Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold412
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: 4645160
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 29 of 32
Found at i:4126013 original size:18 final size:17
Alignment explanation
Indices: 4125982--4126060 Score: 88
Period size: 17 Copynumber: 4.5 Consensus size: 17
4125972 CTTTTCTCTC
* *
4125982 TTTTTCTTTGTTTTGTT
1 TTTTTTTTTGTTTTTTT
*
4125999 TTTTTTTAT-TTTTTTT
1 TTTTTTTTTGTTTTTTT
*
4126015 ATTTTTTTTGTTTTTTT
1 TTTTTTTTTGTTTTTTT
4126032 TTATTTTTTTGTTTTTTGGT
1 TT-TTTTTTTGTTTTTT--T
4126052 TTTTTTTTT
1 TTTTTTTTT
4126061 CTAAAAAGAA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
16 13 0.25
17 15 0.29
18 14 0.27
19 7 0.13
20 3 0.06
ACGTcount: A:0.04, C:0.01, G:0.08, T:0.87
Consensus pattern (17 bp):
TTTTTTTTTGTTTTTTT
Found at i:4126014 original size:28 final size:26
Alignment explanation
Indices: 4125982--4126059 Score: 102
Period size: 28 Copynumber: 2.9 Consensus size: 26
4125972 CTTTTCTCTC
*
4125982 TTTTTCTTTGTTTTGTTTTTTTTTATTT
1 TTTTTATTT-TTTTGTTTTTTTTTA-TT
4126010 TTTTTATTTTTTTTGTTTTTTTTTATT
1 TTTTTA-TTTTTTTGTTTTTTTTTATT
* *
4126037 TTTTTGTTTTTTGGTTTTTTTTT
1 TTTTTATTTTTTTGTTTTTTTTT
4126060 TCTAAAAAGA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
26 16 0.35
27 7 0.15
28 20 0.43
29 3 0.07
ACGTcount: A:0.04, C:0.01, G:0.08, T:0.87
Consensus pattern (26 bp):
TTTTTATTTTTTTGTTTTTTTTTATT
Found at i:4141708 original size:13 final size:13
Alignment explanation
Indices: 4141690--4141715 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4141680 CAATTTTTTG
4141690 TGTATCGATACAT
1 TGTATCGATACAT
4141703 TGTATCGATACAT
1 TGTATCGATACAT
4141716 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4144094 original size:21 final size:21
Alignment explanation
Indices: 4144070--4144116 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
4144060 TTTGATGCTG
4144070 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
4144090 -TATTTGAAGTGAAAAACAAGT
1 AT-TTTGAAGTGAAAAACAAGT
4144111 ATTTTG
1 ATTTTG
4144117 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 9 0.39
22 9 0.39
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:4144255 original size:13 final size:13
Alignment explanation
Indices: 4144237--4144275 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
4144227 ATAATCACCC
*
4144237 TGTATCGATACAG
1 TGTATCGATACAA
4144250 TGTATCGATACAA
1 TGTATCGATACAA
4144263 TGTATCGATACAA
1 TGTATCGATACAA
4144276 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4144286 original size:20 final size:20
Alignment explanation
Indices: 4144261--4144339 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
4144251 GTATCGATAC
4144261 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
4144281 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
4144306 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
4144326 CATGTATCGATACA
1 AATGTATCGATACA
4144340 TTTTGGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:4146374 original size:15 final size:15
Alignment explanation
Indices: 4146354--4146384 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4146344 ATTTCGTTTG
*
4146354 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
4146369 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
4146384 G
1 G
4146385 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:4148219 original size:21 final size:21
Alignment explanation
Indices: 4148190--4148234 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
4148180 AAGTTTTCAT
*
4148190 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
4148210 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
4148232 TTT
1 TTT
4148235 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:4150470 original size:13 final size:13
Alignment explanation
Indices: 4150452--4150477 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4150442 CAATTTTTTG
4150452 TGTATCGATACAT
1 TGTATCGATACAT
4150465 TGTATCGATACAT
1 TGTATCGATACAT
4150478 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4152152 original size:28 final size:28
Alignment explanation
Indices: 4152109--4152266 Score: 173
Period size: 28 Copynumber: 5.6 Consensus size: 28
4152099 GATACAAAGC
4152109 TGGGGTTGGAGTATCCTCTCG-GAAATAA
1 TGGGGTTGGAGTATCC-CTCGAGAAATAA
***
4152137 CAAGGTTGGAGTATCCCT-GATGAAATAA
1 TGGGGTTGGAGTATCCCTCGA-GAAATAA
* *
4152165 TAGGGTTGGAGTATCCCCTC-AAAAATAA
1 TGGGGTTGGAGTAT-CCCTCGAGAAATAA
*
4152193 TGAGGTTGGAGTATCCCT-GATGAAATAA
1 TGGGGTTGGAGTATCCCTCGA-GAAATAA
4152221 TGGGGTTGGAGTATCCC-CGATGAAATAA
1 TGGGGTTGGAGTATCCCTCGA-GAAATAA
*
4152249 CGGGGTTGGAGTATCCCT
1 TGGGGTTGGAGTATCCCT
4152267 AATTGCGGTA
Statistics
Matches: 111, Mismatches: 11, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
26 1 0.01
27 7 0.06
28 98 0.88
29 5 0.05
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.27
Consensus pattern (28 bp):
TGGGGTTGGAGTATCCCTCGAGAAATAA
Found at i:4152199 original size:56 final size:56
Alignment explanation
Indices: 4152111--4152266 Score: 224
Period size: 56 Copynumber: 2.8 Consensus size: 56
4152101 TACAAAGCTG
* * *
4152111 GGGTTGGAGTATCCTCTCGGAAATAACAAGGTTGGAGTATCCCTGATGAAATAATA
1 GGGTTGGAGTATCCCCTCAGAAATAACGAGGTTGGAGTATCCCTGATGAAATAATA
* * *
4152167 GGGTTGGAGTATCCCCTCAAAAATAATGAGGTTGGAGTATCCCTGATGAAATAATG
1 GGGTTGGAGTATCCCCTCAGAAATAACGAGGTTGGAGTATCCCTGATGAAATAATA
* *
4152223 GGGTTGGAGTATCCCC-GATGAAATAACGGGGTTGGAGTATCCCT
1 GGGTTGGAGTATCCCCTCA-GAAATAACGAGGTTGGAGTATCCCT
4152267 AATTGCGGTA
Statistics
Matches: 89, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
55 1 0.01
56 88 0.99
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.26
Consensus pattern (56 bp):
GGGTTGGAGTATCCCCTCAGAAATAACGAGGTTGGAGTATCCCTGATGAAATAATA
Found at i:4153722 original size:20 final size:19
Alignment explanation
Indices: 4153697--4153803 Score: 100
Period size: 20 Copynumber: 5.7 Consensus size: 19
4153687 AAAATGCCTG
*
4153697 AATGTATCGATACATTGTAA
1 AATGTATCGATACAATG-AA
*
4153717 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGA-A
4153737 AATGTATCGAT---AT---
1 AATGTATCGATACAATGAA
* *
4153750 AATGTATCGAAACAATGAGC
1 AATGTATCGATACAATGA-A
4153770 AATGTATCGATACAATGCAA
1 AATGTATCGATACAATG-AA
4153790 AATGTATCGATACA
1 AATGTATCGATACA
4153804 TCTGGGTAAA
Statistics
Matches: 73, Mismatches: 5, Indels: 18
0.76 0.05 0.19
Matches are distributed among these distances:
13 10 0.14
16 2 0.03
17 2 0.03
19 1 0.01
20 57 0.78
21 1 0.01
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (19 bp):
AATGTATCGATACAATGAA
Found at i:4153759 original size:33 final size:33
Alignment explanation
Indices: 4153717--4153786 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
4153707 TACATTGTAA
* *
4153717 AATGTATCGATACAATGAGCAATGTATCGATAT
1 AATGTATCGAAACAATGAGCAATGTATCGATAC
4153750 AATGTATCGAAACAATGAGCAATGTATCGATAC
1 AATGTATCGAAACAATGAGCAATGTATCGATAC
4153783 AATG
1 AATG
4153787 CAAAATGTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (33 bp):
AATGTATCGAAACAATGAGCAATGTATCGATAC
Found at i:4153759 original size:53 final size:53
Alignment explanation
Indices: 4153697--4153801 Score: 142
Period size: 53 Copynumber: 2.0 Consensus size: 53
4153687 AAAATGCCTG
* * *
4153697 AATGTATCGATACATTGTA-AAATGTATCGATACAATG-AGCAATGTATCGATAT
1 AATGTATCGAAACAATG-AGAAATGTATCGATACAATGCA-AAATGTATCGATAT
*
4153750 AATGTATCGAAACAATGAGCAATGTATCGATACAATGCAAAATGTATCGATA
1 AATGTATCGAAACAATGAGAAATGTATCGATACAATGCAAAATGTATCGATA
4153802 CATCTGGGTA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
52 1 0.02
53 44 0.96
54 1 0.02
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (53 bp):
AATGTATCGAAACAATGAGAAATGTATCGATACAATGCAAAATGTATCGATAT
Found at i:4153855 original size:20 final size:20
Alignment explanation
Indices: 4153830--4153886 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
4153820 ATATATCGAT
4153830 ACAATGTATCAATACAATGA
1 ACAATGTATCAATACAATGA
*
4153850 ACAATGTATCGATACAATGA
1 ACAATGTATCAATACAATGA
4153870 ACAATGTATCAATACAA
1 ACAATGTATCAATACAA
4153887 ATTGTGAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.49, C:0.16, G:0.11, T:0.25
Consensus pattern (20 bp):
ACAATGTATCAATACAATGA
Found at i:4155273 original size:21 final size:23
Alignment explanation
Indices: 4155245--4155296 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
4155235 TGTAGTGATT
4155245 CTTT-GTGAAA-AGGTTAG-TTC
1 CTTTAGTGAAAGAGGTTAGTTTC
*
4155265 CTTTAGTGAAAGGGGTTAGTTTC
1 CTTTAGTGAAAGAGGTTAGTTTC
4155288 C-TTAGTGAA
1 CTTTAGTGAA
4155297 GAGATTGATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 4 0.14
21 6 0.21
22 14 0.50
23 4 0.14
ACGTcount: A:0.25, C:0.10, G:0.27, T:0.38
Consensus pattern (23 bp):
CTTTAGTGAAAGAGGTTAGTTTC
Found at i:4155396 original size:44 final size:44
Alignment explanation
Indices: 4155322--4155416 Score: 111
Period size: 44 Copynumber: 2.2 Consensus size: 44
4155312 AATTATAGTT
* * * * *
4155322 ATATGTACATACTGTTATAGTCATATATACATT-TAGTTATTATG
1 ATATGTACAGACTATTATAGTCATACATACATTAT-GTTACTATA
* *
4155366 ATATGTACAGACTATTATTGTGATACATACATTATGTTACTATA
1 ATATGTACAGACTATTATAGTCATACATACATTATGTTACTATA
4155410 ATATGTA
1 ATATGTA
4155417 TGTACTATTA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
44 42 0.98
45 1 0.02
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.43
Consensus pattern (44 bp):
ATATGTACAGACTATTATAGTCATACATACATTATGTTACTATA
Found at i:4156711 original size:26 final size:26
Alignment explanation
Indices: 4156681--4156734 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
4156671 AATAAGTAAC
**
4156681 TTTTAATTACATGTTAACTTTAAGCT
1 TTTTAATTACATCCTAACTTTAAGCT
4156707 TTTTAATTACATCCTAACTTTAAGCT
1 TTTTAATTACATCCTAACTTTAAGCT
4156733 TT
1 TT
4156735 GTTTTTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.30, C:0.15, G:0.06, T:0.50
Consensus pattern (26 bp):
TTTTAATTACATCCTAACTTTAAGCT
Found at i:4158969 original size:2 final size:2
Alignment explanation
Indices: 4158962--4158997 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4158952 AATTTTGTTG
4158962 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4158998 TGTATTTGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4163330 original size:16 final size:16
Alignment explanation
Indices: 4163304--4163336 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4163294 GTTTATCAAG
4163304 AAAAATCTTAGAAGAAA
1 AAAAATCTTAGAA-AAA
4163321 AAAAAT-TTAGAAAAA
1 AAAAATCTTAGAAAAA
4163336 A
1 A
4163337 TCCTTAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 6 0.38
17 6 0.38
ACGTcount: A:0.70, C:0.03, G:0.09, T:0.18
Consensus pattern (16 bp):
AAAAATCTTAGAAAAA
Found at i:4164777 original size:22 final size:22
Alignment explanation
Indices: 4164729--4164778 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
4164719 CGATTCTTTA
* *
4164729 AAAAATAATGTGTAGATATAGT
1 AAAAATAATATGTAGATACAGT
*
4164751 GAAAATAATATGTACG-TACAGT
1 AAAAATAATATGTA-GATACAGT
4164773 AAAAAT
1 AAAAAT
4164779 GGTATTTTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.52, C:0.04, G:0.16, T:0.28
Consensus pattern (22 bp):
AAAAATAATATGTAGATACAGT
Found at i:4165130 original size:24 final size:22
Alignment explanation
Indices: 4165083--4165125 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
4165073 CATTTAGTAA
*
4165083 AAAAACAATATGTATATGTAAT
1 AAAAACAATATGTATATATAAT
*
4165105 AAAAATAATATGTATATATAA
1 AAAAACAATATGTATATATAA
4165126 CATAACTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.58, C:0.02, G:0.07, T:0.33
Consensus pattern (22 bp):
AAAAACAATATGTATATATAAT
Found at i:4165935 original size:15 final size:15
Alignment explanation
Indices: 4165911--4165944 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
4165901 TCCTTTCATA
*
4165911 AAAAATAATAATAAT
1 AAAAACAATAATAAT
4165926 AAAAACAATAATAAT
1 AAAAACAATAATAAT
4165941 AAAA
1 AAAA
4165945 TAATATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAAACAATAATAAT
Found at i:4166062 original size:211 final size:210
Alignment explanation
Indices: 4165785--4166171 Score: 616
Period size: 211 Copynumber: 1.8 Consensus size: 210
4165775 TTTTAGTCCA
* * *
4165785 AAAAGGATGTCTGTCTGTATAGATATAATTTAATAAAATAATCTGTATGTTTAAGACAATTTAAT
1 AAAAGGATATCTGTCTATATAGATATAATTTAATAAAATAATCTGTATGTTTAAGACAAGTTAAT
* * *
4165850 TACCTATAGACATAACTATTTGTTCAAACAAGAATTGTCTGAACAAATATATCCTTTCATAAAAA
66 TACCTACAGACACAACTATTTGTTCAAACAACAATTGTCTGAACAAATATATCCTTTCATAAAAA
*
4165915 ATAATAATAATAAAAACA-ATAA-TAATAAAATAATATAATTAATTAACTAAAAATTAATTAAAA
131 ATAATAATAATAAAAA-ATATAATTAATAAAATAA-AAAATTAATTAACTAAAAATTAATTAAAA
4165978 CATGCATATCTTAGTCT
194 CATGCATATCTTAGTCT
* *
4165995 AAAAGGAATATCTGTCTATATAGATATAATTTAATAAAATAATCTGTCTGTTTAAGACAGGTTAA
1 AAAAGG-ATATCTGTCTATATAGATATAATTTAATAAAATAATCTGTATGTTTAAGACAAGTTAA
* *
4166060 TTACTTACAGACACAACTATTTGTTCAAACAACAATTGTTTGAACAAATATATCCTTTCATAAAA
65 TTACCTACAGACACAACTATTTGTTCAAACAACAATTGTCTGAACAAATATATCCTTTCATAAAA
* *
4166125 AATAATAATAATAAAAAATATAATTAATTAATTAAAAAATTAATTAA
130 AATAATAATAATAAAAAATATAATTAATAAAATAAAAAATTAATTAA
4166172 TTTTGTACCT
Statistics
Matches: 161, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
210 7 0.04
211 145 0.90
212 9 0.06
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.34
Consensus pattern (210 bp):
AAAAGGATATCTGTCTATATAGATATAATTTAATAAAATAATCTGTATGTTTAAGACAAGTTAAT
TACCTACAGACACAACTATTTGTTCAAACAACAATTGTCTGAACAAATATATCCTTTCATAAAAA
ATAATAATAATAAAAAATATAATTAATAAAATAAAAAATTAATTAACTAAAAATTAATTAAAACA
TGCATATCTTAGTCT
Found at i:4166152 original size:16 final size:16
Alignment explanation
Indices: 4166119--4166148 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4166109 ATATCCTTTC
4166119 ATAAAAAATAATAATA
1 ATAAAAAATAATAATA
4166135 ATAAAAAAT-ATAAT
1 ATAAAAAATAATAAT
4166149 TAATTAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
ATAAAAAATAATAATA
Found at i:4166962 original size:22 final size:22
Alignment explanation
Indices: 4166921--4166962 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
4166911 ATCCTCCGCA
* *
4166921 ATAAAAATAAAAAGATAAAGAG
1 ATAAAAATAAAAAAAAAAAGAG
*
4166943 ATAAAATTAAAAAAAAAAAG
1 ATAAAAATAAAAAAAAAAAG
4166963 CAAATTTCAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.14
Consensus pattern (22 bp):
ATAAAAATAAAAAAAAAAAGAG
Found at i:4174085 original size:33 final size:33
Alignment explanation
Indices: 4174048--4174114 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
4174038 TTCAACGATT
4174048 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
4174081 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
4174114 T
1 T
4174115 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:4174086 original size:13 final size:13
Alignment explanation
Indices: 4174068--4174092 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4174058 CATAAAATGT
4174068 TGTATCGATACAA
1 TGTATCGATACAA
4174081 TGTATCGATACA
1 TGTATCGATACA
4174093 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4174173 original size:13 final size:13
Alignment explanation
Indices: 4174155--4174182 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
4174145 ATTACTCAAA
4174155 TGTATCGATACAT
1 TGTATCGATACAT
4174168 TGTATCGATACAT
1 TGTATCGATACAT
4174181 TG
1 TG
4174183 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4174232 original size:52 final size:52
Alignment explanation
Indices: 4174188--4174368 Score: 326
Period size: 52 Copynumber: 3.5 Consensus size: 52
4174178 CATTGATCTT
*
4174188 TGTATCGATACATGCAGGCAAGTTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
4174240 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
* **
4174292 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
4174344 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
4174369 TCATATTTCG
Statistics
Matches: 125, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 125 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
Found at i:4189693 original size:30 final size:29
Alignment explanation
Indices: 4189636--4189841 Score: 209
Period size: 30 Copynumber: 7.0 Consensus size: 29
4189626 TCACCCTTCA
4189636 AAAGCCCACAAGTCAGTGGCATCTTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
*
4189665 AAAGCCCACAAGTTAGTGGCATCTTTTTTC
1 AAAGCCCACAAGTCAGTGGCATC-TTTTTC
* * *
4189695 AAAAGCCCACAAGTTAGTGGCACCCTTTTC
1 -AAAGCCCACAAGTCAGTGGCATCTTTTTC
* *
4189725 AAAAGCCCACAAGTCAGTGGCAAC--CTTC
1 -AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
4189753 AAAGCCCACAAATCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
* * * *
4189783 GAACCCCACAAGTCGGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
4189812 AAAGTCCACAACTCCGTGGCACTCTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
4189842 TTTTGTAAGC
Statistics
Matches: 150, Mismatches: 21, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
27 20 0.13
28 4 0.03
29 45 0.30
30 59 0.39
31 22 0.15
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.25
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCATCTTTTTC
Found at i:4189908 original size:34 final size:35
Alignment explanation
Indices: 4189817--4189908 Score: 107
Period size: 35 Copynumber: 2.7 Consensus size: 35
4189807 TTTCCAAAGT
* *
4189817 CCACAACTCCGTGGCACTCTTTTTCTTTTGTAAGC
1 CCACAACTCTGTGGCACTCTTTTTCCTTTGTAAGC
* *
4189852 TCACAACTCTGTAGCACTCTTTTTCCTTT-TAAGC
1 CCACAACTCTGTGGCACTCTTTTTCCTTTGTAAGC
* *
4189886 CCACAAGT-TAGTGGCACCCTTTT
1 CCACAACTCT-GTGGCACTCTTTT
4189909 CAGCATATTG
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
33 1 0.02
34 22 0.46
35 25 0.52
ACGTcount: A:0.20, C:0.30, G:0.13, T:0.37
Consensus pattern (35 bp):
CCACAACTCTGTGGCACTCTTTTTCCTTTGTAAGC
Found at i:4189990 original size:41 final size:38
Alignment explanation
Indices: 4189911--4189991 Score: 108
Period size: 41 Copynumber: 2.1 Consensus size: 38
4189901 ACCCTTTTCA
*
4189911 GCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTG
1 GCATATTGGCACCTTCATCTTTAAGTCCAATATAGCTG
* *
4189949 GCATATTGGCACCTTTGGCATCTTTAAGTCTAATATCGCTG
1 GCATATTGGCACC-TT--CATCTTTAAGTCCAATATAGCTG
4189990 GC
1 GC
4189992 CTTGAATCAG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
38 13 0.35
39 2 0.05
41 22 0.59
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (38 bp):
GCATATTGGCACCTTCATCTTTAAGTCCAATATAGCTG
Found at i:4190009 original size:90 final size:92
Alignment explanation
Indices: 4189908--4190197 Score: 284
Period size: 97 Copynumber: 3.1 Consensus size: 92
4189898 GGCACCCTTT
** * *
4189908 TCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGG-CAT-ATTGGCACCTTTGG-CAT
1 TCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCATAATCAGCA-CATTGGCCAC
* *
4189970 CTTTAAGTCTAATATCGCTGGCCTTGAA
65 CTTTAAGCCCAATATCGCTGGCCTTGAA
*
4189998 TCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGTACC
1 TCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCAT-AATCAGCACATTGG---C
4190063 TCACCTTTAAGCCCAATATCGCTGGCCTTGAA
62 -CACCTTTAAGCCCAATATCGCTGGCCTTGAA
* * * * * * *
4190095 TCAGCATATTGGCACC-TAATCTTTAAGACCAGTGTCGCCGGCCTTGAATCAGCACATT-GTCAC
1 TCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCAT-AATCAGCACATTGGCCAC
* * * * * * *
4190158 CTTCAAGTCTAACTGTTGCTGACCGTGAA
65 CTTTAAGCCCAA-TATCGCTGGCCTTGAA
4190187 TCAGCATATTG
1 TCAGCATATTG
4190198 ACATCCTTTT
Statistics
Matches: 171, Mismatches: 20, Indels: 16
0.83 0.10 0.08
Matches are distributed among these distances:
90 42 0.25
91 14 0.08
92 28 0.16
93 5 0.03
95 1 0.01
96 37 0.22
97 44 0.26
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (92 bp):
TCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCATAATCAGCACATTGGCCACC
TTTAAGCCCAATATCGCTGGCCTTGAA
Found at i:4190039 original size:49 final size:49
Alignment explanation
Indices: 4189949--4190162 Score: 261
Period size: 48 Copynumber: 4.3 Consensus size: 49
4189939 AATGTAGCTG
*
4189949 GCATATTGGCACCTTTGGCATCTTTAAGTCTAATATCGCTGGCCTTGAATCA
1 GCATATTGGCACC-TT--CATCTTTAAGTCCAATATCGCTGGCCTTGAATCA
* *
4190001 GCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCA
1 GCATATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCA
* * * *
4190050 GCACATTGGTACC-TCACCTTTAAGCCCAATATCGCTGGCCTTGAATCA
1 GCATATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCA
* * * * *
4190098 GCATATTGGCACC-TAATCTTTAAGACCAGTGTCGCCGGCCTTGAATCA
1 GCATATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCA
* *
4190146 GCACATTGTCACCTTCA
1 GCATATTGGCACCTTCA
4190163 AGTCTAACTG
Statistics
Matches: 141, Mismatches: 20, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
48 82 0.58
49 44 0.31
51 2 0.01
52 13 0.09
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.30
Consensus pattern (49 bp):
GCATATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCA
Found at i:4191073 original size:52 final size:52
Alignment explanation
Indices: 4191031--4191211 Score: 299
Period size: 52 Copynumber: 3.5 Consensus size: 52
4191021 CACTGATCTT
* *
4191031 TGTATCGATACATGTAGGCAAGTTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
*
4191083 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATCCATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
* * **
4191135 AGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
4191187 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
4191212 TCATATTTTG
Statistics
Matches: 120, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 120 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
Found at i:4204392 original size:20 final size:19
Alignment explanation
Indices: 4204346--4204422 Score: 73
Period size: 20 Copynumber: 3.9 Consensus size: 19
4204336 TCATACCCTG
* *
4204346 ATGTATCGATGCATTTTTCA
1 ATGTATCGATACA-TTATCA
* *
4204366 ATATATCGATACATGTATGA
1 ATGTATCGATACAT-TATCA
* *
4204386 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTAT-CA
4204406 ATGTATCGATACATTAT
1 ATGTATCGATACATTAT
4204423 GTCTTTTTTA
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
19 3 0.07
20 42 0.93
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (19 bp):
ATGTATCGATACATTATCA
Found at i:4204413 original size:40 final size:39
Alignment explanation
Indices: 4204346--4204423 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
4204336 TCATACCCTG
* * *
4204346 ATGTATCGATGCATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
4204386 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
4204424 TCTTTTTTAC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:4205368 original size:24 final size:24
Alignment explanation
Indices: 4205336--4205392 Score: 100
Period size: 22 Copynumber: 2.5 Consensus size: 24
4205326 AGCCTTTGAC
4205336 CATGCATTTTTTTTTATTATGTTT
1 CATGCATTTTTTTTTATTATGTTT
4205360 CATGCA--TTTTTTTATTATGTTT
1 CATGCATTTTTTTTTATTATGTTT
4205382 CATGCATTTTT
1 CATGCATTTTT
4205393 AACATGTCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
22 22 0.71
24 9 0.29
ACGTcount: A:0.18, C:0.11, G:0.09, T:0.63
Consensus pattern (24 bp):
CATGCATTTTTTTTTATTATGTTT
Found at i:4205399 original size:20 final size:21
Alignment explanation
Indices: 4205345--4205399 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
4205335 CCATGCATTT
**
4205345 TTTTTTATTATGTTTCATGCA
1 TTTTTTAACATGTTTCATGCA
**
4205366 TTTTTTTATTATGTTTCATGCA
1 -TTTTTTAACATGTTTCATGCA
4205388 -TTTTTAACATGT
1 TTTTTTAACATGT
4205400 CCAGCATCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 10 0.32
22 21 0.68
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.62
Consensus pattern (21 bp):
TTTTTTAACATGTTTCATGCA
Found at i:4207741 original size:21 final size:20
Alignment explanation
Indices: 4207688--4207743 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
4207678 TGTAAGGTGG
*
4207688 TTTTGCATCGATACATTCAC
1 TTTTGTATCGATACATTCAC
* * *
4207708 TTATGTCTCGATACATTTAC
1 TTTTGTATCGATACATTCAC
4207728 TGTTTGTATCGATACA
1 T-TTTGTATCGATACA
4207744 AATTGTAGAA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.25, C:0.20, G:0.12, T:0.43
Consensus pattern (20 bp):
TTTTGTATCGATACATTCAC
Found at i:4208975 original size:13 final size:13
Alignment explanation
Indices: 4208957--4208982 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4208947 CAATTTTTTG
4208957 TGTATCGATACAT
1 TGTATCGATACAT
4208970 TGTATCGATACAT
1 TGTATCGATACAT
4208983 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4211358 original size:21 final size:21
Alignment explanation
Indices: 4211334--4211380 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
4211324 TTTAATGCTG
4211334 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
4211354 -TATTTGAAGTGAAAAACAAGT
1 AT-TTTGAAGTGAAAAACAAGT
4211375 ATTTTG
1 ATTTTG
4211381 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 9 0.39
22 9 0.39
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:4211526 original size:20 final size:20
Alignment explanation
Indices: 4211501--4211577 Score: 73
Period size: 20 Copynumber: 3.6 Consensus size: 20
4211491 ATAATCACCC
4211501 TGTATCGATACAAAGAAAAA
1 TGTATCGATACAAAGAAAAA
* *
4211521 TGTATCGATACATAGAATTTCCAGA
1 TGTATCGATACAAAGAA-----AAA
* *
4211546 TGTATCGATACACAGAAACA
1 TGTATCGATACAAAGAAAAA
4211566 TGTATCGATACA
1 TGTATCGATACA
4211578 TTTTGGACAT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
20 30 0.62
25 18 0.38
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.26
Consensus pattern (20 bp):
TGTATCGATACAAAGAAAAA
Found at i:4213594 original size:15 final size:15
Alignment explanation
Indices: 4213574--4213604 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4213564 ATTTCGTTTG
*
4213574 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
4213589 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
4213604 G
1 G
4213605 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:4215598 original size:21 final size:20
Alignment explanation
Indices: 4215570--4215610 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
4215560 AGCTATATTT
* *
4215570 TCAAAATTTGTATCGATACA
1 TCAAAAATTATATCGATACA
4215590 TCAAAAATTATATCGATACA
1 TCAAAAATTATATCGATACA
4215610 T
1 T
4215611 TTACACGGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.34
Consensus pattern (20 bp):
TCAAAAATTATATCGATACA
Found at i:4217768 original size:21 final size:21
Alignment explanation
Indices: 4217735--4217779 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
4217725 TTGCAAGTTG
*
4217735 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
4217757 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
4217777 AAA
1 AAA
4217780 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:4219604 original size:15 final size:15
Alignment explanation
Indices: 4219584--4219614 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4219574 TAAAAACGTC
*
4219584 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
4219599 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
4219614 C
1 C
4219615 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:4221706 original size:20 final size:20
Alignment explanation
Indices: 4221627--4221706 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
4221617 AATGTCCAAA
*
4221627 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
4221647 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
4221672 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
4221692 TTGTATCGATACATT
1 ATGTATCGATACATT
4221707 GTATCGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:4221710 original size:13 final size:13
Alignment explanation
Indices: 4221692--4221730 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
4221682 ACATTTTTCT
4221692 TTGTATCGATACA
1 TTGTATCGATACA
4221705 TTGTATCGATACA
1 TTGTATCGATACA
*
4221718 CTGTATCGATACA
1 TTGTATCGATACA
4221731 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:4221875 original size:21 final size:21
Alignment explanation
Indices: 4221851--4221897 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
4221841 AAATCTTTTG
4221851 CAAAAT-ACTT-GTTTTTCACTT
1 CAAAATAACTTCGTTTTTCA--T
4221872 C-AAATAACTTCGTTTTTCAT
1 CAAAATAACTTCGTTTTTCAT
4221892 CAAAAT
1 CAAAAT
4221898 CAGCATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (21 bp):
CAAAATAACTTCGTTTTTCAT
Found at i:4221894 original size:20 final size:19
Alignment explanation
Indices: 4221853--4221895 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
4221843 ATCTTTTGCA
4221853 AAATACTTGTTTTTCACTTC
1 AAATACTTGTTTTTCAC-TC
4221873 AAATAACTTCGTTTTTCA-TC
1 AAAT-ACTT-GTTTTTCACTC
4221893 AAA
1 AAA
4221896 ATCAGCATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATACTTGTTTTTCACTC
Found at i:4227166 original size:138 final size:138
Alignment explanation
Indices: 4226999--4227255 Score: 453
Period size: 138 Copynumber: 1.9 Consensus size: 138
4226989 TGTTATTTGG
*
4226999 TGGATAATAAAGAATTATGTCACACATGTATGTATTGATGTATCACGCATCCCATTTTTATTTGA
1 TGGATAATAAAGAATTATGTCACACATGTATGTATTGATGTATCACACATCCCATTTTTATTTGA
*
4227064 AAAACAAAAAATAAAAAAATAAATG-AAAAAAAGGATATGCATGGTGCATTGAAAATAAAGAATT
66 AAAACAAAAAAT-AAAAAATAAATGAAAAAAAAAGATATGCATGGTGCATTGAAAATAAAGAATT
4227128 ATGTCACAT
130 ATGTCACAT
*
4227137 TGGATAATAAAGAATTATGTCACATATGTATGTATTGATGTATCACACATCCCATTTTTATTTGA
1 TGGATAATAAAGAATTATGTCACACATGTATGTATTGATGTATCACACATCCCATTTTTATTTGA
*
4227202 AAAACAAAAAATAAAAAATAAATGAAAAAAAAAAGATGTGCATGGTGCATTGAA
66 AAAACAAAAAATAAAAAATAAATG-AAAAAAAAAGATATGCATGGTGCATTGAA
4227256 GCTCAATTTA
Statistics
Matches: 113, Mismatches: 4, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
137 12 0.11
138 75 0.66
139 26 0.23
ACGTcount: A:0.47, C:0.10, G:0.14, T:0.29
Consensus pattern (138 bp):
TGGATAATAAAGAATTATGTCACACATGTATGTATTGATGTATCACACATCCCATTTTTATTTGA
AAAACAAAAAATAAAAAATAAATGAAAAAAAAAGATATGCATGGTGCATTGAAAATAAAGAATTA
TGTCACAT
Found at i:4233654 original size:23 final size:23
Alignment explanation
Indices: 4233628--4233693 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
4233618 AATCGAAGCG
* *
4233628 ACCAAAACAGCAGTAAAAGAACA
1 ACCAAAACAGCAGCAAAACAACA
*
4233651 ACCAAAACAGTAGCAAAACAACA
1 ACCAAAACAGCAGCAAAACAACA
* *
4233674 ACCAAAGCAGTAGCAAAACA
1 ACCAAAACAGCAGCAAAACA
4233694 GCAAAAGAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.59, C:0.24, G:0.12, T:0.05
Consensus pattern (23 bp):
ACCAAAACAGCAGCAAAACAACA
Found at i:4236861 original size:20 final size:20
Alignment explanation
Indices: 4236838--4236910 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
4236828 ACAATTCAAA
4236838 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
4236858 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
4236879 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
4236899 GTATCGATACAT
1 GTATCGATACAT
4236911 AAAAAAGTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:4236882 original size:21 final size:21
Alignment explanation
Indices: 4236856--4236931 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
4236846 ACATGTTGCA
4236856 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
4236877 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
4236897 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
*
4236918 TTGTATCGATACAT
1 ATGTATCGATACAT
4236932 TTCTTGGTAG
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:4236889 original size:41 final size:41
Alignment explanation
Indices: 4236838--4236931 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
4236828 ACAATTCAAA
*
4236838 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
*
4236879 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGTT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
4236920 GTATCGATACAT
1 GTATCGATACAT
4236932 TTCTTGGTAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:4236988 original size:13 final size:13
Alignment explanation
Indices: 4236970--4236995 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4236960 TACAGCAAGT
4236970 ATGTATCGATACA
1 ATGTATCGATACA
4236983 ATGTATCGATACA
1 ATGTATCGATACA
4236996 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:4239242 original size:21 final size:21
Alignment explanation
Indices: 4239209--4239253 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
4239199 TTGCAAGTTG
*
4239209 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
4239231 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
4239251 AAA
1 AAA
4239254 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:4243180 original size:20 final size:20
Alignment explanation
Indices: 4243101--4243180 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
4243091 AATGTCCAAA
*
4243101 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
4243121 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
4243146 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
4243166 TTGTATCGATACATT
1 ATGTATCGATACATT
4243181 GTATCGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:4243184 original size:13 final size:13
Alignment explanation
Indices: 4243166--4243204 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
4243156 ACATTTTTCT
4243166 TTGTATCGATACA
1 TTGTATCGATACA
4243179 TTGTATCGATACA
1 TTGTATCGATACA
*
4243192 CTGTATCGATACA
1 TTGTATCGATACA
4243205 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:4245680 original size:20 final size:20
Alignment explanation
Indices: 4245657--4245729 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
4245647 ACAATTCAAA
4245657 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
4245677 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
4245698 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
4245718 GTATCGATACAT
1 GTATCGATACAT
4245730 AAAAAAGTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:4245701 original size:21 final size:21
Alignment explanation
Indices: 4245675--4245750 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
4245665 ACATGTTGCA
4245675 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
4245696 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
4245716 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
*
4245737 TTGTATCGATACAT
1 ATGTATCGATACAT
4245751 TTCTTGGCAG
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:4245708 original size:41 final size:41
Alignment explanation
Indices: 4245657--4245750 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
4245647 ACAATTCAAA
*
4245657 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
*
4245698 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGTT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
4245739 GTATCGATACAT
1 GTATCGATACAT
4245751 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:4245807 original size:13 final size:13
Alignment explanation
Indices: 4245789--4245814 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4245779 TACAGCAAGT
4245789 ATGTATCGATACA
1 ATGTATCGATACA
4245802 ATGTATCGATACA
1 ATGTATCGATACA
4245815 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:4247616 original size:79 final size:79
Alignment explanation
Indices: 4247457--4247609 Score: 193
Period size: 79 Copynumber: 1.9 Consensus size: 79
4247447 CAAACCCTCC
* * * *
4247457 TAAAGGACACGTTTGACATGAAAGTGCTCAATGATCCTAAAAGACTCGGTTTTTACATGGAACTT
1 TAAAGGACACGTTTGACATGAAAGTGCTCAATGATCCAAAAAGACTCGATTTTTACATGAAAATT
*
4247522 TCCAAAATAACCCT
66 ACCAAAATAACCCT
* *
4247536 TAAAGGACATGTTTGACATGAAAGTGCT-ACATGATCCAAAAAGACTTGATATTTT-CAATGAAA
1 TAAAGGACACGTTTGACATGAAAGTGCTCA-ATGATCCAAAAAGACTCGAT-TTTTAC-ATGAAA
*
4247599 ATTACTAAAAT
63 ATTACCAAAAT
4247610 GGCCTTAGGT
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
78 1 0.02
79 45 0.71
80 17 0.27
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (79 bp):
TAAAGGACACGTTTGACATGAAAGTGCTCAATGATCCAAAAAGACTCGATTTTTACATGAAAATT
ACCAAAATAACCCT
Found at i:4248815 original size:16 final size:17
Alignment explanation
Indices: 4248776--4248818 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
4248766 AAAAATAAAC
4248776 TAAAA-TAATAGAAAAA
1 TAAAATTAATAGAAAAA
4248792 TATGAAATTAATA-AAAAA
1 TA--AAATTAATAGAAAAA
4248810 TAAAATTAA
1 TAAAATTAA
4248819 ATAATGTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
16 9 0.38
18 10 0.42
19 5 0.21
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.26
Consensus pattern (17 bp):
TAAAATTAATAGAAAAA
Found at i:4255640 original size:66 final size:66
Alignment explanation
Indices: 4255570--4255708 Score: 143
Period size: 66 Copynumber: 2.1 Consensus size: 66
4255560 AGATACTAAC
* * * * * * * * *
4255570 TTGACTTTTGACCTATTTAGAAGGATATAGGCTTAACTCTTTTAACCCGTTTATTAGGATACAAG
1 TTGACTTTGGACCTATGTAGAAGGATACAAGCATAACTATTTTAACCCATTCAGTAGGATACAAG
4255635 T
66 T
** * * * *
4255636 TTGACCCTGGACTTGTGTAGAAGGATACAAGCATAACTATTTTGACCCATTCAGTAGGATACGAG
1 TTGACTTTGGACCTATGTAGAAGGATACAAGCATAACTATTTTAACCCATTCAGTAGGATACAAG
4255701 T
66 T
4255702 TTGACTT
1 TTGACTT
4255709 ATTTAACTTG
Statistics
Matches: 56, Mismatches: 17, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
66 56 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (66 bp):
TTGACTTTGGACCTATGTAGAAGGATACAAGCATAACTATTTTAACCCATTCAGTAGGATACAAG
T
Found at i:4255987 original size:33 final size:33
Alignment explanation
Indices: 4255892--4256008 Score: 119
Period size: 33 Copynumber: 3.5 Consensus size: 33
4255882 GTTCAGAAAA
*
4255892 ACACAAGCTTGACTTCTTTAACTTATTTAAAAGG
1 ACACAAGCTTGAC-TCTTTAACTTATTTAGAAGG
* * **
4255926 ATAC-AGGTTGACTCTTTAACTTGGTTAGAAGG
1 ACACAAGCTTGACTCTTTAACTTATTTAGAAGG
* * * **
4255958 ACACAAGCTTAACACTTAAACTTATTTAGAAAA
1 ACACAAGCTTGACTCTTTAACTTATTTAGAAGG
*
4255991 ACACAAGTTTGACTCTTT
1 ACACAAGCTTGACTCTTT
4256009 TTTAACTTAG
Statistics
Matches: 64, Mismatches: 18, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
32 20 0.31
33 41 0.64
34 3 0.05
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (33 bp):
ACACAAGCTTGACTCTTTAACTTATTTAGAAGG
Found at i:4257558 original size:30 final size:27
Alignment explanation
Indices: 4257503--4257559 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 27
4257493 ATTAAGGCTC
*
4257503 TCGTTTAAAAATTTCTCCTCTTGATAA
1 TCGTTTAAAAATTTCTCCCCTTGATAA
4257530 TCGTTTAAAAAATTTTCTCTCCCTTGATAA
1 TCGTTT-AAAAA-TTTCTC-CCCTTGATAA
4257560 AAATTTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 6 0.23
28 5 0.19
29 6 0.23
30 9 0.35
ACGTcount: A:0.30, C:0.19, G:0.07, T:0.44
Consensus pattern (27 bp):
TCGTTTAAAAATTTCTCCCCTTGATAA
Found at i:4258853 original size:20 final size:20
Alignment explanation
Indices: 4258828--4258966 Score: 108
Period size: 20 Copynumber: 6.8 Consensus size: 20
4258818 TTTTCACAAT
4258828 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
*
4258848 TTGTATCGATACACTGTTCA
1 TTGTATCGATACATTGTTCA
4258868 TTGTATCGATACATTG-T-A
1 TTGTATCGATACATTGTTCA
* * *
4258886 TCG-ATAC-ATTC-TGGGTTTACCTA
1 TTGTAT-CGATACAT-TG-TT--C-A
* * *
4258909 GATGTATCGATATATTTTTCA
1 -TTGTATCGATACATTGTTCA
*
4258930 TTGTATCGATACATTATTCA
1 TTGTATCGATACATTGTTCA
4258950 TTGTATCGATACATTGT
1 TTGTATCGATACATTGT
4258967 ATCGATACAT
Statistics
Matches: 92, Mismatches: 15, Indels: 24
0.70 0.11 0.18
Matches are distributed among these distances:
16 1 0.01
17 6 0.07
18 4 0.04
19 2 0.02
20 67 0.73
21 1 0.01
22 1 0.01
23 1 0.01
24 4 0.04
25 4 0.04
26 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:4258884 original size:13 final size:13
Alignment explanation
Indices: 4258866--4258895 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
4258856 ATACACTGTT
4258866 CATTGTATCGATA
1 CATTGTATCGATA
4258879 CATTGTATCGATA
1 CATTGTATCGATA
4258892 CATT
1 CATT
4258896 CTGGGTTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:4258966 original size:13 final size:13
Alignment explanation
Indices: 4258948--4258977 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
4258938 ATACATTATT
4258948 CATTGTATCGATA
1 CATTGTATCGATA
4258961 CATTGTATCGATA
1 CATTGTATCGATA
4258974 CATT
1 CATT
4258978 CCCAGATGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:4258988 original size:33 final size:33
Alignment explanation
Indices: 4258928--4258993 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
4258918 ATATATTTTT
** *
4258928 CATTGTATCGATACATTATTCATTGTATCGATA
1 CATTGTATCGATACATTACCCAATGTATCGATA
4258961 CATTGTATCGATACATT-CCCAGATGTATCGATA
1 CATTGTATCGATACATTACCCA-ATGTATCGATA
4258994 TATTTTACAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 2 0.07
33 27 0.93
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (33 bp):
CATTGTATCGATACATTACCCAATGTATCGATA
Found at i:4258989 original size:20 final size:19
Alignment explanation
Indices: 4258964--4259019 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
4258954 ATCGATACAT
*
4258964 TGTATCGATACATTCCCAGA
1 TGTATCGATACATTCACA-A
* *
4258984 TGTATCGATATATTTTACAA
1 TGTATCGATACA-TTCACAA
4259004 TGTATCGATACATTCA
1 TGTATCGATACATTCA
4259020 GGCGTTTTTG
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 3 0.10
20 23 0.77
21 4 0.13
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATTCACAA
Found at i:4261093 original size:51 final size:51
Alignment explanation
Indices: 4261037--4261160 Score: 142
Period size: 51 Copynumber: 2.4 Consensus size: 51
4261027 ATTTTTCATC
* * * *
4261037 TCGGGGATACTCCAACCCCTG-TTTTATTTCCACAACATCAATTTTCCATAA
1 TCGGGGATACTCCAACCCC-GATTTTATGTCCAAAACACCAATTTTCCACAA
* * *
4261088 TCGGGGATACTCCGACTCCGATTTTATGTCCAAAACACCAATTTTTCACAA
1 TCGGGGATACTCCAACCCCGATTTTATGTCCAAAACACCAATTTTCCACAA
* * *
4261139 TTGGAGATACTCTAACCCCGAT
1 TCGGGGATACTCCAACCCCGAT
4261161 ATTTCATCGG
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
50 1 0.02
51 59 0.98
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.31
Consensus pattern (51 bp):
TCGGGGATACTCCAACCCCGATTTTATGTCCAAAACACCAATTTTCCACAA
Found at i:4261333 original size:28 final size:27
Alignment explanation
Indices: 4261301--4261373 Score: 103
Period size: 28 Copynumber: 2.6 Consensus size: 27
4261291 TTCACAATTT
4261301 GGGATACTCCAACCCCGTTA-TTTCATCG
1 GGGATACTCCAACCCCGTTATTTTCA--G
*
4261329 GGGATACTCTAACCCCGTTATTTTCGAG
1 GGGATACTCCAACCCCGTTATTTTC-AG
4261357 GGGATACTCCAACCCCG
1 GGGATACTCCAACCCCG
4261374 ACTTTATATC
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 36 0.88
29 4 0.10
30 1 0.02
ACGTcount: A:0.22, C:0.32, G:0.21, T:0.26
Consensus pattern (27 bp):
GGGATACTCCAACCCCGTTATTTTCAG
Found at i:4273949 original size:21 final size:22
Alignment explanation
Indices: 4273924--4273966 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
4273914 CATATTTTTT
*
4273924 TTAAAAAAACCAAAAA-AAAAA
1 TTAAAAAAACAAAAAAGAAAAA
4273945 TTAAAAAAACAAAAAAGAAAAA
1 TTAAAAAAACAAAAAAGAAAAA
4273967 AAAAAGAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.81, C:0.07, G:0.02, T:0.09
Consensus pattern (22 bp):
TTAAAAAAACAAAAAAGAAAAA
Found at i:4273971 original size:21 final size:20
Alignment explanation
Indices: 4273926--4273971 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
4273916 TATTTTTTTT
* *
4273926 AAAAAAACCAAAAAAAAAAT
1 AAAAAAAACAAAAAAAAAAA
* *
4273946 TAAAAAAACAAAAAAGAAAA
1 AAAAAAAACAAAAAAAAAAA
4273966 AAAAAA
1 AAAAAA
4273972 GAGAAAAGAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.87, C:0.07, G:0.02, T:0.04
Consensus pattern (20 bp):
AAAAAAAACAAAAAAAAAAA
Found at i:4275057 original size:55 final size:55
Alignment explanation
Indices: 4274973--4275254 Score: 320
Period size: 55 Copynumber: 5.0 Consensus size: 55
4274963 GATGCCTTTT
* *
4274973 CCTTTTAAAGCCCACACAAGTTGGTGGCACCCTTTAGTCCTCAAACAGCAGGACA
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGGACG
* *
4275028 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACG
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGGACG
*** *
4275083 CCTTTTAAAGCCCACACAAGTTGGTGGCATTTTTTAGTCCTCAAAAAGCAGGACG
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGGACG
* * * *
4275138 CCTTTTAAAACCTACACGAGTTGGTGGCA--CTTTCCAGTCCTCAAAGAGCAAGACG
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCCTTT--AGTCCTCAAAGAGCAGGACG
**
4275193 TCTTCTTCTTTTAAAGCCCACACAAGTTGGTGGCA--CTTCCTAGTATTCAAAGAGCAGGACG
1 ----C--CTTTTAAAGCCCACACAAGTTGGTGGCACCCTT--TAGTCCTCAAAGAGCAGGACG
4275254 C
1 C
4275255 TCTCTCCTTT
Statistics
Matches: 197, Mismatches: 20, Indels: 18
0.84 0.09 0.08
Matches are distributed among these distances:
53 3 0.02
55 146 0.74
57 1 0.01
59 1 0.01
61 45 0.23
63 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (55 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGGACG
Found at i:4275143 original size:28 final size:28
Alignment explanation
Indices: 4275059--4275143 Score: 66
Period size: 28 Copynumber: 3.1 Consensus size: 28
4275049 TGGTGGCACC
*
4275059 TTTTAGTCCTCAAAGAGCAGGACGCCTT
1 TTTTAGTCCTCAAAAAGCAGGACGCCTT
** * ** ** *
4275087 TTAAAG-CC-CACACAAGTTGGTGGCATT
1 TTTTAGTCCTCA-AAAAGCAGGACGCCTT
4275114 TTTTAGTCCTCAAAAAGCAGGACGCCTT
1 TTTTAGTCCTCAAAAAGCAGGACGCCTT
4275142 TT
1 TT
4275144 AAAACCTACA
Statistics
Matches: 37, Mismatches: 17, Indels: 6
0.62 0.28 0.10
Matches are distributed among these distances:
26 2 0.05
27 15 0.41
28 18 0.49
29 2 0.05
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (28 bp):
TTTTAGTCCTCAAAAAGCAGGACGCCTT
Found at i:4275390 original size:62 final size:62
Alignment explanation
Indices: 4275293--4275715 Score: 427
Period size: 61 Copynumber: 7.1 Consensus size: 62
4275283 GAGCAGGACG
* * * *
4275293 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAGGAGCAGGACACCTTTT
1 CCTTTTAAAGCCCACACGAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAGGACGCCTTTT
* * * *
4275355 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAAGATGCCTTTT
1 CCTTTTAAAGCCCACACGAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAGGACGCCTTTT
* * * *
4275417 CCTTTTAAAGCCTACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGTAGGATG-CTTTT
1 CCTTTTAAAGCCCACACGAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAGGACGCCTTTT
*
4275477 -C----AAAGCCCACACGAGTTGGTGGCA-TTTTTCAGTCCTCAAAGAGCAGGACGCC-TTT
1 CCTTTTAAAGCCCACACGAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAGGACGCCTTTT
* * * * *
4275532 -C----AAAGCCCACACGAGTTGGTAGCA-TTTTCCAGTCCTAAAAAAGTAGGATG--TTTT
1 CCTTTTAAAGCCCACACGAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAGGACGCCTTTT
* ** * *
4275586 CTCTTTTTAAAGACCACTTGAGTTGGTGGCAC-CTTCCAGTCCTCAAAGAGCAGGATGCCTTTT
1 C-C-TTTTAAAGCCCACACGAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAGGACGCCTTTT
* * * *
4275649 -CTTTTCAAAACCCACACGAGTTGCTGGCACTTTT-TAGTCCTCAAAGAGCAGAACGCCTTTT
1 CCTTTT-AAAGCCCACACGAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAGGACGCCTTTT
*
4275710 TCTTTT
1 CCTTTT
4275716 TCTCCTTTGT
Statistics
Matches: 310, Mismatches: 36, Indels: 30
0.82 0.10 0.08
Matches are distributed among these distances:
54 3 0.01
55 91 0.29
56 2 0.01
59 1 0.00
60 9 0.03
61 107 0.35
62 93 0.30
63 4 0.01
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.30
Consensus pattern (62 bp):
CCTTTTAAAGCCCACACGAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAGGACGCCTTTT
Found at i:4275626 original size:116 final size:115
Alignment explanation
Indices: 4275273--4275647 Score: 402
Period size: 116 Copynumber: 3.2 Consensus size: 115
4275263 TTCGCCTTTT
* *
4275273 AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAA
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAA
* * ** * *
4275338 GGAGCAGGACACCTTTTCC-TTTTAAAGCCCACACAAGTTGGTGGCACTTTTCT
65 AGAGTAGG--ATGTTTTCCTTTTTAAAGCCCACACGAGTTGGTGGCAC-TTTCC
* * *
4275391 AGTCCTCAAAGAGCAAGATGCCTTTTCCTTTTAAAGCCTACACAAGTTGGTGGCATTTTCCAGTC
1 AGTCCTCAAAGAGCAGGACGCC-TTT-C----AAAGCCCACACAAGTTGGTGGCATTTTCCAGTC
* * *
4275456 CTCAAAGAGTAGGATG-----CTTTTCAAAGCCCACACGAGTTGGTGGCATTTTTC
60 CTCAAAGAGTAGGATGTTTTCCTTTTTAAAGCCCACACGAGTTGGTGGCACTTTCC
* * *
4275507 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTAGCATTTTCCAGTCCTAAAA
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAA
* * ** *
4275572 AAGTAGGATGTTTTCTCTTTTTAAAGACCACTTGAGTTGGTGGCACCTTCC
66 GAGTAGGATGTTTTC-CTTTTTAAAGCCCACACGAGTTGGTGGCACTTTCC
*
4275623 AGTCCTCAAAGAGCAGGATGCCTTT
1 AGTCCTCAAAGAGCAGGACGCCTTT
4275648 TCTTTTCAAA
Statistics
Matches: 215, Mismatches: 29, Indels: 28
0.79 0.11 0.10
Matches are distributed among these distances:
110 44 0.20
114 1 0.00
115 3 0.01
116 76 0.35
117 25 0.12
118 20 0.09
119 3 0.01
121 1 0.00
123 20 0.09
124 22 0.10
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (115 bp):
AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAA
GAGTAGGATGTTTTCCTTTTTAAAGCCCACACGAGTTGGTGGCACTTTCC
Found at i:4275792 original size:45 final size:44
Alignment explanation
Indices: 4275706--4275828 Score: 119
Period size: 45 Copynumber: 2.8 Consensus size: 44
4275696 GCAGAACGCC
* * *
4275706 TTTTTCTTTTTCTCC-TTTGTCTTCAAAGAGCAGGACACACTTCA
1 TTTTCCTTTTTC-CCTTTTGTCCTCAAAGAGCAAGACACACTTCA
* ** *
4275750 TTCCTT-TTTTTTCCCTTTTGTCCTCAAAGAGCAAGATGCACTTTA
1 TT--TTCCTTTTTCCCTTTTGTCCTCAAAGAGCAAGACACACTTCA
*
4275795 TTTTCCTCTTT--CTTTTGTCCTCAAAGAGCAAGAC
1 TTTTCCTTTTTCCCTTTTGTCCTCAAAGAGCAAGAC
4275829 GCATTACGTT
Statistics
Matches: 66, Mismatches: 9, Indels: 10
0.78 0.11 0.12
Matches are distributed among these distances:
42 22 0.33
43 2 0.03
44 8 0.12
45 32 0.48
46 2 0.03
ACGTcount: A:0.20, C:0.25, G:0.11, T:0.43
Consensus pattern (44 bp):
TTTTCCTTTTTCCCTTTTGTCCTCAAAGAGCAAGACACACTTCA
Found at i:4275801 original size:444 final size:436
Alignment explanation
Indices: 4274939--4275743 Score: 983
Period size: 444 Copynumber: 1.8 Consensus size: 436
4274929 TTTCTCCTTT
* * *
4274939 CACTTTTCAGTCTTCAAAGAGTAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
1 CACTTTTCAGTCCTCAAAGAGCAAGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA-C
4275004 CTTTAGTCCTCAAACAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCT
65 CTTTAGTCCTCAAACAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCT
* * ** *
4275069 CAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTTTAGTCCTCAAAAAGCAG
130 CAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTAGCATTTTCCAGTCCTAAAAAAGCAG
* *
4275134 GACGCCTTTTAAAACCTACACGAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAAGACGTCTTCT
195 GACGCCTTTTAAAACCTACACGAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAAGACGCCTTCT
* * * *
4275199 TCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTATTCAAAGAGCAGGACGCTCTCTCCTT
260 TCTTTTAAAACCCACACAAGTTGCTGGCACTTCCTAGTACTCAAAGAGCAGAACGCTCTCTCCTT
* *
4275264 TCGCCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCT
325 TCGCCTTTTAGTCCTCAAAGAGCAGGACACC-TTT--A---CACACAAGTTGGTGGCACCTTTCT
* * *
4275329 AGTCCTCAAGGAGCAGGACACCTTTTCCTTTTAAAGCCCACACAAGTTGGTGG
384 AGTCCTCAAAGAGCAAGACACATTTTCCTTTTAAAGCCCACACAAGTTGGTGG
*
4275382 CACTTTTCTAGTCCTCAAAGAGCAAGATGCCTTTTCCTTTTAAAGCCTACACAAGTTGGTGGCA-
1 CACTTTTC-AGTCCTCAAAGAGCAAGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCAC
* * * ** * * *
4275446 TTTTCCAGTCCTCAAAGAGTAGGATGCTTTTCAAAGCCCACACGAGTTGGTGGCA-TTTTTCAGT
65 CTTT--AGTCCTCAAACAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTT-AGT
*
4275510 CCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTAGCATTTTCCAGTCCTAAAAAAG
127 CCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTAGCATTTTCCAGTCCTAAAAAAG
* * ** *
4275575 TAGGATGTTTTCTCTTTTTAAAGACC-ACTTGAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAG
192 CAGGACG----C-C-TTTTAAA-ACCTACACGAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAA
* * ** *
4275639 GATGCCTT-TTCTTTTCAAAACCCACACGAGTTGCTGGCACTTTTTAGTCCTCAAAGAGCAGAAC
250 GACGCCTTCTTCTTTT-AAAACCCACACAAGTTGCTGGCACTTCCTAGTACTCAAAGAGCAGAAC
* * * * *
4275703 GCCTTTTTCTTTTTCTCC-TTT-GTCTTCAAAGAGCAGGACAC
314 G-CTCTCTC-CTTTCGCCTTTTAGTCCTCAAAGAGCAGGACAC
4275744 ACTTCATTCC
Statistics
Matches: 308, Mismatches: 40, Indels: 21
0.83 0.11 0.06
Matches are distributed among these distances:
442 3 0.01
443 12 0.04
444 161 0.52
448 1 0.00
449 8 0.03
450 106 0.34
451 11 0.04
452 6 0.02
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (436 bp):
CACTTTTCAGTCCTCAAAGAGCAAGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
TTTAGTCCTCAAACAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTC
AAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTAGCATTTTCCAGTCCTAAAAAAGCAGG
ACGCCTTTTAAAACCTACACGAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAAGACGCCTTCTT
CTTTTAAAACCCACACAAGTTGCTGGCACTTCCTAGTACTCAAAGAGCAGAACGCTCTCTCCTTT
CGCCTTTTAGTCCTCAAAGAGCAGGACACCTTTACACACAAGTTGGTGGCACCTTTCTAGTCCTC
AAAGAGCAAGACACATTTTCCTTTTAAAGCCCACACAAGTTGGTGG
Found at i:4275854 original size:42 final size:42
Alignment explanation
Indices: 4275685--4275866 Score: 137
Period size: 42 Copynumber: 4.3 Consensus size: 42
4275675 GCACTTTTTA
* *
4275685 GTCCTCAAAGAGC-AGAACGC-CTT--TTTCTTTTTCTCCTTT
1 GTCCTCAAAGAGCAAG-ACGCACTTACTTTTTTTTTTTCCTTT
* * * *
4275724 GTCTTCAAAGAGCAGGACACACTT-CATTCCTTTTTTTTCCCTTTT
1 GTCCTCAAAGAGCAAGACGCACTTAC-TT--TTTTTTTTTCC-TTT
* ** * *
4275769 GTCCTCAAAGAGCAAGATGCACTTTA-TTTTCCTCTTTCTTTT
1 GTCCTCAAAGAGCAAGACGCAC-TTACTTTTTTTTTTTCCTTT
4275811 GTCCTCAAAGAGCAAGACGCA-TTACGTTTTTTTTTTTCCTTT
1 GTCCTCAAAGAGCAAGACGCACTTAC-TTTTTTTTTTTCCTTT
4275853 GTCCTCGAAA-AGCA
1 GTCCTC-AAAGAGCA
4275867 GGATATACTC
Statistics
Matches: 111, Mismatches: 20, Indels: 21
0.73 0.13 0.14
Matches are distributed among these distances:
39 15 0.14
40 7 0.06
42 47 0.42
43 9 0.08
44 8 0.07
45 23 0.21
46 2 0.02
ACGTcount: A:0.21, C:0.25, G:0.13, T:0.40
Consensus pattern (42 bp):
GTCCTCAAAGAGCAAGACGCACTTACTTTTTTTTTTTCCTTT
Found at i:4276580 original size:20 final size:20
Alignment explanation
Indices: 4276555--4276611 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
4276545 TTTTCACAAT
*
4276555 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTATTCA
*
4276575 TTGTATCGATACACTATTCA
1 TTGTATCGATACATTATTCA
*
4276595 GTGTATCGATACATTAT
1 TTGTATCGATACATTAT
4276612 ATAGATACAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (20 bp):
TTGTATCGATACATTATTCA
Found at i:4276663 original size:20 final size:20
Alignment explanation
Indices: 4276638--4276692 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
4276628 TTTACCCAGA
*
4276638 TGTATCAATACATT-TTGCAT
1 TGTATCAATACATTGCT-CAT
*
4276658 TGTATCGATACATTGCTCAT
1 TGTATCAATACATTGCTCAT
4276678 TGTATCAATACATTG
1 TGTATCAATACATTG
4276693 TATCGATACA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (20 bp):
TGTATCAATACATTGCTCAT
Found at i:4276691 original size:13 final size:13
Alignment explanation
Indices: 4276675--4276704 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
4276665 ATACATTGCT
4276675 CATTGTATCAATA
1 CATTGTATCAATA
*
4276688 CATTGTATCGATA
1 CATTGTATCAATA
4276701 CATT
1 CATT
4276705 ACCCAAATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (13 bp):
CATTGTATCAATA
Found at i:4279091 original size:51 final size:51
Alignment explanation
Indices: 4279034--4279155 Score: 163
Period size: 51 Copynumber: 2.4 Consensus size: 51
4279024 ATTTTTCATC
* * * * * *
4279034 TCGGGGATACTATAACCCCGGTTTTATTTCCACAACATCAATTTTCCATAA
1 TCGGGGATACTCTAACCCCGATTTTATGTCCAAAACACCAATTTTCCACAA
* * *
4279085 TCGGGGATACTCCAACTCCGATTTTATGTCCAAAACACCAATTTTTCACAA
1 TCGGGGATACTCTAACCCCGATTTTATGTCCAAAACACCAATTTTCCACAA
4279136 TCGGGGATACTCTAACCCCG
1 TCGGGGATACTCTAACCCCG
4279156 TTATTTCATC
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.30
Consensus pattern (51 bp):
TCGGGGATACTCTAACCCCGATTTTATGTCCAAAACACCAATTTTCCACAA
Found at i:4279197 original size:28 final size:29
Alignment explanation
Indices: 4279138--4279209 Score: 92
Period size: 28 Copynumber: 2.5 Consensus size: 29
4279128 TTTCACAATC
* *
4279138 GGGGATACTCTAACCCCGTTATTTCAT-C
1 GGGGATACTCCAACCCCGTTATTTCATAG
**
4279166 GGGGATACTCCAACCCCGTTATTTTTTAG
1 GGGGATACTCCAACCCCGTTATTTCATAG
*
4279195 GGGGACACTCCAACC
1 GGGGATACTCCAACC
4279210 TCGGTTTTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
28 24 0.63
29 14 0.37
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (29 bp):
GGGGATACTCCAACCCCGTTATTTCATAG
Found at i:4279209 original size:29 final size:28
Alignment explanation
Indices: 4279135--4279189 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
4279125 ATTTTTCACA
*
4279135 ATCGGGGATACTCTAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
4279163 ATCGGGGATACTCCAACCCCGTTATTT
1 ATCGGGGATACTCCAACCCCGTTATTT
4279190 TTTAGGGGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.22, C:0.29, G:0.18, T:0.31
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATTTC
Found at i:4279330 original size:28 final size:28
Alignment explanation
Indices: 4279297--4279362 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
4279287 TTTCACAATC
* *
4279297 GGGGATACTCCGACCCTGTTATTTCATCA
1 GGGGATACTCCAACCCCGTTATTTC-TCA
*
4279326 -GGGATACTCCAACCCCGTTATTTCTGA
1 GGGGATACTCCAACCCCGTTATTTCTCA
4279353 GGGGATACTC
1 GGGGATACTC
4279363 TAACTCCGGC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 2 0.06
28 31 0.94
ACGTcount: A:0.21, C:0.27, G:0.23, T:0.29
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTATTTCTCA
Found at i:4279330 original size:159 final size:159
Alignment explanation
Indices: 4279047--4279348 Score: 453
Period size: 159 Copynumber: 1.9 Consensus size: 159
4279037 GGGATACTAT
* * * *
4279047 AACCCCGGTTTTATTTCCACAACATCAATTTTCCATAATCGGGGATACTCCAACTCCGATTTTAT
1 AACCCCGGTTTTATTTCCAAAACATCAATTTACCACAATCGAGGATACTCCAACTCCGATTTTAT
* * *
4279112 GTCCAAAACACCAATTTTTCACAATCGGGGATACTCTAACCCCGTTATTTCATCGGGGATACTCC
66 GTCAAAAACACCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTCATCAGGGATACTCC
4279177 AACCCCGTTATTTTTTAGGGGGACACTCC
131 AACCCCGTTATTTTTTAGGGGGACACTCC
* * * *
4279206 AACCTCGGTTTTATTTCTAAAACATCGATTTACCGCAATCGAGGATACTCCAACTCC-ATTTTTA
1 AACCCCGGTTTTATTTCCAAAACATCAATTTACCACAATCGAGGATACTCCAACTCCGA-TTTTA
* * * *
4279270 TTTCAAAAACACTAATTTTTCACAATCGGGGATACTCCGACCCTGTTATTTCATCAGGGATACTC
65 TGTCAAAAACACCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTCATCAGGGATACTC
4279335 CAACCCCGTTATTT
130 CAACCCCGTTATTT
4279349 CTGAGGGGAT
Statistics
Matches: 127, Mismatches: 15, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
158 1 0.01
159 126 0.99
ACGTcount: A:0.27, C:0.27, G:0.13, T:0.32
Consensus pattern (159 bp):
AACCCCGGTTTTATTTCCAAAACATCAATTTACCACAATCGAGGATACTCCAACTCCGATTTTAT
GTCAAAAACACCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTCATCAGGGATACTCC
AACCCCGTTATTTTTTAGGGGGACACTCC
Found at i:4279443 original size:28 final size:27
Alignment explanation
Indices: 4279404--4279480 Score: 102
Period size: 28 Copynumber: 2.8 Consensus size: 27
4279394 TTTTTTCATA
*
4279404 ATCGGGGGTACTCCAACCCCGTTATTT
1 ATCGGGGATACTCCAACCCCGTTATTT
*
4279431 CATCGGGGATACTCCAATCCCGTTATTT
1 -ATCGGGGATACTCCAACCCCGTTATTT
4279459 -TCGAAGGGATACTCCAACCCCG
1 ATCG--GGGATACTCCAACCCCG
4279481 ATTTTATTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
26 3 0.07
28 41 0.93
ACGTcount: A:0.22, C:0.31, G:0.21, T:0.26
Consensus pattern (27 bp):
ATCGGGGATACTCCAACCCCGTTATTT
Found at i:4279527 original size:51 final size:51
Alignment explanation
Indices: 4279464--4279633 Score: 214
Period size: 51 Copynumber: 3.3 Consensus size: 51
4279454 TATTTTCGAA
* *
4279464 GGGATACTCCAACCCCGATTTTATTTTTAAAATACCAATTTTTCACAATCG
1 GGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTTCACAATCG
* *
4279515 GGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTCTCACAATCG
1 GGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTTCACAATCG
* ** * * *** * *
4279566 GGGATACTCTAACCCCGACCTTATTTCCAAAGCATTGATTTTCCAGAATCG
1 GGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTTCACAATCG
4279617 GGGATACTCCAACCCCG
1 GGGATACTCCAACCCCG
4279634 TTATTTTCGA
Statistics
Matches: 102, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 102 1.00
ACGTcount: A:0.29, C:0.28, G:0.13, T:0.30
Consensus pattern (51 bp):
GGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTTCACAATCG
Found at i:4279540 original size:110 final size:107
Alignment explanation
Indices: 4279248--4279527 Score: 307
Period size: 110 Copynumber: 2.6 Consensus size: 107
4279238 CCGCAATCGA
* * * *
4279248 GGATACTCCAACTCC-ATTTTTATTTCAAAAACACTAATTTTTCACAATCGGGGATACTCCGACC
1 GGATACTCCAACTCCGA-TTTTATTTCTAAAATACCAATTTTTCACAATCGGGGATACTCCAACC
*
4279312 C-TGTTATTTCATCAGGGATACTCCAACCCCGTTATTTCTGAGG
65 CGT-TTATTTCATCAGGGATACTCCAACCCCGTTATTTCTGAAG
* ** * ** * * *
4279355 GGATACTCTAACTCCGGCTTTATATCTAAAATATTGATCTTTTTTCATAATCGGGGGTACTCCAA
1 GGATACTCCAACTCCGATTTTATTTCTAAAATA-CCA--ATTTTTCACAATCGGGGATACTCCAA
* *
4279420 CCCCG-TTATTTCATCGGGGATACTCCAATCCCGTTATTT-TCGAAG
63 -CCCGTTTATTTCATCAGGGATACTCCAACCCCGTTATTTCT-GAAG
* *
4279465 GGATACTCCAACCCCGATTTTATTTTTAAAATACCAATTTTTCACAATCGGGGATACTCCAAC
1 GGATACTCCAACTCCGATTTTATTTCTAAAATACCAATTTTTCACAATCGGGGATACTCCAAC
4279528 TCCGATTTTA
Statistics
Matches: 140, Mismatches: 26, Indels: 15
0.77 0.14 0.08
Matches are distributed among these distances:
106 1 0.01
107 49 0.35
108 1 0.01
109 2 0.01
110 84 0.60
111 3 0.02
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (107 bp):
GGATACTCCAACTCCGATTTTATTTCTAAAATACCAATTTTTCACAATCGGGGATACTCCAACCC
GTTTATTTCATCAGGGATACTCCAACCCCGTTATTTCTGAAG
Found at i:4281500 original size:13 final size:13
Alignment explanation
Indices: 4281477--4281516 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
4281467 ATAGTAACCC
4281477 ATATATCGATACA
1 ATATATCGATACA
* *
4281490 ATGTGTCGATACA
1 ATATATCGATACA
4281503 ATATATCGATACA
1 ATATATCGATACA
4281516 A
1 A
4281517 AGAATATTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.30
Consensus pattern (13 bp):
ATATATCGATACA
Found at i:4281676 original size:42 final size:42
Alignment explanation
Indices: 4281624--4281706 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
4281614 ATTAGTATCA
*
4281624 AACCTTACCCTATAGACCCTAATTTACATCAAACAAGTATAG
1 AACCTTACCCTATAGACCCTAATTCACATCAAACAAGTATAG
4281666 AACCTTACCCTATAGACCCTAATTCACATCAAACAAGTATA
1 AACCTTACCCTATAGACCCTAATTCACATCAAACAAGTATA
4281707 ATTTGAATAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.41, C:0.28, G:0.06, T:0.25
Consensus pattern (42 bp):
AACCTTACCCTATAGACCCTAATTCACATCAAACAAGTATAG
Found at i:4288187 original size:37 final size:36
Alignment explanation
Indices: 4288146--4288265 Score: 116
Period size: 37 Copynumber: 3.2 Consensus size: 36
4288136 TCTCGATGAT
*
4288146 ATATCCTCCAGAAAGGCTTTGAAAATCTCTTAAAAGA
1 ATATCCTCAAGAAAGGCTTTGAAAATCTCTTAAAA-A
* ** *
4288183 ATATCTTCAAGAGAAGATTTTGAAAATAC-CTTGTAAAA
1 ATATCCTCAAGA-AAGGCTTTGAAAAT-CTCTT-AAAAA
* * *
4288221 ATGTCCTCAAGAGAGGCTTTGAAAATCTCTTAATGAA
1 ATATCCTCAAGAAAGGCTTTGAAAATCTCTTAA-AAA
4288258 ATATCCTC
1 ATATCCTC
4288266 GAAAGTGGGT
Statistics
Matches: 65, Mismatches: 13, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
36 2 0.03
37 33 0.51
38 26 0.40
39 4 0.06
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (36 bp):
ATATCCTCAAGAAAGGCTTTGAAAATCTCTTAAAAA
Found at i:4288643 original size:13 final size:13
Alignment explanation
Indices: 4288625--4288651 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4288615 ACATTATGCT
4288625 TTGTATCGATACA
1 TTGTATCGATACA
4288638 TTGTATCGATACA
1 TTGTATCGATACA
4288651 T
1 T
4288652 GCTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:4288681 original size:20 final size:19
Alignment explanation
Indices: 4288635--4288691 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
4288625 TTGTATCGAT
4288635 ACATTGTATCGATACATGC
1 ACATTGTATCGATACATGC
* *
4288654 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGC
4288673 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
4288692 AGATTGGTAG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Consensus pattern (19 bp):
ACATTGTATCGATACATGC
Found at i:4288759 original size:13 final size:13
Alignment explanation
Indices: 4288741--4288789 Score: 63
Period size: 13 Copynumber: 4.2 Consensus size: 13
4288731 CATGGGACAA
4288741 TGTATCGATACAT
1 TGTATCGATACAT
4288754 TGTATCGATACA-
1 TGTATCGATACAT
4288766 TG-AT-GA-A-AT
1 TGTATCGATACAT
4288775 TGTATCGATACAT
1 TGTATCGATACAT
4288788 TG
1 TG
4288790 CTTGTAACGG
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
8 1 0.03
9 3 0.10
10 4 0.13
11 4 0.13
12 3 0.10
13 16 0.52
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4288762 original size:33 final size:34
Alignment explanation
Indices: 4288720--4288789 Score: 108
Period size: 33 Copynumber: 2.1 Consensus size: 34
4288710 CTATCACTAT
4288720 TTGTATCGATACATG-GGACAA-TGTATCGATACA
1 TTGTATCGATACATGAGGA-AATTGTATCGATACA
*
4288753 TTGTATCGATACATGATGAAATTGTATCGATACA
1 TTGTATCGATACATGAGGAAATTGTATCGATACA
4288787 TTG
1 TTG
4288790 CTTGTAACGG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
33 17 0.50
34 17 0.50
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (34 bp):
TTGTATCGATACATGAGGAAATTGTATCGATACA
Found at i:4292054 original size:39 final size:39
Alignment explanation
Indices: 4292000--4292078 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
4291990 TGTTAAGGGT
4292000 AAGCATAAAAGAAATTCTTTTAAACCTATAAACTTTGTC
1 AAGCATAAAAGAAATTCTTTTAAACCTATAAACTTTGTC
4292039 AAGCATAAAAGAAATTCTTTTAAACCTATAAACTTTGTC
1 AAGCATAAAAGAAATTCTTTTAAACCTATAAACTTTGTC
4292078 A
1 A
4292079 CGACGTCTAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.33
Consensus pattern (39 bp):
AAGCATAAAAGAAATTCTTTTAAACCTATAAACTTTGTC
Found at i:4296852 original size:50 final size:50
Alignment explanation
Indices: 4296797--4296908 Score: 224
Period size: 50 Copynumber: 2.2 Consensus size: 50
4296787 GCTATAACAA
4296797 AAAGGGGGAGAAGATATTGAAAATAAATAAATTTTTATTTGTTATTTGAC
1 AAAGGGGGAGAAGATATTGAAAATAAATAAATTTTTATTTGTTATTTGAC
4296847 AAAGGGGGAGAAGATATTGAAAATAAATAAATTTTTATTTGTTATTTGAC
1 AAAGGGGGAGAAGATATTGAAAATAAATAAATTTTTATTTGTTATTTGAC
4296897 AAAGGGGGAGAA
1 AAAGGGGGAGAA
4296909 ATGCTTTGAT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 62 1.00
ACGTcount: A:0.43, C:0.02, G:0.23, T:0.32
Consensus pattern (50 bp):
AAAGGGGGAGAAGATATTGAAAATAAATAAATTTTTATTTGTTATTTGAC
Found at i:4296968 original size:20 final size:19
Alignment explanation
Indices: 4296902--4296968 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 19
4296892 TTGACAAAGG
*
4296902 GGGAGAAATGCTTTGATTAA
1 GGGAGAAATTCTTT-ATTAA
*
4296922 GGGGGAGAATT-TTT-TTGAA
1 GGGAGA-AATTCTTTATT-AA
4296941 GAGGAGAAATTCTTTAATTAA
1 G-GGAGAAATTCTTT-ATTAA
4296962 GGGAGAA
1 GGGAGAA
4296969 TAAAACGAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
18 2 0.05
19 7 0.18
20 21 0.55
21 6 0.16
22 2 0.05
ACGTcount: A:0.36, C:0.03, G:0.31, T:0.30
Consensus pattern (19 bp):
GGGAGAAATTCTTTATTAA
Found at i:4297529 original size:13 final size:13
Alignment explanation
Indices: 4297511--4297537 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4297501 ACATTATGCT
4297511 TTGTATCGATACA
1 TTGTATCGATACA
4297524 TTGTATCGATACA
1 TTGTATCGATACA
4297537 T
1 T
4297538 GCTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:4297567 original size:20 final size:19
Alignment explanation
Indices: 4297521--4297577 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
4297511 TTGTATCGAT
4297521 ACATTGTATCGATACATGC
1 ACATTGTATCGATACATGC
* *
4297540 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGC
4297559 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
4297578 AGATTGGCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Consensus pattern (19 bp):
ACATTGTATCGATACATGC
Found at i:4297645 original size:13 final size:13
Alignment explanation
Indices: 4297627--4297675 Score: 63
Period size: 13 Copynumber: 4.2 Consensus size: 13
4297617 CATGGGACAA
4297627 TGTATCGATACAT
1 TGTATCGATACAT
4297640 TGTATCGATACA-
1 TGTATCGATACAT
4297652 TG-AT-GA-A-AT
1 TGTATCGATACAT
4297661 TGTATCGATACAT
1 TGTATCGATACAT
4297674 TG
1 TG
4297676 CTTGTAACGG
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
8 1 0.03
9 3 0.10
10 4 0.13
11 4 0.13
12 3 0.10
13 16 0.52
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4297648 original size:33 final size:34
Alignment explanation
Indices: 4297606--4297675 Score: 108
Period size: 33 Copynumber: 2.1 Consensus size: 34
4297596 CTATCACTAT
4297606 TTGTATCGATACATG-GGACAA-TGTATCGATACA
1 TTGTATCGATACATGAGGA-AATTGTATCGATACA
*
4297639 TTGTATCGATACATGATGAAATTGTATCGATACA
1 TTGTATCGATACATGAGGAAATTGTATCGATACA
4297673 TTG
1 TTG
4297676 CTTGTAACGG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
33 17 0.50
34 17 0.50
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (34 bp):
TTGTATCGATACATGAGGAAATTGTATCGATACA
Found at i:4298498 original size:75 final size:74
Alignment explanation
Indices: 4298419--4298609 Score: 244
Period size: 75 Copynumber: 2.6 Consensus size: 74
4298409 TTAGAGAATT
*
4298419 TCATAGTAAAATATCCTTAAATGAAGTTTTCAAAAATATCTTGATGAAATCTCTTCAAAAGAGGC
1 TCATAGTGAAATATCCTTAAATGAAGTTTT-AAAAATATCTTGATGAAATCTCTTCAAAAGAGGC
*
4298484 TTTGAAAATC
65 TTCGAAAATC
* * * *
4298494 TCATAATGAAATAT-TTTCAAGA-GAAGCTTTTAAAAATATCTTGATGAAATGTCTTCAAGAGAG
1 TCATAGTGAAATATCCTT-AA-ATGAAG-TTTTAAAAATATCTTGATGAAATCTCTTCAAAAGAG
4298557 GCTTCGAAAATC
63 GCTTCGAAAATC
* *
4298569 TCCTAGTGAAATATCCTT-AATAGAAGTTTTAAAAATCTCTT
1 TCATAGTGAAATATCCTTAAAT-GAAGTTTTAAAAATATCTT
4298610 ACTAAAGTAT
Statistics
Matches: 100, Mismatches: 10, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
73 1 0.01
74 17 0.17
75 75 0.75
76 7 0.07
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (74 bp):
TCATAGTGAAATATCCTTAAATGAAGTTTTAAAAATATCTTGATGAAATCTCTTCAAAAGAGGCT
TCGAAAATC
Found at i:4298541 original size:38 final size:38
Alignment explanation
Indices: 4298441--4298655 Score: 133
Period size: 37 Copynumber: 5.7 Consensus size: 38
4298431 ATCCTTAAAT
* *
4298441 GAAG-TTTTCAAAAATATCTTGATGAAATCTCTTCAAAA
1 GAAGCTTTT-AAAAATATCTTGATGAAATATCTTCAAGA
* * * * * *
4298479 GAGGC-TTTGAAAATCTCATAATGAAATATTTTCAAGA
1 GAAGCTTTTAAAAATATCTTGATGAAATATCTTCAAGA
*
4298516 GAAGCTTTTAAAAATATCTTGATGAAATGTCTTCAAGA
1 GAAGCTTTTAAAAATATCTTGATGAAATATCTTCAAGA
* ** * * *
4298554 GAGGC-TTCGAAAATCTCCT-AGTGAAATATCCTT-AATA
1 GAAGCTTTTAAAAATATCTTGA-TGAAATAT-CTTCAAGA
* * *
4298591 GAAG-TTTTAAAAATCTCTT-ACT-AAAGTATCCTCTAGA
1 GAAGCTTTTAAAAATATCTTGA-TGAAA-TATCTTCAAGA
* *
4298628 AAAGC-TTTAGAAAATTTCTTGATGAAAT
1 GAAGCTTTTA-AAAATATCTTGATGAAAT
4298656 CTCCTTGAGA
Statistics
Matches: 134, Mismatches: 32, Indels: 22
0.71 0.17 0.12
Matches are distributed among these distances:
36 6 0.04
37 74 0.55
38 50 0.37
39 4 0.03
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.33
Consensus pattern (38 bp):
GAAGCTTTTAAAAATATCTTGATGAAATATCTTCAAGA
Found at i:4301968 original size:25 final size:24
Alignment explanation
Indices: 4301936--4301983 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
4301926 GAATTAAAAT
* *
4301936 AAAATTTTTGATGCAAAGAAATTA
1 AAAAATTTTGATGAAAAGAAATTA
4301960 AAAAATTTTGATGAAAAGAAATTA
1 AAAAATTTTGATGAAAAGAAATTA
4301984 GTTAAAAACC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.54, C:0.02, G:0.12, T:0.31
Consensus pattern (24 bp):
AAAAATTTTGATGAAAAGAAATTA
Found at i:4303820 original size:3 final size:3
Alignment explanation
Indices: 4303812--4303859 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
4303802 GTAAACAGGT
4303812 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
4303860 CTGGATGAGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:4304400 original size:2 final size:2
Alignment explanation
Indices: 4304393--4304428 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4304383 AAATTGTAAC
4304393 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4304429 TCTCTGCAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4310085 original size:76 final size:76
Alignment explanation
Indices: 4309959--4310110 Score: 268
Period size: 76 Copynumber: 2.0 Consensus size: 76
4309949 CATATGTATT
* * *
4309959 ATCCTATTTTATGAGACAAAAACACCAAATAGGCTAATTTGGCACTACATTAAAGATCAGGAATA
1 ATCCTACTTTATGAGACAAAAACACCAAAGAGGCTAATTTGGCACTACATTAAAGATCAAGAATA
4310024 CACAGTAAGCA
66 CACAGTAAGCA
*
4310035 ATCCTACTTTATGAGACAAAAACAGCAAAGAGGCTAATTTGGCACTACATTAAAGATCAAGAATA
1 ATCCTACTTTATGAGACAAAAACACCAAAGAGGCTAATTTGGCACTACATTAAAGATCAAGAATA
4310100 CACAGTAAGCA
66 CACAGTAAGCA
4310111 GTGGTTTCAA
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 72 1.00
ACGTcount: A:0.44, C:0.18, G:0.15, T:0.22
Consensus pattern (76 bp):
ATCCTACTTTATGAGACAAAAACACCAAAGAGGCTAATTTGGCACTACATTAAAGATCAAGAATA
CACAGTAAGCA
Found at i:4312916 original size:16 final size:16
Alignment explanation
Indices: 4312887--4312927 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
4312877 ATGATTTGGG
4312887 TTTTTCTTTCTCTTTT
1 TTTTTCTTTCTCTTTT
* *
4312903 TTTTTTTTTTTCTTTT
1 TTTTTCTTTCTCTTTT
4312919 TTCTTTCTT
1 TT-TTTCTT
4312928 AATGATTCGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (16 bp):
TTTTTCTTTCTCTTTT
Found at i:4319528 original size:21 final size:22
Alignment explanation
Indices: 4319488--4319534 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
4319478 GTTGCCTTAT
* *
4319488 AATAAATATTTTAAAATATTTG
1 AATAAATATTATAAAATATTTA
*
4319510 AATAAA-ATTATAAATTATTTA
1 AATAAATATTATAAAATATTTA
4319531 AATA
1 AATA
4319535 TTTTACATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
AATAAATATTATAAAATATTTA
Found at i:4319753 original size:17 final size:17
Alignment explanation
Indices: 4319728--4319777 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 17
4319718 TAAAATTTTT
*
4319728 GAGTTATTTTTGAGTTC
1 GAGTCATTTTTGAGTTC
*
4319745 GAGTCATTTTAGA-TTC
1 GAGTCATTTTTGAGTTC
* *
4319761 AAGTCA-CTTTGAGTTC
1 GAGTCATTTTTGAGTTC
4319777 G
1 G
4319778 GATTATTTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
15 4 0.15
16 11 0.42
17 11 0.42
ACGTcount: A:0.22, C:0.12, G:0.22, T:0.44
Consensus pattern (17 bp):
GAGTCATTTTTGAGTTC
Done.