Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002647.1 Hibiscus syriacus cultivar Beakdansim tig00005406_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: 7027529
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 21 of 26
Found at i:5617157 original size:24 final size:20
Alignment explanation
Indices: 5617102--5617146 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
5617092 CTTCAAGGTA
5617102 AGCTAGGTGAGTGTCTTGGT
1 AGCTAGGTGAGTGTCTTGGT
5617122 AGCTAGGTGAGTGTCTTGGT
1 AGCTAGGTGAGTGTCTTGGT
5617142 AGCTA
1 AGCTA
5617147 ACTAGGTGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.18, C:0.11, G:0.38, T:0.33
Consensus pattern (20 bp):
AGCTAGGTGAGTGTCTTGGT
Found at i:5619900 original size:23 final size:24
Alignment explanation
Indices: 5619858--5619910 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
5619848 CTTTTCTTTC
5619858 TTTCTTCTTTTCGAGTGCTTTCAA
1 TTTCTTCTTTTCGAGTGCTTTCAA
* *
5619882 TTTCTTCTTTT-GAGTGCTTTTAT
1 TTTCTTCTTTTCGAGTGCTTTCAA
5619905 TTTCTT
1 TTTCTT
5619911 TGCTGATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.09, C:0.17, G:0.11, T:0.62
Consensus pattern (24 bp):
TTTCTTCTTTTCGAGTGCTTTCAA
Found at i:5621094 original size:10 final size:12
Alignment explanation
Indices: 5621061--5621099 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
5621051 GGTCTTCTCA
5621061 ACTC-CTCAGCT
1 ACTCTCTCAGCT
5621072 ACTCTCTCAGCT
1 ACTCTCTCAGCT
5621084 ACT-TC-CAGCT
1 ACTCTCTCAGCT
5621094 AC-CTCT
1 ACTCTCT
5621100 AGTCCACTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 9 0.36
11 6 0.24
12 10 0.40
ACGTcount: A:0.18, C:0.44, G:0.08, T:0.31
Consensus pattern (12 bp):
ACTCTCTCAGCT
Found at i:5622541 original size:15 final size:15
Alignment explanation
Indices: 5622529--5622558 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5622519 GCTATTGATG
5622529 GTGTTGATATTGAAA
1 GTGTTGATATTGAAA
*
5622544 GTGTTGATGTTGAAA
1 GTGTTGATATTGAAA
5622559 TAGAGATGGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.30, T:0.40
Consensus pattern (15 bp):
GTGTTGATATTGAAA
Found at i:5633761 original size:19 final size:19
Alignment explanation
Indices: 5633730--5633769 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
5633720 AGGGAATAAT
5633730 AATATAAGTAATGAAATGA
1 AATATAAGTAATGAAATGA
5633749 AATATTAAG-AATGAAATGA
1 AATA-TAAGTAATGAAATGA
5633768 AA
1 AA
5633770 CAAAGAAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.15, T:0.25
Consensus pattern (19 bp):
AATATAAGTAATGAAATGA
Found at i:5634234 original size:19 final size:20
Alignment explanation
Indices: 5634184--5634225 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
5634174 GAAACCCCTT
*
5634184 TGAAAATACATGAGTTTTGA
1 TGAAAATACATGAGTTTTAA
5634204 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGAGTTTTAA
5634223 TGA
1 TGA
5634226 TGATACATGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.43, C:0.05, G:0.17, T:0.36
Consensus pattern (20 bp):
TGAAAATACATGAGTTTTAA
Found at i:5637729 original size:19 final size:19
Alignment explanation
Indices: 5637698--5637739 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
5637688 AGGGAATAAT
5637698 AATATAAGTAATGAAATGA
1 AATATAAGTAATGAAATGA
5637717 AATATTAAG-AATGAAATGA
1 AATA-TAAGTAATGAAATGA
5637736 AATA
1 AATA
5637740 AATAAAGGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.60, C:0.00, G:0.14, T:0.26
Consensus pattern (19 bp):
AATATAAGTAATGAAATGA
Found at i:5638193 original size:19 final size:20
Alignment explanation
Indices: 5638152--5638200 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
5638142 GAAACCCCTT
*
5638152 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
5638172 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
5638191 TGAAGATACA
1 TGAAAATACA
5638201 CGCTCTTGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:5639203 original size:20 final size:19
Alignment explanation
Indices: 5639166--5639204 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
5639156 AAGTAAAGAT
**
5639166 GTGAAAACATATGTTATGC
1 GTGAAAACATATAATATGC
5639185 GTGAAAATCATATAATATGC
1 GTGAAAA-CATATAATATGC
5639205 AAGTGAATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (19 bp):
GTGAAAACATATAATATGC
Found at i:5641673 original size:14 final size:15
Alignment explanation
Indices: 5641639--5641685 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
5641629 AATTTGGAGT
5641639 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
5641654 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
5641668 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
5641685 G
1 G
5641686 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:5645542 original size:36 final size:35
Alignment explanation
Indices: 5645502--5645580 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 35
5645492 ACTATCTATT
* *
5645502 CATCACCACCTTCCATCACCATTTTCACGCCTATAA
1 CATCACCACATTCCATCACCA-TATCACGCCTATAA
* * * *
5645538 CATCACCATATTCCATTACTATATCACGCCTATAT
1 CATCACCACATTCCATCACCATATCACGCCTATAA
*
5645573 TATCACCA
1 CATCACCA
5645581 ACTTATAAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
35 19 0.53
36 17 0.47
ACGTcount: A:0.30, C:0.37, G:0.03, T:0.30
Consensus pattern (35 bp):
CATCACCACATTCCATCACCATATCACGCCTATAA
Found at i:5647285 original size:15 final size:15
Alignment explanation
Indices: 5647250--5647285 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
5647240 ATGAATAATT
*
5647250 AAGAAATGAAATGGA
1 AAGAATTGAAATGGA
5647265 AAGAATTGAAATGGA
1 AAGAATTGAAATGGA
*
5647280 TAGAAT
1 AAGAAT
5647286 AGTTATCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.25, T:0.19
Consensus pattern (15 bp):
AAGAATTGAAATGGA
Found at i:5647818 original size:19 final size:19
Alignment explanation
Indices: 5647767--5647819 Score: 70
Period size: 21 Copynumber: 2.7 Consensus size: 19
5647757 TGAAACCCCT
5647767 TTGAAAATACATGATTTTA
1 TTGAAAATACATGATTTTA
*
5647786 TGATAAAAATACATGATTTTA
1 T--TGAAAATACATGATTTTA
*
5647807 TTGAAGATACATG
1 TTGAAAATACATG
5647820 CTCTTTACCG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 11 0.38
21 18 0.62
ACGTcount: A:0.43, C:0.06, G:0.13, T:0.38
Consensus pattern (19 bp):
TTGAAAATACATGATTTTA
Found at i:5650288 original size:19 final size:21
Alignment explanation
Indices: 5650244--5650296 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
5650234 TGAAACCCCT
5650244 ATGAAAATACATGATTTTTAA
1 ATGAAAATACATGATTTTTAA
5650265 ATGAAAATACATGA-TTTT-A
1 ATGAAAATACATGATTTTTAA
*
5650284 ATGAAGATACATG
1 ATGAAAATACATG
5650297 CTCTTGGCCG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.42
20 4 0.13
21 14 0.45
ACGTcount: A:0.47, C:0.06, G:0.13, T:0.34
Consensus pattern (21 bp):
ATGAAAATACATGATTTTTAA
Found at i:5652505 original size:15 final size:16
Alignment explanation
Indices: 5652454--5652506 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
5652444 AGATAGTGAA
5652454 ATAAGAAAAGATGAAAG
1 ATAAGAAAA-ATGAAAG
*
5652471 AATAA-AGAAATGAAATG
1 -ATAAGAAAAATGAAA-G
5652488 ATAAGAAAAATG-AAG
1 ATAAGAAAAATGAAAG
5652503 ATAA
1 ATAA
5652507 CTTACAACTC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
15 5 0.16
16 12 0.39
17 10 0.32
18 4 0.13
ACGTcount: A:0.66, C:0.00, G:0.19, T:0.15
Consensus pattern (16 bp):
ATAAGAAAAATGAAAG
Found at i:5652646 original size:11 final size:11
Alignment explanation
Indices: 5652630--5652672 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
5652620 TGCAACTTGC
5652630 TTCTTTTCGTT
1 TTCTTTTCGTT
5652641 TTCTTTTCGTT
1 TTCTTTTCGTT
*
5652652 TTC--TTCTTT
1 TTCTTTTCGTT
5652661 TTCTTTTC-TT
1 TTCTTTTCGTT
5652671 TT
1 TT
5652673 GCACTCCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
9 8 0.28
10 4 0.14
11 17 0.59
ACGTcount: A:0.00, C:0.19, G:0.05, T:0.77
Consensus pattern (11 bp):
TTCTTTTCGTT
Found at i:5652667 original size:5 final size:5
Alignment explanation
Indices: 5652630--5652672 Score: 52
Period size: 5 Copynumber: 8.4 Consensus size: 5
5652620 TGCAACTTGC
*
5652630 TTCTT TTCGTT TTCTT TTCGTT TTCTT CT-TT TTCTT TTCTT TT
1 TTCTT TTC-TT TTCTT TTC-TT TTCTT TTCTT TTCTT TTCTT TT
5652673 GCACTCCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
4 3 0.09
5 20 0.61
6 10 0.30
ACGTcount: A:0.00, C:0.19, G:0.05, T:0.77
Consensus pattern (5 bp):
TTCTT
Found at i:5652723 original size:20 final size:21
Alignment explanation
Indices: 5652698--5652741 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
5652688 TGTAGGAATC
*
5652698 TTTTTCTT-TCTCTTTTTGTT
1 TTTTTCTTATCTCTTTTTCTT
*
5652718 TTTTTCTTATTTCTTTTTCTT
1 TTTTTCTTATCTCTTTTTCTT
5652739 TTT
1 TTT
5652742 GTTGCTATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.82
Consensus pattern (21 bp):
TTTTTCTTATCTCTTTTTCTT
Found at i:5653576 original size:19 final size:20
Alignment explanation
Indices: 5653528--5653579 Score: 79
Period size: 21 Copynumber: 2.6 Consensus size: 20
5653518 GAAACCCCTT
5653528 TGAAAATACATGATTTTATGA
1 TGAAAATACATGATTTTA-GA
5653549 TGAAAATACATGATTTTA-A
1 TGAAAATACATGATTTTAGA
*
5653568 TGAAGATACATG
1 TGAAAATACATG
5653580 CTCTTGACTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 12 0.40
21 18 0.60
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTAGA
Found at i:5654326 original size:20 final size:21
Alignment explanation
Indices: 5654288--5654327 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
5654278 GATCATCTAG
* *
5654288 AAGCTAAGATAACATGCATAT
1 AAGCTAAGATAAAAGGCATAT
5654309 AAGCT-AGATAAAAGGCATA
1 AAGCTAAGATAAAAGGCATA
5654328 GGATGTTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.50, C:0.12, G:0.17, T:0.20
Consensus pattern (21 bp):
AAGCTAAGATAAAAGGCATAT
Found at i:5654736 original size:30 final size:30
Alignment explanation
Indices: 5654700--5654759 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
5654690 ATATAAAGTA
5654700 AGGAAGAACTCCCTTAGATTGATCTTGATG
1 AGGAAGAACTCCCTTAGATTGATCTTGATG
5654730 AGGAAGAACTCCCTTAGATTGATCTTGATG
1 AGGAAGAACTCCCTTAGATTGATCTTGATG
5654760 GATCTTCAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (30 bp):
AGGAAGAACTCCCTTAGATTGATCTTGATG
Found at i:5657607 original size:35 final size:36
Alignment explanation
Indices: 5657567--5657634 Score: 120
Period size: 35 Copynumber: 1.9 Consensus size: 36
5657557 ATTTAGAAGT
5657567 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
*
5657602 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGA
5657635 CAGATTGTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 20 0.65
36 11 0.35
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (36 bp):
TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
Found at i:5660218 original size:33 final size:33
Alignment explanation
Indices: 5660139--5660242 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
5660129 ATACAATCTG
* *
5660139 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
5660175 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
5660208 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
5660241 TC
1 TC
5660243 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:5660854 original size:16 final size:15
Alignment explanation
Indices: 5660828--5660879 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
5660818 GAGTTGTAAG
5660828 TTATC-TTCATTTTT
1 TTATCTTTCATTTTT
*
5660842 TTATCATTTCATTTCT
1 TTATC-TTTCATTTTT
5660858 TTATTCTTTCATCTTTT
1 TTA-TCTTTCAT-TTTT
5660875 CTTAT
1 -TTAT
5660880 TTCATTACCA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
14 5 0.16
16 17 0.55
17 6 0.19
18 3 0.10
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATCTTTCATTTTT
Found at i:5666497 original size:16 final size:18
Alignment explanation
Indices: 5666467--5666515 Score: 68
Period size: 17 Copynumber: 2.8 Consensus size: 18
5666457 AAGACAGTGA
5666467 AATAAGAAAATATGAAA-G
1 AATAAGAAAA-ATGAAATG
5666485 AATAA-AAAAATGAAATG
1 AATAAGAAAAATGAAATG
5666502 -ATAAGAAAAATGAA
1 AATAAGAAAAATGAA
5666516 GATAACTTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
16 10 0.34
17 14 0.48
18 5 0.17
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.16
Consensus pattern (18 bp):
AATAAGAAAAATGAAATG
Found at i:5667173 original size:35 final size:36
Alignment explanation
Indices: 5667126--5667193 Score: 120
Period size: 35 Copynumber: 1.9 Consensus size: 36
5667116 ATTTAGAAGT
5667126 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
*
5667161 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGA
5667194 CAGATTGTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 20 0.65
36 11 0.35
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (36 bp):
TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
Found at i:5670447 original size:15 final size:16
Alignment explanation
Indices: 5670396--5670448 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
5670386 AGATAGTGAA
5670396 ATAAGAAAAGATGAAAG
1 ATAAGAAAA-ATGAAAG
*
5670413 AATAA-AGAAATGAAATG
1 -ATAAGAAAAATGAAA-G
5670430 ATAAGAAAAATG-AAG
1 ATAAGAAAAATGAAAG
5670445 ATAA
1 ATAA
5670449 CTTACAACTC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
15 5 0.16
16 12 0.39
17 10 0.32
18 4 0.13
ACGTcount: A:0.66, C:0.00, G:0.19, T:0.15
Consensus pattern (16 bp):
ATAAGAAAAATGAAAG
Found at i:5670667 original size:16 final size:17
Alignment explanation
Indices: 5670646--5670678 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5670636 TGTAGGAGTC
5670646 TTTTCTT-TTTCTTTTT
1 TTTTCTTCTTTCTTTTT
5670662 TTTTCTTCTTTCTTTTT
1 TTTTCTTCTTTCTTTTT
5670679 CTCTTTTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTCTTCTTTCTTTTT
Found at i:5670670 original size:13 final size:13
Alignment explanation
Indices: 5670654--5670686 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
5670644 TCTTTTCTTT
5670654 TTCTTTTTTTTTC
1 TTCTTTTTTTTTC
*
5670667 TTCTTTCTTTTTC
1 TTCTTTTTTTTTC
5670680 -TCTTTTT
1 TTCTTTTT
5670687 GTTGCTTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (13 bp):
TTCTTTTTTTTTC
Found at i:5674385 original size:15 final size:16
Alignment explanation
Indices: 5674334--5674386 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
5674324 AGATAGTGAA
5674334 ATAAGAAAAGATGAAAG
1 ATAAGAAAA-ATGAAAG
*
5674351 AATAA-AGAAATGAAATG
1 -ATAAGAAAAATGAAA-G
5674368 ATAAGAAAAATG-AAG
1 ATAAGAAAAATGAAAG
5674383 ATAA
1 ATAA
5674387 CTTACAACTC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
15 5 0.16
16 12 0.39
17 10 0.32
18 4 0.13
ACGTcount: A:0.66, C:0.00, G:0.19, T:0.15
Consensus pattern (16 bp):
ATAAGAAAAATGAAAG
Found at i:5675039 original size:13 final size:12
Alignment explanation
Indices: 5675020--5675105 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
5675010 ATATAGCCGT
5675020 GATATGGTGATG
1 GATATGGTGATG
5675032 GAATATGGTGAT-
1 G-ATATGGTGATG
*
5675044 GATATAGGCG-T-
1 GATAT-GGTGATG
5675055 GATAATGGTGATG
1 GAT-ATGGTGATG
5675068 GACTATGGTGAT-
1 GA-TATGGTGATG
*
5675080 GATATAGG-CAT-
1 GATAT-GGTGATG
5675091 GATAATGGTGATG
1 GAT-ATGGTGATG
5675104 GA
1 GA
5675106 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.30, C:0.03, G:0.36, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:5675075 original size:36 final size:36
Alignment explanation
Indices: 5675005--5675106 Score: 161
Period size: 36 Copynumber: 2.9 Consensus size: 36
5674995 TAGAAGTTGA
* * *
5675005 TGATAATATAGCCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
5675040 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
*
5675076 TGATGATATAGGCATGATAATGGTGATGGAC
1 TGATGATATAGGCGTGATAATGGTGATGGAC
5675107 AGATTGTATC
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 16 0.26
36 46 0.74
ACGTcount: A:0.30, C:0.06, G:0.33, T:0.30
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGACTATGG
Found at i:5678933 original size:36 final size:36
Alignment explanation
Indices: 5678860--5678964 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
5678850 ATTTAGAAGT
* *
5678860 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
5678895 TGGTGATGATATAGGCGTAATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
5678931 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
5678965 AGATTGTATC
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 19 0.29
36 46 0.71
ACGTcount: A:0.30, C:0.05, G:0.35, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:5682217 original size:15 final size:16
Alignment explanation
Indices: 5682166--5682218 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
5682156 AGATAGTGAA
5682166 ATAAGAAAAGATGAAAG
1 ATAAGAAAA-ATGAAAG
*
5682183 AATAA-AGAAATGAAATG
1 -ATAAGAAAAATGAAA-G
5682200 ATAAGAAAAATG-AAG
1 ATAAGAAAAATGAAAG
5682215 ATAA
1 ATAA
5682219 CTTACAACTC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
15 5 0.16
16 12 0.39
17 10 0.32
18 4 0.13
ACGTcount: A:0.66, C:0.00, G:0.19, T:0.15
Consensus pattern (16 bp):
ATAAGAAAAATGAAAG
Found at i:5682412 original size:30 final size:30
Alignment explanation
Indices: 5682346--5682419 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
5682336 CTTTGCTTCA
**
5682346 CTTTTTCTTTTGCTTTGAATTTTCTTCTTT
1 CTTTTTCTTTTTTTTTGAATTTTCTTCTTT
* *
5682376 -TCTTTTCTTTTTTTTTTATTTTTCTTCTTT
1 CT-TTTTCTTTTTTTTTGAATTTTCTTCTTT
*
5682406 CTTTTTCTCTTTTT
1 CTTTTTCTTTTTTT
5682420 GTTGCTTTTG
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 1 0.03
30 35 0.95
31 1 0.03
ACGTcount: A:0.04, C:0.16, G:0.03, T:0.77
Consensus pattern (30 bp):
CTTTTTCTTTTTTTTTGAATTTTCTTCTTT
Found at i:5682418 original size:7 final size:6
Alignment explanation
Indices: 5682373--5682418 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
5682363 AATTTTCTTC
*
5682373 TTTTC- TTTTCT TTTT-T TTTTAT TTTTCT TCTTTCT TTTTCT CTTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT T-TTTCT TTTTCT -TTTT
5682419 TGTTGCTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
5 10 0.28
6 16 0.44
7 10 0.28
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTCT
Found at i:5682870 original size:36 final size:36
Alignment explanation
Indices: 5682797--5682901 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
5682787 ATTTAGAAGT
* *
5682797 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
5682832 TGGTGATGATATAGGCGTAATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
5682868 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
5682902 AGGTTGTATC
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 19 0.29
36 46 0.71
ACGTcount: A:0.30, C:0.05, G:0.35, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:5685456 original size:22 final size:23
Alignment explanation
Indices: 5685426--5685468 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
5685416 TTTTCTTTGC
*
5685426 TTTTCCTTT-TTTTTAGTGCTGA
1 TTTTCCTTTCTTTTGAGTGCTGA
*
5685448 TTTTTCTTTCTTTTGAGTGCT
1 TTTTCCTTTCTTTTGAGTGCT
5685469 TCACTTTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.07, C:0.14, G:0.14, T:0.65
Consensus pattern (23 bp):
TTTTCCTTTCTTTTGAGTGCTGA
Found at i:5693071 original size:24 final size:21
Alignment explanation
Indices: 5693036--5693078 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
5693026 TGCTCATTCT
*
5693036 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
5693059 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
5693079 ATCTTGTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:5694321 original size:24 final size:24
Alignment explanation
Indices: 5694294--5694348 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
5694284 CCAACTTTTC
5694294 TTTCTTTTTTCTTC-TTTTGAGTG
1 TTTCTTTTTTCTTCTTTTTGAGTG
**
5694317 TTT-TCAATTTCTTCTTTTTGAGTG
1 TTTCT-TTTTTCTTCTTTTTGAGTG
*
5694341 CTTCTTTT
1 TTTCTTTT
5694349 CTGATTTTTC
Statistics
Matches: 24, Mismatches: 5, Indels: 5
0.71 0.15 0.15
Matches are distributed among these distances:
22 1 0.04
23 10 0.42
24 12 0.50
25 1 0.04
ACGTcount: A:0.07, C:0.15, G:0.11, T:0.67
Consensus pattern (24 bp):
TTTCTTTTTTCTTCTTTTTGAGTG
Found at i:5704547 original size:22 final size:23
Alignment explanation
Indices: 5704510--5704562 Score: 90
Period size: 22 Copynumber: 2.3 Consensus size: 23
5704500 ACAATCTGTC
5704510 CATCACCATTATCACGCCTATAT
1 CATCACCATTATCACGCCTATAT
5704533 CATCACCA-TATCACGCCTATAT
1 CATCACCATTATCACGCCTATAT
*
5704555 TATCACCA
1 CATCACCA
5704563 ACTTCTAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 21 0.72
23 8 0.28
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (23 bp):
CATCACCATTATCACGCCTATAT
Found at i:5704728 original size:15 final size:15
Alignment explanation
Indices: 5704704--5704739 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
5704694 TTTGATAACT
*
5704704 ATTCTATCCATTTCA
1 ATTCTTTCCATTTCA
5704719 ATTCTTTCCATTTCA
1 ATTCTTTCCATTTCA
*
5704734 TTTCTT
1 ATTCTT
5704740 AATTACTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.19, C:0.25, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTCTTTCCATTTCA
Found at i:5705666 original size:20 final size:21
Alignment explanation
Indices: 5705622--5705666 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
5705612 GTGATATAAT
*
5705622 TTATTATAGGATGATGAATTA
1 TTATTATAGGATCATGAATTA
*
5705643 -TATTATAGGATCA-GATTTA
1 TTATTATAGGATCATGAATTA
5705662 TTATT
1 TTATT
5705667 TTATTAGGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.36, C:0.02, G:0.16, T:0.47
Consensus pattern (21 bp):
TTATTATAGGATCATGAATTA
Found at i:5716192 original size:24 final size:24
Alignment explanation
Indices: 5716165--5716211 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
5716155 GTGGATCACC
* *
5716165 AAAAGTCACGTTTATTGATTCTTT
1 AAAAGACACGTTTATTGAATCTTT
* *
5716189 AAAAGACATGTTTCTTGAATCTT
1 AAAAGACACGTTTATTGAATCTT
5716212 CAACTTGAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.43
Consensus pattern (24 bp):
AAAAGACACGTTTATTGAATCTTT
Found at i:5717366 original size:5 final size:5
Alignment explanation
Indices: 5717356--5717397 Score: 59
Period size: 5 Copynumber: 8.6 Consensus size: 5
5717346 TTCAACTTTA
* *
5717356 TTTCT TTTCT TTTCT TTTCT TTTCT TTGCT TTT-T CTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
5717398 TGAGTGCTGG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
4 3 0.09
5 29 0.91
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (5 bp):
TTTCT
Found at i:5717436 original size:25 final size:24
Alignment explanation
Indices: 5717386--5717438 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
5717376 TTTCTTTGCT
* **
5717386 TTTTCTTCTTTTTGAGTGCTGGAA
1 TTTTCTTCTTTTAGAGTGCTCAAA
5717410 TTTTCTTCTTTTAGAGTGCTTCAAA
1 TTTTCTTCTTTTAGAGTGC-TCAAA
5717435 TTTT
1 TTTT
5717439 TTTTGTTGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.15, C:0.13, G:0.15, T:0.57
Consensus pattern (24 bp):
TTTTCTTCTTTTAGAGTGCTCAAA
Found at i:5729267 original size:16 final size:16
Alignment explanation
Indices: 5729233--5729281 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
5729223 GTAAGTTATC
* * *
5729233 TTCACTTTCTTACTAT
1 TTCATTTTCTTATTCT
5729249 TTCATTTTCTTATTCT
1 TTCATTTTCTTATTCT
5729265 TTCATCTATTCTTATTC
1 TTCAT-T-TTCTTATTC
5729282 CATTACCTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 18 0.64
17 1 0.04
18 9 0.32
ACGTcount: A:0.16, C:0.22, G:0.00, T:0.61
Consensus pattern (16 bp):
TTCATTTTCTTATTCT
Found at i:5731029 original size:21 final size:20
Alignment explanation
Indices: 5731001--5731043 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
5730991 TTTGATAACA
5731001 TTTCTTTCCATTTCAATTCT
1 TTTCTTTCCATTTCAATTCT
*
5731021 TTTCATTTCCATTTCATTTCT
1 TTTC-TTTCCATTTCAATTCT
5731042 TT
1 TT
5731044 AATTATCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.14, C:0.23, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTCTTTCCATTTCAATTCT
Found at i:5731853 original size:44 final size:44
Alignment explanation
Indices: 5731790--5731877 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
5731780 GGCAAGAAAT
5731790 TCCTTTTGACGCCACTTTCTCCTAGTCAAGTGAATGAAGATCAA
1 TCCTTTTGACGCCACTTTCTCCTAGTCAAGTGAATGAAGATCAA
*
5731834 TCCTTTTGACGTCACTTTCTCCTAGTCAAGTGAATGAAGATCAA
1 TCCTTTTGACGCCACTTTCTCCTAGTCAAGTGAATGAAGATCAA
5731878 ACTCATTTGA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (44 bp):
TCCTTTTGACGCCACTTTCTCCTAGTCAAGTGAATGAAGATCAA
Found at i:5738752 original size:17 final size:17
Alignment explanation
Indices: 5738707--5738755 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
5738697 ACAAAGTGCT
*
5738707 ACAATAAAAA-AAAACA
1 ACAAGAAAAAGAAAACA
5738723 ACAAGAAAGAAGAAAACA
1 ACAAGAAA-AAGAAAACA
5738741 A-AAGAGAAAAGAAAA
1 ACAAGA-AAAAGAAAA
5738756 AGACTCCTAC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 7 0.24
17 13 0.45
18 9 0.31
ACGTcount: A:0.78, C:0.08, G:0.12, T:0.02
Consensus pattern (17 bp):
ACAAGAAAAAGAAAACA
Found at i:5738814 original size:14 final size:15
Alignment explanation
Indices: 5738780--5738826 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
5738770 AATTTGGAGT
5738780 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
5738795 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
5738809 TCAAAAGCAATAGAAAA
1 GCAAAAG-AA-AGAAAA
5738826 G
1 G
5738827 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
16 1 0.04
17 6 0.24
ACGTcount: A:0.70, C:0.06, G:0.19, T:0.04
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:5744435 original size:17 final size:18
Alignment explanation
Indices: 5744400--5744438 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
5744390 CTACAACAAA
5744400 AAAACAACAAGAAAGAAG
1 AAAACAACAAGAAAGAAG
5744418 AAAACAA-AAGAGAA-AAG
1 AAAACAACAAGA-AAGAAG
5744435 AAAA
1 AAAA
5744439 AGACTCCTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.77, C:0.08, G:0.15, T:0.00
Consensus pattern (18 bp):
AAAACAACAAGAAAGAAG
Found at i:5744488 original size:14 final size:16
Alignment explanation
Indices: 5744465--5744509 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
5744455 TTTGGAGTGC
5744465 AAAAGAAAGAAAAG-A
1 AAAAGAAAGAAAAGCA
5744480 AAAAG-AAGAAAAGCA
1 AAAAGAAAGAAAAGCA
*
5744495 AAATAAAAAGAAAAG
1 AAA-AGAAAGAAAAG
5744510 TGAAGCAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 8 0.31
15 9 0.35
16 1 0.04
17 8 0.31
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (16 bp):
AAAAGAAAGAAAAGCA
Found at i:5751381 original size:11 final size:11
Alignment explanation
Indices: 5751365--5751389 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5751355 TTTTTCTTCT
5751365 TTCACTTGCAC
1 TTCACTTGCAC
5751376 TTCACTTGCAC
1 TTCACTTGCAC
5751387 TTC
1 TTC
5751390 TTTTTGGTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.36, G:0.08, T:0.40
Consensus pattern (11 bp):
TTCACTTGCAC
Found at i:5759376 original size:28 final size:28
Alignment explanation
Indices: 5759344--5759399 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
5759334 CGTGAATTAA
*
5759344 CAAAACAAATGATGAACATACTGTTATG
1 CAAAACAAATAATGAACATACTGTTATG
*
5759372 CAAAACAAATAATGAACATGCTGTTATG
1 CAAAACAAATAATGAACATACTGTTATG
5759400 TGAATGTGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.25
Consensus pattern (28 bp):
CAAAACAAATAATGAACATACTGTTATG
Found at i:5768591 original size:22 final size:22
Alignment explanation
Indices: 5768563--5768617 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
5768553 ATCGAAGAGG
*
5768563 AGTATCGATACCAAAGTATAGT
1 AGTATCGATACCAAAGTATAGA
* *
5768585 AGTATCGGTACCATAGTATAGA
1 AGTATCGATACCAAAGTATAGA
*
5768607 AGTATCAATAC
1 AGTATCGATAC
5768618 TAATGAGTCT
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:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (22 bp):
AGTATCGATACCAAAGTATAGA
Found at i:5769072 original size:46 final size:46
Alignment explanation
Indices: 5769019--5769201 Score: 260
Period size: 46 Copynumber: 4.0 Consensus size: 46
5769009 TAAAATGAAT
* *
5769019 CCATAAATGATATGT-ATGAAAGGATGTATTAAGGCATGAAAGGATG
1 CCATAAATGAAAT-TCATGAAAGGATGCATTAAGGCATGAAAGGATG
* *
5769065 CCATAAATGAAATTCATGAAAGAATGCATTAATGCATGAAAGGATG
1 CCATAAATGAAATTCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * * * *
5769111 CCATAAATAAAATGCATGAAATGATGCATTAAGTCATGAAATGATG
1 CCATAAATGAAATTCATGAAAGGATGCATTAAGGCATGAAAGGATG
*
5769157 ACATAAATGAAATTCATGAAAGGATGCATTAAGGCATGAAAGGAT
1 CCATAAATGAAATTCATGAAAGGATGCATTAAGGCATGAAAGGAT
5769202 TCATTAAGGC
Statistics
Matches: 119, Mismatches: 17, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
45 1 0.01
46 118 0.99
ACGTcount: A:0.45, C:0.09, G:0.21, T:0.25
Consensus pattern (46 bp):
CCATAAATGAAATTCATGAAAGGATGCATTAAGGCATGAAAGGATG
Found at i:5769082 original size:26 final size:25
Alignment explanation
Indices: 5769052--5769261 Score: 118
Period size: 26 Copynumber: 9.0 Consensus size: 25
5769042 ATGTATTAAG
5769052 GCATGAAAGGATGCCATAAATGAAAT
1 GCATGAAAGGATGCCATAAAT-AAAT
* *
5769078 TCATGAAAGAATG-CAT---T-AAT
1 GCATGAAAGGATGCCATAAATAAAT
5769098 GCATGAAAGGATGCCATAAATAAAAT
1 GCATGAAAGGATGCCATAAAT-AAAT
* *
5769124 GCATGAAATGATG-CAT---TAAGT
1 GCATGAAAGGATGCCATAAATAAAT
* *
5769145 -CATGAAATGATGACATAAATGAAAT
1 GCATGAAAGGATGCCATAAAT-AAAT
* *
5769170 TCATGAAAGGATG-CAT---T-AAG
1 GCATGAAAGGATGCCATAAATAAAT
* *
5769190 GCATGAAAGGAT-TCAT---T-AAG
1 GCATGAAAGGATGCCATAAATAAAT
**
5769210 GCATGAAAGGATGTTATAAATGAAAT
1 GCATGAAAGGATGCCATAAAT-AAAT
*
5769236 GCATGAAAGGATGGCATAAATGAAAT
1 GCATGAAAGGATGCCATAAAT-AAAT
5769262 TAATGAATAA
Statistics
Matches: 151, Mismatches: 14, Indels: 38
0.74 0.07 0.19
Matches are distributed among these distances:
20 58 0.38
21 12 0.08
22 3 0.02
24 3 0.02
25 12 0.08
26 63 0.42
ACGTcount: A:0.45, C:0.09, G:0.22, T:0.24
Consensus pattern (25 bp):
GCATGAAAGGATGCCATAAATAAAT
Found at i:5769104 original size:20 final size:20
Alignment explanation
Indices: 5769034--5769222 Score: 110
Period size: 20 Copynumber: 8.6 Consensus size: 20
5769024 AATGATATGT
* *
5769034 ATGAAAGGATGTATTAAGGC
1 ATGAAAGGATGCATTAATGC
*
5769054 ATGAAAGGATGCCATAAATGAAATTC
1 ATGAAAGGATG-CAT---T--AATGC
*
5769080 ATGAAAGAATGCATTAATGC
1 ATGAAAGGATGCATTAATGC
5769100 ATGAAAGGATGCCATAAATAAAATGC
1 ATGAAAGGATG-CAT---T--AATGC
*
5769126 ATGAAATGATGCATTAA-GTC
1 ATGAAAGGATGCATTAATG-C
* *
5769146 ATGAAATGATGACATAAATGAAATTC
1 ATGAAAGGATG-CAT---T--AATGC
*
5769172 ATGAAAGGATGCATTAAGGC
1 ATGAAAGGATGCATTAATGC
* *
5769192 ATGAAAGGATTCATTAAGGC
1 ATGAAAGGATGCATTAATGC
5769212 ATGAAAGGATG
1 ATGAAAGGATG
5769223 TTATAAATGA
Statistics
Matches: 136, Mismatches: 13, Indels: 40
0.72 0.07 0.21
Matches are distributed among these distances:
19 1 0.01
20 71 0.52
21 8 0.06
22 3 0.02
24 3 0.02
25 9 0.07
26 41 0.30
ACGTcount: A:0.44, C:0.09, G:0.23, T:0.24
Consensus pattern (20 bp):
ATGAAAGGATGCATTAATGC
Found at i:5769197 original size:66 final size:66
Alignment explanation
Indices: 5769020--5769248 Score: 191
Period size: 66 Copynumber: 3.4 Consensus size: 66
5769010 AAAATGAATC
* * * **
5769020 CATAAATGATATGTATGAAAGGATGTATTAAGGCATGAAAGGATGCCA-TAA---ATGAAATTCA
1 CATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG-CATTAAGGCATGAAA-GGA
5769081 TGA
64 TGA
* * *
5769084 -A-AGAATGCATTAATGCATGAAAGGATGCCATAAATAAAATGCATGAAATGATGCATTAAGTCA
1 CATA-AATG-A--AATGCATGAAAGGATG-CAT---T--AAGGCATGAAAGGATGCATTAAGGCA
*
5769147 TGAAATGATGA
56 TGAAAGGATGA
* *
5769158 CATAAATGAAATTCATGAAAGGATGCATTAAGGCATGAAAGGATTCATTAAGGCATGAAAGGATG
1 CATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCATTAAGGCATGAAAGGATG
*
5769223 T
66 A
*
5769224 TATAAATGAAATGCATGAAAGGATG
1 CATAAATGAAATGCATGAAAGGATG
5769249 GCATAAATGA
Statistics
Matches: 134, Mismatches: 15, Indels: 30
0.75 0.08 0.17
Matches are distributed among these distances:
62 1 0.01
63 5 0.04
64 1 0.01
66 68 0.51
67 2 0.01
68 1 0.01
70 1 0.01
71 5 0.04
72 32 0.24
74 6 0.04
75 11 0.08
76 1 0.01
ACGTcount: A:0.45, C:0.08, G:0.22, T:0.25
Consensus pattern (66 bp):
CATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCATTAAGGCATGAAAGGATG
A
Found at i:5769241 original size:92 final size:90
Alignment explanation
Indices: 5769034--5769268 Score: 246
Period size: 92 Copynumber: 2.6 Consensus size: 90
5769024 AATGATATGT
* * * *
5769034 ATGAAAGGATGTATT-AAGGCATGAAAGGATGCCATAAATGAAATTCATGAAAGAATGCATTAAT
1 ATGAAAGGATGCATTAAATGCATGAAAGGATGACATAAATGAAATTCATGAAAGAATGCATTAAG
*
5769098 GCATGAAAGGATGCCATAAATAAAATGC
66 GCATGAAAGGATGCCAT--AT-AAAGGC
* * * *
5769126 ATGAAATGATGCATTAAGT-CATGAAATGATGACATAAATGAAATTCATGAAAGGATGCATTAAG
1 ATGAAAGGATGCATTAAATGCATGAAAGGATGACATAAATGAAATTCATGAAAGAATGCATTAAG
*
5769190 GCATGAAAGGAT-TCAT-T-AAGGC
66 GCATGAAAGGATGCCATATAAAGGC
* * *
5769212 ATGAAAGGATGTTATAAATGAAATGCATGAAAGGATGGCATAAATGAAATTAATGAA
1 ATGAAAGGATG-CAT---T-AAATGCATGAAAGGATGACATAAATGAAATTCATGAA
5769269 TAATTACTAA
Statistics
Matches: 120, Mismatches: 16, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
86 14 0.12
87 2 0.02
88 1 0.01
90 1 0.01
91 6 0.05
92 95 0.79
93 1 0.01
ACGTcount: A:0.46, C:0.08, G:0.22, T:0.24
Consensus pattern (90 bp):
ATGAAAGGATGCATTAAATGCATGAAAGGATGACATAAATGAAATTCATGAAAGAATGCATTAAG
GCATGAAAGGATGCCATATAAAGGC
Found at i:5769267 original size:26 final size:26
Alignment explanation
Indices: 5769212--5769268 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
5769202 TCATTAAGGC
** *
5769212 ATGAAAGGATGTTATAAATGAAATGC
1 ATGAAAGGATGGCATAAATGAAATGA
*
5769238 ATGAAAGGATGGCATAAATGAAATTA
1 ATGAAAGGATGGCATAAATGAAATGA
5769264 ATGAA
1 ATGAA
5769269 TAATTACTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.49, C:0.04, G:0.23, T:0.25
Consensus pattern (26 bp):
ATGAAAGGATGGCATAAATGAAATGA
Found at i:5775652 original size:20 final size:20
Alignment explanation
Indices: 5775627--5775889 Score: 112
Period size: 20 Copynumber: 11.9 Consensus size: 20
5775617 TAAATGAAAT
*
5775627 GCATGAAATGATGCAATAAG
1 GCATGAAAGGATGCAATAAG
* *
5775647 GCATGAAATGATGCCATAAATGAAAT
1 GCATGAAAGGATG-C---AAT--AAG
* * *
5775673 GCATGAAAGAATACACTAAG
1 GCATGAAAGGATGCAATAAG
*
5775693 GCATGAAAGGATGCCATAAATGAACA
1 GCATGAAAGGATG-C---AAT-AA-G
* *
5775719 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCAATAAG
* * *
5775739 GCATGAAAGGATGTATTAAT
1 GCATGAAAGGATGCAATAAG
*
5775759 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCAATAAG
* * *
5775779 GTATGAAAAGATGCCATAAATGAAAT
1 GCATGAAAGGATG-C---AAT--AAG
* *
5775805 GTATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCAATAAG
*
5775825 GCATGAAAGGATGCCAAAAATGAAAT
1 GCATGAAAGGATG-C---AAT--AAG
*
5775851 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCAATAAG
* *
5775871 TCATGAAAGGATGCCATAA
1 GCATGAAAGGATGCAATAA
5775890 ATGAAATGCA
Statistics
Matches: 186, Mismatches: 33, Indels: 48
0.70 0.12 0.18
Matches are distributed among these distances:
20 104 0.56
21 6 0.03
22 8 0.04
24 9 0.05
25 6 0.03
26 53 0.28
ACGTcount: A:0.44, C:0.11, G:0.24, T:0.21
Consensus pattern (20 bp):
GCATGAAAGGATGCAATAAG
Found at i:5775668 original size:46 final size:46
Alignment explanation
Indices: 5775615--5776035 Score: 568
Period size: 46 Copynumber: 9.3 Consensus size: 46
5775605 AAAACAAATA
* * *
5775615 CATAAATGAAATGCATGAAATGATGCAATAAGGCATGAAATGATGC
1 CATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* * *
5775661 CATAAATGAAATGCATGAAAGAATACACTAAGGCATGAAAGGATGC
1 CATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
*
5775707 CATAAATGAACA-GCATGAAATGATGCATTAAGGCATGAAAGGATG-
1 CATAAATGAA-ATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* * *
5775752 --T--AT-TAATGCATGAAAGGATGCATTAAGGTATGAAAAGATGC
1 CATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
*
5775793 CATAAATGAAATGTATGAAAGGATGCATTAAGGCATGAAAGGATGC
1 CATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* *
5775839 CAAAAATGAAATGCATGAAAGGATGCATTAAGTCATGAAAGGATGC
1 CATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* * * *
5775885 CATAAATGAAATGCATGAAAAGAGGCATTAAGGCATGAAAGAATGT
1 CATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* * *
5775931 CATAAATGAAATGCACGAAAAGAGGCATTAAGGCATGAAAGGATGC
1 CATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* *
5775977 CATAAATGAAATGCATGAAATGATGCATTAAAGGCATGAAAGGATGG
1 CATAAATGAAATGCATGAAAGGATGCATT-AAGGCATGAAAGGATGC
*
5776024 CATAAAAGAAAT
1 CATAAATGAAAT
5776036 TAATGAATAA
Statistics
Matches: 332, Mismatches: 34, Indels: 17
0.87 0.09 0.04
Matches are distributed among these distances:
39 1 0.00
40 31 0.09
41 2 0.01
43 2 0.01
45 2 0.01
46 266 0.80
47 28 0.08
ACGTcount: A:0.46, C:0.10, G:0.24, T:0.20
Consensus pattern (46 bp):
CATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
Found at i:5775808 original size:26 final size:26
Alignment explanation
Indices: 5775781--5776035 Score: 145
Period size: 26 Copynumber: 10.9 Consensus size: 26
5775771 GCATTAAGGT
* *
5775781 ATGAAAAGATGCCATAAATGAAATGT
1 ATGAAAGGATGCCATAAATGAAATGC
*
5775807 ATGAAAGGATG-CAT---T--AAGGC
1 ATGAAAGGATGCCATAAATGAAATGC
*
5775827 ATGAAAGGATGCCAAAAATGAAATGC
1 ATGAAAGGATGCCATAAATGAAATGC
*
5775853 ATGAAAGGATG-CAT---T-AAGT-C
1 ATGAAAGGATGCCATAAATGAAATGC
5775873 ATGAAAGGATGCCATAAATGAAATGC
1 ATGAAAGGATGCCATAAATGAAATGC
* * *
5775899 ATGAAAAGA-GGCAT---T--AAGGC
1 ATGAAAGGATGCCATAAATGAAATGC
* *
5775919 ATGAAAGAATGTCATAAATGAAATGC
1 ATGAAAGGATGCCATAAATGAAATGC
* * * *
5775945 ACGAAAAGA-GGCAT---T--AAGGC
1 ATGAAAGGATGCCATAAATGAAATGC
5775965 ATGAAAGGATGCCATAAATGAAATGC
1 ATGAAAGGATGCCATAAATGAAATGC
* *
5775991 ATGAAATGATG-CAT---T-AAAGGC
1 ATGAAAGGATGCCATAAATGAAATGC
* *
5776012 ATGAAAGGATGGCATAAAAGAAAT
1 ATGAAAGGATGCCATAAATGAAAT
5776036 TAATGAATAA
Statistics
Matches: 171, Mismatches: 29, Indels: 58
0.66 0.11 0.22
Matches are distributed among these distances:
20 48 0.28
21 31 0.18
22 8 0.05
24 4 0.02
25 19 0.11
26 61 0.36
ACGTcount: A:0.47, C:0.10, G:0.24, T:0.19
Consensus pattern (26 bp):
ATGAAAGGATGCCATAAATGAAATGC
Found at i:5775915 original size:178 final size:181
Alignment explanation
Indices: 5775615--5776035 Score: 591
Period size: 178 Copynumber: 2.3 Consensus size: 181
5775605 AAAACAAATA
* * *
5775615 CATAAATGAAATGCATGAAATGATGCAATAAGGCATGAAATGATGCCATAAATGAAATGCATGAA
1 CATAAATGAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCAAAAATGAAATGCATGAA
* *
5775680 AGAATACACTAAGGCATGAAAGGATGCCATAAATGAACAGCATGAAATGATGCATTAAGGCATGA
66 AGAATACACTAAGGCATGAAAGGATGCCATAAATGAACAGCATGAAAAGAGGCATTAAGGCATGA
* * * * *
5775745 AAGGATGT-AT-T-AATGCATGAAAGGATGCATTAAGGTATGAAAAGATGC
131 AAGAATGTCATATAAATGCACGAAAAGAGGCATTAAGGCATGAAAAGATGC
* *
5775793 CATAAATGAAATGTATGAAAGGATGCATTAAGGCATGAAAGGATGCCAAAAATGAAATGCATGAA
1 CATAAATGAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCAAAAATGAAATGCATGAA
* * * *
5775858 AGGATGCATTAAGTCATGAAAGGATGCCATAAATGAA-ATGCATGAAAAGAGGCATTAAGGCATG
66 AGAATACACTAAGGCATGAAAGGATGCCATAAATGAACA-GCATGAAAAGAGGCATTAAGGCATG
*
5775922 AAAGAATGTCATAAATGAAATGCACGAAAAGAGGCATTAAGGCATGAAAGGATGC
130 AAAGAATGTCAT--AT-AAATGCACGAAAAGAGGCATTAAGGCATGAAAAGATGC
*
5775977 CATAAATGAAATGCATGAAATGATGCATTAAAGGCATGAAAGGATGGCATAAAA-GAAAT
1 CATAAATGAAATGCATGAAATGATGCATT-AAGGCATGAAAGGATGCCA-AAAATGAAAT
5776036 TAATGAATAA
Statistics
Matches: 214, Mismatches: 20, Indels: 11
0.87 0.08 0.04
Matches are distributed among these distances:
177 1 0.00
178 124 0.58
179 2 0.01
182 1 0.00
184 59 0.28
185 23 0.11
186 4 0.02
ACGTcount: A:0.46, C:0.10, G:0.24, T:0.20
Consensus pattern (181 bp):
CATAAATGAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCAAAAATGAAATGCATGAA
AGAATACACTAAGGCATGAAAGGATGCCATAAATGAACAGCATGAAAAGAGGCATTAAGGCATGA
AAGAATGTCATATAAATGCACGAAAAGAGGCATTAAGGCATGAAAAGATGC
Found at i:5779856 original size:20 final size:20
Alignment explanation
Indices: 5779817--5779865 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
5779807 TGATTGTCTA
*
5779817 AGATGTCATATAGGATCATAT
1 AGATG-CATATAGGAGCATAT
*
5779838 AGATGCATTTAGGAGCATAT
1 AGATGCATATAGGAGCATAT
*
5779858 AGTTGCAT
1 AGATGCAT
5779866 GTTGTGGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 20 0.80
21 5 0.20
ACGTcount: A:0.35, C:0.10, G:0.22, T:0.33
Consensus pattern (20 bp):
AGATGCATATAGGAGCATAT
Found at i:5782628 original size:18 final size:18
Alignment explanation
Indices: 5782605--5782648 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
5782595 ATCTGAATTT
*
5782605 TCGGATCGAATCAACATA
1 TCGGATCGAATCAACAGA
5782623 TCGGATCGAATCAACAGA
1 TCGGATCGAATCAACAGA
*
5782641 TTGGATCG
1 TCGGATCG
5782649 GTCGGATCGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (18 bp):
TCGGATCGAATCAACAGA
Found at i:5801282 original size:60 final size:59
Alignment explanation
Indices: 5801187--5801319 Score: 144
Period size: 60 Copynumber: 2.2 Consensus size: 59
5801177 GGGACCAATT
* * * * * *
5801187 AATAAAGAGTCATAGTTTGGGGTGAAATTGAAATATTCAA-AAGTTT-GAGGATTAATTTAT
1 AATAAA-AGTCATAGTTTAGGATGAAAATAAAATATT-AAGAAGTTTAGA-GATCAATTTAA
* *
5801247 AATGATAGTCATAGTTTAAGGATGAAAATAAAATATTAAGAAGTTTAGAGATCAATTTAA
1 AATAAAAGTCATAGTTT-AGGATGAAAATAAAATATTAAGAAGTTTAGAGATCAATTTAA
5801307 AATAAAAGTCATA
1 AATAAAAGTCATA
5801320 ACTTGAGGAT
Statistics
Matches: 60, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
59 13 0.22
60 45 0.75
61 2 0.03
ACGTcount: A:0.46, C:0.04, G:0.18, T:0.32
Consensus pattern (59 bp):
AATAAAAGTCATAGTTTAGGATGAAAATAAAATATTAAGAAGTTTAGAGATCAATTTAA
Found at i:5802036 original size:22 final size:22
Alignment explanation
Indices: 5802009--5802083 Score: 150
Period size: 22 Copynumber: 3.4 Consensus size: 22
5801999 ACAACATCAT
5802009 TTTAATTTTGATTAATGTTAAA
1 TTTAATTTTGATTAATGTTAAA
5802031 TTTAATTTTGATTAATGTTAAA
1 TTTAATTTTGATTAATGTTAAA
5802053 TTTAATTTTGATTAATGTTAAA
1 TTTAATTTTGATTAATGTTAAA
5802075 TTTAATTTT
1 TTTAATTTT
5802084 AATTTTAAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (22 bp):
TTTAATTTTGATTAATGTTAAA
Found at i:5802516 original size:24 final size:24
Alignment explanation
Indices: 5802489--5802535 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
5802479 ATTTAGTTAA
*
5802489 TTAACGGTTTTCATTCAATAAAAT
1 TTAACGGTTTTCATCCAATAAAAT
*
5802513 TTAACGGTTTTTATCCAATAAAA
1 TTAACGGTTTTCATCCAATAAAA
5802536 CTTACTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (24 bp):
TTAACGGTTTTCATCCAATAAAAT
Found at i:5803313 original size:24 final size:23
Alignment explanation
Indices: 5803281--5803358 Score: 68
Period size: 24 Copynumber: 3.3 Consensus size: 23
5803271 GACTATGTTC
5803281 GTGTTCGTTTGTTTATTTTTAAAT
1 GTGTTCGTTT-TTTATTTTTAAAT
**
5803305 GTGTTCGTTTAAT-TTTTTAATAT
1 GTGTTCGTTTTTTATTTTTAA-AT
* * *
5803328 CATGTTCGTTAATTTATTTTTGAAT
1 -GTGTTCGTT-TTTTATTTTTAAAT
5803353 GTGTTC
1 GTGTTC
5803359 TTGTTCATTC
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
22 7 0.17
23 3 0.07
24 23 0.55
25 3 0.07
26 6 0.14
ACGTcount: A:0.19, C:0.06, G:0.15, T:0.59
Consensus pattern (23 bp):
GTGTTCGTTTTTTATTTTTAAAT
Found at i:5803396 original size:23 final size:23
Alignment explanation
Indices: 5803370--5803420 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
5803360 TGTTCATTCA
*
5803370 TTTAACATTCATGAACGTGTTCG
1 TTTAACATTCATGAACATGTTCG
**
5803393 TTTAATGTTCATGAACATGTTCG
1 TTTAACATTCATGAACATGTTCG
5803416 TTTAA
1 TTTAA
5803421 TGTTTGCGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.43
Consensus pattern (23 bp):
TTTAACATTCATGAACATGTTCG
Found at i:5803421 original size:23 final size:23
Alignment explanation
Indices: 5803377--5803424 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
5803367 TCATTTAACA
*
5803377 TTCATGAACGTGTTCGTTTAATG
1 TTCATGAACATGTTCGTTTAATG
5803400 TTCATGAACATGTTCGTTTAATG
1 TTCATGAACATGTTCGTTTAATG
5803423 TT
1 TT
5803425 TGCGAACATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.46
Consensus pattern (23 bp):
TTCATGAACATGTTCGTTTAATG
Found at i:5803431 original size:23 final size:23
Alignment explanation
Indices: 5803377--5803442 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 23
5803367 TCATTTAACA
* *
5803377 TTCATGAACGTGTTCGTTTAATG
1 TTCACGAACATGTTCGTTTAATG
*
5803400 TTCATGAACATGTTCGTTTAATG
1 TTCACGAACATGTTCGTTTAATG
** * *
5803423 TTTGCGAACATATTCATTTA
1 TTCACGAACATGTTCGTTTA
5803443 GTATTCATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.44
Consensus pattern (23 bp):
TTCACGAACATGTTCGTTTAATG
Found at i:5806866 original size:23 final size:23
Alignment explanation
Indices: 5806814--5806859 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
5806804 CACCGAAAAA
*
5806814 CTAAGAAGGAAATAAAATATTTT
1 CTAAGAAGGAAAGAAAATATTTT
*
5806837 CTAAGAAGGAGAGAAAATATTTT
1 CTAAGAAGGAAAGAAAATATTTT
5806860 TCAAGAAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.50, C:0.04, G:0.17, T:0.28
Consensus pattern (23 bp):
CTAAGAAGGAAAGAAAATATTTT
Found at i:5806872 original size:24 final size:23
Alignment explanation
Indices: 5806827--5806873 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
5806817 AGAAGGAAAT
*
5806827 AAAATATTTTCTAAGAAGGAGAG
1 AAAATATTTTCTAAGAAAGAGAG
5806850 AAAATATTTT-TCAAGAAA-AGAG
1 AAAATATTTTCT-AAGAAAGAGAG
5806872 AA
1 AA
5806874 GTTCTTGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.53, C:0.04, G:0.17, T:0.26
Consensus pattern (23 bp):
AAAATATTTTCTAAGAAAGAGAG
Found at i:5809409 original size:116 final size:116
Alignment explanation
Indices: 5809194--5809826 Score: 893
Period size: 116 Copynumber: 5.4 Consensus size: 116
5809184 TCCCATATGA
* * *
5809194 AAATTCATACACTTAGTATGAATCTCTTAACCATTTT-CACCCAAAGTGTCCAATACGGAAATTC
1 AAATTCATACACTTAGTATGAATTTCTTAA-CATTTTGCACACGAAGTG-CCAATACGGAAATTC
* * *
5809258 ATACACTTAGTATGAATCTCTTAACCA--TTTGCACACAAAGTGCCCAATACAG
64 ATACACTTAGTATGAATTTCTTAA-CATTTTTGCACACGAAGTGCCCAATACGG
* * *
5809310 AAATTTATACACTTAGTATGAATTTCTTAAC-TTTTGCACACGAACTGGCCAATACGAAAATTCA
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTGCACACGAAGT-GCCAATACGGAAATTCA
*
5809374 TACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACAG
65 TACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACGG
* *
5809426 AAATTCACACGCTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCTAATACGGAAATTC
1 AAATTCATACACTTAGTATGAATTTCTTAACA-TTTTGCACACGAAGTGCC-AATACGGAAATTC
*
5809491 ATACACTTAGTATGAATTTCTTAAC--TTTTGCACAGGAAGTGCCCAATACGG
64 ATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACGG
*
5809542 AAATTCATACACTTAGTATGAATCTCTTAACATTTTTGCACACGAAGTGCTCAATACGGAAATTC
1 AAATTCATACACTTAGTATGAATTTCTTAACA-TTTTGCACACGAAGTGC-CAATACGGAAATTC
*
5809607 ATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGTCCAATACGG
64 ATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACGG
* * **
5809660 AAATTCATACACTTAGTATGAATTTCTTAA-ATTTTACATACGAAGTGCCAAATACATAAATTCA
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTGCACACGAAGTGCC-AATACGGAAATTCA
* *
5809724 TACACGTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCTCAATACGG
65 TACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACGG
* * * * **
5809776 AAACTCATGCACTTAGTATTAATTTCTTAACATTTTTCACACTTAGTGCCA
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTGCACACGAAGTGCCA
5809827 TTTAGTAATC
Statistics
Matches: 470, Mismatches: 35, Indels: 24
0.89 0.07 0.05
Matches are distributed among these distances:
114 6 0.01
115 46 0.10
116 294 0.63
117 20 0.04
118 104 0.22
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (116 bp):
AAATTCATACACTTAGTATGAATTTCTTAACATTTTGCACACGAAGTGCCAATACGGAAATTCAT
ACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACGG
Found at i:5809430 original size:59 final size:59
Alignment explanation
Indices: 5809194--5809817 Score: 892
Period size: 59 Copynumber: 10.7 Consensus size: 59
5809184 TCCCATATGA
* * * *
5809194 AAATTCATACACTTAGTATGAATCTCTTAACCA-TTTT-CACCCAAAGTGTCCAATACGG
1 AAATTCATACACTTAGTATGAATTTCTTAA-CATTTTTGCACACGAAGTGCCCAATACGG
* * *
5809252 AAATTCATACACTTAGTATGAATCTCTTAACCA--TTTGCACACAAAGTGCCCAATACAG
1 AAATTCATACACTTAGTATGAATTTCTTAA-CATTTTTGCACACGAAGTGCCCAATACGG
* * * *
5809310 AAATTTATACACTTAGTATGAATTTCTTAAC--TTTTGCACACGAACTGGCCAATACGA
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACGG
*
5809367 AAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACAG
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACGG
* * *
5809426 AAATTCACACGCTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCTAATACGG
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACGG
*
5809485 AAATTCATACACTTAGTATGAATTTCTTAAC--TTTTGCACAGGAAGTGCCCAATACGG
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACGG
* *
5809542 AAATTCATACACTTAGTATGAATCTCTTAACATTTTTGCACACGAAGTGCTCAATACGG
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACGG
*
5809601 AAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGTCCAATACGG
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACGG
* * * **
5809660 AAATTCATACACTTAGTATGAATTTCTTAA-A-TTTTACATACGAAGTGCCAAATACAT
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACGG
* *
5809717 AAATTCATACACGTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCTCAATACGG
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACGG
* * *
5809776 AAACTCATGCACTTAGTATTAATTTCTTAACATTTTT-CACAC
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACAC
5809818 TTAGTGCCAT
Statistics
Matches: 512, Mismatches: 46, Indels: 16
0.89 0.08 0.03
Matches are distributed among these distances:
57 157 0.31
58 86 0.17
59 269 0.53
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (59 bp):
AAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACGG
Found at i:5809508 original size:175 final size:174
Alignment explanation
Indices: 5809192--5809826 Score: 915
Period size: 175 Copynumber: 3.6 Consensus size: 174
5809182 TTTCCCATAT
* * *
5809192 GAAAATTCATACACTTAGTATGAATCTCTTAACCA-TTTT-CACCCAAAGTGTCCAATACGGAAA
1 GAAAATTCATACACTTAGTATGAATCTCTTAA-CATTTTTGCACACGAAGTGCCCAATACGGAAA
* * * *
5809255 TTCATACACTTAGTATGAATCTCTTAACCA--TTTGCACACAAAGTGCCCAATACAGAAATTTAT
65 TTCATACACTTAGTATGAATTTCTTAA-CATTTTTGCACACGAAGTG-CCAATACGGAAATTCAT
*
5809318 ACACTTAGTATGAATTTCTTAACTTTTGCACACGAACTGGCCAATAC
128 ACACTTAGTATGAATTTCTTAACTTTTGCACACGAAGTGGCCAATAC
* *
5809365 GAAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACAGAAAT
1 GAAAATTCATACACTTAGTATGAATCTCTTAACATTTTTGCACACGAAGTGCCCAATACGGAAAT
* *
5809430 TCACACGCTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCTAATACGGAAATTCATAC
66 TCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCC-AATACGGAAATTCATAC
* *
5809495 ACTTAGTATGAATTTCTTAACTTTTGCACAGGAAGTGCCCAATAC
130 ACTTAGTATGAATTTCTTAACTTTTGCACACGAAGTGGCCAATAC
* *
5809540 GGAAATTCATACACTTAGTATGAATCTCTTAACATTTTTGCACACGAAGTGCTCAATACGGAAAT
1 GAAAATTCATACACTTAGTATGAATCTCTTAACATTTTTGCACACGAAGTGCCCAATACGGAAAT
5809605 TCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGTCCAATACGGAAATTCATAC
66 TCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTG-CCAATACGGAAATTCATAC
* * *
5809670 ACTTAGTATGAATTTCTTAAATTTTACATACGAAGT-GCCAAATAC
130 ACTTAGTATGAATTTCTTAACTTTTGCACACGAAGTGGCC-AATAC
* * *
5809715 -ATAAATTCATACACGTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCTCAATACGGAAA
1 GA-AAATTCATACACTTAGTATGAATCTCTTAACATTTTTGCACACGAAGTGCCCAATACGGAAA
* * * **
5809779 CTCATGCACTTAGTATTAATTTCTTAACATTTTT-CACACTTAGTGCCA
65 TTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCA
5809827 TTTAGTAATC
Statistics
Matches: 421, Mismatches: 33, Indels: 16
0.90 0.07 0.03
Matches are distributed among these distances:
172 2 0.00
173 40 0.10
174 57 0.14
175 320 0.76
176 2 0.00
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (174 bp):
GAAAATTCATACACTTAGTATGAATCTCTTAACATTTTTGCACACGAAGTGCCCAATACGGAAAT
TCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCAATACGGAAATTCATACA
CTTAGTATGAATTTCTTAACTTTTGCACACGAAGTGGCCAATAC
Found at i:5816038 original size:13 final size:13
Alignment explanation
Indices: 5816002--5816028 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5815992 ATGAGCAGCG
5816002 AATAGTGAACAGT
1 AATAGTGAACAGT
5816015 AATAGTGAACAGT
1 AATAGTGAACAGT
5816028 A
1 A
5816029 CCTGTGAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.22, T:0.22
Consensus pattern (13 bp):
AATAGTGAACAGT
Found at i:5816691 original size:40 final size:43
Alignment explanation
Indices: 5816556--5816691 Score: 172
Period size: 43 Copynumber: 3.2 Consensus size: 43
5816546 ATATACATAT
* * *
5816556 CATTTA-TCACATAAGCTCATAAGCTTATATTACCAACATTCTTAC
1 CATTTATTC-CATAAGCTCGTAAGCTTATTTTACC-A-ATACTTAC
*
5816601 CATTTATTCCATAAGTTCGTAAGCTTATTTTACCAATACTTAC
1 CATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATACTTAC
*
5816644 CATTTATTCCATAAGCTCGTAAGCTTA-TTT-GC-ATACTTAC
1 CATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATACTTAC
5816684 CATTTATT
1 CATTTATT
5816692 AACCAATAAA
Statistics
Matches: 84, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
40 16 0.19
41 1 0.01
42 3 0.04
43 33 0.39
44 1 0.01
45 28 0.33
46 2 0.02
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.40
Consensus pattern (43 bp):
CATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATACTTAC
Found at i:5819519 original size:57 final size:57
Alignment explanation
Indices: 5819431--5819545 Score: 230
Period size: 57 Copynumber: 2.0 Consensus size: 57
5819421 GGATGTCTAT
5819431 TGATCTCCTTACTTAGCGGATATTCTACCTACGAACGAAATAAACATACGTTAAACA
1 TGATCTCCTTACTTAGCGGATATTCTACCTACGAACGAAATAAACATACGTTAAACA
5819488 TGATCTCCTTACTTAGCGGATATTCTACCTACGAACGAAATAAACATACGTTAAACA
1 TGATCTCCTTACTTAGCGGATATTCTACCTACGAACGAAATAAACATACGTTAAACA
5819545 T
1 T
5819546 TACTTAGTGA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.29
Consensus pattern (57 bp):
TGATCTCCTTACTTAGCGGATATTCTACCTACGAACGAAATAAACATACGTTAAACA
Found at i:5820097 original size:118 final size:118
Alignment explanation
Indices: 5819784--5820352 Score: 843
Period size: 116 Copynumber: 4.9 Consensus size: 118
5819774 TTCCCATATA
* **
5819784 AAAATTCATACACTTAGTATGAATCTCTTAACCA--TTTGCACACAAAGTGGC-CAATACTAAAA
1 AAAATTCATACACTTAGTATGAATCTCTTAA-CATTTTTGCACACGAAGT-GCACAATACGGAAA
* * *
5819846 TTCATACACTTAGTATGAATCTCTTAACCA--TTTGCACACAAAGTGCACAATACG
64 TTCATACACTTAGTATGAATTTCTTAA-CATTTTTGCACACGAAGTGCCCAATACG
* * * * *
5819900 GAAATTCATACACTTAGTATGAATTTCCTATC--TTTTGCACACGAAGTG-ACCAATATGGAAAT
1 AAAATTCATACACTTAGTATGAATCTCTTAACATTTTTGCACACGAAGTGCA-CAATACGGAAAT
*
5819962 TCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATATG
65 TCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACG
*
5820016 GAAATTCATACACTTAGTATGAATCTCTTAACATTTTTGCACACGAAGTGCACAATACGGAAATT
1 AAAATTCATACACTTAGTATGAATCTCTTAACATTTTTGCACACGAAGTGCACAATACGGAAATT
*
5820081 CATACACTTAGTATGAATCTCTTAACATTTTTGCACACGAAGTGCCCAATACG
66 CATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACG
* *
5820134 AAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACGGAAATT
1 AAAATTCATACACTTAGTATGAATCTCTTAACATTTTTGCACACGAAGTGCACAATACGGAAATT
*
5820199 CATACACTTAGTATGAATTTCTTAAC--TTTTGCACACGAAGTGCCAAATACG
66 CATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACG
* * * *
5820250 AAAATTCATACACTTAGTATAAATATTTTAACATTTTTGCACACGAAGTGCCCAATACGGAAATT
1 AAAATTCATACACTTAGTATGAATCTCTTAACATTTTTGCACACGAAGTGCACAATACGGAAATT
5820315 CATACACTTAGTATGAATTTCTTAACATTTTTGCACAC
66 CATACACTTAGTATGAATTTCTTAACATTTTTGCACAC
5820353 TTAGTGCCAT
Statistics
Matches: 417, Mismatches: 26, Indels: 18
0.90 0.06 0.04
Matches are distributed among these distances:
114 3 0.01
115 48 0.12
116 189 0.45
118 176 0.42
119 1 0.00
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (118 bp):
AAAATTCATACACTTAGTATGAATCTCTTAACATTTTTGCACACGAAGTGCACAATACGGAAATT
CATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACG
Found at i:5820378 original size:59 final size:59
Alignment explanation
Indices: 5819785--5820352 Score: 866
Period size: 59 Copynumber: 9.7 Consensus size: 59
5819775 TCCCATATAA
* * * **
5819785 AAATTCATACACTTAGTATGAATCTCTTAACCA--TTTGCACACAAAGTGGCCAATACTA
1 AAATTCATACACTTAGTATGAATTTCTTAA-CATTTTTGCACACGAAGTGCCCAATACGG
* * *
5819843 AAATTCATACACTTAGTATGAATCTCTTAACCA--TTTGCACACAAAGTGCACAATACGG
1 AAATTCATACACTTAGTATGAATTTCTTAA-CATTTTTGCACACGAAGTGCCCAATACGG
* * * *
5819901 AAATTCATACACTTAGTATGAATTTCCTATC--TTTTGCACACGAAGTGACCAATATGG
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACGG
*
5819958 AAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATATGG
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACGG
* *
5820017 AAATTCATACACTTAGTATGAATCTCTTAACATTTTTGCACACGAAGTGCACAATACGG
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACGG
* *
5820076 AAATTCATACACTTAGTATGAATCTCTTAACATTTTTGCACACGAAGTGCCCAATACGA
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACGG
5820135 AAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACGG
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACGG
* *
5820194 AAATTCATACACTTAGTATGAATTTCTTAAC--TTTTGCACACGAAGTGCCAAATACGA
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACGG
*
5820251 AAATTCATACACTTAGTATAAATATT-TTAACATTTTTGCACACGAAGTGCCCAATACGG
1 AAATTCATACACTTAGTATGAAT-TTCTTAACATTTTTGCACACGAAGTGCCCAATACGG
5820310 AAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACAC
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACAC
5820353 TTAGTGCCAT
Statistics
Matches: 476, Mismatches: 27, Indels: 13
0.92 0.05 0.03
Matches are distributed among these distances:
57 102 0.21
58 85 0.18
59 289 0.61
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (59 bp):
AAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACGG
Found at i:5820395 original size:175 final size:173
Alignment explanation
Indices: 5819785--5820352 Score: 833
Period size: 175 Copynumber: 3.2 Consensus size: 173
5819775 TCCCATATAA
* * * *
5819785 AAATTCATACACTTAGTATGAATCTCTTAACCA--TTTGCACACAAAGTGGCCAATACT-AAAAT
1 AAATTCATACACTTAGTATGAATTTCTTAA-CATTTTTGCACACGAAGTGCCCAATA-TGGAAAT
* * *
5819847 TCATACACTTAGTATGAATCTCTTAACCATTTGCACACAAAGTGCACAATACGGAAATTCATACA
64 TCATACACTTAG-ATGAATTTCTTAA-CTTTTGCACACGAAGTGCACAATACGGAAATTCATACA
* * * *
5819912 CTTAGTATGAATTTCCTATC--TTTTGCACACGAAGTGACCAATATGG
127 CTTAGTATGAATTT-TTAACATTTTTGCACACGAAGTGCCCAATACGG
5819958 AAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATATGGAAATTC
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATATGGAAATTC
*
5820023 ATACACTTAGTATGAATCTCTTAACATTTTTGCACACGAAGTGCACAATACGGAAATTCATACAC
66 ATACACTTAG-ATGAATTTCTTAAC--TTTTGCACACGAAGTGCACAATACGGAAATTCATACAC
* *
5820088 TTAGTATGAATCTCTTAACATTTTTGCACACGAAGTGCCCAATACGA
128 TTAGTATGAAT-TTTTAACATTTTTGCACACGAAGTGCCCAATACGG
*
5820135 AAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACGGAAATTC
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATATGGAAATTC
*
5820200 ATACACTTAGTATGAATTTCTTAACTTTTGCACACGAAGTGC-CAAATACGAAAATTCATACACT
66 ATACACTTAG-ATGAATTTCTTAACTTTTGCACACGAAGTGCAC-AATACGGAAATTCATACACT
*
5820264 TAGTATAAATATTTTAACATTTTTGCACACGAAGTGCCCAATACGG
129 TAGTATGAAT-TTTTAACATTTTTGCACACGAAGTGCCCAATACGG
5820310 AAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACAC
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACAC
5820353 TTAGTGCCAT
Statistics
Matches: 367, Mismatches: 19, Indels: 16
0.91 0.05 0.04
Matches are distributed among these distances:
172 2 0.01
173 31 0.08
174 51 0.14
175 171 0.47
176 1 0.00
177 111 0.30
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (173 bp):
AAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATATGGAAATTC
ATACACTTAGATGAATTTCTTAACTTTTGCACACGAAGTGCACAATACGGAAATTCATACACTTA
GTATGAATTTTTAACATTTTTGCACACGAAGTGCCCAATACGG
Found at i:5820440 original size:234 final size:234
Alignment explanation
Indices: 5819784--5820352 Score: 731
Period size: 234 Copynumber: 2.4 Consensus size: 234
5819774 TTCCCATATA
* * * **
5819784 AAAATTCATACACTTAGTATGAATCTCTTAACCA--TTTGCACACAAAGTGGC-CAATACTAAAA
1 AAAATTCATACACTTAGTATAAATATCTTAA-CATTTTTGCACACGAAGT-GCACAATACGGAAA
* * * *
5819846 TTCATACACTTAGTATGAATCTCTTAACCA--TTTGCACACAAAGTGCACAATACGGAAATTCAT
64 TTCATACACTTAGTATGAATCTCTTAA-CATTTTTGCACACGAAGTGCCCAATACGAAAATCCAT
* * * * * * * *
5819909 ACACTTAGTATGAATTTCCTATC--TTTTGCACACGAAGTGACCAATATGGAAATTCATACACTT
128 ACACTTAG-ATGAATTTCTTAACAATTATGAACACGAAGTGAACAATACGCAAATTAATACACTT
* *
5819972 AGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATATG
192 AGTATGAATTTCTTAACA-TTTTGCACACGAAGTGCCAAATACG
* * *
5820016 GAAATTCATACACTTAGTATGAATCTCTTAACATTTTTGCACACGAAGTGCACAATACGGAAATT
1 AAAATTCATACACTTAGTATAAATATCTTAACATTTTTGCACACGAAGTGCACAATACGGAAATT
*
5820081 CATACACTTAGTATGAATCTCTTAACATTTTTGCACACGAAGTGCCCAATACGAAAATTCATACA
66 CATACACTTAGTATGAATCTCTTAACATTTTTGCACACGAAGTGCCCAATACGAAAATCCATACA
* * * ** * *
5820146 CTTAGTATGAATTTCTTAACATTTTTGCACACGAAGTGCCCAATACGGAAATTCATACACTTAGT
131 CTTAG-ATGAATTTCTTAACAATTATGAACACGAAGTGAACAATACGCAAATTAATACACTTAGT
5820211 ATGAATTTCTTAAC-TTTTGCACACGAAGTGCCAAATACG
195 ATGAATTTCTTAACATTTTGCACACGAAGTGCCAAATACG
* *
5820250 AAAATTCATACACTTAGTATAAATATTTTAACATTTTTGCACACGAAGTGCCCAATACGGAAATT
1 AAAATTCATACACTTAGTATAAATATCTTAACATTTTTGCACACGAAGTGCACAATACGGAAATT
*
5820315 CATACACTTAGTATGAATTTCTTAACATTTTTGCACAC
66 CATACACTTAGTATGAATCTCTTAACATTTTTGCACAC
5820353 TTAGTGCCAT
Statistics
Matches: 311, Mismatches: 19, Indels: 12
0.91 0.06 0.04
Matches are distributed among these distances:
231 2 0.01
232 34 0.11
233 49 0.16
234 171 0.55
236 55 0.18
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (234 bp):
AAAATTCATACACTTAGTATAAATATCTTAACATTTTTGCACACGAAGTGCACAATACGGAAATT
CATACACTTAGTATGAATCTCTTAACATTTTTGCACACGAAGTGCCCAATACGAAAATCCATACA
CTTAGATGAATTTCTTAACAATTATGAACACGAAGTGAACAATACGCAAATTAATACACTTAGTA
TGAATTTCTTAACATTTTGCACACGAAGTGCCAAATACG
Found at i:5820826 original size:20 final size:21
Alignment explanation
Indices: 5820775--5820826 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
5820765 GTTTCGAAAT
*
5820775 GGTATCGATAC-CTTCCCTTC
1 GGTATCGATACTCTCCCCTTC
*
5820795 GGTATTGATACTC-CCCCTTC
1 GGTATCGATACTCTCCCCTTC
5820815 GGTATCGATACT
1 GGTATCGATACT
5820827 GATTGAATCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.17, C:0.31, G:0.17, T:0.35
Consensus pattern (21 bp):
GGTATCGATACTCTCCCCTTC
Found at i:5822141 original size:18 final size:17
Alignment explanation
Indices: 5822113--5822148 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
5822103 GTCGAGACTA
*
5822113 AGAAAATTTATTATTTT
1 AGAAAATTTATTAATTT
5822130 AGAAAGATTTATTAATTT
1 AGAAA-ATTTATTAATTT
5822148 A
1 A
5822149 TGAAGTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.47
Consensus pattern (17 bp):
AGAAAATTTATTAATTT
Found at i:5822278 original size:2 final size:2
Alignment explanation
Indices: 5822271--5822318 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
5822261 TCATGTTTGA
*
5822271 AT AT AT AT AT AT AT -T AA AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5822312 AT AT AT A
1 AT AT AT A
5822319 AAAAAATGAA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5822477 original size:15 final size:15
Alignment explanation
Indices: 5822457--5822577 Score: 58
Period size: 15 Copynumber: 7.9 Consensus size: 15
5822447 ATAATAATTT
5822457 TTTAATAATTATAAA
1 TTTAATAATTATAAA
*
5822472 TTTAATAATT-TAAC
1 TTTAATAATTATAAA
*
5822486 TTCTAAT-ATAATAAAA
1 TT-TAATAATTAT-AAA
*
5822502 TTACTAATAATAAATAAATTA
1 TT--TAATAAT-TAT-AA--A
5822523 TTTAATCAATT-T-AA
1 TTTAAT-AATTATAAA
5822537 TTTAATAATTA-AAA
1 TTTAATAATTATAAA
* *
5822551 -TTAA-AATTTTTAA
1 TTTAATAATTATAAA
*
5822564 TCTAATAATTATAA
1 TTTAATAATTATAA
5822578 TTAATATAAT
Statistics
Matches: 83, Mismatches: 9, Indels: 28
0.69 0.08 0.23
Matches are distributed among these distances:
12 4 0.05
13 10 0.12
14 19 0.23
15 21 0.25
16 5 0.06
17 5 0.06
18 3 0.04
19 10 0.12
20 3 0.04
21 3 0.04
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (15 bp):
TTTAATAATTATAAA
Found at i:5822664 original size:35 final size:35
Alignment explanation
Indices: 5822541--5822671 Score: 106
Period size: 35 Copynumber: 3.7 Consensus size: 35
5822531 ATTTAATTTA
* *
5822541 ATAATTAA-A-ATTAAAATTTTTAATCTAATAATT
1 ATAATTAATATATAAAAAATTTTAATCTAATAATT
*****
5822574 ATAATTAATATA-ATTTTTTTATTAATCTAATAATT
1 ATAATTAATATATAAAAAATT-TTAATCTAATAATT
* * *
5822609 ATAACTAATTTTTAATTAAAAAAATTTAATCTAATAATT
1 ATAATTAA--TAT-A-TAAAAAATTTTAATCTAATAATT
5822648 ATAATTAATATATAAAAAATTTTA
1 ATAATTAATATATAAAAAATTTTA
5822672 TTAATTTATA
Statistics
Matches: 74, Mismatches: 16, Indels: 14
0.71 0.15 0.13
Matches are distributed among these distances:
33 8 0.11
34 4 0.05
35 33 0.45
36 1 0.01
37 4 0.05
38 1 0.01
39 21 0.28
40 2 0.03
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (35 bp):
ATAATTAATATATAAAAAATTTTAATCTAATAATT
Found at i:5822697 original size:18 final size:18
Alignment explanation
Indices: 5822674--5822709 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
5822664 AAATTTTATT
5822674 AATTTA-TAATCATAATTA
1 AATTTATTAATC-TAATTA
5822692 AATTTATTAATCTAATTA
1 AATTTATTAATCTAATTA
5822710 TCATAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (18 bp):
AATTTATTAATCTAATTA
Found at i:5822701 original size:74 final size:74
Alignment explanation
Indices: 5822559--5822701 Score: 175
Period size: 74 Copynumber: 1.9 Consensus size: 74
5822549 AATTAAAATT
*** * *
5822559 TTTAATCTAATAATTATAATTAATATAATTTTTTTATTAATCTAATAATTATAACTAATTTTTAA
1 TTTAATCTAATAATTATAATTAATATAAAAATTTTATTAATCTAATAATCATAACTAATATTTAA
5822624 TTAAAAAAA
66 TTAAAAAAA
* *
5822633 TTTAATCTAATAATTATAATTAATATATAAAAAATTTTATTAAT-TTATAATCATAATTAA-ATT
1 TTTAATCTAATAATTATAATT-A-ATAT-AAAAATTTTATTAATCTAATAATCATAACTAATATT
5822696 T-ATTAA
63 TAATTAA
5822702 TCTAATTATC
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
74 26 0.44
75 4 0.07
76 17 0.29
77 12 0.20
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (74 bp):
TTTAATCTAATAATTATAATTAATATAAAAATTTTATTAATCTAATAATCATAACTAATATTTAA
TTAAAAAAA
Found at i:5822987 original size:21 final size:21
Alignment explanation
Indices: 5822963--5823016 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
5822953 TATGTAAATA
5822963 TCAAATTATTTAAATAATAAG
1 TCAAATTATTTAAATAATAAG
5822984 TCAAATTATTTAAATAATAAG
1 TCAAATTATTTAAATAATAAG
5823005 TCAAATTATTTA
1 TCAAATTATTTA
5823017 CAGGTTAAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.41
Consensus pattern (21 bp):
TCAAATTATTTAAATAATAAG
Found at i:5823025 original size:21 final size:21
Alignment explanation
Indices: 5822963--5823033 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 21
5822953 TATGTAAATA
*
5822963 TCAAATTATTTAAATAATAAG
1 TCAAATTATTTAAAGAATAAG
*
5822984 TCAAATTATTTAAATAATAAG
1 TCAAATTATTTAAAGAATAAG
* **
5823005 TCAAATTATTTACAGGTTAAG
1 TCAAATTATTTAAAGAATAAG
5823026 -CAAATTAT
1 TCAAATTAT
5823034 AAATCAGTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
20 8 0.17
21 38 0.83
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (21 bp):
TCAAATTATTTAAAGAATAAG
Found at i:5823497 original size:31 final size:31
Alignment explanation
Indices: 5823462--5823529 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
5823452 TTAAAACTTT
* *
5823462 CAATATAATCCC-CTGACATTTAGTCCGTTTG
1 CAATATAATCCCTC-AACATTTAGTCCATTTG
**
5823493 CAATATGGTCCCTCAACATTTAGTCCATTTG
1 CAATATAATCCCTCAACATTTAGTCCATTTG
5823524 CAATAT
1 CAATAT
5823530 GGTCCCCGAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 31 0.97
32 1 0.03
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.35
Consensus pattern (31 bp):
CAATATAATCCCTCAACATTTAGTCCATTTG
Found at i:5823530 original size:31 final size:31
Alignment explanation
Indices: 5823477--5823535 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
5823467 TAATCCCCTG
*
5823477 ACATTTAGTCCGTTTGCAATATGGTCCCTCA
1 ACATTTAGTCCATTTGCAATATGGTCCCTCA
5823508 ACATTTAGTCCATTTGCAATATGGTCCC
1 ACATTTAGTCCATTTGCAATATGGTCCC
5823536 CGACGTAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.36
Consensus pattern (31 bp):
ACATTTAGTCCATTTGCAATATGGTCCCTCA
Found at i:5826149 original size:31 final size:31
Alignment explanation
Indices: 5826114--5826175 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
5826104 CAGTTACGTC
5826114 AGGGACCATATTGCAAACAAACTAAATGTTG
1 AGGGACCATATTGCAAACAAACTAAATGTTG
* * *
5826145 AGGGACCATATTGTAAATAGACTAAATGTTG
1 AGGGACCATATTGCAAACAAACTAAATGTTG
5826176 GGATACTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.26
Consensus pattern (31 bp):
AGGGACCATATTGCAAACAAACTAAATGTTG
Found at i:5827084 original size:14 final size:14
Alignment explanation
Indices: 5827065--5827160 Score: 56
Period size: 14 Copynumber: 7.0 Consensus size: 14
5827055 TATTTACTTC
5827065 AATATTATTATTAA
1 AATATTATTATTAA
*
5827079 AATATTA-AATGTAA
1 AATATTATTAT-TAA
* * *
5827093 AATGTTATAAATAAA
1 AATATTAT-TATTAA
* *
5827108 AATATTAATATTAT
1 AATATTATTATTAA
*
5827122 TATATT-TTATTAA
1 AATATTATTATTAA
** *
5827135 AATAAAATTATTAT
1 AATATTATTATTAA
5827149 AA-ATTA-TATTAA
1 AATATTATTATTAA
5827161 TTATTTATTA
Statistics
Matches: 60, Mismatches: 18, Indels: 10
0.68 0.20 0.11
Matches are distributed among these distances:
12 5 0.08
13 12 0.20
14 32 0.53
15 8 0.13
16 3 0.05
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (14 bp):
AATATTATTATTAA
Found at i:5827168 original size:37 final size:39
Alignment explanation
Indices: 5827127--5827217 Score: 105
Period size: 42 Copynumber: 2.3 Consensus size: 39
5827117 ATTATTATAT
5827127 TTTATTAAAATAA-AAT-TATTATAAATTATATTAATTA
1 TTTATTAAAATAATAATATATTATAAATTATATTAATTA
* * *
5827164 TTTATTAAAATAACAATAATATATTATTAGTTATGTTAATTA
1 TTTATTAAAAT---AATAATATATTATAAATTATATTAATTA
*
5827206 CTTATTAAAATA
1 TTTATTAAAATA
5827218 TAAAAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
37 11 0.24
39 1 0.02
40 2 0.04
41 3 0.07
42 28 0.62
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.47
Consensus pattern (39 bp):
TTTATTAAAATAATAATATATTATAAATTATATTAATTA
Found at i:5827203 original size:42 final size:42
Alignment explanation
Indices: 5827138--5827235 Score: 119
Period size: 42 Copynumber: 2.4 Consensus size: 42
5827128 TTATTAAAAT
* *
5827138 AAAAT-TATTATAAATTATATTAATTATTTATTAAAATA-ACA
1 AAAATATATTATTAATTATATTAATTACTTATTAAAATATA-A
* * *
5827179 ATAATATATTATTAGTTATGTTAATTACTTATTAAAATATAA
1 AAAATATATTATTAATTATATTAATTACTTATTAAAATATAA
*
5827221 AAAATATAATATTAA
1 AAAATATATTATTAA
5827236 AGTAAAAATA
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.09
42 42 0.89
43 1 0.02
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (42 bp):
AAAATATATTATTAATTATATTAATTACTTATTAAAATATAA
Found at i:5827306 original size:18 final size:18
Alignment explanation
Indices: 5827269--5827306 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
5827259 TAAGAATTAT
*
5827269 TAATAAATATATTTTAAA
1 TAATAAATATATTTAAAA
5827287 TAATAAATA-ATTTAATAA
1 TAATAAATATATTTAA-AA
5827305 TA
1 TA
5827307 TTATTTCTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAATAAATATATTTAAAA
Found at i:5827457 original size:13 final size:11
Alignment explanation
Indices: 5827429--5827453 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5827419 TTAATATTTT
5827429 TATTAAAATGA
1 TATTAAAATGA
5827440 TATTAAAATGA
1 TATTAAAATGA
5827451 TAT
1 TAT
5827454 ATTATTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (11 bp):
TATTAAAATGA
Found at i:5829529 original size:22 final size:22
Alignment explanation
Indices: 5829495--5829551 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
5829485 ATATGATTTC
*
5829495 TATGTGTACATGAGTACATGC-T
1 TATGTCTACATGA-TACATGCAT
*
5829517 TATGTCTATATGATACATGCAT
1 TATGTCTACATGATACATGCAT
*
5829539 TAT-TATACATGAT
1 TATGTCTACATGAT
5829552 CTATGTGTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 15 0.50
22 15 0.50
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (22 bp):
TATGTCTACATGATACATGCAT
Found at i:5829833 original size:23 final size:23
Alignment explanation
Indices: 5829807--5829876 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
5829797 GAGTCGATGG
* *
5829807 TTCTACGCAGTCCTTCGAGATAA
1 TTCTACGCGGTCCTTCGGGATAA
* * *
5829830 TTCTACGTGGTCCTTCGGGACAT
1 TTCTACGCGGTCCTTCGGGATAA
*
5829853 TTCTACGCGGTCGTTCGGGATAA
1 TTCTACGCGGTCCTTCGGGATAA
5829876 T
1 T
5829877 ACTATATATG
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.33
Consensus pattern (23 bp):
TTCTACGCGGTCCTTCGGGATAA
Found at i:5830167 original size:6 final size:6
Alignment explanation
Indices: 5830060--5830166 Score: 178
Period size: 6 Copynumber: 17.8 Consensus size: 6
5830050 ATGAACAATG
* * *
5830060 AATGAT AATGAT AATGAT AATGAC AATGAC AATGAC AATGAC AATGAC
1 AATGAC AATGAC AATGAC AATGAC AATGAC AATGAC AATGAC AATGAC
5830108 AATGAC AATGAC AATGAC AATGAC AATGAC AATGAC AATGAC AATGAC
1 AATGAC AATGAC AATGAC AATGAC AATGAC AATGAC AATGAC AATGAC
*
5830156 AATGAT AATGA
1 AATGAC AATGA
5830167 TGTTGTTGAT
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 99 1.00
ACGTcount: A:0.50, C:0.12, G:0.17, T:0.21
Consensus pattern (6 bp):
AATGAC
Found at i:5832509 original size:3 final size:3
Alignment explanation
Indices: 5832501--5832537 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
5832491 CAGTTGTTAA
5832501 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
5832538 AATAATAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:5833100 original size:14 final size:15
Alignment explanation
Indices: 5833081--5833118 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
5833071 AAATATCAGA
5833081 TTTAATCCTTTA-AT
1 TTTAATCCTTTACAT
**
5833095 TTTAATAATTTACAT
1 TTTAATCCTTTACAT
5833110 TTTAATCCT
1 TTTAATCCT
5833119 GAATAGTAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.32, C:0.13, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTAATCCTTTACAT
Found at i:5833800 original size:33 final size:34
Alignment explanation
Indices: 5833738--5833805 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 34
5833728 AGTGTGAAAT
* * *
5833738 AATGTTGGGGTATTTTGAACACTTGTATCA-ACA
1 AATGTTGGGGCATTTTGAACACCTATATCATACA
**
5833771 AATGTTGGGGCATTTTGAAGGCCTATATCATACA
1 AATGTTGGGGCATTTTGAACACCTATATCATACA
5833805 A
1 A
5833806 GAATATAAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
33 25 0.86
34 4 0.14
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.34
Consensus pattern (34 bp):
AATGTTGGGGCATTTTGAACACCTATATCATACA
Found at i:5835015 original size:38 final size:38
Alignment explanation
Indices: 5834959--5835040 Score: 110
Period size: 38 Copynumber: 2.2 Consensus size: 38
5834949 AAGTCAACCA
* *
5834959 TTGACTTCCTAGTGAAGAGAAGTCAATATTTTTTATCC
1 TTGACTTCCTAGTAAAGAGAAGTCAATATTTGTTATCC
* * *
5834997 TTGATTTCCTCGTAAAGAGAAGTCAATCTTTGTTATCC
1 TTGACTTCCTAGTAAAGAGAAGTCAATATTTGTTATCC
*
5835035 CTGACT
1 TTGACT
5835041 CCCCAGTGGA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (38 bp):
TTGACTTCCTAGTAAAGAGAAGTCAATATTTGTTATCC
Found at i:5835084 original size:62 final size:62
Alignment explanation
Indices: 5835011--5835147 Score: 166
Period size: 62 Copynumber: 2.2 Consensus size: 62
5835001 TTTCCTCGTA
* * **
5835011 AAGAGAAGTCAATCTTTGTTATCCCTGACTCCCCAGTGGAGCCAATCTTTGACTTCATCATG
1 AAGAGAAGTCAATCTTTGTTATCCATGACTCCCCAGTAGAGCCAATCCCTGACTTCATCATG
* ** ** * **
5835073 AAGAGAAGTCAACCTTTGTTATTTATGACTCCCCAGTAGAGTTAATCCCTGACTTCCTTGTG
1 AAGAGAAGTCAATCTTTGTTATCCATGACTCCCCAGTAGAGCCAATCCCTGACTTCATCATG
5835135 AAGAGAAGTCAAT
1 AAGAGAAGTCAAT
5835148 ATTGCAGATT
Statistics
Matches: 62, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (62 bp):
AAGAGAAGTCAATCTTTGTTATCCATGACTCCCCAGTAGAGCCAATCCCTGACTTCATCATG
Found at i:5835341 original size:36 final size:36
Alignment explanation
Indices: 5835284--5835981 Score: 900
Period size: 36 Copynumber: 19.1 Consensus size: 36
5835274 ATCAACCTCG
*
5835284 AATCTAAGCCTTCACGAAAGAGTAGTGAAGCAAATC
1 AATCTAAGCCTTCACGGAAGAGTAGTGAAGCAAATC
* * * *
5835320 AATTTAAGCCGTCAAGGAAGAGTAGTGAATCAAATC
1 AATCTAAGCCTTCACGGAAGAGTAGTGAAGCAAATC
* *
5835356 AATCTAAGCCTTCACGAAAGAGTAATGAAGCAAATC
1 AATCTAAGCCTTCACGGAAGAGTAGTGAAGCAAATC
*
5835392 AA-CTTAAGCCCTCACGGAAGAGTAGTGAAGCAAATC
1 AATC-TAAGCCTTCACGGAAGAGTAGTGAAGCAAATC
5835428 AATCTAAGCCTTCACGGAAGAGTAGTGAAGCAAATC
1 AATCTAAGCCTTCACGGAAGAGTAGTGAAGCAAATC
* **
5835464 AA-CTTAAGCCTTCACGAAAGAGTAGTGAATAAAATC
1 AATC-TAAGCCTTCACGGAAGAGTAGTGAAGCAAATC
* *
5835500 AACCTAAGCCTTCACGGATGAGTAGTGAAGCAAATC
1 AATCTAAGCCTTCACGGAAGAGTAGTGAAGCAAATC
* * *
5835536 AACCTAAGCCTTCACGGAAGAGTAGTGGAGAAAATC
1 AATCTAAGCCTTCACGGAAGAGTAGTGAAGCAAATC
* * *
5835572 AATTTAAGCCTTCACGGAAGAGTAGTGGAGCAAACC
1 AATCTAAGCCTTCACGGAAGAGTAGTGAAGCAAATC
*
5835608 AATTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATC
1 AATCTAAGCCTTCACGGAAGAGTAGTGAAGCAAATC
* *
5835644 AATCTAAGCCTTCATGGAAGAGTAGTGAAACAAATC
1 AATCTAAGCCTTCACGGAAGAGTAGTGAAGCAAATC
*
5835680 AATCTAAGCCTTCAAGGAAGAGTAGTGAAGCAAATC
1 AATCTAAGCCTTCACGGAAGAGTAGTGAAGCAAATC
*
5835716 AATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATA
1 AATC-TAAGCCTTCACGGAAGAGTAGTGAAGCAAATC
* * *
5835753 AATCTAAGCCTTCACGGAACAATAATGAAGCAAATC
1 AATCTAAGCCTTCACGGAAGAGTAGTGAAGCAAATC
* *
5835789 AATCTAAGTCTTCACGGAAGAGTAGTAAAGCAAATC
1 AATCTAAGCCTTCACGGAAGAGTAGTGAAGCAAATC
* *
5835825 AATCTAAGCCTTCACGAAAGAGTAGTGAAGAAAATC
1 AATCTAAGCCTTCACGGAAGAGTAGTGAAGCAAATC
*
5835861 AATCTTAAGCCTTCACGGAAGAGTAGTGAAGAAAATC
1 AATC-TAAGCCTTCACGGAAGAGTAGTGAAGCAAATC
* * * *
5835898 AATCTTGAGTCTGATCTCCACGAAAGAGTAGTGGAA-CATATTTC
1 AATC-TAAG-C----CTTCACGGAAGAGTAGT-GAAGCA-A-ATC
* * *
5835942 -TTCTTAGCCTTCACGGAAGAGTAGTGAAACAAATC
1 AATCTAAGCCTTCACGGAAGAGTAGTGAAGCAAATC
5835977 AATCT
1 AATCT
5835982 TGAGTCTTAT
Statistics
Matches: 583, Mismatches: 63, Indels: 32
0.86 0.09 0.05
Matches are distributed among these distances:
35 4 0.01
36 458 0.79
37 92 0.16
38 1 0.00
41 1 0.00
42 19 0.03
43 6 0.01
44 2 0.00
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.21
Consensus pattern (36 bp):
AATCTAAGCCTTCACGGAAGAGTAGTGAAGCAAATC
Found at i:5836103 original size:47 final size:48
Alignment explanation
Indices: 5835986--5836413 Score: 260
Period size: 47 Copynumber: 8.6 Consensus size: 48
5835976 CAATCTTGAG
** * *
5835986 TCTTATCTCCCTGAAAGAAGAGTAAAGTAGATTCGTCTTTCCTT-GTAT
1 TCTTATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTCTTTCTTTCG-AT
* * *
5836034 T-TTATCTCCTTGAAAGAAGAGTGGAGCAGATTTGTCTTTCTTTAGAT
1 TCTTATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTCTTTCTTTCGAT
* ** *
5836081 TC-TATCTCCCTGAAAGAAGAGTGGATCAGACCCGT-TTTCAAAGATTTCTCGAG
1 TCTTATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTCTTTC------TT-TCGAT
* * * * *
5836134 TCTTATCTCCCTGAAAGAATAGTGGAACAAATTCGTCTTTCCTTGGAT
1 TCTTATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTCTTTCTTTCGAT
* * * * *
5836182 TC-TATCTCCCTGAAAAAAGAGTGGAGCAGATCCGTTTTTGTTAGATTTTTCGAG
1 TCTTATCTCCCTGAAAGAAGAGTGGAGCAGATTCG----TCTT---TCTTTCGAT
* * *
5836236 TCTTATCTCCTTGAAAGAAGAGTGGAGCAGATTCGTCTTCCTTTGGA-
1 TCTTATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTCTTTCTTTCGAT
* * ** * * *
5836283 TCTTATCTCCTTGAAAGAAGAGTGTAAAAGATCCAT-TTTCGTTAGATTTCTCGAG
1 TCTTATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTCTTTC-------TT-TCGAT
* * * * **
5836338 TCTTATCTCCCTAAAAGATGAGTGGAGCAGATTCGTCTTCCCTAGGA-
1 TCTTATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTCTTTCTTTCGAT
5836385 TCTTATCTCCCTGAAAGAAGAGTGGAGCA
1 TCTTATCTCCCTGAAAGAAGAGTGGAGCA
5836414 AATCCGTTTT
Statistics
Matches: 292, Mismatches: 59, Indels: 59
0.71 0.14 0.14
Matches are distributed among these distances:
46 7 0.02
47 152 0.52
48 14 0.05
49 2 0.01
51 6 0.02
52 2 0.01
53 7 0.02
54 38 0.13
55 61 0.21
56 3 0.01
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (48 bp):
TCTTATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTCTTTCTTTCGAT
Found at i:5836271 original size:102 final size:102
Alignment explanation
Indices: 5836035--5836494 Score: 570
Period size: 102 Copynumber: 4.5 Consensus size: 102
5836025 TCCTTGTATT
* * *
5836035 TTATCTCCTTGAAAGAAGAGTGGAGCAGATTTGTCTTTCTTTAGATTCTATCTCCCTGAAAGAAG
1 TTATCTCCTTGAAAGAAGAGTGGAGCAGATTCGTCTTTCCTTGGATTCTATCTCCCTGAAAGAAG
* *
5836100 AGTGGATCAGACCCG-TTTTCAAAGATTTCTCGAGTC
66 AGTGGAGCAGATCCGTTTTTCAAAGATTTCTCGAGTC
* * * * *
5836136 TTATCTCCCTGAAAGAATAGTGGAACAAATTCGTCTTTCCTTGGATTCTATCTCCCTGAAAAAAG
1 TTATCTCCTTGAAAGAAGAGTGGAGCAGATTCGTCTTTCCTTGGATTCTATCTCCCTGAAAGAAG
*** *
5836201 AGTGGAGCAGATCCGTTTTTGTTAGATTTTTCGAGTC
66 AGTGGAGCAGATCCGTTTTTCAAAGATTTCTCGAGTC
*
5836238 TTATCTCCTTGAAAGAAGAGTGGAGCAGATTCGTC-TTCCTTTGGA-TCTTATCTCCTTGAAAGA
1 TTATCTCCTTGAAAGAAGAGTGGAGCAGATTCGTCTTTCC-TTGGATTC-TATCTCCCTGAAAGA
* ** * **
5836301 AGAGTGTAAAAGATCC-ATTTTCGTTAGATTTCTCGAGTC
64 AGAGTGGAGCAGATCCGTTTTTC-AAAGATTTCTCGAGTC
* * * * *
5836340 TTATCTCCCTAAAAGATGAGTGGAGCAGATTCGTCTTCCCTAGGA-TCTTATCTCCCTGAAAGAA
1 TTATCTCCTTGAAAGAAGAGTGGAGCAGATTCGTCTTTCCTTGGATTC-TATCTCCCTGAAAGAA
* *
5836404 GAGTGGAGCAAATCCGTTTTACAAAGATTTCTCGAGTC
65 GAGTGGAGCAGATCCGTTTTTCAAAGATTTCTCGAGTC
* * *
5836442 TTATCTCCTTGAAAGAATAGTGGAGCAGACTCGTCTTCCCTTGGATTCTATCT
1 TTATCTCCTTGAAAGAAGAGTGGAGCAGATTCGTCTTTCCTTGGATTCTATCT
5836495 TACTTAAAGA
Statistics
Matches: 306, Mismatches: 46, Indels: 13
0.84 0.13 0.04
Matches are distributed among these distances:
101 80 0.26
102 217 0.71
103 9 0.03
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (102 bp):
TTATCTCCTTGAAAGAAGAGTGGAGCAGATTCGTCTTTCCTTGGATTCTATCTCCCTGAAAGAAG
AGTGGAGCAGATCCGTTTTTCAAAGATTTCTCGAGTC
Found at i:5836408 original size:204 final size:203
Alignment explanation
Indices: 5836035--5836494 Score: 629
Period size: 204 Copynumber: 2.3 Consensus size: 203
5836025 TCCTTGTATT
* * *
5836035 TTATCTCCTTGAAAGAAGAGTGGAGCAGATTTGTCTTTCTTTAGATTCTATCTCCCTGAAAGAAG
1 TTATCTCCTTGAAAGAAGAGTGGAGCAGATTCGTCTTCCTTTGGATTCTATCTCCCTGAAAGAAG
** * *
5836100 AGTGGATCAGACCCGTTTTCAAAGATTTCTCGAGTCTTATCTCCCTGAAAGAATAGTGGAACAAA
66 AGTGGAAAAGACCCATTTTCAAAGATTTCTCGAGTCTTATCTCCCTAAAAGAATAGTGGAACAAA
* * * ****
5836165 TTCGTCTTTCCTTGGATTCTATCTCCCTGAAAAAAGAGTGGAGCAGATCCGTTTTTGTTAGATTT
131 TTCGTCTTCCCTAGGATTCTATCTCCCTGAAAAAAGAGTGGAGCAAATCCGTTTTACAAAGATTT
*
5836230 TTCGAGTC
196 CTCGAGTC
*
5836238 TTATCTCCTTGAAAGAAGAGTGGAGCAGATTCGTCTTCCTTTGGA-TCTTATCTCCTTGAAAGAA
1 TTATCTCCTTGAAAGAAGAGTGGAGCAGATTCGTCTTCCTTTGGATTC-TATCTCCCTGAAAGAA
* * ** *
5836302 GAGTGTAAAAGATCCATTTTCGTTAGATTTCTCGAGTCTTATCTCCCTAAAAG-ATGAGTGGAGC
65 GAGTGGAAAAGACCCATTTTC-AAAGATTTCTCGAGTCTTATCTCCCTAAAAGAAT-AGTGGAAC
* *
5836366 AGATTCGTCTTCCCTAGGA-TCTTATCTCCCTGAAAGAAGAGTGGAGCAAATCCGTTTTACAAAG
128 AAATTCGTCTTCCCTAGGATTC-TATCTCCCTGAAAAAAGAGTGGAGCAAATCCGTTTTACAAAG
5836430 ATTTCTCGAGTC
192 ATTTCTCGAGTC
* * *
5836442 TTATCTCCTTGAAAGAATAGTGGAGCAGACTCGTCTTCCCTTGGATTCTATCT
1 TTATCTCCTTGAAAGAAGAGTGGAGCAGATTCGTCTTCCTTTGGATTCTATCT
5836495 TACTTAAAGA
Statistics
Matches: 226, Mismatches: 26, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
202 2 0.01
203 77 0.34
204 145 0.64
205 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (203 bp):
TTATCTCCTTGAAAGAAGAGTGGAGCAGATTCGTCTTCCTTTGGATTCTATCTCCCTGAAAGAAG
AGTGGAAAAGACCCATTTTCAAAGATTTCTCGAGTCTTATCTCCCTAAAAGAATAGTGGAACAAA
TTCGTCTTCCCTAGGATTCTATCTCCCTGAAAAAAGAGTGGAGCAAATCCGTTTTACAAAGATTT
CTCGAGTC
Found at i:5836652 original size:3 final size:3
Alignment explanation
Indices: 5836644--5836669 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5836634 CCAGTTGTTA
5836644 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
5836670 AATGATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:5838758 original size:2 final size:2
Alignment explanation
Indices: 5838751--5838794 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
5838741 ATCAACTTAA
5838751 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5838793 AT
1 AT
5838795 GTGTGTGTGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5840372 original size:25 final size:24
Alignment explanation
Indices: 5840332--5840424 Score: 125
Period size: 25 Copynumber: 3.8 Consensus size: 24
5840322 CAATTTTGAA
5840332 AGCTCGATTGAAGCTCGAGACTCG
1 AGCTCGATTGAAGCTCGAGACTCG
5840356 AGCTCGATTTGAAGCTCGAGACTCG
1 AGCTCGA-TTGAAGCTCGAGACTCG
** *
5840381 AGCTCGATTTGAAGCTCG-GTTTTG
1 AGCTCGA-TTGAAGCTCGAGACTCG
*
5840405 AGCTCGATTCAAGCTCGAGA
1 AGCTCGATTGAAGCTCGAGA
5840425 ACAGGTTAAT
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
23 9 0.15
24 18 0.29
25 35 0.56
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.26
Consensus pattern (24 bp):
AGCTCGATTGAAGCTCGAGACTCG
Found at i:5840373 original size:12 final size:12
Alignment explanation
Indices: 5840326--5840422 Score: 51
Period size: 11 Copynumber: 8.0 Consensus size: 12
5840316 TCAAAACAAT
5840326 TTTGAAAGCTCGA
1 TTTG-AAGCTCGA
5840339 -TTGAAGCTCGAGA
1 TTTGAAGCTC--GA
* *
5840352 CTCG-AGCTCGA
1 TTTGAAGCTCGA
5840363 TTTGAAGCTCGAGA
1 TTTGAAGCTC--GA
* *
5840377 CTCG-AGCTCGA
1 TTTGAAGCTCGA
*
5840388 TTTGAAGCTCGGT
1 TTTGAAGCTC-GA
5840401 TTTG-AGCTCGA
1 TTTGAAGCTCGA
*
5840412 -TTCAAGCTCGA
1 TTTGAAGCTCGA
5840423 GAACAGGTTA
Statistics
Matches: 65, Mismatches: 10, Indels: 20
0.68 0.11 0.21
Matches are distributed among these distances:
10 2 0.03
11 22 0.34
12 18 0.28
13 17 0.26
14 6 0.09
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.28
Consensus pattern (12 bp):
TTTGAAGCTCGA
Done.