Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 86 of 290
Found at i:28767764 original size:24 final size:24
Alignment explanation
Indices: 28767732--28767859 Score: 166
Period size: 24 Copynumber: 5.0 Consensus size: 24
28767722 ACTTAGCACC
28767732 ATGCCATGGACTTATTTCACTTAG
1 ATGCCATGGACTTATTTCACTTAG
28767756 ATGCCATGGACTTATTTCACTTAG
1 ATGCCATGGACTTATTTCACTTAG
*
28767780 CACATTGCCATGGACTTATTTCACTTTGCAC
1 ---A-TGCCATGGACTTATTTCAC-TT--AG
28767811 ATTGCCATGGACTTATTTCACTTAG
1 A-TGCCATGGACTTATTTCACTTAG
*
28767836 ATGCCATGGTCTTATTTCACTTAG
1 ATGCCATGGACTTATTTCACTTAG
28767860 CACAATTCCA
Statistics
Matches: 94, Mismatches: 3, Indels: 14
0.85 0.03 0.13
Matches are distributed among these distances:
24 46 0.49
25 2 0.02
27 3 0.03
28 40 0.43
29 2 0.02
31 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (24 bp):
ATGCCATGGACTTATTTCACTTAG
Found at i:28767776 original size:52 final size:52
Alignment explanation
Indices: 28767720--28767859 Score: 189
Period size: 52 Copynumber: 2.7 Consensus size: 52
28767710 GGGAAATTTC
28767720 TCACTTAGCACCATGCCATGGACTTATTTCACTTAGA-TGCCATGGACTTATT
1 TCACTTAGCA-CATGCCATGGACTTATTTCACTTAGATTGCCATGGACTTATT
*
28767772 TCACTTAGCACATTGCCATGGACTTATTTCACTTTGCACATTGCCATGGACTTATT
1 TCACTTAGCACA-TGCCATGGACTTATTTCAC-TT--AGATTGCCATGGACTTATT
*
28767828 TCACTTAG---ATGCCATGGTCTTATTTCACTTAG
1 TCACTTAGCACATGCCATGGACTTATTTCACTTAG
28767860 CACAATTCCA
Statistics
Matches: 80, Mismatches: 3, Indels: 13
0.83 0.03 0.14
Matches are distributed among these distances:
49 1 0.01
51 4 0.05
52 47 0.59
53 3 0.04
55 2 0.03
56 23 0.29
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (52 bp):
TCACTTAGCACATGCCATGGACTTATTTCACTTAGATTGCCATGGACTTATT
Found at i:28767789 original size:28 final size:27
Alignment explanation
Indices: 28767720--28767863 Score: 201
Period size: 28 Copynumber: 5.4 Consensus size: 27
28767710 GGGAAATTTC
28767720 TCACTTAGCACCATGCCATGGACTTATT
1 TCACTTAGCA-CATGCCATGGACTTATT
28767748 TCACTTAG---ATGCCATGGACTTATT
1 TCACTTAGCACATGCCATGGACTTATT
28767772 TCACTTAGCACATTGCCATGGACTTATT
1 TCACTTAGCACA-TGCCATGGACTTATT
*
28767800 TCACTTTGCACATTGCCATGGACTTATT
1 TCACTTAGCACA-TGCCATGGACTTATT
*
28767828 TCACTTAG---ATGCCATGGTCTTATT
1 TCACTTAGCACATGCCATGGACTTATT
28767852 TCACTTAGCACA
1 TCACTTAGCACA
28767864 ATTCCATATC
Statistics
Matches: 106, Mismatches: 3, Indels: 15
0.85 0.02 0.12
Matches are distributed among these distances:
24 46 0.43
25 1 0.01
27 2 0.02
28 57 0.54
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.36
Consensus pattern (27 bp):
TCACTTAGCACATGCCATGGACTTATT
Found at i:28775134 original size:48 final size:48
Alignment explanation
Indices: 28775076--28775755 Score: 1189
Period size: 48 Copynumber: 14.2 Consensus size: 48
28775066 ATATACACAC
* * *
28775076 ATCTCCTACATATTTCACACTAGCCATTCGACTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
28775124 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
28775172 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
28775220 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
28775268 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
28775316 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
* *
28775364 ATCTCATATATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
28775412 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
28775460 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
28775508 ATCTCATACATATTTCACATTAGCCATTCAGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
* * *
28775556 ATCTCATTCATATTTCACACTAGCCATTTGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
* * * * *
28775604 ATCTTATATATATTTCACACTGGCCATTCGGCTTTACCACATATACAG
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
* * *
28775652 ATCTCATATATATTTCACATTGGCCATTCGGCTTTACCACATATAAAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
28775700 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
28775748 ATCTCATA
1 ATCTCATA
28775756 NNNNNNNNNN
Statistics
Matches: 606, Mismatches: 26, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 606 1.00
ACGTcount: A:0.31, C:0.27, G:0.06, T:0.35
Consensus pattern (48 bp):
ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
Found at i:28788750 original size:48 final size:48
Alignment explanation
Indices: 28788692--28788880 Score: 315
Period size: 48 Copynumber: 3.9 Consensus size: 48
28788682 ATATACACAC
*
28788692 ATCTCCTACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
28788740 ATCTCATACATATTTCACACTTGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* **
28788788 ATCTTATTTATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* *
28788836 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATA
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATA
28788881 NNNNNNNNNN
Statistics
Matches: 132, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 132 1.00
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.37
Consensus pattern (48 bp):
ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
Found at i:28797715 original size:25 final size:24
Alignment explanation
Indices: 28797687--28797778 Score: 69
Period size: 25 Copynumber: 3.8 Consensus size: 24
28797677 CCATAAAACA
28797687 GGAAGCTCATGTGAGCCATGCAATG
1 GGAAGCTCATGTGAGCCATG-AATG
* * * * *
28797712 GGAAGCTCATATGGGCTATTTAACG
1 GGAAGCTCATGTGAGCCA-TGAATG
* *
28797737 GGAAGCTCATGAGAGTCATG-ATCG
1 GGAAGCTCATGTGAGCCATGAAT-G
* *
28797761 GGAAGCTCGTGCGAGCCA
1 GGAAGCTCATGTGAGCCA
28797779 ATAACAGGTA
Statistics
Matches: 50, Mismatches: 15, Indels: 5
0.71 0.21 0.07
Matches are distributed among these distances:
23 1 0.02
24 17 0.34
25 31 0.62
26 1 0.02
ACGTcount: A:0.27, C:0.20, G:0.33, T:0.21
Consensus pattern (24 bp):
GGAAGCTCATGTGAGCCATGAATG
Found at i:28804163 original size:48 final size:48
Alignment explanation
Indices: 28804088--28804315 Score: 207
Period size: 48 Copynumber: 4.9 Consensus size: 48
28804078 TACATGGTAG
* * * * *
28804088 GATGCCAATTCCATATCTCAAATATGGTCTTACATGGGATCACATATC
1 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATC
* ** **
28804136 GATGCCAATGTCATGTCCCAGACATGGTCTTACATGGGATCGTAGGTC
1 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATC
* * * *
28804184 AATGCCAATGCCATGTCCCAGACATAGTCTTACATGGGATTACATGTC
1 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATC
* * ** **
28804232 GATGCCGAT---A-G-CCCAG-CTATGGTCTTACACGAAATTGCATATC
1 GATGCCAATGCCATGTCCCAGAC-ATGGTCTTACATGGGATCACATATC
* *
28804275 GATGCCAAAGCCATGTCCCAAACATGGTCTTACATGGGATC
1 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATC
28804316 GTACATAACC
Statistics
Matches: 141, Mismatches: 32, Indels: 14
0.75 0.17 0.07
Matches are distributed among these distances:
42 1 0.01
43 31 0.22
44 1 0.01
45 1 0.01
46 1 0.01
47 1 0.01
48 104 0.74
49 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.27
Consensus pattern (48 bp):
GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATC
Found at i:28805835 original size:24 final size:24
Alignment explanation
Indices: 28805803--28805850 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
28805793 AATTTTAATA
28805803 TGCATTTTTTCTTAAAATAGTTAT
1 TGCATTTTTTCTTAAAATAGTTAT
28805827 TGCATTTTTTCTTAAAATAGTTAT
1 TGCATTTTTTCTTAAAATAGTTAT
28805851 GTTAGGCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.08, G:0.08, T:0.54
Consensus pattern (24 bp):
TGCATTTTTTCTTAAAATAGTTAT
Found at i:28808646 original size:150 final size:150
Alignment explanation
Indices: 28808375--28808674 Score: 537
Period size: 150 Copynumber: 2.0 Consensus size: 150
28808365 GCACACTATT
* *
28808375 GATGACATTATTCTCTCAACTAACCAACATTAGTGATGAAATAAATCAAGTTATTATTTTTTCAG
1 GATGACATTATTCTCTCAACTAACCAACAATAGTGATGAAATAAATCAAGTTATTAATTTTTCAG
*
28808440 TTTAGATAATTCAATTAAATAAATTATAAAAAAATATTAGAAAAATAATTCATCGATTTTTTAAT
66 TTTAAATAATTCAATTAAATAAATTATAAAAAAATATTAGAAAAATAATTCATCGATTTTTTAAT
*
28808505 TTAGCTCATATTAGTTCATG
131 TTAACTCATATTAGTTCATG
* *
28808525 GATGACATTATTCTCTCAACTAACTAACAATGGTGATGAAATAAATCAAGTTATTAATTTTTCAG
1 GATGACATTATTCTCTCAACTAACCAACAATAGTGATGAAATAAATCAAGTTATTAATTTTTCAG
28808590 TTTAAATAATTCAATTAAATAAATTATAAAAAAATATTAGAAAAATAATTCATCGATTTTTTAAT
66 TTTAAATAATTCAATTAAATAAATTATAAAAAAATATTAGAAAAATAATTCATCGATTTTTTAAT
*
28808655 TTAACTTATATTAGTTCATG
131 TTAACTCATATTAGTTCATG
28808675 ACTCAACCAA
Statistics
Matches: 143, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
150 143 1.00
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.39
Consensus pattern (150 bp):
GATGACATTATTCTCTCAACTAACCAACAATAGTGATGAAATAAATCAAGTTATTAATTTTTCAG
TTTAAATAATTCAATTAAATAAATTATAAAAAAATATTAGAAAAATAATTCATCGATTTTTTAAT
TTAACTCATATTAGTTCATG
Found at i:28810763 original size:18 final size:17
Alignment explanation
Indices: 28810738--28810771 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
28810728 AAATGGTTTT
28810738 TTTGAAGAAATTAAAAG
1 TTTGAAGAAATTAAAAG
*
28810755 TTTGTAAGAGATTAAAA
1 TTTG-AAGAAATTAAAA
28810772 TAATATTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.50, C:0.00, G:0.18, T:0.32
Consensus pattern (17 bp):
TTTGAAGAAATTAAAAG
Found at i:28814598 original size:34 final size:34
Alignment explanation
Indices: 28814547--28814633 Score: 86
Period size: 34 Copynumber: 2.5 Consensus size: 34
28814537 ATACTGGTCA
* *
28814547 GAAATAGGCTAAGGCCCAGAGTGCCACTATTACT
1 GAAATAGGCTAAGGCCCAGACTGCCACTACTACT
* * *
28814581 GAAATGGGCTCAA-GCCCAGACTGCTACTACTATT
1 GAAATAGGCT-AAGGCCCAGACTGCCACTACTACT
*
28814615 GAAAGAGGGGCTAAGGCCC
1 GAAATA--GGCTAAGGCCC
28814634 TTAACTGAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
34 30 0.71
35 4 0.10
36 8 0.19
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.18
Consensus pattern (34 bp):
GAAATAGGCTAAGGCCCAGACTGCCACTACTACT
Found at i:28826853 original size:29 final size:28
Alignment explanation
Indices: 28826799--28826853 Score: 65
Period size: 29 Copynumber: 1.9 Consensus size: 28
28826789 TATACATCAA
* * * *
28826799 GAAAGACGAAGTTTTGACCTAGATCGGC
1 GAAAGACAAAGTTGTGAACTAAATCGGC
28826827 GAAAGAACAAAGTTGTGAACTAAATCG
1 GAAAG-ACAAAGTTGTGAACTAAATCG
28826854 AACTATTAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 5 0.23
29 17 0.77
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.20
Consensus pattern (28 bp):
GAAAGACAAAGTTGTGAACTAAATCGGC
Found at i:28829742 original size:21 final size:22
Alignment explanation
Indices: 28829718--28829768 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
28829708 GTTGAGAAAA
28829718 TTATTTAATTAAAAAATTA-AT
1 TTATTTAATTAAAAAATTATAT
* **
28829739 TTATCTAATTAATTAATTATTAT
1 TTATTTAATTAAAAAATTA-TAT
28829762 TTATTTA
1 TTATTTA
28829769 TTTATGAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 16 0.67
23 8 0.33
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
TTATTTAATTAAAAAATTATAT
Found at i:28834326 original size:42 final size:42
Alignment explanation
Indices: 28834280--28834360 Score: 162
Period size: 42 Copynumber: 1.9 Consensus size: 42
28834270 CTTTGAAATA
28834280 TGTTGATACTATACATGTGTAAATTAACTTATTGTGCTAATG
1 TGTTGATACTATACATGTGTAAATTAACTTATTGTGCTAATG
28834322 TGTTGATACTATACATGTGTAAATTAACTTATTGTGCTA
1 TGTTGATACTATACATGTGTAAATTAACTTATTGTGCTA
28834361 TGTATCTAAA
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:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (42 bp):
TGTTGATACTATACATGTGTAAATTAACTTATTGTGCTAATG
Found at i:28841448 original size:68 final size:67
Alignment explanation
Indices: 28841376--28841525 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
28841366 CATCATGTGT
* * * *
28841376 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
28841438 ATGTAG
62 ATGTAG
** * *
28841444 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
28841509 AG
66 AG
28841511 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
28841526 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:28841481 original size:64 final size:64
Alignment explanation
Indices: 28841400--28841583 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
28841390 AGACATTATG
* *
28841400 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
28841464 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
28841529 AA
63 AA
* * * *
28841531 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
28841584 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:28857891 original size:20 final size:20
Alignment explanation
Indices: 28857866--28857904 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28857856 AGGGACTAAA
* *
28857866 ATGAAAAGTTTTAAAATTTG
1 ATGAAAAATTCTAAAATTTG
28857886 ATGAAAAATTCTAAAATTT
1 ATGAAAAATTCTAAAATTT
28857905 TAGGAATACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.03, G:0.10, T:0.38
Consensus pattern (20 bp):
ATGAAAAATTCTAAAATTTG
Found at i:28859978 original size:25 final size:25
Alignment explanation
Indices: 28859944--28859994 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
28859934 TTGAATACAT
*
28859944 GCTTGAAATGATGACAAAGGGGTAA
1 GCTTGAAATGATGACAAAAGGGTAA
*
28859969 GCTTGAAATGATGATAAAAGGGTAA
1 GCTTGAAATGATGACAAAAGGGTAA
28859994 G
1 G
28859995 TCCCGATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.41, C:0.06, G:0.31, T:0.22
Consensus pattern (25 bp):
GCTTGAAATGATGACAAAAGGGTAA
Found at i:28860731 original size:25 final size:25
Alignment explanation
Indices: 28860702--28860751 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
28860692 TGATGGTTGG
28860702 AGATCACTGGAACATTGTCACACTA
1 AGATCACTGGAACATTGTCACACTA
*
28860727 AGATCACTGGAGCATTGTCACACTA
1 AGATCACTGGAACATTGTCACACTA
28860752 TCTACTAGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (25 bp):
AGATCACTGGAACATTGTCACACTA
Found at i:28861503 original size:21 final size:22
Alignment explanation
Indices: 28861477--28861521 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
28861467 GTCCAAAGGA
28861477 GTCC-TTGGACCACACGGGCGT
1 GTCCTTTGGACCACACGGGCGT
*
28861498 GTCCTTTGGACCACACGGGTGT
1 GTCCTTTGGACCACACGGGCGT
28861520 GT
1 GT
28861522 GAGTCCTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.13, C:0.29, G:0.33, T:0.24
Consensus pattern (22 bp):
GTCCTTTGGACCACACGGGCGT
Found at i:28866813 original size:16 final size:17
Alignment explanation
Indices: 28866792--28866825 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
28866782 AAAAATTATG
28866792 AAATAAA-ACCAAACAA
1 AAATAAACACCAAACAA
*
28866808 AAATAAACATCAAACAA
1 AAATAAACACCAAACAA
28866825 A
1 A
28866826 TGACATCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.74, C:0.18, G:0.00, T:0.09
Consensus pattern (17 bp):
AAATAAACACCAAACAA
Found at i:28868868 original size:16 final size:15
Alignment explanation
Indices: 28868847--28868876 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
28868837 ATTGTGTAAA
28868847 ATTAATTAATATAATT
1 ATTAATTAAT-TAATT
28868863 ATTAATTAATTAAT
1 ATTAATTAATTAAT
28868877 ATTTTGAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTAATTAATTAATT
Found at i:28878106 original size:21 final size:21
Alignment explanation
Indices: 28878066--28878106 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28878056 AGGTTAAAAA
*
28878066 TATATTTTTAATTGATATTTT
1 TATATTTTTAATTGAAATTTT
28878087 TATATTTTATAATT-AAATTT
1 TATATTTT-TAATTGAAATTT
28878107 AAATAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
TATATTTTTAATTGAAATTTT
Found at i:28878854 original size:21 final size:21
Alignment explanation
Indices: 28878830--28878869 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
28878820 ATTAACTATC
28878830 GAAACGTTAAAATTTTTCAGT
1 GAAACGTTAAAATTTTTCAGT
28878851 GAAACGTTAAAATTTTTCA
1 GAAACGTTAAAATTTTTCA
28878870 ACGAAACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (21 bp):
GAAACGTTAAAATTTTTCAGT
Found at i:28878875 original size:21 final size:21
Alignment explanation
Indices: 28878829--28878881 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
28878819 AATTAACTAT
*
28878829 CGAAACGTTAAAATTTTTCAG
1 CGAAACGTTAAAATTTTTCAA
*
28878850 TGAAACGTTAAAATTTTTCAA
1 CGAAACGTTAAAATTTTTCAA
*
28878871 CGAAACTTTAA
1 CGAAACGTTAA
28878882 TACCACCTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (21 bp):
CGAAACGTTAAAATTTTTCAA
Found at i:28892803 original size:40 final size:39
Alignment explanation
Indices: 28892772--28892981 Score: 242
Period size: 40 Copynumber: 5.3 Consensus size: 39
28892762 GGACTAAGAT
* *
28892772 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGATACAAA-TCCGGGTTAAGTC
* *
28892812 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
* *
28892852 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* * *
28892892 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* * * * *
28892932 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
28892971 CCGAAGGCATT
1 CCGAAGGCATT
28892982 TGAACGAGGA
Statistics
Matches: 156, Mismatches: 11, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
39 34 0.22
40 119 0.76
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:28892935 original size:120 final size:120
Alignment explanation
Indices: 28892719--28892981 Score: 309
Period size: 120 Copynumber: 2.2 Consensus size: 120
28892709 TTGAATGCTG
* *
28892719 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
* *
28892783 TGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
66 CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACTAAA
* * * * **
28892839 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGAT-CCGAAGGCAT
* * * * * *
28892902 TCGTGCGAGTTATTAAA-TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
65 TCGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
* *
28892958 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
28892982 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
119 38 0.31
120 74 0.61
121 9 0.07
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:28893001 original size:79 final size:80
Alignment explanation
Indices: 28892720--28893016 Score: 230
Period size: 80 Copynumber: 3.7 Consensus size: 80
28892710 TGAATGCTGT
* ** * * * **
28892720 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTCGAAC-GAGTGACTAAATCCGGGTTAAG-TCCCGAAGGCATT
* * *
28892783 TGTGCGAGATAC-AAATT
64 CGTGCGAGTTACTAAA-A
* * * * **
28892800 CCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGAT-ACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAG-TGACTAAATCCGGGTTAAGTCCCGAAGGCATTC
* *
28892864 GTGCGAGTTATTAAAT
65 GTGCGAGTTACTAAAA
* ** * * *
28892880 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATT-G
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
*
28892944 TGTGAGTTACTAAAA
66 TGCGAGTTACTAAAA
* * * *
28892959 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGA-CTAAATCCGGGTTAAGTCCCGAAGG
28893017 TACGTGATTT
Statistics
Matches: 183, Mismatches: 28, Indels: 14
0.81 0.12 0.06
Matches are distributed among these distances:
78 15 0.08
79 47 0.26
80 110 0.60
81 11 0.06
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
TGCGAGTTACTAAAA
Found at i:28900753 original size:40 final size:39
Alignment explanation
Indices: 28900722--28900931 Score: 242
Period size: 40 Copynumber: 5.3 Consensus size: 39
28900712 GGACTAAGAT
* *
28900722 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGATACAAA-TCCGGGTTAAGTC
* *
28900762 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
* *
28900802 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* * *
28900842 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* * * * *
28900882 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
28900921 CCGAAGGCATT
1 CCGAAGGCATT
28900932 TGAACGAGGA
Statistics
Matches: 156, Mismatches: 11, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
39 34 0.22
40 119 0.76
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:28900885 original size:120 final size:120
Alignment explanation
Indices: 28900669--28900931 Score: 309
Period size: 120 Copynumber: 2.2 Consensus size: 120
28900659 TTGAATGCTG
* *
28900669 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
* *
28900733 TGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
66 CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACTAAA
* * * * **
28900789 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGAT-CCGAAGGCAT
* * * * * *
28900852 TCGTGCGAGTTATTAAA-TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
65 TCGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
* *
28900908 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
28900932 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
119 38 0.31
120 74 0.61
121 9 0.07
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:28900951 original size:79 final size:80
Alignment explanation
Indices: 28900670--28900966 Score: 230
Period size: 80 Copynumber: 3.7 Consensus size: 80
28900660 TGAATGCTGT
* ** * * * **
28900670 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTCGAAC-GAGTGACTAAATCCGGGTTAAG-TCCCGAAGGCATT
* * *
28900733 TGTGCGAGATAC-AAATT
64 CGTGCGAGTTACTAAA-A
* * * * **
28900750 CCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGAT-ACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAG-TGACTAAATCCGGGTTAAGTCCCGAAGGCATTC
* *
28900814 GTGCGAGTTATTAAAT
65 GTGCGAGTTACTAAAA
* ** * * *
28900830 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATT-G
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
*
28900894 TGTGAGTTACTAAAA
66 TGCGAGTTACTAAAA
* * * *
28900909 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGA-CTAAATCCGGGTTAAGTCCCGAAGG
28900967 TACGTGATTT
Statistics
Matches: 183, Mismatches: 28, Indels: 14
0.81 0.12 0.06
Matches are distributed among these distances:
78 15 0.08
79 47 0.26
80 110 0.60
81 11 0.06
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
TGCGAGTTACTAAAA
Found at i:28912052 original size:12 final size:13
Alignment explanation
Indices: 28912028--28912056 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
28912018 GGGCTATAAC
28912028 TATTGCATTTATT
1 TATTGCATTTATT
28912041 TATTGC-TTTATT
1 TATTGCATTTATT
28912053 TATT
1 TATT
28912057 CATGTATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (13 bp):
TATTGCATTTATT
Found at i:28916449 original size:29 final size:29
Alignment explanation
Indices: 28916407--28916507 Score: 150
Period size: 29 Copynumber: 3.5 Consensus size: 29
28916397 CATGAAATTG
28916407 GCACTAAGTGTGCGGGTTCAAATTGTATA
1 GCACTAAGTGTGCGGGTTCAAATTGTATA
*
28916436 GCACTAAGTGTGCGGGTTCAAGTTGTATA
1 GCACTAAGTGTGCGGGTTCAAATTGTATA
* * *
28916465 GCACTAAGTGTGCGAGTTC-GATTATATA
1 GCACTAAGTGTGCGGGTTCAAATTGTATA
*
28916493 ACACTAAGTGTGCGG
1 GCACTAAGTGTGCGG
28916508 ACTTACTATA
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
28 19 0.29
29 46 0.71
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.30
Consensus pattern (29 bp):
GCACTAAGTGTGCGGGTTCAAATTGTATA
Found at i:28920698 original size:162 final size:162
Alignment explanation
Indices: 28920431--28920753 Score: 628
Period size: 162 Copynumber: 2.0 Consensus size: 162
28920421 AGATAAAAGA
28920431 CTTAAGGATTAATGCATGAAAGGTAAATCACAAAAGGTTATGTTGAATCATGGCTTCTTGTAACT
1 CTTAAGGATTAATGCATGAAAGGTAAATCACAAAAGGTTATGTTGAATCATGGCTTCTTGTAACT
28920496 TAGGTAGCAATGATGCATTGCTAGATGTCACTCATTGTATGTAACATTAGAATCGTTCTAGTATT
66 TAGGTAGCAATGATGCATTGCTAGATGTCACTCATTGTATGTAACATTAGAATCGTTCTAGTATT
28920561 ACTGCTAACGTTACAAGAGCCTACAGGGTCAC
131 ACTGCTAACGTTACAAGAGCCTACAGGGTCAC
28920593 CTTAAGGATTAATGCATGAAAGGTAAATCACAAAAGGTTATGTTGAATCATGGCTTCTTGTAACT
1 CTTAAGGATTAATGCATGAAAGGTAAATCACAAAAGGTTATGTTGAATCATGGCTTCTTGTAACT
28920658 TAGGTAGCAATGATGCATTGCTAGATGTCACTCATTGTATGTAACATTAGAATCGTTCTAGTATT
66 TAGGTAGCAATGATGCATTGCTAGATGTCACTCATTGTATGTAACATTAGAATCGTTCTAGTATT
* *
28920723 ACTGCTAATGTTACAAGAGCTTACAGGGTCA
131 ACTGCTAACGTTACAAGAGCCTACAGGGTCA
28920754 GACCATATGG
Statistics
Matches: 159, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
162 159 1.00
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.32
Consensus pattern (162 bp):
CTTAAGGATTAATGCATGAAAGGTAAATCACAAAAGGTTATGTTGAATCATGGCTTCTTGTAACT
TAGGTAGCAATGATGCATTGCTAGATGTCACTCATTGTATGTAACATTAGAATCGTTCTAGTATT
ACTGCTAACGTTACAAGAGCCTACAGGGTCAC
Found at i:28924648 original size:53 final size:53
Alignment explanation
Indices: 28924580--28924757 Score: 171
Period size: 53 Copynumber: 3.3 Consensus size: 53
28924570 TTCCTTTTTG
* *
28924580 AACTTACCATTGCCATCTCTTGACATGGTCTTACGTGGTATCCTTGCCTTATA
1 AACTTACCAATGCCATCTCTTGACATGGTCTTACATGGTATCCTTGCCTTATA
* * * * *
28924633 AACTCACCAATGCCATGC-CTTGGCATGGTCTTACATGGGA-CCTTTTCCTCATATT
1 AACTTACCAATGCCAT-CTCTTGACATGGTCTTACATGGTATCC-TTGCCT--TATA
** * * *
28924688 AACTTATTAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTATA
1 AACTTACCAATGCCATCTCTTGACATGGTCTTACATGGTATCCTTGCCTTATA
* *
28924741 GAACTTATCAACGCCAT
1 -AACTTACCAATGCCAT
28924758 GCCAACATGA
Statistics
Matches: 99, Mismatches: 19, Indels: 13
0.76 0.15 0.10
Matches are distributed among these distances:
52 2 0.02
53 41 0.41
54 15 0.15
55 39 0.39
56 2 0.02
ACGTcount: A:0.24, C:0.26, G:0.15, T:0.36
Consensus pattern (53 bp):
AACTTACCAATGCCATCTCTTGACATGGTCTTACATGGTATCCTTGCCTTATA
Found at i:28924767 original size:42 final size:42
Alignment explanation
Indices: 28924720--28924802 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
28924710 ACATGGTCTT
28924720 ACATGATTTCCTTGCCTTATAGAACTTATCAACGCCATGCCA
1 ACATGATTTCCTTGCCTTATAGAACTTATCAACGCCATGCCA
* *
28924762 ACATGATTTCCTTGCCTTATAGAACTTATCAATGTCATGCC
1 ACATGATTTCCTTGCCTTATAGAACTTATCAACGCCATGCC
28924803 TTGGCATGGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.28, C:0.27, G:0.12, T:0.34
Consensus pattern (42 bp):
ACATGATTTCCTTGCCTTATAGAACTTATCAACGCCATGCCA
Found at i:28924910 original size:47 final size:47
Alignment explanation
Indices: 28924807--28924968 Score: 143
Period size: 47 Copynumber: 3.5 Consensus size: 47
28924797 CATGCCTTGG
* *
28924807 CATGGTCTTACATGGTATCCTTGTCTTAGTGCCAATGCCACATCTTGA
1 CATGGTCTTACATGGTATCCTTGTC-TAATGCCAATGCCACATCTGGA
** * *
28924855 TTTGGTCTTACATGG-AGTCCTTAGTC-AATGCCGATGCCATATCTGGA
1 CATGGTCTTACATGGTA-TCCTT-GTCTAATGCCAATGCCACATCTGGA
* * * * * ** *
28924902 CATGGTCTTACACGGGATCCTTGCCT--TACCAATGTCATGTCTTGA
1 CATGGTCTTACATGGTATCCTTGTCTAATGCCAATGCCACATCTGGA
28924947 CATGGTCTTACATGGTATCCTT
1 CATGGTCTTACATGGTATCCTT
28924969 AACCATCAAT
Statistics
Matches: 93, Mismatches: 17, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
45 34 0.37
46 2 0.02
47 35 0.38
48 19 0.20
49 3 0.03
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.35
Consensus pattern (47 bp):
CATGGTCTTACATGGTATCCTTGTCTAATGCCAATGCCACATCTGGA
Found at i:28924967 original size:45 final size:45
Alignment explanation
Indices: 28924802--28924968 Score: 147
Period size: 45 Copynumber: 3.6 Consensus size: 45
28924792 AATGTCATGC
* * *
28924802 CTTGGCATGGTCTTACATGGTATCCTTGTCTTAGTGCCAATGCCACAT
1 CTTGACATGGTCTTACATGGTATCCTTGCCTTA---CCAATGCCATAT
** ** * *
28924850 CTTGATTTGGTCTTACATGG-AGTCCTTAGTCAATGCCGATGCCATAT
1 CTTGACATGGTCTTACATGGTA-TCCTT-G-CCTTACCAATGCCATAT
* * * * *
28924897 CTGGACATGGTCTTACACGGGATCCTTGCCTTACCAATGTCATGT
1 CTTGACATGGTCTTACATGGTATCCTTGCCTTACCAATGCCATAT
28924942 CTTGACATGGTCTTACATGGTATCCTT
1 CTTGACATGGTCTTACATGGTATCCTT
28924969 AACCATCAAT
Statistics
Matches: 93, Mismatches: 22, Indels: 11
0.74 0.17 0.09
Matches are distributed among these distances:
45 35 0.38
46 1 0.01
47 32 0.34
48 23 0.25
49 1 0.01
50 1 0.01
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.35
Consensus pattern (45 bp):
CTTGACATGGTCTTACATGGTATCCTTGCCTTACCAATGCCATAT
Found at i:28925639 original size:30 final size:30
Alignment explanation
Indices: 28925594--28925654 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
28925584 TCCCTAACTC
* *
28925594 AAACTTTTTCAAAATTACAATTTTGCCCCT
1 AAACCTTTACAAAATTACAATTTTGCCCCT
**
28925624 AAACCTTTACAAAATTATGATTTTGCCCCT
1 AAACCTTTACAAAATTACAATTTTGCCCCT
28925654 A
1 A
28925655 GGCTCGGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.38
Consensus pattern (30 bp):
AAACCTTTACAAAATTACAATTTTGCCCCT
Found at i:28932186 original size:10 final size:10
Alignment explanation
Indices: 28932151--28932197 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
28932141 GTTTTTACTA
28932151 TTTTTAGTAAT
1 TTTTTA-TAAT
* *
28932162 ATTTT-TAAC
1 TTTTTATAAT
28932171 TTTTTATAAT
1 TTTTTATAAT
28932181 TTTTTATAAT
1 TTTTTATAAT
28932191 TTATTTA
1 TT-TTTA
28932198 AGTAAAATCC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
9 7 0.23
10 15 0.50
11 8 0.27
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:28938440 original size:28 final size:27
Alignment explanation
Indices: 28938400--28938460 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
28938390 ACTTAATGTA
* *
28938400 GAAAATATTAAATTAATT-TTATTTTAT
1 GAAAAAATTAAATAAATTATT-TTTTAT
*
28938427 TAAAAAATTGAAATAAATTATTTTTTAT
1 GAAAAAATT-AAATAAATTATTTTTTAT
28938455 GAAAAA
1 GAAAAA
28938461 TATTCAACTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
27 7 0.25
28 19 0.68
29 2 0.07
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (27 bp):
GAAAAAATTAAATAAATTATTTTTTAT
Found at i:28943783 original size:12 final size:13
Alignment explanation
Indices: 28943763--28943795 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
28943753 AAGTAGATTT
28943763 TTATAATAATTAA
1 TTATAATAATTAA
28943776 TTAT-ATAATTAA
1 TTATAATAATTAA
*
28943788 TTAAAATA
1 TTATAATA
28943796 TTTATAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TTATAATAATTAA
Found at i:28944030 original size:21 final size:21
Alignment explanation
Indices: 28943982--28944023 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28943972 TTTCGCTGTT
* *
28943982 TCTAATCTCACTGCTACAGTA
1 TCTAATCACACTACTACAGTA
*
28944003 TCCAATCACACTACTACAGTA
1 TCTAATCACACTACTACAGTA
28944024 ATTAATCTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.31, G:0.07, T:0.29
Consensus pattern (21 bp):
TCTAATCACACTACTACAGTA
Found at i:28944086 original size:7 final size:7
Alignment explanation
Indices: 28944074--28944098 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
28944064 AAGCCTAAGT
28944074 TTAAAAA
1 TTAAAAA
28944081 TTAAAAA
1 TTAAAAA
28944088 TTAAAAA
1 TTAAAAA
28944095 TTAA
1 TTAA
28944099 TATAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
TTAAAAA
Found at i:28946676 original size:94 final size:95
Alignment explanation
Indices: 28946556--28946729 Score: 237
Period size: 94 Copynumber: 1.8 Consensus size: 95
28946546 TATGAGAGCC
* * *
28946556 AGTGTAAGACCATGTCTGAGAAATGGCATCGGCATTGAGACGA-GTGCTAATGTAAGA-CATGCT
1 AGTGTAAGACCATGTCTGAGAAATGGCATCGAC-TTGAGA-GATGAGCCAATGTAAGACCATGCT
28946619 TGGGACAT-GCATCGGCTACGAGATGATAGTT
64 TGGGACATGGCATCGGCTACGAGATGATAGTT
* * * * *
28946650 AGTGTAAGACCATGTCTGGGACATGGCATCGACTTGAGATATGAGCCAGTGTAAGACCATGTTTG
1 AGTGTAAGACCATGTCTGAGAAATGGCATCGACTTGAGAGATGAGCCAATGTAAGACCATGCTTG
28946715 GGACATGGCATCGGC
66 GGACATGGCATCGGC
28946730 ACCTTACTCC
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
92 1 0.01
93 17 0.25
94 43 0.62
95 8 0.12
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.24
Consensus pattern (95 bp):
AGTGTAAGACCATGTCTGAGAAATGGCATCGACTTGAGAGATGAGCCAATGTAAGACCATGCTTG
GGACATGGCATCGGCTACGAGATGATAGTT
Found at i:28946689 original size:47 final size:47
Alignment explanation
Indices: 28946506--28946729 Score: 194
Period size: 47 Copynumber: 4.8 Consensus size: 47
28946496 AGTTATTGTG
* * * * *
28946506 AGCTAGTGTAAGA-CATGTCTGGGAAAT-ACATCGGCCAT-ATTATGAG
1 AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGG-CTTGA-GATGAT
* * * *
28946552 AGCCAGTGTAAGACCATGTCTGAGAAATGGCATCGGCATTGAGACGAGT
1 AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC-TTGAGATGA-T
* *
28946601 -GCTAATGTAAGA-CATG-CTTGGGACAT-GCATCGGCTACGAGATGAT
1 AGCTAGTGTAAGACCATGTC-TGGGACATGGCATCGGCT-TGAGATGAT
* *
28946646 AGTTAGTGTAAGACCATGTCTGGGACATGGCATCGACTTGAGAT-AT
1 AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCTTGAGATGAT
* *
28946692 GAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGC
1 -AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC
28946730 ACCTTACTCC
Statistics
Matches: 145, Mismatches: 21, Indels: 23
0.77 0.11 0.12
Matches are distributed among these distances:
45 2 0.01
46 39 0.27
47 74 0.51
48 29 0.20
49 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.24
Consensus pattern (47 bp):
AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCTTGAGATGAT
Found at i:28954236 original size:46 final size:46
Alignment explanation
Indices: 28954162--28954372 Score: 178
Period size: 46 Copynumber: 4.5 Consensus size: 46
28954152 TACATCAAAC
** * *
28954162 CATGTCTAAGACATGGCATCGGCATCGAGACG-AGTGCTAGTGTAAGA
1 CATGTCTGGGACAT-GCATCGGCATCGAGACGTA-AGCCAGTGTAAGA
* *
28954209 CATGTTTGGGACATGCATCGGCCTCGAGACGTAAGCCAGTGTAAGA
1 CATGTCTGGGACATGCATCGGCATCGAGACGTAAGCCAGTGTAAGA
* * *
28954255 CATGTCTGGGACATGCATCGGCTAT-AAGATG-ATAGTCAGTGTAAGA
1 CATGTCTGGGACATGCATCGGC-ATCGAGACGTA-AGCCAGTGTAAGA
* * * ** *
28954301 CCATATCTGGGACATGGCATCGAC-TTGAGATATGAGCCAGTGTAAGA
1 -CATGTCTGGGACAT-GCATCGGCATCGAGACGTAAGCCAGTGTAAGA
*
28954348 CCATGTCTGGGACATGGCATTGGCA
1 -CATGTCTGGGACAT-GCATCGGCA
28954373 CCTTACTCCA
Statistics
Matches: 136, Mismatches: 20, Indels: 15
0.80 0.12 0.09
Matches are distributed among these distances:
45 1 0.01
46 65 0.48
47 63 0.46
48 7 0.05
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.23
Consensus pattern (46 bp):
CATGTCTGGGACATGCATCGGCATCGAGACGTAAGCCAGTGTAAGA
Found at i:28954342 original size:47 final size:48
Alignment explanation
Indices: 28954242--28954367 Score: 179
Period size: 47 Copynumber: 2.7 Consensus size: 48
28954232 TCGAGACGTA
*
28954242 AGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTATAAGATGAT
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACTATAAGATGAT
* * *
28954288 AGTCAGTGTAAGACCATATCTGGGACATGGCATCGACT-TGAGAT-AT
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACTATAAGATGAT
28954334 GAGCCAGTGTAAGACCATGTCTGGGACATGGCAT
1 -AGCCAGTGTAAGACCATGTCTGGGACATGGCAT
28954368 TGGCACCTTA
Statistics
Matches: 71, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
46 14 0.20
47 49 0.69
48 8 0.11
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (48 bp):
AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACTATAAGATGAT
Found at i:28954666 original size:33 final size:33
Alignment explanation
Indices: 28954625--28954690 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
28954615 TGTTGTATAA
28954625 TTATTTATATGCAACTTACTAAGCTTTATGCTT
1 TTATTTATATGCAACTTACTAAGCTTTATGCTT
28954658 TTATTTATATGCAACTTACTAAGCTTTATGCTT
1 TTATTTATATGCAACTTACTAAGCTTTATGCTT
28954691 ACTCCTTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.27, C:0.15, G:0.09, T:0.48
Consensus pattern (33 bp):
TTATTTATATGCAACTTACTAAGCTTTATGCTT
Found at i:28955957 original size:18 final size:18
Alignment explanation
Indices: 28955936--28955970 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28955926 GGAATATTCA
*
28955936 TTTATTCAGTATCAGTCG
1 TTTATTCAGTAACAGTCG
*
28955954 TTTATTCTGTAACAGTC
1 TTTATTCAGTAACAGTC
28955971 AATTATTCAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.17, G:0.14, T:0.46
Consensus pattern (18 bp):
TTTATTCAGTAACAGTCG
Found at i:28956123 original size:6 final size:6
Alignment explanation
Indices: 28956114--28956140 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
28956104 CACCGTAAGG
28956114 GTAACA GTAACA GTAACA GTAACA GTA
1 GTAACA GTAACA GTAACA GTAACA GTA
28956141 GCGGTACACA
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:0.48, C:0.15, G:0.19, T:0.19
Consensus pattern (6 bp):
GTAACA
Found at i:28957277 original size:22 final size:21
Alignment explanation
Indices: 28957252--28957292 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
28957242 TCCCCTGTTC
*
28957252 TTCTCTGTTTCGTTTGCTTTGT
1 TTCTCTGTTTCATTT-CTTTGT
*
28957274 TTCTCTTTTTCATTTCTTT
1 TTCTCTGTTTCATTTCTTT
28957293 TATTTCATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.02, C:0.20, G:0.10, T:0.68
Consensus pattern (21 bp):
TTCTCTGTTTCATTTCTTTGT
Found at i:28959185 original size:39 final size:39
Alignment explanation
Indices: 28959127--28959203 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 39
28959117 TATAGAAGTG
*
28959127 TACTTTCTTTGTCTAATATTGATTTGAATAAGGTGTTTT
1 TACTTCCTTTGTCTAATATTGATTTGAATAAGGTGTTTT
* *
28959166 TACTTCCTTTGTTTGATATTGATTTGAATAAGGTGTTT
1 TACTTCCTTTGTCTAATATTGATTTGAATAAGGTGTTT
28959204 CAACCTTACC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.22, C:0.08, G:0.17, T:0.53
Consensus pattern (39 bp):
TACTTCCTTTGTCTAATATTGATTTGAATAAGGTGTTTT
Found at i:28960395 original size:8 final size:8
Alignment explanation
Indices: 28960382--28960414 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
28960372 ACTAAGCAAG
28960382 GACATCTC
1 GACATCTC
28960390 GACATCTC
1 GACATCTC
28960398 GACATCTC
1 GACATCTC
*
28960406 AACATCTC
1 GACATCTC
28960414 G
1 G
28960415 TTAGTAGAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.27, C:0.36, G:0.12, T:0.24
Consensus pattern (8 bp):
GACATCTC
Found at i:28969879 original size:18 final size:19
Alignment explanation
Indices: 28969845--28969880 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
28969835 CACATAGGGT
28969845 TCACAAAGGGCTTTGCATG
1 TCACAAAGGGCTTTGCATG
*
28969864 TCACATAGGG-TTTGCAT
1 TCACAAAGGGCTTTGCAT
28969881 AACATATAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (19 bp):
TCACAAAGGGCTTTGCATG
Found at i:28970316 original size:24 final size:24
Alignment explanation
Indices: 28970280--28970350 Score: 115
Period size: 24 Copynumber: 3.0 Consensus size: 24
28970270 CTGGCAGGAG
*
28970280 AGGATTTAAGAGTTGATAAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
28970304 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
**
28970328 AGGATTTAGGAGCAGATAAGGGA
1 AGGATTTAGGAGTTGATAAGGGA
28970351 GGAAATCTAG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.37, C:0.01, G:0.37, T:0.25
Consensus pattern (24 bp):
AGGATTTAGGAGTTGATAAGGGAT
Found at i:28971811 original size:27 final size:27
Alignment explanation
Indices: 28971771--28971882 Score: 138
Period size: 27 Copynumber: 4.1 Consensus size: 27
28971761 AGGAAGCGTC
*
28971771 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
*
28971798 CTGGTGGCTCTGCCACATATT-TCTGTT
1 CTGGTGGCTCTGCCACA-ATTATCTGAT
*
28971825 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
* * *
28971853 CTGGTGACTCTGTCAC-ATTATCTGTT
1 CTGGTGGCTCTGCCACAATTATCTGAT
28971879 CTGG
1 CTGG
28971883 CAGCCATGCT
Statistics
Matches: 75, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
26 8 0.11
27 49 0.65
28 18 0.24
ACGTcount: A:0.15, C:0.24, G:0.23, T:0.38
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:28971877 original size:54 final size:54
Alignment explanation
Indices: 28971771--28971882 Score: 163
Period size: 54 Copynumber: 2.1 Consensus size: 54
28971761 AGGAAGCGTC
* *
28971771 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATTTCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
* * *
28971825 CTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATATATCTGTT
28971879 CTGG
1 CTGG
28971883 CAGCCATGCT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
54 34 0.65
55 18 0.35
ACGTcount: A:0.15, C:0.24, G:0.23, T:0.38
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
Found at i:28975574 original size:27 final size:27
Alignment explanation
Indices: 28975544--28975651 Score: 94
Period size: 27 Copynumber: 4.0 Consensus size: 27
28975534 AGCGTCCTGA
* *
28975544 TGGCTATGCTAAAATTATCTGATCTGG
1 TGGCTCTGCCAAAATTATCTGATCTGG
* *
28975571 TGGCTCTGCCACATATT-TCTGTTCTGG
1 TGGCTCTGCCA-AAATTATCTGATCTGG
**
28975598 TGGCTCTGCCACGATTATCTGTATCTGG
1 TGGCTCTGCCAAAATTATCTG-ATCTGG
* * * *
28975626 TGACTCTGTC-ACATTATCTGTTCTGG
1 TGGCTCTGCCAAAATTATCTGATCTGG
28975652 CAGCCATGCT
Statistics
Matches: 66, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
26 8 0.12
27 41 0.62
28 17 0.26
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.39
Consensus pattern (27 bp):
TGGCTCTGCCAAAATTATCTGATCTGG
Found at i:28989104 original size:11 final size:11
Alignment explanation
Indices: 28989077--28989142 Score: 64
Period size: 11 Copynumber: 5.9 Consensus size: 11
28989067 AATTCTATAA
28989077 TTCA-TTTCAT
1 TTCATTTTCAT
28989087 TTCCATTTTCAT
1 TT-CATTTTCAT
*
28989099 ATCATTCTT-ATT
1 TTCATT-TTCA-T
28989111 TTCATTTTCAT
1 TTCATTTTCAT
*
28989122 TTCAATTTCAT
1 TTCATTTTCAT
*
28989133 TTCATATTCA
1 TTCATTTTCA
28989143 AATCATAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
10 2 0.04
11 28 0.61
12 16 0.35
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.58
Consensus pattern (11 bp):
TTCATTTTCAT
Found at i:28989119 original size:6 final size:6
Alignment explanation
Indices: 28989077--28989134 Score: 52
Period size: 6 Copynumber: 10.2 Consensus size: 6
28989067 AATTCTATAA
* *
28989077 TTCA-T TTCATT TCCATT TTCA-T ATCATT CTT-ATT TTCATT TTCA-T
1 TTCATT TTCATT TTCATT TTCATT TTCATT -TTCATT TTCATT TTCATT
*
28989122 TTCAAT TTCATT T
1 TTCATT TTCATT T
28989135 CATATTCAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
5 15 0.35
6 27 0.63
7 1 0.02
ACGTcount: A:0.21, C:0.19, G:0.00, T:0.60
Consensus pattern (6 bp):
TTCATT
Found at i:28989130 original size:17 final size:17
Alignment explanation
Indices: 28989110--28989143 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
28989100 TCATTCTTAT
28989110 TTTCATTTTCAT-TTCAA
1 TTTCA-TTTCATATTCAA
28989127 TTTCATTTCATATTCAA
1 TTTCATTTCATATTCAA
28989144 ATCATAAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.26, C:0.18, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTCATTTCATATTCAA
Found at i:28989142 original size:6 final size:5
Alignment explanation
Indices: 28989077--28989142 Score: 51
Period size: 5 Copynumber: 11.8 Consensus size: 5
28989067 AATTCTATAA
* *
28989077 TTCAT TTCAT TTCCATT TTCAT ATCAT TCTTATT TTCATT TTCAT TTCAAT
1 TTCAT TTCAT TT-CA-T TTCAT TTCAT T-TCA-T TTCA-T TTCAT TTC-AT
28989128 TTCAT TTCAT ATTCA
1 TTCAT TTCAT -TTCA
28989143 AATCATAAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
5 23 0.45
6 23 0.45
7 5 0.10
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.58
Consensus pattern (5 bp):
TTCAT
Found at i:28990142 original size:73 final size:73
Alignment explanation
Indices: 28990032--28990185 Score: 220
Period size: 72 Copynumber: 2.1 Consensus size: 73
28990022 AAAAATATTG
* * *
28990032 GAGGGGCCTACTTATTTTTTTGGAAGGGCTATTGTATATATACAAAGGGAGAAATTACAAAAATC
1 GAGGGGCCTACTTATTATTTTGGAAGGGCCATAGTATATATACAAAGGG-GAAATTACAAAAATC
28990097 TTAAACCTT
65 TTAAACCTT
* * * *
28990106 GAGGGGCCTACTTA-TATTTTGGGAGGGCCATAGTATATATACAAAGTGGAAATTGCAAAAATTT
1 GAGGGGCCTACTTATTATTTTGGAAGGGCCATAGTATATATACAAAGGGGAAATTACAAAAATCT
28990170 TAAACCTT
66 TAAACCTT
*
28990178 GGGGGGCC
1 GAGGGGCC
28990186 GTGACTCCTG
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
72 29 0.40
73 29 0.40
74 14 0.19
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (73 bp):
GAGGGGCCTACTTATTATTTTGGAAGGGCCATAGTATATATACAAAGGGGAAATTACAAAAATCT
TAAACCTT
Found at i:28991853 original size:34 final size:34
Alignment explanation
Indices: 28991822--28991946 Score: 180
Period size: 34 Copynumber: 3.7 Consensus size: 34
28991812 AATGCAGTCT
* * *
28991822 GGGCCTAAGCCCACTTCGGTTTCAGTAGCAGTTC
1 GGGCCTTAGCCCATTTCAGTTTCAGTAGCAGTTC
*
28991856 GGGCCTTAGCCCATTTCAGTTTTAGTAGCAGTTC
1 GGGCCTTAGCCCATTTCAGTTTCAGTAGCAGTTC
**
28991890 GATCCTTAGCCCATTTCAGTTTCAGTAGCAGTTC
1 GGGCCTTAGCCCATTTCAGTTTCAGTAGCAGTTC
28991924 GGGCCTTAGCCCATTAT-AGTTTC
1 GGGCCTTAGCCCATT-TCAGTTTC
28991947 GGTATTAGAT
Statistics
Matches: 81, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
34 80 0.99
35 1 0.01
ACGTcount: A:0.18, C:0.26, G:0.22, T:0.33
Consensus pattern (34 bp):
GGGCCTTAGCCCATTTCAGTTTCAGTAGCAGTTC
Found at i:28998815 original size:34 final size:34
Alignment explanation
Indices: 28998784--28998878 Score: 120
Period size: 34 Copynumber: 2.8 Consensus size: 34
28998774 AATGCAGTCT
28998784 GGGCCTAAGCCCACTTCAGTTTCAGTAGCAGTTC
1 GGGCCTAAGCCCACTTCAGTTTCAGTAGCAGTTC
* * *
28998818 GGGCCTTAGCCCATTTCAGTTTTAGTAGCAGTTC
1 GGGCCTAAGCCCACTTCAGTTTCAGTAGCAGTTC
* * *
28998852 AGGCCTTAGCCCA-TTAAAGTTTCAGTA
1 GGGCCTAAGCCCACTT-CAGTTTCAGTA
28998879 TTAGATTGCA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 2 0.04
34 52 0.96
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (34 bp):
GGGCCTAAGCCCACTTCAGTTTCAGTAGCAGTTC
Found at i:29008275 original size:43 final size:44
Alignment explanation
Indices: 29008213--29008296 Score: 125
Period size: 44 Copynumber: 1.9 Consensus size: 44
29008203 ATCACGAATA
29008213 TCACAAAAGCCCATACTCTC-AAGGAGCGCACAGAGTGAGATGC
1 TCACAAAAGCCCATACTCTCAAAGGAGCGCACAGAGTGAGATGC
* * * *
29008256 TCACAATAGCTCATGCTCTCAAAGGATCGCACAGAGTGAGA
1 TCACAAAAGCCCATACTCTCAAAGGAGCGCACAGAGTGAGA
29008297 CTTAACTTGG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 17 0.47
44 19 0.53
ACGTcount: A:0.35, C:0.26, G:0.23, T:0.17
Consensus pattern (44 bp):
TCACAAAAGCCCATACTCTCAAAGGAGCGCACAGAGTGAGATGC
Found at i:29009654 original size:17 final size:17
Alignment explanation
Indices: 29009626--29009688 Score: 51
Period size: 17 Copynumber: 3.8 Consensus size: 17
29009616 TGGCCTTGCT
29009626 CATGTGGGCCCACATGCC
1 CATGT-GGCCCACATGCC
* *
29009644 CATGTGGCCCATATTCC
1 CATGTGGCCCACATGCC
*
29009661 CACTTTGG-CCA-A-GCC
1 CA-TGTGGCCCACATGCC
*
29009676 CGTGTGGCCCACA
1 CATGTGGCCCACA
29009689 CGACCACACT
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
14 4 0.11
15 6 0.17
16 2 0.06
17 15 0.42
18 9 0.25
ACGTcount: A:0.17, C:0.38, G:0.24, T:0.21
Consensus pattern (17 bp):
CATGTGGCCCACATGCC
Found at i:29025310 original size:30 final size:30
Alignment explanation
Indices: 29025276--29025333 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
29025266 GTTTTACACG
29025276 TAAACTCAAATAACCCTAATGTCATGACGT
1 TAAACTCAAATAACCCTAATGTCATGACGT
29025306 TAAACTCAAATAACCCTAATGTCATGAC
1 TAAACTCAAATAACCCTAATGTCATGAC
29025334 ATTTATATCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.41, C:0.24, G:0.09, T:0.26
Consensus pattern (30 bp):
TAAACTCAAATAACCCTAATGTCATGACGT
Found at i:29033007 original size:16 final size:18
Alignment explanation
Indices: 29032974--29033007 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
29032964 TCAGGCTGTA
29032974 TCAGAACTAGAGCTTGAG
1 TCAGAACTAGAGCTTGAG
29032992 TCAGAAC-AGA-CTTGAG
1 TCAGAACTAGAGCTTGAG
29033008 CTTCTTGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 3 0.19
18 7 0.44
ACGTcount: A:0.35, C:0.18, G:0.26, T:0.21
Consensus pattern (18 bp):
TCAGAACTAGAGCTTGAG
Found at i:29044716 original size:22 final size:21
Alignment explanation
Indices: 29044674--29044716 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
29044664 GTTACAACAC
*
29044674 TCAAGGTGTATAAGTCTATAA
1 TCAAGGTGTATAACTCTATAA
29044695 TCAAGGATGTATATACTC-ATAA
1 TCAAGG-TGTATA-ACTCTATAA
29044717 AATAAAATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 6 0.32
22 10 0.53
23 3 0.16
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.33
Consensus pattern (21 bp):
TCAAGGTGTATAACTCTATAA
Found at i:29045233 original size:20 final size:20
Alignment explanation
Indices: 29045208--29045249 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
29045198 AGGACCTCAT
*
29045208 TCATTTCGGGAAATCACATA
1 TCATTTCGAGAAATCACATA
*
29045228 TCATTTCGAGAAATCGCATA
1 TCATTTCGAGAAATCACATA
29045248 TC
1 TC
29045250 CATCGATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.31
Consensus pattern (20 bp):
TCATTTCGAGAAATCACATA
Found at i:29049914 original size:42 final size:42
Alignment explanation
Indices: 29049867--29050104 Score: 231
Period size: 42 Copynumber: 5.7 Consensus size: 42
29049857 ACGATTCAGA
29049867 TATATATATGGCACTTAGTGTGC-A-ATTCGAGATAGCTTCGGC
1 TATATAT-TGGCACTTAGTGTGCGAGATTCGA-ATAGCTTCGGC
**
29049909 TATATATT-GCACTTAGTGTGC--GATTCGAAATAGCTTTAGC
1 TATATATTGGCACTTAGTGTGCGAGATTCG-AATAGCTTCGGC
* *
29049949 TATATA-TGGCACTTAGTGTGCGAGA-CCAAGATAGCTTCGGC
1 TATATATTGGCACTTAGTGTGCGAGATTCGA-ATAGCTTCGGC
* * * * **
29049990 TATGTA-AGGAACTTACTGTGCGAGATTATAATAGCTTCGGC
1 TATATATTGGCACTTAGTGTGCGAGATTCGAATAGCTTCGGC
* * ** *
29050031 TATGTATTGGCACTTACTGTGCGAGATTATAATAGCTTCAGC
1 TATATATTGGCACTTAGTGTGCGAGATTCGAATAGCTTCGGC
*
29050073 TATGTATTGGCACTTAGTGTGCGAGATATCGA
1 TATATATTGGCACTTAGTGTGCGAGAT-TCGA
29050105 GTATTCGACA
Statistics
Matches: 168, Mismatches: 19, Indels: 17
0.82 0.09 0.08
Matches are distributed among these distances:
39 1 0.01
40 47 0.28
41 50 0.30
42 68 0.40
43 2 0.01
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (42 bp):
TATATATTGGCACTTAGTGTGCGAGATTCGAATAGCTTCGGC
Found at i:29050075 original size:83 final size:83
Alignment explanation
Indices: 29049937--29050099 Score: 204
Period size: 83 Copynumber: 2.0 Consensus size: 83
29049927 TGCGATTCGA
* * *
29049937 AATAGCTTTAGCTATATATGGCACTTAGTGTGCGAGACCAAGATAGCTTCGGCTATGTA-AGGAA
1 AATAGCTTCAGCTATATATGGCACTTACTGTGCGAGACCAAGATAGCTTCAGCTATGTATAGGAA
29050001 CTTACTGTGCGAGATTAT
66 CTTACTGTGCGAGATTAT
* * ** *
29050019 AATAGCTTCGGCTATGTATTGGCACTTACTGTGCGAGATTATA-ATAGCTTCAGCTATGTATTGG
1 AATAGCTTCAGCTATATA-TGGCACTTACTGTGCGAGACCA-AGATAGCTTCAGCTATGTATAGG
* *
29050083 CACTTAGTGTGCGAGAT
64 AACTTACTGTGCGAGAT
29050100 ATCGAGTATT
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
82 15 0.22
83 35 0.51
84 18 0.26
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.33
Consensus pattern (83 bp):
AATAGCTTCAGCTATATATGGCACTTACTGTGCGAGACCAAGATAGCTTCAGCTATGTATAGGAA
CTTACTGTGCGAGATTAT
Found at i:29057272 original size:17 final size:17
Alignment explanation
Indices: 29057250--29057291 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
29057240 AATTCGTACA
29057250 AGCTTACTAAGCTTTAT
1 AGCTTACTAAGCTTTAT
29057267 AGCTTACTAAGCTTTAT
1 AGCTTACTAAGCTTTAT
29057284 AGCTTACT
1 AGCTTACT
29057292 TTGTTTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (17 bp):
AGCTTACTAAGCTTTAT
Found at i:29065326 original size:42 final size:42
Alignment explanation
Indices: 29065264--29065359 Score: 147
Period size: 42 Copynumber: 2.3 Consensus size: 42
29065254 GAGTTACACT
** *
29065264 GCCTGGACACACAGTTGTGTCCTTGACCGTGTGACTCACATG
1 GCCTGGACACACAGCCGTGTCCTTAACCGTGTGACTCACATG
*
29065306 GCCTGGGCACACAGCCGTGTCCTTAACCGTGTGACTCACATG
1 GCCTGGACACACAGCCGTGTCCTTAACCGTGTGACTCACATG
*
29065348 GCCTGGCCACAC
1 GCCTGGACACAC
29065360 GCCCATGTGC
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.19, C:0.33, G:0.26, T:0.22
Consensus pattern (42 bp):
GCCTGGACACACAGCCGTGTCCTTAACCGTGTGACTCACATG
Found at i:29065378 original size:42 final size:42
Alignment explanation
Indices: 29065281--29065379 Score: 137
Period size: 42 Copynumber: 2.4 Consensus size: 42
29065271 CACACAGTTG
* *
29065281 TGTCCTTGACCGTGTGACTCACATGGCCTGGGCACACAGCCG
1 TGTCCTTGACCGTGTGACTCACATGGCCTGGCCACACAGCCA
*
29065323 TGTCCTTAACCGTGTGACTCACATGGCCTGGCCACAC-GCCCA
1 TGTCCTTGACCGTGTGACTCACATGGCCTGGCCACACAG-CCA
* *
29065365 TGTGCTTGCCCGTGT
1 TGTCCTTGACCGTGT
29065380 AGTTTTAAGT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
41 1 0.02
42 49 0.98
ACGTcount: A:0.15, C:0.34, G:0.26, T:0.24
Consensus pattern (42 bp):
TGTCCTTGACCGTGTGACTCACATGGCCTGGCCACACAGCCA
Found at i:29071922 original size:31 final size:31
Alignment explanation
Indices: 29071884--29071945 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
29071874 CACCGAAAAC
*
29071884 TACGAATTCTTTACCCGACTCAATCTGAACT
1 TACGAATTCTTTACCCGACTCAAGCTGAACT
29071915 TACGAATTCTTTACCCGACTCAAGCTGAACT
1 TACGAATTCTTTACCCGACTCAAGCTGAACT
29071946 AACACTGGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.29, C:0.29, G:0.11, T:0.31
Consensus pattern (31 bp):
TACGAATTCTTTACCCGACTCAAGCTGAACT
Found at i:29073726 original size:13 final size:13
Alignment explanation
Indices: 29073708--29073740 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
29073698 TTGTCTTTCA
29073708 CACTACTAACACT
1 CACTACTAACACT
29073721 CACTACTAACACT
1 CACTACTAACACT
*
29073734 CGCTACT
1 CACTACT
29073741 GATGTAGCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.33, C:0.39, G:0.03, T:0.24
Consensus pattern (13 bp):
CACTACTAACACT
Found at i:29076523 original size:16 final size:16
Alignment explanation
Indices: 29076504--29076548 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
29076494 CGGCAAATCC
29076504 CGAAAAGCCGAAATGT
1 CGAAAAGCCGAAATGT
**
29076520 CGAAAAGCTAAAATGT
1 CGAAAAGCCGAAATGT
29076536 CGAAAAGCCGAAA
1 CGAAAAGCCGAAA
29076549 GTTTGGCTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.49, C:0.18, G:0.22, T:0.11
Consensus pattern (16 bp):
CGAAAAGCCGAAATGT
Found at i:29077511 original size:11 final size:11
Alignment explanation
Indices: 29077495--29077520 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
29077485 ATTGCACGTA
29077495 TGATATTATTG
1 TGATATTATTG
29077506 TGATATTATTG
1 TGATATTATTG
29077517 TGAT
1 TGAT
29077521 GTGGGCTTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.54
Consensus pattern (11 bp):
TGATATTATTG
Found at i:29080056 original size:39 final size:39
Alignment explanation
Indices: 29080013--29080148 Score: 110
Period size: 39 Copynumber: 3.5 Consensus size: 39
29080003 CCGGACATAT
* * * *
29080013 TTCCAGCGCGTAGCCTGTAGACCTTAAGTCCGGTTATAA
1 TTCCAGCACATAGCCTGCAGACCTTAAGTCCGGGTATAA
* * *
29080052 TTCCAGCACATAGCCTGCGGCCCTTAAGTCTGGGTATAA
1 TTCCAGCACATAGCCTGCAGACCTTAAGTCCGGGTATAA
* * * * *** * *
29080091 TTCTAACATATAGCCTGCGGGTTTTTAAGCCCGGATATAA
1 TTCCAGCACATAGCCTGC-AGACCTTAAGTCCGGGTATAA
*
29080131 TTCCAGCATATAGCCTGC
1 TTCCAGCACATAGCCTGC
29080149 GGGTCTTTAA
Statistics
Matches: 78, Mismatches: 18, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
39 47 0.60
40 31 0.40
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (39 bp):
TTCCAGCACATAGCCTGCAGACCTTAAGTCCGGGTATAA
Found at i:29080130 original size:40 final size:40
Alignment explanation
Indices: 29080036--29080167 Score: 140
Period size: 40 Copynumber: 3.3 Consensus size: 40
29080026 CCTGTAGACC
* * * * * *
29080036 TTAAGTCCGGTTATAATTCCAGCACATAGCCTGC-GGCCC
1 TTAAGCCCGGATATAATTCCAACATATAGCCTGCGGGTCT
* * * * *
29080075 TTAAGTCTGGGTATAATTCTAACATATAGCCTGCGGGTTT
1 TTAAGCCCGGATATAATTCCAACATATAGCCTGCGGGTCT
*
29080115 TTAAGCCCGGATATAATTCCAGCATATAGCCTGCGGGTCT
1 TTAAGCCCGGATATAATTCCAACATATAGCCTGCGGGTCT
*
29080155 TTAAGCCCTGATA
1 TTAAGCCCGGATA
29080168 CACATCAAAT
Statistics
Matches: 77, Mismatches: 15, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
39 29 0.38
40 48 0.62
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.30
Consensus pattern (40 bp):
TTAAGCCCGGATATAATTCCAACATATAGCCTGCGGGTCT
Found at i:29090208 original size:22 final size:21
Alignment explanation
Indices: 29090183--29090223 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
29090173 ACTGAAATGT
*
29090183 CACACGGGCGTGTTGCCCCTCC
1 CACACGAGCGTG-TGCCCCTCC
*
29090205 CACACTAGCGTGTGCCCCT
1 CACACGAGCGTGTGCCCCT
29090224 TTGTTAAGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.12, C:0.44, G:0.24, T:0.20
Consensus pattern (21 bp):
CACACGAGCGTGTGCCCCTCC
Found at i:29102190 original size:55 final size:54
Alignment explanation
Indices: 29102035--29102225 Score: 222
Period size: 53 Copynumber: 3.5 Consensus size: 54
29102025 TTCCTTTTTA
* * *
29102035 AACTTACCATTGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-G
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* * * * *
29102088 AACTCACCATTGCCATGCCTTGGCATGGTCTTACATGGGATCTTTGCCTTATAG
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
** * * * * *
29102142 TAGTTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTGTAG
1 -AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
*
29102197 AACTTACCAATGCCATGCCTTGGCATGGT
1 AACTTACCAATGCCATGCCTTGACATGGT
29102226 ATTATCCTTA
Statistics
Matches: 113, Mismatches: 23, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
53 46 0.41
54 25 0.22
55 42 0.37
ACGTcount: A:0.20, C:0.24, G:0.19, T:0.36
Consensus pattern (54 bp):
AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
Found at i:29122734 original size:46 final size:45
Alignment explanation
Indices: 29122684--29122859 Score: 212
Period size: 46 Copynumber: 3.8 Consensus size: 45
29122674 TGTTTGGGCA
29122684 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
29122730 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
29122777 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
29122823 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
29122860 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 69 0.62
47 32 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:29122839 original size:93 final size:93
Alignment explanation
Indices: 29122680--29122851 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
29122670 AGGATGTTTG
* *
29122680 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
29122745 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* *
29122773 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
29122838 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
29122852 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:29125803 original size:15 final size:15
Alignment explanation
Indices: 29125783--29125851 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
29125773 GTATCTTGGG
29125783 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
29125798 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
29125813 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
29125828 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
29125843 TTTCTTTAT
1 TTTCTTTAT
29125852 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:29125852 original size:30 final size:30
Alignment explanation
Indices: 29125774--29125861 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
29125764 CATAGTATCG
* * * *
29125774 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
29125804 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
29125834 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
29125862 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:29133303 original size:25 final size:26
Alignment explanation
Indices: 29133249--29133303 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
29133239 TTTCATATTT
*
29133249 TATAATAAGGTTAAATATGTAATTAA
1 TATAATAACGTTAAATATGTAATTAA
*
29133275 -ATAAT-ACGTTAATATATGTTA-TAA
1 TATAATAACGTTAA-ATATGTAATTAA
29133299 TATAA
1 TATAA
29133304 CATAAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
24 9 0.36
25 16 0.64
ACGTcount: A:0.49, C:0.02, G:0.09, T:0.40
Consensus pattern (26 bp):
TATAATAACGTTAAATATGTAATTAA
Found at i:29137008 original size:85 final size:85
Alignment explanation
Indices: 29136891--29137062 Score: 344
Period size: 85 Copynumber: 2.0 Consensus size: 85
29136881 TTTTTCTTTG
29136891 ACAAAAATTTGGAATGAAAAGCAAGAGATTAGATTTATTAATATTAATAAATTGAAAATTATTTT
1 ACAAAAATTTGGAATGAAAAGCAAGAGATTAGATTTATTAATATTAATAAATTGAAAATTATTTT
29136956 TCTTGATTGAAAAAAATCTC
66 TCTTGATTGAAAAAAATCTC
29136976 ACAAAAATTTGGAATGAAAAGCAAGAGATTAGATTTATTAATATTAATAAATTGAAAATTATTTT
1 ACAAAAATTTGGAATGAAAAGCAAGAGATTAGATTTATTAATATTAATAAATTGAAAATTATTTT
29137041 TCTTGATTGAAAAAAATCTC
66 TCTTGATTGAAAAAAATCTC
29137061 AC
1 AC
29137063 TTTTTTTTAG
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 87 1.00
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (85 bp):
ACAAAAATTTGGAATGAAAAGCAAGAGATTAGATTTATTAATATTAATAAATTGAAAATTATTTT
TCTTGATTGAAAAAAATCTC
Found at i:29139285 original size:79 final size:81
Alignment explanation
Indices: 29139183--29139366 Score: 213
Period size: 79 Copynumber: 2.3 Consensus size: 81
29139173 GCTCCTCGTT
* *
29139183 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCACAAATGCCTTCGGGA-CTTAACC
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCACAAATGCCTTC-GGATCTTAACC
*
29139245 CGGAT-TTAGTAAC-TCGCA
63 CGGATATT-GTAACTTAGCA
* **
29139263 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACGAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAACCCGG
*
29139327 ATATTGTCACTTAGCA
66 ATATTGTAACTTAGCA
29139343 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
29139367 CATCATCCAA
Statistics
Matches: 91, Mismatches: 7, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
78 14 0.15
79 55 0.60
80 22 0.24
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATTGTAACTTAGCA
Found at i:29139300 original size:39 final size:41
Alignment explanation
Indices: 29139183--29139366 Score: 190
Period size: 40 Copynumber: 4.6 Consensus size: 41
29139173 GCTCCTCGTT
* *
29139183 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAATCTCGCA
* *
29139223 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAA-CTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAATCTCGCA
29139263 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGT-ATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAATCTCGCA
* * * *
29139302 CGAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGTAATC-TCGCA
29139343 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
29139367 CATCATCCAA
Statistics
Matches: 127, Mismatches: 8, Indels: 19
0.82 0.05 0.12
Matches are distributed among these distances:
38 3 0.02
39 47 0.37
40 66 0.52
41 11 0.09
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (41 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAATCTCGCA
Found at i:29139621 original size:32 final size:32
Alignment explanation
Indices: 29139584--29139647 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
29139574 TGTCGAACGA
29139584 TTCCGATAGCTATTCGACCACTTTTTCCTTCC
1 TTCCGATAGCTATTCGACCACTTTTTCCTTCC
29139616 TTCCGATAGCTATTCGACCACTTTTTCCTTCC
1 TTCCGATAGCTATTCGACCACTTTTTCCTTCC
29139648 CCTTATCGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.16, C:0.34, G:0.09, T:0.41
Consensus pattern (32 bp):
TTCCGATAGCTATTCGACCACTTTTTCCTTCC
Found at i:29141503 original size:232 final size:232
Alignment explanation
Indices: 29141097--29141560 Score: 838
Period size: 232 Copynumber: 2.0 Consensus size: 232
29141087 CCCAAGTAGG
*
29141097 TTCCTCGATCCCGTGTTTGAGCCATAACACCTTAACTAACGGAACCCTTTTGTTTCGCAACTCTT
1 TTCCTCGATCCCGTGTTTGAGCCATAACACCTTAACTAACGGAACCCTTTTGTTTCGCAACTCCT
* * *
29141162 TCACTTCACGAGCTAGGACACGCATCGGTTCTTTTTCATAACTCATATCGGCTTGAATTTTAACC
66 TCACTTCACGAGCTAGGACACGCATCGGTTCTTCTTCATAACTCATATCGACTTGAATTTCAACC
29141227 TCTGATGGGCTAATTATATGCGATGGATCAGATCGATAGCGTCGAAGCATCGAAACATGAAAGAC
131 TCTGATGGGCTAATTATATGCGATGGATCAGATCGATAGCGTCGAAGCATCGAAACATGAAAGAC
29141292 GTCGTGAATCTTTTCAAGATCAGGGGGCAAAATCAAT
196 GTCGTGAATCTTTTCAAGATCAGGGGGCAAAATCAAT
* * *
29141329 TTCCTCGATCCCGTGTTTGAGCCATAACACCTTTACTAGCGGAACTCTTTTGTTTCGCAACTCCT
1 TTCCTCGATCCCGTGTTTGAGCCATAACACCTTAACTAACGGAACCCTTTTGTTTCGCAACTCCT
* * *
29141394 TCACTTCACGAGCTAGGATACGCATCGGTTCTTCTTCATAGCTCATGTCGACTTGAATTTCAACC
66 TCACTTCACGAGCTAGGACACGCATCGGTTCTTCTTCATAACTCATATCGACTTGAATTTCAACC
29141459 TCTGATGGGCTAATTATATGCGATGGATCAGATCGATAGCGTCGAAGCATCGAAACATGAAAGAC
131 TCTGATGGGCTAATTATATGCGATGGATCAGATCGATAGCGTCGAAGCATCGAAACATGAAAGAC
29141524 GTCGTGAATCTTTTCAAGATCAGGGGGCAAAATCAAT
196 GTCGTGAATCTTTTCAAGATCAGGGGGCAAAATCAAT
29141561 CTATACGCAA
Statistics
Matches: 222, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
232 222 1.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (232 bp):
TTCCTCGATCCCGTGTTTGAGCCATAACACCTTAACTAACGGAACCCTTTTGTTTCGCAACTCCT
TCACTTCACGAGCTAGGACACGCATCGGTTCTTCTTCATAACTCATATCGACTTGAATTTCAACC
TCTGATGGGCTAATTATATGCGATGGATCAGATCGATAGCGTCGAAGCATCGAAACATGAAAGAC
GTCGTGAATCTTTTCAAGATCAGGGGGCAAAATCAAT
Found at i:29143092 original size:40 final size:39
Alignment explanation
Indices: 29142994--29143216 Score: 207
Period size: 40 Copynumber: 5.6 Consensus size: 39
29142984 TCCTCGTTCA
* * * *
29142994 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
29143033 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
29143072 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGAAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
29143112 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
29143152 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
29143193 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
29143217 CAGCATTCAA
Statistics
Matches: 155, Mismatches: 23, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
39 40 0.26
40 103 0.66
41 12 0.08
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:29143225 original size:41 final size:41
Alignment explanation
Indices: 29143148--29143225 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
29143138 TTTGTATCTC
* * *
29143148 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
29143189 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
29143226 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:29145214 original size:48 final size:48
Alignment explanation
Indices: 29145143--29145364 Score: 408
Period size: 48 Copynumber: 4.6 Consensus size: 48
29145133 CAAGATAAAT
* *
29145143 ATATATATGTGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* *
29145191 ATATGTATATGTAGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
29145239 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
29145287 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
29145335 ATATGTATATGTGGTAAAGCCGAATGGCTA
1 ATATGTATATGTGGTAAAGCCGAATGGCTA
29145365 NNNNNNNNNN
Statistics
Matches: 168, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
48 168 1.00
ACGTcount: A:0.35, C:0.07, G:0.27, T:0.31
Consensus pattern (48 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
Found at i:29149334 original size:53 final size:54
Alignment explanation
Indices: 29149206--29149336 Score: 138
Period size: 53 Copynumber: 2.4 Consensus size: 54
29149196 GGTAATTATG
* **
29149206 TAAGACCATGTCAAGACATGGCATTGATGAGTTAAAATAAAGAAAAGATCCCATG
1 TAAGACCATGTCAAGACATGGCATTGATGAGTT-AAATAAAGAAAAGATACCACA
* * * * * * * * *
29149261 TAAGACCGTGCCAAGGCATGGTATTGGTGAGTT-CATAAGGCAAGGATACCACA
1 TAAGACCATGTCAAGACATGGCATTGATGAGTTAAATAAAGAAAAGATACCACA
29149314 TAAGACCATGTCAAGACATGGCA
1 TAAGACCATGTCAAGACATGGCA
29149337 ATGGTAGGTT
Statistics
Matches: 60, Mismatches: 16, Indels: 2
0.77 0.21 0.03
Matches are distributed among these distances:
53 32 0.53
55 28 0.47
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.21
Consensus pattern (54 bp):
TAAGACCATGTCAAGACATGGCATTGATGAGTTAAATAAAGAAAAGATACCACA
Found at i:29161041 original size:14 final size:13
Alignment explanation
Indices: 29161001--29161041 Score: 55
Period size: 14 Copynumber: 3.0 Consensus size: 13
29160991 GTTTGTTTCA
*
29161001 CTGAAAATGACTTC
1 CTGAAAATGA-TTT
29161015 CTGAAAATGATTT
1 CTGAAAATGATTT
29161028 CTGGAAAATGATTT
1 CT-GAAAATGATTT
29161042 ACTTTTTTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 4 0.16
14 21 0.84
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (13 bp):
CTGAAAATGATTT
Found at i:29165317 original size:28 final size:28
Alignment explanation
Indices: 29165285--29165343 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
29165275 CGTAATATAA
29165285 CATAGTTATTACGTTTAGTTGCAACTAC
1 CATAGTTATTACGTTTAGTTGCAACTAC
*
29165313 CATAGTTATTATGTTTAGTTGCAACTAC
1 CATAGTTATTACGTTTAGTTGCAACTAC
29165341 CAT
1 CAT
29165344 GTTTCATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.41
Consensus pattern (28 bp):
CATAGTTATTACGTTTAGTTGCAACTAC
Found at i:29173239 original size:21 final size:20
Alignment explanation
Indices: 29173205--29173245 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
29173195 GTCAAGAAGG
29173205 CCACACAGACGTGTAGCCCTT
1 CCACACAGACGTGT-GCCCTT
**
29173226 CCACACAGGTGTGTGCCCTT
1 CCACACAGACGTGTGCCCTT
29173246 ATTTCAAGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.20, C:0.37, G:0.22, T:0.22
Consensus pattern (20 bp):
CCACACAGACGTGTGCCCTT
Found at i:29178360 original size:30 final size:30
Alignment explanation
Indices: 29178326--29178382 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
29178316 TAGGCACTTC
*
29178326 CACACGGGTAAACCACACACCCATGTGAGG
1 CACACGGGCAAACCACACACCCATGTGAGG
* * *
29178356 CACACGGGCAGACCACACGCCCGTGTG
1 CACACGGGCAAACCACACACCCATGTG
29178383 TCATGGCCGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.28, C:0.37, G:0.26, T:0.09
Consensus pattern (30 bp):
CACACGGGCAAACCACACACCCATGTGAGG
Found at i:29181545 original size:43 final size:43
Alignment explanation
Indices: 29181479--29181590 Score: 147
Period size: 43 Copynumber: 2.6 Consensus size: 43
29181469 AGGGGTGTTA
** * *
29181479 CAGACATGGTCTTACACAAAATCA-TATAACGATGCCAATGTCC
1 CAGACATGGTCTTACACTTAATCACAAT-ACAATGCCAATGTCC
*
29181522 CAGACATGGTCTTACACTTAATCACAATACAATGTCAATGTCC
1 CAGACATGGTCTTACACTTAATCACAATACAATGCCAATGTCC
29181565 CAGACATGGTCTTACA-TGTAATCACA
1 CAGACATGGTCTTACACT-TAATCACA
29181591 TCTCGACAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
42 1 0.02
43 59 0.95
44 2 0.03
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.26
Consensus pattern (43 bp):
CAGACATGGTCTTACACTTAATCACAATACAATGCCAATGTCC
Found at i:29188009 original size:42 final size:43
Alignment explanation
Indices: 29187953--29188042 Score: 164
Period size: 43 Copynumber: 2.1 Consensus size: 43
29187943 TGTTCTTCTC
*
29187953 TCTCCTACCGAATTTTTA-TTTTTTTCTTTCGAACGTTTCCTT
1 TCTCCTACCGAATTTTTATTTTTTTTCTTTCAAACGTTTCCTT
29187995 TCTCCTACCGAATTTTTATTTTTTTTCTTTCAAACGTTTCCTT
1 TCTCCTACCGAATTTTTATTTTTTTTCTTTCAAACGTTTCCTT
29188038 TCTCC
1 TCTCC
29188043 CTTTTTCTTT
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
42 18 0.39
43 28 0.61
ACGTcount: A:0.14, C:0.26, G:0.06, T:0.54
Consensus pattern (43 bp):
TCTCCTACCGAATTTTTATTTTTTTTCTTTCAAACGTTTCCTT
Found at i:29198842 original size:41 final size:41
Alignment explanation
Indices: 29198797--29198913 Score: 107
Period size: 41 Copynumber: 2.9 Consensus size: 41
29198787 GTCAAGCTCG
* *
29198797 AAGCCTAATATAACACA-TTGACACAAAGCCTATTAGGCACA
1 AAGCCTAACATAACACACTTG-CACAAAGCCTACTAGGCACA
* * * *
29198838 AAGCCTGACATAATACACTTGCACGAAGCCTACTAGGCATA
1 AAGCCTAACATAACACACTTGCACAAAGCCTACTAGGCACA
* * * *
29198879 GAGCCCAA-ATATCAC-C-GGCACAAAGCCTACTAGGC
1 AAGCCTAACATAACACACTTGCACAAAGCCTACTAGGC
29198914 TATAACCCTG
Statistics
Matches: 62, Mismatches: 13, Indels: 5
0.77 0.16 0.06
Matches are distributed among these distances:
38 17 0.27
39 1 0.02
40 5 0.08
41 36 0.58
42 3 0.05
ACGTcount: A:0.38, C:0.28, G:0.16, T:0.17
Consensus pattern (41 bp):
AAGCCTAACATAACACACTTGCACAAAGCCTACTAGGCACA
Found at i:29203251 original size:29 final size:28
Alignment explanation
Indices: 29203195--29203308 Score: 122
Period size: 29 Copynumber: 4.0 Consensus size: 28
29203185 GTGAGCATGA
* * *
29203195 ATATGAATGTGACTGGTCCTAATGGGCC
1 ATATAAATGTGATTGGGCCTAATGGGCC
29203223 ATATAAATGTGATTTGGGCCTAATGGGCC
1 ATATAAATGTGA-TTGGGCCTAATGGGCC
* *
29203252 ATATACAGGTGATTTGGGCCTAATGGGCC
1 ATATAAATGTGA-TTGGGCCTAATGGGCC
* * * *
29203281 A-ATGAATATGATTGGGCTTAATGAGCC
1 ATATAAATGTGATTGGGCCTAATGGGCC
29203308 A
1 A
29203309 GATACAGGTA
Statistics
Matches: 74, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
27 15 0.20
28 17 0.23
29 42 0.57
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (28 bp):
ATATAAATGTGATTGGGCCTAATGGGCC
Found at i:29212294 original size:37 final size:37
Alignment explanation
Indices: 29212121--29212658 Score: 666
Period size: 37 Copynumber: 14.4 Consensus size: 37
29212111 ATAGGTATAG
* * * * *
29212121 AGCCCGAATATCACCGGCGCAAAGCCTACTAGACACAG
1 AGCCC-AAAATCACCGGCACAAAGCCTGCTAGGCACAT
* ** * * *
29212159 AGCCCAAATATCTCTAGCACAGAGCCTGCTAGGCATAG
1 AGCCCAAA-ATCACCGGCACAAAGCCTGCTAGGCACAT
* *** **
29212197 AGCCCGAATATCACTAACACAAAGCCTGCTAGGCACGG
1 AGCCC-AAAATCACCGGCACAAAGCCTGCTAGGCACAT
** *
29212235 AGCTTGAATATCACCGGCACAAAGCCTGCTAGGCACAT
1 AGC-CCAAAATCACCGGCACAAAGCCTGCTAGGCACAT
* * *
29212273 GGCCCAAAATCACCAGCACAAAGCCTGCTAAGCACAT
1 AGCCCAAAATCACCGGCACAAAGCCTGCTAGGCACAT
* *
29212310 AGCCCAAATAACACCGGCACAAAGCCTGCCAGGCACAT
1 AGCCCAAA-ATCACCGGCACAAAGCCTGCTAGGCACAT
29212348 AGCCCAAAATCACCGGCACAAAGCCTGCTAGGCACAT
1 AGCCCAAAATCACCGGCACAAAGCCTGCTAGGCACAT
* * *
29212385 GGCCCAAAATCACCAGCACAAAGCCTGCTAAGCACAT
1 AGCCCAAAATCACCGGCACAAAGCCTGCTAGGCACAT
29212422 AGCCCGAATAA-CACCGGCACAAAGCCTGCTAGGCACAT
1 AGCCC-AA-AATCACCGGCACAAAGCCTGCTAGGCACAT
*
29212460 AGCCCAAAATCACCGGCACAAAGCCTGCTACGCACAT
1 AGCCCAAAATCACCGGCACAAAGCCTGCTAGGCACAT
* ** *
29212497 GGCCCAAAATCACTAGCACAAAGCCTGCTAAGCACAT
1 AGCCCAAAATCACCGGCACAAAGCCTGCTAGGCACAT
*
29212534 AGCCCGAATAA-CACCGGCACAAAGCCTACTAGGCACAT
1 AGCCC-AA-AATCACCGGCACAAAGCCTGCTAGGCACAT
29212572 AGCCCAAAATCACCGGCACAAAGCCTGCTAGGCACAT
1 AGCCCAAAATCACCGGCACAAAGCCTGCTAGGCACAT
29212609 AGCCCAAAATCACCGGCACAAAGCCTGCTAGGCACAT
1 AGCCCAAAATCACCGGCACAAAGCCTGCTAGGCACAT
*
29212646 AGCCCGAAATCAC
1 AGCCCAAAATCAC
29212659 TGCATTTCTA
Statistics
Matches: 437, Mismatches: 53, Indels: 21
0.86 0.10 0.04
Matches are distributed among these distances:
36 4 0.01
37 245 0.56
38 182 0.42
39 6 0.01
ACGTcount: A:0.35, C:0.34, G:0.19, T:0.12
Consensus pattern (37 bp):
AGCCCAAAATCACCGGCACAAAGCCTGCTAGGCACAT
Found at i:29212325 original size:75 final size:75
Alignment explanation
Indices: 29212121--29212658 Score: 679
Period size: 75 Copynumber: 7.2 Consensus size: 75
29212111 ATAGGTATAG
* * * * * * ** *
29212121 AGCCCGAATATCACCGGCGCAAAGCCTACTAGACACAGAGCCCAAATATCTCTAGCACAGAGCCT
1 AGCCC-AAAATCACCGGCACAAAGCCTGCTAGGCACATAGCCCAAATATCACCGGCACAAAGCCT
* *
29212186 GCTAGGCATAG
65 GCTAGGCACAT
* *** ** ***
29212197 AGCCCGAATATCACTAACACAAAGCCTGCTAGGCACGGAGCTTGAATATCACCGGCACAAAGCCT
1 AGCCC-AAAATCACCGGCACAAAGCCTGCTAGGCACATAGCCCAAATATCACCGGCACAAAGCCT
29212262 GCTAGGCACAT
65 GCTAGGCACAT
* * * *
29212273 GGCCCAAAATCACCAGCACAAAGCCTGCTAAGCACATAGCCCAAATAACACCGGCACAAAGCCTG
1 AGCCCAAAATCACCGGCACAAAGCCTGCTAGGCACATAGCCCAAATATCACCGGCACAAAGCCTG
*
29212338 CCAGGCACAT
66 CTAGGCACAT
* *
29212348 AGCCCAAAATCACCGGCACAAAGCCTGCTAGGCACATGGCCCAAA-ATCACCAGCACAAAGCCTG
1 AGCCCAAAATCACCGGCACAAAGCCTGCTAGGCACATAGCCCAAATATCACCGGCACAAAGCCTG
*
29212412 CTAAGCACAT
66 CTAGGCACAT
29212422 AGCCCGAATAA-CACCGGCACAAAGCCTGCTAGGCACATAGCCCAAA-ATCACCGGCACAAAGCC
1 AGCCC-AA-AATCACCGGCACAAAGCCTGCTAGGCACATAGCCCAAATATCACCGGCACAAAGCC
*
29212485 TGCTACGCACAT
64 TGCTAGGCACAT
* ** * * * *
29212497 GGCCCAAAATCACTAGCACAAAGCCTGCTAAGCACATAGCCCGAATAACACCGGCACAAAGCCTA
1 AGCCCAAAATCACCGGCACAAAGCCTGCTAGGCACATAGCCCAAATATCACCGGCACAAAGCCTG
29212562 CTAGGCACAT
66 CTAGGCACAT
29212572 AGCCCAAAATCACCGGCACAAAGCCTGCTAGGCACATAGCCCAAA-ATCACCGGCACAAAGCCTG
1 AGCCCAAAATCACCGGCACAAAGCCTGCTAGGCACATAGCCCAAATATCACCGGCACAAAGCCTG
29212636 CTAGGCACAT
66 CTAGGCACAT
*
29212646 AGCCCGAAATCAC
1 AGCCCAAAATCAC
29212659 TGCATTTCTA
Statistics
Matches: 403, Mismatches: 55, Indels: 10
0.86 0.12 0.02
Matches are distributed among these distances:
73 2 0.00
74 102 0.25
75 233 0.58
76 66 0.16
ACGTcount: A:0.35, C:0.34, G:0.19, T:0.12
Consensus pattern (75 bp):
AGCCCAAAATCACCGGCACAAAGCCTGCTAGGCACATAGCCCAAATATCACCGGCACAAAGCCTG
CTAGGCACAT
Found at i:29212393 original size:112 final size:112
Alignment explanation
Indices: 29212121--29212653 Score: 780
Period size: 112 Copynumber: 4.7 Consensus size: 112
29212111 ATAGGTATAG
* * * * * * *
29212121 AGCCCGAATATCACCGGCGCAAAGCCTACTAGACACA-GAGCCCAAATATCTCTAGCACAGAGCC
1 AGCCC-AAAATCACCGGCACAAAGCCTGCTAGGCACATG-GCCCAAA-ATCACCAGCACAAAGCC
* * * * *** **
29212185 TGCTAGGCATAGAGCCCGAATATCACTAACACAAAGCCTGCTAGGCACGG
63 TGCTAAGCACATAGCCCGAATAACACCGGCACAAAGCCTGCTAGGCACAT
** *
29212235 AGCTTGAATATCACCGGCACAAAGCCTGCTAGGCACATGGCCCAAAATCACCAGCACAAAGCCTG
1 AGC-CCAAAATCACCGGCACAAAGCCTGCTAGGCACATGGCCCAAAATCACCAGCACAAAGCCTG
* *
29212300 CTAAGCACATAGCCCAAATAACACCGGCACAAAGCCTGCCAGGCACAT
65 CTAAGCACATAGCCCGAATAACACCGGCACAAAGCCTGCTAGGCACAT
29212348 AGCCCAAAATCACCGGCACAAAGCCTGCTAGGCACATGGCCCAAAATCACCAGCACAAAGCCTGC
1 AGCCCAAAATCACCGGCACAAAGCCTGCTAGGCACATGGCCCAAAATCACCAGCACAAAGCCTGC
29212413 TAAGCACATAGCCCGAATAACACCGGCACAAAGCCTGCTAGGCACAT
66 TAAGCACATAGCCCGAATAACACCGGCACAAAGCCTGCTAGGCACAT
* *
29212460 AGCCCAAAATCACCGGCACAAAGCCTGCTACGCACATGGCCCAAAATCACTAGCACAAAGCCTGC
1 AGCCCAAAATCACCGGCACAAAGCCTGCTAGGCACATGGCCCAAAATCACCAGCACAAAGCCTGC
*
29212525 TAAGCACATAGCCCGAATAACACCGGCACAAAGCCTACTAGGCACAT
66 TAAGCACATAGCCCGAATAACACCGGCACAAAGCCTGCTAGGCACAT
* *
29212572 AGCCCAAAATCACCGGCACAAAGCCTGCTAGGCACATAGCCCAAAATCACCGGCACAAAGCCTGC
1 AGCCCAAAATCACCGGCACAAAGCCTGCTAGGCACATGGCCCAAAATCACCAGCACAAAGCCTGC
*
29212637 TAGGCACATAGCCCGAA
66 TAAGCACATAGCCCGAA
29212654 ATCACTGCAT
Statistics
Matches: 385, Mismatches: 32, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
112 290 0.75
113 56 0.15
114 38 0.10
115 1 0.00
ACGTcount: A:0.35, C:0.34, G:0.19, T:0.12
Consensus pattern (112 bp):
AGCCCAAAATCACCGGCACAAAGCCTGCTAGGCACATGGCCCAAAATCACCAGCACAAAGCCTGC
TAAGCACATAGCCCGAATAACACCGGCACAAAGCCTGCTAGGCACAT
Found at i:29212589 original size:21 final size:21
Alignment explanation
Indices: 29212565--29212633 Score: 58
Period size: 21 Copynumber: 3.5 Consensus size: 21
29212555 AAGCCTACTA
*
29212565 GGCACATAGCCCAAAATCACC
1 GGCACAAAGCCCAAAATCACC
***
29212586 GGCACAAAG-CC-TGCT-A--
1 GGCACAAAGCCCAAAATCACC
*
29212602 GGCACATAGCCCAAAATCACC
1 GGCACAAAGCCCAAAATCACC
29212623 GGCACAAAGCC
1 GGCACAAAGCC
29212634 TGCTAGGCAC
Statistics
Matches: 34, Mismatches: 9, Indels: 10
0.64 0.17 0.19
Matches are distributed among these distances:
16 8 0.24
17 2 0.06
18 2 0.06
19 2 0.06
20 2 0.06
21 18 0.53
ACGTcount: A:0.36, C:0.36, G:0.19, T:0.09
Consensus pattern (21 bp):
GGCACAAAGCCCAAAATCACC
Found at i:29213560 original size:44 final size:44
Alignment explanation
Indices: 29213500--29213587 Score: 140
Period size: 44 Copynumber: 2.0 Consensus size: 44
29213490 TTATAATTTT
* * * *
29213500 AATACATAGTGTCGTTCAATGTCAATACTAAGGGCTATTTATTA
1 AATACATAATGACGTTCAATGTCAATACTAAAGACTATTTATTA
29213544 AATACATAATGACGTTCAATGTCAATACTAAAGACTATTTATTA
1 AATACATAATGACGTTCAATGTCAATACTAAAGACTATTTATTA
29213588 CATTGGTCCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (44 bp):
AATACATAATGACGTTCAATGTCAATACTAAAGACTATTTATTA
Found at i:29215584 original size:42 final size:42
Alignment explanation
Indices: 29215537--29215626 Score: 162
Period size: 42 Copynumber: 2.1 Consensus size: 42
29215527 GCCCTTAGGC
*
29215537 CCATTTCAATATCACATGTAATGTCAATGGATGTATGCAAGA
1 CCATTTCAATATCACATGTAATGTCAATGAATGTATGCAAGA
*
29215579 CCATTTCAATATCACATGTAATGTCAATGAATGTATGCAAGC
1 CCATTTCAATATCACATGTAATGTCAATGAATGTATGCAAGA
29215621 CCATTT
1 CCATTT
29215627 GGGGAGACTA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.32
Consensus pattern (42 bp):
CCATTTCAATATCACATGTAATGTCAATGAATGTATGCAAGA
Found at i:29215817 original size:26 final size:26
Alignment explanation
Indices: 29215759--29215842 Score: 113
Period size: 26 Copynumber: 3.3 Consensus size: 26
29215749 CTGGAGGCCT
29215759 AGCCTCTTTT-AAT-AACTGGGGCA-A
1 AGCC-CTTTTCAATAAACTGGGGCATA
**
29215783 AGCCCTTTTCGGTAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
29215809 AGCCCTTTTCAATAAACTGGGGCAT-
1 AGCCCTTTTCAATAAACTGGGGCATA
29215834 AGCCCTTTT
1 AGCCCTTTT
29215843 GCACTTCCTC
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
23 5 0.09
24 5 0.09
25 19 0.36
26 24 0.45
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (26 bp):
AGCCCTTTTCAATAAACTGGGGCATA
Found at i:29215917 original size:20 final size:20
Alignment explanation
Indices: 29215892--29215966 Score: 111
Period size: 20 Copynumber: 3.9 Consensus size: 20
29215882 TTATGATTAC
*
29215892 ATCATGTGCATTTCATACAT
1 ATCATGTGCATATCATACAT
29215912 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
29215932 ATCATGTGCATATCATATCA-
1 ATCATGTGCATATCATA-CAT
29215952 ATCATGT--ATATCATA
1 ATCATGTGCATATCATA
29215967 TCCCACGTAT
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
18 8 0.15
20 43 0.81
21 2 0.04
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:29215923 original size:11 final size:11
Alignment explanation
Indices: 29215892--29215947 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
29215882 TTATGATTAC
29215892 ATCATGTGCAT
1 ATCATGTGCAT
* *
29215903 TTCA--TACAT
1 ATCATGTGCAT
29215912 ATCATGTGCAT
1 ATCATGTGCAT
*
29215923 ATCA--TACAT
1 ATCATGTGCAT
29215932 ATCATGTGCAT
1 ATCATGTGCAT
29215943 ATCAT
1 ATCAT
29215948 ATCAATCATG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.38
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:29215964 original size:9 final size:10
Alignment explanation
Indices: 29215909--29215965 Score: 57
Period size: 9 Copynumber: 5.8 Consensus size: 10
29215899 GCATTTCATA
29215909 CATATCATGT
1 CATATCATGT
*
29215919 GCATATCAT-A
1 -CATATCATGT
29215929 CATATCATGT
1 CATATCATGT
*
29215939 GCATATCATAT
1 -CATATCATGT
29215950 CA-ATCATGT
1 CATATCATGT
29215959 -ATATCAT
1 CATATCAT
29215966 ATCCCACGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
8 1 0.03
9 19 0.49
10 2 0.05
11 17 0.44
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (10 bp):
CATATCATGT
Found at i:29216022 original size:25 final size:25
Alignment explanation
Indices: 29215994--29216041 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
29215984 ATAATTAAAC
* * *
29215994 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAATAGTCATTTTTA
29216019 CCTAGGGGCAAAATAGTCATTTT
1 CCTAGGGGCAAAATAGTCATTTT
29216042 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (25 bp):
CCTAGGGGCAAAATAGTCATTTTTA
Found at i:29216730 original size:27 final size:27
Alignment explanation
Indices: 29216669--29216732 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
29216659 GGCGTATTCA
*
29216669 TCATTTTACCATACAAGGGTATTACGG
1 TCATTTTACCATACAAGGCTATTACGG
* *
29216696 TCACTTTACCCTACAGAGGCT-TTACGG
1 TCATTTTACCATACA-AGGCTATTACGG
*
29216723 TCTTTTTACC
1 TCATTTTACC
29216733 TATTAAGGGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 27 0.87
28 4 0.13
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (27 bp):
TCATTTTACCATACAAGGCTATTACGG
Found at i:29216794 original size:27 final size:27
Alignment explanation
Indices: 29216764--29216916 Score: 139
Period size: 27 Copynumber: 5.7 Consensus size: 27
29216754 TTCATCCTAC
* * *
29216764 AAGGGTGTTTTGGTAAATCTACAAATT
1 AAGGGTATTTTGGTAATTTTACAAATT
** *
29216791 AAGGGTATTTCT-GTAATTTTGTAAATC
1 AAGGGTATTT-TGGTAATTTTACAAATT
*
29216818 AGGGGTATTTTGGTAATTTTACAAATT
1 AAGGGTATTTTGGTAATTTTACAAATT
* * * *
29216845 GAGGGTATTTCGGTAATTTCACAAA-C
1 AAGGGTATTTTGGTAATTTTACAAATT
* *
29216871 CAGTGGTATTTTGGTAATTTTACAAACT
1 AAG-GGTATTTTGGTAATTTTACAAATT
* *
29216899 AGGGGTGTTTTGGTAATT
1 AAGGGTATTTTGGTAATT
29216917 CTACCCTATA
Statistics
Matches: 100, Mismatches: 22, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
26 3 0.03
27 95 0.95
28 2 0.02
ACGTcount: A:0.29, C:0.08, G:0.23, T:0.41
Consensus pattern (27 bp):
AAGGGTATTTTGGTAATTTTACAAATT
Done.