Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 135 of 185
Found at i:41831841 original size:22 final size:21
Alignment explanation
Indices: 41831802--41831844 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
41831792 TGACCTTTTC
*
41831802 AAGGTATGGGTAGGTATGGGA
1 AAGGTATGGGAAGGTATGGGA
41831823 AAGGTATGGGCAAGGTATGGGA
1 AAGGTATGGG-AAGGTATGGGA
41831845 TATATTCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.30, C:0.02, G:0.47, T:0.21
Consensus pattern (21 bp):
AAGGTATGGGAAGGTATGGGA
Found at i:41841803 original size:17 final size:18
Alignment explanation
Indices: 41841734--41841803 Score: 54
Period size: 20 Copynumber: 3.8 Consensus size: 18
41841724 AAAAATTAAA
41841734 AAAAATATTCTTTAAAAAAT
1 AAAAATA-T-TTTAAAAAAT
*
41841754 AAAAAAATTTATGAAAAAAT
1 AAAAATATTT-T-AAAAAAT
* * *
41841774 AAAACT-CTGT-AAAAAT
1 AAAAATATTTTAAAAAAT
41841790 AAAAATATTTTAAA
1 AAAAATATTTTAAA
41841804 TATATAAACA
Statistics
Matches: 38, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
16 11 0.29
17 2 0.05
18 5 0.13
19 3 0.08
20 17 0.45
ACGTcount: A:0.63, C:0.04, G:0.03, T:0.30
Consensus pattern (18 bp):
AAAAATATTTTAAAAAAT
Found at i:41842282 original size:31 final size:31
Alignment explanation
Indices: 41842233--41842306 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
41842223 ATTTAAACAA
* * *
41842233 AAAACATAAAAATTTAAAAATTATAATT-TTT
1 AAAATATAAAAA-TTAAAAATAAAAATTCTTT
41842264 AAAATATATAAAATTAAAAATAAAAATTCTTT
1 AAAATATA-AAAATTAAAAATAAAAATTCTTT
41842296 AAAAT-TAAAAA
1 AAAATATAAAAA
41842307 AATAAAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
30 4 0.11
31 22 0.58
32 12 0.32
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.34
Consensus pattern (31 bp):
AAAATATAAAAATTAAAAATAAAAATTCTTT
Found at i:41853549 original size:24 final size:25
Alignment explanation
Indices: 41853516--41853570 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
41853506 AACTGAAATA
*
41853516 AAAATTTAAAACCTAGA-AAAAGAG
1 AAAATCTAAAACCTAGACAAAAGAG
* *
41853540 AAAATCTAAAGCCTAGATCGAAAGAG
1 AAAATCTAAAACCTAGA-CAAAAGAG
41853566 AAAAT
1 AAAAT
41853571 TATACATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 15 0.58
26 11 0.42
ACGTcount: A:0.58, C:0.11, G:0.15, T:0.16
Consensus pattern (25 bp):
AAAATCTAAAACCTAGACAAAAGAG
Found at i:41857024 original size:23 final size:23
Alignment explanation
Indices: 41856998--41857043 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
41856988 ACAAACAACA
*
41856998 AATAATTTACTATTACTCCTACT
1 AATAATCTACTATTACTCCTACT
41857021 AATAATCTACTATTACTCCTACT
1 AATAATCTACTATTACTCCTACT
41857044 TCTAACAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.24, G:0.00, T:0.41
Consensus pattern (23 bp):
AATAATCTACTATTACTCCTACT
Found at i:41858341 original size:24 final size:24
Alignment explanation
Indices: 41858311--41858358 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
41858301 GGTAAGCACT
41858311 TTGTGCTTAGTAAGCTCGTGTAAC
1 TTGTGCTTAGTAAGCTCGTGTAAC
*
41858335 TTGTGCTTAGTAAGCTTGTGTAAC
1 TTGTGCTTAGTAAGCTCGTGTAAC
41858359 AAGAATTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.21, C:0.15, G:0.25, T:0.40
Consensus pattern (24 bp):
TTGTGCTTAGTAAGCTCGTGTAAC
Found at i:41861565 original size:17 final size:16
Alignment explanation
Indices: 41861533--41861572 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
41861523 ACAAAAGAAG
41861533 ATTTAG-GTTCTAAAA
1 ATTTAGAGTTCTAAAA
*
41861548 AGTTTAGAGTTTTAAAA
1 A-TTTAGAGTTCTAAAA
41861565 ATTTAGAG
1 ATTTAGAG
41861573 GATTTTGAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 12 0.55
17 9 0.41
ACGTcount: A:0.40, C:0.03, G:0.17, T:0.40
Consensus pattern (16 bp):
ATTTAGAGTTCTAAAA
Found at i:41870147 original size:22 final size:22
Alignment explanation
Indices: 41870121--41870175 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
41870111 TACATAGGTG
41870121 ATGTCGAGACACACCAGGTCCT
1 ATGTCGAGACACACCAGGTCCT
*
41870143 GTGTC-ATGACACACCAGGTCCT
1 ATGTCGA-GACACACCAGGTCCT
*
41870165 ATGTCGCGACA
1 ATGTCGAGACA
41870176 TCGATGGCAG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 1 0.04
22 27 0.96
ACGTcount: A:0.25, C:0.31, G:0.24, T:0.20
Consensus pattern (22 bp):
ATGTCGAGACACACCAGGTCCT
Found at i:41873428 original size:11 final size:11
Alignment explanation
Indices: 41873412--41873504 Score: 60
Period size: 11 Copynumber: 8.9 Consensus size: 11
41873402 TTTTTTTTAA
41873412 TTTTAAAATAT
1 TTTTAAAATAT
*
41873423 TTTTAAGATACTT
1 TTTTAAAATA--T
*
41873436 TTTTAAAAAAAT
1 TTTT-AAAATAT
41873448 TTTT---A-A-
1 TTTTAAAATAT
41873454 TTTTAAAATAT
1 TTTTAAAATAT
41873465 TTTTAAAATACT
1 TTTTAAAATA-T
*
41873477 TTTT-TAAT-T
1 TTTTAAAATAT
41873486 TTTT-AAA-AT
1 TTTTAAAATAT
41873495 TTTTAAAATA
1 TTTTAAAATA
41873505 AAAATGGGCC
Statistics
Matches: 65, Mismatches: 5, Indels: 24
0.69 0.05 0.26
Matches are distributed among these distances:
6 4 0.06
7 1 0.02
8 1 0.02
9 13 0.20
10 4 0.06
11 23 0.35
12 10 0.15
13 5 0.08
14 4 0.06
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:41873459 original size:18 final size:17
Alignment explanation
Indices: 41873436--41873470 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
41873426 TAAGATACTT
41873436 TTTTAAAAAAATTTTTAA
1 TTTT-AAAAAATTTTTAA
*
41873454 TTTTAAAATATTTTTAA
1 TTTTAAAAAATTTTTAA
41873471 AATACTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTTAAAAAATTTTTAA
Found at i:41873468 original size:30 final size:31
Alignment explanation
Indices: 41873423--41873506 Score: 86
Period size: 30 Copynumber: 2.8 Consensus size: 31
41873413 TTTAAAATAT
*
41873423 TTTTAAGATACTTTTTTAAAA-AAATTTTTAA
1 TTTTAAAATAC-TTTTTAAAATAAATTTTTAA
**
41873454 TTTTAAAATA-TTTTTAAAATACTTTTTTAA
1 TTTTAAAATACTTTTTAAAATAAATTTTTAA
*
41873484 TTTTTTAAA-A-TTTTTAAAATAAA
1 -TTTTAAAATACTTTTTAAAATAAA
41873507 AATGGGCCGG
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
29 9 0.20
30 20 0.44
31 16 0.36
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (31 bp):
TTTTAAAATACTTTTTAAAATAAATTTTTAA
Found at i:41876826 original size:19 final size:19
Alignment explanation
Indices: 41876804--41876873 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
41876794 CTTCTATATA
*
41876804 TTTTATAATCTTTTACTAT
1 TTTTATAATCTTTTACAAT
**
41876823 TTTTATAAAATTTTACAAT
1 TTTTATAATCTTTTACAAT
* * *
41876842 TTTTATATTTTTTTACGA-
1 TTTTATAATCTTTTACAAT
41876860 TTTTATAATCTTTT
1 TTTTATAATCTTTT
41876874 TCTAATTATT
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
18 12 0.29
19 30 0.71
ACGTcount: A:0.29, C:0.07, G:0.01, T:0.63
Consensus pattern (19 bp):
TTTTATAATCTTTTACAAT
Found at i:41876931 original size:19 final size:19
Alignment explanation
Indices: 41876898--41876963 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
41876888 AAAATTAAAT
41876898 ATTTCTTATATTTTTTATTA
1 ATTT-TTATATTTTTTATTA
* * *
41876918 AATTTTATAATTTTTATTG
1 ATTTTTATATTTTTTATTA
* *
41876937 ATTTTTATTTTTTTTATCA
1 ATTTTTATATTTTTTATTA
41876956 ATTTTTAT
1 ATTTTTAT
41876964 CACATGTCAC
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 35 0.92
20 3 0.08
ACGTcount: A:0.26, C:0.03, G:0.02, T:0.70
Consensus pattern (19 bp):
ATTTTTATATTTTTTATTA
Found at i:41876965 original size:10 final size:9
Alignment explanation
Indices: 41876804--41876963 Score: 56
Period size: 10 Copynumber: 16.7 Consensus size: 9
41876794 CTTCTATATA
41876804 TTTTATAAT
1 TTTTATAAT
41876813 CTTTTACT-AT
1 -TTTTA-TAAT
*
41876823 TTTTATAAAA
1 TTTTAT-AAT
*
41876833 TTTTACAAT
1 TTTTATAAT
41876842 TTTTAT-AT
1 TTTTATAAT
*
41876850 TTTTTTACGA-
1 TTTTATA--AT
41876860 TTTTATAATCT
1 TTTTATAA--T
*
41876871 TTTTCTAAT
1 TTTTATAAT
* *
41876880 TATTAATAAA
1 T-TTTATAAT
** *
41876890 AATTAAATAT
1 TTTTATA-AT
*
41876900 TTCTTATATT
1 TT-TTATAAT
*
41876910 TTTTATTAAA
1 TTTTA-TAAT
41876920 TTTTATAAT
1 TTTTATAAT
*
41876929 TTTTATTGAT
1 TTTTA-TAAT
**
41876939 TTTTATTTT
1 TTTTATAAT
41876948 TTTTATCAAT
1 TTTTAT-AAT
41876958 TTTTAT
1 TTTTAT
41876964 CACATGTCAC
Statistics
Matches: 108, Mismatches: 27, Indels: 30
0.65 0.16 0.18
Matches are distributed among these distances:
8 9 0.08
9 36 0.33
10 50 0.46
11 13 0.12
ACGTcount: A:0.31, C:0.05, G:0.01, T:0.62
Consensus pattern (9 bp):
TTTTATAAT
Found at i:41879766 original size:15 final size:15
Alignment explanation
Indices: 41879748--41879812 Score: 60
Period size: 15 Copynumber: 4.1 Consensus size: 15
41879738 TAATTTTTTG
41879748 AAAATTAATTTTACAAA
1 AAAATTAATTTT--AAA
*
41879765 AATAATT-ATTTGAAA
1 AA-AATTAATTTTAAA
*
41879780 AAAATTATTTTTAAA
1 AAAATTAATTTTAAA
*
41879795 AAAATTATTTTTTAAA
1 AAAATTA-ATTTTAAA
41879811 AA
1 AA
41879813 GTAAATAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
14 4 0.10
15 18 0.43
16 10 0.24
17 6 0.14
18 4 0.10
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (15 bp):
AAAATTAATTTTAAA
Found at i:41879771 original size:29 final size:29
Alignment explanation
Indices: 41879738--41879812 Score: 78
Period size: 32 Copynumber: 2.5 Consensus size: 29
41879728 CCAATTCGAC
*
41879738 TAATTTTTTGAAAATTAATTTTACAAAAA
1 TAATTTTTTGAAAATTAATTTTAAAAAAA
* *
41879767 TAATTATTTGAAAAAAATTATTTTTAAAAAAA
1 TAATTTTTTG---AAAATTAATTTTAAAAAAA
* *
41879799 TTATTTTTTAAAAA
1 TAATTTTTTGAAAA
41879813 GTAAATAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
29 13 0.35
32 24 0.65
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (29 bp):
TAATTTTTTGAAAATTAATTTTAAAAAAA
Found at i:41879792 original size:32 final size:31
Alignment explanation
Indices: 41879748--41879812 Score: 85
Period size: 32 Copynumber: 2.1 Consensus size: 31
41879738 TAATTTTTTG
*
41879748 AAAATTAATTTTACAAAAATAATTATTTGAAA
1 AAAATTAATTTTAAAAAAATAATT-TTTGAAA
* * *
41879780 AAAATTATTTTTAAAAAAATTATTTTTTAAA
1 AAAATTAATTTTAAAAAAATAATTTTTGAAA
41879811 AA
1 AA
41879813 GTAAATAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 8 0.28
32 21 0.72
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (31 bp):
AAAATTAATTTTAAAAAAATAATTTTTGAAA
Found at i:41879805 original size:14 final size:14
Alignment explanation
Indices: 41879748--41879805 Score: 62
Period size: 15 Copynumber: 3.8 Consensus size: 14
41879738 TAATTTTTTG
41879748 AAAATTAATTTTACAAA
1 AAAATT-ATTTT--AAA
*
41879765 AATAATTATTTGAAA
1 AA-AATTATTTTAAA
41879780 AAAATTATTTTTAAA
1 AAAATTA-TTTTAAA
41879795 AAAATTATTTT
1 AAAATTATTTT
41879806 TTAAAAAGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
14 9 0.24
15 18 0.49
17 6 0.16
18 4 0.11
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (14 bp):
AAAATTATTTTAAA
Found at i:41884606 original size:18 final size:18
Alignment explanation
Indices: 41884585--41884651 Score: 89
Period size: 18 Copynumber: 3.6 Consensus size: 18
41884575 TAAAAATTAT
*
41884585 AAAAAATTTTATTTTTTA
1 AAAAAATTATATTTTTTA
41884603 AAAAAATTATATTTTTTTA
1 AAAAAATTATA-TTTTTTA
*
41884622 TTAAAAATTATATTTTTTA
1 -AAAAAATTATATTTTTTA
*
41884641 AAAATATTATA
1 AAAAAATTATA
41884652 AATTTTTATT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
18 19 0.44
19 14 0.33
20 10 0.23
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
AAAAAATTATATTTTTTA
Found at i:41884628 original size:38 final size:38
Alignment explanation
Indices: 41884563--41884666 Score: 129
Period size: 38 Copynumber: 2.8 Consensus size: 38
41884553 AAAAATTATA
* ** * *
41884563 TTAAAAAAATCATAAA-AATTATAAAAAATTTTATTTT
1 TTAAAAAAATTATAAATTTTTATTAAAAATTATATTTT
**
41884600 TTAAAAAAATTATATTTTTTTATTAAAAATTATATTTT
1 TTAAAAAAATTATAAATTTTTATTAAAAATTATATTTT
*
41884638 TTAAAAATATTATAAATTTTTATTAAAAA
1 TTAAAAAAATTATAAATTTTTATTAAAAA
41884667 ATATCAATAC
Statistics
Matches: 56, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
37 13 0.23
38 43 0.77
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (38 bp):
TTAAAAAAATTATAAATTTTTATTAAAAATTATATTTT
Found at i:41884656 original size:20 final size:18
Alignment explanation
Indices: 41884584--41884659 Score: 75
Period size: 19 Copynumber: 4.1 Consensus size: 18
41884574 ATAAAAATTA
*
41884584 TAAAAAATT-TTATTTTT
1 TAAAAAATTATAATTTTT
*
41884601 TAAAAAAATTATATTTTTT
1 T-AAAAAATTATAATTTTT
41884620 TATTAAAAATTAT-ATTTTT
1 TA--AAAAATTATAATTTTT
*
41884639 TAAAAATATTATAAATTTT
1 TAAAAA-ATTATAATTTTT
41884658 TA
1 TA
41884660 TTAAAAAATA
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
17 5 0.10
18 14 0.29
19 21 0.43
20 9 0.18
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TAAAAAATTATAATTTTT
Found at i:41890383 original size:25 final size:25
Alignment explanation
Indices: 41890355--41890413 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 25
41890345 TTACCCCCAA
*
41890355 TAAAATTTGACAATTTTACCCTTGG
1 TAAAATTTGACAATTTTACCATTGG
** * *
41890380 TAAAATCTTGATGATTTTTCTATTGG
1 TAAAAT-TTGACAATTTTACCATTGG
41890406 TAAAATTT
1 TAAAATTT
41890414 CAAGAAAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
25 8 0.29
26 20 0.71
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.46
Consensus pattern (25 bp):
TAAAATTTGACAATTTTACCATTGG
Found at i:41895374 original size:26 final size:26
Alignment explanation
Indices: 41895345--41895406 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 26
41895335 TATCCCCAAC
*
41895345 AAAATTTTGACAATTTTACCCTTGAT
1 AAAATTTTGACAATTTTACCCCTGAT
* * * *
41895371 AAAATTTTAACGATTTTGCCCCTGGT
1 AAAATTTTGACAATTTTACCCCTGAT
41895397 AAAATTTTGA
1 AAAATTTTGA
41895407 GAAAATATGT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (26 bp):
AAAATTTTGACAATTTTACCCCTGAT
Found at i:41896538 original size:31 final size:30
Alignment explanation
Indices: 41896503--41896567 Score: 89
Period size: 28 Copynumber: 2.2 Consensus size: 30
41896493 TTATTTAATA
41896503 CATTAAAGAAAGTGAGTTTATGATAATTATT
1 CATTAAA-AAAGTGAGTTTATGATAATTATT
* *
41896534 CATT--AATATTGAGTTTATGATAATTATT
1 CATTAAAAAAGTGAGTTTATGATAATTATT
41896562 CATTAA
1 CATTAA
41896568 TATTAAATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
28 25 0.83
29 1 0.03
31 4 0.13
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.43
Consensus pattern (30 bp):
CATTAAAAAAGTGAGTTTATGATAATTATT
Found at i:41896546 original size:28 final size:28
Alignment explanation
Indices: 41896515--41896571 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
41896505 TTAAAGAAAG
41896515 TGAGTTTATGATAATTATTCATTAATAT
1 TGAGTTTATGATAATTATTCATTAATAT
41896543 TGAGTTTATGATAATTATTCATTAATAT
1 TGAGTTTATGATAATTATTCATTAATAT
41896571 T
1 T
41896572 AAATGTCTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.35, C:0.04, G:0.11, T:0.51
Consensus pattern (28 bp):
TGAGTTTATGATAATTATTCATTAATAT
Found at i:41897395 original size:30 final size:29
Alignment explanation
Indices: 41897352--41897433 Score: 119
Period size: 30 Copynumber: 2.8 Consensus size: 29
41897342 TAGGGTCTAG
* *
41897352 GGGTTCTAAAAAAATAATATTGATGAGTT
1 GGGTTCTAAAAAAATAATTTTGATGAGAT
*
41897381 GGGTTCTGAAAAAAATAATTTTTATGAGAT
1 GGGTTCT-AAAAAAATAATTTTGATGAGAT
*
41897411 GGGTTCTAAAGAAATAATTTTGA
1 GGGTTCTAAAAAAATAATTTTGA
41897434 AGAAAAAACA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 21 0.45
30 26 0.55
ACGTcount: A:0.40, C:0.04, G:0.21, T:0.35
Consensus pattern (29 bp):
GGGTTCTAAAAAAATAATTTTGATGAGAT
Found at i:41903877 original size:25 final size:25
Alignment explanation
Indices: 41903849--41903917 Score: 70
Period size: 25 Copynumber: 2.7 Consensus size: 25
41903839 GAGCTTTTCA
41903849 TTATACAGCTCACATGAGCTTCCCG-
1 TTATA-AGCTCACATGAGCTTCCCGT
* *
41903874 TTATATGGCTCGA-AAGAGCTTCCCGT
1 TTATA-AGCTC-ACATGAGCTTCCCGT
*
41903900 TTATATGCTCACATGAGC
1 TTATAAGCTCACATGAGC
41903918 ATTTTTAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
24 1 0.03
25 29 0.81
26 6 0.17
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (25 bp):
TTATAAGCTCACATGAGCTTCCCGT
Found at i:41904108 original size:62 final size:62
Alignment explanation
Indices: 41904037--41904166 Score: 260
Period size: 62 Copynumber: 2.1 Consensus size: 62
41904027 TAGGAGTACG
41904037 AAATGAATTATTACCCGTATAAGCCTGAAATACATGAAAATGATGTTACTTGACATATTGAA
1 AAATGAATTATTACCCGTATAAGCCTGAAATACATGAAAATGATGTTACTTGACATATTGAA
41904099 AAATGAATTATTACCCGTATAAGCCTGAAATACATGAAAATGATGTTACTTGACATATTGAA
1 AAATGAATTATTACCCGTATAAGCCTGAAATACATGAAAATGATGTTACTTGACATATTGAA
41904161 AAATGA
1 AAATGA
41904167 GATGAAAGAT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 68 1.00
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.30
Consensus pattern (62 bp):
AAATGAATTATTACCCGTATAAGCCTGAAATACATGAAAATGATGTTACTTGACATATTGAA
Found at i:41908926 original size:19 final size:18
Alignment explanation
Indices: 41908884--41908919 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
41908874 CGAATTGTAT
*
41908884 ATTTTTTCTCTTATTTTC
1 ATTTTTTCTATTATTTTC
41908902 ATTTTTATCTATTATTTT
1 ATTTTT-TCTATTATTTT
41908920 GTTTTTTCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.72
Consensus pattern (18 bp):
ATTTTTTCTATTATTTTC
Found at i:41909749 original size:18 final size:18
Alignment explanation
Indices: 41909709--41909749 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
41909699 ATTAGTTTAA
* *
41909709 TATTTTCATTATTATTAT
1 TATTATCATTATCATTAT
41909727 TATTATCATTATCATTAT
1 TATTATCATTATCATTAT
41909745 TATTA
1 TATTA
41909750 CTACTACTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (18 bp):
TATTATCATTATCATTAT
Found at i:41909768 original size:3 final size:3
Alignment explanation
Indices: 41909684--41909749 Score: 55
Period size: 3 Copynumber: 22.0 Consensus size: 3
41909674 CCTTTTTGTG
* * *
41909684 TTA TTT TTA TTA TTAA TTA GT- TTA ATA TT- TTCA TTA TTA TTA TTA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA
* *
41909729 TTA TCA TTA TCA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
41909750 CTACTACTTT
Statistics
Matches: 49, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
2 3 0.06
3 41 0.84
4 5 0.10
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:41914354 original size:25 final size:25
Alignment explanation
Indices: 41914332--41914388 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
41914322 ATTGGCTCGT
41914332 AAGAGCTTCCCGTTATACAGCTCAC
1 AAGAGCTTCCCGTTATACAGCTCAC
* * ** *
41914357 ATGAGTTTCCCGTTATATGGCTCAA
1 AAGAGCTTCCCGTTATACAGCTCAC
41914382 AAGAGCT
1 AAGAGCT
41914389 ACTCGTTTCT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (25 bp):
AAGAGCTTCCCGTTATACAGCTCAC
Found at i:41915871 original size:25 final size:24
Alignment explanation
Indices: 41915806--41915903 Score: 90
Period size: 24 Copynumber: 4.0 Consensus size: 24
41915796 AGCGTCTAGT
* *
41915806 TATTAGCTCTCATGAGCATCCCGA
1 TATTGGCTCTCATGAGCTTCCCGA
* *
41915830 TATTGGCTCTCTTGAGCTTCCTGA
1 TATTGGCTCTCATGAGCTTCCCGA
*
41915854 TATTTGGCTCTCACGAGCTTCCC-A
1 TA-TTGGCTCTCATGAGCTTCCCGA
* * * *
41915878 TTAATAGCTCTTATGAGCATCCCGA
1 -TATTGGCTCTCATGAGCTTCCCGA
41915903 T
1 T
41915904 TGGTCGTGAT
Statistics
Matches: 59, Mismatches: 12, Indels: 6
0.77 0.16 0.08
Matches are distributed among these distances:
24 39 0.66
25 20 0.34
ACGTcount: A:0.20, C:0.28, G:0.17, T:0.35
Consensus pattern (24 bp):
TATTGGCTCTCATGAGCTTCCCGA
Found at i:41915973 original size:24 final size:23
Alignment explanation
Indices: 41915943--41915990 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
41915933 CACCGCAGCT
41915943 TTTATGAGCGTCCTAATATTTGGC
1 TTTATGAGCGTCCTAA-ATTTGGC
* *
41915967 TTTATGAGCTTCCTGAATTTGGC
1 TTTATGAGCGTCCTAAATTTGGC
41915990 T
1 T
41915991 CTCTTGAGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.44
Consensus pattern (23 bp):
TTTATGAGCGTCCTAAATTTGGC
Found at i:41916021 original size:48 final size:50
Alignment explanation
Indices: 41915969--41916077 Score: 132
Period size: 49 Copynumber: 2.2 Consensus size: 50
41915959 TATTTGGCTT
* * * ** * * *
41915969 TATGAGCTTCCTGA-ATTTGGCTCTCTTGAGCTTTCTGTT-TATGGCTCG
1 TATGAGCTTCCTGATAATTAGCTCACAAGAGCTTCCTGTTATATAGCTCA
41916017 TATGAGCTTCCTGATAATTAGCTCACAAGAGCTTCCTGTTATATAGCTCA
1 TATGAGCTTCCTGATAATTAGCTCACAAGAGCTTCCTGTTATATAGCTCA
41916067 TATGAGCTTCC
1 TATGAGCTTCC
41916078 CGTTTTATGG
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
48 14 0.27
49 19 0.37
50 18 0.35
ACGTcount: A:0.20, C:0.22, G:0.19, T:0.39
Consensus pattern (50 bp):
TATGAGCTTCCTGATAATTAGCTCACAAGAGCTTCCTGTTATATAGCTCA
Found at i:41916090 original size:25 final size:25
Alignment explanation
Indices: 41915969--41916090 Score: 83
Period size: 25 Copynumber: 5.0 Consensus size: 25
41915959 TATTTGGCTT
**
41915969 TATGAGCTTCCTGAATT-TGGCTC-
1 TATGAGCTTCCTGTTTTATGGCTCA
* * *
41915992 TCTTGAGCTTTCTG-TTTATGGCTCG
1 T-ATGAGCTTCCTGTTTTATGGCTCA
*
41916017 TATGAGCTTCCTGATAATTA--GCTCA
1 TATGAGCTTCCTG-T-TTTATGGCTCA
* * * *
41916042 CAAGAGCTTCCTGTTATATAGCTCA
1 TATGAGCTTCCTGTTTTATGGCTCA
*
41916067 TATGAGCTTCCCGTTTTATGGCTC
1 TATGAGCTTCCTGTTTTATGGCTC
41916091 GAAAGAGTTA
Statistics
Matches: 75, Mismatches: 16, Indels: 14
0.71 0.15 0.13
Matches are distributed among these distances:
23 5 0.07
24 27 0.36
25 40 0.53
27 3 0.04
ACGTcount: A:0.19, C:0.22, G:0.20, T:0.39
Consensus pattern (25 bp):
TATGAGCTTCCTGTTTTATGGCTCA
Found at i:41920311 original size:76 final size:76
Alignment explanation
Indices: 41920210--41920456 Score: 314
Period size: 76 Copynumber: 3.2 Consensus size: 76
41920200 AGGACGTATA
* * *
41920210 CACACATTTAATATTGTCAGTTTATCCGACTAGTGTTGGACACAAATCTTTATCGGTTAATCCGA
1 CACACATTTAATATCGTCGGTTTATCCGACTAGTGTTGGGCACAAATCTTTATCGGTTAATCCGA
*
41920275 CTAGTGTTGGG
66 CTAGTGCTGGG
* * * ** *
41920286 CACATATTTAATATCGTCGGTTTATCCGATTAGTGTTGGGCATAAATCTTTATTAGTTAATCCGG
1 CACACATTTAATATCGTCGGTTTATCCGACTAGTGTTGGGCACAAATCTTTATCGGTTAATCCGA
* *
41920351 CTAGTACTAGG
66 CTAGTGCTGGG
* * * * * *
41920362 CGCACATTTAATATCGTCGGTTTATCTGACTAGTGCTGGGCGCAAATCTTTGTCGGTTAATTCGA
1 CACACATTTAATATCGTCGGTTTATCCGACTAGTGTTGGGCACAAATCTTTATCGGTTAATCCGA
41920427 CTAGTGCTGGG
66 CTAGTGCTGGG
* *
41920438 TACACATTTAGTATCGTCG
1 CACACATTTAATATCGTCG
41920457 ATTGATCTGA
Statistics
Matches: 142, Mismatches: 29, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
76 142 1.00
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.36
Consensus pattern (76 bp):
CACACATTTAATATCGTCGGTTTATCCGACTAGTGTTGGGCACAAATCTTTATCGGTTAATCCGA
CTAGTGCTGGG
Found at i:41920320 original size:40 final size:39
Alignment explanation
Indices: 41920210--41920456 Score: 138
Period size: 36 Copynumber: 6.5 Consensus size: 39
41920200 AGGACGTATA
* * *
41920210 CACACATTTAATATTGTCAGTTTATCCGACTAGTGTTGGA
1 CACAAATTTAATA-TGTCGGTTTATCCGACTAGTGTTGGG
*
41920250 CACAAATCTT--TA--TCGGTTAATCCGACTAGTGTTGGG
1 CACAAAT-TTAATATGTCGGTTTATCCGACTAGTGTTGGG
* *
41920286 CACATATTTAATATCGTCGGTTTATCCGATTAGTGTTGGG
1 CACAAATTTAATAT-GTCGGTTTATCCGACTAGTGTTGGG
* * * * ** *
41920326 CATAAATCTT--TAT-T-AGTTAATCCGGCTAGTACTAGG
1 CACAAAT-TTAATATGTCGGTTTATCCGACTAGTGTTGGG
* * * *
41920362 CGCACATTTAATATCGTCGGTTTATCTGACTAGTGCTGGG
1 CACAAATTTAATAT-GTCGGTTTATCCGACTAGTGTTGGG
* * * * *
41920402 CGCAAATCT--T-TGTCGGTTAATTCGACTAGTGCTGGG
1 CACAAATTTAATATGTCGGTTTATCCGACTAGTGTTGGG
* * *
41920438 TACACATTTAGTATCGTCG
1 CACAAATTTAATAT-GTCG
41920457 ATTGATCTGA
Statistics
Matches: 157, Mismatches: 34, Indels: 32
0.70 0.15 0.14
Matches are distributed among these distances:
35 4 0.03
36 73 0.46
37 7 0.04
38 2 0.01
39 7 0.04
40 60 0.38
41 4 0.03
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.36
Consensus pattern (39 bp):
CACAAATTTAATATGTCGGTTTATCCGACTAGTGTTGGG
Found at i:41921988 original size:17 final size:17
Alignment explanation
Indices: 41921968--41922002 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
41921958 GTAAAAAAAT
* *
41921968 GATAAAAGTATAATTTA
1 GATAAAAATAGAATTTA
41921985 GATAAAAATAGAATTTA
1 GATAAAAATAGAATTTA
41922002 G
1 G
41922003 GAAAAAATTT
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:0.54, C:0.00, G:0.14, T:0.31
Consensus pattern (17 bp):
GATAAAAATAGAATTTA
Found at i:41922091 original size:13 final size:13
Alignment explanation
Indices: 41922075--41922101 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
41922065 AGCAGAGAAT
41922075 TGTGAGAAATGTG
1 TGTGAGAAATGTG
41922088 TGTGAGAAATGTG
1 TGTGAGAAATGTG
41922101 T
1 T
41922102 TGGGGGTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (13 bp):
TGTGAGAAATGTG
Found at i:41927413 original size:20 final size:21
Alignment explanation
Indices: 41927388--41927426 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
41927378 AAACTGACTT
*
41927388 TTGAAAAGCT-TTTGTTTGGC
1 TTGAAAAACTATTTGTTTGGC
41927408 TTGAAAAACTATTTGTTTG
1 TTGAAAAACTATTTGTTTG
41927427 CAATTACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.26, C:0.08, G:0.21, T:0.46
Consensus pattern (21 bp):
TTGAAAAACTATTTGTTTGGC
Found at i:41933438 original size:31 final size:31
Alignment explanation
Indices: 41933403--41933462 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
41933393 GTTTTTTGAA
*
41933403 CTATTCAAAAATTTTTATTTAAGTCACTGAG
1 CTATTCAAAAATTTTTATTTAAATCACTGAG
**
41933434 CTATTCAAATGTTTTTATTTAAATCACTG
1 CTATTCAAAAATTTTTATTTAAATCACTG
41933463 GGTTGTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.45
Consensus pattern (31 bp):
CTATTCAAAAATTTTTATTTAAATCACTGAG
Found at i:41934186 original size:6 final size:6
Alignment explanation
Indices: 41934175--41934228 Score: 99
Period size: 6 Copynumber: 9.0 Consensus size: 6
41934165 AATTCAAAGC
41934175 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
*
41934223 ATAATA
1 AAAATA
41934229 TATTAGTATG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
AAAATA
Found at i:41934358 original size:20 final size:19
Alignment explanation
Indices: 41934313--41934357 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
41934303 TATTCTTTAA
*
41934313 AATTTTTATAAATATTTTG
1 AATTTTTAAAAATATTTTG
41934332 AATTTTTAAAAATTATTTT-
1 AATTTTTAAAAA-TATTTTG
41934351 AATTTTT
1 AATTTTT
41934358 TTATTGTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 18 0.75
20 6 0.25
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
AATTTTTAAAAATATTTTG
Found at i:41937047 original size:18 final size:18
Alignment explanation
Indices: 41936990--41937047 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 18
41936980 AGTTTTTTAA
41936990 TGTTTTTTGCTTAGAAAAT
1 TGTTTTTT-CTTAGAAAAT
*
41937009 TGTTTTTTTATTCAAAGAAAAT
1 TG-TTTTTTCTT---AGAAAAT
41937031 TGTTTTTTCTTAGAAAA
1 TGTTTTTTCTTAGAAAA
41937048 GATGTTAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
18 6 0.18
19 4 0.12
20 6 0.18
21 8 0.24
22 9 0.27
ACGTcount: A:0.31, C:0.05, G:0.12, T:0.52
Consensus pattern (18 bp):
TGTTTTTTCTTAGAAAAT
Found at i:41937503 original size:33 final size:33
Alignment explanation
Indices: 41937439--41937514 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 33
41937429 TGACTATTGA
* * * **
41937439 GGAGGGTGATGTTGAAGGGGTGGAAGTTGATGG
1 GGAGGGTGATGATGAAGGAGTAGAAACTGATGG
41937472 GGAGGGTGATGATGAAGGAGTAGAAACTGATGG
1 GGAGGGTGATGATGAAGGAGTAGAAACTGATGG
* *
41937505 TGATGGTGAT
1 GGAGGGTGAT
41937515 CTAGAAAAGG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.26, C:0.01, G:0.49, T:0.24
Consensus pattern (33 bp):
GGAGGGTGATGATGAAGGAGTAGAAACTGATGG
Found at i:41940608 original size:16 final size:16
Alignment explanation
Indices: 41940587--41940625 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
41940577 GTTTTTGGCT
41940587 TGTATAGGGTGAATGG
1 TGTATAGGGTGAATGG
41940603 TGTATAGGGTGAATGG
1 TGTATAGGGTGAATGG
41940619 TGTATAG
1 TGTATAG
41940626 ACTAATCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.41, T:0.33
Consensus pattern (16 bp):
TGTATAGGGTGAATGG
Found at i:41941014 original size:211 final size:210
Alignment explanation
Indices: 41940649--41941063 Score: 663
Period size: 211 Copynumber: 2.0 Consensus size: 210
41940639 TTTTGTAAAG
* * *
41940649 TACATTTATCCAAATTGCAAAGGGGAAATCATATGCTTAAATGATCAAATTTGTCTTTTTAGTCT
1 TACATTTATCCAAATCGCAAAGGGGAAATCATATGCTTAAATGATCAAAGTTGTCCTTTTAGTCT
* *
41940714 TATGTTTATTGTCACTGCATTATTTATTAAACTAAATTAAATTAGGCATAAACAATAAATATTAG
66 TATGTTTATTGTCACTGCATTATTTACTAAACTAAATTAAATTAGGCATAAACAACAAATATTAG
* *
41940779 CCATTACTTCCAAGCATTATGTTAAATTACATAAAAAAACAACCAATATTAGTTAATCAACATTT
131 CCATTACTTCCAAGCATAATGTTAAATTACAT-AAAAAACAACCAATATTAGTCAATCAACATTT
41940844 GCAACTGCTAGCTGCA
195 GCAACTGCTAGCTGCA
*
41940860 TACATTTATCTAAATCGCAATA-GGGAAATCATATGCTTAAATGATCAAAGTTGTCCTTTTAGTC
1 TACATTTATCCAAATCGCAA-AGGGGAAATCATATGCTTAAATGATCAAAGTTGTCCTTTTAGTC
* *
41940924 TTATGTTTATTGTTACTGCATTATTTACTAAGCTAAATTAAATTAGGCATAAACAACAAATATT-
65 TTATGTTTATTGTCACTGCATTATTTACTAAACTAAATTAAATTAGGCATAAACAACAAATATTA
* *
41940988 GATCATTACTTCCAAGCATAATGTTAAATTACATAAAAAACAACCAATATTTGTCAATCAACATT
130 G-CCATTACTTCCAAGCATAATGTTAAATTACATAAAAAACAACCAATATTAGTCAATCAACATT
* *
41941053 TGTAATTGCTA
194 TGCAACTGCTA
41941064 ATTGCATATG
Statistics
Matches: 188, Mismatches: 14, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
210 39 0.21
211 148 0.79
212 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.36
Consensus pattern (210 bp):
TACATTTATCCAAATCGCAAAGGGGAAATCATATGCTTAAATGATCAAAGTTGTCCTTTTAGTCT
TATGTTTATTGTCACTGCATTATTTACTAAACTAAATTAAATTAGGCATAAACAACAAATATTAG
CCATTACTTCCAAGCATAATGTTAAATTACATAAAAAACAACCAATATTAGTCAATCAACATTTG
CAACTGCTAGCTGCA
Found at i:41943680 original size:31 final size:32
Alignment explanation
Indices: 41943642--41943703 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 32
41943632 GGCAAATTGT
41943642 AAGAGTAATTGAATCCTAAT-AAAACTCTTTC
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTC
41943673 AAGAGTAATTGAATCCTAATAAAAACTCTTT
1 AAGAGTAATTGAATCCTAATAAAAACTCTTT
41943704 AAAATTATCT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 20 0.67
32 10 0.33
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.32
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACTCTTTC
Found at i:41949270 original size:21 final size:21
Alignment explanation
Indices: 41949245--41949291 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
41949235 CAACTTTTTT
41949245 TTTTTGCAGTTTTTTTTGCGC
1 TTTTTGCAGTTTTTTTTGCGC
** *
41949266 TTTTTGCTTTTTTTTTTGCGG
1 TTTTTGCAGTTTTTTTTGCGC
41949287 TTTTT
1 TTTTT
41949292 TTTGCGCTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.02, C:0.11, G:0.17, T:0.70
Consensus pattern (21 bp):
TTTTTGCAGTTTTTTTTGCGC
Found at i:41949281 original size:33 final size:33
Alignment explanation
Indices: 41949240--41949315 Score: 143
Period size: 33 Copynumber: 2.3 Consensus size: 33
41949230 GTAGGCAACT
41949240 TTTTTTTTTTGCAGTTTTTTTTGCGCTTTTTGC
1 TTTTTTTTTTGCAGTTTTTTTTGCGCTTTTTGC
*
41949273 TTTTTTTTTTGCGGTTTTTTTTGCGCTTTTTGC
1 TTTTTTTTTTGCAGTTTTTTTTGCGCTTTTTGC
41949306 TTTTTTTTTT
1 TTTTTTTTTT
41949316 AAGAATAAGA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.01, C:0.11, G:0.14, T:0.74
Consensus pattern (33 bp):
TTTTTTTTTTGCAGTTTTTTTTGCGCTTTTTGC
Found at i:41949315 original size:12 final size:12
Alignment explanation
Indices: 41949242--41949303 Score: 58
Period size: 12 Copynumber: 5.4 Consensus size: 12
41949232 AGGCAACTTT
*
41949242 TTTTTTTTGCAG
1 TTTTTTTTGCGG
41949254 TTTTTTTTGC-G
1 TTTTTTTTGCGG
* **
41949265 --CTTTTTGCTT
1 TTTTTTTTGCGG
41949275 TTTTTTTTGCGG
1 TTTTTTTTGCGG
*
41949287 TTTTTTTTGCGC
1 TTTTTTTTGCGG
41949299 TTTTT
1 TTTTT
41949304 GCTTTTTTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
9 7 0.17
11 1 0.02
12 33 0.80
ACGTcount: A:0.02, C:0.11, G:0.16, T:0.71
Consensus pattern (12 bp):
TTTTTTTTGCGG
Found at i:41951559 original size:22 final size:23
Alignment explanation
Indices: 41951534--41951578 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
41951524 AACACAATTC
41951534 ATAAAAAAT-TGAAAAATATAAA
1 ATAAAAAATATGAAAAATATAAA
* *
41951556 ATAAAAAGTATGAAAATTATAAA
1 ATAAAAAATATGAAAAATATAAA
41951579 TTTTTAGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (23 bp):
ATAAAAAATATGAAAAATATAAA
Found at i:41951806 original size:39 final size:38
Alignment explanation
Indices: 41951723--41951807 Score: 88
Period size: 39 Copynumber: 2.2 Consensus size: 38
41951713 ATTATATTTG
*
41951723 GAATTTTTTTATATTTGAAAAAGAGATTTATATTTTTT
1 GAATTTTTATATATTTGAAAAAGAGATTTATATTTTTT
41951761 -ATATTTTTATATTATTT-AAAAA-A-ATTTATAATTGCTTTT
1 GA-ATTTTTATA-TATTTGAAAAAGAGATTTAT-ATT--TTTT
41951800 GAATTTTT
1 GAATTTTT
41951808 TGAAATTTTC
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
36 6 0.15
37 5 0.12
38 13 0.32
39 15 0.38
40 1 0.03
ACGTcount: A:0.35, C:0.01, G:0.07, T:0.56
Consensus pattern (38 bp):
GAATTTTTATATATTTGAAAAAGAGATTTATATTTTTT
Found at i:41963222 original size:35 final size:35
Alignment explanation
Indices: 41963182--41963262 Score: 162
Period size: 35 Copynumber: 2.3 Consensus size: 35
41963172 GAGAGCGATT
41963182 GAGCAATACATGTTAGAAAATATAGTAGAAAAGCA
1 GAGCAATACATGTTAGAAAATATAGTAGAAAAGCA
41963217 GAGCAATACATGTTAGAAAATATAGTAGAAAAGCA
1 GAGCAATACATGTTAGAAAATATAGTAGAAAAGCA
41963252 GAGCAATACAT
1 GAGCAATACAT
41963263 AATTGAATCT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 46 1.00
ACGTcount: A:0.51, C:0.10, G:0.20, T:0.20
Consensus pattern (35 bp):
GAGCAATACATGTTAGAAAATATAGTAGAAAAGCA
Found at i:41973199 original size:153 final size:153
Alignment explanation
Indices: 41973026--41973312 Score: 459
Period size: 153 Copynumber: 1.9 Consensus size: 153
41973016 TATTTAAATG
*
41973026 TTTATTTGTTACTTTATAACACCATGGCTAAAATGAACATTTTATTTTTTAAAAGCACTTTTTGA
1 TTTATTTGTTACTTTATAACACCATGGCTAAAATGAACATTTTATTTCTTAAAAGCACTTTTTGA
** * *
41973091 CAACAATACT-AACACTTAAATCTTAAACTGAACTTTTCAAAACTACTCCTCAAAATCATTTTTC
66 CAACAATACTAAACACTTAAATCTTAAACCAAAATTTTCAAAACTACTCCTCAAAATCACTTTT-
41973155 TAAAATACTTTTTAAAATAGGCAT
130 TAAAATACTTTTTAAAATAGGCAT
* * *
41973179 TTTATTTGTTACTTTATAACACCATGTCTAAAATGAGCATTTTATTTCTTAAAATCACTTTTTGA
1 TTTATTTGTTACTTTATAACACCATGGCTAAAATGAACATTTTATTTCTTAAAAGCACTTTTTGA
* * *
41973244 CAGCAATATTAAACACTTAAATCTTAAACCAAAATTTTCAAAACTACTTCTCAAAATCACTTTTT
66 CAACAATACTAAACACTTAAATCTTAAACCAAAATTTTCAAAACTACTCCTCAAAATCACTTTTT
41973309 AAAA
131 AAAA
41973313 GCAGTTTGTC
Statistics
Matches: 122, Mismatches: 11, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
153 74 0.61
154 48 0.39
ACGTcount: A:0.38, C:0.17, G:0.05, T:0.39
Consensus pattern (153 bp):
TTTATTTGTTACTTTATAACACCATGGCTAAAATGAACATTTTATTTCTTAAAAGCACTTTTTGA
CAACAATACTAAACACTTAAATCTTAAACCAAAATTTTCAAAACTACTCCTCAAAATCACTTTTT
AAAATACTTTTTAAAATAGGCAT
Found at i:41976346 original size:31 final size:31
Alignment explanation
Indices: 41976311--41976373 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
41976301 TTATACTTGG
41976311 CTATATGCCTTTACTAGAGTAGCCTCACTAT
1 CTATATGCCTTTACTAGAGTAGCCTCACTAT
41976342 CTATATGCCTTTACTAGAGTAGCCTCACTAT
1 CTATATGCCTTTACTAGAGTAGCCTCACTAT
41976373 C
1 C
41976374 ACAACAGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.25, C:0.27, G:0.13, T:0.35
Consensus pattern (31 bp):
CTATATGCCTTTACTAGAGTAGCCTCACTAT
Found at i:41980818 original size:54 final size:53
Alignment explanation
Indices: 41980707--41980847 Score: 187
Period size: 54 Copynumber: 2.6 Consensus size: 53
41980697 CATCTCCTAA
* *
41980707 GGTATTTTGGTCATTTTACCCTATGGGGTATTTCGATCATTTTACCCTATAGC
1 GGTATTTCGGTCATTTTATCCTATGGGGTATTTCGATCATTTTACCCTATAGC
* *
41980760 GGTATTTCGATCATTTTATCCTATGAGGGTATTTC-AGTCATTTTACCTTATGAG-
1 GGTATTTCGGTCATTTTATCCTATG-GGGTATTTCGA-TCATTTTACCCTAT-AGC
*
41980814 GGTATTTCGGTCATTTTATCTTATGGCGGTATTT
1 GGTATTTCGGTCATTTTATCCTATGG-GGTATTT
41980848 TTTGTTATTT
Statistics
Matches: 78, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
53 24 0.31
54 52 0.67
55 2 0.03
ACGTcount: A:0.19, C:0.16, G:0.20, T:0.45
Consensus pattern (53 bp):
GGTATTTCGGTCATTTTATCCTATGGGGTATTTCGATCATTTTACCCTATAGC
Found at i:41980838 original size:27 final size:27
Alignment explanation
Indices: 41980707--41980831 Score: 173
Period size: 27 Copynumber: 4.7 Consensus size: 27
41980697 CATCTCCTAA
*
41980707 GGTATTTTGGTCATTTTACCCTATG-G
1 GGTATTTCGGTCATTTTACCCTATGAG
*
41980733 GGTATTTCGATCATTTTACCCTAT-AG
1 GGTATTTCGGTCATTTTACCCTATGAG
* *
41980759 CGGTATTTCGATCATTTTATCCTATGAG
1 -GGTATTTCGGTCATTTTACCCTATGAG
* *
41980787 GGTATTTCAGTCATTTTACCTTATGAG
1 GGTATTTCGGTCATTTTACCCTATGAG
41980814 GGTATTTCGGTCATTTTA
1 GGTATTTCGGTCATTTTA
41980832 TCTTATGGCG
Statistics
Matches: 88, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
26 23 0.26
27 63 0.72
28 2 0.02
ACGTcount: A:0.20, C:0.16, G:0.19, T:0.45
Consensus pattern (27 bp):
GGTATTTCGGTCATTTTACCCTATGAG
Found at i:41980844 original size:27 final size:26
Alignment explanation
Indices: 41980707--41980847 Score: 165
Period size: 27 Copynumber: 5.3 Consensus size: 26
41980697 CATCTCCTAA
*
41980707 GGTATTTTGGTCATTTTACCCTATGG
1 GGTATTTCGGTCATTTTACCCTATGG
* *
41980733 GGTATTTCGATCATTTTACCCTATAGC
1 GGTATTTCGGTCATTTTACCCTAT-GG
* *
41980760 GGTATTTCGATCATTTTATCCTATGAG
1 GGTATTTCGGTCATTTTACCCTATG-G
* *
41980787 GGTATTTCAGTCATTTTACCTTATGAG
1 GGTATTTCGGTCATTTTACCCTATG-G
* *
41980814 GGTATTTCGGTCATTTTATCTTATGG
1 GGTATTTCGGTCATTTTACCCTATGG
41980840 CGGTATTT
1 -GGTATTT
41980848 TTTGTTATTT
Statistics
Matches: 101, Mismatches: 11, Indels: 5
0.86 0.09 0.04
Matches are distributed among these distances:
26 24 0.24
27 77 0.76
ACGTcount: A:0.19, C:0.16, G:0.20, T:0.45
Consensus pattern (26 bp):
GGTATTTCGGTCATTTTACCCTATGG
Found at i:41983488 original size:36 final size:37
Alignment explanation
Indices: 41983439--41983534 Score: 106
Period size: 37 Copynumber: 2.6 Consensus size: 37
41983429 GTCTCCAATT
* * *
41983439 TCACATTTTAATTCAATTTCACTTTTTCACTTTCAA-
1 TCACAATTCAATTCAATTTCACTTTTCCACTTTCAAG
* *
41983475 TCACAATTCAATTCAAAATTCACTTTTCCATTTTCAAG
1 TCACAATTCAATTC-AATTTCACTTTTCCACTTTCAAG
*
41983513 TCA-ATATTCATTTCAATTTCAC
1 TCACA-ATTCAATTCAATTTCAC
41983535 ACATATATTC
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
36 12 0.24
37 27 0.54
38 11 0.22
ACGTcount: A:0.31, C:0.23, G:0.01, T:0.45
Consensus pattern (37 bp):
TCACAATTCAATTCAATTTCACTTTTCCACTTTCAAG
Found at i:41986239 original size:20 final size:20
Alignment explanation
Indices: 41986201--41986242 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
41986191 AAATAAACAC
**
41986201 ATAACTATTTATTTAATATT
1 ATAACTATTTAAATAATATT
*
41986221 ATAACTATTTAAATGATATT
1 ATAACTATTTAAATAATATT
41986241 AT
1 AT
41986243 TTAAATAGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (20 bp):
ATAACTATTTAAATAATATT
Found at i:41989683 original size:4 final size:4
Alignment explanation
Indices: 41989669--41989715 Score: 85
Period size: 4 Copynumber: 11.8 Consensus size: 4
41989659 GATGCACCTG
*
41989669 CATA AATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CAT
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CAT
41989716 GATCATCTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:41994848 original size:24 final size:24
Alignment explanation
Indices: 41994820--41994868 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
41994810 ACATAACTTA
41994820 CCATTTCATTTGCATAATATAAAG
1 CCATTTCATTTGCATAATATAAAG
41994844 CCATTTCATTTGCATAATATAAAG
1 CCATTTCATTTGCATAATATAAAG
41994868 C
1 C
41994869 ATAAGTATAA
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:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (24 bp):
CCATTTCATTTGCATAATATAAAG
Found at i:42004544 original size:16 final size:17
Alignment explanation
Indices: 42004525--42004556 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
42004515 TTAGGGAAGA
42004525 GAAATAA-TAGTTGGAT
1 GAAATAATTAGTTGGAT
42004541 GAAATAATTAGTTGGA
1 GAAATAATTAGTTGGA
42004557 ATAGATCCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.44, C:0.00, G:0.25, T:0.31
Consensus pattern (17 bp):
GAAATAATTAGTTGGAT
Found at i:42011298 original size:23 final size:23
Alignment explanation
Indices: 42011269--42011366 Score: 153
Period size: 23 Copynumber: 4.3 Consensus size: 23
42011259 ATAAGTGCCA
*
42011269 CACTGATATGTAGTCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
42011292 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
42011315 CACTG-GATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
42011337 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
42011360 CACTGAT
1 CACTGAT
42011367 CAATAACACT
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
22 20 0.29
23 48 0.71
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:42011334 original size:45 final size:45
Alignment explanation
Indices: 42011276--42011364 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
42011266 CCACACTGAT
* * *
42011276 ATGTAGTCGAAGCTACCACTGATATGTAGCCGAAGCTACCACTGG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
42011321 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
42011365 ATCAATAACA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.20
Consensus pattern (45 bp):
ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
Found at i:42015317 original size:41 final size:41
Alignment explanation
Indices: 42015260--42015446 Score: 295
Period size: 41 Copynumber: 4.6 Consensus size: 41
42015250 AGTAAGATGA
* * *
42015260 TTCAGACTTTAAGTCTAGCAGGCTTGACGCCGGTGAAATAT
1 TTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAT
* *
42015301 TTCAGACTTTACGTCTAGCAGGCTTGATGCCAGTGAAATAT
1 TTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAT
*
42015342 TTTAGACTTTACGTCTAGCAGGCTTAATGCCGGTG-AATAT
1 TTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAT
*
42015382 TTCTGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAT
1 TTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAT
*
42015423 TTCTGACTTTACGTCTAGCAGGCT
1 TTCAGACTTTACGTCTAGCAGGCT
42015447 AATTGCTGGT
Statistics
Matches: 137, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
40 38 0.28
41 99 0.72
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (41 bp):
TTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAT
Found at i:42015412 original size:81 final size:83
Alignment explanation
Indices: 42015263--42015446 Score: 293
Period size: 81 Copynumber: 2.3 Consensus size: 83
42015253 AAGATGATTC
* * *
42015263 AGACTTTAAGTCTAGCAGGCTTGACGCCGGTGAAATATTTCAGACTTTACGTCTAGCAGGCTTGA
1 AGACTTTACGTCTAGCAGGCTTAACGCCGGTGAAATATTTCAGACTTTACGTCTAGCAGGCTTAA
42015328 TGCCAGTGAAATATTT-T
66 TGCCAGTGAAATATTTCT
* *
42015345 AGACTTTACGTCTAGCAGGCTTAATGCCGGTG-AATATTTCTGACTTTACGTCTAGCAGGCTTAA
1 AGACTTTACGTCTAGCAGGCTTAACGCCGGTGAAATATTTCAGACTTTACGTCTAGCAGGCTTAA
*
42015409 TGCCGGTGAAATATTTCT
66 TGCCAGTGAAATATTTCT
42015427 -GACTTTACGTCTAGCAGGCT
1 AGACTTTACGTCTAGCAGGCT
42015447 AATTGCTGGT
Statistics
Matches: 95, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
81 65 0.68
82 30 0.32
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.33
Consensus pattern (83 bp):
AGACTTTACGTCTAGCAGGCTTAACGCCGGTGAAATATTTCAGACTTTACGTCTAGCAGGCTTAA
TGCCAGTGAAATATTTCT
Found at i:42015482 original size:122 final size:122
Alignment explanation
Indices: 42015264--42015501 Score: 293
Period size: 122 Copynumber: 2.0 Consensus size: 122
42015254 AGATGATTCA
* *
42015264 GACTTTAAGTCTAGCAGGCTTGACGCCGGTGAAATATTTCAGACTTTACGTCTAGCAGGCTTGAT
1 GACTTTAAGTCTAGCAGGCTTAACGCCGGTGAAATATTTCAGACTTTACGTCTAGCAGGCTTAAT
* * * *
42015329 GCCAGTGAAATATTTTAGACTTTACGTCTAGCAGGCTTAA-TGCCGGTGAATATTTCT
66 GCCAGTGAAATATATCAGACTTTAAGCCTAGCAGGC-TAAGTGCCGGTGAATATTTCT
* * *
42015386 GACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATATTTCTGACTTTACGTCTAGCAGGC-TAAT
1 GACTTTAAGTCTAGCAGGCTTAACGCCGGTGAAATATTTCAGACTTTACGTCTAGCAGGCTTAA-
** * * **
42015450 TGCTGGTGTACTGA-ATCAGGTTTTAAGCCTAGCAGGCTAAGTGCCGGTGAAT
65 TGCCAGTGAAAT-ATATCAGACTTTAAGCCTAGCAGGCTAAGTGCCGGTGAAT
42015502 CTGTTTAAAT
Statistics
Matches: 98, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
121 5 0.05
122 92 0.94
123 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (122 bp):
GACTTTAAGTCTAGCAGGCTTAACGCCGGTGAAATATTTCAGACTTTACGTCTAGCAGGCTTAAT
GCCAGTGAAATATATCAGACTTTAAGCCTAGCAGGCTAAGTGCCGGTGAATATTTCT
Found at i:42018327 original size:22 final size:22
Alignment explanation
Indices: 42018301--42018342 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
42018291 AATACGAGAA
42018301 AATATGGAACTAAAAAGAAATG
1 AATATGGAACTAAAAAGAAATG
*
42018323 AATATGGAACTAAGAAGAAA
1 AATATGGAACTAAAAAGAAA
42018343 AGTTGTCGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.60, C:0.05, G:0.19, T:0.17
Consensus pattern (22 bp):
AATATGGAACTAAAAAGAAATG
Found at i:42018972 original size:22 final size:22
Alignment explanation
Indices: 42018945--42018986 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
42018935 CAAAAGAATA
42018945 ATGATATAAACGTTTATCAATG
1 ATGATATAAACGTTTATCAATG
42018967 ATGATATAAACGTTTATCAA
1 ATGATATAAACGTTTATCAA
42018987 ACTCGTTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.36
Consensus pattern (22 bp):
ATGATATAAACGTTTATCAATG
Found at i:42020133 original size:4 final size:4
Alignment explanation
Indices: 42020124--42020285 Score: 61
Period size: 4 Copynumber: 38.8 Consensus size: 4
42020114 GGGAAAGGAG
* *
42020124 AAGA AAGA AAGA AAGAA AAGGA AAGGA GAGGG AAGA AAG- AA-A AAGA
1 AAGA AAGA AAGA AAG-A AA-GA AA-GA -AAGA AAGA AAGA AAGA AAGA
* *
42020170 AGGA AAGAA AAGGA AAGGA GAAGA AA-A AAGA AAGAA AACGA AGGA AAGAA
1 AAGA AAG-A AA-GA AA-GA -AAGA AAGA AAGA AAG-A AA-GA AAGA AAG-A
* **
42020220 AAGGA AAGGA GAAGA AA-A AAAA AAGA AAG- AAG- AAG- AAG- AAGA GGGA
1 AA-GA AA-GA -AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA
*
42020266 AAGAA AAGA AAGA AAAA AAG
1 AAG-A AAGA AAGA AAGA AAG
42020286 GTAATTTTTG
Statistics
Matches: 126, Mismatches: 15, Indels: 34
0.72 0.09 0.19
Matches are distributed among these distances:
3 22 0.17
4 54 0.43
5 41 0.33
6 9 0.07
ACGTcount: A:0.69, C:0.01, G:0.30, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:42020147 original size:10 final size:10
Alignment explanation
Indices: 42020126--42020281 Score: 71
Period size: 10 Copynumber: 15.9 Consensus size: 10
42020116 GAAAGGAGAA
42020126 GAAAG-AAA-
1 GAAAGAAAAG
42020134 GAAAGAAAAG
1 GAAAGAAAAG
* *
42020144 GAAAGGAGAG
1 GAAAGAAAAG
*
42020154 GGAAG-AAA-
1 GAAAGAAAAG
42020162 GAAA-AAGAAG
1 GAAAGAA-AAG
42020172 GAAAGAAAAG
1 GAAAGAAAAG
*
42020182 GAAAGGAGAA-
1 GAAA-GAAAAG
* *
42020192 GAAAAAAGAAA
1 GAAAGAA-AAG
*
42020203 GAAA-ACGAAG
1 GAAAGA-AAAG
42020213 GAAAGAAAAG
1 GAAAGAAAAG
*
42020223 GAAAGGAGAAG
1 GAAA-GAAAAG
* * *
42020234 AAAAAAAAAA
1 GAAAGAAAAG
42020244 GAAAGAAGAA-
1 GAAAGAA-AAG
*
42020254 G-AAGAAGAGG
1 GAAAGAA-AAG
42020264 GAAAGAAAA-
1 GAAAGAAAAG
42020273 GAAAGAAAA
1 GAAAGAAAA
42020282 AAAGGTAATT
Statistics
Matches: 113, Mismatches: 20, Indels: 29
0.70 0.12 0.18
Matches are distributed among these distances:
8 9 0.08
9 24 0.21
10 54 0.48
11 26 0.23
ACGTcount: A:0.69, C:0.01, G:0.31, T:0.00
Consensus pattern (10 bp):
GAAAGAAAAG
Found at i:42020201 original size:31 final size:31
Alignment explanation
Indices: 42020163--42020277 Score: 85
Period size: 31 Copynumber: 3.8 Consensus size: 31
42020153 GGGAAGAAAG
42020163 AAAAAGAAGGAAAGAAAAGGAAAGGAGAAGA
1 AAAAAGAAGGAAAGAAAAGGAAAGGAGAAGA
* * *
42020194 AAAAAGAAAGAAA-ACGAAGGAAA-GAAAAGGA
1 AAAAAGAAGGAAAGA-AAAGGAAAGGAGAA-GA
** * * * *
42020225 AAGGAGAAGAAAAAAAAAAGAAAGAAGAAG-
1 AAAAAGAAGGAAAGAAAAGGAAAGGAGAAGA
* *
42020255 AAGAAGAGGGAAAGAAAA-GAAAG
1 AAAAAGAAGGAAAGAAAAGGAAAG
42020278 AAAAAAAGGT
Statistics
Matches: 65, Mismatches: 15, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
29 5 0.08
30 19 0.29
31 37 0.57
32 4 0.06
ACGTcount: A:0.70, C:0.01, G:0.30, T:0.00
Consensus pattern (31 bp):
AAAAAGAAGGAAAGAAAAGGAAAGGAGAAGA
Found at i:42020213 original size:41 final size:41
Alignment explanation
Indices: 42020122--42020254 Score: 182
Period size: 41 Copynumber: 3.3 Consensus size: 41
42020112 GAGGGAAAGG
* **
42020122 AGAAGAAAGAAAGAAAGAAAAGGAAAGGAG-AG--GGAAGAA
1 AGAA-AAAGAAGGAAAGAAAAGGAAAGGAGAAGAAAAAAGAA
42020161 AGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAAAAAAGAA
1 AGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAAAAAAGAA
* *
42020202 AGAAAACGAAGGAAAGAAAAGGAAAGGAGAAGAAAAAAAAA
1 AGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAAAAAAGAA
42020243 AGAAAGAAGAAG
1 AGAAA-AAGAAG
42020255 AAGAAGAGGG
Statistics
Matches: 84, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
38 24 0.29
39 6 0.07
41 49 0.58
42 5 0.06
ACGTcount: A:0.68, C:0.01, G:0.31, T:0.00
Consensus pattern (41 bp):
AGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAAAAAAGAA
Found at i:42020235 original size:65 final size:61
Alignment explanation
Indices: 42020115--42020286 Score: 159
Period size: 65 Copynumber: 2.7 Consensus size: 61
42020105 AGAATGAGAG
* **
42020115 GGAAAGGAGAAGAAAGAAAGAAAGAAAAGGAAAGGAGAGGGAA-GAAAGAAAAAGAAGGAAAGAA
1 GGAAAGGAGAAGAAA-AAAGAAAGAAAA-G-AAGGAAAGAAAAGGAAAGAAAAAGAA--AAA-AA
42020179 AA
60 AA
* *
42020181 GGAAAGGAGAAGAAAAAAGAAAGAAAACGAAGGAAAGAAAAGGAAAGGAGAAGAAAAAAAAA
1 GGAAAGGAGAAGAAAAAAGAAAGAAAA-GAAGGAAAGAAAAGGAAAGAAAAAGAAAAAAAAA
* * * *
42020243 AGAAAGAAGAAGAAGAAGAGGGAAAGAAAAGAAAGAAA-AAAAGG
1 GGAAAGGAGAAGAA-AA-A-AGAAAGAAAAGAAGGAAAGAAAAGG
42020287 TAATTTTTGT
Statistics
Matches: 92, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
62 16 0.17
63 11 0.12
64 17 0.18
65 33 0.36
66 15 0.16
ACGTcount: A:0.67, C:0.01, G:0.32, T:0.00
Consensus pattern (61 bp):
GGAAAGGAGAAGAAAAAAGAAAGAAAAGAAGGAAAGAAAAGGAAAGAAAAAGAAAAAAAAA
Found at i:42020267 original size:41 final size:41
Alignment explanation
Indices: 42020122--42020285 Score: 178
Period size: 41 Copynumber: 4.0 Consensus size: 41
42020112 GAGGGAAAGG
* ** *
42020122 AGAAGAAAGAAAGAAAGAAAAGGAAAGGAG-AG--GGAAGAA
1 AGAA-AAAGAAGGAAAGAAAAGGAAAGGAGAAGAAAAAAAAA
*
42020161 AGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAAAAAAGAA
1 AGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAAAAAAAAA
*
42020202 AGAAAACGAAGGAAAGAAAAGGAAAGGAGAAGAAAAAAAAA
1 AGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAAAAAAAAA
* *
42020243 AGAAAGAAGAA-G-AAGAAGAGGGAAA-GAAAAGAAAGAAAAAA
1 AGAAA-AAGAAGGAAAGAA-AAGGAAAGGAGAAGAAA-AAAAAA
42020284 AG
1 AG
42020286 GTAATTTTTG
Statistics
Matches: 111, Mismatches: 8, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
38 24 0.22
39 6 0.05
40 13 0.12
41 64 0.58
42 4 0.04
ACGTcount: A:0.69, C:0.01, G:0.30, T:0.00
Consensus pattern (41 bp):
AGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAAAAAAAAA
Found at i:42020968 original size:160 final size:153
Alignment explanation
Indices: 42020650--42021560 Score: 736
Period size: 160 Copynumber: 5.8 Consensus size: 153
42020640 AATTTCAAAC
* * *
42020650 ATAATGTAAAATAATAAAATTA--AAAATTATGGTA-TTTT-TT-AAAGTAATAAAATGCGAAGA
1 ATAATGTAAAATAATAAAA-TACGAAAATAAT-ATATTTTTATTGAAAGTAATAAAATTCG-AGA
* * * **
42020710 AAA-AATACGAACAAATGGC-TGAAGTAAGAGTGTTTTACTAAATTTTTTAAAAGTTTAGAAATA
63 AAATAATACGAACAAAGGGCAGGAA-TAAG-GTTTTTTACTAAATTTTTTAAAA--ACAGAAATA
*
42020773 ATTAATACAAATATTTCAAAAAAAATGTACTGAA
124 ATTAAT---AA-ATTTCAAACAAAATGTACTGAA
*
42020807 ATAATATAAAATAATAAAATACGAAAATAATATATTTTTATTGAAAGTAATAAAATTCGAGAAAA
1 ATAATGTAAAATAATAAAATACGAAAATAATATATTTTTATTGAAAGTAATAAAATTCGAGAAAA
* * *
42020872 TAATACGAGCAAAGGGCAGGAATAAGGTTTTTTTTTACACTAAATTAATTTTAAAAACA-CACTA
66 TAATACGAACAAAGGGCAGGAATAAGG---TTTTTT--ACTAAATT--TTTTAAAAACAGAAAT-
* *
42020936 AATTAATAAATTTCAAACATAATGCACTGAA
123 AATTAATAAATTTCAAACAAAATGTACTGAA
* * * *
42020967 ATAATTTAAAATTATAAAATTA-G-AAATTATGATA-TTTT-TT-AAAGTAATAAAATGCGGAGA
1 ATAATGTAAAATAATAAAA-TACGAAAATAAT-ATATTTTTATTGAAAGTAATAAAATTC-GAGA
* * *
42021027 AAA-AATACGAACAATGGGC-CGAAGTAAGAGTCTTTTACTAAATTTTTTAAAAATTCAGAAATA
63 AAATAATACGAACAAAGGGCAGGAA-TAAG-GTTTTTTACTAAATTTTTTAAAAA--CAGAAATA
*
42021090 ATGAATACAAATATTTCAAACAAAATGTACTGAA
124 ATTAAT---AA-ATTTCAAACAAAATGTACTGAA
* *
42021124 ATAATATAAAATAATAAAATACGAAAATAATATATTTTCATTGAAAGTAATAAAATTCGAGAAAA
1 ATAATGTAAAATAATAAAATACGAAAATAATATATTTTTATTGAAAGTAATAAAATTCGAGAAAA
* * * *
42021189 TAATAC-AAGCAAAAGACAGGAATAAGGGTTTTTTTTACACTAAATTAATTTTAAAAACA-CACT
66 TAATACGAA-CAAAGGGCAGGAATAA-GG--TTTTTT--ACTAAATT--TTTTAAAAACAGAAAT
* *
42021252 AAATTAATAAATTTCAAACATAATGCACTGAA
123 -AATTAATAAATTTCAAACAAAATGTACTGAA
* * *
42021284 ATAATGTAAAATTATAAAATTA-G-AAATTATGATA-TTTT-TT-AAAGTAATAAAATGCGGAGA
1 ATAATGTAAAATAATAAAA-TACGAAAATAAT-ATATTTTTATTGAAAGTAATAAAATTC-GAGA
* * * * *
42021344 AAAAAATAAGAATAAAGGGC-CGAAGTAAGAGTCTTTTACTAAATTTTTTAAAAATTCAGAAATA
63 AAATAATACGAACAAAGGGCAGGAA-TAAG-GTTTTTTACTAAATTTTTTAAAAA--CAGAAATA
* *
42021408 ATGAATACAAATATTTCAAACAAAATGTATTGAA
124 ATTAAT---AA-ATTTCAAACAAAATGTACTGAA
* * *
42021442 ATAATGTAAAATAATAAAATACAAAAATAATATATTTTTATTAAAAGTAATAAAATTCGGGAAAA
1 ATAATGTAAAATAATAAAATACGAAAATAATATATTTTTATTGAAAGTAATAAAATTCGAGAAAA
* **
42021507 TTATACGAGTAAAGGGCAGGAATAAAGGGGTTTTTTACACTAAA-TTTTTAAAAA
66 TAATACGAACAAAGGGCAGGAAT-AA--GGTTTTTT--ACTAAATTTTTTAAAAA
42021561 TTTATATTGA
Statistics
Matches: 615, Mismatches: 72, Indels: 128
0.75 0.09 0.16
Matches are distributed among these distances:
151 9 0.01
152 9 0.01
153 16 0.03
154 18 0.03
155 7 0.01
156 14 0.02
157 115 0.19
158 92 0.15
159 51 0.08
160 164 0.27
161 34 0.06
162 16 0.03
163 15 0.02
164 38 0.06
166 17 0.03
ACGTcount: A:0.51, C:0.07, G:0.11, T:0.31
Consensus pattern (153 bp):
ATAATGTAAAATAATAAAATACGAAAATAATATATTTTTATTGAAAGTAATAAAATTCGAGAAAA
TAATACGAACAAAGGGCAGGAATAAGGTTTTTTACTAAATTTTTTAAAAACAGAAATAATTAATA
AATTTCAAACAAAATGTACTGAA
Found at i:42021238 original size:317 final size:317
Alignment explanation
Indices: 42020650--42021795 Score: 1542
Period size: 317 Copynumber: 3.7 Consensus size: 317
42020640 AATTTCAAAC
* * *
42020650 ATAATGTAAAATAATAAAATTAAAAATTATGGTATTTTTTAAAGTAATAAAATGCGAAGAAAAAA
1 ATAATGTAAAATTATAAAATTAAAAATTATGATATTTTTTAAAGTAATAAAATGCGGAGAAAAAA
* * * * *
42020715 TACGAACAAATGGCTGAAGTAAGAGTGTTTTACTAAATTTTTTAAAAGTTTAGAAATAATTAATA
66 TACGAACAAATGGCCGAAGTAAGAGTCTTTTACTAAATTTTTTAAAAATTCAGAAATAATGAATA
*
42020780 CAAATATTTCAAAAAAAATGTACTGAAATAATATAAAATAATAAAATACGAAAATAATATATTTT
131 CAAATATTTCAAACAAAATGTACTGAAATAATATAAAATAATAAAATACGAAAATAATATATTTT
*
42020845 TATTGAAAGTAATAAAATTCGAGAAAATAATACGAGCAAAGGGCAGGAATAAGGTTTTTTTTTAC
196 TATTGAAAGTAATAAAATTCGAGAAAATAATACGAGCAAAGGGCAGGAATAAGGGTTTTTTTTAC
42020910 ACTAAATTAATTTTAAAAACACACTAAATTAATAAATTTCAAACATAATGCACTGAA
261 ACTAAATTAATTTTAAAAACACACTAAATTAATAAATTTCAAACATAATGCACTGAA
* *
42020967 ATAATTTAAAATTATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCGGAGAAAAAA
1 ATAATGTAAAATTATAAAATTAAAAATTATGATATTTTTTAAAGTAATAAAATGCGGAGAAAAAA
42021032 TACGAAC-AATGGGCCGAAGTAAGAGTCTTTTACTAAATTTTTTAAAAATTCAGAAATAATGAAT
66 TACGAACAAAT-GGCCGAAGTAAGAGTCTTTTACTAAATTTTTTAAAAATTCAGAAATAATGAAT
42021096 ACAAATATTTCAAACAAAATGTACTGAAATAATATAAAATAATAAAATACGAAAATAATATATTT
130 ACAAATATTTCAAACAAAATGTACTGAAATAATATAAAATAATAAAATACGAAAATAATATATTT
* * * *
42021161 TCATTGAAAGTAATAAAATTCGAGAAAATAATACAAGCAAAAGACAGGAATAAGGGTTTTTTTTA
195 TTATTGAAAGTAATAAAATTCGAGAAAATAATACGAGCAAAGGGCAGGAATAAGGGTTTTTTTTA
42021226 CACTAAATTAATTTTAAAAACACACTAAATTAATAAATTTCAAACATAATGCACTGAA
260 CACTAAATTAATTTTAAAAACACACTAAATTAATAAATTTCAAACATAATGCACTGAA
*
42021284 ATAATGTAAAATTATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCGGAGAAAAAA
1 ATAATGTAAAATTATAAAATTAAAAATTATGATATTTTTTAAAGTAATAAAATGCGGAG-AAAAA
* * *
42021349 ATAAGAATAAAGGGCCGAAGTAAGAGTCTTTTACTAAATTTTTTAAAAATTCAGAAATAATGAAT
65 ATACGAACAAATGGCCGAAGTAAGAGTCTTTTACTAAATTTTTTAAAAATTCAGAAATAATGAAT
* * *
42021414 ACAAATATTTCAAACAAAATGTATTGAAATAATGTAAAATAATAAAATACAAAAATAATATATTT
130 ACAAATATTTCAAACAAAATGTACTGAAATAATATAAAATAATAAAATACGAAAATAATATATTT
* * * * *
42021479 TTATTAAAAGTAATAAAATTCGGGAAAATTATACGAGTAAAGGGCAGGAATAAAGGG-GTTTTTT
195 TTATTGAAAGTAATAAAATTCGAGAAAATAATACGAGCAAAGGGCAGGAAT-AAGGGTTTTTTTT
** * * * *
42021543 ACACTAAA-T--TTTT-AAAA-A-TTTATATT--GAAA-GT-AATA-A-AATTCA--GAA
259 ACACTAAATTAATTTTAAAAACACACTAAATTAATAAATTTCAA-ACATAATGCACTGAA
* * * * *
42021589 ATAAT-T---TTTA-AAAATACAAAAATAAT-ATTTTTTATTGAAAGTAATAAAATTCGG-GAAA
1 ATAATGTAAAATTATAAAAT-TAAAAATTATGATATTTT-TT-AAAGTAATAAAATGCGGAGAAA
* * * *
42021647 AAATACGAACAAATGGCCGAAATAAGGGTTTTTTACTAATTTTTTTTTTGAAAAA---AGAAATA
63 AAATACGAACAAATGGCCGAAGTAAGAGTCTTTTACTAA---ATTTTTT-AAAAATTCAGAAATA
* * * * * *
42021709 ATTAATAC----ACTTCAAACATAATGTAATAAAATAATGTAAAATAATAAAATACGAAAATAAT
124 ATGAATACAAATATTTCAAACAAAATGTACTGAAATAATATAAAATAATAAAATACGAAAATAAT
42021770 ATATTTTTATTGAAAGTAATAAAATT
189 ATATTTTTATTGAAAGTAATAAAATT
42021796 TAGGAAAATA
Statistics
Matches: 759, Mismatches: 58, Indels: 44
0.88 0.07 0.05
Matches are distributed among these distances:
297 73 0.10
300 47 0.06
301 27 0.04
302 16 0.02
303 6 0.01
304 6 0.01
305 8 0.01
307 5 0.01
308 3 0.00
309 2 0.00
310 3 0.00
312 5 0.01
313 1 0.00
314 4 0.01
315 4 0.01
316 3 0.00
317 356 0.47
318 183 0.24
319 7 0.01
ACGTcount: A:0.51, C:0.07, G:0.11, T:0.32
Consensus pattern (317 bp):
ATAATGTAAAATTATAAAATTAAAAATTATGATATTTTTTAAAGTAATAAAATGCGGAGAAAAAA
TACGAACAAATGGCCGAAGTAAGAGTCTTTTACTAAATTTTTTAAAAATTCAGAAATAATGAATA
CAAATATTTCAAACAAAATGTACTGAAATAATATAAAATAATAAAATACGAAAATAATATATTTT
TATTGAAAGTAATAAAATTCGAGAAAATAATACGAGCAAAGGGCAGGAATAAGGGTTTTTTTTAC
ACTAAATTAATTTTAAAAACACACTAAATTAATAAATTTCAAACATAATGCACTGAA
Found at i:42021602 original size:21 final size:22
Alignment explanation
Indices: 42021578--42021619 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
42021568 TGAAAGTAAT
* *
42021578 AAAATTCAGAAATAAT-TTTTA
1 AAAATACAAAAATAATATTTTA
42021599 AAAATACAAAAATAATATTTT
1 AAAATACAAAAATAATATTTT
42021620 TTATTGAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (22 bp):
AAAATACAAAAATAATATTTTA
Found at i:42026759 original size:20 final size:20
Alignment explanation
Indices: 42026734--42026771 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
42026724 TTTGATATTA
42026734 ACAATTAAAATAAATAAAGT
1 ACAATTAAAATAAATAAAGT
*
42026754 ACAATTAAAATAATTAAA
1 ACAATTAAAATAAATAAA
42026772 AATATTCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.26
Consensus pattern (20 bp):
ACAATTAAAATAAATAAAGT
Found at i:42039528 original size:50 final size:47
Alignment explanation
Indices: 42039427--42039551 Score: 126
Period size: 50 Copynumber: 2.5 Consensus size: 47
42039417 CATAGGGGGT
* *
42039427 CTTATGAAAGGTAATAAAAGCCCTACTCTCAGATGAATGGGGGGAGA
1 CTTATGAAAGGTAATAAAAGCCCTACTCTCAAATGAATGGAGGGAGA
* * *
42039474 CTTATGAAAGGTAATAATAATGACCTTACT-TCCAAATGCATGGAGGGAGG
1 CTTATGAAAGGTAATAA-AA-G-CCCTACTCT-CAAATGAATGGAGGGAGA
*
42039524 CTTATGGAAGGTGGTAATAAAAGCCCTA
1 CTTAT-GAA--AGGTAATAAAAGCCCTA
42039552 TTCCCAGACG
Statistics
Matches: 64, Mismatches: 7, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
47 17 0.27
48 2 0.03
49 2 0.03
50 29 0.45
51 4 0.06
52 2 0.03
53 8 0.12
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.24
Consensus pattern (47 bp):
CTTATGAAAGGTAATAAAAGCCCTACTCTCAAATGAATGGAGGGAGA
Found at i:42040734 original size:17 final size:16
Alignment explanation
Indices: 42040712--42040746 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
42040702 CATGAATCGC
42040712 TGGTCTAATATACATCA
1 TGGTCTAATATAC-TCA
42040729 TGGTCTAATATACTCA
1 TGGTCTAATATACTCA
42040745 TG
1 TG
42040747 AACAATTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.37
Consensus pattern (16 bp):
TGGTCTAATATACTCA
Found at i:42044524 original size:43 final size:43
Alignment explanation
Indices: 42044463--42044549 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
42044453 ATTCGATGTA
42044463 TGATCACCCGATTAAGCCATGATTGTATATGCCAATATAAATG
1 TGATCACCCGATTAAGCCATGATTGTATATGCCAATATAAATG
42044506 TGATCACCCGATTAAGCCATGATTGTATATGCCAATATAAATG
1 TGATCACCCGATTAAGCCATGATTGTATATGCCAATATAAATG
42044549 T
1 T
42044550 ATGAAATGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31
Consensus pattern (43 bp):
TGATCACCCGATTAAGCCATGATTGTATATGCCAATATAAATG
Found at i:42059592 original size:18 final size:18
Alignment explanation
Indices: 42059549--42059596 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
42059539 GGATTGTTCG
*
42059549 TCGCCATATTTGGATTGC
1 TCGCCATATTTGGACTGC
*
42059567 TCGTCATATTTGGACTG-
1 TCGCCATATTTGGACTGC
42059584 TCCGCCATATTTG
1 T-CGCCATATTTG
42059597 ATAGTTTGCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 1 0.04
18 25 0.96
ACGTcount: A:0.17, C:0.23, G:0.21, T:0.40
Consensus pattern (18 bp):
TCGCCATATTTGGACTGC
Found at i:42064586 original size:13 final size:13
Alignment explanation
Indices: 42064568--42064592 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42064558 TAATTTATAT
42064568 GTGTGAAAATTTC
1 GTGTGAAAATTTC
42064581 GTGTGAAAATTT
1 GTGTGAAAATTT
42064593 TATTGTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:42067014 original size:42 final size:43
Alignment explanation
Indices: 42066886--42067127 Score: 239
Period size: 43 Copynumber: 5.7 Consensus size: 43
42066876 GATATGATTT
*
42066886 CGTGTAAGACCACGTCTGGGATGTTGGCATCGACTTGTGTTTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTA
* * * *
42066929 CATGTAAGACCACGTCTAGGATGTTGGCATCAACTTGTGTTTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTA
42066972 CGTGTAAGACCACGTCTGGGACGTT-GCATCGACTTGTGTTTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTA
* * * * *
42067014 CGTGTAAAACCATGTTTGGGACATTGGCATCGTA-TT-TGATT-
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCG-ACTTGTGTTTA
* * * *
42067055 CAG-GTAAGACC-CTGTCTGGGACAG-TGGAATTGA-TATATGATTA
1 C-GTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGACT-TGTGTTTA
* *
42067098 CATGTAAGACCACGTTTGGGACGTTGGCAT
1 CGTGTAAGACCACGTCTGGGACGTTGGCAT
42067128 TGTACGAGAT
Statistics
Matches: 167, Mismatches: 21, Indels: 22
0.80 0.10 0.10
Matches are distributed among these distances:
40 2 0.01
41 23 0.14
42 48 0.29
43 92 0.55
44 2 0.01
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (43 bp):
CGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTA
Found at i:42067041 original size:85 final size:86
Alignment explanation
Indices: 42066886--42067044 Score: 239
Period size: 85 Copynumber: 1.9 Consensus size: 86
42066876 GATATGATTT
* * *
42066886 CGTGTAAGACCACGTCTGGGATGTTGGCATCGACTTGTGTTTACATGTAAGACCACGTCTAGGAT
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTACATGTAAAACCACGTCTAGGAC
*
42066951 GTTGGCATCAACTTGTGTTTA
66 ATTGGCATCAACTTGTGTTTA
* * * *
42066972 CGTGTAAGACCACGTCTGGGACGTT-GCATCGACTTGTGTTTACGTGTAAAACCATGTTTGGGAC
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTACATGTAAAACCACGTCTAGGAC
42067036 ATTGGCATC
66 ATTGGCATC
42067045 GTATTTGATT
Statistics
Matches: 65, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
85 41 0.63
86 24 0.37
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.31
Consensus pattern (86 bp):
CGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTACATGTAAAACCACGTCTAGGAC
ATTGGCATCAACTTGTGTTTA
Found at i:42067118 original size:43 final size:42
Alignment explanation
Indices: 42067011--42067119 Score: 105
Period size: 41 Copynumber: 2.6 Consensus size: 42
42067001 CGACTTGTGT
* * * * * *
42067011 TTACGTGTAAAACCATGTTTGGGACATTGGCATCGTATTTGA
1 TTACATGTAAGACCACGTTTGGGACAGTGGAATCGTATATGA
* * *
42067053 TT-CAGGTAAGACC-CTGTCTGGGACAGTGGAATTGATATATGA
1 TTACATGTAAGACCAC-GTTTGGGACAGTGGAATCG-TATATGA
42067095 TTACATGTAAGACCACGTTTGGGAC
1 TTACATGTAAGACCACGTTTGGGAC
42067120 GTTGGCATTG
Statistics
Matches: 52, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
41 23 0.44
42 10 0.19
43 18 0.35
44 1 0.02
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.31
Consensus pattern (42 bp):
TTACATGTAAGACCACGTTTGGGACAGTGGAATCGTATATGA
Found at i:42070563 original size:20 final size:20
Alignment explanation
Indices: 42070525--42070563 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
42070515 ATTTTAACTA
*
42070525 CTTAATTAACTTAATTTAAC
1 CTTAATTAACTTAAATTAAC
42070545 CTTAATTAA-TTAAAATTAA
1 CTTAATTAACTT-AAATTAA
42070564 TCACCATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (20 bp):
CTTAATTAACTTAAATTAAC
Found at i:42072265 original size:24 final size:24
Alignment explanation
Indices: 42072237--42072284 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
42072227 ATTAGGAGAT
42072237 GGTGAATGATGATGACTTTTCCAC
1 GGTGAATGATGATGACTTTTCCAC
42072261 GGTGAATGATGATGACTTTTCCAC
1 GGTGAATGATGATGACTTTTCCAC
42072285 TAAGTATGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (24 bp):
GGTGAATGATGATGACTTTTCCAC
Found at i:42072293 original size:24 final size:24
Alignment explanation
Indices: 42072240--42072294 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
42072230 AGGAGATGGT
**
42072240 GAATGATGATGACTTTTCCACGGT
1 GAATGATGATGACTTTTCCACGAA
*
42072264 GAATGATGATGACTTTTCCACTAA
1 GAATGATGATGACTTTTCCACGAA
*
42072288 GTATGAT
1 GAATGAT
42072295 TAATAATTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.35
Consensus pattern (24 bp):
GAATGATGATGACTTTTCCACGAA
Found at i:42074800 original size:14 final size:14
Alignment explanation
Indices: 42074781--42074807 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
42074771 AAAGGGGATG
42074781 AAATCAGTGTAAAA
1 AAATCAGTGTAAAA
42074795 AAATCAGTGTAAA
1 AAATCAGTGTAAA
42074808 GAGAAAAAAT
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:0.56, C:0.07, G:0.15, T:0.22
Consensus pattern (14 bp):
AAATCAGTGTAAAA
Found at i:42075671 original size:24 final size:24
Alignment explanation
Indices: 42075642--42075891 Score: 155
Period size: 24 Copynumber: 10.7 Consensus size: 24
42075632 GTTTATTGTA
*
42075642 TATTATTATTTTAGATTTATCATG
1 TATTATTATTTTAAATTTATCATG
* *
42075666 TTTTATTATTTGT-AATTTATCA-A
1 TATTATTATTT-TAAATTTATCATG
* *
42075689 TATTATTATTTTAAATTCATCGT-
1 TATTATTATTTTAAATTTATCATG
**
42075712 TAACATTATTTTAAATTTATCATG
1 TATTATTATTTTAAATTTATCATG
*
42075736 TA-TATTTATTTCAAATTTATCAT-
1 TATTA-TTATTTTAAATTTATCATG
* * *
42075759 TAATA-T-TTTTAAATTTATTATA
1 TATTATTATTTTAAATTTATCATG
* ** *
42075781 TACTATTATTTTGGATTTATCACG
1 TATTATTATTTTAAATTTATCATG
* *
42075805 TATGATTATTCTAGAA-TTATCAT-
1 TATTATTATTTTA-AATTTATCATG
* * * *
42075828 CA-AAAT-TTTTAAATTTTAT-ATA
1 TATTATTATTTTAAA-TTTATCATG
* *
42075850 TATTATTATTTTAAATTTATTATA
1 TATTATTATTTTAAATTTATCATG
*
42075874 TATTATTTATTGTAAATT
1 TATTA-TTATTTTAAATT
42075892 ATTCAATTCA
Statistics
Matches: 175, Mismatches: 34, Indels: 33
0.72 0.14 0.14
Matches are distributed among these distances:
20 2 0.01
21 19 0.11
22 13 0.07
23 48 0.27
24 80 0.46
25 13 0.07
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.56
Consensus pattern (24 bp):
TATTATTATTTTAAATTTATCATG
Found at i:42075731 original size:46 final size:46
Alignment explanation
Indices: 42075646--42075866 Score: 55
Period size: 45 Copynumber: 4.8 Consensus size: 46
42075636 ATTGTATATT
* * * * * **
42075646 ATTATTTTAGATTTATCATGTTTTATTATTTGT-AATTTATCAATATT
1 ATTATTTTAAATTTATCA-ATATTATTATTT-TAAATTCATCATTAAC
* ** ** *
42075693 ATTATTTTAAATTCATCGTTAACATTATTTTAAATTTATCATGTATA-
1 ATTATTTTAAATTTATCAATATTATTATTTTAAATTCATCAT-TA-AC
* * * * * *
42075740 TTTATTTCAAATTTATCATTAATA-T-TTTTAAATTTATTA-TATAC
1 ATTATTTTAAATTTATCAATATTATTATTTTAAATTCATCATTA-AC
** * * * *
42075784 TATTATTTTGGATTTATCACGTATGATTATTCTAGAATT-ATCATCAA-
1 -ATTATTTTAAATTTATCA-ATATTATTATTTTA-AATTCATCATTAAC
*
42075831 AAT-TTTTAAATTTTAT-ATATATTATTATTTTAAATT
1 ATTATTTTAAA-TTTATCA-ATATTATTATTTTAAATT
42075867 TATTATATAT
Statistics
Matches: 131, Mismatches: 32, Indels: 25
0.70 0.17 0.13
Matches are distributed among these distances:
43 4 0.03
44 4 0.03
45 45 0.34
46 28 0.21
47 37 0.28
48 8 0.06
49 5 0.04
ACGTcount: A:0.34, C:0.06, G:0.05, T:0.55
Consensus pattern (46 bp):
ATTATTTTAAATTTATCAATATTATTATTTTAAATTCATCATTAAC
Found at i:42075814 original size:69 final size:69
Alignment explanation
Indices: 42075608--42075881 Score: 217
Period size: 69 Copynumber: 4.0 Consensus size: 69
42075598 TATTATCATT
* * * * * *
42075608 AAATTAATCATTAATATTATCTAAGTTTAT-TGTATATTATTATTTTAGATTTATCATGTTTTAT
1 AAATTTATCATTAATATT-TTTAAATTTATATATATACTATTATTTTAGATTTATCATG-TATAT
*
42075672 TATTTG
64 TATTTC
* * * * * *
42075678 TAATTTATCAATATTATTATTTTAAATTCATCGT-TA-AC-ATTATTTTAAATTTATCATGTATA
1 AAATTTATCATTAATA-T-TTTTAAATTTAT-ATATATACTATTATTTTAGATTTATCATGTATA
42075740 TTTATTTC
63 -TTATTTC
* *
42075748 AAATTTATCATTAATATTTTTAAATTTAT-TATATACTATTATTTTGGATTTATCACGTATGATT
1 AAATTTATCATTAATATTTTTAAATTTATATATATACTATTATTTTAGATTTATCATGTAT-ATT
42075812 A-TTC
65 ATTTC
* * * * *
42075816 TAGAA-TTATCATCAAAATTTTTAAATTT-TATATATATTATTATTTTAAATTTAT--TATATAT
1 -A-AATTTATCATTAATATTTTTAAATTTATATATATACTATTATTTTAGATTTATCATGTATAT
42075877 TATTT
64 TATTT
42075882 ATTGTAAATT
Statistics
Matches: 166, Mismatches: 25, Indels: 29
0.75 0.11 0.13
Matches are distributed among these distances:
66 5 0.03
67 7 0.04
68 17 0.10
69 70 0.42
70 53 0.32
71 10 0.06
72 3 0.02
73 1 0.01
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.55
Consensus pattern (69 bp):
AAATTTATCATTAATATTTTTAAATTTATATATATACTATTATTTTAGATTTATCATGTATATTA
TTTC
Found at i:42075862 original size:17 final size:18
Alignment explanation
Indices: 42075840--42075877 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
42075830 AAATTTTTAA
*
42075840 ATTTTATATATATTAT-T
1 ATTTTAAATATATTATAT
*
42075857 ATTTTAAATTTATTATAT
1 ATTTTAAATATATTATAT
42075875 ATT
1 ATT
42075878 ATTTATTGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
ATTTTAAATATATTATAT
Found at i:42085574 original size:18 final size:18
Alignment explanation
Indices: 42085551--42085593 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
42085541 ACCCAATCCA
*
42085551 AACCCAAGTATACAACCC
1 AACCCAAGTACACAACCC
* *
42085569 AACCCAATTACCCAACCC
1 AACCCAAGTACACAACCC
42085587 AACCCAA
1 AACCCAA
42085594 TCATAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.44, G:0.02, T:0.09
Consensus pattern (18 bp):
AACCCAAGTACACAACCC
Found at i:42085711 original size:9 final size:9
Alignment explanation
Indices: 42085697--42085781 Score: 89
Period size: 9 Copynumber: 9.4 Consensus size: 9
42085687 GTAGTGATTC
42085697 AATTCGGTT
1 AATTCGGTT
42085706 AATTCGGTT
1 AATTCGGTT
**
42085715 AATTCGGGC
1 AATTCGGTT
42085724 AATTCGGTT
1 AATTCGGTT
* *
42085733 AATTTGGGT
1 AATTCGGTT
* *
42085742 AATCCGATT
1 AATTCGGTT
*
42085751 AATTCGGCT
1 AATTCGGTT
*
42085760 AATTCGGGT
1 AATTCGGTT
*
42085769 AATTCAGTT
1 AATTCGGTT
42085778 AATT
1 AATT
42085782 TTTAACCAAA
Statistics
Matches: 60, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 60 1.00
ACGTcount: A:0.26, C:0.13, G:0.22, T:0.39
Consensus pattern (9 bp):
AATTCGGTT
Found at i:42088414 original size:15 final size:14
Alignment explanation
Indices: 42088393--42088428 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
42088383 ATAATCCTTA
*
42088393 ATAATTATCTTAAT
1 ATAATTATCCTAAT
42088407 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
42088422 ATAATTA
1 ATAATTA
42088429 AAATAGAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:42089685 original size:19 final size:19
Alignment explanation
Indices: 42089634--42089686 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
42089624 GTAAGTATGA
*
42089634 TTTTTTATTTTATCTTAGT
1 TTTTTTATGTTATCTTAGT
*
42089653 TTTCATTATG-TATCTTAGT
1 TTT-TTTATGTTATCTTAGT
42089672 TTTTTTATGTTATCT
1 TTTTTTATGTTATCT
42089687 CAAGGTAGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 5 0.17
19 20 0.69
20 4 0.14
ACGTcount: A:0.17, C:0.08, G:0.08, T:0.68
Consensus pattern (19 bp):
TTTTTTATGTTATCTTAGT
Found at i:42092799 original size:45 final size:45
Alignment explanation
Indices: 42092724--42092809 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
42092714 TATACGCCTA
*
42092724 AAATGAGTAAGACCATAGCTAAAAGATGCTATTACATCATGATAT
1 AAATGAGTAAGACCATAGCTAAAAGATGCTATGACATCATGATAT
* * *
42092769 AAATGAGTAAGACCATGGCTGAAAGGTGCTATGACATCATG
1 AAATGAGTAAGACCATAGCTAAAAGATGCTATGACATCATG
42092810 TGAAAGTACG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.24
Consensus pattern (45 bp):
AAATGAGTAAGACCATAGCTAAAAGATGCTATGACATCATGATAT
Found at i:42092992 original size:27 final size:27
Alignment explanation
Indices: 42092962--42093053 Score: 114
Period size: 27 Copynumber: 3.4 Consensus size: 27
42092952 TCGACGGGAC
*
42092962 GTTAAACACGGGATAGTCTGTTAGGAT
1 GTTAAACACGGGATAGTCTGATAGGAT
* * *
42092989 GTTAAACA-GGGTATAGCCTAATGGGAT
1 GTTAAACACGGG-ATAGTCTGATAGGAT
* *
42093016 GTTAAATACAGGATAGTCTGATAGGAT
1 GTTAAACACGGGATAGTCTGATAGGAT
42093043 GTTAAACACGG
1 GTTAAACACGG
42093054 TGTAGTACTC
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
26 3 0.06
27 47 0.90
28 2 0.04
ACGTcount: A:0.34, C:0.11, G:0.28, T:0.27
Consensus pattern (27 bp):
GTTAAACACGGGATAGTCTGATAGGAT
Found at i:42100577 original size:27 final size:27
Alignment explanation
Indices: 42100547--42100648 Score: 141
Period size: 27 Copynumber: 3.8 Consensus size: 27
42100537 ATCATAGATT
*
42100547 GTCCGATAGGACGTTAAACACGGGATA
1 GTCCGATGGGACGTTAAACACGGGATA
*
42100574 GTCCGATGGGACGTTAAACACGAGATA
1 GTCCGATGGGACGTTAAACACGGGATA
* * * *
42100601 GTCCGACGGGAAGTTAAACATGGCATA
1 GTCCGATGGGACGTTAAACACGGGATA
*
42100628 GTCTGATGGGACGTTAAACAC
1 GTCCGATGGGACGTTAAACAC
42100649 AAGGTAGTCC
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 64 1.00
ACGTcount: A:0.32, C:0.19, G:0.29, T:0.20
Consensus pattern (27 bp):
GTCCGATGGGACGTTAAACACGGGATA
Found at i:42101855 original size:13 final size:12
Alignment explanation
Indices: 42101826--42101874 Score: 52
Period size: 11 Copynumber: 4.3 Consensus size: 12
42101816 AGACAAAAAT
42101826 AAAAAC-ACAAG
1 AAAAACTACAAG
42101837 -AAAACTACAGAG
1 AAAAACTACA-AG
42101849 AAAAACTA-AAG
1 AAAAACTACAAG
*
42101860 AAAACCTA-AAG
1 AAAAACTACAAG
42101871 AAAA
1 AAAA
42101875 TGAAAACTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
10 5 0.15
11 19 0.56
12 3 0.09
13 7 0.21
ACGTcount: A:0.69, C:0.14, G:0.10, T:0.06
Consensus pattern (12 bp):
AAAAACTACAAG
Found at i:42103819 original size:9 final size:10
Alignment explanation
Indices: 42103799--42103827 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
42103789 CATTTATGTT
42103799 TTTCTATTCA
1 TTTCTATTCA
42103809 TTTCT-TTCA
1 TTTCTATTCA
42103818 TTTCTATTCA
1 TTTCTATTCA
42103828 AACACGCAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.17, C:0.21, G:0.00, T:0.62
Consensus pattern (10 bp):
TTTCTATTCA
Found at i:42104281 original size:128 final size:128
Alignment explanation
Indices: 42104053--42104309 Score: 514
Period size: 128 Copynumber: 2.0 Consensus size: 128
42104043 TTGTCATTAG
42104053 TGTGTTACCCTCATAGGATATCTTTGATCTCCTTGGGATAATATTCATTCTCACAGTATGATCCT
1 TGTGTTACCCTCATAGGATATCTTTGATCTCCTTGGGATAATATTCATTCTCACAGTATGATCCT
42104118 ATTTTATCTCATGGTAACCATTACATCTTCCTTCATTAAAAGTCAATCATTATCAATTAGTGA
66 ATTTTATCTCATGGTAACCATTACATCTTCCTTCATTAAAAGTCAATCATTATCAATTAGTGA
42104181 TGTGTTACCCTCATAGGATATCTTTGATCTCCTTGGGATAATATTCATTCTCACAGTATGATCCT
1 TGTGTTACCCTCATAGGATATCTTTGATCTCCTTGGGATAATATTCATTCTCACAGTATGATCCT
42104246 ATTTTATCTCATGGTAACCATTACATCTTCCTTCATTAAAAGTCAATCATTATCAATTAGTGA
66 ATTTTATCTCATGGTAACCATTACATCTTCCTTCATTAAAAGTCAATCATTATCAATTAGTGA
42104309 T
1 T
42104310 CATGTCATCC
Statistics
Matches: 129, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
128 129 1.00
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (128 bp):
TGTGTTACCCTCATAGGATATCTTTGATCTCCTTGGGATAATATTCATTCTCACAGTATGATCCT
ATTTTATCTCATGGTAACCATTACATCTTCCTTCATTAAAAGTCAATCATTATCAATTAGTGA
Found at i:42105742 original size:31 final size:31
Alignment explanation
Indices: 42105695--42105815 Score: 161
Period size: 31 Copynumber: 3.9 Consensus size: 31
42105685 TATGTGATAG
* * *
42105695 TACATGGTATACATATGCAATTATGAATTAT
1 TACAGGGTATAAATATGCAATTATGAATGAT
* * *
42105726 TACAGGGTATAAATATGTAGTTATGAATGGT
1 TACAGGGTATAAATATGCAATTATGAATGAT
*
42105757 TACAGGGTATAAATATACAATTATGAATGAT
1 TACAGGGTATAAATATGCAATTATGAATGAT
* *
42105788 TACAGGGTATGAATATGCAAATATGAAT
1 TACAGGGTATAAATATGCAATTATGAAT
42105816 AGTTGATGGC
Statistics
Matches: 77, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 77 1.00
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.34
Consensus pattern (31 bp):
TACAGGGTATAAATATGCAATTATGAATGAT
Found at i:42105800 original size:17 final size:17
Alignment explanation
Indices: 42105747--42105801 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
42105737 AATATGTAGT
*
42105747 TATGAATGGTTACAGGG
1 TATGAATGATTACAGGG
* **
42105764 TATAAAT-A-TACA-AT
1 TATGAATGATTACAGGG
42105778 TATGAATGATTACAGGG
1 TATGAATGATTACAGGG
42105795 TATGAAT
1 TATGAAT
42105802 ATGCAAATAT
Statistics
Matches: 28, Mismatches: 7, Indels: 6
0.68 0.17 0.15
Matches are distributed among these distances:
14 6 0.21
15 5 0.18
16 4 0.14
17 13 0.46
ACGTcount: A:0.40, C:0.05, G:0.22, T:0.33
Consensus pattern (17 bp):
TATGAATGATTACAGGG
Found at i:42108384 original size:9 final size:9
Alignment explanation
Indices: 42108370--42108406 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
42108360 CAACTAATTA
42108370 TAACAATAT
1 TAACAATAT
*
42108379 TAACAACATT
1 TAACAATA-T
42108389 TAACAATAT
1 TAACAATAT
42108398 TAACAATAT
1 TAACAATAT
42108407 CACTAACTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 17 0.68
10 8 0.32
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (9 bp):
TAACAATAT
Found at i:42110239 original size:24 final size:23
Alignment explanation
Indices: 42110212--42110256 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
42110202 TTACAAATAG
*
42110212 AAAATAAAGTTAAGTAAGAAATGA
1 AAAATAAAATTAAGTAA-AAATGA
42110236 AAAATAAAATTAAGTAAAAAT
1 AAAATAAAATTAAGTAAAAAT
42110257 TGTCCATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.67, C:0.00, G:0.11, T:0.22
Consensus pattern (23 bp):
AAAATAAAATTAAGTAAAAATGA
Found at i:42114798 original size:51 final size:51
Alignment explanation
Indices: 42114725--42114918 Score: 214
Period size: 51 Copynumber: 3.8 Consensus size: 51
42114715 CAATGATGTT
* * *
42114725 CGGTTCACATAGTAGCCTGCACATAGTACTACACATGTGA-CTATTACCATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCTA-TACCATC
** ** * * * *
42114776 CACTACACGTAGTAGCAAGCACATAGTACTACACACGTGATCGAAACTATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCTATACCATC
* * *
42114827 CGGTACGCATAGTAGCCTGCACATAGTACTACACATGTGACCTAT--CATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCTATACCATC
*
42114876 CTGGTACACGTAGTAGCTTGCACATAGTACTACACACGTGACC
1 C-GGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACC
42114919 ATCACTTTCA
Statistics
Matches: 116, Mismatches: 25, Indels: 5
0.79 0.17 0.03
Matches are distributed among these distances:
49 4 0.03
50 37 0.32
51 73 0.63
52 2 0.02
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.24
Consensus pattern (51 bp):
CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCTATACCATC
Found at i:42114915 original size:101 final size:101
Alignment explanation
Indices: 42114732--42114916 Score: 293
Period size: 101 Copynumber: 1.8 Consensus size: 101
42114722 GTTCGGTTCA
42114732 CATAGTAGCCTGCACATAGTACTACACATGTGACTATTACCATCCACTACACGTAGTAGCAAGCA
1 CATAGTAGCCTGCACATAGTACTACACATGTGACTATTA-CATCCACTACACGTAGTAGCAAGCA
42114797 CATAGTACTACACACGTGATCGAAACTATCCGGTACG
65 CATAGTACTACACACGTGATCGAAACTATCCGGTACG
** **
42114834 CATAGTAGCCTGCACATAGTACTACACATGTGACCTA-T-CATCCTGGTACACGTAGTAGCTTGC
1 CATAGTAGCCTGCACATAGTACTACACATGTGA-CTATTACATCC-ACTACACGTAGTAGCAAGC
42114897 ACATAGTACTACACACGTGA
64 ACATAGTACTACACACGTGA
42114917 CCATCACTTT
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
100 5 0.06
101 35 0.45
102 34 0.44
103 3 0.04
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATGTGACTATTACATCCACTACACGTAGTAGCAAGCAC
ATAGTACTACACACGTGATCGAAACTATCCGGTACG
Found at i:42136644 original size:21 final size:21
Alignment explanation
Indices: 42136598--42136644 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
42136588 AATTTTCAAT
*
42136598 ATTATTAAATATATATTTATA
1 ATTAATAAATATATATTTATA
* *
42136619 TTTAATAAATTATGTATTT-TA
1 ATTAATAAA-TATATATTTATA
42136640 ATTAA
1 ATTAA
42136645 ATCATTTAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
ATTAATAAATATATATTTATA
Found at i:42136687 original size:16 final size:18
Alignment explanation
Indices: 42136666--42136702 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
42136656 TACTAATATT
42136666 ATTAATAA-T-TTTTAAA
1 ATTAATAATTATTTTAAA
42136682 ATTAATAATTATTTTAAA
1 ATTAATAATTATTTTAAA
42136700 ATT
1 ATT
42136703 TAAATAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.42
17 1 0.05
18 10 0.53
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTAATAATTATTTTAAA
Found at i:42136710 original size:20 final size:18
Alignment explanation
Indices: 42136667--42136723 Score: 64
Period size: 20 Copynumber: 3.1 Consensus size: 18
42136657 ACTAATATTA
42136667 TTAATAAT-TTTTAAAA-
1 TTAATAATATTTTAAAAT
42136683 TTAATAATTATTTTAAAAT
1 TTAATAA-TATTTTAAAAT
*
42136702 TTAAATAATATTCTTAATAT
1 TT-AATAATATT-TTAAAAT
42136722 TT
1 TT
42136724 TATATTAACA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
16 7 0.20
17 1 0.03
18 8 0.23
19 6 0.17
20 13 0.37
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
TTAATAATATTTTAAAAT
Found at i:42141297 original size:65 final size:65
Alignment explanation
Indices: 42141217--42141347 Score: 262
Period size: 65 Copynumber: 2.0 Consensus size: 65
42141207 CGACCATGAG
42141217 TAAGCTTCTTCATCCACTTATTCATCCAAAATAGTTATGGTATCATGTAAATTTCCACCCTTTTT
1 TAAGCTTCTTCATCCACTTATTCATCCAAAATAGTTATGGTATCATGTAAATTTCCACCCTTTTT
42141282 TAAGCTTCTTCATCCACTTATTCATCCAAAATAGTTATGGTATCATGTAAATTTCCACCCTTTTT
1 TAAGCTTCTTCATCCACTTATTCATCCAAAATAGTTATGGTATCATGTAAATTTCCACCCTTTTT
42141347 T
1 T
42141348 GTTAAACTCC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.27, C:0.23, G:0.08, T:0.42
Consensus pattern (65 bp):
TAAGCTTCTTCATCCACTTATTCATCCAAAATAGTTATGGTATCATGTAAATTTCCACCCTTTTT
Found at i:42143476 original size:41 final size:40
Alignment explanation
Indices: 42143431--42143513 Score: 123
Period size: 41 Copynumber: 2.0 Consensus size: 40
42143421 ATTTTTTTGT
**
42143431 TTAGGGTTTTGTTAAAATAATTTAGGTTTAGGG-TTGTAGGG
1 TTAGGGTTTCATTAAAATAATTTAGGTTT-GGGATT-TAGGG
42143472 TTAGGGTTTCATTAAAATAATTTAGGTTTGGGATTTAGGG
1 TTAGGGTTTCATTAAAATAATTTAGGTTTGGGATTTAGGG
42143512 TT
1 TT
42143514 TAAGAATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
40 10 0.26
41 29 0.74
ACGTcount: A:0.25, C:0.01, G:0.29, T:0.45
Consensus pattern (40 bp):
TTAGGGTTTCATTAAAATAATTTAGGTTTGGGATTTAGGG
Found at i:42143647 original size:34 final size:34
Alignment explanation
Indices: 42143550--42143648 Score: 96
Period size: 34 Copynumber: 2.9 Consensus size: 34
42143540 TTTAGAGTTA
* * *
42143550 TTTTTAAG-AATTTAATTAAACTAGGTTTTAAGG
1 TTTTTAAGAAAATTAATTAAATTAGGGTTTAAGG
* * **
42143583 GTTTTAA-ATAAATTAATTAATTTAAAGTTT-AGAG
1 TTTTTAAGA-AAATTAATTAAATTAGGGTTTAAG-G
42143617 TTTTTAAGAAAATTAATTAAATTAGGGTTTAA
1 TTTTTAAGAAAATTAATTAAATTAGGGTTTAA
42143649 TTTAAAAAAA
Statistics
Matches: 50, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
33 8 0.16
34 40 0.80
35 2 0.04
ACGTcount: A:0.41, C:0.01, G:0.13, T:0.44
Consensus pattern (34 bp):
TTTTTAAGAAAATTAATTAAATTAGGGTTTAAGG
Done.