Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10
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: 48586650
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2183483 characters in sequence are not A, C, G, or T
File 9 of 145
Found at i:3114508 original size:84 final size:84
Alignment explanation
Indices: 3114400--3114555 Score: 233
Period size: 84 Copynumber: 1.9 Consensus size: 84
3114390 CCAAAGCGGC
* * * *
3114400 GCCGTTTCTTTACTGGAATAAAATCTTTTAGTGGCGTTTTGTATGAAAACGCCGCAA-ATGTGAA
1 GCCGTTTCTCTACTCGAATAAAATCTTATAGTGGCGTTTTGTAAGAAAACGCCGCAAGA-GTGAA
3114464 TTAATGTTGGCCAATACGGT
65 TTAATGTTGGCCAATACGGT
* * *
3114484 GCCGTTTCTCTACTCGAATGAAATCTTATAGTGGCGTTTTTTAAGAAAACGCTGCAAGAGTGAAT
1 GCCGTTTCTCTACTCGAATAAAATCTTATAGTGGCGTTTTGTAAGAAAACGCCGCAAGAGTGAAT
3114549 TAATGTT
66 TAATGTT
3114556 TGGCAATGTG
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
84 63 0.98
85 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (84 bp):
GCCGTTTCTCTACTCGAATAAAATCTTATAGTGGCGTTTTGTAAGAAAACGCCGCAAGAGTGAAT
TAATGTTGGCCAATACGGT
Found at i:3114573 original size:84 final size:84
Alignment explanation
Indices: 3114401--3114574 Score: 208
Period size: 84 Copynumber: 2.1 Consensus size: 84
3114391 CAAAGCGGCG
* * * *
3114401 CCGTTTCTTTACTGGAATAAAATCTTTTAGTGGCGTTTTGTATGAAAACGCCGCAAATGTGAATT
1 CCGTTTCTCTACTCGAATAAAATCTTATAGTGGCGTTTTGTAAGAAAACGCCGCAAATGTGAATT
***
3114466 AATGTTGGCCAATACGGTG
66 AATGTTGGCCAATACGACA
* * *
3114485 CCGTTTCTCTACTCGAATGAAATCTTATAGTGGCGTTTTTTAAGAAAACGCTGCAAGA-GTGAAT
1 CCGTTTCTCTACTCGAATAAAATCTTATAGTGGCGTTTTGTAAGAAAACGCCGCAA-ATGTGAAT
**
3114549 TAATGTTTGG-CAATGTGACA
65 TAATG-TTGGCCAATACGACA
3114569 CCGTTT
1 CCGTTT
3114575 GGCTTCATGA
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
84 71 0.93
85 5 0.07
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (84 bp):
CCGTTTCTCTACTCGAATAAAATCTTATAGTGGCGTTTTGTAAGAAAACGCCGCAAATGTGAATT
AATGTTGGCCAATACGACA
Found at i:3114904 original size:83 final size:84
Alignment explanation
Indices: 3114809--3115057 Score: 235
Period size: 84 Copynumber: 3.0 Consensus size: 84
3114799 TGCCGTTCTT
* * *
3114809 ATGTTTTAAAATTTGTCAAAACGGCGCCGTTTATCT-TGAGGAA-AGAAATATT-TTGTGGCG-T
1 ATGTATTAAAATTTGCCAAAACGGCGCCGTTTATCTAT-AGGAATA-AAATATTATAGTGGCGCT
3114870 TTTTGATAAAAACGCCGCAAGG
64 TTTT-ATAAAAACGCCGCAAGG
* * *
3114892 ATGTATTAAAATTTGCCAAAGCGGCGCCGTTTATCTATTGGAATAAAATCTTATAGTGGCGCTTT
1 ATGTATTAAAATTTGCCAAAACGGCGCCGTTTATCTATAGGAATAAAATATTATAGTGGCGCTTT
3114957 TTATAAAAACGCCGCAA-G
66 TTATAAAAACGCCGCAAGG
* ** * ** * * * *
3114975 AGTGAATTAATCTTTGCCAATACGATGTCGTTTCTCTACT-GGAATGAAATCTTATAGTGGCG-T
1 A-TGTATTAAAATTTGCCAAAACGGCGCCGTTTATCTA-TAGGAATAAAATATTATAGTGGCGCT
*
3115038 TTTTA-AGAAAATGCCGCAAG
64 TTTTATA-AAAACGCCGCAAG
3115058 TGTGAATTAA
Statistics
Matches: 141, Mismatches: 17, Indels: 15
0.82 0.10 0.09
Matches are distributed among these distances:
82 1 0.01
83 62 0.44
84 72 0.51
85 6 0.04
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (84 bp):
ATGTATTAAAATTTGCCAAAACGGCGCCGTTTATCTATAGGAATAAAATATTATAGTGGCGCTTT
TTATAAAAACGCCGCAAGG
Found at i:3114984 original size:84 final size:82
Alignment explanation
Indices: 3114814--3115090 Score: 258
Period size: 83 Copynumber: 3.3 Consensus size: 82
3114804 TTCTTATGTT
* * * * *
3114814 TTAAAATTTGTCAAAACGGCGCCGTTTATCT-TGAGGAA-AGAAATATT-TTGTGGCGTTTTTGA
1 TTAAAATTTGCCAAAGCGGCGCCGTTTATCTAT-TGGAATA-AAATCTTATAGTGGCGTTTTT-A
*
3114876 TAAAAACGCCGCAAGGATGTA
63 TAAAAACGCCGCAAGG-TGAA
3114897 TTAAAATTTGCCAAAGCGGCGCCGTTTATCTATTGGAATAAAATCTTATAGTGGCGCTTTTTATA
1 TTAAAATTTGCCAAAGCGGCGCCGTTTATCTATTGGAATAAAATCTTATAGTGGCG-TTTTTATA
3114962 AAAACGCCGCAAGAGTGAA
65 AAAACGCCGCAAG-GTGAA
** ** * * * *
3114981 TTAATCTTTGCCAATA-CGATGTCGTTTCTCTACTGGAATGAAATCTTATAGTGGCGTTTTTA-A
1 TTAAAATTTGCCAA-AGCGGCGCCGTTTATCTATTGGAATAAAATCTTATAGTGGCGTTTTTATA
*
3115044 GAAAATGCCGCAAGTGTGAA
65 -AAAACGCCGCAAG-GTGAA
** * * *
3115064 TTAATGTTTGTCAATGCGGCACCGTTT
1 TTAAAATTTGCCAAAGCGGCGCCGTTT
3115091 TCTGTTCAGT
Statistics
Matches: 163, Mismatches: 23, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
82 1 0.01
83 81 0.50
84 74 0.45
85 7 0.04
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (82 bp):
TTAAAATTTGCCAAAGCGGCGCCGTTTATCTATTGGAATAAAATCTTATAGTGGCGTTTTTATAA
AAACGCCGCAAGGTGAA
Found at i:3115090 original size:83 final size:82
Alignment explanation
Indices: 3114863--3115090 Score: 260
Period size: 84 Copynumber: 2.7 Consensus size: 82
3114853 GAAATATTTT
* * *
3114863 GTGGCGTTTTTGATAAAAACGCCGCAAGGATGTATTAAAATTTGCCAAAGCGGCGCCGTTTATCT
1 GTGGCGTTTTT-ATAAAAACGCCGCAAGG-TGAATTAATATTTGCCAATGCGGCGCCGTTTATCT
*
3114928 ATTGGAATAAAATCTTATA
64 ACTGGAATAAAATCTTATA
* * ** * *
3114947 GTGGCGCTTTTTATAAAAACGCCGCAAGAGTGAATTAATCTTTGCCAATACGATGTCGTTTCTCT
1 GTGGCG-TTTTTATAAAAACGCCGCAAG-GTGAATTAATATTTGCCAATGCGGCGCCGTTTATCT
*
3115012 ACTGGAATGAAATCTTATA
64 ACTGGAATAAAATCTTATA
* * * *
3115031 GTGGCGTTTTTA-AGAAAATGCCGCAAGTGTGAATTAATGTTTGTCAATGCGGCACCGTTT
1 GTGGCGTTTTTATA-AAAACGCCGCAAG-GTGAATTAATATTTGCCAATGCGGCGCCGTTT
3115091 TCTGTTCAGT
Statistics
Matches: 121, Mismatches: 20, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
82 1 0.01
83 43 0.36
84 71 0.59
85 6 0.05
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.32
Consensus pattern (82 bp):
GTGGCGTTTTTATAAAAACGCCGCAAGGTGAATTAATATTTGCCAATGCGGCGCCGTTTATCTAC
TGGAATAAAATCTTATA
Found at i:3116114 original size:32 final size:32
Alignment explanation
Indices: 3116073--3116137 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
3116063 TGAGTATTGC
3116073 AAATTATCTACAAATGCTTTCCATCTAAAACA
1 AAATTATCTACAAATGCTTTCCATCTAAAACA
*
3116105 AAATTATCTACAAATGCTTTCCATCTGAAACA
1 AAATTATCTACAAATGCTTTCCATCTAAAACA
3116137 A
1 A
3116138 GCTTGTCATC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.43, C:0.22, G:0.05, T:0.31
Consensus pattern (32 bp):
AAATTATCTACAAATGCTTTCCATCTAAAACA
Found at i:3116484 original size:5 final size:5
Alignment explanation
Indices: 3116461--3116500 Score: 53
Period size: 5 Copynumber: 7.6 Consensus size: 5
3116451 ATAACACTTC
*
3116461 TTTTA TTTTAA TATGTA TTTTA TTTTA TTTTA TTTTA TTT
1 TTTTA TTTT-A T-TTTA TTTTA TTTTA TTTTA TTTTA TTT
3116501 AATAATACTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 25 0.81
6 4 0.13
7 2 0.06
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:3117846 original size:2 final size:2
Alignment explanation
Indices: 3117839--3117865 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3117829 NNNNNNNNNN
3117839 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3117866 TCTCGACTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3124055 original size:43 final size:43
Alignment explanation
Indices: 3123994--3124122 Score: 195
Period size: 43 Copynumber: 3.0 Consensus size: 43
3123984 CTGTGTGTTT
*
3123994 TATTTTTTATTCTTATTGCTTTGCGATCTTTTTATATTGTCAC
1 TATTTTTTATTCTTATTGCTTTGCGATCTTTCTATATTGTCAC
* * *
3124037 TATTTTTTATTCTTATTGCTTTGCGATCCTTCTATATTATCAT
1 TATTTTTTATTCTTATTGCTTTGCGATCTTTCTATATTGTCAC
* *
3124080 TATTTTTTTATTCTTATTGCTTTGCTATCTTTCTAAATTGTCA
1 TA-TTTTTTATTCTTATTGCTTTGCGATCTTTCTATATTGTCA
3124123 TTATCGACGT
Statistics
Matches: 77, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
43 41 0.53
44 36 0.47
ACGTcount: A:0.18, C:0.15, G:0.08, T:0.60
Consensus pattern (43 bp):
TATTTTTTATTCTTATTGCTTTGCGATCTTTCTATATTGTCAC
Found at i:3124102 original size:44 final size:44
Alignment explanation
Indices: 3123996--3124126 Score: 201
Period size: 44 Copynumber: 3.0 Consensus size: 44
3123986 GTGTGTTTTA
* *
3123996 TTTTTTATTCTTATTGCTTTGCGATCTTTTTATATTGTCACTA-
1 TTTTTTATTCTTATTGCTTTGCGATCTTTCTATATTGTCATTAT
* *
3124039 TTTTTTATTCTTATTGCTTTGCGATCCTTCTATATTATCATTAT
1 TTTTTTATTCTTATTGCTTTGCGATCTTTCTATATTGTCATTAT
* *
3124083 TTTTTTATTCTTATTGCTTTGCTATCTTTCTAAATTGTCATTAT
1 TTTTTTATTCTTATTGCTTTGCGATCTTTCTATATTGTCATTAT
3124127 CGACGTTTAA
Statistics
Matches: 79, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
43 39 0.49
44 40 0.51
ACGTcount: A:0.18, C:0.15, G:0.08, T:0.60
Consensus pattern (44 bp):
TTTTTTATTCTTATTGCTTTGCGATCTTTCTATATTGTCATTAT
Found at i:3125327 original size:18 final size:18
Alignment explanation
Indices: 3125304--3125352 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
3125294 TCTAAATTAA
3125304 AAAATACAAAAAATGAA-T
1 AAAATACAAAAAAT-AATT
**
3125322 AAAATAGTAAAAATAATT
1 AAAATACAAAAAATAATT
3125340 AAAATACAAAAAA
1 AAAATACAAAAAA
3125353 AAAAAGAAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 2 0.08
18 24 0.92
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.18
Consensus pattern (18 bp):
AAAATACAAAAAATAATT
Found at i:3148810 original size:6 final size:6
Alignment explanation
Indices: 3148799--3148823 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3148789 GGAAGAGAGC
3148799 GAAATA GAAATA GAAATA GAAATA G
1 GAAATA GAAATA GAAATA GAAATA G
3148824 GAAGATAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.20, T:0.16
Consensus pattern (6 bp):
GAAATA
Found at i:3150178 original size:40 final size:40
Alignment explanation
Indices: 3150147--3150224 Score: 95
Period size: 42 Copynumber: 1.9 Consensus size: 40
3150137 GATTTGTGTC
* *
3150147 CACGTA-AGGACATCGCGCTGACGTGGACGCGATGTCCTGA
1 CACGTACAGGACATCACGCTGACGTGGACGCGAT-TTCTGA
**
3150187 CACGTACCCTGACATCACGCTGACGTGGACGCGATTTC
1 CACGTA-CAGGACATCACGCTGACGTGGACGCGATTTC
3150225 GCGAAAAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
40 6 0.19
41 2 0.06
42 24 0.75
ACGTcount: A:0.22, C:0.31, G:0.28, T:0.19
Consensus pattern (40 bp):
CACGTACAGGACATCACGCTGACGTGGACGCGATTTCTGA
Found at i:3154377 original size:191 final size:191
Alignment explanation
Indices: 3154047--3154429 Score: 748
Period size: 191 Copynumber: 2.0 Consensus size: 191
3154037 CATGTGGTTC
* *
3154047 ACATGGCCAAGAGACACGCCCGTATCTTAGGCCATGTGCATATTTGAAATAGGGCACATGGTAGT
1 ACATGACCAAGAGACACGCCCGTATCTTAGGCCATGTGCATATTTGAAATAGGGCACACGGTAGT
3154112 GTCCCAACCCGTGTACATACCCGTGTAACTCTTTAACTTGGGTCACACGGCCAAGCCACACGTAC
66 GTCCCAACCCGTGTACATACCCGTGTAACTCTTTAACTTGGGTCACACGGCCAAGCCACACGTAC
3154177 ATGTGCTAGGCCATGTGAATATGAAAATTTGCATTAAATAGGTGCAATGGTCACACGGCCA
131 ATGTGCTAGGCCATGTGAATATGAAAATTTGCATTAAATAGGTGCAATGGTCACACGGCCA
3154238 ACATGACCAAGAGACACGCCCGTATCTTAGGCCATGTGCATATTTGAAATAGGGCACACGGTAGT
1 ACATGACCAAGAGACACGCCCGTATCTTAGGCCATGTGCATATTTGAAATAGGGCACACGGTAGT
3154303 GTCCCAACCCGTGTACATACCCGTGTAACTCTTTAACTTGGGTCACACGGCCAAGCCACACGTAC
66 GTCCCAACCCGTGTACATACCCGTGTAACTCTTTAACTTGGGTCACACGGCCAAGCCACACGTAC
3154368 ATGTGCTAGGCCATGTGAATATGAAAATTTGCATTAAATAGGTGCAATGGTCACACGGCCA
131 ATGTGCTAGGCCATGTGAATATGAAAATTTGCATTAAATAGGTGCAATGGTCACACGGCCA
3154429 A
1 A
3154430 GCCACACGCC
Statistics
Matches: 190, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
191 190 1.00
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (191 bp):
ACATGACCAAGAGACACGCCCGTATCTTAGGCCATGTGCATATTTGAAATAGGGCACACGGTAGT
GTCCCAACCCGTGTACATACCCGTGTAACTCTTTAACTTGGGTCACACGGCCAAGCCACACGTAC
ATGTGCTAGGCCATGTGAATATGAAAATTTGCATTAAATAGGTGCAATGGTCACACGGCCA
Found at i:3155517 original size:23 final size:23
Alignment explanation
Indices: 3155466--3155531 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 23
3155456 CATTAATCAG
* *
3155466 GAAGCTCTAGATAGCCATATATCGA
1 GAAGCTCAAGAGAGCC--ATATCGA
* * *
3155491 GAAGTTCAAGCGAGCCATATCGG
1 GAAGCTCAAGAGAGCCATATCGA
*
3155514 GAAGCTCCAGAGAGCCAT
1 GAAGCTCAAGAGAGCCAT
3155532 TAATCAGGAA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
23 21 0.64
25 12 0.36
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.18
Consensus pattern (23 bp):
GAAGCTCAAGAGAGCCATATCGA
Found at i:3155564 original size:26 final size:26
Alignment explanation
Indices: 3155449--3155583 Score: 104
Period size: 25 Copynumber: 5.4 Consensus size: 26
3155439 GGGTAGCTCT
*
3155449 AAAGAGCCATTAATCAGGAAGCTC-T
1 AAAGAGCCATTAATCAGGAAGCTCAC
* * *
3155474 AGATAGCCA-TATATC-GAGAAGTTCA-
1 AAAGAGCCATTA-ATCAG-GAAGCTCAC
** *
3155499 AGCGAGCCA-T-ATCGGGAAGCTC-C
1 AAAGAGCCATTAATCAGGAAGCTCAC
*
3155522 AGAGAGCCATTAATCAGGAAGCTCAC
1 AAAGAGCCATTAATCAGGAAGCTCAC
* *
3155548 AAAGGGCCTTTAATCAGGAAGCTCAC
1 AAAGAGCCATTAATCAGGAAGCTCAC
*
3155574 GAAGAGCCAT
1 AAAGAGCCAT
3155584 ATATCAGAAC
Statistics
Matches: 88, Mismatches: 14, Indels: 15
0.75 0.12 0.13
Matches are distributed among these distances:
23 17 0.19
24 5 0.06
25 35 0.40
26 31 0.35
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (26 bp):
AAAGAGCCATTAATCAGGAAGCTCAC
Found at i:3155589 original size:26 final size:27
Alignment explanation
Indices: 3155524--3155598 Score: 86
Period size: 26 Copynumber: 2.9 Consensus size: 27
3155514 GAAGCTCCAG
*
3155524 AGAGCCAT-TAATCAGGAAGCTCACAA
1 AGAGCCATATAATCAGGAAGCTCACGA
* *
3155550 AGGGCC-TTTAATCAGGAAGCTCACGA
1 AGAGCCATATAATCAGGAAGCTCACGA
3155576 AGAGCCATAT-ATCA-GAACGCTCA
1 AGAGCCATATAATCAGGAA-GCTCA
3155599 TAAGAGCTGT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
25 4 0.10
26 36 0.86
27 2 0.05
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.17
Consensus pattern (27 bp):
AGAGCCATATAATCAGGAAGCTCACGA
Found at i:3157919 original size:14 final size:14
Alignment explanation
Indices: 3157900--3157927 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3157890 ACAAATTACA
3157900 TGTTAGAATAGTAT
1 TGTTAGAATAGTAT
3157914 TGTTAGAATAGTAT
1 TGTTAGAATAGTAT
3157928 CATTAGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.43
Consensus pattern (14 bp):
TGTTAGAATAGTAT
Found at i:3157933 original size:14 final size:14
Alignment explanation
Indices: 3157902--3157935 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3157892 AAATTACATG
**
3157902 TTAGAATAGTATTG
1 TTAGAATAGTATCA
3157916 TTAGAATAGTATCA
1 TTAGAATAGTATCA
3157930 TTAGAA
1 TTAGAA
3157936 AAAAAAATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.41, C:0.03, G:0.18, T:0.38
Consensus pattern (14 bp):
TTAGAATAGTATCA
Found at i:3160617 original size:12 final size:12
Alignment explanation
Indices: 3160600--3160647 Score: 64
Period size: 12 Copynumber: 4.2 Consensus size: 12
3160590 TAATCCTCTC
3160600 AATTTCCTTCCA
1 AATTTCCTTCCA
3160612 AATTTCCTTCCA
1 AATTTCCTTCCA
* *
3160624 AAATT-C-TCCC
1 AATTTCCTTCCA
3160634 AATTTCCTTCCA
1 AATTTCCTTCCA
3160646 AA
1 AA
3160648 ATTCTCTCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
10 7 0.23
11 2 0.07
12 21 0.70
ACGTcount: A:0.29, C:0.33, G:0.00, T:0.38
Consensus pattern (12 bp):
AATTTCCTTCCA
Found at i:3160640 original size:22 final size:22
Alignment explanation
Indices: 3160612--3160653 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
3160602 TTTCCTTCCA
3160612 AATTTCCTTCCAAAATTCTCCC
1 AATTTCCTTCCAAAATTCTCCC
3160634 AATTTCCTTCCAAAATTCTC
1 AATTTCCTTCCAAAATTCTC
3160654 TCAAATCCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.29, C:0.33, G:0.00, T:0.38
Consensus pattern (22 bp):
AATTTCCTTCCAAAATTCTCCC
Found at i:3162326 original size:18 final size:18
Alignment explanation
Indices: 3162300--3162334 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3162290 AGTTGTGTTT
* *
3162300 CCTAGCCCTTATATGTAC
1 CCTAACCCTTACATGTAC
3162318 CCTAACCCTTACATGTA
1 CCTAACCCTTACATGTA
3162335 TCCTTTTCCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.34, G:0.09, T:0.31
Consensus pattern (18 bp):
CCTAACCCTTACATGTAC
Found at i:3162767 original size:25 final size:25
Alignment explanation
Indices: 3162738--3162848 Score: 81
Period size: 25 Copynumber: 4.6 Consensus size: 25
3162728 TTTAAATTTA
3162738 TTATTTGATGTAATAAAATAGAATT
1 TTATTTGATGTAATAAAATAGAATT
**
3162763 TTATTTGATGTAATACGCATAGAAATT
1 TTATTTGATGTAATA-AAATAG-AATT
* ** * *
3162790 TT-TTCGA-GT--T-ATTTTG-ATA
1 TTATTTGATGTAATAAAATAGAATT
*
3162809 TTATTTGATGTAATAAAATAGAAAT
1 TTATTTGATGTAATAAAATAGAATT
*
3162834 TTATTTGATATAATA
1 TTATTTGATGTAATA
3162849 GGCATAAAAT
Statistics
Matches: 63, Mismatches: 15, Indels: 16
0.67 0.16 0.17
Matches are distributed among these distances:
19 4 0.06
20 4 0.06
21 4 0.06
23 2 0.03
24 3 0.05
25 32 0.51
26 8 0.13
27 6 0.10
ACGTcount: A:0.39, C:0.03, G:0.13, T:0.46
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAATT
Found at i:3162792 original size:28 final size:27
Alignment explanation
Indices: 3162731--3162792 Score: 74
Period size: 25 Copynumber: 2.3 Consensus size: 27
3162721 TACCGTATTT
3162731 AAATTTATTATTTGATGTAATAAAATAG
1 AAATTT-TTATTTGATGTAATAAAATAG
**
3162759 -AA-TTTTATTTGATGTAATACGCATAG
1 AAATTTTTATTTGATGTAATA-AAATAG
3162785 AAATTTTT
1 AAATTTTT
3162793 TCGAGTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
25 15 0.52
26 6 0.21
27 4 0.14
28 4 0.14
ACGTcount: A:0.40, C:0.03, G:0.11, T:0.45
Consensus pattern (27 bp):
AAATTTTTATTTGATGTAATAAAATAG
Found at i:3162824 original size:71 final size:71
Alignment explanation
Indices: 3162736--3162916 Score: 292
Period size: 71 Copynumber: 2.5 Consensus size: 71
3162726 TATTTAAATT
3162736 TATTATTTGATGTAATAAAATAGAATTTTATTTGATGTAATACGCATAGAAA-TTTTTTCGAGTT
1 TATTATTTGATGTAATAAAATAGAATTTTATTTGATGTAATACGCATA-AAATTTTTTTCGAGTT
3162800 ATTTTGA
65 ATTTTGA
* * *
3162807 TATTATTTGATGTAATAAAATAGAAATTTATTTGATATAATAGGCATAAAATTTTTTTCGAGTTA
1 TATTATTTGATGTAATAAAATAGAATTTTATTTGATGTAATACGCATAAAATTTTTTTCGAGTTA
3162872 TTTTGA
66 TTTTGA
* *
3162878 TATTATTTGATATAATAAAATAGAAGTTATATTTGATGT
1 TATTATTTGATGTAATAAAATAGAA-TTTTATTTGATGT
3162917 TATAAAAACC
Statistics
Matches: 101, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
70 3 0.03
71 88 0.87
72 10 0.10
ACGTcount: A:0.38, C:0.03, G:0.13, T:0.46
Consensus pattern (71 bp):
TATTATTTGATGTAATAAAATAGAATTTTATTTGATGTAATACGCATAAAATTTTTTTCGAGTTA
TTTTGA
Found at i:3162913 original size:36 final size:35
Alignment explanation
Indices: 3162796--3162919 Score: 90
Period size: 36 Copynumber: 3.5 Consensus size: 35
3162786 AATTTTTTCG
*
3162796 AGTTATTTTGATATTATTTGATGTAATAAAATAGA
1 AGTTATTTTGATATTATTTGATATAATAAAATAGA
* * ** * **** *
3162831 AATT-TATTTGATATAATAGGCATAAAATTTTTTTCG-
1 AGTTAT-TTTGATATTATTTG-ATATAA-TAAAATAGA
3162867 AGTTATTTTGATATTATTTGATATAATAAAATAGA
1 AGTTATTTTGATATTATTTGATATAATAAAATAGA
*
3162902 AGTTATATTTGATGTTAT
1 AGTTAT-TTTGATATTAT
3162920 AAAAACCCTA
Statistics
Matches: 61, Mismatches: 22, Indels: 11
0.65 0.23 0.12
Matches are distributed among these distances:
34 4 0.07
35 25 0.41
36 28 0.46
37 4 0.07
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.48
Consensus pattern (35 bp):
AGTTATTTTGATATTATTTGATATAATAAAATAGA
Found at i:3162942 original size:18 final size:18
Alignment explanation
Indices: 3162919--3162971 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 18
3162909 TTTGATGTTA
3162919 TAAAAACCCTAATTTAAT
1 TAAAAACCCTAATTTAAT
3162937 TAAAAACCCTAACATAATTTAAT
1 TAAAAA-CC---C-TAATTTAAT
3162960 TAAAAACCCTAA
1 TAAAAACCCTAA
3162972 CCCTAACCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
18 9 0.30
19 3 0.10
22 3 0.10
23 15 0.50
ACGTcount: A:0.53, C:0.19, G:0.00, T:0.28
Consensus pattern (18 bp):
TAAAAACCCTAATTTAAT
Found at i:3162954 original size:23 final size:23
Alignment explanation
Indices: 3162928--3162972 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
3162918 ATAAAAACCC
3162928 TAATTTAATTAAAAACCCTAACA
1 TAATTTAATTAAAAACCCTAACA
3162951 TAATTTAATTAAAAACCCTAAC
1 TAATTTAATTAAAAACCCTAAC
3162973 CCTAACCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.31
Consensus pattern (23 bp):
TAATTTAATTAAAAACCCTAACA
Found at i:3162974 original size:29 final size:29
Alignment explanation
Indices: 3162941--3163256 Score: 467
Period size: 29 Copynumber: 10.8 Consensus size: 29
3162931 TTTAATTAAA
*
3162941 AACCCTAACATAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
3162970 AACCCTAACCTAATTTAATTAAAAACCC-
1 AACCCTAACCTAATTTAATTAAAAACCCT
* *
3162998 ACTGCCCTAACCTAATTTGATTAAAAACCCT
1 A--ACCCTAACCTAATTTAATTAAAAACCCT
*
3163029 AACACTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
3163058 AACCCTAACCTAATTTAATTAAAAACCC-
1 AACCCTAACCTAATTTAATTAAAAACCCT
* *
3163086 ACTGCCCTAACCTAATTTGATTAAAAACCCT
1 A--ACCCTAACCTAATTTAATTAAAAACCCT
*
3163117 AACACTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
3163146 AACCCTAACCTAATTTAATTAAAAACCC-
1 AACCCTAACCTAATTTAATTAAAAACCCT
* *
3163174 ACTGCCCTAACCTAATTTGATTAAAAACCCT
1 A--ACCCTAACCTAATTTAATTAAAAACCCT
*
3163205 AACACTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
3163234 AACCCTAACCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
3163257 TATCAATTAA
Statistics
Matches: 259, Mismatches: 19, Indels: 18
0.88 0.06 0.06
Matches are distributed among these distances:
28 3 0.01
29 178 0.69
30 75 0.29
31 3 0.01
ACGTcount: A:0.44, C:0.27, G:0.02, T:0.28
Consensus pattern (29 bp):
AACCCTAACCTAATTTAATTAAAAACCCT
Found at i:3163014 original size:59 final size:58
Alignment explanation
Indices: 3162941--3163256 Score: 467
Period size: 59 Copynumber: 5.4 Consensus size: 58
3162931 TTTAATTAAA
*
3162941 AACCCTAACATAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCC-
1 AACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCT
* * *
3162998 ACTGCCCTAACCTAATTTGATTAAAAACCCTAACACTAACCTAATTTAATTAAAAACCCT
1 A--ACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCT
* *
3163058 AACCCTAACCTAATTTAATTAAAAACCC-ACTGCCCTAACCTAATTTGATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCTA--ACCCTAACCTAATTTAATTAAAAACCCT
*
3163117 AACACTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCC-
1 AACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCT
* * *
3163174 ACTGCCCTAACCTAATTTGATTAAAAACCCTAACACTAACCTAATTTAATTAAAAACCCT
1 A--ACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCT
3163234 AACCCTAACCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
3163257 TATCAATTAA
Statistics
Matches: 232, Mismatches: 18, Indels: 17
0.87 0.07 0.06
Matches are distributed among these distances:
57 3 0.01
58 70 0.30
59 156 0.67
60 3 0.01
ACGTcount: A:0.44, C:0.27, G:0.02, T:0.28
Consensus pattern (58 bp):
AACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCT
Found at i:3163069 original size:88 final size:88
Alignment explanation
Indices: 3162945--3163256 Score: 615
Period size: 88 Copynumber: 3.5 Consensus size: 88
3162935 ATTAAAAACC
*
3162945 CTAACATAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCACTGCCCTAACC
1 CTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCACTGCCCTAACC
3163010 TAATTTGATTAAAAACCCTAACA
66 TAATTTGATTAAAAACCCTAACA
3163033 CTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCACTGCCCTAACC
1 CTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCACTGCCCTAACC
3163098 TAATTTGATTAAAAACCCTAACA
66 TAATTTGATTAAAAACCCTAACA
3163121 CTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCACTGCCCTAACC
1 CTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCACTGCCCTAACC
3163186 TAATTTGATTAAAAACCCTAACA
66 TAATTTGATTAAAAACCCTAACA
3163209 CTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAA
1 CTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAA
3163257 TATCAATTAA
Statistics
Matches: 223, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 223 1.00
ACGTcount: A:0.44, C:0.26, G:0.02, T:0.28
Consensus pattern (88 bp):
CTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCACTGCCCTAACC
TAATTTGATTAAAAACCCTAACA
Found at i:3167175 original size:35 final size:35
Alignment explanation
Indices: 3167098--3167168 Score: 103
Period size: 35 Copynumber: 2.1 Consensus size: 35
3167088 ATTTTCCAAT
3167098 AACTAAAAATAAAATCAATCAAATATAAAGAAAAA
1 AACTAAAAATAAAATCAATCAAATATAAAGAAAAA
*
3167133 AACTAAAAATAAAAT-AATCCAAA-CTAAA-AAAAA
1 AACTAAAAATAAAATCAAT-CAAATATAAAGAAAAA
3167166 AAC
1 AAC
3167169 AGTAAAACTC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
33 8 0.24
34 7 0.21
35 19 0.56
ACGTcount: A:0.72, C:0.11, G:0.01, T:0.15
Consensus pattern (35 bp):
AACTAAAAATAAAATCAATCAAATATAAAGAAAAA
Found at i:3172192 original size:8 final size:8
Alignment explanation
Indices: 3172179--3172211 Score: 57
Period size: 8 Copynumber: 4.0 Consensus size: 8
3172169 CATCAATTTT
3172179 ATTTATTC
1 ATTTATTC
3172187 ATTTATTC
1 ATTTATTC
3172195 ATTTATTC
1 ATTTATTC
3172203 ATATTATTC
1 AT-TTATTC
3172212 CTATATCATC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.75
9 6 0.25
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.61
Consensus pattern (8 bp):
ATTTATTC
Found at i:3172927 original size:18 final size:18
Alignment explanation
Indices: 3172906--3172949 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
3172896 AATTTCAAAA
3172906 AAAAATACAAAAAAAATT
1 AAAAATACAAAAAAAATT
* * *
3172924 AAAATTTCATAAAAAATT
1 AAAAATACAAAAAAAATT
3172942 ATAAAATA
1 A-AAAATA
3172950 TCTAAAACAC
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (18 bp):
AAAAATACAAAAAAAATT
Found at i:3175168 original size:41 final size:41
Alignment explanation
Indices: 3175119--3175217 Score: 135
Period size: 41 Copynumber: 2.4 Consensus size: 41
3175109 GACTTTAAGT
*
3175119 CTAGCAGGCTATGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTATGTGCCGGTGATCTGAATCAGGCTATAAAC
* ** **
3175160 CTAGCAGGCTACGTGTTGGTGATCTGAATCAGGCTATAAGT
1 CTAGCAGGCTATGTGCCGGTGATCTGAATCAGGCTATAAAC
*
3175201 CTAGCGGGCTATGTGCC
1 CTAGCAGGCTATGTGCC
3175218 ATTGAATTTG
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.27
Consensus pattern (41 bp):
CTAGCAGGCTATGTGCCGGTGATCTGAATCAGGCTATAAAC
Found at i:3179283 original size:89 final size:88
Alignment explanation
Indices: 3179126--3179305 Score: 288
Period size: 89 Copynumber: 2.0 Consensus size: 88
3179116 ATCCATATAC
* *
3179126 ATTCTGTGACAAAAAGCATATAAATATAATGTTCATCGTCACATTATCTTTAATTCTTGGAGTTT
1 ATTCTGTGACAAAAAGCATATAAATATAACGTTCATCGTCACATTATATTTAATTCTTGGAG-TT
*
3179191 TTTTTTACATTTGTTGGAACATTT
65 TTTTTTACATTTATTGGAACATTT
*
3179215 ATTCTGTGACAAAAAGCATATAAATGTAACGTTCATCGTCACATTATATATTAAATTCTTGGAGT
1 ATTCTGTGACAAAAAGCATATAAATATAACGTTCATCGTCACATTATAT-TT-AATTCTTGGAG-
3179280 TTTTTTTTACATTTATTGGAACATTT
63 TTTTTTTTACATTTATTGGAACATTT
3179306 GATTGCTCCA
Statistics
Matches: 85, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
89 46 0.54
90 2 0.02
91 37 0.44
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (88 bp):
ATTCTGTGACAAAAAGCATATAAATATAACGTTCATCGTCACATTATATTTAATTCTTGGAGTTT
TTTTTACATTTATTGGAACATTT
Found at i:3181188 original size:6 final size:7
Alignment explanation
Indices: 3181163--3181193 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
3181153 TTCAAGCTTT
3181163 TTTTTATA
1 TTTTTA-A
3181171 TTTTTAA
1 TTTTTAA
3181178 TTTTTAA
1 TTTTTAA
3181185 TTTTTAA
1 TTTTTAA
3181192 TT
1 TT
3181194 AATAAGTCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 17 0.74
8 6 0.26
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTTAA
Found at i:3187398 original size:28 final size:28
Alignment explanation
Indices: 3187362--3187416 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
3187352 ATGCCTACAA
*
3187362 GTAGTCATTCATCTTGAACCTAAATCCT
1 GTAGGCATTCATCTTGAACCTAAATCCT
*
3187390 GTAGGCATTCATCTTGAACCTGAATCC
1 GTAGGCATTCATCTTGAACCTAAATCC
3187417 GATCATTGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (28 bp):
GTAGGCATTCATCTTGAACCTAAATCCT
Found at i:3197924 original size:28 final size:28
Alignment explanation
Indices: 3197878--3197936 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
3197868 GAATTCTACT
3197878 TATAAGATAGTCCTAACGGACTTCCACA
1 TATAAGATAGTCCTAACGGACTTCCACA
* * * *
3197906 TATAAGATAGTTCTGACGGGCTTCCATA
1 TATAAGATAGTCCTAACGGACTTCCACA
3197934 TAT
1 TAT
3197937 TTCATAACTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (28 bp):
TATAAGATAGTCCTAACGGACTTCCACA
Found at i:3199678 original size:18 final size:18
Alignment explanation
Indices: 3199649--3199697 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
3199639 AATGAGTACT
*
3199649 TATATA-AATTAAATGAA
1 TATATATAATTAAATAAA
*
3199666 TATATATAATTAATTAAA
1 TATATATAATTAAATAAA
* *
3199684 TAAAAATAATTAAA
1 TATATATAATTAAA
3199698 CATGTACCTG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 6 0.23
18 20 0.77
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (18 bp):
TATATATAATTAAATAAA
Found at i:3201688 original size:51 final size:51
Alignment explanation
Indices: 3201633--3201732 Score: 130
Period size: 51 Copynumber: 2.0 Consensus size: 51
3201623 AATTATTTAA
*
3201633 AAATAGGGATTTAAGAGAAATTTA-AGAGGAAATTAAGAGCAAATTGAGATT
1 AAATAGGAATTTAAGAGAAATTTAGA-AGGAAATTAAGAGCAAATTGAGATT
* * * * *
3201684 AAATATGAATTTGAGAGAAATTTGGAAGGAAATTGAGAGGAAATTGAGA
1 AAATAGGAATTTAAGAGAAATTTAGAAGGAAATTAAGAGCAAATTGAGA
3201733 GGAAATTTGA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
51 41 0.98
52 1 0.02
ACGTcount: A:0.48, C:0.01, G:0.26, T:0.25
Consensus pattern (51 bp):
AAATAGGAATTTAAGAGAAATTTAGAAGGAAATTAAGAGCAAATTGAGATT
Found at i:3201705 original size:11 final size:12
Alignment explanation
Indices: 3201691--3201744 Score: 71
Period size: 11 Copynumber: 4.8 Consensus size: 12
3201681 ATTAAATATG
3201691 AATTTGAGA-GA
1 AATTTGAGAGGA
3201702 AATTTG-GAAGGA
1 AATTTGAG-AGGA
3201714 AA-TTGAGAGGA
1 AATTTGAGAGGA
3201725 AA-TTGAGAGGA
1 AATTTGAGAGGA
3201736 AATTTGAGA
1 AATTTGAGA
3201745 AAGGATTAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
10 1 0.03
11 27 0.69
12 11 0.28
ACGTcount: A:0.44, C:0.00, G:0.31, T:0.24
Consensus pattern (12 bp):
AATTTGAGAGGA
Found at i:3202036 original size:30 final size:30
Alignment explanation
Indices: 3202000--3202059 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
3201990 TTTCACCTAC
3202000 CCTACAACTAGTTTATAATACCAATCTTAG
1 CCTACAACTAGTTTATAATACCAATCTTAG
*
3202030 CCTACAAGTAGTTTATAATACCAATCTTAG
1 CCTACAACTAGTTTATAATACCAATCTTAG
3202060 TATCAATTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.37, C:0.22, G:0.08, T:0.33
Consensus pattern (30 bp):
CCTACAACTAGTTTATAATACCAATCTTAG
Found at i:3205686 original size:28 final size:28
Alignment explanation
Indices: 3205653--3205708 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
3205643 TGTAATATAT
3205653 AAACTCCTGTTCTGGCTCTTTTGTATGC
1 AAACTCCTGTTCTGGCTCTTTTGTATGC
3205681 AAACTCCTGTTCTGGCTCTTTTGTATGC
1 AAACTCCTGTTCTGGCTCTTTTGTATGC
3205709 TTGCCTACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.43
Consensus pattern (28 bp):
AAACTCCTGTTCTGGCTCTTTTGTATGC
Found at i:3210261 original size:23 final size:23
Alignment explanation
Indices: 3210231--3210274 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
3210221 TATTTTAGAT
*
3210231 TTAATTTTTATATTTTA-ATTTAA
1 TTAATTTTAAT-TTTTATATTTAA
3210254 TTAATTTTAATTTTTATATTT
1 TTAATTTTAATTTTTATATTT
3210275 TTAAAATTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (23 bp):
TTAATTTTAATTTTTATATTTAA
Found at i:3210278 original size:15 final size:14
Alignment explanation
Indices: 3210230--3210275 Score: 67
Period size: 14 Copynumber: 3.2 Consensus size: 14
3210220 TTATTTTAGA
3210230 TTTAATTTTTATAT
1 TTTAATTTTTATAT
3210244 TTTAATTTAATTA-AT
1 TTTAATTT--TTATAT
3210259 TTTAATTTTTATAT
1 TTTAATTTTTATAT
3210273 TTT
1 TTT
3210276 TAAAATTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
13 3 0.10
14 13 0.45
15 10 0.34
16 3 0.10
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTAATTTTTATAT
Found at i:3210663 original size:14 final size:13
Alignment explanation
Indices: 3210645--3210691 Score: 58
Period size: 14 Copynumber: 3.5 Consensus size: 13
3210635 CGATATTCGT
3210645 AAATTTTAAAAAA
1 AAATTTTAAAAAA
*
3210658 TAAATTTGAAAGAAA
1 -AAATTTTAAA-AAA
*
3210673 AAATTTTTAAAAA
1 AAATTTTAAAAAA
3210686 AAATTT
1 AAATTT
3210692 AATTGGTGCC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
13 9 0.31
14 17 0.59
15 3 0.10
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (13 bp):
AAATTTTAAAAAA
Found at i:3212407 original size:21 final size:20
Alignment explanation
Indices: 3212383--3212449 Score: 68
Period size: 21 Copynumber: 3.4 Consensus size: 20
3212373 GAACAAAACA
3212383 AAAATTACAAAAATATGAACT
1 AAAATTA-AAAAATATGAACT
**
3212404 AAAATT-AAAAATA--AAAG
1 AAAATTAAAAAATATGAACT
*
3212421 AAAAATAATAAAATATGAACT
1 AAAATTAA-AAAATATGAACT
3212442 AAAATTAA
1 AAAATTAA
3212450 CACCATCGCC
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
17 7 0.19
18 1 0.03
19 13 0.36
21 15 0.42
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.22
Consensus pattern (20 bp):
AAAATTAAAAAATATGAACT
Found at i:3213623 original size:24 final size:24
Alignment explanation
Indices: 3213591--3213639 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
3213581 GGATAATTCA
* *
3213591 ACTTACTTAGGGTTGAGGTAAGTT
1 ACTTACTTAAGATTGAGGTAAGTT
3213615 ACTTACTTAAGATTGAGGTAAGTT
1 ACTTACTTAAGATTGAGGTAAGTT
3213639 A
1 A
3213640 TACTATGAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.08, G:0.24, T:0.37
Consensus pattern (24 bp):
ACTTACTTAAGATTGAGGTAAGTT
Found at i:3219887 original size:43 final size:43
Alignment explanation
Indices: 3219839--3219926 Score: 149
Period size: 43 Copynumber: 2.0 Consensus size: 43
3219829 TCAACCACAT
* * *
3219839 ATCAAATTTAAAGATCAACAAAAGATTGATGCACAAGTAAAGC
1 ATCAAATGTAAACATCAACAAAAGATGGATGCACAAGTAAAGC
3219882 ATCAAATGTAAACATCAACAAAAGATGGATGCACAAGTAAAGC
1 ATCAAATGTAAACATCAACAAAAGATGGATGCACAAGTAAAGC
3219925 AT
1 AT
3219927 GAAGTTACAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.51, C:0.15, G:0.15, T:0.19
Consensus pattern (43 bp):
ATCAAATGTAAACATCAACAAAAGATGGATGCACAAGTAAAGC
Found at i:3221180 original size:15 final size:15
Alignment explanation
Indices: 3221160--3221192 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
3221150 ATTTTAATAT
3221160 TATTTAACCTATAAA
1 TATTTAACCTATAAA
*
3221175 TATTTAGCCTATAAA
1 TATTTAACCTATAAA
3221190 TAT
1 TAT
3221193 GTCATTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.42
Consensus pattern (15 bp):
TATTTAACCTATAAA
Found at i:3221994 original size:30 final size:30
Alignment explanation
Indices: 3221960--3222022 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
3221950 ACTTATTTTA
*
3221960 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
* * *
3221990 TTGTTGATTTTATTATTATTTTAGAGGCAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
3222020 TTG
1 TTG
3222023 CTTGTTAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.03, G:0.14, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTATTATTATTTTAAAGACAT
Found at i:3222333 original size:109 final size:110
Alignment explanation
Indices: 3222141--3222361 Score: 435
Period size: 109 Copynumber: 2.0 Consensus size: 110
3222131 TATTATATAT
3222141 ATATTTAAAAATTATATAAAAATAATATAAAAAATTAATACGGGCGGGCCGGGTCGGGCCCGAAT
1 ATATTTAAAAATTATATAAAAATAATATAAAAAATTAATACGGGCGGGCCGGGTCGGGCCCGAAT
3222206 TTTAGCATTTTTATCCAGGTCGGGCTTGAGCAAAATTTTAGACCC
66 TTTAGCATTTTTATCCAGGTCGGGCTTGAGCAAAATTTTAGACCC
3222251 ATATTT-AAAATTATATAAAAATAATATAAAAAATTAATACGGGCGGGCCGGGTCGGGCCCGAAT
1 ATATTTAAAAATTATATAAAAATAATATAAAAAATTAATACGGGCGGGCCGGGTCGGGCCCGAAT
3222315 TTTAGCATTTTTATCCAGGTCGGGCTTGAGCAAAATTTTAGACCC
66 TTTAGCATTTTTATCCAGGTCGGGCTTGAGCAAAATTTTAGACCC
3222360 AT
1 AT
3222362 TTTTCGGGCG
Statistics
Matches: 111, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
109 105 0.95
110 6 0.05
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.29
Consensus pattern (110 bp):
ATATTTAAAAATTATATAAAAATAATATAAAAAATTAATACGGGCGGGCCGGGTCGGGCCCGAAT
TTTAGCATTTTTATCCAGGTCGGGCTTGAGCAAAATTTTAGACCC
Found at i:3224982 original size:46 final size:46
Alignment explanation
Indices: 3224915--3225099 Score: 300
Period size: 46 Copynumber: 4.0 Consensus size: 46
3224905 CATGGCAAAG
* *
3224915 TGTGAAACGTAAGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* * *
3224961 TGTGAAAAGTAGGTATGGTATTTCGGTAAAGAAAACCAGACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
*
3225007 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
3225053 TGTGAAAAGTAGGTATGGTATTTTC-GTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTA-TTTCAGTGAAGAAAACCATACTGAGT
3225099 T
1 T
3225100 ATAGCCTTGT
Statistics
Matches: 128, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
46 124 0.97
47 4 0.03
ACGTcount: A:0.36, C:0.09, G:0.26, T:0.29
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
Found at i:3229591 original size:47 final size:47
Alignment explanation
Indices: 3229522--3229616 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 47
3229512 GTTCGAGGTA
*
3229522 AGTCCATTGCAGATTTTGGCCGAGAAGGTGTTATAAAAATAAGAGCC
1 AGTCCATGGCAGATTTTGGCCGAGAAGGTGTTATAAAAATAAGAGCC
3229569 AGTCCATGGCAGATTTTGGCCGAGAAGGTGTTATAAAAATAAGAGCC
1 AGTCCATGGCAGATTTTGGCCGAGAAGGTGTTATAAAAATAAGAGCC
3229616 A
1 A
3229617 ATGTGAAAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.35, C:0.15, G:0.26, T:0.24
Consensus pattern (47 bp):
AGTCCATGGCAGATTTTGGCCGAGAAGGTGTTATAAAAATAAGAGCC
Found at i:3234511 original size:21 final size:23
Alignment explanation
Indices: 3234461--3234515 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 23
3234451 TTTTGCTTAT
*
3234461 TCAAATAAAATCATAATTTATACA
1 TCAAATAAAAT-ATAATCTATACA
3234485 TCAAATAAAAT-TAATCTA-ACA
1 TCAAATAAAATATAATCTATACA
*
3234506 TGAAATAAAA
1 TCAAATAAAA
3234516 CACGGTGTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 12 0.41
22 6 0.21
24 11 0.38
ACGTcount: A:0.58, C:0.11, G:0.02, T:0.29
Consensus pattern (23 bp):
TCAAATAAAATATAATCTATACA
Found at i:3234868 original size:8 final size:8
Alignment explanation
Indices: 3234819--3234870 Score: 63
Period size: 8 Copynumber: 6.6 Consensus size: 8
3234809 ATATGTATGT
3234819 ATATATAA
1 ATATATAA
3234827 AT-TATAA
1 ATATATAA
3234834 AGTATA-AA
1 A-TATATAA
3234842 ATATATAA
1 ATATATAA
* *
3234850 GTATGTAA
1 ATATATAA
3234858 ATATATAA
1 ATATATAA
3234866 ATATA
1 ATATA
3234871 CACTTATAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
7 10 0.27
8 25 0.68
9 2 0.05
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.37
Consensus pattern (8 bp):
ATATATAA
Found at i:3234909 original size:16 final size:16
Alignment explanation
Indices: 3234890--3234923 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
3234880 AAATTAAAAT
3234890 ATATATGTAGACATAA
1 ATATATGTAGACATAA
*
3234906 ATATATGTATACATAA
1 ATATATGTAGACATAA
3234922 AT
1 AT
3234924 TATAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.35
Consensus pattern (16 bp):
ATATATGTAGACATAA
Found at i:3234945 original size:22 final size:23
Alignment explanation
Indices: 3234902--3234945 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
3234892 ATATGTAGAC
* * *
3234902 ATAAATATATGTATACATAAATT
1 ATAAATATATATATAAAAAAATT
3234925 ATAAA-ATATATATAAAAAAAT
1 ATAAATATATATATAAAAAAAT
3234946 ATATGAGTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (23 bp):
ATAAATATATATATAAAAAAATT
Found at i:3235991 original size:4 final size:4
Alignment explanation
Indices: 3235982--3236008 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3235972 ATATGAGAGA
3235982 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
3236009 AGCTGAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:3236909 original size:50 final size:50
Alignment explanation
Indices: 3236851--3237172 Score: 221
Period size: 50 Copynumber: 6.4 Consensus size: 50
3236841 AATCTGTCAT
* *
3236851 CTTCAATCTGTTTAACTGCAATGTTGGGGAAGTAAAATTCACTGTTGTAG
1 CTTCAATCTGTTTAACTGCAATGTTGGGGAAGTAAGATTCGCTGTTGTAG
**** ** *** ** ** *
3236901 CTTCAATCTGTTCCGTTGCACCGCCAGAAAAGTAAGATTCGCCATTGTGG
1 CTTCAATCTGTTTAACTGCAATGTTGGGGAAGTAAGATTCGCTGTTGTAG
*
3236951 CTTCAATCTTTTTAACTGCAATGTTGGGGAAGTAAGATTCGCTGTTGTAG
1 CTTCAATCTGTTTAACTGCAATGTTGGGGAAGTAAGATTCGCTGTTGTAG
**** ** *** ** * **
3237001 CTTCAATCTGTTCCGTTGCACCGCCAGAAAAGTAAGATTCACCATTGTAG
1 CTTCAATCTGTTTAACTGCAATGTTGGGGAAGTAAGATTCGCTGTTGTAG
* * * *
3237051 CTTCAATCTTTTTAACTGCAATGTTGGGGGAGCAAGATCCGCTGTTGTAG
1 CTTCAATCTGTTTAACTGCAATGTTGGGGAAGTAAGATTCGCTGTTGTAG
** * ** * * * * * *
3237101 CTTCAATCTGTTCCACTACACCGCTAGGAAAGTAAGATCCGCTATTATAG
1 CTTCAATCTGTTTAACTGCAATGTTGGGGAAGTAAGATTCGCTGTTGTAG
*
3237151 CTTCAATCTTTTTAACTGCAAT
1 CTTCAATCTGTTTAACTGCAAT
3237173 ATCGGAGAAA
Statistics
Matches: 189, Mismatches: 83, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
50 189 1.00
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (50 bp):
CTTCAATCTGTTTAACTGCAATGTTGGGGAAGTAAGATTCGCTGTTGTAG
Found at i:3237024 original size:100 final size:100
Alignment explanation
Indices: 3236851--3237172 Score: 500
Period size: 100 Copynumber: 3.2 Consensus size: 100
3236841 AATCTGTCAT
* * *
3236851 CTTCAATCTGTTTAACTGCAATGTTGGGGAAGTAAAATTCACTGTTGTAGCTTCAATCTGTTCCG
1 CTTCAATCTTTTTAACTGCAATGTTGGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGTTCCG
*
3236916 TTGCACCGCCAGAAAAGTAAGATTCGCCATTGTGG
66 TTGCACCGCCAGAAAAGTAAGATTCGCCATTGTAG
3236951 CTTCAATCTTTTTAACTGCAATGTTGGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGTTCCG
1 CTTCAATCTTTTTAACTGCAATGTTGGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGTTCCG
*
3237016 TTGCACCGCCAGAAAAGTAAGATTCACCATTGTAG
66 TTGCACCGCCAGAAAAGTAAGATTCGCCATTGTAG
* * * *
3237051 CTTCAATCTTTTTAACTGCAATGTTGGGGGAGCAAGATCCGCTGTTGTAGCTTCAATCTGTTCCA
1 CTTCAATCTTTTTAACTGCAATGTTGGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGTTCCG
* * * * * * *
3237116 CTACACCGCTAGGAAAGTAAGATCCGCTATTATAG
66 TTGCACCGCCAGAAAAGTAAGATTCGCCATTGTAG
3237151 CTTCAATCTTTTTAACTGCAAT
1 CTTCAATCTTTTTAACTGCAAT
3237173 ATCGGAGAAA
Statistics
Matches: 205, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
100 205 1.00
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (100 bp):
CTTCAATCTTTTTAACTGCAATGTTGGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGTTCCG
TTGCACCGCCAGAAAAGTAAGATTCGCCATTGTAG
Found at i:3237188 original size:50 final size:50
Alignment explanation
Indices: 3237048--3237188 Score: 122
Period size: 50 Copynumber: 2.8 Consensus size: 50
3237038 TTCACCATTG
* * * * * *
3237048 TAGCTTCAATCTTTTTAACTGCAATGTTGGGGGAGCAAGATCCGCTGTTG
1 TAGCTTCAATCTTTTTAACTGCAATATAGGAGAAGCAAGATCCGCTATTA
* ** * *** *
3237098 TAGCTTCAATCTGTTCCACTACACCGCTAGGA-AAGTAAGATCCGCTATTA
1 TAGCTTCAATCTTTTTAACTGCA-ATATAGGAGAAGCAAGATCCGCTATTA
* *
3237148 TAGCTTCAATCTTTTTAACTGCAATATCGGAGAAACAAGAT
1 TAGCTTCAATCTTTTTAACTGCAATATAGGAGAAGCAAGAT
3237189 TCGTCAATTT
Statistics
Matches: 66, Mismatches: 23, Indels: 4
0.71 0.25 0.04
Matches are distributed among these distances:
49 4 0.06
50 59 0.89
51 3 0.05
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (50 bp):
TAGCTTCAATCTTTTTAACTGCAATATAGGAGAAGCAAGATCCGCTATTA
Found at i:3237209 original size:100 final size:100
Alignment explanation
Indices: 3236851--3237220 Score: 481
Period size: 100 Copynumber: 3.7 Consensus size: 100
3236841 AATCTGTCAT
* * * * *
3236851 CTTCAATCTGTTTAACTGCAATGTTGGGGAAGTAAAATTCACTGTTGTAGCTTCAATCTGTTCCG
1 CTTCAATCTTTTTAACTGCAATGTTGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCA
* *
3236916 TTGCACCGCCAGAAAAGTAAGATTCGCCATTGTGG
66 CTGCACCGCCAGAAAAGTAAGATTCGCCATTGTAG
* *
3236951 CTTCAATCTTTTTAACTGCAATGTTGGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGTTCCG
1 CTTCAATCTTTTTAACTGCAATGTTGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCA
* *
3237016 TTGCACCGCCAGAAAAGTAAGATTCACCATTGTAG
66 CTGCACCGCCAGAAAAGTAAGATTCGCCATTGTAG
* *
3237051 CTTCAATCTTTTTAACTGCAATGTTGGGGGAGCAAGATCCGCTGTTGTAGCTTCAATCTGTTCCA
1 CTTCAATCTTTTTAACTGCAATGTTGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCA
* * * * * *
3237116 CTACACCGCTAGGAAAGTAAGATCCGCTATTATAG
66 CTGCACCGCCAGAAAAGTAAGATTCGCCATTGTAG
* * * * ** * *
3237151 CTTCAATCTTTTTAACTGCAATATCGGAGAAACAAGATTCGTCAATT-TGGCTTTAATCTGTTCC
1 CTTCAATCTTTTTAACTGCAATGTTGGGGAAGCAAGATTCG-CTGTTGTAGCTTCAATCTGTTCC
3237215 ACTGCA
65 ACTGCA
3237221 TCGCTTGGGG
Statistics
Matches: 241, Mismatches: 28, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
100 238 0.99
101 3 0.01
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (100 bp):
CTTCAATCTTTTTAACTGCAATGTTGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCA
CTGCACCGCCAGAAAAGTAAGATTCGCCATTGTAG
Found at i:3237236 original size:100 final size:100
Alignment explanation
Indices: 3236895--3237258 Score: 307
Period size: 100 Copynumber: 3.6 Consensus size: 100
3236885 AAATTCACTG
** * * * * * * *
3236895 TTGTAGCTTCAATCTGTTCCGTTGCACCGCCAGAAAAGTAAGATTCGCCATTGTGGCTTCAATCT
1 TTGTAGCTTCAATCTGTTCCACTACACCGCTAGGAAAGTAAGATCCGCTATTATAGCTTCAATCT
* * * ** * **
3236960 TTTTAACTGCAATGTTGGGGAAGTAAGATTCGCTG
66 TTTTAACTGCAATATCGGAGAAACAAGATCCGCAA
** * * * * * * *
3236995 TTGTAGCTTCAATCTGTTCCGTTGCACCGCCAGAAAAGTAAGATTCACCATTGTAGCTTCAATCT
1 TTGTAGCTTCAATCTGTTCCACTACACCGCTAGGAAAGTAAGATCCGCTATTATAGCTTCAATCT
* * * * * **
3237060 TTTTAACTGCAATGTTGGGGGAGCAAGATCCGCTG
66 TTTTAACTGCAATATCGGAGAAACAAGATCCGCAA
3237095 TTGTAGCTTCAATCTGTTCCACTACACCGCTAGGAAAGTAAGATCCGCTATTATAGCTTCAATCT
1 TTGTAGCTTCAATCTGTTCCACTACACCGCTAGGAAAGTAAGATCCGCTATTATAGCTTCAATCT
*
3237160 TTTTAACTGCAATATCGGAGAAACAAGATTCGTCAA
66 TTTTAACTGCAATATCGGAGAAACAAGATCCG-CAA
* * * * * *** * * *
3237196 TT-TGGCTTTAATCTGTTCCACTGCATCGCTTGGGGCGTAAGATTCGCTATTGTAGCTTTAATC
1 TTGTAGCTTCAATCTGTTCCACTACACCGCTAGGAAAGTAAGATCCGCTATTATAGCTTCAATC
3237259 AAGATTCACC
Statistics
Matches: 230, Mismatches: 33, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
100 227 0.99
101 3 0.01
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (100 bp):
TTGTAGCTTCAATCTGTTCCACTACACCGCTAGGAAAGTAAGATCCGCTATTATAGCTTCAATCT
TTTTAACTGCAATATCGGAGAAACAAGATCCGCAA
Found at i:3237389 original size:75 final size:75
Alignment explanation
Indices: 3237308--3237570 Score: 517
Period size: 75 Copynumber: 3.5 Consensus size: 75
3237298 GTAGGGGAAG
*
3237308 CAAGATTCACCGATGCGGTTTTAATCTGTTCCACTGCATCGCTTGGGGCGTAAGATTCGCTCTTG
1 CAAGATTCGCCGATGCGGTTTTAATCTGTTCCACTGCATCGCTTGGGGCGTAAGATTCGCTCTTG
3237373 TAGCTTTAAT
66 TAGCTTTAAT
3237383 CAAGATTCGCCGATGCGGTTTTAATCTGTTCCACTGCATCGCTTGGGGCGTAAGATTCGCTCTTG
1 CAAGATTCGCCGATGCGGTTTTAATCTGTTCCACTGCATCGCTTGGGGCGTAAGATTCGCTCTTG
3237448 TAGCTTTAAT
66 TAGCTTTAAT
3237458 CAAGATTCGCCGATGCGGTTTTAATCTGTTCCACTGCATCGCTTGGGGCGTAAGATTCGCTCTTG
1 CAAGATTCGCCGATGCGGTTTTAATCTGTTCCACTGCATCGCTTGGGGCGTAAGATTCGCTCTTG
3237523 TAGCTTTAAT
66 TAGCTTTAAT
3237533 CAAGATTCGCCGATGCGGTTTTAATCTGTTCCACTGCA
1 CAAGATTCGCCGATGCGGTTTTAATCTGTTCCACTGCA
3237571 CCGCCTGGAA
Statistics
Matches: 187, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 187 1.00
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.34
Consensus pattern (75 bp):
CAAGATTCGCCGATGCGGTTTTAATCTGTTCCACTGCATCGCTTGGGGCGTAAGATTCGCTCTTG
TAGCTTTAAT
Found at i:3237838 original size:44 final size:45
Alignment explanation
Indices: 3237724--3237855 Score: 153
Period size: 45 Copynumber: 3.0 Consensus size: 45
3237714 TTGAAAACTG
* * *
3237724 TGGTTTCTTCGATCTGCTTCGCTGTTAGTACAAGAAGGCAAGATC
1 TGGTATCTTCGATCTGCTTCGCTGTCAGTACAAGAAGGCAAGAGC
* * *
3237769 TGCTATCTTC-ATTCTACTCCGCTGTCAGTACAAGAAGGCAAG-GC
1 TGGTATCTTCGA-TCTGCTTCGCTGTCAGTACAAGAAGGCAAGAGC
* *
3237813 TGGTGTCTTCGATCTGCTTCGCTGTCAAG-GCAAGAAGGCAAGA
1 TGGTATCTTCGATCTGCTTCGCTGTC-AGTACAAGAAGGCAAGA
3237856 TCTGTTGTCT
Statistics
Matches: 72, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
44 34 0.47
45 38 0.53
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.29
Consensus pattern (45 bp):
TGGTATCTTCGATCTGCTTCGCTGTCAGTACAAGAAGGCAAGAGC
Found at i:3237896 original size:44 final size:44
Alignment explanation
Indices: 3237848--3238074 Score: 121
Period size: 44 Copynumber: 5.2 Consensus size: 44
3237838 CAAGGCAAGA
3237848 AGGCAAGATCTGTTGTCTTCAACCATCTCCACT-ACAATCGAGAG
1 AGGCAAGATCTGTTGTCTTCAACCATCTCCACTCACAATCGAG-G
* * ** * * **
3237892 AGGCAAGGTTTG-TGTCTTTGACC-TGCTTCGCTGTCAAT-GCAGG
1 AGGCAAGATCTGTTGTCTTCAACCAT-CTCCACTCACAATCG-AGG
* * *
3237935 AAGGCAAGATCTTTTGTCTTCAACCAGCTCCA-TCACAACCGAGAG
1 -AGGCAAGATCTGTTGTCTTCAACCATCTCCACTCACAATCGAG-G
* * * * * **
3237980 AGGCAAGGTTTG-TGTCTTCGACC-TGCTTCGCTGTCAAT-GCAGG
1 AGGCAAGATCTGTTGTCTTCAACCAT-CTCCACTCACAATCG-AGG
* * *
3238023 CAGGCAAGATCTGTTGTCTTTAACCAGCTCCA-TCACAACCGAGGG
1 -AGGCAAGATCTGTTGTCTTCAACCATCTCCACTCACAATCGA-GG
3238068 AGGCAAG
1 AGGCAAG
3238075 GGTTTGTTTT
Statistics
Matches: 129, Mismatches: 38, Indels: 32
0.65 0.19 0.16
Matches are distributed among these distances:
42 1 0.01
43 31 0.24
44 68 0.53
45 29 0.22
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.26
Consensus pattern (44 bp):
AGGCAAGATCTGTTGTCTTCAACCATCTCCACTCACAATCGAGG
Found at i:3238353 original size:86 final size:86
Alignment explanation
Indices: 3237731--3238859 Score: 1145
Period size: 86 Copynumber: 13.1 Consensus size: 86
3237721 CTGTGGTTTC
* * * * * * *
3237731 TTCGATCTGCTTCGCTGTTAGTACAAGAAGGCAAGATCTGCTATCTTCATTCTA-CTCCGCTGTC
1 TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCT-TCTTTA-ACCAGCTCCACTG-C
* *
3237795 AGTA-CAA-GAAGGCAAGGCTGGTGTC
63 A--ACCAATGAAGGCAAGGCT-TTGTT
* * * * * * *
3237820 TTCGATCTGCTTCGCTGTCAAGGCAAGAAGGCAAGATCTGTTGTCTTCAACCATCTCCACTACAA
1 TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCT-TCTTTAACCAGCTCCACTGCAA
* *
3237885 TCGA-GAGAGGCAAGG-TTTGTGT
65 CCAATGA-AGGCAAGGCTTTGT-T
* * * ** * *
3237907 CTTTGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCA-TCAC
1 -TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCT-TCTTTAACCAGCTCCACT-GC
*
3237971 AACCGA-GAGAGGCAAGG-TTTGTGT
63 AACCAATGA-AGGCAAGGCTTTGT-T
* * * * *
3237995 CTTCGACCTGCTTCGCTGTCAATGCAGGCAGGCAAGATCTGTTGTCTTTAACCAGCTCCA-TCAC
1 -TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCT-TCTTTAACCAGCTCCACT-GC
* * * *
3238059 AACCGAGGGAGGCAAGGGTTTGTT
63 AACCAATGAAGGCAAGGCTTTGTT
* * *
3238083 TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGGTTCTTCAACCAGCTCCA-TCACAA
1 TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACT-GCAA
*
3238147 CCGA-GAGAGGCAAGG-TTTGTGT
65 CCAATGA-AGGCAAGGCTTTGT-T
* * * * * ** * *
3238169 CTTCGACCTGCTTCGCTATCAATGTAGGAAGACAAGATCTTTTGTCTTCAACCAACTCCA-T-C-
1 -TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCT-TCTTTAACCAGCTCCACTGCA
* *
3238231 A-CAATCGAGAGGCAAGG-TATATT
64 ACCAAT-GA-AGGCAAGGCTTTGTT
*
3238254 TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAAC
1 TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAAC
*
3238319 CAATGAAGGTAAGGCTTTGTT
66 CAATGAAGGCAAGGCTTTGTT
3238340 TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACT-CTAA
1 TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGC-AA
*
3238404 CCAATGAAGGCAA-GTTTTGTGT
65 CCAATGAAGGCAAGGCTTTGT-T
* * * * ** * * *
3238426 CTTCGACCTGCTTCGCTATCAATGTAGGAAGGCAAGATCTTTTGTCTTCAACCAACTCCA-TCAC
1 -TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCT-TCTTTAACCAGCTCCACT-GC
* *
3238490 AACCGA-G-AGGCAAGG-TTTATT
63 AACCAATGAAGGCAAGGCTTTGTT
* *
3238511 TTCGATCTGCTTCGTTGTTAACGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAAC
1 TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAAC
3238576 CAATGAAGGCAAGGCTTTGTT
66 CAATGAAGGCAAGGCTTTGTT
* * *
3238597 TTCGATCTGCTTCGCTGTTAATGTAGGAAGGCAAGATCTACTTCTTTAACCAGCTCCACTGTAAC
1 TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAAC
*
3238662 CAATGAAGGCAAGTC-TTGTT
66 CAATGAAGGCAAGGCTTTGTT
* * *
3238682 TTCGATCTACTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCGATTGCAAC
1 TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAAC
3238747 CAATGAAGGCAAGGCTTTGTT
66 CAATGAAGGCAAGGCTTTGTT
* *
3238768 TTCGATCTGCTTCGCTGTTAATGTAGGAAGGCAAGATCTACTTCTTTAACCAGCTCCACTGCAAC
1 TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAAC
*
3238833 CAATGAAGGCAATGCTTTGTT
66 CAATGAAGGCAAGGCTTTGTT
3238854 TTCGAT
1 TTCGAT
3238860 GTTCACTAAT
Statistics
Matches: 909, Mismatches: 100, Indels: 65
0.85 0.09 0.06
Matches are distributed among these distances:
83 34 0.04
84 73 0.08
85 110 0.12
86 314 0.35
87 122 0.13
88 200 0.22
89 56 0.06
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (86 bp):
TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAAC
CAATGAAGGCAAGGCTTTGTT
Found at i:3238396 original size:257 final size:257
Alignment explanation
Indices: 3237731--3238859 Score: 1418
Period size: 257 Copynumber: 4.4 Consensus size: 257
3237721 CTGTGGTTTC
* * * * * * *
3237731 TTCGATCTGCTTCGCTGTTAGTACAAGAAGGCAAGATCTGCTATCTTCATTCTA-CTCCGCTGTC
1 TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCT-TCTTTA-ACCAGCTCCACTG-C
* * * * *
3237795 AGTA-CAA-GAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCAAGGCAAGAAGGCAAGATC
63 A--ACCAATGAAGGCAAGGCT-TTGTTTTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATC
* * * * *
3237858 TGTTGTCTTCAACCATCTCCACTACAATCGA-GAGAGGCAAGGTTTGTGTCTTTGACCTGCTTCG
125 TGCT-TCTTCAACCAGCTCCACTACAACCAATGA-AGGCAAGGTTTGTGTCTTCGACCTGCTTCG
* *
3237922 CTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAG
188 CTATCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAACTCCATCACAACC--GAGAGGCAAG
*
3237987 GTTTGTGT
251 GTTTAT-T
* * * * *
3237995 CTTCGACCTGCTTCGCTGTCAATGCAGGCAGGCAAGATCTGTTGTCTTTAACCAGCTCCA-TCAC
1 -TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCT-TCTTTAACCAGCTCCACT-GC
* * * * *
3238059 AACCGAGGGAGGCAAGGGTTTGTTTTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGG
63 AACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGC
*
3238124 TTCTTCAACCAGCTCCA-TCACAACCGA-GAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTA
128 TTCTTCAACCAGCTCCACT-ACAACCAATGA-AGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTA
* * * *
3238187 TCAATGTAGGAAGACAAGATCTTTTGTCTTCAACCAACTCCATCACAATCGAGAGGCAAGGTATA
191 TCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAACTCCATCACAACCGAGAGGCAAGGTTTA
3238252 TT
256 TT
*
3238254 TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAAC
1 TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAAC
*
3238319 CAATGAAGGTAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTTC
66 CAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTTC
* *
3238384 TTTAACCAGCTCCACT-CTAACCAATGAAGGCAAGTTTTGTGTCTTCGACCTGCTTCGCTATCAA
131 TTCAACCAGCTCCACTAC-AACCAATGAAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTATCAA
*
3238448 TGTAGGAAGGCAAGATCTTTTGTCTTCAACCAACTCCATCACAACCGAGAGGCAAGGTTTATT
195 TGCAGGAAGGCAAGATCTTTTGTCTTCAACCAACTCCATCACAACCGAGAGGCAAGGTTTATT
* *
3238511 TTCGATCTGCTTCGTTGTTAACGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAAC
1 TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAAC
* *
3238576 CAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGTAGGAAGGCAAGATCTACTTC
66 CAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTTC
* ** * * * *
3238641 TTTAACCAGCTCCACTGTAACCAATGAAGGCAA-GTCTTGT-T-TTCGATCTACTTCGCTGTTAA
131 TTCAACCAGCTCCACTACAACCAATGAAGGCAAGGT-TTGTGTCTTCGACCTGCTTCGCTATCAA
** * * * ** * *
3238703 TGCAGGAAGGCAAGATCTGCT-TCTTTAACCAGCTCGATTGCAACCAATGAAGGCAAGGCTTTGT
195 TGCAGGAAGGCAAGATCTTTTGTCTTCAACCAACTCCATCACAACCGA-G-AGGCAAGG-TTTAT
3238767 T
257 T
* *
3238768 TTCGATCTGCTTCGCTGTTAATGTAGGAAGGCAAGATCTACTTCTTTAACCAGCTCCACTGCAAC
1 TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAAC
*
3238833 CAATGAAGGCAATGCTTTGTTTTCGAT
66 CAATGAAGGCAAGGCTTTGTTTTCGAT
3238860 GTTCACTAAT
Statistics
Matches: 775, Mismatches: 75, Indels: 36
0.87 0.08 0.04
Matches are distributed among these distances:
254 20 0.03
255 36 0.05
256 11 0.01
257 446 0.58
258 41 0.05
259 1 0.00
260 14 0.02
261 1 0.00
262 103 0.13
263 43 0.06
264 15 0.02
265 44 0.06
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (257 bp):
TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAAC
CAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTTC
TTCAACCAGCTCCACTACAACCAATGAAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTATCAAT
GCAGGAAGGCAAGATCTTTTGTCTTCAACCAACTCCATCACAACCGAGAGGCAAGGTTTATT
Found at i:3238417 original size:171 final size:171
Alignment explanation
Indices: 3237731--3238859 Score: 1164
Period size: 171 Copynumber: 6.5 Consensus size: 171
3237721 CTGTGGTTTC
* * * * * *
3237731 TTCGATCTGCTTCGCTGTTAGTACAAGAAGGCAAGATCTGCTATCTTCATTCTA-CTCCGCTGTC
1 TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCT-TCTTCA-ACCAGCTCCACTG-C
* * * *
3237795 AGTA-CAAGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCAAGGCAAGAAGGCAAGATCT
63 A--ACCAAGAAGGCAAGGCT-TTGTTTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
* * * * * *
3237859 GTTGTCTTCAACCATCTCCACTACAATCGA-GAGAGGCAAGGTTTGTGT
125 GCTGTCTTTAACCAGCTCCACTGCAACCAATGA-AGGCAAGGTTTGT-T
* * * ** *
3237907 CTTTGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCA-TCAC
1 -TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCT-TCTTCAACCAGCTCCACT-GC
* * *
3237971 AACCGAGAGAGGCAAGG-TTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGCAGGCAAGATCT
63 AACCAAGA-AGGCAAGGCTTTGT-T-TTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
* * * * *
3238035 GTTGTCTTTAACCAGCTCCA-TCACAACCGAGGGAGGCAAGGGTTTGTT
125 GCTGTCTTTAACCAGCTCCACT-GCAACCAATGAAGGCAA-GGTTTGTT
* *
3238083 TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGGTTCTTCAACCAGCTCCA-TCACAA
1 TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTTCTTCAACCAGCTCCACT-GCAA
* * * * * **
3238147 CCGAGAGAGGCAAGG-TTTGTGTCTTCGACCTGCTTCGCTATCAATGTAGGAAGACAAGATCTTT
65 CCAAGA-AGGCAAGGCTTTGT-T-TTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGC
* * * *
3238211 TGTCTTCAACCAACTCCA-T-C-A-CAATCGAGAGGCAAGGTATATT
127 TGTCTTTAACCAGCTCCACTGCAACCAAT-GA-AGGCAAGGTTTGTT
* *
3238254 TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAAC
1 TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTTCTTCAACCAGCTCCACTGCAAC
* *
3238319 CAATGAAGGTAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCT-T
66 CAA-GAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTGT
*
3238383 CTTTAACCAGCTCCACT-CTAACCAATGAAGGCAAGTTTTGTGT
130 CTTTAACCAGCTCCACTGC-AACCAATGAAGGCAAGGTTTGT-T
* * * * ** * *
3238426 CTTCGACCTGCTTCGCTATCAATGTAGGAAGGCAAGATCTTTTGTCTTCAACCAACTCCA-TCAC
1 -TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCT-TCTTCAACCAGCTCCACT-GC
* * * * *
3238490 AACCGAG-AGGCAAGG-TTTATTTTCGATCTGCTTCGTTGTTAACGCAGGAAGGCAAGATCTGCT
63 AACCAAGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCT
3238553 -TCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTTGTT
128 GTCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGG-TTTGTT
* * * *
3238597 TTCGATCTGCTTCGCTGTTAATGTAGGAAGGCAAGATCTACTTCTTTAACCAGCTCCACTGTAAC
1 TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTTCTTCAACCAGCTCCACTGCAAC
* * *
3238662 CAATGAAGGCAAGTC-TTGTTTTCGATCTACTTCGCTGTTAATGCAGGAAGGCAAGATCTGCT-T
66 CAA-GAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTGT
* *
3238725 CTTTAACCAGCTCGATTGCAACCAATGAAGGCAAGGCTTTGTT
130 CTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGG-TTTGTT
* * *
3238768 TTCGATCTGCTTCGCTGTTAATGTAGGAAGGCAAGATCTACTTCTTTAACCAGCTCCACTGCAAC
1 TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTTCTTCAACCAGCTCCACTGCAAC
*
3238833 CAATGAAGGCAATGCTTTGTTTTCGAT
66 CAA-GAAGGCAAGGCTTTGTTTTCGAT
3238860 GTTCACTAAT
Statistics
Matches: 828, Mismatches: 95, Indels: 63
0.84 0.10 0.06
Matches are distributed among these distances:
169 33 0.04
170 78 0.09
171 336 0.41
172 43 0.05
173 41 0.05
174 122 0.15
175 43 0.05
176 80 0.10
177 52 0.06
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (171 bp):
TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTTCTTCAACCAGCTCCACTGCAAC
CAAGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTGTC
TTTAACCAGCTCCACTGCAACCAATGAAGGCAAGGTTTGTT
Found at i:3240049 original size:14 final size:14
Alignment explanation
Indices: 3240030--3240079 Score: 64
Period size: 14 Copynumber: 3.5 Consensus size: 14
3240020 CCTTAGCCTC
3240030 TTCATTTTTACTTT
1 TTCATTTTTACTTT
* *
3240044 TTCATTTTTTCATT
1 TTCATTTTTACTTT
*
3240058 TTCATTTTTATTTT
1 TTCATTTTTACTTT
3240072 TCTCATTT
1 T-TCATTT
3240080 CTTCTTCTTC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 24 0.80
15 6 0.20
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.72
Consensus pattern (14 bp):
TTCATTTTTACTTT
Found at i:3240086 original size:3 final size:3
Alignment explanation
Indices: 3240078--3240105 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3240068 TTTTTCTCAT
3240078 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
3240106 CTTTTTTTTA
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:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:3242997 original size:153 final size:153
Alignment explanation
Indices: 3242719--3243023 Score: 592
Period size: 153 Copynumber: 2.0 Consensus size: 153
3242709 CTTCATTATC
*
3242719 ATTCCCAAAGTGGACCACTGGGTTTTTTCATTTCTCCAACCTCATATCCAACAACTGTGTTAACT
1 ATTCCCAAAATGGACCACTGGGTTTTTTCATTTCTCCAACCTCATATCCAACAACTGTGTTAACT
3242784 GGCTCATCAGATTTCTCTGGACTCCTAGCATCTGATCCTTCACATCTTGTTGAAATTTGGCCAAT
66 GGCTCATCAGATTTCTCTGGACTCCTAGCATCTGATCCTTCACATCTTGTTGAAATTTGGCCAAT
3242849 TGCTCTAGCATCTGTATCTGCAA
131 TGCTCTAGCATCTGTATCTGCAA
*
3242872 ATTCCCAAAATGGACCACTGGGTTTTTTCCTTTCTCCAACCTCATATCCAACAACTGTGTTAACT
1 ATTCCCAAAATGGACCACTGGGTTTTTTCATTTCTCCAACCTCATATCCAACAACTGTGTTAACT
3242937 GGCTCATCAGATTTCTCTGGACTCCTAGCATCTGATCCTTCACATCTTGTTGAAATTTGGCCAAT
66 GGCTCATCAGATTTCTCTGGACTCCTAGCATCTGATCCTTCACATCTTGTTGAAATTTGGCCAAT
3243002 TGCTCTAGCATCTGTATCTGCA
131 TGCTCTAGCATCTGTATCTGCA
3243024 TTCACTCTAA
Statistics
Matches: 150, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
153 150 1.00
ACGTcount: A:0.23, C:0.27, G:0.15, T:0.35
Consensus pattern (153 bp):
ATTCCCAAAATGGACCACTGGGTTTTTTCATTTCTCCAACCTCATATCCAACAACTGTGTTAACT
GGCTCATCAGATTTCTCTGGACTCCTAGCATCTGATCCTTCACATCTTGTTGAAATTTGGCCAAT
TGCTCTAGCATCTGTATCTGCAA
Found at i:3245110 original size:203 final size:203
Alignment explanation
Indices: 3244761--3245166 Score: 794
Period size: 203 Copynumber: 2.0 Consensus size: 203
3244751 GAGGTGTGAT
3244761 CGGGTCACCTCGAAAAGTAGTTGTTTTTAATAAACGATTTAATTTTTATTAAAACAACGCTTTTG
1 CGGGTCACCTCGAAAAGTAGTTGTTTTTAATAAACGATTTAATTTTTATTAAAACAACGCTTTTG
3244826 GTCTACGAAATTCAGAAAAACGGGTTCGGGAGTCGGTTACGCACGAGGAAGGATTAGCACCCTCG
66 GTCTACGAAATTCAGAAAAACGGGTTCGGGAGTCGGTTACGCACGAGGAAGGATTAGCACCCTCG
*
3244891 ATACGCCCAAAATTGGTACCTAGTTGATTACTTAATGTCTTAGTGTCGAAAATTGAGAACTTTAA
131 ATACGCCCAAAATTGGTACCTAGTTGATTACTTAATGCCTTAGTGTCGAAAATTGAGAACTTTAA
3244956 AGAATTAA
196 AGAATTAA
3244964 CGGGTCACCTCGAAAAGTAGTTGTTTTTAATAAACGATTTAATTTTTATTAAAACAACGCTTTTG
1 CGGGTCACCTCGAAAAGTAGTTGTTTTTAATAAACGATTTAATTTTTATTAAAACAACGCTTTTG
3245029 GTCTACGAAATTCAGAAAAACGGGTTCGGGAGTCGGTTACGCACGAGGAAGGATTAGCACCCTCG
66 GTCTACGAAATTCAGAAAAACGGGTTCGGGAGTCGGTTACGCACGAGGAAGGATTAGCACCCTCG
*
3245094 ATACGCCCAAAATTGGTACCTAGTTGATTACTTAATGCCTTGGTGTCGAAAATTGAGAACTTTAA
131 ATACGCCCAAAATTGGTACCTAGTTGATTACTTAATGCCTTAGTGTCGAAAATTGAGAACTTTAA
3245159 AGAATTAA
196 AGAATTAA
3245167 AAAATACGAT
Statistics
Matches: 201, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
203 201 1.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.30
Consensus pattern (203 bp):
CGGGTCACCTCGAAAAGTAGTTGTTTTTAATAAACGATTTAATTTTTATTAAAACAACGCTTTTG
GTCTACGAAATTCAGAAAAACGGGTTCGGGAGTCGGTTACGCACGAGGAAGGATTAGCACCCTCG
ATACGCCCAAAATTGGTACCTAGTTGATTACTTAATGCCTTAGTGTCGAAAATTGAGAACTTTAA
AGAATTAA
Found at i:3245557 original size:21 final size:23
Alignment explanation
Indices: 3245507--3245561 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 23
3245497 TTTTGCTTAT
*
3245507 TCAAATAAAATCATAATTTATACA
1 TCAAATAAAAT-ATAATCTATACA
3245531 TCAAATAAAAT-TAATCTA-ACA
1 TCAAATAAAATATAATCTATACA
*
3245552 TGAAATAAAA
1 TCAAATAAAA
3245562 CACGGTGTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 12 0.41
22 6 0.21
24 11 0.38
ACGTcount: A:0.58, C:0.11, G:0.02, T:0.29
Consensus pattern (23 bp):
TCAAATAAAATATAATCTATACA
Found at i:3246855 original size:4 final size:4
Alignment explanation
Indices: 3246846--3246872 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3246836 ATATGAGAGA
3246846 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
3246873 AGCTGAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:3250238 original size:13 final size:13
Alignment explanation
Indices: 3250220--3250260 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
3250210 TATCATATTT
3250220 TATATTTCAAAAA
1 TATATTTCAAAAA
3250233 TATATTT-ATAAAA
1 TATATTTCA-AAAA
3250246 -ATATTTCAAAAA
1 TATATTTCAAAAA
3250258 TAT
1 TAT
3250261 TTTATTGGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 11 0.44
13 14 0.56
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (13 bp):
TATATTTCAAAAA
Found at i:3261820 original size:23 final size:24
Alignment explanation
Indices: 3261794--3261847 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
3261784 GACGGCTGGT
3261794 GAGAGGAAGACAAGT-G-GAGAAAG
1 GAGAGGAA-ACAAGTGGAGAGAAAG
* *
3261817 GAGATTGAAACACGTGGAGAGAAAG
1 GAGA-GGAAACAAGTGGAGAGAAAG
3261842 GAGAGG
1 GAGAGG
3261848 TGGGGAAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
23 9 0.36
24 5 0.20
25 11 0.44
ACGTcount: A:0.44, C:0.06, G:0.43, T:0.07
Consensus pattern (24 bp):
GAGAGGAAACAAGTGGAGAGAAAG
Found at i:3263320 original size:3 final size:3
Alignment explanation
Indices: 3263312--3263337 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3263302 GTCCACAGTT
3263312 AGC AGC AGC AGC AGC AGC AGC AGC AG
1 AGC AGC AGC AGC AGC AGC AGC AGC AG
3263338 GCATTGTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.35, T:0.00
Consensus pattern (3 bp):
AGC
Found at i:3265873 original size:23 final size:22
Alignment explanation
Indices: 3265822--3265863 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
3265812 TTTTAATATT
*
3265822 AAATTATTTTTTATCTGAATCA
1 AAATTATTATTTATCTGAATCA
3265844 AATATTATTATTTATC-GAAT
1 AA-ATTATTATTTATCTGAAT
3265864 ATCCAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (22 bp):
AAATTATTATTTATCTGAATCA
Found at i:3267227 original size:20 final size:20
Alignment explanation
Indices: 3267195--3267248 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
3267185 TATATAAATA
*
3267195 ATTTTAAAAAATAAAAACAC
1 ATTTTATAAAATAAAAACAC
* *
3267215 A-TTTATAATAAT-ATAACTC
1 ATTTTATAA-AATAAAAACAC
3267234 ATTTTATAAAATAAA
1 ATTTTATAAAATAAA
3267249 TAGTCTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.35
Consensus pattern (20 bp):
ATTTTATAAAATAAAAACAC
Found at i:3274794 original size:11 final size:11
Alignment explanation
Indices: 3274780--3274819 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
3274770 TATTTTCTCC
3274780 CTATTTTGCTA
1 CTATTTTGCTA
*
3274791 CTATTTTACTA
1 CTATTTTGCTA
* *
3274802 TTATGTTGCTA
1 CTATTTTGCTA
3274813 CTATTTT
1 CTATTTT
3274820 ATTGTTATTG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.20, C:0.15, G:0.07, T:0.57
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:3274894 original size:30 final size:30
Alignment explanation
Indices: 3274860--3274919 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
3274850 TATTTTATTA
3274860 TTAATTTTGTTATTATTTTAAAGGCATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
*
3274890 TTAATTTTGTTATTATTTTAGAGGCATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
3274920 CTTGTTAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.03, G:0.15, T:0.57
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGGCATTTG
Found at i:3276165 original size:55 final size:55
Alignment explanation
Indices: 3276060--3276165 Score: 142
Period size: 55 Copynumber: 1.9 Consensus size: 55
3276050 GTGAGCTTGA
* * *
3276060 AAAATAAGATAGCTTTGAAGACATATCTAGCTACCTTGAAGGTATACAGACATAG
1 AAAATAAGATAGCTTTGAAGACATATCTAGCCACCTTGAAAGTAGACAGACATAG
* * *
3276115 AAAATTAGATAGCTTTGAATG-CATATCTAGCCACTTTGAAAGTAGGCAGAC
1 AAAATAAGATAGCTTTGAA-GACATATCTAGCCACCTTGAAAGTAGACAGAC
3276166 TTTTTTGAGT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
55 43 0.98
56 1 0.02
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (55 bp):
AAAATAAGATAGCTTTGAAGACATATCTAGCCACCTTGAAAGTAGACAGACATAG
Found at i:3280089 original size:23 final size:23
Alignment explanation
Indices: 3280062--3280108 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
3280052 CATGTTAGTT
*
3280062 TTTGATTACTTTCATTAGTCACG
1 TTTGATTACTTTCACTAGTCACG
*
3280085 TTTGATTACTTTCGCTAGTCACG
1 TTTGATTACTTTCACTAGTCACG
3280108 T
1 T
3280109 CAATATTCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.47
Consensus pattern (23 bp):
TTTGATTACTTTCACTAGTCACG
Found at i:3286026 original size:3 final size:3
Alignment explanation
Indices: 3286018--3286092 Score: 150
Period size: 3 Copynumber: 25.0 Consensus size: 3
3286008 ACTACTTAGA
3286018 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
3286066 AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG
3286093 CCAGATGTGG
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:3290013 original size:135 final size:135
Alignment explanation
Indices: 3289766--3290020 Score: 321
Period size: 135 Copynumber: 1.9 Consensus size: 135
3289756 CAAAAACTAT
* * * *
3289766 AATTTCCTCCAGAAAATATAATACTGTCAGCCTCAACGAAGGAACATTTATTCAGATGAACTGCC
1 AATTCCCTCCAGAAAATATAAAACTGTCAGCCTCAACAAAGGAACATTTATTCAGATGAACTCCC
* * * * *
3289831 ACTATAGAATCCCATCATGAACTAGTAGAACTATCATGTTTCAAATGAACTTTTAAAACAGTTCA
66 ACTAGAGAATCCCACCACGAACAAGTAGAACTATCAAGTTTCAAATGAACTTTTAAAACAGTTCA
3289896 ACCAG
131 ACCAG
* * * * ** * * *
3289901 AATTCCCTCCAGAAAATATAAAATTGTTAGCCTCAATAAAGGGATGTTTATTTAGGTGGACTCCC
1 AATTCCCTCCAGAAAATATAAAACTGTCAGCCTCAACAAAGGAACATTTATTCAGATGAACTCCC
* * *
3289966 ACTCGAGAATCCCACCACGAACAAGTAGAATTATGAAGTTTCAAATGAACTTTTA
66 ACTAGAGAATCCCACCACGAACAAGTAGAACTATCAAGTTTCAAATGAACTTTTA
3290021 GAAATGCTGA
Statistics
Matches: 99, Mismatches: 21, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
135 99 1.00
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (135 bp):
AATTCCCTCCAGAAAATATAAAACTGTCAGCCTCAACAAAGGAACATTTATTCAGATGAACTCCC
ACTAGAGAATCCCACCACGAACAAGTAGAACTATCAAGTTTCAAATGAACTTTTAAAACAGTTCA
ACCAG
Found at i:3293237 original size:6 final size:6
Alignment explanation
Indices: 3293226--3293256 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
3293216 AACAAGAAGA
3293226 GATGTG GATGTG GATGTG GATGTG GATGTG G
1 GATGTG GATGTG GATGTG GATGTG GATGTG G
3293257 GTTTTCTTCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.00, G:0.52, T:0.32
Consensus pattern (6 bp):
GATGTG
Found at i:3293809 original size:20 final size:19
Alignment explanation
Indices: 3293766--3293817 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 19
3293756 AATGACATCA
3293766 AAACAACAACAAACAGTAG
1 AAACAACAACAAACAGTAG
* * *
3293785 AAACAACAGCAAAGTAGTGG
1 AAACAACAACAAA-CAGTAG
*
3293805 AAACAATAACAAA
1 AAACAACAACAAA
3293818 ACACAATAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.62, C:0.17, G:0.13, T:0.08
Consensus pattern (19 bp):
AAACAACAACAAACAGTAG
Found at i:3300628 original size:21 final size:21
Alignment explanation
Indices: 3300576--3300617 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
3300566 TTAAAACCAT
* *
3300576 AAAATTTTATAAA-ATTAGAA
1 AAAATTATAAAAATATTAGAA
3300596 AAAATTATAAAAATATTAGAA
1 AAAATTATAAAAATATTAGAA
3300617 A
1 A
3300618 TTAATTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (21 bp):
AAAATTATAAAAATATTAGAA
Found at i:3302276 original size:6 final size:6
Alignment explanation
Indices: 3302255--3302306 Score: 77
Period size: 6 Copynumber: 8.7 Consensus size: 6
3302245 CAAACCACAA
* * *
3302255 CAACAG CATCAG CAACAA CAACAA CAACAG CAACAG CAACAG CAACAG
1 CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG
3302303 CAAC
1 CAAC
3302307 GGGAACATGT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.52, C:0.35, G:0.12, T:0.02
Consensus pattern (6 bp):
CAACAG
Found at i:3302313 original size:18 final size:18
Alignment explanation
Indices: 3302251--3302306 Score: 85
Period size: 18 Copynumber: 3.1 Consensus size: 18
3302241 TCGGCAAACC
*
3302251 ACAACAACAGCATCAGCA
1 ACAACAACAGCAACAGCA
*
3302269 ACAACAACAACAACAGCA
1 ACAACAACAGCAACAGCA
*
3302287 ACAGCAACAGCAACAGCA
1 ACAACAACAGCAACAGCA
3302305 AC
1 AC
3302307 GGGAACATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.54, C:0.34, G:0.11, T:0.02
Consensus pattern (18 bp):
ACAACAACAGCAACAGCA
Found at i:3304386 original size:30 final size:30
Alignment explanation
Indices: 3304326--3304405 Score: 72
Period size: 30 Copynumber: 2.5 Consensus size: 30
3304316 ATCTTATATA
* * *
3304326 TTTATAATTTTTAAAAGATTAAATTAAATT
1 TTTATTATTTTTAAAAGAGTAAATGAAATT
*
3304356 TTTATTATTTTTAAAAG-GTAAAGTGCAATT
1 TTTATTATTTTTAAAAGAGTAAA-TGAAATT
3304386 TTACTATTATTAATTTAAAA
1 TT--TATTATT--TTTAAAA
3304406 TTTTATAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
29 4 0.10
30 23 0.56
32 7 0.17
34 7 0.17
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (30 bp):
TTTATTATTTTTAAAAGAGTAAATGAAATT
Found at i:3307515 original size:5 final size:5
Alignment explanation
Indices: 3307505--3307529 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3307495 CAGATATATG
3307505 TTATA TTATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA
3307530 GGCATATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTATA
Found at i:3326001 original size:43 final size:42
Alignment explanation
Indices: 3325889--3326006 Score: 109
Period size: 43 Copynumber: 2.8 Consensus size: 42
3325879 ATCCCAAAAA
* * *
3325889 CGCCGCTAAAGATCAGGGTCTTTGGCGGCGCTTCTACTAAAG
1 CGCCGCTAAAGATCAGTGTCTTTAGCGGCGTTTCTACTAAAG
* * *
3325931 CACCGCTAAA-AGTCTTA-T-TCTTCAGCGGCGTTTGTGA-TAGAAG
1 CGCCGCTAAAGA-TC--AGTGTCTTTAGCGGCGTTTCT-ACTA-AAG
3325974 CGCCGCTAAAGATCAGTGTCTTTAGCGGCGTTT
1 CGCCGCTAAAGATCAGTGTCTTTAGCGGCGTTT
3326007 TTAGTAAAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 15
0.72 0.10 0.18
Matches are distributed among these distances:
41 2 0.03
42 27 0.45
43 29 0.48
44 2 0.03
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (42 bp):
CGCCGCTAAAGATCAGTGTCTTTAGCGGCGTTTCTACTAAAG
Found at i:3326501 original size:39 final size:40
Alignment explanation
Indices: 3326434--3326512 Score: 115
Period size: 39 Copynumber: 2.0 Consensus size: 40
3326424 TAAAAAGTAT
* * *
3326434 TTATATTAACAAATACTACCATAAATATAATAAATATTTTC
1 TTATATTAAAAAACACTA-CATAAATATAATAAACATTTTC
3326475 TTATATTAAAAAACACTA-ATAAATATAATAAACATTTT
1 TTATATTAAAAAACACTACATAAATATAATAAACATTTT
3326513 ACTGTATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
39 19 0.54
41 16 0.46
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (40 bp):
TTATATTAAAAAACACTACATAAATATAATAAACATTTTC
Found at i:3331076 original size:19 final size:20
Alignment explanation
Indices: 3331039--3331078 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
3331029 TCTTTTCGCA
* *
3331039 TTCATTTCATGCATTTGCAT
1 TTCATTACATGCATATGCAT
3331059 TTCATTACAT-CATATGCAT
1 TTCATTACATGCATATGCAT
3331078 T
1 T
3331079 AAACACAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.25, C:0.20, G:0.07, T:0.47
Consensus pattern (20 bp):
TTCATTACATGCATATGCAT
Found at i:3332845 original size:19 final size:19
Alignment explanation
Indices: 3332821--3332860 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
3332811 GCAAATATTC
*
3332821 TTTCATT-CTTTACGATTTT
1 TTTCATTCCTTCA-GATTTT
3332840 TTTCATTCCTTCAGATTTT
1 TTTCATTCCTTCAGATTTT
3332859 TT
1 TT
3332861 CTGCCAAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.15, C:0.17, G:0.05, T:0.62
Consensus pattern (19 bp):
TTTCATTCCTTCAGATTTT
Found at i:3333813 original size:6 final size:7
Alignment explanation
Indices: 3333801--3333846 Score: 60
Period size: 7 Copynumber: 6.6 Consensus size: 7
3333791 AAAAGTGATG
3333801 TGAAAAA
1 TGAAAAA
3333808 TGAAAAGA
1 TGAAAA-A
3333816 TG-AAAA
1 TGAAAAA
3333822 TGAAAAA
1 TGAAAAA
3333829 TGAAAAA
1 TGAAAAA
3333836 -GTAAAAA
1 TG-AAAAA
3333843 TGAA
1 TGAA
3333847 GAGGCTAAGG
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
6 4 0.11
7 27 0.77
8 4 0.11
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.15
Consensus pattern (7 bp):
TGAAAAA
Found at i:3335173 original size:45 final size:45
Alignment explanation
Indices: 3335073--3335265 Score: 189
Period size: 45 Copynumber: 4.3 Consensus size: 45
3335063 GGCAGGTTGA
* * * *
3335073 AAGAAAGTAGATCTTGTCTT-CATGTACTGG-CGTGAAGTAGATC-
1 AAGAAAGCAGATCTTGTCTTCCCT-TACTGGTGGCGAAGTAGATCG
* * *
3335116 AGAGATACCAGATCTTGCCTTCCCTTACTGGTGGCGAAGTAGATCG
1 A-AGAAAGCAGATCTTGTCTTCCCTTACTGGTGGCGAAGTAGATCG
** * *
3335162 AAGAAAGCAGATCTTGTCTT-TATGTACTGG-CGTGAAGTAGATCG
1 AAGAAAGCAGATCTTGTCTTCCCT-TACTGGTGGCGAAGTAGATCG
** *
3335206 AAGAAAGTGGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCG
1 AAGAAAGCAGATCTTGTCTTCCCTTACTGGTGGCGAAGTAGATCG
*
3335251 AAGAAAACAGATCTT
1 AAGAAAGCAGATCTT
3335266 ATCTCCTTAG
Statistics
Matches: 119, Mismatches: 24, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
43 1 0.01
44 58 0.49
45 59 0.50
46 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.27
Consensus pattern (45 bp):
AAGAAAGCAGATCTTGTCTTCCCTTACTGGTGGCGAAGTAGATCG
Found at i:3335174 original size:89 final size:89
Alignment explanation
Indices: 3335073--3335265 Score: 289
Period size: 89 Copynumber: 2.2 Consensus size: 89
3335063 GGCAGGTTGA
* *
3335073 AAGAAAGTAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC-AGAGATACCAGATCTTGCCTT
1 AAGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCGA-AGAAACCAGATCTTGCCTT
*
3335137 CCCTTACTGGTGGCGAAGTAGATCG
65 CCCATACTGGTGGCGAAGTAGATCG
* *** *
3335162 AAGAAAGCAGATCTTGTCTTTATGTACTGGCGTGAAGTAGATCGAAGAAAGTGGATCTTGTCTTC
1 AAGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCGAAGAAACCAGATCTTGCCTTC
3335227 CCATACTGGTGGCGAAGTAGATCG
66 CCATACTGGTGGCGAAGTAGATCG
*
3335251 AAGAAAACAGATCTT
1 AAGAAAGCAGATCTT
3335266 ATCTCCTTAG
Statistics
Matches: 94, Mismatches: 9, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
89 93 0.99
90 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.27
Consensus pattern (89 bp):
AAGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCGAAGAAACCAGATCTTGCCTTC
CCATACTGGTGGCGAAGTAGATCG
Found at i:3335402 original size:44 final size:44
Alignment explanation
Indices: 3335353--3335844 Score: 275
Period size: 44 Copynumber: 11.2 Consensus size: 44
3335343 CCGGTAATTC
* *
3335353 TATCTCCCTAGGCAGCAGTGGAATAGATTGAATATTACAGATCT
1 TATCTCCCTAGGCAGCAGTGGAGTAGATTGAAGATTACAGATCT
* * * * ** *
3335397 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTT
1 TATCTCCCTAGGCAGCAGTGGAGTAGATTGAAGATTACAGATCT
* ** ** * * *
3335441 TACCTCCCTGAGGTTGCAGCAGAGTATATTGAAGCTGGTA-A-TTC-
1 TATCTCCCT-AGGCAGCAGTGGAGTAGATTGAAGAT--TACAGATCT
* * * *
3335485 TATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTATAGATCT
1 TATCTCCCTAGGCAGCAGTGGAGTAGATTGAAGATTACAGATCT
* * * * * ** *
3335529 TATCTCCCAAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTT
1 TATCTCCCTAGGCAGCAGTGGAGTAGATTGAAGATTACAGATCT
* ** * * * *
3335573 TACCTCCCTAAGGTTGCAGCGGAGTATATTGAAGCCAGTA-A-TTC-
1 TATCTCCCT-AGGCAGCAGTGGAGTAGATTGAAG--ATTACAGATCT
* *
3335617 TATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCT
1 TATCTCCCTAGGCAGCAGTGGAGTAGATTGAAGATTACAGATCT
* * * * ** *
3335661 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTT
1 TATCTCCCTAGGCAGCAGTGGAGTAGATTGAAGATTACAGATCT
* ** * * * *
3335705 TACCTCCCTAAGGTTGCAGCGGAGTATATTGAAG-CTAGTA-AT-T
1 TATCTCCCT-AGGCAGCAGTGGAGTAGATTGAAGATTA-CAGATCT
* * *
3335748 CTATCTCCCTGGGCAGCAGTGGAATAGATTGAAAATTACAGATCT
1 -TATCTCCCTAGGCAGCAGTGGAGTAGATTGAAGATTACAGATCT
* * * * ***
3335793 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACCCCAG-TCT
1 TATCTCCCTAGGCAGCAGTGGAGTAGATTGAAGATTACAGATCT
3335836 TATCTCCCT
1 TATCTCCCT
3335845 GAAGTTGCAG
Statistics
Matches: 317, Mismatches: 113, Indels: 37
0.68 0.24 0.08
Matches are distributed among these distances:
41 5 0.02
42 2 0.01
43 70 0.22
44 185 0.58
45 52 0.16
46 2 0.01
47 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (44 bp):
TATCTCCCTAGGCAGCAGTGGAGTAGATTGAAGATTACAGATCT
Found at i:3335886 original size:264 final size:264
Alignment explanation
Indices: 3335352--3335887 Score: 824
Period size: 264 Copynumber: 2.0 Consensus size: 264
3335342 GCCGGTAATT
*
3335352 CTATCTCCCTAGGCAGCAGTGGAATAGATTGAATATTACAGATCTTATCTCCCTAAGCAGTAGTG
1 CTATCTCCCTAGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTG
* *
3335417 GAGCAGATCGAAGATGGCAGATTTTACCTCCCTGAGGTTGCAGCAGAGTATATTGAAGCTGGTAA
66 GAGCAGATCGAAGATGGCAGATTTTACCTCCCTAAGGTTGCAGCAGAGTATATTGAAGCTAGTAA
* *
3335482 TTCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTATAGATCTTATCTCCCAAAGCAGTAG
131 TTCTATCTCCCTGGGCAACAGTGGAATAGATTGAAAATTACAGATCTTATCTCCCAAAGCAGTAG
*** * * * ** * **
3335547 TGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTAAGGTTGCAGCGGAGTATATTGAAGCCAGT
196 TGGAGCAGATCGAAGACCCCAGATCTTACCTCCCTAAGGTTGCAGCGGAGCAAACAGAAGACACC
*
3335612 AATT
261 AATC
*
3335616 CTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTG
1 CTATCTCCCTAGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTG
*
3335681 GAGCAGATCGAAGATGGCAGATTTTACCTCCCTAAGGTTGCAGCGGAGTATATTGAAGCTAGTAA
66 GAGCAGATCGAAGATGGCAGATTTTACCTCCCTAAGGTTGCAGCAGAGTATATTGAAGCTAGTAA
* *
3335746 TTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAAATTACAGATCTTATCTCCCTAAGCAGTAG
131 TTCTATCTCCCTGGGCAACAGTGGAATAGATTGAAAATTACAGATCTTATCTCCCAAAGCAGTAG
* * *
3335811 TGGAGCAGATCGAAGACCCCAG-TCTTATCTCCCTGAA-GTTGCAGTGGAGCAAACAGAAGTATA
196 TGGAGCAGATCGAAGACCCCAGATCTTACCTCCCT-AAGGTTGCAGCGGAGCAAACAGAAG-ACA
3335874 CCAATC
259 CCAATC
3335880 CTATCTCC
1 CTATCTCC
3335888 TTGAAGTTGC
Statistics
Matches: 246, Mismatches: 24, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
263 27 0.11
264 219 0.89
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (264 bp):
CTATCTCCCTAGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTG
GAGCAGATCGAAGATGGCAGATTTTACCTCCCTAAGGTTGCAGCAGAGTATATTGAAGCTAGTAA
TTCTATCTCCCTGGGCAACAGTGGAATAGATTGAAAATTACAGATCTTATCTCCCAAAGCAGTAG
TGGAGCAGATCGAAGACCCCAGATCTTACCTCCCTAAGGTTGCAGCGGAGCAAACAGAAGACACC
AATC
Found at i:3335887 original size:132 final size:132
Alignment explanation
Indices: 3335257--3335826 Score: 921
Period size: 132 Copynumber: 4.3 Consensus size: 132
3335247 ATCGAAGAAA
* * **
3335257 ACAGATCTTATCT-CCTTAGACAGTAGTGGAGTAGATC-AAGGATGGTGGATTTTACCTCCCTGA
1 ACAGATCTTATCTCCCTAAG-CAGTAGTGGAGCAGATCGAA-GATGGCAGATTTTACCTCCCT-A
* * * ** *
3335320 A-GTTACAGTGGAGTACATTGAAGCCGGTAATTCTATCTCCCTAGGCAGCAGTGGAATAGATTGA
63 AGGTTGCAGCGGAGTATATTGAAGCTAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGA
*
3335384 ATATT
128 AGATT
*
3335389 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGAGG
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTAAGG
* * *
3335454 TTGCAGCAGAGTATATTGAAGCTGGTAATTCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGA
66 TTGCAGCGGAGTATATTGAAGCTAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGA
3335519 TT
131 TT
* *
3335521 ATAGATCTTATCTCCCAAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTAAGG
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTAAGG
*
3335586 TTGCAGCGGAGTATATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGA
66 TTGCAGCGGAGTATATTGAAGCTAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGA
3335651 TT
131 TT
3335653 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTAAGG
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTAAGG
*
3335718 TTGCAGCGGAGTATATTGAAGCTAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAAA
66 TTGCAGCGGAGTATATTGAAGCTAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGA
3335783 TT
131 TT
3335785 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGA
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGA
3335827 CCCCAGTCTT
Statistics
Matches: 411, Mismatches: 24, Indels: 6
0.93 0.05 0.01
Matches are distributed among these distances:
131 1 0.00
132 403 0.98
133 7 0.02
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (132 bp):
ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTAAGG
TTGCAGCGGAGTATATTGAAGCTAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGA
TT
Found at i:3335922 original size:132 final size:132
Alignment explanation
Indices: 3335352--3335930 Score: 464
Period size: 132 Copynumber: 4.4 Consensus size: 132
3335342 GCCGGTAATT
* * **
3335352 CTATCTCCCT-AGGCAGCAGTGGAATAGATTGAATATTACAGATCTTATCTCCCTAAGCAGTAGT
1 CTATCTCCCTGA-GCAGCAATGGAATAGATTGAAAACCACAGATCTTATCTCCCTAAGCAGTAGT
*** * * * * * ** * ***
3335416 GGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGAGGTTGCAGCAGAGTATATTGAAGCTGGTA
65 GGAGCAGATCGAAGACCCCAGATCTTACCTCCCTAAGGTTGCAGCGGAGCAAACAGAAGATACCA
*
3335481 ATT
130 ATC
* * * * ** * *
3335484 CTATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTATAGATCTTATCTCCCAAAGCAGTAGTG
1 CTATCTCCCTGAGCAGCAATGGAATAGATTGAAAACCACAGATCTTATCTCCCTAAGCAGTAGTG
*** * * * ** ** **
3335549 GAGCAGATCGAAGATGGCAGATTTTACCTCCCTAAGGTTGCAGCGGAGTATATTGAAGCCAGTAA
66 GAGCAGATCGAAGACCCCAGATCTTACCTCCCTAAGGTTGCAGCGGAGCAAACAGAAGATACCAA
*
3335614 TT
131 TC
* * * **
3335616 CTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTG
1 CTATCTCCCTGAGCAGCAATGGAATAGATTGAAAACCACAGATCTTATCTCCCTAAGCAGTAGTG
*** * * * ** * **
3335681 GAGCAGATCGAAGATGGCAGATTTTACCTCCCTAAGGTTGCAGCGGAGTATATTGAAGCTAGTAA
66 GAGCAGATCGAAGACCCCAGATCTTACCTCCCTAAGGTTGCAGCGGAGCAAACAGAAGATACCAA
*
3335746 TT
131 TC
* * **
3335748 CTATCTCCCTGGGCAGCAGTGGAATAGATTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTG
1 CTATCTCCCTGAGCAGCAATGGAATAGATTGAAAACCACAGATCTTATCTCCCTAAGCAGTAGTG
* *
3335813 GAGCAGATCGAAGACCCCAG-TCTTATCTCCCTGAA-GTTGCAGTGGAGCAAACAGAAGTATACC
66 GAGCAGATCGAAGACCCCAGATCTTACCTCCCT-AAGGTTGCAGCGGAGCAAACAGAAG-ATACC
3335876 AATC
129 AATC
* ** * * * *
3335880 CTATCTCCTTGAAGTTGCAATGGAGTGGATT-AAAACCGCAGATCTCATCTC
1 CTATCTCCCTG-AGCAGCAATGGAATAGATTGAAAACCACAGATCTTATCTC
3335931 TCTGAAGTTG
Statistics
Matches: 404, Mismatches: 39, Indels: 8
0.90 0.09 0.02
Matches are distributed among these distances:
131 27 0.07
132 364 0.90
133 13 0.03
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (132 bp):
CTATCTCCCTGAGCAGCAATGGAATAGATTGAAAACCACAGATCTTATCTCCCTAAGCAGTAGTG
GAGCAGATCGAAGACCCCAGATCTTACCTCCCTAAGGTTGCAGCGGAGCAAACAGAAGATACCAA
TC
Found at i:3338650 original size:17 final size:17
Alignment explanation
Indices: 3338628--3338664 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
3338618 AGTGCCACAT
3338628 TAAAAGTTTTGATAAAG
1 TAAAAGTTTTGATAAAG
3338645 TAAAAGTTTTGATAAAG
1 TAAAAGTTTTGATAAAG
3338662 TAA
1 TAA
3338665 GAAGGGCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.16, T:0.35
Consensus pattern (17 bp):
TAAAAGTTTTGATAAAG
Found at i:3341718 original size:11 final size:11
Alignment explanation
Indices: 3341702--3341729 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
3341692 AATTATATCT
3341702 TTATTTTTTAA
1 TTATTTTTTAA
3341713 TTATTTTTTAA
1 TTATTTTTTAA
3341724 TTATTT
1 TTATTT
3341730 AAATTTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (11 bp):
TTATTTTTTAA
Found at i:3341952 original size:20 final size:20
Alignment explanation
Indices: 3341906--3341953 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
3341896 CTGTTTTTTA
*
3341906 TTTTATATATTATAATATAAT
1 TTTTA-ATATTATAACATAAT
*
3341927 TATTAATATTATGAACAT-AT
1 TTTTAATATTAT-AACATAAT
3341947 TTTTAAT
1 TTTTAAT
3341954 GGTTTGCCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (20 bp):
TTTTAATATTATAACATAAT
Found at i:3360549 original size:23 final size:21
Alignment explanation
Indices: 3360507--3360550 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
3360497 GATCTCATTT
*
3360507 TTTTTTAAAAAAATCAAATTA
1 TTTTTTAAAAAAATAAAATTA
*
3360528 TTTTTTAACGAAAATAATAATTA
1 TTTTTTAA-AAAAATAA-AATTA
3360551 AAACATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 8 0.42
22 6 0.32
23 5 0.26
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (21 bp):
TTTTTTAAAAAAATAAAATTA
Found at i:3363827 original size:101 final size:100
Alignment explanation
Indices: 3363695--3363911 Score: 301
Period size: 101 Copynumber: 2.1 Consensus size: 100
3363685 TTACCATGAC
* * * * *
3363695 CCAACCATGGTCTTACATTCGTAGTTTCATAACTCAATTATGGTCTTATCATCAGAATGCCATAA
1 CCAACCATGGTCTTACATTCATAG-TCCATAACCCAATTATGGTCTTATCATCAAAATACCATAA
3363760 CCCAACTATGGTCTTACTTATAAATACTGCCATGGT
65 CCCAACTATGGTCTTACTTATAAATACTGCCATGGT
* * *
3363796 CCAACCATGGTCTTACATTCAAATAG-CCATAACCCAATTATGGTCTTTTCATTAAAATATCATA
1 CCAACCATGGTCTTACATTC--ATAGTCCATAACCCAATTATGGTCTTATCATCAAAATACCATA
* * *
3363860 TCTCAGCTATGGTCTTACTTATAAATACTGCCATGGT
64 ACCCAACTATGGTCTTACTTATAAATACTGCCATGGT
3363897 CCAACCATGGTCTTA
1 CCAACCATGGTCTTA
3363912 TCCGTCAATT
Statistics
Matches: 103, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
101 100 0.97
103 3 0.03
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (100 bp):
CCAACCATGGTCTTACATTCATAGTCCATAACCCAATTATGGTCTTATCATCAAAATACCATAAC
CCAACTATGGTCTTACTTATAAATACTGCCATGGT
Found at i:3363839 original size:33 final size:33
Alignment explanation
Indices: 3363688--3363877 Score: 104
Period size: 33 Copynumber: 5.7 Consensus size: 33
3363678 ACATGCATTA
* * *
3363688 CCATGACCCAACCATGGTCTTACATTC--GTAG
1 CCATAACCCAACTATGGTCTTACATTCAAATAG
* * *
3363719 TTTCATAACTCAATTATGGTCTTATCA-TCAGAAT-G
1 --CCATAACCCAACTATGGTCTTA-CATTCA-AATAG
*
3363754 CCATAACCCAACTATGGTCTTAC-TTATAAATACTG
1 CCATAACCCAACTATGGTCTTACATT-CAAATA--G
*** *
3363789 CCATGGTCCAACCATGGTCTTACATTCAAATAG
1 CCATAACCCAACTATGGTCTTACATTCAAATAG
* * *
3363822 CCATAACCCAATTATGGTCTTTTCATTAAAATA-
1 CCATAACCCAACTATGGTC-TTACATTCAAATAG
* * * *
3363855 TCATATCTCAGCTATGGTCTTAC
1 CCATAACCCAACTATGGTCTTAC
3363878 TTATAAATAC
Statistics
Matches: 118, Mismatches: 28, Indels: 23
0.70 0.17 0.14
Matches are distributed among these distances:
32 8 0.07
33 68 0.58
34 13 0.11
35 26 0.22
36 3 0.03
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.33
Consensus pattern (33 bp):
CCATAACCCAACTATGGTCTTACATTCAAATAG
Found at i:3366595 original size:35 final size:36
Alignment explanation
Indices: 3366554--3366635 Score: 96
Period size: 35 Copynumber: 2.3 Consensus size: 36
3366544 TTTAATTATA
*
3366554 TATATATATATACAATTAATGATATTTAAA-TATAATT
1 TATAT-TATAT-CAATTAATGATAATTAAATTATAATT
* *
3366591 TATATTATATGAATTTATGATAATTAAATTATAA-T
1 TATATTATATCAATTAATGATAATTAAATTATAATT
*
3366626 GATATTATAT
1 TATATTATAT
3366636 TATTAAATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
35 25 0.62
36 10 0.25
37 5 0.12
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.48
Consensus pattern (36 bp):
TATATTATATCAATTAATGATAATTAAATTATAATT
Found at i:3366627 original size:25 final size:23
Alignment explanation
Indices: 3366547--3366643 Score: 62
Period size: 24 Copynumber: 4.1 Consensus size: 23
3366537 TTATTTGTTT
3366547 AATTATAT-ATA-TATAT-A-TA
1 AATTATATGATATTATATAATTA
3366566 CAATTA-ATGATATTTAAATATAATTTA
1 -AATTATATGATA-TT--ATATAA-TTA
*
3366593 TATTATATGA-ATTTATGATAATTA
1 AATTATATGATA-TTAT-ATAATTA
*
3366617 AATTATAATGATATTATATTATTA
1 AATTAT-ATGATATTATATAATTA
3366641 AAT
1 AAT
3366644 AAATCAAAAT
Statistics
Matches: 62, Mismatches: 3, Indels: 20
0.73 0.04 0.24
Matches are distributed among these distances:
19 2 0.03
20 8 0.13
22 1 0.02
24 23 0.37
25 13 0.21
26 9 0.15
27 6 0.10
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (23 bp):
AATTATATGATATTATATAATTA
Found at i:3368377 original size:45 final size:45
Alignment explanation
Indices: 3368310--3368410 Score: 130
Period size: 45 Copynumber: 2.2 Consensus size: 45
3368300 GCCGACTACT
* ** * *
3368310 GTTACTGTTACCGATTTGGCACTTTGTGTGTCAAATACTGTTACC
1 GTTACTGTTACAGATTCAGCACTTTGTGTGTCAAATAATGTCACC
** *
3368355 GTTACTGTTACAGATTCAGCACTTTGTGTGTGGAATAATGTCACT
1 GTTACTGTTACAGATTCAGCACTTTGTGTGTCAAATAATGTCACC
3368400 GTTACTGTTAC
1 GTTACTGTTAC
3368411 TGCTACCGTT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.40
Consensus pattern (45 bp):
GTTACTGTTACAGATTCAGCACTTTGTGTGTCAAATAATGTCACC
Found at i:3368586 original size:2 final size:2
Alignment explanation
Indices: 3368579--3368603 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3368569 AATAAGAATG
3368579 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3368604 GTTAATTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3370481 original size:55 final size:55
Alignment explanation
Indices: 3370416--3370527 Score: 224
Period size: 55 Copynumber: 2.0 Consensus size: 55
3370406 ATTGATGTGT
3370416 ATAGATTGAATCGTTATATGATTTGGTTATCTTGAACTCACCTTACTGTTGCAAA
1 ATAGATTGAATCGTTATATGATTTGGTTATCTTGAACTCACCTTACTGTTGCAAA
3370471 ATAGATTGAATCGTTATATGATTTGGTTATCTTGAACTCACCTTACTGTTGCAAA
1 ATAGATTGAATCGTTATATGATTTGGTTATCTTGAACTCACCTTACTGTTGCAAA
3370526 AT
1 AT
3370528 GTAATAACAG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.40
Consensus pattern (55 bp):
ATAGATTGAATCGTTATATGATTTGGTTATCTTGAACTCACCTTACTGTTGCAAA
Found at i:3371012 original size:17 final size:17
Alignment explanation
Indices: 3370990--3371098 Score: 69
Period size: 17 Copynumber: 6.5 Consensus size: 17
3370980 ACGACTATAC
3370990 TTTATATGCAAGTTGTG
1 TTTATATGCAAGTTGTG
** *
3371007 TTTATATGTGAGTTGTC
1 TTTATATGCAAGTTGTG
* * *
3371024 TTTATACGTAAGCTG-G
1 TTTATATGCAAGTTGTG
* * * * *
3371040 GTTATGTACGAGTTGTA
1 TTTATATGCAAGTTGTG
* * * *
3371057 TGTATATGCGAGCTATG
1 TTTATATGCAAGTTGTG
3371074 TTTATATGCAAGTTGTG
1 TTTATATGCAAGTTGTG
3371091 -TTATATGC
1 TTTATATGC
3371099 GAACTGCGTT
Statistics
Matches: 65, Mismatches: 26, Indels: 3
0.69 0.28 0.03
Matches are distributed among these distances:
16 16 0.25
17 49 0.75
ACGTcount: A:0.23, C:0.08, G:0.25, T:0.44
Consensus pattern (17 bp):
TTTATATGCAAGTTGTG
Found at i:3371097 original size:33 final size:32
Alignment explanation
Indices: 3371050--3371145 Score: 84
Period size: 33 Copynumber: 2.8 Consensus size: 32
3371040 GTTATGTACG
*
3371050 AGTTGTATGTATATGCGAGCTATGTTTATATGCA
1 AGTTGT-T-TATATGCGAGCTATGTTTATACGCA
* ** **
3371084 AGTTGTGTTATATGCGAACTGCGTTTATACGTG
1 AGTTGT-TTATATGCGAGCTATGTTTATACGCA
*
3371117 AGTTGCCTTTATATGCGAGCTATGCTTAT
1 AGTTG--TTTATATGCGAGCTATGTTTAT
3371146 CAATGTGTGG
Statistics
Matches: 49, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
33 24 0.49
34 24 0.49
35 1 0.02
ACGTcount: A:0.23, C:0.12, G:0.24, T:0.41
Consensus pattern (32 bp):
AGTTGTTTATATGCGAGCTATGTTTATACGCA
Found at i:3377477 original size:50 final size:50
Alignment explanation
Indices: 3377402--3377500 Score: 162
Period size: 50 Copynumber: 2.0 Consensus size: 50
3377392 TTCGGAATTC
* *
3377402 TGACTTCTGATATATAAAACATAAGGAAGAATACGTTTTGTTGGTAAAAT
1 TGACTTCTGATATATAAAACATAAGGAAGAATACATTTTGTGGGTAAAAT
* *
3377452 TGACTTCTGGTATATAAAACATAAGGAAGGATACATTTTGTGGGTAAAA
1 TGACTTCTGATATATAAAACATAAGGAAGAATACATTTTGTGGGTAAAA
3377501 AACTGACTTC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.39, C:0.08, G:0.20, T:0.32
Consensus pattern (50 bp):
TGACTTCTGATATATAAAACATAAGGAAGAATACATTTTGTGGGTAAAAT
Done.