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 114 of 208
Found at i:34450927 original size:27 final size:27
Alignment explanation
Indices: 34450883--34451053 Score: 121
Period size: 27 Copynumber: 6.4 Consensus size: 27
34450873 ATCCTGTCAT
**
34450883 CCTTTGTAACATACTCTGAATGGATCG
1 CCTTTGTGGCATACTCTGAATGGATCG
* * * * *
34450910 CCTTTGTGGCGTAGTCTGTATGAATCA
1 CCTTTGTGGCATACTCTGAATGGATCG
* * * *
34450937 CCTTTGCGGCATACTCTGTATGAATCA
1 CCTTTGTGGCATACTCTGAATGGATCG
* * * * *
34450964 TCTTTTTGGCATACTCTGTATAGATAG
1 CCTTTGTGGCATACTCTGAATGGATCG
* *
34450991 CCTTTATGGCGA-ACTCTGAATGG-TTG
1 CCTTTGTGGC-ATACTCTGAATGGATCG
* * *
34451017 CCTTTGTAGAATACTCTAAATGGATCG
1 CCTTTGTGGCATACTCTGAATGGATCG
*
34451044 CCTTAGTGGC
1 CCTTTGTGGC
34451054 CTATCTTACA
Statistics
Matches: 111, Mismatches: 30, Indels: 6
0.76 0.20 0.04
Matches are distributed among these distances:
25 1 0.01
26 19 0.17
27 90 0.81
28 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (27 bp):
CCTTTGTGGCATACTCTGAATGGATCG
Found at i:34455180 original size:20 final size:20
Alignment explanation
Indices: 34455155--34455195 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
34455145 TAGAAACAAA
*
34455155 TCAGAAACACATAAAAATTT
1 TCAGAAAAACATAAAAATTT
* *
34455175 TCAGAAAAAGATTAAAATTT
1 TCAGAAAAACATAAAAATTT
34455195 T
1 T
34455196 TAAACTATAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.10, G:0.07, T:0.29
Consensus pattern (20 bp):
TCAGAAAAACATAAAAATTT
Found at i:34456420 original size:30 final size:30
Alignment explanation
Indices: 34456384--34456458 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
34456374 TTACCACTTC
*
34456384 TTTTCATAGTTCGATAGCCGAAGCTATCCA
1 TTTTCATAGTTCGATAGCCGAAGCCATCCA
* *
34456414 TTTTCAT-GTTTTGATAGCCGAAGCCATCCC
1 TTTTCATAG-TTCGATAGCCGAAGCCATCCA
* *
34456444 TTTTAATAATTCGAT
1 TTTTCATAGTTCGAT
34456459 GGTCGTCACC
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
29 1 0.03
30 36 0.97
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (30 bp):
TTTTCATAGTTCGATAGCCGAAGCCATCCA
Found at i:34456498 original size:29 final size:30
Alignment explanation
Indices: 34456437--34456518 Score: 112
Period size: 29 Copynumber: 2.8 Consensus size: 30
34456427 ATAGCCGAAG
34456437 CCATCCCTTTTAATAATTCGATGGTCGTCA
1 CCATCCCTTTTAATAATTCGATGGTCGTCA
**
34456467 CCATCCCTTTTAATTGTT-GATGGTCGTCA
1 CCATCCCTTTTAATAATTCGATGGTCGTCA
* * *
34456496 CCATCCTTTTTCATAATTTGATG
1 CCATCCCTTTTAATAATTCGATG
34456519 CCGAAGCTGT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 25 0.56
30 20 0.44
ACGTcount: A:0.21, C:0.24, G:0.13, T:0.41
Consensus pattern (30 bp):
CCATCCCTTTTAATAATTCGATGGTCGTCA
Found at i:34456555 original size:30 final size:29
Alignment explanation
Indices: 34456503--34456604 Score: 91
Period size: 31 Copynumber: 3.4 Consensus size: 29
34456493 TCACCATCCT
* *
34456503 TTTTCATAATTTGATGCCGAAGCTGT-TCC
1 TTTTCATAATTTGAAGCCGAAGCTATAT-C
*
34456532 TTTTCATAATTTGACAGCTGAAGCTATATC
1 TTTTCATAATTTGA-AGCCGAAGCTATATC
* * *
34456562 TTTTCATAATTTTGATAGTCGAAGCCAT-CC
1 TTTTCATAA-TTTGA-AGCCGAAGCTATATC
34456592 ATTTTCATAATTT
1 -TTTTCATAATTT
34456605 TATAGCCAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
29 14 0.23
30 23 0.38
31 24 0.39
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.43
Consensus pattern (29 bp):
TTTTCATAATTTGAAGCCGAAGCTATATC
Found at i:34456586 original size:31 final size:28
Alignment explanation
Indices: 34456503--34456610 Score: 101
Period size: 30 Copynumber: 3.6 Consensus size: 28
34456493 TCACCATCCT
*
34456503 TTTTCATAATTTGAT-GCCGAAGCTGTTCC
1 TTTTCATAATTTGATAG-CGAAGCTATT-C
*
34456532 TTTTCATAATTTGACAGCTGAAGCTATATC
1 TTTTCATAATTTGATAGC-GAAGCTAT-TC
* *
34456562 TTTTCATAATTTTGATAGTCGAAGCCATCC
1 TTTTCATAA-TTTGATAG-CGAAGCTATTC
*
34456592 ATTTTCATAATTTTATAGC
1 -TTTTCATAATTTGATAGC
34456611 CAAAGCCATC
Statistics
Matches: 67, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
29 16 0.24
30 26 0.39
31 24 0.36
32 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.43
Consensus pattern (28 bp):
TTTTCATAATTTGATAGCGAAGCTATTC
Found at i:34456619 original size:30 final size:31
Alignment explanation
Indices: 34456562--34456621 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
34456552 AAGCTATATC
* *
34456562 TTTTCATAATTTTGATAGTCGAAGCCATCCA
1 TTTTCATAATTTTGATAGCCAAAGCCATCCA
34456593 TTTTCATAATTTT-ATAGCCAAAGCCATCC
1 TTTTCATAATTTTGATAGCCAAAGCCATCC
34456622 CTTTGTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 14 0.52
31 13 0.48
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.38
Consensus pattern (31 bp):
TTTTCATAATTTTGATAGCCAAAGCCATCCA
Found at i:34456713 original size:30 final size:30
Alignment explanation
Indices: 34456675--34456748 Score: 94
Period size: 30 Copynumber: 2.5 Consensus size: 30
34456665 ATGGCCGAGA
*
34456675 CCATCCCTTTTCATAATTCGATAGCTGAAG
1 CCATCCCTTTTCATAATTTGATAGCTGAAG
* * * *
34456705 CTATCCCTTTCCATATTTTGATACCTGAAG
1 CCATCCCTTTTCATAATTTGATAGCTGAAG
*
34456735 CCATCTCTTTTCAT
1 CCATCCCTTTTCAT
34456749 TGGTTGATGA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.23, C:0.28, G:0.09, T:0.39
Consensus pattern (30 bp):
CCATCCCTTTTCATAATTTGATAGCTGAAG
Found at i:34464480 original size:30 final size:30
Alignment explanation
Indices: 34464446--34464651 Score: 139
Period size: 30 Copynumber: 6.6 Consensus size: 30
34464436 ATACTTGAAG
34464446 CCATCCCTTTTCATAATTCGATGGTCGTCA
1 CCATCCCTTTTCATAATTCGATGGTCGTCA
* * **
34464476 CCATCCCTTTTCATTGTTGATGGTGGTGATGGTCACCA
1 CCATCCCTTTTCA----TAAT--T--CGATGGTCGTCA
* * * *
34464514 CCATCCCTTTCCATAATTTGATAGTCG-AA
1 CCATCCCTTTTCATAATTCGATGGTCGTCA
* * *
34464543 GCTATCCCTTTTCATAATTCGATTGTCG-AA
1 -CCATCCCTTTTCATAATTCGATGGTCGTCA
* * *
34464573 GCCATCCATTTTCATAATCCGATGGTCATCA
1 -CCATCCCTTTTCATAATTCGATGGTCGTCA
** *
34464604 CCATCCCTTTTCATTGTT-GATAGTCGTCA
1 CCATCCCTTTTCATAATTCGATGGTCGTCA
*
34464633 CCATCCCTTTTCAAAATTC
1 CCATCCCTTTTCATAATTC
34464652 AATAGCCGAA
Statistics
Matches: 137, Mismatches: 28, Indels: 22
0.73 0.15 0.12
Matches are distributed among these distances:
29 25 0.18
30 82 0.60
31 1 0.01
32 1 0.01
34 6 0.04
36 1 0.01
38 21 0.15
ACGTcount: A:0.22, C:0.28, G:0.14, T:0.37
Consensus pattern (30 bp):
CCATCCCTTTTCATAATTCGATGGTCGTCA
Found at i:34464662 original size:89 final size:89
Alignment explanation
Indices: 34464503--34464677 Score: 210
Period size: 89 Copynumber: 2.0 Consensus size: 89
34464493 TGATGGTGGT
* * * *
34464503 GATGGTCACCACCATCCCTTTCCATAATTTGATAGTCGAAGCTATCCCTTTTCATAATTCGATTG
1 GATGGTCACCACCATCCCTTTCCAT-ATTTGATAGTCGAAGCCATCCCTTTTCAAAATTCAATAG
* *
34464568 TCGAAGCCATCCATTTTCATAATCC
65 CCGAAGCCATCCATTTCCATAATCC
* * *
34464593 GATGGTCATCACCATCCCTTTTCAT-TGTTGATAGTCGTCA-CCATCCCTTTTCAAAATTCAATA
1 GATGGTCACCACCATCCCTTTCCATAT-TTGATAGTCG-AAGCCATCCCTTTTCAAAATTCAATA
* *
34464656 GCCGAAGCTATCCCTTTCCATA
64 GCCGAAGCCATCCATTTCCATA
34464678 TTTTGATAGC
Statistics
Matches: 72, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
88 1 0.01
89 47 0.65
90 24 0.33
ACGTcount: A:0.25, C:0.29, G:0.12, T:0.34
Consensus pattern (89 bp):
GATGGTCACCACCATCCCTTTCCATATTTGATAGTCGAAGCCATCCCTTTTCAAAATTCAATAGC
CGAAGCCATCCATTTCCATAATCC
Found at i:34464714 original size:30 final size:29
Alignment explanation
Indices: 34464604--34464714 Score: 98
Period size: 30 Copynumber: 3.7 Consensus size: 29
34464594 ATGGTCATCA
* *
34464604 CCATCCCTTTTCATTGTTGATAGTCGTCA-
1 CCATCCCTTTTCATTGTTGATAGCCG-AAG
*** *
34464633 CCATCCCTTTTCAAAATTCAATAGCCGAAG
1 CCATCCCTTTTCATTGTT-GATAGCCGAAG
* * *
34464663 CTATCCCTTTCCATATTTTGATAGCCGAAG
1 CCATCCCTTTTCAT-TGTTGATAGCCGAAG
34464693 CCATCCCTTTTCATTGGTTGAT
1 CCATCCCTTTTCATT-GTTGAT
34464715 GACTGTCGAT
Statistics
Matches: 63, Mismatches: 15, Indels: 7
0.74 0.18 0.08
Matches are distributed among these distances:
29 17 0.27
30 44 0.70
31 2 0.03
ACGTcount: A:0.23, C:0.28, G:0.13, T:0.37
Consensus pattern (29 bp):
CCATCCCTTTTCATTGTTGATAGCCGAAG
Found at i:34464976 original size:6 final size:6
Alignment explanation
Indices: 34464965--34464991 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
34464955 TTCAATCCAA
34464965 ATTCAT ATTCAT ATTCAT ATTCAT ATT
1 ATTCAT ATTCAT ATTCAT ATTCAT ATT
34464992 TTTGCAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.52
Consensus pattern (6 bp):
ATTCAT
Found at i:34466761 original size:26 final size:26
Alignment explanation
Indices: 34466732--34466782 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
34466722 TCTTTTCCTT
*
34466732 TCTTTTCATTTTTAGATTAGGTTTTC
1 TCTTTTCATTTTTAGATTAGATTTTC
**
34466758 TCTTTTTTTTTTTAGATTAGATTTT
1 TCTTTTCATTTTTAGATTAGATTTT
34466783 ATTTTTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.16, C:0.08, G:0.10, T:0.67
Consensus pattern (26 bp):
TCTTTTCATTTTTAGATTAGATTTTC
Found at i:34466789 original size:26 final size:26
Alignment explanation
Indices: 34466740--34466796 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
34466730 TTTCTTTTCA
* *
34466740 TTTTTAGATTAGGTTTTCTCTTTTTT
1 TTTTTAGATTAGATTTTATCTTTTTT
34466766 TTTTTAGATTAGATTTTAT-TTTTTT
1 TTTTTAGATTAGATTTTATCTTTTTT
34466791 TATTTT
1 T-TTTT
34466797 CTTTCTTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 7 0.25
26 21 0.75
ACGTcount: A:0.16, C:0.04, G:0.09, T:0.72
Consensus pattern (26 bp):
TTTTTAGATTAGATTTTATCTTTTTT
Found at i:34475143 original size:29 final size:29
Alignment explanation
Indices: 34475110--34475167 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
34475100 ATTGGGAAAT
34475110 TTAAATTAACTATTTGTACTTGTTTCCAA
1 TTAAATTAACTATTTGTACTTGTTTCCAA
34475139 TTAAATTAACTATTTGTACTTGTTTCCAA
1 TTAAATTAACTATTTGTACTTGTTTCCAA
34475168 CGAAAATGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (29 bp):
TTAAATTAACTATTTGTACTTGTTTCCAA
Found at i:34482492 original size:29 final size:28
Alignment explanation
Indices: 34482436--34482492 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
34482426 TTTCCCTTCC
* * *
34482436 TGACGAGTCTAAGGTTAGGAGCTTCCTT
1 TGACGAGTCCAAGGTTAGGAACTCCCTT
34482464 TGACGAGTTCCAAGGTTAGGAACTCCCTT
1 TGACGAG-TCCAAGGTTAGGAACTCCCTT
34482493 CAACAGTTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 7 0.28
29 18 0.72
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (28 bp):
TGACGAGTCCAAGGTTAGGAACTCCCTT
Found at i:34484835 original size:3 final size:3
Alignment explanation
Indices: 34484822--34484855 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
34484812 TGAAAGAGAG
34484822 GAA GAAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA G-AA GAA GAA GAA GAA GAA GAA GAA GAA GAA
34484856 ACAAGGCTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:34485798 original size:10 final size:10
Alignment explanation
Indices: 34485783--34485814 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
34485773 ATGTAAAATC
34485783 GAGTGAGAGA
1 GAGTGAGAGA
34485793 GAGTGAGAGA
1 GAGTGAGAGA
*
34485803 GAGAGAGAGA
1 GAGTGAGAGA
34485813 GA
1 GA
34485815 AGAAGAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.50, T:0.06
Consensus pattern (10 bp):
GAGTGAGAGA
Found at i:34500382 original size:12 final size:12
Alignment explanation
Indices: 34500367--34500399 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
34500357 CTTCTAGCTC
34500367 TACAACCTCACA
1 TACAACCTCACA
34500379 TACAACCTCACA
1 TACAACCTCACA
34500391 TACAACCTC
1 TACAACCTC
34500400 CATCCTCGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.39, C:0.42, G:0.00, T:0.18
Consensus pattern (12 bp):
TACAACCTCACA
Found at i:34502741 original size:25 final size:25
Alignment explanation
Indices: 34502713--34502770 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
34502703 ACATGAGCTA
34502713 TGAATATGAATGCTCACACAAGTTG
1 TGAATATGAATGCTCACACAAGTTG
*
34502738 TGAATATGAATGCTCACACGAGTTG
1 TGAATATGAATGCTCACACAAGTTG
34502763 TGAATATG
1 TGAATATG
34502771 GGTGTGCTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.29
Consensus pattern (25 bp):
TGAATATGAATGCTCACACAAGTTG
Found at i:34522044 original size:38 final size:38
Alignment explanation
Indices: 34522002--34522100 Score: 130
Period size: 38 Copynumber: 2.6 Consensus size: 38
34521992 CGAATATAAT
*
34522002 AATTATAATTACCATAATTATAATAATGTTTGA-CCAAA
1 AATTATAATTACCATAATTATAATAATATTTGATCC-AA
* *
34522040 AATTACAATTA-CAGTAATTATAATAATATTTGATCCTA
1 AATTATAATTACCA-TAATTATAATAATATTTGATCCAA
*
34522078 AATTATAATTACAATAATTATAA
1 AATTATAATTACCATAATTATAA
34522101 CAAAGATTTC
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
37 2 0.04
38 48 0.91
39 3 0.06
ACGTcount: A:0.48, C:0.09, G:0.04, T:0.38
Consensus pattern (38 bp):
AATTATAATTACCATAATTATAATAATATTTGATCCAA
Found at i:34541626 original size:14 final size:14
Alignment explanation
Indices: 34541607--34541638 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
34541597 GAGGAGATAA
34541607 AAGATCTTAAAGAT
1 AAGATCTTAAAGAT
34541621 AAGATCTTAAAGAT
1 AAGATCTTAAAGAT
34541635 AAGA
1 AAGA
34541639 GCTAATCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.53, C:0.06, G:0.16, T:0.25
Consensus pattern (14 bp):
AAGATCTTAAAGAT
Found at i:34545402 original size:6 final size:6
Alignment explanation
Indices: 34545388--34545421 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
34545378 AGGTTTCCAA
* *
34545388 AAATAG AAATGG AAATGG AAATGA AAATGG AAAT
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAAT
34545422 AATCCATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.59, C:0.00, G:0.24, T:0.18
Consensus pattern (6 bp):
AAATGG
Found at i:34569160 original size:30 final size:30
Alignment explanation
Indices: 34569126--34569189 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
34569116 CACACAGGCG
*
34569126 TGTGTCACACACGGGCAACACACATGGGCA
1 TGTGTCACACACGAGCAACACACATGGGCA
*
34569156 TGTGTCACACACGAGCAACACACATGGGCG
1 TGTGTCACACACGAGCAACACACATGGGCA
34569186 TGTG
1 TGTG
34569190 ACCCAAGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.16
Consensus pattern (30 bp):
TGTGTCACACACGAGCAACACACATGGGCA
Found at i:34569637 original size:49 final size:49
Alignment explanation
Indices: 34569565--34569665 Score: 166
Period size: 49 Copynumber: 2.1 Consensus size: 49
34569555 TCTAGAAGGG
* * *
34569565 ATAAATAGTGATAAGAGTGTAGACAGTGGAAGACTAAGTTTAGGAATGT
1 ATAAATAGTGATAACAGTGTAGACAGTGGAAGACCAAGTTTAGCAATGT
*
34569614 ATAAATAGTGATAACAGTGTAGACAGTGGAAGACCAAGTTTAGCATTGT
1 ATAAATAGTGATAACAGTGTAGACAGTGGAAGACCAAGTTTAGCAATGT
34569663 ATA
1 ATA
34569666 GCATGATTAG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.41, C:0.07, G:0.26, T:0.27
Consensus pattern (49 bp):
ATAAATAGTGATAACAGTGTAGACAGTGGAAGACCAAGTTTAGCAATGT
Found at i:34580018 original size:50 final size:50
Alignment explanation
Indices: 34579894--34580184 Score: 334
Period size: 50 Copynumber: 5.8 Consensus size: 50
34579884 GATAATAACA
* ** * *
34579894 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCATGTAC--
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGG
* * * * ** *
34579943 TACCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * ** * * *
34579993 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACATCTCTTCTCAG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
34580043 TGCCAACGCCATGCCCCAAACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
34580093 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
34580143 TGCCAACGCCATGTCCCAGACATGGTTTTACATGGGATCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
34580185 TTACCCAAAC
Statistics
Matches: 206, Mismatches: 34, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
48 1 0.00
49 39 0.19
50 166 0.81
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.26
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:34588106 original size:45 final size:45
Alignment explanation
Indices: 34588042--34588135 Score: 152
Period size: 45 Copynumber: 2.1 Consensus size: 45
34588032 AACAGATACT
* * *
34588042 CGGTGGATTTAGCACATAGCAACCACCTTATTAATCAATGATGTC
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
*
34588087 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTT
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
34588132 CGGT
1 CGGT
34588136 TCACATAGTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
Found at i:34588247 original size:51 final size:50
Alignment explanation
Indices: 34588192--34588319 Score: 156
Period size: 50 Copynumber: 2.5 Consensus size: 50
34588182 CCGATACATG
*
34588192 TAGTAGCCTGCACATAGTACTACACACATGATCGAAACTATC-T-GGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACAT-A-CG-AACTATCATCGGTACACA
* *
34588243 TAGTAGCCTGCACATAGTACTA-A-ACATACGACCTATCATTCCGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACATACGAACTATCA-T-CGGTACACA
34588293 TAGTAGCCTGCACATAGTACTACACAC
1 TAGTAGCCTGCACATAGTACTACACAC
34588320 GTGACCATCA
Statistics
Matches: 68, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
46 6 0.09
47 2 0.03
48 2 0.03
49 4 0.06
50 29 0.43
51 23 0.34
52 2 0.03
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.23
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACACATACGAACTATCATCGGTACACA
Found at i:34588309 original size:50 final size:53
Alignment explanation
Indices: 34588132--34588319 Score: 171
Period size: 51 Copynumber: 3.7 Consensus size: 53
34588122 CAATGATGTT
* * * * * * *
34588132 CGGTTCACATAGTAGCTTACACATAGTACT--ACACATG-TGGAAATTACCATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACATGATCGAAACTATC-TC
* *
34588183 CGATACATGTAGTAGCCTGCACATAGTACTACACACATGATCGAAACTATCT-
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACATGATCGAAACTATCTC
* * *
34588235 -GGTACGCATAGTAGCCTGCACATAGTACTA-A-ACAT-A-CG-ACCTATCATTC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACATGATCGAAACTATC--TC
34588284 CGGTACACGTAGTAGCCTGCACATAGTACTACACAC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACAC
34588320 GTGACCATCA
Statistics
Matches: 112, Mismatches: 16, Indels: 17
0.77 0.11 0.12
Matches are distributed among these distances:
46 6 0.05
47 2 0.02
48 2 0.02
49 4 0.04
50 29 0.26
51 51 0.46
52 2 0.02
53 8 0.07
54 8 0.07
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.24
Consensus pattern (53 bp):
CGGTACACGTAGTAGCCTGCACATAGTACTACACACATGATCGAAACTATCTC
Found at i:34591518 original size:20 final size:20
Alignment explanation
Indices: 34591478--34591521 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
34591468 CTAGTTGAAA
* **
34591478 AAAAATTAAAATTTTGTTTT
1 AAAAATTAAAACTTTCCTTT
34591498 AAAAATTAAAACTTTCCTTT
1 AAAAATTAAAACTTTCCTTT
34591518 AAAA
1 AAAA
34591522 TGACTAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (20 bp):
AAAAATTAAAACTTTCCTTT
Found at i:34591695 original size:148 final size:148
Alignment explanation
Indices: 34591282--34591729 Score: 553
Period size: 148 Copynumber: 3.0 Consensus size: 148
34591272 AGATCATTAC
* * *
34591282 TTTTCTTAAAAATCAAA-AATTTATTTCGAAATAGTTGAAAAAGATCAAAATTTTGTTTTAAAAA
1 TTTTCTTAAAGATCAAAGATTTTATTTTGAAATAGTTGAAAAA-ATCAAAATTTTGTTTT-AAAA
* * *
34591346 ATTCAAACTTTTCCTTTAAAATGACTAAAAAAACGTATTTTTA-TTTTAAAAATCTAAACTTTCT
64 ATT-AAAATTTTCCTTTAAAATGACT-AAAAAACATATTTTTATTTTTTAAAATCTAAACTTTCT
** *
34591410 GCTTTTTCAAAGAAAGAAAAACACCAT
127 -CTTTTTC--TTAAA-AAAAATA-CAT
* *
34591437 TTTTCTTAAAGATCAAAGATTTTATTTTGAACTAGTTGAAAAAAAATTAAAATTTTGTTTTAAAA
1 TTTTCTTAAAGATCAAAGATTTTATTTTGAAATAGTTG--AAAAAATCAAAATTTTGTTTTAAAA
* * *
34591502 ATTAAAACTTTCCTTTAAAATGACTAAAAAATATATTTTTATTTTTTAAAATCTAAACTTCCTCT
64 ATTAAAATTTTCCTTTAAAATGACTAAAAAACATATTTTTATTTTTTAAAATCTAAACTTTCTCT
* *
34591567 TTTTCTTTAAAAAAATA-TT
129 TTTTCTTAAAAAAAATACAT
* * * *
34591586 TTTTTTTAAAGATCAAAGCTTTTATTTTGAAATAGTTGAGAAAAATCAAAACTTTGTTTTAAAAT
1 TTTTCTTAAAGATCAAAGATTTTATTTTGAAATAGTTGA-AAAAATCAAAATTTTGTTTTAAAAA
* *
34591651 TTTAAATTTTTCTTTAAAATGACTAAAAAACATATTTTTATTTTTTAAAATCTAAACTTTCTCTT
65 TTAAAATTTTCCTTTAAAATGACTAAAAAACATATTTTTATTTTTTAAAATCTAAACTTTCTCTT
*
34591716 CTT-TTAAAAAAAAT
130 TTTCTTAAAAAAAAT
34591730 CAAAACTTTT
Statistics
Matches: 259, Mismatches: 29, Indels: 18
0.85 0.09 0.06
Matches are distributed among these distances:
147 11 0.04
148 84 0.32
149 36 0.14
151 6 0.02
152 2 0.01
154 21 0.08
155 55 0.21
156 24 0.09
157 15 0.06
158 5 0.02
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.43
Consensus pattern (148 bp):
TTTTCTTAAAGATCAAAGATTTTATTTTGAAATAGTTGAAAAAATCAAAATTTTGTTTTAAAAAT
TAAAATTTTCCTTTAAAATGACTAAAAAACATATTTTTATTTTTTAAAATCTAAACTTTCTCTTT
TTCTTAAAAAAAATACAT
Found at i:34592634 original size:42 final size:42
Alignment explanation
Indices: 34592574--34592838 Score: 379
Period size: 42 Copynumber: 6.3 Consensus size: 42
34592564 CCTCTAAATG
* *
34592574 CTCTAAATGCAAT-AAAGAGTGAATGGATCTCCACACCTAGGC
1 CTCTAAATGCAATGAAA-AGTGAATGGACCTCCACACCTGGGC
* * *
34592616 CTCTAAATGTAATGAAGAGTAAATGGACCTCCACACCTGGGC
1 CTCTAAATGCAATGAAAAGTGAATGGACCTCCACACCTGGGC
34592658 CTCTAAATGCAATGAAAAGTGAATGGACCTCCACACCTGGGC
1 CTCTAAATGCAATGAAAAGTGAATGGACCTCCACACCTGGGC
* * * *
34592700 CTCTCAATGAAATGAAAAGTGAATGGACCTCCACACCTAGGT
1 CTCTAAATGCAATGAAAAGTGAATGGACCTCCACACCTGGGC
* *
34592742 CTCTAAATGCAATGAAAAGTGAATGAACCTCCACACTTGGGC
1 CTCTAAATGCAATGAAAAGTGAATGGACCTCCACACCTGGGC
** **
34592784 CTCTAAATGCAATGAAAAGAAAATGGGTCTCCACACCTGGGC
1 CTCTAAATGCAATGAAAAGTGAATGGACCTCCACACCTGGGC
34592826 CTCTAAATGCAAT
1 CTCTAAATGCAAT
34592839 AAATGTTTTC
Statistics
Matches: 198, Mismatches: 24, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
42 196 0.99
43 2 0.01
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (42 bp):
CTCTAAATGCAATGAAAAGTGAATGGACCTCCACACCTGGGC
Found at i:34593279 original size:21 final size:21
Alignment explanation
Indices: 34593240--34593279 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
34593230 TACTTTTTGG
*
34593240 TTTCTTTTTTGTTTTATTTTT
1 TTTCTTTTTTGTTTGATTTTT
34593261 TTTCTTTTTT-TCTTGATTT
1 TTTCTTTTTTGT-TTGATTT
34593280 AAGAAAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.05, C:0.07, G:0.05, T:0.82
Consensus pattern (21 bp):
TTTCTTTTTTGTTTGATTTTT
Found at i:34600353 original size:12 final size:13
Alignment explanation
Indices: 34600336--34600364 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
34600326 CTCATACATG
34600336 AATAAATAAA-GC
1 AATAAATAAATGC
34600348 AATAAATAAATGC
1 AATAAATAAATGC
34600361 AATA
1 AATA
34600365 GTTATAGCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.21
Consensus pattern (13 bp):
AATAAATAAATGC
Found at i:34613726 original size:22 final size:22
Alignment explanation
Indices: 34613691--34613735 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
34613681 CAGAATTTTT
*
34613691 AAATTTTTCATTTTAGCAAAATC
1 AAATTTTTCATTTTA-AAAAATC
34613714 AAATTTTTC-TTTTAAAAAATC
1 AAATTTTTCATTTTAAAAAATC
34613735 A
1 A
34613736 TTACTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.33
22 5 0.24
23 9 0.43
ACGTcount: A:0.42, C:0.11, G:0.02, T:0.44
Consensus pattern (22 bp):
AAATTTTTCATTTTAAAAAATC
Found at i:34613819 original size:21 final size:22
Alignment explanation
Indices: 34613776--34613824 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
34613766 CGAAATAGTA
34613776 TAAAAAGATCAAAATTTTGCTT
1 TAAAAAGATCAAAATTTTGCTT
*
34613798 TAAAAA-ATTCAAACTTTT-CTT
1 TAAAAAGA-TCAAAATTTTGCTT
*
34613819 TTAAAA
1 TAAAAA
34613825 TGACTAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.47, C:0.10, G:0.04, T:0.39
Consensus pattern (22 bp):
TAAAAAGATCAAAATTTTGCTT
Found at i:34613976 original size:20 final size:20
Alignment explanation
Indices: 34613939--34613979 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
34613929 AGATGAAAAC
**
34613939 AATTAAAACTTTGTTTTAAA
1 AATTAAAACTTTCCTTTAAA
34613959 AATTAAAACTTTCCTTTAAA
1 AATTAAAACTTTCCTTTAAA
34613979 A
1 A
34613980 TGACTAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.41
Consensus pattern (20 bp):
AATTAAAACTTTCCTTTAAA
Found at i:34614095 original size:146 final size:144
Alignment explanation
Indices: 34613718--34614184 Score: 456
Period size: 146 Copynumber: 3.1 Consensus size: 144
34613708 AAAATCAAAT
* * * * * *
34613718 TTTTCTTTTAAAAAATCATTACTTTTCTTAAAAATCAAAAATTTCTTTCGAAATAGTAT-AAAAA
1 TTTT-TTTTAAAAAA-AATTA-TTTTTTTAAAGATCAAAATTTTATTTTGAAATAGT-TGAAAAA
* * * * *
34613782 GATCAAAATTTTGCTTTAAAAAATTCAAACTTTTCTTTTAAAATGACTAAAAAAAACATATTTTT
62 AATCAAAACTTTG-TTTTAAAAATTAAAAC-TTTCCTTTAAAATGACT---AAAAACATATTTTT
* * *
34613847 ATTTTAAAAATATAAACTTTATCC
122 ATTTTTAAAATCTAAACTTTCT-C
** * *
34613871 TTTTTTAAAGAAAGAAAAACATCATTTTTCTTAAAGATCAAATATTTTATTTTGAAATAGATGAA
1 TTTTTT---TTAA-AAAAA-ATTATTTTT-TTAAAGATCAAA-ATTTTATTTTGAAATAGTTGAA
* * *
34613936 AACAATTAAAACTTTGTTTTAAAAATTAAAACTTTCCTTTAAAATGACTAAAAATATATTTTTAT
59 AAAAATCAAAACTTTGTTTTAAAAATTAAAACTTTCCTTTAAAATGACTAAAAACATATTTTTAT
*
34614001 TTTTAAAATCCAAACTTTCTC
124 TTTTAAAATCTAAACTTTCTC
*
34614022 TTTTTCTTTAAAAAAAATTATTTTTTTAAAGATCAAAGCTTTTATTTTGAAATAGTTGAAAAAAA
1 TTTTT-TTTAAAAAAAATTATTTTTTTAAAGATCAAA-ATTTTATTTTGAAATAGTTGAAAAAAA
* * *
34614087 TCACAACTTTGTTTTAAAATTTTAAAA-TTTTCTTTAAAATGACTAAAACACATA-TTTTATTTT
64 TCAAAACTTTGTTTTAAAA-ATTAAAACTTTCCTTTAAAATGACTAAAA-ACATATTTTTA-TTT
*
34614150 TTAAATTCTAAACTTTCTC
126 TTAAAATCTAAACTTTCTC
*
34614169 -TTCTTTTAAAAAAAAT
1 TTTTTTTTAAAAAAAAT
34614185 AAAACTTTTC
Statistics
Matches: 265, Mismatches: 37, Indels: 32
0.79 0.11 0.10
Matches are distributed among these distances:
145 12 0.05
146 81 0.31
147 38 0.14
148 5 0.02
149 2 0.01
151 6 0.02
152 34 0.13
153 4 0.02
155 22 0.08
156 33 0.12
157 28 0.11
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.43
Consensus pattern (144 bp):
TTTTTTTTAAAAAAAATTATTTTTTTAAAGATCAAAATTTTATTTTGAAATAGTTGAAAAAAATC
AAAACTTTGTTTTAAAAATTAAAACTTTCCTTTAAAATGACTAAAAACATATTTTTATTTTTAAA
ATCTAAACTTTCTC
Found at i:34615034 original size:42 final size:42
Alignment explanation
Indices: 34614987--34615074 Score: 158
Period size: 42 Copynumber: 2.1 Consensus size: 42
34614977 CTTCATATAC
*
34614987 AATGCAATGAAAAGTAAATGGACCTCCACACCTAGGCCTCTA
1 AATGCAACGAAAAGTAAATGGACCTCCACACCTAGGCCTCTA
*
34615029 AATGCAACGAAAAGTAAATGGACCTCCACACCTATGCCTCTA
1 AATGCAACGAAAAGTAAATGGACCTCCACACCTAGGCCTCTA
34615071 AATG
1 AATG
34615075 GACCTCCACA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.39, C:0.26, G:0.16, T:0.19
Consensus pattern (42 bp):
AATGCAACGAAAAGTAAATGGACCTCCACACCTAGGCCTCTA
Found at i:34625279 original size:6 final size:6
Alignment explanation
Indices: 34625270--34625299 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
34625260 TCAATTTCTC
34625270 CATTTT CATTTT CATTTT CATTTT CATTTT
1 CATTTT CATTTT CATTTT CATTTT CATTTT
34625300 GGAGAAAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.67
Consensus pattern (6 bp):
CATTTT
Found at i:34629273 original size:15 final size:18
Alignment explanation
Indices: 34629239--34629275 Score: 53
Period size: 15 Copynumber: 2.2 Consensus size: 18
34629229 TTTAAGCGTG
34629239 CATATCATTAATATAAAA
1 CATATCATTAATATAAAA
34629257 CATAT-ATT-ATA-AAAA
1 CATATCATTAATATAAAA
34629272 CATA
1 CATA
34629276 GAACATAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 8 0.42
16 3 0.16
17 3 0.16
18 5 0.26
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (18 bp):
CATATCATTAATATAAAA
Found at i:34629953 original size:18 final size:20
Alignment explanation
Indices: 34629913--34629953 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
34629903 TATGTACTAA
*
34629913 ATAAAATTATATCTTATATT
1 ATAAAATTATATCTTACATT
34629933 ATAAAA-TATAT-TTACATT
1 ATAAAATTATATCTTACATT
34629951 ATA
1 ATA
34629954 GTTTTTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
19 5 0.25
20 6 0.30
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (20 bp):
ATAAAATTATATCTTACATT
Found at i:34632101 original size:25 final size:25
Alignment explanation
Indices: 34632073--34632123 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
34632063 TTATAGAAGT
34632073 TAACATATGAGAAGGCTGAAATGCA
1 TAACATATGAGAAGGCTGAAATGCA
34632098 TAACATATGAGAAGGCTGAAATGCA
1 TAACATATGAGAAGGCTGAAATGCA
34632123 T
1 T
34632124 GCTTAGGTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.43, C:0.12, G:0.24, T:0.22
Consensus pattern (25 bp):
TAACATATGAGAAGGCTGAAATGCA
Found at i:34651246 original size:28 final size:28
Alignment explanation
Indices: 34651215--34651585 Score: 173
Period size: 28 Copynumber: 13.1 Consensus size: 28
34651205 CTTTTAGAGA
* *
34651215 TTTGCCACAAAGGTTGCCCTTTAATAGG
1 TTTGCCACAAAGGTTACCCTTTAACAGG
* *
34651243 TTTGCCACAAAGGTTTA-CCTTT-CCAGAT
1 TTTGCCACAAAGG-TTACCCTTTAACAG-G
** * *
34651271 TTTTTCACAAAGGCTATCCTTTAACAGG
1 TTTGCCACAAAGGTTACCCTTTAACAGG
* * * * *
34651299 TTCGCCACAAAGGCTTACCTTTTCAGAGT
1 TTTGCCACAAAGG-TTACCCTTTAACAGG
*
34651328 TTTGCCACAAAGGCT-CTCCTTTAACAGG
1 TTTGCCACAAAGGTTAC-CCTTTAACAGG
* * * *
34651356 TTCGCCACAAAGGCTTA-CCTTTCTAGAGT
1 TTTGCCACAAAGG-TTACCCTTT-AACAGG
* * ***
34651385 TTTGCCGCAAAGGCTGTTCTTTAACAGG
1 TTTGCCACAAAGGTTACCCTTTAACAGG
*
34651413 TTTGCCACAAAGGCTTA-CCTTT-CCAGAG
1 TTTGCCACAAAGG-TTACCCTTTAACAG-G
* * ** *
34651441 TTTTTCCATAAAGGTTGTCCTTTAATAGG
1 -TTTGCCACAAAGGTTACCCTTTAACAGG
** * * * * *
34651470 TTCACCACATAGGCTTACCTTTTTAGAGT
1 TTTGCCACAAAGG-TTACCCTTTAACAGG
* *
34651499 TTTGCCACAAAGGCTATCCTTTAACAGG
1 TTTGCCACAAAGGTTACCCTTTAACAGG
* * *
34651527 TTCGCCACAAAGGCTTA-CCTTT-CCAGATT
1 TTTGCCACAAAGG-TTACCCTTTAACAG--G
* * *
34651556 TTTGCCACAAAGGCTATCCTTTAATAGG
1 TTTGCCACAAAGGTTACCCTTTAACAGG
34651584 TT
1 TT
34651586 CACTACATAG
Statistics
Matches: 247, Mismatches: 75, Indels: 42
0.68 0.21 0.12
Matches are distributed among these distances:
27 11 0.04
28 131 0.53
29 101 0.41
30 4 0.02
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.33
Consensus pattern (28 bp):
TTTGCCACAAAGGTTACCCTTTAACAGG
Found at i:34651256 original size:57 final size:57
Alignment explanation
Indices: 34651204--34651737 Score: 615
Period size: 57 Copynumber: 9.4 Consensus size: 57
34651194 TAAGGTGTTT
* * ** * * *
34651204 CCTTT-TAGAGATTTGCCACAAAGGTTGCCCTTTAATAGGTTTGCCACAAAGGTTTA
1 CCTTTCTAGAGTTTTGCCACAAAGGCTATCCTTTAACAGGTTCGCCACAAAGGCTTA
* **
34651260 CCTTTCCAGA-TTTTTTCACAAAGGCTATCCTTTAACAGGTTCGCCACAAAGGCTTA
1 CCTTTCTAGAGTTTTGCCACAAAGGCTATCCTTTAACAGGTTCGCCACAAAGGCTTA
*
34651316 CCTTT-TCAGAGTTTTGCCACAAAGGCTCTCCTTTAACAGGTTCGCCACAAAGGCTTA
1 CCTTTCT-AGAGTTTTGCCACAAAGGCTATCCTTTAACAGGTTCGCCACAAAGGCTTA
* * * *
34651373 CCTTTCTAGAGTTTTGCCGCAAAGGCTGTTCTTTAACAGGTTTGCCACAAAGGCTTA
1 CCTTTCTAGAGTTTTGCCACAAAGGCTATCCTTTAACAGGTTCGCCACAAAGGCTTA
* * * * * * * *
34651430 CCTTTCCAGAGTTTTTCCATAAAGGTTGTCCTTTAATAGGTTCACCACATAGGCTTA
1 CCTTTCTAGAGTTTTGCCACAAAGGCTATCCTTTAACAGGTTCGCCACAAAGGCTTA
*
34651487 CCTTTTTAGAGTTTTGCCACAAAGGCTATCCTTTAACAGGTTCGCCACAAAGGCTTA
1 CCTTTCTAGAGTTTTGCCACAAAGGCTATCCTTTAACAGGTTCGCCACAAAGGCTTA
* * * * * *
34651544 CCTTTCCAGATTTTTGCCACAAAGGCTATCCTTTAATAGGTTCACTACATAGGCTTA
1 CCTTTCTAGAGTTTTGCCACAAAGGCTATCCTTTAACAGGTTCGCCACAAAGGCTTA
* * * * * * ** *
34651601 ACTTTCTAGAGTTTTGCGATAAAGACTTTCCTTTAAAAGGTTTACCATAAAGGCTTA
1 CCTTTCTAGAGTTTTGCCACAAAGGCTATCCTTTAACAGGTTCGCCACAAAGGCTTA
* * * * * * * *
34651658 CATTTCCAGAGTTTTTCCACAAAGGTTGTCCTTTAACAGGTTTGCCATATAGGCTTA
1 CCTTTCTAGAGTTTTGCCACAAAGGCTATCCTTTAACAGGTTCGCCACAAAGGCTTA
34651715 CCTTTCTAGAGTTTTGCCACAAA
1 CCTTTCTAGAGTTTTGCCACAAA
34651738 AGCTTTTCTT
Statistics
Matches: 403, Mismatches: 71, Indels: 7
0.84 0.15 0.01
Matches are distributed among these distances:
56 50 0.12
57 352 0.87
58 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (57 bp):
CCTTTCTAGAGTTTTGCCACAAAGGCTATCCTTTAACAGGTTCGCCACAAAGGCTTA
Found at i:34651512 original size:171 final size:170
Alignment explanation
Indices: 34651204--34651737 Score: 685
Period size: 171 Copynumber: 3.1 Consensus size: 170
34651194 TAAGGTGTTT
* * * *
34651204 CCTTT-TAGAGATTTGCCACAAAGGTTGCCCTTTAATAGGTTTGCCACAAAGGTTTACCTTTCCA
1 CCTTTCTAGAGTTTTGCCACAAAGGCTGTCCTTTAATAGGTTTGCCACAAAGGCTTACCTTTCCA
* * * * *
34651268 GA-TTTTTTCACAAAGGCTATCCTTTAACAGGTTCGCCACAAAGGCTTACCTTTTCAGAGTTTTG
66 GAGTTTTTCCATAAAGG-TTTCCTTTAAAAGGTTCACCACAAAGGCTTACCTTTTCAGAGTTTTG
*
34651332 CCACAAAGGCTCTCCTTTAACAGGTTCGCCACAAAGGCTTA
130 CCACAAAGGCTATCCTTTAACAGGTTCGCCACAAAGGCTTA
* * *
34651373 CCTTTCTAGAGTTTTGCCGCAAAGGCTGTTCTTTAACAGGTTTGCCACAAAGGCTTACCTTTCCA
1 CCTTTCTAGAGTTTTGCCACAAAGGCTGTCCTTTAATAGGTTTGCCACAAAGGCTTACCTTTCCA
* * *
34651438 GAGTTTTTCCATAAAGGTTGTCCTTTAATAGGTTCACCACATAGGCTTACCTTTTTAGAGTTTTG
66 GAGTTTTTCCATAAAGGTT-TCCTTTAAAAGGTTCACCACAAAGGCTTACCTTTTCAGAGTTTTG
34651503 CCACAAAGGCTATCCTTTAACAGGTTCGCCACAAAGGCTTA
130 CCACAAAGGCTATCCTTTAACAGGTTCGCCACAAAGGCTTA
* * * ** * * * *
34651544 CCTTTCCAGATTTTTGCCACAAAGGCTATCCTTTAATAGGTTCACTACATAGGCTTAACTTTCTA
1 CCTTTCTAGAGTTTTGCCACAAAGGCTGTCCTTTAATAGGTTTGCCACAAAGGCTTACCTTTCCA
* * * * * * * *
34651609 GAGTTTTGCGATAAAGACTTTCCTTTAAAAGGTTTACCATAAAGGCTTACATTTCCAGAGTTTTT
66 GAGTTTTTCCATAAAG-GTTTCCTTTAAAAGGTTCACCACAAAGGCTTACCTTTTCAGAGTTTTG
* * * * *
34651674 CCACAAAGGTTGTCCTTTAACAGGTTTGCCATATAGGCTTA
130 CCACAAAGGCTATCCTTTAACAGGTTCGCCACAAAGGCTTA
34651715 CCTTTCTAGAGTTTTGCCACAAA
1 CCTTTCTAGAGTTTTGCCACAAA
34651738 AGCTTTTCTT
Statistics
Matches: 316, Mismatches: 45, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
169 5 0.02
170 55 0.17
171 254 0.80
172 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (170 bp):
CCTTTCTAGAGTTTTGCCACAAAGGCTGTCCTTTAATAGGTTTGCCACAAAGGCTTACCTTTCCA
GAGTTTTTCCATAAAGGTTTCCTTTAAAAGGTTCACCACAAAGGCTTACCTTTTCAGAGTTTTGC
CACAAAGGCTATCCTTTAACAGGTTCGCCACAAAGGCTTA
Found at i:34653565 original size:17 final size:18
Alignment explanation
Indices: 34653507--34653567 Score: 61
Period size: 20 Copynumber: 3.3 Consensus size: 18
34653497 TCCCTCCTAC
*
34653507 TATATTATATGATGTTATA
1 TATATTATATAAT-TTATA
* *
34653526 TCATATTATATAGTATATAA
1 T-ATATTATATAATTTAT-A
34653546 TATATTA-ATAATTTATA
1 TATATTATATAATTTATA
34653563 TATAT
1 TATAT
34653568 GCTGCAATGA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
17 6 0.17
18 7 0.20
19 10 0.29
20 12 0.34
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.51
Consensus pattern (18 bp):
TATATTATATAATTTATA
Found at i:34653756 original size:5 final size:5
Alignment explanation
Indices: 34653746--34653818 Score: 146
Period size: 5 Copynumber: 14.6 Consensus size: 5
34653736 CTCTTCTACT
34653746 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
34653796 ATATA ATATA ATATA ATATA ATA
1 ATATA ATATA ATATA ATATA ATA
34653819 ATAGTTATAT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 68 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:34653865 original size:33 final size:30
Alignment explanation
Indices: 34653817--34653878 Score: 72
Period size: 33 Copynumber: 2.0 Consensus size: 30
34653807 TATAATATAA
*
34653817 TAATAGTTATATATG-TATTAATAGTTTTAG
1 TAATAGTTATATATGTTA-TAATAGGTTTAG
34653847 TAATAGTTATATATTATGTTATAATAGGTTTA
1 TAATAG-T-TATA-TATGTTATAATAGGTTTA
34653879 AGGTTGAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
30 6 0.22
31 1 0.04
32 4 0.15
33 14 0.52
34 2 0.07
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (30 bp):
TAATAGTTATATATGTTATAATAGGTTTAG
Found at i:34653949 original size:28 final size:28
Alignment explanation
Indices: 34653917--34653971 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
34653907 ATAATTATAA
* * *
34653917 AATATATTATTTTATTATGTATTAGTAT
1 AATATATTAATATATTATGTATAAGTAT
34653945 AATATATTAATATATTATGTATAAGTA
1 AATATATTAATATATTATGTATAAGTA
34653972 ATTGATTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (28 bp):
AATATATTAATATATTATGTATAAGTAT
Found at i:34657103 original size:26 final size:29
Alignment explanation
Indices: 34657041--34657104 Score: 89
Period size: 27 Copynumber: 2.3 Consensus size: 29
34657031 CGGCCCGAAT
34657041 ATAATAAATATATATTTTTTATTTTTTTA
1 ATAATAAATATATATTTTTTATTTTTTTA
**
34657070 ATTTTAAA-ATAT-TTTTTTATTTTTTTA
1 ATAATAAATATATATTTTTTATTTTTTTA
34657097 A-AATAAAT
1 ATAATAAAT
34657105 TTTTGGTGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
26 4 0.13
27 16 0.53
28 4 0.13
29 6 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (29 bp):
ATAATAAATATATATTTTTTATTTTTTTA
Found at i:34657225 original size:21 final size:21
Alignment explanation
Indices: 34657200--34657252 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
34657190 TTTTTTTATA
* * *
34657200 GGCCCGGCCTGAACTTGGCCC
1 GGCCCGACCCGAACCTGGCCC
34657221 GGCCCGACCCGAACCTGGCCC
1 GGCCCGACCCGAACCTGGCCC
34657242 GGCCCGACCCG
1 GGCCCGACCCG
34657253 TGATCACCTC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.11, C:0.49, G:0.32, T:0.08
Consensus pattern (21 bp):
GGCCCGACCCGAACCTGGCCC
Found at i:34662224 original size:29 final size:29
Alignment explanation
Indices: 34662161--34662236 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 29
34662151 CGCATTCAGC
* * *
34662161 AGAATCAGCCACAAGGGTTTCTCATACACA
1 AGAATCAGCCACAAAGG-CTCTCATACAAA
34662191 A-AATCAGCCACAAAGGCTCTCATA-AAA
1 AGAATCAGCCACAAAGGCTCTCATACAAA
34662218 TAGAATCAGCCACAAAGGC
1 -AGAATCAGCCACAAAGGC
34662237 ATCCATTTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
27 2 0.05
28 8 0.20
29 30 0.73
30 1 0.02
ACGTcount: A:0.42, C:0.26, G:0.16, T:0.16
Consensus pattern (29 bp):
AGAATCAGCCACAAAGGCTCTCATACAAA
Found at i:34662551 original size:54 final size:54
Alignment explanation
Indices: 34662469--34662591 Score: 210
Period size: 54 Copynumber: 2.3 Consensus size: 54
34662459 TCATTTTTCG
*
34662469 CACATGACGCCATAGTCCCAAACTAGGTCTTACAATATGCGGTATTCATATCCC
1 CACATGATGCCATAGTCCCAAACTAGGTCTTACAATATGCGGTATTCATATCCC
*
34662523 CACATGATGCCATAGTCCCAAACTAGGTCTTACAATATGCGGTCTTCATATCCC
1 CACATGATGCCATAGTCCCAAACTAGGTCTTACAATATGCGGTATTCATATCCC
* *
34662577 CATATGATGCAATAG
1 CACATGATGCCATAG
34662592 CCACCATGAA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 65 1.00
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (54 bp):
CACATGATGCCATAGTCCCAAACTAGGTCTTACAATATGCGGTATTCATATCCC
Found at i:34669724 original size:17 final size:16
Alignment explanation
Indices: 34669695--34669730 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
34669685 ACCATGCTTG
*
34669695 AAAAAAGAGAGAAAGA
1 AAAAAAGAAAGAAAGA
34669711 AAAAAATGAAAGAAAGA
1 AAAAAA-GAAAGAAAGA
34669728 AAA
1 AAA
34669731 GTGAGGATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (16 bp):
AAAAAAGAAAGAAAGA
Found at i:34670885 original size:22 final size:22
Alignment explanation
Indices: 34670831--34670886 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
34670821 CTGCCCAAGA
34670831 TATCGCAATATCCTCTTCTAGG
1 TATCGCAATATCCTCTTCTAGG
*
34670853 TATCACAATATCCTCTTC-AGGG
1 TATCGCAATATCCTCTTCTA-GG
*
34670875 TATCGCGATATC
1 TATCGCAATATC
34670887 ACCTTCATCA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 1 0.03
22 29 0.97
ACGTcount: A:0.25, C:0.27, G:0.14, T:0.34
Consensus pattern (22 bp):
TATCGCAATATCCTCTTCTAGG
Found at i:34672397 original size:25 final size:25
Alignment explanation
Indices: 34672368--34672433 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
34672358 CTACAACTCT
**
34672368 CATGAGCTTCCCGATACTTGGCTTT
1 CATGAGCTTCCCGATACTTGGCTAG
* * *
34672393 TATGAGCTTCTCGATATTTGGCTAG
1 CATGAGCTTCCCGATACTTGGCTAG
*
34672418 CAAGAGCTTCCCGATA
1 CATGAGCTTCCCGATA
34672434 TACAATTCGT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.33
Consensus pattern (25 bp):
CATGAGCTTCCCGATACTTGGCTAG
Found at i:34673821 original size:21 final size:22
Alignment explanation
Indices: 34673797--34673847 Score: 79
Period size: 21 Copynumber: 2.4 Consensus size: 22
34673787 TGCACCTTTG
34673797 AAAATTTTTAATA-TTTTTCAA
1 AAAATTTTTAATATTTTTTCAA
*
34673818 AAAA-TTTTAATATTTTTTGAA
1 AAAATTTTTAATATTTTTTCAA
34673839 AAAATTTTT
1 AAAATTTTT
34673848 GAGTACCCGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 8 0.30
21 15 0.56
22 4 0.15
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
AAAATTTTTAATATTTTTTCAA
Found at i:34676813 original size:28 final size:28
Alignment explanation
Indices: 34676777--34677041 Score: 176
Period size: 28 Copynumber: 9.5 Consensus size: 28
34676767 TTATACTGCA
* *
34676777 CCACGAAGGCATTCCTTT-TCAAAGATAG
1 CCACAAAGGC-TTCCTTTAACAAAGATAG
* * * * * *
34676805 CCACAAAGGCTTCATTTTATAGATATCG
1 CCACAAAGGCTTCCTTTAACAAAGATAG
** * *
34676833 TAACAAAGGCTTCCTTTAACAGAGATTG
1 CCACAAAGGCTTCCTTTAACAAAGATAG
* ** *
34676861 CCACAAATGCTTCCTTTAACGGAGATGG
1 CCACAAAGGCTTCCTTTAACAAAGATAG
* * *
34676889 CCACAAAGGATTCCTTTAACAAAGCTCG
1 CCACAAAGGCTTCCTTTAACAAAGATAG
* *
34676917 CCACAAAGGCTTCTTTTAACAGAGATCA-
1 CCACAAAGGCTTCCTTTAACAAAGAT-AG
* * *
34676945 CCACAAAGGCTTTCTTTAATAGAGATCA-
1 CCACAAAGGCTTCCTTTAACAAAGAT-AG
* * * * *
34676973 CCACAAAGGCTTTCATTAACAGAGGTCG
1 CCACAAAGGCTTCCTTTAACAAAGATAG
* * * * *
34677001 CCACAAATGATTCGTTTAACAGAGATCG
1 CCACAAAGGCTTCCTTTAACAAAGATAG
34677029 CCACAAAGGCTTC
1 CCACAAAGGCTTC
34677042 TCTTCTCTTG
Statistics
Matches: 189, Mismatches: 45, Indels: 6
0.79 0.19 0.03
Matches are distributed among these distances:
27 6 0.03
28 183 0.97
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (28 bp):
CCACAAAGGCTTCCTTTAACAAAGATAG
Found at i:34676866 original size:56 final size:56
Alignment explanation
Indices: 34676777--34677041 Score: 264
Period size: 56 Copynumber: 4.7 Consensus size: 56
34676767 TTATACTGCA
* * * * * * *
34676777 CCACGAAGGCATTCCTTT-TCAAAGATAGCCACAAAGGCTTCATTTTATAGATATCG
1 CCACAAAGGC-TTCCTTTAACAGAGATCGCCACAAAGGCTTCATTTAACAGAGATCG
** * * * * *
34676833 TAACAAAGGCTTCCTTTAACAGAGATTGCCACAAATGCTTCCTTTAACGGAGATGG
1 CCACAAAGGCTTCCTTTAACAGAGATCGCCACAAAGGCTTCATTTAACAGAGATCG
* * * * *
34676889 CCACAAAGGATTCCTTTAACAAAGCTCGCCACAAAGGCTTCTTTTAACAGAGATCA
1 CCACAAAGGCTTCCTTTAACAGAGATCGCCACAAAGGCTTCATTTAACAGAGATCG
* * * *
34676945 CCACAAAGGCTTTCTTTAATAGAGATCACCACAAAGGCTTTCA-TTAACAGAGGTCG
1 CCACAAAGGCTTCCTTTAACAGAGATCGCCACAAAGGC-TTCATTTAACAGAGATCG
* * *
34677001 CCACAAATGATTCGTTTAACAGAGATCGCCACAAAGGCTTC
1 CCACAAAGGCTTCCTTTAACAGAGATCGCCACAAAGGCTTC
34677042 TCTTCTCTTG
Statistics
Matches: 168, Mismatches: 39, Indels: 5
0.79 0.18 0.02
Matches are distributed among these distances:
55 10 0.06
56 155 0.92
57 3 0.02
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (56 bp):
CCACAAAGGCTTCCTTTAACAGAGATCGCCACAAAGGCTTCATTTAACAGAGATCG
Found at i:34676949 original size:84 final size:84
Alignment explanation
Indices: 34676835--34677041 Score: 261
Period size: 84 Copynumber: 2.5 Consensus size: 84
34676825 AGATATCGTA
* * * **
34676835 ACAAAGGCTTCCTTTAACAGAGATTGCCACAAATGCTTCCTTTAACGGAGATGGCCACAAAGGAT
1 ACAAAGGCTTCCTTTAACAGAGATCGCCACAAAGGCTTCCTTTAACAGAGATCACCACAAAGGAT
*
34676900 TCCTTTAACAAAGCTCGCC
66 TCCATTAACAAAGCTCGCC
* * * * *
34676919 ACAAAGGCTTCTTTTAACAGAGATCACCACAAAGGCTTTCTTTAATAGAGATCACCACAAAGGCT
1 ACAAAGGCTTCCTTTAACAGAGATCGCCACAAAGGCTTCCTTTAACAGAGATCACCACAAAGGAT
* * *
34676984 TTCATTAACAGAGGTCGCC
66 TCCATTAACAAAGCTCGCC
* * *
34677003 ACAAATGATTCGTTTAACAGAGATCGCCACAAAGGCTTC
1 ACAAAGGCTTCCTTTAACAGAGATCGCCACAAAGGCTTC
34677042 TCTTCTCTTG
Statistics
Matches: 104, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
84 104 1.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (84 bp):
ACAAAGGCTTCCTTTAACAGAGATCGCCACAAAGGCTTCCTTTAACAGAGATCACCACAAAGGAT
TCCATTAACAAAGCTCGCC
Found at i:34677252 original size:53 final size:53
Alignment explanation
Indices: 34677172--34677314 Score: 180
Period size: 53 Copynumber: 2.7 Consensus size: 53
34677162 CCACATGATG
* * * * *
34677172 CCATAACCTACAAGTTACAGTCTTACACGATATGGTCTTCTTTCTATATCATA
1 CCATAACCCACCAGTTACAGTCTTACACGATATGGTCTTCGTCCCATATCATA
* * * *
34677225 CCATAACCCACCAGTTACAGTTTTACACGATATGATCTTCGTCCCATATGATG
1 CCATAACCCACCAGTTACAGTCTTACACGATATGGTCTTCGTCCCATATCATA
*
34677278 CCATAACCCACCAGTTA-TGATCTTACACGATATGGTC
1 CCATAACCCACCAGTTACAG-TCTTACACGATATGGTC
34677315 CATCAATGCC
Statistics
Matches: 77, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
52 1 0.01
53 76 0.99
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.31
Consensus pattern (53 bp):
CCATAACCCACCAGTTACAGTCTTACACGATATGGTCTTCGTCCCATATCATA
Found at i:34686564 original size:21 final size:21
Alignment explanation
Indices: 34686540--34686589 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
34686530 ATATTAAATA
34686540 ATTTATTAA-AATAATAATTTT
1 ATTTATTAATAATAATAA-TTT
*
34686561 ATTTATTAATATTAATAATTT
1 ATTTATTAATAATAATAATTT
34686582 ATTATATT
1 ATT-TATT
34686590 TCTAAATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 15 0.58
22 11 0.42
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTTATTAATAATAATAATTT
Found at i:34687141 original size:136 final size:136
Alignment explanation
Indices: 34686893--34687165 Score: 501
Period size: 136 Copynumber: 2.0 Consensus size: 136
34686883 ATTTCATGTA
34686893 AGCTATTTTTCATTAAACATATACACCCTAAATAATTAGGACCGCTTCATAATGTTAAAATTATC
1 AGCTATTTTTCATTAAACATATACACCCTAAATAATTAGGACCGCTTCATAATGTTAAAATTATC
* * *
34686958 ATTTTATTATTTTCCTTTATGTACTGTAGGCTCTTTTGTAACATTGTTAGTTTGTTACCTGCTCG
66 ATTTTACTATTTTCCTTTATGTACTGTAGGCTCTGTTGTAACATTGTTAGTCTGTTACCTGCTCG
34687023 AGTAAT
131 AGTAAT
34687029 AGCTATTTTTCATTAAACATATACACCCTAAATAATTAGGACCGCTTCATAATGTTAAAATTATC
1 AGCTATTTTTCATTAAACATATACACCCTAAATAATTAGGACCGCTTCATAATGTTAAAATTATC
* *
34687094 ATTTTACTCTTTTCCTTTATGTACTGTAGGCTCTGTTGTAACGTTGTTAGTCTGTTACCTGCTCG
66 ATTTTACTATTTTCCTTTATGTACTGTAGGCTCTGTTGTAACATTGTTAGTCTGTTACCTGCTCG
34687159 AGTAAT
131 AGTAAT
34687165 A
1 A
34687166 ACAATAATAT
Statistics
Matches: 132, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
136 132 1.00
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.42
Consensus pattern (136 bp):
AGCTATTTTTCATTAAACATATACACCCTAAATAATTAGGACCGCTTCATAATGTTAAAATTATC
ATTTTACTATTTTCCTTTATGTACTGTAGGCTCTGTTGTAACATTGTTAGTCTGTTACCTGCTCG
AGTAAT
Found at i:34689801 original size:21 final size:21
Alignment explanation
Indices: 34689775--34689830 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
34689765 AACAGCGGTG
*
34689775 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
34689796 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
*
34689817 GCTGTGAGATTAGA
1 GCGGTGAGATTAGA
34689831 AACAATGGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.25, C:0.09, G:0.36, T:0.30
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:34690279 original size:29 final size:29
Alignment explanation
Indices: 34690237--34690625 Score: 532
Period size: 29 Copynumber: 13.1 Consensus size: 29
34690227 GAATACGCCG
* *
34690237 AATATACTACATATATTTTTTATTTTTAC
1 AATACACTACATATATTTTTTATTTTTAA
34690266 AATACACTACATATATTTTTTTATTTTTAA
1 AATACACTACATATA-TTTTTTATTTTTAA
34690296 AATACACTACATATA-TTTTTATTTTTAA
1 AATACACTACATATATTTTTTATTTTTAA
34690324 AATACACTACATATATTTTTTTATTTTTAA
1 AATACACTACATATA-TTTTTTATTTTTAA
34690354 AATACACTACATATATTTTTTATTTTTAA
1 AATACACTACATATATTTTTTATTTTTAA
34690383 AATACACTACATATATATTTTTTATTTTTAA
1 AATACACTAC--ATATATTTTTTATTTTTAA
*
34690414 AATACACTACATATATTTTTTTACTTTTAA
1 AATACACTACATATA-TTTTTTATTTTTAA
* * *
34690444 AATACACTTCATATATATATATATATTTTAA
1 AATACACTACATATAT-TTTTTAT-TTTTAA
* *
34690475 AATACACTACATATATTTTTTATTTCTAG
1 AATACACTACATATATTTTTTATTTTTAA
34690504 AATACACTACATATATTTTTTATTTTTAA
1 AATACACTACATATATTTTTTATTTTTAA
* * *
34690533 AATACACTACATATA-TATATATATATTAA
1 AATACACTACATATATTTTTTAT-TTTTAA
34690562 AATACACTACA-AGTATTTTTTTATTTTTAA
1 AATACACTACATA-TA-TTTTTTATTTTTAA
* *
34690592 AATCCATTACATATATATTTTTTATTTTTAA
1 AATACACTAC--ATATATTTTTTATTTTTAA
34690623 AAT
1 AAT
34690626 TTTAAATACA
Statistics
Matches: 323, Mismatches: 22, Indels: 28
0.87 0.06 0.08
Matches are distributed among these distances:
28 34 0.11
29 108 0.33
30 105 0.33
31 72 0.22
32 3 0.01
33 1 0.00
ACGTcount: A:0.39, C:0.11, G:0.01, T:0.50
Consensus pattern (29 bp):
AATACACTACATATATTTTTTATTTTTAA
Found at i:34690288 original size:30 final size:30
Alignment explanation
Indices: 34690237--34690625 Score: 551
Period size: 30 Copynumber: 13.1 Consensus size: 30
34690227 GAATACGCCG
* *
34690237 AATATACTACATATA-TTTTTTATTTTTAC
1 AATACACTACATATATTTTTTTATTTTTAA
34690266 AATACACTACATATATTTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
34690296 AATACACTACATATA--TTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
34690324 AATACACTACATATATTTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
34690354 AATACACTACATATA-TTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
34690383 AATACACTACATATATATTTTTTATTTTTAA
1 AATACACTACATATAT-TTTTTTATTTTTAA
*
34690414 AATACACTACATATATTTTTTTACTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
* * * *
34690444 AATACACTTCATATATATATATATATTTTAA
1 AATACACTACATATATTTTTTTAT-TTTTAA
* *
34690475 AATACACTACATATA-TTTTTTATTTCTAG
1 AATACACTACATATATTTTTTTATTTTTAA
34690504 AATACACTACATATA-TTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
* * * *
34690533 AATACACTACATATATATATATA-TATTAA
1 AATACACTACATATATTTTTTTATTTTTAA
34690562 AATACACTACA-AGTATTTTTTTATTTTTAA
1 AATACACTACATA-TATTTTTTTATTTTTAA
* *
34690592 AATCCATTACATATATATTTTTTATTTTTAA
1 AATACACTACATATAT-TTTTTTATTTTTAA
34690623 AAT
1 AAT
34690626 TTTAAATACA
Statistics
Matches: 323, Mismatches: 26, Indels: 20
0.88 0.07 0.05
Matches are distributed among these distances:
28 29 0.09
29 112 0.35
30 114 0.35
31 68 0.21
ACGTcount: A:0.39, C:0.11, G:0.01, T:0.50
Consensus pattern (30 bp):
AATACACTACATATATTTTTTTATTTTTAA
Found at i:34690409 original size:148 final size:147
Alignment explanation
Indices: 34690247--34690625 Score: 566
Period size: 148 Copynumber: 2.5 Consensus size: 147
34690237 AATATACTAC
*
34690247 ATATATTTTTTATTTTTACAATACACTACATATATTTTTTTATTTTTAAAATACACTACATATAT
1 ATATATTTTTTATTTTTAAAATACACTACATATATTTTTTTATTTTTAAAATACACTACATATAT
*
34690312 TTTTATTTTTAAAATACACTACATATATTTTTTTATTTTTAAAATACACTACATATATTTTTTAT
66 TTTTATTTTTAAAATACACTACATATA-TTTTTTATTTCTAAAATACACTACATATATTTTTTAT
34690377 TTTTAAAATACACTACAT
130 TTTTAAAATACACTACAT
* *
34690395 ATATATTTTTTATTTTTAAAATACACTACATATATTTTTTTACTTTTAAAATACACTTCATATAT
1 ATATATTTTTTATTTTTAAAATACACTACATATATTTTTTTATTTTTAAAATACACTACATATAT
* *
34690460 ATATATATATTTTAAAATACACTACATATATTTTTTATTTCTAGAATACACTACATATATTTTTT
66 -T-TTTAT-TTTTAAAATACACTACATATATTTTTTATTTCTAAAATACACTACATATATTTTTT
34690525 ATTTTTAAAATACACTACAT
128 ATTTTTAAAATACACTACAT
* * * * *
34690545 ATATA-TATATA-TATTAAAATACACTACA-AGTATTTTTTTATTTTTAAAATCCATTACATATA
1 ATATATTTTTTATTTTTAAAATACACTACATA-TATTTTTTTATTTTTAAAATACACTAC--ATA
34690607 TATTTTTTATTTTTAAAAT
63 TA-TTTTTATTTTTAAAAT
34690626 TTTAAATACA
Statistics
Matches: 210, Mismatches: 14, Indels: 14
0.88 0.06 0.06
Matches are distributed among these distances:
147 1 0.00
148 110 0.52
149 9 0.04
150 68 0.32
151 22 0.10
ACGTcount: A:0.39, C:0.10, G:0.01, T:0.51
Consensus pattern (147 bp):
ATATATTTTTTATTTTTAAAATACACTACATATATTTTTTTATTTTTAAAATACACTACATATAT
TTTTATTTTTAAAATACACTACATATATTTTTTATTTCTAAAATACACTACATATATTTTTTATT
TTTAAAATACACTACAT
Found at i:34690810 original size:7 final size:6
Alignment explanation
Indices: 34690789--34690840 Score: 77
Period size: 6 Copynumber: 8.2 Consensus size: 6
34690779 CGTTCCCTCC
34690789 TCCCAT TCCCAT TCCCATT TCCCATT TCCCATT TCCCAT TCCCAT TCCCAT
1 TCCCAT TCCCAT TCCCA-T TCCCA-T TCCCA-T TCCCAT TCCCAT TCCCAT
34690840 T
1 T
34690841 ATCAACAATA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
6 25 0.56
7 20 0.44
ACGTcount: A:0.15, C:0.46, G:0.00, T:0.38
Consensus pattern (6 bp):
TCCCAT
Found at i:34698126 original size:30 final size:30
Alignment explanation
Indices: 34698090--34698169 Score: 160
Period size: 30 Copynumber: 2.7 Consensus size: 30
34698080 TGAATCACAT
34698090 CAAAAACATTACTTAACCTAATTAGCCAAC
1 CAAAAACATTACTTAACCTAATTAGCCAAC
34698120 CAAAAACATTACTTAACCTAATTAGCCAAC
1 CAAAAACATTACTTAACCTAATTAGCCAAC
34698150 CAAAAACATTACTTAACCTA
1 CAAAAACATTACTTAACCTA
34698170 TATTTGTCAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.47, C:0.26, G:0.03, T:0.24
Consensus pattern (30 bp):
CAAAAACATTACTTAACCTAATTAGCCAAC
Found at i:34698976 original size:42 final size:42
Alignment explanation
Indices: 34698874--34699030 Score: 135
Period size: 43 Copynumber: 3.7 Consensus size: 42
34698864 AGCTATTACA
* *
34698874 ATGCCAACGTCCCAGACGAG-GTCTTACATGTAATCAAATATCG
1 ATGCCAACGTCCCAGAC-AGTGTCTTACATGAAATTAAATA-CG
** * *
34698917 ATGCC-ACTGTCTTAGACAGTGTTTTACATGAAATTATATACG
1 ATGCCAAC-GTCCCAGACAGTGTCTTACATGAAATTAAATACG
*
34698959 ATGCCAATGTCCCAGACA-TAGTCTTACATGGAAATCTCAAAT-CG
1 ATGCCAACGTCCCAGACAGT-GTCTTACAT-GAAAT-T-AAATACG
*
34699003 ATGCCACCGTCCCAGAC-GTGGTCTTACA
1 ATGCCAACGTCCCAGACAGT-GTCTTACA
34699031 CAAAAATCAT
Statistics
Matches: 92, Mismatches: 14, Indels: 15
0.76 0.12 0.12
Matches are distributed among these distances:
41 1 0.01
42 27 0.29
43 34 0.37
44 27 0.29
45 3 0.03
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.27
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACAGTGTCTTACATGAAATTAAATACG
Found at i:34700564 original size:29 final size:29
Alignment explanation
Indices: 34700521--34700755 Score: 136
Period size: 29 Copynumber: 8.1 Consensus size: 29
34700511 GTGCTAAACA
* *
34700521 ATGGTCGTAATCATCCCTTTTCATATTCG
1 ATGGTCGAAACCATCCCTTTTCATATTCG
*
34700550 ATGGTCGAAACCATCACTTTTCATTAATT-G
1 ATGGTCGAAACCATCCCTTTTCA-T-ATTCG
** *
34700580 ATGGTCGTCA-CATCCCTTTTCATAATCG
1 ATGGTCGAAACCATCCCTTTTCATATTCG
* * * * * * *
34700608 ATAGCCGAAGCTATCTCTTTTCGTATTTG
1 ATGGTCGAAACCATCCCTTTTCATATTCG
** *
34700637 ATGGTCGTCACCATCCCTTTTCAT-TGTTG
1 ATGGTCGAAACCATCCCTTTTCATAT-TCG
** *
34700666 ATGGTCGTCACTATCCCTTTTCATAATT-G
1 ATGGTCGAAACCATCCCTTTTCAT-ATTCG
* * * * *
34700695 ATAGTCGAATCTATCCATTTTCATATTTG
1 ATGGTCGAAACCATCCCTTTTCATATTCG
* * * * * *
34700724 ATAGCCGAAGCTATCCCTTTACATAATCG
1 ATGGTCGAAACCATCCCTTTTCATATTCG
34700753 ATG
1 ATG
34700756 ATCGTCGATA
Statistics
Matches: 160, Mismatches: 38, Indels: 16
0.75 0.18 0.07
Matches are distributed among these distances:
27 2 0.01
28 11 0.07
29 132 0.82
30 11 0.07
31 4 0.03
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.39
Consensus pattern (29 bp):
ATGGTCGAAACCATCCCTTTTCATATTCG
Found at i:34700628 original size:58 final size:58
Alignment explanation
Indices: 34700521--34700761 Score: 211
Period size: 58 Copynumber: 4.2 Consensus size: 58
34700511 GTGCTAAACA
* * * * * * *
34700521 ATGGTCGTAATCATCCCTTTTCATATTCGATGGTCGAAACCATCACTTTTCATTAATTG
1 ATGGTCGTCACCATCCCTTTTCATATTCGATAGCCGAAGCTATCCCTTTTCA-TAATTG
* * * *
34700580 ATGGTCGTCA-CATCCCTTTTCATAATCGATAGCCGAAGCTATCTCTTTTCGTATTTG
1 ATGGTCGTCACCATCCCTTTTCATATTCGATAGCCGAAGCTATCCCTTTTCATAATTG
* * * *
34700637 ATGGTCGTCACCATCCCTTTTCAT-TGTTGATGGTCGTCA-CTATCCCTTTTCATAATTG
1 ATGGTCGTCACCATCCCTTTTCATAT-TCGATAGCCG-AAGCTATCCCTTTTCATAATTG
* * * * * * *
34700695 ATAGTCG-AATCTATCCATTTTCATATTTGATAGCCGAAGCTATCCCTTTACATAATCG
1 ATGGTCGTCA-CCATCCCTTTTCATATTCGATAGCCGAAGCTATCCCTTTTCATAATTG
*
34700753 ATGATCGTC
1 ATGGTCGTC
34700762 GATATGCTGT
Statistics
Matches: 146, Mismatches: 29, Indels: 14
0.77 0.15 0.07
Matches are distributed among these distances:
57 17 0.12
58 118 0.81
59 11 0.08
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.39
Consensus pattern (58 bp):
ATGGTCGTCACCATCCCTTTTCATATTCGATAGCCGAAGCTATCCCTTTTCATAATTG
Found at i:34700659 original size:87 final size:86
Alignment explanation
Indices: 34700536--34700725 Score: 265
Period size: 87 Copynumber: 2.2 Consensus size: 86
34700526 CGTAATCATC
*
34700536 CCTTTTCATATTCGATGGTCGAAACCATCACTTTTCATTAATTGATGGTCGTCAC-ATCCCTTTT
1 CCTTTTCATATTTGATGGTCGAAACCATCACTTTTCATT-ATTGATGGTCGTCACTATCCCTTTT
34700600 CATAATCGATAGCCGAAGCTAT
65 CATAATCGATAGCCGAAGCTAT
* ** * *
34700622 CTCTTTTCGTATTTGATGGTCGTCACCATCCCTTTTCATTGTTGATGGTCGTCACTATCCCTTTT
1 C-CTTTTCATATTTGATGGTCGAAACCATCACTTTTCATTATTGATGGTCGTCACTATCCCTTTT
* * *
34700687 CATAATTGATAGTCGAATCTAT
65 CATAATCGATAGCCGAAGCTAT
34700709 CCATTTTCATATTTGAT
1 CC-TTTTCATATTTGAT
34700726 AGCCGAAGCT
Statistics
Matches: 91, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
86 16 0.18
87 75 0.82
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.41
Consensus pattern (86 bp):
CCTTTTCATATTTGATGGTCGAAACCATCACTTTTCATTATTGATGGTCGTCACTATCCCTTTTC
ATAATCGATAGCCGAAGCTAT
Found at i:34700740 original size:87 final size:85
Alignment explanation
Indices: 34700536--34700761 Score: 258
Period size: 87 Copynumber: 2.6 Consensus size: 85
34700526 CGTAATCATC
* *
34700536 CCTTTTCATATTCGATGGTCGAAACCATCACTTTTCATTAATTGATGGTCGTCACATCCCTTTTC
1 CCTTTTCATATTTGATGGTCG-AACCATCCCTTTTCATTAATTGATGGTCGTCACATCCCTTTTC
* *
34700601 ATAATCGATAGCCGAAGCTAT
65 ATAATCGATAGTCGAATCTAT
* * *
34700622 CTCTTTTCGTATTTGATGGTCGTCACCATCCCTTTTCATT-GTTGATGGTCGTCACTATCCCTTT
1 C-CTTTTCATATTTGATGGTCG-AACCATCCCTTTTCATTAATTGATGGTCGTCAC-ATCCCTTT
*
34700686 TCATAATTGATAGTCGAATCTAT
63 TCATAATCGATAGTCGAATCTAT
* * * * * *
34700709 CCATTTTCATATTTGATAGCCGAAGCTATCCCTTTACA-TAATCGATGATCGTC
1 CC-TTTTCATATTTGATGGTCGAA-CCATCCCTTTTCATTAATTGATGGTCGTC
34700762 GATATGCTGT
Statistics
Matches: 117, Mismatches: 18, Indels: 9
0.81 0.12 0.06
Matches are distributed among these distances:
86 18 0.15
87 99 0.85
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.39
Consensus pattern (85 bp):
CCTTTTCATATTTGATGGTCGAACCATCCCTTTTCATTAATTGATGGTCGTCACATCCCTTTTCA
TAATCGATAGTCGAATCTAT
Found at i:34704262 original size:21 final size:21
Alignment explanation
Indices: 34704236--34704278 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
34704226 CAAAGTGGCA
34704236 AGTTAACTGGCCACATCAGCT
1 AGTTAACTGGCCACATCAGCT
*
34704257 AGTTAACTGGCCATATCAGCT
1 AGTTAACTGGCCACATCAGCT
34704278 A
1 A
34704279 TCCCGTTGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (21 bp):
AGTTAACTGGCCACATCAGCT
Found at i:34709939 original size:133 final size:133
Alignment explanation
Indices: 34709701--34709963 Score: 517
Period size: 133 Copynumber: 2.0 Consensus size: 133
34709691 AAGTTATTGC
34709701 ATCGACAACGGTTCTCATAATTTATCTTGTTTCTATATAGTTGTTTAATCGAAATTAATAGACAA
1 ATCGACAACGGTTCTCATAATTTATCTTGTTTCTATATAGTTGTTTAATCGAAATTAATAGACAA
34709766 AACACTACCATCCTTGCAGGATCGATATCCGACAAACTCACATCTATCTACTATACTTGCATCGA
66 AACACTACCATCCTTGCAGGATCGATATCCGACAAACTCACATCTATCTACTATACTTGCATCGA
34709831 TAG
131 TAG
34709834 ATCGACAACGGTTCTCATAATTTATCTTGTTTCTATATAGTTGTTTAATCGAAATTAATAGACAA
1 ATCGACAACGGTTCTCATAATTTATCTTGTTTCTATATAGTTGTTTAATCGAAATTAATAGACAA
*
34709899 AAGACTACCATCCTTGCAGGATCGATATCCGACAAACTCACATCTATCTACTATACTTGCATCGA
66 AACACTACCATCCTTGCAGGATCGATATCCGACAAACTCACATCTATCTACTATACTTGCATCGA
34709964 CAGTGTACAC
Statistics
Matches: 129, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
133 129 1.00
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (133 bp):
ATCGACAACGGTTCTCATAATTTATCTTGTTTCTATATAGTTGTTTAATCGAAATTAATAGACAA
AACACTACCATCCTTGCAGGATCGATATCCGACAAACTCACATCTATCTACTATACTTGCATCGA
TAG
Found at i:34716469 original size:21 final size:21
Alignment explanation
Indices: 34716418--34716470 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
34716408 ACTGTTGTTG
*
34716418 AGAAGGAAGTTGTTGCTGCAGA
1 AGAA-GAAGTTGTTGCTGAAGA
34716440 AG-AGAAAGTTGTTGCTGAAGA
1 AGAAG-AAGTTGTTGCTGAAGA
34716461 AGAAGAAGTT
1 AGAAGAAGTT
34716471 ACTGAAAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 1 0.04
21 23 0.82
22 4 0.14
ACGTcount: A:0.38, C:0.06, G:0.34, T:0.23
Consensus pattern (21 bp):
AGAAGAAGTTGTTGCTGAAGA
Found at i:34721155 original size:57 final size:56
Alignment explanation
Indices: 34721094--34721225 Score: 142
Period size: 57 Copynumber: 2.3 Consensus size: 56
34721084 ATAGAAATGG
* * *
34721094 TGAAATGGAAAAATAGCAAA-CTTTTGGAAATGACTAAGTTTTTATCCAAAATGAAAA
1 TGAAATGGAAAAAT-G-AAATCATTTGGAAATGAATAAGGTTTTATCCAAAATGAAAA
* ** *
34721151 TGAAAATGGAGAAATGAAATCATTTGGAAATGAATGTGGTTTTCTCCAAAATGAAAA
1 TG-AAATGGAAAAATGAAATCATTTGGAAATGAATAAGGTTTTATCCAAAATGAAAA
*
34721208 TGAAAAT-GTAAAATGAAA
1 TG-AAATGGAAAAATGAAA
34721226 AAGACCTAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
56 12 0.19
57 41 0.64
58 11 0.17
ACGTcount: A:0.48, C:0.07, G:0.18, T:0.27
Consensus pattern (56 bp):
TGAAATGGAAAAATGAAATCATTTGGAAATGAATAAGGTTTTATCCAAAATGAAAA
Found at i:34728328 original size:13 final size:14
Alignment explanation
Indices: 34728299--34728329 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
34728289 AGGATTAGGG
34728299 TTTTTCTTTTCATT
1 TTTTTCTTTTCATT
34728313 TTTTTCTTTTCATT
1 TTTTTCTTTTCATT
34728327 TTT
1 TTT
34728330 CATTTAGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTTCTTTTCATT
Found at i:34751275 original size:16 final size:16
Alignment explanation
Indices: 34751254--34751284 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
34751244 CCAAGCATGT
34751254 CAATAGCTAGCCATTC
1 CAATAGCTAGCCATTC
*
34751270 CAATAGCTAGTCATT
1 CAATAGCTAGCCATT
34751285 ATCAAATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (16 bp):
CAATAGCTAGCCATTC
Found at i:34755135 original size:32 final size:32
Alignment explanation
Indices: 34755091--34755184 Score: 134
Period size: 32 Copynumber: 2.9 Consensus size: 32
34755081 AAATACAAAA
*
34755091 TTATTTTTAAAAACCTTAAACCCTAATTTAAT
1 TTATTTTAAAAAACCTTAAACCCTAATTTAAT
* * *
34755123 TTATTTTAAAAAATCTTAAACCTTAATTTATT
1 TTATTTTAAAAAACCTTAAACCCTAATTTAAT
* *
34755155 TTATTTTAAAAAACCCTAAAACCTAATTTA
1 TTATTTTAAAAAACCTTAAACCCTAATTTA
34755185 TTTTTTAAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 54 1.00
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.44
Consensus pattern (32 bp):
TTATTTTAAAAAACCTTAAACCCTAATTTAAT
Found at i:34755922 original size:3 final size:3
Alignment explanation
Indices: 34755916--34755950 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
34755906 ACTACTACAC
34755916 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
34755951 GTTTTCGGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:34768428 original size:98 final size:98
Alignment explanation
Indices: 34768250--34768446 Score: 340
Period size: 98 Copynumber: 2.0 Consensus size: 98
34768240 GTACAATAAA
* * *
34768250 ACTTTAAAAGAATATCCGCTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
*
34768315 CCTCTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
34768348 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
* *
34768413 CCTTTAAAATTCCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
34768446 A
1 A
34768447 TGACTTTTTT
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 93 1.00
ACGTcount: A:0.37, C:0.24, G:0.11, T:0.29
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
Found at i:34770611 original size:132 final size:132
Alignment explanation
Indices: 34770374--34771280 Score: 1564
Period size: 132 Copynumber: 6.9 Consensus size: 132
34770364 CACTGCAACT
* * * * * * *
34770374 TCAGGGAGATAAGACTAGATGGCTTAAATATGCTTCCCACTATCTTGGAAAGATAAGATTCGTCG
1 TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCG
* *
34770439 TCTTCGATCTGCTCCACTACTGCTTAGGGAAATAAGATCTACAATCTTCAA-CTATCTCCGCTGC
66 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTTTCAACCTA-CTCCGCTGC
**
34770503 TAC
130 CGC
34770506 TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCG
1 TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCG
*
34770571 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTTTCAACATACTCCGCTGCC
66 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTTTCAACCTACTCCGCTGCC
34770636 GC
131 GC
*
34770638 TCAGGGAGGCAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCG
1 TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCG
*
34770703 TCTTCGATCTGATCCACTACTGCTTAGGGAGATAAGATCTACAATTTTCAACCTACTCCGCTGCC
66 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTTTCAACCTACTCCGCTGCC
34770768 GC
131 GC
*
34770770 TCAAGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCG
1 TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCG
34770835 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTTTCAACCTACTCCGCTGCC
66 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTTTCAACCTACTCCGCTGCC
34770900 GC
131 GC
*
34770902 TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCA
1 TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCG
*
34770967 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTTTCAACCTATTCCGCTGCC
66 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTTTCAACCTACTCCGCTGCC
34771032 GC
131 GC
34771034 TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCG
1 TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCG
* * *
34771099 TCTTCGATCTGTTCCGCTACTGCTTAGGGAGATAAGATCTACAATTTTCAACCTACTCCGCTGCT
66 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTTTCAACCTACTCCGCTGCC
34771164 GC
131 GC
* * * *
34771166 TCAGGGAGACAAGGCTTGGTGACTCAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCA
1 TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCG
* *
34771231 TTTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCAACAATTTTCA
66 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTTTCA
34771281 CTGATCTGTT
Statistics
Matches: 740, Mismatches: 34, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
132 738 1.00
133 2 0.00
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (132 bp):
TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCG
TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTTTCAACCTACTCCGCTGCC
GC
Found at i:34774375 original size:14 final size:14
Alignment explanation
Indices: 34774356--34774385 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
34774346 TAGCCATTCT
34774356 TTCATCCAATGCTG
1 TTCATCCAATGCTG
*
34774370 TTCATCCAATGTTG
1 TTCATCCAATGCTG
34774384 TT
1 TT
34774386 GACTCCATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.20, C:0.23, G:0.13, T:0.43
Consensus pattern (14 bp):
TTCATCCAATGCTG
Found at i:34776271 original size:12 final size:12
Alignment explanation
Indices: 34776254--34776278 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34776244 TTTCCCAACG
34776254 TCTCCTCGATGC
1 TCTCCTCGATGC
34776266 TCTCCTCGATGC
1 TCTCCTCGATGC
34776278 T
1 T
34776279 TTTCTCAACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.40, G:0.16, T:0.36
Consensus pattern (12 bp):
TCTCCTCGATGC
Found at i:34782877 original size:98 final size:98
Alignment explanation
Indices: 34782699--34782895 Score: 331
Period size: 98 Copynumber: 2.0 Consensus size: 98
34782689 GTAAAATAAA
* * *
34782699 ACTTTAAAAGAATATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAACAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
*
34782764 CCTCTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
34782797 ACTTTAAAACAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAACAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
* * *
34782862 CCTTTAAAATTCCAAACTCGGAATATTTTCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
34782895 A
1 A
34782896 TGACTTTTTT
Statistics
Matches: 92, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
98 92 1.00
ACGTcount: A:0.37, C:0.24, G:0.10, T:0.29
Consensus pattern (98 bp):
ACTTTAAAACAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
Found at i:34791044 original size:20 final size:20
Alignment explanation
Indices: 34791015--34791052 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
34791005 AATGTTACAA
*
34791015 ATGGAAAAATGGAGAAATAG
1 ATGGAAAAATAGAGAAATAG
*
34791035 ATGGATAAATAGAGAAAT
1 ATGGAAAAATAGAGAAAT
34791053 GAAATTCCGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.26, T:0.18
Consensus pattern (20 bp):
ATGGAAAAATAGAGAAATAG
Found at i:34796882 original size:22 final size:22
Alignment explanation
Indices: 34796854--34796897 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
34796844 AACATAGGAA
34796854 ATTTTGTTTTCATGCTTTTTCT
1 ATTTTGTTTTCATGCTTTTTCT
34796876 ATTTTGTTTTCATGCTTTTTCT
1 ATTTTGTTTTCATGCTTTTTCT
34796898 TTTACTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.09, C:0.14, G:0.09, T:0.68
Consensus pattern (22 bp):
ATTTTGTTTTCATGCTTTTTCT
Found at i:34804834 original size:2 final size:2
Alignment explanation
Indices: 34804827--34804901 Score: 101
Period size: 2 Copynumber: 41.0 Consensus size: 2
34804817 ATTAAGACAC
34804827 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
34804868 AG -G AG -G AG -G AG AG AG AG AG AG AG -G AG -G AG -G AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
34804902 GAGGAGGGAG
Statistics
Matches: 66, Mismatches: 0, Indels: 14
0.82 0.00 0.17
Matches are distributed among these distances:
1 7 0.11
2 59 0.89
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (2 bp):
AG
Found at i:34804859 original size:24 final size:21
Alignment explanation
Indices: 34804828--34804932 Score: 107
Period size: 21 Copynumber: 5.0 Consensus size: 21
34804818 TTAAGACACA
34804828 GAGAGAGAGAGAGAGAGAGAGAG
1 GAGAGAGAGAGAGAG-GAG-GAG
34804851 AGAGAGAGAGAGAGAGGAGGAG
1 -GAGAGAGAGAGAGAGGAGGAG
34804873 GAG-GAGAGAGAGAGAGAGGAG
1 GAGAGAGAGAGAGAG-GAGGAG
34804894 GAG-GAGAG-GAGGAGGGAGGAG
1 GAGAGAGAGAGA-GA-GGAGGAG
34804915 G-GAG-G-GAG-GAGGAGGAG
1 GAGAGAGAGAGAGAGGAGGAG
34804932 G
1 G
34804933 GAAGGGAGGA
Statistics
Matches: 76, Mismatches: 0, Indels: 17
0.82 0.00 0.18
Matches are distributed among these distances:
17 8 0.11
18 2 0.03
19 1 0.01
20 16 0.21
21 27 0.36
22 4 0.05
23 3 0.04
24 15 0.20
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (21 bp):
GAGAGAGAGAGAGAGGAGGAG
Found at i:34804872 original size:3 final size:3
Alignment explanation
Indices: 34804864--34804946 Score: 80
Period size: 3 Copynumber: 26.0 Consensus size: 3
34804854 GAGAGAGAGA
34804864 GAG GAG GAG GAG GAG AGAG AGAG AGAG GAG GAG GA- GAG GAG GAGG GAG
1 GAG GAG GAG GAG GAG -GAG -GAG -GAG GAG GAG GAG GAG GAG GA-G GAG
*
34804912 GAGG GAGG GAG GAG GAG GAG G-G AAGG GAG GAG GAG
1 GA-G GA-G GAG GAG GAG GAG GAG GA-G GAG GAG GAG
34804947 AGAGANNNNN
Statistics
Matches: 72, Mismatches: 2, Indels: 12
0.84 0.02 0.14
Matches are distributed among these distances:
2 3 0.04
3 46 0.64
4 23 0.32
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:34804880 original size:32 final size:30
Alignment explanation
Indices: 34804828--34804932 Score: 108
Period size: 26 Copynumber: 3.9 Consensus size: 30
34804818 TTAAGACACA
34804828 GAGAGAGAGAGAGAGA-GA-GA-GA-GAGA
1 GAGAGAGAGAGAGAGAGGAGGAGGAGGAGA
34804854 GAGAGAGAGAGAG-GAGGAGGAGGA-GAGA
1 GAGAGAGAGAGAGAGAGGAGGAGGAGGAGA
34804882 GAGAGAGAG-GAG-GAGGA-GAGGAGGAG-
1 GAGAGAGAGAGAGAGAGGAGGAGGAGGAGA
* *
34804908 G-GAG-GAGGGAGGGAGGAGGAGGAGG
1 GAGAGAGAGAGAGAGAGGAGGAGGAGG
34804933 GAAGGGAGGA
Statistics
Matches: 72, Mismatches: 0, Indels: 13
0.85 0.00 0.15
Matches are distributed among these distances:
24 3 0.04
25 8 0.11
26 26 0.36
27 20 0.28
28 15 0.21
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (30 bp):
GAGAGAGAGAGAGAGAGGAGGAGGAGGAGA
Found at i:34804911 original size:18 final size:18
Alignment explanation
Indices: 34804858--34804948 Score: 90
Period size: 18 Copynumber: 5.3 Consensus size: 18
34804848 GAGAGAGAGA
34804858 GAGAGAGAGGA-GGAGGAG
1 GAGAG-GAGGAGGGAGGAG
34804876 GAGAGAGAGAGAGAGGAGGAG
1 GAGAG-GAG-GAG-GGAGGAG
34804897 GAGAGGAGGAGGGAGGAG
1 GAGAGGAGGAGGGAGGAG
34804915 G-GA-G-GGA-GGAGGAG
1 GAGAGGAGGAGGGAGGAG
34804929 GAG-GGA--AGGGAGGAG
1 GAGAGGAGGAGGGAGGAG
34804944 GAGAG
1 GAGAG
34804949 AGANNNNNNN
Statistics
Matches: 65, Mismatches: 0, Indels: 18
0.78 0.00 0.22
Matches are distributed among these distances:
14 9 0.14
15 15 0.23
16 2 0.03
17 2 0.03
18 17 0.26
19 5 0.08
20 3 0.05
21 12 0.18
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (18 bp):
GAGAGGAGGAGGGAGGAG
Found at i:34805193 original size:18 final size:18
Alignment explanation
Indices: 34805166--34805200 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
34805156 GTTTTTTTGT
*
34805166 GGGAAGGAGGGAGAGAGG
1 GGGAAAGAGGGAGAGAGG
34805184 GGGAAAGAGGGAGAGAG
1 GGGAAAGAGGGAGAGAG
34805201 AGAGAGTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.63, T:0.00
Consensus pattern (18 bp):
GGGAAAGAGGGAGAGAGG
Found at i:34805418 original size:6 final size:6
Alignment explanation
Indices: 34805403--34805460 Score: 55
Period size: 6 Copynumber: 9.8 Consensus size: 6
34805393 TATAAGTCTA
* * * * *
34805403 AAAAAT -AAAAT AAAAAT AACAAG AAAAAT ATAAAT ATAAAT ATAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
*
34805450 AAAAAG AAAAA
1 AAAAAT AAAAA
34805461 AATCTAAATA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
5 5 0.11
6 39 0.89
ACGTcount: A:0.78, C:0.02, G:0.03, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:34805454 original size:24 final size:23
Alignment explanation
Indices: 34805364--34805444 Score: 67
Period size: 24 Copynumber: 3.3 Consensus size: 23
34805354 TAATCAATAA
34805364 AAAAATAAC-AGTAAAAATAAAAT
1 AAAAATAACAAG-AAAAATAAAAT
*
34805387 AGAACATATAAGTCTA-AAAAATAAAAT
1 A-AA-A-ATAA--CAAGAAAAATAAAAT
34805414 AAAAATAACAAGAAAAATATAAAT
1 AAAAATAACAAGAAAAATA-AAAT
*
34805438 ATAAATA
1 AAAAATA
34805445 TAAATAAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
22 2 0.04
23 8 0.17
24 16 0.33
25 2 0.04
26 6 0.12
27 12 0.25
28 1 0.02
29 1 0.02
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.20
Consensus pattern (23 bp):
AAAAATAACAAGAAAAATAAAAT
Found at i:34805463 original size:50 final size:50
Alignment explanation
Indices: 34805364--34805463 Score: 116
Period size: 50 Copynumber: 2.0 Consensus size: 50
34805354 TAATCAATAA
* * *
34805364 AAAAATAACAGTAAAAATAAAATAGAACATATAAGTCTAAAAAATAAAAT
1 AAAAATAACAGTAAAAATAAAATAGAACATATAAATCAAAAAAAAAAAAT
*
34805414 AAAAATAACAAG-AAAAATATAAATATAA-ATATAAAT-AAAAAGAAAAAAAT
1 AAAAATAAC-AGTAAAAATA-AAATAGAACATATAAATCAAAAA-AAAAAAAT
34805464 CTAAATAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
49 4 0.09
50 30 0.70
51 9 0.21
ACGTcount: A:0.72, C:0.04, G:0.05, T:0.19
Consensus pattern (50 bp):
AAAAATAACAGTAAAAATAAAATAGAACATATAAATCAAAAAAAAAAAAT
Found at i:34806416 original size:10 final size:10
Alignment explanation
Indices: 34806401--34806436 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
34806391 ACACTTATAG
34806401 TTTTTAATAA
1 TTTTTAATAA
34806411 TTTTT-ATAA
1 TTTTTAATAA
34806420 TTTTTAATAA
1 TTTTTAATAA
34806430 TTTTTAA
1 TTTTTAA
34806437 AACCAATATG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 9 0.36
10 16 0.64
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:34806419 original size:9 final size:9
Alignment explanation
Indices: 34806395--34806435 Score: 55
Period size: 10 Copynumber: 4.3 Consensus size: 9
34806385 TATTCAACAC
*
34806395 TTATAGTTT
1 TTATAATTT
34806404 TTAATAATTT
1 TT-ATAATTT
34806414 TTATAATTT
1 TTATAATTT
34806423 TTAATAATTT
1 TT-ATAATTT
34806433 TTA
1 TTA
34806436 AAACCAATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 12 0.41
10 17 0.59
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (9 bp):
TTATAATTT
Found at i:34806423 original size:19 final size:19
Alignment explanation
Indices: 34806395--34806435 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
34806385 TATTCAACAC
*
34806395 TTATAGTTTTTAATAATTT
1 TTATAATTTTTAATAATTT
34806414 TTATAATTTTTAATAATTT
1 TTATAATTTTTAATAATTT
34806433 TTA
1 TTA
34806436 AAACCAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
TTATAATTTTTAATAATTT
Found at i:34807152 original size:14 final size:14
Alignment explanation
Indices: 34807133--34807160 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
34807123 TAATAACTTA
34807133 TTTGTTGTTTTAAT
1 TTTGTTGTTTTAAT
34807147 TTTGTTGTTTTAAT
1 TTTGTTGTTTTAAT
34807161 CTTATAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.71
Consensus pattern (14 bp):
TTTGTTGTTTTAAT
Found at i:34807415 original size:18 final size:18
Alignment explanation
Indices: 34807392--34807438 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
34807382 ATAAAAATTA
34807392 TTTAAAAATATTTT-AAT
1 TTTAAAAATATTTTAAAT
*
34807409 TTATAAAAGTATTTTAAAT
1 TT-TAAAAATATTTTAAAT
34807428 TTT-AAAATATT
1 TTTAAAAATATT
34807439 AATTAAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 9 0.35
18 12 0.46
19 5 0.19
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
TTTAAAAATATTTTAAAT
Found at i:34807584 original size:23 final size:25
Alignment explanation
Indices: 34807558--34807612 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 25
34807548 ATTGCAAGTT
*
34807558 TAAAATTTTCAAA-AA-TTTTTAAA
1 TAAAATTTTAAAATAATTTTTTAAA
** *
34807581 TAAAAGATTAAAATAATTTTTTATA
1 TAAAATTTTAAAATAATTTTTTAAA
34807606 TAAAATT
1 TAAAATT
34807613 GAAGGGAAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
23 10 0.42
24 2 0.08
25 12 0.50
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (25 bp):
TAAAATTTTAAAATAATTTTTTAAA
Found at i:34810369 original size:11 final size:11
Alignment explanation
Indices: 34810355--34810393 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
34810345 ACATCTAAAT
34810355 AATAATAACAA
1 AATAATAACAA
*
34810366 AATAATAATAA
1 AATAATAACAA
* *
34810377 TATAATAACGA
1 AATAATAACAA
34810388 AATAAT
1 AATAAT
34810394 TGCAAAACAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.26
Consensus pattern (11 bp):
AATAATAACAA
Found at i:34810384 original size:14 final size:14
Alignment explanation
Indices: 34810307--34810376 Score: 54
Period size: 14 Copynumber: 4.6 Consensus size: 14
34810297 AATACTTTAA
34810307 AATAATAACAAAATT
1 AATAATAACAAAA-T
34810322 AATAATAA-AATAA-
1 AATAATAACAA-AAT
34810335 AAGTTATATAACATCTAAAT
1 AA--TA-ATAACA---AAAT
34810355 AATAATAACAAAAT
1 AATAATAACAAAAT
34810369 AATAATAA
1 AATAATAA
34810377 TATAATAACG
Statistics
Matches: 46, Mismatches: 0, Indels: 19
0.71 0.00 0.29
Matches are distributed among these distances:
13 2 0.04
14 14 0.30
15 12 0.26
16 4 0.09
17 7 0.15
18 2 0.04
19 2 0.04
20 3 0.07
ACGTcount: A:0.66, C:0.06, G:0.01, T:0.27
Consensus pattern (14 bp):
AATAATAACAAAAT
Found at i:34810391 original size:36 final size:35
Alignment explanation
Indices: 34810308--34810393 Score: 86
Period size: 36 Copynumber: 2.4 Consensus size: 35
34810298 ATACTTTAAA
* * *
34810308 ATAATAACAAA-ATTAATAATAAAATAAAAGTTAT
1 ATAATAACAAATAATAATAACAAAATAAAAGTAAT
* *
34810342 ATAACATCTAAATAATAATAACAAAATAATAA-TAAT
1 ATAATAAC-AAATAATAATAACAAAATAA-AAGTAAT
34810378 ATAATAACGAAATAAT
1 ATAATAAC-AAATAAT
34810394 TGCAAAACAG
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
34 6 0.15
35 3 0.07
36 30 0.73
37 2 0.05
ACGTcount: A:0.64, C:0.06, G:0.02, T:0.28
Consensus pattern (35 bp):
ATAATAACAAATAATAATAACAAAATAAAAGTAAT
Found at i:34813589 original size:3 final size:3
Alignment explanation
Indices: 34813581--34813621 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
34813571 AAATTAGTTA
34813581 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
34813622 AAGGATATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:34821755 original size:1 final size:1
Alignment explanation
Indices: 34821749--34821773 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
34821739 GTGTGAAGAT
34821749 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
34821774 GGGAGTGGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:34824161 original size:17 final size:17
Alignment explanation
Indices: 34824139--34824171 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
34824129 ATATTTAATA
34824139 TATATTTGATTAAAAAG
1 TATATTTGATTAAAAAG
34824156 TATATTTGATTAAAAA
1 TATATTTGATTAAAAA
34824172 TAAAAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (17 bp):
TATATTTGATTAAAAAG
Found at i:34824285 original size:13 final size:13
Alignment explanation
Indices: 34824267--34824294 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
34824257 TTTGCCCAAA
34824267 CCTATATTTCGGG
1 CCTATATTTCGGG
34824280 CCTATATTTCGGG
1 CCTATATTTCGGG
34824293 CC
1 CC
34824295 AGCCGTCGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.29, G:0.21, T:0.36
Consensus pattern (13 bp):
CCTATATTTCGGG
Found at i:34825616 original size:27 final size:27
Alignment explanation
Indices: 34825567--34825629 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
34825557 GGAAAAGTCA
*
34825567 ACTCCCCTTTAGTAATAGCATCAATGC
1 ACTCCCCTTTAGTAATAGCATCAATAC
* *
34825594 ACTCCACCTTT-GTAGTAGTATCAATAC
1 ACTCC-CCTTTAGTAATAGCATCAATAC
34825621 ACTTCCCCT
1 AC-TCCCCT
34825630 CGATAAGATG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 23 0.74
28 8 0.26
ACGTcount: A:0.27, C:0.32, G:0.10, T:0.32
Consensus pattern (27 bp):
ACTCCCCTTTAGTAATAGCATCAATAC
Found at i:34828423 original size:16 final size:18
Alignment explanation
Indices: 34828388--34828425 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
34828378 TGTACTATTG
34828388 ATTATGTAATTGGATAAT
1 ATTATGTAATTGGATAAT
*
34828406 ATTAT-TAATTTG-TAAT
1 ATTATGTAATTGGATAAT
34828422 ATTA
1 ATTA
34828426 ATTGTGGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (18 bp):
ATTATGTAATTGGATAAT
Found at i:34829330 original size:23 final size:24
Alignment explanation
Indices: 34829304--34829365 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
34829294 CCCATATTAA
34829304 ATATTTAATATATATAAAA-ATAT
1 ATATTTAATATATATAAAATATAT
* * *
34829327 ATATTTGATTAAAAATAAAATATAT
1 ATATTT-AATATATATAAAATATAT
34829352 ATATTTAATATATA
1 ATATTTAATATATA
34829366 ATTTGAGCCA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
23 6 0.19
24 15 0.48
25 10 0.32
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
ATATTTAATATATATAAAATATAT
Found at i:34832103 original size:42 final size:42
Alignment explanation
Indices: 34832056--34832149 Score: 188
Period size: 42 Copynumber: 2.2 Consensus size: 42
34832046 CATAATTTCA
34832056 AATTCATACAAATCATATCAATACTCATCTTAAAACCAATCC
1 AATTCATACAAATCATATCAATACTCATCTTAAAACCAATCC
34832098 AATTCATACAAATCATATCAATACTCATCTTAAAACCAATCC
1 AATTCATACAAATCATATCAATACTCATCTTAAAACCAATCC
34832140 AATTCATACA
1 AATTCATACA
34832150 TATCGTCCCT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.29
Consensus pattern (42 bp):
AATTCATACAAATCATATCAATACTCATCTTAAAACCAATCC
Found at i:34834476 original size:50 final size:50
Alignment explanation
Indices: 34834416--34834607 Score: 174
Period size: 50 Copynumber: 3.9 Consensus size: 50
34834406 TATTGAGTTT
* * *
34834416 ATGAGAGGTCCCATATAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
1 ATGAAAGGTCCCATATAAGACCATGTCTGGGACATGGCATTGGCACCGAC
*** * *
34834466 ATGAAAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGAT
1 ATGAAAGGTCCCATATAAGACCATGTCTGGGACATGGCATTGGCACCGAC
* * * * *
34834516 ATGAGAA-CTCCCATATAAGACCATATCTGAGATATGACATTGGCA--GTAC
1 ATGA-AAGGTCCCATATAAGACCATGTCTGGGACATGGCATTGGCACCG-AC
* ** * * *
34834565 AGGAAACATCCCATGTAAGACCATGTCTAGGACATGGCTTTGG
1 ATGAAAGGTCCCATATAAGACCATGTCTGGGACATGGCATTGG
34834608 TATGTTATTA
Statistics
Matches: 113, Mismatches: 26, Indels: 7
0.77 0.18 0.05
Matches are distributed among these distances:
48 3 0.03
49 32 0.28
50 76 0.67
51 2 0.02
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.21
Consensus pattern (50 bp):
ATGAAAGGTCCCATATAAGACCATGTCTGGGACATGGCATTGGCACCGAC
Found at i:34834844 original size:16 final size:15
Alignment explanation
Indices: 34834811--34834862 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
34834801 ATGAGTCATT
*
34834811 TAAATAAGCAAGTAAG
1 TAAATAAGTAAG-AAG
34834827 TAAATAAGTAAGAGAG
1 TAAATAAGTAAGA-AG
* *
34834843 TAAGTAAATAAGAAAG
1 TAAATAAGTAAG-AAG
34834859 TAAA
1 TAAA
34834863 GATCATGATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
15 1 0.03
16 28 0.93
17 1 0.03
ACGTcount: A:0.60, C:0.02, G:0.19, T:0.19
Consensus pattern (15 bp):
TAAATAAGTAAGAAG
Found at i:34850362 original size:39 final size:39
Alignment explanation
Indices: 34850316--34850490 Score: 230
Period size: 39 Copynumber: 4.5 Consensus size: 39
34850306 ACAATAGGGG
*
34850316 CGTAAGTACGATCAGGGGTA-TCAAAGTACAACAAGGGCA
1 CGTAAGTGCGATCAGGGGTACT-AAAGTACAACAAGGGCA
* * *
34850355 CGTAAGTACGATCAGGGTTACTAAAGTACAA-TAGGGACA
1 CGTAAGTGCGATCAGGGGTACTAAAGTACAACAAGGG-CA
* *
34850394 CGTAAGTGCGATCA-GGGTACTGAAGTACAACAGGGGCA
1 CGTAAGTGCGATCAGGGGTACTAAAGTACAACAAGGGCA
**
34850432 CGTAAGTGCGATCAGGGGTACCGAAGTACAACAAGGGCA
1 CGTAAGTGCGATCAGGGGTACTAAAGTACAACAAGGGCA
*
34850471 CATAAGTGCGATCAGGGGTA
1 CGTAAGTGCGATCAGGGGTA
34850491 TAGTTATATA
Statistics
Matches: 122, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
38 34 0.28
39 87 0.71
40 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.31, T:0.17
Consensus pattern (39 bp):
CGTAAGTGCGATCAGGGGTACTAAAGTACAACAAGGGCA
Found at i:34850383 original size:20 final size:18
Alignment explanation
Indices: 34850318--34850448 Score: 61
Period size: 19 Copynumber: 6.8 Consensus size: 18
34850308 AATAGGGGCG
34850318 TAAGTACGATCAGGGGTATC
1 TAAGTACGATCA-GGGTA-C
* * *
34850338 AAAGTAC-AACAAGGGCAC
1 TAAGTACGATC-AGGGTAC
34850356 GTAAGTACGATCAGGGTTAC
1 -TAAGTACGATCAGGG-TAC
* *
34850376 TAAAGTACAAT-AGGGACAC
1 T-AAGTACGATCAGGG-TAC
*
34850395 GTAAGTGCGATCAGGGTAC
1 -TAAGTACGATCAGGGTAC
* *
34850414 TGAAGTAC-AACAGGGGCAC
1 T-AAGTACGATCA-GGGTAC
*
34850433 GTAAGTGCGATCAGGG
1 -TAAGTACGATCAGGG
34850449 GTACCGAAGT
Statistics
Matches: 83, Mismatches: 17, Indels: 23
0.67 0.14 0.19
Matches are distributed among these distances:
18 5 0.06
19 50 0.60
20 28 0.34
ACGTcount: A:0.35, C:0.17, G:0.31, T:0.18
Consensus pattern (18 bp):
TAAGTACGATCAGGGTAC
Done.