Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008645.1 Hibiscus syriacus cultivar Beakdansim tig00111621_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: 4138222
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 22
Found at i:1956670 original size:27 final size:24
Alignment explanation
Indices: 1956618--1956676 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 24
1956608 ATTATGTTAT
*
1956618 TTTAATTTTTTGAATATTTTTTAA
1 TTTAATTTTTTGAATATTTTTAAA
*
1956642 TTTAATATTTTTTAATATTATTTCAAA
1 TTTAAT-TTTTTGAATATT-TTT-AAA
1956669 TTTTAATT
1 -TTTAATT
1956677 CGTAGAATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
24 6 0.21
25 11 0.38
26 3 0.10
27 3 0.10
28 6 0.21
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (24 bp):
TTTAATTTTTTGAATATTTTTAAA
Found at i:1957713 original size:21 final size:21
Alignment explanation
Indices: 1957659--1957713 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
1957649 GAATATATAT
* *
1957659 CGAGCCCGCAGGATTACATTC
1 CGAGCCCGAAGGGTTACATTC
* *
1957680 TGAGCTCGAAGGGTTACATTC
1 CGAGCCCGAAGGGTTACATTC
*
1957701 CGAGCCCGTAGGG
1 CGAGCCCGAAGGG
1957714 CTTTATGATA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.22, C:0.27, G:0.31, T:0.20
Consensus pattern (21 bp):
CGAGCCCGAAGGGTTACATTC
Found at i:1959721 original size:21 final size:20
Alignment explanation
Indices: 1959697--1959753 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 20
1959687 CCTTCATGAA
*
1959697 TACATATCGAGCCCGCAGGAT
1 TACAT-TCGAGCCCGAAGGAT
* * *
1959718 TACATTTTGAGCTCGAAGGGT
1 TACA-TTCGAGCCCGAAGGAT
1959739 TACATTCCGAGCCCG
1 TACATT-CGAGCCCG
1959754 TAGGGCTTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
20 2 0.07
21 25 0.89
22 1 0.04
ACGTcount: A:0.25, C:0.26, G:0.25, T:0.25
Consensus pattern (20 bp):
TACATTCGAGCCCGAAGGAT
Found at i:1959758 original size:21 final size:21
Alignment explanation
Indices: 1959704--1959758 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
1959694 GAATACATAT
* * *
1959704 CGAGCCCGCAGGATTACATTT
1 CGAGCCCGAAGGGTTACATTC
* *
1959725 TGAGCTCGAAGGGTTACATTC
1 CGAGCCCGAAGGGTTACATTC
*
1959746 CGAGCCCGTAGGG
1 CGAGCCCGAAGGG
1959759 CTTTATGATA
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.22, C:0.25, G:0.31, T:0.22
Consensus pattern (21 bp):
CGAGCCCGAAGGGTTACATTC
Found at i:1961171 original size:8 final size:8
Alignment explanation
Indices: 1961160--1961193 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
1961150 TGCTCTTGAT
1961160 CTCTCAAA
1 CTCTCAAA
1961168 CTCTCAAA
1 CTCTCAAA
* *
1961176 CCCTCACA
1 CTCTCAAA
1961184 CTCTCAAA
1 CTCTCAAA
1961192 CT
1 CT
1961194 ATTAAACTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.32, C:0.44, G:0.00, T:0.24
Consensus pattern (8 bp):
CTCTCAAA
Found at i:1961895 original size:82 final size:82
Alignment explanation
Indices: 1961747--1961905 Score: 239
Period size: 82 Copynumber: 1.9 Consensus size: 82
1961737 TAATACTCAT
* ** *
1961747 ATGAAAAATTCACAAGCTATTACAGAAATGTATGCCACATTTGTTGATGTTCGTGTGATTCGTGG
1 ATGAAAAATTCACAAGCTATTACAGAAATGTATGCCACATTTGTTGATGTTCATGCAATTCATGG
*
1961812 TATGTTATTATGGTCAG
66 TATGTCATTATGGTCAG
**
1961829 ATGAAAAATTCACTTGCTATTACAGAAATGTATGCCACATTTGTTGA-GATTCATGCAATTCATG
1 ATGAAAAATTCACAAGCTATTACAGAAATGTATGCCACATTTGTTGATG-TTCATGCAATTCATG
1961893 GTATGTCATTATG
65 GTATGTCATTATG
1961906 CTCTCACTAT
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
81 1 0.01
82 68 0.99
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.36
Consensus pattern (82 bp):
ATGAAAAATTCACAAGCTATTACAGAAATGTATGCCACATTTGTTGATGTTCATGCAATTCATGG
TATGTCATTATGGTCAG
Found at i:1963141 original size:24 final size:23
Alignment explanation
Indices: 1963114--1963165 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
1963104 AAAAAAACTA
*
1963114 AAACACTTTAACCTAAAAAACCCT
1 AAACACTTCAACCT-AAAAACCCT
*
1963138 AAACCACTTCAACCTAAAAACCTT
1 AAA-CACTTCAACCTAAAAACCCT
1963162 AAAC
1 AAAC
1963166 CATTATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 1 0.04
24 14 0.56
25 10 0.40
ACGTcount: A:0.50, C:0.31, G:0.00, T:0.19
Consensus pattern (23 bp):
AAACACTTCAACCTAAAAACCCT
Found at i:1963166 original size:24 final size:25
Alignment explanation
Indices: 1963102--1963167 Score: 80
Period size: 25 Copynumber: 2.7 Consensus size: 25
1963092 AAACCATTTT
** * *
1963102 TAAAAAAAACTAAAACACTTTAACC
1 TAAAAAACCCTAAACCACTTCAACC
1963127 TAAAAAACCCTAAACCACTTCAACC
1 TAAAAAACCCTAAACCACTTCAACC
*
1963152 T-AAAAACCTTAAACCA
1 TAAAAAACCCTAAACCA
1963168 TTATAAAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
24 14 0.39
25 22 0.61
ACGTcount: A:0.55, C:0.27, G:0.00, T:0.18
Consensus pattern (25 bp):
TAAAAAACCCTAAACCACTTCAACC
Found at i:1966960 original size:41 final size:42
Alignment explanation
Indices: 1966915--1967001 Score: 158
Period size: 42 Copynumber: 2.1 Consensus size: 42
1966905 TAGAAAATAG
*
1966915 AAATATAATAATAAGGATAT-AAAGTCATTTTATATTTATAA
1 AAATATAATAATAAAGATATAAAAGTCATTTTATATTTATAA
1966956 AAATATAATAATAAAGATATAAAAGTCATTTTATATTTATAA
1 AAATATAATAATAAAGATATAAAAGTCATTTTATATTTATAA
1966998 AAAT
1 AAAT
1967002 TCATGCATTT
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 19 0.43
42 25 0.57
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (42 bp):
AAATATAATAATAAAGATATAAAAGTCATTTTATATTTATAA
Found at i:1967153 original size:18 final size:18
Alignment explanation
Indices: 1967130--1967165 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1967120 ACAATGGAAA
1967130 GGAAAGGAAAGTTAACTT
1 GGAAAGGAAAGTTAACTT
1967148 GGAAAGGAAAGTTAACTT
1 GGAAAGGAAAGTTAACTT
1967166 ACTTTCCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.06, G:0.28, T:0.22
Consensus pattern (18 bp):
GGAAAGGAAAGTTAACTT
Found at i:1973736 original size:3 final size:3
Alignment explanation
Indices: 1973723--1973819 Score: 97
Period size: 3 Copynumber: 30.3 Consensus size: 3
1973713 ATTGGGTTTG
* * *
1973723 TAA TAAA TAA TAA TAA TAA TATT TTA TAA TAAA TAA TAA TAA TAA TTTA
1 TAA T-AA TAA TAA TAA TAA TA-A TAA TAA T-AA TAA TAA TAA TAA -TAA
1973772 TAA TAAA TAA TAA TAA TAA TATA TAA TAA TAA TAAA TAA TAA T-A TAA
1 TAA T-AA TAA TAA TAA TAA TA-A TAA TAA TAA T-AA TAA TAA TAA TAA
1973819 T
1 T
1973820 GGTTGAAAAA
Statistics
Matches: 80, Mismatches: 6, Indels: 16
0.78 0.06 0.16
Matches are distributed among these distances:
2 2 0.03
3 60 0.75
4 18 0.22
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:1973757 original size:23 final size:23
Alignment explanation
Indices: 1973731--1973814 Score: 134
Period size: 23 Copynumber: 3.7 Consensus size: 23
1973721 TGTAATAAAT
*
1973731 AATAATAATAATATTTTATAATA
1 AATAATAATAATAATTTATAATA
1973754 AATAATAATAATAATTTATAATA
1 AATAATAATAATAATTTATAATA
*
1973777 AATAATAATAATAATATATAAT-
1 AATAATAATAATAATTTATAATA
1973799 AATAATAAATAATAAT
1 AATAAT-AATAATAAT
1973815 ATAATGGTTG
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
22 6 0.10
23 52 0.90
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
AATAATAATAATAATTTATAATA
Found at i:1973758 original size:26 final size:26
Alignment explanation
Indices: 1973723--1973815 Score: 131
Period size: 26 Copynumber: 3.7 Consensus size: 26
1973713 ATTGGGTTTG
1973723 TAATAAATAATAATAATAATATTTTA
1 TAATAAATAATAATAATAATATTTTA
1973749 TAATAAATAATAATAAT-A-A-TTTA
1 TAATAAATAATAATAATAATATTTTA
* *
1973772 TAATAAATAATAATAATAATATATAA
1 TAATAAATAATAATAATAATATTTTA
1973798 TAAT-AATAAATAATAATA
1 TAATAAAT-AATAATAATA
1973816 TAATGGTTGA
Statistics
Matches: 61, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
23 21 0.34
24 2 0.03
25 5 0.08
26 33 0.54
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (26 bp):
TAATAAATAATAATAATAATATTTTA
Found at i:1974337 original size:118 final size:118
Alignment explanation
Indices: 1974111--1974409 Score: 436
Period size: 118 Copynumber: 2.5 Consensus size: 118
1974101 TCGGTGTTGT
* * * * * *
1974111 TCCAACTCCTTATGTGATGGAATTGAGCTAAAGTTGAATAAGTTCTTCTCATTATGAAATTTTTC
1 TCCACCTCCTTCTATGATGGAATTGAGCTAAGGTTGAATAAGTTCTTCTCATTATGAACTTCTTC
* *
1974176 TCCCTCATTGGATAAGTTCTTCTTATTACAAACCCTTCCATTGGAAATATTGA
66 TCCCTCATCGGATAAGTTCTTCTCATTACAAACCCTTCCATTGGAAATATTGA
* * * * *
1974229 TTCACCTTCTTCTATGATGGAATCGAGCTGAGGTTGAATAAGTTCTTCTCATTACGAACTTCTTC
1 TCCACCTCCTTCTATGATGGAATTGAGCTAAGGTTGAATAAGTTCTTCTCATTATGAACTTCTTC
* * * *
1974294 TCCCTTATCGGATAAGTTCTTCTCATTATAAACCCTTCTATTGGAAATGTTGA
66 TCCCTCATCGGATAAGTTCTTCTCATTACAAACCCTTCCATTGGAAATATTGA
*
1974347 TCCACCTCCTTCTATGATGGAATTGAGCTAAGGTTGAATAAGTTCTTCTTATTATGAACTTCT
1 TCCACCTCCTTCTATGATGGAATTGAGCTAAGGTTGAATAAGTTCTTCTCATTATGAACTTCT
1974410 GAACCTTTCC
Statistics
Matches: 158, Mismatches: 23, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
118 158 1.00
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (118 bp):
TCCACCTCCTTCTATGATGGAATTGAGCTAAGGTTGAATAAGTTCTTCTCATTATGAACTTCTTC
TCCCTCATCGGATAAGTTCTTCTCATTACAAACCCTTCCATTGGAAATATTGA
Found at i:1974479 original size:87 final size:87
Alignment explanation
Indices: 1974324--1974496 Score: 292
Period size: 87 Copynumber: 2.0 Consensus size: 87
1974314 TCTCATTATA
* *
1974324 AACCCTTCTATTGGAAATGTTGATCCACCTCCTTCTATGATGGAATTGAGCTAAGGTTGAATAAG
1 AACCCTTCCATTGGAAATGTTGATCCACCTCCTTCTATGATGGAATTGAGCGAAGGTTGAATAAG
*
1974389 TTCTTCTTATTATGAACTTCTG
66 TTCTTCTCATTATGAACTTCTG
* * *
1974411 AACCTTTCCATTGGAAATGTTGATCCACCTCCTTTTGTGATGGAATTGAGCGAAGGTTGAATAAG
1 AACCCTTCCATTGGAAATGTTGATCCACCTCCTTCTATGATGGAATTGAGCGAAGGTTGAATAAG
1974476 TTCTTCTCATTATGAACTTCT
66 TTCTTCTCATTATGAACTTCT
1974497 TCTCCCCTAT
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 80 1.00
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (87 bp):
AACCCTTCCATTGGAAATGTTGATCCACCTCCTTCTATGATGGAATTGAGCGAAGGTTGAATAAG
TTCTTCTCATTATGAACTTCTG
Found at i:1979058 original size:15 final size:15
Alignment explanation
Indices: 1979035--1979075 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1979025 GAAGTAAGAG
*
1979035 TATCGATACCAGGGA
1 TATCAATACCAGGGA
*
1979050 TATCAATACCAGGGG
1 TATCAATACCAGGGA
*
1979065 TATCAGTACCA
1 TATCAATACCA
1979076 TTTTTGCAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (15 bp):
TATCAATACCAGGGA
Found at i:1979779 original size:32 final size:32
Alignment explanation
Indices: 1979743--1979813 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
1979733 TGAATGTGTA
1979743 TATGTGACAAATATAAATGATAATACCCATGT
1 TATGTGACAAATATAAATGATAATACCCATGT
* *
1979775 TATGTGACAAATATAAATGATAATGCTCATGT
1 TATGTGACAAATATAAATGATAATACCCATGT
1979807 TATGTGA
1 TATGTGA
1979814 TATGAGAGCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (32 bp):
TATGTGACAAATATAAATGATAATACCCATGT
Found at i:1979991 original size:22 final size:21
Alignment explanation
Indices: 1979961--1980041 Score: 74
Period size: 23 Copynumber: 3.7 Consensus size: 21
1979951 CCTTAAGGAG
*
1979961 TGGTCTTTCGGGACATCTATA
1 TGGTCCTTCGGGACATCTATA
* * *
1979982 TGGTCCTTTCAGGG-GATATATG
1 TGGTCC-TTC-GGGACATCTATA
*
1980004 TGGTCCTTCGGGACATCTCTA
1 TGGTCCTTCGGGACATCTATA
1980025 CGTGGTCCTTCGGGACA
1 --TGGTCCTTCGGGACA
1980042 AAATCTATGT
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
20 3 0.06
21 12 0.26
22 14 0.30
23 18 0.38
ACGTcount: A:0.16, C:0.22, G:0.28, T:0.33
Consensus pattern (21 bp):
TGGTCCTTCGGGACATCTATA
Found at i:1981227 original size:14 final size:14
Alignment explanation
Indices: 1981208--1981289 Score: 69
Period size: 14 Copynumber: 5.7 Consensus size: 14
1981198 AAGTCAACGG
1981208 GTTGACTCAGACGA
1 GTTGACTCAGACGA
* *
1981222 GTTGACTCGGATGA
1 GTTGACTCAGACGA
*
1981236 GTTGACT-GGATCTGA
1 GTTGACTCAGA-C-GA
*
1981251 GTTGACT-GGATCTGA
1 GTTGACTCAGA-C-GA
*
1981266 GTTGACTCAGGCGA
1 GTTGACTCAGACGA
1981280 GTTGACTCAG
1 GTTGACTCAG
1981290 TTCAGACTGG
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
13 3 0.05
14 31 0.52
15 25 0.42
16 1 0.02
ACGTcount: A:0.22, C:0.17, G:0.33, T:0.28
Consensus pattern (14 bp):
GTTGACTCAGACGA
Found at i:1981253 original size:15 final size:15
Alignment explanation
Indices: 1981220--1981272 Score: 83
Period size: 15 Copynumber: 3.6 Consensus size: 15
1981210 TGACTCAGAC
1981220 GAGTTGACTCGGA--T
1 GAGTTGACT-GGATCT
1981234 GAGTTGACTGGATCT
1 GAGTTGACTGGATCT
1981249 GAGTTGACTGGATCT
1 GAGTTGACTGGATCT
1981264 GAGTTGACT
1 GAGTTGACT
1981273 CAGGCGAGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
13 3 0.08
14 9 0.24
15 25 0.68
ACGTcount: A:0.21, C:0.13, G:0.34, T:0.32
Consensus pattern (15 bp):
GAGTTGACTGGATCT
Found at i:1992307 original size:20 final size:20
Alignment explanation
Indices: 1992271--1992308 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1992261 ATCATATTCC
**
1992271 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
1992291 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
1992309 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:1992864 original size:19 final size:19
Alignment explanation
Indices: 1992840--1992876 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1992830 AAACCAAAAA
*
1992840 AACTCTCCCTTTTTCTCTC
1 AACTCTCCCTTTTCCTCTC
*
1992859 AACTCTCTCTTTTCCTCT
1 AACTCTCCCTTTTCCTCT
1992877 GCTCGGTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.11, C:0.41, G:0.00, T:0.49
Consensus pattern (19 bp):
AACTCTCCCTTTTCCTCTC
Found at i:1993579 original size:3 final size:3
Alignment explanation
Indices: 1993566--1993676 Score: 170
Period size: 3 Copynumber: 36.3 Consensus size: 3
1993556 ATTGAGTTTG
1993566 TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
1993612 TAA TAA TAA TTTA TAA TAAA TAA TAA TAA TAA TAG TAA TAA TAA TAA
1 TAA TAA TAA -TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1993659 TAA TAA TAA TAA T-A TAA T
1 TAA TAA TAA TAA TAA TAA T
1993677 GGTTAAAAAA
Statistics
Matches: 100, Mismatches: 4, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
2 2 0.02
3 90 0.90
4 8 0.08
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1994151 original size:4 final size:4
Alignment explanation
Indices: 1994138--1994187 Score: 66
Period size: 4 Copynumber: 12.0 Consensus size: 4
1994128 GTTAGATAAC
1994138 AAAT -AAT AAAT AAAT AAAT AAAT AAAT AAAT AAAAT AAAGT AAAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAA-T -AAAT AAAT
1994188 CAAAAGAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
3 3 0.07
4 30 0.71
5 6 0.14
6 3 0.07
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:1994175 original size:9 final size:9
Alignment explanation
Indices: 1994145--1994357 Score: 118
Period size: 9 Copynumber: 22.7 Consensus size: 9
1994135 AACAAATAAT
1994145 AAATAAAT-
1 AAATAAATA
1994153 AAATAAAT-
1 AAATAAATA
1994161 AAATAAATA
1 AAATAAATA
1994170 AAATAAAGTA
1 AAATAAA-TA
1994180 AAATAAATCA
1 AAATAAAT-A
* *
1994190 AAAGAAAAA
1 AAATAAATA
1994199 AAATGAAAATGA
1 AAAT--AAAT-A
*
1994211 AAATAGATA
1 AAATAAATA
1994220 AAA-AAATA
1 AAATAAATA
1994228 TAAA-AAATA
1 -AAATAAATA
*
1994237 TAAAAAATATTA
1 -AAATAA-A-TA
1994249 AAATGACAATA
1 AAAT-A-AATA
*
1994260 ATAAAAAATA
1 A-AATAAATA
* *
1994270 AAGATTAGTGA
1 AA-ATAAAT-A
* *
1994281 AATTAAGTA
1 AAATAAATA
1994290 AAA-AAATA
1 AAATAAATA
*
1994298 AAATAAAAA
1 AAATAAATA
*
1994307 AAATAAAAA
1 AAATAAATA
1994316 AAATAAA-A
1 AAATAAATA
1994324 AAATAAA-A
1 AAATAAATA
1994332 AAATAAGATAGA
1 AAATAA-AT--A
1994344 AAATAAA-A
1 AAATAAATA
1994352 AAATAA
1 AAATAA
1994358 TAATAAAAGG
Statistics
Matches: 169, Mismatches: 16, Indels: 40
0.75 0.07 0.18
Matches are distributed among these distances:
8 49 0.29
9 53 0.31
10 33 0.20
11 15 0.09
12 18 0.11
13 1 0.01
ACGTcount: A:0.75, C:0.01, G:0.06, T:0.19
Consensus pattern (9 bp):
AAATAAATA
Found at i:1994308 original size:8 final size:8
Alignment explanation
Indices: 1994288--1994357 Score: 72
Period size: 8 Copynumber: 8.4 Consensus size: 8
1994278 TGAAATTAAG
1994288 TAAAAAAA
1 TAAAAAAA
*
1994296 T-AAAATA
1 TAAAAAAA
1994303 -AAAAAAA
1 TAAAAAAA
1994310 TAAAAAAAA
1 T-AAAAAAA
1994319 TAAAAAAA
1 TAAAAAAA
1994327 TAAAAAAA
1 TAAAAAAA
1994335 TAAGATAGAAAA
1 T-A-A-A-AAAA
1994347 TAAAAAAA
1 TAAAAAAA
1994355 TAA
1 TAA
1994358 TAATAAAAGG
Statistics
Matches: 53, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
7 10 0.19
8 24 0.45
9 10 0.19
10 2 0.04
11 2 0.04
12 5 0.09
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (8 bp):
TAAAAAAA
Found at i:1995513 original size:2 final size:2
Alignment explanation
Indices: 1995502--1995542 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1995492 ATATGTTTAT
1995502 TA TA -A 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
1995543 AAACACATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1996573 original size:106 final size:106
Alignment explanation
Indices: 1996422--1997123 Score: 1170
Period size: 106 Copynumber: 6.6 Consensus size: 106
1996412 CTCTGGAACC
* * ** ** *
1996422 GGGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTTTGAAGTTGAACTTATGTTGTCTCGAGT
1 GGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
1996487 CCAATATCCTTCTCTGTGAAGTTGAAATTGGCTCTGAAATT
66 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT
1996528 GGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
1 GGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
1996593 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT
66 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT
* * *
1996634 GGGAAGTTGTTTATTGACAACCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGT
1 GGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* *
1996699 CCAATATCCTTCGCTGTGAAATTGAAATTGGCTCTAAAATT
66 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT
* *
1996740 GAGAAATTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
1 GGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* *
1996805 CCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCTGAAATT
66 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT
* * *
1996846 GGAAAATTATTTATTGACAACTAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
1 GGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
1996911 CCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATT
66 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT
* *
1996952 GGGAAATTATTTATTGACAACCAGCGGTCCCTTCGTCTTGAAGTTGAACTTGCGTTGTCTGGAGT
1 GGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
1997017 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT
66 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT
* * *
1997058 GAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
1 GGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
1997123 C
66 C
1997124 AAACTGGATT
Statistics
Matches: 559, Mismatches: 37, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
106 559 1.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.34
Consensus pattern (106 bp):
GGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT
Found at i:2000325 original size:18 final size:19
Alignment explanation
Indices: 2000285--2000329 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
2000275 AGTTAATGTG
2000285 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
2000304 AATGCAAAGAAAATAA-AA
1 AATGCAAAGAAAATAACAA
2000322 AATGCAAA
1 AATGCAAA
2000330 ATGTATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 10 0.38
19 16 0.62
ACGTcount: A:0.69, C:0.09, G:0.11, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:2001600 original size:6 final size:6
Alignment explanation
Indices: 2001589--2001614 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2001579 ATCGAATAAA
2001589 TAAATT TAAATT TAAATT TAAATT TA
1 TAAATT TAAATT TAAATT TAAATT TA
2001615 CTATTTTTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TAAATT
Found at i:2002029 original size:4 final size:4
Alignment explanation
Indices: 2002016--2002067 Score: 52
Period size: 4 Copynumber: 12.0 Consensus size: 4
2002006 GTTAGATAAC
2002016 AAAT -AAT AAAT AAAT AAAT AAAT AAAAT AAAAT AAAAT AAAGT AAAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT -AAAT -AAAT -AAAT AAA-T -AAAT
2002064 AAAT
1 AAAT
2002068 CAAAAGAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
3 3 0.07
4 22 0.50
5 16 0.36
6 3 0.07
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:2002050 original size:10 final size:10
Alignment explanation
Indices: 2002023--2002151 Score: 71
Period size: 10 Copynumber: 13.2 Consensus size: 10
2002013 AACAAATAAT
2002023 AAAT-AAAT-
1 AAATAAAATA
2002031 AAAT-AAATA
1 AAATAAAATA
2002040 AAATAAAATA
1 AAATAAAATA
*
2002050 AAATAAAGTA
1 AAATAAAATA
2002060 AAAT-AAATCA
1 AAATAAAAT-A
*
2002070 AAAGAAAA-A
1 AAATAAAATA
2002079 AAATGAAAATGA
1 AAAT-AAAAT-A
*
2002091 AAAT-AGATA
1 AAATAAAATA
2002100 AAA-AAAATTA
1 AAATAAAA-TA
*
2002110 AAA-AATATA
1 AAATAAAATA
*
2002119 AAA-AATATTA
1 AAATAA-AATA
*
2002129 AAATGACAATA
1 AAAT-AAAATA
2002140 ATAA-AAAATA
1 A-AATAAAATA
2002150 AA
1 AA
2002152 GATTAGTGAA
Statistics
Matches: 96, Mismatches: 12, Indels: 25
0.72 0.09 0.19
Matches are distributed among these distances:
8 8 0.08
9 25 0.26
10 48 0.50
11 7 0.07
12 8 0.08
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.19
Consensus pattern (10 bp):
AAATAAAATA
Found at i:2002212 original size:39 final size:35
Alignment explanation
Indices: 2002160--2002244 Score: 100
Period size: 38 Copynumber: 2.3 Consensus size: 35
2002150 AAGATTAGTG
*
2002160 AAATTAAGTAAAAAAATAAAATAAAAGAATAAAAATAA
1 AAATTAA-TAAAAAAACAAAATAAAA-AATAAAAA-AA
* *
2002198 TAAATTAATAAAAAAACAAGATAGAAAATAAAAAAA
1 -AAATTAATAAAAAAACAAAATAAAAAATAAAAAAA
2002234 AAA-TAATAAAA
1 AAATTAATAAAA
2002245 GGGTTAAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
34 8 0.19
35 3 0.07
36 2 0.05
37 8 0.19
38 15 0.35
39 7 0.16
ACGTcount: A:0.76, C:0.01, G:0.05, T:0.18
Consensus pattern (35 bp):
AAATTAATAAAAAAACAAAATAAAAAATAAAAAAA
Found at i:2002239 original size:31 final size:30
Alignment explanation
Indices: 2002169--2002244 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 30
2002159 GAAATTAAGT
* *
2002169 AAAAAAATAAAATAAAAGAATAAAAATAAT
1 AAAAAAATAAAAAAAAAGAATAAAAATAAA
**
2002199 AAATTAATAAAAAAACAAG-ATAGAAAATAAA
1 AAAAAAATAAAAAAA-AAGAATA-AAAATAAA
*
2002230 AAAAAAATAATAAAA
1 AAAAAAATAAAAAAA
2002245 GGGTTAAATT
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
30 15 0.41
31 22 0.59
ACGTcount: A:0.79, C:0.01, G:0.04, T:0.16
Consensus pattern (30 bp):
AAAAAAATAAAAAAAAAGAATAAAAATAAA
Found at i:2003386 original size:2 final size:2
Alignment explanation
Indices: 2003379--2003450 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
2003369 ATATGTTTAT
2003379 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
2003421 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
2003451 ACACATAAAT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2006784 original size:3 final size:3
Alignment explanation
Indices: 2006761--2006802 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
2006751 ATTTTTCAAC
2006761 TAT TA- TAT TA- TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2006803 AAAATATATA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 6 0.17
3 30 0.83
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:2015835 original size:55 final size:54
Alignment explanation
Indices: 2015776--2016222 Score: 492
Period size: 55 Copynumber: 8.1 Consensus size: 54
2015766 TTCTTTCAAG
* *
2015776 GAGTATA-AGACTCGAACAATCTTCAACAAACGGGTCCACTCGTTATTCCTTGAGA
1 GAGTATAGA-ACTCGAACAATCTTCAACAAACGGGTCCGCTC-TTATTCCTTCAGA
* * * * *
2015831 GAGTATAGGACTTG-ACAATCTTCAACAAATGAGTCCGCTCTCTATTCCTTGAGA
1 GAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGCTCT-TATTCCTTCAGA
** * *
2015885 GAGTATAGGTCTCGAACAATTTTCAACAAACGGGTCCGCTCTTTATTTCTTCAGA
1 GAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGCTC-TTATTCCTTCAGA
* * * * *
2015940 GTGTATAGGACTCGAACAATTTTCAACAAACGGGTACGCTCCCTATT-CTATCAGA
1 GAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGCT-CTTATTCCT-TCAGA
** *
2015995 GAGTATAGAACTCGAACAATCTTCATA-AAATAGGTCTGCTCTCTATTCCTTCAGA
1 GAGTATAGAACTCGAACAATCTTCA-ACAAACGGGTCCGCTCT-TATTCCTTCAGA
* *
2016050 GAGTATAGAACTCGAACAATCTTCATA-AAGCAGGTCCGCTCTCTATTCCTTCAGA
1 GAGTATAGAACTCGAACAATCTTCA-ACAAACGGGTCCGCTCT-TATTCCTTCAGA
* * *
2016105 GAGTATAGAACTCGAACAATCTTCAACAAATGGGTCCGCTCCCTATTCCATCAGA
1 GAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGCT-CTTATTCCTTCAGA
* * *
2016160 GAGTATAGAACTCGAACAATCTTCAACAAACGAGTCCGCTCCCTATT-CTATTAGA
1 GAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGCT-CTTATTCCT-TCAGA
2016215 GAGTATAG
1 GAGTATAG
2016223 GACTTGATCT
Statistics
Matches: 344, Mismatches: 36, Indels: 24
0.85 0.09 0.06
Matches are distributed among these distances:
53 1 0.00
54 52 0.15
55 285 0.83
56 6 0.02
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (54 bp):
GAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGCTCTTATTCCTTCAGA
Found at i:2016009 original size:110 final size:109
Alignment explanation
Indices: 2015753--2016222 Score: 549
Period size: 110 Copynumber: 4.3 Consensus size: 109
2015743 TCTAATGACA
* *
2015753 AGTCCGCTCCCCATTCTTTCA-AGGAGTATA-AGACTCGAACAATCTTCAACAAACGGGTCCACT
1 AGTCCGCTCCCTATTC-TTCAGA-GAGTATAGA-ACTCGAACAATCTTCAACAAACGGGTCCGCT
* * * *
2015816 CGT-TATTCCTTGAGAGAGTATAGGACTTG-ACAATCTTCAACAAATG
63 C-TCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACG
* * ** *
2015862 AGTCCGCTCTCTATTCCTTGAGAGAGTATAGGTCTCGAACAATTTTCAACAAACGGGTCCGCTCT
1 AGTCCGCTCCCTATT-CTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGCTCT
* * * * *
2015927 TTATTTCTTCAGAGTGTATAGGACTCGAACAATTTTCAACAAACG
65 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACG
* * ** *
2015972 GGTACGCTCCCTATTCTATCAGAGAGTATAGAACTCGAACAATCTTCATA-AAATAGGTCTGCTC
1 AGTCCGCTCCCTATTCT-TCAGAGAGTATAGAACTCGAACAATCTTCA-ACAAACGGGTCCGCTC
*
2016036 TCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTC-ATAAA-G
64 TCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACG
* *
2016080 CAGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAATGGGTCCGCT
1 -A-GTCCGCTCCCTATT-CTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGCT
* *
2016145 CCCTATTCCATCAGAGAGTATAGAACTCGAACAATCTTCAACAAACG
63 CTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACG
*
2016192 AGTCCGCTCCCTATTCTATTAGAGAGTATAG
1 AGTCCGCTCCCTATTCT-TCAGAGAGTATAG
2016223 GACTTGATCT
Statistics
Matches: 308, Mismatches: 39, Indels: 27
0.82 0.10 0.07
Matches are distributed among these distances:
108 2 0.01
109 83 0.27
110 214 0.69
111 8 0.03
112 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (109 bp):
AGTCCGCTCCCTATTCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGCTCTC
TATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACG
Found at i:2016069 original size:165 final size:165
Alignment explanation
Indices: 2015754--2016222 Score: 583
Period size: 165 Copynumber: 2.8 Consensus size: 165
2015744 CTAATGACAA
* * * * * *
2015754 GTCCGCTCCCCATTCTTTCA-AGGAGTATAAGACTCGAACAATCTTCAACAAACGGGTCCACTCG
1 GTCCGCTCTCTATTCCTTCAGA-GAGTATAGGACTCGAACAATCTTCAACAAACGGGTCCGCTCC
* * * *
2015818 TTATTCCT-TGAGAGAGTATAGGACTTG-ACAATCTTCAACAAATGAGTCCGCTCTCTATTCCTT
65 CTATT-CTATCAGAGAGTATAGAACTCGAACAATCTTCAACAAATGAGTCCGCTCTCTATTCCTT
* ** * *
2015881 GAGAGAGTATAGGTCTCGAACAATTTTCA-ACAAACGG
129 CAGAGAGTATAGAACTCGAACAATCTTCATA-AAACAG
* * * * *
2015918 GTCCGCTCTTTATTTCTTCAGAGTGTATAGGACTCGAACAATTTTCAACAAACGGGTACGCTCCC
1 GTCCGCTCTCTATTCCTTCAGAGAGTATAGGACTCGAACAATCTTCAACAAACGGGTCCGCTCCC
*
2015983 TATTCTATCAGAGAGTATAGAACTCGAACAATCTTCATA-AAAT-AGGTCTGCTCTCTATTCCTT
66 TATTCTATCAGAGAGTATAGAACTCGAACAATCTTCA-ACAAATGA-GTCCGCTCTCTATTCCTT
*
2016046 CAGAGAGTATAGAACTCGAACAATCTTCATAAAGCAG
129 CAGAGAGTATAGAACTCGAACAATCTTCATAAAACAG
* *
2016083 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAATGGGTCCGCTCCC
1 GTCCGCTCTCTATTCCTTCAGAGAGTATAGGACTCGAACAATCTTCAACAAACGGGTCCGCTCCC
* * * *
2016148 TATTCCATCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGAGTCCGCTCCCTATT-CTATT
66 TATTCTATCAGAGAGTATAGAACTCGAACAATCTTCAACAAATGAGTCCGCTCTCTATTCCT-TC
2016212 AGAGAGTATAG
130 AGAGAGTATAG
2016223 GACTTGATCT
Statistics
Matches: 262, Mismatches: 34, Indels: 17
0.84 0.11 0.05
Matches are distributed among these distances:
163 2 0.01
164 75 0.29
165 182 0.69
166 3 0.01
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (165 bp):
GTCCGCTCTCTATTCCTTCAGAGAGTATAGGACTCGAACAATCTTCAACAAACGGGTCCGCTCCC
TATTCTATCAGAGAGTATAGAACTCGAACAATCTTCAACAAATGAGTCCGCTCTCTATTCCTTCA
GAGAGTATAGAACTCGAACAATCTTCATAAAACAG
Found at i:2016295 original size:37 final size:36
Alignment explanation
Indices: 2016245--2016315 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 36
2016235 ATAAAATAAG
2016245 TTTGCTTCACTACTCTTCCGTAAAGGCTTATAGATGA
1 TTTGCTTCACTACTCTTCCGTAAAGGCTTA-AGATGA
*
2016282 TTTGCTTCACTACTCTTCCGTGAAGGCTTAAGAT
1 TTTGCTTCACTACTCTTCCGTAAAGGCTTAAGAT
2016316 TAAATTGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 4 0.12
37 29 0.88
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.38
Consensus pattern (36 bp):
TTTGCTTCACTACTCTTCCGTAAAGGCTTAAGATGA
Found at i:2016561 original size:16 final size:18
Alignment explanation
Indices: 2016532--2016570 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
2016522 TAGTTATCTT
2016532 TATC-TCAATGCTTCAA-
1 TATCTTCAATGCTTCAAC
2016548 TATCTTCAAT-CTTCAAC
1 TATCTTCAATGCTTCAAC
2016565 TATCTT
1 TATCTT
2016571 TGGGAAACCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.28, C:0.26, G:0.03, T:0.44
Consensus pattern (18 bp):
TATCTTCAATGCTTCAAC
Found at i:2017623 original size:7 final size:7
Alignment explanation
Indices: 2017611--2017795 Score: 161
Period size: 7 Copynumber: 25.7 Consensus size: 7
2017601 TTTCTCTATT
2017611 TTTTTCA
1 TTTTTCA
2017618 TTTTTCA
1 TTTTTCA
2017625 TTTTTCA
1 TTTTTCA
2017632 TTTTTCA
1 TTTTTCA
2017639 TTTTTCA
1 TTTTTCA
2017646 TTTTTCA
1 TTTTTCA
2017653 TTTTTCA
1 TTTTTCA
2017660 TTTTTCA
1 TTTTTCA
*
2017667 TTTTTCTC
1 TTTTTC-A
2017675 TTTCTTC-
1 TTT-TTCA
2017682 TTTTTCA
1 TTTTTCA
*
2017689 TTTTTTA
1 TTTTTCA
2017696 TTTTTTCA
1 -TTTTTCA
2017704 TTTTTTCA
1 -TTTTTCA
2017712 TTTTTCCCA
1 TTTTT--CA
2017721 -TTTTCTA
1 TTTTTC-A
2017728 TTTTTCTA
1 TTTTTC-A
*
2017736 TTTTTCTCTT
1 -TTTT-TC-A
2017746 TTTTTC-
1 TTTTTCA
2017752 TTTTTCA
1 TTTTTCA
2017759 TTTTT--
1 TTTTTCA
*
2017764 TTCATT-A
1 TT-TTTCA
2017771 TTTTTC-
1 TTTTTCA
2017777 TTTTTCCA
1 TTTTT-CA
2017785 -TTTTCA
1 TTTTTCA
2017791 TTTTT
1 TTTTT
2017796 TCATCATTTT
Statistics
Matches: 155, Mismatches: 6, Indels: 34
0.79 0.03 0.17
Matches are distributed among these distances:
5 2 0.01
6 21 0.14
7 86 0.55
8 30 0.19
9 13 0.08
10 3 0.02
ACGTcount: A:0.11, C:0.16, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTTCA
Found at i:2031039 original size:64 final size:63
Alignment explanation
Indices: 2030923--2031063 Score: 171
Period size: 64 Copynumber: 2.2 Consensus size: 63
2030913 CATATTCAAT
* *
2030923 GTGCATCGATGCACTCTTTAAAGAAGAAACATCGAATGCAATTGGTGCATCGATGCATAAGG-A
1 GTGCATCGATGCACTCTTAAAAGAAGAAACATCGAAGGCAATTGGTGCATCGATGCAT-AGGTA
* * * *
2030986 GTGCATCGATGCATCCTCTTAAAATG-A-AAACATCGAAGGTAATTTGTGTATCGATGCATGGGT
1 GTGCATCGATGCA--CTCTTAAAA-GAAGAAACATCGAAGGCAATTGGTGCATCGATGCATAGGT
2031049 A
63 A
2031050 GTGCATCGATGCAC
1 GTGCATCGATGCAC
2031064 ATGTTAAAGA
Statistics
Matches: 68, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
62 1 0.01
63 15 0.22
64 42 0.62
65 9 0.13
66 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (63 bp):
GTGCATCGATGCACTCTTAAAAGAAGAAACATCGAAGGCAATTGGTGCATCGATGCATAGGTA
Found at i:2035708 original size:28 final size:27
Alignment explanation
Indices: 2035677--2035734 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
2035667 CTATAATATT
*
2035677 AAACTCTAATTCC-TAACCCTTAACCCCC
1 AAACTCTAA--CCTTAACCCCTAACCCCC
2035705 AAACTCTAACCTTTAACCCCTAACCCCC
1 AAACTCTAACC-TTAACCCCTAACCCCC
2035733 AA
1 AA
2035735 TCCCAAGCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 2 0.07
28 25 0.93
ACGTcount: A:0.34, C:0.43, G:0.00, T:0.22
Consensus pattern (27 bp):
AAACTCTAACCTTAACCCCTAACCCCC
Found at i:2036769 original size:3 final size:3
Alignment explanation
Indices: 2036761--2036808 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
2036751 TTAAAAATAC
2036761 TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2036808 T
1 T
2036809 CATCATCATT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2037243 original size:39 final size:40
Alignment explanation
Indices: 2037192--2037275 Score: 100
Period size: 41 Copynumber: 2.1 Consensus size: 40
2037182 ATTTAAAAAA
* *
2037192 ATATATAAAAATA-TTAAATTACTA-AAAAAATGGAATAT
1 ATATATAAAAATACTAAAACTACTATAAAAAATGGAATAT
* * *
2037230 ATATATTAAAAATACTAAAACTATTATAAAAAATTGAATGT
1 ATATA-TAAAAATACTAAAACTACTATAAAAAATGGAATAT
2037271 ATATA
1 ATATA
2037276 GGTTATAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
38 5 0.13
39 8 0.21
40 8 0.21
41 17 0.45
ACGTcount: A:0.58, C:0.04, G:0.05, T:0.33
Consensus pattern (40 bp):
ATATATAAAAATACTAAAACTACTATAAAAAATGGAATAT
Found at i:2037608 original size:64 final size:64
Alignment explanation
Indices: 2037507--2037636 Score: 251
Period size: 64 Copynumber: 2.0 Consensus size: 64
2037497 CGACTGCAAG
*
2037507 TTTTTGCCTTTTCTGCAGCTCCCCAGCGCCGGTTGATGTTGTCTATTAGGCTTTATTTAACTTC
1 TTTTTGCCTTTCCTGCAGCTCCCCAGCGCCGGTTGATGTTGTCTATTAGGCTTTATTTAACTTC
2037571 TTTTTGCCTTTCCTGCAGCTCCCCAGCGCCGGTTGATGTTGTCTATTAGGCTTTATTTAACTTC
1 TTTTTGCCTTTCCTGCAGCTCCCCAGCGCCGGTTGATGTTGTCTATTAGGCTTTATTTAACTTC
2037635 TT
1 TT
2037637 AAACTGGAAG
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.12, C:0.25, G:0.18, T:0.44
Consensus pattern (64 bp):
TTTTTGCCTTTCCTGCAGCTCCCCAGCGCCGGTTGATGTTGTCTATTAGGCTTTATTTAACTTC
Found at i:2038936 original size:22 final size:22
Alignment explanation
Indices: 2038911--2038952 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2038901 TAAACAATAG
*
2038911 ATTTCTTAATCATTAAAATCAA
1 ATTTCTTAACCATTAAAATCAA
*
2038933 ATTTCTTAACCATTGAAATC
1 ATTTCTTAACCATTAAAATC
2038953 GTTTAACTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.17, G:0.02, T:0.40
Consensus pattern (22 bp):
ATTTCTTAACCATTAAAATCAA
Found at i:2039688 original size:37 final size:37
Alignment explanation
Indices: 2039599--2039680 Score: 110
Period size: 37 Copynumber: 2.2 Consensus size: 37
2039589 ATATATATGC
* *
2039599 GAACCAATCGATAATTAGATTTATCATTATAACGGAT
1 GAACCAGTCGATAATTAGATTTATCATCATAACGGAT
* * * *
2039636 GAACTAGTCGATAATTGGATTTATCATCCTAATGGAT
1 GAACCAGTCGATAATTAGATTTATCATCATAACGGAT
2039673 GAACCAGT
1 GAACCAGT
2039681 GGGTAATTCA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.32
Consensus pattern (37 bp):
GAACCAGTCGATAATTAGATTTATCATCATAACGGAT
Found at i:2041028 original size:47 final size:47
Alignment explanation
Indices: 2040977--2041081 Score: 156
Period size: 47 Copynumber: 2.2 Consensus size: 47
2040967 CCTCATGTTA
* * *
2040977 TCTAGTTCTCATGATTATTTAGAAAAATAAACCTAATAGCATTCTTT
1 TCTAGTTCTCATCATTATTCAGAAAAATAAACCTAATAACATTCTTT
* * *
2041024 TCTAGTTCTCATCCTTATTCAGATAAATAAACCTTATAACATTCTTT
1 TCTAGTTCTCATCATTATTCAGAAAAATAAACCTAATAACATTCTTT
2041071 TCTAGTTCTCA
1 TCTAGTTCTCA
2041082 GGCTTTATTA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 52 1.00
ACGTcount: A:0.32, C:0.19, G:0.07, T:0.42
Consensus pattern (47 bp):
TCTAGTTCTCATCATTATTCAGAAAAATAAACCTAATAACATTCTTT
Found at i:2045305 original size:25 final size:25
Alignment explanation
Indices: 2045271--2045367 Score: 169
Period size: 25 Copynumber: 3.9 Consensus size: 25
2045261 GAGTAGGGGA
2045271 TTAGGGTTTGAAACCCTAATCTGTT
1 TTAGGGTTTGAAACCCTAATCTGTT
2045296 TTAGGGTTTGAAACCCTAAAT-TGTT
1 TTAGGGTTTGAAACCCT-AATCTGTT
*
2045321 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGTT
2045346 TTAGGGTTTGAAACCCTAATCT
1 TTAGGGTTTGAAACCCTAATCT
2045368 AACGGGTTGC
Statistics
Matches: 69, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
24 3 0.04
25 63 0.91
26 3 0.04
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGTT
Found at i:2045449 original size:22 final size:22
Alignment explanation
Indices: 2045421--2045480 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
2045411 CTTCGGGTTG
2045421 TTGGGCTCCGGGATTGGGCCTT
1 TTGGGCTCCGGGATTGGGCCTT
*
2045443 TTGGGCTTCGGG-TT--G----
1 TTGGGCTCCGGGATTGGGCCTT
2045458 TTGGGCTCCGGGATTGGGCCTT
1 TTGGGCTCCGGGATTGGGCCTT
2045480 T
1 T
2045481 GTAATCTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 14
0.64 0.04 0.31
Matches are distributed among these distances:
15 11 0.38
16 2 0.07
18 1 0.03
19 1 0.03
21 2 0.07
22 12 0.41
ACGTcount: A:0.03, C:0.20, G:0.42, T:0.35
Consensus pattern (22 bp):
TTGGGCTCCGGGATTGGGCCTT
Found at i:2045456 original size:37 final size:37
Alignment explanation
Indices: 2045406--2045480 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
2045396 CAATTCTGAG
2045406 TTGGGCTTCGGGTTGTTGGGCTCCGGGATTGGGCCTT
1 TTGGGCTTCGGGTTGTTGGGCTCCGGGATTGGGCCTT
2045443 TTGGGCTTCGGGTTGTTGGGCTCCGGGATTGGGCCTT
1 TTGGGCTTCGGGTTGTTGGGCTCCGGGATTGGGCCTT
2045480 T
1 T
2045481 GTAATCTGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.03, C:0.19, G:0.43, T:0.36
Consensus pattern (37 bp):
TTGGGCTTCGGGTTGTTGGGCTCCGGGATTGGGCCTT
Found at i:2045530 original size:3 final size:3
Alignment explanation
Indices: 2045522--2045582 Score: 65
Period size: 3 Copynumber: 21.0 Consensus size: 3
2045512 GCAAAAATTG
* **
2045522 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TAA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2045566 TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA
2045583 CGGAAAAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 5 0.10
3 40 0.83
4 3 0.06
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:2045970 original size:43 final size:44
Alignment explanation
Indices: 2045921--2046072 Score: 141
Period size: 43 Copynumber: 3.5 Consensus size: 44
2045911 TCTGGGGATG
*
2045921 ACACGGTTCATAC-TGATGAAACTCTGGCCACCTAAAGGTGATA
1 ACACGGTTCATACGTGATGAAACTCTGGCCATCTAAAGGTGATA
* * * ** * *
2045964 ACACGGTTCCTACGTGATGAGGACGGCTGGTTATCT-ATGGT--TG
1 ACACGGTTCATACGTGATGA-AAC-TCTGGCCATCTAAAGGTGATA
* *
2046007 ACACGGCTCATACGTGATGAAGAGATCTGGCCATCTAAAGGTGATA
1 ACACGGTTCATACGTGATGAA-A-CTCTGGCCATCTAAAGGTGATA
*
2046053 ACACGGTTCCTACGTGATGA
1 ACACGGTTCATACGTGATGA
2046073 GGACGGCTGG
Statistics
Matches: 82, Mismatches: 19, Indels: 13
0.72 0.17 0.11
Matches are distributed among these distances:
43 40 0.49
44 10 0.12
45 6 0.07
46 26 0.32
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (44 bp):
ACACGGTTCATACGTGATGAAACTCTGGCCATCTAAAGGTGATA
Found at i:2046052 original size:89 final size:87
Alignment explanation
Indices: 2045919--2046115 Score: 333
Period size: 89 Copynumber: 2.3 Consensus size: 87
2045909 GGTCTGGGGA
* *
2045919 TGACACGGTTCATAC-TGATGAAACTCTGGCCACCTAAAGGTGATAACACGGTTCCTACGTGATG
1 TGACACGGCTCATACGTGATGAAAATCTGGCCACCTAAAGGTGATAACACGGTTCCTACGTGATG
2045983 AGGACGGCTGGTTATCTATGGT
66 AGGACGGCTGGTTATCTATGGT
*
2046005 TGACACGGCTCATACGTGATGAAGAGATCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
1 TGACACGGCTCATACGTGATGAA-A-ATCTGGCCACCTAAAGGTGATAACACGGTTCCTACGTGA
2046070 TGAGGACGGCTGGTTATCTATGGT
64 TGAGGACGGCTGGTTATCTATGGT
*
2046094 TGACACGGCTCCTACGTGATGA
1 TGACACGGCTCATACGTGATGA
2046116 GGAAGTCCGG
Statistics
Matches: 104, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
86 14 0.13
87 7 0.07
88 1 0.01
89 82 0.79
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (87 bp):
TGACACGGCTCATACGTGATGAAAATCTGGCCACCTAAAGGTGATAACACGGTTCCTACGTGATG
AGGACGGCTGGTTATCTATGGT
Found at i:2046111 original size:43 final size:43
Alignment explanation
Indices: 2045964--2046118 Score: 186
Period size: 43 Copynumber: 3.5 Consensus size: 43
2045954 AAAGGTGATA
*
2045964 ACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTG
1 ACACGGCTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTG
* * * ** * *
2046007 ACACGGCTCATACGTGATGAAGA-GATCTGGCCATCTAAAGGTGATA
1 ACACGGCTCCTACGTGATGAGGACG-GCTGGTTATCT-ATGGT--TG
*
2046053 ACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTG
1 ACACGGCTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTG
2046096 ACACGGCTCCTACGTGATGAGGA
1 ACACGGCTCCTACGTGATGAGGA
2046119 AGTCCGGTCA
Statistics
Matches: 90, Mismatches: 17, Indels: 10
0.77 0.15 0.09
Matches are distributed among these distances:
42 1 0.01
43 51 0.57
44 4 0.04
45 4 0.04
46 29 0.32
47 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.26
Consensus pattern (43 bp):
ACACGGCTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTG
Found at i:2047102 original size:18 final size:20
Alignment explanation
Indices: 2047075--2047119 Score: 58
Period size: 18 Copynumber: 2.3 Consensus size: 20
2047065 TATTTTCTTC
*
2047075 TTTTTCATTTTT-CAT-TTT
1 TTTTTTATTTTTCCATATTT
2047093 TTTTTTATTTTTCCATCATTT
1 TTTTTTATTTTTCCAT-ATTT
2047114 TTTTTT
1 TTTTTT
2047120 TAAGTGTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 11 0.48
19 3 0.13
21 9 0.39
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTTTTATTTTTCCATATTT
Found at i:2060446 original size:3 final size:3
Alignment explanation
Indices: 2060438--2060504 Score: 127
Period size: 3 Copynumber: 22.7 Consensus size: 3
2060428 GTATATTGTA
2060438 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2060486 AAT AAT AAT AAT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AA
2060505 ATATAAAAGA
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 61 0.97
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2060510 original size:6 final size:5
Alignment explanation
Indices: 2060441--2060512 Score: 54
Period size: 6 Copynumber: 12.4 Consensus size: 5
2060431 TATTGTAAAT
2060441 AATAA TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA
1 AATAA -AATAA -AATAA -AATAA -AATAA -AATAA -AATAA -AATAA -AATAA
2060494 TAATAA AATAA ATATAA AA
1 -AATAA AATAA A-ATAA AA
2060513 GACCCGGACA
Statistics
Matches: 65, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
5 7 0.11
6 58 0.89
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (5 bp):
AATAA
Found at i:2062987 original size:18 final size:18
Alignment explanation
Indices: 2062956--2062990 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2062946 AAAGGATATT
*
2062956 TGATCTTTATCTGTGAAA
1 TGATCTTTACCTGTGAAA
*
2062974 TGATCTTTGCCTGTGAA
1 TGATCTTTACCTGTGAA
2062991 TACAGATTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.14, G:0.20, T:0.43
Consensus pattern (18 bp):
TGATCTTTACCTGTGAAA
Found at i:2070029 original size:3 final size:3
Alignment explanation
Indices: 2070023--2070108 Score: 147
Period size: 3 Copynumber: 28.7 Consensus size: 3
2070013 CATTTACTAC
2070023 TAT TAT TAT TAT TATT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
2070069 TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2070109 CAAACGGGCC
Statistics
Matches: 80, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
2 2 0.03
3 75 0.94
4 3 0.04
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2071675 original size:23 final size:22
Alignment explanation
Indices: 2071629--2071673 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2071619 ATATTATAAA
2071629 AAATTATAATTTAATTTTATTT
1 AAATTATAATTTAATTTTATTT
*
2071651 AAATTATTATATTAATATTTATT
1 AAATTATAAT-TTAAT-TTTATT
2071674 AATATCGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 5 0.25
24 6 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
AAATTATAATTTAATTTTATTT
Found at i:2071715 original size:118 final size:125
Alignment explanation
Indices: 2071490--2071732 Score: 277
Period size: 118 Copynumber: 2.0 Consensus size: 125
2071480 TGTAGTCATA
* *
2071490 TAAATATATATATAATAAATAATAATTTATATTTTTTTACATAAATTATTTTAATATTTATTTTT
1 TAAATATATATATAATAAATAATAATTTATATTTTTTTAAATAAATTATATTAATATTTA--TTT
* * * * *
2071555 CAATATCAAAGAAAAGGGCAGTCTTAATACAACTGGATGTCCTATTCTGGTATTT-TAAAAT
64 CAATATCAAAGAAAAGAGCAGTCTTAAGACAACTAGAAGTCCTATTCTGATATTTCTAAAAT
* *
2071616 TAAATAT-TATA-AA-AAATTATAATTTA-ATTTTATTTAAAT-TATTATATTAATATTTA-TT-
1 TAAATATATATATAATAAATAATAATTTATATTTT-TTTAAATAAATTATATTAATATTTATTTC
* * * * *
2071674 AATATCGAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTCCTTTTCTGATATTTCTAAA
65 AATATCAAAGAAAAGAGCAGTCTTAAGACAACTAGAAGTCCTATTCTGATATTTCTAAA
2071733 TAAATAAATA
Statistics
Matches: 101, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
118 44 0.44
119 6 0.06
122 20 0.20
123 18 0.18
124 2 0.02
125 4 0.04
126 7 0.07
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (125 bp):
TAAATATATATATAATAAATAATAATTTATATTTTTTTAAATAAATTATATTAATATTTATTTCA
ATATCAAAGAAAAGAGCAGTCTTAAGACAACTAGAAGTCCTATTCTGATATTTCTAAAAT
Found at i:2071755 original size:23 final size:26
Alignment explanation
Indices: 2071723--2071772 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 26
2071713 CCTTTTCTGA
*
2071723 TATTTCTAAATA-A-ATAAA-TATTT
1 TATTTATAAATATATATAAATTATTT
2071746 TATTTATAAATATATATAAATTATTT
1 TATTTATAAATATATATAAATTATTT
2071772 T
1 T
2071773 TTCTCATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 1 0.04
25 5 0.22
26 6 0.26
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (26 bp):
TATTTATAAATATATATAAATTATTT
Found at i:2072316 original size:24 final size:26
Alignment explanation
Indices: 2072254--2072317 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
2072244 TAATTCTTTC
*
2072254 TTTTCAATTTT-TTTATATATTTATTA
1 TTTTC-ATTTTATTTATATATTTAATA
**
2072280 TTTTCATAGTATTTATATA-TTAATA
1 TTTTCATTTTATTTATATATTTAATA
2072305 -TTTCATTTTATTT
1 TTTTCATTTTATTT
2072318 GCAAGTATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
24 11 0.34
25 8 0.25
26 13 0.41
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.66
Consensus pattern (26 bp):
TTTTCATTTTATTTATATATTTAATA
Found at i:2082925 original size:13 final size:13
Alignment explanation
Indices: 2082907--2082959 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
2082897 ATTATGCTTG
2082907 AAGAAAAAGAAAA
1 AAGAAAAAGAAAA
*
2082920 AAGAAAAA-ATAAT
1 AAGAAAAAGA-AAA
2082933 AAG--AAAGAAAA
1 AAGAAAAAGAAAA
2082944 GAA-AAAAAGAAAA
1 -AAGAAAAAGAAAA
2082957 AAG
1 AAG
2082960 GGTGTCAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
11 5 0.16
12 6 0.19
13 21 0.66
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (13 bp):
AAGAAAAAGAAAA
Found at i:2083955 original size:93 final size:93
Alignment explanation
Indices: 2083796--2084088 Score: 523
Period size: 93 Copynumber: 3.2 Consensus size: 93
2083786 GATTCAAGTA
2083796 GAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCGGATCTGGTTTGATATGAACCC
1 GAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCGGATCTGGTTTGATATGAACCC
2083861 TAAAAACCAATCATTAAATTTGGAAGAT
66 TAAAAACCAATCATTAAATTTGGAAGAT
2083889 GAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCGGATCTGGTTTGATATGAACCC
1 GAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCGGATCTGGTTTGATATGAACCC
* *
2083954 TAAAAACCAATCATTGAATTTAGAAGAT
66 TAAAAACCAATCATTAAATTTGGAAGAT
* *
2083982 GAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAATATGAACCC
1 GAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCGGATCTGGTTTGATATGAACCC
* *
2084047 TAAAAACCAATCATTAAATTTGAAAGAC
66 TAAAAACCAATCATTAAATTTGGAAGAT
*
2084075 GAATGTGCTTATAG
1 GAATGTGCTCATAG
2084089 TATAAATAAG
Statistics
Matches: 191, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 191 1.00
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (93 bp):
GAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCGGATCTGGTTTGATATGAACCC
TAAAAACCAATCATTAAATTTGGAAGAT
Found at i:2084960 original size:40 final size:41
Alignment explanation
Indices: 2084914--2085011 Score: 173
Period size: 40 Copynumber: 2.4 Consensus size: 41
2084904 TTTCCGGAAG
2084914 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA-AA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
*
2084954 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAATAAGAA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
2084995 A-TTCATAATGAGAAGAA
1 AGTTCATAATGAGAAGAA
2085012 TTTGTTCAAC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
40 53 0.95
41 3 0.05
ACGTcount: A:0.50, C:0.09, G:0.21, T:0.19
Consensus pattern (41 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
Found at i:2085411 original size:116 final size:113
Alignment explanation
Indices: 2084948--2085479 Score: 901
Period size: 113 Copynumber: 4.7 Consensus size: 113
2084938 TGAAGAAGGA
*
2084948 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAATAAGAAATTCATAATGAGAAGAAT
1 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAT
*
2085013 TTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAACTTTTCC
66 TTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCC
*
2085061 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAATAAGAAATTCATAATGAGAAGAAT
1 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAT
2085126 TTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCC
66 TTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCC
2085174 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAT
1 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAT
2085239 TTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCC
66 TTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCC
* * *
2085287 AGAAAAAGTTCATAATGAGAAGAACTCGTCACCTGAAGAAGAAAGAAGAAAATCATAATGAGAAG
1 AGAAAAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAG
*
2085352 AATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCC
63 AATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCC
* * * *
2085403 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA-TAAGAAG---TTCACAATGAGAAGAAC
1 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAT
*
2085464 TTGTTCAACTTTTTGC
66 TTGTTCAACCTTTTGC
2085480 ATAATTCTAT
Statistics
Matches: 403, Mismatches: 13, Indels: 10
0.95 0.03 0.02
Matches are distributed among these distances:
109 29 0.07
112 6 0.01
113 259 0.64
114 1 0.00
115 1 0.00
116 107 0.27
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (113 bp):
AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAT
TTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCC
Found at i:2085598 original size:84 final size:82
Alignment explanation
Indices: 2085444--2085630 Score: 214
Period size: 84 Copynumber: 2.3 Consensus size: 82
2085434 GAAGAATAAG
* * * * * * * *
2085444 AAGTTCACAATGAGAAGAACTTGTTCAACTTTTTGCATAATTCTATCACATAAGGAGATAGATTA
1 AAGTTCATAATGAGAAGAACTTATTCAACCTTTTGAATAACTCTATCACAAAAGGAAATAGATCA
*
2085509 GCATCAACCTTTCCAG-AGA
66 ACATCAACC---CCAGCAGA
* * * *
2085528 AAGTTCATAATGAGAAGAGCTTATTTAACCTTTTGAATGACTCTATCACAAAAGGAAATAGGTCA
1 AAGTTCATAATGAGAAGAACTTATTCAACCTTTTGAATAACTCTATCACAAAAGGAAATAGATCA
*
2085593 ACATCATCCCCAGCAGA
66 ACATCAACCCCAGCAGA
2085610 AAGTTCATAATGAGAAGAACT
1 AAGTTCATAATGAGAAGAACT
2085631 CATCTGAAGA
Statistics
Matches: 87, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
81 4 0.05
82 23 0.26
84 60 0.69
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (82 bp):
AAGTTCATAATGAGAAGAACTTATTCAACCTTTTGAATAACTCTATCACAAAAGGAAATAGATCA
ACATCAACCCCAGCAGA
Found at i:2085801 original size:3 final size:3
Alignment explanation
Indices: 2085793--2085840 Score: 73
Period size: 3 Copynumber: 16.7 Consensus size: 3
2085783 CTCCATTTAC
*
2085793 TAT TAT TAT TAT TAT TA- TAT TAT TAT TGT TAT TAT TAT T-T TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2085839 TA
1 TA
2085841 CAAACGGGCC
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 4 0.10
3 37 0.90
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2085818 original size:20 final size:20
Alignment explanation
Indices: 2085793--2085840 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
2085783 CTCCATTTAC
2085793 TATTATTATTATTATTATAT
1 TATTATTATTATTATTATAT
* *
2085813 TATTATTGTTATTATTATTT
1 TATTATTATTATTATTATAT
2085833 TATTATTA
1 TATTATTA
2085841 CAAACGGGCC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
TATTATTATTATTATTATAT
Found at i:2085819 original size:23 final size:23
Alignment explanation
Indices: 2085793--2085840 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
2085783 CTCCATTTAC
2085793 TATTATTATTATTATTATATTAT
1 TATTATTATTATTATTATATTAT
* *
2085816 TATTGTTATTATTATTTTATTAT
1 TATTATTATTATTATTATATTAT
2085839 TA
1 TA
2085841 CAAACGGGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (23 bp):
TATTATTATTATTATTATATTAT
Found at i:2087206 original size:9 final size:11
Alignment explanation
Indices: 2087183--2087217 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
2087173 TTATGTAGTC
2087183 ATATAATATAT
1 ATATAATATAT
*
2087194 ATATAATAAAT
1 ATATAATATAT
*
2087205 ATATAATTTAT
1 ATATAATATAT
2087216 AT
1 AT
2087218 TTTTTCATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
ATATAATATAT
Found at i:2087365 original size:23 final size:22
Alignment explanation
Indices: 2087319--2087363 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2087309 ATATTATAAA
2087319 AAATTATAATTTAATTTTATTT
1 AAATTATAATTTAATTTTATTT
*
2087341 AAATTATTATATTAATATTTATT
1 AAATTATAAT-TTAAT-TTTATT
2087364 AATATCGGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 5 0.25
24 6 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
AAATTATAATTTAATTTTATTT
Found at i:2087405 original size:117 final size:119
Alignment explanation
Indices: 2087190--2087421 Score: 269
Period size: 117 Copynumber: 2.0 Consensus size: 119
2087180 GTCATATAAT
*
2087190 ATATATATAATAAATATATAATTTATATTTTTTCATAAATTATTAATATTTATTTTCAATATCGA
1 ATATATATAAAAAATATATAATTTATATTTTTT-ATAAATTATTAATATTTATTTTCAATATCGA
* * * * *
2087255 AGAAAAGGGCAGTCTTAATACAACTGGATGTCCTATTTGGTATTT-TAAAATTAA
65 AGAAAAGAGCAGTCTTAAGACAACTAGAAGTCCTATTTGATATTTCTAAAATTAA
*
2087309 ATAT-TATAAAAAAT-TATAATTTA-ATTTTATT-TAAATTATT-ATATTAATATTTATTAATAT
1 ATATATATAAAAAATATATAATTTATATTTT-TTATAAATTATTAATATT--TATTT-TCAATAT
* * * * *
2087369 CGGAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTCCTTTTTGATATTTCTAAA
62 CGAAGAAAAGAGCAGTCTTAAGACAACTAGAAGTCCTATTTGATATTTCTAAA
2087422 TAAAAATTTA
Statistics
Matches: 96, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
114 5 0.05
115 9 0.09
116 10 0.10
117 55 0.57
118 13 0.14
119 4 0.04
ACGTcount: A:0.40, C:0.08, G:0.09, T:0.43
Consensus pattern (119 bp):
ATATATATAAAAAATATATAATTTATATTTTTTATAAATTATTAATATTTATTTTCAATATCGAA
GAAAAGAGCAGTCTTAAGACAACTAGAAGTCCTATTTGATATTTCTAAAATTAA
Found at i:2093128 original size:15 final size:16
Alignment explanation
Indices: 2093090--2093129 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
2093080 CCAGAACCTC
* *
2093090 TAAATCATTCAGCATT
1 TAAATCATTCAACACT
2093106 TAAATCATTCAACACT
1 TAAATCATTCAACACT
2093122 T-AATCATT
1 TAAATCATT
2093130 TTGAAGTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.40, C:0.20, G:0.03, T:0.38
Consensus pattern (16 bp):
TAAATCATTCAACACT
Found at i:2097237 original size:18 final size:19
Alignment explanation
Indices: 2097197--2097237 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
2097187 TGGTTCACGA
*
2097197 AATGTAAGATTACCAATGGG
1 AATGTAAGATTACC-AGGGG
2097217 AATGTAAGATTACC-GGGG
1 AATGTAAGATTACCAGGGG
2097235 AAT
1 AAT
2097238 AGGATTACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
20 14 0.70
ACGTcount: A:0.39, C:0.10, G:0.27, T:0.24
Consensus pattern (19 bp):
AATGTAAGATTACCAGGGG
Found at i:2097461 original size:37 final size:37
Alignment explanation
Indices: 2097388--2097462 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
2097378 TTTAGAAAAT
* *
2097388 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
2097425 ATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTGAAAATCATAAA
2097462 A
1 A
2097463 ATGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:2102381 original size:84 final size:81
Alignment explanation
Indices: 2102243--2102409 Score: 307
Period size: 84 Copynumber: 2.0 Consensus size: 81
2102233 AAGAAACCAT
2102243 AATATTAGAAATTGGAAAACACCTTGAACCGGCTAAGCACACTGGAAATTAGTCGGACTAAGCAC
1 AATATTAGAAATTGGAAAACACCTTGAACCGGCTAAGCACACTGGAAATTAGTCGGACTAAGCAC
2102308 ATTGTTTAGATAAAAA
66 ATTGTTTAGATAAAAA
2102324 AATATTAGAAATTGGAAAACAACCTTTGAACCGGACTAAGCACACTGGAAATTAGTCGGACTAAG
1 AATATTAGAAATTGGAAAAC-ACC-TTGAACCGG-CTAAGCACACTGGAAATTAGTCGGACTAAG
2102389 CACATTGTTTAGATAAAAA
63 CACATTGTTTAGATAAAAA
2102408 AA
1 AA
2102410 AAGGTTCAAA
Statistics
Matches: 83, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
81 20 0.24
82 3 0.04
83 9 0.11
84 51 0.61
ACGTcount: A:0.43, C:0.16, G:0.18, T:0.23
Consensus pattern (81 bp):
AATATTAGAAATTGGAAAACACCTTGAACCGGCTAAGCACACTGGAAATTAGTCGGACTAAGCAC
ATTGTTTAGATAAAAA
Found at i:2105649 original size:15 final size:16
Alignment explanation
Indices: 2105629--2105665 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
2105619 TGACGACGAC
2105629 GAAGAAGAA-GAAGAA
1 GAAGAAGAATGAAGAA
*
2105644 GAAGAA-AATGATGAA
1 GAAGAAGAATGAAGAA
2105659 GAAGAAG
1 GAAGAAG
2105666 GCGGAGAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 2 0.11
15 17 0.89
ACGTcount: A:0.62, C:0.00, G:0.32, T:0.05
Consensus pattern (16 bp):
GAAGAAGAATGAAGAA
Found at i:2110622 original size:27 final size:28
Alignment explanation
Indices: 2110587--2110643 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 28
2110577 GCATCTCCAG
2110587 ATCTTCAATACAATCTTT-AATTCTTCC
1 ATCTTCAATACAATCTTTAAATTCTTCC
2110614 ATCTTCAATACAATCTTTAAATTCTTCC
1 ATCTTCAATACAATCTTTAAATTCTTCC
2110642 AT
1 AT
2110644 ATCAGGTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 18 0.62
28 11 0.38
ACGTcount: A:0.32, C:0.25, G:0.00, T:0.44
Consensus pattern (28 bp):
ATCTTCAATACAATCTTTAAATTCTTCC
Found at i:2113293 original size:21 final size:21
Alignment explanation
Indices: 2113267--2113724 Score: 376
Period size: 21 Copynumber: 22.1 Consensus size: 21
2113257 CATATTCTCA
2113267 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
2113288 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
* *
2113309 TTGCGATAGTCGAAGTTCGCA
1 TTGCGATAGTCCAAGTTCGCG
** *
2113330 TTGCGATTTTCCAAATT--CG
1 TTGCGATAGTCCAAGTTCGCG
*
2113349 TTGCGGTAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
* *
2113370 TTGCGATATTCCAAGTTTGCG
1 TTGCGATAGTCCAAGTTCGCG
** * *
2113391 TTGCGATTTTCCAAATT--CT
1 TTGCGATAGTCCAAGTTCGCG
* *
2113410 TTGCGATAGTCAAAGTTCGTG
1 TTGCGATAGTCCAAGTTCGCG
* * *
2113431 TTGCGATTTATTCCAAATT--CA
1 TTGCGA--TAGTCCAAGTTCGCG
* *
2113452 TTGCGATTTATTCCAAATT--CG
1 TTGCGA--TAGTCCAAGTTCGCG
*
2113473 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
*
2113494 TTGCGATTTATTCCAAGTTCG-G
1 TTGCGA--TAGTCCAAGTTCGCG
2113516 TT-CGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
** *
2113536 TTGCGATTTTCCAAATT--CG
1 TTGCGATAGTCCAAGTTCGCG
*
2113555 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
* *
2113576 TTGCGATTTATTCCAAATT--CG
1 TTGCGA--TAGTCCAAGTTCGCG
2113597 TTGCGATAGTCCAAGTTCGCCG
1 TTGCGATAGTCCAAGTTCG-CG
* *
2113619 TTGCAATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
*
2113640 TTGCGATTTATTCCAAGTT--CG
1 TTGCGA--TAGTCCAAGTTCGCG
*
2113661 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
** *
2113682 TTGCGATTTTCCAAATT--CG
1 TTGCGATAGTCCAAGTTCGCG
*
2113701 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
2113722 TTG
1 TTG
2113725 AGATTTATTC
Statistics
Matches: 350, Mismatches: 62, Indels: 50
0.76 0.13 0.11
Matches are distributed among these distances:
19 96 0.27
20 3 0.01
21 193 0.55
22 22 0.06
23 36 0.10
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.35
Consensus pattern (21 bp):
TTGCGATAGTCCAAGTTCGCG
Found at i:2113368 original size:82 final size:84
Alignment explanation
Indices: 2113267--2113646 Score: 401
Period size: 82 Copynumber: 4.6 Consensus size: 84
2113257 CATATTCTCA
* *
2113267 TTGCGATAGTCCAAGTTCGCGTTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCATT
1 TTGCGATAGTCCAAGTTCGCGTTGCGATATTCCAAGTT-GCGTTGCGATAGTCGAAGTTCGCGTT
2113332 GCGA-TT-TTCCAAATTC-G
65 GCGATTTATTCCAAATTCGG
* ** * * *
2113349 TTGCGGTAGTCCAAGTTCGCGTTGCGATATTCCAAGTTTGCGTTGCGATTTTCCAAATT--CTTT
1 TTGCGATAGTCCAAGTTCGCGTTGCGATATTCCAAG-TTGCGTTGCGATAGTCGAAGTTCGCGTT
*
2113412 GCGA--TAGT-CAAAGTTCGTG
65 GCGATTTATTCCAAA-TTCG-G
* * * *
2113431 TTGCGATTTATTCCAAATT--CATTGCGATTTATTCCAAATT-CGTTGCGATAGTCGAAGTTCGC
1 TTGCGA--TAGTCCAAGTTCGCGTTGCGA--TATTCCAAGTTGCGTTGCGATAGTCGAAGTTCGC
*
2113493 GTTGCGATTTATTCCAAGTTCGG
62 GTTGCGATTTATTCCAAATTCGG
* *
2113516 TT-CGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATT-CGTTGCGATAGTCGAAGTTCGCGTTG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATATTCCAAGTTGCGTTGCGATAGTCGAAGTTCGCGTTG
2113579 CGATTTATTCCAAATTC-G
66 CGATTTATTCCAAATTCGG
* * *
2113597 TTGCGATAGTCCAAGTTCGCCGTTGCAATAGTCGAAGTTCGCGTTGCGAT
1 TTGCGATAGTCCAAGTTCG-CGTTGCGATATTCCAAGTT-GCGTTGCGAT
2113647 TTATTCCAAG
Statistics
Matches: 248, Mismatches: 30, Indels: 37
0.79 0.10 0.12
Matches are distributed among these distances:
79 5 0.02
80 11 0.04
81 3 0.01
82 155 0.62
83 18 0.07
84 34 0.14
85 12 0.05
86 7 0.03
87 3 0.01
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.35
Consensus pattern (84 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATATTCCAAGTTGCGTTGCGATAGTCGAAGTTCGCGTTG
CGATTTATTCCAAATTCGG
Found at i:2113705 original size:40 final size:42
Alignment explanation
Indices: 2113617--2113754 Score: 217
Period size: 40 Copynumber: 3.3 Consensus size: 42
2113607 CCAAGTTCGC
* *
2113617 CGTTGCAATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
2113659 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
*
2113699 CGTTGCGATAGTCGAAGTTCGCGTTGAGATTTATTCCAAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCC-AAATT
*
2113742 CGGTGCGATAGTC
1 CGTTGCGATAGTC
2113755 CAAAATCGCA
Statistics
Matches: 89, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
40 36 0.40
41 4 0.04
42 32 0.36
43 17 0.19
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (42 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
Found at i:2113858 original size:6 final size:6
Alignment explanation
Indices: 2113847--2113873 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2113837 GACACGTATT
2113847 ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
2113874 CGAGACGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:2113884 original size:5 final size:5
Alignment explanation
Indices: 2113874--2113905 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
2113864 GACCACGACC
2113874 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CG
1 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CG
2113906 GATGACGGCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.38, C:0.22, G:0.41, T:0.00
Consensus pattern (5 bp):
CGAGA
Found at i:2114442 original size:42 final size:42
Alignment explanation
Indices: 2114380--2114524 Score: 222
Period size: 42 Copynumber: 3.5 Consensus size: 42
2114370 TGCGATTTTG
*
2114380 GACTATCGCAAACGAATTTGGAATAAATCGCAACACGAACTTC
1 GACTATCGC-AACGAATTTGGAATAAATCGCAACGCGAACTTC
* *
2114423 GACTATCGCAACGAATTTGGACT--ATCGCAACGCGAACTTG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
2114463 GACTATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
2114505 GACTATCGCAACGAACTTTG
1 GACTATCGCAACGAA-TTTG
2114525 ACTATCGCAA
Statistics
Matches: 93, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
40 37 0.40
42 43 0.46
43 13 0.14
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.23
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:2114485 original size:82 final size:83
Alignment explanation
Indices: 2114377--2114536 Score: 279
Period size: 82 Copynumber: 1.9 Consensus size: 83
2114367 CGTTGCGATT
2114377 TTGGACTATCGCAAACGAATTTGGAATAAATCGCAACACGAACTTCGACTATCGCAACGAA-TTT
1 TTGGACTATCGCAAACGAATTTGGAATAAATCGCAACACGAACTTCGACTATCGCAACGAACTTT
2114441 GGACTATCGCAACGCGAAC
66 -GACTATCGCAACGCGAAC
**
2114460 TTGGACTATCGC-AACGAATTTGGAATAAATCGCAATGCGAACTTCGACTATCGCAACGAACTTT
1 TTGGACTATCGCAAACGAATTTGGAATAAATCGCAACACGAACTTCGACTATCGCAACGAACTTT
2114524 GACTATCGCAACG
66 GACTATCGCAACG
2114537 AATTTTGAAT
Statistics
Matches: 74, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
82 59 0.80
83 15 0.20
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (83 bp):
TTGGACTATCGCAAACGAATTTGGAATAAATCGCAACACGAACTTCGACTATCGCAACGAACTTT
GACTATCGCAACGCGAAC
Found at i:2114494 original size:61 final size:60
Alignment explanation
Indices: 2114427--2114560 Score: 189
Period size: 61 Copynumber: 2.2 Consensus size: 60
2114417 AACTTCGACT
* *
2114427 ATCGCAA-CGAATTTGGACTATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAA
1 ATCGCAAGCGAACTTCGACTATCGCAA--CGAACTTGGACTATCGCAACGAATTTGGAATAA
* *
2114488 ATCGCAATGCGAACTTCGACTATCGCAACGAACTTTGACTATCGCAACGAATTTTGAATAA
1 ATCGCAA-GCGAACTTCGACTATCGCAACGAACTTGGACTATCGCAACGAATTTGGAATAA
2114549 ATCGCAATGCGA
1 ATCGCAA-GCGA
2114561 TAGTCGAAGT
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
61 50 0.75
63 17 0.25
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.24
Consensus pattern (60 bp):
ATCGCAAGCGAACTTCGACTATCGCAACGAACTTGGACTATCGCAACGAATTTGGAATAA
Found at i:2114544 original size:19 final size:19
Alignment explanation
Indices: 2114376--2114541 Score: 154
Period size: 19 Copynumber: 8.2 Consensus size: 19
2114366 TCGTTGCGAT
2114376 TTTGGACTATCGCAAACGAA
1 TTTGGACTATCGC-AACGAA
*
2114396 TTTGGAATAAATCGCAACACGAA
1 TTTGGACT--ATCGC-A-ACGAA
* *
2114419 CTTCGACTATCGCAACGAA
1 TTTGGACTATCGCAACGAA
2114438 TTTGGACTATCGCAACGCGAA
1 TTTGGACTATCGCAA--CGAA
*
2114459 CTTGGACTATCGCAACGAA
1 TTTGGACTATCGCAACGAA
*
2114478 TTTGGAATAAATCGCAATGCGAA
1 TTTGGACT--ATCGCAA--CGAA
* *
2114501 CTTCGACTATCGCAACGAA
1 TTTGGACTATCGCAACGAA
2114520 CTTT-GACTATCGCAACGAA
1 -TTTGGACTATCGCAACGAA
2114539 TTT
1 TTT
2114542 TGAATAAATC
Statistics
Matches: 123, Mismatches: 13, Indels: 22
0.78 0.08 0.14
Matches are distributed among these distances:
18 3 0.02
19 47 0.38
20 10 0.08
21 37 0.30
22 7 0.06
23 19 0.15
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.25
Consensus pattern (19 bp):
TTTGGACTATCGCAACGAA
Found at i:2115785 original size:187 final size:183
Alignment explanation
Indices: 2115474--2115844 Score: 690
Period size: 187 Copynumber: 2.0 Consensus size: 183
2115464 TAAGGGAATT
2115474 CAGTATTGTTTCCCTTTAATGGAATAATTTACTATGTGTCCTCTTAACTAAAAAATTCTTTTATA
1 CAGTATTGTTTCCCTTTAATGGAATAATTTACTATGTGTCCTCTTAACTAAAAAATTCTTTTATA
2115539 ATCATTAGGCCTACATTTTGTCCGACAATTTTAACTACACTCTCACATTATTCTATAGACCCCTC
66 ATCATTAGGCCTACATTTTGTCCGACAATTTTAACTACACTCTCACATTATTCTATAGACCCCTC
2115604 GGATCAATCCTCATGTTGAGTCGAAAATCCAGGTCGTTACGAGCTATGTGAAG
131 GGATCAATCCTCATGTTGAGTCGAAAATCCAGGTCGTTACGAGCTATGTGAAG
2115657 CAGTATTGTTTCCCTTTAATGGAATAATTTACTATGTGGTCCTCTTTAACT-AAAAATTCACTTT
1 CAGTATTGTTTCCCTTTAATGGAATAATTTACTATGT-GTCCTC-TTAACTAAAAAATT--C-TT
2115721 TTATAATCATTAGGCCTACATTTTGTCCGACAATTTTAACTACACTCTCACATTATTCTATAGAC
61 TTATAATCATTAGGCCTACATTTTGTCCGACAATTTTAACTACACTCTCACATTATTCTATAGAC
2115786 CCCTCGGATCAATCCTCATGTTGAGTCGAAAATCCAGGTCGTTACGAGCTATGTGAAG
126 CCCTCGGATCAATCCTCATGTTGAGTCGAAAATCCAGGTCGTTACGAGCTATGTGAAG
2115844 C
1 C
2115845 CTCAGGCAGT
Statistics
Matches: 183, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
183 37 0.20
184 13 0.07
185 6 0.03
186 1 0.01
187 126 0.69
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.36
Consensus pattern (183 bp):
CAGTATTGTTTCCCTTTAATGGAATAATTTACTATGTGTCCTCTTAACTAAAAAATTCTTTTATA
ATCATTAGGCCTACATTTTGTCCGACAATTTTAACTACACTCTCACATTATTCTATAGACCCCTC
GGATCAATCCTCATGTTGAGTCGAAAATCCAGGTCGTTACGAGCTATGTGAAG
Found at i:2116998 original size:16 final size:16
Alignment explanation
Indices: 2116977--2117009 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2116967 CTCCAAAATA
*
2116977 AAACACATATATAATT
1 AAACACATACATAATT
2116993 AAACACATACATAATT
1 AAACACATACATAATT
2117009 A
1 A
2117010 TAAAAACTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (16 bp):
AAACACATACATAATT
Found at i:2117086 original size:31 final size:31
Alignment explanation
Indices: 2117048--2117181 Score: 175
Period size: 31 Copynumber: 4.3 Consensus size: 31
2117038 TTAGGGTTTG
2117048 TATATATAATTAATATAAAAATAAAAAATAT
1 TATATATAATTAATATAAAAATAAAAAATAT
* *
2117079 TATATATAATTAATAT-AAAA-AAATAGTA-
1 TATATATAATTAATATAAAAATAAAAAATAT
2117107 TATATATAATTAATATAAAAAATAAAAAAAATATT
1 TATATATAATTAATAT-AAAAAT--AAAAAATA-T
*
2117142 ATATATATAATTAATATAAAAATTAAAAATAT
1 -TATATATAATTAATATAAAAATAAAAAATAT
2117174 TATATATA
1 TATATATA
2117182 TATAATTGAG
Statistics
Matches: 90, Mismatches: 5, Indels: 16
0.81 0.05 0.14
Matches are distributed among these distances:
28 16 0.18
29 6 0.07
30 8 0.09
31 24 0.27
32 1 0.01
33 13 0.14
35 6 0.07
36 16 0.18
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.37
Consensus pattern (31 bp):
TATATATAATTAATATAAAAATAAAAAATAT
Found at i:2117145 original size:36 final size:35
Alignment explanation
Indices: 2117090--2117188 Score: 144
Period size: 36 Copynumber: 2.7 Consensus size: 35
2117080 ATATATAATT
2117090 AATATAAAAAAATAGTATATATATAATTAATATAAAA
1 AATA-AAAAAAATA-TATATATATAATTAATATAAAA
2117127 AATAAAAAAAATATTATATATATAATTAATATAAAA
1 AATAAAAAAAATA-TATATATATAATTAATATAAAA
* * *
2117163 ATTAAAAATATTATATATATATAATT
1 AATAAAAAAAATATATATATATAATT
2117189 GAGGTGGGGA
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
35 13 0.22
36 41 0.71
37 4 0.07
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (35 bp):
AATAAAAAAAATATATATATATAATTAATATAAAA
Found at i:2117186 original size:62 final size:62
Alignment explanation
Indices: 2117048--2117181 Score: 184
Period size: 64 Copynumber: 2.1 Consensus size: 62
2117038 TTAGGGTTTG
* *
2117048 TATATATAATTAATAT-AAAAAT--AAAAAATATTATATATAATTAATATAAAAAAATAGTA
1 TATATATAATTAATATAAAAAATAAAAAAAATATTATATATAATTAATATAAAAAAAAAATA
2117107 TATATATAATTAATATAAAAAATAAAAAAAATATTATATATATAATTAATATAAAAATTAAAAAT
1 TATATATAATTAATATAAAAAATAAAAAAAATA-T-TATATATAATTAATATAAAAA--AAAAAT
2117172 A
62 A
2117173 TTATATATA
1 -TATATATA
2117182 TATAATTGAG
Statistics
Matches: 65, Mismatches: 2, Indels: 8
0.87 0.03 0.11
Matches are distributed among these distances:
59 16 0.25
60 6 0.09
62 8 0.12
63 1 0.02
64 21 0.32
66 5 0.08
67 8 0.12
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.37
Consensus pattern (62 bp):
TATATATAATTAATATAAAAAATAAAAAAAATATTATATATAATTAATATAAAAAAAAAATA
Found at i:2129906 original size:21 final size:21
Alignment explanation
Indices: 2129880--2129924 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2129870 GATTTCTGGG
* *
2129880 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
2129901 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
2129922 CAA
1 CAA
2129925 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:2129978 original size:21 final size:22
Alignment explanation
Indices: 2129947--2129988 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
2129937 TCCAGAATGC
2129947 CAGAGGGGAACCGATACCCCCA
1 CAGAGGGGAACCGATACCCCCA
*
2129969 CAGA-GGGAACCGATTCCCCC
1 CAGAGGGGAACCGATACCCCC
2129989 TAAAGGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.29, C:0.38, G:0.26, T:0.07
Consensus pattern (22 bp):
CAGAGGGGAACCGATACCCCCA
Found at i:2131278 original size:59 final size:59
Alignment explanation
Indices: 2131203--2131355 Score: 238
Period size: 59 Copynumber: 2.6 Consensus size: 59
2131193 TCGAGACATA
2131203 TGGACAGTTTACCGAGGATCTTTATGACCTCTGGACAGTTTACCGAGGA-TTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTCTGGACAG-TTACCGAGGACTTTATGACCTC
2131263 TGGACAGTTACCGAGGATCTTTATGACCTCTGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTCTGGACAGTTACCGAGGA-CTTTATGACCTC
* **
2131323 TGGACAGTTACCG-GGGTCTTGGTGACCTCTGGA
1 TGGACAGTTACCGAGGATCTTTATGACCTCTGGA
2131356 TAGGTCCTTC
Statistics
Matches: 88, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
58 10 0.11
59 47 0.53
60 31 0.35
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (59 bp):
TGGACAGTTACCGAGGATCTTTATGACCTCTGGACAGTTACCGAGGACTTTATGACCTC
Found at i:2131288 original size:30 final size:30
Alignment explanation
Indices: 2131203--2131355 Score: 240
Period size: 30 Copynumber: 5.1 Consensus size: 30
2131193 TCGAGACATA
2131203 TGGACAGTTTACCGAGGATCTTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
2131234 TGGACAGTTTACCGAGGA--TTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
2131263 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
2131293 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* **
2131323 TGGACAGTTACCG-GGGTCTTGGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
2131352 TGGA
1 TGGA
2131356 TAGGTCCTTC
Statistics
Matches: 117, Mismatches: 3, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
28 10 0.09
29 35 0.30
30 54 0.46
31 18 0.15
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:2135785 original size:20 final size:20
Alignment explanation
Indices: 2135760--2135797 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2135750 CAATTTATTC
2135760 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
2135780 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
2135798 CACTTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:2137501 original size:23 final size:22
Alignment explanation
Indices: 2137471--2137551 Score: 83
Period size: 23 Copynumber: 3.6 Consensus size: 22
2137461 GCATGGCCTT
2137471 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
2137493 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
* *
2137515 GTGTATCGACGCACATTCAAAGG
1 GTGCATCGATGCACATTC-AAGG
*
2137538 ATGCATCGATGCAC
1 GTGCATCGATGCAC
2137552 TGTTAAGTGT
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
21 14 0.31
22 2 0.04
23 29 0.64
ACGTcount: A:0.25, C:0.26, G:0.26, T:0.23
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:2143033 original size:27 final size:27
Alignment explanation
Indices: 2143003--2143065 Score: 94
Period size: 27 Copynumber: 2.3 Consensus size: 27
2142993 CAAAATAGCC
2143003 TGAGTGCATCGATGCATGGCT-TGTGCA
1 TGAGTGCATCGATGCATGG-TATGTGCA
2143030 TGAGTGCATCGATGCATGGTATGTGCA
1 TGAGTGCATCGATGCATGGTATGTGCA
2143057 TCGA-TGCAT
1 T-GAGTGCAT
2143066 AAAATGCATT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
26 1 0.03
27 31 0.91
28 2 0.06
ACGTcount: A:0.21, C:0.17, G:0.32, T:0.30
Consensus pattern (27 bp):
TGAGTGCATCGATGCATGGTATGTGCA
Found at i:2143101 original size:91 final size:92
Alignment explanation
Indices: 2142961--2143131 Score: 224
Period size: 91 Copynumber: 1.9 Consensus size: 92
2142951 TACACTAAGA
* *
2142961 GTGCATCGATGCATGAAATGAATTCGATGTTTCAAAATAGCCTGAGTGCATCGATGCATGGCTT-
1 GTGCATCGATGCATAAAATGAATTCGATGTTTCAAAATAGCCTGAGTGCATCGATGCATGGATTG
2143025 GTGCAT-GAGTGCATCGATGCATGGTAT
66 GTGCATCG-GTGCATCGATGCATGGTAT
* ** * *
2143052 GTGCATCGATGCATAAAATGCATTCGATG-TTCAATTTATTCATTG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATAAAATGAATTCGATGTTTCAAAATA-GC-CTGAGTGCATCGATGCATGGAT
2143115 TGGTGCATCGGTGCATC
64 TGGTGCATCGGTGCATC
2143132 ACTTTGAAAA
Statistics
Matches: 69, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
90 7 0.10
91 46 0.67
92 15 0.22
93 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (92 bp):
GTGCATCGATGCATAAAATGAATTCGATGTTTCAAAATAGCCTGAGTGCATCGATGCATGGATTG
GTGCATCGGTGCATCGATGCATGGTAT
Found at i:2143118 original size:20 final size:20
Alignment explanation
Indices: 2143093--2143130 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2143083 CAATTTATTC
2143093 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
2143113 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
2143131 CACTTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:2145268 original size:16 final size:16
Alignment explanation
Indices: 2145249--2145288 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
2145239 AATGAGTACC
2145249 GAGCTTAACGAGTAAT
1 GAGCTTAACGAGTAAT
2145265 GAGCTTAACGAGTAAT
1 GAGCTTAACGAGTAAT
2145281 GAGCTTAA
1 GAGCTTAA
2145289 TGAGCAACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.25
Consensus pattern (16 bp):
GAGCTTAACGAGTAAT
Found at i:2150468 original size:18 final size:18
Alignment explanation
Indices: 2150445--2150482 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2150435 TTTATATACC
2150445 AATAAA-AATCTAGATTTA
1 AATAAATAAT-TAGATTTA
*
2150463 AATAAATAATTTGATTTA
1 AATAAATAATTAGATTTA
2150481 AA
1 AA
2150483 CTTATCCCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (18 bp):
AATAAATAATTAGATTTA
Found at i:2151152 original size:21 final size:21
Alignment explanation
Indices: 2151106--2151152 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
2151096 ATACATCGCA
*
2151106 AACGATTTTGTAATAAGATTT
1 AACGTTTTTGTAATAAGATTT
2151127 AACGTTTTTGTAATAAGATTT
1 AACGTTTTTGTAATAAGATTT
2151148 AACGT
1 AACGT
2151153 GTTTCAGTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.36, C:0.06, G:0.15, T:0.43
Consensus pattern (21 bp):
AACGTTTTTGTAATAAGATTT
Found at i:2151494 original size:19 final size:19
Alignment explanation
Indices: 2151470--2151527 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
2151460 CCGAAATCGA
2151470 TTTTTTCGGTTCGGTTCGG
1 TTTTTTCGGTTCGGTTCGG
*
2151489 TTTTTT---TAACGGTTCGG
1 TTTTTTCGGT-TCGGTTCGG
*
2151506 GTTTTTCGGTTCGGTTCGG
1 TTTTTTCGGTTCGGTTCGG
2151525 TTT
1 TTT
2151528 ATCGGTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
16 1 0.03
17 13 0.42
19 16 0.52
20 1 0.03
ACGTcount: A:0.03, C:0.14, G:0.29, T:0.53
Consensus pattern (19 bp):
TTTTTTCGGTTCGGTTCGG
Found at i:2151526 original size:18 final size:18
Alignment explanation
Indices: 2151471--2151534 Score: 71
Period size: 18 Copynumber: 3.6 Consensus size: 18
2151461 CGAAATCGAT
2151471 TTTTTCGGTTCGGTTCGG
1 TTTTTCGGTTCGGTTCGG
2151489 TTTTT---TTAACGGTTCGGG
1 TTTTTCGGTT--CGGTTC-GG
2151507 TTTTTCGGTTCGGTTCGG
1 TTTTTCGGTTCGGTTCGG
*
2151525 TTTATCGGTT
1 TTTTTCGGTT
2151535 TTTCAATAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
15 2 0.05
17 6 0.15
18 23 0.59
19 6 0.15
21 2 0.05
ACGTcount: A:0.05, C:0.14, G:0.30, T:0.52
Consensus pattern (18 bp):
TTTTTCGGTTCGGTTCGG
Found at i:2156903 original size:28 final size:25
Alignment explanation
Indices: 2156868--2156917 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
2156858 AATGCACATA
2156868 ATAATAATAATTAAAAACATTGTAC
1 ATAATAATAATTAAAAACATTGTAC
2156893 ATAATAATAATTAAAAACATTGTAC
1 ATAATAATAATTAAAAACATTGTAC
2156918 CGAATCTCAA
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:0.56, C:0.08, G:0.04, T:0.32
Consensus pattern (25 bp):
ATAATAATAATTAAAAACATTGTAC
Found at i:2158025 original size:12 final size:12
Alignment explanation
Indices: 2158008--2158032 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2157998 TACTAATATT
2158008 ATGAATATGAAA
1 ATGAATATGAAA
2158020 ATGAATATGAAA
1 ATGAATATGAAA
2158032 A
1 A
2158033 AATATGCAGG
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:0.60, C:0.00, G:0.16, T:0.24
Consensus pattern (12 bp):
ATGAATATGAAA
Found at i:2161349 original size:43 final size:42
Alignment explanation
Indices: 2161253--2161452 Score: 231
Period size: 42 Copynumber: 4.7 Consensus size: 42
2161243 CTGCAAAAGG
* * * *
2161253 TAGCGGCG-TTTTCTGAAAAATGCCGTAAAAGGTCAAGATCTA
1 TAGCGGCGTTTTTCT-TAAAACGCCGCAAAAGGTCAAGCTCTA
* *
2161295 TAGCGGCGTTTTTCTTAAAACGCCACAAAAGGCCAAGCTCTA
1 TAGCGGCGTTTTTCTTAAAACGCCGCAAAAGGTCAAGCTCTA
* * *
2161337 TAGCGCCGGTTTTCTTTAAAACGCCGCAAAAGGTCAAACTCTA
1 TAGCGGCGTTTTTC-TTAAAACGCCGCAAAAGGTCAAGCTCTA
* * * *
2161380 TAGCGGCGTTTTTCTTTAAACGTCGTAAAAGGTCAAGCTTTA
1 TAGCGGCGTTTTTCTTAAAACGCCGCAAAAGGTCAAGCTCTA
*
2161422 TAGCGGCGTTTGTTTTCTAAAACGCCGCAAA
1 TAGCGGCGTTT-TTCT-TAAAACGCCGCAAA
2161453 TGTGTGGTCA
Statistics
Matches: 132, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
42 75 0.57
43 46 0.35
44 11 0.08
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.28
Consensus pattern (42 bp):
TAGCGGCGTTTTTCTTAAAACGCCGCAAAAGGTCAAGCTCTA
Found at i:2161410 original size:85 final size:84
Alignment explanation
Indices: 2161253--2161452 Score: 240
Period size: 85 Copynumber: 2.3 Consensus size: 84
2161243 CTGCAAAAGG
* ** * *
2161253 TAGCGGCGTTTTCTGAAAAATGCCGTAAAAGGTCAAGATCTATAGCGGCGTTTTTCTTAAAACGC
1 TAGCGCCGTTTTCTTTAAAACGCCGCAAAAGGTCAAGATCTATAGCGGCGTTTTTCTTAAAACGC
2161318 CACAAAAGGCCAAGCTCTA
66 CACAAAAGGCCAAGCTCTA
*
2161337 TAGCGCCGGTTTTCTTTAAAACGCCGCAAAAGGTCAA-ACTCTATAGCGGCGTTTTTCTTTAAAC
1 TAGCGCC-GTTTTCTTTAAAACGCCGCAAAAGGTCAAGA-TCTATAGCGGCGTTTTTCTTAAAAC
* ** * *
2161401 GTCGTAAAAGGTCAAGCTTTA
64 GCCACAAAAGGCCAAGCTCTA
* *
2161422 TAGCGGCGTTTGTTTTCTAAAACGCCGCAAA
1 TAGCGCCGTTT-TCTT-TAAAACGCCGCAAA
2161453 TGTGTGGTCA
Statistics
Matches: 99, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
84 11 0.11
85 74 0.75
86 14 0.14
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.28
Consensus pattern (84 bp):
TAGCGCCGTTTTCTTTAAAACGCCGCAAAAGGTCAAGATCTATAGCGGCGTTTTTCTTAAAACGC
CACAAAAGGCCAAGCTCTA
Found at i:2165316 original size:41 final size:41
Alignment explanation
Indices: 2165271--2165647 Score: 314
Period size: 41 Copynumber: 9.2 Consensus size: 41
2165261 CGAATCTTTG
*
2165271 GCGGCGTTTGTGCTTAAAATGCCACTAAAGTATAGTATTTA
1 GCGGCGTTTGTGCTTAAAACGCCACTAAAGTATAGTATTTA
* * * * * *
2165312 GCGGCATTTATAC-AAAAACGCCACTAAAGTACAAGCATTTA
1 GCGGCGTTTGTGCTTAAAACGCCACTAAAGTA-TAGTATTTA
* * *
2165353 GCAGCGTTTGTGCTTAAAACACCACTAAAATATAGTATTTA
1 GCGGCGTTTGTGCTTAAAACGCCACTAAAGTATAGTATTTA
* * * * * * * *
2165394 GCGGCGTATATAC-AAAAATGCCACTAAAGTACGAGCACTTA
1 GCGGCGTTTGTGCTTAAAACGCCACTAAAGTA-TAGTATTTA
* * *
2165435 GCGTCGTTTGTGCTTAAAACGCCACTAAAGTATAGCATATA
1 GCGGCGTTTGTGCTTAAAACGCCACTAAAGTATAGTATTTA
* * * * * * * *
2165476 GCGGCGTTTTATAC-AAAAATGCCACTAAAGAACGAGCACTTA
1 GCGGCG-TTTGTGCTTAAAACGCCACTAAAGTA-TAGTATTTA
*
2165518 GCGGCGTTTGTGCTTAAAACGCCACTAAAGTACAGTATTTA
1 GCGGCGTTTGTGCTTAAAACGCCACTAAAGTATAGTATTTA
* * * * * *
2165559 GCGGCGTTTGTGCTTGAAACGCTACTAAAATACATTATTAA
1 GCGGCGTTTGTGCTTAAAACGCCACTAAAGTATAGTATTTA
* * * *
2165600 GCGGCGTTTATAC--AAAACACCACTAAAGTATATTATTTA
1 GCGGCGTTTGTGCTTAAAACGCCACTAAAGTATAGTATTTA
*
2165639 ACGGCGTTT
1 GCGGCGTTT
2165648 ATATAAAAGC
Statistics
Matches: 262, Mismatches: 67, Indels: 16
0.76 0.19 0.05
Matches are distributed among these distances:
39 28 0.11
40 30 0.11
41 141 0.54
42 63 0.24
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (41 bp):
GCGGCGTTTGTGCTTAAAACGCCACTAAAGTATAGTATTTA
Found at i:2165586 original size:83 final size:82
Alignment explanation
Indices: 2165203--2165667 Score: 492
Period size: 82 Copynumber: 5.7 Consensus size: 82
2165193 GTTTATTCAA
** * * * * *
2165203 AAAACGCCACTAAAGTACGGGTATTTAGCGACGTTTATATAGAAACACCTCTAAAGTACGA--AT
1 AAAACGCCACTAAAGTA-TAGTATTTAGCGGCGTTTATACAAAAACGCCACTAAAGTACGAGCA-
*
2165266 CTTTGGCGGCGTTTGTGCTT
64 C-TTAGCGGCGTTTGTGCTT
* * * *
2165286 AAAATGCCACTAAAGTATAGTATTTAGCGGCATTTATACAAAAACGCCACTAAAGTACAAGCATT
1 AAAACGCCACTAAAGTATAGTATTTAGCGGCGTTTATACAAAAACGCCACTAAAGTACGAGCACT
*
2165351 TAGCAGCGTTTGTGCTT
66 TAGCGGCGTTTGTGCTT
* * * *
2165368 AAAACACCACTAAAATATAGTATTTAGCGGCGTATATACAAAAATGCCACTAAAGTACGAGCACT
1 AAAACGCCACTAAAGTATAGTATTTAGCGGCGTTTATACAAAAACGCCACTAAAGTACGAGCACT
*
2165433 TAGCGTCGTTTGTGCTT
66 TAGCGGCGTTTGTGCTT
* * * *
2165450 AAAACGCCACTAAAGTATAGCATATAGCGGCGTTTTATACAAAAATGCCACTAAAGAACGAGCAC
1 AAAACGCCACTAAAGTATAGTATTTAGCGGCG-TTTATACAAAAACGCCACTAAAGTACGAGCAC
2165515 TTAGCGGCGTTTGTGCTT
65 TTAGCGGCGTTTGTGCTT
* * * ** * * **
2165533 AAAACGCCACTAAAGTACAGTATTTAGCGGCGTTTGTGCTTGAAACGCTACTAAAATAC-ATTA-
1 AAAACGCCACTAAAGTATAGTATTTAGCGGCGTTTATAC-AAAAACGCCACTAAAGTACGAGCAC
* *
2165596 TTAAGCGGCGTTTATAC--
65 TT-AGCGGCGTTTGTGCTT
* * * * *
2165613 AAAACACCACTAAAGTATATTATTTAACGGCGTTTATATAAAAGCGCCACTAAAG
1 AAAACGCCACTAAAGTATAGTATTTAGCGGCGTTTATACAAAAACGCCACTAAAG
2165668 AACAAGTATA
Statistics
Matches: 320, Mismatches: 57, Indels: 14
0.82 0.15 0.04
Matches are distributed among these distances:
79 11 0.03
80 32 0.10
81 2 0.01
82 169 0.53
83 105 0.33
84 1 0.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.27
Consensus pattern (82 bp):
AAAACGCCACTAAAGTATAGTATTTAGCGGCGTTTATACAAAAACGCCACTAAAGTACGAGCACT
TAGCGGCGTTTGTGCTT
Found at i:2170793 original size:21 final size:21
Alignment explanation
Indices: 2170767--2170811 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
2170757 AAGACGATGA
2170767 TGGTGGTTGTGATGATCATGT
1 TGGTGGTTGTGATGATCATGT
2170788 TGGTGGTTGTGATGATCATGT
1 TGGTGGTTGTGATGATCATGT
2170809 TGG
1 TGG
2170812 CGATAATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.13, C:0.04, G:0.40, T:0.42
Consensus pattern (21 bp):
TGGTGGTTGTGATGATCATGT
Found at i:2173909 original size:3 final size:3
Alignment explanation
Indices: 2173901--2173954 Score: 56
Period size: 3 Copynumber: 18.3 Consensus size: 3
2173891 CTTTTTTAAA
** ** *
2173901 TAT TAT TAT CGT TAT T-T TAT TAT TAT TAT TAT TAT TAT GCT TAT TTT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2173948 TAT TAT T
1 TAT TAT T
2173955 TTTTTATTTA
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2192600 original size:30 final size:30
Alignment explanation
Indices: 2192487--2192606 Score: 127
Period size: 30 Copynumber: 4.0 Consensus size: 30
2192477 GGCTTAGTCC
* ** *
2192487 ACATCTGCATGGGATTAATTCTCCATTATG
1 ACATCTGCATGAGATTAATTCTCTGTTCTG
* * * *
2192517 ACATTTGCATGAGATCAATTCCCCT-TTTTG
1 ACATCTGCATGAGATTAATT-CTCTGTTCTG
*
2192547 ACATCTGCATGGGATTAATTCTCTGTTCTG
1 ACATCTGCATGAGATTAATTCTCTGTTCTG
2192577 ACATCTGCATGAGATT-ATATCTCTGTTCTG
1 ACATCTGCATGAGATTAAT-TCTCTGTTCTG
2192607 TTTCTGTTGG
Statistics
Matches: 75, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
29 5 0.07
30 68 0.91
31 2 0.03
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.39
Consensus pattern (30 bp):
ACATCTGCATGAGATTAATTCTCTGTTCTG
Done.