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 216 of 438
Found at i:66852788 original size:16 final size:15
Alignment explanation
Indices: 66852769--66852820 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
66852759 TTTCAGATTT
66852769 TTTTTTTCTTTTCGAA
1 TTTTTTT-TTTTCGAA
66852785 -TTTTTTTTTT-GAA
1 TTTTTTTTTTTCGAA
*
66852798 TTGTTTTTTTTCCGAA
1 TT-TTTTTTTTTCGAA
66852814 TTTTTTT
1 TTTTTTT
66852821 GACTTGTATA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
13 3 0.09
14 5 0.16
15 19 0.59
16 5 0.16
ACGTcount: A:0.12, C:0.08, G:0.08, T:0.73
Consensus pattern (15 bp):
TTTTTTTTTTTCGAA
Found at i:66852788 original size:18 final size:18
Alignment explanation
Indices: 66852753--66852794 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
66852743 CATTAAACAC
*
66852753 TTTTTTTTTCAGATTTTT
1 TTTTTTTTTCAGAATTTT
66852771 TTTTTCTTTTC-GAATTTT
1 TTTTT-TTTTCAGAATTTT
66852789 TTTTTT
1 TTTTTT
66852795 GAATTGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 16 0.73
19 5 0.23
ACGTcount: A:0.10, C:0.07, G:0.05, T:0.79
Consensus pattern (18 bp):
TTTTTTTTTCAGAATTTT
Found at i:66854860 original size:26 final size:27
Alignment explanation
Indices: 66854815--66854883 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 27
66854805 TGCTCGTATC
**
66854815 AGGGTAAAATGACAAAAATA-CCATAT
1 AGGGTAAAATGACTGAAATACCCATAT
* * *
66854841 AGGGTAAAATGACTGTAATACCCCTGT
1 AGGGTAAAATGACTGAAATACCCATAT
*
66854868 AAGGTAAAATGACTGA
1 AGGGTAAAATGACTGA
66854884 TTTGCTCTAT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
26 17 0.49
27 18 0.51
ACGTcount: A:0.45, C:0.13, G:0.20, T:0.22
Consensus pattern (27 bp):
AGGGTAAAATGACTGAAATACCCATAT
Found at i:66855334 original size:34 final size:32
Alignment explanation
Indices: 66855288--66855375 Score: 104
Period size: 34 Copynumber: 2.7 Consensus size: 32
66855278 CTGATTACTA
* * *
66855288 TTACTGAAATGGGCTAAGGCCCAGATTGCCACTG
1 TTACTG-AATGGGCTAAGGCCC-CACTGACACTG
* *
66855322 TTACTGATATGGGCTTAGGCCCCACTGATACTG
1 TTACTGA-ATGGGCTAAGGCCCCACTGACACTG
66855355 TTACTGAATGGGCTAAGGCCC
1 TTACTGAATGGGCTAAGGCCC
66855376 TAACTGAAAC
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
32 13 0.28
33 15 0.32
34 19 0.40
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (32 bp):
TTACTGAATGGGCTAAGGCCCCACTGACACTG
Found at i:66855382 original size:33 final size:32
Alignment explanation
Indices: 66855277--66855387 Score: 114
Period size: 33 Copynumber: 3.3 Consensus size: 32
66855267 TGGTTACTGC
*
66855277 ACTGATTACTATTACTGAAATGGGCTAAGGCCCA
1 ACTGA-TACTGTTACTG-AATGGGCTAAGGCCCA
* ** * *
66855311 GATTGCCACTGTTACTGATATGGGCTTAGGCCCC
1 -ACTGATACTGTTACTGA-ATGGGCTAAGGCCCA
66855345 ACTGATACTGTTACTGAATGGGCTAAGGCCCTA
1 ACTGATACTGTTACTGAATGGGCTAAGGCCC-A
*
66855378 ACTGAAACTG
1 ACTGATACTG
66855388 AAAGGGCTTA
Statistics
Matches: 62, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
32 13 0.21
33 24 0.39
34 22 0.35
35 3 0.05
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (32 bp):
ACTGATACTGTTACTGAATGGGCTAAGGCCCA
Found at i:66859492 original size:49 final size:49
Alignment explanation
Indices: 66859410--66859667 Score: 432
Period size: 49 Copynumber: 5.3 Consensus size: 49
66859400 CTCTTCGGGA
* *
66859410 CTTATCACAT-T-TATACACTTTCACATTCATCACATTGGCCATTCA-GC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATT-AGGC
* *
66859457 CCTATCACATATATACACACCTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
* *
66859506 CTTATCACATATATACACACTTTCACATTCATCACAACGGTCATTAGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
66859555 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
66859604 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
66859653 CTTATCACATATATA
1 CTTATCACATATATA
66859668 TATCTCATAC
Statistics
Matches: 198, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
47 9 0.05
48 2 0.01
49 187 0.94
ACGTcount: A:0.31, C:0.30, G:0.07, T:0.31
Consensus pattern (49 bp):
CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:66863174 original size:27 final size:27
Alignment explanation
Indices: 66863137--66863235 Score: 137
Period size: 27 Copynumber: 3.7 Consensus size: 27
66863127 CAAATTAATT
*
66863137 AAATGATTGTTTTGCCCTTATGTGGTA
1 AAATGACTGTTTTGCCCTTATGTGGTA
*
66863164 AAATGACTGTTTTGCCCTTATATGGTA
1 AAATGACTGTTTTGCCCTTATGTGGTA
* *
66863191 AAATGA-TAGTTTTGCCCTTTTGAGGTA
1 AAATGACT-GTTTTGCCCTTATGTGGTA
*
66863218 AAATAACTGTTTTGCCCT
1 AAATGACTGTTTTGCCCT
66863236 ATGCGATGTA
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
26 1 0.02
27 62 0.97
28 1 0.02
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.41
Consensus pattern (27 bp):
AAATGACTGTTTTGCCCTTATGTGGTA
Found at i:66877021 original size:45 final size:45
Alignment explanation
Indices: 66876957--66877130 Score: 217
Period size: 45 Copynumber: 3.8 Consensus size: 45
66876947 TGTAACCCGC
*
66876957 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGCATTCGCAT
*
66877002 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG-ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGCATTCGC-A--T
* *** *
66877048 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGG-CATTCGCAT
*
66877095 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
66877131 ATGCCCAAAT
Statistics
Matches: 110, Mismatches: 12, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 36 0.33
46 33 0.30
47 32 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGCATTCGCAT
Found at i:66877123 original size:93 final size:92
Alignment explanation
Indices: 66876965--66877135 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 92
66876955 GCCCATAAGT
*
66876965 GAACTCGGACTCAACTCAACGAGCTCGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
66877030 GAGCTCGGATGCCTAGTTACATCTCTC
66 GAGCTCGGATGCCTAGTTACATCTCTC
*
66877057 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGG-CATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
66877122 CGAGTTCGGATGCC
65 CGAGCTCGGATGCC
66877136 CAAATATCCT
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
92 27 0.36
93 48 0.64
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.21
Consensus pattern (92 bp):
GAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
GAGCTCGGATGCCTAGTTACATCTCTC
Found at i:66877150 original size:46 final size:44
Alignment explanation
Indices: 66876962--66877150 Score: 129
Period size: 46 Copynumber: 4.1 Consensus size: 44
66876952 CCCGCCCATA
* * * *
66876962 AGTGAACTCGGACTCAACTCAACGAGCTCGGCGTTCGC--ATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGG-ATGCCCAAATCC-T
* *
66877006 AAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA---A-ATC-CT
* * *
66877056 --CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGC--ATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCCCAAATCC-T
66877099 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATATCCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCC-AA-ATCCT
66877146 AGTGA
1 AGTGA
66877151 CATGTCACTT
Statistics
Matches: 115, Mismatches: 12, Indels: 33
0.72 0.08 0.21
Matches are distributed among these distances:
42 1 0.01
43 4 0.03
44 6 0.05
45 31 0.27
46 33 0.29
47 28 0.24
48 4 0.03
49 3 0.03
50 4 0.03
51 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (44 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATCCT
Found at i:66885337 original size:38 final size:40
Alignment explanation
Indices: 66885286--66885394 Score: 143
Period size: 38 Copynumber: 2.8 Consensus size: 40
66885276 CTGGAAATTA
* *
66885286 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAG-T-GGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTTAGGC
**
66885324 TATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTATTC
1 TATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGTTAGGC
*
66885364 TATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC
66885395 ACGTGATTAT
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
37 3 0.05
38 28 0.45
39 1 0.02
40 28 0.45
41 2 0.03
ACGTcount: A:0.23, C:0.24, G:0.29, T:0.24
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTTAGGC
Found at i:66885408 original size:40 final size:40
Alignment explanation
Indices: 66885246--66885410 Score: 162
Period size: 40 Copynumber: 4.2 Consensus size: 40
66885236 AAATTGAATG
* * **
66885246 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTG-GAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC-GAGTGATT
* * *
66885285 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTG--G
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGATT
* *
66885323 CTATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGTGATT
* *
66885363 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGA-GTGATT
66885403 ATATCCGG
1 ATATCCGG
66885411 TTATATTCCG
Statistics
Matches: 104, Mismatches: 15, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
37 3 0.03
38 29 0.28
39 14 0.13
40 56 0.54
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGATT
Found at i:66891590 original size:46 final size:46
Alignment explanation
Indices: 66891540--66891712 Score: 208
Period size: 46 Copynumber: 3.7 Consensus size: 46
66891530 TGGTTGAGCA
*
66891540 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
66891586 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
66891633 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
66891679 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
66891713 GGGGGGGTTA
Statistics
Matches: 107, Mismatches: 13, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 61 0.57
47 29 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:66891696 original size:93 final size:93
Alignment explanation
Indices: 66891537--66891707 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
66891527 GGATGGTTGA
* *
66891537 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
66891602 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
66891630 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
66891695 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
66891708 ACTTAGGGGG
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:66891972 original size:19 final size:20
Alignment explanation
Indices: 66891935--66891972 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
66891925 ATAAGGTGGT
66891935 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
66891955 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
66891973 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:66896784 original size:28 final size:27
Alignment explanation
Indices: 66896744--66896814 Score: 88
Period size: 28 Copynumber: 2.6 Consensus size: 27
66896734 TCTTTCATAT
* **
66896744 GGCCCATTCACATTTATGTGGCCATTA
1 GGCCCAATCACATTTATACGGCCATTA
* *
66896771 GGCCCAAATCACATTCATACGGCCATTT
1 GGCCC-AATCACATTTATACGGCCATTA
66896799 GGCCCAATCACATTTA
1 GGCCCAATCACATTTA
66896815 CAGTCATGCT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
27 15 0.41
28 22 0.59
ACGTcount: A:0.27, C:0.30, G:0.15, T:0.28
Consensus pattern (27 bp):
GGCCCAATCACATTTATACGGCCATTA
Found at i:66897070 original size:16 final size:16
Alignment explanation
Indices: 66897033--66897072 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
66897023 CCAAACTTTT
66897033 GGCTTTTCGACATTTC
1 GGCTTTTCGACATTTC
** *
66897049 AACTTTTCGGCATTTC
1 GGCTTTTCGACATTTC
66897065 GGCTTTTC
1 GGCTTTTC
66897073 AGGATCTGCC
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.45
Consensus pattern (16 bp):
GGCTTTTCGACATTTC
Found at i:66901326 original size:28 final size:27
Alignment explanation
Indices: 66901297--66901396 Score: 112
Period size: 28 Copynumber: 3.6 Consensus size: 27
66901287 TGTATATAGC
*
66901297 CCATTAGGCCCAATCTCTTTCATATGG
1 CCATTAGGCCCAATCACTTTCATATGG
* *
66901324 CCCGTTAGGCCCAATCACATTT-ATGTGG
1 -CCATTAGGCCCAATCAC-TTTCATATGG
*
66901352 CCATTAGGCCCAAATCACATTCATATGG
1 CCATTAGGCCC-AATCACTTTCATATGG
* *
66901380 CCATTTGGCCTAATCAC
1 CCATTAGGCCCAATCAC
66901397 ATTTACAGTC
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
27 18 0.30
28 40 0.66
29 3 0.05
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.29
Consensus pattern (27 bp):
CCATTAGGCCCAATCACTTTCATATGG
Found at i:66901358 original size:55 final size:55
Alignment explanation
Indices: 66901297--66901401 Score: 149
Period size: 55 Copynumber: 1.9 Consensus size: 55
66901287 TGTATATAGC
* * *
66901297 CCATTAGGCCC-AATCTCTTTCATATGGCCCGTTAGGCCCAATCACATTTATGTGG
1 CCATTAGGCCCAAATCACATTCATATGG-CCATTAGGCCCAATCACATTTATGTGG
* *
66901352 CCATTAGGCCCAAATCACATTCATATGGCCATTTGGCCTAATCACATTTA
1 CCATTAGGCCCAAATCACATTCATATGGCCATTAGGCCCAATCACATTTA
66901402 CAGTCATGCT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
55 30 0.68
56 14 0.32
ACGTcount: A:0.26, C:0.29, G:0.15, T:0.30
Consensus pattern (55 bp):
CCATTAGGCCCAAATCACATTCATATGGCCATTAGGCCCAATCACATTTATGTGG
Found at i:66901496 original size:18 final size:19
Alignment explanation
Indices: 66901473--66901509 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
66901463 GAGGCCCAAC
66901473 AGCCCA-TCGGGCCCATTT
1 AGCCCATTCGGGCCCATTT
*
66901491 AGCCCATTCTGGCCCATTT
1 AGCCCATTCGGGCCCATTT
66901510 GGTCAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.16, C:0.38, G:0.19, T:0.27
Consensus pattern (19 bp):
AGCCCATTCGGGCCCATTT
Found at i:66901637 original size:16 final size:16
Alignment explanation
Indices: 66901616--66901659 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
66901606 GTAGCTAAAC
66901616 TTTCGACTTTTCGGCA
1 TTTCGACTTTTCGGCA
*
66901632 TTTCGACTTTTTGGCA
1 TTTCGACTTTTCGGCA
*
66901648 TTTCAACTTTTC
1 TTTCGACTTTTC
66901660 AAGATCTGTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.14, C:0.23, G:0.14, T:0.50
Consensus pattern (16 bp):
TTTCGACTTTTCGGCA
Found at i:66916205 original size:40 final size:40
Alignment explanation
Indices: 66916146--66916290 Score: 120
Period size: 40 Copynumber: 3.6 Consensus size: 40
66916136 TGACGATAAA
* * * *
66916146 TCGGCTATTTGTGGTACTTAGTGTACGAT-TT-GACATAGCT
1 TCGGCTATATATGGCACTTAGTGT--GATATTCGACATAACT
*
66916186 TCGGCTATATATGGCACTTAATGTGATATTCGACATAACT
1 TCGGCTATATATGGCACTTAGTGTGATATTCGACATAACT
*
66916226 TCAGG-TATATATGGCACTTAGTGTGCA-ATTCGAGATATA-T
1 TC-GGCTATATATGGCACTTAGTGTG-ATATTCGACATA-ACT
* * * *
66916266 TCAGCTATGTACGACACTTAGTGTG
1 TCGGCTATATATGGCACTTAGTGTG
66916291 CGTGTCATTG
Statistics
Matches: 88, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
38 3 0.03
39 3 0.03
40 78 0.89
41 4 0.05
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (40 bp):
TCGGCTATATATGGCACTTAGTGTGATATTCGACATAACT
Found at i:66918232 original size:24 final size:26
Alignment explanation
Indices: 66918188--66918236 Score: 75
Period size: 24 Copynumber: 1.9 Consensus size: 26
66918178 CGAGGTAAGT
66918188 TCGTATGTTAAATAAGCTTTAATATAA
1 TCGTATGTTAAAT-AGCTTTAATATAA
66918215 TCGTAT-TTAAAT-GCTTTAATAT
1 TCGTATGTTAAATAGCTTTAATAT
66918237 TGCATGAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 10 0.45
26 6 0.27
27 6 0.27
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.45
Consensus pattern (26 bp):
TCGTATGTTAAATAGCTTTAATATAA
Found at i:66919525 original size:14 final size:14
Alignment explanation
Indices: 66919506--66919535 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
66919496 GTTTCAGCTC
66919506 ATAAATATGTGTTA
1 ATAAATATGTGTTA
*
66919520 ATAAATATGTTTTA
1 ATAAATATGTGTTA
66919534 AT
1 AT
66919536 CTGATTCTAA
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:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (14 bp):
ATAAATATGTGTTA
Found at i:66922826 original size:30 final size:30
Alignment explanation
Indices: 66922741--66922837 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
66922731 TAAACTAAAA
* *
66922741 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
** * * * * *
66922771 TGAGCTGGGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
66922801 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
66922830 ATGAGCTA
1 -TGAGCTA
66922838 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
29 1 0.02
30 49 0.98
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Found at i:66923117 original size:46 final size:47
Alignment explanation
Indices: 66923049--66923171 Score: 160
Period size: 46 Copynumber: 2.6 Consensus size: 47
66923039 CAAGATATTT
* *
66923049 AAGCCAGTGTAAGACATGTCTGGGACATGCATCGACATT-GATACA-
1 AAGCTAGTGTAAGACATATCTGGGACATGCATCGACATTCGATACAC
* * *
66923094 AGAGCTAGTGTAAGACATATCTGGGACATGCATCGGCCTTGCGATATAC
1 A-AGCTAGTGTAAGACATATCTGGGACATGCATCGACATT-CGATACAC
*
66923143 AAGCTAGTGTAAGACCTATCTGGGACATG
1 AAGCTAGTGTAAGACATATCTGGGACATG
66923172 GCGTCAGCTT
Statistics
Matches: 68, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
45 1 0.01
46 34 0.50
48 32 0.47
49 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.24
Consensus pattern (47 bp):
AAGCTAGTGTAAGACATATCTGGGACATGCATCGACATTCGATACAC
Found at i:66923163 original size:48 final size:45
Alignment explanation
Indices: 66923007--66923171 Score: 168
Period size: 48 Copynumber: 3.5 Consensus size: 45
66922997 TCGTATCACG
* * * * * *
66923007 GTGTAAGACATGTTTGGGACATGCATCAGCCTCAAGATATTTAAGCCA
1 GTGTAAGACATATCTGGGACATGCATCGGCCT--TGATA-TAAAGCTA
* * * *
66923055 GTGTAAGACATGTCTGGGACATGCATCGACATTGATACAAGAGCTA
1 GTGTAAGACATATCTGGGACATGCATCGGCCTTGATATAA-AGCTA
66923101 GTGTAAGACATATCTGGGACATGCATCGGCCTTGCGATATACAAGCTA
1 GTGTAAGACATATCTGGGACATGCATCGGCCTT--GATATA-AAGCTA
*
66923149 GTGTAAGACCTATCTGGGACATG
1 GTGTAAGACATATCTGGGACATG
66923172 GCGTCAGCTT
Statistics
Matches: 100, Mismatches: 13, Indels: 8
0.83 0.11 0.07
Matches are distributed among these distances:
45 1 0.01
46 38 0.38
48 60 0.60
49 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.25
Consensus pattern (45 bp):
GTGTAAGACATATCTGGGACATGCATCGGCCTTGATATAAAGCTA
Found at i:66923258 original size:49 final size:50
Alignment explanation
Indices: 66923191--66923323 Score: 153
Period size: 49 Copynumber: 2.7 Consensus size: 50
66923181 TGTGGTGTGT
* * *
66923191 CAGTGTAAGACCTATCTGGTACATGGCATCAACAC-CGATAGATGAGAGC
1 CAGTGTAAGACCTGTCTGGGACATGGCATCAACACTCGATAGATGAAAGC
*** * *
66923240 CAGTGTAAGACCTGTCTGGGACATGGCATTGGC-CTCGCTATATGAAAGC
1 CAGTGTAAGACCTGTCTGGGACATGGCATCAACACTCGATAGATGAAAGC
* *
66923289 TAGTGTAAGACCATGTCCGGGACATGGCATCAACA
1 CAGTGTAAGACC-TGTCTGGGACATGGCATCAACA
66923324 TCTTAACCCA
Statistics
Matches: 68, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
48 1 0.01
49 50 0.74
50 17 0.25
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.22
Consensus pattern (50 bp):
CAGTGTAAGACCTGTCTGGGACATGGCATCAACACTCGATAGATGAAAGC
Found at i:66926904 original size:44 final size:42
Alignment explanation
Indices: 66926751--66926907 Score: 140
Period size: 43 Copynumber: 3.7 Consensus size: 42
66926741 AGCTCATACA
* * * *
66926751 ATGCCAACGTCCTAGATGTGGTCTTACATGT-AATCAAATATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACACGTAAATC-AA-ATCG
** *
66926794 ATGCCTCTGTCCCAGACAG-GGTCTTACAC-AAAATCAAATACG
1 ATGCCAATGTCCCAGAC-GTGGTCTTACACGTAAATCAAAT-CG
* * *
66926836 ATGCCAATGTCCTAGACATAGTCTTACACGTAAATCATAAGTCG
1 ATGCCAATGTCCCAGACGTGGTCTTACACGTAAATCA-AA-TCG
*
66926880 ATGCCAATGTCCCGGACGTGGTCTTACA
1 ATGCCAATGTCCCAGACGTGGTCTTACA
66926908 AGATAACACA
Statistics
Matches: 90, Mismatches: 17, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
41 2 0.02
42 27 0.30
43 31 0.34
44 29 0.32
45 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACGTGGTCTTACACGTAAATCAAATCG
Found at i:66930299 original size:40 final size:40
Alignment explanation
Indices: 66930240--66930408 Score: 173
Period size: 40 Copynumber: 4.2 Consensus size: 40
66930230 CGGGACTTTA
* * *
66930240 CCCGGATATCACGATTTGCACAAATGCCTTCGGGTCTTAG
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* *
66930280 CCCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAG
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* * * * *
66930320 CCCGGATATAGCTACTAGCACAATTGCCTTCGGGTCTTAA
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* * *
66930360 CCCGGATAT-A-AA-TTTCAGCATAATTGTCTTCGGGGCTTAG
1 CCCGGATATAACAACTTGCA-CA-AA-TGCCTTCGGGTCTTAG
66930400 CCCGGATAT
1 CCCGGATAT
66930409 CATTCAATTT
Statistics
Matches: 106, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
37 3 0.03
38 3 0.03
39 1 0.01
40 99 0.93
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (40 bp):
CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
Found at i:66938314 original size:40 final size:40
Alignment explanation
Indices: 66938255--66938423 Score: 173
Period size: 40 Copynumber: 4.2 Consensus size: 40
66938245 CGGGACTTTA
* * *
66938255 CCCGGATATCACGATTTGCACAAATGCCTTCGGGTCTTAG
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* *
66938295 CCCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAG
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* * * * *
66938335 CCCGGATATAGCTACTAGCACAATTGCCTTCGGGTCTTAA
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* * *
66938375 CCCGGATAT-A-AA-TTTCAGCATAATTGTCTTCGGGGCTTAG
1 CCCGGATATAACAACTTGCA-CA-AA-TGCCTTCGGGTCTTAG
66938415 CCCGGATAT
1 CCCGGATAT
66938424 CATTCAATTT
Statistics
Matches: 106, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
37 3 0.03
38 3 0.03
39 1 0.01
40 99 0.93
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (40 bp):
CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
Found at i:66941069 original size:21 final size:20
Alignment explanation
Indices: 66941036--66941075 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
66941026 ATAACTTGAA
*
66941036 AAAGAAAAAGAGAGTGAGAG
1 AAAGAAAAAGAGAATGAGAG
*
66941056 AAAGCAAAACGAGAATGAGA
1 AAAG-AAAAAGAGAATGAGA
66941076 TTGAAAAAGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.60, C:0.05, G:0.30, T:0.05
Consensus pattern (20 bp):
AAAGAAAAAGAGAATGAGAG
Found at i:66941115 original size:18 final size:20
Alignment explanation
Indices: 66941094--66941139 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 20
66941084 GCATGTGAGC
66941094 AAGAAAAGA-AAATTGAA-A
1 AAGAAAAGAGAAATTGAAGA
* *
66941112 AAG-AGAGAGAGATTGAAGA
1 AAGAAAAGAGAAATTGAAGA
66941131 AAGAAAAGA
1 AAGAAAAGA
66941140 TGGTGAGCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
17 4 0.18
18 10 0.45
19 4 0.18
20 4 0.18
ACGTcount: A:0.65, C:0.00, G:0.26, T:0.09
Consensus pattern (20 bp):
AAGAAAAGAGAAATTGAAGA
Found at i:66952375 original size:31 final size:33
Alignment explanation
Indices: 66952313--66952377 Score: 100
Period size: 31 Copynumber: 2.0 Consensus size: 33
66952303 CTCATCAAGT
66952313 AATTCACATAATTACATATTATTCAACATAACC
1 AATTCACATAATTACATATTATTCAACATAACC
66952346 AATTCA-ATAATTACATA-TATTC-ACAATAACC
1 AATTCACATAATTACATATTATTCAAC-ATAACC
66952377 A
1 A
66952378 CAAAACATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
30 2 0.06
31 12 0.39
32 11 0.35
33 6 0.19
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (33 bp):
AATTCACATAATTACATATTATTCAACATAACC
Found at i:66952668 original size:30 final size:30
Alignment explanation
Indices: 66952623--66952682 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
66952613 ATTTAATACG
*
66952623 AACTTTGGCAAAATTACATTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
* *
66952653 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
66952683 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.28, C:0.25, G:0.08, T:0.38
Consensus pattern (30 bp):
AACTTTGGCAAAATTACACTTTTGCCCCTA
Found at i:66953716 original size:14 final size:14
Alignment explanation
Indices: 66953697--66953726 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
66953687 GTTTCAACTT
66953697 ATAAATATGTGTTA
1 ATAAATATGTGTTA
*
66953711 ATAAATATGTTTTA
1 ATAAATATGTGTTA
66953725 AT
1 AT
66953727 CTGATTCTAA
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:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (14 bp):
ATAAATATGTGTTA
Found at i:66968387 original size:34 final size:34
Alignment explanation
Indices: 66968344--66968412 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
66968334 CTCATCAAGT
* *
66968344 AATTCACATAATTACATATTATTCAATAATAACC
1 AATTCACATAATTACATACTATTCAACAATAACC
66968378 AATTCACATAATTACATACTATTCAACAATAACC
1 AATTCACATAATTACATACTATTCAACAATAACC
66968412 A
1 A
66968413 CAAAACATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (34 bp):
AATTCACATAATTACATACTATTCAACAATAACC
Found at i:66968421 original size:34 final size:34
Alignment explanation
Indices: 66968349--66968422 Score: 96
Period size: 34 Copynumber: 2.2 Consensus size: 34
66968339 CAAGTAATTC
* * **
66968349 ACATAATTACATATTATTCAATAATAACCAATTC
1 ACATAATTACATACTATTCAACAATAACCAATAA
66968383 ACATAATTACATACTATTCAACAATAACCACA-AA
1 ACATAATTACATACTATTCAACAATAACCA-ATAA
66968417 ACATAA
1 ACATAA
66968423 CATTTCATGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 34 0.97
35 1 0.03
ACGTcount: A:0.51, C:0.20, G:0.00, T:0.28
Consensus pattern (34 bp):
ACATAATTACATACTATTCAACAATAACCAATAA
Found at i:66969758 original size:14 final size:14
Alignment explanation
Indices: 66969739--66969768 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
66969729 GTTTCAACTT
66969739 ATAAATATGTGTTA
1 ATAAATATGTGTTA
*
66969753 ATAAATATGTTTTA
1 ATAAATATGTGTTA
66969767 AT
1 AT
66969769 CTGATTCTAA
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:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (14 bp):
ATAAATATGTGTTA
Found at i:66970918 original size:24 final size:26
Alignment explanation
Indices: 66970886--66970935 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
66970876 GCCGAATCTT
*
66970886 CATCCTCA-TTCACCTAGCC-ATTTC
1 CATCATCATTTCACCTAGCCAATTTC
*
66970910 CATCATCATTTCACTTAGCCAATTTC
1 CATCATCATTTCACCTAGCCAATTTC
66970936 AGCCCTTCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 7 0.32
25 10 0.45
26 5 0.23
ACGTcount: A:0.24, C:0.36, G:0.04, T:0.36
Consensus pattern (26 bp):
CATCATCATTTCACCTAGCCAATTTC
Found at i:66982743 original size:46 final size:46
Alignment explanation
Indices: 66982693--66982860 Score: 236
Period size: 46 Copynumber: 3.6 Consensus size: 46
66982683 TGGTTGAGCA
66982693 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
66982739 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
66982784 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
66982832 TCCGAACTCGTTGAGTTGAGTCCGAGTTC
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC
66982861 GTGTTGGCAT
Statistics
Matches: 107, Mismatches: 6, Indels: 18
0.82 0.05 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 58 0.54
47 29 0.27
48 3 0.03
50 5 0.05
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:66982849 original size:93 final size:93
Alignment explanation
Indices: 66982690--66982863 Score: 348
Period size: 93 Copynumber: 1.9 Consensus size: 93
66982680 GGATGGTTGA
66982690 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
66982755 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
66982783 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
66982848 TGAGTCCGAGTTCGTG
66 TGAGTCCGAGTTCGTG
66982864 TTGGCATGAG
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 81 1.00
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:66986186 original size:30 final size:29
Alignment explanation
Indices: 66986152--66986239 Score: 88
Period size: 30 Copynumber: 2.9 Consensus size: 29
66986142 CTTGCTTATA
*
66986152 TTCAGCTCACGAGCTAAAGCTTAGCTCAAC
1 TTCAGCTTA-GAGCTAAAGCTTAGCTCAAC
* *
66986182 TTCAGCTTAGGAG-TATAATCTCAGCTCAAC
1 TTCAGCTTA-GAGCTA-AAGCTTAGCTCAAC
* *
66986212 TTTAGCTTAAAGGCTAAAGCTTAGCTCA
1 TTCAGCTTAGA-GCTAAAGCTTAGCTCA
66986240 TTTTAGCTCA
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
29 3 0.06
30 42 0.89
31 2 0.04
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (29 bp):
TTCAGCTTAGAGCTAAAGCTTAGCTCAAC
Found at i:66988483 original size:30 final size:29
Alignment explanation
Indices: 66988411--66988487 Score: 86
Period size: 30 Copynumber: 2.7 Consensus size: 29
66988401 TAATGAATGT
* *
66988411 AAAA-AAGAAAAG-AAAAGTGAGAAAAAT
1 AAAACAAGAAAAGAAAAAGAGAGAAAAAG
*
66988438 AAAACAAGAATAGAAAAAGAGAGAGAAAAG
1 AAAACAAGAAAAGAAAAAGAGAGA-AAAAG
**
66988468 AAAGTAAGAAAAGAAAAAGA
1 AAAACAAGAAAAGAAAAAGA
66988488 TGAACAAGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
27 4 0.10
28 7 0.17
29 9 0.22
30 21 0.51
ACGTcount: A:0.73, C:0.01, G:0.21, T:0.05
Consensus pattern (29 bp):
AAAACAAGAAAAGAAAAAGAGAGAAAAAG
Found at i:66989637 original size:30 final size:30
Alignment explanation
Indices: 66989603--66989700 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
66989593 AGCTCACTCC
66989603 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
66989633 TAGCTCAGCTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * *
66989663 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
66989693 TAGCTCAT
1 TAGCTCAT
66989701 TTTAGTTTAA
Statistics
Matches: 49, Mismatches: 17, Indels: 3
0.71 0.25 0.04
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.29
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:66990631 original size:22 final size:20
Alignment explanation
Indices: 66990599--66990647 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 20
66990589 GCTGAATTTA
66990599 TGAACTATTTTAATACATTAGTG
1 TGAAC-ATTTTAAT-CATT-GTG
* *
66990622 TGAACATTTTTATTATTGTG
1 TGAACATTTTAATCATTGTG
66990642 TGAACA
1 TGAACA
66990648 CCTAGATGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 3 0.12
22 7 0.29
23 5 0.21
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (20 bp):
TGAACATTTTAATCATTGTG
Found at i:66993800 original size:29 final size:29
Alignment explanation
Indices: 66993767--66993823 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
66993757 ATAACCAAAC
*
66993767 CTACAAAAACTTTATATCCATAAACCCAA
1 CTACAAAAACTTCATATCCATAAACCCAA
*
66993796 CTACATAAACTTCATATCCATAAACCCA
1 CTACAAAAACTTCATATCCATAAACCCA
66993824 TCTTTGAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.25
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAA
Found at i:67002688 original size:30 final size:30
Alignment explanation
Indices: 67002654--67002750 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
67002644 TAAACTAAAA
67002654 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * *
67002684 TGAGCTGAGGC-TAAACTCCTAAGCTAAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
67002714 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
67002744 TGAGCTA
1 TGAGCTA
67002751 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
29 2 0.04
30 43 0.83
31 7 0.13
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:67010079 original size:11 final size:10
Alignment explanation
Indices: 67010023--67010082 Score: 59
Period size: 11 Copynumber: 5.7 Consensus size: 10
67010013 AGTAAGTTTA
67010023 AAAAAAATTCG
1 AAAAAAATT-G
*
67010034 AAAAAAATTC
1 AAAAAAATTG
*
67010044 AAAAAAAGTG
1 AAAAAAATTG
67010054 -AAAAAATTAG
1 AAAAAAATT-G
67010064 AAAAAAAACTTG
1 -AAAAAAA-TTG
67010076 AAAAAAA
1 AAAAAAA
67010083 AATTTGACCA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
9 7 0.17
10 9 0.22
11 16 0.39
12 7 0.17
13 2 0.05
ACGTcount: A:0.72, C:0.05, G:0.08, T:0.15
Consensus pattern (10 bp):
AAAAAAATTG
Found at i:67015703 original size:5 final size:5
Alignment explanation
Indices: 67015693--67015748 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
67015683 AAGAGAAAAC
67015693 AAAGA AAAGA AAAGA AAA-A GAAA-A AAAGAA AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAGA AAAGA -AAAGA AAAG-A AAAGA AAA-GA AA-AGA
67015739 AAAGA AAAGA
1 AAAGA AAAGA
67015749 GAGGCAAGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
4 5 0.11
5 30 0.67
6 9 0.20
7 1 0.02
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:67015710 original size:19 final size:20
Alignment explanation
Indices: 67015682--67015746 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 20
67015672 ACATTCTTGT
*
67015682 AAAGAGAAAACAAAGAAAAG-A
1 AAAGA-AAAAGAAA-AAAAGAA
67015703 AAAGAAAAAGAAAAAAAGAA
1 AAAGAAAAAGAAAAAAAGAA
*
67015723 AAAGAAAATGAAATAAAAAGAA
1 AAAGAAAAAG-AA-AAAAAGAA
67015745 AA
1 AA
67015747 GAGAGGCAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
19 5 0.13
20 17 0.44
21 7 0.18
22 10 0.26
ACGTcount: A:0.80, C:0.02, G:0.15, T:0.03
Consensus pattern (20 bp):
AAAGAAAAAGAAAAAAAGAA
Found at i:67015828 original size:11 final size:12
Alignment explanation
Indices: 67015796--67015826 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
67015786 TTGAGAGAAC
67015796 TTGAAAAAGCCT
1 TTGAAAAAGCCT
67015808 TTGAAAAAGCCT
1 TTGAAAAAGCCT
67015820 TTGAAAA
1 TTGAAAA
67015827 GCAAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:67015863 original size:30 final size:31
Alignment explanation
Indices: 67015829--67015910 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 31
67015819 TTTGAAAAGC
* *
67015829 AAAAAAAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
67015859 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
67015889 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
67015911 TGAAACAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
29 8 0.19
30 25 0.60
31 9 0.21
ACGTcount: A:0.66, C:0.01, G:0.21, T:0.12
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:67018053 original size:30 final size:30
Alignment explanation
Indices: 67018019--67018115 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
67018009 AGCTCACTCC
67018019 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
67018049 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * * *
67018079 CAGCTCAACTTTAGCTCACGACCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
67018109 TAGCTCA
1 TAGCTCA
67018116 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:67019971 original size:14 final size:14
Alignment explanation
Indices: 67019952--67019996 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
67019942 AACTCATCTT
*
67019952 AGTTTAATTAAATG
1 AGTTTAATTTAATG
67019966 AGTTT-ATTTAATG
1 AGTTTAATTTAATG
*
67019979 AATTTAATTTAATG
1 AGTTTAATTTAATG
67019993 AGTT
1 AGTT
67019997 GCTTCTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:67021176 original size:11 final size:11
Alignment explanation
Indices: 67021160--67021199 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
67021150 AGTAAGTTTA
67021160 AAAAAAAATCG
1 AAAAAAAATCG
*
67021171 AAAAAAATTC-
1 AAAAAAAATCG
*
67021181 AAAAAAAATTG
1 AAAAAAAATCG
67021192 AAAAAAAA
1 AAAAAAAA
67021200 ACAAAATCTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 8 0.32
11 17 0.68
ACGTcount: A:0.78, C:0.05, G:0.05, T:0.12
Consensus pattern (11 bp):
AAAAAAAATCG
Found at i:67021204 original size:21 final size:21
Alignment explanation
Indices: 67021160--67021205 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
67021150 AGTAAGTTTA
**
67021160 AAAAAAAATCGAAAAAAATTC
1 AAAAAAAATCGAAAAAAAAAC
*
67021181 AAAAAAAATTGAAAAAAAAAC
1 AAAAAAAATCGAAAAAAAAAC
67021202 AAAA
1 AAAA
67021206 TCTGAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.78, C:0.07, G:0.04, T:0.11
Consensus pattern (21 bp):
AAAAAAAATCGAAAAAAAAAC
Found at i:67023397 original size:21 final size:21
Alignment explanation
Indices: 67023333--67023406 Score: 50
Period size: 21 Copynumber: 3.6 Consensus size: 21
67023323 AAAAAAATCA
67023333 GAAAAAGAAAACAAAAGAG-AG
1 GAAAAAGAAAA-AAAAGAGAAG
**
67023354 TG-AAAAG-AAAATCAGTA-AA-
1 -GAAAAAGAAAAAAAAG-AGAAG
67023373 GAAAAAGAAAAAAAAGAGAAG
1 GAAAAAGAAAAAAAAGAGAAG
**
67023394 GAAATTGAAAAAA
1 GAAAAAGAAAAAA
67023407 TGAGTGTCTT
Statistics
Matches: 40, Mismatches: 6, Indels: 13
0.68 0.10 0.22
Matches are distributed among these distances:
18 1 0.03
19 9 0.22
20 13 0.32
21 16 0.40
22 1 0.03
ACGTcount: A:0.70, C:0.03, G:0.20, T:0.07
Consensus pattern (21 bp):
GAAAAAGAAAAAAAAGAGAAG
Found at i:67026535 original size:14 final size:14
Alignment explanation
Indices: 67026516--67026560 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
67026506 AACTCATCTT
*
67026516 AGTTTAATTAAATG
1 AGTTTAATTTAATG
67026530 AGTTT-ATTTAATG
1 AGTTTAATTTAATG
*
67026543 AATTTAATTTAATG
1 AGTTTAATTTAATG
67026557 AGTT
1 AGTT
67026561 GCTTCTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:67030704 original size:21 final size:21
Alignment explanation
Indices: 67030671--67030744 Score: 50
Period size: 21 Copynumber: 3.6 Consensus size: 21
67030661 AAGACACTCA
**
67030671 TTTTTTCAATTTCCTTCTCTT
1 TTTTTTCTTTTTCCTTCTCTT
67030692 TTTTTTCTTTTT-CTT-TAC-T
1 TTTTTTCTTTTTCCTTCT-CTT
**
67030711 GATTTTC-TTTTCAC-TCTCTT
1 TTTTTTCTTTTTC-CTTCTCTT
67030731 TTGTTTTCTTTTTC
1 TT-TTTTCTTTTTC
67030745 TGATTTTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 13
0.68 0.10 0.22
Matches are distributed among these distances:
18 4 0.10
19 9 0.22
20 7 0.17
21 15 0.38
22 5 0.12
ACGTcount: A:0.07, C:0.20, G:0.03, T:0.70
Consensus pattern (21 bp):
TTTTTTCTTTTTCCTTCTCTT
Found at i:67034502 original size:11 final size:11
Alignment explanation
Indices: 67034488--67034517 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
67034478 AGATTTTGTT
67034488 TTTTTTTTCAA
1 TTTTTTTTCAA
67034499 TTTTTTTTCAA
1 TTTTTTTTCAA
67034510 TTTTTTTT
1 TTTTTTTT
67034518 GAAACTTACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:67035705 original size:14 final size:14
Alignment explanation
Indices: 67035683--67035727 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
67035673 TTAAAGAAGC
67035683 AACTCATTAAATTA
1 AACTCATTAAATTA
*
67035697 AATTCATTAAA-TA
1 AACTCATTAAATTA
*
67035710 AACTCATTTAATTA
1 AACTCATTAAATTA
67035724 AACT
1 AACT
67035728 AAGATGAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:67035765 original size:22 final size:22
Alignment explanation
Indices: 67035739--67035808 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
67035729 AGATGAGTTG
67035739 TATTAATGACCAGCAACTCATT
1 TATTAATGACCAGCAACTCATT
* *
67035761 TATTAA--ACTA--AGA-TGAGTT
1 TATTAATGACCAGCA-ACTCA-TT
67035780 GTATTAATGACCAGCAACTCATT
1 -TATTAATGACCAGCAACTCATT
67035803 TATTAA
1 TATTAA
67035809 ACTAAGAGGC
Statistics
Matches: 36, Mismatches: 4, Indels: 16
0.64 0.07 0.29
Matches are distributed among these distances:
18 3 0.08
19 3 0.08
20 9 0.25
22 15 0.42
23 3 0.08
24 3 0.08
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (22 bp):
TATTAATGACCAGCAACTCATT
Found at i:67035771 original size:42 final size:42
Alignment explanation
Indices: 67035710--67035815 Score: 203
Period size: 42 Copynumber: 2.5 Consensus size: 42
67035700 TCATTAAATA
67035710 AACTCATTTAATTAAACTAAGATGAGTTGTATTAATGACCAGC
1 AACTCATTT-ATTAAACTAAGATGAGTTGTATTAATGACCAGC
67035753 AACTCATTTATTAAACTAAGATGAGTTGTATTAATGACCAGC
1 AACTCATTTATTAAACTAAGATGAGTTGTATTAATGACCAGC
67035795 AACTCATTTATTAAACTAAGA
1 AACTCATTTATTAAACTAAGA
67035816 GGCTTAAATA
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 54 0.86
43 9 0.14
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (42 bp):
AACTCATTTATTAAACTAAGATGAGTTGTATTAATGACCAGC
Found at i:67037756 original size:14 final size:14
Alignment explanation
Indices: 67037734--67037779 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
67037724 ACCTAAACCG
* *
67037734 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
67037748 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
67037762 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
67037776 ACCA
1 ACCA
67037780 ATCCATTCGT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.20, C:0.33, G:0.07, T:0.41
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:67039283 original size:15 final size:15
Alignment explanation
Indices: 67039263--67039303 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
67039253 TATCAAGCAT
67039263 GGCCTAAGTTCGGGG
1 GGCCTAAGTTCGGGG
67039278 GGCCTAAGTTCGGGG
1 GGCCTAAGTTCGGGG
*
67039293 GGCCCAAGTTC
1 GGCCTAAGTTC
67039304 AAAATGAAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.15, C:0.24, G:0.41, T:0.20
Consensus pattern (15 bp):
GGCCTAAGTTCGGGG
Found at i:67043002 original size:15 final size:16
Alignment explanation
Indices: 67042984--67043018 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
67042974 GAATATTATA
*
67042984 AAAAAATAA-AAGAAG
1 AAAAAATAAGAAAAAG
67042999 AAAAAATAAGAAAAAG
1 AAAAAATAAGAAAAAG
67043015 AAAA
1 AAAA
67043019 CAAAAGAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.83, C:0.00, G:0.11, T:0.06
Consensus pattern (16 bp):
AAAAAATAAGAAAAAG
Found at i:67043071 original size:21 final size:20
Alignment explanation
Indices: 67042991--67043067 Score: 56
Period size: 19 Copynumber: 4.0 Consensus size: 20
67042981 ATAAAAAAAT
*
67042991 AAAAGAAGAAAAA-ATAAGA
1 AAAAGAAGAAAAAGAGAAGA
*
67043010 AAAAGAAAACAAAAGAG-AGCA
1 AAAAGAAGA-AAAAGAGAAG-A
**
67043031 AAAAG-A-AATCAGCA-AAGA
1 AAAAGAAGAAAAAG-AGAAGA
67043049 AAAAGAAGAAAAAGAGAAG
1 AAAAGAAGAAAAAGAGAAG
67043068 GAAATTGAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 15
0.68 0.09 0.23
Matches are distributed among these distances:
18 9 0.20
19 14 0.32
20 14 0.32
21 7 0.16
ACGTcount: A:0.73, C:0.05, G:0.19, T:0.03
Consensus pattern (20 bp):
AAAAGAAGAAAAAGAGAAGA
Found at i:67043978 original size:14 final size:14
Alignment explanation
Indices: 67043961--67044000 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
67043951 CGAACGGAAT
*
67043961 GGTAGGAACGAAAG
1 GGTAGGAACAAAAG
67043975 GGTAGGAACAAAAG
1 GGTAGGAACAAAAG
* *
67043989 GATATGAACAAA
1 GGTAGGAACAAA
67044001 TTGGTCGATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.50, C:0.07, G:0.33, T:0.10
Consensus pattern (14 bp):
GGTAGGAACAAAAG
Found at i:67044352 original size:15 final size:15
Alignment explanation
Indices: 67044332--67044379 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
67044322 TCAAAGGTGG
67044332 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
67044347 GTTTATGTAGATGGA
1 GTTTATGGATATGAA
*
67044362 -TTTATGGATATAAA
1 GTTTATGGATATGAA
67044376 GTTT
1 GTTT
67044380 TTGTAGGCTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:67052421 original size:14 final size:14
Alignment explanation
Indices: 67052404--67052443 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
67052394 CGAACGGAAT
*
67052404 GGTAGGAACGAAAG
1 GGTAGGAACAAAAG
67052418 GGTAGGAACAAAAG
1 GGTAGGAACAAAAG
* *
67052432 GATATGAACAAA
1 GGTAGGAACAAA
67052444 TTGGTCGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.50, C:0.07, G:0.33, T:0.10
Consensus pattern (14 bp):
GGTAGGAACAAAAG
Found at i:67056443 original size:63 final size:65
Alignment explanation
Indices: 67056309--67056443 Score: 154
Period size: 67 Copynumber: 2.1 Consensus size: 65
67056299 TATGAACTTG
*
67056309 ATTTAATAGATGCTTCTTTAAATAAACTAGTTACTAGGATAATTTAGTGATGCATGAGTTAAAGT
1 ATTTAATAGATGCTTCTTTAAATAAACTAGTTACTAGGATAA--TAGTGATGCATAAGTTAAAGT
67056374 TC
64 TC
* * *
67056376 ATTTAATA-ATGCTTCTATTAATTAAACTAGTTGCT-GGATTAA-A-TGATGCATAAGTGT-TAG
1 ATTTAATAGATGCTTCT-TTAAATAAACTAGTTACTAGGA-TAATAGTGATGCATAAGT-TAAAG
67056436 TTC
63 TTC
67056439 ATTTA
1 ATTTA
67056444 TTTAAGTTAG
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
63 21 0.34
64 2 0.03
66 11 0.18
67 27 0.44
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.41
Consensus pattern (65 bp):
ATTTAATAGATGCTTCTTTAAATAAACTAGTTACTAGGATAATAGTGATGCATAAGTTAAAGTTC
Found at i:67057518 original size:19 final size:19
Alignment explanation
Indices: 67057494--67057533 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
67057484 AGCTCCCATG
*
67057494 TAGCTCCATACCAGCTCAT
1 TAGCTCCAGACCAGCTCAT
**
67057513 TAGCTCGGGACCAGCTCAT
1 TAGCTCCAGACCAGCTCAT
67057532 TA
1 TA
67057534 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (19 bp):
TAGCTCCAGACCAGCTCAT
Found at i:67058852 original size:30 final size:30
Alignment explanation
Indices: 67058818--67058914 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
67058808 AGCTCACTCC
67058818 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
67058848 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
67058878 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
67058908 TAGCTCA
1 TAGCTCA
67058915 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:67059840 original size:22 final size:20
Alignment explanation
Indices: 67059808--67059856 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 20
67059798 GCCGAATTTA
67059808 TGAACTATTTTAATACATTAGTG
1 TGAAC-ATTTTAAT-CATT-GTG
* *
67059831 TGAACATTTTTATTATTGTG
1 TGAACATTTTAATCATTGTG
67059851 TGAACA
1 TGAACA
67059857 CCTAGATGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 3 0.12
22 7 0.29
23 5 0.21
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (20 bp):
TGAACATTTTAATCATTGTG
Found at i:67061528 original size:11 final size:12
Alignment explanation
Indices: 67061496--67061526 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
67061486 ATGAGAGAAC
67061496 TTGAAAAAGCCT
1 TTGAAAAAGCCT
67061508 TTGAAAAAGCCT
1 TTGAAAAAGCCT
67061520 TTGAAAA
1 TTGAAAA
67061527 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:67061605 original size:12 final size:12
Alignment explanation
Indices: 67061588--67061632 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
67061578 ATTTGAGAGA
*
67061588 GAAAAAGAAGTT
1 GAAAAAGAAATT
67061600 GAAAAAGAAATT
1 GAAAAAGAAATT
*
67061612 GAAAAAGAGATT
1 GAAAAAGAAATT
*
67061624 -AAAGAGAAA
1 GAAAAAGAAA
67061633 GAAATTGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
11 7 0.24
12 22 0.76
ACGTcount: A:0.64, C:0.00, G:0.22, T:0.13
Consensus pattern (12 bp):
GAAAAAGAAATT
Found at i:67063837 original size:30 final size:30
Alignment explanation
Indices: 67063803--67063899 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
67063793 AGCTCACTCC
67063803 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
67063833 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
67063863 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
67063893 TAGCTCA
1 TAGCTCA
67063900 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:67072807 original size:14 final size:14
Alignment explanation
Indices: 67072790--67072829 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
67072780 CGAATAGAAT
*
67072790 GGTAGGAACGAAAG
1 GGTAGGAACAAAAG
67072804 GGTAGGAACAAAAG
1 GGTAGGAACAAAAG
* *
67072818 GATATGAACAAA
1 GGTAGGAACAAA
67072830 TTGGTCGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.50, C:0.07, G:0.33, T:0.10
Consensus pattern (14 bp):
GGTAGGAACAAAAG
Found at i:67074672 original size:21 final size:21
Alignment explanation
Indices: 67074646--67074696 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
67074636 TAATAGCATT
67074646 ACTTTGAAGTTATAAAAAAAA
1 ACTTTGAAGTTATAAAAAAAA
*
67074667 ACTTTGAA-ATATAAAAAAAA
1 ACTTTGAAGTTATAAAAAAAA
67074687 A-TTATGAAGT
1 ACTT-TGAAGT
67074697 GCTTAATTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 2 0.08
20 16 0.62
21 8 0.31
ACGTcount: A:0.57, C:0.04, G:0.10, T:0.29
Consensus pattern (21 bp):
ACTTTGAAGTTATAAAAAAAA
Found at i:67078660 original size:29 final size:29
Alignment explanation
Indices: 67078627--67078686 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
67078617 ATAACCAAAC
* *
67078627 CTACAAAAACTTTATATCCATAAATCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
67078656 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
67078685 CT
1 CT
67078687 TTGAATCCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:67078679 original size:15 final size:15
Alignment explanation
Indices: 67078633--67078680 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
67078623 AAACCTACAA
*
67078633 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
67078648 AAA-TCCATCTACAT
1 AAACTTCATATCCAT
67078662 AAACTTCATATCCAT
1 AAACTTCATATCCAT
67078677 AAAC
1 AAAC
67078681 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:67080024 original size:30 final size:28
Alignment explanation
Indices: 67079988--67080043 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
67079978 AAGCGAAAAA
* *
67079988 GAAAAAGAGTGTGTGCAAGAAAGTAAAGTT
1 GAAAAAGAGAGTGAGCAA-AAAG-AAAGTT
67080018 GAAAAAGAGAGTGAGCAAAAAGAAAG
1 GAAAAAGAGAGTGAGCAAAAAGAAAG
67080044 CGTGGAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 4 0.17
30 16 0.67
ACGTcount: A:0.54, C:0.04, G:0.30, T:0.12
Consensus pattern (28 bp):
GAAAAAGAGAGTGAGCAAAAAGAAAGTT
Found at i:67083287 original size:29 final size:29
Alignment explanation
Indices: 67083254--67083313 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
67083244 ATAACCAAAC
* *
67083254 CTACAAAAACTTTATATCCATAAATCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
67083283 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
67083312 CT
1 CT
67083314 TTGAATCCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:67083306 original size:15 final size:15
Alignment explanation
Indices: 67083260--67083307 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
67083250 AAACCTACAA
*
67083260 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
67083275 AAA-TCCATCTACAT
1 AAACTTCATATCCAT
67083289 AAACTTCATATCCAT
1 AAACTTCATATCCAT
67083304 AAAC
1 AAAC
67083308 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:67087472 original size:20 final size:20
Alignment explanation
Indices: 67087427--67087472 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
67087417 TAAATCACTC
*
67087427 TTTTTTTCGATTTTTTTTTA
1 TTTTTTTCGATTTTTTATTA
67087447 TTTTTTTCGAATTTTTTATT-
1 TTTTTTTCG-ATTTTTTATTA
67087467 TTTTTT
1 TTTTTT
67087473 AACTTGTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.11, C:0.04, G:0.04, T:0.80
Consensus pattern (20 bp):
TTTTTTTCGATTTTTTATTA
Found at i:67087887 original size:14 final size:14
Alignment explanation
Indices: 67087840--67087887 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
67087830 GTACGAATGG
*
67087840 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
67087854 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
67087868 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
67087882 ATTGGT
1 AATGGT
67087888 CGGTTTAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:67090521 original size:16 final size:16
Alignment explanation
Indices: 67090480--67090525 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
67090470 TTCTTTGGAA
67090480 ACACTCTTTTC-TTTT
1 ACACTCTTTTCTTTTT
*
67090495 AC-CTCAATTTCTTTTT
1 ACACTC-TTTTCTTTTT
*
67090511 CCACTCTTTTCTTTT
1 ACACTCTTTTCTTTT
67090526 GATCAAACTC
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
14 3 0.12
15 6 0.24
16 13 0.52
17 3 0.12
ACGTcount: A:0.13, C:0.28, G:0.00, T:0.59
Consensus pattern (16 bp):
ACACTCTTTTCTTTTT
Found at i:67090661 original size:14 final size:14
Alignment explanation
Indices: 67090635--67090675 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
67090625 GTCTTTTGAT
67090635 ATCTTTTTGCTTTTC
1 ATCTTTTT-CTTTTC
67090650 ATCTTTTTCTTTTC
1 ATCTTTTTCTTTTC
*
67090664 -TCATTTTCTTTT
1 ATCTTTTTCTTTT
67090676 TACAAGAGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 11 0.44
14 6 0.24
15 8 0.32
ACGTcount: A:0.07, C:0.20, G:0.02, T:0.71
Consensus pattern (14 bp):
ATCTTTTTCTTTTC
Found at i:67091570 original size:30 final size:30
Alignment explanation
Indices: 67091536--67091633 Score: 83
Period size: 30 Copynumber: 3.3 Consensus size: 30
67091526 AGCTCACTCC
67091536 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * * * * *
67091566 TAGCTTAGT-TTCAGCTTAGGAGTTTAATCT
1 TAGCTCA-TATTCAGCTCACGAGCTAAACCT
* * *
67091596 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
67091626 TAGCTCAT
1 TAGCTCAT
67091634 TTTAGTTTAA
Statistics
Matches: 49, Mismatches: 15, Indels: 7
0.69 0.21 0.10
Matches are distributed among these distances:
30 48 0.98
31 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:67092376 original size:30 final size:31
Alignment explanation
Indices: 67092342--67092438 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
67092332 AGCTCACTCC
*
67092342 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
67092372 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
67092402 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
67092432 TAGCTCA
1 TAGCTCA
67092439 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:67098862 original size:25 final size:25
Alignment explanation
Indices: 67098834--67098885 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
67098824 TAAGAGCATG
67098834 AACTAGACATCATAAATATCATGCT
1 AACTAGACATCATAAATATCATGCT
67098859 AACTAGACATCATAAATATCATGCT
1 AACTAGACATCATAAATATCATGCT
67098884 AA
1 AA
67098886 GCTAAACTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.46, C:0.19, G:0.08, T:0.27
Consensus pattern (25 bp):
AACTAGACATCATAAATATCATGCT
Found at i:67100475 original size:47 final size:50
Alignment explanation
Indices: 67100412--67100536 Score: 159
Period size: 47 Copynumber: 2.6 Consensus size: 50
67100402 CTGGTATGCA
* * **
67100412 TAGTAGCCTACACTTAGTACTACACATGCGA-C-CAACAGTCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCTCAACA-TCTAATACACG
* *
67100461 TA-TAG-CTGCACTTAGTACTACACACGTGACCTCACCATCTAATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCTCAACATCTAATACACG
67100509 TAGTAGCCTGCACTTAGTACTACACACG
1 TAGTAGCCTGCACTTAGTACTACACACG
67100537 TGATCACAGT
Statistics
Matches: 66, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
47 21 0.32
48 15 0.23
49 9 0.14
50 21 0.32
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.24
Consensus pattern (50 bp):
TAGTAGCCTGCACTTAGTACTACACACGCGACCTCAACATCTAATACACG
Found at i:67100531 original size:50 final size:49
Alignment explanation
Indices: 67100412--67100539 Score: 163
Period size: 50 Copynumber: 2.6 Consensus size: 49
67100402 CTGGTATGCA
* * * **
67100412 TAGTAGCCTACACTTAGTACTACACATGCGACCAACAGTCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAACAGTCTAATACACG
*
67100461 TA-TAG-CTGCACTTAGTACTACACACGTGACCTCACCA-TCTAATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-C-CAACAGTCTAATACACG
67100509 TAGTAGCCTGCACTTAGTACTACACACGTGA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA
67100540 TCACAGTTTT
Statistics
Matches: 69, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
47 21 0.30
48 15 0.22
49 9 0.13
50 24 0.35
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.24
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAACAGTCTAATACACG
Found at i:67102769 original size:15 final size:15
Alignment explanation
Indices: 67102713--67102777 Score: 73
Period size: 15 Copynumber: 4.4 Consensus size: 15
67102703 TAAAGATAAC
*
67102713 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
67102727 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
*
67102742 GAA-AAACCCAGAATA
1 -AAGAAATCCAGAATA
67102757 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
67102772 AAGAAA
1 AAGAAA
67102778 CCCAAGATAC
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
14 11 0.26
15 29 0.67
16 3 0.07
ACGTcount: A:0.63, C:0.14, G:0.14, T:0.09
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:67102779 original size:30 final size:31
Alignment explanation
Indices: 67102713--67102781 Score: 92
Period size: 30 Copynumber: 2.3 Consensus size: 31
67102703 TAAAGATAAC
*
67102713 AAGAAAACC-GAATAAAGAAATCCAAGATAG
1 AAGAAACCCAGAATAAAGAAATCCAAGATAG
67102743 AA-AAACCCAGAATAAAGAAATCC-AGAATA-
1 AAGAAACCCAGAATAAAGAAATCCAAG-ATAG
67102772 AAGAAACCCA
1 AAGAAACCCA
67102782 AGATACGATA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
29 9 0.26
30 26 0.74
ACGTcount: A:0.61, C:0.17, G:0.13, T:0.09
Consensus pattern (31 bp):
AAGAAACCCAGAATAAAGAAATCCAAGATAG
Found at i:67104640 original size:20 final size:20
Alignment explanation
Indices: 67104617--67104664 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
67104607 AGCTCCGTCC
*
67104617 AGCTCAACTCAGCTCATTTG
1 AGCTCAACTCAACTCATTTG
*** *
67104637 AGCTCGTTTCAACTCGTTTG
1 AGCTCAACTCAACTCATTTG
67104657 AGCTCAAC
1 AGCTCAAC
67104665 CGAGCTTACT
Statistics
Matches: 20, Mismatches: 8, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.23, C:0.29, G:0.17, T:0.31
Consensus pattern (20 bp):
AGCTCAACTCAACTCATTTG
Found at i:67104890 original size:19 final size:18
Alignment explanation
Indices: 67104868--67104915 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
67104858 TTCATTAAAT
*
67104868 TTTTAATTATTAATTATGA
1 TTTTAATTAATAATTAT-A
* * *
67104887 TTTTTATGAATAGTTATA
1 TTTTAATTAATAATTATA
67104905 TTTTAATTAAT
1 TTTTAATTAAT
67104916 TGTGTGTTAA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
18 10 0.43
19 13 0.57
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (18 bp):
TTTTAATTAATAATTATA
Found at i:67107149 original size:18 final size:18
Alignment explanation
Indices: 67107126--67107175 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
67107116 GAAAGAAAAA
*
67107126 GAAAAAGAGATTGAGAGT
1 GAAAAAGAGAATGAGAGT
* *
67107144 GAAAAAGAAAATGAGATT
1 GAAAAAGAGAATGAGAGT
*
67107162 GAACAAGAGAATGA
1 GAAAAAGAGAATGA
67107176 AAAAGAGTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.56, C:0.02, G:0.28, T:0.14
Consensus pattern (18 bp):
GAAAAAGAGAATGAGAGT
Found at i:67107152 original size:24 final size:24
Alignment explanation
Indices: 67107119--67107200 Score: 94
Period size: 24 Copynumber: 3.4 Consensus size: 24
67107109 AAGAAATGAA
67107119 AGAAAAAGAAAAAGAGATTGAGAG
1 AGAAAAAGAAAAAGAGATTGAGAG
* * *
67107143 TGAAAAAGAAAATGAGATTGA-ACA
1 AGAAAAAGAAAAAGAGATTGAGA-G
* * *
67107167 AGAGAATGAAAAAGAGTTTGAGAG
1 AGAAAAAGAAAAAGAGATTGAGAG
67107191 AGAAAAAGAA
1 AGAAAAAGAA
67107201 TGTGAACAAG
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
23 1 0.02
24 43 0.96
25 1 0.02
ACGTcount: A:0.60, C:0.01, G:0.27, T:0.12
Consensus pattern (24 bp):
AGAAAAAGAAAAAGAGATTGAGAG
Found at i:67107229 original size:18 final size:19
Alignment explanation
Indices: 67107193--67107231 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
67107183 TTTGAGAGAG
*
67107193 AAAAAGAATGTGAACAAGA
1 AAAAAGAATGTGAAAAAGA
*
67107212 AAAAAGAGTG-GAAAAAGA
1 AAAAAGAATGTGAAAAAGA
67107230 AA
1 AA
67107232 TTGAGATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.67, C:0.03, G:0.23, T:0.08
Consensus pattern (19 bp):
AAAAAGAATGTGAAAAAGA
Found at i:67110712 original size:39 final size:39
Alignment explanation
Indices: 67110679--67110754 Score: 125
Period size: 39 Copynumber: 1.9 Consensus size: 39
67110669 TTAGTTTGTG
*
67110679 TCTTTAATTATGTTATAGTTTGAACATCATTAGTATGAA
1 TCTTTAATTATGTCATAGTTTGAACATCATTAGTATGAA
* *
67110718 TCTTTAATTATGTCGTAGTTTGAACATCATTAATATG
1 TCTTTAATTATGTCATAGTTTGAACATCATTAGTATG
67110755 TGTTCTGCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.32, C:0.09, G:0.13, T:0.46
Consensus pattern (39 bp):
TCTTTAATTATGTCATAGTTTGAACATCATTAGTATGAA
Found at i:67110891 original size:52 final size:51
Alignment explanation
Indices: 67110762--67110893 Score: 167
Period size: 50 Copynumber: 2.6 Consensus size: 51
67110752 ATGTGTTCTG
* * *
67110762 CATTTAATAAAGTCATGCATTATGTAACTCTCATGTAAGTTAAGTTTGCAT
1 CATTAAATTAAGTCATGCATTATGTAACTCCCATGTAAGTTAAGTTTGCAT
** * * *
67110813 CA-TAAATTGTGACATGCATTATGTAACTCCCATGTTAGTTAAAGTTTGTAT
1 CATTAAATTAAGTCATGCATTATGTAACTCCCATGTAAGTT-AAGTTTGCAT
*
67110864 CATTAAATTAAGTCATGCATTAAGTAACTC
1 CATTAAATTAAGTCATGCATTATGTAACTC
67110894 ATTTGTTCAT
Statistics
Matches: 67, Mismatches: 12, Indels: 3
0.82 0.15 0.04
Matches are distributed among these distances:
50 31 0.46
51 13 0.19
52 23 0.34
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (51 bp):
CATTAAATTAAGTCATGCATTATGTAACTCCCATGTAAGTTAAGTTTGCAT
Found at i:67113493 original size:23 final size:23
Alignment explanation
Indices: 67113463--67113508 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
67113453 ATTTAACAAG
67113463 ATAGGAACCTCGGTATGTTTGAA
1 ATAGGAACCTCGGTATGTTTGAA
67113486 ATAGGAACCTCGGTATGTTTGAA
1 ATAGGAACCTCGGTATGTTTGAA
67113509 CCCTACACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.13, G:0.26, T:0.30
Consensus pattern (23 bp):
ATAGGAACCTCGGTATGTTTGAA
Found at i:67114581 original size:106 final size:107
Alignment explanation
Indices: 67114451--67114667 Score: 409
Period size: 106 Copynumber: 2.0 Consensus size: 107
67114441 AACTAATGTG
67114451 AACTAAATTTAATATGTGGTTTATTAATTAACTAATTAATGAACTTATTAAATAAAAATTTAATA
1 AACTAAATTTAATATGTGGTTTATTAATTAACTAATTAATGAACTTATTAAATAAAAATTTAATA
67114516 GCAGTCAAATGAAGTCAAAGTAGTCTTTATGAGCTAGAGTT-
66 GCAGTCAAATGAAGTCAAAGTAGTCTTTATGAGCTAGAGTTC
*
67114557 AACTAAATTTAATATGTGGTTTATTAATTAACTAATTAATGAACTTATTAAATAAAAATTTAATG
1 AACTAAATTTAATATGTGGTTTATTAATTAACTAATTAATGAACTTATTAAATAAAAATTTAATA
*
67114622 GCAGTCAAATGAAGTCATAGTAGTCTTTATGAGCTAGAGTTC
66 GCAGTCAAATGAAGTCAAAGTAGTCTTTATGAGCTAGAGTTC
67114664 AACT
1 AACT
67114668 CATGAACTAA
Statistics
Matches: 108, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
106 104 0.96
107 4 0.04
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.37
Consensus pattern (107 bp):
AACTAAATTTAATATGTGGTTTATTAATTAACTAATTAATGAACTTATTAAATAAAAATTTAATA
GCAGTCAAATGAAGTCAAAGTAGTCTTTATGAGCTAGAGTTC
Found at i:67115223 original size:6 final size:6
Alignment explanation
Indices: 67115208--67115296 Score: 63
Period size: 6 Copynumber: 14.7 Consensus size: 6
67115198 CAAGTTGTAA
* * * **
67115208 AAAAAT AAAAAG -AAAAG AAAAGAA AAGAAAG AAAAAG AAAATG AAAGTG
1 AAAAAG AAAAAG AAAAAG AAAA-AG AA-AAAG AAAAAG AAAAAG AAAAAG
** * * *
67115257 AAAAAG AAAGTG AAAAAG AAATAG AGAATG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
67115297 TGAGATTGAG
Statistics
Matches: 63, Mismatches: 17, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
5 5 0.08
6 50 0.79
7 6 0.10
8 2 0.03
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.07
Consensus pattern (6 bp):
AAAAAG
Found at i:67115235 original size:15 final size:16
Alignment explanation
Indices: 67115215--67115265 Score: 61
Period size: 15 Copynumber: 3.2 Consensus size: 16
67115205 TAAAAAAATA
67115215 AAAAGAAAAG-AAAAG
1 AAAAGAAAAGAAAAAG
67115230 AAAAG-AAAGAAAAAG
1 AAAAGAAAAGAAAAAG
*
67115245 AAAATGAAAGTGAAAAAG
1 AAAA-GAAA-AGAAAAAG
67115263 AAA
1 AAA
67115266 GTGAAAAAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
14 4 0.13
15 14 0.45
16 1 0.03
17 2 0.06
18 10 0.32
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (16 bp):
AAAAGAAAAGAAAAAG
Found at i:67115240 original size:4 final size:5
Alignment explanation
Indices: 67115215--67115253 Score: 53
Period size: 5 Copynumber: 7.6 Consensus size: 5
67115205 TAAAAAAATA
67115215 AAAAG AAAAG AAAAG AAAAG -AAAG AAAAAG AAAATG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG -AAAAG AAAA-G AAA
67115254 GTGAAAAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
4 4 0.13
5 19 0.61
6 8 0.26
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (5 bp):
AAAAG
Found at i:67115277 original size:18 final size:17
Alignment explanation
Indices: 67115206--67115296 Score: 71
Period size: 18 Copynumber: 5.2 Consensus size: 17
67115196 TTCAAGTTGT
67115206 AAAA-AAAT-AAAAAG-
1 AAAAGAAATGAAAAAGA
*
67115220 AAAAGAAAAGAAAAGAAAGA
1 AAAAGAAATG--AA-AAAGA
**
67115240 AAAAGAAAATGAAAGTGA
1 AAAAG-AAATGAAAAAGA
67115258 AAAAGAAAGTGAAAAAGA
1 AAAAGAAA-TGAAAAAGA
*
67115276 AATAGAGAATGAAAAAGA
1 AAAAGA-AATGAAAAAGA
67115294 AAA
1 AAA
67115297 TGAGATTGAG
Statistics
Matches: 60, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
14 4 0.07
15 3 0.05
17 3 0.05
18 33 0.55
19 8 0.13
20 5 0.08
21 4 0.07
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.07
Consensus pattern (17 bp):
AAAAGAAATGAAAAAGA
Found at i:67115644 original size:9 final size:9
Alignment explanation
Indices: 67115630--67115654 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
67115620 ATGAGCCTAA
67115630 AGGTAAGTT
1 AGGTAAGTT
67115639 AGGTAAGTT
1 AGGTAAGTT
67115648 AGGTAAG
1 AGGTAAG
67115655 GATAATTGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.28
Consensus pattern (9 bp):
AGGTAAGTT
Found at i:67118617 original size:6 final size:6
Alignment explanation
Indices: 67118583--67118683 Score: 53
Period size: 6 Copynumber: 15.7 Consensus size: 6
67118573 AAAAAATAAA
* * *
67118583 AAAAATG AAAAAG AAATGAG AAATGAG AAAAAG AACACAA- AAATAG AAAAAG
1 AAAAA-G AAAAAG AAA-AAG AAA-AAG AAAAAG AA-A-AAG AAAAAG AAAAAG
* * *
67118635 AGAGAG -AAAAG AAAATG AGAAAAG AAAAAG AAGAACAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG A-AAAAG AAAAAG -A-AA-AAG AAAAAG AAAA
67118684 TGGAAAAAAA
Statistics
Matches: 75, Mismatches: 10, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
5 4 0.05
6 35 0.47
7 28 0.37
8 5 0.07
9 3 0.04
ACGTcount: A:0.72, C:0.03, G:0.20, T:0.05
Consensus pattern (6 bp):
AAAAAG
Found at i:67118644 original size:20 final size:18
Alignment explanation
Indices: 67118574--67118696 Score: 65
Period size: 20 Copynumber: 6.6 Consensus size: 18
67118564 AATGAATTTA
*
67118574 AAAAATAAA-AAAAAT-G
1 AAAAAGAAAGAAAAATAG
*
67118590 AAAAAGAAATGAGAAATGAG
1 AAAAAGAAA-GAAAAAT-AG
*
67118610 AAAAAGAACACAAAAATAG
1 AAAAAGAA-AGAAAAATAG
* *
67118629 AAAAAGAGAGAGAAA-AG
1 AAAAAGAAAGAAAAATAG
*
67118646 AAAATGAGAAAAGAAAAAGAAG
1 AAAA--AG-AAAGAAAAA-TAG
* * *
67118668 AACAAGAAAAAGAAAATGG
1 AAAAAGAAAGA-AAAATAG
67118687 AAAAA-AAAGA
1 AAAAAGAAAGA
67118697 TTGATTGCAA
Statistics
Matches: 81, Mismatches: 15, Indels: 20
0.70 0.13 0.17
Matches are distributed among these distances:
16 8 0.10
17 6 0.07
18 14 0.17
19 20 0.25
20 27 0.33
21 1 0.01
22 5 0.06
ACGTcount: A:0.73, C:0.02, G:0.19, T:0.06
Consensus pattern (18 bp):
AAAAAGAAAGAAAAATAG
Found at i:67118676 original size:15 final size:14
Alignment explanation
Indices: 67118639--67118681 Score: 61
Period size: 13 Copynumber: 3.1 Consensus size: 14
67118629 AAAAAGAGAG
*
67118639 AGAAAAGAAAATG-
1 AGAAAAGAAAAAGA
67118652 AGAAAAGAAAAAGA
1 AGAAAAGAAAAAGA
67118666 AGAACAAGAAAAAGA
1 AGAA-AAGAAAAAGA
67118681 A
1 A
67118682 AATGGAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 12 0.44
14 4 0.15
15 11 0.41
ACGTcount: A:0.74, C:0.02, G:0.21, T:0.02
Consensus pattern (14 bp):
AGAAAAGAAAAAGA
Found at i:67118689 original size:28 final size:29
Alignment explanation
Indices: 67118622--67118696 Score: 75
Period size: 28 Copynumber: 2.6 Consensus size: 29
67118612 AAAGAACACA
67118622 AAAATAGAAAAAGAGAGAGAAAAGAAAATGAG
1 AAAAT-GAAAAAGA-AGAGAAAAGAAAA-GAG
*
67118654 AAAA-GAAAAAGAAGA-ACAAGAAAA-AG
1 AAAATGAAAAAGAAGAGAAAAGAAAAGAG
*
67118680 AAAATGGAAAAAAAAGA
1 AAAAT-GAAAAAGAAGA
67118697 TTGATTGCAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
26 6 0.15
28 18 0.46
29 3 0.08
30 8 0.21
32 4 0.10
ACGTcount: A:0.73, C:0.01, G:0.21, T:0.04
Consensus pattern (29 bp):
AAAATGAAAAAGAAGAGAAAAGAAAAGAG
Found at i:67121604 original size:30 final size:30
Alignment explanation
Indices: 67121519--67121606 Score: 90
Period size: 30 Copynumber: 2.9 Consensus size: 30
67121509 TGAGCTAAAA
* *
67121519 TGAGCTAAGCTTTAGC-CCTTAAGCTAAAGT
1 TGAGCTAAGATTTAGCTCC-TAAGCTGAAGT
*
67121549 TGAGCTGAGATTATA-CTCCTAAGCTGAAGT
1 TGAGCTAAGATT-TAGCTCCTAAGCTGAAGT
* * *
67121579 TGAGCTAAGGTTTAGCTCGTGAGCTGAA
1 TGAGCTAAGATTTAGCTCCTAAGCTGAA
67121607 TATAAGCTAG
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
29 2 0.04
30 42 0.88
31 4 0.08
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCCTAAGCTGAAGT
Found at i:67123862 original size:12 final size:12
Alignment explanation
Indices: 67123822--67123877 Score: 58
Period size: 12 Copynumber: 4.4 Consensus size: 12
67123812 GTTTCTTTTG
67123822 TTTCAATTTCTTT
1 TTTCAATTTC-TT
* *
67123835 CTCTTTAATCTCTT
1 -T-TTCAATTTCTT
67123849 TTTCAATTTCTT
1 TTTCAATTTCTT
*
67123861 TTTCAACTTCTT
1 TTTCAATTTCTT
67123873 TTTCA
1 TTTCA
67123878 CTCTCAAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
12 25 0.69
13 1 0.03
14 3 0.08
15 7 0.19
ACGTcount: A:0.16, C:0.21, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTCAATTTCTT
Found at i:67124014 original size:5 final size:5
Alignment explanation
Indices: 67124004--67124060 Score: 53
Period size: 5 Copynumber: 11.0 Consensus size: 5
67123994 CTCTTGCCTC
* * *
67124004 TCTTT TCTTTT TATTT TGTTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TC-TTT TCTTT TCTTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
67124051 TCTTT TCTTT
1 TCTTT TCTTT
67124061 GTTTTCTCTT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
4 3 0.07
5 30 0.70
6 6 0.14
7 4 0.09
ACGTcount: A:0.02, C:0.16, G:0.04, T:0.79
Consensus pattern (5 bp):
TCTTT
Found at i:67124036 original size:25 final size:25
Alignment explanation
Indices: 67124008--67124056 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
67123998 TGCCTCTCTT
*
67124008 TTCTTTT-TATTTTGTTTTCTTTTTC
1 TTCTTTTCT-TTTTCTTTTCTTTTTC
67124033 TTCTTTTGCTTTTTCTTTTCTTTT
1 TTCTTTT-CTTTTTCTTTTCTTTT
67124057 CTTTGTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 13 0.62
27 1 0.05
ACGTcount: A:0.02, C:0.14, G:0.04, T:0.80
Consensus pattern (25 bp):
TTCTTTTCTTTTTCTTTTCTTTTTC
Found at i:67124061 original size:21 final size:20
Alignment explanation
Indices: 67124017--67124071 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 20
67124007 TTTCTTTTTA
67124017 TTTTG-TTTTCTTTTTCTTC
1 TTTTGTTTTTCTTTTTCTTC
*
67124036 TTTTGCTTTTTC-TTTTCTTT
1 TTTTG-TTTTTCTTTTTCTTC
67124056 TCTTTGTTTTCTCTTT
1 T-TTTGTTTT-TCTTT
67124072 ACAAGAATGT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
19 5 0.17
20 12 0.40
21 11 0.37
22 2 0.07
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.78
Consensus pattern (20 bp):
TTTTGTTTTTCTTTTTCTTC
Found at i:67127900 original size:11 final size:12
Alignment explanation
Indices: 67127884--67127937 Score: 69
Period size: 11 Copynumber: 4.7 Consensus size: 12
67127874 CAAGTTTGAA
*
67127884 AAAAAAAACT-G
1 AAAAAAAATTCG
67127895 AAAAAAAATTCG
1 AAAAAAAATTCG
67127907 AAAAAAAAATTCG
1 -AAAAAAAATTCG
67127920 -AAAAAAATT-G
1 AAAAAAAATTCG
67127930 AAAAAAAA
1 AAAAAAAA
67127938 GTGATTTATG
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
10 1 0.03
11 25 0.64
12 1 0.03
13 12 0.31
ACGTcount: A:0.74, C:0.06, G:0.07, T:0.13
Consensus pattern (12 bp):
AAAAAAAATTCG
Done.