Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 93 of 135
Found at i:28985456 original size:26 final size:25
Alignment explanation
Indices: 28985405--28985528 Score: 119
Period size: 26 Copynumber: 5.0 Consensus size: 25
28985395 AGTTACCCTT
*
28985405 TTTAATATTATTTTGTAT-AT-TT-
1 TTTAATATTATTTTGTATGTTGTTC
* *
28985427 TTTAATATTATTTTCATATGCTGTTC
1 TTTAATATTATTTT-GTATGTTGTTC
* * *
28985453 TTTATTGTTTATTTTGTATGTTGTTT
1 TTTAAT-ATTATTTTGTATGTTGTTC
*
28985479 TTTAATATGATTTTGTATGTTGTTC
1 TTTAATATTATTTTGTATGTTGTTC
* *
28985504 TTTATTGTTTATTTTGTATGTTGTT
1 TTTAAT-ATTATTTTGTATGTTGTT
28985529 TTATGATGGC
Statistics
Matches: 82, Mismatches: 14, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
22 14 0.17
23 3 0.04
24 1 0.01
25 23 0.28
26 34 0.41
27 7 0.09
ACGTcount: A:0.19, C:0.03, G:0.12, T:0.66
Consensus pattern (25 bp):
TTTAATATTATTTTGTATGTTGTTC
Found at i:28985508 original size:51 final size:52
Alignment explanation
Indices: 28985424--28985530 Score: 180
Period size: 51 Copynumber: 2.1 Consensus size: 52
28985414 ATTTTGTATA
*
28985424 TTTTTTAATATTATTTTCATATGCTGTTCTTTATTGTTTATTTTGTATGTTG
1 TTTTTTAATATGATTTTCATATGCTGTTCTTTATTGTTTATTTTGTATGTTG
* *
28985476 TTTTTTAATATGATTTT-GTATGTTGTTCTTTATTGTTTATTTTGTATGTTG
1 TTTTTTAATATGATTTTCATATGCTGTTCTTTATTGTTTATTTTGTATGTTG
28985527 TTTT
1 TTTT
28985531 ATGATGGCTT
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
51 36 0.69
52 16 0.31
ACGTcount: A:0.16, C:0.04, G:0.13, T:0.67
Consensus pattern (52 bp):
TTTTTTAATATGATTTTCATATGCTGTTCTTTATTGTTTATTTTGTATGTTG
Found at i:28986397 original size:18 final size:18
Alignment explanation
Indices: 28986364--28986398 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28986354 ATGTTGCCCC
*
28986364 AACTCAACAGTATGCCTT
1 AACTCAACAATATGCCTT
*
28986382 AACTCAACAATCTGCCT
1 AACTCAACAATATGCCT
28986399 CAAGACAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.31, G:0.09, T:0.26
Consensus pattern (18 bp):
AACTCAACAATATGCCTT
Found at i:28986738 original size:27 final size:27
Alignment explanation
Indices: 28986708--28986767 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
28986698 ATTTGGCAAT
*
28986708 AGTTTGCCATTCCTTTATTTTGTAAAC
1 AGTTTGCCATTCCTATATTTTGTAAAC
28986735 AGTTTGCCATTCCTATATTTTGTAAAC
1 AGTTTGCCATTCCTATATTTTGTAAAC
*
28986762 ATTTTG
1 AGTTTG
28986768 GCCTTTAGCC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.23, C:0.17, G:0.12, T:0.48
Consensus pattern (27 bp):
AGTTTGCCATTCCTATATTTTGTAAAC
Found at i:28988452 original size:29 final size:30
Alignment explanation
Indices: 28988407--28988465 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
28988397 CAATCGGATC
28988407 AAATCGAAATTTCATGTATAAAATTACACA
1 AAATCGAAATTTCATGTATAAAATTACACA
*
28988437 AAATC-AAAGTTT-ATGTATATAATTACACA
1 AAATCGAAA-TTTCATGTATAAAATTACACA
28988466 TTAAACCATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 19 0.70
30 8 0.30
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.32
Consensus pattern (30 bp):
AAATCGAAATTTCATGTATAAAATTACACA
Found at i:28988483 original size:30 final size:29
Alignment explanation
Indices: 28988420--28988485 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
28988410 TCGAAATTTC
*
28988420 ATGTATAAAATTACACAAAATCAAAGTTT
1 ATGTATAAAATTACACAAAACCAAAGTTT
* *
28988449 ATGTATATAATTACACATTAAACCATAG-TT
1 ATGTATAAAATTACACA--AAACCAAAGTTT
28988479 ATGTATA
1 ATGTATA
28988486 GTTTTGATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 16 0.50
30 9 0.28
31 7 0.22
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.35
Consensus pattern (29 bp):
ATGTATAAAATTACACAAAACCAAAGTTT
Found at i:28989258 original size:19 final size:20
Alignment explanation
Indices: 28989236--28989274 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
28989226 CATTTAATTA
28989236 ATTTATTTTAAT-TTAAAAT
1 ATTTATTTTAATATTAAAAT
*
28989255 ATTTTTTTTAATATTAAAAT
1 ATTTATTTTAATATTAAAAT
28989275 TAAAAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTTATTTTAATATTAAAAT
Found at i:28989760 original size:11 final size:10
Alignment explanation
Indices: 28989690--28989767 Score: 58
Period size: 10 Copynumber: 7.8 Consensus size: 10
28989680 TAATTATATT
28989690 TTTAAAATTA
1 TTTAAAATTA
28989700 TTTAAAATCT-
1 TTTAAAAT-TA
28989710 TTT-AAATT-
1 TTTAAAATTA
*
28989718 TCTTATAATT-
1 T-TTAAAATTA
*
28989728 TTTAATAA-AA
1 TTTAA-AATTA
28989738 TTTAAAATTTA
1 TTTAAAA-TTA
28989749 TTTTAAAATTA
1 -TTTAAAATTA
28989760 TTTAAAAT
1 TTTAAAAT
28989768 AATGTTAATT
Statistics
Matches: 56, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
8 2 0.04
9 11 0.20
10 31 0.55
11 5 0.09
12 7 0.12
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (10 bp):
TTTAAAATTA
Found at i:28989991 original size:30 final size:29
Alignment explanation
Indices: 28989957--28990027 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 29
28989947 CAGTTTAAAA
* *
28989957 AAAAAGTTTAACTTTTGTTTGAGTACTTTT
1 AAAAAGTTTAACTTTTATTTGAGCA-TTTT
* *
28989987 AAAAATTTTTACTTTTATTTGAGCATTTT
1 AAAAAGTTTAACTTTTATTTGAGCATTTT
* *
28990016 GAAAGGTTTAAC
1 AAAAAGTTTAAC
28990028 GCTTATTCGA
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
29 12 0.36
30 21 0.64
ACGTcount: A:0.32, C:0.07, G:0.13, T:0.48
Consensus pattern (29 bp):
AAAAAGTTTAACTTTTATTTGAGCATTTT
Found at i:28990294 original size:10 final size:10
Alignment explanation
Indices: 28990279--28990323 Score: 65
Period size: 10 Copynumber: 4.6 Consensus size: 10
28990269 TTATCAATTC
28990279 GGTTAATTTT
1 GGTTAATTTT
*
28990289 GGTTAATTTC
1 GGTTAATTTT
*
28990299 GGTTGATTTT
1 GGTTAATTTT
28990309 GGTTAA-TTT
1 GGTTAATTTT
28990318 GGTTAA
1 GGTTAA
28990324 ATGAACATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
9 9 0.29
10 22 0.71
ACGTcount: A:0.20, C:0.02, G:0.24, T:0.53
Consensus pattern (10 bp):
GGTTAATTTT
Found at i:28990301 original size:20 final size:20
Alignment explanation
Indices: 28990276--28990323 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
28990266 ATATTATCAA
28990276 TTCGGTTAATTTTGGTTAAT
1 TTCGGTTAATTTTGGTTAAT
*
28990296 TTCGGTTGATTTTGGTTAAT
1 TTCGGTTAATTTTGGTTAAT
28990316 TT-GGTTAA
1 TTCGGTTAA
28990324 ATGAACATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.19, C:0.04, G:0.23, T:0.54
Consensus pattern (20 bp):
TTCGGTTAATTTTGGTTAAT
Found at i:29001730 original size:51 final size:50
Alignment explanation
Indices: 29001661--29001759 Score: 144
Period size: 50 Copynumber: 2.0 Consensus size: 50
29001651 GCTCTTAAAC
* *
29001661 TTTACACATTCTGTTAGTTTAATCTTGATTTAACAAATTTAGCCCTCAAAG
1 TTTACACATCCTGATAGTTT-ATCTTGATTTAACAAATTTAGCCCTCAAAG
* * *
29001712 TTTATACATCCTGATAGTTTGTCTTGCTTTAACAAATTTAGCCCTCAA
1 TTTACACATCCTGATAGTTTATCTTGATTTAACAAATTTAGCCCTCAA
29001760 CATTCACACA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
50 26 0.60
51 17 0.40
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.41
Consensus pattern (50 bp):
TTTACACATCCTGATAGTTTATCTTGATTTAACAAATTTAGCCCTCAAAG
Found at i:29009234 original size:24 final size:24
Alignment explanation
Indices: 29009202--29009248 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
29009192 TAACAAGCAT
29009202 TAACTTTTCTATCCATTTTGAGGC
1 TAACTTTTCTATCCATTTTGAGGC
29009226 TAACTTTTCTATCCATTTTGAGG
1 TAACTTTTCTATCCATTTTGAGG
29009249 TAATTTGACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.21, C:0.19, G:0.13, T:0.47
Consensus pattern (24 bp):
TAACTTTTCTATCCATTTTGAGGC
Found at i:29010909 original size:7 final size:7
Alignment explanation
Indices: 29010897--29010932 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
29010887 TTGTCTTGTA
29010897 TTCAATG
1 TTCAATG
29010904 TTCAATG
1 TTCAATG
29010911 TTCAATG
1 TTCAATG
29010918 TTCAATG
1 TTCAATG
29010925 TTCAATG
1 TTCAATG
29010932 T
1 T
29010933 CTATCTATCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (7 bp):
TTCAATG
Found at i:29011192 original size:29 final size:30
Alignment explanation
Indices: 29011160--29011247 Score: 106
Period size: 31 Copynumber: 2.9 Consensus size: 30
29011150 TGATTTAATA
29011160 TGCAATTGTATACAT-AAATTTTAATTTGG
1 TGCAATTGTATACATAAAATTTTAATTTGG
* **
29011189 TGCAATTATGCACATAAAATTTTAATTGTGG
1 TGCAATTGTATACATAAAATTTTAATT-TGG
* * *
29011220 TTCAAATGTATACTTAAAATTTTAATTT
1 TGCAATTGTATACATAAAATTTTAATTT
29011248 TGATTTAATT
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
29 12 0.25
30 12 0.25
31 24 0.50
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.44
Consensus pattern (30 bp):
TGCAATTGTATACATAAAATTTTAATTTGG
Found at i:29019448 original size:20 final size:20
Alignment explanation
Indices: 29019423--29019467 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
29019413 CATGATTTTT
*
29019423 ATTAAGAGTAAATAG-GCTTA
1 ATTAAGAGTAAA-AGAGATTA
*
29019443 ATTAAGATTAAAAGAGATTA
1 ATTAAGAGTAAAAGAGATTA
29019463 ATTAA
1 ATTAA
29019468 AGCTTAATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.51, C:0.02, G:0.16, T:0.31
Consensus pattern (20 bp):
ATTAAGAGTAAAAGAGATTA
Found at i:29024872 original size:718 final size:715
Alignment explanation
Indices: 29023492--29024914 Score: 1717
Period size: 718 Copynumber: 2.0 Consensus size: 715
29023482 CAAAAGGTAA
* * *
29023492 GTTATAAAGTGGATTGCCTTGAGACCTTCCGGACAACTACTAGGTACAAGGGGTCAAACAAGCAG
1 GTTATAAAGCGGATTGCCTTGAGACCTTCCAGACAACTACTA-GTACAAGAGGTCAAACAAGCAG
* * * *
29023557 GTTATGCTACGAGGGTTCAGTAGATGAATAGTTTCATTTTTTGTGCGTATTAAAGACACTCCAAG
65 GCTATGCTACGAGGGTTCAATAGATGAAGAGTTTCATTTCTTGTGCGTATTAAAGACACTCCAAG
* * *
29023622 GAAAATGGGGATGAATCGAATATTCTATAACGAATGCATTAATGATGGAACATTATAGTTGTCCT
130 GAAAATGGGGATGAATCGAATATTCTAGAACGAATGCATTAATGATGGAACATTACAATTGTCCT
* * * * *
29023687 TTGGAAATGATGCCAATGATGGAGCAAGCTTTGTATCCTTTCGTAAGACACAAATTTAGTTGGGA
195 TTAGAAACGATACCAATAATGGAGCAAGCTTTGTATCCTTTCATAAGACACAAATTTAGTTGGGA
29023752 ATGGTTCATGAATTATTAGGTCTACTAAGCTCAACATGCAACATTTTAGAGAGCTCCTTTAAATA
260 ATGGTTCATGAATTATTAGGTCTACTAAGCTCAACATGCAACATTTTAGAGAGCTCCTTTAAATA
* ** * * * * * *
29023817 CCCTTAATTTTAGTTATTTGGGGTTCATTTACTTCACCGGAGAAATTTCTTAAGTTTTTCAATTC
325 CCCCTAATCCTAGTGATTTGAGGTTCATTTACTTCACCGGAGAAATTTCCTAAGTTATCCAAGTC
* *
29023882 TTTCTTTTTTCTCTATTTATCAAAATTTCGTGAGTTTTTGTTCTCCAATTTCTTTGCTTTCCCTT
390 TTTCTTTTTTCTCTATTTACCAAAATTTCGTAAGTTTTTGTTCTCCAATTTCTTTGCTTTCCCTT
* * *** * * *
29023947 GCCTTTCCTCACTCTTCTTATTCATCTTTATCATTCCTTTCTTGGAGTTGGAGGTTCTGTTAAAG
455 GCCTTTCCTCACTATTATTATTCATCGCCACCATTCCTTGCTTGGAGTTAGAGGTTCTGTTAAAG
* * *
29024012 GTAAGAGTTCAATTTCTTTGAATCTTTGTACTTTCTTTTTTAATAGAATCAACACCAATGGTTGA
520 ATAAGAGTTCAATATCTTTGAATCTTTGTACTTTCTTTTTTAATAGAAACAACACCAATGGTTGA
* * * *
29024077 GGGTAACAAAAGATCTTAGAAAAATCCTATTAAGATAACAGTTATTTTAGTTGCAGTGGAAGTTT
585 GGGTAACAAAAGATCTTAGAAAAATCCTATTAAGAAAACAATTATTTTAGTTACAGCGGAAGTTT
** *
29024142 AAATTTTTTTTCTTAAACTGAACTTGTTATGTTATTTAT-GTCAATAAACCTATACCGATCAAGT
650 AAATAATTTTTCTTAAACTGAACTTG-TA--TTATTTATAG-CAATAAACCTAAACCGATCAAGT
29024206 GGAAG
711 GGAAG
* * * * * *
29024211 GTTATAAAGCGGATTGCCTTGAGACCTTCCAGACAATTATTA-TGCACGAGGTCAGACAAGCGGG
1 GTTATAAAGCGGATTGCCTTGAGACCTTCCAGACAACTACTAGTACAAGAGGTCAAACAAGCAGG
* ** * *
29024275 CTGTGCCTTA-G-GGGTTCAATAGATGAAGAGTTTCATTTCTTGTGCGTATTGGAGACGCTCCAG
66 CTATG-C-TACGAGGGTTCAATAGATGAAGAGTTTCATTTCTTGTGCGTATTAAAGACACTCCAA
* * * * * * *
29024338 GGAAAA-GAGGGATGTATCGAGTATTCTGGAATGGATGCATTAATGGTGGAGCATTACAATTGTC
129 GGAAAATG-GGGATGAATCGAATATTCTAGAACGAATGCATTAATGATGGAACATTACAATTGTC
* * **
29024402 CTTTTAGAAACGATACCAATAATGGAGTAGGCTTTGTATCCTTTCAT-AGA-ACACGTGTTCAGT
193 C-TTTAGAAACGATACCAATAATGGAGCAAGCTTTGTATCCTTTCATAAGACACAAAT-TT-AGT
* ** * ** * * *
29024465 TGGGAGTGGTTTGTGAATTATTAGGTTTGTTAGGCTCAA-ATTG-AGCCATTTTGGAGAGCTCCT
255 TGGGAATGGTTCATGAATTATTAGGTCTACTAAGCTCAACA-TGCA-ACATTTTAGAGAGCTCCT
* * * * * * *
29024528 TTAAGTACCCCTGATCCTAGTGATTTGAGGTTCATTTGCTTTATCTGATAAATTTCCTAAG-TAT
318 TTAAATACCCCTAATCCTAGTGATTTGAGGTTCATTTACTTCACCGGAGAAATTTCCTAAGTTAT
* * * *
29024592 CCAAGTCTTTTCTCTTTTT-TTTGTTTACCAAAATTT-GATAAGTTTTTGTTCTCCATTTTGTTT
383 CCAAGTC-TTTCT-TTTTTCTCTATTTACCAAAATTTCG-TAAGTTTTTGTTCTCCAATTTCTTT
* **
29024655 GCTTTCTCTTGCCTTTTTTCACTATTATTATTCATCGCCACCATTCCTTGCTTGGAGTTAGAGGC
445 GCTTTCCCTTGCCTTTCCTCACTATTATTATTCATCGCCACCATTCCTTGCTTGGAGTTAGAGG-
* *
29024720 TT-TGTTAAAGATAAGATTTCAATATCTTTGAATCTTTGTACTTTCTTTTTTTAGTAGAAACAAC
509 TTCTGTTAAAGATAAGAGTTCAATATCTTTGAATCTTTGTACTTTC-TTTTTTAATAGAAACAAC
* *
29024784 ACCAATGGTTG-GGAGTAACAACAGATCTTGGAAAAAT-CTGATTAAGAAAACAATTATTTTAGT
573 ACCAATGGTTGAGG-GTAACAAAAGATCTTAGAAAAATCCT-ATTAAGAAAACAATTATTTTAGT
29024847 TACAGCGGAAGTTTAAA-AATTTTTCTTAAACTGAACTTGTATTATTTATAGCAATAAACCTAAA
636 TACAGCGGAAGTTTAAATAATTTTTCTTAAACTGAACTTGTATTATTTATAGCAATAAACCTAAA
29024911 CCGA
701 CCGA
29024915 GATGTCCATG
Statistics
Matches: 595, Mismatches: 93, Indels: 36
0.82 0.13 0.05
Matches are distributed among these distances:
715 24 0.04
716 6 0.01
717 135 0.23
718 299 0.50
719 131 0.22
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.38
Consensus pattern (715 bp):
GTTATAAAGCGGATTGCCTTGAGACCTTCCAGACAACTACTAGTACAAGAGGTCAAACAAGCAGG
CTATGCTACGAGGGTTCAATAGATGAAGAGTTTCATTTCTTGTGCGTATTAAAGACACTCCAAGG
AAAATGGGGATGAATCGAATATTCTAGAACGAATGCATTAATGATGGAACATTACAATTGTCCTT
TAGAAACGATACCAATAATGGAGCAAGCTTTGTATCCTTTCATAAGACACAAATTTAGTTGGGAA
TGGTTCATGAATTATTAGGTCTACTAAGCTCAACATGCAACATTTTAGAGAGCTCCTTTAAATAC
CCCTAATCCTAGTGATTTGAGGTTCATTTACTTCACCGGAGAAATTTCCTAAGTTATCCAAGTCT
TTCTTTTTTCTCTATTTACCAAAATTTCGTAAGTTTTTGTTCTCCAATTTCTTTGCTTTCCCTTG
CCTTTCCTCACTATTATTATTCATCGCCACCATTCCTTGCTTGGAGTTAGAGGTTCTGTTAAAGA
TAAGAGTTCAATATCTTTGAATCTTTGTACTTTCTTTTTTAATAGAAACAACACCAATGGTTGAG
GGTAACAAAAGATCTTAGAAAAATCCTATTAAGAAAACAATTATTTTAGTTACAGCGGAAGTTTA
AATAATTTTTCTTAAACTGAACTTGTATTATTTATAGCAATAAACCTAAACCGATCAAGTGGAAG
Found at i:29025683 original size:14 final size:14
Alignment explanation
Indices: 29025644--29025690 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
29025634 GACTTAACTA
*
29025644 ATTTAATTTC-ATC
1 ATTTAATTTCAATT
* *
29025657 ATTGAACTTCAATT
1 ATTTAATTTCAATT
29025671 ATTTAATTTCAATT
1 ATTTAATTTCAATT
*
29025685 AATTAA
1 ATTTAA
29025691 GTAATAATTC
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
13 8 0.30
14 19 0.70
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (14 bp):
ATTTAATTTCAATT
Found at i:29028035 original size:15 final size:14
Alignment explanation
Indices: 29028016--29028042 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29028006 GGGATAACAA
29028016 AAAAAAAGGAAAAG
1 AAAAAAAGGAAAAG
29028030 AAAAAAAGGAAAA
1 AAAAAAAGGAAAA
29028043 CCTTGAGAAA
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:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AAAAAAAGGAAAAG
Found at i:29028609 original size:24 final size:24
Alignment explanation
Indices: 29028558--29028610 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
29028548 CCTCAAAACT
* *
29028558 TTTTTCCTTTTACTTTCTCCCCAT
1 TTTTTCCTTTTACTTTCTCCCAAA
29028582 TTTTTCCTTTTACTTTC-CCCAAAA
1 TTTTTCCTTTTACTTTCTCCC-AAA
29028606 TTTTT
1 TTTTT
29028611 ACTCCCAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 3 0.12
24 23 0.88
ACGTcount: A:0.13, C:0.28, G:0.00, T:0.58
Consensus pattern (24 bp):
TTTTTCCTTTTACTTTCTCCCAAA
Found at i:29030106 original size:24 final size:24
Alignment explanation
Indices: 29030074--29030124 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
29030064 GTATATTGGT
*
29030074 TAACTATTCTAGGCTCGTAAGAGC
1 TAACCATTCTAGGCTCGTAAGAGC
* *
29030098 TAACCATTCTAGGCTTGTGAGAGC
1 TAACCATTCTAGGCTCGTAAGAGC
29030122 TAA
1 TAA
29030125 TATTATCTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (24 bp):
TAACCATTCTAGGCTCGTAAGAGC
Found at i:29034522 original size:24 final size:24
Alignment explanation
Indices: 29034486--29034536 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
29034476 GTATATTGGT
* *
29034486 TAACTATTTTGGGCTCGTAAGAGC
1 TAACCATTCTGGGCTCGTAAGAGC
* *
29034510 TAACCATTCTGGGCTTGTGAGAGC
1 TAACCATTCTGGGCTCGTAAGAGC
29034534 TAA
1 TAA
29034537 TATTATCTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.31
Consensus pattern (24 bp):
TAACCATTCTGGGCTCGTAAGAGC
Found at i:29035075 original size:21 final size:21
Alignment explanation
Indices: 29035041--29035080 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
29035031 TTGTGATTTG
* *
29035041 CATGCTTGTTTCGGTAGAACC
1 CATGCATGTATCGGTAGAACC
29035062 CATGCATGTATCGGTAGAA
1 CATGCATGTATCGGTAGAA
29035081 GTACAAGGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (21 bp):
CATGCATGTATCGGTAGAACC
Found at i:29036369 original size:125 final size:126
Alignment explanation
Indices: 29036240--29036478 Score: 336
Period size: 125 Copynumber: 1.9 Consensus size: 126
29036230 ATTTTGTCTC
* * * * * *
29036240 ATCTTACCCCGATACACAATACTGACTAATAAAAGTGTGACATGTGAGACGGTCTTATTGGAATT
1 ATCTTACCCCAATACACAATACTAACTAATAAAAATGTGACATATGACACGGTCTTATAGGAATT
* * *
29036305 CATACACCTTTT-TTTGGATAAAATGGGACAAAATTTATAATTTAAGTACCACTAAATTCA
66 CATACACCTTTTATTTGGATAAAATGAGACAAAATCTAAAATTTAAGTACCACTAAATTCA
* * * * *
29036365 ATCTTACCTCAATACACAATGCTAACTAATAAAAATGTGATATATGACATGTTCTTATAGGAATT
1 ATCTTACCCCAATACACAATACTAACTAATAAAAATGTGACATATGACACGGTCTTATAGGAATT
*
29036430 CATACACTTTTTATTTGGATAAAATGAGACAAAATCTAAAATTTAAGTA
66 CATACACCTTTTATTTGGATAAAATGAGACAAAATCTAAAATTTAAGTA
29036479 ATACTGAATT
Statistics
Matches: 98, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
125 65 0.66
126 33 0.34
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (126 bp):
ATCTTACCCCAATACACAATACTAACTAATAAAAATGTGACATATGACACGGTCTTATAGGAATT
CATACACCTTTTATTTGGATAAAATGAGACAAAATCTAAAATTTAAGTACCACTAAATTCA
Found at i:29044677 original size:1 final size:1
Alignment explanation
Indices: 29044642--29044668 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
29044632 TCCAAGAAGT
29044642 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
29044669 TCCCAAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:29048630 original size:39 final size:39
Alignment explanation
Indices: 29048587--29048661 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
29048577 ACATTTGCAA
* *
29048587 CAGCAACAACTC-CCTCAGCTGCAGCAACAGCAGCAGCAG
1 CAGCAACAACTCTCC-CAGCTGCAACAACAACAGCAGCAG
*
29048626 CAGCAGCAACTCTCCCAGCTGCAACAACAACAGCAG
1 CAGCAACAACTCTCCCAGCTGCAACAACAACAGCAG
29048662 TTGCCCCAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
39 30 0.94
40 2 0.06
ACGTcount: A:0.35, C:0.39, G:0.19, T:0.08
Consensus pattern (39 bp):
CAGCAACAACTCTCCCAGCTGCAACAACAACAGCAGCAG
Found at i:29048869 original size:24 final size:24
Alignment explanation
Indices: 29048837--29048885 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
29048827 GGCTTTATGA
29048837 GTTGATCAGTGACACTTGGAATTT
1 GTTGATCAGTGACACTTGGAATTT
29048861 GTTGATCAGTGACACTTGGAATTT
1 GTTGATCAGTGACACTTGGAATTT
29048885 G
1 G
29048886 CTGGCTTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.12, G:0.27, T:0.37
Consensus pattern (24 bp):
GTTGATCAGTGACACTTGGAATTT
Found at i:29058375 original size:80 final size:80
Alignment explanation
Indices: 29058238--29058386 Score: 253
Period size: 80 Copynumber: 1.9 Consensus size: 80
29058228 CACAAAATTT
* * * *
29058238 GTCAATTCATGGCACCCAGTGCCTAATGGATAAACCGCGATAAGTGAGCCCAGCTCTAGTTGGAT
1 GTCAATTCATGGCACCCAATGCCTAACGGATAAACCGCGATAAATGAGCCCAACTCTAGTTGGAT
29058303 TAACCAAAGAATTCC
66 TAACCAAAGAATTCC
*
29058318 GTCAATTCATGGCACCCAATGCCTAGCGGATAAACCGCGATAAATGAGCCCAACTCTAGTTGGAT
1 GTCAATTCATGGCACCCAATGCCTAACGGATAAACCGCGATAAATGAGCCCAACTCTAGTTGGAT
29058383 TAAC
66 TAAC
29058387 TAATGGTTTG
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
80 64 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.22
Consensus pattern (80 bp):
GTCAATTCATGGCACCCAATGCCTAACGGATAAACCGCGATAAATGAGCCCAACTCTAGTTGGAT
TAACCAAAGAATTCC
Found at i:29065086 original size:20 final size:20
Alignment explanation
Indices: 29065061--29065106 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
29065051 TAACCCGCTG
29065061 CTACAATACCTTTGCCATTT
1 CTACAATACCTTTGCCATTT
29065081 CTACAATACCTTTGCCATTT
1 CTACAATACCTTTGCCATTT
29065101 CTACAA
1 CTACAA
29065107 AGATTTAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.28, C:0.30, G:0.04, T:0.37
Consensus pattern (20 bp):
CTACAATACCTTTGCCATTT
Found at i:29071156 original size:17 final size:18
Alignment explanation
Indices: 29071134--29071173 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
29071124 ATAGTTTTCA
*
29071134 TGCATTTT-TATTGTCAT
1 TGCATTTTATATTGTCAC
*
29071151 TGCATTTTATTTTGTCAC
1 TGCATTTTATATTGTCAC
29071169 TGCAT
1 TGCAT
29071174 CCCTTTTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.17, C:0.15, G:0.12, T:0.55
Consensus pattern (18 bp):
TGCATTTTATATTGTCAC
Found at i:29071794 original size:16 final size:16
Alignment explanation
Indices: 29071756--29071810 Score: 58
Period size: 16 Copynumber: 3.3 Consensus size: 16
29071746 TCACTCATTT
*
29071756 GAAAAAGAAACAAAATGA
1 GAAAAAGAAAGAAAA--A
*
29071774 GAAAAAGGAAGAAAAA
1 GAAAAAGAAAGAAAAA
29071790 GAAAAAGAAA-AAGAAA
1 GAAAAAGAAAGAA-AAA
29071806 GAAAA
1 GAAAA
29071811 TTTTGATAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 2 0.06
16 18 0.55
18 13 0.39
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (16 bp):
GAAAAAGAAAGAAAAA
Found at i:29076652 original size:3 final size:3
Alignment explanation
Indices: 29076644--29076684 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
29076634 TTGGAGTGTT
29076644 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
29076685 TATATCTATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:29077081 original size:17 final size:17
Alignment explanation
Indices: 29077042--29077089 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
29077032 ATATATATGG
29077042 AAATGCAATGACAATGA
1 AAATGCAATGACAATGA
* *
29077059 AGATGCAGTGACAA-GAA
1 AAATGCAATGACAATG-A
29077076 AAATGCAATGACAA
1 AAATGCAATGACAA
29077090 ACGAAATGTG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
16 1 0.04
17 25 0.96
ACGTcount: A:0.52, C:0.12, G:0.21, T:0.15
Consensus pattern (17 bp):
AAATGCAATGACAATGA
Found at i:29077096 original size:17 final size:16
Alignment explanation
Indices: 29077041--29077097 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
29077031 AATATATATG
*
29077041 GAAATGCAATGACAAT
1 GAAATGCAATGACAAA
*
29077057 GAAGATGCAGTGACAAGA
1 GAA-ATGCAATGACAA-A
*
29077075 AAAATGCAATGACAAA
1 GAAATGCAATGACAAA
29077091 CGAAATG
1 -GAAATG
29077098 TGATGACAGC
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
16 4 0.12
17 27 0.82
18 2 0.06
ACGTcount: A:0.51, C:0.12, G:0.23, T:0.14
Consensus pattern (16 bp):
GAAATGCAATGACAAA
Found at i:29089000 original size:37 final size:38
Alignment explanation
Indices: 29088959--29089056 Score: 101
Period size: 38 Copynumber: 2.6 Consensus size: 38
29088949 ATACATGTTC
*
29088959 ATGCAGCAACATTCCTGGGTGCAA-TTGAAGAATACTT
1 ATGCAGCAACATTCTTGGGTGCAATTTGAAGAATACTT
* * * * *
29088996 ATGCAGTAATAGTT-TTGGATACAATTTGAAGAATATTT
1 ATGCAGCAACA-TTCTTGGGTGCAATTTGAAGAATACTT
* *
29089034 ATGCAGCGACAGTCTTGGGTGCA
1 ATGCAGCAACATTCTTGGGTGCA
29089057 TTTCGAAAAT
Statistics
Matches: 46, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
37 17 0.37
38 29 0.63
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.31
Consensus pattern (38 bp):
ATGCAGCAACATTCTTGGGTGCAATTTGAAGAATACTT
Found at i:29089124 original size:37 final size:37
Alignment explanation
Indices: 29089078--29089148 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 37
29089068 TTCCTGCAGT
* *
29089078 GACAATTTTGGGTGCAATCTGGAACTGCTCATGCGGC
1 GACAATTTTGGGCGCAATCTAGAACTGCTCATGCGGC
* * *
29089115 GACAGTTTTGGGCGCAATTTAGAAGTGCTCATGC
1 GACAATTTTGGGCGCAATCTAGAACTGCTCATGC
29089149 AGCAACATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.28
Consensus pattern (37 bp):
GACAATTTTGGGCGCAATCTAGAACTGCTCATGCGGC
Found at i:29090218 original size:17 final size:17
Alignment explanation
Indices: 29090198--29090237 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
29090188 TAGATGTAGC
*
29090198 GACAATAAAAATACAGT
1 GACAATAAAAATACAGG
*
29090215 GACAATAAAAATGCAGG
1 GACAATAAAAATACAGG
29090232 GACAAT
1 GACAAT
29090238 TATACTACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.55, C:0.12, G:0.17, T:0.15
Consensus pattern (17 bp):
GACAATAAAAATACAGG
Found at i:29092544 original size:16 final size:16
Alignment explanation
Indices: 29092523--29092553 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29092513 ATAATGCAAA
29092523 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
29092539 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
29092554 GGATCCACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:29106370 original size:2 final size:2
Alignment explanation
Indices: 29106365--29106391 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
29106355 ACACACACAC
29106365 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 T
29106392 TGTTGTGATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29106577 original size:17 final size:18
Alignment explanation
Indices: 29106555--29106618 Score: 57
Period size: 17 Copynumber: 3.7 Consensus size: 18
29106545 ATGTTCAACC
29106555 TTTAACC-TCCATTGACT
1 TTTAACCTTCCATTGACT
29106572 TTTAACCTTCCA-T--CT
1 TTTAACCTTCCATTGACT
* *
29106587 TCCTTAACC-TCCCTTGACC
1 T--TTAACCTTCCATTGACT
29106606 TTTAACCTTCCAT
1 TTTAACCTTCCAT
29106619 CTTCCTTAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 13
0.70 0.06 0.25
Matches are distributed among these distances:
15 3 0.08
16 3 0.08
17 21 0.57
18 8 0.22
19 2 0.05
ACGTcount: A:0.20, C:0.36, G:0.03, T:0.41
Consensus pattern (18 bp):
TTTAACCTTCCATTGACT
Found at i:29106604 original size:34 final size:34
Alignment explanation
Indices: 29106556--29106630 Score: 132
Period size: 34 Copynumber: 2.2 Consensus size: 34
29106546 TGTTCAACCT
*
29106556 TTAACCTCCATTGACTTTTAACCTTCCATCTTCC
1 TTAACCTCCATTGACCTTTAACCTTCCATCTTCC
*
29106590 TTAACCTCCCTTGACCTTTAACCTTCCATCTTCC
1 TTAACCTCCATTGACCTTTAACCTTCCATCTTCC
29106624 TTAACCT
1 TTAACCT
29106631 TTCATATTCT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.20, C:0.37, G:0.03, T:0.40
Consensus pattern (34 bp):
TTAACCTCCATTGACCTTTAACCTTCCATCTTCC
Found at i:29106627 original size:17 final size:17
Alignment explanation
Indices: 29106573--29106631 Score: 70
Period size: 17 Copynumber: 3.5 Consensus size: 17
29106563 CCATTGACTT
29106573 TTAACCTTCCATCTTCC
1 TTAACCTTCCATCTTCC
29106590 TTAACC-TCC--CTTGACC
1 TTAACCTTCCATCTT--CC
29106606 TTTAACCTTCCATCTTCC
1 -TTAACCTTCCATCTTCC
29106624 TTAACCTT
1 TTAACCTT
29106632 TCATATTCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
14 3 0.08
16 5 0.14
17 20 0.56
18 5 0.14
20 3 0.08
ACGTcount: A:0.19, C:0.39, G:0.02, T:0.41
Consensus pattern (17 bp):
TTAACCTTCCATCTTCC
Found at i:29112986 original size:20 final size:20
Alignment explanation
Indices: 29112963--29113007 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
29112953 ATATTTATGA
*
29112963 TTTTTAATGAATTTGTAAA-T
1 TTTTTAATAAATTT-TAAAGT
*
29112983 TTTTTTATAAATTTTAAAGT
1 TTTTTAATAAATTTTAAAGT
29113003 TTTTT
1 TTTTT
29113008 TTATAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (20 bp):
TTTTTAATAAATTTTAAAGT
Found at i:29112987 original size:21 final size:19
Alignment explanation
Indices: 29112972--29113033 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 19
29112962 ATTTTTAATG
29112972 AATTTGTAAA-TTTTTTTAT
1 AATTT-TAAAGTTTTTTTAT
29112991 AAATTTTAAAGTTTTTTTTAT
1 -AATTTTAAAG-TTTTTTTAT
* *
29113012 AATTTTAATG-ATTTTTAT
1 AATTTTAAAGTTTTTTTAT
29113030 AATT
1 AATT
29113034 CAAGAATGTA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
18 11 0.29
19 4 0.11
20 14 0.37
21 9 0.24
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (19 bp):
AATTTTAAAGTTTTTTTAT
Found at i:29113008 original size:20 final size:19
Alignment explanation
Indices: 29112972--29113033 Score: 65
Period size: 18 Copynumber: 3.2 Consensus size: 19
29112962 ATTTTTAATG
29112972 AATTTGTAAA-TTTTTTTAT
1 AATTT-TAAATTTTTTTTAT
29112991 AAATTTTAAAGTTTTTTTTAT
1 -AATTTTAAA-TTTTTTTTAT
**
29113012 AATTTT-AATGATTTTTAT
1 AATTTTAAATTTTTTTTAT
29113030 AATT
1 AATT
29113034 CAAGAATGTA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
18 12 0.32
19 6 0.16
20 11 0.29
21 9 0.24
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (19 bp):
AATTTTAAATTTTTTTTAT
Found at i:29117108 original size:17 final size:17
Alignment explanation
Indices: 29117086--29117120 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
29117076 ATTATAAAAT
*
29117086 CAAATCTTATCAGATTA
1 CAAATCTTATAAGATTA
*
29117103 CAAATCTTCTAAGATTA
1 CAAATCTTATAAGATTA
29117120 C
1 C
29117121 TTGTCCTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.20, G:0.06, T:0.34
Consensus pattern (17 bp):
CAAATCTTATAAGATTA
Found at i:29118143 original size:25 final size:25
Alignment explanation
Indices: 29118113--29118208 Score: 97
Period size: 25 Copynumber: 3.9 Consensus size: 25
29118103 TGCTCTGAGT
** *
29118113 TCTGGCTCGCATGAGCAATATTCTG
1 TCTGGCTCGCAAAAGCAATATTCTA
* *
29118138 TCTGGCTCGTAAAAGCGATATTCTA
1 TCTGGCTCGCAAAAGCAATATTCTA
* *
29118163 TCTGGCTCGTAAAAGCGAT-TTCTA
1 TCTGGCTCGCAAAAGCAATATTCTA
*
29118187 TCTGGCTCG-AAAGAGCGATATT
1 TCTGGCTCGCAAA-AGCAATATT
29118209 ATGAATTCTA
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
23 3 0.05
24 20 0.31
25 41 0.64
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (25 bp):
TCTGGCTCGCAAAAGCAATATTCTA
Found at i:29118190 original size:24 final size:25
Alignment explanation
Indices: 29118130--29118208 Score: 126
Period size: 25 Copynumber: 3.2 Consensus size: 25
29118120 CGCATGAGCA
*
29118130 ATATTCTGTCTGGCTCGTAAAAGCG
1 ATATTCTATCTGGCTCGTAAAAGCG
29118155 ATATTCTATCTGGCTCGTAAAAGCG
1 ATATTCTATCTGGCTCGTAAAAGCG
29118180 AT-TTCTATCTGGCTCG-AAAGAGCG
1 ATATTCTATCTGGCTCGTAAA-AGCG
29118204 ATATT
1 ATATT
29118209 ATGAATTCTA
Statistics
Matches: 51, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
23 3 0.06
24 20 0.39
25 28 0.55
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.33
Consensus pattern (25 bp):
ATATTCTATCTGGCTCGTAAAAGCG
Found at i:29118235 original size:28 final size:28
Alignment explanation
Indices: 29118191--29118264 Score: 103
Period size: 28 Copynumber: 2.6 Consensus size: 28
29118181 TTTCTATCTG
29118191 GCTCGAAAGAGCGATATTATGAATTCTA
1 GCTCGAAAGAGCGATATTATGAATTCTA
* * *
29118219 GCTCGAAAGAGCTATATTTTGAATTTTA
1 GCTCGAAAGAGCGATATTATGAATTCTA
* *
29118247 GCTCGTAAGAGCGTTATT
1 GCTCGAAAGAGCGATATT
29118265 TTGTCTGAGC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.34
Consensus pattern (28 bp):
GCTCGAAAGAGCGATATTATGAATTCTA
Found at i:29134679 original size:25 final size:25
Alignment explanation
Indices: 29134651--29134818 Score: 149
Period size: 25 Copynumber: 6.6 Consensus size: 25
29134641 CTCTGAATTC
* *
29134651 TGGCTCGTATGAGTGATATTCTGTT
1 TGGCTCGTAAGAGCGATATTCTGTT
*
29134676 TGGCTCGTAAGAGCGATATTTTGTT
1 TGGCTCGTAAGAGCGATATTCTGTT
* *
29134701 TGGCTTGTAAGAGCGATATT-TTTT
1 TGGCTCGTAAGAGCGATATTCTGTT
*
29134725 CTGGCTCGTAAGAGCGATATTCTGTC
1 -TGGCTCGTAAGAGCGATATTCTGTT
* * *
29134751 TGGCTTGAAAGAGCTATATTCTGAATT
1 TGGCTCGTAAGAGCGATATTCTG--TT
* * * *
29134778 CTGGCTTGTAAGTGTGTTATTCTGTCT
1 -TGGCTCGTAAGAGCGATATTCTGT-T
* *
29134805 AGGCTCGTTAGAGC
1 TGGCTCGTAAGAGC
29134819 TAAATTTTGG
Statistics
Matches: 115, Mismatches: 22, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
24 3 0.03
25 80 0.70
26 12 0.10
27 2 0.02
28 18 0.16
ACGTcount: A:0.20, C:0.14, G:0.27, T:0.39
Consensus pattern (25 bp):
TGGCTCGTAAGAGCGATATTCTGTT
Found at i:29141101 original size:14 final size:14
Alignment explanation
Indices: 29141076--29141108 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
29141066 AACTTAAATA
29141076 ATTTTATTTAGTTT
1 ATTTTATTTAGTTT
29141090 -TTTTAGTTTAGTTT
1 ATTTTA-TTTAGTTT
29141104 ATTTT
1 ATTTT
29141109 TATGTTTGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 5 0.29
14 8 0.47
15 4 0.24
ACGTcount: A:0.18, C:0.00, G:0.09, T:0.73
Consensus pattern (14 bp):
ATTTTATTTAGTTT
Found at i:29142600 original size:23 final size:23
Alignment explanation
Indices: 29142570--29142613 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
29142560 ATATGTGCAT
29142570 TGTTGATTATGGTCTAAAGCCCA
1 TGTTGATTATGGTCTAAAGCCCA
*
29142593 TGTTGATTATGGTGTAAAGCC
1 TGTTGATTATGGTCTAAAGCC
29142614 TCTGCCTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (23 bp):
TGTTGATTATGGTCTAAAGCCCA
Found at i:29156277 original size:21 final size:21
Alignment explanation
Indices: 29156253--29156299 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
29156243 CTTAAATTTT
29156253 ATTTGTTATTGA-T-TTGTTTCA
1 ATTT-TTATTGACTCTT-TTTCA
*
29156274 ATTTTTGTTGACTCTTTTTCA
1 ATTTTTATTGACTCTTTTTCA
29156295 ATTTT
1 ATTTT
29156300 CTTTTAGGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 6 0.26
21 15 0.65
22 2 0.09
ACGTcount: A:0.17, C:0.09, G:0.11, T:0.64
Consensus pattern (21 bp):
ATTTTTATTGACTCTTTTTCA
Found at i:29156944 original size:171 final size:170
Alignment explanation
Indices: 29156660--29157002 Score: 623
Period size: 171 Copynumber: 2.0 Consensus size: 170
29156650 TATGTTGGTT
*
29156660 TGCCTCATGTAGATGCAAGAAAGCATCTTAAATCTTTTCTAATAATCTGTGCTTCTTTTAGTCAG
1 TGCCTCATGTAGATGCAAGAAAGCATCTTAAATCTTTTCTAATAAACTGTGCTTCTTTTAGTCAG
* *
29156725 CATGGTGTTCCTAATGACGCTTTGAAGATGCAATTGTTTCCTTATTCATTGCAAGAAAGGGCTCG
66 CATGGTGTTCCTAATGACGCTTTGAAGATGCAACTATTTCCTTATTCATTGCAAGAAAGGGCTCG
*
29156790 TACCTGGTTCCTTGGATTACTTGCTGGATCGATTACATAG
131 TACCTGGTTCCTTGGATTACTTGCTAGATCGATTACATAG
*
29156830 TGCCTCATGTAGATGCAAGAGAGCATCTTAAATCTTTTCTTAATAAACTGTGCTTCTTTTAGTCA
1 TGCCTCATGTAGATGCAAGAAAGCATCTTAAATCTTTTC-TAATAAACTGTGCTTCTTTTAGTCA
*
29156895 GCATGGTGTTCCTGATGACGCTTTGAAGATGCAACTATTTCCTTATTCATTGCAAGAAAGGGCTC
65 GCATGGTGTTCCTAATGACGCTTTGAAGATGCAACTATTTCCTTATTCATTGCAAGAAAGGGCTC
29156960 GTACCTGGTTCCTTGGATTACTTGCTAGATCGATTACATAG
130 GTACCTGGTTCCTTGGATTACTTGCTAGATCGATTACATAG
29157001 TG
1 TG
29157003 GAATGCACTT
Statistics
Matches: 166, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
170 38 0.23
171 128 0.77
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (170 bp):
TGCCTCATGTAGATGCAAGAAAGCATCTTAAATCTTTTCTAATAAACTGTGCTTCTTTTAGTCAG
CATGGTGTTCCTAATGACGCTTTGAAGATGCAACTATTTCCTTATTCATTGCAAGAAAGGGCTCG
TACCTGGTTCCTTGGATTACTTGCTAGATCGATTACATAG
Found at i:29163713 original size:24 final size:23
Alignment explanation
Indices: 29163673--29163737 Score: 64
Period size: 24 Copynumber: 2.9 Consensus size: 23
29163663 CTGTGGGTAT
29163673 TGAGGAAGAGAAAGAAGAAGAGAA
1 TGAGGAAGAGAAAGAAGAA-AGAA
*
29163697 TGAGGAGGA-AAAGGAAGAAAGAA
1 TGAGGAAGAGAAA-GAAGAAAGAA
* *
29163720 --AAGAAGAGAAGGAAGAAA
1 TGAGGAAGAGAAAGAAGAAA
29163738 TTTTTGTCGC
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
21 12 0.34
22 2 0.06
23 7 0.20
24 14 0.40
ACGTcount: A:0.60, C:0.00, G:0.37, T:0.03
Consensus pattern (23 bp):
TGAGGAAGAGAAAGAAGAAAGAA
Found at i:29163714 original size:27 final size:27
Alignment explanation
Indices: 29163674--29163733 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
29163664 TGTGGGTATT
* *
29163674 GAGGAAGAGAAAG-AAGAAGAGAATGAG
1 GAGGAAAAGAAAGAAAGAAAAGAA-GAG
*
29163701 GAGGAAAAGGAAGAAAGAAAAGAAGAG
1 GAGGAAAAGAAAGAAAGAAAAGAAGAG
*
29163728 AAGGAA
1 GAGGAA
29163734 GAAATTTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 19 0.68
28 9 0.32
ACGTcount: A:0.60, C:0.00, G:0.38, T:0.02
Consensus pattern (27 bp):
GAGGAAAAGAAAGAAAGAAAAGAAGAG
Found at i:29169545 original size:97 final size:99
Alignment explanation
Indices: 29169444--29169626 Score: 262
Period size: 99 Copynumber: 1.9 Consensus size: 99
29169434 TATACGGTCA
* * * * * *
29169444 TGTGTTTTGAGATAGTATATTACACGAGTGTACAC-GGGGTGA-GACACGACTGTGTGTCCCATA
1 TGTGTTCTGAGACAGTATATTACACGAGTGGACACACGAGTGAGGACACAACTGTGTGTCCCATA
29169507 CTTCGAATGCTCACACGGTCTCCTCACACGGTTG
66 CTTCGAATGCTCACACGGTCTCCTCACACGGTTG
* * *
29169541 TGTGTTCTGAGACAGTATGTTACACGGGTGGACACACGAGTTAGGACACAACTGTGTGTCCCATA
1 TGTGTTCTGAGACAGTATATTACACGAGTGGACACACGAGTGAGGACACAACTGTGTGTCCCATA
*
29169606 CTTCGAATGCTCACATGGTCT
66 CTTCGAATGCTCACACGGTCT
29169627 AAGTAATGTC
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
97 30 0.41
98 4 0.05
99 40 0.54
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.28
Consensus pattern (99 bp):
TGTGTTCTGAGACAGTATATTACACGAGTGGACACACGAGTGAGGACACAACTGTGTGTCCCATA
CTTCGAATGCTCACACGGTCTCCTCACACGGTTG
Found at i:29176328 original size:47 final size:47
Alignment explanation
Indices: 29176274--29176386 Score: 172
Period size: 47 Copynumber: 2.4 Consensus size: 47
29176264 GTCATAGTAA
* *
29176274 TGCAGATAAACTGTCACATAATAAAATTGTAGACAAGCCACCACTTT
1 TGCAGATAAACTGCCACATAATAAAATTGTAGACAAGCCACCACGTT
* * * *
29176321 TGCAGATAAACTGCCACTTTATAATATTGTGGACAAGCCACCACGTT
1 TGCAGATAAACTGCCACATAATAAAATTGTAGACAAGCCACCACGTT
29176368 TGCAGATAAACTGCCACAT
1 TGCAGATAAACTGCCACAT
29176387 CTTTCACCTT
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 59 1.00
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (47 bp):
TGCAGATAAACTGCCACATAATAAAATTGTAGACAAGCCACCACGTT
Found at i:29184166 original size:18 final size:19
Alignment explanation
Indices: 29184124--29184192 Score: 61
Period size: 19 Copynumber: 3.7 Consensus size: 19
29184114 ATCGAAAGAT
* * * *
29184124 CAAAATTTATACCTAATAG
1 CAAAATTTCTAACTGATAC
29184143 CAAAATTTCTAA-TCG-TAC
1 CAAAATTTCTAACT-GATAC
* *
29184161 CAAAATCTCTAACTGATAT
1 CAAAATTTCTAACTGATAC
29184180 CAAAATTTCTAAC
1 CAAAATTTCTAAC
29184193 GCAATACCAA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
18 15 0.38
19 25 0.62
ACGTcount: A:0.43, C:0.20, G:0.04, T:0.32
Consensus pattern (19 bp):
CAAAATTTCTAACTGATAC
Found at i:29189220 original size:21 final size:21
Alignment explanation
Indices: 29189196--29189253 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
29189186 TAGTACAGAT
*
29189196 TTCTACCGATACAGGTGACAG
1 TTCTACCGATACAAGTGACAG
* *
29189217 TTCTATCGATACAAGTGAC-T
1 TTCTACCGATACAAGTGACAG
*
29189237 TTGCTACCGAAACAAGT
1 TT-CTACCGATACAAGT
29189254 CTTACTTCTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 2 0.06
21 29 0.94
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (21 bp):
TTCTACCGATACAAGTGACAG
Found at i:29189990 original size:18 final size:19
Alignment explanation
Indices: 29189954--29190020 Score: 102
Period size: 19 Copynumber: 3.6 Consensus size: 19
29189944 ACCTTGTGAT
29189954 CCAATATTGCTCTTACGAG
1 CCAATATTGCTCTTACGAG
29189973 CCAATATTGCTC-TACGAG
1 CCAATATTGCTCTTACGAG
*
29189991 CCAGTATTGCTCTTACGAG
1 CCAATATTGCTCTTACGAG
29190010 -CAAGTATTGCT
1 CCAA-TATTGCT
29190021 ATTCTCTCTA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
18 19 0.43
19 25 0.57
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (19 bp):
CCAATATTGCTCTTACGAG
Found at i:29197004 original size:19 final size:19
Alignment explanation
Indices: 29196982--29197027 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
29196972 TACAATCCAA
29196982 TATTGCTCTTACGAGCTAG
1 TATTGCTCTTACGAGCTAG
* *
29197001 TATTGCTTTTACGAGGTAG
1 TATTGCTCTTACGAGCTAG
29197020 TATTGCTC
1 TATTGCTC
29197028 AACGAGCCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.41
Consensus pattern (19 bp):
TATTGCTCTTACGAGCTAG
Found at i:29198934 original size:8 final size:8
Alignment explanation
Indices: 29198923--29198977 Score: 65
Period size: 8 Copynumber: 6.5 Consensus size: 8
29198913 AAAAATTAGA
29198923 AAAAATAT
1 AAAAATAT
*
29198931 AAAAATCGT
1 AAAAAT-AT
29198940 AAAAAATAT
1 -AAAAATAT
29198949 AAAATATAT
1 AAAA-ATAT
*
29198958 AGAAATAT
1 AAAAATAT
29198966 AAAAATAT
1 AAAAATAT
29198974 AAAA
1 AAAA
29198978 TTTTATAAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
8 25 0.62
9 9 0.22
10 6 0.15
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.24
Consensus pattern (8 bp):
AAAAATAT
Found at i:29198934 original size:9 final size:9
Alignment explanation
Indices: 29198896--29198977 Score: 62
Period size: 9 Copynumber: 9.0 Consensus size: 9
29198886 AAAAAATTCT
29198896 AATATAAAA
1 AATATAAAA
29198905 AATTTATTAAAA
1 AA--TA-TAAAA
* *
29198917 ATTAGAAAA
1 AATATAAAA
29198926 AATAT-AAA
1 AATATAAAA
*
29198934 AATCGTAAAA
1 AAT-ATAAAA
29198944 AATATAAAA
1 AATATAAAA
* *
29198953 TATAT-AGA
1 AATATAAAA
29198961 AATAT-AAA
1 AATATAAAA
29198969 AATATAAAA
1 AATATAAAA
29198978 TTTTATAAAG
Statistics
Matches: 57, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
8 19 0.33
9 22 0.39
10 8 0.14
11 2 0.04
12 6 0.11
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.27
Consensus pattern (9 bp):
AATATAAAA
Found at i:29198970 original size:18 final size:17
Alignment explanation
Indices: 29198896--29198977 Score: 76
Period size: 18 Copynumber: 4.5 Consensus size: 17
29198886 AAAAAATTCT
29198896 AATATAAAAAATTTATTAAA
1 AATATAAAAAA--TA-TAAA
*
29198916 AATTAGAAAAAATATAAA
1 AA-TATAAAAAATATAAA
*
29198934 AATCGTAAAAAATAT-AA
1 AAT-ATAAAAAATATAAA
*
29198951 AATATATAGAAATATAAA
1 AATATA-AAAAATATAAA
29198969 AATATAAAA
1 AATATAAAA
29198978 TTTTATAAAG
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
16 2 0.04
17 15 0.29
18 23 0.44
19 2 0.04
20 2 0.04
21 8 0.15
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.27
Consensus pattern (17 bp):
AATATAAAAAATATAAA
Found at i:29199015 original size:21 final size:21
Alignment explanation
Indices: 29198991--29199048 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
29198981 TATAAAGTTG
29198991 AAAGAAAATTATACAAAAT-GT
1 AAAGAAAATTATA-AAAATCGT
*
29199012 AAAG-AAA-TATAAAATTCGT
1 AAAGAAAATTATAAAAATCGT
*
29199031 AAAAAAAATTATAAAAAT
1 AAAGAAAATTATAAAAAT
29199049 TATTGTATCA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 4 0.13
19 9 0.29
20 6 0.19
21 12 0.39
ACGTcount: A:0.66, C:0.03, G:0.07, T:0.24
Consensus pattern (21 bp):
AAAGAAAATTATAAAAATCGT
Found at i:29199231 original size:10 final size:9
Alignment explanation
Indices: 29199184--29199237 Score: 56
Period size: 9 Copynumber: 6.0 Consensus size: 9
29199174 AGTCTTTAAT
*
29199184 TTTTTATGA
1 TTTTTATAA
29199193 TTTTTATAAA
1 TTTTTAT-AA
* *
29199203 ATTTTACAA
1 TTTTTATAA
*
29199212 TTTTT-TAT
1 TTTTTATAA
29199220 TTTTTATAA
1 TTTTTATAA
29199229 TTTTTATAA
1 TTTTTATAA
29199238 AACAATTTTC
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
8 6 0.17
9 24 0.67
10 6 0.17
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (9 bp):
TTTTTATAA
Found at i:29199278 original size:25 final size:25
Alignment explanation
Indices: 29199220--29199289 Score: 76
Period size: 25 Copynumber: 2.9 Consensus size: 25
29199210 AATTTTTTAT
29199220 TTTTTATAATTTTT-ATAAAA--CAA
1 TTTTTAT-ATTTTTAATAAAATTCAA
*
29199243 TTTTCTA-ATTTTTAATAAAATTCTA
1 TTTT-TATATTTTTAATAAAATTCAA
*
29199268 TTTTTATATTTTTATTAAAATT
1 TTTTTATATTTTTAATAAAATT
29199290 TAATAAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
22 6 0.15
23 10 0.25
24 4 0.10
25 20 0.50
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (25 bp):
TTTTTATATTTTTAATAAAATTCAA
Found at i:29199514 original size:85 final size:85
Alignment explanation
Indices: 29199364--29199555 Score: 208
Period size: 85 Copynumber: 2.2 Consensus size: 85
29199354 GAGTAGGGGA
* * * * *
29199364 TTAATTACCTTTTTGAAAAATTTTGAGGGTCTTTTTGATACATTTTAAAAGTTTAAGTACTCAAT
1 TTAATT-CTTTTTTTAAAAAGTTTGAGGGTCTTTTTGATACATGTTAAAAGTTCAAGTACTCAAT
** *
29199429 TAGTTG-AAAAAAAATCAGGAGC
65 TAAATGCAAAAAAAA-AAGG-GC
* * * **
29199451 TTAATT-TTTTTTTAAAAAGTTTGAGGGTTTTTTTGATGCATGTTGAAAGTTCAAGTGTTCAATT
1 TTAATTCTTTTTTTAAAAAGTTTGAGGGTCTTTTTGATACATGTTAAAAGTTCAAGTACTCAATT
29199515 AAATGCAAAAAAAAAAGGGC
66 AAATGCAAAAAAAAAAGGGC
29199535 TTAATTGCTTTTTTTGAAAAA
1 TTAATT-CTTTTTTT-AAAAA
29199556 AAATTTAAAC
Statistics
Matches: 88, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
84 8 0.09
85 54 0.61
86 15 0.17
87 11 0.12
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.41
Consensus pattern (85 bp):
TTAATTCTTTTTTTAAAAAGTTTGAGGGTCTTTTTGATACATGTTAAAAGTTCAAGTACTCAATT
AAATGCAAAAAAAAAAGGGC
Found at i:29203749 original size:15 final size:15
Alignment explanation
Indices: 29203726--29203791 Score: 64
Period size: 15 Copynumber: 4.5 Consensus size: 15
29203716 TGGGATCCAA
* *
29203726 TTTATTTTCTCGCAC
1 TTTACTTTCTTGCAC
*
29203741 TTTACTTTCTTTCAC
1 TTTACTTTCTTGCAC
*
29203756 TTTACTTTCTTGCAA
1 TTTACTTTCTTGCAC
* *
29203771 TTAAATTT-TTGCA-
1 TTTACTTTCTTGCAC
29203784 TTTACTTT
1 TTTACTTT
29203792 TCTCGCACTA
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
13 6 0.14
14 5 0.12
15 31 0.74
ACGTcount: A:0.18, C:0.20, G:0.05, T:0.58
Consensus pattern (15 bp):
TTTACTTTCTTGCAC
Found at i:29204007 original size:2 final size:2
Alignment explanation
Indices: 29204000--29204024 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29203990 TTTTATTCTT
29204000 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 T
29204025 TATTTTGCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29208719 original size:21 final size:23
Alignment explanation
Indices: 29208695--29208743 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
29208685 TTTTTCATTT
*
29208695 TTTATATTT-TA-ATTTTTGAAA
1 TTTATATTTATATATTTTAGAAA
*
29208716 TTTATATTTATATATTTTAGAAT
1 TTTATATTTATATATTTTAGAAA
29208739 TTTAT
1 TTTAT
29208744 TAAAAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 9 0.38
22 2 0.08
23 13 0.54
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (23 bp):
TTTATATTTATATATTTTAGAAA
Found at i:29208815 original size:29 final size:32
Alignment explanation
Indices: 29208771--29208829 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
29208761 TTTTTTTAAT
*
29208771 TTTTTTGAATTATTT-AT-ATATTATATATTA
1 TTTTTTGAATTATTTAATCATATAATATATTA
*
29208801 TTTTTT-AATTTTTTAATCATATAATATAT
1 TTTTTTGAATTATTTAATCATATAATATAT
29208830 ATAATATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 7 0.28
30 8 0.32
31 10 0.40
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (32 bp):
TTTTTTGAATTATTTAATCATATAATATATTA
Found at i:29208828 original size:38 final size:39
Alignment explanation
Indices: 29208762--29208838 Score: 97
Period size: 38 Copynumber: 2.0 Consensus size: 39
29208752 TTTTAAAACT
* *
29208762 TTTTTTAATTTTTTTGAATTATTTATATAT-TATATATTA
1 TTTTTTAATTTTTTTGAATCATTAATATATATA-ATATTA
29208801 TTTTTTAA-TTTTTT-AATCATATAATATATATAATATTA
1 TTTTTTAATTTTTTTGAATCAT-TAATATATATAATATTA
29208839 AAAAATATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
37 5 0.15
38 19 0.56
39 10 0.29
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (39 bp):
TTTTTTAATTTTTTTGAATCATTAATATATATAATATTA
Found at i:29209347 original size:20 final size:21
Alignment explanation
Indices: 29209322--29209367 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
29209312 ATTTATGTAT
29209322 TTTAAAA-TTTTATT-AAAAAA
1 TTTAAAACTTTT-TTAAAAAAA
29209342 TTTAAAACTTTTTTAAAAAAA
1 TTTAAAACTTTTTTAAAAAAA
29209363 TTTAA
1 TTTAA
29209368 TTATTTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
TTTAAAACTTTTTTAAAAAAA
Found at i:29211921 original size:25 final size:25
Alignment explanation
Indices: 29211871--29211921 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
29211861 AATGTTTTTG
* * *
29211871 TATTAAAAAGTAAATTATATTTTTT
1 TATTAAAAAATAAATTAAATTATTT
29211896 TATTAAAAAATAAA-TAAATTAATTT
1 TATTAAAAAATAAATTAAATT-ATTT
29211921 T
1 T
29211922 TTTTATGTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (25 bp):
TATTAAAAAATAAATTAAATTATTT
Found at i:29211922 original size:26 final size:25
Alignment explanation
Indices: 29211865--29211915 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
29211855 ATTATGAATG
* * *
29211865 TTTTTGTATTAAAAAGTAAATTATA
1 TTTTTTTATTAAAAAATAAATTAAA
29211890 TTTTTTTATTAAAAAATAAA-TAAA
1 TTTTTTTATTAAAAAATAAATTAAA
29211914 TT
1 TT
29211916 AATTTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 5 0.22
25 18 0.78
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (25 bp):
TTTTTTTATTAAAAAATAAATTAAA
Found at i:29212425 original size:10 final size:9
Alignment explanation
Indices: 29212398--29212495 Score: 63
Period size: 10 Copynumber: 10.1 Consensus size: 9
29212388 TTATTTTTCA
29212398 AAAAATTAT
1 AAAAATTAT
29212407 AAAAA-TAT
1 AAAAATTAT
29212415 AAAGAATTAT
1 AAA-AATTAT
29212425 AAAAATCTTATTT
1 AAAAA--TTA--T
*
29212438 AAAATTTATT
1 AAAAATTA-T
*
29212448 AAGAATTAT
1 AAAAATTAT
29212457 AAGAAATTAT
1 AA-AAATTAT
*
29212467 AAATAATGAT
1 AAA-AATTAT
* *
29212477 TAAAATTTT
1 AAAAATTAT
*
29212486 TAAAATTAT
1 AAAAATTAT
29212495 A
1 A
29212496 TATGCATGTT
Statistics
Matches: 71, Mismatches: 10, Indels: 16
0.73 0.10 0.16
Matches are distributed among these distances:
8 6 0.08
9 25 0.35
10 29 0.41
11 6 0.08
13 5 0.07
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.38
Consensus pattern (9 bp):
AAAAATTAT
Found at i:29212686 original size:44 final size:42
Alignment explanation
Indices: 29212636--29212778 Score: 135
Period size: 43 Copynumber: 3.3 Consensus size: 42
29212626 CCGCTAAAAA
* *
29212636 TAGCGGCGTTTAT-TTAAAAAAATGCCGCTATAGAATATGGTCTT
1 TAGCGGCGTTT-TCTCAAAAAAAT--CGCTAAAGAATATGGTCTT
* *
29212680 TAGCGGCGTTTTCCTCACAAACATCGCTAAAGAATATGGTCTT
1 TAGCGGCGTTTT-CTCAAAAAAATCGCTAAAGAATATGGTCTT
* * *** * *
29212723 TAGCGGCGCTTTCCCAAAAACGCCGCTAAAGAACATGATCTT
1 TAGCGGCGTTTTCTCAAAAAAATCGCTAAAGAATATGGTCTT
29212765 TAGCGGCGCTTTTC
1 TAGCGGCG-TTTTC
29212779 CCACAAACGC
Statistics
Matches: 84, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
42 32 0.38
43 34 0.40
44 11 0.13
45 7 0.08
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.29
Consensus pattern (42 bp):
TAGCGGCGTTTTCTCAAAAAAATCGCTAAAGAATATGGTCTT
Found at i:29212715 original size:43 final size:43
Alignment explanation
Indices: 29212659--29212926 Score: 306
Period size: 43 Copynumber: 6.2 Consensus size: 43
29212649 TTAAAAAAAT
* *
29212659 GCCGCTATAGAATATGGTCTTTAGCGGCG-TTTTCCTCACAAAC
1 GCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCC-CACAAAC
** * *
29212702 ATCGCTAAAGAATATGGTCTTTAGCGGCGC-TTTCCCAAAAAC
1 GCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAAC
*
29212744 GCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTCCCACAAAC
1 GCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAAC
* * * **
29212787 GCCACTAAAGAACATGATCTTCTTTAGCGGTGCTTTTCATACAAAC
1 GCCGCTAAAGAACATG---GTCTTTAGCGGCGCTTTTCCCACAAAC
* * * **
29212833 GCCGCTAAAGAACATGATTTTTAGCGGCGTTTTTCATACAAAC
1 GCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAAC
* *
29212876 GCCGCTAAAGAACATAGTCTTTAGCGGCGCTTTTCCCACAAAT
1 GCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAAC
*
29212919 GCCACTAA
1 GCCGCTAA
29212927 CATTAATAAA
Statistics
Matches: 193, Mismatches: 27, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
42 32 0.17
43 123 0.64
46 38 0.20
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (43 bp):
GCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAAC
Found at i:29212856 original size:89 final size:84
Alignment explanation
Indices: 29212653--29212910 Score: 297
Period size: 89 Copynumber: 3.0 Consensus size: 84
29212643 GTTTATTTAA
* * * * **
29212653 AAAAATGCCGCTATAGAATATGGTCTTTAGCGGCGTTTTCCTCACAAACATCGCTAAAG-A-ATA
1 AAAAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTCC-CACAAACGCCGCTAAAGAACATA
*
29212716 TGGTCTTTAGCGGCGCTTTCCC
65 T-GTCTTTAGCGGCGCTTT-TC
*
29212738 AAAAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTCCCACAAACGCCACTAAAGAACATG
1 AAAAACGCCGCTAAAGAACATGATCTTTAGCGGCG-TTTTCCCACAAACGCCGCTAAAGAACAT-
* *
29212803 ATCTTCTTTAGCGGTGCTTTTC
64 AT-GTCTTTAGCGGCGCTTTTC
* **
29212825 ATACAAACGCCGCTAAAGAACATGATTTTTAGCGGCGTTTTTCATACAAACGCCGCTAAAGAACA
1 A-A-AAACGCCGCTAAAGAACATGATCTTTAGCGGCG-TTTTCCCACAAACGCCGCTAAAGAACA
29212890 TA-GTCTTTAGCGGCGCTTTTC
63 TATGTCTTTAGCGGCGCTTTTC
29212911 CCACAAATGC
Statistics
Matches: 149, Mismatches: 18, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
85 45 0.30
86 24 0.16
87 4 0.03
88 19 0.13
89 57 0.38
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (84 bp):
AAAAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTCCCACAAACGCCGCTAAAGAACATAT
GTCTTTAGCGGCGCTTTTC
Found at i:29212912 original size:132 final size:131
Alignment explanation
Indices: 29212676--29212926 Score: 355
Period size: 132 Copynumber: 1.9 Consensus size: 131
29212666 TAGAATATGG
* * * *
29212676 TCTTTAGCGGCGTTTTCCTCACAAACATCGCTAAAGAATATGGTCTTTAGCGGCGCTTTCCCAAA
1 TCTTTAGCGGCGTTTTCATCACAAACACCGCTAAAGAACATGATCTTTAGCGGCGCTTTCCCAAA
29212741 AACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTCCCACAAACGCCACTAAAGAACATGATC
66 AACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTCCCACAAACGCCACTAAAGAACATGATC
29212806 T
131 T
* * * **
29212807 TCTTTAGCGGTGCTTTTCAT-ACAAACGCCGCTAAAGAACATGATTTTTAGCGGCG-TTTTTCAT
1 TCTTTAGCGGCG-TTTTCATCACAAACACCGCTAAAGAACATGATCTTTAGCGGCGCTTTCCCA-
*
29212870 ACAAACGCCGCTAAAGAACAT-AGTCTTTAGCGGCGCTTTTCCCACAAATGCCACTAA
64 A-AAACGCCGCTAAAGAACATGA-TCTTTAGCGGCGCTTTTCCCACAAACGCCACTAA
29212927 CATTAATAAA
Statistics
Matches: 106, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
130 5 0.05
131 43 0.41
132 58 0.55
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (131 bp):
TCTTTAGCGGCGTTTTCATCACAAACACCGCTAAAGAACATGATCTTTAGCGGCGCTTTCCCAAA
AACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTCCCACAAACGCCACTAAAGAACATGATC
T
Found at i:29216917 original size:41 final size:41
Alignment explanation
Indices: 29216860--29217201 Score: 438
Period size: 41 Copynumber: 8.3 Consensus size: 41
29216850 AAACTCAACT
* * * *
29216860 TTTAGTGGCACTTTCTCATAAGTGTCGCTATTTCTCTGACC
1 TTTAGCGGCGCTTTCTCATAAGCGTCGCTATTGCTCTGACC
*
29216901 TTTAGTGGCGCTTTCTCATAAGCGTCGCTATTGCTCTGACC
1 TTTAGCGGCGCTTTCTCATAAGCGTCGCTATTGCTCTGACC
*
29216942 TTTAGTGGCGCTTTCTCATAAGCGTCGCTATTGCTCTGACC
1 TTTAGCGGCGCTTTCTCATAAGCGTCGCTATTGCTCTGACC
* * *
29216983 TTTAGCGGCGCTTT-TCCATAAGCGCCGTTATTGCTCTAACC
1 TTTAGCGGCGCTTTCT-CATAAGCGTCGCTATTGCTCTGACC
*
29217024 TTTAGCGGCGCTTTAC-CATAAGCGTCGCTATTGCTTTGACC
1 TTTAGCGGCGCTTT-CTCATAAGCGTCGCTATTGCTCTGACC
* * ** * * *
29217065 TTTAGCGGTGCATTCAAATATGCGCCGCTATTGCTCTAACC
1 TTTAGCGGCGCTTTCTCATAAGCGTCGCTATTGCTCTGACC
* *
29217106 TTTAGCGGCGCTTTCCCATAAGCGTCGCTATTGCTTTGACC
1 TTTAGCGGCGCTTTCTCATAAGCGTCGCTATTGCTCTGACC
* * *
29217147 TTTAGCGGCGCTTTCTCATAAACGCCGCTATTGCTCTGATC
1 TTTAGCGGCGCTTTCTCATAAGCGTCGCTATTGCTCTGACC
29217188 TTTAGCTGG-GCTTT
1 TTTAGC-GGCGCTTT
29217202 TCTTTAAGCA
Statistics
Matches: 265, Mismatches: 31, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
40 2 0.01
41 261 0.98
42 2 0.01
ACGTcount: A:0.16, C:0.27, G:0.21, T:0.36
Consensus pattern (41 bp):
TTTAGCGGCGCTTTCTCATAAGCGTCGCTATTGCTCTGACC
Found at i:29224236 original size:31 final size:30
Alignment explanation
Indices: 29224201--29224317 Score: 107
Period size: 31 Copynumber: 3.9 Consensus size: 30
29224191 AAATGATTAA
*
29224201 AATTTGATATCTAAACTTGACATTTTTTCTT
1 AATTTGATACCTAAACTTGACATTTTTTC-T
* * *
29224232 AATTTGGTATCTAAACTT----TTTTTGTCC
1 AATTTGATACCTAAACTTGACATTTTT-TCT
* * * *
29224259 ACTTTAATACCCACACTTGACAATTTTTTCT
1 AATTTGATACCTAAACTTGAC-ATTTTTTCT
29224290 AATTTGATACCTAAACTTGACATTTTTT
1 AATTTGATACCTAAACTTGACATTTTTT
29224318 TTAAGTCGGT
Statistics
Matches: 67, Mismatches: 13, Indels: 13
0.72 0.14 0.14
Matches are distributed among these distances:
27 17 0.25
28 2 0.03
30 7 0.10
31 36 0.54
32 5 0.07
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.48
Consensus pattern (30 bp):
AATTTGATACCTAAACTTGACATTTTTTCT
Found at i:29224335 original size:30 final size:31
Alignment explanation
Indices: 29224273--29224338 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 31
29224263 TAATACCCAC
* *
29224273 ACTTGACAATTTTTTCTAATTTGATACCTAA
1 ACTTGACAATTTTTTCTAAGTCGATACCTAA
* * *
29224304 ACTTGAC-ATTTTTTTTAAGTCGGTACTTAA
1 ACTTGACAATTTTTTCTAAGTCGATACCTAA
29224334 ACTTG
1 ACTTG
29224339 TTGGAGTCCA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 23 0.77
31 7 0.23
ACGTcount: A:0.29, C:0.15, G:0.11, T:0.45
Consensus pattern (31 bp):
ACTTGACAATTTTTTCTAAGTCGATACCTAA
Found at i:29228846 original size:17 final size:18
Alignment explanation
Indices: 29228788--29228850 Score: 63
Period size: 18 Copynumber: 3.2 Consensus size: 18
29228778 CAAAGGTAGA
* *
29228788 CAAAAACGTGCCATAAGG
1 CAAAAGCGTGCCACAAGG
29228806 CAAAAGCGTGCCACAAGG
1 CAAAAGCGTGCCACAAGG
29228824 CAAAGGAAAAGCGTGCCACAAGG
1 C-----AAAAGCGTGCCACAAGG
29228847 CAAA
1 CAAA
29228851 GGAAAAGCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
18 20 0.53
23 18 0.47
ACGTcount: A:0.44, C:0.24, G:0.25, T:0.06
Consensus pattern (18 bp):
CAAAAGCGTGCCACAAGG
Found at i:29228880 original size:24 final size:23
Alignment explanation
Indices: 29228802--29228874 Score: 128
Period size: 23 Copynumber: 3.1 Consensus size: 23
29228792 AACGTGCCAT
29228802 AAGGCAAAAGCGTGCCACAAGGCA
1 AAGG-AAAAGCGTGCCACAAGGCA
29228826 AAGGAAAAGCGTGCCACAAGGCA
1 AAGGAAAAGCGTGCCACAAGGCA
29228849 AAGGAAAAGCGTGCCACAAAGGCA
1 AAGGAAAAGCGTGCCAC-AAGGCA
29228873 AA
1 AA
29228875 TAAAAACTAG
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
23 36 0.75
24 12 0.25
ACGTcount: A:0.45, C:0.22, G:0.29, T:0.04
Consensus pattern (23 bp):
AAGGAAAAGCGTGCCACAAGGCA
Found at i:29228915 original size:18 final size:17
Alignment explanation
Indices: 29228872--29228915 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
29228862 CCACAAAGGC
*
29228872 AAATAAAAACTAGAAGA
1 AAATAAAAACTAAAAGA
**
29228889 AAATCAAAATTTAAAAGA
1 AAAT-AAAAACTAAAAGA
29228907 AAATAAAAA
1 AAATAAAAA
29228916 ATGAATATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.73, C:0.05, G:0.07, T:0.16
Consensus pattern (17 bp):
AAATAAAAACTAAAAGA
Found at i:29231391 original size:21 final size:21
Alignment explanation
Indices: 29231362--29231404 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
29231352 TGCTTTATAA
29231362 TATTAATTAATAA-AATATTAT
1 TATTAATTAA-AATAATATTAT
*
29231383 TATTTATTAAAATAATATTAT
1 TATTAATTAAAATAATATTAT
29231404 T
1 T
29231405 GATAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TATTAATTAAAATAATATTAT
Found at i:29231393 original size:18 final size:18
Alignment explanation
Indices: 29231362--29231415 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
29231352 TGCTTTATAA
* *
29231362 TATTAATTAATAAAATAT
1 TATTATTTATTAAAATAT
*
29231380 TATTATTTATTAAAATAA
1 TATTATTTATTAAAATAT
* *
29231398 TATTATTGATAAAAATAT
1 TATTATTTATTAAAATAT
29231416 CATTTGAAAG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
TATTATTTATTAAAATAT
Found at i:29235399 original size:21 final size:21
Alignment explanation
Indices: 29235373--29235413 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
29235363 TAAATAATCG
29235373 GGCTTTGTGCCGGTGTATTCA
1 GGCTTTGTGCCGGTGTATTCA
29235394 GGCTTTGTGCCGGTGTATTC
1 GGCTTTGTGCCGGTGTATTC
29235414 GAGCTGTGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.07, C:0.20, G:0.34, T:0.39
Consensus pattern (21 bp):
GGCTTTGTGCCGGTGTATTCA
Found at i:29235423 original size:21 final size:21
Alignment explanation
Indices: 29235373--29235425 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
29235363 TAAATAATCG
*
29235373 GGCTTTGTGCCGGTGTATTCA
1 GGCTGTGTGCCGGTGTATTCA
*
29235394 GGCTTTGTGCCGGTGTATTC-
1 GGCTGTGTGCCGGTGTATTCA
29235414 GAGCTGTGTGCC
1 G-GCTGTGTGCC
29235426 TAGTAGGCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 1 0.03
21 29 0.97
ACGTcount: A:0.08, C:0.21, G:0.36, T:0.36
Consensus pattern (21 bp):
GGCTGTGTGCCGGTGTATTCA
Found at i:29235445 original size:37 final size:37
Alignment explanation
Indices: 29235393--29235556 Score: 220
Period size: 37 Copynumber: 4.4 Consensus size: 37
29235383 CGGTGTATTC
29235393 AGGCTTTGTGCCGGTGTATTCGAGCTGTGTGCCTAGT
1 AGGCTTTGTGCCGGTGTATTCGAGCTGTGTGCCTAGT
* * *
29235430 AGGCTTTGTGTCGGTGTTTTCGAGTTGTGTGCCTAGT
1 AGGCTTTGTGCCGGTGTATTCGAGCTGTGTGCCTAGT
* * * * * *
29235467 AAGCTTTATGCCGGTGTAATCGGGCTTTATGCCTAGT
1 AGGCTTTGTGCCGGTGTATTCGAGCTGTGTGCCTAGT
* *
29235504 AGGCTTTGTGCCGGTGTATTCGAGCTTTGTACCTAGT
1 AGGCTTTGTGCCGGTGTATTCGAGCTGTGTGCCTAGT
*
29235541 AGGCTTTGGGCCGGTG
1 AGGCTTTGTGCCGGTG
29235557 AACATAAAGG
Statistics
Matches: 108, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 108 1.00
ACGTcount: A:0.12, C:0.18, G:0.34, T:0.37
Consensus pattern (37 bp):
AGGCTTTGTGCCGGTGTATTCGAGCTGTGTGCCTAGT
Found at i:29239648 original size:21 final size:21
Alignment explanation
Indices: 29239583--29239658 Score: 75
Period size: 21 Copynumber: 3.6 Consensus size: 21
29239573 TCTAGAATTT
*
29239583 GTTGTATCGGTAGAAGGT-TA
1 GTTGTATCGGTAGAACGTCTA
* *
29239603 GATTGTATTGGTAGAAC-TCAGA
1 G-TTGTATCGGTAGAACGTC-TA
29239625 GTTGTATCGGTAGAACGTCTA
1 GTTGTATCGGTAGAACGTCTA
* *
29239646 GTTCTAGCGGTAG
1 GTTGTATCGGTAG
29239659 GATTCTGCAG
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
20 2 0.04
21 39 0.87
22 4 0.09
ACGTcount: A:0.25, C:0.11, G:0.32, T:0.33
Consensus pattern (21 bp):
GTTGTATCGGTAGAACGTCTA
Found at i:29240800 original size:20 final size:21
Alignment explanation
Indices: 29240771--29240810 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
29240761 TTTAAATAAG
*
29240771 GGCACTGAAGTGCA-TACAGA
1 GGCACCGAAGTGCATTACAGA
29240791 GGCACCGAAGTGCATTACAG
1 GGCACCGAAGTGCATTACAG
29240811 GGTTATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.33, C:0.23, G:0.30, T:0.15
Consensus pattern (21 bp):
GGCACCGAAGTGCATTACAGA
Found at i:29241728 original size:37 final size:37
Alignment explanation
Indices: 29241684--29241761 Score: 156
Period size: 37 Copynumber: 2.1 Consensus size: 37
29241674 CCACTAAAAC
29241684 ATAAAATAGTTTATTTATCTATCCAACCCTTCCACTT
1 ATAAAATAGTTTATTTATCTATCCAACCCTTCCACTT
29241721 ATAAAATAGTTTATTTATCTATCCAACCCTTCCACTT
1 ATAAAATAGTTTATTTATCTATCCAACCCTTCCACTT
29241758 ATAA
1 ATAA
29241762 CCTTCAACAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.40
Consensus pattern (37 bp):
ATAAAATAGTTTATTTATCTATCCAACCCTTCCACTT
Found at i:29245442 original size:31 final size:31
Alignment explanation
Indices: 29245389--29245696 Score: 363
Period size: 31 Copynumber: 10.0 Consensus size: 31
29245379 TTTTCGTTTA
* *
29245389 ATATCC-TTTC-AGATACAACCTTTCCAATAG
1 ATATCCATTTCGA-ATATAACCTTTTCAATAG
* * **
29245419 ATATCCATTTCGGATATGACCTTTTCAATTT
1 ATATCCATTTCGAATATAACCTTTTCAATAG
* * **
29245450 AGATCCATTTCGAATATGACCTTTTCAATTT
1 ATATCCATTTCGAATATAACCTTTTCAATAG
29245481 ATATCCATTTC-AGATATAACCTTTTCAATAG
1 ATATCCATTTCGA-ATATAACCTTTTCAATAG
29245512 ATATCCATTTCGAATATAACCTTTTCAATAG
1 ATATCCATTTCGAATATAACCTTTTCAATAG
* * * *
29245543 ATATTCATTCCAAATATAACATTTTCAATAG
1 ATATCCATTTCGAATATAACCTTTTCAATAG
* * *
29245574 ATATCCATTTCGGATATGACCTTTTCAATAT
1 ATATCCATTTCGAATATAACCTTTTCAATAG
**
29245605 ATATCCATTTCGAATATAACCTTTTTGATAG
1 ATATCCATTTCGAATATAACCTTTTCAATAG
* * *
29245636 ATATCCATTACGAATATAACATTTTCAATAT
1 ATATCCATTTCGAATATAACCTTTTCAATAG
29245667 ATATCCATTTC-AGATATAACCTTTTCAATA
1 ATATCCATTTCGA-ATATAACCTTTTCAATA
29245697 TTTGAGCAAA
Statistics
Matches: 238, Mismatches: 35, Indels: 9
0.84 0.12 0.03
Matches are distributed among these distances:
30 8 0.03
31 229 0.96
32 1 0.00
ACGTcount: A:0.34, C:0.19, G:0.07, T:0.40
Consensus pattern (31 bp):
ATATCCATTTCGAATATAACCTTTTCAATAG
Found at i:29245515 original size:18 final size:18
Alignment explanation
Indices: 29245492--29245546 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
29245482 TATCCATTTC
29245492 AGATATAACCTTTTCAAT
1 AGATATAACCTTTTCAAT
* *
29245510 AGATAT--CCATTTC--G
1 AGATATAACCTTTTCAAT
29245524 A-ATATAACCTTTTCAAT
1 AGATATAACCTTTTCAAT
29245541 AGATAT
1 AGATAT
29245547 TCATTCCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 10
0.67 0.10 0.24
Matches are distributed among these distances:
13 4 0.14
14 1 0.04
15 6 0.21
16 6 0.21
17 1 0.04
18 10 0.36
ACGTcount: A:0.38, C:0.16, G:0.07, T:0.38
Consensus pattern (18 bp):
AGATATAACCTTTTCAAT
Found at i:29245697 original size:93 final size:93
Alignment explanation
Indices: 29245389--29245696 Score: 429
Period size: 93 Copynumber: 3.3 Consensus size: 93
29245379 TTTTCGTTTA
* * * * ** *
29245389 ATATCC-TTTCAGATACAACCTTTCCAATAGATATCCATTTCGGATATGACCTTTTCAATTTAGA
1 ATATCCATTTCAGATATAACCTTTTCAATAGATATCCATTTCGAATATAACCTTTTCAATAGATA
* * * *
29245453 TCCATTTCGAATATGACCTTTTCAATTT
66 TCCATTACGAATATAACATTTTCAATAT
29245481 ATATCCATTTCAGATATAACCTTTTCAATAGATATCCATTTCGAATATAACCTTTTCAATAGATA
1 ATATCCATTTCAGATATAACCTTTTCAATAGATATCCATTTCGAATATAACCTTTTCAATAGATA
* * * *
29245546 TTCATTCCAAATATAACATTTTCAATAG
66 TCCATTACGAATATAACATTTTCAATAT
* * * **
29245574 ATATCCATTTCGGATATGACCTTTTCAATATATATCCATTTCGAATATAACCTTTTTGATAGATA
1 ATATCCATTTCAGATATAACCTTTTCAATAGATATCCATTTCGAATATAACCTTTTCAATAGATA
29245639 TCCATTACGAATATAACATTTTCAATAT
66 TCCATTACGAATATAACATTTTCAATAT
29245667 ATATCCATTTCAGATATAACCTTTTCAATA
1 ATATCCATTTCAGATATAACCTTTTCAATA
29245697 TTTGAGCAAA
Statistics
Matches: 190, Mismatches: 25, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
92 6 0.03
93 184 0.97
ACGTcount: A:0.34, C:0.19, G:0.07, T:0.40
Consensus pattern (93 bp):
ATATCCATTTCAGATATAACCTTTTCAATAGATATCCATTTCGAATATAACCTTTTCAATAGATA
TCCATTACGAATATAACATTTTCAATAT
Found at i:29248542 original size:16 final size:17
Alignment explanation
Indices: 29248513--29248546 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
29248503 ACCACAATAA
29248513 AATAAAATTCTAATATT
1 AATAAAATTCTAATATT
*
29248530 AATAAACTT-TAATATT
1 AATAAAATTCTAATATT
29248546 A
1 A
29248547 TGATATTGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (17 bp):
AATAAAATTCTAATATT
Found at i:29249770 original size:2 final size:2
Alignment explanation
Indices: 29249765--29249823 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
29249755 ACTATTGGTG
29249765 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
29249807 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
29249824 TATGTAAAAC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29250051 original size:18 final size:17
Alignment explanation
Indices: 29249998--29250047 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 17
29249988 TGCTTTATAA
29249998 TATTAATTAATAAAATAT
1 TATT-ATTAATAAAATAT
*
29250016 TATTACTTATTAAAATAT
1 TATTA-TTAATAAAATAT
29250034 TATTATTAATAAAA
1 TATTATTAATAAAA
29250048 ATATCATCTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 9 0.31
18 20 0.69
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
TATTATTAATAAAATAT
Found at i:29251914 original size:30 final size:29
Alignment explanation
Indices: 29251884--29252109 Score: 181
Period size: 29 Copynumber: 7.7 Consensus size: 29
29251874 CCCCTTAACT
*
29251884 TTCTAAAAATTTCATTTTAACCCTCGAAC
1 TTCTAAAAATTACATTTTAACCCTCGAAC
* * * *
29251913 TTTCCAAAAATTACAATTTAACCTTCAAAC
1 -TTCTAAAAATTACATTTTAACCCTCGAAC
* *
29251943 TTCTCAAAAATTAAATTTT-ACCCTAGAAC
1 TTCT-AAAAATTACATTTTAACCCTCGAAC
* *
29251972 TTCTCAAAAATTACATTTTTACCC-CTAAAC
1 TTCT-AAAAATTACATTTTAACCCTC-GAAC
* * * **
29252002 TTCTAAAAATCACATTTTTATCCTCGTTC
1 TTCTAAAAATTACATTTTAACCCTCGAAC
* *
29252031 TTCCAAAAATCACATTTTTAACCC-CGAAC
1 TTCTAAAAATTACA-TTTTAACCCTCGAAC
**
29252060 TTCTCAAAAATTACATTTTTGCCCAT-GAAC
1 TTCT-AAAAATTACATTTTAACCC-TCGAAC
*
29252090 TTCCAAAAATTACCATTTTA
1 TTCTAAAAATTA-CATTTTA
29252110 CTCCCGAGCA
Statistics
Matches: 157, Mismatches: 30, Indels: 18
0.77 0.15 0.09
Matches are distributed among these distances:
29 80 0.51
30 77 0.49
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.36
Consensus pattern (29 bp):
TTCTAAAAATTACATTTTAACCCTCGAAC
Found at i:29252116 original size:59 final size:58
Alignment explanation
Indices: 29251884--29252108 Score: 233
Period size: 59 Copynumber: 3.8 Consensus size: 58
29251874 CCCCTTAACT
* * * * *
29251884 TTCT-AAAAATTTCATTTTAACCCTCGAACTTTCCAAAAATTACAATTTAACCTTCAAAC
1 TTCTCAAAAATTACATTTTTACCCTCGAAC-TTCCAAAAATTACATTTTTACC-CCAAAC
* *
29251943 TTCTCAAAAATTA-AATTTTACCCTAGAACTTCTCAAAAATTACATTTTTACCCCTAAAC
1 TTCTCAAAAATTACATTTTTACCCTCGAACTTC-CAAAAATTACATTTTTACCCC-AAAC
* * ** * *
29252002 TTCT-AAAAATCACATTTTTATCCTCGTTCTTCCAAAAATCACATTTTTAACCCCGAAC
1 TTCTCAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTACATTTTT-ACCCCAAAC
*
29252060 TTCTCAAAAATTACATTTTTGCCCAT-GAACTTCCAAAAATTACCATTTT
1 TTCTCAAAAATTACATTTTTACCC-TCGAACTTCCAAAAATTA-CATTTT
29252109 ACTCCCGAGC
Statistics
Matches: 137, Mismatches: 21, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
58 33 0.24
59 90 0.66
60 14 0.10
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.36
Consensus pattern (58 bp):
TTCTCAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTACATTTTTACCCCAAAC
Found at i:29252124 original size:88 final size:88
Alignment explanation
Indices: 29251968--29252128 Score: 218
Period size: 88 Copynumber: 1.8 Consensus size: 88
29251958 TTTTACCCTA
* * ** *
29251968 GAACTTCTCAAAAATTACATTTTTACCCCTAAACTTCTAAAAATCACATTTTTATCCTCGTTCTT
1 GAACTTCTCAAAAATTACATTTTTACCCATAAACTTCCAAAAATCACATTTTTATCCTCGAGCAT
29252033 CCAAAAATCACATTTTTAACCCC
66 CCAAAAATCACATTTTTAACCCC
* * *
29252056 GAACTTCTCAAAAATTACATTTTTGCCCATGAACTTCCAAAAATTACCA-TTTTACTCC-CGAGC
1 GAACTTCTCAAAAATTACATTTTTACCCATAAACTTCCAAAAATCA-CATTTTTA-TCCTCGAGC
29252119 ATCCAAAAAT
64 ATCCAAAAAT
29252129 TTTCCAAGAG
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
88 58 0.92
89 5 0.08
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (88 bp):
GAACTTCTCAAAAATTACATTTTTACCCATAAACTTCCAAAAATCACATTTTTATCCTCGAGCAT
CCAAAAATCACATTTTTAACCCC
Found at i:29261232 original size:49 final size:49
Alignment explanation
Indices: 29261168--29261265 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
29261158 GGTAGAATGG
*
29261168 ATTCAGGCCCGATATTATCAATTGAATTTAATCGAGGAAAAGAGGTTAA
1 ATTCAGGCCCGATATTATCAATTGAATTTAATCAAGGAAAAGAGGTTAA
29261217 ATTCAGGCCCGATATTATCAATTGAATTTAATCAAGGAAAAGAGGTTAA
1 ATTCAGGCCCGATATTATCAATTGAATTTAATCAAGGAAAAGAGGTTAA
29261266 GAGTTATTCG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (49 bp):
ATTCAGGCCCGATATTATCAATTGAATTTAATCAAGGAAAAGAGGTTAA
Found at i:29262620 original size:78 final size:76
Alignment explanation
Indices: 29262536--29263557 Score: 327
Period size: 78 Copynumber: 13.1 Consensus size: 76
29262526 TGAAGATCCG
*
29262536 ATCTCTTACCCCGAGCTTGAGGCAGATT-A-TCATTAGCAAGTCTCTTACCCCGAGC-TAGGGGC
1 ATCTCTTACCCCGAGC-TGAGGCAGATTCAGCCATT--CAA-TCTCTTACCCCGAGCTTA-GGGC
**
29262598 AGATCACCGTCAGCCA
61 AGATCACCACCAGCCA
* * *
29262614 ATCTCTTACCCCGAGGCTGGGGTAGATTGCAGCCATTCGATCTCTTACCCCGAGCTTAGGGCAGA
1 ATCTCTTACCCCGA-GCTGAGGCAGATT-CAGCCATTCAATCTCTTACCCCGAGCTTAGGGCAGA
*
29262679 TCATCACCAGCCA
64 TCACCACCAGCCA
** * ** * * * *
29262692 ATCTCTTACCCCGAGCCT-AGGGCAGATTGCAATCGTTTGATCTCTTACCCCAAACCTGGGGCAG
1 ATCTCTTACCCCGAG-CTGA-GGCAGATT-CAGCCATTCAATCTCTTACCCCGAGCTTAGGGCAG
* * **
29262756 ATCATCATCAGTAA
63 ATCACCACCAGCCA
* * * * * * * * ** * *
29262770 ATCTTTTACCTCGAGCCAGGGGTAGA-TCACCGTCAGTCAATCTTTTTTCCTGAGCTT-GGGTAG
1 ATCTCTTACCCCGAG-CTGAGGCAGATTCA--GCCATTCAATCTCTTACCCCGAGCTTAGGGCAG
*** ** *
29262833 AT-TGTAGCCATTCG
63 ATCACCA-CCAGCCA
* ** * * * ** *
29262847 ATCTCTTATCTTGAGCTTGGGGCAGA-TCATTACTAGCCAATCTCTTACCCCGAGCTT-GGGTAG
1 ATCTCTTACCCCGAGC-TGAGGCAGATTCA--GCCATTCAATCTCTTACCCCGAGCTTAGGGCAG
* * *
29262910 ATTA-CAGCC-GTTCG
63 ATCACCA-CCAG-CCA
* * * * * *
29262924 ATCTCTTATCCCGAGCTTAGGGCAGA-TCA-TCATCAACAAATCTTTTACCCCGAGC-CAGAGGC
1 ATCTCTTACCCCGAGCTGA-GGCAGATTCAGCCAT--TC-AATCTCTTACCCCGAGCTTAG-GGC
* * *
29262986 AGATCACTATCAACCA
61 AGATCACCACCAGCCA
* * * * * *
29263002 ATCTCTTACCCCGAGCTTAGGGCAGATTACAGTCATTCGATCTTTTACCTCGAGCTT-GAGGCAA
1 ATCTCTTACCCCGAGCTGA-GGCAGATT-CAGCCATTCAATCTCTTACCCCGAGCTTAG-GGCAG
* * **
29263066 ATTAACACCAGTAA
63 ATCACCACCAGCCA
* * * * * * * * * *
29263080 ATCTCTTACCCCTAGCCTAAGGTAGATTGCAGTCATTCGATCTTTTACCTCGAGCCTAAGGCAAA
1 ATCTCTTACCCCGAG-CTGAGGCAGATT-CAGCCATTCAATCTCTTACCCCGAGCTTAGGGCAGA
* *
29263145 TCAACACCAGCAA
64 TCACCACCAGCCA
* * * * * *
29263158 ATCTCTTACCCCAAGCTTGAGGCAAATTGCAACCATTCAATCTCTTACCTCGAGCCT-GAGGCAA
1 ATCTCTTACCCCGAGC-TGAGGCAGATT-CAGCCATTCAATCTCTTACCCCGAGCTTAG-GGCAG
* *
29263222 ATCAACACCAGCAA
63 ATCACCACCAGCCA
** * * ** * *
29263236 ATCTCTTACCTTGAGCTTGGGGCAGATTGCAGTCATTTGATCTCTTACCCCGAGCTTGGGGCAGG
1 ATCTCTTACCCCGAGC-TGAGGCAGATT-CAGCCATTCAATCTCTTACCCCGAGCTTAGGGCAGA
* * * *
29263301 TCATCATCAACAA
64 TCACCACCAGCCA
* * * * * * * * *
29263314 ATCTCTTACCCCAACCAT-AGGGCAAATTGCAGCCATCCGATCTCTTACCCCAAGCCTGGGGTAG
1 ATCTCTTACCCCGAGC-TGA-GGCAGATT-CAGCCATTCAATCTCTTACCCCGAGCTTAGGGCAG
* **
29263378 ATTACCATTAGCCA
63 ATCACCACCAGCCA
* * * * * * * * * *
29263392 ATCTCTTACCCTGAGACGGGGGTAGATTACAGTCATCCGATCTTTTACCCCGAACCTAGGGCAGA
1 ATCTCTTACCCCGAG-CTGAGGCAGATT-CAGCCATTCAATCTCTTACCCCGAGCTTAGGGCAGA
* *
29263457 TTACCACTAGCCA
64 TCACCACCAGCCA
* * * * *
29263470 ATCTCTTACCCCGAGCCTG-GGTAAATTGTAGCCATTCGATCTCTTACCTCGAGCTT-GAGGCAG
1 ATCTCTTACCCCGAG-CTGAGGCAGATT-CAGCCATTCAATCTCTTACCCCGAGCTTAG-GGCAG
* * *
29263533 ATCATCATCATCCA
63 ATCACCACCAGCCA
*
29263547 ATCTGTTACCC
1 ATCTCTTACCC
29263558 TGATCATGGA
Statistics
Matches: 731, Mismatches: 178, Indels: 71
0.75 0.18 0.07
Matches are distributed among these distances:
74 1 0.00
76 7 0.01
77 160 0.22
78 538 0.74
79 14 0.02
80 3 0.00
81 8 0.01
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.26
Consensus pattern (76 bp):
ATCTCTTACCCCGAGCTGAGGCAGATTCAGCCATTCAATCTCTTACCCCGAGCTTAGGGCAGATC
ACCACCAGCCA
Found at i:29262773 original size:156 final size:155
Alignment explanation
Indices: 29262576--29263517 Score: 512
Period size: 156 Copynumber: 6.1 Consensus size: 155
29262566 CATTAGCAAG
* * * * *
29262576 TCTCTTACCCCGAGCTAGGGGCAGATCACCGTCAGCCAATCTCTTACCCCGAGGCTGGGGTAGAT
1 TCTCTTACCCCAACCT-GGGGCAGATCAACATCAGCAAATCTCTTACCCCGAGGCTGGGGTAGAT
* *
29262641 TGCAGCCATTCGATCTCTTACCCCGAGCTTAGGGCAGATCATCACCAGCCAATCTCTTACCCCGA
65 TGCAGTCATTCGATCTTTTACCCCGAGCTTAGGGCAGATCATCACCAGCCAATCTCTTACCCCGA
* *
29262706 GCCTAGGGCAGATTGCAATCGTTTGA
130 GCCTAGGGCAGATTGCAATCATTCGA
* * * * * *
29262732 TCTCTTACCCCAAACCTGGGGCAGATCATCATCAGTAAATCTTTTACCTCGAGCCAGGGGTAGAT
1 TCTCTTACCCC-AACCTGGGGCAGATCAACATCAGCAAATCTCTTACCCCGAGGCTGGGGTAGAT
** * * * ** * * ** ** * * **
29262797 CACCGTCAGTCAATCTTTTTTCCTGAGCTT-GGGTAGATTGT-AGCCATTCGATCTCTTATCTTG
65 TGCAGTCATTCGATCTTTTACCCCGAGCTTAGGGCAGATCATCA-CCAGCCAATCTCTTACCCCG
* * * ** *
29262860 AGCTTGGGGCAGA-T-CATTACTAGCCAA
129 AGCCTAGGGCAGATTGCAAT-C-ATTCGA
* * * * * * * * * * *
29262887 TCTCTTACCCCGAGCTTGGGTAGAT-TACAGCCGTTC-GATCTCTTATCCCGA-GCTTAGGGCAG
1 TCTCTTACCCCAACCTGGGGCAGATCAACATCAG--CAAATCTCTTACCCCGAGGC-TGGGGTAG
* * * * *
29262949 A-T-CA-TCATCAACAAATCTTTTACCCCGAGC-CAGAGGCAGATCA-CTATCAACCAATCTCTT
63 ATTGCAGTCAT--TC-GATCTTTTACCCCGAGCTTAG-GGCAGATCATC-ACCAGCCAATCTCTT
* * *
29263009 ACCCCGAGCTTAGGGCAGATTACAGTCATTCGA
123 ACCCCGAGCCTAGGGCAGATTGCAATCATTCGA
* * * * * * * * * * * **
29263042 TCTTTTACCTCGAGCTTGAGGCAAATTAACACCAGTAAATCTCTTACCCCTAGCCTAAGGTAGAT
1 TCTCTTACC-CCAACCTGGGGCAGATCAACATCAGCAAATCTCTTACCCCGAGGCTGGGGTAGAT
* * * * * * *
29263107 TGCAGTCATTCGATCTTTTACCTCGAGCCTAAGGCAAATCAACACCAGCAAATCTCTTACCCCAA
65 TGCAGTCATTCGATCTTTTACCCCGAGCTTAGGGCAGATCATCACCAGCCAATCTCTTACCCCGA
* * * *
29263172 G-CTTGAGGCAAATTGCAACCATTCAA
130 GCCTAG-GGCAGATTGCAATCATTCGA
* * * * * ** *
29263198 TCTCTTACCTCGAGCCTGAGGCAAATCAACACCAGCAAATCTCTTACCTTGA-GCTTGGGGCAGA
1 TCTCTTACC-CCAACCTGGGGCAGATCAACATCAGCAAATCTCTTACCCCGAGGC-TGGGGTAGA
* * * * * * *
29263262 TTGCAGTCATTTGATCTCTTACCCCGAGCTTGGGGCAGGTCATCATCAACAAATCTCTTACCCC-
64 TTGCAGTCATTCGATCTTTTACCCCGAGCTTAGGGCAGATCATCACCAGCCAATCTCTTACCCCG
* * ** *
29263326 AACCATAGGGCAAATTGCAGCCATCCGA
129 AGCC-TAGGGCAGATTGCAATCATTCGA
* * * * * * * *
29263354 TCTCTTACCCCAAGCCTGGGGTAGATTACCATTAGCCAATCTCTTACCCTGAGACGGGGGTAGAT
1 TCTCTTACCCCAA-CCTGGGGCAGATCAACATCAGCAAATCTCTTACCCCGAGGCTGGGGTAGAT
* * * * * * *
29263419 TACAGTCATCCGATCTTTTACCCCGAACCTAGGGCAGATTACCACTAGCCAATCTCTTACCCCGA
65 TGCAGTCATTCGATCTTTTACCCCGAGCTTAGGGCAGATCATCACCAGCCAATCTCTTACCCCGA
* * * **
29263484 GCCT-GGGTAAATTGTAGCCATTCGA
130 GCCTAGGGCAGATTGCAATCATTCGA
29263509 TCTCTTACC
1 TCTCTTACC
29263518 TCGAGCTTGA
Statistics
Matches: 581, Mismatches: 173, Indels: 65
0.71 0.21 0.08
Matches are distributed among these distances:
151 3 0.01
152 1 0.00
153 9 0.02
154 45 0.08
155 120 0.21
156 375 0.65
157 22 0.04
158 2 0.00
159 4 0.01
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.26
Consensus pattern (155 bp):
TCTCTTACCCCAACCTGGGGCAGATCAACATCAGCAAATCTCTTACCCCGAGGCTGGGGTAGATT
GCAGTCATTCGATCTTTTACCCCGAGCTTAGGGCAGATCATCACCAGCCAATCTCTTACCCCGAG
CCTAGGGCAGATTGCAATCATTCGA
Found at i:29262966 original size:77 final size:77
Alignment explanation
Indices: 29262821--29262978 Score: 210
Period size: 77 Copynumber: 2.1 Consensus size: 77
29262811 CTTTTTTCCT
** ** * * * *
29262821 GAGCTTGGGTAGATTGTAGCCATTCGATCTCTTATCTTGAGCTTGGGGCAGATCATTACTAGCCA
1 GAGCTTGGGTAGATTACAGCCATTCGATCTCTTATCCCGAGCTTAGGGCAGATCATCACTAACAA
29262886 ATCTCTTACCCC
66 ATCTCTTACCCC
*
29262898 GAGCTTGGGTAGATTACAGCCGTTCGATCTCTTATCCCGAGCTTAGGGCAGATCATCA-TCAACA
1 GAGCTTGGGTAGATTACAGCCATTCGATCTCTTATCCCGAGCTTAGGGCAGATCATCACT-AACA
*
29262962 AATCTTTTACCCC
65 AATCTCTTACCCC
29262975 GAGC
1 GAGC
29262979 CAGAGGCAGA
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
76 1 0.01
77 69 0.99
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.30
Consensus pattern (77 bp):
GAGCTTGGGTAGATTACAGCCATTCGATCTCTTATCCCGAGCTTAGGGCAGATCATCACTAACAA
ATCTCTTACCCC
Found at i:29263050 original size:39 final size:39
Alignment explanation
Indices: 29262536--29263557 Score: 274
Period size: 39 Copynumber: 26.3 Consensus size: 39
29262526 TGAAGATCCG
29262536 ATCTCTTACCCCGAGCTT-GAGGCAGATT--A-TCATTAGCA
1 ATCTCTTACCCCGAGCTTAG-GGCAGATTACAGTCATT--CA
* * **
29262574 AGTCTCTTACCCCGAGC-TAGGGGCAGATCACCGTCAGCCA
1 A-TCTCTTACCCCGAGCTTA-GGGCAGATTACAGTCATTCA
* * * * *
29262614 ATCTCTTACCCCGAGGC-TGGGGTAGATTGCAGCCATTCG
1 ATCTCTTACCCCGA-GCTTAGGGCAGATTACAGTCATTCA
* * **
29262653 ATCTCTTACCCCGAGCTTAGGGCAGATCATCA-CCAGCCA
1 ATCTCTTACCCCGAGCTTAGGGCAGATTA-CAGTCATTCA
* * * * **
29262692 ATCTCTTACCCCGAGCCTAGGGCAGATTGCAATCGTTTG
1 ATCTCTTACCCCGAGCTTAGGGCAGATTACAGTCATTCA
* * * * * * *
29262731 ATCTCTTACCCCAAACCTGGGGCAGATCATCA-TCAGTAA
1 ATCTCTTACCCCGAGCTTAGGGCAGATTA-CAGTCATTCA
* * * * * * *
29262770 ATCTTTTACCTCGAGC-CAGGGGTAGATCACCGTCAGTCA
1 ATCTCTTACCCCGAGCTTA-GGGCAGATTACAGTCATTCA
* ** * * ** * *
29262809 ATCTTTTTTCCTGAGCTT-GGGTAGATTGTAGCCATTCG
1 ATCTCTTACCCCGAGCTTAGGGCAGATTACAGTCATTCA
* ** * * **
29262847 ATCTCTTATCTTGAGCTTGGGGCAGA-T-CATTACTAGCCA
1 ATCTCTTACCCCGAGCTTAGGGCAGATTACAGT-C-ATTCA
* * * *
29262886 ATCTCTTACCCCGAGCTT-GGGTAGATTACAGCCGTTCG
1 ATCTCTTACCCCGAGCTTAGGGCAGATTACAGTCATTCA
* * *
29262924 ATCTCTTATCCCGAGCTTAGGGCAGATCATCA-TCA-ACAA
1 ATCTCTTACCCCGAGCTTAGGGCAGATTA-CAGTCATTC-A
* * * **
29262963 ATCTTTTACCCCGAGC-CAGAGGCAGATCACTA-TCAACCA
1 ATCTCTTACCCCGAGCTTAG-GGCAGATTAC-AGTCATTCA
*
29263002 ATCTCTTACCCCGAGCTTAGGGCAGATTACAGTCATTCG
1 ATCTCTTACCCCGAGCTTAGGGCAGATTACAGTCATTCA
* * * * * *
29263041 ATCTTTTACCTCGAGCTT-GAGGCAAATTAACA-CCAGTAA
1 ATCTCTTACCCCGAGCTTAG-GGCAGATT-ACAGTCATTCA
* * * * * *
29263080 ATCTCTTACCCCTAGCCTAAGGTAGATTGCAGTCATTCG
1 ATCTCTTACCCCGAGCTTAGGGCAGATTACAGTCATTCA
* * * * * * * *
29263119 ATCTTTTACCTCGAGCCTAAGGCAAATCAACA-CCA-GCAA
1 ATCTCTTACCCCGAGCTTAGGGCAGAT-TACAGTCATTC-A
* * * **
29263158 ATCTCTTACCCCAAGCTT-GAGGCAAATTGCAACCATTCA
1 ATCTCTTACCCCGAGCTTAG-GGCAGATTACAGTCATTCA
* * * * * *
29263197 ATCTCTTACCTCGAGCCT-GAGGCAAATCAACA-CCA-GCAA
1 ATCTCTTACCCCGAGCTTAG-GGCAGAT-TACAGTCATTC-A
** * * **
29263236 ATCTCTTACCTTGAGCTTGGGGCAGATTGCAGTCATTTG
1 ATCTCTTACCCCGAGCTTAGGGCAGATTACAGTCATTCA
* * * *
29263275 ATCTCTTACCCCGAGCTTGGGGCAGGTCATCA-TCA-ACAA
1 ATCTCTTACCCCGAGCTTAGGGCAGATTA-CAGTCATTC-A
* * * * * * * *
29263314 ATCTCTTACCCCAACCATAGGGCAAATTGCAGCCATCCG
1 ATCTCTTACCCCGAGCTTAGGGCAGATTACAGTCATTCA
* * * * * **
29263353 ATCTCTTACCCCAAGCCTGGGGTAGATTACCA-TTAGCCA
1 ATCTCTTACCCCGAGCTTAGGGCAGATTA-CAGTCATTCA
* ** * * *
29263392 ATCTCTTACCCTGAGAC-GGGGGTAGATTACAGTCATCCG
1 ATCTCTTACCCCGAG-CTTAGGGCAGATTACAGTCATTCA
* * * * **
29263431 ATCTTTTACCCCGAACCTAGGGCAGATTACCACT-AGCCA
1 ATCTCTTACCCCGAGCTTAGGGCAGATTA-CAGTCATTCA
* * * ** * *
29263470 ATCTCTTACCCCGAGCCT-GGGTAAATTGTAGCCATTCG
1 ATCTCTTACCCCGAGCTTAGGGCAGATTACAGTCATTCA
* * *
29263508 ATCTCTTACCTCGAGCTT-GAGGCAGATCATCA-TCATCCA
1 ATCTCTTACCCCGAGCTTAG-GGCAGATTA-CAGTCATTCA
*
29263547 ATCTGTTACCC
1 ATCTCTTACCC
29263558 TGATCATGGA
Statistics
Matches: 716, Mismatches: 215, Indels: 105
0.69 0.21 0.10
Matches are distributed among these distances:
37 2 0.00
38 106 0.15
39 568 0.79
40 37 0.05
42 3 0.00
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.26
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCTTAGGGCAGATTACAGTCATTCA
Found at i:29264000 original size:17 final size:17
Alignment explanation
Indices: 29263978--29264074 Score: 106
Period size: 17 Copynumber: 5.8 Consensus size: 17
29263968 GAACTCATTT
* *
29263978 TTTAAATTTGTTTTAGG
1 TTTAAATTTATTTTAAG
* *
29263995 TTTAAAATTATTTTAAA
1 TTTAAATTTATTTTAAG
*
29264012 TTTAAATTAATTTTAAG
1 TTTAAATTTATTTTAAG
* *
29264029 TTTAAACTTATTTTAAA
1 TTTAAATTTATTTTAAG
* *
29264046 TTTAAAATTA-TTTAAA
1 TTTAAATTTATTTTAAG
29264062 TTTAAATTTATTT
1 TTTAAATTTATTT
29264075 AAATCTAAAA
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
16 15 0.22
17 52 0.78
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (17 bp):
TTTAAATTTATTTTAAG
Found at i:29264015 original size:6 final size:6
Alignment explanation
Indices: 29264006--29264083 Score: 60
Period size: 6 Copynumber: 14.0 Consensus size: 6
29263996 TTAAAATTAT
* * * *
29264006 TTTAAA TTTAAA -TTAAT TTTAAG TTTAAA CTT-AT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
29264052 ATT--A TTTAAA TTTAAA TTT--A TTTAAA TCTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
29264084 ATAAATAATG
Statistics
Matches: 56, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
4 7 0.12
5 7 0.12
6 42 0.75
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:29264016 original size:34 final size:34
Alignment explanation
Indices: 29263978--29264083 Score: 119
Period size: 34 Copynumber: 3.2 Consensus size: 34
29263968 GAACTCATTT
** *
29263978 TTTAAATTTGTTTTAGGTTTAAAATTATTTTAAA
1 TTTAAATTAATTTTAAGTTTAAAATTATTTTAAA
*
29264012 TTTAAATTAATTTTAAGTTTAAACTTATTTTAAA
1 TTTAAATTAATTTTAAGTTTAAAATTATTTTAAA
* *
29264046 TTTAAAATT-A-TTTAAATTTAAATTTA-TTTAAA
1 TTT-AAATTAATTTTAAGTTTAAAATTATTTTAAA
*
29264078 TCTAAA
1 TTTAAA
29264084 ATAAATAATG
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
31 3 0.05
32 8 0.12
33 14 0.22
34 34 0.53
35 5 0.08
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (34 bp):
TTTAAATTAATTTTAAGTTTAAAATTATTTTAAA
Found at i:29264020 original size:16 final size:16
Alignment explanation
Indices: 29263999--29264083 Score: 102
Period size: 17 Copynumber: 5.2 Consensus size: 16
29263989 TTTAGGTTTA
29263999 AAATTATTTTAAATTT
1 AAATTATTTTAAATTT
*
29264015 AAATTAATTTTAAGTTT
1 AAATT-ATTTTAAATTT
29264032 AAACTTATTTTAAATTT
1 AAA-TTATTTTAAATTT
29264049 AAAATTA-TTTAAATTT
1 -AAATTATTTTAAATTT
*
29264065 AAATT-TATTTAAATCT
1 AAATTAT-TTTAAATTT
29264081 AAA
1 AAA
29264084 ATAAATAATG
Statistics
Matches: 61, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
15 5 0.08
16 25 0.41
17 26 0.43
18 5 0.08
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (16 bp):
AAATTATTTTAAATTT
Found at i:29265912 original size:31 final size:30
Alignment explanation
Indices: 29265842--29266030 Score: 177
Period size: 30 Copynumber: 6.3 Consensus size: 30
29265832 GTCCATGAAT
* ** * *
29265842 TTTCCAAAAATCATGTTTTGACCCCTAAAC
1 TTTCCAAAAATTACATTTTAACCCTTAAAC
*
29265872 TTTCCAAAAATTACATTTTAACCCTTAAATG
1 TTTCCAAAAATTACATTTTAACCCTTAAA-C
* *
29265903 TTTTCAAAAATTACATTTTGACCCTTAAAC
1 TTTCCAAAAATTACATTTTAACCCTTAAAC
*
29265933 TTTCCAAAAATTATATTTTAACCCTTAAAC
1 TTTCCAAAAATTACATTTTAACCCTTAAAC
* ** *
29265963 -TTCACAAAAATTGCATTTTTGCCCTCAAAC
1 TTTC-CAAAAATTACATTTTAACCCTTAAAC
* * * * *
29265993 TTT-TAAAAATCACATTTTTACCCCTGAAC
1 TTTCCAAAAATTACATTTTAACCCTTAAAC
29266022 -TTCCAAAAA
1 TTTCCAAAAA
29266031 ATTTTACCCC
Statistics
Matches: 130, Mismatches: 25, Indels: 9
0.79 0.15 0.05
Matches are distributed among these distances:
28 2 0.02
29 27 0.21
30 72 0.55
31 29 0.22
ACGTcount: A:0.37, C:0.23, G:0.04, T:0.37
Consensus pattern (30 bp):
TTTCCAAAAATTACATTTTAACCCTTAAAC
Found at i:29265941 original size:61 final size:61
Alignment explanation
Indices: 29265857--29266030 Score: 203
Period size: 61 Copynumber: 2.9 Consensus size: 61
29265847 AAAAATCATG
* * **
29265857 TTTTGACCCCTAAACTTTCCAAAAATTACATTTTAACCCTTAAATGTTTTCAAAAATTACA-
1 TTTTGACCCTTAAACTTTCCAAAAATTACATTTTAACCCTTAAA-CTTCACAAAAATTACAT
* *
29265918 TTTTGACCCTTAAACTTTCCAAAAATTATATTTTAACCCTTAAACTTCACAAAAATTGCAT
1 TTTTGACCCTTAAACTTTCCAAAAATTACATTTTAACCCTTAAACTTCACAAAAATTACAT
* * * * * *
29265979 TTTTG-CCCTCAAACTTT-TAAAAATCACATTTTTACCCCTGAACTTC-CAAAAA
1 TTTTGACCCTTAAACTTTCCAAAAATTACATTTTAACCCTTAAACTTCACAAAAA
29266031 ATTTTACCCC
Statistics
Matches: 99, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
58 6 0.06
59 23 0.23
60 23 0.23
61 47 0.47
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.37
Consensus pattern (61 bp):
TTTTGACCCTTAAACTTTCCAAAAATTACATTTTAACCCTTAAACTTCACAAAAATTACAT
Found at i:29266053 original size:24 final size:24
Alignment explanation
Indices: 29266008--29266054 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
29265998 AAAATCACAT
* * *
29266008 TTTTACCCCTGAACTTCCAAAAAA
1 TTTTACCCCCGAACATCAAAAAAA
*
29266032 TTTTACCCCCGAGCATCAAAAAA
1 TTTTACCCCCGAACATCAAAAAA
29266055 TTACCATTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.38, C:0.30, G:0.06, T:0.26
Consensus pattern (24 bp):
TTTTACCCCCGAACATCAAAAAAA
Found at i:29270345 original size:3 final size:3
Alignment explanation
Indices: 29270337--29270367 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
29270327 ATTTTTCATG
29270337 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
29270368 CAAAATTAAA
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:0.32, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:29274496 original size:26 final size:26
Alignment explanation
Indices: 29274447--29274496 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
29274437 TCTGTTTAAA
**
29274447 TTTGAAATTATTTAATAATTTTTATG
1 TTTGAAATTATTTAATAAGGTTTATG
* *
29274473 TTTGAATTTATTTAATGAGGTTTA
1 TTTGAAATTATTTAATAAGGTTTA
29274497 GCATATGACA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (26 bp):
TTTGAAATTATTTAATAAGGTTTATG
Found at i:29274574 original size:6 final size:6
Alignment explanation
Indices: 29274567--29274602 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
29274557 TGCATGCATG
*
29274567 AACATG AACATA AACATA AACATA AACATA AACATA
1 AACATA AACATA AACATA AACATA AACATA AACATA
29274603 TTTAATTCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.64, C:0.17, G:0.03, T:0.17
Consensus pattern (6 bp):
AACATA
Done.