Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167860.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_13, 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: 22724830
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82000 characters in sequence are not A, C, G, or T
File 100 of 109
Found at i:20022548 original size:36 final size:35
Alignment explanation
Indices: 20022508--20022579 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 35
20022498 ATTTAATCAC
* * *
20022508 ATTTTTATATATATGAATTCACATATAATTCTATTA
1 ATTTTTATACATATGAATT-AAATATAATCCTATTA
*
20022544 ATTTTTATACATATGAATTAAATATGATCCTATTA
1 ATTTTTATACATATGAATTAAATATAATCCTATTA
20022579 A
1 A
20022580 ACTTAATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 14 0.44
36 18 0.56
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.47
Consensus pattern (35 bp):
ATTTTTATACATATGAATTAAATATAATCCTATTA
Found at i:20022704 original size:34 final size:38
Alignment explanation
Indices: 20022666--20022739 Score: 102
Period size: 34 Copynumber: 2.1 Consensus size: 38
20022656 ATTTGAATCA
*
20022666 AATTTAAAAAAAT-TTTAAATT-TTAA-AATAAAT-TC
1 AATTTAAAAAAATATATAAATTATTAATAATAAATATC
*
20022700 AATTTAAATAAATATATAAATTATTAATAATAAATATC
1 AATTTAAAAAAATATATAAATTATTAATAATAAATATC
20022738 AA
1 AA
20022740 CCCGACCATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
34 12 0.35
35 7 0.21
36 4 0.12
37 7 0.21
38 4 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (38 bp):
AATTTAAAAAAATATATAAATTATTAATAATAAATATC
Found at i:20027623 original size:16 final size:16
Alignment explanation
Indices: 20027585--20027662 Score: 52
Period size: 16 Copynumber: 4.9 Consensus size: 16
20027575 ATTGCTGTTT
*
20027585 ACGGAACAACT-ATTC
1 ACGGAACAACTCCTTC
* *
20027600 AAGAAACAACTCCTTC
1 ACGGAACAACTCCTTC
* *
20027616 ACGGAACAACACTTTC
1 ACGGAACAACTCCTTC
* * *
20027632 ATGGAACACCT-GTTC
1 ACGGAACAACTCCTTC
*
20027647 TCGGAACAACTTCCTT
1 ACGGAACAAC-TCCTT
20027663 AAAGAACAAG
Statistics
Matches: 45, Mismatches: 15, Indels: 4
0.70 0.23 0.06
Matches are distributed among these distances:
15 19 0.42
16 24 0.53
17 2 0.04
ACGTcount: A:0.35, C:0.29, G:0.13, T:0.23
Consensus pattern (16 bp):
ACGGAACAACTCCTTC
Found at i:20034239 original size:26 final size:27
Alignment explanation
Indices: 20034209--20034261 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
20034199 AATAAATATG
*
20034209 AATAATCGAATTAAATTT-AAATTTTA
1 AATAATCGAATTAAATTTCAAAGTTTA
*
20034235 AATAATTGAATTAAATTTCAAAGTTTA
1 AATAATCGAATTAAATTTCAAAGTTTA
20034262 GTAACAAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 17 0.71
27 7 0.29
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.42
Consensus pattern (27 bp):
AATAATCGAATTAAATTTCAAAGTTTA
Found at i:20038959 original size:26 final size:26
Alignment explanation
Indices: 20038929--20038979 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
20038919 CAGCCACTTA
20038929 TTAAAACTTTTACTTCTACTATGATT
1 TTAAAACTTTTACTTCTACTATGATT
20038955 TTAAAACTTTTACTTCTACTATGAT
1 TTAAAACTTTTACTTCTACTATGAT
20038980 GCAGCTGCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.31, C:0.16, G:0.04, T:0.49
Consensus pattern (26 bp):
TTAAAACTTTTACTTCTACTATGATT
Found at i:20041986 original size:62 final size:62
Alignment explanation
Indices: 20041909--20042032 Score: 221
Period size: 62 Copynumber: 2.0 Consensus size: 62
20041899 GAAAAGACCG
* *
20041909 TTCGGCCTTTGATGGGTCAGATCAGAGCTCGTTATGTCAAATCCAGCCCACAACATCACCCA
1 TTCGGCCTATGATGGGTCAGATCAGAGCTCGTTAAGTCAAATCCAGCCCACAACATCACCCA
*
20041971 TTCGGCCTATGATGGGTCAGATCAGAGCTCGTTAAGTCAAGTCCAGCCCACAACATCACCCA
1 TTCGGCCTATGATGGGTCAGATCAGAGCTCGTTAAGTCAAATCCAGCCCACAACATCACCCA
20042033 CTATTAAGTA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 59 1.00
ACGTcount: A:0.27, C:0.31, G:0.20, T:0.23
Consensus pattern (62 bp):
TTCGGCCTATGATGGGTCAGATCAGAGCTCGTTAAGTCAAATCCAGCCCACAACATCACCCA
Found at i:20043273 original size:11 final size:11
Alignment explanation
Indices: 20043257--20043286 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
20043247 AAACGCCAAG
*
20043257 CATCATTATCT
1 CATCATTATCC
20043268 CATCATTATCC
1 CATCATTATCC
20043279 CATCATTA
1 CATCATTA
20043287 ATTCATTCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.40
Consensus pattern (11 bp):
CATCATTATCC
Found at i:20044133 original size:13 final size:14
Alignment explanation
Indices: 20044110--20044142 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
20044100 TATATTAAAA
*
20044110 AATTACAAAAAATT
1 AATTACAAAAAATG
20044124 AATT-CAAAAAATG
1 AATTACAAAAAATG
20044137 AATTAC
1 AATTAC
20044143 TCTTTAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.61, C:0.09, G:0.03, T:0.27
Consensus pattern (14 bp):
AATTACAAAAAATG
Found at i:20046197 original size:20 final size:21
Alignment explanation
Indices: 20046167--20046205 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
20046157 TGAAAAGGAC
20046167 AAATGATGCAAATACAAATTA
1 AAATGATGCAAATACAAATTA
20046188 AAAT-ATGCAAATACAAAT
1 AAATGATGCAAATACAAAT
20046206 GATCAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.59, C:0.10, G:0.08, T:0.23
Consensus pattern (21 bp):
AAATGATGCAAATACAAATTA
Found at i:20046642 original size:194 final size:198
Alignment explanation
Indices: 20046253--20046654 Score: 652
Period size: 204 Copynumber: 2.0 Consensus size: 198
20046243 CCTTTCTTAT
* *
20046253 TTTTGTTTTTTATCATTTATTTTGCAAAATATTTAGTGATAAAAGAAATTTTATTTATTATTATT
1 TTTTGTTTTTTATCATTTATTTTGAAAAATATTTACTGATAAAAGAAATTTTATTTATTATTATT
20046318 TTATTTTGTGTTGGAATCTTTTTTAAATTTTCGATATTTTTTCGATATCTAGGCGAAATTTAAGA
66 TTATTTTGTGTTGGAATCTTTTTTAAA---T-G--A-TTTTTCGATATCTAGGCGAAATTTAAGA
*
20046383 AAATTAGTCATTCACTTAAAAAAATTTCAAAATTAATTTTGGGTAAAAGTGAAAATGATGTT-AA
124 AAATTAGTCATTCACTTAAAAAAATTTCAAAATTAATTTTAGGTAAAAGTGAAAATGATGTTAAA
20046447 AAAAATATGA
189 AAAAATATGA
20046457 TTTTGTTTTTTATCATTTATTTTGAAAAATATTTACTGATAAAAGAAATTTTATTTATTATTATT
1 TTTTGTTTTTTATCATTTATTTTGAAAAATATTTACTGATAAAAGAAATTTTATTTATTATTATT
* *
20046522 TTATTTTGTGTTGGAATCTTTTTT-AA-G-TTTTTCGATATTTAGGCGAAATTTAAGAAAATTGG
66 TTATTTTGTGTTGGAATCTTTTTTAAATGATTTTTCGATATCTAGGCGAAATTTAAGAAAATTAG
20046584 TCATTCACTTAAAAAAATTTCAAAATTAATTTTAGGTAAAAGCT-AAAATGATGTTAAAAAAAAT
131 TCATTCACTTAAAAAAATTTCAAAATTAATTTTAGGTAAAAG-TGAAAATGATGTTAAAAAAAAT
20046648 ATGA
195 ATGA
20046652 TTT
1 TTT
20046655 GAATTTCCTC
Statistics
Matches: 191, Mismatches: 5, Indels: 13
0.91 0.02 0.06
Matches are distributed among these distances:
194 85 0.45
195 16 0.08
198 1 0.01
203 2 0.01
204 87 0.46
ACGTcount: A:0.37, C:0.05, G:0.11, T:0.46
Consensus pattern (198 bp):
TTTTGTTTTTTATCATTTATTTTGAAAAATATTTACTGATAAAAGAAATTTTATTTATTATTATT
TTATTTTGTGTTGGAATCTTTTTTAAATGATTTTTCGATATCTAGGCGAAATTTAAGAAAATTAG
TCATTCACTTAAAAAAATTTCAAAATTAATTTTAGGTAAAAGTGAAAATGATGTTAAAAAAAATA
TGA
Found at i:20046712 original size:194 final size:191
Alignment explanation
Indices: 20046278--20046654 Score: 465
Period size: 194 Copynumber: 1.9 Consensus size: 191
20046268 TTTATTTTGC
20046278 AAAATATTTAGTGATAAAAGAAATTTTATTTATTATTATTTTATTTTGTGTTGGAATCTTTTTTA
1 AAAATATTTA-T-ATAAAAGAAA---TA-TTATTATTATTTTATTTTGTGTTGGAATCTTTTTTA
20046343 AATTTTCGATATTTTTTCGATATCTAGGCGAAATTTAAGAAAATTAGTCATTCACTTAAAAAAAT
60 AA---T-G--A-TTTTTCGATATCTAGGCGAAATTTAAGAAAATTAGTCATTCACTTAAAAAAAT
* * *
20046408 TTCAAAATTAATTTTGGGTAAAAGTGAAAATGATGTTAAAAAAATATGATTTTGTTTTTTATCAT
118 TTCAAAATTAATTTTAGGTAAAAGTGAAAATGATGTTAAAAAAATATGATTTTGTTTTATATCAG
* * *
20046473 TTATTTTGA
183 TCATCTTCA
20046482 AAAATATTTACTGATAAAAGAAATTTTATTTATTATTATTTTATTTTGTGTTGGAATCTTTTTT-
1 AAAATATTTA-T-ATAAAAGAAA---TA-TTATTATTATTTTATTTTGTGTTGGAATCTTTTTTA
* *
20046546 AA-G-TTTTTCGATATTTAGGCGAAATTTAAGAAAATTGGTCATTCACTTAAAAAAATTTCAAAA
60 AATGATTTTTCGATATCTAGGCGAAATTTAAGAAAATTAGTCATTCACTTAAAAAAATTTCAAAA
20046609 TTAATTTTAGGTAAAAGCT-AAAATGATGTTAAAAAAAATATGATTT
125 TTAATTTTAGGTAAAAG-TGAAAATGATGTT-AAAAAAATATGATTT
20046655 GAATTTCCTC
Statistics
Matches: 167, Mismatches: 4, Indels: 13
0.91 0.02 0.07
Matches are distributed among these distances:
194 85 0.51
195 16 0.10
198 1 0.01
203 2 0.01
204 63 0.38
ACGTcount: A:0.39, C:0.05, G:0.12, T:0.45
Consensus pattern (191 bp):
AAAATATTTATATAAAAGAAATATTATTATTATTTTATTTTGTGTTGGAATCTTTTTTAAATGAT
TTTTCGATATCTAGGCGAAATTTAAGAAAATTAGTCATTCACTTAAAAAAATTTCAAAATTAATT
TTAGGTAAAAGTGAAAATGATGTTAAAAAAATATGATTTTGTTTTATATCAGTCATCTTCA
Found at i:20047402 original size:16 final size:16
Alignment explanation
Indices: 20047357--20047411 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 16
20047347 TCCAACTTCA
20047357 TTTTCTTTCTCTTCTCC
1 TTTTCTTTCT-TTCTCC
* *
20047374 TTATTTTTTTCTTTTTCC
1 -T-TTTCTTTCTTTCTCC
20047392 TTTTCTTTCTTTCTCC
1 TTTTCTTTCTTTCTCC
20047408 TTTT
1 TTTT
20047412 AGATGTCGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 17 0.53
17 1 0.03
18 6 0.19
19 8 0.25
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTCTTTCTTTCTCC
Found at i:20047472 original size:17 final size:16
Alignment explanation
Indices: 20047431--20047476 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
20047421 AATCAATCTC
20047431 TCTCTTTTT-TT-TTT
1 TCTCTTTTTCTTCTTT
*
20047445 TCTATTTTTCTTCTTT
1 TCTCTTTTTCTTCTTT
20047461 TCTCTTTCTTCTTCTT
1 TCTCTTT-TTCTTCTT
20047477 CTTCGCCACT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 8 0.30
15 2 0.07
16 9 0.33
17 8 0.30
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (16 bp):
TCTCTTTTTCTTCTTT
Found at i:20047637 original size:15 final size:15
Alignment explanation
Indices: 20047602--20047635 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
20047592 TTTCTCTTTA
20047602 TTTTTCATTTCTTAC
1 TTTTTCATTTCTTAC
*
20047617 TTTTTCATTTGTT-C
1 TTTTTCATTTCTTAC
20047631 TTTTT
1 TTTTT
20047636 TCCTATTGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.09, C:0.15, G:0.03, T:0.74
Consensus pattern (15 bp):
TTTTTCATTTCTTAC
Found at i:20063039 original size:9 final size:9
Alignment explanation
Indices: 20063025--20063055 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
20063015 ATGGATATAC
*
20063025 GTTTAATAT
1 GTTTAACAT
20063034 GTTTAACAT
1 GTTTAACAT
20063043 GTTTAACAT
1 GTTTAACAT
20063052 GTTT
1 GTTT
20063056 TTTATGTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.29, C:0.06, G:0.13, T:0.52
Consensus pattern (9 bp):
GTTTAACAT
Found at i:20063528 original size:31 final size:30
Alignment explanation
Indices: 20063479--20063580 Score: 91
Period size: 29 Copynumber: 3.4 Consensus size: 30
20063469 ATTATATTCT
* * *
20063479 TATATATATTCATGTTAATCATATTTATTTA
1 TATATATATTTATATTAATCGTATTTA-TTA
* * *
20063510 TATATATATTTGTATTAATCGCATCTA-TA
1 TATATATATTTATATTAATCGTATTTATTA
* * *
20063539 TATAAATATTTTTATTAATCGTGTTTA-TA
1 TATATATATTTATATTAATCGTATTTATTA
20063568 TATATAATATTTA
1 TATAT-ATATTTA
20063581 AAGTAAATTA
Statistics
Matches: 57, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
29 30 0.53
30 6 0.11
31 21 0.37
ACGTcount: A:0.36, C:0.06, G:0.05, T:0.53
Consensus pattern (30 bp):
TATATATATTTATATTAATCGTATTTATTA
Found at i:20083435 original size:23 final size:23
Alignment explanation
Indices: 20083409--20083458 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
20083399 TTTTATATAG
20083409 AGAATTCATCTAATTTTAGAGAA
1 AGAATTCATCTAATTTTAGAGAA
* *
20083432 AGAATTCATTTGATTTTAGAGAA
1 AGAATTCATCTAATTTTAGAGAA
20083455 AGAA
1 AGAA
20083459 AATTAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.34
Consensus pattern (23 bp):
AGAATTCATCTAATTTTAGAGAA
Found at i:20086480 original size:45 final size:44
Alignment explanation
Indices: 20086431--20086516 Score: 104
Period size: 44 Copynumber: 1.9 Consensus size: 44
20086421 TTGTTGAGTC
*
20086431 TCTACTTAAAGGAG-TCATTT-AAATTTTTTTAAAAGTTGTCAAACT
1 TCTACTTAAAGGAGCT-ATTTGAAA--TTTTCAAAAGTTGTCAAACT
* *
20086476 TCTACTTAGATGAGCTATTTGAAATTTTCAAAAGTTGTCAA
1 TCTACTTAAAGGAGCTATTTGAAATTTTCAAAAGTTGTCAA
20086517 GTATTTGGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
44 16 0.44
45 16 0.44
46 4 0.11
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.41
Consensus pattern (44 bp):
TCTACTTAAAGGAGCTATTTGAAATTTTCAAAAGTTGTCAAACT
Found at i:20086897 original size:15 final size:14
Alignment explanation
Indices: 20086848--20086897 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
20086838 ATTTGTTTTT
20086848 AAATAATAATAATT-
1 AAATAATAAT-ATTA
*
20086862 AAATATTAA-A-TA
1 AAATAATAATATTA
20086874 AAATAATAATTATTA
1 AAATAATAA-TATTA
20086889 AAATAATAA
1 AAATAATAA
20086898 AAAAAAGGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
11 1 0.03
12 9 0.30
14 9 0.30
15 11 0.37
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
AAATAATAATATTA
Found at i:20086902 original size:26 final size:26
Alignment explanation
Indices: 20086848--20086903 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
20086838 ATTTGTTTTT
*
20086848 AAATAATAATAATTAAATATTAAATA
1 AAATAATAATAATTAAATAATAAATA
* *
20086874 AAATAATAATTATTAAAATAATAAAAA
1 AAATAATAATAATT-AAATAATAAATA
20086901 AAA
1 AAA
20086904 GGAAGACAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 13 0.50
27 13 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (26 bp):
AAATAATAATAATTAAATAATAAATA
Found at i:20087954 original size:3 final size:3
Alignment explanation
Indices: 20087942--20087983 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
20087932 AACCTTATAG
20087942 AAT AAT -AT AAT AA- AA- AGAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AA
20087984 ATGAAAATGA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 5 0.14
3 30 0.83
4 1 0.03
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:20088676 original size:25 final size:26
Alignment explanation
Indices: 20088648--20088697 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
20088638 GTACTGAAAC
20088648 ATTTTAAGAA-TATTTCAATAAAAAT
1 ATTTTAAGAATTATTTCAATAAAAAT
20088673 ATTTTAAGAATTATTTCAATAAAAA
1 ATTTTAAGAATTATTTCAATAAAAA
20088698 GGTTCTGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (26 bp):
ATTTTAAGAATTATTTCAATAAAAAT
Found at i:20089599 original size:20 final size:21
Alignment explanation
Indices: 20089571--20089609 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
20089561 ATAAAAAATA
*
20089571 ATTCATTAATTA-TACTTTTC
1 ATTCATTAAATATTACTTTTC
*
20089591 ATTCTTTAAATATTACTTT
1 ATTCATTAAATATTACTTT
20089610 AATCAGTGCC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.31, C:0.13, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTCATTAAATATTACTTTTC
Found at i:20100367 original size:19 final size:19
Alignment explanation
Indices: 20100343--20100380 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
20100333 ATCACGTATA
20100343 TTTATTATGTTTT-CCTTTT
1 TTTATTAT-TTTTCCCTTTT
*
20100362 TTTATTCTTTTTCCCTTTT
1 TTTATTATTTTTCCCTTTT
20100381 GATTTGGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.08, C:0.16, G:0.03, T:0.74
Consensus pattern (19 bp):
TTTATTATTTTTCCCTTTT
Found at i:20116123 original size:22 final size:21
Alignment explanation
Indices: 20116081--20116149 Score: 54
Period size: 22 Copynumber: 3.4 Consensus size: 21
20116071 AAGGTATGTA
* *
20116081 TAATTTAATT-TTAATTGATT
1 TAATTTGATTATTAATTAATT
20116101 TAATTTGATTATTGAATTAATT
1 TAATTTGATTATT-AATTAATT
* * *
20116123 TCAGTTGATTAATAA--AATT
1 TAATTTGATTATTAATTAATT
*
20116142 TATTTTGA
1 TAATTTGA
20116150 AAGAATTTTG
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
19 9 0.23
20 9 0.23
21 4 0.10
22 17 0.44
ACGTcount: A:0.36, C:0.01, G:0.09, T:0.54
Consensus pattern (21 bp):
TAATTTGATTATTAATTAATT
Found at i:20121395 original size:12 final size:12
Alignment explanation
Indices: 20121378--20121436 Score: 66
Period size: 12 Copynumber: 4.7 Consensus size: 12
20121368 GCTGCAATCC
*
20121378 AAGAAAAGAAAG
1 AAGAAAAAAAAG
20121390 AAGAAAAAAAAG
1 AAGAAAAAAAAG
20121402 AAGCCAAAAAAAAAG
1 AAG---AAAAAAAAG
20121417 AGAGAAAAAAAAG
1 A-AGAAAAAAAAG
20121430 AA-AAAAA
1 AAGAAAAA
20121437 GTTGGTTGAA
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
11 5 0.12
12 15 0.36
13 10 0.24
15 10 0.24
16 2 0.05
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (12 bp):
AAGAAAAAAAAG
Found at i:20121423 original size:28 final size:29
Alignment explanation
Indices: 20121376--20121431 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 29
20121366 GCGCTGCAAT
20121376 CCAAGAAAAGAAAGAAGAAAAAAAAGAAG
1 CCAAGAAAAGAAAGAAGAAAAAAAAGAAG
20121405 CCAA-AAAA-AAAGAGAGAAAAAAAAGAA
1 CCAAGAAAAGAAAGA-AGAAAAAAAAGAA
20121432 AAAAAGTTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
27 5 0.19
28 17 0.65
29 4 0.15
ACGTcount: A:0.75, C:0.07, G:0.18, T:0.00
Consensus pattern (29 bp):
CCAAGAAAAGAAAGAAGAAAAAAAAGAAG
Found at i:20121425 original size:15 final size:14
Alignment explanation
Indices: 20121381--20121436 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 14
20121371 GCAATCCAAG
20121381 AAAAGAAAGAAGAAAA
1 AAAAG-AAGAA-AAAA
*
20121397 AAAAGAAGCCAAAAA
1 AAAAGAAG-AAAAAA
*
20121412 AAAAG-AGAGAAAA
1 AAAAGAAGAAAAAA
20121425 AAAAGAA-AAAAA
1 AAAAGAAGAAAAA
20121437 GTTGGTTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
13 13 0.38
14 3 0.09
15 12 0.35
16 6 0.18
ACGTcount: A:0.80, C:0.04, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAGAAGAAAAAA
Found at i:20122956 original size:28 final size:29
Alignment explanation
Indices: 20122917--20122971 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
20122907 TCAATTTTTA
20122917 TTTTAATCACAACTACAAT-AATTTTAGT
1 TTTTAATCACAACTACAATAAATTTTAGT
* * *
20122945 TTTTAATTACAATTATAATAAATTTTA
1 TTTTAATCACAACTACAATAAATTTTA
20122972 TTATTATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 16 0.70
29 7 0.30
ACGTcount: A:0.42, C:0.09, G:0.02, T:0.47
Consensus pattern (29 bp):
TTTTAATCACAACTACAATAAATTTTAGT
Found at i:20125284 original size:29 final size:29
Alignment explanation
Indices: 20125251--20125309 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 29
20125241 TATATTTGAT
20125251 AATTAATATATGTAT-T-ATTTTTATATAAA
1 AATT-ATATAT-TATATAATTTTTATATAAA
*
20125280 AATTATGTATTATATAATTTTTATATAAA
1 AATTATATATTATATAATTTTTATATAAA
20125309 A
1 A
20125310 TTTTATTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 3 0.11
28 6 0.22
29 18 0.67
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (29 bp):
AATTATATATTATATAATTTTTATATAAA
Found at i:20125419 original size:22 final size:23
Alignment explanation
Indices: 20125393--20125438 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
20125383 AATTTTTTAA
20125393 TAAATAAAATTTC-ACTAAAATT
1 TAAATAAAATTTCTACTAAAATT
* * *
20125415 TAAATTAATTTTCTATTAAAATT
1 TAAATAAAATTTCTACTAAAATT
20125438 T
1 T
20125439 GAGTTAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.46
Consensus pattern (23 bp):
TAAATAAAATTTCTACTAAAATT
Found at i:20125452 original size:23 final size:23
Alignment explanation
Indices: 20125408--20125452 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
20125398 AAAATTTCAC
* *
20125408 TAAAATTTAAATTAATTTTCTAT
1 TAAAATTTAAATTAAATATCTAT
* *
20125431 TAAAATTTGAGTTAAATATCTA
1 TAAAATTTAAATTAAATATCTA
20125453 ATATCAAATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (23 bp):
TAAAATTTAAATTAAATATCTAT
Found at i:20125608 original size:60 final size:61
Alignment explanation
Indices: 20125542--20125663 Score: 203
Period size: 60 Copynumber: 2.0 Consensus size: 61
20125532 CAAAATACAA
*
20125542 TAAGCATTTCAATTAATTTTACTTCAATAGGATGATGAGA-T-ATATGTTACTAACTAAGAG
1 TAAGCATTTCAATTAATTTTACTTC-ATAGGATGATGAGACTGATATGTTAATAACTAAGAG
*
20125602 TAAGCATTTCAATTAATTTTACTTCATGGGATGATGAGACTGATATGTTAATAACTAAGAG
1 TAAGCATTTCAATTAATTTTACTTCATAGGATGATGAGACTGATATGTTAATAACTAAGAG
20125663 T
1 T
20125664 TAATTTAGAT
Statistics
Matches: 58, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
59 13 0.22
60 26 0.45
61 19 0.33
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (61 bp):
TAAGCATTTCAATTAATTTTACTTCATAGGATGATGAGACTGATATGTTAATAACTAAGAG
Found at i:20125689 original size:22 final size:21
Alignment explanation
Indices: 20125663--20125708 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
20125653 TAACTAAGAG
20125663 TTAATTTAGATAAATAATAAAA
1 TTAATTTAGATAAA-AATAAAA
* *
20125685 TTAATTTTGATAAAATTAAAA
1 TTAATTTAGATAAAAATAAAA
20125706 TTA
1 TTA
20125709 TTATAATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (21 bp):
TTAATTTAGATAAAAATAAAA
Found at i:20125754 original size:14 final size:13
Alignment explanation
Indices: 20125731--20125762 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
20125721 TTAAAAATTA
20125731 TAAAAAATTTTAT
1 TAAAAAATTTTAT
20125744 TAAATAAATTTTAT
1 TAAA-AAATTTTAT
20125758 TAAAA
1 TAAAA
20125763 TTAATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TAAAAAATTTTAT
Found at i:20126449 original size:13 final size:14
Alignment explanation
Indices: 20126422--20126450 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
20126412 AAAAATACTA
20126422 TAAATATTGAAATT
1 TAAATATTGAAATT
20126436 TAAATATT-AAATT
1 TAAATATTGAAATT
20126449 TA
1 TA
20126451 TTGATTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (14 bp):
TAAATATTGAAATT
Found at i:20129066 original size:30 final size:31
Alignment explanation
Indices: 20129031--20129097 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
20129021 GTTTAATAAA
* * *
20129031 ATATATGTAATTTTTATTTTTA-AT-TTTTAT
1 ATATATGTAA-ATTAATTTTTATATAATTTAT
20129061 ATATATGTAAATTAATTTTTATATAATTTAT
1 ATATATGTAAATTAATTTTTATATAATTTAT
20129092 ATATAT
1 ATATAT
20129098 AATTTATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 9 0.28
30 12 0.38
31 11 0.34
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (31 bp):
ATATATGTAAATTAATTTTTATATAATTTAT
Found at i:20129098 original size:13 final size:13
Alignment explanation
Indices: 20129031--20129117 Score: 60
Period size: 13 Copynumber: 7.0 Consensus size: 13
20129021 GTTTAATAAA
*
20129031 ATATATGTAATTT
1 ATATATATAATTT
* * *
20129044 TTATTTTTAATTT
1 ATATATATAATTT
* *
20129057 TTATATAT-ATGT
1 ATATATATAATTT
20129069 A-A-AT-TAATTT
1 ATATATATAATTT
20129079 -T-TATATAATTT
1 ATATATATAATTT
20129090 ATATATATAATTT
1 ATATATATAATTT
20129103 ATATTATATGAATTT
1 ATA-TATAT-AATTT
20129118 GGATCTGACC
Statistics
Matches: 58, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
9 1 0.02
10 7 0.12
11 7 0.12
12 4 0.07
13 29 0.50
14 5 0.09
15 5 0.09
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (13 bp):
ATATATATAATTT
Found at i:20130372 original size:8 final size:8
Alignment explanation
Indices: 20130359--20130396 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
20130349 TAAAATTATT
20130359 TATTTTTA
1 TATTTTTA
20130367 TATTTTT-
1 TATTTTTA
*
20130374 TAATTTTA
1 TATTTTTA
20130382 TTATTTTTA
1 -TATTTTTA
20130391 TATTTT
1 TATTTT
20130397 ATACATTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
7 6 0.23
8 13 0.50
9 7 0.27
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTTA
Found at i:20139975 original size:21 final size:21
Alignment explanation
Indices: 20139950--20140006 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
20139940 TTAAAAATAA
20139950 TATTTTATAA-ATTTATAATTT
1 TATTTT-TAATATTTATAATTT
20139971 TATTTTTAATATTTATAATATT
1 TATTTTTAATATTTATAAT-TT
*
20139993 T-TTATTTATTATTT
1 TATT-TTTAATATTT
20140007 TTTATTTAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
20 3 0.09
21 17 0.53
22 12 0.38
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TATTTTTAATATTTATAATTT
Found at i:20139981 original size:30 final size:31
Alignment explanation
Indices: 20139947--20140008 Score: 83
Period size: 30 Copynumber: 2.0 Consensus size: 31
20139937 TTATTAAAAA
20139947 TAATATTTTATAA-ATTTATAATT-TTATTTT
1 TAATA-TTTATAATATTTATAATTATTATTTT
* *
20139977 TAATATTTATAATATTTTTATTTATTATTTT
1 TAATATTTATAATATTTATAATTATTATTTT
20140008 T
1 T
20140009 TATTTAAGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 7 0.25
30 13 0.46
31 8 0.29
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (31 bp):
TAATATTTATAATATTTATAATTATTATTTT
Found at i:20140000 original size:15 final size:14
Alignment explanation
Indices: 20139980--20140014 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
20139970 TTATTTTTAA
20139980 TATTTATAATATTTT
1 TATTTATAAT-TTTT
*
20139995 TATTTATTATTTTT
1 TATTTATAATTTTT
20140009 TATTTA
1 TATTTA
20140015 AGGCTCTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TATTTATAATTTTT
Found at i:20140417 original size:4 final size:4
Alignment explanation
Indices: 20140410--20140511 Score: 57
Period size: 4 Copynumber: 23.5 Consensus size: 4
20140400 TTCGATCGAT
20140410 TTAA TTAA TT-- TTAAA TTAA TTAA TTAA TTAAA TTAAA TTAAA TTAAA
1 TTAA TTAA TTAA TT-AA TTAA TTAA TTAA TT-AA TT-AA TT-AA TT-AA
* * *
20140457 TTAA TATATT TTAA -AAA TTAA TTAA TCAAA TTTAA TTAAA TTAA TTAAA
1 TTAA T-TA-A TTAA TTAA TTAA TTAA T-TAA -TTAA TT-AA TTAA TT-AA
20140506 TTAA TT
1 TTAA TT
20140512 TTTTGATTAA
Statistics
Matches: 81, Mismatches: 6, Indels: 22
0.74 0.06 0.20
Matches are distributed among these distances:
2 2 0.02
3 2 0.02
4 38 0.47
5 37 0.46
6 2 0.02
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (4 bp):
TTAA
Found at i:20140430 original size:15 final size:15
Alignment explanation
Indices: 20140410--20140482 Score: 69
Period size: 15 Copynumber: 4.6 Consensus size: 15
20140400 TTCGATCGAT
20140410 TTAATTAATTTTAAA
1 TTAATTAATTTTAAA
20140425 TTAATTAATTAATTAAA
1 TTAATTAATT--TTAAA
*
20140442 TTAAATTAA-ATTAAA
1 TT-AATTAATTTTAAA
20140457 TTAA-TATATTTTAAAAA
1 TTAATTA-ATTTT--AAA
20140474 TTAATTAAT
1 TTAATTAAT
20140483 CAAATTTAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
13 2 0.04
14 3 0.06
15 19 0.40
17 16 0.33
18 8 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TTAATTAATTTTAAA
Found at i:20140443 original size:5 final size:5
Alignment explanation
Indices: 20140420--20140509 Score: 68
Period size: 5 Copynumber: 18.8 Consensus size: 5
20140410 TTAATTAATT
**
20140420 TTAAA TT-AA TT-AA TT-AA TTAAA TTAAA TTAAA TTAAA TT-AA TATATT
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA T-TAAA
* *
20140467 TTAAAAA TT-AA TT-AA TCAAA TTTAA TTAAA TT-AA TTAAA TTAA
1 TT--AAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAA
20140510 TTTTTTGATT
Statistics
Matches: 70, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
4 26 0.37
5 40 0.57
6 1 0.01
7 3 0.04
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (5 bp):
TTAAA
Found at i:20140513 original size:45 final size:46
Alignment explanation
Indices: 20140410--20140513 Score: 142
Period size: 45 Copynumber: 2.3 Consensus size: 46
20140400 TTCGATCGAT
*
20140410 TTAATTAATTTTAAATTAATTAATTAATTAAATTAAATTAAATTAAA
1 TTAATTAATTTTAAA-TAATTAATTAATCAAATTAAATTAAATTAAA
*
20140457 TTAA-TATATTTTAAA-AATTAATTAATCAAATTTAATTAAATT-AA
1 TTAATTA-ATTTTAAATAATTAATTAATCAAATTAAATTAAATTAAA
20140501 TTAAATTAATTTT
1 TT-AATTAATTTT
20140514 TTGATTAATT
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
44 4 0.08
45 32 0.62
46 4 0.08
47 12 0.23
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (46 bp):
TTAATTAATTTTAAATAATTAATTAATCAAATTAAATTAAATTAAA
Found at i:20140603 original size:13 final size:14
Alignment explanation
Indices: 20140572--20140603 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
20140562 TTAAATAGAC
20140572 TAAATAAAATTATT
1 TAAATAAAATTATT
20140586 T-AATAAAA-TATT
1 TAAATAAAATTATT
20140598 TAAATA
1 TAAATA
20140604 TCAAAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 5 0.29
13 11 0.65
14 1 0.06
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TAAATAAAATTATT
Found at i:20140686 original size:16 final size:15
Alignment explanation
Indices: 20140661--20140690 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
20140651 TCATTATTTT
20140661 TTATTTATATTTAAA
1 TTATTTATATTTAAA
20140676 TTATATTATATTTAA
1 TTAT-TTATATTTAA
20140691 GTTAATTCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTATTTATATTTAAA
Found at i:20140758 original size:4 final size:4
Alignment explanation
Indices: 20140749--20140802 Score: 51
Period size: 4 Copynumber: 13.8 Consensus size: 4
20140739 AATTATTTTC
* *
20140749 ATTA ATTA ATTA A--A ATTA ATTTG A-TA ATTA ATTA ATTA ATTTA ATCA
1 ATTA ATTA ATTA ATTA ATTA A-TTA ATTA ATTA ATTA ATTA A-TTA ATTA
20140796 ATTA ATT
1 ATTA ATT
20140803 CAAATAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
2 2 0.05
3 2 0.05
4 30 0.73
5 7 0.17
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (4 bp):
ATTA
Found at i:20154393 original size:23 final size:25
Alignment explanation
Indices: 20154351--20154396 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
20154341 CACATTTGAT
*
20154351 TATTGATTGTTATCTATTACTTCTG
1 TATTGATTGTAATCTATTACTTCTG
20154376 TATTG-TTGTAAT-TATTACTTC
1 TATTGATTGTAATCTATTACTTC
20154397 AAGCGCAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
24 6 0.30
25 5 0.25
ACGTcount: A:0.22, C:0.11, G:0.11, T:0.57
Consensus pattern (25 bp):
TATTGATTGTAATCTATTACTTCTG
Found at i:20156152 original size:20 final size:20
Alignment explanation
Indices: 20156127--20156167 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
20156117 AGAGAAAGAC
20156127 CTCTCCCATGTACAAGAAAG
1 CTCTCCCATGTACAAGAAAG
20156147 CTCTCCCATGTACAAGAAAG
1 CTCTCCCATGTACAAGAAAG
20156167 C
1 C
20156168 AAAGCAGTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.32, G:0.15, T:0.20
Consensus pattern (20 bp):
CTCTCCCATGTACAAGAAAG
Found at i:20161022 original size:18 final size:18
Alignment explanation
Indices: 20160996--20161032 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
20160986 TGAGATGAAG
20160996 TGATATACAAAAGAAACT
1 TGATATACAAAAGAAACT
* *
20161014 TGATGTACAGAAGAAACT
1 TGATATACAAAAGAAACT
20161032 T
1 T
20161033 TTCTGAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.11, G:0.16, T:0.24
Consensus pattern (18 bp):
TGATATACAAAAGAAACT
Found at i:20161452 original size:11 final size:11
Alignment explanation
Indices: 20161436--20161463 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
20161426 TTGAAAAAGA
20161436 TAAATTATTTT
1 TAAATTATTTT
20161447 TAAATTATTTT
1 TAAATTATTTT
20161458 TAAATT
1 TAAATT
20161464 GAGATTAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TAAATTATTTT
Found at i:20161461 original size:228 final size:239
Alignment explanation
Indices: 20160835--20161475 Score: 787
Period size: 249 Copynumber: 2.7 Consensus size: 239
20160825 TTAATGAAAT
* * * * *
20160835 ATATTTAAAAGTTAAAAATAATGTAAGGATTATTTATAAAAAAATATTAAAGATGTTAAATAATA
1 ATATTTAAAAATTGAAGATAATGTAATGATTATTTATAAAAAAATATTAAAGATATTAAATAATA
* *
20160900 TTTTTAAAAGTTATGATAAATTTAAATACTCATGTTAACTATAGATAAATTGAAAAAAATAAATT
66 -TTTTAAAAGTTATGATAAATTTAAATACTCATGTTAACTTTAGATAAATTGAAAAAGATAAATT
*
20160965 A-CTTTAAAGTTAATTTTAAATTGAGATGAAGTGATATACAAAAGAAACTTGATGTACAGAAGAA
130 ATTTTTAAA-TT-ATTTTAAATTGAGATGAAGTG----AC-AAAGAAAC-TGATG-ACA-AAGAA
* *
20161029 ACTTTTCTGAAATTGTTTTGCTATTTATATTTTTTTTACATTTTTTTTGTGAAAT
185 ACTTTTCTGAAATTGTTTTGCTATTTATATTTTTTTTACATTTTTTTTGTAAAAC
*
20161084 ATATTTAAAAACTGAAGATAATGTAATGATTATTTATAAAAAAATATTAAAGATATTAAATAATA
1 ATATTTAAAAATTGAAGATAATGTAATGATTATTTATAAAAAAATATTAAAGATATTAAATAATA
* * *
20161149 CTTTTAAAAGTTGTGATAAATTTAAATACTTATGTTAA-TTCTAGATGAATTGAAAAAGATAAAT
66 -TTTTAAAAGTTATGATAAATTTAAATACTCATGTTAACTT-TAGATAAATTGAAAAAGATAAAT
* * * *
20161213 TATTTTAAAATTGATTTTAAATTGATAT-AAG-G-C-AATATA-T-A-G-C-AA-AAAC-TTTCT
129 TATTTTTAAATT-ATTTTAAATTGAGATGAAGTGACAAAGAAACTGATGACAAAGAAACTTTTC-
* *
20161267 TGAAGTTGTTTTGGT-TTT-T-TTTTTTTT-CATATTTTCTTTGTAAAAC
192 TGAAATTGTTTTGCTATTTATATTTTTTTTACAT-TTTT-TTTGTAAAAC
*
20161313 ATATTTAAAAATTGAAGATAATATAATGATTATTTAT-AAAAAATATTAAAGATATTAAATAATA
1 ATATTTAAAAATTGAAGATAATGTAATGATTATTTATAAAAAAATATTAAAGATATTAAATAATA
20161377 TTTTAAAAAGTTATGATAAATTTAAATACTCATGTTAACTTTAGATAAATTGAAAAAGATAAATT
66 TTTT-AAAAGTTATGATAAATTTAAATACTCATGTTAACTTTAGATAAATTGAAAAAGATAAATT
*
20161442 ATTTTTAAATTATTTTTAAATTGAGATTAAGTGA
130 ATTTTTAAATTA-TTTTAAATTGAGATGAAGTGA
20161476 TGTTACAAGA
Statistics
Matches: 352, Mismatches: 29, Indels: 40
0.84 0.07 0.10
Matches are distributed among these distances:
227 8 0.02
228 116 0.33
229 49 0.14
230 8 0.02
231 17 0.05
232 2 0.01
234 1 0.00
236 1 0.00
237 1 0.00
238 1 0.00
240 4 0.01
242 1 0.00
247 1 0.00
248 4 0.01
249 133 0.38
250 5 0.01
ACGTcount: A:0.44, C:0.04, G:0.10, T:0.41
Consensus pattern (239 bp):
ATATTTAAAAATTGAAGATAATGTAATGATTATTTATAAAAAAATATTAAAGATATTAAATAATA
TTTTAAAAGTTATGATAAATTTAAATACTCATGTTAACTTTAGATAAATTGAAAAAGATAAATTA
TTTTTAAATTATTTTAAATTGAGATGAAGTGACAAAGAAACTGATGACAAAGAAACTTTTCTGAA
ATTGTTTTGCTATTTATATTTTTTTTACATTTTTTTTGTAAAAC
Found at i:20163193 original size:12 final size:13
Alignment explanation
Indices: 20163166--20163200 Score: 54
Period size: 12 Copynumber: 2.7 Consensus size: 13
20163156 TAGTTATATA
20163166 TTAAAACTTATTTT
1 TTAAAA-TTATTTT
20163180 TTAAAATT-TTTT
1 TTAAAATTATTTT
20163192 TTAAAATTA
1 TTAAAATTA
20163201 ATTAAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 12 0.60
13 2 0.10
14 6 0.30
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (13 bp):
TTAAAATTATTTT
Found at i:20163219 original size:22 final size:22
Alignment explanation
Indices: 20163180--20163225 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
20163170 AACTTATTTT
* ** *
20163180 TTAAAATTTTTTTTAAAATTAA
1 TTAAAATTTATTAAAAAAATAA
20163202 TTAAAATTTATTAAAAAAATAA
1 TTAAAATTTATTAAAAAAATAA
20163224 TT
1 TT
20163226 TTTTATCTAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TTAAAATTTATTAAAAAAATAA
Found at i:20164545 original size:32 final size:32
Alignment explanation
Indices: 20164504--20164572 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
20164494 CCCGATCTTG
20164504 AACAGAACCCATTCAACATTTGCAGCAGCTTC
1 AACAGAACCCATTCAACATTTGCAGCAGCTTC
* *
20164536 AACAGAACCCATTCGACGTTTGCAGCAGCTTC
1 AACAGAACCCATTCAACATTTGCAGCAGCTTC
20164568 AACAG
1 AACAG
20164573 TTTGCAGCAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.33, C:0.30, G:0.16, T:0.20
Consensus pattern (32 bp):
AACAGAACCCATTCAACATTTGCAGCAGCTTC
Found at i:20164577 original size:19 final size:19
Alignment explanation
Indices: 20164553--20164591 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
20164543 CCCATTCGAC
20164553 GTTTGCAGCAGCTTCAACA
1 GTTTGCAGCAGCTTCAACA
20164572 GTTTGCAGCAGCTTCAACA
1 GTTTGCAGCAGCTTCAACA
20164591 G
1 G
20164592 AACCCATTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (19 bp):
GTTTGCAGCAGCTTCAACA
Found at i:20164582 original size:51 final size:51
Alignment explanation
Indices: 20164515--20164653 Score: 246
Period size: 51 Copynumber: 2.8 Consensus size: 51
20164505 ACAGAACCCA
20164515 TTCAACA-TTTGCAGCAGCTTCAACAGAACCCATTCGACGTTTGCAGCAGC
1 TTCAACAGTTTGCAGCAGCTTCAACAGAACCCATTCGACGTTTGCAGCAGC
20164565 TTCAACAGTTTGCAGCAGCTTCAACAGAACCCATTCGACGTTTGCAGCAGC
1 TTCAACAGTTTGCAGCAGCTTCAACAGAACCCATTCGACGTTTGCAGCAGC
* *
20164616 TTCAACAGTTTGCAG-ATCTTGAACAGAACCCATTCGAC
1 TTCAACAGTTTGCAGCAGCTTCAACAGAACCCATTCGAC
20164654 AGAACCCATT
Statistics
Matches: 86, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
50 28 0.33
51 58 0.67
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (51 bp):
TTCAACAGTTTGCAGCAGCTTCAACAGAACCCATTCGACGTTTGCAGCAGC
Found at i:20164657 original size:14 final size:14
Alignment explanation
Indices: 20164638--20164666 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
20164628 CAGATCTTGA
20164638 ACAGAACCCATTCG
1 ACAGAACCCATTCG
20164652 ACAGAACCCATTCG
1 ACAGAACCCATTCG
20164666 A
1 A
20164667 TGTTTGCAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.34, G:0.14, T:0.14
Consensus pattern (14 bp):
ACAGAACCCATTCG
Found at i:20164719 original size:57 final size:57
Alignment explanation
Indices: 20164652--20165136 Score: 372
Period size: 57 Copynumber: 8.4 Consensus size: 57
20164642 AACCCATTCG
* *
20164652 ACAGAACCCATTCGATGTTTGCAGCTTGCAGTAGCTTCAACAGTTTGCAGATCTTGA
1 ACAGAACCCATTCGACGTTTGCAGCTTGCAGCAGCTTCAACAGTTTGCAGATCTTGA
* * *
20164709 ACAAAACCCATTCGACG--T-----TTGCAGCAGCTTCAACAGTTTGCAGCAGCTTCA
1 ACAGAACCCATTCGACGTTTGCAGCTTGCAGCAGCTTCAACAGTTTGCAG-ATCTTGA
**** * * *
20164760 ACAGTTTACA---GA--TCTTGAACAGTTTGTAGCAGCTTCAACAGTTTACAGATCTTGA
1 ACAGAACCCATTCGACGT-TTG--CAGCTTGCAGCAGCTTCAACAGTTTGCAGATCTTGA
* *
20164815 ACAGAACCCATTCGACGTTTGCAGCTTGTAGCAGCTTCAACAGTTTACAGATCTTGA
1 ACAGAACCCATTCGACGTTTGCAGCTTGCAGCAGCTTCAACAGTTTGCAGATCTTGA
* * * * * * *
20164872 ACAGTTTACAGCAGCTTCAACAGTTTACAGATCTTGAACAGAACCCATTCGAC-GTTTGCAG--C
1 ACAG--AAC-CCA--TTCGAC-GTTTGCAG--CTTG--CAGCA-GC-TTCAACAGTTTGCAGATC
20164934 TTGCA
54 TTG-A
* ** * * * *
20164939 GCAGCTTCAACAGTT-TACAGATCTTGAACAGTTTGCAGCAGCTTCAACAGTTTACAGATCTTGA
1 ACAG-AAC-CCA-TTCGAC-G-T-TTG--CAGCTTGCAGCAGCTTCAACAGTTTGCAGATCTTGA
20165003 ACAGAACCCATTCGACGTTTGCAGCTTGCAGCAGCTTCAACAGTTTGCAGATCTTGA
1 ACAGAACCCATTCGACGTTTGCAGCTTGCAGCAGCTTCAACAGTTTGCAGATCTTGA
20165060 ACAGAACCCATTCGACGTTTGCAGCTTGCAGCAGCTTCAACAGTTTGCAGATCTTGA
1 ACAGAACCCATTCGACGTTTGCAGCTTGCAGCAGCTTCAACAGTTTGCAGATCTTGA
*
20165117 ACAGAACCCCTTCGACGTTT
1 ACAGAACCCATTCGACGTTT
20165137 ACAGTAGCTT
Statistics
Matches: 343, Mismatches: 48, Indels: 74
0.74 0.10 0.16
Matches are distributed among these distances:
48 2 0.01
49 1 0.00
50 24 0.07
51 10 0.03
55 12 0.03
56 23 0.07
57 164 0.48
58 2 0.01
59 8 0.02
60 4 0.01
61 3 0.01
62 14 0.04
63 16 0.05
64 12 0.03
65 11 0.03
66 14 0.04
67 7 0.02
68 11 0.03
69 5 0.01
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (57 bp):
ACAGAACCCATTCGACGTTTGCAGCTTGCAGCAGCTTCAACAGTTTGCAGATCTTGA
Found at i:20164782 original size:18 final size:19
Alignment explanation
Indices: 20164725--20164995 Score: 119
Period size: 19 Copynumber: 14.4 Consensus size: 19
20164715 CCCATTCGAC
*
20164725 GTTTGCAGCAGCTTCAACA
1 GTTTACAGCAGCTTCAACA
*
20164744 GTTTGCAGCAGCTTCAACA
1 GTTTACAGCAGCTTCAACA
* *
20164763 GTTTACAG-ATCTTGAACA
1 GTTTACAGCAGCTTCAACA
**
20164781 GTTTGTAGCAGCTTCAACA
1 GTTTACAGCAGCTTCAACA
* *
20164800 GTTTACAG-ATCTTGAACA
1 GTTTACAGCAGCTTCAACA
**** * **
20164818 GAACCCATTC-GACGTT-TGCA
1 GTTTACA-GCAG-C-TTCAACA
* **
20164838 GCTTGTAGCAGCTTCAACA
1 GTTTACAGCAGCTTCAACA
* *
20164857 GTTTACAG-ATCTTGAACA
1 GTTTACAGCAGCTTCAACA
20164875 GTTTACAGCAGCTTCAACA
1 GTTTACAGCAGCTTCAACA
* *
20164894 GTTTACAG-ATCTTGAACA
1 GTTTACAGCAGCTTCAACA
**** * **
20164912 GAACCCATTC-GACGTT-TGCA
1 GTTTACA-GCAG-C-TTCAACA
* *
20164932 GCTTGCAGCAGCTTCAACA
1 GTTTACAGCAGCTTCAACA
* *
20164951 GTTTACAG-ATCTTGAACA
1 GTTTACAGCAGCTTCAACA
*
20164969 GTTTGCAGCAGCTTCAACA
1 GTTTACAGCAGCTTCAACA
20164988 GTTTACAG
1 GTTTACAG
20164996 ATCTTGAACA
Statistics
Matches: 178, Mismatches: 59, Indels: 30
0.67 0.22 0.11
Matches are distributed among these distances:
18 71 0.40
19 90 0.51
20 13 0.07
21 4 0.02
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (19 bp):
GTTTACAGCAGCTTCAACA
Found at i:20164791 original size:37 final size:37
Alignment explanation
Indices: 20164740--20165006 Score: 165
Period size: 37 Copynumber: 7.1 Consensus size: 37
20164730 CAGCAGCTTC
20164740 AACAGTTTGCAGCAGCTTCAACAGTTTACAGATCTTG
1 AACAGTTTGCAGCAGCTTCAACAGTTTACAGATCTTG
*
20164777 AACAGTTTGTAGCAGCTTCAACAGTTTACAGATCTTG
1 AACAGTTTGCAGCAGCTTCAACAGTTTACAGATCTTG
**** * ** *
20164814 AACAGAACCCATTC-GACGTT-TGCAGCTTGTAGCAG--CTTC
1 AACAGTTTGCA-GCAG-C-TTCAACAG-TT-TA-CAGATCTTG
* * * * *
20164853 AACAGTTTACAG-ATCTTGAACAGTTTACAGCAGCTTC
1 AACAGTTTGCAGCAGCTTCAACAGTTTACAG-ATCTTG
* * * ****
20164890 AACAGTTTACAG-ATCTTGAACAGAACCCATTCGA-CGTTTG
1 AACAGTTTGCAGCAGCTTCAACAGTTTACA---GATC--TTG
*
20164930 --CAGCTTGCAGCAGCTTCAACAGTTTACAGATCTTG
1 AACAGTTTGCAGCAGCTTCAACAGTTTACAGATCTTG
20164965 AACAGTTTGCAGCAGCTTCAACAGTTTACAGATCTTG
1 AACAGTTTGCAGCAGCTTCAACAGTTTACAGATCTTG
20165002 AACAG
1 AACAG
20165007 AACCCATTCG
Statistics
Matches: 178, Mismatches: 32, Indels: 40
0.71 0.13 0.16
Matches are distributed among these distances:
34 3 0.02
35 5 0.03
36 6 0.03
37 116 0.65
38 14 0.08
39 26 0.15
40 5 0.03
41 3 0.02
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (37 bp):
AACAGTTTGCAGCAGCTTCAACAGTTTACAGATCTTG
Found at i:20164861 original size:94 final size:94
Alignment explanation
Indices: 20164746--20165063 Score: 600
Period size: 94 Copynumber: 3.4 Consensus size: 94
20164736 CTTCAACAGT
*
20164746 TTGCAGCAGCTTCAACAGTTTACAGATCTTGAACAGTTTGTAGCAGCTTCAACAGTTTACAGATC
1 TTGCAGCAGCTTCAACAGTTTACAGATCTTGAACAGTTTGCAGCAGCTTCAACAGTTTACAGATC
20164811 TTGAACAGAACCCATTCGACGTTTGCAGC
66 TTGAACAGAACCCATTCGACGTTTGCAGC
* *
20164840 TTGTAGCAGCTTCAACAGTTTACAGATCTTGAACAGTTTACAGCAGCTTCAACAGTTTACAGATC
1 TTGCAGCAGCTTCAACAGTTTACAGATCTTGAACAGTTTGCAGCAGCTTCAACAGTTTACAGATC
20164905 TTGAACAGAACCCATTCGACGTTTGCAGC
66 TTGAACAGAACCCATTCGACGTTTGCAGC
20164934 TTGCAGCAGCTTCAACAGTTTACAGATCTTGAACAGTTTGCAGCAGCTTCAACAGTTTACAGATC
1 TTGCAGCAGCTTCAACAGTTTACAGATCTTGAACAGTTTGCAGCAGCTTCAACAGTTTACAGATC
20164999 TTGAACAGAACCCATTCGACGTTTGCAGC
66 TTGAACAGAACCCATTCGACGTTTGCAGC
*
20165028 TTGCAGCAGCTTCAACAGTTTGCAGATCTTGAACAG
1 TTGCAGCAGCTTCAACAGTTTACAGATCTTGAACAG
20165064 AACCCATTCG
Statistics
Matches: 218, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
94 218 1.00
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (94 bp):
TTGCAGCAGCTTCAACAGTTTACAGATCTTGAACAGTTTGCAGCAGCTTCAACAGTTTACAGATC
TTGAACAGAACCCATTCGACGTTTGCAGC
Found at i:20164956 original size:151 final size:149
Alignment explanation
Indices: 20164787--20165190 Score: 429
Period size: 151 Copynumber: 2.7 Consensus size: 149
20164777 AACAGTTTGT
20164787 AGCAGCTTCAACAGTTTACAGATCTTGAACAGAACCCATTCGACGTTTGCAGCTTGTAGCAGCTT
1 AGCAGCTTCAACAGTTTACAGATCTTGAACAGAACCCATTCGACGTTT-CAGCTTG-AGCAGCTT
20164852 CAACAGTTTACAGATCTTGAACAGTTTACAGCAGCTTCAACAGTTTACAGATCTTGAACAGAACC
64 CAACAGTTTACAGATCTTGAACAGTTTACAGCAGCTTCAACAGTTTACAGATCTTGAACAGAACC
20164917 CATTCGACGTTTGCAGCTTGC
129 CATTCGACGTTTGCAGCTTGC
** * *
20164938 AGCAGCTTCAACAGTTTACAGATCTTGAACAGTTTGCAGCAGCTTCAACAGTTTACAGATCTTGA
1 AGCAGCTTCAACAGTTTACAGATCTTGAACAG--AAC-CCA--TTCGAC-GTTT-CAG--CTTGA
* ** * * * * *
20165003 ACAG-AAC-CCA-TTCGAC-G-T-TTG--CAGCTTGCAGCAGCTTCAACAGTTTGCAGATCTTGA
57 GCAGCTTCAACAGTT-TACAGATCTTGAACAGTTTACAGCAGCTTCAACAGTTTACAGATCTTGA
20165060 ACAGAACCCATTCGACGTTTGCAGCTTGC
121 ACAGAACCCATTCGACGTTTGCAGCTTGC
* * *
20165089 AGCAGCTTCAACAGTTTGCAGATCTTGAACAGAACCCCTTCGACGTTT-A-C---AGTAGCTTCA
1 AGCAGCTTCAACAGTTTACAGATCTTGAACAGAACCCATTCGACGTTTCAGCTTGAGCAGCTTCA
** * *
20165149 ACAGTTTGTAGCAGCTTCAACAGTTTACAGCAGCTTCAACAG
66 ACAGTTTACAG-ATCTTGAACAGTTTACAGCAGCTTCAACAG
20165191 AACCCATTTG
Statistics
Matches: 204, Mismatches: 31, Indels: 42
0.74 0.11 0.15
Matches are distributed among these distances:
137 3 0.01
138 1 0.00
139 2 0.01
140 4 0.02
143 3 0.01
145 24 0.12
146 5 0.02
148 1 0.00
149 1 0.00
151 125 0.61
153 4 0.02
154 3 0.01
155 3 0.01
156 9 0.04
157 8 0.04
158 4 0.02
159 4 0.02
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (149 bp):
AGCAGCTTCAACAGTTTACAGATCTTGAACAGAACCCATTCGACGTTTCAGCTTGAGCAGCTTCA
ACAGTTTACAGATCTTGAACAGTTTACAGCAGCTTCAACAGTTTACAGATCTTGAACAGAACCCA
TTCGACGTTTGCAGCTTGC
Found at i:20165025 original size:50 final size:52
Alignment explanation
Indices: 20164971--20165156 Score: 232
Period size: 57 Copynumber: 3.4 Consensus size: 52
20164961 CTTGAACAGT
*
20164971 TTGCAGCAGCTTCAACAGTTTACAGATCTTGAACAGAACCCATTCGACGTTTGCAGC
1 TTGCAGCAGCTTCAACAGTTTGCAGATCTTGAACAGAACCCATTCGACG-TT----C
20165028 TTGCAGCAGCTTCAACAGTTTGCAGATCTTGAACAGAACCCATTCGACGTTTGCAGC
1 TTGCAGCAGCTTCAACAGTTTGCAGATCTTGAACAGAACCCATTCGACG-TT----C
*
20165085 TTGCAGCAGCTTCAACAGTTTGCAGATCTTGAACAGAACCCCTTCGACG-T-
1 TTGCAGCAGCTTCAACAGTTTGCAGATCTTGAACAGAACCCATTCGACGTTC
* *
20165135 TTACAGTAGCTTCAACAGTTTG
1 TTGCAGCAGCTTCAACAGTTTG
20165157 TAGCAGCTTC
Statistics
Matches: 125, Mismatches: 4, Indels: 7
0.92 0.03 0.05
Matches are distributed among these distances:
50 20 0.16
55 1 0.01
57 104 0.83
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (52 bp):
TTGCAGCAGCTTCAACAGTTTGCAGATCTTGAACAGAACCCATTCGACGTTC
Found at i:20165164 original size:19 final size:19
Alignment explanation
Indices: 20165133--20165190 Score: 89
Period size: 19 Copynumber: 3.1 Consensus size: 19
20165123 CCCCTTCGAC
*
20165133 GTTTACAGTAGCTTCAACA
1 GTTTACAGCAGCTTCAACA
**
20165152 GTTTGTAGCAGCTTCAACA
1 GTTTACAGCAGCTTCAACA
20165171 GTTTACAGCAGCTTCAACA
1 GTTTACAGCAGCTTCAACA
20165190 G
1 G
20165191 AACCCATTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.29
Consensus pattern (19 bp):
GTTTACAGCAGCTTCAACA
Found at i:20165206 original size:70 final size:69
Alignment explanation
Indices: 20165089--20165222 Score: 196
Period size: 70 Copynumber: 1.9 Consensus size: 69
20165079 TGCAGCTTGC
* * * * *
20165089 AGCAGCTTCAACAGTTTGCAGATCTTGAACAGAACCCCTTCGACGTTTACAGTAGCTTCAACAGT
1 AGCAGCTTCAACAGTTTACAGAGCTTCAACAGAACCCATTCGACGTTTACAGCAGCTTCAACAGT
20165154 TTGT
66 TTGT
* *
20165158 AGCAGCTTCAACAGTTTACAGCAGCTTCAACAGAACCCATTTGACGTTTGCAGCAGCTTCAACAG
1 AGCAGCTTCAACAGTTTACAG-AGCTTCAACAGAACCCATTCGACGTTTACAGCAGCTTCAACAG
20165223 AACCCGATCC
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
69 20 0.35
70 37 0.65
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (69 bp):
AGCAGCTTCAACAGTTTACAGAGCTTCAACAGAACCCATTCGACGTTTACAGCAGCTTCAACAGT
TTGT
Found at i:20165450 original size:25 final size:25
Alignment explanation
Indices: 20165422--20165475 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
20165412 TTTTAAATAA
* **
20165422 GAATGCCTTAATTAAATACTTTTAT
1 GAATGCCTAAATTAAATACCCTTAT
20165447 GAATGCCTAAATTAAATACCCTTAT
1 GAATGCCTAAATTAAATACCCTTAT
20165472 GAAT
1 GAAT
20165476 ATTGTGGGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (25 bp):
GAATGCCTAAATTAAATACCCTTAT
Found at i:20169153 original size:12 final size:12
Alignment explanation
Indices: 20169138--20169164 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
20169128 ATTATTATTA
20169138 TTATTGTTGTTG
1 TTATTGTTGTTG
20169150 TTATTGTTGTTG
1 TTATTGTTGTTG
20169162 TTA
1 TTA
20169165 CTTGAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.11, C:0.00, G:0.22, T:0.67
Consensus pattern (12 bp):
TTATTGTTGTTG
Found at i:20169767 original size:291 final size:291
Alignment explanation
Indices: 20169243--20169826 Score: 1123
Period size: 291 Copynumber: 2.0 Consensus size: 291
20169233 GCTCGAATAA
20169243 TCGAGTATAAAAATCGAGCTTTTTTTTATATATTAATCGAGCTTAATCGAGCGAGCTCGAATAGC
1 TCGAGTATAAAAATCGAGCTTTTTTTTATATATTAATCGAGCTTAATCGAGCGAGCTCGAATAGC
* * *
20169308 TCGAATTTGATCACGAATCGAGTTCGAGCTTAAAAAATAAAACTTGATCGAGCTCGAACCGAGTA
66 TCGAATTCGATCACGAATCGAGTTCGAGCTTAAAAAATAAAACTTAATCGAGCTCGAACCGAATA
20169373 TCGAACCCTGAATTGTGAGTCGAGCTCGAGCTCGAGCTTCTCATTATTCGGCTCGGCTCGACTCG
131 TCGAACCCTGAATTGTGAGTCGAGCTCGAGCTCGAGCTTCTCATTATTCGGCTCGGCTCGACTCG
20169438 TTTACAGCCCTAGTCTCAACCCAAGTTAGATGAACTTCACCGGTTACAACTCCAAGCTTGAAATA
196 TTTACAGCCCTAGTCTCAACCCAAGTTAGATGAACTTCACCGGTTACAACTCCAAGCTTGAAATA
20169503 AACAACTAAATGTGATCTCTGTGACTTTCTT
261 AACAACTAAATGTGATCTCTGTGACTTTCTT
20169534 TCGAGTATAAAAATCGAGCTTTTTTTTATATATTAATCGAGCTTAATCGAGCGAGCTCGAATAGC
1 TCGAGTATAAAAATCGAGCTTTTTTTTATATATTAATCGAGCTTAATCGAGCGAGCTCGAATAGC
*
20169599 TCGAATTCGATCACGAATTGAGTTCGAGCTTAAAAAATAAAACTTAATCGAGCTCGAACCGAATA
66 TCGAATTCGATCACGAATCGAGTTCGAGCTTAAAAAATAAAACTTAATCGAGCTCGAACCGAATA
*
20169664 TCGAGCCCTGAATTGTGAGTCGAGCTCGAGCTCGAGCTTCTCATTATTCGGCTCGGCTCGACTCG
131 TCGAACCCTGAATTGTGAGTCGAGCTCGAGCTCGAGCTTCTCATTATTCGGCTCGGCTCGACTCG
20169729 TTTACAGCCCTAGTCTCAACCCAAGTTAGATGAACTTCACCGGTTACAACTCCAAGCTTGAAATA
196 TTTACAGCCCTAGTCTCAACCCAAGTTAGATGAACTTCACCGGTTACAACTCCAAGCTTGAAATA
20169794 AACAACTAAATGTGATCTCTGTGACTTTCTT
261 AACAACTAAATGTGATCTCTGTGACTTTCTT
20169825 TC
1 TC
20169827 ACTCATCTTT
Statistics
Matches: 288, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
291 288 1.00
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (291 bp):
TCGAGTATAAAAATCGAGCTTTTTTTTATATATTAATCGAGCTTAATCGAGCGAGCTCGAATAGC
TCGAATTCGATCACGAATCGAGTTCGAGCTTAAAAAATAAAACTTAATCGAGCTCGAACCGAATA
TCGAACCCTGAATTGTGAGTCGAGCTCGAGCTCGAGCTTCTCATTATTCGGCTCGGCTCGACTCG
TTTACAGCCCTAGTCTCAACCCAAGTTAGATGAACTTCACCGGTTACAACTCCAAGCTTGAAATA
AACAACTAAATGTGATCTCTGTGACTTTCTT
Found at i:20170103 original size:16 final size:16
Alignment explanation
Indices: 20170082--20170112 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20170072 GGCCTCTTTG
20170082 TTTTTTTCACTTTTTC
1 TTTTTTTCACTTTTTC
*
20170098 TTTTTTTGACTTTTT
1 TTTTTTTCACTTTTT
20170113 AAACTTCCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.06, C:0.13, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTTTTTCACTTTTTC
Found at i:20170244 original size:221 final size:221
Alignment explanation
Indices: 20169861--20170321 Score: 838
Period size: 221 Copynumber: 2.1 Consensus size: 221
20169851 CAACTAACAA
* * * *
20169861 TTTTTTTCACTTTATCCTTTTTTGACTTTTTAAACTTCCTTCTGTCTCTTTTTTTTTTTAACCTA
1 TTTTTTTCACTTTTTCTTTTTTTGACTTTTTAAACTTCCTTCTGTCTCTTTATTTTTTGAACCTA
* *
20169926 AACTATACTACTCGTAACTCCCTCCAAACTTTCCTTCTCTCTTTTATGGCAGGCCTTCCTCTATT
66 AACTATACTACCCGTAACTCCCCCCAAACTTTCCTTCTCTCTTTTATGGCAGGCCTTCCTCTATT
20169991 CTTCCTTCCTTTTCTCTTCCTCTTGTTTTTTTCTTTCCTCTCCCCTTTGCTTTCCACACCCCTCT
131 CTTCCTTCCTTTTCTCTTCCTCTTGTTTTTTTCTTTCCTCTCCCCTTTGCTTTCCACACCCCTCT
20170056 CCTCTCCATGTCAAAGGGCCTCTTTG
196 CCTCTCCATGTCAAAGGGCCTCTTTG
*
20170082 TTTTTTTCACTTTTTCTTTTTTTGACTTTTTAAACTTCCTTCTTTCTCTTTATTTTTTGAACCTA
1 TTTTTTTCACTTTTTCTTTTTTTGACTTTTTAAACTTCCTTCTGTCTCTTTATTTTTTGAACCTA
20170147 AACTATACTACCCGTAACTCCCCCCAAACTTTCCTTCTCTCTTTTATGGCAGGCCTTCCTCTATT
66 AACTATACTACCCGTAACTCCCCCCAAACTTTCCTTCTCTCTTTTATGGCAGGCCTTCCTCTATT
20170212 CTTCCTTCCTTTTCTCTTCCTCTTGTTTTTTTCTTTCCTCTCCCCTTTGCTTTCCACACCCCTCT
131 CTTCCTTCCTTTTCTCTTCCTCTTGTTTTTTTCTTTCCTCTCCCCTTTGCTTTCCACACCCCTCT
20170277 CCTCTCCATGTCAAAGGGCCTCTTTG
196 CCTCTCCATGTCAAAGGGCCTCTTTG
20170303 TTTTTTT---TTTTTCTTTTTT
1 TTTTTTTCACTTTTTCTTTTTT
20170322 GCTTTAACCA
Statistics
Matches: 233, Mismatches: 7, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
218 12 0.05
221 221 0.95
ACGTcount: A:0.12, C:0.31, G:0.06, T:0.51
Consensus pattern (221 bp):
TTTTTTTCACTTTTTCTTTTTTTGACTTTTTAAACTTCCTTCTGTCTCTTTATTTTTTGAACCTA
AACTATACTACCCGTAACTCCCCCCAAACTTTCCTTCTCTCTTTTATGGCAGGCCTTCCTCTATT
CTTCCTTCCTTTTCTCTTCCTCTTGTTTTTTTCTTTCCTCTCCCCTTTGCTTTCCACACCCCTCT
CCTCTCCATGTCAAAGGGCCTCTTTG
Found at i:20170892 original size:19 final size:19
Alignment explanation
Indices: 20170865--20170903 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
20170855 CAAATATCTA
20170865 GTGGATAAGATGAAGGACT
1 GTGGATAAGATGAAGGACT
* * *
20170884 GTGGGTAAGGTGAGGGACT
1 GTGGATAAGATGAAGGACT
20170903 G
1 G
20170904 ATGGCAGCTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.28, C:0.05, G:0.46, T:0.21
Consensus pattern (19 bp):
GTGGATAAGATGAAGGACT
Found at i:20178482 original size:13 final size:15
Alignment explanation
Indices: 20178453--20178484 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
20178443 TTAAGTTCAA
20178453 ATTTAATTAATAATT
1 ATTTAATTAATAATT
20178468 ATTT-ATTAA-AATT
1 ATTTAATTAATAATT
20178481 ATTT
1 ATTT
20178485 GAAATACACG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 5 0.29
15 4 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTTAATTAATAATT
Found at i:20179588 original size:31 final size:33
Alignment explanation
Indices: 20179538--20179599 Score: 85
Period size: 31 Copynumber: 1.9 Consensus size: 33
20179528 TTAAAATTTA
*
20179538 TTTTTATCAAAATTAATTT-A-TATTTTATAAT
1 TTTTTATCAAAATAAATTTAACTATTTTATAAT
20179569 TTTTTAT-AAAATAACATTTAACTATTTTATA
1 TTTTTATCAAAATAA-ATTTAACTATTTTATA
20179600 CATAATTGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 6 0.22
31 11 0.41
32 1 0.04
33 9 0.33
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (33 bp):
TTTTTATCAAAATAAATTTAACTATTTTATAAT
Found at i:20182066 original size:35 final size:35
Alignment explanation
Indices: 20182026--20182093 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
20182016 ATGGTGCTAT
20182026 TTTTGTCTGCTTACATCTGATGCATAACTGAATTA
1 TTTTGTCTGCTTACATCTGATGCATAACTGAATTA
*
20182061 TTTTGTCTGCTTATATCTGATGCATAACTGAAT
1 TTTTGTCTGCTTACATCTGATGCATAACTGAAT
20182094 AGGAAACTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.25, C:0.16, G:0.15, T:0.44
Consensus pattern (35 bp):
TTTTGTCTGCTTACATCTGATGCATAACTGAATTA
Found at i:20184027 original size:27 final size:28
Alignment explanation
Indices: 20183982--20184034 Score: 83
Period size: 27 Copynumber: 1.9 Consensus size: 28
20183972 CAATTATTTA
20183982 ATTTTTTTATAATATAATTATTTAAAGC
1 ATTTTTTTATAATATAATTATTTAAAGC
20184010 ATTTTCTTTATAA-A-AATTATTTAAA
1 ATTTT-TTTATAATATAATTATTTAAA
20184035 TAATAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
27 11 0.46
28 6 0.25
29 7 0.29
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (28 bp):
ATTTTTTTATAATATAATTATTTAAAGC
Found at i:20184048 original size:17 final size:18
Alignment explanation
Indices: 20184026--20184067 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
20184016 TTTATAAAAA
*
20184026 TTATTTAAATAATA-ATT
1 TTATTTAAAAAATATATT
*
20184043 TTATTTTAAAAAATATCTT
1 TTA-TTTAAAAAATATATT
20184062 TTATTT
1 TTATTT
20184068 TAATTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 3 0.14
18 13 0.62
19 5 0.24
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (18 bp):
TTATTTAAAAAATATATT
Found at i:20184050 original size:18 final size:19
Alignment explanation
Indices: 20184029--20184070 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
20184019 ATAAAAATTA
*
20184029 TTTAAATAATA-ATTTTAT
1 TTTAAAAAATATATTTTAT
*
20184047 TTTAAAAAATATCTTTTAT
1 TTTAAAAAATATATTTTAT
20184066 TTTAA
1 TTTAA
20184071 TTTTAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTAAAAAATATATTTTAT
Found at i:20184082 original size:30 final size:28
Alignment explanation
Indices: 20184038--20184094 Score: 69
Period size: 30 Copynumber: 2.0 Consensus size: 28
20184028 ATTTAAATAA
**
20184038 TAATTTTATTTTAAAAAATATCTTTTATTT
1 TAATTTTAAATTAAAAAAT-T-TTTTATTT
*
20184068 TAATTTTAAATTAAATAATTTTTTATT
1 TAATTTTAAATTAAAAAATTTTTTATT
20184095 AAAATGATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 7 0.29
29 1 0.04
30 16 0.67
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60
Consensus pattern (28 bp):
TAATTTTAAATTAAAAAATTTTTTATTT
Found at i:20184270 original size:15 final size:16
Alignment explanation
Indices: 20184250--20184279 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
20184240 TCGTTAAATA
20184250 ATTATTAAAT-TTAAT
1 ATTATTAAATATTAAT
20184265 ATTATTAAATATTAA
1 ATTATTAAATATTAA
20184280 AATCAACATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTATTAAATATTAAT
Found at i:20185041 original size:12 final size:12
Alignment explanation
Indices: 20185026--20185073 Score: 62
Period size: 12 Copynumber: 4.1 Consensus size: 12
20185016 AATTATTTAT
20185026 TTAAAATATAAA
1 TTAAAATATAAA
*
20185038 TTAAAAT-TTAA
1 TTAAAATATAAA
* *
20185049 TTTAAATACAAA
1 TTAAAATATAAA
20185061 TTAAAATATAAA
1 TTAAAATATAAA
20185073 T
1 T
20185074 ATTTATTTGA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
11 9 0.31
12 20 0.69
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (12 bp):
TTAAAATATAAA
Found at i:20185047 original size:23 final size:23
Alignment explanation
Indices: 20185020--20185067 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
20185010 TATGTTAATT
*
20185020 ATTT-ATTTAAAATATAAATTAAA
1 ATTTAATTT-AAATACAAATTAAA
20185043 ATTTAATTTAAATACAAATTAAA
1 ATTTAATTTAAATACAAATTAAA
20185066 AT
1 AT
20185068 ATAAATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
ATTTAATTTAAATACAAATTAAA
Found at i:20185096 original size:30 final size:30
Alignment explanation
Indices: 20185027--20185103 Score: 95
Period size: 30 Copynumber: 2.6 Consensus size: 30
20185017 ATTATTTATT
20185027 TAAAATATAAAT-TAAAATTTAATTTAAATA
1 TAAAATA-AAATATAAAATTTAATTTAAATA
* * *
20185057 CAAATTAAAATATAAATATTT-ATTTGAATA
1 TAAAATAAAATATAAA-ATTTAATTTAAATA
20185087 TAAAATAAAATATAAAA
1 TAAAATAAAATATAAAA
20185104 AAATTTCAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
29 5 0.12
30 31 0.77
31 4 0.10
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (30 bp):
TAAAATAAAATATAAAATTTAATTTAAATA
Found at i:20185134 original size:9 final size:9
Alignment explanation
Indices: 20185120--20185153 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
20185110 CAAGTAAAAG
20185120 AAAATTTAT
1 AAAATTTAT
20185129 AAAATTTAT
1 AAAATTTAT
*
20185138 AAAA-ATAT
1 AAAATTTAT
20185146 AAAATTTA
1 AAAATTTA
20185154 GAGAAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (9 bp):
AAAATTTAT
Found at i:20185604 original size:27 final size:27
Alignment explanation
Indices: 20185569--20185661 Score: 86
Period size: 27 Copynumber: 3.4 Consensus size: 27
20185559 TTTATGTCTT
20185569 AAAAATATTTTAAAAATTTTTATTTTA
1 AAAAATATTTTAAAAATTTTTATTTTA
*
20185596 AAAAATA-TTT-AAGA-TTTT-TTTTA
1 AAAAATATTTTAAAAATTTTTATTTTA
* *
20185619 CAGAAAACACTTTAAATAATAATTTTATTTTA
1 -A-AAAATATTTTAAA-AAT--TTTTATTTTA
20185651 AAAAATATTTT
1 AAAAATATTTT
20185662 TTATTTTTAT
Statistics
Matches: 52, Mismatches: 5, Indels: 15
0.72 0.07 0.21
Matches are distributed among these distances:
23 5 0.10
24 5 0.10
25 8 0.15
26 6 0.12
27 9 0.17
28 1 0.02
30 8 0.15
31 5 0.10
32 5 0.10
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.47
Consensus pattern (27 bp):
AAAAATATTTTAAAAATTTTTATTTTA
Found at i:20185652 original size:18 final size:19
Alignment explanation
Indices: 20185629--20185668 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
20185619 CAGAAAACAC
*
20185629 TTTAAATAATA-ATTTTAT
1 TTTAAAAAATATATTTTAT
*
20185647 TTTAAAAAATATTTTTTAT
1 TTTAAAAAATATATTTTAT
20185666 TTT
1 TTT
20185669 TATAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTAAAAAATATATTTTAT
Found at i:20185952 original size:22 final size:21
Alignment explanation
Indices: 20185926--20185992 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 21
20185916 ATAAAATAAA
20185926 ATAAAAAATTATCATTATATAT
1 ATAAAAAATTAT-ATTATATAT
*
20185948 ATAAAAATATTATAATA-AT-T
1 ATAAAAA-ATTATATTATATAT
20185968 ATATAAAAATTA-ATATATATAT
1 ATA-AAAAATTATAT-TATATAT
20185990 ATA
1 ATA
20185993 GATTCTCATA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
19 1 0.03
20 10 0.26
21 8 0.21
22 14 0.37
23 5 0.13
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (21 bp):
ATAAAAAATTATATTATATAT
Found at i:20186054 original size:17 final size:18
Alignment explanation
Indices: 20186020--20186055 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
20186010 GAATGAATCT
*
20186020 AAATAAAAAATATCTTAA
1 AAATAAAAAATATATTAA
20186038 AAATAAAAAA-ATATTAA
1 AAATAAAAAATATATTAA
20186055 A
1 A
20186056 TATTATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (18 bp):
AAATAAAAAATATATTAA
Found at i:20188323 original size:17 final size:17
Alignment explanation
Indices: 20188297--20188333 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
20188287 TAAGTATTTG
*
20188297 TTAATCAAATTATATTA
1 TTAATAAAATTATATTA
*
20188314 TTAATAAAATTTTATTA
1 TTAATAAAATTATATTA
20188331 TTA
1 TTA
20188334 TTATTACGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (17 bp):
TTAATAAAATTATATTA
Found at i:20190904 original size:4 final size:4
Alignment explanation
Indices: 20190895--20191004 Score: 52
Period size: 4 Copynumber: 28.2 Consensus size: 4
20190885 ATTTTATTAT
** * *
20190895 TTTA TTTA TTTA TAAA TATA TTTA -TTA -TTA -TTA TTTA TCTA TTAATA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT--TA
* * * * *
20190942 TATA TTTA -TTA TTTA TTAA TATA TTT- TTTA -TTA TTTA TCTA TTAA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* *
20190987 TGTA TTTT TTATA TTTA T
1 TTTA TTTA TT-TA TTTA T
20191005 CTATCAATGT
Statistics
Matches: 79, Mismatches: 20, Indels: 14
0.70 0.18 0.12
Matches are distributed among these distances:
3 18 0.23
4 55 0.70
5 3 0.04
6 3 0.04
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.65
Consensus pattern (4 bp):
TTTA
Found at i:20190926 original size:31 final size:31
Alignment explanation
Indices: 20190887--20190959 Score: 107
Period size: 31 Copynumber: 2.4 Consensus size: 31
20190877 TATTTTTAAT
*
20190887 TTTATTATT-TTATTTATTTA-TAA-ATATA
1 TTTATTATTATTATTTATCTATTAATATATA
20190915 TTTATTATTATTATTTATCTATTAATATATA
1 TTTATTATTATTATTTATCTATTAATATATA
20190946 TTTATTATTTATTA
1 TTTATTA-TTATTA
20190960 ATATATTTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 9 0.22
29 10 0.25
30 3 0.08
31 12 0.30
32 6 0.15
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.64
Consensus pattern (31 bp):
TTTATTATTATTATTTATCTATTAATATATA
Found at i:20190928 original size:25 final size:26
Alignment explanation
Indices: 20190891--20191031 Score: 96
Period size: 25 Copynumber: 5.5 Consensus size: 26
20190881 TTTAATTTTA
20190891 TTATT-TTATTTATTTATAAATATAT
1 TTATTATTATTTATTTATAAATATAT
**
20190916 TTATTATTA-TTATTTATCTAT-TA-
1 TTATTATTATTTATTTATAAATATAT
* *
20190939 ATATATATT-TATTATTTATTAATATAT
1 TTAT-TATTAT-TTATTTATAAATATAT
* * * *
20190966 TTTTTATTATTTATCTATTAATGTAT
1 TTATTATTATTTATTTATAAATATAT
* * *
20190992 TTTTTA-TATTTATCTATCAATGTATAT
1 TTATTATTATTTATTTAT-AA-ATATAT
20191019 TTATCTATTATTT
1 TTAT-TATTATTT
20191032 TTTTTTTATT
Statistics
Matches: 92, Mismatches: 13, Indels: 18
0.75 0.11 0.15
Matches are distributed among these distances:
23 3 0.03
24 6 0.07
25 36 0.39
26 30 0.33
27 10 0.11
28 2 0.02
29 5 0.05
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.63
Consensus pattern (26 bp):
TTATTATTATTTATTTATAAATATAT
Found at i:20191002 original size:47 final size:50
Alignment explanation
Indices: 20190892--20191004 Score: 146
Period size: 47 Copynumber: 2.3 Consensus size: 50
20190882 TTAATTTTAT
20190892 TATTTTATT-TATTTATAAATATATTTATTATTATTATTTATCTATTAATA
1 TATTTT-TTATATTTATAAATATATTTATTATTATTATTTATCTATTAATA
* * *
20190942 TA-TATTTATTATTTATTAATATA-TT-TT-TTATTATTTATCTATTAATG
1 TATTTTTTA-TATTTATAAATATATTTATTATTATTATTTATCTATTAATA
20190989 TATTTTTTATATTTAT
1 TATTTTTTATATTTAT
20191005 CTATCAATGT
Statistics
Matches: 56, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
47 28 0.50
48 9 0.16
49 4 0.07
50 15 0.27
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.65
Consensus pattern (50 bp):
TATTTTTTATATTTATAAATATATTTATTATTATTATTTATCTATTAATA
Found at i:20191796 original size:3 final size:3
Alignment explanation
Indices: 20191790--20191848 Score: 55
Period size: 3 Copynumber: 19.7 Consensus size: 3
20191780 TTTTTTTCTC
* * * * * * *
20191790 TTA TTA TTA TTA TTA TTA TTG TTG TTG TTG TTG TTG TTG TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
20191838 TTA TTA TTA TT
1 TTA TTA TTA TT
20191849 TATTGATTAG
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:20203530 original size:86 final size:86
Alignment explanation
Indices: 20203430--20203637 Score: 226
Period size: 86 Copynumber: 2.4 Consensus size: 86
20203420 GCATTTACTT
* *
20203430 TTTC-AAAGTTATGGTGCCTCTGTTTAGAGAAGCTTTATTA-TTTTTCAAAAGTCGTTAAGCCTC
1 TTTCAAAAGTCATGGTGCCTCTGTTTAGAGAAGCTTT-TTACTTTCTC-AAAGTCGTTAAGCCTC
*
20203493 TGATTAGAGGAGCTTTGTTTA-C
64 TGATTAGAGGAGCTTTATTTATC
* * ** * *
20203515 TTTCAAAAGTCATGGTTGCTTCTGTTTAAAGGAA-CAATTTACTTTCTCAAAGTCGTTGAGCTTC
1 TTTCAAAAGTCATGG-TGCCTCTGTTTAGA-GAAGCTTTTTACTTTCTCAAAGTCGTTAAGCCTC
* *
20203579 TGTTTAGAGGAGCTTTATTTATT
64 TGATTAGAGGAGCTTTATTTATC
* * *
20203602 TTTCAAAAGTCATTGAGCCTCTGTTTAGAGGAGCTT
1 TTTCAAAAGTCATGGTGCCTCTGTTTAGAGAAGCTT
20203638 ACCTCTGTTT
Statistics
Matches: 99, Mismatches: 18, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
85 6 0.06
86 57 0.58
87 33 0.33
88 3 0.03
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.41
Consensus pattern (86 bp):
TTTCAAAAGTCATGGTGCCTCTGTTTAGAGAAGCTTTTTACTTTCTCAAAGTCGTTAAGCCTCTG
ATTAGAGGAGCTTTATTTATC
Found at i:20203612 original size:44 final size:44
Alignment explanation
Indices: 20203422--20203637 Score: 201
Period size: 44 Copynumber: 5.0 Consensus size: 44
20203412 GTCAAGGAGC
* * * *
20203422 ATTTACTTTTTC-AAAGTTATGGTGCCTCTGTTTAGAGAAGCTTT
1 ATTTA-TTTTTCAAAAGTCATTGAGCCTCTGTTTAGAGGAGCTTT
* * *
20203466 A-TTATTTTTCAAAAGTCGTTAAGCCTCTGATTAGAGGAGCTTT
1 ATTTATTTTTCAAAAGTCATTGAGCCTCTGTTTAGAGGAGCTTT
* * * * * * * *
20203509 GTTTA-CTTTCAAAAGTCATGGTTGCTTCTGTTTAAAGGAAC--A
1 ATTTATTTTTCAAAAGTCATTG-AGCCTCTGTTTAGAGGAGCTTT
* * *
20203551 ATTTACTTTCTC-AAAGTCGTTGAGCTTCTGTTTAGAGGAGCTTT
1 ATTTA-TTTTTCAAAAGTCATTGAGCCTCTGTTTAGAGGAGCTTT
20203595 ATTTATTTTTCAAAAGTCATTGAGCCTCTGTTTAGAGGAGCTT
1 ATTTATTTTTCAAAAGTCATTGAGCCTCTGTTTAGAGGAGCTT
20203638 ACCTCTGTTT
Statistics
Matches: 134, Mismatches: 30, Indels: 16
0.74 0.17 0.09
Matches are distributed among these distances:
42 26 0.19
43 53 0.40
44 55 0.41
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.42
Consensus pattern (44 bp):
ATTTATTTTTCAAAAGTCATTGAGCCTCTGTTTAGAGGAGCTTT
Found at i:20203644 original size:20 final size:20
Alignment explanation
Indices: 20203619--20203657 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
20203609 AGTCATTGAG
*
20203619 CCTCTGTTTAGAGGAGCTTA
1 CCTCTGTTTAAAGGAGCTTA
20203639 CCTCTGTTTAAAGGAGCTT
1 CCTCTGTTTAAAGGAGCTT
20203658 TGTTTATCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.36
Consensus pattern (20 bp):
CCTCTGTTTAAAGGAGCTTA
Found at i:20203689 original size:65 final size:64
Alignment explanation
Indices: 20203577--20203702 Score: 207
Period size: 65 Copynumber: 2.0 Consensus size: 64
20203567 TCGTTGAGCT
*
20203577 TCTGTTTAGAGGAGCTTTATTTATTTTTCAAAAGTCATTGAGCCTCTGTTTAGAGGAGCTTACC
1 TCTGTTTAAAGGAGCTTTATTTATTTTTCAAAAGTCATTGAGCCTCTGTTTAGAGGAGCTTACC
* **
20203641 TCTGTTTAAAGGAGCTTTGTTTATCTTTTCAAAAGTTGTTGAGCCTCTGTTTAGAGGAGCTT
1 TCTGTTTAAAGGAGCTTTATTTAT-TTTTCAAAAGTCATTGAGCCTCTGTTTAGAGGAGCTT
20203703 TATTTATTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
64 22 0.39
65 35 0.61
ACGTcount: A:0.22, C:0.14, G:0.21, T:0.42
Consensus pattern (64 bp):
TCTGTTTAAAGGAGCTTTATTTATTTTTCAAAAGTCATTGAGCCTCTGTTTAGAGGAGCTTACC
Found at i:20203703 original size:45 final size:43
Alignment explanation
Indices: 20203639--20203968 Score: 349
Period size: 45 Copynumber: 7.5 Consensus size: 43
20203629 GAGGAGCTTA
* *
20203639 CCTCTGTTTAAAGGAGCTTTGTTTATCTTTTCAAAAGTTGTTGAG
1 CCTCTGTTTAGAGGAGCTTTGTTTAT-TTTTC-AAAGTCGTTGAG
* *
20203684 CCTCTGTTTAGAGGAGCTTTATTTATTTTTCAAAGTCGTTGAA
1 CCTCTGTTTAGAGGAGCTTTGTTTATTTTTCAAAGTCGTTGAG
* * *
20203727 CCTCTGTTTAGAAGAGCTTTGTTTATATTTCTAAAAGTCATTGAG
1 CCTCTGTTTAGAGGAGCTTTGTTTAT-TTT-TCAAAGTCGTTGAG
* * * *
20203772 CCTCTGATTAGAAGAGCTTTGTTTACTTTTTCAAAGTCGTGGTTG
1 CCTCTGTTTAGAGGAGCTTTGTTTA-TTTTTCAAAGTCGTTG-AG
* ** *
20203817 CCTCTGTTTAAAGGAGC--AATTTATTTTTCAAAGTCATTGAG
1 CCTCTGTTTAGAGGAGCTTTGTTTATTTTTCAAAGTCGTTGAG
* * * *
20203858 CCTCTGATTAGAGGAGCTGTATTTATATTTTCCAAAGTCATTGAG
1 CCTCTGTTTAGAGGAGCTTTGTTTAT-TTTT-CAAAGTCGTTGAG
* *
20203903 CCTCTGTTTAGATGAGCTTTGTTTATGTTTCTTAAAGTCGTTGAG
1 CCTCTGTTTAGAGGAGCTTTGTTTAT-TTT-TCAAAGTCGTTGAG
**
20203948 CCTCTACTTAGAGGAGCTTTG
1 CCTCTGTTTAGAGGAGCTTTG
20203969 ATCAAAATTT
Statistics
Matches: 241, Mismatches: 35, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
41 16 0.07
42 14 0.06
43 44 0.18
44 21 0.09
45 144 0.60
46 2 0.01
ACGTcount: A:0.23, C:0.15, G:0.20, T:0.42
Consensus pattern (43 bp):
CCTCTGTTTAGAGGAGCTTTGTTTATTTTTCAAAGTCGTTGAG
Found at i:20203789 original size:88 final size:86
Alignment explanation
Indices: 20203638--20203967 Score: 362
Period size: 88 Copynumber: 3.7 Consensus size: 86
20203628 AGAGGAGCTT
** *
20203638 ACCTCTGTTTAAAGGAGCTTTGTTTATCTTTTCAAAAGTTGTTGAGCCTCTGTTTAGAGGAGCTT
1 ACCTCTGTTTAAAGGAGCTTTGTTTAT-TTTT-AAAAGTCATTGAGCCTCTGATTAGAGGAGCTT
20203703 TATTTATTTTTCAAAGTCGTTGA
64 TATTTATTTTTCAAAGTCGTTGA
*
20203726 ACCTCTGTTTAGAA-GAGCTTTGTTTATATTTCTAAAAGTCATTGAGCCTCTGATTAGAAGAGCT
1 ACCTCTGTTTA-AAGGAGCTTTGTTTAT-TTT-TAAAAGTCATTGAGCCTCTGATTAGAGGAGCT
* * *
20203790 TTGTTTACTTTTTCAAAGTCGTGGTT
63 TTATTTA-TTTTTCAAAGTCGTTG-A
* ** * *
20203816 GCCTCTGTTTAAAGGAGC--AATTTATTTTTCAAAGTCATTGAGCCTCTGATTAGAGGAGCTGTA
1 ACCTCTGTTTAAAGGAGCTTTGTTTATTTTTAAAAGTCATTGAGCCTCTGATTAGAGGAGCTTTA
*
20203879 TTTATATTTTCCAAAGTCATTGA
66 TTTAT-TTTT-CAAAGTCGTTGA
* * * * *
20203902 GCCTCTGTTTAGATGAGCTTTGTTTATGTTTCTTAAAGTCGTTGAGCCTCT-ACTTAGAGGAGCT
1 ACCTCTGTTTAAAGGAGCTTTGTTTAT-TTT-TAAAAGTCATTGAGCCTCTGA-TTAGAGGAGCT
20203966 TT
63 TT
20203968 GATCAAAATT
Statistics
Matches: 205, Mismatches: 25, Indels: 22
0.81 0.10 0.09
Matches are distributed among these distances:
85 1 0.00
86 55 0.27
87 12 0.06
88 70 0.34
89 24 0.12
90 43 0.21
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.42
Consensus pattern (86 bp):
ACCTCTGTTTAAAGGAGCTTTGTTTATTTTTAAAAGTCATTGAGCCTCTGATTAGAGGAGCTTTA
TTTATTTTTCAAAGTCGTTGA
Found at i:20203963 original size:131 final size:130
Alignment explanation
Indices: 20203639--20203965 Score: 390
Period size: 131 Copynumber: 2.5 Consensus size: 130
20203629 GAGGAGCTTA
*
20203639 CCTCTGTTTA-AAGGAGCTTTGTTTATCTTTTCAAAAGTTGTTGAGCCTCTGTTTAGAGGAGCTT
1 CCTCTGTTTAGAA-GAGCTTTGTTTAT-TTTT-AAAAGTCGTTGAGCCTCTGTTTAGAGGAGC-T
* * * * *
20203703 TATTTATTTTTCAAAGTCGTTGAACCTCTGTTTAGAAGAGCTTTGTTTATATTTCTAAAAGTCAT
62 AATTTATTTTTCAAAGTCATTGAACCTCTGATTAGAAGAGCTGTATTTATATTTCTAAAAGTCAT
20203768 TGAG
127 TGAG
* * * * *
20203772 CCTCTGATTAGAAGAGCTTTGTTTACTTTTTCAAAGTCGTGGTTGCCTCTGTTTAAAGGAGC-AA
1 CCTCTGTTTAGAAGAGCTTTGTTTA-TTTTTAAAAGTCGTTG-AGCCTCTGTTTAGAGGAGCTAA
* * *
20203836 TTTATTTTTCAAAGTCATTGAGCCTCTGATTAGAGGAGCTGTATTTATATTT-TCCAAAGTCATT
64 TTTATTTTTCAAAGTCATTGAACCTCTGATTAGAAGAGCTGTATTTATATTTCT-AAAAGTCATT
20203900 GAG
128 GAG
* * **
20203903 CCTCTGTTTAGATGAGCTTTGTTTATGTTTCTTAAAGTCGTTGAGCCTCTACTTAGAGGAGCT
1 CCTCTGTTTAGAAGAGCTTTGTTTAT-TTT-TAAAAGTCGTTGAGCCTCTGTTTAGAGGAGCT
20203966 TTGATCAAAA
Statistics
Matches: 165, Mismatches: 22, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
130 2 0.01
131 100 0.61
132 18 0.11
133 42 0.25
134 3 0.02
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.42
Consensus pattern (130 bp):
CCTCTGTTTAGAAGAGCTTTGTTTATTTTTAAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTAATT
TATTTTTCAAAGTCATTGAACCTCTGATTAGAAGAGCTGTATTTATATTTCTAAAAGTCATTGAG
Found at i:20204187 original size:12 final size:12
Alignment explanation
Indices: 20204178--20204416 Score: 59
Period size: 14 Copynumber: 18.8 Consensus size: 12
20204168 TTTGTATTTG
20204178 TATTTTTATTAT
1 TATTTTTATTAT
20204190 TATTTTT-TTA-
1 TATTTTTATTAT
* * *
20204200 T-TTATAAATAT
1 TATTTTTATTAT
20204211 ATAGTTTTTATTAT
1 -TA-TTTTTATTAT
*
20204225 TATTTATCTATTAA
1 TATTT-T-TATTAT
* * *
20204239 TATATATACGTTTT
1 TATTTTTA--TTAT
*
20204253 TATTGTTTATTAA
1 TATT-TTTATTAT
20204266 TATATTTT-TTAT
1 TAT-TTTTATTAT
20204278 TATTTATCTATTAAT
1 TATTT-T-TATT-AT
20204293 GTATATTTT-TTA-
1 -TAT-TTTTATTAT
20204305 TA--TTTATCTAT
1 TATTTTTAT-TAT
*
20204316 TATTTTTATTTT
1 TATTTTTATTAT
*
20204328 TATTTATCTATTAA
1 TATTT-T-TATTAT
20204342 TA-TTTT-TTA-
1 TATTTTTATTAT
*
20204351 TATTTATCTATCAAT
1 TATTT-T-TAT-TAT
*
20204366 GTATATTTATCTAT
1 -TATTTTTAT-TAT
* *
20204380 TACTATTATTAT
1 TATTTTTATTAT
20204392 TATATTATTATTAT
1 TAT-TT-TTATTAT
20204406 TATTATTTATT
1 TATT-TTTATT
20204417 TTTTGGTTGG
Statistics
Matches: 166, Mismatches: 27, Indels: 67
0.64 0.10 0.26
Matches are distributed among these distances:
8 3 0.02
9 6 0.04
10 10 0.06
11 11 0.07
12 34 0.20
13 35 0.21
14 50 0.30
15 7 0.04
16 8 0.05
17 2 0.01
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (12 bp):
TATTTTTATTAT
Found at i:20204226 original size:35 final size:34
Alignment explanation
Indices: 20204180--20204256 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 34
20204170 TGTATTTGTA
* *
20204180 TTTTTATTATTATTTTTTTATTTATAAATATATA-G
1 TTTTTATTATTATTTATCTA-TTA-AAATATATACG
*
20204215 TTTTTATTATTATTTATCTATTAATATATATACG
1 TTTTTATTATTATTTATCTATTAAAATATATACG
20204249 TTTTTATT
1 TTTTTATT
20204257 GTTTATTAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
33 8 0.21
34 12 0.32
35 18 0.47
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (34 bp):
TTTTTATTATTATTTATCTATTAAAATATATACG
Found at i:20204289 original size:8 final size:7
Alignment explanation
Indices: 20204251--20204416 Score: 60
Period size: 8 Copynumber: 22.9 Consensus size: 7
20204241 TATATACGTT
*
20204251 TTTATTG
1 TTTATTA
20204258 TTTATTAA
1 TTTATT-A
* *
20204266 TATATTT
1 TTTATTA
20204273 TTTATTA
1 TTTATTA
20204280 TTTATCTA
1 TTTAT-TA
*
20204288 TTAATGTA
1 TTTAT-TA
20204296 TATT-TT-
1 T-TTATTA
20204302 TTATATTTA
1 TT-TA-TTA
*
20204311 TCTATTA
1 TTTATTA
20204318 TTT-TTA
1 TTTATTA
20204324 TTT-TTA
1 TTTATTA
20204330 TTTATCTA
1 TTTAT-TA
*
20204338 TTAATATTT
1 TT--TATTA
20204347 TTTA-TA
1 TTTATTA
20204353 TTTATCTA
1 TTTAT-TA
**
20204361 TCAATGTA
1 TTTAT-TA
*
20204369 TAT-TTA
1 TTTATTA
*
20204375 TCTATTA
1 TTTATTA
20204382 CTATTATTA
1 -T-TTATTA
20204391 TTATATTA
1 TT-TATTA
20204399 -TTATTA
1 TTTATTA
20204405 -TTATTA
1 TTTATTA
20204411 TTTATT
1 TTTATT
20204417 TTTTGGTTGG
Statistics
Matches: 122, Mismatches: 19, Indels: 36
0.69 0.11 0.20
Matches are distributed among these distances:
5 1 0.01
6 34 0.28
7 36 0.30
8 38 0.31
9 10 0.08
10 3 0.02
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (7 bp):
TTTATTA
Found at i:20204298 original size:53 final size:50
Alignment explanation
Indices: 20204215--20204360 Score: 169
Period size: 53 Copynumber: 2.9 Consensus size: 50
20204205 AAATATATAG
*
20204215 TTTTTATTATTATTTATCTATTAATATATATACGTTTTTATTGTTTAT-TAATA
1 TTTTTATTATTATTTATCTATTAATATATAT---TTTTTA-TATTTATCTAATA
* *
20204268 TATTTT-TTATTATTTATCTATTAATGTATATTTTTTATATTTATCTATTA
1 T-TTTTATTATTATTTATCTATTAATATATATTTTTTATATTTATCTAATA
*
20204318 TTTTTATTTTTATTTATCTA-T--TA-ATATTTTTTATATTTATCTA
1 TTTTTATTATTATTTATCTATTAATATATATTTTTTATATTTATCTA
20204361 TCAATGTATA
Statistics
Matches: 85, Mismatches: 5, Indels: 13
0.83 0.05 0.13
Matches are distributed among these distances:
46 20 0.24
47 1 0.01
49 11 0.13
50 24 0.28
53 25 0.29
54 4 0.05
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (50 bp):
TTTTTATTATTATTTATCTATTAATATATATTTTTTATATTTATCTAATA
Found at i:20204309 original size:27 final size:26
Alignment explanation
Indices: 20204216--20204373 Score: 131
Period size: 23 Copynumber: 6.1 Consensus size: 26
20204206 AATATATAGT
20204216 TTTTATTATTATTTATCTATTAATATATA
1 TTTT-TTA-TATTTATCTATTAAT-TATA
*
20204245 TACGTTTTTAT-TGT-T-TATTAA-TATA
1 T---TTTTTATATTTATCTATTAATTATA
20204270 TTTTTTATTATTTATCTATTAATGTATA
1 TTTTTTA-TATTTATCTATTAAT-TATA
20204298 TTTTTTATATTTATCTATT-ATT-T-
1 TTTTTTATATTTATCTATTAATTATA
20204321 TTATTTT-TATTTATCTATT-A--ATA
1 TT-TTTTATATTTATCTATTAATTATA
*
20204344 TTTTTTATATTTATCTATCAATGTATA
1 TTTTTTATATTTATCTATTAAT-TATA
20204371 TTT
1 TTT
20204374 ATCTATTACT
Statistics
Matches: 109, Mismatches: 3, Indels: 36
0.74 0.02 0.24
Matches are distributed among these distances:
22 11 0.10
23 29 0.27
24 8 0.07
25 7 0.06
26 8 0.07
27 24 0.22
28 12 0.11
29 3 0.03
30 1 0.01
31 3 0.03
32 3 0.03
ACGTcount: A:0.28, C:0.04, G:0.03, T:0.65
Consensus pattern (26 bp):
TTTTTTATATTTATCTATTAATTATA
Found at i:20204334 original size:23 final size:23
Alignment explanation
Indices: 20204277--20204419 Score: 84
Period size: 23 Copynumber: 6.1 Consensus size: 23
20204267 ATATTTTTTA
20204277 TTATTTATCTATTAATGTATATT-TTT
1 TTATTTATCTATT-AT-T-T-TTATTT
20204303 TATATTTATCTATTATTTTTATTT
1 T-TATTTATCTATTATTTTTATTT
*
20204327 TTATTTATCTATTAATATTT-TTT
1 TTATTTATCTATT-ATTTTTATTT
* * * *
20204350 ATATTTATCTATCAATGTATATTT
1 TTATTTATCTAT-TATTTTTATTT
* *
20204374 ATCTA-TTA-CTATTATTATTA-TA
1 -T-TATTTATCTATTATTTTTATTT
20204396 TTA-TTAT-TATTATTATTTATTT
1 TTATTTATCTATTATT-TTTATTT
20204418 TT
1 TT
20204420 TGGTTGGTTT
Statistics
Matches: 94, Mismatches: 13, Indels: 24
0.72 0.10 0.18
Matches are distributed among these distances:
20 12 0.13
21 4 0.04
22 4 0.04
23 36 0.38
24 17 0.18
25 4 0.04
26 5 0.05
27 12 0.13
ACGTcount: A:0.29, C:0.05, G:0.01, T:0.65
Consensus pattern (23 bp):
TTATTTATCTATTATTTTTATTT
Found at i:20204391 original size:3 final size:3
Alignment explanation
Indices: 20204372--20204412 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
20204362 CAATGTATAT
*
20204372 TTA TCTA TTA CTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TT
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
20204413 TATTTTTTGG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:20204397 original size:17 final size:17
Alignment explanation
Indices: 20204377--20204411 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
20204367 TATATTTATC
20204377 TATTACTATTATTATTA
1 TATTACTATTATTATTA
*
20204394 TATTATTATTATTATTA
1 TATTACTATTATTATTA
20204411 T
1 T
20204412 TTATTTTTTG
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:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (17 bp):
TATTACTATTATTATTA
Found at i:20204415 original size:27 final size:26
Alignment explanation
Indices: 20204184--20204416 Score: 88
Period size: 27 Copynumber: 8.8 Consensus size: 26
20204174 TTTGTATTTT
* * *
20204184 TATTATTATTTTTTTATTTATAAATA
1 TATTATTATTTTATTATTTATTATTA
*
20204210 TA-TAGTTTTTATTATTATTTATCTATTA
1 TATTA-TTATT-TTATTATTTAT-TATTA
*
20204238 -ATATATATACGTTT-TTATTGT-TTATTA
1 TAT-TAT-TA-TTTTATTATT-TATTATTA
20204265 -ATATATT-TTTTATTATTTATCTATTA
1 TAT-TATTATTTTATTATTTAT-TATTA
*
20204291 -ATGTA-TATTTTTTATATTTATCTATTA
1 TAT-TATTATTTTAT-TATTTAT-TATTA
20204318 T-TT-TTA-TTT-TTATTTATCTATTA
1 TATTATTATTTTATTATTTAT-TATTA
*
20204341 -A-TATT-TTTTA-TATTTATCTATCA
1 TATTATTATTTTATTATTTAT-TATTA
20204364 -ATGTA-TATTTATCTATTACTATTATTATTA
1 TAT-TATTA-TT-T-TATTA-T-TTATTATTA
20204394 TATTATTATTATTATTATTTATT
1 TATTATTATT-TTATTATTTATT
20204417 TTTTGGTTGG
Statistics
Matches: 166, Mismatches: 11, Indels: 59
0.70 0.05 0.25
Matches are distributed among these distances:
22 1 0.01
23 31 0.19
24 6 0.04
25 14 0.08
26 26 0.16
27 42 0.25
28 13 0.08
29 13 0.08
30 12 0.07
31 8 0.05
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (26 bp):
TATTATTATTTTATTATTTATTATTA
Found at i:20205203 original size:15 final size:16
Alignment explanation
Indices: 20205173--20205208 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
20205163 GTTTTCTTTT
20205173 TTATTTACTATTATTA
1 TTATTTACTATTATTA
*
20205189 TTATTT-CTTTTATTA
1 TTATTTACTATTATTA
20205204 TTATT
1 TTATT
20205209 ATTATTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (16 bp):
TTATTTACTATTATTA
Found at i:20205205 original size:21 final size:21
Alignment explanation
Indices: 20205176--20205215 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
20205166 TTCTTTTTTA
20205176 TTTACTATTATTATTATTTCT
1 TTTACTATTATTATTATTTCT
*
20205197 TTTATTATTATTATTATTT
1 TTTACTATTATTATTATTT
20205216 ATTGATTAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTACTATTATTATTATTTCT
Found at i:20205405 original size:57 final size:57
Alignment explanation
Indices: 20205297--20205509 Score: 345
Period size: 58 Copynumber: 3.7 Consensus size: 57
20205287 AAATTCCAAA
* *
20205297 AAAAAATATTTTTAAGGAAAAGTTGAAAGCATCAATTTTCCTTGAAAATAAGTTTTCT
1 AAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTT-TTTGAAAATAAGTTTTCT
* * *
20205355 AAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTTTCAAAATAAGTTTTCT
1 AAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTTTTGAAAATAAGTTTTCT
* *
20205412 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGTTTTTT
1 AAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTT-TTGAAAATAAGTTTTCT
20205470 AAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTT
1 AAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTT
20205510 CTTGTATAAA
Statistics
Matches: 145, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
57 55 0.38
58 90 0.62
ACGTcount: A:0.44, C:0.05, G:0.12, T:0.39
Consensus pattern (57 bp):
AAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTTTTGAAAATAAGTTTTCT
Found at i:20205448 original size:115 final size:115
Alignment explanation
Indices: 20205297--20205509 Score: 372
Period size: 115 Copynumber: 1.9 Consensus size: 115
20205287 AAATTCCAAA
20205297 AAAAAATATTTTTAAGGAAAAGTTGAAAGCATCAATTTTCCTTGAAAATAAGTTTTCTAAAAAAT
1 AAAAAATATTTTTAAGGAAAAGTTGAAAGCATCAATTTTCCTTGAAAATAAGTTTTCTAAAAAAT
*
20205362 ATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTTTCAAAATAAGTTTTCT
66 ATTTTTAAGAAAAAGTTGAAAGTATCAATTTTTTTCAAAATAAGTTTTCT
* * * *
20205412 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGTTTTTTAAAAAAT
1 AAAAAATATTTTTAAGGAAAAGTTGAAAGCATCAATTTTCCTTGAAAATAAGTTTTCTAAAAAAT
*
20205477 ATTTTTAAGGAAAAGTTGAAAGTATCAATTTTT
66 ATTTTTAAGAAAAAGTTGAAAGTATCAATTTTT
20205510 CTTGTATAAA
Statistics
Matches: 92, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
115 92 1.00
ACGTcount: A:0.44, C:0.05, G:0.12, T:0.39
Consensus pattern (115 bp):
AAAAAATATTTTTAAGGAAAAGTTGAAAGCATCAATTTTCCTTGAAAATAAGTTTTCTAAAAAAT
ATTTTTAAGAAAAAGTTGAAAGTATCAATTTTTTTCAAAATAAGTTTTCT
Found at i:20209040 original size:2 final size:2
Alignment explanation
Indices: 20209033--20209059 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20209023 TTGAGTGGTA
20209033 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
20209060 ATAAAAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20212468 original size:24 final size:22
Alignment explanation
Indices: 20212441--20212491 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
20212431 ATTTGCAAAT
*
20212441 TTTTTATTAAAAATAATTAAAAAA
1 TTTTAATT-AAAA-AATTAAAAAA
* *
20212465 TTTTAATTGATAAATTAAAAAA
1 TTTTAATTAAAAAATTAAAAAA
20212487 TTTTA
1 TTTTA
20212492 TTGCATAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 15 0.62
23 2 0.08
24 7 0.29
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
TTTTAATTAAAAAATTAAAAAA
Found at i:20212484 original size:21 final size:22
Alignment explanation
Indices: 20212455--20212504 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
20212445 TATTAAAAAT
20212455 AATTAAAAAATTTTAATTG-ATA
1 AATTAAAAAATTTT-ATTGCATA
20212477 AATTAAAAAATTTTATTGCATA
1 AATTAAAAAATTTTATTGCATA
20212499 AATTAA
1 AATTAA
20212505 GTGACAGGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 4 0.15
22 23 0.85
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (22 bp):
AATTAAAAAATTTTATTGCATA
Found at i:20215541 original size:17 final size:17
Alignment explanation
Indices: 20215521--20215558 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
20215511 TTAAAAATCG
20215521 AAATAAGATAAATA-AAA
1 AAAT-AGATAAATATAAA
*
20215538 AAATATATAAATATAAA
1 AAATAGATAAATATAAA
20215555 AAAT
1 AAAT
20215559 TAAATTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (17 bp):
AAATAGATAAATATAAA
Done.