Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 137 of 318
Found at i:42512101 original size:43 final size:43
Alignment explanation
Indices: 42512045--42512208 Score: 197
Period size: 43 Copynumber: 3.8 Consensus size: 43
42512035 AGCTCATACA
* * * *
42512045 ATGCCAA-ATCCCAGATATGGTCTTACATGTTATCAT-ATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCATAATAT-G
* * * *
42512087 ATGCCACTGTCCCAGAGAGGGTCTTACACGAAATCATAATATG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCATAATATG
* * *
42512130 ATGCCAATGTCCTAGACATGGTCTTACACGTAATCTTAATATA
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCATAATATG
*
42512173 ATGCCAATGTCCCAGACATGGTCTTACATGTAATCA
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCA
42512209 CATCTTGGTA
Statistics
Matches: 103, Mismatches: 17, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
42 6 0.06
43 93 0.90
44 4 0.04
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGTAATCATAATATG
Found at i:42512675 original size:16 final size:16
Alignment explanation
Indices: 42512639--42512678 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 16
42512629 TTATCTATTA
42512639 TAACTATAATAACCATT
1 TAACTA-AATAACCATT
42512656 TAACTAAACTAACC-TT
1 TAACTAAA-TAACCATT
42512672 TAACTAA
1 TAACTAA
42512679 CATTAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (16 bp):
TAACTAAATAACCATT
Found at i:42518386 original size:49 final size:49
Alignment explanation
Indices: 42518322--42518544 Score: 227
Period size: 49 Copynumber: 4.5 Consensus size: 49
42518312 TTGGTACGCA
*
42518322 TAGTAGCCTGCACTTAGTACTACAGATGCAACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCAACCAATTATCCGGTACACG
* ** ** * * *
42518371 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATATAC-
1 TAGTAGCCTGCACTTAGTACTACACATGCAACC-AATTATCCGGTACACG
* *** * *
42518420 TAGTAGCCTGCAATTAGTACTACACACGTG-ATTGAAGTTAT-CGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACA--TGCAACCAA-TTATCCGGTACACG
* *
42518470 TAGTAGCCTGCACTTAGTACTACACATGCGACTAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCAACCAATTATCCGGTACACG
*
42518519 TAGTAGCCTACACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
42518545 CGTGACCTCA
Statistics
Matches: 138, Mismatches: 29, Indels: 14
0.76 0.16 0.08
Matches are distributed among these distances:
48 6 0.04
49 94 0.68
50 37 0.27
51 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.26
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACATGCAACCAATTATCCGGTACACG
Found at i:42518492 original size:99 final size:100
Alignment explanation
Indices: 42518357--42518549 Score: 264
Period size: 99 Copynumber: 1.9 Consensus size: 100
42518347 ATGCAACCAA
* * * *
42518357 TTATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATATAC-T
1 TTATCCGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGA-CTAACCATCCGATACACGT
*
42518421 AGTAGCCTGCAATTAGTACTACACACGTGATTGAAG
65 AGTAGCCTACAATTAGTACTACACACGTGATTGAAG
* * ** *
42518457 TTAT-CGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACTAATTATCCGGTACACGTA
1 TTATCCGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACTAACCATCCGATACACGTA
*
42518521 GTAGCCTACACTTAGTACTACACACGTGA
66 GTAGCCTACAATTAGTACTACACACGTGA
42518550 CCTCACAATA
Statistics
Matches: 81, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
98 12 0.15
99 65 0.80
100 4 0.05
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (100 bp):
TTATCCGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACTAACCATCCGATACACGTA
GTAGCCTACAATTAGTACTACACACGTGATTGAAG
Found at i:42520957 original size:19 final size:19
Alignment explanation
Indices: 42520922--42520959 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
42520912 TTACAATTTA
*
42520922 AATTTTTATTTTCTTTTCT
1 AATTTTTATTTTATTTTCT
42520941 AATTTTTCA-TTTATTTTCT
1 AATTTTT-ATTTTATTTTCT
42520960 TCTGACAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 16 0.94
20 1 0.06
ACGTcount: A:0.18, C:0.11, G:0.00, T:0.71
Consensus pattern (19 bp):
AATTTTTATTTTATTTTCT
Found at i:42529601 original size:48 final size:48
Alignment explanation
Indices: 42529527--42529951 Score: 414
Period size: 48 Copynumber: 8.9 Consensus size: 48
42529517 TAAATTGCCA
* * * *
42529527 ATGCCATGTCCCAGACATGGTGTTACACTGGCTCACATGTCGAGGCTG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCGAGGCCG
* * * * * *
42529575 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGTCTCAATGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCGAGGCCG
* * * *
42529623 ATTCCATGTCCCAGACATAGTCTTACGCTAGCT-ATCATAAT-GAGGCTG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCA-CAT-ATCGAGGCCG
* * * * * * *
42529671 ATGTCATGTCCCAGACATGGTCTTATACTAACACACATATCAATGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCGAGGCCG
* *
42529719 ATGCCATGTCCCAGACATGGTCTTACACT-GACTCTCATAAT-GTGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAG-CTCACAT-ATCGAGGCCG
* * *
42529767 ATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAATGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCGAGGCCG
* * * *
42529815 ATGCCATGTCCCAGACATGGTCTTACATTAGCACACATATCTACGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCGAGGCCG
* * * *
42529863 ATGCCATGTCCCATACATGGTCTTACACT-GAATCTCATAAT-GTGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAG-CTCACAT-ATCGAGGCCG
* *
42529911 ATGCCATGTCCCA-AGCATGGTCTTACACTAGCACACCTATC
1 ATGCCATGTCCCAGA-CATGGTCTTACACTAGCTCACATATC
42529952 ACCCAAATGG
Statistics
Matches: 305, Mismatches: 59, Indels: 26
0.78 0.15 0.07
Matches are distributed among these distances:
47 8 0.03
48 289 0.95
49 8 0.03
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.27
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCGAGGCCG
Found at i:42529791 original size:144 final size:144
Alignment explanation
Indices: 42529527--42529952 Score: 506
Period size: 144 Copynumber: 3.0 Consensus size: 144
42529517 TAAATTGCCA
* ** * * * * *
42529527 ATGCCATGTCCCAGACATGGTGTTACACTGGCTCACATGTCGAGGCTGATGCCATGTCCCAGACA
1 ATGCCATGTCCCAGACATGGTCTTACACTAACACACATATCAACGCCGATGCCATGTCCCAGACA
* * * *
42529592 TGGTCTTACACT-AGCTCTCGTCTCAATGT---CGATTCCATGTCCCAGACATAGTCTTACGCTA
66 TGGTCTTACACTGA-CTCTC--AT-AATGTGGCCGATGCCATGTCCCAGACATGGTCTTACACTA
* * *
42529653 GCTA-TCATAAT-GAGGCTG
127 GC-ACACAT-ATCAAGGCCG
* * * *
42529671 ATGTCATGTCCCAGACATGGTCTTATACTAACACACATATCAATGTCGATGCCATGTCCCAGACA
1 ATGCCATGTCCCAGACATGGTCTTACACTAACACACATATCAACGCCGATGCCATGTCCCAGACA
42529736 TGGTCTTACACTGACTCTCATAATGTGGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCAC
66 TGGTCTTACACTGACTCTCATAATGTGGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCAC
*
42529801 ACATATCAATGCCG
131 ACATATCAAGGCCG
* * * *
42529815 ATGCCATGTCCCAGACATGGTCTTACATTAGCACACATATCTACGCCGATGCCATGTCCCATACA
1 ATGCCATGTCCCAGACATGGTCTTACACTAACACACATATCAACGCCGATGCCATGTCCCAGACA
*
42529880 TGGTCTTACACTGAATCTCATAATGTGGCCGATGCCATGTCCCA-AGCATGGTCTTACACTAGCA
66 TGGTCTTACACTGACTCTCATAATGTGGCCGATGCCATGTCCCAGA-CATGGTCTTACACTAGCA
*
42529944 CACCTATCA
130 CACATATCA
42529953 CCCAAATGGC
Statistics
Matches: 246, Mismatches: 29, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
141 5 0.02
142 1 0.00
143 4 0.02
144 235 0.96
145 1 0.00
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.27
Consensus pattern (144 bp):
ATGCCATGTCCCAGACATGGTCTTACACTAACACACATATCAACGCCGATGCCATGTCCCAGACA
TGGTCTTACACTGACTCTCATAATGTGGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCAC
ACATATCAAGGCCG
Found at i:42534698 original size:21 final size:20
Alignment explanation
Indices: 42534664--42534706 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
42534654 TAATTAATAT
*
42534664 ATTCAATAAGTATATATATCA
1 ATTCAATAAGTATAAAT-TCA
42534685 ATTCAATTAA-TATAAATTCA
1 ATTCAA-TAAGTATAAATTCA
42534705 AT
1 AT
42534707 AAATTCATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
21 12 0.60
22 3 0.15
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (20 bp):
ATTCAATAAGTATAAATTCA
Found at i:42535423 original size:22 final size:21
Alignment explanation
Indices: 42535389--42535431 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
42535379 AAAGCCCTAA
42535389 CTTTTTCTCCTTT-TTCTTTCT
1 CTTTTTCTCCTTTCTT-TTTCT
*
42535410 CTTTTTCCTTCTTTCTTTTTCT
1 CTTTTT-CTCCTTTCTTTTTCT
42535432 TAAGTTTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 6 0.32
22 11 0.58
23 2 0.11
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (21 bp):
CTTTTTCTCCTTTCTTTTTCT
Found at i:42535424 original size:20 final size:20
Alignment explanation
Indices: 42535391--42535432 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
42535381 AGCCCTAACT
42535391 TTTTCTCCTTTTTCTTTCTC
1 TTTTCTCCTTTTTCTTTCTC
*
42535411 TTTT-TCCTTCTTTCTTTTTC
1 TTTTCTCCTT-TTTCTTTCTC
42535431 TT
1 TT
42535433 AAGTTTTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTCTCCTTTTTCTTTCTC
Found at i:42535532 original size:15 final size:14
Alignment explanation
Indices: 42535499--42535543 Score: 58
Period size: 15 Copynumber: 3.3 Consensus size: 14
42535489 CTTATTCTTT
*
42535499 TATAAT-TATTATA
1 TATAATATAATATA
42535512 -ATAATATAATATGA
1 TATAATATAATAT-A
42535526 TATAATATAATATA
1 TATAATATAATATA
42535540 TATA
1 TATA
42535544 CTTAAGTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 5 0.18
13 5 0.18
14 6 0.21
15 12 0.43
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (14 bp):
TATAATATAATATA
Found at i:42535589 original size:20 final size:19
Alignment explanation
Indices: 42535564--42535611 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
42535554 AAGTATTACA
*
42535564 TATATTATTATATACATATG
1 TATATTATT-TATACACATG
*
42535584 TATATTATTTTTACACATG
1 TATATTATTTATACACATG
42535603 TA-ATTATTT
1 TATATTATTT
42535612 TTACCATACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 7 0.27
19 10 0.38
20 9 0.35
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.54
Consensus pattern (19 bp):
TATATTATTTATACACATG
Found at i:42535610 original size:18 final size:19
Alignment explanation
Indices: 42535564--42535615 Score: 70
Period size: 18 Copynumber: 2.7 Consensus size: 19
42535554 AAGTATTACA
* *
42535564 TATATTATTATATACATATG
1 TATATTATT-TTTACACATG
42535584 TATATTATTTTTACACATG
1 TATATTATTTTTACACATG
42535603 TA-ATTATTTTTAC
1 TATATTATTTTTAC
42535616 CATACACATG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 11 0.37
19 10 0.33
20 9 0.30
ACGTcount: A:0.35, C:0.08, G:0.04, T:0.54
Consensus pattern (19 bp):
TATATTATTTTTACACATG
Found at i:42536044 original size:30 final size:30
Alignment explanation
Indices: 42536009--42536070 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
42535999 ACTTTTTTTA
* * *
42536009 TTGTTATTTTTGTTATTATTTTAAAGATAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
*
42536039 TTGTTAATTTTATTATTATTTTAGAGACAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
42536069 TT
1 TT
42536071 ACTTGTTAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.27, C:0.02, G:0.10, T:0.61
Consensus pattern (30 bp):
TTGTTAATTTTATTATTATTTTAAAGACAT
Found at i:42536171 original size:18 final size:18
Alignment explanation
Indices: 42536150--42536189 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
42536140 GAAATATTTA
*
42536150 TTTTGATGT-TTTTAGTAT
1 TTTTGATGTATTAT-GTAT
42536168 TTTTGATGTATTATGTAT
1 TTTTGATGTATTATGTAT
42536186 TTTT
1 TTTT
42536190 TTAAAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.17, C:0.00, G:0.15, T:0.68
Consensus pattern (18 bp):
TTTTGATGTATTATGTAT
Found at i:42536213 original size:12 final size:12
Alignment explanation
Indices: 42536192--42536225 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
42536182 GTATTTTTTT
*
42536192 AAAATTATATAA
1 AAAATAATATAA
42536204 AAAATAATATAA
1 AAAATAATATAA
*
42536216 AAATTAATAT
1 AAAATAATAT
42536226 GGGCGGGCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:42536790 original size:21 final size:22
Alignment explanation
Indices: 42536755--42536797 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
42536745 AATTGCTAAT
*
42536755 ACACAACAACCAACACTGTAGAC
1 ACACAACAA-CAACACCGTAGAC
42536778 ACACAACAA-AACACCGTAGA
1 ACACAACAACAACACCGTAGA
42536798 TGGAATCTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 10 0.53
23 9 0.47
ACGTcount: A:0.51, C:0.33, G:0.09, T:0.07
Consensus pattern (22 bp):
ACACAACAACAACACCGTAGAC
Found at i:42541364 original size:13 final size:13
Alignment explanation
Indices: 42541329--42541370 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
42541319 AGTATGTATG
42541329 TATATGATTAG-T
1 TATATGATTAGAT
42541341 T-TATGATTAGAT
1 TATATGATTAGAT
*
42541353 TATATTATTAGAT
1 TATATGATTAGAT
*
42541366 GATAT
1 TATAT
42541371 TAAGTTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
11 9 0.35
12 3 0.12
13 14 0.54
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (13 bp):
TATATGATTAGAT
Found at i:42549536 original size:13 final size:13
Alignment explanation
Indices: 42549501--42549542 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
42549491 AGTATGTATG
42549501 TATATGATTAG-T
1 TATATGATTAGAT
42549513 T-TATGATTAGAT
1 TATATGATTAGAT
*
42549525 TATATTATTAGAT
1 TATATGATTAGAT
*
42549538 GATAT
1 TATAT
42549543 TAAGTTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
11 9 0.35
12 3 0.12
13 14 0.54
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (13 bp):
TATATGATTAGAT
Found at i:42553935 original size:12 final size:12
Alignment explanation
Indices: 42553918--42553959 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
42553908 AGACACACGC
42553918 CCCGTGTGTGAG
1 CCCGTGTGTGAG
42553930 CCCGTGTGTG-G
1 CCCGTGTGTGAG
*
42553941 -GCGTGTGTGAG
1 CCCGTGTGTGAG
42553952 CCCGTGTG
1 CCCGTGTG
42553960 ACACACACGG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
10 8 0.31
11 2 0.08
12 16 0.62
ACGTcount: A:0.05, C:0.24, G:0.45, T:0.26
Consensus pattern (12 bp):
CCCGTGTGTGAG
Found at i:42555044 original size:45 final size:45
Alignment explanation
Indices: 42554992--42555121 Score: 136
Period size: 45 Copynumber: 2.8 Consensus size: 45
42554982 CCTGAGCTGA
* * * * *
42554992 TGAACAGTTAGCTCTAACGAGCTGAAATGGTAAGCTTTTTTCAGT
1 TGAACAGTAAGCTCTAACGAGCTGAAATGGTAAGCTCTATTAAGC
* *
42555037 TGAACAGTAAGCTC-ATACGAGTTGAAACGGTAAGCTCTATTAAGC
1 TGAACAGTAAGCTCTA-ACGAGCTGAAATGGTAAGCTCTATTAAGC
**
42555082 TGAACAGTAAGCTCTTTCGAGCTGATATATCGGTAAGCTC
1 TGAACAGTAAGCTCTAACGAGCTGA-A-AT-GGTAAGCTC
42555122 ATACGAGCTG
Statistics
Matches: 69, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
44 1 0.01
45 57 0.83
46 1 0.01
47 1 0.01
48 9 0.13
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (45 bp):
TGAACAGTAAGCTCTAACGAGCTGAAATGGTAAGCTCTATTAAGC
Found at i:42555104 original size:22 final size:22
Alignment explanation
Indices: 42554992--42555106 Score: 74
Period size: 22 Copynumber: 5.1 Consensus size: 22
42554982 CCTGAGCTGA
* **
42554992 TGAACAGTTAGCTCTAACGAGC
1 TGAACAGTAAGCTCTTTCGAGC
* *
42555014 TGAA-ATGGTAAGCTTTTTTC-AGT
1 TGAACA--GTAAGC-TCTTTCGAGC
* * *
42555037 TGAACAGTAAGCTCATACGAGT
1 TGAACAGTAAGCTCTTTCGAGC
* *
42555059 TGAAACGGTAAGCTCTATT-AAGC
1 TG-AACAGTAAGCTCT-TTCGAGC
42555082 TGAACAGTAAGCTCTTTCGAGC
1 TGAACAGTAAGCTCTTTCGAGC
42555104 TGA
1 TGA
42555107 TATATCGGTA
Statistics
Matches: 70, Mismatches: 15, Indels: 16
0.69 0.15 0.16
Matches are distributed among these distances:
21 6 0.09
22 33 0.47
23 26 0.37
24 5 0.07
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (22 bp):
TGAACAGTAAGCTCTTTCGAGC
Found at i:42561210 original size:36 final size:36
Alignment explanation
Indices: 42561163--42561232 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
42561153 TTAGAGTAAT
*
42561163 TCTAAATCCTCCAGAATCCTTTCCATCGACTCCAAG
1 TCTAAATCCTCCAAAATCCTTTCCATCGACTCCAAG
42561199 TCTAAATCCTCCAAAATCCTTTCCATCGACTCCA
1 TCTAAATCCTCCAAAATCCTTTCCATCGACTCCA
42561233 TCCAATATTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.29, C:0.37, G:0.06, T:0.29
Consensus pattern (36 bp):
TCTAAATCCTCCAAAATCCTTTCCATCGACTCCAAG
Found at i:42562805 original size:22 final size:22
Alignment explanation
Indices: 42562780--42562824 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
42562770 ACATATTAGA
*
42562780 TTGTAGTTTAACCACCAATGGT
1 TTGTAGATTAACCACCAATGGT
**
42562802 TTGTAGATTAACTGCCAATGGT
1 TTGTAGATTAACCACCAATGGT
42562824 T
1 T
42562825 GTGGACAGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.38
Consensus pattern (22 bp):
TTGTAGATTAACCACCAATGGT
Found at i:42564028 original size:14 final size:13
Alignment explanation
Indices: 42564002--42564029 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
42563992 CTTGGCAAGG
42564002 ATCATTTTTAAAA
1 ATCATTTTTAAAA
42564015 ATCATTTTTAAAA
1 ATCATTTTTAAAA
42564028 AT
1 AT
42564030 TCCAACCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (13 bp):
ATCATTTTTAAAA
Found at i:42564167 original size:19 final size:19
Alignment explanation
Indices: 42564145--42564217 Score: 53
Period size: 19 Copynumber: 3.8 Consensus size: 19
42564135 ATGAAAAAAT
42564145 AATTTCCAAATAAAAATTA
1 AATTTCCAAATAAAAATTA
* * *
42564164 AA-TTACAAGAAAATAAATAA
1 AATTTCCAA-ATAA-AAATTA
* *
42564184 AATTT-CACATACCAAATTA
1 AATTTCCAAATA-AAAATTA
42564203 AATTTCC-AATAAAAA
1 AATTTCCAAATAAAAA
42564218 AACTATTTTC
Statistics
Matches: 40, Mismatches: 9, Indels: 11
0.67 0.15 0.18
Matches are distributed among these distances:
18 8 0.20
19 20 0.50
20 10 0.25
21 2 0.05
ACGTcount: A:0.59, C:0.12, G:0.01, T:0.27
Consensus pattern (19 bp):
AATTTCCAAATAAAAATTA
Found at i:42572614 original size:35 final size:35
Alignment explanation
Indices: 42572568--42572637 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
42572558 CTCCTCCTTT
**
42572568 AATGAGTCTAGTTGGACTAAAATTCATGTCCTATG
1 AATGAGTCTAGTTAAACTAAAATTCATGTCCTATG
42572603 AATGAGTCTAGTTAAACTAAAATTCATGTCCTATG
1 AATGAGTCTAGTTAAACTAAAATTCATGTCCTATG
42572638 TTAAACTAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (35 bp):
AATGAGTCTAGTTAAACTAAAATTCATGTCCTATG
Found at i:42576838 original size:6 final size:6
Alignment explanation
Indices: 42576820--42576860 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
42576810 TCATTACTGC
*
42576820 AGATGT AGCTGT AGATGT AGATGT AGATGT AGATGT AGATG
1 AGATGT AGATGT AGATGT AGATGT AGATGT AGATGT AGATG
42576861 AATGTGATGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.32, C:0.02, G:0.34, T:0.32
Consensus pattern (6 bp):
AGATGT
Found at i:42581457 original size:26 final size:26
Alignment explanation
Indices: 42581427--42581516 Score: 90
Period size: 26 Copynumber: 3.5 Consensus size: 26
42581417 TATTTTTTAG
* *
42581427 TCAATTCAACTGGTCCATATCGGTTC
1 TCAATCCAACTGATCCATATCGGTTC
** *
42581453 TCAATCCAACCAATCCATATCGGCTC
1 TCAATCCAACTGATCCATATCGGTTC
* * **
42581479 TCAGTCCAATTGATCCATATATGTTC
1 TCAATCCAACTGATCCATATCGGTTC
*
42581505 TCAACCCAACTG
1 TCAATCCAACTG
42581517 GTCAATAACG
Statistics
Matches: 49, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
26 49 1.00
ACGTcount: A:0.28, C:0.31, G:0.11, T:0.30
Consensus pattern (26 bp):
TCAATCCAACTGATCCATATCGGTTC
Found at i:42587244 original size:25 final size:25
Alignment explanation
Indices: 42587190--42587237 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
42587180 AAGCTCCTCT
* *
42587190 AAGCTGAATAATGGAAAGCTCATGA
1 AAGCTAAATAACGGAAAGCTCATGA
* *
42587215 GAGCTAAATAACGGGAAGCTCAT
1 AAGCTAAATAACGGAAAGCTCAT
42587238 ACAAGCTGTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.42, C:0.15, G:0.25, T:0.19
Consensus pattern (25 bp):
AAGCTAAATAACGGAAAGCTCATGA
Found at i:42590833 original size:26 final size:26
Alignment explanation
Indices: 42590797--42590904 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
42590787 TGAAATGCCC
* *
42590797 ATCATGGAACATTTACCTAAACAATT
1 ATCATGGAACATTTACCTAACCCATT
42590823 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
42590849 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
42590875 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
42590901 ATCA
1 ATCA
42590905 ATTTGTACCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.37, C:0.23, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:42592882 original size:19 final size:20
Alignment explanation
Indices: 42592858--42592896 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
42592848 TATAATTAAA
42592858 AAAAATT-CTTCAATT-TTTT
1 AAAAATTACTT-AATTATTTT
42592877 AAAAATTACTTAATTATTTT
1 AAAAATTACTTAATTATTTT
42592897 TAATTTTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (20 bp):
AAAAATTACTTAATTATTTT
Found at i:42593025 original size:7 final size:7
Alignment explanation
Indices: 42593013--42593037 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
42593003 TAAATATTTA
42593013 AAATTAT
1 AAATTAT
42593020 AAATTAT
1 AAATTAT
42593027 AAATTAT
1 AAATTAT
42593034 AAAT
1 AAAT
42593038 ATCTTTTCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
AAATTAT
Found at i:42595060 original size:12 final size:12
Alignment explanation
Indices: 42595043--42595067 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42595033 TTGTGTGTTC
42595043 TTTATTTTATTT
1 TTTATTTTATTT
42595055 TTTATTTTATTT
1 TTTATTTTATTT
42595067 T
1 T
42595068 ATTTTCACAA
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTATTTTATTT
Found at i:42605004 original size:35 final size:35
Alignment explanation
Indices: 42604962--42605057 Score: 97
Period size: 34 Copynumber: 2.8 Consensus size: 35
42604952 GAGAAACCAA
42604962 AGAAGAGCATTTGAAAGAAAAGCTTTTTGAAAAAAC
1 AGAAGAGCATTTGAAAGAAAAGCTTTTTG-AAAAAC
* * * *
42604998 AG-AGAGCGTTTAAAAGAGAAGC-TTTTGAGAAAC
1 AGAAGAGCATTTGAAAGAAAAGCTTTTTGAAAAAC
* * * *
42605031 CGAAGAGTATCTGAAAGACAAGCTTTT
1 AGAAGAGCATTTGAAAGAAAAGCTTTT
42605058 GAGAGAAGTA
Statistics
Matches: 48, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
33 6 0.12
34 20 0.42
35 20 0.42
36 2 0.04
ACGTcount: A:0.44, C:0.10, G:0.23, T:0.23
Consensus pattern (35 bp):
AGAAGAGCATTTGAAAGAAAAGCTTTTTGAAAAAC
Found at i:42605025 original size:72 final size:69
Alignment explanation
Indices: 42604915--42605057 Score: 164
Period size: 72 Copynumber: 2.0 Consensus size: 69
42604905 GAAAGAAACG
* *
42604915 TTTGAAAAATCAAAGAACGTTAGAAAAAGAAGTATTTGAGAAACCAAAGAAGAGCATTTGAAAGA
1 TTTGAAAAAACAAAGAACGTTAGAAAAAGAAGTATTTGAGAAACC---GAAGAGCATCTGAAAGA
42604980 AAAGCTT
63 AAAGCTT
* * * * *
42604987 TTTGAAAAAACAGAGAGCGTTTA-AAAGAGAAGCT-TTTGAGAAACCGAAGAGTATCTGAAAGAC
1 TTTGAAAAAACAAAGAACG-TTAGAAAAAGAAG-TATTTGAGAAACCGAAGAGCATCTGAAAGAA
42605050 AAGCTT
64 AAGCTT
42605056 TT
1 TT
42605058 GAGAGAAGTA
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
69 23 0.37
72 35 0.56
73 4 0.06
ACGTcount: A:0.47, C:0.10, G:0.21, T:0.22
Consensus pattern (69 bp):
TTTGAAAAAACAAAGAACGTTAGAAAAAGAAGTATTTGAGAAACCGAAGAGCATCTGAAAGAAAA
GCTT
Found at i:42607703 original size:9 final size:9
Alignment explanation
Indices: 42607689--42607722 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
42607679 AAATTCGAAT
*
42607689 TTGAATAAC
1 TTGAATAAA
*
42607698 TTGAATAAT
1 TTGAATAAA
42607707 TTGAATAAA
1 TTGAATAAA
42607716 TTGAATA
1 TTGAATA
42607723 TTAAACTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.47, C:0.03, G:0.12, T:0.38
Consensus pattern (9 bp):
TTGAATAAA
Found at i:42607709 original size:18 final size:18
Alignment explanation
Indices: 42607686--42607722 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
42607676 TTCAAATTCG
*
42607686 AATTTGAATAACTTGAAT
1 AATTTGAATAAATTGAAT
42607704 AATTTGAATAAATTGAAT
1 AATTTGAATAAATTGAAT
42607722 A
1 A
42607723 TTAAACTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.11, T:0.38
Consensus pattern (18 bp):
AATTTGAATAAATTGAAT
Found at i:42608650 original size:96 final size:96
Alignment explanation
Indices: 42608484--42608677 Score: 298
Period size: 96 Copynumber: 2.0 Consensus size: 96
42608474 TCGCTTCTTT
* *
42608484 TTGCTCCTCTTTGCCCTCTTGGCTTCGACTTTACCCTTGCTCGAACCAAGCTTCTTGGGCTCCTT
1 TTGCTCCTCTTTGCCCTCTTGGCTTCGACTTTACCCTTGCTCGAACCAAGCTTCCTGGGCTCCGT
* * * * *
42608549 GTCTGCTTCATCGTTCCCTTCGATGACAGAC
66 ATCTGCTTCATCATTCCCATCGATAACAAAC
* *
42608580 TTGCTCCTCTTTGCCCTCTTGGCTTCGGCTTTTCCCTTGCTCGAACCAAGCTTCCTGGGCTCCGT
1 TTGCTCCTCTTTGCCCTCTTGGCTTCGACTTTACCCTTGCTCGAACCAAGCTTCCTGGGCTCCGT
*
42608645 ATCTGCTTGATCATTCCCATCGATAACAAAC
66 ATCTGCTTCATCATTCCCATCGATAACAAAC
42608676 TT
1 TT
42608678 CCTCGGACAC
Statistics
Matches: 88, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
96 88 1.00
ACGTcount: A:0.13, C:0.34, G:0.17, T:0.36
Consensus pattern (96 bp):
TTGCTCCTCTTTGCCCTCTTGGCTTCGACTTTACCCTTGCTCGAACCAAGCTTCCTGGGCTCCGT
ATCTGCTTCATCATTCCCATCGATAACAAAC
Found at i:42616575 original size:62 final size:60
Alignment explanation
Indices: 42616472--42616604 Score: 185
Period size: 62 Copynumber: 2.2 Consensus size: 60
42616462 AGCCGTATGA
* ** * *
42616472 GGTACACGGGCTAGCACACGGGCATGTGACCAGGCTGTGTGACTCATTGATTTGATAAATAG
1 GGTACACGGGTTAGCACACGGGCATGTGACCAGGCCATGTGACAC-TAG-TTTGATAAATAG
*
42616534 GGTACAAGGGTTAGCACACGGGCATGTGACCAGGCCATGTGACACTAGTTTGATAAATAG
1 GGTACACGGGTTAGCACACGGGCATGTGACCAGGCCATGTGACACTAGTTTGATAAATAG
*
42616594 GGCACACGGGT
1 GGTACACGGGT
42616605 GACCACACAG
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
60 21 0.33
61 2 0.03
62 40 0.63
ACGTcount: A:0.27, C:0.20, G:0.32, T:0.22
Consensus pattern (60 bp):
GGTACACGGGTTAGCACACGGGCATGTGACCAGGCCATGTGACACTAGTTTGATAAATAG
Found at i:42630855 original size:5 final size:5
Alignment explanation
Indices: 42630847--42630871 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
42630837 CAGAAAAGAG
42630847 CCGAA CCGAA CCGAA CCGAA CCGAA
1 CCGAA CCGAA CCGAA CCGAA CCGAA
42630872 TTTTATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.40, G:0.20, T:0.00
Consensus pattern (5 bp):
CCGAA
Found at i:42633158 original size:36 final size:36
Alignment explanation
Indices: 42633118--42633188 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 36
42633108 AGAGGTGAAA
* *
42633118 TATGATGCCTTAGAGGTAAGTATGAAAGAATAATGT
1 TATGATGCCTTAGAGGCAAGTATGAAAGAACAATGT
* * *
42633154 TATGATGCCTTGGAGGCGAGTATGGAAGAACAATG
1 TATGATGCCTTAGAGGCAAGTATGAAAGAACAATG
42633189 CTAATAGCTC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.35, C:0.08, G:0.30, T:0.27
Consensus pattern (36 bp):
TATGATGCCTTAGAGGCAAGTATGAAAGAACAATGT
Found at i:42633521 original size:60 final size:59
Alignment explanation
Indices: 42633417--42633554 Score: 136
Period size: 60 Copynumber: 2.3 Consensus size: 59
42633407 ACTCTACAAT
* * ** * * *
42633417 AGTAGATATATAATGAACTCTCCAATAATGTAGTTTACTTAAATGGGTGAACTCTGA-AAG
1 AGTAGATATATAATGAACTCTCCAATAAAG-AGTTCACGCAAATGAGTGAACAC-CATAAG
* *
42633477 TGTAGATATATAATGAACTCTCCGATGAAA-AGGTTCACGCAAATGAGTGAACACCATAAG
1 AGTAGATATATAATGAACTCTCCAAT-AAAGA-GTTCACGCAAATGAGTGAACACCATAAG
*
42633537 AGTAGACATATAATGAAC
1 AGTAGATATATAATGAAC
42633555 GGTTCGCCTG
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
59 2 0.03
60 60 0.94
61 2 0.03
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.27
Consensus pattern (59 bp):
AGTAGATATATAATGAACTCTCCAATAAAGAGTTCACGCAAATGAGTGAACACCATAAG
Found at i:42650786 original size:39 final size:39
Alignment explanation
Indices: 42650689--42650911 Score: 233
Period size: 39 Copynumber: 5.6 Consensus size: 39
42650679 TTGAATGATG
*
42650689 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGA-T-ACTAAT
* *
42650727 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
*
42650768 TCCGGGCTAAGCCTGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
* *
42650807 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
* *
42650846 TCCGGGTTAAGTCCCGAAGGCATTTGTGTGA-ATTACT-AT
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
42650885 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAG-CCCGAAGGCATTTG
42650912 AACGAGGAGC
Statistics
Matches: 160, Mismatches: 17, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
39 91 0.57
40 57 0.36
41 11 0.07
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:42650833 original size:78 final size:80
Alignment explanation
Indices: 42650689--42650911 Score: 253
Period size: 79 Copynumber: 2.8 Consensus size: 80
42650679 TTGAATGATG
* * * * *
42650689 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGACAATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAA-TTACTATAACCGGGCTAAG-TCCCGAAGGCAT
*
42650751 TTGTGCGAGATACTAAT
64 TTGTGCGAGATACTAAA
* *
42650768 TCCGGGCTAAG-CCTGAAGGCATTTGTGCGAGA-TACTA-ATTCCGGGCTAAG-CCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGA-ATTACTATA-ACCGGGCTAAGTCCCGAAGGCAT
*
42650829 TTGTGCGAGTTACTAAA
64 TTGTGCGAGATACTAAA
* * *
42650846 TCCGGGTTAAGTCCCGAAGGCATTTGTGTGAATTACTATAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAATTACTATAACCGGGCTAAGTCCCGAAGGCATTT
42650911 G
66 G
42650912 AACGAGGAGC
Statistics
Matches: 123, Mismatches: 12, Indels: 17
0.81 0.08 0.11
Matches are distributed among these distances:
78 45 0.37
79 55 0.45
80 22 0.18
81 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAATTACTATAACCGGGCTAAGTCCCGAAGGCATTT
GTGCGAGATACTAAA
Found at i:42650933 original size:79 final size:79
Alignment explanation
Indices: 42650741--42650944 Score: 186
Period size: 79 Copynumber: 2.6 Consensus size: 79
42650731 GGACTAAGAT
** * * * *
42650741 CCGAAGGCATTTGTGCGAGAT-ACTAATTCCGGGCT-AAGCCTGAAGGCATTTGTGCGAGATACT
1 CCGAAGGCATTTGAACGAG-TGACTAAATCCGGGTTAAATCCCGAAGGCATTTGTGCGAGATACT
*
42650804 AATTCCGGGCTAAGC
65 AATACCGGGCTAAGC
** * * *
42650819 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGTGA-ATTACT
1 CCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATCCCGAAGGCATTTGTGCGAGA-TACT
*
42650883 -ATAACCGGGCTATGTC
65 AAT-ACCGGGCTAAG-C
* *
42650899 CCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGAAGGCATTTGAACGAGTGA-CTAAATCCGGGTTAAATCCCGAAGG
42650945 TACGTGATTT
Statistics
Matches: 106, Mismatches: 14, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
77 1 0.01
78 34 0.32
79 46 0.43
80 25 0.24
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATCCCGAAGGCATTTGTGCGAGATACTA
ATACCGGGCTAAGC
Found at i:42658741 original size:39 final size:40
Alignment explanation
Indices: 42658646--42658868 Score: 239
Period size: 39 Copynumber: 5.7 Consensus size: 40
42658636 TTGAATGATG
*
42658646 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
* *
42658684 ATCAGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
*
42658725 TCCGGGCTAAG-CCCGAAGGTATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
42658764 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
42658803 TCCGGGTTAAGTCCCGAAGGCATTTGTGTGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
42658842 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
42658869 AACGAGGAGC
Statistics
Matches: 159, Mismatches: 16, Indels: 17
0.83 0.08 0.09
Matches are distributed among these distances:
39 90 0.57
40 57 0.36
41 11 0.07
42 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:42658783 original size:78 final size:80
Alignment explanation
Indices: 42658646--42658868 Score: 244
Period size: 79 Copynumber: 2.8 Consensus size: 80
42658636 TTGAATGATG
* * * * * *
42658646 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGACAATATCAGGACTAAGAT-CCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAA-TTACTATAACCGGGCTAAG-TCCCGAAGGCAT
*
42658708 TTGTGCGAGATACTAAT
64 TTGTGCGAGATACTAAA
* *
42658725 TCCGGGCTAAG-CCCGAAGGTATTTGTGCGAGA-TACTA-ATTCCGGGCTAAG-CCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGA-ATTACTATA-ACCGGGCTAAGTCCCGAAGGCAT
*
42658786 TTGTGCGAGTTACTAAA
64 TTGTGCGAGATACTAAA
* * *
42658803 TCCGGGTTAAGTCCCGAAGGCATTTGTGTGAATTACTATAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAATTACTATAACCGGGCTAAGTCCCGAAGGCATTT
42658868 G
66 G
42658869 AACGAGGAGC
Statistics
Matches: 122, Mismatches: 13, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
78 45 0.37
79 54 0.44
80 22 0.18
81 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAATTACTATAACCGGGCTAAGTCCCGAAGGCATTT
GTGCGAGATACTAAA
Found at i:42658890 original size:79 final size:79
Alignment explanation
Indices: 42658698--42658901 Score: 195
Period size: 79 Copynumber: 2.6 Consensus size: 79
42658688 GGACTAAGAT
** * * *
42658698 CCGAAGGCATTTGTGCGAGAT-ACTAATTCCGGGCTAAG-CCCGAAGGTATTTGTGCGAGATACT
1 CCGAAGGCATTTGAACGAG-TGACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACT
*
42658761 AATTCCGGGCTAAGC
65 AATACCGGGCTAAGC
** * *
42658776 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGTGA-ATTACT
1 CCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-TACT
*
42658840 -ATAACCGGGCTATGTC
65 AAT-ACCGGGCTAAG-C
* * *
42658856 CCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGAAGGCATTTGAACGAGTGA-CTAAATCCGGGTTAAGTCCCGAAGG
42658902 TGCGTGATTT
Statistics
Matches: 108, Mismatches: 12, Indels: 11
0.82 0.09 0.08
Matches are distributed among these distances:
77 1 0.01
78 37 0.34
79 45 0.42
80 25 0.23
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTA
ATACCGGGCTAAGC
Found at i:42661326 original size:20 final size:20
Alignment explanation
Indices: 42661273--42661330 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
42661263 TGCGTAACAA
* *
42661273 AGGCACCAAAGTGAAAACAG
1 AGGCACCAAAGTGCAATCAG
42661293 AGGCA-CAAATGTGCAATCAG
1 AGGCACCAAA-GTGCAATCAG
*
42661313 AGGCACCGAAGTGCAATC
1 AGGCACCAAAGTGCAATC
42661331 CTGTACAAGC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 4 0.12
20 26 0.79
21 3 0.09
ACGTcount: A:0.41, C:0.22, G:0.26, T:0.10
Consensus pattern (20 bp):
AGGCACCAAAGTGCAATCAG
Found at i:42666839 original size:23 final size:24
Alignment explanation
Indices: 42666812--42666868 Score: 66
Period size: 23 Copynumber: 2.4 Consensus size: 24
42666802 AATATTTACG
*
42666812 AAGTTAAGTG-AGTG-ATTAATTTA
1 AAGTTAA-TGAAGTGAATTAACTTA
42666835 AAGTTTAATGAAGTGAATTAACTTA
1 AAG-TTAATGAAGTGAATTAACTTA
42666860 AA-TTAATGA
1 AAGTTAATGA
42666869 TAGTTAGATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
23 12 0.40
24 8 0.27
25 10 0.33
ACGTcount: A:0.44, C:0.02, G:0.18, T:0.37
Consensus pattern (24 bp):
AAGTTAATGAAGTGAATTAACTTA
Found at i:42666854 original size:25 final size:22
Alignment explanation
Indices: 42666822--42666868 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 22
42666812 AAGTTAAGTG
*
42666822 AGTGATTAATTTAAAGTTTAATGA
1 AGTGATTAACTTAAA--TTAATGA
42666846 AGTGAATTAACTTAAATTAATGA
1 AGTG-ATTAACTTAAATTAATGA
42666869 TAGTTAGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 7 0.33
24 4 0.19
25 10 0.48
ACGTcount: A:0.45, C:0.02, G:0.15, T:0.38
Consensus pattern (22 bp):
AGTGATTAACTTAAATTAATGA
Found at i:42667275 original size:15 final size:15
Alignment explanation
Indices: 42667255--42667283 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
42667245 GAAATAAAAG
42667255 AAAGAAATAGAATGA
1 AAAGAAATAGAATGA
42667270 AAAGAAATAGAATG
1 AAAGAAATAGAATG
42667284 TGGAACGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.66, C:0.00, G:0.21, T:0.14
Consensus pattern (15 bp):
AAAGAAATAGAATGA
Found at i:42667328 original size:21 final size:19
Alignment explanation
Indices: 42667304--42667341 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
42667294 CAGGGAAAGG
42667304 AAGAAAG-A-AAAAGAGAA
1 AAGAAAGAAGAAAAGAGAA
42667321 AAGAAAGAAGAAAAGAGAA
1 AAGAAAGAAGAAAAGAGAA
42667340 AA
1 AA
42667342 TTAAATGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.37
18 1 0.05
19 11 0.58
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (19 bp):
AAGAAAGAAGAAAAGAGAA
Found at i:42667961 original size:3 final size:3
Alignment explanation
Indices: 42667953--42667979 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
42667943 GAATGGTAAG
42667953 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
42667980 GGTATTGAAT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:42668575 original size:18 final size:18
Alignment explanation
Indices: 42668532--42668578 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
42668522 GACTGTCTGC
** *
42668532 TACTGAATAATTGACTGT
1 TACTGAATAAACGACTGA
42668550 TA-TAGAATAAACGACTGA
1 TACT-GAATAAACGACTGA
42668568 TACTGAATAAA
1 TACTGAATAAA
42668579 TGAATATTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 1 0.04
18 22 0.92
19 1 0.04
ACGTcount: A:0.45, C:0.11, G:0.15, T:0.30
Consensus pattern (18 bp):
TACTGAATAAACGACTGA
Found at i:42668589 original size:18 final size:19
Alignment explanation
Indices: 42668568--42668608 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
42668558 AAACGACTGA
42668568 TACTGAA-TAAATGAATAT
1 TACTGAATTAAATGAATAT
* *
42668586 TACT-AATTAACTGATTAT
1 TACTGAATTAAATGAATAT
42668604 TACTG
1 TACTG
42668609 TTGACTAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 2 0.11
18 17 0.89
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (19 bp):
TACTGAATTAAATGAATAT
Found at i:42669541 original size:26 final size:26
Alignment explanation
Indices: 42669502--42669554 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
42669492 CACAAGCGTG
*
42669502 TCCCATGCCGTACGGGCATGTTAAAC
1 TCCCATGCCATACGGGCATGTTAAAC
42669528 TCCCATGCCATACGGGCATGTTAAAC
1 TCCCATGCCATACGGGCATGTTAAAC
42669554 T
1 T
42669555 AGCACACAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.25
Consensus pattern (26 bp):
TCCCATGCCATACGGGCATGTTAAAC
Found at i:42670204 original size:12 final size:13
Alignment explanation
Indices: 42670170--42670205 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
42670160 TTTCTTCCAT
42670170 GGAGATACTTTCA
1 GGAGATACTTTCA
42670183 GGAGATACTTTCA
1 GGAGATACTTTCA
42670196 GGA-ATACTTT
1 GGAGATACTTT
42670206 ATCACCAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 7 0.30
13 16 0.70
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (13 bp):
GGAGATACTTTCA
Found at i:42691791 original size:86 final size:86
Alignment explanation
Indices: 42691687--42691860 Score: 321
Period size: 86 Copynumber: 2.0 Consensus size: 86
42691677 AAAGTTTTAC
42691687 ACAACTTTGAGTTATTGTTATTTTTCCCAAAAATAGCGAGAATTTATTTTCTAATTATAAATTAT
1 ACAACTTTGAGTTATTGTTATTTTTCCCAAAAATAGCGAGAATTTATTTTCTAATTATAAATTAT
42691752 ATTTTCCAGGATAACAATTCT
66 ATTTTCCAGGATAACAATTCT
* *
42691773 ACAATTTTGAGTTATTGTTATTTTTCCCGAAAATAGCGAGAATTTATTTTCTAATTATAAATTAT
1 ACAACTTTGAGTTATTGTTATTTTTCCCAAAAATAGCGAGAATTTATTTTCTAATTATAAATTAT
*
42691838 ATTTTCTAGGATAACAATTCT
66 ATTTTCCAGGATAACAATTCT
42691859 AC
1 AC
42691861 CAGTTTTTAT
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
86 85 1.00
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (86 bp):
ACAACTTTGAGTTATTGTTATTTTTCCCAAAAATAGCGAGAATTTATTTTCTAATTATAAATTAT
ATTTTCCAGGATAACAATTCT
Found at i:42693412 original size:60 final size:60
Alignment explanation
Indices: 42693342--42693456 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 60
42693332 TTTATACCTA
* * * *
42693342 CAATGTTTACACATTTTATCAATTTGATGCTAAATCT-AAAAATTCAACAAATTTAGTCTT
1 CAATGTTTACAAAATTAATC-ATTTAATGCTAAATCTAAAAAATTCAACAAATTTAGTCTT
** * *
42693402 CAATGTTTACAAAATTAATCATTTAATTTTAATTCTAAAAAATTCAATAAATTTA
1 CAATGTTTACAAAATTAATCATTTAATGCTAAATCTAAAAAATTCAACAAATTTA
42693457 ACCCTAAACG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
59 12 0.26
60 34 0.74
ACGTcount: A:0.43, C:0.12, G:0.04, T:0.41
Consensus pattern (60 bp):
CAATGTTTACAAAATTAATCATTTAATGCTAAATCTAAAAAATTCAACAAATTTAGTCTT
Found at i:42700630 original size:11 final size:12
Alignment explanation
Indices: 42700609--42700638 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
42700599 AACGGAGCAT
42700609 CATATATTATTC
1 CATATATTATTC
42700621 CATA-ATTATTC
1 CATATATTATTC
42700632 CATATAT
1 CATATAT
42700639 ATATATTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.37, C:0.17, G:0.00, T:0.47
Consensus pattern (12 bp):
CATATATTATTC
Found at i:42700991 original size:15 final size:15
Alignment explanation
Indices: 42700973--42701007 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
42700963 TTACTTATAT
42700973 TATATGTATTTATTA
1 TATATGTATTTATTA
42700988 TATATGTATTTATTA
1 TATATGTATTTATTA
42701003 TATAT
1 TATAT
42701008 TATAAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (15 bp):
TATATGTATTTATTA
Found at i:42701016 original size:11 final size:11
Alignment explanation
Indices: 42701002--42701036 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
42700992 TGTATTTATT
*
42701002 ATATATTATAA
1 ATATATTAAAA
42701013 ATATATTAAAA
1 ATATATTAAAA
42701024 ATA-ATTAAAA
1 ATATATTAAAA
42701034 ATA
1 ATA
42701037 ATATATGGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 10 0.43
11 13 0.57
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
ATATATTAAAA
Found at i:42701019 original size:22 final size:24
Alignment explanation
Indices: 42700968--42701020 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 24
42700958 TTAACTTACT
* *
42700968 TATATTATATGTATTTATTATATA
1 TATATTATATGTATATATTATAAA
*
42700992 TGTATT-TAT-TATATATTATAAA
1 TATATTATATGTATATATTATAAA
42701014 TATATTA
1 TATATTA
42701021 AAAATAATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
22 16 0.67
23 3 0.12
24 5 0.21
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.57
Consensus pattern (24 bp):
TATATTATATGTATATATTATAAA
Found at i:42705203 original size:19 final size:18
Alignment explanation
Indices: 42705163--42705203 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
42705153 AGGGCTATTA
*
42705163 TTTTTTTAGGGTTAGGGT
1 TTTTTTTAGGGTTAGGGG
*
42705181 TTTTGTTTAGGGTTTGGGG
1 TTTT-TTTAGGGTTAGGGG
42705200 TTTT
1 TTTT
42705204 AAAAAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.07, C:0.00, G:0.34, T:0.59
Consensus pattern (18 bp):
TTTTTTTAGGGTTAGGGG
Found at i:42708399 original size:38 final size:38
Alignment explanation
Indices: 42708356--42708433 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
42708346 AAAACTTGGA
*
42708356 GTAAGGATGAGAGTTTTAATTTATTTAGTTATACAAGG
1 GTAAGGATAAGAGTTTTAATTTATTTAGTTATACAAGG
42708394 GTAAGGATAAGAGTTTTAATTTATTTAGTTATACAAGG
1 GTAAGGATAAGAGTTTTAATTTATTTAGTTATACAAGG
42708432 GT
1 GT
42708434 GATGCAGTTG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.35, C:0.03, G:0.23, T:0.40
Consensus pattern (38 bp):
GTAAGGATAAGAGTTTTAATTTATTTAGTTATACAAGG
Found at i:42709419 original size:10 final size:10
Alignment explanation
Indices: 42709392--42709430 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
42709382 TTAAATTCTA
42709392 AAAGATAAAT
1 AAAGATAAAT
42709402 ACAA-ATAAAT
1 A-AAGATAAAT
*
42709412 AAAGATAATT
1 AAAGATAAAT
42709422 AAAGATAAA
1 AAAGATAAA
42709431 AAGCTAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.69, C:0.03, G:0.08, T:0.21
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:42710272 original size:99 final size:99
Alignment explanation
Indices: 42710096--42710297 Score: 271
Period size: 99 Copynumber: 2.0 Consensus size: 99
42710086 TTTAAATTTT
** * * *
42710096 TTAAATTATTTATTTTTGCTTAAGAATATATTGAACCTTTTGACGCGAATAGAGATAACAACCAA
1 TTAAATTATTTATTTTTGCTTAAGAATATACCGAACCTCTTGACACGAAGAGAGATAACAACCAA
*
42710161 GCACCCCACCCCGGTTACTCAGCCCAACATACTC
66 GCACCCCACCCCGGTTACTCAGCCCAACACACTC
* * * *
42710195 TTAATTTATTATATTTTT-CTTAAGAATATACCGAACCTCTTGACACGAAGAGAGATGATAGCCA
1 TTAAATTATT-TATTTTTGCTTAAGAATATACCGAACCTCTTGACACGAAGAGAGATAACAACCA
** *
42710259 AGCACCTTACCCCGGTTACTCAGCCCAACACATTC
65 AGCACCCCACCCCGGTTACTCAGCCCAACACACTC
42710294 TTAA
1 TTAA
42710298 GTATTTTAAC
Statistics
Matches: 89, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
99 82 0.92
100 7 0.08
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (99 bp):
TTAAATTATTTATTTTTGCTTAAGAATATACCGAACCTCTTGACACGAAGAGAGATAACAACCAA
GCACCCCACCCCGGTTACTCAGCCCAACACACTC
Found at i:42711151 original size:26 final size:26
Alignment explanation
Indices: 42711119--42711169 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
42711109 GGAAGAGTTT
42711119 CCTTAAGCTGGTTTTTTCATATTTTC
1 CCTTAAGCTGGTTTTTTCATATTTTC
42711145 CCTTAAGCTGGTTTTTTCATATTTT
1 CCTTAAGCTGGTTTTTTCATATTTT
42711170 ACTTCAAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.16, C:0.18, G:0.12, T:0.55
Consensus pattern (26 bp):
CCTTAAGCTGGTTTTTTCATATTTTC
Found at i:42712702 original size:83 final size:83
Alignment explanation
Indices: 42712563--42712730 Score: 336
Period size: 83 Copynumber: 2.0 Consensus size: 83
42712553 CATCTCTTTG
42712563 GAATTTTATTCTAATATGTTGGAATGAAGTCGATGGTAAAAATAAATAAATAAATAAAAATATTC
1 GAATTTTATTCTAATATGTTGGAATGAAGTCGATGGTAAAAATAAATAAATAAATAAAAATATTC
42712628 GAGGTTCAACCGAATTGT
66 GAGGTTCAACCGAATTGT
42712646 GAATTTTATTCTAATATGTTGGAATGAAGTCGATGGTAAAAATAAATAAATAAATAAAAATATTC
1 GAATTTTATTCTAATATGTTGGAATGAAGTCGATGGTAAAAATAAATAAATAAATAAAAATATTC
42712711 GAGGTTCAACCGAATTGT
66 GAGGTTCAACCGAATTGT
42712729 GA
1 GA
42712731 TTCTGAGAAG
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 85 1.00
ACGTcount: A:0.43, C:0.07, G:0.17, T:0.32
Consensus pattern (83 bp):
GAATTTTATTCTAATATGTTGGAATGAAGTCGATGGTAAAAATAAATAAATAAATAAAAATATTC
GAGGTTCAACCGAATTGT
Found at i:42714894 original size:50 final size:50
Alignment explanation
Indices: 42714814--42714942 Score: 170
Period size: 50 Copynumber: 2.5 Consensus size: 50
42714804 GACCATGACA
* * * *
42714814 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGATAAGTG
1 ACAAATGATAAGTG-TAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
42714865 A-AAATGATAAGTAGTAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
1 ACAAATGATAAGT-GTAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
* *
42714915 ACAAGTGAAAAGTGGTAGCTTCGGCTAC
1 ACAAATGATAAGT-GTAGCTTCGGCTAC
42714943 CTGATCAGTG
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
50 44 0.64
51 25 0.36
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.26
Consensus pattern (50 bp):
ACAAATGATAAGTGTAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
Found at i:42714956 original size:31 final size:31
Alignment explanation
Indices: 42714918--42715065 Score: 208
Period size: 31 Copynumber: 4.8 Consensus size: 31
42714908 ACAAATGACA
42714918 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
** *
42714949 AGTGAAAAGT-GTAGCTTTTGTTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* * *
42714979 AGTGAAAAATGGTAGCTCCGACTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
42715010 AGTGAAAAATGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
42715041 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
42715066 AAGTGACAAG
Statistics
Matches: 103, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
30 26 0.25
31 77 0.75
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:42715013 original size:61 final size:62
Alignment explanation
Indices: 42714918--42715057 Score: 192
Period size: 61 Copynumber: 2.3 Consensus size: 62
42714908 ACAAATGACA
* * * *** *
42714918 AGTGAAAAGTGGTAGCTTCGGCTACCTGATCAGTGAAAAGT-GTAGCTTTTGTTACCTGATC
1 AGTGAAAAGTGGTAGCTCCGACTACCTGATCAGTGAAAAATGGTAGCTCCGGCTACCTGATC
*
42714979 AGTGAAAAATGGTAGCTCCGACTACCTGATCAGTGAAAAATGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTCCGACTACCTGATCAGTGAAAAATGGTAGCTCCGGCTACCTGATC
*
42715041 AGTGAATAGTGGTAGCT
1 AGTGAAAAGTGGTAGCT
42715058 TCGGCTACAA
Statistics
Matches: 68, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
61 37 0.54
62 31 0.46
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (62 bp):
AGTGAAAAGTGGTAGCTCCGACTACCTGATCAGTGAAAAATGGTAGCTCCGGCTACCTGATC
Found at i:42715259 original size:49 final size:48
Alignment explanation
Indices: 42715083--42715256 Score: 194
Period size: 47 Copynumber: 3.7 Consensus size: 48
42715073 AAGTGACTTC
* * * *
42715083 CGTATAAGACCATATCTGGGATATGGCATCG-GTGTGATATATG-CTA
1 CGTATAAGACCATAGCTGGGATATGGCATCGAATGTGATATGTGATTA
* * *
42715129 CTGTATAAGACCATATCTGGGATATGGCATC-AGTGAGATATGTGATT-
1 C-GTATAAGACCATAGCTGGGATATGGCATCGAATGTGATATGTGATTA
* *
42715176 CGTGTAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATTA
1 CGTATAAGACCATAGCTGGGATATGGCATCGA-ATGTGATATGTGATTA
* * *
42715225 CGCATAAGACCATAGCTGGGCTATGACATCGA
1 CGTATAAGACCATAGCTGGGATATGGCATCGA
42715257 TATATAAAGA
Statistics
Matches: 111, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
46 27 0.24
47 41 0.37
48 14 0.13
49 29 0.26
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (48 bp):
CGTATAAGACCATAGCTGGGATATGGCATCGAATGTGATATGTGATTA
Found at i:42717051 original size:5 final size:5
Alignment explanation
Indices: 42717041--42717107 Score: 57
Period size: 5 Copynumber: 12.6 Consensus size: 5
42717031 ATTAATATCC
*
42717041 AAATA AAATA AAGTA ATAATAA ATAATA AAATTA AAATTA AAATA AAA-A
1 AAATA AAATA AAATA A-AAT-A A-AATA AAA-TA AAA-TA AAATA AAATA
42717090 GAAA-A AAATA AAATA AAA
1 -AAATA AAATA AAATA AAA
42717108 ATTGGGTTAC
Statistics
Matches: 55, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
4 4 0.07
5 30 0.55
6 15 0.27
7 6 0.11
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (5 bp):
AAATA
Found at i:42720269 original size:16 final size:16
Alignment explanation
Indices: 42720248--42720287 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
42720238 CTCCGATTGT
42720248 CTTAATCCACCTTGGG
1 CTTAATCCACCTTGGG
42720264 CTTAATCCACCTTGGG
1 CTTAATCCACCTTGGG
*
42720280 CTCAATCC
1 CTTAATCC
42720288 TCGAATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.20, C:0.35, G:0.15, T:0.30
Consensus pattern (16 bp):
CTTAATCCACCTTGGG
Found at i:42727828 original size:10 final size:9
Alignment explanation
Indices: 42727797--42727835 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
42727787 TTGAATCATT
*
42727797 AAAATATTA
1 AAAATATAA
*
42727806 ATAATATAA
1 AAAATATAA
42727815 AAAATATGAA
1 AAAATAT-AA
42727825 AAAATATAA
1 AAAATATAA
42727834 AA
1 AA
42727836 CTAAAAGTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
9 17 0.65
10 9 0.35
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (9 bp):
AAAATATAA
Found at i:42730538 original size:24 final size:24
Alignment explanation
Indices: 42730506--42730573 Score: 127
Period size: 24 Copynumber: 2.8 Consensus size: 24
42730496 CAGCAGCCAA
42730506 TATATTGAATGGTCGTTTTACAAG
1 TATATTGAATGGTCGTTTTACAAG
42730530 TATATTGAATGGTCGTTTTACAAG
1 TATATTGAATGGTCGTTTTACAAG
*
42730554 TATATTGAATGGTTGTTTTA
1 TATATTGAATGGTCGTTTTA
42730574 GGCTTTGGGA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.28, C:0.06, G:0.21, T:0.46
Consensus pattern (24 bp):
TATATTGAATGGTCGTTTTACAAG
Found at i:42732436 original size:44 final size:43
Alignment explanation
Indices: 42732386--42732566 Score: 104
Period size: 44 Copynumber: 4.2 Consensus size: 43
42732376 GCCGCTAAAA
42732386 TTAGCGGCGTTTGTTTGAAAAAACGCCACTAAAGATCATGACTT
1 TTAGCGGCGTTTGTTT-AAAAAACGCCACTAAAGATCATGACTT
* * * *
42732430 TTAGCGGC-TTT-TTT-AAAAATGCGCAGCTAAA-AGCCTG-GTCT
1 TTAGCGGCGTTTGTTTAAAAAACGC-CA-CTAAAGATCATGACT-T
* * * * * * *
42732471 TTAGTGGCG-CTGTTTTAGAAAACGCCATTAAAAACCAAGACTT
1 TTAGCGGCGTTTG-TTTAAAAAACGCCACTAAAGATCATGACTT
* * * * * * *
42732514 TTAGCGGCATTTTTTTAAAAAAAGGCCGCTAAAGCTAATGACCT
1 TTAGCGGCGTTTGTTT-AAAAAACGCCACTAAAGATCATGACTT
42732558 TTAGCGGCG
1 TTAGCGGCG
42732567 CTTTACCCAA
Statistics
Matches: 98, Mismatches: 28, Indels: 22
0.66 0.19 0.15
Matches are distributed among these distances:
40 8 0.08
41 15 0.15
42 12 0.12
43 22 0.22
44 41 0.42
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (43 bp):
TTAGCGGCGTTTGTTTAAAAAACGCCACTAAAGATCATGACTT
Found at i:42732738 original size:25 final size:25
Alignment explanation
Indices: 42732688--42732748 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 25
42732678 TATCCATGAT
* * *
42732688 ATAAATATAAAAATTTTCTATTAAA
1 ATAAAAATAAAAATTTTCAATCAAA
42732713 ATAAAAATAAAAATTTAT-AATCAAA
1 ATAAAAATAAAAATTT-TCAATCAAA
42732738 ACT-AAAATAAA
1 A-TAAAAATAAA
42732749 TAATAAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
25 29 0.94
26 2 0.06
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (25 bp):
ATAAAAATAAAAATTTTCAATCAAA
Found at i:42737788 original size:16 final size:18
Alignment explanation
Indices: 42737752--42737787 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
42737742 TTTGCTGAGA
42737752 TTATATTTTTTGAAATTT
1 TTATATTTTTTGAAATTT
*
42737770 TTAT-TTTTTTTAAATTT
1 TTATATTTTTTGAAATTT
42737787 T
1 T
42737788 AAATATTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (18 bp):
TTATATTTTTTGAAATTT
Found at i:42737849 original size:7 final size:7
Alignment explanation
Indices: 42737839--42737929 Score: 76
Period size: 7 Copynumber: 12.6 Consensus size: 7
42737829 AATATTAAAA
42737839 TTTTAAGT
1 TTTTAA-T
42737847 TTTTAAGT
1 TTTTAA-T
42737855 TTTTAA-
1 TTTTAAT
42737861 TTTTAATT
1 TTTTAA-T
*
42737869 TTTTTAT
1 TTTTAAT
42737876 TTTTCAAT
1 TTTT-AAT
*
42737884 TTTCAAT
1 TTTTAAT
*
42737891 TTTCAAT
1 TTTTAAT
*
42737898 TTTCAAT
1 TTTTAAT
*
42737905 TTTCAAT
1 TTTTAAT
*
42737912 TTTCAAT
1 TTTTAAT
*
42737919 TTTCAAT
1 TTTTAAT
42737926 TTTT
1 TTTT
42737930 TTAAAGATTT
Statistics
Matches: 76, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
6 6 0.08
7 46 0.61
8 24 0.32
ACGTcount: A:0.25, C:0.08, G:0.02, T:0.65
Consensus pattern (7 bp):
TTTTAAT
Found at i:42737900 original size:21 final size:21
Alignment explanation
Indices: 42737876--42737928 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
42737866 ATTTTTTTAT
42737876 TTTTCAATTTTCAATTTTCAA
1 TTTTCAATTTTCAATTTTCAA
42737897 TTTTCAATTTTCAATTTTCAA
1 TTTTCAATTTTCAATTTTCAA
42737918 TTTTCAATTTT
1 TTTTCAATTTT
42737929 TTTAAAGATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.26, C:0.13, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTCAATTTTCAATTTTCAA
Found at i:42737922 original size:14 final size:14
Alignment explanation
Indices: 42737876--42737928 Score: 106
Period size: 14 Copynumber: 3.8 Consensus size: 14
42737866 ATTTTTTTAT
42737876 TTTTCAATTTTCAA
1 TTTTCAATTTTCAA
42737890 TTTTCAATTTTCAA
1 TTTTCAATTTTCAA
42737904 TTTTCAATTTTCAA
1 TTTTCAATTTTCAA
42737918 TTTTCAATTTT
1 TTTTCAATTTT
42737929 TTTAAAGATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 39 1.00
ACGTcount: A:0.26, C:0.13, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTTCAATTTTCAA
Found at i:42739655 original size:40 final size:41
Alignment explanation
Indices: 42739553--42739746 Score: 302
Period size: 41 Copynumber: 4.8 Consensus size: 41
42739543 GTTATATGAC
* *
42739553 TTTTAGCGGCGTTTTACCAAAAACGCCGCTATTGCTCTGTT
1 TTTTAGCGGCGCTTTGCCAAAAACGCCGCTATTGCTCTGTT
*
42739594 TTTTAGCGGCGCTTTGACC-AAAACGCCGCTTTTGCTCTGTT
1 TTTTAGCGGCGCTTTG-CCAAAAACGCCGCTATTGCTCTGTT
*
42739635 TTTTAGCTGCGCTTTGCCAAAAACGCCGCTATTGCTCTGTT
1 TTTTAGCGGCGCTTTGCCAAAAACGCCGCTATTGCTCTGTT
* *
42739676 TTTTAGTGGCGCTTTGCCAAAAACGCCGCTATTACTCTG-T
1 TTTTAGCGGCGCTTTGCCAAAAACGCCGCTATTGCTCTGTT
*
42739716 TTTTAGCGGCGCTTTGTCAAAAACGCCGCTA
1 TTTTAGCGGCGCTTTGCCAAAAACGCCGCTA
42739747 ATGTATAATT
Statistics
Matches: 141, Mismatches: 10, Indels: 5
0.90 0.06 0.03
Matches are distributed among these distances:
40 32 0.23
41 107 0.76
42 2 0.01
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.35
Consensus pattern (41 bp):
TTTTAGCGGCGCTTTGCCAAAAACGCCGCTATTGCTCTGTT
Found at i:42742728 original size:15 final size:15
Alignment explanation
Indices: 42742708--42742739 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
42742698 CATTTCACTA
*
42742708 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
42742723 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
42742738 TT
1 TT
42742740 TGCATGTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:42744382 original size:62 final size:58
Alignment explanation
Indices: 42744298--42744430 Score: 151
Period size: 62 Copynumber: 2.2 Consensus size: 58
42744288 TCCAAAAATA
* * * *
42744298 ATATTATTTTAAT-ATTTTAATATTAGATTTAATTTAATGCTTATCTACAAGATAAATATT
1 ATATTATTTTAATAAATTTAATATTAAATTTAATCTAATACTTATCT--AA-ATAAATATT
* * *
42744358 TTATTATTTTAATAAGATTTAATATTAAATTTAATCTAATATTTATCTTAATAAATATT
1 ATATTATTTTAATAA-ATTTAATATTAAATTTAATCTAATACTTATCTAAATAAATATT
*
42744417 ATATTAATTTAATA
1 ATATTATTTTAATA
42744431 TTAAAGTAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
59 21 0.34
60 13 0.21
61 1 0.02
62 27 0.44
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.51
Consensus pattern (58 bp):
ATATTATTTTAATAAATTTAATATTAAATTTAATCTAATACTTATCTAAATAAATATT
Found at i:42746755 original size:26 final size:25
Alignment explanation
Indices: 42746654--42746894 Score: 100
Period size: 26 Copynumber: 9.5 Consensus size: 25
42746644 AAATAATATA
* ***
42746654 AAAATAAATAATATA-ACAAGGTTT
1 AAAATAAATAATATATAAAAAAATT
** **
42746678 AAAATAAATAATAGGTGAAACCAATT
1 AAAATAAATAATATAT-AAAAAAATT
* * **
42746704 AAAGTAAA-AAGATATAAAAAGTTT
1 AAAATAAATAATATATAAAAAAATT
42746728 AAAAATAAATAATATATAAAAAAATT
1 -AAAATAAATAATATATAAAAAAATT
* **
42746754 AAAATAAATAATATATGAAATGATT
1 AAAATAAATAATATATAAAAAAATT
* * *
42746779 CAGAATAAACAATATATGAAAAAGATT
1 -AAAATAAATAATATAT-AAAAAAATT
* *
42746806 ----TGACATAA-ATATAAAACAATTT
1 AAAAT-AAATAATATATAAAA-AAATT
* *
42746828 AGAATAAAATAATATATAAAACAATTT
1 AAAAT-AAATAATATATAAAA-AAATT
* * * *
42746855 CAAATACATAAATATATGTAATAAATT
1 AAAATAAAT-AATATAT-AAAAAAATT
*
42746882 AAAAGAAATAATA
1 AAAATAAATAATA
42746895 CACAAAGTAA
Statistics
Matches: 161, Mismatches: 41, Indels: 28
0.70 0.18 0.12
Matches are distributed among these distances:
21 4 0.02
22 8 0.05
23 4 0.02
24 18 0.11
25 33 0.20
26 51 0.32
27 41 0.25
28 2 0.01
ACGTcount: A:0.61, C:0.04, G:0.07, T:0.27
Consensus pattern (25 bp):
AAAATAAATAATATATAAAAAAATT
Found at i:42746756 original size:50 final size:51
Alignment explanation
Indices: 42746654--42746761 Score: 123
Period size: 50 Copynumber: 2.2 Consensus size: 51
42746644 AAATAATATA
* * * **
42746654 AAAATAAATA-ATATAACAAGGTTTAAAATAAATAATAGGTGAAACCAATT
1 AAAATAAAAAGATATAACAAAGTTTAAAATAAATAATAGATGAAAAAAATT
* *
42746704 AAAGTAAAAAGATATAA-AAAGTTTAAAAATAAATAATATAT-AAAAAAATT
1 AAAATAAAAAGATATAACAAAGTTT-AAAATAAATAATAGATGAAAAAAATT
42746754 AAAATAAA
1 AAAATAAA
42746762 TAATATATGA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
50 28 0.58
51 20 0.42
ACGTcount: A:0.65, C:0.03, G:0.07, T:0.25
Consensus pattern (51 bp):
AAAATAAAAAGATATAACAAAGTTTAAAATAAATAATAGATGAAAAAAATT
Found at i:42746860 original size:27 final size:26
Alignment explanation
Indices: 42746810--42746870 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 26
42746800 AAGATTTGAC
42746810 ATAAATATAAAACAATTTAGAATAAA
1 ATAAATATAAAACAATTTAGAATAAA
*
42746836 ATAATATATAAAACAATTTCA-AAT-AC
1 ATAA-ATATAAAACAATTT-AGAATAAA
42746862 ATAAATATA
1 ATAAATATA
42746871 TGTAATAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
25 5 0.16
26 9 0.28
27 17 0.53
28 1 0.03
ACGTcount: A:0.62, C:0.07, G:0.02, T:0.30
Consensus pattern (26 bp):
ATAAATATAAAACAATTTAGAATAAA
Found at i:42746971 original size:23 final size:24
Alignment explanation
Indices: 42746941--42746986 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
42746931 TAAAAAAGAG
*
42746941 TTTAAAATAAATAATATA-AAAAT
1 TTTAAAATAAATAACATATAAAAT
*
42746964 TTTAAAATGAATAACATATAAAA
1 TTTAAAATAAATAACATATAAAA
42746987 CAACATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (24 bp):
TTTAAAATAAATAACATATAAAAT
Found at i:42746993 original size:12 final size:12
Alignment explanation
Indices: 42746976--42747001 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42746966 TAAAATGAAT
42746976 AACATATAAAAC
1 AACATATAAAAC
42746988 AACATATAAAAC
1 AACATATAAAAC
42747000 AA
1 AA
42747002 TTTAAACTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.15, G:0.00, T:0.15
Consensus pattern (12 bp):
AACATATAAAAC
Found at i:42747101 original size:27 final size:26
Alignment explanation
Indices: 42747040--42747102 Score: 72
Period size: 27 Copynumber: 2.4 Consensus size: 26
42747030 TTAAACAGAT
* * *
42747040 AATAATATATAAAGTAGTTTAAAATA
1 AATAATATATAAAATACTTAAAAATA
* *
42747066 AAGAGTATATAAAAATACTTAAAAATA
1 AATAATATAT-AAAATACTTAAAAATA
42747093 AATAATATAT
1 AATAATATAT
42747103 GGAAAGTTCA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (26 bp):
AATAATATATAAAATACTTAAAAATA
Found at i:42747205 original size:24 final size:26
Alignment explanation
Indices: 42747167--42747220 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 26
42747157 ATAATATATC
*
42747167 TAAATAACATATAAAA-A-TTTTAAA
1 TAAATAACATATAAAATAGTTTAAAA
* *
42747191 TAAATAATATGTAAAATAGTTTAAAA
1 TAAATAACATATAAAATAGTTTAAAA
42747217 TAAA
1 TAAA
42747221 AGGTATCTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 14 0.56
25 1 0.04
26 10 0.40
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (26 bp):
TAAATAACATATAAAATAGTTTAAAA
Found at i:42748161 original size:19 final size:19
Alignment explanation
Indices: 42748137--42748175 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
42748127 GAAAACTTAG
42748137 ATCCGAAAGAAAAGATTGA
1 ATCCGAAAGAAAAGATTGA
42748156 ATCCGAAAGAAAAGATTGA
1 ATCCGAAAGAAAAGATTGA
42748175 A
1 A
42748176 ATCCACTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.54, C:0.10, G:0.21, T:0.15
Consensus pattern (19 bp):
ATCCGAAAGAAAAGATTGA
Found at i:42748951 original size:44 final size:45
Alignment explanation
Indices: 42748902--42749011 Score: 118
Period size: 44 Copynumber: 2.5 Consensus size: 45
42748892 TCGATTCGCT
*
42748902 CCACTGCAACTTTAGGGAGAT-AGGACTCATAACTTTAAC-CTGCC
1 CCACTGCAACTTTAGGGAGATAAGG-CTCATAACTTTAACTCAGCC
* * * * *
42748946 CCACTGCAACTTCAGGGGGATAAGGCTTATAGCTTTAACTCAGCT
1 CCACTGCAACTTTAGGGAGATAAGGCTCATAACTTTAACTCAGCC
*
42748991 CTACTGCAA-TTTCAGGGAGAT
1 CCACTGCAACTTT-AGGGAGAT
42749012 GAGGTTTGTG
Statistics
Matches: 54, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
44 33 0.61
45 21 0.39
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (45 bp):
CCACTGCAACTTTAGGGAGATAAGGCTCATAACTTTAACTCAGCC
Found at i:42749160 original size:44 final size:44
Alignment explanation
Indices: 42749054--42749684 Score: 289
Period size: 44 Copynumber: 14.0 Consensus size: 44
42749044 TTGTAGCTTG
* * * *
42749054 ATCTGCTCCATTGCAACTTCAAGGAGATAAGATCTTCTATCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGA-CTTGTAACTTCA
* *
42749099 GTCTGCTCCATTGCAACTTCAGGGAGATAAGACTTGTAACTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCA
* * ** *
42749143 A-CTTGCCCCACTGCAACTTCAGGGGGATAAGGTTTGTAGCTTCA
1 ATC-TGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCA
* ** * * **
42749187 ATCTACTCCACTATAACTTCAGGGAGATAAGATTCACCATAGTAAGTTTG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAG----A-C-TTGTAACTTCA
* * * * * * *
42749237 ATC--CAACCTACTGCAACTTCA-GAAGTATAGGATTTATAGCTTTA
1 ATCTGC-TCC-ACTGCAACTTCAGGGAG-ATAAGACTTGTAACTTCA
* * * * *
42749281 ATCTGCTCTACTGCAACTTTAGAGAGATAAGATTTGCTATCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-TAACTTCA
* * * * *
42749326 GTCTGTTCCACTGTAACTTCAGGTG-TATAAGACTCGTAACTTCA
1 ATCTGCTCCACTGCAACTTCAGG-GAGATAAGACTTGTAACTTCA
* * * ** * *** *
42749370 ACCTGCCCCACTACAAAGATAAGTTTTG-T--GA-TCTGTAGCTTCA
1 ATCTGCTCCACTGC-AACTTCAG-GGAGATAAGACT-TGTAACTTCA
* * * **
42749413 ATCTGCCCCACTGCAACTTCAGAGAGATAAGA-TTCACTATTTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGACTT--GTAACTTCA
* * * *
42749458 GTCTGCTCTACT-AAACTTCAGGGAGATAAGACTTGTAATTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCA
* * **
42749501 ACCTGCTCTACTGCAACTTCAGGGAGATAAGGTTTGTGATCTGTAGCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGT-A-----A-CTTCA
* * **
42749552 ATCTGCCCCACTGCAACTTCAGGGAGATAAGA-TTCACTATTTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGACTT--GTAACTTCA
* * * * *
42749597 GTCTGCTCTACTGCAGCTTCAGGGAGATAAGACTTTTAATTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCA
* * * *
42749641 ACCTGCTTCACTGCAACTTTAGGGAGATAAGA-TTTTAACTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCA
42749684 A
1 A
42749685 CTTGTTCCAT
Statistics
Matches: 438, Mismatches: 111, Indels: 76
0.70 0.18 0.12
Matches are distributed among these distances:
41 1 0.00
42 7 0.02
43 52 0.12
44 186 0.42
45 121 0.28
46 5 0.01
48 1 0.00
49 5 0.01
50 26 0.06
51 33 0.08
52 1 0.00
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.31
Consensus pattern (44 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCA
Found at i:42749558 original size:139 final size:140
Alignment explanation
Indices: 42749273--42749671 Score: 514
Period size: 139 Copynumber: 2.9 Consensus size: 140
42749263 ATAGGATTTA
* * * * ** * * *
42749273 TAGCTTTAATCTGCTCTACTGCAACTTTAGAGAGATAAGATTTGCTATCTTCAGTCTGTTCCACT
1 TAGCTTCAATCTGCCCCACTGCAACTTCAGAGAGATAAGATTCACTATTTTCAGTCTGCTCTACT
* * * * * * *
42749338 GTAACTTCAGGTG-TATAAGACTCGTAACTTCAACCTGC-C--C--C-ACTACA--AAGATAAGT
66 GAAACTTCAGG-GAGATAAGACTTGTAATTTCAACCTGCTCTACTGCAACTTCAGGGAGATAAGG
42749394 TTTGTGATCTG
130 TTTGTGATCTG
42749405 TAGCTTCAATCTGCCCCACTGCAACTTCAGAGAGATAAGATTCACTATTTTCAGTCTGCTCTACT
1 TAGCTTCAATCTGCCCCACTGCAACTTCAGAGAGATAAGATTCACTATTTTCAGTCTGCTCTACT
42749470 -AAACTTCAGGGAGATAAGACTTGTAATTTCAACCTGCTCTACTGCAACTTCAGGGAGATAAGGT
66 GAAACTTCAGGGAGATAAGACTTGTAATTTCAACCTGCTCTACTGCAACTTCAGGGAGATAAGGT
42749534 TTGTGATCTG
131 TTGTGATCTG
*
42749544 TAGCTTCAATCTGCCCCACTGCAACTTCAGGGAGATAAGATTCACTATTTTCAGTCTGCTCTACT
1 TAGCTTCAATCTGCCCCACTGCAACTTCAGAGAGATAAGATTCACTATTTTCAGTCTGCTCTACT
* * * *
42749609 GCAGCTTCAGGGAGATAAGACTTTTAATTTCAACCTGCT-TCACTGCAACTTTAGGGAGATAAG
66 GAAACTTCAGGGAGATAAGACTTGTAATTTCAACCTGCTCT-ACTGCAACTTCAGGGAGATAAG
42749672 ATTTTAACTT
Statistics
Matches: 235, Mismatches: 21, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
130 1 0.00
131 31 0.13
132 57 0.24
134 1 0.00
136 1 0.00
137 5 0.02
139 83 0.35
140 56 0.24
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.32
Consensus pattern (140 bp):
TAGCTTCAATCTGCCCCACTGCAACTTCAGAGAGATAAGATTCACTATTTTCAGTCTGCTCTACT
GAAACTTCAGGGAGATAAGACTTGTAATTTCAACCTGCTCTACTGCAACTTCAGGGAGATAAGGT
TTGTGATCTG
Found at i:42749812 original size:88 final size:88
Alignment explanation
Indices: 42749721--42750150 Score: 481
Period size: 88 Copynumber: 4.9 Consensus size: 88
42749711 TAAGGTGTAA
* * ** * **
42749721 TGGCTTCAATCTGCTCCAATATCATTTCAGGGAGAAGAGATCTGTAGCTTCGATCTACTCCATTG
1 TGGCTTCAAGCCGCTCCAATGCCATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCGCTG
* * *
42749786 AAACTTCAAGGGGATACGGATCA
66 AAACTTCAAGGAGATACTGATCG
* * * * *
42749809 TGGCTTCAGGCCGTTCCAGTGCTATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCGCTA
1 TGGCTTCAAGCCGCTCCAATGCCATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCGCTG
* *
42749874 AAACTTCAAGGCGATA-TGAACTG
66 AAACTTCAAGGAGATACTGATC-G
* * *
42749897 TGGCTTCAAGCCGCTCCAACGCCATTTCAGGTAGAAGAGATTTGTAGCTTCGATCTACTCCACTG
1 TGGCTTCAAGCCGCTCCAATGCCATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCGCTG
* ** *
42749962 GAACTTCAAGGAGATACAAATTG
66 AAACTTCAAGGAGATACTGATCG
* ** * * * *
42749985 TAGCTTCGGGCCTCT-CAGTGCCATTTCAGGGAGAAGAGATTTATAGCTTCGATCTACTCTGCTG
1 TGGCTTCAAGCCGCTCCAATGCCATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCGCTG
* * *
42750049 GAACTTTAAGGAGAT-CTGCT-G
66 AAACTTCAAGGAGATACTGATCG
* * *
42750070 TGGCTTCGAGCAGCTCCAATGCCATTTCAGGGAGAAGAGATTTGTAGCCTCGATCTACTCCGCTG
1 TGGCTTCAAGCCGCTCCAATGCCATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCGCTG
*
42750135 AAACTCCAAGGAGATA
66 AAACTTCAAGGAGATA
42750151 TGAATTATTG
Statistics
Matches: 283, Mismatches: 55, Indels: 9
0.82 0.16 0.03
Matches are distributed among these distances:
85 12 0.04
86 59 0.21
87 60 0.21
88 151 0.53
89 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (88 bp):
TGGCTTCAAGCCGCTCCAATGCCATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCGCTG
AAACTTCAAGGAGATACTGATCG
Found at i:42750112 original size:173 final size:175
Alignment explanation
Indices: 42749721--42750150 Score: 560
Period size: 176 Copynumber: 2.5 Consensus size: 175
42749711 TAAGGTGTAA
* * ** * *
42749721 TGGCTTCAATCTGCTCCAATATCATTTCAGGGAGAAGAGATCTGTAGCTTCGATCTACTCCATTG
1 TGGCTTCAAGCAGCTCCAATGCCATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCACTG
* ** * *
42749786 AAACTTCAAGGGGATACGGATCATGGCTTCAGGCCGTTCCAGTGCTATTTCAGGGAGAAGAGATT
66 AAACTTCAAGGAGATACAAATCATAGCTTCAGGCCGTTCCAGTGCCATTTCAGGGAGAAGAGATT
* *
42749851 TGTAGCTTCGATCTACTCCGCTAAAACTTCAAGGCGATATGAACTG
131 TATAGCTTCGATCTACTCCGCTAAAACTTCAAGGAGATATG-ACTG
* * *
42749897 TGGCTTCAAGCCGCTCCAACGCCATTTCAGGTAGAAGAGATTTGTAGCTTCGATCTACTCCACTG
1 TGGCTTCAAGCAGCTCCAATGCCATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCACTG
* ** *
42749962 GAACTTCAAGGAGATACAAATTGTAGCTTCGGGCC--TCTCAGTGCCATTTCAGGGAGAAGAGAT
66 AAACTTCAAGGAGATACAAATCATAGCTTCAGGCCGTTC-CAGTGCCATTTCAGGGAGAAGAGAT
* ** * *
42750025 TTATAGCTTCGATCTACTCTGCTGGAACTTTAAGGAGATCTG-CTG
130 TTATAGCTTCGATCTACTCCGCTAAAACTTCAAGGAGATATGACTG
* * *
42750070 TGGCTTCGAGCAGCTCCAATGCCATTTCAGGGAGAAGAGATTTGTAGCCTCGATCTACTCCGCTG
1 TGGCTTCAAGCAGCTCCAATGCCATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCACTG
*
42750135 AAACTCCAAGGAGATA
66 AAACTTCAAGGAGATA
42750151 TGAATTATTG
Statistics
Matches: 221, Mismatches: 32, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
173 76 0.34
174 2 0.01
175 59 0.27
176 84 0.38
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (175 bp):
TGGCTTCAAGCAGCTCCAATGCCATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCACTG
AAACTTCAAGGAGATACAAATCATAGCTTCAGGCCGTTCCAGTGCCATTTCAGGGAGAAGAGATT
TATAGCTTCGATCTACTCCGCTAAAACTTCAAGGAGATATGACTG
Found at i:42750429 original size:131 final size:131
Alignment explanation
Indices: 42750178--42750432 Score: 404
Period size: 131 Copynumber: 1.9 Consensus size: 131
42750168 CCTGCTCTAT
* * *
42750178 TACTGCTTAGAGAGATAGGATTGTGGCTTAAATCTGCTCCACTACGGTTTAGGGAGACAAGATTT
1 TACTGCTTAGAGAGATAGGATGGTGGCTTAAATCTGCTCCACTACGGTTTAGGAAGACAAGATTC
**
42750243 GTTGTCTTCGATCTGTTCCACTGCAACTTCAAGGAGACAAGATCTACAATCTTCAGCCTACTCTG
66 GCCGTCTTCGATCTGTTCCACTGCAACTTCAAGGAGACAAGATCTACAATCTTCAGCCTACTCTG
42750308 C
131 C
* *
42750309 TACTGCTTAGGGAGATAGGATGGTGGCTTAAATCTGCTCCACTATGGTTTAGGAAGACAAGATTC
1 TACTGCTTAGAGAGATAGGATGGTGGCTTAAATCTGCTCCACTACGGTTTAGGAAGACAAGATTC
* * *
42750374 GCCGTCTTCGATCTGTTCTACTGTAACTTC-AGAGAGACAAGATCTATAATCTTCAGCCT
66 GCCGTCTTCGATCTGTTCCACTGCAACTTCAAG-GAGACAAGATCTACAATCTTCAGCCT
42750433 GTTACCCTAC
Statistics
Matches: 113, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
130 2 0.02
131 111 0.98
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (131 bp):
TACTGCTTAGAGAGATAGGATGGTGGCTTAAATCTGCTCCACTACGGTTTAGGAAGACAAGATTC
GCCGTCTTCGATCTGTTCCACTGCAACTTCAAGGAGACAAGATCTACAATCTTCAGCCTACTCTG
C
Found at i:42750488 original size:44 final size:43
Alignment explanation
Indices: 42750439--42750573 Score: 114
Period size: 44 Copynumber: 3.1 Consensus size: 43
42750429 GCCTGTTACC
42750439 CTACTGCTTAGGGGGTTAAGGTTCACCGTCTTTGATCTGCTCCA
1 CTACTGCTTAGGGGGTTAAGG-TCACCGTCTTTGATCTGCTCCA
* * * ** * * *
42750483 CTACTGCTTAGGGAGATAAGGT--CTGTAATTCAGCCTGTTACC-
1 CTACTGCTTAGGGGGTTAAGGTCACCGTCTTTGA-TCTGCT-CCA
* * *
42750525 CTACTGCTCAAGGGGTTAAGCCTCACCGTCTTTGATCTGCTCCA
1 CTACTGCTTAGGGGGTTAAG-GTCACCGTCTTTGATCTGCTCCA
42750569 CTACT
1 CTACT
42750574 ATCTGTAATT
Statistics
Matches: 66, Mismatches: 19, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
41 6 0.09
42 20 0.30
43 6 0.09
44 28 0.42
45 6 0.09
ACGTcount: A:0.19, C:0.27, G:0.22, T:0.32
Consensus pattern (43 bp):
CTACTGCTTAGGGGGTTAAGGTCACCGTCTTTGATCTGCTCCA
Found at i:42750750 original size:64 final size:64
Alignment explanation
Indices: 42750649--42750772 Score: 212
Period size: 64 Copynumber: 1.9 Consensus size: 64
42750639 GTATCTATGT
* * *
42750649 TTATGCCAAATGATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGTTGTGATGC
1 TTATGCCAAATAATTAGGATGCTATGATCGAAATGAATCAAATACTCCTAACTAGATGTGATGC
*
42750713 TTATGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATACTCCTAACTAGATGTG
1 TTATGCCAAATAATTAGGATGCTATGATCGAAATGAATCAAATACTCCTAACTAGATGTG
42750773 TTATGAATGA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 56 1.00
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (64 bp):
TTATGCCAAATAATTAGGATGCTATGATCGAAATGAATCAAATACTCCTAACTAGATGTGATGC
Found at i:42751939 original size:50 final size:50
Alignment explanation
Indices: 42751884--42751979 Score: 138
Period size: 50 Copynumber: 1.9 Consensus size: 50
42751874 TCCCCTTTGG
*** *
42751884 TCTCAAAGCGTCCTTTGTGGGTTTTCGCCTTAGCCTCTCCCTTTTTTTTT
1 TCTCAAAGCGTCCTTTGCAAGTTTTCACCTTAGCCTCTCCCTTTTTTTTT
* *
42751934 TCTCAAGGCGTCCTTTGCAAGTTTTCACCTTGGCCTCTCCCTTTTT
1 TCTCAAAGCGTCCTTTGCAAGTTTTCACCTTAGCCTCTCCCTTTTT
42751980 AGGTAGAACA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 40 1.00
ACGTcount: A:0.09, C:0.30, G:0.16, T:0.45
Consensus pattern (50 bp):
TCTCAAAGCGTCCTTTGCAAGTTTTCACCTTAGCCTCTCCCTTTTTTTTT
Found at i:42757141 original size:127 final size:126
Alignment explanation
Indices: 42756991--42757222 Score: 285
Period size: 127 Copynumber: 1.8 Consensus size: 126
42756981 TGTGGACGGA
* ** *
42756991 ATTTTAAAGGAATGTTTGATTATTTGGATAAACAGAAA-ATCGAAACCC-ATCACATTAGGGTAC
1 ATTTTAAAGGAATATTTGATTATTTAAATAAAC-GAAAGATCGAAACCCAAT-ACATTAGGGCAC
* *
42757054 GATTTCC-CAAA-TTCTCAAACATCAACCATCGCTTTTGTTTTAAAGTTTAAAAAACGCAAACGA
64 GA--TCCACAAATTTCT-AAACATCAAACATCGCCTTTGTTTTAAAGTTTAAAAAACGCAAACGA
42757117 G
126 G
* *
42757118 ATTTTAAAGGGAA-ATTTGATTATTTAAATAAACGAAAGATCGAAGCCCAATACGTTAGGGCACG
1 ATTTTAAA-GGAATATTTGATTATTTAAATAAACGAAAGATCGAAACCCAATACATTAGGGCACG
*
42757182 ATCCATCGAATTTCTAAACATCAAACATCGCCTTTGTTTTA
65 ATCCA-CAAATTTCTAAACATCAAACATCGCCTTTGTTTTA
42757223 TAAAGTCTAC
Statistics
Matches: 90, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
125 3 0.03
126 4 0.04
127 73 0.81
128 10 0.11
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (126 bp):
ATTTTAAAGGAATATTTGATTATTTAAATAAACGAAAGATCGAAACCCAATACATTAGGGCACGA
TCCACAAATTTCTAAACATCAAACATCGCCTTTGTTTTAAAGTTTAAAAAACGCAAACGAG
Found at i:42757779 original size:26 final size:25
Alignment explanation
Indices: 42757724--42757825 Score: 89
Period size: 26 Copynumber: 4.0 Consensus size: 25
42757714 AGGTGCAACC
* *
42757724 AATTAAAGTAAA-AAGATATAAAAA
1 AATTAAAATAAATAATATATAAAAA
**
42757748 GTTTAAAAATAAATAATATATAAAAA
1 AATT-AAAATAAATAATATATAAAAA
* *
42757774 AATTAAAATAAATAATATATGAAAT
1 AATTAAAATAAATAATATATAAAAA
* * * *
42757799 GATTCAGAATAAACAATATATGAAAA
1 AATT-AAAATAAATAATATATAAAAA
42757825 A
1 A
42757826 GATTTGACAT
Statistics
Matches: 62, Mismatches: 13, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
24 2 0.03
25 29 0.47
26 31 0.50
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.26
Consensus pattern (25 bp):
AATTAAAATAAATAATATATAAAAA
Found at i:42757995 original size:23 final size:26
Alignment explanation
Indices: 42757947--42758010 Score: 82
Period size: 25 Copynumber: 2.6 Consensus size: 26
42757937 TAAGACCCTT
42757947 TAAA-AACATATAAAAGAGTTTAAAA
1 TAAATAACATATAAAAGAGTTTAAAA
*
42757972 TAAAT-A-ATATAAAAG-TTTTAAAA
1 TAAATAACATATAAAAGAGTTTAAAA
*
42757995 TGAATAACATATAAAA
1 TAAATAACATATAAAA
42758011 CAACATATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
23 11 0.32
24 10 0.29
25 13 0.38
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.28
Consensus pattern (26 bp):
TAAATAACATATAAAAGAGTTTAAAA
Found at i:42758017 original size:12 final size:12
Alignment explanation
Indices: 42758000--42758025 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42757990 TAAAATGAAT
42758000 AACATATAAAAC
1 AACATATAAAAC
42758012 AACATATAAAAC
1 AACATATAAAAC
42758024 AA
1 AA
42758026 TTTAAACTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.15, G:0.00, T:0.15
Consensus pattern (12 bp):
AACATATAAAAC
Found at i:42758125 original size:27 final size:26
Alignment explanation
Indices: 42758064--42758126 Score: 72
Period size: 27 Copynumber: 2.4 Consensus size: 26
42758054 TTAAACAGAT
* * *
42758064 AATAATATATAAAGTAGTTTAAAATA
1 AATAATATATAAAATACTTAAAAATA
* *
42758090 AAGAGTATATAAAAATACTTAAAAATA
1 AATAATATAT-AAAATACTTAAAAATA
42758117 AATAATATAT
1 AATAATATAT
42758127 GGAAAGTTCA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (26 bp):
AATAATATATAAAATACTTAAAAATA
Found at i:42758229 original size:24 final size:26
Alignment explanation
Indices: 42758191--42758244 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 26
42758181 ATAATATATC
*
42758191 TAAATAACATATAAAA-A-TTTTAAA
1 TAAATAACATATAAAATAGTTTAAAA
* *
42758215 TAAATAATATGTAAAATAGTTTAAAA
1 TAAATAACATATAAAATAGTTTAAAA
42758241 TAAA
1 TAAA
42758245 AGGTATCTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 14 0.56
25 1 0.04
26 10 0.40
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (26 bp):
TAAATAACATATAAAATAGTTTAAAA
Found at i:42759188 original size:19 final size:19
Alignment explanation
Indices: 42759161--42759204 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
42759151 GAAAACTTAG
42759161 ATCCAAAAGAAAAGATTGA
1 ATCCAAAAGAAAAGATTGA
*
42759180 ATCCGAAAGAAAAGATTGAA
1 ATCCAAAAGAAAAGATTG-A
42759200 ATCCA
1 ATCCA
42759205 CTTTCTAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.55, C:0.14, G:0.16, T:0.16
Consensus pattern (19 bp):
ATCCAAAAGAAAAGATTGA
Found at i:42762230 original size:27 final size:27
Alignment explanation
Indices: 42762200--42762377 Score: 198
Period size: 27 Copynumber: 6.6 Consensus size: 27
42762190 ATATTGAGCC
* * *
42762200 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
* * *
42762227 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAACT
42762254 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
* * *
42762282 CGCACACTTAGTGCCACATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
* **
42762309 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAACT
*
42762336 CGCACACTTAGTGCAACATAGTCGAA-T
1 CGCACACTTAGTGCTACATAGTC-AACT
42762363 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
42762378 GTACAATTTA
Statistics
Matches: 131, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
26 1 0.01
27 104 0.79
28 26 0.20
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:42762339 original size:82 final size:81
Alignment explanation
Indices: 42762221--42762376 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
42762211 TGCTATATAA
* *
42762221 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
42762286 CACTTAGTGCCACATGG
65 CACTTAGTGCCACATGG
* * ** *
42762303 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
42762367 CACTTAGTGC
65 CACTTAGTGC
42762377 TGTACAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 16 0.24
82 50 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCACATGG
Found at i:42762941 original size:13 final size:13
Alignment explanation
Indices: 42762923--42762947 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42762913 TACTAAATTT
42762923 TCATGGATTCAAG
1 TCATGGATTCAAG
42762936 TCATGGATTCAA
1 TCATGGATTCAA
42762948 TATACCATTA
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:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TCATGGATTCAAG
Found at i:42784379 original size:27 final size:27
Alignment explanation
Indices: 42784349--42784526 Score: 198
Period size: 27 Copynumber: 6.6 Consensus size: 27
42784339 ATATTGAGCC
* * *
42784349 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
* * *
42784376 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAACT
42784403 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
* * *
42784431 CGCACACTTAGTGCCACATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
* **
42784458 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAACT
*
42784485 CGCACACTTAGTGCAACATAGTCGAA-T
1 CGCACACTTAGTGCTACATAGTC-AACT
42784512 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
42784527 GTACAATTTA
Statistics
Matches: 131, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
26 1 0.01
27 104 0.79
28 26 0.20
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:42784488 original size:82 final size:81
Alignment explanation
Indices: 42784370--42784525 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
42784360 TGCTATATAA
* *
42784370 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
42784435 CACTTAGTGCCACATGG
65 CACTTAGTGCCACATGG
* * ** *
42784452 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
42784516 CACTTAGTGC
65 CACTTAGTGC
42784526 TGTACAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 16 0.24
82 50 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCACATGG
Found at i:42785090 original size:13 final size:13
Alignment explanation
Indices: 42785072--42785096 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42785062 TACTAAATTT
42785072 TCATGGATTCAAG
1 TCATGGATTCAAG
42785085 TCATGGATTCAA
1 TCATGGATTCAA
42785097 TATACCATTA
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:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TCATGGATTCAAG
Found at i:42791937 original size:26 final size:22
Alignment explanation
Indices: 42791908--42791955 Score: 60
Period size: 26 Copynumber: 2.0 Consensus size: 22
42791898 AGTTGTAGAG
42791908 AGAAAATTCTCTGAAGAGATTATTTT
1 AGAAAATT-TCT--AGAGA-TATTTT
42791934 AGAAAATTTCTAGAGATATTTT
1 AGAAAATTTCTAGAGATATTTT
42791956 TTGGATTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 6 0.27
23 5 0.23
25 3 0.14
26 8 0.36
ACGTcount: A:0.40, C:0.06, G:0.15, T:0.40
Consensus pattern (22 bp):
AGAAAATTTCTAGAGATATTTT
Found at i:42795311 original size:18 final size:19
Alignment explanation
Indices: 42795281--42795317 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
42795271 ATCACTGTCA
42795281 CCCACCGTAATCAAATTTG
1 CCCACCGTAATCAAATTTG
42795300 CCCACC-TAATCAAATTTG
1 CCCACCGTAATCAAATTTG
42795318 TTATTAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.32, C:0.32, G:0.08, T:0.27
Consensus pattern (19 bp):
CCCACCGTAATCAAATTTG
Done.