Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 230 of 438
Found at i:70997079 original size:40 final size:40
Alignment explanation
Indices: 70996952--70997081 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
70996942 ATGCTGGAAA
* *
70996952 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * **
70996992 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCA
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
70997032 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
70997072 TTATATCCGG
1 TTATATCCGG
70997082 TTGTATTCCG
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
39 4 0.05
40 72 0.95
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:70999454 original size:25 final size:25
Alignment explanation
Indices: 70999420--70999470 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
70999410 CACCACCCTT
**
70999420 GAAAAAACCACGGCCATAAGATGTA
1 GAAAAAACCACACCCATAAGATGTA
*
70999445 GAAAAGACCACACCCATAAGATGTA
1 GAAAAAACCACACCCATAAGATGTA
70999470 G
1 G
70999471 GCACTAATCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.12
Consensus pattern (25 bp):
GAAAAAACCACACCCATAAGATGTA
Found at i:71003523 original size:29 final size:29
Alignment explanation
Indices: 71003459--71003555 Score: 117
Period size: 29 Copynumber: 3.4 Consensus size: 29
71003449 TTCACATACC
* **
71003459 TGTATCTGGCCCATTAAGCCC-AATCGTA
1 TGTATATGGCCCATTAAGCCCAAATCACA
*
71003487 T-TCATATGGCCCATTAAGCCCAAATCACC
1 TGT-ATATGGCCCATTAAGCCCAAATCACA
*
71003516 TGTATATGGCCCATTAGGCCCAAATCACA
1 TGTATATGGCCCATTAAGCCCAAATCACA
*
71003545 TTTATATGGCC
1 TGTATATGGCC
71003556 TGTTCATCCC
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
27 1 0.02
28 18 0.31
29 39 0.66
30 1 0.02
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (29 bp):
TGTATATGGCCCATTAAGCCCAAATCACA
Found at i:71003803 original size:8 final size:8
Alignment explanation
Indices: 71003790--71003820 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
71003780 GTAGCCAAAC
*
71003790 TTTCGGCT
1 TTTCGGCA
71003798 TTTCGGCA
1 TTTCGGCA
71003806 TTTCGGCA
1 TTTCGGCA
71003814 TTTCGGC
1 TTTCGGC
71003821 TTTTTCCGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.06, C:0.26, G:0.26, T:0.42
Consensus pattern (8 bp):
TTTCGGCA
Found at i:71005671 original size:97 final size:95
Alignment explanation
Indices: 71005502--71005737 Score: 246
Period size: 97 Copynumber: 2.5 Consensus size: 95
71005492 CCCAGGGTAT
71005502 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGC-TCATCCATCAAGTCAATGCCATGTC
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTCATCCATCAAGTCAATGCCATGTC
71005566 CCAAACATGGTCTTACACTAACTGTCACATATC
66 CCAAACAT-GTCTTACACTAAC--TCACATATC
** * * ** * *
71005599 CGTGCCGATGCCATGTTCCAAACATGGTCTTACACTGGCTTACAT-C-TTGAGGCTGATG-CATG
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTT-CATCCATCAAGTC-AATGCCATG
* * * * * *
71005661 TTCTAGACATGTCTTACATTAGCTCACATCTC
64 TCCCAAACATGTCTTACACTAACTCACATATC
**
71005693 AACACCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCAT
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCT-TCAT
71005738 AATATGGTCG
Statistics
Matches: 115, Mismatches: 20, Indels: 11
0.79 0.14 0.08
Matches are distributed among these distances:
94 45 0.39
95 1 0.01
96 11 0.10
97 50 0.43
98 5 0.04
99 3 0.03
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.28
Consensus pattern (95 bp):
AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTCATCCATCAAGTCAATGCCATGTC
CCAAACATGTCTTACACTAACTCACATATC
Found at i:71005756 original size:47 final size:47
Alignment explanation
Indices: 71005505--71005765 Score: 169
Period size: 47 Copynumber: 5.5 Consensus size: 47
71005495 AGGGTATAAT
71005505 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCCATCA-A--
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTC-T-CAT-ATATG
* * * ** * *
71005552 GTCAATGCCATGTCCCAAACATGGTCTTACACTAACTGTCACATATCCG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATAT--G
* * *
71005601 TGCCGATGCCATGTTCCAAACATGGTCTTACACTGGCT-TACATCT-TGAG
1 -GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCT-CATATAT--G
* * * * * * * **
71005650 GCTGATG-CATGTTCTAGACAT-GTCTTACATTAGCTCACATCTCAAC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAT-ATG
*
71005696 ACCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATATG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCAT-ATATG
* *
71005744 GTCGATG-CATGTCCCATACATG
1 GCCGATGCCATGTCCCAGACATG
71005766 TCTCGCACTA
Statistics
Matches: 164, Mismatches: 37, Indels: 26
0.72 0.16 0.11
Matches are distributed among these distances:
44 1 0.01
45 3 0.02
46 23 0.14
47 70 0.43
48 28 0.17
49 4 0.02
50 35 0.21
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (47 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATATG
Found at i:71005766 original size:94 final size:95
Alignment explanation
Indices: 71005506--71005768 Score: 252
Period size: 94 Copynumber: 2.8 Consensus size: 95
71005496 GGGTATAATG
* *
71005506 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCCATCA-A--GTCAATGCCATGTCCC
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTC-TACAT-ATATGGTCGATG-CATGTCCC
****
71005568 AAACATGGTCTTACACTAACTGTCACATATCCGTG
63 AAACAT-GTCTTACACTAAC-GTCACATATCAACA
* * * * * *
71005603 CCGATGCCATGTTCCAAACATGGTCTTACACTGGCT-TACATCT-TGAGGCTGATGCATGTTCTA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTACATATATG-GTC-GATGCATGTCCCA
* * * *
71005666 GACATGTCTTACATTAGC-TCACATCTCAACA
64 AACATGTCTTACACTAACGTCACATATCAACA
*
71005697 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCT-CATAATATGGTCGATGCATGTCCCAT
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTACAT-ATATGGTCGATGCATGTCCCAA
71005761 ACATGTCT
65 ACATGTCT
71005769 CGCACTAGCA
Statistics
Matches: 135, Mismatches: 23, Indels: 19
0.76 0.13 0.11
Matches are distributed among these distances:
94 64 0.47
95 8 0.06
96 13 0.10
97 47 0.35
98 3 0.02
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.29
Consensus pattern (95 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTACATATATGGTCGATGCATGTCCCAAA
CATGTCTTACACTAACGTCACATATCAACA
Found at i:71008409 original size:31 final size:32
Alignment explanation
Indices: 71008353--71008413 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
71008343 CGAAGTCACT
* *
71008353 AGATATAGATATTGTGGCTAGGCCACCAGAAC
1 AGATATAGATATTGTGGCAAAGCCACCAGAAC
*
71008385 AGATATATATA-TGTGGCAAAGCCACCAGA
1 AGATATAGATATTGTGGCAAAGCCACCAGA
71008414 TTGTAGCGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 16 0.62
32 10 0.38
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.21
Consensus pattern (32 bp):
AGATATAGATATTGTGGCAAAGCCACCAGAAC
Found at i:71008433 original size:71 final size:67
Alignment explanation
Indices: 71008358--71008499 Score: 185
Period size: 67 Copynumber: 2.1 Consensus size: 67
71008348 TCACTAGATA
* * * *
71008358 TAGATATTGTGGCTAGGCCACCAGAACAGATATATATATGTGGCAAAGCCACCAGATTGTAGCGA
1 TAGATATTGTGACGAAGCCACCAGAACAG----ATATATGTGGCAAAGCCACCAGATTGCAGCGA
71008423 GGCTGC
62 GGCTGC
* * *
71008429 TAGATATTGTGACGAAGTCACCAGAACAGATATATGTGGCGAGGCCACCAGATTGCAGCGAGGCT
1 TAGATATTGTGACGAAGCCACCAGAACAGATATATGTGGCAAAGCCACCAGATTGCAGCGAGGCT
71008494 GC
66 GC
71008496 TAGA
1 TAGA
71008500 ACACTTCCTC
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
67 39 0.61
71 25 0.39
ACGTcount: A:0.31, C:0.20, G:0.28, T:0.21
Consensus pattern (67 bp):
TAGATATTGTGACGAAGCCACCAGAACAGATATATGTGGCAAAGCCACCAGATTGCAGCGAGGCT
GC
Found at i:71008477 original size:27 final size:26
Alignment explanation
Indices: 71008430--71008480 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
71008420 CGAGGCTGCT
*
71008430 AGATATTGTGACGAAGTCACCAGAAC
1 AGATATTGTGACGAAGCCACCAGAAC
* *
71008456 AGATATATGTGGCGAGGCCACCAGA
1 AGATAT-TGTGACGAAGCCACCAGA
71008481 TTGCAGCGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.35, C:0.20, G:0.27, T:0.18
Consensus pattern (26 bp):
AGATATTGTGACGAAGCCACCAGAAC
Found at i:71017251 original size:28 final size:28
Alignment explanation
Indices: 71017182--71017282 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
71017172 GACAAGATTG
* * * *
71017182 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
71017212 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
71017240 GCACTAAGTGTGCGAG-TTGAATACATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
71017269 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
71017283 GATTCACTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.05
28 24 0.38
29 19 0.30
30 18 0.28
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:71021404 original size:40 final size:40
Alignment explanation
Indices: 71021359--71021488 Score: 172
Period size: 40 Copynumber: 3.2 Consensus size: 40
71021349 CGGAATATAA
71021359 CCGGATATAACCA-TGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACT-TGCACAAATGCCTTCGGGTCTTAGC
* ** * *
71021399 CCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTTGCACAAATGCCTTCGGGTCTTAGC
* * *
71021439 CCGGATATAGCCACTTGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTTGCACAAATGCCTTCGGGTCTTAGC
71021479 CCGGATATAA
1 CCGGATATAA
71021489 TTTCCAGCAT
Statistics
Matches: 75, Mismatches: 14, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
40 74 0.99
41 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAACCACTTGCACAAATGCCTTCGGGTCTTAGC
Found at i:71021503 original size:40 final size:39
Alignment explanation
Indices: 71021375--71021525 Score: 144
Period size: 40 Copynumber: 3.8 Consensus size: 39
71021365 ATAACCATGT
* * *
71021375 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTC
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCAC-C
** *
71021415 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATATAGCCACTT
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAATCAC-C
* **
71021455 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCC
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCACC
* * *
71021494 AGCATAATTGTCTTCGGG-CTTAGCCTGGATAT
1 -GCACAATTGCCTTCGGGTCTTAGCCCGGATAT
71021526 CATTCAATTT
Statistics
Matches: 93, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
39 14 0.15
40 77 0.83
41 2 0.02
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (39 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCACC
Found at i:71026784 original size:20 final size:20
Alignment explanation
Indices: 71026741--71026786 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
71026731 ACTGTTTTGT
*
71026741 TATGGG-CCAACTGTATTGA
1 TATGGGCCCAACTGTATTAA
* *
71026760 GATGGGCCCAACTGTGTTAA
1 TATGGGCCCAACTGTATTAA
71026780 TATGGGC
1 TATGGGC
71026787 AAGGCCCAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.28
Consensus pattern (20 bp):
TATGGGCCCAACTGTATTAA
Found at i:71026855 original size:60 final size:59
Alignment explanation
Indices: 71026779--71026915 Score: 161
Period size: 60 Copynumber: 2.3 Consensus size: 59
71026769 AACTGTGTTA
* *
71026779 ATATGGGCAAGGCCCAACATA-TCTCGACT-TGTAATAGGGCTACGGCCCAGATTGATACTG
1 ATATGGGCTAGGCCCAACATACTCT-GA-TATGTAA-AGGGCTACGGCCCAGATTAATACTG
* * * *
71026839 ATATGGGCTAGGCCCAATATACTCTGATACTGTAAGGGGCTATGGCCCAGATTAATATTG
1 ATATGGGCTAGGCCCAACATACTCTGATA-TGTAAAGGGCTACGGCCCAGATTAATACTG
71026899 ATATGGGCTAAGGCCCA
1 ATATGGGCT-AGGCCCA
71026916 GTTAACACTG
Statistics
Matches: 67, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
59 1 0.01
60 51 0.76
61 15 0.22
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (59 bp):
ATATGGGCTAGGCCCAACATACTCTGATATGTAAAGGGCTACGGCCCAGATTAATACTG
Found at i:71028552 original size:17 final size:17
Alignment explanation
Indices: 71028530--71028563 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
71028520 CACTTATTCA
*
71028530 CTCACAATGCTTTTATT
1 CTCACAATACTTTTATT
*
71028547 CTCACATTACTTTTATT
1 CTCACAATACTTTTATT
71028564 TACATGACAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.24, G:0.03, T:0.50
Consensus pattern (17 bp):
CTCACAATACTTTTATT
Found at i:71032937 original size:19 final size:20
Alignment explanation
Indices: 71032899--71032937 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
71032889 GTCCTTATGT
*
71032899 TGTAAATAGACCATGGATAG
1 TGTAAATAGACCATGAATAG
*
71032919 TGTAAATTGA-CATGAATAG
1 TGTAAATAGACCATGAATAG
71032938 CTATCCATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.41, C:0.08, G:0.23, T:0.28
Consensus pattern (20 bp):
TGTAAATAGACCATGAATAG
Found at i:71033870 original size:81 final size:82
Alignment explanation
Indices: 71033763--71033944 Score: 199
Period size: 81 Copynumber: 2.2 Consensus size: 82
71033753 CAATTATGTT
* * * * * *
71033763 TGGCACTTAGTGTGTG-TATCGAGATAGCTTCGGCTATATAAAGCACTTAATGTGTGA-ATTGGA
1 TGGCACTTAGTGTGCGAGATTGAGATAGCTTCAGCTAT-TAAAGAACTTAATGTGTGAGATTAGA
**
71033826 ATAGCTTCGGCTAT-ATA
65 ATAGCTTCAACTATGATA
* * * * *
71033843 TGGCATTTAGTGTGCGAGATTGAGATAGCTTTAGCTATTAGAGAACTTAGTGTGTGAGATTATAA
1 TGGCACTTAGTGTGCGAGATTGAGATAGCTTCAGCTATTAAAGAACTTAATGTGTGAGATTAGAA
* *
71033908 TAGCTTCAACTATGCTT
66 TAGCTTCAACTATGATA
71033925 TGGCACTTAGTGTGCGAGAT
1 TGGCACTTAGTGTGCGAGAT
71033945 ATAGAGTATT
Statistics
Matches: 83, Mismatches: 16, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
80 30 0.36
81 33 0.40
82 20 0.24
ACGTcount: A:0.27, C:0.13, G:0.26, T:0.35
Consensus pattern (82 bp):
TGGCACTTAGTGTGCGAGATTGAGATAGCTTCAGCTATTAAAGAACTTAATGTGTGAGATTAGAA
TAGCTTCAACTATGATA
Found at i:71033902 original size:40 final size:41
Alignment explanation
Indices: 71033765--71033903 Score: 144
Period size: 40 Copynumber: 3.5 Consensus size: 41
71033755 ATTATGTTTG
* * *
71033765 GCACTTAGTGTGTG-TATCGAGATAGCTTCGGCTATATAAA
1 GCACTTAGTGTGTGAGATTGAGATAGCTTCGGCTATATAGA
*
71033805 GCACTTAATGTGTGA-ATTG-GAATAGCTTCGGCTATATATG-
1 GCACTTAGTGTGTGAGATTGAG-ATAGCTTCGGCTATATA-GA
* * **
71033845 GCATTTAGTGTGCGAGATTGAGATAGCTTTAGCTAT-TAGA
1 GCACTTAGTGTGTGAGATTGAGATAGCTTCGGCTATATAGA
*
71033885 GAACTTAGTGTGTGAGATT
1 GCACTTAGTGTGTGAGATT
71033904 ATAATAGCTT
Statistics
Matches: 82, Mismatches: 11, Indels: 12
0.78 0.10 0.11
Matches are distributed among these distances:
39 2 0.02
40 63 0.77
41 16 0.20
42 1 0.01
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.35
Consensus pattern (41 bp):
GCACTTAGTGTGTGAGATTGAGATAGCTTCGGCTATATAGA
Found at i:71035523 original size:20 final size:19
Alignment explanation
Indices: 71035482--71035534 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
71035472 TTCCTTAAGC
* *
71035482 AAGAAGAAAGAAAACTAGCA
1 AAGAAG-AAGAAAAATAACA
71035502 AAGAAGAAGAAACAATAACA
1 AAGAAGAAGAAA-AATAACA
* *
71035522 AAAAATAAGAAAA
1 AAGAAGAAGAAAA
71035535 TTTTGAAGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 7 0.25
20 21 0.75
ACGTcount: A:0.72, C:0.08, G:0.15, T:0.06
Consensus pattern (19 bp):
AAGAAGAAGAAAAATAACA
Found at i:71040209 original size:55 final size:53
Alignment explanation
Indices: 71040080--71040275 Score: 189
Period size: 55 Copynumber: 3.6 Consensus size: 53
71040070 CTTACCATTT
* *
71040080 CCATGTCTCGACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAATG
1 CCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATGAACTCACCAATG
* * * * * *
71040133 CCATGCCTTGGCATGGTCTTACATGGGA-CCTTTTCCTTATAGTGACTTATCAATG
1 CCATGTCTTGACATGGTCTTACATGGGATCC-TTGCCTTAT-G-AACTCACCAATG
* * *
71040188 CCATGTGTTGACATGGTCTTACATGGTATCCTTGCCTTA-GAAACCTTACCAATTG
1 CCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATG-AA-CTCACCAA-TG
* * * *
71040243 TCATGCCTTGGCATGGTCTTACATGGTATCCTT
1 CCATGTCTTGACATGGTCTTACATGGGATCCTT
71040276 AAACCCTAAT
Statistics
Matches: 117, Mismatches: 20, Indels: 10
0.80 0.14 0.07
Matches are distributed among these distances:
52 2 0.02
53 34 0.29
54 8 0.07
55 71 0.61
56 2 0.02
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (53 bp):
CCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATGAACTCACCAATG
Found at i:71042103 original size:28 final size:28
Alignment explanation
Indices: 71042049--71042146 Score: 119
Period size: 28 Copynumber: 3.5 Consensus size: 28
71042039 ATAATAAGCC
*
71042049 CGCACACTT-GTGCT-TAATAGTCGAACT
1 CGCACACTTAGTGCTAT-ATAATCGAACT
*
71042076 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCGAACT
* * *
71042104 CGCACACTTAGTGCTATACAATTTGAACC
1 CGCACACTTAGTGCTATATAA-TCGAACT
71042133 CGCACACTTAGTGC
1 CGCACACTTAGTGC
71042147 CAATCTCATG
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
27 9 0.15
28 34 0.55
29 19 0.31
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCGAACT
Found at i:71051331 original size:40 final size:40
Alignment explanation
Indices: 71051272--71051398 Score: 152
Period size: 40 Copynumber: 3.2 Consensus size: 40
71051262 CTGAATACAA
* * *
71051272 CCGGATATAACCACGTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATAGAACGACTTGCACGAATGCCTTCGGGTCTTAGC
71051312 CCGGATAGAACGACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATAGAACGACTTGCACGAATGCCTTCGGGTCTTAGC
* * *
71051352 CCGGAT-GTAGCCG-CTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATAG-A-ACGACTTGCACGAA-TGCCTTCGGGTCTTAGC
71051392 CCGGATA
1 CCGGATA
71051399 TAATTTCCAG
Statistics
Matches: 77, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
39 3 0.04
40 72 0.94
41 2 0.03
ACGTcount: A:0.22, C:0.29, G:0.26, T:0.23
Consensus pattern (40 bp):
CCGGATAGAACGACTTGCACGAATGCCTTCGGGTCTTAGC
Found at i:71059236 original size:40 final size:39
Alignment explanation
Indices: 71059191--71059319 Score: 154
Period size: 40 Copynumber: 3.3 Consensus size: 39
71059181 CGGAATACAA
71059191 CCGGATATAACCACGTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACGAATGCCTTCGGGTCTTAGC
* *
71059231 CCGGATAGAACGACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACGAATGCCTTCGGGTCTTAGC
* * * *
71059271 CCGGATGTAGCCGCTAGCAC-AATTGCCTTC-GGTCTTAAC
1 CCGGATATAACCACT-GCACGAA-TGCCTTCGGGTCTTAGC
71059310 CCGGATATAA
1 CCGGATATAA
71059320 TTTCCAACAT
Statistics
Matches: 76, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
39 19 0.25
40 57 0.75
ACGTcount: A:0.23, C:0.29, G:0.25, T:0.23
Consensus pattern (39 bp):
CCGGATATAACCACTGCACGAATGCCTTCGGGTCTTAGC
Found at i:71071530 original size:43 final size:43
Alignment explanation
Indices: 71071469--71071555 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
71071459 GCATCCATAT
71071469 ACTTAGCTTGAAAAATAGTCTTGAAAAACTCCCAAGTCAAATG
1 ACTTAGCTTGAAAAATAGTCTTGAAAAACTCCCAAGTCAAATG
71071512 ACTTAGCTTGAAAAATAGTCTTGAAAAACTCCCAAGTCAAATG
1 ACTTAGCTTGAAAAATAGTCTTGAAAAACTCCCAAGTCAAATG
71071555 A
1 A
71071556 TCGACTTGTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.25
Consensus pattern (43 bp):
ACTTAGCTTGAAAAATAGTCTTGAAAAACTCCCAAGTCAAATG
Found at i:71076077 original size:21 final size:21
Alignment explanation
Indices: 71076051--71076098 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
71076041 TGAGTCCGAG
71076051 TTCGAGAGATGTAACTAAGCA
1 TTCGAGAGATGTAACTAAGCA
*
71076072 TTCGAGAGATGTAACTAGGCA
1 TTCGAGAGATGTAACTAAGCA
*
71076093 TCCGAG
1 TTCGAG
71076099 CTCGTTGAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.33, C:0.17, G:0.27, T:0.23
Consensus pattern (21 bp):
TTCGAGAGATGTAACTAAGCA
Found at i:71083375 original size:32 final size:32
Alignment explanation
Indices: 71083334--71083397 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
71083324 GTAGGTCTTG
71083334 CATGTGTTGCATGATCATTTTGGTTGGTTGTT
1 CATGTGTTGCATGATCATTTTGGTTGGTTGTT
71083366 CATGTGTTGCATGATCATTTTGGTTGGTTGTT
1 CATGTGTTGCATGATCATTTTGGTTGGTTGTT
71083398 TTAGTATGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.12, C:0.09, G:0.28, T:0.50
Consensus pattern (32 bp):
CATGTGTTGCATGATCATTTTGGTTGGTTGTT
Found at i:71086309 original size:40 final size:40
Alignment explanation
Indices: 71086201--71086410 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
71086191 CGGGATTTAA
* * * * *
71086201 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
71086241 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
71086281 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
71086321 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
71086361 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
71086401 CCGGATATAT
1 CCGGATATAT
71086411 TTCCAATGTT
Statistics
Matches: 153, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 152 0.99
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:71094444 original size:40 final size:40
Alignment explanation
Indices: 71094336--71094545 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
71094326 CGGGATTTAA
* * * * *
71094336 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
71094376 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
71094416 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
71094456 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
71094496 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
71094536 CCGGATATAT
1 CCGGATATAT
71094546 TTCCAATGTT
Statistics
Matches: 153, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 152 0.99
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:71097081 original size:201 final size:201
Alignment explanation
Indices: 71096732--71097131 Score: 773
Period size: 201 Copynumber: 2.0 Consensus size: 201
71096722 GAAAATTTTG
71096732 GAAAACTTAGAAATTTTTCAATCATATAAGGGTCACACGCCCGTGTGAATTGGCCGTGTGCCTTA
1 GAAAACTTAGAAATTTTTCAATCATATAAGGGTCACACGCCCGTGTGAATTGGCCGTGTGCCTTA
*
71096797 CACAGCTAGTAGACATGCTCGTGTCTTAGGCCATGTGGAAACAGGGCATACATACTGACTTGTAT
66 CACAGCTAGTAGACATGCCCGTGTCTTAGGCCATGTGGAAACAGGGCATACATACTGACTTGTAT
71096862 CACATGGCCGACGACATGCCCGTGTACCAGGCCGTTTGAAAGCTAGAGGGTATACTGACTCAGGT
131 CACATGGCCGACGACATGCCCGTGTACCAGGCCGTTTGAAAGCTAGAGGGTATACTGACTCAGGT
71096927 CACATT
196 CACATT
71096933 GAAAACTTAGAAATTTTTCAATCATATAAGGGTCACACGCCCGTGTGAATTGGCCGTGTGCCTTA
1 GAAAACTTAGAAATTTTTCAATCATATAAGGGTCACACGCCCGTGTGAATTGGCCGTGTGCCTTA
*
71096998 CACAGCTAGTAGACATGCCCGTGTCTTAGGCCGTGTGGAAACAGGGCATACATACTGACTTGTAT
66 CACAGCTAGTAGACATGCCCGTGTCTTAGGCCATGTGGAAACAGGGCATACATACTGACTTGTAT
*
71097063 CACATGGCCGATGACATGCCCGTGTACCAGGCCGTTTGAAAGCTAGAGGGTATACTGACTCAGGT
131 CACATGGCCGACGACATGCCCGTGTACCAGGCCGTTTGAAAGCTAGAGGGTATACTGACTCAGGT
71097128 CACA
196 CACA
71097132 CGGCCAACCA
Statistics
Matches: 196, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
201 196 1.00
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (201 bp):
GAAAACTTAGAAATTTTTCAATCATATAAGGGTCACACGCCCGTGTGAATTGGCCGTGTGCCTTA
CACAGCTAGTAGACATGCCCGTGTCTTAGGCCATGTGGAAACAGGGCATACATACTGACTTGTAT
CACATGGCCGACGACATGCCCGTGTACCAGGCCGTTTGAAAGCTAGAGGGTATACTGACTCAGGT
CACATT
Found at i:71101890 original size:24 final size:24
Alignment explanation
Indices: 71101862--71101908 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
71101852 AGTGAAATCT
*
71101862 ATAAATTTCCATCTTCAATTAATG
1 ATAAACTTCCATCTTCAATTAATG
* *
71101886 ATAAACTTCTATCTTCCATTAAT
1 ATAAACTTCCATCTTCAATTAAT
71101909 ATTTAATGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.36, C:0.19, G:0.02, T:0.43
Consensus pattern (24 bp):
ATAAACTTCCATCTTCAATTAATG
Found at i:71107220 original size:46 final size:46
Alignment explanation
Indices: 71107170--71107345 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
71107160 TGGTTGAGCA
71107170 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
71107216 TCCGAACTCGTTGAGTTGAGTCTGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
71107261 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
71107309 CCCGAGCTCATTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
71107346 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 61 0.56
47 28 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:71107326 original size:93 final size:93
Alignment explanation
Indices: 71107167--71107338 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
71107157 GGATGGTTGA
* * *
71107167 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
*
71107232 TGAGTCTGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
71107260 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCATTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
71107325 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
71107339 CTTATGGGCG
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:71118913 original size:14 final size:14
Alignment explanation
Indices: 71118894--71118921 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
71118884 TCCTATTTTG
71118894 GTTATTTTTGATTT
1 GTTATTTTTGATTT
71118908 GTTATTTTTGATTT
1 GTTATTTTTGATTT
71118922 TTTGGCATGT
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:0.14, C:0.00, G:0.14, T:0.71
Consensus pattern (14 bp):
GTTATTTTTGATTT
Found at i:71120827 original size:15 final size:15
Alignment explanation
Indices: 71120809--71120841 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
71120799 TAAGGTGAGT
*
71120809 ATCAACATATATCGC
1 ATCAACATATATCAC
71120824 ATCAACATATATCAC
1 ATCAACATATATCAC
71120839 ATC
1 ATC
71120842 TTATAATAAA
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:0.27, G:0.03, T:0.27
Consensus pattern (15 bp):
ATCAACATATATCAC
Found at i:71129125 original size:46 final size:46
Alignment explanation
Indices: 71129004--71129126 Score: 174
Period size: 46 Copynumber: 2.7 Consensus size: 46
71128994 AACCCGCCCC
* * * *
71129004 TAAGTGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* *
71129050 TAAATGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* *
71129096 TAAGCGAACTCGGACTCAACTCAATGAGTTC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC
71129127 AGATGCTCAA
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 68 1.00
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:71129586 original size:30 final size:30
Alignment explanation
Indices: 71129552--71129611 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
71129542 ATTTAATACG
71129552 AACTTTAAAAAAATTACACTTTTGCCCCTA
1 AACTTTAAAAAAATTACACTTTTGCCCCTA
*** *
71129582 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTAAAAAAATTACACTTTTGCCCCTA
71129612 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (30 bp):
AACTTTAAAAAAATTACACTTTTGCCCCTA
Found at i:71138139 original size:46 final size:46
Alignment explanation
Indices: 71138089--71138214 Score: 207
Period size: 46 Copynumber: 2.7 Consensus size: 46
71138079 TGGTTGAGCA
*
71138089 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
71138135 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
71138181 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
71138215 GGGGCGGGTT
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
46 74 1.00
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:71142085 original size:28 final size:28
Alignment explanation
Indices: 71142053--71142108 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
71142043 ATAACTAAAC
71142053 AATAAACTACATGATTAAATCACCATTG
1 AATAAACTACATGATTAAATCACCATTG
71142081 AATAAACTACATGATTAAATCACCATTG
1 AATAAACTACATGATTAAATCACCATTG
71142109 CTGAATCACA
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:0.46, C:0.18, G:0.07, T:0.29
Consensus pattern (28 bp):
AATAAACTACATGATTAAATCACCATTG
Found at i:71142880 original size:43 final size:43
Alignment explanation
Indices: 71142829--71142957 Score: 117
Period size: 43 Copynumber: 3.0 Consensus size: 43
71142819 ATGTAATAAA
71142829 ATAT-CGATGCCACTGTCCCAGACAAGGGTCTTACACGAAATC
1 ATATACGATGCCACTGTCCCAGACAAGGGTCTTACACGAAATC
* * * *
71142871 ATATACGATGCCAATGTCCAAGAC-ATGGTCTTACATGTAAATC
1 ATATACGATGCCACTGTCCCAGACAAGGGTCTTACACG-AAATC
* *
71142914 -TCAAATCGATGCCAAC-GTCCCAG--ATGTGGTCTTACACGAAATC
1 AT-ATA-CGATGCC-ACTGTCCCAGACAAG-GGTCTTACACGAAATC
71142957 A
1 A
71142958 CATATTGGAA
Statistics
Matches: 69, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
42 16 0.23
43 29 0.42
44 23 0.33
45 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.24
Consensus pattern (43 bp):
ATATACGATGCCACTGTCCCAGACAAGGGTCTTACACGAAATC
Found at i:71142944 original size:44 final size:43
Alignment explanation
Indices: 71142792--71142949 Score: 119
Period size: 44 Copynumber: 3.7 Consensus size: 43
71142782 AGCTCGTAAA
* * * **
71142792 ATGCCAACATCCCAGATGAGATCTTACATGT-AATAAAATATCG
1 ATGCCAACGTCCCAGATGTGGTCTTACATGTAAATTCAA-ATCG
* * *
71142835 ATGCC-ACTGTCCCAGACAAG-GGTCTTACACG-AAA-TCATATACG
1 ATGCCAAC-GTCCCAG--ATGTGGTCTTACATGTAAATTCAAAT-CG
* * **
71142878 ATGCCAATGTCCAAGACATGGTCTTACATGTAAATCTCAAATCG
1 ATGCCAACGTCCCAGATGTGGTCTTACATGTAAAT-TCAAATCG
71142922 ATGCCAACGTCCCAGATGTGGTCTTACA
1 ATGCCAACGTCCCAGATGTGGTCTTACA
71142950 CGAAATCACA
Statistics
Matches: 88, Mismatches: 17, Indels: 19
0.71 0.14 0.15
Matches are distributed among these distances:
41 1 0.01
42 14 0.16
43 28 0.32
44 38 0.43
45 7 0.08
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.25
Consensus pattern (43 bp):
ATGCCAACGTCCCAGATGTGGTCTTACATGTAAATTCAAATCG
Found at i:71144036 original size:13 final size:13
Alignment explanation
Indices: 71144018--71144042 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
71144008 ACAAACGATA
71144018 AAATTTTCACACG
1 AAATTTTCACACG
71144031 AAATTTTCACAC
1 AAATTTTCACAC
71144043 ATATCACATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:71149409 original size:49 final size:49
Alignment explanation
Indices: 71149332--71149569 Score: 287
Period size: 49 Copynumber: 4.8 Consensus size: 49
71149322 TAGCCGAAGC
* *
71149332 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
* * * * *
71149381 TATCCGGTACACGCAGTAGCCTGCACTTAGTACTACACACGTGACCTAAC
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACC-AAT
* ** * * *
71149431 CATCTAATACATGTAGTAGCCTGCACTTAGTACTACACATGTGATCGAAGT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGA-CCAA-T
* * * * *
71149482 TATCAGGTACGCATAGTAGCTTGAACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
71149531 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACA
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACA
71149570 CGTGACCTCA
Statistics
Matches: 154, Mismatches: 32, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
49 75 0.49
50 44 0.29
51 35 0.23
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (49 bp):
TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
Found at i:71151773 original size:46 final size:46
Alignment explanation
Indices: 71151697--71152010 Score: 459
Period size: 46 Copynumber: 6.8 Consensus size: 46
71151687 TGATATCATA
* * * * *
71151697 GTATCTTTCAACTATGGTTTTACTCGTTTTC-TGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTC-ATTTCATATCAGGTTGCCATG
* *** *
71151743 GTATCTTTCAACCATGGTCTTATTCATTTTCCCGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCA-TTTCATATCAGGTTGCCATG
71151790 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
* *
71151836 GTATCTTTCAACCATGGTCTTATTCATTTCATATCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
*
71151882 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
*
71151928 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
* *
71151974 GTATCTTTCAACCATGGTCTTACACATTCCATATCAG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAG
71152011 AGGGCACACT
Statistics
Matches: 250, Mismatches: 16, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
46 211 0.84
47 39 0.16
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.40
Consensus pattern (46 bp):
GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
Found at i:71160844 original size:25 final size:25
Alignment explanation
Indices: 71160815--71160862 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
71160805 TTATAATATG
* * *
71160815 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
71160840 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
71160863 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:71160930 original size:20 final size:20
Alignment explanation
Indices: 71160905--71160968 Score: 110
Period size: 20 Copynumber: 3.2 Consensus size: 20
71160895 ATAAAATGGT
71160905 ATGTATGATATGCACATGAC
1 ATGTATGATATGCACATGAC
*
71160925 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACATGAC
*
71160945 ATGTATGATATGCACATGAG
1 ATGTATGATATGCACATGAC
71160965 ATGT
1 ATGT
71160969 TCATAAATGC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.34, C:0.11, G:0.22, T:0.33
Consensus pattern (20 bp):
ATGTATGATATGCACATGAC
Found at i:71160945 original size:11 final size:11
Alignment explanation
Indices: 71160909--71160963 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
71160899 AATGGTATGT
71160909 ATGATATGCAC
1 ATGATATGCAC
* *
71160920 ATGACATG--T
1 ATGATATGCAC
71160929 ATGATATGCAC
1 ATGATATGCAC
*
71160940 ATGATATG--T
1 ATGATATGCAC
71160949 ATGATATGCAC
1 ATGATATGCAC
71160960 ATGA
1 ATGA
71160964 GATGTTCATA
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:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:71161070 original size:24 final size:23
Alignment explanation
Indices: 71161014--71161180 Score: 237
Period size: 24 Copynumber: 7.0 Consensus size: 23
71161004 GAGGAAGTGA
71161014 AAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
*
71161037 TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
71161060 CAAAAGGGCTTATGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
71161084 CAAAAGGGCTTATGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
71161108 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTA-T
* *
71161132 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTA-T
*
71161156 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
71161180 A
1 A
71161181 TGATAAAGCA
Statistics
Matches: 133, Mismatches: 7, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
23 44 0.33
24 79 0.59
25 10 0.08
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (23 bp):
AAAAGGGCTTATGCCCCAGTTAT
Found at i:71161083 original size:47 final size:46
Alignment explanation
Indices: 71161014--71161179 Score: 244
Period size: 47 Copynumber: 3.5 Consensus size: 46
71161004 GAGGAAGTGA
71161014 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
*
71161060 CAAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT-TAAAGGGCTTATGCCCCAGTTAT
*
71161108 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT-AAAGGGCTTATGCCCCAGTTA-T
*
71161156 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
71161180 ATGATAAAGC
Statistics
Matches: 110, Mismatches: 4, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
47 66 0.60
48 33 0.30
49 11 0.10
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.27
Consensus pattern (46 bp):
AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
Found at i:71161130 original size:71 final size:71
Alignment explanation
Indices: 71161014--71161180 Score: 255
Period size: 71 Copynumber: 2.3 Consensus size: 71
71161004 GAGGAAGTGA
*
71161014 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCA
1 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCA
71161079 GTTATC
66 GTTATC
** *
71161085 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCA
1 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCA
*
71161150 GTTATT
66 GTTATC
*
71161156 AAAAGAGGC-TAGGCCTCCAGTTATA
1 AAAAG-GGCTTATGCC-CCAGTTATA
71161181 TGATAAAGCA
Statistics
Matches: 88, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
71 76 0.86
72 12 0.14
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (71 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCA
GTTATC
Found at i:71161431 original size:30 final size:31
Alignment explanation
Indices: 71161371--71161433 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
71161361 CGTTTACAGT
71161371 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
71161402 AAAGGCTTCGGCCCAGTGTTATG-AATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
71161432 AA
1 AA
71161434 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 9 0.30
31 21 0.70
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.24
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:71167217 original size:25 final size:25
Alignment explanation
Indices: 71167188--71167235 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
71167178 TTATAATATG
* * *
71167188 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
71167213 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
71167236 GTTTATATGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:71167337 original size:20 final size:20
Alignment explanation
Indices: 71167274--71167329 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
71167264 ATAAACATGT
71167274 ATGTATGATATGCACATGAC
1 ATGTATGATATGCACATGAC
*
71167294 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACATGAC
71167314 ATGTATGATATGCACA
1 ATGTATGATATGCACA
71167330 CGAGATGTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (20 bp):
ATGTATGATATGCACATGAC
Found at i:71167438 original size:24 final size:23
Alignment explanation
Indices: 71167382--71167547 Score: 228
Period size: 24 Copynumber: 7.0 Consensus size: 23
71167372 GAGGAAGTGA
71167382 AAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
*
71167405 TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
71167428 CAAAAGGGCTTATGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
71167452 CAAAAGGGCTTATGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
71167476 -AAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTA-T
* *
71167499 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTA-T
*
71167523 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
71167547 A
1 A
71167548 TGATAAAGCA
Statistics
Matches: 132, Mismatches: 6, Indels: 9
0.90 0.04 0.06
Matches are distributed among these distances:
22 21 0.16
23 23 0.17
24 78 0.59
25 10 0.08
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.27
Consensus pattern (23 bp):
AAAAGGGCTTATGCCCCAGTTAT
Found at i:71167497 original size:46 final size:46
Alignment explanation
Indices: 71167382--71167547 Score: 228
Period size: 46 Copynumber: 3.5 Consensus size: 46
71167372 GAGGAAGTGA
*
71167382 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTAT
71167428 CAAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTAT
* *
71167476 -AAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTA-TAAAAGGGCTTATGCCCCAGTTA-T
*
71167523 AAAAGAGGC-TAGGCCTCCAGTTATA
1 AAAAG-GGCTTATGCC-CCAGTTATA
71167548 TGATAAAGCA
Statistics
Matches: 108, Mismatches: 5, Indels: 11
0.87 0.04 0.09
Matches are distributed among these distances:
46 41 0.38
47 25 0.23
48 32 0.30
49 10 0.09
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.27
Consensus pattern (46 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTAT
Found at i:71167497 original size:70 final size:70
Alignment explanation
Indices: 71167382--71167547 Score: 253
Period size: 70 Copynumber: 2.3 Consensus size: 70
71167372 GAGGAAGTGA
71167382 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCA
1 AAAAGGGCTTATGCCCCAGTTA-TAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCA
71167447 GTTATC
65 GTTATC
** *
71167453 AAAAGGGCTTATGCCCCAGTTATAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAG
1 AAAAGGGCTTATGCCCCAGTTATAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAG
*
71167518 TTATT
66 TTATC
*
71167523 AAAAGAGGC-TAGGCCTCCAGTTATA
1 AAAAG-GGCTTATGCC-CCAGTTATA
71167548 TGATAAAGCA
Statistics
Matches: 88, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
70 54 0.61
71 34 0.39
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.27
Consensus pattern (70 bp):
AAAAGGGCTTATGCCCCAGTTATAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAG
TTATC
Found at i:71167798 original size:30 final size:31
Alignment explanation
Indices: 71167738--71167800 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
71167728 CGTTTACAGT
71167738 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
71167769 AAAGGCTTCGGCCCAGTGTTATG-AATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
71167799 AA
1 AA
71167801 CATGAAAAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 9 0.30
31 21 0.70
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.24
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:71172455 original size:39 final size:39
Alignment explanation
Indices: 71172374--71172550 Score: 281
Period size: 39 Copynumber: 4.6 Consensus size: 39
71172364 AATCGTACAA
*
71172374 CCTTCGGGCTTAGCCC---TATGACAATTTGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCACAATTTGCACAATTG
* * *
71172410 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCACAATTTGCACAATTG
*
71172449 CCTTCGGGCTTAGCCCGGGTATCACAATTTGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCACAATTTGCACAATTG
71172488 CCTT-GGGCTTAGCCCGGATATCACAATTTGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCACAATTTGCACAATTG
71172526 CCTTCGGGCTTAGCCCGGATATCAC
1 CCTTCGGGCTTAGCCCGGATATCAC
71172551 TCGAACATTC
Statistics
Matches: 128, Mismatches: 9, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
36 16 0.12
38 37 0.29
39 75 0.59
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.28
Consensus pattern (39 bp):
CCTTCGGGCTTAGCCCGGATATCACAATTTGCACAATTG
Found at i:71172521 original size:77 final size:77
Alignment explanation
Indices: 71172374--71172550 Score: 279
Period size: 77 Copynumber: 2.3 Consensus size: 77
71172364 AATCGTACAA
* *
71172374 CCTTCGGGCTTAGCCC--TATGACAATTTGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAA
1 CCTTCGGGCTTAGCCCGGTATCACAATTTGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAA
71172437 CTCGCACAATTG
66 CTCGCACAATTG
71172449 CCTTCGGGCTTAGCCCGGGTATCACAATTTGCACAATTGCCTT-GGGCTTAGCCCGGATATCACA
1 CCTTCGGGCTTAGCCC-GGTATCACAATTTGCACAATTGCCTTCGGGCTTAGCCCGGATATCACA
* *
71172513 ATTTGCACAATTG
65 ACTCGCACAATTG
71172526 CCTTCGGGCTTAGCCCGGATATCAC
1 CCTTCGGGCTTAGCCCGG-TATCAC
71172551 TCGAACATTC
Statistics
Matches: 94, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
75 16 0.17
76 2 0.02
77 53 0.56
78 23 0.24
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.28
Consensus pattern (77 bp):
CCTTCGGGCTTAGCCCGGTATCACAATTTGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAA
CTCGCACAATTG
Found at i:71180474 original size:39 final size:39
Alignment explanation
Indices: 71180412--71180672 Score: 405
Period size: 39 Copynumber: 6.7 Consensus size: 39
71180402 CCGCTCAAAG
*
71180412 GCCTTCGGGACTTAACCCGGATATCACAATTTGCACAATT
1 GCCTTCGGG-CTTAGCCCGGATATCACAATTTGCACAATT
* * * * *
71180452 GCCTTCAGGCTTAGCCTGGATATCATAACTCGCACAATT
1 GCCTTCGGGCTTAGCCCGGATATCACAATTTGCACAATT
* *
71180491 GCCTTCTGGCTTAGCCCGGGTATCACAATTTGCACAATT
1 GCCTTCGGGCTTAGCCCGGATATCACAATTTGCACAATT
* * *
71180530 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
1 GCCTTCGGGCTTAGCCCGGATATCACAATTTGCACAATT
*
71180569 GCCTTCGGGCTTAGCCCGGGTATCACAATTTGCACAATT
1 GCCTTCGGGCTTAGCCCGGATATCACAATTTGCACAATT
71180608 GCCTTCGGGCTTAGCCCGGATATCACAATTTGCACAATT
1 GCCTTCGGGCTTAGCCCGGATATCACAATTTGCACAATT
71180647 GCCTTCGGGCTTAGCCCGGATATCAC
1 GCCTTCGGGCTTAGCCCGGATATCAC
71180673 TCGAACATTC
Statistics
Matches: 199, Mismatches: 22, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
39 191 0.96
40 8 0.04
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.28
Consensus pattern (39 bp):
GCCTTCGGGCTTAGCCCGGATATCACAATTTGCACAATT
Found at i:71202825 original size:29 final size:29
Alignment explanation
Indices: 71202793--71202895 Score: 118
Period size: 29 Copynumber: 3.6 Consensus size: 29
71202783 GTGACGAGAT
* *
71202793 TGGCACTGAGTGTGCGAGCTTGAAATGTA
1 TGGCACTAAGTGTGCGAGCTTGAAATATA
* * *
71202822 TGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTTGAAATATA
* * *
71202851 TGGCACTATGTGTGCGGGCTT-AAATCACA
1 TGGCACTAAGTGTGCGAGCTTGAAAT-ATA
71202880 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
71202896 TGATCGAGTA
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
28 2 0.03
29 59 0.97
ACGTcount: A:0.23, C:0.17, G:0.32, T:0.28
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTTGAAATATA
Found at i:71210768 original size:29 final size:29
Alignment explanation
Indices: 71210736--71210838 Score: 118
Period size: 29 Copynumber: 3.6 Consensus size: 29
71210726 GTGACGAGAT
* *
71210736 TGGCACTGAGTGTGCGAGCTTGAAATGTA
1 TGGCACTAAGTGTGCGAGCTTGAAATATA
* * *
71210765 TGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTTGAAATATA
* * *
71210794 TGGCACTATGTGTGCGGGCTT-AAATCACA
1 TGGCACTAAGTGTGCGAGCTTGAAAT-ATA
71210823 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
71210839 TGATCGAGTA
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
28 2 0.03
29 59 0.97
ACGTcount: A:0.23, C:0.17, G:0.32, T:0.28
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTTGAAATATA
Found at i:71213944 original size:43 final size:43
Alignment explanation
Indices: 71213851--71213998 Score: 194
Period size: 43 Copynumber: 3.5 Consensus size: 43
71213841 TCGATGCCAC
* * * * *
71213851 TGTCCCAAACAAGGTCTTACACG-TATCAT-A-TACGATGCCAA
1 TGTCCCAAACATGGTCTTACACGTTTTC-TCACTTCGATTCGAA
*
71213892 TGTCCCAAACATGGTCTTACACGTTTTCTCACTTTGATTCGAA
1 TGTCCCAAACATGGTCTTACACGTTTTCTCACTTCGATTCGAA
*
71213935 TGTCCCAAACATGGTCTTACATGTTTTCTCACTTCGATTCGAA
1 TGTCCCAAACATGGTCTTACACGTTTTCTCACTTCGATTCGAA
*
71213978 TGTCCCAGACATGGTCTTACA
1 TGTCCCAAACATGGTCTTACA
71213999 TGAATCACAC
Statistics
Matches: 95, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
41 23 0.24
42 4 0.04
43 68 0.72
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.32
Consensus pattern (43 bp):
TGTCCCAAACATGGTCTTACACGTTTTCTCACTTCGATTCGAA
Found at i:71213999 original size:43 final size:43
Alignment explanation
Indices: 71213890--71214000 Score: 195
Period size: 43 Copynumber: 2.6 Consensus size: 43
71213880 ATACGATGCC
* *
71213890 AATGTCCCAAACATGGTCTTACACGTTTTCTCACTTTGATTCG
1 AATGTCCCAAACATGGTCTTACATGTTTTCTCACTTCGATTCG
71213933 AATGTCCCAAACATGGTCTTACATGTTTTCTCACTTCGATTCG
1 AATGTCCCAAACATGGTCTTACATGTTTTCTCACTTCGATTCG
*
71213976 AATGTCCCAGACATGGTCTTACATG
1 AATGTCCCAAACATGGTCTTACATG
71214001 AATCACACAT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 65 1.00
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.35
Consensus pattern (43 bp):
AATGTCCCAAACATGGTCTTACATGTTTTCTCACTTCGATTCG
Found at i:71223551 original size:43 final size:44
Alignment explanation
Indices: 71223490--71223653 Score: 182
Period size: 43 Copynumber: 3.8 Consensus size: 44
71223480 TAATGCTAGC
* *
71223490 GTCCCAGAC-GTGGTCTTACATGTAATCAAATATCGATGTCACT
1 GTCCCAGACAGTGGTCTTACACGAAATCAAATATCGATGTCACT
71223533 GTCCCAGACAG-GGTCTTACACGAAATCAAATAT-GATGTCA-T
1 GTCCCAGACAGTGGTCTTACACGAAATCAAATATCGATGTCACT
* * *
71223574 GTCCCAGACA-TGGTCTTACACGTAAATCTCAA-ATCAATGCCAAC-
1 GTCCCAGACAGTGGTCTTACACG-AAATC-AAATATCGATGTC-ACT
* *
71223618 GTCCCAGA-TGTGGTCTTACATGAAATCAAATATCGA
1 GTCCCAGACAGTGGTCTTACACGAAATCAAATATCGA
71223654 AATCCTATGT
Statistics
Matches: 103, Mismatches: 9, Indels: 18
0.79 0.07 0.14
Matches are distributed among these distances:
41 22 0.21
42 16 0.16
43 44 0.43
44 21 0.20
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (44 bp):
GTCCCAGACAGTGGTCTTACACGAAATCAAATATCGATGTCACT
Found at i:71224997 original size:53 final size:53
Alignment explanation
Indices: 71224915--71225017 Score: 197
Period size: 53 Copynumber: 1.9 Consensus size: 53
71224905 AGAATTTGTA
71224915 ATTTATAGCGACATGTCATTGAATGATTTAGGTTGCGTATTGATGCAAGAGTG
1 ATTTATAGCGACATGTCATTGAATGATTTAGGTTGCGTATTGATGCAAGAGTG
*
71224968 ATTTATAGCGACATGTCATTGAATTATTTAGGTTGCGTATTGATGCAAGA
1 ATTTATAGCGACATGTCATTGAATGATTTAGGTTGCGTATTGATGCAAGA
71225018 AGGAAAAGTT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.29, C:0.10, G:0.24, T:0.37
Consensus pattern (53 bp):
ATTTATAGCGACATGTCATTGAATGATTTAGGTTGCGTATTGATGCAAGAGTG
Found at i:71230549 original size:48 final size:46
Alignment explanation
Indices: 71230352--71230566 Score: 225
Period size: 46 Copynumber: 4.6 Consensus size: 46
71230342 TGATATGTGT
71230352 GCTAGTGTAAGACATGTCTAGGACATGCATCAGCCACAATATGAAA
1 GCTAGTGTAAGACATGTCTAGGACATGCATCAGCCACAATATGAAA
*
71230398 GCTAGTGTAAGACATGTCTAGGACATGCATCAGCCACAATATGAGA
1 GCTAGTGTAAGACATGTCTAGGACATGCATCAGCCACAATATGAAA
* * * * **
71230444 GCTAATGTAAGACATGTCTAGGACATGCTTCGGCCTCGAGATATTTAA
1 GCTAGTGTAAGACATGTCTAGGACATGCATCAGCCAC-A-ATATGAAA
* * * * * * *
71230492 GCCAATGTAAGACATGTTTGGGACATGCATCGGCCTCGCGATAT-ACAA
1 GCTAGTGTAAGACATGTCTAGGACATGCATCAG-C-CACAATATGA-AA
* * *
71230540 GCTAGTGTAAGACTTATCTGGGACATG
1 GCTAGTGTAAGACATGTCTAGGACATG
71230567 GCGTCAGCTT
Statistics
Matches: 144, Mismatches: 20, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
46 78 0.54
47 1 0.01
48 62 0.43
49 1 0.01
50 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.25
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTCTAGGACATGCATCAGCCACAATATGAAA
Found at i:71244151 original size:30 final size:30
Alignment explanation
Indices: 71244110--71244178 Score: 122
Period size: 30 Copynumber: 2.3 Consensus size: 30
71244100 TAGCCTGTGT
71244110 GCGCTG-TGCTTGCTCCCAACTCCTGCTAC
1 GCGCTGCTGCTTGCTCCCAACTCCTGCTAC
71244139 GCGCTGCTGCTTGCTCCCAACTCCTGCTAC
1 GCGCTGCTGCTTGCTCCCAACTCCTGCTAC
*
71244169 GTGCTGCTGC
1 GCGCTGCTGC
71244179 CTCGCGCACA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
29 6 0.16
30 32 0.84
ACGTcount: A:0.09, C:0.41, G:0.23, T:0.28
Consensus pattern (30 bp):
GCGCTGCTGCTTGCTCCCAACTCCTGCTAC
Found at i:71248640 original size:40 final size:39
Alignment explanation
Indices: 71248595--71248802 Score: 193
Period size: 40 Copynumber: 5.2 Consensus size: 39
71248585 CGGAATACAA
*
71248595 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * * *
71248635 CCGGATAGAACGACTTGCACAAATGCCTTTGGGTATTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
71248675 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* *** *
71248715 CCGGATGTGGTCACTAGCAC-AATGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACT-GCACAAAT-GCCTTCGGGTCTTAGC
** * * *
71248755 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
71248795 CCGGATAT
1 CCGGATAT
71248803 CATTCAATTG
Statistics
Matches: 139, Mismatches: 26, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
39 4 0.03
40 132 0.95
41 3 0.02
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.26
Consensus pattern (39 bp):
CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC
Found at i:71248735 original size:80 final size:80
Alignment explanation
Indices: 71248595--71248801 Score: 229
Period size: 80 Copynumber: 2.6 Consensus size: 80
71248585 CGGAATACAA
* * *
71248595 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTTGCACAAAT-
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCAC-AATG
* *
71248659 GCCTTTGGGTATTAGC
65 GCCTTCGGGTATTAAC
* * **
71248675 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATGTGGTC-ACTAGCACAATG
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT-AGAACGACTAGCACAATG
*
71248739 GCCTTCGGGTCTTAAC
65 GCCTTCGGGTATTAAC
** * ** * *
71248755 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGCCCGGATA
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATA
71248802 TCATTCAATT
Statistics
Matches: 106, Mismatches: 19, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
79 3 0.03
80 101 0.95
81 2 0.02
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.26
Consensus pattern (80 bp):
CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCACAATGG
CCTTCGGGTATTAAC
Found at i:71257470 original size:23 final size:23
Alignment explanation
Indices: 71257444--71257522 Score: 61
Period size: 23 Copynumber: 3.2 Consensus size: 23
71257434 CCATAGCTCA
71257444 AAGCACCACCAATAGTTTAAGCT
1 AAGCACCACCAATAGTTTAAGCT
* ***
71257467 AAGCA-AACCAATATGAAACCATAGCT
1 AAGCACCACCAATA-G--TTTA-AGCT
71257493 CAAAGCACCACCAATAGTTTAAGCT
1 --AAGCACCACCAATAGTTTAAGCT
71257518 AAGCA
1 AAGCA
71257523 AACCTATAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 14
0.65 0.13 0.22
Matches are distributed among these distances:
22 7 0.17
23 11 0.27
25 5 0.12
26 5 0.12
28 6 0.15
29 7 0.17
ACGTcount: A:0.44, C:0.25, G:0.13, T:0.18
Consensus pattern (23 bp):
AAGCACCACCAATAGTTTAAGCT
Found at i:71257502 original size:51 final size:51
Alignment explanation
Indices: 71257426--71257526 Score: 202
Period size: 51 Copynumber: 2.0 Consensus size: 51
71257416 CATAAAAATT
71257426 ATATGAAACCATAGCTCAAAGCACCACCAATAGTTTAAGCTAAGCAAACCA
1 ATATGAAACCATAGCTCAAAGCACCACCAATAGTTTAAGCTAAGCAAACCA
71257477 ATATGAAACCATAGCTCAAAGCACCACCAATAGTTTAAGCTAAGCAAACC
1 ATATGAAACCATAGCTCAAAGCACCACCAATAGTTTAAGCTAAGCAAACC
71257527 TATAAAATAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.45, C:0.26, G:0.12, T:0.18
Consensus pattern (51 bp):
ATATGAAACCATAGCTCAAAGCACCACCAATAGTTTAAGCTAAGCAAACCA
Found at i:71259493 original size:12 final size:12
Alignment explanation
Indices: 71259472--71259510 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
71259462 CACACGCCCG
*
71259472 TGTGCCAGGCCA
1 TGTGCTAGGCCA
*
71259484 TGTGCTAGGCCG
1 TGTGCTAGGCCA
71259496 TGTGCTAGGCCA
1 TGTGCTAGGCCA
71259508 TGT
1 TGT
71259511 AACTTCTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.13, C:0.26, G:0.36, T:0.26
Consensus pattern (12 bp):
TGTGCTAGGCCA
Found at i:71263370 original size:27 final size:27
Alignment explanation
Indices: 71263332--71263395 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
71263322 TTTATCAAGG
* **
71263332 GTATTAGTTTATTGATAAATGAATATT
1 GTATTAATTTATCAATAAATGAATATT
*
71263359 GTATTAATTTATCAATAAATTAATATT
1 GTATTAATTTATCAATAAATGAATATT
71263386 -TATTAATTTA
1 GTATTAATTTA
71263396 GAGAATATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
26 10 0.30
27 23 0.70
ACGTcount: A:0.41, C:0.02, G:0.08, T:0.50
Consensus pattern (27 bp):
GTATTAATTTATCAATAAATGAATATT
Found at i:71265071 original size:40 final size:40
Alignment explanation
Indices: 71265009--71265117 Score: 164
Period size: 40 Copynumber: 2.7 Consensus size: 40
71264999 TCTAGTGTAA
* *
71265009 TTCAGTCGGATTAGCTCTTATGAGCTTTTGTATGGTGTGT
1 TTCAGTTGGATTAGCTCTTATGAGCTTTTGTATAGTGTGT
* *
71265049 TTTAGTTGGATTAGCTCTTATGAGCTTTTGTCTAGTGTGT
1 TTCAGTTGGATTAGCTCTTATGAGCTTTTGTATAGTGTGT
* *
71265089 TTCGGTTGGATTAGCTCATATGAGCTTTT
1 TTCAGTTGGATTAGCTCTTATGAGCTTTT
71265118 ATCTGGTATG
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 62 1.00
ACGTcount: A:0.16, C:0.12, G:0.26, T:0.47
Consensus pattern (40 bp):
TTCAGTTGGATTAGCTCTTATGAGCTTTTGTATAGTGTGT
Found at i:71269564 original size:19 final size:19
Alignment explanation
Indices: 71269540--71269576 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
71269530 CTTTATAAGG
71269540 GACTCTATATTGATGGTTA
1 GACTCTATATTGATGGTTA
71269559 GACTCTATATTGATGGTT
1 GACTCTATATTGATGGTT
71269577 GATCTTTAAT
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:0.24, C:0.11, G:0.22, T:0.43
Consensus pattern (19 bp):
GACTCTATATTGATGGTTA
Found at i:71274106 original size:40 final size:40
Alignment explanation
Indices: 71274062--71274210 Score: 217
Period size: 40 Copynumber: 3.7 Consensus size: 40
71274052 ATATCACGAT
*
71274062 TTGCACAAACGCCTTCGGGTCTTAGCCCGGATTTAACAAC
1 TTGCACAAATGCCTTCGGGTCTTAGCCCGGATTTAACAAC
*
71274102 TTGCACGAATGCCTTCGGGTCTTAGCCCGGATTTAACAAC
1 TTGCACAAATGCCTTCGGGTCTTAGCCCGGATTTAACAAC
* * * *
71274142 TTGCACGAATGCCTTCGGGTCTTAGCCCGGATATAGCTAC
1 TTGCACAAATGCCTTCGGGTCTTAGCCCGGATTTAACAAC
* * *
71274182 TAGCACAATTGCCTTCGGGTCTTAACCCG
1 TTGCACAAATGCCTTCGGGTCTTAGCCCG
71274211 ATAAAATTTT
Statistics
Matches: 100, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 100 1.00
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (40 bp):
TTGCACAAATGCCTTCGGGTCTTAGCCCGGATTTAACAAC
Found at i:71274131 original size:80 final size:80
Alignment explanation
Indices: 71274032--71274210 Score: 225
Period size: 80 Copynumber: 2.2 Consensus size: 80
71274022 CCGCACCAAG
* * * * * *
71274032 GCCTACGGGACTTAACCCGGATATCACGATTTGCACAAACGCCTTCGGGTCTTAGCCCGGATTTA
1 GCCTTCGGGTCTTAACCCGGATATAACAACTTGCACAAACGCCTTCGGGTCTTAGCCCGGATATA
*
71274097 ACAACTTGCACGAA-T
66 ACAACTAGCAC-AATT
* * * *
71274112 GCCTTCGGGTCTTAGCCCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATATA
1 GCCTTCGGGTCTTAACCCGGATATAACAACTTGCACAAACGCCTTCGGGTCTTAGCCCGGATATA
* *
71274177 GCTACTAGCACAATT
66 ACAACTAGCACAATT
71274192 GCCTTCGGGTCTTAACCCG
1 GCCTTCGGGTCTTAACCCG
71274211 ATAAAATTTT
Statistics
Matches: 84, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
79 2 0.02
80 82 0.98
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.26
Consensus pattern (80 bp):
GCCTTCGGGTCTTAACCCGGATATAACAACTTGCACAAACGCCTTCGGGTCTTAGCCCGGATATA
ACAACTAGCACAATT
Found at i:71279626 original size:18 final size:18
Alignment explanation
Indices: 71279578--71279618 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
71279568 AGATATATTA
** *
71279578 ATTATTATTTTTATTGCT
1 ATTATTATTTAAATTGAT
71279596 ATTATTATTTAAATTGAT
1 ATTATTATTTAAATTGAT
71279614 ATTAT
1 ATTAT
71279619 ATTATAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (18 bp):
ATTATTATTTAAATTGAT
Found at i:71279810 original size:18 final size:18
Alignment explanation
Indices: 71279769--71279810 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
71279759 ATAGTTAAGT
*
71279769 AAAGAAACAAAAGAAATA
1 AAAGAAACAAAAGAAAGA
*
71279787 AAAGAAA-AAAAGAAGGA
1 AAAGAAACAAAAGAAAGA
71279804 AACAGAA
1 AA-AGAA
71279811 TAAGGAATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.76, C:0.05, G:0.17, T:0.02
Consensus pattern (18 bp):
AAAGAAACAAAAGAAAGA
Found at i:71280455 original size:20 final size:19
Alignment explanation
Indices: 71280432--71280469 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
71280422 TTTATATTCC
71280432 GAATTTAATATTTAATTGTT
1 GAATTTAATATTT-ATTGTT
*
71280452 GAATTTATTATTTATTGT
1 GAATTTAATATTTATTGT
71280470 GTAGGTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.58
Consensus pattern (19 bp):
GAATTTAATATTTATTGTT
Found at i:71283161 original size:47 final size:47
Alignment explanation
Indices: 71283095--71283565 Score: 736
Period size: 47 Copynumber: 10.3 Consensus size: 47
71283085 GTATGAGATA
*
71283095 TATATATGT-ATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTA
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
71283141 TATATATGTGATAAGGCCTAATGG-CGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
71283187 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
71283234 ----TA--T-AT-----CTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
71283269 TATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
71283316 TATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
71283363 TATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
71283410 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
* * *
71283457 CATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
* * * *
71283504 TATATATGTGATAAGGCCGAGTGGCCAATGTGATGGATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
71283551 TATAAATGTGATAAG
1 TATATATGTGATAAG
71283566 TCCTGAAGGG
Statistics
Matches: 401, Mismatches: 10, Indels: 27
0.92 0.02 0.06
Matches are distributed among these distances:
35 30 0.07
39 1 0.00
40 2 0.00
41 2 0.00
42 2 0.00
43 2 0.00
46 54 0.13
47 308 0.77
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.30
Consensus pattern (47 bp):
TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
Found at i:71283244 original size:35 final size:35
Alignment explanation
Indices: 71283204--71283273 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
71283194 GTGATAAGGC
71283204 CTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 CTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
71283239 CTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 CTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
71283274 GTGTGATAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.31, C:0.09, G:0.29, T:0.31
Consensus pattern (35 bp):
CTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
Found at i:71283742 original size:37 final size:37
Alignment explanation
Indices: 71283683--71283765 Score: 121
Period size: 37 Copynumber: 2.2 Consensus size: 37
71283673 CCGAGCTCTA
* *
71283683 AAGACCCGATGACTACGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATGACCACGGGTGGAGATTATGTCCGGGT
* *
71283720 AAGACCCGATGACCATGGGTGGAGATTTTGTCCGGGT
1 AAGACCCGATGACCACGGGTGGAGATTATGTCCGGGT
*
71283757 AAGCCCCGA
1 AAGACCCGA
71283766 ACTAAAGGTT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.24, C:0.22, G:0.33, T:0.22
Consensus pattern (37 bp):
AAGACCCGATGACCACGGGTGGAGATTATGTCCGGGT
Found at i:71292994 original size:69 final size:67
Alignment explanation
Indices: 71292920--71293071 Score: 232
Period size: 67 Copynumber: 2.2 Consensus size: 67
71292910 AAGACTCAAA
* *
71292920 AATTAAAATTTTTTATTTCTTTTTTTTTTTTTTGTTTTACTTGAAAAGATATATTCTCAGTATCG
1 AATTAAAATTTTTTATTTC--TTTTTTTTGTTTGTTTTACTTGAAAAGATATATTCTCACTATCG
71292985 TTCT
64 TTCT
**
71292989 AATTAAAATTTTAGATTTCTTTTTTTTGTTTGTTTTACTTGAAAAGATATATTCTCACTATCGTT
1 AATTAAAATTTTTTATTTCTTTTTTTTGTTTGTTTTACTTGAAAAGATATATTCTCACTATCGTT
71293054 CT
66 CT
71293056 AACTTAAAAGTTTTTT
1 AA-TTAAAA-TTTTTT
71293072 TTAAAGGAAA
Statistics
Matches: 75, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
67 48 0.64
68 6 0.08
69 21 0.28
ACGTcount: A:0.27, C:0.09, G:0.08, T:0.56
Consensus pattern (67 bp):
AATTAAAATTTTTTATTTCTTTTTTTTGTTTGTTTTACTTGAAAAGATATATTCTCACTATCGTT
CT
Found at i:71293786 original size:23 final size:22
Alignment explanation
Indices: 71293759--71293813 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
71293749 TTTAATATTA
*
71293759 TTTATTTGATATTTGTAAATAAT
1 TTTATTTGATATAT-TAAATAAT
**
71293782 TTTATATACATATATTAAATAAT
1 TTTAT-TTGATATATTAAATAAT
*
71293805 TTTTTTTGA
1 TTTATTTGA
71293814 AAATATCAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
22 2 0.08
23 17 0.68
24 6 0.24
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.56
Consensus pattern (22 bp):
TTTATTTGATATATTAAATAAT
Found at i:71297922 original size:52 final size:52
Alignment explanation
Indices: 71297847--71297951 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 52
71297837 TAATTTAAAG
71297847 AAAAACTATAATTATCAATAGTTGTTACATTGTCATGATATATATCAATAGA
1 AAAAACTATAATTATCAATAGTTGTTACATTGTCATGATATATATCAATAGA
*
71297899 AAAAACTATAATTATCAATAGTTGTTACTTTGTCATGATATATATCAATAGA
1 AAAAACTATAATTATCAATAGTTGTTACATTGTCATGATATATATCAATAGA
71297951 A
1 A
71297952 CTATGATTTA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.37
Consensus pattern (52 bp):
AAAAACTATAATTATCAATAGTTGTTACATTGTCATGATATATATCAATAGA
Found at i:71299355 original size:11 final size:10
Alignment explanation
Indices: 71299329--71299394 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 10
71299319 GATATTAGAG
*
71299329 ATATTTTGATG
1 ATATTTT-ATA
71299340 ATATTTTATA
1 ATATTTTATA
71299350 ATTATTTTATTA
1 A-TATTTTA-TA
71299362 ATATTTTAATGA
1 ATATTTT-AT-A
71299374 GATATTTTATTA
1 -ATATTTTA-TA
*
71299386 TTATTTTAT
1 ATATTTTAT
71299395 TTAGTATATA
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
10 4 0.09
11 28 0.60
12 7 0.15
13 8 0.17
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (10 bp):
ATATTTTATA
Found at i:71299395 original size:11 final size:11
Alignment explanation
Indices: 71299340--71299395 Score: 60
Period size: 11 Copynumber: 4.9 Consensus size: 11
71299330 TATTTTGATG
71299340 ATATTTTA-TA
1 ATATTTTATTA
71299350 ATTATTTTATTA
1 A-TATTTTATTA
*
71299362 ATATTTTAATGA
1 ATATTTT-ATTA
71299374 GATATTTTATTA
1 -ATATTTTATTA
*
71299386 TTATTTTATT
1 ATATTTTATT
71299396 TAGTATATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
10 1 0.03
11 22 0.56
12 9 0.23
13 7 0.18
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (11 bp):
ATATTTTATTA
Found at i:71314763 original size:40 final size:40
Alignment explanation
Indices: 71314708--71314857 Score: 212
Period size: 40 Copynumber: 3.8 Consensus size: 40
71314698 GTGTGCATGA
71314708 GCATTTGTGCGAGTTGTTATATCCGGGCTAAGACCCGAAG
1 GCATTTGTGCGAGTTGTTATATCCGGGCTAAGACCCGAAG
* *
71314748 GCATTCGTGTGAGTTGTTATATCCGGGCTAAGACCCGAAG
1 GCATTTGTGCGAGTTGTTATATCCGGGCTAAGACCCGAAG
* * *
71314788 GCATTTGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAG
1 GCATTTGTGCGAGTTGTTATATCCGGGCTAAGACCCGAAG
* ** *
71314828 GCAATTGTGCTTGTGGTTATATCC-GGCTAA
1 GCATTTGTGCGAGTTGTTATATCCGGGCTAA
71314858 ATTCCGAAGA
Statistics
Matches: 96, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
39 5 0.05
40 91 0.95
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (40 bp):
GCATTTGTGCGAGTTGTTATATCCGGGCTAAGACCCGAAG
Found at i:71319702 original size:22 final size:22
Alignment explanation
Indices: 71319677--71319719 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
71319667 GACTATGCGA
71319677 TCTGAGCTCATGAGT-TATGTGG
1 TCTGAGCTCATGA-TATATGTGG
71319699 TCTGAGCTCATGATATATGTG
1 TCTGAGCTCATGATATATGTG
71319720 ACACATGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.21, C:0.14, G:0.28, T:0.37
Consensus pattern (22 bp):
TCTGAGCTCATGATATATGTGG
Found at i:71320126 original size:2 final size:2
Alignment explanation
Indices: 71320119--71320147 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
71320109 GTGGTAAGAG
71320119 TA 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 TA T
71320148 GAAGAATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:71321924 original size:48 final size:47
Alignment explanation
Indices: 71321870--71322198 Score: 222
Period size: 49 Copynumber: 6.9 Consensus size: 47
71321860 CAGCCACATT
*
71321870 ATGAGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCATTAAG
1 ATGAGAGCCAGTGTAAGACC-TGTCTGGGACATGGCATCGGCATTAAG
* * * * * **
71321918 ACGAGAGCTAGTGTAAGACATGTATGGGACAT-GCATCGGCCTCGAG
1 ATGAGAGCCAGTGTAAGACCTGTCTGGGACATGGCATCGGCATTAAG
* * *
71321964 AT-ATGCAAGCTAGTGTAAGACCTATCTGGGACATGGCATCGGC-TTAAC
1 ATGA-G--AGCCAGTGTAAGACCTGTCTGGGACATGGCATCGGCATTAAG
* * * * * * **
71322012 AT--GTGTCAGTGTAAGACTTGTCTGGGGCATGACATCGACACCGATAG
1 ATGAGAGCCAGTGTAAGACCTGTCTGGGACATGGCATCGGCA-TTA-AG
* * * * *
71322059 ATGAGAGCCAGTGTAAGACCTGTTTGGGACATGCCATCGGCCTCGATAT
1 ATGAGAGCCAGTGTAAGACCTGTCTGGGACATGGCATCGGCAT-TA-AG
* * *
71322108 ATGAAAGTCAGTGTAAGACCTGTCTGGGACATGGCATCGAC-TT-AG
1 ATGAGAGCCAGTGTAAGACCTGTCTGGGACATGGCATCGGCATTAAG
* * * * *
71322153 ATGTGTGAGCCAATGTAAGACCATGTTTGGAACATGGCATTGGCAT
1 A--TGAGAGCCAGTGTAAGACC-TGTCTGGGACATGGCATCGGCAT
71322199 CGTACCCTAT
Statistics
Matches: 217, Mismatches: 50, Indels: 27
0.74 0.17 0.09
Matches are distributed among these distances:
44 28 0.13
45 3 0.01
46 15 0.07
47 29 0.13
48 63 0.29
49 79 0.36
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (47 bp):
ATGAGAGCCAGTGTAAGACCTGTCTGGGACATGGCATCGGCATTAAG
Found at i:71322072 original size:49 final size:49
Alignment explanation
Indices: 71321833--71322148 Score: 190
Period size: 49 Copynumber: 6.7 Consensus size: 49
71321823 GATATGTGCT
* * * * *
71321833 AGTGTAAGACATGTCTGGGTCATG-CATC-AGCCAC-AT-TATGAGAGCC
1 AGTGTAAGACCTGTCTGGGACATGACATCGA-CCTCGATAGATGAAAGCC
* * * * * * * *
71321879 AGTGTAAGACCATGTTTGGGACATGGCATCGGCAT-TA-AGACGAGAGCT
1 AGTGTAAGACC-TGTCTGGGACATGACATCGACCTCGATAGATGAAAGCC
* * * * * * *
71321927 AGTGTAAGACATGTATGGGACATG-CATCGGCCTCGAGATATGCAAGCT
1 AGTGTAAGACCTGTCTGGGACATGACATCGACCTCGATAGATGAAAGCC
* * * * * * *
71321975 AGTGTAAGACCTATCTGGGACATGGCATCG-GCT-TA-ACATG--TGTC
1 AGTGTAAGACCTGTCTGGGACATGACATCGACCTCGATAGATGAAAGCC
* * *
71322019 AGTGTAAGACTTGTCTGGGGCATGACATCGACAC-CGATAGATGAGAGCC
1 AGTGTAAGACCTGTCTGGGACATGACATCGAC-CTCGATAGATGAAAGCC
* * * * *
71322068 AGTGTAAGACCTGTTTGGGACATGCCATCGGCCTCGATATATGAAAGTC
1 AGTGTAAGACCTGTCTGGGACATGACATCGACCTCGATAGATGAAAGCC
*
71322117 AGTGTAAGACCTGTCTGGGACATGGCATCGAC
1 AGTGTAAGACCTGTCTGGGACATGACATCGAC
71322149 TTAGATGTGT
Statistics
Matches: 209, Mismatches: 46, Indels: 27
0.74 0.16 0.10
Matches are distributed among these distances:
44 27 0.13
46 24 0.11
47 29 0.14
48 54 0.26
49 75 0.36
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.24
Consensus pattern (49 bp):
AGTGTAAGACCTGTCTGGGACATGACATCGACCTCGATAGATGAAAGCC
Found at i:71322079 original size:93 final size:95
Alignment explanation
Indices: 71321830--71322198 Score: 301
Period size: 93 Copynumber: 3.9 Consensus size: 95
71321820 ATGGATATGT
* *
71321830 GCTAGTGTAAGACATGTCTGGGTCATGCATCAGCCA-C-AT-TATGAGAGCCAGTGTAAGACCAT
1 GCTAGTGTAAGACATGTCTGGGACATGCATC-GACACCGATATATGAGAGCCAGTGTAAGACC-T
*
71321892 GTTTGGGACATGGCATCGGCATTAAGACGAGA
64 GTTTGGGACATGGCATCGGCATTAACACGAGA
* * * *
71321924 GCTAGTGTAAGACATGTATGGGACATGCATCGGC-CTCGAGATATGCA-AGCTAGTGTAAGACCT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGACAC-CGATATATG-AGAGCCAGTGTAAGACCT
* * * *
71321987 ATCTGGGACATGGCATCGGC-TTAACATGTG-
64 GTTTGGGACATGGCATCGGCATTAACACGAGA
* * * *
71322017 TC-AGTGTAAGACTTGTCTGGGGCATGACATCGACACCGATAGATGAGAGCCAGTGTAAGACCTG
1 GCTAGTGTAAGACATGTCTGGGACATG-CATCGACACCGATATATGAGAGCCAGTGTAAGACCTG
* * * * * *
71322081 TTTGGGACATGCCATCGGCCTCGATATATGAAA
65 TTTGGGACATGGCATCGGCAT-TA-ACACGAGA
* ** * * * *
71322114 G-TCAGTGTAAGACCTGTCTGGGACATGGCATCG--ACTTAGATGTGTGAGCCAATGTAAGACCA
1 GCT-AGTGTAAGACATGTCTGGGACAT-GCATCGACACCGATATATGAGAGCCAGTGTAAGACC-
* *
71322176 TGTTTGGAACATGGCATTGGCAT
63 TGTTTGGGACATGGCATCGGCAT
71322199 CGTACCCTAT
Statistics
Matches: 220, Mismatches: 39, Indels: 29
0.76 0.14 0.10
Matches are distributed among these distances:
92 22 0.10
93 48 0.22
94 39 0.18
95 21 0.10
96 43 0.20
97 20 0.09
98 26 0.12
99 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (95 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGACACCGATATATGAGAGCCAGTGTAAGACCTGT
TTGGGACATGGCATCGGCATTAACACGAGA
Found at i:71338645 original size:37 final size:37
Alignment explanation
Indices: 71338575--71338668 Score: 127
Period size: 37 Copynumber: 2.6 Consensus size: 37
71338565 AGTACATAAG
* * * * *
71338575 TAATCCAACC-AAAACATGCAAAATTCTCATGAGATC
1 TAATCCAACCGATAACACGCCAAATGCTCATGAGAGC
*
71338611 TAATCCAACTGATAACACGCCAAATGCTCATGAGAGC
1 TAATCCAACCGATAACACGCCAAATGCTCATGAGAGC
71338648 TAATCCAACCGATAACACGCC
1 TAATCCAACCGATAACACGCC
71338669 TCCGCACTAA
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
36 9 0.18
37 41 0.82
ACGTcount: A:0.40, C:0.29, G:0.12, T:0.19
Consensus pattern (37 bp):
TAATCCAACCGATAACACGCCAAATGCTCATGAGAGC
Found at i:71350772 original size:51 final size:51
Alignment explanation
Indices: 71350697--71350858 Score: 234
Period size: 51 Copynumber: 3.2 Consensus size: 51
71350687 TTTTAAGAGT
*
71350697 CACACGCCTATGTGGCTTGGGACATGCCTGTGTGGGCAGGCCGTGTGGTCA
1 CACACGCCCATGTGGCTTGGGACATGCCTGTGTGGGCAGGCCGTGTGGTCA
* * *
71350748 CACATGCCCATGTGGCTTGAGACATGCCCGTGTGGGCAGGCCGTGTGGTCA
1 CACACGCCCATGTGGCTTGGGACATGCCTGTGTGGGCAGGCCGTGTGGTCA
* * * ** *
71350799 CACACGCCCATATAGCTTGGGACATGCCTGTGTGAGCAGGCTATATGGTCA
1 CACACGCCCATGTGGCTTGGGACATGCCTGTGTGGGCAGGCCGTGTGGTCA
71350850 CACACGCCC
1 CACACGCCC
71350859 GTGTCCTTAA
Statistics
Matches: 98, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 98 1.00
ACGTcount: A:0.18, C:0.28, G:0.32, T:0.22
Consensus pattern (51 bp):
CACACGCCCATGTGGCTTGGGACATGCCTGTGTGGGCAGGCCGTGTGGTCA
Found at i:71352091 original size:42 final size:43
Alignment explanation
Indices: 71352024--71352110 Score: 124
Period size: 42 Copynumber: 2.0 Consensus size: 43
71352014 TAGGATCTCG
*
71352024 TATCGATACCAATAGCCCAACTATGGTCTTACACGAAAC-CTTA
1 TATCGATACCAATAGCCCAAATATGGTCTTACACG-AACTCTTA
* *
71352067 TATCGATGCC-ATATCCCAAATATGGTCTTACACGAACTCTTA
1 TATCGATACCAATAGCCCAAATATGGTCTTACACGAACTCTTA
71352109 TA
1 TA
71352111 ATGAATCTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
41 3 0.08
42 28 0.70
43 9 0.22
ACGTcount: A:0.33, C:0.26, G:0.11, T:0.29
Consensus pattern (43 bp):
TATCGATACCAATAGCCCAAATATGGTCTTACACGAACTCTTA
Found at i:71359404 original size:3 final size:3
Alignment explanation
Indices: 71359396--71359445 Score: 77
Period size: 3 Copynumber: 17.3 Consensus size: 3
71359386 TTTATTTCTG
*
71359396 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTC TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
71359442 TTA T
1 TTA T
71359446 ATTTTCTTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 4 0.09
3 41 0.91
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:71359456 original size:16 final size:16
Alignment explanation
Indices: 71359405--71359455 Score: 68
Period size: 15 Copynumber: 3.1 Consensus size: 16
71359395 GTTATTATTA
*
71359405 TTATTATTATTATTATT
1 TTATTATTATT-TTCTT
71359422 ATTATTATTATTTTCTT
1 -TTATTATTATTTTCTT
71359439 TTATTA-TATTTTCTT
1 TTATTATTATTTTCTT
71359454 TT
1 TT
71359456 TTTCTTTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
15 11 0.34
16 6 0.19
17 4 0.12
18 11 0.34
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.73
Consensus pattern (16 bp):
TTATTATTATTTTCTT
Found at i:71359636 original size:21 final size:22
Alignment explanation
Indices: 71359612--71359655 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
71359602 GCCCTAGACT
71359612 AGCCCTA-ACCTGCAGCCAAAC
1 AGCCCTACACCTGCAGCCAAAC
71359633 AGCCCTACACCTGCAGCCAAAC
1 AGCCCTACACCTGCAGCCAAAC
71359655 A
1 A
71359656 CCACTTTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.34, C:0.43, G:0.14, T:0.09
Consensus pattern (22 bp):
AGCCCTACACCTGCAGCCAAAC
Found at i:71361512 original size:9 final size:9
Alignment explanation
Indices: 71361479--71361513 Score: 52
Period size: 9 Copynumber: 3.7 Consensus size: 9
71361469 AATTAAAAAG
71361479 AAAAAAGAA
1 AAAAAAGAA
71361488 AAAAAGGAGAA
1 AAAAA--AGAA
71361499 AAAAAAGAA
1 AAAAAAGAA
71361508 AAAAAA
1 AAAAAA
71361514 TATGTAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 15 0.62
11 9 0.38
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:71365301 original size:44 final size:44
Alignment explanation
Indices: 71365231--71365320 Score: 153
Period size: 44 Copynumber: 2.0 Consensus size: 44
71365221 GACATATGCG
71365231 TCGTCGACACAATACCGTTAGACAACTAATCTCAAATAGAATTA
1 TCGTCGACACAATACCGTTAGACAACTAATCTCAAATAGAATTA
* * *
71365275 TCGTTGACACAATACCGTTAGTCAACTAATCTCAAATAGAGTTA
1 TCGTCGACACAATACCGTTAGACAACTAATCTCAAATAGAATTA
71365319 TC
1 TC
71365321 TCTATTATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (44 bp):
TCGTCGACACAATACCGTTAGACAACTAATCTCAAATAGAATTA
Found at i:71367415 original size:20 final size:20
Alignment explanation
Indices: 71367378--71367416 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
71367368 CCTTAAATTG
**
71367378 TTTTATTTATAAGGTTATTA
1 TTTTATTTATAAACTTATTA
71367398 TTTTATTTATAAACTTATT
1 TTTTATTTATAAACTTATT
71367417 TTAATAGACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.62
Consensus pattern (20 bp):
TTTTATTTATAAACTTATTA
Found at i:71370968 original size:76 final size:77
Alignment explanation
Indices: 71370875--71371060 Score: 209
Period size: 79 Copynumber: 2.4 Consensus size: 77
71370865 AGTTTCGCTA
* * * *
71370875 CTTCAATGAAGGAAATAATGTTATTTGAGTTAAAGA-AAAAA-AAA-AGCA-AAAGAAACTTAAA
1 CTTCAGTGAAGTAAATAATGATATTTGAGTTAAA-ATAAAAATAAATA-AATAAAGAAACTTAAA
71370936 AAGTTAGCTGCACCG
64 AAGTT-GCTGCACCG
*
71370951 CTTCAGTGAAGTAAATAATGATGTTTGAGTTTTAAAATAAAAATAAATAAATAAAGAAACTTAAA
1 CTTCAGTGAAGTAAATAATGATATTTGAG--TTAAAATAAAAATAAATAAATAAAGAAACTTAAA
* *
71371016 TAGTTGCTTCACCG
64 AAGTTGCTGCACCG
* * *
71371030 CGTCAGTGAAATAAATAATGGTATTTGAGTT
1 CTTCAGTGAAGTAAATAATGATATTTGAGTT
71371061 TTACACAAAA
Statistics
Matches: 93, Mismatches: 11, Indels: 11
0.81 0.10 0.10
Matches are distributed among these distances:
76 25 0.27
77 3 0.03
78 10 0.11
79 37 0.40
80 18 0.19
ACGTcount: A:0.46, C:0.09, G:0.17, T:0.28
Consensus pattern (77 bp):
CTTCAGTGAAGTAAATAATGATATTTGAGTTAAAATAAAAATAAATAAATAAAGAAACTTAAAAA
GTTGCTGCACCG
Found at i:71372696 original size:45 final size:45
Alignment explanation
Indices: 71372646--71372735 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
71372636 CCTCATGGCA
71372646 ACATTAAAGTGATTGATGATGCAATAATTGTTTATTCTCCAATTT
1 ACATTAAAGTGATTGATGATGCAATAATTGTTTATTCTCCAATTT
*
71372691 ACATTAAAGTGATTGATGATGCAATAGTTGTTTATTCTCCAATTT
1 ACATTAAAGTGATTGATGATGCAATAATTGTTTATTCTCCAATTT
71372736 TTCTTCTCTA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.42
Consensus pattern (45 bp):
ACATTAAAGTGATTGATGATGCAATAATTGTTTATTCTCCAATTT
Found at i:71376525 original size:24 final size:24
Alignment explanation
Indices: 71376498--71376547 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
71376488 TATTTCTGAA
71376498 TTTCTTTTTGCTCCTGAAGATGTG
1 TTTCTTTTTGCTCCTGAAGATGTG
71376522 TTTCTTTTTGCTCCTGAAGATGTG
1 TTTCTTTTTGCTCCTGAAGATGTG
71376546 TT
1 TT
71376548 AACCTAACCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.12, C:0.16, G:0.20, T:0.52
Consensus pattern (24 bp):
TTTCTTTTTGCTCCTGAAGATGTG
Found at i:71378912 original size:18 final size:17
Alignment explanation
Indices: 71378885--71378918 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
71378875 TTCAATTGAT
71378885 AATGAAACCATTAAGTC
1 AATGAAACCATTAAGTC
71378902 AATGTAAACCATTAAGT
1 AATG-AAACCATTAAGT
71378919 TAATCTATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.26
Consensus pattern (17 bp):
AATGAAACCATTAAGTC
Found at i:71383136 original size:92 final size:88
Alignment explanation
Indices: 71383029--71383225 Score: 263
Period size: 92 Copynumber: 2.2 Consensus size: 88
71383019 TTAAGTGTGT
* * * *
71383029 AAAAAACCCTCAAACTTTTTGAAAAAAAGTAATTAAG-CCATTGCTTTTTTTTTTGGCACTCAAT
1 AAAAAACCCTCAAACTTTTTCAAAAAAAGAAATTAAGTCC-CTGC--CTTTTTTT-GCACTCAAT
*
71383093 T-GGATACTTGAACTTTCAAAATGCATCA
62 TAGG-TACTTGAACTATCAAAATGCAT-A
*
71383121 AAAAAACCCTTAAACTTTTTCAAAAAAAGAAATTAAGTCCCTGCCTTTTTTTGCACTCAATTAGG
1 AAAAAACCCTCAAACTTTTTCAAAAAAAGAAATTAAGTCCCTGCCTTTTTTTGCACTCAATTAGG
71383186 TACTTGAACTATCAAAATGCATA
66 TACTTGAACTATCAAAATGCATA
*
71383209 AAAAAGCCCTCAAACTT
1 AAAAAACCCTCAAACTT
71383226 AAAAAAAAAA
Statistics
Matches: 95, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
88 16 0.17
89 31 0.33
90 9 0.09
92 37 0.39
93 2 0.02
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (88 bp):
AAAAAACCCTCAAACTTTTTCAAAAAAAGAAATTAAGTCCCTGCCTTTTTTTGCACTCAATTAGG
TACTTGAACTATCAAAATGCATA
Found at i:71383235 original size:89 final size:87
Alignment explanation
Indices: 71383076--71383305 Score: 257
Period size: 87 Copynumber: 2.6 Consensus size: 87
71383066 CCATTGCTTT
* * * **
71383076 TTTTTTTGGCACTCAATTGGATACTTGAACTTTCAAAATGCATCAAAAAAACCCTTAAACTTTTT
1 TTTTTTT-GCACTCAATTGG-TACTTGAACTATCAAAATGCATCAAAAAAGCCCTCAAAC-TTAA
* * **
71383141 CAAAAAAAGAAATTAAGTCCCTGCC
63 AAAAAAAAGAAATTAAGCCCCTAAC
71383166 TTTTTTTGCACTCAATTAGGTACTTGAACTATCAAAATGCAT-AAAAAAGCCCTCAAACTTAAAA
1 TTTTTTTGCACTCAATT-GGTACTTGAACTATCAAAATGCATCAAAAAAGCCCTCAAACTTAAAA
* *
71383230 AAAAAAGCAATTAAGCCCCTAAT
65 AAAAAAGAAATTAAGCCCCTAAC
* * * * *
71383253 TTTTTTTCCACTCTATTGAGTACTTGAATTGTC-AAATACATCAAAAAAGCCCT
1 TTTTTTTGCACTCAATTG-GTACTTGAACTATCAAAATGCATCAAAAAAGCCCT
71383306 TTGATTGTTA
Statistics
Matches: 121, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
86 8 0.07
87 59 0.49
88 14 0.12
89 31 0.26
90 9 0.07
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.32
Consensus pattern (87 bp):
TTTTTTTGCACTCAATTGGTACTTGAACTATCAAAATGCATCAAAAAAGCCCTCAAACTTAAAAA
AAAAAGAAATTAAGCCCCTAAC
Found at i:71383429 original size:10 final size:9
Alignment explanation
Indices: 71383416--71383546 Score: 59
Period size: 10 Copynumber: 13.8 Consensus size: 9
71383406 AATATTAAAA
71383416 ATAAAAATCT
1 ATAAAAAT-T
*
71383426 ATAAAAGTT
1 ATAAAAATT
*
71383435 ATAAAATTT
1 ATAAAAATT
**
71383444 ATTAAATTTT
1 A-TAAAAATT
71383454 AATAAAAA-T
1 -ATAAAAATT
71383463 ATAAAAATAT
1 ATAAAAAT-T
* **
71383473 TTAAATTTT
1 ATAAAAATT
71383482 ACTAAAAATT
1 A-TAAAAATT
* *
71383492 AGAAATAAAT
1 ATAAA-AATT
71383502 ATAAAAATCGT
1 ATAAAAAT--T
*
71383513 AAAAAAATT
1 ATAAAAATT
71383522 ATAAAAAATT
1 AT-AAAAATT
*
71383532 GT-AAAATT
1 ATAAAAATT
*
71383540 TTAAAAA
1 ATAAAAA
71383547 AAAAATCATA
Statistics
Matches: 92, Mismatches: 19, Indels: 21
0.70 0.14 0.16
Matches are distributed among these distances:
8 14 0.15
9 23 0.25
10 46 0.50
11 9 0.10
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.34
Consensus pattern (9 bp):
ATAAAAATT
Found at i:71383476 original size:28 final size:27
Alignment explanation
Indices: 71383426--71383498 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 27
71383416 ATAAAAATCT
* *
71383426 ATAAAAGTTATAAAATTTATTAAATTTTA
1 ATAAAAATTA-AAAATAT-TTAAATTTTA
71383455 ATAAAAATATAAAAATATTTAAATTTTA
1 ATAAAAAT-TAAAAATATTTAAATTTTA
* *
71383483 CTAAAAATTAGAAATA
1 ATAAAAATTAAAAATA
71383499 AATATAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
27 7 0.18
28 17 0.44
29 13 0.33
30 2 0.05
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (27 bp):
ATAAAAATTAAAAATATTTAAATTTTA
Found at i:71383746 original size:9 final size:9
Alignment explanation
Indices: 71383732--71383867 Score: 60
Period size: 9 Copynumber: 14.2 Consensus size: 9
71383722 TTTTGGTACA
71383732 ATAATTTTT
1 ATAATTTTT
71383741 ATAATTTTTTTT
1 ATAA---TTTTT
*
71383753 ATAAATTTT
1 ATAATTTTT
*
71383762 ATATTTCTTT
1 ATAATT-TTT
* *
71383772 ACATTTTTT
1 ATAATTTTT
71383781 ATAATTTTT
1 ATAATTTTT
* *
71383790 CCTATATTTCT
1 -ATA-ATTTTT
71383801 AT-ATGTTTT
1 ATAAT-TTTT
71383810 ATATATTTTT
1 ATA-ATTTTT
**
71383820 ATAAAATTT
1 ATAATTTTT
*
71383829 ACAATTTTT
1 ATAATTTTT
*
71383838 AGTATTTTATT
1 A-TAATTT-TT
* *
71383849 A-AAATTTA
1 ATAATTTTT
71383857 ATAATTTTT
1 ATAATTTTT
71383866 AT
1 AT
71383868 TGATTATTTT
Statistics
Matches: 93, Mismatches: 22, Indels: 24
0.67 0.16 0.17
Matches are distributed among these distances:
8 4 0.04
9 48 0.52
10 22 0.24
11 10 0.11
12 9 0.10
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.62
Consensus pattern (9 bp):
ATAATTTTT
Found at i:71383772 original size:10 final size:9
Alignment explanation
Indices: 71383747--71383822 Score: 55
Period size: 10 Copynumber: 8.0 Consensus size: 9
71383737 TTTTATAATT
71383747 TTTTTTATA
1 TTTTTTATA
**
71383756 AATTTTATA
1 TTTTTTATA
*
71383765 TTTCTTTACA
1 TTT-TTTATA
71383775 TTTTTTATAA
1 TTTTTTAT-A
71383785 TTTTTCCTATA
1 TTTTT--TATA
*
71383796 -TTTCTATA
1 TTTTTTATA
*
71383804 TGTTTTATA
1 TTTTTTATA
71383813 TATTTTTATA
1 T-TTTTTATA
71383823 AAATTTACAA
Statistics
Matches: 51, Mismatches: 10, Indels: 11
0.71 0.14 0.15
Matches are distributed among these distances:
8 4 0.08
9 19 0.37
10 24 0.47
11 1 0.02
12 3 0.06
ACGTcount: A:0.26, C:0.07, G:0.01, T:0.66
Consensus pattern (9 bp):
TTTTTTATA
Found at i:71387218 original size:44 final size:44
Alignment explanation
Indices: 71387155--71387240 Score: 145
Period size: 44 Copynumber: 2.0 Consensus size: 44
71387145 CCAAAACATG
**
71387155 TGTCACATATATCATGAACTCAGGCCACAACTCATGAGTTCAAA
1 TGTCACATATATCATGAACTCAAACCACAACTCATGAGTTCAAA
*
71387199 TGTCACATATATCATGAACTCAAACCACTACTCATGAGTTCA
1 TGTCACATATATCATGAACTCAAACCACAACTCATGAGTTCA
71387241 GATCACATAG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.36, C:0.26, G:0.12, T:0.27
Consensus pattern (44 bp):
TGTCACATATATCATGAACTCAAACCACAACTCATGAGTTCAAA
Found at i:71387221 original size:24 final size:24
Alignment explanation
Indices: 71387155--71387222 Score: 63
Period size: 22 Copynumber: 3.0 Consensus size: 24
71387145 CCAAAACATG
71387155 TGTCACATATATCATGAACTC--A
1 TGTCACATATATCATGAACTCAAA
* * * **
71387177 GGCCACA-A-CTCATGAGTTCAAA
1 TGTCACATATATCATGAACTCAAA
71387199 TGTCACATATATCATGAACTCAAA
1 TGTCACATATATCATGAACTCAAA
71387223 CCACTACTCA
Statistics
Matches: 32, Mismatches: 10, Indels: 6
0.67 0.21 0.12
Matches are distributed among these distances:
20 8 0.25
21 1 0.03
22 11 0.34
23 1 0.03
24 11 0.34
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.26
Consensus pattern (24 bp):
TGTCACATATATCATGAACTCAAA
Found at i:71388852 original size:43 final size:43
Alignment explanation
Indices: 71388688--71388859 Score: 147
Period size: 43 Copynumber: 4.0 Consensus size: 43
71388678 CATAGGATTC
* * *
71388688 CGATATATGATTTCATGTAGGACCTTGTCTGGGAC-GTTGGCAT
1 CGATATATGATTACATGTAAGACCTCGTCTGGGACAG-TGGCAT
* * * *
71388731 CGATTTGA-GATTTACGTGTAAGACCAT-GTCTGAGACATTGGCAT
1 CGATAT-ATGA-TTACATGTAAGACC-TCGTCTGGGACAGTGGCAT
* * *
71388775 C-ATATATGATTTCGTGTAAGGCC-CTGTCTGGGACAGTGGCAT
1 CGATATATGATTACATGTAAGACCTC-GTCTGGGACAGTGGCAT
* * *
71388817 CGATATTTGATTACATGTAAGACCTCGTCTAGGACATTGGCAT
1 CGATATATGATTACATGTAAGACCTCGTCTGGGACAGTGGCAT
71388860 TGTACGAGCT
Statistics
Matches: 103, Mismatches: 17, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
42 29 0.28
43 45 0.44
44 28 0.27
45 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (43 bp):
CGATATATGATTACATGTAAGACCTCGTCTGGGACAGTGGCAT
Found at i:71390426 original size:30 final size:30
Alignment explanation
Indices: 71390392--71390479 Score: 106
Period size: 30 Copynumber: 2.9 Consensus size: 30
71390382 CTAGCTTATA
71390392 TTCAGCTCACGAGCTAAACCTTAGCTCAAC
1 TTCAGCTCACGAGCTAAACCTTAGCTCAAC
* * * *
71390422 TTCAGCTTAGGAG-TATAATCTCAGCTCAAC
1 TTCAGCTCACGAGCTA-AACCTTAGCTCAAC
* *
71390452 TTTAGCTCACGAGCTAAAGCTTAGCTCA
1 TTCAGCTCACGAGCTAAACCTTAGCTCA
71390480 TTTTAGTTTA
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
29 2 0.04
30 43 0.91
31 2 0.04
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (30 bp):
TTCAGCTCACGAGCTAAACCTTAGCTCAAC
Found at i:71390895 original size:13 final size:13
Alignment explanation
Indices: 71390877--71390901 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
71390867 GTATTGATCA
71390877 TGTGTTCACACCT
1 TGTGTTCACACCT
71390890 TGTGTTCACACC
1 TGTGTTCACACC
71390902 ATGATGACCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTGTTCACACCT
Found at i:71411571 original size:30 final size:31
Alignment explanation
Indices: 71411521--71411581 Score: 115
Period size: 30 Copynumber: 2.0 Consensus size: 31
71411511 CAGGTTGAGG
71411521 AATTGGGGGAGGTGGGGGAGGTCGTACATTT
1 AATTGGGGGAGGTGGGGGAGGTCGTACATTT
71411552 AATTGGGGGAGGT-GGGGAGGTCGTACATTT
1 AATTGGGGGAGGTGGGGGAGGTCGTACATTT
71411582 GGGTTCGTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 17 0.57
31 13 0.43
ACGTcount: A:0.20, C:0.07, G:0.48, T:0.26
Consensus pattern (31 bp):
AATTGGGGGAGGTGGGGGAGGTCGTACATTT
Done.