Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 94 of 167
Found at i:31152479 original size:28 final size:27
Alignment explanation
Indices: 31152335--31152489 Score: 97
Period size: 28 Copynumber: 5.6 Consensus size: 27
31152325 TAGTTATATG
*
31152335 TGGCACTTAACGTGTG-AAGTATCGGGGA
1 TGGCACTT-A-GTGTGCAAGTATCAGGGA
31152363 TGGCACTTAGTGTGCAA-TACATCCA--GA
1 TGGCACTTAGTGTGCAAGT--AT-CAGGGA
* *
31152390 CTGGCACTTAGTGTGCGAAGTAACGGGGA
1 -TGGCACTTAGTGTGC-AAGTATCAGGGA
** *
31152419 TGGCACTTAGTGTGCGAAACATCTA-GAA
1 TGGCACTTAGTGTGC-AAGTATC-AGGGA
* *
31152447 CGGCACTTAGTGTGCAAGGTATCAGGTA
1 TGGCACTTAGTGTGCAA-GTATCAGGGA
31152475 TGGCA-TCTAGTGTGC
1 TGGCACT-TAGTGTGC
31152490 GATACATTGA
Statistics
Matches: 101, Mismatches: 13, Indels: 26
0.72 0.09 0.19
Matches are distributed among these distances:
26 6 0.06
27 10 0.10
28 79 0.78
29 5 0.05
30 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (27 bp):
TGGCACTTAGTGTGCAAGTATCAGGGA
Found at i:31152613 original size:32 final size:32
Alignment explanation
Indices: 31152539--31152637 Score: 126
Period size: 32 Copynumber: 3.1 Consensus size: 32
31152529 TGAGTATGAG
* * * * * *
31152539 ATTGGTACGAGATGATACAGGTATCTACGGAA
1 ATTGGTACAATATGGTACATGTATGTACGAAA
31152571 ATTGGTACAATATGGTACATGTATGTACGAAA
1 ATTGGTACAATATGGTACATGTATGTACGAAA
* *
31152603 ATTGGTACAATATAGTACATGTATGTACAAAA
1 ATTGGTACAATATGGTACATGTATGTACGAAA
31152635 ATT
1 ATT
31152638 CAATTGAGTA
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 59 1.00
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.30
Consensus pattern (32 bp):
ATTGGTACAATATGGTACATGTATGTACGAAA
Found at i:31157474 original size:26 final size:25
Alignment explanation
Indices: 31157366--31157473 Score: 141
Period size: 25 Copynumber: 4.4 Consensus size: 25
31157356 CTGGAGGCCT
*
31157366 AGCCTCTTTTAAT-AACTGGGGC-AA
1 AGCC-CTTTTGATAAACTGGGGCAAA
31157390 AGCCCTTTTGATAAACTGGGGCAAA
1 AGCCCTTTTGATAAACTGGGGCAAA
*
31157415 AGCCCTTTTAATAAACTGGGGCAAA
1 AGCCCTTTTGATAAACTGGGGCAAA
* *
31157440 AGCCCTTTTCGGTAAACTGGGGC-AT
1 AGCCCTTTT-GATAAACTGGGGCAAA
31157465 AGCCCTTTT
1 AGCCCTTTT
31157474 TGCACTTCCT
Statistics
Matches: 76, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
23 7 0.09
24 13 0.17
25 45 0.59
26 11 0.14
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (25 bp):
AGCCCTTTTGATAAACTGGGGCAAA
Found at i:31163975 original size:26 final size:25
Alignment explanation
Indices: 31163879--31163986 Score: 132
Period size: 25 Copynumber: 4.4 Consensus size: 25
31163869 CTAGAGGCCT
*
31163879 AGCCTCTTTTAAT-AACTGGGGC-AA
1 AGCC-CTTTTGATAAACTGGGGCAAA
31163903 AGCCCTTTTGATAAACTGGGGCAAA
1 AGCCCTTTTGATAAACTGGGGCAAA
*
31163928 AGCCCTTTTAATAAACTGGGGCAAA
1 AGCCCTTTTGATAAACTGGGGCAAA
* * *
31163953 AGCCCTATTCGGTAAACTGGGGC-AT
1 AGCCCT-TTTGATAAACTGGGGCAAA
31163978 AGCCCTTTT
1 AGCCCTTTT
31163987 TGCACTTCCT
Statistics
Matches: 74, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
23 7 0.09
24 15 0.20
25 39 0.53
26 13 0.18
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (25 bp):
AGCCCTTTTGATAAACTGGGGCAAA
Found at i:31171965 original size:21 final size:22
Alignment explanation
Indices: 31171939--31171979 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
31171929 CACTTGACAC
31171939 AGGGGC-ACACACCCGTGTGGG
1 AGGGGCAACACACCCGTGTGGG
31171960 AGGGGCAACACACCCGTGTG
1 AGGGGCAACACACCCGTGTG
31171980 AGCATTCCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.22, C:0.29, G:0.39, T:0.10
Consensus pattern (22 bp):
AGGGGCAACACACCCGTGTGGG
Found at i:31172972 original size:9 final size:9
Alignment explanation
Indices: 31172958--31172983 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
31172948 ATGAAAATAA
31172958 TAAAACCAT
1 TAAAACCAT
31172967 TAAAACCAT
1 TAAAACCAT
31172976 TAAAACCA
1 TAAAACCA
31172984 AAGTGTATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.23, G:0.00, T:0.19
Consensus pattern (9 bp):
TAAAACCAT
Found at i:31182717 original size:46 final size:46
Alignment explanation
Indices: 31182634--31182750 Score: 148
Period size: 46 Copynumber: 2.5 Consensus size: 46
31182624 AAGTAGAAGC
31182634 CATGTCCCAGACATGGTCTTACACTGACTATCATCTCGTA-GCCAACG
1 CATGTCCCAGACAT-GTCTTACACTGACTATCATCTCG-AGGCCAACG
* * * *
31182681 CATGTCCTAGACATGTCTTACACTGGCT-TACGTCTCGAGGCCAATG
1 CATGTCCCAGACATGTCTTACACTGACTAT-CATCTCGAGGCCAACG
*
31182727 CATGTCCCCGACATGTCTTACACT
1 CATGTCCCAGACATGTCTTACACT
31182751 AGCACTCGTC
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
45 2 0.03
46 47 0.76
47 13 0.21
ACGTcount: A:0.23, C:0.32, G:0.18, T:0.27
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTGACTATCATCTCGAGGCCAACG
Found at i:31187846 original size:13 final size:14
Alignment explanation
Indices: 31187827--31187859 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
31187817 ATTTATTTTA
31187827 AAAAGTAA-TAATT
1 AAAAGTAATTAATT
*
31187840 TAAAGTAATTAATT
1 AAAAGTAATTAATT
31187854 AAAAGT
1 AAAAGT
31187860 TTCCAATCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (14 bp):
AAAAGTAATTAATT
Found at i:31198260 original size:32 final size:32
Alignment explanation
Indices: 31198212--31198279 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
31198202 AAATTATTGA
31198212 TGCAACTAATTGTTCATGCAATCATTACAATT
1 TGCAACTAATTGTTCATGCAATCATTACAATT
* *
31198244 TGCAACTATTTTTTCATGCAATCATTACAATT
1 TGCAACTAATTGTTCATGCAATCATTACAATT
31198276 TGCA
1 TGCA
31198280 GATGGTTCCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.32, C:0.19, G:0.09, T:0.40
Consensus pattern (32 bp):
TGCAACTAATTGTTCATGCAATCATTACAATT
Found at i:31198765 original size:30 final size:30
Alignment explanation
Indices: 31198731--31198788 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
31198721 ACTTAATAAG
31198731 CAAATACCTCTAAAATAATAACAAAATTGA
1 CAAATACCTCTAAAATAATAACAAAATTGA
* *
31198761 CAAATGCCTTTAAAATAATAACAAAATT
1 CAAATACCTCTAAAATAATAACAAAATT
31198789 AATAATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.55, C:0.16, G:0.03, T:0.26
Consensus pattern (30 bp):
CAAATACCTCTAAAATAATAACAAAATTGA
Found at i:31200506 original size:15 final size:16
Alignment explanation
Indices: 31200480--31200517 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
31200470 GGTTGAACCG
31200480 ATTTTCTTTATTT-TAA
1 ATTTT-TTTATTTGTAA
*
31200496 ATTTTTTTATTTGTAT
1 ATTTTTTTATTTGTAA
31200512 ATTTTT
1 ATTTTT
31200518 AATAATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (16 bp):
ATTTTTTTATTTGTAA
Found at i:31200796 original size:19 final size:19
Alignment explanation
Indices: 31200774--31200831 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 19
31200764 GGTTATGGAG
31200774 CATTACCAAACTTATCACA
1 CATTACCAAACTTATCACA
* * ***
31200793 CATT--TAAACATA-CTGG
1 CATTACCAAACTTATCACA
31200809 CATTACCAAACTTATCACA
1 CATTACCAAACTTATCACA
31200828 CATT
1 CATT
31200832 TAAACATACA
Statistics
Matches: 26, Mismatches: 10, Indels: 6
0.62 0.24 0.14
Matches are distributed among these distances:
16 5 0.19
17 6 0.23
18 6 0.23
19 9 0.35
ACGTcount: A:0.40, C:0.28, G:0.03, T:0.29
Consensus pattern (19 bp):
CATTACCAAACTTATCACA
Found at i:31200819 original size:35 final size:35
Alignment explanation
Indices: 31200773--31200840 Score: 136
Period size: 35 Copynumber: 1.9 Consensus size: 35
31200763 AGGTTATGGA
31200773 GCATTACCAAACTTATCACACATTTAAACATACTG
1 GCATTACCAAACTTATCACACATTTAAACATACTG
31200808 GCATTACCAAACTTATCACACATTTAAACATAC
1 GCATTACCAAACTTATCACACATTTAAACATAC
31200841 ATTTCTCATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.41, C:0.26, G:0.04, T:0.28
Consensus pattern (35 bp):
GCATTACCAAACTTATCACACATTTAAACATACTG
Found at i:31206090 original size:16 final size:16
Alignment explanation
Indices: 31206069--31206109 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
31206059 AGGACTTCCA
31206069 CTATTTAATTTCATAG
1 CTATTTAATTTCATAG
31206085 CTATTTAATTTCATAG
1 CTATTTAATTTCATAG
31206101 CTATTTAAT
1 CTATTTAAT
31206110 ACCTTTAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.32, C:0.12, G:0.05, T:0.51
Consensus pattern (16 bp):
CTATTTAATTTCATAG
Found at i:31207828 original size:20 final size:21
Alignment explanation
Indices: 31207795--31207835 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
31207785 ATAAATAATT
* *
31207795 AAAAAATCATTAAAAATGCAA
1 AAAAAAGCATTAAAAAAGCAA
31207816 AAAAAAGCA-TAAAAAAGCAA
1 AAAAAAGCATTAAAAAAGCAA
31207836 TACAAAACCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.71, C:0.10, G:0.07, T:0.12
Consensus pattern (21 bp):
AAAAAAGCATTAAAAAAGCAA
Found at i:31207991 original size:22 final size:21
Alignment explanation
Indices: 31207963--31208009 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
31207953 AAAATCTCAT
31207963 AATTTTATGA-ATTTTTAAAAA
1 AATTTTATGATA-TTTTAAAAA
*
31207984 GAATTTTATGGTATTTTAAAAA
1 -AATTTTATGATATTTTAAAAA
31208006 AATT
1 AATT
31208010 AGCCATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 4 0.17
22 18 0.78
23 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.47
Consensus pattern (21 bp):
AATTTTATGATATTTTAAAAA
Found at i:31208005 original size:23 final size:22
Alignment explanation
Indices: 31207963--31208006 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
31207953 AAAATCTCAT
*
31207963 AATTTTATGAATTTTTAAAAAG
1 AATTTTATGAATTTTAAAAAAG
*
31207985 AATTTTATGGTATTTTAAAAAA
1 AATTTTAT-GAATTTTAAAAAA
31208007 ATTAGCCATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (22 bp):
AATTTTATGAATTTTAAAAAAG
Found at i:31209412 original size:26 final size:26
Alignment explanation
Indices: 31209383--31209437 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
31209373 TTTTTTGGTA
* *
31209383 TTTTGTATTTTGTAATTTTTCATTTT
1 TTTTATATTTTGTAATTTTTCATATT
31209409 TTTTATATTTTGTAATTTTTCATATT
1 TTTTATATTTTGTAATTTTTCATATT
31209435 TTT
1 TTT
31209438 GGGGATATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.18, C:0.04, G:0.05, T:0.73
Consensus pattern (26 bp):
TTTTATATTTTGTAATTTTTCATATT
Found at i:31211363 original size:26 final size:25
Alignment explanation
Indices: 31211319--31211367 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
31211309 ATCATGAGTA
*
31211319 TAGTAAATTTTATTATTATATATTTT
1 TAGTAAATTATATTATTAT-TATTTT
31211345 TAGTAAATATATATT-TTATTATT
1 TAGTAAAT-TATATTATTATTATT
31211368 GATCTATACT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 4 0.19
26 12 0.57
27 5 0.24
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (25 bp):
TAGTAAATTATATTATTATTATTTT
Found at i:31213675 original size:5 final size:5
Alignment explanation
Indices: 31213665--31213708 Score: 88
Period size: 5 Copynumber: 8.8 Consensus size: 5
31213655 ACTAACTATG
31213665 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
31213709 AACACACAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:31221092 original size:43 final size:43
Alignment explanation
Indices: 31220994--31221152 Score: 148
Period size: 43 Copynumber: 3.7 Consensus size: 43
31220984 CAATGCCATA
* ** * **
31220994 TCCCAGATATGGTCTTACATGTTATCACAT-ATCGATGCTGATAG
1 TCCCAGACATGGTCTTACACATAATCACATAAT-GATGCAAAT-G
* *
31221038 -CCCA-ACTATGGTCTTACACGA-AATTA-ATTAATGATGCTAATG
1 TCCCAGAC-ATGGTCTTACAC-ATAATCACA-TAATGATGCAAATG
*
31221080 TCCTAGACATGGTCTTACACATAATCACATAATGATGCAAATG
1 TCCCAGACATGGTCTTACACATAATCACATAATGATGCAAATG
*
31221123 TCCCAGATATGGTCTTACACATAATCACAT
1 TCCCAGACATGGTCTTACACATAATCACAT
31221153 CTCGAAAATC
Statistics
Matches: 96, Mismatches: 11, Indels: 17
0.77 0.09 0.14
Matches are distributed among these distances:
42 4 0.04
43 87 0.91
44 5 0.05
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.31
Consensus pattern (43 bp):
TCCCAGACATGGTCTTACACATAATCACATAATGATGCAAATG
Found at i:31223300 original size:42 final size:43
Alignment explanation
Indices: 31223145--31223289 Score: 170
Period size: 42 Copynumber: 3.4 Consensus size: 43
31223135 TGTGTTTTTG
** * * *
31223145 TGTAAGACCACATCTGGGACGTTGGCATTGACT-TTTGATTTACA
1 TGTAAGACCATGTTTGGGACATTGGCATCGA-TATTTGA-TTACA
* *
31223189 TGTAAGACCATGTTTGGGACATTGGCATCG-TATTTGATTTCG
1 TGTAAGACCATGTTTGGGACATTGGCATCGATATTTGATTACA
* *
31223231 TGTAAGACCCTGTTTGGGACAATGGCATCGATATTTGATTACA
1 TGTAAGACCATGTTTGGGACATTGGCATCGATATTTGATTACA
31223274 TGTAAGA-CATGTTTGG
1 TGTAAGACCATGTTTGG
31223290 AATGTTGGCA
Statistics
Matches: 87, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
42 40 0.46
43 22 0.25
44 25 0.29
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (43 bp):
TGTAAGACCATGTTTGGGACATTGGCATCGATATTTGATTACA
Found at i:31224575 original size:23 final size:23
Alignment explanation
Indices: 31224545--31224590 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
31224535 TGCATGTTTT
*
31224545 GAGATTGAAATTGGCTAAAAATG
1 GAGATTGAAATTGGATAAAAATG
31224568 GAGATTGAAATTGGATAAAAATG
1 GAGATTGAAATTGGATAAAAATG
31224591 TGGTATATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.46, C:0.02, G:0.26, T:0.26
Consensus pattern (23 bp):
GAGATTGAAATTGGATAAAAATG
Found at i:31228790 original size:16 final size:17
Alignment explanation
Indices: 31228769--31228806 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
31228759 TTTTATATGG
*
31228769 ATTTTACT-TTTATTTT
1 ATTTTACTATGTATTTT
31228785 ATTTTACTACTGTATTTT
1 ATTTTACTA-TGTATTTT
31228803 ATTT
1 ATTT
31228807 AAATAAGGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
18 11 0.58
ACGTcount: A:0.21, C:0.08, G:0.03, T:0.68
Consensus pattern (17 bp):
ATTTTACTATGTATTTT
Found at i:31235561 original size:48 final size:48
Alignment explanation
Indices: 31235488--31235683 Score: 286
Period size: 48 Copynumber: 4.0 Consensus size: 48
31235478 AGATATGCAC
*
31235488 GATCCCATGTAAGACCGTGTCTGGGACATGGCATTGGCATCGATATGT
1 GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGT
* * *
31235536 GATCCCATGTAAGACCATGTATGGGACATGGCATTGGCATCAATATGA
1 GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGT
* *
31235584 GA-CACCATGTATGACCATGTCTGGGACATGGCATTGACATCGATATGT
1 GATC-CCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGT
* *
31235632 GATCCCATGTAAGACCATATCTGGGATATGGCATTGGCATCCGACTATGT
1 GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT-CGA-TATGT
31235682 GA
1 GA
31235684 ATGTGATTTC
Statistics
Matches: 131, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
47 1 0.01
48 119 0.91
49 4 0.03
50 7 0.05
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (48 bp):
GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGT
Found at i:31236666 original size:20 final size:20
Alignment explanation
Indices: 31236638--31236677 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
31236628 ACACGGACAT
*
31236638 GTGTTTAGGCCGTGTGTGAC
1 GTGTCTAGGCCGTGTGTGAC
31236658 GTGTCTAGGCCGTGTGTGAC
1 GTGTCTAGGCCGTGTGTGAC
31236678 ACACGGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.10, C:0.17, G:0.40, T:0.33
Consensus pattern (20 bp):
GTGTCTAGGCCGTGTGTGAC
Found at i:31237457 original size:5 final size:6
Alignment explanation
Indices: 31237441--31237497 Score: 64
Period size: 6 Copynumber: 9.8 Consensus size: 6
31237431 TAATTGAACC
* * *
31237441 ATTTTT ATTTTT ATTTTT A-TTGT A-TTTT ATTTTT ATTTTT AATTTA
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
*
31237487 ATTTTT GTTTT
1 ATTTTT ATTTT
31237498 CTAATTCTTC
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
5 8 0.19
6 35 0.81
ACGTcount: A:0.19, C:0.00, G:0.04, T:0.77
Consensus pattern (6 bp):
ATTTTT
Found at i:31241464 original size:14 final size:15
Alignment explanation
Indices: 31241445--31241488 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
31241435 TCCTTTTCTC
31241445 ATTATTA-TTTATTT
1 ATTATTATTTTATTT
31241459 ATTATTATTTTATTTT
1 ATTATTATTTTA-TTT
31241475 ATT-TTATCTTTATT
1 ATTATTAT-TTTATT
31241489 AGTTTTAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 7 0.26
15 10 0.37
16 10 0.37
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (15 bp):
ATTATTATTTTATTT
Found at i:31250236 original size:12 final size:12
Alignment explanation
Indices: 31250219--31250244 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
31250209 GGCATGTGGC
31250219 TGCACACGGCCA
1 TGCACACGGCCA
31250231 TGCACACGGCCA
1 TGCACACGGCCA
31250243 TG
1 TG
31250245 TCGCACGGTC
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:0.23, C:0.38, G:0.27, T:0.12
Consensus pattern (12 bp):
TGCACACGGCCA
Found at i:31255423 original size:5 final size:5
Alignment explanation
Indices: 31255409--31255469 Score: 54
Period size: 6 Copynumber: 11.6 Consensus size: 5
31255399 GACCTTTGAG
*
31255409 TTTA- TTTAT TTTAT TCTAT TTTATT TTTAAT TTTA- TTTATT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTA-T TTT-AT TTTAT TTTA-T TTTAT
31255455 GTTTATT TTTAT TTT
1 -TTTA-T TTTAT TTT
31255470 CTTAGACTTA
Statistics
Matches: 48, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
4 8 0.17
5 18 0.38
6 20 0.42
7 2 0.04
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.77
Consensus pattern (5 bp):
TTTAT
Found at i:31255430 original size:10 final size:9
Alignment explanation
Indices: 31255409--31255451 Score: 50
Period size: 9 Copynumber: 4.3 Consensus size: 9
31255399 GACCTTTGAG
31255409 TTTATTTAT
1 TTTATTTAT
31255418 TTTATTCTAT
1 TTTATT-TAT
31255428 TTTATTTTTAAT
1 TTTA--TTT-AT
31255440 TTTATTTAT
1 TTTATTTAT
31255449 TTT
1 TTT
31255452 TATGTTTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
9 11 0.37
10 10 0.33
11 1 0.03
12 8 0.27
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTATTTAT
Found at i:31255444 original size:22 final size:22
Alignment explanation
Indices: 31255416--31255468 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
31255406 GAGTTTATTT
*
31255416 ATTTTATTCTA-TTTTATTTTTA
1 ATTTTATT-TATTTTTATGTTTA
31255438 ATTTTATTTATTTTTATGTTTA
1 ATTTTATTTATTTTTATGTTTA
*
31255460 TTTTTATTT
1 ATTTTATTT
31255469 TCTTAGACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 2 0.07
22 26 0.93
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (22 bp):
ATTTTATTTATTTTTATGTTTA
Found at i:31255447 original size:16 final size:15
Alignment explanation
Indices: 31255409--31255462 Score: 65
Period size: 16 Copynumber: 3.5 Consensus size: 15
31255399 GACCTTTGAG
31255409 TTTATTTA-TTTTAT
1 TTTATTTATTTTTAT
*
31255423 TCTATTTTATTTTTAAT
1 TTTA-TTTATTTTT-AT
31255440 TTTATTTATTTTTAT
1 TTTATTTATTTTTAT
31255455 GTTTATTT
1 -TTTATTT
31255463 TTATTTTCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
14 3 0.09
15 6 0.18
16 20 0.59
17 5 0.15
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (15 bp):
TTTATTTATTTTTAT
Found at i:31258165 original size:43 final size:43
Alignment explanation
Indices: 31258046--31258200 Score: 127
Period size: 42 Copynumber: 3.6 Consensus size: 43
31258036 AGCTCGTACA
* ** * * * *
31258046 ATGCCAACGTCCCAGATGTGGTCTTACATG-TATCAAATATTG
1 ATGCCAATGTCCCAGACATGGTCTTAAACGAAATCAAATATCG
* *
31258088 ATGCCACTGTCCCAGACATGGTCTTACACGAAATCAAATA-CG
1 ATGCCAATGTCCCAGACATGGTCTTAAACGAAATCAAATATCG
* * *
31258130 ATGCCAATGTCCTAGACATGGTCTTAAACATAAATCTCAATATC-
1 ATGCCAATGTCCCAGACATGGTCTTAAAC-GAAATC-AAATATCG
* * *
31258174 AGCGCCAATGTCCCGGACGTGGTCTTA
1 A-TGCCAATGTCCCAGACATGGTCTTA
31258201 CATGAAAATA
Statistics
Matches: 92, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
42 52 0.57
43 13 0.14
44 5 0.05
45 22 0.24
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.26
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTAAACGAAATCAAATATCG
Found at i:31261670 original size:23 final size:24
Alignment explanation
Indices: 31261626--31261670 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
31261616 CAAGTCCTAC
*
31261626 CCATCCAGCCTCTACACTCCATCT
1 CCATCCAACCTCTACACTCCATCT
*
31261650 CCATCCAACC-CTATACTCCAT
1 CCATCCAACCTCTACACTCCAT
31261671 GTGGGGATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.24, C:0.49, G:0.02, T:0.24
Consensus pattern (24 bp):
CCATCCAACCTCTACACTCCATCT
Found at i:31271806 original size:43 final size:42
Alignment explanation
Indices: 31271660--31271817 Score: 142
Period size: 43 Copynumber: 3.7 Consensus size: 42
31271650 ATGTGTTTTT
* * *
31271660 GTGTAAGACCACATCTGGGACTTTGGCATCGACT-TATGATTTAC
1 GTGTAAGACCACATCTAGGAC-GTGGCATCGA-TATTTGA-TTAC
* * * *
31271704 GTGTAAGAACACGTCTGGGACGTTGGCATCG-TATTTGATTTC
1 GTGTAAGACCACATCTAGGACG-TGGCATCGATATTTGATTAC
31271746 GTGTAAGACC-CTATCTAGGACAGTGGCATCGATATTTGATTAC
1 GTGTAAGACCAC-ATCTAGGAC-GTGGCATCGATATTTGATTAC
* * *
31271789 ATGTAAGACCACGTCTAGGATGTTGGCAT
1 GTGTAAGACCACATCTAGGACG-TGGCAT
31271818 TGTACGACCT
Statistics
Matches: 95, Mismatches: 12, Indels: 15
0.78 0.10 0.12
Matches are distributed among these distances:
41 1 0.01
42 29 0.31
43 37 0.39
44 28 0.29
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.31
Consensus pattern (42 bp):
GTGTAAGACCACATCTAGGACGTGGCATCGATATTTGATTAC
Found at i:31272586 original size:10 final size:10
Alignment explanation
Indices: 31272546--31272588 Score: 50
Period size: 11 Copynumber: 4.1 Consensus size: 10
31272536 GATTGAAATA
*
31272546 TATGCTTTGG
1 TATGATTTGG
31272556 TATGATTTTGG
1 TATGA-TTTGG
*
31272567 TTTAGATTTGG
1 TAT-GATTTGG
31272578 TATGATTTGG
1 TATGATTTGG
31272588 T
1 T
31272589 TGGTGAATTG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
10 12 0.43
11 14 0.50
12 2 0.07
ACGTcount: A:0.16, C:0.02, G:0.28, T:0.53
Consensus pattern (10 bp):
TATGATTTGG
Found at i:31279545 original size:6 final size:6
Alignment explanation
Indices: 31279534--31279562 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
31279524 CACCCCTCCC
31279534 ATGCAT ATGCAT ATGCAT ATGCA- ATGCAT
1 ATGCAT ATGCAT ATGCAT ATGCAT ATGCAT
31279563 CCATTATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (6 bp):
ATGCAT
Found at i:31281396 original size:4 final size:4
Alignment explanation
Indices: 31281387--31281414 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
31281377 GAGTTTGTGG
31281387 TTGA TTGA TTGA TTGA TTGA TTGA TTGA
1 TTGA TTGA TTGA TTGA TTGA TTGA TTGA
31281415 ATTTAAGCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TTGA
Found at i:31286485 original size:41 final size:41
Alignment explanation
Indices: 31286440--31286536 Score: 167
Period size: 41 Copynumber: 2.4 Consensus size: 41
31286430 ATCAATAGGT
* *
31286440 CTGCTCACACAAGTTGTCAGTCAAGACGTAGCTACGCGGTG
1 CTGCTCACACAAGTTGTCAGTCAAGACATAGCTACGCGATG
*
31286481 CTGCTCACACAAGTTGTCAGTCAAGACATAGCTATGCGATG
1 CTGCTCACACAAGTTGTCAGTCAAGACATAGCTACGCGATG
31286522 CTGCTCACACAAGTT
1 CTGCTCACACAAGTT
31286537 TTCAAGTATC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.24
Consensus pattern (41 bp):
CTGCTCACACAAGTTGTCAGTCAAGACATAGCTACGCGATG
Found at i:31290279 original size:16 final size:17
Alignment explanation
Indices: 31290254--31290291 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
31290244 AGATATGAAA
31290254 TTTA-TTTTTTT-ACAG
1 TTTATTTTTTTTAACAG
31290269 TTTATTTTTTTTAACAG
1 TTTATTTTTTTTAACAG
*
31290286 TATATT
1 TTTATT
31290292 GAGAATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 4 0.20
16 7 0.35
17 9 0.45
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (17 bp):
TTTATTTTTTTTAACAG
Found at i:31294121 original size:40 final size:40
Alignment explanation
Indices: 31294066--31294190 Score: 118
Period size: 40 Copynumber: 3.2 Consensus size: 40
31294056 ACTGATGATA
31294066 GTGTGCCC-TGCACTAGTCAGATAAATCGACGATATCAAAT
1 GTGTGCCCAT-CACTAGTCAGATAAATCGACGATATCAAAT
* * * *
31294106 GTGTGCCCATCACTAGTCAGATAAATC-A-AAAAT-GAGT
1 GTGTGCCCATCACTAGTCAGATAAATCGACGATATCAAAT
* * * *
31294143 -TATGCCCAGT-GCTAGTCGGATAAACCGACGATATCAAAT
1 GTGTGCCCA-TCACTAGTCAGATAAATCGACGATATCAAAT
31294182 GTGTGCCCA
1 GTGTGCCCA
31294191 ACAGTAGTTG
Statistics
Matches: 66, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
36 20 0.30
37 4 0.06
38 6 0.09
39 3 0.05
40 32 0.48
41 1 0.02
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (40 bp):
GTGTGCCCATCACTAGTCAGATAAATCGACGATATCAAAT
Found at i:31294159 original size:76 final size:76
Alignment explanation
Indices: 31294078--31294234 Score: 208
Period size: 76 Copynumber: 2.1 Consensus size: 76
31294068 GTGCCCTGCA
* *
31294078 CTAGTCAGATAAATCGACGATATCAAATGTGTGCCCATCACTAGTCAGATAAATCA-AAAATGAG
1 CTAGTCAGATAAACCGACGATATCAAATGTGTGCCCAACACTAGTCAGATAAA-CAGAAAATGAG
31294142 TTATGCCCAGTG
65 TTATGCCCAGTG
* * ** * *
31294154 CTAGTCGGATAAACCGACGATATCAAATGTGTGCCCAACAGTAGTTGGATAAACAGACAATGATT
1 CTAGTCAGATAAACCGACGATATCAAATGTGTGCCCAACACTAGTCAGATAAACAGAAAATGAGT
*
31294219 TGTGCCCAGTG
66 TATGCCCAGTG
*
31294230 TTAGT
1 CTAGT
31294235 TGGGTAAATA
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
75 2 0.03
76 68 0.97
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.25
Consensus pattern (76 bp):
CTAGTCAGATAAACCGACGATATCAAATGTGTGCCCAACACTAGTCAGATAAACAGAAAATGAGT
TATGCCCAGTG
Found at i:31298370 original size:16 final size:15
Alignment explanation
Indices: 31298349--31298392 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
31298339 AAAAGTGATA
31298349 AAAATATAGAAAAAAG
1 AAAATA-AGAAAAAAG
*
31298365 AAAATACGAAAAAAAG
1 AAAATAAG-AAAAAAG
31298381 AACAATAAGAAA
1 AA-AATAAGAAA
31298393 GTATTCTGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 1 0.04
16 18 0.75
17 5 0.21
ACGTcount: A:0.75, C:0.05, G:0.11, T:0.09
Consensus pattern (15 bp):
AAAATAAGAAAAAAG
Found at i:31298378 original size:17 final size:17
Alignment explanation
Indices: 31298358--31298392 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
31298348 AAAAATATAG
*
31298358 AAAAAAGAA-AATACGA
1 AAAAAAGAACAATAAGA
31298374 AAAAAAGAACAATAAGA
1 AAAAAAGAACAATAAGA
31298391 AA
1 AA
31298393 GTATTCTGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.77, C:0.06, G:0.11, T:0.06
Consensus pattern (17 bp):
AAAAAAGAACAATAAGA
Found at i:31302724 original size:63 final size:63
Alignment explanation
Indices: 31302657--31302780 Score: 239
Period size: 63 Copynumber: 2.0 Consensus size: 63
31302647 AGAAAATAAT
31302657 AAAAAAAGAAATTTAAAGGAAATATTTACATAAAATAATAGGAAATCAATAATGTATACTTGG
1 AAAAAAAGAAATTTAAAGGAAATATTTACATAAAATAATAGGAAATCAATAATGTATACTTGG
*
31302720 AAAAAAAGAAATTTAAAGGAAATATTTACATAAAATAATATGAAATCAATAATGTATACTT
1 AAAAAAAGAAATTTAAAGGAAATATTTACATAAAATAATAGGAAATCAATAATGTATACTT
31302781 AAGAGTAAAA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.56, C:0.05, G:0.10, T:0.28
Consensus pattern (63 bp):
AAAAAAAGAAATTTAAAGGAAATATTTACATAAAATAATAGGAAATCAATAATGTATACTTGG
Found at i:31304732 original size:177 final size:176
Alignment explanation
Indices: 31304423--31304839 Score: 593
Period size: 177 Copynumber: 2.4 Consensus size: 176
31304413 TAGTCTTTCA
* ** * * * * *
31304423 GCAACTTCAGGAAGATCAGGTTTGTGA-CTTCAACCTACTTCACTGCAACTTCAGAGAGACAAAG
1 GCAACTTCAGGAAGATAAGACTAGT-ATCTTCAACCTGC-TCTCTGCAACTTCAGAGAGATAAGG
* * *
31304487 CTGATGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGACTCGCCATCTTTGACCTACTC
64 TTGGTGGCTAAAATCTGATCCATAGCCGATACATGGAGATAAGACTCGCCATCTTTGACCTACTC
* *
31304552 CATAGCCGATACATGGAAATAAGATCTGTTATTTTCAGTCTGCTTCCT
129 CATAGCCGATACATGGAAATAAGATCTGTAATTTTCAGTATGCTTCCT
* * * *
31304600 GCAACTTTAGGAAGATAAGACTTGTATCTTCAACCTGCTCTCTTGCTACTTTAGAGAGATAAGGT
1 GCAACTTCAGGAAGATAAGACTAGTATCTTCAACCTGCTCTC-TGCAACTTCAGAGAGATAAGGT
* * * *
31304665 TGGTGGCTAAAATCTGATCCATAGCTGATACATGGAGATAAGACTCGCCATTTTTGATCTGCTCC
65 TGGTGGCTAAAATCTGATCCATAGCCGATACATGGAGATAAGACTCGCCATCTTTGACCTACTCC
* *
31304730 ATAGCCGATACATGGAGATAAGATCTGTAATTTTCAGTATGTTTCCT
130 ATAGCCGATACATGGAAATAAGATCTGTAATTTTCAGTATGCTTCCT
31304777 GCAACTTCAGGAAGATAAGACTAGTATCTTCAACCTGCTCTCTGCAACTTCAGAGAGATAAGG
1 GCAACTTCAGGAAGATAAGACTAGTATCTTCAACCTGCTCTCTGCAACTTCAGAGAGATAAGG
31304840 CTTGTAATCT
Statistics
Matches: 213, Mismatches: 25, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
176 23 0.11
177 190 0.89
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (176 bp):
GCAACTTCAGGAAGATAAGACTAGTATCTTCAACCTGCTCTCTGCAACTTCAGAGAGATAAGGTT
GGTGGCTAAAATCTGATCCATAGCCGATACATGGAGATAAGACTCGCCATCTTTGACCTACTCCA
TAGCCGATACATGGAAATAAGATCTGTAATTTTCAGTATGCTTCCT
Found at i:31304880 original size:45 final size:43
Alignment explanation
Indices: 31304775--31304882 Score: 117
Period size: 43 Copynumber: 2.5 Consensus size: 43
31304765 AGTATGTTTC
* * *
31304775 CTGCAACTTCAGGAAGATAAGACTAGTATCTTCAACCTGCTCT
1 CTGCAACTTCAGGGAGATAAGACTAGTATCTTCAACCTACTCG
* * * * *
31304818 CTGCAACTTCAGAGAGATAAGGCTTGTAATCTTCAATCTATTCCG
1 CTGCAACTTCAGGGAGATAAGACTAGT-ATCTTCAACCTACT-CG
*
31304863 CTGCAACTTTAGGGAGATAA
1 CTGCAACTTCAGGGAGATAA
31304883 TATCTGACTT
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
43 23 0.43
44 11 0.21
45 19 0.36
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.29
Consensus pattern (43 bp):
CTGCAACTTCAGGGAGATAAGACTAGTATCTTCAACCTACTCG
Found at i:31305053 original size:64 final size:64
Alignment explanation
Indices: 31304952--31305078 Score: 227
Period size: 64 Copynumber: 2.0 Consensus size: 64
31304942 TCATATATCT
31304952 ATGCTTATGCCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCGCCTAACTACATGTG
1 ATGCTTATGCCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCGCCTAACTACATGTG
* * *
31305016 ATGCTTATGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGT
1 ATGCTTATGCCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCGCCTAACTACATGT
31305079 ATTATGAATG
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 60 1.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (64 bp):
ATGCTTATGCCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCGCCTAACTACATGTG
Found at i:31311071 original size:40 final size:40
Alignment explanation
Indices: 31311016--31311098 Score: 148
Period size: 40 Copynumber: 2.1 Consensus size: 40
31311006 TAGCTTCATC
31311016 TTCAGTTACTGGTTCATAAACCAGTGGTTTTGTCCTCTCT
1 TTCAGTTACTGGTTCATAAACCAGTGGTTTTGTCCTCTCT
* *
31311056 TTCAGTTACTGGTTCATTAACCAGTGGTTTTGTCCTCTTT
1 TTCAGTTACTGGTTCATAAACCAGTGGTTTTGTCCTCTCT
31311096 TTC
1 TTC
31311099 CCTTGTTCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.16, C:0.22, G:0.17, T:0.46
Consensus pattern (40 bp):
TTCAGTTACTGGTTCATAAACCAGTGGTTTTGTCCTCTCT
Found at i:31317006 original size:18 final size:17
Alignment explanation
Indices: 31316970--31317013 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
31316960 TTCAAAATAG
*
31316970 ATAAAAATAATAATTAA
1 ATAAAAATAATAATGAA
*
31316987 ATAAAAATCATATATGAA
1 ATAAAAATAATA-ATGAA
*
31317005 ATAATAATA
1 ATAAAAATA
31317014 TTTGAAAGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (17 bp):
ATAAAAATAATAATGAA
Found at i:31322558 original size:19 final size:19
Alignment explanation
Indices: 31322525--31322570 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
31322515 AGTTGTAAGT
* *
31322525 ATATATATGTGAATAATTTG
1 ATAT-TATGTAAATAATGTG
31322545 ATATTATGTAAATAATGTG
1 ATATTATGTAAATAATGTG
*
31322564 ACATTAT
1 ATATTAT
31322571 TATATGTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.41, C:0.02, G:0.13, T:0.43
Consensus pattern (19 bp):
ATATTATGTAAATAATGTG
Found at i:31326231 original size:30 final size:31
Alignment explanation
Indices: 31326166--31326233 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
31326156 CCGTGTACTT
* *
31326166 GCCCGTGTGACTCACATGGCCAGGGTACACA
1 GCCCGTGTAACTCACATAGCCAGGGTACACA
*
31326197 -CCCGTGTAACTCACATAGCCTA-GGTTCA-A
1 GCCCGTGTAACTCACATAGCC-AGGGTACACA
31326226 GCCCGTGT
1 GCCCGTGT
31326234 CCCTGGCTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
29 1 0.03
30 30 0.94
31 1 0.03
ACGTcount: A:0.22, C:0.32, G:0.25, T:0.21
Consensus pattern (31 bp):
GCCCGTGTAACTCACATAGCCAGGGTACACA
Found at i:31336325 original size:17 final size:17
Alignment explanation
Indices: 31336303--31336343 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
31336293 TGAGTTCTAG
31336303 TAGCTATAAGTATCAAA
1 TAGCTATAAGTATCAAA
31336320 TAGCTATAAGTATCAAA
1 TAGCTATAAGTATCAAA
31336337 TAGCTAT
1 TAGCTAT
31336344 GAAATTCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (17 bp):
TAGCTATAAGTATCAAA
Found at i:31336352 original size:17 final size:17
Alignment explanation
Indices: 31336303--31336353 Score: 68
Period size: 17 Copynumber: 3.0 Consensus size: 17
31336293 TGAGTTCTAG
*
31336303 TAGCTATAAGTATCAAA
1 TAGCTATAAATATCAAA
*
31336320 TAGCTATAAGTATCAAA
1 TAGCTATAAATATCAAA
31336337 TAGCTATGAAAT-TCAAA
1 TAGCTAT-AAATATCAAA
31336354 ACTTGAGGCC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 29 0.91
18 3 0.09
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (17 bp):
TAGCTATAAATATCAAA
Found at i:31341262 original size:39 final size:41
Alignment explanation
Indices: 31341167--31341350 Score: 208
Period size: 40 Copynumber: 4.6 Consensus size: 41
31341157 TTGAATGATG
*
31341167 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGT-ACTAATA
*
31341206 TCCGGACTAAGAT-CCGAAGGCATTTGTGCG-AGATACTAAT-
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAAG-TACTAATA
31341246 TCCGGGCTAAG-CCCGAAGGCATTTGTGCG-AGTTACTAA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAG-TACTAATA
* *
31341285 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACT-ATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATA
* *
31341325 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
31341351 AACGAGGAGC
Statistics
Matches: 126, Mismatches: 9, Indels: 19
0.82 0.06 0.12
Matches are distributed among these distances:
39 54 0.43
40 61 0.48
41 11 0.09
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATA
Found at i:31341302 original size:79 final size:81
Alignment explanation
Indices: 31341167--31341350 Score: 222
Period size: 79 Copynumber: 2.3 Consensus size: 81
31341157 TTGAATGATG
31341167 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
31341230 TGTGCGAGA-TACTA-A
66 TGTGCGA-ATTACTATA
* * **
31341245 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAA-ATCCGGGTTAAG-TCCCGAAGGC
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGAC-AATATCCGGACTAAGAT-CCGAAGGC
31341306 ATTTGTGCGAATTACTATA
63 ATTTGTGCGAATTACTATA
* *
31341325 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
31341351 AACGAGGAGC
Statistics
Matches: 92, Mismatches: 6, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
78 11 0.12
79 58 0.63
80 23 0.25
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
TGTGCGAATTACTATA
Found at i:31341372 original size:79 final size:79
Alignment explanation
Indices: 31341219--31341383 Score: 194
Period size: 79 Copynumber: 2.1 Consensus size: 79
31341209 GGACTAAGAT
* ** *
31341219 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
*
31341284 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
*
31341298 CCGAAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAG
1 CCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-
* *
31341360 CTATATCC-GGTTAAATT
62 CTAAATCCGGGTTAAATC
31341377 CCGAAGG
1 CCGAAGG
31341384 TACGTGATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
78 3 0.04
79 46 0.62
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
ATCCGGGTTAAATC
Found at i:31349204 original size:27 final size:27
Alignment explanation
Indices: 31349173--31349350 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
31349163 TAAATTGTAC
31349173 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
31349200 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
31349226 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
31349254 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
31349282 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
31349309 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
31349336 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
31349351 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:31349287 original size:82 final size:81
Alignment explanation
Indices: 31349174--31349329 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
31349164 AAATTGTACA
* *
31349174 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
31349238 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
31349255 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
31349320 TGCGAGTTGA
65 TGCGAATTGA
31349330 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:31349341 original size:82 final size:81
Alignment explanation
Indices: 31349170--31349350 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
31349160 GATTAAATTG
* *
31349170 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
31349235 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
31349251 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
31349315 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
31349333 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
31349351 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:31349847 original size:46 final size:46
Alignment explanation
Indices: 31349780--31349871 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
31349770 ATTGCTTATG
31349780 ACTTACTGAGTTATAAACTCACTCGGTGTTTCCTTGTCACCCATTA
1 ACTTACTGAGTTATAAACTCACTCGGTGTTTCCTTGTCACCCATTA
31349826 ACTTACTGAGTTATAAACTCACTCGGTGTTTCCTTGTCACCCATTA
1 ACTTACTGAGTTATAAACTCACTCGGTGTTTCCTTGTCACCCATTA
31349872 TAGGTTGCTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.24, C:0.26, G:0.13, T:0.37
Consensus pattern (46 bp):
ACTTACTGAGTTATAAACTCACTCGGTGTTTCCTTGTCACCCATTA
Found at i:31355714 original size:18 final size:18
Alignment explanation
Indices: 31355691--31355729 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
31355681 ATTGTGAAAT
31355691 AAGAAAATTCTATTAGTA
1 AAGAAAATTCTATTAGTA
*
31355709 AAGAAAATTCTGTTAGTA
1 AAGAAAATTCTATTAGTA
31355727 AAG
1 AAG
31355730 GTACTGTGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.49, C:0.05, G:0.15, T:0.31
Consensus pattern (18 bp):
AAGAAAATTCTATTAGTA
Found at i:31364202 original size:22 final size:22
Alignment explanation
Indices: 31364163--31364265 Score: 143
Period size: 22 Copynumber: 4.5 Consensus size: 22
31364153 CATCTCGTAT
* *
31364163 GAGCTTACCGATTCAGCTCGATA
1 GAGCTTACTG-TTCAGCTCAATA
31364186 GAGCTTACTGTTCAGCTCAATA
1 GAGCTTACTGTTCAGCTCAATA
31364208 GAGCTTACTGTTCAGCTCAATA
1 GAGCTTACTGTTCAGCTCAATA
* *
31364230 GAGCTTACCGCTTTCAGCCCAATA
1 GAGCTTACTG--TTCAGCTCAATA
31364254 GAGCTTACTGTT
1 GAGCTTACTGTT
31364266 TATCAGCTCG
Statistics
Matches: 73, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
22 44 0.60
23 9 0.12
24 20 0.27
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.30
Consensus pattern (22 bp):
GAGCTTACTGTTCAGCTCAATA
Found at i:31364261 original size:46 final size:44
Alignment explanation
Indices: 31364163--31364265 Score: 143
Period size: 46 Copynumber: 2.3 Consensus size: 44
31364153 CATCTCGTAT
* * * *
31364163 GAGCTTACCGATTCAGCTCGATAGAGCTTACTGTTCAGCTCAATA
1 GAGCTTACTG-TTCAGCTCAATAGAGCTTACCGTTCAGCCCAATA
31364208 GAGCTTACTGTTCAGCTCAATAGAGCTTACCGCTTTCAGCCCAATA
1 GAGCTTACTGTTCAGCTCAATAGAGCTTACCG--TTCAGCCCAATA
31364254 GAGCTTACTGTT
1 GAGCTTACTGTT
31364266 TATCAGCTCG
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
44 20 0.38
45 9 0.17
46 23 0.44
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.30
Consensus pattern (44 bp):
GAGCTTACTGTTCAGCTCAATAGAGCTTACCGTTCAGCCCAATA
Found at i:31364506 original size:20 final size:20
Alignment explanation
Indices: 31364469--31364549 Score: 83
Period size: 20 Copynumber: 4.0 Consensus size: 20
31364459 TAATAATAAG
*
31364469 ATATGTGTTTATATGGATGAA
1 ATAT-TGTTTATACGGATGAA
*
31364490 ATATTGTTGATACGGATGAA
1 ATATTGTTTATACGGATGAA
* *
31364510 TTATTG-TTATTACTGATGAA
1 ATATTGTTTA-TACGGATGAA
* *
31364530 CTATTATTTATACGGATGAA
1 ATATTGTTTATACGGATGAA
31364550 TTACTGGTTA
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
19 2 0.04
20 41 0.82
21 7 0.14
ACGTcount: A:0.33, C:0.05, G:0.20, T:0.42
Consensus pattern (20 bp):
ATATTGTTTATACGGATGAA
Found at i:31364569 original size:40 final size:40
Alignment explanation
Indices: 31364484--31364560 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
31364474 TGTTTATATG
* * *
31364484 GATGAAATATTGTTGATACGGATGAATTATTGTTATTACT
1 GATGAAATATTATTTATACGGATGAATTATGGTTATTACT
*
31364524 GATGAACTATTATTTATACGGATGAATTACTGGTTAT
1 GATGAAATATTATTTATACGGATGAATTA-TGGTTAT
31364561 GTGAATGAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
40 26 0.81
41 6 0.19
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.42
Consensus pattern (40 bp):
GATGAAATATTATTTATACGGATGAATTATGGTTATTACT
Found at i:31364580 original size:40 final size:40
Alignment explanation
Indices: 31364484--31364582 Score: 96
Period size: 40 Copynumber: 2.5 Consensus size: 40
31364474 TGTTTATATG
* * *
31364484 GATGAAATATTGTTGATACGGATGAATTATTGTTATTACT
1 GATGAAATATAGTTTATACGGATGAATTATGGTTATTACT
* *
31364524 GATGAACTATTA-TTTATACGGATGAATTACTGGTTA-T-GT
1 GATGAAATA-TAGTTTATACGGATGAATTA-TGGTTATTACT
*
31364563 GAATGAATTATAGTTTATAC
1 G-ATGAAATATAGTTTATAC
31364583 AAATAGAAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
39 4 0.08
40 39 0.80
41 6 0.12
ACGTcount: A:0.33, C:0.06, G:0.19, T:0.41
Consensus pattern (40 bp):
GATGAAATATAGTTTATACGGATGAATTATGGTTATTACT
Found at i:31367791 original size:20 final size:20
Alignment explanation
Indices: 31367766--31367819 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
31367756 AATAGGGGTC
31367766 ACATGCCCGTGTGGTTTGGG
1 ACATGCCCGTGTGGTTTGGG
31367786 ACATGCCCGTGTGGTTTGGG
1 ACATGCCCGTGTGGTTTGGG
**
31367806 ACACACCCGTGTGG
1 ACATGCCCGTGTGG
31367820 GCAAGCCCTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.13, C:0.24, G:0.37, T:0.26
Consensus pattern (20 bp):
ACATGCCCGTGTGGTTTGGG
Found at i:31369745 original size:40 final size:40
Alignment explanation
Indices: 31369659--31369882 Score: 290
Period size: 40 Copynumber: 5.6 Consensus size: 40
31369649 TATTCGGATG
* *
31369659 ATATCCGGGCTAAGACCCAAAGGCACTTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCA-TTTGTGCTAGTGACT
* * *
31369700 ATATCCGGGTTAAGTCCCGAAGGCATTTGCGCTAGTGACG
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
*
31369740 ATATCCGGGCTAAGACCCGAAGGCATTTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCA-TTTGTGCTAGTGACT
* * *
31369781 ATATCCGGGATAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
31369821 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGATTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTA-GTGACT
* *
31369861 ATATCC-GGTTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
31369883 TACTTGGGTT
Statistics
Matches: 163, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
39 14 0.09
40 90 0.55
41 59 0.36
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:31369795 original size:81 final size:80
Alignment explanation
Indices: 31369658--31369882 Score: 319
Period size: 81 Copynumber: 2.8 Consensus size: 80
31369648 TTATTCGGAT
*
31369658 GATATCCGGGCTAAGACCCAAAGGCACTTTGTGCTAGTGACTATATCCGGGTTAAGTCCCGAAGG
1 GATATCCGGGCTAAGACCCGAAGGCA-TTTGTGCTAGTGACTATATCCGGGTTAAGTCCCGAAGG
*
31369723 CATTTGCGCTAGTGAC
65 CATTTGCGCGAGTGAC
*
31369739 GATATCCGGGCTAAGACCCGAAGGCATTTTGTGCTAGTGACTATATCCGGGATAAGTCCCGAAGG
1 GATATCCGGGCTAAGACCCGAAGGCA-TTTGTGCTAGTGACTATATCCGGGTTAAGTCCCGAAGG
* *
31369804 CATTTGTGCGAGTTAC
65 CATTTGCGCGAGTGAC
* * * * *
31369820 TATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGATTTG-CTATATCC-GGTTAAATCCCGAAGG
1 GATATCCGGGCTAAGACCCGAAGGCATTTGTGCTA-GTGACTATATCCGGGTTAAGTCCCGAAGG
31369883 TACTTGGGTT
Statistics
Matches: 131, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
79 14 0.11
80 16 0.12
81 101 0.77
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.26
Consensus pattern (80 bp):
GATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACTATATCCGGGTTAAGTCCCGAAGGC
ATTTGCGCGAGTGAC
Found at i:31375854 original size:24 final size:24
Alignment explanation
Indices: 31375811--31375856 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
31375801 TGTGTTTTTC
*
31375811 AAGTATATGTTTGATAATATGATA
1 AAGTATATGTTTCATAATATGATA
31375835 AAGTCATATGTTTCAT-ATATGA
1 AAGT-ATATGTTTCATAATATGA
31375857 ACTCAATAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.39, C:0.04, G:0.15, T:0.41
Consensus pattern (24 bp):
AAGTATATGTTTCATAATATGATA
Found at i:31379657 original size:43 final size:43
Alignment explanation
Indices: 31379609--31379779 Score: 154
Period size: 43 Copynumber: 4.0 Consensus size: 43
31379599 GTTATCAAGA
*
31379609 TGAGATTACATGTAAGACCATGCCTGGGACATTGGCATTGTAC
1 TGAGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAC
* * *
31379652 TGAGATTTCATCTAAGACCATGTCTGGGACATTGGCATAAT-TAA
1 TGAGATTACATGTAAGACCATGTCTGGGACATTGGCAT--TGTAC
* * * * *
31379696 T-TGATTTCGTGTAAGA-CATTGTCTGGGACAGTGGCATCGATA-
1 TGAGATTACATGTAAGACCA-TGTCTGGGACATTGGCATTG-TAC
* * * *
31379738 TGTGATAACATGTAAGACCATATCTGGGATA-TGGCATTGTAC
1 TGAGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAC
31379780 GAGCTTATGT
Statistics
Matches: 105, Mismatches: 15, Indels: 17
0.77 0.11 0.12
Matches are distributed among these distances:
41 2 0.02
42 10 0.10
43 87 0.83
44 5 0.05
45 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.31
Consensus pattern (43 bp):
TGAGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAC
Found at i:31382783 original size:47 final size:47
Alignment explanation
Indices: 31382692--31383057 Score: 515
Period size: 47 Copynumber: 7.7 Consensus size: 47
31382682 TCTGTACATG
* *
31382692 ATGTGATGAATGTGAA-AGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAACA-TG--TATATATGTGATAAGGCCGAATGGCCA
* *
31382741 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAACA-TGTATATATGTGATAAGGCCGAATGGCCA
31382788 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACA-TGTATATATGTGATAAGGCCGAATGGCCA
* *
31382835 ATGTGATGAATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA
* *
31382882 ATGTGATGAATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA
* *
31382929 ATGTGATGAATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA
* *
31382976 ATGTGATGAATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA
* * *
31383023 ATGTGATGGATGTGGAA-GTGTATAAATGTGATAAG
1 ATGTGATGAATGT-GAACATGTATATATGTGATAAG
31383058 TCCCGAAGGG
Statistics
Matches: 306, Mismatches: 9, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
47 282 0.92
48 4 0.01
49 20 0.07
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.29
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCA
Found at i:31386902 original size:40 final size:40
Alignment explanation
Indices: 31386837--31387047 Score: 248
Period size: 40 Copynumber: 5.3 Consensus size: 40
31386827 TCTTCGGAAT
* * * *
31386837 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTC
* * * * *
31386876 TTAACCCGGGT-ATAGCAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATAAAATC-ACTAGCACAAATGCCTTCGGGTC
* * *
31386916 TTAGCCCGGAT-ATATCAACTCGCACAAATGCCTTCGGGCC
1 TTAGCCCGGATAAAATC-ACTAGCACAAATGCCTTCGGGTC
*
31386956 TTAGCCCGGATAAAATCACTAGCATAAATGCCTTCGGGTC
1 TTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTC
* *
31386996 TTAACCCGGATAAAATCACTAGCACAAATGCCTTCGGGAC
1 TTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTC
31387036 TTAGCCCGGATA
1 TTAGCCCGGATA
31387048 TCATTCAAAT
Statistics
Matches: 149, Mismatches: 20, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
39 5 0.03
40 140 0.94
41 4 0.03
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.23
Consensus pattern (40 bp):
TTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTC
Found at i:31389159 original size:38 final size:38
Alignment explanation
Indices: 31389095--31389169 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
31389085 AATCCGAGTT
*
31389095 TAAAGACCCGCTGACTATATGAAGAGATTATGTCCGGG
1 TAAAGACCCGATGACTATATGAAGAGATTATGTCCGGG
* *
31389133 TAAAGACCCGATGGCTATGT-ACAGAGATTATGTCCGG
1 TAAAGACCCGATGACTATATGA-AGAGATTATGTCCGG
31389170 ATTAAAATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 1 0.03
38 32 0.97
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.24
Consensus pattern (38 bp):
TAAAGACCCGATGACTATATGAAGAGATTATGTCCGGG
Found at i:31389282 original size:40 final size:40
Alignment explanation
Indices: 31389223--31389586 Score: 532
Period size: 40 Copynumber: 9.1 Consensus size: 40
31389213 AGGTCTCGAC
31389223 GATG-ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
*
31389262 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* * *
31389302 GATGTATCCGTGCTAAGTCCCAAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* * *
31389342 GATGTACCCGGGCTAAGTCCCGAAGAGCATTCATGCTTGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
31389382 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
*
31389422 GATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* *
31389462 GATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* * * ** *
31389502 GATATATCTGTGCTAAACCCCGAAGAGCATTCGTGCTGGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* * * * *
31389542 GTTATATCCGGGCTAGGTCCCGAAGAGCAATCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
31389582 GATGT
1 GATGT
31389587 GTATTCGGGC
Statistics
Matches: 291, Mismatches: 33, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
39 4 0.01
40 287 0.99
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
Found at i:31392986 original size:49 final size:47
Alignment explanation
Indices: 31392920--31393129 Score: 291
Period size: 47 Copynumber: 4.4 Consensus size: 47
31392910 ATTGATGTAC
* *
31392920 AAGTATATATATGTGATAGGGCCGAGTGGCCAATGTGATGAATGTGA
1 AAGTATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
31392967 AAGTATATATATGCGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
1 AAGTATATATAT--GTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* * *
31393016 ACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
1 A-AGTATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* *
31393063 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGGA
1 AAGTATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGT-GA
31393111 AATGTATA-A-ATGTGATAAG
1 AA-GTATATATATGTGATAAG
31393130 TCCCGAAGGG
Statistics
Matches: 148, Mismatches: 9, Indels: 12
0.88 0.05 0.07
Matches are distributed among these distances:
46 1 0.01
47 97 0.66
48 5 0.03
49 44 0.30
50 1 0.01
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (47 bp):
AAGTATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
Found at i:31393054 original size:22 final size:22
Alignment explanation
Indices: 31393027--31393101 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
31393017 CATGTGTATG
31393027 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* * ***
31393049 TGTGATGAATG-TGAAAGTGTATATA
1 TGTGAT-AAGGCCG-AA-TGGCCA-A
31393074 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
31393096 TGTGAT
1 TGTGAT
31393102 GGATGTGGAA
Statistics
Matches: 38, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 14 0.37
23 8 0.21
24 8 0.21
25 8 0.21
ACGTcount: A:0.32, C:0.11, G:0.31, T:0.27
Consensus pattern (22 bp):
TGTGATAAGGCCGAATGGCCAA
Found at i:31393129 original size:94 final size:95
Alignment explanation
Indices: 31392925--31393129 Score: 315
Period size: 96 Copynumber: 2.2 Consensus size: 95
31392915 TGTACAAGTA
* *
31392925 TATATATGTGATAGGGCCGAGTGGCCAATGTGATGAATGTGAAAGTATATATATGCGTGATAAGG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTATATATAT-CGTGATAAGG
31392990 CCGAATGGCCAATGTGATGAATGTGAACATG
65 CCGAATGGCCAATGTGATGAATGTGAACATG
* * *
31393021 TGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATAT-GTGATAAGGC
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTATATATATCGTGATAAGGC
*
31393085 CGAATGGCCAATGTGATGGATGTGGAA-ATG
66 CGAATGGCCAATGTGATGAATGT-GAACATG
*
31393115 TATAAATGTGATAAG
1 TATATATGTGATAAG
31393130 TCCCGAAGGG
Statistics
Matches: 99, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
94 47 0.47
95 3 0.03
96 49 0.49
ACGTcount: A:0.33, C:0.09, G:0.31, T:0.28
Consensus pattern (95 bp):
TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTATATATATCGTGATAAGGC
CGAATGGCCAATGTGATGAATGTGAACATG
Found at i:31396243 original size:6 final size:6
Alignment explanation
Indices: 31396213--31396329 Score: 62
Period size: 6 Copynumber: 19.0 Consensus size: 6
31396203 AAGAAACATT
* * * *
31396213 ATCAGA A-CTAGA ATCAAA ATGAGA ATCAGA ATCAGA ATCAG- GTGACATA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA
* * * *
31396262 ATCAGA ATCAAA ATCAGA ATTA-A GTGACAGA ATCAGA ATCAGT ATCAGGTA
1 ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA ATCAGA ATCA-G-A
*
31396313 AT-AGA ATCAGA ACCAGA
1 ATCAGA ATCAGA ATCAGA
31396330 GTGTGAATGC
Statistics
Matches: 83, Mismatches: 17, Indels: 22
0.68 0.14 0.18
Matches are distributed among these distances:
5 7 0.08
6 65 0.78
7 6 0.07
8 5 0.06
ACGTcount: A:0.49, C:0.15, G:0.18, T:0.19
Consensus pattern (6 bp):
ATCAGA
Found at i:31396271 original size:31 final size:31
Alignment explanation
Indices: 31396234--31396309 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 31
31396224 AATCAAAATG
* *
31396234 AGAATCAGAATCAGAATCAGGTGACATAATC
1 AGAATCAGAATCAGAATCAAGTGACAGAATC
* *
31396265 AGAATCAAAATCAGAATTAAGTGACAGAATC
1 AGAATCAGAATCAGAATCAAGTGACAGAATC
*
31396296 AGAATCAGTATCAG
1 AGAATCAGAATCAG
31396310 GTAATAGAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.47, C:0.14, G:0.18, T:0.20
Consensus pattern (31 bp):
AGAATCAGAATCAGAATCAAGTGACAGAATC
Found at i:31396977 original size:27 final size:27
Alignment explanation
Indices: 31396945--31397165 Score: 203
Period size: 27 Copynumber: 8.2 Consensus size: 27
31396935 GGGGCAAAAT
* * *
31396945 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
31396972 GATAATTCTACACTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
31396999 GGTATTTCTACCGTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
31397026 GGTAATTCTACCCTA-TAGCGGTATTTC
1 GGTAATTCTACCCTACAAG-GGTATTTC
* *
31397053 AGTAATTCTACCCTAC-AGCGGTATTTT
1 GGTAATTCTACCCTACAAG-GGTATTTC
* * * *
31397080 AGTAATTCTACCCTATAGGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
31397107 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
** * * *
31397134 AATAATTTTACCCTACAGGGGTACTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
31397161 AGTAA
1 GGTAA
31397166 CTTGGTAAAC
Statistics
Matches: 167, Mismatches: 24, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
26 2 0.01
27 164 0.98
28 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:31397017 original size:54 final size:54
Alignment explanation
Indices: 31396946--31397165 Score: 255
Period size: 54 Copynumber: 4.1 Consensus size: 54
31396936 GGGCAAAATG
* * * * *
31396946 GTAATTTTACCCCACAAGGGTATCTCGATAATTCTACACTACAGGGGTATTTCG
1 GTAATTCTACCCTACAAGGGTATTTCGATAATTCTACCCTACAGGGGTATTTCA
* * * * *
31397000 GTATTTCTACCGTACAAGGGTATTTCGGTAATTCTACCCTATAGCGGTATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCGATAATTCTACCCTACAGGGGTATTTCA
* * *
31397054 GTAATTCTACCCTAC-AGCGGTATTT-TAGTAATTCTACCCTATAGGGGTATTTTA
1 GTAATTCTACCCTACAAG-GGTATTTCGA-TAATTCTACCCTACAGGGGTATTTCA
* * * *
31397108 GTAATTCTACCCTACAGGGGTATTTCAATAATTTTACCCTACAGGGGTACTTCA
1 GTAATTCTACCCTACAAGGGTATTTCGATAATTCTACCCTACAGGGGTATTTCA
31397162 GTAA
1 GTAA
31397166 CTTGGTAAAC
Statistics
Matches: 140, Mismatches: 22, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
53 2 0.01
54 136 0.97
55 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (54 bp):
GTAATTCTACCCTACAAGGGTATTTCGATAATTCTACCCTACAGGGGTATTTCA
Found at i:31397089 original size:81 final size:81
Alignment explanation
Indices: 31396946--31397165 Score: 253
Period size: 81 Copynumber: 2.7 Consensus size: 81
31396936 GGGCAAAATG
* * * * * * *
31396946 GTAATTTTACCCCACAAG-GGTATCTCGATAATTCTACACTACAGGGGTATTTCGGTATTTCTAC
1 GTAATTCTACCCTAC-AGCGGTATTTCAATAATTCTACCCTACAGGGGTATTTCAGTAATTCTAC
* *
31397010 CGTACAAGGGTATTTCG
65 CCTACAAGGGTATTTCA
* * * *
31397027 GTAATTCTACCCTATAGCGGTATTTCAGTAATTCTACCCTACAGCGGTATTTTAGTAATTCTACC
1 GTAATTCTACCCTACAGCGGTATTTCAATAATTCTACCCTACAGGGGTATTTCAGTAATTCTACC
* * *
31397092 CTATAGGGGTATTTTA
66 CTACAAGGGTATTTCA
* * *
31397108 GTAATTCTACCCTACAGGGGTATTTCAATAATTTTACCCTACAGGGGTACTTCAGTAA
1 GTAATTCTACCCTACAGCGGTATTTCAATAATTCTACCCTACAGGGGTATTTCAGTAA
31397166 CTTGGTAAAC
Statistics
Matches: 115, Mismatches: 23, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
80 2 0.02
81 113 0.98
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (81 bp):
GTAATTCTACCCTACAGCGGTATTTCAATAATTCTACCCTACAGGGGTATTTCAGTAATTCTACC
CTACAAGGGTATTTCA
Found at i:31400134 original size:21 final size:21
Alignment explanation
Indices: 31400110--31400176 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 21
31400100 TGTAATCTCA
31400110 CAACCTCAAAGATTTATAACT
1 CAACCTCAAAGATTTATAACT
*** *
31400131 CAA-CT--AAGCCGTGTAATCT
1 CAACCTCAAAGATTTATAA-CT
31400150 CACAACCTCAAAGATTTATAACT
1 C--AACCTCAAAGATTTATAACT
31400173 CAAC
1 CAAC
31400177 TAACTTATCA
Statistics
Matches: 32, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
18 7 0.22
19 3 0.09
20 2 0.06
21 8 0.25
22 2 0.06
23 3 0.09
24 7 0.22
ACGTcount: A:0.40, C:0.27, G:0.07, T:0.25
Consensus pattern (21 bp):
CAACCTCAAAGATTTATAACT
Found at i:31400146 original size:42 final size:42
Alignment explanation
Indices: 31400099--31400179 Score: 162
Period size: 42 Copynumber: 1.9 Consensus size: 42
31400089 TAAGTACGCT
31400099 GTGTAATCTCACAACCTCAAAGATTTATAACTCAACTAAGCC
1 GTGTAATCTCACAACCTCAAAGATTTATAACTCAACTAAGCC
31400141 GTGTAATCTCACAACCTCAAAGATTTATAACTCAACTAA
1 GTGTAATCTCACAACCTCAAAGATTTATAACTCAACTAA
31400180 CTTATCAAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.40, C:0.25, G:0.09, T:0.27
Consensus pattern (42 bp):
GTGTAATCTCACAACCTCAAAGATTTATAACTCAACTAAGCC
Found at i:31400174 original size:23 final size:23
Alignment explanation
Indices: 31400106--31400174 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 23
31400096 GCTGTGTAAT
31400106 CTCACAACCTCAAAGATTTATAA
1 CTCACAACCTCAAAGATTTATAA
*** *
31400129 CT--CAA-CT--AAGCCGTGTAA
1 CTCACAACCTCAAAGATTTATAA
31400147 TCTCACAACCTCAAAGATTTATAA
1 -CTCACAACCTCAAAGATTTATAA
31400171 CTCA
1 CTCA
31400175 ACTAACTTAT
Statistics
Matches: 32, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
18 7 0.22
19 2 0.06
20 2 0.06
21 6 0.19
22 2 0.06
23 6 0.19
24 7 0.22
ACGTcount: A:0.39, C:0.28, G:0.07, T:0.26
Consensus pattern (23 bp):
CTCACAACCTCAAAGATTTATAA
Found at i:31400350 original size:34 final size:34
Alignment explanation
Indices: 31400312--31400429 Score: 117
Period size: 34 Copynumber: 3.6 Consensus size: 34
31400302 ATTATAGACG
31400312 ATCTATTATTGCATAAATTTTTCGGTGACTTCCA
1 ATCTATTATTGCATAAATTTTTCGGTGACTTCCA
31400346 ATCTATTATTGC----ATTTTTCGGTGAC-T-CA
1 ATCTATTATTGCATAAATTTTTCGGTGACTTCCA
* * * *
31400374 AACT-TAACCT-CAGAAACATTTTTCGGTGACTTCCA
1 ATCTATTA-TTGCA-TAA-ATTTTTCGGTGACTTCCA
31400409 ATCTATTATTGCATAAATTTT
1 ATCTATTATTGCATAAATTTT
31400430 GCTCGGATCA
Statistics
Matches: 66, Mismatches: 7, Indels: 22
0.69 0.07 0.23
Matches are distributed among these distances:
27 3 0.05
28 6 0.09
29 1 0.02
30 13 0.20
33 13 0.20
34 18 0.27
35 8 0.12
36 4 0.06
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.42
Consensus pattern (34 bp):
ATCTATTATTGCATAAATTTTTCGGTGACTTCCA
Found at i:31400364 original size:30 final size:30
Alignment explanation
Indices: 31400328--31400422 Score: 88
Period size: 30 Copynumber: 3.1 Consensus size: 30
31400318 TATTGCATAA
31400328 ATTTTTCGGTGACTTCCAATCTATTATTGC
1 ATTTTTCGGTGACTTCCAATCTATTATTGC
* * *
31400358 ATTTTTCGGTGAC-T-CAAACT-TAACCTCAGAAAC
1 ATTTTTCGGTGACTTCCAATCTATTA--T-TG---C
31400391 ATTTTTCGGTGACTTCCAATCTATTATTGC
1 ATTTTTCGGTGACTTCCAATCTATTATTGC
31400421 AT
1 AT
31400423 AAATTTTGCT
Statistics
Matches: 50, Mismatches: 6, Indels: 18
0.68 0.08 0.24
Matches are distributed among these distances:
27 2 0.04
28 5 0.10
29 2 0.04
30 17 0.34
33 15 0.30
34 2 0.04
35 5 0.10
36 2 0.04
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.41
Consensus pattern (30 bp):
ATTTTTCGGTGACTTCCAATCTATTATTGC
Found at i:31401955 original size:49 final size:49
Alignment explanation
Indices: 31401900--31401995 Score: 192
Period size: 49 Copynumber: 2.0 Consensus size: 49
31401890 TGTTGCGTAA
31401900 TGTAATATGAATTGACAGTAAAAGACCATGGTTAGACCATGGCAATGTG
1 TGTAATATGAATTGACAGTAAAAGACCATGGTTAGACCATGGCAATGTG
31401949 TGTAATATGAATTGACAGTAAAAGACCATGGTTAGACCATGGCAATG
1 TGTAATATGAATTGACAGTAAAAGACCATGGTTAGACCATGGCAATG
31401996 AGCTAAGTGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.38, C:0.12, G:0.24, T:0.26
Consensus pattern (49 bp):
TGTAATATGAATTGACAGTAAAAGACCATGGTTAGACCATGGCAATGTG
Found at i:31402119 original size:82 final size:81
Alignment explanation
Indices: 31401982--31402171 Score: 298
Period size: 82 Copynumber: 2.4 Consensus size: 81
31401972 GACCATGGTT
*
31401982 AGACCATGGCAATGAGCTAAGTGAAATAAGTGATTCACATGTAAGACCATATCTAGGATATGGCA
1 AGACCATGGCAATGTGCTAAGTGAAATAAGTGATTCACATGTAAGACCATATCTAGGAT-TGGCA
*
31402047 TTGTCCTAACTGAAATA
65 TCGTCCTAACTGAAATA
*
31402064 AGACCATAGCAATGTGCTAAGTGAAATAAGTGATTCACATGTAAGACCATATCTAGGATTGGCAT
1 AGACCATGGCAATGTGCTAAGTGAAATAAGTGATTCACATGTAAGACCATATCTAGGATTGGCAT
* *
31402129 CGTGCTAAGTGAAATA
66 CGTCCTAACTGAAATA
31402145 AGACCATGGC-AT-T--TAAGTGAAATAAGT
1 AGACCATGGCAATGTGCTAAGTGAAATAAGT
31402172 TCAAGGCAAC
Statistics
Matches: 102, Mismatches: 6, Indels: 5
0.90 0.05 0.04
Matches are distributed among these distances:
77 14 0.14
79 1 0.01
80 2 0.02
81 28 0.27
82 57 0.56
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.26
Consensus pattern (81 bp):
AGACCATGGCAATGTGCTAAGTGAAATAAGTGATTCACATGTAAGACCATATCTAGGATTGGCAT
CGTCCTAACTGAAATA
Found at i:31402155 original size:28 final size:27
Alignment explanation
Indices: 31402123--31402324 Score: 170
Period size: 28 Copynumber: 7.6 Consensus size: 27
31402113 TATCTAGGAT
*
31402123 TGGCATCGTGCTAAGTGAAATAAGACCA
1 TGGCAT-GTGCTAAGTGAAATAAGTCCA
*
31402151 TGGCAT-T--TAAGTGAAATAAGTTCA
1 TGGCATGTGCTAAGTGAAATAAGTCCA
* * *
31402175 AGGCAACGTGCTAAGTGAAATAAGACCA
1 TGGC-ATGTGCTAAGTGAAATAAGTCCA
31402203 TGGCA--T-CTAAGTGAAATAAGTCCA
1 TGGCATGTGCTAAGTGAAATAAGTCCA
** * * *
31402227 ACGCAACGGGCTAAGTGAAATAAGACCA
1 TGGC-ATGTGCTAAGTGAAATAAGTCCA
*
31402255 TGG--TAT-CTAAGTGAAATAAGTCCA
1 TGGCATGTGCTAAGTGAAATAAGTCCA
* *
31402279 TGGCAATTTGCTAAGTAAAATAAGTCCA
1 TGGC-ATGTGCTAAGTGAAATAAGTCCA
*
31402307 TGGTATGGTGCTAAGTGA
1 TGGCAT-GTGCTAAGTGA
31402325 GAAATTTCTC
Statistics
Matches: 138, Mismatches: 23, Indels: 26
0.74 0.12 0.14
Matches are distributed among these distances:
24 57 0.41
25 3 0.02
26 2 0.01
27 5 0.04
28 71 0.51
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.24
Consensus pattern (27 bp):
TGGCATGTGCTAAGTGAAATAAGTCCA
Found at i:31402166 original size:24 final size:24
Alignment explanation
Indices: 31402133--31402283 Score: 140
Period size: 24 Copynumber: 6.0 Consensus size: 24
31402123 TGGCATCGTG
31402133 CTAAGTGAAATAAGACCATGGCAT
1 CTAAGTGAAATAAGACCATGGCAT
* ** *
31402157 TTAAGTGAAATAAGTTCAAGGCAACGT
1 CTAAGTGAAATAAGACCATGGC-A--T
31402184 GCTAAGTGAAATAAGACCATGGCAT
1 -CTAAGTGAAATAAGACCATGGCAT
* ** *
31402209 CTAAGTGAAATAAGTCCAACGCAACGGG
1 CTAAGTGAAATAAGACCATGGC-A---T
*
31402237 CTAAGTGAAATAAGACCATGGTAT
1 CTAAGTGAAATAAGACCATGGCAT
*
31402261 CTAAGTGAAATAAGTCCATGGCA
1 CTAAGTGAAATAAGACCATGGCA
31402284 ATTTGCTAAG
Statistics
Matches: 100, Mismatches: 19, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
24 58 0.58
25 3 0.03
27 3 0.03
28 36 0.36
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.21
Consensus pattern (24 bp):
CTAAGTGAAATAAGACCATGGCAT
Found at i:31402312 original size:52 final size:52
Alignment explanation
Indices: 31402124--31402309 Score: 273
Period size: 52 Copynumber: 3.6 Consensus size: 52
31402114 ATCTAGGATT
* * *
31402124 GGCATCGTGCTAAGTGAAATAAGACCATGGCATTTAAGTGAAATAAGTTCAA
1 GGCAACGTGCTAAGTGAAATAAGACCATGGCATCTAAGTGAAATAAGTCCAA
31402176 GGCAACGTGCTAAGTGAAATAAGACCATGGCATCTAAGTGAAATAAGTCCAA
1 GGCAACGTGCTAAGTGAAATAAGACCATGGCATCTAAGTGAAATAAGTCCAA
* * * *
31402228 CGCAACGGGCTAAGTGAAATAAGACCATGGTATCTAAGTGAAATAAGTCCAT
1 GGCAACGTGCTAAGTGAAATAAGACCATGGCATCTAAGTGAAATAAGTCCAA
** * *
31402280 GGCAATTTGCTAAGTAAAATAAGTCCATGG
1 GGCAACGTGCTAAGTGAAATAAGACCATGG
31402310 TATGGTGCTA
Statistics
Matches: 121, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 121 1.00
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.23
Consensus pattern (52 bp):
GGCAACGTGCTAAGTGAAATAAGACCATGGCATCTAAGTGAAATAAGTCCAA
Found at i:31402406 original size:51 final size:51
Alignment explanation
Indices: 31402343--31402518 Score: 244
Period size: 51 Copynumber: 3.5 Consensus size: 51
31402333 TCAGTTGAAC
* *
31402343 CTTTGTGAATATAATAGCTTTAGACAAAAGTGTGGTACTATGTGAAGGCCA
1 CTTTGTGAATAAAATAGCTTTGGACAAAAGTGTGGTACTATGTGAAGGCCA
* * * * * * *
31402394 CTATGTGAATATAATAGCTTTGGACATAGGTGCGGTACTAAGTGATGGCCA
1 CTTTGTGAATAAAATAGCTTTGGACAAAAGTGTGGTACTATGTGAAGGCCA
* *
31402445 CTTTGTGAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCAA
1 CTTTGTGAATAAAATAGCTTTGGACAAAAGTGTGGTACTATGTGAAGGCCA
*
31402496 CTTTGTGGATAAAATAGCTTTGG
1 CTTTGTGAATAAAATAGCTTTGG
31402519 CTACAAGGGT
Statistics
Matches: 109, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 109 1.00
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.31
Consensus pattern (51 bp):
CTTTGTGAATAAAATAGCTTTGGACAAAAGTGTGGTACTATGTGAAGGCCA
Found at i:31402525 original size:51 final size:50
Alignment explanation
Indices: 31402343--31402547 Score: 234
Period size: 51 Copynumber: 4.0 Consensus size: 50
31402333 TCAGTTGAAC
* * *
31402343 CTTTGTGAATATAATAGCTTTAGACAAAAGTGTGGTACTATGTGAAGGCCA
1 CTTTGTGAATAAAATAGCTTT-GGCACAAGTGTGGTACTATGTGAAGGCCA
* * * * *
31402394 CTATGTGAATATAATAGCTTTGG-ACATAGGTGCGGTACTAAGTGATGGCCA
1 CTTTGTGAATAAAATAGCTTTGGCACA-A-GTGTGGTACTATGTGAAGGCCA
*
31402445 CTTTGTGAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCAA
1 CTTTGTGAATAAAATAGCTTTGG-CACAAGTGTGGTACTATGTGAAGGCCA
* * * *
31402496 CTTTGTGGATAAAATAGCTTTGGCTACAAGGGTGGTA-TATGTTAAAGCCA
1 CTTTGTGAATAAAATAGCTTTGGC-ACAAGTGTGGTACTATGTGAAGGCCA
31402546 CT
1 CT
31402548 GCGTATGTAA
Statistics
Matches: 132, Mismatches: 17, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
49 2 0.02
50 15 0.11
51 111 0.84
52 1 0.01
53 3 0.02
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.31
Consensus pattern (50 bp):
CTTTGTGAATAAAATAGCTTTGGCACAAGTGTGGTACTATGTGAAGGCCA
Found at i:31403203 original size:18 final size:17
Alignment explanation
Indices: 31403175--31403208 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
31403165 GACCTTAGCC
31403175 CATTACAGAATAAGAAA
1 CATTACAGAATAAGAAA
*
31403192 CATTATCAGAATTAGAA
1 CATTA-CAGAATAAGAA
31403209 CCAAAATAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.53, C:0.12, G:0.12, T:0.24
Consensus pattern (17 bp):
CATTACAGAATAAGAAA
Found at i:31403226 original size:6 final size:6
Alignment explanation
Indices: 31403196--31403559 Score: 324
Period size: 6 Copynumber: 60.3 Consensus size: 6
31403186 AAGAAACATT
* * * *
31403196 ATCAGA ATTAGA ACCAAA ATAAGA ATCAGA ATCAGA ATCAGTA A-CAGA
1 ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAG-A ATCAGA
* *
31403244 ATCAGA ATCAAA ATCA-A TATTAGTA A-CAGA ATCAGA ATCAGA ATCAGA
1 ATCAGA ATCAGA ATCAGA -ATCAG-A ATCAGA ATCAGA ATCAGA ATCAGA
* *
31403292 ATTAG- GTGACAGA ATCAGA ATCAGA ATCAGTA A-CAGA ATCAGA ATCAGA
1 ATCAGA AT--CAGA ATCAGA ATCAGA ATCAG-A ATCAGA ATCAGA ATCAGA
* * *
31403341 ATCA-A TATTAGTA A-CAGA ATCAGA ATCAGA ATCAGA ATTAG- GTGACAGA
1 ATCAGA -ATCAG-A ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA
* *
31403390 ATCAGA ATCAGA ATCAGTA A-CAGA ATCAGA ATCAGA ATCAGT ATTAGTA
1 ATCAGA ATCAGA ATCAG-A ATCAGA ATCAGA ATCAGA ATCAGA ATCAG-A
* * *
31403439 A-CAGA ATCAGA ATCAGA ATCAGA ATTAGA ATTAG- GTGACAGA ATCAG-
1 ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA
* *
31403486 ATCAGTA A-CAGA ATCAGA ATCAGT ATTAGTA A-CAGA ATCAGA ATCAGA
1 ATCAG-A ATCAGA ATCAGA ATCAGA ATCAG-A ATCAGA ATCAGA ATCAGA
31403534 ATCAGA ATCAGA ATCAGA ATCAGA AT
1 ATCAGA ATCAGA ATCAGA ATCAGA AT
31403560 GTGAATGCGA
Statistics
Matches: 295, Mismatches: 33, Indels: 60
0.76 0.09 0.15
Matches are distributed among these distances:
5 26 0.09
6 247 0.84
7 17 0.06
8 5 0.02
ACGTcount: A:0.49, C:0.14, G:0.17, T:0.20
Consensus pattern (6 bp):
ATCAGA
Found at i:31403230 original size:30 final size:30
Alignment explanation
Indices: 31403196--31403559 Score: 363
Period size: 30 Copynumber: 12.9 Consensus size: 30
31403186 AAGAAACATT
* *
31403196 ATCAGAATTAG-AACCAAAATAAGAATCAGA
1 ATCAGAATTAGTAA-CAGAATCAGAATCAGA
* *
31403226 ATCAGAATCAGTAACAGAATCAGAATCAAA
1 ATCAGAATTAGTAACAGAATCAGAATCAGA
31403256 ATCA-ATATTAGTAACAGAATCAGAATCAGA
1 ATCAGA-ATTAGTAACAGAATCAGAATCAGA
31403286 ATCAGAATTAGGT----G-A-CAGAATCAGA
1 ATCAGAATTA-GTAACAGAATCAGAATCAGA
*
31403311 ATCAGAATCAGTAACAGAATCAGAATCAGA
1 ATCAGAATTAGTAACAGAATCAGAATCAGA
31403341 ATCA-ATATTAGTAACAGAATCAGAATCAGA
1 ATCAGA-ATTAGTAACAGAATCAGAATCAGA
31403371 ATCAGAATTAGGT----G-A-CAGAATCAGA
1 ATCAGAATTA-GTAACAGAATCAGAATCAGA
*
31403396 ATCAGAATCAGTAACAGAATCAGAATCAGA
1 ATCAGAATTAGTAACAGAATCAGAATCAGA
*
31403426 ATCAGTATTAGTAACAGAATCAGAATCAGA
1 ATCAGAATTAGTAACAGAATCAGAATCAGA
* *
31403456 ATCAGAATTAG-AATTAG-GT--G-A-CAGA
1 ATCAGAATTAGTAA-CAGAATCAGAATCAGA
*
31403481 ATCAG-ATCAGTAACAGAATCAGAATCAG-
1 ATCAGAATTAGTAACAGAATCAGAATCAGA
31403509 -T----ATTAGTAACAGAATCAGAATCAGA
1 ATCAGAATTAGTAACAGAATCAGAATCAGA
*
31403534 ATCAGAATCAG-AATCAGAATCAGAAT
1 ATCAGAATTAGTAA-CAGAATCAGAAT
31403560 GTGAATGCGA
Statistics
Matches: 282, Mismatches: 19, Indels: 66
0.77 0.05 0.18
Matches are distributed among these distances:
24 32 0.11
25 50 0.18
26 4 0.01
27 5 0.02
28 3 0.01
29 12 0.04
30 168 0.60
31 8 0.03
ACGTcount: A:0.49, C:0.14, G:0.17, T:0.20
Consensus pattern (30 bp):
ATCAGAATTAGTAACAGAATCAGAATCAGA
Found at i:31403319 original size:85 final size:85
Alignment explanation
Indices: 31403217--31403541 Score: 515
Period size: 85 Copynumber: 3.9 Consensus size: 85
31403207 AACCAAAATA
*
31403217 AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAAAATCAATATTAGTAACAGAATCAGAAT
1 AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAATATTAGTAACAGAATCAGAAT
31403282 CAGAATCAGAATTAGGTGAC
66 CAGAATCAGAATTAGGTGAC
31403302 AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAATATTAGTAACAGAATCAGAAT
1 AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAATATTAGTAACAGAATCAGAAT
31403367 CAGAATCAGAATTAGGTGAC
66 CAGAATCAGAATTAGGTGAC
*
31403387 AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAGTATTAGTAACAGAATCAGAAT
1 AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAATATTAGTAACAGAATCAGAAT
* *
31403452 CAGAATCAGAATTAGAATTA-
66 CAGAATCAGAATTAG-GTGAC
* *
31403472 GGTGA-CAGAATCAG-ATCAGTAACAGAATCAGAATCAG------TATTAGTAACAGAATCAGAA
1 AG-AATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAATATTAGTAACAGAATCAGAA
31403529 TCAGAATCAGAAT
65 TCAGAATCAGAAT
31403542 CAGAATCAGA
Statistics
Matches: 232, Mismatches: 6, Indels: 11
0.93 0.02 0.04
Matches are distributed among these distances:
78 33 0.14
84 23 0.10
85 173 0.75
86 3 0.01
ACGTcount: A:0.48, C:0.14, G:0.18, T:0.20
Consensus pattern (85 bp):
AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAATATTAGTAACAGAATCAGAAT
CAGAATCAGAATTAGGTGAC
Found at i:31403714 original size:27 final size:26
Alignment explanation
Indices: 31403677--31403742 Score: 87
Period size: 27 Copynumber: 2.5 Consensus size: 26
31403667 AGCATGGCTG
*
31403677 CCAGAACAGATATCGTGACAGAGTCA
1 CCAGAACAGATATCGTGACAGAGCCA
* *
31403703 CCAGATACAGATATTGTGGCAGAGCCA
1 CCAGA-ACAGATATCGTGACAGAGCCA
31403730 CCAGAATCAGATA
1 CCAGAA-CAGATA
31403743 ATGTGGCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
26 6 0.17
27 29 0.83
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATATCGTGACAGAGCCA
Found at i:31403747 original size:27 final size:27
Alignment explanation
Indices: 31403677--31403750 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 27
31403667 AGCATGGCTG
* *
31403677 CCAGAA-CAGAT-ATCGTGACAGAGTCA
1 CCAGAATCAGATAAT-GTGGCAGAGCCA
*
31403703 CCAG-ATACAGATATTGTGGCAGAGCCA
1 CCAGAAT-CAGATAATGTGGCAGAGCCA
31403730 CCAGAATCAGATAATGTGGCA
1 CCAGAATCAGATAATGTGGCA
31403751 AACCCACCTA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
25 1 0.03
26 4 0.10
27 32 0.80
28 3 0.08
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (27 bp):
CCAGAATCAGATAATGTGGCAGAGCCA
Found at i:31403757 original size:27 final size:27
Alignment explanation
Indices: 31403701--31403758 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
31403691 GTGACAGAGT
* * *
31403701 CACCAGATACAGATATTGTGGCAGAGC
1 CACCAGATACAGATAATGTGGCAAACC
31403728 CACCAGA-ATCAGATAATGTGGCAAACC
1 CACCAGATA-CAGATAATGTGGCAAACC
31403755 CACC
1 CACC
31403759 TAACAGAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 1 0.04
27 26 0.96
ACGTcount: A:0.36, C:0.28, G:0.21, T:0.16
Consensus pattern (27 bp):
CACCAGATACAGATAATGTGGCAAACC
Found at i:31403963 original size:22 final size:22
Alignment explanation
Indices: 31403915--31403973 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
31403905 GTAAATACGT
*
31403915 TTGGCACGAAGCCATAGTCAAG
1 TTGGCACAAAGCCATAGTCAAG
* * * *
31403937 ATGGCACAAAGCCATATTTAGG
1 TTGGCACAAAGCCATAGTCAAG
*
31403959 TTGGCACAGAGCCAT
1 TTGGCACAAAGCCAT
31403974 TAATAACGGG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAGTCAAG
Found at i:31404140 original size:27 final size:26
Alignment explanation
Indices: 31404061--31404143 Score: 112
Period size: 27 Copynumber: 3.1 Consensus size: 26
31404051 TCGATCGGTC
* * *
31404061 AACAGATATTGTGACAGAGTCACCAA
1 AACAGATATTGTGGCAGAGCCACCAG
31404087 ATACAGATATTGTGGCAGAGCCACCAG
1 A-ACAGATATTGTGGCAGAGCCACCAG
*
31404114 AACAGATATTTGTGGCATAGCCACCAG
1 AACAGATA-TTGTGGCAGAGCCACCAG
31404141 AAC
1 AAC
31404144 GCTTCCTCCG
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
26 8 0.16
27 43 0.84
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.19
Consensus pattern (26 bp):
AACAGATATTGTGGCAGAGCCACCAG
Found at i:31404372 original size:27 final size:27
Alignment explanation
Indices: 31404342--31404537 Score: 230
Period size: 27 Copynumber: 7.3 Consensus size: 27
31404332 GGGGCAAAAT
* * *
31404342 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
31404369 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
31404396 GGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
31404423 GATAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
31404450 GGTAATTCTATCCTATAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * * *
31404477 AGTAGTTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
** *
31404504 GAAAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
31404531 AGTAATT
1 GGTAATT
31404538 TCACAATCAA
Statistics
Matches: 142, Mismatches: 27, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 142 1.00
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:31404486 original size:81 final size:81
Alignment explanation
Indices: 31404344--31404537 Score: 262
Period size: 81 Copynumber: 2.4 Consensus size: 81
31404334 GGCAAAATGG
* * * * * * *
31404344 TAATTTTACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTTCGGTATTTCTACCC
1 TAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTCAGTAGTTCTACCC
31404409 TACAAGGGTATTTCGA
66 TACAAGGGTATTTCGA
* * *
31404425 TAATTCTACCCTACAGGGGTATTTTGGTAATTCTATCCTATAAGGGTATTTCAGTAGTTCTACCC
1 TAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTCAGTAGTTCTACCC
* *
31404490 TATAGGGGTATTTCGA
66 TACAAGGGTATTTCGA
* *
31404506 AAATTCTACCCTACAGGGGTATTTCAGTAATT
1 TAATTCTACCCTACAGGGGTATTTCGGTAATT
31404538 TCACAATCAA
Statistics
Matches: 98, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
81 98 1.00
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.36
Consensus pattern (81 bp):
TAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTCAGTAGTTCTACCC
TACAAGGGTATTTCGA
Found at i:31404572 original size:27 final size:27
Alignment explanation
Indices: 31404542--31404970 Score: 581
Period size: 27 Copynumber: 15.9 Consensus size: 27
31404532 GTAATTTCAC
*
31404542 AATCAAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
** * **
31404569 AATCGAGGGTAAAACAATAATTTTAAA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
31404596 AATCGAGGGTAAAACGATAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
31404623 AATCGAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
31404650 AATCAAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
** * **
31404677 AATCGAGGGTAAAACAATAATTTTAAA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
31404704 AATCGAGGGTAAAACGATAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
31404731 AATCGAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
31404758 AATCGAGGGTAAAACAGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
31404785 AA-CTGAGGGTAAAACGGTAATTTTGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
* * **
31404812 AATCAAGGGTAAAACGGTAATTTTACA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
31404839 AATCGAGGGTAAAACGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* **
31404866 AATCGAGGGTAAAACGGTAATTTTAAA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
31404893 AATCGAGGGTAAAATGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
31404920 AATCGAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
31404947 AATCGAGGGTAAAATGGTAATTCT
1 AATCGAGGGTAAAACGGTAATTCT
31404971 ATCTTATTTC
Statistics
Matches: 358, Mismatches: 42, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
26 1 0.00
27 356 0.99
28 1 0.00
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.27
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTCTGTA
Found at i:31405005 original size:27 final size:27
Alignment explanation
Indices: 31404975--31405069 Score: 111
Period size: 27 Copynumber: 3.5 Consensus size: 27
31404965 AATTCTATCT
*
31404975 TATTTCGGTAATTTTACAAATCGAGGA
1 TATTTCGGTAATTTTACAAATCGAGGG
* * *
31405002 TATTTGGGTAATTTTATAAATCGGGGG
1 TATTTCGGTAATTTTACAAATCGAGGG
* *
31405029 TACTTT-GGTAATTTTACAAGTTGAGGG
1 TA-TTTCGGTAATTTTACAAATCGAGGG
*
31405056 TATTTCAGTAATTT
1 TATTTCGGTAATTT
31405070 GGTAAACTAA
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
26 3 0.05
27 51 0.89
28 3 0.05
ACGTcount: A:0.28, C:0.07, G:0.22, T:0.42
Consensus pattern (27 bp):
TATTTCGGTAATTTTACAAATCGAGGG
Found at i:31407335 original size:13 final size:12
Alignment explanation
Indices: 31407307--31407335 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
31407297 TGTGCCCCTG
31407307 TTTTTCATGAAA
1 TTTTTCATGAAA
31407319 TTTTTCATGAAA
1 TTTTTCATGAAA
31407331 TTTTT
1 TTTTT
31407336 AAAAGTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.28, C:0.07, G:0.07, T:0.59
Consensus pattern (12 bp):
TTTTTCATGAAA
Found at i:31412358 original size:49 final size:49
Alignment explanation
Indices: 31412303--31412401 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
31412293 TTGTTGCGTA
31412303 GTGTAATATGAATTGATAGTAAAAGACCATGGTTAGACCATGGCAATGT
1 GTGTAATATGAATTGATAGTAAAAGACCATGGTTAGACCATGGCAATGT
31412352 GTGTAATATGAATTGATAGTAAAAGACCATGGTTAGACCATGGCAATGT
1 GTGTAATATGAATTGATAGTAAAAGACCATGGTTAGACCATGGCAATGT
31412401 G
1 G
31412402 CTAAGTGAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.36, C:0.10, G:0.25, T:0.28
Consensus pattern (49 bp):
GTGTAATATGAATTGATAGTAAAAGACCATGGTTAGACCATGGCAATGT
Found at i:31412489 original size:24 final size:27
Alignment explanation
Indices: 31412456--31412580 Score: 154
Period size: 24 Copynumber: 4.8 Consensus size: 27
31412446 TGGCATCGTG
*
31412456 CTAAGTGAAATAAGACCATGGC-AT-T
1 CTAAGTGAAATAAGTCCATGGCAATGT
*
31412481 -TAAGTGAAATAAGTTCATGGCAATGT
1 CTAAGTGAAATAAGTCCATGGCAATGT
* *
31412507 GCTAAGTTAAATAAGACCATGGC-A--T
1 -CTAAGTGAAATAAGTCCATGGCAATGT
31412532 CTAAGTGAAATAAGTCCATGGCAATGT
1 CTAAGTGAAATAAGTCCATGGCAATGT
31412559 GCTAAGTGAAATAAGTCCATGG
1 -CTAAGTGAAATAAGTCCATGG
31412581 TATGGTGCTA
Statistics
Matches: 85, Mismatches: 7, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
24 39 0.46
25 4 0.05
26 1 0.01
27 2 0.02
28 39 0.46
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.26
Consensus pattern (27 bp):
CTAAGTGAAATAAGTCCATGGCAATGT
Found at i:31412519 original size:52 final size:52
Alignment explanation
Indices: 31412445--31412580 Score: 220
Period size: 52 Copynumber: 2.6 Consensus size: 52
31412435 TATCTAGGAT
* *
31412445 ATGGC-ATCGTGCTAAGTGAAATAAGACCATGGCATTTAAGTGAAATAAGTTC
1 ATGGCAAT-GTGCTAAGTGAAATAAGACCATGGCATCTAAGTGAAATAAGTCC
*
31412497 ATGGCAATGTGCTAAGTTAAATAAGACCATGGCATCTAAGTGAAATAAGTCC
1 ATGGCAATGTGCTAAGTGAAATAAGACCATGGCATCTAAGTGAAATAAGTCC
*
31412549 ATGGCAATGTGCTAAGTGAAATAAGTCCATGG
1 ATGGCAATGTGCTAAGTGAAATAAGACCATGG
31412581 TATGGTGCTA
Statistics
Matches: 78, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
52 76 0.97
53 2 0.03
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.26
Consensus pattern (52 bp):
ATGGCAATGTGCTAAGTGAAATAAGACCATGGCATCTAAGTGAAATAAGTCC
Found at i:31412521 original size:28 final size:27
Alignment explanation
Indices: 31412445--31412595 Score: 179
Period size: 28 Copynumber: 5.7 Consensus size: 27
31412435 TATCTAGGAT
*
31412445 ATGGCATCGTGCTAAGTGAAATAAGACC
1 ATGGCAT-GTGCTAAGTGAAATAAGTCC
*
31412473 ATGGCAT-T--TAAGTGAAATAAGTTC
1 ATGGCATGTGCTAAGTGAAATAAGTCC
* *
31412497 ATGGCAATGTGCTAAGTTAAATAAGACC
1 ATGGC-ATGTGCTAAGTGAAATAAGTCC
31412525 ATGGCA--T-CTAAGTGAAATAAGTCC
1 ATGGCATGTGCTAAGTGAAATAAGTCC
31412549 ATGGCAATGTGCTAAGTGAAATAAGTCC
1 ATGGC-ATGTGCTAAGTGAAATAAGTCC
*
31412577 ATGGTATGGTGCTAAGTGA
1 ATGGCAT-GTGCTAAGTGA
31412596 GAAATTTCCC
Statistics
Matches: 106, Mismatches: 8, Indels: 18
0.80 0.06 0.14
Matches are distributed among these distances:
24 39 0.37
25 4 0.04
26 2 0.02
27 4 0.04
28 57 0.54
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.26
Consensus pattern (27 bp):
ATGGCATGTGCTAAGTGAAATAAGTCC
Found at i:31412669 original size:51 final size:51
Alignment explanation
Indices: 31412614--31412818 Score: 286
Period size: 51 Copynumber: 4.0 Consensus size: 51
31412604 CCAGTTGAAC
* * *
31412614 CTTTGTGAATATAATAGCTTTAGACACAAGTGTGGTACTATGTGAAGGACA
1 CTTTGTGAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCA
* *
31412665 CTTTGTGAATATAATAGCTTTGGACACAAGTGTGGTACTAAGTGAAGGCCA
1 CTTTGTGAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCA
* *
31412716 CTTTGTGAATAAAATAGCTTTGGACACAAGCGTTGTACTATGTGAAGGCCA
1 CTTTGTGAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCA
* * * * *
31412767 TTTTGTGAATAAAATAGCTTTGG-CTACAAGGGTAGCACTATGTTAAGGCCA
1 CTTTGTGAATAAAATAGCTTTGGAC-ACAAGTGTGGTACTATGTGAAGGCCA
31412818 C
1 C
31412819 CGTGTATCCG
Statistics
Matches: 140, Mismatches: 13, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
50 1 0.01
51 139 0.99
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (51 bp):
CTTTGTGAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCA
Found at i:31423011 original size:55 final size:54
Alignment explanation
Indices: 31422911--31423157 Score: 222
Period size: 55 Copynumber: 4.6 Consensus size: 54
31422901 TTAATGGTAC
* * *
31422911 CATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTT-TCTAAGGCAAGGAAAT
1 CATGTAAGACCATGCCAAGACATGGC-ATTGGTAA-GTTCTATAAGGCAAGGATAT
* * * *
31422966 CATGTAAGACCATGTCAATACATGGCATTGATAAGTTACTATAAGGCAAAGG-TCT
1 CATGTAAGACCATGCCAAGACATGGCATTGGTAAGTT-CTATAAGGC-AAGGATAT
* * * * *
31423021 CACGTAAGACCGTGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGCAAGGATAC
1 CATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCTATAAGGCAAGGATAT
* * * *
31423074 CATGTAAGACCATGTCAAGACATGGCAATGGTAAGTT-T-CAA---AAGGATAC
1 CATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCTATAAGGCAAGGATAT
* * * *
31423123 CACGTAAGACCATGACAAGTCATGGCAATGGTAAG
1 CATGTAAGACCATGCCAAGACATGGCATTGGTAAG
31423158 GTACCCGCAT
Statistics
Matches: 161, Mismatches: 26, Indels: 16
0.79 0.13 0.08
Matches are distributed among these distances:
49 40 0.25
52 6 0.04
53 42 0.26
54 8 0.05
55 61 0.38
56 4 0.02
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (54 bp):
CATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCTATAAGGCAAGGATAT
Found at i:31423109 original size:108 final size:110
Alignment explanation
Indices: 31422914--31423159 Score: 305
Period size: 108 Copynumber: 2.3 Consensus size: 110
31422904 ATGGTACCAT
*
31422914 GTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAATCATGTAAGACCAT
1 GTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGACCAT
* *
31422979 GTCAATACATGGCATTGATAAGTTACTATAAGGCAAAGGTCTCAC
66 GTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTCTCAC
* * *
31423024 GTAAGACCGTGCCAAGGCATGGC-ATTGGTGA-G-TTCATAAGGCAAGGATACCATGTAAGACCA
1 GTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTC-TAAGGCAAGGAAACCATGTAAGACCA
* * * *
31423086 TGTCAAGACATGGCAATGGTAAGTTTC-AAAAGG-ATA---C-CAC
65 TGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTCTCAC
* *
31423126 GTAAGACCATGACAAGTCATGGCAA-TGGTAAGGT
1 GTAAGACCATGCCAAGGCATGGCAATTGGTAAGGT
31423160 ACCCGCATAT
Statistics
Matches: 118, Mismatches: 14, Indels: 14
0.81 0.10 0.10
Matches are distributed among these distances:
102 28 0.24
103 3 0.03
106 2 0.02
107 8 0.07
108 48 0.41
109 7 0.06
110 22 0.19
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.22
Consensus pattern (110 bp):
GTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGACCAT
GTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTCTCAC
Found at i:31424786 original size:43 final size:42
Alignment explanation
Indices: 31424723--31424886 Score: 197
Period size: 43 Copynumber: 3.9 Consensus size: 42
31424713 AGCTCGTACA
* * * *
31424723 ATGCC-ATATCCCAGATATGGTCTTACATGTTATCACATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCA-ATATCG
* * *
31424765 ATGCCAGTGTCCCAGACATGGTCTTACACGAAATCATATAACG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCA-ATATCG
31424808 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCGTAATAT-G
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATC--AATATCG
* *
31424851 ATGCCAATGTCCCAAACATGGTCTTACACATAATCA
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCA
31424887 CGTCTTGTTA
Statistics
Matches: 106, Mismatches: 13, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
41 1 0.01
42 5 0.05
43 96 0.91
44 3 0.03
45 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGTAATCAATATCG
Found at i:31424886 original size:86 final size:85
Alignment explanation
Indices: 31424723--31424879 Score: 219
Period size: 86 Copynumber: 1.8 Consensus size: 85
31424713 AGCTCGTACA
* * * * *
31424723 ATGCCATATCCCAGATATGGTCTTACATGTTATCACATATCGATGCCAGTGTCCCAGACATGGTC
1 ATGCCATATCCCAGACATGGTCTTACACGTAATCACATATCGATGCCAATGTCCCAAACATGGTC
31424788 TTACACGAAATCATATAACG
66 TTACACGAAATCATATAACG
*
31424808 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCGTA-ATAT-GATGCCAATGTCCCAAACATG
1 ATGCC-ATATCCCAGACATGGTCTTACACGTAATC--ACATATCGATGCCAATGTCCCAAACATG
31424871 GTCTTACAC
63 GTCTTACAC
31424880 ATAATCACGT
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
85 5 0.08
86 53 0.84
87 4 0.06
88 1 0.02
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (85 bp):
ATGCCATATCCCAGACATGGTCTTACACGTAATCACATATCGATGCCAATGTCCCAAACATGGTC
TTACACGAAATCATATAACG
Done.