Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168049.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_30, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 11202444
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 44000 characters in sequence are not A, C, G, or T
File 18 of 64
Found at i:2420894 original size:12 final size:12
Alignment explanation
Indices: 2420879--2420917 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 12
2420869 AGGTTTTATA
2420879 AATTTTAAAATT
1 AATTTTAAAATT
2420891 AATTTTTAAAATAT
1 AA-TTTTAAAAT-T
2420905 AATTTATAAAATT
1 AATTT-TAAAATT
2420918 TTGCCAACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 2 0.08
13 13 0.54
14 9 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
AATTTTAAAATT
Found at i:2420909 original size:14 final size:14
Alignment explanation
Indices: 2420875--2420916 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
2420865 TAAAAGGTTT
*
2420875 TATAAATTTTAAAA
1 TATAATTTTTAAAA
2420889 T-TAATTTTTAAAA
1 TATAATTTTTAAAA
*
2420902 TATAATTTATAAAA
1 TATAATTTTTAAAA
2420916 T
1 T
2420917 TTTGCCAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 12 0.48
14 13 0.52
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TATAATTTTTAAAA
Found at i:2421001 original size:65 final size:65
Alignment explanation
Indices: 2420774--2421040 Score: 182
Period size: 65 Copynumber: 4.1 Consensus size: 65
2420764 TTTTTAAAAT
* * ** * *
2420774 TAATTCATAAAATCTTAG-CAATATATTAAAGGATTTTA-TAAGTTTGAAAA-TAATTTTTTAAA
1 TAATTCATAAAATCTT-GCCAACATAGTAAAAAATTTTATTAA-TTTGAAAATTAA-TTTATGAA
* *
2420836 AAT
63 CAC
* **** * ** * * * *
2420839 TAATTCACAAAATCCAATCAACATATTAAAAGGTTTTATAAATTTTAAAATTAATTT-TTAAAAT
1 TAATTCATAAAATCTTGCCAACATAGTAAAAAATTTTATTAATTTGAAAATTAATTTATGAACA-
*
2420903 A
65 C
* * * * * * *
2420904 TAATTTATAAAATTTTGCCAACATATTAAAAAATTTTATTGATTTGAAAATTACTTTTTGAAGAC
1 TAATTCATAAAATCTTGCCAACATAGTAAAAAATTTTATTAATTTGAAAATTAATTTATGAACAC
* * * *
2420969 TAATTCATAAAATCTTGTCAACATAGTGAAAAATTTTATTAATTTGACAATTAATTTATGAACAT
1 TAATTCATAAAATCTTGCCAACATAGTAAAAAATTTTATTAATTTGAAAATTAATTTATGAACAC
2421034 TAATTCA
1 TAATTCA
2421041 ATCAAAATAT
Statistics
Matches: 159, Mismatches: 38, Indels: 10
0.77 0.18 0.05
Matches are distributed among these distances:
64 5 0.03
65 145 0.91
66 9 0.06
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.41
Consensus pattern (65 bp):
TAATTCATAAAATCTTGCCAACATAGTAAAAAATTTTATTAATTTGAAAATTAATTTATGAACAC
Found at i:2421006 original size:130 final size:129
Alignment explanation
Indices: 2420764--2421040 Score: 290
Period size: 130 Copynumber: 2.1 Consensus size: 129
2420754 AACAAAGAAT
* ** *
2420764 TTTTTAAAATTAATTCATAAAATCTTAGCAATATATTAAAGGATTTTATAAGTTTGAAAATAATT
1 TTTTTAAAATTAATTCATAAAATCTTAGCAACATATTAAAAAATTTTATAAGTTTGAAAATAACT
* * * *
2420829 TTTTAAAAATTAATTCACAAAATCCAATCAACATATTAAAAGGTTTTATAAATTTTAAAATTAA
66 TTTTAAAAACTAATTCACAAAATCCAATCAACATATGAAAAGATTTTATAAATTTGAAAATTAA
* * * *
2420893 TTTTTAAAATATAATTTATAAAAT-TTTGCCAACATATTAAAAAATTTTAT-TGATTTGAAAATT
1 TTTTTAAAAT-TAATTCATAAAATCTTAG-CAACATATTAAAAAATTTTATAAG-TTTGAAAATA
* * * *** * *
2420956 ACTTTTTGAAGACTAATTCATAAAATCTTGTCAACATAGTGAAAA-ATTTTATTAATTTGACAAT
63 ACTTTTTAAAAACTAATTCACAAAATCCAATCAACATA-TGAAAAGATTTTATAAATTTGAAAAT
2421020 TAA
127 TAA
* *
2421023 TTTATGAACATTAATTCA
1 TTT-TTAAAATTAATTCA
2421041 ATCAAAATAT
Statistics
Matches: 120, Mismatches: 23, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
129 14 0.12
130 96 0.80
131 10 0.08
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.42
Consensus pattern (129 bp):
TTTTTAAAATTAATTCATAAAATCTTAGCAACATATTAAAAAATTTTATAAGTTTGAAAATAACT
TTTTAAAAACTAATTCACAAAATCCAATCAACATATGAAAAGATTTTATAAATTTGAAAATTAA
Found at i:2423152 original size:24 final size:23
Alignment explanation
Indices: 2423125--2423169 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
2423115 CTTCATCTTC
* *
2423125 ATTTTCTTTTTCTTTTTATTTTTA
1 ATTTTCATTTTC-ATTTATTTTTA
2423149 ATTTTCATTTTCATTTATTTT
1 ATTTTCATTTTCATTTATTTT
2423170 CATTTATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.76
Consensus pattern (23 bp):
ATTTTCATTTTCATTTATTTTTA
Found at i:2423164 original size:12 final size:12
Alignment explanation
Indices: 2423116--2423174 Score: 52
Period size: 12 Copynumber: 5.1 Consensus size: 12
2423106 TTTTTATTTC
*
2423116 TTCATCTTCATT
1 TTCATTTTCATT
*
2423128 TTCTTTTTC-TT
1 TTCATTTTCATT
* *
2423139 TTTATTTTTAATT
1 TTCA-TTTTCATT
2423152 TTCATTTTCA-T
1 TTCATTTTCATT
2423163 TT-ATTTTCATT
1 TTCATTTTCATT
2423174 T
1 T
2423175 ATTTATTTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
10 7 0.19
11 9 0.24
12 16 0.43
13 5 0.14
ACGTcount: A:0.15, C:0.14, G:0.00, T:0.71
Consensus pattern (12 bp):
TTCATTTTCATT
Found at i:2423170 original size:16 final size:14
Alignment explanation
Indices: 2423149--2423183 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
2423139 TTTATTTTTA
2423149 ATTTTCATTTTCATTT
1 ATTTTCA-TTT-ATTT
2423165 ATTTTCATTTATTT
1 ATTTTCATTTATTT
2423179 ATTTT
1 ATTTT
2423184 TATTCTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 3 0.16
16 7 0.37
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.71
Consensus pattern (14 bp):
ATTTTCATTTATTT
Found at i:2423183 original size:30 final size:30
Alignment explanation
Indices: 2423122--2423183 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
2423112 TTTCTTCATC
* * *
2423122 TTCATTTTCTTTTTCTTTTTATTTTTAATT
1 TTCATTTTCTATTTATTTTCATTTTTAATT
*
2423152 TTCATTTTC-ATTTATTTTCATTTATTTATT
1 TTCATTTTCTATTTATTTTCATTT-TTAATT
2423182 TT
1 TT
2423184 TATTCTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 11 0.41
30 16 0.59
ACGTcount: A:0.16, C:0.10, G:0.00, T:0.74
Consensus pattern (30 bp):
TTCATTTTCTATTTATTTTCATTTTTAATT
Found at i:2424140 original size:17 final size:15
Alignment explanation
Indices: 2424118--2424152 Score: 52
Period size: 17 Copynumber: 2.2 Consensus size: 15
2424108 TCCCATAAAG
2424118 TTTTCTTTTTCCTTTTT
1 TTTTCTTTTT--TTTTT
2424135 TTTTCTTTTTTTTTT
1 TTTTCTTTTTTTTTT
2424150 TTT
1 TTT
2424153 GGGTTTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.44
17 10 0.56
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (15 bp):
TTTTCTTTTTTTTTT
Found at i:2424178 original size:19 final size:19
Alignment explanation
Indices: 2424156--2424193 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2424146 TTTTTTTGGG
2424156 TTTAATTT-ATCTTTTATTT
1 TTTAATTTAAT-TTTTATTT
*
2424175 TTTATTTTAATTTTTATTT
1 TTTAATTTAATTTTTATTT
2424194 AAATTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTAATTTAATTTTTATTT
Found at i:2424182 original size:12 final size:12
Alignment explanation
Indices: 2424156--2424199 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
2424146 TTTTTTTGGG
* *
2424156 TTTAATTTATCT
1 TTTAATTTTTAT
*
2424168 TTTATTTTTTAT
1 TTTAATTTTTAT
2424180 TTTAATTTTTAT
1 TTTAATTTTTAT
*
2424192 TTAAATTT
1 TTTAATTT
2424200 GAAACAATGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTAATTTTTAT
Found at i:2428404 original size:36 final size:36
Alignment explanation
Indices: 2428364--2428435 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
2428354 ATAAATAAAA
** * *
2428364 TAATAAAAGATTAATA-ATATATAATAATAAAATTTT
1 TAATAAAAGAGAAATATATAAAT-ATAAAAAAATTTT
2428400 TAATAAAAGAGAAATATATAAATATAAAAAAATTTT
1 TAATAAAAGAGAAATATATAAATATAAAAAAATTTT
2428436 ATTTTTTAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 26 0.84
37 5 0.16
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (36 bp):
TAATAAAAGAGAAATATATAAATATAAAAAAATTTT
Found at i:2428600 original size:13 final size:13
Alignment explanation
Indices: 2428578--2428630 Score: 72
Period size: 13 Copynumber: 4.2 Consensus size: 13
2428568 TACAAGACCT
2428578 TAAA-TGAAACCC
1 TAAAGTGAAACCC
*
2428590 TAAAGTGAAACCT
1 TAAAGTGAAACCC
* *
2428603 TAAAATGAAACCT
1 TAAAGTGAAACCC
2428616 TAAAGTGAAACCC
1 TAAAGTGAAACCC
2428629 TA
1 TA
2428631 CGTAAAACCT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
12 4 0.11
13 32 0.89
ACGTcount: A:0.49, C:0.19, G:0.11, T:0.21
Consensus pattern (13 bp):
TAAAGTGAAACCC
Found at i:2428602 original size:25 final size:26
Alignment explanation
Indices: 2428574--2428627 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
2428564 CTAATACAAG
2428574 ACCTT-AAATGAAACCCTAAAGTGAA
1 ACCTTAAAATGAAACCCTAAAGTGAA
*
2428599 ACCTTAAAATGAAACCTTAAAGTGAA
1 ACCTTAAAATGAAACCCTAAAGTGAA
2428625 ACC
1 ACC
2428628 CTACGTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
25 5 0.19
26 22 0.81
ACGTcount: A:0.48, C:0.20, G:0.11, T:0.20
Consensus pattern (26 bp):
ACCTTAAAATGAAACCCTAAAGTGAA
Found at i:2430031 original size:26 final size:27
Alignment explanation
Indices: 2429999--2430054 Score: 87
Period size: 26 Copynumber: 2.1 Consensus size: 27
2429989 GAATTGTAAG
*
2429999 AACAAAATTTAAATCGCTTGAAACA-A
1 AACAAAATTTAAATCGCATGAAACATA
*
2430025 AACAAAATTTAAATTGCATGAAACATA
1 AACAAAATTTAAATCGCATGAAACATA
2430052 AAC
1 AAC
2430055 TGAAAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 23 0.85
27 4 0.15
ACGTcount: A:0.55, C:0.14, G:0.07, T:0.23
Consensus pattern (27 bp):
AACAAAATTTAAATCGCATGAAACATA
Found at i:2433652 original size:3 final size:3
Alignment explanation
Indices: 2433646--2433673 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2433636 AAAATTGATA
2433646 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2433674 TACAGATCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2437710 original size:130 final size:129
Alignment explanation
Indices: 2437555--2437831 Score: 285
Period size: 130 Copynumber: 2.1 Consensus size: 129
2437545 AACAAAGAAT
* * *
2437555 TTTTTAAAATTAATTCGTAATATCTTAG-CAATATATTA-AAGGATTTTATA-AGTTTGAAAATA
1 TTTTTAAAATTAATTCATAACATCTT-GCCAACATATTAGAA-GATTTTATAGA-TTTGAAAATA
* *
2437617 ATTTTTTAAAAATTAATTCACAAAATCCAATCAACATATT-AAAAGGTTTTATAAAATTT-AAAA
63 ACTTTTTAAAAATTAATTCACAAAATCCAATCAACATATTGAAAA-ATTTTAT-AAATTTGAAAA
2437680 TTAA
126 TTAA
* * * *
2437684 TTTTTAAAATATAATTTATAACATCTTGCCAACATATTAGAATATTTTATTGATTTGAAAATTAC
1 TTTTTAAAAT-TAATTCATAACATCTTGCCAACATATTAGAAGATTTTATAGATTTGAAAATAAC
* * * *** * *
2437749 TTTTTGAAGATTAATTCATAAAATCTTGTCAACATATTGAAAAATTTTATTAATTTGACAATTAA
65 TTTTTAAAAATTAATTCACAAAATCCAATCAACATATTGAAAAATTTTATAAATTTGAAAATTAA
* *
2437814 TTTATGAACATTAATTCA
1 TTT-TTAAAATTAATTCA
2437832 ATCAAAATAT
Statistics
Matches: 121, Mismatches: 20, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
129 16 0.13
130 93 0.77
131 12 0.10
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.42
Consensus pattern (129 bp):
TTTTTAAAATTAATTCATAACATCTTGCCAACATATTAGAAGATTTTATAGATTTGAAAATAACT
TTTTAAAAATTAATTCACAAAATCCAATCAACATATTGAAAAATTTTATAAATTTGAAAATTAA
Found at i:2437717 original size:65 final size:64
Alignment explanation
Indices: 2437552--2437831 Score: 237
Period size: 65 Copynumber: 4.3 Consensus size: 64
2437542 AAAAACAAAG
* * * * *
2437552 AATTTTTTAAAATTAATTCGTAATATCTTAG-CAATATATTAAAGGATTTTA-TAAGTTTGAAAA
1 AATTTTTGAAAATTAATTCATAAAATCTT-GCCAACATATTAAA-AATTTTATTAA-TTTGAAAA
2437615 -T
63 TT
* * **** * *
2437616 AATTTTTTAAAAATTAATTCACAAAATCCAATCAACATATTAAAAGGTTTTATAAAATTT-AAAA
1 AA-TTTTTGAAAATTAATTCATAAAATCTTGCCAACATATTAAAA-ATTTTAT-TAATTTGAAAA
2437680 TT
63 TT
* * * *
2437682 AATTTTT-AAAATATAATTTATAACATCTTGCCAACATATTAGAATATTTTATTGATTTGAAAAT
1 AATTTTTGAAAAT-TAATTCATAAAATCTTGCCAACATATTA-AAAATTTTATTAATTTGAAAAT
2437746 T
64 T
* * * *
2437747 ACTTTTTGAAGATTAATTCATAAAATCTTGTCAACATATTGAAAAATTTTATTAATTTGACAATT
1 AATTTTTGAAAATTAATTCATAAAATCTTGCCAACATATT-AAAAATTTTATTAATTTGAAAATT
* *
2437812 AATTTATGAACATTAATTCA
1 AATTTTTGAAAATTAATTCA
2437832 ATCAAAATAT
Statistics
Matches: 172, Mismatches: 33, Indels: 21
0.76 0.15 0.09
Matches are distributed among these distances:
64 11 0.06
65 146 0.85
66 13 0.08
67 2 0.01
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (64 bp):
AATTTTTGAAAATTAATTCATAAAATCTTGCCAACATATTAAAAATTTTATTAATTTGAAAATT
Found at i:2439940 original size:6 final size:6
Alignment explanation
Indices: 2439929--2440020 Score: 64
Period size: 6 Copynumber: 15.5 Consensus size: 6
2439919 ACCCAAATGA
* * * * * *
2439929 ATTTTT ATTTTT A-TTTT ATTTTC ATCTTC ATTTTC ATTTTC ATTTTC
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
* * *
2439976 ATTTTC ATTTTC A--TTT ATTTTT ATTTATTT ATTTTT ATTCTT ATT
1 ATTTTT ATTTTT ATTTTT ATTTTT A-TT-TTT ATTTTT ATTTTT ATT
2440021 ATTTGGTCAA
Statistics
Matches: 76, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
4 3 0.04
5 5 0.07
6 60 0.79
7 4 0.05
8 4 0.05
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.72
Consensus pattern (6 bp):
ATTTTT
Found at i:2439961 original size:12 final size:12
Alignment explanation
Indices: 2439929--2439991 Score: 92
Period size: 12 Copynumber: 5.3 Consensus size: 12
2439919 ACCCAAATGA
* *
2439929 ATTTTTATTTTT
1 ATTTTCATTTTC
2439941 ATTTT-ATTTTC
1 ATTTTCATTTTC
*
2439952 ATCTTCATTTTC
1 ATTTTCATTTTC
2439964 ATTTTCATTTTC
1 ATTTTCATTTTC
2439976 ATTTTCATTTTC
1 ATTTTCATTTTC
2439988 ATTT
1 ATTT
2439992 ATTTTTATTT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
11 9 0.19
12 38 0.81
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (12 bp):
ATTTTCATTTTC
Found at i:2439969 original size:18 final size:17
Alignment explanation
Indices: 2439941--2440001 Score: 81
Period size: 18 Copynumber: 3.6 Consensus size: 17
2439931 TTTTATTTTT
2439941 ATTTT-ATTTTCATCTTC
1 ATTTTCATTTTCAT-TTC
2439958 ATTTTCATTTTCATTTTC
1 ATTTTCATTTTCA-TTTC
2439976 ATTTTCATTTTCATTT-
1 ATTTTCATTTTCATTTC
*
2439992 ATTTTTATTT
1 ATTTTCATTT
2440002 ATTTATTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
16 9 0.22
17 8 0.20
18 23 0.56
19 1 0.02
ACGTcount: A:0.18, C:0.13, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTTCATTTTCATTTC
Found at i:2440007 original size:14 final size:14
Alignment explanation
Indices: 2439988--2440014 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2439978 TTTCATTTTC
2439988 ATTTATTTTTATTT
1 ATTTATTTTTATTT
2440002 ATTTATTTTTATT
1 ATTTATTTTTATT
2440015 CTTATTATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (14 bp):
ATTTATTTTTATTT
Found at i:2441155 original size:13 final size:13
Alignment explanation
Indices: 2441137--2441201 Score: 66
Period size: 13 Copynumber: 5.2 Consensus size: 13
2441127 CATTTTTATT
2441137 ATATTTTTGCATG
1 ATATTTTTGCATG
*
2441150 ATATTTTCT-TATG
1 ATATTTT-TGCATG
2441163 ATATTTTTGCATG
1 ATATTTTTGCATG
*
2441176 -TATCTGTT--ATG
1 ATAT-TTTTGCATG
2441187 ATATTTTTGCATG
1 ATATTTTTGCATG
2441200 AT
1 AT
2441202 TCTATTATGA
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
11 6 0.14
12 7 0.17
13 28 0.67
14 1 0.02
ACGTcount: A:0.23, C:0.08, G:0.14, T:0.55
Consensus pattern (13 bp):
ATATTTTTGCATG
Found at i:2441155 original size:24 final size:24
Alignment explanation
Indices: 2441128--2441216 Score: 101
Period size: 24 Copynumber: 3.6 Consensus size: 24
2441118 TTATTATTAC
*
2441128 ATTTTTATTATATTTTTGCATGAT
1 ATTTTTATGATATTTTTGCATGAT
2441152 ATTTTCTTATGATATTTTTGCATG-T
1 A-TTT-TTATGATATTTTTGCATGAT
*
2441177 ATCTGTTATGATATTTTTGCATGAT
1 AT-TTTTATGATATTTTTGCATGAT
*
2441202 -TCTATTATGATATTT
1 AT-TTTTATGATATTT
2441217 GTAAATGATT
Statistics
Matches: 58, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
24 34 0.59
25 7 0.12
26 17 0.29
ACGTcount: A:0.24, C:0.07, G:0.11, T:0.58
Consensus pattern (24 bp):
ATTTTTATGATATTTTTGCATGAT
Found at i:2441224 original size:24 final size:23
Alignment explanation
Indices: 2441182--2441230 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
2441172 CATGTATCTG
* **
2441182 TTATGATATTTTTGCATGATTCTA
1 TTATGATATTTGTAAATGATT-TA
2441206 TTATGATATTTGTAAATGATTTA
1 TTATGATATTTGTAAATGATTTA
2441229 TT
1 TT
2441231 TTTGTATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.29, C:0.04, G:0.12, T:0.55
Consensus pattern (23 bp):
TTATGATATTTGTAAATGATTTA
Found at i:2453601 original size:13 final size:12
Alignment explanation
Indices: 2453584--2453615 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
2453574 ATTATTTTTA
2453584 AAAAATAAAAAT
1 AAAAATAAAAAT
2453596 AGAAAATAAAAAT
1 A-AAAATAAAAAT
2453609 AAAAATA
1 AAAAATA
2453616 TTTTTCTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (12 bp):
AAAAATAAAAAT
Found at i:2453606 original size:5 final size:6
Alignment explanation
Indices: 2453584--2453615 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
2453574 ATTATTTTTA
2453584 AAAAAT AAAAAT AGAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT A-AAAAT AAAAAT AAAAAT A
2453616 TTTTTCTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:2455058 original size:20 final size:20
Alignment explanation
Indices: 2455017--2455054 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
2455007 GAACATAATA
2455017 ACAATTAAGATGAATGCATG
1 ACAATTAAGATGAATGCATG
2455037 ACAATTAA-A-GAATGCATG
1 ACAATTAAGATGAATGCATG
2455055 TGACCGCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.50
19 1 0.06
20 8 0.44
ACGTcount: A:0.47, C:0.11, G:0.18, T:0.24
Consensus pattern (20 bp):
ACAATTAAGATGAATGCATG
Found at i:2455179 original size:26 final size:26
Alignment explanation
Indices: 2455150--2455210 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 26
2455140 TCTAGGGTTT
2455150 AGGTTTAGGTTTAGGGTTTCAAG-TTA
1 AGGTTTAGGTTTAGGGTTT-AAGATTA
*
2455176 AGG-TTATGGTTTGGGGTTTAAGATTA
1 AGGTTTA-GGTTTAGGGTTTAAGATTA
*
2455202 TGGTTTAGG
1 AGGTTTAGG
2455211 GTTTTATGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
25 6 0.20
26 21 0.70
27 3 0.10
ACGTcount: A:0.21, C:0.02, G:0.34, T:0.43
Consensus pattern (26 bp):
AGGTTTAGGTTTAGGGTTTAAGATTA
Found at i:2455196 original size:20 final size:20
Alignment explanation
Indices: 2455173--2455214 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
2455163 GGGTTTCAAG
* *
2455173 TTAAGGTTATGGTTTGGGGT
1 TTAAGATTATGGTTTAGGGT
2455193 TTAAGATTATGGTTTAGGGT
1 TTAAGATTATGGTTTAGGGT
2455213 TT
1 TT
2455215 TATGGGAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.33, T:0.48
Consensus pattern (20 bp):
TTAAGATTATGGTTTAGGGT
Found at i:2456841 original size:95 final size:95
Alignment explanation
Indices: 2456677--2456865 Score: 240
Period size: 95 Copynumber: 2.0 Consensus size: 95
2456667 TTTAAGATGC
* * *
2456677 AATCAAGGTTTTTAATGTACCAAAAATCATAAAATAATTTTAAAATGTGATATGAAATGTTTCAT
1 AATCAAGGTTTTTAATGTAACAAAAATCATAAAATAATTTTAAAATGTGATATAAAATGTTTCAC
* * *
2456742 GAAAATCCAACCTT-AAAAAGGTCAAATTAT
66 GAAAAT-CAAACTTCAAAAAGATAAAATTAT
* * * *
2456772 AATCAGGGTTTTTGATGTAATAAAAATCATAAAATAATATTT-AAATGTGATCTAAAACT-TTTC
1 AATCAAGGTTTTTAATGTAACAAAAATCATAAAATAAT-TTTAAAATGTGATATAAAA-TGTTTC
2456835 ACGAAAATCAAACTTCAAAAAGATAAAATTA
64 ACGAAAATCAAACTTCAAAAAGATAAAATTA
2456866 CAAAAATACC
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
94 6 0.07
95 71 0.88
96 4 0.05
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.32
Consensus pattern (95 bp):
AATCAAGGTTTTTAATGTAACAAAAATCATAAAATAATTTTAAAATGTGATATAAAATGTTTCAC
GAAAATCAAACTTCAAAAAGATAAAATTAT
Found at i:2457325 original size:41 final size:41
Alignment explanation
Indices: 2457245--2457325 Score: 101
Period size: 41 Copynumber: 2.0 Consensus size: 41
2457235 ACTGTAGATT
* * *
2457245 CACATAAGAGAAAATGATTCATAGATAGAGGCCTTTGGATA
1 CACATAAGAGAAAATGATTCATAGATAGAAGACTCTGGATA
* *
2457286 CACATTAGAGAAAATGATTCAT-GATTGGAAGACTCTGGAT
1 CACATAAGAGAAAATGATTCATAGA-TAGAAGACTCTGGAT
2457326 TTATAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
40 2 0.06
41 32 0.94
ACGTcount: A:0.40, C:0.12, G:0.22, T:0.26
Consensus pattern (41 bp):
CACATAAGAGAAAATGATTCATAGATAGAAGACTCTGGATA
Found at i:2457512 original size:42 final size:42
Alignment explanation
Indices: 2457405--2457795 Score: 338
Period size: 42 Copynumber: 9.3 Consensus size: 42
2457395 GAAAACTCAA
**
2457405 GATTCATAACAAAGTAATTGATTCATAGTTTGGAGGACTTT-
1 GATTCATAACAAAGTAAACGATTCATAGTTTGGAGGACTTTG
* *
2457446 GATTCACAACAAAGTAAACAATTCATAGTTTGGAGGACTTTG
1 GATTCATAACAAAGTAAACGATTCATAGTTTGGAGGACTTTG
* * *
2457488 GATGCATAACAAAATAAATGATTCATAGTTTTGGAGGACTTTG
1 GATTCATAACAAAGTAAACGATTCATAG-TTTGGAGGACTTTG
* * * *
2457531 GATTCACAACAGAGTAAACGATTCACAGTTTGGAGAACTTTG
1 GATTCATAACAAAGTAAACGATTCATAGTTTGGAGGACTTTG
* * * * * * * *
2457573 GATTAATAATAGAGTAAACAATTCACAGTTTGGAAGACTCTA
1 GATTCATAACAAAGTAAACGATTCATAGTTTGGAGGACTTTG
* * ** ** *
2457615 GATTCATAATAAAGTAAACAATTCATAGTTTAAAACACTCTG
1 GATTCATAACAAAGTAAACGATTCATAGTTTGGAGGACTTTG
* ** * * * *
2457657 GATTTATAGTAGAGTAAATGATTCATCA-TTTGAAGGACTCTG
1 GATTCATAACAAAGTAAACGATTCAT-AGTTTGGAGGACTTTG
* * * **
2457699 GATTCGTAACAAAATAAATGATTCATAGTTTAAAGGACTTTG
1 GATTCATAACAAAGTAAACGATTCATAGTTTGGAGGACTTTG
* * * * * *
2457741 GGTTCACAATAAATTAAACAATTCATAG-TTGGAGGACTTCG
1 GATTCATAACAAAGTAAACGATTCATAGTTTGGAGGACTTTG
*
2457782 GATTCACAACAAAG
1 GATTCATAACAAAG
2457796 ATTAAGGCTT
Statistics
Matches: 286, Mismatches: 60, Indels: 8
0.81 0.17 0.02
Matches are distributed among these distances:
41 59 0.21
42 190 0.66
43 37 0.13
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.31
Consensus pattern (42 bp):
GATTCATAACAAAGTAAACGATTCATAGTTTGGAGGACTTTG
Found at i:2457640 original size:127 final size:126
Alignment explanation
Indices: 2457405--2457645 Score: 302
Period size: 127 Copynumber: 1.9 Consensus size: 126
2457395 GAAAACTCAA
* ** * * *
2457405 GATTCATAACAAAGTAATTGATTCATAGTTTGGAGGACTTTGATTCACAACAAAGTAAACAATTC
1 GATTCACAACAAAGTAAACGATTCACAGTTTGGAGAACTTTGATTAACAACAAAGTAAACAATTC
* * * * **
2457470 ATAGTTTGGAGGACTTTGGATGCATAACAAAATAAATGATTCATAGTTTTGGAGGACTTTG
66 ACAGTTTGGAAGACTCTAGATGCATAACAAAATAAACAATTCATAGTTTTGGAGGACTTTG
* * * *
2457531 GATTCACAACAGAGTAAACGATTCACAGTTTGGAGAACTTTGGATTAATAATAGAGTAAACAATT
1 GATTCACAACAAAGTAAACGATTCACAGTTTGGAGAACTTT-GATTAACAACAAAGTAAACAATT
* * *
2457596 CACAGTTTGGAAGACTCTAGATTCATAATAAAGTAAACAATTCATAGTTT
65 CACAGTTTGGAAGACTCTAGATGCATAACAAAATAAACAATTCATAGTTT
2457646 AAAACACTCT
Statistics
Matches: 95, Mismatches: 19, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
126 35 0.37
127 60 0.63
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (126 bp):
GATTCACAACAAAGTAAACGATTCACAGTTTGGAGAACTTTGATTAACAACAAAGTAAACAATTC
ACAGTTTGGAAGACTCTAGATGCATAACAAAATAAACAATTCATAGTTTTGGAGGACTTTG
Found at i:2457902 original size:16 final size:17
Alignment explanation
Indices: 2457881--2457913 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
2457871 ATTAAAAGTG
2457881 TTTCAAGATTCA-AAAA
1 TTTCAAGATTCACAAAA
2457897 TTTCAAGATTCACAAAA
1 TTTCAAGATTCACAAAA
2457914 GTTTTAGGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.48, C:0.15, G:0.06, T:0.30
Consensus pattern (17 bp):
TTTCAAGATTCACAAAA
Found at i:2458270 original size:16 final size:17
Alignment explanation
Indices: 2458233--2458272 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
2458223 AAGAGGGGTT
*
2458233 AAAGATTCACAAATTCC
1 AAAGATTCACAAAATCC
2458250 AAAGATTCACAAAAT-C
1 AAAGATTCACAAAATCC
2458266 AAAGATT
1 AAAGATT
2458273 TAAAATTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.53, C:0.17, G:0.07, T:0.23
Consensus pattern (17 bp):
AAAGATTCACAAAATCC
Found at i:2458326 original size:141 final size:141
Alignment explanation
Indices: 2458083--2458403 Score: 437
Period size: 141 Copynumber: 2.3 Consensus size: 141
2458073 AGTCTCGTAT
* * * *
2458083 GAGGGATTAAAGATTCACAAA-TCTCAAAGATTCACAAGAGTCAAAGTTTTGAAATTTTCAAATA
1 GAGGGGTTAAAGATTCACAAATTC-CAAAGATTCACAA-AATCAAAGATTTAAAATTTTCAAATA
* * * * * * * *
2458147 TTCGTTAGAAGGGTTAAAGATTCACAAATTCCAGAGATTTATAAGAGTTAAAGATTTAAAATTTT
64 TTCATAAAAAGGGTTAAAAATTCACAAATTCCAAAGATTCACAAGAGTCAAAGATTTAAAATTTT
*
2458212 CAAAGGTTTGCAA
129 CAAAGGTTCGCAA
2458225 GAGGGGTTAAAGATTCACAAATTCCAAAGATTCACAAAATCAAAGATTTAAAATTTTCAAATATT
1 GAGGGGTTAAAGATTCACAAATTCCAAAGATTCACAAAATCAAAGATTTAAAATTTTCAAATATT
* * *
2458290 CATAAAAAGGGTTAAAAATTCATAAATTTCAAAGATTCGCAAGAGTCAAAGATTTAAAATTTTCA
66 CATAAAAAGGGTTAAAAATTCACAAATTCCAAAGATTCACAAGAGTCAAAGATTTAAAATTTTCA
*
2458355 AAGGTTCGCCA
131 AAGGTTCGCAA
* * *
2458366 GAGGGGTTAAAGATTCACAAATTCTAGAGATTCGCAAA
1 GAGGGGTTAAAGATTCACAAATTCCAAAGATTCACAAA
2458404 CATAAATGAT
Statistics
Matches: 158, Mismatches: 20, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
141 123 0.78
142 33 0.21
143 2 0.01
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (141 bp):
GAGGGGTTAAAGATTCACAAATTCCAAAGATTCACAAAATCAAAGATTTAAAATTTTCAAATATT
CATAAAAAGGGTTAAAAATTCACAAATTCCAAAGATTCACAAGAGTCAAAGATTTAAAATTTTCA
AAGGTTCGCAA
Found at i:2458402 original size:71 final size:71
Alignment explanation
Indices: 2458020--2458398 Score: 356
Period size: 71 Copynumber: 5.4 Consensus size: 71
2458010 TGCAATGACC
* * * * * * *
2458020 AAAGATCCATAAACTCTAAAGATTTACAAGATTCAAGGACTTGT-AAA-TTTCAAAG-TCTCGTA
1 AAAGATTCACAAATTCTAAAGATTCACAAGAGTCAAAGA-TT-TAAAATTTTCAAAGAT-TCGCA
* *
2458082 TGAGGGATT
63 AGAGGGGTT
* * * **
2458091 AAAGATTCACAAA-TCTCAAAGATTCACAAGAGTCAAAGTTTTGAAATTTTCAAATATTCGTTAG
1 AAAGATTCACAAATTCT-AAAGATTCACAAGAGTCAAAGATTTAAAATTTTCAAAGATTCGCAAG
*
2458155 AAGGGTT
65 AGGGGTT
* * * * * * *
2458162 AAAGATTCACAAATTCCAGAGATTTATAAGAGTTAAAGATTTAAAATTTTCAAAGGTTTGCAAGA
1 AAAGATTCACAAATTCTAAAGATTCACAAGAGTCAAAGATTTAAAATTTTCAAAGATTCGCAAGA
2458227 GGGGTT
66 GGGGTT
* * * ** *
2458233 AAAGATTCACAAATTCCAAAGATTCACAA-AATCAAAGATTTAAAATTTTCAAATATTCATAAAA
1 AAAGATTCACAAATTCTAAAGATTCACAAGAGTCAAAGATTTAAAATTTTCAAAGATTCGCAAGA
*
2458297 AGGGTT
66 GGGGTT
* * * * *
2458303 AAAAATTCATAAATT-TCAAAGATTCGCAAGAGTCAAAGATTTAAAATTTTCAAAGGTTCGCCAG
1 AAAGATTCACAAATTCT-AAAGATTCACAAGAGTCAAAGATTTAAAATTTTCAAAGATTCGCAAG
2458367 AGGGGTT
65 AGGGGTT
*
2458374 AAAGATTCACAAATTCTAGAGATTC
1 AAAGATTCACAAATTCTAAAGATTC
2458399 GCAAACATAA
Statistics
Matches: 249, Mismatches: 51, Indels: 16
0.79 0.16 0.05
Matches are distributed among these distances:
69 1 0.00
70 64 0.26
71 180 0.72
72 4 0.02
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (71 bp):
AAAGATTCACAAATTCTAAAGATTCACAAGAGTCAAAGATTTAAAATTTTCAAAGATTCGCAAGA
GGGGTT
Found at i:2460017 original size:17 final size:20
Alignment explanation
Indices: 2459997--2460037 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
2459987 TCTTTTTTCA
2459997 ATTTTTC-TT-CCTTTT-TT
1 ATTTTTCTTTCCCTTTTCTT
2460014 A-TTTTCTTTCCCTTTTCTT
1 ATTTTTCTTTCCCTTTTCTT
2460033 ATTTT
1 ATTTT
2460038 CTCCTTCGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
16 5 0.25
17 3 0.15
18 6 0.30
19 3 0.15
20 3 0.15
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.73
Consensus pattern (20 bp):
ATTTTTCTTTCCCTTTTCTT
Found at i:2460020 original size:16 final size:17
Alignment explanation
Indices: 2459999--2460043 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 17
2459989 TTTTTTCAAT
2459999 TTTTCTTCCTTTT-TTA
1 TTTTCTTCCTTTTCTTA
2460015 TTTTCTTTCCCTTTTCTTA
1 TTTTC-TT-CCTTTTCTTA
2460034 TTTTC-TCCTT
1 TTTTCTTCCTT
2460044 CGTTCACTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 9 0.35
17 3 0.12
18 6 0.23
19 8 0.31
ACGTcount: A:0.04, C:0.24, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTCTTCCTTTTCTTA
Found at i:2460392 original size:24 final size:23
Alignment explanation
Indices: 2460364--2460414 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 23
2460354 GAAGAAAAGG
2460364 TTTTTTCTCTTTTCTTTTTCAAAAT
1 TTTTTTCT-TTTTC-TTTTCAAAAT
2460389 TTTTTTCTTTTTCTTTTCAAAAT
1 TTTTTTCTTTTTCTTTTCAAAAT
2460412 TTT
1 TTT
2460415 CTTTATTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 13 0.50
24 5 0.19
25 8 0.31
ACGTcount: A:0.16, C:0.14, G:0.00, T:0.71
Consensus pattern (23 bp):
TTTTTTCTTTTTCTTTTCAAAAT
Found at i:2460579 original size:22 final size:23
Alignment explanation
Indices: 2460551--2460594 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
2460541 CAATTAAAGC
2460551 TTTTTTTCA-TTTCATTTTTTTA
1 TTTTTTTCATTTTCATTTTTTTA
2460573 TTTTTTTCATTTTCATTTTTTT
1 TTTTTTTCATTTTCATTTTTTT
2460595 CTTTGCATGC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTTTTTCATTTTCATTTTTTTA
Found at i:2461290 original size:15 final size:15
Alignment explanation
Indices: 2461252--2461306 Score: 76
Period size: 16 Copynumber: 3.6 Consensus size: 15
2461242 TCCTTATTCT
*
2461252 TCTCTTTTTTCATTTT
1 TCTCTTTTTTC-TTTC
2461268 TCTCTTTTTTCTTTC
1 TCTCTTTTTTCTTTC
2461283 TCT-TTTTTTCTTCTC
1 TCTCTTTTTTCTT-TC
2461298 TCTCTTTTT
1 TCTCTTTTT
2461307 AAAAGCACTT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
14 9 0.25
15 11 0.31
16 16 0.44
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.75
Consensus pattern (15 bp):
TCTCTTTTTTCTTTC
Found at i:2461345 original size:5 final size:5
Alignment explanation
Indices: 2461335--2461365 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
2461325 ATTATTATTA
2461335 TTTTC TTTTC TCTTTC TTTTC TTTTC TTTTC
1 TTTTC TTTTC T-TTTC TTTTC TTTTC TTTTC
2461366 ATTTAAAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTC
Found at i:2461356 original size:16 final size:15
Alignment explanation
Indices: 2461335--2461365 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
2461325 ATTATTATTA
2461335 TTTTCTTTTCTCTTTC
1 TTTTCTTTTCT-TTTC
2461351 TTTTCTTTTCTTTTC
1 TTTTCTTTTCTTTTC
2461366 ATTTAAAGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTCTTTTCTTTTC
Found at i:2464255 original size:22 final size:22
Alignment explanation
Indices: 2464225--2464275 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
2464215 TTTTGAAAAA
*
2464225 TTTTG-TTTTTTTT-TTT-GTT
1 TTTTGATTTTTTTTCTTTCTTT
*
2464244 TTTGGATTTTTTTTCTTTCTTT
1 TTTTGATTTTTTTTCTTTCTTT
2464266 TTTTGATTTT
1 TTTTGATTTT
2464276 GTTAGATAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 4 0.15
20 8 0.31
21 3 0.12
22 11 0.42
ACGTcount: A:0.04, C:0.04, G:0.10, T:0.82
Consensus pattern (22 bp):
TTTTGATTTTTTTTCTTTCTTT
Found at i:2465032 original size:19 final size:20
Alignment explanation
Indices: 2465008--2465059 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
2464998 AATCAAAACA
2465008 TTTTTTC-AAATTTTCA-ATT
1 TTTTTTCAAAATTTT-AGATT
2465027 TTTTTTCAAAATTTTAGA-T
1 TTTTTTCAAAATTTTAGATT
2465046 TTTTTT-AAAATTTT
1 TTTTTTCAAAATTTT
2465060 TTCACTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.26
19 15 0.48
20 8 0.26
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.63
Consensus pattern (20 bp):
TTTTTTCAAAATTTTAGATT
Found at i:2465969 original size:7 final size:6
Alignment explanation
Indices: 2465954--2466067 Score: 70
Period size: 7 Copynumber: 17.7 Consensus size: 6
2465944 GGGTTAGGGT
* *
2465954 TTTAGG TTTAGAG TTTAGG ATTA-G ATTAGG ATTTAGGG TTTAGG TTTAGGG
1 TTTAGG TTTAG-G TTTAGG TTTAGG TTTAGG -TTTA-GG TTTAGG TTTA-GG
* * * *
2466005 TTT-GAG TTTATGG TTTAGTA TTTGGG TTTAGGG TTTGGG TTTAAG TTTCAGG
1 TTTAG-G TTTA-GG TTTAG-G TTTAGG TTTA-GG TTTAGG TTTAGG TTT-AGG
2466057 TTTAGGG TTTA
1 TTTA-GG TTTA
2466068 TGATTTTAAT
Statistics
Matches: 86, Mismatches: 10, Indels: 23
0.72 0.08 0.19
Matches are distributed among these distances:
5 6 0.07
6 34 0.40
7 43 0.50
8 3 0.03
ACGTcount: A:0.19, C:0.01, G:0.32, T:0.47
Consensus pattern (6 bp):
TTTAGG
Found at i:2465970 original size:13 final size:13
Alignment explanation
Indices: 2465954--2466067 Score: 65
Period size: 13 Copynumber: 8.3 Consensus size: 13
2465944 GGGTTAGGGT
2465954 TTTAGGTTTAGAG
1 TTTAGGTTTAGAG
*
2465967 TTTAGGATTAGATTAGG
1 TTTAGGTTTAG---A-G
2465984 ATTTAGGGTTTAG-G
1 -TTTA-GGTTTAGAG
2465998 TTTAGGGTTT-GAG
1 TTTA-GGTTTAGAG
2466011 TTTATGGTTTAGTA-
1 TTTA-GGTTTAG-AG
* *
2466025 TTTGGGTTTAGGG
1 TTTAGGTTTAGAG
*
2466038 TTTGGGTTTA-AG
1 TTTAGGTTTAGAG
*
2466050 TTTCAGGTTTAGGG
1 TTT-AGGTTTAGAG
2466064 TTTA
1 TTTA
2466068 TGATTTTAAT
Statistics
Matches: 81, Mismatches: 8, Indels: 24
0.72 0.07 0.21
Matches are distributed among these distances:
12 5 0.06
13 54 0.67
14 9 0.11
15 1 0.01
16 1 0.01
17 1 0.01
18 4 0.05
19 6 0.07
ACGTcount: A:0.19, C:0.01, G:0.32, T:0.47
Consensus pattern (13 bp):
TTTAGGTTTAGAG
Found at i:2465989 original size:25 final size:24
Alignment explanation
Indices: 2465955--2466002 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
2465945 GGTTAGGGTT
2465955 TTAGGTTTAGAGTTTAGGATTAGA
1 TTAGGTTTAGAGTTTAGGATTAGA
* *
2465979 TTAGGATTTAGGGTTTAGGTTTAG
1 TTAGG-TTTAGAGTTTAGGATTAG
2466003 GGTTTGAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (24 bp):
TTAGGTTTAGAGTTTAGGATTAGA
Found at i:2466019 original size:20 final size:19
Alignment explanation
Indices: 2465991--2466066 Score: 82
Period size: 20 Copynumber: 3.9 Consensus size: 19
2465981 AGGATTTAGG
2465991 GTTTAGGTTTAGGGTTTGA
1 GTTTAGGTTTAGGGTTTGA
** *
2466010 GTTTATGGTTTAGTATTTGG
1 GTTTA-GGTTTAGGGTTTGA
*
2466030 GTTTAGGGTTT-GGGTTTAA
1 GTTTA-GGTTTAGGGTTTGA
2466049 GTTTCAGGTTTAGGGTTT
1 GTTT-AGGTTTAGGGTTT
2466067 ATGATTTTAA
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
19 18 0.39
20 28 0.61
ACGTcount: A:0.14, C:0.01, G:0.34, T:0.50
Consensus pattern (19 bp):
GTTTAGGTTTAGGGTTTGA
Found at i:2469046 original size:17 final size:15
Alignment explanation
Indices: 2469013--2469061 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 15
2469003 ATGACTGCTT
* *
2469013 TTTTTTAGTATTGTA
1 TTTTTTATTATTATA
2469028 TTATTTATATTATTATA
1 TT-TTT-TATTATTATA
2469045 TTTTTTATTA-TATA
1 TTTTTTATTATTATA
2469059 TTT
1 TTT
2469062 GCATGATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
14 7 0.23
15 7 0.23
16 6 0.20
17 10 0.33
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (15 bp):
TTTTTTATTATTATA
Found at i:2469156 original size:25 final size:25
Alignment explanation
Indices: 2469041--2469184 Score: 100
Period size: 26 Copynumber: 5.8 Consensus size: 25
2469031 TTTATATTAT
* *
2469041 TATATTTT-TTATTATATATTTGCA
1 TATATTTTATTATGATATTTTTGCA
* *
2469065 TGATATTTTCTTCT-ACTATTTTTGCA
1 T-ATATTTTATTATGA-TATTTTTGCA
* * **
2469091 TGATATTTTATTCTAATAGTTTTTTAA
1 T-ATATTTTATTATGATA-TTTTTGCA
*
2469118 T-TA-TCTATTATGATATTTTTGCA
1 TATATTTTATTATGATATTTTTGCA
*
2469141 TATATTTTATTATGATTTATTTTGCA
1 TATATTTTATTATGATAT-TTTTGCA
* *
2469167 T-GATCTTATTATGATATT
1 TATATTTTATTATGATATT
2469185 GTTGTATTGT
Statistics
Matches: 97, Mismatches: 15, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
23 7 0.07
24 13 0.13
25 34 0.35
26 35 0.36
27 8 0.08
ACGTcount: A:0.26, C:0.07, G:0.08, T:0.59
Consensus pattern (25 bp):
TATATTTTATTATGATATTTTTGCA
Found at i:2469177 original size:50 final size:49
Alignment explanation
Indices: 2469081--2469184 Score: 122
Period size: 50 Copynumber: 2.1 Consensus size: 49
2469071 TTTCTTCTAC
* *
2469081 TATTTTTGCATGATATTTTATTCTAATAGTTTTTTAATTATCTATTATGA
1 TATTTTTGCATGATATTTTATTATAATA-TTTTTTAATGATCTATTATGA
* *
2469131 TATTTTTGCAT-ATATTTTATTATGAT-TTATTTTGCATGATCTTATTATGA
1 TATTTTTGCATGATATTTTATTATAATATT-TTTT-AATGATC-TATTATGA
2469181 TATT
1 TATT
2469185 GTTGTATTGT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
47 2 0.04
48 4 0.09
49 18 0.38
50 23 0.49
ACGTcount: A:0.27, C:0.06, G:0.09, T:0.59
Consensus pattern (49 bp):
TATTTTTGCATGATATTTTATTATAATATTTTTTAATGATCTATTATGA
Found at i:2469981 original size:2 final size:2
Alignment explanation
Indices: 2469974--2469998 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2469964 AAGTGTATCA
2469974 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2469999 CACAGATGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2472304 original size:2 final size:2
Alignment explanation
Indices: 2472293--2472343 Score: 63
Period size: 2 Copynumber: 27.0 Consensus size: 2
2472283 AGGCTTTTAT
* *
2472293 TA TA TA -A TA TA TA TT TA -A TA TA TA TA TA TA TA GA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2472333 TA -A TA TA TA TA
1 TA TA TA TA TA TA
2472344 AAGTTAAAGT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
1 3 0.07
2 39 0.93
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2478156 original size:3 final size:3
Alignment explanation
Indices: 2478148--2478172 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2478138 TCTTAGGGAA
2478148 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
2478173 GAAACCTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2478774 original size:55 final size:55
Alignment explanation
Indices: 2478710--2478997 Score: 184
Period size: 55 Copynumber: 5.3 Consensus size: 55
2478700 AGCTTGTAAT
* *
2478710 TTTTTTTACCTATACCGACGCTTAAAGCCCGTCAGTATAGATTTGTATATTTTAA
1 TTTTCTTACCTATACCGACGCTTAAAGCCCGTCAGTATAGACTTGTATATTTTAA
* * * *
2478765 TTTTCTTACCTATACCGATAGC-TAGCA-CCCGTCAGTATAGACTTATATGTTTTAA
1 TTTTCTTACCTATACCGA-CGCTTA-AAGCCCGTCAGTATAGACTTGTATATTTTAA
* * * * ** * *
2478820 TTTTTCTTACCTATATCGACGATCAATGCTTGTTAGTAGAGACTTGTA-A--TT--
1 -TTTTCTTACCTATACCGACGCTTAAAGCCCGTCAGTATAGACTTGTATATTTTAA
* * * * *
2478871 TTTT-TTACCTATACCGACACTTAGTA-TCCATCAGTATAGACTTGTATTTTTTAA
1 TTTTCTTACCTATACCGACGCTTA-AAGCCCGTCAGTATAGACTTGTATATTTTAA
* * * * * * * * * *
2478925 TTTTCTTACTTATGCCAATCG-TTAGAGACTGTCA-TACAGAATTTTATGTTTTAA
1 TTTTCTTACCTATACCGA-CGCTTAAAGCCCGTCAGTATAGACTTGTATATTTTAA
*
2478979 TTTTCTTACATATACCGAC
1 TTTTCTTACCTATACCGAC
2478998 AGTTAGAGAT
Statistics
Matches: 173, Mismatches: 46, Indels: 30
0.69 0.18 0.12
Matches are distributed among these distances:
49 29 0.17
50 4 0.02
52 2 0.01
53 3 0.02
54 36 0.21
55 62 0.36
56 37 0.21
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.42
Consensus pattern (55 bp):
TTTTCTTACCTATACCGACGCTTAAAGCCCGTCAGTATAGACTTGTATATTTTAA
Found at i:2479032 original size:54 final size:54
Alignment explanation
Indices: 2478900--2479032 Score: 135
Period size: 54 Copynumber: 2.4 Consensus size: 54
2478890 CTTAGTATCC
* * * *
2478900 ATCAGTATAGACTTGTATTTTTTAATTTTCTTACTTATGCCAATCGTTAGAGACT
1 ATCAGTATAGACTTATA-TGTTTAATTTTCTTACATATACCAATCGTTAGAGACT
* * * * * *
2478955 GTCA-TACAGAATTTTATGTTTTAATTTTCTTACATATACCGA-CAGTTAGAGATT
1 ATCAGTATAGACTTATATG-TTTAATTTTCTTACATATACCAATC-GTTAGAGACT
2479009 ATCAGTATAGACTTATATGTTTAA
1 ATCAGTATAGACTTATATGTTTAA
2479033 ATATTTTTAT
Statistics
Matches: 62, Mismatches: 13, Indels: 7
0.76 0.16 0.09
Matches are distributed among these distances:
53 2 0.03
54 46 0.74
55 14 0.23
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.44
Consensus pattern (54 bp):
ATCAGTATAGACTTATATGTTTAATTTTCTTACATATACCAATCGTTAGAGACT
Found at i:2479175 original size:23 final size:24
Alignment explanation
Indices: 2479144--2479189 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
2479134 TTATTTTAAA
*
2479144 AATTATATTT-TAATTATTAATATT
1 AATTATATTTGTAATCA-TAATATT
2479168 AATT-TATTTGTAATCATAATAT
1 AATTATATTTGTAATCATAATAT
2479190 GATATGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (24 bp):
AATTATATTTGTAATCATAATATT
Found at i:2480623 original size:19 final size:19
Alignment explanation
Indices: 2480599--2480654 Score: 80
Period size: 19 Copynumber: 3.0 Consensus size: 19
2480589 AAGCCAAACA
2480599 ATAAACAATTATATATAAT
1 ATAAACAATTATATATAAT
*
2480618 ATAAACAA-TATATA-AAC
1 ATAAACAATTATATATAAT
2480635 ATTAAACAATTATATATAAT
1 A-TAAACAATTATATATAAT
2480655 GTAAGCAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 3 0.09
18 13 0.41
19 14 0.44
20 2 0.06
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (19 bp):
ATAAACAATTATATATAAT
Found at i:2480641 original size:37 final size:37
Alignment explanation
Indices: 2480594--2480674 Score: 126
Period size: 37 Copynumber: 2.2 Consensus size: 37
2480584 TGAAAAAGCC
*
2480594 AAACAATAAACAATTATATATAATATAAACAATATAT
1 AAACAATAAACAATTATATATAATATAAACAATACAT
* * *
2480631 AAACATTAAACAATTATATATAATGTAAGCAATACAT
1 AAACAATAAACAATTATATATAATATAAACAATACAT
2480668 AAACAAT
1 AAACAAT
2480675 TATATAAACC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.59, C:0.10, G:0.02, T:0.28
Consensus pattern (37 bp):
AAACAATAAACAATTATATATAATATAAACAATACAT
Found at i:2480663 original size:19 final size:18
Alignment explanation
Indices: 2480600--2480654 Score: 76
Period size: 18 Copynumber: 3.0 Consensus size: 18
2480590 AGCCAAACAA
2480600 TAAACAATTATATATAAT
1 TAAACAATTATATATAAT
*
2480618 ATAAACAA-TATATAAACAT
1 -TAAACAATTATATATA-AT
2480637 TAAACAATTATATATAAT
1 TAAACAATTATATATAAT
2480655 GTAAGCAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 16 0.50
19 16 0.50
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (18 bp):
TAAACAATTATATATAAT
Found at i:2480856 original size:30 final size:30
Alignment explanation
Indices: 2480820--2480923 Score: 109
Period size: 30 Copynumber: 3.2 Consensus size: 30
2480810 AAGCCAAACA
2480820 ATAAACAATTATATATAATCTAAACAATATAT
1 ATAAACAATTATATATAATCTAAAC-A-ATAT
* *
2480852 AAACAATAAACAATTATATATAACCTAAACAGTAT
1 -----ATAAACAATTATATATAATCTAAACAATAT
*
2480887 GTAAACAATTATATATAATCTAAACAATTAT
1 ATAAACAATTATATATAATCTAAACAA-TAT
2480918 ATAAAC
1 ATAAAC
2480924 CTTATTATGC
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
30 24 0.40
31 8 0.13
35 3 0.05
36 1 0.02
37 24 0.40
ACGTcount: A:0.56, C:0.12, G:0.02, T:0.31
Consensus pattern (30 bp):
ATAAACAATTATATATAATCTAAACAATAT
Found at i:2480861 original size:37 final size:37
Alignment explanation
Indices: 2480815--2480895 Score: 135
Period size: 37 Copynumber: 2.2 Consensus size: 37
2480805 TGAAAAAGCC
*
2480815 AAACAATAAACAATTATATATAATCTAAACAATATAT
1 AAACAATAAACAATTATATATAACCTAAACAATATAT
* *
2480852 AAACAATAAACAATTATATATAACCTAAACAGTATGT
1 AAACAATAAACAATTATATATAACCTAAACAATATAT
2480889 AAACAAT
1 AAACAAT
2480896 TATATATAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.27
Consensus pattern (37 bp):
AAACAATAAACAATTATATATAACCTAAACAATATAT
Found at i:2482069 original size:147 final size:147
Alignment explanation
Indices: 2481798--2482092 Score: 500
Period size: 147 Copynumber: 2.0 Consensus size: 147
2481788 CAACGCTTTC
* *
2481798 AATAATCCCCTTATAAAAAAATGTATACAATTATTGAAAGCATTTTCTACAAGAAATGCCTTTAA
1 AATAATCCCCTCATAAAAAAATGTATACAATTATTGAAAGCATTTTCTACAAGAAACGCCTTTAA
* * *
2481863 TAATTTCACTAAAAATTTTCACAAGCTTATTGAAGGCGTTTTTGGTCAAAAACGACTTCAATAAA
66 TAATTTCACTAAAAAATTTCACAAGCGTATTGAAGGCGTTTTTGGTCAAAAACGACTTCAACAAA
2481928 TATCATATCAAAATTGT
131 TATCATATCAAAATTGT
* * *
2481945 AATAATCTCCTCATAAAAAAATGTATACGATTATTGAAAGCATTTTTTACAAGAAACGCCTTTAA
1 AATAATCCCCTCATAAAAAAATGTATACAATTATTGAAAGCATTTTCTACAAGAAACGCCTTTAA
* *
2482010 TAATTTCACTAAAAAATTTCACAAGCGTATTGAAGGCGTTTTTGGTCAAAAATGGCTTCAACAAA
66 TAATTTCACTAAAAAATTTCACAAGCGTATTGAAGGCGTTTTTGGTCAAAAACGACTTCAACAAA
2482075 TATCATATCAAAATTGT
131 TATCATATCAAAATTGT
2482092 A
1 A
2482093 TACTAAAGGT
Statistics
Matches: 138, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
147 138 1.00
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.33
Consensus pattern (147 bp):
AATAATCCCCTCATAAAAAAATGTATACAATTATTGAAAGCATTTTCTACAAGAAACGCCTTTAA
TAATTTCACTAAAAAATTTCACAAGCGTATTGAAGGCGTTTTTGGTCAAAAACGACTTCAACAAA
TATCATATCAAAATTGT
Found at i:2482965 original size:243 final size:242
Alignment explanation
Indices: 2482523--2482983 Score: 536
Period size: 243 Copynumber: 1.9 Consensus size: 242
2482513 CTCGGCTTCT
2482523 ATAATCCAGTCAATAAATTTTTAGTTAGGATTATTAAAGGCGATTTTTGTCAAAAATACCTTCAA
1 ATAATCCAGTCAATAAATTTTTAGTTAGGATTATTAAAGGCGATTTTTGTCAAAAATACCTTCAA
* *
2482588 TAATCCATAGACAAAAGTTGAAACGGATTCTTGAAGGCGCTTTTGGCTCAAAACGCCTTTAATAT
66 TAATCCATACACAAAAGTTGAAACGGATTCTTGAAGGCGCTTTTGGCCCAAAACGCCTTTAATAT
* ** * * *** **
2482653 ACAGATGATAAACTTAAATGGTTGGATTATTAAAGGTGGTTTTTTCCAAAAACACCTTCATTAAC
131 ACACACAATAAAATTAAATGGTGGGATTATTAAAGGCAATTTTTT-CAAAAACACCTTCAAGAAC
* *
2482718 ATTTTGTTAGGGATTATTCAAGGTGTTATCGATAGGAAAATGTCCTTA
195 ATTTTATTAGGGATGATTCAAGGTGTTATCGATAGGAAAATGTCCTTA
* * * * * ** *
2482766 ATAATCCATTCAATTAATTTTTAGTT-GGTATTATTGAATGCTATTTTT-TTTAAAATGCCTTCA
1 ATAATCCAGTCAATAAATTTTTAGTTAGG-ATTATTAAAGGCGATTTTTGTCAAAAATACCTTCA
* * *
2482829 ATAATCCATACA-AAAATGTTGAAAACGGATTCTTGAAGGCGTTTTTTGCCCAAAATGCCTTTAA
65 ATAATCCATACACAAAA-GTTG-AAACGGATTCTTGAAGGCGCTTTTGGCCCAAAACGCCTTTAA
* ** * **
2482893 TATTCCACACAATAAAATTTTA-GGTGGGATTATTGAAGGCAATTTTAGTT-AAAAATGCCTTCA
128 TA-TACACACAATAAAATTAAATGGTGGGATTATTAAAGGCAATTTT--TTCAAAAACACCTTCA
*
2482956 AGGACATTTTATTAGGGATGATTCAAGG
190 AGAACATTTTATTAGGGATGATTCAAGG
2482984 AATTTTTTTG
Statistics
Matches: 180, Mismatches: 32, Indels: 12
0.80 0.14 0.05
Matches are distributed among these distances:
241 4 0.02
242 29 0.16
243 133 0.74
244 12 0.07
245 2 0.01
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.36
Consensus pattern (242 bp):
ATAATCCAGTCAATAAATTTTTAGTTAGGATTATTAAAGGCGATTTTTGTCAAAAATACCTTCAA
TAATCCATACACAAAAGTTGAAACGGATTCTTGAAGGCGCTTTTGGCCCAAAACGCCTTTAATAT
ACACACAATAAAATTAAATGGTGGGATTATTAAAGGCAATTTTTTCAAAAACACCTTCAAGAACA
TTTTATTAGGGATGATTCAAGGTGTTATCGATAGGAAAATGTCCTTA
Found at i:2483099 original size:35 final size:35
Alignment explanation
Indices: 2483048--2483117 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
2483038 TGTATATGTC
* *
2483048 AAGTTAGTTGTAGGTTTATGCCCAGAAAACGTTTG
1 AAGTCAGTTGTAGGTTTATGCCCAGAAAACATTTG
**
2483083 AAGTCAGTTGTAGGTTTATGCTTAGAAAACATTTG
1 AAGTCAGTTGTAGGTTTATGCCCAGAAAACATTTG
2483118 GTTATATATG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.30, C:0.10, G:0.24, T:0.36
Consensus pattern (35 bp):
AAGTCAGTTGTAGGTTTATGCCCAGAAAACATTTG
Found at i:2486512 original size:39 final size:39
Alignment explanation
Indices: 2486418--2486514 Score: 149
Period size: 39 Copynumber: 2.5 Consensus size: 39
2486408 GACTCCAAGC
* *
2486418 TTAGAGTATCTGGTTAGATGTTTTGGACTTGAAAAGGAG
1 TTAGAGGATCTGGTTGGATGTTTTGGACTTGAAAAGGAG
* *
2486457 TTAGAAGATCTGGTTGGATGTTTTGGACTTGAAAGGGAG
1 TTAGAGGATCTGGTTGGATGTTTTGGACTTGAAAAGGAG
*
2486496 TTAGAGGATCTAGTTGGAT
1 TTAGAGGATCTGGTTGGAT
2486515 ACTTTGGATG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.27, C:0.05, G:0.33, T:0.35
Consensus pattern (39 bp):
TTAGAGGATCTGGTTGGATGTTTTGGACTTGAAAAGGAG
Found at i:2496590 original size:1 final size:1
Alignment explanation
Indices: 2496584--2496613 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
2496574 TCCTTCTTTC
2496584 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2496614 CCCTCCTCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2498733 original size:308 final size:310
Alignment explanation
Indices: 2498368--2498985 Score: 1015
Period size: 309 Copynumber: 2.0 Consensus size: 310
2498358 GTTAGGAACA
* *
2498368 CACCCTGTTGTAAATTCTTATTGCCTTTCTCTCTTTTTTTTTTTATTTTAGGAATGCCTTGAGGT
1 CACCCTGTTGTAAATTCTTACTGCCCTTCTCTCTTTTTTTTTTTATTTTAGGAATGCCTTGAGGT
* * **
2498433 CAAAGCTTCTCAAACATTTGGCATGGCAAGTAAGGGAGCTTTTTTCGCTCATTTGCCTAGTATAA
66 CAAAGCTTCTCAAACATTTGGCATGCCAAGTAAGAGAGCTTTTTTCGCTCATTAACCTAGTATAA
* *
2498498 AACAATGTTAC-AAGGAAAAGAACCTTAGAGGAAAGAGAGATTGTCGTCCCAGTTGGATCAGAAA
131 AACAATGTTACTAAGGAAAAGAACCTTAGAGGAAAGAGAGATGGCCGTCCCAGTTGGATCAGAAA
* *
2498562 CCCACCATAGCTAACTTTTTGTCCGACTTGCCCAACCATAAGCGAGATCGACCATGAAACAATTT
196 CCCACCATAGCCAACTTTTTGTCCGACTTGCCCAACCATAAGCGAGATCGACCATAAAACAATTT
*
2498627 CAAGCCTTAATCGAACAGATATAGGCCATCCAGCAAATGTTACAAACCAT
261 CAAGCCTTAATCGAACAGATATAGGCCATCAAGCAAATGTTACAAACCAT
* * *
2498677 CACCTTGTTGTAAATTTTTACTGCCCTTCTCT-TTTTTTTTTTTTTTTTAGGAATGCCTTGAGGT
1 CACCCTGTTGTAAATTCTTACTGCCCTTCTCTCTTTTTTTTTTTATTTTAGGAATGCCTTGAGGT
* *
2498741 TAGAGCTTCTCAAACATTTGGCATGCCAAGTAAGAGAGCTTTTTTCGCTCATTAACCTAGTATAA
66 CAAAGCTTCTCAAACATTTGGCATGCCAAGTAAGAGAGCTTTTTTCGCTCATTAACCTAGTATAA
* *
2498806 AGCAATGTTACTAAGGAAGAGAACCTTAGAGGAAAGAGAGATGGCCGTCCCAGTTGGATCAGAAA
131 AACAATGTTACTAAGGAAAAGAACCTTAGAGGAAAGAGAGATGGCCGTCCCAGTTGGATCAGAAA
** *
2498871 CCCACCATAGCCAACTTTTTGTTTGACTTGCCTAACCATAAGCGAGATCGACCATAAAACAATTT
196 CCCACCATAGCCAACTTTTTGTCCGACTTGCCCAACCATAAGCGAGATCGACCATAAAACAATTT
* *
2498936 CAAGCCTTGATCGAATAGATATAGGCCATCAAGCAAATGTTACAAACCAT
261 CAAGCCTTAATCGAACAGATATAGGCCATCAAGCAAATGTTACAAACCAT
2498986 AATCTCACTA
Statistics
Matches: 285, Mismatches: 23, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
308 100 0.35
309 185 0.65
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31
Consensus pattern (310 bp):
CACCCTGTTGTAAATTCTTACTGCCCTTCTCTCTTTTTTTTTTTATTTTAGGAATGCCTTGAGGT
CAAAGCTTCTCAAACATTTGGCATGCCAAGTAAGAGAGCTTTTTTCGCTCATTAACCTAGTATAA
AACAATGTTACTAAGGAAAAGAACCTTAGAGGAAAGAGAGATGGCCGTCCCAGTTGGATCAGAAA
CCCACCATAGCCAACTTTTTGTCCGACTTGCCCAACCATAAGCGAGATCGACCATAAAACAATTT
CAAGCCTTAATCGAACAGATATAGGCCATCAAGCAAATGTTACAAACCAT
Found at i:2504398 original size:23 final size:22
Alignment explanation
Indices: 2504372--2504414 Score: 52
Period size: 22 Copynumber: 1.9 Consensus size: 22
2504362 TAAAATAGTC
2504372 TGACATAAGTACATT-GAAAAGGG
1 TGACAT-AGTAC-TTAGAAAAGGG
*
2504395 TGACCTAGTACTTAGAAAAG
1 TGACATAGTACTTAGAAAAG
2504415 TTTAAACCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 2 0.11
22 11 0.61
23 5 0.28
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.23
Consensus pattern (22 bp):
TGACATAGTACTTAGAAAAGGG
Found at i:2517684 original size:21 final size:21
Alignment explanation
Indices: 2517658--2517702 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
2517648 ATTAAAATAT
2517658 AATTAAAT-AAATCTAATATAA
1 AATTAAATCAAATCT-ATATAA
*
2517679 AATTAAATCAAATCTATATTA
1 AATTAAATCAAATCTATATAA
2517700 AAT
1 AAT
2517703 AAAACTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.36
Consensus pattern (21 bp):
AATTAAATCAAATCTATATAA
Found at i:2523329 original size:17 final size:18
Alignment explanation
Indices: 2523302--2523335 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2523292 AGTAAATAAT
2523302 AAAAGAATAAAAAGAAAG
1 AAAAGAATAAAAAGAAAG
2523320 AAAA-AATAAAAAGAAA
1 AAAAGAATAAAAAGAAA
2523336 AGTTTTGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.06
Consensus pattern (18 bp):
AAAAGAATAAAAAGAAAG
Found at i:2525575 original size:32 final size:32
Alignment explanation
Indices: 2525539--2525751 Score: 90
Period size: 32 Copynumber: 6.7 Consensus size: 32
2525529 ATAGTTTAGT
* *
2525539 TGGCACTTATGAAAATTTAAGTTCAACCTAGC
1 TGGCACTTATGAAAATTTAAGTCCAAACTAGC
** * * *
2525571 TGGCACCCATGAGATTTTAAGTCCAAATTAGC
1 TGGCACTTATGAAAATTTAAGTCCAAACTAGC
* * * *** *
2525603 TAGTACTTATG-AAATTTAAGTCTAGTTTAGT
1 TGGCACTTATGAAAATTTAAGTCCAAACTAGC
* ** * *
2525634 TGGCA-TGCAATGAAAATTTAAACCCAATCTAAC
1 TGGCACT--TATGAAAATTTAAGTCCAAACTAGC
* * ** ** *
2525667 TGACACTAATGAAAATTTAAGTTTAGTCTAGT
1 TGGCACTTATGAAAATTTAAGTCCAAACTAGC
* * * *
2525699 TGGTAGC-CATGAAAATTTAAGTCCAATCTAGT
1 TGGCA-CTTATGAAAATTTAAGTCCAAACTAGC
**
2525731 TGGCACCAATGAAAATTTAAG
1 TGGCACTTATGAAAATTTAAG
2525752 CTAAGATTAG
Statistics
Matches: 132, Mismatches: 43, Indels: 12
0.71 0.23 0.06
Matches are distributed among these distances:
30 1 0.01
31 18 0.14
32 94 0.71
33 18 0.14
34 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.32
Consensus pattern (32 bp):
TGGCACTTATGAAAATTTAAGTCCAAACTAGC
Found at i:2525775 original size:32 final size:31
Alignment explanation
Indices: 2525705--2525941 Score: 196
Period size: 32 Copynumber: 7.5 Consensus size: 31
2525695 TAGTTGGTAG
* * * *
2525705 CCATGAAAATTTAAGTCCAATCTAGTTGGC-A
1 CCATGAAAATTTAAG-CCAATTTAGATGACGT
* * *
2525736 CCAATGAAAATTTAAGCTAAGATTAGATGACAT
1 CC-ATGAAAATTTAAGCCAA-TTTAGATGACGT
*
2525769 CCATGAAAATTTAAGCCCAATTTAGCTGACGT
1 CCATGAAAATTTAAG-CCAATTTAGATGACGT
* * * *
2525801 CTATGAAAATTTAAGCTTAATTTAGCTGACGC
1 CCATGAAAATTTAAGC-CAATTTAGATGACGT
* *
2525833 CCATGAAAATTTAAGCCCAAATT--A--ACAT
1 CCATGAAAATTTAAG-CCAATTTAGATGACGT
* *
2525861 CCATGAAAATTTAAGCCCAGTTTAGCTGACGT
1 CCATGAAAATTTAAG-CCAATTTAGATGACGT
* * *
2525893 CTATGAAAATTTAAGCCTAGTTTAGATGACGC
1 CCATGAAAATTTAAGCC-AATTTAGATGACGT
2525925 CCATGAAAATTTAAGCC
1 CCATGAAAATTTAAGCC
2525942 CATATTATTT
Statistics
Matches: 168, Mismatches: 27, Indels: 21
0.78 0.12 0.10
Matches are distributed among these distances:
28 23 0.14
31 8 0.05
32 131 0.78
33 6 0.04
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.29
Consensus pattern (31 bp):
CCATGAAAATTTAAGCCAATTTAGATGACGT
Found at i:2525816 original size:64 final size:64
Alignment explanation
Indices: 2525614--2525940 Score: 252
Period size: 64 Copynumber: 5.2 Consensus size: 64
2525604 AGTACTTATG
* * * * * * **
2525614 AAATTTAAGTCT-AGTTTAGTTGGCATGCAATGAAAATTTAAACCCAATCTAACTGACACTAATG
1 AAATTTAAG-CTAAGTTTAGCTGACAT-CCATGAAAATTTAAGCCCAATTTAGCTGACACCCATG
2525678 A
64 A
* * * * ** * * * * * *
2525679 AAATTTAAGTTTAGTCTAGTTGGTAGCCATGAAAATTTAAGTCCAATCTAGTTGGCACCAATGA
1 AAATTTAAGCTAAGTTTAGCTGACATCCATGAAAATTTAAGCCCAATTTAGCTGACACCCATGA
* * ** *
2525743 AAATTTAAGCTAAGATTAGATGACATCCATGAAAATTTAAGCCCAATTTAGCTGACGTCTATGA
1 AAATTTAAGCTAAGTTTAGCTGACATCCATGAAAATTTAAGCCCAATTTAGCTGACACCCATGA
** * *
2525807 AAATTTAAGCTTAA-TTTAGCTGACGCCCATGAAAATTTAAGCCCAAATTA----ACATCCATGA
1 AAATTTAAGC-TAAGTTTAGCTGACATCCATGAAAATTTAAGCCCAATTTAGCTGACACCCATGA
** * * * * * *
2525867 AAATTTAAGCCCAGTTTAGCTGACGTCTATGAAAATTTAAGCCTAGTTTAGATGACGCCCATGA
1 AAATTTAAGCTAAGTTTAGCTGACATCCATGAAAATTTAAGCCCAATTTAGCTGACACCCATGA
2525931 AAATTTAAGC
1 AAATTTAAGC
2525941 CCATATTATT
Statistics
Matches: 213, Mismatches: 42, Indels: 15
0.79 0.16 0.06
Matches are distributed among these distances:
59 1 0.00
60 49 0.23
64 140 0.66
65 23 0.11
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.30
Consensus pattern (64 bp):
AAATTTAAGCTAAGTTTAGCTGACATCCATGAAAATTTAAGCCCAATTTAGCTGACACCCATGA
Found at i:2525885 original size:92 final size:92
Alignment explanation
Indices: 2525765--2525948 Score: 323
Period size: 92 Copynumber: 2.0 Consensus size: 92
2525755 AGATTAGATG
* *
2525765 ACATCCATGAAAATTTAAGCCCAATTTAGCTGACGTCTATGAAAATTTAAGCTTAATTTAGCTGA
1 ACATCCATGAAAATTTAAGCCCAATTTAGCTGACGTCTATGAAAATTTAAGCCTAATTTAGATGA
2525830 CGCCCATGAAAATTTAAGCCCAAATTA
66 CGCCCATGAAAATTTAAGCCCAAATTA
* *
2525857 ACATCCATGAAAATTTAAGCCCAGTTTAGCTGACGTCTATGAAAATTTAAGCCTAGTTTAGATGA
1 ACATCCATGAAAATTTAAGCCCAATTTAGCTGACGTCTATGAAAATTTAAGCCTAATTTAGATGA
*
2525922 CGCCCATGAAAATTTAAGCCCATATTA
66 CGCCCATGAAAATTTAAGCCCAAATTA
2525949 TTTGGCACCT
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
92 87 1.00
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (92 bp):
ACATCCATGAAAATTTAAGCCCAATTTAGCTGACGTCTATGAAAATTTAAGCCTAATTTAGATGA
CGCCCATGAAAATTTAAGCCCAAATTA
Found at i:2525966 original size:32 final size:32
Alignment explanation
Indices: 2525930--2525991 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
2525920 GACGCCCATG
* *
2525930 AAAATTTAAGCCC-ATATTATTTGGCACCTATA
1 AAAATTAAAGCCCAAT-TTAGTTGGCACCTATA
*
2525962 AAAATTAAAGCTCAATTTAGTTGGCACCTA
1 AAAATTAAAGCCCAATTTAGTTGGCACCTA
2525992 GATTTTAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 24 0.92
33 2 0.08
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (32 bp):
AAAATTAAAGCCCAATTTAGTTGGCACCTATA
Found at i:2525981 original size:64 final size:64
Alignment explanation
Indices: 2525739--2525981 Score: 149
Period size: 64 Copynumber: 3.9 Consensus size: 64
2525729 GTTGGCACCA
** * * * * * * * *
2525739 ATGAAAATTTAAGCTAAGATTAGATGACATCC-ATGAAAATTTAAGCCCAATTTAGCTGACGTCT
1 ATGAAAATTTAAGCCCAGTTTAGCTGACA-CCTATAAAAATTAAAGCCTAATTTAGATGACGCCC
** * * * * * * * **
2525803 ATGAAAATTTAAGCTTAATTTAGCTGACGCCCATGAAAATTTAAGCCCAAATT--A--ACATCC
1 ATGAAAATTTAAGCCCAGTTTAGCTGACACCTATAAAAATTAAAGCCTAATTTAGATGACGCCC
** * * *
2525863 ATGAAAATTTAAGCCCAGTTTAGCTGACGTCTATGAAAATTTAAGCCTAGTTTAGATGACGCCC
1 ATGAAAATTTAAGCCCAGTTTAGCTGACACCTATAAAAATTAAAGCCTAATTTAGATGACGCCC
** *
2525927 ATGAAAATTTAAGCCCA-TATTATTTGGCACCTATAAAAATTAAAG-CTCAATTTAG
1 ATGAAAATTTAAGCCCAGT-TTAGCTGACACCTATAAAAATTAAAGCCT-AATTTAG
2525982 TTGGCACCTA
Statistics
Matches: 145, Mismatches: 27, Indels: 14
0.78 0.15 0.08
Matches are distributed among these distances:
60 49 0.34
62 1 0.01
63 5 0.03
64 90 0.62
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.30
Consensus pattern (64 bp):
ATGAAAATTTAAGCCCAGTTTAGCTGACACCTATAAAAATTAAAGCCTAATTTAGATGACGCCC
Found at i:2526786 original size:15 final size:14
Alignment explanation
Indices: 2526766--2526806 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
2526756 TTGCTTGGTC
2526766 AATAAATAAATAAA
1 AATAAATAAATAAA
2526780 TAAT-AA-AAATAAA
1 -AATAAATAAATAAA
2526793 AATAAAATAAATAA
1 AAT-AAATAAATAA
2526807 GCTTGAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
12 3 0.13
13 7 0.30
14 4 0.17
15 9 0.39
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
AATAAATAAATAAA
Found at i:2526796 original size:12 final size:12
Alignment explanation
Indices: 2526773--2526806 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
2526763 GTCAATAAAT
2526773 AAATAAATAATAA
1 AAATAAATAAT-A
2526786 AAATAAA-AATA
1 AAATAAATAATA
2526797 AAATAAATAA
1 AAATAAATAA
2526807 GCTTGAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 8 0.40
12 5 0.25
13 7 0.35
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (12 bp):
AAATAAATAATA
Found at i:2527230 original size:15 final size:16
Alignment explanation
Indices: 2527207--2527244 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
2527197 AAAGAATAAA
2527207 AACAAAAGGAACCAAC
1 AACAAAAGGAACCAAC
*
2527223 AA-AAAAGGAAGCAAC
1 AACAAAAGGAACCAAC
2527238 AACAAAA
1 AACAAAA
2527245 AAGAAAGCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.68, C:0.18, G:0.13, T:0.00
Consensus pattern (16 bp):
AACAAAAGGAACCAAC
Found at i:2527263 original size:18 final size:18
Alignment explanation
Indices: 2527219--2527254 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2527209 CAAAAGGAAC
*
2527219 CAACAAAAAAGGAAGCAA
1 CAACAAAAAAGAAAGCAA
2527237 CAACAAAAAAGAAAGCAA
1 CAACAAAAAAGAAAGCAA
2527255 AAGAGAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.69, C:0.17, G:0.14, T:0.00
Consensus pattern (18 bp):
CAACAAAAAAGAAAGCAA
Found at i:2530083 original size:21 final size:19
Alignment explanation
Indices: 2530045--2530099 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 19
2530035 TAAGCAAGCA
*
2530045 AAATATAATAATAAATAAT
1 AAATATAAAAATAAATAAT
2530064 AAATATAAAAATCCAAATAAT
1 AAATATAAAAAT--AAATAAT
*
2530085 ACAA-ATAATAATAAA
1 A-AATATAAAAATAAA
2530100 AAACTTAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
19 14 0.45
21 15 0.48
22 2 0.06
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.25
Consensus pattern (19 bp):
AAATATAAAAATAAATAAT
Found at i:2530444 original size:3 final size:3
Alignment explanation
Indices: 2530431--2530510 Score: 58
Period size: 3 Copynumber: 27.0 Consensus size: 3
2530421 AAAATACAAA
** * * **
2530431 AAT AA- AAT AAT AAT AAT AAT AAT AAT TTT AAT GAAG AAG AGG AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
*
2530475 AACT -AT AAT AAT AAT AAT AAT AAC AAT AAT AAT AAT
1 AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2530511 TAGTGTTTAG
Statistics
Matches: 63, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
2 5 0.08
3 56 0.89
4 2 0.03
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:2530633 original size:19 final size:19
Alignment explanation
Indices: 2530609--2530656 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
2530599 CCTAAAAAGG
*
2530609 AAACCCGAAACTTTATGTA
1 AAACCCGAAACTTTAGGTA
* *
2530628 AAACCCTAAACTTTAGGTG
1 AAACCCGAAACTTTAGGTA
*
2530647 AAACCTGAAA
1 AAACCCGAAA
2530657 ACCCTAAGTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.44, C:0.21, G:0.12, T:0.23
Consensus pattern (19 bp):
AAACCCGAAACTTTAGGTA
Found at i:2531184 original size:76 final size:78
Alignment explanation
Indices: 2531100--2531253 Score: 276
Period size: 79 Copynumber: 2.0 Consensus size: 78
2531090 TTGCACTTGT
2531100 TACACACATATATA-TTTTT-ATTATTGATGTTTATGGTTAACTATAGCATTTTTCATTTTTACT
1 TACACACATATATATTTTTTAATTATTGATGTTTATGGTTAACTATAGCATTTTTCATTTTTACT
2531163 ACATAAAAAGTTA
66 ACATAAAAAGTTA
2531176 TACACACATATATATTTTTTTAATTATTGATGTTTATGGTTAACTATAGCATTTTTCATTTTTAC
1 TACACACATATATA-TTTTTTAATTATTGATGTTTATGGTTAACTATAGCATTTTTCATTTTTAC
*
2531241 TGCATAAAAAGTT
65 TACATAAAAAGTT
2531254 CTTTGAAAAA
Statistics
Matches: 74, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
76 14 0.19
78 5 0.07
79 55 0.74
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.48
Consensus pattern (78 bp):
TACACACATATATATTTTTTAATTATTGATGTTTATGGTTAACTATAGCATTTTTCATTTTTACT
ACATAAAAAGTTA
Found at i:2533645 original size:24 final size:24
Alignment explanation
Indices: 2533618--2533679 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
2533608 TGTAATCATG
*
2533618 CAATAAATATTAAATCATACCATA
1 CAATAAATATAAAATCATACCATA
* *
2533642 CAATAAATATAAAATCATATCATG
1 CAATAAATATAAAATCATACCATA
2533666 CAATAAATATAAAA
1 CAATAAATATAAAA
2533680 ACACATTATA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.58, C:0.13, G:0.02, T:0.27
Consensus pattern (24 bp):
CAATAAATATAAAATCATACCATA
Found at i:2533693 original size:24 final size:24
Alignment explanation
Indices: 2533612--2533695 Score: 87
Period size: 24 Copynumber: 3.5 Consensus size: 24
2533602 TAATTATGTA
* * * *
2533612 ATCATGCAATAAATATTAAATCAT
1 ATCATACAATAAATATAAAAACAC
* * *
2533636 ACCATACAATAAATATAAAATCAT
1 ATCATACAATAAATATAAAAACAC
*
2533660 ATCATGCAATAAATATAAAAACAC
1 ATCATACAATAAATATAAAAACAC
*
2533684 ATTATACAATAA
1 ATCATACAATAA
2533696 TAAATATATT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.56, C:0.14, G:0.02, T:0.27
Consensus pattern (24 bp):
ATCATACAATAAATATAAAAACAC
Found at i:2533749 original size:32 final size:32
Alignment explanation
Indices: 2533689--2533751 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
2533679 AACACATTAT
* * *
2533689 ACAATAATAAATATATTAGTAGTAATGCAATC
1 ACAAAAATAAATATATTAATAATAATGCAATC
*
2533721 ACAAAAATAAATATATTAATAATCATGCAAT
1 ACAAAAATAAATATATTAATAATAATGCAAT
2533752 ATTATAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.54, C:0.10, G:0.06, T:0.30
Consensus pattern (32 bp):
ACAAAAATAAATATATTAATAATAATGCAATC
Found at i:2535148 original size:15 final size:17
Alignment explanation
Indices: 2535123--2535154 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2535113 GCTATTGCAT
2535123 TATTGTTGATA-ATTTG
1 TATTGTTGATAGATTTG
2535139 TATT-TTGATAGATTTG
1 TATTGTTGATAGATTTG
2535155 AGCATAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.25, C:0.00, G:0.19, T:0.56
Consensus pattern (17 bp):
TATTGTTGATAGATTTG
Found at i:2540462 original size:17 final size:15
Alignment explanation
Indices: 2540435--2540478 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 15
2540425 GGGATTTGGA
2540435 TTTTC-TTTTTTGTT
1 TTTTCTTTTTTTGTT
2540449 TATCTTCTTTTTTTGTT
1 T-T-TTCTTTTTTTGTT
2540466 TTTTCTTATTTTT
1 TTTTCTT-TTTTT
2540479 CAAAAATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 1 0.04
15 6 0.23
16 9 0.35
17 10 0.38
ACGTcount: A:0.05, C:0.09, G:0.05, T:0.82
Consensus pattern (15 bp):
TTTTCTTTTTTTGTT
Found at i:2540472 original size:18 final size:17
Alignment explanation
Indices: 2540440--2540478 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
2540430 TTGGATTTTC
*
2540440 TTTTTTGTTTATCTTCT
1 TTTTTTGTTTATCTTAT
*
2540457 TTTTTTGTTTTTTCTTAT
1 TTTTTTG-TTTATCTTAT
2540475 TTTT
1 TTTT
2540479 CAAAAATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.05, C:0.08, G:0.05, T:0.82
Consensus pattern (17 bp):
TTTTTTGTTTATCTTAT
Found at i:2540504 original size:13 final size:13
Alignment explanation
Indices: 2540486--2540511 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2540476 TTTCAAAAAT
2540486 ATAAGTAAAATAA
1 ATAAGTAAAATAA
2540499 ATAAGTAAAATAA
1 ATAAGTAAAATAA
2540512 TTTTTAAAAA
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:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (13 bp):
ATAAGTAAAATAA
Found at i:2543058 original size:15 final size:17
Alignment explanation
Indices: 2543030--2543065 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
2543020 CTTTTCCATC
2543030 TTTTCATTTCTCTTTT-
1 TTTTCATTTCTCTTTTA
2543046 TTTTCATTT-TCTTTTA
1 TTTTCATTTCTCTTTTA
2543062 TTTT
1 TTTT
2543066 TCTTTTCCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTCATTTCTCTTTTA
Found at i:2543065 original size:17 final size:16
Alignment explanation
Indices: 2543030--2543077 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
2543020 CTTTTCCATC
2543030 TTTTCA-TTTCTCTTTT
1 TTTTCATTTTCT-TTTT
2543046 TTTTCATTTTCTTTTAT
1 TTTTCATTTTCTTTT-T
2543063 TTTTC-TTTTCCTTTT
1 TTTTCATTTT-CTTTT
2543078 CCTAACATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
16 13 0.45
17 16 0.55
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTCATTTTCTTTTT
Found at i:2548404 original size:64 final size:63
Alignment explanation
Indices: 2548336--2548455 Score: 161
Period size: 63 Copynumber: 1.9 Consensus size: 63
2548326 GTTAGTAGGC
* * *
2548336 TTTTAGGAATTTAATTTTAAAAATTATTTTTAAA-CTCATAAAATCTTCCAATAATTTGATAAGA
1 TTTTAGGAATATAACTTTAAAAATTA-TTTTAAACCT-AAAAAATCTTCCAATAATTTGATAAGA
* * *
2548400 TTTTATGAATATAACTTTAAAATTTATTTTAAGCCTAAAAAATCTTCCAATAATTT
1 TTTTAGGAATATAACTTTAAAAATTATTTTAAACCTAAAAAATCTTCCAATAATTT
2548456 AAGAGAAATT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
63 25 0.51
64 24 0.49
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (63 bp):
TTTTAGGAATATAACTTTAAAAATTATTTTAAACCTAAAAAATCTTCCAATAATTTGATAAGA
Found at i:2551620 original size:17 final size:18
Alignment explanation
Indices: 2551593--2551626 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2551583 TACATTTTTA
2551593 TAATCTAAAAAAATTAAT
1 TAATCTAAAAAAATTAAT
2551611 TAAT-TAAAAAAATTAA
1 TAATCTAAAAAAATTAA
2551627 AGTCAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (18 bp):
TAATCTAAAAAAATTAAT
Found at i:2551644 original size:8 final size:9
Alignment explanation
Indices: 2551631--2551663 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
2551621 AATTAAAGTC
2551631 AAAAAATAA
1 AAAAAATAA
2551640 AAAAAATAA
1 AAAAAATAA
2551649 AAAAAA-AGA
1 AAAAAATA-A
2551658 AAAAAA
1 AAAAAA
2551664 AGACAAACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 1 0.04
9 22 0.96
ACGTcount: A:0.91, C:0.00, G:0.03, T:0.06
Consensus pattern (9 bp):
AAAAAATAA
Found at i:2551651 original size:10 final size:10
Alignment explanation
Indices: 2551631--2551664 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
2551621 AATTAAAGTC
2551631 AAAAAAT-AA
1 AAAAAATAAA
2551640 AAAAAATAAA
1 AAAAAATAAA
*
2551650 AAAAAAGAAA
1 AAAAAATAAA
2551660 AAAAA
1 AAAAA
2551665 GACAAACAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 7 0.30
10 16 0.70
ACGTcount: A:0.91, C:0.00, G:0.03, T:0.06
Consensus pattern (10 bp):
AAAAAATAAA
Found at i:2552802 original size:23 final size:25
Alignment explanation
Indices: 2552756--2552805 Score: 86
Period size: 23 Copynumber: 2.1 Consensus size: 25
2552746 TAATTGTTAT
2552756 TAATAGTAATAAAATGAAAATAATA
1 TAATAGTAATAAAATGAAAATAATA
2552781 TAATA-TAATAAAAT-AAAATAATA
1 TAATAGTAATAAAATGAAAATAATA
2552804 TA
1 TA
2552806 TATTAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 11 0.44
24 9 0.36
25 5 0.20
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (25 bp):
TAATAGTAATAAAATGAAAATAATA
Found at i:2552845 original size:20 final size:19
Alignment explanation
Indices: 2552762--2552845 Score: 57
Period size: 18 Copynumber: 4.2 Consensus size: 19
2552752 TTATTAATAG
2552762 TAATAA-AATGAAAAT-AATA
1 TAATAATAAT-AAAATGAA-A
*
2552781 TAAT-ATAATAAAATAAAA
1 TAATAATAATAAAATGAAA
*
2552799 TAATATATATTAAAAATGTTTAAA
1 TAATA-ATAAT-AAAATG---AAA
2552823 TAATAATAATAATAATGAAA
1 TAATAATAATAA-AATGAAA
2552843 TAA
1 TAA
2552846 ACTTTTTATT
Statistics
Matches: 53, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
18 11 0.21
19 9 0.17
20 10 0.19
21 5 0.09
22 2 0.04
23 8 0.15
24 8 0.15
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (19 bp):
TAATAATAATAAAATGAAA
Found at i:2553130 original size:33 final size:32
Alignment explanation
Indices: 2553110--2553232 Score: 149
Period size: 33 Copynumber: 3.8 Consensus size: 32
2553100 CTAAGTTTTT
2553110 AAAACCCCTAAAAATCCAAAATCCCTAAAATCC
1 AAAACCCCTAAAAATCCAAAAT-CCTAAAATCC
* *
2553143 AAACCCCCTAAAAATCCAAAATCCCTTAAATCC
1 AAAACCCCTAAAAATCCAAAAT-CCTAAAATCC
* * *
2553176 AAACCCCCCCT-AAAATCCGAAACCCTAAAATCC
1 AAA--ACCCCTAAAAATCCAAAATCCTAAAATCC
*
2553209 AAAACCCCTCAAAATCCAAAATCC
1 AAAACCCCTAAAAATCCAAAATCC
2553233 CAAACTTTTA
Statistics
Matches: 79, Mismatches: 8, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
31 5 0.06
32 12 0.15
33 46 0.58
34 10 0.13
35 6 0.08
ACGTcount: A:0.47, C:0.37, G:0.01, T:0.15
Consensus pattern (32 bp):
AAAACCCCTAAAAATCCAAAATCCTAAAATCC
Found at i:2553141 original size:16 final size:16
Alignment explanation
Indices: 2553110--2553307 Score: 142
Period size: 15 Copynumber: 12.5 Consensus size: 16
2553100 CTAAGTTTTT
2553110 AAAACCCCTAAAAATCC
1 AAAACCCCT-AAAATCC
*
2553127 AAAATCCCTAAAATCC
1 AAAACCCCTAAAATCC
*
2553143 AAACCCCCTAAAAATCC
1 AAAACCCCT-AAAATCC
* *
2553160 AAAATCCCTTAAATCC
1 AAAACCCCTAAAATCC
*
2553176 AAACCCCCCCTAAAATCC
1 AAA--ACCCCTAAAATCC
*
2553194 GAAA-CCCTAAAATCC
1 AAAACCCCTAAAATCC
2553209 AAAACCCCTCAAAATCC
1 AAAACCCCT-AAAATCC
* * **
2553226 AAAATCCC-AAACTTT
1 AAAACCCCTAAAATCC
* *
2553241 TAAA-CCCTTAAA-CC
1 AAAACCCCTAAAATCC
*
2553255 TAAACCCCCT-AAATCC
1 -AAAACCCCTAAAATCC
* *
2553271 AAAATCCTTAAAATCC
1 AAAACCCCTAAAATCC
*
2553287 -AAA-CCCTTAAAT-C
1 AAAACCCCTAAAATCC
2553300 AAAACCCC
1 AAAACCCC
2553308 AAACCTCAAA
Statistics
Matches: 141, Mismatches: 28, Indels: 26
0.72 0.14 0.13
Matches are distributed among these distances:
13 1 0.01
14 13 0.09
15 40 0.28
16 39 0.28
17 36 0.26
18 12 0.09
ACGTcount: A:0.46, C:0.36, G:0.01, T:0.17
Consensus pattern (16 bp):
AAAACCCCTAAAATCC
Found at i:2553186 original size:18 final size:19
Alignment explanation
Indices: 2553165--2553200 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2553155 AATCCAAAAT
*
2553165 CCCTTAAATCC-AAACCCC
1 CCCTAAAATCCGAAACCCC
2553183 CCCTAAAATCCGAAACCC
1 CCCTAAAATCCGAAACCC
2553201 TAAAATCCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.36, C:0.47, G:0.03, T:0.14
Consensus pattern (19 bp):
CCCTAAAATCCGAAACCCC
Found at i:2553200 original size:19 final size:18
Alignment explanation
Indices: 2553132--2553228 Score: 68
Period size: 17 Copynumber: 5.8 Consensus size: 18
2553122 AATCCAAAAT
2553132 CCCTAAAATCCAAA--CC
1 CCCTAAAATCCAAACCCC
**
2553148 CCCTAAAAATCCAAA--AT
1 CCCT-AAAATCCAAACCCC
*
2553165 CCCTTAAATCCAAACCCC
1 CCCTAAAATCCAAACCCC
2553183 CCCTAAAATCCGAAA----
1 CCCTAAAATCC-AAACCCC
*
2553198 CCCTAAAATCCAAAACCC
1 CCCTAAAATCCAAACCCC
*
2553216 CTC-AAAATCCAAA
1 CCCTAAAATCCAAA
2553229 ATCCCAAACT
Statistics
Matches: 66, Mismatches: 7, Indels: 15
0.75 0.08 0.17
Matches are distributed among these distances:
14 3 0.05
15 11 0.17
16 13 0.20
17 24 0.36
18 12 0.18
19 3 0.05
ACGTcount: A:0.45, C:0.39, G:0.01, T:0.14
Consensus pattern (18 bp):
CCCTAAAATCCAAACCCC
Found at i:2553323 original size:51 final size:50
Alignment explanation
Indices: 2553265--2553364 Score: 121
Period size: 51 Copynumber: 2.0 Consensus size: 50
2553255 TAAACCCCCT
* * *
2553265 AAATCCAAAATCCTTAAAA-TCCAAACCCTTAAATCAAAACCCCAAACCTCA
1 AAATCC-AAA-CCATAAAACTCCAAACCCTAAAACCAAAACCCCAAACCTCA
* *
2553316 AAATCCAAACCATAAAATCTCCAAACTCTAAAACCAAAACCCTAAACCT
1 AAATCCAAACCATAAAA-CTCCAAACCCTAAAACCAAAACCCCAAACCT
2553365 TTTATATCCT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
49 7 0.17
50 3 0.07
51 32 0.76
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (50 bp):
AAATCCAAACCATAAAACTCCAAACCCTAAAACCAAAACCCCAAACCTCA
Found at i:2554373 original size:17 final size:18
Alignment explanation
Indices: 2554346--2554379 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2554336 GTGGTTTTTA
2554346 TAATCTAAAAAAATTAAT
1 TAATCTAAAAAAATTAAT
2554364 TAAT-TAAAAAAATTAA
1 TAATCTAAAAAAATTAA
2554380 AGTAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (18 bp):
TAATCTAAAAAAATTAAT
Found at i:2554385 original size:14 final size:14
Alignment explanation
Indices: 2554368--2554394 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2554358 ATTAATTAAT
2554368 TAAAAAAATTAAAG
1 TAAAAAAATTAAAG
2554382 TAAAAAAATTAAA
1 TAAAAAAATTAAA
2554395 AAAAAAAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (14 bp):
TAAAAAAATTAAAG
Found at i:2554399 original size:13 final size:14
Alignment explanation
Indices: 2554369--2554402 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
2554359 TTAATTAATT
*
2554369 AAAAAAATTAAAGT
1 AAAAAAATTAAAGA
2554383 AAAAAAATTAAA-A
1 AAAAAAATTAAAGA
2554396 AAAAAAA
1 AAAAAAA
2554403 GAAGAAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (14 bp):
AAAAAAATTAAAGA
Found at i:2554410 original size:23 final size:23
Alignment explanation
Indices: 2554365--2554411 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
2554355 AAAATTAATT
* *
2554365 AATTAAAAAAATTAAAGTAAAAA
1 AATTAAAAAAATAAAAGAAAAAA
*
2554388 AATTAAAAAAA-AAAAGAAGAAA
1 AATTAAAAAAATAAAAGAAAAAA
2554410 AA
1 AA
2554412 GAAAAAAGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (23 bp):
AATTAAAAAAATAAAAGAAAAAA
Found at i:2555398 original size:22 final size:22
Alignment explanation
Indices: 2555370--2555425 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
2555360 AGGTAAAAAA
*
2555370 ATTTTTTTTTTTTTATA-TATAT
1 ATTTTTTTTTATTTA-AGTATAT
*
2555392 ATTTTTTGTTATTTAAGTATAT
1 ATTTTTTTTTATTTAAGTATAT
2555414 ATTTTTTTTTAT
1 ATTTTTTTTTAT
2555426 GCATGATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 1 0.03
22 29 0.97
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.73
Consensus pattern (22 bp):
ATTTTTTTTTATTTAAGTATAT
Found at i:2555506 original size:24 final size:23
Alignment explanation
Indices: 2555472--2555520 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 23
2555462 TAATTGTTAT
2555472 TAATAGTAATAAAATGAAAATAATA
1 TAATAGTAATAAAAT-AAAA-AATA
2555497 TAATA-TAATAAAATAAAAAATA
1 TAATAGTAATAAAATAAAAAATA
2555519 TA
1 TA
2555521 TATTAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 6 0.25
23 4 0.17
24 9 0.38
25 5 0.21
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (23 bp):
TAATAGTAATAAAATAAAAAATA
Found at i:2555853 original size:16 final size:16
Alignment explanation
Indices: 2555822--2555923 Score: 91
Period size: 16 Copynumber: 6.2 Consensus size: 16
2555812 CTAAGTTTTT
2555822 AAAACCCCTAAAAATCC
1 AAAACCCCT-AAAATCC
*
2555839 AAAATCCCTAAAATCC
1 AAAACCCCTAAAATCC
**
2555855 -AAACCCCTAAAAATTG
1 AAAACCCCT-AAAATCC
* * *
2555871 AAAATCTCTTAAATCC
1 AAAACCCCTAAAATCC
2555887 -AAACCCTCATAAAATCC
1 AAAACCC-C-TAAAATCC
*
2555904 GAAACCCCTAAAATCC
1 AAAACCCCTAAAATCC
2555920 AAAA
1 AAAA
2555924 TCCCAAACTT
Statistics
Matches: 67, Mismatches: 13, Indels: 11
0.74 0.14 0.12
Matches are distributed among these distances:
15 11 0.16
16 28 0.42
17 22 0.33
18 6 0.09
ACGTcount: A:0.50, C:0.30, G:0.02, T:0.18
Consensus pattern (16 bp):
AAAACCCCTAAAATCC
Found at i:2555862 original size:32 final size:32
Alignment explanation
Indices: 2555823--2555922 Score: 121
Period size: 32 Copynumber: 3.1 Consensus size: 32
2555813 TAAGTTTTTA
2555823 AAACCCCTAAAAATCCAAAATCCCTAAAATCC
1 AAACCCCTAAAAATCCAAAATCCCTAAAATCC
** * *
2555855 AAACCCCTAAAAATTGAAAATCTCTTAAATCC
1 AAACCCCTAAAAATCCAAAATCCCTAAAATCC
* *
2555887 AAA-CCCTCATAAAATCCGAAACCCCTAAAATCC
1 AAACCCCT-A-AAAATCCAAAATCCCTAAAATCC
2555920 AAA
1 AAA
2555923 ATCCCAAACT
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
31 4 0.07
32 32 0.57
33 20 0.36
ACGTcount: A:0.49, C:0.31, G:0.02, T:0.18
Consensus pattern (32 bp):
AAACCCCTAAAAATCCAAAATCCCTAAAATCC
Found at i:2555995 original size:41 final size:41
Alignment explanation
Indices: 2555914--2555995 Score: 94
Period size: 41 Copynumber: 2.0 Consensus size: 41
2555904 GAAACCCCTA
* *** *
2555914 AAATCCAAAATCCCAAACTTTTAAACTCTTAAACCTAAACC
1 AAATCCAAAATCCCAAAATCCAAAACTCTTAAACCAAAACC
*
2555955 AAATCCAAAATCCCTAAAATCCAAAACT-TTAAATCAAAACC
1 AAATCCAAAATCCC-AAAATCCAAAACTCTTAAACCAAAACC
2555996 CCAAACCTCA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
41 25 0.74
42 9 0.26
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.22
Consensus pattern (41 bp):
AAATCCAAAATCCCAAAATCCAAAACTCTTAAACCAAAACC
Found at i:2557607 original size:27 final size:26
Alignment explanation
Indices: 2557577--2557656 Score: 67
Period size: 26 Copynumber: 3.0 Consensus size: 26
2557567 AATAAAATTC
2557577 AATAAATATAAAAAGATAATTTAATAA
1 AATAAATATAAAAA-ATAATTTAATAA
* *
2557604 AAT-ATTAATAAAAATTAATTATAA-AA
1 AATAAAT-ATAAAAAATAATT-TAATAA
* *
2557630 ACTAACTAT-AAAAATAATATTAATAA
1 AATAAATATAAAAAATAAT-TTAATAA
2557656 A
1 A
2557657 GTTTAATAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
25 11 0.26
26 17 0.40
27 15 0.35
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.31
Consensus pattern (26 bp):
AATAAATATAAAAAATAATTTAATAA
Found at i:2557629 original size:13 final size:13
Alignment explanation
Indices: 2557611--2557644 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
2557601 TAAAATATTA
*
2557611 ATAAAAATTAATT
1 ATAAAAATTAACT
*
2557624 ATAAAAACTAACT
1 ATAAAAATTAACT
2557637 ATAAAAAT
1 ATAAAAAT
2557645 AATATTAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (13 bp):
ATAAAAATTAACT
Found at i:2557795 original size:21 final size:21
Alignment explanation
Indices: 2557771--2557814 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2557761 ATTAATTTTA
2557771 TAAATTAGTTAA-TTAAATTAT
1 TAAA-TAGTTAATTTAAATTAT
* *
2557792 TAAATATTTAATTTTAATTAT
1 TAAATAGTTAATTTAAATTAT
2557813 TA
1 TA
2557815 TGAAATTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
TAAATAGTTAATTTAAATTAT
Done.