Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 7 of 279
Found at i:1994463 original size:28 final size:28
Alignment explanation
Indices: 1994403--1994465 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
1994393 GTCATTATCA
*
1994403 ACCCCATAAGTTATAAAACTCTTCTTAT
1 ACCCCATAAGTTATAAAACTCTTCCTAT
* * * * *
1994431 GCCCCATGAGTTATGAGACTTTTCCTAT
1 ACCCCATAAGTTATAAAACTCTTCCTAT
1994459 ACCCCAT
1 ACCCCAT
1994466 TAATATGGGA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.33
Consensus pattern (28 bp):
ACCCCATAAGTTATAAAACTCTTCCTAT
Found at i:1995507 original size:46 final size:46
Alignment explanation
Indices: 1995412--1995508 Score: 106
Period size: 46 Copynumber: 2.1 Consensus size: 46
1995402 ACAAATTAAT
* * **
1995412 AATATTATCCAATTGCATAATTAGTAGTACACCACATGATAATTAC
1 AATATTATCCAAGTGCATAACTAGTAGTACACCACATGATAAGCAC
* * * *
1995458 AATATTGTCCAAGTGCATTACTAGTATTACACCACATTA-AAGCATC
1 AATATTATCCAAGTGCATAACTAGTAGTACACCACATGATAAGCA-C
1995504 AATAT
1 AATAT
1995509 CTTCAACCTT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
45 3 0.07
46 39 0.93
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.32
Consensus pattern (46 bp):
AATATTATCCAAGTGCATAACTAGTAGTACACCACATGATAAGCAC
Found at i:2011525 original size:20 final size:20
Alignment explanation
Indices: 2011500--2011539 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2011490 AAAAAGAGGT
2011500 TTTCTCTTAAAGTTTTGCTA
1 TTTCTCTTAAAGTTTTGCTA
2011520 TTTCTCTTAAAGTTTTGCTA
1 TTTCTCTTAAAGTTTTGCTA
2011540 AGTGTTGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.55
Consensus pattern (20 bp):
TTTCTCTTAAAGTTTTGCTA
Found at i:2020173 original size:2 final size:2
Alignment explanation
Indices: 2020168--2020192 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2020158 AAAAAAAAAA
2020168 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
2020193 AAGAGGAGTC
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:2021353 original size:23 final size:22
Alignment explanation
Indices: 2021317--2021362 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 22
2021307 ACTTGAATTA
*
2021317 TTTAAAATATAAATATTATATT
1 TTTAAAAAATAAATATTATATT
2021339 TTTAAAGAAATAAATATTATATT
1 TTTAAA-AAATAAATATTATATT
2021362 T
1 T
2021363 CAATCAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
TTTAAAAAATAAATATTATATT
Found at i:2024204 original size:44 final size:44
Alignment explanation
Indices: 2024149--2024262 Score: 210
Period size: 44 Copynumber: 2.6 Consensus size: 44
2024139 GATACAAGCT
*
2024149 AGTGTAAGACCTGTTTGGGACATGGCGTCAGCTTGTTTTGTGTC
1 AGTGTAAGACCTGTTTGGGACATGGCGTCAGCTTGTTTTATGTC
*
2024193 AGTGTAAGACCTGTTTGGGACATGACGTCAGCTTGTTTTATGTC
1 AGTGTAAGACCTGTTTGGGACATGGCGTCAGCTTGTTTTATGTC
2024237 AGTGTAAGACCTGTTTGGGACATGGC
1 AGTGTAAGACCTGTTTGGGACATGGC
2024263 ATCGACACCG
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 67 1.00
ACGTcount: A:0.19, C:0.16, G:0.31, T:0.34
Consensus pattern (44 bp):
AGTGTAAGACCTGTTTGGGACATGGCGTCAGCTTGTTTTATGTC
Found at i:2024207 original size:22 final size:22
Alignment explanation
Indices: 2024182--2024252 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
2024172 GGCGTCAGCT
2024182 TGTTTTGTGTCAGTGTAAGACC
1 TGTTTTGTGTCAGTGTAAGACC
* * * * *
2024204 TG-TTTGGGACATGACGTCAG-CT
1 TGTTTTGTGTCA-G-TGTAAGACC
*
2024226 TGTTTTATGTCAGTGTAAGACC
1 TGTTTTGTGTCAGTGTAAGACC
2024248 TGTTT
1 TGTTT
2024253 GGGACATGGC
Statistics
Matches: 34, Mismatches: 11, Indels: 8
0.64 0.21 0.15
Matches are distributed among these distances:
21 11 0.32
22 13 0.38
23 10 0.29
ACGTcount: A:0.18, C:0.14, G:0.27, T:0.41
Consensus pattern (22 bp):
TGTTTTGTGTCAGTGTAAGACC
Found at i:2027718 original size:30 final size:30
Alignment explanation
Indices: 2027676--2027743 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 30
2027666 ACCCCAGGAG
* *
2027676 ACACATGGCCATGTACCAAGGCCGTGTGTC
1 ACACACGGCCATGTACCAAGGCCATGTGTC
* **
2027706 ATACACGGCCATGTACCAATTCCATGTGTC
1 ACACACGGCCATGTACCAAGGCCATGTGTC
2027736 ACACACGG
1 ACACACGG
2027744 TTGAGCCATA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.26, C:0.31, G:0.22, T:0.21
Consensus pattern (30 bp):
ACACACGGCCATGTACCAAGGCCATGTGTC
Found at i:2028830 original size:43 final size:43
Alignment explanation
Indices: 2028769--2028881 Score: 199
Period size: 43 Copynumber: 2.6 Consensus size: 43
2028759 CAATGCCATT
*
2028769 TCCCAGATATGGTCTTACATGTAATCAAAATACCATGCAAATG
1 TCCCAGATATGGTCTTACATGTAATCAAAATACAATGCAAATG
*
2028812 TCCCACATATGGTCTTACATGTAATCAAAATACAATGCAAATG
1 TCCCAGATATGGTCTTACATGTAATCAAAATACAATGCAAATG
*
2028855 TCCCAGACATGGTCTTACATGTAATCA
1 TCCCAGATATGGTCTTACATGTAATCA
2028882 CATCTCGGTA
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 66 1.00
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.28
Consensus pattern (43 bp):
TCCCAGATATGGTCTTACATGTAATCAAAATACAATGCAAATG
Found at i:2033298 original size:43 final size:42
Alignment explanation
Indices: 2033158--2033320 Score: 184
Period size: 42 Copynumber: 3.9 Consensus size: 42
2033148 TAGGGTTACT
* *
2033158 GAGATTACGTGTAAGACCATATTTGGGATATGGCATCAATAC
1 GAGATTACGTGTAAGACCATATCTGGGATATGGCATCGATAC
* ** * *
2033200 GAGATTTCGTGTAAGACCATATCCAGGATATGACATCGATAT
1 GAGATTACGTGTAAGACCATATCTGGGATATGGCATCGATAC
* * * *
2033242 GAGACTT-TGTGTAAGACTATAGCTGGGCTATTGGCATCGATAC
1 GAGA-TTACGTGTAAGACCATATCTGGGATA-TGGCATCGATAC
* *
2033285 GAGATTACATGTAAGACCATATCTGTGATATGGCAT
1 GAGATTACGTGTAAGACCATATCTGGGATATGGCAT
2033321 TGGTATGGTA
Statistics
Matches: 97, Mismatches: 21, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
42 64 0.66
43 33 0.34
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.29
Consensus pattern (42 bp):
GAGATTACGTGTAAGACCATATCTGGGATATGGCATCGATAC
Found at i:2036170 original size:74 final size:74
Alignment explanation
Indices: 2036092--2036296 Score: 243
Period size: 74 Copynumber: 2.8 Consensus size: 74
2036082 GCCATAATTA
* * * * * * *
2036092 GGAAGCTCATGCGAGCCAATAACGGGTAA-CTCTGAAGAGCCATTAATTAGAAAGCTCTGGATAG
1 GGAAGTTCAAGCGAGCCAATATCGGG-AAGCTCTGAAGAGCCATTAATCAGAAAGCTCCGAATAA
*
2036156 CCATATATCT
65 CCATATATCG
* * *
2036166 GGAAGTTCAAGCAAGCTAATATCGGGAAGCTC-CAGAGAGCCATTAATCAGAAAGCTCCGAATAA
1 GGAAGTTCAAGCGAGCCAATATCGGGAAGCTCTGA-AGAGCCATTAATCAGAAAGCTCCGAATAA
2036230 CCATATATCG
65 CCATATATCG
* * * *
2036240 GGAAGTTTAAGCGAGCCACTATTGGGAAGCTCTGGAGAGCCATTAATCAGAAAGCTC
1 GGAAGTTCAAGCGAGCCAATATCGGGAAGCTCTGAAGAGCCATTAATCAGAAAGCTC
2036297 ACAAAGAACC
Statistics
Matches: 110, Mismatches: 18, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
73 3 0.03
74 107 0.97
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.21
Consensus pattern (74 bp):
GGAAGTTCAAGCGAGCCAATATCGGGAAGCTCTGAAGAGCCATTAATCAGAAAGCTCCGAATAAC
CATATATCG
Found at i:2036450 original size:25 final size:24
Alignment explanation
Indices: 2036405--2036473 Score: 86
Period size: 25 Copynumber: 2.8 Consensus size: 24
2036395 CAAGATGCTC
*
2036405 CGAAGAACTAT-TAACGGGAAGCT
1 CGAAGAACCATATAACGGGAAGCT
2036428 CGCAAGAACCATATAACGGGAAGCT
1 CG-AAGAACCATATAACGGGAAGCT
* *
2036453 CGAGAGGACCATATATCGGGA
1 CGA-AGAACCATATAACGGGA
2036474 TGATCATGAG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
23 2 0.05
24 9 0.22
25 29 0.73
ACGTcount: A:0.38, C:0.20, G:0.28, T:0.14
Consensus pattern (24 bp):
CGAAGAACCATATAACGGGAAGCT
Found at i:2039336 original size:40 final size:38
Alignment explanation
Indices: 2039291--2039386 Score: 95
Period size: 40 Copynumber: 2.5 Consensus size: 38
2039281 ACGGTACTTA
*
2039291 ATGGTGTGTAGGGTTGGATGGG-AAGATTTTATCCCCAT
1 ATGGTGTGTAGGGTTGGATGGGTAA-ATTTTATCCCCAC
* * * * *
2039329 ATTTGGTGTGCAGGGATGGGTGGGTCAATTTTATCCTCAC
1 A--TGGTGTGTAGGGTTGGATGGGTAAATTTTATCCCCAC
*
2039369 ATGGTGTGTTGGGTTGGA
1 ATGGTGTGTAGGGTTGGA
2039387 CGGAGTTGGT
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
38 14 0.31
40 30 0.67
41 1 0.02
ACGTcount: A:0.18, C:0.10, G:0.36, T:0.35
Consensus pattern (38 bp):
ATGGTGTGTAGGGTTGGATGGGTAAATTTTATCCCCAC
Found at i:2056725 original size:17 final size:17
Alignment explanation
Indices: 2056700--2056733 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2056690 TAGACACACA
2056700 GGTGCGTGTCTAGGCCG
1 GGTGCGTGTCTAGGCCG
*
2056717 GGTGTGTGTCTAGGCCG
1 GGTGCGTGTCTAGGCCG
2056734 TATGTGACAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.06, C:0.21, G:0.47, T:0.26
Consensus pattern (17 bp):
GGTGCGTGTCTAGGCCG
Found at i:2056739 original size:17 final size:17
Alignment explanation
Indices: 2056705--2056739 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2056695 ACACAGGTGC
*
2056705 GTGTCTAGGCCGGGTGT
1 GTGTCTAGGCCGGATGT
*
2056722 GTGTCTAGGCCGTATGT
1 GTGTCTAGGCCGGATGT
2056739 G
1 G
2056740 ACACACGAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.09, C:0.17, G:0.43, T:0.31
Consensus pattern (17 bp):
GTGTCTAGGCCGGATGT
Found at i:2059382 original size:23 final size:23
Alignment explanation
Indices: 2059352--2059400 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
2059342 CCCATATTGT
*
2059352 TTGTAAAGAAGAAAGACGGTTCA
1 TTGTAAAGAAGAAAAACGGTTCA
*
2059375 TTGTAAAGAAGAAAAATGGTTCA
1 TTGTAAAGAAGAAAAACGGTTCA
2059398 TTG
1 TTG
2059401 AGGCTATGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.43, C:0.06, G:0.24, T:0.27
Consensus pattern (23 bp):
TTGTAAAGAAGAAAAACGGTTCA
Found at i:2061320 original size:35 final size:34
Alignment explanation
Indices: 2061259--2061327 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 34
2061249 AAATTTCAGG
*
2061259 GTAGCTGGGAAAATACTTGCCATTGGTAGAATTT
1 GTAGCTGGGAAAATACTTGCCATTGGTAAAATTT
***
2061293 GTAGCTGGGAAAAATACTTGTTGTTGGTAAAATTT
1 GTAGCTGGG-AAAATACTTGCCATTGGTAAAATTT
2061328 CCCTACAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 9 0.30
35 21 0.70
ACGTcount: A:0.30, C:0.09, G:0.26, T:0.35
Consensus pattern (34 bp):
GTAGCTGGGAAAATACTTGCCATTGGTAAAATTT
Found at i:2070182 original size:20 final size:20
Alignment explanation
Indices: 2070157--2070230 Score: 130
Period size: 20 Copynumber: 3.7 Consensus size: 20
2070147 AACAGGGGTC
*
2070157 ACACGCCCATGTGGTTTGGG
1 ACACGCCCGTGTGGTTTGGG
2070177 ACACGCCCGTGTGGTTTGGG
1 ACACGCCCGTGTGGTTTGGG
2070197 ACACGCCCGTGTGGTTTGGG
1 ACACGCCCGTGTGGTTTGGG
*
2070217 ACACACCCGTGTGG
1 ACACGCCCGTGTGG
2070231 ATAGGCCGTG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.14, C:0.27, G:0.36, T:0.23
Consensus pattern (20 bp):
ACACGCCCGTGTGGTTTGGG
Found at i:2074653 original size:18 final size:18
Alignment explanation
Indices: 2074610--2074654 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
2074600 TGTGGAACTA
*
2074610 GGCAGAGATGAAGATGGT
1 GGCAGAGGTGAAGATGGT
*
2074628 GGCAGAGGTGAAGGTGGT
1 GGCAGAGGTGAAGATGGT
*
2074646 GGTAGAGGT
1 GGCAGAGGT
2074655 TGGGTTCCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.04, G:0.51, T:0.18
Consensus pattern (18 bp):
GGCAGAGGTGAAGATGGT
Found at i:2075319 original size:15 final size:15
Alignment explanation
Indices: 2075299--2075329 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2075289 GAACCCACAA
2075299 CGACGCTCTATCATC
1 CGACGCTCTATCATC
2075314 CGACGCTCTATCATC
1 CGACGCTCTATCATC
2075329 C
1 C
2075330 TCATGTGGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.42, G:0.13, T:0.26
Consensus pattern (15 bp):
CGACGCTCTATCATC
Found at i:2076709 original size:19 final size:19
Alignment explanation
Indices: 2076685--2076728 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
2076675 GGTGGTGGTC
2076685 GGCTGATGTTGGGGCATAG
1 GGCTGATGTTGGGGCATAG
* *
2076704 GGCTGATGTTGGGGCGTGG
1 GGCTGATGTTGGGGCATAG
2076723 GGCTGA
1 GGCTGA
2076729 GCTTTGTGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.11, C:0.11, G:0.52, T:0.25
Consensus pattern (19 bp):
GGCTGATGTTGGGGCATAG
Found at i:2087777 original size:12 final size:12
Alignment explanation
Indices: 2087760--2087787 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
2087750 TTGGAAAGAA
2087760 TTCATAATGTGT
1 TTCATAATGTGT
2087772 TTCATAATGTGT
1 TTCATAATGTGT
2087784 TTCA
1 TTCA
2087788 CGTGTTGATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.11, G:0.14, T:0.50
Consensus pattern (12 bp):
TTCATAATGTGT
Found at i:2099381 original size:21 final size:20
Alignment explanation
Indices: 2099351--2099389 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
2099341 TCTTTTGGAC
2099351 GTGGACGGTTTGGGACCTTAA
1 GTGGACGGTTTGGG-CCTTAA
*
2099372 GTGGATGGTTTGGGCCTT
1 GTGGACGGTTTGGGCCTT
2099390 TTCCTCCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.13, C:0.13, G:0.41, T:0.33
Consensus pattern (20 bp):
GTGGACGGTTTGGGCCTTAA
Found at i:2101030 original size:31 final size:31
Alignment explanation
Indices: 2100985--2101154 Score: 105
Period size: 31 Copynumber: 5.5 Consensus size: 31
2100975 GAACACTGGC
* * *
2100985 ACATAGTACTTGATAAAATATAAACATCAAC
1 ACATAGTGCCTGATAAAATATAAACATCAAT
* * * *
2101016 ACATTGTGCCTGATACAATATGAACA-CTGAT
1 ACATAGTGCCTGATAAAATATAAACATC-AAT
* * *
2101047 ACATAGTACCTGATAAAATATAATCACCAAT
1 ACATAGTGCCTGATAAAATATAAACATCAAT
* **
2101078 ACATAGT-ACTAGATAAAATATATTCATCCAA-
1 ACATAGTGCCT-GATAAAATATAAACAT-CAAT
* * * * *
2101109 ACATTA-TGCCTGAGACAATATGAATACCAAT
1 ACA-TAGTGCCTGATAAAATATAAACATCAAT
*
2101140 ACATAGTACCTGATA
1 ACATAGTGCCTGATA
2101155 TTTCAAAACC
Statistics
Matches: 105, Mismatches: 26, Indels: 16
0.71 0.18 0.11
Matches are distributed among these distances:
30 8 0.08
31 89 0.85
32 8 0.08
ACGTcount: A:0.45, C:0.18, G:0.10, T:0.27
Consensus pattern (31 bp):
ACATAGTGCCTGATAAAATATAAACATCAAT
Found at i:2101093 original size:93 final size:93
Alignment explanation
Indices: 2100985--2101154 Score: 252
Period size: 93 Copynumber: 1.8 Consensus size: 93
2100975 GAACACTGGC
* * * **
2100985 ACATAGTACTTGATAAAATATAAACAT-CAACACATTGTGCCTGATACAATATGAACACTGATAC
1 ACATAGTACTAGATAAAATATAAACATCCAA-ACATTATGCCTGAGACAATATGAACACCAATAC
2101049 ATAGTACCTGATAAAATATAATCACCAAT
65 ATAGTACCTGATAAAATATAATCACCAAT
** *
2101078 ACATAGTACTAGATAAAATATATTCATCCAAACATTATGCCTGAGACAATATGAATACCAATACA
1 ACATAGTACTAGATAAAATATAAACATCCAAACATTATGCCTGAGACAATATGAACACCAATACA
2101143 TAGTACCTGATA
66 TAGTACCTGATA
2101155 TTTCAAAACC
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
93 65 0.96
94 3 0.04
ACGTcount: A:0.45, C:0.18, G:0.10, T:0.27
Consensus pattern (93 bp):
ACATAGTACTAGATAAAATATAAACATCCAAACATTATGCCTGAGACAATATGAACACCAATACA
TAGTACCTGATAAAATATAATCACCAAT
Found at i:2101098 original size:62 final size:62
Alignment explanation
Indices: 2100961--2101098 Score: 161
Period size: 62 Copynumber: 2.2 Consensus size: 62
2100951 TATCTCAACC
* * * * *
2100961 ACTGATAAGATAATGAACACTGGCACATAGTACTTGATAAAATATAAACATCAACACATTGTG
1 ACTGATAAAAT-ATGAACACTGACACATAGTACCTGATAAAATATAAACACCAACACATAGTG
* * * * *
2101024 CCTGATACAATATGAACACTGATACATAGTACCTGATAAAATATAATCACCAATACATAGT-
1 ACTGATAAAATATGAACACTGACACATAGTACCTGATAAAATATAAACACCAACACATAGTG
2101085 ACTAGATAAAATAT
1 ACT-GATAAAATAT
2101099 ATTCATCCAA
Statistics
Matches: 62, Mismatches: 12, Indels: 3
0.81 0.16 0.04
Matches are distributed among these distances:
61 2 0.03
62 52 0.84
63 8 0.13
ACGTcount: A:0.46, C:0.17, G:0.12, T:0.26
Consensus pattern (62 bp):
ACTGATAAAATATGAACACTGACACATAGTACCTGATAAAATATAAACACCAACACATAGTG
Found at i:2105717 original size:20 final size:20
Alignment explanation
Indices: 2105692--2105734 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
2105682 ATGAAGTATG
2105692 CGAAATTATGCTTTATTACA
1 CGAAATTATGCTTTATTACA
2105712 CGAAATTATGCTTTATTACA
1 CGAAATTATGCTTTATTACA
2105732 CGA
1 CGA
2105735 TTTTTGTGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (20 bp):
CGAAATTATGCTTTATTACA
Found at i:2112042 original size:28 final size:28
Alignment explanation
Indices: 2111989--2112095 Score: 134
Period size: 28 Copynumber: 4.0 Consensus size: 28
2111979 CACTTTGTGC
2111989 TATTCTGGTGTGTTTTGGATGGATTATAT
1 TATTCTGGTGTGTTTTGGA-GGATTATAT
* *
2112018 TATTTTGGTGTGTTTGGGAGGATTATAT
1 TATTCTGGTGTGTTTTGGAGGATTATAT
* *
2112046 GATACTGGTGTGTTTTGGAGGA-T-TA-
1 TATTCTGGTGTGTTTTGGAGGATTATAT
2112071 TA--CTGGTGTGTTTTGGAGGATTATA
1 TATTCTGGTGTGTTTTGGAGGATTATA
2112096 CTGGTGTGTT
Statistics
Matches: 69, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
23 18 0.26
24 1 0.01
25 3 0.04
26 2 0.03
27 1 0.01
28 27 0.39
29 17 0.25
ACGTcount: A:0.19, C:0.03, G:0.32, T:0.47
Consensus pattern (28 bp):
TATTCTGGTGTGTTTTGGAGGATTATAT
Found at i:2112104 original size:25 final size:23
Alignment explanation
Indices: 2112047--2112107 Score: 122
Period size: 23 Copynumber: 2.7 Consensus size: 23
2112037 GGATTATATG
2112047 ATACTGGTGTGTTTTGGAGGATT
1 ATACTGGTGTGTTTTGGAGGATT
2112070 ATACTGGTGTGTTTTGGAGGATT
1 ATACTGGTGTGTTTTGGAGGATT
2112093 ATACTGGTGTGTTTT
1 ATACTGGTGTGTTTT
2112108 TGTAACACCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.16, C:0.05, G:0.33, T:0.46
Consensus pattern (23 bp):
ATACTGGTGTGTTTTGGAGGATT
Found at i:2121715 original size:44 final size:44
Alignment explanation
Indices: 2121664--2121752 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
2121654 AATCACTAAA
2121664 CCCCAAAACTTACTCATCTATGCTCAAACCATGTCCCTAAAAGC
1 CCCCAAAACTTACTCATCTATGCTCAAACCATGTCCCTAAAAGC
2121708 CCCCAAAACTTACTCATCTATGCTCAAACCATGTCCCTAAAAGC
1 CCCCAAAACTTACTCATCTATGCTCAAACCATGTCCCTAAAAGC
2121752 C
1 C
2121753 TTTGAAACCT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.34, C:0.37, G:0.07, T:0.22
Consensus pattern (44 bp):
CCCCAAAACTTACTCATCTATGCTCAAACCATGTCCCTAAAAGC
Found at i:2129229 original size:35 final size:35
Alignment explanation
Indices: 2129178--2129282 Score: 156
Period size: 35 Copynumber: 3.0 Consensus size: 35
2129168 AACTATTATG
*
2129178 TGAGATGTAACAATACACGAGCTATAAGTATTGTA
1 TGAGTTGTAACAATACACGAGCTATAAGTATTGTA
* * * *
2129213 TGAGTTGTAACGATACACGAGCCATAAGTATTATG
1 TGAGTTGTAACAATACACGAGCTATAAGTATTGTA
*
2129248 TGAGTTGTAACAATAAACGAGCTATAAGTATTGTA
1 TGAGTTGTAACAATACACGAGCTATAAGTATTGTA
2129283 CAAAATTGTA
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 60 1.00
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (35 bp):
TGAGTTGTAACAATACACGAGCTATAAGTATTGTA
Found at i:2129280 original size:70 final size:70
Alignment explanation
Indices: 2129129--2129282 Score: 209
Period size: 70 Copynumber: 2.2 Consensus size: 70
2129119 AACATGCAAA
* * ** ** * *
2129129 CTATAAGTATTATGTAAGTTGTAGTGATACGTGAGTCATAACTATTATGTGAGATGTAACAATAC
1 CTATAAGTATTGTATAAGTTGTAACGATACACGAGCCATAACTATTATGTGAGATGTAACAATAA
2129194 ACGAG
66 ACGAG
* * *
2129199 CTATAAGTATTGTATGAGTTGTAACGATACACGAGCCATAAGTATTATGTGAGTTGTAACAATAA
1 CTATAAGTATTGTATAAGTTGTAACGATACACGAGCCATAACTATTATGTGAGATGTAACAATAA
2129264 ACGAG
66 ACGAG
2129269 CTATAAGTATTGTA
1 CTATAAGTATTGTA
2129283 CAAAATTGTA
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
70 73 1.00
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.32
Consensus pattern (70 bp):
CTATAAGTATTGTATAAGTTGTAACGATACACGAGCCATAACTATTATGTGAGATGTAACAATAA
ACGAG
Found at i:2130264 original size:12 final size:12
Alignment explanation
Indices: 2130247--2130280 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
2130237 TTTAGATTAG
2130247 CTTTTTTTTCTTT
1 CTTTTTTTTC-TT
2130260 CTTTTTTTTCTT
1 CTTTTTTTTCTT
2130272 CTTATTTTT
1 CTT-TTTTT
2130281 AGATTAGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (12 bp):
CTTTTTTTTCTT
Found at i:2130315 original size:23 final size:24
Alignment explanation
Indices: 2130265--2130315 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
2130255 TCTTTCTTTT
* * *
2130265 TTTTCTTCTTATTTTTAGATTAGG
1 TTTTCCTCTTATTTTTAGAATAGA
*
2130289 TTTTCCTCTT-TTTTTAGAATATA
1 TTTTCCTCTTATTTTTAGAATAGA
2130312 TTTT
1 TTTT
2130316 ATTTTTTTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.18, C:0.10, G:0.08, T:0.65
Consensus pattern (24 bp):
TTTTCCTCTTATTTTTAGAATAGA
Found at i:2132628 original size:40 final size:40
Alignment explanation
Indices: 2132572--2132759 Score: 177
Period size: 40 Copynumber: 4.7 Consensus size: 40
2132562 ATTGGGTTCT
*
2132572 GTGCCTAGCAAG-CTTTGTGCC-GATGTAGTTATCAGGCTTT
1 GTGCCTAGC-AGCCTTTGTGCCAG-TGTAGTTATCAGGCTTA
* * *
2132612 CTGCCTAGCAGCCTTTGTGCCAGTGTATTTATCGGGCTTA
1 GTGCCTAGCAGCCTTTGTGCCAGTGTAGTTATCAGGCTTA
* * * *
2132652 GTGCCTAACAACCTTTGTGCCGGTGT-GTTTATCAAGCTTA
1 GTGCCTAGCAGCCTTTGTGCCAGTGTAG-TTATCAGGCTTA
* * * *
2132692 GTGCCTAGCAGGCTTCGTGCCAGTGTATTTTATCGGGC-TA
1 GTGCCTAGCAGCCTTTGTGCCAGTGTA-GTTATCAGGCTTA
* *
2132732 TGTGCCTAGCAGGCTTTGTGCTAGTGTA
1 -GTGCCTAGCAGCCTTTGTGCCAGTGTA
2132760 TCAAATTGTC
Statistics
Matches: 121, Mismatches: 21, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
39 2 0.02
40 86 0.71
41 33 0.27
ACGTcount: A:0.16, C:0.22, G:0.27, T:0.35
Consensus pattern (40 bp):
GTGCCTAGCAGCCTTTGTGCCAGTGTAGTTATCAGGCTTA
Found at i:2132697 original size:80 final size:81
Alignment explanation
Indices: 2132571--2132739 Score: 227
Period size: 80 Copynumber: 2.1 Consensus size: 81
2132561 TATTGGGTTC
* * * * *
2132571 TGTGCCTAGCAAGCTTTGTGCCGATGTAGTTATCAGGCTTTCTGCCTAGCAGCCTTTGTGCCAGT
1 TGTGCCTAACAACCTTTGTGCCGATGTAGTTATCAAGCTTACTGCCTAGCAGCCTTCGTGCCAGT
2132636 GTA-TTTATCGGGCT-
66 GTATTTTATCGGGCTA
* * *
2132650 TAGTGCCTAACAACCTTTGTGCCGGTGT-GTTTATCAAGCTTAGTGCCTAGCAGGCTTCGTGCCA
1 T-GTGCCTAACAACCTTTGTGCCGATGTAG-TTATCAAGCTTACTGCCTAGCAGCCTTCGTGCCA
2132714 GTGTATTTTATCGGGCTA
64 GTGTATTTTATCGGGCTA
2132732 TGTGCCTA
1 TGTGCCTA
2132740 GCAGGCTTTG
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
79 2 0.03
80 57 0.73
81 18 0.23
82 1 0.01
ACGTcount: A:0.17, C:0.22, G:0.26, T:0.35
Consensus pattern (81 bp):
TGTGCCTAACAACCTTTGTGCCGATGTAGTTATCAAGCTTACTGCCTAGCAGCCTTCGTGCCAGT
GTATTTTATCGGGCTA
Found at i:2133617 original size:21 final size:21
Alignment explanation
Indices: 2133591--2133630 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2133581 CTATTAGCGT
*
2133591 ACACGGGCGTGTGAAGTAGTC
1 ACACGGACGTGTGAAGTAGTC
2133612 ACACGGACGTGTGAAGTAG
1 ACACGGACGTGTGAAGTAG
2133631 CCATATGGCC
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:0.28, C:0.17, G:0.38, T:0.17
Consensus pattern (21 bp):
ACACGGACGTGTGAAGTAGTC
Found at i:2140664 original size:151 final size:151
Alignment explanation
Indices: 2140390--2140692 Score: 554
Period size: 151 Copynumber: 2.0 Consensus size: 151
2140380 TCTTTCAGTT
* * * *
2140390 CATCGATATACCTGTTGAACTATTTGAATTAATATCAGATACTCGGGGATTGTACACCCTAAGTG
1 CATCGATATACCTGTTGAACTATTTGAATTAATATCAGATACTCAGGAATTGCACACCCCAAGTG
2140455 CCAATACATAGCCAAAGTTATCTCAATCTCATATCTCATATAATGCTCACTCTCGAGCTATCAAC
66 CCAATACATAGCCAAAGTTATCTCAATCTCATATCTCATATAATGCTCACTCTCGAGCTATCAAC
2140520 GGGTCTGCTCACACAAGCTGA
131 GGGTCTGCTCACACAAGCTGA
2140541 CATCGATATACCTGTTGAACTATTTGAATTAATATCAGATACTCAGGAATCT-CACACCCCAAGT
1 CATCGATATACCTGTTGAACTATTTGAATTAATATCAGATACTCAGGAAT-TGCACACCCCAAGT
2140605 GCCAATACATAGCCAAAGTTATCTCAATCTCATATCTCATATAATGCTCACTCTCGAGCTATCAA
65 GCCAATACATAGCCAAAGTTATCTCAATCTCATATCTCATATAATGCTCACTCTCGAGCTATCAA
2140670 CGGGTCTGCTCACACAAGCTGA
130 CGGGTCTGCTCACACAAGCTGA
2140692 C
1 C
2140693 GGTCAAGATG
Statistics
Matches: 147, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
151 146 0.99
152 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.28
Consensus pattern (151 bp):
CATCGATATACCTGTTGAACTATTTGAATTAATATCAGATACTCAGGAATTGCACACCCCAAGTG
CCAATACATAGCCAAAGTTATCTCAATCTCATATCTCATATAATGCTCACTCTCGAGCTATCAAC
GGGTCTGCTCACACAAGCTGA
Found at i:2144565 original size:40 final size:40
Alignment explanation
Indices: 2144521--2144611 Score: 173
Period size: 40 Copynumber: 2.3 Consensus size: 40
2144511 TTTGGTTAAG
*
2144521 AAATTATAAAATTTAGTTAGTTAATTAGAAGAAAGGGAAT
1 AAATTGTAAAATTTAGTTAGTTAATTAGAAGAAAGGGAAT
2144561 AAATTGTAAAATTTAGTTAGTTAATTAGAAGAAAGGGAAT
1 AAATTGTAAAATTTAGTTAGTTAATTAGAAGAAAGGGAAT
2144601 AAATTGTAAAA
1 AAATTGTAAAA
2144612 GCTGCAAAAG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.51, C:0.00, G:0.18, T:0.32
Consensus pattern (40 bp):
AAATTGTAAAATTTAGTTAGTTAATTAGAAGAAAGGGAAT
Found at i:2146825 original size:53 final size:53
Alignment explanation
Indices: 2146745--2146853 Score: 173
Period size: 53 Copynumber: 2.1 Consensus size: 53
2146735 TCATTCCCTA
*
2146745 GAAGGTCAACGCTGAATCAAGGGACCAATTCATAAACAAGTTAAAATTGTAGG
1 GAAGGTCAACGCTGAATCAAGGGACCAATTCATAAACAAGTTAAAATCGTAGG
** * *
2146798 GAAGGTCGGCGCTGAGTCAAGGGACCAATTCGTAAACAAGTTAAAATCGTAGG
1 GAAGGTCAACGCTGAATCAAGGGACCAATTCATAAACAAGTTAAAATCGTAGG
2146851 GAA
1 GAA
2146854 AAAATAACTA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.39, C:0.16, G:0.27, T:0.19
Consensus pattern (53 bp):
GAAGGTCAACGCTGAATCAAGGGACCAATTCATAAACAAGTTAAAATCGTAGG
Found at i:2148121 original size:40 final size:39
Alignment explanation
Indices: 2148066--2148204 Score: 143
Period size: 40 Copynumber: 3.5 Consensus size: 39
2148056 ATCGGGCTAG
* ** *
2148066 TGCCTAGCAAGCTTTGCACCAGTGTAATTATAGGGATTTA
1 TGCCTAGCAGGCTTTGTGCCAGTGTAATTATCGGG-TTTA
** * *
2148106 TGCCTAGCAGGCTTTGTGCTGGTGTATTTATCGGGCTTA
1 TGCCTAGCAGGCTTTGTGCCAGTGTAATTATCGGGTTTA
* * * *
2148145 GTGCCTAGCAGGCTTTGTGTCATTGTAGTTATCGGGCTTGA
1 -TGCCTAGCAGGCTTTGTGCCAGTGTAATTATCGGG-TTTA
2148186 TGCCTAGCAGGCTTTGTGC
1 TGCCTAGCAGGCTTTGTGC
2148205 TGGTGTATCA
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
39 3 0.04
40 76 0.94
41 2 0.02
ACGTcount: A:0.17, C:0.19, G:0.29, T:0.35
Consensus pattern (39 bp):
TGCCTAGCAGGCTTTGTGCCAGTGTAATTATCGGGTTTA
Found at i:2148160 original size:80 final size:79
Alignment explanation
Indices: 2148050--2148212 Score: 236
Period size: 80 Copynumber: 2.1 Consensus size: 79
2148040 CTTGTATTGA
*
2148050 GTATTTATCGGGCTAGTGCCTAGCAAGCTTTGCACCAGTGTAATTATAGGGATTTATGCCTAGCA
1 GTATTTATCGGGCTAGTGCCTAGCAAGCTTTGCACCAGTGTAATTATAGGGATTGATGCCTAGCA
2148115 GGCTTTGTGCTGGT
66 GGCTTTGTGCTGGT
* *** * * * *
2148129 GTATTTATCGGGCTTAGTGCCTAGCAGGCTTTGTGTCATTGTAGTTATCGGGCTTGATGCCTAGC
1 GTATTTATCGGGC-TAGTGCCTAGCAAGCTTTGCACCAGTGTAATTATAGGGATTGATGCCTAGC
2148194 AGGCTTTGTGCTGGT
65 AGGCTTTGTGCTGGT
2148209 GTAT
1 GTAT
2148213 CAAATTGTCT
Statistics
Matches: 74, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
79 13 0.18
80 61 0.82
ACGTcount: A:0.17, C:0.17, G:0.29, T:0.36
Consensus pattern (79 bp):
GTATTTATCGGGCTAGTGCCTAGCAAGCTTTGCACCAGTGTAATTATAGGGATTGATGCCTAGCA
GGCTTTGTGCTGGT
Found at i:2159313 original size:70 final size:69
Alignment explanation
Indices: 2159229--2159495 Score: 250
Period size: 70 Copynumber: 3.8 Consensus size: 69
2159219 AATCTCTTTG
* * *
2159229 CGCCCAGC-ACTAGTTGGATATA-CCAACAATAAGTTTACCCAGCACTAGTCAAATAATTGATAA
1 CGCCCAGCGA-TAGTTGGATA-AGCCAACAATAAGTGTGCCCAACACTAGTCAAATAATTGA-AA
2159292 TGTTTTA
63 TGTTTTA
* * * * * *
2159299 CGCCCAGCGATAGTTGGATAAGCCAACGATAAGTGTGCCCAATACTAGTCGAACAATCGAAGATT
1 CGCCCAGCGATAGTTGGATAAGCCAACAATAAGTGTGCCCAACACTAGTCAAATAATTGAA-ATG
2159364 TTTTA
65 TTTTA
* * * * * ** **
2159369 CGCCCAGTGCTAGTTGGATAAGCCAACAATAAGTGTGGCTAGCACTAGTTGAATAATTGACGGTG
1 CGCCCAGCGATAGTTGGATAAGCCAACAATAAGTGTGCCCAACACTAGTCAAATAATTGA-AATG
*
2159434 TTTTG
65 TTTTA
* * * * * *
2159439 CGCCCAACGCTAGTTGGATAAACCAACGATAATTGTGCCTAACACTAGTCAAATAAT
1 CGCCCAGCGATAGTTGGATAAGCCAACAATAAGTGTGCCCAACACTAGTCAAATAAT
2159496 CAATAAGATT
Statistics
Matches: 161, Mismatches: 32, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
69 2 0.01
70 158 0.98
71 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (69 bp):
CGCCCAGCGATAGTTGGATAAGCCAACAATAAGTGTGCCCAACACTAGTCAAATAATTGAAATGT
TTTA
Found at i:2159486 original size:140 final size:140
Alignment explanation
Indices: 2159229--2159488 Score: 342
Period size: 140 Copynumber: 1.9 Consensus size: 140
2159219 AATCTCTTTG
* *
2159229 CGCCCAGCACTAGTTGGATATACCAACAATAAGTTTACCCAGCACTAGTCAAATAATTGATAATG
1 CGCCCAGCACTAGTTGGATATACCAACAATAAGTGTACCCAGCACTAGTCAAATAATTGACAATG
* * *
2159294 TTTTACGCCCAGCGATAGTTGGATAAGCCAACGATAAGTGTGCCCAATACTAGTCGAACAATCGA
66 TTTTACGCCCAACGATAGTTGGATAAACCAACGATAAGTGTGCCCAACACTAGTCGAACAATCGA
2159359 AGATTTTTTA
131 AGATTTTTTA
** ** * ** **
2159369 CGCCCAGTGCTAGTTGGATA-AGCCAACAATAAGTGTGGCTAGCACTAGTTGAATAATTGACGGT
1 CGCCCAGCACTAGTTGGATATA-CCAACAATAAGTGTACCCAGCACTAGTCAAATAATTGACAAT
* * * *
2159433 GTTTTGCGCCCAACGCTAGTTGGATAAACCAACGATAATTGTGCCTAACACTAGTC
65 GTTTTACGCCCAACGATAGTTGGATAAACCAACGATAAGTGTGCCCAACACTAGTC
2159489 AAATAATCAA
Statistics
Matches: 101, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
139 1 0.01
140 100 0.99
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (140 bp):
CGCCCAGCACTAGTTGGATATACCAACAATAAGTGTACCCAGCACTAGTCAAATAATTGACAATG
TTTTACGCCCAACGATAGTTGGATAAACCAACGATAAGTGTGCCCAACACTAGTCGAACAATCGA
AGATTTTTTA
Found at i:2160660 original size:19 final size:19
Alignment explanation
Indices: 2160636--2160733 Score: 146
Period size: 19 Copynumber: 5.2 Consensus size: 19
2160626 AATCTTTAGG
2160636 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* *
2160655 GATATGCAATATCAGATAT
1 GATATGCAATCTTAGATAT
2160674 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
2160691 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
2160710 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
2160731 GAT
1 GAT
2160734 CTTGTAATCT
Statistics
Matches: 71, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
17 15 0.21
19 47 0.66
21 9 0.13
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:2160683 original size:36 final size:37
Alignment explanation
Indices: 2160636--2160733 Score: 135
Period size: 36 Copynumber: 2.6 Consensus size: 37
2160626 AATCTTTAGG
2160636 GATATGCAATCTTAGATATGATATGCAATATCAGATAT
1 GATA-GCAATCTTAGATATGATATGCAATATCAGATAT
* *
2160674 GATA-CAATCTTAGATATGATATGCAATCTTAGATAT
1 GATAGCAATCTTAGATATGATATGCAATATCAGATAT
2160710 GATATGCAATCTTGAAGATATGAT
1 GATA-GCAATCTT--AGATATGAT
2160734 CTTGTAATCT
Statistics
Matches: 54, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
36 34 0.63
38 11 0.20
40 9 0.17
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (37 bp):
GATAGCAATCTTAGATATGATATGCAATATCAGATAT
Found at i:2168627 original size:120 final size:120
Alignment explanation
Indices: 2168414--2168650 Score: 440
Period size: 120 Copynumber: 2.0 Consensus size: 120
2168404 TGGGCTCACA
*
2168414 AATGCCCCTACGGTATTTATGGATTTGATGAATCGGATCTTCAGACCATATTTGGATCGGTTCGT
1 AATGCCCCTACGGTATTTATGGATTTGATGAATCGGATCTTCAGACCATATTTGGACCGGTTCGT
2168479 AGTTGTGTTCATTGATGACATCTTGGTCTATTCAAGAGATGAGACCGAACATACT
66 AGTTGTGTTCATTGATGACATCTTGGTCTATTCAAGAGATGAGACCGAACATACT
*
2168534 AATGCCCCTGCGGTATTTATGGATTTGATGAATCGGATCTTCAGA-CAGTATTTGGACCGGTTCG
1 AATGCCCCTACGGTATTTATGGATTTGATGAATCGGATCTTCAGACCA-TATTTGGACCGGTTCG
2168598 TAGTTGTGTTCATTGATGACATCTTGGTCTATTCAAGAGATGAGACCGAACAT
65 TAGTTGTGTTCATTGATGACATCTTGGTCTATTCAAGAGATGAGACCGAACAT
2168651 GCTGAGCATC
Statistics
Matches: 114, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
119 2 0.02
120 112 0.98
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (120 bp):
AATGCCCCTACGGTATTTATGGATTTGATGAATCGGATCTTCAGACCATATTTGGACCGGTTCGT
AGTTGTGTTCATTGATGACATCTTGGTCTATTCAAGAGATGAGACCGAACATACT
Found at i:2172638 original size:39 final size:40
Alignment explanation
Indices: 2172543--2172804 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
2172533 TTGAATGATG
*
2172543 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
2172581 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
2172622 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
2172661 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
2172700 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
2172739 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
2172778 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
2172805 AACGAGGAGC
Statistics
Matches: 203, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
39 132 0.65
40 59 0.29
41 11 0.05
42 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:2178452 original size:8 final size:8
Alignment explanation
Indices: 2178438--2178498 Score: 50
Period size: 9 Copynumber: 6.9 Consensus size: 8
2178428 TCTATTTCAA
2178438 AAAAAAAGG
1 AAAAAAA-G
2178447 AAAAAAAG
1 AAAAAAAG
2178455 AAAAGAAAACG
1 -AAA-AAAA-G
*
2178466 AAAAAAAT
1 AAAAAAAG
*
2178474 AAAATAAAA
1 AAAA-AAAG
2178483 AGAAAAAAG
1 A-AAAAAAG
2178492 AAAAAAA
1 AAAAAAA
2178499 ATGGAGAGGC
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
8 11 0.25
9 22 0.50
10 10 0.23
11 1 0.02
ACGTcount: A:0.84, C:0.02, G:0.11, T:0.03
Consensus pattern (8 bp):
AAAAAAAG
Found at i:2178463 original size:19 final size:18
Alignment explanation
Indices: 2178436--2178499 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 18
2178426 CTTCTATTTC
2178436 AAAAAAAAAGGAAAAAAAG
1 AAAAAAAAA-GAAAAAAAG
* *
2178455 AAAAGAAAACGAAAAAAAT
1 AAAA-AAAAAGAAAAAAAG
2178474 AAAATAAAAAG-AAAAAAG
1 AAAA-AAAAAGAAAAAAAG
2178492 AAAAAAAA
1 AAAAAAAA
2178500 TGGAGAGGCC
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
17 4 0.10
18 10 0.26
19 21 0.54
20 4 0.10
ACGTcount: A:0.84, C:0.02, G:0.11, T:0.03
Consensus pattern (18 bp):
AAAAAAAAAGAAAAAAAG
Found at i:2179590 original size:84 final size:84
Alignment explanation
Indices: 2179448--2180401 Score: 1577
Period size: 84 Copynumber: 11.4 Consensus size: 84
2179438 ATTCAGCGCT
2179448 TTAATCCCCTAAGCAGTAGGGTAACAAGTTAAATTTGCAGATCTTATCTCCGTAAGCAGTAGTGG
1 TTAATCCCCTAAGCAGTAGGGTAACAAGTTAAATTTGCAGATCTTATCTCCGTAAGCAGTAGTGG
2179513 AGAAGATCGAAGACTCGCC
66 AGAAGATCGAAGACTCGCC
* * *
2179532 TTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCA-ATTCTTATCTCCCTTAGCAGTAGTG
1 TTAATCCCCTAAGCAGTAGGGTAACAAGTTAAATTTGCAGA-TCTTATCTCCGTAAGCAGTAGTG
*
2179596 GAGCAGATCGAAGACTCGCC
65 GAGAAGATCGAAGACTCGCC
* * * * *
2179616 TTAATCCCCTAAGTAGTAGGGTAACAGGTT-CA----CAGATCTTATCTCCCTAAGCAGTAGCGG
1 TTAATCCCCTAAGCAGTAGGGTAACAAGTTAAATTTGCAGATCTTATCTCCGTAAGCAGTAGTGG
* *
2179676 AGCAGATCGACGACGACTCACC
66 AGAAGATCGA--A-GACTCGCC
*
2179698 TTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCGTAAGCAGTAGTGG
1 TTAATCCCCTAAGCAGTAGGGTAACAAGTTAAATTTGCAGATCTTATCTCCGTAAGCAGTAGTGG
2179763 AGAAGATCGAAGACTCGCC
66 AGAAGATCGAAGACTCGCC
2179782 TTAATCCCCTAAGCAGTAGGGTAACAAGTTAAATTTGCAGATCTTATCTCCGTAAGCAGTAGTGG
1 TTAATCCCCTAAGCAGTAGGGTAACAAGTTAAATTTGCAGATCTTATCTCCGTAAGCAGTAGTGG
2179847 AGAAGATCGAAGACTCGCC
66 AGAAGATCGAAGACTCGCC
2179866 TTAATCCCCTAAGCAGTAGGGTAACAAGTTAAATTTGCAGATCTTATCTCCGTAAGCAGTAGTGG
1 TTAATCCCCTAAGCAGTAGGGTAACAAGTTAAATTTGCAGATCTTATCTCCGTAAGCAGTAGTGG
2179931 AGAAGATCGAAGACTCGCC
66 AGAAGATCGAAGACTCGCC
2179950 TTAATCCCCTAAGCAGTAGGGTAACAAGTTAAATTTGCAGATCTTATCTCCGTAAGCAGTAGTGG
1 TTAATCCCCTAAGCAGTAGGGTAACAAGTTAAATTTGCAGATCTTATCTCCGTAAGCAGTAGTGG
2180015 AGAAGATCGAAGACTCGCC
66 AGAAGATCGAAGACTCGCC
2180034 TTAATCCCCTAAGCAGTAGGGTAACAAGTTAAATTTGCAGATCTTATCTCCGTAAGCAGTAGTGG
1 TTAATCCCCTAAGCAGTAGGGTAACAAGTTAAATTTGCAGATCTTATCTCCGTAAGCAGTAGTGG
2180099 AGAAGATCGAAGACTCGCC
66 AGAAGATCGAAGACTCGCC
2180118 TTAATCCCCTAAGCAGTAGGGTAACAAGTTAAATTTGCAGATCTTATCTCCGTAAGCAGTAGTGG
1 TTAATCCCCTAAGCAGTAGGGTAACAAGTTAAATTTGCAGATCTTATCTCCGTAAGCAGTAGTGG
2180183 AGAAGATCGAAGACTCGCC
66 AGAAGATCGAAGACTCGCC
2180202 TTAATCCCCTAAGCAGTAGGGTAACAAGTTAAATTTGCAGATCTTATCTCCGTAAGCAGTAGTGG
1 TTAATCCCCTAAGCAGTAGGGTAACAAGTTAAATTTGCAGATCTTATCTCCGTAAGCAGTAGTGG
2180267 AGAAGATCGAAGACTCGCC
66 AGAAGATCGAAGACTCGCC
* * * **
2180286 TTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCTGATCTTATC-CC-TAA-TAGTAGCAG
1 TTAATCCCCTAAGCAGTAGGGTAACAAGTTAAATTTGCAGATCTTATCTCCGTAAGCAGTAGTGG
* *
2180348 AGCAGATCGAAGAAGAT-GCGC
66 AGAAGATCGAAG-A-CTCGC-C
* * *
2180369 TTAACCCCCTAAGCAGTAGGGTACCAGGTTAAA
1 TTAATCCCCTAAGCAGTAGGGTAACAAGTTAAA
2180402 GTATAGCAGA
Statistics
Matches: 832, Mismatches: 25, Indels: 27
0.94 0.03 0.03
Matches are distributed among these distances:
79 34 0.04
80 1 0.00
81 18 0.02
82 42 0.05
83 38 0.05
84 663 0.80
85 1 0.00
87 35 0.04
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.25
Consensus pattern (84 bp):
TTAATCCCCTAAGCAGTAGGGTAACAAGTTAAATTTGCAGATCTTATCTCCGTAAGCAGTAGTGG
AGAAGATCGAAGACTCGCC
Found at i:2180704 original size:87 final size:88
Alignment explanation
Indices: 2180526--2180707 Score: 212
Period size: 87 Copynumber: 2.1 Consensus size: 88
2180516 CGGAGAGCAG
* * *
2180526 ATCGAAGACATAGCATATCTGACCTTCTAATATTTCATATTGAAGCAGATCCAAGATGATTTAGC
1 ATCGAAGACATAGCAGATCTGACCTTCTAATATTTCACACTGAAGCAGATCCAAGATGATTTAGC
* *
2180591 ATCCTTGTGTTTACAAGGAGCAA
66 ATCCTTGTATTTACAAGGAACAA
* * *
2180614 ATCGAAGACATAGCAGATCTGACCTTC-AGGTGTTT-ACGCTGAAGCAGATCCAAGATGATTT-G
1 ATCGAAGACATAGCAGATCTGACCTTCTA-ATATTTCACACTGAAGCAGATCCAAGATGATTTAG
*
2180676 ACAT-CTCTGTATTGT-CAAGGAACGA
65 -CATCCT-TGTATT-TACAAGGAACAA
2180701 ATCGAAG
1 ATCGAAG
2180708 GTAGCAGATT
Statistics
Matches: 81, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
86 3 0.04
87 47 0.58
88 31 0.38
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (88 bp):
ATCGAAGACATAGCAGATCTGACCTTCTAATATTTCACACTGAAGCAGATCCAAGATGATTTAGC
ATCCTTGTATTTACAAGGAACAA
Found at i:2181108 original size:19 final size:20
Alignment explanation
Indices: 2181084--2181126 Score: 70
Period size: 19 Copynumber: 2.1 Consensus size: 20
2181074 AATCTTTAAG
2181084 GATATGCAATCTT-AGATAT
1 GATATGCAATCTTAAGATAT
2181103 GATATGCAATCTTAAAGATAT
1 GATATGCAATCTT-AAGATAT
2181124 GAT
1 GAT
2181127 CTTGTAATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 13 0.59
21 9 0.41
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (20 bp):
GATATGCAATCTTAAGATAT
Found at i:2198452 original size:14 final size:14
Alignment explanation
Indices: 2198433--2198462 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2198423 ATTTAACCGA
2198433 ATATACATAAACTC
1 ATATACATAAACTC
*
2198447 ATATACATATACTC
1 ATATACATAAACTC
2198461 AT
1 AT
2198463 GAATCATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (14 bp):
ATATACATAAACTC
Found at i:2198605 original size:19 final size:20
Alignment explanation
Indices: 2198581--2198619 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
2198571 CCGAATGTAC
2198581 TTTTCATATACA-CATATAT
1 TTTTCATATACATCATATAT
*
2198600 TTTTCATTTACATCATATAT
1 TTTTCATATACATCATATAT
2198620 GATTTGCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTTCATATACATCATATAT
Found at i:2199369 original size:33 final size:33
Alignment explanation
Indices: 2199327--2199425 Score: 109
Period size: 33 Copynumber: 3.2 Consensus size: 33
2199317 CAGATCGGTA
* *
2199327 ACAGTCTGGGCCTGAGCCCTATTCAGTATCAGT
1 ACAGTCTGGGCCTAAGCCCTATACAGTATCAGT
*
2199360 ACAGTCTGGGCCTTAGCCCTATACAG--T-A--
1 ACAGTCTGGGCCTAAGCCCTATACAGTATCAGT
* * *
2199388 ACAGTGTGGGCCTAAGCCCAATGCAGTATCAGT
1 ACAGTCTGGGCCTAAGCCCTATACAGTATCAGT
2199421 ACAGT
1 ACAGT
2199426 GTAGTGCAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
28 22 0.40
30 2 0.04
31 2 0.04
33 29 0.53
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.24
Consensus pattern (33 bp):
ACAGTCTGGGCCTAAGCCCTATACAGTATCAGT
Found at i:2199398 original size:61 final size:61
Alignment explanation
Indices: 2199299--2199425 Score: 175
Period size: 61 Copynumber: 2.1 Consensus size: 61
2199289 AGTGAATAAC
* * * *
2199299 ACAGTCTGGGCCTAAGCCCAGATCGGTAACAGTCTGGGCCTGAGCCCTATTCAGTATCAGT
1 ACAGTCTGGGCCTAAGCCCAGATCAGTAACAGTCTGGGCCTAAGCCCAATGCAGTATCAGT
* * *
2199360 ACAGTCTGGGCCTTAGCCC-TATACAGTAACAGTGTGGGCCTAAGCCCAATGCAGTATCAGT
1 ACAGTCTGGGCCTAAGCCCAGAT-CAGTAACAGTCTGGGCCTAAGCCCAATGCAGTATCAGT
2199421 ACAGT
1 ACAGT
2199426 GTAGTGCAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
60 2 0.03
61 56 0.97
ACGTcount: A:0.25, C:0.27, G:0.25, T:0.23
Consensus pattern (61 bp):
ACAGTCTGGGCCTAAGCCCAGATCAGTAACAGTCTGGGCCTAAGCCCAATGCAGTATCAGT
Found at i:2199427 original size:33 final size:31
Alignment explanation
Indices: 2199299--2199425 Score: 108
Period size: 28 Copynumber: 4.2 Consensus size: 31
2199289 AGTGAATAAC
*
2199299 ACAGTCTGGGCCTAAG-CC--CAG-ATCGGT
1 ACAGTCTGGGCCTAAGCCCATCAGTATCAGT
*
2199326 AACAGTCTGGGCCTGAGCCCTATTCAGTATCAGT
1 -ACAGTCTGGGCCTAAGCCC-A-TCAGTATCAGT
*
2199360 ACAGTCTGGGCCTTAGCCC-T-A-TA-CAGT
1 ACAGTCTGGGCCTAAGCCCATCAGTATCAGT
*
2199387 AACAGTGTGGGCCTAAGCCCAATGCAGTATCAGT
1 -ACAGTCTGGGCCTAAGCCC-AT-CAGTATCAGT
2199421 ACAGT
1 ACAGT
2199426 GTAGTGCAAT
Statistics
Matches: 81, Mismatches: 5, Indels: 21
0.76 0.05 0.20
Matches are distributed among these distances:
27 4 0.05
28 34 0.42
29 3 0.04
30 2 0.02
32 1 0.01
33 28 0.35
34 9 0.11
ACGTcount: A:0.25, C:0.27, G:0.25, T:0.23
Consensus pattern (31 bp):
ACAGTCTGGGCCTAAGCCCATCAGTATCAGT
Found at i:2199801 original size:27 final size:27
Alignment explanation
Indices: 2199771--2199963 Score: 278
Period size: 27 Copynumber: 7.1 Consensus size: 27
2199761 GGGCATAATC
* * *
2199771 GTCATTTTACCATATAGGGGTACTACG
1 GTCATTTTACCCTACAGGGGTATTACG
2199798 GTCATTTTACCCTACAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGTATTACG
*
2199825 ATCATTTTACCCTACAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGTATTACG
2199852 GTCATTTTACCCTACAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGTATTACG
* *
2199879 GTCATTTTACCCTACTGGGGTATTACA
1 GTCATTTTACCCTACAGGGGTATTACG
* *
2199906 GTCATTTTACCCTACAGGGCTATTACA
1 GTCATTTTACCCTACAGGGGTATTACG
* * * *
2199933 ATCATTTTACCCTATAAGGGTATTACA
1 GTCATTTTACCCTACAGGGGTATTACG
2199960 GTCA
1 GTCA
2199964 AATAACGACC
Statistics
Matches: 152, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 152 1.00
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGTATTACG
Found at i:2202067 original size:41 final size:43
Alignment explanation
Indices: 2201985--2202122 Score: 113
Period size: 41 Copynumber: 3.2 Consensus size: 43
2201975 TCCCAGAAGT
* * *
2201985 GGTCTTACATGCTATCACATATCGATGCCACTGTCCCAGACAA
1 GGTCTTACATGCAATCAAATATCGATGCCACTATCCCAGACAA
* *
2202028 GGTCTTACATG-AATCAAATA-CGATGCCGA-TATCCTAGACAT
1 GGTCTTACATGCAATCAAATATCGATGCC-ACTATCCCAGACAA
* * * * * *
2202069 GGTTTTACACGTAACCACATATATCGATGCCAAC-GTCCCAGACAT
1 GGTCTTACATGCAATCA-A-ATATCGATGCC-ACTATCCCAGACAA
2202114 GGTCTTACA
1 GGTCTTACA
2202123 CGAGAACACA
Statistics
Matches: 77, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
41 25 0.32
42 12 0.16
43 12 0.16
44 3 0.04
45 25 0.32
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (43 bp):
GGTCTTACATGCAATCAAATATCGATGCCACTATCCCAGACAA
Found at i:2202133 original size:45 final size:43
Alignment explanation
Indices: 2202003--2202135 Score: 128
Period size: 45 Copynumber: 3.0 Consensus size: 43
2201993 ATGCTATCAC
* * *
2202003 ATATCGATGCCACTGTCCCAGACAAGGTCTTACATGAATCA-A-
1 ATATCGATGCCAC-GTCCCAGACATGGTCTTACACGAAACACAT
** * * *
2202045 ATA-CGATGCCGATATCCTAGACATGGTTTTACACGTAACCACAT
1 ATATCGATGCC-ACGTCCCAGACATGGTCTTACACG-AAACACAT
2202089 ATATCGATGCCAACGTCCCAGACATGGTCTTACACGAGAACACAT
1 ATATCGATGCC-ACGTCCCAGACATGGTCTTACACGA-AACACAT
2202134 AT
1 AT
2202136 TAGAAATCCT
Statistics
Matches: 72, Mismatches: 13, Indels: 9
0.77 0.14 0.10
Matches are distributed among these distances:
41 24 0.33
42 8 0.11
43 1 0.01
44 4 0.06
45 35 0.49
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (43 bp):
ATATCGATGCCACGTCCCAGACATGGTCTTACACGAAACACAT
Found at i:2212948 original size:13 final size:14
Alignment explanation
Indices: 2212932--2212961 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
2212922 ATGCTTGATG
2212932 TTAATTGAA-GTAA
1 TTAATTGAATGTAA
2212945 TTAATTGAATGTAA
1 TTAATTGAATGTAA
2212959 TTA
1 TTA
2212962 TCTATTTAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (14 bp):
TTAATTGAATGTAA
Found at i:2215748 original size:19 final size:18
Alignment explanation
Indices: 2215720--2215759 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
2215710 GAATACTTCC
2215720 ATAAACGATAACTTATTCT
1 ATAAACGATAACTTATT-T
*
2215739 ATAAATGATAACTTATTT
1 ATAAACGATAACTTATTT
2215757 ATA
1 ATA
2215760 GGCGGTTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (18 bp):
ATAAACGATAACTTATTT
Found at i:2217024 original size:12 final size:12
Alignment explanation
Indices: 2217000--2217038 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
2216990 TTAAAAAGTT
2217000 TAAACAAATAAA
1 TAAACAAATAAA
2217012 TAAA-AAATGAAA
1 TAAACAAAT-AAA
*
2217024 TAAGCAAATAAA
1 TAAACAAATAAA
2217036 TAA
1 TAA
2217039 TTAAATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
11 4 0.17
12 16 0.67
13 4 0.17
ACGTcount: A:0.72, C:0.05, G:0.05, T:0.18
Consensus pattern (12 bp):
TAAACAAATAAA
Found at i:2217032 original size:20 final size:18
Alignment explanation
Indices: 2217009--2217054 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
2216999 TTAAACAAAT
2217009 AAATAAAAAATGAAATAA
1 AAATAAAAAATGAAATAA
* *
2217027 GCAAATAAATAATTAAATAA
1 --AAATAAAAAATGAAATAA
2217047 AAATAAAA
1 AAATAAAA
2217055 TATAACAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 7 0.30
20 16 0.70
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.20
Consensus pattern (18 bp):
AAATAAAAAATGAAATAA
Found at i:2217044 original size:12 final size:12
Alignment explanation
Indices: 2217005--2217144 Score: 60
Period size: 12 Copynumber: 11.2 Consensus size: 12
2216995 AAGTTTAAAC
2217005 AAATAAATAA-A
1 AAATAAATAATA
**
2217016 AAATGAAATAAGC
1 AAAT-AAATAATA
*
2217029 AAATAAATAATT
1 AAATAAATAATA
2217041 AAATAAA-AATA
1 AAATAAATAATA
*
2217052 AAATATAACAAATTA
1 AAATA-AA-TAA-TA
2217067 CAAATGACAATAATA
1 -AAAT-A-AATAATA
2217082 ATAAT-AATAATA
1 A-AATAAATAATA
*
2217094 ACAT-AATAGA-A
1 AAATAAATA-ATA
2217105 ATAAT-AATAATA
1 A-AATAAATAATA
*
2217117 ATAATAAAGAATA
1 A-AATAAATAATA
*
2217130 ATAAT-AGTAATA
1 A-AATAAATAATA
2217142 AAA
1 AAA
2217145 ATAATATTAA
Statistics
Matches: 105, Mismatches: 11, Indels: 26
0.74 0.08 0.18
Matches are distributed among these distances:
11 23 0.22
12 48 0.46
13 15 0.14
14 3 0.03
15 7 0.07
16 6 0.06
17 3 0.03
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.24
Consensus pattern (12 bp):
AAATAAATAATA
Found at i:2217083 original size:3 final size:3
Alignment explanation
Indices: 2217075--2217226 Score: 137
Period size: 3 Copynumber: 50.3 Consensus size: 3
2217065 TACAAATGAC
*
2217075 AAT AAT AAT AAT AAT AAT AA- CAT AAT AGA- AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT
* * * * * *
2217119 AAT AAAG AAT AAT AAT AGT AAT AAA AAT AAT ATT AAC AGT AAT AAT
1 AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
** * * *
2217165 AAT GGT AAT AAT AAAT AAT AGT AAT AAT AAT AAT AAT AAT AGT AAC
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
2217211 AAT AGT AAC AAT AAT A
1 AAT AAT AAT AAT AAT A
2217227 TATTAAATTA
Statistics
Matches: 116, Mismatches: 28, Indels: 10
0.75 0.18 0.06
Matches are distributed among these distances:
2 2 0.02
3 108 0.93
4 6 0.05
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:2217384 original size:41 final size:41
Alignment explanation
Indices: 2217339--2217420 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
2217329 GAAGGACCAA
2217339 ATTGAAACGCACAAATAACGAGGGACAAAAAGGGAAATTTT
1 ATTGAAACGCACAAATAACGAGGGACAAAAAGGGAAATTTT
2217380 ATTGAAACGCACAAATAACGAGGGACAAAAAGGGAAATTTT
1 ATTGAAACGCACAAATAACGAGGGACAAAAAGGGAAATTTT
2217421 TCCTTCCCTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.49, C:0.12, G:0.22, T:0.17
Consensus pattern (41 bp):
ATTGAAACGCACAAATAACGAGGGACAAAAAGGGAAATTTT
Found at i:2218832 original size:44 final size:44
Alignment explanation
Indices: 2218715--2218849 Score: 139
Period size: 44 Copynumber: 3.0 Consensus size: 44
2218705 AGAGGTATAG
* * *
2218715 GACTTGTCGCCTT-AATCCGCTCCACTGCAACTTCAGGGAGATAG
1 GACTTGT-GCCTTCAATCTGCTCCACTGCAACTTTAGGGAGATAA
* * ** *
2218759 GA-TTAGCTGTCTTCAGTCTGCTCTGCTGCAACTTTAGGGAGAGAA
1 GACTT-G-TGCCTTCAATCTGCTCCACTGCAACTTTAGGGAGATAA
* *
2218804 GACTTGTGGCTTCAATCTGCTCCACTGCAACTTTAGGAAGATAA
1 GACTTGTGCCTTCAATCTGCTCCACTGCAACTTTAGGGAGATAA
2218848 GA
1 GA
2218850 TTTTCCATGA
Statistics
Matches: 73, Mismatches: 14, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
43 2 0.03
44 41 0.56
45 28 0.38
46 2 0.03
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (44 bp):
GACTTGTGCCTTCAATCTGCTCCACTGCAACTTTAGGGAGATAA
Found at i:2219149 original size:45 final size:45
Alignment explanation
Indices: 2219093--2219215 Score: 183
Period size: 45 Copynumber: 2.7 Consensus size: 45
2219083 ATAGCTTCAA
* * * * *
2219093 TCTGTTCCACTGCAACTTTAGAGAAATAAGATTCGCTATCATTAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATCATTAG
*
2219138 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATCTTTAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATCATTAG
*
2219183 TCTGCTCCGCTGCAACTTCAGGGAGATAAGATT
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATT
2219216 TGTGAATTTA
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 71 1.00
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.30
Consensus pattern (45 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATCATTAG
Found at i:2219767 original size:12 final size:12
Alignment explanation
Indices: 2219750--2219774 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2219740 ATCAAAGAAA
2219750 GCAAGCATTGTT
1 GCAAGCATTGTT
2219762 GCAAGCATTGTT
1 GCAAGCATTGTT
2219774 G
1 G
2219775 GAATACAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (12 bp):
GCAAGCATTGTT
Found at i:2219991 original size:3 final size:3
Alignment explanation
Indices: 2219970--2220009 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
2219960 CCTTTCCATT
* *
2219970 TTC TTA TTC TTC TTA TTC TTC TTC TTC TTC TTC TT- TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
2220010 GGAAAAGTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.05, C:0.25, G:0.00, T:0.70
Consensus pattern (3 bp):
TTC
Found at i:2232458 original size:40 final size:40
Alignment explanation
Indices: 2232414--2232675 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
2232404 GCTCCTCGTT
* *
2232414 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
2232454 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
2232494 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
2232533 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
2232572 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
2232611 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
2232652 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
2232676 CATCATTCAA
Statistics
Matches: 205, Mismatches: 9, Indels: 17
0.89 0.04 0.07
Matches are distributed among these distances:
38 2 0.01
39 128 0.62
40 64 0.31
41 11 0.05
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:2238069 original size:17 final size:17
Alignment explanation
Indices: 2238008--2238069 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 17
2237998 AAACAAGGCT
2238008 AACAATATAAAAA-TATA
1 AACAA-ATAAAAAGTATA
* *
2238025 AATAAATAAACAAGTAAA
1 AACAAATAAA-AAGTATA
* * *
2238043 AACTATTAAAAAGTTTA
1 AACAAATAAAAAGTATA
2238060 AACAAATAAA
1 AACAAATAAA
2238070 TAAAAAATGA
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
16 5 0.15
17 19 0.56
18 10 0.29
ACGTcount: A:0.68, C:0.06, G:0.03, T:0.23
Consensus pattern (17 bp):
AACAAATAAAAAGTATA
Found at i:2238072 original size:4 final size:4
Alignment explanation
Indices: 2238058--2238112 Score: 51
Period size: 4 Copynumber: 14.0 Consensus size: 4
2238048 TTAAAAAGTT
* * * *
2238058 TAAA CAAA TAAA TAAA -AAA TGAAA TAAG CAAA TAAA TAAG TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA T-AAA TAAA TAAA TAAA TAAA TAAA TAAA
2238106 -AAA TAAA
1 TAAA TAAA
2238113 ATATAACAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
3 6 0.15
4 30 0.75
5 4 0.10
ACGTcount: A:0.73, C:0.04, G:0.05, T:0.18
Consensus pattern (4 bp):
TAAA
Found at i:2238140 original size:3 final size:3
Alignment explanation
Indices: 2238132--2238263 Score: 102
Period size: 3 Copynumber: 43.0 Consensus size: 3
2238122 ATTACAAATG
* * * * *
2238132 ATA ATA ATA ATA AGA ATA ATA ATA ATA ACA ATA ATA ACAA AGA ACA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA
* * * * * * * *
2238178 AAA ATA GTA ATA AAA ATA ATA TTA ACA GTA ATA ATA ATG GTA ATA ATAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
* *
2238227 ATA ATA ATA ATAA ATA ATA ATA ATA GTA ACA ATA ATA
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA
2238264 TATTAAATTA
Statistics
Matches: 99, Mismatches: 27, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
3 91 0.92
4 8 0.08
ACGTcount: A:0.64, C:0.04, G:0.05, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:2244483 original size:16 final size:15
Alignment explanation
Indices: 2244449--2244493 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
2244439 ATAGGGACCT
*
2244449 TTATAATATACACTA
1 TTATAATATACAATA
*
2244464 TTATAATATTCAAATA
1 TTATAATATAC-AATA
2244480 TTATAATATACAAT
1 TTATAATATACAAT
2244494 TAAGTTTGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (15 bp):
TTATAATATACAATA
Found at i:2250508 original size:46 final size:46
Alignment explanation
Indices: 2250337--2250623 Score: 244
Period size: 50 Copynumber: 6.1 Consensus size: 46
2250327 CATTGTTGTT
* * * *
2250337 ATGTGAGCCAGTGTAAGACATGTTTGGGACATGCATCGGCCAC-ATT
1 ATGTAAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGA-G
* * * *
2250383 ATGAAATGCTAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAAAG
1 ATGTAA-GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCG--AG
* * *
2250432 A-GACGAGAGCTAGTGTAAGACATGTTTGGGACATGCATCGGCCTCGAG
1 ATG--TA-AGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAG
*
2250480 ATGTAAGCCAGTGTAAGACATGTCTGGGACATGCATC-GACTACGAG
1 ATGTAAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAG
* * *
2250526 ATGT--GCTAGTGTAAGACATGTCTGGGACATGCATCGGCAC-AGAT
1 ATGTAAGCCAGTGTAAGACATGTCTGGGACATGCATCGGC-CTCGAG
* * * *
2250570 ATGTGAGAGCCAGTGTAAGACCATATCTGGGATATGGCATCGGCATCGAT
1 ATGT-A-AGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAG
2250620 ATGT
1 ATGT
2250624 GTAAGGTTTC
Statistics
Matches: 198, Mismatches: 25, Indels: 32
0.78 0.10 0.13
Matches are distributed among these distances:
44 36 0.18
45 4 0.02
46 43 0.22
47 33 0.17
48 15 0.08
49 14 0.07
50 52 0.26
51 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.30, T:0.24
Consensus pattern (46 bp):
ATGTAAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAG
Found at i:2250552 original size:44 final size:44
Alignment explanation
Indices: 2250346--2250561 Score: 202
Period size: 46 Copynumber: 4.7 Consensus size: 44
2250336 TATGTGAGCC
* * * *
2250346 AGTGTAAGACATGTTTGGGACATGCATCGGCCAC-ATTATGAAATGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGACTACGA-GATG---TGCT
* * * *
2250393 AGTGTAAGACATGTCTGGGACATGCATCGGCATTGAAAGAGACGAGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATC-G-ACT--ACGAGA--TGTGCT
* * *
2250443 AGTGTAAGACATGTTTGGGACATGCATCGGCCT-CGAGATGTAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATC-GACTACGAGATGT--GCT
2250489 AGTGTAAGACATGTCTGGGACATGCATCGACTACGAGATGTGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGACTACGAGATGTGCT
2250533 AGTGTAAGACATGTCTGGGACATGCATCG
1 AGTGTAAGACATGTCTGGGACATGCATCG
2250562 GCACAGATAT
Statistics
Matches: 141, Mismatches: 18, Indels: 23
0.77 0.10 0.13
Matches are distributed among these distances:
44 32 0.23
45 3 0.02
46 41 0.29
47 27 0.19
48 1 0.01
49 1 0.01
50 32 0.23
51 2 0.01
52 1 0.01
53 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.30, T:0.24
Consensus pattern (44 bp):
AGTGTAAGACATGTCTGGGACATGCATCGACTACGAGATGTGCT
Found at i:2250610 original size:140 final size:141
Alignment explanation
Indices: 2250337--2250623 Score: 357
Period size: 140 Copynumber: 2.0 Consensus size: 141
2250327 CATTGTTGTT
* * * *
2250337 ATGTGAGCCAGTGTAAGACATGTTTGGGACATGCATCGGCCACATTATGAAATGCTAGTGTAAGA
1 ATGTAAGCCAGTGTAAGACATGTCTGGGACATGCATCGACCACATGATG--ATGCTAGTGTAAGA
** * * *
2250402 CATGTCTGGGACATGCATCGGCATTGAAAGAGACGAGAGCTAGTGTAAGACATGTTTGGGACATG
64 CATGTCTGGGACATGCATCGGCACAGAAAGAGACGAGAGCCAGTGTAAGACATATCTGGGACATG
*
2250467 CATCGGCCTCGAG
129 CATCGGCATCGAG
*
2250480 ATGTAAGCCAGTGTAAGACATGTCTGGGACATGCATCGACTACGA-GATG-TGCTAGTGTAAGAC
1 ATGTAAGCCAGTGTAAGACATGTCTGGGACATGCATCGACCAC-ATGATGATGCTAGTGTAAGAC
* * * *
2250543 ATGTCTGGGACATGCATCGGCACAGATA-TG-TGAGAGCCAGTGTAAGACCATATCTGGGATATG
65 ATGTCTGGGACATGCATCGGCACAGAAAGAGACGAGAGCCAGTGTAAGA-CATATCTGGGACAT-
*
2250606 GCATCGGCATCGAT
128 GCATCGGCATCGAG
2250620 ATGT
1 ATGT
2250624 GTAAGGTTTC
Statistics
Matches: 125, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
138 15 0.12
139 12 0.10
140 55 0.44
143 42 0.34
144 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.30, T:0.24
Consensus pattern (141 bp):
ATGTAAGCCAGTGTAAGACATGTCTGGGACATGCATCGACCACATGATGATGCTAGTGTAAGACA
TGTCTGGGACATGCATCGGCACAGAAAGAGACGAGAGCCAGTGTAAGACATATCTGGGACATGCA
TCGGCATCGAG
Found at i:2261738 original size:12 final size:13
Alignment explanation
Indices: 2261702--2261739 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
2261692 AAATATTTGA
2261702 CTTGTTCTTAATT
1 CTTGTTCTTAATT
*
2261715 ATGTGTTCTTAATT
1 CT-TGTTCTTAATT
2261729 CTTG-TCTTAAT
1 CTTGTTCTTAAT
2261740 ATTCCAAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 7 0.32
13 3 0.14
14 12 0.55
ACGTcount: A:0.18, C:0.13, G:0.11, T:0.58
Consensus pattern (13 bp):
CTTGTTCTTAATT
Found at i:2263860 original size:44 final size:44
Alignment explanation
Indices: 2263797--2263887 Score: 173
Period size: 44 Copynumber: 2.1 Consensus size: 44
2263787 CGCCTCTCTC
*
2263797 CTAGCAAAGTTTGGTTTGGTCCCTTGCAATGCATGAATTTTTAA
1 CTAGCAAAGTTTGGTTTGGTCCCTTACAATGCATGAATTTTTAA
2263841 CTAGCAAAGTTTGGTTTGGTCCCTTACAATGCATGAATTTTTAA
1 CTAGCAAAGTTTGGTTTGGTCCCTTACAATGCATGAATTTTTAA
2263885 CTA
1 CTA
2263888 TCTTGCATTT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.38
Consensus pattern (44 bp):
CTAGCAAAGTTTGGTTTGGTCCCTTACAATGCATGAATTTTTAA
Found at i:2264788 original size:27 final size:27
Alignment explanation
Indices: 2264748--2264860 Score: 120
Period size: 27 Copynumber: 4.2 Consensus size: 27
2264738 TGTCTCATTG
*
2264748 GACTATCTCGTGTTTAACATCCTGTCA
1 GACTATCCCGTGTTTAACATCCTGTCA
* * *
2264775 GACTATCCCTTGTTTAGCATCCTATCA
1 GACTATCCCGTGTTTAACATCCTGTCA
* * *
2264802 GACTATCCCATGTTTAACATCTTGTTA
1 GACTATCCCGTGTTTAACATCCTGTCA
* * *
2264829 GACTATTCAGTGTTTAACGT-CTCGTCA
1 GACTATCCCGTGTTTAACATCCT-GTCA
2264856 GACTA
1 GACTA
2264861 ACTATGATGC
Statistics
Matches: 70, Mismatches: 15, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
26 1 0.01
27 69 0.99
ACGTcount: A:0.24, C:0.25, G:0.14, T:0.37
Consensus pattern (27 bp):
GACTATCCCGTGTTTAACATCCTGTCA
Found at i:2265463 original size:22 final size:20
Alignment explanation
Indices: 2265405--2265465 Score: 52
Period size: 22 Copynumber: 2.9 Consensus size: 20
2265395 TACCAAATCA
2265405 TAAATA-ATCAAAAATTTAAT
1 TAAATATAT-AAAAATTTAAT
* * *
2265425 TAAAAATATTTACAATTATAATT
1 TAAATATA-TAAAAATT-TAA-T
2265448 TAAATATATAAAAATTTA
1 TAAATATATAAAAATTTA
2265466 TCAAAACCAT
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
20 5 0.16
21 8 0.26
22 10 0.32
23 8 0.26
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.39
Consensus pattern (20 bp):
TAAATATATAAAAATTTAAT
Found at i:2273375 original size:13 final size:13
Alignment explanation
Indices: 2273357--2273382 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2273347 ACTGTGGATT
2273357 TTGGTTTTAAAGA
1 TTGGTTTTAAAGA
2273370 TTGGTTTTAAAGA
1 TTGGTTTTAAAGA
2273383 AACAATTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (13 bp):
TTGGTTTTAAAGA
Found at i:2280343 original size:29 final size:29
Alignment explanation
Indices: 2280309--2280382 Score: 94
Period size: 29 Copynumber: 2.6 Consensus size: 29
2280299 TAATCAATCG
* * *
2280309 CACACACTTAGTGCCATGCACTTTAAACT
1 CACACACTTAGTGCCATACAATTTAAACC
**
2280338 CACACACTTAGTGCTGTACAATTTAAACC
1 CACACACTTAGTGCCATACAATTTAAACC
*
2280367 CGCACACTTAGTGCCA
1 CACACACTTAGTGCCA
2280383 ATCTCATGAC
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.31, C:0.31, G:0.12, T:0.26
Consensus pattern (29 bp):
CACACACTTAGTGCCATACAATTTAAACC
Found at i:2284499 original size:29 final size:29
Alignment explanation
Indices: 2284465--2284538 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
2284455 TAATCAACCA
*
2284465 CGCACACTTAGTGCCATGTACTTT-AAACT
1 CGCACACTTAGTGCCATGCA-TTTCAAACT
*
2284494 CGCACACTTAGTGCCATGCATTTCAAATT
1 CGCACACTTAGTGCCATGCATTTCAAACT
*
2284523 CGCACACCTAGTGCCA
1 CGCACACTTAGTGCCA
2284539 ATCTCACAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 3 0.07
29 38 0.93
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCATTTCAAACT
Found at i:2297352 original size:11 final size:11
Alignment explanation
Indices: 2297319--2297354 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
2297309 TGAATTGTAG
*
2297319 TAGTTAACAGA
1 TAGTTAACAGT
2297330 TAGTTAATCAGT
1 TAGTTAA-CAGT
2297342 TAGTTAACAGT
1 TAGTTAACAGT
2297353 TA
1 TA
2297355 CTCATCATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.36
Consensus pattern (11 bp):
TAGTTAACAGT
Found at i:2304944 original size:70 final size:70
Alignment explanation
Indices: 2304831--2305470 Score: 643
Period size: 70 Copynumber: 9.1 Consensus size: 70
2304821 TCTTCCCAAA
* * * * * * * * *
2304831 AAAATAGTTAGCGAGACCTCAATCTCTCACCTGTGATCTTAAGGCTTGTAGGTTCAATACTGCAG
1 AAAATAGTTAGCGAGAGCTCAAGCTCCCAACTGTGATCTTAAGGCTCGCAGGTTCAACACCGTAG
2304896 CCTCC
66 CCTCC
* * * * * * * * * * * *
2304901 AAAATAGATAGCGAGAGCTTAAGTTCACAGCTATAATATTAAGGCTTGCATGTTCAACACCATAA
1 AAAATAGTTAGCGAGAGCTCAAGCTCCCAACTGTGATCTTAAGGCTCGCAGGTTCAACACCGTAG
*
2304966 CCTCT
66 CCTCC
* * * * * *
2304971 AAAAAAATTAGCGAGAGCTCAAGCTCCCAACTGTGATTTTAAGGCTCGCAAGTTCAACATCATAG
1 AAAATAGTTAGCGAGAGCTCAAGCTCCCAACTGTGATCTTAAGGCTCGCAGGTTCAACACCGTAG
2305036 CCTCC
66 CCTCC
* * * *
2305041 AAAATAGTTAGTGAGAGCTCAAGCTCCCAAATGTGATCTTAAGGCTCGTAGGTTCAACACAGTAG
1 AAAATAGTTAGCGAGAGCTCAAGCTCCCAACTGTGATCTTAAGGCTCGCAGGTTCAACACCGTAG
2305106 CCTCC
66 CCTCC
* * * *
2305111 AAAATAGTTAGTGAGAGCTCAAGCTCCTAACTATGATCTTAAGGCTCACAGGTTCAACACCGTAG
1 AAAATAGTTAGCGAGAGCTCAAGCTCCCAACTGTGATCTTAAGGCTCGCAGGTTCAACACCGTAG
*
2305176 CCTCT
66 CCTCC
* ** * *
2305181 AAAATAGTTAGCGATAGCTCAAGCTCCCAGTTGTGATCTTAAGGCTCACAGGTTCAACACCTTAG
1 AAAATAGTTAGCGAGAGCTCAAGCTCCCAACTGTGATCTTAAGGCTCGCAGGTTCAACACCGTAG
2305246 CCTCC
66 CCTCC
* ** * * ** *
2305251 AAAATAGTTAGCAAGAGCTCAAGCTCCCAGTTGTGATCTTAAGGCTCGCAAGTTCAATACCACAA
1 AAAATAGTTAGCGAGAGCTCAAGCTCCCAACTGTGATCTTAAGGCTCGCAGGTTCAACACCGTAG
2305316 CCTCC
66 CCTCC
** * * * **
2305321 AAAATAGTTAGCGAGAGCTCAAGCTCTTAGA-TCTGATCTTAAGGCTCGCAAGTTCAATACCACA
1 AAAATAGTTAGCGAGAGCTCAAGCTCCCA-ACTGTGATCTTAAGGCTCGCAGGTTCAACACCGTA
* *
2305385 ACCTCT
65 GCCTCC
* * * * ** * *
2305391 AAAACAGTTAGCGAGAGCTCAAGCTCTCAGCTGTGATCTTAAGGCTCACAAATTCAAGCACTGCA
1 AAAATAGTTAGCGAGAGCTCAAGCTCCCAACTGTGATCTTAAGGCTCGCAGGTTCAA-CACCGTA
*
2305456 GCCTTC
65 GCCTCC
2305462 AAAATAGTT
1 AAAATAGTT
2305471 GAAGCTCGTG
Statistics
Matches: 482, Mismatches: 85, Indels: 5
0.84 0.15 0.01
Matches are distributed among these distances:
70 467 0.97
71 15 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (70 bp):
AAAATAGTTAGCGAGAGCTCAAGCTCCCAACTGTGATCTTAAGGCTCGCAGGTTCAACACCGTAG
CCTCC
Found at i:2305194 original size:210 final size:210
Alignment explanation
Indices: 2304831--2305470 Score: 773
Period size: 210 Copynumber: 3.0 Consensus size: 210
2304821 TCTTCCCAAA
* * * ** * *
2304831 AAAATAGTTAGCGAGACCTCAATCTCTCACCTGTGATCTTAAGGCTTGTAGGTTCAATACTGCAG
1 AAAATAGTTAGCGAGAGCTCAAGCTCCCAAATGTGATCTTAAGGCTCGTAGGTTCAATACAGCAG
* * * * * * * *
2304896 CCTCCAAAATAGATAGCGAGAGCTTAAGTTCAC-AGCTATAATATTAAGGCTTGCATGTTCAACA
66 CCTCCAAAATAGTTAGCGAGAGCTCAAGCTC-CTAACTATGATCTTAAGGCTCGCAAGTTCAACA
* * * *
2304960 CCATAACCTCTAAAAAAATTAGCGAGAGCTCAAGCTCCCAACTGTGATTTTAAGGCTCGCAAGTT
130 CCATAACCTCTAAAAAAGTTAGCGAGAGCTCAAGCTCCCAGCTGTGATCTTAAGGCTCACAAGTT
*
2305025 CAACATCATAGCCTCC
195 CAACACCATAGCCTCC
* * *
2305041 AAAATAGTTAGTGAGAGCTCAAGCTCCCAAATGTGATCTTAAGGCTCGTAGGTTCAACACAGTAG
1 AAAATAGTTAGCGAGAGCTCAAGCTCCCAAATGTGATCTTAAGGCTCGTAGGTTCAATACAGCAG
* * *
2305106 CCTCCAAAATAGTTAGTGAGAGCTCAAGCTCCTAACTATGATCTTAAGGCTCACAGGTTCAACAC
66 CCTCCAAAATAGTTAGCGAGAGCTCAAGCTCCTAACTATGATCTTAAGGCTCGCAAGTTCAACAC
* * * * * *
2305171 CGTAGCCTCTAAAATAGTTAGCGATAGCTCAAGCTCCCAGTTGTGATCTTAAGGCTCACAGGTTC
131 CATAACCTCTAAAAAAGTTAGCGAGAGCTCAAGCTCCCAGCTGTGATCTTAAGGCTCACAAGTTC
*
2305236 AACACCTTAGCCTCC
196 AACACCATAGCCTCC
* ** * *
2305251 AAAATAGTTAGCAAGAGCTCAAGCTCCCAGTTGTGATCTTAAGGCTCGCAAGTTCAATACCA-CA
1 AAAATAGTTAGCGAGAGCTCAAGCTCCCAAATGTGATCTTAAGGCTCGTAGGTTCAATA-CAGCA
* * * *
2305315 ACCTCCAAAATAGTTAGCGAGAGCTCAAGCTCTTAGA-TCTGATCTTAAGGCTCGCAAGTTCAAT
65 GCCTCCAAAATAGTTAGCGAGAGCTCAAGCTCCTA-ACTATGATCTTAAGGCTCGCAAGTTCAAC
* * * *
2305379 ACCACAACCTCTAAAACAGTTAGCGAGAGCTCAAGCTCTCAGCTGTGATCTTAAGGCTCACAAAT
129 ACCATAACCTCTAAAAAAGTTAGCGAGAGCTCAAGCTCCCAGCTGTGATCTTAAGGCTCACAAGT
*** *
2305444 TCAAGCACTGCAGCCTTC
194 TCAA-CACCATAGCCTCC
2305462 AAAATAGTT
1 AAAATAGTT
2305471 GAAGCTCGTG
Statistics
Matches: 366, Mismatches: 60, Indels: 7
0.85 0.14 0.02
Matches are distributed among these distances:
209 1 0.00
210 344 0.94
211 21 0.06
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (210 bp):
AAAATAGTTAGCGAGAGCTCAAGCTCCCAAATGTGATCTTAAGGCTCGTAGGTTCAATACAGCAG
CCTCCAAAATAGTTAGCGAGAGCTCAAGCTCCTAACTATGATCTTAAGGCTCGCAAGTTCAACAC
CATAACCTCTAAAAAAGTTAGCGAGAGCTCAAGCTCCCAGCTGTGATCTTAAGGCTCACAAGTTC
AACACCATAGCCTCC
Found at i:2305574 original size:25 final size:25
Alignment explanation
Indices: 2305544--2305593 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
2305534 ATTTGCTTAA
2305544 GTTAAAATTTTGCTCAAGTTCACGG
1 GTTAAAATTTTGCTCAAGTTCACGG
2305569 GTTAAAATTTTGCTCAAGTTCACGG
1 GTTAAAATTTTGCTCAAGTTCACGG
2305594 AGAAATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (25 bp):
GTTAAAATTTTGCTCAAGTTCACGG
Found at i:2308654 original size:20 final size:20
Alignment explanation
Indices: 2308613--2308662 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
2308603 TGTCAATCCT
* *
2308613 ATGAATAGTGGGGTTAAGTC
1 ATGAATAGTGGAGTGAAGTC
2308633 ATGAATAGTGGAGTCGAA-TC
1 ATGAATAGTGGAGT-GAAGTC
*
2308653 ATGAACAGTG
1 ATGAATAGTG
2308663 ATAATATGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 24 0.92
21 2 0.08
ACGTcount: A:0.34, C:0.08, G:0.32, T:0.26
Consensus pattern (20 bp):
ATGAATAGTGGAGTGAAGTC
Found at i:2311867 original size:69 final size:69
Alignment explanation
Indices: 2311756--2311897 Score: 266
Period size: 69 Copynumber: 2.1 Consensus size: 69
2311746 TTTTTCGGGT
*
2311756 TAGTATACAACCCGTGTACATGGACGAGAAAAGCATACATACATGTTGCGCCTATCTGATAGGCT
1 TAGTATACAACCCGTGTACATAGACGAGAAAAGCATACATACATGTTGCGCCTATCTGATAGGCT
2311821 CAAC
66 CAAC
2311825 TAGTATACAACCCGTGTACATAGACGAGAAAAGCATACATACATGTTGCGCCTATCTGATAGGCT
1 TAGTATACAACCCGTGTACATAGACGAGAAAAGCATACATACATGTTGCGCCTATCTGATAGGCT
*
2311890 CAAG
66 CAAC
2311894 TAGT
1 TAGT
2311898 TGAGCCTATC
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 71 1.00
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (69 bp):
TAGTATACAACCCGTGTACATAGACGAGAAAAGCATACATACATGTTGCGCCTATCTGATAGGCT
CAAC
Found at i:2311924 original size:27 final size:27
Alignment explanation
Indices: 2311869--2311931 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
2311859 ATACATACAT
* * * *
2311869 GTTGCGCCTATCTGATAGGCTCAAGTA
1 GTTGAGCCTATCTGACAGGCACAACTA
*
2311896 GTTGAGCCTATCTGACAGGCACGACTA
1 GTTGAGCCTATCTGACAGGCACAACTA
*
2311923 GTTGTGCCT
1 GTTGAGCCT
2311932 TCTTGGTAGG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.21, C:0.24, G:0.27, T:0.29
Consensus pattern (27 bp):
GTTGAGCCTATCTGACAGGCACAACTA
Found at i:2315608 original size:33 final size:34
Alignment explanation
Indices: 2315571--2315648 Score: 99
Period size: 33 Copynumber: 2.4 Consensus size: 34
2315561 ATAAAATATG
*
2315571 GCGGTGGATATGGAC-CAGGAGGAGTAGAGTACA-
1 GCGGTGGATACGG-CTCAGGAGGAGTAGAGTACAT
* *
2315604 GCGGTGGATACGGCTCTGGAGGAGTTGAGTACAT
1 GCGGTGGATACGGCTCAGGAGGAGTAGAGTACAT
2315638 G-GGTGGATACG
1 GCGGTGGATACG
2315649 AGCCGGAAGG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
32 1 0.03
33 38 0.95
34 1 0.03
ACGTcount: A:0.24, C:0.13, G:0.44, T:0.19
Consensus pattern (34 bp):
GCGGTGGATACGGCTCAGGAGGAGTAGAGTACAT
Found at i:2315844 original size:12 final size:12
Alignment explanation
Indices: 2315819--2315853 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2315809 AGAGTGTAGT
*
2315819 TCCGGCTTTGGC
1 TCCGGCTCTGGC
*
2315831 TCCTGCTCTGGC
1 TCCGGCTCTGGC
2315843 TCCGGCTCTGG
1 TCCGGCTCTGG
2315854 TGCATGATGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.37, G:0.31, T:0.31
Consensus pattern (12 bp):
TCCGGCTCTGGC
Found at i:2318191 original size:116 final size:116
Alignment explanation
Indices: 2317806--2318253 Score: 728
Period size: 115 Copynumber: 3.9 Consensus size: 116
2317796 ATACTAACAC
* *
2317806 AAAATAACTATAAAATTA-TTTTTTTAAAATAAATTACTAAAAAAAATCACAATACACTAATACA
1 AAAATAGCTATAAAATTATTTTTTTTAAAATATATTACTAAAAAAAATCACAATACACTAATACA
2317870 CACTAAACCACTAAACACTAACAA--TATATAACCTAATCTTAAATTACTAAT
66 C-C-AAACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAAT
*
2317921 AAAATAGCTATAAAAATATTTTTTTT-AAATATATTACTAAAAAAAATCACAATACACTAATACA
1 AAAATAGCTATAAAATTATTTTTTTTAAAATATATTACTAAAAAAAATCACAATACACTAATACA
* * *
2317985 CTAAACCACTAAACACTAACAATTTATATAATCTAACCTTAAATTACTAAT
66 CCAAACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAAT
* * *
2318036 AAAATAGCTATAAAACTATTTTTTTTTAAATATATTACT-AAAAAAATTACAATACACTAATACA
1 AAAATAGCTATAAAATTATTTTTTTTAAAATATATTACTAAAAAAAATCACAATACACTAATACA
2318100 CCAAACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAAT
66 CCAAACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAAT
2318151 AAAATAGCTATAAAATTATTTTTTTTAAAAATATATTACT-AAAAAAATCACAATACACTAATAC
1 AAAATAGCTATAAAATTATTTTTTTT-AAAATATATTACTAAAAAAAATCACAATACACTAATAC
* *
2318215 ACTAAACTACTAAACACTAACAATTTATATAACCTAATC
65 ACCAAACCACTAAACACTAACAATTTATATAACCTAATC
2318254 AACTATAAAA
Statistics
Matches: 312, Mismatches: 16, Indels: 9
0.93 0.05 0.03
Matches are distributed among these distances:
113 20 0.06
115 201 0.64
116 91 0.29
ACGTcount: A:0.52, C:0.16, G:0.01, T:0.32
Consensus pattern (116 bp):
AAAATAGCTATAAAATTATTTTTTTTAAAATATATTACTAAAAAAAATCACAATACACTAATACA
CCAAACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAAT
Found at i:2318528 original size:3 final size:3
Alignment explanation
Indices: 2318522--2318598 Score: 102
Period size: 3 Copynumber: 25.3 Consensus size: 3
2318512 TTACCCTTTT
*
2318522 TTC TTC TTC TTC TTC TT- TTC TTT TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* *
2318569 TTCC TTC TTC TTCC TTC TTT TTC TCC TTC T
1 TT-C TTC TTC TT-C TTC TTC TTC TTC TTC T
2318599 CCTTTCTCTC
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
2 2 0.03
3 57 0.88
4 6 0.09
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:2318563 original size:32 final size:33
Alignment explanation
Indices: 2318522--2318604 Score: 107
Period size: 32 Copynumber: 2.6 Consensus size: 33
2318512 TTACCCTTTT
* *
2318522 TTCTTCTTCTTCTTCTTTTCTTTTTCTT-CTTC
1 TTCTTCTTCTTCTTCTTTCCTTCTTCTTCCTTC
2318554 TTCTTCTTCTTCTTC-TTCCTTCTTCTTCCTTC
1 TTCTTCTTCTTCTTCTTTCCTTCTTCTTCCTTC
* * *
2318586 TTTTTCTCCTTCTCCTTTC
1 TTCTTCTTCTTCTTCTTTC
2318605 TCTCCTTTCT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
31 10 0.23
32 31 0.70
33 3 0.07
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (33 bp):
TTCTTCTTCTTCTTCTTTCCTTCTTCTTCCTTC
Found at i:2318821 original size:27 final size:27
Alignment explanation
Indices: 2318783--2318834 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
2318773 AGGTGGGGGT
*
2318783 GTCGTGCCTACCTGTCAGGCACGACTA
1 GTCGTGCCTACCTGACAGGCACGACTA
*
2318810 GTCGTGCCTACCTGACAGGCTCGAC
1 GTCGTGCCTACCTGACAGGCACGAC
2318835 CCGTTTCGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.17, C:0.35, G:0.27, T:0.21
Consensus pattern (27 bp):
GTCGTGCCTACCTGACAGGCACGACTA
Found at i:2319656 original size:24 final size:22
Alignment explanation
Indices: 2319613--2319662 Score: 73
Period size: 24 Copynumber: 2.2 Consensus size: 22
2319603 TGTTATAAAA
*
2319613 ATTAATTAATATAATTAAACCT
1 ATTAATTAATAAAATTAAACCT
2319635 ATTAATTATATAAAAATTAAACCT
1 ATTAATTA-AT-AAAATTAAACCT
2319659 ATTA
1 ATTA
2319663 CTCAAATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 8 0.32
23 2 0.08
24 15 0.60
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (22 bp):
ATTAATTAATAAAATTAAACCT
Found at i:2319690 original size:36 final size:37
Alignment explanation
Indices: 2319592--2319728 Score: 99
Period size: 36 Copynumber: 3.8 Consensus size: 37
2319582 CGGAGTGGCC
*
2319592 CAAATATATTATGTTATAAAAATT-AATTAATATAAT
1 CAAATATATTATGTTATAAAAATTAAACTAATATAAT
* ** *
2319628 TAAACCTATTAAT-TATATAAAAATTAAACCT-AT-TACT
1 CAAATATATT-ATGT-TATAAAAATTAAA-CTAATATAAT
*
2319665 CAAATATATTATGTTATAAAAATT-AA-TTATATAAT
1 CAAATATATTATGTTATAAAAATTAAACTAATATAAT
* * *
2319700 TAAATCTATTAAT-TATATAACAATTAAAC
1 CAAATATATT-ATGT-TATAAAAATTAAAC
2319729 CTATTACCCA
Statistics
Matches: 78, Mismatches: 12, Indels: 20
0.71 0.11 0.18
Matches are distributed among these distances:
33 1 0.01
34 2 0.03
35 14 0.18
36 31 0.40
37 25 0.32
38 4 0.05
39 1 0.01
ACGTcount: A:0.51, C:0.07, G:0.01, T:0.40
Consensus pattern (37 bp):
CAAATATATTATGTTATAAAAATTAAACTAATATAAT
Found at i:2319725 original size:72 final size:73
Alignment explanation
Indices: 2319590--2319740 Score: 268
Period size: 72 Copynumber: 2.1 Consensus size: 73
2319580 CCCGGAGTGG
2319590 CCCAAATATATTATGTTATAAAAATTAATTAATATAATTAAACCTATTAATTATATAAAAATTAA
1 CCCAAATATATTATGTTATAAAAATTAATTAATATAATTAAACCTATTAATTATATAAAAATTAA
2319655 ACCTATTA
66 ACCTATTA
* * *
2319663 CTCAAATATATTATGTTATAAAAATTAATT-ATATAATTAAATCTATTAATTATATAACAATTAA
1 CCCAAATATATTATGTTATAAAAATTAATTAATATAATTAAACCTATTAATTATATAAAAATTAA
2319727 ACCTATTA
66 ACCTATTA
2319735 CCCAAA
1 CCCAAA
2319741 ACCTAAAAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
72 45 0.61
73 29 0.39
ACGTcount: A:0.50, C:0.11, G:0.01, T:0.38
Consensus pattern (73 bp):
CCCAAATATATTATGTTATAAAAATTAATTAATATAATTAAACCTATTAATTATATAAAAATTAA
ACCTATTA
Found at i:2319984 original size:34 final size:34
Alignment explanation
Indices: 2319941--2320008 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
2319931 AAAGGAATAG
*
2319941 GATGACATGAAATCACAATTTCATATAATCTTTT
1 GATGACATGAAATCACAATTTCACATAATCTTTT
*
2319975 GATGACATGAAATTACAATTTCACATAATCTTTT
1 GATGACATGAAATCACAATTTCACATAATCTTTT
2320009 CTCCCCAAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (34 bp):
GATGACATGAAATCACAATTTCACATAATCTTTT
Found at i:2331884 original size:31 final size:31
Alignment explanation
Indices: 2331849--2331913 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
2331839 GTTTGGGTTA
* * *
2331849 CAAATTGAATGTTGAAGCCAAACTT-AGGTAC
1 CAAATTGAATATTGAA-ACAAAATTCAGGTAC
2331880 CAAATTGAATATTGAAACAAAATTCAGGTAC
1 CAAATTGAATATTGAAACAAAATTCAGGTAC
2331911 CAA
1 CAA
2331914 GTGGTATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 6 0.20
31 24 0.80
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (31 bp):
CAAATTGAATATTGAAACAAAATTCAGGTAC
Found at i:2332067 original size:22 final size:22
Alignment explanation
Indices: 2332042--2332097 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
2332032 TTAGGAAGAC
**
2332042 TTTAAAATTTAAAATCATTCTT
1 TTTAAAAAGTAAAATCATTCTT
2332064 TTTAAAAAGTAAAATCATTCTT
1 TTTAAAAAGTAAAATCATTCTT
*
2332086 TTCAAAAAGTAA
1 TTTAAAAAGTAA
2332098 CATATATAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (22 bp):
TTTAAAAAGTAAAATCATTCTT
Found at i:2336850 original size:6 final size:5
Alignment explanation
Indices: 2336814--2336850 Score: 56
Period size: 5 Copynumber: 7.2 Consensus size: 5
2336804 ATATCTTGAG
*
2336814 AAATA AAAAA AAATA AAATA AAATA AAATA AACATA A
1 AAATA AAATA AAATA AAATA AAATA AAATA AA-ATA A
2336851 CTTTTTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 25 0.86
6 4 0.14
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (5 bp):
AAATA
Found at i:2340478 original size:2 final size:2
Alignment explanation
Indices: 2340471--2340495 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2340461 TATAATTGCT
2340471 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 T
2340496 TCCCCTCCAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2341867 original size:13 final size:14
Alignment explanation
Indices: 2341849--2341881 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
2341839 CAAAAACAAC
2341849 TTAATAAG-CTTAA
1 TTAATAAGACTTAA
2341862 TTAAT-AGACTTAA
1 TTAATAAGACTTAA
2341875 TTAATAA
1 TTAATAA
2341882 ACAAATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 2 0.11
13 15 0.83
14 1 0.06
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (14 bp):
TTAATAAGACTTAA
Found at i:2341907 original size:28 final size:28
Alignment explanation
Indices: 2341872--2341936 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
2341862 TTAATAGACT
**
2341872 TAATTAATAAACAAATTTAATGCTTAAC
1 TAATTAATAAACAAATTTAACACTTAAC
* *
2341900 TAATTAATAACCACATTTAACACTTAAC
1 TAATTAATAAACAAATTTAACACTTAAC
2341928 TAACTTAAT
1 TAA-TTAAT
2341937 TAATAAACTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 27 0.84
29 5 0.16
ACGTcount: A:0.48, C:0.15, G:0.02, T:0.35
Consensus pattern (28 bp):
TAATTAATAAACAAATTTAACACTTAAC
Found at i:2352508 original size:19 final size:17
Alignment explanation
Indices: 2352484--2352530 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 17
2352474 AATTAAAGTA
*
2352484 ATAAAAAATAATACTATAT
1 ATAAAAAAT-ATA-TATAC
*
2352503 ATAAAATATATATATAC
1 ATAAAAAATATATATAC
2352520 AT-AAAAATATA
1 ATAAAAAATATA
2352531 CACTAATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 8 0.32
17 6 0.24
18 3 0.12
19 8 0.32
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (17 bp):
ATAAAAAATATATATAC
Found at i:2352526 original size:18 final size:19
Alignment explanation
Indices: 2352487--2352535 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 19
2352477 TAAAGTAATA
*
2352487 AAAAATA-ATACTATATAT
1 AAAAATATATACTATACAT
2352505 -AAAATATATA-TATACAT
1 AAAAATATATACTATACAT
*
2352522 AAAAATATACACTA
1 AAAAATATATACTA
2352536 ATATATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 12 0.46
18 12 0.46
19 2 0.08
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAAATATATACTATACAT
Found at i:2352762 original size:3 final size:3
Alignment explanation
Indices: 2352749--2352834 Score: 60
Period size: 3 Copynumber: 29.3 Consensus size: 3
2352739 GAGGGCATAT
2352749 ATA AT- ATA ATA ATA AT- ATA A-A A-A ATA ATA TATA CATGA GA-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA -AT-A -ATA ATA
* *
2352793 ATA ATA ATA AT- ATAA ATA ATA GTA AAA ATA ATA A-A ATA ATA A
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2352835 AACAAAGCTC
Statistics
Matches: 68, Mismatches: 6, Indels: 18
0.74 0.07 0.20
Matches are distributed among these distances:
2 13 0.19
3 46 0.68
4 7 0.10
5 2 0.03
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:2352775 original size:18 final size:18
Alignment explanation
Indices: 2352754--2352834 Score: 76
Period size: 18 Copynumber: 4.4 Consensus size: 18
2352744 CATATATAAT
2352754 ATAATAATAATATAAAAA
1 ATAATAATAATATAAAAA
* *
2352772 ATAATATATACATGAGAAATA
1 ATAATA-ATA-AT-ATAAAAA
*
2352793 ATAATAATAATATAAATA
1 ATAATAATAATATAAAAA
*
2352811 ATAGTAA-AA-ATAATAAA
1 ATAATAATAATATAA-AAA
2352828 ATAATAA
1 ATAATAA
2352835 AACAAAGCTC
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
16 4 0.08
17 10 0.19
18 18 0.34
19 5 0.09
20 5 0.09
21 11 0.21
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.28
Consensus pattern (18 bp):
ATAATAATAATATAAAAA
Found at i:2353689 original size:21 final size:21
Alignment explanation
Indices: 2353665--2353729 Score: 51
Period size: 21 Copynumber: 3.1 Consensus size: 21
2353655 TCCACTGAAA
2353665 CTTCAAGGAGATCTGCTGTAG
1 CTTCAAGGAGATCTGCTGTAG
* ** ** * *
2353686 CTTCGATTA-ATCCACTGAAA
1 CTTCAAGGAGATCTGCTGTAG
*
2353706 CTTCAAGGAGATCTGCTGTGG
1 CTTCAAGGAGATCTGCTGTAG
2353727 CTT
1 CTT
2353730 TTAGCTGCTC
Statistics
Matches: 28, Mismatches: 15, Indels: 2
0.62 0.33 0.04
Matches are distributed among these distances:
20 13 0.46
21 15 0.54
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.31
Consensus pattern (21 bp):
CTTCAAGGAGATCTGCTGTAG
Found at i:2353979 original size:43 final size:43
Alignment explanation
Indices: 2353777--2354120 Score: 204
Period size: 44 Copynumber: 7.9 Consensus size: 43
2353767 GATTTTCAAC
* * *
2353777 CTGTTACCCTACTGCTTAGGGGGTTAAG-GCTTGT-CATTATTGAT
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATC-TGTAAATT-TAG-T
* * * * * **
2353821 CTGTTTCCCTACTGCTTAGGTGTTTAAGATCTTGTAAAATCAAC
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATC-TGTAAATTTAGT
* * * *
2353865 CTGTTACCCTACTGCTTAGGGGTTTAAGGCTCATCG--CA-TTCGAT
1 CTGTTACCCTACTGCTTAGGGGGTTAA-GATC-T-GTAAATTTAG-T
*
2353909 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATTTAGT
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTTAGT
* ** * * *
2353952 CTGTTACCCTACTGCTTCGGGTTTTAAGA-CT-CATCATCTTCAAT
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTA-AAT-TT-AGT
* * *
2353996 CTGCTT-CCCTACTGCTTAGGGGGTTGAGGTCTGTAAATTTAGC
1 CTG-TTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTTAGT
* * * *
2354039 CTGTTACCCTACTGCTTAGGGGTTTAAGA-CT-CATCATCTTCAAT
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTA-AAT-TT-AGT
* * *
2354083 CTGTTTCTCTACTGCTTAGGGGGTTGAGATCTGTAAAT
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAAT
2354121 CTTCAATCTG
Statistics
Matches: 227, Mismatches: 53, Indels: 39
0.71 0.17 0.12
Matches are distributed among these distances:
41 3 0.01
42 11 0.05
43 59 0.26
44 130 0.57
45 19 0.08
46 5 0.02
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (43 bp):
CTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTTAGT
Found at i:2353985 original size:87 final size:87
Alignment explanation
Indices: 2353776--2354120 Score: 451
Period size: 87 Copynumber: 4.0 Consensus size: 87
2353766 TGATTTTCAA
* * ** **
2353776 CCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTCAT-TATTGATCTGTTTCCCTACTGCTTAG
1 CCTGTTACCCTACTGCTTAGGGGTTTAAGACTCATCATCT-TCAATCTGTTTCCCTACTGCTTAG
* * * * *
2353840 GTGTTTAAGATCTTGTAAAATCAA
65 GGGGTTAAGATC-TGTAAATTTAG
* * *
2353864 CCTGTTACCCTACTGCTTAGGGGTTTAAGGCTCATC-GCATTCGATCTGTTTCCCTACTGCTTAG
1 CCTGTTACCCTACTGCTTAGGGGTTTAAGACTCATCATC-TTCAATCTGTTTCCCTACTGCTTAG
2353928 GGGGTTAAGATCTGTAAATTTAG
65 GGGGTTAAGATCTGTAAATTTAG
* * * *
2353951 TCTGTTACCCTACTGCTTCGGGTTTTAAGACTCATCATCTTCAATCTGCTTCCCTACTGCTTAGG
1 CCTGTTACCCTACTGCTTAGGGGTTTAAGACTCATCATCTTCAATCTGTTTCCCTACTGCTTAGG
* *
2354016 GGGTTGAGGTCTGTAAATTTAG
66 GGGTTAAGATCTGTAAATTTAG
*
2354038 CCTGTTACCCTACTGCTTAGGGGTTTAAGACTCATCATCTTCAATCTGTTTCTCTACTGCTTAGG
1 CCTGTTACCCTACTGCTTAGGGGTTTAAGACTCATCATCTTCAATCTGTTTCCCTACTGCTTAGG
*
2354103 GGGTTGAGATCTGTAAAT
66 GGGTTAAGATCTGTAAAT
2354121 CTTCAATCTG
Statistics
Matches: 229, Mismatches: 25, Indels: 7
0.88 0.10 0.03
Matches are distributed among these distances:
87 161 0.70
88 67 0.29
89 1 0.00
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.37
Consensus pattern (87 bp):
CCTGTTACCCTACTGCTTAGGGGTTTAAGACTCATCATCTTCAATCTGTTTCCCTACTGCTTAGG
GGGTTAAGATCTGTAAATTTAG
Found at i:2354363 original size:88 final size:86
Alignment explanation
Indices: 2354259--2354432 Score: 233
Period size: 88 Copynumber: 2.0 Consensus size: 86
2354249 TGTAAATTTG
* ** *
2354259 GCTTGTTACCCTACTGCTTAGGGGGCTAAAGCTCATTATTTTCGATCTATTTCCCTAATGCTTA-
1 GCTTGTTACCCTACTGCTTAGAGGGCTAAAGCTCATTACCTTCGATCTATTCCCCTAATGCTTAT
2354323 GGGTGATAAGATCTATGAACTTCA
66 GGG-G-TAAGATCTATGAA-TTCA
* * * *
2354347 GCTTGTTACCCTACTGCTTAGAGGGTTAAAGCTCGTTGCCTTCGATCTATTCCCCTACTGCTTAT
1 GCTTGTTACCCTACTGCTTAGAGGGCTAAAGCTCATTACCTTCGATCTATTCCCCTAATGCTTAT
*
2354412 GGGGTAAGATCTGTGAATTCA
66 GGGGTAAGATCTATGAATTCA
2354433 CTGATTCTAG
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
86 4 0.05
87 12 0.16
88 57 0.75
89 3 0.04
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.36
Consensus pattern (86 bp):
GCTTGTTACCCTACTGCTTAGAGGGCTAAAGCTCATTACCTTCGATCTATTCCCCTAATGCTTAT
GGGGTAAGATCTATGAATTCA
Found at i:2362494 original size:19 final size:20
Alignment explanation
Indices: 2362470--2362516 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
2362460 AGAGAAAGTT
2362470 TAATGCAAATGT-TGCAATG
1 TAATGCAAATGTATGCAATG
*
2362489 TAATGCAAATGTATGGAATG
1 TAATGCAAATGTATGCAATG
2362509 -AATGCAAA
1 TAATGCAAA
2362517 AGAAAGGAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 20 0.77
20 6 0.23
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.28
Consensus pattern (20 bp):
TAATGCAAATGTATGCAATG
Found at i:2364966 original size:12 final size:12
Alignment explanation
Indices: 2364951--2364980 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2364941 ACAATAATAC
2364951 TATATATAAATG
1 TATATATAAATG
*
2364963 TATATATATATG
1 TATATATAAATG
2364975 TATATA
1 TATATA
2364981 ATAGAAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (12 bp):
TATATATAAATG
Done.