Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 19 of 172
Found at i:6079111 original size:15 final size:15
Alignment explanation
Indices: 6079091--6079119 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
6079081 GTGGGTCCGT
6079091 TTACTAGGACTTTTG
1 TTACTAGGACTTTTG
6079106 TTACTAGGACTTTT
1 TTACTAGGACTTTT
6079120 TAACAAATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.17, T:0.48
Consensus pattern (15 bp):
TTACTAGGACTTTTG
Found at i:6080943 original size:21 final size:21
Alignment explanation
Indices: 6080898--6080960 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
6080888 TTTGAACCAT
* *
6080898 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
6080920 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
6080941 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
6080961 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 24 0.65
22 13 0.35
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:6083468 original size:9 final size:9
Alignment explanation
Indices: 6083439--6083475 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
6083429 TGAGTTTTCG
6083439 AATTCGAAT
1 AATTCGAAT
*
6083448 AACTCGAAT
1 AATTCGAAT
6083457 AATTCGAAT
1 AATTCGAAT
*
6083466 AATTTGAAT
1 AATTCGAAT
6083475 A
1 A
6083476 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:6086010 original size:36 final size:35
Alignment explanation
Indices: 6085931--6086014 Score: 93
Period size: 36 Copynumber: 2.4 Consensus size: 35
6085921 TATCTACAAG
6085931 ATAAAC-ATTAAATTAAATTTAATATTAAATTAAT
1 ATAAACTATTAAATTAAATTTAATATTAAATTAAT
* *
6085965 AAAATACTATTAAGA-TAAGTTTAA-ATTAAATTTAAT
1 ATAA-ACTATTAA-ATTAAATTTAATATTAAA-TTAAT
6086001 ATTAAACTATTAAA
1 A-TAAACTATTAAA
6086015 ATGATATTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
34 3 0.07
35 9 0.21
36 27 0.64
37 3 0.07
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (35 bp):
ATAAACTATTAAATTAAATTTAATATTAAATTAAT
Found at i:6089309 original size:16 final size:15
Alignment explanation
Indices: 6089290--6089343 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 15
6089280 ACCAAAATTG
6089290 TTAATTAAGCTTAAGT
1 TTAATTAA-CTTAAGT
*
6089306 TTAATTAAACTT-AGG
1 TTAATT-AACTTAAGT
6089321 TTAATTAACTTAA-T
1 TTAATTAACTTAAGT
6089335 TATAATTAA
1 T-TAATTAA
6089344 TAACCAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
14 6 0.18
15 16 0.48
16 9 0.27
17 2 0.06
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.44
Consensus pattern (15 bp):
TTAATTAACTTAAGT
Found at i:6089326 original size:15 final size:15
Alignment explanation
Indices: 6089289--6089332 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
6089279 CACCAAAATT
*
6089289 GTTAATTAAGCTTAAG
1 GTTAATTAAACTT-AG
*
6089305 TTTAATTAAACTTAG
1 GTTAATTAAACTTAG
6089320 GTTAATT-AACTTA
1 GTTAATTAAACTTA
6089333 ATTATAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 6 0.24
15 8 0.32
16 11 0.44
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.43
Consensus pattern (15 bp):
GTTAATTAAACTTAG
Found at i:6089580 original size:13 final size:13
Alignment explanation
Indices: 6089562--6089586 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6089552 ATTTTGCAAA
6089562 ATTGTTGGTTTCC
1 ATTGTTGGTTTCC
6089575 ATTGTTGGTTTC
1 ATTGTTGGTTTC
6089587 TTGACACTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.12, G:0.24, T:0.56
Consensus pattern (13 bp):
ATTGTTGGTTTCC
Found at i:6091277 original size:27 final size:27
Alignment explanation
Indices: 6091238--6091301 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 27
6091228 TCGTAAGTGA
* * *
6091238 GGGTTCACTAGTATTTTGACGAACTAG
1 GGGTTCACCAGTACTTTGACAAACTAG
* * *
6091265 GGGTTTACCAGTACTTTGGCAAACTGG
1 GGGTTCACCAGTACTTTGACAAACTAG
6091292 GGGTTCACCA
1 GGGTTCACCA
6091302 AAAGGACATC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (27 bp):
GGGTTCACCAGTACTTTGACAAACTAG
Found at i:6092148 original size:14 final size:14
Alignment explanation
Indices: 6092126--6092177 Score: 61
Period size: 14 Copynumber: 3.7 Consensus size: 14
6092116 TATGCGAGCC
* *
6092126 TATGATTTTAAAGA
1 TATGTTTTTAAAAA
6092140 TATGTTTTTAAAAA
1 TATGTTTTTAAAAA
*
6092154 TATGGTTTTAAAAA
1 TATGTTTTTAAAAA
6092168 T-TGTGTTTTA
1 TATGT-TTTTA
6092178 CAAGATTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
13 2 0.06
14 31 0.94
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (14 bp):
TATGTTTTTAAAAA
Found at i:6092554 original size:6 final size:6
Alignment explanation
Indices: 6092545--6092577 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
6092535 TAGTGTGTAT
6092545 AAGAAC AAGAAC AAGAAC AAGAAC AAGAAC AAG
1 AAGAAC AAGAAC AAGAAC AAGAAC AAGAAC AAG
6092578 CATAAGTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.67, C:0.15, G:0.18, T:0.00
Consensus pattern (6 bp):
AAGAAC
Found at i:6100336 original size:74 final size:74
Alignment explanation
Indices: 6100240--6100421 Score: 249
Period size: 74 Copynumber: 2.5 Consensus size: 74
6100230 ACGAAAGTTG
* *
6100240 CGCCCAGCGCTAGTCGGATAAACCGACGAATAATTAGTGAGCGCAGCTCTAGTTGAATATACCGA
1 CGCCCAGCGCTAGTCGGATAAACCGACGAATAAATAGTGAGCCCAGCTCTAGTTGAATATACC-A
*
6100305 A-GGTATTTA
65 ATGATATTTA
* * * * *
6100314 CGCCCAACGCTAGTTGGATAAACCAACGAATAAATAGTGAGCCCAGCTCTAGTTGGATTTACCAA
1 CGCCCAGCGCTAGTCGGATAAACCGACGAATAAATAGTGAGCCCAGCTCTAGTTGAATATACCAA
*
6100379 TGATATTTG
66 TGATATTTA
* *
6100388 TGCCCAGCGGTAGTCGGATAAACCGACGAATAAA
1 CGCCCAGCGCTAGTCGGATAAACCGACGAATAAA
6100422 CAATTATTTA
Statistics
Matches: 93, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
73 2 0.02
74 91 0.98
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.23
Consensus pattern (74 bp):
CGCCCAGCGCTAGTCGGATAAACCGACGAATAAATAGTGAGCCCAGCTCTAGTTGAATATACCAA
TGATATTTA
Found at i:6100369 original size:39 final size:39
Alignment explanation
Indices: 6100241--6100421 Score: 103
Period size: 35 Copynumber: 4.8 Consensus size: 39
6100231 CGAAAGTTGC
* * *
6100241 GCCCAGCGCTAGTCGGATAAACCGACGAATAATTAGTGA
1 GCCCAGCGCTAGTTGGATAAACCAACGAATAAATAGTGA
* * * * * *
6100280 GCGCAGCTCTAGTTGAATATACCGAA-G-GT--AT--TTA
1 GCCCAGCGCTAGTTGGATAAACC-AACGAATAAATAGTGA
*
6100314 CGCCCAACGCTAGTTGGATAAACCAACGAATAAATAGTGA
1 -GCCCAGCGCTAGTTGGATAAACCAACGAATAAATAGTGA
* ** * * *
6100354 GCCCAGCTCTAGTTGGATTTACCAATG-AT--AT-TTGT
1 GCCCAGCGCTAGTTGGATAAACCAACGAATAAATAGTGA
* * *
6100389 GCCCAGCGGTAGTCGGATAAACCGACGAATAAA
1 GCCCAGCGCTAGTTGGATAAACCAACGAATAAA
6100422 CAATTATTTA
Statistics
Matches: 101, Mismatches: 30, Indels: 23
0.66 0.19 0.15
Matches are distributed among these distances:
34 4 0.04
35 41 0.41
36 6 0.06
38 6 0.06
39 41 0.41
40 3 0.03
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.23
Consensus pattern (39 bp):
GCCCAGCGCTAGTTGGATAAACCAACGAATAAATAGTGA
Found at i:6105895 original size:27 final size:26
Alignment explanation
Indices: 6105863--6105913 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 26
6105853 AATTTCAAGA
6105863 TAATTAGATATATAAATTTAT-TGTTTT
1 TAATTA-AT-TATAAATTTATATGTTTT
*
6105890 TAATTAATTATATATTTATATGTT
1 TAATTAATTATAAATTTATATGTT
6105914 ATAAAAATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 10 0.45
26 6 0.27
27 6 0.27
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (26 bp):
TAATTAATTATAAATTTATATGTTTT
Found at i:6110062 original size:42 final size:42
Alignment explanation
Indices: 6110013--6110109 Score: 158
Period size: 42 Copynumber: 2.3 Consensus size: 42
6110003 CTCGGTATCG
* *
6110013 CACACTTAGTGCCCGTTATTCAACATCATCATTTTAATTTCA
1 CACACTTAGTGCCCATTATCCAACATCATCATTTTAATTTCA
* *
6110055 CACACTTAGTGCCCATTATCCAACATCATTATTTTAATTTCG
1 CACACTTAGTGCCCATTATCCAACATCATCATTTTAATTTCA
6110097 CACACTTAGTGCC
1 CACACTTAGTGCC
6110110 GTTCATATAG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.28, C:0.28, G:0.08, T:0.36
Consensus pattern (42 bp):
CACACTTAGTGCCCATTATCCAACATCATCATTTTAATTTCA
Found at i:6111010 original size:16 final size:17
Alignment explanation
Indices: 6110977--6111010 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
6110967 CATAAAGTTA
*
6110977 ATATTTACCTTATTACT
1 ATATTAACCTTATTACT
6110994 ATATTAACCTT-TTACT
1 ATATTAACCTTATTACT
6111010 A
1 A
6111011 ATAATTATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATTAACCTTATTACT
Found at i:6112444 original size:49 final size:49
Alignment explanation
Indices: 6112343--6112469 Score: 132
Period size: 49 Copynumber: 2.6 Consensus size: 49
6112333 AGGTAGAAAA
* * *
6112343 CCATCGTTGTCGAGCTATTCTGGATGATAGAATGTATATATAGTGAGAG
1 CCATCGTTGTCGAGCTATTCAGGATGATAGAATATATAGATAGTGAGAG
* * * *
6112392 CCATTGTTGTTGAGCTATTCAGGATGGTAGAATA-ATTAGATATTGA-ATG
1 CCATCGTTGTCGAGCTATTCAGGATGATAGAATATA-TAGATAGTGAGA-G
* * *
6112441 CCATCGTTGTCGAGCCATCCGGGATGATA
1 CCATCGTTGTCGAGCTATTCAGGATGATA
6112470 AAATGTAAGA
Statistics
Matches: 63, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
48 2 0.03
49 61 0.97
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (49 bp):
CCATCGTTGTCGAGCTATTCAGGATGATAGAATATATAGATAGTGAGAG
Found at i:6114074 original size:18 final size:15
Alignment explanation
Indices: 6114035--6114069 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
6114025 GACTCTATTT
6114035 TAATT-ATATTAAGA
1 TAATTAATATTAAGA
6114049 TAATTAATATTAAGA
1 TAATTAATATTAAGA
6114064 TAATTA
1 TAATTA
6114070 TTAATGATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:6117704 original size:37 final size:37
Alignment explanation
Indices: 6117663--6117757 Score: 102
Period size: 37 Copynumber: 2.6 Consensus size: 37
6117653 TAAATATTAG
* *
6117663 TCAGTATAACAGTAAGATTTGCTTAGTTAAG-CTCTAT
1 TCAGTATAACAGTAAGATTTGCTCAATTAAGTCTC-AT
** * *
6117700 TCAGTATAACAGTTTGATTTGCTCAATTGAGTTTCAT
1 TCAGTATAACAGTAAGATTTGCTCAATTAAGTCTCAT
* *
6117737 TTAGTATAACAATAAGATTTG
1 TCAGTATAACAGTAAGATTTG
6117758 GCTCGATAGC
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
37 45 0.96
38 2 0.04
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.40
Consensus pattern (37 bp):
TCAGTATAACAGTAAGATTTGCTCAATTAAGTCTCAT
Found at i:6131479 original size:28 final size:28
Alignment explanation
Indices: 6131436--6131502 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
6131426 TAAACTAATG
*
6131436 AGCTCACCACTTACTACTCATTTGAGGT
1 AGCTCACCACTCACTACTCATTTGAGGT
*
6131464 AGCTCACCACTCACTATTCATTTGAGGT
1 AGCTCACCACTCACTACTCATTTGAGGT
*
6131492 TGCTCACCACT
1 AGCTCACCACT
6131503 TACTGTGAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.24, C:0.31, G:0.13, T:0.31
Consensus pattern (28 bp):
AGCTCACCACTCACTACTCATTTGAGGT
Found at i:6131534 original size:18 final size:18
Alignment explanation
Indices: 6131511--6131555 Score: 74
Period size: 18 Copynumber: 2.5 Consensus size: 18
6131501 CTTACTGTGA
6131511 GTTCGCCAATCTTAGG-GG
1 GTTCGCCAATCTT-GGAGG
6131529 GTTCGCCAATCTTGGAGG
1 GTTCGCCAATCTTGGAGG
6131547 GTTCGCCAA
1 GTTCGCCAA
6131556 ATGTTGCATG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 2 0.08
18 24 0.92
ACGTcount: A:0.18, C:0.24, G:0.31, T:0.27
Consensus pattern (18 bp):
GTTCGCCAATCTTGGAGG
Found at i:6134031 original size:66 final size:66
Alignment explanation
Indices: 6133894--6134040 Score: 197
Period size: 66 Copynumber: 2.2 Consensus size: 66
6133884 CGAAACATAT
* * * *
6133894 TTGGTGTGTTGGAGAGTGTTAGCTTTATGCTTCACTTTTTGGGATATGTTCGACTTTATGACTCA
1 TTGGTGTGTTGGAGAGTGTTAGCTTTATGCTTCACTTTATGGAACATGTTCGACTCTATGACTCA
6133959 A
66 A
* * * *
6133960 TTGGTGTGTTGGAGAGTGTTAGTTTTATGCTTCAC-TTATGGAACATGTTTGACTCTATGAGTCT
1 TTGGTGTGTTGGAGAGTGTTAGCTTTATGCTTCACTTTATGGAACATGTTCGACTCTATGACTCA
6134024 A
66 A
*
6134025 TCTGGTGTGATGGAGA
1 T-TGGTGTGTTGGAGA
6134041 TCCGTGTATC
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
65 24 0.34
66 47 0.66
ACGTcount: A:0.19, C:0.11, G:0.28, T:0.42
Consensus pattern (66 bp):
TTGGTGTGTTGGAGAGTGTTAGCTTTATGCTTCACTTTATGGAACATGTTCGACTCTATGACTCA
A
Found at i:6136723 original size:18 final size:18
Alignment explanation
Indices: 6136700--6136736 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
6136690 TTGCATTGCT
6136700 TACTCTACTACTC-CTCTC
1 TACTCT-CTACTCTCTCTC
6136718 TACTCTCTACTCTCTCTC
1 TACTCTCTACTCTCTCTC
6136736 T
1 T
6136737 TTTTTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.14, C:0.43, G:0.00, T:0.43
Consensus pattern (18 bp):
TACTCTCTACTCTCTCTC
Found at i:6146275 original size:48 final size:48
Alignment explanation
Indices: 6146185--6146381 Score: 198
Period size: 48 Copynumber: 4.1 Consensus size: 48
6146175 AATAGATTTC
* * * * *
6146185 TCGGTGGCCTGCACACAGTCCGTACCACCTTTGTGTAATAACAGATTC
1 TCGGTGGCCTACACACAGTCCGTGCCACCCTTGTGTCATAACAGATTA
* ** *
6146233 TCGGTGGCCTACACATAGTCCGTGCCACCCTTGTACCTTAACA-AGTTA
1 TCGGTGGCCTACACACAGTCCGTGCCACCCTTGTGTCATAACAGA-TTA
** * * * * * * *
6146281 TTAGTGACCTACACACTGGCTGTGCCACCCTTGTGTCACAATAGAATA
1 TCGGTGGCCTACACACAGTCCGTGCCACCCTTGTGTCATAACAGATTA
* *
6146329 TCGGTGGCCTGCACACAGTCCATGCCACCCTTGTGTCATAACAGATTA
1 TCGGTGGCCTACACACAGTCCGTGCCACCCTTGTGTCATAACAGATTA
6146377 TCGGT
1 TCGGT
6146382 ACGCATAGTA
Statistics
Matches: 114, Mismatches: 33, Indels: 4
0.75 0.22 0.03
Matches are distributed among these distances:
47 1 0.01
48 112 0.98
49 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.27
Consensus pattern (48 bp):
TCGGTGGCCTACACACAGTCCGTGCCACCCTTGTGTCATAACAGATTA
Found at i:6148237 original size:48 final size:48
Alignment explanation
Indices: 6148046--6148246 Score: 224
Period size: 48 Copynumber: 4.2 Consensus size: 48
6148036 GCGTACTGAT
* * *
6148046 AATCTATTATGACACAAGGGTGGCACGGACTGTGTACAGGCCACCGAT
1 AATCTGTTATGACACAAGGGTGGCACGGACTGTGTGCAGGCCACCGAG
* * * * * * *
6148094 ATTCTGTTTTGACACAAGGGTGGCACGGATTGTGTGCAAGTCACCAAT
1 AATCTGTTATGACACAAGGGTGGCACGGACTGTGTGCAGGCCACCGAG
* * *
6148142 AA-CTTGTTAAGATACAAGGGTGGCACGGACTATGTGCAGGCCACCGAG
1 AATC-TGTTATGACACAAGGGTGGCACGGACTGTGTGCAGGCCACCGAG
* * * *
6148190 AATCTGTTATTACACAAAGGTGGTACGGACTGTGTGTAGGCCACCGAG
1 AATCTGTTATGACACAAGGGTGGCACGGACTGTGTGCAGGCCACCGAG
6148238 AAATCTGTT
1 -AATCTGTT
6148247 TTTATTCCGA
Statistics
Matches: 125, Mismatches: 25, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
47 1 0.01
48 115 0.92
49 9 0.07
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (48 bp):
AATCTGTTATGACACAAGGGTGGCACGGACTGTGTGCAGGCCACCGAG
Found at i:6152645 original size:252 final size:252
Alignment explanation
Indices: 6152200--6152706 Score: 924
Period size: 252 Copynumber: 2.0 Consensus size: 252
6152190 CTTCAAGAGC
6152200 TTTTCATATTTCCACCGGGGATTACATTAACATGTAGAGATCATACAATTGATTAGACAAGGGTT
1 TTTTCATATTTCCACCGGGGATTACATTAACATGTAGAGATCATACAATTGATTAGACAAGGGTT
* *
6152265 GATAATGTGTTTTCAACATGTGAAATTTTCTTCTTCATGCTTCTTCTTGAGTTTGGCCACTTTCG
66 GATAATGTGTCTTCAACATGTGAAATTGTCTTCTTCATGCTTCTTCTTGAGTTTGGCCACTTTCG
* *
6152330 TAATTTCCTCGTGGCTTGCATTGGGGGCGGGGTCCTCCACAGGTTGTAGTTTTGGATCCAGAATG
131 TAATTTCCTCGTGGCTTCCATTGGGGGCGGGATCCTCCACAGGTTGTAGTTTTGGATCCAGAATG
*
6152395 TACACCACATGTAAGATAGTAAGAAGGAACAACATCTTGTCCTTCCAACGATTGTAG
196 TACACCACATGTAAGATAGTAAGAAGGAACAACATCTTGTCCTTCCAACGATTGAAG
*
6152452 TTTTCATATTTCCACCGTGGATTACATTAACATGTAGAGATCATACAATTGATTAGACAAGGGTT
1 TTTTCATATTTCCACCGGGGATTACATTAACATGTAGAGATCATACAATTGATTAGACAAGGGTT
6152517 GATAATGTGTCTTCAACATGTGAAATTGTCTTCTTCATGCTTCTTCTTGAGTTTGGCCACTTTCG
66 GATAATGTGTCTTCAACATGTGAAATTGTCTTCTTCATGCTTCTTCTTGAGTTTGGCCACTTTCG
* *
6152582 TAATTTCCTTGTGGCTTCCATTGGGGGCGGGATCCTCTACAGGTTGTAGTTTTGGATCCAGAATG
131 TAATTTCCTCGTGGCTTCCATTGGGGGCGGGATCCTCCACAGGTTGTAGTTTTGGATCCAGAATG
* *
6152647 TACACCATATGTAAGGTAGTAAGAAGGAACAACATCTTGTCCTTCCAACGATTGAAG
196 TACACCACATGTAAGATAGTAAGAAGGAACAACATCTTGTCCTTCCAACGATTGAAG
6152704 TTT
1 TTT
6152707 GAAAGATCAA
Statistics
Matches: 245, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
252 245 1.00
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.35
Consensus pattern (252 bp):
TTTTCATATTTCCACCGGGGATTACATTAACATGTAGAGATCATACAATTGATTAGACAAGGGTT
GATAATGTGTCTTCAACATGTGAAATTGTCTTCTTCATGCTTCTTCTTGAGTTTGGCCACTTTCG
TAATTTCCTCGTGGCTTCCATTGGGGGCGGGATCCTCCACAGGTTGTAGTTTTGGATCCAGAATG
TACACCACATGTAAGATAGTAAGAAGGAACAACATCTTGTCCTTCCAACGATTGAAG
Found at i:6160275 original size:36 final size:36
Alignment explanation
Indices: 6160235--6160330 Score: 140
Period size: 36 Copynumber: 2.7 Consensus size: 36
6160225 GTATATTTGA
*
6160235 ATTGATGTACTTGTGATATTATAAGTAATTCGGCCT
1 ATTGATATACTTGTGATATTATAAGTAATTCGGCCT
* *
6160271 ATTGATATACTTGTGATATTATAAGTGATTTGGCCT
1 ATTGATATACTTGTGATATTATAAGTAATTCGGCCT
* *
6160307 AATGATATAGTTGTGATATT-TAAG
1 ATTGATATACTTGTGATATTATAAG
6160331 AGTGATAATT
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
35 4 0.07
36 51 0.93
ACGTcount: A:0.30, C:0.07, G:0.20, T:0.43
Consensus pattern (36 bp):
ATTGATATACTTGTGATATTATAAGTAATTCGGCCT
Found at i:6166475 original size:23 final size:26
Alignment explanation
Indices: 6166446--6166505 Score: 81
Period size: 23 Copynumber: 2.4 Consensus size: 26
6166436 GTATGTTCTT
* *
6166446 ATATTATAAAAT-ATAA-GTAATTAA
1 ATATTATAAAATGAAAATGTAATAAA
6166470 A-ATTATAAAATGAAAATGTAATAAA
1 ATATTATAAAATGAAAATGTAATAAA
6166495 ATATTATAAAA
1 ATATTATAAAA
6166506 CTTAACGTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 10 0.32
24 4 0.13
25 8 0.26
26 9 0.29
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (26 bp):
ATATTATAAAATGAAAATGTAATAAA
Found at i:6167264 original size:16 final size:16
Alignment explanation
Indices: 6167243--6167291 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
6167233 TTCGCTGTAT
6167243 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
*
6167259 TGGAATAGAGGTGTAA
1 TGGAATAGAGGCGTAA
6167275 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
6167291 T
1 T
6167292 AGCAAATCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.37, C:0.04, G:0.37, T:0.22
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:6167321 original size:45 final size:44
Alignment explanation
Indices: 6167270--6167359 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 44
6167260 GGAATAGAGG
6167270 TGTAATGGAATAGAGGCGTAATAGCAAATCAAT-TGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAG-AAATC-ATGTGTTTGGTTGAA
* *
6167315 TGTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGAAATCATGTGTTTGGTTGAA
6167359 T
1 T
6167360 AGAATAGAGG
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
43 1 0.02
44 17 0.40
45 24 0.57
ACGTcount: A:0.32, C:0.06, G:0.28, T:0.34
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGAAATCATGTGTTTGGTTGAA
Found at i:6167637 original size:66 final size:65
Alignment explanation
Indices: 6167565--6167762 Score: 177
Period size: 66 Copynumber: 3.2 Consensus size: 65
6167555 AAAATTCTTA
6167565 ATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTAA
1 ATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAA-ATAATTTAA
6167630 C
65 C
* ** * * * * *
6167631 ATAATTATTATT-AAATAT--A-TTA-T--AAT--TAAAATAT-ATAATTTAATAA-AATTCTTA
1 ATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAATAATT-TAA
6167685 -
65 C
* * *
6167685 ATAATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAA
1 ATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAA-ATAATTTAA
6167750 C
65 C
*
6167751 ATAATTATTATT
1 ATAATTAATATT
6167763 AAATATATTA
Statistics
Matches: 98, Mismatches: 20, Indels: 28
0.67 0.14 0.19
Matches are distributed among these distances:
54 14 0.14
55 7 0.07
56 8 0.08
57 8 0.08
58 3 0.03
59 4 0.04
61 4 0.04
62 3 0.03
63 8 0.08
64 8 0.08
65 7 0.07
66 24 0.24
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.42
Consensus pattern (65 bp):
ATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAATAATTTAAC
Found at i:6167655 original size:120 final size:120
Alignment explanation
Indices: 6167503--6167829 Score: 575
Period size: 120 Copynumber: 2.7 Consensus size: 120
6167493 ATTTAATCAT
* *
6167503 ATTTAAACATAATTAGTATTAAATATATTATAATTAAAATATATAATTTAAAAAAATTCTTAATA
1 ATTT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
6167568 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
65 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
6167624 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
1 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
* * *
6167689 TCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATA
66 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
* *
6167744 AATTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATAA
1 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
6167809 TTAATATTCTTATAT-AATTTA
66 TTAATATTCTTATATGAATTTA
6167830 ATAAAACAAT
Statistics
Matches: 198, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
119 6 0.03
120 188 0.95
121 4 0.02
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (120 bp):
ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
Found at i:6167664 original size:16 final size:16
Alignment explanation
Indices: 6167621--6167666 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
6167611 ACTATAAAAG
*
6167621 ATAATTTAACATA-ATT
1 ATAA-TTAAAATATATT
*
6167637 ATTATT-AAATATATT
1 ATAATTAAAATATATT
6167652 ATAATTAAAATATAT
1 ATAATTAAAATATAT
6167667 AATTTAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 4 0.16
15 10 0.40
16 11 0.44
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
ATAATTAAAATATATT
Found at i:6167673 original size:14 final size:15
Alignment explanation
Indices: 6167621--6167675 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
6167611 ACTATAAAAG
6167621 ATAATTTAACATA-ATT
1 ATAA-TTAA-ATATATT
*
6167637 ATTATTAAATATATT
1 ATAATTAAATATATT
6167652 ATAATTAAA-ATA-T
1 ATAATTAAATATATT
*
6167665 ATAATTTAATA
1 ATAATTAAATA
6167676 AAATTCTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 9 0.26
14 7 0.21
15 15 0.44
16 3 0.09
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAATTAAATATATT
Found at i:6167786 original size:18 final size:18
Alignment explanation
Indices: 6167765--6167812 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
6167755 TTATTATTAA
6167765 ATATATTATAATTAAAAT
1 ATATATTATAATTAAAAT
6167783 ATATAATT-TAA-TAAAAT
1 ATAT-ATTATAATTAAAAT
*
6167800 -TAT-TAATAATTAA
1 ATATATTATAATTAA
6167813 TATTCTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
14 1 0.04
15 3 0.12
16 6 0.23
17 6 0.23
18 7 0.27
19 3 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATATTATAATTAAAAT
Found at i:6167793 original size:14 final size:15
Alignment explanation
Indices: 6167744--6167795 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
6167734 GTAAAATATA
6167744 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
6167759 TATTAAATATATTAT
1 AATTAAATATATTAT
6167774 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
6167787 AATTTAATA
1 AATTAAATA
6167796 AAATTATTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:6167801 original size:44 final size:43
Alignment explanation
Indices: 6167721--6167804 Score: 107
Period size: 43 Copynumber: 1.9 Consensus size: 43
6167711 CTCAAATCAT
* *
6167721 AATATATGATACTGTAAAATATAAATTAACATAATTATTATTA
1 AATATATGATAATGTAAAATATAAATTAACAAAATTATTATTA
* *
6167764 AATATATTATAAT-TAAAATATATAATTTAATAAAATTATTA
1 AATATATGATAATGTAAAATATA-AA-TTAACAAAATTATTA
6167805 ATAATTAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
42 9 0.26
43 13 0.37
44 13 0.37
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (43 bp):
AATATATGATAATGTAAAATATAAATTAACAAAATTATTATTA
Found at i:6170301 original size:8 final size:8
Alignment explanation
Indices: 6170288--6170322 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
6170278 TAAAGATTCT
6170288 AAAAAAGA
1 AAAAAAGA
6170296 AAAAAAGA
1 AAAAAAGA
*
6170304 AACAAAG-
1 AAAAAAGA
6170311 AAAAAAGA
1 AAAAAAGA
6170319 AAAA
1 AAAA
6170323 GTAGAATACC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 6 0.25
8 18 0.75
ACGTcount: A:0.86, C:0.03, G:0.11, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:6170316 original size:15 final size:16
Alignment explanation
Indices: 6170291--6170320 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
6170281 AGATTCTAAA
6170291 AAAGAAAAAAAGAAAC
1 AAAGAAAAAAAGAAAC
6170307 AAAG-AAAAAAGAAA
1 AAAGAAAAAAAGAAA
6170321 AAGTAGAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.83, C:0.03, G:0.13, T:0.00
Consensus pattern (16 bp):
AAAGAAAAAAAGAAAC
Found at i:6173867 original size:5 final size:5
Alignment explanation
Indices: 6173850--6173906 Score: 60
Period size: 5 Copynumber: 11.4 Consensus size: 5
6173840 TTATGTTTTA
* * * * * *
6173850 TATAT TATTT TATAT TATAT TCTTT TATAT CATAT TATAT TATAT TAAAA
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
6173900 TATAT TA
1 TATAT TA
6173907 AAAAAACTAA
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
5 40 1.00
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:6173870 original size:15 final size:15
Alignment explanation
Indices: 6173850--6173896 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
6173840 TTATGTTTTA
6173850 TATATTATTTTATAT
1 TATATTATTTTATAT
*
6173865 TATATTCTTTTATAT
1 TATATTATTTTATAT
* *
6173880 CATATTATATTATAT
1 TATATTATTTTATAT
6173895 TA
1 TA
6173897 AAATATATTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (15 bp):
TATATTATTTTATAT
Found at i:6174127 original size:22 final size:22
Alignment explanation
Indices: 6174089--6174135 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
6174079 ATAAAAAGAC
6174089 AAAGAAACAAGAGAAGA-ACAGA
1 AAAGAAACAAGAGAAGAGAC-GA
6174111 AAAGAAAC-AGAGAAAGAGACGA
1 AAAGAAACAAGAG-AAGAGACGA
6174133 AAA
1 AAA
6174136 CAGGAGAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 4 0.17
22 17 0.74
23 2 0.09
ACGTcount: A:0.68, C:0.09, G:0.23, T:0.00
Consensus pattern (22 bp):
AAAGAAACAAGAGAAGAGACGA
Found at i:6174599 original size:3 final size:3
Alignment explanation
Indices: 6174591--6174618 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
6174581 GATAGAAATT
6174591 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
6174619 AAATTAATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:6175229 original size:23 final size:21
Alignment explanation
Indices: 6175202--6175285 Score: 89
Period size: 21 Copynumber: 4.0 Consensus size: 21
6175192 GGCTTTGATG
6175202 ATCAGGCACTTTATGTGTCGT
1 ATCAGGCACTTTATGTGTCGT
* *
6175223 ACATCAGACATTTTATGTGTCGT
1 --ATCAGGCACTTTATGTGTCGT
* **
6175246 ATCAGGCACCTCGTGTGTCGT
1 ATCAGGCACTTTATGTGTCGT
*
6175267 TTCAGGCAC-TTATGTGTCG
1 ATCAGGCACTTTATGTGTCG
6175286 AGAAAAATGA
Statistics
Matches: 51, Mismatches: 10, Indels: 3
0.80 0.16 0.05
Matches are distributed among these distances:
20 8 0.16
21 24 0.47
23 19 0.37
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.36
Consensus pattern (21 bp):
ATCAGGCACTTTATGTGTCGT
Found at i:6175411 original size:184 final size:184
Alignment explanation
Indices: 6175102--6175469 Score: 736
Period size: 184 Copynumber: 2.0 Consensus size: 184
6175092 ATTTTGAAAT
6175102 AGAAAAATGATTTGAATACCCTATTAACTAGTCGGGCTAAGTCGGATATAGTTGGCATGCCATAG
1 AGAAAAATGATTTGAATACCCTATTAACTAGTCGGGCTAAGTCGGATATAGTTGGCATGCCATAG
6175167 GATTTGGAAGAGTACGAGATTTATCGGCTTTGATGATCAGGCACTTTATGTGTCGTACATCAGAC
66 GATTTGGAAGAGTACGAGATTTATCGGCTTTGATGATCAGGCACTTTATGTGTCGTACATCAGAC
6175232 ATTTTATGTGTCGTATCAGGCACCTCGTGTGTCGTTTCAGGCACTTATGTGTCG
131 ATTTTATGTGTCGTATCAGGCACCTCGTGTGTCGTTTCAGGCACTTATGTGTCG
6175286 AGAAAAATGATTTGAATACCCTATTAACTAGTCGGGCTAAGTCGGATATAGTTGGCATGCCATAG
1 AGAAAAATGATTTGAATACCCTATTAACTAGTCGGGCTAAGTCGGATATAGTTGGCATGCCATAG
6175351 GATTTGGAAGAGTACGAGATTTATCGGCTTTGATGATCAGGCACTTTATGTGTCGTACATCAGAC
66 GATTTGGAAGAGTACGAGATTTATCGGCTTTGATGATCAGGCACTTTATGTGTCGTACATCAGAC
6175416 ATTTTATGTGTCGTATCAGGCACCTCGTGTGTCGTTTCAGGCACTTATGTGTCG
131 ATTTTATGTGTCGTATCAGGCACCTCGTGTGTCGTTTCAGGCACTTATGTGTCG
6175470 TATATAGATC
Statistics
Matches: 184, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
184 184 1.00
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.33
Consensus pattern (184 bp):
AGAAAAATGATTTGAATACCCTATTAACTAGTCGGGCTAAGTCGGATATAGTTGGCATGCCATAG
GATTTGGAAGAGTACGAGATTTATCGGCTTTGATGATCAGGCACTTTATGTGTCGTACATCAGAC
ATTTTATGTGTCGTATCAGGCACCTCGTGTGTCGTTTCAGGCACTTATGTGTCG
Found at i:6175413 original size:23 final size:21
Alignment explanation
Indices: 6175386--6175472 Score: 95
Period size: 21 Copynumber: 4.1 Consensus size: 21
6175376 GGCTTTGATG
6175386 ATCAGGCACTTTATGTGTCGT
1 ATCAGGCACTTTATGTGTCGT
* *
6175407 ACATCAGACATTTTATGTGTCGT
1 --ATCAGGCACTTTATGTGTCGT
* **
6175430 ATCAGGCACCTCGTGTGTCGT
1 ATCAGGCACTTTATGTGTCGT
*
6175451 TTCAGGCAC-TTATGTGTCGT
1 ATCAGGCACTTTATGTGTCGT
6175471 AT
1 AT
6175473 ATAGATCAGG
Statistics
Matches: 53, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
20 10 0.19
21 24 0.45
23 19 0.36
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.37
Consensus pattern (21 bp):
ATCAGGCACTTTATGTGTCGT
Found at i:6179180 original size:56 final size:56
Alignment explanation
Indices: 6179066--6179185 Score: 152
Period size: 56 Copynumber: 2.1 Consensus size: 56
6179056 AACCCTAAAC
* * **
6179066 CCTAAGGCAAACCTTGTTCATGTTTTCTAACAAGTATGTACGAACTGGTCTCTCGA
1 CCTAAGGCAAACCCTGTTCATGTTTTCTAACAAGTATGTACAAACCAGTCTCTCGA
* * * *
6179122 CCTAAGGCAAACCCTGTTCATGTTTTCTGATAAGTATGTGCAAACCAGTCT-TGTGA
1 CCTAAGGCAAACCCTGTTCATGTTTTCTAACAAGTATGTACAAACCAGTCTCT-CGA
6179178 CCTAAGGC
1 CCTAAGGC
6179186 GGACCTTTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
55 1 0.02
56 54 0.98
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (56 bp):
CCTAAGGCAAACCCTGTTCATGTTTTCTAACAAGTATGTACAAACCAGTCTCTCGA
Found at i:6183654 original size:51 final size:52
Alignment explanation
Indices: 6183596--6183733 Score: 185
Period size: 50 Copynumber: 2.7 Consensus size: 52
6183586 TCAGTTCACA
*
6183596 TAGTAGCCTGCACATAGTACTACACATGTGACCATTC-TCA-TCTGATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCA-TCATCATTCCGATACACG
* * * *
6183647 TAGTAGCCTGCACATAATACTACAGATGCGACC--CATCATTCCGGTACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATCATCATTCCGATACACG
*
6183697 TAGTAGCCTGCACATAGTACTACACACGTGACCATCA
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATCA
6183734 CTTTCACTTT
Statistics
Matches: 74, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
48 1 0.01
49 3 0.04
50 38 0.51
51 30 0.41
52 2 0.03
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (52 bp):
TAGTAGCCTGCACATAGTACTACACATGTGACCATCATCATTCCGATACACG
Found at i:6193644 original size:11 final size:11
Alignment explanation
Indices: 6193628--6193676 Score: 89
Period size: 11 Copynumber: 4.5 Consensus size: 11
6193618 TAATTTATTC
6193628 TTTATGATTTA
1 TTTATGATTTA
6193639 TTTATGATTTA
1 TTTATGATTTA
*
6193650 TTTGTGATTTA
1 TTTATGATTTA
6193661 TTTATGATTTA
1 TTTATGATTTA
6193672 TTTAT
1 TTTAT
6193677 CAAGTGTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 36 1.00
ACGTcount: A:0.24, C:0.00, G:0.10, T:0.65
Consensus pattern (11 bp):
TTTATGATTTA
Found at i:6195031 original size:25 final size:24
Alignment explanation
Indices: 6194995--6195092 Score: 90
Period size: 25 Copynumber: 4.0 Consensus size: 24
6194985 GTAATTAGGA
* * *
6194995 TTACGGATTTCAGCTCGTACGAGC
1 TTACCGATTTCAGCTCGAATGAGC
* *
6195019 TTACCGATATTCAGCTCAAAAGAGC
1 TTACCGAT-TTCAGCTCGAATGAGC
* *
6195044 TTACCGTTATTCAGCTGGAATGAGC
1 TTACCGAT-TTCAGCTCGAATGAGC
*
6195069 TTACCG-TTTACAGCTCGTATGAGC
1 TTACCGATTT-CAGCTCGAATGAGC
6195093 ATACATGTAC
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
23 2 0.03
24 20 0.32
25 40 0.65
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (24 bp):
TTACCGATTTCAGCTCGAATGAGC
Found at i:6198191 original size:41 final size:41
Alignment explanation
Indices: 6198146--6198249 Score: 156
Period size: 41 Copynumber: 2.5 Consensus size: 41
6198136 GACTTTAAGT
* *
6198146 CTAGCAGGCTAAGAGCCGGTGATCT-GAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGAT-TGGAATCAGGCTATAAAC
* *
6198187 CTAGCAGGCTAAGTGCCGGTGATTGGAATCGGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATTGGAATCAGGCTATAAAC
6198228 CTAGCAGGCTAAGTGCCGGTGA
1 CTAGCAGGCTAAGTGCCGGTGA
6198250 ATATGTTAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
40 1 0.02
41 57 0.98
ACGTcount: A:0.27, C:0.20, G:0.32, T:0.21
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATTGGAATCAGGCTATAAAC
Found at i:6205497 original size:41 final size:41
Alignment explanation
Indices: 6205452--6205637 Score: 284
Period size: 41 Copynumber: 4.5 Consensus size: 41
6205442 GACTTTAAGT
* *
6205452 CTAGCAGGCTAAGAGCCGGCGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
* * *
6205493 CTAGCAGGCTAAGAGCCGGTGATTTGAACCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
*
6205534 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
* *
6205575 CTAGCAGGCTAAGTGCCGGTGAT-TGGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATCT-GAATCAGGTTATAAAC
6205616 CTAGCAGGCTAAGTGCCGGTGA
1 CTAGCAGGCTAAGTGCCGGTGA
6205638 ATATGTTAAA
Statistics
Matches: 134, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
40 1 0.01
41 133 0.99
ACGTcount: A:0.30, C:0.20, G:0.29, T:0.21
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
Found at i:6205635 original size:82 final size:80
Alignment explanation
Indices: 6205398--6205638 Score: 299
Period size: 82 Copynumber: 2.9 Consensus size: 80
6205388 ATTGAAATTT
* * *
6205398 TCAGGTT-TAAAACCTAGCAGGCTTAAGGCCGGTGAAAT-AATTC-GGACTTTAAGTCTAGCAGG
1 TCAGGTTAT-AAACCTAGCAGGC-TAAGGCCGGTG-ATTGAA-TCAGG-CTATAAGCCTAGCAGG
* * *
6205460 CTAAGAGCCGGCGATCTGAA
61 CTAAGTGCCGGTGAACTGAA
* * *
6205480 TCAGGTTATAAACCTAGCAGGCTAAGAGCCGGTGATTTGAACCAGGTTATAAACCTAGCAGGCTA
1 TCAGGTTATAAACCTAGCAGGCTAAG-GCCGGTGA-TTGAATCAGGCTATAAGCCTAGCAGGCTA
6205545 AGTGCCGGTGAACTGAA
64 AGTGCCGGTGAACTGAA
6205562 TCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATTGGAATCAGGCTATAAGCCTAGCAGGCTA
1 TCAGGTTATAAACCTAGCAGGCTAAG-GCCGGTGATT-GAATCAGGCTATAAGCCTAGCAGGCTA
6205627 AGTGCCGGTGAA
64 AGTGCCGGTGAA
6205639 TATGTTAAAT
Statistics
Matches: 140, Mismatches: 13, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
81 7 0.05
82 128 0.91
83 5 0.04
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (80 bp):
TCAGGTTATAAACCTAGCAGGCTAAGGCCGGTGATTGAATCAGGCTATAAGCCTAGCAGGCTAAG
TGCCGGTGAACTGAA
Found at i:6230738 original size:20 final size:20
Alignment explanation
Indices: 6230710--6230767 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
6230700 AAAAATGTAA
* *
6230710 AAGAGATATATATATATAAT
1 AAGACATATAGATATATAAT
6230730 AAGACATATAGATATATAAT
1 AAGACATATAGATATATAAT
* * *
6230750 AAGATACAAAGATATATA
1 AAGACATATAGATATATA
6230768 GATATAAGGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.57, C:0.03, G:0.10, T:0.29
Consensus pattern (20 bp):
AAGACATATAGATATATAAT
Found at i:6231814 original size:2 final size:2
Alignment explanation
Indices: 6231809--6231848 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
6231799 ATGCACGCGC
6231809 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
6231849 TTGTAACAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:6232786 original size:44 final size:44
Alignment explanation
Indices: 6232733--6232954 Score: 146
Period size: 44 Copynumber: 5.1 Consensus size: 44
6232723 CTATTACTTT
* *
6232733 AATCCGCTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTC
1 AATCCGCTCCACTGCAACTTCAGGGAGATAAGATTATCGGCTTC
* * * **
6232777 AATCTGCTCCACTGTAACTTCAGGGAGATAAGATTTGTCATCTTC
1 AATCCGCTCCACTGCAACTTCAGGGAGATAAGA-TTATCGGCTTC
* * * ** * * * * *
6232822 AGTCTGCCCCACTGTGACCTCAGGGGGATAAGA--CTC-GATGC
1 AATCCGCTCCACTGCAACTTCAGGGAGATAAGATTATCGGCTTC
* * * * ** *
6232863 GATCCACTCTACTGCAACTTCAGAGAGATAAGATCTAT-TACTTT
1 AATCCGCTCCACTGCAACTTCAGGGAGATAAGAT-TATCGGCTTC
* * * *
6232907 AATCCGCTCCACTACAACTTCAGGGAGATAGGATTATAGGCTTA
1 AATCCGCTCCACTGCAACTTCAGGGAGATAAGATTATCGGCTTC
6232951 AATC
1 AATC
6232955 TGCTTCCTTA
Statistics
Matches: 131, Mismatches: 41, Indels: 12
0.71 0.22 0.07
Matches are distributed among these distances:
41 24 0.18
42 2 0.02
43 3 0.02
44 66 0.50
45 36 0.27
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (44 bp):
AATCCGCTCCACTGCAACTTCAGGGAGATAAGATTATCGGCTTC
Found at i:6232834 original size:45 final size:44
Alignment explanation
Indices: 6232713--6232854 Score: 124
Period size: 44 Copynumber: 3.2 Consensus size: 44
6232703 CAGCTTCAAA
* * * * **
6232713 GAGATAAGATCTATTA-CTTTAATCCGCTCCACTACAACTTCAGG
1 GAGATAAGAT-TATCAGCTTCAATCTGCCCCACTGTAACTTCAGG
* * *
6232757 GAGATAGGATTATCGGCTTCAATCTGCTCCACTGTAACTTCAGG
1 GAGATAAGATTATCAGCTTCAATCTGCCCCACTGTAACTTCAGG
* * * * *
6232801 GAGATAAGATTTGTCATCTTCAGTCTGCCCCACTGTGACCTCAGG
1 GAGATAAGA-TTATCAGCTTCAATCTGCCCCACTGTAACTTCAGG
*
6232846 GGGATAAGA
1 GAGATAAGA
6232855 CTCGATGCGA
Statistics
Matches: 80, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
43 3 0.04
44 41 0.51
45 36 0.45
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.28
Consensus pattern (44 bp):
GAGATAAGATTATCAGCTTCAATCTGCCCCACTGTAACTTCAGG
Found at i:6233023 original size:130 final size:130
Alignment explanation
Indices: 6232873--6233524 Score: 959
Period size: 130 Copynumber: 5.0 Consensus size: 130
6232863 GATCCACTCT
* * * * * * * *
6232873 ACTGCAACTTCAG-AGAGATAAGATCT-ATTACTTTAATCCGCTCCACTACAACTTCAGGGAGAT
1 ACTGCAACTTCAGTCGGGATAAGACCTGCTTAC-TTAGTCTGCTCCACTACAACCTCAGGGAGAA
* *
6232936 AGGA-TTATAGGCTTAAATCTGCTTCCTTACACTTGAAGGTAAGATTCGCCGTCTTCGATCTGTC
65 AGGACTCAT-GGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGTC
6233000 CC
129 CC
* ** *
6233002 ACTGCAACTTCAGTCGGGATAAGACCTGCTTACTTAGTCTTCTCCACTGTAACCTCAGAGAGAAA
1 ACTGCAACTTCAGTCGGGATAAGACCTGCTTACTTAGTCTGCTCCACTACAACCTCAGGGAGAAA
* ** * *
6233067 GGAATCGGGGCTTAAATCTACTTTCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGTCCC
66 GGACTCATGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGTCCC
* * *
6233132 ACTGTAACTTCAGTCGGGATAAGACCTGCTTACTTAGTCTGTTCCACTACAACCTCAGAGAGAAA
1 ACTGCAACTTCAGTCGGGATAAGACCTGCTTACTTAGTCTGCTCCACTACAACCTCAGGGAGAAA
* * *
6233197 GGACTCGTGGCTTAAATCTTCTTCCTTACACTTGAAGATAAGATTCGCCATCTTCGATCTGTCCC
66 GGACTCATGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGTCCC
* *
6233262 ACTGCAACTTCAGTCGGGATAAGACCTGCTTACATAGTCTGCTCCACTGCAACCTCAGGGAGAAA
1 ACTGCAACTTCAGTCGGGATAAGACCTGCTTACTTAGTCTGCTCCACTACAACCTCAGGGAGAAA
* *
6233327 GAACTCGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGTCCC
66 GGACTCATGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGTCCC
* * * *
6233392 ACTGCAACTTCAGTTGGGATAAGACCTTCTTACTTAGTCTGCTTCACTACAACCTTAGGGAGAAA
1 ACTGCAACTTCAGTCGGGATAAGACCTGCTTACTTAGTCTGCTCCACTACAACCTCAGGGAGAAA
*
6233457 GGACTCATGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCCTCGATCTGTCCC
66 GGACTCATGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGTCCC
6233522 ACT
1 ACT
6233525 ACTGCTTCGG
Statistics
Matches: 475, Mismatches: 45, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
129 13 0.03
130 457 0.96
131 5 0.01
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (130 bp):
ACTGCAACTTCAGTCGGGATAAGACCTGCTTACTTAGTCTGCTCCACTACAACCTCAGGGAGAAA
GGACTCATGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGTCCC
Found at i:6233064 original size:174 final size:172
Alignment explanation
Indices: 6232712--6233026 Score: 413
Period size: 174 Copynumber: 1.8 Consensus size: 172
6232702 GCAGCTTCAA
* *
6232712 AGAGATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTC
1 AGAGATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGATTATAGGCTTA
* * * **
6232777 AATCTGCTCCACTGTAACTTCAGGGAGATAAGATTTGTCATCTTCAGTCTGCCCCACTGTGACCT
66 AATCTGCTCCACTGTAACTT-A-GAAGATAAGATTCGCCATCTTCAGTCTGCCCCACTGCAACCT
* * * *
6232842 CAGGGGGATAAGACTCGATGCGATCCACTCTACTGCAACTTCAG
129 CAGCGGGATAAGACTCGATGAGATCCACTCCACTGCAACCTCAG
6232886 AGAGATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGATTATAGGCTTA
1 AGAGATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGATTATAGGCTTA
* * * * *
6232951 AATCTGCTTC-CT-TACACTT-GAAGGTAAGATTCGCCGTCTTC-GATCTGTCCCACTGCAACTT
66 AATCTGCTCCACTGTA-ACTTAGAAGATAAGATTCGCCATCTTCAG-TCTGCCCCACTGCAACCT
6233012 CAGTCGGGATAAGAC
129 CAG-CGGGATAAGAC
6233027 CTGCTTACTT
Statistics
Matches: 125, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
169 1 0.01
170 34 0.27
171 10 0.08
172 2 0.02
173 6 0.05
174 72 0.58
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (172 bp):
AGAGATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGATTATAGGCTTA
AATCTGCTCCACTGTAACTTAGAAGATAAGATTCGCCATCTTCAGTCTGCCCCACTGCAACCTCA
GCGGGATAAGACTCGATGAGATCCACTCCACTGCAACCTCAG
Found at i:6233638 original size:131 final size:131
Alignment explanation
Indices: 6233464--6233762 Score: 369
Period size: 131 Copynumber: 2.3 Consensus size: 131
6233454 AAAGGACTCA
* * *
6233464 TGGCTTAAATCTGCTTCCTTACACTT---GAAGATAAGATTCGCCGTCCTCGATCTG-TCCCACT
1 TGGCTTAAATCTGTTTCCCTACTCTTGGGGAAGATAAGATTCGCCGTCCTCGATCTGTTCCC-CT
* * * * * *
6233525 ACTGCTTCGGG-AGACAAGATCTATAAT-TTCCAACCTATTCCACTGCTGGTCAGTGACATAGAA
65 ACT-CCTCGGGAAGACAAGATCCACAATCTT-CAACCTATCCCACTGCTGATCAGGGACATAGAA
6233588 CTTG
128 CTTG
* *
6233592 TGGCTTAAATCTGTTTCCCTACTCTTGGGGAAGATAAGATTCGCCGTCTTCGATCTGTTTCCCTA
1 TGGCTTAAATCTGTTTCCCTACTCTTGGGGAAGATAAGATTCGCCGTCCTCGATCTGTTCCCCTA
* * * *
6233657 CTCCTGGGGAAGATAAGATCCGCAATCTTCAACCTATCCCACTGCTGATCAGGGACATAGGACTT
66 CTCCTCGGGAAGACAAGATCCACAATCTTCAACCTATCCCACTGCTGATCAGGGACATAGAACTT
6233722 G
131 G
*
6233723 TGGCTTAAATCTATTTCCCTACT-TCTGGGGAAGATAAGAT
1 TGGCTTAAATCTGTTTCCCTACTCT-TGGGGAAGATAAGAT
6233763 CCGCAACTTT
Statistics
Matches: 148, Mismatches: 16, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
128 23 0.16
130 6 0.04
131 114 0.77
132 5 0.03
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (131 bp):
TGGCTTAAATCTGTTTCCCTACTCTTGGGGAAGATAAGATTCGCCGTCCTCGATCTGTTCCCCTA
CTCCTCGGGAAGACAAGATCCACAATCTTCAACCTATCCCACTGCTGATCAGGGACATAGAACTT
G
Found at i:6233686 original size:44 final size:44
Alignment explanation
Indices: 6233600--6233686 Score: 138
Period size: 44 Copynumber: 2.0 Consensus size: 44
6233590 TGTGGCTTAA
* * **
6233600 ATCTGTTTCCCTACTCTTGGGGAAGATAAGATTCGCCGTCTTCG
1 ATCTGTTTCCCTACTCCTGGGGAAGATAAGATCCGCAATCTTCG
6233644 ATCTGTTTCCCTACTCCTGGGGAAGATAAGATCCGCAATCTTC
1 ATCTGTTTCCCTACTCCTGGGGAAGATAAGATCCGCAATCTTC
6233687 AACCTATCCC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (44 bp):
ATCTGTTTCCCTACTCCTGGGGAAGATAAGATCCGCAATCTTCG
Found at i:6233701 original size:390 final size:387
Alignment explanation
Indices: 6232945--6233649 Score: 918
Period size: 390 Copynumber: 1.8 Consensus size: 387
6232935 TAGGATTATA
*
6232945 GGCTTAAATCTGCTTCCTTACACTTGAAGGTAAGATTCGCCGTCTTCGATCTGTCCCACTGCAAC
1 GGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGTCCCACTGCAAC
* ** *
6233010 TTCAGTCGGGATAAGACCTGCTTACTTAGTCTTCTCCACTGTAACCTCAGAGAGAAAGGAATCGG
66 TTCAGTCGGGATAAGACCTGCTTACTTAGTCTGCTCCACTACAACCTCAGAGAGAAAGGAATCAG
* * *
6233075 GGCTTAAATCTACTTTCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGTCCCACTGTAAC
131 GGCTTAAATCTACTTCCTTACACTTGAAGATAAGATTCGCCGTCCTCGATCTGTCCCACTCTAAC
* * * ** * * *
6233140 TTCAGTCGGGATAAGACCTGCTTACTTAGTCTGTTCCACTACAACCTCAGAGAGAAAGGACTCGT
196 TTCAG-CGGGACAAGACCTGATAACTTAACCTATTCCACTACAACCTCAGAGACAAAGAACTCGT
*
6233205 GGCTTAAATCTTCTTCCTTACACTTGAAGATAAGATTCGCCATCTTCGATCTGTCCCACTGCAAC
260 GGCTTAAATCTTCTTCCCTACACTTGAAGATAAGATTCGCCATCTTCGATCTGTCCCACT--AAC
* *
6233270 TTCAGTCGGGATAAGACCTGCTTACATAGTCTGCTCCACTGCAACCTCAGGGAGAAAGAACTCGT
323 TCCAGTCGGGATAAGACCTGCTTACATAGCCTGCTCCACTGCAACCTCAGGGAGAAAGAACTCGT
6233335 GGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGTCCCACTGCAAC
1 GGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGTCCCACTGCAAC
* * * * * * *
6233400 TTCAGTTGGGATAAGACCTTCTTACTTAGTCTGCTTCACTACAACCTTAGGGAGAAAGGACTCAT
66 TTCAGTCGGGATAAGACCTGCTTACTTAGTCTGCTCCACTACAACCTCAGAGAGAAAGGAATCAG
* *
6233465 GGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCCTCGATCTGTCCCACTACT-G
131 GGCTTAAATCTACTTCCTTACACTTGAAGATAAGATTCGCCGTCCTCGATCTGTCCCACT-CTAA
* * * *** * *
6233529 CTTC-G-GGAGACAAGATCT-ATAATTTCCAACCTATTCCACTGC-TGGTCAGTGACATAGAACT
195 CTTCAGCGG-GACAAGACCTGATAACTT--AACCTATTCCACTACAACCTCAGAGACAAAGAACT
* * *
6233590 TGTGGCTTAAATCTGT-TTCCCTACTCTTGGGGAAGATAAGATTCGCCGTCTTCGATCTGT
257 CGTGGCTTAAATCT-TCTTCCCTACACTT---GAAGATAAGATTCGCCATCTTCGATCTGT
6233650 TTCCCTACTC
Statistics
Matches: 270, Mismatches: 37, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
387 6 0.02
388 43 0.16
389 13 0.05
390 179 0.66
391 29 0.11
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (387 bp):
GGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGTCCCACTGCAAC
TTCAGTCGGGATAAGACCTGCTTACTTAGTCTGCTCCACTACAACCTCAGAGAGAAAGGAATCAG
GGCTTAAATCTACTTCCTTACACTTGAAGATAAGATTCGCCGTCCTCGATCTGTCCCACTCTAAC
TTCAGCGGGACAAGACCTGATAACTTAACCTATTCCACTACAACCTCAGAGACAAAGAACTCGTG
GCTTAAATCTTCTTCCCTACACTTGAAGATAAGATTCGCCATCTTCGATCTGTCCCACTAACTCC
AGTCGGGATAAGACCTGCTTACATAGCCTGCTCCACTGCAACCTCAGGGAGAAAGAACTCGT
Found at i:6233805 original size:86 final size:87
Alignment explanation
Indices: 6233644--6233810 Score: 291
Period size: 86 Copynumber: 1.9 Consensus size: 87
6233634 GCCGTCTTCG
*
6233644 ATCTGTTTCCCTACTCCTGGGGAAGATAAGATCCGCAATCTTCAACCTATCCCACTGCTGATCAG
1 ATCTATTTCCCTACTCCTGGGGAAGATAAGATCCGCAATCTTCAACCTATCCCACTGCTGATCAG
6233709 GGACATAGGACTTGTGGCTTAA
66 GGACATAGGACTTGTGGCTTAA
* * *
6233731 ATCTATTTCCCTACTTCTGGGGAAGATAAGATCCGCAA-CTTTAACCTATCCTACTGCTGATCAG
1 ATCTATTTCCCTACTCCTGGGGAAGATAAGATCCGCAATCTTCAACCTATCCCACTGCTGATCAG
6233795 GGACATAGGACTTGTG
66 GGACATAGGACTTGTG
6233811 ATTTCACCGA
Statistics
Matches: 76, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
86 40 0.53
87 36 0.47
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (87 bp):
ATCTATTTCCCTACTCCTGGGGAAGATAAGATCCGCAATCTTCAACCTATCCCACTGCTGATCAG
GGACATAGGACTTGTGGCTTAA
Found at i:6235059 original size:21 final size:20
Alignment explanation
Indices: 6235025--6235064 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
6235015 TTAGCCTCTC
6235025 CATTTTACTTTTCATTTTTT
1 CATTTTACTTTTCATTTTTT
*
6235045 CATTTTCCATTTTCATTTTT
1 CATTTTAC-TTTTCATTTTT
6235065 CATCTCCCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.68
Consensus pattern (20 bp):
CATTTTACTTTTCATTTTTT
Found at i:6235077 original size:20 final size:21
Alignment explanation
Indices: 6235033--6235077 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
6235023 TCCATTTTAC
* *
6235033 TTTTCATTTTTTCATTTTCCA
1 TTTTCATTTTTTCATCTCCCA
*
6235054 TTTTCA-TTTTTCATCTCCCT
1 TTTTCATTTTTTCATCTCCCA
6235074 TTTT
1 TTTT
6235078 TTTGAACTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.11, C:0.22, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTCATTTTTTCATCTCCCA
Found at i:6235486 original size:30 final size:28
Alignment explanation
Indices: 6235444--6235503 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 28
6235434 CTTTTTCATA
6235444 TTTTTATTTTGACTTTAATTGATTTCTTT
1 TTTTTATTTTGACTTTAATT-ATTTCTTT
* *
6235473 TTTTTACTTTTGACTTTGATTTTTTCTTT
1 TTTTTA-TTTTGACTTTAATTATTTCTTT
6235502 TT
1 TT
6235504 ATTTTTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 15 0.54
30 13 0.46
ACGTcount: A:0.13, C:0.08, G:0.07, T:0.72
Consensus pattern (28 bp):
TTTTTATTTTGACTTTAATTATTTCTTT
Found at i:6235491 original size:26 final size:26
Alignment explanation
Indices: 6235462--6235521 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
6235452 TTGACTTTAA
6235462 TTGATTTCTTT-TTTTTACTTTTGACT
1 TTGATTT-TTTCTTTTTACTTTTGACT
* * *
6235488 TTGATTTTTTCTTTTTATTTTTTATT
1 TTGATTTTTTCTTTTTACTTTTGACT
6235514 TTGATTTT
1 TTGATTTT
6235522 GATTTTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
25 3 0.10
26 27 0.90
ACGTcount: A:0.12, C:0.07, G:0.07, T:0.75
Consensus pattern (26 bp):
TTGATTTTTTCTTTTTACTTTTGACT
Found at i:6235507 original size:13 final size:13
Alignment explanation
Indices: 6235487--6235521 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
6235477 TACTTTTGAC
*
6235487 TTTGATTTTTTCT
1 TTTGATTTTTTAT
*
6235500 TTTTATTTTTTAT
1 TTTGATTTTTTAT
6235513 TTTGATTTT
1 TTTGATTTT
6235522 GATTTTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.11, C:0.03, G:0.06, T:0.80
Consensus pattern (13 bp):
TTTGATTTTTTAT
Found at i:6239615 original size:18 final size:19
Alignment explanation
Indices: 6239589--6239644 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 19
6239579 AAAAATGTAA
*
6239589 AAGAGATAT-ATATATAAT
1 AAGACATATAATATATAAT
6239607 AAGACATATAGATATATAAT
1 AAGACATATA-ATATATAAT
* *
6239627 AAGATATAAAGATATATA
1 AAGACATATA-ATATATA
6239645 GATATAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
18 8 0.24
20 25 0.76
ACGTcount: A:0.57, C:0.02, G:0.11, T:0.30
Consensus pattern (19 bp):
AAGACATATAATATATAAT
Found at i:6239623 original size:20 final size:20
Alignment explanation
Indices: 6239598--6239644 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
6239588 AAAGAGATAT
*
6239598 ATATATAATAAGACATATAG
1 ATATATAATAAGACATAAAG
*
6239618 ATATATAATAAGATATAAAG
1 ATATATAATAAGACATAAAG
6239638 ATATATA
1 ATATATA
6239645 GATATAAGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.57, C:0.02, G:0.09, T:0.32
Consensus pattern (20 bp):
ATATATAATAAGACATAAAG
Found at i:6241527 original size:13 final size:13
Alignment explanation
Indices: 6241511--6241537 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
6241501 AATATAATAA
6241511 ATTTATATTTTTT
1 ATTTATATTTTTT
6241524 ATTTATATTTTTT
1 ATTTATATTTTTT
6241537 A
1 A
6241538 ATTTTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
ATTTATATTTTTT
Found at i:6257521 original size:101 final size:103
Alignment explanation
Indices: 6257319--6257523 Score: 360
Period size: 101 Copynumber: 2.0 Consensus size: 103
6257309 CCAGGTAATG
*
6257319 TAGTTGGGTCATAAATGAAATATAAATTAATGTGATTGATGTCTAATATATATATATATATGGAT
1 TAGTTGGGTCATAAATGAAATACAAATTAATGTGATTGATGTC--ATATATATATATATATGGAT
6257384 GTCAAGGGAATGTTCCTCGAGTGGATGGGCAGTTGGCTAA
64 GTCAAGGGAATGTTCCTCGAGTGGATGGGCAGTTGGCTAA
*
6257424 TAGTTGGGTCATAAATGAAATACAATTTAATGTGATTGATGTC-TA-ATATATATATATGGATGT
1 TAGTTGGGTCATAAATGAAATACAAATTAATGTGATTGATGTCATATATATATATATATGGATGT
6257487 CAAGGGAATGTTCCTCGAGTGGATGGGCAGTTGGCTA
66 CAAGGGAATGTTCCTCGAGTGGATGGGCAGTTGGCTA
6257524 TGACAAGGGC
Statistics
Matches: 98, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
101 55 0.56
102 2 0.02
105 41 0.42
ACGTcount: A:0.32, C:0.08, G:0.25, T:0.34
Consensus pattern (103 bp):
TAGTTGGGTCATAAATGAAATACAAATTAATGTGATTGATGTCATATATATATATATATGGATGT
CAAGGGAATGTTCCTCGAGTGGATGGGCAGTTGGCTAA
Found at i:6259683 original size:6 final size:6
Alignment explanation
Indices: 6259674--6259702 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
6259664 AATTTTTTTT
6259674 TTTTGC TTTTGC TTTTGC TTTTGC TTTTG
1 TTTTGC TTTTGC TTTTGC TTTTGC TTTTG
6259703 ACTGGAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.14, G:0.17, T:0.69
Consensus pattern (6 bp):
TTTTGC
Found at i:6262887 original size:20 final size:20
Alignment explanation
Indices: 6262862--6262922 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
6262852 CAAGCTAAGG
*
6262862 AGAAAGAGAAGAAGAACGAA
1 AGAAAGAGAAGAAGAAAGAA
*
6262882 AGAAAGAAAAGAAGAGAAGAA
1 AGAAAGAGAAGAAGA-AAGAA
*
6262903 AG-AAGAGAAGAAGAAGGAA
1 AGAAAGAGAAGAAGAAAGAA
6262922 A
1 A
6262923 AAAATTCATG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
19 5 0.14
20 25 0.69
21 6 0.17
ACGTcount: A:0.67, C:0.02, G:0.31, T:0.00
Consensus pattern (20 bp):
AGAAAGAGAAGAAGAAAGAA
Found at i:6262896 original size:12 final size:13
Alignment explanation
Indices: 6262865--6262914 Score: 59
Period size: 12 Copynumber: 3.8 Consensus size: 13
6262855 GCTAAGGAGA
6262865 AAGAGAAGAAGAACG
1 AAGAGAAGAA-AA-G
6262880 AA-AGAAAGAAAAG
1 AAGAG-AAGAAAAG
6262893 AAGAGAAG-AAAG
1 AAGAGAAGAAAAG
6262905 AAGAGAAGAA
1 AAGAGAAGAA
6262915 GAAGGAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
12 12 0.38
13 7 0.22
14 6 0.19
15 7 0.22
ACGTcount: A:0.68, C:0.02, G:0.30, T:0.00
Consensus pattern (13 bp):
AAGAGAAGAAAAG
Found at i:6266536 original size:27 final size:27
Alignment explanation
Indices: 6266501--6266832 Score: 406
Period size: 27 Copynumber: 12.4 Consensus size: 27
6266491 TGCGATTTAT
*
6266501 GGGT-AAATGACCGAAATACCCTCGAT
1 GGGTAAAATGACCGAAATACCCTCGAA
* *
6266527 GGGAAAAATGACCGAAATACCCCCGAA
1 GGGTAAAATGACCGAAATACCCTCGAA
6266554 GGGTAAAATGACCGAAATACCCTCGAA
1 GGGTAAAATGACCGAAATACCCTCGAA
* * *
6266581 GGGTAAAATGACTGAAATATCCTCGAT
1 GGGTAAAATGACCGAAATACCCTCGAA
* * *
6266608 GGGTAAAATGACTGAAATACCTTCAAA
1 GGGTAAAATGACCGAAATACCCTCGAA
*
6266635 GGGTAAAATGACTGAAATACCCTCGAA
1 GGGTAAAATGACCGAAATACCCTCGAA
*
6266662 GGGTAAAATGATCGAAATACCCTC-AA
1 GGGTAAAATGACCGAAATACCCTCGAA
*
6266688 AGGTAAAATGACCGAAATACCCTCGAA
1 GGGTAAAATGACCGAAATACCCTCGAA
* * *
6266715 GAGTAAAATAACCGAAATACTCCTAG-A
1 GGGTAAAATGACCGAAATAC-CCTCGAA
* *
6266742 GGGTAAAATGATCGAAATACCC-CCAGA
1 GGGTAAAATGACCGAAATACCCTCGA-A
** *
6266769 GGGTAAAATGATTGAAATACCCTTGAA
1 GGGTAAAATGACCGAAATACCCTCGAA
* *
6266796 GGGTAAAATAACCAAAATACCCTC-AA
1 GGGTAAAATGACCGAAATACCCTCGAA
6266822 -GGTAAAATGAC
1 GGGTAAAATGAC
6266833 TGTTATACCT
Statistics
Matches: 264, Mismatches: 36, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
25 10 0.04
26 31 0.12
27 218 0.83
28 5 0.02
ACGTcount: A:0.42, C:0.19, G:0.20, T:0.18
Consensus pattern (27 bp):
GGGTAAAATGACCGAAATACCCTCGAA
Found at i:6267227 original size:28 final size:28
Alignment explanation
Indices: 6267191--6267291 Score: 121
Period size: 28 Copynumber: 3.6 Consensus size: 28
6267181 TACTGGTTAT
*
6267191 TGTATTGGGCTACGGCCCACACTATTAC
1 TGTATTGGGCTAAGGCCCACACTATTAC
* *
6267219 TGTACTGGGTTAAGGCCCACACTATTAC
1 TGTATTGGGCTAAGGCCCACACTATTAC
* * * *
6267247 TGTGTTGGGCTAAGGCCCACATTGTTTC
1 TGTATTGGGCTAAGGCCCACACTATTAC
* *
6267275 TATTTTGGGCTAAGGCC
1 TGTATTGGGCTAAGGCC
6267292 TACGCTGTAC
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 62 1.00
ACGTcount: A:0.20, C:0.24, G:0.25, T:0.32
Consensus pattern (28 bp):
TGTATTGGGCTAAGGCCCACACTATTAC
Found at i:6274167 original size:27 final size:27
Alignment explanation
Indices: 6274135--6274413 Score: 253
Period size: 27 Copynumber: 10.3 Consensus size: 27
6274125 ATTCGTGGGC
*
6274135 AAATGACTGAAATACCCTCGATGGGTA
1 AAATGACTGAAATACCCTCGAAGGGTA
* * *
6274162 AAATGACCGAAATACCCCCAAAGGGTA
1 AAATGACTGAAATACCCTCGAAGGGTA
** * *
6274189 AAATGACCAAAATACCCTCTAAAGGTA
1 AAATGACTGAAATACCCTCGAAGGGTA
*
6274216 AAATGA-TCGAAATACCCTCAAAGGGTA
1 AAATGACT-GAAATACCCTCGAAGGGTA
** * *
6274243 AAATGACCAAAATACTCTCAAAGGGTA
1 AAATGACTGAAATACCCTCGAAGGGTA
* *
6274270 AAATGA-TCGAAATACCTTCGGAGGGTA
1 AAATGACT-GAAATACCCTCGAAGGGTA
* * *
6274297 AAATGATTGAAATACCCCCGGAGGGTA
1 AAATGACTGAAATACCCTCGAAGGGTA
* *
6274324 AAATGAC-CAAGATACCCTTGAAGGGTA
1 AAATGACTGAA-ATACCCTCGAAGGGTA
* *
6274351 AAATGACCGAAATACCCCCGAAGGGTA
1 AAATGACTGAAATACCCTCGAAGGGTA
* *
6274378 AAATGA-TCGAAATA-GCTCCATAGGGTA
1 AAATGACT-GAAATACCCTCGA-AGGGTA
*
6274405 AAATAACTG
1 AAATGACTG
6274414 TTATACCCCT
Statistics
Matches: 207, Mismatches: 36, Indels: 18
0.79 0.14 0.07
Matches are distributed among these distances:
26 5 0.02
27 198 0.96
28 4 0.02
ACGTcount: A:0.42, C:0.19, G:0.20, T:0.18
Consensus pattern (27 bp):
AAATGACTGAAATACCCTCGAAGGGTA
Found at i:6274202 original size:54 final size:54
Alignment explanation
Indices: 6274135--6274408 Score: 309
Period size: 54 Copynumber: 5.1 Consensus size: 54
6274125 ATTCGTGGGC
* * * *
6274135 AAATGACTGAAATACCCTCGATGGGTAAAATGACCGAAATACCCCCAAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTAAAATGATCGAAATACCCTCAAAGGGTA
* * *
6274189 AAATGACCAAAATACCCTCTAAAGGTAAAATGATCGAAATACCCTCAAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTAAAATGATCGAAATACCCTCAAAGGGTA
* * * * **
6274243 AAATGACCAAAATACTCTCAAAGGGTAAAATGATCGAAATACCTTCGGAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTAAAATGATCGAAATACCCTCAAAGGGTA
** * * * **
6274297 AAATGATTGAAATACCCCCGGAGGGTAAAATGA-CCAAGATACCCTTGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTAAAATGATCGAA-ATACCCTCAAAGGGTA
* * *
6274351 AAATGACCGAAATACCCCCGAAGGGTAAAATGATCGAAATA-GCTCCATAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTAAAATGATCGAAATACCCT-CAAAGGGTA
6274405 AAAT
1 AAAT
6274409 AACTGTTATA
Statistics
Matches: 185, Mismatches: 32, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
53 5 0.03
54 177 0.96
55 3 0.02
ACGTcount: A:0.42, C:0.19, G:0.20, T:0.18
Consensus pattern (54 bp):
AAATGACCGAAATACCCTCGAAGGGTAAAATGATCGAAATACCCTCAAAGGGTA
Found at i:6274270 original size:81 final size:81
Alignment explanation
Indices: 6274135--6274408 Score: 327
Period size: 81 Copynumber: 3.4 Consensus size: 81
6274125 ATTCGTGGGC
* * * * *
6274135 AAATGA-CTGAAATACCCTCGATGGGTAAAATGACCGAAATACCCCCAAAGGGTAAAATGACCAA
1 AAATGATC-GAAATACCCTCAAAGGGTAAAATGACCAAAATACCCTCAAAGGGTAAAATGACCGA
* *
6274199 AATACCCTCTAAAGGTA
65 AATACCCTCGAAGGGTA
* *
6274216 AAATGATCGAAATACCCTCAAAGGGTAAAATGACCAAAATACTCTCAAAGGGTAAAATGATCGAA
1 AAATGATCGAAATACCCTCAAAGGGTAAAATGACCAAAATACCCTCAAAGGGTAAAATGACCGAA
* *
6274281 ATACCTTCGGAGGGTA
66 ATACCCTCGAAGGGTA
* * ** * **
6274297 AAATGATTGAAATACCCCCGGAGGGTAAAATGACCAAGATACCCTTGAAGGGTAAAATGACCGAA
1 AAATGATCGAAATACCCTCAAAGGGTAAAATGACCAAAATACCCTCAAAGGGTAAAATGACCGAA
*
6274362 ATACCCCCGAAGGGTA
66 ATACCCTCGAAGGGTA
* *
6274378 AAATGATCGAAATA-GCTCCATAGGGTAAAAT
1 AAATGATCGAAATACCCT-CAAAGGGTAAAAT
6274409 AACTGTTATA
Statistics
Matches: 163, Mismatches: 28, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
80 1 0.01
81 161 0.99
82 1 0.01
ACGTcount: A:0.42, C:0.19, G:0.20, T:0.18
Consensus pattern (81 bp):
AAATGATCGAAATACCCTCAAAGGGTAAAATGACCAAAATACCCTCAAAGGGTAAAATGACCGAA
ATACCCTCGAAGGGTA
Found at i:6274805 original size:28 final size:28
Alignment explanation
Indices: 6274773--6274843 Score: 117
Period size: 28 Copynumber: 2.5 Consensus size: 28
6274763 GCTACTATAT
6274773 TGGGCTAAGGCCCACACTATTACTGTAC
1 TGGGCTAAGGCCCACACTATTACTGTAC
*
6274801 TGGGCTAAAGG-CCACACTATTACTGTAT
1 TGGGCT-AAGGCCCACACTATTACTGTAC
6274829 TGGGCTAAGGCCCAC
1 TGGGCTAAGGCCCAC
6274844 GCTGTACTGT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
27 4 0.10
28 32 0.80
29 4 0.10
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (28 bp):
TGGGCTAAGGCCCACACTATTACTGTAC
Found at i:6282112 original size:25 final size:26
Alignment explanation
Indices: 6282053--6282112 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
6282043 TTGTATGTTA
*
6282053 AGCTCGCATACCAAGTTTGCAGATTG
1 AGCTCGCATACCAAGTTTACAGATTG
* * *
6282079 AGCTTGCATATCGAGTTTACA-ATTG
1 AGCTCGCATACCAAGTTTACAGATTG
6282104 AGCTCGCAT
1 AGCTCGCAT
6282113 GATGTTAAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 12 0.41
26 17 0.59
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.30
Consensus pattern (26 bp):
AGCTCGCATACCAAGTTTACAGATTG
Found at i:6287410 original size:44 final size:44
Alignment explanation
Indices: 6287355--6287443 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
6287345 TGTTGCATAG
6287355 TGGGAGCAATCTCTATAATCCAATCCTTTGGTGTGATGTTGATT
1 TGGGAGCAATCTCTATAATCCAATCCTTTGGTGTGATGTTGATT
6287399 TGGGAGCAATCTCTATAATCCAATCCTTTGGTGTGATGTTGATT
1 TGGGAGCAATCTCTATAATCCAATCCTTTGGTGTGATGTTGATT
6287443 T
1 T
6287444 TGAATTTTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.39
Consensus pattern (44 bp):
TGGGAGCAATCTCTATAATCCAATCCTTTGGTGTGATGTTGATT
Found at i:6294910 original size:27 final size:22
Alignment explanation
Indices: 6294854--6295135 Score: 184
Period size: 21 Copynumber: 12.9 Consensus size: 22
6294844 ATATTAGAAT
6294854 ATTACAATATTCATACAAAAAA
1 ATTACAATATTCATACAAAAAA
*
6294876 A-TATAATATTCATACAAAATTACAAA
1 ATTACAATATTCATAC--AA--A-AAA
6294902 ATTACAATATTCATAC-AAAAA
1 ATTACAATATTCATACAAAAAA
6294923 ATTGA-AATATTCATACAAAACTATAA
1 ATT-ACAATATTCATAC-AAA--A-AA
6294949 TATTACAATATTCATACAAAAAA
1 -ATTACAATATTCATACAAAAAA
* *
6294972 TTTATAATATTCATAC---AAA
1 ATTACAATATTCATACAAAAAA
6294991 ATTACAATATTCATAC-AAAAA
1 ATTACAATATTCATACAAAAAA
* * *
6295012 ATTACTA-ATCCA-A-AACTATAA
1 ATTACAATATTCATACAA--AAAA
* * *
6295033 A-TACAA-ATTTAATTATAAAATA
1 ATTACAATA-TTCA-TACAAAAAA
*
6295055 ATTACAATATTCATAC---AAC
1 ATTACAATATTCATACAAAAAA
6295074 ATTACAATATTCAT--AAAAAA
1 ATTACAATATTCATACAAAAAA
* *
6295094 ATTATAATATTCATACGAAAAA
1 ATTACAATATTCATACAAAAAA
* *
6295116 TTTAAAATATTCATACAAAA
1 ATTACAATATTCATACAAAA
6295136 TTCTAATCTA
Statistics
Matches: 206, Mismatches: 24, Indels: 60
0.71 0.08 0.21
Matches are distributed among these distances:
19 34 0.17
20 24 0.12
21 45 0.22
22 44 0.21
23 15 0.07
24 5 0.02
25 2 0.01
26 10 0.05
27 27 0.13
ACGTcount: A:0.55, C:0.12, G:0.01, T:0.32
Consensus pattern (22 bp):
ATTACAATATTCATACAAAAAA
Found at i:6294932 original size:48 final size:48
Alignment explanation
Indices: 6294854--6294997 Score: 227
Period size: 48 Copynumber: 3.0 Consensus size: 48
6294844 ATATTAGAAT
*
6294854 ATTACAATATTCATACAAAAAAATATAATATTCATACAAAATTACAAA
1 ATTACAATATTCATACAAAAAATTATAATATTCATACAAAATTACAAA
* * *
6294902 ATTACAATATTCATACAAAAAATTGA-AATATTCATACAAAACTATAAT
1 ATTACAATATTCATACAAAAAATT-ATAATATTCATACAAAATTACAAA
6294950 ATTACAATATTCATACAAAAAATTTATAATATTCATACAAAATTACAA
1 ATTACAATATTCATACAAAAAA-TTATAATATTCATACAAAATTACAA
6294998 TATTCATACA
Statistics
Matches: 87, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
48 65 0.75
49 22 0.25
ACGTcount: A:0.56, C:0.12, G:0.01, T:0.31
Consensus pattern (48 bp):
ATTACAATATTCATACAAAAAATTATAATATTCATACAAAATTACAAA
Found at i:6295007 original size:41 final size:41
Alignment explanation
Indices: 6294950--6295135 Score: 170
Period size: 41 Copynumber: 4.5 Consensus size: 41
6294940 AAACTATAAT
6294950 ATTACAATATTCATACAAAAAATTTATAATATTCATAC-AAA
1 ATTACAATATTCATACAAAAAA-TTATAATATTCATACAAAA
* * *
6294991 ATTACAATATTCATACAAAAAATTACT-A-ATCCAAAACTATAA
1 ATTACAATATTCATACAAAAAATTA-TAATATTC-ATAC-AAAA
* * * *
6295033 A-TACAA-ATTTAATTATAAAATAATTACAATATTCATAC-AAC
1 ATTACAATA-TTCA-TACAAAA-AATTATAATATTCATACAAAA
6295074 ATTACAATATTCATA-AAAAAATTATAATATTCATACGAAAA
1 ATTACAATATTCATACAAAAAATTATAATATTCATAC-AAAA
*
6295115 ATTTAAAATATTCATACAAAA
1 A-TTACAATATTCATACAAAA
6295136 TTCTAATCTA
Statistics
Matches: 116, Mismatches: 14, Indels: 28
0.73 0.09 0.18
Matches are distributed among these distances:
39 19 0.16
40 12 0.10
41 38 0.33
42 30 0.26
43 14 0.12
44 3 0.03
ACGTcount: A:0.55, C:0.12, G:0.01, T:0.32
Consensus pattern (41 bp):
ATTACAATATTCATACAAAAAATTATAATATTCATACAAAA
Found at i:6295136 original size:83 final size:85
Alignment explanation
Indices: 6294896--6295136 Score: 239
Period size: 83 Copynumber: 2.8 Consensus size: 85
6294886 CATACAAAAT
*
6294896 TACAAAATTACAATATTCATACAAAAAATTGA-AATATTCATACAAAACTATAATATTACAATAT
1 TACAAAATTACAATATTCATACAAAAAATT-ATAATATTCATAC-AAA--A-AAT-TTAAAATAT
*
6294960 TCATACAAAA-AATTTATAATATTCA
60 TCATACAAAATAATTTACAATATTCA
* * * * *
6294985 TACAAAATTACAATATTCATACAAAAAATTACT-A-ATCCAAAACTATAAA--TACAAAT-TTAA
1 TACAAAATTACAATATTCATACAAAAAATTA-TAATATTC-ATACAAAAAATTTA-AAATATTCA
*
6295045 TTATAAAATAA-TTACAATATTCA
63 -TACAAAATAATTTACAATATTCA
* *
6295068 TACAACATTACAATATTCATA-AAAAAATTATAATATTCATACGAAAAATTTAAAATATTCATAC
1 TACAAAATTACAATATTCATACAAAAAATTATAATATTCATACAAAAAATTTAAAATATTCATAC
6295132 AAAAT
66 AAAAT
6295137 TCTAATCTAA
Statistics
Matches: 126, Mismatches: 15, Indels: 28
0.75 0.09 0.17
Matches are distributed among these distances:
81 1 0.01
82 22 0.17
83 54 0.43
84 7 0.06
85 2 0.02
86 1 0.01
88 5 0.04
89 34 0.27
ACGTcount: A:0.55, C:0.12, G:0.01, T:0.32
Consensus pattern (85 bp):
TACAAAATTACAATATTCATACAAAAAATTATAATATTCATACAAAAAATTTAAAATATTCATAC
AAAATAATTTACAATATTCA
Found at i:6295312 original size:3 final size:3
Alignment explanation
Indices: 6295304--6295360 Score: 98
Period size: 3 Copynumber: 19.3 Consensus size: 3
6295294 TTTATAAACT
6295304 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
*
6295351 TTC TCC TTC T
1 TTC TTC TTC T
6295361 CCTCTTCTCC
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 49 0.96
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:6298977 original size:19 final size:18
Alignment explanation
Indices: 6298949--6298993 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 18
6298939 CCAGTTCCAT
6298949 TTCCATTCTTGAAAGTTA
1 TTCCATTCTTGAAAGTTA
6298967 TTCCTATTCTTGAAAGTTA
1 TTCC-ATTCTTGAAAGTTA
6298986 TTCTCATT
1 TTC-CATT
6298994 TAATTTATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.16
19 20 0.80
20 1 0.04
ACGTcount: A:0.24, C:0.18, G:0.09, T:0.49
Consensus pattern (18 bp):
TTCCATTCTTGAAAGTTA
Found at i:6321956 original size:84 final size:82
Alignment explanation
Indices: 6321800--6321963 Score: 193
Period size: 84 Copynumber: 2.0 Consensus size: 82
6321790 AACTTCCTTA
*
6321800 GGGAAATAAATTATTTTGGGATGATGTCTAACCCCATAATTTCCTCAATGAAATCAATTATGTAG
1 GGGAAATAAATTATTTTGGGATGATGTCTAACCCCATAATTTCCTCAAGGAAATCAATTATGTAG
*
6321865 GCAAATGGCTAGCCTCG
66 GCAAATGGCAAGCCTCG
* * ** * ** *
6321882 GGGAAATCAATTATCTTTTGGGCTGATGTCTGGCTCCATAATTTCCTCGGGGAAATCAGTTATGT
1 GGGAAATAAATTA--TTTTGGGATGATGTCTAACCCCATAATTTCCTCAAGGAAATCAATTATGT
* **
6321947 ATGTTAATGGCAAGCCT
64 AGGCAAATGGCAAGCCT
6321964 AATAACTTTC
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
82 12 0.18
84 55 0.82
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (82 bp):
GGGAAATAAATTATTTTGGGATGATGTCTAACCCCATAATTTCCTCAAGGAAATCAATTATGTAG
GCAAATGGCAAGCCTCG
Found at i:6323562 original size:22 final size:22
Alignment explanation
Indices: 6323534--6323579 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
6323524 AGTGGGGGGA
6323534 GAAAACCAAGTTTAGTTGCATT
1 GAAAACCAAGTTTAGTTGCATT
6323556 GAAAACCAAGTTTAGTTGCATT
1 GAAAACCAAGTTTAGTTGCATT
6323578 GA
1 GA
6323580 TGTATTCGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (22 bp):
GAAAACCAAGTTTAGTTGCATT
Found at i:6326963 original size:16 final size:15
Alignment explanation
Indices: 6326942--6326971 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
6326932 TTAAATGCAC
6326942 AACAACATTTATTAAT
1 AACAACATTT-TTAAT
6326958 AACAACATTTTTAA
1 AACAACATTTTTAA
6326972 GTTGAAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (15 bp):
AACAACATTTTTAAT
Found at i:6332260 original size:12 final size:12
Alignment explanation
Indices: 6332245--6332274 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
6332235 AGTATAGCCT
6332245 TATATATATATG
1 TATATATATATG
*
6332257 TATATATATATT
1 TATATATATATG
6332269 TATATA
1 TATATA
6332275 AAGGTTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (12 bp):
TATATATATATG
Found at i:6333990 original size:14 final size:15
Alignment explanation
Indices: 6333966--6334000 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
6333956 TGCTTTAATC
6333966 ATGGATTAGTATTT-T
1 ATGG-TTAGTATTTAT
6333981 ATGGTTAGTATTTAT
1 ATGGTTAGTATTTAT
6333996 ATGGT
1 ATGGT
6334001 AATGTATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (15 bp):
ATGGTTAGTATTTAT
Found at i:6334296 original size:24 final size:24
Alignment explanation
Indices: 6334260--6334343 Score: 77
Period size: 24 Copynumber: 3.5 Consensus size: 24
6334250 ATGAATGTAT
*
6334260 ATGCTGTCAAATTTTGATGTACAA
1 ATGCAGTCAAATTTTGATGTACAA
* *
6334284 ATGCAGTCCAATTATAT-ATGT--AT
1 ATGCAGTCAAATT-T-TGATGTACAA
6334307 ATGCTA-TCAAATTTTGATGTACAA
1 ATGC-AGTCAAATTTTGATGTACAA
*
6334331 ATGCAGTCCAATT
1 ATGCAGTCAAATT
6334344 ATATATGTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
21 1 0.02
22 5 0.11
23 12 0.26
24 23 0.49
25 5 0.11
26 1 0.02
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (24 bp):
ATGCAGTCAAATTTTGATGTACAA
Found at i:6334319 original size:23 final size:23
Alignment explanation
Indices: 6334293--6334366 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 23
6334283 AATGCAGTCC
6334293 AATTATATATGTATATGCTATCA
1 AATTATATATGTATATGCTATCA
* *
6334316 AATT-T-TGATGTACAAATGC-AGTCC
1 AATTATAT-ATGT--ATATGCTA-TCA
*
6334340 AATTATATATGTATATGCTGTCA
1 AATTATATATGTATATGCTATCA
6334363 AATT
1 AATT
6334367 TATGTCAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 14
0.67 0.09 0.24
Matches are distributed among these distances:
21 1 0.03
22 5 0.13
23 16 0.41
24 11 0.28
25 5 0.13
26 1 0.03
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.41
Consensus pattern (23 bp):
AATTATATATGTATATGCTATCA
Found at i:6334386 original size:45 final size:47
Alignment explanation
Indices: 6334254--6334367 Score: 219
Period size: 47 Copynumber: 2.4 Consensus size: 47
6334244 GAGTAAATGA
6334254 ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATAT
1 ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATAT
*
6334301 ATGTATATGCTATCAAATTTTGATGTACAAATGCAGTCCAATTATAT
1 ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATAT
6334348 ATGTATATGCTGTCAAATTT
1 ATGTATATGCTGTCAAATTT
6334368 ATGTCAATAT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 65 1.00
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.39
Consensus pattern (47 bp):
ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATAT
Found at i:6334497 original size:24 final size:23
Alignment explanation
Indices: 6334420--6334521 Score: 75
Period size: 22 Copynumber: 4.4 Consensus size: 23
6334410 GACCGAATTA
6334420 TCAAATTTTCATGTACAAATGCAG
1 TCAAATTTT-ATGTACAAATGCAG
* * *
6334444 TCCAATTATATATGT--ATATGCTG
1 TCAAATT-T-TATGTACAAATGCAG
6334467 TCAAATTTTGATGTACAAATGCAG
1 TCAAATTTT-ATGTACAAATGCAG
* * * *
6334491 TCTAATTTT-TGTATATATGCTG
1 TCAAATTTTATGTACAAATGCAG
*
6334513 TCCAATTTT
1 TCAAATTTT
6334522 TGGTGTGAAA
Statistics
Matches: 62, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
21 1 0.02
22 23 0.37
23 12 0.19
24 20 0.32
25 5 0.08
26 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (23 bp):
TCAAATTTTATGTACAAATGCAG
Found at i:6334523 original size:47 final size:47
Alignment explanation
Indices: 6334420--6334521 Score: 143
Period size: 47 Copynumber: 2.2 Consensus size: 47
6334410 GACCGAATTA
* *
6334420 TCAAATTTTCATGTACAAATGCAGTCCAATTATATATGTATATGCTG
1 TCAAATTTTGATGTACAAATGCAGTCCAATTATATATATATATGCTG
* * *
6334467 TCAAATTTTGATGTACAAATGCAGTCTAATT-TTTGTATATATGCTG
1 TCAAATTTTGATGTACAAATGCAGTCCAATTATATATATATATGCTG
*
6334513 TCCAATTTT
1 TCAAATTTT
6334522 TGGTGTGAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
46 20 0.41
47 29 0.59
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (47 bp):
TCAAATTTTGATGTACAAATGCAGTCCAATTATATATATATATGCTG
Found at i:6334551 original size:46 final size:46
Alignment explanation
Indices: 6334420--6334568 Score: 119
Period size: 47 Copynumber: 3.2 Consensus size: 46
6334410 GACCGAATTA
* * *
6334420 TCAAATTTTCATGTACAAATGCAGTCCAA-TTAT-ATATGTATATGCTG
1 TCAAATTTTGATGTACAAATGCAGTCTAAGTT-TGGTA--TATATGCTG
* *
6334467 TCAAATTTTGATGTACAAATGCAGTCTAATTTTTGTATATATGCTG
1 TCAAATTTTGATGTACAAATGCAGTCTAAGTTTGGTATATATGCTG
* *
6334513 TCCAATTTTTGGTGTGA-AAATGCTA-TCT-AGTTTGGTATATAAATGCTG
1 T-CAAATTTTGATGT-ACAAATGC-AGTCTAAGTTTGGTATAT--ATGCTG
6334561 TTCAAATT
1 -TCAAATT
6334569 GATGTATAAT
Statistics
Matches: 86, Mismatches: 8, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
46 20 0.23
47 48 0.56
48 17 0.20
49 1 0.01
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (46 bp):
TCAAATTTTGATGTACAAATGCAGTCTAAGTTTGGTATATATGCTG
Found at i:6337953 original size:17 final size:17
Alignment explanation
Indices: 6337933--6337969 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
6337923 TTATGTATAT
*
6337933 TATTTTATTATATAATA
1 TATTATATTATATAATA
*
6337950 TATTATATTATATTATA
1 TATTATATTATATAATA
6337967 TAT
1 TAT
6337970 ATTAATAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TATTATATTATATAATA
Found at i:6337955 original size:12 final size:11
Alignment explanation
Indices: 6337938--6337971 Score: 52
Period size: 10 Copynumber: 3.1 Consensus size: 11
6337928 TATATTATTT
6337938 TATTATATAATA
1 TATTATAT-ATA
6337950 TATTATAT-TA
1 TATTATATATA
6337960 TATTATATATA
1 TATTATATATA
6337971 T
1 T
6337972 TAATAAAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.48
11 3 0.14
12 8 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTATATATA
Found at i:6337961 original size:10 final size:10
Alignment explanation
Indices: 6337928--6337973 Score: 53
Period size: 9 Copynumber: 4.7 Consensus size: 10
6337918 TTATGTTATG
6337928 TATATTAT-T
1 TATATTATAT
6337937 T-TATTATAT
1 TATATTATAT
6337946 AATATATTATAT
1 --TATATTATAT
6337958 TATATTATA-
1 TATATTATAT
6337967 TATATTA
1 TATATTA
6337974 ATAAAGTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
8 6 0.18
9 9 0.27
10 9 0.27
11 1 0.03
12 8 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
TATATTATAT
Found at i:6342662 original size:18 final size:19
Alignment explanation
Indices: 6342639--6342677 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
6342629 TTTCTAAAAT
*
6342639 ATATATTTTA-AAACCCAA
1 ATATATTATACAAACCCAA
6342657 ATATATTATACTAAACCCAA
1 ATATATTATAC-AAACCCAA
6342677 A
1 A
6342678 CTCAAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
20 9 0.50
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.31
Consensus pattern (19 bp):
ATATATTATACAAACCCAA
Found at i:6349164 original size:27 final size:27
Alignment explanation
Indices: 6349126--6349179 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
6349116 CAAGGATGAG
6349126 TTAATTATTTTAGTGCATAACTTCATC
1 TTAATTATTTTAGTGCATAACTTCATC
6349153 TTAATTATTTTAGTGCATAACTTCATC
1 TTAATTATTTTAGTGCATAACTTCATC
6349180 CCATTGTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.48
Consensus pattern (27 bp):
TTAATTATTTTAGTGCATAACTTCATC
Found at i:6351371 original size:25 final size:27
Alignment explanation
Indices: 6351343--6351395 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
6351333 TGACTAAATT
6351343 TTAAAA-AA-ATTAAAT-AAGAAAATCA
1 TTAAAATAATATTAAATCAA-AAAATCA
6351368 TTAAAATTAATATTAAATCAAAAAATCA
1 TTAAAA-TAATATTAAATCAAAAAATCA
6351396 AAATTAGTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
25 6 0.25
27 2 0.08
28 14 0.58
29 2 0.08
ACGTcount: A:0.64, C:0.06, G:0.02, T:0.28
Consensus pattern (27 bp):
TTAAAATAATATTAAATCAAAAAATCA
Found at i:6352461 original size:13 final size:13
Alignment explanation
Indices: 6352443--6352468 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6352433 TTTAAATCAT
6352443 GGGTATATATATA
1 GGGTATATATATA
6352456 GGGTATATATATA
1 GGGTATATATATA
6352469 TATTAGACCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.38
Consensus pattern (13 bp):
GGGTATATATATA
Found at i:6355758 original size:9 final size:9
Alignment explanation
Indices: 6355744--6355768 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
6355734 CCTATTTCAT
6355744 AAATTCACA
1 AAATTCACA
6355753 AAATTCACA
1 AAATTCACA
6355762 AAATTCA
1 AAATTCA
6355769 ATATGGCCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.20, G:0.00, T:0.24
Consensus pattern (9 bp):
AAATTCACA
Found at i:6368811 original size:70 final size:70
Alignment explanation
Indices: 6368735--6368869 Score: 202
Period size: 70 Copynumber: 1.9 Consensus size: 70
6368725 TTATATTATT
* * * *
6368735 TCATATGGCCGAATATATAAGTTCAATAT-ATCATCACATGTAACCTAATGTTCAAGTTCAA-AT
1 TCATATGGCCGAATATACAAATTCAATATAATC-TCACATGTAACC-AATATACAAGTTCAATAT
6368798 AAACATC
64 AAACATC
6368805 TCATATGGCCGAATATACAAATTCAATATAATCTCACATGTAACCAATATACAAGTTCAATATAA
1 TCATATGGCCGAATATACAAATTCAATATAATCTCACATGTAACCAATATACAAGTTCAATATAA
6368870 GCTCACATGT
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
69 13 0.22
70 43 0.73
71 3 0.05
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.30
Consensus pattern (70 bp):
TCATATGGCCGAATATACAAATTCAATATAATCTCACATGTAACCAATATACAAGTTCAATATAA
ACATC
Found at i:6368901 original size:35 final size:34
Alignment explanation
Indices: 6368744--6368945 Score: 165
Period size: 35 Copynumber: 5.8 Consensus size: 34
6368734 TTCATATGGC
* * *
6368744 CGAATATATAAGTTCAATATATCATCACATGTAA
1 CGAATATACAAGTTCAATATAACCTCACATGTAA
* * * * **
6368778 CCTAATGTTCAAGTTCAA-ATAAACATCTCATATG-GC
1 -CGAATATACAAGTTCAATAT-AAC--CTCACATGTAA
* *
6368814 CGAATATACAAATTCAATATAATCTCACATGTAA
1 CGAATATACAAGTTCAATATAACCTCACATGTAA
* *
6368848 CCAATATACAAGTTCAATATAAGCTCACATGTAA
1 CGAATATACAAGTTCAATATAACCTCACATGTAA
* * * * *
6368882 TCGGATACACAAGTTCAATATAACCTCATATGCAGC
1 -CGAATATACAAGTTCAATATAACCTCACATGTA-A
*
6368918 CGAACATACAAGTTCAATATAACCTCAC
1 CGAATATACAAGTTCAATATAACCTCAC
6368946 TTATACTTAC
Statistics
Matches: 129, Mismatches: 31, Indels: 14
0.74 0.18 0.08
Matches are distributed among these distances:
33 7 0.05
34 33 0.26
35 81 0.63
36 2 0.02
37 6 0.05
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.28
Consensus pattern (34 bp):
CGAATATACAAGTTCAATATAACCTCACATGTAA
Found at i:6369007 original size:43 final size:43
Alignment explanation
Indices: 6368949--6369041 Score: 168
Period size: 43 Copynumber: 2.2 Consensus size: 43
6368939 ACCTCACTTA
* *
6368949 TACTTACCTATGTGGCCAAATATAGAAGTCATTTAGATCAACT
1 TACTTACCTATGTGGCCAAATATAAAAGTCATTTAGAACAACT
6368992 TACTTACCTATGTGGCCAAATATAAAAGTCATTTAGAACAACT
1 TACTTACCTATGTGGCCAAATATAAAAGTCATTTAGAACAACT
6369035 TACTTAC
1 TACTTAC
6369042 TCACTTTCCA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.32
Consensus pattern (43 bp):
TACTTACCTATGTGGCCAAATATAAAAGTCATTTAGAACAACT
Found at i:6371208 original size:113 final size:112
Alignment explanation
Indices: 6371010--6371234 Score: 414
Period size: 113 Copynumber: 2.0 Consensus size: 112
6371000 AGAACGGATT
6371010 ACAAGCCCAAGTTCTTAAAGACAAGGCCCAATAAGATGTTCCAAGCCCAATCCAGAAATTTAAAT
1 ACAAGCCCAAGTTCTTAAAGACAAGGCCCAATAAGATGTTCCAAGCCCAATCCAGAAATTTAAAT
*
6371075 CAAATTTAGTTGAAAATCAGGCCAAATTGTCAAAGTGGCCCAATTTG
66 AAAATTTAGTTGAAAATCAGGCCAAATTGTCAAAGTGGCCCAATTTG
* *
6371122 NACAAGCCCAAGTTCTTAAAGACAAGGCCTAATAAGATGTTCCACGCCCAATCCAGAAATTTAAA
1 -ACAAGCCCAAGTTCTTAAAGACAAGGCCCAATAAGATGTTCCAAGCCCAATCCAGAAATTTAAA
6371187 TAAAATTTAGTTGAAAATCAGGCCAAATTGTCAAAGTGGCCCAATTTG
65 TAAAATTTAGTTGAAAATCAGGCCAAATTGTCAAAGTGGCCCAATTTG
6371235 TAAAATTTTA
Statistics
Matches: 109, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
113 109 1.00
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.24
Consensus pattern (112 bp):
ACAAGCCCAAGTTCTTAAAGACAAGGCCCAATAAGATGTTCCAAGCCCAATCCAGAAATTTAAAT
AAAATTTAGTTGAAAATCAGGCCAAATTGTCAAAGTGGCCCAATTTG
Found at i:6373854 original size:10 final size:11
Alignment explanation
Indices: 6373834--6373877 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
6373824 ATAGTAATTT
6373834 CTCGAAAAAAA
1 CTCGAAAAAAA
6373845 CTCGAAAAAAAA
1 CTCG-AAAAAAA
*
6373857 TTC-AAAAAAA
1 CTCGAAAAAAA
*
6373867 TTCGAAAAAAA
1 CTCGAAAAAAA
6373878 AACTAGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
10 10 0.33
11 11 0.37
12 9 0.30
ACGTcount: A:0.66, C:0.14, G:0.07, T:0.14
Consensus pattern (11 bp):
CTCGAAAAAAA
Found at i:6373938 original size:12 final size:14
Alignment explanation
Indices: 6373917--6373954 Score: 55
Period size: 12 Copynumber: 2.9 Consensus size: 14
6373907 GGATATCAAG
6373917 TTGT-AAAAAAAAA
1 TTGTGAAAAAAAAA
6373930 -T-TGAAAAAAAAA
1 TTGTGAAAAAAAAA
6373942 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
6373955 GAGAGCTAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 1 0.05
12 10 0.45
13 1 0.05
14 10 0.45
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.21
Consensus pattern (14 bp):
TTGTGAAAAAAAAA
Found at i:6373940 original size:14 final size:14
Alignment explanation
Indices: 6373921--6373954 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
6373911 ATCAAGTTGT
6373921 AAAAAAAAAT-TGA
1 AAAAAAAAATGTGA
*
6373934 AAAAAAAATTGTGA
1 AAAAAAAAATGTGA
6373948 AAAAAAA
1 AAAAAAA
6373955 GAGAGCTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (14 bp):
AAAAAAAAATGTGA
Found at i:6382007 original size:11 final size:11
Alignment explanation
Indices: 6381991--6382016 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
6381981 TAGAAGAGAC
6381991 GAAACAGGGGA
1 GAAACAGGGGA
6382002 GAAACAGGGGA
1 GAAACAGGGGA
6382013 GAAA
1 GAAA
6382017 GAAGAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.08, G:0.42, T:0.00
Consensus pattern (11 bp):
GAAACAGGGGA
Found at i:6382700 original size:18 final size:18
Alignment explanation
Indices: 6382677--6382725 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
6382667 ATGTGAGGTA
*
6382677 AGTATTAATATTAGTATT
1 AGTATTATTATTAGTATT
6382695 AGTATTATTATTAGTATT
1 AGTATTATTATTAGTATT
*
6382713 ATTATTATTATTA
1 AGTATTATTATTA
6382726 TGAGTGGGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (18 bp):
AGTATTATTATTAGTATT
Found at i:6382705 original size:3 final size:3
Alignment explanation
Indices: 6382679--6382726 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
6382669 GTGAGGTAAG
* * * *
6382679 TAT TAA TAT TAG TAT TAG TAT TAT TAT TAG TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
6382727 GAGTGGGAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:6382726 original size:12 final size:12
Alignment explanation
Indices: 6382679--6382726 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
6382669 GTGAGGTAAG
* *
6382679 TATTAATATTAG
1 TATTAGTATTAT
6382691 TATTAGTATTAT
1 TATTAGTATTAT
6382703 TATTAGTATTAT
1 TATTAGTATTAT
*
6382715 TATTATTATTAT
1 TATTAGTATTAT
6382727 GAGTGGGAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (12 bp):
TATTAGTATTAT
Found at i:6382921 original size:24 final size:24
Alignment explanation
Indices: 6382867--6382938 Score: 67
Period size: 24 Copynumber: 2.9 Consensus size: 24
6382857 TGTGTGAAGT
*
6382867 TGTGAAATAATTATTG-ATTG-AAA
1 TGTGAAA-AATGATTGAATTGAAAA
*
6382890 GGTGGAAAAATGATTGAATTGAAAA
1 TGT-GAAAAATGATTGAATTGAAAA
6382915 TGTGAAAAATTGTAATTGAATTGA
1 TGTGAAAAA-TG--ATTGAATTGA
6382939 GAATATATGT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
23 9 0.22
24 14 0.35
25 7 0.17
27 10 0.25
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.33
Consensus pattern (24 bp):
TGTGAAAAATGATTGAATTGAAAA
Found at i:6383141 original size:37 final size:39
Alignment explanation
Indices: 6383082--6383177 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
6383072 CGGATAGATT
* * * *
6383082 CGATGAGGTACTGGGTACCAACT-TT-CTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTAT-C
* *
6383119 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
6383158 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
6383178 TTCTGGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.40
38 2 0.04
39 24 0.50
40 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
Done.