Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 130 of 198
Found at i:41371804 original size:6 final size:6
Alignment explanation
Indices: 41371793--41371819 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
41371783 ATGCCCCCCA
41371793 TTCATT TTCATT TTCATT TTCATT TTC
1 TTCATT TTCATT TTCATT TTCATT TTC
41371820 TTATTTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.19, G:0.00, T:0.67
Consensus pattern (6 bp):
TTCATT
Found at i:41372164 original size:17 final size:17
Alignment explanation
Indices: 41372142--41372177 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
41372132 GTAATCCCCC
41372142 TTAAGTGAAATAATAAG
1 TTAAGTGAAATAATAAG
*
41372159 TTAAGTGATATAATAAG
1 TTAAGTGAAATAATAAG
41372176 TT
1 TT
41372178 GGGCTCTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.17, T:0.36
Consensus pattern (17 bp):
TTAAGTGAAATAATAAG
Found at i:41378427 original size:50 final size:50
Alignment explanation
Indices: 41378311--41378549 Score: 214
Period size: 50 Copynumber: 4.7 Consensus size: 50
41378301 GATAATAACA
* * * ** * * *
41378311 TGCCAAAGCCATGTCTCAGACATGTTCTTACATGGGATGTTTCTTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGG
* * **
41378360 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * ** *
41378410 TTCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
*
41378460 TGCCAATGCCATGTCCCTA-ACATGGTCTTACATGGGACCTCTCATAACTTCAATGA
1 TGCCAATGCCATGTCCC-AGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
*
41378516 TGCCAATGTCATGTCCCAGACATGGTCTTACATG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATG
41378550 AGATCTCTTT
Statistics
Matches: 154, Mismatches: 26, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
48 1 0.01
49 37 0.24
50 80 0.52
51 1 0.01
53 2 0.01
55 1 0.01
56 32 0.21
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.30
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:41380293 original size:12 final size:12
Alignment explanation
Indices: 41380267--41380300 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
41380257 TAATGATACA
41380267 AATAGTAAC-AT
1 AATAGTAACAAT
41380278 AATAGTAACAAT
1 AATAGTAACAAT
*
41380290 AATAATAACAA
1 AATAGTAACAA
41380301 CAAAAGCCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.62, C:0.09, G:0.06, T:0.24
Consensus pattern (12 bp):
AATAGTAACAAT
Found at i:41388837 original size:87 final size:87
Alignment explanation
Indices: 41388691--41388870 Score: 324
Period size: 87 Copynumber: 2.1 Consensus size: 87
41388681 TTACTCCATT
* *
41388691 AATATTGGACAGAATATTTACCTTACTAAAAATCTATTATTTATACCAAACAACAAATAATGTTT
1 AATATTGGACAGAATATTTACCCTACTAAAAATCTATTATTTATACCAAACAACAAATAATATTT
41388756 AAGAATATTTTTATTTGAAATA
66 AAGAATATTTTTATTTGAAATA
*
41388778 AATATTGGACAGAATATTTACCCTACTAAAAATCTATTATTTATACCAAACAATAAATAATATTT
1 AATATTGGACAGAATATTTACCCTACTAAAAATCTATTATTTATACCAAACAACAAATAATATTT
41388843 AAGAATATTTTTATTTGAAATA
66 AAGAATATTTTTATTTGAAATA
*
41388865 ATTATT
1 AATATT
41388871 ATTTTAAAGA
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 89 1.00
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.39
Consensus pattern (87 bp):
AATATTGGACAGAATATTTACCCTACTAAAAATCTATTATTTATACCAAACAACAAATAATATTT
AAGAATATTTTTATTTGAAATA
Found at i:41397769 original size:42 final size:43
Alignment explanation
Indices: 41397712--41397827 Score: 153
Period size: 43 Copynumber: 2.7 Consensus size: 43
41397702 TCAAATATCA
* * *
41397712 ATGCCACTGTCCCAGACAAGGTCTTACATGAAATC-ATATAAG
1 ATGCCAATGTCCCAGACATGGTCTTACACGAAATCTATATAAG
* * * **
41397754 ATGCCGATGTCCCAGACATGGTCTTACACGTAATCTCTATTCG
1 ATGCCAATGTCCCAGACATGGTCTTACACGAAATCTATATAAG
41397797 ATGCCAATGTCCCAGACATGGTCTTACACGA
1 ATGCCAATGTCCCAGACATGGTCTTACACGA
41397828 TATCACATCT
Statistics
Matches: 63, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
42 30 0.48
43 33 0.52
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGAAATCTATATAAG
Found at i:41399339 original size:33 final size:34
Alignment explanation
Indices: 41399254--41399348 Score: 108
Period size: 33 Copynumber: 2.9 Consensus size: 34
41399244 CAGTCCAATA
41399254 CCACCGCAGTACAACACTCCTC-CCGGCTCGTAT
1 CCACCGCAGTACAACACTCCTCTCCGGCTCGTAT
* * * * *
41399287 CTATCGCATTAC-TCTACTCCTCTCTGG-TCGTAT
1 CCACCGCAGTACAAC-ACTCCTCTCCGGCTCGTAT
41399320 CCACCGCAGTACAACACTCCTCT-CGGCTC
1 CCACCGCAGTACAACACTCCTCTCCGGCTC
41399349 AAGTTCATCG
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
32 3 0.06
33 41 0.85
34 4 0.08
ACGTcount: A:0.19, C:0.42, G:0.14, T:0.25
Consensus pattern (34 bp):
CCACCGCAGTACAACACTCCTCTCCGGCTCGTAT
Found at i:41399760 original size:48 final size:48
Alignment explanation
Indices: 41399618--41399752 Score: 218
Period size: 48 Copynumber: 2.8 Consensus size: 48
41399608 AGATTAATTG
* **
41399618 CAACACTAAAACTTGGAACAAACTTTGTGGTCATAAATTAAATACATTA
1 CAACATTAAAACTTGGAACAAACTTTGTAAT-ATAAATTAAATACATTA
41399667 CAACATTAAAA-TTGGAACAAACTTTGTAATATAAATTAAATACATTA
1 CAACATTAAAACTTGGAACAAACTTTGTAATATAAATTAAATACATTA
*
41399714 CAACATTAAAACTTAGAACAAACTTTGTAATATAAATTA
1 CAACATTAAAACTTGGAACAAACTTTGTAATATAAATTA
41399753 GGTACATTGG
Statistics
Matches: 81, Mismatches: 4, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
47 28 0.35
48 43 0.53
49 10 0.12
ACGTcount: A:0.49, C:0.13, G:0.07, T:0.30
Consensus pattern (48 bp):
CAACATTAAAACTTGGAACAAACTTTGTAATATAAATTAAATACATTA
Found at i:41405130 original size:16 final size:16
Alignment explanation
Indices: 41405106--41405136 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41405096 AGATTAAGTA
41405106 AAAAATAAAAAAAATC
1 AAAAATAAAAAAAATC
*
41405122 AAAATTAAAAAAAAT
1 AAAAATAAAAAAAAT
41405137 TGTAATTACA
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:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (16 bp):
AAAAATAAAAAAAATC
Found at i:41406080 original size:14 final size:13
Alignment explanation
Indices: 41406058--41406100 Score: 52
Period size: 14 Copynumber: 3.3 Consensus size: 13
41406048 AACAAGTGAG
*
41406058 GAAAAAGAAAAAT
1 GAAAGAGAAAAAT
41406071 GAGAAGAGAAAAAT
1 GA-AAGAGAAAAAT
*
41406085 GAAAGTGAAAAA-
1 GAAAGAGAAAAAT
41406097 GAAA
1 GAAA
41406101 TTGAAAGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 4 0.15
13 11 0.41
14 12 0.44
ACGTcount: A:0.70, C:0.00, G:0.23, T:0.07
Consensus pattern (13 bp):
GAAAGAGAAAAAT
Found at i:41406094 original size:13 final size:13
Alignment explanation
Indices: 41406064--41406106 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 13
41406054 TGAGGAAAAA
*
41406064 GAAAAATGAGAAGA
1 GAAAAATGA-AAGT
41406078 GAAAAATGAAAGT
1 GAAAAATGAAAGT
*
41406091 GAAAAA-GAAATT
1 GAAAAATGAAAGT
41406103 GAAA
1 GAAA
41406107 GAAAAGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
12 9 0.33
13 9 0.33
14 9 0.33
ACGTcount: A:0.65, C:0.00, G:0.23, T:0.12
Consensus pattern (13 bp):
GAAAAATGAAAGT
Found at i:41406100 original size:33 final size:33
Alignment explanation
Indices: 41406058--41406132 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 33
41406048 AACAAGTGAG
* *
41406058 GAAAAAGAAAAATG-AGAAGAGAAAAATGAAAGT
1 GAAAAAGAAAAATGAAGAAAAGAAAAAT-AAAAT
*
41406091 GAAAAAG-AAATTGAAAGAAAAGAAAAATAAAAT
1 GAAAAAGAAAAATG-AAGAAAAGAAAAATAAAAT
41406124 GAAAAAGAA
1 GAAAAAGAA
41406133 GAAGAGGAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
32 5 0.14
33 18 0.50
34 13 0.36
ACGTcount: A:0.71, C:0.00, G:0.20, T:0.09
Consensus pattern (33 bp):
GAAAAAGAAAAATGAAGAAAAGAAAAATAAAAT
Found at i:41406115 original size:21 final size:21
Alignment explanation
Indices: 41406091--41406135 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
41406081 AAATGAAAGT
*
41406091 GAAAAAGAAATTGAAAGAA-AA
1 GAAAAAGAAAATGAAA-AAGAA
*
41406112 GAAAAATAAAATGAAAAAGAA
1 GAAAAAGAAAATGAAAAAGAA
41406133 GAA
1 GAA
41406136 GAGGAAAGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.09
Consensus pattern (21 bp):
GAAAAAGAAAATGAAAAAGAA
Found at i:41406129 original size:12 final size:12
Alignment explanation
Indices: 41406078--41406132 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
41406068 AATGAGAAGA
*
41406078 GAAAAATGAAAGT
1 GAAAAA-GAAAAT
*
41406091 GAAAAAGAAATT
1 GAAAAAGAAAAT
41406103 G--AAAGAAAA-
1 GAAAAAGAAAAT
*
41406112 GAAAAATAAAAT
1 GAAAAAGAAAAT
41406124 GAAAAAGAA
1 GAAAAAGAA
41406133 GAAGAGGAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
9 1 0.03
10 7 0.20
11 7 0.20
12 14 0.40
13 6 0.17
ACGTcount: A:0.71, C:0.00, G:0.18, T:0.11
Consensus pattern (12 bp):
GAAAAAGAAAAT
Found at i:41411686 original size:4 final size:4
Alignment explanation
Indices: 41411677--41411716 Score: 62
Period size: 4 Copynumber: 9.8 Consensus size: 4
41411667 AAAAATACAT
*
41411677 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTCTC ATTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT-TC TTTC TTT
41411717 TCTTCCTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
4 30 0.91
5 3 0.09
ACGTcount: A:0.03, C:0.25, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTC
Found at i:41411993 original size:13 final size:13
Alignment explanation
Indices: 41411975--41412013 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
41411965 ATGTTTTTTT
41411975 TTCATAAAAAATA
1 TTCATAAAAAATA
*
41411988 TTCATAAAAAATC
1 TTCATAAAAAATA
41412001 TT--TAAAAAATA
1 TTCATAAAAAATA
41412012 TT
1 TT
41412014 AAAATTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 10 0.42
13 14 0.58
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (13 bp):
TTCATAAAAAATA
Found at i:41412037 original size:17 final size:17
Alignment explanation
Indices: 41411994--41412037 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
41411984 AATATTCATA
*
41411994 AAAAATCTTTAAAAAAT
1 AAAAATATTTAAAAAAT
*
41412011 ATTAAA-ATTTAAAAAAT
1 A-AAAATATTTAAAAAAT
41412028 AAAAATATTT
1 AAAAATATTT
41412038 TAATTATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
16 3 0.14
17 16 0.73
18 3 0.14
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAAATATTTAAAAAAT
Found at i:41412042 original size:23 final size:25
Alignment explanation
Indices: 41412005--41412052 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
41411995 AAAATCTTTA
41412005 AAAAATATTAAAATT-TA-AAAAAT
1 AAAAATATTAAAATTATATAAAAAT
**
41412028 AAAAATATTTTAATTATATAAAAAT
1 AAAAATATTAAAATTATATAAAAAT
41412053 TTCAAAATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 13 0.62
24 2 0.10
25 6 0.29
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (25 bp):
AAAAATATTAAAATTATATAAAAAT
Found at i:41413553 original size:3 final size:3
Alignment explanation
Indices: 41413545--41413575 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
41413535 GGATGAACGG
41413545 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
41413576 TAGAGAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:41422803 original size:21 final size:22
Alignment explanation
Indices: 41422774--41422820 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
41422764 CAGAAGGAGT
*
41422774 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
41422796 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
41422817 GAGT
1 GAGT
41422821 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:41426246 original size:10 final size:10
Alignment explanation
Indices: 41426227--41426256 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
41426217 TTACAGTGAA
*
41426227 CCAAACGTTT
1 CCAAAAGTTT
41426237 CCAAAAGTTT
1 CCAAAAGTTT
41426247 CCAAAAGTTT
1 CCAAAAGTTT
41426257 TAAGCGGGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.37, C:0.23, G:0.10, T:0.30
Consensus pattern (10 bp):
CCAAAAGTTT
Found at i:41434946 original size:28 final size:28
Alignment explanation
Indices: 41434915--41434972 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
41434905 TTTTAGGCCC
41434915 AATCTCAAACAAAATGAAAAAGATGAAA
1 AATCTCAAACAAAATGAAAAAGATGAAA
41434943 AATCTCAAACAAAATGAAAAAGATGAAA
1 AATCTCAAACAAAATGAAAAAGATGAAA
41434971 AA
1 AA
41434973 AAATTCGGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.66, C:0.10, G:0.10, T:0.14
Consensus pattern (28 bp):
AATCTCAAACAAAATGAAAAAGATGAAA
Found at i:41440695 original size:91 final size:89
Alignment explanation
Indices: 41440596--41440855 Score: 285
Period size: 92 Copynumber: 2.9 Consensus size: 89
41440586 CTCTCAAATT
* * **
41440596 TTTTAAAAAAAAAAGCAATTAAGC-CC-CTTTTTTTTGCATTCAATTTGGTACTTGAACTTTTAA
1 TTTTAAAAAAAAAAGCAATTAAGCACCGCTTTTTTTTGCACTCAATTAGGTACTTGAACTGCTAA
*
41440659 AATGCATAAAAAAAAGGCCCTCAGAC
66 AATGCATAAAAAAAA--CCCTCAAAC
* * * * *
41440685 GTTTT-CAAAAAAAAGTAATTAAGCTCCTGCTTTTTTTTTCACTCAATTAGGTACTTGAACTGCC
1 -TTTTAAAAAAAAAAGCAATTAAGCACC-GCTTTTTTTTGCACTCAATTAGGTACTTGAACTGCT
* *
41440749 AAAATGCATCAAAAAAACTCTCAAAC
64 AAAATGCATAAAAAAAACCCTCAAAC
* *
41440775 -TTTAAAAAAAAAAGCAATTAAGCACCTGCTTGTTTTTTTGCACTCAATTGGGTACTTAAACTGC
1 TTTTAAAAAAAAAAGCAATTAAGCACC-GC-T-TTTTTTTGCACTCAATTAGGTACTTGAACTGC
* *
41440839 TAAAATGTATTAAAAAA
63 TAAAATGCATAAAAAAA
41440856 GGCTAGGGGC
Statistics
Matches: 144, Mismatches: 20, Indels: 11
0.82 0.11 0.06
Matches are distributed among these distances:
88 3 0.02
89 39 0.27
90 14 0.10
91 43 0.30
92 45 0.31
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (89 bp):
TTTTAAAAAAAAAAGCAATTAAGCACCGCTTTTTTTTGCACTCAATTAGGTACTTGAACTGCTAA
AATGCATAAAAAAAACCCTCAAAC
Found at i:41440739 original size:92 final size:88
Alignment explanation
Indices: 41440597--41440855 Score: 297
Period size: 89 Copynumber: 2.9 Consensus size: 88
41440587 TCTCAAATTT
* * * **
41440597 TTTAAAAAAAAAAGCAATTAAGCCC--CTTTTTTTTGCATTCAATTTGGTACTTGAACTTTTAAA
1 TTTAAAAAAAAAAGCAATTAAGCCCTGCTTTTTTTTTCACTCAATTAGGTACTTGAACTGCTAAA
*
41440660 ATGCATAAAAAAAAGGCCCTCAGAC
66 ATGCATAAAAAAAA--CCCTCAAAC
** * *
41440685 GTTTTCAAAAAAAAGTAATTAAGCTCCTGCTTTTTTTTTCACTCAATTAGGTACTTGAACTGCCA
1 -TTTAAAAAAAAAAGCAATTAAGC-CCTGCTTTTTTTTTCACTCAATTAGGTACTTGAACTGCTA
* *
41440750 AAATGCATCAAAAAAACTCTCAAAC
64 AAATGCATAAAAAAAACCCTCAAAC
* *
41440775 TTTAAAAAAAAAAGCAATTAAGCACCTGCTTGTTTTTTTGCACTCAATTGGGTACTTAAACTGCT
1 TTTAAAAAAAAAAGCAATTAAGC-CCTGCTT-TTTTTTT-CACTCAATTAGGTACTTGAACTGCT
* *
41440840 AAAATGTATTAAAAAA
63 AAAATGCATAAAAAAA
41440856 GGCTAGGGGC
Statistics
Matches: 144, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
89 47 0.33
90 16 0.11
91 36 0.25
92 45 0.31
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.32
Consensus pattern (88 bp):
TTTAAAAAAAAAAGCAATTAAGCCCTGCTTTTTTTTTCACTCAATTAGGTACTTGAACTGCTAAA
ATGCATAAAAAAAACCCTCAAAC
Found at i:41441105 original size:88 final size:84
Alignment explanation
Indices: 41440883--41441104 Score: 243
Period size: 88 Copynumber: 2.6 Consensus size: 84
41440873 GGGGGTTGGC
* *
41440883 AGTTCAAGCACCCAATTGAGTGCAAAAAAAA-GGACTTAATTATTTTTTTTAAAAGTTTAAGGGT
1 AGTTCAAGTACCCAATTGAGTGCAAAAAAAAGGGACTTAATTATTTTTTTTAAAAGTCTAAGGGT
* **
41440947 GTTTTTTATTCATTTTGGC
66 GTTTTTTATGCATTTTGAA
* * * *
41440966 AGTTCAAGTATCCAATTGAGTG-AAGAAAATGTAAGGG-CTTAATCATTTTTTTGAAAAAGTCTG
1 AGTTCAAGTACCCAATTGAGTGCAA-AAAA---AAGGGACTTAATTATTTTTTT-TAAAAGTCTA
*
41441029 AGGGCTTTTTTTTATGCATTTTGAA
61 AGGG-TGTTTTTTATGCATTTTGAA
* * * *
41441054 AGTTTAAGTACCCAATTGAGCGCAAAAAAAAGGGACCTAATTGTTTTTTTT
1 AGTTCAAGTACCCAATTGAGTGCAAAAAAAAGGGACTTAATTATTTTTTTT
41441105 TTTTAAGTTT
Statistics
Matches: 113, Mismatches: 17, Indels: 16
0.77 0.12 0.11
Matches are distributed among these distances:
82 2 0.02
83 24 0.21
85 5 0.04
86 28 0.25
87 13 0.12
88 39 0.35
89 2 0.02
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (84 bp):
AGTTCAAGTACCCAATTGAGTGCAAAAAAAAGGGACTTAATTATTTTTTTTAAAAGTCTAAGGGT
GTTTTTTATGCATTTTGAA
Found at i:41448180 original size:6 final size:6
Alignment explanation
Indices: 41448171--41448198 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
41448161 TGATTTAAAT
41448171 TTAATA TTAATA TTAATA TTAATA TTAA
1 TTAATA TTAATA TTAATA TTAATA TTAA
41448199 ATAAAAATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TTAATA
Found at i:41448351 original size:23 final size:22
Alignment explanation
Indices: 41448299--41448353 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
41448289 TTATATAAAA
41448299 TTTAAATTTATTATTATATTTT
1 TTTAAATTTATTATTATATTTT
* *
41448321 TTGAAAATATTTTTA-TATATTTCT
1 TT-TAAAT-TTATTATTATATTT-T
41448345 TTTAAATTT
1 TTTAAATTT
41448354 TCAGAATTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
22 4 0.15
23 15 0.56
24 8 0.30
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (22 bp):
TTTAAATTTATTATTATATTTT
Found at i:41453722 original size:28 final size:28
Alignment explanation
Indices: 41453682--41453744 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 28
41453672 TGCTTGGAAG
41453682 AACTACAAGGAATTTTATGAGCCTTGCA
1 AACTACAAGGAATTTTATGAGCCTTGCA
*
41453710 AACTACAAGGAATTTTATGAGCCTTGCG
1 AACTACAAGGAATTTTATGAGCCTTGCA
41453738 AACTACA
1 AACTACA
41453745 CCTCACTCTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (28 bp):
AACTACAAGGAATTTTATGAGCCTTGCA
Found at i:41454898 original size:57 final size:57
Alignment explanation
Indices: 41454808--41454961 Score: 202
Period size: 57 Copynumber: 2.7 Consensus size: 57
41454798 ACAATCCTCT
* * *
41454808 AAAATTTTTTAAGTATAAAAAAGTTCGCGGAGTCACATTCCCAACTTATTACTTTAG
1 AAAATTTTCTAAGTATAAAAAAGTTCGCAGAGTCACATTCCCAACATATTACTTTAG
* * * *
41454865 AAAATTTTCTAAGTATAAAAAAGTTTGCAGAGTCACTTTCCCAGCATATTATTTTAG
1 AAAATTTTCTAAGTATAAAAAAGTTCGCAGAGTCACATTCCCAACATATTACTTTAG
* * *
41454922 AAAATTTTCCAAGTATAAAATAGCTCGCAGA-TCCACATTC
1 AAAATTTTCTAAGTATAAAAAAGTTCGCAGAGT-CACATTC
41454962 GCAGTTGATG
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
56 1 0.01
57 83 0.99
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.34
Consensus pattern (57 bp):
AAAATTTTCTAAGTATAAAAAAGTTCGCAGAGTCACATTCCCAACATATTACTTTAG
Found at i:41454976 original size:57 final size:57
Alignment explanation
Indices: 41454808--41454986 Score: 173
Period size: 57 Copynumber: 3.1 Consensus size: 57
41454798 ACAATCCTCT
** * * * * * *
41454808 AAAATTTTTTAAGTATAAAAAAGTTCGCGGAGTCACATTCCCAACTTATTACTTTAG
1 AAAATTTTCCAAGTATAAAAAAGCTCGCAGAGTCACATTCCCAGCATATGATTTTAG
* * * * *
41454865 AAAATTTTCTAAGTATAAAAAAGTTTGCAGAGTCACTTTCCCAGCATATTATTTTAG
1 AAAATTTTCCAAGTATAAAAAAGCTCGCAGAGTCACATTCCCAGCATATGATTTTAG
* * *
41454922 AAAATTTTCCAAGTATAAAATAGCTCGCAGA-TCCACATTCGCAG-TTGATGATTTTAG
1 AAAATTTTCCAAGTATAAAAAAGCTCGCAGAGT-CACATTCCCAGCAT-ATGATTTTAG
*
41454979 AATATTTT
1 AAAATTTT
41454987 ACTTAAAGCC
Statistics
Matches: 104, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
56 2 0.02
57 102 0.98
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (57 bp):
AAAATTTTCCAAGTATAAAAAAGCTCGCAGAGTCACATTCCCAGCATATGATTTTAG
Found at i:41472342 original size:2 final size:2
Alignment explanation
Indices: 41472335--41472375 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
41472325 AAAGAATGAA
41472335 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
41472376 AAAGAAAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:41473496 original size:14 final size:14
Alignment explanation
Indices: 41473477--41473503 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41473467 TTAAGTTTTT
41473477 AATTTCACTCGAAC
1 AATTTCACTCGAAC
41473491 AATTTCACTCGAA
1 AATTTCACTCGAA
41473504 TTCGAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.26, G:0.07, T:0.30
Consensus pattern (14 bp):
AATTTCACTCGAAC
Found at i:41477435 original size:37 final size:37
Alignment explanation
Indices: 41477385--41477459 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
41477375 CGAGAACATT
41477385 GAATTCACTCGTCTAAGCCTCCCCCTACGCCCAAATC
1 GAATTCACTCGTCTAAGCCTCCCCCTACGCCCAAATC
41477422 GAATTCACTCGTCTAAGCCTCCCCCTACGCCCAAATC
1 GAATTCACTCGTCTAAGCCTCCCCCTACGCCCAAATC
41477459 G
1 G
41477460 CAGAGGAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.43, G:0.12, T:0.21
Consensus pattern (37 bp):
GAATTCACTCGTCTAAGCCTCCCCCTACGCCCAAATC
Found at i:41483854 original size:37 final size:37
Alignment explanation
Indices: 41483804--41483878 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
41483794 GATACCAAAG
41483804 AAGGTTTTTCGCATACAAGATAAAAGTAAGAGATCTT
1 AAGGTTTTTCGCATACAAGATAAAAGTAAGAGATCTT
41483841 AAGGTTTTTCGCATACAAGATAAAAGTAAGAGATCTT
1 AAGGTTTTTCGCATACAAGATAAAAGTAAGAGATCTT
41483878 A
1 A
41483879 TGTGGGAAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.29
Consensus pattern (37 bp):
AAGGTTTTTCGCATACAAGATAAAAGTAAGAGATCTT
Found at i:41483985 original size:15 final size:16
Alignment explanation
Indices: 41483959--41484000 Score: 63
Period size: 15 Copynumber: 2.8 Consensus size: 16
41483949 GTTCAGATCC
41483959 AATCCAAAAAAATCAA
1 AATCCAAAAAAATCAA
41483975 AATCC-AAAAAATCAA
1 AATCCAAAAAAATCAA
41483990 AAT--AAAAAAAT
1 AATCCAAAAAAAT
41484001 GAGAGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 7 0.28
15 13 0.52
16 5 0.20
ACGTcount: A:0.71, C:0.14, G:0.00, T:0.14
Consensus pattern (16 bp):
AATCCAAAAAAATCAA
Found at i:41484925 original size:13 final size:13
Alignment explanation
Indices: 41484907--41484936 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
41484897 TTTGAGTCAA
41484907 AAAATGAAAAATG
1 AAAATGAAAAATG
41484920 AAAATGAAAAATG
1 AAAATGAAAAATG
41484933 AAAA
1 AAAA
41484937 AATGAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.13
Consensus pattern (13 bp):
AAAATGAAAAATG
Found at i:41484946 original size:8 final size:7
Alignment explanation
Indices: 41484906--41484945 Score: 64
Period size: 7 Copynumber: 5.7 Consensus size: 7
41484896 CTTTGAGTCA
41484906 AAAAATG
1 AAAAATG
41484913 AAAAATG
1 AAAAATG
41484920 -AAAATG
1 AAAAATG
41484926 AAAAATG
1 AAAAATG
41484933 AAAAAATG
1 -AAAAATG
41484941 AAAAA
1 AAAAA
41484946 AATTAAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.19
7 18 0.58
8 7 0.23
ACGTcount: A:0.75, C:0.00, G:0.12, T:0.12
Consensus pattern (7 bp):
AAAAATG
Found at i:41486437 original size:129 final size:129
Alignment explanation
Indices: 41486207--41486693 Score: 823
Period size: 129 Copynumber: 3.8 Consensus size: 129
41486197 GTGAAGATAG
* *
41486207 CAGATCTTTTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGTGAATCTTATCTTCAAGTGTA
1 CAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGAGAATCTTATCTTCAAGTGTA
*
41486272 AGGAAGCAGATTTAAGCCACAAGTCTTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAAATTA
66 AGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAAATTA
* * *
41486336 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGAGAATCTTATCTTCAAGTTTA
1 CAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGAGAATCTTATCTTCAAGTGTA
*
41486401 AGGAAGCAGATTTAAACCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAAATTA
66 AGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAAATTA
41486465 CAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGAC-GACGAATCTTATCTTCAAGTGT
1 CAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGA-GAATCTTATCTTCAAGTGT
* ** *
41486529 AAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTCGTCAGTTGTGGAATAGGTTAGGAAATTA
65 AAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAAATTA
* *
41486594 CAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGTGAATCTTATCTTCAAGTGTA
1 CAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGAGAATCTTATCTTCAAGTGTA
* *
41486659 AGGAAGCAGATTTAAGCCACAAATCCTATCTCCCT
66 AGGAAGCAGATTTAAGCCACAAGTCCTATATCCCT
41486694 AAAGTTGTAG
Statistics
Matches: 338, Mismatches: 18, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
128 2 0.01
129 335 0.99
130 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (129 bp):
CAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGAGAATCTTATCTTCAAGTGTA
AGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAAATTA
Found at i:41486909 original size:44 final size:43
Alignment explanation
Indices: 41486854--41487224 Score: 273
Period size: 44 Copynumber: 8.6 Consensus size: 43
41486844 GAAGATGGCA
* *
41486854 AATCTTATCTCCCTGAGGTTGCAGTGGAGCAAATTGAAGCCGAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-CGAT
* * * * **
41486898 AATCTTTTCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCGAT
* ** ** * **
41486941 AGATCTTATCTCTCTGAAGTTGCAGTAAAGTGGATTGCA-TTA-
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCGAT
* *
41486983 AATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCCGGT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-CGAT
* * * * **
41487027 AATCCTATCTCCCTAAAGTTGTAGTGGAGCAGATTAAAGTAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCGAT
* * * * ** * * **
41487070 AGATTTTATCTCTCTAAAGTTGCAGTAGAGTGGATCGCA-TTA-
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCGAT
*
41487112 AATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGTCGAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-CGAT
* * * * * **
41487156 AATCCTATCTCCCTGAAGTTGTAGTGAAGCGGATTAAAGTAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCGAT
*
41487199 AGATCTTATCTCTCTGAAGTTGCAGT
1 A-ATCTTATCTCCCTGAAGTTGCAGT
41487225 AGAGTGGATC
Statistics
Matches: 250, Mismatches: 68, Indels: 18
0.74 0.20 0.05
Matches are distributed among these distances:
41 58 0.23
42 2 0.01
43 13 0.05
44 177 0.71
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (43 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCGAT
Found at i:41487009 original size:85 final size:85
Alignment explanation
Indices: 41486855--41487270 Score: 264
Period size: 85 Copynumber: 4.8 Consensus size: 85
41486845 AAGATGGCAA
* * * * ** * *
41486855 ATCTTATCTCCCTGAGGTTGCAGTGGAGCAAATTGAAGCCGATAATCTTTTCTCCCTGAAGTTGT
1 ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGCA--TTA-AATCTTATCTCCCTGAAGTTGC
*
41486920 AGTGGAGCGGATTAAAGTAATAG
63 AGTGGAGCGGATTAAAGCAATAG
* * ** *
41486943 ATCTTATCTCTCTGAAGTTGCAGTAAAGTGGATTGCATTAAATCTTATCTCCCTGAGGTTGCAGT
1 ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGCATTAAATCTTATCTCCCTGAAGTTGCAGT
* * **
41487008 GGAGCAGATTGAAGCCGGTA-
66 GGAGCGGATTAAAG-CAATAG
* * * * * * * * * *
41487028 ATCCTATCTCCCTAAAGTTGTAGTGGAGCAGATTAAAGTAATAGATTTTATCTCTCTAAAGTTGC
1 ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATT---GCATTAAATCTTATCTCCCTGAAGTTGC
* * * * *
41487093 AGTAGAGTGGA-T--CGCATTAA
63 AGTGGAGCGGATTAAAGCAATAG
* * * * * *
41487113 ATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGTCGATAATCCTATCTCCCTGAAGTTGT
1 ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGCA-T-TA-AATCTTATCTCCCTGAAGTTGC
* *
41487178 AGTGAAGCGGATTAAAGTAATAG
63 AGTGGAGCGGATTAAAGCAATAG
* ** * * ** * *
41487201 ATCTTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCATCAGGTTTTATCTCCCTGAGGTTGCAGT
1 ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGCATTAAATCTTATCTCCCTGAAGTTGCAGT
41487266 GGAGC
66 GGAGC
41487271 AGACTGAGAA
Statistics
Matches: 243, Mismatches: 74, Indels: 25
0.71 0.22 0.07
Matches are distributed among these distances:
82 2 0.01
84 4 0.02
85 138 0.57
86 5 0.02
87 2 0.01
88 92 0.38
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.31
Consensus pattern (85 bp):
ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGCATTAAATCTTATCTCCCTGAAGTTGCAGT
GGAGCGGATTAAAGCAATAG
Found at i:41487304 original size:129 final size:129
Alignment explanation
Indices: 41486853--41487273 Score: 698
Period size: 129 Copynumber: 3.3 Consensus size: 129
41486843 CGAAGATGGC
* * *
41486853 AAATCTTATCTCCCTGAGGTTGCAGTGGAGCAAATTGAAGCCGATAATCTTTTCTCCCTGAAGTT
1 AAATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTT
* *
41486918 GTAGTGGAGCGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTGCAGTAAAGTGGATTGCATT
66 GTAGTGGAGCGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCATT
* *
41486982 AAATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCCGGTAATCCTATCTCCCTAAAGTT
1 AAATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTT
* * *
41487047 GTAGTGGAGCAGATTAAAGTAATAGATTTTATCTCTCTAAAGTTGCAGTAGAGTGGATCGCATT
66 GTAGTGGAGCGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCATT
*
41487111 AAATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGTCGATAATCCTATCTCCCTGAAGTT
1 AAATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTT
* *
41487176 GTAGTGAAGCGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCATC
66 GTAGTGGAGCGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCATT
** *
41487240 AGGTTTTATCTCCCTGAGGTTGCAGTGGAGCAGA
1 AAATCTTATCTCCCTGAGGTTGCAGTGGAGCAGA
41487274 CTGAGAAGAC
Statistics
Matches: 271, Mismatches: 21, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
129 271 1.00
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (129 bp):
AAATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTT
GTAGTGGAGCGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCATT
Found at i:41494640 original size:15 final size:14
Alignment explanation
Indices: 41494619--41494654 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
41494609 ATAATCCTTA
*
41494619 ATAATTATCTTAAT
1 ATAATTATCCTAAT
41494633 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
41494648 ATAATTA
1 ATAATTA
41494655 AAATAGAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:41499160 original size:15 final size:17
Alignment explanation
Indices: 41499140--41499171 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
41499130 ACAAAATGAG
41499140 AATAA-TTAAT-ACAAA
1 AATAATTTAATCACAAA
41499155 AATAATTTAATCACAAA
1 AATAATTTAATCACAAA
41499172 TAAATCAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 5 0.33
17 5 0.33
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.28
Consensus pattern (17 bp):
AATAATTTAATCACAAA
Found at i:41499382 original size:20 final size:20
Alignment explanation
Indices: 41499338--41499382 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
41499328 GGTAAAAAAG
*
41499338 AATTTAAAATAATGTTGATA
1 AATTTAAAATAATGTGGATA
*
41499358 AATTT-AAATCATGTGGATA
1 AATTTAAAATAATGTGGATA
41499377 ATATTT
1 A-ATTT
41499383 TAGAAGAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.44, C:0.02, G:0.11, T:0.42
Consensus pattern (20 bp):
AATTTAAAATAATGTGGATA
Found at i:41509842 original size:16 final size:16
Alignment explanation
Indices: 41509820--41509863 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
41509810 TTTTTGTATT
41509820 ATTTTAATATAAAATA
1 ATTTTAATATAAAATA
* * *
41509836 CTTTTAAAATGAAATA
1 ATTTTAATATAAAATA
*
41509852 ATATTAATATAA
1 ATTTTAATATAA
41509864 TTAATTCTAA
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (16 bp):
ATTTTAATATAAAATA
Found at i:41511407 original size:33 final size:33
Alignment explanation
Indices: 41511370--41511452 Score: 78
Period size: 33 Copynumber: 2.5 Consensus size: 33
41511360 CATGGCAATG
* *
41511370 TTTAAATGTAAGACCATAGCTGGGCTATGACA-
1 TTTAAATGTAAGACCATAACTGAGCTATGACAC
* * * *
41511402 TTTTAATGAAAAGACCATAACTGAGTTATGGCAC
1 TTTAAATG-TAAGACCATAACTGAGCTATGACAC
**
41511436 TACAAATGTAAGACCAT
1 TTTAAATGTAAGACCAT
41511453 GGCAGGGTCA
Statistics
Matches: 39, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
32 7 0.18
33 27 0.69
34 5 0.13
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.28
Consensus pattern (33 bp):
TTTAAATGTAAGACCATAACTGAGCTATGACAC
Found at i:41516671 original size:21 final size:21
Alignment explanation
Indices: 41516641--41516683 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
41516631 TGGGTGGATT
*
41516641 AGCTCTTACGAGCTTCTCTTC
1 AGCTCCTACGAGCTTCTCTTC
*
41516662 AGCTCCTACGAGCTTCTGTTC
1 AGCTCCTACGAGCTTCTCTTC
41516683 A
1 A
41516684 ACTTTCGAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.33, G:0.16, T:0.35
Consensus pattern (21 bp):
AGCTCCTACGAGCTTCTCTTC
Found at i:41523136 original size:21 final size:21
Alignment explanation
Indices: 41523110--41523194 Score: 125
Period size: 21 Copynumber: 4.0 Consensus size: 21
41523100 TTGGTGGATT
**
41523110 AGCTCTTATGAGCTTCTGTTC
1 AGCTCTTACAAGCTTCTGTTC
41523131 AGCTCTTACAAGCTTCTGTTC
1 AGCTCTTACAAGCTTCTGTTC
*
41523152 AGCTCTTACAAGCTTCCGTTC
1 AGCTCTTACAAGCTTCTGTTC
**
41523173 AGCTCTTATGAGCTTCTGTTC
1 AGCTCTTACAAGCTTCTGTTC
41523194 A
1 A
41523195 ACTTTCGAGC
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 58 1.00
ACGTcount: A:0.18, C:0.27, G:0.16, T:0.39
Consensus pattern (21 bp):
AGCTCTTACAAGCTTCTGTTC
Found at i:41524083 original size:29 final size:30
Alignment explanation
Indices: 41524040--41524109 Score: 106
Period size: 29 Copynumber: 2.4 Consensus size: 30
41524030 GCGTGTGTCT
*
41524040 CAGCCGTGTGTAACGCACGGCCAAGTGAAA
1 CAGCCATGTGTAACGCACGGCCAAGTGAAA
*
41524070 -AGCCATGTGTAACGCATGGCCAAGTGAAA
1 CAGCCATGTGTAACGCACGGCCAAGTGAAA
*
41524099 CAGCCCTGTGT
1 CAGCCATGTGT
41524110 CCCCTATATC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 27 0.75
30 9 0.25
ACGTcount: A:0.29, C:0.26, G:0.29, T:0.17
Consensus pattern (30 bp):
CAGCCATGTGTAACGCACGGCCAAGTGAAA
Found at i:41524870 original size:20 final size:18
Alignment explanation
Indices: 41524823--41524880 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 18
41524813 TTTTCAAAAC
*
41524823 AATTTTAATTTGATTGAA
1 AATTTTAACTTGATTGAA
*
41524841 AATGTTTAACTCGATTGAA
1 AAT-TTTAACTTGATTGAA
41524860 ATCATTTTAACTTGATT-AA
1 A--ATTTTAACTTGATTGAA
41524879 AA
1 AA
41524881 GTTGATTCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
17 1 0.03
18 3 0.09
19 17 0.50
20 11 0.32
21 2 0.06
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (18 bp):
AATTTTAACTTGATTGAA
Found at i:41525418 original size:31 final size:31
Alignment explanation
Indices: 41525377--41525471 Score: 122
Period size: 31 Copynumber: 3.1 Consensus size: 31
41525367 TAATGCTTAT
* *
41525377 GTGACTAAAATGAAAGCACCCTAAAAGTTAG
1 GTGACCAAAATGAAAGCACCCTAAAAGTTGG
* **
41525408 GTGACCAAAATGAAAGCA-CCT-TATTTTGG
1 GTGACCAAAATGAAAGCACCCTAAAAGTTGG
*
41525437 GTGACCAAAATGAAAACACCCTAAAAGTTGG
1 GTGACCAAAATGAAAGCACCCTAAAAGTTGG
41525468 GTGA
1 GTGA
41525472 TCAACTAGGT
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
29 21 0.40
30 6 0.11
31 26 0.49
ACGTcount: A:0.41, C:0.17, G:0.21, T:0.21
Consensus pattern (31 bp):
GTGACCAAAATGAAAGCACCCTAAAAGTTGG
Found at i:41538388 original size:2 final size:2
Alignment explanation
Indices: 41538378--41538423 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
41538368 AAATGTTAAT
*
41538378 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41538420 TA TA
1 TA TA
41538424 GTAAACTACT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:41547510 original size:33 final size:33
Alignment explanation
Indices: 41547452--41547528 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 33
41547442 TGAGTATGGC
* *
41547452 CGTGTGGG-CCACACGGGCTACGCCAAAT-TGGG
1 CGTGTGGGCCCACACGAGCAACGCC-AATCTGGG
*
41547484 CGTGTGGGCCCACACGAGCAAGGCCAATCTGGG
1 CGTGTGGGCCCACACGAGCAACGCCAATCTGGG
*
41547517 CATGTGGGCCCA
1 CGTGTGGGCCCA
41547529 GGAATTTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
32 11 0.28
33 28 0.72
ACGTcount: A:0.19, C:0.30, G:0.36, T:0.14
Consensus pattern (33 bp):
CGTGTGGGCCCACACGAGCAACGCCAATCTGGG
Found at i:41547993 original size:13 final size:14
Alignment explanation
Indices: 41547955--41547995 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
41547945 ATGGGGGTAG
41547955 GATTCTGTATATCT
1 GATTCTGTATATCT
* *
41547969 G-TTCAGTTTATCT
1 GATTCTGTATATCT
41547982 GATTCTG-ATATCT
1 GATTCTGTATATCT
41547995 G
1 G
41547996 TATCTATTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
13 17 0.77
14 5 0.23
ACGTcount: A:0.20, C:0.15, G:0.17, T:0.49
Consensus pattern (14 bp):
GATTCTGTATATCT
Found at i:41548232 original size:18 final size:20
Alignment explanation
Indices: 41548193--41548234 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
41548183 AAAGAACTAT
*
41548193 TTTTATTTTAGTAATAATGG
1 TTTTATTTTAGAAATAATGG
41548213 TTTTATTTTA-AAAT-ATGG
1 TTTTATTTTAGAAATAATGG
41548231 TTTT
1 TTTT
41548235 TTTAGAGGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.38
19 3 0.14
20 10 0.48
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.60
Consensus pattern (20 bp):
TTTTATTTTAGAAATAATGG
Found at i:41548362 original size:14 final size:15
Alignment explanation
Indices: 41548343--41548372 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
41548333 ACTTTACGTA
41548343 AACAAATG-GTTTTT
1 AACAAATGAGTTTTT
41548357 AACAAATGAGTTTTT
1 AACAAATGAGTTTTT
41548372 A
1 A
41548373 GAAACACGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (15 bp):
AACAAATGAGTTTTT
Found at i:41554019 original size:12 final size:12
Alignment explanation
Indices: 41554002--41554026 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41553992 TACTCTTCCT
41554002 TCTTTTTCTTTC
1 TCTTTTTCTTTC
41554014 TCTTTTTCTTTC
1 TCTTTTTCTTTC
41554026 T
1 T
41554027 ATAACCTTTT
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:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TCTTTTTCTTTC
Found at i:41554551 original size:13 final size:13
Alignment explanation
Indices: 41554533--41554557 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41554523 GTGTGTTGGC
41554533 CCACATGGGCATG
1 CCACATGGGCATG
41554546 CCACATGGGCAT
1 CCACATGGGCAT
41554558 ATGGGTTTTA
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:0.24, C:0.32, G:0.28, T:0.16
Consensus pattern (13 bp):
CCACATGGGCATG
Found at i:41555230 original size:13 final size:13
Alignment explanation
Indices: 41555212--41555236 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41555202 GCGTGTTGGC
41555212 CCACACGGGCATG
1 CCACACGGGCATG
41555225 CCACACGGGCAT
1 CCACACGGGCAT
41555237 ATGGGTTTTG
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:0.24, C:0.40, G:0.28, T:0.08
Consensus pattern (13 bp):
CCACACGGGCATG
Found at i:41556116 original size:14 final size:15
Alignment explanation
Indices: 41556097--41556125 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
41556087 ACTTTACGCA
41556097 AACAAAT-GGTTTTT
1 AACAAATGGGTTTTT
41556111 AACAAATGGGTTTTT
1 AACAAATGGGTTTTT
41556126 GGAAACACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.41
Consensus pattern (15 bp):
AACAAATGGGTTTTT
Found at i:41557266 original size:18 final size:19
Alignment explanation
Indices: 41557251--41557301 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
41557241 AATATATAAT
41557251 TTTTAGAATTTTTATAAATA
1 TTTTA-AATTTTTATAAATA
*
41557271 TTTTAAA-TTTTAAAAATTA
1 TTTTAAATTTTTATAAA-TA
*
41557290 TTTTTAATTTTT
1 TTTTAAATTTTT
41557302 GAAATTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 8 0.30
19 10 0.37
20 9 0.33
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
TTTTAAATTTTTATAAATA
Found at i:41557281 original size:19 final size:20
Alignment explanation
Indices: 41557251--41557318 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
41557241 AATATATAAT
*
41557251 TTTTAGAATTTTTATAAA-TA
1 TTTTA-AATTTTTAAAAATTA
41557271 TTTTAAA-TTTTAAAAATTA
1 TTTTAAATTTTTAAAAATTA
* * *
41557290 TTTTTAATTTTTGAAATTTA
1 TTTTAAATTTTTAAAAATTA
*
41557310 TTTTGAATT
1 TTTTAAATT
41557319 ATTTTAAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
18 8 0.20
19 10 0.24
20 23 0.56
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (20 bp):
TTTTAAATTTTTAAAAATTA
Found at i:41557318 original size:20 final size:19
Alignment explanation
Indices: 41557257--41557329 Score: 60
Period size: 20 Copynumber: 3.7 Consensus size: 19
41557247 TAATTTTTAG
41557257 AATTTTTATAAA--TATTTT
1 AATTTTTA-AAATTTATTTT
* *
41557275 AAATTTTAAAAATTATTTTT
1 AATTTTTAAAATTTA-TTTT
*
41557295 AATTTTTGAAATTTATTTT
1 AATTTTTAAAATTTATTTT
*
41557314 GAATTATTTTAAATTT
1 -AATT-TTTAAAATTT
41557330 TTATTTAGAG
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
17 3 0.07
18 7 0.16
19 6 0.13
20 20 0.44
21 9 0.20
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (19 bp):
AATTTTTAAAATTTATTTT
Found at i:41566754 original size:30 final size:30
Alignment explanation
Indices: 41566688--41566855 Score: 134
Period size: 30 Copynumber: 5.7 Consensus size: 30
41566678 ATGCAAAAAA
* *
41566688 TAAAAATTACATTTTGACCCTTATACTTTT-
1 TAAAATTTACATTTTGACCC-TAAACTTTTC
* *
41566718 TGAAATTTGCATTTTGACCCTAAACTTTTC
1 TAAAATTTACATTTTGACCCTAAACTTTTC
**
41566748 TAAAA-TTACATTTCAACCCCTAAAC-TTTC
1 TAAAATTTACATTTTGA-CCCTAAACTTTTC
*
41566777 TCAAAATTT-CACTTTGACCCCTAAACTTTT-
1 T-AAAATTTACATTTTGA-CCCTAAACTTTTC
* * * *
41566807 TAAAAATTACATCTTGGCCCTATA-TTTTCC
1 TAAAATTTACATTTTGACCCTAAACTTTT-C
*
41566837 TAAAA-TTACATTTTTACCC
1 TAAAATTTACATTTTGACCC
41566856 CAAATATTTT
Statistics
Matches: 111, Mismatches: 19, Indels: 17
0.76 0.13 0.12
Matches are distributed among these distances:
28 4 0.04
29 44 0.40
30 58 0.52
31 5 0.05
ACGTcount: A:0.32, C:0.23, G:0.04, T:0.41
Consensus pattern (30 bp):
TAAAATTTACATTTTGACCCTAAACTTTTC
Found at i:41566842 original size:59 final size:58
Alignment explanation
Indices: 41566688--41566843 Score: 149
Period size: 59 Copynumber: 2.6 Consensus size: 58
41566678 ATGCAAAAAA
* *
41566688 TAAAAATTACATTTTGACCCTTATACTTTT-TGAAATTTGCATTTTGACCCTAAACTTTTC
1 TAAAAATTACA-TTTGACCC-TATA-TTTTCTAAAATTTGCACTTTGACCCTAAACTTTTC
* * *
41566748 T-AAAATTACATTTCAACCCCTAAACTTTCTCAAAATTT-CACTTTGACCCCTAAACTTTT-
1 TAAAAATTACATTT-GA-CCCTATATTTTCT-AAAATTTGCACTTTGA-CCCTAAACTTTTC
*
41566807 TAAAAATTACATCTTGGCCCTATATTTTCCTAAAATT
1 TAAAAATTACAT-TTGACCCTATATTTT-CTAAAATT
41566844 ACATTTTTAC
Statistics
Matches: 79, Mismatches: 9, Indels: 17
0.75 0.09 0.16
Matches are distributed among these distances:
58 6 0.08
59 37 0.47
60 34 0.43
61 2 0.03
ACGTcount: A:0.33, C:0.22, G:0.04, T:0.41
Consensus pattern (58 bp):
TAAAAATTACATTTGACCCTATATTTTCTAAAATTTGCACTTTGACCCTAAACTTTTC
Found at i:41567396 original size:11 final size:11
Alignment explanation
Indices: 41567380--41567420 Score: 57
Period size: 10 Copynumber: 3.7 Consensus size: 11
41567370 TTTTCAAAGG
*
41567380 GAAAAAGAATA
1 GAAAAAGAAAA
41567391 GAAAAAGAAAAA
1 GAAAAAG-AAAA
41567403 GAAAAA-AAAA
1 GAAAAAGAAAA
41567413 GAAAAAGA
1 GAAAAAGA
41567421 GGAAGAAGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
10 10 0.37
11 8 0.30
12 9 0.33
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (11 bp):
GAAAAAGAAAA
Found at i:41567408 original size:7 final size:6
Alignment explanation
Indices: 41567380--41567420 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
41567370 TTTTCAAAGG
*
41567380 GAAAAA G-AATA GAAAAA GAAAAA G-AAAA -AAAAA GAAAAA GA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GA
41567421 GGAAGAAGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
5 12 0.40
6 18 0.60
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (6 bp):
GAAAAA
Found at i:41567411 original size:16 final size:17
Alignment explanation
Indices: 41567380--41567420 Score: 66
Period size: 16 Copynumber: 2.5 Consensus size: 17
41567370 TTTTCAAAGG
*
41567380 GAAAAAGAATAGAAAAA
1 GAAAAAGAATAAAAAAA
41567397 GAAAAAGAA-AAAAAAA
1 GAAAAAGAATAAAAAAA
41567413 GAAAAAGA
1 GAAAAAGA
41567421 GGAAGAAGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (17 bp):
GAAAAAGAATAAAAAAA
Found at i:41567563 original size:14 final size:14
Alignment explanation
Indices: 41567544--41567582 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 14
41567534 GGGGCGAACG
41567544 AAGAAGGAAAAAGA
1 AAGAAGGAAAAAGA
41567558 AAGAA-GAAAAAGA
1 AAGAAGGAAAAAGA
*
41567571 AGGAAGGAAAAA
1 AAGAAGGAAAAA
41567583 AGAGAGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (14 bp):
AAGAAGGAAAAAGA
Found at i:41567595 original size:14 final size:14
Alignment explanation
Indices: 41567551--41567615 Score: 60
Period size: 14 Copynumber: 4.6 Consensus size: 14
41567541 ACGAAGAAGG
*
41567551 AAAAAGAAAG-AAG
1 AAAAAGAAAGAAAA
* *
41567564 AAAAAGAAGGAAGGA
1 AAAAAGAAAGAA-AA
*
41567579 AAAAAGAGAGAAAA
1 AAAAAGAAAGAAAA
**
41567593 AAAGGGAAAGAAAA
1 AAAAAGAAAGAAAA
41567607 AAAAAGAAA
1 AAAAAGAAA
41567616 AAATAATTTT
Statistics
Matches: 39, Mismatches: 11, Indels: 3
0.74 0.21 0.06
Matches are distributed among these distances:
13 9 0.23
14 20 0.51
15 10 0.26
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAGAAAA
Found at i:41567789 original size:14 final size:14
Alignment explanation
Indices: 41567770--41567796 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41567760 TCGGTGGACC
41567770 AGCAGCAGCCCACT
1 AGCAGCAGCCCACT
41567784 AGCAGCAGCCCAC
1 AGCAGCAGCCCAC
41567797 CCGTGCAGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.44, G:0.22, T:0.04
Consensus pattern (14 bp):
AGCAGCAGCCCACT
Found at i:41568461 original size:17 final size:17
Alignment explanation
Indices: 41568422--41568724 Score: 193
Period size: 18 Copynumber: 16.8 Consensus size: 17
41568412 TAAAAATTTC
41568422 AAATTTTCGTGTTTTCTAA
1 AAATTTTCGTG-TTTC-AA
41568441 AAATTTAT-GTGTTTCAA
1 AAATTT-TCGTGTTTCAA
*
41568458 AAATTTTCGTGTTTTCTA
1 AAATTTTCGTG-TTTCAA
* *
41568476 AAATTTTCATATTTTCAA
1 AAATTTTCGT-GTTTCAA
41568494 AAATTTTCGTGTTTTCAA
1 AAATTTTCGTG-TTTCAA
*
41568512 AAATTTTCGTGTTTCCA
1 AAATTTTCGTGTTTCAA
*
41568529 AAATTTTCGTGTTTTTAAAAAA
1 AAATTTTCGTG--TTT---CAA
* *
41568551 AAATTTGCGT-TTTGAAAA
1 AAATTTTCGTGTTT--CAA
*
41568569 AAATTCTCGTGTTTCAA
1 AAATTTTCGTGTTTCAA
*
41568586 AAATTGTCGCT-TTTC-A
1 AAATTTTCG-TGTTTCAA
* *
41568602 AAATTTTTGTGTTTTAA
1 AAATTTTCGTGTTTCAA
*
41568619 AAATTCTCGTGTTTGCAA
1 AAATTTTCGTGTTT-CAA
*
41568637 AAATTTTCGTGTTTTTAAA
1 AAATTTTCGTG--TTTCAA
* * *
41568656 AAACTTTTGCTTTTTTTAAAA
1 AAA-TTTT-C-GTGTTT-CAA
*
41568677 AAAATTTCGTGTTTC-A
1 AAATTTTCGTGTTTCAA
* *
41568693 AAATTCTCGTGTTTAAAA
1 AAATTTTCGTGTTT-CAA
*
41568711 AAATTCTCGTGTTT
1 AAATTTTCGTGTTT
41568725 TAATCGGATC
Statistics
Matches: 229, Mismatches: 32, Indels: 47
0.74 0.10 0.15
Matches are distributed among these distances:
15 1 0.00
16 25 0.11
17 54 0.24
18 93 0.41
19 24 0.10
20 14 0.06
21 7 0.03
22 11 0.05
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.48
Consensus pattern (17 bp):
AAATTTTCGTGTTTCAA
Found at i:41568550 original size:36 final size:35
Alignment explanation
Indices: 41568422--41568657 Score: 216
Period size: 36 Copynumber: 6.6 Consensus size: 35
41568412 TAAAAATTTC
41568422 AAATTTTCGTGTTTTCTAAAAATTTAT-GTGTTTCAA
1 AAATTTTCGTGTTTT-TAAAAATTT-TCGTGTTTCAA
* *
41568458 AAATTTTCGTGTTTTCT-AAAATTTTCATATTTTCAA
1 AAATTTTCGTGTTTT-TAAAAATTTTCGT-GTTTCAA
* *
41568494 AAATTTTCGTGTTTTCAAAAATTTTCGTGTTTCCA
1 AAATTTTCGTGTTTTTAAAAATTTTCGTGTTTCAA
* *
41568529 AAATTTTCGTGTTTTTAAAAAAAAATTTGCGT-TTTGAAAA
1 AAATTTTCGTGTTTTT----AAAAATTTTCGTGTTT--CAA
* * *
41568569 AAATTCTCGTG-TTTCAAAAATTGTCGCT-TTTC-A
1 AAATTTTCGTGTTTTTAAAAATTTTCG-TGTTTCAA
* *
41568602 AAATTTTTGTG-TTTTAAAAATTCTCGTGTTTGCAA
1 AAATTTTCGTGTTTTTAAAAATTTTCGTGTTT-CAA
41568637 AAATTTTCGTGTTTTTAAAAA
1 AAATTTTCGTGTTTTTAAAAA
41568658 ACTTTTGCTT
Statistics
Matches: 166, Mismatches: 20, Indels: 28
0.78 0.09 0.13
Matches are distributed among these distances:
32 1 0.01
33 26 0.16
34 2 0.01
35 48 0.29
36 61 0.37
38 3 0.02
39 14 0.08
40 11 0.07
ACGTcount: A:0.31, C:0.10, G:0.11, T:0.47
Consensus pattern (35 bp):
AAATTTTCGTGTTTTTAAAAATTTTCGTGTTTCAA
Found at i:41568614 original size:33 final size:35
Alignment explanation
Indices: 41568567--41568724 Score: 108
Period size: 33 Copynumber: 4.5 Consensus size: 35
41568557 GCGTTTTGAA
* *
41568567 AAAAATTCTCGTGTTTCAAAAATTGTCGCT-TTT-C
1 AAAAATTTTCGTGTTTCAAAAATTCTCG-TGTTTGC
* *
41568601 -AAAATTTTTGTGTTTTAAAAATTCTCGTGTTTGC
1 AAAAATTTTCGTGTTTCAAAAATTCTCGTGTTTGC
* * * * **
41568635 AAAAATTTTCGTGTTTTTAAAAAACTTTTGCTTTTTTTAA
1 AAAAATTTTCGTG--TTTCAAAAA-TTCT-C-GTGTTTGC
* **
41568675 AAAAAATTTCGTGTTTC-AAAATTCTCGTGTTTAA
1 AAAAATTTTCGTGTTTCAAAAATTCTCGTGTTTGC
*
41568709 AAAAATTCTCGTGTTT
1 AAAAATTTTCGTGTTT
41568725 TAATCGGATC
Statistics
Matches: 98, Mismatches: 18, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
32 1 0.01
33 26 0.27
34 21 0.21
35 12 0.12
36 3 0.03
37 12 0.12
38 6 0.06
39 1 0.01
40 16 0.16
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.46
Consensus pattern (35 bp):
AAAAATTTTCGTGTTTCAAAAATTCTCGTGTTTGC
Found at i:41579608 original size:25 final size:24
Alignment explanation
Indices: 41579573--41579624 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
41579563 CATACCGCAA
*
41579573 CTCTTTATGAG-TGTCCTGATATAGG
1 CTCTTTATGAGCT-TCCTAATAT-GG
*
41579598 CTCTTTGTGAGCTTCCTAATATGG
1 CTCTTTATGAGCTTCCTAATATGG
41579622 CTC
1 CTC
41579625 ACTTGAACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 5 0.21
25 18 0.75
26 1 0.04
ACGTcount: A:0.17, C:0.21, G:0.21, T:0.40
Consensus pattern (24 bp):
CTCTTTATGAGCTTCCTAATATGG
Found at i:41582918 original size:25 final size:25
Alignment explanation
Indices: 41582865--41582921 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
41582855 ATTCCAGTAT
* *
41582865 GAGCTTACCGATACTCAGCTTGTAT
1 GAGCTTACCGATACTCAGCTTGGAG
* * *
41582890 GAGCTTACCGCTATTTAGCTTGGAG
1 GAGCTTACCGATACTCAGCTTGGAG
41582915 GAGCTTA
1 GAGCTTA
41582922 TTTTTTATCA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32
Consensus pattern (25 bp):
GAGCTTACCGATACTCAGCTTGGAG
Found at i:41586693 original size:23 final size:23
Alignment explanation
Indices: 41586665--41586708 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
41586655 CTTTCTTACT
*
41586665 GTAGTAATTTTCGGGGTATTATA
1 GTAGTAATTTTCGGGATATTATA
41586688 GTAGTAATTTTCGGGATATTA
1 GTAGTAATTTTCGGGATATTA
41586709 CATCTATGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.05, G:0.25, T:0.43
Consensus pattern (23 bp):
GTAGTAATTTTCGGGATATTATA
Found at i:41592642 original size:38 final size:40
Alignment explanation
Indices: 41592571--41592652 Score: 105
Period size: 38 Copynumber: 2.1 Consensus size: 40
41592561 ATGTTATACT
* * *
41592571 TTCTGTTTGGCGTGATTCGGGTGGATCAACTCTTACGAGC
1 TTCTGTTTGGCATGATTCGGGAGGACCAACTCTTACGAGC
* *
41592611 TTCTG-TTGGCATG-TTCGGGAGGACCAGCTCTTATGAGC
1 TTCTGTTTGGCATGATTCGGGAGGACCAACTCTTACGAGC
41592649 TTCT
1 TTCT
41592653 ATTGACGGTG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 25 0.68
39 7 0.19
40 5 0.14
ACGTcount: A:0.15, C:0.21, G:0.29, T:0.35
Consensus pattern (40 bp):
TTCTGTTTGGCATGATTCGGGAGGACCAACTCTTACGAGC
Found at i:41610506 original size:80 final size:80
Alignment explanation
Indices: 41610395--41610678 Score: 234
Period size: 80 Copynumber: 3.4 Consensus size: 80
41610385 AGATTACTAT
* * * * * *
41610395 CTTTGATCTGCTCCGCTGTAAGCTCAGGGAGATAAGACCTGATACGATCCACTCTACTATAACTT
1 CTTTAATCCGCTCCACTGTAATCTCAAGGAGATAAGACCTGATACGATCCACTCTACTGTAACTT
41610460 CAGAGAGATAAGATC
66 CAGAGAGATAAGATC
* * ** ***
41610475 CTTTAATCCGCTCCACTGTAATCTCAAGGAGATAGGA--TTACTATCTTTGATCTGCTCCGTTGT
1 CTTTAATCCGCTCCACTGTAATCTCAAGGAGATAAGACCTGA-TA-C---GATCCACTCTACTGT
*
41610538 AA-TCTCAGGGAGATAAGATC
61 AACT-TCAGAGAGATAAGATC
* * * *
41610558 TGCAATTCTTCAGTCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGATACAATCCACTCTACT
1 --C---T-TT-AATCCGCTCCACTGTAATCTCAAGGAGATAAGACCTGATACGATCCACTCTACT
* *
41610623 GTAACTTTAGAGATATAAGATC
59 GTAACTTCAGAGAGATAAGATC
41610645 CTTTAATCCGCTCCACTGTAATCTC-AGAGAGATA
1 CTTTAATCCGCTCCACTGTAATCTCAAG-GAGATA
41610679 GGATAGTGTC
Statistics
Matches: 156, Mismatches: 31, Indels: 34
0.71 0.14 0.15
Matches are distributed among these distances:
78 2 0.01
79 3 0.02
80 57 0.37
81 2 0.01
82 2 0.01
83 26 0.17
85 2 0.01
87 24 0.15
88 2 0.01
89 2 0.01
90 30 0.19
91 2 0.01
92 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (80 bp):
CTTTAATCCGCTCCACTGTAATCTCAAGGAGATAAGACCTGATACGATCCACTCTACTGTAACTT
CAGAGAGATAAGATC
Found at i:41610550 original size:44 final size:44
Alignment explanation
Indices: 41610312--41610854 Score: 262
Period size: 44 Copynumber: 12.6 Consensus size: 44
41610302 TGTGGTTTTA
* * *
41610312 ATCTGCTCCACTGTAA-CTTCAGGGAGATAGGATTACTAGCTCTG
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGATTACTATCTTTG
* *
41610356 ATCTGCTCCGCTGTAATCTCAGGAAGATAAGATTACTATCTTTG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTG
* * *
41610400 ATCTGCTCCGCTGTAAGCTCAGGGAGATAAGA--CCTGATAC---G
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACT-AT-CTTTG
** * * * *
41610441 ATCCACTCTACTATAA-CTTCAGAGAGATAAGA-T-C---CTTTA
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGATTACTATCTTTG
* * *
41610480 ATCCGCTCCACTGTAATCTCAAGGAGATAGGATTACTATCTTTG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTG
** * * *
41610524 ATCTGCTCCGTTGTAATCTCAGGGAGATAAGATCTGCAAT-TCTTC
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGAT-TACTATCT-TTG
* *
41610569 AGTCTGCTCCACTGTAATCTCAGGGAGATAAGA--CCTGATAC---A
1 A-TCTGCTCCACTGTAATCTCAGGGAGATAAGATTACT-AT-CTTTG
** * * * * *
41610611 ATCCACTCTACTGTAA-CTTTAGAGATATAAGA-T-C---CTTTA
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGATTACTATCTTTG
* * * * * *
41610650 ATCCGCTCCACTGTAATCTCAGAGAGATAGGA-TAGTGTCTTCG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTG
** * * *
41610693 ATCTGCTCCGTTGTAATCTCAGGGAGATAAGATCTGCAAT-TCTTC
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGAT-TACTATCT-TTG
* ** **
41610738 AGTCTGCTCCACTGTAATCTCAGGGAGATAATA-T-CTGGCTTCA
1 A-TCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTG
* * * *
41610781 ATCTGCTCCACTGTAACCTCAGGGAGATGAGATTTGA-AATTCTTCG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGA-TT-ACTA-TCTTTG
* *
41610827 GTCTACTCCACTGTAATCTCAGGGAGAT
1 ATCTGCTCCACTGTAATCTCAGGGAGAT
41610855 CAGACCTGTA
Statistics
Matches: 381, Mismatches: 78, Indels: 78
0.71 0.15 0.15
Matches are distributed among these distances:
36 2 0.01
39 51 0.13
40 5 0.01
41 51 0.13
42 31 0.08
43 36 0.09
44 107 0.28
45 12 0.03
46 86 0.23
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (44 bp):
ATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTG
Found at i:41610588 original size:46 final size:45
Alignment explanation
Indices: 41610484--41610854 Score: 251
Period size: 46 Copynumber: 8.5 Consensus size: 45
41610474 CCTTTAATCC
* * * * *
41610484 GCTCCACTGTAATCTCAAGGAGATAGGAT-TACTATCTT-TGATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATCTGCAATCTTCAG-TCT
**
41610528 GCTCCGTTGTAATCTCAGGGAGATAAGATCTGCAATTCTTCAGTCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATCTGCAA-TCTTCAGTCT
* * * *
41610574 GCTCCACTGTAATCTCAGGGAGATAAGACCTG--A--TACAATCC
1 GCTCCACTGTAATCTCAGGGAGATAAGATCTGCAATCTTCAGTCT
* * * * * * *
41610615 ACTCTACTGTAA-CTTTAGAGATATAAGATC--C--T-TT-AATCC
1 GCTCCACTGTAATC-TCAGGGAGATAAGATCTGCAATCTTCAGTCT
* * *
41610654 GCTCCACTGTAATCTCAGAGAGATAGGATAGTG---TCTTC-GATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGAT-CTGCAATCTTCAG-TCT
**
41610697 GCTCCGTTGTAATCTCAGGGAGATAAGATCTGCAATTCTTCAGTCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATCTGCAA-TCTTCAGTCT
* * *
41610743 GCTCCACTGTAATCTCAGGGAGATAATATCTG---GCTTCAATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATCTGCAATCTTCAGTCT
* * * * *
41610785 GCTCCACTGTAACCTCAGGGAGATGAGATTTGAAATTCTTCGGTCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATCTGCAA-TCTTCAGTCT
*
41610831 ACTCCACTGTAATCTCAGGGAGAT
1 GCTCCACTGTAATCTCAGGGAGAT
41610855 CAGACCTGTA
Statistics
Matches: 258, Mismatches: 47, Indels: 42
0.74 0.14 0.12
Matches are distributed among these distances:
39 27 0.10
40 3 0.01
41 28 0.11
42 40 0.16
43 27 0.10
44 26 0.10
45 3 0.01
46 102 0.40
47 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (45 bp):
GCTCCACTGTAATCTCAGGGAGATAAGATCTGCAATCTTCAGTCT
Found at i:41610661 original size:170 final size:170
Alignment explanation
Indices: 41610247--41610768 Score: 723
Period size: 170 Copynumber: 3.1 Consensus size: 170
41610237 CTGCAACATT
* * * * *
41610247 AGGGATATAAGGCCTGATACGATCCACCCTACTGTAACCTCAGAGAGATAAGATCTGTGGTTTTA
1 AGGGAGATAAGACCTGATACGATCCACTCTACTGTAACTTCAGAGAGATAAGATC-----CTTTA
* * * * *
41610312 ATCTGCTCCACTGTAA-CTTCAGGGAGATAGGATTACTAGCTCTGATCTGCTCCGCTGTAATCTC
61 ATCCGCTCCACTGTAATC-TCAAGGAGATAGGATTACTATCTTTGATCTGCTCCGTTGTAATCTC
* * * * * *
41610376 AGGAAGATAAGAT-TACTA-TCTT-TGATCTGCTCCGCTGTAAGCTC
125 AGGGAGATAAGATCTGCAATTCTTCAG-TCTGCTCCACTGTAATCTC
*
41610420 AGGGAGATAAGACCTGATACGATCCACTCTACTATAACTTCAGAGAGATAAGATCCTTTAATCCG
1 AGGGAGATAAGACCTGATACGATCCACTCTACTGTAACTTCAGAGAGATAAGATCCTTTAATCCG
41610485 CTCCACTGTAATCTCAAGGAGATAGGATTACTATCTTTGATCTGCTCCGTTGTAATCTCAGGGAG
66 CTCCACTGTAATCTCAAGGAGATAGGATTACTATCTTTGATCTGCTCCGTTGTAATCTCAGGGAG
41610550 ATAAGATCTGCAATTCTTCAGTCTGCTCCACTGTAATCTC
131 ATAAGATCTGCAATTCTTCAGTCTGCTCCACTGTAATCTC
* * *
41610590 AGGGAGATAAGACCTGATACAATCCACTCTACTGTAACTTTAGAGATATAAGATCCTTTAATCCG
1 AGGGAGATAAGACCTGATACGATCCACTCTACTGTAACTTCAGAGAGATAAGATCCTTTAATCCG
* * *
41610655 CTCCACTGTAATCTC-AGAGAGATAGGA-TAGTGTCTTCGATCTGCTCCGTTGTAATCTCAGGGA
66 CTCCACTGTAATCTCAAG-GAGATAGGATTACTATCTTTGATCTGCTCCGTTGTAATCTCAGGGA
41610718 GATAAGATCTGCAATTCTTCAGTCTGCTCCACTGTAATCTC
130 GATAAGATCTGCAATTCTTCAGTCTGCTCCACTGTAATCTC
41610759 AGGGAGATAA
1 AGGGAGATAA
41610769 TATCTGGCTT
Statistics
Matches: 320, Mismatches: 24, Indels: 14
0.89 0.07 0.04
Matches are distributed among these distances:
168 73 0.23
169 90 0.28
170 106 0.33
171 1 0.00
173 50 0.16
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (170 bp):
AGGGAGATAAGACCTGATACGATCCACTCTACTGTAACTTCAGAGAGATAAGATCCTTTAATCCG
CTCCACTGTAATCTCAAGGAGATAGGATTACTATCTTTGATCTGCTCCGTTGTAATCTCAGGGAG
ATAAGATCTGCAATTCTTCAGTCTGCTCCACTGTAATCTC
Found at i:41610674 original size:39 final size:40
Alignment explanation
Indices: 41610574--41610678 Score: 108
Period size: 39 Copynumber: 2.6 Consensus size: 40
41610564 TCTTCAGTCT
*
41610574 GCTCCACTGTAATCTCAGGGAGATAAGACCTGATACAATCC
1 GCTCCACTGTAATCTCAGAGAGATAAGACCT-ATACAATCC
* * * * *
41610615 ACTCTACTGTAA-CTTTAGAGATATAAGATCCT-T-TAATCC
1 GCTCCACTGTAATC-TCAGAGAGATAAGA-CCTATACAATCC
41610654 GCTCCACTGTAATCTCAGAGAGATA
1 GCTCCACTGTAATCTCAGAGAGATA
41610679 GGATAGTGTC
Statistics
Matches: 51, Mismatches: 10, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
39 24 0.47
40 3 0.06
41 21 0.41
42 3 0.06
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (40 bp):
GCTCCACTGTAATCTCAGAGAGATAAGACCTATACAATCC
Found at i:41620285 original size:20 final size:20
Alignment explanation
Indices: 41620257--41620299 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
41620247 AAAAACTGCT
41620257 CCTTACAAAAAGTATCGATA
1 CCTTACAAAAAGTATCGATA
* *
41620277 CCTTTCAAAAAGTATTGATA
1 CCTTACAAAAAGTATCGATA
41620297 CCT
1 CCT
41620300 ATTGTATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (20 bp):
CCTTACAAAAAGTATCGATA
Found at i:41620402 original size:21 final size:21
Alignment explanation
Indices: 41620376--41620417 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
41620366 CAAACAATCA
41620376 CAAAAAGTA-TCGATACCTTTT
1 CAAAAAGTACT-GATACCTTTT
41620397 CAAAAAGTACTGATACCTTTT
1 CAAAAAGTACTGATACCTTTT
41620418 ACGAGGTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (21 bp):
CAAAAAGTACTGATACCTTTT
Found at i:41620902 original size:285 final size:285
Alignment explanation
Indices: 41620392--41620960 Score: 996
Period size: 285 Copynumber: 2.0 Consensus size: 285
41620382 GTATCGATAC
**
41620392 CTTTTCAAAAAGTACTGATACCTTTTACGAGGTATCGATAAAATTTCTTTGGTATCGTTGTAAAT
1 CTTTTCAAAAAGTACTGATACCTTTTACGAGGTATCGATAAAATGCCTTTGGTATCGTTGTAAAT
* *
41620457 TAACTTTAACAGTCATTGAATCATGTATTAAATTCTAATAGTATCGATACACATAGAAAAAGTAT
66 TAACTTTAACAGTCACTGAATCATGTATTAAATGCTAATAGTATCGATACACATAGAAAAAGTAT
*
41620522 CGATACCTTTTGTTGCAAGTGAATTTAATGATATGGTATTTTCATCCCCAACGACTCTATTCAAT
131 CGATACCTTTTGTTGCAAATGAATTTAATGATATGGTATTTTCATCCCCAACGACTCTATTCAAT
* * *
41620587 TCCTCAACAACCACAACGGTTGAAAATCAATTAGAGGGTATAAATACCAGCTTTTGAAGGCCCTA
196 TCATCAACAACCACAACGGTTGAAAATCAATTAGAGGGTATAAATACCAACTTTTGAAGGCCCCA
*
41620652 CAACAAAAAGTGAGATTGCAATAGT
261 CAACAAAAAGTGAGATTACAATAGT
*
41620677 CTTTTCAAAAAGTATTGATACCTTTTACGAGGTATCGATAAAATGCCTTTGGTATCGTTGTAAAT
1 CTTTTCAAAAAGTACTGATACCTTTTACGAGGTATCGATAAAATGCCTTTGGTATCGTTGTAAAT
41620742 TAACTTTAACAGTCACTGAATCATGTATTAAATGCTAATAGTATCGATACACATAGAAAAAGTAT
66 TAACTTTAACAGTCACTGAATCATGTATTAAATGCTAATAGTATCGATACACATAGAAAAAGTAT
*
41620807 CGATACCTTTTGTTGCAAATGAATTTAATGATAT-GTCATTTTCATCCCCAACGACTCTATTTAA
131 CGATACCTTTTGTTGCAAATGAATTTAATGATATGGT-ATTTTCATCCCCAACGACTCTATTCAA
* *
41620871 TTCATCAACAACCACAACGGTTGGAAATCAATTAGATGGTATAAATACCAACTTTTGAAGGCCCC
195 TTCATCAACAACCACAACGGTTGAAAATCAATTAGAGGGTATAAATACCAACTTTTGAAGGCCCC
*
41620936 AGAACAAAAAGTGAGATTACAATAG
260 ACAACAAAAAGTGAGATTACAATAG
41620961 ATCAAGTGCT
Statistics
Matches: 269, Mismatches: 14, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
284 2 0.01
285 267 0.99
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (285 bp):
CTTTTCAAAAAGTACTGATACCTTTTACGAGGTATCGATAAAATGCCTTTGGTATCGTTGTAAAT
TAACTTTAACAGTCACTGAATCATGTATTAAATGCTAATAGTATCGATACACATAGAAAAAGTAT
CGATACCTTTTGTTGCAAATGAATTTAATGATATGGTATTTTCATCCCCAACGACTCTATTCAAT
TCATCAACAACCACAACGGTTGAAAATCAATTAGAGGGTATAAATACCAACTTTTGAAGGCCCCA
CAACAAAAAGTGAGATTACAATAGT
Found at i:41623171 original size:20 final size:18
Alignment explanation
Indices: 41623124--41623172 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
41623114 CAAGATAAAC
41623124 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
41623141 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
41623161 ATTAAATTAATA
1 ATTAAATTAATA
41623173 AAATACTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:41623680 original size:19 final size:19
Alignment explanation
Indices: 41623642--41623681 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
41623632 AAAATATCAA
* *
41623642 ATTAATTTTAATTAATTTG
1 ATTAATTTAAATTAACTTG
*
41623661 ATTAATTTAAATTTACTTG
1 ATTAATTTAAATTAACTTG
41623680 AT
1 AT
41623682 CAAGATTAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.55
Consensus pattern (19 bp):
ATTAATTTAAATTAACTTG
Found at i:41626995 original size:21 final size:20
Alignment explanation
Indices: 41626963--41627002 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
41626953 TTAGAATGTA
41626963 TAAAAAATTAAAAAATATTTT
1 TAAAAAATTAAAAAA-ATTTT
41626984 TAAATAAA-TAAAAAAATTT
1 TAAA-AAATTAAAAAAATTT
41627003 AATATTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 11 0.61
22 3 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
TAAAAAATTAAAAAAATTTT
Found at i:41628183 original size:37 final size:36
Alignment explanation
Indices: 41628130--41628210 Score: 92
Period size: 36 Copynumber: 2.2 Consensus size: 36
41628120 TCATTTTTTC
* * *
41628130 TTATTTTTATTGTTATTTCGATTTCAATT-ATCTTTA
1 TTATTTTTATTATTA-TTAGATTTAAATTCATCTTTA
* *
41628166 TTATTTTTACTTATTATTAGATTTAAATTCTTCTTTC
1 TTATTTTTA-TTATTATTAGATTTAAATTCATCTTTA
41628203 TTATTTTT
1 TTATTTTT
41628211 GCACAGATTG
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
36 20 0.53
37 18 0.47
ACGTcount: A:0.22, C:0.09, G:0.04, T:0.65
Consensus pattern (36 bp):
TTATTTTTATTATTATTAGATTTAAATTCATCTTTA
Found at i:41629556 original size:46 final size:46
Alignment explanation
Indices: 41629369--41629574 Score: 141
Period size: 51 Copynumber: 4.3 Consensus size: 46
41629359 TCTACCCTGT
* *
41629369 TTGGACAGC-TCTTATACATCAAAAATT-GAGCAGCATATAAATACAAAA
1 TTGGACAGCAT-TTATTCACCAAAAATTAG-GCAGC--ATAAATACAAAA
* * * *
41629417 TTGGACAGCATTTTTTTTTCACCCAAAATTAGGCAGCATACATATACCAAT
1 TTGGACAGCA---TTTATTCACCAAAAATTAGGCAGCATA-A-ATACAAAA
* * * * **
41629468 TTGGACAGCACTTATACA-CAAAATTTA-ACAGCATGTGTATACAAAA
1 TTGGACAGCATTTATTCACCAAAAATTAGGCAGCA--TAAATACAAAA
* *
41629514 TTGGACAGCATTGATTCACCAAAAATTAGGCAGCATAAATACATCAA
1 TTGGACAGCATTTATTCACCAAAAATTAGGCAGCATAAATACA-AAA
*
41629561 TTGGGCAGCATTTA
1 TTGGACAGCATTTA
41629575 AGCATAAAAA
Statistics
Matches: 120, Mismatches: 26, Indels: 25
0.70 0.15 0.15
Matches are distributed among these distances:
46 32 0.27
47 29 0.24
48 20 0.17
49 3 0.03
50 1 0.01
51 33 0.28
52 2 0.02
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (46 bp):
TTGGACAGCATTTATTCACCAAAAATTAGGCAGCATAAATACAAAA
Found at i:41629586 original size:94 final size:95
Alignment explanation
Indices: 41629368--41629570 Score: 230
Period size: 97 Copynumber: 2.1 Consensus size: 95
41629358 ATCTACCCTG
* * * * ** *
41629368 TTTGGACAGCTCTTATACATCAAAAATTGAGCAGCATATAAATACAAAATTGGACAGCATTTTTT
1 TTTGGACAGCACTTATACA--AAAAATTTAACAGCATGTGTATACAAAATTGGACAGCA--TTTG
* * * *
41629433 TTTCACCCAAAATTAGGCAGCATACATATACCAA
62 ATTCACCAAAAATTAGGCAGCATAAATACACCAA
*
41629467 TTTGGACAGCACTTATACACAAAATTTAACAGCATGTGTATACAAAATTGGACAGCA-TTGATTC
1 TTTGGACAGCACTTATACAAAAAATTTAACAGCATGTGTATACAAAATTGGACAGCATTTGATTC
*
41629531 ACCAAAAATTAGGCAGCATAAATACATCAA
66 ACCAAAAATTAGGCAGCATAAATACACCAA
*
41629561 -TTGGGCAGCA
1 TTTGGACAGCA
41629571 TTTAAGCATA
Statistics
Matches: 90, Mismatches: 14, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
93 9 0.10
94 31 0.34
97 32 0.36
99 18 0.20
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (95 bp):
TTTGGACAGCACTTATACAAAAAATTTAACAGCATGTGTATACAAAATTGGACAGCATTTGATTC
ACCAAAAATTAGGCAGCATAAATACACCAA
Found at i:41630388 original size:29 final size:28
Alignment explanation
Indices: 41630297--41630452 Score: 231
Period size: 28 Copynumber: 5.5 Consensus size: 28
41630287 TTTAATAAGT
* ** * *
41630297 TCGCACACTTAGTTCTCAATAATCAAAC
1 TCGCACACTTAGTGCTTTACAATTAAAC
*
41630325 TCGCACACTTAGTGCTTTACCATTAAAC
1 TCGCACACTTAGTGCTTTACAATTAAAC
41630353 TCGCACACTTAGTGCTTTACAAATTAAAC
1 TCGCACACTTAGTGCTTTAC-AATTAAAC
41630382 TCGCACACTTAGTGCTTTACAAATTAAAC
1 TCGCACACTTAGTGCTTTAC-AATTAAAC
*
41630411 TCGCACACTTAGTGCTTTACAATTAAAT
1 TCGCACACTTAGTGCTTTACAATTAAAC
41630439 TCGCACACTTAGTG
1 TCGCACACTTAGTG
41630453 TCGAAAGTCA
Statistics
Matches: 119, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
28 63 0.53
29 56 0.47
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.31
Consensus pattern (28 bp):
TCGCACACTTAGTGCTTTACAATTAAAC
Found at i:41630390 original size:57 final size:57
Alignment explanation
Indices: 41630297--41630452 Score: 233
Period size: 57 Copynumber: 2.7 Consensus size: 57
41630287 TTTAATAAGT
* ** * * *
41630297 TCGCACACTTAGTTCTCAATAATCAAACTCGCACACTTAGTGCTTTAC-CATTAAAC
1 TCGCACACTTAGTGCTTTACAATTAAACTCGCACACTTAGTGCTTTACAAATTAAAC
41630353 TCGCACACTTAGTGCTTTACAAATTAAACTCGCACACTTAGTGCTTTACAAATTAAAC
1 TCGCACACTTAGTGCTTTAC-AATTAAACTCGCACACTTAGTGCTTTACAAATTAAAC
*
41630411 TCGCACACTTAGTGCTTTACAATTAAATTCGCACACTTAGTG
1 TCGCACACTTAGTGCTTTACAATTAAACTCGCACACTTAGTG
41630453 TCGAAAGTCA
Statistics
Matches: 91, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
56 16 0.18
57 48 0.53
58 27 0.30
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.31
Consensus pattern (57 bp):
TCGCACACTTAGTGCTTTACAATTAAACTCGCACACTTAGTGCTTTACAAATTAAAC
Found at i:41636877 original size:46 final size:46
Alignment explanation
Indices: 41636827--41637066 Score: 248
Period size: 46 Copynumber: 5.1 Consensus size: 46
41636817 CAAAATTAGG
41636827 CAGCATACATATACCAATTTGGACAGCACTTATACACAAAATTTAA
1 CAGCATACATATACCAATTTGGACAGCACTTATACACAAAATTTAA
*** * * * * **
41636873 CAGCATGTGTATACAAAATTGGACAGCACTGATTCACCAAAAATTTGGG
1 CAGCATACATATACCAATTTGGACAGCACTTATACA-C-AAAATTT-AA
* *
41636922 CATCATACATATACCAATTTGGATAGCACTTATACACAAAATTTAA
1 CAGCATACATATACCAATTTGGACAGCACTTATACACAAAATTTAA
*** * * * * *
41636968 CAGCATGTGTATACAAAATTGGACAGCA-TTGATTCACTAAAAATTAGG
1 CAGCATACATATACCAATTTGGACAGCACTT-ATACAC-AAAATTTA-A
41637016 CAGCATACATATACCAATTTGGACAGCACTTATACACAAAATTTAA
1 CAGCATACATATACCAATTTGGACAGCACTTATACACAAAATTTAA
41637062 CAGCA
1 CAGCA
41637067 CGTGTATACA
Statistics
Matches: 149, Mismatches: 38, Indels: 14
0.74 0.19 0.07
Matches are distributed among these distances:
45 2 0.01
46 60 0.40
47 22 0.15
48 36 0.24
49 29 0.19
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.26
Consensus pattern (46 bp):
CAGCATACATATACCAATTTGGACAGCACTTATACACAAAATTTAA
Found at i:41636898 original size:23 final size:23
Alignment explanation
Indices: 41636835--41637089 Score: 112
Period size: 23 Copynumber: 10.9 Consensus size: 23
41636825 GGCAGCATAC
* *
41636835 ATATACCAATTTGGACAGCACTT
1 ATATACAAAATTGGACAGCACTT
* **
41636858 ATACACAAAATTTAACAGCA-TGT
1 ATATACAAAATTGGACAGCACT-T
* *
41636881 GTATACAAAATTGGACAGCACTG
1 ATATACAAAATTGGACAGCACTT
* * *
41636904 AT-TCACCAAAAATTTGGGCATCA-TAC
1 ATAT-A-C-AAAA-TTGGACAGCACT-T
* * *
41636930 ATATACCAATTTGGATAGCACTT
1 ATATACAAAATTGGACAGCACTT
* **
41636953 ATACACAAAATTTAACAGCA-TGT
1 ATATACAAAATTGGACAGCACT-T
*
41636976 GTATACAAAATTGGACAGCA-TT
1 ATATACAAAATTGGACAGCACTT
*
41636998 GAT-TCACTAAAAATTAGG-CAGCA-TAC
1 -ATAT-AC--AAAATT-GGACAGCACT-T
* *
41637024 ATATACCAATTTGGACAGCACTT
1 ATATACAAAATTGGACAGCACTT
* ** *
41637047 ATACACAAAATTTAACAGCACGT
1 ATATACAAAATTGGACAGCACTT
*
41637070 GTATACAAAATTGGACAGCA
1 ATATACAAAATTGGACAGCA
41637090 TTGATTCACC
Statistics
Matches: 168, Mismatches: 45, Indels: 38
0.67 0.18 0.15
Matches are distributed among these distances:
22 7 0.04
23 118 0.70
24 6 0.04
25 22 0.13
26 14 0.08
27 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.26
Consensus pattern (23 bp):
ATATACAAAATTGGACAGCACTT
Found at i:41637152 original size:94 final size:94
Alignment explanation
Indices: 41636745--41637116 Score: 564
Period size: 94 Copynumber: 3.9 Consensus size: 94
41636735 ATCTACCCTG
* * * * * *
41636745 TTTGGACAGCTCTTATACATCAAAAATTGAGCAGCATATATATACAAAATTGGACAGCATTTTTT
1 TTTGGACAGCACTTATACA-C-AAAATTTAACAGCATGTGTATACAAAATTGGACAGCA---TTG
* *
41636810 TTTCACCCAAAATTAGGCAGCATACATATACCAA
61 ATTCACCAAAAATTAGGCAGCATACATATACCAA
*
41636844 TTTGGACAGCACTTATACACAAAATTTAACAGCATGTGTATACAAAATTGGACAGCACTGATTCA
1 TTTGGACAGCACTTATACACAAAATTTAACAGCATGTGTATACAAAATTGGACAGCATTGATTCA
* *
41636909 CCAAAAATTTGGGCATCATACATATACCAA
66 CCAAAAA-TTAGGCAGCATACATATACCAA
*
41636939 TTTGGATAGCACTTATACACAAAATTTAACAGCATGTGTATACAAAATTGGACAGCATTGATTCA
1 TTTGGACAGCACTTATACACAAAATTTAACAGCATGTGTATACAAAATTGGACAGCATTGATTCA
*
41637004 CTAAAAATTAGGCAGCATACATATACCAA
66 CCAAAAATTAGGCAGCATACATATACCAA
*
41637033 TTTGGACAGCACTTATACACAAAATTTAACAGCACGTGTATACAAAATTGGACAGCATTGATTCA
1 TTTGGACAGCACTTATACACAAAATTTAACAGCATGTGTATACAAAATTGGACAGCATTGATTCA
41637098 CCAAAAATTAGGCAGCATA
66 CCAAAAATTAGGCAGCATA
41637117 AATACATCAA
Statistics
Matches: 253, Mismatches: 19, Indels: 7
0.91 0.07 0.03
Matches are distributed among these distances:
94 112 0.44
95 89 0.35
97 33 0.13
98 1 0.00
99 18 0.07
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (94 bp):
TTTGGACAGCACTTATACACAAAATTTAACAGCATGTGTATACAAAATTGGACAGCATTGATTCA
CCAAAAATTAGGCAGCATACATATACCAA
Found at i:41637903 original size:28 final size:28
Alignment explanation
Indices: 41637863--41637989 Score: 182
Period size: 28 Copynumber: 4.5 Consensus size: 28
41637853 ATTTATAAGT
* *
41637863 TCGCACACTTAGTGCTCAATAATTAAAC
1 TCGCACACTTAGTGCTTAACAATTAAAC
* *
41637891 TCGCACACTTAGTGCTTTACCATTAAAC
1 TCGCACACTTAGTGCTTAACAATTAAAC
*
41637919 TCGCACACTTAGTGCTTTACAAATTAAAC
1 TCGCACACTTAGTGCTTAAC-AATTAAAC
* *
41637948 TCGCACACTTAGTGCTTTACAATTAAAT
1 TCGCACACTTAGTGCTTAACAATTAAAC
41637976 TCGCACACTTAGTG
1 TCGCACACTTAGTG
41637990 TCGAAAGTCA
Statistics
Matches: 92, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
28 65 0.71
29 27 0.29
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.31
Consensus pattern (28 bp):
TCGCACACTTAGTGCTTAACAATTAAAC
Found at i:41637955 original size:57 final size:56
Alignment explanation
Indices: 41637863--41637989 Score: 202
Period size: 57 Copynumber: 2.2 Consensus size: 56
41637853 ATTTATAAGT
*
41637863 TCGCACACTTAGTGCTCAATAATTAAACTCGCACACTTAGTGCTTTACCATTAAAC
1 TCGCACACTTAGTGCTCAATAATTAAACTCGCACACTTAGTGCTTTACAATTAAAC
* *
41637919 TCGCACACTTAGTGCTTTACA-AATTAAACTCGCACACTTAGTGCTTTACAATTAAAT
1 TCGCACACTTAGTGC-TCA-ATAATTAAACTCGCACACTTAGTGCTTTACAATTAAAC
41637976 TCGCACACTTAGTG
1 TCGCACACTTAGTG
41637990 TCGAAAGTCA
Statistics
Matches: 66, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
56 15 0.23
57 50 0.76
58 1 0.02
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.31
Consensus pattern (56 bp):
TCGCACACTTAGTGCTCAATAATTAAACTCGCACACTTAGTGCTTTACAATTAAAC
Found at i:41638049 original size:2 final size:2
Alignment explanation
Indices: 41638042--41638077 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
41638032 TCACTACATG
41638042 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41638078 CCNNNNNNNN
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41652946 original size:16 final size:16
Alignment explanation
Indices: 41652922--41652959 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
41652912 TTTGGTTCGC
* *
41652922 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
41652938 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
41652954 TGTAAT
1 TGTAAT
41652960 AGCAAATCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:41653308 original size:16 final size:16
Alignment explanation
Indices: 41653271--41653312 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
41653261 TTAATCATAT
*
41653271 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
41653287 TT-AAATATATTATAA
1 TTAAAATATATTATAA
41653302 TTAAAATATAT
1 TTAAAATATAT
41653313 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:41653319 original size:14 final size:15
Alignment explanation
Indices: 41653280--41653321 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
41653270 TTTAAACATA
*
41653280 ATTATTATTAAATAT
1 ATTATAATTAAATAT
41653295 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
41653309 A-TATAATTTAATA
1 ATTATAATTAAATA
41653322 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:41656875 original size:43 final size:41
Alignment explanation
Indices: 41656828--41656933 Score: 142
Period size: 43 Copynumber: 2.5 Consensus size: 41
41656818 TTATATTTTG
*
41656828 GATTTAAATGTATAGTTTTATATT-AATATTATATAATCAAAAT
1 GATTTTAAT-TATA-TTTTA-ATTAAATATTATATAATCAAAAT
*
41656871 GATTTTAATTATATTTCAATTAAAAATATTATATAATCAAAAT
1 GATTTTAATTATATTTTAATT--AAATATTATATAATCAAAAT
41656914 GATTTTAATTATATTTTAAT
1 GATTTTAATTATATTTTAAT
41656934 ATACCTTAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
40 3 0.05
41 4 0.07
42 4 0.07
43 46 0.81
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (41 bp):
GATTTTAATTATATTTTAATTAAATATTATATAATCAAAAT
Found at i:41656882 original size:23 final size:23
Alignment explanation
Indices: 41656855--41656927 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 23
41656845 TTATATTAAT
41656855 ATTATATAATCAAAATGATTTTA
1 ATTATATAATCAAAATGATTTTA
* * * ***
41656878 ATTATAT-TTC-AATTAAAAAT-
1 ATTATATAATCAAAATGATTTTA
41656898 ATTATATAATCAAAATGATTTTA
1 ATTATATAATCAAAATGATTTTA
41656921 ATTATAT
1 ATTATAT
41656928 TTTAATATAC
Statistics
Matches: 35, Mismatches: 12, Indels: 6
0.66 0.23 0.11
Matches are distributed among these distances:
20 7 0.20
21 7 0.20
22 7 0.20
23 14 0.40
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (23 bp):
ATTATATAATCAAAATGATTTTA
Found at i:41657994 original size:50 final size:50
Alignment explanation
Indices: 41657939--41658040 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
41657929 ATTAGCAGTA
41657939 AATGTACTTGGGTGTTAATTCATTTCAAACATTTCAAAGCATTCAAAGTT
1 AATGTACTTGGGTGTTAATTCATTTCAAACATTTCAAAGCATTCAAAGTT
41657989 AATGTACTTGGGTGTTAATTCATTTCAAACATTTCAAAGCATTCAAAGTT
1 AATGTACTTGGGTGTTAATTCATTTCAAACATTTCAAAGCATTCAAAGTT
41658039 AA
1 AA
41658041 CAGTACCAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (50 bp):
AATGTACTTGGGTGTTAATTCATTTCAAACATTTCAAAGCATTCAAAGTT
Found at i:41665508 original size:2 final size:2
Alignment explanation
Indices: 41665501--41665528 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
41665491 CAGGTACATG
41665501 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41665529 GTTTTCTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41666956 original size:12 final size:12
Alignment explanation
Indices: 41666939--41666963 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41666929 TGTCTCATGG
41666939 GTGTGCAATAGA
1 GTGTGCAATAGA
41666951 GTGTGCAATAGA
1 GTGTGCAATAGA
41666963 G
1 G
41666964 ATTCTAGGCC
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:0.32, C:0.08, G:0.36, T:0.24
Consensus pattern (12 bp):
GTGTGCAATAGA
Found at i:41669426 original size:9 final size:9
Alignment explanation
Indices: 41669412--41669505 Score: 134
Period size: 9 Copynumber: 10.4 Consensus size: 9
41669402 TTTGGTTAAA
41669412 AATTAACCG
1 AATTAACCG
41669421 AATTAACCG
1 AATTAACCG
*
41669430 AATTATCCG
1 AATTAACCG
41669439 AATTAACCG
1 AATTAACCG
*
41669448 AATTACCCG
1 AATTAACCG
*
41669457 AATTACCCG
1 AATTAACCG
41669466 AATTAACCG
1 AATTAACCG
*
41669475 AATTACCCG
1 AATTAACCG
*
41669484 AATTAACCA
1 AATTAACCG
*
41669493 AATTAACCA
1 AATTAACCG
41669502 AATT
1 AATT
41669506 GAATCACTAC
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 78 1.00
ACGTcount: A:0.43, C:0.24, G:0.09, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:41675553 original size:30 final size:30
Alignment explanation
Indices: 41675499--41675559 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 30
41675489 ACTAAGCAAA
41675499 TTTCATATACATGTATCATCCATTT-CATG
1 TTTCATATACATGTATCATCCATTTCCATG
41675528 TTTCAATATATCATGTAAT-AT-CATTTCCATG
1 TTTC-ATATA-CATGT-ATCATCCATTTCCATG
41675559 T
1 T
41675560 ATTTCATGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
29 4 0.14
30 10 0.36
31 12 0.43
32 2 0.07
ACGTcount: A:0.30, C:0.18, G:0.07, T:0.46
Consensus pattern (30 bp):
TTTCATATACATGTATCATCCATTTCCATG
Found at i:41675563 original size:10 final size:10
Alignment explanation
Indices: 41675550--41675581 Score: 50
Period size: 9 Copynumber: 3.4 Consensus size: 10
41675540 ATGTAATATC
41675550 ATTTCCATGT
1 ATTTCCATGT
41675560 ATTT-CATGT
1 ATTTCCATGT
41675569 A-TTCCATGT
1 ATTTCCATGT
41675578 ATTT
1 ATTT
41675582 ACCTGTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
8 2 0.10
9 12 0.60
10 6 0.30
ACGTcount: A:0.22, C:0.16, G:0.09, T:0.53
Consensus pattern (10 bp):
ATTTCCATGT
Found at i:41675847 original size:25 final size:26
Alignment explanation
Indices: 41675747--41675858 Score: 137
Period size: 25 Copynumber: 4.5 Consensus size: 26
41675737 GCCAGTTGTG
*
41675747 AATCGGTAAGCTCAT-ACGAGCTGA-G
1 AATCGGTAAGCTC-TCACGAGCTGACA
*
41675772 AATC-GTAAGCTCTCACGAACTG-CA
1 AATCGGTAAGCTCTCACGAGCTGACA
*
41675796 AATCGGTAAGCTCTCACGAG-TGGCA
1 AATCGGTAAGCTCTCACGAGCTGACA
41675821 AATCGGTAAGCTCTCACGAGCT-ACA
1 AATCGGTAAGCTCTCACGAGCTGACA
*
41675846 AATCAGTAAGCTC
1 AATCGGTAAGCTC
41675859 ATATGAGCTG
Statistics
Matches: 77, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
23 1 0.01
24 21 0.27
25 54 0.70
26 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.21
Consensus pattern (26 bp):
AATCGGTAAGCTCTCACGAGCTGACA
Found at i:41686237 original size:16 final size:16
Alignment explanation
Indices: 41686212--41686254 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
41686202 TTGAATTTTT
41686212 GTTA-TAAGAATATTG
1 GTTATTAAGAATATTG
41686227 GTTATTAAGAATATTG
1 GTTATTAAGAATATTG
*
41686243 ATTATTAAGAAT
1 GTTATTAAGAAT
41686255 TTTATTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 4 0.15
16 22 0.85
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (16 bp):
GTTATTAAGAATATTG
Found at i:41686281 original size:18 final size:17
Alignment explanation
Indices: 41686253--41686287 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
41686243 ATTATTAAGA
*
41686253 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
41686270 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
41686288 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:41686379 original size:61 final size:59
Alignment explanation
Indices: 41686312--41686739 Score: 286
Period size: 61 Copynumber: 7.1 Consensus size: 59
41686302 GTTAAATTAT
*
41686312 ATTTTATAGTATCATATATTATGGTTTTAGTAAATTTATATAAGAATATTGATTATTAAGA
1 ATTTTATAGTATCATATATTATGATTTTAGTAAATTTATATAAGAATATTG-TTATTAA-A
* * * * ** * ** * *
41686373 ATTTTATTA-AATTATATATTTTAATTAAAATATTTTTA-ATAATAAT-TATGTTAAATT-AT
1 ATTTTA-TAGTATCATATATTATGATTTTAGTAAATTTATATAAGAATAT-TGTT--ATTAAA
41686432 ATTTTATAGTATCATATATTATGATTTTAGTAAATTTATATAAGAATATTGATTATTAAGA
1 ATTTTATAGTATCATATATTATGATTTTAGTAAATTTATATAAGAATATTG-TTATTAA-A
* * * * ** * ** * *
41686493 ATTTTATTA-AATTATATATTTTAATTAAAATATTTTTA-ATAATAAT-TATGTTAAATT-AT
1 ATTTTA-TAGTATCATATATTATGATTTTAGTAAATTTATATAAGAATAT-TGTT--ATTAAA
*
41686552 ATTTTACAGTATCATATATTATGATTTTAGTAAATTTATATAAGAATATTGGTTATTAAGA
1 ATTTTATAGTATCATATATTATGATTTTAGTAAATTTATATAAGAATATT-GTTATTAA-A
* * * * ** * * * *
41686613 ATTTTATTA-AATTATATATTTTAATTAAAATATATTTA-ATAATAAT-TATGTTAAATT-AT
1 ATTTTA-TAGTATCATATATTATGATTTTAGTAAATTTATATAAGAATAT-TGTT--ATTAAA
41686672 ATTTTATAGTATCATATATTATGATTTTAGTAAATTTATATAAGAATATTGATTATTTAAA
1 ATTTTATAGTATCATATATTATGATTTTAGTAAATTTATATAAGAATATTG-TTA-TTAAA
41686733 ATTTTAT
1 ATTTTAT
41686740 TAAACTATAT
Statistics
Matches: 270, Mismatches: 67, Indels: 60
0.68 0.17 0.15
Matches are distributed among these distances:
58 5 0.02
59 96 0.36
60 59 0.22
61 105 0.39
62 5 0.02
ACGTcount: A:0.42, C:0.01, G:0.07, T:0.50
Consensus pattern (59 bp):
ATTTTATAGTATCATATATTATGATTTTAGTAAATTTATATAAGAATATTGTTATTAAA
Found at i:41686445 original size:120 final size:120
Alignment explanation
Indices: 41686228--41686787 Score: 1043
Period size: 120 Copynumber: 4.7 Consensus size: 120
41686218 AGAATATTGG
*
41686228 TTAT-TAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAA
1 TTATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATTTTTAA
*
41686292 TAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGGTTTTAGTAAAT
66 TAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTTAGTAAAT
41686347 TTATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATTTTTAA
1 TTATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATTTTTAA
41686412 TAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTTAGTAAAT
66 TAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTTAGTAAAT
41686467 TTATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATTTTTAA
1 TTATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATTTTTAA
*
41686532 TAATAATTATGTTAAATTATATTTTACAGTATCATATATTATGATTTTAGTAAAT
66 TAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTTAGTAAAT
* *
41686587 TTATATAAGAATATTGGTTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAA
1 TTATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATTTTTAA
41686652 TAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTTAGTAAAT
66 TAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTTAGTAAAT
*
41686707 TTATATAAGAATATTGATTATTTAA-AATTTTATTAAACTATATATTTTAATTAAAATATTTTTA
1 TTATATAAGAATATTGATTA-TTAAGAATTTTATTAAATTATATATTTTAATTAAAATATTTTTA
41686771 ATAATAATTATGTTAAA
65 ATAATAATTATGTTAAA
41686788 ATATGATTAA
Statistics
Matches: 430, Mismatches: 9, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
119 4 0.01
120 422 0.98
121 4 0.01
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.50
Consensus pattern (120 bp):
TTATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATTTTTAA
TAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTTAGTAAAT
Found at i:41686641 original size:18 final size:17
Alignment explanation
Indices: 41686613--41686647 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
41686603 GTTATTAAGA
*
41686613 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
41686630 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
41686648 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:41686750 original size:61 final size:58
Alignment explanation
Indices: 41686228--41686752 Score: 256
Period size: 59 Copynumber: 8.7 Consensus size: 58
41686218 AGAATATTGG
* * ** * *
41686228 TTAT-TAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATAT
1 TTATATAAGAATATTG-TTATTAA-AATTTTATTAAA-TATATATTATGATTTTAGTAAAT
* * * *
41686288 TTA-ATAATAAT-TATGTTAAATT-ATATTTTA-TAGTATCATATATTATGGTTTTAGTAAAT
1 TTATATAAGAATAT-TGTT--ATTAAAATTTTATTA-AAT-ATATATTATGATTTTAGTAAAT
* * ** * **
41686347 TTATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATTT
1 TTATATAAGAATATTG-TTATTAA-AATTTTATTAAA-TATATATTATGATTTTAGTAAAT
* * *
41686408 TTA-ATAATAAT-TATGTTAAATT-ATATTTTA-TAGTATCATATATTATGATTTTAGTAAAT
1 TTATATAAGAATAT-TGTT--ATTAAAATTTTATTA-AAT-ATATATTATGATTTTAGTAAAT
* * ** * **
41686467 TTATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATTT
1 TTATATAAGAATATTG-TTATTAA-AATTTTATTAAA-TATATATTATGATTTTAGTAAAT
* * * *
41686528 TTA-ATAATAAT-TATGTTAAATT-ATATTTTA-CAGTATCATATATTATGATTTTAGTAAAT
1 TTATATAAGAATAT-TGTT--ATTAAAATTTTATTA-AAT-ATATATTATGATTTTAGTAAAT
* * ** * *
41686587 TTATATAAGAATATTGGTTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATAT
1 TTATATAAGAATATT-GTTATTAA-AATTTTATTAAA-TATATATTATGATTTTAGTAAAT
* * *
41686648 TTA-ATAATAAT-TATGTTAAATT-ATATTTTA-TAGTATCATATATTATGATTTTAGTAAAT
1 TTATATAAGAATAT-TGTT--ATTAAAATTTTATTA-AAT-ATATATTATGATTTTAGTAAAT
41686707 TTATATAAGAATATTGATTATTTAAAATTTTATTAAACTATATATT
1 TTATATAAGAATATTG-TTA-TTAAAATTTTATTAAA-TATATATT
41686753 TTAATTAAAA
Statistics
Matches: 342, Mismatches: 74, Indels: 97
0.67 0.14 0.19
Matches are distributed among these distances:
58 11 0.03
59 124 0.36
60 81 0.24
61 115 0.34
62 11 0.03
ACGTcount: A:0.42, C:0.01, G:0.06, T:0.50
Consensus pattern (58 bp):
TTATATAAGAATATTGTTATTAAAATTTTATTAAATATATATTATGATTTTAGTAAAT
Found at i:41687008 original size:16 final size:16
Alignment explanation
Indices: 41686987--41687019 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
41686977 TTGAATTGCT
*
41686987 ATTACGCCTCTATTCC
1 ATTACGCCTCTACTCC
41687003 ATTACGCCTCTACTCC
1 ATTACGCCTCTACTCC
41687019 A
1 A
41687020 ATACAGCGAA
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:0.21, C:0.39, G:0.06, T:0.33
Consensus pattern (16 bp):
ATTACGCCTCTACTCC
Found at i:41687082 original size:13 final size:13
Alignment explanation
Indices: 41687064--41687088 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41687054 AATTTTAACC
41687064 TTAAAAGATATGG
1 TTAAAAGATATGG
41687077 TTAAAAGATATG
1 TTAAAAGATATG
41687089 ATTTTTTTTT
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:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (13 bp):
TTAAAAGATATGG
Done.