Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397268.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_81.0, 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: 6219335
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 77647 characters in sequence are not A, C, G, or T
File 4 of 13
Found at i:2176709 original size:25 final size:22
Alignment explanation
Indices: 2176681--2176725 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 22
2176671 AATCATGTAA
2176681 AATCTTAAATTTTGTTATTCTTTAT
1 AATCTT-AATTTT-TT-TTCTTTAT
2176706 AATCTTAATTTTTTTTCTTT
1 AATCTTAATTTTTTTTCTTT
2176726 TGGATACATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 6 0.30
23 2 0.10
24 6 0.30
25 6 0.30
ACGTcount: A:0.24, C:0.09, G:0.02, T:0.64
Consensus pattern (22 bp):
AATCTTAATTTTTTTTCTTTAT
Found at i:2182852 original size:32 final size:33
Alignment explanation
Indices: 2182804--2182870 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 33
2182794 ATTCAATTTA
*
2182804 GTAAGCCATTAATTAATAAATGTTATCATTGAT
1 GTAAGCCATTAATTAATAAATGTTATCATCGAT
* *
2182837 GTAAG-CATTGATTAATAAATGTTCTCATCGAT
1 GTAAGCCATTAATTAATAAATGTTATCATCGAT
2182869 GT
1 GT
2182871 GTTCACAATG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
32 26 0.84
33 5 0.16
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.39
Consensus pattern (33 bp):
GTAAGCCATTAATTAATAAATGTTATCATCGAT
Found at i:2187369 original size:13 final size:13
Alignment explanation
Indices: 2187351--2187375 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2187341 TCAACTTTAC
2187351 AGGAAAAGAAAAT
1 AGGAAAAGAAAAT
2187364 AGGAAAAGAAAA
1 AGGAAAAGAAAA
2187376 AGGTTGTGGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.24, T:0.04
Consensus pattern (13 bp):
AGGAAAAGAAAAT
Found at i:2202860 original size:20 final size:20
Alignment explanation
Indices: 2202835--2202876 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
2202825 CGATGTCGAA
2202835 TAGAGCCAACTAGTACAAGC
1 TAGAGCCAACTAGTACAAGC
2202855 TAGAGCCAACTAGTACAAGC
1 TAGAGCCAACTAGTACAAGC
2202875 TA
1 TA
2202877 ACAAAGTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.24, G:0.19, T:0.17
Consensus pattern (20 bp):
TAGAGCCAACTAGTACAAGC
Found at i:2209765 original size:97 final size:97
Alignment explanation
Indices: 2209573--2209753 Score: 317
Period size: 97 Copynumber: 1.9 Consensus size: 97
2209563 TAAAACAAAA
* * *
2209573 TCATTTTCCTTTCTAACTTTTCTTTTTGAAAGGTAATTAAAGAAAAGAACAATCAAATGAACCAT
1 TCATTTTACTTTCTAACTTTTCTTTTTAAAAAGTAATTAAAGAAAAGAACAATCAAATGAACCAT
*
2209638 TTATTTAAATTCCTTCTAAACAAAGAGAATTT
66 TTATATAAATTCCTTCTAAACAAAGAGAATTT
*
2209670 TCATTTTACTTTCTCACTTTTCTTTTTAAAAAGTAATTAAAGAAAAGAACAATCAAATGAACCAT
1 TCATTTTACTTTCTAACTTTTCTTTTTAAAAAGTAATTAAAGAAAAGAACAATCAAATGAACCAT
2209735 TTATATAAATTCCTTCTAA
66 TTATATAAATTCCTTCTAA
2209754 TCATAAAGAA
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
97 79 1.00
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.39
Consensus pattern (97 bp):
TCATTTTACTTTCTAACTTTTCTTTTTAAAAAGTAATTAAAGAAAAGAACAATCAAATGAACCAT
TTATATAAATTCCTTCTAAACAAAGAGAATTT
Found at i:2211556 original size:2 final size:2
Alignment explanation
Indices: 2211549--2211573 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2211539 ACTTAGCAAT
2211549 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2211574 TGGTGTTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2231113 original size:52 final size:52
Alignment explanation
Indices: 2231052--2231156 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 52
2231042 ATGTCCCAGG
2231052 AGTTCCTTGACTTGACACTTTGTTTGCATCTGACCTGAGGAATCAATAGGAA
1 AGTTCCTTGACTTGACACTTTGTTTGCATCTGACCTGAGGAATCAATAGGAA
*
2231104 AGTTCCTTGACTTGATACTTTGTTTGCATCTGACCTGAGGAATCAATAGGAA
1 AGTTCCTTGACTTGACACTTTGTTTGCATCTGACCTGAGGAATCAATAGGAA
2231156 A
1 A
2231157 TTAAAATTAT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (52 bp):
AGTTCCTTGACTTGACACTTTGTTTGCATCTGACCTGAGGAATCAATAGGAA
Found at i:2241616 original size:2 final size:2
Alignment explanation
Indices: 2241609--2241636 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2241599 ATTCGAGGGT
2241609 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
2241637 AAAGGTTACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2257788 original size:148 final size:148
Alignment explanation
Indices: 2257520--2257819 Score: 474
Period size: 148 Copynumber: 2.0 Consensus size: 148
2257510 AGTTTTTTAG
*
2257520 AAAGAGATATGATCAAAATACCGAAATATATACAAATGAAATTATCACCATACTTGCACTGATTT
1 AAAGAGATATGATCAAAATACCGAAATATATACAAATGAAATCATCACCATACTTGCACTGATTT
********** *
2257585 TCATCAAATGAGCTNNNNNNNNNNATTTCCTACAAAAACCATAAGAGAAATTAGCAATAATTACT
66 TCATCAAATGAGCTTTTTTCATCAATTTCCTACAAAAACCATAAAAGAAATTAGCAATAATTACT
2257650 ATTGAAGTAATTTAAAAT
131 ATTGAAGTAATTTAAAAT
2257668 AAAGAGATATGATCAAAATACCGAAATATATACAAATGAAATCATCACCATACTTGCACTGATTT
1 AAAGAGATATGATCAAAATACCGAAATATATACAAATGAAATCATCACCATACTTGCACTGATTT
*
2257733 TTATCAAATGAGCTTTTTTCATCAATTTCCTACAAAAACCATAAAAGAAATTAGCAATAATTACT
66 TCATCAAATGAGCTTTTTTCATCAATTTCCTACAAAAACCATAAAAGAAATTAGCAATAATTACT
*
2257798 GTTGAAGTAATTTAAAAT
131 ATTGAAGTAATTTAAAAT
2257816 AAAG
1 AAAG
2257820 CAACCTAAAA
Statistics
Matches: 138, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
148 138 1.00
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.29
Consensus pattern (148 bp):
AAAGAGATATGATCAAAATACCGAAATATATACAAATGAAATCATCACCATACTTGCACTGATTT
TCATCAAATGAGCTTTTTTCATCAATTTCCTACAAAAACCATAAAAGAAATTAGCAATAATTACT
ATTGAAGTAATTTAAAAT
Found at i:2273877 original size:46 final size:46
Alignment explanation
Indices: 2273816--2273910 Score: 172
Period size: 46 Copynumber: 2.1 Consensus size: 46
2273806 CTGTCATATA
*
2273816 ACCTAGCTAGGTCTCATATCTACGTCCAAATTAATATAGAAACAAC
1 ACCTAACTAGGTCTCATATCTACGTCCAAATTAATATAGAAACAAC
*
2273862 ACCTAACTAGTTCTCATATCTACGTCCAAATTAATATAGAAACAAC
1 ACCTAACTAGGTCTCATATCTACGTCCAAATTAATATAGAAACAAC
2273908 ACC
1 ACC
2273911 AAGCAAAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.40, C:0.25, G:0.08, T:0.26
Consensus pattern (46 bp):
ACCTAACTAGGTCTCATATCTACGTCCAAATTAATATAGAAACAAC
Found at i:2275693 original size:18 final size:18
Alignment explanation
Indices: 2275659--2275696 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2275649 TTGATTACAT
*
2275659 AAGTTAAAAATTATATAG
1 AAGTTAAAAAATATATAG
2275677 AAGTTAAAAAGAT-TATAG
1 AAGTTAAAAA-ATATATAG
2275695 AA
1 AA
2275697 ATAGAGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.58, C:0.00, G:0.13, T:0.29
Consensus pattern (18 bp):
AAGTTAAAAAATATATAG
Found at i:2279321 original size:2 final size:2
Alignment explanation
Indices: 2279316--2279344 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2279306 CATATGTGTG
2279316 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2279345 GTTCACTAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2279686 original size:20 final size:20
Alignment explanation
Indices: 2279650--2279688 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2279640 TTATGGATTC
*
2279650 ATATTTTTAATTCAAAAAAT
1 ATATTTTTAAATCAAAAAAT
2279670 ATATTTATTAAAT-AAAAAA
1 ATATTT-TTAAATCAAAAAA
2279689 AATCTTAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (20 bp):
ATATTTTTAAATCAAAAAAT
Found at i:2279687 original size:21 final size:20
Alignment explanation
Indices: 2279650--2279689 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2279640 TTATGGATTC
* *
2279650 ATATTTTTAATTCAAAAAAT
1 ATATTTTTAAATAAAAAAAT
2279670 ATATTTATTAAATAAAAAAA
1 ATATTT-TTAAATAAAAAAA
2279690 ATCTTAATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (20 bp):
ATATTTTTAAATAAAAAAAT
Found at i:2283447 original size:4 final size:4
Alignment explanation
Indices: 2283438--2283468 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
2283428 CTAATTGGTT
*
2283438 TTTC TTTC TTTC TTTC TTTC TTTC CTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
2283469 TGTTTGGTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTC
Found at i:2285904 original size:30 final size:31
Alignment explanation
Indices: 2285870--2285939 Score: 74
Period size: 30 Copynumber: 2.3 Consensus size: 31
2285860 ATAAATTATC
* *
2285870 ATTTTTTATTAT-ATTCAA-TCAACTTCTTAA
1 ATTTTTTATTATAAGTCAATTAAAC-TCTTAA
* *
2285900 A-TTTTTATTTTAAGTCAATTAAACTCTTAT
1 ATTTTTTATTATAAGTCAATTAAACTCTTAA
2285930 ATTTTTTATT
1 ATTTTTTATT
2285940 TTGAATCAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
29 9 0.27
30 12 0.36
31 12 0.36
ACGTcount: A:0.31, C:0.10, G:0.01, T:0.57
Consensus pattern (31 bp):
ATTTTTTATTATAAGTCAATTAAACTCTTAA
Found at i:2286186 original size:30 final size:30
Alignment explanation
Indices: 2286146--2286205 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
2286136 AATTATTAAT
* *
2286146 TATAAAAATTT-ATTTAATTTAAAATAAAAA
1 TATAAAAATTTGATTGAATGT-AAATAAAAA
*
2286176 TATAATAATTTGATTGAATGTAAATAAAAA
1 TATAAAAATTTGATTGAATGTAAATAAAAA
2286206 ATTACAGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 19 0.73
31 7 0.27
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (30 bp):
TATAAAAATTTGATTGAATGTAAATAAAAA
Found at i:2286341 original size:25 final size:25
Alignment explanation
Indices: 2286307--2286357 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
2286297 TGAGAAAGAA
*
2286307 GAAAGGATATCTGGTAGGTATAAAC
1 GAAAGGATATCTGGCAGGTATAAAC
2286332 GAAAGGATATCTGGCAGGTATAAAC
1 GAAAGGATATCTGGCAGGTATAAAC
2286357 G
1 G
2286358 GATTTTAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.39, C:0.10, G:0.29, T:0.22
Consensus pattern (25 bp):
GAAAGGATATCTGGCAGGTATAAAC
Found at i:2293684 original size:22 final size:21
Alignment explanation
Indices: 2293656--2293707 Score: 65
Period size: 19 Copynumber: 2.6 Consensus size: 21
2293646 ATAAAAATAT
2293656 AATAATTTATTTAATTTTTTTA
1 AATAATTTA-TTAATTTTTTTA
2293678 AATAATTTA--AATTTTTTTA
1 AATAATTTATTAATTTTTTTA
*
2293697 AA-AATATATTA
1 AATAATTTATTA
2293708 TGTCATTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 5 0.19
19 12 0.44
20 1 0.04
22 9 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
AATAATTTATTAATTTTTTTA
Found at i:2294257 original size:24 final size:24
Alignment explanation
Indices: 2294195--2294257 Score: 58
Period size: 24 Copynumber: 2.5 Consensus size: 24
2294185 GATAAATTTT
2294195 ATTTAGTTTAAAATAAAAATATAAAA
1 ATTTA-TTT-AAATAAAAATATAAAA
* *
2294221 ACTTGATGT-AAT-AAAATAATAAAA
1 A-TTTATTTAAATAAAAAT-ATAAAA
2294245 ATTTATTTAAATA
1 ATTTATTTAAATA
2294258 TTTTAAATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 9
0.69 0.10 0.21
Matches are distributed among these distances:
23 10 0.34
24 13 0.45
26 3 0.10
27 3 0.10
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.37
Consensus pattern (24 bp):
ATTTATTTAAATAAAAATATAAAA
Found at i:2303666 original size:28 final size:27
Alignment explanation
Indices: 2303629--2303689 Score: 63
Period size: 27 Copynumber: 2.2 Consensus size: 27
2303619 ACTTTTAGAG
*
2303629 TTTTAATTTTGT-TAAGTTTTTTAA-TTT
1 TTTTAATTTTATGT-AG-TTTTTAATTTT
*
2303656 TTTTTATTTTTATGTAGTTTTTAATTTT
1 TTTTAATTT-TATGTAGTTTTTAATTTT
2303684 TTTTAA
1 TTTTAA
2303690 AAAAATATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
27 15 0.54
28 12 0.43
29 1 0.04
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.72
Consensus pattern (27 bp):
TTTTAATTTTATGTAGTTTTTAATTTT
Found at i:2305390 original size:27 final size:30
Alignment explanation
Indices: 2305342--2305396 Score: 89
Period size: 28 Copynumber: 1.9 Consensus size: 30
2305332 TTTTATTTAA
2305342 AATAAAAATATATAAATTTGA-TTAAATAT
1 AATAAAAATATATAAATTTGATTTAAATAT
2305371 AATAAAAA-ATA-AAATTTGATTTAAAT
1 AATAAAAATATATAAATTTGATTTAAAT
2305397 TTTTTAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
27 8 0.32
28 9 0.36
29 8 0.32
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (30 bp):
AATAAAAATATATAAATTTGATTTAAATAT
Found at i:2317529 original size:2 final size:2
Alignment explanation
Indices: 2317522--2317547 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2317512 TTATGGTAGA
2317522 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
2317548 GTGTGTGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2326584 original size:4 final size:4
Alignment explanation
Indices: 2326577--2326603 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2326567 AGCAAACAAA
2326577 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
2326604 TATTATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:2332718 original size:25 final size:25
Alignment explanation
Indices: 2332690--2332737 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
2332680 TAAATTTTTA
2332690 TAATTAACAAT-TAACTAGTTATTAT
1 TAATTAA-AATATAACTAGTTATTAT
*
2332715 TAATTAAAATATCACTAGTTATT
1 TAATTAAAATATAACTAGTTATT
2332738 TATATTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 3 0.14
25 18 0.86
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (25 bp):
TAATTAAAATATAACTAGTTATTAT
Found at i:2334943 original size:15 final size:15
Alignment explanation
Indices: 2334925--2334970 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
2334915 ATTTTAAGTC
2334925 ATAATATTTTGGATT
1 ATAATATTTTGGATT
*
2334940 ATAATAGATTTGGATT
1 ATAATA-TTTTGGATT
*
2334956 -TCATATTTT-GATT
1 ATAATATTTTGGATT
2334969 AT
1 AT
2334971 TTTAGTTTCG
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
13 4 0.15
14 4 0.15
15 10 0.38
16 8 0.31
ACGTcount: A:0.33, C:0.02, G:0.13, T:0.52
Consensus pattern (15 bp):
ATAATATTTTGGATT
Found at i:2338806 original size:30 final size:29
Alignment explanation
Indices: 2338772--2338832 Score: 68
Period size: 33 Copynumber: 1.9 Consensus size: 29
2338762 CCCCCCCCCT
2338772 CGGCCCTCCCACGAACTCCCAGTCTCCGCC
1 CGGCCCTCCCACG-ACTCCCAGTCTCCGCC
*
2338802 CGGCCCCCCTCCCACGGCTCCCAGGTCTCCG
1 CGG---CCCTCCCACGACTCCCA-GTCTCCG
2338833 ACACCCCCCC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
30 3 0.12
32 6 0.23
33 17 0.65
ACGTcount: A:0.10, C:0.57, G:0.20, T:0.13
Consensus pattern (29 bp):
CGGCCCTCCCACGACTCCCAGTCTCCGCC
Found at i:2338809 original size:40 final size:40
Alignment explanation
Indices: 2338746--2338872 Score: 139
Period size: 40 Copynumber: 3.4 Consensus size: 40
2338736 ACGACTCCGG
2338746 ACTCCCAGTCTCCCGACCCCCCCCCTCGGCCCTCCCACGA
1 ACTCCCAGTCTCCCGACCCCCCCCCTCGGCCCTCCCACGA
**
2338786 ACTCCCAGTCT-CCG---CCCGGCC-C--CCCTCCCACG-
1 ACTCCCAGTCTCCCGACCCCCCCCCTCGGCCCTCCCACGA
*
2338818 GCTCCCAGGTCT-CCGACACCCCCCCCTCGG-CCTCCCACGA
1 ACTCCCA-GTCTCCCGAC-CCCCCCCCTCGGCCCTCCCACGA
2338858 ACTCCCAGTCTCCCG
1 ACTCCCAGTCTCCCG
2338873 CCCGACCCCC
Statistics
Matches: 71, Mismatches: 6, Indels: 20
0.73 0.06 0.21
Matches are distributed among these distances:
32 6 0.08
33 17 0.24
35 1 0.01
36 5 0.07
37 5 0.07
38 1 0.01
39 16 0.23
40 20 0.28
ACGTcount: A:0.12, C:0.60, G:0.15, T:0.13
Consensus pattern (40 bp):
ACTCCCAGTCTCCCGACCCCCCCCCTCGGCCCTCCCACGA
Found at i:2338840 original size:72 final size:71
Alignment explanation
Indices: 2338747--2339023 Score: 280
Period size: 72 Copynumber: 4.2 Consensus size: 71
2338737 CGACTCCGGA
*
2338747 CTCCCAGTCTCCCGACCCCCCCCCTCGGCCCTCCCACGAACTCCCAGTCTCCGCCCGGCCCCCCT
1 CTCCCAGTCTCCCGACACCCCCCCTCGG-CCTCCCACGAACTCCCAGTCTCCGCCCGGCCCCCCT
2338812 CCCACGG
65 CCCACGG
*
2338819 CTCCCAGGTCT-CCGACACCCCCCCCTCGGCCTCCCACGAACTCCCAGTCTCCCGCCC-GACCCC
1 CTCCCA-GTCTCCCGACA-CCCCCCCTCGGCCTCCCACGAACTCCCAGTCT-CCGCCCGGCCCCC
2338882 CTCCCACGG
63 CTCCCACGG
* *
2338891 CTCCCAATCTCCCG--A-CCCCCCT-----TCCCACGAACTCCC-GAT-TCCCCCCGGCCCCCCT
1 CTCCCAGTCTCCCGACACCCCCCCTCGGCCTCCCACGAACTCCCAG-TCTCCGCCCGGCCCCCCT
2338946 -CCACGG
65 CCCACGG
*
2338952 CTCCCAGTCTCCCG--A----CCC-C--CCTCCCACGAACTCCGAGTC-CC-CCCGGCCCCCCT-
1 CTCCCAGTCTCCCGACACCCCCCCTCGGCCTCCCACGAACTCCCAGTCTCCGCCCGGCCCCCCTC
*
2339005 CCACGA
66 CCACGG
2339011 CTCCCAGTCTCCC
1 CTCCCAGTCTCCC
2339024 ACGAGTCCCT
Statistics
Matches: 186, Mismatches: 8, Indels: 35
0.81 0.03 0.15
Matches are distributed among these distances:
58 3 0.02
59 30 0.16
60 16 0.09
61 26 0.14
62 9 0.05
63 15 0.08
68 7 0.04
70 1 0.01
71 3 0.02
72 55 0.30
73 21 0.11
ACGTcount: A:0.12, C:0.61, G:0.14, T:0.13
Consensus pattern (71 bp):
CTCCCAGTCTCCCGACACCCCCCCTCGGCCTCCCACGAACTCCCAGTCTCCGCCCGGCCCCCCTC
CCACGG
Found at i:2338841 original size:32 final size:32
Alignment explanation
Indices: 2338775--2339026 Score: 140
Period size: 30 Copynumber: 7.9 Consensus size: 32
2338765 CCCCCCTCGG
*
2338775 CCCTCCCACGAACTCCCAGTCTCCGCCCGGCCC
1 CCCTCCCACGAACTCCCAGTCTCCGCAC-GCCC
* *
2338808 CCCTCCCACG-GCTCCCAGGTCTCCGACACCCCCCCC
1 CCCTCCCACGAACTCCCA-GTCTCCG-CA---CGCCC
* *
2338844 TCGGCCTCCCACGAACTCCCAGTCTCCCGCCCGACC
1 -C--CCTCCCACGAACTCCCAGTCT-CCGCACGCCC
* *
2338880 CCCTCCCACG-GCTCCCAATCTCC-CGAC-CCC
1 CCCTCCCACGAACTCCCAGTCTCCGC-ACGCCC
* * *
2338910 CCTTCCCACGAACTCCC-GAT-TCCCCCCGGCCC
1 CCCTCCCACGAACTCCCAG-TCTCCGCAC-GCCC
*
2338942 CCCT-CCACG-GCTCCCAGTCT-C-C-CGACCC
1 CCCTCCCACGAACTCCCAGTCTCCGCACG-CCC
* *
2338970 CCCTCCCACGAACTCCGAGTC-CC-CCCGGCCC
1 CCCTCCCACGAACTCCCAGTCTCCGCAC-GCCC
2339001 CCCT-CCACG-ACTCCCAGTCTCC-CACG
1 CCCTCCCACGAACTCCCAGTCTCCGCACG
2339027 AGTCCCTTCC
Statistics
Matches: 173, Mismatches: 21, Indels: 54
0.70 0.08 0.22
Matches are distributed among these distances:
27 1 0.01
28 8 0.05
29 16 0.09
30 42 0.24
31 25 0.14
32 22 0.13
33 26 0.15
34 1 0.01
35 1 0.01
36 6 0.03
37 2 0.01
39 14 0.08
40 9 0.05
ACGTcount: A:0.13, C:0.60, G:0.14, T:0.13
Consensus pattern (32 bp):
CCCTCCCACGAACTCCCAGTCTCCGCACGCCC
Found at i:2339009 original size:30 final size:30
Alignment explanation
Indices: 2338848--2339019 Score: 156
Period size: 30 Copynumber: 5.6 Consensus size: 30
2338838 CCCCCCTCGG
2338848 CCTCCCACGAACTCCCAGTCTCCCGCCCGA-CCC
1 CCTCCCACG-ACTCCCAG--TCCC-CCCGACCCC
* * *
2338881 CCTCCCACGGCTCCCAAT-CTCCCGACCCC
1 CCTCCCACGACTCCCAGTCCCCCCGACCCC
* *
2338910 CCTTCCCACGAACTCCCGATTCCCCCCGGCCCC
1 CC-TCCCACG-ACTCCC-AGTCCCCCCGACCCC
* *
2338943 CCT-CCACGGCTCCCAGT-CTCCCGACCCC
1 CCTCCCACGACTCCCAGTCCCCCCGACCCC
* *
2338971 CCTCCCACGAACTCCGAGTCCCCCCGGCCCC
1 CCTCCCACG-ACTCCCAGTCCCCCCGACCCC
2339002 CCT-CCACGACTCCCAGTC
1 CCTCCCACGACTCCCAGTC
2339020 TCCCACGAGT
Statistics
Matches: 115, Mismatches: 16, Indels: 20
0.76 0.11 0.13
Matches are distributed among these distances:
28 17 0.15
29 22 0.19
30 25 0.22
31 22 0.19
32 9 0.08
33 20 0.17
ACGTcount: A:0.13, C:0.60, G:0.13, T:0.13
Consensus pattern (30 bp):
CCTCCCACGACTCCCAGTCCCCCCGACCCC
Found at i:2339017 original size:59 final size:59
Alignment explanation
Indices: 2338848--2339023 Score: 253
Period size: 59 Copynumber: 2.9 Consensus size: 59
2338838 CCCCCCTCGG
* * * *
2338848 CCTCCCACGAACTCCCAGTCTCCCGCCCGACCCCCTCCCACGGCTCCCAATCTCCCGACCCC
1 CCTCCCACGAACTCCGAGTC-CCC-CCGGCCCCCCT-CCACGGCTCCCAGTCTCCCGACCCC
*
2338910 CCTTCCCACGAACTCCCGATTCCCCCCGGCCCCCCTCCACGGCTCCCAGTCTCCCGACCCC
1 CC-TCCCACGAACT-CCGAGTCCCCCCGGCCCCCCTCCACGGCTCCCAGTCTCCCGACCCC
*
2338971 CCTCCCACGAACTCCGAGTCCCCCCGGCCCCCCTCCACGACTCCCAGTCTCCC
1 CCTCCCACGAACTCCGAGTCCCCCCGGCCCCCCTCCACGGCTCCCAGTCTCCC
2339024 ACGAGTCCCT
Statistics
Matches: 105, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
59 38 0.36
60 11 0.10
61 26 0.25
62 11 0.10
63 14 0.13
64 5 0.05
ACGTcount: A:0.13, C:0.61, G:0.12, T:0.14
Consensus pattern (59 bp):
CCTCCCACGAACTCCGAGTCCCCCCGGCCCCCCTCCACGGCTCCCAGTCTCCCGACCCC
Found at i:2339161 original size:26 final size:26
Alignment explanation
Indices: 2339126--2339183 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
2339116 AAAACCGACC
2339126 AAAA-CGACCGAAACCGATACTCCAA
1 AAAACCGACCGAAACCGATACTCCAA
2339151 AAAACCGACCGAAACCGATACTCCAA
1 AAAACCGACCGAAACCGATACTCCAA
2339177 AAAACCG
1 AAAACCG
2339184 TTCGGTCGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 4 0.12
26 28 0.88
ACGTcount: A:0.48, C:0.33, G:0.12, T:0.07
Consensus pattern (26 bp):
AAAACCGACCGAAACCGATACTCCAA
Found at i:2346177 original size:27 final size:27
Alignment explanation
Indices: 2346123--2346177 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 27
2346113 TAATTATTTT
*
2346123 TTAAAAAATATAATTATCACAATTAAA
1 TTAAAAAATATAATTATCACAATGAAA
2346150 TTAAAATACATATAATTA-CA-AATGAAA
1 TTAAAA-A-ATATAATTATCACAATGAAA
2346177 T
1 T
2346178 ATAACTTCGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 13 0.52
28 3 0.12
29 9 0.36
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (27 bp):
TTAAAAAATATAATTATCACAATGAAA
Found at i:2350137 original size:15 final size:16
Alignment explanation
Indices: 2350114--2350156 Score: 65
Period size: 14 Copynumber: 2.9 Consensus size: 16
2350104 GATTTAGATC
2350114 AATTTTAAAAATCATA
1 AATTTTAAAAATCATA
2350130 AA-TTTAAAAAT--TA
1 AATTTTAAAAATCATA
2350143 AATTTTAAAAATCA
1 AATTTTAAAAATCA
2350157 AAAGTGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 4 0.17
14 9 0.38
15 9 0.38
16 2 0.08
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (16 bp):
AATTTTAAAAATCATA
Found at i:2351936 original size:26 final size:26
Alignment explanation
Indices: 2351866--2351938 Score: 92
Period size: 27 Copynumber: 2.8 Consensus size: 26
2351856 CTTGCCGTTA
2351866 GGAACATCCTTGTGCATTACGCACTT
1 GGAACATCCTTGTGCATTACGCACTT
* * *
2351892 GGGACAATCCTTGGGCATTATGCACTT
1 GGAAC-ATCCTTGTGCATTACGCACTT
* *
2351919 GGAACAGCCTTATGCATTAC
1 GGAACATCCTTGTGCATTAC
2351939 CCAATTAGGA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
26 15 0.39
27 23 0.61
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.29
Consensus pattern (26 bp):
GGAACATCCTTGTGCATTACGCACTT
Found at i:2355104 original size:26 final size:26
Alignment explanation
Indices: 2355068--2355117 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
2355058 AAAGAAGATG
2355068 GTGGATTTCATGAAAGATGTTCTCCA
1 GTGGATTTCATGAAAGATGTTCTCCA
2355094 GTGGATTTCATGAAAGATGTTCTC
1 GTGGATTTCATGAAAGATGTTCTC
2355118 AACTCTGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (26 bp):
GTGGATTTCATGAAAGATGTTCTCCA
Found at i:2355601 original size:53 final size:53
Alignment explanation
Indices: 2355506--2355611 Score: 158
Period size: 53 Copynumber: 2.0 Consensus size: 53
2355496 AGCCAAACTC
* * *
2355506 TCTAGAACATTTTAAACATAAAAATAATTTGTGAACCCTGCCACTTATTCTGA
1 TCTAGAACATCTTAAACATAAAAATAACTTGTAAACCCTGCCACTTATTCTGA
* * *
2355559 TCTAGAATATCTTAAACATAAAAATAACTTGTAAACCTTGCCACTTGTTCTGA
1 TCTAGAACATCTTAAACATAAAAATAACTTGTAAACCCTGCCACTTATTCTGA
2355612 GTTGCTATCA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (53 bp):
TCTAGAACATCTTAAACATAAAAATAACTTGTAAACCCTGCCACTTATTCTGA
Found at i:2355706 original size:45 final size:45
Alignment explanation
Indices: 2355630--2355762 Score: 122
Period size: 45 Copynumber: 3.0 Consensus size: 45
2355620 CACTTCTTTC
* * * * *
2355630 TATGAAATAGCTATTTCATGCTTTTTCCTATTCTGTAGCACAACA
1 TATGAAATAGATATTCCATACTTGTTCCTATTCTGTAACACAACA
* * *
2355675 TATGAAATAGATGTTCCATACTTGTTGCTATTTTGTAACACAACA
1 TATGAAATAGATATTCCATACTTGTTCCTATTCTGTAACACAACA
* * * * * * * *
2355720 TATAAAATAGCTATTTCATGCTTATTCTTATTTTGTAGCACAA
1 TATGAAATAGATATTCCATACTTGTTCCTATTCTGTAACACAA
2355763 TGCTTCCATA
Statistics
Matches: 71, Mismatches: 17, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
45 71 1.00
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.41
Consensus pattern (45 bp):
TATGAAATAGATATTCCATACTTGTTCCTATTCTGTAACACAACA
Found at i:2358877 original size:2 final size:2
Alignment explanation
Indices: 2358870--2358899 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2358860 CTGAAGTAAC
2358870 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2358900 TAATCAGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2364709 original size:2 final size:2
Alignment explanation
Indices: 2364702--2364732 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2364692 ATTATAGGTG
2364702 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2364733 TCTCATACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2394103 original size:2 final size:2
Alignment explanation
Indices: 2394096--2394128 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2394086 AGACAAGATC
*
2394096 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2394129 CACATGCATG
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:2395107 original size:22 final size:21
Alignment explanation
Indices: 2395079--2395120 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
2395069 ATTTTTATAA
2395079 TAAAAAACAA-AAATATAGAAAT
1 TAAAAAA-AATAAATA-AGAAAT
2395101 TAAAAAAAATAAATAAGAAA
1 TAAAAAAAATAAATAAGAAA
2395121 ACAAAGATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (21 bp):
TAAAAAAAATAAATAAGAAAT
Found at i:2397980 original size:121 final size:122
Alignment explanation
Indices: 2397828--2398053 Score: 337
Period size: 121 Copynumber: 1.9 Consensus size: 122
2397818 CAACTCCAAT
* * **
2397828 ATTGAGAAGTAAGAAGAACGGACAACAAAGATTGCAACAGAAATGGCAAAAACTCGAGATTTTCA
1 ATTGAGAAGTAAGAAGAACAGACAACAAAGATTGCAACAGAAATGGCAAAAACTAGAGATGATCA
2397893 AAAGACAAGAAGCTACT-AACAAAACAAGCTAACCTGAGATGAAAATGAGAAAGCTG
66 AAAGACAAGAAGCTACTAAACAAAACAAGCTAACCTGAGATGAAAATGAGAAAGCTG
* * ** *
2397949 ATTGAGAAGTGAGAAGAACAGACAATAAAGATTGCAATGGAAATGGCTAAAACTAGAGATGATCA
1 ATTGAGAAGTAAGAAGAACAGACAACAAAGATTGCAACAGAAATGGCAAAAACTAGAGATGATCA
* * *
2398014 AAAGACAAGAAGCTTCTAAACAACACAGGCTAACCTGAGA
66 AAAGACAAGAAGCTACTAAACAAAACAAGCTAACCTGAGA
2398054 AAGCTGGTGG
Statistics
Matches: 92, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
121 72 0.78
122 20 0.22
ACGTcount: A:0.49, C:0.15, G:0.21, T:0.15
Consensus pattern (122 bp):
ATTGAGAAGTAAGAAGAACAGACAACAAAGATTGCAACAGAAATGGCAAAAACTAGAGATGATCA
AAAGACAAGAAGCTACTAAACAAAACAAGCTAACCTGAGATGAAAATGAGAAAGCTG
Found at i:2401492 original size:176 final size:179
Alignment explanation
Indices: 2401245--2401644 Score: 416
Period size: 176 Copynumber: 2.3 Consensus size: 179
2401235 TTACAATTGA
* ** **
2401245 TTAACTA-CTATTAATCAAAACGTCACTTGTCATTTTATATAT-ATTTAACGTAAATGTGGAAGA
1 TTAACTATC-ATTAATCAAAACATCACTTGTCATTTTATAT-TCATACAACGTAAATGTAAAAGA
* ** * * * **
2401308 TAAAAATATCATATGGTTACGTTATTATGTCATATCAATATG-CACGTCA-GTATCCACTATAAC
64 TAAAAATATCACATGACTACGTCATCATGTCATATCAACATGTCACGTCACCCATCCACTATAAC
* * * * * *
2401371 ATGTTAAGTTGCCACGTCAACATTATATGATATAAAATAAGAAGTGATGTT
129 ATATTAACTTGCCACGTCAACATTATATGATATAAAATAAAAAATAATATT
* *
2401422 TTAACTATCATTAATC-AAACATCATTTGTCATTTTATATTCATACAACGTTAATGTAAAATG-T
1 TTAACTATCATTAATCAAAACATCACTTGTCATTTTATATTCATACAACGTAAATGTAAAA-GAT
* * * * * *
2401485 GAAAATATCACGTGACTATGTCATCATGTTATATCAACATGTCACGTCACCCATCCACTATGATA
65 AAAAATATCACATGACTACGTCATCATGTCATATCAACATGTCACGTCACCCATCCACTATAACA
* * *
2401550 TATTAACTTGCCATGTTAACATTATGTGATATAAAATAAAAAATAATATT
130 TATTAACTTGCCACGTCAACATTATATGATATAAAATAAAAAATAATATT
* * * * *
2401600 TTAACTGTCATTAGTCAAAACATCACTTGTTAATTTATACTCATA
1 TTAACTATCATTAATCAAAACATCACTTGTCATTTTATATTCATA
2401645 TAATACTGAT
Statistics
Matches: 181, Mismatches: 36, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
175 1 0.01
176 67 0.37
177 22 0.12
178 67 0.37
179 24 0.13
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.36
Consensus pattern (179 bp):
TTAACTATCATTAATCAAAACATCACTTGTCATTTTATATTCATACAACGTAAATGTAAAAGATA
AAAATATCACATGACTACGTCATCATGTCATATCAACATGTCACGTCACCCATCCACTATAACAT
ATTAACTTGCCACGTCAACATTATATGATATAAAATAAAAAATAATATT
Found at i:2402230 original size:27 final size:28
Alignment explanation
Indices: 2402161--2402231 Score: 81
Period size: 27 Copynumber: 2.5 Consensus size: 28
2402151 TATCGTTAGT
*
2402161 AATAAAAACTTATTTAGTACAAAATAAAA
1 AATAAAAACTTA-TTAGAACAAAATAAAA
* * *
2402190 ATATAAAAATTTATT-GAACAAAGTTAAA
1 A-ATAAAAACTTATTAGAACAAAATAAAA
2402218 AATAAAAACTTATT
1 AATAAAAACTTATT
2402232 TAAATTTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 12 0.33
28 11 0.31
29 3 0.08
30 10 0.28
ACGTcount: A:0.59, C:0.06, G:0.04, T:0.31
Consensus pattern (28 bp):
AATAAAAACTTATTAGAACAAAATAAAA
Found at i:2408990 original size:7 final size:7
Alignment explanation
Indices: 2408974--2409003 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
2408964 ATTGTTTTTC
2408974 TTTTATTT
1 TTTTA-TT
2408982 TTTTATT
1 TTTTATT
2408989 TTTTATT
1 TTTTATT
2408996 TTTTATT
1 TTTTATT
2409003 T
1 T
2409004 AATGAAGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 17 0.77
8 5 0.23
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTATT
Found at i:2414660 original size:116 final size:113
Alignment explanation
Indices: 2414459--2414687 Score: 327
Period size: 116 Copynumber: 2.0 Consensus size: 113
2414449 CAATTTGGAT
* * *
2414459 TTTTGTCAAGATTTTTCTTCAATTTACACTTTTTTTTTAAAAGCAACATTCTTGTATATTAACTA
1 TTTTGTCAAAATTTTTCTCCAATTTACACTTTTTTTTTAAAAGCAACATTCTTATATATTAACTA
*
2414524 AAATTAAAATTACATCAATGTCAAATCTAGTCTACATCTAATGAACAG
66 AAATTAAAATTACATCAATGTCAAATCAAGTCTACATCTAATGAACAG
2414572 TTTTGTCAAAATTTTTCTCCAATTTACACTTTATTTTTTTTAAAAGCAACAATT-TTATATATTA
1 TTTTGTCAAAATTTTTCTCCAATTTACAC--T-TTTTTTTTAAAAGCAAC-ATTCTTATATATTA
* * **
2414636 ATTAAAATTAAAATTATA-CGAATGTCAAATCAAGTCTGTATCTAATGAACAG
62 ACTAAAATTAAAATTACATC-AATGTCAAATCAAGTCTACATCTAATGAACAG
2414688 GCATTTAACT
Statistics
Matches: 103, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
113 27 0.26
115 2 0.02
116 71 0.69
117 3 0.03
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.42
Consensus pattern (113 bp):
TTTTGTCAAAATTTTTCTCCAATTTACACTTTTTTTTTAAAAGCAACATTCTTATATATTAACTA
AAATTAAAATTACATCAATGTCAAATCAAGTCTACATCTAATGAACAG
Found at i:2415351 original size:16 final size:17
Alignment explanation
Indices: 2415330--2415371 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
2415320 CACGGCAAAA
2415330 ATAAATAAATA-AATAT
1 ATAAATAAATATAATAT
*
2415346 ATAAAT-AATATTATAT
1 ATAAATAAATATAATAT
2415362 ATAATATAAA
1 ATAA-ATAAA
2415372 ATCCATAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 4 0.18
16 14 0.64
17 2 0.09
18 2 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
ATAAATAAATATAATAT
Found at i:2422344 original size:66 final size:66
Alignment explanation
Indices: 2422236--2422428 Score: 278
Period size: 66 Copynumber: 2.9 Consensus size: 66
2422226 GATAGAAGCA
* * * * *
2422236 CAGCTGGTGGTCTTCCTGAGTCTGGATAAGCATCCTTTGGAGGAGACGCTTGGGGAGAATGAACA
1 CAGCTGGAGGTTTTCCTGACTCTGGGTAAGCATCCTTTGGAGGAGACTCTTGGGGAGAATGAACA
2422301 T
66 T
** * *
2422302 TGGCTGGAGGTTTTCCTGACTCTGGGTAACCATCCTTTGGAGGAGACTCTTGGGGAGAATGAACC
1 CAGCTGGAGGTTTTCCTGACTCTGGGTAAGCATCCTTTGGAGGAGACTCTTGGGGAGAATGAACA
2422367 T
66 T
* * *
2422368 CAGTTGGAGGTTTTCCTGACTCTGGGTAAGCATCCTTTGGGGGCGACTCTTGGGGAGAATG
1 CAGCTGGAGGTTTTCCTGACTCTGGGTAAGCATCCTTTGGAGGAGACTCTTGGGGAGAATG
2422429 GCTCATCTTC
Statistics
Matches: 112, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
66 112 1.00
ACGTcount: A:0.20, C:0.19, G:0.34, T:0.28
Consensus pattern (66 bp):
CAGCTGGAGGTTTTCCTGACTCTGGGTAAGCATCCTTTGGAGGAGACTCTTGGGGAGAATGAACA
T
Found at i:2440701 original size:17 final size:15
Alignment explanation
Indices: 2440657--2440703 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
2440647 TATATATAAA
2440657 TTATTATAA-ATTTT
1 TTATTATAATATTTT
*
2440671 TTATTACTATTATTTT
1 TTATTA-TAATATTTT
2440687 TTATTTTATAATATTTT
1 TTA--TTATAATATTTT
2440704 ATTTAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 6 0.22
15 2 0.07
16 8 0.30
17 8 0.30
18 3 0.11
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (15 bp):
TTATTATAATATTTT
Found at i:2440718 original size:20 final size:18
Alignment explanation
Indices: 2440694--2440743 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
2440684 TTTTTATTTT
2440694 ATAATATTTTATTTAAAAA
1 ATAATATTTTATTT-AAAA
*
2440713 ATTAATATATT-TTTAAAA
1 A-TAATATTTTATTTAAAA
2440731 ATAATAATTTTAT
1 ATAAT-ATTTTAT
2440744 ATTTATTATG
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 4 0.15
18 9 0.35
19 5 0.19
20 8 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATAATATTTTATTTAAAA
Found at i:2446858 original size:27 final size:27
Alignment explanation
Indices: 2446810--2447036 Score: 251
Period size: 27 Copynumber: 8.4 Consensus size: 27
2446800 TTCCACAGCG
* * * *
2446810 CAACTAGCACTAGAACCTGCTGTAACA
1 CAACAAGCATTAGAACTTGCTGCAACA
* * * *
2446837 CTACTAGCATGAGAACTCGCTGCAACA
1 CAACAAGCATTAGAACTTGCTGCAACA
* * **
2446864 CAAGAAGCATTACAACTCACTGCAACA
1 CAACAAGCATTAGAACTTGCTGCAACA
2446891 CTAAC-AGCATTAGAACTTGCTGCAACA
1 C-AACAAGCATTAGAACTTGCTGCAACA
* *
2446918 CAAGAAGCATTAGAACTAGCTGCAACA
1 CAACAAGCATTAGAACTTGCTGCAACA
*
2446945 CAAGAAGCATTAGAACTTGCTGCAACA
1 CAACAAGCATTAGAACTTGCTGCAACA
*
2446972 CAAGAAGCATTAGAACTTGCTGCAACA
1 CAACAAGCATTAGAACTTGCTGCAACA
*
2446999 CTAAC-AGCATAAGAACTTGCTGCAACA
1 C-AACAAGCATTAGAACTTGCTGCAACA
* *
2447026 CTACCAGCATT
1 CAACAAGCATT
2447037 TGCATTCGAA
Statistics
Matches: 173, Mismatches: 23, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
26 4 0.02
27 165 0.95
28 4 0.02
ACGTcount: A:0.39, C:0.26, G:0.16, T:0.19
Consensus pattern (27 bp):
CAACAAGCATTAGAACTTGCTGCAACA
Found at i:2447036 original size:54 final size:54
Alignment explanation
Indices: 2446815--2447026 Score: 293
Period size: 54 Copynumber: 3.9 Consensus size: 54
2446805 CAGCGCAACT
* * * * *
2446815 AGCACTAGAACCTGCTGTAACACT-ACTAGCATGAGAACTCGCTGCAACACAAGA
1 AGCATTAGAACTTGCTGCAACACTAAC-AGCATTAGAACTTGCTGCAACACAAGA
* **
2446869 AGCATTACAACTCACTGCAACACTAACAGCATTAGAACTTGCTGCAACACAAGA
1 AGCATTAGAACTTGCTGCAACACTAACAGCATTAGAACTTGCTGCAACACAAGA
* *
2446923 AGCATTAGAACTAGCTGCAACAC-AAGAAGCATTAGAACTTGCTGCAACACAAGA
1 AGCATTAGAACTTGCTGCAACACTAA-CAGCATTAGAACTTGCTGCAACACAAGA
*
2446977 AGCATTAGAACTTGCTGCAACACTAACAGCATAAGAACTTGCTGCAACAC
1 AGCATTAGAACTTGCTGCAACACTAACAGCATTAGAACTTGCTGCAACAC
2447027 TACCAGCATT
Statistics
Matches: 140, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
53 2 0.01
54 134 0.96
55 4 0.03
ACGTcount: A:0.40, C:0.26, G:0.17, T:0.18
Consensus pattern (54 bp):
AGCATTAGAACTTGCTGCAACACTAACAGCATTAGAACTTGCTGCAACACAAGA
Found at i:2447048 original size:33 final size:33
Alignment explanation
Indices: 2447019--2447104 Score: 154
Period size: 33 Copynumber: 2.6 Consensus size: 33
2447009 AAGAACTTGC
2447019 TGCAACACTACCAGCATTTGCATTCGAACTAGT
1 TGCAACACTACCAGCATTTGCATTCGAACTAGT
2447052 TGCAACACTACCAGCATTTGCATTCGAACTAGT
1 TGCAACACTACCAGCATTTGCATTCGAACTAGT
* *
2447085 TGCAACACCACTAGCATTTG
1 TGCAACACTACCAGCATTTG
2447105 AACTTGCTGC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (33 bp):
TGCAACACTACCAGCATTTGCATTCGAACTAGT
Found at i:2447122 original size:27 final size:27
Alignment explanation
Indices: 2447071--2447162 Score: 105
Period size: 27 Copynumber: 3.4 Consensus size: 27
2447061 ACCAGCATTT
* * * *
2447071 GCATTCGAACTAGTTGCAACACCACTA
1 GCATTTGAACTTGCTGCTACACCACTA
*
2447098 GCATTTGAACTTGCTGCTACGCCACTA
1 GCATTTGAACTTGCTGCTACACCACTA
2447125 -CTATTTGAACTTGCTGCTACACCACTA
1 GC-ATTTGAACTTGCTGCTACACCACTA
**
2447152 GTGTTTGAACT
1 GCATTTGAACT
2447163 CACTCCAACA
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
26 1 0.02
27 54 0.98
ACGTcount: A:0.26, C:0.27, G:0.16, T:0.30
Consensus pattern (27 bp):
GCATTTGAACTTGCTGCTACACCACTA
Found at i:2447199 original size:27 final size:27
Alignment explanation
Indices: 2447153--2447243 Score: 92
Period size: 27 Copynumber: 3.4 Consensus size: 27
2447143 ACACCACTAG
** *
2447153 TGTTTGAACTCACTCCAACAACACTGA
1 TGTTTGAACTCACTAAAACAACACCGA
* * *
2447180 TGTTTGAACTCGCTAAAACACCGCCGA
1 TGTTTGAACTCACTAAAACAACACCGA
* * *
2447207 TGTTTGAACTCATTAAAACACCACCGG
1 TGTTTGAACTCACTAAAACAACACCGA
*
2447234 TATTTGAACT
1 TGTTTGAACT
2447244 TGCTGCAACA
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.27
Consensus pattern (27 bp):
TGTTTGAACTCACTAAAACAACACCGA
Found at i:2447869 original size:21 final size:21
Alignment explanation
Indices: 2447843--2447885 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2447833 ACAGCTAAAG
*
2447843 AGAGGTT-CACAAAATAATTAA
1 AGAGGTTCCAC-AAATAAATAA
2447864 AGAGGTTCCACAAATAAATAA
1 AGAGGTTCCACAAATAAATAA
2447885 A
1 A
2447886 CTAGCACAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.53, C:0.12, G:0.14, T:0.21
Consensus pattern (21 bp):
AGAGGTTCCACAAATAAATAA
Found at i:2452057 original size:42 final size:42
Alignment explanation
Indices: 2451978--2452063 Score: 138
Period size: 42 Copynumber: 2.0 Consensus size: 42
2451968 AGGATTTGAG
2451978 TATTTTATGTTTGGGTTTTGGGGTAAGCTTGGATAAAAATATT
1 TATTTTATGTTTGGGTTTTGGGGTAAGCTTGGATAAAAA-ATT
* *
2452021 TATTTTATGTTTGGG-TTTGGGGTAAGTTTGGGTAAAAAATT
1 TATTTTATGTTTGGGTTTTGGGGTAAGCTTGGATAAAAAATT
2452062 TA
1 TA
2452064 CTATCTATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
41 5 0.12
42 21 0.51
43 15 0.37
ACGTcount: A:0.26, C:0.01, G:0.27, T:0.47
Consensus pattern (42 bp):
TATTTTATGTTTGGGTTTTGGGGTAAGCTTGGATAAAAAATT
Found at i:2457465 original size:2 final size:2
Alignment explanation
Indices: 2457458--2457488 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2457448 TCTTGTTTTG
2457458 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
2457489 ATATTCACTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:2466573 original size:21 final size:20
Alignment explanation
Indices: 2466545--2466589 Score: 81
Period size: 21 Copynumber: 2.2 Consensus size: 20
2466535 TTGGTGCAGA
2466545 AAACGCCCAACAACTTGAGG
1 AAACGCCCAACAACTTGAGG
2466565 AAACTGCCCAACAACTTGAGG
1 AAAC-GCCCAACAACTTGAGG
2466586 AAAC
1 AAAC
2466590 AGTCCGGAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.42, C:0.29, G:0.18, T:0.11
Consensus pattern (20 bp):
AAACGCCCAACAACTTGAGG
Found at i:2471356 original size:16 final size:15
Alignment explanation
Indices: 2471335--2471369 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
2471325 ATATTGTCAC
2471335 TTTATTAATAAATAAA
1 TTTATTAATAAA-AAA
*
2471351 TTTATTAATTAAAAA
1 TTTATTAATAAAAAA
2471366 TTTA
1 TTTA
2471370 AAAAATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TTTATTAATAAAAAA
Found at i:2473122 original size:18 final size:17
Alignment explanation
Indices: 2473101--2473143 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
2473091 ATTGGCCGCC
2473101 TCTCTCTTTTAATTCCTT
1 TCTCTCTTTTAATT-CTT
* *
2473119 TCTCATCCTTTCATTCTT
1 TCTC-TCTTTTAATTCTT
2473137 TCTCTCT
1 TCTCTCT
2473144 CTATCACTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
17 2 0.10
18 11 0.52
19 8 0.38
ACGTcount: A:0.09, C:0.33, G:0.00, T:0.58
Consensus pattern (17 bp):
TCTCTCTTTTAATTCTT
Found at i:2479012 original size:2 final size:2
Alignment explanation
Indices: 2479005--2479036 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2478995 CATGGACAAT
2479005 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
2479037 AATAAAGCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2479579 original size:11 final size:11
Alignment explanation
Indices: 2479545--2479584 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
2479535 AAGTTGTAAT
2479545 ATTTTTAATAA
1 ATTTTTAATAA
2479556 ATTATTTAA-AA
1 ATT-TTTAATAA
*
2479567 ATTTTAAATAA
1 ATTTTTAATAA
2479578 ATTTTTA
1 ATTTTTA
2479585 TTTTTTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 4 0.16
11 16 0.64
12 5 0.20
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
ATTTTTAATAA
Found at i:2488577 original size:33 final size:33
Alignment explanation
Indices: 2488540--2488628 Score: 88
Period size: 33 Copynumber: 2.7 Consensus size: 33
2488530 TATCATATCC
* * * *
2488540 TATTAATATGTCATGTTATTTTTAATTATTATG
1 TATTAATATGTCATGTTATTATCAATTATAATA
* * **
2488573 TATTAACATGTTAAATTATTATCAATTATAATA
1 TATTAATATGTCATGTTATTATCAATTATAATA
* *
2488606 TTTTAATATGTCATGTTAATATC
1 TATTAATATGTCATGTTATTATC
2488629 TTGTGATATA
Statistics
Matches: 42, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.36, C:0.06, G:0.07, T:0.52
Consensus pattern (33 bp):
TATTAATATGTCATGTTATTATCAATTATAATA
Found at i:2507891 original size:2 final size:2
Alignment explanation
Indices: 2507884--2507915 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2507874 AAACCTCAAA
*
2507884 CT CT CT CT CT CT CT CT CT CT CT CT CT TT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2507916 TTTATCTCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:2510264 original size:2 final size:2
Alignment explanation
Indices: 2510259--2510284 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2510249 CTTGATTTTC
2510259 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
2510285 AACTTGGTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2515868 original size:15 final size:15
Alignment explanation
Indices: 2515850--2515902 Score: 79
Period size: 15 Copynumber: 3.5 Consensus size: 15
2515840 CACAAATGCT
2515850 AAGGAAACGAATGGC
1 AAGGAAACGAATGGC
*
2515865 AAGGACACGAATGGC
1 AAGGAAACGAATGGC
* *
2515880 AAGGACACGAATGAC
1 AAGGAAACGAATGGC
2515895 AAGGAAAC
1 AAGGAAAC
2515903 AAGCAGCATC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.47, C:0.17, G:0.30, T:0.06
Consensus pattern (15 bp):
AAGGAAACGAATGGC
Found at i:2532602 original size:2 final size:2
Alignment explanation
Indices: 2532595--2532621 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2532585 CCCCTTTATT
2532595 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2532622 TGAATATGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2536780 original size:52 final size:51
Alignment explanation
Indices: 2536672--2536786 Score: 140
Period size: 52 Copynumber: 2.2 Consensus size: 51
2536662 ACATAATAAT
* * * * * * *
2536672 TTTGATATTTTATGAAATATTTTAACAGTTAGAATTTGAGATTTTATTTGAT
1 TTTGA-ATTTTATGAAATATTTTAACAGTTAAAATTTAAAAATTAATTTAAA
*
2536724 TTTGACATTTTATGCAATATTTTAACAGTTAAAATTTAAAAATTAATTTAAA
1 TTTGA-ATTTTATGAAATATTTTAACAGTTAAAATTTAAAAATTAATTTAAA
2536776 TTTGAATTTTA
1 TTTGAATTTTA
2536787 AGAGTCCTAT
Statistics
Matches: 54, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
51 6 0.11
52 48 0.89
ACGTcount: A:0.37, C:0.03, G:0.10, T:0.50
Consensus pattern (51 bp):
TTTGAATTTTATGAAATATTTTAACAGTTAAAATTTAAAAATTAATTTAAA
Found at i:2553748 original size:19 final size:19
Alignment explanation
Indices: 2553712--2553750 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
2553702 CTATATTAAC
*
2553712 AAAAAAAATCTTATATTAT
1 AAAAAAAATCTTAAATTAT
* *
2553731 AAAAATAATTTTAAATTAT
1 AAAAAAAATCTTAAATTAT
2553750 A
1 A
2553751 TTTCTTTTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAAAAAATCTTAAATTAT
Found at i:2560137 original size:13 final size:13
Alignment explanation
Indices: 2560119--2560150 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
2560109 TTTAACGAGT
2560119 TTTTTATTTTTTA
1 TTTTTATTTTTTA
2560132 TTTTTATTTTTTA
1 TTTTTATTTTTTA
*
2560145 CTTTTA
1 TTTTTA
2560151 GTAAACTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:2562548 original size:123 final size:123
Alignment explanation
Indices: 2562319--2562565 Score: 334
Period size: 123 Copynumber: 2.0 Consensus size: 123
2562309 CTGCATATGT
** *
2562319 AAGTAAATTACCTGCAGGGAAAGTAACAAAATTTCTGATGCAATTTCAGATTATCATGGAATCAA
1 AAGTAAATTACCTGCAGCAAAAGTAACAAAATGTCTGATGCAATTTCAGATTATCATGGAATCAA
* * * * *
2562384 GATGTTACTTTTGATGAAACAAAAGTTGCTAATATTGTAACAACTTAGACCATATGAA
66 GATGTTACTATTGATGAAACAAAAGTAGCTAATAATATAACAACTTAGACCACATGAA
* ** * *
2562442 AAGTAAATTACCTGCAGCAAAAGTGACATTATGTGTGATGCAGTTTCAGATTATCATGGAATCAA
1 AAGTAAATTACCTGCAGCAAAAGTAACAAAATGTCTGATGCAATTTCAGATTATCATGGAATCAA
* * *
2562507 GATTTTACTATTGATGAAACAAAGGTAG-TGAATAATATAACAACTTTGACCACATGAA
66 GATGTTACTATTGATGAAACAAAAGTAGCT-AATAATATAACAACTTAGACCACATGAA
2562565 A
1 A
2562566 TCACCAGCTT
Statistics
Matches: 107, Mismatches: 16, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
122 1 0.01
123 106 0.99
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (123 bp):
AAGTAAATTACCTGCAGCAAAAGTAACAAAATGTCTGATGCAATTTCAGATTATCATGGAATCAA
GATGTTACTATTGATGAAACAAAAGTAGCTAATAATATAACAACTTAGACCACATGAA
Found at i:2564824 original size:14 final size:15
Alignment explanation
Indices: 2564805--2564835 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
2564795 AAATTATATT
2564805 TTAATTAATAA-TAA
1 TTAATTAATAATTAA
2564819 TTAATTAATAATTAA
1 TTAATTAATAATTAA
2564834 TT
1 TT
2564836 TAAAATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TTAATTAATAATTAA
Found at i:2564827 original size:11 final size:11
Alignment explanation
Indices: 2564806--2564835 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
2564796 AATTATATTT
2564806 TAATTAA-TAA
1 TAATTAATTAA
2564816 TAATTAATTAA
1 TAATTAATTAA
2564827 TAATTAATT
1 TAATTAATT
2564836 TAAAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.37
11 12 0.63
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TAATTAATTAA
Found at i:2592066 original size:22 final size:22
Alignment explanation
Indices: 2592011--2592052 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2592001 TGGACCAGTT
*
2592011 ATTC-AAAAGAGAAAAAGAGGC
1 ATTCAAAAATAGAAAAAGAGGC
2592032 ATTCAAAAATAGAAAAAGAGG
1 ATTCAAAAATAGAAAAAGAGG
2592053 ATTTAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.60, C:0.07, G:0.21, T:0.12
Consensus pattern (22 bp):
ATTCAAAAATAGAAAAAGAGGC
Found at i:2593175 original size:2 final size:2
Alignment explanation
Indices: 2593168--2593193 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2593158 AGATTAAGCA
2593168 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2593194 GTATTAATCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2600651 original size:28 final size:28
Alignment explanation
Indices: 2600611--2600667 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
2600601 GTCAAATAAA
*
2600611 CAAGTCTGCTTTGATATCATTTTGTCAT
1 CAAGTCTGCTTTGATATCATTTTATCAT
2600639 CAAGTCTGCTTTGATATCATTTTATCAT
1 CAAGTCTGCTTTGATATCATTTTATCAT
2600667 C
1 C
2600668 GATGATATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.23, C:0.19, G:0.12, T:0.46
Consensus pattern (28 bp):
CAAGTCTGCTTTGATATCATTTTATCAT
Found at i:2601905 original size:16 final size:16
Alignment explanation
Indices: 2601884--2601915 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2601874 TTTGAGTTTT
2601884 AATAATAATTTTAAAA
1 AATAATAATTTTAAAA
2601900 AATAATAATTTTAAAA
1 AATAATAATTTTAAAA
2601916 TATATATCGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AATAATAATTTTAAAA
Found at i:2602017 original size:20 final size:20
Alignment explanation
Indices: 2601989--2602031 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
2601979 AAATAATAAC
2601989 TTTTAATATTAAATT-TTTA
1 TTTTAATATTAAATTATTTA
*
2602008 TTTTATATATTATATTATTTA
1 TTTTA-ATATTAAATTATTTA
2602029 TTT
1 TTT
2602032 AAAATTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
20 9 0.43
21 7 0.33
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTAATATTAAATTATTTA
Found at i:2602794 original size:14 final size:14
Alignment explanation
Indices: 2602777--2602803 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2602767 TATATATTCA
2602777 TTTTTATTATTACT
1 TTTTTATTATTACT
2602791 TTTTTATTATTAC
1 TTTTTATTATTAC
2602804 ATGTATTAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTTTATTATTACT
Found at i:2604978 original size:84 final size:84
Alignment explanation
Indices: 2604820--2604978 Score: 196
Period size: 84 Copynumber: 1.9 Consensus size: 84
2604810 GCTCCAATTC
* * * *
2604820 TTCATTTTTTTAATGGTAATTTCTTGGTAATTGATTCTTTAGTCATAGATATATAGGGATTATTG
1 TTCATTTTTTTAATGCTAATCTCTTGATAATTGATTCTTTAGTCATAGATATATAGGGATAATTG
* **
2604885 AGGTGAAATATAATAATGG
66 ACGACAAATATAATAATGG
* * *
2604904 TTCATTTTTTTAATGCTAATCTCTTGATTATTGATTCTTTAGTTATAGTTA-ATA-GGATAATTG
1 TTCATTTTTTTAATGCTAATCTCTTGATAATTGATTCTTTAGTCATAGATATATAGGGATAATTG
2604967 TTACGACAAATA
66 --ACGACAAATA
2604979 GATGAGATGG
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
82 8 0.13
83 3 0.05
84 52 0.83
ACGTcount: A:0.31, C:0.07, G:0.16, T:0.47
Consensus pattern (84 bp):
TTCATTTTTTTAATGCTAATCTCTTGATAATTGATTCTTTAGTCATAGATATATAGGGATAATTG
ACGACAAATATAATAATGG
Found at i:2618378 original size:2 final size:2
Alignment explanation
Indices: 2618371--2618396 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2618361 TAGGCAAGGA
2618371 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2618397 CTGACCTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2622962 original size:28 final size:30
Alignment explanation
Indices: 2622922--2622985 Score: 96
Period size: 28 Copynumber: 2.2 Consensus size: 30
2622912 AATCATTAGT
*
2622922 TATAAGAGCTTATTTAGCTT-AAA-AAAAA
1 TATAAAAGCTTATTTAGCTTAAAATAAAAA
*
2622950 TATAAAAGCTTATTTAGTTTAAAATAAAAA
1 TATAAAAGCTTATTTAGCTTAAAATAAAAA
2622980 TATAAA
1 TATAAA
2622986 GTTTAATTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 18 0.56
29 3 0.09
30 11 0.34
ACGTcount: A:0.53, C:0.05, G:0.08, T:0.34
Consensus pattern (30 bp):
TATAAAAGCTTATTTAGCTTAAAATAAAAA
Found at i:2627697 original size:26 final size:26
Alignment explanation
Indices: 2627658--2627715 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 26
2627648 CTTTATGGCA
* * *
2627658 AAAAAATCAAATTACCAATAAATAATT
1 AAAAAATCAAATTA-AAAGAAAAAATT
*
2627685 AAAAAAT-ATATTAAAAGAAAAAATT
1 AAAAAATCAAATTAAAAGAAAAAATT
2627710 AAAAAA
1 AAAAAA
2627716 ATAAAAATCT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 15 0.56
26 5 0.19
27 7 0.26
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.22
Consensus pattern (26 bp):
AAAAAATCAAATTAAAAGAAAAAATT
Found at i:2629324 original size:2 final size:2
Alignment explanation
Indices: 2629317--2629342 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2629307 ACTCAATTTG
2629317 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
2629343 GTTTGGAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2632398 original size:7 final size:7
Alignment explanation
Indices: 2632382--2632435 Score: 90
Period size: 7 Copynumber: 7.7 Consensus size: 7
2632372 AGGTAAACAT
2632382 AAAAAAG
1 AAAAAAG
*
2632389 AAAAAGG
1 AAAAAAG
2632396 AAAAAAG
1 AAAAAAG
*
2632403 AAAAAAC
1 AAAAAAG
2632410 AAAAAAG
1 AAAAAAG
2632417 AAAAAAG
1 AAAAAAG
2632424 AAAAAAG
1 AAAAAAG
2632431 AAAAA
1 AAAAA
2632436 TATAATAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 43 1.00
ACGTcount: A:0.85, C:0.02, G:0.13, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:2640804 original size:2 final size:2
Alignment explanation
Indices: 2640797--2640827 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2640787 CATTGTCCTT
*
2640797 TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2640828 TTTTCCATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (2 bp):
TC
Found at i:2643416 original size:14 final size:14
Alignment explanation
Indices: 2643397--2643429 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
2643387 GATTGCTATT
2643397 GAAGAATGTTCGAC
1 GAAGAATGTTCGAC
*
2643411 GAAGAATGTTTGAC
1 GAAGAATGTTCGAC
2643425 GAAGA
1 GAAGA
2643430 GAGGCGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.39, C:0.09, G:0.30, T:0.21
Consensus pattern (14 bp):
GAAGAATGTTCGAC
Found at i:2653320 original size:85 final size:86
Alignment explanation
Indices: 2653227--2653391 Score: 242
Period size: 85 Copynumber: 1.9 Consensus size: 86
2653217 TCATATAGTA
* * * *
2653227 AACTTGGAAATTACAACCAAATTCACATCAAGCATGGAAATTTATTATACAAATTCCAAACAAGC
1 AACTTGGAAATTACAACCAAATTCACAACAAACATGAAAATTTATTATACAAAATCCAAACAAGC
2653292 ACAATTAT-CCAAAGTAAAAG
66 ACAATTATCCCAAAGTAAAAG
* ***
2653312 AACTTGGAAATTACATCCAAATTGGTAACAAACATGAAAATTTATTATACAAAATCCAAACAAGC
1 AACTTGGAAATTACAACCAAATTCACAACAAACATGAAAATTTATTATACAAAATCCAAACAAGC
*
2653377 ACAGTTATCCCAAAG
66 ACAATTATCCCAAAG
2653392 AAGAGAAATT
Statistics
Matches: 70, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
85 64 0.91
86 6 0.09
ACGTcount: A:0.48, C:0.19, G:0.10, T:0.24
Consensus pattern (86 bp):
AACTTGGAAATTACAACCAAATTCACAACAAACATGAAAATTTATTATACAAAATCCAAACAAGC
ACAATTATCCCAAAGTAAAAG
Found at i:2655231 original size:16 final size:16
Alignment explanation
Indices: 2655212--2655242 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2655202 TATATAAAAA
2655212 AATCAATAAATAAACC
1 AATCAATAAATAAACC
*
2655228 AATCAATTAATAAAC
1 AATCAATAAATAAAC
2655243 ATATAATTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.16, G:0.00, T:0.23
Consensus pattern (16 bp):
AATCAATAAATAAACC
Found at i:2656332 original size:2 final size:2
Alignment explanation
Indices: 2656325--2656352 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2656315 TATTAGAACT
2656325 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
2656353 ATAGATCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2656534 original size:24 final size:26
Alignment explanation
Indices: 2656485--2656535 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
2656475 ATTGAGAATT
*
2656485 ATGCCTTAATCATGATACATAGACAAC
1 ATGCCTTAATCATGA-ACATAAACAAC
2656512 ATGCCTTAATCA-G-ACATAAACAAC
1 ATGCCTTAATCATGAACATAAACAAC
2656536 TAGCAACTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 10 0.43
26 1 0.04
27 12 0.52
ACGTcount: A:0.43, C:0.24, G:0.10, T:0.24
Consensus pattern (26 bp):
ATGCCTTAATCATGAACATAAACAAC
Found at i:2660483 original size:12 final size:13
Alignment explanation
Indices: 2660435--2660489 Score: 51
Period size: 14 Copynumber: 4.2 Consensus size: 13
2660425 AACTAAATTA
2660435 ATTTTTTATA-AT
1 ATTTTTTATATAT
*
2660447 A-TATTTATATAT
1 ATTTTTTATATAT
* *
2660459 ATTAATATATATAAT
1 ATT-TTTTATAT-AT
2660474 ATTTTTTATATAT
1 ATTTTTTATATAT
2660487 ATT
1 ATT
2660490 AAGAATAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
11 7 0.20
12 4 0.11
13 6 0.17
14 13 0.37
15 5 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
ATTTTTTATATAT
Found at i:2660484 original size:18 final size:18
Alignment explanation
Indices: 2660435--2660488 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 18
2660425 AACTAAATTA
*
2660435 ATTTTTTATAATATATTTAT
1 ATTTTTTAT-ATATA-TAAT
* *
2660455 ATATATTAATATATATAAT
1 AT-TTTTTATATATATAAT
2660474 ATTTTTTATATATAT
1 ATTTTTTATATATAT
2660489 TAAGAATAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
18 11 0.39
19 5 0.18
20 7 0.25
21 5 0.18
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTTTTTATATATATAAT
Found at i:2660520 original size:16 final size:16
Alignment explanation
Indices: 2660495--2660529 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2660485 ATATTAAGAA
*
2660495 TAATTGATAATAAACT
1 TAATTAATAATAAACT
*
2660511 TAATTAATAATATACT
1 TAATTAATAATAAACT
2660527 TAA
1 TAA
2660530 AATATATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (16 bp):
TAATTAATAATAAACT
Found at i:2660787 original size:28 final size:27
Alignment explanation
Indices: 2660745--2660803 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 27
2660735 ATGCTTCATA
* *
2660745 ATATAAAATGTTATAAATATATATGTAT
1 ATATAAAATGTTATAAACAT-TATATAT
2660773 ATATAAAAT-TATATAAACATTATATAT
1 ATATAAAATGT-TATAAACATTATATAT
2660800 ATAT
1 ATAT
2660804 TTAATTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 11 0.39
28 17 0.61
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (27 bp):
ATATAAAATGTTATAAACATTATATAT
Found at i:2661812 original size:28 final size:29
Alignment explanation
Indices: 2661770--2661828 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 29
2661760 TATGAAGAGT
* *
2661770 ATTTTTATATTATTTTTTA-AATAATTAA
1 ATTTTTAAATAATTTTTTATAATAATTAA
*
2661798 ATTTTTAAATAATTTTTTATAATTATTAA
1 ATTTTTAAATAATTTTTTATAATAATTAA
2661827 AT
1 AT
2661829 AGTGAATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 17 0.63
29 10 0.37
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (29 bp):
ATTTTTAAATAATTTTTTATAATAATTAA
Found at i:2667696 original size:4 final size:4
Alignment explanation
Indices: 2667687--2667725 Score: 62
Period size: 4 Copynumber: 10.0 Consensus size: 4
2667677 CCTATCTTTT
*
2667687 TGTA TGTA TGTA T-CA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
2667726 AGCATCTGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 2 0.06
4 30 0.94
ACGTcount: A:0.26, C:0.03, G:0.23, T:0.49
Consensus pattern (4 bp):
TGTA
Found at i:2667835 original size:125 final size:125
Alignment explanation
Indices: 2667706--2667932 Score: 303
Period size: 125 Copynumber: 1.8 Consensus size: 125
2667696 GTATCATGTA
* * * * *
2667706 TGTATGTATGTATGTATGTAAGCATCTGAGTATGGTAATTTTTACATATATGCATCTAGGTATCT
1 TGTATGTATGGATGGATGTAAGCATCTGAGTATGGTAATTTATACAAATATGCATCTAGGTATCA
*
2667771 CTTTGTTTGTTAAAAT-TCTGATAAATGATTAATGGGTTTTTTTCCCGATTTTGAGGTTTG
66 CTTTGTTTGTTAAAATAT-TGACAAATGATTAATGGGTTTTTTTCCCGATTTTGAGGTTTG
** * * * * * * *
2667831 TGTATGTATGGATGGATGTGTGCATTTGGGTATGTTTATTTATGCAAATATGCATCTGGGTTTCA
1 TGTATGTATGGATGGATGTAAGCATCTGAGTATGGTAATTTATACAAATATGCATCTAGGTATCA
2667896 CTTTGTTTGTTAAAATATTGACAAATGATTAATGGGT
66 CTTTGTTTGTTAAAATATTGACAAATGATTAATGGGT
2667933 ACTGATGGGT
Statistics
Matches: 86, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
125 85 0.99
126 1 0.01
ACGTcount: A:0.25, C:0.08, G:0.22, T:0.45
Consensus pattern (125 bp):
TGTATGTATGGATGGATGTAAGCATCTGAGTATGGTAATTTATACAAATATGCATCTAGGTATCA
CTTTGTTTGTTAAAATATTGACAAATGATTAATGGGTTTTTTTCCCGATTTTGAGGTTTG
Found at i:2674137 original size:2 final size:2
Alignment explanation
Indices: 2674130--2674176 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
2674120 GCCATCACTC
2674130 CT CT CT CT CT CT CT CT -T CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2674171 CT CT CT
1 CT CT CT
2674177 TCATCCTCAA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:2675343 original size:5 final size:5
Alignment explanation
Indices: 2675333--2675370 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
2675323 CTTTTTTATC
*
2675333 CTTTT CTTTT CTTTT CTTTT CTTTT -TTCT CTTGTT CTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTT-TT CTT
2675371 GATGGAATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
4 3 0.10
5 22 0.76
6 4 0.14
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (5 bp):
CTTTT
Found at i:2675351 original size:15 final size:14
Alignment explanation
Indices: 2675323--2675370 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
2675313 GCCATTAACC
*
2675323 CTTTTTTATCCTTTT
1 CTTTTTTCT-CTTTT
*
2675338 CTTTTCTTTTCTTTT
1 CTTTT-TTCTCTTTT
2675353 CTTTTTTCTCTTGTT
1 CTTTTTTCTCTT-TT
2675368 CTT
1 CTT
2675371 GATGGAATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 6 0.21
15 20 0.69
16 3 0.10
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.75
Consensus pattern (14 bp):
CTTTTTTCTCTTTT
Found at i:2677273 original size:2 final size:2
Alignment explanation
Indices: 2677262--2677295 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2677252 TGCACTTGTC
2677262 AT AT -T AT 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 AT A
2677296 ATCTACCTAA
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:2679793 original size:2 final size:2
Alignment explanation
Indices: 2679786--2679814 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2679776 TTTAACTTGT
2679786 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2679815 TTCAAATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2687050 original size:21 final size:21
Alignment explanation
Indices: 2687024--2687072 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
2687014 ATTTTTTCTT
2687024 ATTTTA-TT-TTAAATATTTATA
1 ATTTTACTTATTAAATA-TTA-A
2687045 ATTTTATCTTATTAAATATTAA
1 ATTTTA-CTTATTAAATATTAA
2687067 ATTTTA
1 ATTTTA
2687073 AAATCTAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 6 0.24
22 7 0.28
23 5 0.20
24 7 0.28
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
ATTTTACTTATTAAATATTAA
Found at i:2687067 original size:31 final size:32
Alignment explanation
Indices: 2687006--2687076 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 32
2686996 AGTTTCAAAA
* ** *
2687006 ATTTATAAATTTTTTCTTATTTTATTTTAAAT
1 ATTTATAAATTTTATCTTATTAAATATTAAAT
2687038 ATTTAT-AATTTTATCTTATTAAATATTAAAT
1 ATTTATAAATTTTATCTTATTAAATATTAAAT
2687069 -TTTA-AAAT
1 ATTTATAAAT
2687077 CTAACTCTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
30 7 0.21
31 21 0.62
32 6 0.18
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (32 bp):
ATTTATAAATTTTATCTTATTAAATATTAAAT
Found at i:2688944 original size:2 final size:2
Alignment explanation
Indices: 2688937--2688967 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2688927 NNNNNNNNNN
2688937 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
2688968 GGAGTGATGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2693688 original size:33 final size:33
Alignment explanation
Indices: 2693639--2694460 Score: 340
Period size: 33 Copynumber: 24.9 Consensus size: 33
2693629 CTTTGGTCAT
* * * *
2693639 GAAACTCCAACCATTCCCGCAAGCTTGGGTGAA
1 GAAACTCCTAGCATTCCCACAACCTTGGGTGAA
* *
2693672 GAAACTCCTAGTATTCCCACAAGCTTGGGTGAA
1 GAAACTCCTAGCATTCCCACAACCTTGGGTGAA
*
2693705 GAAACTCCTAGCATTCCCACAACCTTGGATGAA
1 GAAACTCCTAGCATTCCCACAACCTTGGGTGAA
**
2693738 GAAA-TGCCTAGTGTTCCCACAACCTTGGGTGAA
1 GAAACT-CCTAGCATTCCCACAACCTTGGGTGAA
2693771 GAAACTCCTAGCATTCCCACAACCTTGGGTGAA
1 GAAACTCCTAGCATTCCCACAACCTTGGGTGAA
* * * * *
2693804 GAAATTCTTACCATTCCCACAAACTTGGGCGAA
1 GAAACTCCTAGCATTCCCACAACCTTGGGTGAA
* **** **
2693837 GAAACTCCTATC-TATCCTGTGACCTTGGCAGAA
1 GAAACTCCTAGCAT-TCCCACAACCTTGGGTGAA
* * * **
2693870 GAAACCCCT-GCCATTACCATAA-CTGTGGGCCAA
1 GAAACTCCTAG-CATTCCCACAACCT-TGGGTGAA
* *
2693903 GAAACTCCT-G-ATCTACACACAACATTGGGTGAA
1 GAAACTCCTAGCAT-T-CCCACAACCTTGGGTGAA
***
2693936 GAAACTCC-AGTCATTCCTC-CAACCTTGGACAAA
1 GAAACTCCTAG-CATTCC-CACAACCTTGGGTGAA
** *
2693969 GAAACTCC-AGTCATTCCTTCGACCTTGGGTGAA
1 GAAACTCCTAG-CATTCCCACAACCTTGGGTGAA
* ** * *
2694002 GAAACTCCT-GCCATTTCTC-CAACCTTTTGCGAC
1 GAAACTCCTAG-CA-TTCCCACAACCTTGGGTGAA
* * * ** * * *
2694035 GAAACTTCAACCA-TCACTGCAACCCTGGGTCAG
1 GAAACTCCTAGCATTC-CCACAACCTTGGGTGAA
** * * * * *
2694068 GAAACTCAGACCATTACTACAACCTTCGGTGAG
1 GAAACTCCTAGCATTCCCACAACCTTGGGTGAA
* * * * * ** * * *
2694101 GAAAATACAACCGTTCCTGCAACGTTGGTTGAG
1 GAAACTCCTAGCATTCCCACAACCTTGGGTGAA
* * **
2694134 GAAACTAC-AACTATTCCCACAACCTTGCATGAA
1 GAAACTCCTAGC-ATTCCCACAACCTTGGGTGAA
* * *
2694167 GAAACT-CTAGCTGTTCCCACAACCTTGGCTGAG
1 GAAACTCCTAGC-ATTCCCACAACCTTGGGTGAA
* *
2694200 GAAACT-CTAACTATTCCCACAACCTTGGG-CAA
1 GAAACTCCTAGC-ATTCCCACAACCTTGGGTGAA
* * * * * *
2694232 GGAAACTGCAAGTATTCCCACCACCTTGGGCGAG
1 -GAAACTCCTAGCATTCCCACAACCTTGGGTGAA
* * * * *
2694266 GAAACTGCAAGTATTCCCAAAACCTTGGGTGAG
1 GAAACTCCTAGCATTCCCACAACCTTGGGTGAA
*
2694299 GAAACATCAACTA--ATT-CCACAACCTTGGGTGAG
1 GAAAC-TC--CTAGCATTCCCACAACCTTGGGTGAA
* * * *
2694332 GAAACTTCTA-CTATTCCAACAACCTTGGCTGAG
1 GAAACTCCTAGC-ATTCCCACAACCTTGGGTGAA
* * * * * ** *
2694365 GAAATTCC-AACTAATCCGACAACCGTGACTGAG
1 GAAACTCCTAGC-ATTCCCACAACCTTGGGTGAA
* * * * *
2694398 GAAACTTCGA-CTATTCCCGCAACCTTGGGCGAG
1 GAAACTCCTAGC-ATTCCCACAACCTTGGGTGAA
* *
2694431 GAAACT-TTGGCTATTCCCACAACCTTGGGT
1 GAAACTCCTAGC-ATTCCCACAACCTTGGGT
2694461 TTGGAAGCTT
Statistics
Matches: 611, Mismatches: 144, Indels: 68
0.74 0.17 0.08
Matches are distributed among these distances:
30 3 0.00
31 4 0.01
32 14 0.02
33 569 0.93
34 17 0.03
35 2 0.00
36 2 0.00
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (33 bp):
GAAACTCCTAGCATTCCCACAACCTTGGGTGAA
Found at i:2698372 original size:2 final size:2
Alignment explanation
Indices: 2698360--2698397 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
2698350 TCACTTTTCC
* *
2698360 CT CT CT TT CT CT CT CT CT CT CT GT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2698398 GTTTCTTTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.45, G:0.03, T:0.53
Consensus pattern (2 bp):
CT
Found at i:2698373 original size:8 final size:8
Alignment explanation
Indices: 2698360--2698413 Score: 54
Period size: 8 Copynumber: 6.5 Consensus size: 8
2698350 TCACTTTTCC
2698360 CTCTCTTT
1 CTCTCTTT
*
2698368 CTCTCTCT
1 CTCTCTTT
2698376 CTCTCTGTCT
1 CTCTCT-T-T
*
2698386 CTCTCTCT
1 CTCTCTTT
*
2698394 CTCTGTTT
1 CTCTCTTT
*
2698402 CTTTCTTT
1 CTCTCTTT
2698410 CTCT
1 CTCT
2698414 TTTATTCTCT
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
8 29 0.81
10 7 0.19
ACGTcount: A:0.00, C:0.39, G:0.04, T:0.57
Consensus pattern (8 bp):
CTCTCTTT
Found at i:2698379 original size:16 final size:16
Alignment explanation
Indices: 2698360--2698415 Score: 69
Period size: 16 Copynumber: 3.5 Consensus size: 16
2698350 TCACTTTTCC
2698360 CTCTCTTTCTCTCTCT
1 CTCTCTTTCTCTCTCT
*
2698376 CTCTCTGTCTCTCTCT
1 CTCTCTTTCTCTCTCT
*
2698392 CTCTCTGTT-TCTTTCT
1 CTCTCT-TTCTCTCTCT
*
2698408 TTCTCTTT
1 CTCTCTTT
2698416 TATTCTCTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
15 2 0.06
16 32 0.91
17 1 0.03
ACGTcount: A:0.00, C:0.38, G:0.04, T:0.59
Consensus pattern (16 bp):
CTCTCTTTCTCTCTCT
Found at i:2699163 original size:20 final size:21
Alignment explanation
Indices: 2699131--2699175 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2699121 GACTGAAAAA
2699131 ATTCTAAGTGCTTTT-ATATC
1 ATTCTAAGTGCTTTTCATATC
*
2699151 ATTCTTAAG-GCTTTTCATGTC
1 ATTC-TAAGTGCTTTTCATATC
2699172 ATTC
1 ATTC
2699176 ATGATTGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.22, C:0.18, G:0.11, T:0.49
Consensus pattern (21 bp):
ATTCTAAGTGCTTTTCATATC
Found at i:2701244 original size:29 final size:29
Alignment explanation
Indices: 2701211--2701270 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
2701201 CTCTGTTTGT
2701211 TTTCTTATCTATTTGCTTTATTCCATTGG
1 TTTCTTATCTATTTGCTTTATTCCATTGG
2701240 TTTCTTATCTATTTGCTTTATTCCATTGG
1 TTTCTTATCTATTTGCTTTATTCCATTGG
2701269 TT
1 TT
2701271 AGTCAGTATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.13, C:0.17, G:0.10, T:0.60
Consensus pattern (29 bp):
TTTCTTATCTATTTGCTTTATTCCATTGG
Found at i:2712196 original size:14 final size:14
Alignment explanation
Indices: 2712177--2712203 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2712167 ATGTTGCACC
2712177 TAGTTGAGAAATAA
1 TAGTTGAGAAATAA
2712191 TAGTTGAGAAATA
1 TAGTTGAGAAATA
2712204 TTTTTCTTGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.22, T:0.30
Consensus pattern (14 bp):
TAGTTGAGAAATAA
Found at i:2713373 original size:8 final size:8
Alignment explanation
Indices: 2713357--2713397 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
2713347 GCAATTGCTA
*
2713357 TTTTAATT
1 TTTTTATT
2713365 TTTTTA-T
1 TTTTTATT
2713372 TTTTTA-T
1 TTTTTATT
2713379 TTTTTATT
1 TTTTTATT
*
2713387 TTTTTGTT
1 TTTTTATT
2713395 TTT
1 TTT
2713398 CGTTTTAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 14 0.47
8 16 0.53
ACGTcount: A:0.12, C:0.00, G:0.02, T:0.85
Consensus pattern (8 bp):
TTTTTATT
Found at i:2713397 original size:7 final size:7
Alignment explanation
Indices: 2713364--2713390 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
2713354 CTATTTTAAT
2713364 TTTTTTA
1 TTTTTTA
2713371 TTTTTTA
1 TTTTTTA
2713378 TTTTTTA
1 TTTTTTA
2713385 TTTTTT
1 TTTTTT
2713391 TGTTTTTCGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTA
Found at i:2713445 original size:21 final size:20
Alignment explanation
Indices: 2713421--2713459 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
2713411 ATGAAGCAAC
*
2713421 TCTTGGTGTGTTTGTTTTAGA
1 TCTTGGTGTATTT-TTTTAGA
*
2713442 TCTTTGTGTATTTTTTTA
1 TCTTGGTGTATTTTTTTA
2713460 ATTTGTTCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.10, C:0.05, G:0.21, T:0.64
Consensus pattern (20 bp):
TCTTGGTGTATTTTTTTAGA
Found at i:2717873 original size:22 final size:22
Alignment explanation
Indices: 2717845--2717887 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2717835 GTTGGAGTTC
2717845 GGATAAATGGTCTTCAAAGAAT
1 GGATAAATGGTCTTCAAAGAAT
2717867 GGATAAATGGTCTTCAAAGAA
1 GGATAAATGGTCTTCAAAGAA
2717888 CTCAACATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.26
Consensus pattern (22 bp):
GGATAAATGGTCTTCAAAGAAT
Done.