Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 64 of 203
Found at i:20511918 original size:93 final size:93
Alignment explanation
Indices: 20511805--20512176 Score: 701
Period size: 93 Copynumber: 4.0 Consensus size: 93
20511795 CACTCATGAC
* * *
20511805 TTTCAAAAGAAGGTATATATGCTTAGCAAATAC-ATTATAATGGTAATTTGAAAAGCTAGTATTC
1 TTTCAAAAGAATGTATATATGCTTAGCAAATACAATCA-AATGGTCATTTGAAAAGCTAGTATTC
20511869 AAGATTCAATACATAGAATATTAGATATT
65 AAGATTCAATACATAGAATATTAGATATT
20511898 TTTCAAAAGAATGTATATATGCTTAGCAAATACAATCAAATGGTCATTTGAAAAGCTAGTATTCA
1 TTTCAAAAGAATGTATATATGCTTAGCAAATACAATCAAATGGTCATTTGAAAAGCTAGTATTCA
20511963 AGATTCAATACATAGAATATTAGATATT
66 AGATTCAATACATAGAATATTAGATATT
20511991 TTTCAAAAGAATGTATATATGCTTAGCAAATACAATCAAATGGTCATTTGAAAAGCTAGTATTCA
1 TTTCAAAAGAATGTATATATGCTTAGCAAATACAATCAAATGGTCATTTGAAAAGCTAGTATTCA
20512056 AGATTCAATACATAGAATATTAGATATT
66 AGATTCAATACATAGAATATTAGATATT
20512084 TTTCAAAAGAATGTATATATGCTTAGCAAATACAATCAAATGGTCATTTGAAAAGCTAGTATTCA
1 TTTCAAAAGAATGTATATATGCTTAGCAAATACAATCAAATGGTCATTTGAAAAGCTAGTATTCA
20512149 AGATTCAATACATAGAATATTAGATATT
66 AGATTCAATACATAGAATATTAGATATT
20512177 ATGTGATGTT
Statistics
Matches: 275, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
93 272 0.99
94 3 0.01
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (93 bp):
TTTCAAAAGAATGTATATATGCTTAGCAAATACAATCAAATGGTCATTTGAAAAGCTAGTATTCA
AGATTCAATACATAGAATATTAGATATT
Found at i:20519612 original size:32 final size:32
Alignment explanation
Indices: 20519571--20519632 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
20519561 CATCTATTTT
20519571 CATTGTTCAACTCTTTGACAACACGAAAAATC
1 CATTGTTCAACTCTTTGACAACACGAAAAATC
*
20519603 CATTGTTCAACTCTTTGACAACATGAAAAA
1 CATTGTTCAACTCTTTGACAACACGAAAAA
20519633 ACCAAAAGCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.39, C:0.23, G:0.10, T:0.29
Consensus pattern (32 bp):
CATTGTTCAACTCTTTGACAACACGAAAAATC
Found at i:20525683 original size:21 final size:21
Alignment explanation
Indices: 20525659--20525702 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
20525649 GAATCTTTAG
*
20525659 TATTTATTGTATCATTT-TATT
1 TATTTAAT-TATCATTTCTATT
*
20525680 TATTTAATTATCCTTTCTATT
1 TATTTAATTATCATTTCTATT
20525701 TA
1 TA
20525703 ATTAGGTCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.25, C:0.09, G:0.02, T:0.64
Consensus pattern (21 bp):
TATTTAATTATCATTTCTATT
Found at i:20526174 original size:27 final size:27
Alignment explanation
Indices: 20526144--20526198 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
20526134 AATTTTGAAT
20526144 TCTAAAAATATGTCTTGATTTATTTTC
1 TCTAAAAATATGTCTTGATTTATTTTC
20526171 TCTAAAAATATGTCTTGATTTATTTTC
1 TCTAAAAATATGTCTTGATTTATTTTC
20526198 T
1 T
20526199 TATATTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.11, G:0.07, T:0.53
Consensus pattern (27 bp):
TCTAAAAATATGTCTTGATTTATTTTC
Found at i:20528566 original size:45 final size:45
Alignment explanation
Indices: 20528512--20528633 Score: 244
Period size: 45 Copynumber: 2.7 Consensus size: 45
20528502 GTATATTTAT
20528512 TTTTAACTAATAATTGTAAATTAAAATAATTATAATTATCACAAA
1 TTTTAACTAATAATTGTAAATTAAAATAATTATAATTATCACAAA
20528557 TTTTAACTAATAATTGTAAATTAAAATAATTATAATTATCACAAA
1 TTTTAACTAATAATTGTAAATTAAAATAATTATAATTATCACAAA
20528602 TTTTAACTAATAATTGTAAATTAAAATAATTA
1 TTTTAACTAATAATTGTAAATTAAAATAATTA
20528634 AAATAACTAT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 77 1.00
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (45 bp):
TTTTAACTAATAATTGTAAATTAAAATAATTATAATTATCACAAA
Found at i:20528577 original size:20 final size:20
Alignment explanation
Indices: 20528554--20528623 Score: 52
Period size: 22 Copynumber: 3.2 Consensus size: 20
20528544 TAATTATCAC
20528554 AAATTTTAACTAATAATTGT
1 AAATTTTAACTAATAATTGT
* * *
20528574 AAATTAAAATAA-TTATAATTAT
1 AAATT---TTAACTAATAATTGT
20528596 CACAAATTTTAACTAATAATTGT
1 ---AAATTTTAACTAATAATTGT
20528619 AAATT
1 AAATT
20528624 AAAATAATTA
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
20 10 0.27
22 11 0.30
23 11 0.30
25 5 0.14
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (20 bp):
AAATTTTAACTAATAATTGT
Found at i:20529547 original size:3 final size:3
Alignment explanation
Indices: 20529539--20529564 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
20529529 AAATCAATGT
20529539 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
20529565 TATTAAATCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:20532290 original size:39 final size:37
Alignment explanation
Indices: 20532247--20532330 Score: 96
Period size: 37 Copynumber: 2.2 Consensus size: 37
20532237 TAAGTGAAAG
* *
20532247 TTATAAAAATTATTAAATTTTATTAAAAATAAAAAAAAA
1 TTATAAAAATGATAAAATTTTA-T-AAAATAAAAAAAAA
* ***
20532286 TTATAAAAATGGTAAAATTTTATAAAATTCTAAAAAA
1 TTATAAAAATGATAAAATTTTATAAAATAAAAAAAAA
20532323 TTATAAAA
1 TTATAAAA
20532331 TTTTATAAAG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
37 19 0.49
38 1 0.03
39 19 0.49
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.36
Consensus pattern (37 bp):
TTATAAAAATGATAAAATTTTATAAAATAAAAAAAAA
Found at i:20532293 original size:9 final size:9
Alignment explanation
Indices: 20532217--20532380 Score: 57
Period size: 10 Copynumber: 17.3 Consensus size: 9
20532207 ATGGACAAAT
*
20532217 AAAATGATA
1 AAAATTATA
20532226 AAAA--ATA
1 AAAATTATA
* *
20532233 AAAATAAGTG
1 AAAATTA-TA
*
20532243 AAAGTTATA
1 AAAATTATA
20532252 AAAATTATTA
1 AAAATTA-TA
**
20532262 AATTTTATTA
1 AAAATTA-TA
* *
20532272 AAAATAAAAA
1 AAAAT-TATA
20532282 AAAATTATA
1 AAAATTATA
**
20532291 AAAATGGT-
1 AAAATTATA
*
20532299 AAAATTTTA
1 AAAATTATA
*
20532308 TAAAATTCTAA
1 -AAAATTAT-A
20532319 AAAATTATA
1 AAAATTATA
*
20532328 AAATTTTATAAA
1 AAA-ATTAT--A
20532340 GAAAATTATA
1 -AAAATTATA
*
20532350 AAAAATATA
1 AAAATTATA
*
20532359 AAGAAATAT-
1 AA-AATTATA
20532368 AAAATTCATA
1 AAAATT-ATA
20532378 AAA
1 AAA
20532381 GAATTATCAT
Statistics
Matches: 117, Mismatches: 23, Indels: 29
0.69 0.14 0.17
Matches are distributed among these distances:
7 7 0.06
8 9 0.08
9 38 0.32
10 53 0.45
11 2 0.02
12 5 0.04
13 3 0.03
ACGTcount: A:0.63, C:0.01, G:0.05, T:0.30
Consensus pattern (9 bp):
AAAATTATA
Found at i:20532293 original size:10 final size:10
Alignment explanation
Indices: 20532247--20532371 Score: 64
Period size: 10 Copynumber: 12.8 Consensus size: 10
20532237 TAAGTGAAAG
20532247 TTAT-AAAAA
1 TTATAAAAAA
* **
20532256 TTATTAAATT
1 TTATAAAAAA
*
20532266 TTATTAAAAA
1 TTATAAAAAA
* *
20532276 TAAAAAAAAA
1 TTATAAAAAA
20532286 TTAT-AAAAA
1 TTATAAAAAA
**
20532295 TGGT--AAAA
1 TTATAAAAAA
* *
20532303 TTTTATAAAA
1 TTATAAAAAA
*
20532313 TTCTAAAAAA
1 TTATAAAAAA
**
20532323 TTATAAAATT
1 TTATAAAAAA
20532333 TTATAAAGAAAA
1 TTAT-AA-AAAA
20532345 TTATAAAAAA
1 TTATAAAAAA
20532355 -TATAAAGAAA
1 TTATAAA-AAA
20532365 -TATAAAA
1 TTATAAAA
20532372 TTCATAAAAG
Statistics
Matches: 90, Mismatches: 20, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
8 6 0.07
9 18 0.20
10 56 0.62
11 4 0.04
12 6 0.07
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (10 bp):
TTATAAAAAA
Found at i:20532302 original size:18 final size:19
Alignment explanation
Indices: 20532280--20532330 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
20532270 TAAAAATAAA
*
20532280 AAAAAATTATAAAAATGGT
1 AAAAAATTATAAAAATGCT
** *
20532299 AAAATTTTAT-AAAATTCT
1 AAAAAATTATAAAAATGCT
20532317 AAAAAATTATAAAA
1 AAAAAATTATAAAA
20532331 TTTTATAAAG
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
18 14 0.56
19 11 0.44
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (19 bp):
AAAAAATTATAAAAATGCT
Found at i:20532312 original size:28 final size:29
Alignment explanation
Indices: 20532280--20532353 Score: 80
Period size: 28 Copynumber: 2.5 Consensus size: 29
20532270 TAAAAATAAA
*
20532280 AAAAAATTATAAAAATGGTAAAATTTTAT
1 AAAAAATTATAAAAATGATAAAATTTTAT
* *
20532309 --AAAATTCTAAAAAATTATAAAATTTTAT
1 AAAAAATTAT-AAAAATGATAAAATTTTAT
20532337 AAAGAAAATTATAAAAA
1 -AA-AAAATTATAAAAA
20532354 ATATAAAGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
27 7 0.19
28 17 0.47
31 5 0.14
32 7 0.19
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.32
Consensus pattern (29 bp):
AAAAAATTATAAAAATGATAAAATTTTAT
Found at i:20532360 original size:21 final size:22
Alignment explanation
Indices: 20532319--20532372 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
20532309 AAAATTCTAA
**
20532319 AAAATTATAAAATTTTATAAAG
1 AAAATTATAAAATAATATAAAG
20532341 AAAATTATAAAA-AATATAAAG
1 AAAATTATAAAATAATATAAAG
20532362 -AAA-TATAAAAT
1 AAAATTATAAAAT
20532373 TCATAAAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 7 0.24
20 3 0.10
21 7 0.24
22 12 0.41
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.30
Consensus pattern (22 bp):
AAAATTATAAAATAATATAAAG
Found at i:20532589 original size:29 final size:29
Alignment explanation
Indices: 20532557--20532684 Score: 116
Period size: 29 Copynumber: 4.4 Consensus size: 29
20532547 TTTTTGATGC
*
20532557 ATTTTATAATTATTT-ATGATTTTTATAAA
1 ATTTTATAATTATTTAATAATTTTTAT-AA
* * *
20532586 ATTTTACAATTTTTTTATAATTTTTTATAA
1 ATTTTATAATTATTTAATAA-TTTTTATAA
* * * *
20532616 ACTTTATAATTTTTTCATAATTTTTATTA
1 ATTTTATAATTATTTAATAATTTTTATAA
* *
20532645 TTTTTATTAA-AATTTAATAATTTTTATAA
1 ATTTTA-TAATTATTTAATAATTTTTATAA
*
20532674 TTTTTATAATT
1 ATTTTATAATT
20532685 TTTTTGCTAC
Statistics
Matches: 81, Mismatches: 14, Indels: 8
0.79 0.14 0.08
Matches are distributed among these distances:
28 3 0.04
29 46 0.57
30 25 0.31
31 7 0.09
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.62
Consensus pattern (29 bp):
ATTTTATAATTATTTAATAATTTTTATAA
Found at i:20532609 original size:9 final size:9
Alignment explanation
Indices: 20532558--20532687 Score: 107
Period size: 9 Copynumber: 13.4 Consensus size: 9
20532548 TTTTGATGCA
20532558 TTTTATAAT
1 TTTTATAAT
*
20532567 TATTTATGAT
1 T-TTTATAAT
*
20532577 TTTTATAAAA
1 TTTTAT-AAT
*
20532587 TTTTACAATTT
1 TTTTATAA--T
20532598 TTTTATAATT
1 TTTTATAA-T
*
20532608 TTTTATAAA
1 TTTTATAAT
*
20532617 CTTTATAATT
1 TTTTATAA-T
20532627 TTTTCATAAT
1 TTTT-ATAAT
*
20532637 TTTTATTAT
1 TTTTATAAT
*
20532646 TTTTATTAAAA
1 TTTTA-T-AAT
*
20532657 TTTAATAAT
1 TTTTATAAT
20532666 TTTTATAAT
1 TTTTATAAT
20532675 TTTTATAAT
1 TTTTATAAT
20532684 TTTT
1 TTTT
20532688 TTGCTACACG
Statistics
Matches: 97, Mismatches: 16, Indels: 16
0.75 0.12 0.12
Matches are distributed among these distances:
9 47 0.48
10 34 0.35
11 16 0.16
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (9 bp):
TTTTATAAT
Found at i:20532621 original size:19 final size:19
Alignment explanation
Indices: 20532557--20532688 Score: 97
Period size: 19 Copynumber: 6.8 Consensus size: 19
20532547 TTTTTGATGC
* *
20532557 ATTTTATAATTATTTATGA
1 ATTTTATAATTTTTTATAA
* ** *
20532576 TTTTTATAAAATTTTACAA
1 ATTTTATAATTTTTTATAA
*
20532595 TTTTTTTATAATTTTTTATAA
1 --ATTTTATAATTTTTTATAA
*
20532616 ACTTTATAATTTTTTCATAA
1 ATTTTATAATTTTTT-ATAA
* *
20532636 TTTTTATTA-TTTTTATTAAA
1 ATTTTATAATTTTTTA-T-AA
*
20532656 ATTTAATAA-TTTTTATAA
1 ATTTTATAATTTTTTATAA
*
20532674 TTTTTATAATTTTTT
1 ATTTTATAATTTTTT
20532689 TGCTACACGT
Statistics
Matches: 88, Mismatches: 19, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
18 10 0.11
19 38 0.43
20 24 0.27
21 16 0.18
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (19 bp):
ATTTTATAATTTTTTATAA
Found at i:20532638 original size:11 final size:10
Alignment explanation
Indices: 20532558--20532688 Score: 94
Period size: 10 Copynumber: 13.4 Consensus size: 10
20532548 TTTTGATGCA
20532558 TTTTATAATT
1 TTTTATAATT
* *
20532568 ATTTATGA-T
1 TTTTATAATT
**
20532577 TTTTATAAAA
1 TTTTATAATT
*
20532587 TTTTACAATTT
1 TTTTATAA-TT
20532598 TTTTATAATT
1 TTTTATAATT
*
20532608 TTTTATAA-A
1 TTTTATAATT
*
20532617 CTTTATAATT
1 TTTTATAATT
20532627 TTTTCATAA-T
1 TTTT-ATAATT
*
20532637 TTTTATTA-T
1 TTTTATAATT
**
20532646 TTTTATTAAAA
1 TTTTA-TAATT
*
20532657 TTTAATAA-T
1 TTTTATAATT
20532666 TTTTATAA-T
1 TTTTATAATT
20532675 TTTTATAATT
1 TTTTATAATT
20532685 TTTT
1 TTTT
20532689 TGCTACACGT
Statistics
Matches: 95, Mismatches: 19, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
9 39 0.41
10 41 0.43
11 15 0.16
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (10 bp):
TTTTATAATT
Found at i:20533347 original size:20 final size:21
Alignment explanation
Indices: 20533308--20533347 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
20533298 AGTTTTAAAA
20533308 TCACCCTATATTTTCTGCCTT
1 TCACCCTATATTTTCTGCCTT
*
20533329 TCACCCTATTTTTTC-GCCT
1 TCACCCTATATTTTCTGCCT
20533348 GAATGAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.12, C:0.35, G:0.05, T:0.47
Consensus pattern (21 bp):
TCACCCTATATTTTCTGCCTT
Found at i:20543400 original size:27 final size:28
Alignment explanation
Indices: 20543370--20543428 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 28
20543360 ACACACTCGG
**
20543370 AATAATAT-AAATCCTCCTTAACACACA
1 AATAATATCAAATCCTCCCAAACACACA
* *
20543397 AAT-ATATCATATCCTCCCAAACACACC
1 AATAATATCAAATCCTCCCAAACACACA
20543424 AATAA
1 AATAA
20543429 GGCATTAGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 4 0.15
27 21 0.81
28 1 0.04
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (28 bp):
AATAATATCAAATCCTCCCAAACACACA
Found at i:20543701 original size:29 final size:29
Alignment explanation
Indices: 20543664--20543720 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
20543654 CATATAATTC
20543664 AATATTCACACATATTCTTACTTAATTTT
1 AATATTCACACATATTCTTACTTAATTTT
20543693 AATATTCACACATATTCTTACTTAATTT
1 AATATTCACACATATTCTTACTTAATTT
20543721 CAAATGTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.35, C:0.18, G:0.00, T:0.47
Consensus pattern (29 bp):
AATATTCACACATATTCTTACTTAATTTT
Found at i:20543749 original size:24 final size:23
Alignment explanation
Indices: 20543705--20543751 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
20543695 TATTCACACA
20543705 TATTCTTACTTAATTTCAAATGT
1 TATTCTTACTTAATTTCAAATGT
*
20543728 TATTACTTACCTTACTTT-AAATGT
1 TATT-CTTA-CTTAATTTCAAATGT
20543752 CCCATGATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 10 0.48
25 7 0.33
ACGTcount: A:0.30, C:0.15, G:0.04, T:0.51
Consensus pattern (23 bp):
TATTCTTACTTAATTTCAAATGT
Found at i:20544028 original size:22 final size:24
Alignment explanation
Indices: 20543987--20544030 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
20543977 TAACTAAGCT
*
20543987 TACTTACTTTTCTAACTTAATTCA
1 TACTTACTTTTATAACTTAATTCA
20544011 TACTTA-TTTTAT-ACTTAATT
1 TACTTACTTTTATAACTTAATT
20544031 TCTTGCCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 5 0.26
24 6 0.32
ACGTcount: A:0.30, C:0.16, G:0.00, T:0.55
Consensus pattern (24 bp):
TACTTACTTTTATAACTTAATTCA
Found at i:20546614 original size:46 final size:46
Alignment explanation
Indices: 20546547--20547592 Score: 1939
Period size: 46 Copynumber: 22.6 Consensus size: 46
20546537 TTTGAGTACT
20546547 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
20546593 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
20546639 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
20546685 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
20546731 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
20546777 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
20546823 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
20546869 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
20546915 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
20546961 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
20547007 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
20547053 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
20547099 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
20547145 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
20547191 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
20547237 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
20547283 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
20547329 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
20547375 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* **
20547421 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* ** *
20547467 TCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGAC------AAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* * *
20547519 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTATACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
20547565 TCTGATCAAGAGACAAAGTGATAAGTGG
1 TCTGATCAAGTGACAAAGTGATAAGTGG
20547593 CTACACTTAT
Statistics
Matches: 986, Mismatches: 8, Indels: 12
0.98 0.01 0.01
Matches are distributed among these distances:
46 942 0.96
52 44 0.04
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (46 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:20547604 original size:37 final size:37
Alignment explanation
Indices: 20547555--20547663 Score: 168
Period size: 37 Copynumber: 3.0 Consensus size: 37
20547545 GATAGCTTTA
*
20547555 GCTATACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
* *
20547592 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
20547629 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
20547664 ATCATACGTA
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
35 11 0.17
36 4 0.06
37 51 0.77
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.26
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
Found at i:20548076 original size:31 final size:31
Alignment explanation
Indices: 20548002--20548076 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
20547992 TATAAAATAG
* *
20548002 TCACTTAACTATTTGAAAGTATTCATTTAAT
1 TCACTGAACTATTCGAAAGTATTCATTTAAT
* * *
20548033 TCATTGAACTATTCGAAAGTTTTTATTTAAGT
1 TCACTGAACTATTCGAAAGTATTCATTTAA-T
*
20548065 T-ACTGAGCTATT
1 TCACTGAACTATT
20548077 AAGTTTTTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
31 34 0.94
32 2 0.06
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (31 bp):
TCACTGAACTATTCGAAAGTATTCATTTAAT
Found at i:20550652 original size:14 final size:14
Alignment explanation
Indices: 20550633--20550662 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
20550623 GATATGTCGA
20550633 AACATATTAATACC
1 AACATATTAATACC
20550647 AACATATTAATACC
1 AACATATTAATACC
20550661 AA
1 AA
20550663 TACCAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.20, G:0.00, T:0.27
Consensus pattern (14 bp):
AACATATTAATACC
Found at i:20555661 original size:15 final size:15
Alignment explanation
Indices: 20555641--20555671 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
20555631 CACTTTCAAC
20555641 ATTTTATTCTATTTT
1 ATTTTATTCTATTTT
*
20555656 ATTTTATTGTATTTT
1 ATTTTATTCTATTTT
20555671 A
1 A
20555672 AAATTTCAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.71
Consensus pattern (15 bp):
ATTTTATTCTATTTT
Found at i:20558532 original size:19 final size:20
Alignment explanation
Indices: 20558500--20558537 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
20558490 TTCTACTAAA
20558500 TTTTATATTATTTTAATATT
1 TTTTATATTATTTTAATATT
*
20558520 TTTTTTATT-TTTTAATAT
1 TTTTATATTATTTTAATAT
20558538 CTAAATATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTATATTATTTTAATATT
Found at i:20562863 original size:17 final size:18
Alignment explanation
Indices: 20562836--20562877 Score: 68
Period size: 17 Copynumber: 2.3 Consensus size: 18
20562826 TTACTGTTAA
20562836 TATAGTTTATATTTATA-T
1 TATA-TTTATATTTATATT
20562854 TATATTTATATTTATATT
1 TATATTTATATTTATATT
20562872 TATATT
1 TATATT
20562878 AGTCTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 12 0.52
18 11 0.48
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (18 bp):
TATATTTATATTTATATT
Found at i:20562885 original size:23 final size:22
Alignment explanation
Indices: 20562836--20562892 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 22
20562826 TTACTGTTAA
*
20562836 TATAGTTTATATTTATATTATATT
1 TATA-TTTATATTTATATTATA-C
20562860 TATATTTATATTTATATTAGT-C
1 TATATTTATATTTATATTA-TAC
20562882 T-TATTTATATT
1 TATATTTATATT
20562893 ATTGTAGTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
21 10 0.32
22 1 0.03
23 15 0.48
24 5 0.16
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.63
Consensus pattern (22 bp):
TATATTTATATTTATATTATAC
Found at i:20562892 original size:6 final size:6
Alignment explanation
Indices: 20562836--20562877 Score: 68
Period size: 6 Copynumber: 7.0 Consensus size: 6
20562826 TTACTGTTAA
20562836 TATAGTT TATATT TATA-T TATATT TATATT TATATT TATATT
1 TATA-TT TATATT TATATT TATATT TATATT TATATT TATATT
20562878 AGTCTTATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.15
6 25 0.74
7 4 0.12
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (6 bp):
TATATT
Found at i:20564226 original size:31 final size:31
Alignment explanation
Indices: 20564165--20564230 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
20564155 AACAATCCAT
*
20564165 TGACTTAAATAAAAATTAGTGGATAATTCAA
1 TGACTTAAATAAAAATTAGTGAATAATTCAA
* * *
20564196 TGACTTCAATAAAAACTT-TTGAATAGTTCAA
1 TGACTTAAATAAAAA-TTAGTGAATAATTCAA
20564227 TGAC
1 TGAC
20564231 CACTTTATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 28 0.93
32 2 0.07
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (31 bp):
TGACTTAAATAAAAATTAGTGAATAATTCAA
Found at i:20570956 original size:60 final size:60
Alignment explanation
Indices: 20570889--20571063 Score: 334
Period size: 60 Copynumber: 2.9 Consensus size: 60
20570879 GTTCAAACAC
*
20570889 ACTCATAATAAAAATCAGGGTAAACTAAACTCAAGGTGCACTAAATAATTAGTAACCTAA
1 ACTCATAATAAAAATCAGGGTAAACTAAACTCAAGGTGCACTAAATAATTAGTAAACTAA
20570949 ACTCATAATAAAAATCAGGGTAAACTAAACTCAAGGTGCACTAAATAATTAGTAAACTAA
1 ACTCATAATAAAAATCAGGGTAAACTAAACTCAAGGTGCACTAAATAATTAGTAAACTAA
20571009 ACTCATAATAAAAATCAGGGTAAACTAAACTCAAGGT-CACTAAATAATTAGTAAA
1 ACTCATAATAAAAATCAGGGTAAACTAAACTCAAGGTGCACTAAATAATTAGTAAA
20571064 TTTACATTTT
Statistics
Matches: 114, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
59 18 0.16
60 96 0.84
ACGTcount: A:0.50, C:0.15, G:0.11, T:0.23
Consensus pattern (60 bp):
ACTCATAATAAAAATCAGGGTAAACTAAACTCAAGGTGCACTAAATAATTAGTAAACTAA
Found at i:20571147 original size:31 final size:31
Alignment explanation
Indices: 20571106--20571171 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
20571096 CAAATGATTG
*
20571106 TTGAACTATTCAAAAGTTTTCATTTAAGTTA
1 TTGAACTATTCAAAAGTTTTCATTTAAGTCA
* *
20571137 TTGAATTATTCAAAAGTTTTTATTTAAGTCA
1 TTGAACTATTCAAAAGTTTTCATTTAAGTCA
20571168 TTGA
1 TTGA
20571172 GTTGTTAAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.47
Consensus pattern (31 bp):
TTGAACTATTCAAAAGTTTTCATTTAAGTCA
Found at i:20577452 original size:16 final size:16
Alignment explanation
Indices: 20577418--20577451 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
20577408 AAAAAAGGCA
*
20577418 TTATATCAGATTAATT
1 TTATATCAAATTAATT
20577434 TTATCATCAAATTAATT
1 TTAT-ATCAAATTAATT
20577451 T
1 T
20577452 ACTTTATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.38, C:0.09, G:0.03, T:0.50
Consensus pattern (16 bp):
TTATATCAAATTAATT
Found at i:20581498 original size:27 final size:27
Alignment explanation
Indices: 20581468--20581531 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
20581458 TTTATCGAGG
*
20581468 TTATTAGTTTATCGATAAATTAATATT
1 TTATTAATTTATCGATAAATTAATATT
20581495 TTATTAATTTATCGATAAATTAATA-T
1 TTATTAATTTATCGATAAATTAATATT
*
20581521 TCATTAATTTA
1 TTATTAATTTA
20581532 GAGAATATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
26 11 0.31
27 24 0.69
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.52
Consensus pattern (27 bp):
TTATTAATTTATCGATAAATTAATATT
Found at i:20581650 original size:34 final size:35
Alignment explanation
Indices: 20581610--20581680 Score: 110
Period size: 34 Copynumber: 2.0 Consensus size: 35
20581600 TGAATCAACG
20581610 TTAATTGGTTCATGTATA-AAAAA-AAAAGAGTTAA
1 TTAATTGGTTCATGTA-ACAAAAAGAAAAGAGTTAA
20581644 TTAATTGGTTCATGTAACCAAAAAGAAAAGAGTTAA
1 TTAATTGGTTCATGTAA-CAAAAAGAAAAGAGTTAA
20581680 T
1 T
20581681 GGTTTCAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 1 0.03
34 16 0.47
35 5 0.15
36 12 0.35
ACGTcount: A:0.48, C:0.06, G:0.15, T:0.31
Consensus pattern (35 bp):
TTAATTGGTTCATGTAACAAAAAGAAAAGAGTTAA
Found at i:20593928 original size:54 final size:54
Alignment explanation
Indices: 20593846--20593954 Score: 200
Period size: 54 Copynumber: 2.0 Consensus size: 54
20593836 TGTTTAAAAT
20593846 AGAAGATACTTTGTGTTTAAACACATTAGACCTCACAACTATTTGAATGCCGCC
1 AGAAGATACTTTGTGTTTAAACACATTAGACCTCACAACTATTTGAATGCCGCC
* *
20593900 AGAAGATACTTTGTGTTTAAACTCATTAGCCCTCACAACTATTTGAATGCCGCC
1 AGAAGATACTTTGTGTTTAAACACATTAGACCTCACAACTATTTGAATGCCGCC
20593954 A
1 A
20593955 TAGACGAATC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (54 bp):
AGAAGATACTTTGTGTTTAAACACATTAGACCTCACAACTATTTGAATGCCGCC
Found at i:20597050 original size:31 final size:31
Alignment explanation
Indices: 20597012--20597129 Score: 139
Period size: 31 Copynumber: 3.6 Consensus size: 31
20597002 TTATATATAA
20597012 TATATTAATCGAAATAAATCCCTCAATTTTT
1 TATATTAATCGAAATAAATCCCTCAATTTTT
***
20597043 TATATTAATCGAAATAAATAAGAT-ATATTATATAT
1 TATATTAATCGAAATAAAT-CCCTCA-ATT-T-T-T
20597078 AATATATTAATCGAAATAAATCCCTCAATTTTT
1 --TATATTAATCGAAATAAATCCCTCAATTTTT
20597111 TATATTAATCGAAATAAAT
1 TATATTAATCGAAATAAAT
20597130 AAGATATATT
Statistics
Matches: 73, Mismatches: 6, Indels: 16
0.77 0.06 0.17
Matches are distributed among these distances:
31 39 0.53
32 4 0.05
33 2 0.03
34 2 0.03
35 2 0.03
36 4 0.05
37 20 0.27
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.40
Consensus pattern (31 bp):
TATATTAATCGAAATAAATCCCTCAATTTTT
Found at i:20597068 original size:68 final size:68
Alignment explanation
Indices: 20596990--20597153 Score: 328
Period size: 68 Copynumber: 2.4 Consensus size: 68
20596980 TTATTATATA
20596990 AAATAAGATATATTATATATAATATATTAATCGAAATAAATCCCTCAATTTTTTATATTAATCGA
1 AAATAAGATATATTATATATAATATATTAATCGAAATAAATCCCTCAATTTTTTATATTAATCGA
20597055 AAT
66 AAT
20597058 AAATAAGATATATTATATATAATATATTAATCGAAATAAATCCCTCAATTTTTTATATTAATCGA
1 AAATAAGATATATTATATATAATATATTAATCGAAATAAATCCCTCAATTTTTTATATTAATCGA
20597123 AAT
66 AAT
20597126 AAATAAGATATATTATATATAATATATT
1 AAATAAGATATATTATATATAATATATT
20597154 TTTTTGAACT
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 96 1.00
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.40
Consensus pattern (68 bp):
AAATAAGATATATTATATATAATATATTAATCGAAATAAATCCCTCAATTTTTTATATTAATCGA
AAT
Found at i:20603962 original size:14 final size:15
Alignment explanation
Indices: 20603942--20603983 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
20603932 ATAATGTAAC
20603942 ATATATTTTAATGTT
1 ATATATTTTAATGTT
* *
20603957 -TATATTGTAGTGTT
1 ATATATTTTAATGTT
20603971 ATATATTATTAAT
1 ATATATT-TTAAT
20603984 TTAATTTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
14 12 0.57
15 6 0.29
16 3 0.14
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (15 bp):
ATATATTTTAATGTT
Found at i:20605895 original size:8 final size:8
Alignment explanation
Indices: 20605884--20605916 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
20605874 TAACCTTTTC
20605884 AAAAA-AA
1 AAAAACAA
20605891 AAAAACAA
1 AAAAACAA
20605899 AAAAACAA
1 AAAAACAA
20605907 AAAAACAA
1 AAAAACAA
20605915 AA
1 AA
20605917 CAACTAGGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 5 0.20
8 20 0.80
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAACAA
Found at i:20610301 original size:23 final size:21
Alignment explanation
Indices: 20610262--20610308 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
20610252 ACAAATTCTA
* *
20610262 TATTATTATTGTTATTGCATTGT
1 TATTATTATTATAATTG-ATT-T
20610285 TATTATTATTATAATTGATTT
1 TATTATTATTATAATTGATTT
20610306 TAT
1 TAT
20610309 AGATATATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 4 0.18
22 3 0.14
23 15 0.68
ACGTcount: A:0.28, C:0.02, G:0.09, T:0.62
Consensus pattern (21 bp):
TATTATTATTATAATTGATTT
Found at i:20610330 original size:22 final size:23
Alignment explanation
Indices: 20610305--20610350 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
20610295 ATAATTGATT
20610305 TTATAGATATATACATATA-TTA
1 TTATAGATATATACATATACTTA
* * *
20610327 TTATATATTTCTACATATACTTA
1 TTATAGATATATACATATACTTA
20610350 T
1 T
20610351 ACACATTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.50
Consensus pattern (23 bp):
TTATAGATATATACATATACTTA
Found at i:20610358 original size:22 final size:22
Alignment explanation
Indices: 20610316--20610358 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
20610306 TATAGATATA
* *
20610316 TACATATATTATTATATATTTC
1 TACATATATTATTACACATTTC
20610338 TACATATACTTA-TACACATTT
1 TACATATA-TTATTACACATTT
20610359 TTTTTGTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.37, C:0.14, G:0.00, T:0.49
Consensus pattern (22 bp):
TACATATATTATTACACATTTC
Found at i:20610807 original size:5 final size:5
Alignment explanation
Indices: 20610792--20610821 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
20610782 TACATAAGTG
20610792 TTTTA -TTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
20610822 ATTGTTTCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:20616679 original size:18 final size:18
Alignment explanation
Indices: 20616653--20616701 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 18
20616643 AATCTAAACT
*
20616653 TGAACCATGAACTTGAAA
1 TGAATCATGAACTTGAAA
20616671 TGAATCATGATGAACTTGAAA
1 TGAATC---ATGAACTTGAAA
20616692 TGAATCATGA
1 TGAATCATGA
20616702 TCCTTAACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 9 0.33
21 18 0.67
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (18 bp):
TGAATCATGAACTTGAAA
Found at i:20616685 original size:21 final size:21
Alignment explanation
Indices: 20616659--20616702 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
20616649 AACTTGAACC
20616659 ATGAACTTGAAATGAATCATG
1 ATGAACTTGAAATGAATCATG
20616680 ATGAACTTGAAATGAATCATG
1 ATGAACTTGAAATGAATCATG
20616701 AT
1 AT
20616703 CCTTAACATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.43, C:0.09, G:0.18, T:0.30
Consensus pattern (21 bp):
ATGAACTTGAAATGAATCATG
Found at i:20617060 original size:11 final size:11
Alignment explanation
Indices: 20617044--20617068 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
20617034 GATACAATAA
20617044 AATCTTAATTT
1 AATCTTAATTT
20617055 AATCTTAATTT
1 AATCTTAATTT
20617066 AAT
1 AAT
20617069 TGTTGAGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (11 bp):
AATCTTAATTT
Found at i:20619044 original size:30 final size:31
Alignment explanation
Indices: 20618969--20619055 Score: 86
Period size: 31 Copynumber: 2.8 Consensus size: 31
20618959 AAACTTAATG
*
20618969 GGTTTTAGTGAGAATTTTCAAAAATTTTGGTA
1 GGTTTTA-TGAAAATTTTCAAAAATTTTGGTA
* * * * *
20619001 GGTCTAATTAAAATTTTCAAAATTTTTTG-A
1 GGTTTTATGAAAATTTTCAAAAATTTTGGTA
*
20619031 GGTTTTATGAAAATTTATAAAAAAT
1 GGTTTTATGAAAATTT-TCAAAAAT
20619056 GAAGAGTCTA
Statistics
Matches: 43, Mismatches: 11, Indels: 3
0.75 0.19 0.05
Matches are distributed among these distances:
30 14 0.33
31 24 0.56
32 5 0.12
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.44
Consensus pattern (31 bp):
GGTTTTATGAAAATTTTCAAAAATTTTGGTA
Found at i:20622212 original size:33 final size:33
Alignment explanation
Indices: 20622175--20622237 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
20622165 CTTTTTTTGC
*
20622175 AGCATGTAATTACTAATTAGTATGTTCTTATGT
1 AGCATGTAATTACTAATCAGTATGTTCTTATGT
20622208 AGCATGTAATTACTAATCAGTATGTTCTTA
1 AGCATGTAATTACTAATCAGTATGTTCTTA
20622238 ATAACCAAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (33 bp):
AGCATGTAATTACTAATCAGTATGTTCTTATGT
Found at i:20624056 original size:45 final size:45
Alignment explanation
Indices: 20623957--20624049 Score: 150
Period size: 45 Copynumber: 2.0 Consensus size: 45
20623947 TGAATCGAAA
*
20623957 TTGGGTTTTTGTCTTTTGGTATGAACAAAAACATGAGGAGGTTTT
1 TTGGGTTTTTGTCTTTTGGTATGAACAAAAACAGGAGGAGGTTTT
* *
20624002 TTGGGTTTTTGTCTTTTGGTATGAACAAAAACACGGGGGAGTTTTT
1 TTGGGTTTTTGTCTTTTGGTATGAACAAAAACA-GGAGGAGGTTTT
20624048 TT
1 TT
20624050 TTTTTTTTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
45 33 0.75
46 11 0.25
ACGTcount: A:0.23, C:0.08, G:0.27, T:0.43
Consensus pattern (45 bp):
TTGGGTTTTTGTCTTTTGGTATGAACAAAAACAGGAGGAGGTTTT
Found at i:20631382 original size:31 final size:30
Alignment explanation
Indices: 20631346--20631458 Score: 95
Period size: 31 Copynumber: 3.6 Consensus size: 30
20631336 GATTGACTAA
20631346 AATTTTTAAAAATTTTGAAGGTTTTAATGAG
1 AATTTTTAAAAATTTTGAAGG-TTTAATGAG
* * * *
20631377 AATTTTTAAACAATTTTGTATGTTAAACT-AA
1 AATTTTTAAA-AATTTTGAAGGTTTAA-TGAG
**
20631408 AACTTTCAAAAAAAATTTTGAAAGGTTTAATGAG
1 AA-TTT--TTAAAAATTTTG-AAGGTTTAATGAG
20631442 AA-TTTTAAAAATTTTGA
1 AATTTTTAAAAATTTTGA
20631459 GCGGGCTAAT
Statistics
Matches: 63, Mismatches: 12, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
29 1 0.02
30 10 0.16
31 17 0.27
32 15 0.24
33 8 0.13
34 12 0.19
ACGTcount: A:0.43, C:0.04, G:0.12, T:0.42
Consensus pattern (30 bp):
AATTTTTAAAAATTTTGAAGGTTTAATGAG
Found at i:20640752 original size:100 final size:100
Alignment explanation
Indices: 20640479--20640949 Score: 722
Period size: 100 Copynumber: 4.7 Consensus size: 100
20640469 AAAATTACAT
20640479 TAAAAAATCACAAAACAC-TAAACT-AACACTAACAATTTATATAACCTAATCATAAATTACAAA
1 TAAAAAATCACAAAACACAT-AACTAAACACTAACAATTTATATAACCTAATCATAAATTACAAA
20640542 CAAAATAACTATAAAATTATTTATTAAATACATTAC
65 CAAAATAACTATAAAATTATTTATTAAATACATTAC
20640578 TAAAAAATCACAAAACAC-TAAACT-AACACTAACAATTTATATAACCTAATCATAAATTACAAA
1 TAAAAAATCACAAAACACAT-AACTAAACACTAACAATTTATATAACCTAATCATAAATTACAAA
20640641 CAAAATAACTATAAAATTATTTATTAAATACATTAC
65 CAAAATAACTATAAAATTATTTATTAAATACATTAC
20640677 TAAAAAATCACAAAACACATAACTAAACACTAACAATTTATATAACCTAATCATAAATTACAAAC
1 TAAAAAATCACAAAACACATAACTAAACACTAACAATTTATATAACCTAATCATAAATTACAAAC
20640742 AAAATAACTATAAAATTATTTATTAAATACATTAC
66 AAAATAACTATAAAATTATTTATTAAATACATTAC
*
20640777 TAAAAAATCACAAAACACATAACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAAC
1 TAAAAAATCACAAAACACATAACTAAACACTAACAATTTATATAACCTAATCATAAATTACAAAC
* * * **
20640842 AAAATAATTATAAATTTTTTTAAAAAAAAGTTACATTAC
66 AAAATAACTATAAAATTATTT--ATTAAA--TACATTAC
* * **
20640881 TAAAAGATCACAAAAC-CATATACTAAACACTAACAA-TT-TGTAACCTAATCCCATAAATTATT
1 TAAAAAATCACAAAACACATA-ACTAAACACTAACAATTTATATAACCTAAT--CATAAATTACA
20640943 AACAAAA
63 AACAAAA
20640950 ATAAATAACT
Statistics
Matches: 354, Mismatches: 9, Indels: 13
0.94 0.02 0.03
Matches are distributed among these distances:
99 121 0.34
100 158 0.45
102 14 0.04
103 6 0.02
104 55 0.16
ACGTcount: A:0.55, C:0.16, G:0.01, T:0.28
Consensus pattern (100 bp):
TAAAAAATCACAAAACACATAACTAAACACTAACAATTTATATAACCTAATCATAAATTACAAAC
AAAATAACTATAAAATTATTTATTAAATACATTAC
Found at i:20641222 original size:60 final size:60
Alignment explanation
Indices: 20641144--20641258 Score: 203
Period size: 60 Copynumber: 1.9 Consensus size: 60
20641134 TAAACTAAAC
*
20641144 ACAAAAATTTATAACATAATCCTAAATTACTAATAAATTAATTTTAAAATAATTACAAAT
1 ACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTACAAAT
* *
20641204 ACAACAATTTATAGCATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
1 ACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
20641259 TAAAAAAATT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.53, C:0.11, G:0.01, T:0.35
Consensus pattern (60 bp):
ACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTACAAAT
Found at i:20642170 original size:6 final size:6
Alignment explanation
Indices: 20642159--20642349 Score: 382
Period size: 6 Copynumber: 31.8 Consensus size: 6
20642149 TAGAAATTAA
20642159 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
20642207 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
20642255 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
20642303 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATA
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATA
20642350 ATCATTGAAA
Statistics
Matches: 185, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 185 1.00
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAC
Found at i:20644047 original size:20 final size:20
Alignment explanation
Indices: 20644008--20644047 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
20643998 CTTATTCTTG
**
20644008 AGTAATTTTCATGTCTTTTT
1 AGTAATTTTCATGTAATTTT
*
20644028 AGTAGTTTTCATGTAATTTT
1 AGTAATTTTCATGTAATTTT
20644048 TATTCTTTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.07, G:0.12, T:0.57
Consensus pattern (20 bp):
AGTAATTTTCATGTAATTTT
Found at i:20644421 original size:22 final size:22
Alignment explanation
Indices: 20644366--20644423 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
20644356 CTGATAAGGA
*
20644366 TATCACGATACCCTCCCATGGG
1 TATCACGATACCCTCCCATGAG
** * *
20644388 TATTGCGGTACCCTCCCCTGAG
1 TATCACGATACCCTCCCATGAG
20644410 TATCACGATACCCT
1 TATCACGATACCCT
20644424 TGTTGTATAA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.21, C:0.36, G:0.17, T:0.26
Consensus pattern (22 bp):
TATCACGATACCCTCCCATGAG
Found at i:20644655 original size:17 final size:18
Alignment explanation
Indices: 20644633--20644666 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
20644623 AGGGTTAGGG
20644633 TTTTTCTTTTC-TTTTTC
1 TTTTTCTTTTCATTTTTC
20644650 TTTTTCTTTTCATTTTT
1 TTTTTCTTTTCATTTTT
20644667 AGTTTAGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTTCTTTTCATTTTTC
Found at i:20644685 original size:25 final size:24
Alignment explanation
Indices: 20644651--20644703 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
20644641 TTCTTTTTCT
* *
20644651 TTTTCTTTTCATTTTTAGTTTAGG
1 TTTTCTTTTCATTTTTAGATTAGA
*
20644675 TTTTCTCTTTCCTTTTTAGATTAGA
1 TTTTCT-TTTCATTTTTAGATTAGA
20644700 TTTT
1 TTTT
20644704 ATTATTGTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 6 0.24
25 19 0.76
ACGTcount: A:0.13, C:0.11, G:0.09, T:0.66
Consensus pattern (24 bp):
TTTTCTTTTCATTTTTAGATTAGA
Found at i:20647302 original size:37 final size:37
Alignment explanation
Indices: 20647241--20647387 Score: 235
Period size: 37 Copynumber: 4.0 Consensus size: 37
20647231 TACGTATGAT
* *
20647241 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
20647276 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
20647313 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
* *
20647350 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
20647387 C
1 C
20647388 GAAGCTATCA
Statistics
Matches: 104, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 92 0.88
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:20647414 original size:14 final size:14
Alignment explanation
Indices: 20647395--20647433 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
20647385 GCCGAAGCTA
*
20647395 TCACTTATCACTTT
1 TCACTTATCACTTG
*
20647409 TCACTTTTCACTTG
1 TCACTTATCACTTG
20647423 TCACTTGATCA
1 TCACTT-ATCA
20647434 GATAAGTGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 18 0.86
15 3 0.14
ACGTcount: A:0.21, C:0.28, G:0.05, T:0.46
Consensus pattern (14 bp):
TCACTTATCACTTG
Found at i:20647446 original size:59 final size:61
Alignment explanation
Indices: 20647350--20647479 Score: 210
Period size: 59 Copynumber: 2.1 Consensus size: 61
20647340 TAAGTGTAGC
*
20647350 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTT-T
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTGT
* *
20647410 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTGT
20647470 CACTTGATCA
1 CACTT-ATCA
20647480 GATAAGTATA
Statistics
Matches: 64, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
59 46 0.72
60 15 0.23
61 3 0.05
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (61 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTGT
Found at i:20647465 original size:52 final size:52
Alignment explanation
Indices: 20647400--20647573 Score: 234
Period size: 52 Copynumber: 3.4 Consensus size: 52
20647390 AGCTATCACT
*
20647400 TATCACTTTTCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGC
1 TATCACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGC
*
20647452 TATCACTTATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGC
1 TATCACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGC
* * **
20647498 TATTACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGC
1 TATCACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGC
*
20647550 TACCACTTATCACTTTGTCACTTG
1 TATCACTTATCACTTT-TCACTTG
20647574 ATCAGAAGTA
Statistics
Matches: 105, Mismatches: 10, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
46 43 0.41
49 1 0.01
52 55 0.52
53 6 0.06
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (52 bp):
TATCACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGC
Found at i:20647477 original size:46 final size:46
Alignment explanation
Indices: 20647409--20647579 Score: 227
Period size: 46 Copynumber: 3.6 Consensus size: 46
20647399 TTATCACTTT
*
20647409 TCACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTA
1 TCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTA
*
20647454 TCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTA
1 TCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTA
* **
20647500 TTACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTA
1 TCACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTA
*
20647552 CCACTTATCACTTTGTCACTTGATCAGA
1 TCACTTATCACTTTGTCACTTGATCAGA
20647580 AGTACTCAAA
Statistics
Matches: 111, Mismatches: 8, Indels: 13
0.84 0.06 0.10
Matches are distributed among these distances:
45 10 0.09
46 59 0.53
48 1 0.01
50 1 0.01
52 40 0.36
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.35
Consensus pattern (46 bp):
TCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTA
Found at i:20647537 original size:98 final size:101
Alignment explanation
Indices: 20647349--20647579 Score: 360
Period size: 98 Copynumber: 2.3 Consensus size: 101
20647339 ATAAGTGTAG
*
20647349 CCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACT
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTT-AC-
*
20647414 TTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTA
64 --TCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTA
* *
20647454 TCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCAC-TTT-C-C
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTACTC
*
20647516 ACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTA
66 ACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTA
20647552 CCACTTATCACTTTGTCACTTGATCAGA
1 CCACTTATCACTTTGTCACTTGATCAGA
20647580 AGTACTCAAA
Statistics
Matches: 120, Mismatches: 6, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
98 62 0.52
102 1 0.01
104 3 0.03
105 54 0.45
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (101 bp):
CCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTACTC
ACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTA
Found at i:20664094 original size:49 final size:49
Alignment explanation
Indices: 20664033--20664176 Score: 225
Period size: 49 Copynumber: 2.9 Consensus size: 49
20664023 ATGTGAACAT
* *
20664033 GTGATTATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
1 GTGA-TATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCGGTAA
* *
20664083 GTGATATGTGATTTCGTGTAAGACCATAGTTGGGCTATGGCATCGGTAT
1 GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCGGTAA
* *
20664132 GTGATTTGTGATTACGTGTAAGACCATAGTTGGACTATGGCATCG
1 GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCG
20664177 AGAAAACGAA
Statistics
Matches: 88, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
49 84 0.95
50 4 0.05
ACGTcount: A:0.24, C:0.14, G:0.30, T:0.33
Consensus pattern (49 bp):
GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCGGTAA
Found at i:20667572 original size:46 final size:46
Alignment explanation
Indices: 20667554--20667710 Score: 149
Period size: 46 Copynumber: 3.3 Consensus size: 46
20667544 TGACAAGTGG
* * *
20667554 AAAGTGATAAGTAATAGCT-TCGGCTATACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTAT-AGCTACACTTATCTGATCAAGTGAC
*
20667600 AAAGTGATAAGTGATAGCT-TCGGCTACACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTAT-AGCTACACTTATCTGATCAAGTGAC
* * *
20667646 AAGTGAAAAGTGATAAGTGATAGCT-TCGGCTATACTTATCTGATCAAGAGAC
1 ------AAAGTGATAAGTGATAGCTAT-AGCTACACTTATCTGATCAAGTGAC
20667698 AAAGTGATAAGTG
1 AAAGTGATAAGTG
20667711 GCTACACTTA
Statistics
Matches: 101, Mismatches: 4, Indels: 12
0.86 0.03 0.10
Matches are distributed among these distances:
46 57 0.56
52 44 0.44
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (46 bp):
AAAGTGATAAGTGATAGCTATAGCTACACTTATCTGATCAAGTGAC
Found at i:20667573 original size:52 final size:51
Alignment explanation
Indices: 20667502--20667710 Score: 284
Period size: 52 Copynumber: 4.1 Consensus size: 51
20667492 ATCAAGTGAC
* **
20667502 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGT-G
* *
20667554 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC-----
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
20667600 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
* *
20667651 AAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTG
1 -AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-AAGTG
20667704 ATAAGTG
1 A-AAGTG
20667711 GCTACACTTA
Statistics
Matches: 140, Mismatches: 9, Indels: 15
0.85 0.05 0.09
Matches are distributed among these distances:
46 44 0.31
52 86 0.61
53 10 0.07
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (51 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
Found at i:20667608 original size:98 final size:98
Alignment explanation
Indices: 20667488--20667711 Score: 394
Period size: 98 Copynumber: 2.3 Consensus size: 98
20667478 TTTGAGTACT
*
20667488 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
*
20667553 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* *
20667586 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
*
20667651 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
*
20667684 TCTGATCAAGAGACAAAGTGATAAGTGG
1 TCTGATCAAGTGACAAAGTGATAAGTGG
20667712 CTACACTTAT
Statistics
Matches: 119, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 119 1.00
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.28
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:20667720 original size:37 final size:37
Alignment explanation
Indices: 20667673--20667782 Score: 170
Period size: 37 Copynumber: 3.0 Consensus size: 37
20667663 TGATAGCTTC
*
20667673 GGCTATACTTATCTGATCAAGAGACAAAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
* *
20667710 GGCTACACTTATCTGATCAAGAAACAAAGTGATAGGT
1 GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
*
20667747 GGCTACACTTATCTGATC-AGGGAC-AAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
20667782 G
1 G
20667783 ATCATACGTA
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
35 11 0.16
36 4 0.06
37 52 0.78
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.25
Consensus pattern (37 bp):
GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
Found at i:20668440 original size:41 final size:41
Alignment explanation
Indices: 20668383--20668508 Score: 252
Period size: 41 Copynumber: 3.1 Consensus size: 41
20668373 GGGTGTTACA
20668383 GACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCGGT
1 GACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCGGT
20668424 GACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCGGT
1 GACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCGGT
20668465 GACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCGGT
1 GACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCGGT
20668506 GAC
1 GAC
20668509 TTCTTTTTCC
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 85 1.00
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (41 bp):
GACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCGGT
Found at i:20671290 original size:5 final size:5
Alignment explanation
Indices: 20671280--20671323 Score: 88
Period size: 5 Copynumber: 8.8 Consensus size: 5
20671270 TCCTTCATCA
20671280 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATA
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATA
20671324 AATATTAGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (5 bp):
CATAT
Found at i:20682213 original size:27 final size:28
Alignment explanation
Indices: 20682174--20682230 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
20682164 ATATCATTTG
* *
20682174 ACAAGTTTAAGTACT-AAATTAGATAAAA
1 ACAAGTTTAAGTA-TGAAATAAGAAAAAA
20682202 ACAAG-TTAAGTATGAAATAAGAAAAAA
1 ACAAGTTTAAGTATGAAATAAGAAAAAA
20682229 AC
1 AC
20682231 TAAATTAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 1 0.04
27 20 0.77
28 5 0.19
ACGTcount: A:0.58, C:0.07, G:0.12, T:0.23
Consensus pattern (28 bp):
ACAAGTTTAAGTATGAAATAAGAAAAAA
Found at i:20700230 original size:27 final size:27
Alignment explanation
Indices: 20700189--20700333 Score: 136
Period size: 27 Copynumber: 5.4 Consensus size: 27
20700179 AACACGCTAG
* *
20700189 GAAATGAATGCCTTTGTGGCAATTTAT
1 GAAAGGAATGCCTTTGTGGCAATATAT
* *
20700216 GAAAGGAATGACTTTGTGACAATATAT
1 GAAAGGAATGCCTTTGTGGCAATATAT
* *
20700243 GGAAGGAATGTCTTTGTGGCAATATAT
1 GAAAGGAATGCCTTTGTGGCAATATAT
* * *
20700270 G-AATGAATGCCTTCGTGGCAGACTCTA-
1 GAAAGGAATGCCTTTGTGGCA-A-TATAT
* *
20700297 -AAGGGAATGCCTTTGTGGCAA-ACTCT
1 GAAAGGAATGCCTTTGTGGCAATA-TAT
20700323 GAAAGGAATGC
1 GAAAGGAATGC
20700334 ATTAACAGTG
Statistics
Matches: 95, Mismatches: 17, Indels: 12
0.77 0.14 0.10
Matches are distributed among these distances:
25 1 0.01
26 17 0.18
27 74 0.78
28 3 0.03
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (27 bp):
GAAAGGAATGCCTTTGTGGCAATATAT
Found at i:20702685 original size:14 final size:14
Alignment explanation
Indices: 20702666--20702693 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
20702656 CGCATACATA
20702666 TCAAAATATCAATC
1 TCAAAATATCAATC
20702680 TCAAAATATCAATC
1 TCAAAATATCAATC
20702694 ATCATATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (14 bp):
TCAAAATATCAATC
Found at i:20702952 original size:47 final size:48
Alignment explanation
Indices: 20702833--20702977 Score: 166
Period size: 47 Copynumber: 2.9 Consensus size: 48
20702823 CTCGTCCATT
* *
20702833 TGAAACACAATTTGTGGACAAACCACCACTGATTTGCAGATAAACTGCAAC
1 TGAAACAC--TTTGTGGACAAGCCACCAC-GATATGCAGATAAACTGCAAC
* * *
20702884 TGATAACACTTTGTGGACAAGCCACCAC-ATATGTAGATATACTGCCAC
1 TGA-AACACTTTGTGGACAAGCCACCACGATATGCAGATAAACTGCAAC
* **
20702932 TGAAACACTTTGTGGACAAGCCACCACTGATTTATAGATAAACTGC
1 TGAAACACTTTGTGGACAAGCCACCAC-GATATGCAGATAAACTGC
20702978 CACATACTTC
Statistics
Matches: 83, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
47 24 0.29
48 19 0.23
49 14 0.17
50 18 0.22
51 3 0.04
52 5 0.06
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (48 bp):
TGAAACACTTTGTGGACAAGCCACCACGATATGCAGATAAACTGCAAC
Found at i:20705109 original size:23 final size:21
Alignment explanation
Indices: 20705036--20705100 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
20705026 CCTGATCAGT
* *
20705036 ATACGACACA-TAAGTGCCTG
1 ATACGACACACGAGGTGCCTG
*
20705056 AAACGACACACGAGGTGCCTG
1 ATACGACACACGAGGTGCCTG
20705077 ATACGACACACGAGGTGCCTG
1 ATACGACACACGAGGTGCCTG
20705098 ATA
1 ATA
20705101 TATGACACAT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 9 0.22
21 31 0.77
ACGTcount: A:0.34, C:0.26, G:0.25, T:0.15
Consensus pattern (21 bp):
ATACGACACACGAGGTGCCTG
Found at i:20706294 original size:3 final size:3
Alignment explanation
Indices: 20706286--20706314 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
20706276 TATTCCTAGT
20706286 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
20706315 TATTTTAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:20706457 original size:14 final size:14
Alignment explanation
Indices: 20706438--20706483 Score: 83
Period size: 14 Copynumber: 3.3 Consensus size: 14
20706428 TATTTAAAAT
20706438 ATAATAATAATTTA
1 ATAATAATAATTTA
*
20706452 ATAATACTAATTTA
1 ATAATAATAATTTA
20706466 ATAATAATAATTTA
1 ATAATAATAATTTA
20706480 ATAA
1 ATAA
20706484 AATTTTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAATAATAATTTA
Found at i:20708101 original size:12 final size:12
Alignment explanation
Indices: 20708084--20708111 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
20708074 CTTCTCGAAG
20708084 AATCAACTCTTT
1 AATCAACTCTTT
20708096 AATCAACTCTTT
1 AATCAACTCTTT
20708108 AATC
1 AATC
20708112 TCAAAAGTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (12 bp):
AATCAACTCTTT
Found at i:20713113 original size:14 final size:14
Alignment explanation
Indices: 20713094--20713139 Score: 83
Period size: 14 Copynumber: 3.3 Consensus size: 14
20713084 TATTTAAAAT
20713094 ATAATAATAATTTA
1 ATAATAATAATTTA
*
20713108 ATAATACTAATTTA
1 ATAATAATAATTTA
20713122 ATAATAATAATTTA
1 ATAATAATAATTTA
20713136 ATAA
1 ATAA
20713140 AATTTTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAATAATAATTTA
Found at i:20714327 original size:32 final size:32
Alignment explanation
Indices: 20714291--20714354 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
20714281 GTTACAACAA
*
20714291 AGTAAGTACTCCGAGGA-TCGTACCTTAGGGAT
1 AGTAAGTACTCCGAGGAGT-GTACCTAAGGGAT
*
20714323 AGTAAGTACTCTGAGGAGTGTACCTAAGGGAT
1 AGTAAGTACTCCGAGGAGTGTACCTAAGGGAT
20714355 TGCAATTTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 28 0.97
33 1 0.03
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.25
Consensus pattern (32 bp):
AGTAAGTACTCCGAGGAGTGTACCTAAGGGAT
Found at i:20721915 original size:50 final size:50
Alignment explanation
Indices: 20721841--20722027 Score: 178
Period size: 50 Copynumber: 3.6 Consensus size: 50
20721831 TCTTGTACTA
* * ** *
20721841 CCAATGCCATTTCCCAGATATGGTCTTACATGGGAGTTCCCTTATCGGTG
1 CCAATGCCATGTCCCAGAAATGGTCTTACATGGGACCTCCCATATCGGTG
* * * *
20721891 CCCATGCCATGTCCGAGAAATGGTCTTACGA-GGGACCTCTCATCTCGGTG
1 CCAATGCCATGTCCCAGAAATGGTCTTAC-ATGGGACCTCCCATATCGGTG
* * * *
20721941 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGATG
1 CCAATGCCATGTCCCAGAAATGGTCTTACATGGGACCTCCCAT-A--TC---GGTG
*
20721997 CCAATGCCATGTCCCAGACATGGTCTTACAT
1 CCAATGCCATGTCCCAGAAATGGTCTTACAT
20722028 AGGATCTCTT
Statistics
Matches: 113, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
49 1 0.01
50 76 0.67
51 1 0.01
53 2 0.02
56 33 0.29
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (50 bp):
CCAATGCCATGTCCCAGAAATGGTCTTACATGGGACCTCCCATATCGGTG
Found at i:20727109 original size:30 final size:30
Alignment explanation
Indices: 20727073--20727132 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
20727063 TGGGAGGTTC
20727073 TGCATGTTGCAACAGTTGTTGGAATAAACG
1 TGCATGTTGCAACAGTTGTTGGAATAAACG
20727103 TGCATGTTGCAACAGTTGTTGGAATAAACG
1 TGCATGTTGCAACAGTTGTTGGAATAAACG
20727133 GTAGAGTGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.30
Consensus pattern (30 bp):
TGCATGTTGCAACAGTTGTTGGAATAAACG
Found at i:20731702 original size:33 final size:33
Alignment explanation
Indices: 20731665--20731760 Score: 111
Period size: 33 Copynumber: 2.9 Consensus size: 33
20731655 GATATTCTAG
* * * *
20731665 TGGGATAGTAAACATAAAATAGAGATAGTCCGT
1 TGGGACAGTAAACACAAAACAGAGATAGTCCGC
* *
20731698 TGGGACGGTAAACACAGAACAGAGATAGTCCGC
1 TGGGACAGTAAACACAAAACAGAGATAGTCCGC
* * *
20731731 TAGGACAGTAAACACAGAACAAAGATAGTC
1 TGGGACAGTAAACACAAAACAGAGATAGTC
20731761 TATCAGGACA
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.43, C:0.16, G:0.25, T:0.17
Consensus pattern (33 bp):
TGGGACAGTAAACACAAAACAGAGATAGTCCGC
Found at i:20732378 original size:56 final size:55
Alignment explanation
Indices: 20732226--20732378 Score: 131
Period size: 56 Copynumber: 2.8 Consensus size: 55
20732216 CGGGATAGAA
* *
20732226 ATAA-TTTTTTTCATATACTTGTTTATTGAATGATTA-ATTATCGAGGTGAGTAT
1 ATAATTTTTTTTCATATGCTTGTTTATTGAATGATTAGAATATCGAGGTGAGTAT
* * * * *
20732279 ATCATTTTCGTATGAATTGATTTGC-TG-TGATTGAA-G-TT-GAATATTGAGGTGAGTAT
1 ATAATTTT--T-T---TTCATATGCTTGTTTATTGAATGATTAGAATATCGAGGTGAGTAT
20732335 ATAATTTTTTTTCATATGCTTGTTTATTGAATGATTAGTAATAT
1 ATAATTTTTTTTCATATGCTTGTTTATTGAATGATTAG-AATAT
20732379 GATTTAATTA
Statistics
Matches: 75, Mismatches: 11, Indels: 25
0.68 0.10 0.23
Matches are distributed among these distances:
50 7 0.09
51 2 0.03
52 7 0.09
53 5 0.07
54 6 0.08
55 1 0.01
56 30 0.40
57 2 0.03
58 7 0.09
59 2 0.03
60 6 0.08
ACGTcount: A:0.29, C:0.05, G:0.18, T:0.48
Consensus pattern (55 bp):
ATAATTTTTTTTCATATGCTTGTTTATTGAATGATTAGAATATCGAGGTGAGTAT
Found at i:20733758 original size:17 final size:15
Alignment explanation
Indices: 20733728--20733761 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
20733718 CTCCCAGACT
20733728 TAATAAAATAATAAA
1 TAATAAAATAATAAA
20733743 TAATAAAACTTAATAAA
1 TAATAAAA--TAATAAA
20733760 TA
1 TA
20733762 CAATATTGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
17 9 0.53
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (15 bp):
TAATAAAATAATAAA
Found at i:20746174 original size:17 final size:18
Alignment explanation
Indices: 20746152--20746187 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
20746142 ACTTTATGTC
20746152 TTAAAA-AATATAATATA
1 TTAAAATAATATAATATA
20746169 TTAAAATTAATATAATATA
1 TTAAAA-TAATATAATATA
20746188 AGCCATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
19 11 0.65
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TTAAAATAATATAATATA
Found at i:20770861 original size:59 final size:59
Alignment explanation
Indices: 20770769--20770886 Score: 227
Period size: 59 Copynumber: 2.0 Consensus size: 59
20770759 AAATACAGAC
20770769 TTGATTTTAATTGAAAACATGATCGATTGAGGCAAAAACATTATAAGCATGAATCAAAT
1 TTGATTTTAATTGAAAACATGATCGATTGAGGCAAAAACATTATAAGCATGAATCAAAT
*
20770828 TTGATTTTAATTGAAAACATGATCGATTGAGGCACAAACATTATAAGCATGAATCAAAT
1 TTGATTTTAATTGAAAACATGATCGATTGAGGCAAAAACATTATAAGCATGAATCAAAT
20770887 AAATATTATT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (59 bp):
TTGATTTTAATTGAAAACATGATCGATTGAGGCAAAAACATTATAAGCATGAATCAAAT
Found at i:20774781 original size:20 final size:20
Alignment explanation
Indices: 20774756--20774805 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
20774746 AGGAAGATGA
20774756 TACTTAATTCA-TCTTTTATT
1 TACTTAATT-ATTCTTTTATT
*
20774776 TACTTAGTTATTCTTTTATT
1 TACTTAATTATTCTTTTATT
*
20774796 TACTAAATTA
1 TACTTAATTA
20774806 CTACTTTAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 1 0.04
20 25 0.96
ACGTcount: A:0.28, C:0.12, G:0.02, T:0.58
Consensus pattern (20 bp):
TACTTAATTATTCTTTTATT
Found at i:20775382 original size:10 final size:10
Alignment explanation
Indices: 20775369--20775450 Score: 80
Period size: 10 Copynumber: 8.4 Consensus size: 10
20775359 TTTTGATACA
20775369 TTTTATAATT
1 TTTTATAATT
*
20775379 TTTTATGA-T
1 TTTTATAATT
**
20775388 TTTTATAAAA
1 TTTTATAATT
*
20775398 TTTTACAATT
1 TTTTATAATT
20775408 TTTTATATATT
1 TTTTATA-ATT
**
20775419 TTTTACGA-T
1 TTTTATAATT
20775428 TTTTATAA-T
1 TTTTATAATT
20775437 TTTTATAATT
1 TTTTATAATT
20775447 TTTT
1 TTTT
20775451 TCTGTTTTTA
Statistics
Matches: 58, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
9 24 0.41
10 26 0.45
11 8 0.14
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (10 bp):
TTTTATAATT
Found at i:20775390 original size:29 final size:27
Alignment explanation
Indices: 20775358--20775449 Score: 87
Period size: 29 Copynumber: 3.2 Consensus size: 27
20775348 TTAAAGTGCC
20775358 TTTTTGATACATTTTATAATTTTTTATGA
1 TTTTT-ATACATTTTATAATTTTTTAT-A
* *
20775387 TTTTTATAAAATTTTACAATTTTTTATA
1 TTTTTAT-ACATTTTATAATTTTTTATA
*
20775415 TATTTTTTACGATTTTTATAA-TTTTTATAA
1 T-TTTTATAC-A-TTTTATAATTTTTTAT-A
20775445 TTTTT
1 TTTTT
20775450 TTCTGTTTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
28 5 0.09
29 39 0.74
30 9 0.17
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.64
Consensus pattern (27 bp):
TTTTTATACATTTTATAATTTTTTATA
Found at i:20775450 original size:29 final size:29
Alignment explanation
Indices: 20775369--20775468 Score: 82
Period size: 29 Copynumber: 3.4 Consensus size: 29
20775359 TTTTGATACA
* * * *
20775369 TTTTATAATTTTTTATGATTTTTATA-AAA
1 TTTTATAA-TTTTTATAATTTTTTTACGAT
*
20775398 TTTTACAATTTTT-TATATATTTTTTACGAT
1 TTTTATAATTTTTATA-AT-TTTTTTACGAT
20775428 TTTTATAATTTTTATAATTTTTTT-CTG-T
1 TTTTATAATTTTTATAATTTTTTTAC-GAT
20775456 TTTTATATATTTT
1 TTTTATA-ATTTT
20775469 GAATTAAAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
27 1 0.02
28 16 0.27
29 25 0.42
30 15 0.25
31 2 0.03
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.67
Consensus pattern (29 bp):
TTTTATAATTTTTATAATTTTTTTACGAT
Found at i:20775733 original size:86 final size:86
Alignment explanation
Indices: 20775633--20775809 Score: 230
Period size: 86 Copynumber: 2.1 Consensus size: 86
20775623 CCTAATGGTC
* * ** *
20775633 TTTTTTATGTATTTTGACAGTTCAAGTACCCAATTAAGTGCAAAAAAAA-GGGGTTTAACTGCTT
1 TTTTTTATGCATTTTGAAAGTTCAAGTACCCAATTAAGTGCAAAAAAAAGGGGGGCTAACTGCTG
* *
20775697 TTTTTGAAAAAGTTTGAGAAT
66 TTTTAGAAAAAATTTGAGAAT
* * * *
20775718 TTTTTTGATGCATTTTGAAAGTTTAAGTACCTAATTGAGTGCAAAAAAAAGGGGGGCTAATTGCT
1 TTTTTT-ATGCATTTTGAAAGTTCAAGTACCCAATTAAGTGCAAAAAAAAGGGGGGCTAACTGCT
*
20775783 GTTTTAGAAAAAATTTGAGAGT
65 GTTTTAGAAAAAATTTGAGAAT
20775805 TTTTT
1 TTTTT
20775810 ACGCCCTTAA
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
85 6 0.08
86 38 0.49
87 34 0.44
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (86 bp):
TTTTTTATGCATTTTGAAAGTTCAAGTACCCAATTAAGTGCAAAAAAAAGGGGGGCTAACTGCTG
TTTTAGAAAAAATTTGAGAAT
Found at i:20776785 original size:31 final size:30
Alignment explanation
Indices: 20776746--20776808 Score: 90
Period size: 31 Copynumber: 2.1 Consensus size: 30
20776736 ACTGATTAAT
20776746 TGAATAAAATTCATACATAATAATACATGG
1 TGAATAAAATTCATACATAATAATACATGG
* * *
20776776 TGAAGTAAAATTTATACGTAATAATATATGG
1 TGAA-TAAAATTCATACATAATAATACATGG
20776807 TG
1 TG
20776809 GAACTCAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 4 0.14
31 25 0.86
ACGTcount: A:0.46, C:0.06, G:0.14, T:0.33
Consensus pattern (30 bp):
TGAATAAAATTCATACATAATAATACATGG
Found at i:20776826 original size:34 final size:31
Alignment explanation
Indices: 20776746--20776833 Score: 83
Period size: 31 Copynumber: 2.8 Consensus size: 31
20776736 ACTGATTAAT
20776746 TGAA-TAAAAT-TCATACATAATAATACATGG
1 TGAACTAAAATCT-ATACATAATAATACATGG
* * * *
20776776 TGAAGTAAAATTTATACGTAATAATATATGG
1 TGAACTAAAATCTATACATAATAATACATGG
20776807 TGGAACTCAAAGATCTATACAT-ATAAT
1 T-GAACT-AAA-ATCTATACATAATAAT
20776834 TTACAAGATG
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
30 4 0.08
31 23 0.48
32 5 0.10
33 8 0.17
34 8 0.17
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.32
Consensus pattern (31 bp):
TGAACTAAAATCTATACATAATAATACATGG
Found at i:20778309 original size:14 final size:14
Alignment explanation
Indices: 20778292--20778318 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
20778282 GAGTATGGTA
20778292 AAATATTTAAAAAT
1 AAATATTTAAAAAT
20778306 AAATATTTAAAAA
1 AAATATTTAAAAA
20778319 GGTACTAATA
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:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATATTTAAAAAT
Found at i:20780116 original size:44 final size:43
Alignment explanation
Indices: 20780067--20780198 Score: 192
Period size: 44 Copynumber: 3.0 Consensus size: 43
20780057 ACTAATGTAA
** *
20780067 TATTTGATAGTACAAAATTAGTTGAAAATTTTAGAAGAGCTAAT
1 TATTTG-TAGTACAAAATTAGTTGAAAGCTCTAGAAGAGCTAAT
*
20780111 TATTTGCTAGTTCAAAATTAGTTGAAAGCTCTAGAAGAGCTAAT
1 TATTTG-TAGTACAAAATTAGTTGAAAGCTCTAGAAGAGCTAAT
*
20780155 TATTTTGTAGTATAAAATTAGTTGAAAGCTCTAGAAGAGCTAAT
1 TA-TTTGTAGTACAAAATTAGTTGAAAGCTCTAGAAGAGCTAAT
20780199 ATATCAATAT
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
44 76 0.95
45 4 0.05
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.36
Consensus pattern (43 bp):
TATTTGTAGTACAAAATTAGTTGAAAGCTCTAGAAGAGCTAAT
Found at i:20783195 original size:27 final size:27
Alignment explanation
Indices: 20783147--20783442 Score: 260
Period size: 27 Copynumber: 11.0 Consensus size: 27
20783137 AAATCCATAA
**
20783147 CAGTCATTTTATCTCCTA--GGGGTATAA
1 CAGTCATTTTA-C-CCTATGGGGGTATTT
20783174 CAGTCATTTTACCCTATGGGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
* * *
20783201 CAGTCATTCTACCCCATTGGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
*
20783228 CGGTCATTTTACCCTATGGGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
* * * *
20783255 C-GATTATTTTACCTTAT-AGGGTGTTT
1 CAG-TCATTTTACCCTATGGGGGTATTT
* * *
20783281 CGGTCATTCTACCCTATAGGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
* * * *
20783308 CAGTCATTCTATCTTATAGGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
* * *
20783335 C-GATCATTCTACCTTATGCGGGTATTT
1 CAG-TCATTTTACCCTATGGGGGTATTT
* * *
20783362 CGGTCATTTTACCCTATGGAGGTGTTT
1 CAGTCATTTTACCCTATGGGGGTATTT
* *
20783389 CAGTCATTCTACCCTATAGGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
* * * *
20783416 CGGTTATTTTATCCTATGGAGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
20783443 TGGTCATAAC
Statistics
Matches: 222, Mismatches: 40, Indels: 14
0.80 0.14 0.05
Matches are distributed among these distances:
25 4 0.02
26 22 0.10
27 195 0.88
28 1 0.00
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.41
Consensus pattern (27 bp):
CAGTCATTTTACCCTATGGGGGTATTT
Found at i:20783251 original size:81 final size:81
Alignment explanation
Indices: 20783177--20783449 Score: 325
Period size: 81 Copynumber: 3.4 Consensus size: 81
20783167 GGTATAACAG
* * * *
20783177 TCATTTTACCCTATGGGGGTATTTCAGTCATTCTACCCCATTGGGGTATTTCGGTCATTTTACCC
1 TCATTTTACCCTATGGGGGTATTTCGGTCATTCTACCCTATTGGGGTATTTCAGTCATTCTACCC
*
20783242 TATGGGGGTATTTCGA
66 TATAGGGGTATTTCGA
* * * * * * *
20783258 TTATTTTACCTTAT-AGGGTGTTTCGGTCATTCTACCCTATAGGGGTATTTCAGTCATTCTATCT
1 TCATTTTACCCTATGGGGGTATTTCGGTCATTCTACCCTATTGGGGTATTTCAGTCATTCTACCC
20783322 TATAGGGGTATTTCGA
66 TATAGGGGTATTTCGA
* * * * *
20783338 TCATTCTACCTTATGCGGGTATTTCGGTCATTTTACCCTA-TGGAGGTGTTTCAGTCATTCTACC
1 TCATTTTACCCTATGGGGGTATTTCGGTCATTCTACCCTATTGG-GGTATTTCAGTCATTCTACC
*
20783402 CTATAGGGGTATTTCGG
65 CTATAGGGGTATTTCGA
* * * *
20783419 TTATTTTATCCTATGGAGGTATTTTGGTCAT
1 TCATTTTACCCTATGGGGGTATTTCGGTCAT
20783450 AACAATGTAA
Statistics
Matches: 161, Mismatches: 29, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
80 70 0.43
81 91 0.57
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.42
Consensus pattern (81 bp):
TCATTTTACCCTATGGGGGTATTTCGGTCATTCTACCCTATTGGGGTATTTCAGTCATTCTACCC
TATAGGGGTATTTCGA
Found at i:20783309 original size:107 final size:108
Alignment explanation
Indices: 20783174--20783416 Score: 344
Period size: 107 Copynumber: 2.3 Consensus size: 108
20783164 AGGGGTATAA
* * * * *
20783174 CAGTCATTTTACCCTATGGGGGTATTTCAGTCATTCTACCCCATTGGGGTATTTCGGTCATTTTA
1 CAGTCATTCTACCCTATAGGGGTATTTCAGTCATTCTACCCCATAGGGGTATTTCGATCATTCTA
* * *
20783239 CCCTATGGGGGTATTTCGATTATTTTACCTTATAG-GGTGTTT
66 CCCTATGCGGGTATTTCGATCATTTTACCCTATAGAGGTGTTT
* * **
20783281 CGGTCATTCTACCCTATAGGGGTATTTCAGTCATTCTATCTTATAGGGGTATTTCGATCATTCTA
1 CAGTCATTCTACCCTATAGGGGTATTTCAGTCATTCTACCCCATAGGGGTATTTCGATCATTCTA
* * *
20783346 CCTTATGCGGGTATTTCGGTCATTTTACCCTATGGAGGTGTTT
66 CCCTATGCGGGTATTTCGATCATTTTACCCTATAGAGGTGTTT
20783389 CAGTCATTCTACCCTATAGGGGTATTTC
1 CAGTCATTCTACCCTATAGGGGTATTTC
20783417 GGTTATTTTA
Statistics
Matches: 119, Mismatches: 16, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
107 85 0.71
108 34 0.29
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.41
Consensus pattern (108 bp):
CAGTCATTCTACCCTATAGGGGTATTTCAGTCATTCTACCCCATAGGGGTATTTCGATCATTCTA
CCCTATGCGGGTATTTCGATCATTTTACCCTATAGAGGTGTTT
Found at i:20783449 original size:54 final size:53
Alignment explanation
Indices: 20783149--20783449 Score: 291
Period size: 54 Copynumber: 5.6 Consensus size: 53
20783139 ATCCATAACA
** * * * *
20783149 GTCATTTTATCTCCTA-GGGGTATAACAGTCATTTTACCCTATGGGGGTATTTCA
1 GTCATTTTA-C-CCTATGGGGTATTTCGGTCATTCTACCCTATAGGGGTATTTCG
* * * *
20783203 GTCATTCTACCCCATTGGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTA-TGGGGTATTTCGGTCATTCTACCCTATAGGGGTATTTCG
* * * * * *
20783257 ATTATTTTACCTTATAGGGTGTTTCGGTCATTCTACCCTATAGGGGTATTTCA
1 GTCATTTTACCCTATGGGGTATTTCGGTCATTCTACCCTATAGGGGTATTTCG
* * * * *
20783310 GTCATTCTATCTTATAGGGGTATTTCGATCATTCTACCTTAT-GCGGGTATTTCG
1 GTCATTTTACCCTAT-GGGGTATTTCGGTCATTCTACCCTATAG-GGGTATTTCG
* *
20783364 GTCATTTTACCCTATGGAGGTGTTTCAGTCATTCTACCCTATAGGGGTATTTCG
1 GTCATTTTACCCTATGG-GGTATTTCGGTCATTCTACCCTATAGGGGTATTTCG
* * *
20783418 GTTATTTTATCCTATGGAGGTATTTTGGTCAT
1 GTCATTTTACCCTATGG-GGTATTTCGGTCAT
20783450 AACAATGTAA
Statistics
Matches: 204, Mismatches: 37, Indels: 12
0.81 0.15 0.05
Matches are distributed among these distances:
52 3 0.01
53 49 0.24
54 151 0.74
55 1 0.00
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.42
Consensus pattern (53 bp):
GTCATTTTACCCTATGGGGTATTTCGGTCATTCTACCCTATAGGGGTATTTCG
Found at i:20788124 original size:29 final size:29
Alignment explanation
Indices: 20788032--20788151 Score: 170
Period size: 30 Copynumber: 4.0 Consensus size: 29
20788022 CATATTTATG
* *
20788032 GAAAATCAAAGATATGGGTATCAAATAAT
1 GAAAGTCAAAGATATGGGTATCAAATATT
20788061 GAAAAGTCAAAGATATGGGTATCAAATATT
1 G-AAAGTCAAAGATATGGGTATCAAATATT
20788091 GGAAAGTCAAAGATAT-GGTATCAAATATT
1 -GAAAGTCAAAGATATGGGTATCAAATATT
*
20788120 AGAAAGTCAAAGATATGGGTATCGAGATATT
1 -GAAAGTCAAAGATATGGGTATC-AAATATT
20788151 G
1 G
20788152 GCATAATAAA
Statistics
Matches: 83, Mismatches: 4, Indels: 7
0.88 0.04 0.07
Matches are distributed among these distances:
29 29 0.35
30 47 0.57
31 7 0.08
ACGTcount: A:0.46, C:0.07, G:0.22, T:0.26
Consensus pattern (29 bp):
GAAAGTCAAAGATATGGGTATCAAATATT
Found at i:20788128 original size:59 final size:61
Alignment explanation
Indices: 20788030--20788152 Score: 189
Period size: 59 Copynumber: 2.0 Consensus size: 61
20788020 TCCATATTTA
20788030 TGGAAAATCAAAGATATGGGTATCAAATAATGAAAAGTCAAAGATATGGGTATC-AAATAT
1 TGGAAAATCAAAGATATGGGTATCAAATAATGAAAAGTCAAAGATATGGGTATCGAAATAT
* * *
20788090 TGGAAAGTCAAAGATAT-GGTATCAAAT-ATTAGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAATCAAAGATATGGGTATCAAATAATGA-AAAGTCAAAGATATGGGTATCGAAATAT
20788150 TGG
1 TGG
20788153 CATAATAAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
58 3 0.05
59 31 0.53
60 24 0.41
ACGTcount: A:0.45, C:0.07, G:0.23, T:0.26
Consensus pattern (61 bp):
TGGAAAATCAAAGATATGGGTATCAAATAATGAAAAGTCAAAGATATGGGTATCGAAATAT
Found at i:20792748 original size:15 final size:15
Alignment explanation
Indices: 20792728--20792805 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 15
20792718 TTTATGGAAA
20792728 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* **
20792743 ATCAAATA-ATGGAA
1 ATCAAAGATATGGGT
20792757 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
20792773 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
20792787 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
20792803 ATC
1 ATC
20792806 GAGATATTGG
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
14 9 0.19
15 29 0.62
16 9 0.19
ACGTcount: A:0.44, C:0.08, G:0.23, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:20792757 original size:30 final size:30
Alignment explanation
Indices: 20792721--20792805 Score: 152
Period size: 30 Copynumber: 2.8 Consensus size: 30
20792711 ATCCATATTT
*
20792721 ATGGAAAATCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
20792751 ATGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
20792781 TTGGAAAGTCAAAGATATGGGTATC
1 ATGGAAAGTCAAAGATATGGGTATC
20792806 GAGATATTGG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.45, C:0.07, G:0.24, T:0.25
Consensus pattern (30 bp):
ATGGAAAGTCAAAGATATGGGTATCAAATA
Found at i:20797901 original size:42 final size:42
Alignment explanation
Indices: 20797854--20797952 Score: 137
Period size: 42 Copynumber: 2.4 Consensus size: 42
20797844 TTCAGTATAG
* * * *
20797854 CTGATGATGCACTTATGTGCCAGTATATTTGCATCGATTTC-T
1 CTGATGATGCACTTATGTGCCAATATAATTACATCGA-TACAT
*
20797896 CTGATGATGCACTTATGTGCCAATATAATTACTTCGATACAT
1 CTGATGATGCACTTATGTGCCAATATAATTACATCGATACAT
20797938 CTGATGATGCACTTA
1 CTGATGATGCACTTA
20797953 CGTGGAAGTA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
41 2 0.04
42 49 0.96
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.37
Consensus pattern (42 bp):
CTGATGATGCACTTATGTGCCAATATAATTACATCGATACAT
Found at i:20803328 original size:24 final size:23
Alignment explanation
Indices: 20803294--20803340 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
20803284 TTTACGTTCT
20803294 GGAAAGCTAAAAGAAAAAGAAAAA
1 GGAAAGCTAAAAG-AAAAGAAAAA
*
20803318 GGAAAGTTAAAAGAAAAGAAAAA
1 GGAAAGCTAAAAGAAAAGAAAAA
20803341 TTAAAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.70, C:0.02, G:0.21, T:0.06
Consensus pattern (23 bp):
GGAAAGCTAAAAGAAAAGAAAAA
Found at i:20803335 original size:17 final size:18
Alignment explanation
Indices: 20803308--20803346 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
20803298 AGCTAAAAGA
* *
20803308 AAAAGAAAAAGGAAAGTT
1 AAAAGAAAAAGAAAAATT
20803326 AAAAG-AAAAGAAAAATT
1 AAAAGAAAAAGAAAAATT
20803343 AAAA
1 AAAA
20803347 TTATAGGGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.10
Consensus pattern (18 bp):
AAAAGAAAAAGAAAAATT
Found at i:20806689 original size:17 final size:16
Alignment explanation
Indices: 20806667--20806698 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
20806657 AATAGTTGTG
20806667 ATAATTATACATTTAAC
1 ATAATTATA-ATTTAAC
20806684 ATAATTATAATTTAA
1 ATAATTATAATTTAA
20806699 TAGAAGTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (16 bp):
ATAATTATAATTTAAC
Found at i:20806720 original size:43 final size:44
Alignment explanation
Indices: 20806649--20806752 Score: 111
Period size: 44 Copynumber: 2.3 Consensus size: 44
20806639 TTTAAAAAGT
* * * * *
20806649 TGAAATAAAATAGTTGTGATAATTATACATTTA-ACATAATTATAA
1 TGAAAT-AAA-AGTTATGGTAATAATACATTTACAAATAATTAGAA
** *
20806694 TTTAATAGAAGTTATGGTAATAATACATTTACAAATAATTAGAA
1 TGAAATAAAAGTTATGGTAATAATACATTTACAAATAATTAGAA
20806738 TGAAATAAAAGTTAT
1 TGAAATAAAAGTTAT
20806753 TCCAATTTTA
Statistics
Matches: 47, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
43 19 0.40
44 24 0.51
45 4 0.09
ACGTcount: A:0.49, C:0.04, G:0.11, T:0.37
Consensus pattern (44 bp):
TGAAATAAAAGTTATGGTAATAATACATTTACAAATAATTAGAA
Found at i:20808275 original size:11 final size:11
Alignment explanation
Indices: 20808259--20808288 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
20808249 TTTTTTAAAT
20808259 AAAAATAATAA
1 AAAAATAATAA
20808270 AAAAATAATAA
1 AAAAATAATAA
20808281 AAAAATAA
1 AAAAATAA
20808289 GATACTTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAAATAATAA
Found at i:20808430 original size:16 final size:17
Alignment explanation
Indices: 20808409--20808450 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
20808399 TTTAAAAAAA
20808409 TATAAAATTTAG-ATTT
1 TATAAAATTTAGAATTT
*
20808425 TATAAATATTTTGAATTT
1 TATAAA-ATTTAGAATTT
20808443 TA-AAAATT
1 TATAAAATT
20808451 ATTTTGAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 9 0.39
17 8 0.35
18 6 0.26
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (17 bp):
TATAAAATTTAGAATTT
Found at i:20808483 original size:20 final size:20
Alignment explanation
Indices: 20808422--20808476 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
20808412 AAAATTTAGA
*
20808422 TTTTATAAA-TATTTTGAA-
1 TTTTAAAAATTATTTTGAAC
20808440 TTTTAAAAATTATTTTGAAC
1 TTTTAAAAATTATTTTGAAC
*
20808460 TTTTGAAAATTATTTTG
1 TTTTAAAAATTATTTTG
20808477 TGTTTTTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.24
19 9 0.27
20 16 0.48
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (20 bp):
TTTTAAAAATTATTTTGAAC
Found at i:20830296 original size:27 final size:27
Alignment explanation
Indices: 20830252--20830305 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
20830242 CCATAATCCT
*
20830252 CGTGTTTACTATCCTGTTAGAATATTC
1 CGTGTTTAATATCCTGTTAGAATATTC
* * *
20830279 CGTGTTTAATGTCTTGTTAGACTATTC
1 CGTGTTTAATATCCTGTTAGAATATTC
20830306 TACGATGCCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.20, C:0.17, G:0.17, T:0.46
Consensus pattern (27 bp):
CGTGTTTAATATCCTGTTAGAATATTC
Found at i:20834622 original size:48 final size:48
Alignment explanation
Indices: 20834553--20834650 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
20834543 TTACATAGTT
20834553 TTTTTTCCTTTACTTTTTAGATTATGAGAAGCTCGATCGGGTTGGAAG
1 TTTTTTCCTTTACTTTTTAGATTATGAGAAGCTCGATCGGGTTGGAAG
20834601 TTTTTTCCTTTACTTTTTAGATTATGAGAAGCTCGATCGGGTTGGAAG
1 TTTTTTCCTTTACTTTTTAGATTATGAGAAGCTCGATCGGGTTGGAAG
20834649 TT
1 TT
20834651 CGTCGAAGAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.20, C:0.12, G:0.22, T:0.45
Consensus pattern (48 bp):
TTTTTTCCTTTACTTTTTAGATTATGAGAAGCTCGATCGGGTTGGAAG
Found at i:20840913 original size:6 final size:6
Alignment explanation
Indices: 20840902--20840942 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
20840892 AGGATTTCTA
*
20840902 ATTATC ATTATC ATTATC ATTATC ATTATC ATTATT ATTAT
1 ATTATC ATTATC ATTATC ATTATC ATTATC ATTATC ATTAT
20840943 ATTTACACAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.34, C:0.12, G:0.00, T:0.54
Consensus pattern (6 bp):
ATTATC
Found at i:20844730 original size:45 final size:45
Alignment explanation
Indices: 20844679--20844769 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
20844669 GAATTAAGAT
20844679 AGGTGAATCAGCCTTCTAGTAAGCCTTATAGTTTTGCACATTATG
1 AGGTGAATCAGCCTTCTAGTAAGCCTTATAGTTTTGCACATTATG
20844724 AGGTGAATCAGCCTTCTAGTAAGCCTTATAGTTTTGCACATTATG
1 AGGTGAATCAGCCTTCTAGTAAGCCTTATAGTTTTGCACATTATG
20844769 A
1 A
20844770 CTATATAAGG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (45 bp):
AGGTGAATCAGCCTTCTAGTAAGCCTTATAGTTTTGCACATTATG
Found at i:20847391 original size:36 final size:36
Alignment explanation
Indices: 20847351--20847428 Score: 111
Period size: 36 Copynumber: 2.2 Consensus size: 36
20847341 ACAAAGACTA
* * *
20847351 TCACATGGCATGAATAACATACCCACATATTTACTG
1 TCACATGGCATGAACAACACACCCACATATTCACTG
* *
20847387 TCACATGGCATGAACAACACACCCTCATATTCACTT
1 TCACATGGCATGAACAACACACCCACATATTCACTG
20847423 TCACAT
1 TCACAT
20847429 CATTCATCAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.35, C:0.29, G:0.09, T:0.27
Consensus pattern (36 bp):
TCACATGGCATGAACAACACACCCACATATTCACTG
Done.