Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 125 of 186
Found at i:41517962 original size:100 final size:100
Alignment explanation
Indices: 41517789--41517993 Score: 340
Period size: 100 Copynumber: 2.1 Consensus size: 100
41517779 CATTTTACTC
* * ** *
41517789 GTTTTCGCTTAAAACCAAGTAGCACAAGTTGTCTAACATAATTTAAAACCTCATATTCTATCATA
1 GTTTTCACTTAAAACCAAGTAGCACAACTTACCTAACATAATTTAAAACCTCATATTCTAGCATA
*
41517854 AAACACCAAAATACACAAATTTCACCTATGGATAT
66 AAACACCAAAATACAAAAATTTCACCTATGGATAT
*
41517889 GTTTTCACTTAAAACCGAGTAGCACAACTTACCTAACATAATTTAAAACCTCATATTCTAGCATA
1 GTTTTCACTTAAAACCAAGTAGCACAACTTACCTAACATAATTTAAAACCTCATATTCTAGCATA
41517954 AAACACCAAAATACAAAAATTTCACCTATGGATAT
66 AAACACCAAAATACAAAAATTTCACCTATGGATAT
41517989 -TTTTC
1 GTTTTC
41517994 CAAATATGAA
Statistics
Matches: 98, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
99 5 0.05
100 93 0.95
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.30
Consensus pattern (100 bp):
GTTTTCACTTAAAACCAAGTAGCACAACTTACCTAACATAATTTAAAACCTCATATTCTAGCATA
AAACACCAAAATACAAAAATTTCACCTATGGATAT
Found at i:41519001 original size:20 final size:20
Alignment explanation
Indices: 41518976--41519015 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
41518966 GGATTAAACT
*
41518976 GAACTTATTCAGAAT-TTTCA
1 GAACTTAATCA-AATATTTCA
41518996 GAACTTAATCAAATATTTCA
1 GAACTTAATCAAATATTTCA
41519016 AAGCTGTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.38
Consensus pattern (20 bp):
GAACTTAATCAAATATTTCA
Found at i:41523620 original size:43 final size:43
Alignment explanation
Indices: 41523573--41523674 Score: 109
Period size: 42 Copynumber: 2.4 Consensus size: 43
41523563 TCCCAGACGT
* ** *
41523573 GGTCTTATATGTAATTCA-ATATCGATGCCTTTGTCCCAAATAG
1 GGTCTTATATGTAAATCAGATA-CGATGCCAATGTCCCAAACAG
* * * *
41523616 GGTCTTACACG-AAATCAGATACGATGCCAATGTCCCAGACAT
1 GGTCTTATATGTAAATCAGATACGATGCCAATGTCCCAAACAG
41523658 GGTCTTATATGTAAATC
1 GGTCTTATATGTAAATC
41523675 TAAATCGAGG
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
42 30 0.64
43 17 0.36
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (43 bp):
GGTCTTATATGTAAATCAGATACGATGCCAATGTCCCAAACAG
Found at i:41523662 original size:42 final size:43
Alignment explanation
Indices: 41523562--41523711 Score: 110
Period size: 43 Copynumber: 3.5 Consensus size: 43
41523552 CAATGCCGAC
* * * * **
41523562 GTCCCAGACGTGGTCTTATATGTAATTCAATATCGATGCCTTT
1 GTCCCAGACATGGTCTTACACGTAAATCAATATCGATGCCAAT
* * *
41523605 GTCCCAAATAGGGTCTTACACG-AAATCAGATA-CGATGCCAAT
1 GTCCCAGACATGGTCTTACACGTAAATCA-ATATCGATGCCAAT
* * * *
41523647 GTCCCAGACATGGTCTTATATGTAAATCTAA-ATCGA-GGCATGT
1 GTCCCAGACATGGTCTTACACGTAAATC-AATATCGATGCCA-AT
* *
41523690 GTCCCACACAAGGTCTTACACG
1 GTCCCAGACATGGTCTTACACG
41523712 ATGTCGCAGA
Statistics
Matches: 82, Mismatches: 20, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
42 34 0.41
43 47 0.57
44 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.28
Consensus pattern (43 bp):
GTCCCAGACATGGTCTTACACGTAAATCAATATCGATGCCAAT
Found at i:41527872 original size:51 final size:50
Alignment explanation
Indices: 41527812--41527944 Score: 169
Period size: 51 Copynumber: 2.6 Consensus size: 50
41527802 TATTGTGAGG
* *
41527812 TCACGTGTGTAGTACTAAGTGCAGGCTACTATACGTACTC-GATAACTTCGA
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACACGTA-TCAGAT-ACTTAGA
** ** *
41527863 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGG
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACACGTATCAGATACTTAGA
*
41527913 TCACGTGTGTAGTACTAAGTGTAGGCTACTAC
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTAC
41527945 GTGTACCGGA
Statistics
Matches: 73, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
50 36 0.49
51 37 0.51
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.30
Consensus pattern (50 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTACACGTATCAGATACTTAGA
Found at i:41527939 original size:50 final size:51
Alignment explanation
Indices: 41527809--41527992 Score: 198
Period size: 50 Copynumber: 3.7 Consensus size: 51
41527799 ATCTATTGTG
***
41527809 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATACGTACTCGATAACTT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACTCGATAACTT
* * **
41527860 CGATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTA-TCAGAT-GGTT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACTC-GATAACTT
*
41527910 AGGTCACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTAC-CGGATAA-TT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACTC-GATAACTT
* * * * *
41527960 -GGTCGCATGTGTATTACTAGGTGCAAGCTACTA
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTA
41527993 TGCGTACCAG
Statistics
Matches: 112, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
49 27 0.24
50 47 0.42
51 38 0.34
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.30
Consensus pattern (51 bp):
AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACTCGATAACTT
Found at i:41536683 original size:47 final size:49
Alignment explanation
Indices: 41536559--41536687 Score: 147
Period size: 49 Copynumber: 2.7 Consensus size: 49
41536549 AGGGTATAAT
*
41536559 GCCGATGCCATGTCCCAGACATGGTCTTACACTGACTATTGAAATCGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGACTATTGAAATCGAA
* * * **
41536608 GCCGACGCCATCTCCCAAACATGGTCTTACACTGACTCA-T-CCATC-AA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGACT-ATTGAAATCGAA
** *
41536655 GTTGATGCCATGTCCTAGACATGGTCTTACACT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACT
41536688 AGCTCACAAT
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
47 28 0.42
48 3 0.04
49 35 0.52
50 1 0.01
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.26
Consensus pattern (49 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTGACTATTGAAATCGAA
Found at i:41541215 original size:23 final size:23
Alignment explanation
Indices: 41541163--41541260 Score: 80
Period size: 22 Copynumber: 4.3 Consensus size: 23
41541153 GCAGACAAAC
* *
41541163 GGTAAGCTCAATTA-AGCTGAACA
1 GGTAAGCTCCA-TAGAGCTGAAAA
*
41541186 -GTAAGCTCCATAGTGCTGAAAA
1 GGTAAGCTCCATAGAGCTGAAAA
* *
41541208 GGTAAGCTTCGA-AGAGCT-AAAC
1 GGTAAGC-TCCATAGAGCTGAAAA
*
41541230 GGTAAGCT-CATAAGAGCTGAAAC
1 GGTAAGCTCCAT-AGAGCTGAAAA
41541253 GGTAAGCT
1 GGTAAGCT
41541261 TGTACGAGCT
Statistics
Matches: 62, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
20 1 0.02
21 3 0.05
22 32 0.52
23 23 0.37
24 3 0.05
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.20
Consensus pattern (23 bp):
GGTAAGCTCCATAGAGCTGAAAA
Found at i:41541236 original size:22 final size:24
Alignment explanation
Indices: 41541200--41541261 Score: 85
Period size: 22 Copynumber: 2.7 Consensus size: 24
41541190 GCTCCATAGT
*
41541200 GCTGAAAAGGTAAGCTTC-GAAGA
1 GCTGAAACGGTAAGCTTCAGAAGA
*
41541223 GCT-AAACGGTAAGC-TCATAAGA
1 GCTGAAACGGTAAGCTTCAGAAGA
41541245 GCTGAAACGGTAAGCTT
1 GCTGAAACGGTAAGCTT
41541262 GTACGAGCTG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 2 0.06
22 17 0.50
23 14 0.41
24 1 0.03
ACGTcount: A:0.37, C:0.16, G:0.27, T:0.19
Consensus pattern (24 bp):
GCTGAAACGGTAAGCTTCAGAAGA
Found at i:41541269 original size:23 final size:23
Alignment explanation
Indices: 41541200--41541271 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
41541190 GCTCCATAGT
*
41541200 GCTGAAAAGGTAAGCTTCG-AAGA
1 GCTGAAACGGTAAGCTT-GTAAGA
**
41541223 GCT-AAACGGTAAGCTCATAAGA
1 GCTGAAACGGTAAGCTTGTAAGA
*
41541245 GCTGAAACGGTAAGCTTGTACGA
1 GCTGAAACGGTAAGCTTGTAAGA
41541268 GCTG
1 GCTG
41541272 TGGTGAGTCT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
22 18 0.44
23 23 0.56
ACGTcount: A:0.35, C:0.17, G:0.29, T:0.19
Consensus pattern (23 bp):
GCTGAAACGGTAAGCTTGTAAGA
Found at i:41548420 original size:129 final size:129
Alignment explanation
Indices: 41548188--41548441 Score: 280
Period size: 129 Copynumber: 2.0 Consensus size: 129
41548178 TCATATAGGC
** * * *
41548188 ATGTGACCCACTCACACAGCCATATGGCCTATCTTATACGAGCATGGCTCTTCTACACGGTTTAC
1 ATGTGACCCACTCACACAGCCATATGGCCTATCACACACGAGCATGGCTCTTCTAAAAGGTTTAC
**
41548253 CAACATAGTTGTGTGGTTAATCCCACACAAGCTAAGCTTTCA-CACACGGCCAAGGGACACGGGA
66 CAACATAGCAGTGTGGTTAATCCCACACAAGCTAAGCTTT-AGCACACGGCCAAGGGACACGGGA
* * * *
41548317 ATGTGACCCACTCACACGGCCATGTGGCCTATCACACATGAGCATGGCTCTTGTAAAAGGTTTAT
1 ATGTGACCCACTCACACAGCCATATGGCCTATCACACACGAGCATGGCTCTTCTAAAAGGTTTA-
* * * *** * * *
41548382 CGATACA-A-CAGTGTGGTTAATTCCTCATGGGCTGAGCTTTAGTACATGGCCAAGGGACAC
65 CCA-ACATAGCAGTGTGGTTAATCCCACACAAGCTAAGCTTTAGCACACGGCCAAGGGACAC
41548442 AGTCATGTAA
Statistics
Matches: 102, Mismatches: 20, Indels: 6
0.80 0.16 0.05
Matches are distributed among these distances:
128 1 0.01
129 95 0.93
130 3 0.03
131 3 0.03
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.24
Consensus pattern (129 bp):
ATGTGACCCACTCACACAGCCATATGGCCTATCACACACGAGCATGGCTCTTCTAAAAGGTTTAC
CAACATAGCAGTGTGGTTAATCCCACACAAGCTAAGCTTTAGCACACGGCCAAGGGACACGGGA
Found at i:41549661 original size:30 final size:30
Alignment explanation
Indices: 41549625--41549684 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
41549615 TTCCCAAGCC
*
41549625 TAGGGGCAAAAGTGTAATTATGCAAAAGTT
1 TAGGGGCAAAAATGTAATTATGCAAAAGTT
* *
41549655 TAGGGGCAAAAATGTAATTTTGCCAAAGTT
1 TAGGGGCAAAAATGTAATTATGCAAAAGTT
41549685 CATATTAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.28
Consensus pattern (30 bp):
TAGGGGCAAAAATGTAATTATGCAAAAGTT
Found at i:41552352 original size:24 final size:23
Alignment explanation
Indices: 41552308--41552352 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
41552298 TACATCAGTG
41552308 AAAGATTTATTGATTAGAAGCGT
1 AAAGATTTATTGATTAGAAGCGT
*
41552331 AAAGAGTTTCTTGAATTA-AAGC
1 AAAGA-TTTATTG-ATTAGAAGC
41552353 AGGGGAACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.26
24 10 0.53
25 4 0.21
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (23 bp):
AAAGATTTATTGATTAGAAGCGT
Found at i:41571937 original size:27 final size:27
Alignment explanation
Indices: 41571907--41572084 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
41571897 ATATTGAGTC
* * * *
41571907 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
41571934 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
41571961 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
41571989 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
41572016 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
41572043 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
41572070 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41572085 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:41572046 original size:82 final size:81
Alignment explanation
Indices: 41571928--41572083 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
41571918 TGCTATATAA
* *
41571928 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
41571993 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
41572010 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
41572074 CACTTAGTGC
65 CACTTAGTGC
41572084 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:41580000 original size:27 final size:27
Alignment explanation
Indices: 41579970--41580147 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
41579960 ATATTGAGTC
* * * *
41579970 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
41579997 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
41580024 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
41580052 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
41580079 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
41580106 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
41580133 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41580148 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:41580109 original size:82 final size:81
Alignment explanation
Indices: 41579991--41580146 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
41579981 TGCTATATAA
* *
41579991 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
41580056 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
41580073 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
41580137 CACTTAGTGC
65 CACTTAGTGC
41580147 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:41589090 original size:24 final size:24
Alignment explanation
Indices: 41589063--41589109 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
41589053 AAGATTTAGT
**
41589063 ATTTATTAGTATAATATATTTGAC
1 ATTTATTAACATAATATATTTGAC
*
41589087 ATTTATTAACATAATTTATTTGA
1 ATTTATTAACATAATATATTTGA
41589110 TTTACGAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.51
Consensus pattern (24 bp):
ATTTATTAACATAATATATTTGAC
Found at i:41592936 original size:17 final size:17
Alignment explanation
Indices: 41592915--41593016 Score: 69
Period size: 17 Copynumber: 6.0 Consensus size: 17
41592905 CTGTTTATAT
*
41592915 AAAATAATAGTTCATAC
1 AAAATAACAGTTCATAC
* * * *
41592932 CAAATGACAGCTCATGC
1 AAAATAACAGTTCATAC
* * *
41592949 AAAATAATATTTCATAT
1 AAAATAACAGTTCATAC
* **
41592966 GAAATATTAGTTCATAC
1 AAAATAACAGTTCATAC
** * *
41592983 TGAATAACAATTCATGC
1 AAAATAACAGTTCATAC
41593000 AAAATAACAGTTCATAC
1 AAAATAACAGTTCATAC
41593017 TTCATTATAA
Statistics
Matches: 59, Mismatches: 26, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
17 59 1.00
ACGTcount: A:0.46, C:0.16, G:0.09, T:0.29
Consensus pattern (17 bp):
AAAATAACAGTTCATAC
Found at i:41592977 original size:51 final size:51
Alignment explanation
Indices: 41592911--41593015 Score: 129
Period size: 51 Copynumber: 2.1 Consensus size: 51
41592901 ATATCTGTTT
* * * *
41592911 ATATAAAATAATAGTTCATACCAAATGACAGCTCATGCAAAATAATATTTC
1 ATATAAAATAATAGTTCATACCAAATAACAACTCATGCAAAATAACAGTTC
* * ** *
41592962 ATATGAAATATTAGTTCATACTGAATAACAATTCATGCAAAATAACAGTTC
1 ATATAAAATAATAGTTCATACCAAATAACAACTCATGCAAAATAACAGTTC
41593013 ATA
1 ATA
41593016 CTTCATTATA
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.47, C:0.14, G:0.09, T:0.30
Consensus pattern (51 bp):
ATATAAAATAATAGTTCATACCAAATAACAACTCATGCAAAATAACAGTTC
Found at i:41593674 original size:18 final size:18
Alignment explanation
Indices: 41593648--41593696 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
41593638 CATAGTTTGG
41593648 CAAATTAATACA-ATTCAC
1 CAAATTAATACAGA-TCAC
*
41593666 CATATTAATACAGATCAC
1 CAAATTAATACAGATCAC
*
41593684 CAAATTAACACAG
1 CAAATTAATACAG
41593697 TTCGCCTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 26 0.96
19 1 0.04
ACGTcount: A:0.49, C:0.22, G:0.04, T:0.24
Consensus pattern (18 bp):
CAAATTAATACAGATCAC
Found at i:41595748 original size:11 final size:11
Alignment explanation
Indices: 41595732--41595760 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
41595722 AGGGAATGAA
41595732 GAGAGAAAAGT
1 GAGAGAAAAGT
41595743 GAGAGAAAAGT
1 GAGAGAAAAGT
41595754 GA-AGAAA
1 GAGAGAAA
41595761 TAAATGAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.59, C:0.00, G:0.34, T:0.07
Consensus pattern (11 bp):
GAGAGAAAAGT
Found at i:41597697 original size:15 final size:15
Alignment explanation
Indices: 41597641--41597697 Score: 55
Period size: 15 Copynumber: 3.8 Consensus size: 15
41597631 CTTAACCTAA
41597641 AATTA-TTAATTC-T
1 AATTATTTAATTCTT
*
41597654 AATTATTTTAATATTTT
1 AATTA-TTTAAT-TCTT
* *
41597671 ATTTAATTAATTCTT
1 AATTATTTAATTCTT
41597686 AATTATTTAATT
1 AATTATTTAATT
41597698 ATCTAATCTA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
13 5 0.15
15 18 0.53
16 6 0.18
17 5 0.15
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.60
Consensus pattern (15 bp):
AATTATTTAATTCTT
Found at i:41597710 original size:32 final size:31
Alignment explanation
Indices: 41597645--41597711 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 31
41597635 ACCTAAAATT
* * *
41597645 ATTAATTCTAATTATTTTAATATTTTATTTA
1 ATTAATTCTAATTATTTTAATATCTAATCTA
41597676 ATTAATTCTTAATTA-TTTAATTATCTAATCTA
1 ATTAATTC-TAATTATTTTAA-TATCTAATCTA
41597708 ATTA
1 ATTA
41597712 TAGTTTCCAG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 13 0.42
32 18 0.58
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (31 bp):
ATTAATTCTAATTATTTTAATATCTAATCTA
Found at i:41603179 original size:45 final size:45
Alignment explanation
Indices: 41603098--41603341 Score: 245
Period size: 45 Copynumber: 5.3 Consensus size: 45
41603088 AGGTATAAGT
* * * ** * *
41603098 TATATATAATAATTGTCGGTTTTACTAACCAATGCTGGGTACACA
1 TATATATAATATTTGTTGGTTTCACCGACCAGTGCTGGGCACACA
* * * *
41603143 TATATAAAATATTTGCTAGTTTCACCGTCCAGTGCTGGGCACACA
1 TATATATAATATTTGTTGGTTTCACCGACCAGTGCTGGGCACACA
* * *
41603188 CATATATAATATTTGTTGGTTTCACCGACTAGTGCTGGACACACA
1 TATATATAATATTTGTTGGTTTCACCGACCAGTGCTGGGCACACA
* * * *
41603233 TATATATAATAATAATTGTCGGTGTCACCGACCAGTGCTAGGTACACGTA
1 TATATATAAT-AT--TTGTTGGTTTCACCGACCAGTGCTGGGCACAC--A
* * *
41603283 TATATATAATATTTGTTGGTTTCACTGAGCAATGCTGGGCACACA
1 TATATATAATATTTGTTGGTTTCACCGACCAGTGCTGGGCACACA
*
41603328 CATATATAATATTT
1 TATATATAATATTT
41603342 TCCAGTCACA
Statistics
Matches: 161, Mismatches: 33, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
45 95 0.59
46 2 0.01
47 25 0.16
48 26 0.16
49 2 0.01
50 11 0.07
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (45 bp):
TATATATAATATTTGTTGGTTTCACCGACCAGTGCTGGGCACACA
Found at i:41603304 original size:95 final size:93
Alignment explanation
Indices: 41603138--41603338 Score: 246
Period size: 95 Copynumber: 2.2 Consensus size: 93
41603128 AATGCTGGGT
* * * * *
41603138 ACACATATATAA-AATATTTG-CTAGTTTCACCGTCCAGTGCTGGGCACACACATATATAATATT
1 ACACATATATAATAATAATTGTC-GGTGTCACCGACCAGTGCTAGGCACACACATATATAATATT
*
41603201 TGTTGGTTTCACCGA-CTAGTGCTGGACAC
65 TGTTGGTTTCACCGAGC-AATGCTGGACAC
* * *
41603230 ACATATATATAATAATAATTGTCGGTGTCACCGACCAGTGCTAGGTACACGTATATATATAATAT
1 ACACATATATAATAATAATTGTCGGTGTCACCGACCAGTGCTAGGCACAC--ACATATATAATAT
* *
41603295 TTGTTGGTTTCACTGAGCAATGCTGGGCAC
64 TTGTTGGTTTCACCGAGCAATGCTGGACAC
41603325 ACACATATATAATA
1 ACACATATATAATA
41603339 TTTTCCAGTC
Statistics
Matches: 92, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
92 11 0.12
93 29 0.32
94 1 0.01
95 50 0.54
96 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (93 bp):
ACACATATATAATAATAATTGTCGGTGTCACCGACCAGTGCTAGGCACACACATATATAATATTT
GTTGGTTTCACCGAGCAATGCTGGACAC
Found at i:41611876 original size:15 final size:15
Alignment explanation
Indices: 41611856--41611904 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
41611846 AGGTAAGATA
41611856 AACATAACACATCCC
1 AACATAACACATCCC
* *
41611871 AACAT-A-AGAT--A
1 AACATAACACATCCC
41611882 AACATAACACATCCC
1 AACATAACACATCCC
41611897 AACATAAC
1 AACATAAC
41611905 TTGGCCAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
11 5 0.19
12 1 0.04
13 6 0.23
14 1 0.04
15 13 0.50
ACGTcount: A:0.53, C:0.31, G:0.02, T:0.14
Consensus pattern (15 bp):
AACATAACACATCCC
Found at i:41611878 original size:26 final size:26
Alignment explanation
Indices: 41611849--41611903 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
41611839 ACAAAATAGG
41611849 TAAGATAAACATAACACATCCCAACA
1 TAAGATAAACATAACACATCCCAACA
41611875 TAAGATAAACATAACACATCCCAACA
1 TAAGATAAACATAACACATCCCAACA
41611901 TAA
1 TAA
41611904 CTTGGCCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.55, C:0.25, G:0.04, T:0.16
Consensus pattern (26 bp):
TAAGATAAACATAACACATCCCAACA
Found at i:41613641 original size:14 final size:14
Alignment explanation
Indices: 41613622--41613651 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
41613612 TGTTCGGTTG
*
41613622 AATTTTTTAAAAAT
1 AATTTTTGAAAAAT
41613636 AATTTTTGAAAAAT
1 AATTTTTGAAAAAT
41613650 AA
1 AA
41613652 AAATGAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (14 bp):
AATTTTTGAAAAAT
Found at i:41614267 original size:26 final size:27
Alignment explanation
Indices: 41614238--41614289 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
41614228 TGTGTTTTTC
*
41614238 ATTTTTTTAAAATGAAAATG-AAAATT
1 ATTTTTTGAAAATGAAAATGTAAAATT
41614264 ATTTTTTGAAAATGAAAATGTAAAAT
1 ATTTTTTGAAAATGAAAATGTAAAAT
41614290 AAAACTAGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 19 0.79
27 5 0.21
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (27 bp):
ATTTTTTGAAAATGAAAATGTAAAATT
Found at i:41618369 original size:19 final size:19
Alignment explanation
Indices: 41618345--41618392 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
41618335 ATAACAACAT
* *
41618345 AATAGTGAAATGGTAGTAA
1 AATAGTGAAATGATAGCAA
41618364 AATAGTGAAATGATAGCAA
1 AATAGTGAAATGATAGCAA
41618383 AATAGTGAAA
1 AATAGTGAAA
41618393 AAAAGAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.52, C:0.02, G:0.23, T:0.23
Consensus pattern (19 bp):
AATAGTGAAATGATAGCAA
Found at i:41620159 original size:18 final size:19
Alignment explanation
Indices: 41620126--41620161 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
41620116 AATAACGAGG
41620126 AAAACAAAATATGCATAAC
1 AAAACAAAATATGCATAAC
*
41620145 AAAACTAAA-ATGCATAA
1 AAAACAAAATATGCATAA
41620162 AATAATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.64, C:0.14, G:0.06, T:0.17
Consensus pattern (19 bp):
AAAACAAAATATGCATAAC
Found at i:41623006 original size:20 final size:20
Alignment explanation
Indices: 41622969--41623008 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
41622959 TAGATAAGCT
*
41622969 TTTATATTTTTATTAAATAA
1 TTTATATTTCTATTAAATAA
41622989 TTTATA-TTCTATTCAAATAA
1 TTTATATTTCTATT-AAATAA
41623009 GTTCTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTATATTTCTATTAAATAA
Found at i:41627838 original size:50 final size:50
Alignment explanation
Indices: 41627773--41628103 Score: 345
Period size: 50 Copynumber: 6.9 Consensus size: 50
41627763 ATGGGGTAAG
* * *
41627773 GTGCCAATGCCATGTCCTAGACATGGTCTTACACTAGCTCTCGCATATCT
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACATATCT
* *
41627823 GTGCTGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGCATATCT
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACATATCT
* *
41627873 GTGCCGATGCCATGTCCTAGACATGGTCTTACACTAG--CTCACATA-AT
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACATATCT
* *
41627920 GTGGCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCT-T-ACATCTC-
1 GT-GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACATATCT
* * * * *
41627966 GAGGCCGATG-CATGTCCCAAACAT-GTCTTACACTGGCTCT--CATCTCA
1 G-TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACATATCT
** * *
41628013 ACGCCGATGCCATGTCCCAGGCATGGTCTTACACTAG--CTCACATA-AT
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACATATCT
*
41628060 GTGGCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCACACA
1 GT-GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACA
41628104 AGTGACCCTA
Statistics
Matches: 242, Mismatches: 25, Indels: 30
0.81 0.08 0.10
Matches are distributed among these distances:
46 77 0.32
47 43 0.18
48 40 0.17
50 82 0.34
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.27
Consensus pattern (50 bp):
GTGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACATATCT
Found at i:41628042 original size:140 final size:143
Alignment explanation
Indices: 41627828--41628093 Score: 430
Period size: 140 Copynumber: 1.9 Consensus size: 143
41627818 TATCTGTGCT
* *** *
41627828 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGCATATCTGTGCCGATGCCATGTCCTAG
1 GATGCCATGTCCCAAACATGGTCTTACACTAGCTCTC-CATATCAACGCCGATGCCATGTCCCAG
41627893 ACATGGTCTTACACTAGCTCACATAATGTGGCCGATGCATGTCCCAGACATGTCTTACACTGGCT
65 ACATGGTCTTACACTAGCTCACATAATGTGGCCGATGCATGTCCCAGACATGTCTTACACTGGCT
41627958 TACATCTCGAGGCC
130 TACATCTCGAGGCC
* * *
41627972 GATG-CATGTCCCAAACAT-GTCTTACACTGGCTCT-CATCTCAACGCCGATGCCATGTCCCAGG
1 GATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCCATATCAACGCCGATGCCATGTCCCAGA
41628034 CATGGTCTTACACTAGCTCACATAATGTGGCCGATGCATGTCCCAGACATGTCTTACACT
66 CATGGTCTTACACTAGCTCACATAATGTGGCCGATGCATGTCCCAGACATGTCTTACACT
41628094 AGCTCACACA
Statistics
Matches: 114, Mismatches: 8, Indels: 4
0.90 0.06 0.03
Matches are distributed among these distances:
140 82 0.72
142 15 0.13
143 13 0.11
144 4 0.04
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (143 bp):
GATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCCATATCAACGCCGATGCCATGTCCCAGA
CATGGTCTTACACTAGCTCACATAATGTGGCCGATGCATGTCCCAGACATGTCTTACACTGGCTT
ACATCTCGAGGCC
Found at i:41628066 original size:94 final size:93
Alignment explanation
Indices: 41627828--41628101 Score: 320
Period size: 94 Copynumber: 2.9 Consensus size: 93
41627818 TATCTGTGCT
* * *
41627828 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGCATATCTGTGCCGATGCCATGTCCTAG
1 GATGCCATGTCCCAGACATGGTCTTACACTAG--CTCACATATGTG-GCCGATG-CATGTCCCAG
***
41627893 ACATGGTCTTACACTAGCTCACATAATGTGGCC
62 ACAT-GTCTTACACTAGCTCACATAATAACGCC
* * * * *
41627926 GATG-CATGTCCCAGACAT-GTCTTACACTGGCTTACATCTCGAGGCCGATGCATGTCCCAAACA
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATAT-GTGGCCGATGCATGTCCCAGACA
* * *
41627989 TGTCTTACACTGGCTCTCAT-CTCAACGCC
65 TGTCTTACACTAGCTCACATAAT-AACGCC
*
41628018 GATGCCATGTCCCAGGCATGGTCTTACACTAGCTCACATAATGTGGCCGATGCATGTCCCAGACA
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACAT-ATGTGGCCGATGCATGTCCCAGACA
41628083 TGTCTTACACTAGCTCACA
65 TGTCTTACACTAGCTCACA
41628102 CAAGTGACCC
Statistics
Matches: 149, Mismatches: 22, Indels: 14
0.81 0.12 0.08
Matches are distributed among these distances:
91 1 0.01
92 24 0.16
93 25 0.17
94 68 0.46
95 2 0.01
96 11 0.07
97 14 0.09
98 4 0.03
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (93 bp):
GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATGTGGCCGATGCATGTCCCAGACAT
GTCTTACACTAGCTCACATAATAACGCC
Found at i:41628098 original size:46 final size:47
Alignment explanation
Indices: 41627779--41628101 Score: 343
Period size: 46 Copynumber: 6.8 Consensus size: 47
41627769 TAAGGTGCCA
* * * *
41627779 ATGCCATGTCCTAGACATGGTCTTACACTAGCTCTCGCATATCTGTGCTG
1 ATGCCATGTCCCAGACATGGTCTTACACTAG--CTCACATATGTG-GCCG
* *
41627829 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGCATATCTGTGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAG--CTCACATATGTG-GCCG
*
41627879 ATGCCATGTCCTAGACATGGTCTTACACTAGCTCACATAATGTGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACAT-ATGTGGCCG
* * * *
41627927 ATG-CATGTCCCAGACAT-GTCTTACACTGGCTTACATCTCGAGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATAT-GTGGCCG
* * * * ***
41627973 ATG-CATGTCCCAAACAT-GTCTTACACTGGCTCTCATCTCAACGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATAT-GTGGCCG
*
41628019 ATGCCATGTCCCAGGCATGGTCTTACACTAGCTCACATAATGTGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACAT-ATGTGGCCG
41628067 ATG-CATGTCCCAGACAT-GTCTTACACTAGCTCACA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACA
41628102 CAAGTGACCC
Statistics
Matches: 244, Mismatches: 24, Indels: 14
0.87 0.09 0.05
Matches are distributed among these distances:
45 1 0.00
46 85 0.35
47 38 0.16
48 37 0.15
49 5 0.02
50 78 0.32
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (47 bp):
ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATGTGGCCG
Found at i:41629882 original size:22 final size:22
Alignment explanation
Indices: 41629835--41629881 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
41629825 AGATTTAGGA
41629835 TTTTAAAAACAATTTTATTTTC
1 TTTTAAAAACAATTTTATTTTC
41629857 TTTTAAAAACAATTTTA-TTTC
1 TTTTAAAAACAATTTTATTTTC
41629878 TTTT
1 TTTT
41629882 TTTTTAACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 8 0.32
22 17 0.68
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTAAAAACAATTTTATTTTC
Found at i:41633171 original size:29 final size:29
Alignment explanation
Indices: 41633139--41633197 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
41633129 TAAAGTTGTG
41633139 AAAATTTAGCTTGTTTTAGGTTAATTATC
1 AAAATTTAGCTTGTTTTAGGTTAATTATC
41633168 AAAATTTAGCTTGTTTTAGGTTAATTATC
1 AAAATTTAGCTTGTTTTAGGTTAATTATC
41633197 A
1 A
41633198 TGGTTCTTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.47
Consensus pattern (29 bp):
AAAATTTAGCTTGTTTTAGGTTAATTATC
Found at i:41634756 original size:39 final size:39
Alignment explanation
Indices: 41634663--41634838 Score: 212
Period size: 39 Copynumber: 4.5 Consensus size: 39
41634653 GATTTTAACA
* * * * *
41634663 GGGCTAAGACCCGCAGGCCTT-GTG-TGAGATTTATGTCC
1 GGGCTAAGTCCCGAAGGCATTCGTGCTGATA-TTATATCC
* * * **
41634701 AGGCTAAGTCCCGAAGGCATTCGCGCTGGTATTATATTT
1 GGGCTAAGTCCCGAAGGCATTCGTGCTGATATTATATCC
41634740 GGGCTAAGTCCCGAAGGCATTCGTGCTGATATTATATCC
1 GGGCTAAGTCCCGAAGGCATTCGTGCTGATATTATATCC
*
41634779 GGGCTAAGTCCCGAAGGCATTCGTGCTGATGTTATATCC
1 GGGCTAAGTCCCGAAGGCATTCGTGCTGATATTATATCC
* *
41634818 GAGCTAAGTTCCGAAGGCATT
1 GGGCTAAGTCCCGAAGGCATT
41634839 TGGGTTGGAA
Statistics
Matches: 118, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
38 17 0.14
39 98 0.83
40 3 0.03
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (39 bp):
GGGCTAAGTCCCGAAGGCATTCGTGCTGATATTATATCC
Found at i:41642572 original size:39 final size:39
Alignment explanation
Indices: 41642517--41642701 Score: 298
Period size: 39 Copynumber: 4.7 Consensus size: 39
41642507 TGTGTGAGAT
*
41642517 TTATATCCGCGCTAAGTCCCGAAGGCATTCGTGCTGATA
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGATA
* * * *
41642556 TTATATTCGGGTTAAGTCTCGAAGGCATTCGTGCTGGTA
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGATA
*
41642595 TTATATCCGGGCTAAGTCTCGAAGGCATTCGTGCTGATA
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGATA
*
41642634 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGATG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGATA
*
41642673 TTATATCCGGGCTAAGTTCCGAAGGCATT
1 TTATATCCGGGCTAAGTCCCGAAGGCATT
41642702 TGGGTTGGAA
Statistics
Matches: 135, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 135 1.00
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.31
Consensus pattern (39 bp):
TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGATA
Found at i:41646514 original size:39 final size:39
Alignment explanation
Indices: 41646467--41646616 Score: 230
Period size: 39 Copynumber: 3.9 Consensus size: 39
41646457 GGTTGTGTAT
* *
41646467 TGAT-TTATATCCGCGCTAAGACCCGAAGGCATTCGTGC
1 TGATATTATATCCGGGCTAAGTCCCGAAGGCATTCGTGC
* *
41646505 TGATATTATATCTGGGTTAAGTCCCGAAGGCATTCGTGC
1 TGATATTATATCCGGGCTAAGTCCCGAAGGCATTCGTGC
*
41646544 TGGTATTATATCCGGGCTAAGTCCCGAAGGCATTCGTGC
1 TGATATTATATCCGGGCTAAGTCCCGAAGGCATTCGTGC
* *
41646583 TGATGTTATATCCGGGCTAAGTTCCGAAGGCATT
1 TGATATTATATCCGGGCTAAGTCCCGAAGGCATT
41646617 TGGGTTGGAA
Statistics
Matches: 101, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
38 4 0.04
39 97 0.96
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (39 bp):
TGATATTATATCCGGGCTAAGTCCCGAAGGCATTCGTGC
Found at i:41652202 original size:93 final size:93
Alignment explanation
Indices: 41652090--41652260 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
41652080 GCCCATAAGT
* *
41652090 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
41652155 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
41652183 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
41652248 CGAGTTCGGATGC
66 CGAGTTCGGATGC
41652261 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:41652257 original size:46 final size:46
Alignment explanation
Indices: 41652082--41652257 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
41652072 TGTAACCCGC
* * *
41652082 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
41652128 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
41652178 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
41652221 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
41652258 TGCTCAACCA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 64 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:41658000 original size:68 final size:67
Alignment explanation
Indices: 41657928--41658077 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
41657918 CATCATGTGT
* * * *
41657928 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
41657990 ATGTAG
62 ATGTAG
** * *
41657996 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
41658061 AG
66 AG
41658063 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
41658078 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:41658033 original size:64 final size:64
Alignment explanation
Indices: 41657952--41658135 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
41657942 AGACATTATG
* *
41657952 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
41658016 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
41658081 AA
63 AA
* * * *
41658083 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
41658136 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:41669241 original size:29 final size:29
Alignment explanation
Indices: 41669178--41669294 Score: 173
Period size: 29 Copynumber: 4.1 Consensus size: 29
41669168 AGCATGACTG
*
41669178 TAAATGTGTTTTGGGCCTAAT-GGCCATA
1 TAAATGTGATTTGGGCCTAATGGGCCATA
**
41669206 GGAATGTGATTTGGGCCTAATGGGCCATA
1 TAAATGTGATTTGGGCCTAATGGGCCATA
*
41669235 TAAATGTGATTTGGGCCTCATGGGCCATA
1 TAAATGTGATTTGGGCCTAATGGGCCATA
* *
41669264 TAAATGTGATTTGGGCCTAGTGGGCTATA
1 TAAATGTGATTTGGGCCTAATGGGCCATA
41669293 TA
1 TA
41669295 CAGGTATGTG
Statistics
Matches: 79, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
28 18 0.23
29 61 0.77
ACGTcount: A:0.25, C:0.14, G:0.29, T:0.32
Consensus pattern (29 bp):
TAAATGTGATTTGGGCCTAATGGGCCATA
Found at i:41673226 original size:27 final size:26
Alignment explanation
Indices: 41673191--41673448 Score: 246
Period size: 27 Copynumber: 9.6 Consensus size: 26
41673181 AAATAGGGGT
* *
41673191 AAAACAGTCATCTTACCATAAAAGGGC
1 AAAACAGTCATTTTACC-TATAAGGGC
* *
41673218 AAAATAGTCATTTTACCTCATAAAGGC
1 AAAACAGTCATTTTACCT-ATAAGGGC
* *
41673245 AAAACAGTCATTTTACCCCATAAGGGA
1 AAAACAGTCATTTTA-CCTATAAGGGC
* *
41673272 AAAACAATCATTTTACCTCATAAGGGA
1 AAAACAGTCATTTTACCT-ATAAGGGC
*
41673299 AAAACAGTCATTTTACCTCATAAAGGC
1 AAAACAGTCATTTTACCT-ATAAGGGC
* *
41673326 AAAACAATCATTTTACCTTATAAGTGC
1 AAAACAGTCATTTTACC-TATAAGGGC
* *
41673353 AAAATAGTCATTTTACCCCATAAGGGC
1 AAAACAGTCATTTTA-CCTATAAGGGC
* * *
41673380 AAAACAATCATTTTCCCTTATAAGAGC
1 AAAACAGTCATTTTACC-TATAAGGGC
* * * *
41673407 AAAACAATTATTTTACCCCATAAGGAC
1 AAAACAGTCATTTTA-CCTATAAGGGC
*
41673434 AAAATAGTCATTTTA
1 AAAACAGTCATTTTA
41673449 TCGATTAAGG
Statistics
Matches: 191, Mismatches: 33, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
26 5 0.03
27 179 0.94
28 7 0.04
ACGTcount: A:0.42, C:0.20, G:0.11, T:0.27
Consensus pattern (26 bp):
AAAACAGTCATTTTACCTATAAGGGC
Found at i:41673254 original size:54 final size:54
Alignment explanation
Indices: 41673191--41673448 Score: 311
Period size: 54 Copynumber: 4.8 Consensus size: 54
41673181 AAATAGGGGT
* ** * * *
41673191 AAAACAGTCATCTTACCATAAAAGGGCAAAATAGTCATTTTACCTCATAA-AGGC
1 AAAACAGTCATTTTACCCCATAAGGGCAAAACAATCATTTTACCTCATAAGA-GC
* * *
41673245 AAAACAGTCATTTTACCCCATAAGGGAAAAACAATCATTTTACCTCATAAGGGA
1 AAAACAGTCATTTTACCCCATAAGGGCAAAACAATCATTTTACCTCATAAGAGC
* * * *
41673299 AAAACAGTCATTTTACCTCATAAAGGCAAAACAATCATTTTACCTTATAAGTGC
1 AAAACAGTCATTTTACCCCATAAGGGCAAAACAATCATTTTACCTCATAAGAGC
* * *
41673353 AAAATAGTCATTTTACCCCATAAGGGCAAAACAATCATTTTCCCTTATAAGAGC
1 AAAACAGTCATTTTACCCCATAAGGGCAAAACAATCATTTTACCTCATAAGAGC
* * * * *
41673407 AAAACAATTATTTTACCCCATAAGGACAAAATAGTCATTTTA
1 AAAACAGTCATTTTACCCCATAAGGGCAAAACAATCATTTTA
41673449 TCGATTAAGG
Statistics
Matches: 176, Mismatches: 27, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
54 176 1.00
ACGTcount: A:0.42, C:0.20, G:0.11, T:0.27
Consensus pattern (54 bp):
AAAACAGTCATTTTACCCCATAAGGGCAAAACAATCATTTTACCTCATAAGAGC
Found at i:41673326 original size:81 final size:81
Alignment explanation
Indices: 41673212--41673448 Score: 316
Period size: 81 Copynumber: 2.9 Consensus size: 81
41673202 CTTACCATAA
* * *
41673212 AAGGGCAAAATAGTCATTTTACCTCATAAAGGCAAAACAGTCATTTTACCCCATAAGGGAAAAAC
1 AAGGGCAAAACAGTCATTTTACCTCATAAAGGCAAAACAATCATTTTACCCCATAAGGGAAAAAT
* *
41673277 AATCATTTTACCTCAT
66 AGTCATTTTACCCCAT
* ** * *
41673293 AAGGGAAAAACAGTCATTTTACCTCATAAAGGCAAAACAATCATTTTACCTTATAAGTGCAAAAT
1 AAGGGCAAAACAGTCATTTTACCTCATAAAGGCAAAACAATCATTTTACCCCATAAGGGAAAAAT
41673358 AGTCATTTTACCCCAT
66 AGTCATTTTACCCCAT
* * * *
41673374 AAGGGCAAAACAATCATTTTCCCTTAT-AAGAGCAAAACAATTATTTTACCCCATAA-GGACAAA
1 AAGGGCAAAACAGTCATTTTACCTCATAAAG-GCAAAACAATCATTTTACCCCATAAGGGA-AAA
41673437 ATAGTCATTTTA
64 ATAGTCATTTTA
41673449 TCGATTAAGG
Statistics
Matches: 135, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
80 4 0.03
81 131 0.97
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.27
Consensus pattern (81 bp):
AAGGGCAAAACAGTCATTTTACCTCATAAAGGCAAAACAATCATTTTACCCCATAAGGGAAAAAT
AGTCATTTTACCCCAT
Found at i:41676425 original size:20 final size:20
Alignment explanation
Indices: 41676400--41676449 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
41676390 CCGTGGGGCC
41676400 ACACGGCCCATTTTGGCCCA
1 ACACGGCCCATTTTGGCCCA
* * *
41676420 ACACGGTCGATTTTGGCCTA
1 ACACGGCCCATTTTGGCCCA
*
41676440 ACATGGCCCA
1 ACACGGCCCA
41676450 GATCAGCCTT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.34, G:0.22, T:0.22
Consensus pattern (20 bp):
ACACGGCCCATTTTGGCCCA
Found at i:41678016 original size:20 final size:20
Alignment explanation
Indices: 41677991--41678040 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
41677981 CCGTGGGGCC
41677991 ACACGGCCCATTTTGGCCCA
1 ACACGGCCCATTTTGGCCCA
* * *
41678011 ACACGGTCGATTTTGGCCTA
1 ACACGGCCCATTTTGGCCCA
*
41678031 ACATGGCCCA
1 ACACGGCCCA
41678041 GATCAGCCTT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.34, G:0.22, T:0.22
Consensus pattern (20 bp):
ACACGGCCCATTTTGGCCCA
Found at i:41682386 original size:39 final size:40
Alignment explanation
Indices: 41682272--41682456 Score: 207
Period size: 40 Copynumber: 4.7 Consensus size: 40
41682262 GCTACTCGTT
* *
41682272 CAAATACCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
41682312 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
41682352 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * * *
41682391 CAAATGCCTTC-GAATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
41682432 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
41682457 CATCATTCGA
Statistics
Matches: 122, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
38 1 0.01
39 32 0.26
40 78 0.64
41 11 0.09
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:41682416 original size:79 final size:81
Alignment explanation
Indices: 41682278--41682456 Score: 206
Period size: 79 Copynumber: 2.2 Consensus size: 81
41682268 CGTTCAAATA
* * * * *
41682278 CCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTA
1 CCTTCGGGACTTAGCCCGGAATATAGTAACTCACACAAATGCCTTCGGAACTTAACCCGGATATA
* *
41682342 GTAAC-TCGCACCAATG
66 GTAACTTAGCA-CAAAG
**
41682358 CCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCACACAAATGCCTTC-GAATCTTAGTCCGGATAT
1 CCTTCGGGACTTAGCCCGGAATATAGTAACTCACACAAATGCCTTCGGAA-CTTAACCCGGATAT
* *
41682420 GGTCACTTAGCACAAAG
65 AGTAACTTAGCACAAAG
41682437 CCTTCGGGACTTAGCCCGGA
1 CCTTCGGGACTTAGCCCGGA
41682457 CATCATTCGA
Statistics
Matches: 84, Mismatches: 11, Indels: 8
0.82 0.11 0.08
Matches are distributed among these distances:
78 2 0.02
79 58 0.69
80 24 0.29
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (81 bp):
CCTTCGGGACTTAGCCCGGAATATAGTAACTCACACAAATGCCTTCGGAACTTAACCCGGATATA
GTAACTTAGCACAAAG
Found at i:41692821 original size:31 final size:31
Alignment explanation
Indices: 41692783--41692845 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
41692773 CTTTTCACAC
41692783 TTCATATTTCATAACACTGGGCCGAAGCCTT
1 TTCATATTTCATAACACTGGGCCGAAGCCTT
** *
41692814 TTCATATTTCATATTACTGGGCTGAAGCCTT
1 TTCATATTTCATAACACTGGGCCGAAGCCTT
41692845 T
1 T
41692846 ACTGTAAACG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (31 bp):
TTCATATTTCATAACACTGGGCCGAAGCCTT
Found at i:41693116 original size:48 final size:49
Alignment explanation
Indices: 41693030--41693160 Score: 160
Period size: 48 Copynumber: 2.6 Consensus size: 49
41693020 AGCATAGCTG
*
41693030 CTTTATCATATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGCCA-AAGCC
1 CTTTAT-A-ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGCCATAAGCC
* *
41693081 CTTT-TAATAACTGGGGCATAAGCCCTTTATCATAACTGGGGCATAAGCC
1 CTTTATAATAACTGGGGCATAAGCCCTTT-TAATAACTGGGCCATAAGCC
*
41693130 CTTTATCATAACTGGGGCATAAGCCCTTTTA
1 CTTTATAATAACTGGGGCATAAGCCCTTTTA
41693161 CACTTCCTCC
Statistics
Matches: 71, Mismatches: 5, Indels: 10
0.83 0.06 0.12
Matches are distributed among these distances:
47 8 0.11
48 24 0.34
49 11 0.15
50 24 0.34
51 4 0.06
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (49 bp):
CTTTATAATAACTGGGGCATAAGCCCTTTTAATAACTGGGCCATAAGCC
Found at i:41693121 original size:25 final size:25
Alignment explanation
Indices: 41693030--41693158 Score: 158
Period size: 25 Copynumber: 5.2 Consensus size: 25
41693020 AGCATAGCTG
*
41693030 CTTTATCATATAACTGGAGGCCT-AGCC
1 CTTTATC--ATAACTGG-GGCATAAGCC
* *
41693057 TCTTT-TAATAACTGGGCCA-AAGCC
1 -CTTTATCATAACTGGGGCATAAGCC
*
41693081 CTTT-TAATAACTGGGGCATAAGCC
1 CTTTATCATAACTGGGGCATAAGCC
41693105 CTTTATCATAACTGGGGCATAAGCC
1 CTTTATCATAACTGGGGCATAAGCC
41693130 CTTTATCATAACTGGGGCATAAGCC
1 CTTTATCATAACTGGGGCATAAGCC
41693155 CTTT
1 CTTT
41693159 TACACTTCCT
Statistics
Matches: 93, Mismatches: 5, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
23 17 0.18
24 15 0.16
25 56 0.60
27 1 0.01
28 4 0.04
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (25 bp):
CTTTATCATAACTGGGGCATAAGCC
Found at i:41693234 original size:20 final size:20
Alignment explanation
Indices: 41693209--41693275 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 20
41693199 TTATGAATAC
41693209 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
* *
41693229 ATCATGTACATATCATAGAT
1 ATCATGTGCATATCATACAT
* **
41693249 GTCACATGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
41693269 ACCATGT
1 ATCATGT
41693276 TTATCAAAAT
Statistics
Matches: 36, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:41695108 original size:12 final size:12
Alignment explanation
Indices: 41695091--41695115 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41695081 TTATTTTATT
41695091 CTTCCATTAACA
1 CTTCCATTAACA
41695103 CTTCCATTAACA
1 CTTCCATTAACA
41695115 C
1 C
41695116 AACATGTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (12 bp):
CTTCCATTAACA
Found at i:41695135 original size:56 final size:56
Alignment explanation
Indices: 41695068--41695411 Score: 600
Period size: 56 Copynumber: 6.1 Consensus size: 56
41695058 TATTAGTTTA
* ** ** **
41695068 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACTTCCAT-TAACACAACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACAC-AACATGTTTCATGACATGTT
41695124 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
41695180 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
*
41695236 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
41695292 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
41695348 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
41695404 TTGCCCAT
1 TTGCCCAT
41695412 CATCCCTTGT
Statistics
Matches: 278, Mismatches: 9, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
55 3 0.01
56 275 0.99
ACGTcount: A:0.23, C:0.23, G:0.08, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:41699686 original size:56 final size:56
Alignment explanation
Indices: 41699619--41699735 Score: 207
Period size: 56 Copynumber: 2.1 Consensus size: 56
41699609 TAGTTTATCT
*
41699619 CCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTGATGACATGTTTTG
1 CCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTTTTG
* *
41699675 CCCATGCTTCTTATTTTATTTTTCCATTAGCACAACATGTTTCATGACATGTTTTG
1 CCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTTTTG
41699731 CCCAT
1 CCCAT
41699736 CATCCCTTGT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.22, C:0.23, G:0.10, T:0.44
Consensus pattern (56 bp):
CCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTTTTG
Found at i:41701906 original size:150 final size:150
Alignment explanation
Indices: 41701633--41701938 Score: 594
Period size: 150 Copynumber: 2.0 Consensus size: 150
41701623 CAACTCTACC
41701633 CTCCTTAAAGAAATTTCAGCCTTGAAATTTACCTGATCCAAACAGTTGAGGGTACTGCTGACGCA
1 CTCCTTAAAGAAATTTCAGCCTTGAAATTTACCTGATCCAAACAGTTGAGGGTACTGCTGACGCA
41701698 TTGCCTCTTCGGTCTCCCAAGTAGCTTCTTTCTTGCCATGGTTCCTCCAAAGTACCTTCACTAAT
66 TTGCCTCTTCGGTCTCCCAAGTAGCTTCTTTCTTGCCATGGTTCCTCCAAAGTACCTTCACTAAT
41701763 GGGACTGACCTCCTTCTTAA
131 GGGACTGACCTCCTTCTTAA
41701783 CTCCTTAAAGAAATTTCAGCCTTGAAATTTACCTGATCCAAACAGTTGAGGGTACTGCTGACGCA
1 CTCCTTAAAGAAATTTCAGCCTTGAAATTTACCTGATCCAAACAGTTGAGGGTACTGCTGACGCA
*
41701848 TTGCCTCTTCGGTCTCCCAAGTAGCTTCTTTCTTGCCATGGTTCCTCCAAAGTCCCTTCACTAAT
66 TTGCCTCTTCGGTCTCCCAAGTAGCTTCTTTCTTGCCATGGTTCCTCCAAAGTACCTTCACTAAT
41701913 GGGACTGACCTCCTTCTTAA
131 GGGACTGACCTCCTTCTTAA
*
41701933 CACCTT
1 CTCCTT
41701939 GACATCGCGA
Statistics
Matches: 154, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
150 154 1.00
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.32
Consensus pattern (150 bp):
CTCCTTAAAGAAATTTCAGCCTTGAAATTTACCTGATCCAAACAGTTGAGGGTACTGCTGACGCA
TTGCCTCTTCGGTCTCCCAAGTAGCTTCTTTCTTGCCATGGTTCCTCCAAAGTACCTTCACTAAT
GGGACTGACCTCCTTCTTAA
Found at i:41707730 original size:20 final size:20
Alignment explanation
Indices: 41707705--41707789 Score: 125
Period size: 20 Copynumber: 4.2 Consensus size: 20
41707695 CCCCATGTAG
41707705 CATGTGCATATCATACATAT
1 CATGTGCATATCATACATAT
*
41707725 CATGTGCGTATCATACATAT
1 CATGTGCATATCATACATAT
* * *
41707745 CATGTACATATCATAGATGT
1 CATGTGCATATCATACATAT
*
41707765 CATGTGCATATCATACATAC
1 CATGTGCATATCATACATAT
41707785 CATGT
1 CATGT
41707790 TTATCAAAAT
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34
Consensus pattern (20 bp):
CATGTGCATATCATACATAT
Found at i:41707752 original size:11 final size:11
Alignment explanation
Indices: 41707705--41707758 Score: 53
Period size: 11 Copynumber: 5.3 Consensus size: 11
41707695 CCCCATGTAG
*
41707705 CATGTGCATAT
1 CATGTACATAT
41707716 CA--TACATAT
1 CATGTACATAT
* *
41707725 CATGTGCGTAT
1 CATGTACATAT
41707736 CA--TACATAT
1 CATGTACATAT
41707745 CATGTACATAT
1 CATGTACATAT
41707756 CAT
1 CAT
41707759 AGATGTCATG
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.35
Consensus pattern (11 bp):
CATGTACATAT
Found at i:41709820 original size:18 final size:17
Alignment explanation
Indices: 41709799--41709832 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
41709789 TAACTTGTTT
*
41709799 ATCAATCTCATTATTCAA
1 ATCAATC-CATAATTCAA
41709817 ATCAATCCATAATTCA
1 ATCAATCCATAATTCA
41709833 TGCTTTGGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.24, G:0.00, T:0.35
Consensus pattern (17 bp):
ATCAATCCATAATTCAA
Found at i:41709879 original size:18 final size:17
Alignment explanation
Indices: 41709856--41709889 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
41709846 TTACCTTTTT
*
41709856 ATCAATCTCATTATTCAA
1 ATCAATC-CATAATTCAA
41709874 ATCAATCCATAATTCA
1 ATCAATCCATAATTCA
41709890 TGCTTTGGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.24, G:0.00, T:0.35
Consensus pattern (17 bp):
ATCAATCCATAATTCAA
Found at i:41709884 original size:57 final size:57
Alignment explanation
Indices: 41709796--41709928 Score: 266
Period size: 57 Copynumber: 2.3 Consensus size: 57
41709786 ATTTAACTTG
41709796 TTTATCAATCTCATTATTCAAATCAATCCATAATTCATGCTTTGGTAAAATTACCTT
1 TTTATCAATCTCATTATTCAAATCAATCCATAATTCATGCTTTGGTAAAATTACCTT
41709853 TTTATCAATCTCATTATTCAAATCAATCCATAATTCATGCTTTGGTAAAATTACCTT
1 TTTATCAATCTCATTATTCAAATCAATCCATAATTCATGCTTTGGTAAAATTACCTT
41709910 TTTATCAATCTCATTATTC
1 TTTATCAATCTCATTATTC
41709929 TCTAGGCTCG
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 76 1.00
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.44
Consensus pattern (57 bp):
TTTATCAATCTCATTATTCAAATCAATCCATAATTCATGCTTTGGTAAAATTACCTT
Found at i:41715918 original size:30 final size:30
Alignment explanation
Indices: 41715884--41715944 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
41715874 TCCTTAACTC
41715884 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
41715914 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
41715944 A
1 A
41715945 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:41729185 original size:50 final size:50
Alignment explanation
Indices: 41729110--41729210 Score: 184
Period size: 50 Copynumber: 2.0 Consensus size: 50
41729100 AGAATGCTCA
*
41729110 GTAGTAAACACATGAGCAGAGACACGGCCGTGTGTCTCAGCCGTGTGGAG
1 GTAGTAAACACATGAGCAGAGACACGGCCGTGTGTCTCAGCCGTGTAGAG
*
41729160 GTAGTAAACACATGGGCAGAGACACGGCCGTGTGTCTCAGCCGTGTAGAG
1 GTAGTAAACACATGAGCAGAGACACGGCCGTGTGTCTCAGCCGTGTAGAG
41729210 G
1 G
41729211 CCACGGCCTA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.26, C:0.22, G:0.35, T:0.18
Consensus pattern (50 bp):
GTAGTAAACACATGAGCAGAGACACGGCCGTGTGTCTCAGCCGTGTAGAG
Found at i:41730799 original size:39 final size:39
Alignment explanation
Indices: 41730735--41730881 Score: 231
Period size: 39 Copynumber: 3.8 Consensus size: 39
41730725 TTCGAGCACG
* * *
41730735 TAGCCTGCGGACTTCAAGTCCGGATATATTTCTAGCATA
1 TAGCCTGCGGACCTCATGTCCGGATATATTTCCAGCATA
*
41730774 TAGCCTGCGGACCTCATGTCTGGATATATTTCCAGCATA
1 TAGCCTGCGGACCTCATGTCCGGATATATTTCCAGCATA
* *
41730813 TAGCCTGCGGACCTCATGTCCGGGTATATTCCCAGCATA
1 TAGCCTGCGGACCTCATGTCCGGATATATTTCCAGCATA
*
41730852 TAGCCTGCGGACCTTATGTCCGGATATATT
1 TAGCCTGCGGACCTCATGTCCGGATATATT
41730882 CCCAATATCA
Statistics
Matches: 99, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 99 1.00
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (39 bp):
TAGCCTGCGGACCTCATGTCCGGATATATTTCCAGCATA
Found at i:41733553 original size:37 final size:37
Alignment explanation
Indices: 41733499--41733583 Score: 125
Period size: 37 Copynumber: 2.3 Consensus size: 37
41733489 TTTGAGTACG
*
41733499 TGTAAGACCATAGCTGGGCTATGGCATCGTAATGACA
1 TGTAAGACCATAGCTGGGCTATGGCATCGTAATCACA
* * * *
41733536 TGTAAGACCATATCTGGGCTATGGCATTGTGATCCCA
1 TGTAAGACCATAGCTGGGCTATGGCATCGTAATCACA
41733573 TGTAAGACCAT
1 TGTAAGACCAT
41733584 GTTTGGGACA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (37 bp):
TGTAAGACCATAGCTGGGCTATGGCATCGTAATCACA
Found at i:41733616 original size:48 final size:48
Alignment explanation
Indices: 41733563--41733743 Score: 254
Period size: 48 Copynumber: 3.8 Consensus size: 48
41733553 GCTATGGCAT
*
41733563 TGTGATCCCATGTAAGACCATGTTTGGGACATGGCATTGGCATCGATA
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATA
* *
41733611 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATCGGCATTGATA
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATA
* ** * *
41733659 TGTGATCCTATGTAAGACCATGTCTAAGACATGGCTTTGGCATCTATA
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATA
** * *
41733707 TGTGATTTCGTGTAAGACCATGCCTGGGACATGGCAT
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCAT
41733744 CGATATGGGA
Statistics
Matches: 115, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 115 1.00
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (48 bp):
TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATA
Found at i:41738317 original size:13 final size:12
Alignment explanation
Indices: 41738279--41738319 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
41738269 CTAAAATATC
*
41738279 AAAAACTAAAAA
1 AAAAATTAAAAA
*
41738291 GAAAATTAAAAA
1 AAAAATTAAAAA
41738303 AAAAATTAACAAA
1 AAAAATTAA-AAA
41738316 AAAA
1 AAAA
41738320 GCCACATGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
12 18 0.72
13 7 0.28
ACGTcount: A:0.80, C:0.05, G:0.02, T:0.12
Consensus pattern (12 bp):
AAAAATTAAAAA
Found at i:41739309 original size:19 final size:19
Alignment explanation
Indices: 41739272--41739320 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
41739262 TTCCTATTAT
* *
41739272 TTTATTATTTTATTTTTAG
1 TTTATTATTATATTGTTAG
*
41739291 TTTATTATTATCTTGTTAG
1 TTTATTATTATATTGTTAG
* *
41739310 TGTATTCTTAT
1 TTTATTATTAT
41739321 TATGATTATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.20, C:0.04, G:0.08, T:0.67
Consensus pattern (19 bp):
TTTATTATTATATTGTTAG
Found at i:41740917 original size:33 final size:33
Alignment explanation
Indices: 41740879--41740955 Score: 79
Period size: 33 Copynumber: 2.3 Consensus size: 33
41740869 TAGCTGATTT
*
41740879 TATTTT-TT-TGTCTATTTTCTCTATTCTTTTT-TC
1 TATTTTGTTATGTCT-TTATCT-TATT-TTTTTGTC
*
41740912 TATTTTGTTATTTCTTTATCTTATTTTTTTGTC
1 TATTTTGTTATGTCTTTATCTTATTTTTTTGTC
*
41740945 TATTTTCTTAT
1 TATTTTGTTAT
41740956 TTAGTTTGCT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
32 5 0.13
33 22 0.58
34 7 0.18
35 4 0.11
ACGTcount: A:0.12, C:0.12, G:0.04, T:0.73
Consensus pattern (33 bp):
TATTTTGTTATGTCTTTATCTTATTTTTTTGTC
Found at i:41740926 original size:21 final size:21
Alignment explanation
Indices: 41740878--41740928 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
41740868 TTAGCTGATT
41740878 TTATTT-TTTTGTCTATTTTC
1 TTATTTCTTTTGTCTATTTTC
* *
41740898 TCTA-TTCTTTTTTCTATTTTG
1 T-TATTTCTTTTGTCTATTTTC
41740919 TTATTTCTTT
1 TTATTTCTTT
41740929 ATCTTATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 5 0.19
21 21 0.81
ACGTcount: A:0.10, C:0.12, G:0.04, T:0.75
Consensus pattern (21 bp):
TTATTTCTTTTGTCTATTTTC
Found at i:41741842 original size:23 final size:22
Alignment explanation
Indices: 41741816--41741859 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
41741806 ATTTTATTAG
*
41741816 AAAACGAGAAAAAAATTAAAAAA
1 AAAAAGAGAAAAAAA-TAAAAAA
*
41741839 AAAAAGTGAAAAAAATAAAAA
1 AAAAAGAGAAAAAAATAAAAA
41741860 TGAAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.80, C:0.02, G:0.09, T:0.09
Consensus pattern (22 bp):
AAAAAGAGAAAAAAATAAAAAA
Found at i:41741851 original size:15 final size:14
Alignment explanation
Indices: 41741824--41741869 Score: 65
Period size: 14 Copynumber: 3.2 Consensus size: 14
41741814 AGAAAACGAG
*
41741824 AAAAAAATTAAAAA
1 AAAAAAATGAAAAA
*
41741838 AAAAAAGTGAAAAA
1 AAAAAAATGAAAAA
41741852 AATAAAAATGAAAAA
1 AA-AAAAATGAAAAA
41741867 AAA
1 AAA
41741870 GAGATTGAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 15 0.54
15 13 0.46
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.11
Consensus pattern (14 bp):
AAAAAAATGAAAAA
Found at i:41741852 original size:16 final size:15
Alignment explanation
Indices: 41741824--41741869 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
41741814 AGAAAACGAG
*
41741824 AAAAAAAT-TAAAAA
1 AAAAAAATGAAAAAA
*
41741838 AAAAAAGTGAAAAAA
1 AAAAAAATGAAAAAA
*
41741853 ATAAAAATGAAAAAA
1 AAAAAAATGAAAAAA
41741868 AA
1 AA
41741870 GAGATTGAGC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 7 0.27
15 19 0.73
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.11
Consensus pattern (15 bp):
AAAAAAATGAAAAAA
Found at i:41748312 original size:13 final size:13
Alignment explanation
Indices: 41748294--41748333 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
41748284 GTCTATAGAC
41748294 CTCAGATGTGATT
1 CTCAGATGTGATT
41748307 CTCAGATGTGATT
1 CTCAGATGTGATT
*
41748320 CCCAGTAT-TGATT
1 CTCAG-ATGTGATT
41748333 C
1 C
41748334 CTCTTCACTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 23 0.92
14 2 0.08
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.38
Consensus pattern (13 bp):
CTCAGATGTGATT
Found at i:41759292 original size:29 final size:29
Alignment explanation
Indices: 41759239--41759512 Score: 171
Period size: 29 Copynumber: 9.4 Consensus size: 29
41759229 TCAATGATCA
* * *
41759239 ATGAAAAGGGATAGCTTC-AGGTATCGAAT
1 ATGAAAAGGGATAGTTTCGA-CTATCGATT
* *
41759268 ATGGAAAGGGATAGTTTCGACTATCTATT
1 ATGAAAAGGGATAGTTTCGACTATCGATT
* ** * * * *
41759297 ATGAAAAGGGATGGTGACAACCATCAACT
1 ATGAAAAGGGATAGTTTCGACTATCGATT
* ** * **
41759326 ATGAAAAGGGATGGTGACGACCATCGAAA
1 ATGAAAAGGGATAGTTTCGACTATCGATT
*
41759355 ATGAAAAGGGATAGCTTT-GGCTATCGATT
1 ATGAAAAGGGATAG-TTTCGACTATCGATT
* *
41759384 ATGAAAAAGGATAGCTTC-AGCTATCGATT
1 ATGAAAAGGGATAGTTTCGA-CTATCGATT
* * * *
41759413 ATGAAAGGGGATGGCTTCGGCTATCGATT
1 ATGAAAAGGGATAGTTTCGACTATCGATT
* * **
41759442 ATGAAAAAGGATGGTGACGAGC-ATCGATT
1 ATGAAAAGGGATAGTTTCGA-CTATCGATT
** *
41759471 ATGAAAAGGGATAGTGACGACCATTCG-TT
1 ATGAAAAGGGATAGTTTCGACTA-TCGATT
41759500 AATGAAAAGGGAT
1 -ATGAAAAGGGAT
41759513 GGTTAAGACC
Statistics
Matches: 197, Mismatches: 39, Indels: 17
0.78 0.15 0.07
Matches are distributed among these distances:
28 3 0.02
29 176 0.89
30 18 0.09
ACGTcount: A:0.36, C:0.12, G:0.28, T:0.24
Consensus pattern (29 bp):
ATGAAAAGGGATAGTTTCGACTATCGATT
Found at i:41759387 original size:58 final size:58
Alignment explanation
Indices: 41759239--41759484 Score: 203
Period size: 58 Copynumber: 4.2 Consensus size: 58
41759229 TCAATGATCA
* * * * ** * *
41759239 ATGAAAAGGGATAGCTTCAGG-TATCGAATATGGAAAGGGATAGTTTCGACTATCTATT
1 ATGAAAAGGGATAGCTTC-GGCTATCGATTATGAAAAAGGATGGTGACGACCATCGATT
* * ** * * * * **
41759297 ATGAAAAGGGAT-GGTGACAACCATCAACTATGAAAAGGGATGGTGACGACCATCGAAA
1 ATGAAAAGGGATAGCT-TCGGCTATCGATTATGAAAAAGGATGGTGACGACCATCGATT
* * * *
41759355 ATGAAAAGGGATAGCTTTGGCTATCGATTATGAAAAAGGATAGCT-TC-AGCTATCGATT
1 ATGAAAAGGGATAGCTTCGGCTATCGATTATGAAAAAGGAT-GGTGACGA-CCATCGATT
* * *
41759413 ATGAAAGGGGATGGCTTCGGCTATCGATTATGAAAAAGGATGGTGACGAGCATCGATT
1 ATGAAAAGGGATAGCTTCGGCTATCGATTATGAAAAAGGATGGTGACGACCATCGATT
41759471 ATGAAAAGGGATAG
1 ATGAAAAGGGATAG
41759485 TGACGACCAT
Statistics
Matches: 143, Mismatches: 38, Indels: 14
0.73 0.19 0.07
Matches are distributed among these distances:
57 5 0.03
58 133 0.93
59 5 0.03
ACGTcount: A:0.36, C:0.12, G:0.28, T:0.24
Consensus pattern (58 bp):
ATGAAAAGGGATAGCTTCGGCTATCGATTATGAAAAAGGATGGTGACGACCATCGATT
Found at i:41759439 original size:87 final size:87
Alignment explanation
Indices: 41759239--41759482 Score: 210
Period size: 87 Copynumber: 2.8 Consensus size: 87
41759229 TCAATGATCA
* * *
41759239 ATGAAAAGGGATAGCTTCAGG-TATCGAATATGGAAAGGGATAGTTTCGACTATCTATTATGAAA
1 ATGAAAAGGGATGGCTTC-GGCTATCGAATATGAAAAGGGATAGTTTCGACTATCGATTATGAAA
* *
41759303 AGGGATGGTGACAACCATCAACT
65 AAGGATGCTGACAACCATCAACT
* * * * *
41759326 ATGAAAAGGGATGG-TGACGACCATCGAAAATGAAAAGGGATAGCTTT-GGCTATCGATTATGAA
1 ATGAAAAGGGATGGCT-TCGGCTATCGAATATGAAAAGGGATAG-TTTCGACTATCGATTATGAA
* * * * *
41759389 AAAGGATAGCT-TCAGCTATCGATT
64 AAAGGAT-GCTGACAACCATCAACT
* * * * **
41759413 ATGAAAGGGGATGGCTTCGGCTATCGATTATGAAAAAGGATGGTGACGAGC-ATCGATTATGAAA
1 ATGAAAAGGGATGGCTTCGGCTATCGAATATGAAAAGGGATAGTTTCGA-CTATCGATTATGAAA
*
41759477 AGGGAT
65 AAGGAT
41759483 AGTGACGACC
Statistics
Matches: 123, Mismatches: 27, Indels: 14
0.75 0.16 0.09
Matches are distributed among these distances:
86 3 0.02
87 113 0.92
88 7 0.06
ACGTcount: A:0.36, C:0.12, G:0.28, T:0.24
Consensus pattern (87 bp):
ATGAAAAGGGATGGCTTCGGCTATCGAATATGAAAAGGGATAGTTTCGACTATCGATTATGAAAA
AGGATGCTGACAACCATCAACT
Found at i:41759445 original size:116 final size:116
Alignment explanation
Indices: 41759238--41759484 Score: 293
Period size: 116 Copynumber: 2.1 Consensus size: 116
41759228 ATCAATGATC
* * * *
41759238 AATGAAAAGGGATAGCTTCAGGTATCGAATATGGAAAGGGATAGTTTCGACTATCTATTATGAAA
1 AATGAAAAGGGATAGCTTCAGGTATCGAATATGAAAAAGGATAGCTTCGACTATCGATTATGAAA
*
41759303 AGGGATGGTGACAACCATCAACTATGAAAAGGGATGGTGACGACCATCGAA
66 AGGGATGGTGACAACCATCAACTATGAAAAAGGATGGTGACGACCATCGAA
* *
41759354 AATGAAAAGGGATAGCTT-TGGCTATCGATTATGAAAAAGGATAGCTTC-AGCTATCGATTATGA
1 AATGAAAAGGGATAGCTTCAGG-TATCGAATATGAAAAAGGATAGCTTCGA-CTATCGATTATGA
* * ** * * * * *
41759417 AAGGGGATGGCT-TCGGCTATCGATTATGAAAAAGGATGGTGACGAGCATCGAT
64 AAAGGGATGG-TGACAACCATCAACTATGAAAAAGGATGGTGACGACCATCGAA
*
41759470 TATGAAAAGGGATAG
1 AATGAAAAGGGATAG
41759485 TGACGACCAT
Statistics
Matches: 111, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
115 3 0.03
116 107 0.96
117 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.28, T:0.24
Consensus pattern (116 bp):
AATGAAAAGGGATAGCTTCAGGTATCGAATATGAAAAAGGATAGCTTCGACTATCGATTATGAAA
AGGGATGGTGACAACCATCAACTATGAAAAAGGATGGTGACGACCATCGAA
Found at i:41759507 original size:30 final size:29
Alignment explanation
Indices: 41759261--41759555 Score: 170
Period size: 29 Copynumber: 10.1 Consensus size: 29
41759251 AGCTTCAGGT
* * ** *
41759261 ATCGAATATGGAAAGGGATAGTTTCGACT
1 ATCGATTATGAAAAGGGATAGTGACGACC
* * *
41759290 ATCTATTATGAAAAGGGATGGTGACAACC
1 ATCGATTATGAAAAGGGATAGTGACGACC
* * *
41759319 ATCAACTATGAAAAGGGATGGTGACGACC
1 ATCGATTATGAAAAGGGATAGTGACGACC
** ** * *
41759348 ATCGAAAATGAAAAGGGATAGCT-TTGGCT
1 ATCGATTATGAAAAGGGATAG-TGACGACC
* * *
41759377 ATCGATTATGAAAAAGGATAGCT-TC-AGCT
1 ATCGATTATGAAAAGGGATAG-TGACGA-CC
* * * * *
41759406 ATCGATTATGAAAGGGGATGGCT-TCGGCT
1 ATCGATTATGAAAAGGGATAG-TGACGACC
* * *
41759435 ATCGATTATGAAAAAGGATGGTGACGAGC
1 ATCGATTATGAAAAGGGATAGTGACGACC
41759464 ATCGATTATGAAAAGGGATAGTGACGACC
1 ATCGATTATGAAAAGGGATAGTGACGACC
* * *
41759493 ATTCG-TTAATGAAAAGGGATGGTTAAGACC
1 A-TCGATT-ATGAAAAGGGATAGTGACGACC
* ** *
41759523 AAT-GAATATGAAAAGGGACGGTTACGACC
1 -ATCGATTATGAAAAGGGATAGTGACGACC
41759552 ATCG
1 ATCG
41759556 TTTAACACAC
Statistics
Matches: 214, Mismatches: 43, Indels: 18
0.78 0.16 0.07
Matches are distributed among these distances:
28 3 0.01
29 185 0.86
30 25 0.12
31 1 0.00
ACGTcount: A:0.36, C:0.13, G:0.27, T:0.23
Consensus pattern (29 bp):
ATCGATTATGAAAAGGGATAGTGACGACC
Found at i:41773187 original size:27 final size:27
Alignment explanation
Indices: 41773156--41773324 Score: 196
Period size: 27 Copynumber: 6.2 Consensus size: 27
41773146 TAAATTGTAC
41773156 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
41773183 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
41773209 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
41773237 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
41773265 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
41773292 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
41773319 AGCACT
1 AGCACT
41773325 GNNNNNNNNN
Statistics
Matches: 121, Mismatches: 18, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
27 98 0.81
28 23 0.19
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:41773270 original size:82 final size:81
Alignment explanation
Indices: 41773157--41773312 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
41773147 AAATTGTACA
* *
41773157 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
41773221 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
41773238 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
41773303 TGCGAGTTGA
65 TGCGAATTGA
41773313 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:41782652 original size:40 final size:40
Alignment explanation
Indices: 41782593--41782820 Score: 411
Period size: 40 Copynumber: 5.7 Consensus size: 40
41782583 NNNNNNNNNN
* *
41782593 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
41782633 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
41782673 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
41782713 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
41782753 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
41782793 ATATGTCCGGGTTAAGACCCGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
41782821 AGGTGTTTGC
Statistics
Matches: 183, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 183 1.00
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
Found at i:41795529 original size:34 final size:34
Alignment explanation
Indices: 41795456--41795542 Score: 95
Period size: 34 Copynumber: 2.6 Consensus size: 34
41795446 TGTACTGAAT
*
41795456 TGGGCTAAGGCCCACACTGATACTATTACCGTAA
1 TGGGCTAAGGCCCACACTGATACTACTACCGTAA
* * * *
41795490 TGGGCTGAGGCCCACACTGATATTGCTACTGTTAA
1 TGGGCTAAGGCCCACACTGATACTACTACCG-TAA
* *
41795525 -GGGCTTAGGCCCAAACTG
1 TGGGCTAAGGCCCACACTG
41795543 TTTGCACTGC
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
34 42 0.93
35 3 0.07
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.24
Consensus pattern (34 bp):
TGGGCTAAGGCCCACACTGATACTACTACCGTAA
Found at i:41804880 original size:22 final size:20
Alignment explanation
Indices: 41804837--41804875 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
41804827 CAATTTAAAA
41804837 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
*
41804857 TATATAAATTTATTAATAT
1 TATAAAAATTTATTAATAT
41804876 ATGTAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:41804998 original size:20 final size:20
Alignment explanation
Indices: 41804973--41805012 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
41804963 AAATATTTTC
41804973 AGTAAATCATTTTCCAGAAA
1 AGTAAATCATTTTCCAGAAA
41804993 AGTAAATCATTTTCCAGAAA
1 AGTAAATCATTTTCCAGAAA
41805013 TCATTTTCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.15, G:0.10, T:0.30
Consensus pattern (20 bp):
AGTAAATCATTTTCCAGAAA
Found at i:41805026 original size:14 final size:14
Alignment explanation
Indices: 41804996--41805038 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
41804986 CCAGAAAAGT
**
41804996 AAATCATTTTCCAG
1 AAATCATTTTCTGG
41805010 AAATCATTTTCTGG
1 AAATCATTTTCTGG
*
41805024 AAAACATTTTACTGG
1 AAATCATTTT-CTGG
41805039 TAAACAAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 21 0.84
15 4 0.16
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (14 bp):
AAATCATTTTCTGG
Found at i:41810632 original size:380 final size:380
Alignment explanation
Indices: 41809911--41810669 Score: 1374
Period size: 380 Copynumber: 2.0 Consensus size: 380
41809901 GCAATCATCG
41809911 AAAATCCCTCGACAAAACGTCTATAATACCCGGCTAAGCCTAAAAAGCTTCTAACCTCGGATACA
1 AAAATCCCTCGACAAAACGTCTATAATACCCGGCTAAGCCTAAAAAGCTTCTAACCTCGGATACA
*
41809976 TTCTTTGGCGGTTTCCAGTCAACGATCGCGGAAATCTTGCTCGGATCCACCCGAATACCATCACC
66 TTCTTTGGCGGTTTCCAATCAACGATCGCGGAAATCTTGCTCGGATCCACCCGAATACCATCACC
41810041 TGAGACTATATGTCCCAAAAATCTGACTTCACGAAGCCAAAACTCACTTTTACTAAACTTAGCAA
131 TGAGACTATATGTCCCAAAAATCTGACTTCACGAAGCCAAAACTCACTTTTACTAAACTTAGCAA
* *
41810106 ACAGTTTCTTTTCTCTCAAGATCTGTAATATGGTTCTCAAGTGTTCGGCATGCTCAGACTCGTCT
196 ACAGTTTCTTTTCTCTCAAGATCTGTAATATGGTTCTCAAGTGTTCGGCATGCTCAGACTCATCC
*
41810171 CGAGAATAAATTAGAATGTCATCTATGAACACTACTACAAAATTATACAAATATGGCAGAAAGAT
261 CGAGAATAAATTAGAATGTCATCTATAAACACTACTACAAAATTATACAAATATGGCAGAAAGAT
*
41810236 TCAATTCATCAAGTCCATAAATATAGCTGGAGCATTTGTTAAGCCAAAAGGCATA
326 CCAATTCATCAAGTCCATAAATATAGCTGGAGCATTTGTTAAGCCAAAAGGCATA
*
41810291 AAAATCTCTCGACAAAACGTCTATAATACCCGGCTAAGCCTAAAAAGCTTCTAACCTCGGATACA
1 AAAATCCCTCGACAAAACGTCTATAATACCCGGCTAAGCCTAAAAAGCTTCTAACCTCGGATACA
* *
41810356 TTCTTTGGCGGTTTCCAATCAACGATCGTGGAAATCTTGCTTGGATCCACCCGAATACCATCACC
66 TTCTTTGGCGGTTTCCAATCAACGATCGCGGAAATCTTGCTCGGATCCACCCGAATACCATCACC
* *
41810421 TGAGACTATATGTCCCAAAAATCTGACTTCACGAAGCTAAAACTCACTTTTACTGAACTTAGCAA
131 TGAGACTATATGTCCCAAAAATCTGACTTCACGAAGCCAAAACTCACTTTTACTAAACTTAGCAA
*
41810486 ACAGTTTCTTTTCTCTCAAGATCTGTAATATGGTTCTCAAGTGTTCGGCATGTTCAGACTCATCC
196 ACAGTTTCTTTTCTCTCAAGATCTGTAATATGGTTCTCAAGTGTTCGGCATGCTCAGACTCATCC
* * *
41810551 CGAGAATAAATTAGAATGTCATCTATAAACACTACTACAAACTTATCCAAATATGGCCGAAAGAT
261 CGAGAATAAATTAGAATGTCATCTATAAACACTACTACAAAATTATACAAATATGGCAGAAAGAT
* *
41810616 CCGATTCATTAAGTCCATAAATATAGCTGGAGCATTTGTTAAGCCAAAAGGCAT
326 CCAATTCATCAAGTCCATAAATATAGCTGGAGCATTTGTTAAGCCAAAAGGCAT
41810670 CACAAGAAAC
Statistics
Matches: 363, Mismatches: 16, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
380 363 1.00
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.28
Consensus pattern (380 bp):
AAAATCCCTCGACAAAACGTCTATAATACCCGGCTAAGCCTAAAAAGCTTCTAACCTCGGATACA
TTCTTTGGCGGTTTCCAATCAACGATCGCGGAAATCTTGCTCGGATCCACCCGAATACCATCACC
TGAGACTATATGTCCCAAAAATCTGACTTCACGAAGCCAAAACTCACTTTTACTAAACTTAGCAA
ACAGTTTCTTTTCTCTCAAGATCTGTAATATGGTTCTCAAGTGTTCGGCATGCTCAGACTCATCC
CGAGAATAAATTAGAATGTCATCTATAAACACTACTACAAAATTATACAAATATGGCAGAAAGAT
CCAATTCATCAAGTCCATAAATATAGCTGGAGCATTTGTTAAGCCAAAAGGCATA
Found at i:41840703 original size:147 final size:147
Alignment explanation
Indices: 41840436--41840724 Score: 472
Period size: 147 Copynumber: 2.0 Consensus size: 147
41840426 CGCTAACAGG
*
41840436 TATAAACCAATTTAAATAAATCCCCATTTAAAGATAAAACTTAAAACGACCGAATTACATAATAT
1 TATAAACCAATTTAAATAAATCCCCAATTAAAGATAAAACTTAAAACGACCGAATTACATAATAT
* ** **
41840501 TTAACCCAAATAAAGCTACCATAATTTAAAGGTCCAGTATGTAATATAGTAGTGGTGTGGCCTTT
66 TTAACCCAAATAAAGCTACCATAATTTAAAGATCCAGTACATAATATAACAGTGGTGTGGCCTTT
41840566 CCCGAGTCCCTCGGTGA
131 CCCGAGTCCCTCGGTGA
* *
41840583 TATAAACCAATTTCAATAAATCCCTAATTAAAGATAAAACTTAAAACGGA-CGAATTACATAATA
1 TATAAACCAATTTAAATAAATCCCCAATTAAAGATAAAACTTAAAAC-GACCGAATTACATAATA
* *
41840647 TTTAACGCATATAAAGCTACCATAATTTAAAGATCCAGTACATAATATAACAGTGGTGTGGCCTT
65 TTTAACCCAAATAAAGCTACCATAATTTAAAGATCCAGTACATAATATAACAGTGGTGTGGCCTT
41840712 TCCCGAGTCCCTC
130 TCCCGAGTCCCTC
41840725 ACAGTACTGA
Statistics
Matches: 131, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
147 129 0.98
148 2 0.02
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.28
Consensus pattern (147 bp):
TATAAACCAATTTAAATAAATCCCCAATTAAAGATAAAACTTAAAACGACCGAATTACATAATAT
TTAACCCAAATAAAGCTACCATAATTTAAAGATCCAGTACATAATATAACAGTGGTGTGGCCTTT
CCCGAGTCCCTCGGTGA
Found at i:41844526 original size:22 final size:23
Alignment explanation
Indices: 41844487--41844529 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
41844477 GAGATTCTAC
*
41844487 CCGTCCATCCTCTACACTCCACT
1 CCGTCCAACCTCTACACTCCACT
41844510 CCGTCCAACC-CTACACTCCA
1 CCGTCCAACCTCTACACTCCA
41844530 TGTGGGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.21, C:0.53, G:0.05, T:0.21
Consensus pattern (23 bp):
CCGTCCAACCTCTACACTCCACT
Found at i:41849417 original size:24 final size:24
Alignment explanation
Indices: 41849371--41849422 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
41849361 CTTATAAAAC
*
41849371 ATTTTAACATTTAATTCACATATA
1 ATTTTAACATTTAATTCAAATATA
* *
41849395 ATTTT-ACATTTCATTGCAAATATT
1 ATTTTAACATTTAATT-CAAATATA
41849419 ATTT
1 ATTT
41849423 AAACTCAAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.37, C:0.12, G:0.02, T:0.50
Consensus pattern (24 bp):
ATTTTAACATTTAATTCAAATATA
Found at i:41852475 original size:39 final size:39
Alignment explanation
Indices: 41852418--41852495 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
41852408 ATACATACAA
*
41852418 CTTTCATATTCCTCAATAAAACATCAAAGAATAAACATG
1 CTTTCATATTCCTCAATAAAACATCAAAAAATAAACATG
*
41852457 CTTTCATATTCCTTAATAAAACATCAAAAAATAAACATG
1 CTTTCATATTCCTCAATAAAACATCAAAAAATAAACATG
41852496 GCACACATGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.47, C:0.19, G:0.04, T:0.29
Consensus pattern (39 bp):
CTTTCATATTCCTCAATAAAACATCAAAAAATAAACATG
Found at i:41858088 original size:40 final size:40
Alignment explanation
Indices: 41858016--41858092 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
41858006 GCTACTCGTT
* *
41858016 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGATTATAGTAACTCACA
*
41858056 CAAATGCCTTCGGGACTTAACCCAGATT-TAGTAACTC
1 CAAATGCCTTCGGGACATAACCC-GATTATAGTAACTC
41858093 GCACCAAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 30 0.91
41 3 0.09
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGATTATAGTAACTCACA
Found at i:41860274 original size:75 final size:75
Alignment explanation
Indices: 41860151--41860294 Score: 288
Period size: 75 Copynumber: 1.9 Consensus size: 75
41860141 TTTTCGTACT
41860151 CCCCGGGTGAATTGACATTCGGCTACAATGGGCTTCGTTCAGAATCATCGAAATGAGTTTCGAAT
1 CCCCGGGTGAATTGACATTCGGCTACAATGGGCTTCGTTCAGAATCATCGAAATGAGTTTCGAAT
41860216 TCCTCGTTCG
66 TCCTCGTTCG
41860226 CCCCGGGTGAATTGACATTCGGCTACAATGGGCTTCGTTCAGAATCATCGAAATGAGTTTCGAAT
1 CCCCGGGTGAATTGACATTCGGCTACAATGGGCTTCGTTCAGAATCATCGAAATGAGTTTCGAAT
41860291 TCCT
66 TCCT
41860295 TGGAACACAC
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 69 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (75 bp):
CCCCGGGTGAATTGACATTCGGCTACAATGGGCTTCGTTCAGAATCATCGAAATGAGTTTCGAAT
TCCTCGTTCG
Found at i:41861199 original size:74 final size:74
Alignment explanation
Indices: 41861063--41861214 Score: 232
Period size: 74 Copynumber: 2.1 Consensus size: 74
41861053 CCAGGAAGCT
* * * * *
41861063 CCGAACTTCGGTAATATTTCTTGGATGCTTCCAGTTAAGTATGGCTGAAATTTTGCTCGGGTCAA
1 CCGAACTTCAGTAACATTTCTCGGAGGCTTCCAGTCAAGTATGGCTGAAATTTTGCTCGGGTCAA
41861128 CTCGAATAC
66 CTCGAATAC
* * *
41861137 CCGATCTTCAGTAACATTTCTCGGAGGTTTCCAGTCAAGTATGGCTGAAATTTTGTTCGGGTCAA
1 CCGAACTTCAGTAACATTTCTCGGAGGCTTCCAGTCAAGTATGGCTGAAATTTTGCTCGGGTCAA
41861202 CTCGAATAC
66 CTCGAATAC
41861211 CCGA
1 CCGA
41861215 CGCGGATACC
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
74 70 1.00
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (74 bp):
CCGAACTTCAGTAACATTTCTCGGAGGCTTCCAGTCAAGTATGGCTGAAATTTTGCTCGGGTCAA
CTCGAATAC
Found at i:41865253 original size:40 final size:40
Alignment explanation
Indices: 41865216--41865507 Score: 498
Period size: 40 Copynumber: 7.3 Consensus size: 40
41865206 GCTACTCGTT
* *
41865216 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
41865256 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
41865296 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
41865336 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
41865376 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
41865416 CAAATGCCTTCGGGACTTAACGCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
41865456 CAAATGGCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
41865495 CAAATGCCTTCGG
1 CAAATGCCTTCGG
41865508 ATCTTAGTCC
Statistics
Matches: 242, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
39 33 0.14
40 207 0.86
41 2 0.01
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:41865537 original size:80 final size:80
Alignment explanation
Indices: 41865216--41865558 Score: 505
Period size: 80 Copynumber: 4.3 Consensus size: 80
41865206 GCTACTCGTT
*
41865216 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
41865280 GATTTAGTAACTCGCA
65 GATTTAGTAACTCGCA
*
41865296 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
41865361 ATTTAGTAACTCGCA
66 ATTTAGTAACTCGCA
* *
41865376 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACGCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
41865441 ATTTAGTAACTCGCA
66 ATTTAGTAACTCGCA
* * * ** *
41865456 CAAATGGCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCG
* * * *
41865519 GATATGGTCACTTAGCA
65 GATTTAGTAAC-TCGCA
41865536 CAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCG
41865559 AACATCATTC
Statistics
Matches: 243, Mismatches: 16, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
78 3 0.01
79 54 0.22
80 184 0.76
81 2 0.01
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.25
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATTTAGTAACTCGCA
Found at i:41873238 original size:39 final size:39
Alignment explanation
Indices: 41873074--41873256 Score: 170
Period size: 40 Copynumber: 4.6 Consensus size: 39
41873064 TTGAATGCTG
* * * * * * *
41873074 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTATGTCCCGAAGGCATTGTGC-GAGTTACTAAA
* * * *
41873114 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTATG-TCCCGAAGG-CATTGTGCGAGTTACTAAA
* **
41873154 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTATGTCCCGAAGGCATT-GTGCGAGTTACTAAA
*
41873194 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTATGTCCCGAAGGCATTGTGCGAGTTACTAAA
* *
41873233 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTATGTCCCGAAGGCATT
41873257 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
39 38 0.31
40 74 0.61
41 9 0.07
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (39 bp):
TCCGGGTTATGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:41873276 original size:79 final size:80
Alignment explanation
Indices: 41873110--41873291 Score: 190
Period size: 79 Copynumber: 2.3 Consensus size: 80
41873100 GCTAAGTGAA
* * * *
41873110 TATATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGG
1 TATATCCGGGTTAAG-TCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGG
** ** *
41873174 CATTCGTGCGAGTTGT
65 CATTCGAACGAGGAGC
* * * * *
41873190 TAAATCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGC
1 TATATCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGC
*
41873254 ATTTGAACGAGGAGC
66 ATTCGAACGAGGAGC
*
41873269 TATATCC-GGTTAAATCCCGAAGG
1 TATATCCGGGTTAAGTCCCGAAGG
41873292 TACGTGATTT
Statistics
Matches: 83, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
78 14 0.17
79 50 0.60
80 19 0.23
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.26
Consensus pattern (80 bp):
TATATCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGC
ATTCGAACGAGGAGC
Found at i:41887975 original size:40 final size:40
Alignment explanation
Indices: 41886999--41887974 Score: 1803
Period size: 40 Copynumber: 24.4 Consensus size: 40
41886989 AGCCCAAGTA
* * *
41886999 CCTTCGGGATTTAG-CCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
* *
41887038 CCTTCGGGACCTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
* *
41887078 CCTTCGGGACCTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
* *
41887118 CCTTCGGGACCTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
41887158 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
41887198 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
41887238 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
41887278 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
41887318 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
41887358 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
41887398 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
41887438 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
41887478 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
41887518 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
41887558 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
41887598 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
41887638 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
41887678 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
41887718 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
41887758 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
41887798 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
41887838 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
*
41887878 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
* * * *
41887918 CCATCGGGACTTAGCCC-GAAATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCAGATA-TAGTAACTCGCACAAATG
41887958 CCTTCGGGACTTAGCCC
1 CCTTCGGGACTTAGCCC
41887975 GGTTGTCATC
Statistics
Matches: 924, Mismatches: 11, Indels: 3
0.99 0.01 0.00
Matches are distributed among these distances:
39 15 0.02
40 909 0.98
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
Found at i:41895825 original size:40 final size:40
Alignment explanation
Indices: 41895638--41895818 Score: 181
Period size: 40 Copynumber: 4.5 Consensus size: 40
41895628 ATGATGTCCA
* * * *
41895638 GGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCG
* * * * *
41895678 GACTAAGAT-ACGAAGGTATTTGTGTGAGTTACTAATTCCG
1 GGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAATCCG
* * *
41895718 GGCTAAG-CCGGAAGGCATTGGTGCGAGTTACTAAATCTG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCG
*
41895757 GGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATCCG
*
41895797 GGCTATGTCCCGAAGGCATTTG
1 GGCTAAGTCCCGAAGGCATTTG
41895819 AACGAGTAGC
Statistics
Matches: 113, Mismatches: 23, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
39 30 0.27
40 74 0.65
41 9 0.08
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (40 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCG
Found at i:41895840 original size:79 final size:79
Alignment explanation
Indices: 41895688--41895841 Score: 170
Period size: 79 Copynumber: 1.9 Consensus size: 79
41895678 GACTAAGATA
* * * * **
41895688 CGAAGGTATTTGTGTGAGTTACTAATTCCGGGCTAAGCCGGAAGGCATTGGTGCGAGTTACTAAA
1 CGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAA
*
41895753 TCTGGGTTAAGTCC
66 TCTCGGTTAAGTCC
* *
41895767 CGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCT
1 CGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-CT
*
41895830 ATATC-CGGTTAA
63 AAATCTCGGTTAA
41895842 ATTTCGAAGG
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
78 2 0.03
79 38 0.61
80 22 0.35
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (79 bp):
CGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAA
TCTCGGTTAAGTCC
Found at i:41899333 original size:49 final size:47
Alignment explanation
Indices: 41899220--41899777 Score: 864
Period size: 49 Copynumber: 11.6 Consensus size: 47
41899210 TATTTGAATA
** *
41899220 AATGTGAAAGTGTATATATGTGATAAGGCCTAACGGCCGATGCGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
41899267 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
41899314 AATGTGAAAGTGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAA--GTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
41899363 AATGTGAAAGTGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAA--GTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
41899412 AATGTGAAAGTGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAA--GTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
41899461 AATGTGAAAGTGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAA--GTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
41899510 AATGTGAAAGTGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAA--GTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
41899559 AATGTGAAAGTGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAA--GTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
41899608 AATGTGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AA--TGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
**
41899657 AATGTGAAAGTGTATATATGTGATAAGGCCTAACGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
* * * * * * *
41899704 AATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
* *
41899751 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
41899778 TCCCGAAGGA
Statistics
Matches: 491, Mismatches: 16, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
47 159 0.32
49 325 0.66
51 7 0.01
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
Found at i:41899997 original size:37 final size:37
Alignment explanation
Indices: 41899896--41899997 Score: 177
Period size: 37 Copynumber: 2.8 Consensus size: 37
41899886 CCGAGCTCTA
*
41899896 AAGACCCGATGACTACGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGT
41899933 AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGT
1 AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGT
* *
41899970 AAGACCCGATAACTTCGTGTGGAGATTT
1 AAGACCCGATGACTACGTGTGGAGATTT
41899998 CGTCTGAGCT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 62 1.00
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (37 bp):
AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGT
Found at i:41903622 original size:92 final size:92
Alignment explanation
Indices: 41903465--41903648 Score: 359
Period size: 92 Copynumber: 2.0 Consensus size: 92
41903455 CTTGCGTATG
41903465 TACTTGATGACAAAGAATTAGAAAAGAAACCCGAATCTGTGCCGGTGGTTTGTGAATACCCGGAT
1 TACTTGATGACAAAGAATTAGAAAAGAAACCCGAATCTGTGCCGGTGGTTTGTGAATACCCGGAT
*
41903530 GTTTTTCCTGAAGAATTACCGGGTTTA
66 GTTTTTCCGGAAGAATTACCGGGTTTA
41903557 TACTTGATGACAAAGAATTAGAAAAGAAACCCGAATCTGTGCCGGTGGTTTGTGAATACCCGGAT
1 TACTTGATGACAAAGAATTAGAAAAGAAACCCGAATCTGTGCCGGTGGTTTGTGAATACCCGGAT
41903622 GTTTTTCCGGAAGAATTACCGGGTTTA
66 GTTTTTCCGGAAGAATTACCGGGTTTA
41903649 CCACCTGTTC
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
92 91 1.00
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.29
Consensus pattern (92 bp):
TACTTGATGACAAAGAATTAGAAAAGAAACCCGAATCTGTGCCGGTGGTTTGTGAATACCCGGAT
GTTTTTCCGGAAGAATTACCGGGTTTA
Found at i:41909850 original size:15 final size:16
Alignment explanation
Indices: 41909814--41909843 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
41909804 ACATATCATT
41909814 TATTTCATTATATCAA
1 TATTTCATTATATCAA
41909830 TATTTCA-TATATCA
1 TATTTCATTATATCA
41909844 TAGTTTCCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (16 bp):
TATTTCATTATATCAA
Found at i:41912107 original size:43 final size:42
Alignment explanation
Indices: 41912055--41912310 Score: 206
Period size: 43 Copynumber: 6.0 Consensus size: 42
41912045 TTATAAAAAC
* * *
41912055 GCCGCTAAAGATCGTGTTCTTTAGCGGCATTTGTAGGCAAAGT
1 GCCGCTAAAGGTCGTGTTCTTTAGTGGCATTTGT-GGAAAAGT
* *
41912098 GTCGCTAAAGGTCGTGTTCTTTAGTGGTATTTGTGGAAAAGT
1 GCCGCTAAAGGTCGTGTTCTTTAGTGGCATTTGTGGAAAAGT
* * * *
41912140 GCCGCTAAAGGTCATTTTATTTAGTGGCATTTGTGGAAGAAGC
1 GCCGCTAAAGGTCGTGTTCTTTAGTGGCATTTGTGGAA-AAGT
* * * * * * * *
41912183 GCCACTAAAGGTCATGATCTATAGTAGCGTTTGGAGGAAAAGC
1 GCCGCTAAAGGTCGTGTTCTTTAGTGGCATTT-GTGGAAAAGT
* * * * * *
41912226 GCTGCTAAATGTCATGTTCTATAGCGGCGTTTGTGGGAAAAGT
1 GCCGCTAAAGGTCGTGTTCTTTAGTGGCATTTGT-GGAAAAGT
* * * * * *
41912269 GCCGCTAAAAGTCATGGTCTATATTGGCATTTTTGTGAAAAG
1 GCCGCTAAAGGTCGTGTTCTTTAGTGGCATTTGTG-GAAAAG
41912311 CACCATTAAA
Statistics
Matches: 175, Mismatches: 34, Indels: 8
0.81 0.16 0.04
Matches are distributed among these distances:
42 42 0.24
43 128 0.73
44 5 0.03
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.32
Consensus pattern (42 bp):
GCCGCTAAAGGTCGTGTTCTTTAGTGGCATTTGTGGAAAAGT
Found at i:41912309 original size:86 final size:84
Alignment explanation
Indices: 41912049--41912343 Score: 257
Period size: 86 Copynumber: 3.5 Consensus size: 84
41912039 ACACTTTTAT
* * * * * * *
41912049 AAAAACGCCGCTAAAGATCGTGTTCTTTAGCGGCATTTGTAGGCAAAGTGTCGCTAAAGGTCGTG
1 AAAAGCGCCGCTAAAGGTCATGTTCTATAGCGGCATTTGT-GGAAAAGTGCCGCTAAAGGTCATG
* * * *
41912114 TTCTTTAGTGGTATTTGTGG
65 ATCTATAGTGGCATTTTTGG
* * * * * * *
41912134 AAAAGTGCCGCTAAAGGTCATTTTATTTAGTGGCATTTGTGGAAGAAGCGCCACTAAAGGTCATG
1 AAAAGCGCCGCTAAAGGTCATGTTCTATAGCGGCATTTGTGGAA-AAGTGCCGCTAAAGGTCATG
* * **
41912199 ATCTATAGTAGCGTTTGGAGG
65 ATCTATAGTGGCATTT-TTGG
* * * *
41912220 AAAAGCGCTGCTAAATGTCATGTTCTATAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAAGTCATG
1 AAAAGCGCCGCTAAAGGTCATGTTCTATAGCGGCATTTGT-GGAAAAGTGCCGCTAAAGGTCATG
* *
41912285 GTCTATATTGGCATTTTTGTG
65 ATCTATAGTGGCATTTTTG-G
* ** *
41912306 AAAAGCACCATTAAAGGTCAAGTTCTATAGCGGCATTT
1 AAAAGCGCCGCTAAAGGTCATGTTCTATAGCGGCATTT
41912344 TTCCACAAAA
Statistics
Matches: 164, Mismatches: 42, Indels: 7
0.77 0.20 0.03
Matches are distributed among these distances:
84 3 0.02
85 61 0.37
86 96 0.59
87 4 0.02
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.31
Consensus pattern (84 bp):
AAAAGCGCCGCTAAAGGTCATGTTCTATAGCGGCATTTGTGGAAAAGTGCCGCTAAAGGTCATGA
TCTATAGTGGCATTTTTGG
Found at i:41916913 original size:35 final size:36
Alignment explanation
Indices: 41916852--41916919 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 36
41916842 TGAAAGAGAA
* ** *
41916852 TATGTGGGTATGTTATTCATGTCATGTGACAGTAAG
1 TATGTGAGTATGTTATTCATACCATGTAACAGTAAG
41916888 TATGTGAGTATGTT-TTCATACCATGTAACAGT
1 TATGTGAGTATGTTATTCATACCATGTAACAGT
41916920 GATTATAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 15 0.54
36 13 0.46
ACGTcount: A:0.26, C:0.10, G:0.24, T:0.40
Consensus pattern (36 bp):
TATGTGAGTATGTTATTCATACCATGTAACAGTAAG
Found at i:41918202 original size:12 final size:12
Alignment explanation
Indices: 41918187--41918211 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41918177 AGTTTAGTAC
41918187 TTATTTTATGAT
1 TTATTTTATGAT
41918199 TTATTTTATGAT
1 TTATTTTATGAT
41918211 T
1 T
41918212 AATGAATGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (12 bp):
TTATTTTATGAT
Found at i:41918913 original size:12 final size:12
Alignment explanation
Indices: 41918898--41918922 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41918888 AGTTTAGTAC
41918898 TTATTTTATGAT
1 TTATTTTATGAT
41918910 TTATTTTATGAT
1 TTATTTTATGAT
41918922 T
1 T
41918923 AATGAATGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (12 bp):
TTATTTTATGAT
Found at i:41921657 original size:12 final size:12
Alignment explanation
Indices: 41921640--41921667 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
41921630 TCAACTCACC
41921640 CAAACTTATTTT
1 CAAACTTATTTT
41921652 CAAACTTATTTT
1 CAAACTTATTTT
41921664 CAAA
1 CAAA
41921668 GAACATTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.39, C:0.18, G:0.00, T:0.43
Consensus pattern (12 bp):
CAAACTTATTTT
Found at i:41924160 original size:46 final size:46
Alignment explanation
Indices: 41924091--41924182 Score: 125
Period size: 46 Copynumber: 2.0 Consensus size: 46
41924081 AGACTCACCA
*
41924091 CAGCTCATATGAGCTTACCGATTCAGCTTG-TAAGAGCTTACCGTTT
1 CAGCTCATATGAGCTTACCGATTCAGCTCGAT-AGAGCTTACCGTTT
* *
41924137 CAGCTCAT-TGGAGCTTACTGATTCAGCTCGATAGAGCTTACTGTTT
1 CAGCTCATAT-GAGCTTACCGATTCAGCTCGATAGAGCTTACCGTTT
41924183 TTCAGCTCGG
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
45 1 0.02
46 39 0.95
47 1 0.02
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.34
Consensus pattern (46 bp):
CAGCTCATATGAGCTTACCGATTCAGCTCGATAGAGCTTACCGTTT
Found at i:41924179 original size:23 final size:22
Alignment explanation
Indices: 41924091--41924177 Score: 93
Period size: 23 Copynumber: 3.8 Consensus size: 22
41924081 AGACTCACCA
41924091 CAGCTCATATGAGCTTACCGATT
1 CAGCTCATA-GAGCTTACCGATT
** *
41924114 CAGCTTGTAAGAGCTTACCGTTT
1 CAGCTCAT-AGAGCTTACCGATT
* *
41924137 CAGCTCATTGGAGCTTACTGATT
1 CAGCTCA-TAGAGCTTACCGATT
41924160 CAGCTCGATAGAGCTTAC
1 CAGCTC-ATAGAGCTTAC
41924178 TGTTTTTCAG
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
23 49 0.94
24 3 0.06
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (22 bp):
CAGCTCATAGAGCTTACCGATT
Found at i:41924395 original size:20 final size:20
Alignment explanation
Indices: 41924370--41924408 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
41924360 ATTGATAAAT
*
41924370 TACTGGTTATATGGATGAAC
1 TACTGGTTATATGAATGAAC
41924390 TACTGGTTATATGAATGAA
1 TACTGGTTATATGAATGAA
41924409 TTACAGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.08, G:0.23, T:0.36
Consensus pattern (20 bp):
TACTGGTTATATGAATGAAC
Done.