Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold71
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: 5741892
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.33
Warning! 121862 characters in sequence are not A, C, G, or T
File 16 of 33
Found at i:2520735 original size:71 final size:71
Alignment explanation
Indices: 2520652--2520795 Score: 225
Period size: 71 Copynumber: 2.0 Consensus size: 71
2520642 AGTAATTAAA
* * *
2520652 ATTATCTTAAATAGACAGATTATTGTATTAAATTATATCTATACAGATAAATATCCCTTTTAGAC
1 ATTATCTTAAATAGACAAATTATTATATTAAATTATATCTATACAGATAAATATCCCTTCTAGAC
2520717 TAAGAT
66 TAAGAT
* * * *
2520723 ATTATCTTAAATAGATAAATTATTATATTAAATTATATTTATACAGATAGATATCTCTTCTAGAC
1 ATTATCTTAAATAGACAAATTATTATATTAAATTATATCTATACAGATAAATATCCCTTCTAGAC
2520788 TAAGAT
66 TAAGAT
2520794 AT
1 AT
2520796 ACTTGTTTAA
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 66 1.00
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.41
Consensus pattern (71 bp):
ATTATCTTAAATAGACAAATTATTATATTAAATTATATCTATACAGATAAATATCCCTTCTAGAC
TAAGAT
Found at i:2521427 original size:40 final size:40
Alignment explanation
Indices: 2521371--2521451 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
2521361 GGAGATCATC
* *
2521371 ACATCAGAATTGCAGTAGCTTTGAAATGAACTTATACCAT
1 ACATCAGAATTACAGTAGCTTTAAAATGAACTTATACCAT
2521411 ACATCAGAATTACAGTAGCTTTAAAATGAACTTATACCAT
1 ACATCAGAATTACAGTAGCTTTAAAATGAACTTATACCAT
2521451 A
1 A
2521452 TACAAATAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.30
Consensus pattern (40 bp):
ACATCAGAATTACAGTAGCTTTAAAATGAACTTATACCAT
Found at i:2524717 original size:2 final size:2
Alignment explanation
Indices: 2524710--2524740 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2524700 ATAAAAATCT
2524710 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2524741 GGATTTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2525140 original size:3 final size:3
Alignment explanation
Indices: 2525134--2525166 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
2525124 CTTGTTTATA
*
2525134 AAG AAG AAG AAG AAG ACG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
2525167 CTGGATATCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.03, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2525216 original size:2 final size:2
Alignment explanation
Indices: 2525209--2525240 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2525199 TGAAGGAGAA
2525209 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2525241 TAATTATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2526503 original size:35 final size:36
Alignment explanation
Indices: 2526457--2526528 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
2526447 ATCGAAAATG
2526457 ATTTTTAATAAA-TTTTTTAAGTAAAAATATTAATC
1 ATTTTTAATAAATTTTTTTAAGTAAAAATATTAATC
2526492 ATTTTTAATAAATTTTTTTAAGTAAAAATATTAATC
1 ATTTTTAATAAATTTTTTTAAGTAAAAATATTAATC
2526528 A
1 A
2526529 ATCTAAAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 12 0.33
36 24 0.67
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (36 bp):
ATTTTTAATAAATTTTTTTAAGTAAAAATATTAATC
Found at i:2527362 original size:22 final size:22
Alignment explanation
Indices: 2527335--2527380 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
2527325 ATACTTTAAT
*
2527335 ATTTATATTATATATTATGATA
1 ATTTATATTATATAATATGATA
* *
2527357 ATTTATTTTATATAATATTATA
1 ATTTATATTATATAATATGATA
2527379 AT
1 AT
2527381 ATAAATATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
ATTTATATTATATAATATGATA
Found at i:2527411 original size:33 final size:34
Alignment explanation
Indices: 2527374--2527438 Score: 82
Period size: 33 Copynumber: 1.9 Consensus size: 34
2527364 TTATATAATA
2527374 TTATAATATAAATA-TT-A-AAAAATATTAAATTTT
1 TTATAAT-TAAATATTTGATAAAAA-ATTAAATTTT
*
2527407 TTATAATTTAATATTTGATAAAAAATTAAATT
1 TTATAATTAAATATTTGATAAAAAATTAAATT
2527439 ATTAAATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
32 5 0.18
33 9 0.32
34 9 0.32
35 5 0.18
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (34 bp):
TTATAATTAAATATTTGATAAAAAATTAAATTTT
Found at i:2529206 original size:24 final size:25
Alignment explanation
Indices: 2529179--2529226 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
2529169 ACTTATATAT
2529179 TTATATAAA-ATTAATATATTTATG
1 TTATATAAATATTAATATATTTATG
* *
2529203 TTATATAAATTTTATTATATTTAT
1 TTATATAAATATTAATATATTTAT
2529227 ATATTTGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (25 bp):
TTATATAAATATTAATATATTTATG
Found at i:2529232 original size:18 final size:18
Alignment explanation
Indices: 2529206--2529260 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
2529196 ATTTATGTTA
*
2529206 TATAAATTTTATTATATT
1 TATATATTTTATTATATT
*
2529224 TATATATTTGTATAATA-T
1 TATATATTT-TATTATATT
*
2529242 TATAT-TTTAATTATTATT
1 TATATATTTTATTA-TATT
2529260 T
1 T
2529261 TTTATATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
16 3 0.10
17 5 0.17
18 16 0.53
19 6 0.20
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
TATATATTTTATTATATT
Found at i:2530026 original size:14 final size:14
Alignment explanation
Indices: 2530007--2530053 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
2529997 TTTATTAAAA
*
2530007 TAATATTTTTATAT
1 TAATATTTATATAT
2530021 TAATATTTATATATT
1 TAATATTTATATA-T
* *
2530036 TTATATTTAAATA-
1 TAATATTTATATAT
2530049 TAATA
1 TAATA
2530054 ATCCGAACCT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
13 4 0.14
14 12 0.43
15 12 0.43
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TAATATTTATATAT
Found at i:2530989 original size:15 final size:15
Alignment explanation
Indices: 2530969--2531001 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
2530959 TAAATCCGGA
2530969 CTTACAAAGCATTTG
1 CTTACAAAGCATTTG
2530984 CTTACAAAGCATTTG
1 CTTACAAAGCATTTG
2530999 CTT
1 CTT
2531002 TGTGGGTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.36
Consensus pattern (15 bp):
CTTACAAAGCATTTG
Found at i:2531349 original size:3 final size:3
Alignment explanation
Indices: 2531343--2531368 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2531333 TTGTTTTTTT
2531343 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
2531369 CTATTTTAAA
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2532644 original size:2 final size:2
Alignment explanation
Indices: 2532637--2532672 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2532627 GGTACAAAAT
2532637 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2532673 AACATGGCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2533265 original size:2 final size:2
Alignment explanation
Indices: 2533260--2533293 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2533250 ATATATATAT
2533260 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2533294 GTTTTGTGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2533442 original size:15 final size:16
Alignment explanation
Indices: 2533424--2533453 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2533414 CTACTTTTAC
2533424 TTTTTCCTT-TTTTTT
1 TTTTTCCTTATTTTTT
2533439 TTTTTCCTTATTTTT
1 TTTTTCCTTATTTTT
2533454 CATCTTCAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTTCCTTATTTTTT
Found at i:2535236 original size:2 final size:2
Alignment explanation
Indices: 2535229--2535256 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2535219 TTATTGTATG
2535229 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2535257 GTGTGTGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2544866 original size:14 final size:15
Alignment explanation
Indices: 2544831--2544875 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
2544821 TATTTTTAAT
2544831 ATTAATATAAAATTAA
1 ATTAATATAAAA-TAA
2544847 A-T-ATATAAAA-AA
1 ATTAATATAAAATAA
2544859 ATTAATATAAATATAA
1 ATTAATATAAA-ATAA
2544875 A
1 A
2544876 ATTTTTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
12 3 0.12
13 1 0.04
14 15 0.60
15 2 0.08
16 4 0.16
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
ATTAATATAAAATAA
Found at i:2545014 original size:19 final size:18
Alignment explanation
Indices: 2544985--2545027 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
2544975 ATTATTATCA
2544985 TAAATTTATTATTATAAAAT
1 TAAA-TTATTATTA-AAAAT
*
2545005 TAAATTATTATTAAATAT
1 TAAATTATTATTAAAAAT
2545023 TAAAT
1 TAAAT
2545028 AAATTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.41
19 9 0.41
20 4 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TAAATTATTATTAAAAAT
Found at i:2545043 original size:27 final size:27
Alignment explanation
Indices: 2545008--2545074 Score: 68
Period size: 27 Copynumber: 2.4 Consensus size: 27
2544998 ATAAAATTAA
*
2545008 ATTATTATTAAATATTAA-ATAA-ATTTT
1 ATTAATATTAAATA--AATATAATATTTT
2545035 ATTAATATTATAATAAATATAATTATTTT
1 ATTAATATTA-AATAAATATAA-TATTTT
2545064 ATTAAT-TTAAA
1 ATTAATATTAAA
2545075 ATTTTTATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
26 2 0.06
27 15 0.43
28 7 0.20
29 11 0.31
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
ATTAATATTAAATAAATATAATATTTT
Found at i:2545059 original size:21 final size:20
Alignment explanation
Indices: 2545018--2545059 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
2545008 ATTATTATTA
* *
2545018 AATATTAAATAAATTTTATT
1 AATATTAAATAAATATAATT
2545038 AATATTATAATAAATATAATT
1 AATATTA-AATAAATATAATT
2545059 A
1 A
2545060 TTTTATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AATATTAAATAAATATAATT
Found at i:2545519 original size:2 final size:2
Alignment explanation
Indices: 2545507--2545553 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
2545497 TCTTCTAGGG
* *
2545507 GA GA AA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA AA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2545549 GA GA G
1 GA GA G
2545554 CGCATGATGA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2546007 original size:22 final size:22
Alignment explanation
Indices: 2545921--2546008 Score: 63
Period size: 22 Copynumber: 3.9 Consensus size: 22
2545911 CTCATTCATT
* *
2545921 TTAATTAAAATATTATAAAATAA
1 TTAATTTAAAT-TTATAAAATTA
* *
2545944 TAAATTTAAATTTAAAATAATCT-
1 TTAATTTAAATTTATAA-AAT-TA
* **
2545967 TTCATATT-AATCAATAAAATTA
1 TTAAT-TTAAATTTATAAAATTA
2545989 TTAATTTAAATTTATAAAAT
1 TTAATTTAAATTTATAAAAT
2546009 ATAAAATTAA
Statistics
Matches: 48, Mismatches: 12, Indels: 11
0.68 0.17 0.15
Matches are distributed among these distances:
21 3 0.06
22 22 0.46
23 21 0.44
24 2 0.04
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (22 bp):
TTAATTTAAATTTATAAAATTA
Found at i:2546528 original size:25 final size:25
Alignment explanation
Indices: 2546464--2546528 Score: 62
Period size: 25 Copynumber: 2.6 Consensus size: 25
2546454 TTAAATTAAG
* *
2546464 TTAAAGATTAAATTATAAATTTAATTT
1 TTAAATATT-AATT-TAAATTTAAATT
*
2546491 TTATATATT-ATTTAAATTTTAAATT
1 TTAAATATTAATTTAAA-TTTAAATT
2546516 TTAAAT-TTAATTT
1 TTAAATATTAATTT
2546529 TTATATAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
24 6 0.19
25 19 0.59
27 7 0.22
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (25 bp):
TTAAATATTAATTTAAATTTAAATT
Found at i:2546540 original size:20 final size:20
Alignment explanation
Indices: 2546478--2546557 Score: 76
Period size: 20 Copynumber: 4.1 Consensus size: 20
2546468 AGATTAAATT
2546478 ATAAATTTAATTTTTATAT-
1 ATAAATTTAATTTTTATATA
* * * *
2546497 AT-TATTTAAATTTTAAATT
1 ATAAATTTAATTTTTATATA
*
2546516 TTAAATTTAATTTTTATATA
1 ATAAATTTAATTTTTATATA
*
2546536 ATAAATTTTATTTATT-TATA
1 ATAAATTTAATTT-TTATATA
2546556 AT
1 AT
2546558 TGAATCAAAT
Statistics
Matches: 48, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
18 13 0.27
19 3 0.06
20 30 0.62
21 2 0.04
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
ATAAATTTAATTTTTATATA
Found at i:2546972 original size:13 final size:14
Alignment explanation
Indices: 2546956--2546987 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
2546946 ATATTTAAAA
2546956 AAAATTAAAAAT-C
1 AAAATTAAAAATAC
2546969 AAAA-TAAAAATAC
1 AAAATTAAAAATAC
2546982 AAAATT
1 AAAATT
2546988 GTAATAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.41
13 9 0.53
14 1 0.06
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (14 bp):
AAAATTAAAAATAC
Found at i:2547658 original size:17 final size:17
Alignment explanation
Indices: 2547636--2547669 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2547626 ATCTTCACTC
2547636 CTTCTCTGGTTTCTATT
1 CTTCTCTGGTTTCTATT
2547653 CTTCTCTGGTTTCTATT
1 CTTCTCTGGTTTCTATT
2547670 ACAACTCATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.06, C:0.24, G:0.12, T:0.59
Consensus pattern (17 bp):
CTTCTCTGGTTTCTATT
Found at i:2549338 original size:18 final size:16
Alignment explanation
Indices: 2549309--2549342 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
2549299 TTAGGGGAAA
2549309 TTTTTTAATTATTAAT
1 TTTTTTAATTATTAAT
2549325 TTTTTTAAATTTATTAAT
1 TTTTTT-AA-TTATTAAT
2549343 AAAATATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 2 0.12
18 8 0.50
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTTTAATTATTAAT
Found at i:2550838 original size:3 final size:3
Alignment explanation
Indices: 2550830--2550868 Score: 69
Period size: 3 Copynumber: 12.7 Consensus size: 3
2550820 ATTATACAAT
2550830 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATAA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA AT
2550869 TGTGTATATT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2551633 original size:16 final size:15
Alignment explanation
Indices: 2551612--2551643 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
2551602 AAATATTTTT
2551612 AATTATTATTAAATTA
1 AATTATTATT-AATTA
2551628 AATTATTATTAATTA
1 AATTATTATTAATTA
2551643 A
1 A
2551644 TATTCTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATTATTATTAATTA
Found at i:2552343 original size:22 final size:20
Alignment explanation
Indices: 2552313--2552355 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
2552303 GTAAATATAT
*
2552313 TTATATAAAATTTTTATAAAAA
1 TTATAT-AAACTTTTA-AAAAA
*
2552335 TTATCTAAACTTTTAAAAAA
1 TTATATAAACTTTTAAAAAA
2552355 T
1 T
2552356 AAATAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 6 0.32
21 8 0.42
22 5 0.26
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (20 bp):
TTATATAAACTTTTAAAAAA
Found at i:2552407 original size:48 final size:49
Alignment explanation
Indices: 2552355--2552450 Score: 151
Period size: 48 Copynumber: 2.0 Consensus size: 49
2552345 TTTTAAAAAA
2552355 TAAATAAAATTATTTTTAAATCTAAAAAATCATA-ATACT-TATATATAG
1 TAAATAAAATTATTTTTAAATCTAAAAAATCATATATA-TATATATATAG
* *
2552403 TAAATAAAATTATTTTTAAATTTAAATAATCATATATATATATATATA
1 TAAATAAAATTATTTTTAAATCTAAAAAATCATATATATATATATATA
2552451 AACCCAATGC
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
48 33 0.75
49 11 0.25
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (49 bp):
TAAATAAAATTATTTTTAAATCTAAAAAATCATATATATATATATATAG
Found at i:2552835 original size:19 final size:19
Alignment explanation
Indices: 2552807--2552887 Score: 67
Period size: 19 Copynumber: 4.3 Consensus size: 19
2552797 GCTTAATTAA
2552807 ATAATA-AATATTTAATAT
1 ATAATATAATATTTAATAT
*
2552825 ATAATATAATAATTAATTAAT
1 ATAATATAATATTTAA-T-AT
* ** * *
2552846 AAAATATTTTTTTTATTAT
1 ATAATATAATATTTAATAT
*
2552865 ATAATATAATTTTTAATAT
1 ATAATATAATATTTAATAT
2552884 -TAAT
1 ATAAT
2552888 TAAAAAATTA
Statistics
Matches: 49, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
18 10 0.20
19 25 0.51
20 2 0.04
21 12 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATAATATAATATTTAATAT
Found at i:2557212 original size:17 final size:17
Alignment explanation
Indices: 2557187--2557222 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
2557177 TCTCATCCCT
2557187 TATCAGAAGATAAATTC
1 TATCAGAAGATAAATTC
*
2557204 TATCTGAAGATAAATTC
1 TATCAGAAGATAAATTC
2557221 TA
1 TA
2557223 GCATAGAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (17 bp):
TATCAGAAGATAAATTC
Found at i:2561989 original size:26 final size:24
Alignment explanation
Indices: 2561960--2562034 Score: 73
Period size: 26 Copynumber: 3.0 Consensus size: 24
2561950 CGATTTTAAT
2561960 TTAAATTATTTAATAATAATAAAATA
1 TTAAATTATTTAAT-ATAA-AAAATA
* *
2561986 TTAATTTATATAATTATAAAAATATA
1 TTAAATTATTTAA-TATAAAAA-ATA
2562012 TATAAA-TA-TTAATATAAAAAATA
1 T-TAAATTATTTAATATAAAAAATA
2562035 ATATTTTAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
23 3 0.07
24 8 0.19
25 6 0.14
26 21 0.50
27 4 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
TTAAATTATTTAATATAAAAAATA
Found at i:2562019 original size:34 final size:31
Alignment explanation
Indices: 2561955--2562029 Score: 87
Period size: 31 Copynumber: 2.3 Consensus size: 31
2561945 TTAATCGATT
* *
2561955 TTAATTTAAATTATTTAATAATAATAAAATA
1 TTAATTTAAATAATTTAAAAATAATAAAATA
*
2561986 TTAATTTATATAATTATAAAAATATATATAAATA
1 TTAATTTAAATAATT-TAAAAATA-ATA-AAATA
*
2562020 TTAATATAAA
1 TTAATTTAAA
2562030 AAATAATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
31 13 0.36
32 7 0.19
33 3 0.08
34 13 0.36
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (31 bp):
TTAATTTAAATAATTTAAAAATAATAAAATA
Found at i:2563379 original size:2 final size:2
Alignment explanation
Indices: 2563372--2563408 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2563362 CACACGTGTG
2563372 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
2563409 CAACCCTTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.51, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:2565059 original size:2 final size:2
Alignment explanation
Indices: 2565018--2565048 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2565008 CAATAGGAAG
2565018 AT AT 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 AT AT A
2565049 GTACAATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2567069 original size:56 final size:51
Alignment explanation
Indices: 2567008--2567154 Score: 177
Period size: 52 Copynumber: 2.7 Consensus size: 51
2566998 ATCCAAATTA
* * * *
2567008 AATTAATCAAATCAATGAAGTTTAATTTAGTCATTAATCAGTCCACTCAATTTGGT
1 AATTAATTAAAT-AATAAAATTTAATTTAGTAATTAATCAGT---C-CAATTTGGT
2567064 AATTAATTAAATAGATAAAATTTAATTTAGTAATTAATCAGTCCAATTTGGT
1 AATTAATTAAATA-ATAAAATTTAATTTAGTAATTAATCAGTCCAATTTGGT
* *
2567116 AATTAATTAAATGGATAAAATTTAATTTGGTAATTAATC
1 AATTAATTAAAT-AATAAAATTTAATTTAGTAATTAATC
2567155 GGCTCATTTA
Statistics
Matches: 83, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
52 45 0.54
53 1 0.01
55 1 0.01
56 36 0.43
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.39
Consensus pattern (51 bp):
AATTAATTAAATAATAAAATTTAATTTAGTAATTAATCAGTCCAATTTGGT
Found at i:2567133 original size:52 final size:54
Alignment explanation
Indices: 2567028--2567154 Score: 195
Period size: 52 Copynumber: 2.4 Consensus size: 54
2567018 ATCAATGAAG
*
2567028 TTTAATTTAGTCATTAATCAGTCCACTCAATTTGGTAATTAATTAAATAGATAAAA
1 TTTAATTTAGTAATTAATCAGT-C-CTCAATTTGGTAATTAATTAAATAGATAAAA
*
2567084 TTTAATTTAGTAATTAATCAGT-C-CAATTTGGTAATTAATTAAATGGATAAAA
1 TTTAATTTAGTAATTAATCAGTCCTCAATTTGGTAATTAATTAAATAGATAAAA
*
2567136 TTTAATTTGGTAATTAATC
1 TTTAATTTAGTAATTAATC
2567155 GGCTCATTTA
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
52 46 0.68
53 1 0.01
56 21 0.31
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.42
Consensus pattern (54 bp):
TTTAATTTAGTAATTAATCAGTCCTCAATTTGGTAATTAATTAAATAGATAAAA
Found at i:2567510 original size:2 final size:2
Alignment explanation
Indices: 2567503--2567531 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2567493 ACATACATAC
2567503 AT 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 AT A
2567532 ACACGATGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2567953 original size:30 final size:31
Alignment explanation
Indices: 2567913--2567977 Score: 105
Period size: 30 Copynumber: 2.1 Consensus size: 31
2567903 CACCCTTCTA
2567913 ATTACCAATGAAAACCCATAGAATAGAAA-C
1 ATTACCAATGAAAACCCATAGAATAGAAACC
* *
2567943 ATTACTAATGAAATCCCATAGAATAGAAACC
1 ATTACCAATGAAAACCCATAGAATAGAAACC
2567974 ATTA
1 ATTA
2567978 GCTTCATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 27 0.84
31 5 0.16
ACGTcount: A:0.51, C:0.18, G:0.09, T:0.22
Consensus pattern (31 bp):
ATTACCAATGAAAACCCATAGAATAGAAACC
Found at i:2568419 original size:3 final size:3
Alignment explanation
Indices: 2568405--2568447 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
2568395 CAACAGCATC
* *
2568405 AAG AAG ATG AAG AAG AAG AAG AAG AAG AAG AAA AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
2568448 GCCAAAACTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:2570842 original size:4 final size:4
Alignment explanation
Indices: 2570786--2570813 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
2570776 AAATGTGTAC
2570786 ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT
2570814 GTGTGTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:2571876 original size:14 final size:16
Alignment explanation
Indices: 2571845--2571881 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
2571835 CGACATAATA
2571845 TTTAA-AATAAATTAT
1 TTTAATAATAAATTAT
2571860 TTTAATAATAAA-T-T
1 TTTAATAATAAATTAT
2571874 TTTAATAA
1 TTTAATAA
2571882 AACAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.43
15 6 0.29
16 6 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TTTAATAATAAATTAT
Found at i:2573897 original size:14 final size:14
Alignment explanation
Indices: 2573878--2573915 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
2573868 TAATATTTAC
*
2573878 TTAAATATTTATAT
1 TTAAATATATATAT
2573892 TTAAATATATATAT
1 TTAAATATATATAT
2573906 TTAAATATAT
1 TTAAATATAT
2573916 GTAAACATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTAAATATATATAT
Found at i:2574047 original size:3 final size:3
Alignment explanation
Indices: 2574039--2574069 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2574029 TGCAAATATG
2574039 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2574070 AAATCCTTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2575011 original size:2 final size:2
Alignment explanation
Indices: 2575004--2575033 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2574994 TGTATTAGCC
2575004 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2575034 GAGGATATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2577262 original size:21 final size:20
Alignment explanation
Indices: 2577218--2577263 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
2577208 ATAATTCATA
2577218 ATTTTAATAAAAAAATTTAT
1 ATTTTAATAAAAAAATTTAT
**
2577238 -TTTTAATATAAAATTTTTAT
1 ATTTTAATA-AAAAAATTTAT
2577258 ATTTTA
1 ATTTTA
2577264 GTTTATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 8 0.36
20 9 0.41
21 5 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
ATTTTAATAAAAAAATTTAT
Found at i:2583503 original size:11 final size:11
Alignment explanation
Indices: 2583487--2583513 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2583477 TTTAATTTGA
2583487 TTATTTTTTAT
1 TTATTTTTTAT
2583498 TTATTTTTTAT
1 TTATTTTTTAT
2583509 TTATT
1 TTATT
2583514 AAATTCCCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (11 bp):
TTATTTTTTAT
Found at i:2584229 original size:14 final size:15
Alignment explanation
Indices: 2584210--2584239 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2584200 TTTTTTAGTT
2584210 TAAATAA-TAAAAAA
1 TAAATAAGTAAAAAA
2584224 TAAATAAGTAAAAAA
1 TAAATAAGTAAAAAA
2584239 T
1 T
2584240 TATTATCTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (15 bp):
TAAATAAGTAAAAAA
Found at i:2584648 original size:25 final size:21
Alignment explanation
Indices: 2584587--2584635 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
2584577 CAACTTAATT
2584587 AATAAATTTATTAAAAATCAA
1 AATAAATTTATTAAAAATCAA
2584608 AATAAATTTATTAAAAATCAA
1 AATAAATTTATTAAAAATCAA
2584629 AATAAAT
1 AATAAAT
2584636 ATATAATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (21 bp):
AATAAATTTATTAAAAATCAA
Found at i:2586382 original size:24 final size:26
Alignment explanation
Indices: 2586343--2586394 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 26
2586333 GCATCAATTA
*
2586343 TTTAAAAATTATTTAAT-TAATATTT
1 TTTAAAAATTAATTAATATAATATTT
2586368 TTTAAAAA-TAATTAATATAATATTT
1 TTTAAAAATTAATTAATATAATATTT
2586393 TT
1 TT
2586395 ATTAAATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 7 0.28
25 18 0.72
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
TTTAAAAATTAATTAATATAATATTT
Found at i:2587059 original size:13 final size:13
Alignment explanation
Indices: 2587040--2587075 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
2587030 TGATTAATTG
*
2587040 TAAAAATTATATA
1 TAAAAATAATATA
*
2587053 TATAAATAATATA
1 TAAAAATAATATA
2587066 TAAAAATAAT
1 TAAAAATAAT
2587076 TAAAAATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TAAAAATAATATA
Found at i:2587112 original size:23 final size:24
Alignment explanation
Indices: 2587086--2587143 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
2587076 TAAAAATTAA
2587086 ATTTATTAACATATA-AAATA-ATT
1 ATTTATTAA-ATATATAAATATATT
*
2587109 ATTTAATAAATATATAAATATATT
1 ATTTATTAAATATATAAATATATT
2587133 -TTTATTTAAAT
1 ATTTA-TTAAAT
2587144 TTAATTATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
22 5 0.17
23 17 0.57
24 8 0.27
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
ATTTATTAAATATATAAATATATT
Found at i:2587512 original size:14 final size:13
Alignment explanation
Indices: 2587482--2587531 Score: 57
Period size: 14 Copynumber: 3.8 Consensus size: 13
2587472 ATATATATAT
2587482 TAAA-AAAATTTA
1 TAAATAAAATTTA
2587494 TAAATAAAATTTA
1 TAAATAAAATTTA
* *
2587507 TGAAATAATATGTA
1 T-AAATAAAATTTA
2587521 TATAATAAAAT
1 TA-AATAAAAT
2587532 ATATTTAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
12 4 0.12
13 10 0.31
14 18 0.56
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (13 bp):
TAAATAAAATTTA
Found at i:2587553 original size:28 final size:29
Alignment explanation
Indices: 2587476--2587563 Score: 71
Period size: 28 Copynumber: 3.2 Consensus size: 29
2587466 TATTTTATAT
**
2587476 ATATATT-AAAAAA-ATTTATA-AATAAA
1 ATATATTGAAAAAATAAGTATATAATAAA
* * *
2587502 ATTTA-TGAAATAATATGTATATAATAAA
1 ATATATTGAAAAAATAAGTATATAATAAA
* *
2587530 ATATATTTAAAAAATAAGTA-ATAAT-TA
1 ATATATTGAAAAAATAAGTATATAATAAA
2587557 ATATATT
1 ATATATT
2587564 ACATATTATT
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
25 1 0.02
26 9 0.18
27 14 0.28
28 15 0.30
29 11 0.22
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (29 bp):
ATATATTGAAAAAATAAGTATATAATAAA
Found at i:2588854 original size:21 final size:21
Alignment explanation
Indices: 2588825--2588865 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2588815 TAAATTACAC
2588825 AAATAGAAT-ATATTAAAAAAT
1 AAATAGAATAAT-TTAAAAAAT
*
2588846 AAATTGAATAATTTAAAAAA
1 AAATAGAATAATTTAAAAAA
2588866 ATTAAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (21 bp):
AAATAGAATAATTTAAAAAAT
Found at i:2588873 original size:24 final size:21
Alignment explanation
Indices: 2588839--2588885 Score: 51
Period size: 23 Copynumber: 2.1 Consensus size: 21
2588829 AGAATATATT
2588839 AAAAAATAAAT-TGAATAATTTA
1 AAAAAATAAATATG-AT-ATTTA
2588861 AAAAAATTAAAATATGATATTTA
1 AAAAAA-T-AAATATGATATTTA
2588884 AA
1 AA
2588886 TCTCACTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
22 6 0.27
23 8 0.36
24 6 0.27
25 2 0.09
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (21 bp):
AAAAAATAAATATGATATTTA
Found at i:2589482 original size:2 final size:2
Alignment explanation
Indices: 2589475--2589523 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
2589465 ACCTAATTAA
2589475 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2589517 AT AT AT A
1 AT AT AT A
2589524 GATGCACTTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2589951 original size:29 final size:28
Alignment explanation
Indices: 2589918--2589977 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
2589908 AATCAATTCA
2589918 ATTTAAA-TTATTATTTAATTAATAAAAAT
1 ATTTAAATTTA-TATTTAATT-ATAAAAAT
* *
2589947 ATTTATATTTATATTTAATTATAAATAT
1 ATTTAAATTTATATTTAATTATAAAAAT
2589975 ATT
1 ATT
2589978 AATTAATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 10 0.36
29 15 0.54
30 3 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
ATTTAAATTTATATTTAATTATAAAAAT
Found at i:2589981 original size:15 final size:14
Alignment explanation
Indices: 2589935--2590001 Score: 54
Period size: 12 Copynumber: 5.0 Consensus size: 14
2589925 TTATTATTTA
2589935 ATTAATA-AAA-AT
1 ATTAATATAAATAT
* **
2589947 ATTTATATTTATAT
1 ATTAATATAAATAT
2589961 -TTAATTATAAATAT
1 ATTAA-TATAAATAT
2589975 ATTAAT-T-AATAT
1 ATTAATATAAATAT
2589987 ATTAATATACAATAT
1 ATTAATATA-AATAT
2590002 TTTTAATATT
Statistics
Matches: 42, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
12 17 0.40
13 6 0.14
14 10 0.24
15 9 0.21
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (14 bp):
ATTAATATAAATAT
Found at i:2589987 original size:28 final size:28
Alignment explanation
Indices: 2589929--2590016 Score: 75
Period size: 27 Copynumber: 3.3 Consensus size: 28
2589919 TTTAAATTAT
*
2589929 TATTTAATTAATAAAAATATTTATATT--TA
1 TATTTAATT-ATAAATATA-TTA-ATTAATA
2589958 TATTTAATTATAAATATATTAATTAATA
1 TATTTAATTATAAATATATTAATTAATA
2589986 TA-TTAA-TATACAATAT-TT--TTAATA
1 TATTTAATTATA-AATATATTAATTAATA
2590010 T-TTTAAT
1 TATTTAAT
2590017 ATATTTTAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 14
0.78 0.01 0.21
Matches are distributed among these distances:
24 11 0.21
26 9 0.17
27 12 0.23
28 12 0.23
29 9 0.17
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (28 bp):
TATTTAATTATAAATATATTAATTAATA
Found at i:2590428 original size:2 final size:2
Alignment explanation
Indices: 2590421--2590454 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2590411 TTGATTCATC
2590421 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2590455 CAATTACTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2591651 original size:22 final size:24
Alignment explanation
Indices: 2591626--2591677 Score: 74
Period size: 23 Copynumber: 2.2 Consensus size: 24
2591616 AATATTTTAA
2591626 TTAAAAT-TTAAT-TATAAAATA-T
1 TTAAAATATTAATATA-AAAATATT
2591648 TTAAAATATTAATATAAAAATATT
1 TTAAAATATTAATATAAAAATATT
2591672 TTAAAA
1 TTAAAA
2591678 ATAATTCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
22 7 0.26
23 11 0.41
24 9 0.33
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
TTAAAATATTAATATAAAAATATT
Found at i:2591667 original size:23 final size:23
Alignment explanation
Indices: 2591626--2591677 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
2591616 AATATTTTAA
2591626 TTAAAATTTAATTATAAAATA-T
1 TTAAAATTTAATTATAAAATATT
2591648 TTAAAATATTAA-TATAAAAATATT
1 TTAAAAT-TTAATTAT-AAAATATT
2591672 TTAAAA
1 TTAAAA
2591678 ATAATTCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
22 10 0.37
23 10 0.37
24 7 0.26
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
TTAAAATTTAATTATAAAATATT
Found at i:2591682 original size:22 final size:23
Alignment explanation
Indices: 2591611--2591679 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 23
2591601 TATTTCATAA
2591611 ATAAAAATATTTTAATTAAAATTTAAT
1 ATAAAAATATTTT-A--AAAA-TTAAT
2591638 -TATAAAATA-TTTAAAATATTAAT
1 ATA-AAAATATTTTAAAA-ATTAAT
2591661 ATAAAAATATTTTAAAAAT
1 ATAAAAATATTTTAAAAAT
2591680 AATTCAAACT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
23 16 0.42
24 10 0.26
25 1 0.03
26 5 0.13
27 6 0.16
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
ATAAAAATATTTTAAAAATTAAT
Found at i:2591789 original size:2 final size:2
Alignment explanation
Indices: 2591777--2591811 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2591767 ATAAATCTAA
2591777 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2591812 GTATGTGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2592355 original size:21 final size:21
Alignment explanation
Indices: 2592329--2592384 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
2592319 CCACTTAAAA
*
2592329 TTATAATTGTTTTATGTAT-TT
1 TTATAATT-TTTTATATATATT
2592350 TTATAATTTTTTATATATATT
1 TTATAATTTTTTATATATATT
*
2592371 TTATAGTTTATTTA
1 TTATAATTT-TTTA
2592385 ATTTAATCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
20 9 0.29
21 18 0.58
22 4 0.13
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (21 bp):
TTATAATTTTTTATATATATT
Found at i:2593377 original size:16 final size:16
Alignment explanation
Indices: 2593356--2593397 Score: 52
Period size: 14 Copynumber: 2.7 Consensus size: 16
2593346 TTTTTTTGTA
*
2593356 ATATTTTATATGATTT
1 ATATTTTATATGAATT
2593372 ATA-TTTAT-TGAATT
1 ATATTTTATATGAATT
2593386 ATATTATTATAT
1 ATATT-TTATAT
2593398 TTTATATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
14 8 0.36
15 6 0.27
16 7 0.32
17 1 0.05
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (16 bp):
ATATTTTATATGAATT
Found at i:2593454 original size:25 final size:26
Alignment explanation
Indices: 2593426--2593497 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 26
2593416 GTAAGCAAAA
*
2593426 TATTAAATAAATTAAAAAATTTAAT-
1 TATTAAATAAAATAAAAAATTTAATC
** *
2593451 TATTTATTTAAAATAAAAATTTTAATC
1 TA-TTAAATAAAATAAAAAATTTAATC
2593478 T-TTAAATATAAATAAAAAAT
1 TATTAAATA-AAATAAAAAAT
2593498 AATATTTTTA
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
25 7 0.19
26 29 0.78
27 1 0.03
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (26 bp):
TATTAAATAAAATAAAAAATTTAATC
Found at i:2595073 original size:20 final size:20
Alignment explanation
Indices: 2595036--2595073 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2595026 TTCATGAAAA
*
2595036 AATTAACATATAATTTAATC
1 AATTAACATATAAATTAATC
2595056 AATTCAACATA-AAATTAA
1 AATT-AACATATAAATTAA
2595074 ATTAATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (20 bp):
AATTAACATATAAATTAATC
Found at i:2596411 original size:49 final size:50
Alignment explanation
Indices: 2596316--2596421 Score: 121
Period size: 49 Copynumber: 2.1 Consensus size: 50
2596306 AAAATTATTT
* * *
2596316 TAAATATTATATAATATAAATTATTGATGTATCAAAATTTATAT-AAATA
1 TAAATATTATATAATATAAATTATTGATATATCAAAATATAAATAAAATA
*
2596365 TAGAATATTATA-AATAT-AATTA-TGATATGATTAAATATATAAATAAAATA
1 TA-AATATTATATAATATAAATTATTGATAT-ATCAAA-ATATAAATAAAATA
2596415 TAAATAT
1 TAAATAT
2596422 GCTAATTGCC
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
47 5 0.10
48 10 0.20
49 18 0.37
50 16 0.33
ACGTcount: A:0.54, C:0.01, G:0.05, T:0.41
Consensus pattern (50 bp):
TAAATATTATATAATATAAATTATTGATATATCAAAATATAAATAAAATA
Found at i:2596695 original size:10 final size:11
Alignment explanation
Indices: 2596674--2596699 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2596664 ACTTGCATTA
2596674 TTAAAAATTTT
1 TTAAAAATTTT
2596685 TTAAAAATTTT
1 TTAAAAATTTT
2596696 TTAA
1 TTAA
2596700 GAGTTTGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
TTAAAAATTTT
Found at i:2602184 original size:2 final size:2
Alignment explanation
Indices: 2602177--2602207 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2602167 ATTTAATACC
2602177 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2602208 TGCAAATCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2605341 original size:31 final size:30
Alignment explanation
Indices: 2605297--2605354 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
2605287 AGTTAAAAAT
*
2605297 TATTTATTTATTATTTTAATAAAATTTTTG
1 TATTTATATATTATTTTAATAAAATTTTTG
* *
2605327 TATTTAATATATTATTTTTATTAAATTT
1 TATTT-ATATATTATTTTAATAAAATTT
2605355 AAAAATTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 5 0.21
31 19 0.79
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (30 bp):
TATTTATATATTATTTTAATAAAATTTTTG
Found at i:2605693 original size:21 final size:22
Alignment explanation
Indices: 2605652--2605693 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
2605642 ATTAAAAAAA
2605652 AAAGATTGAAATTTATGAGATT
1 AAAGATTGAAATTTATGAGATT
* *
2605674 AAAGATT-AATTTTATTAGAT
1 AAAGATTGAAATTTATGAGAT
2605694 GGGAGAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.40
Consensus pattern (22 bp):
AAAGATTGAAATTTATGAGATT
Found at i:2606068 original size:24 final size:24
Alignment explanation
Indices: 2606007--2606071 Score: 62
Period size: 28 Copynumber: 2.6 Consensus size: 24
2605997 ATATAAATTT
*
2606007 ATATATTATT-AATAAATTAAATA
1 ATATATTTTTAAATAAATTAAATA
2606030 ATATTAATTTATTTAAATAAAATT-AATA
1 ATA-T-A-TT-TTTAAAT-AAATTAAATA
2606058 ATATATTTTTAAAT
1 ATATATTTTTAAAT
2606072 TTTTTTAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 11
0.74 0.02 0.23
Matches are distributed among these distances:
23 3 0.09
24 8 0.23
25 3 0.09
26 3 0.09
27 3 0.09
28 10 0.29
29 5 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
ATATATTTTTAAATAAATTAAATA
Found at i:2610137 original size:84 final size:88
Alignment explanation
Indices: 2610014--2610192 Score: 267
Period size: 84 Copynumber: 2.0 Consensus size: 88
2610004 TATTAATTTC
2610014 CATGAAAGTCAGTATTGTTTGTCTTGATATTATTTAATTTC-ATT-TT-TTGTAATTTTATTTAT
1 CATGAAAGTCAGTATTGTTTGTCTTGATATTATTTAATTTCTATTCTTATTGTAATTTTATTTAT
2610076 GCTTC-AAAATACTTTAGACTTG
66 GCTTCAAAAATACTTTAGACTTG
* * *
2610098 CATGAAATTCAGTATTGTTTGTTTTGATATTATTTAATTTCATTATTCTTAATTTTAATTTTATT
1 CATGAAAGTCAGTATTGTTTGTCTTGATATTATTTAATTTC--TATTCTT-ATTGTAATTTTATT
*
2610163 TATGCTTCAAAAATGCTTTAGACTTG
63 TATGCTTCAAAAATACTTTAGACTTG
2610189 CATG
1 CATG
2610193 TAATAATTCA
Statistics
Matches: 84, Mismatches: 4, Indels: 7
0.88 0.04 0.07
Matches are distributed among these distances:
84 39 0.46
87 3 0.04
88 2 0.02
90 20 0.24
91 20 0.24
ACGTcount: A:0.28, C:0.09, G:0.11, T:0.51
Consensus pattern (88 bp):
CATGAAAGTCAGTATTGTTTGTCTTGATATTATTTAATTTCTATTCTTATTGTAATTTTATTTAT
GCTTCAAAAATACTTTAGACTTG
Found at i:2611303 original size:15 final size:15
Alignment explanation
Indices: 2611283--2611311 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2611273 TTTGATTTAA
2611283 TTAAATTTAAAATAT
1 TTAAATTTAAAATAT
2611298 TTAAATTTAAAATA
1 TTAAATTTAAAATA
2611312 AATTAAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAAATTTAAAATAT
Found at i:2614713 original size:24 final size:24
Alignment explanation
Indices: 2614686--2614731 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
2614676 AATAGGATTG
2614686 TGATTAGGAAATTTAATTATTTTT
1 TGATTAGGAAATTTAATTATTTTT
2614710 TGATTAGGAAATTTAATTATTT
1 TGATTAGGAAATTTAATTATTT
2614732 CATTAAATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (24 bp):
TGATTAGGAAATTTAATTATTTTT
Found at i:2615493 original size:14 final size:14
Alignment explanation
Indices: 2615470--2615496 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2615460 TTAAAAATAT
2615470 TTATATAAATTTAA
1 TTATATAAATTTAA
2615484 TTATATAAATTTA
1 TTATATAAATTTA
2615497 TAAATAAATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTATATAAATTTAA
Found at i:2616372 original size:29 final size:28
Alignment explanation
Indices: 2616305--2616373 Score: 68
Period size: 29 Copynumber: 2.5 Consensus size: 28
2616295 TCATATTAAC
* *
2616305 AAAATTTC-TTAAGATATATAATATTCT
1 AAAATTTCTTTAAGATATAAAAAATTCT
** *
2616332 AAAATTGATTTAGGATATAAAAAAATTCT
1 AAAATTTCTTTAAGATAT-AAAAAATTCT
*
2616361 CAAATTTCTTTAA
1 AAAATTTCTTTAA
2616374 ACATGTAGGG
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
27 6 0.19
28 8 0.26
29 17 0.55
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.41
Consensus pattern (28 bp):
AAAATTTCTTTAAGATATAAAAAATTCT
Found at i:2618230 original size:16 final size:16
Alignment explanation
Indices: 2618209--2618240 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2618199 AATTAGAATA
*
2618209 TAATTTAATAATAATT
1 TAATTTAACAATAATT
2618225 TAATTTAACAATAATT
1 TAATTTAACAATAATT
2618241 AAAGATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
TAATTTAACAATAATT
Found at i:2618709 original size:2 final size:2
Alignment explanation
Indices: 2618702--2618744 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2618692 ATAAATTTTG
2618702 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2618744 A
1 A
2618745 AGAAATAGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2618809 original size:13 final size:13
Alignment explanation
Indices: 2618791--2618816 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2618781 AAAGCACAAA
2618791 ATGAATTAATTTT
1 ATGAATTAATTTT
2618804 ATGAATTAATTTT
1 ATGAATTAATTTT
2618817 CATTTTAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
ATGAATTAATTTT
Found at i:2619249 original size:21 final size:22
Alignment explanation
Indices: 2619207--2619262 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 22
2619197 ATTTAAAATA
*
2619207 ATTTAATTTAATTTAAATTATT
1 ATTTAATTTAATTAAAATTATT
2619229 ATTT-ATTTAA-TAAAATATATT
1 ATTTAATTTAATTAAAAT-TATT
* *
2619250 -TTAAAATTAATTA
1 ATTTAATTTAATTA
2619263 TAAAAATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 7 0.25
21 15 0.54
22 6 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
ATTTAATTTAATTAAAATTATT
Found at i:2619252 original size:19 final size:20
Alignment explanation
Indices: 2619199--2619252 Score: 51
Period size: 19 Copynumber: 2.8 Consensus size: 20
2619189 ATTTTGTAAT
*
2619199 TTAAAATA-ATTTAATTTAA
1 TTAAAATATATTTTATTTAA
*
2619218 TTTAAAT-TATTATTTATTTAA
1 TTAAAATATA-T-TTTATTTAA
2619239 -TAAAATATATTTTA
1 TTAAAATATATTTTA
2619253 AAATTAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
19 11 0.39
20 7 0.25
21 10 0.36
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTAAAATATATTTTATTTAA
Found at i:2620628 original size:13 final size:12
Alignment explanation
Indices: 2620606--2620640 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
2620596 TATTTTTATT
2620606 TAAAATTAATTA
1 TAAAATTAATTA
2620618 TAAATATTAA-TA
1 TAAA-ATTAATTA
2620630 TAAAATTAATT
1 TAAAATTAATT
2620641 TTTAATATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 5 0.24
12 11 0.52
13 5 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
TAAAATTAATTA
Found at i:2620638 original size:24 final size:24
Alignment explanation
Indices: 2620606--2620655 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
2620596 TATTTTTATT
2620606 TAAAATTAATTATAAATATTAATA
1 TAAAATTAATTATAAATATTAATA
* * *
2620630 TAAAATTAATTTTTAATATTATTA
1 TAAAATTAATTATAAATATTAATA
2620654 TA
1 TA
2620656 GATAATAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TAAAATTAATTATAAATATTAATA
Found at i:2620669 original size:36 final size:36
Alignment explanation
Indices: 2620575--2620669 Score: 97
Period size: 36 Copynumber: 2.7 Consensus size: 36
2620565 TAATTTAAAT
* *
2620575 TATTATT-TAAATAATAAAA-AATATTTTTATTTAA
1 TATTATTATAAATAATAAAATAAAATTATTATTTAA
* * *
2620609 AATTAATTATAAATATTAATATAAAATTAATT-TTTAA
1 TATT-ATTATAAATAATAAAATAAAATT-ATTATTTAA
*
2620646 TATTATTATAGATAATAAAATAAA
1 TATTATTATAAATAATAAAATAAA
2620670 CTTTTGAACA
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
34 3 0.06
35 3 0.06
36 27 0.56
37 13 0.27
38 2 0.04
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (36 bp):
TATTATTATAAATAATAAAATAAAATTATTATTTAA
Found at i:2620815 original size:2 final size:2
Alignment explanation
Indices: 2620808--2620878 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
2620798 TAAACTCTTT
2620808 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2620850 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2620879 GATTGTTAAG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2621005 original size:13 final size:13
Alignment explanation
Indices: 2620987--2621030 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
2620977 CTGTGTACAT
2620987 TTTTTAAAAATAA
1 TTTTTAAAAATAA
*
2621000 TTTTTAAAAA-CA
1 TTTTTAAAAATAA
*
2621012 -TTTTAAAAATAT
1 TTTTTAAAAATAA
2621024 TTTTTAA
1 TTTTTAA
2621031 CTATTGTGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 9 0.35
12 1 0.04
13 16 0.62
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (13 bp):
TTTTTAAAAATAA
Found at i:2621540 original size:18 final size:19
Alignment explanation
Indices: 2621517--2621560 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
2621507 GAGTTAAAAG
* *
2621517 TTTATTATTTATTTTA-TT
1 TTTATTATTTAATTAATTT
2621535 TTTATT-TTTAATTAATTT
1 TTTATTATTTAATTAATTT
2621553 TTTATTAT
1 TTTATTAT
2621561 AATGATATGG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 7 0.32
18 14 0.64
19 1 0.05
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (19 bp):
TTTATTATTTAATTAATTT
Found at i:2621637 original size:2 final size:2
Alignment explanation
Indices: 2621632--2621658 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2621622 ATAATTTTTC
2621632 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
2621659 AAATAAATGC
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:2624076 original size:2 final size:2
Alignment explanation
Indices: 2624069--2624106 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2624059 ATGGATCACA
2624069 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2624107 TTGCACCATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2624306 original size:2 final size:2
Alignment explanation
Indices: 2624299--2624328 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2624289 ATAATGCCCT
2624299 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2624329 AATTGACTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2629792 original size:2 final size:2
Alignment explanation
Indices: 2629785--2629816 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2629775 GGTAAAGGGG
*
2629785 GA GA GA GA AA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2629817 TGGACATGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2631161 original size:15 final size:16
Alignment explanation
Indices: 2631141--2631170 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2631131 AGCTTTCAAT
2631141 GAAAAAAAA-AAAAAA
1 GAAAAAAAATAAAAAA
2631156 GAAAAAAAATAAAAA
1 GAAAAAAAATAAAAA
2631171 TCAACTATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.90, C:0.00, G:0.07, T:0.03
Consensus pattern (16 bp):
GAAAAAAAATAAAAAA
Found at i:2631535 original size:21 final size:22
Alignment explanation
Indices: 2631509--2631550 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2631499 TGCAGTTTGC
*
2631509 ACAG-AAAGATAAATTAATAAT
1 ACAGAAAAGATAAATAAATAAT
*
2631530 ACAGAAAATATAAATAAATAA
1 ACAGAAAAGATAAATAAATAA
2631551 ATAATCTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.67, C:0.05, G:0.07, T:0.21
Consensus pattern (22 bp):
ACAGAAAAGATAAATAAATAAT
Found at i:2634225 original size:30 final size:30
Alignment explanation
Indices: 2634189--2634253 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
2634179 TATTTTATTA
* *
2634189 TTAAAAATAAAATTAATTTTATATTAAT-AT
1 TTAAAAATAAAATTAAATTTA-AATAATAAT
*
2634219 TTAAAAATATAATTAAATTTAAATAATAAT
1 TTAAAAATAAAATTAAATTTAAATAATAAT
2634249 TTAAA
1 TTAAA
2634254 GTGAACTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 5 0.16
30 26 0.84
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (30 bp):
TTAAAAATAAAATTAAATTTAAATAATAAT
Found at i:2635515 original size:14 final size:14
Alignment explanation
Indices: 2635496--2635525 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2635486 AACTATTATT
2635496 ATAGCGAACTAATC
1 ATAGCGAACTAATC
*
2635510 ATAGCGACCTAATC
1 ATAGCGAACTAATC
2635524 AT
1 AT
2635526 GCCGTCAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.23, G:0.13, T:0.23
Consensus pattern (14 bp):
ATAGCGAACTAATC
Found at i:2635732 original size:17 final size:17
Alignment explanation
Indices: 2635707--2635771 Score: 71
Period size: 17 Copynumber: 3.7 Consensus size: 17
2635697 TTTAACATTA
2635707 AATAT-AATAAATATTT
1 AATATAAATAAATATTT
*
2635723 AATATAAATATATATTT
1 AATATAAATAAATATTT
2635740 AAT-TAAATAATATAATTTT
1 AATATAAATAA-AT-A-TTT
2635759 AAATATAAATAAA
1 -AATATAAATAAA
2635772 AAAATTAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
16 11 0.27
17 15 0.37
18 1 0.02
19 3 0.07
20 4 0.10
21 7 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AATATAAATAAATATTT
Found at i:2635916 original size:2 final size:2
Alignment explanation
Indices: 2635905--2635941 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2635895 TTTGTTATTT
2635905 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2635942 ATCAAACAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2637014 original size:20 final size:21
Alignment explanation
Indices: 2636984--2637035 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
2636974 TAATTTATAT
2636984 ATTTAAT-TATTTAAAAAATA
1 ATTTAATATATTTAAAAAATA
* *
2637004 ATTT-ATATATTTATAATATA
1 ATTTAATATATTTAAAAAATA
*
2637024 TTTTAATATATT
1 ATTTAATATATT
2637036 ATAATTATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.07
20 18 0.67
21 7 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTTAATATATTTAAAAAATA
Found at i:2637032 original size:10 final size:10
Alignment explanation
Indices: 2637008--2637081 Score: 59
Period size: 10 Copynumber: 7.7 Consensus size: 10
2636998 AAAATAATTT
2637008 ATATATTTATA
1 ATATATTT-TA
2637019 ATATATTTTA
1 ATATATTTTA
*
2637029 ATATATTATA
1 ATATATTTTA
2637039 AT-TATATTTA
1 ATATAT-TTTA
*
2637049 AT-T-TATT-
1 ATATATTTTA
*
2637056 ATATATTAT-
1 ATATATTTTA
*
2637065 ATAAATTTTA
1 ATATATTTTA
2637075 ATATATT
1 ATATATT
2637082 AATAATTTAT
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
7 2 0.04
8 3 0.06
9 13 0.25
10 25 0.49
11 8 0.16
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
ATATATTTTA
Found at i:2637037 original size:20 final size:20
Alignment explanation
Indices: 2637004--2637066 Score: 76
Period size: 20 Copynumber: 3.1 Consensus size: 20
2636994 TTAAAAAATA
2637004 ATTT-ATATATTTATAA-TAT
1 ATTTAATATA-TTATAATTAT
2637023 ATTTTAATATATTATAATTAT
1 A-TTTAATATATTATAATTAT
*
2637044 ATTTAATTTATTATATATTAT
1 ATTTAATATATTATA-ATTAT
2637065 AT
1 AT
2637067 AAATTTTAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
19 1 0.03
20 22 0.56
21 16 0.41
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTTAATATATTATAATTAT
Found at i:2637044 original size:26 final size:25
Alignment explanation
Indices: 2637009--2637093 Score: 81
Period size: 25 Copynumber: 3.5 Consensus size: 25
2636999 AAATAATTTA
*
2637009 TATATTTATAATATATTTTAATATAT
1 TATAATTAT-ATATATTTTAATATAT
* *
2637035 TATAATTATATTTAATTT-AT-TA-
1 TATAATTATATATATTTTAATATAT
*
2637057 TAT-ATTATATAAATTTTAATATAT
1 TATAATTATATATATTTTAATATAT
2637081 TAATAATT-TATAT
1 T-ATAATTATATAT
2637094 TATTAAATTT
Statistics
Matches: 47, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
21 11 0.23
22 5 0.11
23 4 0.09
24 3 0.06
25 13 0.28
26 11 0.23
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TATAATTATATATATTTTAATATAT
Found at i:2637053 original size:25 final size:25
Alignment explanation
Indices: 2637025--2637148 Score: 75
Period size: 23 Copynumber: 5.0 Consensus size: 25
2637015 TATAATATAT
2637025 TTTAATATATTATAATTATATTTAA
1 TTTAATATATTATAATTATATTTAA
*
2637050 TTT-AT-TA-TAT-ATTATA-TAAA
1 TTTAATATATTATAATTATATTTAA
2637070 TTTTAATATATTAATAATTTATATTATTAAA
1 -TTTAATATATT-ATAA-TTATA-T-TT-AA
* * **
2637101 TTTAATAATATT-TATTTTTATAAAA
1 TTTAAT-ATATTATAATTATATTTAA
*
2637126 TATAATAT-TTA-AATTATATTTAA
1 TTTAATATATTATAATTATATTTAA
2637149 ATTTTTTTGT
Statistics
Matches: 75, Mismatches: 11, Indels: 28
0.66 0.10 0.25
Matches are distributed among these distances:
20 3 0.04
21 9 0.12
22 5 0.07
23 14 0.19
24 5 0.07
25 12 0.16
26 1 0.01
27 6 0.08
28 4 0.05
29 2 0.03
30 7 0.09
31 7 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
TTTAATATATTATAATTATATTTAA
Found at i:2637062 original size:37 final size:36
Alignment explanation
Indices: 2637012--2637148 Score: 105
Period size: 32 Copynumber: 4.0 Consensus size: 36
2637002 TAATTTATAT
* *
2637012 ATTTATAATATATTTTAATATATTATAATTATATTTA
1 ATTTATTATATATTAT-ATATATTATAATTATATTTA
* *
2637049 ATTTATTATATATTATATAAATTTTAA-TATA-TTA
1 ATTTATTATATATTATATATATTATAATTATATTTA
* * *
2637083 A-TAATT-TATATTAT-TAAATT-TAATAATATTT-
1 ATTTATTATATATTATATATATTATAATTATATTTA
* *
2637114 ATTT-TTATAAAATATA-ATATT-TAAATTATATTTA
1 ATTTATTATATATTATATATATTAT-AATTATATTTA
2637148 A
1 A
2637149 ATTTTTTTGT
Statistics
Matches: 82, Mismatches: 11, Indels: 17
0.75 0.10 0.15
Matches are distributed among these distances:
30 3 0.04
31 12 0.15
32 22 0.27
33 13 0.16
34 5 0.06
35 4 0.05
36 9 0.11
37 14 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (36 bp):
ATTTATTATATATTATATATATTATAATTATATTTA
Found at i:2637075 original size:46 final size:47
Alignment explanation
Indices: 2637002--2637094 Score: 138
Period size: 46 Copynumber: 2.0 Consensus size: 47
2636992 ATTTAAAAAA
*
2637002 TAATTTATATATTTATAATATATTTTAATATATT-ATAA-TTATATT
1 TAATTTATATATTTATAATAAATTTTAATATATTAATAATTTATATT
2637047 TAATTTATTATATATTAT-ATAAATTTTAATATATTAATAATTTATATT
1 TAATTTA-TATAT-TTATAATAAATTTTAATATATTAATAATTTATATT
2637095 ATTAAATTTA
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
45 7 0.16
46 21 0.49
47 8 0.19
48 7 0.16
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (47 bp):
TAATTTATATATTTATAATAAATTTTAATATATTAATAATTTATATT
Found at i:2637121 original size:30 final size:31
Alignment explanation
Indices: 2637049--2637147 Score: 87
Period size: 30 Copynumber: 3.2 Consensus size: 31
2637039 ATTATATTTA
*
2637049 ATTTA-TTATATATTATATAAATTTTAATAT
1 ATTTATTTTTATATTATATAAATTTTAATAT
* *
2637079 ATTAATAATTTATATTAT-TAAA-TTTAATAAT
1 ATTTAT-TTTTATATTATATAAATTTTAAT-AT
** *
2637110 ATTTATTTTTATAAAATATAATATTTAAATTAT
1 ATTTATTTTTATATTATATAA-ATTTTAA-TAT
2637143 ATTTA
1 ATTTA
2637148 AATTTTTTTG
Statistics
Matches: 54, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
30 18 0.33
31 14 0.26
32 10 0.19
33 11 0.20
34 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (31 bp):
ATTTATTTTTATATTATATAAATTTTAATAT
Found at i:2637364 original size:6 final size:7
Alignment explanation
Indices: 2637349--2637373 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2637339 GACCACCAAC
2637349 TTTTATT
1 TTTTATT
2637356 TTTTATT
1 TTTTATT
2637363 TTTTATT
1 TTTTATT
2637370 TTTT
1 TTTT
2637374 CCTTCAAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTATT
Found at i:2637464 original size:6 final size:6
Alignment explanation
Indices: 2637456--2637497 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
2637446 AGGCATACAT
* *
2637456 AGCCAT AGCCAT AGCCAC AGCCAC AGCCAC AGCCAC AGCCAC
1 AGCCAC AGCCAC AGCCAC AGCCAC AGCCAC AGCCAC AGCCAC
2637498 TCAAATTGCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.33, C:0.45, G:0.17, T:0.05
Consensus pattern (6 bp):
AGCCAC
Found at i:2637636 original size:6 final size:6
Alignment explanation
Indices: 2637620--2637662 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
2637610 TTAAACCTTA
* * *
2637620 AGTGCC CGTGCC AGTGCC AGCGCC GGTGCC AGTGCC AGTGCC A
1 AGTGCC AGTGCC AGTGCC AGTGCC AGTGCC AGTGCC AGTGCC A
2637663 CCGAATTGGC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.14, C:0.37, G:0.35, T:0.14
Consensus pattern (6 bp):
AGTGCC
Found at i:2646029 original size:22 final size:22
Alignment explanation
Indices: 2645981--2646029 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
2645971 AATAATATTT
* *
2645981 TAATTTAAATTTAATTATAAAA
1 TAATATAAATTTAATTAAAAAA
2646003 T-ATATAAATATTAA-TAAAAAA
1 TAATATAAAT-TTAATTAAAAAA
2646024 TAATAT
1 TAATAT
2646030 TTTAATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
TAATATAAATTTAATTAAAAAA
Found at i:2646391 original size:16 final size:17
Alignment explanation
Indices: 2646369--2646416 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
2646359 AATATATAAA
2646369 ATAAATAAATTAAATAT
1 ATAAATAAATTAAATAT
* *
2646386 -TAAATATTATT-AGTAT
1 ATAAATA-AATTAAATAT
2646402 ATAAATAAATTAAAT
1 ATAAATAAATTAAAT
2646417 TAAATCTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 6
0.71 0.12 0.18
Matches are distributed among these distances:
16 13 0.54
17 11 0.46
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (17 bp):
ATAAATAAATTAAATAT
Found at i:2648016 original size:2 final size:2
Alignment explanation
Indices: 2648011--2648051 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2648001 TCTCACTATG
2648011 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2648052 GTTTTTTTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2652626 original size:13 final size:13
Alignment explanation
Indices: 2652608--2652632 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2652598 TAAAACAAAT
2652608 TTTTTTAATTGTG
1 TTTTTTAATTGTG
2652621 TTTTTTAATTGT
1 TTTTTTAATTGT
2652633 CTTTAAGTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.12, T:0.72
Consensus pattern (13 bp):
TTTTTTAATTGTG
Found at i:2662227 original size:21 final size:22
Alignment explanation
Indices: 2662187--2662264 Score: 69
Period size: 22 Copynumber: 3.7 Consensus size: 22
2662177 ATATTTAATG
2662187 ATTAAAAAAATAAAATAAATTA
1 ATTAAAAAAATAAAATAAATTA
*
2662209 ATTAAAAAAAT---GTAAA--A
1 ATTAAAAAAATAAAATAAATTA
2662226 ATTAAAAAAATAAAAATAAA-TA
1 ATTAAAAAAAT-AAAATAAATTA
*
2662248 ATATAAACAACATAAAA
1 AT-TAAA-AAAATAAAA
2662265 ATTCATTATA
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
17 12 0.26
19 4 0.09
21 4 0.09
22 14 0.30
23 8 0.17
24 4 0.09
ACGTcount: A:0.73, C:0.03, G:0.01, T:0.23
Consensus pattern (22 bp):
ATTAAAAAAATAAAATAAATTA
Done.