Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007800.1 Hibiscus syriacus cultivar Beakdansim tig00110114_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4652821
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 23
Found at i:3060156 original size:122 final size:128
Alignment explanation
Indices: 3059935--3060417 Score: 791
Period size: 122 Copynumber: 3.9 Consensus size: 128
3059925 TTATATTTAC
3059935 CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
1 CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
3060000 AC-AAATAATGGAAGGCGC-CCCCCGGGAACGCGCC-TCATGTGAATAGTGAAATAATAGGTA
66 ACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTA
*
3060060 CTGATATATCTAGTGT-CCCGAGGGAC-TGA-TGACGTAATAGGGCAATGATAACATA-T-TCTG
1 CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
*
3060120 ACAAAATAATGGAAGGCGCGCCCCCGGGAACACGCCTTCATGTGAATAGTGAAATAATAGGTA
66 ACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTA
*
3060183 CTG--ATATCTAGTGTCCCCGA--GACATGAGTGATATAATAGGGCAATGAT-A-ATA-TCTCTG
1 CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
* *
3060241 ACAAAAT-ATGGAAGGAGCGCCCCCGGGAATGCGCCTTCATGTGAATAGTGAAATAATAGGTA
66 ACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTA
3060303 CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
1 CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
* *
3060368 ATAAAATAATGGAAGACGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
66 ACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
3060418 ACTCCGATTA
Statistics
Matches: 331, Mismatches: 12, Indels: 27
0.89 0.03 0.07
Matches are distributed among these distances:
120 68 0.21
121 43 0.13
122 80 0.24
123 32 0.10
124 37 0.11
125 17 0.05
126 3 0.01
127 12 0.04
128 39 0.12
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (128 bp):
CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
ACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTA
Found at i:3060456 original size:25 final size:26
Alignment explanation
Indices: 3060406--3060458 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
3060396 AACGCGCCTT
3060406 CATGTGAATAGTACTCCGATTATAGA
1 CATGTGAATAGTACTCCGATTATAGA
3060432 CATGTGAATAGTACT-CGATTATAGA
1 CATGTGAATAGTACTCCGATTATAGA
3060457 CA
1 CA
3060459 CTATTATATG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 12 0.44
26 15 0.56
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (26 bp):
CATGTGAATAGTACTCCGATTATAGA
Found at i:3060525 original size:8 final size:8
Alignment explanation
Indices: 3060512--3060552 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
3060502 TCACAAGCTT
3060512 TCAAATTC
1 TCAAATTC
3060520 TCAAATTC
1 TCAAATTC
* *
3060528 CCAAACTC
1 TCAAATTC
3060536 T-AAATTC
1 TCAAATTC
3060543 TCAAATTC
1 TCAAATTC
3060551 TC
1 TC
3060553 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:3064771 original size:17 final size:17
Alignment explanation
Indices: 3064749--3064783 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
3064739 TTAGCCCGAT
3064749 AAGTGAATAACTCACTA
1 AAGTGAATAACTCACTA
3064766 AAGTGAATAACTCACTA
1 AAGTGAATAACTCACTA
3064783 A
1 A
3064784 CACACTAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.17, G:0.11, T:0.23
Consensus pattern (17 bp):
AAGTGAATAACTCACTA
Found at i:3066725 original size:24 final size:25
Alignment explanation
Indices: 3066675--3066726 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
3066665 GGAAAATAAT
* **
3066675 AAATAAAAAAATAAAATAAGTTTAA
1 AAATAAAAAAATAAAATAAATAGAA
*
3066700 AAATAAAATAA-AAAATAAATAGAA
1 AAATAAAAAAATAAAATAAATAGAA
3066724 AAA
1 AAA
3066727 AATGATAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (25 bp):
AAATAAAAAAATAAAATAAATAGAA
Found at i:3066774 original size:14 final size:15
Alignment explanation
Indices: 3066755--3066789 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
3066745 GATTTTTTTT
3066755 AAAAAAT-ATAAAGA
1 AAAAAATGATAAAGA
*
3066769 AAAAAATGATAATGA
1 AAAAAATGATAAAGA
3066784 AAAAAA
1 AAAAAA
3066790 AAATAGTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (15 bp):
AAAAAATGATAAAGA
Found at i:3068177 original size:69 final size:69
Alignment explanation
Indices: 3068093--3068390 Score: 265
Period size: 68 Copynumber: 4.3 Consensus size: 69
3068083 AATATAATAT
* * *
3068093 AAACTATATAATATATATA-TTTCAAAAATATTTTTTAAAACTATATATTATATTCTTAAAA-AA
1 AAACTATATATTATATATATTTTCAAAAATATTTTTAAAAACTATATATTATATT-TCAAAATAA
3068156 TTTCCA
65 TTT-CA
* * *
3068162 AAACTATATATTATATA-GTTTTCAAAAATGA--TTTAAAAA-TATTATATAAGATTTCAAAATA
1 AAACTATATATTATATATATTTTCAAAAAT-ATTTTTAAAAACTA-TATATTATATTTCAAAATA
* *
3068223 TGTTTTTA
64 --ATTTCA
* * *
3068231 AAACTATATATTATATAAATTTTCAAAAATGTTTTTAAAAACTATATATATATATTTCAAAATGA
1 AAACTATATATTATATATATTTTCAAAAATATTTTTAAAAACTATATAT-TATATTTCAAAATAA
3068296 TTTCA
65 TTTCA
*** * * *
3068301 AAAC--TATATTATATATATTTTCAAATGCATTTTCAAAAACTATACATTATATGTTTC-AAATT
1 AAACTATATATTATATATATTTTCAAAAATATTTTTAAAAACTATATATTATA--TTTCAAAATA
* *
3068363 TTTTAA
64 ATTTCA
*
3068369 AAACT-TATACTATATATATTTT
1 AAACTATATATTATATATATTTT
3068391 TGAAATGTTT
Statistics
Matches: 189, Mismatches: 26, Indels: 28
0.78 0.11 0.12
Matches are distributed among these distances:
67 11 0.06
68 65 0.34
69 64 0.34
70 23 0.12
71 13 0.07
72 13 0.07
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (69 bp):
AAACTATATATTATATATATTTTCAAAAATATTTTTAAAAACTATATATTATATTTCAAAATAAT
TTCA
Found at i:3068261 original size:70 final size:70
Alignment explanation
Indices: 3068093--3068325 Score: 232
Period size: 69 Copynumber: 3.4 Consensus size: 70
3068083 AATATAATAT
* * * * * * * *
3068093 AAACTATATAATATATATA-TTTCAAAAATATTTTTTAAAACTATATAT-TATATTCTTAAAA-A
1 AAACTATATATTATATAAATTTTCAAAAATGTATTTAAAAACTATATATATAGATT-TCAAAATG
3068155 ATTTCCA
65 ATTT-CA
*
3068162 AAACTATATATTATAT-AGTTTTCAAAAATG-ATTTAAAAA-TAT-TATATAAGATTTCAAAATA
1 AAACTATATATTATATAAATTTTCAAAAATGTATTTAAAAACTATATATAT-AGATTTC-AAA-A
* *
3068223 TGTTTTTA
63 TGATTTCA
* *
3068231 AAACTATATATTATATAAATTTTCAAAAATGTTTTTAAAAACTATATATATATATTTCAAAATGA
1 AAACTATATATTATATAAATTTTCAAAAATGTATTTAAAAACTATATATATAGATTTCAAAATGA
3068296 TTTCA
66 TTTCA
*
3068301 AAAC--TATATTATATATATTTTCAAA
1 AAACTATATATTATATAAATTTTCAAA
3068326 TGCATTTTCA
Statistics
Matches: 137, Mismatches: 17, Indels: 21
0.78 0.10 0.12
Matches are distributed among these distances:
66 3 0.02
67 5 0.04
68 34 0.25
69 43 0.31
70 27 0.20
71 11 0.08
72 9 0.07
73 5 0.04
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (70 bp):
AAACTATATATTATATAAATTTTCAAAAATGTATTTAAAAACTATATATATAGATTTCAAAATGA
TTTCA
Found at i:3068293 original size:33 final size:34
Alignment explanation
Indices: 3068103--3068389 Score: 206
Period size: 33 Copynumber: 8.4 Consensus size: 34
3068093 AAACTATATA
* *
3068103 ATATATATATTTCAAAAATATTTTTTAAAACTAT
1 ATATATATATTTCAAAAATGTTTTTAAAAACTAT
* * **
3068137 ATAT-TATATTCTTAAAAA--ATTTCCAAAACTAT
1 ATATATATATT-TCAAAAATGTTTTTAAAAACTAT
*
3068169 ATATTATATAGTTTTCAAAAATG-ATTTAAAAA-TAT
1 ATA-TATATA--TTTCAAAAATGTTTTTAAAAACTAT
*
3068204 -TATATAAGATTTCAAAATATGTTTTT-AAAACTAT
1 ATATAT-ATATTTCAAAA-ATGTTTTTAAAAACTAT
3068238 ATATTATATAAATTTTCAAAAATGTTTTTAAAAACTAT
1 ATA-TATAT--A-TTTCAAAAATGTTTTTAAAAACTAT
* *
3068276 ATATATATATTTC-AAAATG-ATTTCAAAACTAT
1 ATATATATATTTCAAAAATGTTTTTAAAAACTAT
*
3068308 ATTATATATATTTTC--AAATGCATTTTCAAAAACTAT
1 A-TATATATA-TTTCAAAAATG--TTTTTAAAAACTAT
* *
3068344 ACATTATATGTTTC--AAAT-TTTTTAAAAACTTAT
1 ATA-TATATATTTCAAAAATGTTTTTAAAAAC-TAT
3068377 ACTATATATATTT
1 A-TATATATATTT
3068390 TTGAAATGTT
Statistics
Matches: 207, Mismatches: 21, Indels: 51
0.74 0.08 0.18
Matches are distributed among these distances:
32 44 0.21
33 48 0.23
34 33 0.16
35 22 0.11
36 27 0.13
37 14 0.07
38 19 0.09
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.45
Consensus pattern (34 bp):
ATATATATATTTCAAAAATGTTTTTAAAAACTAT
Found at i:3068314 original size:35 final size:34
Alignment explanation
Indices: 3068093--3068429 Score: 186
Period size: 35 Copynumber: 9.8 Consensus size: 34
3068083 AATATAATAT
*
3068093 AAACTATATAATATATATATTTCAAAAAT-ATTTTTTA
1 AAACTATAT-ATATATATATTTC-AAAATGA--TTTCA
*
3068130 AAACTATATAT-TATAT-TCTT-AAAA-AATTTCCA
1 AAACTATATATATATATAT-TTCAAAATGATTT-CA
3068162 AAACTATATAT-TATATAGTTTTCAAAAATGATTT-A
1 AAACTATATATATATATA--TTTC-AAAATGATTTCA
* * * *
3068197 AAAATAT-TATATA-AGATTTCAAAATATGTTTTTA
1 AAACTATATATATATATATTTC-AAA-ATGATTTCA
* * *
3068231 AAACTATATATTATATAAATTTTCAAAAATGTTTTTA
1 AAACTATATA-TATATATA-TTTC-AAAATGATTTCA
3068268 AAA--ACTATATATATATATTTCAAAATGATTTCA
1 AAACTA-TATATATATATATTTCAAAATGATTTCA
3068301 AAACTATAT-TATATATATTTTC-AAATGCATTTTCAA
1 AAACTATATATATATATA-TTTCAAAATG-A-TTTC-A
* * ** *
3068337 AAACTATACAT-TATATGTTTC-AAATTTTTTAA
1 AAACTATATATATATATATTTCAAAATGATTTCA
** *
3068369 AAACT-TATACTATATATATTTTTGAAATG-TTTCG
1 AAACTATATA-TATATATA-TTTCAAAATGATTTCA
* *
3068403 AAACTATATAGTACATATATTTTAAAA
1 AAACTATATA-TATATATATTTCAAAA
3068430 ACATTTTCAA
Statistics
Matches: 247, Mismatches: 24, Indels: 61
0.74 0.07 0.18
Matches are distributed among these distances:
31 6 0.02
32 32 0.13
33 45 0.18
34 45 0.18
35 55 0.22
36 28 0.11
37 28 0.11
38 8 0.03
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.44
Consensus pattern (34 bp):
AAACTATATATATATATATTTCAAAATGATTTCA
Found at i:3069167 original size:84 final size:85
Alignment explanation
Indices: 3069064--3069229 Score: 217
Period size: 84 Copynumber: 2.0 Consensus size: 85
3069054 AAGGTCTTTA
* * * * * *
3069064 GCAGATAGCCCTTCTCGACTTAAGCTATGTTGCAAATAATGTG-CCTTGGAGATGAGCGTAGTCG
1 GCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATAATATGCCCTCGAAGATGAGCGTAATCG
3069128 AACTCAAAGGTCTTTGGTTT
66 AACTCAAAGGTCTTTGGTTT
* * * *
3069148 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGTGTAATCG
1 GCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATAATATGCCCTCGAAGATGAGCGTAATCG
* *
3069213 AACTCGAGGGTCTTTGG
66 AACTCAAAGGTCTTTGG
3069230 CAGATAGCCC
Statistics
Matches: 69, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
84 38 0.55
85 31 0.45
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (85 bp):
GCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATAATATGCCCTCGAAGATGAGCGTAATCG
AACTCAAAGGTCTTTGGTTT
Found at i:3069575 original size:106 final size:106
Alignment explanation
Indices: 3069391--3070412 Score: 1693
Period size: 106 Copynumber: 9.6 Consensus size: 106
3069381 GCATTGTTCC
* * * * * *
3069391 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAATCGGGAAATTGTTTGTTGATAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
** * * *
3069456 CCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
3069497 GAGTGCAATATCCTTTGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
3069562 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
3069603 GACTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
3069668 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
3069709 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
3069774 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
3069815 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
3069880 CCAGCGGTCCCTTCGCCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
3069921 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
3069986 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
3070027 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
3070092 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
3070133 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
3070198 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
3070239 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
3070304 CCAGCGGTCTCTTCGCCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * *
3070345 GAGTCCAATTTTCTTCGTTGCGAAGTTGAAATAGACTCTGAATGAAGTTGGAAAGTTGTTTGTTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-A--AA-TTGGGAAGTTGTTTGTTG
3070410 ACA
62 ACA
3070413 GACAACTTTT
Statistics
Matches: 865, Mismatches: 47, Indels: 4
0.94 0.05 0.00
Matches are distributed among these distances:
106 843 0.97
107 1 0.00
109 2 0.00
110 19 0.02
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:3074388 original size:16 final size:15
Alignment explanation
Indices: 3074359--3074392 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
3074349 TTTTTTTTAT
3074359 AAAATATAAAGAAAA
1 AAAATATAAAGAAAA
*
3074374 AAAATGATAATGAAAA
1 AAAAT-ATAAAGAAAA
3074390 AAA
1 AAA
3074393 GAAAATTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (15 bp):
AAAATATAAAGAAAA
Found at i:3075759 original size:32 final size:31
Alignment explanation
Indices: 3075716--3075789 Score: 78
Period size: 32 Copynumber: 2.3 Consensus size: 31
3075706 AAACTATATA
**
3075716 ATATATATATTTC-AAAAAATATTTTTTAAAACT
1 ATATAT-TATTTCTAAAAAA-A-TTTCGAAAACT
*
3075749 ATATATTATTTTCTTAAAAAATTTCGAAAACT
1 ATATATTA-TTTCTAAAAAAATTTCGAAAACT
3075781 ATATATTAT
1 ATATATTAT
3075790 ATAGTTTTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
31 1 0.03
32 19 0.53
33 11 0.31
34 5 0.14
ACGTcount: A:0.46, C:0.07, G:0.01, T:0.46
Consensus pattern (31 bp):
ATATATTATTTCTAAAAAAATTTCGAAAACT
Found at i:3075821 original size:31 final size:36
Alignment explanation
Indices: 3075775--3075985 Score: 165
Period size: 38 Copynumber: 5.8 Consensus size: 36
3075765 AAAAATTTCG
3075775 AAAACTATATATTATAT-AGTTTTCAAAAATG-ATTT
1 AAAA-TATATATTATATAAGTTTTCAAAAATGTATTT
* *
3075810 -AAA-A-ATATTATATAAGATTTCAAAATATGTTTTT
1 AAAATATATATTATATAAGTTTTCAAAA-ATGTATTT
* *
3075844 AAAATTATATATTATATAATTTTTCAAAAATGTTTTTT
1 AAAA-TATATATTATATAAGTTTTCAAAAATG-TATTT
3075882 AAAAACTATATATTATATATA-TTTTC-AAAATG-ATTT
1 -AAAA-TATATATTATATA-AGTTTTCAAAAATGTATTT
3075918 CAAAACTATATATTATATATA-TTTTC--AAATGTATTTT
1 -AAAA-TATATATTATATA-AGTTTTCAAAAATGTA-TTT
* *
3075955 CAAAAACTATACATTATATATGTTTTCAAAA
1 --AAAA-TATATATTATATAAGTTTTCAAAA
3075986 TTTTTTAAAA
Statistics
Matches: 150, Mismatches: 10, Indels: 27
0.80 0.05 0.14
Matches are distributed among these distances:
31 9 0.06
32 11 0.07
33 3 0.02
34 6 0.04
35 8 0.05
36 29 0.19
37 7 0.05
38 52 0.35
39 22 0.15
40 3 0.02
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (36 bp):
AAAATATATATTATATAAGTTTTCAAAAATGTATTT
Found at i:3075855 original size:33 final size:31
Alignment explanation
Indices: 3075783--3075848 Score: 87
Period size: 33 Copynumber: 2.1 Consensus size: 31
3075773 CGAAAACTAT
*
3075783 ATATTATATAGTTTTCAAAAATGATTTAAAA
1 ATATTATATAGATTTCAAAAATGATTTAAAA
* *
3075814 ATATTATATAAGATTTCAAAATATGTTTTTAAA
1 ATATTATAT-AGATTTCAAAA-ATGATTTAAAA
3075847 AT
1 AT
3075849 TATATATTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 9 0.30
32 10 0.33
33 11 0.37
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (31 bp):
ATATTATATAGATTTCAAAAATGATTTAAAA
Found at i:3075930 original size:36 final size:36
Alignment explanation
Indices: 3075706--3076080 Score: 244
Period size: 36 Copynumber: 10.4 Consensus size: 36
3075696 AATATAATAT
* *
3075706 AAACTATATAATATATATA-TTTCAAAAAAT-ATTTTTTA
1 AAACTATATATTATATATATTTTC--AAAATGA--TTTCA
* *
3075744 AAACTATATATTAT-T-T-TCTT-AAAA-AATTTCGA
1 AAACTATATATTATATATATTTTCAAAATGATTTC-A
*
3075776 AAACTATATATTATATA-GTTTTCAAAAATGATTT-A
1 AAACTATATATTATATATATTTTC-AAAATGATTTCA
* * * *
3075811 AAAATAT-TA-TATA-AGA-TTTCAAAATATGTTTTTA
1 AAACTATATATTATATATATTTTC-AAA-ATGATTTCA
* * *
3075845 AAATTATATATTATATA-ATTTTTCAAAAATGTTTTTTAA
1 AAACTATATATTATATATA-TTTTC-AAAATG--ATTTCA
3075884 AAACTATATATTATATATATTTTCAAAATGATTTCA
1 AAACTATATATTATATATATTTTCAAAATGATTTCA
3075920 AAACTATATATTATATATATTTTC-AAATGTATTTTCAA
1 AAACTATATATTATATATATTTTCAAAATG-A-TTTC-A
* * ** *
3075958 AAACTATACATTATATATGTTTTCAAAATTTTTTAA
1 AAACTATATATTATATATATTTTCAAAATGATTTCA
** * * *
3075994 AAACTATATACAATATATATTTTCGAAATGTTTTCG
1 AAACTATATATTATATATATTTTCAAAATGATTTCA
* * **
3076030 AAACTATATAGTACATATATTTT-AAAAACATTTTCA
1 AAACTATATATTATATATATTTTCAAAATGA-TTTCA
*
3076066 AAAAT-TATATTATAT
1 AAACTATATATTATAT
3076081 TTCTATAAAA
Statistics
Matches: 275, Mismatches: 37, Indels: 53
0.75 0.10 0.15
Matches are distributed among these distances:
31 3 0.01
32 24 0.09
33 16 0.06
34 12 0.04
35 25 0.09
36 98 0.36
37 16 0.06
38 50 0.18
39 30 0.11
40 1 0.00
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (36 bp):
AAACTATATATTATATATATTTTCAAAATGATTTCA
Found at i:3075981 original size:74 final size:74
Alignment explanation
Indices: 3075816--3076027 Score: 248
Period size: 74 Copynumber: 2.8 Consensus size: 74
3075806 ATTTAAAAAT
* * * *
3075816 ATTATATAAGATTTCAAAATATGTTTTTAAAATTATATATTATATA-ATTTTTCAAAAATGTTTT
1 ATTATATATGTTTTC-AAA-ATGTTTTAAAAACTATATATTATATATA-TTTTC-AAAATGTTTT
* *
3075880 TTAAAAACTATAT
62 TCAAAAACTATAC
* * *
3075893 ATTATATATATTTTCAAAATGATTTCAAAACTATATATTATATATATTTTC-AAATGTATTTTCA
1 ATTATATATGTTTTCAAAATGTTTTAAAAACTATATATTATATATATTTTCAAAATGT-TTTTCA
3075957 AAAACTATAC
65 AAAACTATAC
* ** *
3075967 ATTATATATGTTTTCAAAATTTTTTAAAAACTATATACAATATATATTTTCGAAATGTTTT
1 ATTATATATGTTTTCAAAATGTTTTAAAAACTATATATTATATATATTTTCAAAATGTTTT
3076028 CGAAACTATA
Statistics
Matches: 118, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
73 6 0.05
74 62 0.53
75 34 0.29
76 4 0.03
77 12 0.10
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (74 bp):
ATTATATATGTTTTCAAAATGTTTTAAAAACTATATATTATATATATTTTCAAAATGTTTTTCAA
AAACTATAC
Found at i:3076063 original size:74 final size:73
Alignment explanation
Indices: 3075814--3076075 Score: 226
Period size: 74 Copynumber: 3.5 Consensus size: 73
3075804 TGATTTAAAA
* * * ** *
3075814 ATATTATATA-AGATTTCAAAATATGTTTTTAAAATTATATATTATATA-ATTTTTCAAAAATGT
1 ATATTATATATA-TTTTCAAAAT-T-TTTTAAAAACTATATACAATATATA-TTTTC--AAATGA
*
3075877 TTTTTAAAAACTAT
60 TTTTCAAAAACTAT
** * **
3075891 ATATTATATATATTTTCAAAATGATTTCAAAACTATATATTATATATATTTTCAAATGTATTTTC
1 ATATTATATATATTTTCAAAATTTTTTAAAAACTATATACAATATATATTTTCAAATG-ATTTTC
3075956 AAAAACTAT
65 AAAAACTAT
* *
3075965 ACATTATATATGTTTTCAAAATTTTTTAAAAACTATATACAATATATATTTTCGAAATG-TTTTC
1 ATATTATATATATTTTCAAAATTTTTTAAAAACTATATACAATATATATTTTC-AAATGATTTTC
*
3076029 -GAAACTAT
65 AAAAACTAT
* * * * * *
3076037 ATAGTACATATATTTTAAAAACATTTTCAAAAATTATAT
1 ATATTATATATATTTTCAAAA-TTTTTTAAAAACTATAT
3076076 TATATTTCTA
Statistics
Matches: 157, Mismatches: 23, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
72 23 0.15
73 24 0.15
74 59 0.38
75 30 0.19
76 1 0.01
77 19 0.12
78 1 0.01
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (73 bp):
ATATTATATATATTTTCAAAATTTTTTAAAAACTATATACAATATATATTTTCAAATGATTTTCA
AAAACTAT
Found at i:3079720 original size:23 final size:23
Alignment explanation
Indices: 3079687--3079731 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3079677 CATCTTATAT
*
3079687 GGCACTACGGTGCATTTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
3079710 GGCACTTCGGTGTAATTCTACG
1 GGCACTACGGTGCAATTCTACG
3079732 TGGTTCTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.29
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:3082129 original size:19 final size:19
Alignment explanation
Indices: 3082105--3082152 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
3082095 TTGAAGGTGT
3082105 ATCGATGCACAGGTAGTGC
1 ATCGATGCACAGGTAGTGC
3082124 ATCGATGCACAGGTAGTGC
1 ATCGATGCACAGGTAGTGC
3082143 ATCGATGCAC
1 ATCGATGCAC
3082153 TCTTTTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.21
Consensus pattern (19 bp):
ATCGATGCACAGGTAGTGC
Found at i:3083533 original size:31 final size:31
Alignment explanation
Indices: 3083445--3083569 Score: 132
Period size: 31 Copynumber: 4.1 Consensus size: 31
3083435 AGAGTCGAGG
3083445 GTATACCTATGTTCTACGGAACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* *
3083476 -TAATTACCTGTCTT-T-C-GAGACATATGGACA
1 GT-A-TACCTATGTTCTACGGA-ACATATGGACA
*
3083506 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* * * *
3083537 GTTTACCTAGGTTCTTCGGAACCTATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
3083568 GT
1 GT
3083570 TGTCGAGGAT
Statistics
Matches: 77, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
29 10 0.13
30 15 0.19
31 42 0.55
32 10 0.13
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (31 bp):
GTATACCTATGTTCTACGGAACATATGGACA
Found at i:3095297 original size:23 final size:23
Alignment explanation
Indices: 3095261--3095307 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
3095251 AGTTATCTCT
* * * *
3095261 CGTTATTTTGTTCTTTTTCTTCC
1 CGTTATCTTCTTCTTCTTCCTCC
3095284 CGTTATCTTCTTCTTCTTCCTCC
1 CGTTATCTTCTTCTTCTTCCTCC
3095307 C
1 C
3095308 CCCAGACAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.04, C:0.32, G:0.06, T:0.57
Consensus pattern (23 bp):
CGTTATCTTCTTCTTCTTCCTCC
Found at i:3102529 original size:10 final size:10
Alignment explanation
Indices: 3102514--3102540 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
3102504 CTTAAACCGA
3102514 GAGAGAAATT
1 GAGAGAAATT
3102524 GAGAGAAATT
1 GAGAGAAATT
3102534 GAGAGAA
1 GAGAGAA
3102541 TTTGGTGTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.33, T:0.15
Consensus pattern (10 bp):
GAGAGAAATT
Found at i:3103399 original size:72 final size:75
Alignment explanation
Indices: 3103281--3103428 Score: 187
Period size: 72 Copynumber: 2.0 Consensus size: 75
3103271 TATAAAAGAG
* * *
3103281 TTTGAAAAAAGTATTTTTTAATTAATATTTCACCGACATCAATATTTACTTTATATAATTGTTAA
1 TTTGAAAAAAGTA-TTTTTAATTAATATTTCACCAACATCAATATTTAATTTATATAATTATTAA
3103346 AATAAA-ATTA
65 AATAAATATTA
* * *
3103356 TTTGAAAAAA-TA-TTTTAGATT-ATATTTCATCAATATCATTATTTAATTTATATAATTATTAA
1 TTTGAAAAAAGTATTTTTA-ATTAATATTTCACCAACATCAATATTTAATTTATATAATTATTAA
*
3103418 ACTAAATATTA
65 AATAAATATTA
3103429 AATTATTTAT
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
72 45 0.70
73 7 0.11
74 2 0.03
75 10 0.16
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (75 bp):
TTTGAAAAAAGTATTTTTAATTAATATTTCACCAACATCAATATTTAATTTATATAATTATTAAA
ATAAATATTA
Found at i:3110905 original size:62 final size:60
Alignment explanation
Indices: 3110785--3110905 Score: 172
Period size: 62 Copynumber: 2.0 Consensus size: 60
3110775 CAATGTCACG
3110785 ACCAACTTATCACTTCACATTTATCCAATTTCCATAACATTTTATCCAATATATTCAAAA
1 ACCAACTTATCACTTCACATTTATCCAATTTCCATAACATTTTATCCAATATATTCAAAA
* * * *
3110845 ACCAA-TTGATCACTTTACATTTATTCAATTTATTCATAACATTTTATCCAATTTATTCAAA
1 ACCAACTT-ATCACTTCACATTTATCCAA-TT-TCCATAACATTTTATCCAATATATTCAAA
3110906 CTTCACATAC
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
59 2 0.04
60 23 0.43
61 2 0.04
62 27 0.50
ACGTcount: A:0.37, C:0.21, G:0.01, T:0.40
Consensus pattern (60 bp):
ACCAACTTATCACTTCACATTTATCCAATTTCCATAACATTTTATCCAATATATTCAAAA
Found at i:3111542 original size:134 final size:136
Alignment explanation
Indices: 3111034--3111618 Score: 913
Period size: 136 Copynumber: 4.3 Consensus size: 136
3111024 CCATCCATCT
* *
3111034 ATAGTTCCCCGTGGACATGAGTGACATAATAGGGTAATGATAACATATTCTCTGAC-AAATAATG
1 ATAGTTCCCCGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATG
* * * *
3111098 TAA-ACGCCCCCCCCGGGAATGCGCTTTCACCACTTTGCCAAGTCCCCTT-AGAAATAATAGGTA
66 GAAGGCG-CCCCCCC-GGAACGCACTTTCACCACTTTGCCAAGT-CCCTTCAGAAATAATAGGTA
3111161 CTGACATGA
128 CTGACATGA
*
3111170 ATAGTTCCCCGGGGACATGAGTGACATAATAGGGCCATGATAACATATTCTCTGACAAAATAATG
1 ATAGTTCCCCGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATG
*
3111235 GAAGGCGCGCCCCCGGAACGCACTTTCACCACTTTGCCAAGTCCCTTCAGAAATAATAGGTACTG
66 GAAGGCGCCCCCCCGGAACGCACTTTCACCACTTTGCCAAGTCCCTTCAGAAATAATAGGTACTG
3111300 ACATGA
131 ACATGA
3111306 ATAGTTCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 ATAGTTCCCC-GGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
*
3111371 GGAAGGCGCGCCCCCGGAACGCACTTTCACCAC-TTGCCAAGTCCCTTCAG-AA-AATAGGTACT
65 GGAAGGCGCCCCCCCGGAACGCACTTTCACCACTTTGCCAAGTCCCTTCAGAAATAATAGGTACT
3111433 GACATGA
130 GACATGA
*
3111440 ATAGTTCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATA-TCTCTAACAAAATAAT
1 ATAGTTCCCC-GGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
*** *
3111504 GGAAGGCGCCCCCCCGGAACGTGTTTTCACCACTTTGCCAAGTCCCCTCAGAAAATAATAGGTAC
65 GGAAGGCGCCCCCCCGGAACGCACTTTCACCACTTTGCCAAGTCCCTTCAG-AAATAATAGGTAC
3111569 TGACATG-
129 TGACATGA
3111576 --AGTTCCCCGGGGACA-GAGTGACATAATAGGGCAATGATAACAT
1 ATAGTTCCCCGGGGACATGAGTGACATAATAGGGCAATGATAACAT
3111619 TATATGACAA
Statistics
Matches: 426, Mismatches: 15, Indels: 20
0.92 0.03 0.04
Matches are distributed among these distances:
132 28 0.07
133 51 0.12
134 89 0.21
135 7 0.02
136 131 0.31
137 118 0.28
138 2 0.00
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.22
Consensus pattern (136 bp):
ATAGTTCCCCGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATG
GAAGGCGCCCCCCCGGAACGCACTTTCACCACTTTGCCAAGTCCCTTCAGAAATAATAGGTACTG
ACATGA
Found at i:3114523 original size:26 final size:25
Alignment explanation
Indices: 3114468--3114517 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
3114458 ATTAATATTC
*
3114468 TATTTAAATGAATGCTTTTTTCTAA
1 TATTTAAATGAATGCTATTTTCTAA
3114493 TATTTAAATGTAATTGC-ATTTTCTA
1 TATTTAAATG-AA-TGCTATTTTCTA
3114518 TAATTTCTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 10 0.45
26 9 0.41
27 3 0.14
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (25 bp):
TATTTAAATGAATGCTATTTTCTAA
Found at i:3114599 original size:22 final size:20
Alignment explanation
Indices: 3114573--3114635 Score: 65
Period size: 22 Copynumber: 3.1 Consensus size: 20
3114563 TTTATGATAT
3114573 TTATTTAATATAATAATTAATA
1 TTATTTAATATAATAATT-A-A
* *
3114595 TTATTTATTATAAAAATTAA
1 TTATTTAATATAATAATTAA
* *
3114615 TTATTTAAAATTATAA-TAA
1 TTATTTAATATAATAATTAA
3114634 TT
1 TT
3114636 CCACCTTCTA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
19 5 0.14
20 13 0.37
21 1 0.03
22 16 0.46
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTATTTAATATAATAATTAA
Found at i:3119874 original size:80 final size:80
Alignment explanation
Indices: 3119772--3120225 Score: 680
Period size: 80 Copynumber: 5.7 Consensus size: 80
3119762 CAGAAAAAAG
* * ** * * * *
3119772 GGGAGCCAACCTAAGGATATACCTT-GGATCTACTTGAGGACATCCTTAGATCCATAGGGTAACC
1 GGGAACCAACCTAAGGATATACCTTGGGACCTAC-CCAAGATATCCTTAGGTCCATAGGGTTACC
* *
3119836 TTAAGCACACAGCTAA
65 TTATGCACACAGCAAA
* *
3119852 GGGAACCAACCTAAGGATATACCTTGGG-CCTACCCAAGACATCCTTAGGTCCGTAGGGTTACCT
1 GGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCATAGGGTTACCT
3119916 TATGCACACAGCAAA
66 TATGCACACAGCAAA
* * *
3119931 GGGAACCAACTTAAGGATATACCTTAGGACCTACCCAAGATATCCTTAGGTACATAGGGTTACCT
1 GGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCATAGGGTTACCT
3119996 TATGCACACAGCAAA
66 TATGCACACAGCAAA
*
3120011 GGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCATAGGGTTACCC
1 GGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCATAGGGTTACCT
*
3120076 TATGCACACAACAAA
66 TATGCACACAGCAAA
*
3120091 GGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
1 GGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCATAGGGTTACCT
3120156 TATGCACACAGCAAA
66 TATGCACACAGCAAA
* * * *
3120171 GGGAACCAACTTAAAGATATGCCTTGGG-GCTACCCAAGATATCCTTAGGTCCATA
1 GGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCATA
3120226 AGGACTTACA
Statistics
Matches: 344, Mismatches: 28, Indels: 5
0.91 0.07 0.01
Matches are distributed among these distances:
79 89 0.26
80 253 0.74
81 2 0.01
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (80 bp):
GGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCATAGGGTTACCT
TATGCACACAGCAAA
Found at i:3120206 original size:239 final size:239
Alignment explanation
Indices: 3119772--3120225 Score: 714
Period size: 239 Copynumber: 1.9 Consensus size: 239
3119762 CAGAAAAAAG
* * ** * *
3119772 GGGAGCCAACCTAAGGATATACCTTGGATCTACTTGAGGACATCCTTAGATCCATAGGGTAACCT
1 GGGAACCAACCTAAGGATATACCTTGGACCTACTCCAAGACATCCTTAGATCCATAGGGTAACCC
* *
3119837 TAAGCACACAGCTAAGGGAACCAACCTAAGGATATACCTTGGGCCTACCCAAGACATCCTTAGGT
66 TAAGCACACAACAAAGGGAACCAACCTAAGGATATACCTTGGGCCTACCCAAGACATCCTTAGGT
*
3119902 CCGTAGGGTTACCTTATGCACACAGCAAAGGGAACCAACTTAAGGATATACCTTAGGACCTACCC
131 CCGTAGGGTTACCTTATGCACACAGCAAAGGGAACCAACTTAAAGATATACCTTAGGACCTACCC
3119967 AAGATATCCTTAGGTACATAGGGTTACCTTATGCACACAGCAAA
196 AAGATATCCTTAGGTACATAGGGTTACCTTATGCACACAGCAAA
* * *
3120011 GGGAACCAACCTAAGGATATACCTTGGGACCTAC-CCAAGATATCCTTAGGTCCATAGGGTTACC
1 GGGAACCAACCTAAGGATATACCTT-GGACCTACTCCAAGACATCCTTAGATCCATAGGGTAACC
* *
3120075 CTATGCACACAACAAAGGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAG
65 CTAAGCACACAACAAAGGGAACCAACCTAAGGATATACCTTGGG-CCTACCCAAGACATCCTTAG
* **
3120140 GTCCGTAGGGTTACCTTATGCACACAGCAAAGGGAACCAACTTAAAGATATGCCTT-GGGGCTAC
129 GTCCGTAGGGTTACCTTATGCACACAGCAAAGGGAACCAACTTAAAGATATACCTTAGGACCTAC
*
3120204 CCAAGATATCCTTAGGTCCATA
194 CCAAGATATCCTTAGGTACATA
3120226 AGGACTTACA
Statistics
Matches: 195, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
239 115 0.59
240 80 0.41
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (239 bp):
GGGAACCAACCTAAGGATATACCTTGGACCTACTCCAAGACATCCTTAGATCCATAGGGTAACCC
TAAGCACACAACAAAGGGAACCAACCTAAGGATATACCTTGGGCCTACCCAAGACATCCTTAGGT
CCGTAGGGTTACCTTATGCACACAGCAAAGGGAACCAACTTAAAGATATACCTTAGGACCTACCC
AAGATATCCTTAGGTACATAGGGTTACCTTATGCACACAGCAAA
Found at i:3125117 original size:80 final size:80
Alignment explanation
Indices: 3124887--3125341 Score: 684
Period size: 80 Copynumber: 5.7 Consensus size: 80
3124877 CAGCAAAAAG
* * *
3124887 GGGAGCCAACCTAAGGATATACCTT-AGATCTACCCAAGGATATCCTTAGATCCGTAGGGTTACC
1 GGGAACCAACCTAAGGATATACCTTGAGACCTACCCAA-GATATCCTTAGGTCCGTAGGGTTACC
** *
3124951 TTAACCACACAGCTAA
65 TTATGCACACAGCAAA
* * * *
3124967 GGGAACCAACCTAAGGATATACCTTG-GGCCTACCCAAGACATCTTTAGGTCCGTAGGGTTATCT
1 GGGAACCAACCTAAGGATATACCTTGAGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
3125031 TATGCACACAGCAAA
66 TATGCACACAGCAAA
*
3125046 GGGAACCAACCTAAGGATATACCTTGAGACCTACCCAAGATATCCTTAGGTTCGTAGGGTTACCT
1 GGGAACCAACCTAAGGATATACCTTGAGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
3125111 TATGCACACAGCAAA
66 TATGCACACAGCAAA
* * *
3125126 GGGAACCAACCTAAGGATATACCTTGGGACCTACCCAATATATCCTTAGGTCCGTAGGGTTACCC
1 GGGAACCAACCTAAGGATATACCTTGAGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
3125191 TATGCACACAGCAAA
66 TATGCACACAGCAAA
*
3125206 GGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
1 GGGAACCAACCTAAGGATATACCTTGAGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
3125271 TATGCACACAGCAAA
66 TATGCACACAGCAAA
** * *
3125286 GGGAACCAACCTAAGGATATGTCTT-ATGGA-CTACCCAAGATATCTTTAGGTTCGTA
1 GGGAACCAACCTAAGGATATACCTTGA--GACCTACCCAAGATATCCTTAGGTCCGTA
3125342 AGAACTTACA
Statistics
Matches: 345, Mismatches: 26, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
79 61 0.18
80 282 0.82
81 2 0.01
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.23
Consensus pattern (80 bp):
GGGAACCAACCTAAGGATATACCTTGAGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
TATGCACACAGCAAA
Found at i:3139001 original size:21 final size:23
Alignment explanation
Indices: 3138954--3139015 Score: 92
Period size: 21 Copynumber: 2.8 Consensus size: 23
3138944 CTTCGCATTA
* *
3138954 GTACCGATACCATCCTTGAATGG
1 GTACCGATACCCTCCATGAATGG
3138977 GTACCGATACCCTCCATG-A-GG
1 GTACCGATACCCTCCATGAATGG
3138998 GTACCGATACCCTCCATG
1 GTACCGATACCCTCCATG
3139016 GGTTCTGGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 20 0.54
22 1 0.03
23 16 0.43
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.23
Consensus pattern (23 bp):
GTACCGATACCCTCCATGAATGG
Found at i:3139427 original size:14 final size:14
Alignment explanation
Indices: 3139408--3139436 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3139398 AATTTTGAAA
3139408 TAATAAAAAATTAT
1 TAATAAAAAATTAT
3139422 TAATAAAAAATTAT
1 TAATAAAAAATTAT
3139436 T
1 T
3139437 TTGATTTTAA
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TAATAAAAAATTAT
Found at i:3139505 original size:13 final size:13
Alignment explanation
Indices: 3139480--3139520 Score: 64
Period size: 13 Copynumber: 3.1 Consensus size: 13
3139470 TAAAAACTAC
3139480 ACATTGATTTTCAA
1 ACATTG-TTTTCAA
3139494 ACATTGTTTTCAA
1 ACATTGTTTTCAA
*
3139507 ACATAGTTTTCAA
1 ACATTGTTTTCAA
3139520 A
1 A
3139521 ATTTGCCCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 20 0.77
14 6 0.23
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (13 bp):
ACATTGTTTTCAA
Found at i:3143899 original size:46 final size:46
Alignment explanation
Indices: 3143830--3143918 Score: 142
Period size: 46 Copynumber: 1.9 Consensus size: 46
3143820 AATGATCGAA
* *
3143830 ATATAATAAATCAATATCGTAAATGATTAAAATATTATTTATTAAG
1 ATATAATAAATCAATAACATAAATGATTAAAATATTATTTATTAAG
**
3143876 ATATAATAAATTTATAACATAAATGATTAAAATATTATTTATT
1 ATATAATAAATCAATAACATAAATGATTAAAATATTATTTATT
3143919 TAAAATCGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.42
Consensus pattern (46 bp):
ATATAATAAATCAATAACATAAATGATTAAAATATTATTTATTAAG
Found at i:3143913 original size:23 final size:22
Alignment explanation
Indices: 3143849--3143913 Score: 53
Period size: 23 Copynumber: 2.9 Consensus size: 22
3143839 ATCAATATCG
**
3143849 TAAATGATTAAAATATTATTTA
1 TAAATGATTAAAATATTATACA
*
3143871 TTAA-GATATAATAA-ATTTATAACA
1 TAAATGAT-TAA-AATA-TTAT-ACA
3143895 TAAATGATTAAAATATTAT
1 TAAATGATTAAAATATTAT
3143914 TTATTTAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 11
0.69 0.08 0.23
Matches are distributed among these distances:
21 3 0.09
22 7 0.21
23 12 0.36
24 8 0.24
25 3 0.09
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.42
Consensus pattern (22 bp):
TAAATGATTAAAATATTATACA
Found at i:3146125 original size:20 final size:23
Alignment explanation
Indices: 3146081--3146126 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
3146071 TATTAGGATA
3146081 ATGGGTTAGAAAGAAAAATGATAT
1 ATGGGTTAGAAAGAAAAAT-ATAT
*
3146105 ATGGGTTAGAAA-AAAATTATAT
1 ATGGGTTAGAAAGAAAAATATAT
3146127 TATTAATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 4 0.19
23 5 0.24
24 12 0.57
ACGTcount: A:0.50, C:0.00, G:0.22, T:0.28
Consensus pattern (23 bp):
ATGGGTTAGAAAGAAAAATATAT
Found at i:3146126 original size:22 final size:24
Alignment explanation
Indices: 3146077--3146120 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
3146067 AAAATATTAG
3146077 GATA-ATGGGTTAGAAAGAAAAAT
1 GATATATGGGTTAGAAAGAAAAAT
3146100 GATATATGGGTTAGAAA-AAAA
1 GATATATGGGTTAGAAAGAAAA
3146121 TTATATTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.52, C:0.00, G:0.25, T:0.23
Consensus pattern (24 bp):
GATATATGGGTTAGAAAGAAAAAT
Found at i:3146317 original size:13 final size:13
Alignment explanation
Indices: 3146284--3146317 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
3146274 CGAAACAAAC
3146284 AAAAAAATCCACA
1 AAAAAAATCCACA
* *
3146297 AAAGAAATCCCCA
1 AAAAAAATCCACA
3146310 AAAAAAAT
1 AAAAAAAT
3146318 ATACATATTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.68, C:0.21, G:0.03, T:0.09
Consensus pattern (13 bp):
AAAAAAATCCACA
Found at i:3147158 original size:19 final size:19
Alignment explanation
Indices: 3147134--3147170 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3147124 GTTTGATAAT
3147134 TTTTTAGTAGTAAAAATTA
1 TTTTTAGTAGTAAAAATTA
*
3147153 TTTTTAGTAGTAGAAATT
1 TTTTTAGTAGTAAAAATT
3147171 TTGCCTATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.49
Consensus pattern (19 bp):
TTTTTAGTAGTAAAAATTA
Found at i:3147812 original size:34 final size:34
Alignment explanation
Indices: 3147773--3147857 Score: 152
Period size: 34 Copynumber: 2.5 Consensus size: 34
3147763 TATATATATA
* *
3147773 TATATATATAATATTTTATATTTTTTATATTAAT
1 TATATATAAAATATTTTATATATTTTATATTAAT
3147807 TATATATAAAATATTTTATATATTTTATATTAAT
1 TATATATAAAATATTTTATATATTTTATATTAAT
3147841 TATATATAAAATATTTT
1 TATATATAAAATATTTT
3147858 TGGGTTCGGG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (34 bp):
TATATATAAAATATTTTATATATTTTATATTAAT
Found at i:3160638 original size:43 final size:43
Alignment explanation
Indices: 3160556--3160647 Score: 107
Period size: 43 Copynumber: 2.2 Consensus size: 43
3160546 GGTGAAATTC
*** *
3160556 TATGTGACAATATTATCCATTCGTTCTTAGAGACGTGAGTCTT
1 TATGTGACAATATTATCCATTCAACCTTAGAGACATGAGTCTT
* * *
3160599 TATGTGATAATATTATCCATTCAACCTTAGCGATATGAGTC--
1 TATGTGACAATATTATCCATTCAACCTTAGAGACATGAGTCTT
3160640 TATGTGAC
1 TATGTGAC
3160648 CCTATGTGAC
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 7 0.17
43 34 0.83
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.38
Consensus pattern (43 bp):
TATGTGACAATATTATCCATTCAACCTTAGAGACATGAGTCTT
Found at i:3171511 original size:26 final size:27
Alignment explanation
Indices: 3171481--3171539 Score: 77
Period size: 26 Copynumber: 2.2 Consensus size: 27
3171471 TTAAATTAGT
*
3171481 GAAATATTGTGTTT-TAAAA-AGTTAAA
1 GAAATATTGT-TTTGAAAAATAGTTAAA
*
3171507 GAAATATTGTTTTGAAAAATATTTAAA
1 GAAATATTGTTTTGAAAAATAGTTAAA
3171534 GAAATA
1 GAAATA
3171540 AGGTGAATGC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 3 0.10
26 14 0.48
27 12 0.41
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (27 bp):
GAAATATTGTTTTGAAAAATAGTTAAA
Found at i:3171828 original size:2 final size:2
Alignment explanation
Indices: 3171821--3171859 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
3171811 GATAAAAGCA
3171821 AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3171860 CAAATTATTG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3172436 original size:20 final size:20
Alignment explanation
Indices: 3172411--3172451 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
3172401 TCAATGGTAA
3172411 AAGAGAATATTATTCTACCT
1 AAGAGAATATTATTCTACCT
3172431 AAGAGAATATTATTCTACCT
1 AAGAGAATATTATTCTACCT
3172451 A
1 A
3172452 GAGGTTCTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.34
Consensus pattern (20 bp):
AAGAGAATATTATTCTACCT
Found at i:3179334 original size:25 final size:25
Alignment explanation
Indices: 3179293--3179364 Score: 119
Period size: 25 Copynumber: 2.9 Consensus size: 25
3179283 CATTAGGGGA
* *
3179293 TTAGGG-TTAAAACCCTAATTTGTT
1 TTAGGGTTTGAAACCCTAATCTGTT
3179317 TTAGGGTTTGAAACCCTAATCTGTT
1 TTAGGGTTTGAAACCCTAATCTGTT
3179342 TTAGGGTTTGAAACCCTAATCTG
1 TTAGGGTTTGAAACCCTAATCTG
3179365 ATGGGTTGGT
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
24 6 0.13
25 39 0.87
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.39
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGTT
Found at i:3179488 original size:3 final size:3
Alignment explanation
Indices: 3179480--3179536 Score: 80
Period size: 3 Copynumber: 18.3 Consensus size: 3
3179470 ATTAATAAAC
3179480 ATA ATA ATAA ATA ATA ATA ATA ATA ATA ATA ATA ATAA ATA AT- ATAA
1 ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA AT-A
3179527 ATA ATA ATA A
1 ATA ATA ATA A
3179537 AAAAGACCCG
Statistics
Matches: 50, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
2 2 0.04
3 40 0.80
4 8 0.16
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3179505 original size:28 final size:28
Alignment explanation
Indices: 3179472--3179536 Score: 98
Period size: 28 Copynumber: 2.3 Consensus size: 28
3179462 AATATGTAAT
3179472 TAATAA-ACATAATAATAAATAATA-ATAA
1 TAATAATA-ATAATAATAAATAATATA-AA
3179500 TAATAATAATAATAATAAATAATATAAA
1 TAATAATAATAATAATAAATAATATAAA
3179528 TAATAATAA
1 TAATAATAA
3179537 AAAAGACCCG
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
28 33 0.94
29 2 0.06
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.31
Consensus pattern (28 bp):
TAATAATAATAATAATAAATAATATAAA
Found at i:3179508 original size:25 final size:25
Alignment explanation
Indices: 3179472--3179536 Score: 82
Period size: 25 Copynumber: 2.6 Consensus size: 25
3179462 AATATGTAAT
3179472 TAATAA-ACATAATAATAAATAATAA
1 TAATAATA-ATAATAATAAATAATAA
3179497 TAATAATAATAATAAT-AATAAATAA
1 TAATAATAATAATAATAAAT-AATAA
3179522 T-ATAAATAATAATAA
1 TAAT-AATAATAATAA
3179537 AAAAGACCCG
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
24 5 0.14
25 31 0.84
26 1 0.03
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.31
Consensus pattern (25 bp):
TAATAATAATAATAATAAATAATAA
Found at i:3179920 original size:40 final size:42
Alignment explanation
Indices: 3179831--3180196 Score: 150
Period size: 40 Copynumber: 8.4 Consensus size: 42
3179821 ATAACACGAT
* *
3179831 TCCTACATGATGAGGACGG-CTGGTTATCTA--GGATGACACGGC
1 TCCTACGTGATGAGGA-GGTCTGG--ATCTAGGGGATGACACTGC
3179873 TCCTACGTGATGAGGAGGTCTGG-TC-AGGGGATGACACTGC
1 TCCTACGTGATGAGGAGGTCTGGATCTAGGGGATGACACTGC
* * * * * *
3179913 TCATACGTGATGAAGAGTTCTGGACATCTTTAGGTAGGGCGATAACACGGT
1 TCCTACGTGATGAGGAGGTCTGG--ATC------TAGGG-GATGACACTGC
* *
3179964 TCCTACGTGATGAGGACGG-CTGGTTATCTA-TGGTTGACA-TGGC
1 TCCTACGTGATGAGGA-GGTCTGG--ATCTAGGGGATGACACT-GC
*
3180007 TCCTACATGATGAGGAGGTCTGG-TC-AGGGGATGACACTGC
1 TCCTACGTGATGAGGAGGTCTGGATCTAGGGGATGACACTGC
* * * * * *
3180047 TCATACGTGATGAAGAGTTCTGGACATCTTTAGGTAGGGCGATAACACGGT
1 TCCTACGTGATGAGGAGGTCTGG--ATC------TAGGG-GATGACACTGC
* *
3180098 TCCTACGTGATGAGGACGG-CTGGTTATCTA-TGGTTGACA-TGGC
1 TCCTACGTGATGAGGA-GGTCTGG--ATCTAGGGGATGACACT-GC
* * * *
3180141 TCCTACATGATGAGGAGATCTGG-TC-AGGGGATGACACGGT
1 TCCTACGTGATGAGGAGGTCTGGATCTAGGGGATGACACTGC
*
3180181 TCCTATGTGATGAGGA
1 TCCTACGTGATGAGGA
3180197 CTACTGGCCA
Statistics
Matches: 243, Mismatches: 46, Indels: 72
0.67 0.13 0.20
Matches are distributed among these distances:
38 1 0.00
39 4 0.02
40 85 0.35
41 3 0.01
42 22 0.09
43 54 0.22
44 2 0.01
45 4 0.02
50 8 0.03
51 58 0.24
52 2 0.01
ACGTcount: A:0.23, C:0.18, G:0.33, T:0.26
Consensus pattern (42 bp):
TCCTACGTGATGAGGAGGTCTGGATCTAGGGGATGACACTGC
Found at i:3180209 original size:134 final size:134
Alignment explanation
Indices: 3179731--3180177 Score: 736
Period size: 134 Copynumber: 3.3 Consensus size: 134
3179721 CATCTAAAAG
* * * * * *
3179731 TGACAAGGTTCCTACATGATGAGGAAATCTGATCAAGGGATGACACTGCTCATACATGATGAAGA
1 TGACATGGCTCCTACATGATGAGGAGATCTGGTCAGGGGATGACACTGCTCATACGTGATGAAGA
* * * *
3179796 GTTCTGGTCATCTTTAGG-AGGAGTGATAACACGATTCCTACATGATGAGGACGGCTGGTTATCT
66 GTTCTGGACATCTTTAGGTAGG-GCGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCT
*
3179860 A-GGA
130 ATGGT
* * *
3179864 TGACACGGCTCCTACGTGATGAGGAGGTCTGGTCAGGGGATGACACTGCTCATACGTGATGAAGA
1 TGACATGGCTCCTACATGATGAGGAGATCTGGTCAGGGGATGACACTGCTCATACGTGATGAAGA
3179929 GTTCTGGACATCTTTAGGTAGGGCGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTA
66 GTTCTGGACATCTTTAGGTAGGGCGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTA
3179994 TGGT
131 TGGT
*
3179998 TGACATGGCTCCTACATGATGAGGAGGTCTGGTCAGGGGATGACACTGCTCATACGTGATGAAGA
1 TGACATGGCTCCTACATGATGAGGAGATCTGGTCAGGGGATGACACTGCTCATACGTGATGAAGA
3180063 GTTCTGGACATCTTTAGGTAGGGCGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTA
66 GTTCTGGACATCTTTAGGTAGGGCGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTA
3180128 TGGT
131 TGGT
3180132 TGACATGGCTCCTACATGATGAGGAGATCTGGTCAGGGGATGACAC
1 TGACATGGCTCCTACATGATGAGGAGATCTGGTCAGGGGATGACAC
3180178 GGTTCCTATG
Statistics
Matches: 296, Mismatches: 16, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
133 114 0.39
134 182 0.61
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (134 bp):
TGACATGGCTCCTACATGATGAGGAGATCTGGTCAGGGGATGACACTGCTCATACGTGATGAAGA
GTTCTGGACATCTTTAGGTAGGGCGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTA
TGGT
Found at i:3180588 original size:35 final size:36
Alignment explanation
Indices: 3180547--3180642 Score: 108
Period size: 36 Copynumber: 2.7 Consensus size: 36
3180537 ACAAAATTCA
**
3180547 TTTCAAGAGAAACGATCTCAAAGAT-GTTTATTTTG
1 TTTCAAGAGAAACGATCTCAAAGATGGTAAATTTTG
*
3180582 TTTCAAGGGAAACAGAT-TCAAAGATGGTAAATTTTG
1 TTTCAAGAGAAAC-GATCTCAAAGATGGTAAATTTTG
* *
3180618 TTTCCAA-AGAAACAAACTCAAAGAT
1 TTT-CAAGAGAAACGATCTCAAAGAT
3180643 TTTTCCCAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
35 21 0.41
36 27 0.53
37 3 0.06
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (36 bp):
TTTCAAGAGAAACGATCTCAAAGATGGTAAATTTTG
Found at i:3181075 original size:62 final size:63
Alignment explanation
Indices: 3181008--3181133 Score: 200
Period size: 63 Copynumber: 2.0 Consensus size: 63
3180998 AAGATGTTTT
* *
3181008 TTTTTTCAAAAGAAGTTGTC-TCAAGAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGA
1 TTTTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGA
* * *
3181070 TTTTTTCAAAAGAAATTGTCTTTAAGAGATAAAATTTTGTTTCAAAAGAAACAGACTCAAAGA
1 TTTTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGA
3181133 T
1 T
3181134 GGATCACATC
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
62 19 0.33
63 39 0.67
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (63 bp):
TTTTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGA
Found at i:3181252 original size:120 final size:118
Alignment explanation
Indices: 3181032--3181254 Score: 272
Period size: 120 Copynumber: 1.9 Consensus size: 118
3181022 GTTGTCTCAA
* * *
3181032 GAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTCAAAAGAAATTGTCTTTAAGA
1 GAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGAGTTTTTCAAAAGAAACTGTCTTCAAGA
*
3181097 GATAAAATTTTGTTTCAAAAGAAACAGACTCAAAGATGGATCACATCTTAAGT
66 GAGAAAATTTTGTTTCAAAAGAAACAGACTCAAAGATGGATCACATCTTAAGT
* * * **
3181150 GAGACCAAA-TTTGTTTCAAATGAAACAATCTCAAAAGTTAGTTTTTCATTAGAAACTGTC-TCA
1 GAGACAAAATTTTGTTTCAAAGGAAACAAACTC-AAAG--AGTTTTTCAAAAGAAACTGTCTTCA
** *
3181213 AGAGAGACAACA-TTTGTTTTTAAAGAAATAGACTCAAAGATG
63 AGAGAGA-AA-ATTTTGTTTCAAAAGAAACAGACTCAAAGATG
3181255 ATTTTGTTAA
Statistics
Matches: 88, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
117 21 0.24
118 12 0.14
119 8 0.09
120 46 0.52
121 1 0.01
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.30
Consensus pattern (118 bp):
GAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGAGTTTTTCAAAAGAAACTGTCTTCAAGA
GAGAAAATTTTGTTTCAAAAGAAACAGACTCAAAGATGGATCACATCTTAAGT
Found at i:3181777 original size:36 final size:36
Alignment explanation
Indices: 3181693--3181795 Score: 122
Period size: 36 Copynumber: 2.9 Consensus size: 36
3181683 GAGAAACTGA
* * *
3181693 TGTCTCAAGCGAGACGAAATTTG-CTTTA-AGATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
* **
3181727 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
*
3181763 TGTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAA
3181796 CGATCTCAAG
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
34 19 0.33
35 9 0.16
36 29 0.51
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
Found at i:3182137 original size:3 final size:3
Alignment explanation
Indices: 3182124--3182156 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
3182114 GACACTTTAT
3182124 TTA TTA TTTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TT
3182157 TTTTAGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:3182500 original size:14 final size:14
Alignment explanation
Indices: 3182473--3182514 Score: 66
Period size: 14 Copynumber: 2.9 Consensus size: 14
3182463 ATGCAAATTT
3182473 TATGTATCATGTATG
1 TATGTAT-ATGTATG
3182488 TATGTATATGTATG
1 TATGTATATGTATG
*
3182502 TATGTATGTGTAT
1 TATGTATATGTAT
3182515 ACTTTTCTCG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 19 0.73
15 7 0.27
ACGTcount: A:0.26, C:0.02, G:0.21, T:0.50
Consensus pattern (14 bp):
TATGTATATGTATG
Found at i:3182829 original size:66 final size:66
Alignment explanation
Indices: 3182745--3182881 Score: 265
Period size: 66 Copynumber: 2.1 Consensus size: 66
3182735 GAGATTATCT
*
3182745 TGTTTGAAAATGTTTTTCTTCTTCTTTTATTTTCAAAAGTCTGACAATATCAATAGTTTTGAAAA
1 TGTTTGAAAATGTCTTTCTTCTTCTTTTATTTTCAAAAGTCTGACAATATCAATAGTTTTGAAAA
3182810 A
66 A
3182811 TGTTTGAAAATGTCTTTCTTCTTCTTTTATTTTCAAAAGTCTGACAATATCAATAGTTTTGAAAA
1 TGTTTGAAAATGTCTTTCTTCTTCTTTTATTTTCAAAAGTCTGACAATATCAATAGTTTTGAAAA
3182876 A
66 A
3182877 TGTTT
1 TGTTT
3182882 AATCAAAAGA
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 70 1.00
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.47
Consensus pattern (66 bp):
TGTTTGAAAATGTCTTTCTTCTTCTTTTATTTTCAAAAGTCTGACAATATCAATAGTTTTGAAAA
A
Found at i:3183776 original size:13 final size:13
Alignment explanation
Indices: 3183758--3183956 Score: 92
Period size: 13 Copynumber: 14.5 Consensus size: 13
3183748 GCTTTTGTCT
*
3183758 TCTTTTTCCTTGC
1 TCTTTTTCTTTGC
3183771 TCTTTTTTCTTTG-
1 TC-TTTTTCTTTGC
*
3183784 TTTTTTTCTTTGC
1 TCTTTTTCTTTGC
*
3183797 TCTTCTGTGTTCTTTTTC
1 TC-T-T-T-TTC-TTTGC
3183815 TCTTTTTTCTTTGC
1 TC-TTTTTCTTTGC
3183829 T-TTTTCTCTTTGC
1 TCTTTT-TCTTTGC
3183842 T-TATTTTCCGTTTGC
1 TCT-TTTT-C-TTTGC
3183857 TC--TTT-TTT--
1 TCTTTTTCTTTGC
3183865 TC-TTTTCTTTGC
1 TCTTTTTCTTTGC
* *
3183877 TATTTGTTTCTTTGT
1 T-CTT-TTTCTTTGC
*
3183892 TTTTTTTCTTTGC
1 TCTTTTTCTTTGC
*
3183905 TCTTCTGTGTTCTTTTTC
1 TC-T-T-T-TTC-TTTGC
3183923 TCTTTTTCTTTGC
1 TCTTTTTCTTTGC
*
3183936 TTTTTTTCTTTGC
1 TCTTTTTCTTTGC
3183949 TTCTTTTT
1 -TCTTTTT
3183957 TGTTTGCTTT
Statistics
Matches: 148, Mismatches: 13, Indels: 49
0.70 0.06 0.23
Matches are distributed among these distances:
8 2 0.01
9 3 0.02
10 6 0.04
12 15 0.10
13 42 0.28
14 33 0.22
15 21 0.14
16 4 0.03
17 8 0.05
18 14 0.09
ACGTcount: A:0.01, C:0.19, G:0.09, T:0.71
Consensus pattern (13 bp):
TCTTTTTCTTTGC
Found at i:3183794 original size:32 final size:33
Alignment explanation
Indices: 3183747--3183902 Score: 79
Period size: 35 Copynumber: 4.4 Consensus size: 33
3183737 TTTGTCTTTG
3183747 TGCTTTTGTCTTCTTTTTCCTTGCTCTTTTTTCTT
1 TGCTTTT-T-TTCTTTTTCCTTGCTCTTTTTTCTT
* *
3183782 TG-TTTTTTTCTTTGCTCTTCTGTGTTCTTTTTCTCTT
1 TGCTTTTTTTCTTT--T-TCCT-TGCTCTTTTT-TCTT
* *
3183819 T--TTTCTTTGCTTTTTCTCTTTGCT-TATTTTCCGTT
1 TGCTTT-TTTTCTTTTTC-C-TTGCTCT-TTTTTC-TT
* *
3183854 TGCTCTTTTTT-TCTTTTCTTTGCTATTTGTTTCTT
1 TGCT-TTTTTTCT-TTTTCCTTGCTCTTT-TTTCTT
*
3183889 TGTTTTTTTTCTTT
1 TGCTTTTTTTCTTT
3183903 GCTCTTCTGT
Statistics
Matches: 94, Mismatches: 10, Indels: 35
0.68 0.07 0.25
Matches are distributed among these distances:
32 6 0.06
33 1 0.01
34 16 0.17
35 30 0.32
36 18 0.19
37 21 0.22
38 2 0.02
ACGTcount: A:0.01, C:0.19, G:0.09, T:0.71
Consensus pattern (33 bp):
TGCTTTTTTTCTTTTTCCTTGCTCTTTTTTCTT
Found at i:3183815 original size:35 final size:35
Alignment explanation
Indices: 3183774--3183923 Score: 98
Period size: 35 Copynumber: 4.2 Consensus size: 35
3183764 TCCTTGCTCT
3183774 TTTTTCTTTG-TTTTTTTCTTTGCTCTTCTGTGTTC
1 TTTTTCTTTGCTTTTTTTCTTTGCTCTT-TGTGTTC
* * *
3183809 TTTTTCTCTT--TTTTCTTTGCTTTTTCTCTTTG-CTTA
1 TTTTTCT-TTGCTTTT-TTT-C-TTTGCTCTTTGTGTTC
* *
3183845 TTTTCCGTTTGCTCTTTTTTTCTTT--TCTTTGCTATT-
1 TTTTTC-TTTG--CTTTTTTTCTTTGCTCTTTG-TGTTC
* *
3183881 TGTTTCTTTGTTTTTTTTCTTTGCTCTTCTGTGTTC
1 TTTTTCTTTGCTTTTTTTCTTTGCTCTT-TGTGTTC
3183917 TTTTTCT
1 TTTTTCT
3183924 CTTTTTCTTT
Statistics
Matches: 90, Mismatches: 10, Indels: 29
0.70 0.08 0.22
Matches are distributed among these distances:
33 11 0.12
35 28 0.31
36 26 0.29
37 9 0.10
38 9 0.10
39 3 0.03
40 4 0.04
ACGTcount: A:0.01, C:0.18, G:0.09, T:0.71
Consensus pattern (35 bp):
TTTTTCTTTGCTTTTTTTCTTTGCTCTTTGTGTTC
Found at i:3183864 original size:43 final size:45
Alignment explanation
Indices: 3183767--3183874 Score: 118
Period size: 44 Copynumber: 2.5 Consensus size: 45
3183757 TTCTTTTTCC
* * *
3183767 TTGCTCTTTTTTCTTTG-TTTTTTTCTTTGCTCTTCTGTGTTCTT
1 TTGCTCTTTTTTCTTTGCTTTTTCTCTTTGCTCTTCTGTGTCCGT
*
3183811 TTTCTCTTTTTTCTTTGCTTTTTCTCTTTGCT-TAT-T-T-TCCGT
1 TTGCTCTTTTTTCTTTGCTTTTTCTCTTTGCTCT-TCTGTGTCCGT
*
3183853 TTGCTCTTTTTTTCTTTTCTTT
1 TTGCTC-TTTTTTCTTTGCTTT
3183875 GCTATTTGTT
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
42 8 0.15
43 15 0.27
44 18 0.33
45 14 0.25
ACGTcount: A:0.01, C:0.19, G:0.08, T:0.71
Consensus pattern (45 bp):
TTGCTCTTTTTTCTTTGCTTTTTCTCTTTGCTCTTCTGTGTCCGT
Found at i:3183904 original size:48 final size:46
Alignment explanation
Indices: 3183819--3183957 Score: 133
Period size: 44 Copynumber: 3.0 Consensus size: 46
3183809 TTTTTCTCTT
* * *
3183819 TTTTCTTTGCTTTTTCTCTTTGCTTATTTTCCGTTTGCTCTTTTTTTC
1 TTTTCTTTGCTTTTTTTCTTTG-TTTTTTTTC-TTTGCTCTTTTTTTC
*
3183867 TTTTCTTTGCTATTTGTTTCTTTGTTTTTTTTCTTTGCTCTTCTGTGTTC
1 TTTTCTTTGCT-TTT-TTTCTTTGTTTTTTTTCTTTGCTCTT-T-TTTTC
* *
3183917 --TT-TTT-CTCTTTTTCTTTGCTTTTTTTCTTTGCTTCTTTTTT
1 TTTTCTTTGCTTTTTTTCTTTGTTTTTTTTCTTTGC-TCTTTTTT
3183958 GTTTGCTTTT
Statistics
Matches: 79, Mismatches: 7, Indels: 15
0.78 0.07 0.15
Matches are distributed among these distances:
43 2 0.03
44 22 0.28
45 6 0.08
46 2 0.03
47 3 0.04
48 22 0.28
49 11 0.14
50 11 0.14
ACGTcount: A:0.01, C:0.18, G:0.09, T:0.72
Consensus pattern (46 bp):
TTTTCTTTGCTTTTTTTCTTTGTTTTTTTTCTTTGCTCTTTTTTTC
Found at i:3183932 original size:31 final size:28
Alignment explanation
Indices: 3183860--3183956 Score: 103
Period size: 28 Copynumber: 3.4 Consensus size: 28
3183850 CGTTTGCTCT
3183860 TTTTTTC-TTTTCTTTGCTATTTGTTTC
1 TTTTTTCTTTTTCTTTGCTATTTGTTTC
*
3183887 TTTGTTT-TTTTTCTTTGCTCTTCTGTGTTC
1 TTT-TTTCTTTTTCTTTGCTATT-TGT-TTC
3183917 TTTTTCTCTTTTTCTTTGCT-TTT-TTTC
1 TTTTT-TCTTTTTCTTTGCTATTTGTTTC
*
3183944 TTTGCTTCTTTTT
1 TTT-TTTCTTTTT
3183957 TGTTTGCTTT
Statistics
Matches: 61, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
27 16 0.26
28 18 0.30
29 6 0.10
30 9 0.15
31 12 0.20
ACGTcount: A:0.01, C:0.16, G:0.08, T:0.74
Consensus pattern (28 bp):
TTTTTTCTTTTTCTTTGCTATTTGTTTC
Found at i:3183946 original size:107 final size:106
Alignment explanation
Indices: 3183761--3183964 Score: 329
Period size: 107 Copynumber: 1.9 Consensus size: 106
3183751 TTTGTCTTCT
*
3183761 TTTTCCTTGCTCTTTTTTCTTTGTTTTTTTCTTTGCTCTTCTGTGTTCTTTTTCTCTTTTTTCTT
1 TTTTCCTTGCTATTTTTTCTTTGTTTTTTTCTTTGCTCTTCTGTGTTCTTTTTCTCTTTTTTCTT
3183826 TGCTTTTTCTCTTTGCTTATTTTCCGTTTGCTCTTTTTTTC
66 TGCTTTTTCTCTTTGCTTATTTTCCGTTTGCTCTTTTTTTC
*
3183867 TTTTCTTTGCTATTTGTTTCTTTGTTTTTTTTCTTTGCTCTTCTGTGTTCTTTTTCTC-TTTTTC
1 TTTTCCTTGCTATTT-TTTCTTTG-TTTTTTTCTTTGCTCTTCTGTGTTCTTTTTCTCTTTTTTC
* * **
3183931 TTTGCTTTTTTTCTTTGCTTCTTTTTTGTTTGCT
64 TTTGCTTTTTCTCTTTGCTTATTTTCCGTTTGCT
3183965 TTTCTTGTCT
Statistics
Matches: 90, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
106 13 0.14
107 44 0.49
108 33 0.37
ACGTcount: A:0.01, C:0.19, G:0.09, T:0.71
Consensus pattern (106 bp):
TTTTCCTTGCTATTTTTTCTTTGTTTTTTTCTTTGCTCTTCTGTGTTCTTTTTCTCTTTTTTCTT
TGCTTTTTCTCTTTGCTTATTTTCCGTTTGCTCTTTTTTTC
Found at i:3183963 original size:59 final size:58
Alignment explanation
Indices: 3183856--3183977 Score: 160
Period size: 59 Copynumber: 2.1 Consensus size: 58
3183846 TTTCCGTTTG
*
3183856 CTCTTTTTTTCTTTTCTTTGCTATTTGTTTCTTTGTTTTTTTTCTTTGCTCTTCTGTGT
1 CTCTTTTTCTCTTTTCTTTGCTATTTGTTTCTTTGTTTTTTTTCTTTGCTCTTCT-TGT
* *
3183915 -TCTTTTTCTCTTTTTCTTTGCT-TTT-TTTCTTTGCTTCTTTTTTGTTTGCTTTTCTTGT
1 CTCTTTTTCTC-TTTTCTTTGCTATTTGTTTCTTTG-TT-TTTTTTCTTTGCTCTTCTTGT
3183973 CTCTT
1 CTCTT
3183978 CACTTTGATT
Statistics
Matches: 56, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
57 8 0.14
58 17 0.30
59 31 0.55
ACGTcount: A:0.01, C:0.18, G:0.09, T:0.72
Consensus pattern (58 bp):
CTCTTTTTCTCTTTTCTTTGCTATTTGTTTCTTTGTTTTTTTTCTTTGCTCTTCTTGT
Found at i:3183972 original size:13 final size:13
Alignment explanation
Indices: 3183925--3183972 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
3183915 TCTTTTTCTC
*
3183925 TTTTTCTTTGCTT
1 TTTTTGTTTGCTT
*
3183938 TTTTTCTTTGCTTCT
1 TTTTTGTTTGC-T-T
3183953 TTTTTGTTTGCTT
1 TTTTTGTTTGCTT
*
3183966 TTCTTGT
1 TTTTTGT
3183973 CTCTTCACTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 18 0.58
14 2 0.06
15 11 0.35
ACGTcount: A:0.00, C:0.15, G:0.10, T:0.75
Consensus pattern (13 bp):
TTTTTGTTTGCTT
Found at i:3186987 original size:32 final size:32
Alignment explanation
Indices: 3186946--3187008 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
3186936 TGACAAAATG
3186946 ACACAAAC-AAAAGAGAAGAAATAAGTTAGTAT
1 ACACAAACAAAAAGAGAA-AAATAAGTTAGTAT
3186978 ACACAAACAAAAAGAGAAAAATAAGTTAGTA
1 ACACAAACAAAAAGAGAAAAATAAGTTAGTA
3187009 CATGTAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 21 0.70
33 9 0.30
ACGTcount: A:0.62, C:0.10, G:0.14, T:0.14
Consensus pattern (32 bp):
ACACAAACAAAAAGAGAAAAATAAGTTAGTAT
Found at i:3190983 original size:25 final size:25
Alignment explanation
Indices: 3190942--3191013 Score: 119
Period size: 25 Copynumber: 2.9 Consensus size: 25
3190932 CATTAGGGGA
* *
3190942 TTAGGG-TTAAAACCCTAATTTGTT
1 TTAGGGTTTGAAACCCTAATCTGTT
3190966 TTAGGGTTTGAAACCCTAATCTGTT
1 TTAGGGTTTGAAACCCTAATCTGTT
3190991 TTAGGGTTTGAAACCCTAATCTG
1 TTAGGGTTTGAAACCCTAATCTG
3191014 ATGGGTTAGT
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
24 6 0.13
25 39 0.87
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.39
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGTT
Found at i:3191139 original size:3 final size:3
Alignment explanation
Indices: 3191131--3191187 Score: 80
Period size: 3 Copynumber: 18.3 Consensus size: 3
3191121 TAATAAACAT
3191131 ATA ATA ATAA ATA ATA ATA ATA ATA ATA ATA ATA ATAA ATA AT- ATAA
1 ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA AT-A
3191178 ATA ATA ATA A
1 ATA ATA ATA A
3191188 AAAAGACCCG
Statistics
Matches: 50, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
2 2 0.04
3 40 0.80
4 8 0.16
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3191143 original size:18 final size:19
Alignment explanation
Indices: 3191131--3191187 Score: 91
Period size: 19 Copynumber: 3.1 Consensus size: 19
3191121 TAATAAACAT
3191131 ATAATAATAAATAATAATA
1 ATAATAATAAATAATAATA
3191150 ATAATAAT-AATAATAATAA
1 ATAATAATAAATAATAAT-A
3191169 ATAAT-ATAAATAATAATA
1 ATAATAATAAATAATAATA
3191187 A
1 A
3191188 AAAAGACCCG
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
18 13 0.36
19 23 0.64
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
ATAATAATAAATAATAATA
Found at i:3191163 original size:28 final size:28
Alignment explanation
Indices: 3191131--3191187 Score: 98
Period size: 28 Copynumber: 2.0 Consensus size: 28
3191121 TAATAAACAT
3191131 ATAATAATAAATAATA-ATAATAATAATA
1 ATAATAATAAATAATATA-AATAATAATA
3191159 ATAATAATAAATAATATAAATAATAATA
1 ATAATAATAAATAATATAAATAATAATA
3191187 A
1 A
3191188 AAAAGACCCG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 27 0.96
29 1 0.04
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (28 bp):
ATAATAATAAATAATATAAATAATAATA
Found at i:3194515 original size:12 final size:11
Alignment explanation
Indices: 3194500--3194526 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
3194490 TTCAAAACGT
3194500 AAAAAAAAAAG
1 AAAAAAAAAAG
3194511 AAAAAAAAAAG
1 AAAAAAAAAAG
3194522 AAAAA
1 AAAAA
3194527 GGAGAACCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:3204745 original size:26 final size:26
Alignment explanation
Indices: 3204710--3204761 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
3204700 ATCTGTTTTC
*
3204710 ACCCCCTTAAAATTTTATAAGTTCAT
1 ACCCCCTTAAAATTTTATAAATTCAT
*
3204736 ACCCCTTTAAAATTTTATAAATTCAT
1 ACCCCCTTAAAATTTTATAAATTCAT
3204762 TCCTCTAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.37, C:0.21, G:0.02, T:0.40
Consensus pattern (26 bp):
ACCCCCTTAAAATTTTATAAATTCAT
Found at i:3211714 original size:66 final size:64
Alignment explanation
Indices: 3211603--3211773 Score: 252
Period size: 66 Copynumber: 2.6 Consensus size: 64
3211593 AAAACCTCCA
* * *
3211603 GGGGTATCGATTCCCCTACAGGGGGAATCGGTTCCCCTACAGGGAGGAATCGATTCCCCTTCAAA
1 GGGGAATCGATTCCCCTTCAAGGGGAATCGGTTCCCCTACAGGGAGGAATCGATTCCCC-T-AAA
3211668 G
64 G
*
3211669 GGGGAATCGATTCCCCTTCAAGGGGAATCGGTTCCCCTACAGGGAGGAATCGATTCCCCTACAG
1 GGGGAATCGATTCCCCTTCAAGGGGAATCGGTTCCCCTACAGGGAGGAATCGATTCCCCTAAAG
*
3211733 GGAGGAATCGATTCCCCTTCAAAGGGGGAATCGATTCCCCT
1 GG-GGAATCGATTCCCCTTC-AA-GGGGAATCGGTTCCCCT
3211774 TCAAGGTATT
Statistics
Matches: 97, Mismatches: 5, Indels: 5
0.91 0.05 0.05
Matches are distributed among these distances:
64 5 0.05
65 18 0.19
66 58 0.60
67 16 0.16
ACGTcount: A:0.23, C:0.27, G:0.28, T:0.21
Consensus pattern (64 bp):
GGGGAATCGATTCCCCTTCAAGGGGAATCGGTTCCCCTACAGGGAGGAATCGATTCCCCTAAAG
Found at i:3211750 original size:88 final size:87
Alignment explanation
Indices: 3211602--3211779 Score: 320
Period size: 88 Copynumber: 2.0 Consensus size: 87
3211592 CAAAACCTCC
* *
3211602 AGGGGTATCGATTCCCCTACAGGGGGAATCGGTTCCCCTACAGGGAGGAATCGATTCCCCTTCAA
1 AGGGGAATCGATTCCCCTACAGGGGGAATCGATTCCCCTACAGGGAGGAATCGATTCCCCTTCAA
3211667 AGGGGGAATCGATTCCCCTTCA
66 AGGGGGAATCGATTCCCCTTCA
*
3211689 AGGGGAATCGGTTCCCCTACAGGGAGGAATCGATTCCCCTACAGGGAGGAATCGATTCCCCTTCA
1 AGGGGAATCGATTCCCCTACAGGG-GGAATCGATTCCCCTACAGGGAGGAATCGATTCCCCTTCA
3211754 AAGGGGGAATCGATTCCCCTTCA
65 AAGGGGGAATCGATTCCCCTTCA
3211777 AGG
1 AGG
3211780 TATTTTTCTA
Statistics
Matches: 87, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
87 22 0.25
88 65 0.75
ACGTcount: A:0.24, C:0.27, G:0.28, T:0.21
Consensus pattern (87 bp):
AGGGGAATCGATTCCCCTACAGGGGGAATCGATTCCCCTACAGGGAGGAATCGATTCCCCTTCAA
AGGGGGAATCGATTCCCCTTCA
Found at i:3211779 original size:22 final size:21
Alignment explanation
Indices: 3211603--3211773 Score: 216
Period size: 22 Copynumber: 7.8 Consensus size: 21
3211593 AAAACCTCCA
*
3211603 GGGGTATCGATTCCCCTACAG
1 GGGGAATCGATTCCCCTACAG
*
3211624 GGGGAATCGGTTCCCCTACAG
1 GGGGAATCGATTCCCCTACAG
*
3211645 GGAGGAATCGATTCCCCTTCAAAG
1 GG-GGAATCGATTCCCC-T-ACAG
* *
3211669 GGGGAATCGATTCCCCTTCAA
1 GGGGAATCGATTCCCCTACAG
*
3211690 GGGGAATCGGTTCCCCTACAG
1 GGGGAATCGATTCCCCTACAG
3211711 GGAGGAATCGATTCCCCTACAG
1 GG-GGAATCGATTCCCCTACAG
*
3211733 GGAGGAATCGATTCCCCTTCAAAG
1 GG-GGAATCGATTCCCC-T-ACAG
3211757 GGGGAATCGATTCCCCT
1 GGGGAATCGATTCCCCT
3211774 TCAAGGTATT
Statistics
Matches: 132, Mismatches: 12, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
21 42 0.32
22 50 0.38
23 30 0.23
24 10 0.08
ACGTcount: A:0.23, C:0.27, G:0.28, T:0.21
Consensus pattern (21 bp):
GGGGAATCGATTCCCCTACAG
Found at i:3217921 original size:31 final size:31
Alignment explanation
Indices: 3217886--3217957 Score: 110
Period size: 31 Copynumber: 2.3 Consensus size: 31
3217876 ATTAATGATA
*
3217886 TGACATGTTTCATGTCATCA-AAGTGATGGCG
1 TGACATGTTTCATGTCA-CAGAAGTGATAGCG
*
3217917 TGACATGTTTCATGTCACAGAAGTGATAGTG
1 TGACATGTTTCATGTCACAGAAGTGATAGCG
3217948 TGACATGTTT
1 TGACATGTTT
3217958 TATATCACCC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 2 0.05
31 36 0.95
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.35
Consensus pattern (31 bp):
TGACATGTTTCATGTCACAGAAGTGATAGCG
Found at i:3218124 original size:15 final size:15
Alignment explanation
Indices: 3218104--3218132 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3218094 ATTAATTTGA
3218104 TCAAAAATTAAAATT
1 TCAAAAATTAAAATT
3218119 TCAAAAATTAAAAT
1 TCAAAAATTAAAAT
3218133 ACCTTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (15 bp):
TCAAAAATTAAAATT
Found at i:3221043 original size:16 final size:16
Alignment explanation
Indices: 3221004--3221076 Score: 105
Period size: 16 Copynumber: 4.7 Consensus size: 16
3220994 TAATAAATAA
*
3221004 ACGAACATAAACGAAT
1 ACGAACATAAACGAAC
3221020 ACG-A-ATAAACGAAC
1 ACGAACATAAACGAAC
*
3221034 ACGAATATAAACGAAC
1 ACGAACATAAACGAAC
*
3221050 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
3221066 ACGAACATAAA
1 ACGAACATAAA
3221077 TGAATATAAC
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
14 12 0.23
15 2 0.04
16 38 0.73
ACGTcount: A:0.58, C:0.19, G:0.12, T:0.11
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:3221077 original size:16 final size:16
Alignment explanation
Indices: 3220996--3221121 Score: 103
Period size: 16 Copynumber: 8.6 Consensus size: 16
3220986 TCGTTCATTA
3220996 ATAAAT-AA-ACGAAC
1 ATAAATGAACACGAAC
* *
3221010 ATAAACGAATACG-A-
1 ATAAATGAACACGAAC
* *
3221024 ATAAACGAACACGAAT
1 ATAAATGAACACGAAC
*
3221040 ATAAACGAACACGAAC
1 ATAAATGAACACGAAC
3221056 ATAAATGAACACGAAC
1 ATAAATGAACACGAAC
*
3221072 ATAAAT------GAAT
1 ATAAATGAACACGAAC
* *
3221082 AT-AACGAACATGAAC
1 ATAAATGAACACGAAC
3221097 ATAAATGAACACGAAC
1 ATAAATGAACACGAAC
3221113 ATAAATGAA
1 ATAAATGAA
3221122 TATAAATGTT
Statistics
Matches: 92, Mismatches: 9, Indels: 20
0.76 0.07 0.17
Matches are distributed among these distances:
9 2 0.02
10 5 0.05
14 17 0.18
15 9 0.10
16 59 0.64
ACGTcount: A:0.58, C:0.16, G:0.12, T:0.14
Consensus pattern (16 bp):
ATAAATGAACACGAAC
Found at i:3221091 original size:41 final size:41
Alignment explanation
Indices: 3221036--3221126 Score: 164
Period size: 41 Copynumber: 2.2 Consensus size: 41
3221026 AAACGAACAC
3221036 GAATATAAACGAACACGAACATAAATGAACACGAACATAAAT
1 GAATAT-AACGAACACGAACATAAATGAACACGAACATAAAT
*
3221078 GAATATAACGAACATGAACATAAATGAACACGAACATAAAT
1 GAATATAACGAACACGAACATAAATGAACACGAACATAAAT
3221119 GAATATAA
1 GAATATAA
3221127 ATGTTGAAGA
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 42 0.88
42 6 0.12
ACGTcount: A:0.57, C:0.14, G:0.12, T:0.16
Consensus pattern (41 bp):
GAATATAACGAACACGAACATAAATGAACACGAACATAAAT
Found at i:3222589 original size:55 final size:55
Alignment explanation
Indices: 3222505--3222645 Score: 239
Period size: 55 Copynumber: 2.6 Consensus size: 55
3222495 TACTTTTTGG
*
3222505 GTCCATTCAGTTATGTATTTCTTCAATATTTGTACTTTTTTTGGGGTCTATAACA
1 GTCCATTCAGTTATGTATTTCTTCAATATTTATACTTTTTTTGGGGTCTATAACA
*
3222560 GTCCATTCAGTTATGTATTTCTTCAATATTTATACTTTTTTTTGGGTCTATAACA
1 GTCCATTCAGTTATGTATTTCTTCAATATTTATACTTTTTTTGGGGTCTATAACA
*
3222615 GTCCACTCA-TCTATGTATTTCTTCAATATTT
1 GTCCATTCAGT-TATGTATTTCTTCAATATTT
3222646 TTTTGGGGTC
Statistics
Matches: 82, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
54 1 0.01
55 81 0.99
ACGTcount: A:0.23, C:0.16, G:0.11, T:0.50
Consensus pattern (55 bp):
GTCCATTCAGTTATGTATTTCTTCAATATTTATACTTTTTTTGGGGTCTATAACA
Found at i:3234320 original size:14 final size:14
Alignment explanation
Indices: 3234303--3234353 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
3234293 GTGAATAAAT
3234303 AAATGGTTTTAATG
1 AAATGGTTTTAATG
** *
3234317 AAATGTGAATAAAT-
1 AAATG-GTTTTAATG
3234331 AAATGGTTTTAATG
1 AAATGGTTTTAATG
3234345 AAAT-GTTTT
1 AAATGGTTTT
3234354 GGAGTCGCCA
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
13 10 0.34
14 14 0.48
15 5 0.17
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (14 bp):
AAATGGTTTTAATG
Found at i:3234320 original size:28 final size:28
Alignment explanation
Indices: 3234288--3234350 Score: 126
Period size: 28 Copynumber: 2.2 Consensus size: 28
3234278 TGACGGAAAA
3234288 GAAATGTGAATAAATAAATGGTTTTAAT
1 GAAATGTGAATAAATAAATGGTTTTAAT
3234316 GAAATGTGAATAAATAAATGGTTTTAAT
1 GAAATGTGAATAAATAAATGGTTTTAAT
3234344 GAAATGT
1 GAAATGT
3234351 TTTGGAGTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.19, T:0.35
Consensus pattern (28 bp):
GAAATGTGAATAAATAAATGGTTTTAAT
Found at i:3234808 original size:15 final size:16
Alignment explanation
Indices: 3234775--3234811 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
3234765 TAAACATAAT
*
3234775 ATTAAAATAATTGATA
1 ATTAAAATAAATGATA
3234791 ATTAAAATAAAT-ATA
1 ATTAAAATAAATGATA
3234806 ATTAAA
1 ATTAAA
3234812 GTAGACATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (16 bp):
ATTAAAATAAATGATA
Found at i:3237001 original size:123 final size:123
Alignment explanation
Indices: 3236777--3237343 Score: 676
Period size: 124 Copynumber: 4.6 Consensus size: 123
3236767 GATTAAGATG
* * * ** * *
3236777 AAAATGTTGAACAAGTTTTTCTTATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTTATT
1 AAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCTTATT
* * * * * *
3236842 ACGAACTCCTTATGGAAAT-GTTGATGCTGCTTTATCTCCTTCTGCGATAGAGTCAAGC
66 ACGAACTCTTTCTGGAAATGGCT-ATGTTACTCTATCTCCTTCTGCGATAGAGTCAAGC
*
3236900 AAAAGGTTGAATACGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCTTATT
1 AAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCTTATT
* ** * *
3236965 ACAAACTCTTTCTGGAAAT-ATTGATGTTACTCTATCTCCTTCTGCGATAGAATCGAGC
66 ACGAACTCTTTCTGGAAATGGCT-ATGTTACTCTATCTCCTTCTGCGATAGAGTCAAGC
* * * **
3237023 AAAAAGGTTGAATACA-TCCTTCAGATTATGAACTTCTTCTTCATATTCAGACGAGTTCTTCAGA
1 -AAAAGGTTGAATA-AGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCTTA
* * * * *
3237087 TTATGAAAT-TGTT-TGGAAATGGCTCTGTTGCTCTATCTCCTTCTGCAATAGAGTCAAGC
64 TTACGAACTCT-TTCTGGAAATGGCTATGTTACTCTATCTCCTTCTGCGATAGAGTCAAGC
* * * **
3237146 AAAAGGTTGAATAAGTTCTTCATACTATGAACTTCTTATTCCTCTTCAGACGAGTTCTTCAGATT
1 AAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCTTATT
* * * *
3237211 ATGAACTCCTGTCTGGAAATGGCTCTGTTACTCTATCTCCTTCTGCGATAGAGTCAAGA
66 ACGAACT-CTTTCTGGAAATGGCTATGTTACTCTATCTCCTTCTGCGATAGAGTCAAGC
* * *
3237270 AAAAGGTTGAATAAGTTCTTCAGACTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTTATT
1 AAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCTTATT
3237335 ACGAACTCT
66 ACGAACTCT
3237344 ATAAATCAAG
Statistics
Matches: 385, Mismatches: 51, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
121 1 0.00
122 63 0.16
123 147 0.38
124 174 0.45
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (123 bp):
AAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCTTATT
ACGAACTCTTTCTGGAAATGGCTATGTTACTCTATCTCCTTCTGCGATAGAGTCAAGC
Found at i:3237275 original size:246 final size:247
Alignment explanation
Indices: 3236800--3237339 Score: 703
Period size: 246 Copynumber: 2.2 Consensus size: 247
3236790 AGTTTTTCTT
* ** * *
3236800 ATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTATGGAAATGTTG
1 ATTATGAACTTCTTCTTCATCTTCAGATGAGTTCTTCAGATTACGAAATCCTTATGGAAATGCTG
* * * *
3236865 ATGCTGCTTTATCTCCTTCTGCGATAGAGTCAAGCAAAAGGTTGAATACGTTCTTCAGATTATGA
66 ATGCTGCTCTATCTCCTTCTGCAATAGAGTCAAGCAAAAGGTTGAATAAGTTCTTCAGACTATGA
* ** * *
3236930 ACTTCTTCTTCCTCTTCAGACGAGTTCTTCTTATTACAAACTCTTTCTGGAAATATTGATGTTAC
131 ACTTCTTATTCCTCTTCAGACGAGTTCTTCAGATTACAAACTCTGTCTGGAAATACTGATGTTAC
*
3236995 TCTATCTCCTTCTGCGATAGAATCGAGCAAAAAGGTTGAATACA-TCCTTCAG
196 TCTATCTCCTTCTGCGATAGAATCAAGCAAAAAGGTTGAATA-AGTCCTTCAG
* * * **
3237047 ATTATGAACTTCTTCTTCATATTCAGACGAGTTCTTCAGATTATGAAATTGTT-TGGAAATGGCT
1 ATTATGAACTTCTTCTTCATCTTCAGATGAGTTCTTCAGATTACGAAATCCTTATGGAAAT-GCT
* * *
3237111 -CTGTTGCTCTATCTCCTTCTGCAATAGAGTCAAGCAAAAGGTTGAATAAGTTCTTCATACTATG
65 GATGCTGCTCTATCTCCTTCTGCAATAGAGTCAAGCAAAAGGTTGAATAAGTTCTTCAGACTATG
** * *
3237175 AACTTCTTATTCCTCTTCAGACGAGTTCTTCAGATTATGAACTCCTGTCTGGAAATGGCT-CTGT
130 AACTTCTTATTCCTCTTCAGACGAGTTCTTCAGATTACAAACT-CTGTCTGGAAAT-ACTGATGT
* *
3237239 TACTCTATCTCCTTCTGCGATAGAGTCAAG-AAAAAGGTTGAATAAGTTCTTCAG
193 TACTCTATCTCCTTCTGCGATAGAATCAAGCAAAAAGGTTGAATAAGTCCTTCAG
* * * **
3237293 ACTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAA
1 ATTATGAACTTCTTCTTCATCTTCAGATGAGTTCTTCAGATTACGAA
3237340 CTCTATAAAT
Statistics
Matches: 252, Mismatches: 37, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
245 1 0.00
246 162 0.64
247 88 0.35
248 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (247 bp):
ATTATGAACTTCTTCTTCATCTTCAGATGAGTTCTTCAGATTACGAAATCCTTATGGAAATGCTG
ATGCTGCTCTATCTCCTTCTGCAATAGAGTCAAGCAAAAGGTTGAATAAGTTCTTCAGACTATGA
ACTTCTTATTCCTCTTCAGACGAGTTCTTCAGATTACAAACTCTGTCTGGAAATACTGATGTTAC
TCTATCTCCTTCTGCGATAGAATCAAGCAAAAAGGTTGAATAAGTCCTTCAG
Found at i:3238007 original size:353 final size:353
Alignment explanation
Indices: 3237343--3238061 Score: 1172
Period size: 353 Copynumber: 2.0 Consensus size: 353
3237333 TTACGAACTC
* *
3237343 TATAAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTATTAGGCTTA
1 TATAAATCAAGAAACCCCCGAAGGATTAGTTTCTTAGTTGTCAAGAAACCCCTTTATTAGGCTTA
* * ** * * *
3237408 ACTTCCTTTAACATCTCTTTTGAGATAATTAGTAAACCCTTGCAGTCTTGGTTTCTAAAATCTTA
66 ACTTCCTTTAACAACTCATTTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTCTAAAATCTCA
* *
3237473 TTTGAAAACATCCTGCACTGAAGGTCTTATGGATAATCTGTAGGACTTACAAATCAAGAAACCCC
131 TTTGAAAACATCCTGCACTAAAGGTCTTATGGATAATCCGTAGGACTTACAAATCAAGAAACCCC
3237538 CGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTATTAGGCTTAGCTTCCTTTAACAGATCT
196 CGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTATTAGGCTTAGCTTCCTTTAACAGATCT
*
3237603 TTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTCTAAAATCTTATTTGAAAACATCCTGCACT
261 TTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTCTAAAATCTCATTTGAAAACATCCTGCACT
3237668 GAAGGTCTTATGGATGACCCATAGGACT
326 GAAGGTCTTATGGATGACCCATAGGACT
* * *
3237696 TATAAATCAAGAAACCCCTGAAGGATTAGTTTCTTAGTTGTCAATAAACCCCTTTGTTAGGCTTA
1 TATAAATCAAGAAACCCCCGAAGGATTAGTTTCTTAGTTGTCAAGAAACCCCTTTATTAGGCTTA
*
3237761 ACTTCCTTTAACAACT-ATTTGAGATTATTAGTAAACCCCCGAAGGCTTGGTTTCTAAAATCTCA
66 ACTTCCTTTAACAACTCATTTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTCTAAAATCTCA
* *
3237825 TTTGAAAACATCCTGCACTAAAGGTCTTATGGAT-GTCCCGTAGGACTTACAAATCTAGAAACCC
131 TTTGAAAACATCCTGCACTAAAGGTCTTATGGATAAT-CCGTAGGACTTACAAATCAAGAAACCC
* * * * *
3237889 CCGAAGGTTTGGTTTCTTAGTTGTTAAGGAACCCCTTTGTTAGGCTTAGCTTCCTTTAACAGCTC
195 CCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTATTAGGCTTAGCTTCCTTTAACAGATC
3237954 TTTTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTCTAAAATCTCATTTGAAAACATCCTGCA
260 -TTTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTCTAAAATCTCATTTGAAAACATCCTGCA
* * *
3238019 CTGAAGGTCTTTTGGATGGCCCGTAGGACT
324 CTGAAGGTCTTATGGATGACCCATAGGACT
3238049 TATAAATCAAGAA
1 TATAAATCAAGAA
3238062 TATAGATGTA
Statistics
Matches: 338, Mismatches: 26, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
351 1 0.00
352 159 0.47
353 178 0.53
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.33
Consensus pattern (353 bp):
TATAAATCAAGAAACCCCCGAAGGATTAGTTTCTTAGTTGTCAAGAAACCCCTTTATTAGGCTTA
ACTTCCTTTAACAACTCATTTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTCTAAAATCTCA
TTTGAAAACATCCTGCACTAAAGGTCTTATGGATAATCCGTAGGACTTACAAATCAAGAAACCCC
CGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTATTAGGCTTAGCTTCCTTTAACAGATCT
TTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTCTAAAATCTCATTTGAAAACATCCTGCACT
GAAGGTCTTATGGATGACCCATAGGACT
Found at i:3238044 original size:177 final size:177
Alignment explanation
Indices: 3237346--3238061 Score: 1121
Period size: 176 Copynumber: 4.1 Consensus size: 177
3237336 CGAACTCTAT
3237346 AAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTATTAGGCTTAACT
1 AAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTATTAGGCTTAACT
* ** * * *
3237411 TCCTTTAACATCTCTTTTGAGATAATTAGTAAACCCTTGCAGTCTTGGTTTCTAAAATCTTATTT
66 TCCTTTAACAGCTCTTTTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTCTAAAATCTCATTT
* * *
3237476 GAAAACATCCTGCACTGAAGGTCTTATGGATAATCTGTAGGACTTAC
131 GAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGTAGGACTTAC
*
3237523 AAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTATTAGGCTTAGCT
1 AAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTATTAGGCTTAACT
* *
3237588 TCCTTTAACAGATC-TTTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTCTAAAATCTTATTT
66 TCCTTTAACAGCTCTTTTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTCTAAAATCTCATTT
* *
3237652 GAAAACATCCTGCACTGAAGGTCTTATGGATGACCCATAGGACTTAT
131 GAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGTAGGACTTAC
* * ** *
3237699 AAATCAAGAAACCCCTGAAGGATTAGTTTCTTAGTTGTCAATAAACCCCTTTGTTAGGCTTAACT
1 AAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTATTAGGCTTAACT
* * *
3237764 TCCTTTAACAACT-ATTTGAGATTATTAGTAAACCCCCGAAGGCTTGGTTTCTAAAATCTCATTT
66 TCCTTTAACAGCTCTTTTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTCTAAAATCTCATTT
* *
3237828 GAAAACATCCTGCACTAAAGGTCTTATGGATGTCCCGTAGGACTTAC
131 GAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGTAGGACTTAC
* * * * * *
3237875 AAATCTAGAAACCCCCGAAGGTTTGGTTTCTTAGTTGTTAAGGAACCCCTTTGTTAGGCTTAGCT
1 AAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTATTAGGCTTAACT
3237940 TCCTTTAACAGCTCTTTTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTCTAAAATCTCATTT
66 TCCTTTAACAGCTCTTTTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTCTAAAATCTCATTT
* * *
3238005 GAAAACATCCTGCACTGAAGGTCTTTTGGATGGCCCGTAGGACTTAT
131 GAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGTAGGACTTAC
3238052 AAATCAAGAA
1 AAATCAAGAA
3238062 TATAGATGTA
Statistics
Matches: 495, Mismatches: 42, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
176 318 0.64
177 177 0.36
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.33
Consensus pattern (177 bp):
AAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTATTAGGCTTAACT
TCCTTTAACAGCTCTTTTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTCTAAAATCTCATTT
GAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGTAGGACTTAC
Found at i:3238507 original size:54 final size:54
Alignment explanation
Indices: 3238420--3238528 Score: 173
Period size: 54 Copynumber: 2.0 Consensus size: 54
3238410 TAATCGTTGG
* *
3238420 TTCGTAAAACATTTAACAACACATTCATTCTTTCATGTGGCTTCTTCCCAGATT
1 TTCGTAAAACATTTAACAACACATTCATCCTTTCATGTGGCTTCTGCCCAGATT
* * *
3238474 TTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCCTAGATT
1 TTCGTAAAACATTTAACAACACATTCATCCTTTCATGTGGCTTCTGCCCAGATT
3238528 T
1 T
3238529 CTTGTCAGTA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.26, C:0.25, G:0.11, T:0.39
Consensus pattern (54 bp):
TTCGTAAAACATTTAACAACACATTCATCCTTTCATGTGGCTTCTGCCCAGATT
Found at i:3239069 original size:52 final size:52
Alignment explanation
Indices: 3238993--3239194 Score: 246
Period size: 52 Copynumber: 3.9 Consensus size: 52
3238983 TATCCCAACC
* *
3238993 TTTTCATGCTGGTATGAGCCTTCAAGATGCCCCACATGGATTACTTCTGTCT
1 TTTTCATGCTGATATGAGCCTTCAAGATGCCCCAGATGGATTACTTCTGTCT
* * *
3239045 TTTTCATGCTGATGTGAGCCTTCAAGATACCCCAGATGGATTACTTATGTCT
1 TTTTCATGCTGATATGAGCCTTCAAGATGCCCCAGATGGATTACTTCTGTCT
* ** * *
3239097 TTTTTATGCTGATGCGAGCCTTCAATATGCCCCAGATGGATTACTTCTATC-
1 TTTTCATGCTGATATGAGCCTTCAAGATGCCCCAGATGGATTACTTCTGTCT
* * * * * *
3239148 -TTTCATACTGACATGATCCTTCAAGATTCCCCAAATAGATTACTTCT
1 TTTTCATGCTGATATGAGCCTTCAAGATGCCCCAGATGGATTACTTCT
3239195 ATGTTGATGT
Statistics
Matches: 129, Mismatches: 21, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
50 37 0.29
52 92 0.71
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.37
Consensus pattern (52 bp):
TTTTCATGCTGATATGAGCCTTCAAGATGCCCCAGATGGATTACTTCTGTCT
Found at i:3240705 original size:19 final size:19
Alignment explanation
Indices: 3240678--3240767 Score: 100
Period size: 19 Copynumber: 4.8 Consensus size: 19
3240668 CTTGATTCAA
3240678 TTTTT-CTTTTTTCTTTCT
1 TTTTTCCTTTTTTCTTTCT
3240696 TTTTTCCTTTTTT-TTTCT
1 TTTTTCCTTTTTTCTTTCT
3240714 CTTTTTCCTTTTTT-TCTTCT
1 -TTTTTCCTTTTTTCT-TTCT
*
3240734 TTTTTCTCTTTTTCCTTT-T
1 TTTTTC-CTTTTTTCTTTCT
3240753 TTTCTT-CTTTTTTCT
1 TTT-TTCCTTTTTTCT
3240768 CTAAGGGATG
Statistics
Matches: 64, Mismatches: 2, Indels: 12
0.82 0.03 0.15
Matches are distributed among these distances:
18 18 0.28
19 31 0.48
20 14 0.22
21 1 0.02
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTTCCTTTTTTCTTTCT
Found at i:3240707 original size:9 final size:9
Alignment explanation
Indices: 3240695--3240766 Score: 65
Period size: 9 Copynumber: 7.8 Consensus size: 9
3240685 TTTTTCTTTC
3240695 TTTTTTCCTT
1 TTTTTTCC-T
*
3240705 TTTTTTTCT
1 TTTTTTCCT
*
3240714 CTTTTTCCT
1 TTTTTTCCT
3240723 TTTTTT-CT
1 TTTTTTCCT
*
3240731 TCTTTTTTCT
1 T-TTTTTCCT
*
3240741 CTTTTTCCT
1 TTTTTTCCT
*
3240750 TTTTTTCTT
1 TTTTTTCCT
3240759 CTTTTTTC
1 -TTTTTTC
3240767 TCTAAGGGAT
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
8 3 0.06
9 32 0.63
10 16 0.31
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTTCCT
Found at i:3240724 original size:27 final size:27
Alignment explanation
Indices: 3240694--3240769 Score: 134
Period size: 27 Copynumber: 2.8 Consensus size: 27
3240684 TTTTTTCTTT
* *
3240694 CTTTTTTCCTTTTTTTTTCTCTTTTTC
1 CTTTTTTTCTTCTTTTTTCTCTTTTTC
3240721 CTTTTTTTCTTCTTTTTTCTCTTTTTC
1 CTTTTTTTCTTCTTTTTTCTCTTTTTC
3240748 CTTTTTTTCTTCTTTTTTCTCT
1 CTTTTTTTCTTCTTTTTTCTCT
3240770 AAGGGATGAG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (27 bp):
CTTTTTTTCTTCTTTTTTCTCTTTTTC
Found at i:3244487 original size:14 final size:15
Alignment explanation
Indices: 3244470--3244511 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
3244460 ATGTGAATGT
*
3244470 AAAATGAAAATGCAAA
1 AAAATAAAAATGC-AA
*
3244486 AAAAAAAAAATGC-A
1 AAAATAAAAATGCAA
3244500 AAAATAAAAATG
1 AAAATAAAAATG
3244512 TAAATTGTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 12 0.52
16 11 0.48
ACGTcount: A:0.74, C:0.05, G:0.10, T:0.12
Consensus pattern (15 bp):
AAAATAAAAATGCAA
Found at i:3244495 original size:16 final size:17
Alignment explanation
Indices: 3244476--3244509 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
3244466 ATGTAAAATG
3244476 AAAATGCAAAAA-AAAA
1 AAAATGCAAAAATAAAA
3244492 AAAATGCAAAAATAAAA
1 AAAATGCAAAAATAAAA
3244509 A
1 A
3244510 TGTAAATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.79, C:0.06, G:0.06, T:0.09
Consensus pattern (17 bp):
AAAATGCAAAAATAAAA
Found at i:3248700 original size:3 final size:3
Alignment explanation
Indices: 3248692--3248726 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
3248682 ATTTATCATT
3248692 TAA TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3248727 ATGGGACAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:3249573 original size:27 final size:27
Alignment explanation
Indices: 3249521--3249583 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
3249511 ACAATGGCTA
**
3249521 CCTTCATTTGCATAATCAGCCTGGTTC
1 CCTTCATTTGCATAATCAGAATGGTTC
* *
3249548 CCTTCATTTGCATGATCA-AATAGGTTT
1 CCTTCATTTGCATAATCAGAAT-GGTTC
*
3249575 CCTTGATTT
1 CCTTCATTT
3249584 CCACAACAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 1 0.03
27 29 0.97
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.41
Consensus pattern (27 bp):
CCTTCATTTGCATAATCAGAATGGTTC
Found at i:3257439 original size:343 final size:343
Alignment explanation
Indices: 3256784--3257470 Score: 1349
Period size: 343 Copynumber: 2.0 Consensus size: 343
3256774 TTCTGCACCT
3256784 GCACAGATAAAGAGGTGAACTTCATGTACAAGTTAACAGTCTTTGTTTTGTTTAAAAAACGTTAA
1 GCACAGATAAAGAGGTGAACTTCATGTACAAGTTAACAGTCTTTGTTTTGTTTAAAAAACGTTAA
3256849 ATATGTAACATTGTTTAGCCGTACACCTTTCATTGCTCTGAGAACTATAGTAAGTGATTTCATAA
66 ATATGTAACATTGTTTAGCCGTACACCTTTCATTGCTCTGAGAACTATAGTAAGTGATTTCATAA
3256914 TCAGACATAATCAAAGAAACAAATGGTCATAAGGATTTCCTATAAAATTATAATAAAATACCAGA
131 TCAGACATAATCAAAGAAACAAATGGTCATAAGGATTTCCTATAAAATTATAATAAAATACCAGA
3256979 TGAATAAGCAAAATTTGAATTCCACTTTTCTAGTTTTTCTGTCTTCAATTGACTTCACTTATATG
196 TGAATAAGCAAAATTTGAATTCCACTTTTCTAGTTTTTCTGTCTTCAATTGACTTCACTTATATG
3257044 AAATGGGATGGTTATTGATCCCTAGCAGGAACTACAACACCAATATTTTTTTTATTCCAAAAGTA
261 AAATGGGATGGTTATTGATCCCTAGCAGGAACTACAACACCAATATTTTTTTTATTCCAAAAGTA
3257109 AAAGAAAA-ATGCAAATG
326 AAAGAAAACATGCAAATG
3257126 GCACAGATAAAGAGGTGAACTTCATGTACAAGTTAACAGTCTTTGTTTTGTTTAAAAAACGTTAA
1 GCACAGATAAAGAGGTGAACTTCATGTACAAGTTAACAGTCTTTGTTTTGTTTAAAAAACGTTAA
3257191 ATATGTAACATTGTTTAGCCGTACACCTTTCATTGCTCTGAGAACTATAGTTAAGTGATTTCATA
66 ATATGTAACATTGTTTAGCCGTACACCTTTCATTGCTCTGAGAACTATAG-TAAGTGATTTCATA
3257256 ATCAGACATAATCAAAGAAACAAATGGTCATAAGGATTTCCTATAAAATTATAATAAAATACCAG
130 ATCAGACATAATCAAAGAAACAAATGGTCATAAGGATTTCCTATAAAATTATAATAAAATACCAG
3257321 ATGAATAAGCAAAATTTGAATTCCACTTTTCTAGTTTTTCTGTCTTCAATTGACTTCACTTATAT
195 ATGAATAAGCAAAATTTGAATTCCACTTTTCTAGTTTTTCTGTCTTCAATTGACTTCACTTATAT
3257386 GAAATGGGATGGTTTATTGATCCCTAGCAGGAACTACAACACCAATATTTTTTTTATTCCAAAAG
260 GAAATGGGATGG-TTATTGATCCCTAGCAGGAACTACAACACCAATATTTTTTTTATTCCAAAAG
3257451 TAAAAGAAAACATGCAAATG
324 TAAAAGAAAACATGCAAATG
3257471 AATGCAAAGA
Statistics
Matches: 342, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
342 115 0.34
343 156 0.46
344 62 0.18
345 9 0.03
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (343 bp):
GCACAGATAAAGAGGTGAACTTCATGTACAAGTTAACAGTCTTTGTTTTGTTTAAAAAACGTTAA
ATATGTAACATTGTTTAGCCGTACACCTTTCATTGCTCTGAGAACTATAGTAAGTGATTTCATAA
TCAGACATAATCAAAGAAACAAATGGTCATAAGGATTTCCTATAAAATTATAATAAAATACCAGA
TGAATAAGCAAAATTTGAATTCCACTTTTCTAGTTTTTCTGTCTTCAATTGACTTCACTTATATG
AAATGGGATGGTTATTGATCCCTAGCAGGAACTACAACACCAATATTTTTTTTATTCCAAAAGTA
AAAGAAAACATGCAAATG
Found at i:3260513 original size:3 final size:3
Alignment explanation
Indices: 3260505--3260570 Score: 80
Period size: 3 Copynumber: 22.0 Consensus size: 3
3260495 TATATATATT
* * * *
3260505 TAA TAA TAA TAA TAA TAA TAG TAA TAT TTA TGA TAA TAA T-A TAA TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
3260553 TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
3260571 ATAAATCAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
2 2 0.04
3 49 0.91
4 3 0.06
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3261021 original size:37 final size:37
Alignment explanation
Indices: 3260949--3261038 Score: 139
Period size: 37 Copynumber: 2.5 Consensus size: 37
3260939 TTGAACAAGC
*
3260949 TCTTCTCATTGTGAAC-TTCTTCTTCTTCAGATGAGT
1 TCTTCTCATTATGAACTTTCTTCTTCTTCAGATGAGT
3260985 TCTTCTCATTATGAACTTTC-TCTTTCTTCAGATGAGT
1 TCTTCTCATTATGAACTTTCTTC-TTCTTCAGATGAGT
*
3261022 TTTTCTCATTATGAACT
1 TCTTCTCATTATGAACT
3261039 CTACCTGGCA
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
36 17 0.34
37 33 0.66
ACGTcount: A:0.19, C:0.21, G:0.11, T:0.49
Consensus pattern (37 bp):
TCTTCTCATTATGAACTTTCTTCTTCTTCAGATGAGT
Found at i:3261167 original size:38 final size:38
Alignment explanation
Indices: 3261092--3261348 Score: 148
Period size: 38 Copynumber: 6.6 Consensus size: 38
3261082 AGGTTGAACA
* *
3261092 AATTCTTCTCATTATGAACTTATTCTTCATTCTTCAGATGACT
1 AATTCTTCTAATTATGAAC----TCTTC-TTCTTCAGATGACG
3261135 AATTCTTCTAATTATGAACTCTTCTTCTTCAGATGACG
1 AATTCTTCTAATTATGAACTCTTCTTCTTCAGATGACG
* * ** **
3261173 AGTTCTTCTGATTATGAACTCTATC-T-GGCA-ATG-TT
1 AATTCTTCTAATTATGAACTCT-TCTTCTTCAGATGACG
* * * * *** *** * *
3261208 AATCCATCAAATGATGAA-T-TTAAACAAAAGGTTGAACA
1 AATTCTTCTAATTATGAACTCTTCTTCTTCA-GATG-ACG
*
3261246 AATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGACG
1 AATTCTTCTAATTATGAAC----TCTT-CTTCTTCAGATGACG
3261289 AATTCTTCTAATTATGAACTCTTCTTCTTCAGATGACG
1 AATTCTTCTAATTATGAACTCTTCTTCTTCAGATGACG
* *
3261327 AGTTCTTCTGATTATGAACTCT
1 AATTCTTCTAATTATGAACTCT
3261349 ATCTGGCAAT
Statistics
Matches: 162, Mismatches: 38, Indels: 33
0.70 0.16 0.14
Matches are distributed among these distances:
32 1 0.01
33 1 0.01
34 2 0.01
35 12 0.07
36 5 0.03
37 2 0.01
38 82 0.51
39 11 0.07
43 39 0.24
44 5 0.03
45 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.41
Consensus pattern (38 bp):
AATTCTTCTAATTATGAACTCTTCTTCTTCAGATGACG
Found at i:3261216 original size:154 final size:153
Alignment explanation
Indices: 3260932--3261459 Score: 817
Period size: 154 Copynumber: 3.5 Consensus size: 153
3260922 TAGAATTATG
** * *
3260932 CAAAAGGTTGAACAAGCTCTTCTCATTGTGAAC---TTCTT-CTTCTTCAGATG--AGTTCTTCT
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGACAATTCTTCT
* * * * *
3260991 CATTATGAACTTTCTCTTTCTTCAGAT---GAGTTTTTCTCATTATGAACTCTACCTGGCAATGT
66 AATTATGAACTCT-TC-TTCTTCAGATGACGAGTTCTTCTGATTATGAACTCTATCTGGCAATGT
3261053 TAATCCATCAAATGATGAATTTAAA
129 TAATCCATCAAATGATGAATTTAAA
*
3261078 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCATTCTTCAGATGACTAATTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAC-AATTCTTC
3261143 TAATTATGAACTCTTCTTCTTCAGATGACGAGTTCTTCTGATTATGAACTCTATCTGGCAATGTT
65 TAATTATGAACTCTTCTTCTTCAGATGACGAGTTCTTCTGATTATGAACTCTATCTGGCAATGTT
3261208 AATCCATCAAATGATGAATTTAAA
130 AATCCATCAAATGATGAATTTAAA
3261232 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGACGAATTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAC-AATTCTTC
3261297 TAATTATGAACTCTTCTTCTTCAGATGACGAGTTCTTCTGATTATGAACTCTATCTGGCAATGTT
65 TAATTATGAACTCTTCTTCTTCAGATGACGAGTTCTTCTGATTATGAACTCTATCTGGCAATGTT
*
3261362 AATCCATCAATTGATGAATTTAAA
130 AATCCATCAAATGATGAATTTAAA
* *
3261386 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG--AGTTCTTCT
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGACAATTCTTCT
*
3261449 CATTATGAACT
66 AATTATGAACT
3261460 TTTTCTGGAA
Statistics
Matches: 356, Mismatches: 16, Indels: 15
0.92 0.04 0.04
Matches are distributed among these distances:
146 30 0.08
149 5 0.01
150 11 0.03
151 28 0.08
152 2 0.01
153 19 0.05
154 261 0.73
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.39
Consensus pattern (153 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGACAATTCTTCT
AATTATGAACTCTTCTTCTTCAGATGACGAGTTCTTCTGATTATGAACTCTATCTGGCAATGTTA
ATCCATCAAATGATGAATTTAAA
Found at i:3261458 original size:113 final size:113
Alignment explanation
Indices: 3261289--3261707 Score: 637
Period size: 113 Copynumber: 3.7 Consensus size: 113
3261279 TCAGATGACG
* ** * * * *
3261289 AATTCTTCTAATTATGAAC-TCTTCTT-CTTC-AGATGACGAGTTCTTCTGATTATGAACTCTAT
1 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA-GATGAGTTCTTCTCATTATGAACTTTCT
* * * * **
3261351 CTGGCAATGTTAATCCATCAATTGATGAATTTAAACAAAAGGTTGAACA
65 CTGGAAATGCTGATCCATCAATTGATGAATTCAGGCAAAAGGTTGAACA
*
3261400 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTC
1 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
*
3261465 TGGAAAGGCTGATCCATCAATTGATGAATTCAGGCAAAAGGTTGAACA
66 TGGAAATGCTGATCCATCAATTGATGAATTCAGGCAAAAGGTTGAACA
*
3261513 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* *
3261578 TGGAAAAGCTGATCCATCAAGTGATGAATTCAGGCAAAAGGTTGAACA
66 TGGAAATGCTGATCCATCAATTGATGAATTCAGGCAAAAGGTTGAACA
3261626 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
*
3261691 TGGAAATGTTGATCCAT
66 TGGAAATGCTGATCCAT
3261708 TGTTATGGAT
Statistics
Matches: 284, Mismatches: 21, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
111 18 0.06
112 7 0.02
113 258 0.91
114 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.39
Consensus pattern (113 bp):
AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
TGGAAATGCTGATCCATCAATTGATGAATTCAGGCAAAAGGTTGAACA
Found at i:3262773 original size:83 final size:83
Alignment explanation
Indices: 3262556--3263031 Score: 663
Period size: 83 Copynumber: 5.6 Consensus size: 83
3262546 GGTTTCATAT
**
3262556 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTACT-AGCACATTCCTCTTCCAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATTTATCTTCCAA
* *
3262620 ATTCAATAACTGGTTTTAC
65 ATTCAATGATTGGTTTTAC
*
3262639 CAAACCAGATCA-ATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTTATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTTATCTTCCAAA
3262703 TTCAATGATTGGTTTTAC
66 TTCAATGATTGGTTTTAC
3262721 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTACT-AGCACATTCT-TCTTCCA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATT-TATCTTCCA
* *
3262784 AATTCAATAACTGGTTTTAC
64 AATTCAATGATTGGTTTTAC
*
3262804 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTTATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTTATCTTCCAAA
* *
3262869 TTCAATAACTGGTTCTGTGGTTCATAC
66 TTC---AA-T-G--AT-TGGTT-TTAC
* **
3262896 CAAAACAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTTATCTTCCAAA
*
3262961 TTCAATGATTGATTTTAC
66 TTCAATGATTGGTTTTAC
** *
3262979 CAAATTAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATGAGCACAT
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACAT
3263032 GGCATTTGTT
Statistics
Matches: 355, Mismatches: 23, Indels: 30
0.87 0.06 0.07
Matches are distributed among these distances:
81 1 0.00
82 77 0.22
83 191 0.54
84 6 0.02
85 1 0.00
86 2 0.01
87 2 0.01
88 1 0.00
89 2 0.01
91 5 0.01
92 67 0.19
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (83 bp):
CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTTATCTTCCAAA
TTCAATGATTGGTTTTAC
Found at i:3262958 original size:175 final size:174
Alignment explanation
Indices: 3262504--3263031 Score: 815
Period size: 175 Copynumber: 3.1 Consensus size: 174
3262494 CTTATTTCTA
* * * * *
3262504 CTATGAGCAAATTCATCTTTCAAATTTAATGATTGGTTCTGTGGTTTCATATCAAACCAGATCAG
1 CTATGAGCACATTTATCTTTCAAATTCAAT-AATGGTTCTGTGG-TTCATACCAAACCAGATCAG
3262569 ATAACTCAAAGAACACTTCCAGAAGATGCTACTAGCACATTCCTCTTCCAAATTCAATAACTGGT
64 ATAACTCAAAGAACACTTCCAGAAGATGCTACTAGCACATTCCTCTTCCAAATTCAATAACTGGT
3262634 TTTACCAAACCAGATCA-ATAACTCAAAGAACACTTCCAGAAGATG
129 TTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
* *
3262679 CTATGAGCACATTTATCTTTCAAATTC---AAT-G--AT-TGGTT-TTACCAAACCAGATCAGAT
1 CTATGAGCACATTTATCTTTCAAATTCAATAATGGTTCTGTGGTTCATACCAAACCAGATCAGAT
*
3262736 AACTCAAAGAACACTTCCAGAAGATGCTACTAGCACATTCTTCTTCCAAATTCAATAACTGGTTT
66 AACTCAAAGAACACTTCCAGAAGATGCTACTAGCACATTCCTCTTCCAAATTCAATAACTGGTTT
3262801 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
131 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
*
3262845 CTATGAGCACATTTATCTTTCAAATTCAATAACTGGTTCTGTGGTTCATACCAAAACAGATCAGA
1 CTATGAGCACATTTATCTTTCAAATTCAATAA-TGGTTCTGTGGTTCATACCAAACCAGATCAGA
* * *
3262910 TAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATTCCTCTTCCAAATTCAATGATTGAT
65 TAACTCAAAGAACACTTCCAGAAGATGCTACT-AGCACATTCCTCTTCCAAATTCAATAACTGGT
** *
3262974 TTTACCAAATTAGATCAGATAACTCAAAGAACACTTCTAGAAGATG
129 TTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
3263020 CTATGAGCACAT
1 CTATGAGCACAT
3263032 GGCATTTGTT
Statistics
Matches: 324, Mismatches: 18, Indels: 22
0.89 0.05 0.06
Matches are distributed among these distances:
165 96 0.30
166 57 0.18
167 3 0.01
168 1 0.00
169 2 0.01
170 2 0.01
171 3 0.01
173 1 0.00
174 6 0.02
175 153 0.47
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (174 bp):
CTATGAGCACATTTATCTTTCAAATTCAATAATGGTTCTGTGGTTCATACCAAACCAGATCAGAT
AACTCAAAGAACACTTCCAGAAGATGCTACTAGCACATTCCTCTTCCAAATTCAATAACTGGTTT
TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
Found at i:3263003 original size:258 final size:248
Alignment explanation
Indices: 3262556--3263031 Score: 731
Period size: 258 Copynumber: 1.9 Consensus size: 248
3262546 GGTTTCATAT
*
3262556 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTACTAGCACATTCCTCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTACTAGCACATTCATCTTCCAAA
*
3262621 TTCAATAACTGGTTTTACCAAACCAGATCAATAACTCAAAGAACACTTCCAGAAGATGCTATGAG
66 TTCAATAACTGGTTTTACCAAAACAGATCAATAACTCAAAGAACACTTCCAGAAGATGCTATGAG
* * *
3262686 CACATTTATCTTTCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACT
131 CACATTCATCTTCCAAATTCAATGATTGATTTTACCAAACCAGATCAGATAACTCAAAGAACACT
3262751 TCCAGAAGATGCTACT-AGCACATTCTTCTTCCAAATTCAATAACTGGTTTTAC
196 TCCAGAAGATGCTA-TGAGCACATTCTTCTTCCAAATTCAATAACTGGTTTTAC
* *
3262804 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATTTATCTTTCAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTACT-AGCACATTCATCTTCCAA
3262868 ATTCAATAACTGGTTCTGTGGTTCATACCAAAACAGATCAGATAACTCAAAGAACACTTCCAGAA
65 ATTCAATAACT-G----GT--TT--TACCAAAACAGATCA-ATAACTCAAAGAACACTTCCAGAA
* **
3262933 GATGCTATGAGCACATTCCTCTTCCAAATTCAATGATTGATTTTACCAAATTAGATCAGATAACT
120 GATGCTATGAGCACATTCATCTTCCAAATTCAATGATTGATTTTACCAAACCAGATCAGATAACT
*
3262998 CAAAGAACACTTCTAGAAGATGCTATGAGCACAT
185 CAAAGAACACTTCCAGAAGATGCTATGAGCACAT
3263032 GGCATTTGTT
Statistics
Matches: 205, Mismatches: 11, Indels: 14
0.89 0.05 0.06
Matches are distributed among these distances:
247 1 0.00
248 70 0.34
249 1 0.00
253 2 0.01
255 2 0.01
257 15 0.07
258 114 0.56
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (248 bp):
CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTACTAGCACATTCATCTTCCAAA
TTCAATAACTGGTTTTACCAAAACAGATCAATAACTCAAAGAACACTTCCAGAAGATGCTATGAG
CACATTCATCTTCCAAATTCAATGATTGATTTTACCAAACCAGATCAGATAACTCAAAGAACACT
TCCAGAAGATGCTATGAGCACATTCTTCTTCCAAATTCAATAACTGGTTTTAC
Found at i:3264189 original size:6 final size:6
Alignment explanation
Indices: 3264178--3264219 Score: 59
Period size: 6 Copynumber: 6.8 Consensus size: 6
3264168 CCCCTTTTTC
3264178 TTCTTT TTCTTT TTCTTTT TTCTTT TTCTCTT TT-TTT TTCTT
1 TTCTTT TTCTTT TTC-TTT TTCTTT TTCT-TT TTCTTT TTCTT
3264220 CAAGCATAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
5 4 0.12
6 19 0.58
7 10 0.30
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTCTTT
Found at i:3264191 original size:15 final size:14
Alignment explanation
Indices: 3264171--3264216 Score: 69
Period size: 13 Copynumber: 3.4 Consensus size: 14
3264161 CCTTGACCCC
3264171 CTTTTTCTTCTTTTT
1 CTTTTTC-TCTTTTT
3264186 CTTTTTCT-TTTTT
1 CTTTTTCTCTTTTT
3264199 CTTTTTCTCTTTTT
1 CTTTTTCTCTTTTT
3264213 -TTTT
1 CTTTT
3264217 CTTCAAGCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 17 0.57
14 6 0.20
15 7 0.23
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
CTTTTTCTCTTTTT
Found at i:3277003 original size:3 final size:3
Alignment explanation
Indices: 3276995--3277069 Score: 96
Period size: 3 Copynumber: 25.0 Consensus size: 3
3276985 TATATATATT
* * * * *
3276995 TAA TAA TAA TAA TAA TAA TAA TAG TAA TAT TTA TGA TAA TAA TAC TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
3277043 TAA TAA TGA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
3277070 ATAAATCAAA
Statistics
Matches: 61, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3283407 original size:29 final size:29
Alignment explanation
Indices: 3283365--3283444 Score: 151
Period size: 29 Copynumber: 2.8 Consensus size: 29
3283355 CACCTAACTA
3283365 AATTGATGTAAGCAATGACATCTTCATCT
1 AATTGATGTAAGCAATGACATCTTCATCT
*
3283394 AATTGATGTAAGCAATGGCATCTTCATCT
1 AATTGATGTAAGCAATGACATCTTCATCT
3283423 AATTGATGTAAGCAATGACATC
1 AATTGATGTAAGCAATGACATC
3283445 AATTTAGTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (29 bp):
AATTGATGTAAGCAATGACATCTTCATCT
Found at i:3292432 original size:13 final size:13
Alignment explanation
Indices: 3292414--3292444 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3292404 AATGACGCTC
*
3292414 AATGCGCGTCATA
1 AATGCGCATCATA
3292427 AATGCGCATCATA
1 AATGCGCATCATA
3292440 AATGC
1 AATGC
3292445 ACGTTATAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (13 bp):
AATGCGCATCATA
Found at i:3308297 original size:2 final size:2
Alignment explanation
Indices: 3308292--3308319 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3308282 TCTTAATGAA
3308292 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3308320 TATTAACCTA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3308824 original size:14 final size:14
Alignment explanation
Indices: 3308805--3308832 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3308795 ATCATAACAA
3308805 AATTATATAACTAT
1 AATTATATAACTAT
3308819 AATTATATAACTAT
1 AATTATATAACTAT
3308833 TCTTTCACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTATATAACTAT
Found at i:3309465 original size:3 final size:3
Alignment explanation
Indices: 3309457--3309504 Score: 87
Period size: 3 Copynumber: 15.7 Consensus size: 3
3309447 AAAATATTAG
3309457 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT
3309503 AT
1 AT
3309505 GTTTATTGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:3309659 original size:37 final size:36
Alignment explanation
Indices: 3309617--3309736 Score: 133
Period size: 34 Copynumber: 3.3 Consensus size: 36
3309607 AGTTGGAAAA
3309617 TTCATCTTTGGTAGGT-GCCAACTTTGCACATGAGAAT
1 TTCATCTTTGGTAGGTGGCCAACTTTGCA-ATG-GAAT
* * *
3309654 TTCATC-TTGGTTGGTGGCCAAC-TT--ATTGGAAAA
1 TTCATCTTTGGTAGGTGGCCAACTTTGCAATGG-AAT
3309687 TTCATCTTTGGTAGGTGGCCAACTTTGCATATGGGAAT
1 TTCATCTTTGGTAGGTGGCCAACTTTGCA-AT-GGAAT
3309725 TTCATCTTTGGT
1 TTCATCTTTGGT
3309737 CCCTAAAATA
Statistics
Matches: 69, Mismatches: 6, Indels: 15
0.77 0.07 0.17
Matches are distributed among these distances:
32 1 0.01
33 10 0.14
34 16 0.23
35 2 0.03
36 10 0.14
37 13 0.19
38 15 0.22
39 2 0.03
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.38
Consensus pattern (36 bp):
TTCATCTTTGGTAGGTGGCCAACTTTGCAATGGAAT
Found at i:3314353 original size:33 final size:34
Alignment explanation
Indices: 3314306--3314371 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 34
3314296 ATTTGGCAAG
*
3314306 TTGGAAAATTCATCTTTGGTAGGT-GCCAACTTA
1 TTGGAAAATACATCTTTGGTAGGTGGCCAACTTA
*
3314339 TTGGATAATACATCTTTGGTAGGTGGCCAACTT
1 TTGGAAAATACATCTTTGGTAGGTGGCCAACTT
3314372 TGCATATGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 22 0.73
34 8 0.27
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (34 bp):
TTGGAAAATACATCTTTGGTAGGTGGCCAACTTA
Found at i:3318265 original size:17 final size:17
Alignment explanation
Indices: 3318243--3318275 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
3318233 TGGAAGAAAG
3318243 AATGTCCCATGCTAAAT
1 AATGTCCCATGCTAAAT
3318260 AATGTCCCATGCTAAA
1 AATGTCCCATGCTAAA
3318276 GAATAAAGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.27
Consensus pattern (17 bp):
AATGTCCCATGCTAAAT
Done.