Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007993.1 Hibiscus syriacus cultivar Beakdansim tig00110443_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: 2245901
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 12
Found at i:2096376 original size:151 final size:151
Alignment explanation
Indices: 2096086--2096621 Score: 907
Period size: 151 Copynumber: 3.5 Consensus size: 151
2096076 TAAAGCCTTA
2096086 GGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTT
1 GGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTT
*
2096151 T-AAAGCCTTC-GGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAGAGCCTTCGGGAGC
66 TCAAATCC-TCAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAGAGCCTTCGGGAGC
*
2096214 TTTTTGATGTTTTCAAATCCTC
130 TTTTTGATGTTTTCAAACCCTC
* *
2096236 GGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAGAGCCTTCGAGAGCTTTTTGATGTTT
1 GGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTT
*
2096301 TCAAATCCTCAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCT
66 TCAAATCCTCAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAGAGCCTTCGGGAGCT
*
2096366 TTTTGATGTTTT-AAAGCCTTC
131 TTTTGATGTTTTCAAA-CCCTC
*
2096387 GGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAGAGCCTTCGGGAGCTTTTTGATGTTT
1 GGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTT
*
2096452 TCAAATCCTCAGGGTCATCTGTAAGTCCTTTAGTGCATGATGTTTCCAAAGAGCCTTCGGGAGCT
66 TCAAATCCTCAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAGAGCCTTCGGGAGCT
2096517 TTTTGATGTTTTCAAACCCTC
131 TTTTGATGTTTTCAAACCCTC
* *
2096538 AGGGTCATCTGTAAGTCCTGCAGTGTATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTT
1 -GGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTT
* * *
2096603 TTTAAACCCTCGGGGTCAT
65 TTCAAATCCTCAGGGTCAT
2096622 TCATAAGACC
Statistics
Matches: 365, Mismatches: 16, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
150 69 0.19
151 216 0.59
152 80 0.22
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.36
Consensus pattern (151 bp):
GGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTT
TCAAATCCTCAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAGAGCCTTCGGGAGCT
TTTTGATGTTTTCAAACCCTC
Found at i:2096787 original size:3 final size:3
Alignment explanation
Indices: 2096779--2096844 Score: 62
Period size: 3 Copynumber: 21.3 Consensus size: 3
2096769 TTTTACTTAA
** * *
2096779 ATT ATT ATT AAA ATT ATT ATT ATT ATT AAAT ATT ATT ATT ATA ATAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT AT-T
2096826 ATAT ATT A-T ATT ATT ATT A
1 AT-T ATT ATT ATT ATT ATT A
2096845 AATAATTTTA
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
2 2 0.04
3 42 0.81
4 8 0.15
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (3 bp):
ATT
Found at i:2096819 original size:22 final size:21
Alignment explanation
Indices: 2096779--2096844 Score: 70
Period size: 19 Copynumber: 3.3 Consensus size: 21
2096769 TTTTACTTAA
2096779 ATTATTATTAAA-ATTATTATT
1 ATTATTA-TAAATATTATTATT
2096800 ATTA-T-TAAATATTATTATT
1 ATTATTATAAATATTATTATT
* *
2096819 A-TAATATATATATTA-TATT
1 ATTATTATAAATATTATTATT
2096838 ATTATTA
1 ATTATTA
2096845 AATAATTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
18 6 0.15
19 16 0.41
20 13 0.33
21 4 0.10
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTATTATAAATATTATTATT
Found at i:2096832 original size:14 final size:14
Alignment explanation
Indices: 2096779--2096844 Score: 71
Period size: 14 Copynumber: 4.5 Consensus size: 14
2096769 TTTTACTTAA
*
2096779 ATTATTATTAAAATT
1 ATTATTATTATAA-T
2096794 ATTATTATTATTAAAT
1 ATTATTATTA-T-AAT
2096810 ATTATTATTATAAT
1 ATTATTATTATAAT
*
2096824 A-TATATATTATATT
1 ATTAT-TATTATAAT
2096838 ATTATTA
1 ATTATTA
2096845 AATAATTTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
13 3 0.07
14 15 0.33
15 14 0.31
16 11 0.24
17 2 0.04
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
ATTATTATTATAAT
Found at i:2099582 original size:20 final size:20
Alignment explanation
Indices: 2099545--2099583 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2099535 TTTTCATCAC
*
2099545 TTTATATCTTTATTTTATTA
1 TTTATATCTTTATATTATTA
2099565 TTTATAT-TTTATAATTATT
1 TTTATATCTTTAT-ATTATT
2099584 TAATCGCGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTATATCTTTATATTATTA
Found at i:2102270 original size:21 final size:22
Alignment explanation
Indices: 2102227--2102271 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
2102217 TTAAGATAAT
*
2102227 ATTTGAAAATTTATATTTCAAA
1 ATTTGAAAATTCATATTTCAAA
*
2102249 ATTT-AAAATTCATACTTTAAAA
1 ATTTGAAAATTCATA-TTTCAAA
2102271 A
1 A
2102272 ACCCATACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (22 bp):
ATTTGAAAATTCATATTTCAAA
Found at i:2103787 original size:20 final size:21
Alignment explanation
Indices: 2103732--2103776 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2103722 TGATTTTGAA
* *
2103732 AAAATTGAAAGTTTAGGTACT
1 AAAACTGATAGTTTAGGTACT
*
2103753 AAAACTGATAGTTTATGTACT
1 AAAACTGATAGTTTAGGTACT
2103774 AAA
1 AAA
2103777 CACGTAGTTT
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:0.44, C:0.07, G:0.16, T:0.33
Consensus pattern (21 bp):
AAAACTGATAGTTTAGGTACT
Found at i:2104849 original size:45 final size:46
Alignment explanation
Indices: 2104769--2104857 Score: 135
Period size: 45 Copynumber: 2.0 Consensus size: 46
2104759 GAAAAAGCCT
* * *
2104769 GAGTGCATTGATGCATGGTCTTGTGCATCGATGCATCAAATGCACA
1 GAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCACA
*
2104815 GAGTGTATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 GAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
2104858 TTCGATGTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 22 0.56
46 17 0.44
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (46 bp):
GAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCACA
Found at i:2104902 original size:20 final size:20
Alignment explanation
Indices: 2104877--2104914 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2104867 TGAAAAATTA
2104877 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
2104897 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
2104915 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:2113016 original size:45 final size:46
Alignment explanation
Indices: 2112930--2113018 Score: 135
Period size: 45 Copynumber: 2.0 Consensus size: 46
2112920 GAAAAAGCCT
** * *
2112930 GAGTGCATTGATGCATGGTCTTGTGCATCGATGCATCAAATGCACA
1 GAGTGCATCAATGCATGGTCATGTGCATCGATGCATAAAATGCACA
2112976 GAGTGCATCAATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 GAGTGCATCAATGCATGGTCATGTGCATCGATGCATAAAATGCA
2113019 TTCGATGTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 22 0.56
46 17 0.44
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (46 bp):
GAGTGCATCAATGCATGGTCATGTGCATCGATGCATAAAATGCACA
Found at i:2113063 original size:20 final size:20
Alignment explanation
Indices: 2113038--2113075 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2113028 TGAAAAATTA
2113038 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
2113058 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
2113076 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:2114487 original size:29 final size:29
Alignment explanation
Indices: 2114440--2114549 Score: 73
Period size: 29 Copynumber: 3.7 Consensus size: 29
2114430 TTATGACTCT
* *
2114440 TATTTCAAATTAATTCTTAAATTTTTAAA
1 TATTTCAAATTCATCCTTAAATTTTTAAA
* * *
2114469 TATTTCAATTTCATCCTTAAACTATGATT-CA
1 TATTTCAAATTCATCCTTAAA-T-T-TTTAAA
* *
2114500 TATTTTAAATT-AGTCCTTAAACTTTTAAA
1 TATTTCAAATTCA-TCCTTAAATTTTTAAA
* *
2114529 TATTAT-AATTTCATCCCTAAA
1 TATT-TCAAATTCATCCTTAAA
2114550 CTATGACCCT
Statistics
Matches: 62, Mismatches: 12, Indels: 14
0.70 0.14 0.16
Matches are distributed among these distances:
28 2 0.03
29 35 0.56
30 4 0.06
31 19 0.31
32 2 0.03
ACGTcount: A:0.37, C:0.14, G:0.02, T:0.47
Consensus pattern (29 bp):
TATTTCAAATTCATCCTTAAATTTTTAAA
Found at i:2114526 original size:60 final size:59
Alignment explanation
Indices: 2114431--2114605 Score: 181
Period size: 60 Copynumber: 2.9 Consensus size: 59
2114421 GTCCCCCAAT
* * * * *
2114431 TATGACTCTTATTTCAAATTAATTCTTAAATTTTTAAATATTTCAATTTCATCCTTAAAC
1 TATGA-TCATATTTTAAATTAGTCCTTAAATTTTTAAATATTTCAATTTCATCCCTAAAC
*
2114491 TATGATTCATATTTTAAATTAGTCCTTAAACTTTTAAATATTAT-AATTTCATCCCTAAAC
1 TATGA-TCATATTTTAAATTAGTCCTTAAATTTTTAAATATT-TCAATTTCATCCCTAAAC
* * * * * * * *
2114551 TATGACCCTCTTTCTAAGTTGGTCCCTAAATTTTTGAATATTCCAATTTCATCCC
1 TATGATCATATTT-TAAATTAGTCCTTAAATTTTTAAATATTTCAATTTCATCCC
2114606 CAAATTCATC
Statistics
Matches: 96, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
59 5 0.05
60 90 0.94
61 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.05, T:0.45
Consensus pattern (59 bp):
TATGATCATATTTTAAATTAGTCCTTAAATTTTTAAATATTTCAATTTCATCCCTAAAC
Found at i:2114550 original size:29 final size:28
Alignment explanation
Indices: 2114455--2114551 Score: 81
Period size: 29 Copynumber: 3.3 Consensus size: 28
2114445 CAAATTAATT
*
2114455 CTTAAATTTTTAAATATTTCAATTTCATC
1 CTTAAACTTTTAAATATTT-AATTTCATC
* *
2114484 CTTAAACTATGATT-CATATTTTAAATT-AGTC
1 CTTAAACT-T--TTAAATA-TTTAATTTCA-TC
2114515 CTTAAACTTTTAAATATTATAATTTCATC
1 CTTAAACTTTTAAATATT-TAATTTCATC
*
2114544 CCTAAACT
1 CTTAAACT
2114552 ATGACCCTCT
Statistics
Matches: 54, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
28 4 0.07
29 24 0.44
30 4 0.07
31 17 0.31
32 5 0.09
ACGTcount: A:0.36, C:0.15, G:0.02, T:0.46
Consensus pattern (28 bp):
CTTAAACTTTTAAATATTTAATTTCATC
Found at i:2116585 original size:24 final size:24
Alignment explanation
Indices: 2116524--2116585 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 24
2116514 TCTTAAATGT
2116524 AAAAATAATAA-CAATTGAAGTAAA
1 AAAAATAA-AACCAATTGAAGTAAA
* *
2116548 AAAACATAAAACCAATTTAAGTAAC
1 AAAA-ATAAAACCAATTGAAGTAAA
*
2116573 TAAAATAAAACCA
1 AAAAATAAAACCA
2116586 TGGTTATCAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
24 15 0.45
25 18 0.55
ACGTcount: A:0.65, C:0.11, G:0.05, T:0.19
Consensus pattern (24 bp):
AAAAATAAAACCAATTGAAGTAAA
Found at i:2118367 original size:91 final size:90
Alignment explanation
Indices: 2118186--2118433 Score: 367
Period size: 91 Copynumber: 2.7 Consensus size: 90
2118176 CATCGTTGGA
*
2118186 TTGAACAAGTTCTTCTCATTATGAATTTCTTCTTTCT-TGTTGGATGAG--TTCTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTCT-TTGGATGAGTTTTCTCATTATGAAC
*
2118248 TCTACACTGGAAACACTGATGTAAGG
65 TCTACACTGGAAACACTGATGCAAGG
* *
2118274 TTGAACAAGTTATCCTCATTATGAACTTCTTCTTTCTCTTTGGATGAGTTCTTCTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTCTTTGGATGAGTT-TTCTCATTATGAAC
** *
2118339 TCTTTATTGGAAACACTGATGCAAGG
65 TCTACACTGGAAACACTGATGCAAGG
*
2118365 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTTGGATGAGTTTTTTCTCATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTCTTTGGATGAG--TTTTCTCATTATGAA
2118430 CTCT
64 CTCT
2118434 CCATTGAAAA
Statistics
Matches: 144, Mismatches: 10, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
88 43 0.30
89 1 0.01
91 81 0.56
92 17 0.12
93 2 0.01
ACGTcount: A:0.24, C:0.19, G:0.15, T:0.42
Consensus pattern (90 bp):
TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTCTTTGGATGAGTTTTCTCATTATGAACT
CTACACTGGAAACACTGATGCAAGG
Found at i:2118832 original size:74 final size:76
Alignment explanation
Indices: 2118682--2118832 Score: 200
Period size: 74 Copynumber: 2.0 Consensus size: 76
2118672 AGATCTCTTG
* * * * *
2118682 AGTGAGATAAAATTTCTTGTTTCAAGGGAAAATTGTCTCAAGCGAGACGAAATTAGTTTTAAGAA
1 AGTGAGATAAAATTTCTTGTTTCAAGGGAAAACTGTCTCAAGAGAGACAAAACTAGTTTCAAGAA
2118747 AAACCATCTCA
66 AAACCATCTCA
* * *
2118758 AGTGAGAT-ACATTTCTTGTTTCAAGGG-AAACTGTCTCAAGAGAGACAAAACTCGTTTCAAGGA
1 AGTGAGATAAAATTTCTTGTTTCAAGGGAAAACTGTCTCAAGAGAGACAAAACTAGTTTCAAGAA
2118821 AAA-CAGTCTCA
66 AAACCA-TCTCA
2118832 A
1 A
2118833 AGATTTTTGT
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
73 2 0.03
74 38 0.58
75 18 0.27
76 8 0.12
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.27
Consensus pattern (76 bp):
AGTGAGATAAAATTTCTTGTTTCAAGGGAAAACTGTCTCAAGAGAGACAAAACTAGTTTCAAGAA
AAACCATCTCA
Found at i:2118881 original size:66 final size:67
Alignment explanation
Indices: 2118768--2118898 Score: 167
Period size: 66 Copynumber: 2.0 Consensus size: 67
2118758 AGTGAGATAC
* **
2118768 ATTTCTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTCGTTTC-AAGGAAAACAGTCTCA
1 ATTTCTTGTTTCAAGAGAAACAATCTCAAGAGAGACAAAACTCGTTTCAAAGG-AAACAGTCTCA
2118832 AAG
65 AAG
* * * * *
2118835 ATTT-TTGTTTTAAGAGAAACAATCTCAAGGGAGACAAAATTTGTTTCAAAGGAAACTGTCTCAA
1 ATTTCTTGTTTCAAGAGAAACAATCTCAAGAGAGACAAAACTCGTTTCAAAGGAAACAGTCTCAA
2118899 GCGAGACAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
66 47 0.85
67 8 0.15
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.28
Consensus pattern (67 bp):
ATTTCTTGTTTCAAGAGAAACAATCTCAAGAGAGACAAAACTCGTTTCAAAGGAAACAGTCTCAA
AG
Found at i:2118966 original size:39 final size:39
Alignment explanation
Indices: 2118912--2119143 Score: 401
Period size: 39 Copynumber: 5.9 Consensus size: 39
2118902 AGACAAAATC
* * *
2118912 TTCGAGAGAAACTATCTCATGCGAGATAAAATGTTCTGT
1 TTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCTGT
*
2118951 TTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTTTGT
1 TTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCTGT
2118990 TTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCTGT
1 TTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCTGT
* *
2119029 TTCGAGGGAAAATATCTCAAGCGAGATAAAATCTTATGT
1 TTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCTGT
*
2119068 TTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTATGT
1 TTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCTGT
2119107 TTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCT
1 TTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCT
2119144 TTAAAAAAAT
Statistics
Matches: 184, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 184 1.00
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (39 bp):
TTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCTGT
Found at i:2119084 original size:22 final size:22
Alignment explanation
Indices: 2119059--2119123 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 22
2119049 GCGAGATAAA
2119059 ATCTTATGTTTCGAGGGAAACT
1 ATCTTATGTTTCGAGGGAAACT
* * **
2119081 ATCTCAAG---CGAGATAAA--
1 ATCTTATGTTTCGAGGGAAACT
2119098 ATCTTATGTTTCGAGGGAAACT
1 ATCTTATGTTTCGAGGGAAACT
2119120 ATCT
1 ATCT
2119124 CAAGCGAGAT
Statistics
Matches: 30, Mismatches: 8, Indels: 10
0.62 0.17 0.21
Matches are distributed among these distances:
17 6 0.20
19 7 0.23
20 7 0.23
22 10 0.33
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.32
Consensus pattern (22 bp):
ATCTTATGTTTCGAGGGAAACT
Found at i:2120299 original size:40 final size:39
Alignment explanation
Indices: 2120246--2120321 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 39
2120236 TATTTAGTTA
* *
2120246 AACTTGATTTAATTTGCCATTGTCTGGCTAGTTGAATTT
1 AACTTGATTTAATTTGCCATTATCAGGCTAGTTGAATTT
* *
2120285 AACTTTATTGTAATTTGCCTTTATCAGGCTAGTTGAA
1 AACTTGATT-TAATTTGCCATTATCAGGCTAGTTGAA
2120322 GGGTTCATCT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
39 8 0.25
40 24 0.75
ACGTcount: A:0.25, C:0.13, G:0.17, T:0.45
Consensus pattern (39 bp):
AACTTGATTTAATTTGCCATTATCAGGCTAGTTGAATTT
Found at i:2127391 original size:3 final size:3
Alignment explanation
Indices: 2127385--2127441 Score: 62
Period size: 3 Copynumber: 19.0 Consensus size: 3
2127375 ATGATATTAT
* * * *
2127385 TAA TAA TAC TAA TAA TAA GAA TAA GAA TAA TAA TCA TAA T-A TAA TATA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A
2127433 TAA TAA TAA
1 TAA TAA TAA
2127442 ATAAAATATA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
2 2 0.05
3 39 0.89
4 3 0.07
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:2127451 original size:24 final size:24
Alignment explanation
Indices: 2127369--2127449 Score: 60
Period size: 24 Copynumber: 3.4 Consensus size: 24
2127359 CTGCATTGTA
* *
2127369 AATAAAATGATATTAT-TAATAAT
1 AATAAAATAATAATATATAATAAT
* * *
2127392 ACTAATAATAAGAATA-AGAATAAT
1 AATAA-AATAATAATATATAATAAT
*
2127416 AATCATAAT-ATAATATATAATAAT
1 AAT-AAAATAATAATATATAATAAT
2127440 AAATAAAATA
1 -AATAAAATA
2127450 TATATTTTAA
Statistics
Matches: 42, Mismatches: 10, Indels: 10
0.68 0.16 0.16
Matches are distributed among these distances:
23 9 0.21
24 29 0.69
25 4 0.10
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (24 bp):
AATAAAATAATAATATATAATAAT
Found at i:2127452 original size:21 final size:21
Alignment explanation
Indices: 2127385--2127454 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
2127375 ATGATATTAT
*
2127385 TAATA-ATACTAATAATAAGAA
1 TAATATATAATAATAATAA-AA
* * *
2127406 TAAGA-ATAATAATCATAATA
1 TAATATATAATAATAATAAAA
2127426 TAATATATAATAATAAATAAAA
1 TAATATATAATAAT-AATAAAA
2127448 T-ATATAT
1 TAATATAT
2127455 TTTAATCCCA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
20 5 0.12
21 29 0.73
22 6 0.15
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (21 bp):
TAATATATAATAATAATAAAA
Found at i:2130448 original size:41 final size:41
Alignment explanation
Indices: 2130402--2130481 Score: 97
Period size: 41 Copynumber: 2.0 Consensus size: 41
2130392 TATAGTGGCG
* * * *
2130402 TTTTCAACAAACGCCGTAAAATAATAGTAATTTAGCGGCTT
1 TTTTCAAAAAACACCGCAAAATAATAATAATTTAGCGGCTT
* * *
2130443 TTTTCAAAAAACACTGCAATATAGTAATAATTTAGCGGC
1 TTTTCAAAAAACACCGCAAAATAATAATAATTTAGCGGC
2130482 GTTTGTATAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (41 bp):
TTTTCAAAAAACACCGCAAAATAATAATAATTTAGCGGCTT
Found at i:2131179 original size:22 final size:23
Alignment explanation
Indices: 2131151--2131198 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 23
2131141 GTTTTTATGC
2131151 TTTCGAAT-GGAAAAATAATAG-T
1 TTTCGAATAGG-AAAATAATAGCT
2131173 TTTCGAATAGGAAAATAATAGCT
1 TTTCGAATAGGAAAATAATAGCT
2131196 TTT
1 TTT
2131199 GAAAATGTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.35
Consensus pattern (23 bp):
TTTCGAATAGGAAAATAATAGCT
Found at i:2142446 original size:139 final size:139
Alignment explanation
Indices: 2142196--2142456 Score: 504
Period size: 139 Copynumber: 1.9 Consensus size: 139
2142186 TAGTATGTTG
2142196 TTTTGTGTATAGGTTCTTGGGCAAGTTGAAGTCTTACTGTCGTAATAAGCGTTATCCGGAAGGAT
1 TTTTGTGTATAGGTTCTTGGGCAAGTTGAAGTCTTACTGTCGTAATAAGCGTTATCCGGAAGGAT
2142261 CAATTACTGAAGGGTATTTGGCAGAGGAATGTAGAACATTTTGCTCTAGATATTTGGCAGAGGAA
66 CAATTACTGAAGGGTATTTGGCAGAGGAATGTAGAACATTTTGCTCTAGATATTTGGCAGAGGAA
2142326 TGTATAACA
131 TGTATAACA
2142335 TTTTGTGTATAGGTTCTTGGGCAAGTTGAAGTCTTACTGTCGTAATAAGCGTTATCCGGAAGGAT
1 TTTTGTGTATAGGTTCTTGGGCAAGTTGAAGTCTTACTGTCGTAATAAGCGTTATCCGGAAGGAT
* *
2142400 CAATTCCTGAAGGGTATTTGGCAGAGGAATGTATAACATTTTGCTCTAGATATTTGG
66 CAATTACTGAAGGGTATTTGGCAGAGGAATGTAGAACATTTTGCTCTAGATATTTGG
2142457 AAGATGTTGA
Statistics
Matches: 120, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
139 120 1.00
ACGTcount: A:0.27, C:0.12, G:0.26, T:0.34
Consensus pattern (139 bp):
TTTTGTGTATAGGTTCTTGGGCAAGTTGAAGTCTTACTGTCGTAATAAGCGTTATCCGGAAGGAT
CAATTACTGAAGGGTATTTGGCAGAGGAATGTAGAACATTTTGCTCTAGATATTTGGCAGAGGAA
TGTATAACA
Found at i:2145030 original size:42 final size:42
Alignment explanation
Indices: 2144984--2145144 Score: 164
Period size: 42 Copynumber: 3.7 Consensus size: 42
2144974 CGTTTTCGGA
* *
2144984 AAAACACCGCTAAATCTCAACACTTATTGCGATGTTTGTGAG
1 AAAACACCGCTAAATCTCAACACCTATTGCGATGTTTGTGGG
** * *
2145026 AAAACGTCGCTAAATCTCAACACCTATTAC-AGCGTTTGTGGG
1 AAAACACCGCTAAATCTCAACACCTATTGCGA-TGTTTGTGGG
* *
2145068 AAAAAAATGCCGCTAAATCTCAACACCTATTGCGGCT-TTTGTGGG
1 -AAAACA--CCGCTAAATCTCAACACCTATTGC-GATGTTTGTGGG
* *
2145113 ACAAACGCCGTTAAATCTCAACACCTATTGCG
1 A-AAACACCGCTAAATCTCAACACCTATTGCG
2145145 GCATTTGTAG
Statistics
Matches: 97, Mismatches: 15, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
41 1 0.01
42 35 0.36
43 27 0.28
44 1 0.01
45 33 0.34
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.26
Consensus pattern (42 bp):
AAAACACCGCTAAATCTCAACACCTATTGCGATGTTTGTGGG
Found at i:2145090 original size:45 final size:43
Alignment explanation
Indices: 2144981--2145141 Score: 173
Period size: 45 Copynumber: 3.7 Consensus size: 43
2144971 CGACGTTTTC
* * * *
2144981 GGAAAAACACCGCTAAATCTCAACACTTATTGC-GATGTTTGTG
1 GGAAAAACGCCGCTAAATCTCAACACCTATTACAG-CGTTTGTG
* *
2145024 AG-AAAACGTCGCTAAATCTCAACACCTATTACAGCGTTTGTG
1 GGAAAAACGCCGCTAAATCTCAACACCTATTACAGCGTTTGTG
* * * *
2145066 GGAAAAAAATGCCGCTAAATCTCAACACCTATTGCGGCTTTTGTG
1 GG--AAAAACGCCGCTAAATCTCAACACCTATTACAGCGTTTGTG
* *
2145111 GGACAAACGCCGTTAAATCTCAACACCTATT
1 GGAAAAACGCCGCTAAATCTCAACACCTATT
2145142 GCGGCATTTG
Statistics
Matches: 99, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
42 34 0.34
43 28 0.28
45 37 0.37
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (43 bp):
GGAAAAACGCCGCTAAATCTCAACACCTATTACAGCGTTTGTG
Found at i:2145142 original size:43 final size:43
Alignment explanation
Indices: 2144985--2145160 Score: 194
Period size: 43 Copynumber: 4.1 Consensus size: 43
2144975 GTTTTCGGAA
* * * *
2144985 AAACACCGCTAAATCTCAACACTTATTGC-GATGTTTGTGAGA-
1 AAACGCCGCTAAATCTCAACACCTATTGCGGCT-TTTGTGGGAC
* * * * *
2145027 AAACGTCGCTAAATCTCAACACCTATTACAGCGTTTGTGGGAAAA
1 AAACGCCGCTAAATCTCAACACCTATTGCGGCTTTTGTGGG--AC
*
2145072 AAATGCCGCTAAATCTCAACACCTATTGCGGCTTTTGTGGGAC
1 AAACGCCGCTAAATCTCAACACCTATTGCGGCTTTTGTGGGAC
* * *
2145115 AAACGCCGTTAAATCTCAACACCTATTGCGGCATTTGTAGGAC
1 AAACGCCGCTAAATCTCAACACCTATTGCGGCTTTTGTGGGAC
2145158 AAA
1 AAA
2145161 ATCTGCTATA
Statistics
Matches: 113, Mismatches: 17, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
42 32 0.28
43 44 0.39
44 1 0.01
45 36 0.32
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.26
Consensus pattern (43 bp):
AAACGCCGCTAAATCTCAACACCTATTGCGGCTTTTGTGGGAC
Found at i:2147813 original size:32 final size:33
Alignment explanation
Indices: 2147767--2147849 Score: 150
Period size: 33 Copynumber: 2.5 Consensus size: 33
2147757 CTTTATTTTG
2147767 TTCGGGTCGGGTCGGGTTTT-TTAAGTGTGATA
1 TTCGGGTCGGGTCGGGTTTTATTAAGTGTGATA
*
2147799 TTCGGGTCGAGTCGGGTTTTATTAAGTGTGATA
1 TTCGGGTCGGGTCGGGTTTTATTAAGTGTGATA
2147832 TTCGGGTCGGGTCGGGTT
1 TTCGGGTCGGGTCGGGTT
2147850 CGGGTTTAGG
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 19 0.40
33 29 0.60
ACGTcount: A:0.12, C:0.11, G:0.39, T:0.39
Consensus pattern (33 bp):
TTCGGGTCGGGTCGGGTTTTATTAAGTGTGATA
Found at i:2147931 original size:254 final size:247
Alignment explanation
Indices: 2147563--2148115 Score: 837
Period size: 254 Copynumber: 2.2 Consensus size: 247
2147553 TCGGTTCAGA
**
2147563 TCGGGTTTTTTAAGTGTGATA-T----TCGGGTCGGGTTCGGGTTTAGGGTGAAAAAACCGGACC
1 TCGGGTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAACCAAACC
2147623 GACCCAAAAATATATATAATTCAGGTCGGGTCGGATTAAGTCACTATTTTTATTAAATAAAAATA
66 GACCCAAAAATATATATAATTCAGGTCGGGTCGGATTAAGTCACTATTTTTATTAAATAAAAATA
* *
2147688 ATTTTTTATTATTTCGGGTCGGGTCGGGTTGGATTTCTAATTCATATATTCGGGTCGGGTCGGAT
131 ACTTTTTATTATTTC---T--GGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGAT
*
2147753 GAAACTTTATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGAG
191 AAAACTTTATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGAG
2147810 TCGGGTTTTATTAAGTGTGATATTCGGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCAAA
1 TCGGGTTTT-TTAAGTGTGATATTCGGGTCGGGTCGGGTTCGGGTTTAGGGTG-AAAAAACCAAA
* * *
2147875 CCGACCCGAAAATATATATATTTCGGGTCGGGTCGGATTAAGTCACTATTTTTATTAAATAAAAA
64 CCGACCCAAAAATATATATAATTCAGGTCGGGTCGGATTAAGTCACTATTTTTATTAAATAAAAA
*
2147940 TAACTTTTTATTATTTCTGGTCGGGTCGGATTTCTAATTCATATATTTGGGTCGGGTCGGATAAA
129 TAACTTTTTATTATTTCTGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGATAAA
2148005 ACTTTATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGAGTCGGG
194 ACTTTATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGA-----G
* *
2148064 TCTGGGTTTTTTAAGTGTTATATTCGGGTCGGGTTCGGGTTTAGGGTTTAGG
1 TC-GGGTTTTTTAAGTGTGATATTCGGGTCGGG-TCGGG-TTCGGGTTTAGG
2148116 ACCGGACCGA
Statistics
Matches: 280, Mismatches: 11, Indels: 21
0.90 0.04 0.07
Matches are distributed among these distances:
247 9 0.03
248 12 0.04
249 98 0.35
251 1 0.00
253 25 0.09
254 112 0.40
255 12 0.04
256 11 0.04
ACGTcount: A:0.22, C:0.12, G:0.28, T:0.37
Consensus pattern (247 bp):
TCGGGTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAACCAAACC
GACCCAAAAATATATATAATTCAGGTCGGGTCGGATTAAGTCACTATTTTTATTAAATAAAAATA
ACTTTTTATTATTTCTGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGATAAAAC
TTTATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGAG
Found at i:2148079 original size:38 final size:38
Alignment explanation
Indices: 2148021--2148112 Score: 132
Period size: 38 Copynumber: 2.4 Consensus size: 38
2148011 TTTTGTTCGG
2148021 GTCGGGTC-GGGTTTTTTAAGTGTGATATTCGGGTCGA
1 GTCGGGTCTGGGTTTTTTAAGTGTGATATTCGGGTCGA
* *
2148058 GTCGGGTCTGGGTTTTTTAAGTGTTATATTCGGGTCGG
1 GTCGGGTCTGGGTTTTTTAAGTGTGATATTCGGGTCGA
*
2148096 GTTCGGGTTTAGGGTTT
1 G-TCGGGTCT-GGGTTT
2148113 AGGACCGGAC
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
37 8 0.16
38 28 0.57
39 7 0.14
40 6 0.12
ACGTcount: A:0.11, C:0.10, G:0.38, T:0.41
Consensus pattern (38 bp):
GTCGGGTCTGGGTTTTTTAAGTGTGATATTCGGGTCGA
Found at i:2148093 original size:249 final size:248
Alignment explanation
Indices: 2147565--2148110 Score: 859
Period size: 249 Copynumber: 2.2 Consensus size: 248
2147555 GGTTCAGATC
**
2147565 GGGTTTTTTAAGTGTGATATTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAACCGGACCGACCCAA
1 GGGTTTTTTAAGTGTGATATTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAACCAAACCGACCCAA
*
2147630 AAATATATATAATTCAGGTCGGGTCGGATTAAGTCACTATTTTTATTAAATAAAAATAATTTTTT
66 AAATATATATAATTCAGGTCGGGTCGGATTAAGTCACTATTTTTATTAAATAAAAATAACTTTTT
* *
2147695 ATTATTTCGGGTCGGGTCGGGTTGGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTT
131 ATTATTTC--GTC-GGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGATAAAACTT
2147760 TATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGAGTCGGGT
193 TATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGAGTCGGGT
*
2147816 ---TTTATTAAGTGTGATATTCGGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCAAACCG
1 GGGTTTTTTAAGTGTGATA-T----TCGGGTCGGGTTCGGGTTTAGGGTG-AAAAAACCAAACCG
* * *
2147878 ACCCGAAAATATATATATTTCGGGTCGGGTCGGATTAAGTCACTATTTTTATTAAATAAAAATAA
60 ACCCAAAAATATATATAATTCAGGTCGGGTCGGATTAAGTCACTATTTTTATTAAATAAAAATAA
*
2147943 CTTTTTATTATTTC-T-GGTCGGGTCGGATTTCTAATTCATATATTTGGGTCGGGTCGGATAAAA
125 CTTTTTATTATTTCGTCGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGATAAAA
2148006 CTTTATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGAGTCGGGTCT
190 CTTTATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGAGTCGGG--T
*
2148067 GGGTTTTTTAAGTGTTATATTCGGGTCGGGTTCGGGTTTAGGGT
1 GGGTTTTTTAAGTGTGATATTCGGGTCGGGTTCGGGTTTAGGGT
2148111 TTAGGACCGG
Statistics
Matches: 272, Mismatches: 12, Indels: 24
0.88 0.04 0.08
Matches are distributed among these distances:
248 15 0.06
249 128 0.47
251 2 0.01
253 26 0.10
254 101 0.37
ACGTcount: A:0.23, C:0.12, G:0.28, T:0.37
Consensus pattern (248 bp):
GGGTTTTTTAAGTGTGATATTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAACCAAACCGACCCAA
AAATATATATAATTCAGGTCGGGTCGGATTAAGTCACTATTTTTATTAAATAAAAATAACTTTTT
ATTATTTCGTCGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGATAAAACTTTAT
TTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGAGTCGGGT
Found at i:2148655 original size:38 final size:38
Alignment explanation
Indices: 2148604--2148677 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
2148594 CACATGTCTG
*
2148604 CGACCAAACAGAATATGGAATTTGATTCCAATTCCTGC
1 CGACCAAACAGAATATGGAATTGGATTCCAATTCCTGC
2148642 CGACCAAACAGAATATGGAATTGGATTCCAATTCCT
1 CGACCAAACAGAATATGGAATTGGATTCCAATTCCT
2148678 ACAGATTCCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (38 bp):
CGACCAAACAGAATATGGAATTGGATTCCAATTCCTGC
Found at i:2148686 original size:16 final size:18
Alignment explanation
Indices: 2148665--2148710 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
2148655 TATGGAATTG
2148665 GATTCCAATTCC-T-ACA
1 GATTCCAATTCCTTCACA
2148681 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
*
2148699 TATTCCAATTCC
1 GATTCCAATTCC
2148711 CTCATAAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 12 0.44
17 1 0.04
18 14 0.52
ACGTcount: A:0.28, C:0.33, G:0.04, T:0.35
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:2149074 original size:60 final size:59
Alignment explanation
Indices: 2149008--2149166 Score: 146
Period size: 59 Copynumber: 2.7 Consensus size: 59
2148998 GGAATGTTCA
* * *
2149008 AAAAGTTTAGGGACCAATTTAGATTGAAGGTCATATTTTGGGGTTGAAATTAAAATATTC
1 AAAAGTTTAGGGACCAATTTAGAATAAAGGTCATATTTT-GGGATGAAATTAAAATATTC
** * * *
2149068 AAAAGTTT-GAGGATTAATTTAGAA-ACATA-GTCATAGTTTT-GGATGAAATTGAGATATTT
1 AAAAGTTTAG-GGACCAATTTAGAATA-A-AGGTCATA-TTTTGGGATGAAATTAAAATATTC
* * *
2149127 AAAAGTTTAGAGACCAATTTAAAATAAAGGTCATAATTTG
1 AAAAGTTTAGGGACCAATTTAGAATAAAGGTCATATTTTG
2149167 AGAACATGTT
Statistics
Matches: 78, Mismatches: 13, Indels: 17
0.72 0.12 0.16
Matches are distributed among these distances:
58 4 0.05
59 41 0.53
60 28 0.36
61 5 0.06
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.35
Consensus pattern (59 bp):
AAAAGTTTAGGGACCAATTTAGAATAAAGGTCATATTTTGGGATGAAATTAAAATATTC
Found at i:2149969 original size:31 final size:30
Alignment explanation
Indices: 2149934--2150031 Score: 83
Period size: 31 Copynumber: 3.2 Consensus size: 30
2149924 GTAACTTATA
*
2149934 ATAGTCGATAGACTCAACAAAGTAACGTCTT
1 ATAGTCGAAAGACTCAACAAAGTAAC-TCTT
**** *
2149965 ATAGTCGAAAGA-TC-ATTTTGTAACTTTT
1 ATAGTCGAAAGACTCAACAAAGTAACTCTT
* *
2149993 AATAGTCGAGAGACTCAACAAAATAACTTCTT
1 -ATAGTCGAAAGACTCAACAAAGTAAC-TCTT
2150025 ATAGTCG
1 ATAGTCG
2150032 GAGGACTATT
Statistics
Matches: 50, Mismatches: 13, Indels: 8
0.70 0.18 0.11
Matches are distributed among these distances:
28 3 0.06
29 17 0.34
30 4 0.08
31 23 0.46
32 3 0.06
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (30 bp):
ATAGTCGAAAGACTCAACAAAGTAACTCTT
Found at i:2149998 original size:60 final size:60
Alignment explanation
Indices: 2149919--2150031 Score: 190
Period size: 60 Copynumber: 1.9 Consensus size: 60
2149909 TCATGTGATT
* *
2149919 ATTTTGTAACTTATAATAGTCGATAGACTCAACAAAGTAACGTCTTATAGTCGAAAGATC
1 ATTTTGTAACTTATAATAGTCGAGAGACTCAACAAAATAACGTCTTATAGTCGAAAGATC
* *
2149979 ATTTTGTAACTTTTAATAGTCGAGAGACTCAACAAAATAACTTCTTATAGTCG
1 ATTTTGTAACTTATAATAGTCGAGAGACTCAACAAAATAACGTCTTATAGTCG
2150032 GAGGACTATT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 49 1.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (60 bp):
ATTTTGTAACTTATAATAGTCGAGAGACTCAACAAAATAACGTCTTATAGTCGAAAGATC
Found at i:2151358 original size:20 final size:20
Alignment explanation
Indices: 2151335--2151381 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 20
2151325 AACTTAAATC
2151335 AAAATAATTAAAATAA-ATAT
1 AAAATAATT-AAATAATATAT
*
2151355 AAAAT--TTTAATAATATAT
1 AAAATAATTAAATAATATAT
2151373 AAAATAATT
1 AAAATAATT
2151382 TATATGATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
17 5 0.22
18 11 0.48
20 7 0.30
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAATAATTAAATAATATAT
Found at i:2151410 original size:17 final size:18
Alignment explanation
Indices: 2151369--2151415 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
2151359 TTTTAATAAT
* *
2151369 ATATAAAATAATTTATATG
1 ATATAAAATTATCTATA-G
2151388 ATATAAAATTATCTATA-
1 ATATAAAATTATCTATAG
*
2151405 ATATAATATTA
1 ATATAAAATTA
2151416 AAAAATTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 10 0.40
19 15 0.60
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (18 bp):
ATATAAAATTATCTATAG
Found at i:2151419 original size:24 final size:25
Alignment explanation
Indices: 2151392--2151472 Score: 85
Period size: 26 Copynumber: 3.2 Consensus size: 25
2151382 TATATGATAT
2151392 AAAATTATCTATAATATAATATTAA
1 AAAATTATCTATAATATAATATTAA
* * *
2151417 AAAATTAATATTTAAT-TTAT-TTAA
1 AAAATT-ATCTATAATATAATATTAA
2151441 AAAATTAATATCTATAATATAATATTAA
1 AAAA-T--TATCTATAATATAATATTAA
2151469 AAAA
1 AAAA
2151473 CTAATATTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
24 8 0.18
25 10 0.23
26 14 0.32
27 4 0.09
28 8 0.18
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (25 bp):
AAAATTATCTATAATATAATATTAA
Found at i:2151453 original size:52 final size:52
Alignment explanation
Indices: 2151397--2151503 Score: 196
Period size: 52 Copynumber: 2.1 Consensus size: 52
2151387 GATATAAAAT
* *
2151397 TATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTAA
1 TATCTATAATATAATATTAAAAAACTAATATTTAATTTATATAAAAAATTAA
2151449 TATCTATAATATAATATTAAAAAACTAATATTTAATTTATATAAAAAATTAA
1 TATCTATAATATAATATTAAAAAACTAATATTTAATTTATATAAAAAATTAA
2151501 TAT
1 TAT
2151504 TAAAATTAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (52 bp):
TATCTATAATATAATATTAAAAAACTAATATTTAATTTATATAAAAAATTAA
Found at i:2151472 original size:28 final size:25
Alignment explanation
Indices: 2151403--2151504 Score: 127
Period size: 24 Copynumber: 4.0 Consensus size: 25
2151393 AAATTATCTA
2151403 TAATATAATATTAAAAAATTAATATT
1 TAAT-TAATATTAAAAAATTAATATT
*
2151429 TAATTTAT-TTAAAAAATTAATATCT
1 TAATTAATATTAAAAAATTAATAT-T
*
2151454 ATAATATAATATTAAAAAACTAATATT
1 -TAAT-TAATATTAAAAAATTAATATT
*
2151481 TAATTTATA-TAAAAAATTAATATT
1 TAATTAATATTAAAAAATTAATATT
2151505 AAAATTAAAA
Statistics
Matches: 67, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
24 29 0.43
25 8 0.12
26 12 0.18
27 4 0.06
28 14 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (25 bp):
TAATTAATATTAAAAAATTAATATT
Found at i:2151539 original size:12 final size:11
Alignment explanation
Indices: 2151493--2151543 Score: 50
Period size: 12 Copynumber: 4.4 Consensus size: 11
2151483 ATTTATATAA
2151493 AAAATTAATATT
1 AAAATTAATA-T
*
2151505 AAAATTAAAAT
1 AAAATTAATAT
2151516 CAAATATT-ATAT
1 -AAA-ATTAATAT
2151528 AAAATTAAATAT
1 AAAATT-AATAT
2151540 AAAA
1 AAAA
2151544 CTTCTTTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
10 3 0.09
11 4 0.12
12 23 0.70
13 3 0.09
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (11 bp):
AAAATTAATAT
Found at i:2155386 original size:25 final size:25
Alignment explanation
Indices: 2155336--2155393 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
2155326 CTTAATTTTT
* *
2155336 ATTTTAAAAATTAAATTAAATTAAA
1 ATTTTAATAATTAAATTAAATGAAA
*
2155361 ATTTTAATAA-TAGATTAAATCGAAA
1 ATTTTAATAATTAAATTAAAT-GAAA
*
2155386 AATTTAAT
1 ATTTTAAT
2155394 TTTTTTCTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 9 0.32
25 19 0.68
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (25 bp):
ATTTTAATAATTAAATTAAATGAAA
Found at i:2157886 original size:9 final size:9
Alignment explanation
Indices: 2157872--2157896 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2157862 ACACCTTGTA
2157872 GATGAAGAT
1 GATGAAGAT
2157881 GATGAAGAT
1 GATGAAGAT
2157890 GATGAAG
1 GATGAAG
2157897 TTGTTATGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.36, T:0.20
Consensus pattern (9 bp):
GATGAAGAT
Found at i:2160507 original size:26 final size:26
Alignment explanation
Indices: 2160478--2160536 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
2160468 GATTTCTTAT
*
2160478 AGTCTTGAAGTCCTCTTTTGCATACA
1 AGTCTTGAAGTCATCTTTTGCATACA
2160504 AGTCTTGAAGTCATCTTTTGCATACA
1 AGTCTTGAAGTCATCTTTTGCATACA
2160530 AGTCTTG
1 AGTCTTG
2160537 TAATATGATG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (26 bp):
AGTCTTGAAGTCATCTTTTGCATACA
Found at i:2163417 original size:12 final size:12
Alignment explanation
Indices: 2163400--2163429 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2163390 ATTTTGGTTT
*
2163400 TTTTTTCTGGCC
1 TTTTTTCTGACC
2163412 TTTTTTCTGACC
1 TTTTTTCTGACC
2163424 TTTTTT
1 TTTTTT
2163430 TGTTTTATTT
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:0.03, C:0.20, G:0.10, T:0.67
Consensus pattern (12 bp):
TTTTTTCTGACC
Found at i:2164865 original size:21 final size:21
Alignment explanation
Indices: 2164841--2164892 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
2164831 GTCCAAAGAA
*
2164841 GCATGTATTATGGAATCTGGT
1 GCATGTATCATGGAATCTGGT
*
2164862 GCATGTATCATGGGATCTGGT
1 GCATGTATCATGGAATCTGGT
*
2164883 GGATGTATCA
1 GCATGTATCA
2164893 AAAACCAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.23, C:0.12, G:0.31, T:0.35
Consensus pattern (21 bp):
GCATGTATCATGGAATCTGGT
Found at i:2165916 original size:47 final size:45
Alignment explanation
Indices: 2165862--2165956 Score: 172
Period size: 47 Copynumber: 2.1 Consensus size: 45
2165852 ATTTTTGAGT
2165862 TTCATCTTAAGAACAAAATGGATATGAATTGATATTTTTTTTTATCG
1 TTCATCTTAAGAACAAAATGGATATGAATTGATA--TTTTTTTATCG
2165909 TTCATCTTAAGAACAAAATGGATATGAATTGATATTTTTTTATCG
1 TTCATCTTAAGAACAAAATGGATATGAATTGATATTTTTTTATCG
2165954 TTC
1 TTC
2165957 TTTACGGAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
45 14 0.29
47 34 0.71
ACGTcount: A:0.34, C:0.09, G:0.13, T:0.44
Consensus pattern (45 bp):
TTCATCTTAAGAACAAAATGGATATGAATTGATATTTTTTTATCG
Found at i:2170055 original size:31 final size:30
Alignment explanation
Indices: 2170020--2170087 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 30
2170010 TTTGAATTGG
* *
2170020 TGATATGTCTTATTTTATTA-ATATTTTTCTA
1 TGATATATCATATTTTATTAGAT-TTTTT-TA
2170051 TGATATATCATATTTTATTAGATTTTTTTA
1 TGATATATCATATTTTATTAGATTTTTTTA
*
2170081 TCATATA
1 TGATATA
2170088 AGATCTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 8 0.24
31 23 0.70
32 2 0.06
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.59
Consensus pattern (30 bp):
TGATATATCATATTTTATTAGATTTTTTTA
Found at i:2170668 original size:24 final size:24
Alignment explanation
Indices: 2170617--2170736 Score: 134
Period size: 24 Copynumber: 5.0 Consensus size: 24
2170607 TTTAATGTTA
**
2170617 TTTAGGTTGGAGTGGTTTAAGGTTT
1 TTTAGGTTAAAGTGGTTT-AGGTTT
*
2170642 TTTAGGTTAAAGTGATTTAGGTTT
1 TTTAGGTTAAAGTGGTTTAGGTTT
* *
2170666 TTTAGGTTAAAGTGGTTTTGGGTT
1 TTTAGGTTAAAGTGGTTTAGGTTT
* * * *
2170690 TTTAGATTGAAGTGGTTTTGG-GT
1 TTTAGGTTAAAGTGGTTTAGGTTT
*
2170713 TTTAGGTTAAAATGGTTTAGGTTT
1 TTTAGGTTAAAGTGGTTTAGGTTT
2170737 AAGGTTAGAT
Statistics
Matches: 80, Mismatches: 14, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
23 18 0.22
24 47 0.59
25 15 0.19
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.49
Consensus pattern (24 bp):
TTTAGGTTAAAGTGGTTTAGGTTT
Found at i:2170839 original size:28 final size:27
Alignment explanation
Indices: 2170794--2170939 Score: 128
Period size: 28 Copynumber: 5.5 Consensus size: 27
2170784 ATGGATTTTT
2170794 TTAGAAAATACACA-TACATTGAAAAATA
1 TTAGAAAATACACATTACATTG--AAATA
*
2170822 TTAGAACATACA-ATTACATTGAAATA
1 TTAGAAAATACACATTACATTGAAATA
* *
2170848 TTTGAAAATA-AGATTACATTGAAATA
1 TTAGAAAATACACATTACATTGAAATA
* *
2170874 TTAGAAAA-GCACA-TACATTAAAATA
1 TTAGAAAATACACATTACATTGAAATA
*
2170899 GTAGAAAA-ACACA-TACAATATTGAAATA
1 TTAGAAAATACACATTAC---ATTGAAATA
*
2170927 TTATAAAA-ACACA
1 TTAGAAAATACACA
2170940 AACATAAAAA
Statistics
Matches: 100, Mismatches: 12, Indels: 12
0.81 0.10 0.10
Matches are distributed among these distances:
25 26 0.26
26 36 0.36
27 1 0.01
28 37 0.37
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (27 bp):
TTAGAAAATACACATTACATTGAAATA
Found at i:2170863 original size:26 final size:26
Alignment explanation
Indices: 2170794--2170906 Score: 108
Period size: 26 Copynumber: 4.3 Consensus size: 26
2170784 ATGGATTTTT
2170794 TTAGAAAATACACA-TACATTGAAAAATA
1 TTAGAAAATACA-ATTACATTG--AAATA
*
2170822 TTAGAACATACAATTACATTGAAATA
1 TTAGAAAATACAATTACATTGAAATA
*
2170848 TTTGAAAATA-AGATTACATTGAAATA
1 TTAGAAAATACA-ATTACATTGAAATA
* *
2170874 TTAGAAAA-GCACA-TACATTAAAATA
1 TTAGAAAATACA-ATTACATTGAAATA
*
2170899 GTAGAAAA
1 TTAGAAAA
2170907 ACACATACAA
Statistics
Matches: 74, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
25 19 0.26
26 36 0.49
27 1 0.01
28 18 0.24
ACGTcount: A:0.54, C:0.09, G:0.10, T:0.27
Consensus pattern (26 bp):
TTAGAAAATACAATTACATTGAAATA
Found at i:2173529 original size:45 final size:45
Alignment explanation
Indices: 2173418--2173540 Score: 153
Period size: 45 Copynumber: 2.7 Consensus size: 45
2173408 GCAGTTTATG
*
2173418 CATTG-ATGCACTCTCCATGCATAGATGCACTCAGGTTTTAATGAAAA
1 CATTGAATGCACT-T-CATGCATCGATGCACTCAGGTTTT-ATGAAAA
* *
2173465 CATTGAATGCATTTGATGCATCGATGCACTCAGGATATTT-TG-AAA
1 CATTGAATGCACTTCATGCATCGATGCACTCAGG-T-TTTATGAAAA
2173510 CATTGAATGCACTTCATGCATCGATGCACTC
1 CATTGAATGCACTTCATGCATCGATGCACTC
2173541 TTAGTGCACC
Statistics
Matches: 68, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
45 32 0.47
46 20 0.29
47 7 0.10
48 9 0.13
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (45 bp):
CATTGAATGCACTTCATGCATCGATGCACTCAGGTTTTATGAAAA
Found at i:2173538 original size:17 final size:19
Alignment explanation
Indices: 2173516--2173594 Score: 99
Period size: 19 Copynumber: 4.3 Consensus size: 19
2173506 GAAACATTGA
*
2173516 ATGCACT-TCA-TGCATCG
1 ATGCACTCTCAGTGCACCG
*
2173533 ATGCACTCTTAGTGCACCG
1 ATGCACTCTCAGTGCACCG
* *
2173552 ATGCACTCTTAGTGCACTG
1 ATGCACTCTCAGTGCACCG
*
2173571 ATGCACTCTTAGTGCACCG
1 ATGCACTCTCAGTGCACCG
2173590 ATGCA
1 ATGCA
2173595 TTAAGGGTCC
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
17 7 0.12
18 2 0.04
19 47 0.84
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (19 bp):
ATGCACTCTCAGTGCACCG
Found at i:2173553 original size:19 final size:19
Alignment explanation
Indices: 2173526--2173594 Score: 120
Period size: 19 Copynumber: 3.6 Consensus size: 19
2173516 ATGCACTTCA
*
2173526 TGCATCGATGCACTCTTAG
1 TGCACCGATGCACTCTTAG
2173545 TGCACCGATGCACTCTTAG
1 TGCACCGATGCACTCTTAG
*
2173564 TGCACTGATGCACTCTTAG
1 TGCACCGATGCACTCTTAG
2173583 TGCACCGATGCA
1 TGCACCGATGCA
2173595 TTAAGGGTCC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 47 1.00
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.28
Consensus pattern (19 bp):
TGCACCGATGCACTCTTAG
Found at i:2179386 original size:24 final size:22
Alignment explanation
Indices: 2179354--2179431 Score: 79
Period size: 24 Copynumber: 3.5 Consensus size: 22
2179344 GCACTTAACA
2179354 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCAT-CC-TTGAAT
* * *
2179378 GTGCATCGATACA-CCATCAA-
1 GTGCATCGATGCATCCTTGAAT
*
2179398 GTGCACCGATGCATACCTTGAAT
1 GTGCATCGATGCAT-CCTTGAAT
2179421 GTGCATCGATG
1 GTGCATCGATG
2179432 AACAAGACCA
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
20 11 0.26
21 3 0.07
22 7 0.16
23 10 0.23
24 12 0.28
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.27
Consensus pattern (22 bp):
GTGCATCGATGCATCCTTGAAT
Found at i:2179451 original size:43 final size:44
Alignment explanation
Indices: 2179335--2179454 Score: 122
Period size: 43 Copynumber: 2.8 Consensus size: 44
2179325 TTAAAACAAA
* * *
2179335 TGCATCGATGCACTTAAC-AGTGCATCGATGCATCCCTTTGAATG
1 TGCATCGATACAC-AAACAAGTGCATCGATGCATACCTTTGAATG
* * *
2179379 TGCATCGATACACCATCAAGTGCACCGATGCATACC-TTGAATG
1 TGCATCGATACACAAACAAGTGCATCGATGCATACCTTTGAATG
*
2179422 TGCATCGATGA-ACAAGACCA-TGCATCGATGCAT
1 TGCATCGAT-ACACAA-ACAAGTGCATCGATGCAT
2179455 CTGACAGGTT
Statistics
Matches: 64, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
43 33 0.52
44 31 0.48
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (44 bp):
TGCATCGATACACAAACAAGTGCATCGATGCATACCTTTGAATG
Found at i:2181698 original size:18 final size:18
Alignment explanation
Indices: 2181665--2181699 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2181655 GGGGAGAGTA
*
2181665 ATTTCAAACTTGATTTTG
1 ATTTCAAAATTGATTTTG
*
2181683 ATTTCAAAATTTATTTT
1 ATTTCAAAATTGATTTT
2181700 CAAAGAATCT
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:0.31, C:0.09, G:0.06, T:0.54
Consensus pattern (18 bp):
ATTTCAAAATTGATTTTG
Found at i:2182025 original size:20 final size:20
Alignment explanation
Indices: 2181996--2182033 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2181986 TTTCAAAGGG
2181996 ATGCACCGATGAACCAATCC
1 ATGCACCGATGAACCAATCC
* *
2182016 ATGCATCGATGCACCAAT
1 ATGCACCGATGAACCAAT
2182034 GAATAAATTG
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:0.34, C:0.32, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGAACCAATCC
Found at i:2182089 original size:64 final size:63
Alignment explanation
Indices: 2182012--2182162 Score: 184
Period size: 64 Copynumber: 2.4 Consensus size: 63
2182002 CGATGAACCA
*
2182012 ATCCATGCATCGATGCAC-CAATGAATAAATTG-AACATCGAATGTAGTTT-ATGCATCGATGCA
1 ATCCATGCATCGATGCACTC-AGGAATAAA-TGAAACATCGAATGTA-TTTGATGCATCGATGCA
2182074 C
63 C
** *
2182075 -TCTCTATGCATCGATGCACTCAGGTTTTAATGAAAACATCGAATGTATTTGATGCATCGATGCA
1 ATC-C-ATGCATCGATGCACTCAGGAATAAATG-AAACATCGAATGTATTTGATGCATCGATGCA
2182139 C
63 C
2182140 ATCCATGCATCGATGCACTCAGG
1 ATCCATGCATCGATGCACTCAGG
2182163 CTATTTTTAA
Statistics
Matches: 77, Mismatches: 4, Indels: 13
0.82 0.04 0.14
Matches are distributed among these distances:
62 2 0.03
63 3 0.04
64 41 0.53
65 29 0.38
66 2 0.03
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (63 bp):
ATCCATGCATCGATGCACTCAGGAATAAATGAAACATCGAATGTATTTGATGCATCGATGCAC
Found at i:2182113 original size:65 final size:63
Alignment explanation
Indices: 2182044--2182220 Score: 204
Period size: 65 Copynumber: 2.8 Consensus size: 63
2182034 GAATAAATTG
2182044 AACATCGAATGTAGTTTATGCATCGATGCACTCTCTATGCATCGATGCACTCAGG-T-TTTAATG
1 AACATCGAATGTA-TTTATGCATCGATGCACTCTCTATGCATCGATGCACTCAGGCTATTT--T-
2182107 AA
62 AA
*
2182109 AACATCGAATGTATTTGATGCATCGATGCACATC-C-ATGCATCGATGCACTCAGGCTATTTTTA
1 AACATCGAATGTATTT-ATGCATCGATGCAC-TCTCTATGCATCGATGCACTCAGGCTATTTTAA
* * *
2182172 AACATCG-ATGCACTTCATGCATCGATGCACTCT-TAGTGCACCGATGCAC
1 AACATCGAATGTA-TTTATGCATCGATGCACTCTCTA-TGCATCGATGCAC
2182221 AAAGGGTCCA
Statistics
Matches: 100, Mismatches: 4, Indels: 18
0.82 0.03 0.15
Matches are distributed among these distances:
61 2 0.02
62 19 0.19
63 22 0.22
64 23 0.23
65 29 0.29
66 5 0.05
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (63 bp):
AACATCGAATGTATTTATGCATCGATGCACTCTCTATGCATCGATGCACTCAGGCTATTTTAA
Found at i:2182216 original size:19 final size:17
Alignment explanation
Indices: 2182177--2182220 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 17
2182167 TTTTAAACAT
*
2182177 CGATGCACTTCATGCAT
1 CGATGCACTTCATGCAC
*
2182194 CGATGCACTCTTAGTGCAC
1 CGATGCACT-TCA-TGCAC
2182213 CGATGCAC
1 CGATGCAC
2182221 AAAGGGTCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 9 0.39
18 2 0.09
19 12 0.52
ACGTcount: A:0.23, C:0.32, G:0.20, T:0.25
Consensus pattern (17 bp):
CGATGCACTTCATGCAC
Found at i:2183949 original size:18 final size:18
Alignment explanation
Indices: 2183926--2183976 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
2183916 GCGTAGAATT
*
2183926 TGTCCCGAAGGACCAATA
1 TGTCCCAAAGGACCAATA
*
2183944 TGTCCCAAAGGACCACTA
1 TGTCCCAAAGGACCAATA
2183962 TGTCCCAAAGGACCA
1 TGTCCCAAAGGACCA
2183977 TATAGAACAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.33, C:0.31, G:0.20, T:0.16
Consensus pattern (18 bp):
TGTCCCAAAGGACCAATA
Found at i:2184894 original size:21 final size:21
Alignment explanation
Indices: 2184868--2184945 Score: 95
Period size: 21 Copynumber: 3.7 Consensus size: 21
2184858 CAAGTTCCCT
2184868 GGTATCGATACCCTTCACATA
1 GGTATCGATACCCTTCACATA
2184889 GGTATCGATACCTCTTC-CATA
1 GGTATCGATACC-CTTCACATA
** * *
2184910 TGGTATCGATACAGTTCATACA
1 -GGTATCGATACCCTTCACATA
2184932 GGTATCGATACCCT
1 GGTATCGATACCCT
2184946 ATGCATCAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
21 31 0.65
22 17 0.35
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.31
Consensus pattern (21 bp):
GGTATCGATACCCTTCACATA
Found at i:2191462 original size:24 final size:24
Alignment explanation
Indices: 2191406--2191455 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
2191396 AGGTATACTC
2191406 TTAAGCATACTATTATTATGAGAA
1 TTAAGCATACTATTATTATGAGAA
2191430 TTAAGCATACTATTATTATGAGAA
1 TTAAGCATACTATTATTATGAGAA
2191454 TT
1 TT
2191456 GAACATATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (24 bp):
TTAAGCATACTATTATTATGAGAA
Found at i:2196629 original size:20 final size:20
Alignment explanation
Indices: 2196604--2196651 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
2196594 ATGTTTCTAT
2196604 TCTAATGTAAGGTAATGTAC
1 TCTAATGTAAGGTAATGTAC
**
2196624 TCTAATGTAAGGTAATGTTT
1 TCTAATGTAAGGTAATGTAC
2196644 TCTAATGT
1 TCTAATGT
2196652 TCCTAATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.42
Consensus pattern (20 bp):
TCTAATGTAAGGTAATGTAC
Found at i:2199393 original size:18 final size:18
Alignment explanation
Indices: 2199366--2199400 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2199356 TTTGAAAAGA
2199366 TTGAAGTAAATAATAAGT
1 TTGAAGTAAATAATAAGT
*
2199384 TTGAATTAAATAATAAG
1 TTGAAGTAAATAATAAG
2199401 ACCGGATGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.14, T:0.34
Consensus pattern (18 bp):
TTGAAGTAAATAATAAGT
Found at i:2199930 original size:20 final size:21
Alignment explanation
Indices: 2199902--2199942 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
2199892 TGGTAATTAG
* *
2199902 AAACGTCTGAATTAATCTGGA
1 AAACGTCTGAAGTAACCTGGA
2199923 AAAC-TCTGAAGTAACCTGGA
1 AAACGTCTGAAGTAACCTGGA
2199943 TAGACTTGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (21 bp):
AAACGTCTGAAGTAACCTGGA
Found at i:2201267 original size:90 final size:87
Alignment explanation
Indices: 2201010--2201278 Score: 299
Period size: 89 Copynumber: 3.0 Consensus size: 87
2201000 AGTTGGTAAG
* * * *
2201010 ACCTTACGGATCTAAGGATACCCTTGGGTAGGCTCATAGGCCCAGGGCATATCCTTAGGTTGGTT
1 ACCTTACGGATCTAAGGATATCCTT-GGTAGGC-CATAGGCCCAAGGTATATCCTTAAGTTGGTT
*
2201075 CCATTTTGTTTTGTGCTTA-GGTA
64 CCATTTTGTTGTGTGCTTAGGGTA
* *
2201098 ACCTTACGGATCTAAGGATATCCTTAGGTAGGCCCATATGCCTGAAGGTATATCCTTAAGTTGGT
1 ACCTTACGGATCTAAGGATATCCTT-GGTAGG-CCATAGGCC-CAAGGTATATCCTTAAGTTGGT
* * *
2201163 TCCCTTATGCTGTGTGCTTAGGGTA
63 TCCATTTTGTTGTGTGCTTAGGGTA
* * * *
2201188 ACCTTATGGATCTAAGGATATCCTTGG-ATGGTCCAGAGGCTCCAAGGTATATCCTTATGTTAGC
1 ACCTTACGGATCTAAGGATATCCTTGGTA-GG-CCATAGGC-CCAAGGTATATCCTTAAGTT-GG
* *
2201252 TTCCTTTTTGTTGTGTGCTGAGGGTA
62 TTCCATTTTGTTGTGTGCTTAGGGTA
2201278 A
1 A
2201279 GCCCTACTGA
Statistics
Matches: 153, Mismatches: 22, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
88 38 0.25
89 62 0.41
90 53 0.35
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (87 bp):
ACCTTACGGATCTAAGGATATCCTTGGTAGGCCATAGGCCCAAGGTATATCCTTAAGTTGGTTCC
ATTTTGTTGTGTGCTTAGGGTA
Found at i:2205299 original size:273 final size:273
Alignment explanation
Indices: 2204812--2205358 Score: 1040
Period size: 273 Copynumber: 2.0 Consensus size: 273
2204802 CGTGTTCGTC
*
2204812 TTCTCAAGTTTGGATTGATGATAATTCTAGAAGTACTTGGCTCAGCACAACTCTAGATCGCATTC
1 TTCTCAAGTTTGGATTGATGATAATTCTAGAAGTACTTGGCTCAGCACAACTCTAGATCACATTC
2204877 GGTACTAAGAAGTGGATATTCGTGAGATAAATCAACCATGAATACCAGCATGACTTTATTATATG
66 GGTACTAAGAAGTGGATATTCGTGAGATAAATCAACCATGAATACCAGCATGACTTTATTATATG
2204942 ACTAAATTGAAATGAAAGGAAGTATAGTATGTATCAGAAATTCAAAAAAATCTGAATTAATTTGG
131 ACTAAATTGAAATGAAAGGAAGTATAGTATGTATCAGAAATTCAAAAAAATCTGAATTAATTTGG
2205007 AAAACTCCGAAGTAACCGGGATAGACTTACTTGCTAAACGAACTAAGTAACCTCAATGACTGAGG
196 AAAACTCCGAAGTAACCGGGATAGACTTACTTGCTAAACGAACTAAGTAACCTCAATGACTGAGG
2205072 ATTAAATAAGTGA
261 ATTAAATAAGTGA
2205085 TTCTCAAGTTTGGATTGATGATAATTCTAGAAGTACTTGGCTCAGCACAACTCTAGATCACATTC
1 TTCTCAAGTTTGGATTGATGATAATTCTAGAAGTACTTGGCTCAGCACAACTCTAGATCACATTC
*
2205150 GGTACTAAGTAGTGGATATTCGTGAGATAAATCAACCATGAATACCAGCATGACTTTATTATATG
66 GGTACTAAGAAGTGGATATTCGTGAGATAAATCAACCATGAATACCAGCATGACTTTATTATATG
* * *
2205215 ACTAAATTGAAATGAAATGAAGTATAGTATTTATCAGAAATTCAAAAAAGTCTGAATTAATTTGG
131 ACTAAATTGAAATGAAAGGAAGTATAGTATGTATCAGAAATTCAAAAAAATCTGAATTAATTTGG
*
2205280 AAAACTCTGAAGTAACCGGGATAGACTTACTTGCTAAACGAACTAAGTAACCTCAATGACTGAGG
196 AAAACTCCGAAGTAACCGGGATAGACTTACTTGCTAAACGAACTAAGTAACCTCAATGACTGAGG
2205345 ATTAAATAAGTGA
261 ATTAAATAAGTGA
2205358 T
1 T
2205359 GGGATGAGTC
Statistics
Matches: 268, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
273 268 1.00
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.29
Consensus pattern (273 bp):
TTCTCAAGTTTGGATTGATGATAATTCTAGAAGTACTTGGCTCAGCACAACTCTAGATCACATTC
GGTACTAAGAAGTGGATATTCGTGAGATAAATCAACCATGAATACCAGCATGACTTTATTATATG
ACTAAATTGAAATGAAAGGAAGTATAGTATGTATCAGAAATTCAAAAAAATCTGAATTAATTTGG
AAAACTCCGAAGTAACCGGGATAGACTTACTTGCTAAACGAACTAAGTAACCTCAATGACTGAGG
ATTAAATAAGTGA
Found at i:2207042 original size:74 final size:74
Alignment explanation
Indices: 2206913--2207054 Score: 212
Period size: 74 Copynumber: 1.9 Consensus size: 74
2206903 GTTGAACAGG
* * ** *
2206913 GGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAACAAAACTGTTTAGGGGGGAATCGGT
1 GGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCAGAACAAAACCATTCAGGGGGGAATCGGT
2206978 TCCTCCTAT
66 TCCTCCTAT
* * *
2206987 GGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCAGAGCCAAACCATTCAGGGGGGAATCGGT
1 GGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCAGAACAAAACCATTCAGGGGGGAATCGGT
2207052 TCC
66 TCC
2207055 CTCTGAGCAA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
74 60 1.00
ACGTcount: A:0.23, C:0.25, G:0.29, T:0.23
Consensus pattern (74 bp):
GGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCAGAACAAAACCATTCAGGGGGGAATCGGT
TCCTCCTAT
Found at i:2207701 original size:17 final size:17
Alignment explanation
Indices: 2207679--2207722 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
2207669 TTCATAAATC
2207679 CAAAATCCAACAATCCA
1 CAAAATCCAACAATCCA
*
2207696 CAAAATCAAACAATCCA
1 CAAAATCCAACAATCCA
2207713 -AAATATCCAA
1 CAAA-ATCCAA
2207723 AATGTTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.57, C:0.30, G:0.00, T:0.14
Consensus pattern (17 bp):
CAAAATCCAACAATCCA
Found at i:2207714 original size:9 final size:8
Alignment explanation
Indices: 2207674--2207724 Score: 52
Period size: 9 Copynumber: 6.2 Consensus size: 8
2207664 CACCATTCAT
2207674 AAATCC-A
1 AAATCCAA
2207681 AAATCCAA
1 AAATCCAA
*
2207689 CAATCCACA
1 AAATCCA-A
2207698 AAAT-CAA
1 AAATCCAA
2207705 ACAATCCAA
1 A-AATCCAA
2207714 AATATCCAA
1 AA-ATCCAA
2207723 AA
1 AA
2207725 TGTTGAAACA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
7 8 0.22
8 13 0.35
9 16 0.43
ACGTcount: A:0.59, C:0.27, G:0.00, T:0.14
Consensus pattern (8 bp):
AAATCCAA
Found at i:2209687 original size:21 final size:21
Alignment explanation
Indices: 2209661--2209700 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2209651 CAGAACCCCA
*
2209661 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
2209682 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
2209701 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:2209729 original size:20 final size:21
Alignment explanation
Indices: 2209683--2209743 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
2209673 TTCCCCTGTG
2209683 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
2209706 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
2209726 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
2209744 TACACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:2213585 original size:22 final size:21
Alignment explanation
Indices: 2213543--2213582 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2213533 GAGTTTGTTT
*
2213543 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
2213564 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
2213583 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:2215708 original size:77 final size:77
Alignment explanation
Indices: 2215506--2215710 Score: 267
Period size: 75 Copynumber: 2.7 Consensus size: 77
2215496 CCGTTGAACA
* * * *
2215506 GGGGGAATCGGTACCCCCT-TGGGGGGG-ATCGGTTCCCTCCGAGC-ATACTGGAATTCTCGGAA
1 GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCAAT-CTGGAAATCCCGGAA
** *
2215568 CAAAACTGTTTAG
65 CAAAACCATTCAG
* *
2215581 GGGGGAATCGGTTCCTCCTAT--GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCCCGGAGC
1 GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCAATCTGGAAATCCCGGAAC
*
2215644 CAAACCATTCAG
66 AAAACCATTCAG
*
2215656 GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCAATCTGGAA
1 GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCAATCTGGAA
2215711 TTTTTGGCTT
Statistics
Matches: 113, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
74 5 0.04
75 76 0.67
76 2 0.02
77 30 0.27
ACGTcount: A:0.20, C:0.25, G:0.32, T:0.22
Consensus pattern (77 bp):
GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCAATCTGGAAATCCCGGAAC
AAAACCATTCAG
Found at i:2216306 original size:89 final size:90
Alignment explanation
Indices: 2216187--2216408 Score: 313
Period size: 90 Copynumber: 2.5 Consensus size: 90
2216177 GGCCCAGGGC
*
2216187 ATATCCTTAGGTTGATTCCCTTTTGCTGTGTGCTTA-GGTAAC-CTTACGGATCTAAGGATATCC
1 ATATCCTTAGGTTGATTCCCTTTTGCTGTGTGCTTAGGGTAACTC-TACGGATCTAAGGATATCA
2216250 TTGGGTAGACCCATAGACCCCAAGGT
65 TTGGGTAGACCCATAGACCCCAAGGT
* * * * * *
2216276 ATATCCTTAGATTGGTTCCCTTATGTTGTGTGCCTAGGGTAACTCTACGGATCTAATGATATCAT
1 ATATCCTTAGGTTGATTCCCTTTTGCTGTGTGCTTAGGGTAACTCTACGGATCTAAGGATATCAT
* * *
2216341 TGGGTAGGCCCATAGGCTCCAAGGT
66 TGGGTAGACCCATAGACCCCAAGGT
*
2216366 ATATCCTTAGGTTGACTTCCCTTTTGCTGTGTGCTGAGGGTAA
1 ATATCCTTAGGTTGA-TTCCCTTTTGCTGTGTGCTTAGGGTAA
2216409 GCCCTATGGA
Statistics
Matches: 114, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
89 31 0.27
90 59 0.52
91 24 0.21
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (90 bp):
ATATCCTTAGGTTGATTCCCTTTTGCTGTGTGCTTAGGGTAACTCTACGGATCTAAGGATATCAT
TGGGTAGACCCATAGACCCCAAGGT
Found at i:2221901 original size:271 final size:272
Alignment explanation
Indices: 2221418--2221961 Score: 973
Period size: 271 Copynumber: 2.0 Consensus size: 272
2221408 ATAAACACCC
** *
2221418 CTATCTCTAACCGTCTATGAATAACTCTATAAAATCTTAAATCCTAAATCAAACTAAATCTCCAA
1 CTATCTCTAACCGTCTATGAATAACTCTATAAAATCTTAAATCCTAAATCAAAAGAAAGCTCCAA
*
2221483 AACCCTAACCTTTCTCTAACAAAATTAAAATATATTGATTACATTTTATTTTTAAGGATAATTTT
66 AACCCTAACCTTTCTCTAACAAAATTAAAATATATTGATTACATTTTATTTTTAAAGATAATTTT
*
2221548 ATCGAGTACCATTAGATAATGATAGATATTTTTCTTTAAAGTTAATAAGTTTTAATATAAATTAT
131 ATCGAGTACCATTAGATAATGATAGATATTTTTCTTTAAAGCTAATAAGTTTTAATATAAATTAT
2221613 GAATTTTTTTATTAAGCTAAAGGTGATTATAAA-GTAGTATATGTTTTAAATACTCTTAATCATT
196 GAATTTTTTTATTAAGCTAAAGGTGATTATAAAGGTAGTATATGTTTTAAATACTCTTAATCATT
2221677 TGACAATGAACT
261 TGACAATGAACT
*
2221689 CTATCTCTAACCGTCTATGAATAACTCTATAAAATCTTAAATCCTAAATCAAAAGAAAGCTCTAA
1 CTATCTCTAACCGTCTATGAATAACTCTATAAAATCTTAAATCCTAAATCAAAAGAAAGCTCCAA
2221754 AACCCTAACCTTTCTCTAACAAAATTAAAATATATTGATTACATTTTATTTTTAAAGATAATTTT
66 AACCCTAACCTTTCTCTAACAAAATTAAAATATATTGATTACATTTTATTTTTAAAGATAATTTT
*
2221819 ATTGAGTACCATTAGATAATGATAGATATTTTTCTTTAAAGCTAATAAGTTTTAATATAAATTAT
131 ATCGAGTACCATTAGATAATGATAGATATTTTTCTTTAAAGCTAATAAGTTTTAATATAAATTAT
* * *
2221884 GATTTTTTTTATTAAGCTCAAGGTGATTATAAAGTGGTAGTATATGTTTTAAATATTCTTAATCA
196 GAATTTTTTTATTAAGCTAAAGGTGATTATAAA--GGTAGTATATGTTTTAAATACTCTTAATCA
2221949 TTTGACAATGAAC
259 TTTGACAATGAAC
2221962 GCTTAATCAC
Statistics
Matches: 260, Mismatches: 10, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
271 219 0.84
274 41 0.16
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (272 bp):
CTATCTCTAACCGTCTATGAATAACTCTATAAAATCTTAAATCCTAAATCAAAAGAAAGCTCCAA
AACCCTAACCTTTCTCTAACAAAATTAAAATATATTGATTACATTTTATTTTTAAAGATAATTTT
ATCGAGTACCATTAGATAATGATAGATATTTTTCTTTAAAGCTAATAAGTTTTAATATAAATTAT
GAATTTTTTTATTAAGCTAAAGGTGATTATAAAGGTAGTATATGTTTTAAATACTCTTAATCATT
TGACAATGAACT
Found at i:2223082 original size:10 final size:10
Alignment explanation
Indices: 2223067--2223114 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
2223057 TATAAATTAA
2223067 AAATATAAAT
1 AAATATAAAT
2223077 AAATATAAAT
1 AAATATAAAT
* *
2223087 AAAAATATAT
1 AAATATAAAT
* *
2223097 AATTATAATAA
1 AAATATAA-AT
2223108 AAATATA
1 AAATATA
2223115 TTTTATGATA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
10 23 0.77
11 7 0.23
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
AAATATAAAT
Found at i:2223108 original size:19 final size:20
Alignment explanation
Indices: 2223057--2223115 Score: 75
Period size: 19 Copynumber: 2.9 Consensus size: 20
2223047 AAAATTATTT
2223057 TATAAATTAAAAATATAAATAAA
1 TATAAA-TAAAAATAT--ATAAA
*
2223080 TATAAATAAAAATATATAAT
1 TATAAATAAAAATATATAAA
2223100 TAT-AATAAAAATATAT
1 TATAAATAAAAATATAT
2223116 TTTATGATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
19 13 0.37
20 7 0.20
22 9 0.26
23 6 0.17
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
TATAAATAAAAATATATAAA
Found at i:2223218 original size:20 final size:21
Alignment explanation
Indices: 2223167--2223219 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
2223157 GAATTTTATT
2223167 TATTTTTAAGTAATTAAAATA
1 TATTTTTAAGTAATTAAAATA
* * **
2223188 AATTATTAAGTAA-TAAGTTA
1 TATTTTTAAGTAATTAAAATA
2223208 TATTTTTAAGTA
1 TATTTTTAAGTA
2223220 TGTTAGTATT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (21 bp):
TATTTTTAAGTAATTAAAATA
Found at i:2228543 original size:15 final size:14
Alignment explanation
Indices: 2228523--2228557 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
2228513 TAATTATATG
2228523 TTTAATATTTTATAA
1 TTTAATATTTT-TAA
2228538 TTTAATATTTTTAA
1 TTTAATATTTTTAA
*
2228552 ATTAAT
1 TTTAAT
2228558 TTAATGGTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTAATATTTTTAA
Found at i:2232777 original size:18 final size:18
Alignment explanation
Indices: 2232754--2232791 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
2232744 CTCCACCACT
2232754 CAGTCGTCCTACGCCTGA
1 CAGTCGTCCTACGCCTGA
2232772 CAGTCGTCCTACGCCTGA
1 CAGTCGTCCTACGCCTGA
2232790 CA
1 CA
2232792 CTGGTCCTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.18, C:0.39, G:0.21, T:0.21
Consensus pattern (18 bp):
CAGTCGTCCTACGCCTGA
Found at i:2232798 original size:18 final size:18
Alignment explanation
Indices: 2232757--2232799 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
2232747 CACCACTCAG
*
2232757 TCGTCCTACGCCTGACAG
1 TCGTCCTACGCCTGACAC
2232775 TCGTCCTACGCCTGACAC
1 TCGTCCTACGCCTGACAC
*
2232793 TGGTCCT
1 TCGTCCT
2232800 GATTTTTCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.40, G:0.21, T:0.26
Consensus pattern (18 bp):
TCGTCCTACGCCTGACAC
Found at i:2242675 original size:20 final size:21
Alignment explanation
Indices: 2242641--2242683 Score: 79
Period size: 20 Copynumber: 2.1 Consensus size: 21
2242631 CTGGAGGTTC
2242641 ATTACTCTAAATAGTATCGTT
1 ATTACTCTAAATAGTATCGTT
2242662 ATTACTCT-AATAGTATCGTT
1 ATTACTCTAAATAGTATCGTT
2242682 AT
1 AT
2242684 ATTGTGCTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (21 bp):
ATTACTCTAAATAGTATCGTT
Found at i:2244340 original size:19 final size:20
Alignment explanation
Indices: 2244318--2244361 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
2244308 ATATTATATT
*
2244318 GAATTAAAATA-AAAGGAAA
1 GAATTAAAAAATAAAGGAAA
2244337 GAA-TAAAAAATAAAGGAAA
1 GAATTAAAAAATAAAGGAAA
2244356 -AATTAA
1 GAATTAA
2244362 TTTAGGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.70, C:0.00, G:0.14, T:0.16
Consensus pattern (20 bp):
GAATTAAAAAATAAAGGAAA
Done.