Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 96 of 208
Found at i:28660747 original size:15 final size:14
Alignment explanation
Indices: 28660729--28660776 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 14
28660719 AAGTGAAGTG
28660729 AAAAAA-TGAGAAGA
1 AAAAAATTGA-AAGA
28660743 AAAAAATTGAAAAGGA
1 AAAAAATTG-AAA-GA
28660759 AAAGAAATTGAAAGA
1 AAA-AAATTGAAAGA
28660774 AAA
1 AAA
28660777 GAGAAAGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
14 6 0.20
15 9 0.30
16 9 0.30
17 6 0.20
ACGTcount: A:0.71, C:0.00, G:0.19, T:0.10
Consensus pattern (14 bp):
AAAAAATTGAAAGA
Found at i:28660777 original size:15 final size:16
Alignment explanation
Indices: 28660739--28660778 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
28660729 AAAAAATGAG
28660739 AAGAAAA-AAATTGAA
1 AAGAAAAGAAATTGAA
28660754 AAGGAAAAGAAATTG-A
1 AA-GAAAAGAAATTGAA
28660770 AAGAAAAGA
1 AAGAAAAGA
28660779 GAAAGAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 9 0.39
16 8 0.35
17 6 0.26
ACGTcount: A:0.70, C:0.00, G:0.20, T:0.10
Consensus pattern (16 bp):
AAGAAAAGAAATTGAA
Found at i:28660781 original size:17 final size:17
Alignment explanation
Indices: 28660742--28660782 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
28660732 AAATGAGAAG
*
28660742 AAAA-AAATTGAAAAGG
1 AAAAGAAATTGAAAAGA
28660758 AAAAGAAATTG-AAAGA
1 AAAAGAAATTGAAAAGA
28660774 AAAGAGAAA
1 AAA-AGAAA
28660783 GAAAAAGAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.71, C:0.00, G:0.20, T:0.10
Consensus pattern (17 bp):
AAAAGAAATTGAAAAGA
Found at i:28663042 original size:26 final size:27
Alignment explanation
Indices: 28663013--28663065 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
28663003 ATGACCGTAG
*
28663013 TGCCCCTAGAAGGTAAATGACT-ATTT
1 TGCCCCTAGAAGGTAAATAACTGATTT
* *
28663039 TGCCCCTCGAGGGTAAATAACTGATTT
1 TGCCCCTAGAAGGTAAATAACTGATTT
28663066 GTGTTATAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (27 bp):
TGCCCCTAGAAGGTAAATAACTGATTT
Found at i:28668168 original size:16 final size:16
Alignment explanation
Indices: 28668147--28668179 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
28668137 GGAAGATTTG
28668147 AAAATGA-TTGAGAAAA
1 AAAATGAGTTG-GAAAA
28668163 AAAATGAGTTGGAAAA
1 AAAATGAGTTGGAAAA
28668179 A
1 A
28668180 GAAAAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.61, C:0.00, G:0.21, T:0.18
Consensus pattern (16 bp):
AAAATGAGTTGGAAAA
Found at i:28670531 original size:5 final size:5
Alignment explanation
Indices: 28670521--28670545 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
28670511 CATTGGAACT
28670521 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
28670546 CTTAGTTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:28681497 original size:183 final size:183
Alignment explanation
Indices: 28681189--28681545 Score: 597
Period size: 183 Copynumber: 2.0 Consensus size: 183
28681179 AGTCTTGGGC
*
28681189 TGTGTAATGGAGTATTTATTTTAATGTTTGAGCTATGCACGTAGTGGAGTTGGACTGAAATATAG
1 TGTGTAATGGAGTATTTATTTTAATGCTTGAGCTATGCACGTAGTGGAGTTGGACTGAAATATAG
*
28681254 CTATAGGGAGTTTGATTTGAATTTGAATGGAGTTGTGGAGGGAGTTGAGGAGAAATTGGTGGAGT
66 CTATAGGGAGTTTGATTTGAATTTGAATGGAGTTGTGGAGGGAGTTGAAGAGAAATTGGTGGAGT
*
28681319 AATCCAAGGAGGGATAAGGGGAGAGATTTTAGGAGAAAATCGTGGGAGTGTGT
131 AATCCAAGGAGGGATAAAGGGAGAGATTTTAGGAGAAAATCGTGGGAGTGTGT
** * * * *
28681372 TGTGTAATGGAGTATTTATTTTGCTGCTTGAGTTGTGTAGGTAGTGGAGTTGGACTGAAATATAG
1 TGTGTAATGGAGTATTTATTTTAATGCTTGAGCTATGCACGTAGTGGAGTTGGACTGAAATATAG
* *
28681437 CTATGGGGAGTTTGATTTGAATTTGAATGGAGTTGTTGAGGGAGTTGAAGAGAAATTGGTGGAGT
66 CTATAGGGAGTTTGATTTGAATTTGAATGGAGTTGTGGAGGGAGTTGAAGAGAAATTGGTGGAGT
* *
28681502 ACTCCAAGGAGTGATAAAGGGAGAGATTTTAGGAGAAAATCGTG
131 AATCCAAGGAGGGATAAAGGGAGAGATTTTAGGAGAAAATCGTG
28681546 AAAGTGGGGT
Statistics
Matches: 161, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
183 161 1.00
ACGTcount: A:0.29, C:0.04, G:0.35, T:0.32
Consensus pattern (183 bp):
TGTGTAATGGAGTATTTATTTTAATGCTTGAGCTATGCACGTAGTGGAGTTGGACTGAAATATAG
CTATAGGGAGTTTGATTTGAATTTGAATGGAGTTGTGGAGGGAGTTGAAGAGAAATTGGTGGAGT
AATCCAAGGAGGGATAAAGGGAGAGATTTTAGGAGAAAATCGTGGGAGTGTGT
Found at i:28682646 original size:27 final size:28
Alignment explanation
Indices: 28682594--28682707 Score: 130
Period size: 27 Copynumber: 4.2 Consensus size: 28
28682584 GGAGGTCAAC
*
28682594 AAATGACCGACAT-CCCTCTATA-GGTA
1 AAATGACCGAAATACCCTCTATAGGGTA
28682620 AAATGACCGAAATACCCTC-ATAGGGTA
1 AAATGACCGAAATACCCTCTATAGGGTA
* *
28682647 AAATGATCGAAATACCC-CCATAGGGTA
1 AAATGACCGAAATACCCTCTATAGGGTA
* * **
28682674 AAATAACCCAAATA-CCTCTATTCGGTA
1 AAATGACCGAAATACCCTCTATAGGGTA
28682701 AAATGAC
1 AAATGAC
28682708 TGTTATACTC
Statistics
Matches: 75, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
26 18 0.24
27 57 0.76
ACGTcount: A:0.40, C:0.24, G:0.15, T:0.21
Consensus pattern (28 bp):
AAATGACCGAAATACCCTCTATAGGGTA
Found at i:28682950 original size:26 final size:26
Alignment explanation
Indices: 28682875--28682977 Score: 98
Period size: 26 Copynumber: 4.0 Consensus size: 26
28682865 GGAAGTATAT
* * * *
28682875 TGTTACTGGCAGCTTTGGTGTGAGAC
1 TGTTACTGGCAGCTCTGCTGCGATAC
* * *
28682901 TGTTATTGGAAGCTCTGCTGCGATCC
1 TGTTACTGGCAGCTCTGCTGCGATAC
*
28682927 TGTTACTGGCAGCTCTGCTGCGATAT
1 TGTTACTGGCAGCTCTGCTGCGATAC
* * * *
28682953 TATTACTGACAGCTTTGCTACGATA
1 TGTTACTGGCAGCTCTGCTGCGATA
28682978 TTGGTGTGTT
Statistics
Matches: 62, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 62 1.00
ACGTcount: A:0.18, C:0.20, G:0.26, T:0.35
Consensus pattern (26 bp):
TGTTACTGGCAGCTCTGCTGCGATAC
Found at i:28693143 original size:16 final size:15
Alignment explanation
Indices: 28693103--28693144 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
28693093 AGATGATAAT
28693103 TATTAATATATAAATA
1 TATTAAT-TATAAATA
28693119 TATCT-ATTATAATATA
1 TAT-TAATTATAA-ATA
28693135 TATTAATTAT
1 TATTAATTAT
28693145 TATCAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 6 0.26
16 16 0.70
17 1 0.04
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (15 bp):
TATTAATTATAAATA
Found at i:28693723 original size:20 final size:20
Alignment explanation
Indices: 28693695--28693733 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
28693685 AATTTTTCTC
28693695 CTAAATTTT-AATTTTATTAT
1 CTAAATTTTCAA-TTTATTAT
*
28693715 CTAATTTTTCAATTTATTA
1 CTAAATTTTCAATTTATTA
28693734 AATTATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (20 bp):
CTAAATTTTCAATTTATTAT
Found at i:28696827 original size:22 final size:22
Alignment explanation
Indices: 28696801--28696845 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
28696791 ATTATATGTA
*
28696801 TTAATTCATAATATAA-TTAATT
1 TTAATTCAT-ATACAATTTAATT
*
28696823 TTAATTTATATACAATTTAATT
1 TTAATTCATATACAATTTAATT
28696845 T
1 T
28696846 GGGTTGATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (22 bp):
TTAATTCATATACAATTTAATT
Found at i:28708207 original size:23 final size:23
Alignment explanation
Indices: 28708176--28708226 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
28708166 ACATACTTCC
* *
28708176 TTACTGTAGTAATTTTCGGGGTA
1 TTACAGTAGTAATTTTCGGGATA
*
28708199 TTACAGTAGTAATTTTTGGGATA
1 TTACAGTAGTAATTTTCGGGATA
28708222 TTACA
1 TTACA
28708227 CCATAGCTCG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.27, C:0.08, G:0.22, T:0.43
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGGGATA
Found at i:28709504 original size:53 final size:53
Alignment explanation
Indices: 28709438--28709552 Score: 149
Period size: 53 Copynumber: 2.2 Consensus size: 53
28709428 CGTGTGACTT
* * * *
28709438 GGCCGTGTAACCCAAGTCAAAGAGTTACAGGACATAGACACGGGCTGGGACAC
1 GGCCGTGTGACCCAAGCCAAAGAGTTACAGGACACAGACACAGGCTGGGACAC
** * *
28709491 GGCCGTGTGACCCAAGCCAAAGAGTTTTAGGGCACAGACACATGCTGGGACAC
1 GGCCGTGTGACCCAAGCCAAAGAGTTACAGGACACAGACACAGGCTGGGACAC
*
28709544 GGCTGTGTG
1 GGCCGTGTG
28709553 TCCCTGCTTC
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.28, C:0.24, G:0.32, T:0.16
Consensus pattern (53 bp):
GGCCGTGTGACCCAAGCCAAAGAGTTACAGGACACAGACACAGGCTGGGACAC
Found at i:28713661 original size:8 final size:8
Alignment explanation
Indices: 28713648--28713673 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
28713638 AATTTCAATT
28713648 TTATTTAA
1 TTATTTAA
28713656 TTATTTAA
1 TTATTTAA
28713664 TTATTTAA
1 TTATTTAA
28713672 TT
1 TT
28713674 TATTGAATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (8 bp):
TTATTTAA
Found at i:28721485 original size:23 final size:24
Alignment explanation
Indices: 28721432--28721485 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
28721422 TATCTTTGTT
** *
28721432 TTAATTATTTTACTATATTAATCC
1 TTAATTAAATTACTAAATTAATCC
*
28721456 -TATTTAAATTACTAAATTAA-CC
1 TTAATTAAATTACTAAATTAATCC
28721478 TTAATTAA
1 TTAATTAA
28721486 TAGCCTTGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
22 2 0.08
23 22 0.92
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (24 bp):
TTAATTAAATTACTAAATTAATCC
Found at i:28721733 original size:11 final size:11
Alignment explanation
Indices: 28721717--28721741 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28721707 TGACTTTGAG
28721717 TAATAATAAAA
1 TAATAATAAAA
28721728 TAATAATAAAA
1 TAATAATAAAA
28721739 TAA
1 TAA
28721742 ATTTTTTGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
TAATAATAAAA
Found at i:28724242 original size:26 final size:27
Alignment explanation
Indices: 28724208--28724269 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
28724198 AGGGGTAAAA
*
28724208 CGGTAATTTTACCC-CCAAGGGTATTT
1 CGGTCATTTTACCCTCCAAGGGTATTT
* * *
28724234 TGGTCATTTTACCCTTCGAGGGTATTT
1 CGGTCATTTTACCCTCCAAGGGTATTT
28724261 CGGTCATTT
1 CGGTCATTT
28724270 AACAACCTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 12 0.40
27 18 0.60
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.40
Consensus pattern (27 bp):
CGGTCATTTTACCCTCCAAGGGTATTT
Found at i:28732676 original size:22 final size:22
Alignment explanation
Indices: 28732651--28732695 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
28732641 ATTATGATGA
28732651 TTGATAAGT-TGAGATTAATATT
1 TTGATAAGTATGAGATT-ATATT
* *
28732673 TTGATATGTATGCGATTATATT
1 TTGATAAGTATGAGATTATATT
28732695 T
1 T
28732696 GTGTTGATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.31, C:0.02, G:0.18, T:0.49
Consensus pattern (22 bp):
TTGATAAGTATGAGATTATATT
Found at i:28735809 original size:99 final size:100
Alignment explanation
Indices: 28735686--28735884 Score: 330
Period size: 99 Copynumber: 2.0 Consensus size: 100
28735676 TATAAAATGC
* * * *
28735686 AACTTTGAACAATTTGGTGTTGAAAGCAAATTTTGATATTAAAAAGTGTTATGAAAACTAAAAGT
1 AACTTTGAACAATTTGGTGTTGAAAACAAATGTTAATATTAAAAAGTGTTATGAAAACTAAAACT
*
28735751 TAACTAAATAATTTAACTAA-AAAAATTGTTCCAA
66 TAACTAAATAATTTAACTAAGAAAAAATGTTCCAA
28735785 AACTTT-AAGCAATTTGGTGTTGAAAACAAATGTTAATATTAAAAAGTGTTATGAAAACTAAAAC
1 AACTTTGAA-CAATTTGGTGTTGAAAACAAATGTTAATATTAAAAAGTGTTATGAAAACTAAAAC
28735849 TTAACTAAATAATTTAACTAAGAAAAAATGTTCCAA
65 TTAACTAAATAATTTAACTAAGAAAAAATGTTCCAA
28735885 TGCATGATTT
Statistics
Matches: 93, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
98 2 0.02
99 78 0.84
100 13 0.14
ACGTcount: A:0.48, C:0.09, G:0.12, T:0.32
Consensus pattern (100 bp):
AACTTTGAACAATTTGGTGTTGAAAACAAATGTTAATATTAAAAAGTGTTATGAAAACTAAAACT
TAACTAAATAATTTAACTAAGAAAAAATGTTCCAA
Found at i:28739711 original size:20 final size:20
Alignment explanation
Indices: 28739688--28739726 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
28739678 GTGTCCCTAT
28739688 TTGCAC-TACGGTGCCCCTGC
1 TTGCACATAC-GTGCCCCTGC
*
28739708 TTGCACATTCGTGCCCCTG
1 TTGCACATACGTGCCCCTG
28739727 TTCGCACTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.10, C:0.38, G:0.23, T:0.28
Consensus pattern (20 bp):
TTGCACATACGTGCCCCTGC
Found at i:28740374 original size:34 final size:34
Alignment explanation
Indices: 28740331--28740396 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
28740321 CTAAATAGAA
28740331 TTACTCATAGTTGAATAATTTTTTTTACAACTGG
1 TTACTCATAGTTGAATAATTTTTTTTACAACTGG
*
28740365 TTACTCATAGTTGATTAATTTTTTTTACAACT
1 TTACTCATAGTTGAATAATTTTTTTTACAACT
28740397 AGTGAGTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.29, C:0.12, G:0.09, T:0.50
Consensus pattern (34 bp):
TTACTCATAGTTGAATAATTTTTTTTACAACTGG
Found at i:28741242 original size:16 final size:16
Alignment explanation
Indices: 28741200--28741243 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
28741190 TGCTAAGGTG
28741200 AACTGATGAGCTAGCA
1 AACTGATGAGCTAGCA
* * *
28741216 AAATAATGAGCTTGCA
1 AACTGATGAGCTAGCA
*
28741232 AACTGACGAGCT
1 AACTGATGAGCT
28741244 CGCACAGCGA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.20
Consensus pattern (16 bp):
AACTGATGAGCTAGCA
Found at i:28743777 original size:20 final size:21
Alignment explanation
Indices: 28743738--28743780 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
28743728 CGATGCTTAC
*
28743738 TATTATTCGCACTTCAGTTCT
1 TATTATTCGCACTCCAGTTCT
*
28743759 TATTATT-GCACTCCGGTTCT
1 TATTATTCGCACTCCAGTTCT
28743779 TA
1 TA
28743781 ATGCTACTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.19, C:0.23, G:0.12, T:0.47
Consensus pattern (21 bp):
TATTATTCGCACTCCAGTTCT
Found at i:28744481 original size:12 final size:12
Alignment explanation
Indices: 28744464--28744491 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
28744454 CAGCAACACA
28744464 ACCAAGATGCTT
1 ACCAAGATGCTT
28744476 ACCAAGATGCTT
1 ACCAAGATGCTT
28744488 ACCA
1 ACCA
28744492 GGTATGGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.36, C:0.29, G:0.14, T:0.21
Consensus pattern (12 bp):
ACCAAGATGCTT
Found at i:28748603 original size:107 final size:108
Alignment explanation
Indices: 28748321--28748644 Score: 472
Period size: 107 Copynumber: 3.0 Consensus size: 108
28748311 GGAACTTATT
* *
28748321 AACAACATTGATGCAAAACTTAATTCAATGTAATTAAGGATGATGGTTCAAACTAACACA-AATG
1 AACAACATTGATGCAAAACTTAATTCAATATAATTAAGGATGATGGTTCAAACTAACA-AGAAAG
* *
28748385 AAAGATTCAAAAGTTATTTGCCCAGCTAGCTCTAGCATTTGGCA
65 AAAGATTCAAAAGTTATTTGCTCAGCTTGCTCTAGCATTTGGCA
* ** *
28748429 AGCAACATTGATGCAAAACTTAATTCAATATAATTAAGGATGACAGTTCAAACTAATAAGAAAGA
1 AACAACATTGATGCAAAACTTAATTCAATATAATTAAGGATGATGGTTCAAACTAACAAGAAAGA
* * *
28748494 AAGTTTCAAGAGTTATTTGCTCAGCTTGCCCTAGCATTTGG-A
66 AAGATTCAAAAGTTATTTGCTCAGCTTGCTCTAGCATTTGGCA
* * * * *
28748536 AACAAAATTGATGCAAATCTTAATTCAATATAATTATGGATGATGGTTCAAACTAACATGAACGA
1 AACAACATTGATGCAAAACTTAATTCAATATAATTAAGGATGATGGTTCAAACTAACAAGAAAGA
*
28748601 AAGCTTCAAAAGTTATTTGCTCAGCTTGCTCTAGCATTTGGCA
66 AAGATTCAAAAGTTATTTGCTCAGCTTGCTCTAGCATTTGGCA
28748644 A
1 A
28748645 TTTCTAATTT
Statistics
Matches: 191, Mismatches: 23, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
107 96 0.50
108 95 0.50
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (108 bp):
AACAACATTGATGCAAAACTTAATTCAATATAATTAAGGATGATGGTTCAAACTAACAAGAAAGA
AAGATTCAAAAGTTATTTGCTCAGCTTGCTCTAGCATTTGGCA
Found at i:28772033 original size:49 final size:44
Alignment explanation
Indices: 28771837--28772496 Score: 350
Period size: 44 Copynumber: 14.7 Consensus size: 44
28771827 TTTTAATCCA
* *
28771837 CTCCACTGCAACTTCAGGGAGATAGGATTAGTAGCTTCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTG
* * * * * * * *
28771881 CTCCATTGTAACTTCAGAGATATAAGATTGGTATCTTTAACCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTG
* * * * *
28771925 CTCCACTGCAACTTCAGGAAAATAAGGTTTGTGGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTG
*
28771969 CTCCACTGCAGCTTCAGGGAGATAAGATTTGTAGCCCGTCTTCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTA----G-CTTCAATCTG
*
28772018 CTCCACTGCAACTTCAGGGAGATGAAG-TTTG-A--TAT-GATCTG
1 CTCCACTGCAACTTCAGGGAGAT-AAGATTTGTAGCT-TCAATCTG
* * ** *
28772059 CTCTACTGCAACTTTAAAGAGATAAGATTTGTAATTTATAGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTG-------TAGCTTCAATCTG
* * * * * * * * *
28772110 TTCCACTACAACTTCAGGGAAATACGATTCGCTATCTTCAGTTTA
1 CTCCACTGCAACTTCAGGGAGATAAGATTTG-TAGCTTCAATCTG
* * *
28772155 CTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTG
* * * *
28772199 CCCCACTACAACTTCAAGGG-GATAAG-GTT-T-GCTAT-GATCTG
1 CTCCACTGCAACTTC-AGGGAGATAAGATTTGTAGCT-TCAATCTG
* * *
28772240 CTCTACTGCAACTTCAGAGAGATAAGATTTGCAATTTATAACTTCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTG-------TAGCTTCAATCTG
* * * * * *
28772291 TTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTTAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTG-TAGCTTCAATCTG
* * * * * * * *
28772336 TTCCACTACAACCTCAGGGAGATAAAACTCGTAACTTCAACCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTG
* * * * * * * * *
28772380 TTCCACTACAACTTTAAGGAGATAAGACTCGTAACTTCAACCTC
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTG
* * * ** * * * *
28772424 CCCCATTGCAACTTCAGGGGGATCTGAATTGTGGCTTTAATCTA
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTG
* *
28772468 CTCTACTGTAACTTCAGGGAGATAAGATT
1 CTCCACTGCAACTTCAGGGAGATAAGATT
28772497 CGTCATGATG
Statistics
Matches: 465, Mismatches: 118, Indels: 66
0.72 0.18 0.10
Matches are distributed among these distances:
40 6 0.01
41 53 0.11
42 5 0.01
43 2 0.00
44 221 0.48
45 73 0.16
48 2 0.00
49 36 0.08
50 6 0.01
51 61 0.13
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (44 bp):
CTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTG
Found at i:28772187 original size:96 final size:95
Alignment explanation
Indices: 28771838--28772369 Score: 295
Period size: 92 Copynumber: 5.8 Consensus size: 95
28771828 TTTAATCCAC
* * * * * * * * *
28771838 TCCACTGCAACTTCAGGGAGATAGGATTAG-TAGCTTCAATCTGCTCCATTGTAACTTCAGAGAT
1 TCCACTACAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTCAGAGAG
* * * *
28771902 ATAAGA-TTG----GTAT-CTTTAACCTGC
66 ATAAGACTTGTAATTTATACTTCAATCTGT
* * * * ** * * * *
28771926 TCCACTGCAACTTCAGGAAAATAAGGTTTG-TGGCTTTAATCTGCTCCACTGCAGCTTCAGGGAG
1 TCCACTACAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTCAGAGAG
* ***** *
28771990 ATAAGATTTGTAGCCCGT-CTTCAATCTGC
66 ATAAGACTTGTAATTTATACTTCAATCTGT
* * * * * * * *
28772019 TCCACTGCAACTTCAGGGAGATGAAG-TTTG--AT-ATGA-TCTGCTCTACTGCAACTTTAAAGA
1 TCCACTACAACTTCAGGGAAAT-AAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTCAGAGA
* *
28772079 GATAAGATTTGTAATTTATAGCTTTAATCTGT
65 GATAAGACTTGTAATTTATA-CTTCAATCTGT
* * * *
28772111 TCCACTACAACTTCAGGGAAATACGATTCGCTATCTTCAGTTTACTCCACTGCAACTTCAGGGAG
1 TCCACTACAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTCAGAGAG
* *
28772176 ATAAGACTTG-----TA-ACTTCAACCTGC
66 ATAAGACTTGTAATTTATACTTCAATCTGT
* * * * * *
28772200 CCCACTACAACTTCAAGGG-GATAAGGTTTGCTA---TGA-TCTGCTCTACTGCAACTTCAGAGA
1 TCCACTACAACTTC-AGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTCAGAGA
* *
28772260 GATAAGATTTGCAATTTATAACTTCAATCTGT
65 GATAAGACTTGTAATTTAT-ACTTCAATCTGT
* * * * * *
28772292 TCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTTAGTCTGTTCCACTACAACCTCAGGGAG
1 TCCACTACAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTCAGAGAG
* *
28772357 ATAAAACTCGTAA
66 ATAAGACTTGTAA
28772370 CTTCAACCTG
Statistics
Matches: 339, Mismatches: 79, Indels: 44
0.73 0.17 0.10
Matches are distributed among these distances:
85 30 0.09
86 2 0.01
88 58 0.17
89 34 0.10
90 40 0.12
91 10 0.03
92 65 0.19
93 34 0.10
94 5 0.01
95 4 0.01
96 57 0.17
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (95 bp):
TCCACTACAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTCAGAGAG
ATAAGACTTGTAATTTATACTTCAATCTGT
Found at i:28772213 original size:181 final size:181
Alignment explanation
Indices: 28771969--28772405 Score: 572
Period size: 181 Copynumber: 2.4 Consensus size: 181
28771959 CTTTAATCTG
* * * * *
28771969 CTCCACTGCAGCTTCAGGGAGATAAGATTTGTAGCCCGTCTTCAATCTGCTCCACTGCAACTTCA
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTA-----ACTTCAACCTGCTCCACTACAACTTCA
* *
28772034 GGGAGATGAA-GTTTGATATGATCTGCTCTACTGCAACTTTAAAGAGATAAGATTTGTAATTTAT
61 GGGAGAT-AAGGTTTGATATGATCTGCTCTACTGCAACTTCAAAGAGATAAGATTTGCAATTTAT
* * * *
28772098 AGCTTTAATCTGTTCCACTACAACTTCAGGGAAATACGATTCGCTATCTTCAGTTTA
125 AACTTCAATCTGTTCCACTACAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTA
*
28772155 CTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCCCCACTACAACTTCAAGGG-
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTACAACTTC-AGGGA
* *
28772219 GATAAGGTTTGCTATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGCAATTTATAACTT
65 GATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAAAGAGATAAGATTTGCAATTTATAACTT
* * *
28772284 CAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTTAGTCTG
130 CAATCTGTTCCACTACAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTA
* * * * * * * *
28772336 TTCCACTACAACCTCAGGGAGATAAAACTCGTAACTTCAACCTGTTCCACTACAACTTTAAGGAG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTACAACTTCAGGGAG
28772401 ATAAG
66 ATAAG
28772406 ACTCGTAACT
Statistics
Matches: 222, Mismatches: 26, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
180 5 0.02
181 182 0.82
182 4 0.02
186 31 0.14
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (181 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTACAACTTCAGGGAG
ATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAAAGAGATAAGATTTGCAATTTATAACTTC
AATCTGTTCCACTACAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTA
Found at i:28772392 original size:89 final size:89
Alignment explanation
Indices: 28772107--28772442 Score: 279
Period size: 89 Copynumber: 3.8 Consensus size: 89
28772097 TAGCTTTAAT
* * *
28772107 CTGTTCCACTACAACTTCAGGGAAATACGATTCGCTATCTTCAGTTTACTCCACTGCAACTTCAG
1 CTGTTCCACTACAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTCAG
*
28772172 GGAGATAAGACTTGTAACTTCAAC
66 GGAGATAAAACTTGTAACTTCAAC
** * * * * *
28772196 CTGCCCCACTACAACTTCAAGGG-GATAAGGTTTGCTA---TGA-TCTGCTCTACTGCAACTTCA
1 CTGTTCCACTACAACTTC-AGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTCA
* * * *
28772256 GAGAGATAAGATTTGCAATTTATAACTTCAAT
65 GGGAGAT-A-A-----AACTTGTAACTTCAAC
* * * * *
28772288 CTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTTAGTCTGTTCCACTACAACCTCAG
1 CTGTTCCACTACAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTCAG
*
28772353 GGAGATAAAACTCGTAACTTCAAC
66 GGAGATAAAACTTGTAACTTCAAC
* * * * * ** * * *
28772377 CTGTTCCACTACAACTTTAAGGAGATAAGACTCG-TAACTTCAACCTCCCCCATTGCAACTTCAG
1 CTGTTCCACTACAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTCAG
28772441 GG
66 GG
28772443 GGATCTGAAT
Statistics
Matches: 188, Mismatches: 46, Indels: 27
0.72 0.18 0.10
Matches are distributed among these distances:
85 23 0.12
86 3 0.02
87 1 0.01
88 22 0.12
89 67 0.36
90 4 0.02
91 4 0.02
92 38 0.20
94 1 0.01
95 3 0.02
96 22 0.12
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.29
Consensus pattern (89 bp):
CTGTTCCACTACAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTCAG
GGAGATAAAACTTGTAACTTCAAC
Found at i:28778499 original size:27 final size:27
Alignment explanation
Indices: 28778469--28778527 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
28778459 AATTAATAAT
28778469 CAAAGACAAATGAAA-TAAAATAATATA
1 CAAAGACAAATGAAAGT-AAATAATATA
* * *
28778496 CAAAAACAATTTAAAGTAAATAATATA
1 CAAAGACAAATGAAAGTAAATAATATA
*
28778523 AAAAG
1 CAAAG
28778528 GTTTAAAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
27 25 0.96
28 1 0.04
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.20
Consensus pattern (27 bp):
CAAAGACAAATGAAAGTAAATAATATA
Found at i:28778547 original size:26 final size:24
Alignment explanation
Indices: 28778503--28778895 Score: 220
Period size: 26 Copynumber: 15.1 Consensus size: 24
28778493 ATACAAAAAC
*
28778503 AATTTAAAGTAAATAATATA-AAA
1 AATTTAAAATAAATAATATATAAA
*
28778526 AGGTTTAAAATAAATAATATATGAAA
1 A-ATTTAAAATAAATAATATAT-AAA
*** *
28778552 AGAACAAAAATTTAAATAAATAATACAAAA
1 A-ATTTAAAA--TAAAT-AAT-ATA-TAAA
* *
28778582 AATTGTTCAAAATAAACAATATGTGAAA
1 AA-T-TT-AAAATAAATAATATAT-AAA
* * *
28778610 ATTTTTTTAACATAAATAAAATATAAA
1 A---ATTTAAAATAAATAATATATAAA
* *
28778637 ACTGTTTGAAATAAATAAT-T-TAAA
1 A--ATTTAAAATAAATAATATATAAA
* *
28778661 GCAATTTAAAATAAACAATACATAAA
1 --AATTTAAAATAAATAATATATAAA
* *
28778687 ACACTTTAAAAGAAATAATATGTGAAAAA
1 A-A-TTTAAAATAAATAATA--T-ATAAA
*
28778716 AATCTAAAATAAATAATATATATAAA
1 AATTTAAAATAAAT-A-ATATATAAA
28778742 ATAGTTTAAAATAAAATAATATATAAA
1 A-A-TTTAAAAT-AAATAATATATAAA
*
28778769 GCAATTCAAAATAAATAATATATGAAA
1 --AATTTAAAATAAATAATATAT-AAA
28778796 CAATTTAAAATAAATAATATA-AAA
1 -AATTTAAAATAAATAATATATAAA
*
28778820 TAATTTAATATAAATAATATAT-AA
1 -AATTTAAAATAAATAATATATAAA
*
28778844 AATTTAAAATAAATAAAATATAAA
1 AATTTAAAATAAATAATATATAAA
* *
28778868 ACCGTTAAAAATAAATAATATATAAA
1 A--ATTTAAAATAAATAATATATAAA
28778894 AA
1 AA
28778896 CAATTAAAAA
Statistics
Matches: 289, Mismatches: 45, Indels: 71
0.71 0.11 0.18
Matches are distributed among these distances:
23 20 0.07
24 62 0.21
25 2 0.01
26 98 0.34
27 35 0.12
28 34 0.12
29 22 0.08
30 12 0.04
32 4 0.01
ACGTcount: A:0.61, C:0.04, G:0.05, T:0.30
Consensus pattern (24 bp):
AATTTAAAATAAATAATATATAAA
Found at i:28778750 original size:55 final size:50
Alignment explanation
Indices: 28778649--28778914 Score: 161
Period size: 53 Copynumber: 5.2 Consensus size: 50
28778639 TGTTTGAAAT
* * * * * *
28778649 AAATAAT-TTAAAGCAATTTAAAATAAACAATACATA-AAACACTTTAAAAG
1 AAATAATATTAAA-AAAATTAAAATAAATAATATATATAAA-AATTTAAAAA
28778699 AAATAATATGTGAAAAAAATCTAAAATAAATAATATATATAAAATAGTTTAAAATA
1 AAATAATAT-T-AAAAAAAT-TAAAATAAATAATATATATAAAA-A-TTTAAAA-A
** * *
28778755 AAATAATATATAAAGCAATTCAAAATAAATAATATATGA-AACAATTTAAAAT
1 AAATAATAT-TAAAAAAATT-AAAATAAATAATATAT-ATAAAAATTTAAAAA
* * *
28778807 AAATAATA-TAAAATAATTTAATATAAAT-A-ATATAT-AAAATTTAAAAT
1 AAATAATATTAAAA-AAATTAAAATAAATAATATATATAAAAATTTAAAAA
* *** *
28778854 AAATAAAATATAAAACCGTTAAAAATAAATAATATATA-AAAACAATTAAAAA
1 AAATAATAT-TAAAAAAATT-AAAATAAATAATATATATAAAA-ATTTAAAAA
*
28778906 GAAAAAATA
1 -AAATAATA
28778915 AATAACAAAT
Statistics
Matches: 171, Mismatches: 25, Indels: 37
0.73 0.11 0.16
Matches are distributed among these distances:
47 19 0.11
48 6 0.04
49 14 0.08
50 20 0.12
51 12 0.07
52 19 0.11
53 33 0.19
54 5 0.03
55 32 0.19
56 11 0.06
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.28
Consensus pattern (50 bp):
AAATAATATTAAAAAAATTAAAATAAATAATATATATAAAAATTTAAAAA
Found at i:28778759 original size:132 final size:125
Alignment explanation
Indices: 28778615--28778914 Score: 300
Period size: 132 Copynumber: 2.3 Consensus size: 125
28778605 TGAAAATTTT
* * ** **
28778615 TTTAACATAAATAAAATATAAAACTGTTTGAAATAAATAAT-T-T-AAAGCAATTTAAAATAAAC
1 TTTAAAATAAATAATATATAAAACAATTCAAAATAAATAATATATGAAA-CAATTTAAAATAAAC
*
28778677 AATACATAAAACACTTTAAAAGAAATAATATGTGAAAAAAATCTAAAATAAATAATATATATAAA
65 AAT--ATAAAACAATTTAAAAGAAATAATA--T--AAAAAATCTAAAATAAATAA-A-ATATAAA
*
28778742 ATAG
122 ACAG
* *
28778746 TTTAAAATAAAATAATATATAAAGCAATTCAAAATAAATAATATATGAAACAATTTAAAATAAAT
1 TTTAAAAT-AAATAATATATAAAACAATTCAAAATAAATAATATATGAAACAATTTAAAATAAAC
* * * * * *
28778811 AATATAAAATAATTTAATATAAATAATATATAAAATTTAAAATAAATAAAATATAAAACCG
65 AATATAAAACAATTTAAAAGAAATAATATAAAAAATCTAAAATAAATAAAATATAAAACAG
* * * *
28778872 TTAAAAATAAATAATATATAAAAACAATTAAAAAGAAAAAATA
1 TTTAAAATAAATAATATAT-AAAACAATTCAAAATAAATAATA
28778915 AATAACAAAT
Statistics
Matches: 143, Mismatches: 21, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
125 11 0.08
126 35 0.24
127 1 0.01
128 18 0.13
130 1 0.01
131 7 0.05
132 48 0.34
133 1 0.01
134 18 0.13
135 3 0.02
ACGTcount: A:0.63, C:0.05, G:0.04, T:0.29
Consensus pattern (125 bp):
TTTAAAATAAATAATATATAAAACAATTCAAAATAAATAATATATGAAACAATTTAAAATAAACA
ATATAAAACAATTTAAAAGAAATAATATAAAAAATCTAAAATAAATAAAATATAAAACAG
Found at i:28778858 original size:77 final size:72
Alignment explanation
Indices: 28778623--28778889 Score: 164
Period size: 81 Copynumber: 3.5 Consensus size: 72
28778613 TTTTTAACAT
** ** * ** * *
28778623 AAATAAAATATAAAACTGTTTGAAATAAATAATTTAAAGCAATTTAAAAT-AAACAATACATAAA
1 AAATAAAATATAAAACAATTAAAAATAAATAATATAAAATAATTTAAAATAAAATAATATAT-AA
*
28778687 ACACTTTAA
65 ACA-ATTAA
* * *
28778696 AAGA-AATAATATGTGAAAAAAATCTAAAATAAATAATATATATAAAATAGTTTAAAATAAAATA
1 AA-ATAA-AATA--T-AAAACAAT-TAAAA-ATA-AATA-ATATAAAATAATTTAAAATAAAATA
*
28778760 ATATATAAAGCAATTCA
57 ATATATAAA-CAATTAA
* *
28778777 AAATAAATAATATATGAAACAATTTAAAATAAATAATATAAAATAATTTAATAT-AAATAATATA
1 AAAT-AA-AATATA--AAACAATTAAAAATAAATAATATAAAATAATTTAAAATAAAATAATATA
*
28778841 TAAA-ATTTAAAA
62 TAAACAATT--AA
**
28778853 TAAATAAAATATAAAACCGTTAAAAATAAATAATATA
1 -AAATAAAATATAAAACAATTAAAAATAAATAATATA
28778890 TAAAAACAAT
Statistics
Matches: 152, Mismatches: 24, Indels: 36
0.72 0.11 0.17
Matches are distributed among these distances:
73 25 0.16
74 8 0.05
75 6 0.04
76 18 0.12
77 26 0.17
78 7 0.05
79 5 0.03
80 10 0.07
81 29 0.19
82 18 0.12
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (72 bp):
AAATAAAATATAAAACAATTAAAAATAAATAATATAAAATAATTTAAAATAAAATAATATATAAA
CAATTAA
Found at i:28778902 original size:27 final size:26
Alignment explanation
Indices: 28778615--28778919 Score: 266
Period size: 26 Copynumber: 11.8 Consensus size: 26
28778605 TGAAAATTTT
* * **
28778615 TTTAACATAAATAAAATATAAAACTG
1 TTTAAAATAAATAATATATAAAACAA
* *
28778641 TTTGAAATAAATAAT-T-TAAAGCAA
1 TTTAAAATAAATAATATATAAAACAA
* * *
28778665 TTTAAAATAAACAATACATAAAACAC
1 TTTAAAATAAATAATATATAAAACAA
* * *
28778691 TTTAAAAGAAATAATATGTGAAAAAAA
1 TTTAAAATAAATAATATAT-AAAACAA
*
28778718 TCTAAAATAAATAATATATATAAA-ATA
1 TTTAAAATAAATAATATATA-AAACA-A
*
28778745 GTTTAAAATAAAATAATATATAAAGCAA
1 -TTTAAAAT-AAATAATATATAAAACAA
* *
28778773 TTCAAAATAAATAATATATGAAACAA
1 TTTAAAATAAATAATATATAAAACAA
*
28778799 TTTAAAATAAAT-A-ATATAAAATAA
1 TTTAAAATAAATAATATATAAAACAA
*
28778823 TTTAATATAAATAATATAT--AA-AA
1 TTTAAAATAAATAATATATAAAACAA
* **
28778846 TTTAAAATAAATAAAATATAAAACCG
1 TTTAAAATAAATAATATATAAAACAA
*
28778872 TTAAAAATAAATAATATATAAAAACAA
1 TTTAAAATAAATAATATAT-AAAACAA
* * * *
28778899 TTAAAAAGAAAAAATAAATAA
1 TTTAAAATAAATAATATATAA
28778920 CAAATTAAAA
Statistics
Matches: 225, Mismatches: 40, Indels: 28
0.77 0.14 0.10
Matches are distributed among these distances:
23 19 0.08
24 40 0.18
25 5 0.02
26 85 0.38
27 53 0.24
28 10 0.04
29 13 0.06
ACGTcount: A:0.63, C:0.05, G:0.04, T:0.29
Consensus pattern (26 bp):
TTTAAAATAAATAATATATAAAACAA
Found at i:28778916 original size:49 final size:48
Alignment explanation
Indices: 28778721--28778929 Score: 161
Period size: 49 Copynumber: 4.1 Consensus size: 48
28778711 AAAAAAATCT
* * *
28778721 AAAATAAATAATATATATAAAATAGTTTAAAATAAAATAATATATAAAGCAATTC
1 AAAATAAATAATATATA-AACA-A--TTAAAA-AAAA-AA-ATATAAAACAATTA
* * * *
28778776 AAAATAAATAATATATGAAACAATTTAAAATAAATAATATAAAATAATTT
1 AAAATAAATAATATAT-AAACAA-TTAAAAAAAAAAATATAAAACAATTA
* * **
28778826 AATATAAATAATATATAAA-ATTTAAAATAAATAAAATATAAAACCGTTA
1 AAAATAAATAATATATAAACAATTAAAA-AAA-AAAATATAAAACAATTA
28778875 AAAATAAATAATATATAAAAACAATTAAAAAGAAAAAATA-AATAACAAATTA
1 AAAATAAATAATATAT--AAACAATTAAAAA-AAAAAATATAA-AAC-AATTA
28778927 AAA
1 AAA
28778930 GGTTAAAATC
Statistics
Matches: 127, Mismatches: 18, Indels: 21
0.77 0.11 0.13
Matches are distributed among these distances:
47 6 0.05
48 3 0.02
49 30 0.24
50 28 0.22
51 14 0.11
52 18 0.14
53 7 0.06
54 1 0.01
55 19 0.15
56 1 0.01
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.28
Consensus pattern (48 bp):
AAAATAAATAATATATAAACAATTAAAAAAAAAAATATAAAACAATTA
Found at i:28787510 original size:23 final size:22
Alignment explanation
Indices: 28787484--28787538 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
28787474 CCATTTCTTG
*
28787484 TTTAGTTT-TATTTCTAATTGTAA
1 TTTAGTTTCT-TTTC-AATTATAA
28787507 TTTATGTTTCTTTTCAATTATAA
1 TTTA-GTTTCTTTTCAATTATAA
28787530 TTCTAGTTT
1 TT-TAGTTT
28787539 AGTTTTTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
23 17 0.61
24 10 0.36
25 1 0.04
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.62
Consensus pattern (22 bp):
TTTAGTTTCTTTTCAATTATAA
Found at i:28791345 original size:67 final size:67
Alignment explanation
Indices: 28791259--28791393 Score: 252
Period size: 67 Copynumber: 2.0 Consensus size: 67
28791249 TCATTTGTTT
*
28791259 CTTGTTCTGAATGGAGGGAGATTGGCGAGGTTTTGAAGGTATTCGTCGCTTTCTCCAACCTGCAT
1 CTTGTTCTGAATGGAGGGAGATTGGCGAGGCTTTGAAGGTATTCGTCGCTTTCTCCAACCTGCAT
28791324 TG
66 TG
*
28791326 CTTGTTCTGAATGGGGGGAGATTGGCGAGGCTTTGAAGGTATTCGTCGCTTTCTCCAACCTGCAT
1 CTTGTTCTGAATGGAGGGAGATTGGCGAGGCTTTGAAGGTATTCGTCGCTTTCTCCAACCTGCAT
28791391 TG
66 TG
28791393 C
1 C
28791394 GTCTATTCTT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.17, C:0.19, G:0.30, T:0.33
Consensus pattern (67 bp):
CTTGTTCTGAATGGAGGGAGATTGGCGAGGCTTTGAAGGTATTCGTCGCTTTCTCCAACCTGCAT
TG
Found at i:28792003 original size:27 final size:27
Alignment explanation
Indices: 28791946--28792047 Score: 111
Period size: 27 Copynumber: 3.8 Consensus size: 27
28791936 AAAATCATTC
28791946 AAATACCCTCGAA-GGTAAAATTATCG
1 AAATACCCTCGAAGGGTAAAATTATCG
28791972 AAATACCCTCGAAGGGTAAAATTA-CTG
1 AAATACCCTCGAAGGGTAAAATTATC-G
* * *
28791999 GAATACTCTCGAAGGGTAAAATGATCG
1 AAATACCCTCGAAGGGTAAAATTATCG
* * *
28792026 CAATTCCC-CTGTAGGGTAAAAT
1 AAATACCCTC-GAAGGGTAAAAT
28792048 GACTGTAATG
Statistics
Matches: 65, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
26 15 0.23
27 49 0.75
28 1 0.02
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.24
Consensus pattern (27 bp):
AAATACCCTCGAAGGGTAAAATTATCG
Found at i:28792045 original size:54 final size:54
Alignment explanation
Indices: 28791984--28792238 Score: 280
Period size: 54 Copynumber: 4.7 Consensus size: 54
28791974 ATACCCTCGA
* * * * * *
28791984 AGGGTAAAATTACTGGAATA-CTCTCGAAGGGTAAAATGATCGCAATTCCCCTGT
1 AGGGTAAAATGACTGTAATACCCCT-GAAGGGTAAAATGATCGTAATGCCCCTAT
* * * *
28792038 AGGGTAAAATGACTGTAATGCCCCTGTAGGGTAAAATGACCGTAATGCCCCAAT
1 AGGGTAAAATGACTGTAATACCCCTGAAGGGTAAAATGATCGTAATGCCCCTAT
* *
28792092 AGGGTAAAATGACTGTAATGCCCCTGTAGGGTAAAATGATCGTAATGCCCCTAT
1 AGGGTAAAATGACTGTAATACCCCTGAAGGGTAAAATGATCGTAATGCCCCTAT
* * * * * * *
28792146 AGGGTAAAATGACCGTAATGCCCCAGTAGGGTAAAATGGTCGTAATACTCCTAT
1 AGGGTAAAATGACTGTAATACCCCTGAAGGGTAAAATGATCGTAATGCCCCTAT
* * *
28792200 AGGGTTAAATGA-TCGTAATGCCCCTGTAGGGTAAAATGA
1 AGGGTAAAATGACT-GTAATACCCCTGAAGGGTAAAATGA
28792239 CTATTTTGCC
Statistics
Matches: 178, Mismatches: 21, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
54 175 0.98
55 3 0.02
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (54 bp):
AGGGTAAAATGACTGTAATACCCCTGAAGGGTAAAATGATCGTAATGCCCCTAT
Found at i:28792049 original size:27 final size:27
Alignment explanation
Indices: 28792011--28792238 Score: 307
Period size: 27 Copynumber: 8.4 Consensus size: 27
28792001 ATACTCTCGA
* *
28792011 AGGGTAAAATGATCGCAATTCCCCTGT
1 AGGGTAAAATGATCGTAATGCCCCTGT
28792038 AGGGTAAAATGA-CTGTAATGCCCCTGT
1 AGGGTAAAATGATC-GTAATGCCCCTGT
* **
28792065 AGGGTAAAATGACCGTAATGCCCCAAT
1 AGGGTAAAATGATCGTAATGCCCCTGT
28792092 AGGGTAAAATGA-CTGTAATGCCCCTGT
1 AGGGTAAAATGATC-GTAATGCCCCTGT
*
28792119 AGGGTAAAATGATCGTAATGCCCCTAT
1 AGGGTAAAATGATCGTAATGCCCCTGT
* *
28792146 AGGGTAAAATGACCGTAATGCCCCAGT
1 AGGGTAAAATGATCGTAATGCCCCTGT
* * * *
28792173 AGGGTAAAATGGTCGTAATACTCCTAT
1 AGGGTAAAATGATCGTAATGCCCCTGT
*
28792200 AGGGTTAAATGATCGTAATGCCCCTGT
1 AGGGTAAAATGATCGTAATGCCCCTGT
28792227 AGGGTAAAATGA
1 AGGGTAAAATGA
28792239 CTATTTTGCC
Statistics
Matches: 175, Mismatches: 22, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
26 2 0.01
27 171 0.98
28 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (27 bp):
AGGGTAAAATGATCGTAATGCCCCTGT
Found at i:28792096 original size:81 final size:81
Alignment explanation
Indices: 28792011--28792239 Score: 345
Period size: 81 Copynumber: 2.8 Consensus size: 81
28792001 ATACTCTCGA
* *
28792011 AGGGTAAAATGATCGCAATTCCCCTGTAGGGTAAAATGA-CTGTAATGCCCCTGTAGGGTAAAAT
1 AGGGTAAAATGATCGTAATACCCCTGTAGGGTAAAATGATC-GTAATGCCCCTGTAGGGTAAAAT
28792075 GACCGTAATGCCCCAAT
65 GACCGTAATGCCCCAAT
* *
28792092 AGGGTAAAATGA-CTGTAATGCCCCTGTAGGGTAAAATGATCGTAATGCCCCTATAGGGTAAAAT
1 AGGGTAAAATGATC-GTAATACCCCTGTAGGGTAAAATGATCGTAATGCCCCTGTAGGGTAAAAT
*
28792156 GACCGTAATGCCCCAGT
65 GACCGTAATGCCCCAAT
* * * *
28792173 AGGGTAAAATGGTCGTAATACTCCTATAGGGTTAAATGATCGTAATGCCCCTGTAGGGTAAAATG
1 AGGGTAAAATGATCGTAATACCCCTGTAGGGTAAAATGATCGTAATGCCCCTGTAGGGTAAAATG
28792238 AC
66 AC
28792240 TATTTTGCCC
Statistics
Matches: 135, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
80 1 0.01
81 132 0.98
82 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.24
Consensus pattern (81 bp):
AGGGTAAAATGATCGTAATACCCCTGTAGGGTAAAATGATCGTAATGCCCCTGTAGGGTAAAATG
ACCGTAATGCCCCAAT
Found at i:28792360 original size:24 final size:24
Alignment explanation
Indices: 28792257--28792347 Score: 137
Period size: 24 Copynumber: 3.8 Consensus size: 24
28792247 CCCCTCGGGG
28792257 TTAAATGACTGATTTGTCTGTAAT
1 TTAAATGACTGATTTGTCTGTAAT
*
28792281 TTAAATGGCTGATTTGTCTGTAAT
1 TTAAATGACTGATTTGTCTGTAAT
* * **
28792305 TTAAATGACTGATTTATTTGTGGT
1 TTAAATGACTGATTTGTCTGTAAT
28792329 TTAAATGACTGATTTGTCT
1 TTAAATGACTGATTTGTCT
28792348 ATGATTTGTA
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.26, C:0.08, G:0.19, T:0.47
Consensus pattern (24 bp):
TTAAATGACTGATTTGTCTGTAAT
Found at i:28792469 original size:27 final size:27
Alignment explanation
Indices: 28792431--28792495 Score: 91
Period size: 27 Copynumber: 2.4 Consensus size: 27
28792421 ATTGAGGAAG
28792431 TACTG-TACTGGTGGCTCT-GCCACA-A
1 TACTGTTACTGGTGGCT-TGGCCACATA
28792456 TCACTGTTACTGGTGGCTTGGCCACATA
1 T-ACTGTTACTGGTGGCTTGGCCACATA
28792484 TACTGTTACTGG
1 TACTGTTACTGG
28792496 CAGCTTTGCT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
25 1 0.03
26 5 0.14
27 28 0.78
28 2 0.06
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.32
Consensus pattern (27 bp):
TACTGTTACTGGTGGCTTGGCCACATA
Found at i:28792501 original size:27 final size:27
Alignment explanation
Indices: 28792449--28792501 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
28792439 TGGTGGCTCT
**
28792449 GCCACAATCACTGTTACTGGTGGCTTG
1 GCCACAATCACTGTTACTGGCAGCTTG
28792476 GCCACATAT-ACTGTTACTGGCAGCTT
1 GCCACA-ATCACTGTTACTGGCAGCTT
28792502 TGCTGCGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 21 0.91
28 2 0.09
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (27 bp):
GCCACAATCACTGTTACTGGCAGCTTG
Found at i:28792587 original size:32 final size:32
Alignment explanation
Indices: 28792542--28792709 Score: 196
Period size: 32 Copynumber: 5.3 Consensus size: 32
28792532 ATGATGCTAT
* *
28792542 TGATGGCTTTGTGCCGATCATATTACCATTAC
1 TGATGGCTTTGTGCCGATCATATTACTACTAC
*
28792574 TGATGG-TTGTGTGCCGATCATATTACTACTAT
1 TGATGGCTT-TGTGCCGATCATATTACTACTAC
* * * *
28792606 TGATGGCTTTGTACTGATCATACTACTATTAC
1 TGATGGCTTTGTGCCGATCATATTACTACTAC
* * *
28792638 TAATGGCTGTGTGCCGATCATATTATTACTAC
1 TGATGGCTTTGTGCCGATCATATTACTACTAC
* *
28792670 TGATGGCTTTGTGCCAATCATATTAATA-TAC
1 TGATGGCTTTGTGCCGATCATATTACTACTAC
*
28792701 TTATGGCTT
1 TGATGGCTT
28792710 GTAACCATTC
Statistics
Matches: 114, Mismatches: 20, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
31 13 0.11
32 99 0.87
33 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40
Consensus pattern (32 bp):
TGATGGCTTTGTGCCGATCATATTACTACTAC
Found at i:28792617 original size:64 final size:64
Alignment explanation
Indices: 28792538--28792694 Score: 233
Period size: 64 Copynumber: 2.5 Consensus size: 64
28792528 TGCTATGATG
* *
28792538 CTATTGATGGCTTTGTGCCGATCATATTACCATTACTGATGGTTGTGTGCCGATCATATTACTA
1 CTATTGATGGCTTTGTGCCGATCATATTACCATTACTAATGGCTGTGTGCCGATCATATTACTA
* * * * *
28792602 CTATTGATGGCTTTGTACTGATCATACTACTATTACTAATGGCTGTGTGCCGATCATATTATTA
1 CTATTGATGGCTTTGTGCCGATCATATTACCATTACTAATGGCTGTGTGCCGATCATATTACTA
* *
28792666 CTACTGATGGCTTTGTGCCAATCATATTA
1 CTATTGATGGCTTTGTGCCGATCATATTA
28792695 ATATACTTAT
Statistics
Matches: 81, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
64 81 1.00
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.39
Consensus pattern (64 bp):
CTATTGATGGCTTTGTGCCGATCATATTACCATTACTAATGGCTGTGTGCCGATCATATTACTA
Found at i:28812186 original size:18 final size:17
Alignment explanation
Indices: 28812163--28812201 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
28812153 ATATTTTTAT
28812163 ATTAATCAAATCATAATA
1 ATTAATCAAAT-ATAATA
**
28812181 ATTAATTGAATATAATA
1 ATTAATCAAATATAATA
28812198 ATTA
1 ATTA
28812202 TAATTACCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (17 bp):
ATTAATCAAATATAATA
Found at i:28812241 original size:40 final size:38
Alignment explanation
Indices: 28812197--28812297 Score: 116
Period size: 40 Copynumber: 2.6 Consensus size: 38
28812187 TGAATATAAT
*
28812197 AATTATAATTACCATAATTATAATAATGTTTGA-CCAAAA
1 AATTATAATTACCATAATTATAATAATATTTGATCC--AA
* *
28812236 CAATTATAATTA-CAGTAATTATAATAATATTTTATCCTA
1 -AATTATAATTACCA-TAATTATAATAATATTTGATCCAA
*
28812275 AATTATAATTACAATAATTATAA
1 AATTATAATTACCATAATTATAA
28812298 CAAGGATTTC
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
38 20 0.37
39 4 0.07
40 28 0.52
41 2 0.04
ACGTcount: A:0.49, C:0.09, G:0.03, T:0.40
Consensus pattern (38 bp):
AATTATAATTACCATAATTATAATAATATTTGATCCAA
Found at i:28813954 original size:27 final size:25
Alignment explanation
Indices: 28813918--28813967 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
28813908 ATTTTTGATA
* *
28813918 ATTTTACCCTCGATAAAATTTTGACG
1 ATTTTACCCT-AATAAAAATTTGACG
28813944 ATTTTACCCCTAATAAAAATTTGA
1 ATTTTA-CCCTAATAAAAATTTGA
28813968 GAAATTTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 17 0.81
27 4 0.19
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (25 bp):
ATTTTACCCTAATAAAAATTTGACG
Found at i:28814234 original size:9 final size:10
Alignment explanation
Indices: 28814206--28814243 Score: 55
Period size: 9 Copynumber: 4.1 Consensus size: 10
28814196 AATGTTTCTT
28814206 ATTTCTATT-
1 ATTTCTATTC
28814215 -TTTCTATTC
1 ATTTCTATTC
28814224 ATTTC-ATTC
1 ATTTCTATTC
28814233 ATTTCTATTC
1 ATTTCTATTC
28814243 A
1 A
28814244 AACACGTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 8 0.31
9 9 0.35
10 9 0.35
ACGTcount: A:0.21, C:0.18, G:0.00, T:0.61
Consensus pattern (10 bp):
ATTTCTATTC
Found at i:28825483 original size:50 final size:50
Alignment explanation
Indices: 28825424--28825604 Score: 281
Period size: 50 Copynumber: 3.6 Consensus size: 50
28825414 GGGTAAAGAG
*
28825424 GTCCCATGTAAGACCATGTCTGGGACATGGCGTTGACACCGAGATGAGAC
1 GTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAC
*
28825474 GTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAG
1 GTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAC
** * * *
28825524 GTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAAC
1 GTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAG-AC
*
28825575 ATCCCATGTAAGACCATGTCTGGGACATGG
1 GTCCCATGTAAGACCATGTCTGGGACATGG
28825605 ATTTGGCATG
Statistics
Matches: 119, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
50 91 0.76
51 28 0.24
ACGTcount: A:0.25, C:0.24, G:0.30, T:0.20
Consensus pattern (50 bp):
GTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAC
Found at i:28828511 original size:4 final size:4
Alignment explanation
Indices: 28828504--28828530 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
28828494 TTGAATGATG
28828504 AATA AATA AATA AATA AATA AATA AAT
1 AATA AATA AATA AATA AATA AATA AAT
28828531 TTAATTTCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:28830308 original size:44 final size:43
Alignment explanation
Indices: 28830231--28830345 Score: 112
Period size: 44 Copynumber: 2.7 Consensus size: 43
28830221 CCCGATATGT
*
28830231 GATTTCGTGTAAGACTGCGTCTAGGACGTTGGCATCGATTTGA
1 GATTTCGTGTAAGACTCCGTCTAGGACGTTGGCATCGATTTGA
* *
28830274 GATTTACGTGTAAGAC-CCTGTCTGGGACAG-TGGCATCGATATT-T
1 GATTT-CGTGTAAGACTCC-GTCTAGGAC-GTTGGCATCGAT-TTGA
* *
28830318 GATTACATGTAAGAC-CACGTCTAGGACG
1 GATTTCGTGTAAGACTC-CGTCTAGGACG
28830346 ACGAGCTGTT
Statistics
Matches: 61, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
42 1 0.02
43 24 0.39
44 33 0.54
45 3 0.05
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (43 bp):
GATTTCGTGTAAGACTCCGTCTAGGACGTTGGCATCGATTTGA
Found at i:28836364 original size:25 final size:25
Alignment explanation
Indices: 28836336--28836388 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
28836326 TATAAGGGAG
*
28836336 AAAGCAAAACGAGGTAAGCTTATGT
1 AAAGCAAAACGAGGTAAGCTTACGT
**
28836361 AAAGCTTAACGAGGTAAGCTTACGT
1 AAAGCAAAACGAGGTAAGCTTACGT
28836386 AAA
1 AAA
28836389 ACTTAGTAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.43, C:0.13, G:0.23, T:0.21
Consensus pattern (25 bp):
AAAGCAAAACGAGGTAAGCTTACGT
Found at i:28836393 original size:25 final size:25
Alignment explanation
Indices: 28836343--28836393 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
28836333 GAGAAAGCAA
* *
28836343 AACGAGGTAAGCTTATGTAAAGCTT
1 AACGAGGTAAGCTTACGTAAAACTT
28836368 AACGAGGTAAGCTTACGTAAAACTT
1 AACGAGGTAAGCTTACGTAAAACTT
28836393 A
1 A
28836394 GTAAGTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (25 bp):
AACGAGGTAAGCTTACGTAAAACTT
Found at i:28839927 original size:36 final size:36
Alignment explanation
Indices: 28839851--28839932 Score: 96
Period size: 36 Copynumber: 2.3 Consensus size: 36
28839841 CTCTCTATTT
* * *
28839851 TGGTGTGTTTCGGATGGATGATGTCTTCTGAACATT
1 TGGTGTGTTTCAGATGGATGATGTCTTATGAACATC
*
28839887 TGGTGTGTTTCAGATGGACT-A-GCTCTTATGAGCATC
1 TGGTGTGTTTCAGATGGA-TGATG-TCTTATGAACATC
28839923 TGGTGTGTTT
1 TGGTGTGTTT
28839933 TGGTAGGATT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
35 1 0.03
36 38 0.95
37 1 0.03
ACGTcount: A:0.16, C:0.12, G:0.30, T:0.41
Consensus pattern (36 bp):
TGGTGTGTTTCAGATGGATGATGTCTTATGAACATC
Found at i:28849882 original size:23 final size:23
Alignment explanation
Indices: 28849856--28849899 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
28849846 CAAGTAAAAT
28849856 AGATTTCAAAGTATATAAGCTAG
1 AGATTTCAAAGTATATAAGCTAG
*
28849879 AGATTTCAAAGTATGTAAGCT
1 AGATTTCAAAGTATATAAGCT
28849900 CTTCTATCCT
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:0.41, C:0.09, G:0.18, T:0.32
Consensus pattern (23 bp):
AGATTTCAAAGTATATAAGCTAG
Found at i:28854800 original size:12 final size:12
Alignment explanation
Indices: 28854783--28854815 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
28854773 CAGCCCGCCC
28854783 ATATTAATTTTT
1 ATATTAATTTTT
28854795 ATATT-ATTTTT
1 ATATTAATTTTT
28854806 ATA-TAATTTT
1 ATATTAATTTT
28854816 AAATATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:28856280 original size:30 final size:30
Alignment explanation
Indices: 28856236--28856298 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
28856226 ACTTAACAAG
*
28856236 CAAATGCCTCTAAAATAATAACAAAAATAA
1 CAAATGCCTCTAAAATAAAAACAAAAATAA
* * * *
28856266 CAAATGTCTTTAAAATAAAAACAATATTAA
1 CAAATGCCTCTAAAATAAAAACAAAAATAA
28856296 CAA
1 CAA
28856299 TAAAATAAGT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.59, C:0.14, G:0.03, T:0.24
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAAAAACAAAAATAA
Found at i:28856353 original size:22 final size:22
Alignment explanation
Indices: 28856328--28856370 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
28856318 TATTCAAACA
28856328 ATAACAACAAAATAGTAGCAAC
1 ATAACAACAAAATAGTAGCAAC
* **
28856350 ATAATAGTAAAATAGTAGCAA
1 ATAACAACAAAATAGTAGCAA
28856371 AATAGGGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATAGTAGCAAC
Found at i:28856374 original size:11 final size:11
Alignment explanation
Indices: 28856335--28856375 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
28856325 ACAATAACAA
28856335 CAAAATAGTAG
1 CAAAATAGTAG
* *
28856346 CAACATAATAG
1 CAAAATAGTAG
*
28856357 TAAAATAGTAG
1 CAAAATAGTAG
28856368 CAAAATAG
1 CAAAATAG
28856376 GGAGAAAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:28859304 original size:21 final size:21
Alignment explanation
Indices: 28859279--28859344 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
28859269 AAGGTGCAAT
28859279 TGGTATATAAGTGGCCTTAAA
1 TGGTATATAAGTGGCCTTAAA
* * * *
28859300 TGGTA-AT--TTGACCAGTAAT
1 TGGTATATAAGTGGCC-TTAAA
28859319 TGGTATATAAGTGGCCTTAAA
1 TGGTATATAAGTGGCCTTAAA
28859340 TGGTA
1 TGGTA
28859345 ATTAGACCAG
Statistics
Matches: 33, Mismatches: 8, Indels: 8
0.67 0.16 0.16
Matches are distributed among these distances:
18 4 0.12
19 8 0.24
20 4 0.12
21 13 0.39
22 4 0.12
ACGTcount: A:0.32, C:0.09, G:0.24, T:0.35
Consensus pattern (21 bp):
TGGTATATAAGTGGCCTTAAA
Found at i:28859320 original size:40 final size:40
Alignment explanation
Indices: 28859276--28859358 Score: 157
Period size: 40 Copynumber: 2.1 Consensus size: 40
28859266 CATAAGGTGC
*
28859276 AATTGGTATATAAGTGGCCTTAAATGGTAATTTGACCAGT
1 AATTGGTATATAAGTGGCCTTAAATGGTAATTAGACCAGT
28859316 AATTGGTATATAAGTGGCCTTAAATGGTAATTAGACCAGT
1 AATTGGTATATAAGTGGCCTTAAATGGTAATTAGACCAGT
28859356 AAT
1 AAT
28859359 ATTAATAGTG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.35, C:0.10, G:0.22, T:0.34
Consensus pattern (40 bp):
AATTGGTATATAAGTGGCCTTAAATGGTAATTAGACCAGT
Found at i:28859456 original size:15 final size:15
Alignment explanation
Indices: 28859432--28859466 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
28859422 TAAGTAATTT
* *
28859432 AATAATTAAAACCAA
1 AATAAGTAAAAACAA
28859447 AATAAGTAAAAACAA
1 AATAAGTAAAAACAA
28859462 AATAA
1 AATAA
28859467 TTATTCTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.71, C:0.09, G:0.03, T:0.17
Consensus pattern (15 bp):
AATAAGTAAAAACAA
Found at i:28861848 original size:44 final size:44
Alignment explanation
Indices: 28861780--28861867 Score: 149
Period size: 44 Copynumber: 2.0 Consensus size: 44
28861770 TGGACGTGCA
*
28861780 TCCCTACTTCGAATGTCCACATGGCCTAGCCACATGGCCATGTG
1 TCCCTACTTCGAATATCCACATGGCCTAGCCACATGGCCATGTG
* *
28861824 TCCCTACTTCGAATATTCAGATGGCCTAGCCACATGGCCATGTG
1 TCCCTACTTCGAATATCCACATGGCCTAGCCACATGGCCATGTG
28861868 ACCCCTGCAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.22, C:0.32, G:0.20, T:0.26
Consensus pattern (44 bp):
TCCCTACTTCGAATATCCACATGGCCTAGCCACATGGCCATGTG
Found at i:28862907 original size:21 final size:22
Alignment explanation
Indices: 28862881--28862922 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
28862871 GAAATTGTAT
28862881 TAAAAATAAAGAG-AATAAAAA
1 TAAAAATAAAGAGAAATAAAAA
*
28862902 TAAAAATAAAGGGAAATAAAA
1 TAAAAATAAAGAGAAATAAAA
28862923 TGGAAAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.14
Consensus pattern (22 bp):
TAAAAATAAAGAGAAATAAAAA
Found at i:28876372 original size:26 final size:29
Alignment explanation
Indices: 28876331--28876383 Score: 85
Period size: 26 Copynumber: 1.9 Consensus size: 29
28876321 TTGTTAAAAC
28876331 TCTTGTAAAAGAAAAA-TC-AAGAGAAAT
1 TCTTGTAAAAGAAAAACTCAAAGAGAAAT
28876358 TCTTG-AAAAGAAAAACTCAAAGAGAA
1 TCTTGTAAAAGAAAAACTCAAAGAGAA
28876384 TTTATGAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 10 0.42
27 7 0.29
28 7 0.29
ACGTcount: A:0.57, C:0.09, G:0.15, T:0.19
Consensus pattern (29 bp):
TCTTGTAAAAGAAAAACTCAAAGAGAAAT
Found at i:28876401 original size:20 final size:20
Alignment explanation
Indices: 28876371--28876408 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28876361 TGAAAAGAAA
28876371 AACTCAAAGAGAA-TTTATG
1 AACTCAAAGAGAAGTTTATG
28876390 AACTCAAAAGAGAAGTTTA
1 AACTC-AAAGAGAAGTTTA
28876409 ATAATAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 8 0.47
21 4 0.24
ACGTcount: A:0.50, C:0.11, G:0.16, T:0.24
Consensus pattern (20 bp):
AACTCAAAGAGAAGTTTATG
Found at i:28876564 original size:8 final size:8
Alignment explanation
Indices: 28876523--28876547 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
28876513 TTGGAATAAG
28876523 AAATAATA
1 AAATAATA
28876531 AAATAATA
1 AAATAATA
28876539 AAATAATA
1 AAATAATA
28876547 A
1 A
28876548 GAGCTAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AAATAATA
Found at i:28882799 original size:20 final size:20
Alignment explanation
Indices: 28882776--28882840 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
28882766 AAGCTCAAAC
28882776 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGTAAGCTAAATT
*
28882796 GAGCTTAAA-CAAGCTAAATT
1 GAGC-TAAAGTAAGCTAAATT
* * * * *
28882816 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGTAAGCTAAATT
28882836 GAGCT
1 GAGCT
28882841 GGGAAAAACT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
19 2 0.06
20 29 0.83
21 4 0.11
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (20 bp):
GAGCTAAAGTAAGCTAAATT
Found at i:28884419 original size:17 final size:19
Alignment explanation
Indices: 28884389--28884426 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
28884379 TTTATTGTCT
28884389 AAATTAATATATTTA-ATG
1 AAATTAATATATTTAGATG
*
28884407 AAATTATTA-ATTTAGATG
1 AAATTAATATATTTAGATG
28884425 AA
1 AA
28884427 GATCGAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (19 bp):
AAATTAATATATTTAGATG
Found at i:28884868 original size:27 final size:26
Alignment explanation
Indices: 28884816--28884885 Score: 79
Period size: 27 Copynumber: 2.7 Consensus size: 26
28884806 CGTTTCGACC
*
28884816 CACAGCTCGTGTGAGCAGGCCCATTTT
1 CACAGCTCGTGTGAGCATGCCCA-TTT
* **
28884843 CACAGCTCGTGTGAGCATTCTTATTT
1 CACAGCTCGTGTGAGCATGCCCATTT
*
28884869 -AGAGCTCGTGTGAGCAT
1 CACAGCTCGTGTGAGCAT
28884886 ACATGTGCAT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
25 16 0.42
26 3 0.08
27 19 0.50
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.30
Consensus pattern (26 bp):
CACAGCTCGTGTGAGCATGCCCATTT
Found at i:28890024 original size:37 final size:37
Alignment explanation
Indices: 28889983--28890077 Score: 181
Period size: 37 Copynumber: 2.6 Consensus size: 37
28889973 CATCTACTAT
28889983 CATGCCAAATTTATTGTAAATATAATCAACCTATATA
1 CATGCCAAATTTATTGTAAATATAATCAACCTATATA
28890020 CATGCCAAATTTATTGTAAATATAATCAACCTATATA
1 CATGCCAAATTTATTGTAAATATAATCAACCTATATA
*
28890057 CATGCCAAATTTATAGTAAAT
1 CATGCCAAATTTATTGTAAAT
28890078 GCCCTTACTG
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.43, C:0.16, G:0.06, T:0.35
Consensus pattern (37 bp):
CATGCCAAATTTATTGTAAATATAATCAACCTATATA
Found at i:28891582 original size:30 final size:30
Alignment explanation
Indices: 28891548--28891604 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
28891538 ATTATTCACA
28891548 TTTTC-ATATATTTAATTTCCTTTTTTTTTC
1 TTTTCTATAT-TTTAATTTCCTTTTTTTTTC
* **
28891578 TTTTCTTTATTTTCTTTTCCTTTTTTT
1 TTTTCTATATTTTAATTTCCTTTTTTT
28891605 CCTTTTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 20 0.87
31 3 0.13
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (30 bp):
TTTTCTATATTTTAATTTCCTTTTTTTTTC
Found at i:28891592 original size:14 final size:14
Alignment explanation
Indices: 28891573--28891614 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
28891563 TTTCCTTTTT
28891573 TTTTCTTTTCTTTA
1 TTTTCTTTTCTTTA
28891587 TTTTCTTTTCCTTT-
1 TTTTCTTTT-CTTTA
28891601 TTTTCCTTTT-TTTA
1 TTTT-CTTTTCTTTA
28891615 ATGGAAACCA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 3 0.12
14 13 0.52
15 9 0.36
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTCTTTTCTTTA
Found at i:28903684 original size:15 final size:17
Alignment explanation
Indices: 28903666--28903706 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
28903656 ACAAAAAATC
28903666 TTAATAAAA-TAT-TAA
1 TTAATAAAATTATCTAA
28903681 TTAAATAAAATTTATCTAA
1 TT-AATAAAA-TTATCTAA
28903700 TTAATAA
1 TTAATAA
28903707 TAAAAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 2 0.09
16 7 0.32
18 8 0.36
19 5 0.23
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
TTAATAAAATTATCTAA
Found at i:28909709 original size:22 final size:22
Alignment explanation
Indices: 28909681--28909724 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
28909671 TTTTGAACCA
28909681 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
28909703 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
28909725 AAATACCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:28931083 original size:19 final size:19
Alignment explanation
Indices: 28931053--28931090 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
28931043 TTACTAATTA
28931053 ATTCTTTATTTTTTATTTT
1 ATTCTTTATTTTTTATTTT
*
28931072 ATTCTTTATTTTTTGTTTT
1 ATTCTTTATTTTTTATTTT
28931091 TGATTTTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.13, C:0.05, G:0.03, T:0.79
Consensus pattern (19 bp):
ATTCTTTATTTTTTATTTT
Found at i:28932718 original size:34 final size:34
Alignment explanation
Indices: 28932662--28932727 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
28932652 TTAATTAATT
* *
28932662 AGCTTGACAATTGAAGTCCCCGAATAGTCATTGA
1 AGCTTGACAATTAAAGTCCCCGAACAGTCATTGA
* *
28932696 AGCTTGACACTTAAAGTTCCCGAACAGTCATT
1 AGCTTGACAATTAAAGTCCCCGAACAGTCATT
28932728 AGAGTGGACT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (34 bp):
AGCTTGACAATTAAAGTCCCCGAACAGTCATTGA
Found at i:28935958 original size:13 final size:13
Alignment explanation
Indices: 28935940--28935966 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28935930 GATGTAAATG
28935940 AAAAGGAAAAGGA
1 AAAAGGAAAAGGA
28935953 AAAAGGAAAAGGA
1 AAAAGGAAAAGGA
28935966 A
1 A
28935967 TGGTTTCAAC
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:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (13 bp):
AAAAGGAAAAGGA
Found at i:28942966 original size:19 final size:21
Alignment explanation
Indices: 28942942--28942983 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
28942932 TTTAAAACTC
28942942 ATTTTC-AAAAAT-TAATTTA
1 ATTTTCTAAAAATATAATTTA
28942961 ATTTTCTAAAAATCATAATTTA
1 ATTTTCTAAAAAT-ATAATTTA
28942983 A
1 A
28942984 AACATTACTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 6 0.30
22 8 0.40
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (21 bp):
ATTTTCTAAAAATATAATTTA
Found at i:28943261 original size:26 final size:26
Alignment explanation
Indices: 28943232--28943378 Score: 181
Period size: 26 Copynumber: 5.7 Consensus size: 26
28943222 ACAGAATTTT
* *
28943232 CCACAAAATCATTCTTTCATATTACA
1 CCACAAAAGCTTTCTTTCATATTACA
** *
28943258 CCACAATGGCTTTCTTTCATATTACG
1 CCACAAAAGCTTTCTTTCATATTACA
28943284 CCACAAAAGCTTTCTTTCATATTACA
1 CCACAAAAGCTTTCTTTCATATTACA
*
28943310 CCAC-AAAGACTTT-TTTCATATTACT
1 CCACAAAAG-CTTTCTTTCATATTACA
* **
28943335 CCACAAAGGCTTTCTTTCATATTATG
1 CCACAAAAGCTTTCTTTCATATTACA
*
28943361 CCACAAAGGCTTTCTTTC
1 CCACAAAAGCTTTCTTTC
28943379 TAGACGTGTT
Statistics
Matches: 106, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
25 23 0.22
26 83 0.78
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.37
Consensus pattern (26 bp):
CCACAAAAGCTTTCTTTCATATTACA
Found at i:28943322 original size:22 final size:22
Alignment explanation
Indices: 28943297--28943348 Score: 59
Period size: 25 Copynumber: 2.2 Consensus size: 22
28943287 CAAAAGCTTT
28943297 CTTTCATATTACACCACAAAGA
1 CTTTCATATTACACCACAAAGA
* *
28943319 CTTTTTTCATATTACTCCACAAAGG
1 C---TTTCATATTACACCACAAAGA
28943344 CTTTC
1 CTTTC
28943349 TTTCATATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
22 5 0.20
25 20 0.80
ACGTcount: A:0.31, C:0.27, G:0.06, T:0.37
Consensus pattern (22 bp):
CTTTCATATTACACCACAAAGA
Found at i:28943347 original size:51 final size:52
Alignment explanation
Indices: 28943232--28943378 Score: 215
Period size: 51 Copynumber: 2.8 Consensus size: 52
28943222 ACAGAATTTT
* * *
28943232 CCACAAAATCATTCTTTCATATTACACCACAATGGCTTTCTTTCATATTACG
1 CCACAAAAGCTTTCTTTCATATTACACCACAAAGGCTTTCTTTCATATTACG
* *
28943284 CCACAAAAGCTTTCTTTCATATTACACCACAAAGACTTT-TTTCATATTACT
1 CCACAAAAGCTTTCTTTCATATTACACCACAAAGGCTTTCTTTCATATTACG
* **
28943335 CCACAAAGGCTTTCTTTCATATTATGCCACAAAGGCTTTCTTTC
1 CCACAAAAGCTTTCTTTCATATTACACCACAAAGGCTTTCTTTC
28943379 TAGACGTGTT
Statistics
Matches: 85, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
51 46 0.54
52 39 0.46
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.37
Consensus pattern (52 bp):
CCACAAAAGCTTTCTTTCATATTACACCACAAAGGCTTTCTTTCATATTACG
Found at i:28947818 original size:12 final size:12
Alignment explanation
Indices: 28947801--28947828 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
28947791 CCCCAAATGG
28947801 CACAGCTCTCCT
1 CACAGCTCTCCT
28947813 CACAGCTCTCCT
1 CACAGCTCTCCT
28947825 CACA
1 CACA
28947829 TAACAACTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.21, C:0.50, G:0.07, T:0.21
Consensus pattern (12 bp):
CACAGCTCTCCT
Found at i:28954686 original size:25 final size:24
Alignment explanation
Indices: 28954637--28954690 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
28954627 GTCATTAGGG
* * *
28954637 TTACCGATTCCAGCTCTTATGAGC
1 TTACCGATACCAACTCGTATGAGC
28954661 TTACCGATACTCAACTCGTATGAGC
1 TTACCGATAC-CAACTCGTATGAGC
28954686 TTACC
1 TTACC
28954691 ATTATTCAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 9 0.35
25 17 0.65
ACGTcount: A:0.24, C:0.30, G:0.15, T:0.31
Consensus pattern (24 bp):
TTACCGATACCAACTCGTATGAGC
Found at i:28954699 original size:25 final size:25
Alignment explanation
Indices: 28954654--28954733 Score: 69
Period size: 25 Copynumber: 3.3 Consensus size: 25
28954644 TTCCAGCTCT
*
28954654 TATGAGCTTACCGA-TACTCAACTCG
1 TATGAGCTTACC-ATTATTCAACTCG
*
28954679 TATGAGCTTACCATTATTCAATTCAG
1 TATGAGCTTACCATTATTCAACTC-G
* * *
28954705 -AGGAGCTTATCATTATT--GCTCG
1 TATGAGCTTACCATTATTCAACTCG
28954727 TATGAGC
1 TATGAGC
28954734 ATACATGTAC
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
22 1 0.02
23 7 0.16
24 1 0.02
25 35 0.78
26 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (25 bp):
TATGAGCTTACCATTATTCAACTCG
Found at i:28966145 original size:19 final size:19
Alignment explanation
Indices: 28966116--28966158 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
28966106 CGTTATAGGC
28966116 CTCGT-TGGGCTGAAATGGG
1 CTCGTGTGGGCT-AAATGGG
*
28966135 -TCGTGTGGGCTCAATGGG
1 CTCGTGTGGGCTAAATGGG
28966153 CTCGTG
1 CTCGTG
28966159 GGCCTCACAC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.12, C:0.19, G:0.42, T:0.28
Consensus pattern (19 bp):
CTCGTGTGGGCTAAATGGG
Found at i:28966405 original size:27 final size:27
Alignment explanation
Indices: 28966369--28966601 Score: 340
Period size: 27 Copynumber: 8.6 Consensus size: 27
28966359 AAAGGTTGTT
28966369 AAATGACCGTAATACCCCTGTAGGGTA
1 AAATGACCGTAATACCCCTGTAGGGTA
28966396 AAATGACCGTAATACCCCTGTAGGGTA
1 AAATGACCGTAATACCCCTGTAGGGTA
* * *
28966423 AAATGACCATAATGCCCTTGTAGGGTA
1 AAATGACCGTAATACCCCTGTAGGGTA
* *
28966450 AAATTACCGTAATACCCCTATAGGGTA
1 AAATGACCGTAATACCCCTGTAGGGTA
*
28966477 AAATGACCGTAATACCCCGGTAGGGTA
1 AAATGACCGTAATACCCCTGTAGGGTA
* * *
28966504 AAATGATCATAATGCCCCTGTAGGGTA
1 AAATGACCGTAATACCCCTGTAGGGTA
* *
28966531 AAATGACCATAATACCCCTATAGGGTA
1 AAATGACCGTAATACCCCTGTAGGGTA
* * *
28966558 GAATGACCATAATGCCCCTGTAGGGTA
1 AAATGACCGTAATACCCCTGTAGGGTA
28966585 AAATGACCGTAATACCC
1 AAATGACCGTAATACCC
28966602 TCGAGGTCAA
Statistics
Matches: 182, Mismatches: 24, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 182 1.00
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.23
Consensus pattern (27 bp):
AAATGACCGTAATACCCCTGTAGGGTA
Found at i:28966667 original size:24 final size:24
Alignment explanation
Indices: 28966611--28966692 Score: 96
Period size: 24 Copynumber: 3.5 Consensus size: 24
28966601 CTCGAGGTCA
* * * *
28966611 AATGATTGAATTGTCTGTG-GTTA
1 AATGACTGATTTGTCTGTGATTTG
28966634 AATGACTGATTTGTCTGTG-TTTGG
1 AATGACTGATTTGTCTGTGATTT-G
*
28966658 TATGACTGATTTGTCTGTGATTTG
1 AATGACTGATTTGTCTGTGATTTG
28966682 AATGACTGATT
1 AATGACTGATT
28966693 CTGAGCATGG
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
23 19 0.37
24 29 0.57
25 3 0.06
ACGTcount: A:0.22, C:0.07, G:0.26, T:0.45
Consensus pattern (24 bp):
AATGACTGATTTGTCTGTGATTTG
Found at i:28966804 original size:27 final size:26
Alignment explanation
Indices: 28966761--28966819 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 26
28966751 GGAAGTACGG
28966761 TACTGGTGGCTCTGCCACA-ATCACTA
1 TACTGGTGGCTCTGCCACATAT-ACTA
28966787 TTACTGGTGGCT-TGGCCACATATACTA
1 -TACTGGTGGCTCT-GCCACATATACTA
28966814 TACTGG
1 TACTGG
28966820 CAACTTTACT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
26 7 0.23
27 21 0.70
28 2 0.07
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (26 bp):
TACTGGTGGCTCTGCCACATATACTA
Found at i:28966904 original size:32 final size:32
Alignment explanation
Indices: 28966863--28967065 Score: 275
Period size: 32 Copynumber: 6.4 Consensus size: 32
28966853 GCTGCGATGC
* *
28966863 TACTGATGGCTTTGTGTCGGTCATATTACAGT
1 TACTGATGGCTTTGTGCCGATCATATTACAGT
*
28966895 TACTGATGGCTTTGTGCCGATCATATTACTGT
1 TACTGATGGCTTTGTGCCGATCATATTACAGT
*
28966927 TACTGATGGTTTTGTGCCGATCATATTACCA-T
1 TACTGATGGCTTTGTGCCGATCATATTA-CAGT
* *
28966959 TATTGATGGCTTTGTGCCGATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACAGT
*
28966991 TACTGATGGCTTTGTGCCGATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACAGT
* * * *
28967023 TATTGATGGCTTTGTGCCAAACATATTACTG-
1 TACTGATGGCTTTGTGCCGATCATATTACAGT
*
28967054 TACTTATGGCTT
1 TACTGATGGCTT
28967066 GTAGCCATTC
Statistics
Matches: 154, Mismatches: 15, Indels: 5
0.89 0.09 0.03
Matches are distributed among these distances:
31 11 0.07
32 142 0.92
33 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.40
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATATTACAGT
Found at i:28967082 original size:22 final size:21
Alignment explanation
Indices: 28967057--28967120 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 21
28967047 ATTACTGTAC
28967057 TTATGGCTTGTAGCCATTCTGT
1 TTATGGCTT-TAGCCATTCTGT
* *
28967079 TTATAGCTTATAGCTA-TCTTGT
1 TTATGGCTT-TAGCCATTC-TGT
*
28967101 TTACGGCTCTTAGCCATTCT
1 TTATGGCT-TTAGCCATTCT
28967121 AACTACTAGC
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
21 2 0.06
22 28 0.85
23 3 0.09
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.45
Consensus pattern (21 bp):
TTATGGCTTTAGCCATTCTGT
Found at i:28977071 original size:30 final size:30
Alignment explanation
Indices: 28977037--28977168 Score: 183
Period size: 30 Copynumber: 4.4 Consensus size: 30
28977027 CTATCGAATT
* * *
28977037 ATGAAAAGGGATGGTGACAACAATCAAACA
1 ATGAAAAGGGATGCTGACGACCATCAAACA
* * * *
28977067 ATGAAAAGGGATGGTGATGACCGTCGAACA
1 ATGAAAAGGGATGCTGACGACCATCAAACA
*
28977097 ATGAAAAGGGATGCTGACGACCATCGAACA
1 ATGAAAAGGGATGCTGACGACCATCAAACA
*
28977127 ATGAAAAGGGATGCTGACGACCATCAAACT
1 ATGAAAAGGGATGCTGACGACCATCAAACA
28977157 ATGAAAAGGGAT
1 ATGAAAAGGGAT
28977169 AGCTTCGGCT
Statistics
Matches: 92, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 92 1.00
ACGTcount: A:0.42, C:0.15, G:0.27, T:0.15
Consensus pattern (30 bp):
ATGAAAAGGGATGCTGACGACCATCAAACA
Found at i:28980047 original size:2 final size:2
Alignment explanation
Indices: 28980040--28980064 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28980030 CTAACTTAAG
28980040 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
28980065 CTCAAGATTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28980612 original size:3 final size:3
Alignment explanation
Indices: 28980604--28980646 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
28980594 TGTTGCTGAA
* * *
28980604 TAT TAT TAT TAT CAT TAT TAT TAC TAC TAT TAT TAT T-T TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
28980647 ATTACTTAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:28981794 original size:6 final size:6
Alignment explanation
Indices: 28981783--28981813 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
28981773 AGGTGAGTTT
*
28981783 CTCGAC CTCGAC CTCGAC CTTGAC CTCGAC C
1 CTCGAC CTCGAC CTCGAC CTCGAC CTCGAC C
28981814 CTTACCCTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.16, C:0.48, G:0.16, T:0.19
Consensus pattern (6 bp):
CTCGAC
Found at i:28983619 original size:27 final size:27
Alignment explanation
Indices: 28983589--28983882 Score: 319
Period size: 27 Copynumber: 10.9 Consensus size: 27
28983579 TTTCATCTCT
**
28983589 TAGGGGTATAACAGTCATTTTACCCTA
1 TAGGGGTATTTCAGTCATTTTACCCTA
**
28983616 TAGGGGTATTTTGGTCATTTTACCCTA
1 TAGGGGTATTTCAGTCATTTTACCCTA
*
28983643 TAGGGGTATTTCAGTCATTTTACCTTA
1 TAGGGGTATTTCAGTCATTTTACCCTA
* * * *
28983670 TAGGGGTATTCCAGTTATTTTGCACTA
1 TAGGGGTATTTCAGTCATTTTACCCTA
* *
28983697 TAAGGGTATTTCGGTCATTTTACCCTA
1 TAGGGGTATTTCAGTCATTTTACCCTA
* *
28983724 TATGGGTAATTC-GATCATTTTACCCTA
1 TAGGGGTATTTCAG-TCATTTTACCCTA
28983751 T-GGGGATATTTCAGTCATTTTACCCTA
1 TAGGGG-TATTTCAGTCATTTTACCCTA
* **
28983778 TGGGGGTATTTTGGTCATTTTACCCTA
1 TAGGGGTATTTCAGTCATTTTACCCTA
* *
28983805 TGGGGGTATTTCGGTCATTTTACCCTA
1 TAGGGGTATTTCAGTCATTTTACCCTA
*
28983832 T-GAGGGTATTTC-GATCATTTTACCTTA
1 TAG-GGGTATTTCAG-TCATTTTACCCTA
* *
28983859 T-GAGGGTATTTTAATCATTTTACC
1 TAG-GGGTATTTCAGTCATTTTACC
28983883 TATTTTAGGG
Statistics
Matches: 232, Mismatches: 28, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
26 6 0.03
27 221 0.95
28 5 0.02
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.42
Consensus pattern (27 bp):
TAGGGGTATTTCAGTCATTTTACCCTA
Found at i:28990915 original size:17 final size:17
Alignment explanation
Indices: 28990893--28990929 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
28990883 TTGAAAAACC
28990893 CTTCTTGAAATTTCAAA
1 CTTCTTGAAATTTCAAA
**
28990910 CTTCTTGCCATTTCAAA
1 CTTCTTGAAATTTCAAA
28990927 CTT
1 CTT
28990930 GTACAAAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.27, C:0.24, G:0.05, T:0.43
Consensus pattern (17 bp):
CTTCTTGAAATTTCAAA
Found at i:28991746 original size:22 final size:22
Alignment explanation
Indices: 28991721--28991767 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
28991711 CTAAGAGTCG
* * *
28991721 TAAACAGGATAGCTATAAGCTA
1 TAAACAGAATAGCTACAAGCCA
*
28991743 TAAACAGAATGGCTACAAGCCA
1 TAAACAGAATAGCTACAAGCCA
28991765 TAA
1 TAA
28991768 GTACAGTAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.19
Consensus pattern (22 bp):
TAAACAGAATAGCTACAAGCCA
Found at i:28991856 original size:26 final size:26
Alignment explanation
Indices: 28991808--28991857 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
28991798 AGTAGCATCG
28991808 CAGCAAAGCTGCCAGCAACAGTATCA
1 CAGCAAAGCTGCCAGCAACAGTATCA
* *
28991834 CAGCAAAGCTGCCAGTAATAGTAT
1 CAGCAAAGCTGCCAGCAACAGTAT
28991858 ATGTGGCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.38, C:0.26, G:0.20, T:0.16
Consensus pattern (26 bp):
CAGCAAAGCTGCCAGCAACAGTATCA
Found at i:28991875 original size:27 final size:27
Alignment explanation
Indices: 28991845--28991908 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
28991835 AGCAAAGCTG
*
28991845 CCAGTAATAGT-ATATGTGGCCA-AGCCA
1 CCAGTAACAGTGAT-TGTGG-CAGAGCCA
28991872 CCAGTAACAGTGATTGTGGCAGAGCCA
1 CCAGTAACAGTGATTGTGGCAGAGCCA
28991899 CCAGT-ACAGT
1 CCAGTAACAGT
28991909 ACTTCCTCCA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
26 7 0.21
27 25 0.74
28 2 0.06
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.20
Consensus pattern (27 bp):
CCAGTAACAGTGATTGTGGCAGAGCCA
Found at i:28992058 original size:24 final size:24
Alignment explanation
Indices: 28991994--28992059 Score: 105
Period size: 24 Copynumber: 2.8 Consensus size: 24
28991984 CCATTCATAG
*
28991994 ACAAATCAATCATTTAAATCACAA
1 ACAAATCAATCATTTACATCACAA
* *
28992018 ACAAATCAGTCATTTACATCACGA
1 ACAAATCAATCATTTACATCACAA
28992042 ACAAATCAATCATTTACA
1 ACAAATCAATCATTTACA
28992060 CTCGAGGGGT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.48, C:0.23, G:0.03, T:0.26
Consensus pattern (24 bp):
ACAAATCAATCATTTACATCACAA
Found at i:28992133 original size:27 final size:27
Alignment explanation
Indices: 28992103--28992647 Score: 589
Period size: 27 Copynumber: 20.2 Consensus size: 27
28992093 GGCATTACGG
*
28992103 TCATTTAACCCTATGAGGGTATTTCGA
1 TCATTTTACCCTATGAGGGTATTTCGA
* *
28992130 TCATTTTACCCTATGGGGGTATTTCGG
1 TCATTTTACCCTATGAGGGTATTTCGA
* *
28992157 TCATTTTACCCTATGGGGGTACTTC-A
1 TCATTTTACCCTATGAGGGTATTTCGA
28992183 GTCATTTTACCCTATGAGGGTATTT-GA
1 -TCATTTTACCCTATGAGGGTATTTCGA
28992210 GTCA-TTTAGCCCTATGAGGGTATTTCGA
1 -TCATTTTA-CCCTATGAGGGTATTTCGA
* * *
28992238 TCATTTTACCTTATGGGGGTATTT-GG
1 TCATTTTACCCTATGAGGGTATTTCGA
* * *
28992264 TTATTTTACCCTATGGGGGTATTTCGG
1 TCATTTTACCCTATGAGGGTATTTCGA
*
28992291 TCATTTTACCCTATGAGGGTATTTCGG
1 TCATTTTACCCTATGAGGGTATTTCGA
* * * * * *
28992318 TCATTCTATCTTATGGGGGTATTTTGG
1 TCATTTTACCCTATGAGGGTATTTCGA
* * * * * *
28992345 TCATTTAAACTTATGGGGGTATTTTGG
1 TCATTTTACCCTATGAGGGTATTTCGA
* *
28992372 TCATTTTACCCTATGGGGGTATTTTGA
1 TCATTTTACCCTATGAGGGTATTTCGA
* * * *
28992399 TCATTCTACCTTATGAAGGTATTTCGG
1 TCATTTTACCCTATGAGGGTATTTCGA
* *
28992426 TCATTCTACCCTAAGAGGGTATTTC-A
1 TCATTTTACCCTATGAGGGTATTTCGA
* * *
28992452 GTCATTCTACCCTATGAGAGTATTTCGG
1 -TCATTTTACCCTATGAGGGTATTTCGA
*
28992480 TCATTTAACCCTATGAGGGTATTTCGA
1 TCATTTTACCCTATGAGGGTATTTCGA
*
28992507 TCATTCTACCCTATGAGGGTATTTCGA
1 TCATTTTACCCTATGAGGGTATTTCGA
*
28992534 TCATTTTACCCTATGGGGGTATTTCGA
1 TCATTTTACCCTATGAGGGTATTTCGA
* *
28992561 TCATTCTACCCTATGAGAGTATTTC-A
1 TCATTTTACCCTATGAGGGTATTTCGA
* * *
28992587 GTCATTCTACCCTATGTGGGTATTTCGG
1 -TCATTTTACCCTATGAGGGTATTTCGA
* * *
28992615 TAATTTTACCCTTTGAGGGTATTTCGG
1 TCATTTTACCCTATGAGGGTATTTCGA
28992642 TCATTT
1 TCATTT
28992648 AAAAACCTTT
Statistics
Matches: 450, Mismatches: 58, Indels: 20
0.85 0.11 0.04
Matches are distributed among these distances:
26 28 0.06
27 416 0.92
28 6 0.01
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.41
Consensus pattern (27 bp):
TCATTTTACCCTATGAGGGTATTTCGA
Found at i:28994643 original size:13 final size:13
Alignment explanation
Indices: 28994625--28994700 Score: 98
Period size: 13 Copynumber: 5.8 Consensus size: 13
28994615 AGTTCTTCAT
28994625 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
28994638 TGCTTTTAAAAAG
1 TGCTTTTGAAAAG
* *
28994651 TGCTGTAGAAAAG
1 TGCTTTTGAAAAG
* *
28994664 TGCTGTAGAAAAG
1 TGCTTTTGAAAAG
*
28994677 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
28994690 TGCTTTTGAAA
1 TGCTTTTGAAA
28994701 GGTTTGGTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 55 1.00
ACGTcount: A:0.33, C:0.08, G:0.25, T:0.34
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:28997814 original size:19 final size:19
Alignment explanation
Indices: 28997772--28997816 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
28997762 ATATCTGTCA
*
28997772 ATTTCATTATTTAAATTAT
1 ATTTTATTATTTAAATTAT
* *
28997791 GTTTTATTATTTAAATTTT
1 ATTTTATTATTTAAATTAT
28997810 ATTTTAT
1 ATTTTAT
28997817 CCATATTATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (19 bp):
ATTTTATTATTTAAATTAT
Found at i:28998592 original size:59 final size:57
Alignment explanation
Indices: 28998432--28998594 Score: 186
Period size: 59 Copynumber: 2.8 Consensus size: 57
28998422 ATATTATATA
* * *
28998432 TTATGATTTTTATTAATTCATATTTTAATAATAATTATACTAAAAATATTATTAAATTAT
1 TTATTATTTTTATTAATT-ATA-TTTAATAATAATTATA-TTAAAATATGATTAAATTAT
* * *
28998492 ATATTA-TTTTATTAAATTGTATTTAATAATAATTATGTTAAAATATGATTAAATTAT
1 TTATTATTTTTATT-AATTATATTTAATAATAATTATATTAAAATATGATTAAATTAT
*
28998549 TTATTATTTATTATTAAGTTATATTTATTAATAATCT-TATTAAAAT
1 TTATTATTT-TTATTAA-TTATATTTAATAATAAT-TATATTAAAAT
28998595 TTAATAATAA
Statistics
Matches: 88, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
57 23 0.26
58 19 0.22
59 37 0.42
60 9 0.10
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (57 bp):
TTATTATTTTTATTAATTATATTTAATAATAATTATATTAAAATATGATTAAATTAT
Found at i:29000695 original size:13 final size:13
Alignment explanation
Indices: 29000677--29000736 Score: 86
Period size: 13 Copynumber: 4.6 Consensus size: 13
29000667 TTAACAATAT
29000677 TTTTGAAAAGTGC
1 TTTTGAAAAGTGC
29000690 TTTTGAAAAGTGC
1 TTTTGAAAAGTGC
29000703 TTTTGAAAAGTG-
1 TTTTGAAAAGTGC
* *
29000715 TTGTGGAAAAGTAC
1 TT-TTGAAAAGTGC
29000729 TTTTGAAA
1 TTTTGAAA
29000737 TGTTTGGTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
12 2 0.05
13 38 0.90
14 2 0.05
ACGTcount: A:0.33, C:0.05, G:0.23, T:0.38
Consensus pattern (13 bp):
TTTTGAAAAGTGC
Found at i:29001650 original size:15 final size:15
Alignment explanation
Indices: 29001632--29001680 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
29001622 AATCATTATT
29001632 AATAAAATTTATTCA
1 AATAAAATTTATTCA
29001647 AATAAAA--TATT-A
1 AATAAAATTTATTCA
* *
29001659 TATAAGATTTTATTCA
1 AATAA-AATTTATTCA
29001675 AATAAA
1 AATAAA
29001681 TATATATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
12 5 0.19
13 5 0.19
15 12 0.44
16 5 0.19
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (15 bp):
AATAAAATTTATTCA
Found at i:29001698 original size:28 final size:28
Alignment explanation
Indices: 29001604--29001685 Score: 76
Period size: 28 Copynumber: 2.8 Consensus size: 28
29001594 TTTTTATATT
*
29001604 CATTTTATTCTAAAACAAAATCATTATTAATAA
1 CATTTTATTC--AAATAAAAT-ATTA-T-ATAA
*
29001637 -AATTTATTCAAATAAAATATTATATAA
1 CATTTTATTCAAATAAAATATTATATAA
*
29001664 GATTTTATTCAAATAAATATAT
1 CATTTTATTCAAATAAA-ATAT
29001686 ATTTTTCATT
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
27 4 0.09
28 16 0.36
29 8 0.18
30 8 0.18
32 8 0.18
ACGTcount: A:0.50, C:0.07, G:0.01, T:0.41
Consensus pattern (28 bp):
CATTTTATTCAAATAAAATATTATATAA
Found at i:29004252 original size:24 final size:24
Alignment explanation
Indices: 29004225--29004272 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
29004215 AGTAACTCAT
29004225 TTCCTTAAAAAAACAAATTACGGG
1 TTCCTTAAAAAAACAAATTACGGG
*
29004249 TTCCTTCAAAAAACAAATTACGGG
1 TTCCTTAAAAAAACAAATTACGGG
29004273 CTACCAAGTG
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:0.44, C:0.19, G:0.12, T:0.25
Consensus pattern (24 bp):
TTCCTTAAAAAAACAAATTACGGG
Found at i:29004990 original size:8 final size:8
Alignment explanation
Indices: 29004977--29005007 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
29004967 ACAAATATTT
29004977 AATAATAA
1 AATAATAA
29004985 AATAATAA
1 AATAATAA
29004993 AATAATAA
1 AATAATAA
29005001 AATAATA
1 AATAATA
29005008 TATTTAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (8 bp):
AATAATAA
Found at i:29005234 original size:8 final size:8
Alignment explanation
Indices: 29005221--29005272 Score: 58
Period size: 8 Copynumber: 6.8 Consensus size: 8
29005211 TCATTTTAAA
29005221 AATATTTT
1 AATATTTT
29005229 AATA--TT
1 AATATTTT
29005235 AATATTTT
1 AATATTTT
29005243 AATATTCATT
1 AATATT--TT
29005253 -A-ATTTT
1 AATATTTT
29005259 AATATTTT
1 AATATTTT
29005267 AATATT
1 AATATT
29005273 AAAATTTAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
6 8 0.21
7 1 0.03
8 26 0.68
9 1 0.03
10 2 0.05
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (8 bp):
AATATTTT
Found at i:29005240 original size:14 final size:14
Alignment explanation
Indices: 29005221--29005279 Score: 63
Period size: 14 Copynumber: 4.5 Consensus size: 14
29005211 TCATTTTAAA
29005221 AATATTTTAATATT
1 AATATTTTAATATT
29005235 AATATTTTAATATT
1 AATATTTTAATATT
* *
29005249 --CA--TTAATTTT
1 AATATTTTAATATT
29005259 AATATTTTAATATT
1 AATATTTTAATATT
*
29005273 AAAATTT
1 AATATTT
29005280 AATTAAATTA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
10 7 0.19
12 2 0.06
14 27 0.75
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (14 bp):
AATATTTTAATATT
Found at i:29005260 original size:24 final size:24
Alignment explanation
Indices: 29005227--29005272 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
29005217 TAAAAATATT
29005227 TTAATATTAATATTTTAATATTCA
1 TTAATATTAATATTTTAATATTCA
*
29005251 TTAATTTTAATATTTTAATATT
1 TTAATATTAATATTTTAATATT
29005273 AAAATTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (24 bp):
TTAATATTAATATTTTAATATTCA
Found at i:29012093 original size:42 final size:41
Alignment explanation
Indices: 29012013--29012462 Score: 471
Period size: 42 Copynumber: 10.8 Consensus size: 41
29012003 GGATCCCGGT
* * * *
29012013 GGAATCAACACTTAGCAACCACC-TTATAATCAATGATACGG
1 GGAATCAGCACATAGCAACC-CCTTTACAATCAAGGATACGG
* *
29012054 GGAATCAACACATAGTAACCCCTTTCACAATCAAGGATACGG
1 GGAATCAGCACATAGCAACCCCTTT-ACAATCAAGGATACGG
* * * * *
29012096 TGGGATCAGCACTTAGCAACCACC-TTATAATCAATGATATGG
1 -GGAATCAGCACATAGCAACC-CCTTTACAATCAAGGATACGG
29012138 GGAATCAGCACATAGCAACCCCTTTCACAATCAAGGATACGG
1 GGAATCAGCACATAGCAACCCCTTT-ACAATCAAGGATACGG
29012180 GGAATCAGCACATAGCAACCCCTTTCACAATCAAGGATACGG
1 GGAATCAGCACATAGCAACCCCTTT-ACAATCAAGGATACGG
*
29012222 GGAATCAGCACATAGCAACCCTTTTCACAATCAAGGATACGG
1 GGAATCAGCACATAGCAACCCCTTT-ACAATCAAGGATACGG
* * * *
29012264 TGGAATCAACACTTAGCAACCACC-TTATAATCAATGATACGG
1 -GGAATCAGCACATAGCAACC-CCTTTACAATCAAGGATACGG
*
29012306 GGAATCAGCACATACCAACCCCTTTCACAATCAAGGATACGG
1 GGAATCAGCACATAGCAACCCCTTT-ACAATCAAGGATACGG
* * * *
29012348 TGGAATCAGCACTTAGCAACCACC-TTATAATCAATGTTACGG
1 -GGAATCAGCACATAGCAACC-CCTTTACAATCAAGGATACGG
* * *** * *
29012390 TGAATCAACACATAGCAACCCCTTTTTGATCAATGATTCGG
1 GGAATCAGCACATAGCAACCCCTTTACAATCAAGGATACGG
* *
29012431 GGAATCTA-CACTTAGCAACCCC-TTACATTCAA
1 GGAATC-AGCACATAGCAACCCCTTTACAATCAA
29012463 AGAATCCCGG
Statistics
Matches: 350, Mismatches: 45, Indels: 29
0.83 0.11 0.07
Matches are distributed among these distances:
40 14 0.04
41 108 0.31
42 165 0.47
43 58 0.17
44 5 0.01
ACGTcount: A:0.36, C:0.26, G:0.16, T:0.22
Consensus pattern (41 bp):
GGAATCAGCACATAGCAACCCCTTTACAATCAAGGATACGG
Found at i:29012115 original size:84 final size:84
Alignment explanation
Indices: 29012009--29012455 Score: 654
Period size: 84 Copynumber: 5.4 Consensus size: 84
29011999 CAAAGGATCC
* * *
29012009 CGGTGGAATCAACACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAACACATAGTAACC
1 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACC
29012074 CCTTTCACAATCAAGGATA
66 CCTTTCACAATCAAGGATA
* *
29012093 CGGTGGGATCAGCACTTAGCAACCACCTTATAATCAATGATATGGGGAATCAGCACATAGCAACC
1 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACC
29012158 CCTTTCACAATCAAGGATA
66 CCTTTCACAATCAAGGATA
* * *
29012177 CGG-GGAATCAGCACATAGCAACC-CCTTTCACAATCAAGGATACGGGGAATCAGCACATAGCAA
1 CGGTGGAATCAGCACTTAGCAACCACC-TT-ATAATCAATGATACGGGGAATCAGCACATAGCAA
*
29012240 CCCTTTTCACAATCAAGGATA
64 CCCCTTTCACAATCAAGGATA
* *
29012261 CGGTGGAATCAACACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATACCAACC
1 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACC
29012326 CCTTTCACAATCAAGGATA
66 CCTTTCACAATCAAGGATA
* * *
29012345 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGTTACGGTGAATCAACACATAGCAACC
1 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACC
*** * *
29012410 CCTTT-TTGATCAATGATT
66 CCTTTCACAATCAAGGATA
29012428 CGG-GGAATCTA-CACTTAGCAACC-CCTTA
1 CGGTGGAATC-AGCACTTAGCAACCACCTTA
29012456 CATTCAAAGA
Statistics
Matches: 331, Mismatches: 27, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
81 5 0.02
82 20 0.06
83 32 0.10
84 252 0.76
85 20 0.06
86 2 0.01
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (84 bp):
CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACC
CCTTTCACAATCAAGGATA
Found at i:29017122 original size:5 final size:5
Alignment explanation
Indices: 29017110--29017147 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
29017100 AAAAGTTAAG
*
29017110 TATA- TATAT TATA- GATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
29017148 AATAAAAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
4 7 0.23
5 23 0.77
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (5 bp):
TATAT
Done.