Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008003.1 Hibiscus syriacus cultivar Beakdansim tig00110462_pilon, whole genome shotgun sequence
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: 3297763
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 14
Found at i:1888688 original size:2 final size:2
Alignment explanation
Indices: 1888681--1888721 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1888671 AAAATTTAAT
1888681 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1888722 TCAATTGTAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1889239 original size:2 final size:2
Alignment explanation
Indices: 1889232--1889319 Score: 176
Period size: 2 Copynumber: 44.0 Consensus size: 2
1889222 TACCCTAACA
1889232 AT AT AT AT AT 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 AT AT AT AT AT
1889274 AT AT AT AT AT 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 AT AT AT AT AT
1889316 AT AT
1 AT AT
1889320 TTAAGAAATA
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 86 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1892669 original size:2 final size:2
Alignment explanation
Indices: 1892662--1892758 Score: 80
Period size: 2 Copynumber: 50.5 Consensus size: 2
1892652 ATTTATGTAA
*
1892662 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT -T AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
1892702 TT AT -T AT AT AT AT AT TT AT AT GACT AT AT A- AT A- AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT -A-T AT AT AT AT AT AT AT AT AT
* *
1892743 A- AT AT TT AA AT AT AT A
1 AT AT AT AT AT AT AT AT A
1892759 AACAAGTAAA
Statistics
Matches: 75, Mismatches: 12, Indels: 16
0.73 0.12 0.16
Matches are distributed among these distances:
1 6 0.08
2 66 0.88
3 2 0.03
4 1 0.01
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1894169 original size:3 final size:3
Alignment explanation
Indices: 1894163--1894201 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
1894153 TATTATTTTT
*
1894163 TAA TAA TAA TAA T-A TATA TAA TAA TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
1894202 AATGGGTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.84
4 3 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:1894554 original size:124 final size:120
Alignment explanation
Indices: 1894349--1894629 Score: 365
Period size: 124 Copynumber: 2.3 Consensus size: 120
1894339 TCTTCTCTTT
* * * *
1894349 CTTCGGATGAGTTCTTCTCATTATGAACTTT-TCGTTGG---GGATGATGTTGACCTATTTCCTT
1 CTTCAGATGAGTTCTTCTCATTATGAACTTTCTC--TGGAAAGGATGATGCTAACCTATCTCCTT
* *
1894410 CTGTGATAGAGTCATTCAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTCTTCTTTCTC
64 CTGTGATAGAATCATGCAAAAGGTTGAATAAGCTCTTCTCATTATGAA---CTT-TTTCTC
* * *
1894471 CTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGTTGATGCTAATCTATCTGCTTCT
1 CTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGATGATGCTAACCTATCTCCTTCT
* * *
1894536 GTGATAGAATTATGCAAAAGGTTGAATAAGCTCTTCTCATTGTGAACTTTTTCTT
66 GTGATAGAATCATGCAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTTTTCTC
1894591 CTTCAGATGAGTTCTTCTCATTATGAAC-TTCTCTGGAAA
1 CTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA
1894630 AACTGATCCA
Statistics
Matches: 143, Mismatches: 12, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
119 11 0.08
120 33 0.23
121 6 0.04
122 30 0.21
123 2 0.01
124 61 0.43
ACGTcount: A:0.23, C:0.18, G:0.17, T:0.41
Consensus pattern (120 bp):
CTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGATGATGCTAACCTATCTCCTTCT
GTGATAGAATCATGCAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTTTTCTC
Found at i:1894765 original size:113 final size:113
Alignment explanation
Indices: 1894549--1895224 Score: 841
Period size: 113 Copynumber: 6.0 Consensus size: 113
1894539 ATAGAATTAT
* ** *
1894549 GCAAAAGGTTGAATAAGCTCTTCTCATTGTGAAC-T-TT-TT-CTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
1894610 ATTATGAACT-TCTCTGGAAAAACTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTCTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
* * *
1894657 GCAAAAAGTTAAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTTTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*** *
1894722 ATTATGAACTCAAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTCTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
*
1894770 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGATGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC--A-GATGAGTTCTT
** * * * * *
1894835 CTCATTATGAACTCTACCTGGCAATA-TTAATCCATCAAATGATGAATTTAA
63 CTCATTATGAACTCTTTCTGG-AAAAGCTGATCCATCAAATGATGGATTTGA
*
1894886 ACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
1894951 ATTATGAACTTTTTCTGGAAAAGTTGAT-CTTCAAATGATGGATTTGA
66 ATTATGAACTCTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
** * * *
1894998 GTGAAAGGCTGAATAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGAATGATGAGTTCT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC---A-GATGAGTTCT
** * * * * *
1895063 TCTCATTATGAA--CTTTCT-TCAATGTTAATCCATCAAATGATGAATTTAA
62 TCTCATTATGAACTCTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
* *
1895112 ACAAAAGGTTGAACAAATTCTTCTCATTTTGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
1895177 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
66 ATTATGAACTCTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
1895225 ATCTTTGCTA
Statistics
Matches: 488, Mismatches: 62, Indels: 31
0.84 0.11 0.05
Matches are distributed among these distances:
108 28 0.06
109 1 0.00
110 24 0.05
111 3 0.01
112 99 0.20
113 143 0.29
114 65 0.13
115 2 0.00
116 120 0.25
117 3 0.01
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTCTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
Found at i:1894930 original size:229 final size:227
Alignment explanation
Indices: 1894549--1895224 Score: 983
Period size: 229 Copynumber: 3.0 Consensus size: 227
1894539 ATAGAATTAT
** * *
1894549 GCAAAAGGTTGAATAAGCTCTTCTCATTGTGAA---CTT-TTTCTTCTTC--A-GATGAGTTCTT
1 GCAAAAGGTTGAATAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGATGAGTTCTT
* * * * * * * * * *
1894607 CTCATTATGAACTTCTCTGGAAAAACTGATCCATCAAGTGATGGATTTGAGCAAAAAGTTAAACA
66 CTCATTATGAACTTC-CTGGCAATATTAATCCATCAAATGATGAATTTAAACAAAAGGTTGAACA
* ****
1894672 AATTCTTCTCATTATGAACTTCTTCTTCCTTTTTCAGATGAGTTCTTCTCATTATGAACTCAAAC
130 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTC
*
1894737 TGGAAAAGCTGATCCATCAAGTGATGGATTTGA
195 TGGAAAAGCTGATCCATCAAATGATGGATTTGA
*
1894770 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGATGAGTTCTT
1 GCAAAAGGTTGAATAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGATGAGTTCTT
1894835 CTCATTATGAACTCTACCTGGCAATATTAATCCATCAAATGATGAATTTAAACAAAAGGTTGAAC
66 CTCATTATGAACT-T-CCTGGCAATATTAATCCATCAAATGATGAATTTAAACAAAAGGTTGAAC
1894900 AAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTT
129 AAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTT
* *
1894965 CTGGAAAAGTTGAT-CTTCAAATGATGGATTTGA
194 CTGGAAAAGCTGATCCATCAAATGATGGATTTGA
** *
1894998 GTGAAAGGCTGAATAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGAATGATGAGTTCT
1 GCAAAAGGTTGAATAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAG-ATGATGAGTTCT
* * *
1895063 TCTCATTATGAACTTTCT-TCAATGTTAATCCATCAAATGATGAATTTAAACAAAAGGTTGAACA
65 TCTCATTATGAACTTCCTGGCAATATTAATCCATCAAATGATGAATTTAAACAAAAGGTTGAACA
*
1895127 AATTCTTCTCATTTTGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTC
130 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTC
1895192 TGGAAAAGCTGATCCATCAAATGATGGATTTGA
195 TGGAAAAGCTGATCCATCAAATGATGGATTTGA
1895225 ATCTTTGCTA
Statistics
Matches: 411, Mismatches: 33, Indels: 16
0.89 0.07 0.03
Matches are distributed among these distances:
221 29 0.07
224 3 0.01
225 9 0.02
226 120 0.29
227 21 0.05
228 90 0.22
229 138 0.34
230 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (227 bp):
GCAAAAGGTTGAATAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGATGAGTTCTT
CTCATTATGAACTTCCTGGCAATATTAATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAA
ATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCT
GGAAAAGCTGATCCATCAAATGATGGATTTGA
Found at i:1896187 original size:94 final size:94
Alignment explanation
Indices: 1896010--1896314 Score: 549
Period size: 94 Copynumber: 3.3 Consensus size: 94
1896000 TTTATTTCTA
* * *
1896010 CTATGAGCACATTCATCTTTCAAATTCAATGATTGGTTTTT-GTGGTTCTTACCAAACCAGATCA
1 CTATGAGCACATTCATCTTTCAAATTAAATGATTGGTTTTTCGGGGTTCATACCAAACCAGATCA
1896074 GATAACTCAAAGAACACTTCCAGAAGATG
66 GATAACTCAAAGAACACTTCCAGAAGATG
1896103 CTATGAGCACATTCATCTTTCAAATTAAATGATTGGTTTTTCGGGGTTCATACCAAACCAGATCA
1 CTATGAGCACATTCATCTTTCAAATTAAATGATTGGTTTTTCGGGGTTCATACCAAACCAGATCA
1896168 GATAACTCAAAGAACACTTCCAGAAGATG
66 GATAACTCAAAGAACACTTCCAGAAGATG
*
1896197 CTATGAGCATATTCATCTTTCAAATTAAATGATTGGTTTTTCGGGGTTCATACCAAACCAGATCA
1 CTATGAGCACATTCATCTTTCAAATTAAATGATTGGTTTTTCGGGGTTCATACCAAACCAGATCA
*
1896262 GATAACTCAAAGAACACTTCCAAAAGATG
66 GATAACTCAAAGAACACTTCCAGAAGATG
*
1896291 CTATGAGCACATTCATCTTCCAAA
1 CTATGAGCACATTCATCTTTCAAA
1896315 AGATGCTATG
Statistics
Matches: 204, Mismatches: 7, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
93 40 0.20
94 164 0.80
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.30
Consensus pattern (94 bp):
CTATGAGCACATTCATCTTTCAAATTAAATGATTGGTTTTTCGGGGTTCATACCAAACCAGATCA
GATAACTCAAAGAACACTTCCAGAAGATG
Found at i:1896311 original size:29 final size:29
Alignment explanation
Indices: 1896278--1896343 Score: 132
Period size: 29 Copynumber: 2.3 Consensus size: 29
1896268 TCAAAGAACA
1896278 CTTCCAAAAGATGCTATGAGCACATTCAT
1 CTTCCAAAAGATGCTATGAGCACATTCAT
1896307 CTTCCAAAAGATGCTATGAGCACATTCAT
1 CTTCCAAAAGATGCTATGAGCACATTCAT
1896336 CTTCCAAA
1 CTTCCAAA
1896344 TTCAATGATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.35, C:0.26, G:0.12, T:0.27
Consensus pattern (29 bp):
CTTCCAAAAGATGCTATGAGCACATTCAT
Found at i:1896449 original size:123 final size:121
Alignment explanation
Indices: 1896184--1896425 Score: 371
Period size: 123 Copynumber: 2.0 Consensus size: 121
1896174 TCAAAGAACA
* * *
1896184 CTTCCAGAAGATGCTATGAGCATATTCATCTTTCAAATTAAATGATTGGTTTTTCGGGGTTCATA
1 CTTCCAAAAGATGCTATGAGCACATTCATCTTCCAAATTAAATGATTGGTTTTTCGGGGTTCATA
**
1896249 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAGCACATTCAT
66 CC--ACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAGCACAGGCAT
*
1896307 CTTCCAAAAGATGCTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTT-GGGGTTCATA
1 CTTCCAAAAGATGCTATGAGCACATTCATCTTCCAAATTAAATGATTGGTTTTTCGGGGTTCATA
* *
1896371 CC-CTAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACACGGCA
66 CCACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAGCACA-GGCA
1896426 CTTGTTCCAC
Statistics
Matches: 110, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
119 46 0.42
120 2 0.02
122 12 0.11
123 50 0.45
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (121 bp):
CTTCCAAAAGATGCTATGAGCACATTCATCTTCCAAATTAAATGATTGGTTTTTCGGGGTTCATA
CCACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAGCACAGGCAT
Found at i:1905134 original size:15 final size:15
Alignment explanation
Indices: 1905111--1905142 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1905101 TGCAATGAAT
1905111 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
1905126 AATGCATGTATGCAA
1 AATGAATGTATGCAA
1905141 AA
1 AA
1905143 AGGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:1910731 original size:3 final size:3
Alignment explanation
Indices: 1910725--1910761 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
1910715 CTTTTTTTTT
* *
1910725 ATA ATA ATA ATA ATT ATA ATA ATT ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1910762 AATGGGTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:1915382 original size:22 final size:22
Alignment explanation
Indices: 1915354--1915396 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1915344 TACCAATCAT
*
1915354 TGATTTTGTATAGGTTGTGCAC
1 TGATTTTGTATAGGCTGTGCAC
1915376 TGATTTTGTATAGGCTGTGCA
1 TGATTTTGTATAGGCTGTGCA
1915397 GATTTATTTT
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:0.19, C:0.09, G:0.28, T:0.44
Consensus pattern (22 bp):
TGATTTTGTATAGGCTGTGCAC
Found at i:1923304 original size:23 final size:23
Alignment explanation
Indices: 1923278--1923343 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
1923268 TACCACAGCT
*
1923278 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * * *
1923301 CGTAGAATTGCATCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
1923324 CGTAGAAATGCACCGAAGTG
1 CGTAGAAATGCACCGAAGTG
1923344 TCATATAATA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.30, C:0.23, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:1924792 original size:20 final size:21
Alignment explanation
Indices: 1924763--1924806 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
1924753 TTTTGTTCGT
*
1924763 TTGAAGGGGTATCG-TTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1924783 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1924804 TTG
1 TTG
1924807 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.32
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1928411 original size:23 final size:23
Alignment explanation
Indices: 1928377--1928445 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
1928367 TACCACATCT
*
1928377 CGTACAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
1928400 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
1928423 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
1928446 TATAATAATG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:1929893 original size:20 final size:21
Alignment explanation
Indices: 1929864--1929907 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
1929854 TTTTGTTCGT
*
1929864 TTGAAGGGGTATCG-TTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1929884 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1929905 TTG
1 TTG
1929908 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.32
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1932845 original size:31 final size:31
Alignment explanation
Indices: 1932807--1932901 Score: 129
Period size: 31 Copynumber: 3.1 Consensus size: 31
1932797 GAGTCGAGGG
1932807 TTTACCTATG-TCTTTCGGGACATATGGACAA
1 TTTACCTATGTTC-TTCGGGACATATGGACAA
* * *
1932838 TTTACCTATGTTCTACGGGACATATGGATAG
1 TTTACCTATGTTCTTCGGGACATATGGACAA
* *
1932869 TTTACCTAGGTTCTTCGGGACCTATGGACAA
1 TTTACCTATGTTCTTCGGGACATATGGACAA
1932900 TT
1 TT
1932902 GTCGAGGTTC
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
31 53 0.96
32 2 0.04
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (31 bp):
TTTACCTATGTTCTTCGGGACATATGGACAA
Found at i:1936977 original size:9 final size:9
Alignment explanation
Indices: 1936963--1936990 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
1936953 AACTAAAAAT
1936963 AAAATTTTA
1 AAAATTTTA
1936972 AAAATTTTA
1 AAAATTTTA
1936981 AAAATTTTA
1 AAAATTTTA
1936990 A
1 A
1936991 TACTCATAAT
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:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
AAAATTTTA
Found at i:1946752 original size:170 final size:170
Alignment explanation
Indices: 1946464--1946797 Score: 591
Period size: 170 Copynumber: 2.0 Consensus size: 170
1946454 TTTATTATAA
*
1946464 TAAAATTATTAATAAAATAAAAAAGATATGTGATTGTATTTAAATATTATGTGTGCAATTAAAAA
1 TAAAAATATTAATAAAATAAAAAAGATATGTGATTGTATTTAAATATTATGTGTGCAATTAAAAA
1946529 ATAGGGTAAAGCACACAAATAGTCCATGACTATACGATACTATTTTGTTAAGTCCTCTAACTATT
66 ATAGGGTAAAGCACACAAATAGTCCATGACTATACGATACTATTTTGTTAAGTCCTCTAACTATT
* *
1946594 AAAAATTATAAAATGATCCTC-CGATTATAAGGAGTTGATT
131 AAAAATTACAAAATGA-CCCCACGATTATAAGGAGTTGATT
1946634 TAAAAATATTAATAAAATAAAAAAGATATGTGATTGTATTTAAATATTATGTGTGCAATTAAAAA
1 TAAAAATATTAATAAAATAAAAAAGATATGTGATTGTATTTAAATATTATGTGTGCAATTAAAAA
*
1946699 ATAGGGTAAAGCACACAAATGGTCTC-TGACTATACGATACTATTTTGTTAAGTCCTCTAACTAT
66 ATAGGGTAAAGCACACAAATAGTC-CATGACTATACGATACTATTTTGTTAAGTCCTCTAACTAT
*
1946763 TAAAAGTTACAAAATGACCCCACGATTATAAGGAG
130 TAAAAATTACAAAATGACCCCACGATTATAAGGAG
1946798 ATTTTTTTTG
Statistics
Matches: 157, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
169 3 0.02
170 153 0.97
171 1 0.01
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (170 bp):
TAAAAATATTAATAAAATAAAAAAGATATGTGATTGTATTTAAATATTATGTGTGCAATTAAAAA
ATAGGGTAAAGCACACAAATAGTCCATGACTATACGATACTATTTTGTTAAGTCCTCTAACTATT
AAAAATTACAAAATGACCCCACGATTATAAGGAGTTGATT
Found at i:1946951 original size:8 final size:8
Alignment explanation
Indices: 1946938--1946962 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1946928 GATAGTCGTT
1946938 TGAGATTA
1 TGAGATTA
1946946 TGAGATTA
1 TGAGATTA
1946954 TGAGATTA
1 TGAGATTA
1946962 T
1 T
1946963 ATTTTATCAT
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:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (8 bp):
TGAGATTA
Found at i:1947335 original size:20 final size:21
Alignment explanation
Indices: 1947310--1947350 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1947300 TTATAATAAT
1947310 TTTTTAA-ATCTATTTTTTTA
1 TTTTTAATATCTATTTTTTTA
*
1947330 TTTTTAATATCTTTTTTTTTA
1 TTTTTAATATCTATTTTTTTA
1947351 ATATGAGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTTTAATATCTATTTTTTTA
Found at i:1947350 original size:15 final size:16
Alignment explanation
Indices: 1947325--1947354 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1947315 AAATCTATTT
1947325 TTTTATTTTTAATATC
1 TTTTATTTTTAATATC
1947341 TTTT-TTTTTAATAT
1 TTTTATTTTTAATAT
1947355 GAGCAATTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTATTTTTAATATC
Found at i:1951059 original size:22 final size:22
Alignment explanation
Indices: 1951034--1951082 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
1951024 ACGTAGATCA
*
1951034 TTTATAGAGAATAATATTTCTT
1 TTTATAGAGAACAATATTTCTT
1951056 TTTATAGAGAACAATATTTCTT
1 TTTATAGAGAACAATATTTCTT
1951078 TTTAT
1 TTTAT
1951083 TATTGACGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.35, C:0.06, G:0.08, T:0.51
Consensus pattern (22 bp):
TTTATAGAGAACAATATTTCTT
Found at i:1955264 original size:16 final size:16
Alignment explanation
Indices: 1955241--1955282 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1955231 CCAGAACCCA
*
1955241 AAAATGATCCAGACTC
1 AAAATGATCCAAACTC
* *
1955257 ACAATGATCCAAATTC
1 AAAATGATCCAAACTC
1955273 AAAATGATCC
1 AAAATGATCC
1955283 CATAACTTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.45, C:0.24, G:0.10, T:0.21
Consensus pattern (16 bp):
AAAATGATCCAAACTC
Found at i:1969579 original size:15 final size:15
Alignment explanation
Indices: 1969557--1969610 Score: 65
Period size: 15 Copynumber: 3.6 Consensus size: 15
1969547 TTTTTATCAA
1969557 AAATTAAAACGTTAC
1 AAATTAAAACGTTAC
* **
1969572 AGATTAAAATATT-C
1 AAATTAAAACGTTAC
1969586 TAAATTAAAACGTTAC
1 -AAATTAAAACGTTAC
1969602 AAATTAAAA
1 AAATTAAAA
1969611 TATTCTAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
14 1 0.03
15 29 0.94
16 1 0.03
ACGTcount: A:0.56, C:0.09, G:0.06, T:0.30
Consensus pattern (15 bp):
AAATTAAAACGTTAC
Found at i:1969593 original size:30 final size:30
Alignment explanation
Indices: 1969557--1969622 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
1969547 TTTTTATCAA
*
1969557 AAATTAAAACGTTACAGATTAAAATATTCT
1 AAATTAAAACGTTACAAATTAAAATATTCT
1969587 AAATTAAAACGTTACAAATTAAAATATTCT
1 AAATTAAAACGTTACAAATTAAAATATTCT
1969617 AAATTA
1 AAATTA
1969623 TTTTTTTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.53, C:0.09, G:0.05, T:0.33
Consensus pattern (30 bp):
AAATTAAAACGTTACAAATTAAAATATTCT
Found at i:1969620 original size:15 final size:15
Alignment explanation
Indices: 1969574--1969622 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
1969564 AACGTTACAG
1969574 ATTAAAATATTCTAA
1 ATTAAAATATTCTAA
**
1969589 ATTAAAACGTTAC-AA
1 ATTAAAATATT-CTAA
1969604 ATTAAAATATTCTAA
1 ATTAAAATATTCTAA
1969619 ATTA
1 ATTA
1969623 TTTTTTTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 1 0.04
15 26 0.93
16 1 0.04
ACGTcount: A:0.53, C:0.08, G:0.02, T:0.37
Consensus pattern (15 bp):
ATTAAAATATTCTAA
Found at i:1988662 original size:19 final size:18
Alignment explanation
Indices: 1988634--1988669 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1988624 AAGGAATCTC
1988634 AATTTGATTAAACGTATAA
1 AATTTGATTAAA-GTATAA
*
1988653 AATTTTATTAAAGTATA
1 AATTTGATTAAAGTATA
1988670 TTTTTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (18 bp):
AATTTGATTAAAGTATAA
Found at i:1989368 original size:520 final size:506
Alignment explanation
Indices: 1988609--1989633 Score: 1586
Period size: 520 Copynumber: 2.0 Consensus size: 506
1988599 AAAAAGAGCA
* * *
1988609 GAATACATTAATAATAAGGAATCTCAATTTGATTAAACGTATAAAATTTTATTAAAGTATATTTT
1 GAATACATTAATAATAAGGAATCTCAATTTGATTAAAAGTACAAAATTTTATTAAAGTAGATTTT
* * *
1988674 TATTTTATTTAATTTTTCTTTGTAATCAAGTATATGTTTTTATAAATATATATTAAGGATCAGAG
66 TACTTTATTTAATTTTTCTTTGTAATCAAGTATATATTTTTATAAATATATATTAAGGATCACAG
*
1988739 TTAAAAATCAAGTTTTCTTTTATTAAAACCTTCTTTTATTTTATTCCTTCATATTAGTAAAATTA
131 TTAAAAATCAAGTTTTCTTTTATCAAAACCTTCTTTTATTTTATTCCTTCATATTAGTAAAATTA
* * * * *
1988804 TTTTTTTATGTTTGTGGTTTTTCATTTTTAGGTTTACTACGTAAATTTTGATATTCTATGTTTTT
196 TTTTTCTATGTTCGTGGTTTTTCATTTTTAGGTTTACCACGTAAATTCTGATATTATATGTTTTT
*
1988869 CCTTTTCGATCGTATTTATTTGTTTATTCATAATCGTCGTTTCGATATTATAACAAACTGGTATC
261 CCTTTTCGATCGTATTTATTTGTTTATTCATAATCGTCGTTTCGATATTATAACAAACTGATATC
* * *
1988934 AGAGTTTTGTGTTCAAGATTATGAACAATGAAGTATGATATTCCGCTGTTGGATCGAAATACCAT
326 AGAGTTTTGGGTTCAAGATTATG-AC-------------ATTCCGCTGTTGGATCGAAACACCAG
*
1988999 GTTCTCGTTATGGCAAGTGAAGATTTGGAATGTTCTTGCACAATTATATCTCGACGATGCAATAG
377 GTTCTCGCTATGGCAAGTGAAGATTTGGAATGTTCTTGCACAATTATATCTCGACGATGCAATAG
* * *
1989064 AAGGATTTGATGAAAAGTCGGTAACACAATGGACGAATGAGGAAAAGCGTAAGGATTGTAAAGCC
442 AAGGATTTGATGAAAAGTCAGTAACACAATGGACGAATGAGGAAAAACGTAAGGATCGTAAAGCC
*
1989129 GAATACATTAATCAA-GAGGAATCTCAATTTGATTAAAAGTACAAAATTTTATTAAAGTAGATTT
1 GAATACATTAAT-AATAAGGAATCTCAATTTGATTAAAAGTACAAAATTTTATTAAAGTAGATTT
* *
1989193 TTACTTTATTTAATTTTTCTTTGTAATCAAGTATATATTTTTATAAATATATATTAAGTATTACA
65 TTACTTTATTTAATTTTTCTTTGTAATCAAGTATATATTTTTATAAATATATATTAAGGATCACA
* *
1989258 GTTAAAAATCAAGTTTTCTTTTATCAAAATCTTCTTTTATTTTATTCCTTCATATTAGTCAAATT
130 GTTAAAAATCAAGTTTTCTTTTATCAAAACCTTCTTTTATTTTATTCCTTCATATTAGTAAAATT
* * *
1989323 ATTTTTCTATGTTCGTGGTTTTTCATTTTT-GGATTTTCCACGTAAATTCTGGTATTATTTGTTT
195 ATTTTTCTATGTTCGTGGTTTTTCATTTTTAGG-TTTACCACGTAAATTCTGATATTATATGTTT
*
1989387 TTCCTTTTCGATCGTATTTATTTGTTTGTTCATAATCGTCGTTTCGATATTATAACAAACTGATA
259 TTCCTTTTCGATCGTATTTATTTGTTTATTCATAATCGTCGTTTCGATATTATAACAAACTGATA
* * *
1989452 TCAGAGTTTTGGGTTCAAGATTATGACATTCCGCTGTTGGATTGAAACATCAGGTTCTTGCTATG
324 TCAGAGTTTTGGGTTCAAGATTATGACATTCCGCTGTTGGATCGAAACACCAGGTTCTCGCTATG
*
1989517 GCAAGTGAAGATTTGGAATGTTCTTGCATAATTATATCTCGACGATGCAATAGAAGGATTTGATG
389 GCAAGTGAAGATTTGGAATGTTCTTGCACAATTATATCTCGACGATGCAATAGAAGGATTTGATG
*
1989582 AAAAGTCAGTAACACAATTGACGAATGAGGAAAAACGTAAGGATCGTAAAGC
454 AAAAGTCAGTAACACAATGGACGAATGAGGAAAAACGTAAGGATCGTAAAGC
1989634 TTTTTCTCAG
Statistics
Matches: 469, Mismatches: 34, Indels: 18
0.90 0.07 0.03
Matches are distributed among these distances:
506 144 0.31
519 4 0.01
520 319 0.68
521 2 0.00
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (506 bp):
GAATACATTAATAATAAGGAATCTCAATTTGATTAAAAGTACAAAATTTTATTAAAGTAGATTTT
TACTTTATTTAATTTTTCTTTGTAATCAAGTATATATTTTTATAAATATATATTAAGGATCACAG
TTAAAAATCAAGTTTTCTTTTATCAAAACCTTCTTTTATTTTATTCCTTCATATTAGTAAAATTA
TTTTTCTATGTTCGTGGTTTTTCATTTTTAGGTTTACCACGTAAATTCTGATATTATATGTTTTT
CCTTTTCGATCGTATTTATTTGTTTATTCATAATCGTCGTTTCGATATTATAACAAACTGATATC
AGAGTTTTGGGTTCAAGATTATGACATTCCGCTGTTGGATCGAAACACCAGGTTCTCGCTATGGC
AAGTGAAGATTTGGAATGTTCTTGCACAATTATATCTCGACGATGCAATAGAAGGATTTGATGAA
AAGTCAGTAACACAATGGACGAATGAGGAAAAACGTAAGGATCGTAAAGCC
Found at i:1990117 original size:19 final size:18
Alignment explanation
Indices: 1990093--1990142 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
1990083 AATGACCAAT
1990093 AAAATCGCAACGCGATATC
1 AAAATCGCAACGCGAT-TC
*
1990112 AAAATCGCAACGCGATTT
1 AAAATCGCAACGCGATTC
1990130 AGAAATCGCAACG
1 A-AAATCGCAACG
1990143 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 2 0.07
19 27 0.93
ACGTcount: A:0.42, C:0.24, G:0.18, T:0.16
Consensus pattern (18 bp):
AAAATCGCAACGCGATTC
Found at i:1990242 original size:20 final size:20
Alignment explanation
Indices: 1990217--1990367 Score: 151
Period size: 20 Copynumber: 7.4 Consensus size: 20
1990207 TTTAGAAGAA
**
1990217 AATCGCAATGCGATTGATTG
1 AATCGCAATGCGATTGAGAG
* *
1990237 AATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTGAGAG
*
1990257 AATTGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGAGAG
* * *
1990277 AGTCGCAACGCGATTTAGAAGAA
1 AATCGCAATGCGA-TT-G-AGAG
*
1990300 AATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAG
1990320 AA-CTGCAATGCGATTGAGAG
1 AATC-GCAATGCGATTGAGAG
* * *
1990340 AATCGCAACGCGATTTAGAA
1 AATCGCAATGCGATTGAGAG
1990360 AATCGCAA
1 AATCGCAA
1990368 CGGTCAAAAG
Statistics
Matches: 109, Mismatches: 17, Indels: 10
0.80 0.12 0.07
Matches are distributed among these distances:
19 1 0.01
20 88 0.81
21 4 0.04
22 2 0.02
23 14 0.13
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (20 bp):
AATCGCAATGCGATTGAGAG
Found at i:1990291 original size:83 final size:83
Alignment explanation
Indices: 1990196--1990369 Score: 242
Period size: 83 Copynumber: 2.1 Consensus size: 83
1990186 GCTTCCAAGT
* ** * *
1990196 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATTGAA-TCGCAATGCGATTTATAGAAT
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAACT-GCAATGCGATTGAGAGAAT
* * * *
1990260 TGCAATGCGATTGAGAGAG
65 CGCAACGCGATTGAGAAAA
1990279 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAACTGCAATGCGATTGAGAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAACTGCAATGCGATTGAGAGAATC
*
1990344 GCAACGCGATTTAGAAAA
66 GCAACGCGATTGAGAAAA
1990362 TCGCAACG
1 TCGCAACG
1990370 GTCAAAAGAA
Statistics
Matches: 80, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
83 79 0.99
84 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.21
Consensus pattern (83 bp):
TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAACTGCAATGCGATTGAGAGAATC
GCAACGCGATTGAGAAAA
Found at i:1990305 original size:63 final size:63
Alignment explanation
Indices: 1990237--1990359 Score: 201
Period size: 63 Copynumber: 2.0 Consensus size: 63
1990227 CGATTGATTG
* * * * *
1990237 AATCGCAATGCGATTTATAGAATTGCAATGCGATTGAGAGAGTCGCAACGCGATTTAGAAGAA
1 AATCGCAATGCGACTGAGAGAACTGCAATGCGATTGAGAGAATCGCAACGCGATTTAGAAGAA
1990300 AATCGCAATGCGACTGAGAGAACTGCAATGCGATTGAGAGAATCGCAACGCGATTTAGAA
1 AATCGCAATGCGACTGAGAGAACTGCAATGCGATTGAGAGAATCGCAACGCGATTTAGAA
1990360 AATCGCAACG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.21
Consensus pattern (63 bp):
AATCGCAATGCGACTGAGAGAACTGCAATGCGATTGAGAGAATCGCAACGCGATTTAGAAGAA
Found at i:1990368 original size:20 final size:20
Alignment explanation
Indices: 1990093--1990369 Score: 123
Period size: 20 Copynumber: 13.6 Consensus size: 20
1990083 AATGACCAAT
* *
1990093 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
1990112 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
1990132 -AAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
1990151 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
1990171 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
1990192 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
1990215 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
** * *
1990235 TGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * * *
1990255 AGAATTGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
1990275 AGAGTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
1990298 AAAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * *
1990318 AGAA-CTGCAATGCGATTGAG
1 AAAATC-GCAACGCGATTTAG
*
1990338 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
1990358 AAAATCGCAACG
1 AAAATCGCAACG
1990370 GTCAAAAGAA
Statistics
Matches: 198, Mismatches: 45, Indels: 29
0.73 0.17 0.11
Matches are distributed among these distances:
19 32 0.16
20 122 0.62
21 15 0.08
23 29 0.15
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:1990468 original size:6 final size:6
Alignment explanation
Indices: 1990457--1990506 Score: 93
Period size: 6 Copynumber: 8.5 Consensus size: 6
1990447 GACACGTATT
1990457 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1990504 ACC
1 ACC
1990507 CGAGACGAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.11
6 39 0.89
ACGTcount: A:0.32, C:0.52, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1991099 original size:20 final size:20
Alignment explanation
Indices: 1991077--1991268 Score: 215
Period size: 20 Copynumber: 9.3 Consensus size: 20
1991067 CTTTTTAACG
*
1991077 TTGCGATTTTCTAAATCG-A
1 TTGCGATTCTCTAAATCGCA
* *
1991096 GTTGCAATTCTCTCAATCGCA
1 -TTGCGATTCTCTAAATCGCA
*
1991117 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTAAATCGCA
* *
1991137 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTAAATCGCA
* *
1991157 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTAAATCGCA
1991177 TTGCGATTTTCTTCTAAATCGCA
1 TTGCGA--TTC-TCTAAATCGCA
*
1991200 TTGCGATTCTCTCAATCGCA
1 TTGCGATTCTCTAAATCGCA
*
1991220 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTAAATCGCA
*
1991240 TTGCGATTTTCTTCTAAATCGCG
1 TTGCGA--TTC-TCTAAATCGCA
1991263 TTGCGA
1 TTGCGA
1991269 ACTTGGAAGC
Statistics
Matches: 149, Mismatches: 16, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
20 109 0.73
21 4 0.03
22 6 0.04
23 30 0.20
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTCTAAATCGCA
Found at i:1991212 original size:63 final size:63
Alignment explanation
Indices: 1991057--1991268 Score: 267
Period size: 63 Copynumber: 3.5 Consensus size: 63
1991047 TTGACAACCG
* * * * *
1991057 TTGCGATTTTCTTTTTAA-CG--TTGCGATTTTCTAAATCG-AGTTGCAATTCTCTCAATCGCA
1 TTGCGATTTTCTTCTAAATCGCATTGCGATTCTCTCAATCGCA-TTGCGATTCTCTCAATCGCA
* * *
1991117 TTGCGA--TTC-TATAAATCGCATTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCA
1 TTGCGATTTTCTTCTAAATCGCATTGCGATTCTCTCAATCGCATTGCGATTCTCTCAATCGCA
* *
1991177 TTGCGATTTTCTTCTAAATCGCATTGCGATTCTCTCAATCGCATTGCGATTCTATAAATCGCA
1 TTGCGATTTTCTTCTAAATCGCATTGCGATTCTCTCAATCGCATTGCGATTCTCTCAATCGCA
*
1991240 TTGCGATTTTCTTCTAAATCGCGTTGCGA
1 TTGCGATTTTCTTCTAAATCGCATTGCGA
1991269 ACTTGGAAGC
Statistics
Matches: 132, Mismatches: 13, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
57 4 0.03
58 5 0.04
60 45 0.34
61 1 0.01
62 3 0.02
63 74 0.56
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.39
Consensus pattern (63 bp):
TTGCGATTTTCTTCTAAATCGCATTGCGATTCTCTCAATCGCATTGCGATTCTCTCAATCGCA
Found at i:1991345 original size:20 final size:20
Alignment explanation
Indices: 1991075--1991372 Score: 161
Period size: 20 Copynumber: 14.6 Consensus size: 20
1991065 TTCTTTTTAA
1991075 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
1991095 AGTTGCAATTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
1991115 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
1991135 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * * *
1991155 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
*
1991175 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
* * *
1991198 CATTGCGATTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
1991218 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
*
1991238 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
1991261 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
1991282 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
1991300 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
1991322 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
1991342 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
1991361 CGTTGCGATTTT
1 CGTTGCGATTTT
1991373 ATTGGTCATT
Statistics
Matches: 225, Mismatches: 42, Indels: 23
0.78 0.14 0.08
Matches are distributed among these distances:
18 2 0.01
19 17 0.08
20 155 0.69
21 15 0.07
22 6 0.03
23 30 0.13
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.40
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:1991362 original size:19 final size:20
Alignment explanation
Indices: 1991322--1991372 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
1991312 TTCTTTTTAA
*
1991322 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
1991342 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
1991361 CGTTGCGATTTT
1 CGTTGCGATTTT
1991373 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:1992485 original size:280 final size:280
Alignment explanation
Indices: 1991984--1992824 Score: 1666
Period size: 280 Copynumber: 3.0 Consensus size: 280
1991974 GTATGTTGCC
1991984 ATGTTTTTCAACTTCAAACCTCTGACTAGTGTCTCCGTAATTCTCTAACTACGAGAATGTTTTAT
1 ATGTTTTTCAACTTCAAACCTCTGACTAGTGTCTCCGTAATTCTCTAACTACGAGAATGTTTTAT
1992049 ATAAAAATAATTAAAATTTAAAACTAACTAATATTAAAACTCATTGAAATCTTAATAATAAAATA
66 ATAAAAATAATTAAAATTTAAAACTAACTAATATTAAAACTCATTGAAATCTTAATAATAAAATA
1992114 TTCTATCGTCTTCTTTAAGAATTTTATGATTGAATAATTAAGTTTGTAAAATATGTATATTAATA
131 TTCTATCGTCTTCTTTAAGAATTTTATGATTGAATAATTAAGTTTGTAAAATATGTATATTAATA
1992179 ATAATAAGAAATTAATTAGATATTATTTACAATCACCTTAAATTATTTAAAAATATATTAATTAA
196 ATAATAAGAAATTAATTAGATATTATTTACAATCACCTTAAATTATTTAAAAATATATTAATTAA
1992244 TATTAAATATAAATATAAAT
261 TATTAAATATAAATATAAAT
*
1992264 ATGTTTTTCAACTTCAAACCTCCGACTAGTGTCTCCGTAATTCTCTAACTACGAGAATGTTTTAT
1 ATGTTTTTCAACTTCAAACCTCTGACTAGTGTCTCCGTAATTCTCTAACTACGAGAATGTTTTAT
1992329 ATAAAAATAATTAAAATTTAAAACTAACTAATATTAAAACTCATTGAAATCTTAATAATAAAATA
66 ATAAAAATAATTAAAATTTAAAACTAACTAATATTAAAACTCATTGAAATCTTAATAATAAAATA
1992394 TTCTATCGTCTTCTTTAAGAATTTTATGATTGAATAATTAAGTTTGTAAAATATGTATATTAATA
131 TTCTATCGTCTTCTTTAAGAATTTTATGATTGAATAATTAAGTTTGTAAAATATGTATATTAATA
1992459 ATAATAAGAAATTAATTAGATATTATTTACAATCACCTTAAATTATTTAAAAATATATTAATTAA
196 ATAATAAGAAATTAATTAGATATTATTTACAATCACCTTAAATTATTTAAAAATATATTAATTAA
1992524 TATTAAATATAAATATAAAT
261 TATTAAATATAAATATAAAT
1992544 ATGTTTTTCAACTTCAAACCTCTGACTAGTGTCTCCGTAATTCTCTAACTACGAGAATGTTTTAT
1 ATGTTTTTCAACTTCAAACCTCTGACTAGTGTCTCCGTAATTCTCTAACTACGAGAATGTTTTAT
1992609 ATAAAAATAATTAAAATTTAAAACTAACTAATATTAAAACTCATTGAAATCTTAATAATAAAATA
66 ATAAAAATAATTAAAATTTAAAACTAACTAATATTAAAACTCATTGAAATCTTAATAATAAAATA
1992674 TTCTATCGTCTTCTTTAAGAATTTTATGATTGAATAATTAAGTTTGTAAAATATGTATATTAATA
131 TTCTATCGTCTTCTTTAAGAATTTTATGATTGAATAATTAAGTTTGTAAAATATGTATATTAATA
1992739 ATAATAAGAAATTAATTAGATATTATTTACAATCACCTTAAATTATTT-AAAATATATTAATTAA
196 ATAATAAGAAATTAATTAGATATTATTTACAATCACCTTAAATTATTTAAAAATATATTAATTAA
1992803 TATTAAATATAAATATAAAT
261 TATTAAATATAAATATAAAT
1992823 AT
1 AT
1992825 AAATATAAAT
Statistics
Matches: 559, Mismatches: 2, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
279 38 0.07
280 521 0.93
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (280 bp):
ATGTTTTTCAACTTCAAACCTCTGACTAGTGTCTCCGTAATTCTCTAACTACGAGAATGTTTTAT
ATAAAAATAATTAAAATTTAAAACTAACTAATATTAAAACTCATTGAAATCTTAATAATAAAATA
TTCTATCGTCTTCTTTAAGAATTTTATGATTGAATAATTAAGTTTGTAAAATATGTATATTAATA
ATAATAAGAAATTAATTAGATATTATTTACAATCACCTTAAATTATTTAAAAATATATTAATTAA
TATTAAATATAAATATAAAT
Found at i:1993094 original size:6 final size:6
Alignment explanation
Indices: 1992806--1993091 Score: 448
Period size: 6 Copynumber: 47.7 Consensus size: 6
1992796 TAATTAATAT
* * * * * * * *
1992806 TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA
1 TAAACA TAAACA TAAACA TAAACA TAAACA TAAACA TAAACA TAAACA
* * *
1992854 TAATA-T TAAATA TTAACA TAAACA TAAACA TAAACA TAAACA TAAACA
1 TAA-ACA TAAACA TAAACA TAAACA TAAACA TAAACA TAAACA TAAACA
1992902 TAAACA TAAACA TAAACA TAAACA TAAACA TAAACA TAAACA TAAACA
1 TAAACA TAAACA TAAACA TAAACA TAAACA TAAACA TAAACA TAAACA
1992950 TAAACA TAAACA TAAACA TAAACA TAAACA TAAACA TAAACA TAAACA
1 TAAACA TAAACA TAAACA TAAACA TAAACA TAAACA TAAACA TAAACA
1992998 TAAACA TAAACA TAAACA TAAACA TAAACA TAAACA TAAACA TAAACA
1 TAAACA TAAACA TAAACA TAAACA TAAACA TAAACA TAAACA TAAACA
*
1993046 TAAACA TAAACA TAAACA TAAACA TAAACA TAAACA TAAATA TAAA
1 TAAACA TAAACA TAAACA TAAACA TAAACA TAAACA TAAACA TAAA
1993092 TATGTAAAAA
Statistics
Matches: 272, Mismatches: 6, Indels: 4
0.96 0.02 0.01
Matches are distributed among these distances:
5 1 0.00
6 270 0.99
7 1 0.00
ACGTcount: A:0.66, C:0.13, G:0.00, T:0.21
Consensus pattern (6 bp):
TAAACA
Found at i:2001901 original size:28 final size:28
Alignment explanation
Indices: 2001861--2001918 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
2001851 TGGAAGTAAA
2001861 GAACCCACAACCCATCATTACCAAATCT
1 GAACCCACAACCCATCATTACCAAATCT
*
2001889 GAACCCACTACCCATCATTACCAAATCT
1 GAACCCACAACCCATCATTACCAAATCT
2001917 GA
1 GA
2001919 TGGACGAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.38, C:0.38, G:0.05, T:0.19
Consensus pattern (28 bp):
GAACCCACAACCCATCATTACCAAATCT
Found at i:2011976 original size:17 final size:17
Alignment explanation
Indices: 2011954--2011997 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
2011944 TGATTAAGTG
2011954 TTGAATGATTTAATGGA
1 TTGAATGATTTAATGGA
*
2011971 TTGAATGATTTAATGGT
1 TTGAATGATTTAATGGA
2011988 TTGAATGATT
1 TTGAATGATT
2011998 CAAAAGCTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.32, C:0.00, G:0.23, T:0.45
Consensus pattern (17 bp):
TTGAATGATTTAATGGA
Found at i:2016802 original size:23 final size:23
Alignment explanation
Indices: 2016776--2016839 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
2016766 CAGCTCATAT
2016776 AATTACACCGAAGTGCCACGTAG
1 AATTACACCGAAGTGCCACGTAG
* *
2016799 AATTGCACC-AGAGTGCCGCGTAG
1 AATTACACCGA-AGTGCCACGTAG
*
2016822 AATTACACCGTAGTGCCA
1 AATTACACCGAAGTGCCA
2016840 TATAATAATG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
22 1 0.03
23 33 0.97
ACGTcount: A:0.31, C:0.27, G:0.23, T:0.19
Consensus pattern (23 bp):
AATTACACCGAAGTGCCACGTAG
Found at i:2017038 original size:103 final size:103
Alignment explanation
Indices: 2016859--2017072 Score: 367
Period size: 103 Copynumber: 2.1 Consensus size: 103
2016849 GTCCATAAGG
* *
2016859 ACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGACT
1 ACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACT
2016924 TCACACATGTTCCAAAGAATACATATATATCCCGAAGA
66 TCACACATGTTCCAAAGAATACATATATATCCCGAAGA
*
2016962 ACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACC-GAAC
1 ACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAG-AC
* *
2017026 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAGG
65 TTCACACATGTTCCAAAGAATACATATATATCCCGAAGA
2017065 ACCACATA
1 ACCACATA
2017073 GACATATTAT
Statistics
Matches: 105, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
102 1 0.01
103 104 0.99
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.26
Consensus pattern (103 bp):
ACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACT
TCACACATGTTCCAAAGAATACATATATATCCCGAAGA
Found at i:2017617 original size:64 final size:67
Alignment explanation
Indices: 2017507--2017634 Score: 192
Period size: 64 Copynumber: 2.0 Consensus size: 67
2017497 ATTTTCATCT
2017507 TTTAATGGAGGTATGCATCGATGCACTACACCATGCATCGATGCATAAATCCAAGTCGATGTTTG
1 TTTAATGGAGGTATGCATCGATGCACTACACCATGCATCGATGCATAAATCCAAGTCGATGTTTG
2017572 TA
66 TA
* * *
2017574 TTTAATGG-GG-ATGCATCGATGCACT-C-CTTATGCATCGATGCATAAATCCTATTCGATGTTT
1 TTTAATGGAGGTATGCATCGATGCACTACAC-CATGCATCGATGCATAAATCCAAGTCGATGTTT
2017635 TCTTTTTAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
63 1 0.02
64 31 0.54
65 15 0.26
66 2 0.04
67 8 0.14
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (67 bp):
TTTAATGGAGGTATGCATCGATGCACTACACCATGCATCGATGCATAAATCCAAGTCGATGTTTG
TA
Found at i:2017652 original size:64 final size:62
Alignment explanation
Indices: 2017519--2017679 Score: 171
Period size: 64 Copynumber: 2.5 Consensus size: 62
2017509 TAATGGAGGT
* * *
2017519 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCAAGTCGATGTTTGTATTTAATGGGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCCAAGTCGATGTTTCTATTTAAT-GGA
* * * *
2017584 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTTTTTAAAT-TA
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCCAAGTCGATG-TTTCTATTT-AATGGA
* *
2017648 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
2017680 CCTTAAACAA
Statistics
Matches: 83, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
63 1 0.01
64 56 0.67
65 23 0.28
66 3 0.04
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (62 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCCAAGTCGATGTTTCTATTTAATGGA
Found at i:2027461 original size:29 final size:29
Alignment explanation
Indices: 2027419--2027505 Score: 156
Period size: 29 Copynumber: 3.0 Consensus size: 29
2027409 TTCCTCCATA
* *
2027419 GCCATTTTGTACTGATCAGTCCCAAGGCC
1 GCCATTTTCTACTGATCAGTCCAAAGGCC
2027448 GCCATTTTCTACTGATCAGTCCAAAGGCC
1 GCCATTTTCTACTGATCAGTCCAAAGGCC
2027477 GCCATTTTCTACTGATCAGTCCAAAGGCC
1 GCCATTTTCTACTGATCAGTCCAAAGGCC
2027506 TTAACCCTTC
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 56 1.00
ACGTcount: A:0.23, C:0.31, G:0.18, T:0.28
Consensus pattern (29 bp):
GCCATTTTCTACTGATCAGTCCAAAGGCC
Found at i:2030735 original size:2 final size:2
Alignment explanation
Indices: 2030728--2030752 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2030718 AAGGAGAATC
2030728 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 A
2030753 AACAAAATCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2032029 original size:20 final size:17
Alignment explanation
Indices: 2032004--2032055 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 17
2031994 CAGTTGAACG
*
2032004 GTATCGATACTAATGTACTA
1 GTATCGATACTAA-GT--GA
2032024 GTATCGATACTGAAGTGA
1 GTATCGATACT-AAGTGA
2032042 GTATCGATACTAAG
1 GTATCGATACTAAG
2032056 AAAAAGGTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 3 0.10
18 12 0.40
20 13 0.43
21 2 0.07
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (17 bp):
GTATCGATACTAAGTGA
Found at i:2032148 original size:95 final size:94
Alignment explanation
Indices: 2032048--2032234 Score: 245
Period size: 94 Copynumber: 2.0 Consensus size: 94
2032038 GTGAGTATCG
*
2032048 ATACTAAGA-AAAAGGTATCGATACC-TAGGAATCCTA-AAGGTAGAAATGATATCGATACTGAA
1 ATACTAAGAGAAAA-GTATCAATACCAT-GG-ATCC-AGAAGGTAGAAATGATATCGATACTGAA
* *
2032110 AAGGAGTATCGATATCATAGTATATAAGTATTA
62 AAGGAGTATCGATACCATAGTATAGAAGTATTA
* * * *
2032143 ATACTAGGAGAAAAGTATCAATACCATGGATCCAGAATGTAGAAATGGTATCGATACTGAAAGGG
1 ATACTAAGAGAAAAGTATCAATACCATGGATCCAGAAGGTAGAAATGATATCGATACTGAAAAGG
*
2032208 AGTATCGGTACCATAGTATAGAAGTAT
66 AGTATCGATACCATAGTATAGAAGTAT
2032235 CGATACCATG
Statistics
Matches: 81, Mismatches: 8, Indels: 7
0.84 0.08 0.07
Matches are distributed among these distances:
93 1 0.01
94 55 0.68
95 20 0.25
96 5 0.06
ACGTcount: A:0.42, C:0.11, G:0.21, T:0.25
Consensus pattern (94 bp):
ATACTAAGAGAAAAGTATCAATACCATGGATCCAGAAGGTAGAAATGATATCGATACTGAAAAGG
AGTATCGATACCATAGTATAGAAGTATTA
Found at i:2032667 original size:54 final size:54
Alignment explanation
Indices: 2032585--2032867 Score: 273
Period size: 54 Copynumber: 5.0 Consensus size: 54
2032575 ACCCAATTAG
* * *
2032585 CACTATGTGTGCAACCTAAGAATTTCATAATAAATTTATGAATTTCCGTATTGA
1 CACTATTTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGA
* *
2032639 CACTATTTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGG
1 CACTATTTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGA
* * *
2032693 CATTATGTGTTCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTA-TGAA
1 CACTATTTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTG-A
* * *
2032747 TTTCCGTATTGGCATTATGTGTACAACCTAATAAATTCATAATAAGTTTATGAATTTCCTTATTG
1 ----C--ACT---ATT-TGTG--CAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTG
2032812 A
54 A
* * * *
2032813 CACTGTGTGTTTGCAACCTAAGAAATTCATAATGAA-TTTATAAATTTTCGTATTG
1 CACTAT-T-TGTGCAACCTAAGAAATTCATAAT-AAGTTTATGAATTTCCGTATTG
2032868 GTATTAAATG
Statistics
Matches: 191, Mismatches: 22, Indels: 30
0.79 0.09 0.12
Matches are distributed among these distances:
53 2 0.01
54 95 0.50
56 35 0.18
57 3 0.02
58 5 0.03
60 5 0.03
62 1 0.01
63 2 0.01
64 3 0.02
66 38 0.20
67 2 0.01
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.39
Consensus pattern (54 bp):
CACTATTTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGA
Found at i:2032746 original size:12 final size:12
Alignment explanation
Indices: 2032729--2032755 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2032719 ATAATAAGTT
2032729 TATGAATTTCCG
1 TATGAATTTCCG
2032741 TATGAATTTCCG
1 TATGAATTTCCG
2032753 TAT
1 TAT
2032756 TGGCATTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (12 bp):
TATGAATTTCCG
Found at i:2032783 original size:66 final size:66
Alignment explanation
Indices: 2032675--2032805 Score: 235
Period size: 66 Copynumber: 2.0 Consensus size: 66
2032665 ATAATAAGTT
* *
2032675 TATGAATTTTCGTATTGGCATTATGTGTTCAACCTAAGAAATTCATAATAAGTTTATGAATTTCC
1 TATGAATTTCCGTATTGGCATTATGTGTACAACCTAAGAAATTCATAATAAGTTTATGAATTTCC
2032740 G
66 G
*
2032741 TATGAATTTCCGTATTGGCATTATGTGTACAACCTAATAAATTCATAATAAGTTTATGAATTTCC
1 TATGAATTTCCGTATTGGCATTATGTGTACAACCTAAGAAATTCATAATAAGTTTATGAATTTCC
2032806 TTATTGACAC
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (66 bp):
TATGAATTTCCGTATTGGCATTATGTGTACAACCTAAGAAATTCATAATAAGTTTATGAATTTCC
G
Found at i:2036883 original size:18 final size:15
Alignment explanation
Indices: 2036848--2036879 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2036838 ATAGTTCGAG
2036848 TGCTACACAAAATGA
1 TGCTACACAAAATGA
*
2036863 TGCTACACAAGATGA
1 TGCTACACAAAATGA
2036878 TG
1 TG
2036880 ATGCACATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (15 bp):
TGCTACACAAAATGA
Found at i:2039290 original size:102 final size:104
Alignment explanation
Indices: 2039164--2039368 Score: 315
Period size: 102 Copynumber: 2.0 Consensus size: 104
2039154 TTTGGCTGCC
* ** *
2039164 ATATATATATATATGTTTCGTTTTGCCAAATAATTGTTTTAATT-TTTCATGTTCTTCTACATGT
1 ATATATATACATACATTTCGTTTTGCCAAATAATTGTTTTAATTATTCCATGTTCTTCTACATGT
2039228 A-GGGCAAGCTGTATGTTCTAGCTACACTATGTATGGAT
66 AGGGGCAAGCTGTATGTTCTAGCTACACTATGTATGGAT
* * *
2039266 ATATATATACATACATTTCTTTTTGCCAAATAATTGTTTTAATTATTCCGTGTTTTTCTACATGT
1 ATATATATACATACATTTCGTTTTGCCAAATAATTGTTTTAATTATTCCATGTTCTTCTACATGT
* *
2039331 AGGGGCAAGCTTTATGTTCTAGCTACACTATTTATGGA
66 AGGGGCAAGCTGTATGTTCTAGCTACACTATGTATGGA
2039369 CTGCAAATAT
Statistics
Matches: 92, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
102 40 0.43
103 18 0.20
104 34 0.37
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.45
Consensus pattern (104 bp):
ATATATATACATACATTTCGTTTTGCCAAATAATTGTTTTAATTATTCCATGTTCTTCTACATGT
AGGGGCAAGCTGTATGTTCTAGCTACACTATGTATGGAT
Found at i:2041207 original size:12 final size:12
Alignment explanation
Indices: 2041190--2041215 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2041180 TAGTACTATT
2041190 TTATAGACCGGC
1 TTATAGACCGGC
2041202 TTATAGACCGGC
1 TTATAGACCGGC
2041214 TT
1 TT
2041216 GAATTAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (12 bp):
TTATAGACCGGC
Found at i:2049187 original size:6 final size:6
Alignment explanation
Indices: 2049170--2049222 Score: 52
Period size: 6 Copynumber: 8.8 Consensus size: 6
2049160 AGTACACGAT
* * * * * *
2049170 GGACAT GGACAC GGACAC GAACAC GGTCAC GGCCAC GGCCAC GGCCAC
1 GGACAC GGACAC GGACAC GGACAC GGACAC GGACAC GGACAC GGACAC
2049218 GGACA
1 GGACA
2049223 TGGGCATGGA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.28, C:0.36, G:0.32, T:0.04
Consensus pattern (6 bp):
GGACAC
Found at i:2052988 original size:2 final size:2
Alignment explanation
Indices: 2052981--2053016 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2052971 TAATAATTTT
*
2052981 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2053017 CCTCGTGAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2056566 original size:36 final size:37
Alignment explanation
Indices: 2056521--2056594 Score: 123
Period size: 36 Copynumber: 2.0 Consensus size: 37
2056511 CCACCGAAAG
2056521 TGGCCTCCAAAATCCACCGAAAATT-CCCACCAATTT
1 TGGCCTCCAAAATCCACCGAAAATTGCCCACCAATTT
* *
2056557 TGGCTTCCAAAATCCACCGAAAATTGGCCACCAATTT
1 TGGCCTCCAAAATCCACCGAAAATTGCCCACCAATTT
2056594 T
1 T
2056595 AACTTTTCCA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
36 24 0.69
37 11 0.31
ACGTcount: A:0.32, C:0.32, G:0.11, T:0.24
Consensus pattern (37 bp):
TGGCCTCCAAAATCCACCGAAAATTGCCCACCAATTT
Found at i:2063280 original size:21 final size:21
Alignment explanation
Indices: 2063248--2063301 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
2063238 GTACGGTTAC
*
2063248 GGTGGACATGGAAGTTACAGT
1 GGTGGACATGGAAGTAACAGT
* *
2063269 GGTGGACGTGGAAGTAACGGT
1 GGTGGACATGGAAGTAACAGT
*
2063290 GGTGGCCATGGA
1 GGTGGACATGGA
2063302 GGGTACAAAG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.24, C:0.11, G:0.44, T:0.20
Consensus pattern (21 bp):
GGTGGACATGGAAGTAACAGT
Found at i:2063314 original size:21 final size:21
Alignment explanation
Indices: 2063290--2063442 Score: 270
Period size: 21 Copynumber: 7.3 Consensus size: 21
2063280 AAGTAACGGT
*
2063290 GGTGGCCATGGAGGGTACAAA
1 GGTGGACATGGAGGGTACAAA
2063311 GGTGGACATGGAGGGTACAAA
1 GGTGGACATGGAGGGTACAAA
2063332 GGTGGACATGGAGGGTACAAA
1 GGTGGACATGGAGGGTACAAA
2063353 GGTGGACATGGAGGGTACAAA
1 GGTGGACATGGAGGGTACAAA
2063374 GGTGGACATGGAGGGTACAAA
1 GGTGGACATGGAGGGTACAAA
*
2063395 GGTGGACATGGAGGATACAAA
1 GGTGGACATGGAGGGTACAAA
* *
2063416 GTTGGCCATGGAGGGTACAAA
1 GGTGGACATGGAGGGTACAAA
2063437 GGTGGA
1 GGTGGA
2063443 GAGCAGAACG
Statistics
Matches: 125, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 125 1.00
ACGTcount: A:0.32, C:0.10, G:0.42, T:0.15
Consensus pattern (21 bp):
GGTGGACATGGAGGGTACAAA
Found at i:2076129 original size:6 final size:6
Alignment explanation
Indices: 2076118--2076143 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2076108 GCTAACATCA
2076118 GGAGCT GGAGCT GGAGCT GGAGCT GG
1 GGAGCT GGAGCT GGAGCT GGAGCT GG
2076144 TGCAGGCATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.54, T:0.15
Consensus pattern (6 bp):
GGAGCT
Found at i:2080579 original size:3 final size:3
Alignment explanation
Indices: 2080571--2080661 Score: 150
Period size: 3 Copynumber: 30.3 Consensus size: 3
2080561 CAATTATTCA
2080571 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT
2080617 AAT -AT AAT AAAT AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2080661 A
1 A
2080662 CAACATGCAT
Statistics
Matches: 84, Mismatches: 0, Indels: 8
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.05
3 74 0.88
4 6 0.07
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2083141 original size:20 final size:20
Alignment explanation
Indices: 2083116--2083155 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2083106 ATTATCTATT
2083116 CATTCATTCAGGGTTTTGTA
1 CATTCATTCAGGGTTTTGTA
*
2083136 CATTCATTTAGGGTTTTGTA
1 CATTCATTCAGGGTTTTGTA
2083156 TTTGATGTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.20, C:0.12, G:0.20, T:0.47
Consensus pattern (20 bp):
CATTCATTCAGGGTTTTGTA
Found at i:2083659 original size:35 final size:37
Alignment explanation
Indices: 2083620--2083695 Score: 113
Period size: 36 Copynumber: 2.1 Consensus size: 37
2083610 GGTAAGGGAT
*
2083620 TGGTGGTTA-TATAGGCGTG-AAATGGTGATAGAAGA
1 TGGTGGATATTATAGGCGTGAAAATGGTGATAGAAGA
*
2083655 TGGT-GATATTATAGGCGTGAAAATGGTGATGGAAGA
1 TGGTGGATATTATAGGCGTGAAAATGGTGATAGAAGA
2083691 TGGTG
1 TGGTG
2083696 ATGTTTAGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
34 3 0.08
35 14 0.39
36 19 0.53
ACGTcount: A:0.30, C:0.03, G:0.38, T:0.29
Consensus pattern (37 bp):
TGGTGGATATTATAGGCGTGAAAATGGTGATAGAAGA
Found at i:2083690 original size:36 final size:35
Alignment explanation
Indices: 2083629--2083697 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 35
2083619 TTGGTGGTTA
2083629 TATAGGCGTGAAATGGTGATAGAAGATGGTGATAT
1 TATAGGCGTGAAATGGTGATAGAAGATGGTGATAT
*
2083664 TATAGGCGTGAAAATGGTGATGGAAGATGGTGAT
1 TATAGGCGTG-AAATGGTGATAGAAGATGGTGAT
2083698 GTTTAGGTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 10 0.31
36 22 0.69
ACGTcount: A:0.33, C:0.03, G:0.36, T:0.28
Consensus pattern (35 bp):
TATAGGCGTGAAATGGTGATAGAAGATGGTGATAT
Found at i:2085609 original size:40 final size:41
Alignment explanation
Indices: 2085565--2085650 Score: 138
Period size: 41 Copynumber: 2.1 Consensus size: 41
2085555 TTGCATTTCG
*
2085565 CGTTGCGATAGTCTA-CAATGTCGTTGCGATTTTTCAAATT
1 CGTTGCGATAGTCTACCAATGTCGTTGCGATTTTCCAAATT
**
2085605 CGTTGCGATAGTCTACCGTTGTCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCTACCAATGTCGTTGCGATTTTCCAAATT
2085646 CGTTG
1 CGTTG
2085651 ATAGTTAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 15 0.36
41 27 0.64
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.40
Consensus pattern (41 bp):
CGTTGCGATAGTCTACCAATGTCGTTGCGATTTTCCAAATT
Found at i:2085650 original size:19 final size:19
Alignment explanation
Indices: 2085585--2085650 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 19
2085575 GTCTACAATG
*
2085585 TCGTTGCGATTTTTCAAAT
1 TCGTTGCGATTTTCCAAAT
* **
2085604 TCGTTGCGATAGTCTACC-GTT
1 TCGTTGCGAT--T-TTCCAAAT
2085625 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
2085645 TCGTTG
1 TCGTTG
2085651 ATAGTTAAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 10
0.67 0.13 0.19
Matches are distributed among these distances:
19 19 0.54
20 2 0.06
21 2 0.06
22 12 0.34
ACGTcount: A:0.17, C:0.20, G:0.21, T:0.42
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:2085745 original size:6 final size:6
Alignment explanation
Indices: 2085734--2085758 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2085724 TACGTATTAT
2085734 CACGAC CACGAC CACGAC CACGAC C
1 CACGAC CACGAC CACGAC CACGAC C
2085759 CGAGACGGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.52, G:0.16, T:0.00
Consensus pattern (6 bp):
CACGAC
Found at i:2086279 original size:6 final size:6
Alignment explanation
Indices: 2086253--2086343 Score: 161
Period size: 6 Copynumber: 15.7 Consensus size: 6
2086243 TCTCGTCTCG
2086253 GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
2086298 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTC
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTC
2086344 ATACGTGTCT
Statistics
Matches: 85, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 15 0.18
6 70 0.82
ACGTcount: A:0.00, C:0.18, G:0.52, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:2086762 original size:15 final size:13
Alignment explanation
Indices: 2086735--2086759 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2086725 GGTGCGTTTA
2086735 TATTTTTTAAAAT
1 TATTTTTTAAAAT
2086748 TATTTTTTAAAA
1 TATTTTTTAAAA
2086760 AATAAAAGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TATTTTTTAAAAT
Found at i:2087062 original size:10 final size:11
Alignment explanation
Indices: 2087042--2087084 Score: 52
Period size: 10 Copynumber: 3.9 Consensus size: 11
2087032 GGACCGGCTG
2087042 AAAACCGGGAA
1 AAAACCGGGAA
*
2087053 AAAACCGGAAAA
1 AAAACCGG-GAA
*
2087065 AAAAACGGG-A
1 AAAACCGGGAA
2087075 AAAACCGGGA
1 AAAACCGGGA
2087085 TTTTTGTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
10 9 0.35
11 8 0.31
12 9 0.35
ACGTcount: A:0.58, C:0.16, G:0.26, T:0.00
Consensus pattern (11 bp):
AAAACCGGGAA
Found at i:2088741 original size:17 final size:15
Alignment explanation
Indices: 2088706--2088744 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
2088696 AAATTCTAAA
*
2088706 TATTTAAATAAAAAT
1 TATTTATATAAAAAT
2088721 TATTTATATAAAAAAT
1 TATTTATAT-AAAAAT
2088737 CTATTTAT
1 -TATTTAT
2088745 TGATAATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.38
16 6 0.29
17 7 0.33
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (15 bp):
TATTTATATAAAAAT
Found at i:2096516 original size:26 final size:27
Alignment explanation
Indices: 2096487--2096544 Score: 68
Period size: 25 Copynumber: 2.2 Consensus size: 27
2096477 CCGCTTAATT
2096487 TAAAATTTATAA-AATTTTAGAG-AAAA
1 TAAAATTTA-AAGAATTTTAGAGAAAAA
* *
2096513 T-AAACTTAAAGAATTTTATAGAAAAA
1 TAAAATTTAAAGAATTTTAGAGAAAAA
2096539 TAAAAT
1 TAAAAT
2096545 AAATTACCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
24 2 0.08
25 15 0.58
26 6 0.23
27 3 0.12
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.33
Consensus pattern (27 bp):
TAAAATTTAAAGAATTTTAGAGAAAAA
Found at i:2101739 original size:2 final size:2
Alignment explanation
Indices: 2101732--2101782 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
2101722 CAATTCGAAA
2101732 AT AT AT AT AT 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 AT AT AT AT AT
2101774 AT AT AT AT A
1 AT AT AT AT A
2101783 GTGCTTAAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2109260 original size:42 final size:41
Alignment explanation
Indices: 2109168--2109279 Score: 106
Period size: 42 Copynumber: 2.7 Consensus size: 41
2109158 GTAAAAATGT
* *
2109168 CGCAATAGAGTAG-ACATTTAGCGGCGTTTTAGCCCAAACGC
1 CGCAATAGAGTGGTA-AATTAGCGGCGTTTTAGCCCAAACGC
* *
2109209 CGTAATAGAGT-GTTAATGTAGCGGCGTTTATA-CCACAAACGC
1 CGCAATAGAGTGGTAAAT-TAGCGGCGTTT-TAGCC-CAAACGC
*
2109251 TC-CAATAGAGTGGTAAATTAGTGGCGTTT
1 -CGCAATAGAGTGGTAAATTAGCGGCGTTT
2109280 GTATCTAAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
40 3 0.05
41 23 0.39
42 27 0.46
43 6 0.10
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (41 bp):
CGCAATAGAGTGGTAAATTAGCGGCGTTTTAGCCCAAACGC
Found at i:2110716 original size:41 final size:41
Alignment explanation
Indices: 2110647--2110843 Score: 127
Period size: 41 Copynumber: 4.8 Consensus size: 41
2110637 TGAGTAGTAC
* *
2110647 ATTAGCGGCA-TTTTTATACAAACACCGCAATAGGTGTA-AT
1 ATTAGTGGCATTTTTTA-ACAAACGCCGCAATAGGTGTACAT
* **
2110687 ATATAGTGGCTTTTTTTAACAAACGCCGCAACATATTTGTAC-T
1 AT-TAGTGGCATTTTTTAACAAACGCCGC-A-ATAGGTGTACAT
* * * ** * *
2110730 -TTAGTGGCATTTTTAAACTCAAACGTCGCAAAAAATTTAGAT
1 ATTAGTGGCATTTTTTAA--CAAACGCCGCAATAGGTGTACAT
* * * *
2110772 AGTAGTGGC-GTTTATAACAAACGCCGCAGTAGGTGTACA-
1 ATTAGTGGCATTTTTTAACAAACGCCGCAATAGGTGTACAT
* *
2110811 ATTTAGTGGCATTTTTCACCAAACGCCGCAATA
1 A-TTAGTGGCATTTTTTAACAAACGCCGCAATA
2110844 TATTTGAATT
Statistics
Matches: 116, Mismatches: 30, Indels: 21
0.69 0.18 0.13
Matches are distributed among these distances:
39 1 0.01
40 24 0.21
41 52 0.45
42 15 0.13
43 24 0.21
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (41 bp):
ATTAGTGGCATTTTTTAACAAACGCCGCAATAGGTGTACAT
Found at i:2110884 original size:124 final size:123
Alignment explanation
Indices: 2110659--2110884 Score: 276
Period size: 124 Copynumber: 1.8 Consensus size: 123
2110649 TAGCGGCATT
* *
2110659 TTTATACAAACACCGCAATAGGTGTAATATATAGTGGCTTTTTTTAACAAACGCCGCAACATATT
1 TTTATACAAACACCGCAATAGGTGTAATATATAGTGGCATTTTTCAACAAACGCCGCAACATATT
* * * * *
2110724 TGTACTTTAGTGGCATTTTTAAACTCAAACGTCGCAAAAAATTTAGATAGTAGTGGCG
66 TGAACTTTAGCGGCATTTCTAAACACAAACGCCGCAAAAAATTTAGATAGTAGTGGCG
* * * * *
2110782 TTTATAACAAACGCCGCAGTAGGTGTACA-ATTTAGTGGCATTTTTCACCAAACGCCGCAATATA
1 TTTAT-ACAAACACCGCAATAGGTGTA-ATATATAGTGGCATTTTTCAACAAACGCCGCAACATA
* * *
2110846 TTTGAATTGTTA-CGGCGTTTCTAGACACAAACGCCGCAA
64 TTTGAACT-TTAGCGGCATTTCTAAACACAAACGCCGCAA
2110885 TATATATGGA
Statistics
Matches: 85, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
123 5 0.06
124 76 0.89
125 4 0.05
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Consensus pattern (123 bp):
TTTATACAAACACCGCAATAGGTGTAATATATAGTGGCATTTTTCAACAAACGCCGCAACATATT
TGAACTTTAGCGGCATTTCTAAACACAAACGCCGCAAAAAATTTAGATAGTAGTGGCG
Found at i:2110907 original size:124 final size:123
Alignment explanation
Indices: 2110659--2110910 Score: 265
Period size: 124 Copynumber: 2.0 Consensus size: 123
2110649 TAGCGGCATT
* *
2110659 TTTATACAAACACCGCAATAGGTGTAATATATAGTGGCTTTTTTTAACAAACGCCGCAACATATT
1 TTTATACAAACACCGCAATAGGTGTAATATATAGTGGCATTTTTCAACAAACGCCGCAACATATT
* * * * * * *
2110724 TGTACTTTAGTGGCATTTTTAAACTCAAACGTCGCAAAAAATTTAGATAGTAGTGGCG
66 TGAACTTTAGCGGCATTTCTAAACACAAACGCCGCAAAAAATATAGACAGTAGTGGCG
* * * * *
2110782 TTTATAACAAACGCCGCAGTAGGTGTACA-ATTTAGTGGCATTTTTCACCAAACGCCGCAATATA
1 TTTAT-ACAAACACCGCAATAGGTGTA-ATATATAGTGGCATTTTTCAACAAACGCCGCAACATA
* * * * * * * *
2110846 TTTGAATTGTTA-CGGCGTTTCTAGACACAAACGCCGCAATATATATGGACATTAGTTGCG
64 TTTGAACT-TTAGCGGCATTTCTAAACACAAACGCCGCAAAAAATATAGACAGTAGTGGCG
2110906 TTTAT
1 TTTAT
2110911 TAAAAATGCT
Statistics
Matches: 104, Mismatches: 22, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
123 5 0.05
124 95 0.91
125 4 0.04
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (123 bp):
TTTATACAAACACCGCAATAGGTGTAATATATAGTGGCATTTTTCAACAAACGCCGCAACATATT
TGAACTTTAGCGGCATTTCTAAACACAAACGCCGCAAAAAATATAGACAGTAGTGGCG
Found at i:2111317 original size:81 final size:81
Alignment explanation
Indices: 2111169--2111330 Score: 225
Period size: 81 Copynumber: 2.0 Consensus size: 81
2111159 GTATGCTTTA
* * *
2111169 ACACCGTCGCTGCCCGGTACTCAACTGCTGCTGCTTGTCGCCGCTTGAAGCCTTCAATCCTGCTG
1 ACACCGTCGCTGCCCGGTACTCAACTGCTGCTGCTCGTCGCCGCTTGAAGCCGTCAATCCTGATG
*
2111234 CTGCTCGTCATCACCT
66 CTGCTCATCATCACCT
* * * ** *
2111250 ACACCGTCGCTGCCCGGTACTCAACTGCTGCTGCTCGTTGGCGCTTGAAGTCGTCGTTCTTGATG
1 ACACCGTCGCTGCCCGGTACTCAACTGCTGCTGCTCGTCGCCGCTTGAAGCCGTCAATCCTGATG
*
2111315 CTGCTCATTATCACCT
66 CTGCTCATCATCACCT
2111331 CCATTGTTAC
Statistics
Matches: 70, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
81 70 1.00
ACGTcount: A:0.14, C:0.35, G:0.22, T:0.29
Consensus pattern (81 bp):
ACACCGTCGCTGCCCGGTACTCAACTGCTGCTGCTCGTCGCCGCTTGAAGCCGTCAATCCTGATG
CTGCTCATCATCACCT
Found at i:2114006 original size:17 final size:17
Alignment explanation
Indices: 2113981--2114014 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2113971 GTAACTTACA
*
2113981 AAAACAAAATATTTATT
1 AAAACAAAATAATTATT
*
2113998 AAAATAAAATAATTATT
1 AAAACAAAATAATTATT
2114015 TTATCATAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
AAAACAAAATAATTATT
Found at i:2114303 original size:31 final size:30
Alignment explanation
Indices: 2114171--2114303 Score: 77
Period size: 34 Copynumber: 4.1 Consensus size: 30
2114161 CTGTGACTAG
* * *
2114171 ATAATTTTGTTACAATTTGTTATTGTGAAAGA
1 ATAAATTTGTCACAATTT-TTATTTTGAAA-A
* * **
2114203 ATATTATTTGTCACATTTTTTTATAAATGAGAAA
1 ATA-AATTTGTCACA-ATTTTTAT-TTTGA-AAA
* * * *
2114237 TTAATATTTGTTACAAATTGTTATTTTGATTAA
1 ATAA-ATTTGTCAC-AATTTTTATTTTGA-AAA
2114270 ATAAATTTGTCACAATTTTTATTTTGACAAA
1 ATAAATTTGTCACAATTTTTATTTTGA-AAA
2114301 ATA
1 ATA
2114304 TTGAGACGAA
Statistics
Matches: 75, Mismatches: 20, Indels: 13
0.69 0.19 0.12
Matches are distributed among these distances:
31 18 0.24
32 11 0.15
33 20 0.27
34 23 0.31
35 3 0.04
ACGTcount: A:0.37, C:0.05, G:0.10, T:0.48
Consensus pattern (30 bp):
ATAAATTTGTCACAATTTTTATTTTGAAAA
Found at i:2114516 original size:198 final size:195
Alignment explanation
Indices: 2114166--2114670 Score: 708
Period size: 198 Copynumber: 2.6 Consensus size: 195
2114156 TTTTACTGTG
* *
2114166 ACTAGATAATTTTGTTACAATTTGTTATTGTGAAAGAATATTATTTGTCACATTTTTTTATAAAT
1 ACTAAATAATTTTGTTACAATTTGTTATTGTGAAAGAATATTATTTGTCACAATTTTTTAT--AT
*
2114231 GAGAAATTAATATTTGTTACAAATTGTTATTTTGATTAAATAAATTTGTCACAATTTTTATTTTG
64 GAGAAATTAATATTTGTTATAAATTGTTATTTTGATTAAATAAATTTGTCACAATTTTTATTTTG
* * * *
2114296 ACAAAATATTGAGACGAAATAAATTTGACATAACTGTTTACTTTGACTAAATTTA-ACGTGTTAT
129 AAAAAATATTGAGACAAAATAAATTTGACACAACTGTTTACTTTGAATAAATTTATAC--GTTAT
2114360 TGTGA
192 TGT-A
* * *
2114365 A-TAAATCATTTTGTTACAATTTGTTATTGTGAAAGAATATTACTTGTCACAATTCTTTATGATG
1 ACTAAATAATTTTGTTACAATTTGTTATTGTGAAAGAATATTATTTGTCACAATTTTTTAT-ATG
* *
2114429 AGAAATTAATATTTGTTATAAATTATTATTTTGATTAAATAAATTTGTCAGAATTTTTTATTTTG
65 AGAAATTAATATTTGTTATAAATTGTTATTTTGATTAAATAAATTTGTCACAA-TTTTTATTTTG
* * * *
2114494 AAAAAATATTGTGACAAAATAAATTTGACACAATTTTTTATTTTGAATAAATTTATTACGTTATT
129 AAAAAATATTGAGACAAAATAAATTTGACACAACTGTTTACTTTGAATAAATTTA-TACGTTATT
2114559 GTA
193 GTA
* * * *
2114562 ACTAAATAAATTTGTTACAATTTGTTATTATGAAAGAATATTTTTTGTCATAATTTTTTATATTG
1 ACTAAATAATTTTGTTACAATTTGTTATTGTGAAAGAATATTATTTGTCACAATTTTTTATA-TG
* * *
2114627 AGAAATTAATAATTGTTATAAATTGTTATTATGACTAAATAAAT
65 AGAAATTAATATTTGTTATAAATTGTTATTTTGATTAAATAAAT
2114671 ATCGAAATCC
Statistics
Matches: 273, Mismatches: 28, Indels: 11
0.88 0.09 0.04
Matches are distributed among these distances:
197 56 0.21
198 214 0.78
199 1 0.00
200 2 0.01
ACGTcount: A:0.38, C:0.06, G:0.11, T:0.46
Consensus pattern (195 bp):
ACTAAATAATTTTGTTACAATTTGTTATTGTGAAAGAATATTATTTGTCACAATTTTTTATATGA
GAAATTAATATTTGTTATAAATTGTTATTTTGATTAAATAAATTTGTCACAATTTTTATTTTGAA
AAAATATTGAGACAAAATAAATTTGACACAACTGTTTACTTTGAATAAATTTATACGTTATTGTA
Found at i:2119321 original size:66 final size:66
Alignment explanation
Indices: 2119210--2119341 Score: 237
Period size: 66 Copynumber: 2.0 Consensus size: 66
2119200 ATTAGAAATC
*
2119210 ATACTATTGCCTTCTCTCATCTTATTATAAAATCCATGTACGATTTCTAATCAAGGTCTTGTTAA
1 ATACTATTGCCTTCTCTCATCTTATTACAAAATCCATGTACGATTTCTAATCAAGGTCTTGTTAA
2119275 T
66 T
* *
2119276 ATACTATTGCCTTCTCTCATCTTATTACAAAATCCATGTATGATTTTTAATCAAGGTCTTGTTAA
1 ATACTATTGCCTTCTCTCATCTTATTACAAAATCCATGTACGATTTCTAATCAAGGTCTTGTTAA
2119341 T
66 T
2119342 GATGATGACA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.29, C:0.19, G:0.09, T:0.43
Consensus pattern (66 bp):
ATACTATTGCCTTCTCTCATCTTATTACAAAATCCATGTACGATTTCTAATCAAGGTCTTGTTAA
T
Found at i:2120162 original size:43 final size:43
Alignment explanation
Indices: 2120066--2120181 Score: 133
Period size: 43 Copynumber: 2.7 Consensus size: 43
2120056 CTTTTGCATA
* * * * * *
2120066 AAAAACGCCACTAAATCTCAACACTTATTGCGACGTTTGTGAT
1 AAAAACGCCGCTAAATCTCAACACCTATTGCGACATTTATAAG
2120109 AAAAACGCCGCTAAATCTCAACACCTATTGCGACATTTATAAG
1 AAAAACGCCGCTAAATCTCAACACCTATTGCGACATTTATAAG
* * * **
2120152 ACAAATGCCGCTAAATATCAGTACCTATTG
1 AAAAACGCCGCTAAATCTCAACACCTATTG
2120182 TGGCGTTTGT
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 62 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (43 bp):
AAAAACGCCGCTAAATCTCAACACCTATTGCGACATTTATAAG
Found at i:2122229 original size:2 final size:2
Alignment explanation
Indices: 2122222--2122250 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2122212 GTTATTAAAT
2122222 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2122251 TTGCTTTAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2128866 original size:29 final size:29
Alignment explanation
Indices: 2128829--2128917 Score: 151
Period size: 29 Copynumber: 3.1 Consensus size: 29
2128819 CCCCAACACC
* **
2128829 CCTACAAGGTCGCCAAACACTCCCAGCGA
1 CCTACAAGGCCGCCATGCACTCCCAGCGA
2128858 CCTACAAGGCCGCCATGCACTCCCAGCGA
1 CCTACAAGGCCGCCATGCACTCCCAGCGA
2128887 CCTACAAGGCCGCCATGCACTCCCAGCGA
1 CCTACAAGGCCGCCATGCACTCCCAGCGA
2128916 CC
1 CC
2128918 AAGCCTCGAC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 57 1.00
ACGTcount: A:0.26, C:0.45, G:0.19, T:0.10
Consensus pattern (29 bp):
CCTACAAGGCCGCCATGCACTCCCAGCGA
Found at i:2128998 original size:32 final size:32
Alignment explanation
Indices: 2128957--2129021 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
2128947 ACTTAACCCT
2128957 GCTCCCTCGTGCATGGGTTGCATCCATAGCTG
1 GCTCCCTCGTGCATGGGTTGCATCCATAGCTG
2128989 GCTCCCTCGTGCATGGGTTGCATCCATAGCTG
1 GCTCCCTCGTGCATGGGTTGCATCCATAGCTG
2129021 G
1 G
2129022 GAGATTGTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.12, C:0.31, G:0.29, T:0.28
Consensus pattern (32 bp):
GCTCCCTCGTGCATGGGTTGCATCCATAGCTG
Found at i:2129491 original size:28 final size:30
Alignment explanation
Indices: 2129451--2129512 Score: 110
Period size: 28 Copynumber: 2.1 Consensus size: 30
2129441 AATTTAGTTA
2129451 ATTAGTTTGTTAGTTTAAG-T-TATATTAT
1 ATTAGTTTGTTAGTTTAAGTTATATATTAT
2129479 ATTAGTTTGTTAGTTTAAGTTATATATTAT
1 ATTAGTTTGTTAGTTTAAGTTATATATTAT
2129509 ATTA
1 ATTA
2129513 TATAAAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 19 0.59
29 1 0.03
30 12 0.38
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (30 bp):
ATTAGTTTGTTAGTTTAAGTTATATATTAT
Found at i:2129850 original size:20 final size:21
Alignment explanation
Indices: 2129806--2129850 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
2129796 AAATATTGTG
**
2129806 TTTAAAAATATTTAGTGTTGT
1 TTTAAAAATATTTAGTGTTAA
*
2129827 TTTAAAAATATTTTGT-TTAA
1 TTTAAAAATATTTAGTGTTAA
2129847 TTTA
1 TTTA
2129851 TATTATATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (21 bp):
TTTAAAAATATTTAGTGTTAA
Found at i:2133070 original size:49 final size:49
Alignment explanation
Indices: 2133013--2133348 Score: 388
Period size: 49 Copynumber: 6.4 Consensus size: 49
2133003 TTATAAGATT
*
2133013 TAGTAATGATTAGTAATGATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTT-A--A--TGAT--T--TGA
2133071 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGA
1 --TAGTAATGATTAGTAATAATGAAATTATTATTAATATTT-A--A--TG--ATT--TGA
*
2133131 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
1 --TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
* * * *
2133182 TAGTAATTATCAGTAATAATGAAATTATTATTAATTTTTAATAATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
*
2133231 TAGTAATGATTAGTAATAATGAAATTATTAGTAATATTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
*
2133280 TAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
2133329 TAGTAATGATT--TAATAATGA
1 TAGTAATGATTAGTAATAATGA
2133349 TTAGTAATAA
Statistics
Matches: 262, Mismatches: 12, Indels: 17
0.90 0.04 0.06
Matches are distributed among these distances:
47 9 0.03
49 148 0.56
51 3 0.01
53 3 0.01
55 2 0.01
57 1 0.00
59 1 0.00
60 93 0.35
62 2 0.01
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (49 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
Found at i:2133080 original size:60 final size:59
Alignment explanation
Indices: 2133012--2133465 Score: 359
Period size: 60 Copynumber: 8.1 Consensus size: 59
2133002 TTTATAAGAT
*
2133012 TTAGTAATGATTAGTAATGATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
*
2133071 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
*
2133131 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAG---T-A
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
* * *
2133187 --A-T--T-ATCAGTAATAATGAAATTATTATTAATTTTTAATAATTTGATAGTAATGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
* * * * * *
2133240 TTAGTAAT-AAT-GAAATTATTAGTAA-TA-T-TTAATGATTTGAT-AGTAATGATTAGTAAT-A
1 TTAGTAATGATTAGTAA-TAAT-GAAATTATTATTAAT-ATTTAATGA-T-TTGA-TAGTAATGA
* * * ** * * *
2133298 AT-GAAATTG-TTATTAAT-ATTTAATGA-T-TTGATA-GTAATGATTT-A-A-TAATG-
1 TTAGTAA-TGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
*
2133348 --A-T--T-A---GTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
* *
2133398 TTTAGTAATGATTAGTAATAATGAAATTATTATTATTTTTTAATGATTTGATAGTAATGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
2133458 TTAGTAAT
1 TTAGTAAT
2133466 AATGAAATTA
Statistics
Matches: 316, Mismatches: 37, Indels: 83
0.72 0.08 0.19
Matches are distributed among these distances:
42 4 0.01
43 5 0.02
44 1 0.00
45 6 0.02
46 9 0.03
47 1 0.00
48 1 0.00
49 47 0.15
50 5 0.02
51 1 0.00
52 2 0.01
53 4 0.01
54 2 0.01
55 5 0.02
56 14 0.04
57 22 0.07
58 15 0.05
59 20 0.06
60 152 0.48
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (59 bp):
TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
Found at i:2133086 original size:21 final size:21
Alignment explanation
Indices: 2133009--2133149 Score: 68
Period size: 21 Copynumber: 7.0 Consensus size: 21
2132999 GTATTTATAA
2133009 GATTTAGTAATGATTAGTAAT
1 GATTTAGTAATGATTAGTAAT
* * *
2133030 GA--T-GAAATTATTATTAAT
1 GATTTAGTAATGATTAGTAAT
* *
2133048 -ATTTAATGATTTGA-TAGTAAT
1 GATTTAGT-A-ATGATTAGTAAT
2133069 GATTTAGTAATGATTAGTAAT
1 GATTTAGTAATGATTAGTAAT
* * * *
2133090 -A-AT-GAAATTATTATTAAT
1 GATTTAGTAATGATTAGTAAT
* * *
2133108 -ATTTAATGATTTGA-TATTAAT
1 GATTTAGT-A-ATGATTAGTAAT
2133129 GATTTAGTAATGATTAGTAAT
1 GATTTAGTAATGATTAGTAAT
2133150 AATGAAATTA
Statistics
Matches: 85, Mismatches: 22, Indels: 26
0.64 0.17 0.20
Matches are distributed among these distances:
17 1 0.01
18 25 0.29
19 4 0.05
20 7 0.08
21 32 0.38
22 16 0.19
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.45
Consensus pattern (21 bp):
GATTTAGTAATGATTAGTAAT
Found at i:2133356 original size:207 final size:207
Alignment explanation
Indices: 2133073--2133889 Score: 1117
Period size: 207 Copynumber: 3.8 Consensus size: 207
2133063 AGTAATGATT
* *
2133073 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAATA
* * *
2133138 ATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATTATCAGTAATAATG
66 ATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATG
* * *
2133203 AAATTATTATTAATTTTTAATAATTTGATAGTAATGATTAGTAATAATGAAATTATTAGTAATAT
131 AAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATTT
2133268 TTAATGATTTGA
196 TTAATGATTTGA
*
2133280 TAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTAATA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAATA
*
2133345 ATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGAT
66 ATGATTAGTAATAATGAAATTATTATTAATATTT-A--A--TGAT--T--TGA--TAGTAATGAT
*
2133410 TAGTAATAATGAAATTATTATTATTTTTTAATGATTTGATAGTAATGATTAGTAATAATGAAATT
120 TAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAATGAAATT
2133475 ATTATTAATTTTTAATGATTTGA
185 ATTATTAATTTTTAATGATTTGA
*
2133498 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATT--TAA
* * * * *
2133563 TAATGAAATTATTATTAAT--ATTTAATGATTTGATA-TTAATGA-TT--TAGTAATGATTAGTA
64 TAATG--ATTAGTAATAATGAAATT-ATTA-TTAATATTTAATGATTTGATAGTAATGATTAGTA
*
2133622 ATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAATAATAATGAAATTATTAT
125 ATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTAT
2133687 TAATTTTTAATGATTTGATAGTAATGA
190 TAATTTTT-A--A--TGAT--T--TGA
* *
2133714 TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGT
1 -TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAAT
*
2133779 AATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTAGTAATAAT
65 AATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAAT
* * *
2133844 -AATTTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAAT
130 GAAATTATTATTAATTTTTAATGATTTGATAGTAATGA-TTAGTAAT
2133890 GATTTGATAG
Statistics
Matches: 542, Mismatches: 34, Indels: 58
0.85 0.05 0.09
Matches are distributed among these distances:
207 180 0.33
208 2 0.00
210 2 0.00
211 1 0.00
212 8 0.01
213 16 0.03
214 12 0.02
215 12 0.02
216 43 0.08
217 84 0.15
218 151 0.28
220 12 0.02
221 4 0.01
222 15 0.03
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (207 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAATA
ATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATG
AAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATTT
TTAATGATTTGA
Found at i:2133461 original size:49 final size:49
Alignment explanation
Indices: 2133400--2133889 Score: 595
Period size: 49 Copynumber: 9.3 Consensus size: 49
2133390 AGTAATGATT
*
2133400 TAGTAATGATTAGTAATAATGAAATTATTATTATTTTTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
2133449 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
2133498 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
*
2133547 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAAT-TTT--T-A-ATG--ATT--TGA
2133605 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
1 --TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
*
2133656 TAGTAATGATTAATAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTT-A--A--TGAT--T--TGA
*
2133714 TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGA
1 -TAGTAATGATTAGTAATAATGAAATTATTATTAAT-TTT--T-A-ATG--ATT--TGA
*
2133773 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
1 --TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
* * *
2133824 TATTAATGATTAGTAATAAT-AATTTATTATTAATATTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
*
2133872 TATTAATGATTTAGTAAT
1 TAGTAATGA-TTAGTAAT
2133890 GATTTGATAG
Statistics
Matches: 401, Mismatches: 12, Indels: 56
0.86 0.03 0.12
Matches are distributed among these distances:
48 36 0.09
49 197 0.49
50 4 0.01
51 6 0.01
52 2 0.00
53 7 0.02
54 6 0.01
55 4 0.01
56 6 0.01
57 2 0.00
58 6 0.01
59 47 0.12
60 74 0.18
61 2 0.00
62 2 0.00
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (49 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
Found at i:2133488 original size:267 final size:267
Alignment explanation
Indices: 2133013--2133893 Score: 1333
Period size: 267 Copynumber: 3.3 Consensus size: 267
2133003 TTATAAGATT
*
2133013 TAGTAATGATTAGTAATGATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTA
*
2133078 ATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGAT
66 ATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGAT
* * *
2133143 TAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATTATCAGTAATAATGAAATT
131 TAGTAATAATGAAATTATTATTATTTTTTAATGATTTGATAGTAATGATTAGTAATAATGAAATT
*
2133208 ATTATTAATTTTTAATAATTTGATAGTAATGATTAGTAATAATGAAATTATTAGTAATATTTAAT
196 ATTATTAATTTTTAATAATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAAT
2133273 GATTTGA
261 GATTTGA
* *
2133280 TAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTAATA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTA
*
2133345 ATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGAT
66 ATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGAT
2133410 TAGTAATAATGAAATTATTATTATTTTTTAATGATTTGATAGTAATGATTAGTAATAATGAAATT
131 TAGTAATAATGAAATTATTATTATTTTTTAATGATTTGATAGTAATGATTAGTAATAATGAAATT
* *
2133475 ATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAAT
196 ATTATTAATTTTTAATAATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAAT
2133540 GATTTGA
261 GATTTGA
*
2133547 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTA
* *
2133612 ATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAATAATAATG
66 ATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATT--TAGTAATG
* * * * * * ** * *
2133677 A--AATTATTAT-TAATTTTTAATGATTTGATAGT-A-ATGATTAGTAATGATTAGTAATAATGA
129 ATTAGTAATAATGAAATTATT-ATTATTTTTTAATGATTTGA-TAGTAATGATTAGTAATAATGA
*
2133737 AATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGATTAGTAATAATGAAATTA
192 AATTATTATTAAT-TTT--T-A-AT-A-ATT--TGA--TAGTAATGATTAGTAATAATGAAATTA
2133802 TTATTAATATTTAATGATTTGA
246 TTATTAATATTTAATGATTTGA
* * *
2133824 TATTAATGATTAGTAATAAT-AATTTATTATTAATATTTAATGATTTGATATTAATGATTTAGTA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTA
2133888 ATGATT
66 ATGATT
2133894 TGATAGTAAT
Statistics
Matches: 567, Mismatches: 32, Indels: 21
0.91 0.05 0.03
Matches are distributed among these distances:
265 3 0.01
266 42 0.07
267 389 0.69
269 9 0.02
270 1 0.00
271 1 0.00
273 3 0.01
275 3 0.01
276 49 0.09
277 67 0.12
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.46
Consensus pattern (267 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTA
ATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGAT
TAGTAATAATGAAATTATTATTATTTTTTAATGATTTGATAGTAATGATTAGTAATAATGAAATT
ATTATTAATTTTTAATAATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAAT
GATTTGA
Found at i:2133620 original size:60 final size:60
Alignment explanation
Indices: 2133547--2133666 Score: 222
Period size: 60 Copynumber: 2.0 Consensus size: 60
2133537 AATGATTTGA
*
2133547 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATT
*
2133607 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATT
2133667 AATAATAATG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (60 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATT
Found at i:2133667 original size:28 final size:28
Alignment explanation
Indices: 2133636--2133716 Score: 77
Period size: 28 Copynumber: 3.1 Consensus size: 28
2133626 TGAAATTATT
2133636 ATTAATTTTTAATGATTTGATAGTAATG
1 ATTAATTTTTAATGATTTGATAGTAATG
* * * *
2133664 ATTAA----TAAT-A-ATGA-AATTATT
1 ATTAATTTTTAATGATTTGATAGTAATG
2133685 ATTAATTTTTAATGATTTGATAGTAATG
1 ATTAATTTTTAATGATTTGATAGTAATG
2133713 ATTA
1 ATTA
2133717 GTAATGATTA
Statistics
Matches: 38, Mismatches: 8, Indels: 14
0.63 0.13 0.23
Matches are distributed among these distances:
21 9 0.24
22 3 0.08
23 1 0.03
24 4 0.11
25 4 0.11
26 1 0.03
27 3 0.08
28 13 0.34
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (28 bp):
ATTAATTTTTAATGATTTGATAGTAATG
Found at i:2133718 original size:10 final size:10
Alignment explanation
Indices: 2133705--2133731 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
2133695 AATGATTTGA
2133705 TAGTAATGAT
1 TAGTAATGAT
2133715 TAGTAATGAT
1 TAGTAATGAT
2133725 TAGTAAT
1 TAGTAAT
2133732 AATGAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (10 bp):
TAGTAATGAT
Found at i:2133729 original size:168 final size:168
Alignment explanation
Indices: 2133547--2133893 Score: 624
Period size: 168 Copynumber: 2.1 Consensus size: 168
2133537 AATGATTTGA
2133547 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTA
*
2133612 ATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAATAATAATG
66 ATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTAATAATAAT-
*
2133677 AAATTATTATTAATTTTTAATGATTTGATAGTAATGA-T
130 AAATTATTATTAATATTTAATGATTTGATAGTAATGATT
2133715 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTA
* *
2133780 ATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTAGTAATAATA
66 ATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTAATAATAATA
* *
2133845 ATTTATTATTAATATTTAATGATTTGATATTAATGATT
131 AATTATTATTAATATTTAATGATTTGATAGTAATGATT
2133883 TAGTAATGATT
1 TAGTAATGATT
2133894 TGATAGTAAT
Statistics
Matches: 172, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
167 34 0.20
168 138 0.80
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (168 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTA
ATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTAATAATAATA
AATTATTATTAATATTTAATGATTTGATAGTAATGATT
Found at i:2133831 original size:14 final size:14
Alignment explanation
Indices: 2133812--2133908 Score: 65
Period size: 14 Copynumber: 6.7 Consensus size: 14
2133802 TTATTAATAT
2133812 TTAATGATTTGATA
1 TTAATGATTTGATA
*
2133826 TTAATGATTAGTAATA
1 TTAATGATT--TGATA
* * *
2133842 ATAATTTATTATTAATA
1 TTAA-TGA-T-TTGATA
2133859 TTTAATGATTTGATA
1 -TTAATGATTTGATA
2133874 TTAATGA-TT--TA
1 TTAATGATTTGATA
*
2133885 GTAATGATTTGATA
1 TTAATGATTTGATA
*
2133899 GTAATGATTT
1 TTAATGATTT
2133909 ACGACTTAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 18
0.73 0.08 0.20
Matches are distributed among these distances:
11 8 0.12
12 2 0.03
13 2 0.03
14 28 0.42
15 5 0.07
16 8 0.12
17 9 0.13
18 4 0.06
19 1 0.01
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.49
Consensus pattern (14 bp):
TTAATGATTTGATA
Found at i:2133831 original size:119 final size:108
Alignment explanation
Indices: 2133547--2133893 Score: 396
Period size: 119 Copynumber: 3.1 Consensus size: 108
2133537 AATGATTTGA
* *
2133547 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTA
1 TAGTAATGATTAATAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA-TTAGTA
* * * * * * * * *
2133612 ATGATTAGTAATAATGAA-A-TT-ATTA-TTAATTTTTAATGATTT
65 ATAATAATTTATTATTAATATTTAATGATTTGA-TATTAATGA-TT
*
2133654 GATAGTAATGATTAATAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGT
1 --TAGTAATGATTAATAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTAG-
2133719 AATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATT
63 --T-A--A-TAATAAT----TTATTATTAATATTTAATGATTTGATATTAATGATT
* *
2133775 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTAGTAA
1 TAGTAATGATTAATAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTAGTAA
2133840 TAATAATTTATTATTAATATTTAATGATTTGATATTAATGATT
66 TAATAATTTATTATTAATATTTAATGATTTGATATTAATGATT
2133883 TAGTAATGATT
1 TAGTAATGATT
2133894 TGATAGTAAT
Statistics
Matches: 208, Mismatches: 15, Indels: 31
0.82 0.06 0.12
Matches are distributed among these distances:
108 51 0.25
109 55 0.26
111 1 0.00
112 8 0.04
113 1 0.00
114 1 0.00
115 5 0.02
116 1 0.00
119 66 0.32
120 1 0.00
121 4 0.02
122 11 0.05
123 3 0.01
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (108 bp):
TAGTAATGATTAATAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTAGTAA
TAATAATTTATTATTAATATTTAATGATTTGATATTAATGATT
Found at i:2133863 original size:48 final size:49
Alignment explanation
Indices: 2133778--2133889 Score: 199
Period size: 48 Copynumber: 2.3 Consensus size: 49
2133768 AATGATTTAG
2133778 TAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAT
1 TAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAT
*
2133827 TAATGATTAGTAATAAT-AATTTATTATTAATATTTAATGATTTGATAT
1 TAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAT
2133875 TAATGATTTAGTAAT
1 TAATGA-TTAGTAAT
2133890 GATTTGATAG
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
48 36 0.59
49 25 0.41
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (49 bp):
TAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAT
Found at i:2136455 original size:22 final size:21
Alignment explanation
Indices: 2136417--2136457 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
2136407 TTTATGTATA
*
2136417 ATATAACTTAAACTAACAATC
1 ATATAACCTAAACTAACAATC
*
2136438 ATATAACCCTAAATTAACAA
1 ATATAA-CCTAAACTAACAA
2136458 ACTAATTAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.54, C:0.20, G:0.00, T:0.27
Consensus pattern (21 bp):
ATATAACCTAAACTAACAATC
Found at i:2136991 original size:29 final size:29
Alignment explanation
Indices: 2136915--2136996 Score: 119
Period size: 29 Copynumber: 2.8 Consensus size: 29
2136905 CTTGGTCGTC
* ***
2136915 GGGACTGCTTGGCGACCTACAAGGTCGCT
1 GGGAGTGCTTGGCGACCTTGTAGGTCGCT
*
2136944 GGGAGTGCATGGCGACCTTGTAGGTCGCT
1 GGGAGTGCTTGGCGACCTTGTAGGTCGCT
2136973 GGGAGTGCTTGGCGACCTTGTAGG
1 GGGAGTGCTTGGCGACCTTGTAGG
2136997 GGTGTTGGGG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.15, C:0.22, G:0.40, T:0.23
Consensus pattern (29 bp):
GGGAGTGCTTGGCGACCTTGTAGGTCGCT
Found at i:2144942 original size:2 final size:2
Alignment explanation
Indices: 2144935--2144970 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2144925 AAAATATGAA
2144935 AT AT 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 AT AT
2144971 TGTATATTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2147655 original size:20 final size:21
Alignment explanation
Indices: 2147616--2147656 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
2147606 CGTTTGATTC
*
2147616 ATAAAATATAATATTTTATAA
1 ATAAAATATAATATTATATAA
*
2147637 ATAAAAT-TAATGTTATATAA
1 ATAAAATATAATATTATATAA
2147657 GATTATTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
ATAAAATATAATATTATATAA
Found at i:2160431 original size:15 final size:16
Alignment explanation
Indices: 2160411--2160453 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
2160401 TTAAAGTTTT
*
2160411 ATTAAAATAAAT-GTA
1 ATTAAAATAAATAATA
*
2160426 ATTAAAATATATAATA
1 ATTAAAATAAATAATA
2160442 A-TAAAATAAATA
1 ATTAAAATAAATA
2160454 TCTCAATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 21 0.88
16 3 0.12
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (16 bp):
ATTAAAATAAATAATA
Found at i:2161552 original size:44 final size:44
Alignment explanation
Indices: 2161489--2161577 Score: 160
Period size: 44 Copynumber: 2.0 Consensus size: 44
2161479 AACTAAAGGA
*
2161489 GGTTCGCGATTTGTTTAACCACTTCTACTCTCCCACTCCCAATG
1 GGTTCGCAATTTGTTTAACCACTTCTACTCTCCCACTCCCAATG
*
2161533 GGTTCGCAATTTGTTTAACCACTTCTACTCTCCCCCTCCCAATG
1 GGTTCGCAATTTGTTTAACCACTTCTACTCTCCCACTCCCAATG
2161577 G
1 G
2161578 CATAACTTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.18, C:0.35, G:0.13, T:0.34
Consensus pattern (44 bp):
GGTTCGCAATTTGTTTAACCACTTCTACTCTCCCACTCCCAATG
Found at i:2179911 original size:60 final size:60
Alignment explanation
Indices: 2179829--2180011 Score: 242
Period size: 60 Copynumber: 3.0 Consensus size: 60
2179819 ATATATCCTT
* *
2179829 AAACTATGACTCTCACTT-TAAATTGATCCTTGAACTTTTAAACATTATAATTTCATCCCC
1 AAACTATGACTCTCA-TTCTAAATTGATCCTTAAACTTTTAAACATTCTAATTTCATCCCC
* * * * * *
2179889 AAGCTTTGACTCTCATTCTAAATTAATCCTTAAAATTTTGAACATTCTAATTTCATCTCC
1 AAACTATGACTCTCATTCTAAATTGATCCTTAAACTTTTAAACATTCTAATTTCATCCCC
* * * *
2179949 AAACTATGAGTCTCATTCTAAATTGATCCCTAAACTTTTAAATATTCCAATTTCATCCCC
1 AAACTATGACTCTCATTCTAAATTGATCCTTAAACTTTTAAACATTCTAATTTCATCCCC
2180009 AAA
1 AAA
2180012 TTCATCCTAA
Statistics
Matches: 104, Mismatches: 18, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
59 2 0.02
60 102 0.98
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.38
Consensus pattern (60 bp):
AAACTATGACTCTCATTCTAAATTGATCCTTAAACTTTTAAACATTCTAATTTCATCCCC
Found at i:2192994 original size:127 final size:127
Alignment explanation
Indices: 2192777--2193145 Score: 589
Period size: 127 Copynumber: 2.9 Consensus size: 127
2192767 TGAAGGCGTC
* * *
2192777 TTCCCGGGGGCGCGCCTTCCATTATTTTGTTAGAGAATATGTTATTATTGCCCTATTATGTCACT
1 TTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTATGTCACT
* *
2192842 TATGTCCCTC-AGGAACTATTTATGTCAATACCTATTATTCCTTATGGGACCGTGAAGGCACG
66 TATGTCCCCCGA-GAACTATTCATGTCAATACCTATTATTCCTTATGGGACCGTGAAGGCACG
2192904 TTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTATGTCACT
1 TTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTATGTCACT
** * *
2192969 TATGTCCCCCGAGAACTATTCATGTCAATACCTATTATTTATTAGGGGACCGTGAAGGCGCG
66 TATGTCCCCCGAGAACTATTCATGTCAATACCTATTATTCCTTATGGGACCGTGAAGGCACG
* *
2193031 TTCCCGGGAGG-GTGCCTTCCATTATTTTTTCAGAGAATATGTTATCATTACCCTATTATGTCAC
1 TTCCCGGG-GGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTATGTCAC
* *
2193095 TTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTCATGGGAC
65 TTATGTCCCCCGAGAACTATTCATGTCAATACCTATTATTCCTTATGGGAC
2193146 TTTAAAGCGC
Statistics
Matches: 224, Mismatches: 16, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
127 221 0.99
128 3 0.01
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.35
Consensus pattern (127 bp):
TTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTATGTCACT
TATGTCCCCCGAGAACTATTCATGTCAATACCTATTATTCCTTATGGGACCGTGAAGGCACG
Found at i:2193617 original size:34 final size:34
Alignment explanation
Indices: 2193579--2193675 Score: 140
Period size: 34 Copynumber: 2.9 Consensus size: 34
2193569 TTAATGTTAG
*
2193579 ATTTTGAATACTATAATTTATATTTTAAATTTAA
1 ATTTTGAATACTATAATTTGTATTTTAAATTTAA
* * * *
2193613 ATTTTGAATAATATTATTTGCATTTTAATTTTAA
1 ATTTTGAATACTATAATTTGTATTTTAAATTTAA
*
2193647 ATTTCGAATACTATAATTTGTATTTTAAA
1 ATTTTGAATACTATAATTTGTATTTTAAA
2193676 AACATTTATT
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 53 1.00
ACGTcount: A:0.38, C:0.04, G:0.05, T:0.53
Consensus pattern (34 bp):
ATTTTGAATACTATAATTTGTATTTTAAATTTAA
Found at i:2194104 original size:21 final size:21
Alignment explanation
Indices: 2194078--2194135 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
2194068 TCCAAATGGA
*
2194078 GGGCTAGGCATGTAACC-TGGC
1 GGGCTAGGAATGTAACCAT-GC
2194099 GGGCTAGGAATGTAACCATGC
1 GGGCTAGGAATGTAACCATGC
*
2194120 GGGCTAGGAATATAAC
1 GGGCTAGGAATGTAAC
2194136 ACTGCAGAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
21 33 0.97
22 1 0.03
ACGTcount: A:0.28, C:0.19, G:0.34, T:0.19
Consensus pattern (21 bp):
GGGCTAGGAATGTAACCATGC
Found at i:2195893 original size:21 final size:21
Alignment explanation
Indices: 2195864--2195910 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
2195854 ATTCTGACTA
2195864 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
2195885 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
2195906 TCGCA
1 TCGCA
2195911 ACGCGAATAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:2196530 original size:19 final size:20
Alignment explanation
Indices: 2196485--2196532 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
2196475 TTCGAGAATG
**
2196485 AAAATCGCAACGCGGAAATG
1 AAAATCGCAACGCGGAAACC
**
2196505 ACTATCGCAACGC-GAAACC
1 AAAATCGCAACGCGGAAACC
2196524 AAAATCGCA
1 AAAATCGCA
2196533 TTGCGATTTT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.44, C:0.27, G:0.19, T:0.10
Consensus pattern (20 bp):
AAAATCGCAACGCGGAAACC
Found at i:2196606 original size:20 final size:19
Alignment explanation
Indices: 2196528--2196631 Score: 74
Period size: 19 Copynumber: 5.6 Consensus size: 19
2196518 GAAACCAAAA
* **
2196528 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATAGTCATT
2196547 TCGCGTTGCGAT--TC---
1 TCGCGTTGCGATAGTCATT
* **
2196561 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATAGTCATT
2196580 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATAGTCATT
**
2196599 TCCGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATAGTCATT
*
2196619 CTCTCGTTGCGAT
1 -TCGCGTTGCGAT
2196632 TTTCATTTCA
Statistics
Matches: 70, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
14 11 0.16
16 2 0.03
17 2 0.03
19 28 0.40
20 26 0.37
21 1 0.01
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATAGTCATT
Found at i:2196632 original size:20 final size:19
Alignment explanation
Indices: 2196528--2196640 Score: 128
Period size: 20 Copynumber: 6.1 Consensus size: 19
2196518 GAAACCAAAA
*
2196528 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2196547 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
2196561 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
2196580 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
2196599 TCCGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
*
2196619 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
2196639 TC
1 TC
2196641 AACCAAAAGA
Statistics
Matches: 79, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
14 10 0.13
16 3 0.04
17 3 0.04
19 29 0.37
20 33 0.42
21 1 0.01
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2196638 original size:40 final size:39
Alignment explanation
Indices: 2196533--2196640 Score: 129
Period size: 33 Copynumber: 2.9 Consensus size: 39
2196523 CAAAATCGCA
*
2196533 TTGCGATTTTCATTTCGCGTTGCGAT--TC---T-CTCG
1 TTGCGATTTTCATTTCGCGTTGCGATAGTCATTTCCGCG
2196566 TTGCGATTTTCATTTCGCGTTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATAGTCATTTCCGCG
* **
2196605 TTGCGATTTTCATTCTCTCGTTGCGATTTTCATTTC
1 TTGCGATTTTCATT-TCGCGTTGCGATAGTCATTTC
2196641 AACCAAAAGA
Statistics
Matches: 64, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
33 26 0.41
35 2 0.03
38 1 0.02
39 17 0.27
40 18 0.28
ACGTcount: A:0.11, C:0.23, G:0.19, T:0.46
Consensus pattern (39 bp):
TTGCGATTTTCATTTCGCGTTGCGATAGTCATTTCCGCG
Done.