Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 18 of 163
Found at i:5118673 original size:20 final size:20
Alignment explanation
Indices: 5118629--5118674 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
5118619 ATCATATTTA
5118629 GATATATTATTTTTTAAAAT
1 GATATATTATTTTTTAAAAT
*
5118649 AATAT-TTA-TTTTTAATAGAT
1 GATATATTATTTTTTAA-A-AT
5118669 GATATA
1 GATATA
5118675 CACTGTGAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
18 7 0.33
19 4 0.19
20 10 0.48
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (20 bp):
GATATATTATTTTTTAAAAT
Found at i:5142134 original size:26 final size:26
Alignment explanation
Indices: 5142119--5142168 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
5142109 ATGCATATCA
*
5142119 AAGTTTGGCATTGGAAATGTTAATAC
1 AAGTTTGGCATTGGAAATGATAATAC
* *
5142145 AAGTTTGGCCTTGGAAATGTTAAT
1 AAGTTTGGCATTGGAAATGATAAT
5142169 TATTATTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (26 bp):
AAGTTTGGCATTGGAAATGATAATAC
Found at i:5144159 original size:22 final size:22
Alignment explanation
Indices: 5144134--5144179 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
5144124 ATATAATTTT
5144134 TTAAAAA-ATATAATAA-AAAATA
1 TTAAAAACA-ATAA-AATAAAATA
5144156 TTAAAAACAATAAAATAAAATA
1 TTAAAAACAATAAAATAAAATA
5144178 TT
1 TT
5144180 TCTCAACAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 2 0.09
22 19 0.86
23 1 0.05
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (22 bp):
TTAAAAACAATAAAATAAAATA
Found at i:5155147 original size:27 final size:27
Alignment explanation
Indices: 5155093--5155147 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
5155083 CAACACTTTT
*
5155093 TTTTTCATCTTTGACTTTTCTTTTTAA
1 TTTTTCATCTTTGACTTTTCTTTATAA
*
5155120 TTTTTCATCTTTTACTTTAT-TTTATAA
1 TTTTTCATCTTTGACTTT-TCTTTATAA
5155147 T
1 T
5155148 CTCATTATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 24 0.96
28 1 0.04
ACGTcount: A:0.18, C:0.13, G:0.02, T:0.67
Consensus pattern (27 bp):
TTTTTCATCTTTGACTTTTCTTTATAA
Found at i:5158910 original size:18 final size:19
Alignment explanation
Indices: 5158882--5158919 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
5158872 GACTTAATTC
*
5158882 TAAAAACATATATTAAAAT
1 TAAAAACATATATAAAAAT
5158901 TAAAAA-ATATATAAAAAT
1 TAAAAACATATATAAAAAT
5158919 T
1 T
5158920 TAAATAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAAACATATATAAAAAT
Found at i:5158922 original size:19 final size:19
Alignment explanation
Indices: 5158877--5158936 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
5158867 ATTTAGACTT
*
5158877 AATTCTAAAAACATATATTAA
1 AATT-TAAAAA-ATATATAAA
5158898 AA-TTAAAAAATATATAAA
1 AATTTAAAAAATATATAAA
*
5158916 AATTTAAATAATA-A-AAA
1 AATTTAAAAAATATATAAA
5158933 AATT
1 AATT
5158937 GTATAAACAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
17 7 0.19
18 11 0.31
19 15 0.42
20 1 0.03
21 2 0.06
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (19 bp):
AATTTAAAAAATATATAAA
Found at i:5159170 original size:29 final size:29
Alignment explanation
Indices: 5159111--5159170 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
5159101 TTTGGTTTAA
* *
5159111 TGTGCAATTGTATACATGAACTTTGATTT
1 TGTGCAATTGTATACATGAAATTTGAATT
* * *
5159140 TGTGTAATTTTATACATGAAATTTTAATT
1 TGTGCAATTGTATACATGAAATTTGAATT
5159169 TG
1 TG
5159171 ATCAAATTCT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.48
Consensus pattern (29 bp):
TGTGCAATTGTATACATGAAATTTGAATT
Found at i:5159706 original size:14 final size:14
Alignment explanation
Indices: 5159687--5159715 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5159677 TTCAGTACTT
5159687 ATTGTTAAAGTCAA
1 ATTGTTAAAGTCAA
5159701 ATTGTTAAAGTCAA
1 ATTGTTAAAGTCAA
5159715 A
1 A
5159716 GGGAAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.34
Consensus pattern (14 bp):
ATTGTTAAAGTCAA
Found at i:5160756 original size:21 final size:21
Alignment explanation
Indices: 5160732--5160796 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
5160722 GAACATTTAA
5160732 ATTTTTTAAAATTTAAAAAAT
1 ATTTTTTAAAATTTAAAAAAT
* * *
5160753 ATTTTTTATAATTT-TAAAAG
1 ATTTTTTAAAATTTAAAAAAT
*
5160773 A-TTATTAAAATTTATAAAAAT
1 ATTTTTTAAAATTTA-AAAAAT
5160794 ATT
1 ATT
5160797 AAAAAAAGTT
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
19 10 0.29
20 5 0.15
21 18 0.53
22 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
ATTTTTTAAAATTTAAAAAAT
Found at i:5160796 original size:18 final size:19
Alignment explanation
Indices: 5160762--5160800 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
5160752 TATTTTTTAT
5160762 AATTTTAAAAGATTATTAA
1 AATTTTAAAAGATTATTAA
5160781 AATTTATAAAA-A-TATTAA
1 AATTT-TAAAAGATTATTAA
5160799 AA
1 AA
5160801 AAAGTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.42
19 6 0.32
20 5 0.26
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
AATTTTAAAAGATTATTAA
Found at i:5167744 original size:22 final size:22
Alignment explanation
Indices: 5167714--5167760 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
5167704 AAGAGAGGCA
*
5167714 ATACTCAGGAAAGAGCCAACTT
1 ATACCCAGGAAAGAGCCAACTT
5167736 ATACCCAGGAAAGAGCCAACTT
1 ATACCCAGGAAAGAGCCAACTT
5167758 ATA
1 ATA
5167761 TTTCATCTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.43, C:0.23, G:0.17, T:0.17
Consensus pattern (22 bp):
ATACCCAGGAAAGAGCCAACTT
Found at i:5168864 original size:55 final size:55
Alignment explanation
Indices: 5168754--5168952 Score: 182
Period size: 55 Copynumber: 3.5 Consensus size: 55
5168744 AGCACTTATC
* * *
5168754 AACAATCGATTCAAAAGAAGAAGAAGTAATATCCCACAATAACAATTGATTTAAACATATA
1 AACAATCGATTCAAAAG-A-AACAA-T-AT-TCCAAC-ATGACAATTGATTTAAACATATA
* * * * *
5168815 AACAATCGATTTAAAAGAAACAGTATTCCAGCATGACAATCGATCTAAACATATA
1 AACAATCGATTCAAAAGAAACAATATTCCAACATGACAATTGATTTAAACATATA
* * ** *
5168870 AACAATCTATTCAAAAGAAGCAATATTTGAACATGACAATTGATTTAAACATAAA
1 AACAATCGATTCAAAAGAAACAATATTCCAACATGACAATTGATTTAAACATATA
* ** * *
5168925 AATAATTTATCCAAAAGAAGCAATATTC
1 AACAATCGATTCAAAAGAAACAATATTC
5168953 TTAGGAAATT
Statistics
Matches: 116, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
55 89 0.77
56 4 0.03
57 2 0.02
58 1 0.01
59 3 0.03
60 1 0.01
61 16 0.14
ACGTcount: A:0.50, C:0.15, G:0.10, T:0.25
Consensus pattern (55 bp):
AACAATCGATTCAAAAGAAACAATATTCCAACATGACAATTGATTTAAACATATA
Found at i:5170131 original size:15 final size:15
Alignment explanation
Indices: 5170113--5170154 Score: 84
Period size: 15 Copynumber: 2.8 Consensus size: 15
5170103 ATTTAATCAC
5170113 TAAATATTTTAAAAT
1 TAAATATTTTAAAAT
5170128 TAAATATTTTAAAAT
1 TAAATATTTTAAAAT
5170143 TAAATATTTTAA
1 TAAATATTTTAA
5170155 TCACTCTGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TAAATATTTTAAAAT
Found at i:5173552 original size:19 final size:20
Alignment explanation
Indices: 5173520--5173562 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
5173510 ATATCATTTC
5173520 ATATCATTATTCAA-TTCAA
1 ATATCATTATTCAAGTTCAA
*
5173539 ATATCATT-TATCAAGTTCAT
1 ATATCATTAT-TCAAGTTCAA
5173559 ATAT
1 ATAT
5173563 TATAATCTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 12 0.57
20 8 0.38
ACGTcount: A:0.40, C:0.14, G:0.02, T:0.44
Consensus pattern (20 bp):
ATATCATTATTCAAGTTCAA
Found at i:5173665 original size:19 final size:19
Alignment explanation
Indices: 5173641--5173711 Score: 81
Period size: 19 Copynumber: 3.7 Consensus size: 19
5173631 GGCATCGCAA
*
5173641 TGCATACTAGCACATGAAG
1 TGCATACTGGCACATGAAG
*
5173660 TGCATA-TCGGCACACGAAG
1 TGCATACT-GGCACATGAAG
*
5173679 TGCATACTGGCACATGAAA
1 TGCATACTGGCACATGAAG
* *
5173698 CGCATCCTGGCACA
1 TGCATACTGGCACA
5173712 CAAAATACAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
18 1 0.02
19 42 0.95
20 1 0.02
ACGTcount: A:0.32, C:0.27, G:0.23, T:0.18
Consensus pattern (19 bp):
TGCATACTGGCACATGAAG
Found at i:5177310 original size:71 final size:71
Alignment explanation
Indices: 5177226--5177435 Score: 330
Period size: 71 Copynumber: 3.0 Consensus size: 71
5177216 ACTCGACATG
* * * *
5177226 TCAAATTCGAATACATGTGTACAAAGTACAAATTTAAGAACCTGTGTGCAAGGTGTAAACATCGA
1 TCAAATTCAAATACATGTGTGCAAGGTACAAATTTAAGAACCTGTGTGCAAGGTGTGAACATCGA
5177291 AAAATA
66 AAAATA
*
5177297 TCAAATTCAAATACATGTGTGCAAGGTACAAATTTAAAAACCTGTGTGCAAGGTGTGAACATCGA
1 TCAAATTCAAATACATGTGTGCAAGGTACAAATTTAAGAACCTGTGTGCAAGGTGTGAACATCGA
*
5177362 AAAATG
66 AAAATA
* * * *
5177368 TCGAATTCAAATACATGTGTGCAAGGTACGAATTTAAGAACCTGTGTGCAAGTTGTGAACATAGA
1 TCAAATTCAAATACATGTGTGCAAGGTACAAATTTAAGAACCTGTGTGCAAGGTGTGAACATCGA
5177433 AAA
66 AAA
5177436 TATGAACAGA
Statistics
Matches: 128, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
71 128 1.00
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.26
Consensus pattern (71 bp):
TCAAATTCAAATACATGTGTGCAAGGTACAAATTTAAGAACCTGTGTGCAAGGTGTGAACATCGA
AAAATA
Found at i:5177328 original size:27 final size:27
Alignment explanation
Indices: 5177298--5177350 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
5177288 CGAAAAATAT
*
5177298 CAAATTCAAATACATGTGTGCAAGGTA
1 CAAATTCAAAAACATGTGTGCAAGGTA
* *
5177325 CAAATTTAAAAACCTGTGTGCAAGGT
1 CAAATTCAAAAACATGTGTGCAAGGT
5177351 GTGAACATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (27 bp):
CAAATTCAAAAACATGTGTGCAAGGTA
Found at i:5181363 original size:3 final size:3
Alignment explanation
Indices: 5181355--5181401 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
5181345 GAAAAGAATA
5181355 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
5181402 ATAAATTAGG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:5186285 original size:12 final size:13
Alignment explanation
Indices: 5186268--5186304 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
5186258 TGTGTATCCC
5186268 TTATTTATTTCT-
1 TTATTTATTTCTA
5186280 TTATTTATTT-TA
1 TTATTTATTTCTA
*
5186292 TTATTGATTTCTA
1 TTATTTATTTCTA
5186305 AGTTTGTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
11 1 0.05
12 19 0.86
13 2 0.09
ACGTcount: A:0.22, C:0.05, G:0.03, T:0.70
Consensus pattern (13 bp):
TTATTTATTTCTA
Found at i:5191508 original size:391 final size:390
Alignment explanation
Indices: 5190787--5191566 Score: 1524
Period size: 391 Copynumber: 2.0 Consensus size: 390
5190777 AAGAATTCCA
5190787 AAGTTATCAATTGGATTAAATTGTAAAGTTTTGCACACTTGTACCTTATTAAATGTTTGTAACAT
1 AAGTTATCAATTGGATTAAATTGTAAAGTTTTGCACACTTGTACCTTATTAAATGTTTGTAACAT
5190852 CCGTGTGTTTGAACTGGATTTGGAACAGTGATAAAATAGAATTGAGAATTAGAAATGTTTAGTTG
66 CCGTGTGTTTGAACTGGATTTGGAACAGTGATAAAATAGAATTGAGAATTAGAAATGTTTAGTTG
*
5190917 AAGTAAGGAAGGTTAGAAAAATTTAAGGATTAAATGGTAAAGGAGAGAAAATATGGGGGACTAAA
131 AAGTAAGGAAGGTTAGAAAAATTTAAGGATTAAATAGTAAAGGAGAGAAAATATGGGGGACTAAA
*
5190982 TAGCGAATTATCCAAATTGAGTTTTGAGTCATCATGAGAATTAGATTGATTGAGGAGGGGAAAAA
196 TAGCGAATTATCCAAATTGAGTTTTGAGTCATCATGAGAATTAGATTGATTAAGGAGGGGAAAAA
5191047 GAGTAATTTGGTAGAAGATATTTTTGGAGACAAAGTTTTGGGCTAAAGTGTAAAGTTGAAAGGGC
261 GAGTAATTTGGTAGAAGATATTTTTGGAGACAAAGTTTTGGGCTAAAGTGTAAAGTTGAAAGGGC
5191112 CAAGGATTAAAAGTGCAGTTTTACCATTTTTTTAAGCGAGATGTTTTAAGTGAAATTTCTAGAGA
326 CAAGGATTAAAAGTGCAGTTTTACCA-TTTTTTAAGCGAGATGTTTTAAGTGAAATTTCTAGAGA
5191177 C
390 C
5191178 AAGTTATCAATTGGATTAAATTGTAAAGTTTTGCACACTTGTACCTTATTAAATGTTTGTAACAT
1 AAGTTATCAATTGGATTAAATTGTAAAGTTTTGCACACTTGTACCTTATTAAATGTTTGTAACAT
5191243 CCGTGTGTTTGAACTGGATTTGGAACAGTGATAAAATAGAATTGAGAATTAGAAATGTTTAGTTG
66 CCGTGTGTTTGAACTGGATTTGGAACAGTGATAAAATAGAATTGAGAATTAGAAATGTTTAGTTG
5191308 AAGTAAGGAAGGTTAGAAAAATTTAAGGATTAAATAGTAAAGGAGAGAAAATATGGGGGACTAAA
131 AAGTAAGGAAGGTTAGAAAAATTTAAGGATTAAATAGTAAAGGAGAGAAAATATGGGGGACTAAA
*
5191373 TAGTGAATTATCCAAATTGAGTTTTGAGTCATCATGAGAATTAGATTGATTAAGGAGGGGAAAAA
196 TAGCGAATTATCCAAATTGAGTTTTGAGTCATCATGAGAATTAGATTGATTAAGGAGGGGAAAAA
5191438 GAGTAATTTGGTAGAAGATATTTTTGGAGACAAAGTTTTGGGCTAAAGTGTAAAGTTGAAAGGGC
261 GAGTAATTTGGTAGAAGATATTTTTGGAGACAAAGTTTTGGGCTAAAGTGTAAAGTTGAAAGGGC
5191503 CAAGGATTAAAAGTGCAGTTTTACCATTTTTTAAGCGAGATGTTTTAAGTGAAATTTCTAGAGA
326 CAAGGATTAAAAGTGCAGTTTTACCATTTTTTAAGCGAGATGTTTTAAGTGAAATTTCTAGAGA
5191567 ATTTGAGAGA
Statistics
Matches: 386, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
390 38 0.10
391 348 0.90
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.32
Consensus pattern (390 bp):
AAGTTATCAATTGGATTAAATTGTAAAGTTTTGCACACTTGTACCTTATTAAATGTTTGTAACAT
CCGTGTGTTTGAACTGGATTTGGAACAGTGATAAAATAGAATTGAGAATTAGAAATGTTTAGTTG
AAGTAAGGAAGGTTAGAAAAATTTAAGGATTAAATAGTAAAGGAGAGAAAATATGGGGGACTAAA
TAGCGAATTATCCAAATTGAGTTTTGAGTCATCATGAGAATTAGATTGATTAAGGAGGGGAAAAA
GAGTAATTTGGTAGAAGATATTTTTGGAGACAAAGTTTTGGGCTAAAGTGTAAAGTTGAAAGGGC
CAAGGATTAAAAGTGCAGTTTTACCATTTTTTAAGCGAGATGTTTTAAGTGAAATTTCTAGAGAC
Found at i:5192987 original size:23 final size:22
Alignment explanation
Indices: 5192922--5192994 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 22
5192912 TCGCACCTTG
* * *
5192922 TGTGCCTACTGATTTGCGCTATG
1 TGTGCCTACTGA-TTGCACTGTA
* *
5192945 TGCGCCTACTGATTGCACTGTT
1 TGTGCCTACTGATTGCACTGTA
5192967 TGTGCCTACTGGATTGCACTGTA
1 TGTGCCTACT-GATTGCACTGTA
5192990 TGTGC
1 TGTGC
5192995 TTATTGTTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
22 16 0.37
23 27 0.63
ACGTcount: A:0.14, C:0.23, G:0.26, T:0.37
Consensus pattern (22 bp):
TGTGCCTACTGATTGCACTGTA
Found at i:5198897 original size:23 final size:23
Alignment explanation
Indices: 5198870--5198915 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
5198860 AAGAAAGAGA
5198870 TTAACTCTATGTATTGGGTTGAT
1 TTAACTCTATGTATTGGGTTGAT
5198893 TTAACTCTATGTATTGGGTTGAT
1 TTAACTCTATGTATTGGGTTGAT
5198916 AGTCAGGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.09, G:0.22, T:0.48
Consensus pattern (23 bp):
TTAACTCTATGTATTGGGTTGAT
Found at i:5203412 original size:29 final size:27
Alignment explanation
Indices: 5203310--5203412 Score: 84
Period size: 29 Copynumber: 3.7 Consensus size: 27
5203300 TAAAAACAAT
*
5203310 AAATTTGGACCCTTAAAATTTTAAAAAAA
1 AAATTTGGACCCTTAAAA-GTT-AAAAAA
* * **
5203339 AAATTGGGGCCCTTAAAAGTTGGTAAAA
1 AAATTTGGACCCTTAAAAGTT-AAAAAA
*
5203367 AAATTT--AACCTATAAAAGTTAAAAAA
1 AAATTTGGACCCT-TAAAAGTTAAAAAA
5203393 AAATTTTGGATCCCTTAAAA
1 AAA-TTTGGA-CCCTTAAAA
5203413 ATTTTAAAAA
Statistics
Matches: 57, Mismatches: 12, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
26 10 0.18
27 11 0.19
28 11 0.19
29 22 0.39
30 3 0.05
ACGTcount: A:0.49, C:0.11, G:0.12, T:0.29
Consensus pattern (27 bp):
AAATTTGGACCCTTAAAAGTTAAAAAA
Found at i:5203460 original size:97 final size:97
Alignment explanation
Indices: 5203359--5203553 Score: 356
Period size: 97 Copynumber: 2.0 Consensus size: 97
5203349 CCTTAAAAGT
5203359 TGGT-AAAAAAATTTAACCTATAAAAGTTAAAAAAAAATTTTGGATCCCTTAAAAATTTTAAAAA
1 TGGTAAAAAAAATTTAACCTATAAAAGTTAAAAAAAAA-TTTGGATCCCTTAAAAATTTTAAAAA
5203423 AACAAAAATTTAAACTCTTTTAACCTTGGGCCC
65 AACAAAAATTTAAACTCTTTTAACCTTGGGCCC
*
5203456 TGGTAAAAAAAATTTAACCTATAAAAGTTTAAAAAAAATTTGGATCCCTTAAAAATTTTAAAAAA
1 TGGTAAAAAAAATTTAACCTATAAAAGTTAAAAAAAAATTTGGATCCCTTAAAAATTTTAAAAAA
*
5203521 ACAAAAATTTAAACTCTTTTAACTTTGGGCCC
66 ACAAAAATTTAAACTCTTTTAACCTTGGGCCC
5203553 T
1 T
5203554 AAACGATTAC
Statistics
Matches: 95, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
97 63 0.66
98 32 0.34
ACGTcount: A:0.47, C:0.13, G:0.08, T:0.32
Consensus pattern (97 bp):
TGGTAAAAAAAATTTAACCTATAAAAGTTAAAAAAAAATTTGGATCCCTTAAAAATTTTAAAAAA
ACAAAAATTTAAACTCTTTTAACCTTGGGCCC
Found at i:5205077 original size:10 final size:11
Alignment explanation
Indices: 5205060--5205087 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
5205050 CTCATCGTTG
5205060 ATTTTTTTAAA
1 ATTTTTTTAAA
5205071 ATTTTTTTAAA
1 ATTTTTTTAAA
5205082 ATTTTT
1 ATTTTT
5205088 ATTTTTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
ATTTTTTTAAA
Found at i:5205098 original size:5 final size:6
Alignment explanation
Indices: 5205082--5205106 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5205072 TTTTTTTAAA
5205082 ATTTTT ATTTTT ATTTTT ATTTTT A
1 ATTTTT ATTTTT ATTTTT ATTTTT A
5205107 AGAATATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
ATTTTT
Found at i:5207983 original size:17 final size:17
Alignment explanation
Indices: 5207963--5207998 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
5207953 CTCTGACTTA
5207963 TTTTTATAATTA-ATTAT
1 TTTTTAT-ATTATATTAT
5207980 TTTTTATATTATATTAT
1 TTTTTATATTATATTAT
5207997 TT
1 TT
5207999 AAAAAGCCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTTATATTATATTAT
Found at i:5209173 original size:19 final size:20
Alignment explanation
Indices: 5209139--5209176 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
5209129 ATTTTTTATT
5209139 ATTTTAAAAATATAATATAA
1 ATTTTAAAAATATAATATAA
*
5209159 ATTTT-AAATTATAATATA
1 ATTTTAAAAATATAATATA
5209177 TTATTTGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTTTAAAAATATAATATAA
Found at i:5212015 original size:8 final size:7
Alignment explanation
Indices: 5212001--5212060 Score: 59
Period size: 7 Copynumber: 8.4 Consensus size: 7
5211991 ATTAAAAAAA
5212001 TAATTTT
1 TAATTTT
5212008 TAATTTT
1 TAATTTT
5212015 TAATTTT
1 TAATTTT
***
5212022 TAA-ACA
1 TAATTTT
5212028 TAAGTTTT
1 TAA-TTTT
*
5212036 ATATTTTT
1 -TAATTTT
5212044 TAATTTT
1 TAATTTT
5212051 TAATTTT
1 TAATTTT
5212058 TAA
1 TAA
5212061 AAATTAATTA
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
6 3 0.07
7 33 0.79
8 4 0.10
9 2 0.05
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (7 bp):
TAATTTT
Found at i:5212019 original size:36 final size:37
Alignment explanation
Indices: 5211978--5212067 Score: 96
Period size: 36 Copynumber: 2.5 Consensus size: 37
5211968 TAGCAATTAA
5211978 TTAATTTTTTAAAATTAA-AAAAATAATTTTTAATTT
1 TTAATTTTTTAAAATTAAGAAAAATAATTTTTAATTT
**** *
5212014 TTAA-TTTTTAAACA-TAAGTTTTATATTTTTTAATTT
1 TTAATTTTTTAAA-ATTAAGAAAAATAATTTTTAATTT
*
5212050 TTAATTTTTAAAAATTAA
1 TTAATTTTTTAAAATTAA
5212068 TTAATTTCTA
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
35 11 0.25
36 23 0.52
37 10 0.23
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (37 bp):
TTAATTTTTTAAAATTAAGAAAAATAATTTTTAATTT
Found at i:5212024 original size:29 final size:31
Alignment explanation
Indices: 5211992--5212053 Score: 78
Period size: 29 Copynumber: 2.1 Consensus size: 31
5211982 TTTTTTAAAA
5211992 TTAAAAAAATAA-TTTT-TAATTTTTAATTT
1 TTAAAAAAATAAGTTTTATAATTTTTAATTT
* *
5212021 TT--AAACATAAGTTTTATATTTTTTAATTT
1 TTAAAAAAATAAGTTTTATAATTTTTAATTT
5212050 TTAA
1 TTAA
5212054 TTTTTAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
27 7 0.26
28 4 0.15
29 16 0.59
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (31 bp):
TTAAAAAAATAAGTTTTATAATTTTTAATTT
Found at i:5212371 original size:13 final size:13
Alignment explanation
Indices: 5212353--5212378 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5212343 GCGCGTAAAT
5212353 AAATAAAATAATA
1 AAATAAAATAATA
5212366 AAATAAAATAATA
1 AAATAAAATAATA
5212379 TTAATTTCAT
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:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AAATAAAATAATA
Found at i:5212814 original size:20 final size:18
Alignment explanation
Indices: 5212781--5212823 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
5212771 TAAAATTTTT
*
5212781 TAAAAATTGAAAAAGAAATA
1 TAAAAATCG-AAAA-AAATA
*
5212801 TAAAAATCGTAAAAAATA
1 TAAAAATCGAAAAAAATA
5212819 TAAAA
1 TAAAA
5212824 GATTTGTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 10 0.48
19 3 0.14
20 8 0.38
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.21
Consensus pattern (18 bp):
TAAAAATCGAAAAAAATA
Found at i:5222712 original size:63 final size:63
Alignment explanation
Indices: 5222628--5222757 Score: 179
Period size: 63 Copynumber: 2.1 Consensus size: 63
5222618 TTGACCATCT
* *
5222628 TGAAGAATCTGACATGCTTGTTAATGATGAAAAAGGCGCTGAAGTTGATTACAGTGAGGAAGA
1 TGAACAATCTGACATGCTTGTTAATGAAGAAAAAGGCGCTGAAGTTGATTACAGTGAGGAAGA
* *** ** *
5222691 TGAACAATCTGACTTGCTTGTTAATGAAGAAAAATTTGCTGAAGTTGATTTTAGTGATGAAGA
1 TGAACAATCTGACATGCTTGTTAATGAAGAAAAAGGCGCTGAAGTTGATTACAGTGAGGAAGA
5222754 TGAA
1 TGAA
5222758 GATTATCTTC
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
63 58 1.00
ACGTcount: A:0.36, C:0.08, G:0.25, T:0.30
Consensus pattern (63 bp):
TGAACAATCTGACATGCTTGTTAATGAAGAAAAAGGCGCTGAAGTTGATTACAGTGAGGAAGA
Found at i:5225004 original size:6 final size:6
Alignment explanation
Indices: 5224972--5225034 Score: 55
Period size: 6 Copynumber: 11.2 Consensus size: 6
5224962 CAACTTGGAT
* *
5224972 TTTAAA -TTAAG TTTGAAA -TTAAT TTTAAA TTT--A TTTAAA TTTAAA
1 TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
5225017 TTT-AT TTTAAA TTTAAA T
1 TTTAAA TTTAAA TTTAAA T
5225035 ACATTTGAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
4 4 0.09
5 10 0.22
6 29 0.64
7 2 0.04
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:5225012 original size:17 final size:17
Alignment explanation
Indices: 5224990--5225034 Score: 74
Period size: 16 Copynumber: 2.7 Consensus size: 17
5224980 AAGTTTGAAA
*
5224990 TTAATTTTAAATTTA-T
1 TTAAATTTAAATTTATT
5225006 TTAAATTTAAATTTATT
1 TTAAATTTAAATTTATT
5225023 TTAAATTTAAAT
1 TTAAATTTAAAT
5225035 ACATTTGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
16 14 0.52
17 13 0.48
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTAAATTTAAATTTATT
Found at i:5225017 original size:27 final size:28
Alignment explanation
Indices: 5224978--5225054 Score: 86
Period size: 27 Copynumber: 2.8 Consensus size: 28
5224968 GGATTTTAAA
*
5224978 TTAAGTTTGAAATTAATTTTAAATTTAT
1 TTAAATTTGAAATTAATTTTAAATTTAT
* *
5225006 TTAAATTT-AAATTTATTTTAAATTTAA
1 TTAAATTTGAAATTAATTTTAAATTTAT
* * *
5225033 ATACATTTGAAA-TAACTTTAAA
1 TTAAATTTGAAATTAATTTTAAA
5225055 CTTAAAATTT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
27 31 0.76
28 10 0.24
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.49
Consensus pattern (28 bp):
TTAAATTTGAAATTAATTTTAAATTTAT
Found at i:5225031 original size:11 final size:11
Alignment explanation
Indices: 5224970--5225012 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
5224960 TCCAACTTGG
5224970 ATTTTAAATTA
1 ATTTTAAATTA
*
5224981 AGTTTGAAATTA
1 A-TTTTAAATTA
*
5224993 ATTTTAAATTT
1 ATTTTAAATTA
5225004 A-TTTAAATT
1 ATTTTAAATT
5225013 TAAATTTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 8 0.29
11 10 0.36
12 10 0.36
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (11 bp):
ATTTTAAATTA
Found at i:5225040 original size:17 final size:17
Alignment explanation
Indices: 5225005--5225045 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
5224995 TTTAAATTTA
**
5225005 TTTAAATTTAAATTTAT
1 TTTAAATTTAAATACAT
5225022 TTTAAATTTAAATACAT
1 TTTAAATTTAAATACAT
*
5225039 TTGAAAT
1 TTTAAAT
5225046 AACTTTAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (17 bp):
TTTAAATTTAAATACAT
Found at i:5225581 original size:21 final size:21
Alignment explanation
Indices: 5225544--5225583 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5225534 AGAATAGACT
*
5225544 CACATCCAGTGTTCGAATACA
1 CACATCCAGTGTCCGAATACA
5225565 CACATCCAGTAG-CCGAATA
1 CACATCCAGT-GTCCGAATA
5225584 GGCTCAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.35, C:0.30, G:0.15, T:0.20
Consensus pattern (21 bp):
CACATCCAGTGTCCGAATACA
Found at i:5227048 original size:60 final size:59
Alignment explanation
Indices: 5226966--5227222 Score: 351
Period size: 59 Copynumber: 4.4 Consensus size: 59
5226956 AACTGTCCAG
* *
5226966 AAATTACCATTTTACCCCCGAACTTTCTAAAATCCCATTTTTAACCTCGATTCCACCAA
1 AAATTACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCTCGATTTCACCAA
* *
5227025 AAATTACCATTTTTACCCTCGAACTTTCCAAAATCCCATTTTTAACC-CTAGTTTCACCAA
1 AAATTACCA-TTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCTCGA-TTTCACCAA
** * *
5227085 AAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCTCGATTTTACCAA
1 AAATTACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCTCGATTTCACCAA
* * *
5227144 AAATTACCATTTTACCCCCAAACTATCCAAAATCCCA-TTTTAACCCCGATTTCACC-A
1 AAATTACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCTCGATTTCACCAA
*
5227201 AAATT-CCATTTTTACCCTCGAA
1 AAATTACCA-TTTTACCCCCGAA
5227223 AGTTGAAAAT
Statistics
Matches: 177, Mismatches: 17, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
56 3 0.02
57 17 0.10
58 17 0.10
59 86 0.49
60 54 0.31
ACGTcount: A:0.33, C:0.31, G:0.03, T:0.33
Consensus pattern (59 bp):
AAATTACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCTCGATTTCACCAA
Found at i:5227213 original size:29 final size:28
Alignment explanation
Indices: 5226994--5227214 Score: 116
Period size: 30 Copynumber: 7.5 Consensus size: 28
5226984 CGAACTTTCT
* * *
5226994 AAAATCCCATTTTTAACCTCGATTCCACC
1 AAAATTCCATTTTTAACCCCGATT-TACC
5227023 AAAAATTACCATTTTT-ACCCTCGAACTTT-CC
1 -AAAATT-CCATTTTTAACCC-CG-A-TTTACC
* *
5227054 AAAATCCCATTTTTAA-CCCTAGTTTCACC
1 AAAATTCCATTTTTAACCCCGA-TTT-ACC
*
5227083 AAAAATTACCA-TTTT-ACCCCTAAACTTT-CC
1 -AAAATT-CCATTTTTAACCCC--GA-TTTACC
*
5227113 AAAATTCCATTTTTAACCTCGATTTTACC
1 AAAATTCCATTTTTAACCCCGA-TTTACC
* * **
5227142 AAAAATTACCA-TTTTACCCCCAAACTATCC
1 -AAAATT-CCATTTTTAACCCCGATTTA-CC
*
5227172 AAAATCCCA-TTTTAACCCCGATTTCACC
1 AAAATTCCATTTTTAACCCCGATTT-ACC
5227200 AAAATTCCATTTTTA
1 AAAATTCCATTTTTA
5227215 CCCTCGAAAG
Statistics
Matches: 148, Mismatches: 23, Indels: 41
0.70 0.11 0.19
Matches are distributed among these distances:
27 4 0.03
28 32 0.22
29 38 0.26
30 49 0.33
31 18 0.12
32 5 0.03
33 2 0.01
ACGTcount: A:0.34, C:0.30, G:0.02, T:0.34
Consensus pattern (28 bp):
AAAATTCCATTTTTAACCCCGATTTACC
Found at i:5233651 original size:28 final size:28
Alignment explanation
Indices: 5233611--5233666 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
5233601 CACGGGCTTT
*
5233611 AATTTGCGAGAGACTTGGGATTCTCGTC
1 AATTTACGAGAGACTTGGGATTCTCGTC
5233639 AATTTACGAGAGACTTGGGATTCTCGTC
1 AATTTACGAGAGACTTGGGATTCTCGTC
5233667 GATCTTAGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (28 bp):
AATTTACGAGAGACTTGGGATTCTCGTC
Found at i:5247634 original size:31 final size:30
Alignment explanation
Indices: 5247562--5247634 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
5247552 GAACTTAATC
**
5247562 AAATCAAAATTTCATGTATAAAATTGTACA
1 AAATCAAAATTTCATGTATAAAATTACACA
*
5247592 AAATCAAAATTT-ATGTATACAATTACACA
1 AAATCAAAATTTCATGTATAAAATTACACA
*
5247621 TTAAATCATAATTT
1 --AAATCAAAATTT
5247635 GAAATTATCC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 14 0.38
30 12 0.32
31 11 0.30
ACGTcount: A:0.49, C:0.11, G:0.04, T:0.36
Consensus pattern (30 bp):
AAATCAAAATTTCATGTATAAAATTACACA
Found at i:5248811 original size:42 final size:42
Alignment explanation
Indices: 5248749--5248833 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
5248739 TGTCTTTTGC
* *
5248749 TTTACAATTATTTACCCAAACATAATATAAAAGTTTTATTAA
1 TTTACAATTATTTACCCAAACATAATATAAAAATTTCATTAA
*
5248791 TTTACAATTATTTACTCAAACATAATATAAAAATTTCATTAA
1 TTTACAATTATTTACCCAAACATAATATAAAAATTTCATTAA
5248833 T
1 T
5248834 AATTTAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.46, C:0.12, G:0.01, T:0.41
Consensus pattern (42 bp):
TTTACAATTATTTACCCAAACATAATATAAAAATTTCATTAA
Found at i:5250387 original size:22 final size:21
Alignment explanation
Indices: 5250344--5250387 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
5250334 TTCATCCCAT
*
5250344 TTATGTTTACATCATTATCCC
1 TTATGTTTACATAATTATCCC
5250365 TTATGCTTTACATTAATTA-CCC
1 TTATG-TTTACA-TAATTATCCC
5250387 T
1 T
5250388 AGTCATTCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 10 0.50
23 5 0.25
ACGTcount: A:0.25, C:0.23, G:0.05, T:0.48
Consensus pattern (21 bp):
TTATGTTTACATAATTATCCC
Found at i:5250875 original size:17 final size:16
Alignment explanation
Indices: 5250853--5250913 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 16
5250843 AAATATAAAA
5250853 TAAAATTTTTATTAATT
1 TAAAATTTTTA-TAATT
* * *
5250870 TAAAATTATCATAATA
1 TAAAATTTTTATAATT
5250886 TAAAAGTTTCATTAATAATT
1 TAAAA-TTT--TT-ATAATT
5250906 TAAAATTT
1 TAAAATTT
5250914 CCATTTAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
16 9 0.26
17 11 0.32
19 4 0.12
20 10 0.29
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.48
Consensus pattern (16 bp):
TAAAATTTTTATAATT
Found at i:5250889 original size:33 final size:35
Alignment explanation
Indices: 5250847--5250912 Score: 91
Period size: 36 Copynumber: 1.9 Consensus size: 35
5250837 TTACCGAAAT
*
5250847 ATAAAATAAAA-TTT-TTATTAATTTAAAATTATC
1 ATAAAATAAAAGTTTATTAATAATTTAAAATTATC
*
5250880 ATAATATAAAAGTTTCATTAATAATTTAAAATT
1 ATAAAATAAAAGTTT-ATTAATAATTTAAAATT
5250913 TCCATTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 10 0.36
34 3 0.11
36 15 0.54
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (35 bp):
ATAAAATAAAAGTTTATTAATAATTTAAAATTATC
Found at i:5250897 original size:16 final size:17
Alignment explanation
Indices: 5250852--5250902 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
5250842 GAAATATAAA
* *
5250852 ATAAAATTTTTATTAAT
1 ATAAAATTATCATTAAT
*
5250869 TTAAAATTATCA-TAAT
1 ATAAAATTATCATTAAT
5250885 ATAAAAGTT-TCATTAAT
1 ATAAAA-TTATCATTAAT
5250902 A
1 A
5250903 ATTTAAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 12 0.43
17 16 0.57
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (17 bp):
ATAAAATTATCATTAAT
Found at i:5254548 original size:52 final size:52
Alignment explanation
Indices: 5254467--5254701 Score: 362
Period size: 52 Copynumber: 4.5 Consensus size: 52
5254457 TTCTCATTTA
* ** * *
5254467 ATACTCACGATAACATGTAGTCATTGGACCTCATAATCCGTAAAAGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
5254519 ATACTCATGATGACACATAGTCATCGGACCTCATAATTCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * *
5254571 ATACTGACGATGATACATAATCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
5254623 ATACTCACGATAACACATAGTCATCGGACCTTATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
5254675 ATACTCACGATGACACATAGTCATCGG
1 ATACTCACGATGACACATAGTCATCGG
5254702 GCCTTTTGCA
Statistics
Matches: 165, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 165 1.00
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:5255274 original size:18 final size:16
Alignment explanation
Indices: 5255243--5255278 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
5255233 CCTCAATACC
5255243 ATTTCATTTCAATTTA
1 ATTTCATTTCAATTTA
5255259 ATTTCATTCCTCAATTTA
1 ATTTCATT--TCAATTTA
5255277 AT
1 AT
5255279 ATTTACTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
18 10 0.56
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTCATTTCAATTTA
Found at i:5266902 original size:13 final size:13
Alignment explanation
Indices: 5266884--5266919 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
5266874 ATATTATTGT
5266884 TACAAAATTTAAC
1 TACAAAATTTAAC
5266897 TACAAAATTTAAC
1 TACAAAATTTAAC
5266910 TACAAAATTT
1 TACAAAATTT
5266920 GAGTATATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (13 bp):
TACAAAATTTAAC
Found at i:5273005 original size:28 final size:28
Alignment explanation
Indices: 5272974--5273040 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
5272964 TAACATAATG
*
5272974 ATATATATAAATATATATTTTTTTCAT-T
1 ATATATATAAATATATATTATTTT-ATCT
* *
5273002 ATATA-ATTACATATTTATTATTTTATCT
1 ATATATA-TAAATATATATTATTTTATCT
5273030 ATATATATAAA
1 ATATATATAAA
5273041 GAAGTTATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
27 3 0.09
28 28 0.88
29 1 0.03
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (28 bp):
ATATATATAAATATATATTATTTTATCT
Found at i:5273579 original size:31 final size:31
Alignment explanation
Indices: 5273539--5273604 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
5273529 TTACATTTTG
5273539 GTCACTAAACTACTCAAAAATTTTCATTTAA
1 GTCACTAAACTACTCAAAAATTTTCATTTAA
* * * ** *
5273570 GTCATTAAACTATTTAAATTTTTTTATTTAA
1 GTCACTAAACTACTCAAAAATTTTCATTTAA
5273601 GTCA
1 GTCA
5273605 ATGAATTGTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.38, C:0.14, G:0.05, T:0.44
Consensus pattern (31 bp):
GTCACTAAACTACTCAAAAATTTTCATTTAA
Found at i:5274901 original size:2 final size:2
Alignment explanation
Indices: 5274894--5274953 Score: 104
Period size: 2 Copynumber: 30.5 Consensus size: 2
5274884 GCTATCTATC
*
5274894 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA TA 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
5274936 TA TA TA T- TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
5274954 GTTAAGATTA
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5277023 original size:102 final size:102
Alignment explanation
Indices: 5276912--5277130 Score: 429
Period size: 102 Copynumber: 2.1 Consensus size: 102
5276902 ATAAAATTCC
5276912 TTTACAAAATAGTCCTAAACAACAATCAAGTTCACAAACTCATCATTTAATCACAAGAACACTTA
1 TTTACAAAATAGTCCTAAACAACAATCAAGTTCACAAACTCATCATTTAATCACAAGAACACTTA
5276977 GAATTCATTAATGGCAAATTTCAAAATCTTTAACAAT
66 GAATTCATTAATGGCAAATTTCAAAATCTTTAACAAT
5277014 TTTACAAAATAGTCCTAAACAACAATCAAGTTCACAAACTCATCATTTAATCACAAGAACACTTA
1 TTTACAAAATAGTCCTAAACAACAATCAAGTTCACAAACTCATCATTTAATCACAAGAACACTTA
5277079 GAATTCATTAATGGCAAATTTCAAAATCTTTAACAAT
66 GAATTCATTAATGGCAAATTTCAAAATCTTTAACAAT
*
5277116 TTTATAAAATAGTCC
1 TTTACAAAATAGTCC
5277131 CTAGATTAGC
Statistics
Matches: 116, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
102 116 1.00
ACGTcount: A:0.45, C:0.19, G:0.06, T:0.30
Consensus pattern (102 bp):
TTTACAAAATAGTCCTAAACAACAATCAAGTTCACAAACTCATCATTTAATCACAAGAACACTTA
GAATTCATTAATGGCAAATTTCAAAATCTTTAACAAT
Found at i:5277321 original size:41 final size:41
Alignment explanation
Indices: 5277241--5277538 Score: 393
Period size: 41 Copynumber: 7.3 Consensus size: 41
5277231 TTTACATAAA
* * *
5277241 CGCCGC-AAAAGAT-AGAGCAATAGCGGCGATTACGAAAAAG
1 CGCCGCTAAAAG-TCAGAGCAATAGCGGCGCTTATGGAAAAG
* * * *
5277281 CACCGCTAAAGGTCAGAGCAATCGCGGTGCTTATGGAAAAG
1 CGCCGCTAAAAGTCAGAGCAATAGCGGCGCTTATGGAAAAG
* * *
5277322 CGCCGCTAAAGGTAAGAGCAGTAGCGGCGCTTATGGAAAAG
1 CGCCGCTAAAAGTCAGAGCAATAGCGGCGCTTATGGAAAAG
*
5277363 CGCCGCTAAAAGTCGGAGCAATAGCGGCGCTTATGGAAAAG
1 CGCCGCTAAAAGTCAGAGCAATAGCGGCGCTTATGGAAAAG
* * * *
5277404 CGCCGTTAAAGGTCGGAGAAATAGCGGCGCTTATGGAAAAG
1 CGCCGCTAAAAGTCAGAGCAATAGCGGCGCTTATGGAAAAG
* **
5277445 TGCCATTAAAAGTCAGAGCAAATAGCGGCGCTTATGGAAAAG
1 CGCCGCTAAAAGTCAGAGC-AATAGCGGCGCTTATGGAAAAG
*
5277487 CGCCGTTAAAAGTCAGAGCAATAGCGGCGCTTATGGAAAAG
1 CGCCGCTAAAAGTCAGAGCAATAGCGGCGCTTATGGAAAAG
5277528 CGCCGCTAAAA
1 CGCCGCTAAAA
5277539 TTTTTACATT
Statistics
Matches: 228, Mismatches: 27, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
40 6 0.03
41 183 0.80
42 39 0.17
ACGTcount: A:0.35, C:0.20, G:0.30, T:0.15
Consensus pattern (41 bp):
CGCCGCTAAAAGTCAGAGCAATAGCGGCGCTTATGGAAAAG
Found at i:5277626 original size:15 final size:15
Alignment explanation
Indices: 5277603--5277640 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
5277593 ACAGATTTCG
*
5277603 AAATTCCTAAATTCT
1 AAATCCCTAAATTCT
*
5277618 AAATCCCTAATTTCT
1 AAATCCCTAAATTCT
5277633 AAATCCCT
1 AAATCCCT
5277641 CTCCTCCTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.37, C:0.26, G:0.00, T:0.37
Consensus pattern (15 bp):
AAATCCCTAAATTCT
Found at i:5280878 original size:18 final size:18
Alignment explanation
Indices: 5280855--5280900 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
5280845 TTGATGATAT
5280855 CGATATTGATGCTAGTGA
1 CGATATTGATGCTAGTGA
5280873 CGATATTGATGCTAGTGA
1 CGATATTGATGCTAGTGA
*
5280891 CGCTATTGAT
1 CGATATTGAT
5280901 CGTGACCTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.35
Consensus pattern (18 bp):
CGATATTGATGCTAGTGA
Found at i:5285227 original size:34 final size:34
Alignment explanation
Indices: 5285187--5285288 Score: 105
Period size: 38 Copynumber: 2.9 Consensus size: 34
5285177 TTAAATTTTA
*
5285187 AATTAGTAAAAACAACCCAAATACTTAATTATTT
1 AATTAGTAAAAACAACCCAAATATTTAATTATTT
* * * *
5285221 AATTAGTTAAATCTACCCAATTATTTATTTATTTATTT
1 AATTAGTAAAAACAACCCAA--A--TATTTAATTATTT
* *
5285259 AAATATTAAAAACAACCCAAATATTTAATT
1 AATTAGTAAAAACAACCCAAATATTTAATT
5285289 CAAAACATTT
Statistics
Matches: 53, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
34 25 0.47
36 2 0.04
38 26 0.49
ACGTcount: A:0.46, C:0.13, G:0.02, T:0.39
Consensus pattern (34 bp):
AATTAGTAAAAACAACCCAAATATTTAATTATTT
Found at i:5285333 original size:8 final size:8
Alignment explanation
Indices: 5285295--5285319 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
5285285 AATTCAAAAC
5285295 ATTTAATT
1 ATTTAATT
5285303 ATTTAATT
1 ATTTAATT
5285311 ATTTAATT
1 ATTTAATT
5285319 A
1 A
5285320 AATATTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
ATTTAATT
Found at i:5285342 original size:68 final size:68
Alignment explanation
Indices: 5285239--5285506 Score: 227
Period size: 68 Copynumber: 3.7 Consensus size: 68
5285229 AAATCTACCC
* * * * *
5285239 AATTATTTATTTATTTATTTAAATATTAAAAACAACCCAAATATTTAATTCAAAACATTTAATTA
1 AATTATTTAATTAATTATTTAATTATTAAAAACAACCCAAATACTTAATTCAAAATATTTAATTA
5285304 TTT
66 TTT
* *
5285307 AATTATTTAATTAAATATTTAATTATTAAAAACAACCCAAATACTTAATT-ATTTAATTATTTAA
1 AATTATTTAATTAATTATTTAATTATTAAAAACAACCCAAATACTTAATTCA---AAATATTT-A
* ***
5285371 ATCAACCC
62 AT-TATTT
* * *
5285379 AATTAATTAATTAATTAATTATTTATTTATTTAAATATTAAAAACAACTCAAATATTTAATTCAA
1 AATT-A-T--TTAATTAATTATTTA-A----T---TATTAAAAACAACCCAAATACTTAATTCAA
5285444 AATATTTAATTATTT
54 AATATTTAATTATTT
*
5285459 AATTA--TATTTAATTATTTAATTATTAAAAACAACCCAAATACTTAATT
1 AATTATTTAATTAATTATTTAATTATTAAAAACAACCCAAATACTTAATT
5285507 ATTTAATTAG
Statistics
Matches: 158, Mismatches: 24, Indels: 38
0.72 0.11 0.17
Matches are distributed among these distances:
66 25 0.16
67 1 0.01
68 45 0.28
69 1 0.01
70 6 0.04
71 3 0.02
72 5 0.03
73 1 0.01
74 14 0.09
76 14 0.09
79 1 0.01
80 5 0.03
81 4 0.03
82 7 0.04
84 25 0.16
85 1 0.01
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (68 bp):
AATTATTTAATTAATTATTTAATTATTAAAAACAACCCAAATACTTAATTCAAAATATTTAATTA
TTT
Found at i:5285402 original size:34 final size:34
Alignment explanation
Indices: 5285313--5285403 Score: 128
Period size: 34 Copynumber: 2.7 Consensus size: 34
5285303 ATTTAATTAT
* *
5285313 TTAATTAAATATTTAATTATTAAAAACAACCCAA
1 TTAATTAATTATTTAATTATTTAAAACAACCCAA
* * *
5285347 ATACTTAATTATTTAATTATTTAAATCAACCCAA
1 TTAATTAATTATTTAATTATTTAAAACAACCCAA
*
5285381 TTAATTAATTAATTAATTATTTA
1 TTAATTAATTATTTAATTATTTA
5285404 TTTATTTAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (34 bp):
TTAATTAATTATTTAATTATTTAAAACAACCCAA
Found at i:5285459 original size:8 final size:8
Alignment explanation
Indices: 5285446--5285483 Score: 58
Period size: 8 Copynumber: 4.5 Consensus size: 8
5285436 TAATTCAAAA
5285446 TATTTAAT
1 TATTTAAT
5285454 TATTTAATT
1 TATTTAA-T
5285463 ATATTTAAT
1 -TATTTAAT
5285472 TATTTAAT
1 TATTTAAT
5285480 TATT
1 TATT
5285484 AAAAACAACC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
8 19 0.68
9 2 0.07
10 7 0.25
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
TATTTAAT
Found at i:5285468 original size:18 final size:18
Alignment explanation
Indices: 5285445--5285482 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
5285435 TTAATTCAAA
5285445 ATATTTAATTATTTAATT
1 ATATTTAATTATTTAATT
5285463 ATATTTAATTATTTAATT
1 ATATTTAATTATTTAATT
5285481 AT
1 AT
5285483 TAAAAACAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
ATATTTAATTATTTAATT
Found at i:5285486 original size:66 final size:68
Alignment explanation
Indices: 5285381--5285779 Score: 226
Period size: 66 Copynumber: 5.5 Consensus size: 68
5285371 ATCAACCCAA
* * *
5285381 TTAATTAATTAATTAATTATTTATTTATTTAAATATTAAAAACAACTCAAATATTTAATTCAAAA
1 TTAATTAATTAATTAATTATTTAATTATTTAAATATTAAAAACAACCCAAATACTTAATTCAAAA
5285446 TAT
66 TAT
* *
5285449 TTAATTATTTAATT-A-TATTTAATTATTTAATTATTAAAAACAACCCAAATACTTAATT-ATTT
1 TTAATTAATTAATTAATTATTTAATTATTTAAATATTAAAAACAACCCAAATACTTAATTCA---
*
5285511 AATTAGT
63 AAATA-T
** **
5285518 TAAATCAACCCAATTAATTAATTAATTAATTAATTATTTATTTATTTAAATATTAAAAACAACCC
1 T---T-AA-TTAATTAATTAATT-A-T--TTAATTATTTAAATA-TT-------AAAAACAACCC
*
5285583 AAATATTTAATTCAAAATAT
49 AAATACTTAATTCAAAATAT
*
5285603 TTAATT-ATT-A--AA-TATTTAATTATTTAATTATTAAAAACAACCCAAATACTTAATT-ATTT
1 TTAATTAATTAATTAATTATTTAATTATTTAAATATTAAAAACAACCCAAATACTTAATTCA---
5285662 AATTATTTAAAT
63 AA--A--T--AT
* * **
5285674 CAACCTAATTAATTAATTAATTATTTATTTATTTATTTAAATATTAAAAACAACTCAAATGTTTA
1 ----TTAATTAATTAATTAATTATTTA---A-TTATTTAAATATTAAAAACAACCCAAATACTTA
5285739 ATTCAAAATAT
58 ATTCAAAATAT
*
5285750 TTAATTATTTAATT-A-TATTTAATTATTTAA
1 TTAATTAATTAATTAATTATTTAATTATTTAA
5285780 TTAAATATTT
Statistics
Matches: 261, Mismatches: 23, Indels: 96
0.69 0.06 0.25
Matches are distributed among these distances:
62 1 0.00
63 22 0.08
65 3 0.01
66 47 0.18
67 3 0.01
68 17 0.07
69 3 0.01
70 8 0.03
71 17 0.07
72 13 0.05
73 3 0.01
74 8 0.03
75 7 0.03
76 8 0.03
77 2 0.01
78 3 0.01
79 5 0.02
80 21 0.08
81 4 0.02
82 3 0.01
83 1 0.00
84 32 0.12
85 3 0.01
86 4 0.02
88 22 0.08
89 1 0.00
ACGTcount: A:0.46, C:0.08, G:0.01, T:0.46
Consensus pattern (68 bp):
TTAATTAATTAATTAATTATTTAATTATTTAAATATTAAAAACAACCCAAATACTTAATTCAAAA
TAT
Found at i:5285510 original size:34 final size:34
Alignment explanation
Indices: 5285467--5285549 Score: 114
Period size: 34 Copynumber: 2.4 Consensus size: 34
5285457 TTAATTATAT
*
5285467 TTAATTATTTAATTA-TTAAAAACAACCCAAATAC
1 TTAATTATTTAATTAGTT-AAAACAACCCAAATAA
* *
5285501 TTAATTATTTAATTAGTTAAATCAACCCAATTAA
1 TTAATTATTTAATTAGTTAAAACAACCCAAATAA
*
5285535 TTAATTAATTAATTA
1 TTAATTATTTAATTA
5285550 ATTATTTATT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
34 42 0.95
35 2 0.05
ACGTcount: A:0.47, C:0.11, G:0.01, T:0.41
Consensus pattern (34 bp):
TTAATTATTTAATTAGTTAAAACAACCCAAATAA
Found at i:5285538 original size:4 final size:4
Alignment explanation
Indices: 5285529--5285553 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
5285519 AAATCAACCC
5285529 AATT AATT AATT AATT AATT AATT A
1 AATT AATT AATT AATT AATT AATT A
5285554 TTTATTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:5285565 original size:54 final size:53
Alignment explanation
Indices: 5285501--5285626 Score: 137
Period size: 54 Copynumber: 2.3 Consensus size: 53
5285491 ACCCAAATAC
* * *
5285501 TTAATTATTTAATTAGTTAAATCAACCCAATTAATTAATT-AATTAATTAATTA
1 TTAATTATTTAATTA-TTAAAACAACCCAAATAATTAATTAAAATAATTAATTA
* * * *
5285554 TTTATTTATTTAAATATTAAAAACAACCCAAATATTTAATTCAAAATATTTAATTA
1 -TTAATTATTTAATTATT-AAAACAACCCAAATAATTAATT-AAAATAATTAATTA
*
5285610 TTAAATATTTAATTATT
1 TTAATTATTTAATTATT
5285627 TAATTATTAA
Statistics
Matches: 59, Mismatches: 10, Indels: 5
0.80 0.14 0.07
Matches are distributed among these distances:
53 2 0.03
54 32 0.54
55 14 0.24
56 11 0.19
ACGTcount: A:0.46, C:0.07, G:0.01, T:0.46
Consensus pattern (53 bp):
TTAATTATTTAATTATTAAAACAACCCAAATAATTAATTAAAATAATTAATTA
Found at i:5285591 original size:34 final size:34
Alignment explanation
Indices: 5285552--5285692 Score: 105
Period size: 34 Copynumber: 4.3 Consensus size: 34
5285542 ATTAATTAAT
*
5285552 TATTTATTTATTTAAATATTAAAAACAACCCAAA
1 TATTTAATTATTTAAATATTAAAAACAACCCAAA
* ** **
5285586 TATTTAATTCA---AAATATT--TAATTA-TTAAA
1 TATTTAATT-ATTTAAATATTAAAAACAACCCAAA
*
5285615 TATTTAATTATTTAATTATTAAAAACAACCCAAA
1 TATTTAATTATTTAAATATTAAAAACAACCCAAA
* * * * * *
5285649 TACTTAATTATTTAATTATTTAAATCAACCTAAT
1 TATTTAATTATTTAAATATTAAAAACAACCCAAA
*
5285683 TAATTAATTA
1 TATTTAATTA
5285693 ATTATTTATT
Statistics
Matches: 82, Mismatches: 18, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
28 1 0.01
29 12 0.15
30 3 0.04
31 6 0.07
32 7 0.09
33 3 0.04
34 49 0.60
35 1 0.01
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (34 bp):
TATTTAATTATTTAAATATTAAAAACAACCCAAA
Found at i:5285602 original size:14 final size:14
Alignment explanation
Indices: 5285583--5285625 Score: 61
Period size: 14 Copynumber: 3.0 Consensus size: 14
5285573 AAAACAACCC
5285583 AAATATTTAATTCA-
1 AAATATTTAATT-AT
5285597 AAATATTTAATTATT
1 AAATATTTAATTA-T
5285612 AAATATTTAATTAT
1 AAATATTTAATTAT
5285626 TTAATTATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 1 0.04
14 13 0.48
15 13 0.48
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (14 bp):
AAATATTTAATTAT
Found at i:5285617 original size:15 final size:15
Alignment explanation
Indices: 5285583--5285626 Score: 65
Period size: 15 Copynumber: 3.0 Consensus size: 15
5285573 AAAACAACCC
5285583 AAATATTTAATTCA--
1 AAATATTTAATT-ATT
5285597 AAATATTTAATTATT
1 AAATATTTAATTATT
5285612 AAATATTTAATTATT
1 AAATATTTAATTATT
5285627 TAATTATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
13 1 0.04
14 12 0.43
15 15 0.54
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (15 bp):
AAATATTTAATTATT
Found at i:5285621 original size:8 final size:8
Alignment explanation
Indices: 5285600--5285634 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
5285590 TAATTCAAAA
5285600 TATTTAAT
1 TATTTAAT
*
5285608 TA-TTAAA
1 TATTTAAT
5285615 TATTTAAT
1 TATTTAAT
5285623 TATTTAAT
1 TATTTAAT
5285631 TATT
1 TATT
5285635 AAAAACAACC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 6 0.25
8 18 0.75
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
TATTTAAT
Found at i:5285636 original size:15 final size:16
Alignment explanation
Indices: 5285597--5285634 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
5285587 ATTTAATTCA
5285597 AAATATTTAATTA-TT
1 AAATATTTAATTATTT
5285612 AAATATTTAATTATTT
1 AAATATTTAATTATTT
*
5285628 AATTATT
1 AAATATT
5285635 AAAAACAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
AAATATTTAATTATTT
Found at i:5285702 original size:34 final size:34
Alignment explanation
Indices: 5285612--5285704 Score: 114
Period size: 34 Copynumber: 2.7 Consensus size: 34
5285602 TTTAATTATT
* *
5285612 AAATATTTAATTATTTAATTATTAAAAACAACCC
1 AAATAATTAATTATTTAATTATTTAAAACAACCC
* * *
5285646 AAATACTTAATTATTTAATTATTTAAATCAACCT
1 AAATAATTAATTATTTAATTATTTAAAACAACCC
* * *
5285680 AATTAATTAATTAATTATTTATTTA
1 AAATAATTAATTATTTAATTATTTA
5285705 TTTATTTAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 51 1.00
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.45
Consensus pattern (34 bp):
AAATAATTAATTATTTAATTATTTAAAACAACCC
Found at i:5285769 original size:18 final size:19
Alignment explanation
Indices: 5285745--5285796 Score: 88
Period size: 18 Copynumber: 2.7 Consensus size: 19
5285735 TTTAATTCAA
5285745 AATATTTAATTATTTAATT
1 AATATTTAATTATTTAATT
5285764 -ATATTTAATTATTTAATT
1 AATATTTAATTATTTAATT
5285782 AAATATTTAATTATT
1 -AATATTTAATTATT
5285797 AAAAACAACC
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
18 18 0.58
20 13 0.42
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
AATATTTAATTATTTAATT
Found at i:5285796 original size:8 final size:8
Alignment explanation
Indices: 5285747--5285782 Score: 54
Period size: 8 Copynumber: 4.2 Consensus size: 8
5285737 TAATTCAAAA
5285747 TATTTAAT
1 TATTTAAT
5285755 TATTTAATT
1 TATTTAA-T
5285764 ATATTTAAT
1 -TATTTAAT
5285773 TATTTAAT
1 TATTTAAT
5285781 TA
1 TA
5285783 AATATTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 17 0.65
9 2 0.08
10 7 0.27
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
TATTTAAT
Found at i:5292010 original size:43 final size:43
Alignment explanation
Indices: 5291846--5292029 Score: 196
Period size: 43 Copynumber: 4.3 Consensus size: 43
5291836 ATCTGTTAAT
* * * * * *
5291846 TTTAGTGGCGTTTGTAGAAAAAACGCCGCTAAAGAACACTATT-
1 TTTAGCGGCGTTTGTTGATAAAGCGCCGCTAAAGACCA-TGTTC
* * * *
5291889 TATAGCGGCGTTT-TTAGAGTAAA-CGCCACTAAAGATCATGCTC
1 TTTAGCGGCGTTTGTT-GA-TAAAGCGCCGCTAAAGACCATGTTC
*
5291932 TTTAGTGGCGTTTGTTGATAAAGCGCCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTTGATAAAGCGCCGCTAAAGACCATGTTC
*
5291975 TTTAGCAGCGTTTGTTGA-AGAAGCGCCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTTGATA-AAGCGCCGCTAAAGACCATGTTC
5292018 TTTAGCGGCGTT
1 TTTAGCGGCGTT
5292030 ATCTTTAGCG
Statistics
Matches: 119, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
42 8 0.07
43 106 0.89
44 5 0.04
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTTGATAAAGCGCCGCTAAAGACCATGTTC
Found at i:5292393 original size:20 final size:20
Alignment explanation
Indices: 5292368--5292408 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
5292358 TAAATAAACA
*
5292368 TAACTTAATATATAAATTAC
1 TAACTTAATAGATAAATTAC
*
5292388 TAACTTAATAGATGAATTAC
1 TAACTTAATAGATAAATTAC
5292408 T
1 T
5292409 TCAAAACAAT
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:0.46, C:0.10, G:0.05, T:0.39
Consensus pattern (20 bp):
TAACTTAATAGATAAATTAC
Found at i:5293656 original size:14 final size:15
Alignment explanation
Indices: 5293621--5293652 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
5293611 TATATTACAA
5293621 ATTTATAGATATAAT
1 ATTTATAGATATAAT
5293636 ATTTATA-ATAT-AT
1 ATTTATAGATATAAT
5293649 ATTT
1 ATTT
5293653 TATATGCACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 6 0.35
14 4 0.24
15 7 0.41
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
ATTTATAGATATAAT
Found at i:5299042 original size:2 final size:2
Alignment explanation
Indices: 5299035--5299062 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5299025 ATATGAACAT
5299035 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
5299063 CATCTTAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:5302166 original size:93 final size:92
Alignment explanation
Indices: 5302069--5302342 Score: 476
Period size: 93 Copynumber: 2.9 Consensus size: 92
5302059 AAGGGATCAG
* * *
5302069 CAGATGCAAGTCAGGATTCTAACTGGGGTAAGAAAAGTTGGAGCACTGGAAATGATGCTGGCCAA
1 CAGATGCAAGTCAGGATTC-AACTGGGGTAAGAAAAGTTGGGGTACTGGAAATGATTCTGGCCAA
5302134 GACTCTGGTTGGGGCAAAAAAGGATCGA
65 GACTCTGGTTGGGGCAAAAAAGGATCGA
5302162 CAGATGCAAGTCAGGATTCAAGCTGGGGTAAGAAAAGTTGGGGTACTGGAAATGATTCTGGCCAA
1 CAGATGCAAGTCAGGATTCAA-CTGGGGTAAGAAAAGTTGGGGTACTGGAAATGATTCTGGCCAA
*
5302227 GACTCTGGTTGGGGCAAAAAAGGATCGG
65 GACTCTGGTTGGGGCAAAAAAGGATCGA
*
5302255 CAGATGCAAGTCAGGATTCAAACTGGGGTAAGAAAAGTTGGGGTGCTGGAAATGATTCTGGCCAA
1 CAGATGCAAGTCAGGATTC-AACTGGGGTAAGAAAAGTTGGGGTACTGGAAATGATTCTGGCCAA
5302320 GACTCTGGTTGGGGCAAAAAAGG
65 GACTCTGGTTGGGGCAAAAAAGG
5302343 TGGTTGGAAC
Statistics
Matches: 174, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
92 2 0.01
93 170 0.98
94 2 0.01
ACGTcount: A:0.32, C:0.14, G:0.34, T:0.20
Consensus pattern (92 bp):
CAGATGCAAGTCAGGATTCAACTGGGGTAAGAAAAGTTGGGGTACTGGAAATGATTCTGGCCAAG
ACTCTGGTTGGGGCAAAAAAGGATCGA
Found at i:5302730 original size:15 final size:15
Alignment explanation
Indices: 5302651--5302730 Score: 58
Period size: 15 Copynumber: 5.3 Consensus size: 15
5302641 TTTGGTGGCA
*
5302651 GAGGTGGTGATGGTG
1 GAGGCGGTGATGGTG
* *
5302666 GAGGCTACG-GA-GGTA
1 GAGGC--GGTGATGGTG
5302681 GAGGCGGTGATGGTG
1 GAGGCGGTGATGGTG
** *
5302696 GAGGCTATGGA-GGTA
1 GAGGCGGT-GATGGTG
5302711 GAGGCGGTGATGGTG
1 GAGGCGGTGATGGTG
5302726 GAGGC
1 GAGGC
5302731 TACAGAGGTA
Statistics
Matches: 48, Mismatches: 11, Indels: 12
0.68 0.15 0.17
Matches are distributed among these distances:
13 1 0.02
14 4 0.08
15 38 0.79
16 4 0.08
17 1 0.02
ACGTcount: A:0.19, C:0.07, G:0.55, T:0.19
Consensus pattern (15 bp):
GAGGCGGTGATGGTG
Found at i:5302756 original size:30 final size:30
Alignment explanation
Indices: 5302650--5302744 Score: 163
Period size: 30 Copynumber: 3.2 Consensus size: 30
5302640 TTTTGGTGGC
*
5302650 AGAGGTGGTGATGGTGGAGGCTACGGAGGT
1 AGAGGCGGTGATGGTGGAGGCTACGGAGGT
*
5302680 AGAGGCGGTGATGGTGGAGGCTATGGAGGT
1 AGAGGCGGTGATGGTGGAGGCTACGGAGGT
*
5302710 AGAGGCGGTGATGGTGGAGGCTACAGAGGT
1 AGAGGCGGTGATGGTGGAGGCTACGGAGGT
5302740 AGAGG
1 AGAGG
5302745 TGGAAGAGGT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 61 1.00
ACGTcount: A:0.22, C:0.07, G:0.53, T:0.18
Consensus pattern (30 bp):
AGAGGCGGTGATGGTGGAGGCTACGGAGGT
Found at i:5303194 original size:120 final size:121
Alignment explanation
Indices: 5302916--5303208 Score: 419
Period size: 120 Copynumber: 2.4 Consensus size: 121
5302906 CTGATCAAGG
5302916 AGGAGGCCAATCCTCCAGTTGGAGTCAATCTGGTGGCTGGAACAAAGAGGGGGGGAACCAGGGCT
1 AGGAGGCCAATCCTCCAGTTGGAGTCAATCTGGTGGCTGGAACAAAGA--GGGGGAACCAGGGCT
* * **
5302981 GGAATGGTGGAACAAGTGGAGGTGGAGGTAGTAAGAGTTGGAATCAATCTGGTGCTGATCA
64 GGAATGGTGGAACAAGTGGAGGT---GGTAGCAAGACTTGGAATCAATCCAGTGCTGATCA
* *
5303042 AGGAGGCCAATCCTCCAGTTGGAGTCAGTCTGGTGGCTGGAACAAAGA-GGGGAACCAGGGGTGG
1 AGGAGGCCAATCCTCCAGTTGGAGTCAATCTGGTGGCTGGAACAAAGAGGGGGAACCAGGGCTGG
*
5303106 AATGGTGGATCAAGTGGAGGT-GTAGCCAAGACTTGGAATCAATCCAGTGCTGATCA
66 AATGGTGGAACAAGTGGAGGTGGTAG-CAAGACTTGGAATCAATCCAGTGCTGATCA
* * * *
5303162 AGGAGGCCAATTCTGCAGTTGGAATCAATCTGGTGGGTGGAACAAAG
1 AGGAGGCCAATCCTCCAGTTGGAGTCAATCTGGTGGCTGGAACAAAG
5303209 GCTCTATTTC
Statistics
Matches: 154, Mismatches: 12, Indels: 8
0.89 0.07 0.05
Matches are distributed among these distances:
119 4 0.03
120 68 0.44
123 35 0.23
126 47 0.31
ACGTcount: A:0.28, C:0.16, G:0.37, T:0.19
Consensus pattern (121 bp):
AGGAGGCCAATCCTCCAGTTGGAGTCAATCTGGTGGCTGGAACAAAGAGGGGGAACCAGGGCTGG
AATGGTGGAACAAGTGGAGGTGGTAGCAAGACTTGGAATCAATCCAGTGCTGATCA
Found at i:5304023 original size:68 final size:68
Alignment explanation
Indices: 5303914--5304051 Score: 258
Period size: 68 Copynumber: 2.0 Consensus size: 68
5303904 GTTTATATAT
* *
5303914 TTCTTGTTATAAAATATGGAACAGTGAAGTGCTTGAACTATAGGGTTTAGTGTTCTTCAAAGTTC
1 TTCTTGTTATAAAATATGGAACAGTGAAGTGCTTGAACTATAGAGTTTAGTGTTCTCCAAAGTTC
5303979 TCA
66 TCA
5303982 TTCTTGTTATAAAATATGGAACAGTGAAGTGCTTGAACTATAGAGTTTAGTGTTCTCCAAAGTTC
1 TTCTTGTTATAAAATATGGAACAGTGAAGTGCTTGAACTATAGAGTTTAGTGTTCTCCAAAGTTC
5304047 TCA
66 TCA
5304050 TT
1 TT
5304052 TTCTAGGATG
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (68 bp):
TTCTTGTTATAAAATATGGAACAGTGAAGTGCTTGAACTATAGAGTTTAGTGTTCTCCAAAGTTC
TCA
Found at i:5305879 original size:196 final size:196
Alignment explanation
Indices: 5305545--5305937 Score: 777
Period size: 196 Copynumber: 2.0 Consensus size: 196
5305535 TCTAAAATAA
5305545 TTAATAACATGCAGGTGCATTGAAATCTCTTATTACAAATGCAATTGAATGAGCAGCGATGCGAA
1 TTAATAACATGCAGGTGCATTGAAATCTCTTATTACAAATGCAATTGAATGAGCAGCGATGCGAA
5305610 TGGGTTTCAAACCATTCACAAGCTTTGGCTTCAACTCTAGTAGCTCCAAAGAGTCTGAAAGTTTC
66 TGGGTTTCAAACCATTCACAAGCTTTGGCTTCAACTCTAGTAGCTCCAAAGAGTCTGAAAGTTTC
5305675 AAAGGTGTTCCGTTCAACAATACGACACTGCTTAAGATGTTTTCATCTTTTGGAGTCAAATGATA
131 AAAGGTGTTCCGTTCAACAATACGACACTGCTTAAGATGTTTTCATCTTTTGGAGTCAAATGATA
5305740 T
196 T
*
5305741 TTAATAACATGCAGGTGCATTGAAATCTCTTATTACAAATGCAGTTGAATGAGCAGCGATGCGAA
1 TTAATAACATGCAGGTGCATTGAAATCTCTTATTACAAATGCAATTGAATGAGCAGCGATGCGAA
5305806 TGGGTTTCAAACCATTCACAAGCTTTGGCTTCAACTCTAGTAGCTCCAAAGAGTCTGAAAGTTTC
66 TGGGTTTCAAACCATTCACAAGCTTTGGCTTCAACTCTAGTAGCTCCAAAGAGTCTGAAAGTTTC
5305871 AAAGGTGTTCCGTTCAACAATACGACACTGCTTAAGATGTTTTCATCTTTTGGAGTCAAATGATA
131 AAAGGTGTTCCGTTCAACAATACGACACTGCTTAAGATGTTTTCATCTTTTGGAGTCAAATGATA
5305936 T
196 T
5305937 T
1 T
5305938 CTTCTCGCTC
Statistics
Matches: 196, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
196 196 1.00
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Consensus pattern (196 bp):
TTAATAACATGCAGGTGCATTGAAATCTCTTATTACAAATGCAATTGAATGAGCAGCGATGCGAA
TGGGTTTCAAACCATTCACAAGCTTTGGCTTCAACTCTAGTAGCTCCAAAGAGTCTGAAAGTTTC
AAAGGTGTTCCGTTCAACAATACGACACTGCTTAAGATGTTTTCATCTTTTGGAGTCAAATGATA
T
Found at i:5306121 original size:15 final size:15
Alignment explanation
Indices: 5306084--5306122 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
5306074 AATAAAAATT
5306084 TAATTAATTAATAAA
1 TAATTAATTAATAAA
*
5306099 TAAATAATTAAATAAA
1 TAATTAATT-AATAAA
5306115 -AATTAATT
1 TAATTAATT
5306123 GAGTCAACGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TAATTAATTAATAAA
Found at i:5306282 original size:15 final size:16
Alignment explanation
Indices: 5306262--5306291 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5306252 TTAACTAATA
5306262 AAATTAA-AACAAATG
1 AAATTAACAACAAATG
5306277 AAATTAACAACAAAT
1 AAATTAACAACAAAT
5306292 ACAACGGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.67, C:0.10, G:0.03, T:0.20
Consensus pattern (16 bp):
AAATTAACAACAAATG
Found at i:5311122 original size:15 final size:16
Alignment explanation
Indices: 5311104--5311142 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
5311094 AAGATATTTT
5311104 AACAAATAAAATTAA-
1 AACAAATAAAATTAAC
* *
5311119 AACAAATGAAGTTAAC
1 AACAAATAAAATTAAC
5311135 AACAAATA
1 AACAAATA
5311143 TGGTGGTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.67, C:0.10, G:0.05, T:0.18
Consensus pattern (16 bp):
AACAAATAAAATTAAC
Found at i:5320685 original size:305 final size:305
Alignment explanation
Indices: 5320134--5320743 Score: 1193
Period size: 305 Copynumber: 2.0 Consensus size: 305
5320124 ACGCCCAAAA
5320134 TTGGTACCGCATTGATTGCTTTCGGGTCTTTTGTTCTAAAACTTTAAAAACTAGAGTAAAGCTTA
1 TTGGTACCGCATTGATTGCTTTCGGGTCTTTTGTTCTAAAACTTTAAAAACTAGAGTAAAGCTTA
5320199 AAATACGATTTTTAAAAGACTTCGCGTGATTTTCAAAAATACTATTCGAGGGAAATTATCCGTAT
66 AAATACGATTTTTAAAAGACTTCGCGTGATTTTCAAAAATACTATTCGAGGGAAATTATCCGTAT
*
5320264 GTTTCGAATTTCTAAAAGAACTGGAAATTGTGCTCAACACGTTAGGGCACTATGTTCTCAGATTT
131 GTTTCGAATTTCTAAAAGAACTGGAAATCGTGCTCAACACGTTAGGGCACTATGTTCTCAGATTT
5320329 TCGAAGCTGAAGGACATTTTGAAAGACTTTAAAGAGAATATTCGATCGTGTGAGTTATACGAAAG
196 TCGAAGCTGAAGGACATTTTGAAAGACTTTAAAGAGAATATTCGATCGTGTGAGTTATACGAAAG
5320394 TCACACCCAGCACGTTAGGGCATGATTTTTCGAAGTCTTCGCACG
261 TCACACCCAGCACGTTAGGGCATGATTTTTCGAAGTCTTCGCACG
*
5320439 TTGGTACCGCATTGATTGCTTTCGGGTCTTTTGTTCTAAAACTTTAAAAACTAGATTAAAGCTTA
1 TTGGTACCGCATTGATTGCTTTCGGGTCTTTTGTTCTAAAACTTTAAAAACTAGAGTAAAGCTTA
*
5320504 AAATACGATTTTTAAAAGACTTTGCGTGATTTTCAAAAATACTATTCGAGGGAAATTATCCGTAT
66 AAATACGATTTTTAAAAGACTTCGCGTGATTTTCAAAAATACTATTCGAGGGAAATTATCCGTAT
5320569 GTTTCGAATTTCTAAAAGAACTGGAAATCGTGCTCAACACGTTAGGGCACTATGTTCTCAGATTT
131 GTTTCGAATTTCTAAAAGAACTGGAAATCGTGCTCAACACGTTAGGGCACTATGTTCTCAGATTT
5320634 TCGAAGCTGAAGGACATTTTGAAAGACTTTAAAGAGAATATTCGATCGTGTGAGTTATACGAAAG
196 TCGAAGCTGAAGGACATTTTGAAAGACTTTAAAGAGAATATTCGATCGTGTGAGTTATACGAAAG
5320699 TCACACCCAGCACGTTAGGGCATGATTTTTCGAAGTCTTCGCACG
261 TCACACCCAGCACGTTAGGGCATGATTTTTCGAAGTCTTCGCACG
5320744 AAAGGATATT
Statistics
Matches: 302, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
305 302 1.00
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (305 bp):
TTGGTACCGCATTGATTGCTTTCGGGTCTTTTGTTCTAAAACTTTAAAAACTAGAGTAAAGCTTA
AAATACGATTTTTAAAAGACTTCGCGTGATTTTCAAAAATACTATTCGAGGGAAATTATCCGTAT
GTTTCGAATTTCTAAAAGAACTGGAAATCGTGCTCAACACGTTAGGGCACTATGTTCTCAGATTT
TCGAAGCTGAAGGACATTTTGAAAGACTTTAAAGAGAATATTCGATCGTGTGAGTTATACGAAAG
TCACACCCAGCACGTTAGGGCATGATTTTTCGAAGTCTTCGCACG
Found at i:5321097 original size:29 final size:29
Alignment explanation
Indices: 5321064--5321201 Score: 107
Period size: 29 Copynumber: 4.7 Consensus size: 29
5321054 TTGGGATGAT
* *
5321064 GGGGGTAAAATGATAATTTTTAGACACTC
1 GGGGGTAAAATGGTAATTTTTAGACATTC
* ** **
5321093 GGGGGCAAAATGGTAATTTTCGGAGGTTC
1 GGGGGTAAAATGGTAATTTTTAGACATTC
* * * *
5321122 AGGGGTAAAATGGTCATTTTTGGAAAGTTC
1 GGGGGTAAAATGGTAATTTTTAGACA-TTC
** * *
5321152 GGGATTAAAAAT-GAAATTTTTAAACATTC
1 GGGGGT-AAAATGGTAATTTTTAGACATTC
5321181 GGGGGTAAAAATGGTAATTTT
1 GGGGGT-AAAATGGTAATTTT
5321202 CAAAAATTTT
Statistics
Matches: 82, Mismatches: 24, Indels: 5
0.74 0.22 0.05
Matches are distributed among these distances:
29 55 0.67
30 22 0.27
31 5 0.06
ACGTcount: A:0.33, C:0.07, G:0.28, T:0.32
Consensus pattern (29 bp):
GGGGGTAAAATGGTAATTTTTAGACATTC
Found at i:5321171 original size:30 final size:30
Alignment explanation
Indices: 5321099--5321398 Score: 183
Period size: 29 Copynumber: 10.1 Consensus size: 30
5321089 ACTCGGGGGC
* *
5321099 AAAATGGTAATTTTCGG-AGGTTCAGGGG-T-
1 AAAAT-GTAATTTTTGGAAAGTTC-GGGGTTA
* *
5321128 AAAATGGTCATTTTTGGAAAGTTCGGGATTA
1 AAAAT-GTAATTTTTGGAAAGTTCGGGGTTA
* * *
5321159 AAAATGAAATTTTT--AAACATTCGGGGGTA
1 AAAATGTAATTTTTGGAAA-GTTCGGGGTTA
*** * * *
5321188 AAAATGGTAATTTTCAAAAATTTTGGGGTCA
1 AAAAT-GTAATTTTTGGAAAGTTCGGGGTTA
* *
5321219 AAAATGGAATTTTTGG-AAGTTTGAGGG-TA
1 AAAATGTAATTTTTGGAAAGTTCG-GGGTTA
* * ** *
5321248 GAAATGTGATTTTTGGAAAGTTTAGGGTCA
1 AAAATGTAATTTTTGGAAAGTTCGGGGTTA
*
5321278 AAAATGTAATTTTTGG-ATGTTCGGGGGTT-
1 AAAATGTAATTTTTGGAAAGTTC-GGGGTTA
* *
5321307 AAAATGTAATTTTTAGAAAGTTCAGGGGTCA
1 AAAATGTAATTTTTGGAAAGTTC-GGGGTTA
** * *
5321338 AAATATG--ATTTTTTAAAAGTTTGGGG-TC
1 AAA-ATGTAATTTTTGGAAAGTTCGGGGTTA
*
5321366 AAAATGTAATTTTTGGAAAGTTCGGGGTCA
1 AAAATGTAATTTTTGGAAAGTTCGGGGTTA
5321396 AAA
1 AAA
5321399 TATGATTTCT
Statistics
Matches: 208, Mismatches: 46, Indels: 33
0.72 0.16 0.11
Matches are distributed among these distances:
27 3 0.01
28 6 0.03
29 93 0.45
30 80 0.38
31 20 0.10
32 6 0.03
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.35
Consensus pattern (30 bp):
AAAATGTAATTTTTGGAAAGTTCGGGGTTA
Found at i:5321187 original size:59 final size:56
Alignment explanation
Indices: 5321123--5321403 Score: 222
Period size: 59 Copynumber: 4.8 Consensus size: 56
5321113 CGGAGGTTCA
* * *
5321123 GGGGTAAAATGGTCATTTTTGGAAAGTTCGGGATTAAAAATGAAATTTTTAAACATTCG
1 GGGGTAAAAT-GTAATTTTTGGAAAGTTCGGGGTCAAAAATG-AATTTTTAAA-ATTCG
*** * * * * *
5321182 GGGGTAAAAATGGTAATTTTCAAAAATTTTGGGGTCAAAAATGGAATTTTTGGAAGTTTG
1 GGGGT-AAAAT-GTAATTTTTGGAAAGTTCGGGGTCAAAAAT-GAATTTTT-AAAATTCG
* * ** * **
5321242 AGGGTAGAAATGTGATTTTTGGAAAGTTTAGGGTCAAAAATGTAATTTTTGGATGTTCG
1 GGGGTA-AAATGTAATTTTTGGAAAGTTCGGGGTCAAAAATG-AATTTTT-AAAATTCG
* * *
5321301 GGGGTTAAAATGTAATTTTTAGAAAGTTCAGGGGTCAAAATATGATTTTTTAAAAGTT-T
1 GGGG-TAAAATGTAATTTTTGGAAAGTTC-GGGGTCAAAA-ATGAATTTTTAAAA-TTCG
5321360 GGGGTCAAAATGTAATTTTTGGAAAGTTCGGGGTCAAAATATGA
1 GGGGT-AAAATGTAATTTTTGGAAAGTTCGGGGTCAAAA-ATGA
5321404 TTTCTGGACA
Statistics
Matches: 181, Mismatches: 31, Indels: 21
0.78 0.13 0.09
Matches are distributed among these distances:
58 17 0.09
59 93 0.51
60 65 0.36
61 6 0.03
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.35
Consensus pattern (56 bp):
GGGGTAAAATGTAATTTTTGGAAAGTTCGGGGTCAAAAATGAATTTTTAAAATTCG
Found at i:5321385 original size:29 final size:29
Alignment explanation
Indices: 5321182--5321399 Score: 190
Period size: 29 Copynumber: 7.4 Consensus size: 29
5321172 TAAACATTCG
* *** *
5321182 GGGGTAAAAATGGTAATTTTCAAAAATTTT
1 GGGGTCAAAAT-GTAATTTTTGGAAAGTTT
*
5321212 GGGGTCAAAAATGGAATTTTTGG-AAGTTT
1 GGGGTC-AAAATGTAATTTTTGGAAAGTTT
*
5321241 GAGGGT-AGAAATGTGATTTTTGGAAAGTTT
1 G-GGGTCA-AAATGTAATTTTTGGAAAGTTT
* * *
5321271 AGGGTCAAAAATGTAATTTTTGG-ATGTTCG
1 GGGGTC-AAAATGTAATTTTTGGAAAGTT-T
* * *
5321301 GGGGTTAAAATGTAATTTTTAGAAAGTTCA
1 GGGGTCAAAATGTAATTTTTGGAAAGTT-T
* * **
5321331 GGGGTCAAAATATGATTTTTTAAAAGTTT
1 GGGGTCAAAATGTAATTTTTGGAAAGTTT
*
5321360 GGGGTCAAAATGTAATTTTTGGAAAGTTC
1 GGGGTCAAAATGTAATTTTTGGAAAGTTT
5321389 GGGGTCAAAAT
1 GGGGTCAAAAT
5321400 ATGATTTCTG
Statistics
Matches: 152, Mismatches: 28, Indels: 17
0.77 0.14 0.09
Matches are distributed among these distances:
28 1 0.01
29 77 0.51
30 68 0.45
31 6 0.04
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.36
Consensus pattern (29 bp):
GGGGTCAAAATGTAATTTTTGGAAAGTTT
Found at i:5325271 original size:15 final size:16
Alignment explanation
Indices: 5325253--5325290 Score: 69
Period size: 15 Copynumber: 2.4 Consensus size: 16
5325243 AAGATATTTT
5325253 AACAAATGAAATTAA-
1 AACAAATGAAATTAAC
5325268 AACAAATGAAATTAAC
1 AACAAATGAAATTAAC
5325284 AACAAAT
1 AACAAAT
5325291 ACGGTGGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 15 0.68
16 7 0.32
ACGTcount: A:0.66, C:0.11, G:0.05, T:0.18
Consensus pattern (16 bp):
AACAAATGAAATTAAC
Found at i:5329417 original size:305 final size:305
Alignment explanation
Indices: 5328866--5329471 Score: 1194
Period size: 305 Copynumber: 2.0 Consensus size: 305
5328856 CCAAAATTGA
5328866 TACCGCATTGATTGCTTTCGGGTCTTTTGTTCTAAAACTTTAAAAACTAGAGTAAAGCTTAAAAT
1 TACCGCATTGATTGCTTTCGGGTCTTTTGTTCTAAAACTTTAAAAACTAGAGTAAAGCTTAAAAT
5328931 ACGATTTTTAAAAGACTTCGCGTGATTTTCAAAAATACTATTCGAGGGAAATTATCCGTATGTTT
66 ACGATTTTTAAAAGACTTCGCGTGATTTTCAAAAATACTATTCGAGGGAAATTATCCGTATGTTT
*
5328996 CGAATTTCTAAAAGAACTGGAAATTGTGCTCAACACGTTAGGGCACTATGTTCTCAGATTTTCGA
131 CGAATTTCTAAAAGAACTGGAAATCGTGCTCAACACGTTAGGGCACTATGTTCTCAGATTTTCGA
5329061 AGCTGAAGGACATTTTGAAAGACTTTAAAGAGAATATTCGATCGTGTGAGTTATACGAAAGTCAC
196 AGCTGAAGGACATTTTGAAAGACTTTAAAGAGAATATTCGATCGTGTGAGTTATACGAAAGTCAC
5329126 ACCCAGCACGTTAGGGCATGATTTTTCGAAGTCTTCGCACGTTGG
261 ACCCAGCACGTTAGGGCATGATTTTTCGAAGTCTTCGCACGTTGG
5329171 TACCGCATTGATTGCTTTCGGGTCTTTTGTTCTAAAACTTTAAAAACTAGAGTAAAGCTTAAAAT
1 TACCGCATTGATTGCTTTCGGGTCTTTTGTTCTAAAACTTTAAAAACTAGAGTAAAGCTTAAAAT
*
5329236 ACGATTTTTAAAAGACTTTGCGTGATTTTCAAAAATACTATTCGAGGGAAATTATCCGTATGTTT
66 ACGATTTTTAAAAGACTTCGCGTGATTTTCAAAAATACTATTCGAGGGAAATTATCCGTATGTTT
5329301 CGAATTTCTAAAAGAACTGGAAATCGTGCTCAACACGTTAGGGCACTATGTTCTCAGATTTTCGA
131 CGAATTTCTAAAAGAACTGGAAATCGTGCTCAACACGTTAGGGCACTATGTTCTCAGATTTTCGA
5329366 AGCTGAAGGACATTTTGAAAGACTTTAAAGAGAATATTCGATCGTGTGAGTTATACGAAAGTCAC
196 AGCTGAAGGACATTTTGAAAGACTTTAAAGAGAATATTCGATCGTGTGAGTTATACGAAAGTCAC
5329431 ACCCAGCACGTTAGGGCATGATTTTTCGAAGTCTTCGCACG
261 ACCCAGCACGTTAGGGCATGATTTTTCGAAGTCTTCGCACG
5329472 AAAGGATATT
Statistics
Matches: 299, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
305 299 1.00
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (305 bp):
TACCGCATTGATTGCTTTCGGGTCTTTTGTTCTAAAACTTTAAAAACTAGAGTAAAGCTTAAAAT
ACGATTTTTAAAAGACTTCGCGTGATTTTCAAAAATACTATTCGAGGGAAATTATCCGTATGTTT
CGAATTTCTAAAAGAACTGGAAATCGTGCTCAACACGTTAGGGCACTATGTTCTCAGATTTTCGA
AGCTGAAGGACATTTTGAAAGACTTTAAAGAGAATATTCGATCGTGTGAGTTATACGAAAGTCAC
ACCCAGCACGTTAGGGCATGATTTTTCGAAGTCTTCGCACGTTGG
Found at i:5329899 original size:30 final size:30
Alignment explanation
Indices: 5329827--5330126 Score: 183
Period size: 29 Copynumber: 10.1 Consensus size: 30
5329817 ACTCGGGGGC
* *
5329827 AAAATGGTAA-TTTTCGAAGGTTCAGGGG-T-
1 AAAAT-GTAATTTTTGGAAAGTTC-GGGGTTA
* *
5329856 AAAATGGTCATTTTTGGAAAGTTCGGGATTA
1 AAAAT-GTAATTTTTGGAAAGTTCGGGGTTA
* * *
5329887 AAAATGAAATTTTT--AAACATTCGGGGGTA
1 AAAATGTAATTTTTGGAAA-GTTCGGGGTTA
*** * * *
5329916 AAAATGGTAATTTTCAAAAATTTTGGGGTCA
1 AAAAT-GTAATTTTTGGAAAGTTCGGGGTTA
* *
5329947 AAAATGGAATTTTTGG-AAGTTTGAGGG-TA
1 AAAATGTAATTTTTGGAAAGTTCG-GGGTTA
* * ** *
5329976 GAAATGTGATTTTTGGAAAGTTTAGGGTCA
1 AAAATGTAATTTTTGGAAAGTTCGGGGTTA
*
5330006 AAAATGTAATTTTTGG-ATGTTCGGGGGTT-
1 AAAATGTAATTTTTGGAAAGTTC-GGGGTTA
* *
5330035 AAAATGTAATTTTTAGAAAGTTCAGGGGTCA
1 AAAATGTAATTTTTGGAAAGTTC-GGGGTTA
** * *
5330066 AAATATG--ATTTTTTAAAAGTTTGGGG-TC
1 AAA-ATGTAATTTTTGGAAAGTTCGGGGTTA
*
5330094 AAAATGTAATTTTTGGAAAGTTCGGGGTCA
1 AAAATGTAATTTTTGGAAAGTTCGGGGTTA
5330124 AAA
1 AAA
5330127 TATGATTTCT
Statistics
Matches: 208, Mismatches: 46, Indels: 33
0.72 0.16 0.11
Matches are distributed among these distances:
27 3 0.01
28 6 0.03
29 87 0.42
30 86 0.41
31 20 0.10
32 6 0.03
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.35
Consensus pattern (30 bp):
AAAATGTAATTTTTGGAAAGTTCGGGGTTA
Found at i:5329915 original size:59 final size:56
Alignment explanation
Indices: 5329851--5330131 Score: 222
Period size: 59 Copynumber: 4.8 Consensus size: 56
5329841 CGAAGGTTCA
* * *
5329851 GGGGTAAAATGGTCATTTTTGGAAAGTTCGGGATTAAAAATGAAATTTTTAAACATTCG
1 GGGGTAAAAT-GTAATTTTTGGAAAGTTCGGGGTCAAAAATG-AATTTTTAAA-ATTCG
*** * * * * *
5329910 GGGGTAAAAATGGTAATTTTCAAAAATTTTGGGGTCAAAAATGGAATTTTTGGAAGTTTG
1 GGGGT-AAAAT-GTAATTTTTGGAAAGTTCGGGGTCAAAAAT-GAATTTTT-AAAATTCG
* * ** * **
5329970 AGGGTAGAAATGTGATTTTTGGAAAGTTTAGGGTCAAAAATGTAATTTTTGGATGTTCG
1 GGGGTA-AAATGTAATTTTTGGAAAGTTCGGGGTCAAAAATG-AATTTTT-AAAATTCG
* * *
5330029 GGGGTTAAAATGTAATTTTTAGAAAGTTCAGGGGTCAAAATATGATTTTTTAAAAGTT-T
1 GGGG-TAAAATGTAATTTTTGGAAAGTTC-GGGGTCAAAA-ATGAATTTTTAAAA-TTCG
5330088 GGGGTCAAAATGTAATTTTTGGAAAGTTCGGGGTCAAAATATGA
1 GGGGT-AAAATGTAATTTTTGGAAAGTTCGGGGTCAAAA-ATGA
5330132 TTTCTGGACA
Statistics
Matches: 181, Mismatches: 31, Indels: 21
0.78 0.13 0.09
Matches are distributed among these distances:
58 17 0.09
59 93 0.51
60 65 0.36
61 6 0.03
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.35
Consensus pattern (56 bp):
GGGGTAAAATGTAATTTTTGGAAAGTTCGGGGTCAAAAATGAATTTTTAAAATTCG
Found at i:5329929 original size:29 final size:30
Alignment explanation
Indices: 5329792--5329959 Score: 96
Period size: 29 Copynumber: 5.7 Consensus size: 30
5329782 TTGGGATGAT
* * * *
5329792 GGGGGT-AAAATGATAATTTTTAGACACTC
1 GGGGGTAAAAATGGTAATTTTCAAACATTC
* * **
5329821 GGGGG-CAAAATGGTAATTTTCGAAGGTTC
1 GGGGGTAAAAATGGTAATTTTCAAACATTC
* * * *
5329850 AGGGGT-AAAATGGTCATTTTTGGAAA-GTTC
1 GGGGGTAAAAATGGT-AATTTT-CAAACATTC
** * *
5329880 GGGATTAAAAAT-GAAATTTTTAAACATTC
1 GGGGGTAAAAATGGTAATTTTCAAACATTC
* *
5329909 GGGGGTAAAAATGGTAATTTTCAAAAATTT
1 GGGGGTAAAAATGGTAATTTTCAAACATTC
*
5329939 TGGGGTCAAAAATGG-AATTTT
1 GGGGGT-AAAAATGGTAATTTT
5329960 TGGAAGTTTG
Statistics
Matches: 106, Mismatches: 25, Indels: 15
0.73 0.17 0.10
Matches are distributed among these distances:
28 3 0.03
29 51 0.48
30 37 0.35
31 15 0.14
ACGTcount: A:0.35, C:0.07, G:0.26, T:0.32
Consensus pattern (30 bp):
GGGGGTAAAAATGGTAATTTTCAAACATTC
Found at i:5329967 original size:89 final size:89
Alignment explanation
Indices: 5329798--5329964 Score: 212
Period size: 89 Copynumber: 1.9 Consensus size: 89
5329788 TGATGGGGGT
* * * **
5329798 AAAATGATAATTTTTAGACACTCGGGGGCAAAATGGTAATTTTCGAAGGTTCAGGGGTAAAATGG
1 AAAATGATAATTTTTAAACACTCGGGGGAAAAATGGTAATTTTCAAAAATTCAGGGGTAAAATGG
*
5329863 TCATTTTTGGAAAGTTCGGGATTA
66 TAATTTTTGGAAAGTTCGGGATTA
* **
5329887 AAAATGA-AATTTTTAAACATTCGGGGGTAAAAATGGTAATTTTCAAAAATTTTGGGGTCAAAAA
1 AAAATGATAATTTTTAAACACTCGGGGG-AAAAATGGTAATTTTCAAAAATTCAGGGGT--AAAA
5329951 TGG-AATTTTTGGAA
63 TGGTAATTTTTGGAA
5329965 GTTTGAGGGT
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
88 18 0.27
89 31 0.47
90 10 0.15
91 7 0.11
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.32
Consensus pattern (89 bp):
AAAATGATAATTTTTAAACACTCGGGGGAAAAATGGTAATTTTCAAAAATTCAGGGGTAAAATGG
TAATTTTTGGAAAGTTCGGGATTA
Found at i:5330113 original size:29 final size:29
Alignment explanation
Indices: 5329910--5330127 Score: 190
Period size: 29 Copynumber: 7.4 Consensus size: 29
5329900 TAAACATTCG
* *** *
5329910 GGGGTAAAAATGGTAATTTTCAAAAATTTT
1 GGGGTCAAAAT-GTAATTTTTGGAAAGTTT
*
5329940 GGGGTCAAAAATGGAATTTTTGG-AAGTTT
1 GGGGTC-AAAATGTAATTTTTGGAAAGTTT
*
5329969 GAGGGT-AGAAATGTGATTTTTGGAAAGTTT
1 G-GGGTCA-AAATGTAATTTTTGGAAAGTTT
* * *
5329999 AGGGTCAAAAATGTAATTTTTGG-ATGTTCG
1 GGGGTC-AAAATGTAATTTTTGGAAAGTT-T
* * *
5330029 GGGGTTAAAATGTAATTTTTAGAAAGTTCA
1 GGGGTCAAAATGTAATTTTTGGAAAGTT-T
* * **
5330059 GGGGTCAAAATATGATTTTTTAAAAGTTT
1 GGGGTCAAAATGTAATTTTTGGAAAGTTT
*
5330088 GGGGTCAAAATGTAATTTTTGGAAAGTTC
1 GGGGTCAAAATGTAATTTTTGGAAAGTTT
5330117 GGGGTCAAAAT
1 GGGGTCAAAAT
5330128 ATGATTTCTG
Statistics
Matches: 152, Mismatches: 28, Indels: 17
0.77 0.14 0.09
Matches are distributed among these distances:
28 1 0.01
29 77 0.51
30 68 0.45
31 6 0.04
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.36
Consensus pattern (29 bp):
GGGGTCAAAATGTAATTTTTGGAAAGTTT
Found at i:5333991 original size:15 final size:16
Alignment explanation
Indices: 5333973--5334010 Score: 69
Period size: 15 Copynumber: 2.4 Consensus size: 16
5333963 AAGATATTTT
5333973 AACAAATGAAATTAA-
1 AACAAATGAAATTAAC
5333988 AACAAATGAAATTAAC
1 AACAAATGAAATTAAC
5334004 AACAAAT
1 AACAAAT
5334011 ACGGTGGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 15 0.68
16 7 0.32
ACGTcount: A:0.66, C:0.11, G:0.05, T:0.18
Consensus pattern (16 bp):
AACAAATGAAATTAAC
Found at i:5338132 original size:305 final size:305
Alignment explanation
Indices: 5337581--5338190 Score: 1202
Period size: 305 Copynumber: 2.0 Consensus size: 305
5337571 ACGCCCAAAA
5337581 TTGGTACCGCATTGATTGCTTTCGGGTCTTTTGTTCTAAAACTTTAAAAACTAGAGTAAAGCTTA
1 TTGGTACCGCATTGATTGCTTTCGGGTCTTTTGTTCTAAAACTTTAAAAACTAGAGTAAAGCTTA
5337646 AAATACGATTTTTAAAAGACTTCGCGTGATTTTCAAAAATACTATTCGAGGGAAATTATCCGTAT
66 AAATACGATTTTTAAAAGACTTCGCGTGATTTTCAAAAATACTATTCGAGGGAAATTATCCGTAT
*
5337711 GTTTCGAATTTCTAAAAGAACTGGAAATTGTGCTCAACACGTTAGGGCACTATGTTCTCAGATTT
131 GTTTCGAATTTCTAAAAGAACTGGAAATCGTGCTCAACACGTTAGGGCACTATGTTCTCAGATTT
5337776 TCGAAGCTGAAGGACATTTTGAAAGACTTTAAAGAGAATATTCGATCGTGTGAGTTATACGAAAG
196 TCGAAGCTGAAGGACATTTTGAAAGACTTTAAAGAGAATATTCGATCGTGTGAGTTATACGAAAG
5337841 TCACACCCAGCACGTTAGGGCATGATTTTTCGAAGTCTTCGCACG
261 TCACACCCAGCACGTTAGGGCATGATTTTTCGAAGTCTTCGCACG
5337886 TTGGTACCGCATTGATTGCTTTCGGGTCTTTTGTTCTAAAACTTTAAAAACTAGAGTAAAGCTTA
1 TTGGTACCGCATTGATTGCTTTCGGGTCTTTTGTTCTAAAACTTTAAAAACTAGAGTAAAGCTTA
*
5337951 AAATACGATTTTTAAAAGACTTTGCGTGATTTTCAAAAATACTATTCGAGGGAAATTATCCGTAT
66 AAATACGATTTTTAAAAGACTTCGCGTGATTTTCAAAAATACTATTCGAGGGAAATTATCCGTAT
5338016 GTTTCGAATTTCTAAAAGAACTGGAAATCGTGCTCAACACGTTAGGGCACTATGTTCTCAGATTT
131 GTTTCGAATTTCTAAAAGAACTGGAAATCGTGCTCAACACGTTAGGGCACTATGTTCTCAGATTT
5338081 TCGAAGCTGAAGGACATTTTGAAAGACTTTAAAGAGAATATTCGATCGTGTGAGTTATACGAAAG
196 TCGAAGCTGAAGGACATTTTGAAAGACTTTAAAGAGAATATTCGATCGTGTGAGTTATACGAAAG
5338146 TCACACCCAGCACGTTAGGGCATGATTTTTCGAAGTCTTCGCACG
261 TCACACCCAGCACGTTAGGGCATGATTTTTCGAAGTCTTCGCACG
5338191 AAAGGATATT
Statistics
Matches: 303, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
305 303 1.00
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.32
Consensus pattern (305 bp):
TTGGTACCGCATTGATTGCTTTCGGGTCTTTTGTTCTAAAACTTTAAAAACTAGAGTAAAGCTTA
AAATACGATTTTTAAAAGACTTCGCGTGATTTTCAAAAATACTATTCGAGGGAAATTATCCGTAT
GTTTCGAATTTCTAAAAGAACTGGAAATCGTGCTCAACACGTTAGGGCACTATGTTCTCAGATTT
TCGAAGCTGAAGGACATTTTGAAAGACTTTAAAGAGAATATTCGATCGTGTGAGTTATACGAAAG
TCACACCCAGCACGTTAGGGCATGATTTTTCGAAGTCTTCGCACG
Found at i:5338544 original size:29 final size:29
Alignment explanation
Indices: 5338511--5338648 Score: 107
Period size: 29 Copynumber: 4.7 Consensus size: 29
5338501 TTGGGATGAT
* *
5338511 GGGGGTAAAATGATAATTTTTAGACACTC
1 GGGGGTAAAATGGTAATTTTTAGACATTC
* ** **
5338540 GGGGGCAAAATGGTAATTTTCGGAGGTTC
1 GGGGGTAAAATGGTAATTTTTAGACATTC
* * * *
5338569 AGGGGTAAAATGGTCATTTTTGGAAAGTTC
1 GGGGGTAAAATGGTAATTTTTAGACA-TTC
** * *
5338599 GGGATTAAAAAT-GAAATTTTTAAACATTC
1 GGGGGT-AAAATGGTAATTTTTAGACATTC
5338628 GGGGGTAAAAATGGTAATTTT
1 GGGGGT-AAAATGGTAATTTT
5338649 CAAAAATTTT
Statistics
Matches: 82, Mismatches: 24, Indels: 5
0.74 0.22 0.05
Matches are distributed among these distances:
29 55 0.67
30 22 0.27
31 5 0.06
ACGTcount: A:0.33, C:0.07, G:0.28, T:0.32
Consensus pattern (29 bp):
GGGGGTAAAATGGTAATTTTTAGACATTC
Found at i:5338618 original size:30 final size:30
Alignment explanation
Indices: 5338546--5338845 Score: 174
Period size: 29 Copynumber: 10.1 Consensus size: 30
5338536 ACTCGGGGGC
* *
5338546 AAAATGGTAATTTTCGG-AGGTTCAGGGG-T-
1 AAAAT-GTAATTTTTGGAAAGTTC-GGGGTTA
* *
5338575 AAAATGGTCATTTTTGGAAAGTTCGGGATTA
1 AAAAT-GTAATTTTTGGAAAGTTCGGGGTTA
* * *
5338606 AAAATGAAATTTTT--AAACATTCGGGGGTA
1 AAAATGTAATTTTTGGAAA-GTTCGGGGTTA
*** * * *
5338635 AAAATGGTAATTTTCAAAAATTTTGGGGTCA
1 AAAAT-GTAATTTTTGGAAAGTTCGGGGTTA
* *
5338666 AAAATGGAATTTTTGG-AAGTTTGAGGG-TA
1 AAAATGTAATTTTTGGAAAGTTCG-GGGTTA
* * ** *
5338695 GAAATGTGATTTTTGGAAAGTTTAGGGTCA
1 AAAATGTAATTTTTGGAAAGTTCGGGGTTA
* *
5338725 AAAATGGAATTTTTGG-ATGTTCGGGGGTT-
1 AAAATGTAATTTTTGGAAAGTTC-GGGGTTA
* *
5338754 AAAATGTAATTTTTAGAAAGTTCAGGGGTCA
1 AAAATGTAATTTTTGGAAAGTTC-GGGGTTA
** * *
5338785 AAATATG--ATTTTTTAAAAGTTTGGGG-TC
1 AAA-ATGTAATTTTTGGAAAGTTCGGGGTTA
*
5338813 AAAATGTAATTTTTGGAAAGTTCGGGGTCA
1 AAAATGTAATTTTTGGAAAGTTCGGGGTTA
5338843 AAA
1 AAA
5338846 TATGATTTCT
Statistics
Matches: 206, Mismatches: 48, Indels: 33
0.72 0.17 0.11
Matches are distributed among these distances:
27 3 0.01
28 6 0.03
29 92 0.45
30 79 0.38
31 20 0.10
32 6 0.03
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.35
Consensus pattern (30 bp):
AAAATGTAATTTTTGGAAAGTTCGGGGTTA
Found at i:5338634 original size:59 final size:57
Alignment explanation
Indices: 5338570--5338845 Score: 232
Period size: 59 Copynumber: 4.7 Consensus size: 57
5338560 CGGAGGTTCA
* * * *
5338570 GGGGTAAAATGGTCATTTTTGGAAAGTTCGGGATTAAAAATGAAATTTTTAAACATTCG
1 GGGGTAAAAT-GTAATTTTTGGAAAGTTCGGGGTCAAAAATGGAATTTTTAAA-ATTCG
*** * * * * *
5338629 GGGGTAAAAATGGTAATTTTCAAAAATTTTGGGGTCAAAAATGGAATTTTTGGAAGTTTG
1 GGGGT-AAAAT-GTAATTTTTGGAAAGTTCGGGGTCAAAAATGGAATTTTT-AAAATTCG
* * ** * **
5338689 AGGGTAGAAATGTGATTTTTGGAAAGTTTAGGGTCAAAAATGGAATTTTTGGATGTTCG
1 GGGGTA-AAATGTAATTTTTGGAAAGTTCGGGGTCAAAAATGGAATTTTT-AAAATTCG
* * *
5338748 GGGGTTAAAATGTAATTTTTAGAAAGTTCAGGGGTCAAAATAT-GATTTTTTAAAAGTT-T
1 GGGG-TAAAATGTAATTTTTGGAAAGTTC-GGGGTCAAAA-ATGGAATTTTTAAAA-TTCG
5338807 GGGGTCAAAATGTAATTTTTGGAAAGTTCGGGGTCAAAA
1 GGGGT-AAAATGTAATTTTTGGAAAGTTCGGGGTCAAAA
5338846 TATGATTTCT
Statistics
Matches: 177, Mismatches: 32, Indels: 17
0.78 0.14 0.08
Matches are distributed among these distances:
58 11 0.06
59 95 0.54
60 67 0.38
61 4 0.02
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.35
Consensus pattern (57 bp):
GGGGTAAAATGTAATTTTTGGAAAGTTCGGGGTCAAAAATGGAATTTTTAAAATTCG
Found at i:5338832 original size:29 final size:29
Alignment explanation
Indices: 5338629--5338846 Score: 181
Period size: 29 Copynumber: 7.4 Consensus size: 29
5338619 TAAACATTCG
* *** *
5338629 GGGGTAAAAATGGTAATTTTCAAAAATTTT
1 GGGGTCAAAAT-GTAATTTTTGGAAAGTTT
*
5338659 GGGGTCAAAAATGGAATTTTTGG-AAGTTT
1 GGGGTC-AAAATGTAATTTTTGGAAAGTTT
*
5338688 GAGGGT-AGAAATGTGATTTTTGGAAAGTTT
1 G-GGGTCA-AAATGTAATTTTTGGAAAGTTT
* * * *
5338718 AGGGTCAAAAATGGAATTTTTGG-ATGTTCG
1 GGGGTC-AAAATGTAATTTTTGGAAAGTT-T
* * *
5338748 GGGGTTAAAATGTAATTTTTAGAAAGTTCA
1 GGGGTCAAAATGTAATTTTTGGAAAGTT-T
* * **
5338778 GGGGTCAAAATATGATTTTTTAAAAGTTT
1 GGGGTCAAAATGTAATTTTTGGAAAGTTT
*
5338807 GGGGTCAAAATGTAATTTTTGGAAAGTTC
1 GGGGTCAAAATGTAATTTTTGGAAAGTTT
5338836 GGGGTCAAAAT
1 GGGGTCAAAAT
5338847 ATGATTTCTG
Statistics
Matches: 150, Mismatches: 30, Indels: 17
0.76 0.15 0.09
Matches are distributed among these distances:
28 1 0.01
29 76 0.51
30 67 0.45
31 6 0.04
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.35
Consensus pattern (29 bp):
GGGGTCAAAATGTAATTTTTGGAAAGTTT
Found at i:5342717 original size:15 final size:16
Alignment explanation
Indices: 5342699--5342736 Score: 69
Period size: 15 Copynumber: 2.4 Consensus size: 16
5342689 AAGATATTTT
5342699 AACAAATGAAATTAA-
1 AACAAATGAAATTAAC
5342714 AACAAATGAAATTAAC
1 AACAAATGAAATTAAC
5342730 AACAAAT
1 AACAAAT
5342737 ACGGTGGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 15 0.68
16 7 0.32
ACGTcount: A:0.66, C:0.11, G:0.05, T:0.18
Consensus pattern (16 bp):
AACAAATGAAATTAAC
Found at i:5349580 original size:5 final size:5
Alignment explanation
Indices: 5349570--5349602 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
5349560 AATAAATGGA
5349570 TATTC TATTC TATTC TATTC TATTC TATTC TAT
1 TATTC TATTC TATTC TATTC TATTC TATTC TAT
5349603 ATATCAATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.21, C:0.18, G:0.00, T:0.61
Consensus pattern (5 bp):
TATTC
Found at i:5350333 original size:6 final size:6
Alignment explanation
Indices: 5350322--5350354 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
5350312 TCTATGATTT
5350322 AATATA AATATA AATATA AATATA AATATA AAT
1 AATATA AATATA AATATA AATATA AATATA AAT
5350355 TAATTTCAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
AATATA
Found at i:5351817 original size:29 final size:30
Alignment explanation
Indices: 5351776--5351855 Score: 76
Period size: 29 Copynumber: 2.7 Consensus size: 30
5351766 TTTTTGGCTC
**
5351776 TCGAGGGCGAAAAT-GTAATTTCGGGAAAAT
1 TCGAGGGTAAAAATAGTAATTT-GGGAAAAT
* * *
5351806 TCGAGGTTAAAAATAG-AATTTTGGAAAGT
1 TCGAGGGTAAAAATAGTAATTTGGGAAAAT
*
5351835 TCGAGGGT-AAAATGGTAATTT
1 TCGAGGGTAAAAATAGTAATTT
5351856 TTGGTGAAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
28 6 0.15
29 18 0.44
30 16 0.39
31 1 0.02
ACGTcount: A:0.38, C:0.06, G:0.28, T:0.29
Consensus pattern (30 bp):
TCGAGGGTAAAAATAGTAATTTGGGAAAAT
Found at i:5351856 original size:29 final size:29
Alignment explanation
Indices: 5351776--5352012 Score: 129
Period size: 30 Copynumber: 8.0 Consensus size: 29
5351766 TTTTTGGCTC
** * * *
5351776 TCGAGGGCGAAAATGTAATTTCGGGAAAAT
1 TCGAGGGTAAAAATGGAATTT-TGGAAAGT
* *
5351806 TCGAGGTTAAAAATAGAATTTTGGAAAGT
1 TCGAGGGTAAAAATGGAATTTTGGAAAGT
5351835 TCGAGGGT-AAAATGGTAATTTTTGGTGAAA--
1 TCGAGGGTAAAAATGG-AA-TTTT-G-GAAAGT
5351865 TC-AGGGTTAAAAATGGAATTTTGGAAAGT
1 TCGAGGG-TAAAAATGGAATTTTGGAAAGT
* *
5351894 T-TAGGGGT-AAAATAGTAATTTTGGGTGAAA--
1 TCGA-GGGTAAAAAT-GGAATTTT--G-GAAAGT
* *
5351924 TC-AAGGTCAAAAATAGAATTTTGGAAAGT
1 TCGAGGGT-AAAAATGGAATTTTGGAAAGT
*
5351953 T-TAGGGGT-AAAATGGTAATTTTTGG-AAGTT
1 TCGA-GGGTAAAAATGG-AA-TTTTGGAAAG-T
*
5351983 TCGAGGTTAAAAATGGAATTTTGGAAAGT
1 TCGAGGGTAAAAATGGAATTTTGGAAAGT
5352012 T
1 T
5352013 TGGGGACTAG
Statistics
Matches: 163, Mismatches: 17, Indels: 55
0.69 0.07 0.23
Matches are distributed among these distances:
27 8 0.05
28 19 0.12
29 51 0.31
30 55 0.34
31 22 0.13
32 8 0.05
ACGTcount: A:0.37, C:0.04, G:0.27, T:0.32
Consensus pattern (29 bp):
TCGAGGGTAAAAATGGAATTTTGGAAAGT
Found at i:5351873 original size:59 final size:59
Alignment explanation
Indices: 5351810--5352017 Score: 273
Period size: 59 Copynumber: 3.5 Consensus size: 59
5351800 GAAAATTCGA
*
5351810 GGTTAAAAATAGAATTTTGGAAAG-TTCGAGGGTAAAATGGTAATTTTTGGTGAAATCAG
1 GGTTAAAAATAGAATTTTGGAAAGTTTAG-GGGTAAAATGGTAATTTTTGGTGAAATCAG
* * * *
5351869 GGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATAGTAATTTTGGGTGAAATCAA
1 GGTTAAAAATAGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGTGAAATCAG
* *
5351928 GGTCAAAAATAGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTT-G-GAAGTTTC-G
1 GGTTAAAAATAGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGTGAA--ATCAG
*
5351986 AGGTTAAAAATGGAATTTTGGAAAGTTT-GGGG
1 -GGTTAAAAATAGAATTTTGGAAAGTTTAGGGG
5352018 ACTAGAGAGC
Statistics
Matches: 132, Mismatches: 13, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
57 3 0.02
58 5 0.04
59 121 0.92
60 3 0.02
ACGTcount: A:0.37, C:0.02, G:0.28, T:0.33
Consensus pattern (59 bp):
GGTTAAAAATAGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGTGAAATCAG
Found at i:5351978 original size:30 final size:28
Alignment explanation
Indices: 5351815--5352017 Score: 121
Period size: 29 Copynumber: 7.0 Consensus size: 28
5351805 TTCGAGGTTA
* *
5351815 AAAATAGAATTTTGGAAAG-TTCGAGGGT
1 AAAATGGAATTTTGGAAAGTTTAG-GGGT
* *
5351843 AAAATGGTAATTTTTGGTGAAA--TCAGGGTT
1 AAAATGG-AA-TTTT-G-GAAAGTTTAGGGGT
5351873 AAAAATGGAATTTTGGAAAGTTTAGGGGT
1 -AAAATGGAATTTTGGAAAGTTTAGGGGT
* ** ***
5351902 AAAATAGTAATTTTGGGTGAAA-TCAAGGTCA
1 AAAAT-GGAATTTT--G-GAAAGTTTAGGGGT
*
5351933 AAAATAGAATTTTGGAAAGTTTAGGGGT
1 AAAATGGAATTTTGGAAAGTTTAGGGGT
* *
5351961 AAAATGGTAATTTTTGG-AAGTTTCGAGGTT
1 AAAATGG-AA-TTTTGGAAAGTTTAG-GGGT
5351991 AAAAATGGAATTTTGGAAAGTTT-GGGG
1 -AAAATGGAATTTTGGAAAGTTTAGGGG
5352018 ACTAGAGAGC
Statistics
Matches: 135, Mismatches: 23, Indels: 34
0.70 0.12 0.18
Matches are distributed among these distances:
27 8 0.06
28 25 0.19
29 35 0.26
30 32 0.24
31 27 0.20
32 8 0.06
ACGTcount: A:0.37, C:0.02, G:0.28, T:0.33
Consensus pattern (28 bp):
AAAATGGAATTTTGGAAAGTTTAGGGGT
Found at i:5353797 original size:14 final size:15
Alignment explanation
Indices: 5353776--5353818 Score: 56
Period size: 13 Copynumber: 3.1 Consensus size: 15
5353766 CATTGCGCCT
5353776 ATTTGGGCCTTTGTA
1 ATTTGGGCCTTTGTA
*
5353791 A-TTGGGCC-CT-TA
1 ATTTGGGCCTTTGTA
5353803 ATTTGGGCCTTTGTA
1 ATTTGGGCCTTTGTA
5353818 A
1 A
5353819 ATGGACTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
12 3 0.13
13 8 0.35
14 8 0.35
15 4 0.17
ACGTcount: A:0.16, C:0.16, G:0.26, T:0.42
Consensus pattern (15 bp):
ATTTGGGCCTTTGTA
Found at i:5353879 original size:11 final size:11
Alignment explanation
Indices: 5353840--5353922 Score: 55
Period size: 11 Copynumber: 7.5 Consensus size: 11
5353830 TATTTGGACT
*
5353840 TTTAATTTAAA
1 TTTAAATTAAA
*
5353851 TTTTAATTAAA
1 TTTAAATTAAA
5353862 TTTAAATT-AA
1 TTTAAATTAAA
*
5353872 TTTCAAA-T-AT
1 TTT-AAATTAAA
5353882 TTTAAATTTAAA
1 TTTAAA-TTAAA
* * *
5353894 ATGAATTTAAA
1 TTTAAATTAAA
*
5353905 TTTAATAATAAA
1 TTTAA-ATTAAA
5353917 TTTAAA
1 TTTAAA
5353923 CCTAAAACAT
Statistics
Matches: 55, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
9 3 0.05
10 10 0.18
11 29 0.53
12 13 0.24
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (11 bp):
TTTAAATTAAA
Found at i:5353895 original size:16 final size:16
Alignment explanation
Indices: 5353870--5353922 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 16
5353860 AATTTAAATT
* *
5353870 AATTTCAAATATTTTA
1 AATTTAAAATAATTTA
5353886 AATTTAAAATGAATTTA
1 AATTTAAAAT-AATTTA
5353903 AATTTAATAATAAATTTA
1 AATTTAA-AAT-AATTTA
5353921 AA
1 AA
5353923 CCTAAAACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
16 9 0.28
17 12 0.38
18 11 0.34
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (16 bp):
AATTTAAAATAATTTA
Found at i:5353904 original size:17 final size:18
Alignment explanation
Indices: 5353882--5353922 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
5353872 TTTCAAATAT
*
5353882 TTTAAATTTAA-AATGAA
1 TTTAAATTTAATAATAAA
5353899 TTTAAATTTAATAATAAA
1 TTTAAATTTAATAATAAA
5353917 TTTAAA
1 TTTAAA
5353923 CCTAAAACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
TTTAAATTTAATAATAAA
Found at i:5354665 original size:200 final size:200
Alignment explanation
Indices: 5354278--5354770 Score: 707
Period size: 200 Copynumber: 2.5 Consensus size: 200
5354268 TCCTTGTGTA
** * * * *
5354278 TCATCAGGAAGATGACCGCAATCATCTGTTTTAATTCGCTTCTTTGGATCTCCTCAGGAAGACGA
1 TCATCAGGAAGATGACCGCCTTGAT-TGTTTTAATTTGCTTCTCTGGATCTCCTCAGGAAGACAA
* * * * * * *
5354343 ATTTGGTCCACTTCTCTGTGTCTTATCAGGAAGCTAACCTTTTTATTGCTTCAACCTGCTTCTTA
65 ATTTGGTCCACTTCTCTGTATCTCATCAAGAAACTAACCATGTTATTGCTTCAACCTGCTTCTCA
* * *
5354408 GTATCTCATCAAGAAGCTGGGTTCGAAGGTTTGCTCACATTGAGTGTTGAGTTGGTATTCTTCTC
130 GTATCTCATCAAGAAGCTGGGTACGAAGATTTGCTCACATTGAGCGTTGAGTTGGTATTCTTCTC
*
5354473 TGTATC
195 TATATC
5354479 TCATCAGGAAGATGACCGCCTTGATTGTTTTAATTTGCTTCTCTGGATCTCCTCAGGAAGACAAA
1 TCATCAGGAAGATGACCGCCTTGATTGTTTTAATTTGCTTCTCTGGATCTCCTCAGGAAGACAAA
* * *
5354544 TTTGGTCCACTTCTCTATATCTCATCAAGAAACTAACCATGTTATTGTTTCGACCTGCTTCTCAG
66 TTTGGTCCACTTCTCTGTATCTCATCAAGAAACTAACCATGTTATTGCTTCAACCTGCTTCTCAG
* * * * *
5354609 TGTCTCATCAGGAAGCTGGGTACGAAGATTTGCTCGCTTTGAGCGTTGATTTGGTATTCTTCTCT
131 TATCTCATCAAGAAGCTGGGTACGAAGATTTGCTCACATTGAGCGTTGAGTTGGTATTCTTCTCT
*
5354674 ATGTC
196 ATATC
* * * *
5354679 TCATCAGGAAGATGACCGCCTCGCTTATTTTAATTTGCTTCTCTAGATCTCCTCAGGAAGACAAA
1 TCATCAGGAAGATGACCGCCTTGATTGTTTTAATTTGCTTCTCTGGATCTCCTCAGGAAGACAAA
5354744 TTTGGTCCACTTCTCTGTATCTCATCA
66 TTTGGTCCACTTCTCTGTATCTCATCA
5354771 GGAAGATGAC
Statistics
Matches: 261, Mismatches: 31, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
200 239 0.92
201 22 0.08
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.37
Consensus pattern (200 bp):
TCATCAGGAAGATGACCGCCTTGATTGTTTTAATTTGCTTCTCTGGATCTCCTCAGGAAGACAAA
TTTGGTCCACTTCTCTGTATCTCATCAAGAAACTAACCATGTTATTGCTTCAACCTGCTTCTCAG
TATCTCATCAAGAAGCTGGGTACGAAGATTTGCTCACATTGAGCGTTGAGTTGGTATTCTTCTCT
ATATC
Done.