Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr5
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: 43060996
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2186021 characters in sequence are not A, C, G, or T
File 16 of 128
Found at i:4639648 original size:27 final size:25
Alignment explanation
Indices: 4639607--4639657 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
4639597 ATAGATTAAA
4639607 TGTTGTTAATAATAAATT-AAAATT
1 TGTTGTTAATAATAAATTGAAAATT
4639631 TGTTGTTAATAAATATAATTTGAAAAT
1 TGTTGTTAAT-AATA-AA-TTGAAAAT
4639658 ATTAAAACGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 10 0.43
25 4 0.17
26 2 0.09
27 2 0.09
28 5 0.22
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (25 bp):
TGTTGTTAATAATAAATTGAAAATT
Found at i:4645339 original size:14 final size:15
Alignment explanation
Indices: 4645312--4645341 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
4645302 AAAAAGAGAG
4645312 TAAAATATGAAAAGT
1 TAAAATATGAAAAGT
4645327 TAAAATA-GAAAAGT
1 TAAAATATGAAAAGT
4645341 T
1 T
4645342 GACTGACTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.60, C:0.00, G:0.13, T:0.27
Consensus pattern (15 bp):
TAAAATATGAAAAGT
Found at i:4661036 original size:23 final size:22
Alignment explanation
Indices: 4660966--4661047 Score: 98
Period size: 21 Copynumber: 3.8 Consensus size: 22
4660956 CCTGATCAGT
*
4660966 ATACGACACAT-AAGTGCCTGT
1 ATACGACACATAAAGTGCCTGG
** *
4660987 A-ACGACACACGAGGTGCCT-G
1 ATACGACACATAAAGTGCCTGG
4661007 ATACGACACATAAAGTGCCTGAG
1 ATACGACACATAAAGTGCCTG-G
4661030 ATACGACACATAAAGTGC
1 ATACGACACATAAAGTGC
4661048 TTGATCGGCA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
20 9 0.18
21 23 0.45
23 19 0.37
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (22 bp):
ATACGACACATAAAGTGCCTGG
Found at i:4674491 original size:21 final size:21
Alignment explanation
Indices: 4674444--4674491 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
4674434 CTGTTGAAGT
* *
4674444 TAGTTAAAAGGAGTTAGTTAG
1 TAGTTAAAAGGAATTAGTTAA
*
4674465 TTGTTAAACA-GAATTAGTTAA
1 TAGTTAAA-AGGAATTAGTTAA
4674486 TAGTTA
1 TAGTTA
4674492 GCTATTATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.40, C:0.02, G:0.21, T:0.38
Consensus pattern (21 bp):
TAGTTAAAAGGAATTAGTTAA
Found at i:4679349 original size:16 final size:17
Alignment explanation
Indices: 4679322--4679356 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
4679312 GCATTTGGAT
4679322 TAAAATTTTTAAAAATA
1 TAAAATTTTTAAAAATA
4679339 TAAAA-TTTTAAAAATA
1 TAAAATTTTTAAAAATA
4679355 TA
1 TA
4679357 CCAAACTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAAATTTTTAAAAATA
Found at i:4681503 original size:24 final size:24
Alignment explanation
Indices: 4681475--4681524 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
4681465 CATTTTTGGA
4681475 AATCGAATTTTTATTTTAAATACG
1 AATCGAATTTTTATTTTAAATACG
*
4681499 AATCGAGTTTTTATTTTAAATACG
1 AATCGAATTTTTATTTTAAATACG
4681523 AA
1 AA
4681525 GATGGAGTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (24 bp):
AATCGAATTTTTATTTTAAATACG
Found at i:4682196 original size:28 final size:28
Alignment explanation
Indices: 4682165--4682219 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
4682155 CAACATAAAT
4682165 AATAAAATAA-AACGACAATAAT-ATAATG
1 AATAAAATAATAA-GA-AATAATAATAATG
*
4682193 AATACAATAATAAGAAATAATAATAAT
1 AATAAAATAATAAGAAATAATAATAAT
4682220 TATTCAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 6 0.25
28 16 0.67
29 2 0.08
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.24
Consensus pattern (28 bp):
AATAAAATAATAAGAAATAATAATAATG
Found at i:4688516 original size:29 final size:28
Alignment explanation
Indices: 4688448--4688519 Score: 72
Period size: 29 Copynumber: 2.5 Consensus size: 28
4688438 TCTTTTCTTA
**
4688448 CTCGTATTCTTTTTCTTTCTCTTTTTTTT
1 CTCGT-TTCTTTTTCTTTCAATTTTTTTT
** *
4688477 CAAGCTCTCTTTTTCTTTCAATTTTTTTCT
1 CTCG-TTTCTTTTTCTTTCAATTTTTTT-T
4688507 CTCGTTTCTTTTT
1 CTCGTTTCTTTTT
4688520 TTCTTCTCTC
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
29 29 0.88
30 4 0.12
ACGTcount: A:0.07, C:0.22, G:0.04, T:0.67
Consensus pattern (28 bp):
CTCGTTTCTTTTTCTTTCAATTTTTTTT
Found at i:4688537 original size:21 final size:19
Alignment explanation
Indices: 4688498--4688556 Score: 73
Period size: 21 Copynumber: 2.9 Consensus size: 19
4688488 TTTCTTTCAA
*
4688498 TTTTTTTCTCTCGTTTCTT
1 TTTTTTTCTCTCATTTCTT
4688517 TTTTTCTTCTCTCAATTTCTT
1 TTTTT-TTCTCTC-ATTTCTT
*
4688538 TTATTTTTCGCTCATTTCT
1 TT-TTTTTCTCTCATTTCT
4688557 CTCATTAACA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
19 5 0.14
20 13 0.37
21 14 0.40
22 3 0.09
ACGTcount: A:0.07, C:0.22, G:0.03, T:0.68
Consensus pattern (19 bp):
TTTTTTTCTCTCATTTCTT
Found at i:4690863 original size:39 final size:38
Alignment explanation
Indices: 4690787--4690876 Score: 110
Period size: 39 Copynumber: 2.4 Consensus size: 38
4690777 TTAAAACACT
* *
4690787 TAATTAAA-ACACATATTAGTGAGTTCAAAATAAGACA
1 TAATTAAAGACATATATTAATGAGTTCAAAATAAGACA
* * *
4690824 TAATTAAAGACATATATTAATGGTGTTCAAACTACGACA
1 TAATTAAAGACATATATTAAT-GAGTTCAAAATAAGACA
*
4690863 TAATTAAGGACATA
1 TAATTAAAGACATA
4690877 ACTAAGACAT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
37 8 0.18
38 10 0.22
39 27 0.60
ACGTcount: A:0.48, C:0.11, G:0.12, T:0.29
Consensus pattern (38 bp):
TAATTAAAGACATATATTAATGAGTTCAAAATAAGACA
Found at i:4690876 original size:12 final size:12
Alignment explanation
Indices: 4690859--4690898 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
4690849 TTCAAACTAC
4690859 GACATAATTAAG
1 GACATAATTAAG
*
4690871 GACATAACTAA-
1 GACATAATTAAG
4690882 GACATAATTAAG
1 GACATAATTAAG
4690894 GACAT
1 GACAT
4690899 GAACTAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.50, C:0.12, G:0.15, T:0.23
Consensus pattern (12 bp):
GACATAATTAAG
Found at i:4690880 original size:23 final size:24
Alignment explanation
Indices: 4690853--4690905 Score: 90
Period size: 23 Copynumber: 2.2 Consensus size: 24
4690843 ATGGTGTTCA
*
4690853 AACTACGACATAATTAAGGACAT-
1 AACTAAGACATAATTAAGGACATG
4690876 AACTAAGACATAATTAAGGACATG
1 AACTAAGACATAATTAAGGACATG
4690900 AACTAA
1 AACTAA
4690906 AATAACTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 22 0.79
24 6 0.21
ACGTcount: A:0.51, C:0.15, G:0.13, T:0.21
Consensus pattern (24 bp):
AACTAAGACATAATTAAGGACATG
Found at i:4690914 original size:9 final size:9
Alignment explanation
Indices: 4690900--4690926 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
4690890 TAAGGACATG
4690900 AACTAAAAT
1 AACTAAAAT
4690909 AACTAAAAT
1 AACTAAAAT
4690918 AACTAAAAT
1 AACTAAAAT
4690927 GGATTGAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (9 bp):
AACTAAAAT
Found at i:4691742 original size:10 final size:10
Alignment explanation
Indices: 4691727--4691758 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
4691717 CCTTGACCTT
4691727 CTCCTTGCTC
1 CTCCTTGCTC
4691737 CTCCTTGCTC
1 CTCCTTGCTC
4691747 CTCCTTGC-C
1 CTCCTTGCTC
4691756 CTC
1 CTC
4691759 TTCCCTTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.00, C:0.53, G:0.09, T:0.38
Consensus pattern (10 bp):
CTCCTTGCTC
Found at i:4693213 original size:104 final size:104
Alignment explanation
Indices: 4693093--4693299 Score: 371
Period size: 104 Copynumber: 2.0 Consensus size: 104
4693083 CCCCATTCCC
* * *
4693093 GCTTCTGTTTTGCCCAAAATCCATGTCTTC-TGTTTCTTCCTTCTAGCTTTCTTCTCCACTCTCA
1 GCTTCTGTTTTACCCAAAATCAACGTC-TCATGTTTCTTCCTTCTAGCTTTCTTCTCCACTCTCA
4693157 TCGCCTCTTCTCCTTCTCTTTTTTACCTCTCTTTTTTATT
65 TCGCCTCTTCTCCTTCTCTTTTTTACCTCTCTTTTTTATT
4693197 GCTTCTGTTTTACCCAAAATCAACGTCTCATGTTTCTTCCTTCTAGCTTTCTTCTCCACTCTCAT
1 GCTTCTGTTTTACCCAAAATCAACGTCTCATGTTTCTTCCTTCTAGCTTTCTTCTCCACTCTCAT
4693262 CGCCTCTTCTCCTTCTCTTTTTTACCTCTCTTTTTTAT
66 CGCCTCTTCTCCTTCTCTTTTTTACCTCTCTTTTTTAT
4693300 ATAGGTTTTT
Statistics
Matches: 99, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
103 2 0.02
104 97 0.98
ACGTcount: A:0.11, C:0.33, G:0.06, T:0.50
Consensus pattern (104 bp):
GCTTCTGTTTTACCCAAAATCAACGTCTCATGTTTCTTCCTTCTAGCTTTCTTCTCCACTCTCAT
CGCCTCTTCTCCTTCTCTTTTTTACCTCTCTTTTTTATT
Found at i:4697141 original size:45 final size:44
Alignment explanation
Indices: 4697042--4697151 Score: 131
Period size: 45 Copynumber: 2.6 Consensus size: 44
4697032 TTTTCTATTA
4697042 TGCTATTACACCTCTATT-C--T--ATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
* * ***
4697081 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGA-T
4697126 TGCTATTACACCTCTATTCCATTACA
1 TGCTATTACACCTCTATTCCATTACA
4697152 CATCTAATCC
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
42 1 0.02
44 15 0.26
45 25 0.43
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (44 bp):
TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
Found at i:4697151 original size:16 final size:16
Alignment explanation
Indices: 4697132--4697183 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
4697122 GATTTGCTAT
* *
4697132 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
*
4697148 TACACATCTAATCCAA
1 TACACCTCTAATCCAA
4697164 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
4697180 TACA
1 TACA
4697184 GCGAACTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.37, C:0.35, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:4702403 original size:14 final size:14
Alignment explanation
Indices: 4702386--4702428 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
4702376 TCATTTAAGA
4702386 TTTAATTTTTATAT
1 TTTAATTTTTATAT
*
4702400 TTTAATTTTTA-AC
1 TTTAATTTTTATAT
*
4702413 TTTGA-TTTTATAT
1 TTTAATTTTTATAT
4702426 TTT
1 TTT
4702429 TATAATATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
12 5 0.20
13 9 0.36
14 11 0.44
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (14 bp):
TTTAATTTTTATAT
Found at i:4712864 original size:25 final size:25
Alignment explanation
Indices: 4712836--4712886 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
4712826 AAAGACTTGA
4712836 GCCTATTACAGAAGAATGTTAGGAT
1 GCCTATTACAGAAGAATGTTAGGAT
4712861 GCCTATTACAGAAGAATGTTAGGAT
1 GCCTATTACAGAAGAATGTTAGGAT
4712886 G
1 G
4712887 ACATACTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.27
Consensus pattern (25 bp):
GCCTATTACAGAAGAATGTTAGGAT
Found at i:4714606 original size:11 final size:11
Alignment explanation
Indices: 4714588--4714620 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
4714578 CACATATATC
4714588 TCTTTTC-TTT
1 TCTTTTCTTTT
4714598 TCTTTTTCTTTT
1 TC-TTTTCTTTT
4714610 TCTTTTCTTTT
1 TCTTTTCTTTT
4714621 ATCTCATTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 2 0.10
11 14 0.67
12 5 0.24
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (11 bp):
TCTTTTCTTTT
Found at i:4716283 original size:29 final size:31
Alignment explanation
Indices: 4716238--4716309 Score: 89
Period size: 29 Copynumber: 2.4 Consensus size: 31
4716228 TAGCTTATAT
4716238 ACTTAATTAATATTTAATTAA-TCTAAT-TTA
1 ACTTAATTAATATTTAATTAAGT-TAATCTTA
4716268 ACTT-ATTAA-ATCTTAATTAAGTTAATCTTA
1 ACTTAATTAATAT-TTAATTAAGTTAATCTTA
4716298 ACTTTAATTAAT
1 AC-TTAATTAAT
4716310 CAATTTAGTG
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
28 2 0.06
29 17 0.47
30 10 0.28
31 2 0.06
32 5 0.14
ACGTcount: A:0.42, C:0.08, G:0.01, T:0.49
Consensus pattern (31 bp):
ACTTAATTAATATTTAATTAAGTTAATCTTA
Found at i:4721702 original size:29 final size:30
Alignment explanation
Indices: 4721665--4721737 Score: 73
Period size: 29 Copynumber: 2.5 Consensus size: 30
4721655 CAGCCAAAGT
* *
4721665 TTCATGTATATAATTACAC-CAAATTAAAA
1 TTCAAGTATATAATTACACACAAATCAAAA
*
4721694 TTCAAGTAT-TATATTACACATTAAATCAAAA
1 TTCAAGTATATA-ATTACACA-CAAATCAAAA
4721725 TTC-A-TATATAATT
1 TTCAAGTATATAATT
4721738 CTAAAATTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
28 2 0.05
29 21 0.57
30 3 0.08
31 11 0.30
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (30 bp):
TTCAAGTATATAATTACACACAAATCAAAA
Found at i:4728261 original size:75 final size:76
Alignment explanation
Indices: 4728181--4728332 Score: 297
Period size: 75 Copynumber: 2.0 Consensus size: 76
4728171 AAATTATAAA
4728181 ATATTATTTTATTATATTAAAAATTAAATTAATATATGCTTATAATAAGATTTAAACTCAAACCT
1 ATATTATTTTATTATATTAAAAATTAAATTAATATATGCTTATAATAAGATTTAAACTCAAACCT
4728246 A-TACATTAAT
66 ATTACATTAAT
4728256 ATATTATTTTATTATATTAAAAATTAAATTAATATATGCTTATAATAAGATTTAAACTCAAACCT
1 ATATTATTTTATTATATTAAAAATTAAATTAATATATGCTTATAATAAGATTTAAACTCAAACCT
4728321 ATTACATTAAT
66 ATTACATTAAT
4728332 A
1 A
4728333 AAATTTTTGA
Statistics
Matches: 76, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
75 66 0.87
76 10 0.13
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.43
Consensus pattern (76 bp):
ATATTATTTTATTATATTAAAAATTAAATTAATATATGCTTATAATAAGATTTAAACTCAAACCT
ATTACATTAAT
Found at i:4733137 original size:16 final size:16
Alignment explanation
Indices: 4733116--4733165 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
4733106 GAAATTTAAT
4733116 TATTTTATTGAA-ATAA
1 TATTTTATT-AATATAA
4733132 TATTTTAATTAATATAA
1 TATTTT-ATTAATATAA
4733149 T-TTTTATTTAATA-AA
1 TATTTTA-TTAATATAA
4733164 TA
1 TA
4733166 ATAATTAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
15 4 0.13
16 18 0.60
17 8 0.27
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (16 bp):
TATTTTATTAATATAA
Found at i:4736112 original size:41 final size:41
Alignment explanation
Indices: 4736055--4736299 Score: 400
Period size: 41 Copynumber: 6.0 Consensus size: 41
4736045 NNNNNNNNNN
4736055 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
** *
4736096 CCTAGCAGGCTAAGTGCCGGTGATTTGAATCAAGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
*
4736137 CCTAGCAGGCTAAGTGCCGGTGAACTAAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
* *
4736178 CCTAGCAGGCTAAGTGCAGGTGAACTAAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
**
4736219 CCTAGCAGGCTAAGTGCCGGTGATTTGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
* *
4736260 CCTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGCTATAA
1 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAA
4736300 TAAGCTATAA
Statistics
Matches: 190, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 190 1.00
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (41 bp):
CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
Found at i:4745807 original size:44 final size:46
Alignment explanation
Indices: 4745721--4745813 Score: 138
Period size: 44 Copynumber: 2.1 Consensus size: 46
4745711 ATAGGGCTGT
*
4745721 AATGGAATAGAGTTGTAATCAGTAATTCAATTGTTTGGTTGAATGG
1 AATGGAATAGAGCTGTAATCAGTAATTCAATTGTTTGGTTGAATGG
*
4745767 AATGGAATAGAGCTGTAAT-AG-AATTC-TTGTGTTTGGTTGAATGG
1 AATGGAATAGAGCTGTAATCAGTAATTCAAT-TGTTTGGTTGAATGG
4745811 AAT
1 AAT
4745814 AGATGTTGTA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
43 1 0.02
44 23 0.52
45 2 0.05
46 18 0.41
ACGTcount: A:0.32, C:0.04, G:0.27, T:0.37
Consensus pattern (46 bp):
AATGGAATAGAGCTGTAATCAGTAATTCAATTGTTTGGTTGAATGG
Found at i:4751996 original size:9 final size:9
Alignment explanation
Indices: 4751982--4752013 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
4751972 TTTGGTTAAA
4751982 AATTAACCG
1 AATTAACCG
4751991 AATTAACCG
1 AATTAACCG
*
4752000 AATTAACCA
1 AATTAACCG
4752009 AATTA
1 AATTA
4752014 TCCTGGGCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.50, C:0.19, G:0.06, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:4758424 original size:13 final size:13
Alignment explanation
Indices: 4758403--4758466 Score: 85
Period size: 13 Copynumber: 4.9 Consensus size: 13
4758393 ACACTCAAAT
4758403 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
* *
4758416 TTCTCAAAAGTAC
1 TTTTCAAAAGCAC
*
4758429 TTTTTC-ACAGCAC
1 -TTTTCAAAAGCAC
4758442 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
4758455 TTTTCAAAAGCA
1 TTTTCAAAAGCA
4758467 ATAAAGAACT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
12 5 0.12
13 34 0.79
14 4 0.09
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.33
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:4766091 original size:5 final size:6
Alignment explanation
Indices: 4766076--4766100 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
4766066 ATATGAAACA
4766076 AAAAAG AAAAAG AAAAAG AAAAAG A
1 AAAAAG AAAAAG AAAAAG AAAAAG A
4766101 TGATATTGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:4767791 original size:27 final size:27
Alignment explanation
Indices: 4767760--4767811 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
4767750 ACAAACAACA
*
4767760 AAATTCAAAACAAAGGAAAACAGAAGC
1 AAATTCAAAAAAAAGGAAAACAGAAGC
* *
4767787 AAATTCAAAAAAAATGATAACAGAA
1 AAATTCAAAAAAAAGGAAAACAGAA
4767812 AATTTCAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.65, C:0.12, G:0.12, T:0.12
Consensus pattern (27 bp):
AAATTCAAAAAAAAGGAAAACAGAAGC
Found at i:4770964 original size:27 final size:28
Alignment explanation
Indices: 4770931--4771024 Score: 90
Period size: 27 Copynumber: 3.5 Consensus size: 28
4770921 AAACAAACAA
*
4770931 CAAAATTCAAAACAAAGGAAAACAGCAG
1 CAAAATTCAAAACAAAGGAAAACACCAG
* * *
4770959 C-AAATTCAAAATAAATGATAACACCAG
1 CAAAATTCAAAACAAAGGAAAACACCAG
*
4770986 CAAAATTC-AAATAAA-GAATAACACCAG
1 CAAAATTCAAAACAAAGGAA-AACACCAG
*
4771013 -AAAGTT-AAAACA
1 CAAAATTCAAAACA
4771025 CATGATTAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
26 11 0.20
27 38 0.68
28 7 0.12
ACGTcount: A:0.60, C:0.17, G:0.10, T:0.14
Consensus pattern (28 bp):
CAAAATTCAAAACAAAGGAAAACACCAG
Found at i:4771790 original size:27 final size:27
Alignment explanation
Indices: 4771763--4771822 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
4771753 AACAAAAAAA
* *
4771763 TTCAAAATAAATGATAACACCAGCAAAT
1 TTCAAAATAAAGGATAACACCAG-AAAG
*
4771791 TTC-AAATAAAGGATAACCCCAGAAAG
1 TTCAAAATAAAGGATAACACCAGAAAG
4771817 TTCAAA
1 TTCAAA
4771823 CACATTCTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 6 0.21
27 19 0.68
28 3 0.11
ACGTcount: A:0.52, C:0.18, G:0.10, T:0.20
Consensus pattern (27 bp):
TTCAAAATAAAGGATAACACCAGAAAG
Found at i:4779225 original size:1 final size:1
Alignment explanation
Indices: 4779219--4779260 Score: 66
Period size: 1 Copynumber: 42.0 Consensus size: 1
4779209 AAACGCTCAA
**
4779219 CCCCCCCCCCCCCCCCCCCCNNCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
4779261 AAAACAGAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.00, C:0.95, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:4780093 original size:40 final size:40
Alignment explanation
Indices: 4780038--4780115 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
4780028 GATGTCAGGG
* * * *
4780038 GACGTGTCAGCAAATCGCGTCCACATCAGCGTGGTTTGCT
1 GACGTGGCAGCAAATCCCGTCCACATAAGCGCGGTTTGCT
*
4780078 GACGTGGCAGCAAATCCCGTCCACGTAAGCGCGGTTTG
1 GACGTGGCAGCAAATCCCGTCCACATAAGCGCGGTTTG
4780116 TGTCCACGCC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.21, C:0.28, G:0.29, T:0.22
Consensus pattern (40 bp):
GACGTGGCAGCAAATCCCGTCCACATAAGCGCGGTTTGCT
Found at i:4780273 original size:19 final size:19
Alignment explanation
Indices: 4780246--4780282 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
4780236 CCAACGGTCC
*
4780246 AAAACAAACTATAAATACT
1 AAAAAAAACTATAAATACT
4780265 AAAAAAAACTATAAATAC
1 AAAAAAAACTATAAATAC
4780283 CCCACCCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.68, C:0.14, G:0.00, T:0.19
Consensus pattern (19 bp):
AAAAAAAACTATAAATACT
Found at i:4780329 original size:12 final size:12
Alignment explanation
Indices: 4780312--4780354 Score: 56
Period size: 11 Copynumber: 3.8 Consensus size: 12
4780302 AACTAATCCT
4780312 CTCTCAAATTTC
1 CTCTCAAATTTC
4780324 CTCTCAAA-TTC
1 CTCTCAAATTTC
4780335 CT-TCAAAATTT-
1 CTCTC-AAATTTC
4780346 CTCTCAAAT
1 CTCTCAAAT
4780355 CCATATTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
10 2 0.07
11 14 0.50
12 12 0.43
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.40
Consensus pattern (12 bp):
CTCTCAAATTTC
Found at i:4781312 original size:7 final size:7
Alignment explanation
Indices: 4781300--4781324 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
4781290 GTGGACCACC
4781300 TATTTAG
1 TATTTAG
4781307 TATTTAG
1 TATTTAG
4781314 TATTTAG
1 TATTTAG
4781321 TATT
1 TATT
4781325 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:4782644 original size:22 final size:22
Alignment explanation
Indices: 4782592--4783256 Score: 818
Period size: 22 Copynumber: 30.8 Consensus size: 22
4782582 CCTTAACCCT
4782592 AACCCT-AACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
* *
4782613 AA-CCTTAACCCTTAAATTAAA
1 AACCCTAAACCCTTAACTTAAA
*
4782634 AACCCTAAACCCTTAACCTAAA
1 AACCCTAAACCCTTAACTTAAA
*
4782656 AACCCT-AACCCTTAACCTAAA
1 AACCCTAAACCCTTAACTTAAA
* *
4782677 AACTCTAACCCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
* *
4782699 AACACTAAACCCTTAAATTAAA
1 AACCCTAAACCCTTAACTTAAA
4782721 AACCCTAAACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
4782743 AACCCT-AACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
* *
4782764 AACCATAAACCCTTAAATTAAA
1 AACCCTAAACCCTTAACTTAAA
* *
4782786 AATCCTAAACCTTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
*
4782808 AACCCT-AACCCTTAACTTTAA
1 AACCCTAAACCCTTAACTTAAA
*
4782829 AACCCT-AACCTCTTGACTTAAA
1 AACCCTAAACC-CTTAACTTAAA
*
4782851 AACCCTAAACCCTTAAATTAAA
1 AACCCTAAACCCTTAACTTAAA
* *
4782873 AACCATAAACCCTTAATTTAAA
1 AACCCTAAACCCTTAACTTAAA
* *
4782895 AACACT-ACCCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
*
4782916 AACCTTAAACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
*
4782938 AACCCTAACCCCTTAACTT-AA
1 AACCCTAAACCCTTAACTTAAA
* *
4782959 AACCCTAAGCCCTTAAATTAAA
1 AACCCTAAACCCTTAACTTAAA
*
4782981 AACCCCAAACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
* *
4783003 AACTCT-AACCCTTAAATTAAA
1 AACCCTAAACCCTTAACTTAAA
*
4783024 AACCCTAAACCCTTAAATTAAA
1 AACCCTAAACCCTTAACTTAAA
*
4783046 AACCCTAAACCTTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
* *
4783068 AACCCT-AACCTTTAACTTTAA
1 AACCCTAAACCCTTAACTTAAA
*
4783089 AACCCTAACCCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
* *
4783111 AACCCTAAACACTTAAATTAAA
1 AACCCTAAACCCTTAACTTAAA
* ** * *
4783133 AACCCAAAACTTTTAAGTTATA
1 AACCCTAAACCCTTAACTTAAA
*
4783155 AACCCT-AACCCTTAACTTTAA
1 AACCCTAAACCCTTAACTTAAA
*
4783176 AACCCTAAACACTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
** * *
4783198 AACTGT-AACCCTTAAATAAAA
1 AACCCTAAACCCTTAACTTAAA
*
4783219 AACCCT-AACACTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
4783240 AACCCT-AACCCTTAACT
1 AACCCTAAACCCTTAACT
4783257 AAATATAATT
Statistics
Matches: 555, Mismatches: 78, Indels: 22
0.85 0.12 0.03
Matches are distributed among these distances:
20 3 0.01
21 216 0.39
22 332 0.60
23 4 0.01
ACGTcount: A:0.45, C:0.29, G:0.01, T:0.25
Consensus pattern (22 bp):
AACCCTAAACCCTTAACTTAAA
Found at i:4782721 original size:65 final size:65
Alignment explanation
Indices: 4782592--4783256 Score: 842
Period size: 65 Copynumber: 10.3 Consensus size: 65
4782582 CCTTAACCCT
* * *
4782592 AACCCT-AACCCTTAACTTAAAAACCTTAACCCTTAAATTAAAAACCCTAAACCCTTAACCTAAA
1 AACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAA
* * * *
4782656 AACCCT-AACCCTTAACCTAAAAACTCTAACCCCTTAACTTAAAAACACTAAACCCTTAAATTAA
1 AACCCTAAACCCTTAACTTAAAAACCCTAA-CCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
4782720 A
65 A
* *
4782721 AACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCATAAACCCTTAAATTAAA
1 AACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAA
* * * *
4782786 AATCCTAAACCTTTAACTTAAAAACCCTAACCCTTAACTTTAAAACCCT-AACCTCTTGACTTAA
1 AACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAAACC-CTTAACTTAA
4782850 A
65 A
* * * * *
4782851 AACCCTAAACCCTTAAATTAAAAACCATAAACCCTTAATTTAAAAACACT-ACCCCTTAACTTAA
1 AACCCTAAACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
4782915 A
65 A
* * *
4782916 AACCTTAAACCCTTAACTTAAAAACCCTAACCCCTTAACTT-AAAACCCTAAGCCCTTAAATTAA
1 AACCCTAAACCCTTAACTTAAAAACCCTAA-CCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
4782980 A
65 A
* * * *
4782981 AACCCCAAACCCTTAACTTAAAAACTCTAACCCTTAAATTAAAAACCCTAAACCCTTAAATTAAA
1 AACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAA
* * * *
4783046 AACCCTAAACCTTTAACTTAAAAACCCTAACCTTTAACTTTAAAACCCTAACCCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAA
* * * ** * * *
4783111 AACCCTAAACACTTAAATTAAAAACCCAAAACTTTTAAGTTATAAACCCT-AACCCTTAACTTTA
1 AACCCTAAACCCTTAACTTAAAAACCC-TAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
4783175 A
65 A
* ** * * *
4783176 AACCCTAAACACTTAACTTAAAAACTGTAACCCTTAAATAAAAAACCCT-AACACTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAA
4783240 AACCCT-AACCCTTAACT
1 AACCCTAAACCCTTAACT
4783257 AAATATAATT
Statistics
Matches: 525, Mismatches: 68, Indels: 17
0.86 0.11 0.03
Matches are distributed among these distances:
63 10 0.02
64 83 0.16
65 373 0.71
66 59 0.11
ACGTcount: A:0.45, C:0.29, G:0.01, T:0.25
Consensus pattern (65 bp):
AACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAA
Found at i:4782725 original size:87 final size:86
Alignment explanation
Indices: 4782592--4783256 Score: 854
Period size: 87 Copynumber: 7.7 Consensus size: 86
4782582 CCTTAACCCT
* * *
4782592 AACCCT-AACCCTTAACTTAAAAA-CCTTAACCCTTAAATTAAAAACCCTAAACCCTTAACCTAA
1 AACCCTAAACCCTTAAATTAAAAACCCTAAACCCTTAAATTAAAAACCCT-AACCCTTAACTTAA
*
4782655 AAACCCTAACCCTTAACCTAAA
65 AAACCCTAACCCTTAACTTAAA
* * * *
4782677 AACTCTAACCCCTTAACTTAAAAACACTAAACCCTTAAATTAAAAACCCTAAACCCTTAACTTAA
1 AACCCTAAACCCTTAAATTAAAAACCCTAAACCCTTAAATTAAAAACCCT-AACCCTTAACTTAA
4782742 AAACCCTAACCCTTAACTTAAA
65 AAACCCTAACCCTTAACTTAAA
* * * * *
4782764 AACCATAAACCCTTAAATTAAAAATCCTAAACCTTTAACTTAAAAACCCTAACCCTTAACTTTAA
1 AACCCTAAACCCTTAAATTAAAAACCCTAAACCCTTAAATTAAAAACCCTAACCCTTAACTTAAA
*
4782829 AACCCTAACCTCTTGACTTAAA
66 AACCCTAACC-CTTAACTTAAA
* * * *
4782851 AACCCTAAACCCTTAAATTAAAAACCATAAACCCTTAATTTAAAAACACTACCCCTTAACTTAAA
1 AACCCTAAACCCTTAAATTAAAAACCCTAAACCCTTAAATTAAAAACCCTAACCCTTAACTTAAA
*
4782916 AACCTTAAACCCTTAACTTAAA
66 AACCCT-AACCCTTAACTTAAA
* * * *
4782938 AACCCTAACCCCTTAACTT-AAAACCCTAAGCCCTTAAATTAAAAACCCCAAACCCTTAACTTAA
1 AACCCTAAACCCTTAAATTAAAAACCCTAAACCCTTAAATTAAAAA-CCCTAACCCTTAACTTAA
* *
4783002 AAACTCTAACCCTTAAATTAAA
65 AAACCCTAACCCTTAACTTAAA
* * * *
4783024 AACCCTAAACCCTTAAATTAAAAACCCTAAACCTTTAACTTAAAAACCCTAACCTTTAACTTTAA
1 AACCCTAAACCCTTAAATTAAAAACCCTAAACCCTTAAATTAAAAACCCTAACCCTTAACTTAAA
4783089 AACCCTAACCCCTTAACTTAAA
66 AACCCTAA-CCCTTAACTTAAA
* * ** * * *
4783111 AACCCTAAACACTTAAATTAAAAACCCAAAACTTTTAAGTTATAAACCCTAACCCTTAACTTTAA
1 AACCCTAAACCCTTAAATTAAAAACCCTAAACCCTTAAATTAAAAACCCTAACCCTTAACTTAAA
*
4783176 AACCCTAAACACTTAACTTAAA
66 AACCCT-AACCCTTAACTTAAA
** * * *
4783198 AACTGT-AACCCTTAAATAAAAAACCCT-AACACTTAACTTAAAAACCCTAACCCTTAACT
1 AACCCTAAACCCTTAAATTAAAAACCCTAAACCCTTAAATTAAAAACCCTAACCCTTAACT
4783257 AAATATAATT
Statistics
Matches: 509, Mismatches: 63, Indels: 16
0.87 0.11 0.03
Matches are distributed among these distances:
85 33 0.06
86 135 0.27
87 335 0.66
88 6 0.01
ACGTcount: A:0.45, C:0.29, G:0.01, T:0.25
Consensus pattern (86 bp):
AACCCTAAACCCTTAAATTAAAAACCCTAAACCCTTAAATTAAAAACCCTAACCCTTAACTTAAA
AACCCTAACCCTTAACTTAAA
Found at i:4786848 original size:127 final size:125
Alignment explanation
Indices: 4786425--4786885 Score: 656
Period size: 126 Copynumber: 3.7 Consensus size: 125
4786415 AACATGCTAT
* * * * *
4786425 TGTAACAAAAACGCGTCCACGTGGGCGCGATTTCACAAATTCTTTTCATAAAGCATCCTGCTAGA
1 TGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGA
* * *
4786490 AGCG-ATTTTATACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTTTCCAGTACCTAC
66 AGCGTTTTTTAAACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTTTCCAGGACCTAC
*
4786549 TGTAGCAAAAGCGCGTCCACGAGGGTGCGATTTCACAAATTCTTCTCA-AATAGCATCCTGCTTG
1 TGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAA-AGCATCCTGCTTG
* * * * * *
4786613 CAGCGTTGTTTTATACTACTTGCTTAGAAATGTCAAGTCGAAATTATTTTTTCAGGACCTAC
65 AAGCGTT-TTTTAAACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTTTCCAGGACCTAC
* *
4786675 TGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTACTTGA
1 TGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGA
* *
4786740 AGCGTTTTTCTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGACCAAC
66 AGCGTTTTT-TAAACTATTTGCTCAGAAACGTCAAGTCGAAATTATTT-TTCCAGGACCTAC
* * * * *
4786802 TGTAGCAAAAGCGCATCCACGAGGGCGCAATTTCACAAATTTTTCTCATAAAGCATCTTGTTTGA
1 TGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGA
4786867 AGCGTTTTTTAAACTATTT
66 AGCGTTTTTTAAACTATTT
4786886 TCCAGGACCT
Statistics
Matches: 300, Mismatches: 31, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
123 2 0.01
124 59 0.20
125 3 0.01
126 156 0.52
127 80 0.27
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.31
Consensus pattern (125 bp):
TGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGA
AGCGTTTTTTAAACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTTTCCAGGACCTAC
Found at i:4787381 original size:12 final size:13
Alignment explanation
Indices: 4787353--4787382 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
4787343 TAATTGTTAA
4787353 TATTATTAAATTT
1 TATTATTAAATTT
4787366 TATTATTAAA-TT
1 TATTATTAAATTT
4787378 TATTA
1 TATTA
4787383 GATGTGATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TATTATTAAATTT
Found at i:4799925 original size:17 final size:17
Alignment explanation
Indices: 4799903--4799966 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 17
4799893 AATCTTAGAG
4799903 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
* *
4799920 TTCTAATTGTGT-CTTAGAG
1 TTCTAATTGTATAC--AG-C
4799939 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
*
4799956 TTTTAATTGTA
1 TTCTAATTGTA
4799967 GCCTTTGATG
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
16 1 0.03
17 21 0.55
18 4 0.11
19 11 0.29
20 1 0.03
ACGTcount: A:0.27, C:0.12, G:0.14, T:0.47
Consensus pattern (17 bp):
TTCTAATTGTATACAGC
Found at i:4799942 original size:36 final size:36
Alignment explanation
Indices: 4799895--4799965 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
4799885 GATTATGTAA
4799895 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
*
4799931 TCTTAGAGTTCTAATTGTATACAGCTTTTAATTGT
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGT
4799966 AGCCTTTGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.25, C:0.13, G:0.15, T:0.46
Consensus pattern (36 bp):
TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
Found at i:4799944 original size:19 final size:19
Alignment explanation
Indices: 4799894--4799950 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
4799884 AGATTATGTA
4799894 ATCTTAGAGTTCTAATTGT
1 ATCTTAGAGTTCTAATTGT
*
4799913 ATAC--AG-CTTCTAATTGT
1 AT-CTTAGAGTTCTAATTGT
*
4799930 GTCTTAGAGTTCTAATTGT
1 ATCTTAGAGTTCTAATTGT
4799949 AT
1 AT
4799951 ACAGCTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
16 1 0.03
17 11 0.37
18 4 0.13
19 13 0.43
20 1 0.03
ACGTcount: A:0.26, C:0.12, G:0.16, T:0.46
Consensus pattern (19 bp):
ATCTTAGAGTTCTAATTGT
Found at i:4800246 original size:48 final size:48
Alignment explanation
Indices: 4800174--4800265 Score: 148
Period size: 48 Copynumber: 1.9 Consensus size: 48
4800164 GGAAATTCTG
*
4800174 TTGAATCATTTATCATTGCAAGTTAGGCCGACTTAGGCGTTTTTGCTT
1 TTGAATCATTTATCATTGCAAGTTAGGCCGACTTAGGCATTTTTGCTT
* * *
4800222 TTGAATCCTTTATCATTGCGAGTTAGGCTGACTTAGGCATTTTT
1 TTGAATCATTTATCATTGCAAGTTAGGCCGACTTAGGCATTTTT
4800266 TAAGCAAAGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.21, C:0.16, G:0.21, T:0.42
Consensus pattern (48 bp):
TTGAATCATTTATCATTGCAAGTTAGGCCGACTTAGGCATTTTTGCTT
Found at i:4805083 original size:36 final size:36
Alignment explanation
Indices: 4805031--4805101 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
4805021 GATTATGTAA
*
4805031 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
1 TCTTAGAGTTCTAATTGTATACAACTTCTAATTGTG
* *
4805067 TCTTGGAGTTCTAATTGTATACAACTTTTAATTGT
1 TCTTAGAGTTCTAATTGTATACAACTTCTAATTGT
4805102 AGCCTTTGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.25, C:0.13, G:0.15, T:0.46
Consensus pattern (36 bp):
TCTTAGAGTTCTAATTGTATACAACTTCTAATTGTG
Found at i:4805381 original size:48 final size:48
Alignment explanation
Indices: 4805306--4805400 Score: 172
Period size: 48 Copynumber: 2.0 Consensus size: 48
4805296 TGAGGGAATT
*
4805306 CTGTTGAATCCTTTATCATTGCAAGTTAGGCTGACTTAGGCGTTTTTG
1 CTGTTGAATCCTTTATCATTGCAAGTTAGGCTGACTTAGGCATTTTTG
*
4805354 CTGTTGAATCCTTTATCATTGCGAGTTAGGCTGACTTAGGCATTTTT
1 CTGTTGAATCCTTTATCATTGCAAGTTAGGCTGACTTAGGCATTTTT
4805401 TAAGCAAAGA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.19, C:0.17, G:0.22, T:0.42
Consensus pattern (48 bp):
CTGTTGAATCCTTTATCATTGCAAGTTAGGCTGACTTAGGCATTTTTG
Found at i:4807972 original size:42 final size:42
Alignment explanation
Indices: 4807914--4808037 Score: 239
Period size: 42 Copynumber: 3.0 Consensus size: 42
4807904 GATGCAAGGG
4807914 ACACACGGCCAAACCACACGTTCGTGTGCATGACCGTGTGTC
1 ACACACGGCCAAACCACACGTTCGTGTGCATGACCGTGTGTC
*
4807956 ACACACGGCCAAACCACACGTTCGTGTGCATGATCGTGTGTC
1 ACACACGGCCAAACCACACGTTCGTGTGCATGACCGTGTGTC
4807998 ACACACGGCCAAACCACACGTTCGTGTGCATGACCGTGTG
1 ACACACGGCCAAACCACACGTTCGTGTGCATGACCGTGTG
4808038 GATGAAAATA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 80 1.00
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.19
Consensus pattern (42 bp):
ACACACGGCCAAACCACACGTTCGTGTGCATGACCGTGTGTC
Found at i:4808659 original size:25 final size:25
Alignment explanation
Indices: 4808630--4808715 Score: 70
Period size: 25 Copynumber: 3.5 Consensus size: 25
4808620 GCCCTCTCTC
4808630 GAGCCATATAACAAGAAGCTCATGT
1 GAGCCATATAACAAGAAGCTCATGT
* ** *
4808655 GAGCCATGTAACGGGAAGCTTATCCG-
1 GAGCCATATAACAAGAAGCTCAT--GT
** *
4808681 GA-CTGTATAACAAGAAGCTCATAT
1 GAGCCATATAACAAGAAGCTCATGT
4808705 GAGCCA-ATAAC
1 GAGCCATATAAC
4808716 GGGTAGCTCC
Statistics
Matches: 44, Mismatches: 13, Indels: 9
0.67 0.20 0.14
Matches are distributed among these distances:
24 7 0.16
25 34 0.77
26 2 0.05
27 1 0.02
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.20
Consensus pattern (25 bp):
GAGCCATATAACAAGAAGCTCATGT
Found at i:4808908 original size:24 final size:25
Alignment explanation
Indices: 4808881--4808928 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
4808871 GGATGCTCCG
*
4808881 AAGAACTAT-TAACGAGAAGCTCGC
1 AAGAACCATATAACGAGAAGCTCGC
4808905 AAGAACCATATAACGAGAAGCTCG
1 AAGAACCATATAACGAGAAGCTCG
4808929 AGAGGGCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.44, C:0.21, G:0.21, T:0.15
Consensus pattern (25 bp):
AAGAACCATATAACGAGAAGCTCGC
Found at i:4809579 original size:99 final size:100
Alignment explanation
Indices: 4809408--4809606 Score: 391
Period size: 99 Copynumber: 2.0 Consensus size: 100
4809398 ATTTAATCCT
4809408 TATTCCAAGCCTAACCGATTTTTACATATAACATTTGCAGCCCATGTAATTCATAAAATTCATAA
1 TATTCCAAGCCTAACCGATTTTTACATATAACATTTGCAGCCCATGTAATTCATAAAATTCATAA
4809473 TTTTTCCATGAATTTTAAATCTTT-CAATTTAGTC
66 TTTTTCCATGAATTTTAAATCTTTACAATTTAGTC
4809507 TATTCCAAGCCTAACCGATTTTTACATATAACATTTGCAGCCCATGTAATTCATAAAATTCATAA
1 TATTCCAAGCCTAACCGATTTTTACATATAACATTTGCAGCCCATGTAATTCATAAAATTCATAA
4809572 TTTTTCCATGAATTTTAAATCTTTACAATTTAGTC
66 TTTTTCCATGAATTTTAAATCTTTACAATTTAGTC
4809607 CCTAAATCAC
Statistics
Matches: 99, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
99 89 0.90
100 10 0.10
ACGTcount: A:0.34, C:0.19, G:0.07, T:0.40
Consensus pattern (100 bp):
TATTCCAAGCCTAACCGATTTTTACATATAACATTTGCAGCCCATGTAATTCATAAAATTCATAA
TTTTTCCATGAATTTTAAATCTTTACAATTTAGTC
Found at i:4811382 original size:58 final size:58
Alignment explanation
Indices: 4811320--4811462 Score: 173
Period size: 58 Copynumber: 2.5 Consensus size: 58
4811310 AAATTAGAAA
* * ** *
4811320 AAAAAGTGTCAAGTT-TAGATACCACATTGGACCGAAAAAACTAATGTA-ATAAATTAAG
1 AAAAAGTGTCAAGTTCAAG-TACCAAATTGGACAAAAAAAACTAATATATATAAA-TAAG
* *
4811378 AAAAAGTGTCAAGTTCAAGTACCAAATTGGACAAAAAAAACTTATATATCTAAATAAG
1 AAAAAGTGTCAAGTTCAAGTACCAAATTGGACAAAAAAAACTAATATATATAAATAAG
* *
4811436 AAAAAGTGTCAAATTCATGTACCAAAT
1 AAAAAGTGTCAAGTTCAAGTACCAAAT
4811463 ACTATATTAA
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
58 68 0.92
59 6 0.08
ACGTcount: A:0.50, C:0.13, G:0.13, T:0.24
Consensus pattern (58 bp):
AAAAAGTGTCAAGTTCAAGTACCAAATTGGACAAAAAAAACTAATATATATAAATAAG
Found at i:4813863 original size:21 final size:22
Alignment explanation
Indices: 4813822--4813864 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
4813812 TAAATAAATG
4813822 TGTAATAAATATATGTATACATT
1 TGTAATAAATATATG-ATACATT
*
4813845 TGTAATTAATATATG-TACAT
1 TGTAATAAATATATGATACAT
4813865 ACTTATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
23 14 0.74
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (22 bp):
TGTAATAAATATATGATACATT
Found at i:4814005 original size:27 final size:26
Alignment explanation
Indices: 4813958--4814014 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
4813948 GCAGAATAGC
* * *
4813958 AAAACGAAAACAGGGGAGAAAGGAAAG
1 AAAAAGAAAACAGGGAAGAAA-CAAAG
4813985 AAAAAGAAAA-AGGGAAGGAAACAAAG
1 AAAAAGAAAACAGGGAA-GAAACAAAG
4814011 AAAA
1 AAAA
4814015 TTTAGGATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 13 0.50
27 13 0.50
ACGTcount: A:0.67, C:0.05, G:0.28, T:0.00
Consensus pattern (26 bp):
AAAAAGAAAACAGGGAAGAAACAAAG
Found at i:4819481 original size:14 final size:14
Alignment explanation
Indices: 4819415--4819474 Score: 52
Period size: 14 Copynumber: 4.2 Consensus size: 14
4819405 GATATTTTAG
4819415 TTAATATATATTATA
1 TTAAT-TATATTATA
*
4819430 TTTATT-TACTTA-A
1 TTAATTATA-TTATA
* *
4819443 TAAATAAGTATTATA
1 TTAATTA-TATTATA
4819458 TTAATTATATTATA
1 TTAATTATATTATA
4819472 TTA
1 TTA
4819475 TATATATGTA
Statistics
Matches: 35, Mismatches: 6, Indels: 9
0.70 0.12 0.18
Matches are distributed among these distances:
13 6 0.17
14 17 0.49
15 12 0.34
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (14 bp):
TTAATTATATTATA
Found at i:4820825 original size:18 final size:17
Alignment explanation
Indices: 4820767--4820825 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 17
4820757 TTTTTTTGAG
*
4820767 AACACGAAAAATTTTTAA
1 AACACG-AAAATTCTTAA
**
4820785 AACACGAGGA-TCTTAGA
1 AACACGAAAATTCTTA-A
4820802 AACACGAAAATTCTTAA
1 AACACGAAAATTCTTAA
4820819 AAGCACG
1 AA-CACG
4820826 GGGATTTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
16 4 0.12
17 14 0.42
18 15 0.45
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.20
Consensus pattern (17 bp):
AACACGAAAATTCTTAA
Found at i:4820849 original size:38 final size:38
Alignment explanation
Indices: 4820800--4820873 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
4820790 GAGGATCTTA
*
4820800 GAAACACGAAAATTCTT-AAAAGCACGGGGATTTTTTTT
1 GAAACACGAAAATTCTTGAAAA-CACGGGAATTTTTTTT
* * *
4820838 GAAACATGAAAATTTTTGAAAACACGGTAATTTTTT
1 GAAACACGAAAATTCTTGAAAACACGGGAATTTTTT
4820874 AAAACACGGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 27 0.87
39 4 0.13
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (38 bp):
GAAACACGAAAATTCTTGAAAACACGGGAATTTTTTTT
Found at i:4820860 original size:18 final size:18
Alignment explanation
Indices: 4820833--4821190 Score: 103
Period size: 18 Copynumber: 19.9 Consensus size: 18
4820823 ACGGGGATTT
*
4820833 TTTTTG-AAACATGAAAA
1 TTTTTGAAAACACGAAAA
**
4820850 TTTTTGAAAACACGGTAA
1 TTTTTGAAAACACGAAAA
* **
4820868 TTTTTTAAAACACGGGAA
1 TTTTTGAAAACACGAAAA
* *
4820886 TTTTTGGAAACATGAAAA
1 TTTTTGAAAACACGAAAA
*
4820904 -TTTTG-AAACACCG-AAG
1 TTTTTGAAAACA-CGAAAA
4820920 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
*** * * ***
4820938 TTTTTTTTATCGCCTGAA
1 TTTTTGAAAACACGAAAA
* * *
4820956 TTTTTGGAAACGCGGAAA
1 TTTTTGAAAACACGAAAA
*
4820974 TTTTTG-AAACACCGAAATTT
1 TTTTTGAAAACA-CGAAA--A
* *
4820994 TTTTTAAAAAAACACGAAGA
1 TTTTT--GAAAACACGAAAA
* **
4821014 TTTTTG-AAACACAGTATT
1 TTTTTGAAAACAC-GAAAA
4821032 TTTTTG-AAACACAGAAAA
1 TTTTTGAAAACAC-GAAAA
*** **
4821050 -TTTTGAAAATTTGAATTTT
1 TTTTTGAAAACACGAA--AA
* * *
4821069 TTTTATGAAAATACGGGAAT
1 TTTT-TGAAAACAC-GAAAA
* *
4821089 TTTTTGAAAAAATGAAAA
1 TTTTTGAAAACACGAAAA
* *
4821107 ATTTTG-AAACACG--AG
1 TTTTTGAAAACACGAAAA
*
4821122 TTTTTGAAAATACGAAAA
1 TTTTTGAAAACACGAAAA
* * *
4821140 TTTTTTAAAACGCAAAAA
1 TTTTTGAAAACACGAAAA
**
4821158 TTTTT--AAACACGAGATT
1 TTTTTGAAAACACGA-AAA
*
4821175 TTTTTTAAAACACGAA
1 TTTTTGAAAACACGAA
4821191 TATATTTTTT
Statistics
Matches: 248, Mismatches: 69, Indels: 47
0.68 0.19 0.13
Matches are distributed among these distances:
15 6 0.02
16 19 0.08
17 48 0.19
18 124 0.50
19 15 0.06
20 18 0.07
21 7 0.03
22 6 0.02
23 5 0.02
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.35
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:4820924 original size:70 final size:71
Alignment explanation
Indices: 4820834--4820995 Score: 184
Period size: 70 Copynumber: 2.3 Consensus size: 71
4820824 CGGGGATTTT
* ** *
4820834 TTTTGAAACA-TGAAAATTTTTGAAAACACGGTAATTTTTTAAAACACGGGAATTTTTGGAAAC-
1 TTTTGAAACACCG-AAATTTTTGAAAACACGAAAATTTTTTAAAACACCGGAATTTTTGGAAACG
*
4820897 ATGAAAA
65 AGGAAAA
* ** * * * *
4820904 TTTTGAAACACCGAAGTTTTTGAAAACACGAAAATTTTTTTTATCGCCTGAATTTTTGGAAACGC
1 TTTTGAAACACCGAAATTTTTGAAAACACGAAAATTTTTTAAAACACCGGAATTTTTGGAAACGA
*
4820969 GGAAAT
66 GGAAAA
4820975 TTTTGAAACACCGAAATTTTT
1 TTTTGAAACACCGAAATTTTT
4820996 TTTAAAAAAA
Statistics
Matches: 76, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
70 51 0.67
71 25 0.33
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (71 bp):
TTTTGAAACACCGAAATTTTTGAAAACACGAAAATTTTTTAAAACACCGGAATTTTTGGAAACGA
GGAAAA
Found at i:4820995 original size:17 final size:17
Alignment explanation
Indices: 4820833--4820995 Score: 82
Period size: 17 Copynumber: 9.3 Consensus size: 17
4820823 ACGGGGATTT
*
4820833 TTTTTGAAACA-TGAAAA
1 TTTTTGAAACACCG-AAA
* *
4820850 TTTTTGAAAACACGGTAAT
1 TTTTTG-AAACACCG-AAA
* * *
4820869 TTTTTAAAACACGGGAA
1 TTTTTGAAACACCGAAA
*
4820886 TTTTTGGAAACA-TGAAA
1 TTTTT-GAAACACCGAAA
* *
4820903 ATTTTGAAACACCGAAG
1 TTTTTGAAACACCGAAA
4820920 TTTTTGAAA-ACACGAAAA
1 TTTTTGAAACAC-CG-AAA
** * *
4820938 TTTTTTTTATCGCCTG-AA
1 -TTTTTGAAACACC-GAAA
* *
4820956 TTTTTGGAAACGCGGAAA
1 TTTTT-GAAACACCGAAA
4820974 TTTTTGAAACACCGAAA
1 TTTTTGAAACACCGAAA
4820991 TTTTT
1 TTTTT
4820996 TTTAAAAAAA
Statistics
Matches: 111, Mismatches: 24, Indels: 22
0.71 0.15 0.14
Matches are distributed among these distances:
16 8 0.07
17 53 0.48
18 33 0.30
19 15 0.14
20 2 0.02
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (17 bp):
TTTTTGAAACACCGAAA
Found at i:4821025 original size:17 final size:17
Alignment explanation
Indices: 4821003--4821057 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
4820993 TTTTTTAAAA
4821003 AAACAC-GAAGATTTTTG
1 AAACACAGAA-ATTTTTG
**
4821020 AAACACAGTATTTTTTTG
1 AAACACAG-AAATTTTTG
*
4821038 AAACACAGAAAATTTTG
1 AAACACAGAAATTTTTG
4821055 AAA
1 AAA
4821058 ATTTGAATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
17 15 0.48
18 15 0.48
19 1 0.03
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (17 bp):
AAACACAGAAATTTTTG
Found at i:4821178 original size:52 final size:51
Alignment explanation
Indices: 4821068--4821178 Score: 127
Period size: 52 Copynumber: 2.1 Consensus size: 51
4821058 ATTTGAATTT
** *
4821068 TTTTTATGAAAATACGGGAATTTTTTGAAAAAATGAAAAATTTTGAAACACGAG
1 TTTTT-TGAAAATACGAAAATTTTTT--AAAAACGAAAAATTTTGAAACACGAG
*
4821122 -TTTTTGAAAATACGAAAATTTTTT-AAAACGCAAAAATTTTTAAACACGAG
1 TTTTTTGAAAATACGAAAATTTTTTAAAAACG-AAAAATTTTGAAACACGAG
4821172 ATTTTTT
1 -TTTTTT
4821179 TTAAAACACG
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
49 5 0.10
50 18 0.36
52 23 0.46
53 4 0.08
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.37
Consensus pattern (51 bp):
TTTTTTGAAAATACGAAAATTTTTTAAAAACGAAAAATTTTGAAACACGAG
Found at i:4821180 original size:19 final size:21
Alignment explanation
Indices: 4821158--4821208 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 21
4821148 AACGCAAAAA
4821158 TTTTTAAACACG-AGAT-TTT
1 TTTTTAAACACGAAGATATTT
* *
4821177 TTTTAAAACACGAATATATTT
1 TTTTTAAACACGAAGATATTT
4821198 TTTTTGAAACA
1 TTTTT-AAACA
4821209 TGGGAAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 11 0.42
20 3 0.12
21 7 0.27
22 5 0.19
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.45
Consensus pattern (21 bp):
TTTTTAAACACGAAGATATTT
Found at i:4821251 original size:17 final size:17
Alignment explanation
Indices: 4821229--4821272 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
4821219 ATTATTATTT
4821229 TTTTGAAACACGAGAAA-
1 TTTTGAAACACGA-AAAC
*
4821246 TTTTGAAAACATGAAAAC
1 TTTTG-AAACACGAAAAC
4821264 TTTTGAAAC
1 TTTTGAAAC
4821273 CCGATTAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.30
Consensus pattern (17 bp):
TTTTGAAACACGAAAAC
Found at i:4821255 original size:18 final size:18
Alignment explanation
Indices: 4821229--4821271 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
4821219 ATTATTATTT
4821229 TTTTG-AAACACGAGAAA-
1 TTTTGAAAACACGA-AAAC
*
4821246 TTTTGAAAACATGAAAAC
1 TTTTGAAAACACGAAAAC
4821264 TTTTGAAA
1 TTTTGAAA
4821272 CCCGATTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.47, C:0.09, G:0.14, T:0.30
Consensus pattern (18 bp):
TTTTGAAAACACGAAAAC
Found at i:4821391 original size:21 final size:22
Alignment explanation
Indices: 4821366--4821408 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
4821356 AGATTCTAAT
4821366 AAAACACG-AGAATTTTTATTA
1 AAAACACGAAGAATTTTTATTA
*
4821387 AAAACACGAAGATTTTTTATTA
1 AAAACACGAAGAATTTTTATTA
4821409 TATATTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.35
Consensus pattern (22 bp):
AAAACACGAAGAATTTTTATTA
Found at i:4821943 original size:10 final size:10
Alignment explanation
Indices: 4821925--4821989 Score: 53
Period size: 10 Copynumber: 6.4 Consensus size: 10
4821915 ACTTTTTTAT
4821925 TTTCTTTTTTC
1 TTTC-TTTTTC
*
4821936 TTTATTTTTC
1 TTTCTTTTTC
**
4821946 ACTCTTTTTC
1 TTTCTTTTTC
4821956 TTTCTTCTTTC
1 TTTCTT-TTTC
*
4821967 -TTCTTGTTCC
1 TTTCTT-TTTC
4821977 TTT-TTTTTC
1 TTTCTTTTTC
4821986 TTTC
1 TTTC
4821990 AAGCCCTAGC
Statistics
Matches: 42, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
9 6 0.14
10 27 0.64
11 9 0.21
ACGTcount: A:0.03, C:0.22, G:0.02, T:0.74
Consensus pattern (10 bp):
TTTCTTTTTC
Found at i:4822092 original size:16 final size:14
Alignment explanation
Indices: 4822071--4822113 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
4822061 GCCTTCTATT
4822071 CTTTTCTTCCTTCCTC
1 CTTTTCTT-CTT-CTC
*
4822087 CTTTTCTTCTTTTC
1 CTTTTCTTCTTCTC
4822101 CTTTTC-TCTTCTC
1 CTTTTCTTCTTCTC
4822114 TTTCCCCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 6 0.24
14 8 0.32
15 3 0.12
16 8 0.32
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (14 bp):
CTTTTCTTCTTCTC
Found at i:4822124 original size:18 final size:17
Alignment explanation
Indices: 4822081--4822126 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
4822071 CTTTTCTTCC
4822081 TTCCTCCTTT-TCTTCTT
1 TTCC-CCTTTCTCTTCTT
*
4822098 TT-CCTTTTCTCTTCTCT
1 TTCCCCTTTCTCTTCT-T
4822115 TTCCCCTTTCTC
1 TTCCCCTTTCTC
4822127 CCCTTCCCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
15 4 0.17
16 7 0.29
17 5 0.21
18 8 0.33
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (17 bp):
TTCCCCTTTCTCTTCTT
Found at i:4823339 original size:19 final size:19
Alignment explanation
Indices: 4823315--4823364 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
4823305 AAATGAGAAA
4823315 GTGAATTGTG-AATTGATAT
1 GTGAATT-TGAAATTGATAT
4823334 GTGAATTTGAAATTGATAT
1 GTGAATTTGAAATTGATAT
*
4823353 ATGAGATTTGAA
1 GTGA-ATTTGAA
4823365 GATATGAACC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 2 0.07
19 19 0.68
20 7 0.25
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (19 bp):
GTGAATTTGAAATTGATAT
Found at i:4828608 original size:14 final size:15
Alignment explanation
Indices: 4828579--4828611 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
4828569 AAATATAAAC
4828579 ATACAATTGAAACAA
1 ATACAATTGAAACAA
*
4828594 ATACAATT-CAACAA
1 ATACAATTGAAACAA
4828608 ATAC
1 ATAC
4828612 TTTAGTAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.58, C:0.18, G:0.03, T:0.21
Consensus pattern (15 bp):
ATACAATTGAAACAA
Found at i:4835720 original size:7 final size:7
Alignment explanation
Indices: 4835706--4835757 Score: 50
Period size: 7 Copynumber: 7.3 Consensus size: 7
4835696 TTTAATTTTT
4835706 AACCCTA
1 AACCCTA
*
4835713 AACTCTA
1 AACCCTA
4835720 AACCCTA
1 AACCCTA
**
4835727 AACATTAA
1 AACCCT-A
4835735 AACCCTA
1 AACCCTA
*
4835742 AACCTTA
1 AACCCTA
*
4835749 AAACCTA
1 AACCCTA
4835756 AA
1 AA
4835758 AACGGGCAAA
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
7 30 0.86
8 5 0.14
ACGTcount: A:0.50, C:0.31, G:0.00, T:0.19
Consensus pattern (7 bp):
AACCCTA
Found at i:4835739 original size:15 final size:14
Alignment explanation
Indices: 4835706--4835757 Score: 63
Period size: 14 Copynumber: 3.6 Consensus size: 14
4835696 TTTAATTTTT
4835706 AACCCTAAACTCT-A
1 AACCCTAAACT-TAA
4835720 AACCCTAAACATTAA
1 AACCCTAAAC-TTAA
4835735 AACCCTAAACCTTAA
1 AACCCTAAA-CTTAA
4835750 AA-CCTAAA
1 AACCCTAAA
4835758 AACGGGCAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
14 17 0.49
15 17 0.49
16 1 0.03
ACGTcount: A:0.50, C:0.31, G:0.00, T:0.19
Consensus pattern (14 bp):
AACCCTAAACTTAA
Found at i:4839795 original size:30 final size:32
Alignment explanation
Indices: 4839759--4839824 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
4839749 TTTAGAAAAT
4839759 ATTAATACAAAT-CCTT-AA-AAAATAGGATTG
1 ATTAATAC-AATCCCTTGAAGAAAATAGGATTG
* *
4839789 ATTAATACAATCCCTTGAAGAAATTAGGTTTG
1 ATTAATACAATCCCTTGAAGAAAATAGGATTG
4839821 ATTA
1 ATTA
4839825 GAAATTTATC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 3 0.10
30 12 0.39
31 2 0.06
32 14 0.45
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (32 bp):
ATTAATACAATCCCTTGAAGAAAATAGGATTG
Found at i:4841357 original size:30 final size:30
Alignment explanation
Indices: 4841323--4841386 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
4841313 TGGCCAAGCT
* *
4841323 GTGTGGCTCACACGGCCAAGAGACATGCCC
1 GTGTGGCTCACACGGCAAAGAGACACGCCC
*
4841353 GTGTGGCTCACACGGCAAAGAGATACGCCC
1 GTGTGGCTCACACGGCAAAGAGACACGCCC
4841383 GTGT
1 GTGT
4841387 CTTAGGTTGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.23, C:0.30, G:0.31, T:0.16
Consensus pattern (30 bp):
GTGTGGCTCACACGGCAAAGAGACACGCCC
Found at i:4842399 original size:21 final size:21
Alignment explanation
Indices: 4842375--4842415 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
4842365 AAGGATTAAA
4842375 CAGAAGCTCAAAAGAGCTGAG
1 CAGAAGCTCAAAAGAGCTGAG
* *
4842396 CAGAAGCTCATAGGAGCTGA
1 CAGAAGCTCAAAAGAGCTGA
4842416 ATGGAAACCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.20, G:0.29, T:0.12
Consensus pattern (21 bp):
CAGAAGCTCAAAAGAGCTGAG
Found at i:4842491 original size:21 final size:21
Alignment explanation
Indices: 4842355--4842491 Score: 62
Period size: 21 Copynumber: 6.5 Consensus size: 21
4842345 AGTGCTAAAT
* ** *
4842355 AGAAACCCATAAGGATTAAAC
1 AGAAACTCATAAGGGCTGAAC
* * * *
4842376 AGAAGCTCAAAAGAGCTGAGC
1 AGAAACTCATAAGGGCTGAAC
* *
4842397 AGAAGCTCAT-AGGAGCTGAAT
1 AGAAACTCATAAGG-GCTGAAC
* * * * *
4842418 GGAAACCCTTAAGGGTTAAAC
1 AGAAACTCATAAGGGCTGAAC
* * * *
4842439 AGAAGCTTAAAAGAGCTGAAC
1 AGAAACTCATAAGGGCTGAAC
*
4842460 AGAAA-TCCATAAGGGTTGAAC
1 AGAAACT-CATAAGGGCTGAAC
4842481 AGAAACTCATA
1 AGAAACTCATA
4842492 TAAGTTAACA
Statistics
Matches: 79, Mismatches: 33, Indels: 8
0.66 0.28 0.07
Matches are distributed among these distances:
20 3 0.04
21 72 0.91
22 4 0.05
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.16
Consensus pattern (21 bp):
AGAAACTCATAAGGGCTGAAC
Found at i:4846158 original size:25 final size:26
Alignment explanation
Indices: 4846130--4846178 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
4846120 ACATACCGTA
4846130 GCTC-TTATGAGCGTCCCGATATATG
1 GCTCTTTATGAGCGTCCCGATATATG
* *
4846155 GCTCTTTATGAGCTTCCTGATATA
1 GCTCTTTATGAGCGTCCCGATATA
4846179 GCTCACTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.37
Consensus pattern (26 bp):
GCTCTTTATGAGCGTCCCGATATATG
Found at i:4846218 original size:25 final size:24
Alignment explanation
Indices: 4846164--4846238 Score: 66
Period size: 25 Copynumber: 3.1 Consensus size: 24
4846154 GGCTCTTTAT
4846164 GAGCTTCCTGAT-ATAGCTCACTT--
1 GAGCTTCCTGATAATAGCT-A-TTCG
* *
4846187 GAACTTCCTGATATATGGCTATTCG
1 GAGCTTCCTGATA-ATAGCTATTCG
* *
4846212 GAGCTTCTTGATAATAGCTCTTCG
1 GAGCTTCCTGATAATAGCTATTCG
4846236 GAG
1 GAG
4846239 TTACCCGTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
23 13 0.31
24 13 0.31
25 16 0.38
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (24 bp):
GAGCTTCCTGATAATAGCTATTCG
Found at i:4855826 original size:18 final size:18
Alignment explanation
Indices: 4855803--4855840 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
4855793 TTTAGTTAAG
*
4855803 TCTTTCATT-AAGTGTTTT
1 TCTTTC-TTCAAGTATTTT
4855821 TCTTTCTTCAAGTATTTT
1 TCTTTCTTCAAGTATTTT
4855839 TC
1 TC
4855841 ATTTAGTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.16, C:0.16, G:0.08, T:0.61
Consensus pattern (18 bp):
TCTTTCTTCAAGTATTTT
Found at i:4855956 original size:12 final size:11
Alignment explanation
Indices: 4855850--4855952 Score: 55
Period size: 12 Copynumber: 8.5 Consensus size: 11
4855840 CATTTAGTTC
4855850 TTTTATCAAGT
1 TTTTATCAAGT
4855861 TTTTAATTACCAAGT
1 TTTT-A-T--CAAGT
4855876 TTTCTATCAAGT
1 TTT-TATCAAGT
*
4855888 TTTGTAGCAAGT
1 TTT-TATCAAGT
*
4855900 TCTTT-TTAAGT
1 T-TTTATCAAGT
4855911 TTTTCATCAAGT
1 TTTT-ATCAAGT
* *
4855923 CTTTTCATAAAAT
1 -TTTT-ATCAAGT
*
4855936 TTTCCATCAAGT
1 TTT-TATCAAGT
4855948 TTTTA
1 TTTTA
4855953 ATCATTTCTT
Statistics
Matches: 71, Mismatches: 11, Indels: 20
0.70 0.11 0.20
Matches are distributed among these distances:
10 3 0.04
11 10 0.14
12 34 0.48
13 13 0.18
14 1 0.01
15 9 0.13
16 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.09, T:0.50
Consensus pattern (11 bp):
TTTTATCAAGT
Found at i:4865222 original size:16 final size:16
Alignment explanation
Indices: 4865201--4865232 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4865191 GTGGGGGAAT
*
4865201 GTCGAGATTAGAAGAA
1 GTCGAGATTAAAAGAA
4865217 GTCGAGATTAAAAGAA
1 GTCGAGATTAAAAGAA
4865233 ATATGTTGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.06, G:0.28, T:0.19
Consensus pattern (16 bp):
GTCGAGATTAAAAGAA
Found at i:4865302 original size:94 final size:94
Alignment explanation
Indices: 4865123--4865310 Score: 277
Period size: 94 Copynumber: 2.0 Consensus size: 94
4865113 TGTGGGAAGT
* *
4865123 GTCGATATTAGAAGAAATATGTTGTAATCTTTGACCTTAAGTAATTGATATTAAAATCCAGTTAA
1 GTCGAGATTAAAAGAAATATGTTGTAATCTTTGACCTTAAGTAATTGATATTAAAATCCAGTTAA
* * * *
4865188 CTTGTGGGGGAATGTCGAGATTAGAAGAA
66 CTTATGGGAGAATGTAGAGATTAAAAGAA
** * *
4865217 GTCGAGATTAAAAGAAATATGTTGTAATCTTTGACCTTAAGTAATTGATATTAATGTCTAGTTAG
1 GTCGAGATTAAAAGAAATATGTTGTAATCTTTGACCTTAAGTAATTGATATTAAAATCCAGTTAA
*
4865282 CTTATGGGAGAGTGTAGAGATTAAAAGAA
66 CTTATGGGAGAATGTAGAGATTAAAAGAA
4865311 ATCTTTGACC
Statistics
Matches: 83, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
94 83 1.00
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (94 bp):
GTCGAGATTAAAAGAAATATGTTGTAATCTTTGACCTTAAGTAATTGATATTAAAATCCAGTTAA
CTTATGGGAGAATGTAGAGATTAAAAGAA
Found at i:4865326 original size:68 final size:70
Alignment explanation
Indices: 4865242--4865607 Score: 272
Period size: 78 Copynumber: 4.9 Consensus size: 70
4865232 AATATGTTGT
* * *
4865242 AATCTTTGACCTTAAGTAATTGATATTAATG-TCTAGTTAGCTTATGGGAGAGTGTAGAGATT-A
1 AATCTTTGACCTTAAGTAATTGATATTAA-GATCCAGTTAACTTATGGGAGAGTGTCGAGATTAA
4865305 AAA-GA
65 AAATGA
* * * *
4865310 AATCTTTGACCTTAAGTAATTGATATTAGGATCTAGTTAACTTGTGGGGGAGTGTCGAGATTAGA
1 AATCTTTGACCTTAAGTAATTGATATTAAGATCCAGTTAACTTATGGGAGAGTGTCGAGATT--A
*
4865375 AGAAATTTGTTGT
64 A-AAA-----TGA
* *
4865388 AATCTTTGACCTTAAGTAATTGATATTAAGATCCAGTTAACTTGTGGGGGAGTGTCGAGATTAGA
1 AATCTTTGACCTTAAGTAATTGATATTAAGATCCAGTTAACTTATGGGAGAGTGTCGAGATT---
*
4865453 AGAAATATGTTGT
63 A-AAA-A---TGA
* * * *
4865466 AATCTTTGACCTTAATTAATTGATATTAAAATCCAGTTAGCTTATGGGAGAGTATCGAGATTAAA
1 AATCTTTGACCTTAAGTAATTGATATTAAGATCCAGTTAACTTATGGGAGAGTGTCGAGATT---
*
4865531 AGAAATATGTTGT
63 A-AAA-A---TGA
* * * * * * *
4865544 AATATTTGACCTTCAGTAATTTATATTAGGATCCAATTAACTTGTGGG-GAATGTCGAGATTAAA
1 AATCTTTGACCTTAAGTAATTGATATTAAGATCCAGTTAACTTATGGGAGAGTGTCGAGATTAAA
4865608 TGAAATATGT
Statistics
Matches: 256, Mismatches: 28, Indels: 23
0.83 0.09 0.07
Matches are distributed among these distances:
67 1 0.00
68 55 0.21
71 1 0.00
72 3 0.01
73 2 0.01
74 1 0.00
77 11 0.04
78 177 0.69
79 3 0.01
80 2 0.01
ACGTcount: A:0.34, C:0.09, G:0.22, T:0.36
Consensus pattern (70 bp):
AATCTTTGACCTTAAGTAATTGATATTAAGATCCAGTTAACTTATGGGAGAGTGTCGAGATTAAA
AATGA
Found at i:4865368 original size:162 final size:164
Alignment explanation
Indices: 4865046--4865378 Score: 440
Period size: 162 Copynumber: 2.0 Consensus size: 164
4865036 GTGGGGGAGT
*
4865046 GTCGAGGTTAAAAGAAATATGTTGTAACCTTTGACCTTAACTAATTGATATTAGGATCTAGTTAA
1 GTCGAGATTAAAAGAAATATGTTGTAACCTTTGACCTTAACTAATTGATATTAGGATCTAGTTAA
* * * *
4865111 CTTGTGGGAAGTGTCGATATTAGAAGAAATATGTTGTAATCTTTGACCTTAAGTAATTGATATTA
66 CTTATGGGAAGTGTAGAGATT---A-AAATA---TGAAATCTTTGACCTTAAGTAATTGATATTA
4865176 AAATCCAGTTAACTTGTGGGGGAATGTCGAGATTAGAAGAA
124 AAATCCAGTTAACTTGTGGGGGAATGTCGAGATTAGAAGAA
* * *
4865217 GTCGAGATTAAAAGAAATATGTTGTAATCTTTGACCTTAAGTAATTGATATTAATG-TCTAGTTA
1 GTCGAGATTAAAAGAAATATGTTGTAACCTTTGACCTTAACTAATTGATATT-AGGATCTAGTTA
* **
4865281 GCTTATGGGAGAGTGTAGAGATT-AAA-A-GAAATCTTTGACCTTAAGTAATTGATATTAGGATC
65 ACTTATGGGA-AGTGTAGAGATTAAAATATGAAATCTTTGACCTTAAGTAATTGATATTAAAATC
* *
4865343 TAGTTAACTTGTGGGGGAGTGTCGAGATTAGAAGAA
129 CAGTTAACTTGTGGGGGAATGTCGAGATTAGAAGAA
4865379 ATTTGTTGTA
Statistics
Matches: 147, Mismatches: 13, Indels: 13
0.85 0.08 0.08
Matches are distributed among these distances:
162 66 0.45
166 1 0.01
167 3 0.02
171 65 0.44
172 12 0.08
ACGTcount: A:0.35, C:0.08, G:0.23, T:0.34
Consensus pattern (164 bp):
GTCGAGATTAAAAGAAATATGTTGTAACCTTTGACCTTAACTAATTGATATTAGGATCTAGTTAA
CTTATGGGAAGTGTAGAGATTAAAATATGAAATCTTTGACCTTAAGTAATTGATATTAAAATCCA
GTTAACTTGTGGGGGAATGTCGAGATTAGAAGAA
Found at i:4865439 original size:78 final size:78
Alignment explanation
Indices: 4865310--4865633 Score: 472
Period size: 78 Copynumber: 4.2 Consensus size: 78
4865300 GATTAAAAGA
* *
4865310 AATCTTTGACCTTAAGTAATTGATATTAGGATCTAGTTAACTTGTGGGGGAGTGTCGAGATTAGA
1 AATCTTTGACCTTAAGTAATTGATATTAAGATCCAGTTAACTTGTGGGGGAGTGTCGAGATTAGA
*
4865375 AGAAATTTGTTGT
66 AGAAATATGTTGT
4865388 AATCTTTGACCTTAAGTAATTGATATTAAGATCCAGTTAACTTGTGGGGGAGTGTCGAGATTAGA
1 AATCTTTGACCTTAAGTAATTGATATTAAGATCCAGTTAACTTGTGGGGGAGTGTCGAGATTAGA
4865453 AGAAATATGTTGT
66 AGAAATATGTTGT
* * * * * * *
4865466 AATCTTTGACCTTAATTAATTGATATTAAAATCCAGTTAGCTTATGGGAGAGTATCGAGATTAAA
1 AATCTTTGACCTTAAGTAATTGATATTAAGATCCAGTTAACTTGTGGGGGAGTGTCGAGATTAGA
4865531 AGAAATATGTTGT
66 AGAAATATGTTGT
* * * * * *
4865544 AATATTTGACCTTCAGTAATTTATATTAGGATCCAATTAACTTGT-GGGGAATGTCGAGATTA-A
1 AATCTTTGACCTTAAGTAATTGATATTAAGATCCAGTTAACTTGTGGGGGAGTGTCGAGATTAGA
4865607 ATGAAATATGTTGT
66 A-GAAATATGTTGT
*
4865621 AATATTTGACCTT
1 AATCTTTGACCTT
4865634 TTAAGTATTT
Statistics
Matches: 223, Mismatches: 22, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
76 2 0.01
77 39 0.17
78 182 0.82
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.37
Consensus pattern (78 bp):
AATCTTTGACCTTAAGTAATTGATATTAAGATCCAGTTAACTTGTGGGGGAGTGTCGAGATTAGA
AGAAATATGTTGT
Found at i:4869593 original size:17 final size:18
Alignment explanation
Indices: 4869567--4869600 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
4869557 GACTGAACCA
*
4869567 ATTTTTAAATT-TTTATG
1 ATTTTAAAATTATTTATG
4869584 ATTTTAAAATTATTTAT
1 ATTTTAAAATTATTTAT
4869601 TTAATTATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
ATTTTAAAATTATTTATG
Found at i:4870165 original size:18 final size:17
Alignment explanation
Indices: 4870135--4870168 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
4870125 CTCATCGTTT
*
4870135 CTTTTTTTTTTCTTTTC
1 CTTTTTTTGTTCTTTTC
4870152 CTTTTTTTCGTTCTTTT
1 CTTTTTTT-GTTCTTTT
4870169 GGCGTTGTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (17 bp):
CTTTTTTTGTTCTTTTC
Found at i:4880474 original size:14 final size:14
Alignment explanation
Indices: 4880455--4880495 Score: 75
Period size: 14 Copynumber: 3.0 Consensus size: 14
4880445 CAAAAGAAAG
4880455 AAGAAAAGGAAAAA
1 AAGAAAAGGAAAAA
4880469 AAGAAAAGGAAAAA
1 AAGAAAAGGAAAAA
4880483 AAGAAAA-GAAAAA
1 AAGAAAAGGAAAAA
4880496 GAAACAGTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 6 0.22
14 21 0.78
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (14 bp):
AAGAAAAGGAAAAA
Found at i:4885129 original size:78 final size:78
Alignment explanation
Indices: 4884995--4885421 Score: 613
Period size: 78 Copynumber: 5.5 Consensus size: 78
4884985 AAATACTTAA
* * * * *
4884995 AAGGTCAAATATTACAACA-ATTTTTTTTAATCTCGACATTCCCCCACAAGTTAATTGGATCCTA
1 AAGGTCAAAGATTACAACATATTTCTTTTAATCTCGACACTCCCCCACAAGTTAACTGGATCTTA
*
4885059 ATATAAATTACTT
66 ATATCAATTACTT
* * * * * * * *
4885072 AAGGTCAAATACTACAACATATTTCTTTTAATCTCGATACTCTCCCATAAGCTAATTGGATTTTA
1 AAGGTCAAAGATTACAACATATTTCTTTTAATCTCGACACTCCCCCACAAGTTAACTGGATCTTA
*
4885137 ATATCAATTAATT
66 ATATCAATTACTT
*
4885150 AAGGTCAAAGATTACAACATATTTCTTCTAATCTCGACACTCCCCCACAAGTTAACTGGATCTTA
1 AAGGTCAAAGATTACAACATATTTCTTTTAATCTCGACACTCCCCCACAAGTTAACTGGATCTTA
*
4885215 AAATCAATTACTT
66 ATATCAATTACTT
* * * * *
4885228 AAGGTCAAAGATTACAACAAATTTCTTCTAATCTTGACACTCCCCCACAAGTTAACTAGATCCTA
1 AAGGTCAAAGATTACAACATATTTCTTTTAATCTCGACACTCCCCCACAAGTTAACTGGATCTTA
4885293 ATATCAATTACTT
66 ATATCAATTACTT
* * * *
4885306 AAGGTCAAAGATTTCAACATATTTCTTTTAATCTCTACACTCCCCCATAAGCTAACTGGATCTTA
1 AAGGTCAAAGATTACAACATATTTCTTTTAATCTCGACACTCCCCCACAAGTTAACTGGATCTTA
4885371 ATATCAATTACTT
66 ATATCAATTACTT
4885384 AAGGTCAAAGATTACAACATATTTCTTTTAATCTCGAC
1 AAGGTCAAAGATTACAACATATTTCTTTTAATCTCGAC
4885422 TTCTTCTAAT
Statistics
Matches: 311, Mismatches: 38, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
77 18 0.06
78 293 0.94
ACGTcount: A:0.36, C:0.22, G:0.08, T:0.34
Consensus pattern (78 bp):
AAGGTCAAAGATTACAACATATTTCTTTTAATCTCGACACTCCCCCACAAGTTAACTGGATCTTA
ATATCAATTACTT
Found at i:4885308 original size:156 final size:156
Alignment explanation
Indices: 4884995--4885608 Score: 737
Period size: 156 Copynumber: 3.8 Consensus size: 156
4884985 AAATACTTAA
* * * * *
4884995 AAGGTCAAATATTACAACA-ATTTTTTTTAATCTCGACATTCCCCCACAAGTTAATTGGATCCTA
1 AAGGTCAAAGATTACAACATATTTCTTCTAATCTCGACACTCCCCCACAAGTTAACTGGATCCTA
* * * * * * * * *
4885059 ATATAAATTACTTAAGGTCAAATACTACAACATATTTCTTTTAATCTCGATACTCTCCCATAAGC
66 ATATCAATTACTTAAGGTCAAAGATTACAACAAATTTCTTCTAATCTCGACACTCCCCCACAAGT
* *
4885124 TAATTGGATTTTAATATCAATTAATT
131 TAACTGGATTTTAATATCAATTACTT
*
4885150 AAGGTCAAAGATTACAACATATTTCTTCTAATCTCGACACTCCCCCACAAGTTAACTGGATCTTA
1 AAGGTCAAAGATTACAACATATTTCTTCTAATCTCGACACTCCCCCACAAGTTAACTGGATCCTA
* *
4885215 AAATCAATTACTTAAGGTCAAAGATTACAACAAATTTCTTCTAATCTTGACACTCCCCCACAAGT
66 ATATCAATTACTTAAGGTCAAAGATTACAACAAATTTCTTCTAATCTCGACACTCCCCCACAAGT
* **
4885280 TAACTAGATCCTAATATCAATTACTT
131 TAACTGGATTTTAATATCAATTACTT
* * * * * *
4885306 AAGGTCAAAGATTTCAACATATTTCTTTTAATCTCTACACTCCCCCATAAGCTAACTGGATCTTA
1 AAGGTCAAAGATTACAACATATTTCTTCTAATCTCGACACTCCCCCACAAGTTAACTGGATCCTA
4885371 ATATCAATTACTTAAGGTCAAAGATTACAACATATTTCTTTTAATCTCGACTTCTTCTAATCTCG
66 ATATCAATTACTTAAGGTCAAAGATTACAAC--A--------AA--T----TTCTTCTAATCTCG
*
4885436 ACATTCCCCCACAAGTTAACTGGATTTTAATATCAATTACTT
115 ACACTCCCCCACAAGTTAACTGGATTTTAATATCAATTACTT
* * *
4885478 AAGGTCAAAGATTACAACATATTTCTTCTAATATCGACACTTCCCCACAAGTTAACTAGATCCTA
1 AAGGTCAAAGATTACAACATATTTCTTCTAATCTCGACACTCCCCCACAAGTTAACTGGATCCTA
* * * *
4885543 ATATCAATTAGTTAAGGTCAAATG-TTACAACATATTTCTTTTAATCTCGACACTCCTCCACAAG
66 ATATCAATTACTTAAGGTCAAA-GATTACAACAAATTTCTTCTAATCTCGACACTCCCCCACAAG
4885607 TT
130 TT
4885609 GGTGCGTAGA
Statistics
Matches: 394, Mismatches: 47, Indels: 35
0.83 0.10 0.07
Matches are distributed among these distances:
155 18 0.05
156 233 0.59
158 1 0.00
160 1 0.00
162 1 0.00
166 2 0.01
168 1 0.00
170 1 0.00
172 135 0.34
173 1 0.00
ACGTcount: A:0.35, C:0.22, G:0.08, T:0.35
Consensus pattern (156 bp):
AAGGTCAAAGATTACAACATATTTCTTCTAATCTCGACACTCCCCCACAAGTTAACTGGATCCTA
ATATCAATTACTTAAGGTCAAAGATTACAACAAATTTCTTCTAATCTCGACACTCCCCCACAAGT
TAACTGGATTTTAATATCAATTACTT
Found at i:4885431 original size:16 final size:16
Alignment explanation
Indices: 4885406--4885437 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4885396 TACAACATAT
*
4885406 TTCTTTTAATCTCGAC
1 TTCTTCTAATCTCGAC
4885422 TTCTTCTAATCTCGAC
1 TTCTTCTAATCTCGAC
4885438 ATTCCCCCAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.28, G:0.06, T:0.47
Consensus pattern (16 bp):
TTCTTCTAATCTCGAC
Found at i:4885489 original size:94 final size:94
Alignment explanation
Indices: 4885328--4885515 Score: 304
Period size: 94 Copynumber: 2.0 Consensus size: 94
4885318 TTCAACATAT
* * *
4885328 TTCTTTTAATCTCTACACTCCCCCATAAGCTAACTGGATCTTAATATCAATTACTTAAGGTCAAA
1 TTCTTCTAATCTCGACACTCCCCCACAAGCTAACTGGATCTTAATATCAATTACTTAAGGTCAAA
* *
4885393 GATTACAACATATTTCTTTTAATCTCGAC
66 GATTACAACATATTTCTTCTAATATCGAC
* * *
4885422 TTCTTCTAATCTCGACATTCCCCCACAAGTTAACTGGATTTTAATATCAATTACTTAAGGTCAAA
1 TTCTTCTAATCTCGACACTCCCCCACAAGCTAACTGGATCTTAATATCAATTACTTAAGGTCAAA
4885487 GATTACAACATATTTCTTCTAATATCGAC
66 GATTACAACATATTTCTTCTAATATCGAC
4885516 ACTTCCCCAC
Statistics
Matches: 86, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
94 86 1.00
ACGTcount: A:0.32, C:0.23, G:0.08, T:0.37
Consensus pattern (94 bp):
TTCTTCTAATCTCGACACTCCCCCACAAGCTAACTGGATCTTAATATCAATTACTTAAGGTCAAA
GATTACAACATATTTCTTCTAATATCGAC
Found at i:4885547 original size:172 final size:172
Alignment explanation
Indices: 4885250--4885593 Score: 537
Period size: 172 Copynumber: 2.0 Consensus size: 172
4885240 TACAACAAAT
*
4885250 TTCTTCTAATCTTGACACTCCCCCACAAGTTAACTAGATCCTAATATCAATTACTTAAGGTCAAA
1 TTCTTCTAATCTCGACACTCCCCCACAAGTTAACTAGATCCTAATATCAATTACTTAAGGTCAAA
* * * * * * *
4885315 GATTTCAACATATTTCTTTTAATCTCTACACTCCCCCATAAGCTAACTGGATCTTAATATCAATT
66 GATTACAACATATTTCTTCTAATATCGACACTCCCCCACAAGCTAACTAGATCCTAATATCAATT
4885380 ACTTAAGGTCAAA-GATTACAACATATTTCTTTTAATCTCGAC
131 ACTTAAGGTCAAATG-TTACAACATATTTCTTTTAATCTCGAC
* * **
4885422 TTCTTCTAATCTCGACATTCCCCCACAAGTTAACTGGATTTTAATATCAATTACTTAAGGTCAAA
1 TTCTTCTAATCTCGACACTCCCCCACAAGTTAACTAGATCCTAATATCAATTACTTAAGGTCAAA
* *
4885487 GATTACAACATATTTCTTCTAATATCGACACTTCCCCACAAGTTAACTAGATCCTAATATCAATT
66 GATTACAACATATTTCTTCTAATATCGACACTCCCCCACAAGCTAACTAGATCCTAATATCAATT
*
4885552 AGTTAAGGTCAAATGTTACAACATATTTCTTTTAATCTCGAC
131 ACTTAAGGTCAAATGTTACAACATATTTCTTTTAATCTCGAC
4885594 ACTCCTCCAC
Statistics
Matches: 156, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
172 155 0.99
173 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.08, T:0.35
Consensus pattern (172 bp):
TTCTTCTAATCTCGACACTCCCCCACAAGTTAACTAGATCCTAATATCAATTACTTAAGGTCAAA
GATTACAACATATTTCTTCTAATATCGACACTCCCCCACAAGCTAACTAGATCCTAATATCAATT
ACTTAAGGTCAAATGTTACAACATATTTCTTTTAATCTCGAC
Found at i:4885551 original size:78 final size:78
Alignment explanation
Indices: 4885422--4885608 Score: 272
Period size: 78 Copynumber: 2.4 Consensus size: 78
4885412 TAATCTCGAC
* **
4885422 TTCTTCTAATCTCGACA-TTCCCCCACAAGTTAACTGGATTTTAATATCAATTACTTAAGGTCAA
1 TTCTTCTAATCTCGACACTT-CCCCACAAGTTAACTAGATCCTAATATCAATTACTTAAGGTCAA
4885486 A-GATTACAACATAT
65 ATG-TTACAACATAT
* *
4885500 TTCTTCTAATATCGACACTTCCCCACAAGTTAACTAGATCCTAATATCAATTAGTTAAGGTCAAA
1 TTCTTCTAATCTCGACACTTCCCCACAAGTTAACTAGATCCTAATATCAATTACTTAAGGTCAAA
4885565 TGTTACAACATAT
66 TGTTACAACATAT
*
4885578 TTCTTTTAATCTCGACAC-TCCTCCACAAGTT
1 TTCTTCTAATCTCGACACTTCC-CCACAAGTT
4885609 GGTGCGTAGA
Statistics
Matches: 99, Mismatches: 7, Indels: 6
0.88 0.06 0.05
Matches are distributed among these distances:
77 3 0.03
78 93 0.94
79 3 0.03
ACGTcount: A:0.33, C:0.24, G:0.09, T:0.35
Consensus pattern (78 bp):
TTCTTCTAATCTCGACACTTCCCCACAAGTTAACTAGATCCTAATATCAATTACTTAAGGTCAAA
TGTTACAACATAT
Found at i:4888640 original size:6 final size:6
Alignment explanation
Indices: 4888629--4888655 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
4888619 CTATTAACAT
4888629 GACTCG GACTCG GACTCG GACTCG GAC
1 GACTCG GACTCG GACTCG GACTCG GAC
4888656 GGATACATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.33, G:0.33, T:0.15
Consensus pattern (6 bp):
GACTCG
Found at i:4890290 original size:105 final size:104
Alignment explanation
Indices: 4890079--4890315 Score: 291
Period size: 105 Copynumber: 2.3 Consensus size: 104
4890069 GTGAGCAACA
* * *
4890079 GACATGGGCATGTGTCTAGG-CTGTGTAACTCACTATTTATGATTTAGGACCACACAGCTAGGGA
1 GACATGGGCGTGTGTCTAGGTC-GTGTAACTCACTATTTACGATTTAAGACCACACAGCTAGGGA
* * *
4890143 CATGGGCATGTGCCCAGGCCATATGAGTCATACGGGCAAG
65 CATGGGCATGCGCCCAGGCCATATGACTCACACGGGCAAG
* * *
4890183 GACATGGGCGTGTGTTTAGGTCGTGTAACTCACTGTTTACGA-TTAAGATCCACATGAGC-AGAG
1 GACATGGGCGTGTGTCTAGGTCGTGTAACTCACTATTTACGATTTAAGA-CCACA-CAGCTAG-G
* * *
4890246 GACATGGGCGTGCGTCCAGGCCATGTGACTCACACGGGCAAG
63 GACATGGGCATGCGCCCAGGCCATATGACTCACACGGGCAAG
* *
4890288 GACATGGGCGTGTATCCAGGTCGTGTAA
1 GACATGGGCGTGTGTCTAGGTCGTGTAA
4890316 GCCATATGGG
Statistics
Matches: 114, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
103 5 0.04
104 43 0.38
105 66 0.58
ACGTcount: A:0.24, C:0.21, G:0.31, T:0.24
Consensus pattern (104 bp):
GACATGGGCGTGTGTCTAGGTCGTGTAACTCACTATTTACGATTTAAGACCACACAGCTAGGGAC
ATGGGCATGCGCCCAGGCCATATGACTCACACGGGCAAG
Found at i:4890306 original size:42 final size:42
Alignment explanation
Indices: 4890244--4890350 Score: 126
Period size: 42 Copynumber: 2.5 Consensus size: 42
4890234 ACATGAGCAG
* *
4890244 AGGACATGGGCGTGCGTCCAGGCCATGTGA-CTCACACGGGCA
1 AGGACATGGGCGTGTGTCCAGGCCATGTAAGC-CACACGGGCA
* * * * *
4890286 AGGACATGGGCGTGTATCCAGGTCGTGTAAGCCATATGGGCA
1 AGGACATGGGCGTGTGTCCAGGCCATGTAAGCCACACGGGCA
*
4890328 AGTACATGGGCGTGTGTCCAGGC
1 AGGACATGGGCGTGTGTCCAGGC
4890351 TTTGTGGCAT
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
42 53 0.98
43 1 0.02
ACGTcount: A:0.21, C:0.23, G:0.36, T:0.19
Consensus pattern (42 bp):
AGGACATGGGCGTGTGTCCAGGCCATGTAAGCCACACGGGCA
Found at i:4890914 original size:22 final size:22
Alignment explanation
Indices: 4890855--4890915 Score: 68
Period size: 24 Copynumber: 2.7 Consensus size: 22
4890845 CATATGGATA
* *
4890855 TGATATGTTCTGTATATGAAAT
1 TGATTTGTTCTGTATATGAAAC
* *
4890877 TGAAATTGCTTCTGTATATGTAAC
1 TG-ATTTG-TTCTGTATATGAAAC
4890901 TGATTTGTTCTGTAT
1 TGATTTGTTCTGTAT
4890916 CTGAGCTGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
22 10 0.31
23 7 0.22
24 15 0.47
ACGTcount: A:0.26, C:0.08, G:0.18, T:0.48
Consensus pattern (22 bp):
TGATTTGTTCTGTATATGAAAC
Found at i:4894142 original size:18 final size:17
Alignment explanation
Indices: 4894119--4894152 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
4894109 ATAGCTGTGT
4894119 ACTGAAACCATGCTAAAG
1 ACTGAAACCATG-TAAAG
*
4894137 ACTGAAGCCATGTAAA
1 ACTGAAACCATGTAAA
4894153 TCTAAGTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.44, C:0.21, G:0.18, T:0.18
Consensus pattern (17 bp):
ACTGAAACCATGTAAAG
Found at i:4905688 original size:8 final size:8
Alignment explanation
Indices: 4905677--4905706 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
4905667 TGCTCTTCTT
4905677 TGCTTTAC
1 TGCTTTAC
4905685 TGCTTTAC
1 TGCTTTAC
4905693 TGCTTTAC
1 TGCTTTAC
4905701 TGCTTT
1 TGCTTT
4905707 GCTTTACTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.10, C:0.23, G:0.13, T:0.53
Consensus pattern (8 bp):
TGCTTTAC
Found at i:4905709 original size:13 final size:13
Alignment explanation
Indices: 4905674--4905721 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
4905664 CTTTGCTCTT
4905674 CTTTGCTTTACTG
1 CTTTGCTTTACTG
4905687 CTTTACTGCTTTACTG
1 C-TT--TGCTTTACTG
4905703 CTTTGCTTTACTG
1 CTTTGCTTTACTG
*
4905716 TTTTGC
1 CTTTGC
4905722 CAAGGAAGCC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
13 16 0.52
14 2 0.06
15 2 0.06
16 11 0.35
ACGTcount: A:0.08, C:0.23, G:0.15, T:0.54
Consensus pattern (13 bp):
CTTTGCTTTACTG
Found at i:4910444 original size:4 final size:4
Alignment explanation
Indices: 4910435--4910460 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
4910425 TTTATCATAT
4910435 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
4910461 ATTAGTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:4910482 original size:20 final size:21
Alignment explanation
Indices: 4910414--4910482 Score: 72
Period size: 20 Copynumber: 3.3 Consensus size: 21
4910404 GATAACTTTA
4910414 TTTTATTATGTTTTATCATA-
1 TTTTATTATGTTTTATCATAT
* *
4910434 TTTTATTTATTTATTTAT-TTAT
1 TTTTA-TTATGT-TTTATCATAT
4910456 TTATTATTA-GTTTTATCATAT
1 TT-TTATTATGTTTTATCATAT
4910477 TTTTAT
1 TTTTAT
4910483 CTTAAATAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
20 14 0.35
21 13 0.32
22 10 0.25
23 3 0.08
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.70
Consensus pattern (21 bp):
TTTTATTATGTTTTATCATAT
Found at i:4912710 original size:23 final size:25
Alignment explanation
Indices: 4912682--4912729 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
4912672 GTCTTGATTC
4912682 TTAAAAA-TTTAAAA-TTAATTTTT
1 TTAAAAATTTTAAAAGTTAATTTTT
*
4912705 TTAAAAATTTTAAAAGTTTATTTTT
1 TTAAAAATTTTAAAAGTTAATTTTT
4912730 CAATTAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.32
24 7 0.32
25 8 0.36
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (25 bp):
TTAAAAATTTTAAAAGTTAATTTTT
Found at i:4912858 original size:20 final size:20
Alignment explanation
Indices: 4912835--4912883 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
4912825 ATTTATTTAT
*
4912835 TAAAATAATAATTTTATAAA
1 TAAAATAATAATCTTATAAA
4912855 TAAAATAATAATCTTATAAA
1 TAAAATAATAATCTTATAAA
*
4912875 CAAAATAAT
1 TAAAATAAT
4912884 TCAAGGGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (20 bp):
TAAAATAATAATCTTATAAA
Found at i:4919047 original size:10 final size:10
Alignment explanation
Indices: 4919012--4919054 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
4919002 AATAAGGCGC
*
4919012 ATACATATAT
1 ATACACATAT
*
4919022 ATACACACAT
1 ATACACATAT
*
4919032 ACACACATAT
1 ATACACATAT
*
4919042 ATACACGTAT
1 ATACACATAT
4919052 ATA
1 ATA
4919055 TTACATTATT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.49, C:0.21, G:0.02, T:0.28
Consensus pattern (10 bp):
ATACACATAT
Found at i:4922425 original size:20 final size:20
Alignment explanation
Indices: 4922400--4922440 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
4922390 TGGTTGTTTA
4922400 TAGTCATCATAAGTAGCAAG
1 TAGTCATCATAAGTAGCAAG
4922420 TAGTCATCATAAGTAGCAAG
1 TAGTCATCATAAGTAGCAAG
4922440 T
1 T
4922441 TGTACTGTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.27
Consensus pattern (20 bp):
TAGTCATCATAAGTAGCAAG
Found at i:4934077 original size:23 final size:22
Alignment explanation
Indices: 4934051--4934095 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
4934041 GAATTAAATC
4934051 TCTAAGATTACAAAATCATATCT
1 TCTAAGATTAC-AAATCATATCT
* *
4934074 TCTAAGATTGCATATCATATCT
1 TCTAAGATTACAAATCATATCT
4934096 AAGATTGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.38
Consensus pattern (22 bp):
TCTAAGATTACAAATCATATCT
Found at i:4934118 original size:17 final size:17
Alignment explanation
Indices: 4934067--4934110 Score: 70
Period size: 19 Copynumber: 2.5 Consensus size: 17
4934057 ATTACAAAAT
4934067 CATATCTTCTAAGATTG
1 CATATCTTCTAAGATTG
4934084 CATATCATATCTAAGATTG
1 CATATC-T-TCTAAGATTG
4934103 CATATCTT
1 CATATCTT
4934111 TGAAGATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.28
18 2 0.08
19 16 0.64
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.41
Consensus pattern (17 bp):
CATATCTTCTAAGATTG
Found at i:4934945 original size:132 final size:132
Alignment explanation
Indices: 4934533--4934945 Score: 560
Period size: 131 Copynumber: 3.1 Consensus size: 132
4934523 AATTGGTAAT
* ** ** * *
4934533 TTCAACCTGCTCCACTGCAACTTCAGGGAGATA-AGGTTGGTGGCTTAAATCTACTTCTCTACTT
1 TTCAACCTACTCCACTGCTGC-TCAGGGAGATAGA-ACTGGTGGCTTAAATCTACTTCCCTACTA
* * *
4934597 CCTCGGGAAGATAAGACTCGCTGTCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATATAC
64 CCTCGGGAAGATAAGATTCGCCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTAC
*
4934662 AATC
129 AATA
* * * * *
4934666 TTCAACCTACTCCACTACTGCTCAGGGAGATAGAACTGGTGGCATAAATTTTCTTCCC-ACTATC
1 TTCAACCTACTCCACTGCTGCTCAGGGAGATAGAACTGGTGGCTTAAATCTACTTCCCTACTACC
* * *
4934730 TCGAGAAGATAAGATTCGCCGTCTTCGATCTGATCCACTACTGCTTAGGGAGACAGGATCTACAA
66 TCGGGAAGATAAGATTCGCCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAA
*
4934795 TT
131 TA
* *
4934797 TTCAACCTACTCCACTGCTGCTCAGGGAGATAGAACTGGTGGCTTAAATCTGCTTCCCTGCTACC
1 TTCAACCTACTCCACTGCTGCTCAGGGAGATAGAACTGGTGGCTTAAATCTACTTCCCTACTACC
* * * *
4934862 TTGGGAAGATAAGATTCACCATCTTTGATCTGCTCCACTGCTGCTTAGGGAGACAGGATCTACAA
66 TCGGGAAGATAAGATTCGCCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAA
4934927 TA
131 TA
4934929 TTCAACCTACTCCACTG
1 TTCAACCTACTCCACTG
4934946 TAAACTTAGA
Statistics
Matches: 245, Mismatches: 33, Indels: 5
0.87 0.12 0.02
Matches are distributed among these distances:
131 118 0.48
132 109 0.44
133 18 0.07
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.29
Consensus pattern (132 bp):
TTCAACCTACTCCACTGCTGCTCAGGGAGATAGAACTGGTGGCTTAAATCTACTTCCCTACTACC
TCGGGAAGATAAGATTCGCCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAA
TA
Found at i:4935049 original size:89 final size:89
Alignment explanation
Indices: 4934936--4935142 Score: 252
Period size: 89 Copynumber: 2.3 Consensus size: 89
4934926 ATATTCAACC
* * * * * * *
4934936 TACTCCACTGTAAACTTAGAGAGGCAAGGCTGGTGTTTTCGATCTGCTTCACTGCCAGTACAAGA
1 TACTCCGCTGCAAACTCAGGGAGGCAAGGCTGGTGTCTTCGATCTACTTCACTGCCAATACAAGA
* * *
4935001 AGACAAGATCTGCTATTTTCAGTC
66 AGACAAGATCTGCTATCTTCAATA
* * * * *
4935025 TACTCCGCTGCAAATTCAGGGAGGCAAGGTTGGTGTCTTCGATCTACTTCGCTGTCAATACAGGA
1 TACTCCGCTGCAAACTCAGGGAGGCAAGGCTGGTGTCTTCGATCTACTTCACTGCCAATACAAGA
*
4935090 AGACAAGATCTGTTATCTTCAATA
66 AGACAAGATCTGCTATCTTCAATA
* *
4935114 TGCTCCGCTGCAAACTCAGGGAGGTAAGG
1 TACTCCGCTGCAAACTCAGGGAGGCAAGG
4935143 ATTTGTAGCT
Statistics
Matches: 99, Mismatches: 19, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
89 99 1.00
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.28
Consensus pattern (89 bp):
TACTCCGCTGCAAACTCAGGGAGGCAAGGCTGGTGTCTTCGATCTACTTCACTGCCAATACAAGA
AGACAAGATCTGCTATCTTCAATA
Found at i:4935170 original size:45 final size:46
Alignment explanation
Indices: 4935106--4935907 Score: 264
Period size: 45 Copynumber: 17.9 Consensus size: 46
4935096 GATCTGTTAT
* ** * *
4935106 CTTCAATATGCTCCGCTGCAAAC-TCAGGGAGGTAAGGATTTG-TAG
1 CTTCAATCTGCTCTACTGC-AACTTCAGGGAGATAAGGATTCGCTAG
* * *
4935151 CTTCAATCTGTTCTACTGCAACTTTAGGGAGATAA-GATTCGCTAT
1 CTTCAATCTGCTCTACTGCAACTTCAGGGAGATAAGGATTCGCTAG
* ** *
4935196 CTTCAGTCTGCTCTACTGCAACTTCAGGGAGATAA-GATT-ATTGG
1 CTTCAATCTGCTCTACTGCAACTTCAGGGAGATAAGGATTCGCTAG
* * * * *
4935240 CTTTAATCTGCTCCACTGCAACTTTAGAGAGATAA-GATTTGC---
1 CTTCAATCTGCTCTACTGCAACTTCAGGGAGATAAGGATTCGCTAG
* * * * * **
4935282 CAT-GATCTGCTCTATTACAACTTCAGAGAGATAAGATCTGTGATT-TATAG
1 CTTCAATCTGCTCTACTGCAACTTCAGGGAGAT-A-A---G-GATTCGCTAG
* * * * * *
4935332 CTTTAATCT-ATTTCACTGCAACTTTAGGGAAATAA-GATTCGCTAT
1 CTTCAATCTGCTCT-ACTGCAACTTCAGGGAGATAAGGATTCGCTAG
* * * * *
4935377 CTTCAGTCTGCTCCACTACAACTTCAGAGAGATAA-GACTT-G-TAA
1 CTTCAATCTGCTCTACTGCAACTTCAGGGAGATAAGGA-TTCGCTAG
* * *** ** *
4935421 CTTTAATCTGCTCTACTGCAACCTCAAAAAGAT-AGGATT-ATTGG
1 CTTCAATCTGCTCTACTGCAACTTCAGGGAGATAAGGATTCGCTAG
* * * * *
4935465 CTTTAATCTGCTCCACTACAACTTCAGGGAGATAA-GATTTGCTAT
1 CTTCAATCTGCTCTACTGCAACTTCAGGGAGATAAGGATTCGCTAG
* * * * * **
4935510 CTTCAGTCTGCCCTACTGCAACTTCAGGGGGATAA-TACTT-GTTTT
1 CTTCAATCTGCTCTACTGCAACTTCAGGGAGATAAGGA-TTCGCTAG
* * * * * *
4935555 CTTTAGTCTACTCCACTACAACTTCAGGGAGATAA-GACTT-G-TAA
1 CTTCAATCTGCTCTACTGCAACTTCAGGGAGATAAGGA-TTCGCTAG
* * * ** *
4935599 CTTTAAT-TCGCTCCACTGCAACTTCAGAGAGAT-AGGATT-ATTGG
1 CTTCAATCT-GCTCTACTGCAACTTCAGGGAGATAAGGATTCGCTAG
* * * * *
4935643 CTTTAATCTGCTCCACTGCAACTTCAGGGAGATAA-GATTTGCCAT
1 CTTCAATCTGCTCTACTGCAACTTCAGGGAGATAAGGATTCGCTAG
* * * * **
4935688 CTTTAATTTG-TCCCACTGCAACTTCAGGGGGATAA-GACTT-GCTTT
1 CTTCAATCTGCT-CTACTGCAACTTCAGGGAGATAAGGA-TTCGCTAG
* * * * **
4935733 CTTCAGTATGCT-TCACTACAACTTCAGGGGGATAA-GACTT-GCTTT
1 CTTCAATCTGCTCT-ACTGCAACTTCAGGGAGATAAGGA-TTCGCTAG
* * * *
4935778 CTTCAGTTTGCTCCACTGCAACTTCAGGGAGATAA-GACTT-G-TAA
1 CTTCAATCTGCTCTACTGCAACTTCAGGGAGATAAGGA-TTCGCTAG
* * * * * * *
4935822 CTTTAATCCGCTCCACTGTAACTTCAGGAAGAT-AGGATT--ATTG
1 CTTCAATCTGCTCTACTGCAACTTCAGGGAGATAAGGATTCGCTAG
* * * *
4935865 CCTTTAATCTGCTCCACTACAACTTCAAGGAGATAA-GATTCGC
1 -CTTCAATCTGCTCTACTGCAACTTCAGGGAGATAAGGATTCGC
4935908 CATCTTCTTC
Statistics
Matches: 585, Mismatches: 132, Indels: 79
0.73 0.17 0.10
Matches are distributed among these distances:
41 24 0.04
42 3 0.01
43 12 0.02
44 237 0.41
45 273 0.47
46 8 0.01
48 4 0.01
49 1 0.00
50 5 0.01
51 18 0.03
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (46 bp):
CTTCAATCTGCTCTACTGCAACTTCAGGGAGATAAGGATTCGCTAG
Found at i:4935358 original size:92 final size:94
Alignment explanation
Indices: 4935142--4935413 Score: 247
Period size: 89 Copynumber: 2.9 Consensus size: 94
4935132 GGGAGGTAAG
* * ** * * * *
4935142 GATTTGTAGCTTCAATCTGTTCTACTGCAACTTTAGGGAGATAAGATTCGCTATCTTCAGTCTGC
1 GATTTATAGCTTTAATCTACTCCACTGCAACTTTAGAGAAATAAGATTCGC--TCATCAGTCTGC
* * *
4935207 TCTACTGCAACTTCAGGGAGATAAGA--T-T
64 TCCACTACAACTTCAGAGAGATAAGATCTGT
* * * * *
4935235 -A--T-TGGCTTTAATCTGCTCCACTGCAACTTTAGAGAGATAAGATTTGC-CATGA-TCTGCTC
1 GATTTATAGCTTTAATCTACTCCACTGCAACTTTAGAGAAATAAGATTCGCTCATCAGTCTGCTC
* *
4935294 TATTACAACTTCAGAGAGATAAGATCTGT
66 CACTACAACTTCAGAGAGATAAGATCTGT
* * * *
4935323 GATTTATAGCTTTAATCTATTTCACTGCAACTTTAGGGAAATAAGATTCGCTATCTTCAGTCTGC
1 GATTTATAGCTTTAATCTACTCCACTGCAACTTTAGAGAAATAAGATTCGC--TCATCAGTCTGC
4935388 TCCACTACAACTTCAGAGAGATAAGA
64 TCCACTACAACTTCAGAGAGATAAGA
4935414 CTTGTAACTT
Statistics
Matches: 146, Mismatches: 22, Indels: 19
0.78 0.12 0.10
Matches are distributed among these distances:
85 28 0.19
86 3 0.02
87 1 0.01
88 1 0.01
89 40 0.27
90 1 0.01
91 1 0.01
92 39 0.27
95 3 0.02
96 29 0.20
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.33
Consensus pattern (94 bp):
GATTTATAGCTTTAATCTACTCCACTGCAACTTTAGAGAAATAAGATTCGCTCATCAGTCTGCTC
CACTACAACTTCAGAGAGATAAGATCTGT
Found at i:4935487 original size:88 final size:88
Alignment explanation
Indices: 4935383--4935904 Score: 390
Period size: 89 Copynumber: 5.9 Consensus size: 88
4935373 CTATCTTCAG
* * *
4935383 TCTGCTCCACTACAACTTCAGAGAGATAAGACTTGTAACTTTAATCTGCTCTACTGCAACCTCAA
1 TCTGCTCCACTACAACTTCAGGGAGATAAGACTTGTAACTTTAATCTGCTCTACTGCAACTTCAG
*
4935448 AAAGATAGGATTATTGGCTTTAA
66 AGAGATAGGATTATTGGCTTTAA
* * * * *
4935471 TCTGCTCCACTACAACTTCAGGGAGATAAGATTTGCTATCTTCAGTCTGCCCTACTGCAACTTCA
1 TCTGCTCCACTACAACTTCAGGGAGATAAGACTTG-TAACTTTAATCTGCTCTACTGCAACTTCA
* * ** * ** *
4935536 GGGGGATAATACTTGTTTTCTTTAG
65 GAGAGATAGGA-TTATTGGCTTTAA
* *
4935561 TCTACTCCACTACAACTTCAGGGAGATAAGACTTGTAACTTTAAT-TCGCTCCACTGCAACTTCA
1 TCTGCTCCACTACAACTTCAGGGAGATAAGACTTGTAACTTTAATCT-GCTCTACTGCAACTTCA
4935625 GAGAGATAGGATTATTGGCTTTAA
65 GAGAGATAGGATTATTGGCTTTAA
* * * * * *
4935649 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTTAATTTG-TCCCACTGCAACTTC
1 TCTGCTCCACTACAACTTCAGGGAGATAAGACTTG-TAACTTTAATCTGCT-CTACTGCAACTTC
* * * * * * *
4935713 AGGGGGATAAGACTTGCTT-TCTTCAG
64 AGAGAGATAGGA-TT-ATTGGCTTTAA
* * * ** * * * *
4935739 TATGCTTCACTACAACTTCAGGGGGATAAGACTTGCTTTCTTCAGTTTGCTCCACTGCAACTTCA
1 TCTGCTCCACTACAACTTCAGGGAGATAAGACTTG-TAACTTTAATCTGCTCTACTGCAACTTCA
* * * **
4935804 GGGAGATAAGACTT-GTAACTTTAA
65 GAGAGATAGGA-TTATTGGCTTTAA
* ** * * * ** * *
4935828 TCCGCTCCACTGTAACTTCAGGAAGATAGGA-TTATTGCCTTTAATCTGCTCCACTACAACTTCA
1 TCTGCTCCACTACAACTTCAGGGAGATAAGACTT-GTAACTTTAATCTGCTCTACTGCAACTTCA
*
4935892 -AGGAGATAAGATT
65 GA-GAGATAGGATT
4935905 CGCCATCTTC
Statistics
Matches: 348, Mismatches: 74, Indels: 25
0.78 0.17 0.06
Matches are distributed among these distances:
87 2 0.01
88 111 0.32
89 116 0.33
90 116 0.33
91 3 0.01
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.32
Consensus pattern (88 bp):
TCTGCTCCACTACAACTTCAGGGAGATAAGACTTGTAACTTTAATCTGCTCTACTGCAACTTCAG
AGAGATAGGATTATTGGCTTTAA
Found at i:4935589 original size:178 final size:178
Alignment explanation
Indices: 4935129--4935773 Score: 644
Period size: 178 Copynumber: 3.6 Consensus size: 178
4935119 CGCTGCAAAC
* * * * * * *
4935129 TCAGGGAGGTAAGGATTTG-TAGCTTCAATCTGTTCTACTGCAACTTTAGGGAGATAAGA-TTCG
1 TCAGGGAGATAA-GATTTGCCATCTTCAATCTGTCCCACTGCAACTTCAGGGGGATAAGACTT-G
* * * * **
4935192 CTATCTTCAGTCTGCTCTACTGCAACTTCAGGGAGATAAGA-TTATTGGCTTTAA-TCTGCTCCA
64 CTTTCTTCAGTCTGCTCCACTACAACTTCAGGGAGATAAGACTT-GTAACTTTAATTC-GCTCCA
* * * * * ** * * *
4935255 CTGCAACTTTAGAGAGATAAGA-T-TT-GCCATGATCTGCTCTATTACAACT
127 CTGCAACCTCAAAAAGATAGGATTATTGGCTTTAATCTGCTCCACTACAACT
* ** * * ** * **
4935304 TCAGAGAGATAAGATCTGTGATTTATAGCTTTAATCTATTTCACTGCAACTTTAGGGAAATAAGA
1 TCAGGGAGATAAGAT-T-TG--CCAT--CTTCAATCTGTCCCACTGCAACTTCAGGGGGATAAGA
* *
4935369 -TTCGCTATCTTCAGTCTGCTCCACTACAACTTCAGAGAGATAAGACTTGTAACTTTAA-TCTGC
60 CTT-GCTTTCTTCAGTCTGCTCCACTACAACTTCAGGGAGATAAGACTTGTAACTTTAATTC-GC
*
4935432 TCTACTGCAACCTCAAAAAGATAGGATTATTGGCTTTAATCTGCTCCACTACAACT
123 TCCACTGCAACCTCAAAAAGATAGGATTATTGGCTTTAATCTGCTCCACTACAACT
* * * *
4935488 TCAGGGAGATAAGATTTGCTATCTTCAGTCTG-CCCTACTGCAACTTCAGGGGGATAATACTTGT
1 TCAGGGAGATAAGATTTGCCATCTTCAATCTGTCCC-ACTGCAACTTCAGGGGGATAAGACTTGC
* *
4935552 TTTCTTTAGTCTACTCCACTACAACTTCAGGGAGATAAGACTTGTAACTTTAATTCGCTCCACTG
65 TTTCTTCAGTCTGCTCCACTACAACTTCAGGGAGATAAGACTTGTAACTTTAATTCGCTCCACTG
* * * *
4935617 CAACTTCAGAGAGATAGGATTATTGGCTTTAATCTGCTCCACTGCAACT
130 CAACCTCAAAAAGATAGGATTATTGGCTTTAATCTGCTCCACTACAACT
* *
4935666 TCAGGGAGATAAGATTTGCCATCTTTAATTTGTCCCACTGCAACTTCAGGGGGATAAGACTTGCT
1 TCAGGGAGATAAGATTTGCCATCTTCAATCTGTCCCACTGCAACTTCAGGGGGATAAGACTTGCT
* * *
4935731 TTCTTCAGTATGCTTCACTACAACTTCAGGGGGATAAGACTTG
66 TTCTTCAGTCTGCTCCACTACAACTTCAGGGAGATAAGACTTG
4935774 CTTTCTTCAG
Statistics
Matches: 398, Mismatches: 57, Indels: 27
0.83 0.12 0.06
Matches are distributed among these distances:
174 3 0.01
175 11 0.03
176 2 0.01
177 1 0.00
178 222 0.56
179 9 0.02
180 3 0.01
181 106 0.27
182 5 0.01
183 3 0.01
184 33 0.08
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (178 bp):
TCAGGGAGATAAGATTTGCCATCTTCAATCTGTCCCACTGCAACTTCAGGGGGATAAGACTTGCT
TTCTTCAGTCTGCTCCACTACAACTTCAGGGAGATAAGACTTGTAACTTTAATTCGCTCCACTGC
AACCTCAAAAAGATAGGATTATTGGCTTTAATCTGCTCCACTACAACT
Found at i:4935794 original size:223 final size:223
Alignment explanation
Indices: 4935477--4935913 Score: 671
Period size: 223 Copynumber: 2.0 Consensus size: 223
4935467 TTAATCTGCT
* * *
4935477 CCACTACAACTTCAGGGAGATAAGATTTGCTATCTTCAGTCTGCCCTACTGCAACTTCAGGGGGA
1 CCACTACAACTTCAGGGAGATAAGACTTGCTATCTTCAGTATGCCCTACTACAACTTCAGGGGGA
* * * *
4935542 TAATACTTGTTTTCTTTAGTCTACTCCACTACAACTTCAGGGAGATAAGACTTGTAACTTTAATT
66 TAAGACTTGCTTTCTTCAGTCTACTCCACTACAACTTCAGGGAGATAAGACTTGTAACTTTAATC
* * *
4935607 CGCTCCACTGCAACTTCA-GAGAGATAGGATTATTGGCTTTAATCTGCTCCACTGCAACTTCAGG
131 CGCTCCACTGCAACTTCAGGA-AGATAGGATTATTGCCTTTAATCTGCTCCACTACAACTTCAAG
*
4935671 GAGATAAGATTTGCCATCTTTAATTTGTC
195 GAGATAAGATTCGCCATCTTTAATTTGTC
* * * *
4935700 CCACTGCAACTTCAGGGGGATAAGACTTGCTTTCTTCAGTATG-CTTCACTACAACTTCAGGGGG
1 CCACTACAACTTCAGGGAGATAAGACTTGCTATCTTCAGTATGCCCT-ACTACAACTTCAGGGGG
* * *
4935764 ATAAGACTTGCTTTCTTCAGTTTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTTAAT
65 ATAAGACTTGCTTTCTTCAGTCTACTCCACTACAACTTCAGGGAGATAAGACTTGTAACTTTAAT
*
4935829 CCGCTCCACTGTAACTTCAGGAAGATAGGATTATTGCCTTTAATCTGCTCCACTACAACTTCAAG
130 CCGCTCCACTGCAACTTCAGGAAGATAGGATTATTGCCTTTAATCTGCTCCACTACAACTTCAAG
4935894 GAGATAAGATTCGCCATCTT
195 GAGATAAGATTCGCCATCTT
4935914 CTTCAATCCA
Statistics
Matches: 193, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
222 2 0.01
223 189 0.98
224 2 0.01
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (223 bp):
CCACTACAACTTCAGGGAGATAAGACTTGCTATCTTCAGTATGCCCTACTACAACTTCAGGGGGA
TAAGACTTGCTTTCTTCAGTCTACTCCACTACAACTTCAGGGAGATAAGACTTGTAACTTTAATC
CGCTCCACTGCAACTTCAGGAAGATAGGATTATTGCCTTTAATCTGCTCCACTACAACTTCAAGG
AGATAAGATTCGCCATCTTTAATTTGTC
Found at i:4936263 original size:24 final size:24
Alignment explanation
Indices: 4936236--4936311 Score: 107
Period size: 24 Copynumber: 3.2 Consensus size: 24
4936226 TTTCCCACAT
* *
4936236 TGTAATTTTTAAGGTTCAATCCAC
1 TGTAATCTTCAAGGTTCAATCCAC
* *
4936260 TGTAATCTTCAAGGATCAATCTAC
1 TGTAATCTTCAAGGTTCAATCCAC
*
4936284 TATAATCTTCAAGGTTCAATCCAC
1 TGTAATCTTCAAGGTTCAATCCAC
4936308 TGTA
1 TGTA
4936312 CTTTTGGGAC
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.37
Consensus pattern (24 bp):
TGTAATCTTCAAGGTTCAATCCAC
Found at i:4938974 original size:373 final size:374
Alignment explanation
Indices: 4938289--4939035 Score: 1487
Period size: 373 Copynumber: 2.0 Consensus size: 374
4938279 GGACAAGCTC
4938289 CAATCTCTTTCTCTTCTCTTAGGCTTACTGTCCACTGACTTTTGTAAGGTAGGATCTGTTTTTTC
1 CAATCTCTTTCTCTTCTCTTAGGCTTACTGTCCACTGACTTTTGTAAGGTAGGATCTGTTTTTTC
4938354 ATCTTGTTCTATCATCCTTAACAAATCAAGAGATAGGTTACAATCTCAGTCATATTCAAAGTTCT
66 ATCTTGTTCTATCATCCTTAACAAATCAAGAGATAGGTTACAATCTCAGTCATATTCAAAGTTCT
4938419 GAGATCCCCCTGGACACATATCTTACTCAAAAGGAGATTCTGAGTCAGTAGCAACATCGCTCATG
131 GAGATCCCCCTGGACACATATCTTACTCAAAAGGAGATTCTGAGTCAGTAGCAACATCGCTCATG
4938484 TTGTTGATATCTGAAGACCTATTGTAGGTACAAAGGTGGATTCCAAAGAATAAATAAATCTAAGG
196 TTGTTGATATCTGAAGACCTATTGTAGGTACAAAGGTGGATTCCAAAGAATAAATAAATCTAAGG
4938549 ACAATTATTTGTATGAATGAAGAATAAAATAATATTTAAAAGAAAGTCCAAAGAGTAAAAGAATC
261 ACAATTATTTGTATGAATGAAGAATAAAATAATATTTAAAAGAAAGTCCAAAGAGTAAAAGAATC
4938614 TATAAATGAAAAGAATGAAAGAATGTTTGCTCAAAAAG-TACATTTTAT
326 TATAAATGAAAAGAATGAAAGAATGTTTGCTCAAAAAGATACATTTTAT
4938662 CAATCTCTTTCTCTTCTCTTAGGCTTACTGTCCACTGACTTTTGTAAGGTAGGATCTGTTTTTTC
1 CAATCTCTTTCTCTTCTCTTAGGCTTACTGTCCACTGACTTTTGTAAGGTAGGATCTGTTTTTTC
4938727 ATCTTGTTCTATCATCCTTAACAAATCAAGAGATAGGTTACAATCTCAGTCATATTCAAAGTTCT
66 ATCTTGTTCTATCATCCTTAACAAATCAAGAGATAGGTTACAATCTCAGTCATATTCAAAGTTCT
4938792 GAGATCCCCCTGGACACATATCTTACTCAAAAGGAGATTCTGAGTCAGTAGCAACATCGCTCATG
131 GAGATCCCCCTGGACACATATCTTACTCAAAAGGAGATTCTGAGTCAGTAGCAACATCGCTCATG
4938857 TTGTTGATATCTGAAGACCTATTGTAGGTACAAAGGTGGATTCCAAAGAATAAATAAATCTAAGG
196 TTGTTGATATCTGAAGACCTATTGTAGGTACAAAGGTGGATTCCAAAGAATAAATAAATCTAAGG
4938922 ACAATTATTTGTATGAATGAAGAATAAAATAATATTTAAAAGAAAGTCCAAAGAGTAAAAGAATC
261 ACAATTATTTGTATGAATGAAGAATAAAATAATATTTAAAAGAAAGTCCAAAGAGTAAAAGAATC
4938987 TATAAATGAAAAGAATGAAAGAATGTTTGCTCAAAAAGATACATTTTAT
326 TATAAATGAAAAGAATGAAAGAATGTTTGCTCAAAAAGATACATTTTAT
4939036 TGAAACAAAG
Statistics
Matches: 373, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
373 363 0.97
374 10 0.03
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (374 bp):
CAATCTCTTTCTCTTCTCTTAGGCTTACTGTCCACTGACTTTTGTAAGGTAGGATCTGTTTTTTC
ATCTTGTTCTATCATCCTTAACAAATCAAGAGATAGGTTACAATCTCAGTCATATTCAAAGTTCT
GAGATCCCCCTGGACACATATCTTACTCAAAAGGAGATTCTGAGTCAGTAGCAACATCGCTCATG
TTGTTGATATCTGAAGACCTATTGTAGGTACAAAGGTGGATTCCAAAGAATAAATAAATCTAAGG
ACAATTATTTGTATGAATGAAGAATAAAATAATATTTAAAAGAAAGTCCAAAGAGTAAAAGAATC
TATAAATGAAAAGAATGAAAGAATGTTTGCTCAAAAAGATACATTTTAT
Done.