATTTTTTCTTTTGATTTAT
1 TTTATC-TTTTTTCTTTTAATTTAT
2012492 TT
1 TT
2012494 AATATATTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
23 1 0.02
24 18 0.41
25 19 0.43
26 5 0.11
27 1 0.02
ACGTcount: A:0.16, C:0.08, G:0.01, T:0.75
Consensus pattern (24 bp):
TTTATCTTTTTTCTTTTAATTTAT
Found at i:2012459 original size:24 final size:24
Alignment explanation
Indices: 2012418--2012519 Score: 73
Period size: 25 Copynumber: 4.1 Consensus size: 24
2012408 TATTTTTTTC
* *
2012418 TTTATCTTTTTTCCTTTTAATTTAT
1 TTTATCATTTTT-ATTTTAATTTAT
* *
2012443 TTTATCATTTTTATTTTTTATTTTT
1 TTTATCATTTTTA-TTTTAATTTAT
* *
2012468 TTTA-CATTTTTTCTTTTGATTTAT
1 TTTATCA-TTTTTATTTTAATTTAT
* *
2012492 TTAATAT-ATTATTATTTTATTTTAT
1 TT--TATCATTTTTATTTTAATTTAT
2012517 TTT
1 TTT
2012520 CCCTTTTGAT
Statistics
Matches: 61, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
23 1 0.02
24 13 0.21
25 44 0.72
26 3 0.05
ACGTcount: A:0.20, C:0.06, G:0.01, T:0.74
Consensus pattern (24 bp):
TTTATCATTTTTATTTTAATTTAT
Found at i:2012493 original size:49 final size:50
Alignment explanation
Indices: 2012424--2012519 Score: 126
Period size: 49 Copynumber: 1.9 Consensus size: 50
2012414 TTTCTTTATC
* *
2012424 TTTTTTCCTTTTAATTTATTTTATCATTTTTATT-TTTTATTTT-TTTTACA
1 TTTTTTCCTTTTAATTTATTTAAT-A-TATTATTATTTTATTTTATTTTACA
*
2012474 TTTTTT-CTTTTGATTTATTTAATATATTATTATTTTATTTTATTTT
1 TTTTTTCCTTTTAATTTATTTAATATATTATTATTTTATTTTATTTT
2012520 CCCTTTTGAT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
47 6 0.15
48 10 0.24
49 19 0.46
50 6 0.15
ACGTcount: A:0.20, C:0.05, G:0.01, T:0.74
Consensus pattern (50 bp):
TTTTTTCCTTTTAATTTATTTAATATATTATTATTTTATTTTATTTTACA
Found at i:2012571 original size:14 final size:15
Alignment explanation
Indices: 2012549--2012590 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
2012539 ATTTATTTGT
2012549 TTATTTGTTTATTTA
1 TTATTTGTTTATTTA
2012564 TT-TTTGTTT-TATTA
1 TTATTTGTTTAT-TTA
2012578 TTATTT-TTTATTT
1 TTATTTGTTTATTT
2012591 TCATTCTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
13 1 0.04
14 17 0.71
15 6 0.25
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.79
Consensus pattern (15 bp):
TTATTTGTTTATTTA
Found at i:2014339 original size:19 final size:18
Alignment explanation
Indices: 2014305--2014348 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
2014295 ATTTAGACAT
2014305 TTTGCA-TTTCTTATTTTC
1 TTTGCATTTTCTTA-TTTC
*
2014323 TTTGCATTTTGTTATTTC
1 TTTGCATTTTCTTATTTC
2014341 TTTGCATT
1 TTTGCATT
2014349 CACATTAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.11, C:0.14, G:0.09, T:0.66
Consensus pattern (18 bp):
TTTGCATTTTCTTATTTC
Found at i:2015576 original size:22 final size:22
Alignment explanation
Indices: 2015559--2015624 Score: 123
Period size: 22 Copynumber: 3.0 Consensus size: 22
2015549 CTCGTATAAA
*
2015559 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGTAGTGCCCGTAGAAT
2015581 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGTAGTGCCCGTAGAAT
2015603 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGTAGTGCCCGTAGAAT
2015625 GATCCATAAG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.21
Consensus pattern (22 bp):
TGCACCGTAGTGCCCGTAGAAT
Found at i:2015590 original size:13 final size:13
Alignment explanation
Indices: 2015572--2015612 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
2015562 ACCGAAGTGC
2015572 CCGTAGAATTGCA
1 CCGTAGAATTGCA
2015585 CCGTAG---TGC-
1 CCGTAGAATTGCA
2015594 CCGTAGAATTGCA
1 CCGTAGAATTGCA
2015607 CCGTAG
1 CCGTAG
2015613 TGCCCGTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
9 6 0.25
10 3 0.12
12 3 0.12
13 12 0.50
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (13 bp):
CCGTAGAATTGCA
Found at i:2017262 original size:21 final size:21
Alignment explanation
Indices: 2017223--2017262 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2017213 TCTTGTTCGT
* *
2017223 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2017244 TTGAATGGGTACCGATTCC
1 TTGAAGGGGTACCGATTCC
2017263 TTGCCCAGAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.17, C:0.23, G:0.30, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:2020323 original size:21 final size:22
Alignment explanation
Indices: 2020281--2020345 Score: 114
Period size: 21 Copynumber: 3.0 Consensus size: 22
2020271 CTCGTATAAA
*
2020281 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGTAGTGCCCGTAGAAT
2020303 TGCACCGTAGTGCCC-TAGAAT
1 TGCACCGTAGTGCCCGTAGAAT
2020324 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGTAGTGCCCGTAGAAT
2020346 GATGTCCATA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
21 21 0.51
22 20 0.49
ACGTcount: A:0.25, C:0.28, G:0.26, T:0.22
Consensus pattern (22 bp):
TGCACCGTAGTGCCCGTAGAAT
Found at i:2021561 original size:2 final size:2
Alignment explanation
Indices: 2021520--2021552 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2021510 TCAGTTTCAC
*
2021520 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2021553 CCTTATATAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2021636 original size:16 final size:16
Alignment explanation
Indices: 2021600--2021638 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
2021590 AAATGTCAAC
2021600 ACATATATTCATGCAT
1 ACATATATTCATGCAT
2021616 ACATA-ATTCATGTCAT
1 ACATATATTCATG-CAT
*
2021632 TCATATA
1 ACATATA
2021639 CGTATAATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 7 0.35
16 12 0.60
17 1 0.05
ACGTcount: A:0.38, C:0.18, G:0.05, T:0.38
Consensus pattern (16 bp):
ACATATATTCATGCAT
Found at i:2022030 original size:21 final size:20
Alignment explanation
Indices: 2021987--2022026 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2021977 TCTTGTTCGT
* *
2021987 TTGAAGGGGTATCGGTTCCC
1 TTGAAGGGGTACCGATTCCC
*
2022007 TTGAATGGGTACCGATTCCC
1 TTGAAGGGGTACCGATTCCC
2022027 CTTGCCCAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.17, C:0.23, G:0.30, T:0.30
Consensus pattern (20 bp):
TTGAAGGGGTACCGATTCCC
Found at i:2025670 original size:84 final size:84
Alignment explanation
Indices: 2025486--2026269 Score: 865
Period size: 84 Copynumber: 9.4 Consensus size: 84
2025476 TAAACAAACT
* * ** * *
2025486 ATTTGCAGCATAGCTTAAGTCGAGAAAGGTTATCTG----CCAAAGACCCCCGAGTTCGATTACA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
* * *
2025547 CTCAGCTTCGAGGGCACATT
66 CTCAGC-TCCAAGGCACATC
*
2025567 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGCTT-GACTAC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAG-TTCGACTAC
2025631 GCTCAGCTCCAAGGCACATC
65 GCTCAGCTCCAAGGCACATC
* * ** * * *
2025651 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCCCAAGTTCGATTACA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
* *
2025712 CTCAGCTTCGAGGGCACATC
66 CTCAGC-TCCAAGGCACATC
*
2025732 ATTTGCAGCATAAACTTAAGTCGAGAAGGGTTATCTACCAACCAAAGACCTTCGAGTTCGACTAC
1 ATTTGCAGCAT-AACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
*
2025797 GCTCAGCTCCAAGGCATATC
65 GCTCAGCTCCAAGGCACATC
* * * * * * *
2025817 ATTTGCAGCACAACTTAAGTCTACAAGGGTTGTCTGCCAACAAAAGACCTTTGAGCTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
2025882 CTCAGCTCCAAGGCACATC
66 CTCAGCTCCAAGGCACATC
* ** * ** * * *
2025901 ATTTGCAGCATAGCTTAAGTCGAGAAAAGTTATCTGTCAA-CAAAGACCCCCAAGTTCGATTACA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
* * *
2025965 TTCAGCTTCGAGGGCACATC
66 CTCAGC-TCCAAGGCACATC
2025985 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
*
2026050 CTCAGCTCCAAGGCATATC
66 CTCAGCTCCAAGGCACATC
* * * * * *
2026069 ATTTGCAGCACAACTTAAGTCTACAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
*
2026134 CTCAGCT-CAACGACACATC
66 CTCAGCTCCAA-GGCACATC
* * * * **
2026153 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG-TGACCAAAAGACCTTCGAGTTCGACTAC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGACTAC
*
2026217 GCTCAGCT-CAACGACACATC
65 GCTCAGCTCCAA-GGCACATC
* * * * *
2026237 ATTTACAGCATAGCTCAAGGCAAGAAGGGTTAT
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTAT
2026270 ATGTCAATAA
Statistics
Matches: 595, Mismatches: 92, Indels: 29
0.83 0.13 0.04
Matches are distributed among these distances:
79 2 0.00
80 22 0.04
81 56 0.09
82 22 0.04
83 26 0.04
84 372 0.63
85 67 0.11
86 28 0.05
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.24
Consensus pattern (84 bp):
ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
CTCAGCTCCAAGGCACATC
Found at i:2026187 original size:252 final size:251
Alignment explanation
Indices: 2025486--2026269 Score: 1073
Period size: 252 Copynumber: 3.1 Consensus size: 251
2025476 TAAACAAACT
* * ** * *
2025486 ATTTGCAGCATAGCTTAAGTCGAGAAAGGTTATCTG----CCAAAGACCCCCGAGTTCGATTACA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
* * * * * * * * *
2025547 CTCAGCTTCGAGGGCACATTATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAA
66 CTCAGC-TCCAAGGCATATCATTTGCAGCACAACTTAAGTCTACAAGGGTTGTCTGCCAACAAAA
2025612 GACCTTTGAGCTT-GACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGA
130 GACCTTTGAG-TTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGA
*
2025676 AGGGCTATCTG-C-CAAAGACCCCCAAGTTCGATTACACTCAGCTTCGAGGGCACATC
194 AGGGTTATCTGTCACAAAGACCCCCAAGTTCGATTACACTCAGCTTCGAGGGCACATC
*
2025732 ATTTGCAGCATAAACTTAAGTCGAGAAGGGTTATCTACCAACCAAAGACCTTCGAGTTCGACTAC
1 ATTTGCAGCAT-AACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
2025797 GCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTACAAGGGTTGTCTGCCAACAAAA
65 GCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTACAAGGGTTGTCTGCCAACAAAA
*
2025862 GACCTTTGAGCTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAA
130 GACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAA
** *
2025927 AAGTTATCTGTCAACAAAGACCCCCAAGTTCGATTACATTCAGCTTCGAGGGCACATC
195 GGGTTATCTGTC-ACAAAGACCCCCAAGTTCGATTACACTCAGCTTCGAGGGCACATC
2025985 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
2026050 CTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTACAAGGGTTGTCTGCCAACAAAAG
66 CTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTACAAGGGTTGTCTGCCAACAAAAG
* * * * * *
2026115 ACCTTTGAGTTCGACTACGCTCAGCT-CAACGACACATCATTTACAGCATAACTCAAGGCTAGAA
131 ACCTTTGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAGCTTAAGTCGAGAA
* ** * * * * * *
2026179 GGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGC-TCAACGACACATC
195 GGGTTATCTGTCA-C-AAAGACCCCCAAGTTCGATTACACTCAGCTTCGAGGGCACATC
* * * * *
2026237 ATTTACAGCATAGCTCAAGGCAAGAAGGGTTAT
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTAT
2026270 ATGTCAATAA
Statistics
Matches: 480, Mismatches: 46, Indels: 18
0.88 0.08 0.03
Matches are distributed among these distances:
246 11 0.02
247 22 0.05
249 1 0.00
250 118 0.25
251 32 0.07
252 219 0.46
253 77 0.16
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.24
Consensus pattern (251 bp):
ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
CTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTACAAGGGTTGTCTGCCAACAAAAG
ACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAG
GGTTATCTGTCACAAAGACCCCCAAGTTCGATTACACTCAGCTTCGAGGGCACATC
Found at i:2028020 original size:14 final size:14
Alignment explanation
Indices: 2028003--2028032 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2027993 TTCCTTTTAA
2028003 TTATTTTATCATTT
1 TTATTTTATCATTT
2028017 TTATTTTATCATTT
1 TTATTTTATCATTT
2028031 TT
1 TT
2028033 TTACATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (14 bp):
TTATTTTATCATTT
Found at i:2028025 original size:47 final size:46
Alignment explanation
Indices: 2027974--2028082 Score: 105
Period size: 48 Copynumber: 2.3 Consensus size: 46
2027964 TATTCTTTGA
** *
2027974 TTTATTTTTCTTTATCTTTTTCCTTTT-AATTATTT-TATCATTTTTAT
1 TTTATTTTT-TTTACATTTTT-CTTTTGAATTATTTATAT-ATTATTAT
*
2028021 TTTATCATTTTTTTACATTTTTCTTTTGATTTATTTAATATATTATTAT
1 TTTAT--TTTTTTTACATTTTTCTTTTGAATTATTT-ATATATTATTAT
2028070 TTTATTTTATTTT
1 TTTATTTT-TTTT
2028083 CCCTTTTGAT
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
47 13 0.25
48 20 0.38
49 16 0.31
50 3 0.06
ACGTcount: A:0.20, C:0.07, G:0.01, T:0.72
Consensus pattern (46 bp):
TTTATTTTTTTTACATTTTTCTTTTGAATTATTTATATATTATTAT
Found at i:2032556 original size:1 final size:1
Alignment explanation
Indices: 2032552--2032576 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
2032542 TATTTTTTTT
2032552 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
2032577 AACACTTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:2033099 original size:2 final size:2
Alignment explanation
Indices: 2033094--2033145 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
2033084 ATAATTTCTA
2033094 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- 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
2033135 AT AT AT AT AT A
1 AT AT AT AT AT A
2033146 AACTCACAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2033374 original size:20 final size:21
Alignment explanation
Indices: 2033343--2033383 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
2033333 ATTTAATTAT
2033343 TATTTAATAATTTCAAAAATA
1 TATTTAATAATTTCAAAAATA
2033364 TATTT-ATAATTTCAAAAATA
1 TATTTAATAATTTCAAAAATA
2033384 AATTGTAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (21 bp):
TATTTAATAATTTCAAAAATA
Found at i:2034566 original size:45 final size:45
Alignment explanation
Indices: 2034450--2034568 Score: 125
Period size: 45 Copynumber: 2.6 Consensus size: 45
2034440 ATTTAAGCAT
* * * *
2034450 TAATTATCCGTTAATAATGTC-AATAGGTTGGTGGTTGGTGATTAA
1 TAATTATCCATTAATAA-CTCGAGTAGGTTAGTGGTTGGTGATTAA
* * * *
2034495 TAATTATTCTTTAATAACTCGAGTAGGTTAGTGGTTGGTGGTTAT
1 TAATTATCCATTAATAACTCGAGTAGGTTAGTGGTTGGTGATTAA
*
2034540 TAATTATCCATTAATATCTCTG-GTAGGTT
1 TAATTATCCATTAATAACTC-GAGTAGGTT
2034569 GGTTGTTGCA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 2 0.03
45 59 0.95
46 1 0.02
ACGTcount: A:0.27, C:0.08, G:0.22, T:0.43
Consensus pattern (45 bp):
TAATTATCCATTAATAACTCGAGTAGGTTAGTGGTTGGTGATTAA
Found at i:2045602 original size:27 final size:27
Alignment explanation
Indices: 2045571--2045625 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
2045561 TATTATACTC
*
2045571 ATCCAGCAAAGAAAGAAAAAAAGAAAA
1 ATCCAGCAAAAAAAGAAAAAAAGAAAA
*
2045598 ATCCAGCAAAAAAAGGAAAAAAGAAAA
1 ATCCAGCAAAAAAAGAAAAAAAGAAAA
2045625 A
1 A
2045626 AAGAGGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.71, C:0.11, G:0.15, T:0.04
Consensus pattern (27 bp):
ATCCAGCAAAAAAAGAAAAAAAGAAAA
Found at i:2045626 original size:18 final size:18
Alignment explanation
Indices: 2045605--2045646 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
2045595 AAAATCCAGC
2045605 AAAAAAAGGAAAAAAGAA
1 AAAAAAAGGAAAAAAGAA
*
2045623 AAAAAGAGGAAAAAAGAA
1 AAAAAAAGGAAAAAAGAA
2045641 AAAAAA
1 AAAAAA
2045647 TAAAAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (18 bp):
AAAAAAAGGAAAAAAGAA
Found at i:2045635 original size:27 final size:27
Alignment explanation
Indices: 2045582--2045685 Score: 95
Period size: 27 Copynumber: 3.8 Consensus size: 27
2045572 TCCAGCAAAG
*** *
2045582 AAAGAAAAAAAGAAAAATCCAGCAAAA
1 AAAGAAAAAAAGAAAAAAAGAGGAAAA
*
2045609 AAAGGAAAAAAGAAAAAAAGAGG-AAA
1 AAAGAAAAAAAGAAAAAAAGAGGAAAA
* *
2045635 AAAGAAAAAAAATAAAAAAAAAGGAAAGA
1 AAAG-AAAAAAAGAAAAAAAGAGGAAA-A
2045664 AAA-AAACAAAAGGAAAAAAAGA
1 AAAGAAA-AAAA-GAAAAAAAGA
2045686 AAAATTGAAT
Statistics
Matches: 62, Mismatches: 10, Indels: 8
0.77 0.12 0.10
Matches are distributed among these distances:
26 7 0.11
27 37 0.60
28 6 0.10
29 12 0.19
ACGTcount: A:0.79, C:0.04, G:0.15, T:0.02
Consensus pattern (27 bp):
AAAGAAAAAAAGAAAAAAAGAGGAAAA
Found at i:2045653 original size:18 final size:17
Alignment explanation
Indices: 2045582--2045689 Score: 63
Period size: 18 Copynumber: 5.9 Consensus size: 17
2045572 TCCAGCAAAG
*
2045582 AAAGAAAAAAAGAAAAAT
1 AAAGAAAAAAA-AAAAAA
** * **
2045600 CCAGCAAAAAAAGGAAA
1 AAAGAAAAAAAAAAAAA
**
2045617 AAAGAAAAAAAGAGGAAA
1 AAAGAAAAAAA-AAAAAA
2045635 AAAGAAAAAAAATAAAAAA
1 AAAG-AAAAAAA-AAAAAA
*
2045654 AAAGGAAAGAAAAAAACAA
1 AAA-GAAA-AAAAAAAAAA
*
2045673 AAGGAAAAAAAGAAAAA
1 AAAGAAAAAAA-AAAAA
2045690 TTGAATCAAT
Statistics
Matches: 70, Mismatches: 15, Indels: 10
0.74 0.16 0.11
Matches are distributed among these distances:
17 15 0.21
18 26 0.37
19 24 0.34
20 5 0.07
ACGTcount: A:0.80, C:0.04, G:0.15, T:0.02
Consensus pattern (17 bp):
AAAGAAAAAAAAAAAAA
Found at i:2048137 original size:114 final size:114
Alignment explanation
Indices: 2047931--2048156 Score: 353
Period size: 114 Copynumber: 2.0 Consensus size: 114
2047921 AAGTGCCACG
* * *
2047931 TTCTCGTAGTAGAAATAAGGAGACCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TTCTCATAGTAGAAATAAGGAAACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * * * *
2047996 TAATTTGGTATGAACCCCAAAATCAATCATTGGATTTGAAAGATGAATT
66 TAATTCGGTAGGAACCCCAAAACCAATCATTGGAATTAAAAGATGAATT
2048045 TTCTCATAGTAGAAATAAGGAAACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TTCTCATAGTAGAAATAAGGAAACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
** *
2048110 TGGTTCGGTAGGAACCCCATAACCAATCATTGGAATTAAAAGATGAA
66 TAATTCGGTAGGAACCCCAAAACCAATCATTGGAATTAAAAGATGAA
2048157 CTGCATGATC
Statistics
Matches: 101, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
114 101 1.00
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.32
Consensus pattern (114 bp):
TTCTCATAGTAGAAATAAGGAAACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TAATTCGGTAGGAACCCCAAAACCAATCATTGGAATTAAAAGATGAATT
Found at i:2049793 original size:54 final size:54
Alignment explanation
Indices: 2049709--2049863 Score: 247
Period size: 54 Copynumber: 2.9 Consensus size: 54
2049699 GAAATTTTGA
* *
2049709 CAGAAACCACAGAAAAGGATGAATGTGTTGTCAAACGCTTTACGAACATCTGAG
1 CAGAAACCACAGGAAAGGATGAATGTGTTGTCAAACGTTTTACGAACATCTGAG
* *
2049763 CAGAAACCACAGGAAAGGATGAATGCGTTGTCAAATGTTTTACGAACATCTGAG
1 CAGAAACCACAGGAAAGGATGAATGTGTTGTCAAACGTTTTACGAACATCTGAG
* * *
2049817 CAGAAGCCATAGGAAATGATGAATGTGTTGTCAAACGTTTTACGAAC
1 CAGAAACCACAGGAAAGGATGAATGTGTTGTCAAACGTTTTACGAAC
2049864 CAGTGATTAT
Statistics
Matches: 92, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 92 1.00
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (54 bp):
CAGAAACCACAGGAAAGGATGAATGTGTTGTCAAACGTTTTACGAACATCTGAG
Found at i:2050260 original size:22 final size:22
Alignment explanation
Indices: 2050229--2050283 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
2050219 CATCTACTTC
*
2050229 TTCAAAGATGATAGATTCCCTT
1 TTCAAAGATGACAGATTCCCTT
* *
2050251 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCCCTT
*
2050273 TTCAAAAATGA
1 TTCAAAGATGA
2050284 AAGCTTTATT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCCCTT
Found at i:2050875 original size:113 final size:113
Alignment explanation
Indices: 2050683--2051591 Score: 1169
Period size: 113 Copynumber: 7.9 Consensus size: 113
2050673 TAGCAAAGAT
*
2050683 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAG-AAAAAGTTCATAATGAGAAGAACTCATCTG
* *
2050748 AAGAATGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
2050797 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATATGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
*
2050862 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* *
2050910 TCAAATCCATCATTTGATGGATCAGTTTTTCTAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
* * *
2050975 AGAAGGAAGAAAAAATTCATAACGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * *
2051023 TCAAATCCATCATTTGATGGATTAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTAATCTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
*
2051088 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-GC
** * * * * * ****
2051136 TTGAATTCATCATTCGATAGATCAGCATTGCCAGGGCGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
* * *
2051201 AGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAA-CTTTTCGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-GC
* * * ** * *
2051249 TCGAATTCATCATTCGATGGATCAATTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
* ** *
2051314 AGAAAGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
** * * ** *
2051362 AT-AATTCTATCACAAAAAGAGATAGATCAACATCAGCTTTTCCAGAGAAAGTTCATAATGAGAA
1 -TCAA----ATC-C---ATCA-TTTGAT--GGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAA
*
2051426 GAACTCATTTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
54 GAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * * * *
2051486 TTAAATTCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAAAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
2051551 AGAAGGAAGAA-AGAGTTCATAATGAGAAGAATTTGTTCAAC
66 AGAAGGAAGAAGA-AGTTCATAATGAGAAGAATTTGTTCAAC
2051592 ATTGCCCTCT
Statistics
Matches: 709, Mismatches: 70, Indels: 33
0.87 0.09 0.04
Matches are distributed among these distances:
112 6 0.01
113 558 0.79
114 39 0.06
115 4 0.01
116 2 0.00
117 2 0.00
118 1 0.00
119 1 0.00
120 2 0.00
121 2 0.00
122 4 0.01
123 1 0.00
124 87 0.12
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (113 bp):
TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:2051757 original size:31 final size:31
Alignment explanation
Indices: 2051720--2051783 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
2051710 ATCCCGGTTC
*
2051720 TATTATT-TTATTATAATAATTATAATTATTT
1 TATTATTAGTATTA-AATAATTATAATTATTT
* *
2051751 TATTATTAGTATTAAATAATTTTATTTATTT
1 TATTATTAGTATTAAATAATTATAATTATTT
2051782 TA
1 TA
2051784 CAGGCCCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 24 0.83
32 5 0.17
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (31 bp):
TATTATTAGTATTAAATAATTATAATTATTT
Found at i:2051764 original size:23 final size:22
Alignment explanation
Indices: 2051721--2051776 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
2051711 TCCCGGTTCT
2051721 ATTATTTTATTATAATAATTATA
1 ATTATTTTATTATAATAATTA-A
*
2051744 ATTATTTTATTATTAGT-ATTAA
1 ATTATTTTATTA-TAATAATTAA
*
2051766 ATAATTTTATT
1 ATTATTTTATT
2051777 TATTTTACAG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
22 11 0.37
23 16 0.53
24 3 0.10
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
ATTATTTTATTATAATAATTAA
Found at i:2053114 original size:21 final size:21
Alignment explanation
Indices: 2053085--2053124 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2053075 TCATTGTTTA
*
2053085 TTTATATTTTAATTC-TATATG
1 TTTAAATTTT-ATTCATATATG
2053106 TTTAAATTTTATTCATATA
1 TTTAAATTTTATTCATATA
2053125 AATATATACC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.60
Consensus pattern (21 bp):
TTTAAATTTTATTCATATATG
Found at i:2057756 original size:21 final size:21
Alignment explanation
Indices: 2057732--2057792 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
2057722 TTCAAAGAAA
*
2057732 CATTTACCAAACTTTGAAAAC
1 CATTTATCAAACTTTGAAAAC
2057753 CATTT-TCAAA----G-AAA-
1 CATTTATCAAACTTTGAAAAC
2057767 CATTTATCAAACTTTGAAAAC
1 CATTTATCAAACTTTGAAAAC
2057788 CATTT
1 CATTT
2057793 TTTCAAAGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 14
0.68 0.02 0.30
Matches are distributed among these distances:
14 5 0.16
15 8 0.25
16 1 0.03
19 1 0.03
20 7 0.22
21 10 0.31
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.33
Consensus pattern (21 bp):
CATTTATCAAACTTTGAAAAC
Done.