Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 141 of 143
Found at i:42083109 original size:33 final size:33
Alignment explanation
Indices: 42083071--42083153 Score: 98
Period size: 33 Copynumber: 2.5 Consensus size: 33
42083061 GCTAGTGCTG
*
42083071 TAAGCAGGAC-AGTTAG-TACGGATGATGCTCCTT
1 TAAGCAGGACAAG-TAGCT-CGGATGATACTCCTT
*
42083104 TAAGCAGGACAAGTAGCTGGGATGATACTCCTT
1 TAAGCAGGACAAGTAGCTCGGATGATACTCCTT
* *
42083137 TGAGCAGGAAAAGTAGC
1 TAAGCAGGACAAGTAGC
42083154 AGGGACGTGT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
33 41 0.93
34 3 0.07
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.23
Consensus pattern (33 bp):
TAAGCAGGACAAGTAGCTCGGATGATACTCCTT
Found at i:42083210 original size:33 final size:33
Alignment explanation
Indices: 42083090--42083231 Score: 112
Period size: 33 Copynumber: 4.4 Consensus size: 33
42083080 CAGTTAGTAC
* * * *
42083090 GGATGATGCTCCTTTAAGCAGGACAAGTAGCTG
1 GGATGATGCCCCTTCAAGCAGGCCAAGTAGCAG
* * ** **
42083123 GGATGATACTCCTTTGAGCAGGAAAAGTAGCAG
1 GGATGATGCCCCTTCAAGCAGGCCAAGTAGCAG
* * * * *
42083156 GGACG-TG--TCTAT-AAGCCGGCCAATTAGTAG
1 GGATGATGCCCCT-TCAAGCAGGCCAAGTAGCAG
42083186 GGATGATGCCCCTTCAAGCAGGCCAAGTAGCAG
1 GGATGATGCCCCTTCAAGCAGGCCAAGTAGCAG
42083219 GGATGATGCCCCT
1 GGATGATGCCCCT
42083232 ATAATCAGAT
Statistics
Matches: 86, Mismatches: 18, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
30 18 0.21
31 3 0.03
32 2 0.02
33 63 0.73
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.21
Consensus pattern (33 bp):
GGATGATGCCCCTTCAAGCAGGCCAAGTAGCAG
Found at i:42086754 original size:52 final size:51
Alignment explanation
Indices: 42086653--42086754 Score: 125
Period size: 52 Copynumber: 2.0 Consensus size: 51
42086643 TATATATTCA
* * *
42086653 ACTTAACATTTTTTAAATTTAATATTTTATTTTTTTTAATTTGATATTTAG
1 ACTTAACATTTTTTAAATTTAATATCTAATTTTTTTTAATTTGAAATTTAG
* * *
42086704 ACTTGACATTTTTTTTAATTTGATATCTAATTTTTTTTATATTT-AAATTTA
1 ACTTAACA-TTTTTTAAATTTAATATCTAATTTTTTTTA-ATTTGAAATTTA
42086755 TTAAATATTA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
51 7 0.16
52 32 0.74
53 4 0.09
ACGTcount: A:0.30, C:0.05, G:0.04, T:0.61
Consensus pattern (51 bp):
ACTTAACATTTTTTAAATTTAATATCTAATTTTTTTTAATTTGAAATTTAG
Found at i:42086950 original size:11 final size:11
Alignment explanation
Indices: 42086930--42086968 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
42086920 AAAGCAAAAC
42086930 AACAAAATAAT
1 AACAAAATAAT
*
42086941 AACAATATAAT
1 AACAAAATAAT
*
42086952 AACAAAATGAT
1 AACAAAATAAT
42086963 AACAAA
1 AACAAA
42086969 TAAAAAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.69, C:0.10, G:0.03, T:0.18
Consensus pattern (11 bp):
AACAAAATAAT
Found at i:42086980 original size:22 final size:22
Alignment explanation
Indices: 42086930--42086974 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
42086920 AAAGCAAAAC
*
42086930 AACAAAATAATAACAATATAAT
1 AACAAAATAATAACAATATAAA
*
42086952 AACAAAATGATAACAA-ATAAA
1 AACAAAATAATAACAATATAAA
42086973 AA
1 AA
42086975 ATAAAAAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.71, C:0.09, G:0.02, T:0.18
Consensus pattern (22 bp):
AACAAAATAATAACAATATAAA
Found at i:42087664 original size:31 final size:31
Alignment explanation
Indices: 42087586--42087669 Score: 109
Period size: 29 Copynumber: 2.7 Consensus size: 31
42087576 AAAGAATTGA
*
42087586 ATTAAATTAAAATCTCATGTATAAAATTACAC
1 ATTAAATTAAAAT-TTATGTATAAAATTACAC
* *
42087618 A--AAAATAAAATTTATGTATACAATTACAC
1 ATTAAATTAAAATTTATGTATAAAATTACAC
*
42087647 ATTAAATTATAATTTATGTATAA
1 ATTAAATTAAAATTTATGTATAA
42087670 TTTTGAGATT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
29 17 0.39
30 9 0.20
31 17 0.39
32 1 0.02
ACGTcount: A:0.51, C:0.08, G:0.04, T:0.37
Consensus pattern (31 bp):
ATTAAATTAAAATTTATGTATAAAATTACAC
Found at i:42087671 original size:29 final size:30
Alignment explanation
Indices: 42087586--42087669 Score: 100
Period size: 31 Copynumber: 2.8 Consensus size: 30
42087576 AAAGAATTGA
*
42087586 ATTAAATTAAAATCTCATGTATAAAATTACAC
1 ATTAAATTAAAAT-TTATGTAT-AAATTACAC
*
42087618 A--AAAATAAAATTTATGTATACAATTACAC
1 ATTAAATTAAAATTTATGTATA-AATTACAC
*
42087647 ATTAAATTATAATTTATGTATAA
1 ATTAAATTAAAATTTATGTATAA
42087670 TTTTGAGATT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
28 1 0.02
29 16 0.36
30 10 0.22
31 17 0.38
32 1 0.02
ACGTcount: A:0.51, C:0.08, G:0.04, T:0.37
Consensus pattern (30 bp):
ATTAAATTAAAATTTATGTATAAATTACAC
Found at i:42088297 original size:28 final size:28
Alignment explanation
Indices: 42088242--42088297 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
42088232 CTAATCTCTT
* * * *
42088242 TATTATTAAATATATTAATTTAATTTTG
1 TATTATTAAATAAATTAAATAAACTTTG
42088270 TATTATTAAATAAATTAAATAAACTTTG
1 TATTATTAAATAAATTAAATAAACTTTG
42088298 AAAATTATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.50
Consensus pattern (28 bp):
TATTATTAAATAAATTAAATAAACTTTG
Found at i:42088911 original size:15 final size:17
Alignment explanation
Indices: 42088893--42088929 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
42088883 TGATTTTTAA
42088893 AAATTATA-AAA-AATT
1 AAATTATATAAATAATT
*
42088908 AAATTATATAAATAGTT
1 AAATTATATAAATAATT
42088925 AAATT
1 AAATT
42088930 TCGCCACCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 8 0.42
16 3 0.16
17 8 0.42
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
AAATTATATAAATAATT
Found at i:42092313 original size:24 final size:24
Alignment explanation
Indices: 42092268--42092324 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
42092258 TGGAATTCAG
*
42092268 TACATACATATGTAAACAGTGTCA
1 TACATACATATATAAACAGTGTCA
* ** *
42092292 TACATACATATATAGATGGTGTTA
1 TACATACATATATAAACAGTGTCA
42092316 TACATACAT
1 TACATACAT
42092325 TCATAAATGC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.33
Consensus pattern (24 bp):
TACATACATATATAAACAGTGTCA
Found at i:42092460 original size:20 final size:20
Alignment explanation
Indices: 42092435--42092504 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
42092425 GTGGATTTCA
42092435 ATACATACATAGGTGGTGTC
1 ATACATACATAGGTGGTGTC
* *
42092455 ATACATACATAGAG-AGTTTC
1 ATACATACATAG-GTGGTGTC
** **
42092475 ATGTATACATATATGGTGTC
1 ATACATACATAGGTGGTGTC
42092495 ATACATACAT
1 ATACATACAT
42092505 TCATACATGC
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
20 37 0.97
21 1 0.03
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (20 bp):
ATACATACATAGGTGGTGTC
Found at i:42092517 original size:180 final size:184
Alignment explanation
Indices: 42092307--42092650 Score: 470
Period size: 180 Copynumber: 1.9 Consensus size: 184
42092297 ACATATATAG
* *
42092307 ATGGTGTTATACATACATTCATAAATGCTCTGAGTACTCTGAGGGTCT-ACTATGGGTGCTTTTA
1 ATGGTGTCATACATACATTCATAAATGCTCTGAGTACTCTGAGGGTCTAACTATGGGTGCATTTA
42092371 TA-ATATCTCTGGTGTACCATCCTAG-TCCCAGTTAGCCATCTGAA-TTTCC-TACTAGTGG-AT
66 TACATATCTCTGGTGTACCATCCT-GTTCCCAGTTAGCCATCTGAATTTTCCATACTAGTGGCAT
42092431 T-TCA-ATACATACATAGGTGGTGTCATACATACATAGAGAGTTTCATGTATACATAT
130 TATCACATACATACATA-GT--TGTCATACATACATAGAGAGTTTCATGTATACATAT
* * *
42092487 ATGGTGTCATACATACATTCATACATGCTCTGAGTACTCTTAGGTTCTAACTATGGGTGCATTTA
1 ATGGTGTCATACATACATTCATAAATGCTCTGAGTACTCTGAGGGTCTAACTATGGGTGCATTTA
* * ** * *
42092552 TACTATTTCTCTGGTGTACCATTCTGTTCCTGGTTAGCTATCTGAATTTTCCATTCTAGTGGCAT
66 TAC-ATATCTCTGGTGTACCATCCTGTTCCCAGTTAGCCATCTGAATTTTCCATACTAGTGGCAT
*
42092617 TAATTACATACATACATAGTTGTCATACATACAT
130 T-ATCACATACATACATAGTTGTCATACATACAT
42092651 GCTCTGAGGA
Statistics
Matches: 142, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
180 44 0.31
181 17 0.12
182 1 0.01
183 35 0.25
184 5 0.04
185 8 0.06
186 17 0.12
188 4 0.03
189 11 0.08
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.38
Consensus pattern (184 bp):
ATGGTGTCATACATACATTCATAAATGCTCTGAGTACTCTGAGGGTCTAACTATGGGTGCATTTA
TACATATCTCTGGTGTACCATCCTGTTCCCAGTTAGCCATCTGAATTTTCCATACTAGTGGCATT
ATCACATACATACATAGTTGTCATACATACATAGAGAGTTTCATGTATACATAT
Found at i:42094933 original size:21 final size:24
Alignment explanation
Indices: 42094903--42094948 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
42094893 ATATTAATAA
*
42094903 TTTTATTATAA-GTTTTG-ATTAT
1 TTTTATTATAATGTTTAGAATTAT
42094925 TTTTA-TATAATGTTTAGAATTAT
1 TTTTATTATAATGTTTAGAATTAT
42094948 T
1 T
42094949 CATAAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 5 0.24
22 10 0.48
23 6 0.29
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (24 bp):
TTTTATTATAATGTTTAGAATTAT
Found at i:42096221 original size:3 final size:3
Alignment explanation
Indices: 42096215--42096246 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
42096205 GCAATCTCTA
42096215 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CA
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CA
42096247 ACAAAATCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.34, G:0.31, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:42116289 original size:3 final size:3
Alignment explanation
Indices: 42116281--42116305 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
42116271 ACAGTGACAG
42116281 TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA T
42116306 CACAATTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (3 bp):
TGA
Found at i:42117235 original size:19 final size:18
Alignment explanation
Indices: 42117196--42117240 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
42117186 ATAAAAAGTT
42117196 TTTTAAATTGTCATTTTGA
1 TTTTAAATTGT-ATTTTGA
42117215 TTTTAAATTG-ATTTTTAGA
1 TTTTAAATTGTA-TTTT-GA
42117234 TTTTAAA
1 TTTTAAA
42117241 AGTTATTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 1 0.04
18 4 0.17
19 19 0.79
ACGTcount: A:0.31, C:0.02, G:0.09, T:0.58
Consensus pattern (18 bp):
TTTTAAATTGTATTTTGA
Found at i:42117322 original size:19 final size:21
Alignment explanation
Indices: 42117290--42117341 Score: 63
Period size: 19 Copynumber: 2.5 Consensus size: 21
42117280 CAATTAAGTC
*
42117290 TATAATTATCAATTTAAACAT-
1 TATAA-TATTAATTTAAACATA
*
42117311 TA-AATATTAATTTAAATATA
1 TATAATATTAATTTAAACATA
42117331 TATAATATTAA
1 TATAATATTAA
42117342 ATATATTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 13 0.48
20 4 0.15
21 10 0.37
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (21 bp):
TATAATATTAATTTAAACATA
Found at i:42117341 original size:16 final size:14
Alignment explanation
Indices: 42117314--42117348 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 14
42117304 TAAACATTAA
42117314 ATATTAATTTAAAT
1 ATATTAATTTAAAT
42117328 ATATATAATATTAAAT
1 ATAT-TAAT-TTAAAT
42117344 ATATT
1 ATATT
42117349 TCAATAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 4 0.21
15 5 0.26
16 10 0.53
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
ATATTAATTTAAAT
Found at i:42123485 original size:46 final size:48
Alignment explanation
Indices: 42123435--42123531 Score: 119
Period size: 51 Copynumber: 2.0 Consensus size: 48
42123425 ACGCATTTTG
* *
42123435 TCAATTTGGT-C-TTAATAAATTTAGCAC-GCAACATTTACATATTCTA
1 TCAATTTGGTCCTTTAACAAATTTAGC-CTACAACATTTACATATTCTA
42123481 TCAATTTGGTCCTGATTTAACAAATTTAGCCTACAACATTTACATATTCTA
1 TCAATTTGGTCC---TTTAACAAATTTAGCCTACAACATTTACATATTCTA
42123532 ACATTTATGT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
46 10 0.23
47 1 0.02
50 1 0.02
51 31 0.72
ACGTcount: A:0.34, C:0.19, G:0.08, T:0.39
Consensus pattern (48 bp):
TCAATTTGGTCCTTTAACAAATTTAGCCTACAACATTTACATATTCTA
Found at i:42123724 original size:8 final size:8
Alignment explanation
Indices: 42123708--42123740 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
42123698 GTTTGCAATA
*
42123708 TTGAATAT
1 TTGATTAT
42123716 TTGATTAT
1 TTGATTAT
42123724 TTGATTAT
1 TTGATTAT
42123732 TTGATTAT
1 TTGATTAT
42123740 T
1 T
42123741 CAAATATAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.61
Consensus pattern (8 bp):
TTGATTAT
Found at i:42123942 original size:19 final size:19
Alignment explanation
Indices: 42123918--42123954 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
42123908 GAAGGTATCC
**
42123918 ATATTTGATTATACCTTCT
1 ATATTTGAAAATACCTTCT
42123937 ATATTTGAAAATACCTTC
1 ATATTTGAAAATACCTTC
42123955 CAAATTTGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.16, G:0.05, T:0.46
Consensus pattern (19 bp):
ATATTTGAAAATACCTTCT
Found at i:42125714 original size:32 final size:32
Alignment explanation
Indices: 42125677--42125738 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
42125667 CACAATTCAC
42125677 AAAATATATAAACATTAAAGATTTAATTTGAT
1 AAAATATATAAACATTAAAGATTTAATTTGAT
42125709 AAAATATATAAACATTAAAGATTTAATTTG
1 AAAATATATAAACATTAAAGATTTAATTTG
42125739 TTATCATATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.37
Consensus pattern (32 bp):
AAAATATATAAACATTAAAGATTTAATTTGAT
Found at i:42126841 original size:31 final size:32
Alignment explanation
Indices: 42126782--42126841 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
42126772 TTCTTGATCC
* *
42126782 AATTTGATTACTCAAACTTGACACTTTTTCCT
1 AATTTGATTACTCAAACTTAACAATTTTTCCT
42126814 AATTTGA-TAC-CTAAACTTAACAATTTTT
1 AATTTGATTACTC-AAACTTAACAATTTTT
42126842 TTTTAAGTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 1 0.04
31 17 0.68
32 7 0.28
ACGTcount: A:0.33, C:0.18, G:0.05, T:0.43
Consensus pattern (32 bp):
AATTTGATTACTCAAACTTAACAATTTTTCCT
Found at i:42126885 original size:60 final size:59
Alignment explanation
Indices: 42126814--42126925 Score: 136
Period size: 59 Copynumber: 1.9 Consensus size: 59
42126804 ACTTTTTCCT
*
42126814 AATTTGATACCTAAACTTAACAAT-TTTTTTTTAAGTTGGTACATAAACTTTTTGGGGTCA
1 AATTTGATACCTAAACTTAAC--TCTTTTTTGTAAGTTGGTACATAAACTTTTTGGGGTCA
* * * * * *
42126874 AATTTGGTACCTGAACTTGACTCTTTTTTGTAATTTGGTACCTAATCTTTTT
1 AATTTGATACCTAAACTTAACTCTTTTTTGTAAGTTGGTACATAAACTTTTT
42126926 TTAATATTAA
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
58 1 0.02
59 25 0.57
60 18 0.41
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.46
Consensus pattern (59 bp):
AATTTGATACCTAAACTTAACTCTTTTTTGTAAGTTGGTACATAAACTTTTTGGGGTCA
Found at i:42127137 original size:31 final size:31
Alignment explanation
Indices: 42127096--42127170 Score: 107
Period size: 31 Copynumber: 2.4 Consensus size: 31
42127086 AAAAAAAAGC
* *
42127096 TTAGGCACCAAATTAA-AAAAAAGTGCCAAGT
1 TTAGGTACCAAATTAAGAAAAAA-TACCAAGT
*
42127127 TTAGGTACCAAATTAAGAAAAAATATCAAGT
1 TTAGGTACCAAATTAAGAAAAAATACCAAGT
42127158 TTAGGTACCAAAT
1 TTAGGTACCAAAT
42127171 GTTGTATTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
31 34 0.85
32 6 0.15
ACGTcount: A:0.48, C:0.13, G:0.15, T:0.24
Consensus pattern (31 bp):
TTAGGTACCAAATTAAGAAAAAATACCAAGT
Found at i:42127558 original size:18 final size:19
Alignment explanation
Indices: 42127524--42127567 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
42127514 AATACATTCA
*
42127524 ATATTTGAATAAGCTTTCT
1 ATATTTGAATAAGCTTTCC
42127543 ATATTT-AAT-AGACTTTCC
1 ATATTTGAATAAG-CTTTCC
42127561 ATATTTG
1 ATATTTG
42127568 TAAAAATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 2 0.09
18 14 0.64
19 6 0.27
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.48
Consensus pattern (19 bp):
ATATTTGAATAAGCTTTCC
Found at i:42127697 original size:19 final size:18
Alignment explanation
Indices: 42127653--42127703 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 18
42127643 TATGGAAGGT
**
42127653 ATACCTTCCATATCAGAA
1 ATACCTTCCATATTTGAA
42127671 AT--CTTCCATATTTGACA
1 ATACCTTCCATATTTGA-A
*
42127688 ATACCTTCCAAATTTG
1 ATACCTTCCATATTTG
42127704 TGTTAAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
16 11 0.41
17 3 0.11
18 2 0.07
19 11 0.41
ACGTcount: A:0.33, C:0.25, G:0.06, T:0.35
Consensus pattern (18 bp):
ATACCTTCCATATTTGAA
Found at i:42134266 original size:25 final size:24
Alignment explanation
Indices: 42134238--42134290 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
42134228 ATAAATATTT
* *
42134238 AATTGAAGAAAAAACTCAATAACTA
1 AATTGAA-AAAAAACTCAAAAACCA
*
42134263 AATTGAAAAAAACCTCAAAAACCA
1 AATTGAAAAAAAACTCAAAAACCA
42134287 AATT
1 AATT
42134291 AAATAATGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.60, C:0.15, G:0.06, T:0.19
Consensus pattern (24 bp):
AATTGAAAAAAAACTCAAAAACCA
Found at i:42142662 original size:911 final size:903
Alignment explanation
Indices: 42141076--42143509 Score: 3001
Period size: 911 Copynumber: 2.7 Consensus size: 903
42141066 TTTTGTGCCA
* * * ***
42141076 TTAGGACTAGTTTACCATTTAGAACCATACATAGTTGCCTAAGAGTTAATTTGTTATTGAGGTTG
1 TTAGGACTAGTTTACCATTTAGAACCATACACAGTTGCCTAAGGGCTAATTTACCATTGAGGTTG
* * * * *
42141141 AAAAATATTTTTGAAAAGTGTCGTGAAAAAGAA-CTTTTGAAAAGTTTGATAATGTTTA-A---C
66 AAAAGTGTTTTTGAAAAATGT-GTGAAAAA-AAGCTTTTGAAAAGTTTGATAGTGTTTACATTGT
* * * *
42141201 TGTCAAAAAATGCTTTTGAGAAGATAAAATATTAATTTTAGACACGATGTTATAAAGTGAAAGAT
129 TGTC-AAAAACGTTTTTGAGAAGATAAAATGTTAATTTTAGACACGATTTTATAAAGTGAAAGAT
* * *
42141266 TTAATGGGATATAAAAAAAGGTAGCTTAATTGAAAAATACTTTTCCAAAATTTTTGACTTGGTTA
193 TTAATGGG-T-TATAAAAAGGTAGCTTCATTGAAAAATACTTTTTCAAAATTTTTGACTTGGTTA
* ** * ***** *
42141331 AAATCTTAGTTTAAAATCATGTTCAGTTTAAAATGCTGCTTTTTTACAAAAAAAAATTTGTTTGC
256 AAATCTTAGTTTAAAATCATGTTCAGTTTAAAAAGCTGCTTGCTTAC-CAATTTTTTTTGTTTAC
* * * *
42141396 TGCTTTCCAACCTTAATAGTAAACAAAAAAAATTGTAAACAAAGA-TCTTTTCAAAT-CAAACCA
320 TGCTTTCCAGCCTCAATAGTAAAC-AAAAAATTTGTAAACAAAGAGT-TCTTCAAATCCAAACCA
* * * * * * *
42141459 TGATTTCAAACTGCAATTCTAACC---CAATCCAAAATTTTTAACCTTCGGCTTTTGAAAAAATA
383 TGATTAC-AACT--AA-CCCAACCAAACAAGCCAAAATTTTTAACCTTCAGCTTTTGGAAAAATG
* * *
42141521 TTTTTCAATGAATTTACTTTTTTATCCCCCATTAAATCTTTCACTTTATAATATGTTTAAAATTG
444 TTTTTCAATGAATTTACTTTTTTATCCCTCATTAAATCTTTCACTTTATAACATGTCTAAAATTG
* * * *
42141586 ACATTTTATCTTCTTAAAAGCACTTTTTAATAATAAT-AGTAAACACTATCAAACTTTTTAAAAG
509 ACATTTTATCTTCTCAAAAGCACTTTTTAACAGTAATGA-TAAACACTATCAAACTTTTCAAAAG
* *** * * *
42141650 CATTTTTTAAAAGTTTTTTTCACAACACTTTTCAATCTCAATAGTAAACTAGCCGTTAGACAACT
573 CATTTTTCAAAAGCAGTTTTCAAAACACTTTTCAATCTCAATAGTAAACTAGCCCTTAGACAAAT
42141715 ATATATGGTTCTAAATGGTAAACGTAGTCCTAAGTAGAGTTGTCCATGGGTCGTACCGGACCCTA
638 ATATATGGTTCTAAATGGTAAACGTAGTCCTAAGTAGAGTTGTCCATGGGTCGTACCGGACCCTA
*
42141780 ACAAAATTTTAGGCCTAGACCCAA-CCCTAACTATGTATTTGGTGCGTATTATATTTTTAAAAAA
703 ACAAAATTTTAGGCCTAGA-CCAAGCCCTAACTATATATTTGGTGCGTATTATATTTTTAAAAAA
* * ** *
42141844 TATATATAAAAAATAAAATTAATACGGGCTAGGCTGGGCCAGGACAGTGTTTTAGTATTTTTATT
767 TATATATAAAAAATAAAATTAATACAGGCTAGGCTAGGCCAGGACAAAGTTTTAGCATTTTTATT
* ** *
42141909 CGGGTCGAGTTTGGATAAAAATTTAGGCTCATTTTTTAAGCTGGATTCGATACGATCCATGGACA
832 CGGGTCGAGTTTGGATAAAAATTTAGACTCATTTTTTAAGCTGGACCCGACACGATCCATGGACA
42141974 ACTCTAC
897 ACTCTAC
* *
42141981 TTAGGATTAATTTACCATTTAGAACCATACACAGTTGCCTAAGGGCTAATTTACCATTGAGGTTG
1 TTAGGACTAGTTTACCATTTAGAACCATACACAGTTGCCTAAGGGCTAATTTACCATTGAGGTTG
* * *
42142046 AAAGGTGTTTTTGAAAAATGATGTGAAAAATAGCTTTTGAAAAGTTTGATAGTATTTACTATTGT
66 AAAAGTGTTTTTGAAAAATG-TGTGAAAAAAAGCTTTTGAAAAGTTTGATAGTGTTTAC-ATTGT
42142111 TGTCAAAAAGCGTTTTTGAGAAGATAAAATGTTAATGTTT-GACAC-AGTTTTATAAAGTGAAAG
129 TGTCAAAAA-CGTTTTTGAGAAGATAAAATGTTAAT-TTTAGACACGA-TTTTATAAAGTGAAAG
* * *
42142174 ATTTAACGAGGTTATAAAAAGGTAGCTTCATTAAAAAATACTTTTTCAAAATTTTTGACTTGATT
191 ATTTAATG-GGTTATAAAAAGGTAGCTTCATTGAAAAATACTTTTTCAAAATTTTTGACTTGGTT
* * * *
42142239 AAAATCTTAATTTAAAATCATGTTCAATTTAAAAAGTTGCTTGCTTACCACTTTTTTTTGTTTAC
255 AAAATCTTAGTTTAAAATCATGTTCAGTTTAAAAAGCTGCTTGCTTACCAATTTTTTTTGTTTAC
* *
42142304 TGCTTTCCAGCCTCAATAGTAAACAAAAAATTTGATAAACAAATAGTTCTT-AAATCCAAAGCAT
320 TGCTTTCCAGCCTCAATAGTAAACAAAAAATTTG-TAAACAAAGAGTTCTTCAAATCCAAACCAT
* * *
42142368 GATCTACAATTCTAACCCAAGCCAAAAAAGCCAAAATTTTTAACCTTCAACTTTTGGAAAAATGC
384 GAT-TACAA--CTAACCCAA-CCAAACAAGCCAAAATTTTTAACCTTCAGCTTTTGGAAAAATGT
* * *
42142433 TTTTCAAT-ATATTTACTTTTTTATCCCTCATTAAATCTTTCACCTAATAACATGTCTAAAATTA
445 TTTTCAATGA-ATTTACTTTTTTATCCCTCATTAAATCTTTCACTTTATAACATGTCTAAAATTG
42142497 ACATTTTATCTTCTCAAAAGCACTTTTTAACAGTAATGATAAACACTATCAAACTTTTCAAAAGC
509 ACATTTTATCTTCTCAAAAGCACTTTTTAACAGTAATGATAAACACTATCAAACTTTTCAAAAGC
** * *
42142562 -TCTTTTCCGAAGCAGTTTTCAAAAACATTTTTCAATCTCAATAGTAAACTTA-CCCTTAGATAA
574 AT-TTTTCAAAAGCAGTTTTC-AAAACACTTTTCAATCTCAATAGTAAAC-TAGCCCTTAGACAA
* * * **
42142625 ATATGTATGGTTCTAAATGGTAAAC-TAGTCTTAAGTAGAGTTGTCCATGTGTCGTGTCGGACCC
636 ATATATATGGTTCTAAATGGTAAACGTAGTCCTAAGTAGAGTTGTCCATGGGTCGTACCGGACCC
* * * * *
42142689 TAACAAAATTTTAGGCTTGGACTAAGCCCTAACTATATATTTGGTGTGTATTATATTTTTTAAAA
701 TAACAAAATTTTAGGCCTAGACCAAGCCCTAACTATATATTTGGTGCGTATTATATTTTTAAAAA
* *
42142754 ATATATATAAAAAATAAATTTAATACAGGCTAGGCTAGGCCGGGACAAAGTTTTAGCATTTTTAT
766 ATATATATAAAAAATAAAATTAATACAGGCTAGGCTAGGCCAGGACAAAGTTTTAGCATTTTTAT
* **
42142819 TCGGGTCGAGTTTGGGTAAAAATTTAGACTCATTTTTTGGGCTGGACCCGACACGATCCATGGAC
831 TCGGGTCGAGTTTGGATAAAAATTTAGACTCATTTTTTAAGCTGGACCCGACACGATCCATGGAC
42142884 AACTCTAC
896 AACTCTAC
* * * * * * * *
42142892 TTAAGACTAGTTTGCCATTTAGAGCCATAAACAATTACCTAATGGCTAGTTTACCATTGAGGTTG
1 TTAGGACTAGTTTACCATTTAGAACCATACACAGTTGCCTAAGGGCTAATTTACCATTGAGGTTG
*
42142957 AAAAGTG-TTTTGAAAAATGCTGTTAAAAAAAATGCTTTTGAAAAGTTTGATAGTGTTTACCATT
66 AAAAGTGTTTTTGAAAAATG-TG-TGAAAAAAA-GCTTTTGAAAAGTTTGATAGTGTTTA-CATT
* *
42143021 GTTGTCAAAAACTGTTTTTGAGAAGATAAAATGTAAATTTTAGACATGATTTTATAAAGTGAAAG
127 GTTGTCAAAAAC-GTTTTTGAGAAGATAAAATGTTAATTTTAGACACGATTTTATAAAGTGAAAG
* * ** ** *
42143086 ATTTAATGGGGATATAAAAAAGTAATTTCATTGAAAAATACTTTTTCAATTTTTTTGGCTTGGTT
191 ATTTAAT-GGGTTATAAAAAGGTAGCTTCATTGAAAAATACTTTTTCAAAATTTTTGACTTGGTT
* *
42143151 AAAATCCTAGTTTAAAATCATGTTCGGTTTAAAAAGCTGCTTGCTTACCAAATTTTTTTTGTTTA
255 AAAATCTTAGTTTAAAATCATGTTCAGTTTAAAAAGCTGCTTGCTTACC-AATTTTTTTTGTTTA
* * * *
42143216 CTGGTTTCCTGCCTCAATAATAAACAAAAAATTTGGTAAACAAAGAGCTCTTCAAA-CCAAACCA
319 CTGCTTTCCAGCCTCAATAGTAAACAAAAAATTT-GTAAACAAAGAGTTCTTCAAATCCAAACCA
* * * * *
42143280 TGATTTTA-AACT--GCGATTCTAAACCAAGCCAACAA-TTTTAACCTTCAGTTTTTGGAAAAAT
383 TGA--TTACAACTAACCCA-ACCAAA-CAAGCCAA-AATTTTTAACCTTCAGCTTTTGGAAAAAT
* * *
42143341 GTTTTTCAATGAAGTTATTTTTTTATCCCTTATTAAATCTTTCACTTTATAACATCATGTCTAAA
443 GTTTTTCAATGAATTTACTTTTTTATCCCTCATTAAATCTTTCACTTTAT-A-A-CATGTCTAAA
* * *
42143406 ATTGACATTTTATCTTTTCAAAAGCACTTTTTGACAGCAATGATAAACACTATCAAACTTTTCAA
505 ATTGACATTTTATCTTCTCAAAAGCACTTTTTAACAGTAATGATAAACACTATCAAACTTTTCAA
* *** *
42143471 AAGCATTTTTTAAAAGTTTTTTTTCACAACACTTTTCAA
570 AAGCATTTTTCAAAAG-CAGTTTTCAAAACACTTTTCAA
42143510 AAACACTTTT
Statistics
Matches: 1315, Mismatches: 166, Indels: 88
0.84 0.11 0.06
Matches are distributed among these distances:
904 1 0.00
905 104 0.08
906 1 0.00
907 17 0.01
908 59 0.04
909 105 0.08
910 149 0.11
911 456 0.35
912 240 0.18
913 170 0.13
914 12 0.01
915 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (903 bp):
TTAGGACTAGTTTACCATTTAGAACCATACACAGTTGCCTAAGGGCTAATTTACCATTGAGGTTG
AAAAGTGTTTTTGAAAAATGTGTGAAAAAAAGCTTTTGAAAAGTTTGATAGTGTTTACATTGTTG
TCAAAAACGTTTTTGAGAAGATAAAATGTTAATTTTAGACACGATTTTATAAAGTGAAAGATTTA
ATGGGTTATAAAAAGGTAGCTTCATTGAAAAATACTTTTTCAAAATTTTTGACTTGGTTAAAATC
TTAGTTTAAAATCATGTTCAGTTTAAAAAGCTGCTTGCTTACCAATTTTTTTTGTTTACTGCTTT
CCAGCCTCAATAGTAAACAAAAAATTTGTAAACAAAGAGTTCTTCAAATCCAAACCATGATTACA
ACTAACCCAACCAAACAAGCCAAAATTTTTAACCTTCAGCTTTTGGAAAAATGTTTTTCAATGAA
TTTACTTTTTTATCCCTCATTAAATCTTTCACTTTATAACATGTCTAAAATTGACATTTTATCTT
CTCAAAAGCACTTTTTAACAGTAATGATAAACACTATCAAACTTTTCAAAAGCATTTTTCAAAAG
CAGTTTTCAAAACACTTTTCAATCTCAATAGTAAACTAGCCCTTAGACAAATATATATGGTTCTA
AATGGTAAACGTAGTCCTAAGTAGAGTTGTCCATGGGTCGTACCGGACCCTAACAAAATTTTAGG
CCTAGACCAAGCCCTAACTATATATTTGGTGCGTATTATATTTTTAAAAAATATATATAAAAAAT
AAAATTAATACAGGCTAGGCTAGGCCAGGACAAAGTTTTAGCATTTTTATTCGGGTCGAGTTTGG
ATAAAAATTTAGACTCATTTTTTAAGCTGGACCCGACACGATCCATGGACAACTCTAC
Found at i:42143520 original size:13 final size:13
Alignment explanation
Indices: 42143498--42143522 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42143488 TTTTTTTCAC
42143498 AACACTTTTCAAA
1 AACACTTTTCAAA
42143511 AACACTTTTCAA
1 AACACTTTTCAA
42143523 CCTCAATAGT
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:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (13 bp):
AACACTTTTCAAA
Found at i:42145065 original size:39 final size:35
Alignment explanation
Indices: 42144982--42145065 Score: 82
Period size: 35 Copynumber: 2.3 Consensus size: 35
42144972 ATATAAACAA
* *
42144982 ATATTTAATTAATAATGAGAAAAAATATATATTAT
1 ATATTTAATTAACAATGAGAAAAAATATATATAAT
42145017 A-ATTATAATTAACAATGA-AAAACTAATGATAATAATAAT
1 ATATT-TAATTAACAATGAGAAAA--AAT-AT-AT-ATAAT
42145056 ATATTTAATT
1 ATATTTAATT
42145066 GACATAAGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
34 7 0.17
35 13 0.32
36 3 0.08
37 2 0.05
38 2 0.05
39 10 0.25
40 3 0.08
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (35 bp):
ATATTTAATTAACAATGAGAAAAAATATATATAAT
Found at i:42160812 original size:24 final size:24
Alignment explanation
Indices: 42160785--42160835 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
42160775 TACTATTTTT
42160785 TAAGTAAAAAATTAAAATATAATC
1 TAAGTAAAAAATTAAAATATAATC
42160809 TAAGTAAAAAATTAAAATATAATC
1 TAAGTAAAAAATTAAAATATAATC
42160833 TAA
1 TAA
42160836 CTCTTAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (24 bp):
TAAGTAAAAAATTAAAATATAATC
Found at i:42163363 original size:35 final size:35
Alignment explanation
Indices: 42163312--42163382 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
42163302 ACTACTACTA
*
42163312 ATAATAATAACAGCCCTTCAGTAGTGCTGAACTTC
1 ATAAAAATAACAGCCCTTCAGTAGTGCTGAACTTC
42163347 ATAAAAATAACAGCCCTTCAGTAGTGCTGAACTTC
1 ATAAAAATAACAGCCCTTCAGTAGTGCTGAACTTC
42163382 A
1 A
42163383 ACTTACATGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.27
Consensus pattern (35 bp):
ATAAAAATAACAGCCCTTCAGTAGTGCTGAACTTC
Found at i:42167610 original size:24 final size:23
Alignment explanation
Indices: 42167583--42167643 Score: 61
Period size: 25 Copynumber: 2.6 Consensus size: 23
42167573 TTTTTATCGA
*
42167583 AATAAACTAAAAAT-TAGTCTATAC
1 AATAAACTAAAAATATA-TATAT-C
*
42167607 AATAGAAATAAAAATATATATATC
1 AATA-AACTAAAAATATATATATC
*
42167631 AATAAACTCAAAA
1 AATAAACTAAAAA
42167644 CGATGTATCT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
23 7 0.23
24 9 0.29
25 13 0.42
26 2 0.06
ACGTcount: A:0.61, C:0.10, G:0.03, T:0.26
Consensus pattern (23 bp):
AATAAACTAAAAATATATATATC
Found at i:42170284 original size:17 final size:17
Alignment explanation
Indices: 42170261--42170304 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
42170251 CAAATTTTTA
42170261 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATGAT
*
42170277 ATAAATTATTAAAATGAT
1 A-AAATTATAAAAATGAT
*
42170295 AGAATTATAA
1 AAAATTATAA
42170305 TTTTATTATC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 1 0.04
17 19 0.83
18 3 0.13
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATGAT
Found at i:42170603 original size:66 final size:66
Alignment explanation
Indices: 42170526--42170658 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
42170516 GGTAAACTTC
42170526 ACTCAAGGTCTTTATATTATTAGTAAGTTTACGTTTTGGTCAATCGATTTCAAAAATTTACAAAA
1 ACTCAAGGTCTTTATATTATTAGTAAGTTTACGTTTTGGTCAATCGATTTCAAAAATTTACAAAA
42170591 T
66 T
42170592 ACTCAAGGTCTTTATATTATTAGTAAGTTTACGTTTTGGTCAATCGATTTCAAAAATTTACAAAA
1 ACTCAAGGTCTTTATATTATTAGTAAGTTTACGTTTTGGTCAATCGATTTCAAAAATTTACAAAA
42170657 T
66 T
42170658 A
1 A
42170659 GTTATTAAAG
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (66 bp):
ACTCAAGGTCTTTATATTATTAGTAAGTTTACGTTTTGGTCAATCGATTTCAAAAATTTACAAAA
T
Found at i:42172050 original size:7 final size:7
Alignment explanation
Indices: 42172038--42172083 Score: 83
Period size: 7 Copynumber: 6.6 Consensus size: 7
42172028 CCCACCAACT
42172038 TTACTTC
1 TTACTTC
42172045 TTACTTC
1 TTACTTC
42172052 TTACTTC
1 TTACTTC
*
42172059 TTGCTTC
1 TTACTTC
42172066 TTACTTC
1 TTACTTC
42172073 TTACTTC
1 TTACTTC
42172080 TTAC
1 TTAC
42172084 ACAATGTTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.13, C:0.28, G:0.02, T:0.57
Consensus pattern (7 bp):
TTACTTC
Found at i:42172138 original size:13 final size:13
Alignment explanation
Indices: 42172120--42172145 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42172110 ATTCCTTTTG
42172120 TTCTCGCCGGAAA
1 TTCTCGCCGGAAA
42172133 TTCTCGCCGGAAA
1 TTCTCGCCGGAAA
42172146 AAATGGCTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.31, G:0.23, T:0.23
Consensus pattern (13 bp):
TTCTCGCCGGAAA
Found at i:42176471 original size:13 final size:14
Alignment explanation
Indices: 42176443--42176477 Score: 54
Period size: 13 Copynumber: 2.5 Consensus size: 14
42176433 AAAGTATATG
42176443 AATTAAAAATAATTA
1 AATT-AAAATAATTA
42176458 AATTAAAA-AATTA
1 AATTAAAATAATTA
42176471 AATTAAA
1 AATTAAA
42176478 TTTACAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 12 0.60
14 4 0.20
15 4 0.20
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AATTAAAATAATTA
Found at i:42178520 original size:279 final size:275
Alignment explanation
Indices: 42177993--42178531 Score: 611
Period size: 279 Copynumber: 1.9 Consensus size: 275
42177983 ACTTTAGATT
* ** *
42177993 CTGCCATTGTTGACTGCAATAACATAGTTGAAACATGTTCTTTCTGGTTCCCATAGATTATAAAT
1 CTGCCATTGTTGACTGCAATAACATAGCTGAAACATGTTCTTTCTCATTCCCATAGATTATAAAG
* * * * * *
42178058 GATGGATTTTCTTTGCATTTGTAATAATATTTTTGTGATTCATTGGTATTTCGAATTTGATTCTG
66 GATGGATTTTCTTGGCATTTATAATAATATTTTCGTGATTCATTGGTATATCGAATTCGATTCTC
* * * *
42178123 TGTTAACTGATAATCCAAGAACCATGAACATGGAACTGAAATGTTGCTCCTTCTTTGTCAATATC
131 TCTTAACTGATAATCCAAGAACCATGAACATGGAACTGAAATATTGATCCATCTTTGTC-ATATC
* * * * *
42178188 TGCTAGCATGATTTTTGTTAAATTATGTGACTAACAATGGGAAATGGTTCAAATTCTAAGGCTAT
195 T-CTAG-A-GATTTTTGTTAAACTACGGGACTAACAATAGGAAATGCTTCAAATTCTAAGGCTAT
42178253 TAGTCTCAAATTTTAGAGA
257 TAGTCTCAAATTTTAGAGA
* * * * *
42178272 CTGCCATTGTTGACTGCTATAACATAGCTGAAGCATGTTCTTTTTCATTTCCATAGGTTATAAAG
1 CTGCCATTGTTGACTGCAATAACATAGCTGAAACATGTTCTTTCTCATTCCCATAGATTATAAAG
* *
42178337 GATGGATTTTCTTGGCATTTATAATCATATTTAAGGACAATACGTGATTCATTGGTATATCGACT
66 GATGGATTTTCTTGGCATTTATAATAATATTT--------T-CGTGATTCATTGGTATATCGAAT
* * * *
42178402 TCGATTCTCTCTTAACTGATAATCCGAG-ACCATTAACATGGAACTGAAATATTTATTCATCTTT
122 TCGATTCTCTCTTAACTGATAATCCAAGAACCATGAACATGGAACTGAAATATTGATCCATCTTT
* * * * *
42178466 TTC-TATCT-T-G-GATTTTTGTTGAACTACGGGACTAATAATATGAAATGCTTCAAATTCTAAT
187 GTCATATCTCTAGAGATTTTTGTTAAACTACGGGACTAACAATAGGAAATGCTTCAAATTCTAAG
42178527 GCTAT
252 GCTAT
42178532 AGTTGACTGC
Statistics
Matches: 216, Mismatches: 35, Indels: 18
0.80 0.13 0.07
Matches are distributed among these distances:
279 132 0.61
282 1 0.00
283 1 0.00
285 5 0.02
287 33 0.15
288 44 0.20
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.39
Consensus pattern (275 bp):
CTGCCATTGTTGACTGCAATAACATAGCTGAAACATGTTCTTTCTCATTCCCATAGATTATAAAG
GATGGATTTTCTTGGCATTTATAATAATATTTTCGTGATTCATTGGTATATCGAATTCGATTCTC
TCTTAACTGATAATCCAAGAACCATGAACATGGAACTGAAATATTGATCCATCTTTGTCATATCT
CTAGAGATTTTTGTTAAACTACGGGACTAACAATAGGAAATGCTTCAAATTCTAAGGCTATTAGT
CTCAAATTTTAGAGA
Found at i:42181170 original size:196 final size:200
Alignment explanation
Indices: 42180820--42181189 Score: 529
Period size: 196 Copynumber: 1.8 Consensus size: 200
42180810 TTTTTAATCT
* * *
42180820 AAGAAGAAGAAGATAATTGCATGCAATTATGTATTGTAAGATAAGTAGAATTCTACGTTTTCTCA
1 AAGAAGAAGAAGACAATTGCATGCAATTAGGTAGTGTAAGATAAGTAGAATTCTA--TTTTCTCA
* * * *
42180885 TTAATTTTTTTCTCTCTTGCTCTTGCTGGGAATTCTTGATCCTGTTTTGAGGTTTCTATTTTTTA
64 TTAATTTTTTTCTCTCTT-CTCTTGAT--GAATTCGTGAGCCTGTTTTGAGGTTTCTATTTCTTA
42180950 TTTTCCTTTATTATTGTAAGATAAGTAAAATTTTA-CTTTTTTTAAAATTAATTTTTAATCTAAG
126 TTTTCCTTTATTATTGTAAGATAAGTAAAATTTTACCTTTTTTTAAAATTAATTTTTAATCTAAG
42181014 AAGTAAGAAG
191 AAGTAAGAAG
* *
42181024 AAGAAGAAGAAGACAGTTGCATGCAATTAGGTAGTGTAAGATAAGTAGAAATT-T-TTTTTTCAT
1 AAGAAGAAGAAGACAATTGCATGCAATTAGGTAGTGTAAGATAAGTAG-AATTCTATTTTCTCAT
42181087 T-ATTATTTTTCTCTCTT-TCTT-AT-AATTCGTGAGCCTGTTTATGAGGTTTCTATTTCTTATT
65 TAATT-TTTTTCTCTCTTCTCTTGATGAATTCGTGAGCCTGTTT-TGAGGTTTCTATTTCTTATT
*
42181148 TTCCTTTATTATTGTAAGATAAGTAGAATTTTACCTTTTTTT
128 TTCCTTTATTATTGTAAGATAAGTAAAATTTTACCTTTTTTT
42181190 TCCCCTTTCA
Statistics
Matches: 152, Mismatches: 10, Indels: 15
0.86 0.06 0.08
Matches are distributed among these distances:
195 15 0.10
196 51 0.34
197 8 0.05
198 1 0.01
199 4 0.03
200 3 0.02
201 21 0.14
204 45 0.30
205 4 0.03
ACGTcount: A:0.29, C:0.10, G:0.15, T:0.46
Consensus pattern (200 bp):
AAGAAGAAGAAGACAATTGCATGCAATTAGGTAGTGTAAGATAAGTAGAATTCTATTTTCTCATT
AATTTTTTTCTCTCTTCTCTTGATGAATTCGTGAGCCTGTTTTGAGGTTTCTATTTCTTATTTTC
CTTTATTATTGTAAGATAAGTAAAATTTTACCTTTTTTTAAAATTAATTTTTAATCTAAGAAGTA
AGAAG
Found at i:42184293 original size:192 final size:192
Alignment explanation
Indices: 42183966--42184541 Score: 1091
Period size: 192 Copynumber: 3.0 Consensus size: 192
42183956 TCAATGCTAT
42183966 GAACAAGGCATAAACTAAATAAGGAAGTTGTATTTTGAGGTTTGGTTTAACACAAAGGAATAAAC
1 GAACAAGGCATAAACTAAATAAGGAAGTTGTATTTTGAGGTTTGGTTTAACACAAAGGAATAAAC
42184031 ATATTTTCTTAGAAGTGGCCCGACTGTTTGTTTCGTTTTCACCGGCCGGGCAGAAAGGCTTACAT
66 ATATTTTCTTAGAAGTGGCCCGACTGTTTGTTTCGTTTTCACCGGCCGGGCAGAAAGGCTTACAT
42184096 CTTAAACAAACTGCTTCCGTTATTTGTTTGTGGGAACATTGTGTTTTCAATGGCTATAACTA
131 CTTAAACAAACTGCTTCCGTTATTTGTTTGTGGGAACATTGTGTTTTCAATGGCTATAACTA
42184158 GAACAAGGCATAAACTAAATAAGGAAGTTGTATTTTGAGGTTTGGTTTAACACAAAGGAATAAAC
1 GAACAAGGCATAAACTAAATAAGGAAGTTGTATTTTGAGGTTTGGTTTAACACAAAGGAATAAAC
*
42184223 ATATTTTCTTAGAAGTGGCCCGACTGTTTGTTTCGTTTTCACCAGCCGGGCAGAAAGGCTTACAT
66 ATATTTTCTTAGAAGTGGCCCGACTGTTTGTTTCGTTTTCACCGGCCGGGCAGAAAGGCTTACAT
42184288 CTTAAACAAACTGCTTCCGTTATTTGTTTGTGGGAACATTGTGTTTTCAATGGCTATAACTA
131 CTTAAACAAACTGCTTCCGTTATTTGTTTGTGGGAACATTGTGTTTTCAATGGCTATAACTA
42184350 GAACAAGGCATAAACTAAATAAGGAAGTTGTATTTTGAGGTTTGGTTTAACACAAAGGAATAAAC
1 GAACAAGGCATAAACTAAATAAGGAAGTTGTATTTTGAGGTTTGGTTTAACACAAAGGAATAAAC
* * *
42184415 ATTTTTTCTTAGAAGTGGCCTGACTGTTTGTTTCGTTTTCTCCGGCCGGGCAGAAAGGCTTACAT
66 ATATTTTCTTAGAAGTGGCCCGACTGTTTGTTTCGTTTTCACCGGCCGGGCAGAAAGGCTTACAT
*
42184480 CTT-AACAAAACTGCTTCCGTTATTTGTTTGCGGGAACATTGTGTTTTCAATGGCTATAACTA
131 CTTAAAC-AAACTGCTTCCGTTATTTGTTTGTGGGAACATTGTGTTTTCAATGGCTATAACTA
42184542 ATTACAGTTT
Statistics
Matches: 377, Mismatches: 6, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
191 3 0.01
192 374 0.99
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.34
Consensus pattern (192 bp):
GAACAAGGCATAAACTAAATAAGGAAGTTGTATTTTGAGGTTTGGTTTAACACAAAGGAATAAAC
ATATTTTCTTAGAAGTGGCCCGACTGTTTGTTTCGTTTTCACCGGCCGGGCAGAAAGGCTTACAT
CTTAAACAAACTGCTTCCGTTATTTGTTTGTGGGAACATTGTGTTTTCAATGGCTATAACTA
Found at i:42190080 original size:94 final size:93
Alignment explanation
Indices: 42189813--42190137 Score: 379
Period size: 94 Copynumber: 3.4 Consensus size: 93
42189803 TTGTTTCCAA
* * * * **
42189813 CAATTATGAATGT-AAAAGATCCAATTCATGAACATACATACATGCATACATACGTACAAGGAAA
1 CAATTATGAATGTGAAAA-AGCCAATTCAAGACCATACATACATACATACATATATA-AAGGAAA
*
42189877 ACACGGTAGCTCAAGTCCCTTTGTTTCAA-T
64 ACATGGTAGCTCAAGTCCCTTTGTTT-AAGT
* * * *
42189907 CAATTATGAATGTGAAAAAGCCAATTCAAGATCATGCATGCATGCATGCAAATACACATAT-AAG
1 CAATTATGAATGTGAAAAAGCCAATTCAAGA-C---CATACATACAT--ACATACATATATAAAG
*
42189971 GAAAACATGGTAGCTCAAGTCCCTTCGTTTAAGT
60 GAAAACATGGTAGCTCAAGTCCCTTTGTTTAAGT
*
42190005 CAAAATTATGAATGTGAAAAAGCCAATTAAAGACCATACATACATACATACATATATAAAGG-AA
1 C--AATTATGAATGTGAAAAAGCCAATTCAAGACCATACATACATACATACATATATAAAGGAAA
*
42190069 ACATGGTAGCTCAAGTCCCTTTGTTTCAGT
64 ACATGGTAGCTCAAGTCCCTTTGTTTAAGT
* *
42190099 CAATTATGAATGCGAAAAGGCCAATTCAAGACCATACAT
1 CAATTATGAATGTGAAAAAGCCAATTCAAGACCATACAT
42190138 GCATGCGCGC
Statistics
Matches: 198, Mismatches: 22, Indels: 24
0.81 0.09 0.10
Matches are distributed among these distances:
92 35 0.18
94 65 0.33
95 8 0.04
96 9 0.05
97 2 0.01
98 42 0.21
99 1 0.01
100 36 0.18
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.26
Consensus pattern (93 bp):
CAATTATGAATGTGAAAAAGCCAATTCAAGACCATACATACATACATACATATATAAAGGAAAAC
ATGGTAGCTCAAGTCCCTTTGTTTAAGT
Found at i:42190385 original size:281 final size:266
Alignment explanation
Indices: 42189893--42190418 Score: 676
Period size: 281 Copynumber: 1.9 Consensus size: 266
42189883 TAGCTCAAGT
* * * * *
42189893 CCCTTTGTTTCAATCAATTATGAATGTGAAAAAGCCAATTCAAGATCATGCATGCATGCATGCAA
1 CCCTTAGTTTCAATCAATTATGAATGTGAAAAAGCCAATTCAAGACCATACATACATGCATCCAA
*
42189958 ATACACATATAAGGAAAACATGGTAGCTCAAGTCCCTTCGTTTAAGTCAAAATTATGAATGTGAA
66 ACACACATATAAGGAAAACATGGTAGCTCAAGTCCCTTCGTTTAAGTC-AAATTATGAATGTGAA
* *
42190023 AAAGCCAATTAAAGACCATACATACATACATACATATATAAAGGAAACATGGTAGCTCAAGTCCC
130 AAAGCCAATTAAAGACCATACATACATACATACACAGATAAAGGAAACATGGTAGCTCAAGTCCC
* *
42190088 TTTGTTTCAGTCAATTATGAATGCGAAAAGGCCAATTCAAGACCATACATGCATGCGCGCGCACA
195 TTTGTTTCAATCAATTATGAATACGAAAAGGCCAATTCAAGACCATACATGCATGCGCGCGCACA
42190153 CACAGAC
260 CACAGAC
* * *
42190160 CCCTTAGTTTCAGTCAATTATGAATGTGAAAAGGCCACTTCAAGACCATACATACATGCATCCAT
1 CCCTTAGTTTCAATCAATTATGAATGTGAAAAAGCCAATTCAAGACCATACATACATGCATCCA-
** * *
42190225 ACACACACATATATATACAAGGAAAACATGGTAGCTCAAGTCCCTTTTTTTCAGTC-ACTTATGA
65 A-ACACAC----ATAT--AAGGAAAACATGGTAGCTCAAGTCCCTTCGTTTAAGTCAAATTATGA
* * * * *
42190289 ATGTGGAAATGCCAATTCAAGACCCTAAATACATGCATGCATTCACACAGATATAAGGAAAACAT
123 ATGTGAAAAAGCCAATTAAAGA-CC---ATACATACATACA-T-ACACAGATA-AAGG-AAACAT
* *
42190354 GGTAGCTCAAGTCCCTTTGTTTCAATCAATTATGAATATGGAAAGGCCAATTCAAGACCATACAT
180 GGTAGCTCAAGTCCCTTTGTTTCAATCAATTATGAATACGAAAAGGCCAATTCAAGACCATACAT
42190419 ACACACATAT
Statistics
Matches: 219, Mismatches: 24, Indels: 18
0.84 0.09 0.07
Matches are distributed among these distances:
267 56 0.26
268 1 0.00
269 5 0.02
273 30 0.14
274 2 0.01
275 35 0.16
277 11 0.05
278 1 0.00
279 7 0.03
280 4 0.02
281 67 0.31
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (266 bp):
CCCTTAGTTTCAATCAATTATGAATGTGAAAAAGCCAATTCAAGACCATACATACATGCATCCAA
ACACACATATAAGGAAAACATGGTAGCTCAAGTCCCTTCGTTTAAGTCAAATTATGAATGTGAAA
AAGCCAATTAAAGACCATACATACATACATACACAGATAAAGGAAACATGGTAGCTCAAGTCCCT
TTGTTTCAATCAATTATGAATACGAAAAGGCCAATTCAAGACCATACATGCATGCGCGCGCACAC
ACAGAC
Found at i:42190389 original size:100 final size:103
Alignment explanation
Indices: 42190160--42190421 Score: 359
Period size: 100 Copynumber: 2.5 Consensus size: 103
42190150 ACACACAGAC
* * *
42190160 CCCTTAGTTTCAGTCAATTATGAATGTGAAAAGGCCACTTCAAGACCATACATACATGCATCCAT
1 CCCTTTGTTTCAGTCAATTATGAATGTGGAAAGGCCAATTCAAGACCATACATACATGCATCCAT
*
42190225 ACACACACATATATATACAAGGAAAACATGGTAGCTCAAGT
66 A-ACACACA-AGATATA-AAGGAAAACATGGTAGCTCAAGT
* * * * * *
42190266 CCCTTTTTTTCAGTCACTTATGAATGTGGAAATGCCAATTCAAGACCCTAAATACATGCATGCAT
1 CCCTTTGTTTCAGTCAATTATGAATGTGGAAAGGCCAATTCAAGACCATACATACATGCATCCAT
*
42190331 -TCACAC-AGATAT-AAGGAAAACATGGTAGCTCAAGT
66 AACACACAAGATATAAAGGAAAACATGGTAGCTCAAGT
* *
42190366 CCCTTTGTTTCAATCAATTATGAATATGGAAAGGCCAATTCAAGACCATACATACA
1 CCCTTTGTTTCAGTCAATTATGAATGTGGAAAGGCCAATTCAAGACCATACATACA
42190422 CACATATATA
Statistics
Matches: 138, Mismatches: 18, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
100 72 0.52
102 5 0.04
104 5 0.04
106 56 0.41
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.27
Consensus pattern (103 bp):
CCCTTTGTTTCAGTCAATTATGAATGTGGAAAGGCCAATTCAAGACCATACATACATGCATCCAT
AACACACAAGATATAAAGGAAAACATGGTAGCTCAAGT
Found at i:42190635 original size:19 final size:19
Alignment explanation
Indices: 42190607--42190663 Score: 53
Period size: 22 Copynumber: 2.8 Consensus size: 19
42190597 AATATAGCCT
*
42190607 AAAA-AAATAATCAAAACA
1 AAAATAAATAATCAAAAAA
42190625 AAAATAAATAAATCAGTAAAAA
1 AAAATAAAT-AATCA--AAAAA
*
42190647 AAAATCAAATAACCAAA
1 AAAAT-AAATAATCAAA
42190664 CTTTTGAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 4 0.12
19 4 0.12
20 7 0.22
22 13 0.41
23 4 0.12
ACGTcount: A:0.74, C:0.11, G:0.02, T:0.14
Consensus pattern (19 bp):
AAAATAAATAATCAAAAAA
Found at i:42190637 original size:23 final size:22
Alignment explanation
Indices: 42190606--42190658 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
42190596 TAATATAGCC
*
42190606 TAAAAAAAT-AATCAAAACAAAAA
1 TAAATAAATCAAT-AAAA-AAAAA
*
42190629 TAAATAAATCAGTAAAAAAAAA
1 TAAATAAATCAATAAAAAAAAA
42190651 TCAAATAA
1 T-AAATAA
42190659 CCAAACTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 6 0.23
23 18 0.69
24 2 0.08
ACGTcount: A:0.74, C:0.08, G:0.02, T:0.17
Consensus pattern (22 bp):
TAAATAAATCAATAAAAAAAAA
Found at i:42191630 original size:28 final size:30
Alignment explanation
Indices: 42191574--42191630 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
42191564 TAAAAGTTGG
*
42191574 TAAAAACAATAAATTTGGGCCCTTAAAAAC
1 TAAAAACAATAAAATTGGGCCCTTAAAAAC
42191604 TAAAAA-AA-AAAATTGGGACCCTTAAAA
1 TAAAAACAATAAAATTGGG-CCCTTAAAA
42191631 GTTAATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 8 0.32
29 11 0.44
30 6 0.24
ACGTcount: A:0.54, C:0.14, G:0.11, T:0.21
Consensus pattern (30 bp):
TAAAAACAATAAAATTGGGCCCTTAAAAAC
Found at i:42191692 original size:29 final size:28
Alignment explanation
Indices: 42191594--42191698 Score: 97
Period size: 28 Copynumber: 3.7 Consensus size: 28
42191584 AAATTTGGGC
* * * *
42191594 CCTTAAAAACTAAAAAAAAAAATTGGGAC
1 CCTTAAAAA-TTAAAAAAAAATTTTGGAA
* *
42191623 CCTTAAAAGTTAATAAAAAATTTT--AA
1 CCTTAAAAATTAAAAAAAAATTTTGGAA
*
42191649 CCTATAAAAGTTTAAAAAAAAATTTTGAGAA
1 CCT-TAAAA-ATTAAAAAAAAATTTTG-GAA
42191680 CCTTAAAAATTAAAAAAAA
1 CCTTAAAAATTAAAAAAAA
42191699 TAAAAATTTA
Statistics
Matches: 62, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
26 4 0.06
27 5 0.08
28 25 0.40
29 18 0.29
30 5 0.08
31 5 0.08
ACGTcount: A:0.58, C:0.10, G:0.07, T:0.26
Consensus pattern (28 bp):
CCTTAAAAATTAAAAAAAAATTTTGGAA
Found at i:42192713 original size:3 final size:3
Alignment explanation
Indices: 42192705--42192741 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
42192695 CTCCGTGTCG
42192705 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
42192742 TGTTGTTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:42193492 original size:15 final size:17
Alignment explanation
Indices: 42193474--42193505 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
42193464 TTTAAAATGA
42193474 TAAAAT-AT-AAATTAT
1 TAAAATAATAAAATTAT
42193489 TAAAATAATAAAATTAT
1 TAAAATAATAAAATTAT
42193506 ATTTTTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 2 0.13
17 7 0.47
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAAATAATAAAATTAT
Found at i:42193494 original size:23 final size:23
Alignment explanation
Indices: 42193465--42193533 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
42193455 TTTAATTATT
*
42193465 TTAAAATGATAAAATATAAATTA
1 TTAAAATAATAAAATATAAATTA
* *
42193488 TTAAAATAATAAAAT-TATATTT
1 TTAAAATAATAAAATATAAATTA
*
42193510 TTAATATAATAAAAATATATAATT
1 TTAAAATAAT-AAAATATA-AATT
42193534 TAATTTCGAC
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
22 14 0.37
23 19 0.50
24 2 0.05
25 3 0.08
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (23 bp):
TTAAAATAATAAAATATAAATTA
Found at i:42193518 original size:22 final size:22
Alignment explanation
Indices: 42193463--42193529 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
42193453 TATTTAATTA
* *
42193463 TTTTAAAATGATAAAATATAAAT
1 TTTTAAAATAATAAAAT-TATAT
*
42193486 TATTAAAATAATAAAATTATAT
1 TTTTAAAATAATAAAATTATAT
* *
42193508 TTTTAATATAATAAAAATATAT
1 TTTTAAAATAATAAAATTATAT
42193530 AATTTAATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
22 23 0.61
23 15 0.39
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (22 bp):
TTTTAAAATAATAAAATTATAT
Found at i:42205323 original size:16 final size:17
Alignment explanation
Indices: 42205289--42205323 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
42205279 AAAATATTGG
*
42205289 AATATAAAATTTATTTA
1 AATATAAAATATATTTA
42205306 AATATAAAATAT-TTTA
1 AATATAAAATATATTTA
42205322 AA
1 AA
42205324 CATCATTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AATATAAAATATATTTA
Found at i:42210912 original size:2 final size:2
Alignment explanation
Indices: 42210905--42210934 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
42210895 TAAACATTCG
42210905 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42210935 TTAAAAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42211862 original size:19 final size:19
Alignment explanation
Indices: 42211832--42211876 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
42211822 AATTAAGAGA
* *
42211832 AGTTGAATATAGTTACTGTC
1 AGTTG-ATATAGGTACTATC
*
42211852 AGTTGATATAGGTGCTATC
1 AGTTGATATAGGTACTATC
42211871 AGTTGA
1 AGTTGA
42211877 AGTCAGTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (19 bp):
AGTTGATATAGGTACTATC
Found at i:42212368 original size:40 final size:39
Alignment explanation
Indices: 42212314--42212389 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 39
42212304 ATGTTAAATT
*
42212314 AACTATGTAAGTTATTGGGGTTGCAAGACGTGTGATGTC
1 AACTATGTAAGTTATTGGGGTTACAAGACGTGTGATGTC
42212353 AACTATGTTAAGTTATTGGGGTTACAAGACGTGTGAT
1 AACTATG-TAAGTTATTGGGGTTACAAGACGTGTGAT
42212390 TAGATGGAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 7 0.20
40 28 0.80
ACGTcount: A:0.28, C:0.09, G:0.29, T:0.34
Consensus pattern (39 bp):
AACTATGTAAGTTATTGGGGTTACAAGACGTGTGATGTC
Found at i:42213179 original size:16 final size:17
Alignment explanation
Indices: 42213154--42213195 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
42213144 GTTTGGATTA
*
42213154 TTTAAGTTAACATC-AAT
1 TTTAA-TTAAAATCAAAT
42213171 TTTAATTAAAATCAAAT
1 TTTAATTAAAATCAAAT
*
42213188 TGTAATTA
1 TTTAATTA
42213196 TTATAAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (17 bp):
TTTAATTAAAATCAAAT
Found at i:42214846 original size:30 final size:29
Alignment explanation
Indices: 42214777--42214856 Score: 81
Period size: 30 Copynumber: 2.7 Consensus size: 29
42214767 TTTAATAGTT
* *
42214777 TATATTTTTATAATTTTTAAAGGGTTAAA
1 TATAATTTTATAATTTTTAAAGGGTAAAA
*
42214806 TCA-AATTTTTATTATTTTTAAAGGGTCAAAA
1 T-ATAA-TTTTATAATTTTTAAAGGGT-AAAA
* *
42214837 TATAATTTTATCATTATTAA
1 TATAATTTTATAATTTTTAA
42214857 TTTAAAATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
29 2 0.05
30 34 0.81
31 6 0.14
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (29 bp):
TATAATTTTATAATTTTTAAAGGGTAAAA
Found at i:42218961 original size:18 final size:19
Alignment explanation
Indices: 42218940--42218976 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
42218930 CAATAGACTT
42218940 ATCAAATT-AAATATTAAA
1 ATCAAATTCAAATATTAAA
*
42218958 ATCAAATTCAGATATTAAA
1 ATCAAATTCAAATATTAAA
42218977 TAATACATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.57, C:0.08, G:0.03, T:0.32
Consensus pattern (19 bp):
ATCAAATTCAAATATTAAA
Found at i:42225117 original size:19 final size:17
Alignment explanation
Indices: 42225093--42225127 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
42225083 TATTATATGA
42225093 TGAATTGATGAATTGATGT
1 TGAATTGA-GAA-TGATGT
42225112 TGAATTGAGAATGATG
1 TGAATTGAGAATGATG
42225128 GGATGTTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 3 0.19
19 8 0.50
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (17 bp):
TGAATTGAGAATGATGT
Found at i:42233748 original size:31 final size:31
Alignment explanation
Indices: 42233712--42233783 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
42233702 AAAACTTAAC
*
42233712 AATTCAGTGACTTAAATAAAAA-TTTTCGAAT
1 AATTCAGTGACTTAAATAAAAACTTTT-AAAT
* *
42233743 AATTCAGTAACTTGAATAAAAACTTTTAAAT
1 AATTCAGTGACTTAAATAAAAACTTTTAAAT
*
42233774 AGTTCAGTGA
1 AATTCAGTGA
42233784 TTATTTTGTA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 31 0.89
32 4 0.11
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.35
Consensus pattern (31 bp):
AATTCAGTGACTTAAATAAAAACTTTTAAAT
Found at i:42239985 original size:241 final size:236
Alignment explanation
Indices: 42239482--42240125 Score: 821
Period size: 241 Copynumber: 2.7 Consensus size: 236
42239472 CACCCGTGTC
**
42239482 GGGTATAAGGGTATAGGAAAATGATCTTTCAAAGACAACCAAATACATGAATTTTTTTT-AAAGA
1 GGGTATAAGGGTATAGGAAAATGATCTTTCAAAGACCTCCAAATACAT--ATTTTTTTTAAAAGA
* * * * * * * * * *
42239546 AAAATTGAACATACCCGTGTCCTAAATAGACTTACATCTGCCAATTACAATCGGGTCCGATTAAC
64 AAAATGGAAAAAACCCGTGTTCTAAATAGGCTTATATCTGGCAATCACACTCGAGTCCGATTAAC
* * *
42239611 AAAAAAGTACTAGCATGC-AACTACATGAAAGTATGGCTGCAATTACAGGCTCCAACTCATCATT
129 AAAAAAGTACTAGCATGCTAACTATATGAAAGAATGGTTGCAATTACAGGCTCCAACTCATCATT
*
42239675 TCAATTGAAGTACTCATGTCTGATACAACACATATTCATGCAA
194 TCAAGTGAAGTACTCATGTCTGATACAACACATATTCATGCAA
* * * * *
42239718 AGGAACAAGAGTATAGGAATATGATCTTTCAAAGACCTCCAAATACAT-TTTTTTTTAAAAAGGA
1 GGGTATAAGGGTATAGGAAAATGATCTTTCAAAGACCTCCAAATACATATTTTTTTT-AAAA-GA
* * * *
42239782 AAAATGGAAAAAACCCGTGTTCTAAATAGGCTTATATTTGGCACTCATACTCGAGTCCAATTAAC
64 AAAATGGAAAAAACCCGTGTTCTAAATAGGCTTATATCTGGCAATCACACTCGAGTCCGATTAAC
* *
42239847 AGAAAAAGTACTAGCATGTAACTAACTATATGAAAGAATGGTTGCAATTACTA-GCTCCGACTCG
129 A-AAAAAGTACTAGCATG---CTAACTATATGAAAGAATGGTTGCAATTAC-AGGCTCCAACTCA
** *
42239911 TTGTTTCAAGTGAAGTACTCATGTCTGATACGACACATATTCATGCAA
189 TCATTTCAAGTGAAGTACTCATGTCTGATACAACACATATTCATGCAA
* * * ** *
42239959 GGGTATAAGGGTAGAGGAACATGATCTTTCAAAGACCTCCAAATACATAATTTTTTTAGTAGTAA
1 GGGTATAAGGGTATAGGAAAATGATCTTTCAAAGACCTCCAAATACATATTTTTTTTAAAAGAAA
*
42240024 AATGGAACAAAACCCGTGTTCTAAATAGGCTTATATCTGGCATTCACACTCGAGTCCGATTAACA
66 AATGGAA-AAAACCCGTGTTCTAAATAGGCTTATATCTGGCAATCACACTCGAGTCCGATTAACA
*
42240089 AAAAAGTACTGGCATG-TAACTATATGAAAGAATGGTT
130 AAAAAGTACTAGCATGCTAACTATATGAAAGAATGGTT
42240126 ACAGAGAAGG
Statistics
Matches: 352, Mismatches: 45, Indels: 22
0.84 0.11 0.05
Matches are distributed among these distances:
233 8 0.02
235 3 0.01
236 116 0.33
237 16 0.05
240 26 0.07
241 175 0.50
242 8 0.02
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (236 bp):
GGGTATAAGGGTATAGGAAAATGATCTTTCAAAGACCTCCAAATACATATTTTTTTTAAAAGAAA
AATGGAAAAAACCCGTGTTCTAAATAGGCTTATATCTGGCAATCACACTCGAGTCCGATTAACAA
AAAAGTACTAGCATGCTAACTATATGAAAGAATGGTTGCAATTACAGGCTCCAACTCATCATTTC
AAGTGAAGTACTCATGTCTGATACAACACATATTCATGCAA
Found at i:42241904 original size:29 final size:26
Alignment explanation
Indices: 42241872--42241940 Score: 66
Period size: 28 Copynumber: 2.5 Consensus size: 26
42241862 ATAATCATAT
*
42241872 AATTAAAAATAATTTTGCAAAATATTAA
1 AATTAAAAATAATTTT--AAAATATGAA
**
42241900 CAATTAAACTTAAATTTTAAAATATGAA
1 -AATTAAAAAT-AATTTTAAAATATGAA
*
42241928 AAATAAAAATAAT
1 AATTAAAAATAAT
42241941 AAATTTCATA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
26 3 0.09
27 7 0.21
28 9 0.27
29 8 0.24
30 6 0.18
ACGTcount: A:0.59, C:0.04, G:0.03, T:0.33
Consensus pattern (26 bp):
AATTAAAAATAATTTTAAAATATGAA
Found at i:42241943 original size:23 final size:23
Alignment explanation
Indices: 42241919--42241961 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
42241909 TTAAATTTTA
*
42241919 AAATATGA-AAAATAAAAATAAT
1 AAATATCATAAAATAAAAATAAT
*
42241941 AAATTTCATAAAATAAAAATA
1 AAATATCATAAAATAAAAATA
42241962 CAATGACTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (23 bp):
AAATATCATAAAATAAAAATAAT
Found at i:42243208 original size:23 final size:23
Alignment explanation
Indices: 42243182--42243227 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
42243172 ACTTGAGACA
42243182 TTCCATAATAAACACATAAAACT
1 TTCCATAATAAACACATAAAACT
*
42243205 TTCCATAATAAACACATGAAACT
1 TTCCATAATAAACACATAAAACT
42243228 GGCATTCTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.50, C:0.22, G:0.02, T:0.26
Consensus pattern (23 bp):
TTCCATAATAAACACATAAAACT
Found at i:42255757 original size:16 final size:18
Alignment explanation
Indices: 42255730--42255764 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
42255720 TCTTTTCAAA
42255730 TTTGTGTCGTTTTG-GTT
1 TTTGTGTCGTTTTGAGTT
42255747 TTTGT-TCGTTTTGAGTT
1 TTTGTGTCGTTTTGAGTT
42255764 T
1 T
42255765 CGGTTATTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.03, C:0.06, G:0.26, T:0.66
Consensus pattern (18 bp):
TTTGTGTCGTTTTGAGTT
Found at i:42265662 original size:14 final size:14
Alignment explanation
Indices: 42265643--42265670 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
42265633 TCTTATTTAC
42265643 ATCCCTAATTGTAA
1 ATCCCTAATTGTAA
42265657 ATCCCTAATTGTAA
1 ATCCCTAATTGTAA
42265671 TGAGGTTAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (14 bp):
ATCCCTAATTGTAA
Found at i:42266655 original size:31 final size:31
Alignment explanation
Indices: 42266619--42266678 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
42266609 AGACAAAAAA
*
42266619 AGTTCAAA-CTCCAATGTGAAAATAATTACCT
1 AGTTCAAACCT-CAATATGAAAATAATTACCT
* *
42266650 AGTTCAAGCCTTAATATGAAAATAATTAC
1 AGTTCAAACCTCAATATGAAAATAATTAC
42266679 TAAATTTAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 23 0.92
32 2 0.08
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.30
Consensus pattern (31 bp):
AGTTCAAACCTCAATATGAAAATAATTACCT
Found at i:42266728 original size:28 final size:28
Alignment explanation
Indices: 42266697--42266784 Score: 81
Period size: 28 Copynumber: 3.1 Consensus size: 28
42266687 AGGGCTAATT
42266697 TAAAGAAAAAAAAGTTTAAACCCCGATA
1 TAAAGAAAAAAAAGTTTAAACCCCGATA
* *** ** *
42266725 TAAA-AAATACTAAA-TTTAAGGGCTAATT
1 TAAAGAAA-A-AAAAGTTTAAACCCCGATA
42266753 TAAAGAAAAAAAAGTTTAAACCCCGATA
1 TAAAGAAAAAAAAGTTTAAACCCCGATA
42266781 TAAA
1 TAAA
42266785 TTTAAGGTAT
Statistics
Matches: 42, Mismatches: 14, Indels: 8
0.66 0.22 0.12
Matches are distributed among these distances:
27 6 0.14
28 30 0.71
29 6 0.14
ACGTcount: A:0.56, C:0.11, G:0.10, T:0.23
Consensus pattern (28 bp):
TAAAGAAAAAAAAGTTTAAACCCCGATA
Found at i:42266743 original size:56 final size:56
Alignment explanation
Indices: 42266676--42266784 Score: 218
Period size: 56 Copynumber: 1.9 Consensus size: 56
42266666 TGAAAATAAT
42266676 TACTAAATTTAAGGGCTAATTTAAAGAAAAAAAAGTTTAAACCCCGATATAAAAAA
1 TACTAAATTTAAGGGCTAATTTAAAGAAAAAAAAGTTTAAACCCCGATATAAAAAA
42266732 TACTAAATTTAAGGGCTAATTTAAAGAAAAAAAAGTTTAAACCCCGATATAAA
1 TACTAAATTTAAGGGCTAATTTAAAGAAAAAAAAGTTTAAACCCCGATATAAA
42266785 TTTAAGGTAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.52, C:0.11, G:0.11, T:0.26
Consensus pattern (56 bp):
TACTAAATTTAAGGGCTAATTTAAAGAAAAAAAAGTTTAAACCCCGATATAAAAAA
Found at i:42272956 original size:31 final size:31
Alignment explanation
Indices: 42272921--42273012 Score: 125
Period size: 31 Copynumber: 3.0 Consensus size: 31
42272911 AATAACCGCA
* *
42272921 ACTTAAATAAAAACTTTTGAATAGTTCAGTG
1 ACTTAAATGAAGACTTTTGAATAGTTCAGTG
* *
42272952 ACTTAAATGAAGACTTTTGAATAGTCCAATG
1 ACTTAAATGAAGACTTTTGAATAGTTCAGTG
*
42272983 ATTTAAATGAAGAC--TTGAATAGTTCAGTG
1 ACTTAAATGAAGACTTTTGAATAGTTCAGTG
42273012 A
1 A
42273013 TCATTTTATA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
29 14 0.26
31 40 0.74
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (31 bp):
ACTTAAATGAAGACTTTTGAATAGTTCAGTG
Found at i:42281401 original size:42 final size:42
Alignment explanation
Indices: 42281318--42281556 Score: 169
Period size: 42 Copynumber: 5.7 Consensus size: 42
42281308 TATCACGTGA
* * *
42281318 CCTTCTATAGTATCGATCATCAGGTGAGTAAGAATGGTCCCG
1 CCTTCTATAGTATCGATCATCAGGAGAGTAAGAACGATCCCG
*
42281360 CCTTCTATAGTATTGATCATCAGGAGAGTAAGAACGATCCCG
1 CCTTCTATAGTATCGATCATCAGGAGAGTAAGAACGATCCCG
* * * ** * * ***
42281402 TCTGC-AGT-GATAACGATCATTGGGAGAGTAAGACCTATTATG
1 CCTTCTA-TAG-TATCGATCATCAGGAGAGTAAGAACGATCCCG
* * *
42281444 CCTTCTATAATATCTATCATCAGGAGAGTAAGAACGATCCCA
1 CCTTCTATAGTATCGATCATCAGGAGAGTAAGAACGATCCCG
* * * * * * * * * *
42281486 TCTAT-GATAATAACGATCGTAAGGCGAGTATGACCGATCACG
1 CCT-TCTATAGTATCGATCATCAGGAGAGTAAGAACGATCCCG
* *
42281528 CCTTCTATAGTATCGACCTTCAGGAGAGT
1 CCTTCTATAGTATCGATCATCAGGAGAGT
42281557 CGGAACGGTA
Statistics
Matches: 144, Mismatches: 47, Indels: 12
0.71 0.23 0.06
Matches are distributed among these distances:
41 3 0.02
42 139 0.97
43 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.27
Consensus pattern (42 bp):
CCTTCTATAGTATCGATCATCAGGAGAGTAAGAACGATCCCG
Found at i:42281563 original size:84 final size:84
Alignment explanation
Indices: 42281331--42281556 Score: 231
Period size: 84 Copynumber: 2.7 Consensus size: 84
42281321 TCTATAGTAT
* * ** * * *
42281331 CGATCATCAGGTGAGTAAGAATGGTCCCGCCTTCTATAGTATTGATCATCAGGAGAGTAAGAACG
1 CGATCATAAGGAGAGTAAGACCGATCACGCCTTCTATAGTATCGATCATCAGGAGAGTAAGAACG
* *
42281396 ATCCCGTCTGCAGTGATAA
66 ATCCCATCTGCAGTAATAA
** * * * * *
42281415 CGATCATTGGGAGAGTAAGACCTATTATGCCTTCTATAATATCTATCATCAGGAGAGTAAGAACG
1 CGATCATAAGGAGAGTAAGACCGATCACGCCTTCTATAGTATCGATCATCAGGAGAGTAAGAACG
42281480 ATCCCATCT--ATGATAATAA
66 ATCCCATCTGCA-G-TAATAA
* * * * *
42281499 CGATCGTAAGGCGAGTATGACCGATCACGCCTTCTATAGTATCGACCTTCAGGAGAGT
1 CGATCATAAGGAGAGTAAGACCGATCACGCCTTCTATAGTATCGATCATCAGGAGAGT
42281557 CGGAACGGTA
Statistics
Matches: 113, Mismatches: 27, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
82 1 0.01
83 1 0.01
84 111 0.98
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (84 bp):
CGATCATAAGGAGAGTAAGACCGATCACGCCTTCTATAGTATCGATCATCAGGAGAGTAAGAACG
ATCCCATCTGCAGTAATAA
Found at i:42300006 original size:16 final size:16
Alignment explanation
Indices: 42299985--42300035 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
42299975 AGTGGAAAAG
42299985 AAATTGGAAGGATGGA
1 AAATTGGAAGGATGGA
* * *
42300001 AAATTGAAAGGGTAGA
1 AAATTGGAAGGATGGA
* *
42300017 AAACTAGAAGGATGGA
1 AAATTGGAAGGATGGA
42300033 AAA
1 AAA
42300036 CATAATTTTT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.51, C:0.02, G:0.31, T:0.16
Consensus pattern (16 bp):
AAATTGGAAGGATGGA
Found at i:42303430 original size:30 final size:31
Alignment explanation
Indices: 42303376--42303435 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 31
42303366 TAGACCTATA
42303376 CATCATAATTCATGCAATAGCAAAGAACATT
1 CATCATAATTCATGCAATAGCAAAGAACATT
*
42303407 CATCATAATTCA-GCAATATCAAAGAACAT
1 CATCATAATTCATGCAATAGCAAAGAACAT
42303436 CTTCAACTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 16 0.57
31 12 0.43
ACGTcount: A:0.47, C:0.20, G:0.08, T:0.25
Consensus pattern (31 bp):
CATCATAATTCATGCAATAGCAAAGAACATT
Found at i:42317933 original size:17 final size:17
Alignment explanation
Indices: 42317911--42317944 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
42317901 TTCAGACCTC
*
42317911 AAATATAATGGACCAAA
1 AAATATAAAGGACCAAA
42317928 AAATATAAAGGACCAAA
1 AAATATAAAGGACCAAA
42317945 TTGAAAAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.62, C:0.12, G:0.12, T:0.15
Consensus pattern (17 bp):
AAATATAAAGGACCAAA
Found at i:42318550 original size:4 final size:4
Alignment explanation
Indices: 42318541--42318581 Score: 82
Period size: 4 Copynumber: 10.2 Consensus size: 4
42318531 TAGTATAAAT
42318541 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
42318582 CAGTTTGAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:42318953 original size:127 final size:128
Alignment explanation
Indices: 42318722--42318981 Score: 369
Period size: 127 Copynumber: 2.0 Consensus size: 128
42318712 ATGCATGCAT
* * * * * *
42318722 ATATACATACATAGTTTGAATAATATTCTGTTGTGGTTTACGTGATTGGGATGACGGTAGCTGCT
1 ATATACATACACAGTTTGAATAATATGCTGTTGTGGTTTACATAACTGGGATGACGGTAGCTGCA
* * * *
42318787 GAATGGATATTGATTTGGGTTTTGATTCCAAGTCTCTGATTCACC-TTTTTTTTGTTATAGAC
66 GAATGGACATTGATTTGGGGTTTGAGTCCAAGTCACTGATTCACCATTTTTTTTGTTATAGAC
* * * *
42318849 ATATACATATACAGTTTGAATAATATGCTTTTGTGGTTTACATAACTGGGATTATGGTAGCTGCA
1 ATATACATACACAGTTTGAATAATATGCTGTTGTGGTTTACATAACTGGGATGACGGTAGCTGCA
* *
42318914 GAATGGACATTGGTTTGGGGTTTGAGTCCAAGTCACTGATTCACCATTTTTTTTGTTATATAC
66 GAATGGACATTGATTTGGGGTTTGAGTCCAAGTCACTGATTCACCATTTTTTTTGTTATAGAC
42318977 ATATA
1 ATATA
42318982 TGTGTATGAT
Statistics
Matches: 116, Mismatches: 16, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
127 95 0.82
128 21 0.18
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.41
Consensus pattern (128 bp):
ATATACATACACAGTTTGAATAATATGCTGTTGTGGTTTACATAACTGGGATGACGGTAGCTGCA
GAATGGACATTGATTTGGGGTTTGAGTCCAAGTCACTGATTCACCATTTTTTTTGTTATAGAC
Found at i:42325288 original size:20 final size:20
Alignment explanation
Indices: 42325238--42325288 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
42325228 AATTTGTTTA
42325238 AGAAA-ATAATAAAATACAT
1 AGAAATATAATAAAATACAT
* * *
42325257 AGAAATAAAATAAATTTCAT
1 AGAAATATAATAAAATACAT
42325277 A-AATATATAATA
1 AGAA-ATATAATA
42325289 TCAAAATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (20 bp):
AGAAATATAATAAAATACAT
Found at i:42336808 original size:10 final size:10
Alignment explanation
Indices: 42336785--42336821 Score: 51
Period size: 9 Copynumber: 3.8 Consensus size: 10
42336775 TTATTAATTT
42336785 AAAATTTT-A
1 AAAATTTTAA
42336794 AAAATTTTAA
1 AAAATTTTAA
42336804 AAAA-TTTAA
1 AAAATTTTAA
42336813 ATAAATTTT
1 A-AAATTTT
42336822 TTTTTTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 14 0.56
10 8 0.32
11 3 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
AAAATTTTAA
Found at i:42359229 original size:22 final size:19
Alignment explanation
Indices: 42359184--42359230 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 19
42359174 ACTCATGTTT
42359184 TTTTTA-TTTTAAAAAATA
1 TTTTTATTTTTAAAAAATA
*
42359202 TATTTATTTTTAATATATAATA
1 TTTTTATTTTTAA-A-A-AATA
42359224 TTTTTAT
1 TTTTTAT
42359231 ATACTTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 5 0.22
19 6 0.26
20 1 0.04
21 1 0.04
22 10 0.43
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTTATTTTTAAAAAATA
Found at i:42360348 original size:14 final size:14
Alignment explanation
Indices: 42360329--42360356 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
42360319 GCAGTCATGC
42360329 CTTGAAGACTCCAT
1 CTTGAAGACTCCAT
42360343 CTTGAAGACTCCAT
1 CTTGAAGACTCCAT
42360357 TTTGCTAAAC
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:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (14 bp):
CTTGAAGACTCCAT
Found at i:42362088 original size:31 final size:31
Alignment explanation
Indices: 42362053--42362112 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
42362043 TACAAAATGC
**
42362053 TCACTAAACTATTCGGCAGTTTTCATTTAAG
1 TCACTAAACTATTCGAAAGTTTTCATTTAAG
* *
42362084 TCACTGAACTATTCGAAAGTTTTTATTTA
1 TCACTAAACTATTCGAAAGTTTTCATTTA
42362113 CGCTATTAGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.42
Consensus pattern (31 bp):
TCACTAAACTATTCGAAAGTTTTCATTTAAG
Found at i:42366362 original size:21 final size:23
Alignment explanation
Indices: 42366319--42366364 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
42366309 CACAGGAGAA
*
42366319 GGTGATCTACGTCGCATGGGAGGT
1 GGTGATCTACGTCG-ATGAGAGGT
42366343 GGTGATCTACGTCG-T-AGAGGT
1 GGTGATCTACGTCGATGAGAGGT
42366364 G
1 G
42366365 ATGGAGACCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 6 0.29
22 1 0.05
24 14 0.67
ACGTcount: A:0.17, C:0.15, G:0.41, T:0.26
Consensus pattern (23 bp):
GGTGATCTACGTCGATGAGAGGT
Found at i:42366625 original size:48 final size:48
Alignment explanation
Indices: 42366568--42366671 Score: 190
Period size: 48 Copynumber: 2.2 Consensus size: 48
42366558 TCGGATGGGT
*
42366568 GAACGAGATCTACGATGCACAGGTGTAGGTGACCTGCGCCGATAAGGA
1 GAACGAGATCTACGACGCACAGGTGTAGGTGACCTGCGCCGATAAGGA
*
42366616 GAACGAGATCTATGACGCACAGGTGTAGGTGACCTGCGCCGATAAGGA
1 GAACGAGATCTACGACGCACAGGTGTAGGTGACCTGCGCCGATAAGGA
42366664 GAACGAGA
1 GAACGAGA
42366672 CTGAGATCTA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 54 1.00
ACGTcount: A:0.31, C:0.20, G:0.34, T:0.15
Consensus pattern (48 bp):
GAACGAGATCTACGACGCACAGGTGTAGGTGACCTGCGCCGATAAGGA
Found at i:42376014 original size:196 final size:197
Alignment explanation
Indices: 42375509--42376542 Score: 1174
Period size: 197 Copynumber: 5.2 Consensus size: 197
42375499 AATGTTTATG
* * * *
42375509 GGTAATTTTTAAGCTATGAGAAGCTAATGTAGAACCACATTGTGCATTTTGATATTTGACTTTAT
1 GGTAATTTCTAAGCTATGAGAA-CTAATGAAAAACCACATTGTGCATTTTGATATTTGAATTTAT
* * * * *
42375574 AGTTTTTGACCTTCATTGCTAGTTAGCTGTG-TACAGGGACTTGGGTGTGTGCGTTGAATAACCT
65 AGTTTTTGACCTTCATTGCTAGTTAGCAGTGTTACCGGGACTTGGGTGTGAGCGTTGGATAGCCT
* *
42375638 ATATGTCTGATATGCATTAGATATGGGTACTTAAAGAAAAATGAGGAGTCCAAGCAATATAGCTA
130 ATATGTCTGATATGCATTAGATATGGGTACTTCAAGAAAAATGAGGAGTCCGAGCAATATAGCTA
42375703 GTT
195 GTT
* * *
42375706 GGTAATTTCTAATCTATGAGAATCTAATGGAAAACCACATTGTGCATTTTGACATTTGAATTTAT
1 GGTAATTTCTAAGCTATGAGAA-CTAATGAAAAACCACATTGTGCATTTTGATATTTGAATTTAT
* * * *
42375771 ACTTCTTGGCCTTCATTGCTAGTTAGCAGTGTTACCGGGACTTGGGTGTGAGCTTTGGATAGCCT
65 AGTTTTTGACCTTCATTGCTAGTTAGCAGTGTTACCGGGACTTGGGTGTGAGCGTTGGATAGCCT
* * *
42375836 ATATGTCTGATGTGCATTAGATATGGGTACTTCAAGAAACAT-AGGAGTCCGAGCAGTATAGCTA
130 ATATGTCTGATATGCATTAGATATGGGTACTTCAAGAAAAATGAGGAGTCCGAGCAATATAGCTA
*
42375900 GTA
195 GTT
* * *
42375903 AGTAATTTCTAAGCTATGAGAACTAATGAAAAACCACATTGTGCATTTTGATACTTGACTTTATA
1 GGTAATTTCTAAGCTATGAGAACTAATGAAAAACCACATTGTGCATTTTGATATTTGAATTTATA
* ** * * * *
42375968 GTTTTTGACCTTCAATGCTAGTTAGTTGTGTTACTGGTACTTGGGTGTGAGTGTTGGGTAGCCTA
66 GTTTTTGACCTTCATTGCTAGTTAGCAGTGTTACCGGGACTTGGGTGTGAGCGTTGGATAGCCTA
* * *
42376033 CATGTCTAATATGCATTAGATATGGATGTTAGATAAGGGTACTTCAAGAAAAATGAGGAGTCTGA
131 TATGTCTGATATGCA-T---TA--GA---T--AT--GGGTACTTCAAGAAAAATGAGGAGTCCGA
42376098 GCAATATAGCTAGTT
183 GCAATATAGCTAGTT
* * *
42376113 GGTAATTT-TGAAGCTATGAGAAACTAATG---AACCACATTGTGCATTTTGATAATGGAATCTA
1 GGTAATTTCT-AAGCTATGAG-AACTAATGAAAAACCACATTGTGCATTTTGATATTTGAATTTA
* * * * * * *
42376174 TAG-TTTTCAGTCTTTAGTGCTAGTTAACAGTGTTACTGGGACTTGGGTGTTAGCGTTGGATAGC
64 TAGTTTTTGA-CCTTCATTGCTAGTTAGCAGTGTTACCGGGACTTGGGTGTGAGCGTTGGATAGC
* * * * * **
42376238 CTATATGTCTCAAATGCATCATATATGGGTACTTAAAGAAAAATGAGGAGTTTGAGCAATATAGC
128 CTATATGTCTGATATGCATTAGATATGGGTACTTCAAGAAAAATGAGGAGTCCGAGCAATATAGC
42376303 TAGTT
193 TAGTT
* * * *
42376308 GGTAATCTCTAAGCTATGAAAACTAATGAAGAACCACATTGTGCATTTTGGTATTTGAATTTATA
1 GGTAATTTCTAAGCTATGAGAACTAATGAAAAACCACATTGTGCATTTTGATATTTGAATTTATA
* *
42376373 GGTTTTGACCTTCATTGCTA--TAGTCA-TGTTACCGGGACTTGGGTGTGA-CGTTGGATATCCT
66 GTTTTTGACCTTCATTGCTAGTTAG-CAGTGTTACCGGGACTTGGGTGTGAGCGTTGGATAGCCT
** * ** * **
42376434 ATATGTCCAATATGCATTAGATGTTTGTACTTCAAGAAAAATGAGGAGTCCAAATAATATAGC-A
130 ATATGTCTGATATGCATTAGATATGGGTACTTCAAGAAAAATGAGGAGTCCGAGCAATATAGCTA
42376498 GGTT
195 -GTT
* * *
42376502 GGTAATTTCTAAGCTATGGGAAATTAATGAATAACCACATT
1 GGTAATTTCTAAGCTATGAG-AACTAATGAAAAACCACATT
42376543 TTTCATTCTT
Statistics
Matches: 709, Mismatches: 102, Indels: 54
0.82 0.12 0.06
Matches are distributed among these distances:
193 1 0.00
194 89 0.13
195 98 0.14
196 108 0.15
197 170 0.24
198 72 0.10
199 1 0.00
200 2 0.00
202 3 0.00
204 1 0.00
205 1 0.00
207 8 0.01
208 90 0.13
209 18 0.03
210 39 0.06
211 8 0.01
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (197 bp):
GGTAATTTCTAAGCTATGAGAACTAATGAAAAACCACATTGTGCATTTTGATATTTGAATTTATA
GTTTTTGACCTTCATTGCTAGTTAGCAGTGTTACCGGGACTTGGGTGTGAGCGTTGGATAGCCTA
TATGTCTGATATGCATTAGATATGGGTACTTCAAGAAAAATGAGGAGTCCGAGCAATATAGCTAG
TT
Found at i:42395870 original size:23 final size:25
Alignment explanation
Indices: 42395835--42395884 Score: 61
Period size: 23 Copynumber: 2.1 Consensus size: 25
42395825 AATAATTTAA
42395835 TTTGAAATATTTT-TTAATTATTATT
1 TTTGAAATATTTTATTAA-TATTATT
*
42395860 TTTG-AAT-TTTTATTTATATTATT
1 TTTGAAATATTTTATTAATATTATT
42395883 TT
1 TT
42395885 AATTTCTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 13 0.57
24 6 0.26
25 4 0.17
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (25 bp):
TTTGAAATATTTTATTAATATTATT
Found at i:42395871 original size:21 final size:21
Alignment explanation
Indices: 42395845--42395889 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
42395835 TTTGAAATAT
42395845 TTTTTAATTATTATT-TTTGAA
1 TTTTTAATTA-TATTATTTGAA
* *
42395866 TTTTTATTTATATTATTTTAA
1 TTTTTAATTATATTATTTGAA
42395887 TTT
1 TTT
42395890 CTTTACTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (21 bp):
TTTTTAATTATATTATTTGAA
Found at i:42401277 original size:3 final size:3
Alignment explanation
Indices: 42401263--42401292 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
42401253 GTCCGATCCT
*
42401263 CAA CAT CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
42401293 AATGCTGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.33, G:0.00, T:0.03
Consensus pattern (3 bp):
CAA
Found at i:42401519 original size:12 final size:12
Alignment explanation
Indices: 42401502--42401526 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42401492 CAAATATGGT
42401502 CACGTAATGAAC
1 CACGTAATGAAC
42401514 CACGTAATGAAC
1 CACGTAATGAAC
42401526 C
1 C
42401527 CATAAATGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.28, G:0.16, T:0.16
Consensus pattern (12 bp):
CACGTAATGAAC
Found at i:42401995 original size:10 final size:10
Alignment explanation
Indices: 42401980--42402028 Score: 62
Period size: 11 Copynumber: 4.6 Consensus size: 10
42401970 TTCTAGCAAA
42401980 TTTTTAATTT
1 TTTTTAATTT
42401990 TTTTTAACTTT
1 TTTTTAA-TTT
42402001 TTTTTACATTT
1 TTTTTA-ATTT
*
42402012 TTTTAGAATTT
1 TTTT-TAATTT
42402023 TTTTTA
1 TTTTTA
42402029 GAATTTTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
10 8 0.24
11 24 0.71
12 2 0.06
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.73
Consensus pattern (10 bp):
TTTTTAATTT
Found at i:42402001 original size:11 final size:11
Alignment explanation
Indices: 42401980--42402028 Score: 57
Period size: 10 Copynumber: 4.5 Consensus size: 11
42401970 TTCTAGCAAA
42401980 TTTTTAA-TTT
1 TTTTTAACTTT
42401990 TTTTTAACTTT
1 TTTTTAACTTT
*
42402001 TTTTT-ACATT
1 TTTTTAACTTT
*
42402011 TTTTTAGAATTT
1 TTTTTA-ACTTT
42402023 TTTTTA
1 TTTTTA
42402029 GAATTTTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
10 16 0.48
11 8 0.24
12 9 0.27
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.73
Consensus pattern (11 bp):
TTTTTAACTTT
Found at i:42402024 original size:12 final size:11
Alignment explanation
Indices: 42401980--42402036 Score: 64
Period size: 12 Copynumber: 5.2 Consensus size: 11
42401970 TTCTAGCAAA
42401980 TTTTT-AATTT
1 TTTTTAAATTT
*
42401990 TTTTTAACTTT
1 TTTTTAAATTT
*
42402001 TTTTTACA-TT
1 TTTTTAAATTT
42402011 TTTTTAGAATTT
1 TTTTTA-AATTT
42402023 TTTTTAGAATTT
1 TTTTTA-AATTT
42402035 TT
1 TT
42402037 ATAAATATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
10 13 0.32
11 11 0.28
12 16 0.40
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.72
Consensus pattern (11 bp):
TTTTTAAATTT
Found at i:42408368 original size:79 final size:78
Alignment explanation
Indices: 42408148--42408377 Score: 215
Period size: 73 Copynumber: 3.0 Consensus size: 78
42408138 ATATATATAT
* * *
42408148 ATATATAGCATGTATCGACATTTTCCTTCTCTTTTTCCTTTTCCTTCACTTTC-GTCAAAGCCAA
1 ATATATATCATGTATCGACATTTTCCTTCTCCTTTTCCTTTTCCTTCACTTTCTGTTAAAGCCAA
*
42408212 ACCGAGCAAGAAACAC
66 ACAGAGCAAG---CAC
* * * * * * * * *
42408228 ACACATATCATGCATTGACGTTTTACATT-TCATTTTCC--TTCAC-TC-C-CTC-GTTGAAGCC
1 ATATATATCATGTATCGACATTTT-CCTTCTCCTTTTCCTTTTC-CTTCACTTTCTGTTAAAGCC
42408286 AAACAGAGCAAGCAC
64 AAACAGAGCAAGCAC
*
42408301 ATATATATCATGTATCGACATTTTCCTTCTCCTTTTCCTTTTCCTTCACTTTCTTGTTAAAGTCA
1 ATATATATCATGTATCGACATTTTCCTTCTCCTTTTCCTTTTCCTTCACTTTC-TGTTAAAGCCA
*
42408366 AACAGAGTAAGC
65 AACAGAGCAAGC
42408378 GCGCACGCGC
Statistics
Matches: 117, Mismatches: 23, Indels: 21
0.73 0.14 0.13
Matches are distributed among these distances:
72 3 0.03
73 30 0.26
74 1 0.01
75 5 0.04
76 21 0.18
77 3 0.03
78 5 0.04
79 20 0.17
80 26 0.22
81 3 0.03
ACGTcount: A:0.27, C:0.27, G:0.10, T:0.36
Consensus pattern (78 bp):
ATATATATCATGTATCGACATTTTCCTTCTCCTTTTCCTTTTCCTTCACTTTCTGTTAAAGCCAA
ACAGAGCAAGCAC
Found at i:42413990 original size:32 final size:32
Alignment explanation
Indices: 42413929--42413991 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
42413919 AAATTATTAT
* *
42413929 AATTAAAATCAATATATAACAATACATAAATG
1 AATTAAAATCAAAATATAACAAAACATAAATG
* *
42413961 AATTAAAATCAAAATATATCAAAATATAAAT
1 AATTAAAATCAAAATATAACAAAACATAAAT
42413992 CATAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.62, C:0.08, G:0.02, T:0.29
Consensus pattern (32 bp):
AATTAAAATCAAAATATAACAAAACATAAATG
Found at i:42423254 original size:3 final size:3
Alignment explanation
Indices: 42423246--42423272 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
42423236 TCATAAAAAC
42423246 ACA ACA ACA ACA ACA ACA ACA ACA ACA
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA
42423273 TGCAGAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:42424843 original size:24 final size:25
Alignment explanation
Indices: 42424811--42424857 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
42424801 ATTAAACATC
42424811 AAAATTAAATTCAAATACCAAATTG
1 AAAATTAAATTCAAATACCAAATTG
*
42424836 AAAA-TAAATTCATATACCAAAT
1 AAAATTAAATTCAAATACCAAAT
42424858 GGTATATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (25 bp):
AAAATTAAATTCAAATACCAAATTG
Found at i:42427333 original size:28 final size:28
Alignment explanation
Indices: 42427284--42427337 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
42427274 ATTAAATCAA
**
42427284 AATTTTATCATTTTGAGGATTAAAATGT
1 AATTTTATCATTTTGAAAATTAAAATGT
42427312 AATTTTATCATTTAT-AAAATTAAAAT
1 AATTTTATCATTT-TGAAAATTAAAAT
42427338 ATTGCAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 22 0.96
29 1 0.04
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (28 bp):
AATTTTATCATTTTGAAAATTAAAATGT
Found at i:42432371 original size:25 final size:28
Alignment explanation
Indices: 42432334--42432394 Score: 76
Period size: 26 Copynumber: 2.3 Consensus size: 28
42432324 GCCTACAAAG
42432334 TTTTATATAAAAATA-TTAT-TATTTAT
1 TTTTATATAAAAATATTTATCTATTTAT
*
42432360 TTTTA-ATTAAAATATTTATCTATTTA-
1 TTTTATATAAAAATATTTATCTATTTAT
*
42432386 TATTATATA
1 TTTTATATA
42432395 CTATATTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
25 8 0.28
26 13 0.45
27 8 0.28
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (28 bp):
TTTTATATAAAAATATTTATCTATTTAT
Found at i:42433465 original size:31 final size:31
Alignment explanation
Indices: 42433421--42433482 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
42433411 GAAAAACTTG
* * **
42433421 GATACCAATTTGAATATTGAAGTCAAATTCA
1 GATACCAAATTGAACATTGAAACCAAATTCA
*
42433452 GATATCAAATTGAACATTGAAACCAAATTCA
1 GATACCAAATTGAACATTGAAACCAAATTCA
42433483 AGCACTAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.29
Consensus pattern (31 bp):
GATACCAAATTGAACATTGAAACCAAATTCA
Found at i:42438173 original size:24 final size:24
Alignment explanation
Indices: 42438140--42438190 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
42438130 AGAATTAATC
*
42438140 TTTCATTTAAATTCTGTTTATTTG
1 TTTCAATTAAATTCTGTTTATTTG
42438164 TTTCAATTAAATTCTGTTTATTTG
1 TTTCAATTAAATTCTGTTTATTTG
42438188 TTT
1 TTT
42438191 GAGTCAAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.22, C:0.08, G:0.08, T:0.63
Consensus pattern (24 bp):
TTTCAATTAAATTCTGTTTATTTG
Found at i:42441501 original size:31 final size:31
Alignment explanation
Indices: 42441466--42441544 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
42441456 GATCTAACGT
42441466 AAATAAATTAATTTATTATTTTTTAAATAAA
1 AAATAAATTAATTTATTATTTTTTAAATAAA
* *
42441497 AAATAAATTAATCTATTATTTTTTGAATAAA
1 AAATAAATTAATTTATTATTTTTTAAATAAA
42441528 AAATAAAATATAATTTA
1 AAAT-AAAT-TAATTTA
42441545 ATTCATATTA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
31 33 0.77
32 4 0.09
33 6 0.14
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (31 bp):
AAATAAATTAATTTATTATTTTTTAAATAAA
Found at i:42443051 original size:18 final size:18
Alignment explanation
Indices: 42443004--42443054 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
42442994 GGTCCGACAT
* * *
42443004 CAGCTCCAACGACTGCCA
1 CAGCTCCATCGGCGGCCA
42443022 CAGCTCCATCGGCGGCCA
1 CAGCTCCATCGGCGGCCA
*
42443040 CAGCTCCGTCGGCGG
1 CAGCTCCATCGGCGG
42443055 GAAAGGCGCC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.18, C:0.43, G:0.27, T:0.12
Consensus pattern (18 bp):
CAGCTCCATCGGCGGCCA
Found at i:42452892 original size:54 final size:54
Alignment explanation
Indices: 42452823--42452925 Score: 163
Period size: 54 Copynumber: 1.9 Consensus size: 54
42452813 ATAACAAACT
*
42452823 TAAACTCATTTGTGATAAAATTTATACAT-AAATAAAATACAAATACAACAGACG
1 TAAACTCATTTGTGATAAAATTTACAC-TGAAATAAAATACAAATACAACAGACG
* *
42452877 TAAATTCATTTGTGATAAAATTTACACTGAAATAAAATATAAATACAAC
1 TAAACTCATTTGTGATAAAATTTACACTGAAATAAAATACAAATACAAC
42452926 CTAAATGATT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
53 1 0.02
54 44 0.98
ACGTcount: A:0.51, C:0.12, G:0.07, T:0.30
Consensus pattern (54 bp):
TAAACTCATTTGTGATAAAATTTACACTGAAATAAAATACAAATACAACAGACG
Found at i:42453598 original size:18 final size:16
Alignment explanation
Indices: 42453567--42453610 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
42453557 GGTTTAGAGT
*
42453567 TTAAAAATTTTAATTAA
1 TTAAAAA-TTTATTTAA
42453584 TT--AAATTTATTTAA
1 TTAAAAATTTATTTAA
42453598 TTAAAAATTTATT
1 TTAAAAATTTATT
42453611 CTTATCCCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 9 0.38
17 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAAAAATTTATTTAA
Found at i:42457705 original size:176 final size:175
Alignment explanation
Indices: 42456989--42457927 Score: 855
Period size: 176 Copynumber: 5.4 Consensus size: 175
42456979 TAATCATTAA
* * * * * * *
42456989 ATCAATTAAACAGATAACGGATACATACAATCCCCTACAAAATTATCACAATGCTTAGCAAAACC
1 ATCAATTAAACTGAGAGCGAATACATACAAT-TCCTACAAAATTATCACAATGCTAAGCAAAATC
* * * * * * * * * *
42457054 ATATCGAAAACCAACAATTTATGACGTTATATAATAAAA-ATGGAATATGAAGTTTTAATCTGTT
65 AGATCGAAAATCATCAA-TTATGATGTTATATAATAAAACA-AGAATCTGAAATTTTCATCTATA
* * ** * *
42457118 GTCATATTTGTTTCTTATATATTCTCAGGAACCAAACAGTAGATAAAGG
128 GTCTTCTTT-TTTCCAATATATTCTCAGGAACCAAACAGTAGCTAAAAG
* *
42457167 AT-AGATTAAACTGAGAGTGAATACATACAATTCCTACAAGATTATCACAATGCTAAGCAAAATC
1 ATCA-ATTAAACTGAGAGCGAATACATACAATTCCTACAAAATTATCACAATGCTAAGCAAAATC
* * *** * * *
42457231 AGATCGAAAATCAT-AATTCAT-A--CTAAATAATAAAACGTCAATCTGAAAGTTTAATCTATTG
65 AGATCGAAAATCATCAATT-ATGATGTTATATAATAAAACAAGAATCTGAAATTTTCATCTATAG
* * *
42457292 TCTTCTTCTTT-CATATATATTCTCAGAAACCAAACAGTAGCTAAACG
129 TCTTCTTTTTTCCA-ATATATTCTCAGGAACCAAACAGTAGCTAAAAG
* * *
42457339 ATCAATTAAACTGAGAGAC-AATACATAAAATT-CTGACAAAAGTATCACAACGCTAAGCAAAAT
1 ATCAATTAAACTGAGAG-CGAATACATACAATTCCT-ACAAAATTATCACAATGCTAAGCAAAAT
* * *** * *
42457402 CAGATACGAAGATCATCAAACTATGATGTTATATAAT-AAATGTGAATCTGAAATTTCCGTCTAT
64 CAGAT-CGAAAATCATC-AATTATGATGTTATATAATAAAACAAGAATCTGAAATTTTCATCTAT
* * **
42457466 TGTACTT-TTTTTT-CTATATATTCTCAGGAACCAAACAGTAGCTAAATT
127 AGT-CTTCTTTTTTCCAATATATTCTCAGGAACCAAACAGTAGCTAAAAG
* * * * * *
42457514 ATCAATTAAACTGAGAGCGGATACATACAATTCCAACAAAATTATCACAATTCCAAACAAAAGCA
1 ATCAATTAAACTGAGAGCGAATACATACAATTCCTACAAAATTATCACAATGCTAAGCAAAATCA
** * * *
42457579 GATCGAAAAGAATCAATGTATGATGTCACATAATAAAACAAGAATCTGAAATTTTCATATATAGT
66 GATCGAAAATCATCAAT-TATGATGTTATATAATAAAACAAGAATCTGAAATTTTCATCTATAGT
* * *
42457644 CTTCTTTTTTCCAGTATACTCTCAAGAACCAAACAGTAGCTAAAAG
130 CTTCTTTTTTCCAATATATTCTCAGGAACCAAACAGTAGCTAAAAG
* * * * * * * *
42457690 ATCAATTAAACTGAGAACGGAGACGTACATTTCCTACAAACTTATCGCAATGCTAGGCAAAATCA
1 ATCAATTAAACTGAGAGCGAATACATACAATTCCTACAAAATTATCACAATGCTAAGCAAAATCA
*
42457755 GATCGAAAATCATCAATTTATGATGTTATAAAATAAAACAAGAATCTGAAATTTTCATCTATAGT
66 GATCGAAAATCATCAA-TTATGATGTTATATAATAAAACAAGAATCTGAAATTTTCATCTATAGT
42457820 CTTC-TTTTTCCAATATATTCTCAGGAACC--A-A--A-C-----G
130 CTTCTTTTTTCCAATATATTCTCAGGAACCAAACAGTAGCTAAAAG
* * * * * * *
42457854 ATCGATTAAAATGAGAGCGGATACGTACATTTCCTATAAAATTATCGCAATGCTAAGCAAAATCA
1 ATCAATTAAACTGAGAGCGAATACATACAATTCCTACAAAATTATCACAATGCTAAGCAAAATCA
*
42457919 GATTGAAAA
66 GATCGAAAA
42457928 AAATAAACAG
Statistics
Matches: 634, Mismatches: 106, Indels: 56
0.80 0.13 0.07
Matches are distributed among these distances:
164 67 0.11
169 1 0.00
170 1 0.00
171 2 0.00
172 91 0.14
173 47 0.07
174 28 0.04
175 143 0.23
176 178 0.28
177 52 0.08
178 24 0.04
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (175 bp):
ATCAATTAAACTGAGAGCGAATACATACAATTCCTACAAAATTATCACAATGCTAAGCAAAATCA
GATCGAAAATCATCAATTATGATGTTATATAATAAAACAAGAATCTGAAATTTTCATCTATAGTC
TTCTTTTTTCCAATATATTCTCAGGAACCAAACAGTAGCTAAAAG
Found at i:42457802 original size:351 final size:344
Alignment explanation
Indices: 42456989--42457852 Score: 930
Period size: 351 Copynumber: 2.5 Consensus size: 344
42456979 TAATCATTAA
* * ** *
42456989 ATCAATTAAACAGATAACGGATACATACAATCCCCTACAAAATTATCACAATGCTTAGCAAAACC
1 ATCAATTAAACTGAGAACGGATACATAC-ATTTCCTACAAAATTATCACAATGC-TAGCAAAATC
* * * * * * * * *
42457054 ATATCGAAAACCAACAATTTATGACGTTATATAATAAAAATGGAATATGAAGTTTTAATCTGTTG
64 AGATCGAAAATCATCAATTTATGATGTTATATAATAAAAA-AGAATCTGAAATTTTCATCTATTG
*
42457119 TCATATTTGTTTCTTATATATTCTCAGGAACCAAACAGTAGATAAAGGATAGATTAAACTGAGAG
128 TC-T-TTTTTTTC-TATATATTCTCAGGAACCAAACAGTAGATAAAGGATAGATTAAACTGAGAG
* * * * * * **
42457184 TGAATACATACAATTCCTACAAGATTATCACAATGCTAAGCAAAATCAGATCGAAAATCATAATT
190 CGAATACATACAATTCCAACAAAATTATCACAATGCCAAACAAAAGCAGATCGAAAAGAATAATT
** * * *
42457249 CATACTAAATAATAAAACGTCAATCTGAAAGTTTAATCTATTGTCTTCTTCTTTCATATATATTC
255 CATACTAAATAATAAAACAACAATCTGAAAGTTTAATATATAGTCTTCTTCTTTCATATATACTC
*
42457314 TCAGAAACCAAACAGTAGCTAAACG
320 TCAGAAACCAAACAGTAGCTAAAAG
* * * * *
42457339 ATCAATTAAACTGAGAGAC-AATACATAAAATT-CTGACAAAAGTATCACAACGCTAAGCAAAAT
1 ATCAATTAAACTGAGA-ACGGATACATACATTTCCT-ACAAAATTATCACAATGCT-AGCAAAAT
* ** *** * *
42457402 CAGATACGAAGATCATCAAACTATGATGTTATATAATAAATGTGAATCTGAAATTTCCGTCTATT
63 CAGAT-CGAAAATCATCAATTTATGATGTTATATAATAAAAAAGAATCTGAAATTTTCATCTATT
* **
42457467 GTACTTTTTTTTCTATATATTCTCAGGAACCAAACAGTAGCTAAATTATCA-ATTAAACTGAGAG
127 GT-CTTTTTTTTCTATATATTCTCAGGAACCAAACAGTAGATAAAGGAT-AGATTAAACTGAGAG
* *
42457531 CGGATACATACAATTCCAACAAAATTATCACAATTCCAAACAAAAGCAGATCGAAAAGAATCAAT
190 CGAATACATACAATTCCAACAAAATTATCACAATGCCAAACAAAAGCAGATCGAAAAGAAT-AAT
* * * * * * *
42457596 GT-ATGATGTCACATAATAAAACAAGAATCTGAAATTTTCATATATAGTCTTCTTTTTTCCA-GT
254 -TCAT-A-CT-AAATAATAAAACAACAATCTGAAAGTTTAATATATAGTCTTCTTCTTT-CATAT
42457659 ATACTCTCA-AGAACCAAACAGTAGCTAAAAG
314 ATACTCTCAGA-AACCAAACAGTAGCTAAAAG
* * * *
42457690 ATCAATTAAACTGAGAACGGAGACGTACATTTCCTACAAACTTATCGCAATGCTAGGCAAAATCA
1 ATCAATTAAACTGAGAACGGATACATACATTTCCTACAAAATTATCACAATGCTA-GCAAAATCA
* *
42457755 GATCGAAAATCATCAATTTATGATGTTATAAAATAAAACAAGAATCTGAAATTTTCATCTATAGT
65 GATCGAAAATCATCAATTTATGATGTTATATAATAAAA-AAGAATCTGAAATTTTCATCTATTGT
* *
42457820 CTTCTTTTTCCAATATATTCTCAGGAACCAAAC
129 CTT-TTTTTTCTATATATTCTCAGGAACCAAAC
42457853 GATCGATTAA
Statistics
Matches: 422, Mismatches: 74, Indels: 35
0.79 0.14 0.07
Matches are distributed among these distances:
347 97 0.23
348 16 0.04
349 49 0.12
350 88 0.21
351 168 0.40
352 4 0.01
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.29
Consensus pattern (344 bp):
ATCAATTAAACTGAGAACGGATACATACATTTCCTACAAAATTATCACAATGCTAGCAAAATCAG
ATCGAAAATCATCAATTTATGATGTTATATAATAAAAAAGAATCTGAAATTTTCATCTATTGTCT
TTTTTTTCTATATATTCTCAGGAACCAAACAGTAGATAAAGGATAGATTAAACTGAGAGCGAATA
CATACAATTCCAACAAAATTATCACAATGCCAAACAAAAGCAGATCGAAAAGAATAATTCATACT
AAATAATAAAACAACAATCTGAAAGTTTAATATATAGTCTTCTTCTTTCATATATACTCTCAGAA
ACCAAACAGTAGCTAAAAG
Found at i:42461716 original size:14 final size:14
Alignment explanation
Indices: 42461684--42461716 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
42461674 TTGTTTCATT
42461684 GAAAATAATTTTTA
1 GAAAATAATTTTTA
*
42461698 -TAAATAATTTTTA
1 GAAAATAATTTTTA
42461711 GAAAAT
1 GAAAAT
42461717 CTGCCAAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 2
0.80 0.10 0.10
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (14 bp):
GAAAATAATTTTTA
Found at i:42462897 original size:18 final size:19
Alignment explanation
Indices: 42462874--42462913 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
42462864 GAAATACTAA
*
42462874 AATAATAAAT-TAAAGATT
1 AATAATAAATATAAACATT
*
42462892 AATAATATATATAAACATT
1 AATAATAAATATAAACATT
42462911 AAT
1 AAT
42462914 TTTATTATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.35
Consensus pattern (19 bp):
AATAATAAATATAAACATT
Found at i:42463246 original size:22 final size:23
Alignment explanation
Indices: 42463208--42463250 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
42463198 CAAAAGTTTT
*
42463208 ATTCATTATGATTTAAATAAAGC
1 ATTCATTATCATTTAAATAAAGC
42463231 ATTCATTA-CATTTAAATAAA
1 ATTCATTATCATTTAAATAAA
42463251 AAAAATTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.40
Consensus pattern (23 bp):
ATTCATTATCATTTAAATAAAGC
Found at i:42466666 original size:40 final size:44
Alignment explanation
Indices: 42466621--42466707 Score: 112
Period size: 40 Copynumber: 2.1 Consensus size: 44
42466611 AATGAGATAT
42466621 TTATAAATAAATACT-AATAATTT-TATTT-A-AA-TATAATTAA
1 TTATAAATAAATACTCAAT-ATTTATATTTAATAATTATAATTAA
* *
42466661 TTATAAATAAATGCTCAATATTTATTTTTAATAATTATAATTAA
1 TTATAAATAAATACTCAATATTTATATTTAATAATTATAATTAA
42466705 TTA
1 TTA
42466708 ATATTTAGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
40 18 0.45
41 7 0.17
42 1 0.03
43 2 0.05
44 12 0.30
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.47
Consensus pattern (44 bp):
TTATAAATAAATACTCAATATTTATATTTAATAATTATAATTAA
Found at i:42466671 original size:20 final size:20
Alignment explanation
Indices: 42466621--42466672 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
42466611 AATGAGATAT
42466621 TTATAAATAAATACTAATAA
1 TTATAAATAAATACTAATAA
* **
42466641 TTTTATTTAAATA-TAATTAA
1 TTATAAATAAATACTAA-TAA
42466661 TTATAAATAAAT
1 TTATAAATAAAT
42466673 GCTCAATATT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 3 0.12
20 22 0.88
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
TTATAAATAAATACTAATAA
Found at i:42466688 original size:44 final size:40
Alignment explanation
Indices: 42466621--42466707 Score: 95
Period size: 44 Copynumber: 2.1 Consensus size: 40
42466611 AATGAGATAT
*
42466621 TTATAAATAAATACTAATAA-TTTTATTTAAATATAATTAA
1 TTATAAATAAATACTAATAATTTTTA-ATAAATATAATTAA
* *
42466661 TTATAAATAAATGCTCAATATTTATTTTTAATAATTATAATTAA
1 TTATAAATAAATACT-AATA---ATTTTTAATAAATATAATTAA
42466705 TTA
1 TTA
42466708 ATATTTAGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
40 14 0.36
41 4 0.10
44 16 0.41
45 5 0.13
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.47
Consensus pattern (40 bp):
TTATAAATAAATACTAATAATTTTTAATAAATATAATTAA
Found at i:42466818 original size:25 final size:26
Alignment explanation
Indices: 42466773--42466821 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
42466763 TAGTAGTGAG
*
42466773 ATATCATGATATTATTCATTATTTAT
1 ATATCATGATATCATTCATTATTTAT
42466799 ATATCAT-ATATCATAT-ATTATTT
1 ATATCATGATATCAT-TCATTATTT
42466822 TTTTCTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.53
Consensus pattern (26 bp):
ATATCATGATATCATTCATTATTTAT
Found at i:42473439 original size:28 final size:27
Alignment explanation
Indices: 42473383--42473439 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 27
42473373 ATGGACCGAC
*
42473383 TATTTAACTAGTAAACGAAATATAAGAT
1 TATTTAACTAATAAAC-AAATATAAGAT
42473411 TATTTAACTACATAAAC-AATATAATGAT
1 TATTTAACTA-ATAAACAAATATAA-GAT
42473439 T
1 T
42473440 TTGACTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 7 0.27
28 14 0.54
29 5 0.19
ACGTcount: A:0.49, C:0.09, G:0.07, T:0.35
Consensus pattern (27 bp):
TATTTAACTAATAAACAAATATAAGAT
Found at i:42488456 original size:83 final size:83
Alignment explanation
Indices: 42488317--42488470 Score: 263
Period size: 83 Copynumber: 1.9 Consensus size: 83
42488307 GGTCTTACGT
* * *
42488317 GCATATCTGTGATATTTGGTGCGAAATGCGCTGTAAGAGTTATTGATGGGTTATCTCTTACAAGT
1 GCATATCTATGATATTTGGTGCGAAATGCGCTGTAAGAATTATTAATGGGTTATCTCTTACAAGT
42488382 TCGCAAGTAATAATCTGC
66 TCGCAAGTAATAATCTGC
* *
42488400 GCATATCTATGATATTTGGTGCGAGATGCGCTGTGAGAATTATTAATGGGTTATCTCTTACAAGT
1 GCATATCTATGATATTTGGTGCGAAATGCGCTGTAAGAATTATTAATGGGTTATCTCTTACAAGT
42488465 TCGCAA
66 TCGCAA
42488471 CAATATCATT
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
83 66 1.00
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (83 bp):
GCATATCTATGATATTTGGTGCGAAATGCGCTGTAAGAATTATTAATGGGTTATCTCTTACAAGT
TCGCAAGTAATAATCTGC
Found at i:42488854 original size:16 final size:17
Alignment explanation
Indices: 42488833--42488865 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
42488823 AAAATTAAAT
42488833 TTATAAT-TAAACATTA
1 TTATAATATAAACATTA
*
42488849 TTATAATATAAATATTA
1 TTATAATATAAACATTA
42488866 AAAAATGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
TTATAATATAAACATTA
Found at i:42506687 original size:63 final size:63
Alignment explanation
Indices: 42506614--42506759 Score: 220
Period size: 63 Copynumber: 2.3 Consensus size: 63
42506604 ATATAAAGCG
*
42506614 ACTAATATATTGAAATGTTATACCAGATTATAATTTTCATATATTATTCACCCAGAAAATTTC
1 ACTAATATATTGAAATGTTATACCAGATTATAAGTTTCATATATTATTCACCCAGAAAATTTC
* * * * *
42506677 ACTAACATATTGTAATGTTTTATCAGATTATAAGTTTCATATATTATTCACTCAGAAAATTTC
1 ACTAATATATTGAAATGTTATACCAGATTATAAGTTTCATATATTATTCACCCAGAAAATTTC
* *
42506740 ACTAATAAATTGAACTGTTA
1 ACTAATATATTGAAATGTTA
42506760 CCATTTGTGT
Statistics
Matches: 72, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
63 72 1.00
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.40
Consensus pattern (63 bp):
ACTAATATATTGAAATGTTATACCAGATTATAAGTTTCATATATTATTCACCCAGAAAATTTC
Found at i:42506895 original size:23 final size:24
Alignment explanation
Indices: 42506869--42506915 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
42506859 TAACTGTTAT
42506869 TATTT-GTTTCAGACTGAAATTTC
1 TATTTAGTTTCAGACTGAAATTTC
* *
42506892 TATTTATTTTGAGACTGAAATTTC
1 TATTTAGTTTCAGACTGAAATTTC
42506916 AAAATTCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.28, C:0.11, G:0.13, T:0.49
Consensus pattern (24 bp):
TATTTAGTTTCAGACTGAAATTTC
Done.