Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001840.1 Hibiscus syriacus cultivar Beakdansim tig00003725_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: 2412736
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 12
Found at i:2167515 original size:17 final size:17
Alignment explanation
Indices: 2167495--2167554 Score: 68
Period size: 17 Copynumber: 3.6 Consensus size: 17
2167485 AAGGAAGTAG
2167495 TTCATTAATTAAACTAA
1 TTCATTAATTAAACTAA
* *
2167512 TTCATTAATCAAACTAG
1 TTCATTAATTAAACTAA
* * *
2167529 TTCGTTTATTAAATTAA
1 TTCATTAATTAAACTAA
2167546 TTC-TTAATT
1 TTCATTAATT
2167555 GTTTCATGCA
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
16 5 0.14
17 30 0.86
ACGTcount: A:0.38, C:0.12, G:0.03, T:0.47
Consensus pattern (17 bp):
TTCATTAATTAAACTAA
Found at i:2169350 original size:18 final size:18
Alignment explanation
Indices: 2169327--2169361 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2169317 GTTCAGTATT
*
2169327 TGTCCCGAAGGACCACTA
1 TGTCCCGAAAGACCACTA
2169345 TGTCCCGAAAGACCACT
1 TGTCCCGAAAGACCACT
2169362 GGATACATCC
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:0.29, C:0.34, G:0.20, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAAGACCACTA
Found at i:2169375 original size:22 final size:22
Alignment explanation
Indices: 2169347--2169423 Score: 109
Period size: 22 Copynumber: 3.5 Consensus size: 22
2169337 GACCACTATG
*
2169347 TCCCGAAAGACCACTGGATACA
1 TCCCGAAGGACCACTGGATACA
2169369 TCCCGAAGGACCACTGGATACA
1 TCCCGAAGGACCACTGGATACA
* * **
2169391 TCTCGAAGGACCACTGAATATG
1 TCCCGAAGGACCACTGGATACA
2169413 TCCCGAAGGAC
1 TCCCGAAGGAC
2169424 TAATATACCC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.32, C:0.30, G:0.22, T:0.16
Consensus pattern (22 bp):
TCCCGAAGGACCACTGGATACA
Found at i:2169418 original size:44 final size:40
Alignment explanation
Indices: 2169327--2169423 Score: 104
Period size: 44 Copynumber: 2.3 Consensus size: 40
2169317 GTTCAGTATT
* *
2169327 TGTCCCGAAGGACCACTATGTCCCGAAAGACCACTGGATA
1 TGTCCCGAAGGACCACTATATCCCGAAAGACCACTGAATA
** * *
2169367 CATCCCGAAGGACCACTGGATACATCTCGAAGGACCACTGAATA
1 TGTCCCGAAGGACCACT--AT--ATCCCGAAAGACCACTGAATA
2169411 TGTCCCGAAGGAC
1 TGTCCCGAAGGAC
2169424 TAATATACCC
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
40 15 0.33
42 2 0.04
44 28 0.62
ACGTcount: A:0.31, C:0.30, G:0.23, T:0.16
Consensus pattern (40 bp):
TGTCCCGAAGGACCACTATATCCCGAAAGACCACTGAATA
Found at i:2174053 original size:24 final size:24
Alignment explanation
Indices: 2174021--2174071 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
2174011 TTACATAAAG
2174021 AGATCACGAAATACAAAATCGATC
1 AGATCACGAAATACAAAATCGATC
2174045 AGATCACGAAATACAAAATCGATC
1 AGATCACGAAATACAAAATCGATC
2174069 AGA
1 AGA
2174072 GCATTCGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.51, C:0.20, G:0.14, T:0.16
Consensus pattern (24 bp):
AGATCACGAAATACAAAATCGATC
Found at i:2175831 original size:46 final size:44
Alignment explanation
Indices: 2175768--2175856 Score: 151
Period size: 46 Copynumber: 2.0 Consensus size: 44
2175758 TTGTTTAAAT
*
2175768 AATTATTTGGTTCATATTTTTAGAGATGCTAATTTTTAATATTTTA
1 AATTATTTGGTTCATATTTTTAGAG-T-ATAATTTTTAATATTTTA
2175814 AATTATTTGGTTCATATTTTTAGAGTATAATTTTTAATATTTT
1 AATTATTTGGTTCATATTTTTAGAGTATAATTTTTAATATTTT
2175857 TTTTAAGATA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
44 16 0.38
45 1 0.02
46 25 0.60
ACGTcount: A:0.30, C:0.03, G:0.10, T:0.56
Consensus pattern (44 bp):
AATTATTTGGTTCATATTTTTAGAGTATAATTTTTAATATTTTA
Found at i:2176629 original size:2 final size:2
Alignment explanation
Indices: 2176622--2176655 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2176612 TTACCGCCAC
2176622 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2176656 GAATTTGACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2176979 original size:11 final size:11
Alignment explanation
Indices: 2176963--2176991 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
2176953 GAGGGTGGAC
2176963 ATACGAGCCAT
1 ATACGAGCCAT
2176974 ATACGAGCCAT
1 ATACGAGCCAT
2176985 ATACGAG
1 ATACGAG
2176992 TTCGAGCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.17
Consensus pattern (11 bp):
ATACGAGCCAT
Found at i:2177100 original size:60 final size:60
Alignment explanation
Indices: 2177028--2177201 Score: 289
Period size: 60 Copynumber: 2.9 Consensus size: 60
2177018 AGGCAATGGG
*
2177028 GCATGCAGGAATAGAGAGCCAATGGGAGCATGCAAACGAG-CATATACGAGCCCACGGGGA
1 GCATGCAGGAATAGAGAGCCAATGGGAGCATGC-AACGAGCCATATACGAGCCAACGGGGA
*
2177088 GCATGCAGGAATAGAGAGCCAATGGGGAGCATGCAACGAGCCATATACGA-CCAATGGGGA
1 GCATGCAGGAATAGAGAGCCAAT-GGGAGCATGCAACGAGCCATATACGAGCCAACGGGGA
2177148 GCATGCAGGAATAGAGAGCCAATTGGGAGCATGCAACGAGCCATATACGAGCCA
1 GCATGCAGGAATAGAGAGCCAA-TGGGAGCATGCAACGAGCCATATACGAGCCA
2177202 TGCCGAGCCA
Statistics
Matches: 108, Mismatches: 2, Indels: 7
0.92 0.02 0.06
Matches are distributed among these distances:
60 85 0.79
61 23 0.21
ACGTcount: A:0.35, C:0.21, G:0.32, T:0.11
Consensus pattern (60 bp):
GCATGCAGGAATAGAGAGCCAATGGGAGCATGCAACGAGCCATATACGAGCCAACGGGGA
Found at i:2177115 original size:28 final size:28
Alignment explanation
Indices: 2177021--2177182 Score: 143
Period size: 28 Copynumber: 5.6 Consensus size: 28
2177011 TGCAACGAGG
2177021 CAAT-GGG-GCATGCAGGAATAGAGAGC
1 CAATGGGGAGCATGCAGGAATAGAGAGC
* *
2177047 CAAT-GGGAGCATGCAAACGAGCATATACGAGC
1 CAATGGGGAGCATGC--A-G-GAATAGA-GAGC
* *
2177079 CCACGGGGAGCATGCAGGAATAGAGAGC
1 CAATGGGGAGCATGCAGGAATAGAGAGC
* *
2177107 CAATGGGGAGCATGCAACGAGCCATATACGA-C
1 CAATGGGGAGCATGC-A-G-G-AATAGA-GAGC
2177139 CAATGGGGAGCATGCAGGAATAGAGAGC
1 CAATGGGGAGCATGCAGGAATAGAGAGC
*
2177167 CAATTGGGAGCATGCA
1 CAATGGGGAGCATGCA
2177183 ACGAGCCATA
Statistics
Matches: 110, Mismatches: 13, Indels: 24
0.75 0.09 0.16
Matches are distributed among these distances:
26 7 0.06
27 8 0.07
28 37 0.34
29 8 0.07
30 4 0.04
31 8 0.07
32 26 0.24
33 12 0.11
ACGTcount: A:0.35, C:0.20, G:0.34, T:0.12
Consensus pattern (28 bp):
CAATGGGGAGCATGCAGGAATAGAGAGC
Found at i:2177147 original size:32 final size:32
Alignment explanation
Indices: 2177043--2177201 Score: 158
Period size: 28 Copynumber: 5.2 Consensus size: 32
2177033 CAGGAATAGA
2177043 GAGCCAAT-GGGAGCATGCAAACGAGCATATAC
1 GAGCCAATGGGGAGCATGC-AACGAGCATATAC
* * * *
2177075 GAGCCCACGGGGAGCATGC-A-G-GAATAGA-
1 GAGCCAATGGGGAGCATGCAACGAGCATATAC
2177103 GAGCCAATGGGGAGCATGCAACGAGCCATATAC
1 GAGCCAATGGGGAGCATGCAACGAG-CATATAC
* *
2177136 GA-CCAATGGGGAGCATGC-A-G-GAATAGA-
1 GAGCCAATGGGGAGCATGCAACGAGCATATAC
*
2177163 GAGCCAATTGGGAGCATGCAACGAGCCATATAC
1 GAGCCAATGGGGAGCATGCAACGAG-CATATAC
2177196 GAGCCA
1 GAGCCA
2177202 TGCCGAGCCA
Statistics
Matches: 102, Mismatches: 13, Indels: 23
0.74 0.09 0.17
Matches are distributed among these distances:
27 2 0.02
28 36 0.35
29 8 0.08
30 4 0.04
31 4 0.04
32 30 0.29
33 18 0.18
ACGTcount: A:0.35, C:0.22, G:0.32, T:0.11
Consensus pattern (32 bp):
GAGCCAATGGGGAGCATGCAACGAGCATATAC
Found at i:2177258 original size:29 final size:29
Alignment explanation
Indices: 2177223--2177328 Score: 178
Period size: 29 Copynumber: 3.7 Consensus size: 29
2177213 GCAAATAGAG
* *
2177223 AGGTCGCCATGCAG-CCTAGGCGACCTTGT
1 AGGTCGCCATGTAGTCC-CGGCGACCTTGT
2177252 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
2177281 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
2177310 AGGTCGCCATGTAGTCCCG
1 AGGTCGCCATGTAGTCCCG
2177329 CCCATTCCAT
Statistics
Matches: 74, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
29 72 0.97
30 2 0.03
ACGTcount: A:0.15, C:0.31, G:0.31, T:0.23
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:2177447 original size:36 final size:37
Alignment explanation
Indices: 2177379--2177450 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
2177369 CATAGATTCC
2177379 TTCACGTGCTCCCCGCTGCATTGCCTACACCTCCCAA
1 TTCACGTGCTCCCCGCTGCATTGCCTACACCTCCCAA
2177416 TTCACGTGCTCCCCGCTGCA-TGCCTACACCTCCCA
1 TTCACGTGCTCCCCGCTGCATTGCCTACACCTCCCA
2177451 TGCATGTGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 15 0.43
37 20 0.57
ACGTcount: A:0.15, C:0.47, G:0.14, T:0.24
Consensus pattern (37 bp):
TTCACGTGCTCCCCGCTGCATTGCCTACACCTCCCAA
Found at i:2177601 original size:23 final size:23
Alignment explanation
Indices: 2177573--2177618 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
2177563 AAAAGAAAGA
2177573 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
2177596 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
2177619 CCGAGAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.04, G:0.39, T:0.09
Consensus pattern (23 bp):
AAGAAAGGGAGAAGAGATTGCAG
Found at i:2177665 original size:20 final size:21
Alignment explanation
Indices: 2177635--2177676 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
2177625 AAGAAGAAAG
2177635 AAGGGAGAAAGGAAAGGAAGA
1 AAGGGAGAAAGGAAAGGAAGA
*
2177656 AAGGGA-AAAGGAAAGTAAGA
1 AAGGGAGAAAGGAAAGGAAGA
2177676 A
1 A
2177677 GAAGAAAGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.60, C:0.00, G:0.38, T:0.02
Consensus pattern (21 bp):
AAGGGAGAAAGGAAAGGAAGA
Found at i:2178710 original size:29 final size:29
Alignment explanation
Indices: 2178668--2178738 Score: 142
Period size: 29 Copynumber: 2.4 Consensus size: 29
2178658 GCAACTAATG
2178668 GGATTGCATGGCGACCTCCAAGGTCGCCT
1 GGATTGCATGGCGACCTCCAAGGTCGCCT
2178697 GGATTGCATGGCGACCTCCAAGGTCGCCT
1 GGATTGCATGGCGACCTCCAAGGTCGCCT
2178726 GGATTGCATGGCG
1 GGATTGCATGGCG
2178739 TCCTATGGCG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.17, C:0.28, G:0.34, T:0.21
Consensus pattern (29 bp):
GGATTGCATGGCGACCTCCAAGGTCGCCT
Found at i:2179108 original size:25 final size:22
Alignment explanation
Indices: 2179080--2179129 Score: 73
Period size: 25 Copynumber: 2.1 Consensus size: 22
2179070 TATTAGTTTG
2179080 TTAGTTTAAGTTAATTATATTAGTA
1 TTAGTTTAAGTT-A-TATATTA-TA
2179105 TTAGTTTAAGTTATATATTATA
1 TTAGTTTAAGTTATATATTATA
2179127 TTA
1 TTA
2179130 TATAAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 5 0.20
23 7 0.28
24 1 0.04
25 12 0.48
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.54
Consensus pattern (22 bp):
TTAGTTTAAGTTATATATTATA
Found at i:2179945 original size:26 final size:25
Alignment explanation
Indices: 2179916--2179974 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
2179906 AAATCATATT
*
2179916 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AGTAAATATCAAATC
*
2179942 ATTAGATT-AATAGTAATTATCAAATC
1 ATT--ATTAAATAGTAAATATCAAATC
2179968 ATTATTA
1 ATTATTA
2179975 GGTTTATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
24 3 0.11
26 19 0.68
27 3 0.11
28 3 0.11
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (25 bp):
ATTATTAAATAGTAAATATCAAATC
Found at i:2182800 original size:26 final size:25
Alignment explanation
Indices: 2182771--2182962 Score: 184
Period size: 26 Copynumber: 7.7 Consensus size: 25
2182761 TTTGATGATT
2182771 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTT-ATAATAATCATTA
2182797 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTT-ATAATAATCATTA
*
2182823 TAATAATGATTTAGTAATAATCATTA
1 TAGTAATGATTTA-TAATAATCATTA
** *
2182849 TAAAAATGA-TT-TAATAATGATT-
1 TAGTAATGATTTATAATAATCATTA
* * *
2182871 TA--AAT-ATTTAATGATTGATGATT-
1 TAGTAATGATTT-AT-AATAATCATTA
2182894 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTT-ATAATAATCATTA
2182920 TAGTAATGATTTAGTAATAATCATTA
1 TAGTAATGATTTA-TAATAATCATTA
*
2182946 TA-AAATGATTTAATAAT
1 TAGTAATGATTT-ATAAT
2182963 GATTTAAATA
Statistics
Matches: 145, Mismatches: 10, Indels: 23
0.81 0.06 0.13
Matches are distributed among these distances:
19 1 0.01
20 5 0.03
22 3 0.02
23 20 0.14
25 26 0.18
26 90 0.62
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.43
Consensus pattern (25 bp):
TAGTAATGATTTATAATAATCATTA
Found at i:2182906 original size:97 final size:97
Alignment explanation
Indices: 2182797--2183022 Score: 399
Period size: 97 Copynumber: 2.4 Consensus size: 97
2182787 ATAATCATTA
2182797 TAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATTATAAAAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATTAT-AAAATGATTTA
2182862 ATAATGATTTAAATATTTAATGA-TTGATGATT
65 ATAATGATTTAAATATTTAATGATTTGATGATT
*
2182894 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTAGTAATAATCATTATAAAATGATTTAA
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATTATAAAATGATTTAA
2182959 TAATGATTTAAATATTTAATGATTTGATGATT
66 TAATGATTTAAATATTTAATGATTTGATGATT
2182991 TAGTAATGATTTG---ATAATCATTAT-ATAATGAT
1 TAGTAATGATTTGATAATAATCATTATAATAATGAT
2183023 AAATAATTTG
Statistics
Matches: 126, Mismatches: 2, Indels: 6
0.94 0.01 0.04
Matches are distributed among these distances:
93 7 0.06
94 11 0.09
96 34 0.27
97 74 0.59
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.44
Consensus pattern (97 bp):
TAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATTATAAAATGATTTAA
TAATGATTTAAATATTTAATGATTTGATGATT
Found at i:2182933 original size:37 final size:36
Alignment explanation
Indices: 2182810--2182968 Score: 130
Period size: 37 Copynumber: 4.4 Consensus size: 36
2182800 TAATGATTTG
* *
2182810 ATAATAATCATTATAATAATGATTTAGTAATAATCATT
1 ATAATAATGATT-TAGTAATGATTTA-TAATAATCATT
* * * *
2182848 ATAAAAATGATTTAATAATGATTTA-AATATT--TA
1 ATAATAATGATTTAGTAATGATTTATAATAATCATT
* *
2182881 ATGATTGATGATTTAGTAATGATTTGATAATAATCATT
1 AT-AATAATGATTTAGTAATGATTT-ATAATAATCATT
* * *
2182919 ATAGTAATGATTTAGTAATAATCATTATAA-AATGATT
1 ATAATAATGATTTAGTAATGAT--TTATAATAATCATT
2182956 -TAATAATGATTTA
1 ATAATAATGATTTA
2182969 AATATTTAAT
Statistics
Matches: 99, Mismatches: 15, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
33 3 0.03
34 18 0.18
35 6 0.06
36 17 0.17
37 36 0.36
38 17 0.17
39 2 0.02
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.43
Consensus pattern (36 bp):
ATAATAATGATTTAGTAATGATTTATAATAATCATT
Found at i:2182938 original size:123 final size:123
Alignment explanation
Indices: 2182716--2182962 Score: 453
Period size: 123 Copynumber: 2.0 Consensus size: 123
2182706 TATGTATTAT
2182716 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
*
2182781 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAA-AATGATTTAATAA
2182840 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGA-TTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
2182904 TTGATAATAATCATTATAGTAATGATTT-AGTAATAATCATTATAAAATGATTTAATAA
66 TTGATAATAATCATTATAGTAATGATTTGA-TAATAATCATTATAAAATGATTTAATAA
2182962 T
1 T
2182963 GATTTAAATA
Statistics
Matches: 121, Mismatches: 1, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
122 14 0.12
123 62 0.51
124 45 0.37
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.43
Consensus pattern (123 bp):
TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAAAATGATTTAATAA
Found at i:2183001 original size:11 final size:11
Alignment explanation
Indices: 2182888--2183002 Score: 52
Period size: 11 Copynumber: 10.6 Consensus size: 11
2182878 TTAATGATTG
2182888 ATGATTTAGTA
1 ATGATTTAGTA
*
2182899 ATGATTTGATAATA
1 ATGA-TT--TAGTA
*
2182913 ATCATTATAGTA
1 ATGATT-TAGTA
2182925 ATGATTTAGTA
1 ATGATTTAGTA
*
2182936 ATAATCATTA-TAAA
1 ATGAT--TTAGT--A
*
2182950 ATGATTTAATA
1 ATGATTTAGTA
2182961 ATGATTTA--A
1 ATGATTTAGTA
2182970 AT-A-TT--TA
1 ATGATTTAGTA
2182977 ATGATTT-G--
1 ATGATTTAGTA
2182985 ATGATTTAGTA
1 ATGATTTAGTA
2182996 ATGATTT
1 ATGATTT
2183003 GATAATCATT
Statistics
Matches: 83, Mismatches: 6, Indels: 30
0.70 0.05 0.25
Matches are distributed among these distances:
7 5 0.06
8 9 0.11
9 6 0.07
11 29 0.35
12 16 0.19
13 6 0.07
14 12 0.14
ACGTcount: A:0.41, C:0.02, G:0.12, T:0.45
Consensus pattern (11 bp):
ATGATTTAGTA
Found at i:2183008 original size:11 final size:10
Alignment explanation
Indices: 2182949--2183022 Score: 52
Period size: 11 Copynumber: 7.6 Consensus size: 10
2182939 ATCATTATAA
2182949 AATGATTTAAT
1 AATGATTT-AT
2182960 AATGATTTA-
1 AATGATTTAT
2182969 AAT-A-TT-T
1 AATGATTTAT
2182976 AATGA-TT-T
1 AATGATTTAT
*
2182984 GATGATTTAGT
1 AATGATTTA-T
2182995 AATGATTTGAT
1 AATGATTT-AT
*
2183006 AATCATTATAT
1 AATGATT-TAT
2183017 AATGAT
1 AATGAT
2183023 AAATAATTTG
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
7 5 0.10
8 9 0.17
9 5 0.10
10 1 0.02
11 30 0.58
12 2 0.04
ACGTcount: A:0.41, C:0.01, G:0.12, T:0.46
Consensus pattern (10 bp):
AATGATTTAT
Found at i:2185320 original size:34 final size:33
Alignment explanation
Indices: 2185257--2185320 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 33
2185247 CTAAACCCTT
*
2185257 AAACAACTAATAAAATATTCTTTTATATAACTA
1 AAACAACTAATAAAATATTCTTTCATATAACTA
*
2185290 AAACTAACTAATAAACTATT-TTTCATTATAA
1 AAAC-AACTAATAAAATATTCTTTCA-TATAA
2185321 TATACTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
33 8 0.30
34 19 0.70
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (33 bp):
AAACAACTAATAAAATATTCTTTCATATAACTA
Found at i:2185455 original size:46 final size:48
Alignment explanation
Indices: 2185378--2185468 Score: 134
Period size: 46 Copynumber: 1.9 Consensus size: 48
2185368 CAACAAACAA
2185378 ATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTTTTT
1 ATATAACTTAACTATTTAACTAACACAAACTAATT-AATAATTTTTTTT
* *
2185427 ATATAAC-TAACTA-TTAAC-AATACAAACTAATTAATTATTTTT
1 ATATAACTTAACTATTTAACTAACACAAACTAATTAATAATTTTT
2185469 AACTATATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
45 9 0.22
46 13 0.32
47 5 0.12
48 6 0.15
49 7 0.17
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (48 bp):
ATATAACTTAACTATTTAACTAACACAAACTAATTAATAATTTTTTTT
Found at i:2185476 original size:46 final size:48
Alignment explanation
Indices: 2185378--2185481 Score: 133
Period size: 46 Copynumber: 2.2 Consensus size: 48
2185368 CAACAAACAA
**
2185378 ATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTTTTT
1 ATATAAC-TAACTATTTAACTAACACAAACTAATTAAATAATTTTTACT
* *
2185427 ATATAACTAACTA-TTAAC-AATACAAACTAATT-AATTATTTTTAACT
1 ATATAACTAACTATTTAACTAACACAAACTAATTAAATAATTTTT-ACT
2185473 ATATAACTA
1 ATATAACTA
2185482 TCAAACATAT
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
45 9 0.18
46 23 0.46
47 5 0.10
48 6 0.12
49 7 0.14
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.40
Consensus pattern (48 bp):
ATATAACTAACTATTTAACTAACACAAACTAATTAAATAATTTTTACT
Found at i:2185537 original size:41 final size:39
Alignment explanation
Indices: 2185450--2185537 Score: 88
Period size: 41 Copynumber: 2.2 Consensus size: 39
2185440 TTAACAATAC
*
2185450 AAACTAATTAATTATTTTTAACTATATAACTATCAAACAT
1 AAACTAATTAATAATTTTTAACTATATAACTAT-AAACAT
* * * *
2185490 ATACTAATTAAATAATTTTTAATTTATGTATACTAT-AACTT
1 AAACTAATT-AATAATTTTTAA-CTATATA-ACTATAAACAT
2185531 AAACTAA
1 AAACTAA
2185538 CAATCATATA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
40 8 0.21
41 21 0.54
42 5 0.13
43 5 0.13
ACGTcount: A:0.47, C:0.10, G:0.01, T:0.42
Consensus pattern (39 bp):
AAACTAATTAATAATTTTTAACTATATAACTATAAACAT
Found at i:2185700 original size:21 final size:21
Alignment explanation
Indices: 2185670--2185728 Score: 93
Period size: 21 Copynumber: 2.9 Consensus size: 21
2185660 CCCTTTCTTC
2185670 TTCTTACTTTCCTTTCTCCCT
1 TTCTTACTTTCCTTTCTCCCT
*
2185691 TTCTTCCTTTCCTTTCTCCCT
1 TTCTTACTTTCCTTTCTCCCT
*
2185712 TTCTTTCTTT-CTTTCTC
1 TTCTTACTTTCCTTTCTC
2185729 GGCTGCAATC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 7 0.19
21 29 0.81
ACGTcount: A:0.02, C:0.37, G:0.00, T:0.61
Consensus pattern (21 bp):
TTCTTACTTTCCTTTCTCCCT
Found at i:2185761 original size:23 final size:23
Alignment explanation
Indices: 2185731--2185776 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
2185721 TCTTTCTCGG
2185731 CTGCAATCTCTTCTCCCTTTCTT
1 CTGCAATCTCTTCTCCCTTTCTT
2185754 CTGCAATCTCTTCTCCCTTTCTT
1 CTGCAATCTCTTCTCCCTTTCTT
2185777 TCTTTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.09, C:0.39, G:0.04, T:0.48
Consensus pattern (23 bp):
CTGCAATCTCTTCTCCCTTTCTT
Found at i:2185888 original size:18 final size:18
Alignment explanation
Indices: 2185865--2185899 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
2185855 GTACCAATAA
2185865 TCAAATGGTTCACATGCC
1 TCAAATGGTTCACATGCC
2185883 TCAAATGGTTCACATGC
1 TCAAATGGTTCACATGC
2185900 ATGCATTGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (18 bp):
TCAAATGGTTCACATGCC
Found at i:2185951 original size:36 final size:37
Alignment explanation
Indices: 2185904--2185977 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
2185894 ACATGCATGC
2185904 ATTGGGAGGTGTAGGC-ATGCAGCGGGGAGCACGTGA
1 ATTGGGAGGTGTAGGCAATGCAGCGGGGAGCACGTGA
2185940 ATTGGGAGGTGTAGGCAATGCAGCGGGGAGCACGTGA
1 ATTGGGAGGTGTAGGCAATGCAGCGGGGAGCACGTGA
2185977 A
1 A
2185978 GGAATCTATG
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 16 0.43
37 21 0.57
ACGTcount: A:0.24, C:0.14, G:0.46, T:0.16
Consensus pattern (37 bp):
ATTGGGAGGTGTAGGCAATGCAGCGGGGAGCACGTGA
Found at i:2186060 original size:29 final size:29
Alignment explanation
Indices: 2186027--2186135 Score: 184
Period size: 29 Copynumber: 3.8 Consensus size: 29
2186017 GATGGAATGG
2186027 CGCCGGGACTACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
2186056 CGCCGGGACTACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
2186085 CGCCGGGACTACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
* *
2186114 CGCCTAGG-CTGCATGGCGACCT
1 CGCC-GGGACTACATGGCGACCT
2186136 CTCTATTCCT
Statistics
Matches: 77, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
29 75 0.97
30 2 0.03
ACGTcount: A:0.22, C:0.32, G:0.31, T:0.15
Consensus pattern (29 bp):
CGCCGGGACTACATGGCGACCTACAAGGT
Found at i:2186218 original size:28 final size:28
Alignment explanation
Indices: 2186178--2186343 Score: 188
Period size: 28 Copynumber: 5.6 Consensus size: 28
2186168 TATGGCTCGT
2186178 TGCATGCTCCCCATTGGCTCTCTATTCC
1 TGCATGCTCCCCATTGGCTCTCTATTCC
* *
2186206 TGCATGCTCCCCATTGGCTCGTATATGGCTCGT
1 TGCATGCTCCCCATTGGCTC-TCTAT---TC-C
2186239 TGCATGCTCCCCATTGGCTCTCTATTCC
1 TGCATGCTCCCCATTGGCTCTCTATTCC
* * * *
2186267 TGCATGCTCCCCGTGGGCTCGTATATGGCTCGT
1 TGCATGCTCCCCATTGGCTC-TCTAT---TC-C
2186300 TGCATGCTCCCCATTGGCTCTCTATTCC
1 TGCATGCTCCCCATTGGCTCTCTATTCC
2186328 TGCATGCTCCCCATTG
1 TGCATGCTCCCCATTG
2186344 CCTCGTTGCA
Statistics
Matches: 116, Mismatches: 12, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
28 54 0.47
29 12 0.10
32 12 0.10
33 38 0.33
ACGTcount: A:0.11, C:0.36, G:0.20, T:0.34
Consensus pattern (28 bp):
TGCATGCTCCCCATTGGCTCTCTATTCC
Found at i:2186317 original size:22 final size:22
Alignment explanation
Indices: 2186292--2186371 Score: 79
Period size: 22 Copynumber: 3.4 Consensus size: 22
2186282 GGCTCGTATA
2186292 TGGCTCGTTGCATGCTCCCCAT
1 TGGCTCGTTGCATGCTCCCCAT
*
2186314 TGGCTCTCTATTCCTGCATGCTCCCCAT
1 TGG--CTC--GT--TGCATGCTCCCCAT
* *
2186342 TGCCTCGTTGCATCCTCCCCAT
1 TGGCTCGTTGCATGCTCCCCAT
2186364 TGGCTCGT
1 TGGCTCGT
2186372 ATGACTCGTA
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
22 23 0.49
24 4 0.09
26 4 0.09
28 16 0.34
ACGTcount: A:0.09, C:0.39, G:0.19, T:0.34
Consensus pattern (22 bp):
TGGCTCGTTGCATGCTCCCCAT
Found at i:2186349 original size:61 final size:61
Alignment explanation
Indices: 2186134--2186349 Score: 371
Period size: 61 Copynumber: 3.5 Consensus size: 61
2186124 GCATGGCGAC
**
2186134 CTCTCTATTCCTGCATGGCTCGGCA-TGGCTCGTATATGGCTCGTTGCATGCTCCCCATTGG
1 CTCTCTATTCCTGCAT-GCTCCCCATTGGCTCGTATATGGCTCGTTGCATGCTCCCCATTGG
2186195 CTCTCTATTCCTGCATGCTCCCCATTGGCTCGTATATGGCTCGTTGCATGCTCCCCATTGG
1 CTCTCTATTCCTGCATGCTCCCCATTGGCTCGTATATGGCTCGTTGCATGCTCCCCATTGG
* *
2186256 CTCTCTATTCCTGCATGCTCCCCGTGGGCTCGTATATGGCTCGTTGCATGCTCCCCATTGG
1 CTCTCTATTCCTGCATGCTCCCCATTGGCTCGTATATGGCTCGTTGCATGCTCCCCATTGG
*
2186317 CTCTCTATTCCTGCATGCTCCCCATTGCCTCGT
1 CTCTCTATTCCTGCATGCTCCCCATTGGCTCGT
2186350 TGCATCCTCC
Statistics
Matches: 147, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
60 6 0.04
61 141 0.96
ACGTcount: A:0.11, C:0.35, G:0.21, T:0.34
Consensus pattern (61 bp):
CTCTCTATTCCTGCATGCTCCCCATTGGCTCGTATATGGCTCGTTGCATGCTCCCCATTGG
Found at i:2186390 original size:11 final size:11
Alignment explanation
Indices: 2186371--2186404 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
2186361 CATTGGCTCG
*
2186371 TATGACTCGTA
1 TATGGCTCGTA
2186382 TATGGCTCGTA
1 TATGGCTCGTA
2186393 TATGGCTCGTA
1 TATGGCTCGTA
2186404 T
1 T
2186405 GTCACCCTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.38
Consensus pattern (11 bp):
TATGGCTCGTA
Found at i:2186431 original size:11 final size:13
Alignment explanation
Indices: 2186398--2186424 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2186388 TCGTATATGG
2186398 CTCGTATGTCACC
1 CTCGTATGTCACC
2186411 CTCGTATGTCACC
1 CTCGTATGTCACC
2186424 C
1 C
2186425 GTATGTCGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.41, G:0.15, T:0.30
Consensus pattern (13 bp):
CTCGTATGTCACC
Found at i:2187978 original size:7 final size:7
Alignment explanation
Indices: 2187966--2188118 Score: 306
Period size: 7 Copynumber: 21.9 Consensus size: 7
2187956 AAAGAAATCT
2187966 TTTTACC
1 TTTTACC
2187973 TTTTACC
1 TTTTACC
2187980 TTTTACC
1 TTTTACC
2187987 TTTTACC
1 TTTTACC
2187994 TTTTACC
1 TTTTACC
2188001 TTTTACC
1 TTTTACC
2188008 TTTTACC
1 TTTTACC
2188015 TTTTACC
1 TTTTACC
2188022 TTTTACC
1 TTTTACC
2188029 TTTTACC
1 TTTTACC
2188036 TTTTACC
1 TTTTACC
2188043 TTTTACC
1 TTTTACC
2188050 TTTTACC
1 TTTTACC
2188057 TTTTACC
1 TTTTACC
2188064 TTTTACC
1 TTTTACC
2188071 TTTTACC
1 TTTTACC
2188078 TTTTACC
1 TTTTACC
2188085 TTTTACC
1 TTTTACC
2188092 TTTTACC
1 TTTTACC
2188099 TTTTACC
1 TTTTACC
2188106 TTTTACC
1 TTTTACC
2188113 TTTTAC
1 TTTTAC
2188119 GGGTTAATTA
Statistics
Matches: 146, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 146 1.00
ACGTcount: A:0.14, C:0.28, G:0.00, T:0.58
Consensus pattern (7 bp):
TTTTACC
Found at i:2189911 original size:16 final size:17
Alignment explanation
Indices: 2189870--2189914 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
2189860 ATTTTAGTCC
*
2189870 TTTAATT-TTTTTTTAT
1 TTTAATTATTTATTTAT
*
2189886 TTTTATTATTTATTTA-
1 TTTAATTATTTATTTAT
2189902 TTTAATTATTTAT
1 TTTAATTATTTAT
2189915 ATATATATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 18 0.72
17 7 0.28
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTAATTATTTATTTAT
Found at i:2190007 original size:16 final size:17
Alignment explanation
Indices: 2189988--2190024 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
2189978 AATATTTAAT
*
2189988 TTTTTATTTC-ATTTTA
1 TTTTTATTCCAATTTTA
2190004 TTTTTATTCCAATTTTA
1 TTTTTATTCCAATTTTA
2190021 TTTT
1 TTTT
2190025 GGTTTGTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTTATTCCAATTTTA
Found at i:2190076 original size:3 final size:3
Alignment explanation
Indices: 2190070--2190100 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
2190060 TCTCTCTTTG
2190070 TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2190101 TATCTCATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2190103 original size:12 final size:11
Alignment explanation
Indices: 2190070--2190100 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
2190060 TCTCTCTTTG
2190070 TTATTATTATTA
1 TTATTATTA-TA
2190082 TTATTATTATA
1 TTATTATTATA
2190093 TTATTATT
1 TTATTATT
2190101 TATCTCATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTATTATTATA
Found at i:2194369 original size:95 final size:95
Alignment explanation
Indices: 2194204--2194454 Score: 306
Period size: 95 Copynumber: 2.6 Consensus size: 95
2194194 TTATAATATT
* * *
2194204 ATATACAATAAAGCTTGAGTTGTCCCTCTAAAGAAATTGGTTAAACGCCCCGGCTTTATAGATAA
1 ATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCAGGCTTTATAGATAA
* **
2194269 TATTCAGCTAACCTGATAAAGGTGATTATA
66 AATTCAGCTAACCTGATAAAGGCAATTATA
* * *
2194299 ATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGGCTAGGCTTTATGGATAA
1 ATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCAGGCTTTATAGATAA
*
2194364 AATTCAGCTAGCCTGATAAAGGCAATTATA
66 AATTCAGCTAACCTGATAAAGGCAATTATA
* * * * * * *
2194394 ATAT-CTATACAATGATATTAAGCTGTCCCTCTAGAACAATTGGTTAAATGCCCCGGCTTTA
1 ATATACAATA-AA-G--CTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCAGGCTTTA
2194455 CGGATTCAGC
Statistics
Matches: 133, Mismatches: 19, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
94 4 0.03
95 91 0.68
96 1 0.01
98 37 0.28
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Consensus pattern (95 bp):
ATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCAGGCTTTATAGATAA
AATTCAGCTAACCTGATAAAGGCAATTATA
Found at i:2195788 original size:36 final size:36
Alignment explanation
Indices: 2195736--2195852 Score: 180
Period size: 36 Copynumber: 3.2 Consensus size: 36
2195726 TAATTTACTC
*
2195736 AAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTT
1 AAAACAAA-TTTTGTCTCTCTTGAGACAGTTTCCCTT
*
2195773 AAAACAAATTTTGTCTCTCTTGAGACAATTTCCCTT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTT
* *
2195809 GAATCAAATTTTGTCTCTCTTGAGACAGTTTCCCTT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTT
*
2195845 GAAACAAA
1 AAAACAAA
2195853 ATCTTTGAAT
Statistics
Matches: 74, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
36 66 0.89
37 8 0.11
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.38
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTT
Found at i:2195800 original size:21 final size:21
Alignment explanation
Indices: 2195767--2195835 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 21
2195757 TGAGACAGTT
* *
2195767 TCTCTTAAAACAAATTTTGTC
1 TCTCTTGAGACAAATTTTGTC
2195788 TCTCTTGAGAC-AA--TT-TC
1 TCTCTTGAGACAAATTTTGTC
2195805 -C-CTTGA-ATCAAATTTTGTC
1 TCTCTTGAGA-CAAATTTTGTC
2195824 TCTCTTGAGACA
1 TCTCTTGAGACA
2195836 GTTTCCCTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 16
0.68 0.04 0.29
Matches are distributed among these distances:
14 1 0.03
15 6 0.16
16 3 0.08
17 2 0.05
18 4 0.11
19 2 0.05
20 3 0.08
21 16 0.42
22 1 0.03
ACGTcount: A:0.28, C:0.22, G:0.10, T:0.41
Consensus pattern (21 bp):
TCTCTTGAGACAAATTTTGTC
Found at i:2195946 original size:21 final size:22
Alignment explanation
Indices: 2195920--2195968 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 22
2195910 GAGCCAGTTT
*
2195920 CTCTTGAAACAAA-TTTTGTCA
1 CTCTTGAAACAAAGTTGTGTCA
*
2195941 CTCTTGAAACAAAGTTGTGTCT
1 CTCTTGAAACAAAGTTGTGTCA
2195963 CTCTTG
1 CTCTTG
2195969 GGATAGTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (22 bp):
CTCTTGAAACAAAGTTGTGTCA
Found at i:2197613 original size:16 final size:17
Alignment explanation
Indices: 2197594--2197630 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
2197584 AATATTTAAT
*
2197594 TTTTTATT-TAATTTTA
1 TTTTTATTCCAATTTTA
2197610 TTTTTATTCCAATTTTA
1 TTTTTATTCCAATTTTA
2197627 TTTT
1 TTTT
2197631 GGTATTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTTATTCCAATTTTA
Found at i:2198800 original size:2 final size:2
Alignment explanation
Indices: 2198793--2198876 Score: 168
Period size: 2 Copynumber: 42.0 Consensus size: 2
2198783 TACATATAAG
2198793 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2198835 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2198877 CATTTTTTTC
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 82 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2199674 original size:16 final size:16
Alignment explanation
Indices: 2199650--2199683 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2199640 CTGATTTCTC
2199650 AATTCAATTTAAGTCA
1 AATTCAATTTAAGTCA
* *
2199666 AATTGAATTTGAGTCA
1 AATTCAATTTAAGTCA
2199682 AA
1 AA
2199684 CTCTTATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (16 bp):
AATTCAATTTAAGTCA
Found at i:2203088 original size:11 final size:11
Alignment explanation
Indices: 2203072--2203127 Score: 60
Period size: 11 Copynumber: 5.2 Consensus size: 11
2203062 CCAACACACC
2203072 ATAACAAACTA
1 ATAACAAACTA
2203083 ATAACAAACTA
1 ATAACAAACTA
* ** *
2203094 GTATTAAGCTA
1 ATAACAAACTA
*
2203105 ATAACAAAC-C
1 ATAACAAACTA
2203115 ATAACAAACTA
1 ATAACAAACTA
2203126 AT
1 AT
2203128 TGCACTCTAA
Statistics
Matches: 34, Mismatches: 10, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
10 9 0.26
11 25 0.74
ACGTcount: A:0.57, C:0.18, G:0.04, T:0.21
Consensus pattern (11 bp):
ATAACAAACTA
Found at i:2211754 original size:41 final size:40
Alignment explanation
Indices: 2211695--2211771 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
2211685 AATAAAATAA
*
2211695 TAATAAAATAATCAAACTAAAAATCCTGAATAAAAAAAAGT
1 TAATAAAATAATCAAACT-AAAATCCTAAATAAAAAAAAGT
* *
2211736 TAATAATAA-AATCTAACTAAAATCCTAAATATAAAA
1 TAATAA-AATAATCAAACTAAAATCCTAAATAAAAAA
2211772 GGTTATCACA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
40 16 0.50
41 14 0.44
42 2 0.06
ACGTcount: A:0.62, C:0.10, G:0.03, T:0.25
Consensus pattern (40 bp):
TAATAAAATAATCAAACTAAAATCCTAAATAAAAAAAAGT
Found at i:2213426 original size:297 final size:296
Alignment explanation
Indices: 2212846--2213438 Score: 1113
Period size: 298 Copynumber: 2.0 Consensus size: 296
2212836 ATCCATGGGT
2212846 GATAAAAGAAGGCAATGCGATTTGGTTTTGATTTCATAATTTTCAAATATGATGTAAACAAAATA
1 GATAAAAGAAGGCAATGCGATTTGGTTTTGATTTCATAATTTTCAAATATGATGTAAACAAAATA
2212911 GCACAACTGATGCATTCCACTGTAAGGCCCTTTAGAGAGCATTTCTATTTCAGTTCTCATGAATC
66 GCACAACTGATGCATTCCACTGTAAGGCCCTTTAGAGAGCATTTCTATTTCAGTTCTCATGAATC
2212976 TTTATTTGTTCAAGTTTCACAGACTCCTTAAGCAAAGATAGCGCCAAATATTGATCTAAAACAAA
131 TTTATTTGTTCAAGTTTCACAGACTCCTTAAGCAAAGATAGCGCCAAATATTGATCTAAAACAAA
2213041 ACCCCTGAGTGCTTTTGTGTAGTCAACTATAACAGATGTTTCCTGACTCTTTTAGTCTACATTTC
196 ACCCCTGAGTGCTTTTGTGTAGTCAACTATAACAGATGTTTCCTGACTCTTTTAGTCTACATTTC
2213106 ATCAAAATTTAATTTCAAATCCACGGGTTTATTTCAGGC
261 ATCAAAATTTAATTTCAAATCCAC--G-TTATTTCAGGC
2213145 GATAAAAGAAGGC-ATGCGATTTGGTTTTGATTTCATAATTTTCAAATATGATGTAAACAAAATA
1 GATAAAAGAAGGCAATGCGATTTGGTTTTGATTTCATAATTTTCAAATATGATGTAAACAAAATA
2213209 GCACAACTGATGCATTCCACTGTAAGGCCCTTTAGAGAGCATTTCTATTTCAGTTCTCATGAATC
66 GCACAACTGATGCATTCCACTGTAAGGCCCTTTAGAGAGCATTTCTATTTCAGTTCTCATGAATC
2213274 TTT-TATT-TTCAAGTTTCACAGACTCCTT-AGCAAAGATAGCGCCAAATATTGATCTAAAAACA
131 TTTAT-TTGTTCAAGTTTCACAGACTCCTTAAGCAAAGATAGCGCCAAATATTGATCT-AAAACA
2213336 AAACCCCTGAGTGCTTTTGTGTAGTCAACTATAACAGATGTTTCCTGACTCTTTTAGTCTACATT
194 AAACCCCTGAGTGCTTTTGTGTAGTCAACTATAACAGATGTTTCCTGACTCTTTTAGTCTACATT
2213401 TCATCAAAATTTAATTTCAAATCCACGTTATTTCAGGC
259 TCATCAAAATTTAATTTCAAATCCACGTTATTTCAGGC
2213439 TTTATCATTT
Statistics
Matches: 292, Mismatches: 0, Indels: 9
0.97 0.00 0.03
Matches are distributed among these distances:
294 11 0.04
295 1 0.00
296 27 0.09
297 119 0.41
298 121 0.41
299 13 0.04
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.35
Consensus pattern (296 bp):
GATAAAAGAAGGCAATGCGATTTGGTTTTGATTTCATAATTTTCAAATATGATGTAAACAAAATA
GCACAACTGATGCATTCCACTGTAAGGCCCTTTAGAGAGCATTTCTATTTCAGTTCTCATGAATC
TTTATTTGTTCAAGTTTCACAGACTCCTTAAGCAAAGATAGCGCCAAATATTGATCTAAAACAAA
ACCCCTGAGTGCTTTTGTGTAGTCAACTATAACAGATGTTTCCTGACTCTTTTAGTCTACATTTC
ATCAAAATTTAATTTCAAATCCACGTTATTTCAGGC
Found at i:2228032 original size:44 final size:44
Alignment explanation
Indices: 2227984--2228067 Score: 141
Period size: 44 Copynumber: 1.9 Consensus size: 44
2227974 CCTAATAAAA
*
2227984 TAATAATAAAATAATCAAACTAAAAATCCTGAATAAAAAAAAGT
1 TAATAATAAAATAATCAAACTAAAAATCCTAAATAAAAAAAAGT
* *
2228028 TAATAATAAAATAATCTAACTAAAAATCCTAAATATAAAA
1 TAATAATAAAATAATCAAACTAAAAATCCTAAATAAAAAA
2228068 GGTTTATCAC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.63, C:0.10, G:0.02, T:0.25
Consensus pattern (44 bp):
TAATAATAAAATAATCAAACTAAAAATCCTAAATAAAAAAAAGT
Found at i:2239959 original size:44 final size:44
Alignment explanation
Indices: 2239911--2239994 Score: 150
Period size: 44 Copynumber: 1.9 Consensus size: 44
2239901 CCTAATAAAA
*
2239911 TAATAATAAAATAATCAAACTAAAAATCCTGAATAAAAAAAAGT
1 TAATAATAAAATAATCAAACTAAAAATCCTAAATAAAAAAAAGT
*
2239955 TAATAATAAAATAATCAAACTAAAAATCCTAAATATAAAA
1 TAATAATAAAATAATCAAACTAAAAATCCTAAATAAAAAA
2239995 TGTTTATCAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.64, C:0.10, G:0.02, T:0.24
Consensus pattern (44 bp):
TAATAATAAAATAATCAAACTAAAAATCCTAAATAAAAAAAAGT
Found at i:2239988 original size:22 final size:22
Alignment explanation
Indices: 2239919--2239989 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
2239909 AATAATAATA
2239919 AAATAATCAAACTAAAAATCCT
1 AAATAATCAAACTAAAAATCCT
* ** * * *
2239941 GAATAAAAAAAAGTTAATAAT--A
1 AAAT-AATCAAA-CTAAAAATCCT
2239963 AAATAATCAAACTAAAAATCCT
1 AAATAATCAAACTAAAAATCCT
2239985 AAATA
1 AAATA
2239990 TAAAATGTTT
Statistics
Matches: 33, Mismatches: 12, Indels: 8
0.62 0.23 0.15
Matches are distributed among these distances:
20 6 0.18
21 5 0.15
22 11 0.33
23 5 0.15
24 6 0.18
ACGTcount: A:0.63, C:0.11, G:0.03, T:0.23
Consensus pattern (22 bp):
AAATAATCAAACTAAAAATCCT
Found at i:2245617 original size:11 final size:11
Alignment explanation
Indices: 2245603--2245636 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
2245593 TTAACGGGGT
*
2245603 AAAAACGAAAC
1 AAAAACAAAAC
2245614 AAAAACAAAAC
1 AAAAACAAAAC
2245625 AAAAACAAAAC
1 AAAAACAAAAC
2245636 A
1 A
2245637 TTAGGTATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.79, C:0.18, G:0.03, T:0.00
Consensus pattern (11 bp):
AAAAACAAAAC
Found at i:2247666 original size:41 final size:41
Alignment explanation
Indices: 2247579--2247666 Score: 115
Period size: 41 Copynumber: 2.2 Consensus size: 41
2247569 CTAATTCCTA
* * * *
2247579 ATAAAA-TAATAATCAAATAATCAAATTAAAAGTCCTAAAT
1 ATAAAAGTAATAATAAAATAATCAAACTAAAAATCATAAAT
*
2247619 AAAAAAGTAATAATAAAATAATCAAACTAAAAATCATAAAT
1 ATAAAAGTAATAATAAAATAATCAAACTAAAAATCATAAAT
*
2247660 CTAAAAG
1 ATAAAAG
2247667 GTTTATAACA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
40 5 0.12
41 35 0.88
ACGTcount: A:0.64, C:0.09, G:0.03, T:0.24
Consensus pattern (41 bp):
ATAAAAGTAATAATAAAATAATCAAACTAAAAATCATAAAT
Found at i:2249930 original size:14 final size:14
Alignment explanation
Indices: 2249907--2249939 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2249897 TTCTCAATTT
2249907 AAAT-AAATAAATA
1 AAATAAAATAAATA
2249920 AAATAAAATAAATA
1 AAATAAAATAAATA
*
2249934 GAATAA
1 AAATAA
2249940 TATAGAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (14 bp):
AAATAAAATAAATA
Found at i:2250821 original size:16 final size:16
Alignment explanation
Indices: 2250800--2250830 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2250790 TAATATTGAA
2250800 ACTTGAACTCAAAAAG
1 ACTTGAACTCAAAAAG
2250816 ACTTGAACTCAAAAA
1 ACTTGAACTCAAAAA
2250831 AAAATTAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.19, G:0.10, T:0.19
Consensus pattern (16 bp):
ACTTGAACTCAAAAAG
Found at i:2251184 original size:9 final size:9
Alignment explanation
Indices: 2251172--2251216 Score: 58
Period size: 9 Copynumber: 5.0 Consensus size: 9
2251162 CGGTTCTTCC
2251172 GACCGGTCG
1 GACCGGTCG
2251181 GACCGGTTC-
1 GACCGG-TCG
2251190 GACCGGTCG
1 GACCGGTCG
2251199 GACCGGTTC-
1 GACCGG-TCG
2251208 GACCGGTCG
1 GACCGGTCG
2251217 AACCAGTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
8 4 0.12
9 24 0.75
10 4 0.12
ACGTcount: A:0.11, C:0.33, G:0.40, T:0.16
Consensus pattern (9 bp):
GACCGGTCG
Found at i:2251186 original size:22 final size:21
Alignment explanation
Indices: 2251161--2251207 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 21
2251151 ATGACGTCGT
2251161 CCGGTTCTTCCGACCGGTCGGA
1 CCGGTTCTT-CGACCGGTCGGA
2251183 CCGG---TTCGACCGGTCGGA
1 CCGGTTCTTCGACCGGTCGGA
2251201 CCGGTTC
1 CCGGTTC
2251208 GACCGGTCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
18 16 0.73
19 2 0.09
22 4 0.18
ACGTcount: A:0.09, C:0.36, G:0.34, T:0.21
Consensus pattern (21 bp):
CCGGTTCTTCGACCGGTCGGA
Found at i:2251194 original size:18 final size:18
Alignment explanation
Indices: 2251171--2251216 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
2251161 CCGGTTCTTC
2251171 CGACCGGTCGGACCGGTT
1 CGACCGGTCGGACCGGTT
2251189 CGACCGGTCGGACCGGTT
1 CGACCGGTCGGACCGGTT
2251207 CGACCGGTCG
1 CGACCGGTCG
2251217 AACCAGTGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.11, C:0.35, G:0.39, T:0.15
Consensus pattern (18 bp):
CGACCGGTCGGACCGGTT
Found at i:2252736 original size:47 final size:47
Alignment explanation
Indices: 2252667--2252762 Score: 149
Period size: 47 Copynumber: 2.0 Consensus size: 47
2252657 GTTGGGGGAT
*
2252667 GATGGTGATAAATCAGGCGATTGGAGTGTC-GAGTTGGGTCGCCAGTC
1 GATGGCGATAAATCAGGCGATTGGAGT-TCAGAGTTGGGTCGCCAGTC
*
2252714 GATGGCGATAAATCAGGCGATTGGAGTTCTAGGGTTGGGTCGCCAGTC
1 GATGGCGATAAATCAGGCGATTGGAGTTC-AGAGTTGGGTCGCCAGTC
2252762 G
1 G
2252763 TTGCTGAGAC
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
46 2 0.04
47 26 0.58
48 17 0.38
ACGTcount: A:0.21, C:0.16, G:0.39, T:0.25
Consensus pattern (47 bp):
GATGGCGATAAATCAGGCGATTGGAGTTCAGAGTTGGGTCGCCAGTC
Found at i:2253102 original size:20 final size:21
Alignment explanation
Indices: 2253077--2253128 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
2253067 TTTTCCCAAT
*
2253077 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
2253097 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
2253118 TCGCAATGCGA
1 TCGCAATGCGA
2253129 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:2253142 original size:20 final size:20
Alignment explanation
Indices: 2253117--2253251 Score: 121
Period size: 20 Copynumber: 6.7 Consensus size: 20
2253107 AATTGGGAAA
2253117 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
2253137 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
2253157 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
2253178 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * **
2253198 TTCGCAACGCGATTTTGACT
1 ATCGCAATGCGATACTGACT
* *
2253218 TTCGCAATGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
2253238 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
2253252 TTTCAAAGCG
Statistics
Matches: 95, Mismatches: 15, Indels: 9
0.80 0.13 0.08
Matches are distributed among these distances:
19 4 0.04
20 64 0.67
21 25 0.26
22 2 0.02
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:2253161 original size:61 final size:61
Alignment explanation
Indices: 2253114--2253245 Score: 167
Period size: 61 Copynumber: 2.2 Consensus size: 61
2253104 GCGAATTGGG
* * * *
2253114 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTTACTATCGCAACGCGATAATAC
* * * *
2253175 AAAATCGCAACGAGATACTGACTTTCGCAACGCGAT-TTTGACTTTCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTT-ACTATCGCAACGCGATAATAC
*
2253236 ATAATCGCAA
1 AAAATCGCAA
2253246 TGCGATTTTC
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
60 2 0.03
61 61 0.97
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.25
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTTACTATCGCAACGCGATAATAC
Found at i:2253447 original size:22 final size:22
Alignment explanation
Indices: 2253419--2253462 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2253409 CACTCTCTCA
2253419 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
2253441 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
2253463 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:2253779 original size:20 final size:20
Alignment explanation
Indices: 2253725--2253783 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
2253715 GCGATTCTCT
**
2253725 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
2253745 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
2253765 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
2253784 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:2255123 original size:18 final size:18
Alignment explanation
Indices: 2255102--2255146 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
2255092 TCTACTTCGG
*
2255102 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
2255120 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
2255138 GAGCCATCA
1 GAGCCATCA
2255147 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:2255562 original size:17 final size:17
Alignment explanation
Indices: 2255528--2255573 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
2255518 TACTGCTAAC
*
2255528 TGTTTTT-GTTAGTATT
1 TGTTTTTGGTTTGTATT
*
2255544 TGTTTTTGGTTTGTTTT
1 TGTTTTTGGTTTGTATT
2255561 TGTCTTTTGGTTT
1 TGT-TTTTGGTTT
2255574 AAGTAATGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 7 0.27
17 10 0.38
18 9 0.35
ACGTcount: A:0.04, C:0.02, G:0.22, T:0.72
Consensus pattern (17 bp):
TGTTTTTGGTTTGTATT
Found at i:2255728 original size:32 final size:33
Alignment explanation
Indices: 2255669--2255755 Score: 149
Period size: 32 Copynumber: 2.7 Consensus size: 33
2255659 ATGGCTATCA
*
2255669 CAATGCGAAATGAAAATCGCAATGACAAAATCG
1 CAATGCGAAATGAAAATCGCAACGACAAAATCG
2255702 CAATGCGAAATG-AAATCGCAACGACAAAATCG
1 CAATGCGAAATGAAAATCGCAACGACAAAATCG
*
2255734 CAACGCGAAATGAAAATCGCAA
1 CAATGCGAAATGAAAATCGCAA
2255756 TGCAATTTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
32 30 0.59
33 21 0.41
ACGTcount: A:0.48, C:0.21, G:0.18, T:0.13
Consensus pattern (33 bp):
CAATGCGAAATGAAAATCGCAACGACAAAATCG
Found at i:2255737 original size:14 final size:14
Alignment explanation
Indices: 2255681--2255738 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
2255671 ATGCGAAATG
*
2255681 AAAATCGCAATGAC
1 AAAATCGCAACGAC
*
2255695 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
2255711 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
2255727 AAAATCGCAACG
1 AAAATCGCAACG
2255739 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 21 0.57
16 7 0.19
18 9 0.24
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:2255811 original size:14 final size:14
Alignment explanation
Indices: 2255792--2255848 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
2255782 TCATTTCGCA
2255792 TTGCGATTTTGTCG
1 TTGCGATTTTGTCG
*
2255806 TTGCGATTTTCATTTCG
1 TTGCGA-TTT--TGTCG
*
2255823 CATTGCTATTTTGTCG
1 --TTGCGATTTTGTCG
2255839 TTGCGATTTT
1 TTGCGATTTT
2255849 CATTTCGCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 15 0.44
15 3 0.09
16 4 0.12
17 4 0.12
18 3 0.09
19 5 0.15
ACGTcount: A:0.11, C:0.16, G:0.21, T:0.53
Consensus pattern (14 bp):
TTGCGATTTTGTCG
Found at i:2255822 original size:33 final size:33
Alignment explanation
Indices: 2255772--2255864 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
2255762 TTGTGTTTCG
2255772 CGTTGCGA-TTTCATTTCGCATTGCGATTTTGT
1 CGTTGCGATTTTCATTTCGCATTGCGATTTTGT
*
2255804 CGTTGCGATTTTCATTTCGCATTGCTATTTTGT
1 CGTTGCGATTTTCATTTCGCATTGCGATTTTGT
2255837 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
2255865 AGCCATTTCC
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 8 0.14
33 50 0.86
ACGTcount: A:0.13, C:0.19, G:0.20, T:0.47
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTTTGT
Found at i:2255833 original size:19 final size:19
Alignment explanation
Indices: 2255767--2255907 Score: 88
Period size: 20 Copynumber: 7.9 Consensus size: 19
2255757 GCAATTTGTG
*
2255767 TTTCGCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTCA
2255785 TTTCGCATTGCGA-TTT--
1 TTTCGCATTGCGATTTTCA
*
2255801 TGTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
*
2255818 TTTCGCATTGCTA-TTT--
1 TTTCGCATTGCGATTTTCA
*
2255834 TGTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
***
2255851 TTTCGCATTGCGATAGCCA
1 TTTCGCATTGCGATTTTCA
* **
2255870 TTTCCGCGTTGCGATAGTCA
1 TTT-CGCATTGCGATTTTCA
*
2255890 TTTTCGCGTTGCGATTTT
1 -TTTCGCATTGCGATTTT
2255908 AAGTTTCGTG
Statistics
Matches: 97, Mismatches: 14, Indels: 22
0.73 0.11 0.17
Matches are distributed among these distances:
14 11 0.11
15 6 0.06
16 8 0.08
17 8 0.08
18 18 0.19
19 17 0.18
20 26 0.27
21 3 0.03
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.45
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:2256325 original size:42 final size:40
Alignment explanation
Indices: 2256266--2256356 Score: 128
Period size: 42 Copynumber: 2.2 Consensus size: 40
2256256 GCCCGACTCA
*
2256266 CCTATCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCCC-CC-ACCGTTCAAGAGGCC
*
2256308 CCTATCCTCCCTCAAGAGTCCCCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCCCCCACCGTTCAAGAGGCC
* *
2256348 ACTGTCATC
1 CCTATCATC
2256357 GTTGAAGAGG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
40 20 0.45
41 2 0.05
42 22 0.50
ACGTcount: A:0.22, C:0.43, G:0.14, T:0.21
Consensus pattern (40 bp):
CCTATCATCCCTCAAGAGTCCCCCCACCGTTCAAGAGGCC
Found at i:2257789 original size:14 final size:14
Alignment explanation
Indices: 2257770--2257805 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2257760 ATTGTTTAAT
2257770 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
2257784 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
2257798 TGATTTGT
1 TGATTTGT
2257806 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2257966 original size:19 final size:19
Alignment explanation
Indices: 2257942--2258009 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
2257932 ATCGCAACGA
2257942 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
2257961 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
2257980 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
2257994 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
2258010 TTTTCATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 30 0.65
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:2258053 original size:20 final size:20
Alignment explanation
Indices: 2258028--2258103 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
2258018 TCGCATTGCG
*
2258028 ATTTTCTAGTTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
* ***
2258048 ATTTTCGCGTTGCGATTTTTC
1 ATTTTCGAGTTGCGA-TAGCC
*
2258069 A-TTTCGAATTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
*
2258088 ATTTTCGCGTTGCGAT
1 ATTTTCGAGTTGCGAT
2258104 TTCCCCGTTG
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
19 3 0.07
20 36 0.86
21 3 0.07
ACGTcount: A:0.17, C:0.20, G:0.21, T:0.42
Consensus pattern (20 bp):
ATTTTCGAGTTGCGATAGCC
Found at i:2258061 original size:34 final size:34
Alignment explanation
Indices: 2258016--2258119 Score: 109
Period size: 40 Copynumber: 2.9 Consensus size: 34
2258006 GCGATTTTCA
*
2258016 TTTCGCATTGCGATTTTCTAGTTGCGATAGCCAT
1 TTTCGCGTTGCGATTTTCTAGTTGCGATAGCCAT
*
2258050 TTTCGCGTTGCGATTTTTCATTTCGAATTGCGATAGCCAT
1 TTTCGCGTTGCGA-TTTTC---T--AGTTGCGATAGCCAT
* **
2258090 TTTCGCGTTGCGATTTCCCCGTTGCGATAG
1 TTTCGCGTTGCGATTTTCTAGTTGCGATAG
2258120 TCAAATGAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
34 21 0.36
35 5 0.09
38 1 0.02
39 4 0.07
40 27 0.47
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.40
Consensus pattern (34 bp):
TTTCGCGTTGCGATTTTCTAGTTGCGATAGCCAT
Found at i:2258341 original size:20 final size:20
Alignment explanation
Indices: 2258316--2258387 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
2258306 TTGAAGATGA
*
2258316 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGTATCTCG
* *
2258336 TTGCGATTTTGTATTATCTCG
1 TTGCGATTTT-CAGTATCTCG
** * *
2258357 TTGCGATAGTCAGTATCGCA
1 TTGCGATTTTCAGTATCTCG
2258377 TTGCGATTTTC
1 TTGCGATTTTC
2258388 CAAATTCGCA
Statistics
Matches: 40, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 25 0.62
21 15 0.38
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.43
Consensus pattern (20 bp):
TTGCGATTTTCAGTATCTCG
Found at i:2258416 original size:20 final size:21
Alignment explanation
Indices: 2258372--2258423 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
2258362 ATAGTCAGTA
*
2258372 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
2258393 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
2258413 TCGCATTGCGA
1 TCGCATTGCGA
2258424 ATTAGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:2258638 original size:12 final size:12
Alignment explanation
Indices: 2258619--2258652 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2258609 CTCTCCGGCG
2258619 ACATCCGTTCCT
1 ACATCCGTTCCT
*
2258631 ATATCCGTTCCT
1 ACATCCGTTCCT
2258643 ACATCC-TTCC
1 ACATCCGTTCC
2258653 CCATCTGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:2259396 original size:12 final size:12
Alignment explanation
Indices: 2259379--2259408 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
2259369 ATATAATCCT
2259379 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2259391 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2259403 GAAGAA
1 GAAGAA
2259409 AAAGTCCCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:2261735 original size:33 final size:32
Alignment explanation
Indices: 2261693--2261806 Score: 134
Period size: 33 Copynumber: 3.7 Consensus size: 32
2261683 GGAAATTACT
2261693 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATG-AAATCGCAACGAGAGA
**
2261726 ATCGCAATGCGAAATGAAATCGCAAC--GCTA
1 ATCGCAATGCGAAATGAAATCGCAACGAGAGA
*
2261756 ATCGCAATGC-----GAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAATCGCAACGAGAGA
2261783 ATCGCAATGCGAAATGAAAATCGC
1 ATCGCAATGCGAAATG-AAATCGC
2261807 GAATTTAATT
Statistics
Matches: 69, Mismatches: 4, Indels: 16
0.78 0.04 0.18
Matches are distributed among these distances:
25 11 0.16
27 12 0.17
30 12 0.17
32 11 0.16
33 23 0.33
ACGTcount: A:0.41, C:0.21, G:0.24, T:0.14
Consensus pattern (32 bp):
ATCGCAATGCGAAATGAAATCGCAACGAGAGA
Found at i:2261760 original size:12 final size:13
Alignment explanation
Indices: 2261741--2261797 Score: 53
Period size: 13 Copynumber: 4.4 Consensus size: 13
2261731 AATGCGAAAT
2261741 GAAATCGCAACGC
1 GAAATCGCAACGC
* *
2261754 -TAATCGCAATGC
1 GAAATCGCAACGC
*
2261766 GAAATCGCAACGAG
1 GAAATCGCAACG-C
* *
2261780 GGAATCGCAATGC
1 GAAATCGCAACGC
2261793 GAAAT
1 GAAAT
2261798 GAAAATCGCG
Statistics
Matches: 33, Mismatches: 9, Indels: 4
0.72 0.20 0.09
Matches are distributed among these distances:
12 10 0.30
13 13 0.39
14 10 0.30
ACGTcount: A:0.39, C:0.23, G:0.25, T:0.14
Consensus pattern (13 bp):
GAAATCGCAACGC
Found at i:2261793 original size:27 final size:27
Alignment explanation
Indices: 2261710--2261797 Score: 99
Period size: 27 Copynumber: 3.1 Consensus size: 27
2261700 TGCGAAATGA
2261710 AAATCGCAACGAGAGAATCGCAATGCG
1 AAATCGCAACGAGAGAATCGCAATGCG
*
2261737 AAAT-GAAATCGCA-ACGCTAATCGCAATGCG
1 AAATCGCAA-CG-AGA-G--AATCGCAATGCG
*
2261767 AAATCGCAACGAGGGAATCGCAATGCG
1 AAATCGCAACGAGAGAATCGCAATGCG
2261794 AAAT
1 AAAT
2261798 GAAAATCGCG
Statistics
Matches: 51, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
26 3 0.06
27 23 0.45
28 2 0.04
29 2 0.04
30 18 0.35
31 3 0.06
ACGTcount: A:0.41, C:0.22, G:0.24, T:0.14
Consensus pattern (27 bp):
AAATCGCAACGAGAGAATCGCAATGCG
Found at i:2261858 original size:19 final size:19
Alignment explanation
Indices: 2261834--2261880 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
2261824 GCGATTCTCT
2261834 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
2261853 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
2261872 CATTGCGAT
1 CGTTGCGAT
2261881 AGTACTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:2262005 original size:14 final size:14
Alignment explanation
Indices: 2261986--2262019 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2261976 CATCAATTAA
2261986 ACAAATAAACTTTT
1 ACAAATAAACTTTT
* *
2262000 ACAAATCACCTTTT
1 ACAAATAAACTTTT
2262014 ACAAAT
1 ACAAAT
2262020 CAATTAAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATAAACTTTT
Found at i:2262020 original size:14 final size:14
Alignment explanation
Indices: 2261995--2262021 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2261985 AACAAATAAA
2261995 CTTTTACAAATCAC
1 CTTTTACAAATCAC
2262009 CTTTTACAAATCA
1 CTTTTACAAATCA
2262022 ATTAAACAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.26, G:0.00, T:0.37
Consensus pattern (14 bp):
CTTTTACAAATCAC
Found at i:2263432 original size:42 final size:41
Alignment explanation
Indices: 2263373--2263577 Score: 164
Period size: 42 Copynumber: 4.9 Consensus size: 41
2263363 GTGAATCGGG
* ***
2263373 CTCTTGAATGGTGGGAGGGACCTCTTCAACTATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGA-CTCTTCAGGAATGACAGTGGC
* *
2263415 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTC-AGGAATGACAGTGGC
* * * * *
2263457 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGTGGC
1 CTCTTGAACGGTGGGAG-GGACTCTTCAGGAATGACAGTGGC
* *
2263499 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTC-AGGAATGACAGTGGC
* * * * *
2263541 CT-TTCAACGATAGGAGTGGACTCTTGAGGGATGACAG
1 CTCTTGAACGGTGGGAG-GGACTCTTCAGGAATGACAG
2263578 GCGAGTCGGG
Statistics
Matches: 129, Mismatches: 26, Indels: 17
0.75 0.15 0.10
Matches are distributed among these distances:
40 1 0.01
41 29 0.22
42 93 0.72
43 6 0.05
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGACTCTTCAGGAATGACAGTGGC
Found at i:2263439 original size:21 final size:21
Alignment explanation
Indices: 2263415--2263523 Score: 53
Period size: 21 Copynumber: 5.2 Consensus size: 21
2263405 TGACAGTGGC
2263415 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
* ** *
2263436 CTCTCG-A-GGAATGATAGGGGC
1 CTCTTGAACGG--TGGGAGGGGA
* * * *
2263457 CTCTTCAACGATAGGAGTGGA
1 CTCTTGAACGGTGGGAGGGGA
* ** * *
2263478 CTCTTG-AGGGATGACAGTGGC
1 CTCTTGAACGG-TGGGAGGGGA
2263499 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
2263520 CTCT
1 CTCT
2263524 CGAGGAATGA
Statistics
Matches: 58, Mismatches: 24, Indels: 12
0.62 0.26 0.13
Matches are distributed among these distances:
19 2 0.03
20 3 0.05
21 48 0.83
22 4 0.07
23 1 0.02
ACGTcount: A:0.21, C:0.18, G:0.39, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:2263514 original size:84 final size:83
Alignment explanation
Indices: 2263404--2263577 Score: 339
Period size: 84 Copynumber: 2.1 Consensus size: 83
2263394 CTCTTCAACT
2263404 ATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGAT
1 ATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCT-TTCAACGAT
2263469 AGGAGTGGACTCTTGAGGG
65 AGGAGTGGACTCTTGAGGG
2263488 ATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTTTCAACGATA
1 ATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTTTCAACGATA
2263553 GGAGTGGACTCTTGAGGG
66 GGAGTGGACTCTTGAGGG
2263571 ATGACAG
1 ATGACAG
2263578 GCGAGTCGGG
Statistics
Matches: 90, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
83 35 0.39
84 55 0.61
ACGTcount: A:0.24, C:0.17, G:0.38, T:0.21
Consensus pattern (83 bp):
ATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTTTCAACGATA
GGAGTGGACTCTTGAGGG
Found at i:2263974 original size:91 final size:90
Alignment explanation
Indices: 2263793--2263974 Score: 276
Period size: 91 Copynumber: 2.0 Consensus size: 90
2263783 ATTTCAAACT
*
2263793 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
2263858 AGAATTGGCAGCAACCAAATAAATTTAC
63 AGAATTGGCAGCAACCAAATAAATTTAC
2263886 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
* * *
2263950 GTATTGGCAGTAACCGAATAAATTT
64 GAATTGGCAGCAACCAAATAAATTT
2263975 CCTAAGCAAT
Statistics
Matches: 83, Mismatches: 4, Indels: 6
0.89 0.04 0.06
Matches are distributed among these distances:
91 37 0.45
93 19 0.23
95 27 0.33
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCAAATAAATTTAC
Found at i:2265645 original size:20 final size:19
Alignment explanation
Indices: 2265614--2265754 Score: 104
Period size: 19 Copynumber: 7.8 Consensus size: 19
2265604 TCTTTTGGTT
2265614 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
2265633 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
2265654 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
2265673 G--A-G--AATCGCAATGA
1 GAAATGAAAATCGCAACGA
** *
2265687 GAAATGACTATCGCGACGA
1 GAAATGAAAATCGCAACGA
*
2265706 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
2265720 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
2265739 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
2265755 TGCGATTTTG
Statistics
Matches: 97, Mismatches: 13, Indels: 24
0.72 0.10 0.18
Matches are distributed among these distances:
14 19 0.20
16 4 0.04
17 4 0.04
19 39 0.40
20 29 0.30
21 2 0.02
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:2265696 original size:33 final size:33
Alignment explanation
Indices: 2265639--2265737 Score: 135
Period size: 33 Copynumber: 3.0 Consensus size: 33
2265629 ACGAGATAAT
*
2265639 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACG-AGAAATGACTATCGCAACGA
* *
2265673 GAGAATCGCAATGAGAAATGACTATCGCGACGA
1 GAGAATCGCAACGAGAAATGACTATCGCAACGA
* **
2265706 GAGAATCGCAACGCGAAATGAAAATCGCAACG
1 GAGAATCGCAACGAGAAATGACTATCGCAACG
2265738 CGAAATGAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 45 0.79
34 12 0.21
ACGTcount: A:0.40, C:0.21, G:0.26, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGAGAAATGACTATCGCAACGA
Found at i:2265788 original size:19 final size:19
Alignment explanation
Indices: 2265755--2265821 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
2265745 AAAATCGCAA
**
2265755 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
2265774 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
2265793 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
2265813 TGCGATTTT
1 TGCGATTTT
2265822 CATTCTCGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 29 0.71
20 12 0.29
ACGTcount: A:0.10, C:0.16, G:0.25, T:0.48
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:2266362 original size:20 final size:20
Alignment explanation
Indices: 2266337--2266389 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
2266327 GCGCTATGTA
2266337 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
2266357 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
2266377 TATCTCGTTGCGA
1 AATCGCGTTGCGA
2266390 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:2266423 original size:20 final size:20
Alignment explanation
Indices: 2266398--2266451 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
2266388 GATTTTGTAT
2266398 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
2266418 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
2266438 TATCGCATTGCGAT
1 TATCGCATTGCGAT
2266452 TTTCCCAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:2266436 original size:61 final size:61
Alignment explanation
Indices: 2266338--2266454 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
2266328 CGCTATGTAA
* * * * *
2266338 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
2266399 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
2266455 CCCAAATCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:2266464 original size:61 final size:60
Alignment explanation
Indices: 2266336--2266472 Score: 157
Period size: 61 Copynumber: 2.2 Consensus size: 60
2266326 GGCGCTATGT
* * * * * **
2266336 AAATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGT
1 AAATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCC
* * * *
2266396 ATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCC
1 A-AATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CC
2266458 AAATCGCGTTGCGAT
1 AAATCGCGTTGCGAT
2266473 TTACTTATTC
Statistics
Matches: 62, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
60 1 0.02
61 60 0.97
62 1 0.02
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (60 bp):
AAATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCC
Found at i:2266720 original size:17 final size:19
Alignment explanation
Indices: 2266698--2266739 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
2266688 AAAACAATTG
*
2266698 TTTTTATTT-T-AACTTAT
1 TTTTTATTTGTAAAATTAT
2266715 TTTTTATTTGTAAAATTAT
1 TTTTTATTTGTAAAATTAT
2266734 TTTTTA
1 TTTTTA
2266740 ATATTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.41
18 1 0.05
19 12 0.55
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (19 bp):
TTTTTATTTGTAAAATTAT
Found at i:2266747 original size:19 final size:19
Alignment explanation
Indices: 2266711--2266748 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2266701 TTATTTTAAC
*
2266711 TTATTTTTTATTTGTAAAA
1 TTATTTTTTATATGTAAAA
2266730 TTATTTTTTAATAT-TAAAA
1 TTATTTTTT-ATATGTAAAA
2266749 AATATGCCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (19 bp):
TTATTTTTTATATGTAAAA
Found at i:2267474 original size:3 final size:3
Alignment explanation
Indices: 2267466--2267498 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
2267456 GTCCGGGTCT
2267466 TTA TTA TTA TTA TTA TTA CTT- TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
2267499 ATTACATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 24 0.86
4 2 0.07
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2267508 original size:18 final size:18
Alignment explanation
Indices: 2267467--2267509 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
2267457 TCCGGGTCTT
2267467 TATTATTATTATTATTAC
1 TATTATTATTATTATTAC
*
2267485 TTTTATTATTATTAATTAC
1 TATTATTATTATT-ATTAC
2267504 -ATTATT
1 TATTATT
2267510 TTTTATGCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.63
Consensus pattern (18 bp):
TATTATTATTATTATTAC
Found at i:2273325 original size:10 final size:10
Alignment explanation
Indices: 2273310--2273343 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
2273300 TAATTATAAT
2273310 CTAAATGCAG
1 CTAAATGCAG
2273320 CTAAATGCAG
1 CTAAATGCAG
*
2273330 CTAAATGCAA
1 CTAAATGCAG
2273340 CTAA
1 CTAA
2273344 TATGTTGTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.44, C:0.21, G:0.15, T:0.21
Consensus pattern (10 bp):
CTAAATGCAG
Found at i:2278506 original size:80 final size:78
Alignment explanation
Indices: 2278406--2278551 Score: 197
Period size: 80 Copynumber: 1.8 Consensus size: 78
2278396 ATTAAGTAAG
*
2278406 AATTAAAAGAATGTAATTTAGATTACAATTCTTTTAATTGATATATATAATTAAGAA-TAATTAA
1 AATTAAAAGAATGTAATTTAGATTACAAGTC-TTTAA-TG-TATATATAATT-AGAATTAATTAA
2278470 ATAATTTTCTAAATAAA
62 ATAATTTTCTAAATAAA
* * * *
2278487 AATT-AAAGATTGTAATTTAGATTATAAGTCTTTAATGTATATTTAATTTGAATTAATTAAATAA
1 AATTAAAAGAATGTAATTTAGATTACAAGTCTTTAATGTATATATAATTAGAATTAATTAAATAA
2278551 T
66 T
2278552 ATTTTATTTA
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
76 3 0.05
77 22 0.37
78 2 0.03
79 5 0.08
80 23 0.39
81 4 0.07
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.43
Consensus pattern (78 bp):
AATTAAAAGAATGTAATTTAGATTACAAGTCTTTAATGTATATATAATTAGAATTAATTAAATAA
TTTTCTAAATAAA
Found at i:2285529 original size:146 final size:149
Alignment explanation
Indices: 2285302--2285600 Score: 543
Period size: 147 Copynumber: 2.0 Consensus size: 149
2285292 ATTTAGATTA
2285302 CATGTATTTAATGTACATTTAATTTGATTAATTAAATAATATTTTATTTATTAATTCAAAATAAC
1 CATGTATTTAATGTACATTTAATTTGATTAATTAAATAATATTTTATTTATTAATTCAAAATAAC
2285367 TTTAAAAATTCCTAAGATGTTAGGGTAATTGATATA-TTAAAAGGAGGAAAGGTCT-AG-CATTT
66 TTTAAAAATTCCTAAGATGTTAGGGTAATTGATATATTTAAAAGGAGGAAAGGTCTAAGCCATTT
2285429 TACACTTCAGCCGTTTTCT
131 TACACTTCAGCCGTTTTCT
2285448 CATGTATTTAATGTACATTTAATTTGAATTAATTAAATAATATTTTATTTATTAATTCAAAATAA
1 CATGTATTTAATGTACATTTAATTTG-ATTAATTAAATAATATTTTATTTATTAATTCAAAATAA
2285513 CTTT-AAAATTCCTAAGATGTTAGGGTAATTGATATATTTAAAAGGAGGAAAGGTCTAGCAGCCA
65 CTTTAAAAATTCCTAAGATGTTAGGGTAATTGATATATTTAAAAGGAGGAAAGGTCTA--AGCCA
2285577 TTTTACACTTCAGCCGTTTTCT
128 TTTTACACTTCAGCCGTTTTCT
2285599 CA
1 CA
2285601 AAACAAATTT
Statistics
Matches: 147, Mismatches: 0, Indels: 7
0.95 0.00 0.05
Matches are distributed among these distances:
146 58 0.39
147 61 0.41
150 2 0.01
151 26 0.18
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.40
Consensus pattern (149 bp):
CATGTATTTAATGTACATTTAATTTGATTAATTAAATAATATTTTATTTATTAATTCAAAATAAC
TTTAAAAATTCCTAAGATGTTAGGGTAATTGATATATTTAAAAGGAGGAAAGGTCTAAGCCATTT
TACACTTCAGCCGTTTTCT
Found at i:2293144 original size:2 final size:2
Alignment explanation
Indices: 2293137--2293168 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2293127 TATACCCATA
2293137 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2293169 GTATGTATAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2294667 original size:36 final size:37
Alignment explanation
Indices: 2294627--2294699 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 37
2294617 TTTGAGATTG
* * *
2294627 TTTTCTC-TAAAAACAAATTTTGTCTCGCTTTAGACA
1 TTTTCTCTTAAAAACAAATTTCGTCTCACTTGAGACA
*
2294663 TTTTCTCTTAAAAATAAATTTCGTCTCACTTGAGACA
1 TTTTCTCTTAAAAACAAATTTCGTCTCACTTGAGACA
2294700 GTCTTCCTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
36 7 0.22
37 25 0.78
ACGTcount: A:0.32, C:0.19, G:0.08, T:0.41
Consensus pattern (37 bp):
TTTTCTCTTAAAAACAAATTTCGTCTCACTTGAGACA
Found at i:2294710 original size:37 final size:37
Alignment explanation
Indices: 2294629--2294710 Score: 96
Period size: 37 Copynumber: 2.2 Consensus size: 37
2294619 TGAGATTGTT
* * * *
2294629 TTCTC-TAAAAACAAATTTTGTCTCGCTTTAGACATT
1 TTCTCTTAAAAACAAATTTCGTCTCACTTGAGACATC
*
2294665 TTCTCTTAAAAATAAATTTCGTCTCACTTGAGACAGTC
1 TTCTCTTAAAAACAAATTTCGTCTCACTTGAGACA-TC
2294703 TTC-CTTAA
1 TTCTCTTAA
2294711 GACAAAACAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
36 5 0.13
37 30 0.77
38 4 0.10
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.40
Consensus pattern (37 bp):
TTCTCTTAAAAACAAATTTCGTCTCACTTGAGACATC
Found at i:2294795 original size:64 final size:67
Alignment explanation
Indices: 2294663--2294797 Score: 154
Period size: 64 Copynumber: 2.1 Consensus size: 67
2294653 GCTTTAGACA
* * * *
2294663 TTTTCTCTTAAAAATAAATTTCGTCTCACTTGAGACAGTCTTCCTTAAGACAAAACATTTGAGAT
1 TTTTCTCTTAAAAATAAATTTCGTCTCACTTGAGACAGTCTCCCCTAAGACAAAACATTTCAAAT
2294728 TG
66 TG
* * *
2294730 TTTT-TCTTAAAAA-ATA-TTCGTCTCACTTGAGACAGT-TCCCCTCAGAACACAA-ATTTCAAA
1 TTTTCTCTTAAAAATAAATTTCGTCTCACTTGAGACAGTCTCCCCTAAG-ACAAAACATTTCAAA
2294790 GTTG
65 -TTG
2294794 TTTT
1 TTTT
2294798 ACTTGAAACA
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
63 12 0.20
64 32 0.54
65 2 0.03
66 9 0.15
67 4 0.07
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (67 bp):
TTTTCTCTTAAAAATAAATTTCGTCTCACTTGAGACAGTCTCCCCTAAGACAAAACATTTCAAAT
TG
Found at i:2295049 original size:36 final size:36
Alignment explanation
Indices: 2294927--2295153 Score: 153
Period size: 36 Copynumber: 6.4 Consensus size: 36
2294917 CTTTGAGATT
* *
2294927 GTTTCTCTTGAAACAAATTTTGTCTCTCTTTAGACA
1 GTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACA
* * * *
2294963 GTCTCACTTGAAACAAA-ATTGATCTCGCTTGAGATTA
1 GTTTCTCTTGAAACAAATTTTG-TCTCGCTTGAGA-CA
* * ** *
2295000 TTTTCCCTAAAAACAAATTTTTTCTCGCTTGAGACA
1 GTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACA
* * *
2295036 GTTTCTCTTAAAACAAAGTTTTGTATCTCTTGAGACA
1 GTTTCTCTTGAAACAAA-TTTTGTCTCGCTTGAGACA
* * ** * **
2295073 TTTTTTCTTGAAACAAA----AAC-C-TTTGAGATT
1 GTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACA
* * * *
2295103 GTTTCTGTTGAAACAAGTTTTATCTCTCTTGAGACA
1 GTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACA
2295139 GTTTCTCTTGAAACA
1 GTTTCTCTTGAAACA
2295154 TAAACATTGA
Statistics
Matches: 143, Mismatches: 38, Indels: 20
0.71 0.19 0.10
Matches are distributed among these distances:
30 19 0.13
31 1 0.01
34 2 0.01
35 4 0.03
36 60 0.42
37 55 0.38
38 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (36 bp):
GTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACA
Found at i:2295087 original size:73 final size:72
Alignment explanation
Indices: 2294928--2295089 Score: 166
Period size: 73 Copynumber: 2.2 Consensus size: 72
2294918 TTTGAGATTG
* * *
2294928 TTTCTCTTGAAACAAATTTTGTCTCTCTTTAGACAGTCTCACTTGAAACAAAATTGATCTCGCTT
1 TTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACAGTCTCACTTAAAACAAAATTGATCTC-CTT
*
2294993 GAGATTAT
65 GAGATCAT
* ** * * * *
2295001 TTTCCCTAAAAACAAATTTTTTCTCGCTTGAGACAGTTTCTCTTAAAACAAAGTTTTGTATCT-C
1 TTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACAGTCTCACTTAAAACAAA--ATTG-ATCTCC
2295065 TTGAGA-CAT
63 TTGAGATCAT
*
2295074 TTTTTCTTGAAACAAA
1 TTTCTCTTGAAACAAA
2295090 AACCTTTGAG
Statistics
Matches: 71, Mismatches: 15, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
73 57 0.80
74 7 0.10
75 3 0.04
76 4 0.06
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (72 bp):
TTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACAGTCTCACTTAAAACAAAATTGATCTCCTTG
AGATCAT
Found at i:2295194 original size:65 final size:66
Alignment explanation
Indices: 2295036--2295216 Score: 213
Period size: 65 Copynumber: 2.7 Consensus size: 66
2295026 GCTTGAGACA
* * * *
2295036 GTTTCTCTTAAAACAAAGTTTTGTATCTCTTGAGACATTTTTTCTTGAAACAAAAACCTTTGAGA
1 GTTTCTCTTAAAAC-AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAAACCATTGAGA
2295101 TT
65 TT
* * * *
2295103 GTTTCTGTTGAAACAAGTTTTATCTCTCTTGAGACAGTTTCTCTTGAAACATAAA-CATTGAGAT
1 GTTTCTCTTAAAACAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAAACCATTGAGAT
2295167 T
66 T
* * ** *
2295168 GTTTCCCTTCAAACATA-TTTTGTCTCTCTTGAGATTGTTTCCCTTGAAA
1 GTTTCTCTTAAAACA-AGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA
2295217 TATATTTTGT
Statistics
Matches: 98, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
65 49 0.50
66 37 0.38
67 12 0.12
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (66 bp):
GTTTCTCTTAAAACAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAAACCATTGAGAT
T
Found at i:2295207 original size:36 final size:36
Alignment explanation
Indices: 2295160--2295273 Score: 156
Period size: 36 Copynumber: 3.2 Consensus size: 36
2295150 AACATAAACA
*
2295160 TTGAGATTGTTTCCCTTCAAACATATTTTGTCTCTC
1 TTGAGATTGTTTCCCTTGAAACATATTTTGTCTCTC
* *
2295196 TTGAGATTGTTTCCCTTGAAATATATTTTGTATCTC
1 TTGAGATTGTTTCCCTTGAAACATATTTTGTCTCTC
* ** * *
2295232 TTGAGATAGAGTCTCTTGAAACATGTTTTGTCTCTC
1 TTGAGATTGTTTCCCTTGAAACATATTTTGTCTCTC
2295268 TTGAGA
1 TTGAGA
2295274 GAACTTCCCT
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 68 1.00
ACGTcount: A:0.22, C:0.17, G:0.16, T:0.46
Consensus pattern (36 bp):
TTGAGATTGTTTCCCTTGAAACATATTTTGTCTCTC
Found at i:2295286 original size:36 final size:35
Alignment explanation
Indices: 2295170--2295288 Score: 130
Period size: 36 Copynumber: 3.3 Consensus size: 35
2295160 TTGAGATTGT
* **
2295170 TTCCCTTCAAACATATTTTGTCTCTCTTGAGATTGT
1 TTCCCTTGAAACATATTTTGTCTCTCTTGAGA-TAA
* *
2295206 TTCCCTTGAAATATATTTTGTATCTCTTGAGATAGA
1 TTCCCTTGAAACATATTTTGTCTCTCTTGAGATA-A
* * * *
2295242 GTCTCTTGAAACATGTTTTGTCTCTCTTGAGAGAA
1 TTCCCTTGAAACATATTTTGTCTCTCTTGAGATAA
2295277 CTTCCCTTGAAA
1 -TTCCCTTGAAA
2295289 AATTATCCCT
Statistics
Matches: 68, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
35 2 0.03
36 66 0.97
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.43
Consensus pattern (35 bp):
TTCCCTTGAAACATATTTTGTCTCTCTTGAGATAA
Found at i:2295536 original size:137 final size:138
Alignment explanation
Indices: 2295314--2295699 Score: 551
Period size: 138 Copynumber: 2.8 Consensus size: 138
2295304 TGGTCAGCCA
* * * *
2295314 TCCTCATCACGTAAGAACCGTGTCATCCATCGACCAGATCTCCTCATCACGTAGGAGTCACGTCA
1 TCCTCATCACGTAGGAACTGTGTCATCCACCGACCAGATCTCCTCATCACGTAGGAGTCGCGTCA
* *
2295379 CCCTTAGATAACCAACCATCCTCATCACGTAGGAACCATGTTATCTACA-TTATCAATAAAGATG
66 CCCTTAGATAACCAGCCATCCTCATCACGTAGGAATCATGTTATCTACATTTATCAATAAAGATG
2295443 ACCAACCG
131 ACCAACCG
* * * *
2295451 TCCTTATCACGTAGGAACTGTGTCATCCACCGACCATATATCCTCATCACGTAAGAGTCGCGTCA
1 TCCTCATCACGTAGGAACTGTGTCATCCACCGACCAGATCTCCTCATCACGTAGGAGTCGCGTCA
* * * **
2295516 CCCTTAGATAACCAGCCATCCTCATCACGTAAGAATCGTGTTATCTATATTTATCCCTAAAGATG
66 CCCTTAGATAACCAGCCATCCTCATCACGTAGGAATCATGTTATCTACATTTATCAATAAAGATG
* *
2295581 GCCAATCG
131 ACCAACCG
*
2295589 TCCTCATCACGTAGGAACTGTGTCATCCACCGACCAGATCTCCTCATCACGTAGGAG-CAGTGTC
1 TCCTCATCACGTAGGAACTGTGTCATCCACCGACCAGATCTCCTCATCACGTAGGAGTC-GCGTC
* * * *
2295653 ACCCTTAGATAAACAGACTTCCTCATCACGTAGGAATTATGTTATCT
65 ACCCTTAGATAACCAGCCATCCTCATCACGTAGGAATCATGTTATCT
2295700 CCTAATTTAC
Statistics
Matches: 219, Mismatches: 28, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
137 102 0.47
138 117 0.53
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.26
Consensus pattern (138 bp):
TCCTCATCACGTAGGAACTGTGTCATCCACCGACCAGATCTCCTCATCACGTAGGAGTCGCGTCA
CCCTTAGATAACCAGCCATCCTCATCACGTAGGAATCATGTTATCTACATTTATCAATAAAGATG
ACCAACCG
Found at i:2295640 original size:138 final size:137
Alignment explanation
Indices: 2295290--2295699 Score: 570
Period size: 137 Copynumber: 3.0 Consensus size: 137
2295280 CCCTTGAAAA
* * * * * *
2295290 ATTATCCCTAAAGATGGTCAGCCATCCTCATCACGTAAGAACCGTGTCATCCATCGACCAGATCT
1 ATTATCCCTAAAGATGGCCAACCGTCCTCATCACGTAGGAACTGTGTCATCCACCGACCAGATCT
* * *
2295355 CCTCATCACGTAGGAGTCACGTCACCCTTAGATAACCAACCATCCTCATCACGTAGGAACCATGT
66 CCTCATCACGTAGGAGTCGCGTCACCCTTAGATAACCAGCCATCCTCATCACGTAGGAATCATGT
2295420 TATCTAC
131 TATCTAC
** * * * *
2295427 ATTATCAATAAAGATGACCAACCGTCCTTATCACGTAGGAACTGTGTCATCCACCGACCATATAT
1 ATTATCCCTAAAGATGGCCAACCGTCCTCATCACGTAGGAACTGTGTCATCCACCGACCAGATCT
* * *
2295492 CCTCATCACGTAAGAGTCGCGTCACCCTTAGATAACCAGCCATCCTCATCACGTAAGAATCGTGT
66 CCTCATCACGTAGGAGTCGCGTCACCCTTAGATAACCAGCCATCCTCATCACGTAGGAATCATGT
*
2295557 TATCTAT
131 TATCTAC
*
2295564 ATTTATCCCTAAAGATGGCCAATCGTCCTCATCACGTAGGAACTGTGTCATCCACCGACCAGATC
1 A-TTATCCCTAAAGATGGCCAACCGTCCTCATCACGTAGGAACTGTGTCATCCACCGACCAGATC
* * * * *
2295629 TCCTCATCACGTAGGAG-CAGTGTCACCCTTAGATAAACAGACTTCCTCATCACGTAGGAATTAT
65 TCCTCATCACGTAGGAGTC-GCGTCACCCTTAGATAACCAGCCATCCTCATCACGTAGGAATCAT
2295693 GTTATCT
129 GTTATCT
2295700 CCTAATTTAC
Statistics
Matches: 237, Mismatches: 34, Indels: 3
0.86 0.12 0.01
Matches are distributed among these distances:
137 120 0.51
138 117 0.49
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.26
Consensus pattern (137 bp):
ATTATCCCTAAAGATGGCCAACCGTCCTCATCACGTAGGAACTGTGTCATCCACCGACCAGATCT
CCTCATCACGTAGGAGTCGCGTCACCCTTAGATAACCAGCCATCCTCATCACGTAGGAATCATGT
TATCTAC
Done.