Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001444.1 Hibiscus syriacus cultivar Beakdansim tig00002793_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: 2564052
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 12
Found at i:1328039 original size:27 final size:28
Alignment explanation
Indices: 1328009--1328089 Score: 83
Period size: 27 Copynumber: 2.8 Consensus size: 28
1327999 ATATATTTAT
* *
1328009 TAATATTTCTAATAATATAATATAAT-A
1 TAATATTTATAATAATATAATAAAATAA
* *
1328036 TAATATTTTTAATATTATAATAAAATAA
1 TAATATTTATAATAATATAATAAAATAA
1328064 TCAATTATATTATAAATAATATAATA
1 T-AA-TAT-TTAT-AATAATATAATA
1328090 GAAGATATTA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
27 23 0.52
28 2 0.05
29 2 0.05
30 3 0.07
31 3 0.07
32 11 0.25
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (28 bp):
TAATATTTATAATAATATAATAAAATAA
Found at i:1328074 original size:32 final size:34
Alignment explanation
Indices: 1327999--1328089 Score: 87
Period size: 32 Copynumber: 2.6 Consensus size: 34
1327989 AATATTTAAA
* * *
1327999 ATATATTTATTAATATTTCTAATAATATAATATAAT
1 ATATATTT-TTAATA-TTATAATAAAATAATACAAT
1328035 ATAATATTTTTAATATTATAATAAAATAAT-CAAT
1 AT-ATATTTTTAATATTATAATAAAATAATACAAT
* * *
1328069 -TATATTATAAATAATATAATA
1 ATATATTTTTAATATTATAATA
1328090 GAAGATATTA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
32 17 0.35
33 1 0.02
34 3 0.06
35 13 0.27
36 8 0.17
37 6 0.12
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (34 bp):
ATATATTTTTAATATTATAATAAAATAATACAAT
Found at i:1328204 original size:19 final size:18
Alignment explanation
Indices: 1328180--1328250 Score: 54
Period size: 19 Copynumber: 3.6 Consensus size: 18
1328170 ATATTATTAA
1328180 ATTATTAATAATGAATAAT
1 ATTATTAATAAT-AATAAT
* *
1328199 ATTATTTATATATATTTAAT
1 ATTATTAATA-ATA-ATAAT
1328219 ATTAATATAATAATCTAATAAT
1 ATT-AT-TAATAA--TAATAAT
1328241 ATT-TTAATAA
1 ATTATTAATAA
1328251 AGATATTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
19 16 0.38
20 10 0.24
21 3 0.07
22 11 0.26
23 2 0.05
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (18 bp):
ATTATTAATAATAATAAT
Found at i:1328271 original size:23 final size:23
Alignment explanation
Indices: 1328245--1328289 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1328235 AATAATATTT
1328245 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
1328268 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
1328290 ATATAACACT
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:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:1328577 original size:14 final size:14
Alignment explanation
Indices: 1328558--1328587 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1328548 CAGAAAATAT
*
1328558 AATTCATTTTCCAG
1 AATTCAATTTCCAG
1328572 AATTCAATTTCCAG
1 AATTCAATTTCCAG
1328586 AA
1 AA
1328588 AACCAATTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.37
Consensus pattern (14 bp):
AATTCAATTTCCAG
Found at i:1334779 original size:20 final size:22
Alignment explanation
Indices: 1334730--1334787 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
1334720 GCATGGGTAG
1334730 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
*
1334754 TACATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
1334774 TGCATCGATGCACT
1 TGCATCGATGCACT
1334788 TCAAGGGGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 17 0.53
22 1 0.03
23 2 0.06
24 12 0.38
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:1336072 original size:52 final size:52
Alignment explanation
Indices: 1335994--1336092 Score: 180
Period size: 52 Copynumber: 1.9 Consensus size: 52
1335984 ATTATAATAT
*
1335994 CCTTGTGATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTATGTG
1 CCTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTATGTG
*
1336046 CCTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTTTCCTATTT
1 CCTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTT
1336093 CTATGTACCA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.20, C:0.23, G:0.15, T:0.41
Consensus pattern (52 bp):
CCTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTATGTG
Found at i:1336341 original size:15 final size:15
Alignment explanation
Indices: 1336317--1336363 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
1336307 TATTCACACC
* *
1336317 ATCTTTTTTTGTTTT
1 ATCTTATTTTATTTT
1336332 ATCTTATTTTATTTT
1 ATCTTATTTTATTTT
*
1336347 -TCATAATTTTATTTT
1 ATC-TTATTTTATTTT
1336362 AT
1 AT
1336364 ACCCCTGAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 2 0.07
15 24 0.89
16 1 0.04
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.72
Consensus pattern (15 bp):
ATCTTATTTTATTTT
Found at i:1336574 original size:2 final size:2
Alignment explanation
Indices: 1336567--1336627 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
1336557 AGTTAAAAAC
1336567 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1336609 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
1336628 GTTATATTAA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1336692 original size:3 final size:3
Alignment explanation
Indices: 1336684--1336725 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1336674 TAAGTTTATG
1336684 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1336726 ATATTCAAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1341162 original size:15 final size:15
Alignment explanation
Indices: 1341142--1341177 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
1341132 AAAATCTTTC
1341142 TTTCCCGTTCTTGAT
1 TTTCCCGTTCTTGAT
1341157 TTTCCCGTTCTTGAT
1 TTTCCCGTTCTTGAT
1341172 TTTCCC
1 TTTCCC
1341178 CTGCTGGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.06, C:0.31, G:0.11, T:0.53
Consensus pattern (15 bp):
TTTCCCGTTCTTGAT
Found at i:1346751 original size:18 final size:18
Alignment explanation
Indices: 1346730--1346782 Score: 106
Period size: 18 Copynumber: 2.9 Consensus size: 18
1346720 ACATATAAAT
1346730 ATTAATAAAAATATTTTA
1 ATTAATAAAAATATTTTA
1346748 ATTAATAAAAATATTTTA
1 ATTAATAAAAATATTTTA
1346766 ATTAATAAAAATATTTT
1 ATTAATAAAAATATTTT
1346783 CCTCTTGTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATTAATAAAAATATTTTA
Found at i:1348803 original size:33 final size:34
Alignment explanation
Indices: 1348728--1348803 Score: 82
Period size: 33 Copynumber: 2.3 Consensus size: 34
1348718 TTGTGTTCGC
* **
1348728 ATTTGTTTACTTATTTTTGAATGTATTTGTATTT
1 ATTTGTTTACTTATTTTTGAAAGTATTCATATTT
* ** *
1348762 GTCCGTTTA-TTTTTTTTGAAAGTATTCATATTT
1 ATTTGTTTACTTATTTTTGAAAGTATTCATATTT
1348795 ATTTGTTTA
1 ATTTGTTTA
1348804 GCGTTTACAA
Statistics
Matches: 32, Mismatches: 10, Indels: 1
0.74 0.23 0.02
Matches are distributed among these distances:
33 26 0.81
34 6 0.19
ACGTcount: A:0.21, C:0.05, G:0.12, T:0.62
Consensus pattern (34 bp):
ATTTGTTTACTTATTTTTGAAAGTATTCATATTT
Found at i:1348849 original size:22 final size:22
Alignment explanation
Indices: 1348806--1348849 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1348796 TTTGTTTAGC
* *
1348806 GTTTACAAACATGTTCGCTTAT
1 GTTTACAAACATGGTAGCTTAT
* *
1348828 GTTTGCAAACATGGTAGTTTAT
1 GTTTACAAACATGGTAGCTTAT
1348850 AAATTTAAAC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (22 bp):
GTTTACAAACATGGTAGCTTAT
Found at i:1354487 original size:40 final size:41
Alignment explanation
Indices: 1354425--1354519 Score: 97
Period size: 40 Copynumber: 2.3 Consensus size: 41
1354415 AAATGACCAA
*
1354425 CAAATTCGCAACGCAAACTCC-AATTTCGC-A-ACTCAGTTT
1 CAAATTCGCAACGCAAACTCCAAATTT-GCAATACTCAATTT
** ** *
1354464 CCAAATTCGCAACGTGATTTCCAAATTTGCAATACTGAATTT
1 -CAAATTCGCAACGCAAACTCCAAATTTGCAATACTCAATTT
1354506 CAAATTCGCAACGC
1 CAAATTCGCAACGC
1354520 GAATTTTGTT
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
40 19 0.42
41 19 0.42
42 7 0.16
ACGTcount: A:0.34, C:0.27, G:0.12, T:0.27
Consensus pattern (41 bp):
CAAATTCGCAACGCAAACTCCAAATTTGCAATACTCAATTT
Found at i:1354525 original size:20 final size:20
Alignment explanation
Indices: 1354425--1354577 Score: 85
Period size: 20 Copynumber: 7.6 Consensus size: 20
1354415 AAATGACCAA
* * *
1354425 CAAATTCGCAACGCAAACTC
1 CAAATTCGCAACGCGAATTT
* * *
1354445 CAATTTCGCAACTC-AGTTT
1 CAAATTCGCAACGCGAATTT
*
1354464 CCAAATTCGCAACGTG-ATTT
1 -CAAATTCGCAACGCGAATTT
* **
1354484 CCAAATTTGCAATACTGAATTT
1 -CAAATTCGCAACGC-GAATTT
1354506 CAAATTCGCAACGCGAATTT
1 CAAATTCGCAACGCGAATTT
**** * *
1354526 TGTTTTCGCAACTCGATTTT
1 CAAATTCGCAACGCGAATTT
* *
1354546 CGAATTCGCAACACGAATTT
1 CAAATTCGCAACGCGAATTT
* *
1354566 TAATTTCGCAAC
1 CAAATTCGCAAC
1354578 AAGTTTTAGT
Statistics
Matches: 99, Mismatches: 30, Indels: 8
0.72 0.22 0.06
Matches are distributed among these distances:
19 2 0.02
20 81 0.82
21 12 0.12
22 4 0.04
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.31
Consensus pattern (20 bp):
CAAATTCGCAACGCGAATTT
Found at i:1354578 original size:20 final size:20
Alignment explanation
Indices: 1354487--1354596 Score: 77
Period size: 20 Copynumber: 5.6 Consensus size: 20
1354477 GTGATTTCCA
* *
1354487 AATTT-GCAATACTGAATTTC
1 AATTTCGCAACAC-GAATTTT
* *
1354507 AAATTCGCAACGCGAATTTT
1 AATTTCGCAACACGAATTTT
** *
1354527 GTTTTCGCAACTCG-ATTTT
1 AATTTCGCAACACGAATTTT
1354546 CGAA-TTCGCAACACGAATTTT
1 --AATTTCGCAACACGAATTTT
*
1354567 AATTTCGCAACA--AGTTTT
1 AATTTCGCAACACGAATTTT
*
1354585 AGTTTCGCAACA
1 AATTTCGCAACA
1354597 AAAATGTTTT
Statistics
Matches: 72, Mismatches: 13, Indels: 12
0.74 0.13 0.12
Matches are distributed among these distances:
18 16 0.22
19 7 0.10
20 39 0.54
21 10 0.14
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (20 bp):
AATTTCGCAACACGAATTTT
Found at i:1354590 original size:18 final size:18
Alignment explanation
Indices: 1354563--1354597 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1354553 GCAACACGAA
1354563 TTTTAATTTCGCAACAAG
1 TTTTAATTTCGCAACAAG
*
1354581 TTTTAGTTTCGCAACAA
1 TTTTAATTTCGCAACAA
1354598 AAATGTTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.40
Consensus pattern (18 bp):
TTTTAATTTCGCAACAAG
Found at i:1354754 original size:15 final size:16
Alignment explanation
Indices: 1354734--1354771 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1354724 TCCCCATCTC
*
1354734 TAATTTTCTTT-TACA
1 TAATTTTATTTCTACA
*
1354749 TAATTTTATTTCTATA
1 TAATTTTATTTCTACA
1354765 TAATTTT
1 TAATTTT
1354772 TCAATGATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (16 bp):
TAATTTTATTTCTACA
Found at i:1355387 original size:12 final size:12
Alignment explanation
Indices: 1355366--1355399 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1355356 ACCATATTTC
*
1355366 CAATACCAAACA
1 CAATATCAAACA
1355378 CAATATCAAACA
1 CAATATCAAACA
*
1355390 CAATCTCAAA
1 CAATATCAAA
1355400 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:1355552 original size:24 final size:24
Alignment explanation
Indices: 1355525--1355578 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1355515 GTATTTGAAA
1355525 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1355549 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1355573 TTTGAT
1 TTTGAT
1355579 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1355761 original size:3 final size:3
Alignment explanation
Indices: 1355753--1355780 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1355743 ATATAACCCT
1355753 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1355781 TCCCCGAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1355915 original size:18 final size:18
Alignment explanation
Indices: 1355878--1355924 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
1355868 TAAAGATAGC
1355878 AGTTGATTGTTACAAAAA
1 AGTTGATTGTTACAAAAA
*
1355896 AGTT-ATTGTTATCAAGAA
1 AGTTGATTGTTA-CAAAAA
*
1355914 AGATGATTGTT
1 AGTTGATTGTT
1355925 TTGATACAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.28
18 12 0.48
19 6 0.24
ACGTcount: A:0.38, C:0.04, G:0.19, T:0.38
Consensus pattern (18 bp):
AGTTGATTGTTACAAAAA
Found at i:1357876 original size:18 final size:18
Alignment explanation
Indices: 1357842--1357877 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1357832 AAGCAAAAGG
**
1357842 AAATCAAAATCGTAATCA
1 AAATCAAAATCCCAATCA
1357860 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
1357878 CAACCGTCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:1358309 original size:37 final size:37
Alignment explanation
Indices: 1358259--1358393 Score: 116
Period size: 37 Copynumber: 3.5 Consensus size: 37
1358249 CAAATCAACT
1358259 TTTACAAATCAATTAAACAAGCAAAAAATAATTCTTA
1 TTTACAAATCAATTAAACAAGCAAAAAATAATTCTTA
* *
1358296 TTTACACATCAATTAAACAAATCAACTTTTACAAATCAA--C-T-
1 TTTACAAATCAATTAAAC-AAGCAA-----A-AAAT-AATTCTTA
*
1358337 TTTACAAATCAATTAATCAAGCAAAAAATAATTCTTA
1 TTTACAAATCAATTAAACAAGCAAAAAATAATTCTTA
* **
1358374 TTTCCTCATCAATTAAACAA
1 TTTACAAATCAATTAAACAA
1358394 ATCAACTTTT
Statistics
Matches: 77, Mismatches: 9, Indels: 24
0.70 0.08 0.22
Matches are distributed among these distances:
33 2 0.03
34 4 0.05
35 2 0.03
36 1 0.01
37 33 0.43
38 5 0.06
40 5 0.06
41 16 0.21
42 1 0.01
43 2 0.03
44 4 0.05
45 2 0.03
ACGTcount: A:0.49, C:0.18, G:0.01, T:0.32
Consensus pattern (37 bp):
TTTACAAATCAATTAAACAAGCAAAAAATAATTCTTA
Found at i:1358331 original size:14 final size:14
Alignment explanation
Indices: 1358312--1358348 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
1358302 CATCAATTAA
1358312 ACAAATCAACTTTT
1 ACAAATCAACTTTT
1358326 ACAAATCAACTTTT
1 ACAAATCAACTTTT
1358340 ACAAATCAA
1 ACAAATCAA
1358349 TTAATCAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1358384 original size:78 final size:78
Alignment explanation
Indices: 1358248--1358412 Score: 303
Period size: 78 Copynumber: 2.1 Consensus size: 78
1358238 ATTTAAAACA
1358248 ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTAAA
1 ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTAAA
1358313 CAAATCAACTTTT
66 CAAATCAACTTTT
* * *
1358326 ACAAATCAACTTTTACAAATCAATTAATCAAGCAAAAAATAATTCTTATTTCCTCATCAATTAAA
1 ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTAAA
1358391 CAAATCAACTTTT
66 CAAATCAACTTTT
1358404 ACAAATCAA
1 ACAAATCAA
1358413 TTAAACAAGA
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 84 1.00
ACGTcount: A:0.49, C:0.19, G:0.01, T:0.31
Consensus pattern (78 bp):
ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTAAA
CAAATCAACTTTT
Found at i:1359784 original size:21 final size:21
Alignment explanation
Indices: 1359760--1359851 Score: 121
Period size: 21 Copynumber: 4.4 Consensus size: 21
1359750 GTGAATCGGG
*
1359760 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGGTGGGAGGGGT
* *
1359781 CTCTCGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGT
* *
1359802 CTCTTAAATGGTGGGAGGGGT
1 CTCTTGAACGGTGGGAGGGGT
* *
1359823 CTTTTGAACGGTGGGAAGGGT
1 CTCTTGAACGGTGGGAGGGGT
1359844 CTCTTGAA
1 CTCTTGAA
1359852 TGACGAGAGA
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 60 1.00
ACGTcount: A:0.18, C:0.15, G:0.42, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGT
Found at i:1360529 original size:42 final size:42
Alignment explanation
Indices: 1360454--1360550 Score: 140
Period size: 42 Copynumber: 2.3 Consensus size: 42
1360444 GTGATGGAAT
* * * * * *
1360454 AGGTGATGGCTCTTGTTGTGGAGGTGTATAATCGGCTCGATC
1 AGGTGATGGCTCTGGGTGTCGAGCTGTAGAATCGGCTCGATA
1360496 AGGTGATGGCTCTGGGTGTCGAGCTGTAGAATCGGCTCGATA
1 AGGTGATGGCTCTGGGTGTCGAGCTGTAGAATCGGCTCGATA
1360538 AGGTGATGGCTCT
1 AGGTGATGGCTCT
1360551 CGAAGTGGGG
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.18, C:0.15, G:0.37, T:0.30
Consensus pattern (42 bp):
AGGTGATGGCTCTGGGTGTCGAGCTGTAGAATCGGCTCGATA
Found at i:1362070 original size:19 final size:20
Alignment explanation
Indices: 1362036--1362117 Score: 116
Period size: 19 Copynumber: 4.2 Consensus size: 20
1362026 AAACTTAAAT
1362036 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
*
1362056 TCGCAACGC-AAAATGAAAT
1 TCGCAACGCGAAAATGAAAA
*
1362075 TCGCAACGC-AAAATGAAAT
1 TCGCAACGCGAAAATGAAAA
*
1362094 TCGCAACGCGAAACT-AAAA
1 TCGCAACGCGAAAATGAAAA
1362113 TCGCA
1 TCGCA
1362118 TTGCGATTTT
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
19 45 0.78
20 13 0.22
ACGTcount: A:0.46, C:0.23, G:0.17, T:0.13
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:1362117 original size:38 final size:39
Alignment explanation
Indices: 1362025--1362117 Score: 127
Period size: 38 Copynumber: 2.4 Consensus size: 39
1362015 AGTAGTTTCT
1362025 GAAACTTAAATTCGCAACGCGAAAATGAAAATCGCAACGC
1 GAAAC-TAAATTCGCAACGCGAAAATGAAAATCGCAACGC
* *
1362065 -AAAATGAAATTCGCAACGC-AAAATGAAATTCGCAACGC
1 GAAACT-AAATTCGCAACGCGAAAATGAAAATCGCAACGC
*
1362103 GAAACTAAAATCGCA
1 GAAACTAAATTCGCA
1362118 TTGCGATTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
38 27 0.57
39 20 0.43
ACGTcount: A:0.47, C:0.22, G:0.16, T:0.15
Consensus pattern (39 bp):
GAAACTAAATTCGCAACGCGAAAATGAAAATCGCAACGC
Found at i:1362717 original size:20 final size:20
Alignment explanation
Indices: 1362692--1362740 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
1362682 TAAACGCGCT
1362692 TTGCGAATTTGACTTATGTG
1 TTGCGAATTTGACTTATGTG
*
1362712 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTTATGTG
1362732 TTGCGAATT
1 TTGCGAATT
1362741 ACAAATTCGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.18, C:0.10, G:0.24, T:0.47
Consensus pattern (20 bp):
TTGCGAATTTGACTTATGTG
Found at i:1362821 original size:20 final size:20
Alignment explanation
Indices: 1362731--1362822 Score: 98
Period size: 20 Copynumber: 4.6 Consensus size: 20
1362721 TGACTTTTGT
** *
1362731 GTTGCGAATTACAAATTCGC
1 GTTGCGAATTTGAAAATCGC
*
1362751 GTTGCG-ATTT-ATATATTCGC
1 GTTGCGAATTTGA-A-AATCGC
*
1362771 GTTGCAAATTTGAAAATCGC
1 GTTGCGAATTTGAAAATCGC
*
1362791 GTTGCAAATTTGAAAATCGC
1 GTTGCGAATTTGAAAATCGC
1362811 GTTGCGAATTTG
1 GTTGCGAATTTG
1362823 GAAACTGAGT
Statistics
Matches: 64, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
18 1 0.02
19 4 0.06
20 53 0.83
21 5 0.08
22 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (20 bp):
GTTGCGAATTTGAAAATCGC
Found at i:1368225 original size:13 final size:13
Alignment explanation
Indices: 1368209--1368235 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1368199 TTTTCGTCCA
1368209 TATTTTTTTATTT
1 TATTTTTTTATTT
1368222 TATTTTTTTATTT
1 TATTTTTTTATTT
1368235 T
1 T
1368236 TGGGTCATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TATTTTTTTATTT
Found at i:1368387 original size:74 final size:72
Alignment explanation
Indices: 1368274--1368593 Score: 371
Period size: 74 Copynumber: 4.3 Consensus size: 72
1368264 AATATATATG
* * *
1368274 TATATATTATATAATTTTGAAAACATTTTAAAAATATATAGATATATAGTTTTTAAAACATTTTT
1 TATATATTATATAGTTTTTAAAACATTTTAAAAATATATATATATATAGTTTTTAAAACATTTTT
1368339 GAAAACATA
66 GAAAAC--A
*
1368348 TATATATTATATAGTTTTTAAATCATTTTGAAAAAATATATATATTATATAGTTTTTAAAACA-T
1 TATATATTATATAGTTTTTAAAACATTTT--AAAAATATATATA-TATATAGTTTTTAAAACATT
1368412 TTTGAAAACA
63 TTTGAAAACA
* *
1368422 TATATATTATATAGTTTTTAAAACATTTAAAAAATATATATATATTATA-TAATTTTAAAACGTT
1 TATATATTATATAGTTTTTAAAACATTTTAAAAATATATATATA-TATAGT--TTTTAAAACATT
1368486 TTTGAAAA-A
63 TTTGAAAACA
* * * *
1368495 TATATATAATATATAAGTTTTTAAAACAATTTTTGAAAATATATAT-TTTATAGTTTTGAAAATT
1 TATATAT--TATAT-AGTTTTTAAAAC-A-TTTTAAAAATATATATATATATAGTTTTTAAAA-C
*
1368559 ATTTTT-TAAACA
60 ATTTTTGAAAACA
*
1368571 TATATATTATATAGTTTTAAAAA
1 TATATATTATATAGTTTTTAAAA
1368594 AAATGTTTTT
Statistics
Matches: 216, Mismatches: 15, Indels: 31
0.82 0.06 0.12
Matches are distributed among these distances:
71 3 0.01
72 17 0.08
73 27 0.12
74 68 0.31
75 15 0.07
76 51 0.24
77 21 0.10
78 14 0.06
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (72 bp):
TATATATTATATAGTTTTTAAAACATTTTAAAAATATATATATATATAGTTTTTAAAACATTTTT
GAAAACA
Found at i:1368409 original size:112 final size:110
Alignment explanation
Indices: 1368274--1368593 Score: 387
Period size: 112 Copynumber: 2.9 Consensus size: 110
1368264 AATATATATG
* * *
1368274 TATATATTATATAATTTTGAAAACATTTTAAAAATATATAGATATATAGTTTTTAAAACATTTTT
1 TATATATTATATAGTTTTTAAAACATTTTAAAAATATATA-TTATATAGTTTTTAAAACATTTTT
*
1368339 GAAAACATATATATATTATATAGTTTTTAAATC-ATTTTGAAAAAATA
65 -AAAACATATATATATTATATAGTTTTTAAAACGATTTTG-AAAAATA
*
1368386 TATATATTATATAGTTTTTAAAACATTTTGAAAACATATATATTATATAGTTTTTAAAACATTTA
1 TATATATTATATAGTTTTTAAAACATTTT-AAAA-ATATATATTATATAGTTTTTAAAACATTTT
* * * *
1368451 AAAAATATATATATATTATATA-ATTTTAAAACGTTTTTGAAAAATA
64 TAAAACATATATATATTATATAGTTTTTAAAACGATTTTGAAAAATA
* * * * *
1368497 TATATAATATATAAGTTTTTAAAACAATTTTTGAAAATATATATTTTATAGTTTTGAAAATTATT
1 TATATATTATAT-AGTTTTTAAAAC-A-TTTTAAAAATATATATTATATAGTTTTTAAAA-CATT
* *
1368562 TTTTAAAC--ATATATATTATATAGTTTTAAAAA
62 TTTAAAACATATATATATTATATAGTTTTTAAAA
1368594 AAATGTTTTT
Statistics
Matches: 180, Mismatches: 20, Indels: 16
0.83 0.09 0.07
Matches are distributed among these distances:
111 40 0.22
112 93 0.52
113 36 0.20
114 11 0.06
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (110 bp):
TATATATTATATAGTTTTTAAAACATTTTAAAAATATATATTATATAGTTTTTAAAACATTTTTA
AAACATATATATATTATATAGTTTTTAAAACGATTTTGAAAAATA
Found at i:1368615 original size:4 final size:4
Alignment explanation
Indices: 1368601--1368689 Score: 52
Period size: 4 Copynumber: 23.5 Consensus size: 4
1368591 AAAAAATGTT
*
1368601 TTTA TTATA TTTA TTTA TTTA TTTA -TTA -TTA TTT- TTACA TGTT- TTTA
1 TTTA TT-TA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT-TA T-TTA TTTA
* *
1368648 -TT- TTTA TTTA TTTTA TTT- TTTG TTTA -TTA CTTA -TTA TTTA TT
1 TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
1368690 CTTTTTTCTC
Statistics
Matches: 70, Mismatches: 3, Indels: 24
0.72 0.03 0.25
Matches are distributed among these distances:
3 23 0.33
4 37 0.53
5 9 0.13
6 1 0.01
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:1368647 original size:22 final size:22
Alignment explanation
Indices: 1368596--1368659 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
1368586 TTTAAAAAAA
*
1368596 ATGTTTTTATTA-TATTTATTT
1 ATGTTTTTATTATTATTTATTC
1368617 AT-TTATTTATTATTATTT-TTAC
1 ATGTT-TTTATTATTATTTATT-C
*
1368639 ATGTTTTTATTTTTATTTATT
1 ATGTTTTTATTATTATTTATT
1368660 TTATTTTTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
20 2 0.06
21 11 0.31
22 19 0.53
23 4 0.11
ACGTcount: A:0.23, C:0.02, G:0.03, T:0.72
Consensus pattern (22 bp):
ATGTTTTTATTATTATTTATTC
Found at i:1368695 original size:49 final size:49
Alignment explanation
Indices: 1368599--1368695 Score: 119
Period size: 49 Copynumber: 2.0 Consensus size: 49
1368589 AAAAAAAATG
*
1368599 TTTTTATTATATTTATTTATTTATTTATTATTATTTTTACATGTTTTTA
1 TTTTTATTATATTTATTTATTTATTTATTATTATTTTTACATCTTTTTA
* *
1368648 TTTTTATT-TATTTTATTT-TTTGTTTATTACTTATTATTTA-TTCTTTTT
1 TTTTTATTATA-TTTATTTATTTATTTATTA-TTATT-TTTACATCTTTTT
1368696 TCTCGTTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
48 12 0.29
49 26 0.62
50 4 0.10
ACGTcount: A:0.21, C:0.03, G:0.02, T:0.74
Consensus pattern (49 bp):
TTTTTATTATATTTATTTATTTATTTATTATTATTTTTACATCTTTTTA
Found at i:1372982 original size:19 final size:18
Alignment explanation
Indices: 1372949--1373004 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 18
1372939 AGATCCAATC
1372949 AGAACAAAA-AAAGAAAAA
1 AGAA-AAAAGAAAGAAAAA
*
1372967 AGAGAAAAGCAAAGAAAAA
1 AGAAAAAAG-AAAGAAAAA
* *
1372986 ATAAAAAAGAAATAAAAA
1 AGAAAAAAGAAAGAAAAA
1373004 A
1 A
1373005 AACAAAGGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
17 4 0.12
18 12 0.38
19 16 0.50
ACGTcount: A:0.80, C:0.04, G:0.12, T:0.04
Consensus pattern (18 bp):
AGAAAAAAGAAAGAAAAA
Found at i:1373931 original size:24 final size:23
Alignment explanation
Indices: 1373877--1373940 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 23
1373867 GAAAGGGGAA
*
1373877 ATATTTTCAAAACTTTTGGTTAC
1 ATATTTTCAAAACTTTTAGTTAC
*
1373900 ATATTTTTCAAAACCCTTTTAGTT-G
1 ATA-TTTTCAAAA--CTTTTAGTTAC
*
1373925 ATATTTTCAGAACTTT
1 ATATTTTCAAAACTTT
1373941 GAAAATAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
22 4 0.11
23 3 0.09
24 17 0.49
25 3 0.09
26 8 0.23
ACGTcount: A:0.30, C:0.14, G:0.08, T:0.48
Consensus pattern (23 bp):
ATATTTTCAAAACTTTTAGTTAC
Found at i:1374115 original size:32 final size:32
Alignment explanation
Indices: 1374079--1374148 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
1374069 AGGAGAAATG
* *
1374079 GGGGCACCTTT-GAAGATTCAACATTAAATGTT
1 GGGGCACCTTTAG-AGATTCAACATCAAATATT
* * *
1374111 GGGGCATCTTTAGAGATTTAACATCGAATATT
1 GGGGCACCTTTAGAGATTCAACATCAAATATT
1374143 GGGGCA
1 GGGGCA
1374149 TCTTCGGGGA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 31 0.97
33 1 0.03
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (32 bp):
GGGGCACCTTTAGAGATTCAACATCAAATATT
Found at i:1374700 original size:110 final size:110
Alignment explanation
Indices: 1374411--1375144 Score: 984
Period size: 110 Copynumber: 6.9 Consensus size: 110
1374401 GATGGTGGTT
1374411 GCTCAACTTCACAGCGAA-GGG-G-C-GACTGTCAACAAACAACTTTTCAGTTTCATGT-AGAGT
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCAT-TCAGAGT
* *
1374471 CAATTTCAACTTCACAGTGAAGGATATTGGACTCGAGACAACACAT
65 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
*
1374517 GCTCAACTTCACAGCGAAGGGGCGA-T---TGTCAACAAACAACTTTTCAGTTTCATACAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
1374578 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* * * *
1374623 GCTCAACTTCACAACGAATGGGTGACTGACTGTCAACAAATAACTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
* * *
1374688 AACTTCAACTTCATAGCGAAGGATATTAGACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* *
1374733 GCTCAACTTCACAGCGAAGGGGCGATTGACTGT-------CAACTTTTCAGTTTCATTCAGAGTT
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
* *
1374791 AATTTCAACTTCACAACGAAAGATATTGGACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* * * *
1374836 GCTCAACTTCACAACCAATGGGTGACTGACTGT-------CAACTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
*
1374894 AATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* * *
1374939 GCTCAACTTCACAACGAAGGGGCGACTGACTGTCAACAAACAACTTTTCTGTTTCATTCAGAGCC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
* *
1375004 AATTTCAACTTTACAGCAAAGGATATTGGACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* * * *
1375049 GCTCAACTTCACGGCGAAGGGGCGGCTGGCTGTCAACAAACAACTTTCCAG-TT--TT-AGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
* *
1375110 AATTTCAACTTCAC-GACGAAGAATATTGGCCTCGA
66 AATTTCAACTTCACAG-CGAAGGATATTGGACTCGA
1375145 AATAACACTA
Statistics
Matches: 561, Mismatches: 50, Indels: 34
0.87 0.08 0.05
Matches are distributed among these distances:
103 187 0.33
105 1 0.00
106 150 0.27
107 6 0.01
108 1 0.00
109 2 0.00
110 214 0.38
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.25
Consensus pattern (110 bp):
GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
Found at i:1374824 original size:103 final size:103
Alignment explanation
Indices: 1374411--1375085 Score: 857
Period size: 103 Copynumber: 6.4 Consensus size: 103
1374401 GATGGTGGTT
***
1374411 GCTCAACTTCACAGCGAAGGGGCGACTGTCAACAAACAACTTTTCAGTTTCATGT-AGAGTCAAT
1 GCTCAACTTCACAGCGAAGGGGCGACTG---ACTGTCAACTTTTCAGTTTCAT-TCAGAGTCAAT
* *
1374475 TTCAACTTCACAGTGAAGGATATTGGACTCGAGACAACACAT
62 TTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* *** *
1374517 GCTCAACTTCACAGCGAAGGGGCGATTGTCAACAAACAACTTTTCAGTTTCATACAGAGTCAATT
1 GCTCAACTTCACAGCGAAGGGGCGACTG---ACTGTCAACTTTTCAGTTTCATTCAGAGTCAATT
1374582 TCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
63 TCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* * *
1374623 GCTCAACTTCACAACGAATGGGTGACTGACTGTCAACAAATAACTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGT---C----AACTTTTCAGTTTCATTCAGAGTC
* * *
1374688 AACTTCAACTTCATAGCGAAGGATATTAGACTCGAGACAACACAA
59 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* *
1374733 GCTCAACTTCACAGCGAAGGGGCGATTGACTGTCAACTTTTCAGTTTCATTCAGAGTTAATTTCA
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACTTTTCAGTTTCATTCAGAGTCAATTTCA
* *
1374798 ACTTCACAACGAAAGATATTGGACTCGAGACAACACAA
66 ACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* * * *
1374836 GCTCAACTTCACAACCAATGGGTGACTGACTGTCAACTTTTCAGTTTCATTCAGAGTCAATTTCA
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACTTTTCAGTTTCATTCAGAGTCAATTTCA
*
1374901 ACTTCACAGCGAAGGATATTAGACTCGAGACAACACAA
66 ACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* * *
1374939 GCTCAACTTCACAACGAAGGGGCGACTGACTGTCAACAAACAACTTTTCTGTTTCATTCAGAGCC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGT-------CAACTTTTCAGTTTCATTCAGAGTC
* *
1375004 AATTTCAACTTTACAGCAAAGGATATTGGACTCGAGACAACACAA
59 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* * *
1375049 GCTCAACTTCACGGCGAAGGGGCGGCTGGCTGTCAAC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAAC
1375086 AAACAACTTT
Statistics
Matches: 508, Mismatches: 46, Indels: 33
0.87 0.08 0.06
Matches are distributed among these distances:
103 193 0.38
106 126 0.25
107 1 0.00
110 188 0.37
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (103 bp):
GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACTTTTCAGTTTCATTCAGAGTCAATTTCA
ACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
Found at i:1375028 original size:316 final size:320
Alignment explanation
Indices: 1374411--1375144 Score: 1020
Period size: 316 Copynumber: 2.3 Consensus size: 320
1374401 GATGGTGGTT
1374411 GCTCAACTTCACAGCGAAGGGGCGACTGTCAACAAACAACTTTTCAGTTTCATGTAGAGTCAATT
1 GCTCAACTTCACAGCGAAGGGGCGACTGTCAACAAACAACTTTTCAGTTTCATGTAGAGTCAATT
** * * * *
1374476 TCAACTTCACAGTGAAGGATATTGGACTCGAGACAACACATGCTCAACTTCACAGCGAAGGGGCG
66 TCAACTTCACAACGAAAGATATTGGACTCGAGACAACACAAGCTCAACTTCACAACCAAGGGGCG
* *
1374541 ATTGTCAACAAACAACTTTTCAGTTTCATACAGAGTCAATTTCAACTTCACAGCGAAGGATATTG
131 ACTG--AACAAACAACTTTTCAGTTTCATACAGAGTCAATTTCAACTTCACAGCGAAGGATATTA
* * *
1374606 GACTCGAGACAACACAAGCTCAACTTCACAACGAATGGGTGACTGACTGTCAACAAATAACTTTT
194 GACTCGAGACAACACAAGCTCAACTTCACAACGAAGGGGCGACTGACTGTCAACAAACAACTTTT
* * *
1374671 CAGTTTCATTCAGAGTCAACTTCAACTTCATAGCGAAGGATATTAGACTCGAGACAACACAA
259 CAGTTTCATTCAGAGCCAACTTCAACTTCACAGCAAAGGATATTAGACTCGAGACAACACAA
* *** *
1374733 GCTCAACTTCACAGCGAAGGGGCGA-T-T-GACTGTCAACTTTTCAGTTTCAT-TCAGAGTTAAT
1 GCTCAACTTCACAGCGAAGGGGCGACTGTCAACAAACAACTTTTCAGTTTCATGT-AGAGTCAAT
* *
1374794 TTCAACTTCACAACGAAAGATATTGGACTCGAGACAACACAAGCTCAACTTCACAACCAATGGGT
65 TTCAACTTCACAACGAAAGATATTGGACTCGAGACAACACAAGCTCAACTTCACAACCAAGGGGC
*** *
1374859 GACTG-ACTGTCAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTAG
130 GACTGAACAAACAACTTTTCAGTTTCATACAGAGTCAATTTCAACTTCACAGCGAAGGATATTAG
1374923 ACTCGAGACAACACAAGCTCAACTTCACAACGAAGGGGCGACTGACTGTCAACAAACAACTTTTC
195 ACTCGAGACAACACAAGCTCAACTTCACAACGAAGGGGCGACTGACTGTCAACAAACAACTTTTC
* * * *
1374988 TGTTTCATTCAGAGCCAATTTCAACTTTACAGCAAAGGATATTGGACTCGAGACAACACAA
260 AGTTTCATTCAGAGCCAACTTCAACTTCACAGCAAAGGATATTAGACTCGAGACAACACAA
* * *
1375049 GCTCAACTTCACGGCGAAGGGGCGGCTGGCTGTCAACAAACAACTTTCCAG-TT--T-TAGAGTC
1 GCTCAACTTCACAGCGAA--GG-GGC-GACTGTCAACAAACAACTTTTCAGTTTCATGTAGAGTC
* *
1375110 AATTTCAACTTCACGACG-AAGAATATTGGCCTCGA
62 AATTTCAACTTCACAACGAAAG-ATATTGGACTCGA
1375145 AATAACACTA
Statistics
Matches: 364, Mismatches: 39, Indels: 21
0.86 0.09 0.05
Matches are distributed among these distances:
316 187 0.51
318 6 0.02
319 125 0.34
320 4 0.01
321 2 0.01
322 28 0.08
323 12 0.03
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.25
Consensus pattern (320 bp):
GCTCAACTTCACAGCGAAGGGGCGACTGTCAACAAACAACTTTTCAGTTTCATGTAGAGTCAATT
TCAACTTCACAACGAAAGATATTGGACTCGAGACAACACAAGCTCAACTTCACAACCAAGGGGCG
ACTGAACAAACAACTTTTCAGTTTCATACAGAGTCAATTTCAACTTCACAGCGAAGGATATTAGA
CTCGAGACAACACAAGCTCAACTTCACAACGAAGGGGCGACTGACTGTCAACAAACAACTTTTCA
GTTTCATTCAGAGCCAACTTCAACTTCACAGCAAAGGATATTAGACTCGAGACAACACAA
Found at i:1375628 original size:84 final size:82
Alignment explanation
Indices: 1375363--1375817 Score: 375
Period size: 84 Copynumber: 5.5 Consensus size: 82
1375353 ACCTCCAAGA
* * * * *
1375363 CACATCATTTACAGCATAGCTTAAGTCGAAAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCG
1 CACATCATTTACAGCATAACTCAAGGCTAGAAGGGCTATCTG-C-ACCAAAGACCTTCGAGTTCG
* ** *
1375428 ACTATGCTCAGCTCCAAGG
64 ATTACACTCAGCTCTAAGG
* * *
1375447 CACATCATTTGCAGCATAACGT-AA-GTTGAGAAGGGCTATCTG--CCAAAGACCCTCGAGTTCG
1 CACATCATTTACAGCATAAC-TCAAGGCT-AGAAGGGCTATCTGCACCAAAGACCTTCGAGTTCG
* * *
1375508 ATTCCACTCAGCTTCGAGGG
64 ATTACACTCAGC-TCTAAGG
* *
1375528 CACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAAGACCTTCGAGTTCG
1 CACATCATTTACAGCATAACTCAAGGCTAGAAGGGCTATCTG-CACC-AAAGACCTTCGAGTTCG
* * *
1375593 AGTACAGTAAGCTCTAAGG
64 ATTACACTCAGCTCTAAGG
* * * * * * * * * *
1375612 CAAATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTTTCT--ACTATAGACCCTCGAGTTCGAT
1 CACATCATTTACAGCATAACTCAAGGCTAGAAGGGCTATCTGCACCAAAGACCTTCGAGTTCGAT
*
1375675 TACACTCAGCTTCTAGGG
66 TACACTCAGC-TCTAAGG
* * * * * *
1375693 CACATCATTTACAGTATAGCTCAAGGCTATAAGGGCTATTTCCCACCAAAAGACCTTCGAGTTTG
1 CACATCATTTACAGCATAACTCAAGGCTAGAAGGGCTATCT-GCACC-AAAGACCTTCGAGTTCG
1375758 ATTACACTCAGCTC-AGAGG
64 ATTACACTCAGCTCTA-AGG
* * * *
1375777 CAAACCAAATTTACAACATAACTCAAGGCAAGAAGGGCTAT
1 CACATC--ATTTACAGCATAACTCAAGGCTAGAAGGGCTAT
1375818 ATGTCAACAA
Statistics
Matches: 295, Mismatches: 59, Indels: 32
0.76 0.15 0.08
Matches are distributed among these distances:
80 51 0.17
81 79 0.27
82 2 0.01
83 1 0.00
84 83 0.28
85 51 0.17
86 28 0.09
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (82 bp):
CACATCATTTACAGCATAACTCAAGGCTAGAAGGGCTATCTGCACCAAAGACCTTCGAGTTCGAT
TACACTCAGCTCTAAGG
Found at i:1375780 original size:165 final size:164
Alignment explanation
Indices: 1375363--1375780 Score: 523
Period size: 165 Copynumber: 2.5 Consensus size: 164
1375353 ACCTCCAAGA
* * * *
1375363 CACATCATTTACAGCATAGCTTAAGTCGAAAAGGGCTATCTGCCAACC-AAAGACCTTCGAGTTC
1 CACATCATTTACAGCATAGCTCAAGGCTAAAAGGGCTAT-TTCCAACCAAAAGACCTTCGAGTTC
** * * *
1375427 GACTATGCTCAGCTCCAAGGCACATCATTTGCAGCATAACGTAAGTTGAGAAGGGCTATCTGCCA
65 GACTACACTCAGCT-CAAGGCAAATCATTTGCAGCATAACGTAAGTCGAGAAGGGCTATCTACCA
*
1375492 AAGACCCTCGAGTTCGATTCCACTCAGCTTCGAGGG
129 AAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGG
* * * * **
1375528 CACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAAGACCTTCGAGTTCG
1 CACATCATTTACAGCATAGCTCAAGGCTAAAAGGGCTATTTCCAACCAAAAGACCTTCGAGTTCG
* * * * * * * *
1375593 AGTACAGTAAGCTCTAAGGCAAATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTTTCTACTAT
66 ACTACACTCAGCTC-AAGGCAAATCATTTGCAGCATAACGTAAGTCGAGAAGGGCTATCTACCAA
*
1375658 AGACCCTCGAGTTCGATTACACTCAGCTTCTAGGG
130 AGACCCTCGAGTTCGATTACACTCAGCTTCGAGGG
* * * *
1375693 CACATCATTTACAGTATAGCTCAAGGCTATAAGGGCTATTTCCCACCAAAAGACCTTCGAGTTTG
1 CACATCATTTACAGCATAGCTCAAGGCTAAAAGGGCTATTTCCAACCAAAAGACCTTCGAGTTCG
*
1375758 ATTACACTCAGCTCAGAGGCAAA
66 ACTACACTCAGCTCA-AGGCAAA
1375781 CCAAATTTAC
Statistics
Matches: 213, Mismatches: 37, Indels: 6
0.83 0.14 0.02
Matches are distributed among these distances:
164 6 0.03
165 207 0.97
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.25
Consensus pattern (164 bp):
CACATCATTTACAGCATAGCTCAAGGCTAAAAGGGCTATTTCCAACCAAAAGACCTTCGAGTTCG
ACTACACTCAGCTCAAGGCAAATCATTTGCAGCATAACGTAAGTCGAGAAGGGCTATCTACCAAA
GACCCTCGAGTTCGATTACACTCAGCTTCGAGGG
Found at i:1376523 original size:38 final size:37
Alignment explanation
Indices: 1376409--1376730 Score: 370
Period size: 38 Copynumber: 8.6 Consensus size: 37
1376399 AATATATATG
* *
1376409 TATATATTATATAATTTTGAAAACATTTTG-AAAATA
1 TATATATTATATAGTTTTTAAAACATTTTGAAAAATA
* *
1376445 TATATGA-TATATATTTTTTAACACATTTTTGAAAACATA
1 TATAT-ATTATATAGTTTTTAAAACA-TTTTGAAAA-ATA
1376484 TATATATTATATAGTTTTTAAAACATTTTGAAAAA-A
1 TATATATTATATAGTTTTTAAAACATTTTGAAAAATA
1376520 TATATATTATATAGTTTTTAAAACATTTTGAAAACATA
1 TATATATTATATAGTTTTTAAAACATTTTGAAAA-ATA
* * *
1376558 TATATATTATACAATTTTTAAAACATTTTAAAAACATA
1 TATATATTATATAGTTTTTAAAACATTTTGAAAA-ATA
* *
1376596 TATATATTATATAATTTTTAAAACGTTTTTGAAAAATA
1 TATATATTATATAGTTTTTAAAAC-ATTTTGAAAAATA
1376634 TATATATTATATAAGTTTTTAAAACAATTTTTG--AAA-A
1 TATATATTATAT-AGTTTTTAAAAC-A-TTTTGAAAAATA
* * ** *
1376671 TATATATTATATAGTTTTGAAAATTATTTT-TTAAACA
1 TATATATTATATAGTTTTTAAAA-CATTTTGAAAAATA
*
1376708 TATATATTATATAGTTTTAAAAA
1 TATATATTATATAGTTTTTAAAA
1376731 AATGTTTTTA
Statistics
Matches: 255, Mismatches: 17, Indels: 27
0.85 0.06 0.09
Matches are distributed among these distances:
35 4 0.02
36 69 0.27
37 44 0.17
38 90 0.35
39 43 0.17
40 5 0.02
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (37 bp):
TATATATTATATAGTTTTTAAAACATTTTGAAAAATA
Found at i:1376744 original size:3 final size:3
Alignment explanation
Indices: 1376738--1376831 Score: 61
Period size: 3 Copynumber: 30.7 Consensus size: 3
1376728 AAAAATGTTT
* * *
1376738 TTA TTA -TA TTTA TTA TTA TTA TTA TTA TTA TTA TTT TTA CCTA TTT
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
* *
1376784 TTA TTT TTA TTTA TT- TTA TT- TT- TTG TCTA TTA CTTA TTA TTTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA T-TA TTA -TTA TTA -TTA TTA
1376830 TT
1 TT
1376832 TTTTCTTGTT
Statistics
Matches: 73, Mismatches: 9, Indels: 18
0.73 0.09 0.18
Matches are distributed among these distances:
2 8 0.11
3 50 0.68
4 15 0.21
ACGTcount: A:0.24, C:0.04, G:0.01, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:1376801 original size:25 final size:25
Alignment explanation
Indices: 1376738--1376800 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 25
1376728 AAAAATGTTT
*
1376738 TTATTA-TATTTATTA-TTATTATTA
1 TTATTATTATTT-TTACCTATTATTA
*
1376762 TTATTATTATTTTTACCTATTTTTA
1 TTATTATTATTTTTACCTATTATTA
*
1376787 TTTTTATTTATTTT
1 TTATTA-TTATTTT
1376801 ATTTTTTGTC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
24 9 0.27
25 17 0.52
26 7 0.21
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.71
Consensus pattern (25 bp):
TTATTATTATTTTTACCTATTATTA
Found at i:1378067 original size:19 final size:19
Alignment explanation
Indices: 1378043--1378079 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1378033 TATATCGATT
1378043 TTTTTTATTATGTATTTTA
1 TTTTTTATTATGTATTTTA
1378062 TTTTTTATTATGTATTTT
1 TTTTTTATTATGTATTTT
1378080 TTTCTTCCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.76
Consensus pattern (19 bp):
TTTTTTATTATGTATTTTA
Found at i:1378082 original size:16 final size:16
Alignment explanation
Indices: 1378040--1378082 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 16
1378030 ACATATATCG
1378040 ATTTTTTTTATTATGT
1 ATTTTTTTTATTATGT
1378056 ATTTTATTTTTTATTATGT
1 A--TT-TTTTTTATTATGT
1378075 ATTTTTTT
1 ATTTTTTT
1378083 CTTCCTTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
16 6 0.25
17 2 0.08
18 2 0.08
19 14 0.58
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.77
Consensus pattern (16 bp):
ATTTTTTTTATTATGT
Found at i:1383411 original size:3 final size:3
Alignment explanation
Indices: 1383405--1383525 Score: 145
Period size: 3 Copynumber: 40.0 Consensus size: 3
1383395 AATAATTATT
* *
1383405 TAA TAA TAA T-A TAA TATA TAT TAA TAA TATT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TA-A TAA TAA TAA TAA TAA
** * *
1383451 TAA TTT TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
1383499 TAA TAA TAA TAA TTT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1383526 ACGAAAAATT
Statistics
Matches: 99, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
2 2 0.02
3 92 0.93
4 5 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:1384241 original size:76 final size:76
Alignment explanation
Indices: 1383690--1384214 Score: 987
Period size: 76 Copynumber: 6.9 Consensus size: 76
1383680 TGCACTGAAG
*
1383690 GGCTTTGAAAACATCAAAAAGCTCCTGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACA
1 GGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACA
1383755 GATGACCCTAA
66 GATGACCCTAA
*
1383766 GGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACA
1 GGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACA
1383831 GATGACCCTAA
66 GATGACCCTAA
1383842 GGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACA
1 GGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACA
1383907 GATGACCCTAA
66 GATGACCCTAA
* * * *
1383918 GGTTTTGAAAACGTCAAAAAGCTCTCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACA
1 GGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACA
1383983 GATGACCCTAA
66 GATGACCCTAA
1383994 GGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACA
1 GGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACA
1384059 GATGACCCTAA
66 GATGACCCTAA
1384070 GGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACA
1 GGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACA
1384135 GATGACCCTAA
66 GATGACCCTAA
*
1384146 GGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTATA
1 GGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACA
1384211 GATG
66 GATG
1384215 TAGGAAATAG
Statistics
Matches: 437, Mismatches: 12, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 437 1.00
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (76 bp):
GGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACA
GATGACCCTAA
Found at i:1384874 original size:22 final size:23
Alignment explanation
Indices: 1384849--1384903 Score: 96
Period size: 22 Copynumber: 2.5 Consensus size: 23
1384839 CATAAAGCAT
1384849 TCATCTTTGAAAAA-AGAATCTA
1 TCATCTTTGAAAAAGAGAATCTA
1384871 TCATCTTT-AAAAAGAGAATCTA
1 TCATCTTTGAAAAAGAGAATCTA
1384893 TCATCTTTGAA
1 TCATCTTTGAA
1384904 GAGTGTAGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
21 5 0.16
22 24 0.77
23 2 0.06
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.35
Consensus pattern (23 bp):
TCATCTTTGAAAAAGAGAATCTA
Found at i:1387587 original size:115 final size:114
Alignment explanation
Indices: 1387205--1387545 Score: 603
Period size: 114 Copynumber: 3.0 Consensus size: 114
1387195 GATCATGTAG
* * * * *
1387205 TTCATCTTTCAATTCTAATGATTGGTTCTGGGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1387270 ACACTTCCAGAAGATGCTATTGGGT-TTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTT-CTTATTTCTACTATGAGCAAA
1387319 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
1387384 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCATA
66 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
1387433 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGG-TTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
1387498 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCA
65 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCA
1387546 CATGGAACTT
Statistics
Matches: 219, Mismatches: 6, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
114 130 0.59
115 89 0.41
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
Found at i:1394874 original size:20 final size:20
Alignment explanation
Indices: 1394836--1394874 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1394826 ATAAATAATG
*
1394836 AAAATAAAATACTTGAAAAT
1 AAAATAAAATACTTAAAAAT
1394856 AAAATAAAAATA-TTAAAAA
1 AAAAT-AAAATACTTAAAAA
1394875 ATAATATACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (20 bp):
AAAATAAAATACTTAAAAAT
Found at i:1394913 original size:26 final size:25
Alignment explanation
Indices: 1394828--1394914 Score: 69
Period size: 21 Copynumber: 3.6 Consensus size: 25
1394818 ACAGATAAAT
* *
1394828 AAATAATGAAAATA-AAATACT-TGA
1 AAATAAT-AATATATAAATATTATGA
*
1394852 AAATAA-AATA-A-AAATATTA-AA
1 AAATAATAATATATAAATATTATGA
*
1394873 AAATAATATACATATAAATATTATGA
1 AAATAATA-ATATATAAATATTATGA
1394899 AAATAATAAGTATATA
1 AAATAATAA-TATATA
1394915 TAAAAATTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
21 14 0.28
22 4 0.08
23 2 0.04
24 7 0.14
25 9 0.18
26 14 0.28
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (25 bp):
AAATAATAATATATAAATATTATGA
Found at i:1394928 original size:29 final size:28
Alignment explanation
Indices: 1394859--1394930 Score: 71
Period size: 29 Copynumber: 2.6 Consensus size: 28
1394849 TGAAAATAAA
1394859 ATAAAAATA-T-T-AAAAAATAATATAC
1 ATAAAAATATTATGAAAAAATAATATAC
* *
1394884 ATATAAATATTATGAAAATAATAAGTATAT
1 ATAAAAATATTATGAAAA-AATAA-TATAC
*
1394914 ATAAAAAT-TTTTGAAAA
1 ATAAAAATATTATGAAAA
1394931 GAAAGAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
25 8 0.21
26 1 0.03
27 1 0.03
28 4 0.11
29 13 0.34
30 11 0.29
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.33
Consensus pattern (28 bp):
ATAAAAATATTATGAAAAAATAATATAC
Found at i:1397112 original size:3 final size:3
Alignment explanation
Indices: 1397106--1397187 Score: 85
Period size: 3 Copynumber: 27.0 Consensus size: 3
1397096 AATAATTATT
* *
1397106 TAA TAA TAA T-A TAA TATA TAT TAA TAA TATT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TA-A TAA TAA TAA TAA TAA
* * **
1397152 TAA TAT TTA TAA TAA TAA TAA TTT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1397188 ACGAAAAATT
Statistics
Matches: 64, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
2 2 0.03
3 57 0.89
4 5 0.08
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (3 bp):
TAA
Found at i:1397184 original size:18 final size:18
Alignment explanation
Indices: 1397095--1397187 Score: 90
Period size: 18 Copynumber: 5.3 Consensus size: 18
1397085 TTTGGGCTTG
*
1397095 TAATAATTA-TTTAATAA
1 TAATAATAATTTTAATAA
* *
1397112 TAAT-ATAA-TAT-ATAT
1 TAATAATAATTTTAATAA
1397127 TAATAAT-ATTTAATAATAA
1 TAATAATAATTT--TAATAA
1397146 TAATAATAATATTT-ATAA
1 TAATAATAAT-TTTAATAA
1397164 TAATAATAATTTTAATAA
1 TAATAATAATTTTAATAA
1397182 TAATAA
1 TAATAA
1397188 ACGAAAAATT
Statistics
Matches: 63, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
15 8 0.13
16 8 0.13
17 7 0.11
18 25 0.40
19 11 0.17
20 2 0.03
21 2 0.03
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TAATAATAATTTTAATAA
Found at i:1397187 original size:15 final size:16
Alignment explanation
Indices: 1397095--1397187 Score: 82
Period size: 15 Copynumber: 5.6 Consensus size: 16
1397085 TTTGGGCTTG
*
1397095 TAATAATTATTTAATAA
1 TAATAATAATTT-ATAA
* *
1397112 TAAT-ATAATATATAT
1 TAATAATAATTTATAA
*
1397127 TAATAATATTTAATAATAA
1 TAATAATAATT--T-ATAA
1397146 TAATAATAATATTTATAA
1 TAATAAT-A-ATTTATAA
1397164 TAATAATAATTT-TAA
1 TAATAATAATTTATAA
1397179 TAATAATAA
1 TAATAATAA
1397188 ACGAAAAATT
Statistics
Matches: 63, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
15 19 0.30
16 13 0.21
17 5 0.08
18 12 0.19
19 11 0.17
20 1 0.02
21 2 0.03
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAATAATAATTTATAA
Found at i:1404802 original size:22 final size:22
Alignment explanation
Indices: 1404776--1404851 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
1404766 CGAGGGTAGA
1404776 GTATCGATACTCCCCAAAAGGG
1 GTATCGATACTCCCCAAAAGGG
1404798 GTATCGATACTCCCCAAAAGGG
1 GTATCGATACTCCCCAAAAGGG
*
1404820 GCATCGATACTCCCCAAAA-GG
1 GTATCGATACTCCCCAAAAGGG
*
1404841 GTATCAATACT
1 GTATCGATACT
1404852 TAAGTATTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
21 11 0.22
22 40 0.78
ACGTcount: A:0.33, C:0.28, G:0.20, T:0.20
Consensus pattern (22 bp):
GTATCGATACTCCCCAAAAGGG
Found at i:1411521 original size:23 final size:23
Alignment explanation
Indices: 1411495--1411538 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
1411485 ATGCGAACTC
1411495 CATTCTAATATGTAAATCACCAT
1 CATTCTAATATGTAAATCACCAT
1411518 CATTCTAATATGTAAATCACC
1 CATTCTAATATGTAAATCACC
1411539 GTAATTGACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.39, C:0.23, G:0.05, T:0.34
Consensus pattern (23 bp):
CATTCTAATATGTAAATCACCAT
Found at i:1412994 original size:132 final size:135
Alignment explanation
Indices: 1412632--1413223 Score: 640
Period size: 132 Copynumber: 4.3 Consensus size: 135
1412622 TGTGAAAGTG
* * *
1412632 CGTTTCATGGGGCG-CGCCTT-CCTTTTTTGTCAGAATAGGTTATAATTGCCCTATTTTGTGTGA
1 CGTTTCA-GGGG-GACGCCTTCCCTTTTTTGTCAGAATAGGTTATAATTGCCCTATTCTATGTCA
** * ** * ** * *
1412695 TGTCCCCCGGTGGGGTACTATTCATGTCAGTACCTAAAATCTTTGAGGGGACATAGCAATGTGAT
64 TGTCCCCCGGAAGGGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAACAATGTGGT
1412760 TAAAGCA
129 TAAAGCA
* * *
1412767 CATTTCAGGGGGTACGCCTTCCCTTTTTTGTTAGAATAGGTTATAATTGCCCTATTCTGTGTCAT
1 CGTTTCAGGGGG-ACGCCTTCCCTTTTTTGTCAGAATAGGTTATAATTGCCCTATTCTATGTCAT
* * *
1412832 GTCCCCCGG-TGGGCACTATTCATATCAGTACCTATCATGTTTGAGGGGACGCAAAAATGTGGTT
65 GTCCCCCGGAAGGGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAACAATGTGGTT
*
1412896 AAAGTA
130 AAAGCA
* * * *
1412902 CGTTTCA-GGGGATGCCTTCCCTTTTTT-TCAGAATAGGTTATAATTACCCTGTTTTATGTCATG
1 CGTTTCAGGGGGACGCCTTCCCTTTTTTGTCAGAATAGGTTATAATTGCCCTATTCTATGTCATG
* * * * * *
1412965 TCCCCC-GACGGGCACTATTCATGTTAGTACTTATCATGCTTGAGGGGACGCATCATTGTGGTTA
66 TCCCCCGGAAGGGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAACAATGTGGTTA
*
1413029 AAGCG
131 AAGCA
* * * *
1413034 TGTTTCAGGGGGGACACCTTCCCTTTTTTTGTCAGAGAATATGTTATAATTGCCCTATTCTATAT
1 CGTTTCA-GGGGGACGCCTTCCC-TTTTTTGTC--AGAATAGGTTATAATTGCCCTATTCTATGT
*** * *
1413099 CATGTCCCCCGGAATAACACTATTCAAGTCAGTACCTATCATGTTTGAGGGGACGCAATAATGTG
62 CATGTCCCCCGGAAGGGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAACAATGTG
*
1413164 GTTAAAGCG
127 GTTAAAGCA
* *
1413173 CAG-TTCAGGGGGCGCGCCTTCCCTTTTTTTGTCAGAGAATATGTTATAATT
1 C-GTTTCAGGGGG-ACGCCTTCCC-TTTTTTGTC--AGAATAGGTTATAATT
1413224 CTCTATTATG
Statistics
Matches: 389, Mismatches: 55, Indels: 22
0.83 0.12 0.05
Matches are distributed among these distances:
131 1 0.00
132 94 0.24
133 16 0.04
134 20 0.05
135 73 0.19
136 52 0.13
138 40 0.10
139 92 0.24
140 1 0.00
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (135 bp):
CGTTTCAGGGGGACGCCTTCCCTTTTTTGTCAGAATAGGTTATAATTGCCCTATTCTATGTCATG
TCCCCCGGAAGGGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAACAATGTGGTTA
AAGCA
Found at i:1413148 original size:139 final size:135
Alignment explanation
Indices: 1412632--1413223 Score: 619
Period size: 139 Copynumber: 4.4 Consensus size: 135
1412622 TGTGAAAGTG
* * * *
1412632 CGTTTCATGGGGCG-CGCCTT-CCTTTTTTGTCAGAATAGGTTATAATTGCCCTATTTTGTGTGA
1 CGTTTCA-GGGGGGACGCCTTCCCTTTTTTGTCAGAATAGGTTATAATTGCCCTATTCTATGTCA
* * * ** * ** * *
1412695 TGTCCCCCGGTGGGGTACTATTCATGTCAGTACCTAAAATCTTTGAGGGGACATAGCAATGTGAT
65 TGTCCCCCGG-AGGGCACTATTCAAGTCAGTACCTATCATGTTTGAGGGGACGCATCAATGTGGT
1412760 TAAAGCA
129 TAAAGCA
* * * *
1412767 CATTTCAGGGGGTACGCCTTCCCTTTTTTGTTAGAATAGGTTATAATTGCCCTATTCTGTGTCAT
1 CGTTTCAGGGGGGACGCCTTCCCTTTTTTGTCAGAATAGGTTATAATTGCCCTATTCTATGTCAT
* **
1412832 GTCCCCCGGTGGGCACTATTCATA-TCAGTACCTATCATGTTTGAGGGGACGCAAAAATGTGGTT
66 GTCCCCCGGAGGGCACTATTCA-AGTCAGTACCTATCATGTTTGAGGGGACGCATCAATGTGGTT
*
1412896 AAAGTA
130 AAAGCA
* * * *
1412902 CGTTTCA--GGGGATGCCTTCCCTTTTTT-TCAGAATAGGTTATAATTACCCTGTTTTATGTCAT
1 CGTTTCAGGGGGGACGCCTTCCCTTTTTTGTCAGAATAGGTTATAATTGCCCTATTCTATGTCAT
* * * * *
1412964 GTCCCCC-GACGGGCACTATTCATGTTAGTACTTATCATGCTTGAGGGGACGCATCATTGTGGTT
66 GTCCCCCGGA-GGGCACTATTCAAGTCAGTACCTATCATGTTTGAGGGGACGCATCAATGTGGTT
*
1413028 AAAGCG
130 AAAGCA
* * * *
1413034 TGTTTCAGGGGGGACACCTTCCCTTTTTTTGTCAGAGAATATGTTATAATTGCCCTATTCTATAT
1 CGTTTCAGGGGGGACGCCTTCCC-TTTTTTGTC--AGAATAGGTTATAATTGCCCTATTCTATGT
***
1413099 CATGTCCCCCGGAATAACACTATTCAAGTCAGTACCTATCATGTTTGAGGGGACGCAAT-AATGT
63 CATGTCCCCCGG-AGGGCACTATTCAAGTCAGTACCTATCATGTTTGAGGGGACGC-ATCAATGT
*
1413163 GGTTAAAGCG
126 GGTTAAAGCA
*
1413173 CAG-TTCAGGGGGCG-CGCCTTCCCTTTTTTTGTCAGAGAATATGTTATAATT
1 C-GTTTCAGGGGG-GACGCCTTCCC-TTTTTTGTC--AGAATAGGTTATAATT
1413224 CTCTATTATG
Statistics
Matches: 387, Mismatches: 54, Indels: 28
0.83 0.12 0.06
Matches are distributed among these distances:
131 1 0.00
132 93 0.24
133 18 0.05
134 16 0.04
135 72 0.19
136 52 0.13
138 35 0.09
139 95 0.25
140 5 0.01
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (135 bp):
CGTTTCAGGGGGGACGCCTTCCCTTTTTTGTCAGAATAGGTTATAATTGCCCTATTCTATGTCAT
GTCCCCCGGAGGGCACTATTCAAGTCAGTACCTATCATGTTTGAGGGGACGCATCAATGTGGTTA
AAGCA
Found at i:1413319 original size:20 final size:18
Alignment explanation
Indices: 1413294--1413332 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1413284 AAAGTATTAA
*
1413294 TAAATTTTAAGATTTTATAT
1 TAAA-TTTAA-ATATTATAT
1413314 TAAATTTAAATATTATAT
1 TAAATTTAAATATTATAT
1413332 T
1 T
1413333 CGATTTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 5 0.28
20 4 0.22
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
TAAATTTAAATATTATAT
Found at i:1414433 original size:21 final size:21
Alignment explanation
Indices: 1414409--1414449 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1414399 ATAACCTTAC
* * *
1414409 GGGCTGGGTATGTACCCCTGT
1 GGGCTAGGAATGTAACCCTGT
1414430 GGGCTAGGAATGTAACCCTG
1 GGGCTAGGAATGTAACCCTG
1414450 CGGAGATGAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.22, G:0.37, T:0.24
Consensus pattern (21 bp):
GGGCTAGGAATGTAACCCTGT
Found at i:1414474 original size:42 final size:42
Alignment explanation
Indices: 1414428--1414532 Score: 106
Period size: 42 Copynumber: 2.5 Consensus size: 42
1414418 ATGTACCCCT
1414428 GTGGGCTAGGAATGTAACCCTGCGGAGAT-GACATATGAACTG
1 GTGGGCTAGGAATGTAACCCTGCGGAGATGGA-ATATGAACTG
* * ** *
1414470 GTGGGCTTGGCACAT-ACCCTTGCGGAGATGGAATCTGAACTG
1 GTGGGCTAGGAATGTAACCC-TGCGGAGATGGAATATGAACTG
* * *
1414512 GTGGGATGGGAATGTACCCCT
1 GTGGGCTAGGAATGTAACCCT
1414533 ATGGCATCAT
Statistics
Matches: 49, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
41 4 0.08
42 40 0.82
43 5 0.10
ACGTcount: A:0.24, C:0.19, G:0.34, T:0.23
Consensus pattern (42 bp):
GTGGGCTAGGAATGTAACCCTGCGGAGATGGAATATGAACTG
Found at i:1415110 original size:17 final size:17
Alignment explanation
Indices: 1415088--1415123 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
1415078 AAACAGAAAC
1415088 ATAAATAT-ATAATTCTA
1 ATAAATATAAT-ATTCTA
1415105 ATAAATATAATATTCTA
1 ATAAATATAATATTCTA
1415122 AT
1 AT
1415124 TATATCAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 16 0.89
18 2 0.11
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (17 bp):
ATAAATATAATATTCTA
Found at i:1416297 original size:30 final size:28
Alignment explanation
Indices: 1416236--1416298 Score: 74
Period size: 30 Copynumber: 2.2 Consensus size: 28
1416226 AGCACAAATG
* *
1416236 ATAATTAATTAATATATTTAAATAAATA
1 ATAATTAATAAATATATTTAAATAAAAA
1416264 ATAATTATATAAATATTATTGT-AATAAAAA
1 ATAATTA-ATAAATA-TATT-TAAATAAAAA
1416294 ATAAT
1 ATAAT
1416299 ATTATTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 7 0.23
29 6 0.20
30 16 0.53
31 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (28 bp):
ATAATTAATAAATATATTTAAATAAAAA
Found at i:1416301 original size:21 final size:20
Alignment explanation
Indices: 1416275--1416313 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1416265 TAATTATATA
1416275 AATATTATTGTAATAAAAAAT
1 AATATTATTGTAA-AAAAAAT
*
1416296 AATATTATTTTAAAAAAA
1 AATATTATTGTAAAAAAA
1416314 TATTTATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (20 bp):
AATATTATTGTAAAAAAAAT
Found at i:1416325 original size:14 final size:13
Alignment explanation
Indices: 1416301--1416330 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
1416291 AAAATAATAT
1416301 TATTTTAAAAAAA
1 TATTTTAAAAAAA
1416314 TATTTATAAAAAAA
1 TATTT-TAAAAAAA
1416328 TAT
1 TAT
1416331 AACAATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TATTTTAAAAAAA
Found at i:1420405 original size:17 final size:17
Alignment explanation
Indices: 1420383--1420417 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1420373 ATAATATACT
1420383 CCCTCACATTTTATTGA
1 CCCTCACATTTTATTGA
*
1420400 CCCTCATATTTTATTGA
1 CCCTCACATTTTATTGA
1420417 C
1 C
1420418 ATCAAAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.23, C:0.29, G:0.06, T:0.43
Consensus pattern (17 bp):
CCCTCACATTTTATTGA
Found at i:1434635 original size:85 final size:86
Alignment explanation
Indices: 1434553--1434976 Score: 350
Period size: 85 Copynumber: 5.0 Consensus size: 86
1434543 AAAGACTTGG
** * *
1434553 CATCCTTTAGTTAAATGAGCAAGATCGTT-TCCTGATTTGGCT-TCCTTTAGAGAAAGAAGAAGA
1 CATCCTTTAGAGAAATGAGCAAGATCATTATCC-GATTTGGCTATCCTTTAGAGAAAGAAGAATA
* *
1434616 TCAACCATTGATCATGACTTGA
65 TCAACCATTGATTATGACTTAA
* * * *
1434638 CATCCTTCAAATAAATGAGCAAGATCATT-TCTCGATTTGGC-ATCCTTTAGAGAAGGAA-ACAT
1 CATCCTTTAGAGAAATGAGCAAGATCATTATC-CGATTTGGCTATCCTTTAGAGAAAGAAGA-AT
1434700 ATCAACC-TTCGATTATGACTTAA
64 ATCAACCATT-GATTATGACTTAA
* * * * * *
1434723 CGTCCTTTAGAGAAAAGAGCACGATTATTATCCGATTT-GATATCCTTTAGAGAAAGAAGCATAT
1 CATCCTTTAGAGAAATGAGCAAGATCATTATCCGATTTGGCTATCCTTTAGAGAAAGAAGAATAT
* *
1434787 CAACCCTTGATTATGGCTTAA
66 CAACCATTGATTATGACTTAA
* * * * * * *
1434808 AATGCTTTAGAGAAAGGAGCAAGACCATTCTCCGATTTGG-TATCCTTTAGAGAAAGGAGAAAAT
1 CATCCTTTAGAGAAATGAGCAAGATCATTATCCGATTTGGCTATCCTTTAGAGAAAGAAGAATAT
* * *
1434872 CAACCCGTTGATTATGAATTGA
66 CAA-CCATTGATTATGACTTAA
* * * * * * * * *
1434894 CAT-CTTTCAGAAGAAA-GAGTAAGATTATTCTTCAATTTGAC-ATCCTTTAAATGAAGGAACAA
1 CATCCTTT-AG-AGAAATGAGCAAGATCATTATCCGATTTGGCTATCCTTTAGA-GAAAGAAGAA
*
1434956 -ATCAACCACTGATTATGACTT
63 TATCAACCATTGATTATGACTT
1434977 GGCATCATTG
Statistics
Matches: 277, Mismatches: 48, Indels: 28
0.78 0.14 0.08
Matches are distributed among these distances:
84 4 0.01
85 205 0.74
86 56 0.20
87 12 0.04
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (86 bp):
CATCCTTTAGAGAAATGAGCAAGATCATTATCCGATTTGGCTATCCTTTAGAGAAAGAAGAATAT
CAACCATTGATTATGACTTAA
Found at i:1434791 original size:170 final size:171
Alignment explanation
Indices: 1434595--1434982 Score: 407
Period size: 170 Copynumber: 2.3 Consensus size: 171
1434585 TGATTTGGCT
* * *
1434595 TCCTTTAGAGAAAGAAG-AAGATCAACCATTGATCATGACTTGACATCCTTCAAATAAATGAGCA
1 TCCTTTAGAGAAAGAAGCAA-ATCAACCATTGATTATGACTTGACATCCTTCAAAGAAAGGAGCA
* *
1434659 AGATCATT-TCTCGATTTGGCATCCTTTAGAG-AAGGA-AACATATCAA-CC-TTCGATTATGAC
65 AGACCATTCTC-CGATTTGGCATCCTTTAGAGAAAGGAGAA-A-ATCAACCCGTT-GATTATGAA
* * * *
1434719 TTAACGTCCTTT-AG-AGAAAAGAGCACGATTATTATCCGATTTGATA
126 TTAACAT-CTTTCAGAAG-AAAGAGCAAGATTATTATCCAATTTGACA
* * * * * * * *
1434765 TCCTTTAGAGAAAGAAGCATATCAACCCTTGATTATGGCTTAAAATGCTTTAGAGAAAGGAGCAA
1 TCCTTTAGAGAAAGAAGCAAATCAACCATTGATTATGACTTGACATCCTTCAAAGAAAGGAGCAA
* *
1434830 GACCATTCTCCGATTTGGTATCCTTTAGAGAAAGGAGAAAATCAACCCGTTGATTATGAATTGAC
66 GACCATTCTCCGATTTGGCATCCTTTAGAGAAAGGAGAAAATCAACCCGTTGATTATGAATTAAC
* * *
1434895 ATCTTTCAGAAGAAAGAGTAAGATTATTCTTCAATTTGACA
131 ATCTTTCAGAAGAAAGAGCAAGATTATTATCCAATTTGACA
* * * *
1434936 TCCTTTAAATGAAGGAA-CAAATCAACCACTGATTATGACTTGGCATC
1 TCCTTTAGA-GAAAGAAGCAAATCAACCATTGATTATGACTTGACATC
1434983 ATTGATTTCG
Statistics
Matches: 177, Mismatches: 32, Indels: 17
0.78 0.14 0.08
Matches are distributed among these distances:
170 86 0.49
171 79 0.45
172 12 0.07
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (171 bp):
TCCTTTAGAGAAAGAAGCAAATCAACCATTGATTATGACTTGACATCCTTCAAAGAAAGGAGCAA
GACCATTCTCCGATTTGGCATCCTTTAGAGAAAGGAGAAAATCAACCCGTTGATTATGAATTAAC
ATCTTTCAGAAGAAAGAGCAAGATTATTATCCAATTTGACA
Found at i:1437641 original size:106 final size:106
Alignment explanation
Indices: 1437456--1437664 Score: 418
Period size: 106 Copynumber: 2.0 Consensus size: 106
1437446 GTATTTCTTA
1437456 TTAGATAATAACGAATACTAACGATGAAACTTTGGGCTAGATCATGAACACATGGAATAAAAAAT
1 TTAGATAATAACGAATACTAACGATGAAACTTTGGGCTAGATCATGAACACATGGAATAAAAAAT
1437521 ACGAACAAGTTGTTGAAAGACAACGGGTTTGATCTTAAGGT
66 ACGAACAAGTTGTTGAAAGACAACGGGTTTGATCTTAAGGT
1437562 TTAGATAATAACGAATACTAACGATGAAACTTTGGGCTAGATCATGAACACATGGAATAAAAAAT
1 TTAGATAATAACGAATACTAACGATGAAACTTTGGGCTAGATCATGAACACATGGAATAAAAAAT
1437627 ACGAACAAGTTGTTGAAAGACAACGGGTTTGATCTTAA
66 ACGAACAAGTTGTTGAAAGACAACGGGTTTGATCTTAA
1437665 AGGTGTTGTC
Statistics
Matches: 103, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
106 103 1.00
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.25
Consensus pattern (106 bp):
TTAGATAATAACGAATACTAACGATGAAACTTTGGGCTAGATCATGAACACATGGAATAAAAAAT
ACGAACAAGTTGTTGAAAGACAACGGGTTTGATCTTAAGGT
Found at i:1438210 original size:26 final size:25
Alignment explanation
Indices: 1438181--1438252 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 25
1438171 AATATGTGTG
* *
1438181 ATATATATATGATAAAAATATTATAT
1 ATATATATATGATAAAAATA-AAAAT
* *
1438207 ATATATATATAACAACAAATAAAAAT
1 ATATATATATGATAA-AAATAAAAAT
1438233 ATATATATAATGTATAAAAA
1 ATATATAT-ATG-ATAAAAA
1438253 CAATTTGGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
26 24 0.65
27 10 0.27
28 3 0.08
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.35
Consensus pattern (25 bp):
ATATATATATGATAAAAATAAAAAT
Found at i:1438675 original size:458 final size:458
Alignment explanation
Indices: 1437814--1438646 Score: 1316
Period size: 458 Copynumber: 1.8 Consensus size: 458
1437804 ACAAGGTTAG
* * *
1437814 TTAAAGCAAAAAGTTTGGATTGTGAGCTAATTTAGATTTTGAATGGGAATATGAATAGAATTTGG
1 TTAAAGCAAAAAGTTTGGATTGTGAGCTAATTTAGATTTTGAACGAGAATATGAATAGAATTTAG
* *
1437879 AGGTGGATTTGGAGGAGGGGCTCGAAGAGATGGATTTGTACGAGAAGCTCAAGGACGTTTAAACA
66 AGGTAGATTTAGAGGAGGGGCTCGAAGAGATGGATTTGTACGAGAAGCTCAAGGACGTTTAAACA
* * * **
1437944 TATTGGGATAAAAAATCAGGATAGGAAAACCTAAAAAATGAAATAATGTATGTGTATACTTGCAT
131 TATTGGCATAAAAAATCAAGATAGGAAAACCTAAAAAATGAAACAATGTACATGTATACTTGCAT
* *
1438009 CAAATTTCAAATCCCAATGATCATCAACTAATCAAGGTTAAAACATGAAAGTATATGGTGTATAA
196 CAAATTTCAAATCCCAATGATCATCAACTAATCAAGGTTAAAACATGAAAGTATAAGGTATATAA
1438074 ATATATATTTTAAAGACTTGAGGGCTTAAAAAACAGTGCATATATACTTATAATATACAAAATTT
261 ATATATATTTTAAAGACTTGAGGGCTTAAAAAACAGTGCATATATACTTATAATATACAAAATTT
*
1438139 TGAATACATAGTTAGCAAGGAAAAAGAAAATAAATATGTGTGATATATATATGATAAAAATATTA
326 TGAATACATAGTTAGCAA-GAAAAAGAAAATAAATATATGTGATATATATATGATAAAAATATTA
*
1438204 TATATATATATATAACAACAAATAAAAATATATATATAATGTATAAAAACAATTTGGCGATCGGG
390 AATATATATATATAACAACAAATAAAAATATATATATAATGTATAAAAACAATTTGGCGATCGGG
1438269 TTCA
455 TTCA
* * * * *
1438273 TTAAAGCAAGAATTTTGGATTGTGAGCTCATTTAGATTTTGAACGAGAATATGGATAGGATTTAG
1 TTAAAGCAAAAAGTTTGGATTGTGAGCTAATTTAGATTTTGAACGAGAATATGAATAGAATTTAG
* * * *
1438338 AGGTAGATTTAGAGGAGGGGCTCGAAGAGATGGATTTGTATGAGAAGTTCAGGGACGTTTAGACA
66 AGGTAGATTTAGAGGAGGGGCTCGAAGAGATGGATTTGTACGAGAAGCTCAAGGACGTTTAAACA
* ** * *
1438403 TATTGGCAT-AAAAATCAAGATAGGCAAACCTGCAAAATGAAGCAATGTACATGTATGCTTGCAT
131 TATTGGCATAAAAAATCAAGATAGGAAAACCTAAAAAATGAAACAATGTACATGTATACTTGCAT
* *
1438467 CAAATTTCAAATCTCAATGATCATCAACTAATCAAGGTTAAAACATGAAAGTATAAGGTATATAC
196 CAAATTTCAAATCCCAATGATCATCAACTAATCAAGGTTAAAACATGAAAGTATAAGGTATATAA
*
1438532 ATATATATTTTAAAGACTTGAGGGCTTAAAAAACTAGTGTATATATA--TATATATATACAAAA-
261 ATATATATTTTAAAGACTTGAGGGCTTAAAAAAC-AGTGCATATATACTTATA-ATATACAAAAT
1438594 TTTGAATACATAGTTAGCAA-AACAAAGAAAATAAATATATGTGATATATATAT
324 TTTGAATACATAGTTAGCAAGAA-AAAGAAAATAAATATATGTGATATATATAT
1438647 ATATATATAT
Statistics
Matches: 341, Mismatches: 30, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
455 2 0.01
456 29 0.09
457 24 0.07
458 151 0.44
459 135 0.40
ACGTcount: A:0.42, C:0.09, G:0.19, T:0.30
Consensus pattern (458 bp):
TTAAAGCAAAAAGTTTGGATTGTGAGCTAATTTAGATTTTGAACGAGAATATGAATAGAATTTAG
AGGTAGATTTAGAGGAGGGGCTCGAAGAGATGGATTTGTACGAGAAGCTCAAGGACGTTTAAACA
TATTGGCATAAAAAATCAAGATAGGAAAACCTAAAAAATGAAACAATGTACATGTATACTTGCAT
CAAATTTCAAATCCCAATGATCATCAACTAATCAAGGTTAAAACATGAAAGTATAAGGTATATAA
ATATATATTTTAAAGACTTGAGGGCTTAAAAAACAGTGCATATATACTTATAATATACAAAATTT
TGAATACATAGTTAGCAAGAAAAAGAAAATAAATATATGTGATATATATATGATAAAAATATTAA
ATATATATATATAACAACAAATAAAAATATATATATAATGTATAAAAACAATTTGGCGATCGGGT
TCA
Found at i:1438751 original size:2 final size:2
Alignment explanation
Indices: 1438744--1438775 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1438734 CATAACATGA
1438744 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1438776 GTTATTTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1439292 original size:22 final size:23
Alignment explanation
Indices: 1439262--1439305 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1439252 GTACTTGACT
*
1439262 AACAGTATCGATACTG-AAGAAG
1 AACAATATCGATACTGTAAGAAG
*
1439284 AACAATATCGGTACTGTAAGAA
1 AACAATATCGATACTGTAAGAA
1439306 TAGTATCGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.45, C:0.14, G:0.20, T:0.20
Consensus pattern (23 bp):
AACAATATCGATACTGTAAGAAG
Found at i:1439311 original size:42 final size:42
Alignment explanation
Indices: 1439239--1439318 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
1439229 ACGATACTAT
**
1439239 AAGAACAATATCAGTACTTGACTAACAGTATCGATACTGAAG
1 AAGAACAATATCAGTACTTGAAGAACAGTATCGATACTGAAG
* *
1439281 AAGAACAATATCGGTAC-TGTAAGAATAGTATCGATACT
1 AAGAACAATATCAGTACTTG-AAGAACAGTATCGATACT
1439319 AATGCTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 2 0.06
42 31 0.94
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.25
Consensus pattern (42 bp):
AAGAACAATATCAGTACTTGAAGAACAGTATCGATACTGAAG
Found at i:1440789 original size:65 final size:64
Alignment explanation
Indices: 1440672--1440879 Score: 226
Period size: 65 Copynumber: 3.2 Consensus size: 64
1440662 TTTCAAAGTG
* **
1440672 ATGCATCGATGCATCAATCCATGCATCGATGCAC-CATGGAATAAATTG-AACATCGAATGCATT
1 ATGCATCGATGCACCAA-CCATGCATCGATGCACTCA-GG-ATATTTTGAAACATCGAATGCATT
1440735 TC
63 TC
* * * *
1440737 ATGCATTGATGCA-TATACCATGCATCGATGCATTGAGGAT-TTTATGAAAACATCGAATGCATT
1 ATGCATCGATGCACCA-ACCATGCATCGATGCACTCAGGATATTT-TG-AAACATCGAATGCATT
*
1440800 TG
63 TC
* * * *
1440802 ATGTATCGATGCACCAGCCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTT
1 ATGCATCGATGCACCAACCATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATTTC
1440866 ATGCATCGATGCAC
1 ATGCATCGATGCAC
1440880 TCTTAGTGCA
Statistics
Matches: 120, Mismatches: 16, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 48 0.40
65 63 0.52
66 4 0.03
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (64 bp):
ATGCATCGATGCACCAACCATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATTTC
Found at i:1446736 original size:21 final size:21
Alignment explanation
Indices: 1446671--1446765 Score: 86
Period size: 23 Copynumber: 4.4 Consensus size: 21
1446661 TTGTGCTTAA
*
1446671 TGCATCGATACACC-T-AACAG
1 TGCATCGATACACCTTGAA-TG
*
1446691 TGCATCGATGCATCCTTGAATG
1 TGCATCGATACA-CCTTGAATG
* *
1446713 TGCATCGATACACCATGAAGG
1 TGCATCGATACACCTTGAATG
* *
1446734 TGCACCGATGCACGCCTTGAATG
1 TGCATCGAT--ACACCTTGAATG
1446757 TGCATCGAT
1 TGCATCGAT
1446766 GCATGCACAA
Statistics
Matches: 60, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
20 11 0.18
21 17 0.28
22 13 0.22
23 19 0.32
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.24
Consensus pattern (21 bp):
TGCATCGATACACCTTGAATG
Found at i:1446759 original size:23 final size:23
Alignment explanation
Indices: 1446690--1446768 Score: 92
Period size: 23 Copynumber: 3.6 Consensus size: 23
1446680 ACACCTAACA
*
1446690 GTGCATCGATGCA-TCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
* *
1446712 GTGCATCGAT--ACACCATGAAG
1 GTGCATCGATGCACACCTTGAAT
* *
1446733 GTGCACCGATGCACGCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
1446756 GTGCATCGATGCA
1 GTGCATCGATGCA
1446769 TGCACAAGGC
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
20 1 0.02
21 15 0.33
22 10 0.22
23 20 0.43
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.24
Consensus pattern (23 bp):
GTGCATCGATGCACACCTTGAAT
Found at i:1446761 original size:44 final size:42
Alignment explanation
Indices: 1446671--1446765 Score: 129
Period size: 44 Copynumber: 2.2 Consensus size: 42
1446661 TTGTGCTTAA
* *
1446671 TGCATCGATACACCTAACAGTGCATCGATGCATCCTTGAATG
1 TGCATCGATACACCTAACAGTGCACCGATGCAGCCTTGAATG
*
1446713 TGCATCGATACACCATGAA-GGTGCACCGATGCACGCCTTGAATG
1 TGCATCGATACACC-T-AACAGTGCACCGATGCA-GCCTTGAATG
1446757 TGCATCGAT
1 TGCATCGAT
1446766 GCATGCACAA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
42 14 0.30
43 13 0.28
44 20 0.43
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.24
Consensus pattern (42 bp):
TGCATCGATACACCTAACAGTGCACCGATGCAGCCTTGAATG
Found at i:1448321 original size:14 final size:15
Alignment explanation
Indices: 1448296--1448324 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1448286 TTGATTTTGA
1448296 TGTTTCTGGATTGTT
1 TGTTTCTGGATTGTT
1448311 TGTTT-TGGATTGTT
1 TGTTTCTGGATTGTT
1448325 AAATGTTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.07, C:0.03, G:0.28, T:0.62
Consensus pattern (15 bp):
TGTTTCTGGATTGTT
Found at i:1449101 original size:65 final size:63
Alignment explanation
Indices: 1448991--1449191 Score: 237
Period size: 65 Copynumber: 3.1 Consensus size: 63
1448981 GTGATGCACT
* **
1448991 GATGCACCAATCCATACATCGATGCAC-CATGGAATAAATTG-AACATCGAATGCATTTCATGCA
1 GATGCA-CAA-CCATGCATCGATGCACTCA-GG-ATATTTTGAAACATCGAATGCATTTCATGCA
1449054 TC
62 TC
* *
1449056 GATGCACATACCATGCATCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCATTTGATGCAT
1 GATGCACA-ACCATGCATCGATGCACTCAGGATATTT-TG-AAACATCGAATGCATTTCATGCAT
1449120 C
63 C
* * *
1449121 GATGCACCAGCCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTTATGCATC
1 GATGCA-CAACCATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATTTCATGCATC
1449185 GATGCAC
1 GATGCAC
1449192 TCTTAGTGCA
Statistics
Matches: 120, Mismatches: 9, Indels: 16
0.83 0.06 0.11
Matches are distributed among these distances:
62 1 0.01
63 5 0.04
64 49 0.41
65 60 0.50
66 5 0.04
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.26
Consensus pattern (63 bp):
GATGCACAACCATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATTTCATGCATC
Found at i:1450724 original size:25 final size:25
Alignment explanation
Indices: 1450669--1450749 Score: 65
Period size: 25 Copynumber: 3.1 Consensus size: 25
1450659 TATTTTTATA
* * *
1450669 ATAATTATATAGTAATATACAGTATAAT
1 ATAATTATATAATAAAATA-A--ATAGT
1450697 ATAATTATATAATAAAATAAATAGT
1 ATAATTATATAATAAAATAAATAGT
* * *
1450722 ATAGTT-TTTAGAAAAAATAAATAGT
1 ATAATTATATA-ATAAAATAAATAGT
1450747 ATA
1 ATA
1450750 TATATTTTTC
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
24 3 0.07
25 25 0.54
27 1 0.02
28 17 0.37
ACGTcount: A:0.54, C:0.01, G:0.07, T:0.37
Consensus pattern (25 bp):
ATAATTATATAATAAAATAAATAGT
Found at i:1450741 original size:30 final size:29
Alignment explanation
Indices: 1450707--1450785 Score: 92
Period size: 29 Copynumber: 2.8 Consensus size: 29
1450697 ATAATTATAT
*
1450707 AATAAAATAAATAGTATAGTTTTT-AGAA
1 AATAAAATATATAGTATAGTTTTTCAGAA
*
1450735 AAAATAAATAGTATA-TATA-TTTTTCAGAA
1 AATA-AAATA-TATAGTATAGTTTTTCAGAA
*
1450764 AATAATATATATAGTATAGTTT
1 AATAAAATATATAGTATAGTTT
1450786 AAAATATATA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
27 4 0.10
28 16 0.38
29 19 0.45
30 3 0.07
ACGTcount: A:0.51, C:0.01, G:0.09, T:0.39
Consensus pattern (29 bp):
AATAAAATATATAGTATAGTTTTTCAGAA
Found at i:1456371 original size:23 final size:23
Alignment explanation
Indices: 1456345--1456429 Score: 91
Period size: 23 Copynumber: 3.7 Consensus size: 23
1456335 CACCGAAGTG
*
1456345 CCACATAGTTTTGTCCTGAAGGA
1 CCACATAGATTTGTCCTGAAGGA
* *
1456368 CCACGTAGAATTTGTCCCGAAGGA
1 CCACATAG-ATTTGTCCTGAAGGA
* ** *
1456392 CCACGTAGAAATGTCATGAAGGA
1 CCACATAGATTTGTCCTGAAGGA
1456415 CCACATAGA-TTGTCC
1 CCACATAGATTTGTCC
1456430 CAAAGGATTG
Statistics
Matches: 51, Mismatches: 10, Indels: 3
0.80 0.16 0.05
Matches are distributed among these distances:
22 4 0.08
23 26 0.51
24 21 0.41
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.24
Consensus pattern (23 bp):
CCACATAGATTTGTCCTGAAGGA
Found at i:1464795 original size:14 final size:14
Alignment explanation
Indices: 1464776--1464802 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1464766 TATAATAAGA
1464776 AAATAACATAATAC
1 AAATAACATAATAC
1464790 AAATAACATAATA
1 AAATAACATAATA
1464803 TGATATGGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (14 bp):
AAATAACATAATAC
Found at i:1468033 original size:128 final size:131
Alignment explanation
Indices: 1467843--1468093 Score: 348
Period size: 130 Copynumber: 1.9 Consensus size: 131
1467833 AGGGGATTAG
* * *
1467843 CCTTTTAGGACAAGGTGTAACCCTACAACAACACATTTAGACTTGTACCATAAAGTCTCAAGTGT
1 CCTTTTACGACAAGGTGTAACCCTACAACAACACA-TTAGACTTATACCACAAAGTCTCAAGTGT
*
1467908 -AACCCTTCCA-AAGAAGAAATTAAAAATAAAAAACTTTGAAAAATCTCTTACAAGGATTTATTC
65 AAACCCTT-CATAAGAAGAAATTAAAAAGAAAAAACTTTGAAAAATCTCTTACAAGGATTTATTC
1467971 AAA
129 AAA
* *
1467974 CCTTTTACGACAAGGTGTAACCTTACAAC-ACAC-TTAGACTTATACCCCAAAGTCTCAAGTGTA
1 CCTTTTACGACAAGGTGTAACCCTACAACAACACATTAGACTTATACCACAAAGTCTCAAGTGTA
* * ** *
1468037 CAACCCTTCATAAGGAGAAATTAGAAAGAGCAAACTTTGAAAAATCTTTTACAAGGA
66 -AACCCTTCATAAGAAGAAATTAAAAAGAAAAAACTTTGAAAAATCTCTTACAAGGA
1468094 ATGTGTTTAC
Statistics
Matches: 106, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
128 26 0.25
129 2 0.02
130 51 0.48
131 27 0.25
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.26
Consensus pattern (131 bp):
CCTTTTACGACAAGGTGTAACCCTACAACAACACATTAGACTTATACCACAAAGTCTCAAGTGTA
AACCCTTCATAAGAAGAAATTAAAAAGAAAAAACTTTGAAAAATCTCTTACAAGGATTTATTCAA
A
Found at i:1469023 original size:174 final size:170
Alignment explanation
Indices: 1468692--1469067 Score: 398
Period size: 174 Copynumber: 2.2 Consensus size: 170
1468682 AGTAGATCAT
* * * *
1468692 CGATTATGAGTTAGTGTTCTTTAGAGGAAGAAGTAAGATTATTTCCCGATTTGGCACCCTTCAAA
1 CGATTATGAATTAGTGTTCTTCAGAGGAAGAAGTAAGATTATTTCCCAATTTGGCACACTTCAAA
* * * * * * *
1468757 AAAATGACCATACCAACCATTAATTACTAGTTGGCTTCCTTTAGAGAAATGAGCAAGATTATTTC
66 AAAAGGACCATACCAACCATTAATTACTACTTGGCATCCTTCAGAGAAATGACCAAGATGATTCC
* * * *
1468822 TCGATTTGGCATCCTTCATATAAAGGAGTAGATCATCCAC
131 TCGATTTGGCATCCTTCAGAGAAAGGAGTAAATCACCCAC
* * * * * * *
1468862 CGATTAATGACTTAGCGTTCTTCAGAGGGAGGAGTAAGATTGTTTCCCAATTTGGCATATTTCAA
1 CGATT-ATGAATTAGTGTTCTTCAGAGGAAGAAGTAAGATTATTTCCCAATTTGGCACACTTC--
* * *
1468927 AAAAAAAAGGAGCATATCAACCATTGATTA-TGACTTGGCATCCTTCAGAGAAATGACCAAGATC
63 -AAAAAAAGGACCATACCAACCATTAATTACT-ACTTGGCATCCTTCAGAGAAATGACCAAGAT-
* * *
1468991 GA-TCCTTGA-TTGGGAGTCCTTTAGAGAAAGGAGTAAATCACCCAC
125 GATTCCTCGATTTGGCA-TCCTTCAGAGAAAGGAGTAAATCACCCAC
* *
1469036 CAATTATGAATTAGTGTCCTTCAGAGGAAGAA
1 CGATTATGAATTAGTGTTCTTCAGAGGAAGAA
1469068 AGAAAATAGT
Statistics
Matches: 166, Mismatches: 33, Indels: 11
0.79 0.16 0.05
Matches are distributed among these distances:
170 5 0.03
171 47 0.28
173 28 0.17
174 85 0.51
175 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.29
Consensus pattern (170 bp):
CGATTATGAATTAGTGTTCTTCAGAGGAAGAAGTAAGATTATTTCCCAATTTGGCACACTTCAAA
AAAAGGACCATACCAACCATTAATTACTACTTGGCATCCTTCAGAGAAATGACCAAGATGATTCC
TCGATTTGGCATCCTTCAGAGAAAGGAGTAAATCACCCAC
Found at i:1469208 original size:45 final size:44
Alignment explanation
Indices: 1469084--1469291 Score: 137
Period size: 45 Copynumber: 4.9 Consensus size: 44
1469074 TAGTAGATAA
* * * * * *
1469084 ACCATTGATTACGACTTAACATCATTTAGAGAAAGTAGCA-A-G
1 ACCATTGATTACAACTTGACATCCTTCAAAGAAAGGAGCATATG
* ** *
1469126 ACCATT-ATT-CAATTTGTTATCCAT-AAGAGAAAGGAGCATATCG
1 ACCATTGATTACAACTTGACATCCTTCAA-AGAAAGGAGCATAT-G
* *
1469169 ACCATTGATTACGACTTGACATCCTTCAAAGAAATGAGCA-A-G
1 ACCATTGATTACAACTTGACATCCTTCAAAGAAAGGAGCATATG
* * * * * *
1469211 ATCATT--TTTCAATTTGGCATCCTTTAAAGAAAGGAGCATATAA
1 ACCATTGATTACAACTTGACATCCTTCAAAGAAAGGAGCATAT-G
* * *
1469254 ACCATTGATTACAACTTGACGTCCTTTAGAGAAAGGAG
1 ACCATTGATTACAACTTGACATCCTTCAAAGAAAGGAG
1469292 TAAGATCGTT
Statistics
Matches: 125, Mismatches: 29, Indels: 21
0.71 0.17 0.12
Matches are distributed among these distances:
39 1 0.01
40 44 0.35
41 5 0.04
42 12 0.10
43 12 0.10
44 4 0.03
45 45 0.36
46 2 0.02
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (44 bp):
ACCATTGATTACAACTTGACATCCTTCAAAGAAAGGAGCATATG
Found at i:1469211 original size:85 final size:85
Alignment explanation
Indices: 1469080--1469362 Score: 264
Period size: 85 Copynumber: 3.3 Consensus size: 85
1469070 AAAATAGTAG
* * * * **
1469080 ATAAACCATTGATTACGACTTAACATCATTTAGAGAAAGTAGCAAGACCATTATTCAATTTGTTA
1 ATAAACCATTGATTACGACTTGACATCCTTCAAAGAAAGTAGCAAGACCATTATTCAATTTGGCA
1469145 TCC-ATAAGAGAAAGGAGCAT
66 TCCTATAA-AGAAAGGAGCAT
** * *
1469165 ATCGACCATTGATTACGACTTGACATCCTTCAAAGAAA-TGAGCAAGATCATTTTTCAATTTGGC
1 ATAAACCATTGATTACGACTTGACATCCTTCAAAGAAAGT-AGCAAGACCATTATTCAATTTGGC
*
1469229 ATCCTTTAAAGAAAGGAGCAT
65 ATCCTATAAAGAAAGGAGCAT
* * * * * * * * * *
1469250 ATAAACCATTGATTACAACTTGACGTCCTTTAGAGAAAGGAGTAAGATCGTTCTTCGATTTGGCA
1 ATAAACCATTGATTACGACTTGACATCCTTCAAAGAAAGTAGCAAGACCATTATTCAATTTGGCA
* * * *
1469315 TCCTTTAGAGAAAGGATCAG
66 TCCTATAAAGAAAGGAGCAT
* * ** *
1469335 ATCAACTATTGACGACGACTTGGCATCC
1 ATAAACCATTGATTACGACTTGACATCC
1469363 CCATTCTAAG
Statistics
Matches: 163, Mismatches: 32, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
84 1 0.01
85 159 0.98
86 3 0.02
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (85 bp):
ATAAACCATTGATTACGACTTGACATCCTTCAAAGAAAGTAGCAAGACCATTATTCAATTTGGCA
TCCTATAAAGAAAGGAGCAT
Found at i:1469248 original size:40 final size:40
Alignment explanation
Indices: 1469188--1469338 Score: 115
Period size: 40 Copynumber: 3.7 Consensus size: 40
1469178 TACGACTTGA
* *
1469188 CATCCTTCAAAGAAATGAGCAAGATCATTTTTCAATTTGG
1 CATCCTTTAAAGAAAGGAGCAAGATCATTTTTCAATTTGG
* * * * *
1469228 CATCCTTTAAAGAAAGGAGCATATAAACCATTGATTACAACTTGA
1 CATCCTTTAAAGAAAGGAGC--A-AGATCATT--TTTCAATTTGG
* * * * * *
1469273 CGTCCTTTAGAGAAAGGAGTAAGATCGTTCTTCGATTTGG
1 CATCCTTTAAAGAAAGGAGCAAGATCATTTTTCAATTTGG
* *
1469313 CATCCTTTAGAGAAAGGATC-AGATCA
1 CATCCTTTAAAGAAAGGAGCAAGATCA
1469339 ACTATTGACG
Statistics
Matches: 84, Mismatches: 22, Indels: 11
0.72 0.19 0.09
Matches are distributed among these distances:
39 5 0.06
40 41 0.49
42 6 0.07
43 7 0.08
45 25 0.30
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (40 bp):
CATCCTTTAAAGAAAGGAGCAAGATCATTTTTCAATTTGG
Found at i:1469885 original size:91 final size:91
Alignment explanation
Indices: 1469730--1469908 Score: 358
Period size: 91 Copynumber: 2.0 Consensus size: 91
1469720 AAACACCTCA
1469730 ACCGGACATAAGGAGCTTAAGATATGCTTATTTTAGAGAAGATAGTGCGTGCAGAAAATTGAATA
1 ACCGGACATAAGGAGCTTAAGATATGCTTATTTTAGAGAAGATAGTGCGTGCAGAAAATTGAATA
1469795 CGAGTTTAATACGAGAATTTTAACGG
66 CGAGTTTAATACGAGAATTTTAACGG
1469821 ACCGGACATAAGGAGCTTAAGATATGCTTATTTTAGAGAAGATAGTGCGTGCAGAAAATTGAATA
1 ACCGGACATAAGGAGCTTAAGATATGCTTATTTTAGAGAAGATAGTGCGTGCAGAAAATTGAATA
1469886 CGAGTTTAATACGAGAATTTTAA
66 CGAGTTTAATACGAGAATTTTAA
1469909 TTTATTATGA
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 88 1.00
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.28
Consensus pattern (91 bp):
ACCGGACATAAGGAGCTTAAGATATGCTTATTTTAGAGAAGATAGTGCGTGCAGAAAATTGAATA
CGAGTTTAATACGAGAATTTTAACGG
Found at i:1475224 original size:22 final size:22
Alignment explanation
Indices: 1475199--1475243 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1475189 GACTTAACAC
1475199 TTGTAATTGAGCTAAGTTTACA
1 TTGTAATTGAGCTAAGTTTACA
1475221 TTGTAATTGAGCTAAGTTTACA
1 TTGTAATTGAGCTAAGTTTACA
1475243 T
1 T
1475244 ACTTCTTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.42
Consensus pattern (22 bp):
TTGTAATTGAGCTAAGTTTACA
Found at i:1481080 original size:9 final size:9
Alignment explanation
Indices: 1481065--1481135 Score: 67
Period size: 9 Copynumber: 7.9 Consensus size: 9
1481055 TTGTTTTTAT
1481065 TATTATTAA
1 TATTATTAA
* *
1481074 AATTATTAT
1 TATTATTAA
1481083 TATTATTAA
1 TATTATTAA
1481092 TATTA-TATA
1 TATTATTA-A
1481101 TATTATT-A
1 TATTATTAA
*
1481109 TATTA-TAT
1 TATTATTAA
1481117 TATTATTAAA
1 TATTATT-AA
1481127 TAATTATTA
1 T-ATTATTA
1481136 CAAGCCCAGA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
7 1 0.02
8 13 0.26
9 26 0.52
10 4 0.08
11 6 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TATTATTAA
Found at i:1481084 original size:18 final size:17
Alignment explanation
Indices: 1481061--1481135 Score: 91
Period size: 18 Copynumber: 4.4 Consensus size: 17
1481051 ATTTTTGTTT
1481061 TTATTATTATTAAAATTA
1 TTATTATTATT-AAATTA
1481079 TTATTATTATTAATATTA
1 TTATTATTATTAA-ATTA
*
1481097 -TATATATTATTATATTA
1 TTAT-TATTATTAAATTA
*
1481114 -TATTATTATTAAATAA
1 TTATTATTATTAAATTA
1481130 TTATTA
1 TTATTA
1481136 CAAGCCCAGA
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
16 11 0.22
17 17 0.33
18 23 0.45
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTATTATTATTAAATTA
Found at i:1481135 original size:3 final size:3
Alignment explanation
Indices: 1481061--1481124 Score: 71
Period size: 3 Copynumber: 22.0 Consensus size: 3
1481051 ATTTTTGTTT
** *
1481061 TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA ATA TTA -TA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
1481106 TTA -TA TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
1481125 AATAATTATT
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
2 6 0.12
3 42 0.82
4 3 0.06
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:1482852 original size:31 final size:31
Alignment explanation
Indices: 1482817--1482875 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
1482807 ATATTTCTAA
1482817 ATAAATAAATATTTTATTT-ATAAATATATAT
1 ATAAATAAATATTTT-TTTCATAAATATATAT
* *
1482848 ATAAATTAATATTTTTTTCATAATTATA
1 ATAAATAAATATTTTTTTCATAAATATA
1482876 ATTTTGAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 3 0.12
31 22 0.88
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (31 bp):
ATAAATAAATATTTTTTTCATAAATATATAT
Found at i:1483377 original size:27 final size:27
Alignment explanation
Indices: 1483345--1483398 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
1483335 TAATTCTTCC
1483345 TTTTCAAAAT-TTTATATATACTTATTA
1 TTTTCAAAATATTTATATATA-TTATTA
* *
1483372 TTTTCATAGTATTTATATATATTATTA
1 TTTTCAAAATATTTATATATATTATTA
1483399 ATATTTCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 14 0.58
28 10 0.42
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.57
Consensus pattern (27 bp):
TTTTCAAAATATTTATATATATTATTA
Found at i:1488716 original size:17 final size:16
Alignment explanation
Indices: 1488694--1488786 Score: 89
Period size: 17 Copynumber: 5.5 Consensus size: 16
1488684 TCCAGCAAAG
1488694 AAAGAAAAAAGATGAAA
1 AAAGAAAAAAGA-GAAA
*
1488711 AAAGAAAAATGAGAAAA
1 AAAGAAAAAAGAG-AAA
*
1488728 AAAGAAAAAATATGAAA
1 AAAGAAAAAAGA-GAAA
* *
1488745 AAGGAAAAATGAGAAA
1 AAAGAAAAAAGAGAAA
1488761 AAAGGAAAAAA-AGGAAA
1 AAA-GAAAAAAGA-GAAA
1488778 AAAGGAAAA
1 AAA-GAAAA
1488787 TTGAATCATG
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
16 8 0.12
17 55 0.86
18 1 0.02
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.05
Consensus pattern (16 bp):
AAAGAAAAAAGAGAAA
Found at i:1488732 original size:34 final size:33
Alignment explanation
Indices: 1488694--1488787 Score: 134
Period size: 34 Copynumber: 2.8 Consensus size: 33
1488684 TCCAGCAAAG
1488694 AAAGAAAAAAGATGAAAAAAGAAAAATGAGAAAA
1 AAAGAAAAAA-ATGAAAAAAGAAAAATGAGAAAA
*
1488728 AAAGAAAAAATATGAAAAAGGAAAAATGAGAAAA
1 AAAGAAAAAA-ATGAAAAAAGAAAAATGAGAAAA
* * *
1488762 AAGGAAAAAAAGGAAAAAAGGAAAAT
1 AAAGAAAAAAATGAAAAAAGAAAAAT
1488788 TGAATCATGA
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
33 13 0.24
34 41 0.76
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.06
Consensus pattern (33 bp):
AAAGAAAAAAATGAAAAAAGAAAAATGAGAAAA
Found at i:1488770 original size:9 final size:9
Alignment explanation
Indices: 1488758--1488786 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1488748 GAAAAATGAG
1488758 AAAAAAGGA
1 AAAAAAGGA
1488767 AAAAAAGG-
1 AAAAAAGGA
1488775 AAAAAAGGA
1 AAAAAAGGA
1488784 AAA
1 AAA
1488787 TTGAATCATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (9 bp):
AAAAAAGGA
Found at i:1491247 original size:114 final size:114
Alignment explanation
Indices: 1491036--1491254 Score: 339
Period size: 114 Copynumber: 1.9 Consensus size: 114
1491026 ACGTTCTCGC
* *
1491036 AGTAAAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
1 AGTAAAAATAAGGAGACCCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTCG
* * * *
1491101 GTATGAACCCTAAAACCAATCATTAGATTTGAAATATGAATTTGCTCAT
66 GTAAGAACCCCAAAACCAATCATTAGAATTGAAAGATGAATTTGCTCAT
* * *
1491150 AGTAGAAATAAGGAGACCCAATAACATCTTCTGGAAGTGTTCTTTGGGTTATTTGATCTGGTTCG
1 AGTAAAAATAAGGAGACCCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTCG
* *
1491215 GTAAGAACCCCAAAACTAATCATTGGAATTGAAAGATGAA
66 GTAAGAACCCCAAAACCAATCATTAGAATTGAAAGATGAA
1491255 CTGCATGATC
Statistics
Matches: 94, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
114 94 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (114 bp):
AGTAAAAATAAGGAGACCCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTCG
GTAAGAACCCCAAAACCAATCATTAGAATTGAAAGATGAATTTGCTCAT
Found at i:1494517 original size:76 final size:76
Alignment explanation
Indices: 1494418--1495144 Score: 1253
Period size: 76 Copynumber: 9.6 Consensus size: 76
1494408 CTATTTCCAA
*
1494418 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1494483 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
1494494 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCTTTCGGGATCTTTTTGAT-TTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1494558 AGCCTTAGGGT
66 AGCCTTAGGGT
* * *
1494569 CATTTGTAAGTCCTACAGTGCATGATGTTTCTAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1494634 AGCCTTAGGGT
66 AGCCTTAGGGT
*
1494645 CATCTGTAAGTCCTACAGTGCATGATGTTTACAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1494710 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
1494721 CATCTGTAAGTCCTACAGTGCATGATATTTCCAAAAAGCCTTCGGGAGCTTTTTAATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1494786 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
1494797 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCATTCGAGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1494862 AGACTTAGGGT
66 AGCCTTAGGGT
*
1494873 CATCTGTAAGTCCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1494938 AGCCTTAGGGT
66 AGCCTTAGGGT
*
1494949 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1495014 AGCCTTAGGGT
66 AGCCTTAGGGT
* * * *
1495025 CATCTATAAGTCCTACAATGCATGATGTTTCCTAAAAGCCTTCGGGAGCTTTGTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1495090 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
1495101 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAA-CCTTCGGG
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGG
1495145 TCATCTGTAA
Statistics
Matches: 617, Mismatches: 33, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
74 8 0.01
75 74 0.12
76 535 0.87
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:1495131 original size:45 final size:45
Alignment explanation
Indices: 1495078--1495179 Score: 168
Period size: 45 Copynumber: 2.3 Consensus size: 45
1495068 GGGAGCTTTG
* **
1495078 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTAGGGTCATCTGTAAACCCTTCAGTGCA
*
1495123 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAACCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTAGGGTCATCTGTAAACCCTTCAGTGCA
1495168 TGATGTTTTCAA
1 TGATGTTTTCAA
1495180 CATTTCCATC
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 53 1.00
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.36
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTAGGGTCATCTGTAAACCCTTCAGTGCA
Found at i:1495331 original size:9 final size:9
Alignment explanation
Indices: 1495316--1495386 Score: 67
Period size: 9 Copynumber: 7.9 Consensus size: 9
1495306 TTGTTTTTAT
1495316 TATTATTAA
1 TATTATTAA
* *
1495325 AATTATTAT
1 TATTATTAA
1495334 TATTATTAA
1 TATTATTAA
1495343 TATTA-TATA
1 TATTATTA-A
1495352 TATTATT-A
1 TATTATTAA
*
1495360 TATTA-TAT
1 TATTATTAA
1495368 TATTATTAAA
1 TATTATT-AA
1495378 TAATTATTA
1 T-ATTATTA
1495387 CAAGCCCAGA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
7 1 0.02
8 13 0.26
9 26 0.52
10 4 0.08
11 6 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TATTATTAA
Found at i:1495335 original size:18 final size:17
Alignment explanation
Indices: 1495312--1495386 Score: 91
Period size: 18 Copynumber: 4.4 Consensus size: 17
1495302 ATTTTTGTTT
1495312 TTATTATTATTAAAATTA
1 TTATTATTATT-AAATTA
1495330 TTATTATTATTAATATTA
1 TTATTATTATTAA-ATTA
*
1495348 -TATATATTATTATATTA
1 TTAT-TATTATTAAATTA
*
1495365 -TATTATTATTAAATAA
1 TTATTATTATTAAATTA
1495381 TTATTA
1 TTATTA
1495387 CAAGCCCAGA
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
16 11 0.22
17 17 0.33
18 23 0.45
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTATTATTATTAAATTA
Found at i:1495386 original size:3 final size:3
Alignment explanation
Indices: 1495312--1495375 Score: 71
Period size: 3 Copynumber: 22.0 Consensus size: 3
1495302 ATTTTTGTTT
** *
1495312 TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA ATA TTA -TA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
1495357 TTA -TA TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
1495376 AATAATTATT
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
2 6 0.12
3 42 0.82
4 3 0.06
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:1497092 original size:29 final size:29
Alignment explanation
Indices: 1497059--1497115 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
1497049 ATATTTCTAA
1497059 ATAAATAAATATTTTATTT-ATAAATATAT
1 ATAAATAAATATTTT-TTTCATAAATATAT
* *
1497088 ATAAATTAATATTTTTTTCATAATTATA
1 ATAAATAAATATTTTTTTCATAAATATA
1497116 ATTTTGAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 22 0.88
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (29 bp):
ATAAATAAATATTTTTTTCATAAATATAT
Found at i:1498426 original size:14 final size:14
Alignment explanation
Indices: 1498409--1498457 Score: 80
Period size: 14 Copynumber: 3.5 Consensus size: 14
1498399 CTTTCTCTAC
*
1498409 TTCATCATCTCGCA
1 TTCATCATCTCACA
1498423 TTCATCATCTCACA
1 TTCATCATCTCACA
1498437 TTCATCATCTCACA
1 TTCATCATCTCACA
*
1498451 TTTATCA
1 TTCATCA
1498458 CAATTTGGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.27, C:0.33, G:0.02, T:0.39
Consensus pattern (14 bp):
TTCATCATCTCACA
Found at i:1507650 original size:34 final size:32
Alignment explanation
Indices: 1507611--1507680 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
1507601 TTTTGTAAAG
*
1507611 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
1507645 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
1507677 GGGA
1 GGGA
1507681 GTTGTAAGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:1509898 original size:30 final size:29
Alignment explanation
Indices: 1509864--1509921 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
1509854 CAATTTAAGG
1509864 CAAAATATATTTGGACTTGAATTGAATTTA
1 CAAAATATATTTGGA-TTGAATTGAATTTA
* * * *
1509894 CAAAATGTTTTTTGATTTAATTGAATTT
1 CAAAATATATTTGGATTGAATTGAATTT
1509922 TTTCAAAGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 12 0.50
30 12 0.50
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.47
Consensus pattern (29 bp):
CAAAATATATTTGGATTGAATTGAATTTA
Found at i:1510070 original size:20 final size:19
Alignment explanation
Indices: 1510045--1510135 Score: 57
Period size: 20 Copynumber: 4.9 Consensus size: 19
1510035 CACCTGCACT
1510045 AATGCATCGATGCATCATGC
1 AATGCATCGATGCATCAT-C
*
1510065 AATGCATCCATGCA--ATC
1 AATGCATCGATGCATCATC
* *
1510082 AA-ACATCGAATGCA-C-TT
1 AATGCATCG-ATGCATCATC
* *
1510099 AGTGCATCGATGCATCCTGC
1 AATGCATCGATGCATCAT-C
* *
1510119 TATGCATCCATGCATCA
1 AATGCATCGATGCATCA
1510136 AGGCTGCAAC
Statistics
Matches: 54, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
16 4 0.07
17 15 0.28
18 8 0.15
19 1 0.02
20 26 0.48
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.25
Consensus pattern (19 bp):
AATGCATCGATGCATCATC
Found at i:1510283 original size:20 final size:22
Alignment explanation
Indices: 1510245--1510284 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
1510235 TTTGAGTAGA
1510245 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
1510267 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
1510285 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:1510538 original size:34 final size:32
Alignment explanation
Indices: 1510499--1510568 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 32
1510489 TTTTGTAAAG
*
1510499 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
1510533 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
1510565 GGGA
1 GGGA
1510569 GTTGTAAGGT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
32 11 0.31
33 1 0.03
34 23 0.66
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.20
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Done.