Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 193 of 427
Found at i:53632632 original size:43 final size:43
Alignment explanation
Indices: 53632566--53632729 Score: 229
Period size: 43 Copynumber: 3.8 Consensus size: 43
53632556 CAGGTTAAAT
* * * *
53632566 CTAGCAGGCTTCGTGTCGATGATGTGTATTCGAGCCTTTGTGC
1 CTAGCAGGCTTCATGTCGGTGATGTGTATTCGGGCCTTCGTGC
**
53632609 CTAGCAGGCTTCATGTTAGTGATGTGTATTCGGGCCTTCGTGC
1 CTAGCAGGCTTCATGTCGGTGATGTGTATTCGGGCCTTCGTGC
* * *
53632652 CTAGCAGGCTTCATGGCGGTGATATGTATTTGGGCCTTCGTGC
1 CTAGCAGGCTTCATGTCGGTGATGTGTATTCGGGCCTTCGTGC
* *
53632695 CTAGCAGGCTTCTTATCGGTGATGTGTATTCGGGC
1 CTAGCAGGCTTCATGTCGGTGATGTGTATTCGGGC
53632730 TGGTGATGTG
Statistics
Matches: 105, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 105 1.00
ACGTcount: A:0.14, C:0.21, G:0.31, T:0.34
Consensus pattern (43 bp):
CTAGCAGGCTTCATGTCGGTGATGTGTATTCGGGCCTTCGTGC
Found at i:53632736 original size:19 final size:19
Alignment explanation
Indices: 53632712--53632748 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
53632702 GCTTCTTATC
53632712 GGTGATGTGTATTCGGGCT
1 GGTGATGTGTATTCGGGCT
53632731 GGTGATGTGTATTCGGGC
1 GGTGATGTGTATTCGGGC
53632749 CTTCGTGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.43, T:0.35
Consensus pattern (19 bp):
GGTGATGTGTATTCGGGCT
Found at i:53632794 original size:45 final size:44
Alignment explanation
Indices: 53632740--53632898 Score: 198
Period size: 45 Copynumber: 3.6 Consensus size: 44
53632730 TGGTGATGTG
*
53632740 TATTCGGGCCTTCGTGCCTAGCAGGCTATGATGCCGGTGAAATAC
1 TATTCGGGCCTTCGAGCCTAGCAGGCTAT-ATGCCGGTGAAATAC
* * *
53632785 TATTCGGGCCTTTGAGCCTAGTAGGCTATAATGCCGGTGAGATAC
1 TATTCGGGCCTTCGAGCCTAGCAGGCTAT-ATGCCGGTGAAATAC
* * *
53632830 TATTCGGGCTTTCAAGCCTAGCAGGCTATAGTGCCTGTGAAATGA-
1 TATTCGGGCCTTCGAGCCTAGCAGGCTATA-TGCCGGTGAAAT-AC
53632875 TATT-GGGCC-TCGAGCCTAGCAGGC
1 TATTCGGGCCTTCGAGCCTAGCAGGC
53632899 GAAATATCGG
Statistics
Matches: 99, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
43 14 0.14
44 5 0.05
45 79 0.80
46 1 0.01
ACGTcount: A:0.21, C:0.23, G:0.29, T:0.27
Consensus pattern (44 bp):
TATTCGGGCCTTCGAGCCTAGCAGGCTATATGCCGGTGAAATAC
Found at i:53635558 original size:9 final size:9
Alignment explanation
Indices: 53635546--53635580 Score: 52
Period size: 9 Copynumber: 3.7 Consensus size: 9
53635536 CTTAAACACC
53635546 TTGAGTGAT
1 TTGAGTGAT
53635555 TTGAGTGAAT
1 TTGAGTG-AT
53635565 CTTGAGTGAT
1 -TTGAGTGAT
53635575 TTGAGT
1 TTGAGT
53635581 CCTGATTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 13 0.54
10 4 0.17
11 7 0.29
ACGTcount: A:0.23, C:0.03, G:0.31, T:0.43
Consensus pattern (9 bp):
TTGAGTGAT
Found at i:53636264 original size:37 final size:37
Alignment explanation
Indices: 53636158--53636266 Score: 173
Period size: 37 Copynumber: 2.9 Consensus size: 37
53636148 AGCTCAGACG
* * * *
53636158 AAATCTCCACACGAAGTTATTGGGTCTTACCCAGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
53636195 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
53636232 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
53636267 ATATATTTCC
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 67 1.00
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:53636477 original size:47 final size:47
Alignment explanation
Indices: 53636426--53636551 Score: 180
Period size: 47 Copynumber: 2.7 Consensus size: 47
53636416 TTTCACACTA
* * ** **
53636426 GCCATTCGGCTTTACCACATATATGCATTTTCATGTTCACCACATTG
1 GCCATTCGGCCTTATCACATATATGCATGCTCACATTCACCACATTG
* *
53636473 GCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTG
1 GCCATTCGGCCTTATCACATATATGCATGCTCACATTCACCACATTG
53636520 GCCATTCGGCCTTATCACATATATGCATGCTC
1 GCCATTCGGCCTTATCACATATATGCATGCTC
53636552 TGTGACAGCC
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 70 1.00
ACGTcount: A:0.24, C:0.30, G:0.13, T:0.33
Consensus pattern (47 bp):
GCCATTCGGCCTTATCACATATATGCATGCTCACATTCACCACATTG
Found at i:53638367 original size:40 final size:40
Alignment explanation
Indices: 53638312--53638561 Score: 385
Period size: 40 Copynumber: 6.2 Consensus size: 40
53638302 AACATTGGAA
53638312 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
53638352 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
53638392 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
53638432 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
53638472 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
53638511 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
53638552 CTATATCCGG
1 ATATATCCGG
53638562 TTAAATCCCG
Statistics
Matches: 191, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
39 2 0.01
40 189 0.99
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:53646538 original size:40 final size:40
Alignment explanation
Indices: 53646483--53646719 Score: 268
Period size: 40 Copynumber: 6.2 Consensus size: 40
53646473 AACATTGGAA
53646483 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
53646523 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
53646563 ATATATCCGGGCTAAGACCCGAAGGCATTCGT---AGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
53646600 ----A-CCGGGCTAAGA--C---GGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
53646630 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
53646669 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
53646710 CTATATCCGG
1 ATATATCCGG
53646720 TTAAATCCCG
Statistics
Matches: 165, Mismatches: 17, Indels: 30
0.78 0.08 0.14
Matches are distributed among these distances:
27 9 0.05
30 6 0.04
32 11 0.07
33 1 0.01
34 1 0.01
35 11 0.07
37 6 0.04
39 2 0.01
40 118 0.72
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:53646692 original size:107 final size:107
Alignment explanation
Indices: 53646506--53646701 Score: 295
Period size: 107 Copynumber: 1.8 Consensus size: 107
53646496 AAGACCCGAA
* * * *
53646506 GGCATTCGTGCGAGTTGATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGATATATCC
1 GGCATTCGTGCGAGTTGATATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTCACAAATCC
*
53646571 GGGCTAAGACCCGAAGGCATTCGTAGTTGACCGGGCTAAGAC
66 GGGCTAAGACCCGAAGGCAATCGTAGTTGACCGGGCTAAGAC
* *
53646613 GGCATTCGTGCGAGTTGATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TCACCAAATC
1 GGCATTCGTGCGAGTTGATATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTCA-CAAATC
* *
53646677 CGGGTTATGACCCGAAGGCAATCGT
65 CGGGCTAAGACCCGAAGGCAATCGT
53646702 GCGAGTCGCT
Statistics
Matches: 79, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
106 2 0.03
107 77 0.97
ACGTcount: A:0.24, C:0.23, G:0.30, T:0.22
Consensus pattern (107 bp):
GGCATTCGTGCGAGTTGATATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTCACAAATCC
GGGCTAAGACCCGAAGGCAATCGTAGTTGACCGGGCTAAGAC
Found at i:53652109 original size:29 final size:29
Alignment explanation
Indices: 53652076--53652235 Score: 180
Period size: 29 Copynumber: 5.5 Consensus size: 29
53652066 GTGACGAGAT
53652076 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
53652105 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
53652134 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
* ** * ***
53652163 CGGCACTGGGTGTGCGA-GCTCGAAGGGTA
1 TGGCACTAAGTGTGC-ATGCTGGAAATATA
* ** * *
53652192 TGGCACTATGTGTGCGGGCT-TAAATCACA
1 TGGCACTAAGTGTGCATGCTGGAAAT-ATA
53652221 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
53652236 GAAATCGAGT
Statistics
Matches: 111, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
28 2 0.02
29 108 0.97
30 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:53655226 original size:25 final size:25
Alignment explanation
Indices: 53655198--53655255 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
53655188 GTATGCTCTC
*
53655198 ACGAGCTGCAG-ATCGGTAAGATCAT
1 ACGAGCTG-AGAATAGGTAAGATCAT
** *
53655223 ACGATTTGAGAATAGGTAAGCTCAT
1 ACGAGCTGAGAATAGGTAAGATCAT
53655248 ACGAGCTG
1 ACGAGCTG
53655256 TGGTGTGTCT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
24 2 0.08
25 24 0.92
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.22
Consensus pattern (25 bp):
ACGAGCTGAGAATAGGTAAGATCAT
Found at i:53657700 original size:18 final size:19
Alignment explanation
Indices: 53657656--53657702 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
53657646 AAAGGTTAGT
**
53657656 AATGTAAATTGTTAAATAA
1 AATGTAAATTAATAAATAA
53657675 AA-GATAAATTAATAAA-AA
1 AATG-TAAATTAATAAATAA
53657693 AATGTAAATT
1 AATGTAAATT
53657703 TTCTTCATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.32
Consensus pattern (19 bp):
AATGTAAATTAATAAATAA
Found at i:53663940 original size:29 final size:30
Alignment explanation
Indices: 53663871--53663994 Score: 125
Period size: 29 Copynumber: 4.3 Consensus size: 30
53663861 ACCCCTACAT
* *
53663871 ATATGCATATGGCCTA-CTAGGCCCAA-TC
1 ATATTCATATGGCCCATCTAGGCCCAATTC
* *
53663899 TTATTCAAATGGCCCATCT-GGCCCAATTC
1 ATATTCATATGGCCCATCTAGGCCCAATTC
* *
53663928 ATATTCTTATGGCCCA-CTATGCCCAATTC
1 ATATTCATATGGCCCATCTAGGCCCAATTC
* * *
53663957 ACATTCATATGACCCAT-TAGGCCCAAATC
1 ATATTCATATGGCCCATCTAGGCCCAATTC
53663986 ATATT-ATAT
1 ATATTCATAT
53663995 TCATGCTCAC
Statistics
Matches: 78, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
28 25 0.32
29 53 0.68
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.31
Consensus pattern (30 bp):
ATATTCATATGGCCCATCTAGGCCCAATTC
Found at i:53663940 original size:57 final size:58
Alignment explanation
Indices: 53663878--53663990 Score: 140
Period size: 58 Copynumber: 2.0 Consensus size: 58
53663868 CATATATGCA
* ** * *
53663878 TATGGCCTACTAGGCCCAA-TCTTATTCAAATGGCCCATCT-GGCCCAATTCATATTCT
1 TATGGCCCACTAGGCCCAATTCACATTCAAATGACCCAT-TAGGCCCAAATCATATTCT
* *
53663935 TATGGCCCACTATGCCCAATTCACATTCATATGACCCATTAGGCCCAAATCATATT
1 TATGGCCCACTAGGCCCAATTCACATTCAAATGACCCATTAGGCCCAAATCATATT
53663991 ATATTCATGC
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
57 18 0.38
58 29 0.62
ACGTcount: A:0.27, C:0.30, G:0.12, T:0.30
Consensus pattern (58 bp):
TATGGCCCACTAGGCCCAATTCACATTCAAATGACCCATTAGGCCCAAATCATATTCT
Found at i:53664096 original size:19 final size:19
Alignment explanation
Indices: 53664063--53664108 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
53664053 TGGGCCCAAC
*
53664063 AGCCCA-TCAGGCCCATTT
1 AGCCCATTCTGGCCCATTT
53664081 AGCCCATTCTGGCCCATTT
1 AGCCCATTCTGGCCCATTT
*
53664100 -GCCAATTCT
1 AGCCCATTCT
53664109 TAACCCAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 14 0.56
19 11 0.44
ACGTcount: A:0.20, C:0.37, G:0.15, T:0.28
Consensus pattern (19 bp):
AGCCCATTCTGGCCCATTT
Found at i:53664254 original size:16 final size:15
Alignment explanation
Indices: 53664204--53664256 Score: 61
Period size: 16 Copynumber: 3.4 Consensus size: 15
53664194 CGTAGCCCAA
53664204 CTTTTGGCTTTTCGG
1 CTTTTGGCTTTTCGG
**
53664219 CATTTTGGCTTTTCAA
1 C-TTTTGGCTTTTCGG
*
53664235 CTTTTCGGCATTTCGG
1 CTTTT-GGCTTTTCGG
53664251 CTTTTG
1 CTTTTG
53664257 CCTATTCATT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
15 6 0.19
16 25 0.81
ACGTcount: A:0.08, C:0.21, G:0.21, T:0.51
Consensus pattern (15 bp):
CTTTTGGCTTTTCGG
Found at i:53665493 original size:16 final size:16
Alignment explanation
Indices: 53665468--53665500 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
53665458 AAAAATTCAA
*
53665468 GATTTTGGGATTTTTG
1 GATTTCGGGATTTTTG
53665484 GATTTCGGGATTTTTG
1 GATTTCGGGATTTTTG
53665500 G
1 G
53665501 GCGTTACATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.03, G:0.33, T:0.52
Consensus pattern (16 bp):
GATTTCGGGATTTTTG
Found at i:53678938 original size:39 final size:39
Alignment explanation
Indices: 53678893--53679036 Score: 198
Period size: 39 Copynumber: 3.7 Consensus size: 39
53678883 TGTGTGAGAT
* * *
53678893 TTATATCCGGGCTAAGTCCCAAAGGCATTCGTGCTGATG
1 TTATATCCAGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
53678932 TTATATCCAGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCAGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* * * *
53678971 TTATATCTAGGCTAAATCCTGAAGGCATTTGTGCTGGTG
1 TTATATCCAGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
** *
53679010 TTATATCTGGGCAAAGTCCCGAAGGCA
1 TTATATCCAGGCTAAGTCCCGAAGGCA
53679037 ATTGTGTTGG
Statistics
Matches: 94, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 94 1.00
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (39 bp):
TTATATCCAGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
Found at i:53684822 original size:14 final size:14
Alignment explanation
Indices: 53684803--53684832 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
53684793 GACTCTATGA
53684803 AAGGTCGATACCCT
1 AAGGTCGATACCCT
*
53684817 AAGGTCGATATCCT
1 AAGGTCGATACCCT
53684831 AA
1 AA
53684833 CTTATTCACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.23
Consensus pattern (14 bp):
AAGGTCGATACCCT
Found at i:53686960 original size:39 final size:39
Alignment explanation
Indices: 53686913--53687056 Score: 207
Period size: 39 Copynumber: 3.7 Consensus size: 39
53686903 TGTGTGAGAT
* * *
53686913 TTATATTCGGGCTAAGTCTCGAAGGCATTCGTGCTGATG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* * *
53686952 TTATATTCGGGCAAAGTCCCAAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* *
53686991 TTATATCCGGGCTAAATCCCGAAGGCATTTGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
*
53687030 TTATATCCGGGCTAAGTCACGAAGGCA
1 TTATATCCGGGCTAAGTCCCGAAGGCA
53687057 ATTATGTTGG
Statistics
Matches: 94, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 94 1.00
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (39 bp):
TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
Found at i:53688832 original size:40 final size:40
Alignment explanation
Indices: 53688766--53688932 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
53688756 AAATTGAATG
* * *
53688766 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
53688805 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
*
53688845 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
53688885 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
53688925 ATATCCGG
1 ATATCCGG
53688933 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:53696028 original size:40 final size:40
Alignment explanation
Indices: 53695962--53696128 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
53695952 AAATTGAATG
* * *
53695962 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
53696001 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
*
53696041 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
53696081 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
53696121 ATATCCGG
1 ATATCCGG
53696129 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:53699772 original size:79 final size:80
Alignment explanation
Indices: 53699644--53699833 Score: 280
Period size: 79 Copynumber: 2.4 Consensus size: 80
53699634 ATGTCCGGGC
* *
53699644 TAAGTCCCGAAGGC-TTTGTGCTAAG-TGACTATATCCGGACTAAGATCCGAAGGCATTTGTGCG
1 TAAGTCCCGAAGGCATTTGTGC-GAGCT-ACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCG
53699707 AGTTACTAAATCCGGAA
64 AGTTACTAAATCCGGAA
*
53699724 TAAGAT-CCGAA-GCATTTGTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGA
1 TAAG-TCCCGAAGGCATTTGTGCGAGCTACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGA
**
53699787 GTTACTAAATCCGGGT
65 GTTACTAAATCCGGAA
53699803 TAAGTCCCGAAGGCATTTGTGCGAGCTACTA
1 TAAGTCCCGAAGGCATTTGTGCGAGCTACTA
53699834 TAACTGGGCT
Statistics
Matches: 100, Mismatches: 5, Indels: 10
0.87 0.04 0.09
Matches are distributed among these distances:
78 1 0.01
79 63 0.63
80 35 0.35
81 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.26
Consensus pattern (80 bp):
TAAGTCCCGAAGGCATTTGTGCGAGCTACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAG
TTACTAAATCCGGAA
Found at i:53699855 original size:40 final size:40
Alignment explanation
Indices: 53699637--53699833 Score: 267
Period size: 40 Copynumber: 5.0 Consensus size: 40
53699627 TCGAATGATG
* * * *
53699637 TCCGGGCTAAG-TCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGACTAAGAT-CCGAAGGCATTTGTGC-GAGTTACTAAA
53699677 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
*
53699717 TCCGGAATAAGATCCGAA-GCATTTGTGCGAGTTACTAAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
53699756 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
** *
53699796 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGCTACTA
1 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA
53699834 TAACTGGGCT
Statistics
Matches: 144, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
39 39 0.27
40 97 0.67
41 8 0.06
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (40 bp):
TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:53699861 original size:40 final size:40
Alignment explanation
Indices: 53699637--53699861 Score: 230
Period size: 40 Copynumber: 5.7 Consensus size: 40
53699627 TCGAATGATG
* *
53699637 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAG-TGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGCT-ACTAAA
* *
53699677 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGCTACTAAA
** *
53699717 TCCGGAATAAGAT-CCGAA-GCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGCTACTAAA
* *
53699756 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGCTACTAAA
*
53699796 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGCTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTA-AA
* * *
53699837 -CTGGGCTATGTCCCGAAGGTATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
53699862 AACGAGTAGC
Statistics
Matches: 167, Mismatches: 12, Indels: 12
0.87 0.06 0.06
Matches are distributed among these distances:
39 39 0.23
40 117 0.70
41 11 0.07
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTAAA
Found at i:53703707 original size:29 final size:29
Alignment explanation
Indices: 53703674--53703832 Score: 171
Period size: 29 Copynumber: 5.5 Consensus size: 29
53703664 GTGACGAGAT
53703674 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
53703703 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
53703732 TGGCACTAAGTGTGCATGCTGGAAAT-TA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
* ** * ***
53703760 CGGCACTGGGTGTGCGA-GCTCGAAGGGTA
1 TGGCACTAAGTGTGC-ATGCTGGAAATATA
* ** * *
53703789 TGGCACTATGTGTGCGGGCT-TAAATCACA
1 TGGCACTAAGTGTGCATGCTGGAAAT-ATA
53703818 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
53703833 GAAATCGAGT
Statistics
Matches: 110, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
28 22 0.20
29 88 0.80
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:53703744 original size:58 final size:58
Alignment explanation
Indices: 53703670--53703834 Score: 176
Period size: 57 Copynumber: 2.9 Consensus size: 58
53703660 TACGGTGACG
*
53703670 AGAT-TGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGC-ATGCTGGAA
1 AGATATGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCGA-GCTCGAA
* * **
53703727 ATATATGGCACTAAGTGTGCATGCTGGAAAT-TACGGCACTGGGTGTGCGAGCTCGAA
1 AGATATGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCGAGCTCGAA
* * * ** * *
53703784 GGGTATGGCACTATGTGTGCGGGCT-TAAATCACATGGCACTAAGTGTGCGA
1 AGATATGGCACTAAGTGTGCATGCTGGAAAT-ATATGGCACTAAGTGTGCGA
53703835 AATCGAGTAT
Statistics
Matches: 88, Mismatches: 16, Indels: 7
0.79 0.14 0.06
Matches are distributed among these distances:
56 4 0.05
57 42 0.48
58 42 0.48
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.25
Consensus pattern (58 bp):
AGATATGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCGAGCTCGAA
Found at i:53711763 original size:29 final size:29
Alignment explanation
Indices: 53711730--53711889 Score: 180
Period size: 29 Copynumber: 5.5 Consensus size: 29
53711720 GTGACGAGAT
53711730 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
53711759 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
53711788 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
* ** * ***
53711817 CGGCACTGGGTGTGCGA-GCTCGAAGGGTA
1 TGGCACTAAGTGTGC-ATGCTGGAAATATA
* ** * *
53711846 TGGCACTATGTGTGCGGGCT-TAAATCACA
1 TGGCACTAAGTGTGCATGCTGGAAAT-ATA
53711875 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
53711890 GAAATCGAGT
Statistics
Matches: 111, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
28 2 0.02
29 108 0.97
30 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:53726569 original size:40 final size:40
Alignment explanation
Indices: 53726524--53726615 Score: 157
Period size: 40 Copynumber: 2.3 Consensus size: 40
53726514 ATAACCACAA
* *
53726524 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGGTATAACAACTC
*
53726564 GCACAAATGCCTTCGGGTCTTAGCCCGGGTATAACAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGGTATAACAACTC
53726604 GCACAAATGCCT
1 GCACAAATGCCT
53726616 AAACGGTCGG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.23
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGGTATAACAACTC
Found at i:53741283 original size:47 final size:47
Alignment explanation
Indices: 53741196--53741508 Score: 429
Period size: 47 Copynumber: 6.7 Consensus size: 47
53741186 GATTTTACGC
* *
53741196 GATGAATGTGAATGTGTATAAATATGAGATAAGGCCTAATGGCCGATGT
1 GATGAATGTGAAAGTGTAT--ATATGTGATAAGGCCTAATGGCCGATGT
53741245 GATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGT
1 GATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGT
*
53741292 GATGAATGTGAAAGTGTATATATATGCGATAAGGCCTAATGGCCGATGT
1 GATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGT
53741341 GATGAATGTGAAAGTGTATATATGTG---AGGCCTAATGGCCG-TGT
1 GATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGT
* *
53741384 GATGAATGTGAAGGTGTATATATGTGATAAGG-CTGAATGGCCAATGT
1 GATGAATGTGAAAGTGTATATATGTGATAAGGCCT-AATGGCCGATGT
* * * * **
53741431 GATGAATGTGAAAGTGTATATATGTGATAGGGCCGAGTGGCCAACAT
1 GATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGT
* *
53741478 GATGGATGTGAAAGTGTATAAATGTGATAAG
1 GATGAATGTGAAAGTGTATATATGTGATAAG
53741509 TCCGAAGGGC
Statistics
Matches: 241, Mismatches: 15, Indels: 18
0.88 0.05 0.07
Matches are distributed among these distances:
43 28 0.12
44 14 0.06
45 2 0.01
46 10 0.04
47 122 0.51
48 1 0.00
49 64 0.27
ACGTcount: A:0.33, C:0.08, G:0.31, T:0.29
Consensus pattern (47 bp):
GATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGT
Found at i:53741386 original size:139 final size:138
Alignment explanation
Indices: 53741227--53741504 Score: 416
Period size: 139 Copynumber: 2.0 Consensus size: 138
53741217 ATATGAGATA
*
53741227 AGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT-AATGGCCGATG
1 AGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGG-CTGAATGGCCAATG
* * **
53741291 TGATGAATGTGAAAGTGTATATATATGCGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGT
65 TGATGAATGTGAAAGTG--TATATATGCGATAAGGCCGAATGGCCAACATGATGAATGTGAAAGT
*
53741356 GTATATATGTG
128 GTATAAATGTG
*
53741367 AGGCCTAATGGCCG-TGTGATGAATGTGAAGGTGTATATATGTGATAAGGCTGAATGGCCAATGT
1 AGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCTGAATGGCCAATGT
* * * *
53741431 GATGAATGTGAAAGTGTATATATGTGATAGGGCCGAGTGGCCAACATGATGGATGTGAAAGTGTA
66 GATGAATGTGAAAGTGTATATATGCGATAAGGCCGAATGGCCAACATGATGAATGTGAAAGTGTA
53741496 TAAATGTG
131 TAAATGTG
53741504 A
1 A
53741505 TAAGTCCGAA
Statistics
Matches: 126, Mismatches: 11, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
137 49 0.39
138 2 0.02
139 61 0.48
140 14 0.11
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.28
Consensus pattern (138 bp):
AGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCTGAATGGCCAATGT
GATGAATGTGAAAGTGTATATATGCGATAAGGCCGAATGGCCAACATGATGAATGTGAAAGTGTA
TAAATGTG
Found at i:53741411 original size:25 final size:24
Alignment explanation
Indices: 53741381--53741458 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 24
53741371 CTAATGGCCG
53741381 TGTGATGAATGTGAAGGTGTATATA
1 TGTGATGAATGTGAA-GTGTATATA
* ***
53741406 TGTGAT-AAGGCTGAA-TGGCCA-A
1 TGTGATGAATG-TGAAGTGTATATA
53741428 TGTGATGAATGTGAAAGTGTATATA
1 TGTGATGAATGTG-AAGTGTATATA
53741453 TGTGAT
1 TGTGAT
53741459 AGGGCCGAGT
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
22 9 0.22
23 8 0.20
24 6 0.15
25 17 0.43
ACGTcount: A:0.32, C:0.04, G:0.31, T:0.33
Consensus pattern (24 bp):
TGTGATGAATGTGAAGTGTATATA
Found at i:53749719 original size:26 final size:26
Alignment explanation
Indices: 53749683--53749735 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
53749673 AATCCAAGTT
53749683 AGAAAAATATTTAAAAATTATTTTCA
1 AGAAAAATATTTAAAAATTATTTTCA
53749709 AGAAAAATATTTAAAAATTATTTTCA
1 AGAAAAATATTTAAAAATTATTTTCA
53749735 A
1 A
53749736 TGTTTATTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.38
Consensus pattern (26 bp):
AGAAAAATATTTAAAAATTATTTTCA
Found at i:53750953 original size:43 final size:41
Alignment explanation
Indices: 53750906--53751061 Score: 116
Period size: 43 Copynumber: 3.7 Consensus size: 41
53750896 ATGTTCACAT
* *
53750906 GTAAGACCACGTCTAGGACGTTGGCATCGATATGTGATTTTGA
1 GTAAGACCACGTCTAGGACATTGGCATC-ATATGTGA-TTAGA
* * * * *
53750949 GTAAGACCATGTCTGGGACATCGGCATCATAATTGTGATTCGT
1 GTAAGACCACGTCTAGGACATTGGCATCAT-A-TGTGATTAGA
* * * *
53750992 GTAAGACC-CTGTCTAGGACAATGGTATCAACATGTGATTACA
1 GTAAGACCAC-GTCTAGGACATTGGCATC-ATATGTGATTAGA
* * *
53751034 TGTAAGACCATGTCTGGGACGTTGGCAT
1 -GTAAGACCACGTCTAGGACATTGGCAT
53751062 TGTATGATAT
Statistics
Matches: 87, Mismatches: 20, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
42 9 0.10
43 72 0.83
44 6 0.07
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (41 bp):
GTAAGACCACGTCTAGGACATTGGCATCATATGTGATTAGA
Found at i:53751699 original size:2 final size:2
Alignment explanation
Indices: 53751692--53751731 Score: 62
Period size: 2 Copynumber: 19.5 Consensus size: 2
53751682 CGGTTTAACG
*
53751692 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT GAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
53751732 GAAATGTGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (2 bp):
AT
Found at i:53754765 original size:23 final size:22
Alignment explanation
Indices: 53754714--53754767 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 22
53754704 CAATAAATAG
53754714 AATAAAAACGTAATACAAAATT
1 AATAAAAACGTAATACAAAATT
* **
53754736 AATTAAAAACCTTAATACAATTTT
1 AA-TAAAAA-CGTAATACAAAATT
53754760 AATAAAAA
1 AATAAAAA
53754768 AAATGACAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.07
23 12 0.44
24 13 0.48
ACGTcount: A:0.61, C:0.09, G:0.02, T:0.28
Consensus pattern (22 bp):
AATAAAAACGTAATACAAAATT
Found at i:53754806 original size:22 final size:22
Alignment explanation
Indices: 53754778--53754849 Score: 110
Period size: 22 Copynumber: 3.3 Consensus size: 22
53754768 AAATGACAAA
53754778 GAATTGAGAGAGGATTGAGAAT
1 GAATTGAGAGAGGATTGAGAAT
*
53754800 GAGTTGAGAGAGGATTGAGAAT
1 GAATTGAGAGAGGATTGAGAAT
*
53754822 GAATTGAGAGA-GAGTTGAGAGT
1 GAATTGAGAGAGGA-TTGAGAAT
53754844 GAATTG
1 GAATTG
53754850 TGAGTGAATT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
21 2 0.04
22 44 0.96
ACGTcount: A:0.38, C:0.00, G:0.39, T:0.24
Consensus pattern (22 bp):
GAATTGAGAGAGGATTGAGAAT
Found at i:53754828 original size:33 final size:33
Alignment explanation
Indices: 53754777--53754861 Score: 91
Period size: 33 Copynumber: 2.6 Consensus size: 33
53754767 AAAATGACAA
* **
53754777 AGAATTGAGAGA-GGATTGAGAATGAGTTGAGAG
1 AGAATTGAGA-ATGAATTGAGAGAGAGTTGAGAG
*
53754810 AGGATTGAGAATGAATTGAGAGAGAGTTGAGAG
1 AGAATTGAGAATGAATTGAGAGAGAGTTGAGAG
* * *
53754843 TGAATTGTGAGTGAATTGA
1 AGAATTGAGAATGAATTGA
53754862 AAAGGTGGGA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
32 1 0.02
33 42 0.98
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.25
Consensus pattern (33 bp):
AGAATTGAGAATGAATTGAGAGAGAGTTGAGAG
Found at i:53754854 original size:11 final size:11
Alignment explanation
Indices: 53754778--53754861 Score: 78
Period size: 11 Copynumber: 7.6 Consensus size: 11
53754768 AAATGACAAA
*
53754778 GAATTGAGAGA
1 GAATTGAGAGT
* *
53754789 GGATTGAGAAT
1 GAATTGAGAGT
* *
53754800 GAGTTGAGAGA
1 GAATTGAGAGT
* *
53754811 GGATTGAGAAT
1 GAATTGAGAGT
*
53754822 GAATTGAGAGA
1 GAATTGAGAGT
*
53754833 GAGTTGAGAGT
1 GAATTGAGAGT
*
53754844 GAATTGTGAGT
1 GAATTGAGAGT
53754855 GAATTGA
1 GAATTGA
53754862 AAAGGTGGGA
Statistics
Matches: 54, Mismatches: 19, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
11 54 1.00
ACGTcount: A:0.37, C:0.00, G:0.38, T:0.25
Consensus pattern (11 bp):
GAATTGAGAGT
Found at i:53754861 original size:22 final size:22
Alignment explanation
Indices: 53754778--53754861 Score: 105
Period size: 22 Copynumber: 3.8 Consensus size: 22
53754768 AAATGACAAA
*
53754778 GAATTGAGAGAGGATTGAGAAT
1 GAATTGAGAGAGAATTGAGAAT
* *
53754800 GAGTTGAGAGAGGATTGAGAAT
1 GAATTGAGAGAGAATTGAGAAT
* *
53754822 GAATTGAGAGAGAGTTGAGAGT
1 GAATTGAGAGAGAATTGAGAAT
* *
53754844 GAATTGTGAGTGAATTGA
1 GAATTGAGAGAGAATTGA
53754862 AAAGGTGGGA
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 54 1.00
ACGTcount: A:0.37, C:0.00, G:0.38, T:0.25
Consensus pattern (22 bp):
GAATTGAGAGAGAATTGAGAAT
Found at i:53755248 original size:18 final size:19
Alignment explanation
Indices: 53755225--53755263 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
53755215 ACAAATTGAG
*
53755225 TTATTTGAGTTAA-TCGAA
1 TTATTTGAGTCAAGTCGAA
53755243 TTATTTGAGTCAAGTCGAA
1 TTATTTGAGTCAAGTCGAA
53755262 TT
1 TT
53755264 TTTTTCGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.44
Consensus pattern (19 bp):
TTATTTGAGTCAAGTCGAA
Found at i:53757268 original size:12 final size:11
Alignment explanation
Indices: 53757247--53757282 Score: 56
Period size: 12 Copynumber: 3.3 Consensus size: 11
53757237 AATGATGGTC
53757247 TTTTTTTTTCT
1 TTTTTTTTTCT
53757258 TTTTCTTTTTCT
1 TTTT-TTTTTCT
53757270 TTTTTTTTT-T
1 TTTTTTTTTCT
53757280 TTT
1 TTT
53757283 CAATTGGCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.17
11 9 0.38
12 11 0.46
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTTTCT
Found at i:53757293 original size:22 final size:22
Alignment explanation
Indices: 53757246--53757293 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
53757236 AAATGATGGT
* **
53757246 CTTTTTTTTTCTTTTTCTTTTT
1 CTTTTTTTTTCTTTTTCATTGG
53757268 CTTTTTTTTT-TTTTTCAATTGG
1 CTTTTTTTTTCTTTTTC-ATTGG
53757290 CTTT
1 CTTT
53757294 CATAGAATAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.04, C:0.12, G:0.04, T:0.79
Consensus pattern (22 bp):
CTTTTTTTTTCTTTTTCATTGG
Found at i:53767287 original size:34 final size:33
Alignment explanation
Indices: 53767226--53767292 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 33
53767216 CCGACACTAA
53767226 AATGGGCTAAGGCCCACACTAATACTGATACTGT
1 AATGGGCTAAGGCCCACACTAATACTGA-ACTGT
53767260 AATGGGCTAAGGCCCTA-ACTGAA-ACTGAACTGT
1 AATGGGCTAAGGCCC-ACACT-AATACTGAACTGT
53767293 TATTGATATG
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
33 5 0.16
34 23 0.74
35 3 0.10
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (33 bp):
AATGGGCTAAGGCCCACACTAATACTGAACTGT
Found at i:53769260 original size:43 final size:43
Alignment explanation
Indices: 53769116--53769265 Score: 155
Period size: 43 Copynumber: 3.5 Consensus size: 43
53769106 TGTGTTATCG
* * *
53769116 TGTAAGACCACGTCTGGGA-TGTTGGCATCGAT-TTGAGATTTACC
1 TGTAAGACCACGTCTGGGACAG-TGGCATCGATATT-TGA-TTACA
* * * * *
53769160 TGTAAGACTATGTCTGGGACATTGGCATCG-TATATGATTTCA
1 TGTAAGACCACGTCTGGGACAGTGGCATCGATATTTGATTACA
*
53769202 TATAAGACC-CTGTCTGGGACAGTGGCATCGATATTTGATTACA
1 TGTAAGACCAC-GTCTGGGACAGTGGCATCGATATTTGATTACA
53769245 TGTAAGACCACGTCTGGGACA
1 TGTAAGACCACGTCTGGGACA
53769266 TTGACATTGT
Statistics
Matches: 86, Mismatches: 15, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
42 28 0.33
43 31 0.36
44 27 0.31
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACAGTGGCATCGATATTTGATTACA
Found at i:53771046 original size:54 final size:54
Alignment explanation
Indices: 53770976--53771084 Score: 155
Period size: 54 Copynumber: 2.0 Consensus size: 54
53770966 GTGTTCTTGG
* * *
53770976 ATGTTTTTCCTGAAATACTATGGAGATTTATGGCTTGGAGAATGATCAAAATCT
1 ATGTTTTTCCTGAAATAATATAGAGATATATGGCTTGGAGAATGATCAAAATCT
* * * *
53771030 ATGTTTTTCTTTAAATAATATAGAGATATATGGCTTGGGGAATGATCGAAATCT
1 ATGTTTTTCCTGAAATAATATAGAGATATATGGCTTGGAGAATGATCAAAATCT
53771084 A
1 A
53771085 AGGAATTATG
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.38
Consensus pattern (54 bp):
ATGTTTTTCCTGAAATAATATAGAGATATATGGCTTGGAGAATGATCAAAATCT
Found at i:53783388 original size:19 final size:20
Alignment explanation
Indices: 53783348--53783394 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
53783338 CTTATTTCTA
*
53783348 TTAAGTT-TTTTTAATTCAT
1 TTAAGTTGTTTTTAATACAT
*
53783367 TTAAGTTGTTTTTAA-ACTT
1 TTAAGTTGTTTTTAATACAT
53783386 TTACAGTTG
1 TTA-AGTTG
53783395 AAAGTTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.26, C:0.06, G:0.11, T:0.57
Consensus pattern (20 bp):
TTAAGTTGTTTTTAATACAT
Found at i:53783900 original size:13 final size:13
Alignment explanation
Indices: 53783882--53783911 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
53783872 TTAAACTTGA
53783882 ATGAATTGAGATG
1 ATGAATTGAGATG
53783895 ATGAATTGAGATG
1 ATGAATTGAGATG
53783908 -TGAA
1 ATGAA
53783912 ACTTGAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.40, C:0.00, G:0.30, T:0.30
Consensus pattern (13 bp):
ATGAATTGAGATG
Found at i:53789340 original size:17 final size:17
Alignment explanation
Indices: 53789318--53789362 Score: 90
Period size: 17 Copynumber: 2.6 Consensus size: 17
53789308 CACACAGACA
53789318 AAGACACGGCCGTGTGG
1 AAGACACGGCCGTGTGG
53789335 AAGACACGGCCGTGTGG
1 AAGACACGGCCGTGTGG
53789352 AAGACACGGCC
1 AAGACACGGCC
53789363 TAGCACACGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.27, C:0.27, G:0.38, T:0.09
Consensus pattern (17 bp):
AAGACACGGCCGTGTGG
Found at i:53794183 original size:3 final size:3
Alignment explanation
Indices: 53794175--53794215 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
53794165 TATATATATT
53794175 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
53794216 TAAAATGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:53799068 original size:19 final size:19
Alignment explanation
Indices: 53799043--53799112 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
53799033 ATGTGTTACG
53799043 CGAATGAATTACTGTTATA
1 CGAATGAATTACTGTTATA
* * *
53799062 TGGATGAAGTACTGTTTATA
1 CGAATGAATTACTG-TTATA
*
53799082 CGAATGAGTTACTGTTAT-
1 CGAATGAATTACTGTTATA
*
53799100 CAAATGAATTACT
1 CGAATGAATTACT
53799113 ATTTACATGA
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
18 11 0.27
19 15 0.37
20 15 0.37
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.37
Consensus pattern (19 bp):
CGAATGAATTACTGTTATA
Found at i:53799088 original size:20 final size:20
Alignment explanation
Indices: 53799043--53799097 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
53799033 ATGTGTTACG
*
53799043 CGAATGAATTACTG-TTATA
1 CGAATGAAGTACTGTTTATA
* *
53799062 TGGATGAAGTACTGTTTATA
1 CGAATGAAGTACTGTTTATA
53799082 CGAATG-AGTTACTGTT
1 CGAATGAAG-TACTGTT
53799098 ATCAAATGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (20 bp):
CGAATGAAGTACTGTTTATA
Found at i:53801003 original size:40 final size:40
Alignment explanation
Indices: 53800944--53801085 Score: 124
Period size: 40 Copynumber: 3.5 Consensus size: 40
53800934 AAATTGAATG
* * *
53800944 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ***
53800984 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ** *
53801024 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTATT
1 ATATCCGGGCTAAGACCCGAAGACAATT-ATGCTAGAAACT
*
53801064 CTATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
53801086 GCATTTGTGC
Statistics
Matches: 86, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
39 3 0.03
40 83 0.97
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
Found at i:53801086 original size:40 final size:39
Alignment explanation
Indices: 53800983--53801111 Score: 152
Period size: 40 Copynumber: 3.2 Consensus size: 39
53800973 TGCTGGAAAT
* * *
53800983 TATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC
1 TATATCCGGGCTAAGACCCGAAGGC-ATTGTGCGAGTGAC
* *
53801023 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTAT
1 TATATCCGGGCTAAGACCCGAAGGCATT-GTGCGAGTGAC
* *
53801063 TCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGAT
1 TATATCCGGGCTAAGACCCGAAGGCA-TTGTGCGA-GTGAC
53801103 TATATCCGG
1 TATATCCGG
53801112 TTATATTCCG
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
39 4 0.05
40 72 0.92
41 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TATATCCGGGCTAAGACCCGAAGGCATTGTGCGAGTGAC
Found at i:53811680 original size:40 final size:40
Alignment explanation
Indices: 53811621--53811762 Score: 124
Period size: 40 Copynumber: 3.5 Consensus size: 40
53811611 AAATTGAATG
* * *
53811621 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ***
53811661 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ** *
53811701 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTATT
1 ATATCCGGGCTAAGACCCGAAGACAATT-ATGCTAGAAACT
*
53811741 CTATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
53811763 GCATTTGTGC
Statistics
Matches: 86, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
39 3 0.03
40 83 0.97
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
Found at i:53811763 original size:40 final size:39
Alignment explanation
Indices: 53811660--53811788 Score: 152
Period size: 40 Copynumber: 3.2 Consensus size: 39
53811650 TGCTGGAAAT
* * *
53811660 TATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC
1 TATATCCGGGCTAAGACCCGAAGGC-ATTGTGCGAGTGAC
* *
53811700 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTAT
1 TATATCCGGGCTAAGACCCGAAGGCATT-GTGCGAGTGAC
* *
53811740 TCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGAT
1 TATATCCGGGCTAAGACCCGAAGGCA-TTGTGCGA-GTGAC
53811780 TATATCCGG
1 TATATCCGG
53811789 TTATATTCCG
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
39 4 0.05
40 72 0.92
41 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TATATCCGGGCTAAGACCCGAAGGCATTGTGCGAGTGAC
Found at i:53815974 original size:28 final size:28
Alignment explanation
Indices: 53815892--53815981 Score: 137
Period size: 29 Copynumber: 3.1 Consensus size: 28
53815882 TAAGCATGAC
53815892 TATAAATGTGAATTGGGCCT-GATGGGCCA
1 TATAAATGTG-ATTGGGCCTAG-TGGGCCA
*
53815921 TATAAATGTGATTTGGGCCTAATGGGCCA
1 TATAAATGTGA-TTGGGCCTAGTGGGCCA
53815950 TATAAATGTGATTGGGCCTAGTGGGCCA
1 TATAAATGTGATTGGGCCTAGTGGGCCA
53815978 TATA
1 TATA
53815982 CAAGTATGTG
Statistics
Matches: 57, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
28 21 0.37
29 36 0.63
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.30
Consensus pattern (28 bp):
TATAAATGTGATTGGGCCTAGTGGGCCA
Found at i:53818043 original size:16 final size:17
Alignment explanation
Indices: 53818006--53818049 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
53817996 GGAATATAGA
53818006 TTTGAATCCCATCAGTT
1 TTTGAATCCCATCAGTT
53818023 TTTGAATCCCATCAG-T
1 TTTGAATCCCATCAGTT
53818039 TTTGAATCCCA
1 TTTGAATCCCA
53818050 CACACAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 12 0.44
17 15 0.56
ACGTcount: A:0.25, C:0.25, G:0.11, T:0.39
Consensus pattern (17 bp):
TTTGAATCCCATCAGTT
Found at i:53822870 original size:32 final size:32
Alignment explanation
Indices: 53822823--53822885 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
53822813 GAAATTTTAG
* *
53822823 TTTGTTGGATTTTGAAATTATTATGTCTTAAA
1 TTTGTTAGATATTGAAATTATTATGTCTTAAA
* *
53822855 TTTGTTAGATATTGAATTTATTATGTTTTAA
1 TTTGTTAGATATTGAAATTATTATGTCTTAA
53822886 GCTTGTTGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.29, C:0.02, G:0.14, T:0.56
Consensus pattern (32 bp):
TTTGTTAGATATTGAAATTATTATGTCTTAAA
Found at i:53822892 original size:32 final size:32
Alignment explanation
Indices: 53822824--53822892 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 32
53822814 AAATTTTAGT
* * *
53822824 TTGTTGGATTTTGAAATTATTATGTCTTAAAT
1 TTGTTAGATATTGAAATTATTATGTCTTAAAC
* * *
53822856 TTGTTAGATATTGAATTTATTATGTTTTAAGC
1 TTGTTAGATATTGAAATTATTATGTCTTAAAC
53822888 TTGTT
1 TTGTT
53822893 GAATTTATTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.26, C:0.03, G:0.16, T:0.55
Consensus pattern (32 bp):
TTGTTAGATATTGAAATTATTATGTCTTAAAC
Found at i:53822932 original size:21 final size:21
Alignment explanation
Indices: 53822857--53822922 Score: 78
Period size: 25 Copynumber: 3.0 Consensus size: 21
53822847 GTCTTAAATT
53822857 TGTTAGATATTGAATTTATTA
1 TGTTAGATATTGAATTTATTA
* *
53822878 TGTTTTAAGCTTGTTGAATTTATTA
1 TG--TT-AG-ATATTGAATTTATTA
53822903 TGTTAGATATTGAATTTATT
1 TGTTAGATATTGAATTTATT
53822923 TGGTTGGATA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
21 14 0.38
22 2 0.05
23 4 0.11
24 2 0.05
25 15 0.41
ACGTcount: A:0.29, C:0.02, G:0.15, T:0.55
Consensus pattern (21 bp):
TGTTAGATATTGAATTTATTA
Found at i:53824217 original size:28 final size:27
Alignment explanation
Indices: 53824182--53824236 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 27
53824172 CAATATATGT
53824182 AAAAAATTTAAAGTATAAATTTATTAA
1 AAAAAATTTAAAGTATAAATTTATTAA
*
53824209 AAAATAATTTAAAGTATATATTTATTAA
1 AAAA-AATTTAAAGTATAAATTTATTAA
53824237 TATATATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 4 0.15
28 22 0.85
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (27 bp):
AAAAAATTTAAAGTATAAATTTATTAA
Found at i:53824249 original size:18 final size:18
Alignment explanation
Indices: 53824223--53824264 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
53824213 TAATTTAAAG
*
53824223 TATATATTTATTAATATA
1 TATAAATTTATTAATATA
53824241 TATAAATTTATTAATATA
1 TATAAATTTATTAATATA
*
53824259 TGTAAA
1 TATAAA
53824265 AACAGCTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
TATAAATTTATTAATATA
Found at i:53824365 original size:19 final size:19
Alignment explanation
Indices: 53824341--53824378 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
53824331 ATCCAAACAC
*
53824341 TAGAAAAGTAAATCATTTT
1 TAGAAAAGAAAATCATTTT
53824360 TAGAAAAGAAAATCATTTT
1 TAGAAAAGAAAATCATTTT
53824379 CCAGAAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.05, G:0.11, T:0.34
Consensus pattern (19 bp):
TAGAAAAGAAAATCATTTT
Found at i:53825088 original size:179 final size:179
Alignment explanation
Indices: 53824788--53825112 Score: 499
Period size: 179 Copynumber: 1.8 Consensus size: 179
53824778 TAGAGAGTTG
* * *
53824788 TACCATGAGATAAATAATTTTTAGTGAAGAGAGGTCAGAAATGTCGAATAGTGAAATAGAGGTAT
1 TACCATGAAATAAATAATTTTTAGTGAAAAGAGGTCAGAAATATCGAATAGTGAAATAGAGGTAT
* * * *
53824853 CTTTAATGAATAAACTGTACAAATTGGCTGAACTAAAAATTCTAAAAATTTTATGGTAAGAATAT
66 ATTTAATGAATAAACTGTACAAATTGGCTAAACCAAAAATTCTAAAAATTTTATGGTAAGAAGAT
* *
53824918 ATGTGAGTCTAGTTTCTGGGAAAATTAGTGGTTCTCAATTTGAAGTCGT
131 ATATGAGTCTAATTTCTGGGAAAATTAGTGGTTCTCAATTTGAAGTCGT
** * *
53824967 TACCATGAAATAAATAATTTTTAGTGAAAAGAGGTTGGAACTATC-AGATAGTGAAATAGGGGTA
1 TACCATGAAATAAATAATTTTTAGTGAAAAGAGGTCAGAAATATCGA-ATAGTGAAATAGAGGTA
* *
53825031 TATTTAATGAATAAACTGTACTAATTGGCTAAACCAAAAATTCTGAAAATTTTATGGTAAGAAGA
65 TATTTAATGAATAAACTGTACAAATTGGCTAAACCAAAAATTCTAAAAATTTTATGGTAAGAAGA
53825096 TATATGAGTCTAATTTC
130 TATATGAGTCTAATTTC
53825113 ATATAAAATT
Statistics
Matches: 130, Mismatches: 15, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
178 1 0.01
179 129 0.99
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.33
Consensus pattern (179 bp):
TACCATGAAATAAATAATTTTTAGTGAAAAGAGGTCAGAAATATCGAATAGTGAAATAGAGGTAT
ATTTAATGAATAAACTGTACAAATTGGCTAAACCAAAAATTCTAAAAATTTTATGGTAAGAAGAT
ATATGAGTCTAATTTCTGGGAAAATTAGTGGTTCTCAATTTGAAGTCGT
Found at i:53827772 original size:2 final size:2
Alignment explanation
Indices: 53827765--53827796 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
53827755 GCTCTGTTTG
53827765 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53827797 GGGAAGGTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53827958 original size:15 final size:15
Alignment explanation
Indices: 53827938--53827981 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
53827928 TATGATACTG
53827938 TATCTTGGATTTC-C
1 TATCTTGGATTTCTC
53827952 TTATCTTGGATTTCTC
1 -TATCTTGGATTTCTC
*
53827968 TATCTTGGACTTCT
1 TATCTTGGATTTCT
53827982 TAATCCTGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 26 0.96
16 1 0.04
ACGTcount: A:0.14, C:0.20, G:0.14, T:0.52
Consensus pattern (15 bp):
TATCTTGGATTTCTC
Found at i:53827996 original size:30 final size:30
Alignment explanation
Indices: 53827938--53827996 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
53827928 TATGATACTG
* *
53827938 TATCTTGGATTTCCTTATCTTGGATTTCTC
1 TATCTTGGACTTCCTTATCCTGGATTTCTC
*
53827968 TATCTTGGACTT-CTTAATCCTGGTTTTCT
1 TATCTTGGACTTCCTT-ATCCTGGATTTCT
53827997 TGTTATCTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 3 0.12
30 22 0.88
ACGTcount: A:0.14, C:0.20, G:0.14, T:0.53
Consensus pattern (30 bp):
TATCTTGGACTTCCTTATCCTGGATTTCTC
Found at i:53830258 original size:40 final size:40
Alignment explanation
Indices: 53830174--53830323 Score: 139
Period size: 40 Copynumber: 3.8 Consensus size: 40
53830164 AAATTGAATG
* * *
53830174 ATATCCGGGCTAAG-CCCGAAGACAATATGCTG-GA--AATT
1 ATATCCGGGCTAAGACCCGAAGGCAAT-TG-TGCGAGTGACT
* * *
53830212 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGACT
* * *
53830252 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGCGAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGTGACT
* *
53830292 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC
53830324 ACGTGATTAA
Statistics
Matches: 91, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
37 2 0.02
38 16 0.18
39 14 0.15
40 57 0.63
41 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGACT
Found at i:53838238 original size:40 final size:40
Alignment explanation
Indices: 53838154--53838319 Score: 146
Period size: 40 Copynumber: 4.2 Consensus size: 40
53838144 AAATTGAATG
* * *
53838154 ATATCCGGGCTAAG-CCCGAAGACAATATGCTG-GA--AATT
1 ATATCCGGGCTAAGACCCGAAGGCAAT-TG-TGCGAGTGACT
* * *
53838192 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGACT
* * *
53838232 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGCGAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGTGACT
* * *
53838272 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGA-GTGACT
53838312 ATATCCGG
1 ATATCCGG
53838320 TTATATTCCG
Statistics
Matches: 104, Mismatches: 17, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
37 2 0.02
38 16 0.15
39 15 0.14
40 69 0.66
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGACT
Found at i:53840764 original size:29 final size:29
Alignment explanation
Indices: 53840674--53840833 Score: 180
Period size: 29 Copynumber: 5.5 Consensus size: 29
53840664 ACTCGATTTC
* * **
53840674 GCACACTTAGTGCCATGTGATTT-AAGCCC
1 GCACACTTAGTGCCATAT-ATTTCCAGCAT
* *** *
53840703 GCACACATAGTGCCATACCCTTCGAGC-T
1 GCACACTTAGTGCCATATATTTCCAGCAT
** *
53840731 CGCACACCCAGTGCCGTATATTTCCAGCAT
1 -GCACACTTAGTGCCATATATTTCCAGCAT
53840761 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
53840790 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
53840819 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
53840834 ATCTCGTCAC
Statistics
Matches: 111, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
28 2 0.02
29 108 0.97
30 1 0.01
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (29 bp):
GCACACTTAGTGCCATATATTTCCAGCAT
Found at i:53848696 original size:29 final size:29
Alignment explanation
Indices: 53848606--53848765 Score: 180
Period size: 29 Copynumber: 5.5 Consensus size: 29
53848596 ACTCGATTTC
* * **
53848606 GCACACTTAGTGCCATGTGATTT-AAGCCC
1 GCACACTTAGTGCCATAT-ATTTCCAGCAT
* *** *
53848635 GCACACATAGTGCCATACCCTTCGAGC-T
1 GCACACTTAGTGCCATATATTTCCAGCAT
** *
53848663 CGCACACCCAGTGCCGTATATTTCCAGCAT
1 -GCACACTTAGTGCCATATATTTCCAGCAT
53848693 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
53848722 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
53848751 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
53848766 ATCTCGTCAC
Statistics
Matches: 111, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
28 2 0.02
29 108 0.97
30 1 0.01
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (29 bp):
GCACACTTAGTGCCATATATTTCCAGCAT
Found at i:53859549 original size:40 final size:40
Alignment explanation
Indices: 53859501--53859786 Score: 466
Period size: 40 Copynumber: 7.2 Consensus size: 40
53859491 GGACTAAGAT
* *
53859501 CCGAAGGCATTGGTGCCAGTGACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
* *
53859541 TCGAAGGCATTTGTGCTAATGACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
*
53859581 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
53859621 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
* *
53859661 CGGAAGGCATTTGTGCTAGTGACTATATCTGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
*
53859701 CCGAAGGCATTTGTGCTAGTGATTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
* * *
53859741 CCGAAGGCATTTGTGCGAGTTACTATATCC-GGCTAAATC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
53859780 CCGAAGG
1 CCGAAGG
53859787 TACTCGGGTT
Statistics
Matches: 229, Mismatches: 17, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
39 15 0.07
40 214 0.93
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
Found at i:53865452 original size:28 final size:28
Alignment explanation
Indices: 53865406--53865496 Score: 137
Period size: 28 Copynumber: 3.2 Consensus size: 28
53865396 TGGCCCCTTT
*
53865406 AGGCCCAATCTCATTCATATGGCCCATC
1 AGGCCCAATCACATTCATATGGCCCATC
* *
53865434 GGGCCCAATCACATACATATGGCCCATC
1 AGGCCCAATCACATTCATATGGCCCATC
* *
53865462 AGGCCCAATCACTTTCATATGGCCCGTC
1 AGGCCCAATCACATTCATATGGCCCATC
53865490 AGGCCCA
1 AGGCCCA
53865497 GTGACACTCA
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 56 1.00
ACGTcount: A:0.25, C:0.36, G:0.18, T:0.21
Consensus pattern (28 bp):
AGGCCCAATCACATTCATATGGCCCATC
Found at i:53873239 original size:28 final size:28
Alignment explanation
Indices: 53873198--53873293 Score: 124
Period size: 28 Copynumber: 3.5 Consensus size: 28
53873188 TGGCCTCTTT
*
53873198 AGGCCC-ATCTCATTTATATGGCCCATC
1 AGGCCCAATCACATTTATATGGCCCATC
* * *
53873225 GGGCCCAATCACATTCATATGACCCATC
1 AGGCCCAATCACATTTATATGGCCCATC
*
53873253 AGGCCCAATCAC-TTTCATATGGCCCGTC
1 AGGCCCAATCACATTT-ATATGGCCCATC
53873281 AGGCCCAATCACA
1 AGGCCCAATCACA
53873294 CTCGTAGTCA
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
27 7 0.12
28 51 0.88
ACGTcount: A:0.26, C:0.35, G:0.16, T:0.23
Consensus pattern (28 bp):
AGGCCCAATCACATTTATATGGCCCATC
Found at i:53878179 original size:40 final size:40
Alignment explanation
Indices: 53878124--53878265 Score: 135
Period size: 40 Copynumber: 3.5 Consensus size: 40
53878114 ACAACCACAA
* *** *
53878124 GCACAATTGCCTTCGGGTCTTAACCCAGATTTGGTAACTT
1 GCACAATTGCCTTCGGGTCTTAACCCAGATATAACAACTC
* *
53878164 GCACCATTGCCTTCGGGTCTTAGCCCAGATATAACAACTC
1 GCACAATTGCCTTCGGGTCTTAACCCAGATATAACAACTC
* * *
53878204 GCACGAA-TGCCTTCGGGTCTTAACCCGGACATAATC-ACTA
1 GCAC-AATTGCCTTCGGGTCTTAACCCAGATATAA-CAACTC
* * *
53878244 GCATAAATGCCTTCGGGACTTA
1 GCACAATTGCCTTCGGGTCTTA
53878266 GCCCGTATAT
Statistics
Matches: 85, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
39 2 0.02
40 81 0.95
41 2 0.02
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAACCCAGATATAACAACTC
Found at i:53882671 original size:68 final size:67
Alignment explanation
Indices: 53882599--53882748 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
53882589 CATCATGTGT
* * * *
53882599 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
53882661 ATGTAG
62 ATGTAG
** * *
53882667 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
53882732 AG
66 AG
53882734 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
53882749 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:53882704 original size:64 final size:64
Alignment explanation
Indices: 53882623--53882806 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
53882613 AGACATTATG
* *
53882623 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
53882687 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
53882752 AA
63 AA
* * * *
53882754 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
53882807 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:53883760 original size:37 final size:37
Alignment explanation
Indices: 53883702--53883772 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
53883692 GCTCAGATGA
*
53883702 AATCTCCACACGAAGTTATCGGGTCTTACCCGGACAT
1 AATCTCCACACGAAGTCATCGGGTCTTACCCGGACAT
*
53883739 AATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AATCTCCACACGAAGTCATCGGGTCTTACCCGGA
53883773 ATATATTTCC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.24
Consensus pattern (37 bp):
AATCTCCACACGAAGTCATCGGGTCTTACCCGGACAT
Found at i:53883973 original size:48 final size:48
Alignment explanation
Indices: 53883919--53884053 Score: 207
Period size: 48 Copynumber: 2.8 Consensus size: 48
53883909 GCACATCGCC
*
53883919 TACATATTTCACACTAGCCATTCAGCTTTACCACATATACATACCTCA
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATACCTCA
** *
53883967 TACATATTTTGCACTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATACCTCA
* * *
53884015 TACATATTTCACATTAGCCATTCGGCCTTATCACATATA
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATA
53884054 TGCATGTTCA
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 78 1.00
ACGTcount: A:0.31, C:0.28, G:0.07, T:0.34
Consensus pattern (48 bp):
TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATACCTCA
Found at i:53884088 original size:47 final size:47
Alignment explanation
Indices: 53884023--53884310 Score: 468
Period size: 47 Copynumber: 6.1 Consensus size: 47
53884013 CATACATATT
* * * *
53884023 TCACATTAGCCATTCGGCCTTATCACATATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
*
53884070 TCATATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
* * *
53884117 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
* *
53884164 TCATATTGACCATTCGGCCTTATCACACATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
53884211 TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
* *
53884258 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
53884305 TCACAT
1 TCACAT
53884311 AAAATCCTAA
Statistics
Matches: 223, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 223 1.00
ACGTcount: A:0.26, C:0.28, G:0.12, T:0.33
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
Found at i:53884214 original size:25 final size:25
Alignment explanation
Indices: 53884185--53884262 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 25
53884175 ATTCGGCCTT
53884185 ATCACACATATGCATGCTCACATTC
1 ATCACACATATGCATGCTCACATTC
* *
53884210 AT--CACAT-TGGCCAT--TCGGCCTT-
1 ATCACACATAT-G-CATGCTC-ACATTC
53884232 ATCACACATATGCATGCTCACATTC
1 ATCACACATATGCATGCTCACATTC
53884257 ATCACA
1 ATCACA
53884263 TTGGCCATTC
Statistics
Matches: 40, Mismatches: 4, Indels: 18
0.65 0.06 0.29
Matches are distributed among these distances:
22 5 0.12
23 12 0.30
24 12 0.30
25 11 0.28
ACGTcount: A:0.29, C:0.32, G:0.10, T:0.28
Consensus pattern (25 bp):
ATCACACATATGCATGCTCACATTC
Found at i:53884237 original size:22 final size:22
Alignment explanation
Indices: 53884210--53884285 Score: 59
Period size: 22 Copynumber: 3.3 Consensus size: 22
53884200 GCTCACATTC
53884210 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* *
53884232 ATCACACATAT-G-CATGCTC-ACATT
1 AT--CACAT-TGGCCAT--TCGGCCTT
53884256 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
53884279 ATCACAT
1 ATCACAT
53884286 ATATGCATGT
Statistics
Matches: 41, Mismatches: 4, Indels: 18
0.65 0.06 0.29
Matches are distributed among these distances:
22 12 0.29
23 12 0.29
24 12 0.29
25 5 0.12
ACGTcount: A:0.25, C:0.32, G:0.13, T:0.30
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:53893458 original size:39 final size:39
Alignment explanation
Indices: 53893404--53893574 Score: 234
Period size: 39 Copynumber: 4.4 Consensus size: 39
53893394 AATGTTTGAG
53893404 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
*
53893443 TGATATCCGGGCTAAGCCCGAAGGCAATTGGGCGAGTTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* * *
53893482 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* ** *
53893521 TGATATCCGGGTTAAGTCCCGAAGGCCTTTGTGCGGGTTA
1 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTA
** *
53893561 CCATAACCGGGCTA
1 TGATATCCGGGCTA
53893575 TGTCCTGAAG
Statistics
Matches: 115, Mismatches: 16, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
39 88 0.77
40 27 0.23
ACGTcount: A:0.25, C:0.22, G:0.30, T:0.23
Consensus pattern (39 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
Found at i:53895837 original size:33 final size:33
Alignment explanation
Indices: 53895800--53895866 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
53895790 CGATGGTTAG
*
53895800 AATTGCTAAAAGACTATGAGCTTATAATTGACT
1 AATTGCTAAAAGACTACGAGCTTATAATTGACT
*
53895833 AATTGCTAAAAGACTACGAGCTTATAATTTACT
1 AATTGCTAAAAGACTACGAGCTTATAATTGACT
53895866 A
1 A
53895867 TCATCCGAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (33 bp):
AATTGCTAAAAGACTACGAGCTTATAATTGACT
Found at i:53898851 original size:2 final size:2
Alignment explanation
Indices: 53898844--53898874 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
53898834 ATATGAATGA
53898844 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53898875 GTTTTATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53903624 original size:38 final size:35
Alignment explanation
Indices: 53903565--53903682 Score: 135
Period size: 31 Copynumber: 3.5 Consensus size: 35
53903555 TCAATCATGC
*
53903565 ACTGGGCCGTAGCCCTTTTCATATTTCATATTTCATAAT
1 ACTGGGCCGAAG-CCTTTTCATATTTCATATTT-AT--T
53903604 ACTGGGCCGAAGCCTTTTCATATTTC--A--TATT
1 ACTGGGCCGAAGCCTTTTCATATTTCATATTTATT
53903635 ACTGGGCCGAAGCCTTTTCATATTTC--A--TATT
1 ACTGGGCCGAAGCCTTTTCATATTTCATATTTATT
53903666 ACTGGGCCGAAGCCTTT
1 ACTGGGCCGAAGCCTTT
53903683 ACTGTAAACG
Statistics
Matches: 78, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
31 49 0.63
33 2 0.03
34 1 0.01
36 1 0.01
38 14 0.18
39 11 0.14
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (35 bp):
ACTGGGCCGAAGCCTTTTCATATTTCATATTTATT
Found at i:53903626 original size:31 final size:31
Alignment explanation
Indices: 53903588--53903682 Score: 181
Period size: 31 Copynumber: 3.1 Consensus size: 31
53903578 CCTTTTCATA
*
53903588 TTTCATATTTCATAATACTGGGCCGAAGCCT
1 TTTCATATTTCATATTACTGGGCCGAAGCCT
53903619 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATATTACTGGGCCGAAGCCT
53903650 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATATTACTGGGCCGAAGCCT
53903681 TT
1 TT
53903683 ACTGTAAACG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39
Consensus pattern (31 bp):
TTTCATATTTCATATTACTGGGCCGAAGCCT
Found at i:53903925 original size:24 final size:24
Alignment explanation
Indices: 53903874--53904016 Score: 209
Period size: 24 Copynumber: 6.0 Consensus size: 24
53903864 GCTTTATCAT
*
53903874 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
53903899 ATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGGGGCATAAGCCCTTTTA
53903923 ATAACTGGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTA
*
53903946 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
53903970 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
53903994 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
53904017 TCACTTCCTC
Statistics
Matches: 111, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
23 23 0.21
24 76 0.68
25 12 0.11
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:53903953 original size:47 final size:48
Alignment explanation
Indices: 53903874--53904015 Score: 207
Period size: 47 Copynumber: 3.0 Consensus size: 48
53903864 GCTTTATCAT
* *
53903874 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCATAAGCCCTTTCA
**
53903923 ATAACTGGGGCATAAGCCCTTTT-ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA
*
53903970 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTT
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTT
53904016 TTCACTTCCT
Statistics
Matches: 87, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
47 44 0.51
48 31 0.36
49 12 0.14
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.28
Consensus pattern (48 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA
Found at i:53903974 original size:71 final size:72
Alignment explanation
Indices: 53903873--53904016 Score: 220
Period size: 71 Copynumber: 2.0 Consensus size: 72
53903863 TGCTTTATCA
*
53903873 TATAACTGGAGGCCTAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAA
1 TATAACTGGAGGCATAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAA
53903938 GCCCTTT
66 GCCCTTT
* * **
53903945 TATAACTGG-GGCATAAGCC-CTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATA
1 TATAACTGGAGGCAT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATA
53904008 AGCCCTTT
65 AGCCCTTT
53904016 T
1 T
53904017 TCACTTCCTC
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
71 53 0.80
72 13 0.20
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (72 bp):
TATAACTGGAGGCATAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAA
GCCCTTT
Found at i:53904092 original size:20 final size:20
Alignment explanation
Indices: 53904067--53904126 Score: 111
Period size: 20 Copynumber: 3.0 Consensus size: 20
53904057 TATGATTACC
53904067 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
*
53904087 TCATGTGCATATCATACATT
1 TCATGTGCATATCATACATA
53904107 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
53904127 CCATATTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (20 bp):
TCATGTGCATATCATACATA
Found at i:53904097 original size:11 final size:11
Alignment explanation
Indices: 53904067--53904121 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
53904057 TATGATTACC
53904067 TCATGTGCATA
1 TCATGTGCATA
*
53904078 TCA--TACATA
1 TCATGTGCATA
53904087 TCATGTGCATA
1 TCATGTGCATA
* *
53904098 TCA--TACATT
1 TCATGTGCATA
53904107 TCATGTGCATA
1 TCATGTGCATA
53904118 TCAT
1 TCAT
53904122 ACATACCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:53904197 original size:25 final size:25
Alignment explanation
Indices: 53904169--53904216 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
53904159 ATACATAAAC
* * *
53904169 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
53904194 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
53904217 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:53905438 original size:27 final size:27
Alignment explanation
Indices: 53905374--53905430 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
53905364 AGGCATATTC
*
53905374 GTCAGTTTACCATACAGGGGTATTACG
1 GTCACTTTACCATACAGGGGTATTACG
*
53905401 GTCACTTTACCCTACAGGGGCT-TTACG
1 GTCACTTTACCATACAGGGG-TATTACG
53905428 GTC
1 GTC
53905431 TTTTTACCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 26 0.96
28 1 0.04
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.30
Consensus pattern (27 bp):
GTCACTTTACCATACAGGGGTATTACG
Found at i:53905522 original size:27 final size:27
Alignment explanation
Indices: 53905492--53905748 Score: 131
Period size: 27 Copynumber: 9.4 Consensus size: 27
53905482 GTAAATCTAC
*
53905492 AAACCAAGGGTATTTCAGTAATTTTGT
1 AAACCAAGGGTATTTCAGTAATTTTAT
* *
53905519 AAACCAATGGTATTTCTA-TAATTTTTAG
1 AAACCAAGGGTATTTC-AGTAA-TTTTAT
* ** * *
53905547 AAAGTCAAGGGTATTTCTCTAACTTTGT
1 AAA-CCAAGGGTATTTCAGTAATTTTAT
* * ** *
53905575 AAATCAGGGGTATTTTGGTAATTTTAC
1 AAACCAAGGGTATTTCAGTAATTTTAT
*** * * *
53905602 AAATTGAGGGTATTTCGGTAATTTCAC
1 AAACCAAGGGTATTTCAGTAATTTTAT
* *
53905629 AAACCAAGGGTATTT-TGATAATTTTAC
1 AAACCAAGGGTATTTCAG-TAATTTTAT
* * ** *
53905656 AAACTAGGGGTATTTTGGTAATTTTAC
1 AAACCAAGGGTATTTCAGTAATTTTAT
* * *
53905683 AAACTAAGGGTATTTTAGTAATTTTGT
1 AAACCAAGGGTATTTCAGTAATTTTAT
* * *** * *
53905710 AAATCGAGGGTAAAACAGTAATTCTGT
1 AAACCAAGGGTATTTCAGTAATTTTAT
*
53905737 AAATCAAGGGTA
1 AAACCAAGGGTA
53905749 AAACGGTAAT
Statistics
Matches: 182, Mismatches: 42, Indels: 12
0.77 0.18 0.05
Matches are distributed among these distances:
26 1 0.01
27 152 0.84
28 15 0.08
29 14 0.08
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.37
Consensus pattern (27 bp):
AAACCAAGGGTATTTCAGTAATTTTAT
Found at i:53905640 original size:54 final size:54
Alignment explanation
Indices: 53905582--53905721 Score: 183
Period size: 54 Copynumber: 2.6 Consensus size: 54
53905572 TGTAAATCAG
53905582 GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAA
1 GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAA
* * * * *
53905636 GGGTATTTTGATAATTTTACAAACT-AGGGGTATTTTGGTAATTTTACAAACTAA
1 GGGTATTTTGGTAATTTTACAAATTGA-GGGTATTTCGGTAATTTCACAAACCAA
* ** *
53905690 GGGTATTTTAGTAATTTTGTAAATCGAGGGTA
1 GGGTATTTTGGTAATTTTACAAATTGAGGGTA
53905722 AAACAGTAAT
Statistics
Matches: 73, Mismatches: 11, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
53 1 0.01
54 71 0.97
55 1 0.01
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.39
Consensus pattern (54 bp):
GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAA
Found at i:53905746 original size:54 final size:54
Alignment explanation
Indices: 53905688--53905868 Score: 186
Period size: 54 Copynumber: 3.4 Consensus size: 54
53905678 TTTACAAACT
* *
53905688 AAGGGTATTTTAGTAATTTTGTAAATCGAGGGTAAAAC-AGTAATTCTGTAAATC
1 AAGGGTAATTTGGTAATTTTGTAAATCGAGGGTAAAACGA-TAATTCTGTAAATC
*** * * * *
53905742 AAGGGTAAAACGGTAATTCTGTAAGTCGAGGGTAAAACGATAATTATGTAAATT
1 AAGGGTAATTTGGTAATTTTGTAAATCGAGGGTAAAACGATAATTCTGTAAATC
* *** * *
53905796 AGGGGTAAAACGGTAATTATGTAAATCGGGGGTAAAACGATAATTCTGTAAATC
1 AAGGGTAATTTGGTAATTTTGTAAATCGAGGGTAAAACGATAATTCTGTAAATC
* *
53905850 -GGGGTACTTTGGTAATTTT
1 AAGGGTAATTTGGTAATTTT
53905869 ACAAGTCGAA
Statistics
Matches: 106, Mismatches: 20, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
53 14 0.13
54 91 0.86
55 1 0.01
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.31
Consensus pattern (54 bp):
AAGGGTAATTTGGTAATTTTGTAAATCGAGGGTAAAACGATAATTCTGTAAATC
Found at i:53905749 original size:27 final size:26
Alignment explanation
Indices: 53905700--53905855 Score: 181
Period size: 27 Copynumber: 5.8 Consensus size: 26
53905690 GGGTATTTTA
*
53905700 GTAATTTTGTAAATCGAGGGTAAAAC
1 GTAATTCTGTAAATCGAGGGTAAAAC
*
53905726 AGTAATTCTGTAAATCAAGGGTAAAAC
1 -GTAATTCTGTAAATCGAGGGTAAAAC
*
53905753 GGTAATTCTGTAAGTCGAGGGTAAAAC
1 -GTAATTCTGTAAATCGAGGGTAAAAC
* *
53905780 GATAATTATGTAAAT-TAGGGGTAAAAC
1 G-TAATTCTGTAAATCGA-GGGTAAAAC
* *
53905807 GGTAATTATGTAAATCGGGGGTAAAAC
1 -GTAATTCTGTAAATCGAGGGTAAAAC
53905834 GATAATTCTGTAAATCG-GGGTA
1 G-TAATTCTGTAAATCGAGGGTA
53905856 CTTTGGTAAT
Statistics
Matches: 113, Mismatches: 11, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
26 8 0.07
27 104 0.92
28 1 0.01
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.28
Consensus pattern (26 bp):
GTAATTCTGTAAATCGAGGGTAAAAC
Found at i:53905774 original size:81 final size:80
Alignment explanation
Indices: 53905689--53905868 Score: 195
Period size: 81 Copynumber: 2.2 Consensus size: 80
53905679 TTACAAACTA
*
53905689 AGGGTATTTTAGTAATTTTGTAAATCGA-GGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAAC
1 AGGGTA-TTTAGTAATTTTGTAAAT-GAGGGGTAAAACAGTAATTATGTAAATCAAGGGTAAAAC
* *
53905753 GGTAATTCTGTAAGTCG
64 GATAATTCTGTAAATCG
** * * * **
53905770 AGGGTA-AAACGATAATTATGTAAATTAGGGGTAAAACGGTAATTATGTAAATCGGGGGTAAAAC
1 AGGGTATTTA-G-TAATTTTGTAAATGAGGGGTAAAACAGTAATTATGTAAATCAAGGGTAAAAC
53905834 GATAATTCTGTAAATCG
64 GATAATTCTGTAAATCG
*
53905851 -GGGTACTTTGGTAATTTT
1 AGGGTA-TTTAGTAATTTT
53905869 ACAAGTCGAA
Statistics
Matches: 80, Mismatches: 14, Indels: 11
0.76 0.13 0.10
Matches are distributed among these distances:
79 1 0.01
80 13 0.16
81 66 0.82
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.32
Consensus pattern (80 bp):
AGGGTATTTAGTAATTTTGTAAATGAGGGGTAAAACAGTAATTATGTAAATCAAGGGTAAAACGA
TAATTCTGTAAATCG
Found at i:53905891 original size:27 final size:26
Alignment explanation
Indices: 53905861--53905950 Score: 99
Period size: 27 Copynumber: 3.3 Consensus size: 26
53905851 GGGTACTTTG
53905861 GTAATTTTACAAGTCGAAGGTATTTCA
1 GTAATTTTACAA-TCGAAGGTATTTCA
* *
53905888 GTAATTTTACAAATCGAGGGTATTTTA
1 GTAATTTTAC-AATCGAAGGTATTTCA
* * * *
53905915 GTATTTTTACAAACTAAGGGTATTTCG
1 GTAATTTTACAATCGAA-GGTATTTCA
53905942 GTAATTTTA
1 GTAATTTTA
53905951 GTAAACTAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
26 4 0.08
27 46 0.88
28 2 0.04
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.41
Consensus pattern (26 bp):
GTAATTTTACAATCGAAGGTATTTCA
Found at i:53905937 original size:54 final size:53
Alignment explanation
Indices: 53905845--53905950 Score: 133
Period size: 54 Copynumber: 2.0 Consensus size: 53
53905835 ATAATTCTGT
* *
53905845 AAATCGGGGTACTTTGGTAATTTTACAAGTCGAAGGTATTTCAGTAATTTTAC
1 AAATCGGGGTACTTTAGTAATTTTACAAGACGAAGGTATTTCAGTAATTTTAC
* * * *
53905898 AAATCGAGGGTATTTTAGTATTTTTACAA-ACTAAGGGTATTTCGGTAATTTTA
1 AAATCG-GGGTACTTTAGTAATTTTACAAGACGAA-GGTATTTCAGTAATTTTA
53905951 GTAAACTAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
53 9 0.20
54 36 0.80
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (53 bp):
AAATCGGGGTACTTTAGTAATTTTACAAGACGAAGGTATTTCAGTAATTTTAC
Found at i:53909181 original size:27 final size:27
Alignment explanation
Indices: 53909151--53909214 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 27
53909141 TGCCAGAAAC
*
53909151 AGTAAATGTGGCAAAGCCACCAGTATT
1 AGTAAATGTGGCAAAGCCACCAGTAAT
* * * *
53909178 AGTAATTGTGGCATAGCCTCTAGTAAT
1 AGTAAATGTGGCAAAGCCACCAGTAAT
*
53909205 AGTGAATGTG
1 AGTAAATGTG
53909215 ACATAGTCAC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (27 bp):
AGTAAATGTGGCAAAGCCACCAGTAAT
Found at i:53909340 original size:27 final size:27
Alignment explanation
Indices: 53909311--53909473 Score: 182
Period size: 27 Copynumber: 6.0 Consensus size: 27
53909301 GGGCATAATA
* *
53909311 GTCATTTTACCCTATAGGGGCATTACA
1 GTCATTTTACCCTACAGGGGCATTACG
* *
53909338 GTCATTCTACCCTACAGGGACATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* * *
53909365 GTCATTCTACCTTACAGGAGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* * *
53909392 GTCATTTCACCCTACAAGGGCATTATG
1 GTCATTTTACCCTACAGGGGCATTACG
* ** * *
53909419 ATCATTTTACATTATAGGGGCATTATG
1 GTCATTTTACCCTACAGGGGCATTACG
*
53909446 GTCATTTTACCCTACAAGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
53909473 G
1 G
53909474 CCAGATAACA
Statistics
Matches: 111, Mismatches: 25, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 111 1.00
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.31
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGCATTACG
Found at i:53909388 original size:54 final size:53
Alignment explanation
Indices: 53909311--53909473 Score: 202
Period size: 54 Copynumber: 3.0 Consensus size: 53
53909301 GGGCATAATA
* *
53909311 GTCATTTTACCCTATAGGGGCATTACAGTCATTCTACCCTAC-AGGGACATTACG
1 GTCATTTTACCTTATAGGGGCATTACGGTCATT-TACCCTACAAGGG-CATTACG
* * * *
53909365 GTCATTCTACCTTACAGGAGCATTACGGTCATTTCACCCTACAAGGGCATTATG
1 GTCATTTTACCTTATAGGGGCATTACGGTCATTT-ACCCTACAAGGGCATTACG
* * *
53909419 ATCATTTTACATTATAGGGGCATTATGGTCATTTTACCCTACAAGGGCATTACG
1 GTCATTTTACCTTATAGGGGCATTACGGTCA-TTTACCCTACAAGGGCATTACG
53909473 G
1 G
53909474 CCAGATAACA
Statistics
Matches: 92, Mismatches: 14, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
53 1 0.01
54 84 0.91
55 7 0.08
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.31
Consensus pattern (53 bp):
GTCATTTTACCTTATAGGGGCATTACGGTCATTTACCCTACAAGGGCATTACG
Found at i:53914011 original size:27 final size:27
Alignment explanation
Indices: 53913981--53914050 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 27
53913971 AGCATAGCTG
*
53913981 CCAGAAACAGTAAATGTGGCAAAGCCA
1 CCAGTAACAGTAAATGTGGCAAAGCCA
* * *
53914008 CCAGTATCAGTAATTGTGGCATAGCCA
1 CCAGTAACAGTAAATGTGGCAAAGCCA
*
53914035 CCAGTAACAGTGAATG
1 CCAGTAACAGTAAATG
53914051 AGACATAGTC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.37, C:0.21, G:0.23, T:0.19
Consensus pattern (27 bp):
CCAGTAACAGTAAATGTGGCAAAGCCA
Found at i:53914057 original size:27 final size:27
Alignment explanation
Indices: 53914003--53914072 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
53913993 AATGTGGCAA
* * *
53914003 AGCCACCAGTATCAGTAATTGTGGCAT
1 AGCCACCAGTAACAGTAATTGAGACAT
53914030 AGCCACCAGTAACAGTGAA-TGAGACAT
1 AGCCACCAGTAACAGT-AATTGAGACAT
* *
53914057 AGTCACTAGT-ACAGTA
1 AGCCACCAGTAACAGTA
53914073 CTTCCTCCAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
25 1 0.03
26 5 0.14
27 29 0.78
28 2 0.05
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (27 bp):
AGCCACCAGTAACAGTAATTGAGACAT
Found at i:53914242 original size:27 final size:27
Alignment explanation
Indices: 53914208--53914426 Score: 224
Period size: 27 Copynumber: 8.1 Consensus size: 27
53914198 GGGCATAATC
* *
53914208 GTCATTTTACCCTACAGGGGCAGTACA
1 GTCATTTTACCCTACAGGGGCATTACG
* * *
53914235 GTCGTTTTACCCTATAGGGACATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* * * * * *
53914262 ATCATTCTACCTTATAGAGGCATTATG
1 GTCATTTTACCCTACAGGGGCATTACG
* * *
53914289 GTCTTTTTACCCTATATGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* *
53914316 GTCATTTTACCCTACAAGGGCATTATG
1 GTCATTTTACCCTACAGGGGCATTACG
* * *
53914343 GTCATTTTACCTTACAAGGGTATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* ** *
53914370 TTCATTTTACCCTACAATGGCATTAAG
1 GTCATTTTACCCTACAGGGGCATTACG
53914397 GTCATTTTACCCTACA-GGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
53914423 GTCA
1 GTCA
53914427 GATAACGACC
Statistics
Matches: 158, Mismatches: 34, Indels: 1
0.82 0.18 0.01
Matches are distributed among these distances:
26 12 0.08
27 146 0.92
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.34
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGCATTACG
Found at i:53914655 original size:17 final size:18
Alignment explanation
Indices: 53914635--53914669 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
53914625 AACCTGTGTG
53914635 GGGCCCAC-CAGCCCATT
1 GGGCCCACACAGCCCATT
*
53914652 GGGCCCACATAGCCCATT
1 GGGCCCACACAGCCCATT
53914670 TTGACCCAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.20, C:0.43, G:0.23, T:0.14
Consensus pattern (18 bp):
GGGCCCACACAGCCCATT
Found at i:53923389 original size:83 final size:82
Alignment explanation
Indices: 53923233--53923390 Score: 194
Period size: 83 Copynumber: 1.9 Consensus size: 82
53923223 CTGATGTGTG
* * * *
53923233 ATTCGTGTAAGACTATGTCTGGGACATTGGCATCGAAGTGAGAAAATAAGTAAGACCATGTCTGG
1 ATTCGTGTAAGACCATGTCTGGGACAGTGGCATCGAAGTGAGAAAAT-AGTAAGACCATATCGGG
53923298 ACATTGGCATCATATATT
65 ACATTGGCATCATATATT
* * *
53923316 ATTCGTGTAAGACCCTGTCTGGGACAGTGGCATCGATATGTGATAACAT-GTAAGACCATATCCG
1 ATTCGTGTAAGACCATGTCTGGGACAGTGGCATCGA-A-GTGAGAAAATAGTAAGACCATAT-CG
*
53923380 GGATA-TGGCAT
63 GGACATTGGCAT
53923391 TGTACGAGCT
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
83 50 0.78
84 6 0.09
85 8 0.12
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.28
Consensus pattern (82 bp):
ATTCGTGTAAGACCATGTCTGGGACAGTGGCATCGAAGTGAGAAAATAGTAAGACCATATCGGGA
CATTGGCATCATATATT
Found at i:53925642 original size:21 final size:22
Alignment explanation
Indices: 53925618--53925660 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
53925608 CATATCCCAG
*
53925618 ATAT-TGTAACACCCCTAACCC
1 ATATCTGTAACACCCCGAACCC
53925639 ATATCTGTAACACCCCGAACCC
1 ATATCTGTAACACCCCGAACCC
53925661 GAGACCATCG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.33, C:0.40, G:0.07, T:0.21
Consensus pattern (22 bp):
ATATCTGTAACACCCCGAACCC
Found at i:53927114 original size:40 final size:39
Alignment explanation
Indices: 53927023--53927172 Score: 117
Period size: 40 Copynumber: 3.8 Consensus size: 39
53927013 ATAAGCATGT
* * *
53927023 GCACAAATGCCTTCAGGTCTTAGCCCGGATAGAATGTCTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATAGAATGACTA
*
53927063 GCACGAATGCCTTCGGGTCTTAGCCCGGAT-GTA-GCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATAGAATG--ACTA
* * ** *
53927103 GCACAATTGCCTTCGGGTCTTAACCCGG-TATAATTTCCA
1 GCACAA-TGCCTTCGGGTCTTAGCCCGGATAGAATGACTA
* * *
53927142 GCATAATTGTCTTCGGGGCTTAGCCCGGATA
1 GCACAA-TGCCTTCGGGTCTTAGCCCGGATA
53927173 TCATTCAACT
Statistics
Matches: 89, Mismatches: 15, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
38 1 0.01
39 31 0.35
40 57 0.64
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (39 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTA
Found at i:53930452 original size:43 final size:43
Alignment explanation
Indices: 53930381--53930488 Score: 103
Period size: 43 Copynumber: 2.5 Consensus size: 43
53930371 ATACATATCG
* * * * * *
53930381 ATGCCACTGTCCTAAACAAGGTCTTACACGAAAT-TATAATACGA
1 ATGCCAATGTCCCAGACATGGTATTACACGAAATCT-CAATAC-A
* *
53930425 A-GCCAATGTCCCAGATATGGTATTACACGTAATCTCAATACA
1 ATGCCAATGTCCCAGACATGGTATTACACGAAATCTCAATACA
*
53930467 ATGCCAATGTCTCAGACATGGT
1 ATGCCAATGTCCCAGACATGGT
53930489 CTTTCATGTA
Statistics
Matches: 52, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
42 2 0.04
43 48 0.92
44 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTATTACACGAAATCTCAATACA
Found at i:53935516 original size:27 final size:26
Alignment explanation
Indices: 53935475--53935586 Score: 134
Period size: 27 Copynumber: 4.2 Consensus size: 26
53935465 AGGAAGCGTC
*
53935475 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
* *
53935502 CTAGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
53935529 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTG-AT
* * *
53935557 CTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGAT
53935583 CTGG
1 CTGG
53935587 AAGCTATGCT
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
26 7 0.09
27 50 0.68
28 17 0.23
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.37
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:53935579 original size:54 final size:54
Alignment explanation
Indices: 53935475--53935595 Score: 163
Period size: 54 Copynumber: 2.2 Consensus size: 54
53935465 AGGAAGCGTC
*
53935475 CTGGTGGCTATGCCACAATTATCTGATCTAGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTAGTGACTCTGCCACATATATCTGTT
* * * *
53935529 CTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAATTATCTG-ATCTAGTGACTCTGCCACATATATCTGTT
**
53935583 CTGGAAGCTATGC
1 CTGGTGGCTATGC
53935596 TGCATATTTC
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
54 41 0.71
55 17 0.29
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTAGTGACTCTGCCACATATATCTGTT
Found at i:53940991 original size:39 final size:40
Alignment explanation
Indices: 53940941--53941072 Score: 115
Period size: 40 Copynumber: 3.3 Consensus size: 40
53940931 AGCGACTGCT
* * * *
53940941 CAAAAGCCTTCGGGACATAGCCCGG-TATAATAGCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATATAAGAACTCGCA
* * **
53940980 CAAATGCCTTCGGGACTTAACCCGGATTTGGGAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATATAAGAACTCGCA
* ** * **
53941020 CAAATGCCTTC-GGATCTTAGTCCGGATTTGGGAACTCGCA
1 CAAATGCCTTCGGGA-CATAACCCGGATATAAGAACTCGCA
53941060 CAAATGCCTTCGG
1 CAAATGCCTTCGG
53941073 ATCTTAGTCC
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
39 25 0.31
40 54 0.68
41 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.24, T:0.23
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATATAAGAACTCGCA
Found at i:53941029 original size:40 final size:40
Alignment explanation
Indices: 53940974--53941125 Score: 202
Period size: 40 Copynumber: 3.8 Consensus size: 40
53940964 GGTATAATAG
*
53940974 CTCGCACAAATGCCTTCGGGA-CTTAACCCGGATTTGGGAA
1 CTCGCACAAATGCCTTC-GGATCTTAGCCCGGATTTGGGAA
*
53941014 CTCGCACAAATGCCTTCGGATCTTAGTCCGGATTTGGGAA
1 CTCGCACAAATGCCTTCGGATCTTAGCCCGGATTTGGGAA
* * **
53941054 CTCGCACAAATGCCTTCGGATCTTAGTCCGGATATGGTCA
1 CTCGCACAAATGCCTTCGGATCTTAGCCCGGATTTGGGAA
53941094 CTCAGCACAAA-GCCTTCGGGA-CTTAGCCCGGA
1 CTC-GCACAAATGCCTTC-GGATCTTAGCCCGGA
53941126 CATCATTCGA
Statistics
Matches: 103, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
39 3 0.03
40 90 0.87
41 10 0.10
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (40 bp):
CTCGCACAAATGCCTTCGGATCTTAGCCCGGATTTGGGAA
Found at i:53941061 original size:80 final size:80
Alignment explanation
Indices: 53940943--53941125 Score: 203
Period size: 80 Copynumber: 2.3 Consensus size: 80
53940933 CGACTGCTCA
* * *** *
53940943 AAAGCCTTCGGGACATAGCCCGG-TATAATAGCTCGCACAAATGCCTTCGGGA-CTTAACCCGGA
1 AAAGCCTTCGGGACTTAGCCCGGATTTGGGAACTCGCACAAATGCCTTC-GGATCTTAACCCGGA
*
53941006 TTTGGGAACTC-GCAC
65 TATGGGAACTCAGCAC
* **
53941021 AAATGCCTTC-GGATCTTAGTCCGGATTTGGGAACTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 AAA-GCCTTCGGGA-CTTAGCCCGGATTTGGGAACTCGCACAAATGCCTTCGGATCTTAACCCGG
**
53941085 ATATGGTCACTCAGCAC
64 ATATGGGAACTCAGCAC
53941102 AAAGCCTTCGGGACTTAGCCCGGA
1 AAAGCCTTCGGGACTTAGCCCGGA
53941126 CATCATTCGA
Statistics
Matches: 86, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
78 6 0.07
79 17 0.20
80 53 0.62
81 10 0.12
ACGTcount: A:0.25, C:0.27, G:0.25, T:0.23
Consensus pattern (80 bp):
AAAGCCTTCGGGACTTAGCCCGGATTTGGGAACTCGCACAAATGCCTTCGGATCTTAACCCGGAT
ATGGGAACTCAGCAC
Found at i:53946727 original size:27 final size:26
Alignment explanation
Indices: 53946651--53946727 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 26
53946641 AAGCGTCCTG
*
53946651 GTGGCTATGCCACAATTATCTGATCTA
1 GTGGCTATGCCAC-ATTATCTGTTCTA
*
53946678 GTGGCTTTGCCACATATATCTGTTCTA
1 GTGGCTATGCCACAT-TATCTGTTCTA
* *
53946705 GTGGCTCTGCAACGATTATCTGT
1 GTGGCTATGCCAC-ATTATCTGT
53946728 ATTTGGTGAC
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
26 2 0.05
27 40 0.91
28 2 0.05
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (26 bp):
GTGGCTATGCCACATTATCTGTTCTA
Found at i:53948563 original size:13 final size:13
Alignment explanation
Indices: 53948545--53948570 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
53948535 GCTCAACAAG
53948545 GACACACCCGTGT
1 GACACACCCGTGT
53948558 GACACACCCGTGT
1 GACACACCCGTGT
53948571 ACGATTGCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.38, G:0.23, T:0.15
Consensus pattern (13 bp):
GACACACCCGTGT
Done.