Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 163 of 259
Found at i:53072433 original size:5 final size:6
Alignment explanation
Indices: 53072416--53072459 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 6
53072406 AGATAAGTCA
* * *
53072416 TATTTT TATTTT TATTTT TATTTT AATATC TATTTT TATTTT TA
1 TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TA
53072460 ATTAGTATTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (6 bp):
TATTTT
Found at i:53078001 original size:5 final size:5
Alignment explanation
Indices: 53077993--53078021 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
53077983 ATTAAATTAC
53077993 ATAAA ATAAA ATAAA ATAAA ATAAA ATAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAA
53078022 CTATCCCCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
ATAAA
Found at i:53079279 original size:25 final size:22
Alignment explanation
Indices: 53079233--53079283 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 22
53079223 TTTATTTTAA
*
53079233 TATAATAATTTTTATTTAATTT
1 TATAATAATTTTTATATAATTT
53079255 TATAATAATTATTTATAATACATTT
1 TATAATAATT-TTTAT-ATA-ATTT
53079280 TATA
1 TATA
53079284 TTTTTAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 10 0.40
23 5 0.20
24 2 0.08
25 8 0.32
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
TATAATAATTTTTATATAATTT
Found at i:53081907 original size:14 final size:14
Alignment explanation
Indices: 53081888--53081918 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
53081878 AGTAACATGT
53081888 TTTCTGGAAAATAA
1 TTTCTGGAAAATAA
*
53081902 TTTCTGGAAAATGA
1 TTTCTGGAAAATAA
53081916 TTT
1 TTT
53081919 ACTTTTCTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.42
Consensus pattern (14 bp):
TTTCTGGAAAATAA
Found at i:53081945 original size:20 final size:20
Alignment explanation
Indices: 53081902--53081943 Score: 77
Period size: 19 Copynumber: 2.1 Consensus size: 20
53081892 TGGAAAATAA
53081902 TTTCTGGAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
53081922 TTTCT-GAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
53081941 TTT
1 TTT
53081944 TCGGTGTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:53082053 original size:20 final size:20
Alignment explanation
Indices: 53082028--53082067 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
53082018 CTATATTTAC
53082028 ATATATTAATAAATTTATAT
1 ATATATTAATAAATTTATAT
53082048 ATATATTAATAAATTTATAT
1 ATATATTAATAAATTTATAT
53082068 TTTAAATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATATTAATAAATTTATAT
Found at i:53082066 original size:18 final size:18
Alignment explanation
Indices: 53082022--53082067 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 18
53082012 GAAAAGCTAT
*
53082022 ATTTACATATATTAATAA
1 ATTTATATATATTAATAA
53082040 ATTTATATATATATTAATAA
1 A-TT-TATATATATTAATAA
53082060 ATTTATAT
1 ATTTATAT
53082068 TTTAAATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 6 0.24
19 4 0.16
20 15 0.60
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTTATATATATTAATAA
Found at i:53084506 original size:6 final size:6
Alignment explanation
Indices: 53084492--53084547 Score: 85
Period size: 6 Copynumber: 9.3 Consensus size: 6
53084482 GATGAGTGAG
* * *
53084492 GGGGAA GGAGAA GGAGAA GGGGAA GGGGAA GGGGAA GGGGAA GGAGAA
1 GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA
53084540 GGGGAA GG
1 GGGGAA GG
53084548 AGCTTCATGT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (6 bp):
GGGGAA
Found at i:53084515 original size:18 final size:18
Alignment explanation
Indices: 53084492--53084547 Score: 94
Period size: 18 Copynumber: 3.1 Consensus size: 18
53084482 GATGAGTGAG
*
53084492 GGGGAAGGAGAAGGAGAA
1 GGGGAAGGAGAAGGGGAA
*
53084510 GGGGAAGGGGAAGGGGAA
1 GGGGAAGGAGAAGGGGAA
53084528 GGGGAAGGAGAAGGGGAA
1 GGGGAAGGAGAAGGGGAA
53084546 GG
1 GG
53084548 AGCTTCATGT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (18 bp):
GGGGAAGGAGAAGGGGAA
Found at i:53087736 original size:14 final size:14
Alignment explanation
Indices: 53087717--53087756 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
53087707 GAAAAGGTTG
53087717 AAAAGCTTTT-CTGC
1 AAAAGCTTTTAC-GC
53087731 AAAAGCTTTTACGC
1 AAAAGCTTTTACGC
53087745 AAAAGCTTTTAC
1 AAAAGCTTTTAC
53087757 CCCTAAACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 24 0.96
15 1 0.04
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (14 bp):
AAAAGCTTTTACGC
Found at i:53092689 original size:6 final size:7
Alignment explanation
Indices: 53092671--53092696 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
53092661 TCTACTATTT
53092671 TAAAAAA
1 TAAAAAA
53092678 TAAAAAA
1 TAAAAAA
53092685 TAAAAAA
1 TAAAAAA
53092692 TAAAA
1 TAAAA
53092697 TATCTAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
TAAAAAA
Found at i:53094426 original size:29 final size:30
Alignment explanation
Indices: 53094387--53094444 Score: 91
Period size: 29 Copynumber: 1.9 Consensus size: 30
53094377 AATTGGTCTC
53094387 TTCTTTTTGAGAA-ACTCTGTAATTATTCT
1 TTCTTTTTGAGAAGACTCTGTAATTATTCT
*
53094416 TTCTTTTTGAGAAGGTCTCTGTAATTATT
1 TTCTTTTTGAGAA-GACTCTGTAATTATT
53094445 ATAGTGAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 13 0.50
31 13 0.50
ACGTcount: A:0.22, C:0.12, G:0.14, T:0.52
Consensus pattern (30 bp):
TTCTTTTTGAGAAGACTCTGTAATTATTCT
Found at i:53103262 original size:23 final size:26
Alignment explanation
Indices: 53103222--53103269 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 26
53103212 AGTTTTTATA
53103222 TTTTTATTTTTAAGAATTT-AGTCTT
1 TTTTTATTTTTAAGAATTTAAGTCTT
53103247 TTTTTA-TTTTAA-AATTTAAGTCT
1 TTTTTATTTTTAAGAATTTAAGTCT
53103270 AATTGTTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.23
24 11 0.50
25 6 0.27
ACGTcount: A:0.27, C:0.04, G:0.06, T:0.62
Consensus pattern (26 bp):
TTTTTATTTTTAAGAATTTAAGTCTT
Found at i:53112776 original size:52 final size:51
Alignment explanation
Indices: 53112717--53112870 Score: 173
Period size: 52 Copynumber: 2.9 Consensus size: 51
53112707 GACGGAAAAG
*
53112717 ATGTGATATGTGCTTTCGTATAAGACCATAGCTGGGCTATGGCATCGGTGCA
1 ATGTGATATGTG-TTTCGTATAAGACCATAACTGGGCTATGGCATCGGTGCA
* * * **
53112769 ATGTGATACGTGTTCCCGTATAAGACCATAACTGGGCTATGACATCGGTGTT
1 ATGTGATATGTGTT-TCGTATAAGACCATAACTGGGCTATGGCATCGGTGCA
* * * * *
53112821 ATGTGATAATATGATTCTGTATAAGACTATATCTGGGATATGGCATCGGT
1 ATGTGAT-ATGTGTTTC-GTATAAGACCATAACTGGGCTATGGCATCGGT
53112871 ATGATATGTG
Statistics
Matches: 85, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
51 2 0.02
52 51 0.60
53 32 0.38
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (51 bp):
ATGTGATATGTGTTTCGTATAAGACCATAACTGGGCTATGGCATCGGTGCA
Found at i:53117017 original size:18 final size:17
Alignment explanation
Indices: 53116966--53117030 Score: 73
Period size: 18 Copynumber: 3.8 Consensus size: 17
53116956 GGCACGTAAC
53116966 ATATATAAATTTTTAAA
1 ATATATAAATTTTTAAA
53116983 AT-TA-AAATTTTTAAAA
1 ATATATAAATTTTT-AAA
*
53116999 ATATATAAATTAATTAAA
1 ATATATAAATT-TTTAAA
53117017 A-AGTATAAATTTTT
1 ATA-TATAAATTTTT
53117031 TCCACATCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
15 8 0.20
16 7 0.17
17 7 0.17
18 17 0.41
19 2 0.05
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (17 bp):
ATATATAAATTTTTAAA
Found at i:53117336 original size:3 final size:3
Alignment explanation
Indices: 53117328--53117364 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
53117318 ACATATTAAC
*
53117328 TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
53117365 TAAAGAATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:53122880 original size:70 final size:70
Alignment explanation
Indices: 53122728--53122972 Score: 232
Period size: 71 Copynumber: 3.6 Consensus size: 70
53122718 AGATGGAATC
* * *
53122728 ATCATTTACACTGATCTTAGGACTTTTATCTCATTTTATCAGAA-T-T--T-T-GAACAAACAAG
1 ATCATTTACACTGATCTTAGGACTTCTATCTCATTTTATCGGAATTCTAGTCTAGAACAAACAAA
53122787 ATGGG
66 ATGGG
* * ** * *
53122792 GTCATTTATACCAATTTTAGGACTTCTATCTCATTTTATCGGAATTCTAGTCTAGACCAAACAAA
1 ATCATTTACACTGATCTTAGGACTTCTATCTCATTTTATCGGAATTCTAGTCTAGAACAAACAAA
*
53122857 ATGGT
66 ATGGG
* * * * * ***
53122862 TTCATTTACACTGATTTTAGGACTTCTATCTCATCTTTTTCGGAGTTCTAGTCTAGATCAAGTTA
1 ATCATTTACACTGATCTTAGGACTTCTATCTCAT-TTTATCGGAATTCTAGTCTAGAACAAACAA
53122927 AATGGG
65 AATGGG
* ** * *
53122933 ATCATTTTCGTTGGTCTTAGGACTTCTATCTCATCTTATC
1 ATCATTTACACTGATCTTAGGACTTCTATCTCATTTTATC
53122973 AGCTGTATGG
Statistics
Matches: 145, Mismatches: 29, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
64 37 0.26
65 1 0.01
66 1 0.01
68 1 0.01
69 1 0.01
70 47 0.32
71 57 0.39
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.40
Consensus pattern (70 bp):
ATCATTTACACTGATCTTAGGACTTCTATCTCATTTTATCGGAATTCTAGTCTAGAACAAACAAA
ATGGG
Found at i:53128443 original size:20 final size:20
Alignment explanation
Indices: 53128418--53128459 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
53128408 GAACAATTAG
53128418 ATATTACAACCCAAGAATCA
1 ATATTACAACCCAAGAATCA
53128438 ATATTACAACCCAAGAATCA
1 ATATTACAACCCAAGAATCA
53128458 AT
1 AT
53128460 TATGAGCCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.50, C:0.24, G:0.05, T:0.21
Consensus pattern (20 bp):
ATATTACAACCCAAGAATCA
Found at i:53135203 original size:14 final size:14
Alignment explanation
Indices: 53135184--53135211 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
53135174 GCATGTACAT
53135184 AAGTGTTAATATAA
1 AAGTGTTAATATAA
53135198 AAGTGTTAATATAA
1 AAGTGTTAATATAA
53135212 GAGACTTTAG
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:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (14 bp):
AAGTGTTAATATAA
Found at i:53140893 original size:16 final size:16
Alignment explanation
Indices: 53140872--53140903 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
53140862 TAGAGACAAG
53140872 TTGGATATGCTATTTA
1 TTGGATATGCTATTTA
53140888 TTGGATATGCTATTTA
1 TTGGATATGCTATTTA
53140904 GACTTAGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.06, G:0.19, T:0.50
Consensus pattern (16 bp):
TTGGATATGCTATTTA
Found at i:53143699 original size:42 final size:42
Alignment explanation
Indices: 53143637--53143794 Score: 138
Period size: 42 Copynumber: 3.6 Consensus size: 42
53143627 TAAGTGATTT
*
53143637 CGTATAAGACCATGTCTGGGACATGGCATTGATATGAGGTCC
1 CGTATAAGACCATGTCTGGGACATGGCATTGATATGAGGACC
* * *
53143679 CGTATAAGACCATGTTTGGGATATGGCATCAGCATCGATATGA-GACTT
1 CGTATAAGACCATGTCTGGGACATGGCAT-----T-GATATGAGGAC-C
* * * * * *
53143727 CGTATAAGACCATATTTGGGATATGACATCGATATGCGGACC
1 CGTATAAGACCATGTCTGGGACATGGCATTGATATGAGGACC
* *
53143769 CATGTAAGACCATGTCTGGGACATGG
1 CGTATAAGACCATGTCTGGGACATGG
53143795 ATTTGGCACT
Statistics
Matches: 93, Mismatches: 15, Indels: 16
0.75 0.12 0.13
Matches are distributed among these distances:
42 53 0.57
43 3 0.03
47 3 0.03
48 34 0.37
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (42 bp):
CGTATAAGACCATGTCTGGGACATGGCATTGATATGAGGACC
Found at i:53143704 original size:90 final size:90
Alignment explanation
Indices: 53143496--53143794 Score: 244
Period size: 90 Copynumber: 3.2 Consensus size: 90
53143486 AGATCCTGTG
* * * * *
53143496 TAAGACCATGTCTGGGACATGGCATCAGCATCCGAGATGAGAGC--CAGTGTAAGACCACATCTG
1 TAAGACCATGTCTGGGATATGGCATCAGCAT-CGATAAGAGA-CTTC-GTATAAGACCATATCTG
* * * *
53143559 GGATATGGCATCAGTACCAATATGTGATCCCGTA
63 GGACAT-G-A-CA-T--CGATATGAGGTCCCGTA
* * * * * * *
53143593 TAAGACCATATCAGGGATATGGCTTC-GACATCGTTAAGTGATTTCGTATAAGACCATGTCTGGG
1 TAAGACCATGTCTGGGATATGGCATCAG-CATCGATAAGAGACTTCGTATAAGACCATATCTGGG
* *
53143657 ACATGGCATTGATATGAGGTCCCGTA
65 ACATGACATCGATATGAGGTCCCGTA
* * *
53143683 TAAGACCATGTTTGGGATATGGCATCAGCATCGATATGAGACTTCGTATAAGACCATATTTGGGA
1 TAAGACCATGTCTGGGATATGGCATCAGCATCGATAAGAGACTTCGTATAAGACCATATCTGGGA
* * * * *
53143748 TATGACATCGATATGCGGACCCATG
66 CATGACATCGATATGAGGTCCCGTA
*
53143773 TAAGACCATGTCTGGGACATGG
1 TAAGACCATGTCTGGGATATGG
53143795 ATTTGGCACT
Statistics
Matches: 161, Mismatches: 37, Indels: 15
0.76 0.17 0.07
Matches are distributed among these distances:
90 104 0.65
91 1 0.01
92 1 0.01
93 2 0.01
95 1 0.01
96 26 0.16
97 26 0.16
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (90 bp):
TAAGACCATGTCTGGGATATGGCATCAGCATCGATAAGAGACTTCGTATAAGACCATATCTGGGA
CATGACATCGATATGAGGTCCCGTA
Found at i:53143738 original size:48 final size:48
Alignment explanation
Indices: 53143483--53143756 Score: 183
Period size: 48 Copynumber: 5.8 Consensus size: 48
53143473 ACCATGGTTA
* * * *
53143483 ATGAGA-TCCTGTGTAAGACCATGTCTGGGACATGGCATCAGCATCCGAG
1 ATGAGACTCC-GTATAAGACCATATCTGGGATATGGCATCAGCAT-CGAT
* * * * * *
53143532 ATGAGAGC-CAGTGTAAGACCACATCTGGGATATGGCATCAGTACCAAT
1 ATGAGA-CTCCGTATAAGACCATATCTGGGATATGGCATCAGCATCGAT
* * * *
53143580 ATGTGA-TCCCGTATAAGACCATATCAGGGATATGGCTTC-GACATCGTT
1 ATGAGACT-CCGTATAAGACCATATCTGGGATATGGCATCAG-CATCGAT
* * * * * *
53143628 AAGTGATTTCGTATAAGACCATGTCTGGGACATGGCAT-----T-GAT
1 ATGAGACTCCGTATAAGACCATATCTGGGATATGGCATCAGCATCGAT
* * *
53143670 ATGAG-GTCCCGTATAAGACCATGTTTGGGATATGGCATCAGCATCGAT
1 ATGAGACT-CCGTATAAGACCATATCTGGGATATGGCATCAGCATCGAT
* * *
53143718 ATGAGACTTCGTATAAGACCATATTTGGGATATGACATC
1 ATGAGACTCCGTATAAGACCATATCTGGGATATGGCATC
53143757 GATATGCGGA
Statistics
Matches: 176, Mismatches: 35, Indels: 29
0.73 0.15 0.12
Matches are distributed among these distances:
41 1 0.01
42 32 0.18
43 1 0.01
47 2 0.01
48 102 0.58
49 37 0.21
50 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (48 bp):
ATGAGACTCCGTATAAGACCATATCTGGGATATGGCATCAGCATCGAT
Found at i:53146568 original size:10 final size:10
Alignment explanation
Indices: 53146535--53146568 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
53146525 GAATTAGATC
53146535 AAAATTACTA
1 AAAATTACTA
*
53146545 AAAA-TAATA
1 AAAATTACTA
53146554 AAAATTACTA
1 AAAATTACTA
53146564 AAAAT
1 AAAAT
53146569 AACTTCACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (10 bp):
AAAATTACTA
Found at i:53148110 original size:20 final size:20
Alignment explanation
Indices: 53148041--53148110 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
53148031 TGTACAAAAA
* *
53148041 GCATACTTGGCACACGAAGT
1 GCATTCTTGGCACATGAAGT
* * * *
53148061 ACATTCCTAGCATAT-AAGT
1 GCATTCTTGGCACATGAAGT
53148080 GCATATC-TGGCACATGAAGT
1 GCAT-TCTTGGCACATGAAGT
53148100 GCATTCTTGGC
1 GCATTCTTGGC
53148111 GCATAAATGC
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 15 0.39
20 23 0.61
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (20 bp):
GCATTCTTGGCACATGAAGT
Found at i:53150521 original size:36 final size:36
Alignment explanation
Indices: 53150481--53150551 Score: 142
Period size: 36 Copynumber: 2.0 Consensus size: 36
53150471 GCTCGAGAAG
53150481 AGCTAATATATCAATATTTAAAGGAACAAATTTTTA
1 AGCTAATATATCAATATTTAAAGGAACAAATTTTTA
53150517 AGCTAATATATCAATATTTAAAGGAACAAATTTTT
1 AGCTAATATATCAATATTTAAAGGAACAAATTTTT
53150552 TTATAATTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.37
Consensus pattern (36 bp):
AGCTAATATATCAATATTTAAAGGAACAAATTTTTA
Found at i:53151863 original size:43 final size:44
Alignment explanation
Indices: 53151780--53151865 Score: 120
Period size: 44 Copynumber: 2.0 Consensus size: 44
53151770 CTATGTATAT
* * * *
53151780 ATTAATATGGTTAAATCATATGAGATGGTAAACCAGAAGTTTAC
1 ATTAATATCGTTAAATCATATGACATAGTAAACCAAAAGTTTAC
*
53151824 ATTAGTATCGTTAAATCATATG-CATAGTAAACCAAAAGTTTA
1 ATTAATATCGTTAAATCATATGACATAGTAAACCAAAAGTTTA
53151866 TTAGTCCAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
43 17 0.46
44 20 0.54
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (44 bp):
ATTAATATCGTTAAATCATATGACATAGTAAACCAAAAGTTTAC
Found at i:53155733 original size:23 final size:23
Alignment explanation
Indices: 53155701--53155752 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
53155691 GGACTCACCA
*
53155701 CAGCTTATTGGAGCTTACCGATT
1 CAGCTCATTGGAGCTTACCGATT
*
53155724 CAGCTCATTGGAGCTTACTGATT
1 CAGCTCATTGGAGCTTACCGATT
53155747 CAGCTC
1 CAGCTC
53155753 GAAAAAGCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.33
Consensus pattern (23 bp):
CAGCTCATTGGAGCTTACCGATT
Found at i:53155815 original size:24 final size:24
Alignment explanation
Indices: 53155722--53155824 Score: 99
Period size: 24 Copynumber: 4.4 Consensus size: 24
53155712 AGCTTACCGA
* * *
53155722 TTCAGCTCATTGGAGCTTACTG-A
1 TTCAGCTCAATAGAGCTTACTGTT
*
53155745 TTCAGCTCGAA-AAAGCTTACTG--
1 TTCAGCTC-AATAGAGCTTACTGTT
53155767 TTCAGCTCAATAGAGCTTA-TCGTT
1 TTCAGCTCAATAGAGCTTACT-GTT
*
53155791 TTCAACTCAATAGAGCTTACTGTT
1 TTCAGCTCAATAGAGCTTACTGTT
53155815 TATCAGCTCA
1 T-TCAGCTCA
53155825 GGAGGAGTTT
Statistics
Matches: 67, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
21 3 0.04
22 16 0.24
23 17 0.25
24 23 0.34
25 8 0.12
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (24 bp):
TTCAGCTCAATAGAGCTTACTGTT
Found at i:53156057 original size:20 final size:20
Alignment explanation
Indices: 53156029--53156108 Score: 106
Period size: 20 Copynumber: 4.0 Consensus size: 20
53156019 ATATTGTATT
*
53156029 AATGCATGAATTACTGTTGA
1 AATGAATGAATTACTGTTGA
53156049 AATGAATGAATTACTGTTGA
1 AATGAATGAATTACTGTTGA
* * * *
53156069 TATGGATGAGTTACTGCTGA
1 AATGAATGAATTACTGTTGA
*
53156089 AATGAATGAATTACAGTTGA
1 AATGAATGAATTACTGTTGA
53156109 TACGGATAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.36, C:0.07, G:0.23, T:0.34
Consensus pattern (20 bp):
AATGAATGAATTACTGTTGA
Found at i:53156094 original size:40 final size:40
Alignment explanation
Indices: 53156034--53156124 Score: 137
Period size: 40 Copynumber: 2.3 Consensus size: 40
53156024 GTATTAATGC
* * *
53156034 ATGAATTACTGTTGAAATGAATGAATTACTGTTGATATGG
1 ATGAATTACTGCTGAAATGAATGAATTACAGTTGATACGG
*
53156074 ATGAGTTACTGCTGAAATGAATGAATTACAGTTGATACGG
1 ATGAATTACTGCTGAAATGAATGAATTACAGTTGATACGG
*
53156114 ATAAATTACTG
1 ATGAATTACTG
53156125 TTATTACTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.36, C:0.08, G:0.22, T:0.34
Consensus pattern (40 bp):
ATGAATTACTGCTGAAATGAATGAATTACAGTTGATACGG
Found at i:53156137 original size:40 final size:39
Alignment explanation
Indices: 53156090--53156192 Score: 102
Period size: 40 Copynumber: 2.6 Consensus size: 39
53156080 TACTGCTGAA
*
53156090 ATGAATGAATTACAGTTGATACGGATAAATTACT-GTTATT
1 ATGAATGAATTACAGTT-ATACGGATAAACTACTAGTTA-T
* * *
53156130 ACT-AATGAGTTACTGGTTATACGGATGAACTACTAGTTAT
1 A-TGAATGAATTAC-AGTTATACGGATAAACTACTAGTTAT
*
53156170 ATGAATGAATTAGAGTTTATACG
1 ATGAATGAATTACAG-TTATACG
53156193 AATAGAAATG
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
39 2 0.04
40 41 0.80
41 8 0.16
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (39 bp):
ATGAATGAATTACAGTTATACGGATAAACTACTAGTTAT
Found at i:53156177 original size:20 final size:20
Alignment explanation
Indices: 53156092--53156178 Score: 52
Period size: 20 Copynumber: 4.3 Consensus size: 20
53156082 CTGCTGAAAT
*
53156092 GAATGAATTAC-AGTTGATAC
1 GAATGAACTACTAGTT-ATAC
* * *
53156112 GGATAAATTACT-GTTATTAC
1 GAATGAACTACTAGTTA-TAC
* ** *
53156132 TAATGAGTTACTGGTTATAC
1 GAATGAACTACTAGTTATAC
* *
53156152 GGATGAACTACTAGTTATAT
1 GAATGAACTACTAGTTATAC
53156172 GAATGAA
1 GAATGAA
53156179 TTAGAGTTTA
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
19 1 0.02
20 46 0.90
21 4 0.08
ACGTcount: A:0.37, C:0.09, G:0.20, T:0.34
Consensus pattern (20 bp):
GAATGAACTACTAGTTATAC
Found at i:53157685 original size:20 final size:21
Alignment explanation
Indices: 53157654--53157694 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
53157644 AGAGGGGAAG
53157654 GAAAGAAAGAAAAAGAGAAAA
1 GAAAGAAAGAAAAAGAGAAAA
*
53157675 GAAAG-AAGAAAAAGGGAAAA
1 GAAAGAAAGAAAAAGAGAAAA
53157695 TTGAAGGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (21 bp):
GAAAGAAAGAAAAAGAGAAAA
Found at i:53159916 original size:46 final size:46
Alignment explanation
Indices: 53159864--53160137 Score: 345
Period size: 46 Copynumber: 6.0 Consensus size: 46
53159854 GCTCTTTGAA
** *
53159864 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
**
53159910 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
**
53159956 GGGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * ***
53160002 -GGAAAATGAATAAGACCATGGTTGAAAGATACAATGGCAGTGTGAC
1 ATG-AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
*
53160048 ATAAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* ** * * *
53160094 A-GAAAATGAGTAAGACCACAGTTGAAAGACACTATGGCATCATG
1 ATG-AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATG
53160138 TTAAAGATAA
Statistics
Matches: 203, Mismatches: 22, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
45 2 0.01
46 201 0.99
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.20
Consensus pattern (46 bp):
ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:53160118 original size:138 final size:138
Alignment explanation
Indices: 53159874--53160137 Score: 384
Period size: 138 Copynumber: 1.9 Consensus size: 138
53159864 ATGAAATGTG
* * * **
53159874 TAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACAATGGCAACATGACATAAAATGAATAAGACCATGGTTGAAAGA
* * ** *
53159939 TACCATGGCAACATGACGGGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACGG
66 TACCATGGCAACATGACAGAAAATGAATAAGACCACAGTTGAAAGACACCATGGCAACATGACGG
53160004 AAAATGAA
131 AAAATGAA
***
53160012 TAAGACCATGGTTGAAAGATACAATGGCAGTGTGACATAAAATGAATAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACAATGGCAACATGACATAAAATGAATAAGACCATGGTTGAAAGA
* * *
53160077 TACCATGGCAACATGACAGAAAATGAGTAAGACCACAGTTGAAAGACACTATGGCATCATG
66 TACCATGGCAACATGACAGAAAATGAATAAGACCACAGTTGAAAGACACCATGGCAACATG
53160138 TTAAAGATAA
Statistics
Matches: 110, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
138 110 1.00
ACGTcount: A:0.42, C:0.15, G:0.24, T:0.20
Consensus pattern (138 bp):
TAAGACCATGGTTGAAAGATACAATGGCAACATGACATAAAATGAATAAGACCATGGTTGAAAGA
TACCATGGCAACATGACAGAAAATGAATAAGACCACAGTTGAAAGACACCATGGCAACATGACGG
AAAATGAA
Found at i:53160418 original size:16 final size:17
Alignment explanation
Indices: 53160397--53160428 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
53160387 ATGATGGAGC
53160397 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
53160413 ATGAAATGATTGATAT
1 ATGAAATGATTGATAT
53160429 GTACTTATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.38
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:53162756 original size:42 final size:42
Alignment explanation
Indices: 53162644--53162778 Score: 116
Period size: 42 Copynumber: 3.2 Consensus size: 42
53162634 CTGAAGGCTG
* * * * *
53162644 AACAGAAGCTC-ATGAGAGCTAAACAAAAACCCGTAAGGGTTG
1 AACAGAAGCTCAAT-AGAGCTGAACAGAAACCCATAAGAGTTA
* * *
53162686 AAC-GAAAG-TC-GTAAGAGCTGAACGGAAACCCATAAGGGTTA
1 AACAG-AAGCTCAAT-AGAGCTGAACAGAAACCCATAAGAGTTA
* * *
53162727 AATAGAAGCTCAATAGAGCTGAACAGAAACTCATATGAGTTA
1 AACAGAAGCTCAATAGAGCTGAACAGAAACCCATAAGAGTTA
53162769 AACAGAAGCT
1 AACAGAAGCT
53162779 TATGAGATCT
Statistics
Matches: 75, Mismatches: 14, Indels: 8
0.77 0.14 0.08
Matches are distributed among these distances:
41 32 0.43
42 42 0.56
43 1 0.01
ACGTcount: A:0.44, C:0.17, G:0.23, T:0.16
Consensus pattern (42 bp):
AACAGAAGCTCAATAGAGCTGAACAGAAACCCATAAGAGTTA
Found at i:53163696 original size:57 final size:57
Alignment explanation
Indices: 53163608--53163725 Score: 186
Period size: 57 Copynumber: 2.1 Consensus size: 57
53163598 ATGAAGCTAA
* *
53163608 AATATGAAATCCGGAATTAAGAGCTTTTCAATGGTGTTTTTGGA-AAAAAATTTGGAG
1 AATATGAAATCCGGAATTAAGAGCTCTTCAATGGTGTTTTTGGACAAAAAA-TCGGAG
53163665 AATATGAAATCC-GACATTAAGAGCTCTTCAATGGTGTTTTTGGACAAAAAATCGGAG
1 AATATGAAATCCGGA-ATTAAGAGCTCTTCAATGGTGTTTTTGGACAAAAAATCGGAG
53163722 AATA
1 AATA
53163726 AATGGTCTAG
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
56 2 0.04
57 49 0.86
58 6 0.11
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (57 bp):
AATATGAAATCCGGAATTAAGAGCTCTTCAATGGTGTTTTTGGACAAAAAATCGGAG
Found at i:53174740 original size:23 final size:22
Alignment explanation
Indices: 53174695--53174738 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
53174685 ATGTTATTGT
*
53174695 TTGTTAAATTTTAATTATAAAA
1 TTGTTAAATATTAATTATAAAA
53174717 TTGTATAAATATTAA-TATAAAA
1 TTGT-TAAATATTAATTATAAAA
53174739 ATAATTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (22 bp):
TTGTTAAATATTAATTATAAAA
Found at i:53179955 original size:6 final size:6
Alignment explanation
Indices: 53179941--53179989 Score: 80
Period size: 6 Copynumber: 8.2 Consensus size: 6
53179931 ACCGTGCCCG
* *
53179941 ACATAT ACATGT ACATAT ACATAT ACATAT ACATAT ACATAT ACGTAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
53179989 A
1 A
53179990 TAACACTCGT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.47, C:0.16, G:0.04, T:0.33
Consensus pattern (6 bp):
ACATAT
Found at i:53180573 original size:16 final size:16
Alignment explanation
Indices: 53180552--53180584 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
53180542 TCAACAATTC
53180552 GAAGAAAAAAAAAGAA
1 GAAGAAAAAAAAAGAA
*
53180568 GAAGAAGAAAAAAGAA
1 GAAGAAAAAAAAAGAA
53180584 G
1 G
53180585 CTTATGTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (16 bp):
GAAGAAAAAAAAAGAA
Found at i:53180692 original size:13 final size:13
Alignment explanation
Indices: 53180665--53180702 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
53180655 GTCGTAGGTA
*
53180665 AATTCATTTTCTGT
1 AATT-ATTTTTTGT
53180679 AATTATTTTTTGT
1 AATTATTTTTTGT
53180692 AATTATTTTTT
1 AATTATTTTTT
53180703 AAAATAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 19 0.83
14 4 0.17
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (13 bp):
AATTATTTTTTGT
Found at i:53182827 original size:21 final size:21
Alignment explanation
Indices: 53182801--53182841 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
53182791 TTTACCCTAG
53182801 TTTTAATTTCAATGTAATTCA
1 TTTTAATTTCAATGTAATTCA
*
53182822 TTTTAATTTCAATGTGATTC
1 TTTTAATTTCAATGTAATTC
53182842 GAAAAAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.10, G:0.07, T:0.54
Consensus pattern (21 bp):
TTTTAATTTCAATGTAATTCA
Found at i:53184402 original size:56 final size:55
Alignment explanation
Indices: 53184287--53184427 Score: 144
Period size: 55 Copynumber: 2.5 Consensus size: 55
53184277 TCAGGAATTG
* * * *
53184287 AAAAAAAAATTTGGGTGCTGGGTCATTGATGGCCAGCACCCTTGTAATAGATTTAA
1 AAAAAAAAATTT-GGTGCTGGGACACTGATAGCCAGCACCCTTGTAACAGATTTAA
* *
53184343 AAAAAAAAATTTGGTGCTGGGACACTGATAGCC-GACACCTTTGTACCAGATTT--
1 AAAAAAAAATTTGGTGCTGGGACACTGATAGCCAG-CACCCTTGTAACAGATTTAA
**
53184396 TTAAAAAAATTCTAAGGTGCTGGGACACTGAT
1 AAAAAAAAATT-T--GGTGCTGGGACACTGAT
53184428 GGTCAGGACC
Statistics
Matches: 73, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
53 9 0.12
54 2 0.03
55 33 0.45
56 29 0.40
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.28
Consensus pattern (55 bp):
AAAAAAAAATTTGGTGCTGGGACACTGATAGCCAGCACCCTTGTAACAGATTTAA
Found at i:53185324 original size:3 final size:3
Alignment explanation
Indices: 53185316--53185341 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
53185306 AGTAAAAATA
53185316 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
53185342 AGCTATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:53185490 original size:32 final size:30
Alignment explanation
Indices: 53185450--53185512 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 30
53185440 TACATTTGTA
53185450 TTATTTTATGTA-TAATTAGTGAAAAGATATT
1 TTATTTTAT-TATTAATTAGT-AAAAGATATT
*
53185481 TTATATTTATTATTAATTAGTAAAATATATT
1 TTAT-TTTATTATTAATTAGTAAAAGATATT
53185512 T
1 T
53185513 ATTAGATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 16 0.55
32 13 0.45
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (30 bp):
TTATTTTATTATTAATTAGTAAAAGATATT
Found at i:53186640 original size:18 final size:18
Alignment explanation
Indices: 53186609--53186652 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
53186599 TGAATATGTG
53186609 AATTGAAAATTGATTGAA
1 AATTGAAAATTGATTGAA
53186627 AATTGGAAAA-TGATTG--
1 AATT-GAAAATTGATTGAA
53186643 AATTGAAAAT
1 AATTGAAAAT
53186653 GTGAGAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
15 5 0.21
16 4 0.17
18 10 0.42
19 5 0.21
ACGTcount: A:0.50, C:0.00, G:0.18, T:0.32
Consensus pattern (18 bp):
AATTGAAAATTGATTGAA
Found at i:53186885 original size:38 final size:38
Alignment explanation
Indices: 53186783--53186915 Score: 108
Period size: 38 Copynumber: 3.4 Consensus size: 38
53186773 GACCTCGAGT
* * * *
53186783 CGATGAAACACTGGGTGTCACTATTTTACTTCGGATAGATT
1 CGATGAGACACTGGGTGTCA--ACTTTACTTCGGCTAG-TC
** * * *
53186824 CGATGAGGTACTGGGT-ACCACTTTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAACTTTACTTCGGCTAGTC
* *
53186861 CGATGAGACACTGGGTGTCAACTTTGCTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAACTTTACTTCG-GCTAGTC
*
53186899 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
53186916 CCAAATTGGT
Statistics
Matches: 73, Mismatches: 17, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
37 14 0.19
38 42 0.58
39 3 0.04
40 1 0.01
41 13 0.18
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.29
Consensus pattern (38 bp):
CGATGAGACACTGGGTGTCAACTTTACTTCGGCTAGTC
Found at i:53188204 original size:90 final size:89
Alignment explanation
Indices: 53187985--53188218 Score: 269
Period size: 90 Copynumber: 2.6 Consensus size: 89
53187975 GGTGTTACAC
* * *
53187985 AAAATGTTCGTATTA-TTTTGTAT-TCGTAAAT-CAATTGTAGTCAGTATTATTTTTTGGTCAAA
1 AAAATGTTCGTATTATTTTTGTATCT-GTAAATAAAATT-TAGTC-GTATTATTTGTCGGTCAAA
* *
53188047 TTTTATATTTTCGTATATCAGTTTTGT
63 TTTTATATTTTCGTATATCAATTTTCT
* * * * * *
53188074 AAAATATTTGTGTTATTTTTGGATCTGTAAA-AATATTTTAGAACGTATTATTTGTCGGTCAAAT
1 AAAATGTTCGTATTATTTTTGTATCTGTAAATAA-AATTTAG-TCGTATTATTTGTCGGTCAAAT
*
53188138 TTTATATTTTTGTATATCAATTTTCT
64 TTTATATTTTCGTATATCAATTTTCT
*
53188164 AAAATGTTCGTATTATTTTTGTATCTGTAAATAAAATTTAGTTGGTATTATTTGT
1 AAAATGTTCGTATTATTTTTGTATCTGTAAATAAAATTTAG-TCGTATTATTTGT
53188219 TTATTGAATT
Statistics
Matches: 119, Mismatches: 20, Indels: 11
0.79 0.13 0.07
Matches are distributed among these distances:
89 12 0.10
90 100 0.84
91 7 0.06
ACGTcount: A:0.29, C:0.06, G:0.13, T:0.51
Consensus pattern (89 bp):
AAAATGTTCGTATTATTTTTGTATCTGTAAATAAAATTTAGTCGTATTATTTGTCGGTCAAATTT
TATATTTTCGTATATCAATTTTCT
Found at i:53188282 original size:16 final size:17
Alignment explanation
Indices: 53188257--53188290 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
53188247 GAATGCTTGT
53188257 ATTTTCTTATATATGTA
1 ATTTTCTTATATATGTA
*
53188274 ATTTT-TTATATCTGTA
1 ATTTTCTTATATATGTA
53188290 A
1 A
53188291 ATAAAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.59
Consensus pattern (17 bp):
ATTTTCTTATATATGTA
Found at i:53191364 original size:16 final size:16
Alignment explanation
Indices: 53191343--53191377 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
53191333 TTAATTATGA
53191343 ATATTAATATTCATGG
1 ATATTAATATTCATGG
*
53191359 ATATTACTATTCATGG
1 ATATTAATATTCATGG
53191375 ATA
1 ATA
53191378 GATGAGGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.43
Consensus pattern (16 bp):
ATATTAATATTCATGG
Found at i:53203456 original size:31 final size:29
Alignment explanation
Indices: 53203412--53203476 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
53203402 TGTTTTGTTA
*
53203412 TGGTACTTATATTTTTATAAAATATAAAATG
1 TGGTACATATA-TTTTA-AAAATATAAAATG
* **
53203443 TGGTACATGTATTTTAAAAATATTTAATG
1 TGGTACATATATTTTAAAAATATAAAATG
53203472 TGGTA
1 TGGTA
53203477 TCTAAACTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 16 0.53
30 5 0.17
31 9 0.30
ACGTcount: A:0.38, C:0.03, G:0.14, T:0.45
Consensus pattern (29 bp):
TGGTACATATATTTTAAAAATATAAAATG
Found at i:53205496 original size:26 final size:28
Alignment explanation
Indices: 53205435--53205497 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
53205425 TATATATATA
*
53205435 TTTATATATTTATAATTTTTTTAATAAT
1 TTTATATATTTATAATTTTATTAATAAT
* * *
53205463 TTTCTATATTTCTTA-TTTATTAA-AAT
1 TTTATATATTTATAATTTTATTAATAAT
53205489 TTTATATAT
1 TTTATATAT
53205498 AATCATCTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 11 0.37
27 7 0.23
28 12 0.40
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (28 bp):
TTTATATATTTATAATTTTATTAATAAT
Found at i:53209167 original size:20 final size:20
Alignment explanation
Indices: 53209144--53209183 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
53209134 TATTCAAACT
* *
53209144 ATATTACTTGAATAGTTATA
1 ATATTACATGAATAATTATA
*
53209164 ATATTAGATGAATAATTATA
1 ATATTACATGAATAATTATA
53209184 TGTCTTTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.03, G:0.10, T:0.42
Consensus pattern (20 bp):
ATATTACATGAATAATTATA
Found at i:53211852 original size:11 final size:11
Alignment explanation
Indices: 53211836--53211863 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
53211826 TGACTTTAGA
53211836 GTATGTATTTT
1 GTATGTATTTT
53211847 GTATGTATTTT
1 GTATGTATTTT
53211858 GTATGT
1 GTATGT
53211864 TAGACTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.18, C:0.00, G:0.21, T:0.61
Consensus pattern (11 bp):
GTATGTATTTT
Found at i:53212048 original size:15 final size:16
Alignment explanation
Indices: 53212028--53212057 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
53212018 CAATATTGCC
53212028 TTGTTTTGGT-TAAAG
1 TTGTTTTGGTATAAAG
53212043 TTGTTTTGGTATAAA
1 TTGTTTTGGTATAAA
53212058 TGATGTGCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.53
Consensus pattern (16 bp):
TTGTTTTGGTATAAAG
Found at i:53215589 original size:18 final size:18
Alignment explanation
Indices: 53215552--53215603 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
53215542 AAAAGTCTAG
*
53215552 AAAAATACAAATAAACAA
1 AAAAATAAAAATAAACAA
53215570 AAAAATAAAAATAAGA-AA
1 AAAAATAAAAATAA-ACAA
*
53215588 AAATATAAAAAATAAA
1 AAAAAT-AAAAATAAA
53215604 TGGATTCAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 21 0.70
19 9 0.30
ACGTcount: A:0.81, C:0.04, G:0.02, T:0.13
Consensus pattern (18 bp):
AAAAATAAAAATAAACAA
Found at i:53217275 original size:21 final size:23
Alignment explanation
Indices: 53217240--53217363 Score: 146
Period size: 24 Copynumber: 5.2 Consensus size: 23
53217230 AAACTTATAT
*
53217240 TAATA-AATGAATAA-AA-AATAT
1 TAATATAAT-AATAATAATAATAA
*
53217261 TAATATATTAATAAATAAATGAATAA
1 TAATATAATAAT-AAT-AAT-AATAA
53217287 TAATAATAATAATAATAATAATAA
1 TAAT-ATAATAATAATAATAATAA
53217311 TAATAATAATAATAATAATAATAA
1 TAAT-ATAATAATAATAATAATAA
53217335 TAATAATAATAATAATAATAATAA
1 TAAT-ATAATAATAATAATAATAA
53217359 TAATA
1 TAATA
53217364 GAAGAAATGT
Statistics
Matches: 93, Mismatches: 3, Indels: 12
0.86 0.03 0.11
Matches are distributed among these distances:
21 8 0.09
22 4 0.04
23 1 0.01
24 59 0.63
25 3 0.03
26 11 0.12
27 7 0.08
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (23 bp):
TAATATAATAATAATAATAATAA
Found at i:53217290 original size:3 final size:3
Alignment explanation
Indices: 53217282--53217363 Score: 164
Period size: 3 Copynumber: 27.3 Consensus size: 3
53217272 TAAATAAATG
53217282 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
53217330 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
53217364 GAAGAAATGT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 79 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:53219459 original size:42 final size:43
Alignment explanation
Indices: 53219353--53219469 Score: 166
Period size: 43 Copynumber: 2.7 Consensus size: 43
53219343 TACCAGTGCT
* *
53219353 ATATCCCAGATATGGTCTTACATGTAATCTCGTATCGATGCCA
1 ATATCCCAGATATGGTCTTACATGTAATCTCATATCAATGCCA
* *
53219396 ATAGCCCAGCTATGGTCTTACATG-AAGTCTCATATCAATGCC-
1 ATATCCCAGATATGGTCTTACATGTAA-TCTCATATCAATGCCA
*
53219438 ATATCCCAGATATAGTCTTACATGTAATCTCA
1 ATATCCCAGATATGGTCTTACATGTAATCTCA
53219470 GTAACCCTAA
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
42 28 0.43
43 37 0.57
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.32
Consensus pattern (43 bp):
ATATCCCAGATATGGTCTTACATGTAATCTCATATCAATGCCA
Found at i:53223684 original size:7 final size:7
Alignment explanation
Indices: 53223651--53223682 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
53223641 ACATTTCTAA
53223651 TCATCCC
1 TCATCCC
53223658 TCATCCC
1 TCATCCC
53223665 TCATCCC
1 TCATCCC
*
53223672 TCATTCC
1 TCATCCC
53223679 TCAT
1 TCAT
53223683 TCATTATCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.50, G:0.00, T:0.34
Consensus pattern (7 bp):
TCATCCC
Found at i:53229600 original size:29 final size:29
Alignment explanation
Indices: 53229558--53229628 Score: 112
Period size: 29 Copynumber: 2.6 Consensus size: 29
53229548 GTTCTTCAAC
*
53229558 ATAGTTTGATTTGATTGTTAATTGGTGTG
1 ATAGTTTGATTTGATTGTTAATTGGTGCG
53229587 ATAGTTTGATTTGATTGTTAATTGGTGCG
1 ATAGTTTGATTTGATTGTTAATTGGTGCG
53229616 A-A--TTGATTTGATT
1 ATAGTTTGATTTGATT
53229629 AAATCATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
26 11 0.27
28 1 0.02
29 29 0.71
ACGTcount: A:0.23, C:0.01, G:0.25, T:0.51
Consensus pattern (29 bp):
ATAGTTTGATTTGATTGTTAATTGGTGCG
Found at i:53229948 original size:125 final size:127
Alignment explanation
Indices: 53229799--53230097 Score: 338
Period size: 125 Copynumber: 2.4 Consensus size: 127
53229789 GCCACACGGC
* * * * *
53229799 TGTGTGT-CAGGCCGTGTAACTCACTGTTTGTGAATTAAGGTCACATACGCTAGAAACACGAGCA
1 TGTGTGTCCAGGCTGTGTAACTCACTGTTTGTGAATTAGGGTCACACACGCAAGAAACACGAACA
* **
53229863 TGTGTCTAGGCATG-CAACTCA-T-TGTTTGTGAATTAGGGTCACACGG-GCTAAAGACATGGG
66 TGTGTCCAGGC-TGACAACTCACTAT-TTTGTGAATTAGGGTCACACGGAGCTAAAGACACCGG
* * ** * **
53229923 TGTGTGTCCAGGCTGTGTAATTCACTGTTTGTGAATTAGGGTCAGACGGGCAAGAGACACGAATG
1 TGTGTGTCCAGGCTGTGTAACTCACTGTTTGTGAATTAGGGTCACACACGCAAGAAACACGAACA
* * *
53229988 TGTGTCCAGGCTGTATAACTCACTATTTTTTGAATTAGGGTCACACGGAGCTAAAGACCCCGG
66 TGTGTCCAGGCTG-ACAACTCACTATTTTGTGAATTAGGGTCACACGGAGCTAAAGACACCGG
* * * *
53230051 CGTGTGTCTAGGCTGTGTAACTCACTATTTATGAATTAGGGTCACAC
1 TGTGTGTCCAGGCTGTGTAACTCACTGTTTGTGAATTAGGGTCACAC
53230098 GATCCAGAGA
Statistics
Matches: 145, Mismatches: 24, Indels: 8
0.82 0.14 0.05
Matches are distributed among these distances:
124 9 0.06
125 55 0.38
126 6 0.04
127 22 0.15
128 53 0.37
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (127 bp):
TGTGTGTCCAGGCTGTGTAACTCACTGTTTGTGAATTAGGGTCACACACGCAAGAAACACGAACA
TGTGTCCAGGCTGACAACTCACTATTTTGTGAATTAGGGTCACACGGAGCTAAAGACACCGG
Found at i:53229960 original size:63 final size:63
Alignment explanation
Indices: 53229799--53230098 Score: 304
Period size: 63 Copynumber: 4.8 Consensus size: 63
53229789 GCCACACGGC
* * ***
53229799 TGTGTGT-CAGGCCGTGTAACTCACTGTTTGTGAATTAAGGTCACATACGCTAGAA-ACACGAG
1 TGTGTGTCCAGGCTGTGTAACTCACTGTTTGTGAATTAGGGTCACACGGGCTA-AAGACACGAG
** * * * * * *
53229861 CATGTGTCTAGGC-ATGCAACTCATTGTTTGTGAATTAGGGTCACACGGGCTAAAGACATGGG
1 TGTGTGTCCAGGCTGTGTAACTCACTGTTTGTGAATTAGGGTCACACGGGCTAAAGACACGAG
* * *
53229923 TGTGTGTCCAGGCTGTGTAATTCACTGTTTGTGAATTAGGGTCAGACGGGC-AAGAGACACGAA
1 TGTGTGTCCAGGCTGTGTAACTCACTGTTTGTGAATTAGGGTCACACGGGCTAA-AGACACGAG
* * * *
53229986 TGTGTGTCCAGGCTGTATAACTCACTATTTTTTGAATTAGGGTCACACGGAGCTAAAGACCCCG-
1 TGTGTGTCCAGGCTGTGTAACTCACT-GTTTGTGAATTAGGGTCACACGG-GCTAAAGA-CACGA
53230050 G
63 G
* * * *
53230051 CGTGTGTCTAGGCTGTGTAACTCACTATTTATGAATTAGGGTCACACG
1 TGTGTGTCCAGGCTGTGTAACTCACTGTTTGTGAATTAGGGTCACACG
53230099 ATCCAGAGAC
Statistics
Matches: 195, Mismatches: 35, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
61 2 0.01
62 54 0.28
63 66 0.34
64 40 0.21
65 28 0.14
66 5 0.03
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (63 bp):
TGTGTGTCCAGGCTGTGTAACTCACTGTTTGTGAATTAGGGTCACACGGGCTAAAGACACGAG
Found at i:53236517 original size:16 final size:16
Alignment explanation
Indices: 53236496--53236526 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53236486 TTTGCTATTA
*
53236496 TGTCTTTTGTATTTTC
1 TGTCTTTTATATTTTC
53236512 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
53236527 GCATGCATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.10, G:0.10, T:0.71
Consensus pattern (16 bp):
TGTCTTTTATATTTTC
Found at i:53238014 original size:24 final size:24
Alignment explanation
Indices: 53237986--53238031 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
53237976 CAGTGGTGCC
53237986 GGCGGTTGCGTCA-CAATGGTTGGT
1 GGCGGTTG-GTCATCAATGGTTGGT
*
53238010 GGCGGTTGGTCATCAGTGGTTG
1 GGCGGTTGGTCATCAATGGTTG
53238032 AGTAGTGGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.11, C:0.15, G:0.43, T:0.30
Consensus pattern (24 bp):
GGCGGTTGGTCATCAATGGTTGGT
Found at i:53240157 original size:19 final size:19
Alignment explanation
Indices: 53240133--53240182 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
53240123 ATTCTAACCT
53240133 TGTCTCATAAAAATTCAAA
1 TGTCTCATAAAAATTCAAA
53240152 TGTCTCATAAAAATTCAAA
1 TGTCTCATAAAAATTCAAA
*
53240171 TATCTCATAAAA
1 TGTCTCATAAAA
53240183 TGAAATTCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.48, C:0.16, G:0.04, T:0.32
Consensus pattern (19 bp):
TGTCTCATAAAAATTCAAA
Found at i:53242014 original size:26 final size:26
Alignment explanation
Indices: 53241981--53242033 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
53241971 AAAAATTACA
53241981 TTTTTGCCCCTAAACTTTGTCATATT
1 TTTTTGCCCCTAAACTTTGTCATATT
53242007 TTTTTGCCCCTAAACTTTGTCATATT
1 TTTTTGCCCCTAAACTTTGTCATATT
53242033 T
1 T
53242034 ACACTTTGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.19, C:0.23, G:0.08, T:0.51
Consensus pattern (26 bp):
TTTTTGCCCCTAAACTTTGTCATATT
Found at i:53247173 original size:42 final size:42
Alignment explanation
Indices: 53247113--53247193 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
53247103 GTGCAGGTTT
* *
53247113 CACACGGCCAAGATACACACCTATGT-TCTAGGCCATGTGTTA
1 CACACGGCCAAGACACACACCTATGTCTCT-GCCCATGTGTTA
**
53247155 CACACGGCTGAGACACACACCTATGTCTCTGCCCATGTG
1 CACACGGCCAAGACACACACCTATGTCTCTGCCCATGTG
53247194 CTTAATTCTG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 31 0.91
43 3 0.09
ACGTcount: A:0.26, C:0.32, G:0.20, T:0.22
Consensus pattern (42 bp):
CACACGGCCAAGACACACACCTATGTCTCTGCCCATGTGTTA
Found at i:53250644 original size:16 final size:16
Alignment explanation
Indices: 53250620--53250652 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
53250610 TTTTATATAT
*
53250620 TAAATTATTATATTAA
1 TAAAATATTATATTAA
53250636 TAAAATATTATATTAA
1 TAAAATATTATATTAA
53250652 T
1 T
53250653 TAGATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TAAAATATTATATTAA
Found at i:53250852 original size:5 final size:5
Alignment explanation
Indices: 53250842--53250873 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
53250832 TTATTAATTA
53250842 AATAT AATAT AATAT AATAT AATAT AATAT AA
1 AATAT AATAT AATAT AATAT AATAT AATAT AA
53250874 AGTAAATAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AATAT
Found at i:53251389 original size:44 final size:44
Alignment explanation
Indices: 53251339--53251427 Score: 119
Period size: 44 Copynumber: 2.0 Consensus size: 44
53251329 TGTTTAGGGA
* *
53251339 TACTTCGACCTT-GAGTCGATGAGGCA-CTATGAGTGTCGTACTGT
1 TACTTCGA-CTTCAAGTCGATAAGGCACCT-TGAGTGTCGTACTGT
*
53251383 TACTTCGACTTCAAGTCGATAAGGCACCTTGTGTGTCGTACTGT
1 TACTTCGACTTCAAGTCGATAAGGCACCTTGAGTGTCGTACTGT
53251427 T
1 T
53251428 GCTATTACTT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
43 3 0.08
44 35 0.88
45 2 0.05
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.34
Consensus pattern (44 bp):
TACTTCGACTTCAAGTCGATAAGGCACCTTGAGTGTCGTACTGT
Found at i:53254758 original size:22 final size:22
Alignment explanation
Indices: 53254719--53254760 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
53254709 ATATTGTGTA
*
53254719 ACATATCATAACACATCTCATG
1 ACATATCATAACAAATCTCATG
* *
53254741 ACATATCTTAGCAAATCTCA
1 ACATATCATAACAAATCTCA
53254761 AATCATATCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.26, G:0.05, T:0.29
Consensus pattern (22 bp):
ACATATCATAACAAATCTCATG
Found at i:53256028 original size:206 final size:206
Alignment explanation
Indices: 53255669--53256075 Score: 672
Period size: 206 Copynumber: 2.0 Consensus size: 206
53255659 AAACTTGGCA
*
53255669 TCCTGAGGTACTTTTGATAGGGCATTGGTTGGGGATGGCTTTGGTGGCTAACGTGGTAGTTTGGG
1 TCCTAAGGTACTTTTGATAGGGCATTGGTTGGGGATGGCTTTGGTGGCTAACGTGGTAGTTTGGG
* * *
53255734 GGCTATTTTGGGATGGTTTCATGACCTTCCCGACGGCCACACGGGCGTGTGCTGAGGCACACGAC
66 GGCTATTTTGGGATGGTTTCATGACCTCCCCGACGGCCACACGGGCATGTGCTAAGGCACACGAC
* *
53255799 TGTGTGGATTTGGGGATTAGGGTTT-TGAGCCAAATTTGGTGCAACACGACTGTGTGACCGATTG
131 TGTGTGGATTTGGGGATTAGGGTTTCAG-GCCAAATTTGGTGCAACACGACCGTGTGACCGATTG
53255863 GGGGATTAGGCT
195 GGGGATTAGGCT
*
53255875 TCCTAAGGTACTTTTGATAGGGCATTGGTTGGGGATGGCTTTGGTGGCTAACGTGGTGGTTTGGG
1 TCCTAAGGTACTTTTGATAGGGCATTGGTTGGGGATGGCTTTGGTGGCTAACGTGGTAGTTTGGG
* * * * *
53255940 GGCTATTTTGGGGTGGTTTCGTGACCTCCCCTACTGCCACACGGGCATGTGCTAAGGCACACGGC
66 GGCTATTTTGGGATGGTTTCATGACCTCCCCGACGGCCACACGGGCATGTGCTAAGGCACACGAC
* *
53256005 TGTGTGGATTTGGGGATTAGGGTTTCAGGCCAAATTTGGTGCAATACGACCGTGTGATCGATTGG
131 TGTGTGGATTTGGGGATTAGGGTTTCAGGCCAAATTTGGTGCAACACGACCGTGTGACCGATTGG
53256070 GGGATT
196 GGGATT
53256076 TTGTCATTTC
Statistics
Matches: 186, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
206 185 0.99
207 1 0.01
ACGTcount: A:0.17, C:0.17, G:0.36, T:0.30
Consensus pattern (206 bp):
TCCTAAGGTACTTTTGATAGGGCATTGGTTGGGGATGGCTTTGGTGGCTAACGTGGTAGTTTGGG
GGCTATTTTGGGATGGTTTCATGACCTCCCCGACGGCCACACGGGCATGTGCTAAGGCACACGAC
TGTGTGGATTTGGGGATTAGGGTTTCAGGCCAAATTTGGTGCAACACGACCGTGTGACCGATTGG
GGGATTAGGCT
Found at i:53259243 original size:16 final size:15
Alignment explanation
Indices: 53259225--53259298 Score: 71
Period size: 17 Copynumber: 4.8 Consensus size: 15
53259215 TCTCATTTTA
*
53259225 ATTATTCTTTTTATT
1 ATTATTATTTTTATT
53259240 AATTATTTATTTTTATT
1 -ATTA-TTATTTTTATT
*
53259257 GTTATAATATTTTTATT
1 ATTAT--TATTTTTATT
*
53259274 ATTCTTATTTTTA-T
1 ATTATTATTTTTATT
53259288 -TTATTATTTTT
1 ATTATTATTTTT
53259299 CTTTTCTGTT
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
13 10 0.20
14 1 0.02
15 9 0.18
16 7 0.14
17 23 0.46
ACGTcount: A:0.24, C:0.03, G:0.01, T:0.72
Consensus pattern (15 bp):
ATTATTATTTTTATT
Found at i:53262519 original size:8 final size:8
Alignment explanation
Indices: 53262507--53262546 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
53262497 CAAGAGCACC
*
53262507 AAAAGAAC
1 AAAAGAAA
53262515 AAAAGAAA
1 AAAAGAAA
53262523 ACAAAGAAA
1 A-AAAGAAA
*
53262532 GAAAGAAA
1 AAAAGAAA
53262540 AAAAGAA
1 AAAAGAA
53262547 TAGGAAGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
8 21 0.75
9 7 0.25
ACGTcount: A:0.80, C:0.05, G:0.15, T:0.00
Consensus pattern (8 bp):
AAAAGAAA
Found at i:53262530 original size:17 final size:17
Alignment explanation
Indices: 53262516--53262561 Score: 67
Period size: 17 Copynumber: 2.7 Consensus size: 17
53262506 CAAAAGAACA
53262516 AAAGAAAACAAAGAAAG
1 AAAGAAAACAAAGAAAG
53262533 AAAGAAAA-AAAGAATAG
1 AAAGAAAACAAAGAA-AG
*
53262550 GAAGAAAACAAA
1 AAAGAAAACAAA
53262562 ACAAAATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 6 0.23
17 17 0.65
18 3 0.12
ACGTcount: A:0.76, C:0.04, G:0.17, T:0.02
Consensus pattern (17 bp):
AAAGAAAACAAAGAAAG
Found at i:53264443 original size:17 final size:18
Alignment explanation
Indices: 53264401--53264443 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
53264391 TAAATAAATC
53264401 TAAA-TAAAACTCTTAAG
1 TAAACTAAAACTCTTAAG
* *
53264418 TATACTAAAACTC-TAAT
1 TAAACTAAAACTCTTAAG
53264435 TAAACTAAA
1 TAAACTAAA
53264444 CAAGAAGAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.53, C:0.14, G:0.02, T:0.30
Consensus pattern (18 bp):
TAAACTAAAACTCTTAAG
Found at i:53265180 original size:13 final size:14
Alignment explanation
Indices: 53265157--53265185 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
53265147 TAACCATAAA
53265157 TTTAGCCTTTTATG
1 TTTAGCCTTTTATG
53265171 TTTA-CCTTTTATG
1 TTTAGCCTTTTATG
53265184 TT
1 TT
53265186 ATATTGGCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.14, C:0.14, G:0.10, T:0.62
Consensus pattern (14 bp):
TTTAGCCTTTTATG
Found at i:53266533 original size:30 final size:31
Alignment explanation
Indices: 53266487--53266571 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 31
53266477 TTGTTGGTGA
*
53266487 AACTTAAA-AAACAAATTTTAACA-ACTT-TGT
1 AACTTAAATAAA-AAATTTTAA-ATACTTCAGT
* *
53266517 AATTTAAATAAAAAATTTTAAATAGTTCAGT
1 AACTTAAATAAAAAATTTTAAATACTTCAGT
*
53266548 AACTTAAATAAAAATTTTTAAATA
1 AACTTAAATAAAAAATTTTAAATA
53266572 ATTGACCAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 1 0.02
30 19 0.40
31 27 0.57
ACGTcount: A:0.53, C:0.07, G:0.04, T:0.36
Consensus pattern (31 bp):
AACTTAAATAAAAAATTTTAAATACTTCAGT
Found at i:53266582 original size:26 final size:28
Alignment explanation
Indices: 53266553--53266609 Score: 64
Period size: 26 Copynumber: 2.1 Consensus size: 28
53266543 TCAGTAACTT
*
53266553 AAATAAAAATTTTTA-AAT-AATTGACC
1 AAATAAAAATTTTTATAATCAAGTGACC
** *
53266579 AAATTTAACTTTTTATAATCAAGTGACC
1 AAATAAAAATTTTTATAATCAAGTGACC
53266607 AAA
1 AAA
53266610 ACGAAAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 12 0.48
27 3 0.12
28 10 0.40
ACGTcount: A:0.49, C:0.11, G:0.05, T:0.35
Consensus pattern (28 bp):
AAATAAAAATTTTTATAATCAAGTGACC
Found at i:53278035 original size:135 final size:138
Alignment explanation
Indices: 53277752--53278165 Score: 649
Period size: 138 Copynumber: 3.0 Consensus size: 138
53277742 AGTGGGAGGC
*
53277752 TCTGGATCATATTGTCTATATCCAATGGTATTAGTTTCGTTATTATTAACAGCATTCACCGGCCT
1 TCTGGATCATATTGTCTATATCCAATGGTATTAGTTTCGTTATTATTAACAGCATTCACCTGCCT
*
53277817 CGAGTTTGAAGCAGACGAATCAGATCCTCCTCCGTCTTTCTTGGCCCAATTCCTCGTCTTTTCCG
66 CGAGTTTGAAGCAGACGAATCAGATCCTCCTCCGTCTTTCTTGGCCCAATTCCTCGTCTTTTCCA
53277882 GTTTTTCT
131 GTTTTTCT
* * *
53277890 TCTGGATCATATTGTCTACT-TCCGACGGTATTAGTTTCATTATTATTAACAGCATTCACCTGCC
1 TCTGGATCATATTGTCTA-TATCCAATGGTATTAGTTTCGTTATTATTAACAGCATTCACCTGCC
* ** *
53277954 TCAAGTTTGAAGCAGAAAAATCGGATCCTCCAT-C-T-TTT-TTGGCCCAATTCCTCGTCTTTTC
65 TCGAGTTTGAAGCAGACGAATCAGATCCTCC-TCCGTCTTTCTTGGCCCAATTCCTCGTCTTTTC
*
53278015 CTGTTTTTCT
129 CAGTTTTTCT
*
53278025 TCTGGATCATATTGTCTATGTCCAATGGTATTAGTTTCGTTATTATTAACAGCATTCACCTGCCT
1 TCTGGATCATATTGTCTATATCCAATGGTATTAGTTTCGTTATTATTAACAGCATTCACCTGCCT
* * *
53278090 CGAGTTTGAAGCATACGAATCAGATCCTCCTCCGTCTTTCTTTGCCCAATTCCTTGTCTTTTCCA
66 CGAGTTTGAAGCAGACGAATCAGATCCTCCTCCGTCTTTCTTGGCCCAATTCCTCGTCTTTTCCA
53278155 GTTTTTCT
131 GTTTTTCT
53278163 TCT
1 TCT
53278166 CTAGTTGCTT
Statistics
Matches: 249, Mismatches: 20, Indels: 14
0.88 0.07 0.05
Matches are distributed among these distances:
134 2 0.01
135 118 0.47
136 4 0.02
137 4 0.02
138 119 0.48
139 2 0.01
ACGTcount: A:0.20, C:0.25, G:0.15, T:0.40
Consensus pattern (138 bp):
TCTGGATCATATTGTCTATATCCAATGGTATTAGTTTCGTTATTATTAACAGCATTCACCTGCCT
CGAGTTTGAAGCAGACGAATCAGATCCTCCTCCGTCTTTCTTGGCCCAATTCCTCGTCTTTTCCA
GTTTTTCT
Found at i:53282364 original size:73 final size:73
Alignment explanation
Indices: 53282245--53282448 Score: 239
Period size: 73 Copynumber: 2.7 Consensus size: 73
53282235 GTCATGAGAG
* * * *
53282245 TGTTCACCAAATAAGTTCATAAAAAATGACAATTTTAAATAAATTAAAAGTATACATTAATCAAA
1 TGTTCACCAAATAAGTTTAAAAAAAATGACAATTTAAAATAAATTAAAAGTATACATTAACCAAA
53282310 TTCAATTA
66 TTCAATTA
* * *
53282318 TGTTCACCGAATAAGTTTAAAAAAAATAACAATTTAAAATAAATTAAAGCCATTAAATATATACA
1 TGTTCACCAAATAAGTTTAAAAAAAATGACAATTTAAAATAAATT------A--AAA-GTATACA
53282383 TTAACCAAATTCAATTA
57 TTAACCAAATTCAATTA
* *
53282400 TGTTCACCAAATAAG-TTCATAAAAATGACAATTTAAAATAAATTAAAAG
1 TGTTCACCAAATAAGTTTAAAAAAAATGACAATTTAAAATAAATTAAAAG
53282449 CAATTAAATA
Statistics
Matches: 110, Mismatches: 12, Indels: 19
0.78 0.09 0.13
Matches are distributed among these distances:
73 43 0.39
75 1 0.01
79 1 0.01
81 29 0.26
82 36 0.33
ACGTcount: A:0.52, C:0.11, G:0.06, T:0.31
Consensus pattern (73 bp):
TGTTCACCAAATAAGTTTAAAAAAAATGACAATTTAAAATAAATTAAAAGTATACATTAACCAAA
TTCAATTA
Found at i:53282374 original size:82 final size:82
Alignment explanation
Indices: 53282286--53282478 Score: 291
Period size: 82 Copynumber: 2.4 Consensus size: 82
53282276 ATTTTAAATA
* *
53282286 AATTAAA-AGTATACATTAATCAAATTCAATTATGTTCACCGAATAAGTTTAAAAAAAATAACAA
1 AATTAAATA-TATACATTAACCAAATTCAATTATGTTCACCAAATAAG-TTAAAAAAAATAACAA
53282350 TTTAAAATAAATT-AAAGC
64 TTTAAAATAAATTAAAAGC
* * * *
53282368 CATTAAATATATACATTAACCAAATTCAATTATGTTCACCAAATAAGTTCATAAAAATGACAATT
1 AATTAAATATATACATTAACCAAATTCAATTATGTTCACCAAATAAGTTAAAAAAAATAACAATT
53282433 TAAAATAAATTAAAAGC
66 TAAAATAAATTAAAAGC
*
53282450 AATTAAATATATACATTAACCGAATTCAA
1 AATTAAATATATACATTAACCAAATTCAA
53282479 ATTGCCGCAT
Statistics
Matches: 101, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
81 26 0.26
82 74 0.73
83 1 0.01
ACGTcount: A:0.52, C:0.12, G:0.05, T:0.31
Consensus pattern (82 bp):
AATTAAATATATACATTAACCAAATTCAATTATGTTCACCAAATAAGTTAAAAAAAATAACAATT
TAAAATAAATTAAAAGC
Found at i:53285194 original size:20 final size:20
Alignment explanation
Indices: 53285169--53285222 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
53285159 AAGTTAAGTA
*
53285169 TTTATATTAAATTAATATAT
1 TTTATATTAAATTAAGATAT
*
53285189 TTTATAATAAATTTAAGATAT
1 TTTATATTAAA-TTAAGATAT
53285210 TTTATATTTAAAT
1 TTTATA-TTAAAT
53285223 ATATTCTACC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 10 0.34
21 15 0.52
22 4 0.14
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
TTTATATTAAATTAAGATAT
Found at i:53285209 original size:21 final size:20
Alignment explanation
Indices: 53285156--53285215 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 20
53285146 TTGTAGATTA
*
53285156 AATAAGTTAAG-TA-TTTAT
1 AATAAATTAAGATATTTTAT
* *
53285174 ATTAAATTAATATATTTTAT
1 AATAAATTAAGATATTTTAT
53285194 AATAAATTTAAGATATTTTAT
1 AATAAA-TTAAGATATTTTAT
53285215 A
1 A
53285216 TTTAAATATA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
18 8 0.24
19 2 0.06
20 10 0.29
21 14 0.41
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (20 bp):
AATAAATTAAGATATTTTAT
Found at i:53285268 original size:18 final size:20
Alignment explanation
Indices: 53285245--53285283 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
53285235 ATTAATAGTT
*
53285245 TATA-TTATA-ATTTTTTTA
1 TATATTTATATATTATTTTA
53285263 TATATTTATATATTATTTTA
1 TATATTTATATATTATTTTA
53285283 T
1 T
53285284 TTTTATTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 5 0.28
20 9 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TATATTTATATATTATTTTA
Found at i:53288466 original size:43 final size:43
Alignment explanation
Indices: 53288385--53288466 Score: 98
Period size: 43 Copynumber: 1.9 Consensus size: 43
53288375 AAGTCGTACA
**
53288385 ATGCCAACGTCCCAGACGTGGTCTTACATGTAGTCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACATGTAAACACATATCG
53288428 ATGCC-ACAGTCCCAGACAG-GGTCTTAC-TCGTAAACACAT
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACAT-GTAAACACAT
53288467 CTCGGAATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
42 3 0.09
43 30 0.88
44 1 0.03
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.23
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACATGTAAACACATATCG
Found at i:53288524 original size:30 final size:30
Alignment explanation
Indices: 53288490--53288549 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
53288480 ATCGATGCCA
53288490 TGGTCTTACTCGCACACATATATCAGAATC
1 TGGTCTTACTCGCACACATATATCAGAATC
53288520 TGGTCTTACTCGCACACATATATCAGAATC
1 TGGTCTTACTCGCACACATATATCAGAATC
53288550 CTATGTCATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.27, G:0.13, T:0.30
Consensus pattern (30 bp):
TGGTCTTACTCGCACACATATATCAGAATC
Found at i:53294610 original size:29 final size:30
Alignment explanation
Indices: 53294572--53294686 Score: 128
Period size: 30 Copynumber: 3.9 Consensus size: 30
53294562 TAAAAAATAA
* *
53294572 AAATTGCATTTTGACCCCTAAACTTTTC-CT
1 AAATTTCATTTTGACCCCTAAAC-TTTCATT
* *
53294602 -AATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTCATT
* *
53294631 AAATTTCACTTAGACCCCTAAACTTTCATT
1 AAATTTCATTTTGACCCCTAAACTTTCATT
* *
53294661 AAATTTCATTTT-AACCCTAAATTTTC
1 AAATTTCATTTTGACCCCTAAACTTTC
53294687 TAAAAATTAC
Statistics
Matches: 72, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
28 4 0.06
29 33 0.46
30 35 0.49
ACGTcount: A:0.30, C:0.23, G:0.03, T:0.43
Consensus pattern (30 bp):
AAATTTCATTTTGACCCCTAAACTTTCATT
Found at i:53294638 original size:30 final size:30
Alignment explanation
Indices: 53294572--53294687 Score: 130
Period size: 29 Copynumber: 3.9 Consensus size: 30
53294562 TAAAAAATAA
* *
53294572 AAATTGCATTTTGACCCCTAAACTTT-TCCT
1 AAATTTCATTTTGACCCCTAAACTTTCT-TT
*
53294602 -AATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTCTTT
* * *
53294631 AAATTTCACTTAGACCCCTAAACTTTCATT
1 AAATTTCATTTTGACCCCTAAACTTTCTTT
* *
53294661 AAATTTCATTTT-AACCCTAAATTTTCT
1 AAATTTCATTTTGACCCCTAAACTTTCT
53294688 AAAAATTACA
Statistics
Matches: 72, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
29 36 0.50
30 36 0.50
ACGTcount: A:0.29, C:0.23, G:0.03, T:0.44
Consensus pattern (30 bp):
AAATTTCATTTTGACCCCTAAACTTTCTTT
Found at i:53294693 original size:29 final size:29
Alignment explanation
Indices: 53294569--53294700 Score: 90
Period size: 29 Copynumber: 4.5 Consensus size: 29
53294559 ATTTAAAAAA
* *
53294569 TAAAAATTGCATTTTGACCCCTAAACTTT-
1 TAAAAATTTCATTTT-AACCCTAAACTTTC
*** *
53294598 TCCTAATTTCATTTTGACCCTTAAACTTTC
1 TAAAAATTTCATTTTAACCC-TAAACTTTC
** *
53294628 TTTAAATTTCA-CTTAGACCCCTAAACTTTC
1 TAAAAATTTCATTTTA-A-CCCTAAACTTTC
* *
53294658 -ATTAAATTTCATTTTAACCCTAAATTTTC
1 TA-AAAATTTCATTTTAACCCTAAACTTTC
*
53294687 TAAAAATTACATTT
1 TAAAAATTTCATTT
53294701 AGCCCCAGAA
Statistics
Matches: 80, Mismatches: 16, Indels: 14
0.73 0.15 0.13
Matches are distributed among these distances:
28 3 0.04
29 42 0.52
30 29 0.36
31 6 0.08
ACGTcount: A:0.33, C:0.21, G:0.03, T:0.43
Consensus pattern (29 bp):
TAAAAATTTCATTTTAACCCTAAACTTTC
Found at i:53294694 original size:59 final size:59
Alignment explanation
Indices: 53294569--53294694 Score: 148
Period size: 59 Copynumber: 2.1 Consensus size: 59
53294559 ATTTAAAAAA
* * *
53294569 TAAAAATTGCATTTTGACCCCTAAACTTTTCCTAATTTCATTTTGACCCTTAAACTTTC
1 TAAAAATTGCACTTAGACCCCTAAACTTTTCCTAATTTCATTTTAACCCTTAAACTTTC
** * * *
53294628 TTTAAATTTCACTTAGACCCCTAAAC-TTTCATTAAATTTCATTTTAACCC-TAAATTTTC
1 TAAAAATTGCACTTAGACCCCTAAACTTTTC-CT-AATTTCATTTTAACCCTTAAACTTTC
53294687 TAAAAATT
1 TAAAAATT
53294695 ACATTTAGCC
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
58 4 0.07
59 36 0.65
60 15 0.27
ACGTcount: A:0.33, C:0.21, G:0.03, T:0.43
Consensus pattern (59 bp):
TAAAAATTGCACTTAGACCCCTAAACTTTTCCTAATTTCATTTTAACCCTTAAACTTTC
Found at i:53295221 original size:23 final size:24
Alignment explanation
Indices: 53295195--53295265 Score: 94
Period size: 23 Copynumber: 3.0 Consensus size: 24
53295185 AGCCCAAAAA
*
53295195 AAAACAAAGCAAA-AAA-AAGCAGC
1 AAAA-AAAGAAAAGAAAGAAGCAGC
53295218 AAAAAAAGAAGAAGAAAGAAGCAG-
1 AAAAAAAGAA-AAGAAAGAAGCAGC
53295242 AAAAAAAGAAAAGAAAGAAGCAGC
1 AAAAAAAGAAAAGAAAGAAGCAGC
53295266 CCACTTTGTG
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
22 5 0.12
23 19 0.44
24 13 0.30
25 6 0.14
ACGTcount: A:0.70, C:0.10, G:0.20, T:0.00
Consensus pattern (24 bp):
AAAAAAAGAAAAGAAAGAAGCAGC
Found at i:53295894 original size:17 final size:17
Alignment explanation
Indices: 53295851--53295898 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
53295841 AGAAAAAAAT
53295851 CGTGTTTCAAAAATTTTCA
1 CGTGTTTC-AAAA-TTTCA
53295870 --TGTCTTCAAAATTTCA
1 CGTGT-TTCAAAATTTCA
53295886 CGTGTTTCAAAAT
1 CGTGTTTCAAAAT
53295899 AATAATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
16 5 0.19
17 15 0.58
18 6 0.23
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (17 bp):
CGTGTTTCAAAATTTCA
Found at i:53296000 original size:16 final size:16
Alignment explanation
Indices: 53295952--53296000 Score: 64
Period size: 16 Copynumber: 3.0 Consensus size: 16
53295942 TTTCTTTCTA
*
53295952 AAAAAATCGTGTTTTC
1 AAAAATTCGTGTTTTC
53295968 AAAAATTTCCGTG-TTTC
1 AAAAA-TT-CGTGTTTTC
53295985 AAAAATTCGTGTTTTC
1 AAAAATTCGTGTTTTC
53296001 GTGTTTTCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
15 4 0.14
16 11 0.38
17 10 0.34
18 4 0.14
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (16 bp):
AAAAATTCGTGTTTTC
Found at i:53296029 original size:19 final size:20
Alignment explanation
Indices: 53295999--53296036 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
53295989 ATTCGTGTTT
53295999 TCGTGTTTTCAAAAAAAATC
1 TCGTGTTTTCAAAAAAAATC
53296019 TCGTG-TTTCAAAAAAAAT
1 TCGTGTTTTCAAAAAAAAT
53296037 AAAAATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (20 bp):
TCGTGTTTTCAAAAAAAATC
Found at i:53296046 original size:15 final size:14
Alignment explanation
Indices: 53296028--53296060 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
53296018 CTCGTGTTTC
53296028 AAAAAAAATAAAAA
1 AAAAAAAATAAAAA
53296042 TAAAAAAAATAAAAA
1 -AAAAAAAATAAAAA
53296057 AAAA
1 AAAA
53296061 TTCTCGTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.91, C:0.00, G:0.00, T:0.09
Consensus pattern (14 bp):
AAAAAAAATAAAAA
Found at i:53296175 original size:17 final size:18
Alignment explanation
Indices: 53296124--53296548 Score: 228
Period size: 18 Copynumber: 25.0 Consensus size: 18
53296114 AAATTTAGTG
53296124 TTTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
53296142 TTTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
*
53296160 -TCT-GTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* * *
53296176 TTCTGGCG-TTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
**
53296193 TTTTCGTGTTTAAAAAAA
1 TTTTCGTGTTTTCAAAAA
* *
53296211 TTTACGTGTTTTCACAAA
1 TTTTCGTGTTTTCAAAAA
*
53296229 TTTTCGTG-TTTCACAAA
1 TTTTCGTGTTTTCAAAAA
*
53296246 TTCTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* * *
53296264 -CTCCAGTG-TTTC-AAAG
1 TTTTC-GTGTTTTCAAAAA
* *
53296280 TTTCCATGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* *
53296298 TTCTCGCG-TTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
**
53296314 AATTCGTG-TTTCAAAATA
1 TTTTCGTGTTTTCAAAA-A
* **
53296332 TTCTCG-CATTTC---AA
1 TTTTCGTGTTTTCAAAAA
**
53296346 TTTT--TGTTTT-TTAAA
1 TTTTCGTGTTTTCAAAAA
53296361 ---TCGTG-TTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
*
53296375 -TGTCGTGTTTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
*
53296391 TTTTCGTG-TTTCTAAAA
1 TTTTCGTGTTTTCAAAAA
* *
53296408 TTTCCCTGTTTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
**
53296425 TTCCCGTG-TTTCAAAAAAA
1 TTTTCGTGTTTTC--AAAAA
* *
53296444 ATGTCGTGTTTT-AAGAAA
1 TTTTCGTGTTTTCAA-AAA
* *
53296462 ATTTCGTTTTTTCTAAAAA
1 TTTTCGTGTTTTC-AAAAA
*
53296481 TTTTCGTG-TTTCTAAAA
1 TTTTCGTGTTTTCAAAAA
*
53296498 TTTTCGTG-TTT-ACAAA
1 TTTTCGTGTTTTCAAAAA
*
53296514 TTCTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* *
53296532 TTCTCGTATTTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
53296549 AAACTTTCGT
Statistics
Matches: 316, Mismatches: 58, Indels: 67
0.72 0.13 0.15
Matches are distributed among these distances:
12 1 0.00
13 6 0.02
14 9 0.03
15 3 0.01
16 56 0.18
17 108 0.34
18 109 0.34
19 19 0.06
20 5 0.02
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.45
Consensus pattern (18 bp):
TTTTCGTGTTTTCAAAAA
Found at i:53296254 original size:35 final size:35
Alignment explanation
Indices: 53296124--53296549 Score: 184
Period size: 34 Copynumber: 12.5 Consensus size: 35
53296114 AAATTTAGTG
*
53296124 TTTTCGTGTTTTCAAAAATTTTCGTGTTTTCAAAA
1 TTTTCGTGTTTTCAAAAATTCTCGTGTTTTCAAAA
* * * *
53296159 ATCT-GTGTTTTCAAAAATTCTGGCG-TTTCAAAAA
1 TTTTCGTGTTTTCAAAAATTCTCGTGTTTTC-AAAA
**
53296193 TTTTCGTGTTTAAAAAAATT-TACGTGTTTTCACAAA
1 TTTTCGTGTTTTCAAAAATTCT-CGTGTTTTCA-AAA
*
53296229 TTTTCGTG-TTTCACAAATTCTCGTGTTTTCAAAA
1 TTTTCGTGTTTTCAAAAATTCTCGTGTTTTCAAAA
** * ** *
53296263 ACTCCAGTG-TTTCAAAGTTTC-CATGTTTTCAAAAA
1 TTTTC-GTGTTTTCAAAAATTCTCGTGTTTTC-AAAA
* * * *
53296298 TTCTCGCG-TTTAAAAAAAT-TCGTG-TTTCAAAA
1 TTTTCGTGTTTTCAAAAATTCTCGTGTTTTCAAAA
** * **
53296330 TATTCTCG-CATTTC---AATT-T-TTGTTTTTTAAA
1 T-TT-TCGTGTTTTCAAAAATTCTCGTGTTTTCAAAA
* *
53296361 ---TCGTG-TTTCAAAAA-TGTCGTGTTTTAAAAA
1 TTTTCGTGTTTTCAAAAATTCTCGTGTTTTCAAAA
* * *
53296391 TTTTCGTG-TTTCTAAAATT-TCCCTGTTTTAAAAA
1 TTTTCGTGTTTTCAAAAATTCT-CGTGTTTTCAAAA
** * * *
53296425 TTCCCGTG-TTTCAAAAAAAATGTCGTGTTTTAAGAAA
1 TTTTCGTGTTTTC--AAAAATTCTCGTGTTTTCA-AAA
* * *
53296462 ATTTCGTTTTTTCTAAAAATTTTCGTG-TTTCTAAAA
1 TTTTCGTGTTTTC-AAAAATTCTCGTGTTTTC-AAAA
*
53296498 TTTTCGTG-TTT-ACAAATTCTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAATTCTCGTGTTTTC-AAAA
* * *
53296532 TTCTCGTATTTTAAAAAA
1 TTTTCGTGTTTTCAAAAA
53296550 AACTTTCGTT
Statistics
Matches: 293, Mismatches: 65, Indels: 65
0.69 0.15 0.15
Matches are distributed among these distances:
26 7 0.02
28 1 0.00
29 3 0.01
30 11 0.04
31 10 0.03
32 5 0.02
33 34 0.12
34 93 0.32
35 59 0.20
36 46 0.16
37 20 0.07
38 4 0.01
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.45
Consensus pattern (35 bp):
TTTTCGTGTTTTCAAAAATTCTCGTGTTTTCAAAA
Found at i:53296263 original size:53 final size:51
Alignment explanation
Indices: 53296124--53296548 Score: 234
Period size: 51 Copynumber: 8.3 Consensus size: 51
53296114 AAATTTAGTG
53296124 TTTTCGTGTTTTCAAAAATTTTCGTGTTTTCAAAAATCTGTGTTTTCAAAAA
1 TTTTCGTG-TTTCAAAAATTTTCGTGTTTTCAAAAATCTGTGTTTTCAAAAA
* * * ** * *
53296176 TTCTGGCGTTTCAAAAATTTTCGTGTTTAAAAAAATTTACGTGTTTTCACAAA
1 TTTTCGTGTTTCAAAAATTTTCGTGTTTTCAAAAATCT--GTGTTTTCAAAAA
* * * *
53296229 TTTTCGTGTTTCACAAATTCTCGTGTTTTCAAAAACTCCAGTG-TTTC-AAAG
1 TTTTCGTGTTTCAAAAATTTTCGTGTTTTCAAAAA-T-CTGTGTTTTCAAAAA
* * * * **
53296280 TTTCCATGTTTTCAAAAATTCTCGCGTTTAAAAAAAT-TCGTG-TTTCAAAATA
1 TTTTCGTG-TTTCAAAAATTTTCGTGTTTTCAAAAATCT-GTGTTTTCAAAA-A
* ** **
53296332 TTCTCGCATTTC---AATTTT--TGTTTT-TTAAATC-GTG-TTTCAAAAA
1 TTTTCGTGTTTCAAAAATTTTCGTGTTTTCAAAAATCTGTGTTTTCAAAAA
* * * **
53296375 -TGTCGTGTTTTAAAAATTTTCGTG-TTTCTAAAATTTCCCTGTTTT-AAAAA
1 TTTTCGTGTTTCAAAAATTTTCGTGTTTTC-AAAA-ATCTGTGTTTTCAAAAA
** * * * * *
53296425 TTCCCGTGTTTCAAAAAAAATGTCGTGTTTTAAGAAAATTTCGTTTTTTCTAAAAA
1 TTTTCGTGTTTC--AAAAATTTTCGTGTTTTCA-AAAATCT-GTGTTTTC-AAAAA
* * *
53296481 TTTTCGTGTTTCTAAAATTTTCGTGTTTAC-AAATTCTCGTGTTTTCAAAAA
1 TTTTCGTGTTTCAAAAATTTTCGTGTTTTCAAAAATCT-GTGTTTTCAAAAA
* * *
53296532 TTCTCGTATTTTAAAAA
1 TTTTCGTGTTTCAAAAA
53296549 AAACTTTCGT
Statistics
Matches: 277, Mismatches: 69, Indels: 55
0.69 0.17 0.14
Matches are distributed among these distances:
42 7 0.03
43 1 0.00
44 11 0.04
45 10 0.04
46 7 0.03
47 2 0.01
48 7 0.03
49 2 0.01
50 14 0.05
51 72 0.26
52 48 0.17
53 56 0.20
54 25 0.09
56 15 0.05
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.45
Consensus pattern (51 bp):
TTTTCGTGTTTCAAAAATTTTCGTGTTTTCAAAAATCTGTGTTTTCAAAAA
Found at i:53308521 original size:123 final size:123
Alignment explanation
Indices: 53308299--53309031 Score: 981
Period size: 123 Copynumber: 5.9 Consensus size: 123
53308289 AGGAAATTCA
** * *
53308299 ACTCATATCACGAGAGGTGAGTTGAGCCTTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGC
1 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAAATCAACTCATATTGC
* * *
53308364 GAGAAGTGAGTTGAGCCTCGGGGCACGCCAAGGTATTTTTAGTTTATGTTTTAAATTG
66 GAGAAGTGAGTTGAGCCTCAGGACACGCCGAGGTATTTTTAGTTTATGTTTTAAATTG
53308422 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAAATCAACTCATATTGC
1 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAAATCAACTCATATTGC
* * * ** *
53308487 TAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTAT-TTTTCAAAAATC
66 GAGAAGTGAGTTGAGCCTCAGGACACGCCGAGGT-ATTT---TTAGT-TTATGTTTT---AAATT
*
53308551 A
123 G
* *
53308552 ACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTTT-ATTTTCAAAAATCAACTCATATTGC
1 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAAATCAACTCATATTGC
* * * ** *
53308616 TAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTAT-TTTTCAAAAATC
66 GAGAAGTGAGTTGAGCCTCAGGACACGCCGAGGT-ATTT---TTAGT-TTATGTTTT---AAATT
*
53308680 A
123 G
* *
53308681 ACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGC
1 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAAATCAACTCATATTGC
*
53308746 GAGAAGTGAGTTGAGCCTC-GGGCACGCCGAGGTATTTTTTAGTTTATGTTTTAAATTG
66 GAGAAGTGAGTTGAGCCTCAGGACACGCCGAGGTA-TTTTTAGTTTATGTTTTAAATTG
53308804 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAAATCAACTCATATTGC
1 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAAATCAACTCATATTGC
* * *
53308869 GAGAAATGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTATGTTTTAAATTG
66 GAGAAGTGAGTTGAGCCTCAGGACACGCCGAGGTATTTTTAGTTTATGTTTTAAATTG
53308927 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC-AAAATCAACTCATATTGC
1 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAAATCAACTCATATTGC
* * **
53308991 GAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTA
66 GAGAAGTGAGTTGAGCCTCAGGACACGCCGAGGTATTTTTA
53309032 AATTTAAAAA
Statistics
Matches: 564, Mismatches: 34, Indels: 25
0.91 0.05 0.04
Matches are distributed among these distances:
122 54 0.10
123 243 0.43
124 19 0.03
125 4 0.01
126 7 0.01
127 7 0.01
128 5 0.01
129 142 0.25
130 83 0.15
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.37
Consensus pattern (123 bp):
ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAAATCAACTCATATTGC
GAGAAGTGAGTTGAGCCTCAGGACACGCCGAGGTATTTTTAGTTTATGTTTTAAATTG
Found at i:53309073 original size:191 final size:192
Alignment explanation
Indices: 53308850--53309201 Score: 661
Period size: 191 Copynumber: 1.8 Consensus size: 192
53308840 TTTGTTTTTC
53308850 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTA
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTA
53308915 TGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC-AAAATC
66 TGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAAATC
*
53308979 AACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTAAAA
131 AACTCATATTGCAAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTAAAA
*
53309041 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTA
1 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTA
53309106 TGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAAATC
66 TGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAAATC
**
53309171 AACTCATATTGCAAGAGGTGAGTTGAGCCTC
131 AACTCATATTGCAAGAAATGAGTTGAGCCTC
53309202 GGCTCACATG
Statistics
Matches: 156, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
191 122 0.78
192 34 0.22
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.34
Consensus pattern (192 bp):
AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTA
TGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAAATC
AACTCATATTGCAAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTAAAA
Found at i:53309241 original size:16 final size:17
Alignment explanation
Indices: 53309220--53309253 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
53309210 TGCTGAGGTA
*
53309220 TTTTCAATTTATG-TTT
1 TTTTCAATCTATGCTTT
53309236 TTTTCAATCTATGCTTT
1 TTTTCAATCTATGCTTT
53309253 T
1 T
53309254 CAAAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.18, C:0.12, G:0.06, T:0.65
Consensus pattern (17 bp):
TTTTCAATCTATGCTTT
Found at i:53309365 original size:85 final size:88
Alignment explanation
Indices: 53309159--53309402 Score: 311
Period size: 91 Copynumber: 2.8 Consensus size: 88
53309149 TAATTTTTGT
53309159 TTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC-GGCTCACATGCTGAGGTATTT
1 TTTTC-AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGC-CACA-GCTGAGGTATTT
* **
53309223 TCAATTTATGTTTTTTTCAATCTATGC
63 TCAATTTATGCTTTACTCAATCTA-GC
* *
53309250 TTTTCAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAAGG-CAC-GCTGAGGTATTTT
1 TTTTC-AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC-AGGCCACAGCTGAGGTATTTT
53309313 CAATTTATGCTTTACT-AATTCTA-C
64 CAATTTATGCTTTACTCAA-TCTAGC
* *
53309337 TTTTC-AAATCAACTCATATTGCAAGAGGTGAGTTGAGTCTCAGGCCACATGCTGAGGTCTTTTC
1 TTTTCAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGCCACA-GCTGAGGTATTTTC
53309401 AA
65 AA
53309403 ATGCTGTTTT
Statistics
Matches: 138, Mismatches: 9, Indels: 16
0.85 0.06 0.10
Matches are distributed among these distances:
84 3 0.02
85 36 0.26
87 21 0.15
88 2 0.01
89 30 0.22
91 44 0.32
93 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (88 bp):
TTTTCAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGCCACAGCTGAGGTATTTTCA
ATTTATGCTTTACTCAATCTAGC
Found at i:53309710 original size:55 final size:54
Alignment explanation
Indices: 53309512--53309729 Score: 273
Period size: 54 Copynumber: 4.1 Consensus size: 54
53309502 TCAATTTCTA
* *
53309512 CTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 CTTTTTAAATTCTG-TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
* * *
53309567 C-TTTTAATTTCTATTTTTCAAAAACCAACTCATATTGCGAGA-GTGAGTTGAGC
1 CTTTTTAAATTCT-GTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
** ***
53309620 CTTTTTCTATT-T-TTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 CTTTTTAAATTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
* *
53309672 CTTTTGTAAATTCTGTTTTCAAAAATCAACTTATATTGCGAGAAGTGAGTTGAGC
1 CTTTT-TAAATTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
53309727 CTT
1 CTT
53309730 GGCTCACGTG
Statistics
Matches: 140, Mismatches: 17, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
51 24 0.17
52 16 0.11
53 17 0.12
54 44 0.31
55 39 0.28
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (54 bp):
CTTTTTAAATTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
Found at i:53310037 original size:29 final size:30
Alignment explanation
Indices: 53309999--53310113 Score: 128
Period size: 30 Copynumber: 3.9 Consensus size: 30
53309989 TTAAAAATAA
* *
53309999 AAATTGCATTTTGACCCCTAAACTTTTC-CT
1 AAATTTCATTTTGACCCCTAAAC-TTTCATT
* *
53310029 -AATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTCATT
* *
53310058 AAATTTCACTTAGACCCCTAAACTTTCATT
1 AAATTTCATTTTGACCCCTAAACTTTCATT
* *
53310088 AAATTTCATTTT-AACCCTAAATTTTC
1 AAATTTCATTTTGACCCCTAAACTTTC
53310114 TAAAAATTAC
Statistics
Matches: 72, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
28 4 0.06
29 33 0.46
30 35 0.49
ACGTcount: A:0.30, C:0.23, G:0.03, T:0.43
Consensus pattern (30 bp):
AAATTTCATTTTGACCCCTAAACTTTCATT
Found at i:53310065 original size:30 final size:30
Alignment explanation
Indices: 53309999--53310114 Score: 130
Period size: 29 Copynumber: 3.9 Consensus size: 30
53309989 TTAAAAATAA
* *
53309999 AAATTGCATTTTGACCCCTAAACTTT-TCCT
1 AAATTTCATTTTGACCCCTAAACTTTCT-TT
*
53310029 -AATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTCTTT
* * *
53310058 AAATTTCACTTAGACCCCTAAACTTTCATT
1 AAATTTCATTTTGACCCCTAAACTTTCTTT
* *
53310088 AAATTTCATTTT-AACCCTAAATTTTCT
1 AAATTTCATTTTGACCCCTAAACTTTCT
53310115 AAAAATTACA
Statistics
Matches: 72, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
29 36 0.50
30 36 0.50
ACGTcount: A:0.29, C:0.23, G:0.03, T:0.44
Consensus pattern (30 bp):
AAATTTCATTTTGACCCCTAAACTTTCTTT
Found at i:53310120 original size:29 final size:29
Alignment explanation
Indices: 53309996--53310127 Score: 90
Period size: 29 Copynumber: 4.5 Consensus size: 29
53309986 AAATTAAAAA
* *
53309996 TAAAAATTGCATTTTGACCCCTAAACTTT-
1 TAAAAATTTCATTTT-AACCCTAAACTTTC
*** *
53310025 TCCTAATTTCATTTTGACCCTTAAACTTTC
1 TAAAAATTTCATTTTAACCC-TAAACTTTC
** *
53310055 TTTAAATTTCA-CTTAGACCCCTAAACTTTC
1 TAAAAATTTCATTTTA-A-CCCTAAACTTTC
* *
53310085 -ATTAAATTTCATTTTAACCCTAAATTTTC
1 TA-AAAATTTCATTTTAACCCTAAACTTTC
*
53310114 TAAAAATTACATTT
1 TAAAAATTTCATTT
53310128 AGCCCCAGAA
Statistics
Matches: 80, Mismatches: 16, Indels: 14
0.73 0.15 0.13
Matches are distributed among these distances:
28 3 0.04
29 42 0.52
30 29 0.36
31 6 0.08
ACGTcount: A:0.33, C:0.21, G:0.03, T:0.43
Consensus pattern (29 bp):
TAAAAATTTCATTTTAACCCTAAACTTTC
Found at i:53310121 original size:59 final size:59
Alignment explanation
Indices: 53309996--53310121 Score: 148
Period size: 59 Copynumber: 2.1 Consensus size: 59
53309986 AAATTAAAAA
* * *
53309996 TAAAAATTGCATTTTGACCCCTAAACTTTTCCTAATTTCATTTTGACCCTTAAACTTTC
1 TAAAAATTGCACTTAGACCCCTAAACTTTTCCTAATTTCATTTTAACCCTTAAACTTTC
** * * *
53310055 TTTAAATTTCACTTAGACCCCTAAAC-TTTCATTAAATTTCATTTTAACCC-TAAATTTTC
1 TAAAAATTGCACTTAGACCCCTAAACTTTTC-CT-AATTTCATTTTAACCCTTAAACTTTC
53310114 TAAAAATT
1 TAAAAATT
53310122 ACATTTAGCC
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
58 4 0.07
59 36 0.65
60 15 0.27
ACGTcount: A:0.33, C:0.21, G:0.03, T:0.43
Consensus pattern (59 bp):
TAAAAATTGCACTTAGACCCCTAAACTTTTCCTAATTTCATTTTAACCCTTAAACTTTC
Found at i:53310666 original size:24 final size:24
Alignment explanation
Indices: 53310639--53310693 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
53310629 AAGCAAAAAA
53310639 AAGCAGCAAAAAAGAAGAAGAAAG
1 AAGCAGCAAAAAAGAAGAAGAAAG
*
53310663 AAGCAGAAAAAAAGAAGAAGAAAG
1 AAGCAGCAAAAAAGAAGAAGAAAG
53310687 AAGCAGC
1 AAGCAGC
53310694 CCACTTTGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.65, C:0.09, G:0.25, T:0.00
Consensus pattern (24 bp):
AAGCAGCAAAAAAGAAGAAGAAAG
Found at i:53311322 original size:17 final size:17
Alignment explanation
Indices: 53311279--53311326 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
53311269 AGAAAAAAAT
53311279 CGTGTTTCAAAAATTTTCA
1 CGTGTTTC-AAAA-TTTCA
53311298 --TGTCTTCAAAATTTCA
1 CGTGT-TTCAAAATTTCA
53311314 CGTGTTTCAAAAT
1 CGTGTTTCAAAAT
53311327 AATAATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
16 5 0.19
17 15 0.58
18 6 0.23
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (17 bp):
CGTGTTTCAAAATTTCA
Found at i:53311428 original size:16 final size:16
Alignment explanation
Indices: 53311375--53311428 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 16
53311365 TTCGTGTTTC
*
53311375 TTTCTAAAAAATCGTGT
1 TTTC-AAAAATTCGTGT
53311392 TTTCAAAAATTTCCGTG-
1 TTTCAAAAA-TT-CGTGT
53311409 TTTCAAAAATTCGTGT
1 TTTCAAAAATTCGTGT
53311425 TTTC
1 TTTC
53311429 GTGTTTTCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
15 4 0.12
16 11 0.33
17 14 0.42
18 4 0.12
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.44
Consensus pattern (16 bp):
TTTCAAAAATTCGTGT
Found at i:53311461 original size:1 final size:1
Alignment explanation
Indices: 53311457--53311495 Score: 51
Period size: 1 Copynumber: 39.0 Consensus size: 1
53311447 CTCGTGTTTC
* * *
53311457 AAAAAAATAAAAAAAAAAAAATAAAAAAATAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
53311496 TTCTCGTGAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (1 bp):
A
Found at i:53311470 original size:8 final size:8
Alignment explanation
Indices: 53311457--53311493 Score: 60
Period size: 8 Copynumber: 4.9 Consensus size: 8
53311447 CTCGTGTTTC
53311457 AAAAAAAT
1 AAAAAAAT
53311465 -AAAAAA-
1 AAAAAAAT
53311471 AAAAAAAT
1 AAAAAAAT
53311479 AAAAAAAT
1 AAAAAAAT
53311487 AAAAAAA
1 AAAAAAA
53311494 AATTCTCGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 12 0.44
8 15 0.56
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (8 bp):
AAAAAAAT
Found at i:53311476 original size:14 final size:14
Alignment explanation
Indices: 53311457--53311492 Score: 63
Period size: 14 Copynumber: 2.5 Consensus size: 14
53311447 CTCGTGTTTC
53311457 AAAAAAATAAAAAA
1 AAAAAAATAAAAAA
53311471 AAAAAAATAAAAAA
1 AAAAAAATAAAAAA
53311485 ATAAAAAA
1 A-AAAAAA
53311493 AAATTCTCGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (14 bp):
AAAAAAATAAAAAA
Found at i:53311604 original size:16 final size:17
Alignment explanation
Indices: 53311563--53311986 Score: 111
Period size: 18 Copynumber: 24.9 Consensus size: 17
53311553 TTTAGTGTTT
*
53311563 TCGTGTTTTCAAAAATTT
1 TCGTGTTTTCAAAAA-TC
53311581 TCGTGTTTTCAAAAATC
1 TCGTGTTTTCAAAAATC
53311598 T-GTGTTTTCAAAAATTC
1 TCGTGTTTTCAAAAA-TC
* * *
53311615 TGGCG-TTTCAAAAATTT
1 TCGTGTTTTCAAAAA-TC
** *
53311632 TCGTGTTTAAAAAAAATT
1 TCGTGTTT-TCAAAAATC
* *
53311650 TACGTGTTTTCACAAATTT
1 T-CGTGTTTTCA-AAAATC
*
53311669 TCGTG-TTTCACAAATTC
1 TCGTGTTTTCA-AAAATC
53311686 TCGTGTTTTCAAAAA-C
1 TCGTGTTTTCAAAAATC
* *
53311702 TCCAGTG-TTTC-AAAGTT
1 T-C-GTGTTTTCAAAAATC
*
53311719 TCCATGTTTTCAAAAATTC
1 T-CGTGTTTTCAAAAA-TC
* **
53311738 TCGCGTTTAAAAAAAAT-
1 TCGTGTTT-TCAAAAATC
53311755 TCGTG-TTTCAAAATATTC
1 TCGTGTTTTCAAAA-A-TC
**
53311773 TCG-CATTTC---AAT-
1 TCGTGTTTTCAAAAATC
** **
53311785 TTTTGTTTT-TTAAA--
1 TCGTGTTTTCAAAAATC
*
53311799 TCGTG-TTTCAAAAATG
1 TCGTGTTTTCAAAAATC
*
53311815 TCGTGTTTT-AAAAATT
1 TCGTGTTTTCAAAAATC
* * *
53311831 TTGTG-TTTCTAAAATT
1 TCGTGTTTTCAAAAATC
*
53311847 TCCCTGTTTT-AAAAATTC
1 T-CGTGTTTTCAAAAA-TC
* *
53311865 CCGTG-TTTCAAAAAAAATG
1 TCGTGTTTTC---AAAAATC
* *
53311884 TCGTGTTTTAAGAAAATT
1 TCGTGTTTTCA-AAAATC
* *
53311902 TCGTTTTTTCTAAAAATTT
1 TCGTGTTTTC-AAAAA-TC
* *
53311921 TCGTG-TTTCTAAAATTT
1 TCGTGTTTTC-AAAAATC
* *
53311938 TCGTGTTTAC-AAATTC
1 TCGTGTTTTCAAAAATC
53311954 TCGTGTTTTCAAAAATTC
1 TCGTGTTTTCAAAAA-TC
* *
53311972 TCGTATTTTTAAAAA
1 TCGTGTTTTCAAAAA
53311987 AAAACTTTCG
Statistics
Matches: 309, Mismatches: 56, Indels: 82
0.69 0.13 0.18
Matches are distributed among these distances:
12 1 0.00
13 7 0.02
14 7 0.02
15 10 0.03
16 62 0.20
17 78 0.25
18 99 0.32
19 37 0.12
20 8 0.03
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.45
Consensus pattern (17 bp):
TCGTGTTTTCAAAAATC
Found at i:53311611 original size:17 final size:18
Alignment explanation
Indices: 53311560--53311986 Score: 212
Period size: 17 Copynumber: 25.0 Consensus size: 18
53311550 AAATTTAGTG
53311560 TTTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
53311578 TTTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
*
53311596 -TCT-GTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* * *
53311612 TTCTGGCG-TTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
**
53311629 TTTTCGTGTTTAAAAAAAA
1 TTTTCGTGTTT-TCAAAAA
* *
53311648 TTTACGTGTTTTCACAAA
1 TTTTCGTGTTTTCAAAAA
*
53311666 TTTTCGTG-TTTCACAAA
1 TTTTCGTGTTTTCAAAAA
*
53311683 TTCTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* * *
53311701 -CTCCAGTG-TTTC-AAAG
1 TTTTC-GTGTTTTCAAAAA
* *
53311717 TTTCCATGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* * *
53311735 TTCTCGCG-TTTAAAAAA
1 TTTTCGTGTTTTCAAAAA
**
53311752 AATTCGTG-TTTCAAAATA
1 TTTTCGTGTTTTCAAAA-A
* **
53311770 TTCTCG-CATTTC---AA
1 TTTTCGTGTTTTCAAAAA
**
53311784 TTTT--TGTTTT-TTAAA
1 TTTTCGTGTTTTCAAAAA
53311799 ---TCGTG-TTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
*
53311813 -TGTCGTGTTTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
*
53311829 TTTT-GTG-TTTCTAAAA
1 TTTTCGTGTTTTCAAAAA
* *
53311845 TTTCCCTGTTTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
**
53311862 TTCCCGTG-TTTCAAAAAAA
1 TTTTCGTGTTTTC--AAAAA
* *
53311881 ATGTCGTGTTTT-AAGAAA
1 TTTTCGTGTTTTCAA-AAA
* *
53311899 ATTTCGTTTTTTCTAAAAA
1 TTTTCGTGTTTTC-AAAAA
*
53311918 TTTTCGTG-TTTCTAAAA
1 TTTTCGTGTTTTCAAAAA
*
53311935 TTTTCGTG-TTT-ACAAA
1 TTTTCGTGTTTTCAAAAA
*
53311951 TTCTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* * *
53311969 TTCTCGTATTTTTAAAAA
1 TTTTCGTGTTTTCAAAAA
53311987 AAAACTTTCG
Statistics
Matches: 314, Mismatches: 61, Indels: 68
0.71 0.14 0.15
Matches are distributed among these distances:
12 1 0.00
13 6 0.02
14 9 0.03
15 6 0.02
16 51 0.16
17 103 0.33
18 99 0.32
19 34 0.11
20 5 0.02
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.45
Consensus pattern (18 bp):
TTTTCGTGTTTTCAAAAA
Found at i:53311734 original size:88 final size:88
Alignment explanation
Indices: 53311564--53311727 Score: 215
Period size: 88 Copynumber: 1.9 Consensus size: 88
53311554 TTAGTGTTTT
* **
53311564 CGTGTTTTCAAAAATTTTCGTGTTTTCAAAAATCTGTGTTTTCAAAAATTCTGGCGTTTCAAAAA
1 CGTGTTTTCAAAAATTTTCGTGTTTTCAAAAATCTGTGTTTTCAAAAACTCCAGCGTTTCAAAAA
* *
53311629 TTTTCGTGTTTAAAAAAAATTTA
66 TTTCCATGTTTAAAAAAAATTTA
* * *
53311652 CGTGTTTTCACAAATTTTCGTG-TTTCACAAATTCTCGTGTTTTCAAAAACTCCAGTGTTTC-AA
1 CGTGTTTTCAAAAATTTTCGTGTTTTCA-AAAATCT-GTGTTTTCAAAAACTCCAGCGTTTCAAA
*
53311715 AGTTTCCATGTTT
64 AATTTCCATGTTT
53311728 TCAAAAATTC
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
87 5 0.08
88 39 0.60
89 21 0.32
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (88 bp):
CGTGTTTTCAAAAATTTTCGTGTTTTCAAAAATCTGTGTTTTCAAAAACTCCAGCGTTTCAAAAA
TTTCCATGTTTAAAAAAAATTTA
Done.