Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 129432109
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: 129432109
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 96 of 425
Found at i:27828667 original size:21 final size:21
Alignment explanation
Indices: 27828641--27828682 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
27828631 GTAATGAGTG
27828641 AGGTTCGCAAGAGTAGGTACT
1 AGGTTCGCAAGAGTAGGTACT
*
27828662 AGGTTCGCAAGAGTGGGTACT
1 AGGTTCGCAAGAGTAGGTACT
27828683 TGAAATGATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.14, G:0.36, T:0.24
Consensus pattern (21 bp):
AGGTTCGCAAGAGTAGGTACT
Found at i:27840878 original size:20 final size:20
Alignment explanation
Indices: 27840828--27840879 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
27840818 AAGGCAATGC
*
27840828 ACACGCCCGTGTGCTTTTGG
1 ACACGCCCGTGTGCTTTGGG
* *
27840848 ACATGCTCGTGTGCTTTGGG
1 ACACGCCCGTGTGCTTTGGG
27840868 ACACGCCCGTGT
1 ACACGCCCGTGT
27840880 CCCCTACCCA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.12, C:0.29, G:0.31, T:0.29
Consensus pattern (20 bp):
ACACGCCCGTGTGCTTTGGG
Found at i:27845733 original size:39 final size:40
Alignment explanation
Indices: 27845624--27845767 Score: 211
Period size: 39 Copynumber: 3.6 Consensus size: 40
27845614 TCGTTCAAAC
* * * * * *
27845624 GCCTTCGGGACATAGCCCGGTTATGATAACCCGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATCACAACTCGCACAATT
*
27845664 GCCTTCGGGACTTAACCCGGATATCACAACTCGCACAATT
1 GCCTTCGGGACTTAGCCCGGATATCACAACTCGCACAATT
27845704 GCCTTCGGG-CTTAGCCCGGATATCACAACTCGCACAATT
1 GCCTTCGGGACTTAGCCCGGATATCACAACTCGCACAATT
27845743 GCCTTCGGG-CTTAGCCCGGATATCA
1 GCCTTCGGGACTTAGCCCGGATATCA
27845768 TTCGAACATT
Statistics
Matches: 96, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 54 0.56
40 42 0.44
ACGTcount: A:0.24, C:0.32, G:0.22, T:0.22
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATCACAACTCGCACAATT
Found at i:27853675 original size:39 final size:40
Alignment explanation
Indices: 27853566--27853709 Score: 202
Period size: 39 Copynumber: 3.6 Consensus size: 40
27853556 TCGTTCAAAC
* * * * * *
27853566 GCCTTCGGGACATAGCCCGGTTATGATAACCCGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATCACAACTCGCACAATT
*
27853606 GCCTTCGGGACTTAACCCGGATATCACAACTCGCACAATT
1 GCCTTCGGGACTTAGCCCGGATATCACAACTCGCACAATT
27853646 GCCTTCGGG-CTTAGCCCGGATATCACAACTCGCACAATT
1 GCCTTCGGGACTTAGCCCGGATATCACAACTCGCACAATT
*
27853685 GCCTTCGGG-CTTAGCCCGAATATCA
1 GCCTTCGGGACTTAGCCCGGATATCA
27853710 TTCGAACATT
Statistics
Matches: 95, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 53 0.56
40 42 0.44
ACGTcount: A:0.25, C:0.32, G:0.21, T:0.22
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATCACAACTCGCACAATT
Found at i:27869210 original size:48 final size:49
Alignment explanation
Indices: 27869139--27869371 Score: 218
Period size: 48 Copynumber: 4.9 Consensus size: 49
27869129 TAAGGATATG
27869139 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAA-A
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAATA
* * *
27869187 TGTGATCCCATGTAAGACAATGTCTTGGACATGGCATTGGCAT-TAATA
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAATA
* * * * * * *
27869235 TGAGA-CATCGTGTAAGACCATAAT-TGGG-C-T---ATCGACTTCG-ATA
1 TGTGATC-CCATGTAAGACCAT-GTCTGGGACATGGCATTGGCATCGAATA
* *
27869278 TGCATAATCCCATGTAAGACCATGTCCGGGACATGGCATTGGCATC-AATA
1 TG--TGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAATA
* * *
27869328 TGTGATCCCATGTAAGACCATTTTTGGGATATGGCATTGGCATC
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATC
27869372 CTACTATGTA
Statistics
Matches: 144, Mismatches: 27, Indels: 28
0.72 0.14 0.14
Matches are distributed among these distances:
43 10 0.07
44 1 0.01
45 16 0.11
46 3 0.02
47 5 0.03
48 97 0.67
49 1 0.01
50 11 0.08
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (49 bp):
TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAATA
Found at i:27872702 original size:42 final size:42
Alignment explanation
Indices: 27872624--27872703 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
27872614 GTATAGGTTT
*
27872624 CACACGGCCAAGACACACGCCCGTGTTCTAGGCCGTGTAGCA
1 CACACGGCCAAGACACACGCCCGTGTTCTAGCCCGTGTAGCA
**
27872666 CACACGGCTGAGACACACGCCCGTGTCTCTA-CCCGTGT
1 CACACGGCCAAGACACACGCCCGTGT-TCTAGCCCGTGT
27872704 GCTCAATTCT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
42 30 0.88
43 4 0.12
ACGTcount: A:0.21, C:0.38, G:0.25, T:0.16
Consensus pattern (42 bp):
CACACGGCCAAGACACACGCCCGTGTTCTAGCCCGTGTAGCA
Found at i:27875722 original size:22 final size:22
Alignment explanation
Indices: 27875647--27875722 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
27875637 ACATGCATAT
*
27875647 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCCGAACGGCCA
* * * *
27875669 ATGTGATGAATG-TGAACATGCATA
1 ATGTGAT-AAGGCCGAAC-GGC-CA
27875693 TATGTGATAAGGCCGAACGGCCA
1 -ATGTGATAAGGCCGAACGGCCA
27875716 ATGTGAT
1 ATGTGAT
27875723 GAATGTGAAC
Statistics
Matches: 40, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
22 17 0.43
23 6 0.15
24 6 0.15
25 11 0.28
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.24
Consensus pattern (22 bp):
ATGTGATAAGGCCGAACGGCCA
Found at i:27875769 original size:22 final size:22
Alignment explanation
Indices: 27875744--27875863 Score: 59
Period size: 22 Copynumber: 5.2 Consensus size: 22
27875734 TGCATATACA
27875744 TGATAAGGCCGAATGGCCAATG
1 TGATAAGGCCGAATGGCCAATG
* * * *
27875766 TGATGAATG-TGAACTTG-CATTTG
1 TGAT-AAGGCCGAA-TGGCCA-ATG
27875789 TGTGATAAGGCCGAATGGCCAATG
1 T--GATAAGGCCGAATGGCCAATG
* * *
27875813 TGATGAATG-TGAACAT-GCATATATG
1 TGAT-AAGGCCG-A-ATGGC-CA-ATG
27875838 TGATAAGGCCGAATGGCCAATG
1 TGATAAGGCCGAATGGCCAATG
27875860 TGAT
1 TGAT
27875864 GAATGTGAAC
Statistics
Matches: 70, Mismatches: 14, Indels: 28
0.62 0.12 0.25
Matches are distributed among these distances:
22 20 0.29
23 17 0.24
24 17 0.24
25 16 0.23
ACGTcount: A:0.31, C:0.13, G:0.29, T:0.27
Consensus pattern (22 bp):
TGATAAGGCCGAATGGCCAATG
Found at i:27875948 original size:47 final size:47
Alignment explanation
Indices: 27875626--27875913 Score: 504
Period size: 47 Copynumber: 6.1 Consensus size: 47
27875616 GATTTTATGA
27875626 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
*
27875673 GATGAATGTGAACATGCATATATGTGATAAGGCCGAACGGCCAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
**
27875720 GATGAATGTGAACATGCATATACATGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
* * *
27875767 GATGAATGTGAACTTGCATTTGTGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
27875814 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
**
27875861 GATGAATGTGAACATGCATATATGTGATAAGGTAGAATGGCCAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
27875908 GATGAA
1 GATGAA
27875914 CGTGGAAGTG
Statistics
Matches: 227, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 227 1.00
ACGTcount: A:0.34, C:0.12, G:0.28, T:0.26
Consensus pattern (47 bp):
GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
Found at i:27875991 original size:46 final size:46
Alignment explanation
Indices: 27875941--27876109 Score: 284
Period size: 46 Copynumber: 3.7 Consensus size: 46
27875931 GTGGCGAAGC
*
27875941 CGAATGGCTAATGCGAAATGTGTATGAGATGGATATGAGGTAAAGT
1 CGAATGGCTAATGCGAAACGTGTATGAGATGGATATGAGGTAAAGT
*
27875987 CGAATGGCTAATGCGAAACGTGTATGAGATGGATATGAGGTAAAGC
1 CGAATGGCTAATGCGAAACGTGTATGAGATGGATATGAGGTAAAGT
27876033 CGAATGGCTAATGCGAAACGTGTATGAGATGGATATGAGGTAAAGT
1 CGAATGGCTAATGCGAAACGTGTATGAGATGGATATGAGGTAAAGT
* * **
27876079 CGAATGGCTAATGTGAGATATGTATGAGATG
1 CGAATGGCTAATGCGAAACGTGTATGAGATG
27876110 TGTATATATA
Statistics
Matches: 116, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 116 1.00
ACGTcount: A:0.34, C:0.08, G:0.33, T:0.25
Consensus pattern (46 bp):
CGAATGGCTAATGCGAAACGTGTATGAGATGGATATGAGGTAAAGT
Found at i:27881145 original size:26 final size:26
Alignment explanation
Indices: 27881103--27881152 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
27881093 ACATATTTTC
27881103 TCAAAATTTTACAAGGGGCAAAATTA
1 TCAAAATTTTACAAGGGGCAAAATTA
* * *
27881129 TCAAAATTTTGCTAGGGGTAAAAT
1 TCAAAATTTTACAAGGGGCAAAAT
27881153 AGGGATGAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.42, C:0.10, G:0.18, T:0.30
Consensus pattern (26 bp):
TCAAAATTTTACAAGGGGCAAAATTA
Found at i:27881658 original size:49 final size:49
Alignment explanation
Indices: 27881540--27881663 Score: 124
Period size: 49 Copynumber: 2.5 Consensus size: 49
27881530 AAAGTAATCG
* ** * * *
27881540 TTGTCTAGCCATTCTTGATGGTAGATTATGAAAACAGTGAAAGCCATCA
1 TTGTCAAGCCATTCAAGATGGTAGAATATGAAAACAATGAAAACCATCA
* * * * *
27881589 TTGTCAAGCTATACAGGATGGAAGAATATTAAAACAATGAAAACCATCA
1 TTGTCAAGCCATTCAAGATGGTAGAATATGAAAACAATGAAAACCATCA
*
27881638 TTGT-AGGGCCATTCAAGATGGTAGAA
1 TTGTCA-AGCCATTCAAGATGGTAGAA
27881664 AATTCATTTT
Statistics
Matches: 59, Mismatches: 15, Indels: 2
0.78 0.20 0.03
Matches are distributed among these distances:
48 1 0.02
49 58 0.98
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.27
Consensus pattern (49 bp):
TTGTCAAGCCATTCAAGATGGTAGAATATGAAAACAATGAAAACCATCA
Found at i:27883267 original size:27 final size:27
Alignment explanation
Indices: 27883227--27883284 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
27883217 TAAACTTGAT
* *
27883227 ACTTTTTTTTTCTAATTTGGTACGTAA
1 ACTTTTTTTGTCTAATTTGGTACCTAA
27883254 ACTTTTTTTGTCTAATTTGGTACCTAA
1 ACTTTTTTTGTCTAATTTGGTACCTAA
27883281 ACTT
1 ACTT
27883285 GTCAAATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.22, C:0.14, G:0.10, T:0.53
Consensus pattern (27 bp):
ACTTTTTTTGTCTAATTTGGTACCTAA
Found at i:27884425 original size:25 final size:25
Alignment explanation
Indices: 27884391--27884477 Score: 129
Period size: 25 Copynumber: 3.5 Consensus size: 25
27884381 TAGGGATTTT
*
27884391 ATATGCGAGCCTGTATGCTAGTGTA
1 ATATGCGAGCCTGTATGTTAGTGTA
* *
27884416 ATATGCGAGCATGCATGTTAGTGTA
1 ATATGCGAGCCTGTATGTTAGTGTA
* *
27884441 ATATGCGAGCCTATCTGTTAGTGTA
1 ATATGCGAGCCTGTATGTTAGTGTA
27884466 ATATGCGAGCCT
1 ATATGCGAGCCT
27884478 ATTTGTAGTA
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 55 1.00
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.32
Consensus pattern (25 bp):
ATATGCGAGCCTGTATGTTAGTGTA
Found at i:27884962 original size:16 final size:17
Alignment explanation
Indices: 27884943--27884975 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
27884933 CTTGTAGGTA
*
27884943 CGAACCATCT-TGTATG
1 CGAACCACCTATGTATG
27884959 CGAACCACCTATGTATG
1 CGAACCACCTATGTATG
27884976 AGAGCCTTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.27
Consensus pattern (17 bp):
CGAACCACCTATGTATG
Found at i:27890615 original size:47 final size:47
Alignment explanation
Indices: 27890544--27890711 Score: 159
Period size: 47 Copynumber: 3.6 Consensus size: 47
27890534 TAAGGTGCCA
* *
27890544 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCAT-ATCTC-AAGATG
1 ATGCCATGTCCCAGACAT-GTCTTACACTGACT-ATCATCTCGAAGACG
* *
27890591 ATGCCATGTCCCAGACATGATCTTACACTGACTATCATCTCGTAGCCG
1 ATGCCATGTCCCAGACATG-TCTTACACTGACTATCATCTCGAAGACG
* ** ** *
27890639 ATG-CATGTCCCAGACATGTCTTACATTCG-CT-TACGCCTCGGGGCCG
1 ATGCCATGTCCCAGACATGTCTTACACT-GACTAT-CATCTCGAAGACG
27890685 ATG-CATGTCCCAGACATGTCTTACACT
1 ATGCCATGTCCCAGACATGTCTTACACT
27890712 AGCCCTCATT
Statistics
Matches: 106, Mismatches: 10, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
45 1 0.01
46 48 0.45
47 51 0.48
48 6 0.06
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.27
Consensus pattern (47 bp):
ATGCCATGTCCCAGACATGTCTTACACTGACTATCATCTCGAAGACG
Found at i:27890800 original size:140 final size:140
Alignment explanation
Indices: 27890548--27890803 Score: 351
Period size: 140 Copynumber: 1.8 Consensus size: 140
27890538 GTGCCAATGC
*
27890548 CATGTCCCAGACATGGTCTTACACTGGCTCATATCTCAAGATGATGCCATGTCCCAGACATGATC
1 CATGTCCCAGACATGGTCTTACACTGCCTCATATCTCAAGATGATGCCATGTCCCAGACATGATC
* *
27890613 TTACACTGACTATCATCTCGTAGCCGATGCATGTCCCAGACATGTCTTACATTCGCTTACGCCTC
66 TTACACTGACTATCATATCATAGCCGATGCATGTCCCAGACATGTCTTACATTCGCTTACGCCTC
27890678 GGGGCCGATG
131 GGGGCCGATG
* *
27890688 CATGTCCCAGACAT-GTCTTACACTAGCCCTCAT-T-TCAATG-TAGTTGCCATGTCTCAGACAT
1 CATGTCCCAGACATGGTCTTACACT-G-CCTCATATCTCAA-GAT-GATGCCATGTCCCAGACAT
* * * *
27890749 GGTCTTACACTGGCTCTCATAAT-ATGGCCGATGCATGTCCCAGACATGTCTTACA
62 GATCTTACACTGACTATCAT-ATCATAGCCGATGCATGTCCCAGACATGTCTTACA
27890804 GTAGCTCACA
Statistics
Matches: 102, Mismatches: 9, Indels: 10
0.84 0.07 0.08
Matches are distributed among these distances:
139 15 0.15
140 81 0.79
141 6 0.06
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (140 bp):
CATGTCCCAGACATGGTCTTACACTGCCTCATATCTCAAGATGATGCCATGTCCCAGACATGATC
TTACACTGACTATCATATCATAGCCGATGCATGTCCCAGACATGTCTTACATTCGCTTACGCCTC
GGGGCCGATG
Found at i:27891674 original size:31 final size:31
Alignment explanation
Indices: 27891636--27891698 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
27891626 AAGAGATGAG
27891636 AAGAAAATAAATTGACAACTTTTTCTATTTT
1 AAGAAAATAAATTGACAACTTTTTCTATTTT
27891667 AAGAAAATAAATTGACAACTTTTTCTATTTT
1 AAGAAAATAAATTGACAACTTTTTCTATTTT
27891698 A
1 A
27891699 TTTCTTTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.41
Consensus pattern (31 bp):
AAGAAAATAAATTGACAACTTTTTCTATTTT
Found at i:27904274 original size:17 final size:17
Alignment explanation
Indices: 27904252--27904288 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
27904242 AATCGAAATT
27904252 TATTTTATAATAATAAA
1 TATTTTATAATAATAAA
*
27904269 TATTTTGTAATAATAAA
1 TATTTTATAATAATAAA
27904286 TAT
1 TAT
27904289 CATATATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (17 bp):
TATTTTATAATAATAAA
Found at i:27904847 original size:15 final size:15
Alignment explanation
Indices: 27904827--27904878 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
27904817 ACTACAAAAC
27904827 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
27904842 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
27904861 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
27904876 ATT
1 ATT
27904879 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:27905009 original size:16 final size:16
Alignment explanation
Indices: 27904980--27905010 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
27904970 AATTTATTAA
27904980 AATAATTAATTATATC
1 AATAATTAATTATATC
27904996 AATAATTAATTATAT
1 AATAATTAATTATAT
27905011 GATTAGATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
AATAATTAATTATATC
Found at i:27905607 original size:9 final size:9
Alignment explanation
Indices: 27905595--27905630 Score: 54
Period size: 9 Copynumber: 3.8 Consensus size: 9
27905585 TCAAAAATAT
27905595 ATTTTTATA
1 ATTTTTATA
27905604 ATTTTTATA
1 ATTTTTATA
27905613 ATTTTTTAATA
1 A-TTTTT-ATA
27905624 ATTTTTA
1 ATTTTTA
27905631 ATTTTTTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 11 0.44
10 10 0.40
11 4 0.16
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
ATTTTTATA
Found at i:27905630 original size:10 final size:10
Alignment explanation
Indices: 27905590--27905632 Score: 54
Period size: 10 Copynumber: 4.3 Consensus size: 10
27905580 AAAAATCAAA
27905590 AATATATTTTT
1 AATA-ATTTTT
27905601 -ATAATTTTT
1 AATAATTTTT
27905610 -ATAATTTTTT
1 AATAA-TTTTT
27905620 AATAATTTTT
1 AATAATTTTT
27905630 AAT
1 AAT
27905633 TTTTTGAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
9 10 0.33
10 16 0.53
11 4 0.13
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
AATAATTTTT
Found at i:27905782 original size:17 final size:19
Alignment explanation
Indices: 27905760--27905803 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
27905750 TAATACAAGT
27905760 TTAAAAGTTAAA-AAA-AA
1 TTAAAAGTTAAATAAAGAA
* *
27905777 TTAAAAATTAAATAAAGAG
1 TTAAAAGTTAAATAAAGAA
27905796 TTAAAAGT
1 TTAAAAGT
27905804 GATTTTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 11 0.50
18 3 0.14
19 8 0.36
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (19 bp):
TTAAAAGTTAAATAAAGAA
Found at i:27910209 original size:17 final size:15
Alignment explanation
Indices: 27910175--27910218 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 15
27910165 TTTAATTTAT
27910175 AATA-TAAATTTAAA
1 AATATTAAATTTAAA
27910189 AATATTAAATTGTATAA
1 AATATTAAATT-TA-AA
27910206 AATATTCAAATTT
1 AATATT-AAATTT
27910219 TTTATAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 4 0.15
15 6 0.23
16 2 0.08
17 9 0.35
18 5 0.19
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (15 bp):
AATATTAAATTTAAA
Found at i:27911917 original size:42 final size:42
Alignment explanation
Indices: 27911870--27911954 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
27911860 TTGATAACCT
27911870 CTGTTAGCATTGTTTTCTTCCCCCTTAGTTGCTTGTCTTGAC
1 CTGTTAGCATTGTTTTCTTCCCCCTTAGTTGCTTGTCTTGAC
*
27911912 CTGTTAGCATTGTTTTCTTCCTCCTTAGTTGCTTGTCTTGAC
1 CTGTTAGCATTGTTTTCTTCCCCCTTAGTTGCTTGTCTTGAC
27911954 C
1 C
27911955 AGGGGCGAAG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.09, C:0.26, G:0.16, T:0.48
Consensus pattern (42 bp):
CTGTTAGCATTGTTTTCTTCCCCCTTAGTTGCTTGTCTTGAC
Found at i:27914013 original size:2 final size:2
Alignment explanation
Indices: 27914006--27914045 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
27913996 TTAATATCCC
*
27914006 TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27914046 GAGAGAGAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:27914128 original size:3 final size:3
Alignment explanation
Indices: 27914120--27914189 Score: 104
Period size: 3 Copynumber: 23.3 Consensus size: 3
27914110 GTGTTCTTTG
*
27914120 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
27914168 TAT TGT TGT TGT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT T
27914190 GTTTCATAAT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:27915422 original size:30 final size:29
Alignment explanation
Indices: 27915358--27915423 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
27915348 AATTGAATCA
**
27915358 TCCATCAAAATACAAACATAAATAAAGTG
1 TCCATCAAAATACAAACATAAATAAACCG
*
27915387 TCCATCAAAATAC-AACTATCAATTAAACCG
1 TCCATCAAAATACAAAC-AT-AAATAAACCG
27915417 TCCATCA
1 TCCATCA
27915424 TTGAAATACA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 3 0.09
29 15 0.47
30 14 0.44
ACGTcount: A:0.48, C:0.24, G:0.05, T:0.23
Consensus pattern (29 bp):
TCCATCAAAATACAAACATAAATAAACCG
Found at i:27916351 original size:13 final size:13
Alignment explanation
Indices: 27916333--27916359 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
27916323 ATAGTGCTAA
27916333 ACATAACATACAT
1 ACATAACATACAT
27916346 ACATAACATACAT
1 ACATAACATACAT
27916359 A
1 A
27916360 AACATTAATA
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:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (13 bp):
ACATAACATACAT
Found at i:27916449 original size:12 final size:13
Alignment explanation
Indices: 27916432--27916810 Score: 155
Period size: 12 Copynumber: 28.8 Consensus size: 13
27916422 CACATAATAG
27916432 TAATATACA-ACA
1 TAATATACATACA
27916444 TAATATACATACA
1 TAATATACATACA
* *
27916457 TTAAACATGCCATACA
1 -T-AATAT-ACATACA
* *
27916473 TAGTATACAAACA
1 TAATATACATACA
* *
27916486 TAACAGTAAATAACACA
1 TAATA-TACAT---ACA
* *
27916503 TAACAAACATACA
1 TAATATACATACA
27916516 -AATATACATACA
1 TAATATACATACA
27916528 TAATATACATAACA
1 TAATATACAT-ACA
*
27916542 T--TATATA-ACA
1 TAATATACATACA
*
27916552 TAACATACATACA
1 TAATATACATACA
*
27916565 -AATATACAAACA
1 TAATATACATACA
*
27916577 TAACAGTA-A-ACA
1 TAATA-TACATACA
* *
27916589 TAACATACATATA
1 TAATATACATACA
* *
27916602 TAACAAAACATAACA
1 TAA-TATACAT-ACA
*
27916617 TAACATACATACA
1 TAATATACATACA
*
27916630 -AATATACAAACA
1 TAATATACATACA
*
27916642 TAAAAGTA-A-ACA
1 TAATA-TACATACA
*
27916654 TAACATACATACA
1 TAATATACATACA
* *
27916667 TAACAGTTCATAACA
1 TAATA-TACAT-ACA
*
27916682 TAACATACATACA
1 TAATATACATACA
*
27916695 -AATATACAAACA
1 TAATATACATACA
*
27916707 TAACATTA-A-ACA
1 TAATA-TACATACA
* *
27916719 TAACATACATGCA
1 TAATATACATACA
*
27916732 TAACAGTACATAACA
1 TAATA-TACAT-ACA
27916747 TACATA-ACATA-A
1 TA-ATATACATACA
* *
27916759 TAGTAAACATAACA
1 TAATATACAT-ACA
*
27916773 T-ACATACATAACAA
1 TAATATACAT-AC-A
27916787 TACATA-ACATACA
1 TA-ATATACATACA
27916800 TAATATACATA
1 TAATATACATA
27916811 ACAGTTTAAA
Statistics
Matches: 285, Mismatches: 43, Indels: 77
0.70 0.11 0.19
Matches are distributed among these distances:
10 4 0.01
11 8 0.03
12 94 0.33
13 82 0.29
14 50 0.18
15 26 0.09
16 13 0.05
17 8 0.03
ACGTcount: A:0.56, C:0.18, G:0.02, T:0.23
Consensus pattern (13 bp):
TAATATACATACA
Found at i:27916525 original size:51 final size:49
Alignment explanation
Indices: 27916483--27916666 Score: 153
Period size: 49 Copynumber: 3.6 Consensus size: 49
27916473 TAGTATACAA
27916483 ACATAACAGTAAATAACACATAACAAACATACAAATATACATACATAATAT
1 ACATAACAGTAAAT-A-ACATAACAAACATACAAATATACATACATAATAT
* * * * *
27916534 ACATAACATTATATAACATAACATACATACAAATATACAAACATAACAGTAA
1 ACATAACAGTAAATAACATAACAAACATACAAATATACATACAT-A-A-TAT
* * *
27916586 ACATAACA-TACAT-ATATAACAAAACATAACATAACATACATACA-AATAT
1 ACATAACAGTAAATAACATAAC-AAACAT-ACA-AATATACATACATAATAT
*
27916635 ACA-AACA-TAAAAGTAAACATAACATACATACA
1 ACATAACAGT-AAA-T-AACATAACAAACATACA
27916667 TAACAGTTCA
Statistics
Matches: 109, Mismatches: 14, Indels: 21
0.76 0.10 0.15
Matches are distributed among these distances:
48 5 0.05
49 34 0.31
50 13 0.12
51 28 0.26
52 19 0.17
53 10 0.09
ACGTcount: A:0.59, C:0.18, G:0.02, T:0.21
Consensus pattern (49 bp):
ACATAACAGTAAATAACATAACAAACATACAAATATACATACATAATAT
Found at i:27916537 original size:25 final size:26
Alignment explanation
Indices: 27916500--27916801 Score: 193
Period size: 25 Copynumber: 11.5 Consensus size: 26
27916490 AGTAAATAAC
*
27916500 ACATAACAAACATACA-AATATACAT
1 ACATAACATACATACATAATATACAT
* *
27916525 ACATAATATACATAACAT--TATATA-
1 ACATAACATACAT-ACATAATATACAT
*
27916549 ACATAACATACATACA-AATATACAA
1 ACATAACATACATACATAATATACAT
*
27916574 ACATAACAGTA-A-ACATAACATACAT
1 ACATAACA-TACATACATAATATACAT
* * *
27916599 ATATAACAAAACATAACATAACATACAT
1 ACATAAC-ATACAT-ACATAATATACAT
* * *
27916627 ACA-AATATACAAACATAAAAGTA-A-
1 ACATAACATACATACATAATA-TACAT
* *
27916651 ACATAACATACATACATAACAGTTCAT
1 ACATAACATACATACATAATA-TACAT
*
27916678 AACATAACATACATACA-AATATACAA
1 -ACATAACATACATACATAATATACAT
*
27916704 ACATAACATTA-A-ACATAACATACAT
1 ACATAACA-TACATACATAATATACAT
*
27916729 GCATAACAGTACATAACATACATA-ACAT
1 ACATAACA-TACAT-ACATA-ATATACAT
*
27916757 AATAGTAAACATAACATACATACATA-ACAAT
1 -ACA-T-AACAT-ACATACATA-ATATAC-AT
27916788 ACATAACATACATA
1 ACATAACATACATA
27916802 ATATACATAA
Statistics
Matches: 221, Mismatches: 29, Indels: 52
0.73 0.10 0.17
Matches are distributed among these distances:
23 3 0.01
24 26 0.12
25 88 0.40
26 20 0.09
27 10 0.05
28 45 0.20
29 4 0.02
30 15 0.07
31 10 0.05
ACGTcount: A:0.57, C:0.19, G:0.02, T:0.22
Consensus pattern (26 bp):
ACATAACATACATACATAATATACAT
Found at i:27916578 original size:65 final size:65
Alignment explanation
Indices: 27916478--27916813 Score: 268
Period size: 65 Copynumber: 5.1 Consensus size: 65
27916468 ATACATAGTA
* *
27916478 TACA-AACATAACAGTAAATAACACATA-ACAAACATACAAATATACATACATAATATACATAAC
1 TACATAACATAACA-TACAT-ACAAATATACAAACATACAAATATACATACATAATATACATAAC
27916541 AT
64 AT
* * *
27916543 TATATAACATAACATACATACAAATATACAAACATA-ACAGTAAACATAACATACATAT--ATAA
1 TACATAACATAACATACATACAAATATACAAACATACA-AATATACAT-ACATA-ATATACATAA
*
27916605 CAA
63 CAT
* * *
27916608 AACATAACATAACATACATACAAATATACAAACATA-AAAGTAAACATAACAT-ACATACATAAC
1 TACATAACATAACATACATACAAATATACAAACATACAAA-TATACAT-ACATAATATACATAAC
27916671 AGT
64 A-T
* * * *
27916674 T-CATAACATAACATACATACAAATATACAAACATA-ACATTAAACATAACAT-ACATGCATAAC
1 TACATAACATAACATACATACAAATATACAAACATACA-AATATACAT-ACATAATATACATAAC
*
27916736 AG
64 AT
* * *
27916738 TACATAACAT-ACATAACATA-ATAGTAAACATAACATACATACATA-ACAATACATAACATACA
1 TACATAACATAACAT-ACATACA-AATATACA-AACATACA-A-ATATAC-ATACATAATATACA
*
27916800 TAATA-
60 TAACAT
27916805 TACATAACA
1 TACATAACA
27916814 GTTTAAAAAC
Statistics
Matches: 232, Mismatches: 21, Indels: 34
0.81 0.07 0.12
Matches are distributed among these distances:
63 3 0.01
64 14 0.06
65 159 0.69
66 21 0.09
67 21 0.09
68 14 0.06
ACGTcount: A:0.57, C:0.18, G:0.02, T:0.22
Consensus pattern (65 bp):
TACATAACATAACATACATACAAATATACAAACATACAAATATACATACATAATATACATAACAT
Found at i:27918017 original size:22 final size:22
Alignment explanation
Indices: 27917992--27918034 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
27917982 TAACATAGTC
27917992 AAATTACTTGTAATTTATTTTT
1 AAATTACTTGTAATTTATTTTT
27918014 AAATTACTTGTAATTTATTTT
1 AAATTACTTGTAATTTATTTT
27918035 GTGACTGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.58
Consensus pattern (22 bp):
AAATTACTTGTAATTTATTTTT
Found at i:27920429 original size:43 final size:41
Alignment explanation
Indices: 27920274--27920429 Score: 154
Period size: 43 Copynumber: 3.7 Consensus size: 41
27920264 TGCATTATTG
* **
27920274 TGTAAGACCACATCTGGGACGTTGGCATTTACTTATGATTTACA
1 TGTAAGACCACGTCTGGGACGTTGGCACGTA-TT-TGA-TTACA
* * * * *
27920318 TGTAAGACCACGTATGGGACGTTGTCATCGTGTTTGATTTCG
1 TGTAAGACCACGTCTGGGACGTTGGCA-CGTATTTGATTACA
27920360 TGTAAGACC-CTGTCTGGGACAG-TGGCACCGATATTTGATTACA
1 TGTAAGACCAC-GTCTGGGAC-GTTGGCA-CG-TATTTGATTACA
27920403 TGTAAGACCACGTCTGGGACGTTGGCA
1 TGTAAGACCACGTCTGGGACGTTGGCA
27920430 TTGTACGAGA
Statistics
Matches: 92, Mismatches: 14, Indels: 13
0.77 0.12 0.11
Matches are distributed among these distances:
41 1 0.01
42 27 0.29
43 36 0.39
44 27 0.29
45 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (41 bp):
TGTAAGACCACGTCTGGGACGTTGGCACGTATTTGATTACA
Found at i:27921549 original size:30 final size:30
Alignment explanation
Indices: 27921515--27921572 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
27921505 CCGAGCCTAG
27921515 GGGCAAAAGTGTAAATATGCAAAAGTTTAA
1 GGGCAAAAGTGTAAATATGCAAAAGTTTAA
* * * *
27921545 GGGCAAAATTGTAATTTTTCAAAAGTTT
1 GGGCAAAAGTGTAAATATGCAAAAGTTT
27921573 GAGTTAAGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.31
Consensus pattern (30 bp):
GGGCAAAAGTGTAAATATGCAAAAGTTTAA
Found at i:27922147 original size:68 final size:64
Alignment explanation
Indices: 27922037--27922289 Score: 246
Period size: 68 Copynumber: 3.9 Consensus size: 64
27922027 ATACAGATGG
* * * *
27922037 TATGTAGCTAGGTCACATGTATGGTGCTGA-GTGCACATCATGT-GTACAAGAGAGCTACGAGAC
1 TATGTAGCTAGGTCACATGGATGGTACT-ATGTGTACACCATGTAG-ACAAGAGAGCTACGAG--
27922100 ATTA
62 A-TA
* *
27922104 TGATGTAGCTAGGTCACATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATA
1 T-ATGTAGCTAGGTCACATGGATGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATA
* * * * *
27922169 TATGTAGCTAGGTCACATGCATGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGA
1 TATGTAGCTAGGTCACATGGATGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGA
27922234 TA
63 TA
* * *
27922236 AACTG--GCTAGGTCACATGGATGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 TA-TGTAGCTAGGTCACATGGATGGTACTATGTGTACACCATGTAG-ACAAGAGAGC
27922290 CAAAATTATG
Statistics
Matches: 157, Mismatches: 21, Indels: 20
0.79 0.11 0.10
Matches are distributed among these distances:
62 1 0.01
63 19 0.12
64 24 0.15
65 3 0.02
66 23 0.15
67 34 0.22
68 52 0.33
69 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.24
Consensus pattern (64 bp):
TATGTAGCTAGGTCACATGGATGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATA
Found at i:27924229 original size:40 final size:40
Alignment explanation
Indices: 27924173--27924336 Score: 175
Period size: 41 Copynumber: 4.0 Consensus size: 40
27924163 GCAAAAATTG
* * * *
27924173 TAAAATACAGAGCAATAGTGGCGTTTTTGGTAAAACACCGC
1 TAAAA-ACAGAGCAATAGCGGCGCTTTCGGTAAAACGCCGC
* * * *
27924214 TAAAAACAGAGCAATAGCGGCGTTTTTTGCTAAAATGCCGC
1 TAAAAACAGAGCAATAGCGGCG-CTTTCGGTAAAACGCCGC
** * * *
27924255 TAAAAACAGAGCAATAGTAGCACTTTCGGTAAAATGCTGC
1 TAAAAACAGAGCAATAGCGGCGCTTTCGGTAAAACGCCGC
*
27924295 TAAAAACCAGAGCATTAGCGGCGCTTTCGGTAAAACGCCGC
1 TAAAAA-CAGAGCAATAGCGGCGCTTTCGGTAAAACGCCGC
27924336 T
1 T
27924337 GAAAGTCATA
Statistics
Matches: 104, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
40 36 0.35
41 68 0.65
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (40 bp):
TAAAAACAGAGCAATAGCGGCGCTTTCGGTAAAACGCCGC
Found at i:27924329 original size:81 final size:82
Alignment explanation
Indices: 27924173--27924336 Score: 197
Period size: 81 Copynumber: 2.0 Consensus size: 82
27924163 GCAAAAATTG
* ** * *
27924173 TAAAATACAGAGCAATAGTGGCGTTTTTGGTAAAACACCGCTAAAAACAGAGCAATAGCGGCGTT
1 TAAAATACAGAGCAATAGTAGCACTTTCGGTAAAACACCGCTAAAAACAGAGCAATAGCGGCGTC
* *
27924238 TTTTGCTAAAATGCCGC
66 TTTCGCTAAAACGCCGC
** * *
27924255 TAAAA-ACAGAGCAATAGTAGCACTTTCGGTAAAATGCTGCTAAAAACCAGAGCATTAGCGGCG-
1 TAAAATACAGAGCAATAGTAGCACTTTCGGTAAAACACCGCTAAAAA-CAGAGCAATAGCGGCGT
*
27924318 CTTTCGGTAAAACGCCGC
65 CTTTCGCTAAAACGCCGC
27924336 T
1 T
27924337 GAAAGTCATA
Statistics
Matches: 69, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
81 49 0.71
82 20 0.29
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (82 bp):
TAAAATACAGAGCAATAGTAGCACTTTCGGTAAAACACCGCTAAAAACAGAGCAATAGCGGCGTC
TTTCGCTAAAACGCCGC
Found at i:27924529 original size:7 final size:7
Alignment explanation
Indices: 27924513--27924559 Score: 58
Period size: 7 Copynumber: 6.7 Consensus size: 7
27924503 TATCATTATA
27924513 GTTTAAG
1 GTTTAAG
*
27924520 GTTTATG
1 GTTTAAG
27924527 GTTTAAG
1 GTTTAAG
* * *
27924534 ATATATG
1 GTTTAAG
27924541 GTTTAAG
1 GTTTAAG
27924548 GTTTAAG
1 GTTTAAG
27924555 GTTTA
1 GTTTA
27924560 GGAGTTAATT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.47
Consensus pattern (7 bp):
GTTTAAG
Found at i:27924530 original size:14 final size:14
Alignment explanation
Indices: 27924508--27924559 Score: 68
Period size: 14 Copynumber: 3.7 Consensus size: 14
27924498 TTAATTATCA
*
27924508 TTATAGTTTAAGGT
1 TTATGGTTTAAGGT
*
27924522 TTATGGTTTAAGAT
1 TTATGGTTTAAGGT
*
27924536 ATATGGTTTAAGGT
1 TTATGGTTTAAGGT
*
27924550 TTAAGGTTTA
1 TTATGGTTTA
27924560 GGAGTTAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.29, C:0.00, G:0.23, T:0.48
Consensus pattern (14 bp):
TTATGGTTTAAGGT
Found at i:27924624 original size:7 final size:7
Alignment explanation
Indices: 27924598--27924732 Score: 60
Period size: 7 Copynumber: 19.0 Consensus size: 7
27924588 ATGAATTACA
27924598 GGTTTAG
1 GGTTTAG
* * *
27924605 AGATTAT
1 GGTTTAG
27924612 GGTTTAG
1 GGTTTAG
27924619 GGTTTAG
1 GGTTTAG
27924626 GG-TT-G
1 GGTTTAG
*
27924631 GAGTTTAA
1 G-GTTTAG
* *
27924639 GGTGTCAA
1 GGT-TTAG
27924647 GGTTTAG
1 GGTTTAG
*
27924654 GGTTAAG
1 GGTTTAG
*
27924661 GGTTAAG
1 GGTTTAG
* *
27924668 GATTTAA
1 GGTTTAG
27924675 GGTTTAG
1 GGTTTAG
*
27924682 GGTTAAG
1 GGTTTAG
*
27924689 TGTTTAG
1 GGTTTAG
* *
27924696 TGTTTATA
1 GGTTTA-G
*
27924704 GG-ATAGG
1 GGTTTA-G
*
27924711 GGTTAAG
1 GGTTTAG
27924718 AGGTTTAG
1 -GGTTTAG
27924726 GGTTTAG
1 GGTTTAG
27924733 ATTAATTAGT
Statistics
Matches: 94, Mismatches: 27, Indels: 14
0.70 0.20 0.10
Matches are distributed among these distances:
5 2 0.02
6 3 0.03
7 74 0.79
8 15 0.16
ACGTcount: A:0.24, C:0.01, G:0.37, T:0.39
Consensus pattern (7 bp):
GGTTTAG
Found at i:27924659 original size:21 final size:20
Alignment explanation
Indices: 27924635--27924695 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 20
27924625 GGGTTGGAGT
*
27924635 TTAAGGTGTCAAGGTTTAGGG
1 TTAAGG-GTTAAGGTTTAGGG
*
27924656 TTAAGGGTTAAGGATTTAAGG
1 TTAAGGGTTAAGG-TTTAGGG
*
27924677 TTTAGGGTTAAGTGTTTAG
1 TTAAGGGTTAAG-GTTTAG
27924696 TGTTTATAGG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
20 6 0.18
21 27 0.79
22 1 0.03
ACGTcount: A:0.26, C:0.02, G:0.34, T:0.38
Consensus pattern (20 bp):
TTAAGGGTTAAGGTTTAGGG
Found at i:27924666 original size:28 final size:30
Alignment explanation
Indices: 27924619--27924688 Score: 87
Period size: 28 Copynumber: 2.5 Consensus size: 30
27924609 TATGGTTTAG
27924619 GGTTTAGGGTT--GGAGTTTAAGG-TGTCAA
1 GGTTTAGGGTTAAGGAGTTTAAGGAT-TCAA
*
27924647 GGTTTAGGGTTAAGG-G-TTAAGGATTTAA
1 GGTTTAGGGTTAAGGAGTTTAAGGATTCAA
27924675 GGTTTAGGGTTAAG
1 GGTTTAGGGTTAAG
27924689 TGTTTAGTGT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
28 34 0.89
29 2 0.05
30 2 0.05
ACGTcount: A:0.24, C:0.01, G:0.39, T:0.36
Consensus pattern (30 bp):
GGTTTAGGGTTAAGGAGTTTAAGGATTCAA
Found at i:27931906 original size:22 final size:22
Alignment explanation
Indices: 27931874--27931917 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
27931864 GATTAATATT
*
27931874 TTATATTTAATATTTATAAATA
1 TTATATATAATATTTATAAATA
* *
27931896 TTATATATAATTTTTTTAAATA
1 TTATATATAATATTTATAAATA
27931918 ACAATAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTATATATAATATTTATAAATA
Found at i:27935679 original size:46 final size:46
Alignment explanation
Indices: 27935629--27935800 Score: 208
Period size: 46 Copynumber: 3.7 Consensus size: 46
27935619 GGTTGAGCAT
27935629 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGC
* * *
27935675 CCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--GC
* * *
27935720 ATCCGAACTCGTTGAGTTGAGTCCAAGTTCATTTATGGATGCGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGC
*
27935768 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
27935801 GGGGTGGGTT
Statistics
Matches: 106, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 4 0.04
46 58 0.55
47 27 0.25
48 4 0.04
50 4 0.04
51 2 0.02
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGC
Found at i:27935784 original size:93 final size:93
Alignment explanation
Indices: 27935625--27935795 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
27935615 GGATGGTTGA
* *
27935625 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
27935690 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
27935718 GCATCCGAACTCGTTGAGTTGAGTCCAAGTTCATTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
27935783 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
27935796 ACTTAGGGGT
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:27936062 original size:19 final size:20
Alignment explanation
Indices: 27936025--27936062 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
27936015 ATAAGGTGGT
27936025 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
27936045 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
27936063 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:27938092 original size:54 final size:54
Alignment explanation
Indices: 27938009--27938141 Score: 194
Period size: 54 Copynumber: 2.5 Consensus size: 54
27937999 CTTACGGCGA
* * * *
27938009 GATTACCAGTCCAGGCTAAATCCCCCGTATCGTAAACTCATAAGGTGATGTCAG
1 GATTACTAGTCCAGGCTAAATCCCTCGTATAGTAAACTCATAAGGTAATGTCAG
* * *
27938063 GATTACTAGTTCAGGCTAAATCCCTCGTATAGTAGACTCATAAGGTAATGTCGG
1 GATTACTAGTCCAGGCTAAATCCCTCGTATAGTAAACTCATAAGGTAATGTCAG
*
27938117 GATTACTAGTCCGGGCTAAATCCCT
1 GATTACTAGTCCAGGCTAAATCCCT
27938142 TATAATGGCA
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 70 1.00
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (54 bp):
GATTACTAGTCCAGGCTAAATCCCTCGTATAGTAAACTCATAAGGTAATGTCAG
Found at i:27942890 original size:28 final size:29
Alignment explanation
Indices: 27942859--27942915 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
27942849 TAAAGTGATT
*
27942859 TTTGACAAAAATGTCAATTAGGGA-TTAA
1 TTTGACAAAAATGTAAATTAGGGAGTTAA
* *
27942887 TTTGAGAAAAATGTAAATTGGGGAGTTAA
1 TTTGACAAAAATGTAAATTAGGGAGTTAA
27942916 ATTGTGAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 21 0.84
29 4 0.16
ACGTcount: A:0.42, C:0.04, G:0.23, T:0.32
Consensus pattern (29 bp):
TTTGACAAAAATGTAAATTAGGGAGTTAA
Found at i:27942924 original size:29 final size:28
Alignment explanation
Indices: 27942860--27942924 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
27942850 AAAGTGATTT
* * *
27942860 TTGACAAAAATGTCAATTAGGGATTAAT
1 TTGAGAAAAATGTAAATTAGGGATTAAA
*
27942888 TTGAGAAAAATGTAAATTGGGGAGTTAAA
1 TTGAGAAAAATGTAAATTAGGGA-TTAAA
*
27942917 TTGTGAAA
1 TTGAGAAA
27942925 CAAATGATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
28 20 0.65
29 11 0.35
ACGTcount: A:0.43, C:0.03, G:0.23, T:0.31
Consensus pattern (28 bp):
TTGAGAAAAATGTAAATTAGGGATTAAA
Found at i:27945451 original size:29 final size:28
Alignment explanation
Indices: 27945409--27945529 Score: 129
Period size: 28 Copynumber: 4.2 Consensus size: 28
27945399 ATCCATACTT
* *
27945409 ATTCATTTGGCCCATTTAGGCCCAATCTC
1 ATTCATATGGCCCA-TTAGGCCCAATCAC
*
27945438 ATTCATATGGCCCATTAGACCCAAATCAC
1 ATTCATATGGCCCATTAGGCCC-AATCAC
* * *
27945467 TTTCATATGACCCA-TCGGCCCCAATCAC
1 ATTCATATGGCCCATTAGG-CCCAATCAC
*
27945495 ATTCATATGGCCCATT-GACCCCAATCAC
1 ATTCATATGGCCCATTAG-GCCCAATCAC
27945523 ATTCATA
1 ATTCATA
27945530 GTCATGCAAT
Statistics
Matches: 78, Mismatches: 10, Indels: 9
0.80 0.10 0.09
Matches are distributed among these distances:
28 44 0.56
29 34 0.44
ACGTcount: A:0.28, C:0.33, G:0.11, T:0.28
Consensus pattern (28 bp):
ATTCATATGGCCCATTAGGCCCAATCAC
Found at i:27945501 original size:28 final size:28
Alignment explanation
Indices: 27945429--27945529 Score: 130
Period size: 28 Copynumber: 3.6 Consensus size: 28
27945419 CCCATTTAGG
*
27945429 CCCAATCTCATTCATATGGCCCATTAGAC
1 CCCAATCACATTCATATGGCCCA-TAGAC
* * * * *
27945458 CCAAATCACTTTCATATGACCCATCGGC
1 CCCAATCACATTCATATGGCCCATAGAC
*
27945486 CCCAATCACATTCATATGGCCCATTGAC
1 CCCAATCACATTCATATGGCCCATAGAC
27945514 CCCAATCACATTCATA
1 CCCAATCACATTCATA
27945530 GTCATGCAAT
Statistics
Matches: 61, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
28 42 0.69
29 19 0.31
ACGTcount: A:0.30, C:0.36, G:0.09, T:0.26
Consensus pattern (28 bp):
CCCAATCACATTCATATGGCCCATAGAC
Found at i:27947169 original size:23 final size:24
Alignment explanation
Indices: 27947124--27947179 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
27947114 ATGGTATATT
*
27947124 TTGGTATGATTTATAGATGATGAA
1 TTGGTATGATTTATAGAAGATGAA
*
27947148 TTGGTATG-TTTA-AGAAGCATGAT
1 TTGGTATGATTTATAGAAG-ATGAA
27947171 TTGGT-TGAT
1 TTGGTATGAT
27947180 AGAAAGGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 6 0.21
23 14 0.50
24 8 0.29
ACGTcount: A:0.29, C:0.02, G:0.27, T:0.43
Consensus pattern (24 bp):
TTGGTATGATTTATAGAAGATGAA
Found at i:27951402 original size:46 final size:46
Alignment explanation
Indices: 27951350--27951702 Score: 440
Period size: 46 Copynumber: 7.7 Consensus size: 46
27951340 GTTTTCTGAA
*
27951350 ATGAAATGTGTAAGACCATGGCTGAAAGACACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGACACCATGGCAACATGAT
*
27951396 ATGAAATGTGTAAGACCATGGTTGAAAGACACCATGGGAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGACACCATGGCAACATGAT
*
27951442 ATGAAATGTGTAAGACCATGGTTGAAAGACACCATGGCAACAGGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGACACCATGGCAACATGAT
* * * *
27951488 ATAAAATGTGCAAGACCATGGTTGAAAGATACCATGGCAACAGGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGACACCATGGCAACATGAT
* *
27951534 ATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGA-
1 ATGAAATGTGTAAGACCATGGTTGAAAGACACCATGGCAACATGAT
** * ** * ** * *
27951579 CGGGAATGAATAAGACCATGGTTGAAAGATACCATGGCAATGTAAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGACACCATGGCAACATGAT
*** * * *
27951625 ATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAACCTGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGACACCATGGCAACATGAT
* *
27951671 A-GAAAATGAGTAAGACCATAGTTGAAAGACAC
1 ATG-AAATGTGTAAGACCATGGTTGAAAGACAC
27951703 TATGACATCA
Statistics
Matches: 276, Mismatches: 29, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
45 37 0.13
46 239 0.87
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (46 bp):
ATGAAATGTGTAAGACCATGGTTGAAAGACACCATGGCAACATGAT
Found at i:27951657 original size:137 final size:138
Alignment explanation
Indices: 27951361--27951702 Score: 454
Period size: 137 Copynumber: 2.5 Consensus size: 138
27951351 TGAAATGTGT
* * *
27951361 AAGACCATGGCTGAAAGACACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTGAAAGAC
1 AAGACCATGGTTGAAAGATACCATGGCAACATGATATAAAATGTGTAAGACCATGGTTGAAAGAC
* * ** * *
27951426 ACCATGGGAACATGATATGAAATGTGTAAGACCATGGTTGAAAGACACCATGGCAACAGGATATA
66 ACCATGGCAACATGATAGGAAATGAATAAGACCATGGTTGAAAGACACCATGGCAACAGAACATA
**
27951491 AAATGTGC
131 AAATGAAC
* *
27951499 AAGACCATGGTTGAAAGATACCATGGCAACAGGATATAAAATGTGTAAGACCATGGTTGAAAGAT
1 AAGACCATGGTTGAAAGATACCATGGCAACATGATATAAAATGTGTAAGACCATGGTTGAAAGAC
* * * *
27951564 ACCATGGCAACATGA-CGGGAATGAATAAGACCATGGTTGAAAGATACCATGGCAA-TGTAACAT
66 ACCATGGCAACATGATAGGAAATGAATAAGACCATGGTTGAAAGACACCATGGCAACAG-AACAT
*
27951627 GAAATGAAC
130 AAAATGAAC
* * * * *
27951636 AAGACCATGGTTGAAAGATACCATGGCAACCTGACAGAAAATGAGTAAGACCATAGTTGAAAGAC
1 AAGACCATGGTTGAAAGATACCATGGCAACATGATATAAAATGTGTAAGACCATGGTTGAAAGAC
27951701 AC
66 AC
27951703 TATGACATCA
Statistics
Matches: 178, Mismatches: 25, Indels: 3
0.86 0.12 0.01
Matches are distributed among these distances:
136 1 0.01
137 103 0.58
138 74 0.42
ACGTcount: A:0.41, C:0.16, G:0.24, T:0.19
Consensus pattern (138 bp):
AAGACCATGGTTGAAAGATACCATGGCAACATGATATAAAATGTGTAAGACCATGGTTGAAAGAC
ACCATGGCAACATGATAGGAAATGAATAAGACCATGGTTGAAAGACACCATGGCAACAGAACATA
AAATGAAC
Found at i:27952016 original size:16 final size:17
Alignment explanation
Indices: 27951995--27952027 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
27951985 ATGATGGAGC
27951995 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
27952011 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
27952028 TACTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:27954915 original size:29 final size:29
Alignment explanation
Indices: 27954873--27954986 Score: 149
Period size: 29 Copynumber: 4.0 Consensus size: 29
27954863 GCATGTATAT
*
27954873 GAATGTGATTTGGGCCTAATGGGCCGTAC
1 GAATGTGATTTGGGCCTAATGGGCCATAC
*
27954902 GAATGTGATTTGGGCCCAATGGGCCATAC
1 GAATGTGATTTGGGCCTAATGGGCCATAC
* *
27954931 GAATGTGATTTGGGCCTAGTGGGCCATAT
1 GAATGTGATTTGGGCCTAATGGGCCATAC
** * *
27954960 GAATAAGA-TTGGGCCTAGTAGGCCATA
1 GAATGTGATTTGGGCCTAATGGGCCATA
27954987 TGCATGTATG
Statistics
Matches: 77, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
28 18 0.23
29 59 0.77
ACGTcount: A:0.25, C:0.17, G:0.32, T:0.26
Consensus pattern (29 bp):
GAATGTGATTTGGGCCTAATGGGCCATAC
Found at i:27957979 original size:42 final size:42
Alignment explanation
Indices: 27957933--27958017 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
27957923 TAGGGACTTA
27957933 GTCATTTTATGTATGTGTCATTATGATATGGCCAAATGAATT
1 GTCATTTTATGTATGTGTCATTATGATATGGCCAAATGAATT
*
27957975 GTCATTTTATGTATGTGTCATTATGATATGGCCAAATGTATT
1 GTCATTTTATGTATGTGTCATTATGATATGGCCAAATGAATT
27958017 G
1 G
27958018 GCTTGTAATG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.27, C:0.09, G:0.20, T:0.44
Consensus pattern (42 bp):
GTCATTTTATGTATGTGTCATTATGATATGGCCAAATGAATT
Found at i:27960810 original size:77 final size:77
Alignment explanation
Indices: 27960683--27960839 Score: 314
Period size: 77 Copynumber: 2.0 Consensus size: 77
27960673 TTTATTTGAG
27960683 GATCCATAGGTGTAGATGCTGGTATACAGTTGAAAAGATCAAACTTTTTAAGCACCTTTTCAATG
1 GATCCATAGGTGTAGATGCTGGTATACAGTTGAAAAGATCAAACTTTTTAAGCACCTTTTCAATG
27960748 TAATGTGATTGT
66 TAATGTGATTGT
27960760 GATCCATAGGTGTAGATGCTGGTATACAGTTGAAAAGATCAAACTTTTTAAGCACCTTTTCAATG
1 GATCCATAGGTGTAGATGCTGGTATACAGTTGAAAAGATCAAACTTTTTAAGCACCTTTTCAATG
27960825 TAATGTGATTGT
66 TAATGTGATTGT
27960837 GAT
1 GAT
27960840 AAAGCTATAG
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 80 1.00
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (77 bp):
GATCCATAGGTGTAGATGCTGGTATACAGTTGAAAAGATCAAACTTTTTAAGCACCTTTTCAATG
TAATGTGATTGT
Found at i:27965027 original size:20 final size:20
Alignment explanation
Indices: 27965002--27965073 Score: 54
Period size: 20 Copynumber: 3.3 Consensus size: 20
27964992 TAACTAGGCA
27965002 TCCGAGCTCATTGAGTTGAG
1 TCCGAGCTCATTGAGTTGAG
* *
27965022 TCCGAGTTCACTTATAGATGTGAACG
1 TCCGAGCTCA-TT-GAG-T-TG-A-G
* *
27965048 CCCGAGCTCGTTGAGTTGAG
1 TCCGAGCTCATTGAGTTGAG
27965068 TCCGAG
1 TCCGAG
27965074 TTCGTTTATG
Statistics
Matches: 39, Mismatches: 7, Indels: 12
0.67 0.12 0.21
Matches are distributed among these distances:
20 15 0.38
21 3 0.08
22 4 0.10
23 2 0.05
24 4 0.10
25 3 0.08
26 8 0.21
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (20 bp):
TCCGAGCTCATTGAGTTGAG
Found at i:27965933 original size:22 final size:22
Alignment explanation
Indices: 27965903--27965952 Score: 91
Period size: 22 Copynumber: 2.2 Consensus size: 22
27965893 TAGGTAAATG
27965903 AGTTATATTTTATGAGATATTTA
1 AGTT-TATTTTATGAGATATTTA
27965926 AGTTTATTTTATGAGATATTTA
1 AGTTTATTTTATGAGATATTTA
27965948 AGTTT
1 AGTTT
27965953 TGGTGGAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 23 0.85
23 4 0.15
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (22 bp):
AGTTTATTTTATGAGATATTTA
Found at i:27968369 original size:40 final size:40
Alignment explanation
Indices: 27968310--27968517 Score: 211
Period size: 40 Copynumber: 5.2 Consensus size: 40
27968300 CAATTGAATG
* * * *
27968310 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * *
27968350 ATATCCGGGTTAAGACCCGAAGGCCA-TTGTGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGG-CATTTGTGCAAGTAATT
* * **
27968390 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
27968430 AAATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * **
27968470 CTATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
27968510 ATATCCGG
1 ATATCCGG
27968518 TTGTATTCCG
Statistics
Matches: 142, Mismatches: 24, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
39 2 0.01
40 138 0.97
41 2 0.01
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
Found at i:27968448 original size:80 final size:80
Alignment explanation
Indices: 27968311--27968517 Score: 240
Period size: 80 Copynumber: 2.6 Consensus size: 80
27968301 AATTGAATGA
* * ** * * *
27968311 TATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATTATATCCGGGTTAAGACCCGAAGGCCA
1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGG-CA
*
27968376 -TTGTGCTAGT-G-AC
65 TTTGTGCAAGTCGTAC
* * *
27968389 TACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAAATCCGGGCTAATACCCGAAGGC
1 T--ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGC
*
27968454 ATTTGTGCAAGTCGTTC
64 ATTTGTGCAAGTCGTAC
* *
27968471 TATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTTATATCCGG
1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGG
27968518 TTGTATTCCG
Statistics
Matches: 109, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
78 1 0.01
79 2 0.02
80 103 0.94
81 1 0.01
82 2 0.02
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (80 bp):
TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAT
TTGTGCAAGTCGTAC
Found at i:27973742 original size:17 final size:17
Alignment explanation
Indices: 27973710--27973742 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
27973700 GATAAACATA
27973710 TACTAAATATATAATAC
1 TACTAAATATATAATAC
27973727 TACTATAATATA-AATA
1 TACTA-AATATATAATA
27973743 TTAAAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (17 bp):
TACTAAATATATAATAC
Found at i:27980914 original size:15 final size:15
Alignment explanation
Indices: 27980894--27980962 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
27980884 GTATCTTGGG
27980894 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
27980909 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
27980924 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
27980939 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
27980954 TTTCTTTAT
1 TTTCTTTAT
27980963 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:27980963 original size:30 final size:30
Alignment explanation
Indices: 27980885--27980972 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
27980875 CATAGTATCG
* * * *
27980885 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
27980915 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
27980945 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
27980973 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:27993457 original size:26 final size:26
Alignment explanation
Indices: 27993400--27993506 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
27993390 TGAAATGCCC
*
27993400 ATCATGGAACATTTACCTAA-ACATT
1 ATCATGGAACATTTACCTAACCCATT
27993425 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
27993451 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
27993477 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
27993503 ATCA
1 ATCA
27993507 ATTTGTACCA
Statistics
Matches: 76, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
25 20 0.26
26 56 0.74
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:28000448 original size:26 final size:26
Alignment explanation
Indices: 28000417--28000524 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
28000407 TGAAATGCCC
*
28000417 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
28000443 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
28000469 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
28000495 ATTATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
28000521 ATCA
1 ATCA
28000525 ATTTGTACCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:28005359 original size:46 final size:46
Alignment explanation
Indices: 28005287--28005374 Score: 158
Period size: 46 Copynumber: 1.9 Consensus size: 46
28005277 GATTGGATGG
* *
28005287 TATGTGAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACAT
1 TATGAGAGCTAGTGTAAGACATGTCTGCGACATGCATCGGCCACAT
28005333 TATGAGAGCTAGTGTAAGACATGTCTGCGACATGCATCGGCC
1 TATGAGAGCTAGTGTAAGACATGTCTGCGACATGCATCGGCC
28005375 TCGGGATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.25
Consensus pattern (46 bp):
TATGAGAGCTAGTGTAAGACATGTCTGCGACATGCATCGGCCACAT
Found at i:28005492 original size:49 final size:49
Alignment explanation
Indices: 28005435--28005544 Score: 123
Period size: 49 Copynumber: 2.2 Consensus size: 49
28005425 GTTGTGTGTT
* * * *
28005435 AGTGTAAGACCTGCCTGGGAGACGGCATCGACACT-GATAGATGAGAGCC
1 AGTGTAAGACCTGCCTGGGACACGGCAGCGAC-CTCGATAGACGAAAGCC
* * * * *
28005484 AGTGTAAGACTTGTCTGGGACATGGCAGCGACCTCGATATACGAAAGTC
1 AGTGTAAGACCTGCCTGGGACACGGCAGCGACCTCGATAGACGAAAGCC
28005533 AGTGTAAGACCT
1 AGTGTAAGACCT
28005545 ATCATGGACA
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
48 2 0.04
49 48 0.96
ACGTcount: A:0.29, C:0.21, G:0.30, T:0.20
Consensus pattern (49 bp):
AGTGTAAGACCTGCCTGGGACACGGCAGCGACCTCGATAGACGAAAGCC
Found at i:28006662 original size:31 final size:31
Alignment explanation
Indices: 28006624--28006682 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
28006614 GAGGAGAGTA
*
28006624 GGCATACCCTTCTTGGCTGATCCCTTTCGCT
1 GGCATACCCTTCTTGACTGATCCCTTTCGCT
28006655 GGCATACCCTTCTTGACTGATCCCTTTC
1 GGCATACCCTTCTTGACTGATCCCTTTC
28006683 TCTTTGTGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.12, C:0.36, G:0.17, T:0.36
Consensus pattern (31 bp):
GGCATACCCTTCTTGACTGATCCCTTTCGCT
Found at i:28007601 original size:27 final size:26
Alignment explanation
Indices: 28007557--28007608 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
28007547 CTCGCTGCAA
*
28007557 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
28007584 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
28007609 GCAGCCTTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:28008818 original size:6 final size:6
Alignment explanation
Indices: 28008800--28008939 Score: 99
Period size: 6 Copynumber: 22.8 Consensus size: 6
28008790 AAGAAACATT
*
28008800 ATCAGA A-CTAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAG- GTGACAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA
* * * *
28008849 ATTAGA ATCAGA ATCAGA ATCAGT ATCGGGTA A-CAGA ATCAAA ATCAGA
1 ATCAGA ATCAGA ATCAGA ATCAGA ATC-AG-A ATCAGA ATCAGA ATCAGA
* * * * *
28008898 ATCAGT ATTAGGTA A-CAGA ATCAAA ATTAGA ATCAGT ATCAG
1 ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA ATCAGA ATCAG
28008940 GTAACGGAAT
Statistics
Matches: 104, Mismatches: 19, Indels: 22
0.72 0.13 0.15
Matches are distributed among these distances:
5 6 0.06
6 87 0.84
7 8 0.08
8 3 0.03
ACGTcount: A:0.46, C:0.14, G:0.19, T:0.21
Consensus pattern (6 bp):
ATCAGA
Found at i:28008887 original size:31 final size:31
Alignment explanation
Indices: 28008852--28008962 Score: 159
Period size: 31 Copynumber: 3.5 Consensus size: 31
28008842 TGACAGAATT
* *
28008852 AGAATCAGAATCAGAATCAGTATCGGGTAAC
1 AGAATCAAAATCAGAATCAGTATCAGGTAAC
*
28008883 AGAATCAAAATCAGAATCAGTATTAGGTAAC
1 AGAATCAAAATCAGAATCAGTATCAGGTAAC
*
28008914 AGAATCAAAATTAGAATCAGTATCAGGTAAC
1 AGAATCAAAATCAGAATCAGTATCAGGTAAC
* *
28008945 GGAATAAAAAATCAGAAT
1 AGAAT-CAAAATCAGAAT
28008963 GTGAATGCAA
Statistics
Matches: 71, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
31 61 0.86
32 10 0.14
ACGTcount: A:0.49, C:0.13, G:0.18, T:0.21
Consensus pattern (31 bp):
AGAATCAAAATCAGAATCAGTATCAGGTAAC
Found at i:28008932 original size:37 final size:37
Alignment explanation
Indices: 28008784--28008939 Score: 148
Period size: 37 Copynumber: 4.4 Consensus size: 37
28008774 TAACCCATTA
* * *
28008784 CAGAATAAGAAACATTATCA-G-AACTAGAATCAGAAT
1 CAGAATCAGAATCAGTATCAGGTAAC-AGAATCAGAAT
* * *
28008820 CAGAATCAGAATCAGAATCAGGTGACAGAATTAGAAT
1 CAGAATCAGAATCAGTATCAGGTAACAGAATCAGAAT
*
28008857 CAGAATCAGAATCAGTATCGGGTAACAGAATC---A-
1 CAGAATCAGAATCAGTATCAGGTAACAGAATCAGAAT
* *
28008890 -A-AATCAGAATCAGTATTAGGTAACAGAATCAAAAT
1 CAGAATCAGAATCAGTATCAGGTAACAGAATCAGAAT
* *
28008925 TAGAATCAGTATCAG
1 CAGAATCAGAATCAG
28008940 GTAACGGAAT
Statistics
Matches: 99, Mismatches: 13, Indels: 15
0.78 0.10 0.12
Matches are distributed among these distances:
31 27 0.27
32 1 0.01
34 2 0.02
36 17 0.17
37 50 0.51
38 2 0.02
ACGTcount: A:0.47, C:0.14, G:0.18, T:0.21
Consensus pattern (37 bp):
CAGAATCAGAATCAGTATCAGGTAACAGAATCAGAAT
Found at i:28009170 original size:26 final size:27
Alignment explanation
Indices: 28009100--28009172 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
28009090 CTCAGTTATC
* *
28009100 AGATATTGTGACAGAGTCACCAGATAC
1 AGATATTGTGACAGAGCCACCAGATAA
* *
28009127 AGATATTATGGCAGAGCCACCAGA-AA
1 AGATATTGTGACAGAGCCACCAGATAA
* *
28009153 AGATAATGTGACAAAGCCAC
1 AGATATTGTGACAGAGCCAC
28009173 TTAACAGAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
26 17 0.45
27 21 0.55
ACGTcount: A:0.41, C:0.19, G:0.22, T:0.18
Consensus pattern (27 bp):
AGATATTGTGACAGAGCCACCAGATAA
Found at i:28009368 original size:22 final size:22
Alignment explanation
Indices: 28009343--28009395 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
28009333 GGCACACATC
* *
28009343 CATAATCAGGTTGGCACAGAGA
1 CATAATCAGGTTGACACAAAGA
* *
28009365 CAT-ATGTAGGTTGACACAAAGC
1 CATAAT-CAGGTTGACACAAAGA
28009387 CATAATCAG
1 CATAATCAG
28009396 AAGGCTTTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
21 2 0.08
22 20 0.83
23 2 0.08
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.21
Consensus pattern (22 bp):
CATAATCAGGTTGACACAAAGA
Found at i:28009879 original size:27 final size:27
Alignment explanation
Indices: 28009822--28010043 Score: 302
Period size: 27 Copynumber: 8.3 Consensus size: 27
28009812 GGGGCAAATT
* * * *
28009822 GGTAATTTTACCCCACA-AGGTATCTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
28009848 GGTAATTCCACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
*
28009875 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
28009902 GATAATTCTACCCTACAGGGGTATTGC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
28009929 GATAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
28009956 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
28009983 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
** * *
28010010 GGTAATTCTATTCTATAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
28010037 GGTAATT
1 GGTAATT
28010044 TTGTAAATCG
Statistics
Matches: 175, Mismatches: 20, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
26 14 0.08
27 161 0.92
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:28010058 original size:27 final size:27
Alignment explanation
Indices: 28010028--28010368 Score: 278
Period size: 27 Copynumber: 12.6 Consensus size: 27
28010018 TATTCTATAG
** *
28010028 GGGTATTTTGGTAATTTTGTAAATCGA
1 GGGTATTTTGGTAATTTTACAAATCAA
** ** * *
28010055 GGGTAAATCAGTAATTCTATAAATCAA
1 GGGTATTTTGGTAATTTTACAAATCAA
* * *
28010082 GGGTACTTTGGTAATTTTACAAGTCGA
1 GGGTATTTTGGTAATTTTACAAATCAA
*** ** *
28010109 GGGTATTTCCATAATTTTACAGGTCGA
1 GGGTATTTTGGTAATTTTACAAATCAA
**** *
28010136 GGGTATTCCAATAATTTCACAAATC-A
1 GGGTATTTTGGTAATTTTACAAATCAA
*
28010162 GGTTTATTTTGGTAATTTTACAAA-CTAA
1 GG-GTATTTTGGTAATTTTACAAATC-AA
*
28010190 GGGTATTTTGATAATTTTACAAATC-A
1 GGGTATTTTGGTAATTTTACAAATCAA
*
28010216 GGGATATTTTGGTAATTTTACAAA-CCA
1 GGG-TATTTTGGTAATTTTACAAATCAA
** *
28010243 GTGGTATTTTGGTAATTTTGTAAACCAA
1 G-GGTATTTTGGTAATTTTACAAATCAA
*
28010271 GGGTATTTTGGTAATTTTACAAA-CTAG
1 GGGTATTTTGGTAATTTTACAAATC-AA
* * *
28010298 GGGTATTTTGGTGATTTTATAAACCAA
1 GGGTATTTTGGTAATTTTACAAATCAA
* * *
28010325 GGGTATTTTAGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAATCAA
28010352 GGGTATTTTGGTAATTT
1 GGGTATTTTGGTAATTT
28010369 GGTAAACTAA
Statistics
Matches: 256, Mismatches: 48, Indels: 20
0.79 0.15 0.06
Matches are distributed among these distances:
26 10 0.04
27 236 0.92
28 10 0.04
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAATCAA
Found at i:28010069 original size:81 final size:81
Alignment explanation
Indices: 28009850--28010073 Score: 213
Period size: 81 Copynumber: 2.8 Consensus size: 81
28009840 GGTATCTCGG
* * ** ** **
28009850 TAATTCCACCCTACAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTC-GATAATTCTACC
1 TAATTCTACCCTATAGGGGTATTTCGGTAATTCTACAATACAGGGGTAAATCAG-TAATTCTACC
28009914 CTACAGGGGTATTGCGA
65 CTACAGGGGTATTGCGA
** ** *
28009931 TAATTCTACCCTATAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCC
1 TAATTCTACCCTATAGGGGTATTTCGGTAATTCTACAATACAGGGGTAAATCAGTAATTCTACCC
* *
28009996 TACAGGGGTATTTCGG
66 TACAGGGGTATTGCGA
** * *
28010012 TAATTCTATTCTATAGGGGTATTTTGGTAATTTTGTA-AAT-C-GAGGGTAAATCAGTAATTCTA
1 TAATTCTACCCTATAGGGGTATTTCGGTAA--TTCTACAATACAG-GGGTAAATCAGTAATTCTA
28010074 TAAATCAAGG
Statistics
Matches: 124, Mismatches: 15, Indels: 8
0.84 0.10 0.05
Matches are distributed among these distances:
80 1 0.01
81 117 0.94
82 2 0.02
83 4 0.03
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.36
Consensus pattern (81 bp):
TAATTCTACCCTATAGGGGTATTTCGGTAATTCTACAATACAGGGGTAAATCAGTAATTCTACCC
TACAGGGGTATTGCGA
Found at i:28010375 original size:27 final size:27
Alignment explanation
Indices: 28010147--28010368 Score: 282
Period size: 27 Copynumber: 8.2 Consensus size: 27
28010137 GGTATTCCAA
* * **
28010147 TAATTTCACAAATCAGGTTTATTTTGG
1 TAATTTTACAAACCAGGGGTATTTTGG
* * *
28010174 TAATTTTACAAACTAAGGGTATTTTGA
1 TAATTTTACAAACCAGGGGTATTTTGG
* *
28010201 TAATTTTACAAATCAGGGATATTTTGG
1 TAATTTTACAAACCAGGGGTATTTTGG
*
28010228 TAATTTTACAAACCAGTGGTATTTTGG
1 TAATTTTACAAACCAGGGGTATTTTGG
** *
28010255 TAATTTTGTAAACCAAGGGTATTTTGG
1 TAATTTTACAAACCAGGGGTATTTTGG
*
28010282 TAATTTTACAAACTAGGGGTATTTTGG
1 TAATTTTACAAACCAGGGGTATTTTGG
* * * *
28010309 TGATTTTATAAACCAAGGGTATTTTAG
1 TAATTTTACAAACCAGGGGTATTTTGG
28010336 TAATTTTACAAACCAGGGGTATTTTGG
1 TAATTTTACAAACCAGGGGTATTTTGG
28010363 TAATTT
1 TAATTT
28010369 GGTAAACTAA
Statistics
Matches: 163, Mismatches: 32, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 163 1.00
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.41
Consensus pattern (27 bp):
TAATTTTACAAACCAGGGGTATTTTGG
Found at i:28012361 original size:20 final size:21
Alignment explanation
Indices: 28012323--28012361 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28012313 TCAACAGGGC
28012323 CACACGGACGTGTTGCCCTTT
1 CACACGGACGTGTTGCCCTTT
*
28012344 CACACGGGCGTG-TGCCCT
1 CACACGGACGTGTTGCCCT
28012362 GTTCCAAGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.13, C:0.36, G:0.28, T:0.23
Consensus pattern (21 bp):
CACACGGACGTGTTGCCCTTT
Found at i:28015733 original size:266 final size:266
Alignment explanation
Indices: 28015135--28015934 Score: 1188
Period size: 266 Copynumber: 3.0 Consensus size: 266
28015125 TCGAGTCTTA
*
28015135 TAGACTTGCGGATATTTTAGCCCGGTATGTAATCTTAATTTTCCTTAGCAGAGCTTATCATTTTG
1 TAGACTTGCGGATATTTTAGCCCGATATGTAATCTTAATTTTCCTTAGCAGAGCTTATCATTTTG
* *
28015200 GAATTAAAAGGAGTTAATGCCTTTAATTCAAAAATTAATTTAGGTTTAAATGACTCCAATCTTAC
66 GAATTAAAAGGAGTTAATGCCTTTAATTCAAAAATTAATTTAGGTTTAAATGGCTCCAATCTAAC
* * * * * *
28015265 AGGGAAAAGATAGAGAGATTTTTTTTCCCTGTATATTTTTTAAACTATTTTTCGATGCTAGGCAA
131 AGGGAAAAGATAGAGAGA-TTTTTTTCCCTGCATATTTTTCAAACTGTTTTCCGATGATAGACAA
* * * *
28015330 AGGCAAGGCTACTGCTCGTTGATCACTACAACCATGCTACTGCTGTGCTCATCTTGTTGTTGTAT
195 AGGCAAGGCTACTGTTCGTTGATCACTGCAACCGTGCTACTGCTGTGCTCATCCTGTTGTTGTAT
28015395 CCTGAGC
260 CCTGAGC
* * * * *
28015402 TAGACTTGCTGATATTTTAGCTCAATACGTAATCTTAATTTTCCTTAGCAGAGCTTATAATTTTG
1 TAGACTTGCGGATATTTTAGCCCGATATGTAATCTTAATTTTCCTTAGCAGAGCTTATCATTTTG
* * * *
28015467 GAGTTAAAAGGAGTTAATACCTTTAATTCAAAATTTAATTTAGGTTTAAATGGCTCTAATCTAAC
66 GAATTAAAAGGAGTTAATGCCTTTAATTCAAAAATTAATTTAGGTTTAAATGGCTCCAATCTAAC
* *
28015532 AGGGAAAAGATAGAGAGATTTTTTTCCCTGCATATTTTTCAGACTGTTTTCCGGTGATAGACAAA
131 AGGGAAAAGATAGAGAGATTTTTTTCCCTGCATATTTTTCAAACTGTTTTCCGATGATAGACAAA
* * *
28015597 GGTAAGGCTACTGTTCGTTGATCACTGTAACCGTGCTATTGCTGTGCTCATCCTGTTGTTGTATC
196 GGCAAGGCTACTGTTCGTTGATCACTGCAACCGTGCTACTGCTGTGCTCATCCTGTTGTTGTATC
*
28015662 TTGAGC
261 CTGAGC
* * * *
28015668 TAGACTTGCGGATATTTTAGCCCGATATATAATCTGAAGTTTCCTCAGCAGAGCTTATCATTTTG
1 TAGACTTGCGGATATTTTAGCCCGATATGTAATCTTAATTTTCCTTAGCAGAGCTTATCATTTTG
* * *
28015733 GAATTAAAAGGAGTTAATGCCTTTAATTCAAAAATTAATTTTGGTTTAAATGGATCCAATCTGAC
66 GAATTAAAAGGAGTTAATGCCTTTAATTCAAAAATTAATTTAGGTTTAAATGGCTCCAATCTAAC
* *
28015798 AGTGAAAAGATAGAGAGATATTTTTTTCCTTGCATATTTTTCAAACTGTTTTCCGATGATAGACA
131 AGGGAAAAGATAGAGAG--ATTTTTTTCCCTGCATATTTTTCAAACTGTTTTCCGATGATAGACA
** **
28015863 AAGGCAAGGCTACTGTTCGTTGATCACTGCAATTGTGCTACTATTGTGCTCA-CCTTGTTGTTGT
194 AAGGCAAGGCTACTGTTCGTTGATCACTGCAACCGTGCTACTGCTGTGCTCATCC-TGTTGTTGT
28015927 ATCCTGAG
258 ATCCTGAG
28015935 AGATAGCTGA
Statistics
Matches: 474, Mismatches: 56, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
266 232 0.49
267 138 0.29
268 104 0.22
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.37
Consensus pattern (266 bp):
TAGACTTGCGGATATTTTAGCCCGATATGTAATCTTAATTTTCCTTAGCAGAGCTTATCATTTTG
GAATTAAAAGGAGTTAATGCCTTTAATTCAAAAATTAATTTAGGTTTAAATGGCTCCAATCTAAC
AGGGAAAAGATAGAGAGATTTTTTTCCCTGCATATTTTTCAAACTGTTTTCCGATGATAGACAAA
GGCAAGGCTACTGTTCGTTGATCACTGCAACCGTGCTACTGCTGTGCTCATCCTGTTGTTGTATC
CTGAGC
Found at i:28016414 original size:29 final size:29
Alignment explanation
Indices: 28016350--28016418 Score: 120
Period size: 29 Copynumber: 2.4 Consensus size: 29
28016340 TAAAATGATA
* *
28016350 AATTTTGTAAACAATGGCTAAATTTATTG
1 AATTTTTTAGACAATGGCTAAATTTATTG
28016379 AATTTTTTAGACAATGGCTAAATTTATTG
1 AATTTTTTAGACAATGGCTAAATTTATTG
28016408 AATTTTTTAGA
1 AATTTTTTAGA
28016419 TTTACAATCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.36, C:0.06, G:0.13, T:0.45
Consensus pattern (29 bp):
AATTTTTTAGACAATGGCTAAATTTATTG
Found at i:28021836 original size:20 final size:20
Alignment explanation
Indices: 28021811--28021855 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
28021801 AGGGACTAAA
* *
28021811 ATGAAAAGTTGTAAAATTTG
1 ATGAAAAATTATAAAATTTG
*
28021831 ATGAAAAATTATAAAATTTT
1 ATGAAAAATTATAAAATTTG
28021851 ATGAA
1 ATGAA
28021856 TACATGCACT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGAAAAATTATAAAATTTG
Found at i:28025051 original size:21 final size:21
Alignment explanation
Indices: 28025025--28025068 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
28025015 GGTCACACAA
28025025 AAAATTCACACGAAGTGTTCT
1 AAAATTCACACGAAGTGTTCT
28025046 AAAATTCACACGAAGTGTTCT
1 AAAATTCACACGAAGTGTTCT
28025067 AA
1 AA
28025069 CACATGGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.27
Consensus pattern (21 bp):
AAAATTCACACGAAGTGTTCT
Found at i:28030103 original size:20 final size:20
Alignment explanation
Indices: 28030080--28030130 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
28030070 TAAACATGGT
28030080 ATGTATGATATACACATGAC
1 ATGTATGATATACACATGAC
* *
28030100 ATGTATGATATTCACATGAT
1 ATGTATGATATACACATGAC
28030120 ATGTATGATAT
1 ATGTATGATAT
28030131 GCACTTGCTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (20 bp):
ATGTATGATATACACATGAC
Found at i:28030248 original size:23 final size:24
Alignment explanation
Indices: 28030189--28030307 Score: 188
Period size: 24 Copynumber: 5.0 Consensus size: 24
28030179 GAGGAAGTGG
28030189 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
28030213 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
28030237 AAAA-GGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
28030260 AAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
28030284 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
28030308 ATGATAAAGC
Statistics
Matches: 89, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
23 23 0.26
24 55 0.62
25 11 0.12
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:28030259 original size:47 final size:47
Alignment explanation
Indices: 28030189--28030288 Score: 182
Period size: 47 Copynumber: 2.1 Consensus size: 47
28030179 GAGGAAGTGG
28030189 AAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTATT
1 AAAA-GGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTATT
*
28030237 AAAAGGCTTATGCCCCAGTTATTAAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTATT
28030284 AAAAG
1 AAAAG
28030289 AGGCTAGGCC
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 47 0.92
48 4 0.08
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (47 bp):
AAAAGGCTTATGCCCCAGTTATTAAAAGGGCTTATGCCCCAGTTATT
Found at i:28038029 original size:25 final size:25
Alignment explanation
Indices: 28038000--28038047 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
28037990 CCTTATAATG
* * *
28038000 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
28038025 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
28038048 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:28038112 original size:20 final size:20
Alignment explanation
Indices: 28038083--28038127 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
28038073 ATTTTGATAA
*
28038083 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
28038103 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
28038123 ACATG
1 ACATG
28038128 CTGTATTCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:28038252 original size:23 final size:24
Alignment explanation
Indices: 28038179--28038272 Score: 122
Period size: 23 Copynumber: 4.0 Consensus size: 24
28038169 GAGGAAGTGA
28038179 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
28038203 -AAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
**
28038226 AAAAGGGCTT-TTACCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
28038249 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
28038273 ATGATAAAGC
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
23 40 0.66
24 13 0.21
25 8 0.13
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:28038451 original size:31 final size:32
Alignment explanation
Indices: 28038405--28038469 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 32
28038395 TGTTTATAGT
*
28038405 AAAGGCCTTGGGCCCAGTAATATGAAATATGA
1 AAAGGCCTTCGGCCCAGTAATATGAAATATGA
**
28038437 AAAGG-CTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCCTTCGGCCCAGTAATATGAAATATGA
28038468 AA
1 AA
28038470 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 25 0.83
32 5 0.17
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.23
Consensus pattern (32 bp):
AAAGGCCTTCGGCCCAGTAATATGAAATATGA
Found at i:28040515 original size:38 final size:38
Alignment explanation
Indices: 28040384--28040531 Score: 149
Period size: 40 Copynumber: 3.8 Consensus size: 38
28040374 AATTGAATGA
* * * *
28040384 TATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATTA
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC--GAGATTC
* * *
28040423 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAG-TGGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGAT-TC
28040461 TACATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGATTC
1 T--ATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGATTC
*
28040501 TATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC
28040532 ACATGGTTAT
Statistics
Matches: 91, Mismatches: 11, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
37 1 0.01
38 28 0.31
39 17 0.19
40 44 0.48
41 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.28, T:0.22
Consensus pattern (38 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGATTC
Found at i:28040546 original size:78 final size:78
Alignment explanation
Indices: 28040383--28040547 Score: 192
Period size: 78 Copynumber: 2.1 Consensus size: 78
28040373 AAATTGAATG
*
28040383 ATATCCGGGCTAAGCCCGAAGACAATTATGCTGGAAATTATATCCGGGTTAAGACCCGAAGGCAA
1 ATATCCGGGCTAAGCCCGAAGACAATTATGC-GGAAATTATATCCGGGCTAAGACCCGAAGGCAA
*
28040448 TTGTGCTAGTGGCT
65 TTGTGCTAATGGCT
* * * * *
28040462 ACATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGATTCTATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAG-CCCGAAGACAATT-ATGCGGAAATTATATCCGGGCTAAGACCCGAAGGCA
* *
28040525 TTTGTGC-ACATGGTT
64 ATTGTGCTA-ATGGCT
28040540 ATATCCGG
1 ATATCCGG
28040548 TTATATTCCG
Statistics
Matches: 73, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
77 1 0.01
78 45 0.62
79 16 0.22
80 11 0.15
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (78 bp):
ATATCCGGGCTAAGCCCGAAGACAATTATGCGGAAATTATATCCGGGCTAAGACCCGAAGGCAAT
TGTGCTAATGGCT
Found at i:28046734 original size:40 final size:40
Alignment explanation
Indices: 28046649--28046799 Score: 134
Period size: 40 Copynumber: 3.8 Consensus size: 40
28046639 AATTGAATGA
* * *
28046649 TATCCGGGCTAA-ATCCCGAAGACAATTATGCTG-GAAATTA-
1 TATCCGGGCTAAGA-CCCGAAGGCAATTGTGC-GAGACA-TAC
* * *
28046689 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC-TAC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC--GAGACATAC
*
28046730 -ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGACATTC
1 TATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGACATAC
*
28046769 TATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC
28046800 ACATGGTTAT
Statistics
Matches: 92, Mismatches: 11, Indels: 16
0.77 0.09 0.13
Matches are distributed among these distances:
38 3 0.03
39 5 0.05
40 79 0.86
41 4 0.04
42 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGACATAC
Found at i:28046813 original size:40 final size:40
Alignment explanation
Indices: 28046686--28046815 Score: 138
Period size: 40 Copynumber: 3.2 Consensus size: 40
28046676 ATGCTGGAAA
* * * *
28046686 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG
* * * **
28046726 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGA-CA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG
*
28046766 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACATGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG
28046806 TTATATCCGG
1 TTATATCCGG
28046816 TTATATTCCG
Statistics
Matches: 71, Mismatches: 17, Indels: 4
0.77 0.18 0.04
Matches are distributed among these distances:
39 2 0.03
40 69 0.97
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG
Found at i:28054283 original size:25 final size:25
Alignment explanation
Indices: 28054255--28054305 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
28054245 CCCTTATAAT
* * *
28054255 GTGAAAATGACCTTTTTGCCCCTAG
1 GTGAAAATGACCATTATACCCCTAG
28054280 GTGAAAATGACCATTATACCCCTAG
1 GTGAAAATGACCATTATACCCCTAG
28054305 G
1 G
28054306 GTTATGTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (25 bp):
GTGAAAATGACCATTATACCCCTAG
Found at i:28054361 original size:10 final size:10
Alignment explanation
Indices: 28054346--28054384 Score: 69
Period size: 10 Copynumber: 3.8 Consensus size: 10
28054336 TGCTTTTGTA
28054346 CATGATATGC
1 CATGATATGC
28054356 CATGATATGC
1 CATGATATGC
28054366 ACATGATATGC
1 -CATGATATGC
28054377 CATGATAT
1 CATGATAT
28054385 ATTCACATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 18 0.64
11 10 0.36
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (10 bp):
CATGATATGC
Found at i:28054370 original size:21 final size:21
Alignment explanation
Indices: 28054345--28054384 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
28054335 CTGCTTTTGT
28054345 ACATGATATGCCATGATATGC
1 ACATGATATGCCATGATATGC
28054366 ACATGATATGCCATGATAT
1 ACATGATATGCCATGATAT
28054385 ATTCACATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (21 bp):
ACATGATATGCCATGATATGC
Found at i:28054472 original size:25 final size:25
Alignment explanation
Indices: 28054431--28054497 Score: 98
Period size: 25 Copynumber: 2.7 Consensus size: 25
28054421 AGGAAGTACT
* *
28054431 AAAAGGGCTTTGTCCCAGTTTATCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
*
28054456 AAATGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
*
28054481 AAAAGGGCTTTACCCCA
1 AAAAGGGCTTTGCCCCA
28054498 ATTATTAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.27
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCG
Found at i:28055648 original size:35 final size:35
Alignment explanation
Indices: 28055608--28055760 Score: 164
Period size: 35 Copynumber: 4.4 Consensus size: 35
28055598 GTATGTACAT
28055608 ATGTGATGATATATTGATCTTGTATATTTGGCCAC
1 ATGTGATGATATATTGATCTTGTATATTTGGCCAC
* * * * * *
28055643 ATGTGATGTTATATTAAACTTGAATATTTGACTAC
1 ATGTGATGATATATTGATCTTGTATATTTGGCCAC
* * * * *
28055678 ATGTGATGTTTTATTGATCTTGTATATTCGGTCAT
1 ATGTGATGATATATTGATCTTGTATATTTGGCCAC
* *
28055713 ATATGATGATATATTG-TACTTGTATATTTGGCCAT
1 ATGTGATGATATATTGAT-CTTGTATATTTGGCCAC
*
28055748 ATGTGATTATATA
1 ATGTGATGATATA
28055761 ATGAACCTTA
Statistics
Matches: 95, Mismatches: 22, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
34 1 0.01
35 94 0.99
ACGTcount: A:0.28, C:0.08, G:0.18, T:0.46
Consensus pattern (35 bp):
ATGTGATGATATATTGATCTTGTATATTTGGCCAC
Found at i:28058029 original size:40 final size:40
Alignment explanation
Indices: 28057965--28058116 Score: 164
Period size: 39 Copynumber: 3.9 Consensus size: 40
28057955 GCTACTCGTT
* * * ***
28057965 CAAACGCCTTCGGGACATAGCCCGGTTATGGTAACCCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATCACAACCCGCA
* *
28058005 CAAATGCCTTCGGGACTTAACCCGGATATCACAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATCACAACCCGCA
* * * *
28058045 CAATTGCCTTCGGG-CTTAGCCCGGATATCATAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATCACAACCCGCA
* *
28058084 CCATTGCCTTCGGG-CTTAGCCCGGATATCACAA
1 CAAATGCCTTCGGGACTTAGCCCGGATATCACAA
28058117 TTCGCACATT
Statistics
Matches: 97, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
39 52 0.54
40 45 0.46
ACGTcount: A:0.24, C:0.32, G:0.22, T:0.22
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATCACAACCCGCA
Found at i:28058082 original size:39 final size:39
Alignment explanation
Indices: 28058001--28058124 Score: 185
Period size: 39 Copynumber: 3.2 Consensus size: 39
28057991 TATGGTAACC
* *
28058001 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
28058041 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
* *
28058080 CGCACCATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
28058119 CGCACA
1 CGCACA
28058125 TTCATACACA
Statistics
Matches: 75, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
39 58 0.77
40 17 0.23
ACGTcount: A:0.24, C:0.33, G:0.20, T:0.23
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:28076228 original size:29 final size:28
Alignment explanation
Indices: 28076126--28076227 Score: 141
Period size: 29 Copynumber: 3.5 Consensus size: 28
28076116 GTGACGAGAT
*
28076126 TGGCACTAAGTGTGCAAGCTTGAAATGTA
1 TGGCACTAAGTGTGCAAGCTT-AAATATA
28076155 TGGCACTAAGTGTGCAAGCTTAAATTATA
1 TGGCACTAAGTGTGCAAGCTTAAA-TATA
* * *
28076184 TGGCACTATGTGTGCGAGCTTAAATCACA
1 TGGCACTAAGTGTGCAAGCTTAAAT-ATA
28076213 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
28076228 GTGATCGATT
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
28 4 0.06
29 62 0.94
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.28
Consensus pattern (28 bp):
TGGCACTAAGTGTGCAAGCTTAAATATA
Found at i:28081698 original size:2 final size:2
Alignment explanation
Indices: 28081691--28081717 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28081681 ATGATTTGTG
28081691 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
28081718 GTTAAAATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28089160 original size:2 final size:2
Alignment explanation
Indices: 28089153--28089183 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
28089143 ATGATTTGTG
28089153 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28089184 AGTTAAAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28093175 original size:25 final size:25
Alignment explanation
Indices: 28093146--28093271 Score: 110
Period size: 25 Copynumber: 5.3 Consensus size: 25
28093136 CGAACGGCCA
28093146 ATGTGATGAATGCGAACATGCATAT
1 ATGTGATGAATGCGAACATGCATAT
* *
28093171 ATGTGAT-AAGGCCG-A-ATGGC-CA-
1 ATGTGATGAATG-CGAACAT-GCATAT
28093193 ATGTGATGAATGCGAACATGCATAT
1 ATGTGATGAATGCGAACATGCATAT
* *
28093218 ATGTGAT-AAGGCCG-A-ATGGC-CA-
1 ATGTGATGAATG-CGAACAT-GCATAT
28093240 ATGTGATGAATGCGAACATGCATAT
1 ATGTGATGAATGCGAACATGCATAT
28093265 ATGTGAT
1 ATGTGAT
28093272 AGGGTAGAAT
Statistics
Matches: 79, Mismatches: 8, Indels: 28
0.69 0.07 0.24
Matches are distributed among these distances:
22 18 0.23
23 18 0.23
24 18 0.23
25 25 0.32
ACGTcount: A:0.34, C:0.13, G:0.27, T:0.25
Consensus pattern (25 bp):
ATGTGATGAATGCGAACATGCATAT
Found at i:28093255 original size:22 final size:22
Alignment explanation
Indices: 28093136--28093255 Score: 77
Period size: 22 Copynumber: 5.2 Consensus size: 22
28093126 GAGATAAGGC
*
28093136 CGAACGGCCAATGTGATGAATG
1 CGAATGGCCAATGTGATGAATG
* *
28093158 CGAACAT-GCATATATGTGAT-AAGG
1 CG-A-ATGGC-CA-ATGTGATGAATG
28093182 CCGAATGGCCAATGTGATGAATG
1 -CGAATGGCCAATGTGATGAATG
* *
28093205 CGAACAT-GCATATATGTGAT-AAGG
1 CG-A-ATGGC-CA-ATGTGATGAATG
28093229 CCGAATGGCCAATGTGATGAATG
1 -CGAATGGCCAATGTGATGAATG
28093252 CGAA
1 CGAA
28093256 CATGCATATA
Statistics
Matches: 75, Mismatches: 9, Indels: 28
0.67 0.08 0.25
Matches are distributed among these distances:
22 22 0.29
23 18 0.24
24 17 0.23
25 18 0.24
ACGTcount: A:0.34, C:0.16, G:0.28, T:0.22
Consensus pattern (22 bp):
CGAATGGCCAATGTGATGAATG
Found at i:28093316 original size:94 final size:94
Alignment explanation
Indices: 28093103--28093296 Score: 298
Period size: 94 Copynumber: 2.1 Consensus size: 94
28093093 GATTTTATGA
* ** * *
28093103 GATGAATGTGAATGTGTATATTTGAGATAAGGCCGAACGGCCAATGTGATGAATGCGAACATGCA
1 GATGAATGCGAACATGTATATATGTGATAAGGCCGAACGGCCAATGTGATGAATGCGAACATGCA
*
28093168 TATATGTGATAAGGCCGAATGGCCAATGT
66 TATATGTGATAAGGCAGAATGGCCAATGT
* *
28093197 GATGAATGCGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGCGAACATGCA
1 GATGAATGCGAACATGTATATATGTGATAAGGCCGAACGGCCAATGTGATGAATGCGAACATGCA
* *
28093262 TATATGTGATAGGGTAGAATGGCCAATGT
66 TATATGTGATAAGGCAGAATGGCCAATGT
28093291 GATGAA
1 GATGAA
28093297 CGTGGAAGAG
Statistics
Matches: 90, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
94 90 1.00
ACGTcount: A:0.34, C:0.12, G:0.29, T:0.25
Consensus pattern (94 bp):
GATGAATGCGAACATGTATATATGTGATAAGGCCGAACGGCCAATGTGATGAATGCGAACATGCA
TATATGTGATAAGGCAGAATGGCCAATGT
Found at i:28093331 original size:47 final size:47
Alignment explanation
Indices: 28093128--28093296 Score: 302
Period size: 47 Copynumber: 3.6 Consensus size: 47
28093118 GTATATTTGA
*
28093128 GATAAGGCCGAACGGCCAATGTGATGAATGCGAACATGCATATATGT
1 GATAAGGCCGAATGGCCAATGTGATGAATGCGAACATGCATATATGT
28093175 GATAAGGCCGAATGGCCAATGTGATGAATGCGAACATGCATATATGT
1 GATAAGGCCGAATGGCCAATGTGATGAATGCGAACATGCATATATGT
28093222 GATAAGGCCGAATGGCCAATGTGATGAATGCGAACATGCATATATGT
1 GATAAGGCCGAATGGCCAATGTGATGAATGCGAACATGCATATATGT
* **
28093269 GATAGGGTAGAATGGCCAATGTGATGAA
1 GATAAGGCCGAATGGCCAATGTGATGAA
28093297 CGTGGAAGAG
Statistics
Matches: 118, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 118 1.00
ACGTcount: A:0.34, C:0.14, G:0.29, T:0.22
Consensus pattern (47 bp):
GATAAGGCCGAATGGCCAATGTGATGAATGCGAACATGCATATATGT
Found at i:28094947 original size:40 final size:40
Alignment explanation
Indices: 28094892--28095069 Score: 284
Period size: 40 Copynumber: 4.4 Consensus size: 40
28094882 AGAGTTATAT
28094892 ATATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTG
1 ATATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTG
**
28094932 ATATATCCGGGCTAAGTTCCGAAGAGCATTATTGCTAGTG
1 ATATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTG
28094972 ATATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTG
1 ATATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTG
**
28095012 ATATATCCGGGCTAAGTTTTGAAGAAGAGCATTCGTGCTAGTG
1 ATATATCCGGGCTAAG--TT-CCGAAGAGCATTCGTGCTAGTG
*
28095055 ATATATCTGGGCTAA
1 ATATATCCGGGCTAA
28095070 ACCTCGAAGG
Statistics
Matches: 128, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
40 92 0.72
42 2 0.02
43 34 0.27
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.29
Consensus pattern (40 bp):
ATATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTG
Found at i:28095141 original size:28 final size:27
Alignment explanation
Indices: 28095101--28095257 Score: 143
Period size: 28 Copynumber: 5.6 Consensus size: 27
28095091 GAGTTATGAG
* * *
28095101 GCACTGTGTGTGCAAGTTCTTCAACCGA
1 GCACTATGTGTGCGAGTTCTT-AATCGA
* * * * *
28095129 GCACTATGTGTGCCAGATCAGTAGTTGA
1 GCACTATGTGTGCGAGTTC-TTAATCGA
28095157 GGCACTATGTGTGCGAGTTCTTCAATCGA
1 -GCACTATGTGTGCGAGTTCTT-AATCGA
** *
28095186 GCACTATGTGTGCGAGATTGGTAATTGA
1 GCACTATGTGTGCGAG-TTCTTAATCGA
28095214 GGCACTATGTGTGCGAGTTCTTTAATCGA
1 -GCACTATGTGTGCGAGTTC-TTAATCGA
*
28095243 GCGCTATGTGTGCGA
1 GCACTATGTGTGCGA
28095258 AATCAGTCAG
Statistics
Matches: 104, Mismatches: 19, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
28 57 0.55
29 47 0.45
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (27 bp):
GCACTATGTGTGCGAGTTCTTAATCGA
Found at i:28095164 original size:29 final size:28
Alignment explanation
Indices: 28095129--28095257 Score: 118
Period size: 29 Copynumber: 4.5 Consensus size: 28
28095119 CTTCAACCGA
* *
28095129 GCACTATGTGTGCCAGATCAGTAGTTGAG
1 GCACTATGTGTGCGAGATC-GTAATTGAG
* * *
28095158 GCACTATGTGTGCGAGTTCTTCAATCGA-
1 GCACTATGTGTGCGAGATCGT-AATTGAG
*
28095186 GCACTATGTGTGCGAGATTGGTAATTGAG
1 GCACTATGTGTGCGAGA-TCGTAATTGAG
* * *
28095215 GCACTATGTGTGCGAGTTCTTTAATCGA-
1 GCACTATGTGTGCGAGATC-GTAATTGAG
*
28095243 GCGCTATGTGTGCGA
1 GCACTATGTGTGCGA
28095258 AATCAGTCAG
Statistics
Matches: 82, Mismatches: 14, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
28 37 0.45
29 45 0.55
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.31
Consensus pattern (28 bp):
GCACTATGTGTGCGAGATCGTAATTGAG
Found at i:28095187 original size:57 final size:57
Alignment explanation
Indices: 28095097--28095285 Score: 247
Period size: 57 Copynumber: 3.3 Consensus size: 57
28095087 GCTGGAGTTA
* * * *
28095097 TGAGGCACTGTGTGTGCAAGTTCTTCAACCGAGCACTATGTGTGCCAGATCAGTAGT
1 TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCGAGATCAGTAGT
** *
28095154 TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCGAGATTGGTAAT
1 TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCGAGATCAGTAGT
* * *
28095211 TGAGGCACTATGTGTGCGAGTTCTTTAATCGAGCGCTATGTGTGCGAAATCAGTCAG-
1 TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCGAGATCAGT-AGT
* *
28095268 TG-GGCACTGTGTATGCGA
1 TGAGGCACTATGTGTGCGA
28095286 AGTGTGTTTC
Statistics
Matches: 116, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
56 14 0.12
57 101 0.87
58 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.30
Consensus pattern (57 bp):
TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCGAGATCAGTAGT
Found at i:28098656 original size:22 final size:22
Alignment explanation
Indices: 28098585--28098703 Score: 66
Period size: 22 Copynumber: 5.1 Consensus size: 22
28098575 GTATATTTGA
*
28098585 GATAAGGCCGAATGGCCAATGT
1 GATAAGGCTGAATGGCCAATGT
* *
28098607 GATGAATG-TGAACAT-GCATATATGT
1 GAT-AAGGCTG-A-ATGGC-CA-ATGT
28098632 GATAAGGCTGAATGGCCAATGT
1 GATAAGGCTGAATGGCCAATGT
* *
28098654 GATGAATG-TGAACAT-GCATATATGT
1 GAT-AAGGCTG-A-ATGGC-CA-ATGT
*
28098679 GATAAGGCCGAATGGCCAATGT
1 GATAAGGCTGAATGGCCAATGT
28098701 GAT
1 GAT
28098704 GAATGTGAAC
Statistics
Matches: 73, Mismatches: 10, Indels: 28
0.66 0.09 0.25
Matches are distributed among these distances:
22 20 0.27
23 18 0.25
24 18 0.25
25 17 0.23
ACGTcount: A:0.34, C:0.13, G:0.29, T:0.25
Consensus pattern (22 bp):
GATAAGGCTGAATGGCCAATGT
Found at i:28098758 original size:22 final size:22
Alignment explanation
Indices: 28098593--28098759 Score: 69
Period size: 23 Copynumber: 7.2 Consensus size: 22
28098583 GAGATAAGGC
28098593 CGAATGGCCAATGTGATGAATG
1 CGAATGGCCAATGTGATGAATG
* * *
28098615 TGAACAT-GCATATATGTGAT-AAGG
1 CG-A-ATGGC-CA-ATGTGATGAATG
28098639 CTGAATGGCCAATGTGATGAATG
1 C-GAATGGCCAATGTGATGAATG
* * *
28098662 TGAACAT-GCATATATGTGAT-AAGG
1 CG-A-ATGGC-CA-ATGTGATGAATG
28098686 CCGAATGGCCAATGTGATGAATG
1 -CGAATGGCCAATGTGATGAATG
* *
28098709 TGAACAT-G-CATATATG-TGATATGGG
1 CG-A-ATGGCCA-ATGTGATGA-AT--G
28098734 CGAATGGCCAATGTGATGAATG
1 CGAATGGCCAATGTGATGAATG
28098756 CGAA
1 CGAA
28098760 CATGCATATA
Statistics
Matches: 106, Mismatches: 16, Indels: 46
0.63 0.10 0.27
Matches are distributed among these distances:
22 27 0.25
23 28 0.26
24 28 0.26
25 23 0.22
ACGTcount: A:0.34, C:0.12, G:0.29, T:0.26
Consensus pattern (22 bp):
CGAATGGCCAATGTGATGAATG
Found at i:28098830 original size:141 final size:141
Alignment explanation
Indices: 28098560--28098840 Score: 388
Period size: 141 Copynumber: 2.0 Consensus size: 141
28098550 GATTTTATGA
** * * *
28098560 GATGAATGTGAATGTGTATATTTGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCA
1 GATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGCGAACATGCA
* *
28098625 TATATGTGATAAGGCTGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGA
66 TATATGTGATAAGGCTGAATGGCCAATGTGATGAACGTGAACATGCATATATGTGAGAAGGCCGA
28098690 ATGGCCAATGT
131 ATGGCCAATGT
* * *
28098701 GATGAATGTGAACATGCATATATGTGATATGGGCGAATGGCCAATGTGATGAATGCGAACATGCA
1 GATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGCGAACATGCA
* * *
28098766 TATATGTGATAAGG-TAGAATGGCCAATGTGATGAACGTGGAAGA-GTATATATGTGGCGAA-GC
66 TATATGTGATAAGGCT-GAATGGCCAATGTGATGAACGT-GAACATGCATATATGT-GAGAAGGC
*
28098828 CGAATGGCTAATG
128 CGAATGGCCAATG
28098841 CGAAACGTGT
Statistics
Matches: 123, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
140 1 0.01
141 115 0.93
142 7 0.06
ACGTcount: A:0.33, C:0.11, G:0.30, T:0.26
Consensus pattern (141 bp):
GATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGCGAACATGCA
TATATGTGATAAGGCTGAATGGCCAATGTGATGAACGTGAACATGCATATATGTGAGAAGGCCGA
ATGGCCAATGT
Done.