Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 181 of 208
Found at i:55326064 original size:5 final size:5
Alignment explanation
Indices: 55325995--55326158 Score: 59
Period size: 5 Copynumber: 34.6 Consensus size: 5
55325985 AGAAGGAGAG
*
55325995 GGAAA -GAAA -GAAA -GAAA -GAAA -GAAA -GAAA GG-AA GGAGA GGAAA
1 GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA
* * * * ** *
55326038 -GAAA GAAAA AG-AA TGTAA GGAAA GGAAA GGAGAA GAGAAA AAAAA AGAAA
1 GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA GGA-AA G-GAAA GGAAA GGAAA
* * *
55326088 -GAAGA AGAAGA AGAAGA GGAAA GGAAA GGAGA GGAAA --AAA -GAAA
1 GGAA-A GGAA-A GGAA-A GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA
* * *
55326132 GAAAA AG-AA GGAAA GAAAA GGAAA GGA
1 GGAAA GGAAA GGAAA GGAAA GGAAA GGA
55326159 GAAGAGAAAA
Statistics
Matches: 128, Mismatches: 20, Indels: 22
0.75 0.12 0.13
Matches are distributed among these distances:
3 3 0.02
4 44 0.34
5 60 0.47
6 19 0.15
7 2 0.02
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.01
Consensus pattern (5 bp):
GGAAA
Found at i:55326088 original size:46 final size:44
Alignment explanation
Indices: 55326035--55326172 Score: 172
Period size: 46 Copynumber: 3.0 Consensus size: 44
55326025 GAAGGAGAGG
55326035 AAAGAAAGAAAAAGAATGTAAGGAAAGGAAAGGAGAAGAGAAAAAA
1 AAAGAAAGAAAAAGAA-G-AAGGAAAGGAAAGGAGAAGAGAAAAAA
* **
55326081 AAAGAAAGAAGAAGAAGAA-GAAGAGGAAAGGA-AAGGAGAGGAAA
1 AAAGAAAGAAAAAGAAGAAGGAA-AGGAAAGGAGAA-GAGAAAAAA
*
55326125 AAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAA
1 AAAGAAAGAAAAAGAA-G-AAGGAAAGGAAAGGAGAAGAGAAAAAA
55326171 AA
1 AA
55326173 GAAGAAGAAG
Statistics
Matches: 79, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
43 5 0.06
44 33 0.42
45 2 0.03
46 35 0.44
47 4 0.05
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.01
Consensus pattern (44 bp):
AAAGAAAGAAAAAGAAGAAGGAAAGGAAAGGAGAAGAGAAAAAA
Found at i:55326126 original size:44 final size:41
Alignment explanation
Indices: 55325987--55326182 Score: 199
Period size: 41 Copynumber: 4.7 Consensus size: 41
55325977 GGGGGGGGAG
*
55325987 AAGGAGAGGGAAAGAAAGAAAG-A-AAGAAAGAAA-GAAAGG-
1 AAGGAGA-GGAAA-AAAGAAAGAAGAAGAAGGAAAGGAAAGGA
55326026 AAGGAGAGGAAAGAAAGAAA-AAGAATGTAAGGAAAGGAAAGGA
1 AAGGAGAGGAAA-AAAGAAAGAAGAA-G-AAGGAAAGGAAAGGA
**
55326069 GAA-GAGAAAAAAAAAGAAAGAAGAAGAAGAAGAAGAGGAAAGGA
1 -AAGGAGAGGAAAAAAGAAAGAAGAAGAAG--GAA-AGGAAAGGA
* *
55326113 AAGGAGAGGAAAAAAGAAAGAAAAAGAAGGAAAGAAAAGGA
1 AAGGAGAGGAAAAAAGAAAGAAGAAGAAGGAAAGGAAAGGA
*
55326154 AAGGAGAAGAGAAAAA-AAAGAAGAAGAAG
1 AAGGAGAGGA-AAAAAGAAAGAAGAAGAAG
55326183 CGGGAAGGAA
Statistics
Matches: 135, Mismatches: 9, Indels: 24
0.80 0.05 0.14
Matches are distributed among these distances:
38 14 0.10
39 9 0.07
40 1 0.01
41 38 0.28
42 22 0.16
43 17 0.13
44 34 0.25
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.01
Consensus pattern (41 bp):
AAGGAGAGGAAAAAAGAAAGAAGAAGAAGGAAAGGAAAGGA
Found at i:55326869 original size:9 final size:8
Alignment explanation
Indices: 55326855--55326879 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
55326845 AAAATATTAC
55326855 AAAAAAAT
1 AAAAAAAT
55326863 AAAAAAAT
1 AAAAAAAT
55326871 AAAAAAAT
1 AAAAAAAT
55326879 A
1 A
55326880 TTATAAACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAAAAT
Found at i:55331952 original size:18 final size:18
Alignment explanation
Indices: 55331929--55331966 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
55331919 ATCCCAATGA
55331929 TCGCCACCACCTTCTTCT
1 TCGCCACCACCTTCTTCT
* *
55331947 TCGCCAGCACCTTTTTCT
1 TCGCCACCACCTTCTTCT
55331965 TC
1 TC
55331967 ACTACCAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.45, G:0.08, T:0.37
Consensus pattern (18 bp):
TCGCCACCACCTTCTTCT
Found at i:55332838 original size:3 final size:3
Alignment explanation
Indices: 55332830--55332855 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
55332820 TCTTAATACT
55332830 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
55332856 TAATAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:55333153 original size:27 final size:27
Alignment explanation
Indices: 55333082--55333154 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
55333072 ACACGAGTAA
*
55333082 TGCCGCCAATCA-GTATGGCACCATTGG
1 TGCCGCCAATCACCT-TGGCACCATTGG
** * *
55333109 TGCCGCCAATGGCTTTGGCACCTTTGG
1 TGCCGCCAATCACCTTGGCACCATTGG
55333136 TGCCGCCAATCACCTTGGC
1 TGCCGCCAATCACCTTGGC
55333155 CTGACCAGAG
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
27 37 0.97
28 1 0.03
ACGTcount: A:0.16, C:0.33, G:0.26, T:0.25
Consensus pattern (27 bp):
TGCCGCCAATCACCTTGGCACCATTGG
Found at i:55333850 original size:9 final size:9
Alignment explanation
Indices: 55333819--55333869 Score: 57
Period size: 10 Copynumber: 5.3 Consensus size: 9
55333809 TAAAAAATCT
*
55333819 TTAAAATAA
1 TTAAAATTA
*
55333828 TTATAAAGTA
1 TTA-AAATTA
55333838 TTAAAATTA
1 TTAAAATTA
55333847 TTAAAAATATA
1 TT-AAAAT-TA
55333858 TTAAAATTA
1 TTAAAATTA
55333867 TTA
1 TTA
55333870 TTTTAGCATA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
9 15 0.42
10 17 0.47
11 4 0.11
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (9 bp):
TTAAAATTA
Found at i:55333916 original size:23 final size:23
Alignment explanation
Indices: 55333885--55333935 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
55333875 GCATAAATTT
*
55333885 TAATAATTTTAATATAATCTTAA
1 TAATAATTTTAACATAATCTTAA
* *
55333908 TAATTATTTTAACATAATTTTAA
1 TAATAATTTTAACATAATCTTAA
55333931 -AATAA
1 TAATAA
55333936 AATCGGAGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (23 bp):
TAATAATTTTAACATAATCTTAA
Found at i:55333927 original size:11 final size:11
Alignment explanation
Indices: 55333886--55333935 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
55333876 CATAAATTTT
55333886 AATAATTTTAA
1 AATAATTTTAA
* *
55333897 TATAATCTTAA
1 AATAATTTTAA
*
55333908 TAATTATTTTAA
1 -AATAATTTTAA
*
55333920 CATAATTTTAA
1 AATAATTTTAA
55333931 AATAA
1 AATAA
55333936 AATCGGAGAA
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
11 22 0.73
12 8 0.27
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (11 bp):
AATAATTTTAA
Found at i:55334727 original size:14 final size:14
Alignment explanation
Indices: 55334703--55334749 Score: 69
Period size: 13 Copynumber: 3.4 Consensus size: 14
55334693 AACAAAATAA
55334703 AAAATAAAAAAAATT
1 AAAAT-AAAAAAATT
*
55334718 AAAAT-TAAAAATT
1 AAAATAAAAAAATT
55334731 AAAATAAAAAAATT
1 AAAATAAAAAAATT
55334745 AAAAT
1 AAAAT
55334750 CTTAAATCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 12 0.41
14 12 0.41
15 5 0.17
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
AAAATAAAAAAATT
Found at i:55334756 original size:21 final size:22
Alignment explanation
Indices: 55334718--55334767 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
55334708 AAAAAAAATT
55334718 AAAATTAAAAATTAAAAT-AAA
1 AAAATTAAAAATTAAAATCAAA
*
55334739 AAAATT-AAAATCTTAAATCCAAA
1 AAAATTAAAAAT-TAAAAT-CAAA
55334762 AAAATT
1 AAAATT
55334768 GAATTTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 5 0.20
21 11 0.44
23 9 0.36
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (22 bp):
AAAATTAAAAATTAAAATCAAA
Found at i:55334931 original size:2 final size:2
Alignment explanation
Indices: 55334924--55334962 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
55334914 ATACTTGCAA
55334924 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
55334963 CACACACACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:55335801 original size:3 final size:3
Alignment explanation
Indices: 55335793--55335830 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
55335783 GCAGTACATC
55335793 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
55335831 CCCAAACCAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:55340096 original size:23 final size:23
Alignment explanation
Indices: 55340035--55340097 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
55340025 AAGTGTGTGG
* *
55340035 TAAT-TATAAATACATGTGTAAT
1 TAATATATATATACATTTGTAAT
* *
55340057 AAATATATGTATACATTTGTAAT
1 TAATATATATATACATTTGTAAT
55340080 TAATATATATATACATTT
1 TAATATATATATACATTT
55340098 ATATATTATA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
22 3 0.09
23 31 0.91
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.44
Consensus pattern (23 bp):
TAATATATATATACATTTGTAAT
Found at i:55340108 original size:23 final size:23
Alignment explanation
Indices: 55340035--55340105 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 23
55340025 AAGTGTGTGG
* * *
55340035 TAAT-TATAAATACATGTGTAAT
1 TAATATATATATACATTTATAAT
* * *
55340057 AAATATATGTATACATTTGTAAT
1 TAATATATATATACATTTATAAT
55340080 TAATATATATATACATTTATATAT
1 TAATATATATATACATTTATA-AT
55340104 TA
1 TA
55340106 TATTATTATT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
22 3 0.08
23 33 0.82
24 4 0.10
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (23 bp):
TAATATATATATACATTTATAAT
Found at i:55340157 original size:18 final size:18
Alignment explanation
Indices: 55340124--55340162 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
55340114 TTAATTAAAC
55340124 AAAAGAAAGAAATGAAAAT
1 AAAAGAAAGAAATG-AAAT
*
55340143 AAAAGAAA-CAATGAAAT
1 AAAAGAAAGAAATGAAAT
55340160 AAA
1 AAA
55340163 GATTAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 4 0.21
19 8 0.42
ACGTcount: A:0.74, C:0.03, G:0.13, T:0.10
Consensus pattern (18 bp):
AAAAGAAAGAAATGAAAT
Found at i:55344405 original size:20 final size:20
Alignment explanation
Indices: 55344382--55344419 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
55344372 ACTCTATCAT
55344382 TATAAGTCCACTTCTACCGA
1 TATAAGTCCACTTCTACCGA
**
55344402 TATAAGTTTACTTCTACC
1 TATAAGTCCACTTCTACC
55344420 CATACATCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.26, G:0.08, T:0.37
Consensus pattern (20 bp):
TATAAGTCCACTTCTACCGA
Found at i:55351742 original size:37 final size:37
Alignment explanation
Indices: 55351688--55351841 Score: 157
Period size: 37 Copynumber: 4.1 Consensus size: 37
55351678 AAGTACACTT
*
55351688 TCGAGCCAAATCTTACCGTTATACTGAATAAAGCTCAA
1 TCGAG-CAAATCTTACCGTTATACTGAATGAAGCTCAA
* *
55351726 TCGAGCAAATCATACCGTTATACTGAATGGAGCTCAA
1 TCGAGCAAATCTTACCGTTATACTGAATGAAGCTCAA
* * ** * *
55351763 TTGAGCAAACCTTACTATTATACTGAATGATGTTCAA
1 TCGAGCAAATCTTACCGTTATACTGAATGAAGCTCAA
* * * *
55351800 TAGAGCAAAT-TCTACTGTAATACTGAGTGAAGCTCAA
1 TCGAGCAAATCT-TACCGTTATACTGAATGAAGCTCAA
*
55351837 ACGAG
1 TCGAG
55351842 TAGAAATCTA
Statistics
Matches: 95, Mismatches: 20, Indels: 3
0.81 0.17 0.03
Matches are distributed among these distances:
36 1 0.01
37 89 0.94
38 5 0.05
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.27
Consensus pattern (37 bp):
TCGAGCAAATCTTACCGTTATACTGAATGAAGCTCAA
Found at i:55355807 original size:62 final size:63
Alignment explanation
Indices: 55355666--55355807 Score: 151
Period size: 62 Copynumber: 2.3 Consensus size: 63
55355656 ACACAGCCTG
* * * * **
55355666 GACACACGCCTATGTCCTCTGCCCGTGTAGTTTTGAAGCATAAAAAATGAGTTATACGGCCTG
1 GACACACGCCTATGTCCTCTGCCCGTGTAGTCTTGAACCACAAAAAATGAGTTACACGGCCCA
** * * * * *
55355729 GACACACGCCCGTGTCC-CTGGCCGTGTGGTCTTGTACCACAAACAGTGAGTTACACGGCCCA
1 GACACACGCCTATGTCCTCTGCCCGTGTAGTCTTGAACCACAAAAAATGAGTTACACGGCCCA
*
55355791 GACACACGTCTATGTCC
1 GACACACGCCTATGTCC
55355808 GTTTCCCGTG
Statistics
Matches: 63, Mismatches: 16, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
62 48 0.76
63 15 0.24
ACGTcount: A:0.24, C:0.30, G:0.23, T:0.23
Consensus pattern (63 bp):
GACACACGCCTATGTCCTCTGCCCGTGTAGTCTTGAACCACAAAAAATGAGTTACACGGCCCA
Found at i:55370441 original size:49 final size:49
Alignment explanation
Indices: 55370387--55370486 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
55370377 TTAGAATGTT
55370387 GTGCCCTAACGCATTGGGTGTGACATTTTCTTTCTCTGAAATGATAAGG
1 GTGCCCTAACGCATTGGGTGTGACATTTTCTTTCTCTGAAATGATAAGG
55370436 GTGCCCTAACGCATTGGGTGTGACATTTTCTTTCTCTGAAATGATAAGG
1 GTGCCCTAACGCATTGGGTGTGACATTTTCTTTCTCTGAAATGATAAGG
55370485 GT
1 GT
55370487 CTTAATGCGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (49 bp):
GTGCCCTAACGCATTGGGTGTGACATTTTCTTTCTCTGAAATGATAAGG
Found at i:55374480 original size:494 final size:492
Alignment explanation
Indices: 55373542--55374520 Score: 1376
Period size: 494 Copynumber: 2.0 Consensus size: 492
55373532 GTACCAAAAC
* ** * *
55373542 ATACTAAACATGAAGTCAAAGCATTATTAGCATATTTGACATTTCAATACGCATTATCAATTTTA
1 ATACCAAACATGAAGTCAAAGCATTACCAGCATATTTGACATCTCAATACACATTATCAATTTTA
* *
55373607 ACCTTATATAAGGAGGTTTTGGATTGAGAGTGAGAGCATACAAGCTGTCCGATCTTTGTGGTTGT
66 ACCTTATATAAGGAGGTTTTGGATTGAGAGTGAGAGCATACAAGCTGTACGATCTTTGTGATTGT
* * *
55373672 AATTATCCTTGGTGAACTTGGGTAGATTGGGTTGGTTAGCAAATCTGTAATGTGAAAAAATTGTA
131 AATTACCCTTGGTGAACTTGAGTAGATTGGGTTGGTTAGAAAATCTGTAATGTGAAAAAATTGTA
* * * * *
55373737 TAATGGACTCATTATCTAGGTAAGGCCCTACAGAGGTAGATTGTTGAAACGAATTACATCAATAA
196 TAATAGACTCATTATCTAGATAAGGCCCCACAGAGGTAGATTATTGAAACGAATTACATCAACAA
*
55373802 ATTTTCGGTCTCCATCTTCATTTATCTTATTTTTATTCTCTTGCCCTAACTATCAAAACTCACAT
261 ATTCTCGGTCTCCATCTTCATTTATCTTATTTTTATTCTCTTGCCCTAACTATCAAAACTCACAT
* * * * *
55373867 TGCAACATTAATAATGTCTACTAACTAAAATTTTCTATAACCATACTTAATCAACCTTACAGAAT
326 TGCAACATCAATAACGTCTACTAACTAAAATGTTCTATAACCAGACTTAATCAACCTTACAAAAT
*
55373932 TAAAAGGACGGGATTCCAATTATCAAAATCAAAGTTTCTCAACAAAAAAAACTTAGAATTGTTGA
391 TAAAAGGACAGGATTCCAATTATCAAAATCAAAGTTTCTCAACAAAAAAAACTTAGAATTGTTGA
*
55373997 CGTTCTCCTTCAATCTAAGTATTTAATGGAGTCAAAT
456 CATTCTCCTTCAATCTAAGTATTTAATGGAGTCAAAT
* *
55374034 ATACCAAACATGAAGTCAAAGCATTACCAGCATATTTGATATCTCAATACATATTATCAATTTTA
1 ATACCAAACATGAAGTCAAAGCATTACCAGCATATTTGACATCTCAATACACATTATCAATTTTA
* * *
55374099 GCTTTATATATATGGAGGTTTTGGATTGAGAGTGAGAGCATACAAGCTGTATGATCTTTGTGATT
66 ACCTTATATA-A-GGAGGTTTTGGATTGAGAGTGAGAGCATACAAGCTGTACGATCTTTGTGATT
* * **
55374164 GTAATTACCCTTGGTGAGCTTGAGTAGATTGGGTTGTTTAGAAAATCTGTAATGTGAAAATTTTG
129 GTAATTACCCTTGGTGAACTTGAGTAGATTGGGTTGGTTAGAAAATCTGTAATGTGAAAAAATTG
* ** *
55374229 TATAATAGACTCATTATCTAGATAAGGCCCCATAGAGGTAGATTATTGAATGGAATTGCATCAAC
194 TATAATAGACTCATTATCTAGATAAGGCCCCACAGAGGTAGATTATTGAAACGAATTACATCAAC
* * ** * * *
55374294 AAGTTCTCGGTCTTCATCTTTGTTTATCTTGTTGTTTTTATTCTCTTGTCGC-AACTATTAAAAC
259 AAATTCTCGGTCTCCATCTTCATTTATC---TTATTTTTATTCTCTTG-CCCTAACTATCAAAAC
*
55374358 TCACATTGCAACATCAATAGCGTCTACTAACTAAAATCGTT-TATAACCAGACTTAATCAACCTT
320 TCACATTGCAACATCAATAACGTCTACTAACTAAAAT-GTTCTATAACCAGACTTAATCAACCTT
* * * ** * *
55374422 TCAAAATT-GAAGTACATTATTCTAATTA-CCAAATCAAAGTTTCT-AA-AAAAACAAACTTAGA
384 ACAAAATTAAAAGGACAGGATTCCAATTATCAAAATCAAAGTTTCTCAACAAAAA-AAACTTAGA
*
55374483 ATTGTTGACATTCTCCTTCAATCTAAGTATTTGATGGA
448 ATTGTTGACATTCTCCTTCAATCTAAGTATTTAATGGA
55374521 AAGTTATGCC
Statistics
Matches: 427, Mismatches: 52, Indels: 14
0.87 0.11 0.03
Matches are distributed among these distances:
492 66 0.15
493 6 0.01
494 233 0.55
495 15 0.04
496 14 0.03
497 89 0.21
498 4 0.01
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (492 bp):
ATACCAAACATGAAGTCAAAGCATTACCAGCATATTTGACATCTCAATACACATTATCAATTTTA
ACCTTATATAAGGAGGTTTTGGATTGAGAGTGAGAGCATACAAGCTGTACGATCTTTGTGATTGT
AATTACCCTTGGTGAACTTGAGTAGATTGGGTTGGTTAGAAAATCTGTAATGTGAAAAAATTGTA
TAATAGACTCATTATCTAGATAAGGCCCCACAGAGGTAGATTATTGAAACGAATTACATCAACAA
ATTCTCGGTCTCCATCTTCATTTATCTTATTTTTATTCTCTTGCCCTAACTATCAAAACTCACAT
TGCAACATCAATAACGTCTACTAACTAAAATGTTCTATAACCAGACTTAATCAACCTTACAAAAT
TAAAAGGACAGGATTCCAATTATCAAAATCAAAGTTTCTCAACAAAAAAAACTTAGAATTGTTGA
CATTCTCCTTCAATCTAAGTATTTAATGGAGTCAAAT
Found at i:55376786 original size:18 final size:19
Alignment explanation
Indices: 55376738--55376795 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 19
55376728 TAAATCTCAA
*
55376738 AAAAATCAAAAATATATAT
1 AAAAATTAAAAATATATAT
* *
55376757 AAAAATTGAAAATGT-TAT
1 AAAAATTAAAAATATATAT
*
55376775 AAAAATTAAAAA-ATATTT
1 AAAAATTAAAAATATATAT
55376793 AAA
1 AAA
55376796 TTTCAAGTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
17 1 0.03
18 19 0.59
19 12 0.38
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (19 bp):
AAAAATTAAAAATATATAT
Found at i:55376888 original size:17 final size:16
Alignment explanation
Indices: 55376868--55376903 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
55376858 TATTTTAGAA
55376868 TTTAATAATTTTTTATT
1 TTTAA-AATTTTTTATT
*
55376885 TTTAAACTTTTTTATT
1 TTTAAAATTTTTTATT
55376901 TTT
1 TTT
55376904 TTTAGAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTAAAATTTTTTATT
Found at i:55376914 original size:18 final size:18
Alignment explanation
Indices: 55376902--55376938 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
55376892 TTTTTTATTT
*
55376902 TTTTTAGAATTTTAATAA
1 TTTTTAGAATTTTTATAA
55376920 TTTTTAGAATTTTTATAA
1 TTTTTAGAATTTTTATAA
55376938 T
1 T
55376939 ATTATTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.59
Consensus pattern (18 bp):
TTTTTAGAATTTTTATAA
Found at i:55384252 original size:20 final size:19
Alignment explanation
Indices: 55384222--55384262 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
55384212 TAATATATAT
*
55384222 ATCAATTTAATCCATTTCA
1 ATCAATTTAATCCAATTCA
*
55384241 ATCAACTTTAATTCAATTCA
1 ATCAA-TTTAATCCAATTCA
55384261 AT
1 AT
55384263 ATCAAAGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.39, C:0.20, G:0.00, T:0.41
Consensus pattern (19 bp):
ATCAATTTAATCCAATTCA
Found at i:55386296 original size:34 final size:34
Alignment explanation
Indices: 55386257--55386349 Score: 100
Period size: 34 Copynumber: 2.7 Consensus size: 34
55386247 TGTTTGTCTA
55386257 TTATTTCGT-TTATTATTCTTT-ATTTTTCTTAAAT
1 TTATTT-GTATTATTATTCTTTCA-TTTTCTTAAAT
* * *
55386291 TTATTTTTATTTTTATTTTTTCATTTTCTTAAAT
1 TTATTTGTATTATTATTCTTTCATTTTCTTAAAT
* * *
55386325 TTATTTTTATTTTTATTTTTTCATT
1 TTATTTGTATTATTATTCTTTCATT
55386350 CTTTTTCTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
33 1 0.02
34 52 0.96
35 1 0.02
ACGTcount: A:0.19, C:0.06, G:0.01, T:0.73
Consensus pattern (34 bp):
TTATTTGTATTATTATTCTTTCATTTTCTTAAAT
Found at i:55386309 original size:5 final size:6
Alignment explanation
Indices: 55386290--55386377 Score: 70
Period size: 6 Copynumber: 13.5 Consensus size: 6
55386280 TTTTCTTAAA
**
55386290 TTTATT TTTATT TTTATTT TTTCATTT TCTTAAA TTTATT TTTATT TTTATTT
1 TTTATT TTTATT TTTA-TT TTT-A-TT T-TTATT TTTATT TTTATT TTTA-TT
*
55386343 TTTCATT CTTT-TT CTTTGTT TTTATT TTTATT TTT
1 TTT-ATT -TTTATT -TTTATT TTTATT TTTATT TTT
55386378 TATATATCTA
Statistics
Matches: 70, Mismatches: 5, Indels: 14
0.79 0.06 0.16
Matches are distributed among these distances:
6 43 0.61
7 15 0.21
8 10 0.14
9 2 0.03
ACGTcount: A:0.15, C:0.06, G:0.01, T:0.78
Consensus pattern (6 bp):
TTTATT
Found at i:55386378 original size:34 final size:34
Alignment explanation
Indices: 55386280--55386378 Score: 148
Period size: 34 Copynumber: 2.9 Consensus size: 34
55386270 TATTCTTTAT
55386280 TTTTCTTAAATTTATTTTTATTTTTATTTTTTCA
1 TTTTCTTAAATTTATTTTTATTTTTATTTTTTCA
55386314 TTTTCTTAAATTTATTTTTATTTTTATTTTTTCA
1 TTTTCTTAAATTTATTTTTATTTTTATTTTTTCA
** *
55386348 TTCTT-TT-TCTTTGTTTTTATTTTTATTTTTT
1 TT-TTCTTAAATTTATTTTTATTTTTATTTTTT
55386379 ATATATCTAT
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
33 21 0.34
34 38 0.62
35 2 0.03
ACGTcount: A:0.16, C:0.06, G:0.01, T:0.77
Consensus pattern (34 bp):
TTTTCTTAAATTTATTTTTATTTTTATTTTTTCA
Found at i:55394475 original size:50 final size:50
Alignment explanation
Indices: 55394415--55394594 Score: 233
Period size: 50 Copynumber: 3.7 Consensus size: 50
55394405 AAGGAAAAGG
55394415 GACCAAGGCGAAAACCCGCAAAGGGCGCTTTGAGTCCTAAAAAAAAGAAA
1 GACCAAGGCGAAAACCCGCAAAGGGCGCTTTGAGTCCTAAAAAAAAGAAA
* *
55394465 GACCAAGGCGAAAACCCGTAAAGAGCGCTTTGAGTCCT---AAAAA-AAA
1 GACCAAGGCGAAAACCCGCAAAGGGCGCTTTGAGTCCTAAAAAAAAGAAA
*** *
55394511 GACCAAATTGAAAACCCGCAAAGGGCGCTTTGAGTCCTAAAAAAAAGAGA
1 GACCAAGGCGAAAACCCGCAAAGGGCGCTTTGAGTCCTAAAAAAAAGAAA
* * * * *
55394561 GGCCAAGGTGAAAACCCGTAAAGGGAGCCTTGAG
1 GACCAAGGCGAAAACCCGCAAAGGGCGCTTTGAG
55394595 ACCAAAGGGG
Statistics
Matches: 112, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
46 36 0.32
47 5 0.04
49 5 0.04
50 66 0.59
ACGTcount: A:0.42, C:0.21, G:0.25, T:0.12
Consensus pattern (50 bp):
GACCAAGGCGAAAACCCGCAAAGGGCGCTTTGAGTCCTAAAAAAAAGAAA
Found at i:55394539 original size:46 final size:46
Alignment explanation
Indices: 55394415--55394558 Score: 198
Period size: 46 Copynumber: 3.0 Consensus size: 46
55394405 AAGGAAAAGG
*
55394415 GACCAAGGCGAAAACCCGCAAAGGGCGCTTTGAGTCCTAAAAAAAAGAAA
1 GACCAAAGCGAAAACCCGCAAAGGGCGCTTTGAGTCCT---AAAAA-AAA
* * *
55394465 GACCAAGGCGAAAACCCGTAAAGAGCGCTTTGAGTCCTAAAAAAAA
1 GACCAAAGCGAAAACCCGCAAAGGGCGCTTTGAGTCCTAAAAAAAA
**
55394511 GACCAAATTGAAAACCCGCAAAGGGCGCTTTGAGTCCTAAAAAAAA
1 GACCAAAGCGAAAACCCGCAAAGGGCGCTTTGAGTCCTAAAAAAAA
55394557 GA
1 GA
55394559 GAGGCCAAGG
Statistics
Matches: 87, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
46 46 0.53
47 5 0.06
50 36 0.41
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (46 bp):
GACCAAAGCGAAAACCCGCAAAGGGCGCTTTGAGTCCTAAAAAAAA
Found at i:55395926 original size:44 final size:43
Alignment explanation
Indices: 55395815--55395935 Score: 145
Period size: 43 Copynumber: 2.8 Consensus size: 43
55395805 TTTATGGCGG
55395815 ATCTTATCCCCCTGAAGTTGCAGTGGAGTAGATTAAAGCCACTA
1 ATCTTA-CCCCCTGAAGTTGCAGTGGAGTAGATTAAAGCCACTA
* **
55395859 ATCTTACCCCCTGAAGTTGCAGTGGGGTAGATTAAAGTTAC-A
1 ATCTTACCCCCTGAAGTTGCAGTGGAGTAGATTAAAGCCACTA
* * * *
55395901 AGTTTTGTCTCCCTGAAGTTGCAGTGGAGCAGATT
1 A-TCTT-ACCCCCTGAAGTTGCAGTGGAGTAGATT
55395936 GAGGATAACT
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
42 2 0.03
43 35 0.52
44 30 0.45
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (43 bp):
ATCTTACCCCCTGAAGTTGCAGTGGAGTAGATTAAAGCCACTA
Found at i:55396150 original size:179 final size:179
Alignment explanation
Indices: 55395951--55396296 Score: 469
Period size: 179 Copynumber: 1.9 Consensus size: 179
55395941 TAACTAATCC
* * * * *
55395951 TATCTTCCTGAGGTTGCAGTGGATTAGACTGAAGATAGCATATCTCATGTCCCTAAAGTTACAGT
1 TATCTTCCAGAAGTTGCAGTGGAGTAGACTGAAGATAACAAATCTCATGTCCCTAAAGTTACAG-
* * * * *
55396016 GG-AACAGATTAAAGCTATAAATTATAGATCTTACCTCTCTGAAGTTGCAGTAGAGCAGATCATA
65 GGAAAAAAATTAAAGCTATAAATTACAGATCTCACCTCTCTGAAGTTGCAGTAGAACAGATCATA
* *
55396080 GCAAACCCTATCTCTCTAAAGTTGCAGTAGAGTAGGTTGAAGACAAGTCT
130 GCAAACCCTATCTCCCTAAAGTTACAGTAGAGTAGGTTGAAGACAAGTCT
* * * *
55396130 TATCTTCCAGAAGTTGCAGTGGAGTAGACTGAAGATAACAAATCTCATTTCCGTGAAGTTGCAGG
1 TATCTTCCAGAAGTTGCAGTGGAGTAGACTGAAGATAACAAATCTCATGTCCCTAAAGTTACAGG
* * *
55396195 GAAAAAAATTGAAGCTATAAATTACAGATCTCATCTCTCTGAAGTTGCAGTAGAACAGATCATAT
66 GAAAAAAATTAAAGCTATAAATTACAGATCTCACCTCTCTGAAGTTGCAGTAGAACAGATCATAG
* * * *
55396260 CAAACCTTATCTCCCTGAAGTTACCGTGGAGTAGGTT
131 CAAACCCTATCTCCCTAAAGTTACAGTAGAGTAGGTT
55396297 ACAAAGAAGC
Statistics
Matches: 143, Mismatches: 23, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
178 2 0.01
179 141 0.99
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.29
Consensus pattern (179 bp):
TATCTTCCAGAAGTTGCAGTGGAGTAGACTGAAGATAACAAATCTCATGTCCCTAAAGTTACAGG
GAAAAAAATTAAAGCTATAAATTACAGATCTCACCTCTCTGAAGTTGCAGTAGAACAGATCATAG
CAAACCCTATCTCCCTAAAGTTACAGTAGAGTAGGTTGAAGACAAGTCT
Found at i:55400674 original size:5 final size:5
Alignment explanation
Indices: 55400654--55400691 Score: 58
Period size: 5 Copynumber: 7.4 Consensus size: 5
55400644 CCTAAAGAGT
*
55400654 ATTAA ATAATA ATTAA ATTAA ATTAA ATTAA ATTAA AT
1 ATTAA ATTA-A ATTAA ATTAA ATTAA ATTAA ATTAA AT
55400692 ATTGGACTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 26 0.87
6 4 0.13
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATTAA
Found at i:55411646 original size:2 final size:2
Alignment explanation
Indices: 55411639--55411681 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
55411629 ATCAGCTCTT
55411639 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
55411681 T
1 T
55411682 NNNNNNNNNN
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:55412088 original size:9 final size:9
Alignment explanation
Indices: 55412074--55412101 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
55412064 GAGTTAAACG
55412074 AATCGAGTT
1 AATCGAGTT
55412083 AATCGAGTT
1 AATCGAGTT
55412092 AATCGAGTT
1 AATCGAGTT
55412101 A
1 A
55412102 TTTGAATCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (9 bp):
AATCGAGTT
Found at i:55412547 original size:20 final size:18
Alignment explanation
Indices: 55412522--55412597 Score: 59
Period size: 20 Copynumber: 4.1 Consensus size: 18
55412512 TTTTTAATAT
55412522 TTTCCCTCCAAACTATTTAC
1 TTTCCCT-CAAACT-TTTAC
55412542 TTTCCCTCAAACTTTTA-
1 TTTCCCTCAAACTTTTAC
* * *
55412559 -TTCTCTAAAACTTTTTATT
1 TTTCCCTCAAAC-TTTTA-C
55412578 TTTCCC-CTAAACTTTTAC
1 TTTCCCTC-AAACTTTTAC
55412596 TT
1 TT
55412598 CTCACCCTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
16 9 0.20
17 5 0.11
18 6 0.13
19 11 0.24
20 15 0.33
ACGTcount: A:0.24, C:0.28, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTCCCTCAAACTTTTAC
Found at i:55412741 original size:17 final size:17
Alignment explanation
Indices: 55412683--55412763 Score: 60
Period size: 17 Copynumber: 4.6 Consensus size: 17
55412673 TTATATCTAC
55412683 TATTTATATTATTAAAT
1 TATTTATATTATTAAAT
* *
55412700 TAAATTTCACATT-TTATAT
1 T--ATTT-ATATTATTAAAT
55412719 TATTTATATTATTAAAT
1 TATTTATATTATTAAAT
* *
55412736 TGTTTAT-TCATATTGAA-
1 TATTTATAT--TATTAAAT
55412753 TATTTATATTA
1 TATTTATATTA
55412764 AAATTGAATT
Statistics
Matches: 50, Mismatches: 7, Indels: 15
0.69 0.10 0.21
Matches are distributed among these distances:
16 7 0.14
17 22 0.44
18 7 0.14
19 10 0.20
20 4 0.08
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (17 bp):
TATTTATATTATTAAAT
Found at i:55413199 original size:5 final size:5
Alignment explanation
Indices: 55413189--55413245 Score: 53
Period size: 5 Copynumber: 11.2 Consensus size: 5
55413179 GAACAAATAT
* * * *
55413189 ATTCG ATTCG ATTCG ATTTG ATTCG ATTCG TATTCC ATCTC- ACTCG ACTCG
1 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG -ATTCG AT-TCG ATTCG ATTCG
55413240 ATTCG A
1 ATTCG A
55413246 GAAAACTTCA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
4 2 0.05
5 36 0.82
6 6 0.14
ACGTcount: A:0.21, C:0.25, G:0.16, T:0.39
Consensus pattern (5 bp):
ATTCG
Found at i:55413836 original size:3 final size:3
Alignment explanation
Indices: 55413828--55413874 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
55413818 AAATTGAATG
*
55413828 TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
55413875 GTATGTATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:55418540 original size:16 final size:16
Alignment explanation
Indices: 55418519--55418572 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
55418509 ACAATAGTAG
55418519 TAATTACACTTTCATT
1 TAATTACACTTTCATT
*
55418535 TAATTACTACTTT-A-G
1 TAATTAC-ACTTTCATT
* *
55418550 TAGTTACATTTTCATT
1 TAATTACACTTTCATT
55418566 TAATTAC
1 TAATTAC
55418573 TCTATGTTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
14 4 0.13
15 7 0.23
16 14 0.47
17 5 0.17
ACGTcount: A:0.31, C:0.15, G:0.04, T:0.50
Consensus pattern (16 bp):
TAATTACACTTTCATT
Found at i:55429029 original size:44 final size:44
Alignment explanation
Indices: 55428972--55429903 Score: 713
Period size: 44 Copynumber: 20.5 Consensus size: 44
55428962 GAAATGTAAT
* * *
55428972 TTCAACCTACTCCACTGCAACTTTAGGGAGATAAGATTTGTAGC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
* *
55429016 TTTAATCTGCTCCACTGTAACTTCAGGGAGATAAGATTTGTAGC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
* * ** * * * *
55429060 TTCAATCAGGTTTACTGTAGCTTCAGAGAGATAAGATTTGCTATC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TAGC
* * *
55429105 TTCAATTTGCTCCACTGTAACTTCAGGGAAATAAGATTTGTAGC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
* * *
55429149 TTCAATCTGCTCCACTACAACTTTAGGGAGATGAGATTTGTAGC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
* * *
55429193 TTCAATCTGCTCCACTGCAACTTCAGGGAGATGAGATTCGCTATC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TAGC
** * *
55429238 TTCAATCTATTCCACCGCAACTTCAGGAAGATAAGATTTGTAGC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
* *
55429282 -TCTAACCTGCTCCACTGCAACTTCAGGGAGATGAGATTTGTAACTTGCAGC
1 TTC-AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-----T--AGC
* * * * * * * *
55429333 TTTAATCTGTTCCACTACAACTTCGGGGAAATAATATTTTCTATC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTTGTAGC
* * * * **
55429378 TTCAATCTGCTCCATTGCAACTTCAGGGAAATAAGATTCGCATA
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
* * * *
55429422 TTCAATCTGCTCCATTGTAACTTCAGAGAGATAAGGTTTGTAACTTGTAGC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAA-----G--ATTTGTAGC
* ** * * * *
55429473 TTTAATCTATTCCCCTGC-ACTTCAAGGAAATAAGACTCATTACGGTAGA
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-T--TT---GTAGC
* * * * *
55429522 TTTAATCTGAC-CCACTGCAACTTCAGAGG-TATATGATTTATCGC
1 TTCAATCTG-CTCCACTGCAACTTCAG-GGAGATAAGATTTGTAGC
* * * *
55429566 TTCAATCTACTCTACTGTAACTTCAGGGAGATAAGATTTGCTATC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TAGC
* * *
55429611 TTCAATCTGTTCCACTGCAACTTCAGGGAGAAAAGATTTGTAAC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
* * *
55429655 TTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTTATGGC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
* *
55429699 TTTAATCTGCTCCACTGCAACTTCAGGGGGATAAGATTCACTACAGT-GAC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT---T---GTAG-C
* * * *
55429749 TTCAATTTGCTCTACTGCAACTTCAGAGAGATAAGATTTGTTATC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TAGC
* * * *
55429794 TTCAATCTACTCTACTACAACTTCAGGGAGATAAGATTTGTAAC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
* * ** * ** **
55429838 TTCAATTTGTTGTACTGCAACTTTAGAAAGATAAGATTTGTTATT
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TAGC
*
55429883 TTCAATTTGCTCCACTGCAAC
1 TTCAATCTGCTCCACTGCAAC
55429904 CTAAAGGAGA
Statistics
Matches: 705, Mismatches: 142, Indels: 81
0.76 0.15 0.09
Matches are distributed among these distances:
43 6 0.01
44 361 0.51
45 200 0.28
46 2 0.00
47 5 0.01
49 22 0.03
50 58 0.08
51 47 0.07
52 4 0.01
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (44 bp):
TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
Found at i:55429217 original size:133 final size:133
Alignment explanation
Indices: 55428972--55429903 Score: 730
Period size: 133 Copynumber: 6.8 Consensus size: 133
55428962 GAAATGTAAT
* * * * * *
55428972 TTCAACCTACTCCACTGCAACTTTAGGGAGATAAGATTTGTAGCTTTAATCTGCTCCACTGTAAC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTTGTAGCTTCAATCTGCTCCACTGCAAC
* * ** * *
55429037 TTCAGGGAGATAAGATTTGTAGCTTCAATCAGGTTTACTGTAGCTTCAGAGAGATAAGATTTGCT
66 TTCAGGGAGATAAGATTTGTAGCTTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTTGCT
55429102 ATC
131 ATC
* * *
55429105 TTCAATTTGCTCCACTGTAACTTCAGGGAAATAAGATTTGTAGCTTCAATCTGCTCCACTACAAC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTTGTAGCTTCAATCTGCTCCACTGCAAC
* * * * *
55429170 TTTAGGGAGATGAGATTTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATGAGATTCGCT
66 TTCAGGGAGATAAGATTTGTAGCTTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTTGCT
55429235 ATC
131 ATC
** * *
55429238 TTCAATCTATTCCACCGCAACTTCA-GGAAGATAAGATTTGTAGC-TCTAACCTGCTCCACTGCA
1 TTCAATCTGCTCCACTGCAACTTCAGGGAA-ATAAGATTTGTAGCTTC-AATCTGCTCCACTGCA
* * * * * * *
55429301 ACTTCAGGGAGATGAGATTTGTAACTTGCAGCTTTAATCTGTTCCACTACAACTTCGGGGAAATA
64 ACTTCAGGGAGATAAGATTTG-----T--AGCTTCAATCTGCTCCACTGCAACTTCAGAGAGATA
* *
55429366 ATATTTTCTATC
122 AGATTTGCTATC
* * * ** * *
55429378 TTCAATCTGCTCCATTGCAACTTCAGGGAAATAAGATTCGCATATTCAATCTGCTCCATTGTAAC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTTGTAGCTTCAATCTGCTCCACTGCAAC
* * * ** * *
55429443 TTCAGAGAGATAAGGTTTGTAACTTGTAGCTTTAATCTATTCCCCTGC-ACTTCA-AGGAAATAA
66 TTCAGGGAGATAA-----G--ATTTGTAGCTTCAATCTGCTCCACTGCAACTTCAGA-GAGATAA
* **
55429506 GACTCATTACGGTAGA
123 GA-T--TT--GCTATC
* * * * * * * *
55429522 TTTAATCTGAC-CCACTGCAACTTCAGAGG-TATATGATTTATCGCTTCAATCTACTCTACTGTA
1 TTCAATCTG-CTCCACTGCAACTTCAG-GGAAATAAGATTTGTAGCTTCAATCTGCTCCACTGCA
* * * *
55429585 ACTTCAGGGAGATAAGATTTGCTATCTTCAATCTGTTCCACTGCAACTTCAGGGAGAAAAGATTT
64 ACTTCAGGGAGATAAGATTTG-TAGCTTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTT
*
55429650 G-TAAC
128 GCTATC
* * *
55429655 TTCAATCTGCTCCACTGCAACTTCA-GGAAGATAAGATTTATGGCTTTAATCTGCTCCACTGCAA
1 TTCAATCTGCTCCACTGCAACTTCAGGGAA-ATAAGATTTGTAGCTTCAATCTGCTCCACTGCAA
* * *
55429719 CTTCAGGGGGATAAGATTCACTACAGT-GACTTCAATTTGCTCTACTGCAACTTCAGAGAGATAA
65 CTTCAGGGAGATAAGATT---T---GTAG-CTTCAATCTGCTCCACTGCAACTTCAGAGAGATAA
*
55429783 GATTTGTTATC
123 GATTTGCTATC
* * * * * * * **
55429794 TTCAATCTACTCTACTACAACTTCAGGGAGATAAGATTTGTAACTTCAATTTGTTGTACTGCAAC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTTGTAGCTTCAATCTGCTCCACTGCAAC
* ** ** *
55429859 TTTAGAAAGATAAGATTTGTTATTTTCAATTTGCTCCACTGCAAC
66 TTCAGGGAGATAAGATTTG-TAGCTTCAATCTGCTCCACTGCAAC
55429904 CTAAAGGAGA
Statistics
Matches: 636, Mismatches: 120, Indels: 85
0.76 0.14 0.10
Matches are distributed among these distances:
131 2 0.00
132 7 0.01
133 251 0.39
134 22 0.03
136 4 0.01
137 4 0.01
138 57 0.09
139 93 0.15
140 118 0.19
141 6 0.01
142 3 0.00
144 61 0.10
145 4 0.01
147 4 0.01
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (133 bp):
TTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTTGTAGCTTCAATCTGCTCCACTGCAAC
TTCAGGGAGATAAGATTTGTAGCTTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTTGCT
ATC
Found at i:55429914 original size:89 final size:89
Alignment explanation
Indices: 55428972--55429903 Score: 554
Period size: 89 Copynumber: 10.2 Consensus size: 89
55428962 GAAATGTAAT
* * * * * * * *
55428972 TTCAACCTACTCCACTGCAACTTTAGGGAGATAAGATTTGTAGCTTTAATCTGCTCCACTGTAAC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTCAATTTGCTCTACTGCAAC
** *
55429037 TTCAGGGAGATAAGATTTG-TAGC
66 TTCAGAAAGATAAGATTTGTTATC
* * ** * * * * * *
55429060 TTCAATCAGGTTTACTGTAGCTTCAGAGAGATAAGATTTGCTATCTTCAATTTGCTCCACTGTAA
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TAACTTCAATTTGCTCTACTGCAA
* *
55429125 CTTCAGGGAA-ATAAGATTTG-TAGC
65 CTTCA-GAAAGATAAGATTTGTTATC
* * * * * *
55429149 TTCAATCTGCTCCACTACAACTTTAGGGAGATGAGATTTGTAGCTTCAATCTGCTCCACTGCAAC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTCAATTTGCTCTACTGCAAC
** * * *
55429214 TTCAGGGAGATGAGATTCGCTATC
66 TTCAGAAAGATAAGATTTGTTATC
** * * * ** *
55429238 TTCAATCTATTCCACCGCAACTTCAGGAAGATAAGATTTGTAGC-TCTAACCTGCTCCACTGCAA
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTC-AATTTGCTCTACTGCAA
** * *
55429302 CTTCAGGGAGATGAGATTTGTAACTTGCAGC
65 CTTCAGAAAGATAAGATTTG----TT--ATC
* * * * * * * * * * *
55429333 TTTAATCTGTTCCACTACAACTTCGGGGAAATAATATTTTCTATCTTCAATCTGCTCCATTGCAA
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTTGTAACTTCAATTTGCTCTACTGCAA
* * * *
55429398 CTTCAGGGAA-ATAAGATTCG-CATA
65 CTTCA-GAAAGATAAGATTTGTTATC
* * * * * * **
55429422 TTCAATCTGCTCCATTGTAACTTCAGAGAGATAAGGTTTGTAACTTGTAGCTTTAATCTATTCCC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTT-CA-ATTTGCTCTA-----
* * **
55429487 CTGC-ACTTCAAGGAA-ATAAGACTCATTACGGTAGA
59 CTGCAACTTC-AGAAAGATAAGA-T--TT--GTTATC
* * * * ** * * *
55429522 TTTAATCTGAC-CCACTGCAACTTCAGAGG-TATATGATTTATCGCTTCAATCTACTCTACTGTA
1 TTCAATCTG-CTCCACTGCAACTTCAG-GGAGATAAGATTTGTAACTTCAATTTGCTCTACTGCA
** *
55429585 ACTTCAGGGAGATAAGATTTGCTATC
64 ACTTCAGAAAGATAAGATTTGTTATC
* * * *
55429611 TTCAATCTGTTCCACTGCAACTTCAGGGAGAAAAGATTTGTAACTTCAATCTGCTCCACTGCAAC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTCAATTTGCTCTACTGCAAC
* * **
55429676 TTCAGGAAGATAAGATTT-ATGGC
66 TTCAGAAAGATAAGATTTGTTATC
* * *
55429699 TTTAATCTGCTCCACTGCAACTTCAGGGGGATAAGATTCACTACAGTGACTTCAATTTGCTCTAC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT---T---GTAACTTCAATTTGCTCTAC
*
55429764 TGCAACTTCAGAGAGATAAGATTTGTTATC
60 TGCAACTTCAGAAAGATAAGATTTGTTATC
* * * * *
55429794 TTCAATCTACTCTACTACAACTTCAGGGAGATAAGATTTGTAACTTCAATTTGTTGTACTGCAAC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTCAATTTGCTCTACTGCAAC
* *
55429859 TTTAGAAAGATAAGATTTGTTATT
66 TTCAGAAAGATAAGATTTGTTATC
*
55429883 TTCAATTTGCTCCACTGCAAC
1 TTCAATCTGCTCCACTGCAAC
55429904 CTAAAGGAGA
Statistics
Matches: 660, Mismatches: 143, Indels: 81
0.75 0.16 0.09
Matches are distributed among these distances:
87 3 0.00
88 112 0.17
89 304 0.46
90 8 0.01
91 3 0.00
92 1 0.00
93 9 0.01
94 65 0.10
95 70 0.11
96 34 0.05
97 6 0.01
98 7 0.01
99 2 0.00
100 34 0.05
101 2 0.00
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (89 bp):
TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTCAATTTGCTCTACTGCAAC
TTCAGAAAGATAAGATTTGTTATC
Found at i:55438713 original size:17 final size:17
Alignment explanation
Indices: 55438691--55438723 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
55438681 ATGAAGAAAT
*
55438691 ATTATAATAATAACATA
1 ATTATAACAATAACATA
55438708 ATTATAACAATAACAT
1 ATTATAACAATAACAT
55438724 TGACATTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (17 bp):
ATTATAACAATAACATA
Found at i:55447886 original size:17 final size:16
Alignment explanation
Indices: 55447813--55447892 Score: 56
Period size: 17 Copynumber: 4.9 Consensus size: 16
55447803 ATAAAAATAT
*
55447813 TTTTAAA-AATTATAT
1 TTTTAAATAATTATAA
* * *
55447828 TTTTAATTAATAAAAA
1 TTTTAAATAATTATAA
55447844 TTTTAAATAAATTTATAA
1 TTTTAAAT-AA-TTATAA
** *
55447862 AATAAAATATATTATAA
1 TTTTAAATA-ATTATAA
55447879 TTTTAAAT-ATTATA
1 TTTTAAATAATTATA
55447893 TATATATGAA
Statistics
Matches: 48, Mismatches: 13, Indels: 8
0.70 0.19 0.12
Matches are distributed among these distances:
15 12 0.25
16 12 0.25
17 14 0.29
18 10 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTTAAATAATTATAA
Found at i:55449753 original size:2 final size:2
Alignment explanation
Indices: 55449746--55449777 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
55449736 TGTTTCAAAC
55449746 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55449778 GGTTCAGATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55454753 original size:13 final size:14
Alignment explanation
Indices: 55454734--55454772 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
55454724 ATCCCACCTC
55454734 AAATACAGATACAG
1 AAATACAGATACAG
*
55454748 -AATACAGAAACAG
1 AAATACAGATACAG
55454761 AAATAACAGATA
1 AAAT-ACAGATA
55454773 TAACATGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
13 12 0.57
14 3 0.14
15 6 0.29
ACGTcount: A:0.62, C:0.13, G:0.13, T:0.13
Consensus pattern (14 bp):
AAATACAGATACAG
Found at i:55459057 original size:20 final size:20
Alignment explanation
Indices: 55459032--55459084 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
55459022 TATTTTGTAA
55459032 AAAGTATAGATACT-TGGTGC
1 AAAGTATAGATACTCT-GTGC
*
55459052 AAAGTATCGATACTCTGTGC
1 AAAGTATAGATACTCTGTGC
55459072 AAAGTATAGATAC
1 AAAGTATAGATAC
55459085 CTTGACCTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (20 bp):
AAAGTATAGATACTCTGTGC
Found at i:55462525 original size:27 final size:28
Alignment explanation
Indices: 55462471--55462535 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 28
55462461 ATAAAAAATA
*
55462471 ACCAAAATAGTATAACTTTTTTTTATTT
1 ACCAAAATATTATAACTTTTTTTTATTT
55462499 ACCAAAATATTATAA-TTTTTTTTATTT
1 ACCAAAATATTATAACTTTTTTTTATTT
55462526 ACCAAAATAT
1 ACCAAAATAT
55462536 ACAAAAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 22 0.61
28 14 0.39
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.48
Consensus pattern (28 bp):
ACCAAAATATTATAACTTTTTTTTATTT
Found at i:55462971 original size:19 final size:19
Alignment explanation
Indices: 55462947--55463012 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
55462937 ATTAAAATAG
55462947 TTTAATTTAATAACTCTAT
1 TTTAATTTAATAACTCTAT
* *
55462966 TTTAATGTAATAA-ACTAT
1 TTTAATTTAATAACTCTAT
* *
55462984 TCTCATTTAATAACTCTAT
1 TTTAATTTAATAACTCTAT
55463003 TTTAATTTAA
1 TTTAATTTAA
55463013 AAAAATTAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
18 14 0.37
19 24 0.63
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.50
Consensus pattern (19 bp):
TTTAATTTAATAACTCTAT
Found at i:55463438 original size:26 final size:27
Alignment explanation
Indices: 55463391--55463455 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 27
55463381 TGTTTTTTGG
* **
55463391 TATATTTTGATAAAT-ATGAAAA-TTAA
1 TATATTTTGGTAAATAAAAAAAAGTT-A
55463417 TATATTTTGGTAAATAAAAAAAAGTTA
1 TATATTTTGGTAAATAAAAAAAAGTTA
55463444 TAATATTTTGGT
1 T-ATATTTTGGT
55463456 TATTTTTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 14 0.42
27 7 0.21
28 12 0.36
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (27 bp):
TATATTTTGGTAAATAAAAAAAAGTTA
Found at i:55465490 original size:19 final size:18
Alignment explanation
Indices: 55465457--55465493 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
55465447 TCCGGGATTT
*
55465457 AGAAACATATAAATTACA
1 AGAAAAATATAAATTACA
55465475 AGAAAAATACTAAATTACA
1 AGAAAAATA-TAAATTACA
55465494 CTAACCAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.62, C:0.11, G:0.05, T:0.22
Consensus pattern (18 bp):
AGAAAAATATAAATTACA
Found at i:55470044 original size:18 final size:20
Alignment explanation
Indices: 55470007--55470044 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
55469997 ACCAAATACA
55470007 TAAACATCAATCTGACATATT
1 TAAACATCAATC-GACATATT
55470028 TAAACAT-AATC-ACATAT
1 TAAACATCAATCGACATAT
55470045 ACTTCCCAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.35
20 4 0.24
21 7 0.41
ACGTcount: A:0.47, C:0.18, G:0.03, T:0.32
Consensus pattern (20 bp):
TAAACATCAATCGACATATT
Found at i:55470858 original size:27 final size:28
Alignment explanation
Indices: 55470782--55470862 Score: 101
Period size: 28 Copynumber: 2.9 Consensus size: 28
55470772 GGAATTTAGT
* *
55470782 TGAATCAAGTATAACACACATAAAGTAC
1 TGAATCAAATATAACACACATAAAGCAC
*
55470810 TGAATCAAATATAACACACATAAAGCAT
1 TGAATCAAATATAACACACATAAAGCAC
* * *
55470838 TGGATC-CATATAACACGCATAAAGC
1 TGAATCAAATATAACACACATAAAGC
55470863 GTTAGATCTC
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 17 0.36
28 30 0.64
ACGTcount: A:0.48, C:0.20, G:0.11, T:0.21
Consensus pattern (28 bp):
TGAATCAAATATAACACACATAAAGCAC
Found at i:55470870 original size:27 final size:27
Alignment explanation
Indices: 55470791--55470870 Score: 81
Period size: 27 Copynumber: 2.9 Consensus size: 27
55470781 TTGAATCAAG
* * *
55470791 TATAACACACATAAAGTACT-GAATCAAA
1 TATAACACACATAAAGCATTAG-ATC-CA
*
55470819 TATAACACACATAAAGCATTGGATCCA
1 TATAACACACATAAAGCATTAGATCCA
* *
55470846 TATAACACGCATAAAGCGTTAGATC
1 TATAACACACATAAAGCATTAGATC
55470871 TCCCGCCTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
27 23 0.51
28 21 0.47
29 1 0.02
ACGTcount: A:0.46, C:0.20, G:0.11, T:0.23
Consensus pattern (27 bp):
TATAACACACATAAAGCATTAGATCCA
Found at i:55472454 original size:21 final size:22
Alignment explanation
Indices: 55472428--55472473 Score: 76
Period size: 23 Copynumber: 2.1 Consensus size: 22
55472418 AATCTATATA
55472428 TATACATGT-ATATTTATTTTT
1 TATACATGTAATATTTATTTTT
55472449 TATACATGTACATATTTATTTTT
1 TATACATGTA-ATATTTATTTTT
55472472 TA
1 TA
55472474 ACTAATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 9 0.39
23 14 0.61
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.59
Consensus pattern (22 bp):
TATACATGTAATATTTATTTTT
Found at i:55472948 original size:19 final size:20
Alignment explanation
Indices: 55472907--55472948 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
55472897 ATTTCTATGC
* *
55472907 CATTGTAATATTTATTATTG
1 CATTGTAATATTTAATATAG
*
55472927 CATTGT-ATATTTAATGTAG
1 CATTGTAATATTTAATATAG
55472946 CAT
1 CAT
55472949 CACATCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (20 bp):
CATTGTAATATTTAATATAG
Found at i:55477650 original size:11 final size:11
Alignment explanation
Indices: 55477591--55477653 Score: 53
Period size: 11 Copynumber: 5.8 Consensus size: 11
55477581 ATATATACTA
*
55477591 AATAAAATAAT
1 AATAAAATATT
55477602 AAT-AAA-A-T
1 AATAAAATATT
55477610 AATAAAATATT
1 AATAAAATATT
*
55477621 ATTTAAAA-ATT
1 A-ATAAAATATT
55477632 AAATTAAAATATT
1 -AA-TAAAATATT
55477645 AATAAAATA
1 AATAAAATA
55477654 ATATTTATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 14
0.73 0.03 0.24
Matches are distributed among these distances:
8 4 0.09
9 4 0.09
10 4 0.09
11 15 0.35
12 13 0.30
13 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AATAAAATATT
Found at i:55478129 original size:23 final size:23
Alignment explanation
Indices: 55478103--55478147 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
55478093 TTTCTTATTG
55478103 TAGTAATTTTCGAGG-TATTACAA
1 TAGTAATTTTCG-GGATATTACAA
55478126 TAGTAATTTTCGGGATATTACA
1 TAGTAATTTTCGGGATATTACA
55478148 CGTATACATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 2 0.10
23 19 0.90
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (23 bp):
TAGTAATTTTCGGGATATTACAA
Found at i:55492168 original size:30 final size:30
Alignment explanation
Indices: 55492132--55492222 Score: 121
Period size: 30 Copynumber: 3.0 Consensus size: 30
55492122 GGTGAATTAA
55492132 GTTGCTCACACAAGCTAACATTATATCAGG
1 GTTGCTCACACAAGCTAACATTATATCAGG
* *
55492162 GTTGCTCACACAAACTAACATTATATCAAG
1 GTTGCTCACACAAGCTAACATTATATCAGG
* *
55492192 GTTGTTCACATAAGCTTAA-ATTTATATCAGG
1 GTTGCTCACACAAGC-TAACA-TTATATCAGG
55492223 TTACCCATCT
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
30 41 0.77
31 12 0.23
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (30 bp):
GTTGCTCACACAAGCTAACATTATATCAGG
Found at i:55492785 original size:21 final size:19
Alignment explanation
Indices: 55492748--55492789 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
55492738 TTTTCACCTC
*
55492748 AATATTAAATCATGCAATT
1 AATATTAAATCAGGCAATT
55492767 AATATATAAATGCAGGCAATT
1 AATAT-TAAAT-CAGGCAATT
55492788 AA
1 AA
55492790 ATCTATCTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 5 0.25
21 10 0.50
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.31
Consensus pattern (19 bp):
AATATTAAATCAGGCAATT
Found at i:55494832 original size:82 final size:80
Alignment explanation
Indices: 55494694--55494924 Score: 275
Period size: 82 Copynumber: 2.8 Consensus size: 80
55494684 GGAGAAGTAG
** * * * *
55494694 GTTCAAATATTGAGGACTACATTGTTGGGAGGGGCAGCCATAATTCCTAAACATAGATCGTAAAA
1 GTTCAAACCTTGAGGACGATATTGTT-GGAAGGGCAGCCATAA-TCCTGAACATAGATCGTAAAA
*
55494759 TGGACACAGAGACGTAA
64 TGGACACAAAGACGTAA
* *
55494776 GTTCAAACCTTGAGGATGATATTGTTGGAAGAGGCAACCATGAATCCTGAACATAGATCGTAAAA
1 GTTCAAACCTTGAGGACGATATTGTTGGAAG-GGCAGCCAT-AATCCTGAACATAGATCGTAAAA
*
55494841 TAGACACAAAGACGTAA
64 TGGACACAAAGACGTAA
* * *
55494858 GTTCAAACCTTGAGGACGATATTGTTAGAAGGAGCAGCCATAAAT-CTCGAACATAAAGCGTAAA
1 GTTCAAACCTTGAGGACGATATTGTTGGAAGG-GCAGCCAT-AATCCT-GAACATAGATCGTAAA
55494922 ATG
63 ATG
55494925 AATATGAAGA
Statistics
Matches: 128, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
81 7 0.05
82 119 0.93
83 2 0.02
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.23
Consensus pattern (80 bp):
GTTCAAACCTTGAGGACGATATTGTTGGAAGGGCAGCCATAATCCTGAACATAGATCGTAAAATG
GACACAAAGACGTAA
Found at i:55498407 original size:24 final size:24
Alignment explanation
Indices: 55498379--55498427 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
55498369 CTTAGAACCT
55498379 TAGGTCAGCTTTGTTAGAGAGTGA
1 TAGGTCAGCTTTGTTAGAGAGTGA
55498403 TAGGTCAGCTTTGTTAGAGAGTGA
1 TAGGTCAGCTTTGTTAGAGAGTGA
55498427 T
1 T
55498428 CCCACATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.08, G:0.33, T:0.35
Consensus pattern (24 bp):
TAGGTCAGCTTTGTTAGAGAGTGA
Found at i:55503706 original size:5 final size:5
Alignment explanation
Indices: 55503696--55503766 Score: 67
Period size: 5 Copynumber: 14.0 Consensus size: 5
55503686 TTTGGAAAGT
*
55503696 TTTAA TTTAA TTTAA TTTAA TTT-T TTTATA TTTTAA TTTAA TTATAA
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTA-A -TTTAA TTTAA TT-TAA
*
55503743 --TAT TTTAA TTTAA TTATAA TTTAA
1 TTTAA TTTAA TTTAA TT-TAA TTTAA
55503767 AAATGTCACA
Statistics
Matches: 55, Mismatches: 4, Indels: 14
0.75 0.05 0.19
Matches are distributed among these distances:
3 2 0.04
4 3 0.05
5 37 0.67
6 9 0.16
7 4 0.07
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTTAA
Found at i:55503747 original size:19 final size:19
Alignment explanation
Indices: 55503723--55503762 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
55503713 TAATTTTTTT
55503723 ATATTTTAATTTAATTATA
1 ATATTTTAATTTAATTATA
55503742 ATATTTTAATTTAATTATA
1 ATATTTTAATTTAATTATA
55503761 AT
1 AT
55503763 TTAAAAATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATATTTTAATTTAATTATA
Found at i:55511495 original size:31 final size:31
Alignment explanation
Indices: 55511435--55511495 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
55511425 ATTATGCACG
*
55511435 TAAAACTTTAATTGTGATTCAAACCTATACT
1 TAAAACTTTAATTGTGATTCAAACATATACT
* * * *
55511466 TAAAATTTTAATTTTGATTTAATCATATAC
1 TAAAACTTTAATTGTGATTCAAACATATAC
55511496 ATTTAAAGAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.39, C:0.11, G:0.05, T:0.44
Consensus pattern (31 bp):
TAAAACTTTAATTGTGATTCAAACATATACT
Found at i:55511672 original size:29 final size:30
Alignment explanation
Indices: 55511619--55511675 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
55511609 TAATTTGATC
* * *
55511619 AAATTAAAATTTATTGTATAGAATTACACA
1 AAATCAAAATTTATTATATACAATTACACA
55511649 AAATCAAAATTTA-TATATACAATTACA
1 AAATCAAAATTTATTATATACAATTACA
55511676 TATTAAACCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 12 0.50
30 12 0.50
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.35
Consensus pattern (30 bp):
AAATCAAAATTTATTATATACAATTACACA
Found at i:55512557 original size:15 final size:15
Alignment explanation
Indices: 55512536--55512576 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
55512526 TATTTTGTTC
55512536 AAAATTTTA-GTATT
1 AAAATTTTATGTATT
55512550 ACAAA-TTTATGTATT
1 A-AAATTTTATGTATT
55512565 AATAATTTTATG
1 AA-AATTTTATG
55512577 CTGTAACAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 6 0.26
15 11 0.48
16 6 0.26
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (15 bp):
AAAATTTTATGTATT
Found at i:55513226 original size:3 final size:3
Alignment explanation
Indices: 55513218--55513244 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
55513208 TCCTAAAATT
55513218 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
55513245 AGGATAATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:55521532 original size:25 final size:25
Alignment explanation
Indices: 55521478--55521600 Score: 74
Period size: 25 Copynumber: 4.9 Consensus size: 25
55521468 ATGTAAACGA
** *
55521478 GAAGCTCTTTCGAGCCATATAAT-AG
1 GAAGCTCTTGAGAGCCAAAT-ATCAG
* *
55521503 AAAGCTCTTGCGAGCCAAATATCAG
1 GAAGCTCTTGAGAGCCAAATATCAG
* * *
55521528 GAAGCT-TAAGAGAGCC-ATTAACCAG
1 GAAGCTCT-TGAGAGCCAAAT-ATCAG
* * *
55521553 GAAGCTCATGGGAGCCAATTATCAG
1 GAAGCTCTTGAGAGCCAAATATCAG
*
55521578 GAAGCT-TGTGAGAGCCAAGTATC
1 GAAGCTCT-TGAGAGCCAAATATC
55521601 GAGAAGATCA
Statistics
Matches: 77, Mismatches: 15, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
24 5 0.06
25 69 0.90
26 3 0.04
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.21
Consensus pattern (25 bp):
GAAGCTCTTGAGAGCCAAATATCAG
Found at i:55527716 original size:82 final size:82
Alignment explanation
Indices: 55527579--55527742 Score: 328
Period size: 82 Copynumber: 2.0 Consensus size: 82
55527569 GCTAGGGCTT
55527579 TTCTTGAGGGCGACAAGATGTAGTCGCCAATGAGTTTTGGTGGGAGTTTTATGGTAAAAGAGTAT
1 TTCTTGAGGGCGACAAGATGTAGTCGCCAATGAGTTTTGGTGGGAGTTTTATGGTAAAAGAGTAT
55527644 TTTATATTCTTTTTGTG
66 TTTATATTCTTTTTGTG
55527661 TTCTTGAGGGCGACAAGATGTAGTCGCCAATGAGTTTTGGTGGGAGTTTTATGGTAAAAGAGTAT
1 TTCTTGAGGGCGACAAGATGTAGTCGCCAATGAGTTTTGGTGGGAGTTTTATGGTAAAAGAGTAT
55527726 TTTATATTCTTTTTGTG
66 TTTATATTCTTTTTGTG
55527743 AGTGCTCTAT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 82 1.00
ACGTcount: A:0.23, C:0.09, G:0.28, T:0.40
Consensus pattern (82 bp):
TTCTTGAGGGCGACAAGATGTAGTCGCCAATGAGTTTTGGTGGGAGTTTTATGGTAAAAGAGTAT
TTTATATTCTTTTTGTG
Found at i:55529421 original size:2 final size:2
Alignment explanation
Indices: 55529414--55529441 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
55529404 TGCATACGGA
55529414 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55529442 TGATGTTCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55531894 original size:4 final size:4
Alignment explanation
Indices: 55531885--55531923 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
55531875 AAGAGCTGAT
* * *
55531885 AGAA AGAA AGCA AGAA TGAA AGAT AGAA AGAA AGAA AGA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGA
55531924 GAGGAGAGTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.67, C:0.03, G:0.26, T:0.05
Consensus pattern (4 bp):
AGAA
Found at i:55532698 original size:12 final size:11
Alignment explanation
Indices: 55532668--55532701 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
55532658 TCTATTAAGC
55532668 TTTTTATTTAA
1 TTTTTATTTAA
*
55532679 TATTTATTTATA
1 TTTTTATTTA-A
55532691 TTTTTATTTAA
1 TTTTTATTTAA
55532702 AAATAGTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTTTATTTAA
Found at i:55533671 original size:13 final size:14
Alignment explanation
Indices: 55533653--55533681 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
55533643 TCAATAATAA
55533653 AAAATAAAAT-ACC
1 AAAATAAAATAACC
55533666 AAAATAAAATAACC
1 AAAATAAAATAACC
55533680 AA
1 AA
55533682 GAAATCCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.72, C:0.14, G:0.00, T:0.14
Consensus pattern (14 bp):
AAAATAAAATAACC
Found at i:55535226 original size:16 final size:17
Alignment explanation
Indices: 55535198--55535232 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
55535188 TTATGTTAAG
55535198 TATTTTCATGTTATAAA
1 TATTTTCATGTTATAAA
55535215 TATTTT-ATGTTATAAA
1 TATTTTCATGTTATAAA
55535231 TA
1 TA
55535233 GGTGAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.37, C:0.03, G:0.06, T:0.54
Consensus pattern (17 bp):
TATTTTCATGTTATAAA
Found at i:55543294 original size:19 final size:17
Alignment explanation
Indices: 55543250--55543298 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
55543240 GTGTCGTTCG
*
55543250 TTTCCAAAACATTATTCA
1 TTTCC-AAACGTTATTCA
*
55543268 TTTACAAATCGTTATTCAA
1 TTTCCAAA-CGTTATTC-A
55543287 TTTCCAAACGTT
1 TTTCCAAACGTT
55543299 TTTTATTGCG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 3 0.12
18 15 0.58
19 8 0.31
ACGTcount: A:0.35, C:0.20, G:0.04, T:0.41
Consensus pattern (17 bp):
TTTCCAAACGTTATTCA
Found at i:55544273 original size:17 final size:18
Alignment explanation
Indices: 55544237--55544273 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
55544227 CCATGATGTT
*
55544237 TGCCCGTGTAGGCCCGCA
1 TGCCCGTGTAGGCCCACA
55544255 TGCCCGTGT-GGCCCACA
1 TGCCCGTGTAGGCCCACA
55544272 TG
1 TG
55544274 GCTGTAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.11, C:0.38, G:0.32, T:0.19
Consensus pattern (18 bp):
TGCCCGTGTAGGCCCACA
Found at i:55559424 original size:51 final size:51
Alignment explanation
Indices: 55559348--55559536 Score: 231
Period size: 51 Copynumber: 3.7 Consensus size: 51
55559338 CATGAGAACT
* * * **
55559348 CATGTGTAGTACTATGTGTAGGCTACTATGAGTATAAGATAGTTATGGTCA
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGTTATGGTCA
55559399 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGCTT-TGGTCA
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAG-TTATGGTCA
* * * *
55559450 -AGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAT-GGTATTGGTCA
1 CA-TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGTTA-TGGTCA
* *
55559501 CGTGTGTAGTACTAAGTGTAGGCTACTATGTGTACC
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACC
55559537 GAATAGCATT
Statistics
Matches: 120, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
49 1 0.01
50 2 0.02
51 115 0.96
52 2 0.02
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.33
Consensus pattern (51 bp):
CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGTTATGGTCA
Found at i:55559543 original size:102 final size:102
Alignment explanation
Indices: 55559350--55559536 Score: 277
Period size: 102 Copynumber: 1.8 Consensus size: 102
55559340 TGAGAACTCA
* * *
55559350 TGTGTAGTACTATGTGTAGGCTACTATGAGTATAAGATAGTTATGGTCACATGTGTAGTACTAAG
1 TGTGTAGTACTATGTGCAGGCTACTACGAGTACAAGATAGTTATGGTCACATGTGTAGTACTAAG
55559415 TGCAGGCTACTATGTGTACCAGATAGCTTTGGTCAAG
66 TGCAGGCTACTATGTGTACCAGATAGCTTTGGTCAAG
* ** * *
55559452 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAT-GGTATTGGTCACGTGTGTAGTACTAA
1 TGTGTAGTACTATGTGCAGGCTACTACGAGTACAAGATAGTTA-TGGTCACATGTGTAGTACTAA
*
55559516 GTGTAGGCTACTATGTGTACC
65 GTGCAGGCTACTATGTGTACC
55559537 GAATAGCATT
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
101 3 0.04
102 72 0.96
ACGTcount: A:0.25, C:0.14, G:0.28, T:0.33
Consensus pattern (102 bp):
TGTGTAGTACTATGTGCAGGCTACTACGAGTACAAGATAGTTATGGTCACATGTGTAGTACTAAG
TGCAGGCTACTATGTGTACCAGATAGCTTTGGTCAAG
Found at i:55559564 original size:51 final size:50
Alignment explanation
Indices: 55559404--55559570 Score: 160
Period size: 51 Copynumber: 3.3 Consensus size: 50
55559394 GGTCACATGT
*
55559404 GTAGTACTAAGTGCAGGCTACTATGTGTACC-AGATAGCTTTGGTC-AAGTG
1 GTAGTACTAAGTGCAGGCTACTATGTGTACCGA-ATAGCATTGGTCAAAG-G
* * * * * *
55559454 TGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGGTATTGGTC-ACGTG
1 -GTAGTACTAAGTGCAGGCTACTATGTGTACCGAATAGCATTGGTCAAAG-G
* *
55559505 TGTAGTACTAAGTGTAGGCTACTATGTGTACCGAATAGCATTGATCATAAGG
1 -GTAGTACTAAGTGCAGGCTACTATGTGTACCGAATAGCATTGGTCA-AAGG
* *
55559557 GTGGTACTATGTGC
1 GTAGTACTAAGTGC
55559571 GGAACCACCG
Statistics
Matches: 95, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
51 92 0.97
52 1 0.01
53 2 0.02
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.31
Consensus pattern (50 bp):
GTAGTACTAAGTGCAGGCTACTATGTGTACCGAATAGCATTGGTCAAAGG
Found at i:55561921 original size:39 final size:39
Alignment explanation
Indices: 55561877--55562019 Score: 223
Period size: 39 Copynumber: 3.7 Consensus size: 39
55561867 CATATTCACT
*
55561877 TTTAAGCATATATCACATTACACATATAATCACATAACA
1 TTTAAGCATATATCACAATACACATATAATCACATAACA
* * *
55561916 TTTAAGCAAATATCACAATACTCATATAATCACATAAAA
1 TTTAAGCATATATCACAATACACATATAATCACATAACA
*
55561955 TTTAAGCATATATCACAATACTCATATAATCACATAACA
1 TTTAAGCATATATCACAATACACATATAATCACATAACA
* *
55561994 TTCAAGTATATATCACAATACACATA
1 TTTAAGCATATATCACAATACACATA
55562020 ACATGTTTAT
Statistics
Matches: 95, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 95 1.00
ACGTcount: A:0.48, C:0.20, G:0.03, T:0.30
Consensus pattern (39 bp):
TTTAAGCATATATCACAATACACATATAATCACATAACA
Found at i:55578706 original size:28 final size:30
Alignment explanation
Indices: 55578674--55578733 Score: 88
Period size: 28 Copynumber: 2.1 Consensus size: 30
55578664 TGGATATGAA
55578674 TGAAAAGTGGAACTTTAATGCAA-T-ACAG
1 TGAAAAGTGGAACTTTAATGCAACTGACAG
* *
55578702 TGAAAAGTGGCACTTTGATGCAACTGACAG
1 TGAAAAGTGGAACTTTAATGCAACTGACAG
55578732 TG
1 TG
55578734 GCACTATGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 21 0.75
29 1 0.04
30 6 0.21
ACGTcount: A:0.37, C:0.13, G:0.25, T:0.25
Consensus pattern (30 bp):
TGAAAAGTGGAACTTTAATGCAACTGACAG
Found at i:55580326 original size:3 final size:3
Alignment explanation
Indices: 55580318--55580382 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
55580308 CATTTAATTG
55580318 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
55580366 TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
55580383 AAAACTAGAT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:55584098 original size:22 final size:22
Alignment explanation
Indices: 55584073--55584115 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
55584063 ATAAGCTTCT
*
55584073 TTACATTCAATTAATAAATGTA
1 TTACATTCAATCAATAAATGTA
55584095 TTACATTCAATCAATAAATGT
1 TTACATTCAATCAATAAATGT
55584116 GAATTAAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.40
Consensus pattern (22 bp):
TTACATTCAATCAATAAATGTA
Found at i:55585418 original size:19 final size:19
Alignment explanation
Indices: 55585394--55585433 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
55585384 ACAATTGATT
55585394 TTACGTGAAATGGGAATTC
1 TTACGTGAAATGGGAATTC
*
55585413 TTACGTGAATTGGGAATTC
1 TTACGTGAAATGGGAATTC
55585432 TT
1 TT
55585434 TGTTGCCTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.28, C:0.10, G:0.25, T:0.38
Consensus pattern (19 bp):
TTACGTGAAATGGGAATTC
Found at i:55588302 original size:274 final size:274
Alignment explanation
Indices: 55587813--55588369 Score: 828
Period size: 274 Copynumber: 2.0 Consensus size: 274
55587803 TACTCAAAAA
* * *
55587813 TTGAGGGATGCTTTGTCCCTATTCCAGGACGAAGCTTATCAGTGGTGGTTGATAGTTGAGCAAGG
1 TTGAGGGATGCTTTGTCCCTATTCCAGGACGAAGCTTATCAGTGGTGGTTGACAGTTGAACAAAG
* * *
55587878 TGTTCAGCTTGAACAGGTGAACTGAGACTATTTCAAGAACACCTTCTAAGGTAAGTATGTGAGGG
66 TGTTCAGCCTGAACAGGTGAACTGAGACTATTTCAAGAACACATTCCAAGGTAAGTATGTGAGGG
* * * *
55587943 CAAATTATGTTGAGGCTCACCGATATGAGTTCATGAGCCTAGTTCAAGGCGACCGATCGGTGGCC
131 CAAATTATGTTGAAGCTCACCAATACGAGTTCATGAGCCTAGTTCAAGGCAACCGATCGGTGGCC
* * * * * *
55588008 AAATAGGAAGTCGAGTTTTTACGACTGAGTAGGTATGTATGGACTCTAGTAGCGTCTAATTATGA
196 AAATAGGAAGCCAAGTTTTTACAACTAAGTAGGTATGCATGGACTCTAGTAGCGTCTAATTACGA
*
55588073 AAAGTGTTTAAAGT
261 AAAGTGTGTAAAGT
* * * *
55588087 TTGAGGGGTGCTGTT-TCCTTATTTCGGGACGAAGCTTATCAGTGGTGGTTGACAGTTGAACAAA
1 TTGAGGGATGCT-TTGTCCCTATTCCAGGACGAAGCTTATCAGTGGTGGTTGACAGTTGAACAAA
* * *
55588151 GTGTTCATCCTGAACAGGTGAACTGGGACTATTTCAAGAACACATTCCAAGGTTAGTATGTGAGG
65 GTGTTCAGCCTGAACAGGTGAACTGAGACTATTTCAAGAACACATTCCAAGGTAAGTATGTGAGG
*
55588216 GCAAATTATGTTGAAGCTCACCAATACGAGTTCATGAGCCTAGTTCAGGGCAACCGATCGGTGGC
130 GCAAATTATGTTGAAGCTCACCAATACGAGTTCATGAGCCTAGTTCAAGGCAACCGATCGGTGGC
* *
55588281 CAAATATGAAGCCAAGTTTTTACAACTAAGTAGGTATGCATGGACTCTAGTAGCGTCTGATTACG
195 CAAATAGGAAGCCAAGTTTTTACAACTAAGTAGGTATGCATGGACTCTAGTAGCGTCTAATTACG
* * *
55588346 ATAAGTGTGTGAGGT
260 AAAAGTGTGTAAAGT
55588361 TTGAGGGAT
1 TTGAGGGAT
55588370 TAAGATATGA
Statistics
Matches: 251, Mismatches: 31, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
274 249 0.99
275 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.29
Consensus pattern (274 bp):
TTGAGGGATGCTTTGTCCCTATTCCAGGACGAAGCTTATCAGTGGTGGTTGACAGTTGAACAAAG
TGTTCAGCCTGAACAGGTGAACTGAGACTATTTCAAGAACACATTCCAAGGTAAGTATGTGAGGG
CAAATTATGTTGAAGCTCACCAATACGAGTTCATGAGCCTAGTTCAAGGCAACCGATCGGTGGCC
AAATAGGAAGCCAAGTTTTTACAACTAAGTAGGTATGCATGGACTCTAGTAGCGTCTAATTACGA
AAAGTGTGTAAAGT
Found at i:55596136 original size:30 final size:30
Alignment explanation
Indices: 55596100--55596164 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
55596090 GGAAATAAAC
55596100 CTTAAAATTC-AGAATTTTGGA-GGAAGAGGA
1 CTTAAAATTCGA-AATTTTGGAGGGAA-AGGA
55596130 CTTAAAATTCGAAATTTTGGAGGGAAAGGA
1 CTTAAAATTCGAAATTTTGGAGGGAAAGGA
55596160 -TTAAA
1 CTTAAA
55596165 TAGTAAAGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
29 5 0.15
30 23 0.70
31 5 0.15
ACGTcount: A:0.42, C:0.06, G:0.25, T:0.28
Consensus pattern (30 bp):
CTTAAAATTCGAAATTTTGGAGGGAAAGGA
Found at i:55601803 original size:22 final size:22
Alignment explanation
Indices: 55601778--55601820 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
55601768 ATAAGCTCCT
*
55601778 TTACATTCAATTAATAAATGTA
1 TTACATTCAATCAATAAATGTA
55601800 TTACATTCAATCAATAAATGT
1 TTACATTCAATCAATAAATGT
55601821 GAATTAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.40
Consensus pattern (22 bp):
TTACATTCAATCAATAAATGTA
Found at i:55604986 original size:3 final size:3
Alignment explanation
Indices: 55604978--55605009 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
55604968 CATTTAACTG
55604978 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
55605010 ACTAGATGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:55606940 original size:18 final size:18
Alignment explanation
Indices: 55606913--55606948 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
55606903 GCAAGATATC
*
55606913 CCAAATTAAAATCCAAAT
1 CCAAAATAAAATCCAAAT
55606931 CCAAAATAAAATCCAAAT
1 CCAAAATAAAATCCAAAT
55606949 GTCTAGAGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.22, G:0.00, T:0.19
Consensus pattern (18 bp):
CCAAAATAAAATCCAAAT
Found at i:55608710 original size:101 final size:102
Alignment explanation
Indices: 55608589--55608773 Score: 311
Period size: 101 Copynumber: 1.8 Consensus size: 102
55608579 AAAGTGATAG
* *
55608589 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCAGA-A-TGATAGGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCCACTACGTGTATCAGATAGTGAT-GGTCACATGTGTAGT
55608652 ACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
65 ACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
*
55608690 TCACGTGTGTAGTACTATGTGCAGGCCACTACGTGTATCGGATAGTGATGGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCCACTACGTGTATCAGATAGTGATGGTCACATGTGTAGTA
*
55608755 CTATGTGCATGCTACTATG
66 CTATGTGCAGGCTACTATG
55608774 TGAACCGGTA
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
101 40 0.51
102 34 0.44
103 4 0.05
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAGGCCACTACGTGTATCAGATAGTGATGGTCACATGTGTAGTA
CTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
Found at i:55608732 original size:51 final size:49
Alignment explanation
Indices: 55608588--55608771 Score: 208
Period size: 51 Copynumber: 3.7 Consensus size: 49
55608578 GAAAGTGATA
* * *
55608588 GTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCAGA-ATGATAG
1 GTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATA-G-TTG
* * * *
55608638 GTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCG
1 GTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAG-TT-G
* * *
55608689 ATCACGTGTGTAGTACTATGTGCAGGCCACTACGTGTATCGGATAGTGATG
1 GTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGT--TG
*
55608740 GTCACATGTGTAGTACTATGTGCATGCTACTA
1 GTCACATGTGTAGTACTATGTGCAGGCTACTA
55608772 TGTGAACCGG
Statistics
Matches: 111, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
50 40 0.36
51 70 0.63
52 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.30
Consensus pattern (49 bp):
GTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTTG
Found at i:55608775 original size:26 final size:26
Alignment explanation
Indices: 55608695--55608775 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 26
55608685 TTCGATCACG
* *
55608695 TGTGTAGTACTATGTGCAGGCCACTA
1 TGTGTAGTACTATGTGCATGCTACTA
* * *
55608721 CGTGTA-T-CGGATAGTG-ATGGTCAC-A
1 TGTGTAGTAC-TAT-GTGCATGCT-ACTA
55608746 TGTGTAGTACTATGTGCATGCTACTA
1 TGTGTAGTACTATGTGCATGCTACTA
55608772 TGTG
1 TGTG
55608776 AACCGGTATC
Statistics
Matches: 40, Mismatches: 8, Indels: 14
0.65 0.13 0.23
Matches are distributed among these distances:
24 1 0.03
25 16 0.40
26 22 0.55
27 1 0.03
ACGTcount: A:0.22, C:0.16, G:0.28, T:0.33
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCATGCTACTA
Found at i:55608812 original size:101 final size:100
Alignment explanation
Indices: 55608591--55608781 Score: 276
Period size: 102 Copynumber: 1.9 Consensus size: 100
55608581 AGTGATAGTC
* *
55608591 ACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCAGAATGATAGGTCGCATGTGTAGTACTA
1 ACGTGTGTA-TACTATGTGCAGGCCACTACGTGTATCAGAATGATAGGTCACATGTGTAGTACTA
* *
55608656 TGTGCAGGCTACTATGCGTACCGGATAGCTTCGATC
65 TGTGCAGGCTACTATGCGAACCGGATAGCTTCGATA
*
55608692 ACGTGTGTAGTACTATGTGCAGGCCACTACGTGTATCGGATAGTGAT-GGTCACATGTGTAGTAC
1 ACGTGTGTA-TACTATGTGCAGGCCACTACGTGTATCAGA-A-TGATAGGTCACATGTGTAGTAC
* *
55608756 TATGTGCATGCTACTATGTGAACCGG
63 TATGTGCAGGCTACTATGCGAACCGG
55608782 TATCATTAAT
Statistics
Matches: 82, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
101 38 0.46
102 40 0.49
103 4 0.05
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (100 bp):
ACGTGTGTATACTATGTGCAGGCCACTACGTGTATCAGAATGATAGGTCACATGTGTAGTACTAT
GTGCAGGCTACTATGCGAACCGGATAGCTTCGATA
Found at i:55608868 original size:46 final size:43
Alignment explanation
Indices: 55608777--55608861 Score: 116
Period size: 46 Copynumber: 1.9 Consensus size: 43
55608767 TACTATGTGA
*
55608777 ACCGGTATCATTAATTATAAGGTGGTTGCTATGTGCTGATCCC
1 ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCTGATCCC
* *
55608820 ACCGGATATCATTGATTACAAAGGGTGGTTGCTGTGTGCTGA
1 ACCGG-TATCATTAATTA-AAA-GGTGGTTGCTATGTGCTGA
55608862 ATCCACCATG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
43 5 0.14
44 11 0.31
45 2 0.06
46 18 0.50
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (43 bp):
ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCTGATCCC
Found at i:55609020 original size:16 final size:16
Alignment explanation
Indices: 55608999--55609030 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
55608989 TGATTGAAAG
*
55608999 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
55609015 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
55609031 CCAACAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:55613110 original size:91 final size:91
Alignment explanation
Indices: 55612952--55613209 Score: 464
Period size: 91 Copynumber: 2.8 Consensus size: 91
55612942 TTAAATGTAT
*
55612952 AAATTATATATCATTATTAAATTATATTTAATATTCATTATTTTAAATTATATAAATTCATATAA
1 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATATAA
55613017 GAAAATTTATTATCAAGAATTTTATG
66 GAAAATTTATTATCAAGAATTTTATG
*
55613043 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATAAAA
1 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATATAA
55613108 GAAAATTTATTATCAAGAATTTTATG
66 GAAAATTTATTATCAAGAATTTTATG
* * *
55613134 AAATTATATATTATTATTAAATTATATTT-ATAATAATTATTTTAAATTATACAAATTCATATAA
1 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATATAA
55613198 GAAAATTTATTA
66 GAAAATTTATTA
55613210 GTTATAATTG
Statistics
Matches: 161, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
90 44 0.27
91 117 0.73
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (91 bp):
AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATATAA
GAAAATTTATTATCAAGAATTTTATG
Found at i:55613155 original size:18 final size:17
Alignment explanation
Indices: 55613129--55613164 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
55613119 ATCAAGAATT
55613129 TTATGAAATTATATATTA
1 TTATGAAATTATAT-TTA
*
55613147 TTATTAAATTATATTTA
1 TTATGAAATTATATTTA
55613164 T
1 T
55613165 AATAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
TTATGAAATTATATTTA
Found at i:55613265 original size:16 final size:16
Alignment explanation
Indices: 55613246--55613305 Score: 66
Period size: 16 Copynumber: 3.4 Consensus size: 16
55613236 ATCATATATT
55613246 TTATTAAGAATATTGA
1 TTATTAAGAATATTGA
*
55613262 TTATTAAGAATTTTATTAAA
1 TTATTAAGAA---TATT-GA
55613282 TTATATAAGAATATTGA
1 TTAT-TAAGAATATTGA
55613299 TTATTAA
1 TTATTAA
55613306 AAATTTTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
16 13 0.35
17 5 0.14
18 4 0.11
19 4 0.11
20 5 0.14
21 6 0.16
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (16 bp):
TTATTAAGAATATTGA
Found at i:55613293 original size:37 final size:37
Alignment explanation
Indices: 55613246--55613325 Score: 144
Period size: 37 Copynumber: 2.2 Consensus size: 37
55613236 ATCATATATT
*
55613246 TTAT-TAAGAATATTGATTATTAAGAATTTTATTAAA
1 TTATATAAGAATATTGATTATTAAAAATTTTATTAAA
55613282 TTATATAAGAATATTGATTATTAAAAATTTTATTAAA
1 TTATATAAGAATATTGATTATTAAAAATTTTATTAAA
55613319 TTATATA
1 TTATATA
55613326 TTTTAATTAT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
36 4 0.10
37 38 0.90
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.47
Consensus pattern (37 bp):
TTATATAAGAATATTGATTATTAAAAATTTTATTAAA
Found at i:55613342 original size:16 final size:16
Alignment explanation
Indices: 55613321--55613362 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
55613311 TTATTAAATT
*
55613321 ATATATTTTAATTATA
1 ATATATTTTAATAATA
55613337 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
55613352 AT-TATGTTTAA
1 ATATAT-TTTAA
55613363 ATATGCTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:55613347 original size:15 final size:15
Alignment explanation
Indices: 55613312--55613353 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
55613302 TTAAAAATTT
*
55613312 TATTAAATTAT-ATA
1 TATTTAATTATAATA
55613326 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
55613340 TATTTAATAATAAT
1 TATTTAATTATAAT
55613354 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:55613597 original size:16 final size:16
Alignment explanation
Indices: 55613576--55613640 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
55613566 TTGATTTGCT
55613576 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
55613592 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
55613608 ATTACGTCTCTATTCC
1 ATTACGCCTCTATTCC
*
55613624 ATTACGCCTATATTCC
1 ATTACGCCTCTATTCC
55613640 A
1 A
55613641 ATACAGCGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.22, C:0.34, G:0.06, T:0.38
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:55624946 original size:27 final size:28
Alignment explanation
Indices: 55624918--55624971 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
55624908 AAATAGGATA
*
55624918 AAAT-AAATAATAA-GTTAATAATAATT
1 AAATAAAATAATAATGGTAATAATAATT
*
55624944 AAATAAAATAATAATGGTATTAATAATT
1 AAATAAAATAATAATGGTAATAATAATT
55624972 GGGGAAATAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 4 0.17
27 9 0.38
28 11 0.46
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (28 bp):
AAATAAAATAATAATGGTAATAATAATT
Found at i:55626201 original size:28 final size:27
Alignment explanation
Indices: 55626133--55626201 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 27
55626123 TATATATATA
* * *
55626133 ATATATACGTATAGGGGTTTTGTTATTT
1 ATATATA-ATATATGGGTTTTGGTATTT
*
55626161 ATATATAATATATGGGTTTTGGTGTTAT
1 ATATATAATATATGGGTTTTGGTATT-T
*
55626189 ATGTATAATATAT
1 ATATATAATATAT
55626202 TTACGTGGGT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 15 0.43
28 20 0.57
ACGTcount: A:0.30, C:0.01, G:0.19, T:0.49
Consensus pattern (27 bp):
ATATATAATATATGGGTTTTGGTATTT
Found at i:55626287 original size:29 final size:28
Alignment explanation
Indices: 55626230--55626297 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 28
55626220 CACATAGTAC
*
55626230 ATATATATGCGTGGTTTTGCTATACATA
1 ATATATATGCGTGGTTTTACTATACATA
* * *
55626258 ATATATATGTGTGGGTTTTATTATATATA
1 ATATATATGCGT-GGTTTTACTATACATA
*
55626287 ATAAATATGCG
1 ATATATATGCG
55626298 GTTATAGATT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 11 0.33
29 22 0.67
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (28 bp):
ATATATATGCGTGGTTTTACTATACATA
Found at i:55629889 original size:22 final size:22
Alignment explanation
Indices: 55629847--55629893 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
55629837 TTTTTGTAAA
55629847 AAGGATAAAGTGTTTAAAATGTT
1 AAGGATAAAGTG-TTAAAATGTT
55629870 AAGGACTAAAGTG-TAAAATGTT
1 AAGGA-TAAAGTGTTAAAATGTT
55629892 AA
1 AA
55629894 AATATTAGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 11 0.48
23 5 0.22
24 7 0.30
ACGTcount: A:0.47, C:0.02, G:0.21, T:0.30
Consensus pattern (22 bp):
AAGGATAAAGTGTTAAAATGTT
Found at i:55631736 original size:51 final size:51
Alignment explanation
Indices: 55631660--55631854 Score: 225
Period size: 51 Copynumber: 3.8 Consensus size: 51
55631650 CATGAGAACT
* * * **
55631660 CATGTGTAGTACTATGTGTAGGCTACTATGAGTATAAGATAGTTATGGTCA
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGTTATGGTCA
55631711 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGCTT-TGGTCA
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAG-TTATGGTCA
* * * * *
55631762 -AGTATGTAGTACTATGTGCAGGCTACTACGTGTACCGGAT-GGTATTGGTCA
1 CA-TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGTTA-TGGTCA
* * *
55631813 CGTGTGTAGTACTAAGTGTAGGCTACTATGTGTACCAAATAG
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAG
55631855 CATTGATCAT
Statistics
Matches: 121, Mismatches: 17, Indels: 11
0.81 0.11 0.07
Matches are distributed among these distances:
49 1 0.01
50 2 0.02
51 115 0.95
52 3 0.02
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (51 bp):
CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGTTATGGTCA
Found at i:55631840 original size:102 final size:102
Alignment explanation
Indices: 55631664--55631855 Score: 278
Period size: 102 Copynumber: 1.9 Consensus size: 102
55631654 AGAACTCATG
* * *
55631664 TGTAGTACTATGTGTAGGCTACTATGAGTATAAGATAGTTATGGTCACATGTGTAGTACTAAGTG
1 TGTAGTACTATGTGCAGGCTACTACGAGTACAAGATAGTTATGGTCACATGTGTAGTACTAAGTG
*
55631729 CAGGCTACTATGTGTACCAGATAGCTTTGGTCAAGTA
66 CAGGCTACTATGTGTACCAAATAGCTTTGGTCAAGTA
* ** * *
55631766 TGTAGTACTATGTGCAGGCTACTACGTGTACCGGAT-GGTATTGGTCACGTGTGTAGTACTAAGT
1 TGTAGTACTATGTGCAGGCTACTACGAGTACAAGATAGTTA-TGGTCACATGTGTAGTACTAAGT
*
55631830 GTAGGCTACTATGTGTACCAAATAGC
65 GCAGGCTACTATGTGTACCAAATAGC
55631856 ATTGATCATA
Statistics
Matches: 79, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
101 3 0.04
102 76 0.96
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.32
Consensus pattern (102 bp):
TGTAGTACTATGTGCAGGCTACTACGAGTACAAGATAGTTATGGTCACATGTGTAGTACTAAGTG
CAGGCTACTATGTGTACCAAATAGCTTTGGTCAAGTA
Found at i:55631876 original size:51 final size:50
Alignment explanation
Indices: 55631663--55631884 Score: 187
Period size: 51 Copynumber: 4.4 Consensus size: 50
55631653 GAGAACTCAT
* * * ** * *
55631663 GTGTAGTACTATGTGTAGGCTACTATGAGTATAAGATAG-TTATGGTCACAT
1 GTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGCAT-TGGTCA-AA
*
55631714 GTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGCTTTGGTC-AA
1 GTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGCATTGGTCAAA
* * * * * **
55631763 GTATGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGGTATTGGTCACGT
1 G--TGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGCATTGGTCA-AA
* * *
55631816 GTGTAGTACTAAGTGTAGGCTACTATGTGTACCAAATAGCATTGATCATAA
1 GTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGCATTGGTCA-AA
* * *
55631867 GGGTGGTACTATGTGCAG
1 GTGTAGTACTAAGTGCAG
55631885 AACCACCATG
Statistics
Matches: 137, Mismatches: 29, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
49 2 0.01
51 132 0.96
52 2 0.01
53 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (50 bp):
GTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGCATTGGTCAAA
Found at i:55634194 original size:39 final size:39
Alignment explanation
Indices: 55634150--55634292 Score: 223
Period size: 39 Copynumber: 3.7 Consensus size: 39
55634140 CATATTCACT
*
55634150 TTTAAGCATATATCACATTACACATATAATCACATAACA
1 TTTAAGCATATATCACAATACACATATAATCACATAACA
* * *
55634189 TTTAAGCAAATATCACAATACTCATATAATCACATAAAA
1 TTTAAGCATATATCACAATACACATATAATCACATAACA
*
55634228 TTTAAGCATATATCACAATACTCATATAATCACATAACA
1 TTTAAGCATATATCACAATACACATATAATCACATAACA
* *
55634267 TTCAAGTATATATCACAATACACATA
1 TTTAAGCATATATCACAATACACATA
55634293 ACATGTTTAT
Statistics
Matches: 95, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 95 1.00
ACGTcount: A:0.48, C:0.20, G:0.03, T:0.30
Consensus pattern (39 bp):
TTTAAGCATATATCACAATACACATATAATCACATAACA
Found at i:55650563 original size:28 final size:30
Alignment explanation
Indices: 55650531--55650590 Score: 88
Period size: 28 Copynumber: 2.1 Consensus size: 30
55650521 TGGATATGAA
55650531 TGAAAAGTGGAACTTTAATGCAA-T-ACAG
1 TGAAAAGTGGAACTTTAATGCAACTGACAG
* *
55650559 TGAAAAGTGGCACTTTGATGCAACTGACAG
1 TGAAAAGTGGAACTTTAATGCAACTGACAG
55650589 TG
1 TG
55650591 GCACTATGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 21 0.75
29 1 0.04
30 6 0.21
ACGTcount: A:0.37, C:0.13, G:0.25, T:0.25
Consensus pattern (30 bp):
TGAAAAGTGGAACTTTAATGCAACTGACAG
Found at i:55652184 original size:3 final size:3
Alignment explanation
Indices: 55652176--55652219 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
55652166 CATTTAATTG
55652176 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
55652220 AAAACTAGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:55655871 original size:22 final size:22
Alignment explanation
Indices: 55655846--55655888 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
55655836 ATAAGCTTCT
*
55655846 TTACATTCAATTAATAAATGTA
1 TTACATTCAATCAATAAATGTA
55655868 TTACATTCAATCAATAAATGT
1 TTACATTCAATCAATAAATGT
55655889 GAATTAAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.40
Consensus pattern (22 bp):
TTACATTCAATCAATAAATGTA
Found at i:55657177 original size:15 final size:17
Alignment explanation
Indices: 55657149--55657197 Score: 50
Period size: 19 Copynumber: 2.9 Consensus size: 17
55657139 TTTATTTTTC
55657149 TTCTTAC-TGCAATTG-A
1 TTCTTACGTG-AATTGAA
55657165 TT-TTACGTGAATTGGGAA
1 TTCTTACGTGAATT--GAA
55657183 TTCTTACGTGAATTG
1 TTCTTACGTGAATTG
55657198 GGAATTCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
15 8 0.29
16 4 0.14
17 2 0.07
18 3 0.11
19 11 0.39
ACGTcount: A:0.24, C:0.12, G:0.20, T:0.43
Consensus pattern (17 bp):
TTCTTACGTGAATTGAA
Found at i:55657191 original size:19 final size:19
Alignment explanation
Indices: 55657167--55657206 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
55657157 GCAATTGATT
55657167 TTACGTGAATTGGGAATTC
1 TTACGTGAATTGGGAATTC
55657186 TTACGTGAATTGGGAATTC
1 TTACGTGAATTGGGAATTC
55657205 TT
1 TT
55657207 TGTTGCCTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.40
Consensus pattern (19 bp):
TTACGTGAATTGGGAATTC
Found at i:55660104 original size:274 final size:274
Alignment explanation
Indices: 55659610--55660138 Score: 833
Period size: 274 Copynumber: 1.9 Consensus size: 274
55659600 CCCTATTCCA
* * *
55659610 GGACAAAGCTTATCAGTGGTGGTTGATAGTTGAGCAAGGTGTTCAGCCTGAACAGGTGAACTGAG
1 GGACAAAGCTTATCAGTGGTGGTTGACAGTTGAACAAAGTGTTCAGCCTGAACAGGTGAACTGAG
* * *
55659675 ACTATTTCAAGAACACCTTCTAAGGTAAGTATGTGAGGGCAAATTATGTTGAGGCTCACCGATAC
66 ACTATTTCAAGAACACATTCCAAGGTAAGTATGTGAGGGCAAATTATGTTGAAGCTCACCGATAC
* *** *
55659740 GAGTCCATGAGCCTAGTTCAAGGCGACCGATCGGTGGCCAAATAGGAAGTTGAGTTTTTACGACT
131 GAGTCCATGAGCCTAGTTCAAGGCAACCGATCGGTGGCCAAATAGGAAGCCAAGTTTTTACAACT
* * *
55659805 GAGTAGGTATGTATGGACTCTAGTAGCGTCTAATTATGAAAAGTGTGTAAAGTTTGAGGGGTGTT
196 AAGTAGGTATGCATGGACTCTAGTAGCGTCTAATTACGAAAAGTGTGTAAAGTTTGAGGGGTGTT
55659870 GTTTCCTTATTTCG
261 GTTTCCTTATTTCG
* * *
55659884 GGACGAAGCTTATCAGTGGTGGTTGACAGTTGAACAAAGTGTTCAGCCTGAATAGGTGAACTGGG
1 GGACAAAGCTTATCAGTGGTGGTTGACAGTTGAACAAAGTGTTCAGCCTGAACAGGTGAACTGAG
*
55659949 ACTATTTCAAGAACACATTCCAAGGTTAGTATGTGAGGGCAAATTATGTTGAAGCTCACCGATAC
66 ACTATTTCAAGAACACATTCCAAGGTAAGTATGTGAGGGCAAATTATGTTGAAGCTCACCGATAC
* * *
55660014 GAGTTCATGAGCCTAGTTCAGGGCAACCGATCGGTGGCCAAATATGAAGCCAAGTTTTTACAACT
131 GAGTCCATGAGCCTAGTTCAAGGCAACCGATCGGTGGCCAAATAGGAAGCCAAGTTTTTACAACT
* * * *
55660079 AAGTAGGTATGCATGGACTCTAGTAGCGTCTGATTACGATAAGTGTGTGAGGTTTGAGGG
196 AAGTAGGTATGCATGGACTCTAGTAGCGTCTAATTACGAAAAGTGTGTAAAGTTTGAGGG
55660139 ATTAAGATAT
Statistics
Matches: 230, Mismatches: 25, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
274 230 1.00
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (274 bp):
GGACAAAGCTTATCAGTGGTGGTTGACAGTTGAACAAAGTGTTCAGCCTGAACAGGTGAACTGAG
ACTATTTCAAGAACACATTCCAAGGTAAGTATGTGAGGGCAAATTATGTTGAAGCTCACCGATAC
GAGTCCATGAGCCTAGTTCAAGGCAACCGATCGGTGGCCAAATAGGAAGCCAAGTTTTTACAACT
AAGTAGGTATGCATGGACTCTAGTAGCGTCTAATTACGAAAAGTGTGTAAAGTTTGAGGGGTGTT
GTTTCCTTATTTCG
Found at i:55667908 original size:30 final size:30
Alignment explanation
Indices: 55667872--55667936 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
55667862 GGAAATAAAC
55667872 CTTAAAATTCAGAATTTTGGA-GGAAGAGGA
1 CTTAAAATTCAGAATTTTGGAGGGAA-AGGA
*
55667902 CTTAAAATTCGGAATTTTGGAGGGAAAGGA
1 CTTAAAATTCAGAATTTTGGAGGGAAAGGA
55667932 -TTAAA
1 CTTAAA
55667937 TAGTAAAGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
29 5 0.15
30 24 0.73
31 4 0.12
ACGTcount: A:0.40, C:0.06, G:0.26, T:0.28
Consensus pattern (30 bp):
CTTAAAATTCAGAATTTTGGAGGGAAAGGA
Done.