Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008933.1 Hibiscus syriacus cultivar Beakdansim tig00112249_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: 2862162
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 14
Found at i:1910214 original size:2 final size:2
Alignment explanation
Indices: 1910207--1910241 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1910197 TTCTTTTAAC
1910207 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1910242 CACGGACGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1911791 original size:15 final size:13
Alignment explanation
Indices: 1911761--1911789 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1911751 TAAATTTATT
1911761 TATTTTGATAATA
1 TATTTTGATAATA
1911774 TATTTTGATAATA
1 TATTTTGATAATA
1911787 TAT
1 TAT
1911790 ATCTTATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (13 bp):
TATTTTGATAATA
Found at i:1913342 original size:21 final size:23
Alignment explanation
Indices: 1913280--1913327 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
1913270 CAGTGTGGAA
1913280 AAACCTATGTGGTCCTTCGGGAC
1 AAACCTATGTGGTCCTTCGGGAC
1913303 AAACCTATGTGGTCCTTCGGGAC
1 AAACCTATGTGGTCCTTCGGGAC
1913326 AA
1 AA
1913328 TTATGTGGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (23 bp):
AAACCTATGTGGTCCTTCGGGAC
Found at i:1919593 original size:43 final size:42
Alignment explanation
Indices: 1919528--1919613 Score: 138
Period size: 43 Copynumber: 2.0 Consensus size: 42
1919518 TAAATGTATG
*
1919528 AGCATTGTCAAGTTTATCTGGTAAACTACGCTTCATTTTTTAT
1 AGCATTGTCAAGTTTATCTGGTAAACTACGCTTC-TTTATTAT
1919571 AGCATTGTCAAGTTTA-CTTGGTAAACTACGCTTCTTTATTAT
1 AGCATTGTCAAGTTTATC-TGGTAAACTACGCTTCTTTATTAT
1919613 A
1 A
1919614 CAAATTAAGC
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
42 9 0.22
43 32 0.78
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (42 bp):
AGCATTGTCAAGTTTATCTGGTAAACTACGCTTCTTTATTAT
Found at i:1919914 original size:44 final size:43
Alignment explanation
Indices: 1919850--1920122 Score: 249
Period size: 44 Copynumber: 6.4 Consensus size: 43
1919840 GAAAATGACT
* *
1919850 AAATTAGGGGCCTAAATTATAAA-AGTAAAAAGTGAGATTGAAA
1 AAATTAAGGGCCTCAATTATAAAGA-TAAAAAGTGAGATTGAAA
* * *
1919893 ACAATTAAGGGTCTCAATTATAAAGATAAAAAGTTAGATTAAAA
1 A-AATTAAGGGCCTCAATTATAAAGATAAAAAGTGAGATTGAAA
*
1919937 AAATTTAGGGGCCTCAATTAT--AGATATAAAAGTGAGATT-AAA
1 AAA-TTAAGGGCCTCAATTATAAAGATA-AAAAGTGAGATTGAAA
* * * *
1919979 AATATTAGGGGCCTAAACTATAAA-AGT-AAAAGGGA-ATTGAAA
1 AA-ATTAAGGGCCTCAATTATAAAGA-TAAAAAGTGAGATTGAAA
* * * * *
1920021 AAA-GAGGGGCATCAATTATAAAAGTTAAAAA-TGAGAATGAAA
1 AAATTAAGGGCCTCAATTAT-AAAGATAAAAAGTGAGATTGAAA
* *
1920063 AAATTAAGGGCCTCAATTATAATGATTAAAAGTGAGATTGAAAA
1 AAATTAAGGGCCTCAATTATAAAGATAAAAAGTGAGATTG-AAA
*
1920107 AAATTAAGAGCCTCAA
1 AAATTAAGGGCCTCAA
1920123 AGTGAGATTA
Statistics
Matches: 188, Mismatches: 26, Indels: 31
0.77 0.11 0.13
Matches are distributed among these distances:
40 12 0.06
41 10 0.05
42 58 0.31
43 36 0.19
44 71 0.38
45 1 0.01
ACGTcount: A:0.50, C:0.07, G:0.19, T:0.24
Consensus pattern (43 bp):
AAATTAAGGGCCTCAATTATAAAGATAAAAAGTGAGATTGAAA
Found at i:1920197 original size:43 final size:42
Alignment explanation
Indices: 1920121--1920343 Score: 189
Period size: 43 Copynumber: 5.2 Consensus size: 42
1920111 TAAGAGCCTC
* * *
1920121 AAAGTGAGATTAAAAAAGATAGGGGCCTAAATTATAAAAATTA
1 AAAGTGGGATT-AAAAAGATAGAGACCTAAATTATAAAAATTA
* * * *
1920164 AAAGTGGGATTGAAATGATTAGAGACCTCAATTATAAAGA-TA
1 AAAGTGGGATTAAAAAGA-TAGAGACCTAAATTATAAAAATTA
** * * *
1920206 GAAAGTGATAATAAAAAAGATAGGGGCCTAAATTATAAAAATTA
1 -AAAGTG-GGATTAAAAAGATAGAGACCTAAATTATAAAAATTA
* * * *
1920250 AAAGTGGGATTGAAATGATTAGAGACCTCAATTATAAAGA-TA
1 AAAGTGGGATTAAAAAGA-TAGAGACCTAAATTATAAAAATTA
** * *
1920292 GAAAGTGATATTAAAAAAGATAGGGGCCTAAATTATAAAAATTA
1 -AAAGTGGGATT-AAAAAGATAGAGACCTAAATTATAAAAATTA
1920336 AAAGTGGG
1 AAAGTGGG
1920344 TTTGTTTTAT
Statistics
Matches: 137, Mismatches: 35, Indels: 16
0.73 0.19 0.09
Matches are distributed among these distances:
42 16 0.12
43 105 0.77
44 16 0.12
ACGTcount: A:0.50, C:0.05, G:0.21, T:0.24
Consensus pattern (42 bp):
AAAGTGGGATTAAAAAGATAGAGACCTAAATTATAAAAATTA
Found at i:1920211 original size:86 final size:86
Alignment explanation
Indices: 1920121--1920343 Score: 428
Period size: 86 Copynumber: 2.6 Consensus size: 86
1920111 TAAGAGCCTC
*
1920121 AAAGTGAGATTAAAAAAGATAGGGGCCTAAATTATAAAAATTAAAAGTGGGATTGAAATGATTAG
1 AAAGTGATATTAAAAAAGATAGGGGCCTAAATTATAAAAATTAAAAGTGGGATTGAAATGATTAG
1920186 AGACCTCAATTATAAAGATAG
66 AGACCTCAATTATAAAGATAG
*
1920207 AAAGTGATAATAAAAAAGATAGGGGCCTAAATTATAAAAATTAAAAGTGGGATTGAAATGATTAG
1 AAAGTGATATTAAAAAAGATAGGGGCCTAAATTATAAAAATTAAAAGTGGGATTGAAATGATTAG
1920272 AGACCTCAATTATAAAGATAG
66 AGACCTCAATTATAAAGATAG
1920293 AAAGTGATATTAAAAAAGATAGGGGCCTAAATTATAAAAATTAAAAGTGGG
1 AAAGTGATATTAAAAAAGATAGGGGCCTAAATTATAAAAATTAAAAGTGGG
1920344 TTTGTTTTAT
Statistics
Matches: 134, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
86 134 1.00
ACGTcount: A:0.50, C:0.05, G:0.21, T:0.24
Consensus pattern (86 bp):
AAAGTGATATTAAAAAAGATAGGGGCCTAAATTATAAAAATTAAAAGTGGGATTGAAATGATTAG
AGACCTCAATTATAAAGATAG
Found at i:1920255 original size:159 final size:156
Alignment explanation
Indices: 1919965--1920264 Score: 354
Period size: 159 Copynumber: 1.9 Consensus size: 156
1919955 TATAGATATA
* * *
1919965 AAAGTGAGATTAAAAATATTAGGGGCCTAAACTATAAAAGTAAAAGGGAATTGAAAAAAGAGGGG
1 AAAGTGAGATTAAAAATAATAGGGGCCTAAACTATAAAAGTAAAAGGGAATTGAAAAAAGAGAGA
* * * **
1920030 CATCAATTATAAAAGTTAAAAATGAGAATGAAAAAATTAAGGGCCTCAATTATAATGATTAAAAG
66 CATCAATTATAAAAGATAAAAATGAGAATGAAAAAAATAAGGGCCTAAATTATAAAAATTAAAAG
1920095 TGAGATTGAAAAAAATTAAGAGCCTC
131 TGAGATTGAAAAAAATTAAGAGCCTC
* * * * **
1920121 AAAGTGAGATTAAAAA-AGATAGGGGCCTAAATTATAAAAATTAAAAGTGGGATTGAAATGATTA
1 AAAGTGAGATTAAAAATA-ATAGGGGCCTAAACTAT-AAAAGTAAAAG-GGAATTGAAA-AAAGA
* * * *
1920185 GAGACCTCAATTAT-AAAGATAGAAAGTGATAAT-AAAAAAGATAGGGGCCTAAATTATAAAAAT
62 GAGACATCAATTATAAAAGATA-AAAATGAGAATGAAAAAA-ATAAGGGCCTAAATTATAAAAAT
*
1920248 TAAAAGTGGGATTGAAA
125 TAAAAGTGAGATTGAAA
1920265 TGATTAGAGA
Statistics
Matches: 119, Mismatches: 19, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
155 1 0.01
156 31 0.26
157 10 0.08
158 21 0.18
159 56 0.47
ACGTcount: A:0.51, C:0.06, G:0.20, T:0.23
Consensus pattern (156 bp):
AAAGTGAGATTAAAAATAATAGGGGCCTAAACTATAAAAGTAAAAGGGAATTGAAAAAAGAGAGA
CATCAATTATAAAAGATAAAAATGAGAATGAAAAAAATAAGGGCCTAAATTATAAAAATTAAAAG
TGAGATTGAAAAAAATTAAGAGCCTC
Found at i:1928504 original size:9 final size:9
Alignment explanation
Indices: 1928490--1928517 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
1928480 TCCATCTATA
1928490 ATTTAATCT
1 ATTTAATCT
1928499 ATTTAATCT
1 ATTTAATCT
1928508 ATTTAATCT
1 ATTTAATCT
1928517 A
1 A
1928518 AAATCTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.54
Consensus pattern (9 bp):
ATTTAATCT
Found at i:1933086 original size:2 final size:2
Alignment explanation
Indices: 1933079--1933118 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1933069 ATGAAATACG
*
1933079 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1933119 GCCAGAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1933862 original size:18 final size:17
Alignment explanation
Indices: 1933839--1933872 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
1933829 AATAATACGC
1933839 TTAAGACTAACATGTTAT
1 TTAAGACTAACA-GTTAT
1933857 TTAAGACTAACAGTTA
1 TTAAGACTAACAGTTA
1933873 AAAAAGGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (17 bp):
TTAAGACTAACAGTTAT
Found at i:1941488 original size:29 final size:29
Alignment explanation
Indices: 1941454--1941512 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
1941444 CCTAAATTAA
1941454 TTTGATGTCATTGCTAACATCAATTTAGT
1 TTTGATGTCATTGCTAACATCAATTTAGT
*
1941483 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTAACATCAATTTAGT
1941512 T
1 T
1941513 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.47
Consensus pattern (29 bp):
TTTGATGTCATTGCTAACATCAATTTAGT
Found at i:1946143 original size:29 final size:29
Alignment explanation
Indices: 1946109--1946167 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1946099 CCTAAATTAA
1946109 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1946138 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1946167 T
1 T
1946168 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:1952684 original size:2 final size:2
Alignment explanation
Indices: 1952677--1952726 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
1952667 ATGAAATACG
*
1952677 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1952719 AT AG AT AT
1 AT AT AT AT
1952727 CCCAGAATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1959026 original size:2 final size:2
Alignment explanation
Indices: 1959019--1959048 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1959009 AACAAAATTA
1959019 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
1959049 GTTAAATAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1965430 original size:2 final size:2
Alignment explanation
Indices: 1965423--1965462 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1965413 TTTAATGAAA
1965423 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
1965463 GTGGATAGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1967181 original size:2 final size:2
Alignment explanation
Indices: 1967174--1967213 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1967164 ATGAAATACG
*
1967174 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1967214 GCCAGAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1967957 original size:18 final size:17
Alignment explanation
Indices: 1967934--1967967 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
1967924 AATAATACGC
1967934 TTAAGACTAACATGTTAT
1 TTAAGACTAACA-GTTAT
1967952 TTAAGACTAACAGTTA
1 TTAAGACTAACAGTTA
1967968 AAAAAGGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (17 bp):
TTAAGACTAACAGTTAT
Found at i:1971789 original size:25 final size:25
Alignment explanation
Indices: 1971756--1971803 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
1971746 TAGTATGTTG
* *
1971756 CTCTCTGTTTTCGGTTTCTCTCTGT
1 CTCTCTGTTCTCGGTCTCTCTCTGT
* *
1971781 CTCTGTGTTCTCTGTCTCTCTCT
1 CTCTCTGTTCTCGGTCTCTCTCT
1971804 CTGTTTTTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.00, C:0.31, G:0.15, T:0.54
Consensus pattern (25 bp):
CTCTCTGTTCTCGGTCTCTCTCTGT
Found at i:1972289 original size:3 final size:3
Alignment explanation
Indices: 1972281--1972378 Score: 187
Period size: 3 Copynumber: 32.7 Consensus size: 3
1972271 AATATATATT
*
1972281 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1972329 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1972377 TA
1 TA
1972379 TGGGTAAAAA
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 93 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1972972 original size:113 final size:113
Alignment explanation
Indices: 1972695--1973356 Score: 988
Period size: 113 Copynumber: 5.9 Consensus size: 113
1972685 GATAGAATTA
* *
1972695 TTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* *
1972760 CTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGCAAAAGG
66 CTTTCTCTGGAAAAGATAATCCATCAA-GTGATGAATTCAAGCAAAAGG
* *
1972809 TTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGAAGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * * *
1972874 CTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAAGTAAAAGG
66 CTTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCAAGCAAAAGG
*
1972922 TTTAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * *
1972987 CTTTCTCTGGAAAAAATAATCCATCAAGTGATGGATTCAAGTAAAAGG
66 CTTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCAAGCAAAAGG
*
1973035 TTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * *
1973100 CCTTCTCTGGCAAAA-ATAATCCATCAAGTGATGAATTCAAACAAAAAG
66 CTTTCTCTGG-AAAAGATAATCCATCAAGTGATGAATTCAAGCAAAAGG
* *
1973148 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTATTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * * * * * * *
1973213 C-TTCTCTGGCAATGTTGATCCATCAAATTATGAATTCAAACAAAAAG
66 CTTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCAAGCAAAAGG
*
1973260 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * * *
1973325 C-TTCTCTGGCAATGTTGATCCATCAAGTGATG
66 CTTTCTCTGGAAAAGATAATCCATCAAGTGATG
1973357 GATTTGAATC
Statistics
Matches: 512, Mismatches: 34, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
111 2 0.00
112 131 0.26
113 288 0.56
114 91 0.18
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (113 bp):
TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
CTTTCTCTGGAAAAGATAATCCATCAAGTGATGAATTCAAGCAAAAGG
Found at i:1974226 original size:83 final size:83
Alignment explanation
Indices: 1974087--1975126 Score: 1983
Period size: 83 Copynumber: 12.5 Consensus size: 83
1974077 GTTCCTACCA
*
1974087 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATTCTATTGGCAAATTCATCTTCTAAACT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACT
1974152 CAATGATTGGTTCTGTCC
66 CAATGATTGGTTCTGTCC
* *
1974170 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATTGGCAAATTCATCTTCTAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACT
1974235 CAATGATTGGTTCTGTCC
66 CAATGATTGGTTCTGTCC
*
1974253 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACT
1974318 CAATGATTGGTTCTGTCC
66 CAATGATTGGTTCTGTCC
*
1974336 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACT
1974401 CAATGATTGGTTCTGTCC
66 CAATGATTGGTTCTGTCC
*
1974419 AACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACT
1974484 CAATGATTGGTTCTGTCC
66 CAATGATTGGTTCTGTCC
1974502 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACT
*
1974567 CAATGATTGGTTCTGTCT
66 CAATGATTGGTTCTGTCC
*
1974585 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACT
1974650 CAATGATTGGTTCTGTCC
66 CAATGATTGGTTCTGTCC
1974668 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACT
1974733 CAATGATTGGTTCTGTCC
66 CAATGATTGGTTCTGTCC
1974751 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGC-AATTCATCTTCTAAACT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACT
1974815 CAATGATTGGTTCTGTCC
66 CAATGATTGGTTCTGTCC
*
1974833 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACT
1974898 CAATGATTGGTTCTGTCC
66 CAATGATTGGTTCTGTCC
1974916 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACT
1974981 CAATGATTGGTTCTGTCC
66 CAATGATTGGTTCTGTCC
1974999 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACT
*
1975064 CAATGATTGGTTCTGTCT
66 CAATGATTGGTTCTGTCC
1975082 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG
1975127 AGTCTCTTTC
Statistics
Matches: 942, Mismatches: 14, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
82 82 0.09
83 860 0.91
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.28
Consensus pattern (83 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACT
CAATGATTGGTTCTGTCC
Found at i:1976261 original size:1 final size:1
Alignment explanation
Indices: 1976257--1976322 Score: 60
Period size: 1 Copynumber: 66.0 Consensus size: 1
1976247 TTGACCCCCC
* * * * * * * *
1976257 TTTTTTCTTTTTTTCTTTTTTTTTCTTTCTTTTTTTTTTCTTTTTTTTTCTCTTTTTTTTCTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1976322 T
1 T
1976323 CTTCAAGCAT
Statistics
Matches: 49, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (1 bp):
T
Found at i:1976280 original size:11 final size:11
Alignment explanation
Indices: 1976257--1976322 Score: 91
Period size: 11 Copynumber: 6.1 Consensus size: 11
1976247 TTGACCCCCC
1976257 TTTTTTCTTTT
1 TTTTTTCTTTT
1976268 TTTCTTT-TTTT
1 TTT-TTTCTTTT
*
1976279 TTCTTTCTTTT
1 TTTTTTCTTTT
1976290 TTTTTTC-TTT
1 TTTTTTCTTTT
*
1976300 TTTTTTCTCTT
1 TTTTTTCTTTT
1976311 TTTTTTCTTTT
1 TTTTTTCTTTT
1976322 T
1 T
1976323 CTTCAAGCAT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
10 13 0.27
11 32 0.67
12 3 0.06
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:1976289 original size:27 final size:26
Alignment explanation
Indices: 1976256--1976325 Score: 106
Period size: 25 Copynumber: 2.7 Consensus size: 26
1976246 CTTGACCCCC
1976256 CTTTTTTCTTTTTTTCTTTTTTTTTCT
1 CTTTTTT-TTTTTTTCTTTTTTTTTCT
*
1976283 -TTCTTTTTTTTTTCTTTTTTTTTCT
1 CTTTTTTTTTTTTTCTTTTTTTTTCT
1976308 CTTTTTTTTCTTTTTCTT
1 CTTTTTTTT-TTTTTCTT
1976326 CAAGCATAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
25 19 0.49
26 12 0.31
27 8 0.21
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (26 bp):
CTTTTTTTTTTTTTCTTTTTTTTTCT
Found at i:1976291 original size:21 final size:20
Alignment explanation
Indices: 1976257--1976325 Score: 79
Period size: 21 Copynumber: 3.5 Consensus size: 20
1976247 TTGACCCCCC
*
1976257 TTTTTTC-TT-TTTTTCTTT
1 TTTTTTCTTTCTTTTTTTTT
1976275 TTTTTTCTTTCTTTTTTTTT
1 TTTTTTCTTTCTTTTTTTTT
*
1976295 TCTTTTTTTTTCTCTTTTTTTT
1 T-TTTTTCTTTCT-TTTTTTTT
*
1976317 CTTTTTCTT
1 TTTTTTCTT
1976326 CAAGCATAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
18 7 0.16
19 2 0.05
20 9 0.21
21 17 0.40
22 8 0.19
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (20 bp):
TTTTTTCTTTCTTTTTTTTT
Found at i:1988436 original size:25 final size:25
Alignment explanation
Indices: 1988403--1988450 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
1988393 TAGTATGTTG
* *
1988403 CTCTCTGTTTTCGGTTTCTCTCTGT
1 CTCTCTGTTCTCGGTCTCTCTCTGT
* *
1988428 CTCTGTGTTCTCTGTCTCTCTCT
1 CTCTCTGTTCTCGGTCTCTCTCT
1988451 CTGTTTTTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.00, C:0.31, G:0.15, T:0.54
Consensus pattern (25 bp):
CTCTCTGTTCTCGGTCTCTCTCTGT
Found at i:1988935 original size:3 final size:3
Alignment explanation
Indices: 1988927--1989008 Score: 148
Period size: 3 Copynumber: 27.7 Consensus size: 3
1988917 AATATATATT
*
1988927 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1988975 T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1989009 TGGGTAAAAA
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 74 0.97
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1992554 original size:2 final size:2
Alignment explanation
Indices: 1992549--1992595 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1992539 TTAACAAAAA
1992549 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
1992591 AT AT A
1 AT AT A
1992596 ATGTTAAATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1998950 original size:2 final size:2
Alignment explanation
Indices: 1998943--1998997 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
1998933 TAATGAAAAC
1998943 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1998985 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
1998998 GTGTGTGTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2000729 original size:2 final size:2
Alignment explanation
Indices: 2000722--2000757 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2000712 ATGAAATACG
*
2000722 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2000758 GCCAGAATTT
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:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2001498 original size:18 final size:17
Alignment explanation
Indices: 2001475--2001508 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
2001465 AATAATACGC
2001475 TTAAGACTAACATGTTAT
1 TTAAGACTAACA-GTTAT
2001493 TTAAGACTAACAGTTA
1 TTAAGACTAACAGTTA
2001509 AAAAAGGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (17 bp):
TTAAGACTAACAGTTAT
Found at i:2006732 original size:2 final size:2
Alignment explanation
Indices: 2006725--2006760 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2006715 AACAAAATTA
2006725 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
2006761 GTTAAATAGC
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:2008639 original size:37 final size:34
Alignment explanation
Indices: 2008598--2008697 Score: 123
Period size: 34 Copynumber: 2.8 Consensus size: 34
2008588 ATCAAACTTG
2008598 AGTCTTCACGAAAGG-GTAGTGAAGCAAATCATCTGAA
1 AGTCTTCAC--AAGGAGTAGTGAAGCAAA--ATCTGAA
2008635 AGTCTTCACAAGGAAGTAGTGAAGC-AAATCTGAA
1 AGTCTTCACAAGG-AGTAGTGAAGCAAAATCTGAA
*
2008669 AATCTTCACAAGGAAGTAGTGAAGCAAAA
1 AGTCTTCACAAGG-AGTAGTGAAGCAAAA
2008698 GAAGATTATT
Statistics
Matches: 59, Mismatches: 1, Indels: 8
0.87 0.01 0.12
Matches are distributed among these distances:
34 31 0.53
35 7 0.12
36 2 0.03
37 19 0.32
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.20
Consensus pattern (34 bp):
AGTCTTCACAAGGAGTAGTGAAGCAAAATCTGAA
Found at i:2008675 original size:34 final size:34
Alignment explanation
Indices: 2008613--2008696 Score: 132
Period size: 34 Copynumber: 2.4 Consensus size: 34
2008603 TCACGAAAGG
*
2008613 GTAGTGAAGCAAATCATCTGAAAGTCTTCACAAGGAA
1 GTAGTGAAGC-AA--ATCTGAAAATCTTCACAAGGAA
2008650 GTAGTGAAGCAAATCTGAAAATCTTCACAAGGAA
1 GTAGTGAAGCAAATCTGAAAATCTTCACAAGGAA
2008684 GTAGTGAAGCAAA
1 GTAGTGAAGCAAA
2008697 AGAAGATTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
34 34 0.74
36 2 0.04
37 10 0.22
ACGTcount: A:0.43, C:0.14, G:0.23, T:0.20
Consensus pattern (34 bp):
GTAGTGAAGCAAATCTGAAAATCTTCACAAGGAA
Found at i:2008778 original size:53 final size:53
Alignment explanation
Indices: 2008706--2009629 Score: 1390
Period size: 53 Copynumber: 17.4 Consensus size: 53
2008696 AAGAAGATTA
2008706 TTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGC-GAGCCCGTAGGAAGATTATTG
1 TTCGAGTTC-TACTCCCTGAAGAAAAAGAGAGCGGA-CCCGTAGGAAGATTATTG
* *
2008760 TTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGATCCGTAGGAATATTATTG
1 TTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTG
* * * *
2008813 TTCGAATTCTACTCCCTCAAG-AAAAGAGAGCGGACCCGTAGGAAGATTACTA
1 TTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTG
* *
2008865 TTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCAGTAGGAAGATTACTG
1 TTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTG
* *
2008918 TTCGAGTTCTACTCCCTGAAG-AAAAGAGAGTGGACCCGTAGGAAGATTACTG
1 TTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTG
* * *
2008970 TTCAAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAATATTAATG
1 TTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTG
* * *
2009023 TTCGAGTTATACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGACTACTG
1 TTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTG
** * *
2009076 TTCGAGTTCTACTCCCTGAAGAAAAAGAGAGTAGACTCGTAGGAAGATTACTG
1 TTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTG
*
2009129 TTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGAACCCGTAGGAAGATTATTG
1 TTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTG
*
2009182 TTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGATCCGTAGGAAGATTATTG
1 TTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTG
* * *
2009235 TTCGAGTTCTACTCCATGAAGAAAAAGAGAGCGGACCCGTAAGAAGATTACTG
1 TTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTG
*
2009288 TTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCAGACCCGTAGGAAGATTATTG
1 TTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTG
* * *
2009341 TTCGAGTTCTACTCCTTGAAGAAAAAGAGAGCGGACCCGTAGGAAAATTACTGG
1 TTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTA-TTG
* * *
2009395 TT-GAGTTCTACTCTCTGAAGAAAAAAAGAGCGGACCCATAGGAAGATTATTG
1 TTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTG
* * *
2009447 TTCGAGTTCTTACTCCCTGAAGAAAAAGAGAACGGACACATAGGAAGATTATTG
1 TTCGAGTTC-TACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTG
*
2009501 TTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATCG
1 TTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTG
* * * *
2009554 TTCAAGTTCTTACTCCCTGATGAAATAGAGAGC-GAGCTCGTAGGAAGATTATTG
1 TTCGAGTTC-TACTCCCTGAAGAAAAAGAGAGCGGA-CCCGTAGGAAGATTATTG
2009608 TTCGAGTTCTTACTCCCTGAAG
1 TTCGAGTTC-TACTCCCTGAAG
2009630 CGATAGAGAG
Statistics
Matches: 794, Mismatches: 68, Indels: 16
0.90 0.08 0.02
Matches are distributed among these distances:
52 99 0.12
53 574 0.72
54 121 0.15
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (53 bp):
TTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTG
Found at i:2009928 original size:8 final size:8
Alignment explanation
Indices: 2009912--2009952 Score: 64
Period size: 8 Copynumber: 5.0 Consensus size: 8
2009902 TATGGATAAG
2009912 TAATTAAA
1 TAATTAAA
*
2009920 TAGTTAAA
1 TAATTAAA
2009928 TAATTAAA
1 TAATTAAA
2009936 TAATTAAA
1 TAATTAAA
2009944 TATATTAAA
1 TA-ATTAAA
2009953 CATGCACTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
8 24 0.80
9 6 0.20
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (8 bp):
TAATTAAA
Found at i:2011139 original size:25 final size:26
Alignment explanation
Indices: 2011111--2011159 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
2011101 TCCATATATC
*
2011111 TGGTTAG-TGAAGCGACGTCGTTTAA
1 TGGTTAGCTGAAACGACGTCGTTTAA
* *
2011136 TGGTTGGCTGAAACGATGTCGTTT
1 TGGTTAGCTGAAACGACGTCGTTT
2011160 CTGCGTCTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 6 0.30
26 14 0.70
ACGTcount: A:0.20, C:0.12, G:0.33, T:0.35
Consensus pattern (26 bp):
TGGTTAGCTGAAACGACGTCGTTTAA
Found at i:2013295 original size:42 final size:41
Alignment explanation
Indices: 2013180--2013684 Score: 278
Period size: 43 Copynumber: 11.7 Consensus size: 41
2013170 AGGGGGGCTA
* *
2013180 AATTATAAAAGTAAAAAGTGGGATTGAAAAAAAATTAAGGGTCTC
1 AATTAT-AAAGT-AAAAGTGAGATTG--AAAAAATTAAGGGCCTC
* * * * *
2013225 ATTTTATAAAGCTAAAAAATTATATT-AAAAAATTTACGGGCCTC
1 A-ATTATAAAG-T-AAAAGTGAGATTGAAAAAA-TTAAGGGCCTC
* * * *
2013269 AATAATAGAAGTAAAAGTGAGATTAAAAAAATT-AGAGGCGTA
1 AATTATA-AAGTAAAAGTGAGATTGAAAAAATTAAG-GGCCTC
* *
2013311 AACTATAAAAGTAAAAG-GGGATT-AAAAAA--AAGAGGCAC-C
1 AATTAT-AAAGTAAAAGTGAGATTGAAAAAATTAAG-GGC-CTC
*
2013350 AATTATAAAAGTTAAAAGTGAGATTGAAAAAATTAAGGGTCTC
1 AATTAT-AAAG-TAAAAGTGAGATTGAAAAAATTAAGGGCCTC
*
2013393 AATTATAAAGATTAAAAGTGAGATTGAAAAAAAAATAAGGGCCTC
1 AATTATAAAG--TAAAAGTGAGATTG--AAAAAATTAAGGGCCTC
* * * * *
2013438 AATTATAAAGATAGAAATTGAGACT-AAAAAAGATAGGGGCCTA
1 AATTATAAAG-TA-AAAGTGAGATTGAAAAAA-TTAAGGGCCTC
* * ** *
2013481 AATTATAAAAATTAAAAGTGGGATTGAAATGATT-AGAGACCTC
1 AATTAT--AAAGTAAAAGTGAGATTGAAAAAATTAAG-GGCCTC
* ** *
2013524 AATTATAAAGGTGAAAGTGAGATTGAAAAAAATTTGGGGCCTA
1 AATTATAAA-GTAAAAGTGAGATTG-AAAAAATTAAGGGCCTC
* *
2013567 AATTATAGAAGTAAAAAGT-AGGGTTGAAAAAAAATTAAGAG-CTC
1 AATTATA-AAGT-AAAAGTGA-GATTG--AAAAAATTAAGGGCCTC
* * *
2013611 AATTATAAAGGTAAAAAATGAGATT-AAAAAATTAAGAGCTTC
1 AATTATAAA-GT-AAAAGTGAGATTGAAAAAATTAAGGGCCTC
* *
2013653 AATTATACAGGTAAAAAGTGAAATTGAAAAAA
1 AATTATA-AAGT-AAAAGTGAGATTGAAAAAA
2013685 ATTATAAGCA
Statistics
Matches: 364, Mismatches: 60, Indels: 74
0.73 0.12 0.15
Matches are distributed among these distances:
39 16 0.04
40 12 0.03
41 27 0.07
42 80 0.22
43 105 0.29
44 56 0.15
45 54 0.15
46 14 0.04
ACGTcount: A:0.51, C:0.06, G:0.19, T:0.24
Consensus pattern (41 bp):
AATTATAAAGTAAAAGTGAGATTGAAAAAATTAAGGGCCTC
Found at i:2013598 original size:131 final size:131
Alignment explanation
Indices: 2013350--2013685 Score: 303
Period size: 130 Copynumber: 2.6 Consensus size: 131
2013340 AAGAGGCACC
* ** *
2013350 AATTATAAAAGTTAAAAGTGAGATTGAAAAAATTAAGGGTCTCAATTATAAAGATTAAAAGTGAG
1 AATTATAAAAATTAAAAGTGAGATTGAAAAAATTAAGGACCTCAATTATAAAGAGTAAAAGTGAG
* * *
2013415 ATTGAAAAAAAAATAAGGGCCTCAATTATAAAGATAGAAATTGAGACTAAAAAAGATAGGGGCCT
66 ATTGAAAAAAAAATAAGGGCCTAAATTATAAAGATAAAAATAGAGACTAAAAAAGATAGGGGCCT
2013480 A
131 A
* ** *
2013481 AATTATAAAAATTAAAAGTGGGATTGAAATGATT-AGAGACCTCAATTATAAAG-GTGAAAGTGA
1 AATTATAAAAATTAAAAGTGAGATTGAAAAAATTAAG-GACCTCAATTATAAAGAGTAAAAGTGA
* ** ** * *
2013544 GATTG-AAAAAAATTTGGGGCCTAAATTATAGAAG-TAAAAAGTAG-GGTTGAAAAAAAATTAAG
65 GATTGAAAAAAAAATAAGGGCCTAAATTATA-AAGATAAAAA-TAGAGACT-AAAAAAGA-TAGG
* *
2013606 AG-CTC
126 GGCCTA
** * * * *
2013611 AATTATAAAGGTAAAAAATGAGATT-AAAAAATTAA-GAGCTTCAATTATACAG-GTAAAAAGTG
1 AATTATAAAAATTAAAAGTGAGATTGAAAAAATTAAGGA-CCTCAATTATAAAGAGT-AAAAGTG
*
2013673 AAATTGAAAAAAA
64 AGATTGAAAAAAA
2013686 TTATAAGCAT
Statistics
Matches: 165, Mismatches: 31, Indels: 18
0.77 0.14 0.08
Matches are distributed among these distances:
128 2 0.01
129 48 0.29
130 61 0.37
131 54 0.33
ACGTcount: A:0.51, C:0.05, G:0.19, T:0.24
Consensus pattern (131 bp):
AATTATAAAAATTAAAAGTGAGATTGAAAAAATTAAGGACCTCAATTATAAAGAGTAAAAGTGAG
ATTGAAAAAAAAATAAGGGCCTAAATTATAAAGATAAAAATAGAGACTAAAAAAGATAGGGGCCT
A
Found at i:2013657 original size:86 final size:86
Alignment explanation
Indices: 2013180--2013715 Score: 320
Period size: 86 Copynumber: 6.2 Consensus size: 86
2013170 AGGGGGGCTA
* * * ** *
2013180 AATTATAAAAGTAAAAAGTGGGATTGAAAAAAAATTAAGGGTCTCATTTTATAAAGCTAAAAAAT
1 AATTATAAAGGTAAAAAGTGAGATTG--AAAAAATTAAGGGCCT-AAATTATAAAG-TAAAAAGT
* * *
2013245 TATATT-AAAAAATTTACG-G-GCCTC
62 GAGATTGAAAAAAATTA-GAGAG-CTC
* * * *
2013269 AATAATAGAA-GT-AAAAGTGAGATTAAAAAAATT-AGAGGCGTAAACTATAAAAGT-AAAAG-G
1 AATTATA-AAGGTAAAAAGTGAGATTGAAAAAATTAAG-GGCCTAAATTAT-AAAGTAAAAAGTG
* *
2013329 GGATT-AAAAAAA--AGAG-GCACC
63 AGATTGAAAAAAATTAGAGAGC-TC
* * * * *
2013350 AATTATAAAAGTTAAAAGTGAGATTGAAAAAATTAAGGGTCTCAATTATAAAGATTAAAAGTGAG
1 AATTATAAAGGTAAAAAGTGAGATTGAAAAAATTAAGGGCCTAAATTATAAAG-TAAAAAGTGAG
* *
2013415 ATTGAAAAAAAAATA-AGGGCCTC
65 ATTG-AAAAAAATTAGAGAG-CTC
* * * * * * * * *
2013438 AATTATAAAGATAGAAATTGAGACT-AAAAAAGATAGGGGCCTAAATTATAAAAATTAAAAGTGG
1 AATTATAAAGGTAAAAAGTGAGATTGAAAAAA-TTAAGGGCCTAAATTAT-AAAGTAAAAAGTGA
** *
2013502 GATTG-AAATGATTAGAGACCTC
64 GATTGAAAAAAATTAGAGAGCTC
* **
2013524 AATTATAAAGGT-GAAAGTGAGATTGAAAAAAATTTGGGGCCTAAATTATAGAAGTAAAAAGT-A
1 AATTATAAAGGTAAAAAGTGAGATTG-AAAAAATTAAGGGCCTAAATTATA-AAGTAAAAAGTGA
*
2013587 GGGTTGAAAAAAAATTA-AGAGCTC
64 -GATTG-AAAAAAATTAGAGAGCTC
* * * * * *
2013611 AATTATAAAGGTAAAAAATGAGATT-AAAAAATTAAGAGCTTCAATTATACAGGTAAAAAGTGAA
1 AATTATAAAGGTAAAAAGTGAGATTGAAAAAATTAAGGGCCTAAATTATA-AAGTAAAAAGTGAG
*
2013675 ATTGAAAAAAATTATA-AGCATC
65 ATTGAAAAAAATTAGAGAGC-TC
* *
2013697 GATTATAAAGATAAAAAGT
1 AATTATAAAGGTAAAAAGT
2013716 ACACGAATTG
Statistics
Matches: 352, Mismatches: 65, Indels: 63
0.73 0.14 0.13
Matches are distributed among these distances:
80 4 0.01
81 16 0.05
82 29 0.08
83 16 0.05
84 9 0.03
85 31 0.09
86 121 0.34
87 35 0.10
88 77 0.22
89 12 0.03
90 2 0.01
ACGTcount: A:0.51, C:0.06, G:0.18, T:0.24
Consensus pattern (86 bp):
AATTATAAAGGTAAAAAGTGAGATTGAAAAAATTAAGGGCCTAAATTATAAAGTAAAAAGTGAGA
TTGAAAAAAATTAGAGAGCTC
Found at i:2013669 original size:41 final size:43
Alignment explanation
Indices: 2013595--2013713 Score: 138
Period size: 44 Copynumber: 2.8 Consensus size: 43
2013585 TAGGGTTGAA
*
2013595 AAAAAATTAAGAGCTCAATTATAAAGGTAAAAAA-TGAGATT-
1 AAAAAATTAAGAGCTCAATTATAAAGGTAAAAAAGTGAAATTG
*
2013636 AAAAAATTAAGAGCTTCAATTATACAGGT-AAAAAGTGAAATTG
1 AAAAAATTAAGAGC-TCAATTATAAAGGTAAAAAAGTGAAATTG
* *
2013679 AAAAAAATTATA-AGCATCGATTATAAAGATAAAAA
1 -AAAAAATTA-AGAGC-TCAATTATAAAGGTAAAAA
2013714 GTACACGAAT
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
41 19 0.29
42 19 0.29
44 23 0.35
45 5 0.08
ACGTcount: A:0.56, C:0.06, G:0.13, T:0.24
Consensus pattern (43 bp):
AAAAAATTAAGAGCTCAATTATAAAGGTAAAAAAGTGAAATTG
Found at i:2015367 original size:132 final size:135
Alignment explanation
Indices: 2015127--2015388 Score: 413
Period size: 132 Copynumber: 2.0 Consensus size: 135
2015117 CCTGTATAAT
*
2015127 GATATAACAAGAGATTAACTAATACTAATTTATTTGTGCATTTATCAGATGTAATAGAGAAGCAA
1 GATATAACAAGAGATTAACTAATACTAATTTATTTGTGCAGTTATCAGATGTAATAGAGAAGCAA
* * * * * *
2015192 ATGTATTTCTGAGTTCCACTCACCTGTTACCCTGTGCCGCTTTGATCTCCTTGTTCTTGTTTCTG
66 ATGTACTGCTAAGTTCCAATCACCTGTGACCCTGTGCCGCTTTGATCTCCTTGTGCTTGTTTCTG
2015257 CATCA
131 CATCA
* *
2015262 GATATAACAAGAGTTTAACT-A-A-TAATTTATTTGTGCAGTTATCAGATGTCATAGAGAAGCAA
1 GATATAACAAGAGATTAACTAATACTAATTTATTTGTGCAGTTATCAGATGTAATAGAGAAGCAA
*
2015324 ATGTACTGCTAAGTTCCAATCACCTGTGATCCTGTGCCGCTTTGATCTCCTTGTGCTTGTTTCTG
66 ATGTACTGCTAAGTTCCAATCACCTGTGACCCTGTGCCGCTTTGATCTCCTTGTGCTTGTTTCTG
2015389 TAGCTGAATG
Statistics
Matches: 117, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
132 96 0.82
133 1 0.01
134 1 0.01
135 19 0.16
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (135 bp):
GATATAACAAGAGATTAACTAATACTAATTTATTTGTGCAGTTATCAGATGTAATAGAGAAGCAA
ATGTACTGCTAAGTTCCAATCACCTGTGACCCTGTGCCGCTTTGATCTCCTTGTGCTTGTTTCTG
CATCA
Found at i:2026208 original size:12 final size:12
Alignment explanation
Indices: 2026191--2026216 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2026181 AATACCCCTT
2026191 CTAAAAGCTCAC
1 CTAAAAGCTCAC
2026203 CTAAAAGCTCAC
1 CTAAAAGCTCAC
2026215 CT
1 CT
2026217 GACAATTGCA
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:0.38, C:0.35, G:0.08, T:0.19
Consensus pattern (12 bp):
CTAAAAGCTCAC
Found at i:2028060 original size:2 final size:2
Alignment explanation
Indices: 2028053--2028079 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2028043 TAATGAAAAC
2028053 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 T
2028080 GGATAGATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2029787 original size:2 final size:2
Alignment explanation
Indices: 2029780--2029819 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
2029770 ATGAAATACG
* *
2029780 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2029820 CCCAGAATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2030563 original size:18 final size:17
Alignment explanation
Indices: 2030540--2030573 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
2030530 AATAATATGC
2030540 TTAAGACTAACATGTTAT
1 TTAAGACTAACA-GTTAT
2030558 TTAAGACTAACAGTTA
1 TTAAGACTAACAGTTA
2030574 AAAAAGGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (17 bp):
TTAAGACTAACAGTTAT
Found at i:2042995 original size:29 final size:29
Alignment explanation
Indices: 2042961--2043019 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
2042951 CCTAAATTAA
2042961 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
2042990 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
2043019 T
1 T
2043020 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:2046758 original size:2 final size:2
Alignment explanation
Indices: 2046751--2046783 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2046741 TAATGAAAAC
2046751 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 T
2046784 GGATAGATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2048000 original size:10 final size:10
Alignment explanation
Indices: 2047987--2048032 Score: 60
Period size: 9 Copynumber: 4.8 Consensus size: 10
2047977 TGACCAGTTT
2047987 TGAACCGGTC
1 TGAACCGGTC
*
2047997 TGAACCGGTT
1 TGAACCGGTC
*
2048007 TG-ACCGGTT
1 TGAACCGGTC
2048016 TG-ACCGGTC
1 TGAACCGGTC
2048025 TGAACCGG
1 TGAACCGG
2048033 GTTGACCCGA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
9 17 0.52
10 16 0.48
ACGTcount: A:0.17, C:0.26, G:0.33, T:0.24
Consensus pattern (10 bp):
TGAACCGGTC
Found at i:2048014 original size:9 final size:9
Alignment explanation
Indices: 2047970--2048039 Score: 68
Period size: 10 Copynumber: 7.3 Consensus size: 9
2047960 CTGCTGGAAA
2047970 ACCGGTTTG
1 ACCGGTTTG
*
2047979 ACCAGTTTTG
1 ACC-GGTTTG
*
2047989 AACCGGTCTG
1 -ACCGGTTTG
2047999 AACCGGTTTG
1 -ACCGGTTTG
2048009 ACCGGTTTG
1 ACCGGTTTG
*
2048018 ACCGGTCTG
1 ACCGGTTTG
*
2048027 AACCGGGTTG
1 -ACCGGTTTG
2048037 ACC
1 ACC
2048040 CGACCCGACT
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
9 23 0.45
10 25 0.49
11 3 0.06
ACGTcount: A:0.17, C:0.26, G:0.30, T:0.27
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:2048030 original size:28 final size:30
Alignment explanation
Indices: 2047969--2048039 Score: 110
Period size: 28 Copynumber: 2.4 Consensus size: 30
2047959 GCTGCTGGAA
*
2047969 AACCGGTTTGACCAGTTTTGAACCGGTCTG
1 AACCGGTTTGACCAGGTTTGAACCGGTCTG
2047999 AACCGGTTTGACC-GGTTTG-ACCGGTCTG
1 AACCGGTTTGACCAGGTTTGAACCGGTCTG
*
2048027 AACCGGGTTGACC
1 AACCGGTTTGACC
2048040 CGACCCGACT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
28 21 0.54
29 5 0.13
30 13 0.33
ACGTcount: A:0.18, C:0.25, G:0.30, T:0.27
Consensus pattern (30 bp):
AACCGGTTTGACCAGGTTTGAACCGGTCTG
Found at i:2048082 original size:17 final size:17
Alignment explanation
Indices: 2048060--2048109 Score: 91
Period size: 17 Copynumber: 2.9 Consensus size: 17
2048050 GACCCGGCCT
2048060 GACCCGACTGTTGACCC
1 GACCCGACTGTTGACCC
2048077 GACCCGACTGTTGACCC
1 GACCCGACTGTTGACCC
*
2048094 GACCCGACCGTTGACC
1 GACCCGACTGTTGACC
2048110 GTTGACCGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.18, C:0.42, G:0.24, T:0.16
Consensus pattern (17 bp):
GACCCGACTGTTGACCC
Found at i:2048111 original size:7 final size:7
Alignment explanation
Indices: 2048099--2048129 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
2048089 GACCCGACCC
2048099 GACCGTT
1 GACCGTT
2048106 GACCGTT
1 GACCGTT
2048113 GACCGTT
1 GACCGTT
2048120 GACCGTT
1 GACCGTT
2048127 GAC
1 GAC
2048130 TTTCTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:2049083 original size:32 final size:31
Alignment explanation
Indices: 2048999--2049075 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
2048989 CTAATGTGAC
* *
2048999 TCTTAGGTAGGCTCTGCGGCCCTGAGATTAT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGATTAT
** *
2049030 TCTCGGGTAGGCCCTGCGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGAT-TAT
2049062 TCTTAGGTAGGCCC
1 TCTTAGGTAGGCCC
2049076 CACGGCCCCG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 24 0.63
32 14 0.37
ACGTcount: A:0.14, C:0.26, G:0.31, T:0.29
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGCGGCCCTAAGATTAT
Found at i:2049101 original size:63 final size:63
Alignment explanation
Indices: 2048999--2049122 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
2048989 CTAATGTGAC
* ** * *
2048999 TCTTAGGTAGGCTCTGCGGCCCTGAGATTATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATTATTCTCGGGTAGGCCCT-CAGGCCCTAAGATGTGT
* *
2049062 TCTTAGGTAGGCCCCACGGCCCCGAAATCTA-TCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAAT-TATTCTCGGGTAGGCCCTCAGGCCCTAAGATGT
2049123 TCCCTTAGGG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 49 0.94
64 2 0.04
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (63 bp):
TCTTAGGTAGGCCCCACGGCCCCGAAATTATTCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:2050096 original size:514 final size:514
Alignment explanation
Indices: 2049129--2050157 Score: 2031
Period size: 514 Copynumber: 2.0 Consensus size: 514
2049119 ATGTTCCCTT
2049129 AGGGTAACGCTTTTTAAAGAGATTTACTGCAGTATAATTTTATGAGACTTTTTGGACTATGATAT
1 AGGGTAACGCTTTTTAAAGAGATTTACTGCAGTATAATTTTATGAGACTTTTTGGACTATGATAT
2049194 GTTTAGTGTACCTATAGCGATTTTATGATAATATTGGGACACACTGAGCCTAGCTCACTTTTCGA
66 GTTTAGTGTACCTATAGCGATTTTATGATAATATTGGGACACACTGAGCCTAGCTCACTTTTCGA
2049259 AAATGTTTTTCCCCTGTCAGATACTGTTGGTTAGATACCCTGGATTGAGCACTTGGAGGATCAAC
131 AAATGTTTTTCCCCTGTCAGATACTGTTGGTTAGATACCCTGGATTGAGCACTTGGAGGATCAAC
2049324 ATATCTCTTGAAGTATATCTGATTGAAATGTTTTTACCTTACAAGTTGACTTTATTTTGTTGACA
196 ATATCTCTTGAAGTATATCTGATTGAAATGTTTTTACCTTACAAGTTGACTTTATTTTGTTGACA
2049389 TGGACCTTATTTTAAAGTATGAGATTTTAATATGATGACATTTTTACTATTACTATTCGGGTTAT
261 TGGACCTTATTTTAAAGTATGAGATTTTAATATGATGACATTTTTACTATTACTATTCGGGTTAT
2049454 CGTGATTTGATTTTTAAGATATGTTTTAAATTAATTTATTACTTATTGGTATTATATTTACAAGT
326 CGTGATTTGATTTTTAAGATATGTTTTAAATTAATTTATTACTTATTGGTATTATATTTACAAGT
2049519 TAGGTTTTGATAGTATGATTTATTATAATTTCATGTCATTTATAATGTGATTTTACATTGTTTGA
391 TAGGTTTTGATAGTATGATTTATTATAATTTCATGTCATTTATAATGTGATTTTACATTGTTTGA
*
2049584 ATAACGGTTTCGGAAAAATGTCTTAAAGAATCATAATGTGACCCCCTAGACTTAGTCGA
456 ATAACGGTTTCGGAAAAATGTCTTAAAGAATCATAATGTGACCCACTAGACTTAGTCGA
*
2049643 AGGGTAACGCTTTTTAAAGAGATTTATTGCAGTATAATTTTATGAGACTTTTTGGACTATGATAT
1 AGGGTAACGCTTTTTAAAGAGATTTACTGCAGTATAATTTTATGAGACTTTTTGGACTATGATAT
2049708 GTTTAGTGTACCTATAGCGATTTTATGATAATATTGGGACACACTGAGCCTAGCTCACTTTTCGA
66 GTTTAGTGTACCTATAGCGATTTTATGATAATATTGGGACACACTGAGCCTAGCTCACTTTTCGA
2049773 AAATGTTTTTCCCCTGTCAGATACTGTTGGTTAGATACCCTGGATTGAGCACTTGGAGGATCAAC
131 AAATGTTTTTCCCCTGTCAGATACTGTTGGTTAGATACCCTGGATTGAGCACTTGGAGGATCAAC
2049838 ATATCTCTTGAAGTATATCTGATTGAAATGTTTTTACCTTACAAGTTGACTTTATTTTGTTGACA
196 ATATCTCTTGAAGTATATCTGATTGAAATGTTTTTACCTTACAAGTTGACTTTATTTTGTTGACA
2049903 TGGACCTTATTTTAAAGTATGAGATTTTAATATGATGACATTTTTACTATTACTATTCGGGTTAT
261 TGGACCTTATTTTAAAGTATGAGATTTTAATATGATGACATTTTTACTATTACTATTCGGGTTAT
2049968 CGTGATTTGATTTTTAAGATATGTTTTAAATTAATTTATTACTTATTGGTATTATATTTACAAGT
326 CGTGATTTGATTTTTAAGATATGTTTTAAATTAATTTATTACTTATTGGTATTATATTTACAAGT
2050033 TAGGTTTTGATAGTATGATTTATTATAATTTCATGTCATTTATAATGTGATTTTACATTGTTTGA
391 TAGGTTTTGATAGTATGATTTATTATAATTTCATGTCATTTATAATGTGATTTTACATTGTTTGA
*
2050098 ATAACGGTTTCGGAAAAATGTCTTAAAGAATCATAATGTGATCCACTAGACTTAGTCGA
456 ATAACGGTTTCGGAAAAATGTCTTAAAGAATCATAATGTGACCCACTAGACTTAGTCGA
2050157 A
1 A
2050158 ACGCATAGGC
Statistics
Matches: 512, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
514 512 1.00
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (514 bp):
AGGGTAACGCTTTTTAAAGAGATTTACTGCAGTATAATTTTATGAGACTTTTTGGACTATGATAT
GTTTAGTGTACCTATAGCGATTTTATGATAATATTGGGACACACTGAGCCTAGCTCACTTTTCGA
AAATGTTTTTCCCCTGTCAGATACTGTTGGTTAGATACCCTGGATTGAGCACTTGGAGGATCAAC
ATATCTCTTGAAGTATATCTGATTGAAATGTTTTTACCTTACAAGTTGACTTTATTTTGTTGACA
TGGACCTTATTTTAAAGTATGAGATTTTAATATGATGACATTTTTACTATTACTATTCGGGTTAT
CGTGATTTGATTTTTAAGATATGTTTTAAATTAATTTATTACTTATTGGTATTATATTTACAAGT
TAGGTTTTGATAGTATGATTTATTATAATTTCATGTCATTTATAATGTGATTTTACATTGTTTGA
ATAACGGTTTCGGAAAAATGTCTTAAAGAATCATAATGTGACCCACTAGACTTAGTCGA
Found at i:2055869 original size:9 final size:9
Alignment explanation
Indices: 2055837--2055915 Score: 86
Period size: 9 Copynumber: 8.3 Consensus size: 9
2055827 CTGCTGGAAA
2055837 ACCGGTTTG
1 ACCGGTTTG
*
2055846 ACCAGTTTTG
1 ACC-GGTTTG
2055856 AACCGGTTTG
1 -ACCGGTTTG
*
2055866 ACCGGTCTG
1 ACCGGTTTG
2055875 AACCGGTTTG
1 -ACCGGTTTG
2055885 ACCGGTTTG
1 ACCGGTTTG
*
2055894 ACCGGTCTG
1 ACCGGTTTG
*
2055903 AACCGGGTTG
1 -ACCGGTTTG
2055913 ACC
1 ACC
2055916 CGACCCGACT
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
9 31 0.53
10 25 0.42
11 3 0.05
ACGTcount: A:0.16, C:0.25, G:0.30, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:2055878 original size:19 final size:19
Alignment explanation
Indices: 2055836--2055913 Score: 95
Period size: 19 Copynumber: 4.1 Consensus size: 19
2055826 GCTGCTGGAA
*
2055836 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTTTG
*
2055856 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTTTG
2055875 AACCGGTTTGACCGGTTTG
1 AACCGGTTTGACCGGTTTG
* *
2055894 -ACCGGTCTGAACCGGGTTG
1 AACCGGTTTG-ACCGGTTTG
2055913 A
1 A
2055914 CCCGACCCGA
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
18 8 0.16
19 30 0.59
20 13 0.25
ACGTcount: A:0.18, C:0.23, G:0.31, T:0.28
Consensus pattern (19 bp):
AACCGGTTTGACCGGTTTG
Found at i:2055895 original size:28 final size:28
Alignment explanation
Indices: 2055852--2055915 Score: 110
Period size: 28 Copynumber: 2.2 Consensus size: 28
2055842 TTTGACCAGT
2055852 TTTGAACCGGTTTGACCGGTCTGAACCGG
1 TTTG-ACCGGTTTGACCGGTCTGAACCGG
2055881 TTTGACCGGTTTGACCGGTCTGAACCGG
1 TTTGACCGGTTTGACCGGTCTGAACCGG
*
2055909 GTTGACC
1 TTTGACC
2055916 CGACCCGACT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 30 0.88
29 4 0.12
ACGTcount: A:0.16, C:0.25, G:0.31, T:0.28
Consensus pattern (28 bp):
TTTGACCGGTTTGACCGGTCTGAACCGG
Found at i:2055930 original size:14 final size:14
Alignment explanation
Indices: 2055911--2055938 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2055901 TGAACCGGGT
2055911 TGACCCGACCCGAC
1 TGACCCGACCCGAC
2055925 TGACCCGACCCGAC
1 TGACCCGACCCGAC
2055939 CCGACTGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.50, G:0.21, T:0.07
Consensus pattern (14 bp):
TGACCCGACCCGAC
Found at i:2055953 original size:17 final size:17
Alignment explanation
Indices: 2055909--2055985 Score: 109
Period size: 17 Copynumber: 4.4 Consensus size: 17
2055899 TCTGAACCGG
2055909 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
**
2055926 GACCCGACCCGACCCGACT
1 G--TTGACCCGACCCGACT
2055945 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
*
2055962 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACT
2055979 GTTGACC
1 GTTGACC
2055986 GTTGACCGTT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
17 38 0.72
19 15 0.28
ACGTcount: A:0.18, C:0.44, G:0.23, T:0.14
Consensus pattern (17 bp):
GTTGACCCGACCCGACT
Found at i:2055987 original size:7 final size:7
Alignment explanation
Indices: 2055975--2056005 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
2055965 GACCCGACCC
2055975 GACCGTT
1 GACCGTT
2055982 GACCGTT
1 GACCGTT
2055989 GACCGTT
1 GACCGTT
2055996 GACCGTT
1 GACCGTT
2056003 GAC
1 GAC
2056006 TTTCTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:2056959 original size:32 final size:31
Alignment explanation
Indices: 2056875--2056951 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
2056865 CTAATGTGAC
* *
2056875 TCTTAGGTAGGCTCTGCGGCCCTGAGATTAT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGATTAT
** *
2056906 TCTCGGGTAGGCCCTGCGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGAT-TAT
2056938 TCTTAGGTAGGCCC
1 TCTTAGGTAGGCCC
2056952 CACGGCCCCG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 24 0.63
32 14 0.37
ACGTcount: A:0.14, C:0.26, G:0.31, T:0.29
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGCGGCCCTAAGATTAT
Found at i:2056977 original size:63 final size:63
Alignment explanation
Indices: 2056875--2056998 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
2056865 CTAATGTGAC
* ** * *
2056875 TCTTAGGTAGGCTCTGCGGCCCTGAGATTATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATTATTCTCGGGTAGGCCCT-CAGGCCCTAAGATGTGT
* *
2056938 TCTTAGGTAGGCCCCACGGCCCCGAAATCTA-TCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAAT-TATTCTCGGGTAGGCCCTCAGGCCCTAAGATGT
2056999 TCCCTTAGGG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 49 0.94
64 2 0.04
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (63 bp):
TCTTAGGTAGGCCCCACGGCCCCGAAATTATTCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:2063339 original size:2 final size:2
Alignment explanation
Indices: 2063332--2063359 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2063322 ATGAAATACG
2063332 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
2063360 GACAGAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2064103 original size:18 final size:17
Alignment explanation
Indices: 2064080--2064113 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
2064070 AATAATACGC
2064080 TTAAGACTAACATGTTAT
1 TTAAGACTAACA-GTTAT
2064098 TTAAGACTAACAGTTA
1 TTAAGACTAACAGTTA
2064114 AAAAAGGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (17 bp):
TTAAGACTAACAGTTAT
Found at i:2076050 original size:2 final size:2
Alignment explanation
Indices: 2076043--2076069 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2076033 TAATGAAAAC
2076043 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 T
2076070 GGATAGATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2078554 original size:18 final size:17
Alignment explanation
Indices: 2078531--2078564 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
2078521 AATAATACGC
2078531 TTAAGACTAACATGTTAT
1 TTAAGACTAACA-GTTAT
2078549 TTAAGACTAACAGTTA
1 TTAAGACTAACAGTTA
2078565 AAAAAGGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (17 bp):
TTAAGACTAACAGTTAT
Found at i:2080218 original size:29 final size:29
Alignment explanation
Indices: 2080176--2080234 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
2080166 ATTTTCACCT
2080176 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
2080205 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
2080234 A
1 A
2080235 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:2084900 original size:29 final size:29
Alignment explanation
Indices: 2084858--2084916 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
2084848 ATTTTCACCT
2084858 AACTAAATTGATGTAAGCAATGAAATCAA
1 AACTAAATTGATGTAAGCAATGAAATCAA
*
2084887 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGAAATCAA
2084916 A
1 A
2084917 TTAATTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.51, C:0.12, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGAAATCAA
Found at i:2089508 original size:2 final size:2
Alignment explanation
Indices: 2089501--2089530 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2089491 TAACAAATTA
2089501 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
2089531 GTTAAATAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2091360 original size:29 final size:29
Alignment explanation
Indices: 2091326--2091384 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
2091316 CCTAAATTAA
2091326 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
2091355 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
2091384 T
1 T
2091385 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:2092819 original size:168 final size:167
Alignment explanation
Indices: 2092497--2092834 Score: 651
Period size: 168 Copynumber: 2.0 Consensus size: 167
2092487 AAGCAGAGGC
2092497 ACTTTTCAGCGGTATACTGGCAGTGGATCTAAAAAGGATGGTGACAAAGTGAAAATTACCAAGGA
1 ACTTTTCAGCGGTATACTGGCAGTGGATCTAAAAAGGATGGTGACAAAGTGAAAATTACCAAGGA
2092562 AAAGGAGGCCCTCATTCAGGGGGAGCATCCAAGAACGCGGTAATAGTAGAAAGTTCGATGGCAAG
66 AAAGGAGGCCCTCATTCAGGGGGAGCATCCAAGAACGCGGTAATAGTAGAAAGTTCGATGGCAAG
2092627 TGTTATAACTGCGGGAAGATGGGTCACATGGC-AAAG
131 TGTTATAACTGCGGGAAGATGGGTCACATGGCAAAAG
2092663 ACTTTTCAGCGGTATACTGGCAGTGGATCTAAAAAGGATGGTGACAAAGTGAAAAATTACCAAGG
1 ACTTTTCAGCGGTATACTGGCAGTGGATCTAAAAAGGATGGTGACAAAGTG-AAAATTACCAAGG
2092728 AAAAGGAGGCCCTCATTCAGGGGGAGCATCCAAGAATCGCGGTAATAGTAGAAAGTTCGATGGCA
65 AAAAGGAGGCCCTCATTCAGGGGGAGCATCCAAGAA-CGCGGTAATAGTAGAAAGTTCGATGGCA
2092793 AGTGTTATAACTGCGGGAAGATGGGTCACATGGCAAAAG
129 AGTGTTATAACTGCGGGAAGATGGGTCACATGGCAAAAG
2092832 ACT
1 ACT
2092835 GTTGGACCAA
Statistics
Matches: 169, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
166 51 0.30
167 49 0.29
168 62 0.37
169 7 0.04
ACGTcount: A:0.35, C:0.16, G:0.30, T:0.20
Consensus pattern (167 bp):
ACTTTTCAGCGGTATACTGGCAGTGGATCTAAAAAGGATGGTGACAAAGTGAAAATTACCAAGGA
AAAGGAGGCCCTCATTCAGGGGGAGCATCCAAGAACGCGGTAATAGTAGAAAGTTCGATGGCAAG
TGTTATAACTGCGGGAAGATGGGTCACATGGCAAAAG
Found at i:2096775 original size:28 final size:29
Alignment explanation
Indices: 2096743--2096800 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
2096733 CCTAAATTAA
2096743 TTTGATGTCATTGC-TACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
2096771 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
2096800 T
1 T
2096801 AGGTGAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 14 0.48
29 15 0.52
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.48
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:2097676 original size:57 final size:57
Alignment explanation
Indices: 2097582--2097697 Score: 216
Period size: 57 Copynumber: 2.0 Consensus size: 57
2097572 ATAGTTCCAC
2097582 TCAAGATACCTCAACTCATTGGAAGATATACAATATCAACTCCA-TTGTAGGTTGTT
1 TCAAGATACCTCAACTCATTGGAAGATATACAATATCAACTCCATTTGTAGGTTGTT
2097638 TCAAGATACCTCAACTCATTTGGAAGATATACAATATCAACTCCATTTGTAGGTTGTT
1 TCAAGATACCTCAACTCA-TTGGAAGATATACAATATCAACTCCATTTGTAGGTTGTT
2097696 TC
1 TC
2097698 TCCGTCCAAC
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
56 18 0.31
57 26 0.45
58 14 0.24
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.34
Consensus pattern (57 bp):
TCAAGATACCTCAACTCATTGGAAGATATACAATATCAACTCCATTTGTAGGTTGTT
Found at i:2101606 original size:2 final size:2
Alignment explanation
Indices: 2101599--2101648 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
2101589 ATTAATGAAC
2101599 TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2101640 TA TA TA TA T
1 TA TA TA TA T
2101649 GATAGATTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2103360 original size:2 final size:2
Alignment explanation
Indices: 2103353--2103397 Score: 72
Period size: 2 Copynumber: 22.0 Consensus size: 2
2103343 ATGAAATACG
*
2103353 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT GAT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT
2103396 AT
1 AT
2103398 GCCAGAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 38 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2104139 original size:18 final size:17
Alignment explanation
Indices: 2104113--2104146 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2104103 AATAATACGC
*
2104113 TTAAGACTAACATGTTAT
1 TTAAAACTAACA-GTTAT
2104131 TTAAAACTAACAGTTA
1 TTAAAACTAACAGTTA
2104147 AAAAAGGCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (17 bp):
TTAAAACTAACAGTTAT
Found at i:2112352 original size:82 final size:82
Alignment explanation
Indices: 2112262--2112564 Score: 265
Period size: 82 Copynumber: 3.7 Consensus size: 82
2112252 AAAATGCCAT
* *
2112262 TATAGATGAACCCTATTACGACATTTGTATAAAAAATCCGCTAAAGAACTACTCTGTTAC-AGCG
1 TATAGATGAACCCTATTGCGGCATTTGTATAAAAAATCCGCTAAAGAACTACTCTGTTACGA-CG
2112326 TTTGTTGAAAAACACTAC
65 TTTGTTGAAAAACACTAC
** ** * * * **
2112344 TATAGATGAACCCTATTGTTGTGTTTTTATACAAACA-CCGCTAAAGTACTACTCTGTCGCGACG
1 TATAGATGAACCCTATTGCGGCATTTGTATA-AAAAATCCGCTAAAGAACTACTCTGTTACGACG
* *
2112408 TTTGTTGAGAAACGCTAC
65 TTTGTTGAAAAACACTAC
* * * * * * *** * *
2112426 TATGGATGAA-CCTATTGTGGCGTTTGTATAAAAACTCCACTATAGATGAACCCTATTACGAC-T
1 TATAGATGAACCCTATTGCGGCATTTGTATAAAAAATCCGCTAAAGAACTACTCTGTTACGACGT
*
2112489 TTATTGAAAAAACACTAC
66 TTGTTG-AAAAACACTAC
* * **
2112507 TATAGATGAACCCTATTGCGGCATTTTTTATACAAACGCCGCTAAAGGAA-TACTCTGT
1 TATAGATGAACCCTATTGCGGCA-TTTGTATAAAAAATCCGCTAAA-GAACTACTCTGT
2112565 CGTGACATTT
Statistics
Matches: 170, Mismatches: 44, Indels: 13
0.75 0.19 0.06
Matches are distributed among these distances:
80 9 0.05
81 51 0.30
82 81 0.48
83 27 0.16
84 2 0.01
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (82 bp):
TATAGATGAACCCTATTGCGGCATTTGTATAAAAAATCCGCTAAAGAACTACTCTGTTACGACGT
TTGTTGAAAAACACTAC
Found at i:2114567 original size:29 final size:29
Alignment explanation
Indices: 2114534--2114643 Score: 166
Period size: 29 Copynumber: 3.8 Consensus size: 29
2114524 CACCCATTTC
* *
2114534 GAATTAATTACCAGAATAGCACCAAAACC
1 GAATTATTTACCAGAATAGCACCAAAACT
* *
2114563 AAATTATTTACCATAATAGCACCAAAACT
1 GAATTATTTACCAGAATAGCACCAAAACT
*
2114592 GAATTATTTACCAGAATAGCATCAAAACT
1 GAATTATTTACCAGAATAGCACCAAAACT
*
2114621 GAATTATTTACCCGAATAGCACC
1 GAATTATTTACCAGAATAGCACC
2114644 GATCAACGGT
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 72 1.00
ACGTcount: A:0.45, C:0.22, G:0.09, T:0.25
Consensus pattern (29 bp):
GAATTATTTACCAGAATAGCACCAAAACT
Found at i:2114581 original size:58 final size:59
Alignment explanation
Indices: 2114506--2114643 Score: 165
Period size: 58 Copynumber: 2.4 Consensus size: 59
2114496 CCCTTTTTTT
***
2114506 AAATT-TTTACCAAAATAGCACCCATTTC-GAATTAATTACCAGAATAGCACCAAAACC
1 AAATTATTTACCAAAATAGCACCCAAAACTGAATTAATTACCAGAATAGCACCAAAACC
* * * *
2114563 AAATTATTTACCATAATAGCA-CCAAAACTGAATTATTTACCAGAATAGCATCAAAACT
1 AAATTATTTACCAAAATAGCACCCAAAACTGAATTAATTACCAGAATAGCACCAAAACC
* **
2114621 GAATTATTTACCCGAATAGCACC
1 AAATTATTTACCAAAATAGCACC
2114644 GATCAACGGT
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
57 9 0.13
58 58 0.85
59 1 0.01
ACGTcount: A:0.43, C:0.22, G:0.08, T:0.26
Consensus pattern (59 bp):
AAATTATTTACCAAAATAGCACCCAAAACTGAATTAATTACCAGAATAGCACCAAAACC
Found at i:2114673 original size:17 final size:18
Alignment explanation
Indices: 2114651--2114685 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2114641 ACCGATCAAC
2114651 GGTCAAC-GATCGGGTCG
1 GGTCAACGGATCGGGTCG
*
2114668 GGTCAACGGGTCGGGTCG
1 GGTCAACGGATCGGGTCG
2114686 TGACCGGTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.14, C:0.23, G:0.46, T:0.17
Consensus pattern (18 bp):
GGTCAACGGATCGGGTCG
Found at i:2116375 original size:3 final size:3
Alignment explanation
Indices: 2116367--2116416 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
2116357 TATGTTGAAT
2116367 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2116415 AT
1 AT
2116417 TTGACTTAGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2117575 original size:202 final size:200
Alignment explanation
Indices: 2117307--2117708 Score: 786
Period size: 202 Copynumber: 2.0 Consensus size: 200
2117297 GGTGAAACAT
2117307 TAATTTTTTCGGGTCGGGTCGGGTCGGGTGGAGAACCCTTTCTTCTCGGGTCGGGTCGGGTGGCC
1 TAATTTTTTCGGGTCGGGTCGGGTCGGGTGGAGAACCCTTTCTTCTCGGGTCGGGTCGGGTGGCC
2117372 CAAAAACCCGACCCGACCCGACCCATTACCATCCCTAAGAACAACCCTGGTCGGTGAACAATTAA
66 CAAAAACCCGACCCGACCCGACCCATTACCATCCCTAAGAACAACCCTGGTCGGTGAACAATTAA
2117437 TCTGGGTACATTCAGGTATCTGCTGGAATTTTCAGTTTTCGGGAGTCGATTACATGTGGGGAAGG
131 TCTGGGTACATTCAGGTATCTGCTGGAATTTTCAGTTTTCGGGAGTCGATTACATGTGGGGAAGG
2117502 GTGAG
196 GTGAG
2117507 TAATTTTTTCGGGTCGGGTCGGGTCACGGGTGGAGAACCCTTTCTTCTCGGGTCGGGTCGGGTGG
1 TAATTTTTTCGGGTCGGGTCGGGT--CGGGTGGAGAACCCTTTCTTCTCGGGTCGGGTCGGGTGG
2117572 CCCAAAAACCCGACCCGACCCGACCCATTACCATCCCTAAGAACAACCCTGGTCGGTGAACAATT
64 CCCAAAAACCCGACCCGACCCGACCCATTACCATCCCTAAGAACAACCCTGGTCGGTGAACAATT
2117637 AATCTGGGTACATTCAGGTATCTGCTGGAATTTTCAGTTTTCGGGAGTCGATTACATGTGGGGAA
129 AATCTGGGTACATTCAGGTATCTGCTGGAATTTTCAGTTTTCGGGAGTCGATTACATGTGGGGAA
2117702 GGGTGAG
194 GGGTGAG
2117709 CACCCCACAA
Statistics
Matches: 200, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
200 24 0.12
202 176 0.88
ACGTcount: A:0.21, C:0.24, G:0.29, T:0.26
Consensus pattern (200 bp):
TAATTTTTTCGGGTCGGGTCGGGTCGGGTGGAGAACCCTTTCTTCTCGGGTCGGGTCGGGTGGCC
CAAAAACCCGACCCGACCCGACCCATTACCATCCCTAAGAACAACCCTGGTCGGTGAACAATTAA
TCTGGGTACATTCAGGTATCTGCTGGAATTTTCAGTTTTCGGGAGTCGATTACATGTGGGGAAGG
GTGAG
Found at i:2118235 original size:43 final size:41
Alignment explanation
Indices: 2118170--2118254 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 41
2118160 TAAATGTATG
*
2118170 AGCATTGTCAAGTTTATATGGTAAACTACGCTTCATTTTTTAT
1 AGCATTGTCAAGTTTATATGGTAAA-TACGCTTC-TTTATTAT
2118213 AGCATTGTCAAGTTTACT-TGGTAAATACGCTTCTTTATTAT
1 AGCATTGTCAAGTTTA-TATGGTAAATACGCTTCTTTATTAT
2118254 A
1 A
2118255 CAAATTAAGC
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
41 8 0.20
42 8 0.20
43 23 0.57
44 1 0.03
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (41 bp):
AGCATTGTCAAGTTTATATGGTAAATACGCTTCTTTATTAT
Found at i:2123258 original size:13 final size:13
Alignment explanation
Indices: 2123240--2123286 Score: 78
Period size: 12 Copynumber: 3.6 Consensus size: 13
2123230 TAAAACACAT
2123240 GGGCTGCTAAGGG
1 GGGCTGCTAAGGG
2123253 GGGCTGCTAA-GG
1 GGGCTGCTAAGGG
2123265 GGGCTGCTAAGGGG
1 GGGCTGCTAA-GGG
2123279 GGGCTGCT
1 GGGCTGCT
2123287 GTAATTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.38
13 10 0.31
14 10 0.31
ACGTcount: A:0.13, C:0.17, G:0.53, T:0.17
Consensus pattern (13 bp):
GGGCTGCTAAGGG
Found at i:2123702 original size:16 final size:16
Alignment explanation
Indices: 2123681--2123711 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2123671 TTACTATTCA
2123681 CGTGAATAGTGAATTT
1 CGTGAATAGTGAATTT
2123697 CGTGAATAGTGAATT
1 CGTGAATAGTGAATT
2123712 CGGTCGGCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.35
Consensus pattern (16 bp):
CGTGAATAGTGAATTT
Found at i:2124482 original size:15 final size:16
Alignment explanation
Indices: 2124462--2124493 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
2124452 TGGCAGATCC
2124462 AAATCCAG-ACGGGAA
1 AAATCCAGAACGGGAA
2124477 AAATCCAGAACGGGAA
1 AAATCCAGAACGGGAA
2124493 A
1 A
2124494 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.50, C:0.19, G:0.25, T:0.06
Consensus pattern (16 bp):
AAATCCAGAACGGGAA
Found at i:2127774 original size:14 final size:14
Alignment explanation
Indices: 2127755--2127802 Score: 82
Period size: 14 Copynumber: 3.6 Consensus size: 14
2127745 TAAAACACAT
2127755 GGGCTGCTAAGGGG
1 GGGCTGCTAAGGGG
2127769 GGGCTGCTAA--GG
1 GGGCTGCTAAGGGG
2127781 GGGCTGCTAAGGGG
1 GGGCTGCTAAGGGG
2127795 GGGCTGCT
1 GGGCTGCT
2127803 GTAATTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.38
14 20 0.62
ACGTcount: A:0.12, C:0.17, G:0.54, T:0.17
Consensus pattern (14 bp):
GGGCTGCTAAGGGG
Found at i:2127794 original size:11 final size:12
Alignment explanation
Indices: 2127755--2127795 Score: 64
Period size: 12 Copynumber: 3.2 Consensus size: 12
2127745 TAAAACACAT
2127755 GGGCTGCTAAGGGG
1 GGGCTGCTAA--GG
2127769 GGGCTGCTAAGG
1 GGGCTGCTAAGG
2127781 GGGCTGCTAAGG
1 GGGCTGCTAAGG
2127793 GGG
1 GGG
2127796 GGCTGCTGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 17 0.63
14 10 0.37
ACGTcount: A:0.15, C:0.15, G:0.56, T:0.15
Consensus pattern (12 bp):
GGGCTGCTAAGG
Found at i:2131466 original size:24 final size:24
Alignment explanation
Indices: 2131439--2131494 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
2131429 CGAACGATTC
2131439 AGCGGTTCTGGCCAGTTCACTAGT
1 AGCGGTTCTGGCCAGTTCACTAGT
*
2131463 AGCGGTTCTGGCCGGTTCACTAGT
1 AGCGGTTCTGGCCAGTTCACTAGT
2131487 AGCGGTTC
1 AGCGGTTC
2131495 AACCGGTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.14, C:0.25, G:0.32, T:0.29
Consensus pattern (24 bp):
AGCGGTTCTGGCCAGTTCACTAGT
Found at i:2135827 original size:132 final size:135
Alignment explanation
Indices: 2135618--2135879 Score: 440
Period size: 132 Copynumber: 2.0 Consensus size: 135
2135608 CCGTGCATAC
* *
2135618 GATATAACAAGAGATTAACTAATACTAATTTATTTGTGCAGTTGTCAGATGTGATAGAGAAGCAA
1 GATATAACAAGAGATTAACTAATACTAATTTATTTGTGCAGTTATCAGATGTCATAGAGAAGCAA
* * * *
2135683 ATGTATTTCTAAGTTCCAATCACCTGTGACCCTGTGCCGCTTTGATCTCCTTGTTCTTGTTTCTG
66 ATGTACTGCTAAGCTCCAATCACCTGTGACCCTGTGCCGCTTTGATCTCCTTGTGCTTGTTTCTG
2135748 CATCT
131 CATCT
2135753 GATATAACAAGAGATTAACT-A-A-TAATTTATTTGTGCAGTTATCAGATGTCATAGAGAAGCAA
1 GATATAACAAGAGATTAACTAATACTAATTTATTTGTGCAGTTATCAGATGTCATAGAGAAGCAA
*
2135815 ATGTACTGCTAAGCTCCAATCACCTGTGATCCTGTGCCGCTTTGATCTCCTTGTGCTTGTTTCTG
66 ATGTACTGCTAAGCTCCAATCACCTGTGACCCTGTGCCGCTTTGATCTCCTTGTGCTTGTTTCTG
2135880 TAGCAGAATG
Statistics
Matches: 120, Mismatches: 7, Indels: 3
0.92 0.05 0.02
Matches are distributed among these distances:
132 98 0.82
133 1 0.01
134 1 0.01
135 20 0.17
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (135 bp):
GATATAACAAGAGATTAACTAATACTAATTTATTTGTGCAGTTATCAGATGTCATAGAGAAGCAA
ATGTACTGCTAAGCTCCAATCACCTGTGACCCTGTGCCGCTTTGATCTCCTTGTGCTTGTTTCTG
CATCT
Found at i:2140178 original size:2 final size:2
Alignment explanation
Indices: 2140171--2140205 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2140161 TAATGAAAAC
2140171 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 T
2140206 GATGTAATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2142678 original size:18 final size:17
Alignment explanation
Indices: 2142655--2142688 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
2142645 AATAATACGC
2142655 TTAAGACTAACATGTTAT
1 TTAAGACTAACA-GTTAT
2142673 TTAAGACTAACAGTTA
1 TTAAGACTAACAGTTA
2142689 AAAAAAGGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (17 bp):
TTAAGACTAACAGTTAT
Found at i:2145217 original size:30 final size:29
Alignment explanation
Indices: 2145170--2145260 Score: 145
Period size: 25 Copynumber: 3.2 Consensus size: 29
2145160 GTCGATGTGA
2145170 TAATTTTTAATAAAATATAATTTTTTTAT
1 TAATTTTTAATAAAATATAATTTTTTTAT
2145199 TAATTTTTAATAAAA-AT-A--TTTTTAT
1 TAATTTTTAATAAAATATAATTTTTTTAT
2145224 TAATTTTTAATAAAATATAATTTTTTTTAT
1 TAATTTTTAATAAAATATAA-TTTTTTTAT
2145254 TAATTTT
1 TAATTTT
2145261 CATTAAATCC
Statistics
Matches: 57, Mismatches: 0, Indels: 9
0.86 0.00 0.14
Matches are distributed among these distances:
25 22 0.39
26 2 0.04
27 2 0.04
28 2 0.04
29 15 0.26
30 14 0.25
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (29 bp):
TAATTTTTAATAAAATATAATTTTTTTAT
Found at i:2152217 original size:19 final size:19
Alignment explanation
Indices: 2152176--2152218 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
2152166 CATATTATTT
*
2152176 TTTTGTTATTTTTTACTTGC
1 TTTTGTTATTTTTTA-TTCC
2152196 TTTTGTTATTTTCTT-TTCC
1 TTTTGTTATTTT-TTATTCC
2152215 TTTT
1 TTTT
2152219 CTTTGTTACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 7 0.33
20 12 0.57
21 2 0.10
ACGTcount: A:0.07, C:0.12, G:0.07, T:0.74
Consensus pattern (19 bp):
TTTTGTTATTTTTTATTCC
Found at i:2152325 original size:15 final size:17
Alignment explanation
Indices: 2152307--2152338 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
2152297 AATAATATAA
2152307 TAAATT-CAAG-TAGAT
1 TAAATTGCAAGATAGAT
2152322 TAAATTGCAAGATAGAT
1 TAAATTGCAAGATAGAT
2152339 ACAAATACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.47, C:0.06, G:0.16, T:0.31
Consensus pattern (17 bp):
TAAATTGCAAGATAGAT
Found at i:2152849 original size:195 final size:195
Alignment explanation
Indices: 2152504--2152912 Score: 518
Period size: 195 Copynumber: 2.1 Consensus size: 195
2152494 AGATGGCCTA
* * *
2152504 ATAGTGTCTCATTCCACTAAACCAATTGATTATTGATATTAGTTTTGATTTTTTAATCAATCATT
1 ATAGTGCCTCATCCCACTAAACCAACTGATTATTGATATTAGTTTTGATTTTTTAATCAATCATT
* * * *
2152569 AGTATCAGATTTATTGATCGACTAGTCCAGATTGAGTTTTATAGAAACTCATTATGGAGACGACC
66 AGAATCAGATTTATTAATCGACTAGTCCAGATCGAGTTTTATAGAAACCCATTATGGAGACGACC
* * * * * * *
2152634 CTCCCAACCCAATTTGTTCTATACGCAAACGTCAGGATTTAAACCCCTGACATTT-TTTAAGGAA
131 ATCCAAACCCAATTTGTTCTATACACAAACATCAGGATTTAAACCCCTGAC-TTTGCTGAACGAA
2152698 T
195 T
* * * * * *
2152699 CTAGTGCCTCATCCCACTAAATCAACTGATTGTTGGTATTTG-TTTGATTTTTTAAATTAATCAT
1 ATAGTGCCTCATCCCACTAAACCAACTGATTATTGATATTAGTTTTGATTTTTT-AATCAATCAT
* * *
2152763 TAGAATCGGATTTATTAATCGACTAGTCCATATCGAGTTTTATAGAAACCCATTAT-GAGGACTA
65 TAGAATCAGATTTATTAATCGACTAGTCCAGATCGAGTTTTATAGAAACCCATTATGGA-GACGA
* * * *
2152827 CCATCCAAACTCAATTTGTTCTATACACAAATATCAGGATTTGAACCTCTGACTTTGCTGAACGA
129 CCATCCAAACCCAATTTGTTCTATACACAAACATCAGGATTTAAACCCCTGACTTTGCTGAACGA
2152892 AT
194 AT
*
2152894 ATAGTGCCTCATCTCACTA
1 ATAGTGCCTCATCCCACTA
2152913 GACTAGCTGT
Statistics
Matches: 182, Mismatches: 29, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
194 16 0.09
195 166 0.91
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (195 bp):
ATAGTGCCTCATCCCACTAAACCAACTGATTATTGATATTAGTTTTGATTTTTTAATCAATCATT
AGAATCAGATTTATTAATCGACTAGTCCAGATCGAGTTTTATAGAAACCCATTATGGAGACGACC
ATCCAAACCCAATTTGTTCTATACACAAACATCAGGATTTAAACCCCTGACTTTGCTGAACGAAT
Found at i:2157942 original size:21 final size:23
Alignment explanation
Indices: 2157894--2157946 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 23
2157884 ACGTATAATT
* *
2157894 ATAAATTAGTTAATAATTTAAAG
1 ATAAATTATTTAATAATTAAAAG
2157917 ATAAATTATTTAA-AA-TAAAAG
1 ATAAATTATTTAATAATTAAAAG
*
2157938 GTAAATTAT
1 ATAAATTAT
2157947 ACAAGTTACC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 13 0.48
22 2 0.07
23 12 0.44
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.38
Consensus pattern (23 bp):
ATAAATTATTTAATAATTAAAAG
Found at i:2158285 original size:17 final size:17
Alignment explanation
Indices: 2158263--2158295 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2158253 GACATATTCT
2158263 AAATTTATAACAAAACA
1 AAATTTATAACAAAACA
2158280 AAATTTATAACAAAAC
1 AAATTTATAACAAAAC
2158296 TTTTTTCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATTTATAACAAAACA
Found at i:2158448 original size:16 final size:16
Alignment explanation
Indices: 2158427--2158461 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
2158417 ACTGAGAATC
2158427 TTATCATTATAAACTT
1 TTATCATTATAAACTT
*
2158443 TTATCATTATAAATTT
1 TTATCATTATAAACTT
2158459 TTA
1 TTA
2158462 AAATTATGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (16 bp):
TTATCATTATAAACTT
Found at i:2160572 original size:30 final size:30
Alignment explanation
Indices: 2160527--2160585 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
2160517 GTTTTATAAT
* * *
2160527 GTTTAGTGACTATTTTGTAATTATTAAAAA
1 GTTTAATGACAATTTTATAATTATTAAAAA
*
2160557 GTTTAATGACAATTTTATAATTTTTAAAA
1 GTTTAATGACAATTTTATAATTATTAAAA
2160586 CTTGAATTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.39, C:0.03, G:0.10, T:0.47
Consensus pattern (30 bp):
GTTTAATGACAATTTTATAATTATTAAAAA
Found at i:2165102 original size:20 final size:20
Alignment explanation
Indices: 2165074--2165115 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
2165064 AAAAACAAGG
*
2165074 AAAATATAATTCCTAAAAAT
1 AAAAGATAATTCCTAAAAAT
*
2165094 AAAAGATAATTCCTAAAGAT
1 AAAAGATAATTCCTAAAAAT
2165114 AA
1 AA
2165116 TTATTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.60, C:0.10, G:0.05, T:0.26
Consensus pattern (20 bp):
AAAAGATAATTCCTAAAAAT
Found at i:2178618 original size:21 final size:21
Alignment explanation
Indices: 2178594--2178633 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2178584 AGTTACATCT
*
2178594 TGACAAATGTAACTTGGGATG
1 TGACAAATGTAACTCGGGATG
2178615 TGACAAATGTAACTCGGGA
1 TGACAAATGTAACTCGGGA
2178634 ATGCCTCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.12, G:0.28, T:0.25
Consensus pattern (21 bp):
TGACAAATGTAACTCGGGATG
Found at i:2181945 original size:26 final size:26
Alignment explanation
Indices: 2181884--2181961 Score: 120
Period size: 26 Copynumber: 2.9 Consensus size: 26
2181874 CTGCAGGTCT
2181884 TTAGGGGTCATTTTTCCAAATAATGATGA
1 TTAGGGGTCATTTTTCC-AATAA--ATGA
2181913 TTAGGGGTCATTTTTCCAATAAATGA
1 TTAGGGGTCATTTTTCCAATAAATGA
*
2181939 TTAGGGGTCATTTTTCTAATAAA
1 TTAGGGGTCATTTTTCCAATAAA
2181962 ATAAAAAGGT
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
26 26 0.54
28 5 0.10
29 17 0.35
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (26 bp):
TTAGGGGTCATTTTTCCAATAAATGA
Found at i:2188270 original size:164 final size:165
Alignment explanation
Indices: 2187999--2188353 Score: 612
Period size: 164 Copynumber: 2.2 Consensus size: 165
2187989 TTGTGTGTTA
2187999 CAGATGACTCTCTCGTCGTGAAGTTGAGTCAATCTGTTTGTGAAGTTGGAATTGGGAATTGTTAT
1 CAGATGACTCTCTCGTCGTGAAGTTGAGTCAATCTGTTTGTGAAGTTGGAATTGGGAATTGTTAT
2188064 TGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGGGCCCAATATCCTTCGT
66 TGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCT-GGGCCCAATATCCTTCGT
2188129 TGTGAAGTTGAAATTGGG-AA-TGTTTATTGACAAC
130 TGTGAAGTTGAAATTGGGAAATTGTTTATTGACAAC
2188163 CAGATGACTCTCTCGTCGTGAAGTTGAGTCAATCTG-TT-TGAAGTTGGAATTGGGAAATTGTTT
1 CAGATGACTCTCTCGTCGTGAAGTTGAGTCAATCTGTTTGTGAAGTTGGAATTGGG-AATTG-TT
2188226 ATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGGCCCAATATCCTTCG
64 ATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGGCCCAATATCCTTCG
2188291 TTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAAC
129 TTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAAC
** * *
2188328 CAGCGGTCCCT-TCGTCGTGAAGTTGA
1 CAGATGACTCTCTCGTCGTGAAGTTGA
2188354 ACTTACGTTG
Statistics
Matches: 183, Mismatches: 4, Indels: 8
0.94 0.02 0.04
Matches are distributed among these distances:
162 16 0.09
163 43 0.23
164 103 0.56
165 21 0.11
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (165 bp):
CAGATGACTCTCTCGTCGTGAAGTTGAGTCAATCTGTTTGTGAAGTTGGAATTGGGAATTGTTAT
TGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGGCCCAATATCCTTCGTT
GTGAAGTTGAAATTGGGAAATTGTTTATTGACAAC
Found at i:2188627 original size:105 final size:104
Alignment explanation
Indices: 2188417--2188713 Score: 549
Period size: 105 Copynumber: 2.8 Consensus size: 104
2188407 GAAATTATTA
*
2188417 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCATATCCTTCGT
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCAATATCCTTCGT
2188482 TGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTG
66 TGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTG
*
2188521 TTGACAACCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCTAATATCCTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTC-AATATCCTTCG
2188586 TTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTG
65 TTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTG
*
2188626 TTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT-CAATATCCTTCG
2188691 TTGTGAAGTTGAAATTGGCTCTG
65 TTGTGAAGTTGAAATTGGCTCTG
2188714 GGTAAAACCT
Statistics
Matches: 187, Mismatches: 4, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
104 52 0.28
105 134 0.72
106 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.34
Consensus pattern (104 bp):
TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCAATATCCTTCGT
TGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTG
Found at i:2189490 original size:21 final size:21
Alignment explanation
Indices: 2189462--2189505 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
2189452 ACCCACCTTA
2189462 TTTTCTCTTCTT-TTGTTCTT
1 TTTTCTCTTCTTCTTGTTCTT
* *
2189482 TTTTCCTCTTTTTCTTTTTCTT
1 TTTT-CTCTTCTTCTTGTTCTT
2189504 TT
1 TT
2189506 CTCAAATTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 7 0.35
22 9 0.45
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.77
Consensus pattern (21 bp):
TTTTCTCTTCTTCTTGTTCTT
Found at i:2196955 original size:15 final size:15
Alignment explanation
Indices: 2196937--2196965 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2196927 TTCAGATTAT
2196937 TTTGATTTCAAGACA
1 TTTGATTTCAAGACA
2196952 TTTGATTTCAAGAC
1 TTTGATTTCAAGAC
2196966 TGAATCCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (15 bp):
TTTGATTTCAAGACA
Found at i:2198873 original size:14 final size:14
Alignment explanation
Indices: 2198856--2198883 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2198846 AAAACCTCAC
2198856 CATAAACCATATAA
1 CATAAACCATATAA
2198870 CATAAACCATATAA
1 CATAAACCATATAA
2198884 ATTCCATTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.21, G:0.00, T:0.21
Consensus pattern (14 bp):
CATAAACCATATAA
Found at i:2201839 original size:41 final size:41
Alignment explanation
Indices: 2201644--2201847 Score: 206
Period size: 41 Copynumber: 5.0 Consensus size: 41
2201634 TTAGTGGTAA
* * * *
2201644 TTATATATAAACGCCGCTATAGACTAATACTTTCGTGGCGT
1 TTATATACAAACGCCGCTATAAACTCATACTTTTGTGGCGT
* * * *
2201685 TTATATACAAACGCCGCTAAAAAATCGTA-TTGTAGTGGCGT
1 TTATATACAAACGCCGCTATAAACTCATACTT-TTGTGGCGT
2201726 TT-TAATACAAACGCCGCTATAAACT-AGTA-TTTTAGTGGCGT
1 TTAT-ATACAAACGCCGCTATAAACTCA-TACTTTT-GTGGCGT
* *
2201767 TT-TATACAAACGCCGGTAT-AA-TTATACTTTTGTGGCGT
1 TTATATACAAACGCCGCTATAAACTCATACTTTTGTGGCGT
* * *
2201805 TTATATACAAATGCCGCTATATACTCATACTTTTGTGGTGT
1 TTATATACAAACGCCGCTATAAACTCATACTTTTGTGGCGT
2201846 TT
1 TT
2201848 TTTATGTTCT
Statistics
Matches: 137, Mismatches: 17, Indels: 18
0.80 0.10 0.10
Matches are distributed among these distances:
38 12 0.09
39 22 0.16
40 20 0.15
41 83 0.61
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.36
Consensus pattern (41 bp):
TTATATACAAACGCCGCTATAAACTCATACTTTTGTGGCGT
Found at i:2214192 original size:2 final size:2
Alignment explanation
Indices: 2214185--2214210 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2214175 CAGATTAATC
2214185 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
2214211 GAATAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2217215 original size:82 final size:81
Alignment explanation
Indices: 2217093--2217276 Score: 296
Period size: 82 Copynumber: 2.2 Consensus size: 81
2217083 GATCTTTCTA
* * *
2217093 ACATGCAATAGTTCATCATTCAACTTGATTCGATCATGGTAGCATGCAATAATTCACCATTCGAT
1 ACATACAATAGTTCATCATCCAACTTGATTCGATCATGGTAGCATGCAATAATTAACCATTCGAT
*
2217158 TCAGTTCAATCATGGC
66 TCAATTCAATCATGGC
* *
2217174 GACATACAATAGTTCATCATCCAACTTGATTCGATCATGGTAGCATGCAATGATTAATCATTCGA
1 -ACATACAATAGTTCATCATCCAACTTGATTCGATCATGGTAGCATGCAATAATTAACCATTCGA
2217239 TTCAATTCAATCATGGC
65 TTCAATTCAATCATGGC
2217256 AGCATACAATAGTTCATCATC
1 A-CATACAATAGTTCATCATC
2217277 ATTCAACTTG
Statistics
Matches: 95, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
81 1 0.01
82 94 0.99
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.32
Consensus pattern (81 bp):
ACATACAATAGTTCATCATCCAACTTGATTCGATCATGGTAGCATGCAATAATTAACCATTCGAT
TCAATTCAATCATGGC
Found at i:2217234 original size:41 final size:41
Alignment explanation
Indices: 2217094--2217289 Score: 175
Period size: 41 Copynumber: 4.7 Consensus size: 41
2217084 ATCTTTCTAA
2217094 CATGCAATAGTTCATCATTCAACTTGATTCGATCATGGTAG
1 CATGCAATAGTTCATCATTCAACTTGATTCGATCATGGTAG
* * * * * *
2217135 CATGCAATAATTCACCATTCGA-TTCAGTTCAATCATGG-CG
1 CATGCAATAGTTCATCATTCAACTTGA-TTCGATCATGGTAG
* *
2217175 ACATACAATAGTTCATCATCCAACTTGATTCGATCATGGTAG
1 -CATGCAATAGTTCATCATTCAACTTGATTCGATCATGGTAG
* * * * *
2217217 CATGCAAT-GATTAATCATTCGA-TTCAATTCAATCATGGCAG
1 CATGCAATAG-TTCATCATTCAACTT-GATTCGATCATGGTAG
*
2217258 CATACAATAGTTCATCATCATTCAACTTGATT
1 CATGCAATAG-T--TCATCATTCAACTTGATT
2217290 TGATTTATAG
Statistics
Matches: 119, Mismatches: 26, Indels: 17
0.73 0.16 0.10
Matches are distributed among these distances:
40 7 0.06
41 92 0.77
42 6 0.05
44 12 0.10
45 2 0.02
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (41 bp):
CATGCAATAGTTCATCATTCAACTTGATTCGATCATGGTAG
Found at i:2220112 original size:13 final size:13
Alignment explanation
Indices: 2220094--2220135 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
2220084 TGCGTCATAA
*
2220094 ATTTATGACGCGC
1 ATTTATGACGCAC
*
2220107 ATTTATGACACAC
1 ATTTATGACGCAC
*
2220120 ATTTATGACGCTC
1 ATTTATGACGCAC
2220133 ATT
1 ATT
2220136 GCGCGTCATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (13 bp):
ATTTATGACGCAC
Found at i:2220199 original size:85 final size:85
Alignment explanation
Indices: 2220107--2220270 Score: 215
Period size: 85 Copynumber: 1.9 Consensus size: 85
2220097 TATGACGCGC
* * * *
2220107 ATTTATGACACACATTTATGACGCT-CATTGCGCGTCATTGAAGCCCCCGTCA-TAAATGAAGAC
1 ATTTATGACACACATGTATGAC-CTACATTGCGCGTCATTGAAGCACACGTCATTAAA-AAAGAC
2220170 GACACACATTCGTGTGTCATAA
64 GACACACATTCGTGTGTCATAA
* * * * *
2220192 ATTTATGACACGCATGTATGACTTACATTGTGTGTCATTGAAGCACACGTCATTAAAAAAGATGA
1 ATTTATGACACACATGTATGACCTACATTGCGCGTCATTGAAGCACACGTCATTAAAAAAGACGA
2220257 CACACATTCGTGTG
66 CACACATTCGTGTG
2220271 GCGTGATTGT
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
84 1 0.01
85 63 0.93
86 4 0.06
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (85 bp):
ATTTATGACACACATGTATGACCTACATTGCGCGTCATTGAAGCACACGTCATTAAAAAAGACGA
CACACATTCGTGTGTCATAA
Found at i:2221171 original size:2 final size:2
Alignment explanation
Indices: 2221164--2221209 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
2221154 AAAATAGTAC
2221164 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
2221206 AT AT
1 AT AT
2221210 CCGACCATTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2230459 original size:17 final size:17
Alignment explanation
Indices: 2230433--2230481 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
2230423 AAAGTCAACG
*
2230433 GTCAACGGGTCAGGTCA
1 GTCAAAGGGTCAGGTCA
* *
2230450 TTCAATGGGTCAGGTCA
1 GTCAAAGGGTCAGGTCA
*
2230467 GTCAAAAGGTCAGGT
1 GTCAAAGGGTCAGGT
2230482 GATTGGTCTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.27, C:0.18, G:0.33, T:0.22
Consensus pattern (17 bp):
GTCAAAGGGTCAGGTCA
Found at i:2231205 original size:18 final size:19
Alignment explanation
Indices: 2231184--2231219 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2231174 TTTGGAGAAA
2231184 TTTAGG-ATTTTTGAAAAT
1 TTTAGGCATTTTTGAAAAT
*
2231202 TTTAGGCTTTTTTGAAAA
1 TTTAGGCATTTTTGAAAA
2231220 ATTATTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.31, C:0.03, G:0.17, T:0.50
Consensus pattern (19 bp):
TTTAGGCATTTTTGAAAAT
Done.