Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008955.1 Hibiscus syriacus cultivar Beakdansim tig00112285_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: 4658001
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 23
Found at i:3579703 original size:18 final size:18
Alignment explanation
Indices: 3579642--3579710 Score: 50
Period size: 18 Copynumber: 3.6 Consensus size: 18
3579632 TTATAGTGTG
*
3579642 TATACATATAATGTAAAC
1 TATACATGTAATGTAAAC
* *
3579660 TATATATGTGACTTATAGTATA-
1 TATACATGT-A---AT-GTAAAC
3579682 TATACATGTAATGTAAAC
1 TATACATGTAATGTAAAC
*
3579700 TATATATGTAA
1 TATACATGTAA
3579711 CTTATATGTA
Statistics
Matches: 39, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
17 4 0.10
18 19 0.49
19 1 0.03
21 1 0.03
22 10 0.26
23 4 0.10
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.39
Consensus pattern (18 bp):
TATACATGTAATGTAAAC
Found at i:3579718 original size:11 final size:12
Alignment explanation
Indices: 3579621--3579721 Score: 55
Period size: 13 Copynumber: 7.8 Consensus size: 12
3579611 ACAATAGTTA
3579621 ATATATGTAACTT
1 ATATATGTAAC-T
*
3579634 ATAGTGTGTATAC-
1 ATA-TATGTA-ACT
3579647 ATATAATGTAAACT
1 ATAT-ATGT-AACT
*
3579661 ATATATGTGACTT
1 ATATATGTAAC-T
*
3579674 ATAGTATATATAC-
1 ATA-TATGTA-ACT
*
3579687 ATGTAATGTAAACT
1 ATAT-ATGT-AACT
3579701 ATATATGTAACT
1 ATATATGTAACT
3579713 -TATATGTAA
1 ATATATGTAA
3579722 GTACATGTAT
Statistics
Matches: 69, Mismatches: 8, Indels: 24
0.68 0.08 0.24
Matches are distributed among these distances:
11 9 0.13
12 8 0.12
13 30 0.43
14 18 0.26
15 4 0.06
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.41
Consensus pattern (12 bp):
ATATATGTAACT
Found at i:3579742 original size:40 final size:38
Alignment explanation
Indices: 3579621--3579734 Score: 140
Period size: 40 Copynumber: 2.9 Consensus size: 38
3579611 ACAATAGTTA
* *
3579621 ATATATGTAACTTATAGTGTGTATACATATAATGTAAACT
1 ATATATGTAACTTATA-TGT-AATACATGTAATGTAAACT
* *
3579661 ATATATGTGACTTATAGTATATATACATGTAATGTAAACT
1 ATATATGTAACTTATA-TGTA-ATACATGTAATGTAAACT
3579701 ATATATGTAACTTATATGTAAGTACATGT-ATGTA
1 ATATATGTAACTTATATGTAA-TACATGTAATGTA
3579735 TAAACTATGT
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
38 6 0.09
39 10 0.15
40 50 0.76
ACGTcount: A:0.39, C:0.07, G:0.13, T:0.40
Consensus pattern (38 bp):
ATATATGTAACTTATATGTAATACATGTAATGTAAACT
Found at i:3580021 original size:37 final size:36
Alignment explanation
Indices: 3579959--3580028 Score: 95
Period size: 37 Copynumber: 1.9 Consensus size: 36
3579949 ATAGTTAATA
*
3579959 TATATATATAACCTATAATATATGTATACATGTAAAT
1 TATATATATAACCTATAATACATGTAT-CATGTAAAT
* * *
3579996 TATATATGTAACTTATAGTACATGTATCATGTA
1 TATATATATAACCTATAATACATGTATCATGTA
3580029 TGTATAAACT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
36 6 0.21
37 23 0.79
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (36 bp):
TATATATATAACCTATAATACATGTATCATGTAAAT
Found at i:3581488 original size:14 final size:14
Alignment explanation
Indices: 3581469--3581515 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
3581459 ATTATTTTTT
3581469 TATATAAATTAAAC
1 TATATAAATTAAAC
3581483 TATAT-AATT----
1 TATATAAATTAAAC
3581492 TATATAAATTAAAC
1 TATATAAATTAAAC
*
3581506 TATATTAATT
1 TATATAAATT
3581516 TTTCTTTGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 5 0.19
10 4 0.15
13 4 0.15
14 14 0.52
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATAAATTAAAC
Found at i:3581493 original size:23 final size:24
Alignment explanation
Indices: 3581467--3581516 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
3581457 ATATTATTTT
3581467 TTTATATAAATTAAACTATA-TAA
1 TTTATATAAATTAAACTATATTAA
3581490 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAACTATATTAA
3581514 TTT
1 TTT
3581517 TTCTTTGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTATATAAATTAAACTATATTAA
Found at i:3581791 original size:16 final size:16
Alignment explanation
Indices: 3581770--3581824 Score: 83
Period size: 16 Copynumber: 3.4 Consensus size: 16
3581760 CGGATCATTT
* *
3581770 ACAGGTCATGTTAAAA
1 ACAGGTCAGGTTGAAA
3581786 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTGAAA
*
3581802 ACAAGTCAGGTTGAAA
1 ACAGGTCAGGTTGAAA
3581818 ACAGGTC
1 ACAGGTC
3581825 GGGTAATACC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.20
Consensus pattern (16 bp):
ACAGGTCAGGTTGAAA
Found at i:3581966 original size:25 final size:25
Alignment explanation
Indices: 3581881--3581966 Score: 66
Period size: 25 Copynumber: 3.3 Consensus size: 25
3581871 ATCAGTTCGG
3581881 ATTCGGGTATCATATTTTCGGTTCA
1 ATTCGGGTATCATATTTTCGGTTCA
** *** * *
3581906 ATTCGGGTTATGGTCGGATGCAGG-TCGG
1 ATTCGGG-TATCAT-ATTTTC-GGTTC-A
3581934 ATTCGGGTATCATATTTTCGGTTCA
1 ATTCGGGTATCATATTTTCGGTTCA
3581959 ATTCGGGT
1 ATTCGGGT
3581967 TATGGTCGTT
Statistics
Matches: 42, Mismatches: 14, Indels: 10
0.64 0.21 0.15
Matches are distributed among these distances:
25 17 0.40
26 8 0.19
27 8 0.19
28 9 0.21
ACGTcount: A:0.17, C:0.15, G:0.29, T:0.38
Consensus pattern (25 bp):
ATTCGGGTATCATATTTTCGGTTCA
Found at i:3592490 original size:142 final size:139
Alignment explanation
Indices: 3592223--3592667 Score: 450
Period size: 142 Copynumber: 3.2 Consensus size: 139
3592213 TTAATATACA
* *
3592223 TATATAAATAAGATATTTATTTATTTAGAAATATCAAAAAATGA-CTTCTAGGTGCCTTAAGACG
1 TATA-AAATAAGATATTTATTTATTTAGAAATATCAGAAAA-GAGCTTCTAGGTGCCTTAAGACA
* *
3592287 GCTCTTTTCTTCGATATTGAAAAATGAATAAATATAAAACATTTTTCTAAAAATAAAAAAAAAAA
64 GCTCTTTTCTTCGATATT-AAAAATGAATAAATATAAAACA-TTTTCTTAAAATAATAAAAAAAA
3592352 TAGATATATAATT
127 TAGATATATAATT
* ***
3592365 TATAAAAGTAAGATATTTACTTATTTAGAAATATCAGAAAAGAGCTTCTAGGTATTTTAAGACAG
1 TATAAAA-TAAGATATTTATTTATTTAGAAATATCAGAAAAGAGCTTCTAGGTGCCTTAAGACAG
*
3592430 CTCTTTTCTTTGATATTAAAAAAT-AAGTAAATAAATAAAACATTTTCTTAAAA-AAT---AAAA
65 CTCTTTTCTTCGATATT-AAAAATGAA-TAAAT--ATAAAACATTTTCTTAAAATAATAAAAAAA
3592490 AT---T-TAT--TT
126 ATAGATATATAATT
* * *
3592498 TAATATAATAAGATATTTATTTATTT-GAAAATATCAGAAAAGGGTTTCTAGGTGCCTTAAGACA
1 T-ATAAAATAAGATATTTATTTATTTAG-AAATATCAGAAAAGAGCTTCTAGGTGCCTTAAGACA
* * * * *
3592562 ACTATTCTCTTCGATATTGAAAATGAATAAATATAAAATCATTTT-TATAAAAATAATAATAATA
64 GCTCTTTTCTTCGATATTAAAAATGAATAAATATAAAA-CATTTTCT-T-AAAATAATAA-AAAA
3592626 AATAGATTAATATATAATT
125 AATAG----ATATATAATT
*
3592645 TATAAATGTAAGATATTTATTTA
1 TATAAA-ATAAGATATTTATTTA
3592668 ATATATATAA
Statistics
Matches: 251, Mismatches: 25, Indels: 49
0.77 0.08 0.15
Matches are distributed among these distances:
130 7 0.03
131 7 0.03
132 15 0.06
133 70 0.28
134 5 0.02
135 3 0.01
136 1 0.00
137 5 0.02
139 6 0.02
141 7 0.03
142 81 0.32
143 10 0.04
144 9 0.04
145 3 0.01
146 4 0.02
147 18 0.07
ACGTcount: A:0.46, C:0.07, G:0.09, T:0.37
Consensus pattern (139 bp):
TATAAAATAAGATATTTATTTATTTAGAAATATCAGAAAAGAGCTTCTAGGTGCCTTAAGACAGC
TCTTTTCTTCGATATTAAAAATGAATAAATATAAAACATTTTCTTAAAATAATAAAAAAAATAGA
TATATAATT
Found at i:3592500 original size:20 final size:20
Alignment explanation
Indices: 3592457--3592519 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 20
3592447 AAAAAATAAG
*
3592457 TAAATAAATAAAACATTT-TCT
1 TAAA-AAATAAAA-ATTTATTT
3592478 TAAAAAATAAAAATTTATTT
1 TAAAAAATAAAAATTTATTT
* *
3592498 TAATATAATAAGATATTTATTT
1 TAA-AAAATAA-AAATTTATTT
3592520 ATTTGAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
19 4 0.11
20 13 0.36
21 10 0.28
22 9 0.25
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (20 bp):
TAAAAAATAAAAATTTATTT
Found at i:3592620 original size:133 final size:132
Alignment explanation
Indices: 3592373--3592614 Score: 305
Period size: 133 Copynumber: 1.8 Consensus size: 132
3592363 TTTATAAAAG
** * * *
3592373 TAAGATATTTACTTATTTAGAAATATCAGAAAAGAGCTTCTAGGTATTTTAAGACAGCTCTTTTC
1 TAAGATATTTACTTATTTAGAAATATCAGAAAAGAGCTTCTAGGTACCTTAAGACAACTATTCTC
*
3592438 TTTGATATTAAAAAATAAGTAAATAAATAAAACATTTTCTTAAAAAATAAAAATTTATTTTAATA
66 TTCGATATTAAAAAATAAGTAAAT-AATAAAACATTTTCTTAAAAAATAAAAATTTATTTTAATA
3592503 TAA
130 TAA
* * * *
3592506 TAAGATATTTATTTATTT-GAAAATATCAGAAAAGGGTTTCTAGGTGCCTTAAGACAACTATTCT
1 TAAGATATTTACTTATTTAG-AAATATCAGAAAAGAGCTTCTAGGTACCTTAAGACAACTATTCT
*
3592570 CTTCGATATT-GAAAATGAA-TAAAT-ATAAAATCATTTT-TATAAAAA
65 CTTCGATATTAAAAAAT-AAGTAAATAATAAAA-CATTTTCT-TAAAAA
3592615 TAATAATAAT
Statistics
Matches: 94, Mismatches: 11, Indels: 10
0.82 0.10 0.09
Matches are distributed among these distances:
130 7 0.07
131 12 0.13
132 11 0.12
133 64 0.68
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (132 bp):
TAAGATATTTACTTATTTAGAAATATCAGAAAAGAGCTTCTAGGTACCTTAAGACAACTATTCTC
TTCGATATTAAAAAATAAGTAAATAATAAAACATTTTCTTAAAAAATAAAAATTTATTTTAATAT
AA
Found at i:3594311 original size:17 final size:17
Alignment explanation
Indices: 3594289--3594348 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 17
3594279 GTTGAATAAG
3594289 TTCTTCTCATTACGAAC
1 TTCTTCTCATTACGAAC
*
3594306 TTCTTCTTC-TT-CAGATGAG
1 TTCTTC-TCATTAC-GA--AC
*
3594325 TTCTTCTCATTATGAAC
1 TTCTTCTCATTACGAAC
3594342 TTCTTCT
1 TTCTTCT
3594349 GGCAAAGTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 12
0.69 0.06 0.24
Matches are distributed among these distances:
16 1 0.03
17 18 0.53
18 4 0.12
19 11 0.32
ACGTcount: A:0.18, C:0.25, G:0.08, T:0.48
Consensus pattern (17 bp):
TTCTTCTCATTACGAAC
Found at i:3594427 original size:103 final size:101
Alignment explanation
Indices: 3594312--3594623 Score: 308
Period size: 102 Copynumber: 3.0 Consensus size: 101
3594302 GAACTTCTTC
* * * *
3594312 TTCTTCAGATGAGTTCTTCTCATTATGAACTTCTTCTGGCAAAGTTGATGTTGATCTACCTTATG
1 TTCTTCAGATGAGTTCTTCTTATTATGAACTTTTTCTGG-AAAGATGAT-TTGATCTACCTTCTG
3594377 TGATAGAATCAAGCAAAAGGTTGAACAAGTTCTCCTCA
64 TGATAGAATCAAGCAAAAGGTTGAACAAGTTCTCCTCA
* * * ** *
3594415 TTCTTCTGATGAGTTCTTCTTATTATGAACTTTTTCGCTGGGGATGACAATTT-ATCT-TCTTCT
1 TTCTTCAGATGAGTTCTTCTTATTATGAACTTTTT--CT-GGAAAGATGATTTGATCTACCTTCT
* * * * *
3594478 GTGAT-GTAATCTAGCAAAAAGTTGAACAAATTCTCTTCC
63 GTGATAG-AATCAAGCAAAAGGTTGAACAAGTTCTCCTCA
* * *
3594517 TTCTTCAGATGAGTTCTTCTTATTATGAACTTTTTATGGAAATGCTGATACTGATCTATCTCATT
1 TTCTTCAGATGAGTTCTTCTTATTATGAACTTTTTCTGGAAA-GATGAT-TTGATCTA-C-C-TT
* * *
3594582 CTGTGATAGAATCAAAC-AAAGGTTGAACAAGCTCTTCTCA
61 CTGTGATAGAATCAAGCAAAAGGTTGAACAAGTTCTCCTCA
3594622 TT
1 TT
3594624 ATGAACTTCT
Statistics
Matches: 165, Mismatches: 32, Indels: 22
0.75 0.15 0.10
Matches are distributed among these distances:
99 3 0.02
100 4 0.02
101 2 0.01
102 74 0.45
103 36 0.22
104 2 0.01
105 26 0.16
106 17 0.10
107 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (101 bp):
TTCTTCAGATGAGTTCTTCTTATTATGAACTTTTTCTGGAAAGATGATTTGATCTACCTTCTGTG
ATAGAATCAAGCAAAAGGTTGAACAAGTTCTCCTCA
Found at i:3594804 original size:120 final size:120
Alignment explanation
Indices: 3594511--3595036 Score: 404
Period size: 113 Copynumber: 4.5 Consensus size: 120
3594501 GAACAAATTC
** *
3594511 TCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTTTATGGAAATGCTGATACTGATCTAT
1 TCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAAC-TTTCCTGGAAATGTTGATACTGATCTAT
* *
3594576 CTCATTCTGTGATAGAATCAAACAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCT
65 CTCATTCTGGGATAGAATCAAACAAAGGTTGAACAAGCTCTTCTCATTATGAA--TAT
*
3594634 TCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGAAATGTTGATGA-TGATTTA
1 TCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTC-CTGGAAATGTTGAT-ACTGATCTA
* * * * * * *
3594698 TCTCCTTCTGGGATAGAGTCGAGCAAAAGGTTTAACAAGTTCTTCTTATTATGAA-AT
64 TCTCATTCTGGGATAGAATCAAAC-AAAGGTTGAACAAGCTCTTCTCATTATGAATAT
* * *
3594755 TCTTCC-TCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTGAT-C----C-AT
1 TCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACT-TTCCTGGAAATGTTGATACTGATCTAT
* * * * * *
3594813 C-GA--AT--GAT-GAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCT
65 CTCATTCTGGGATAGAA-TCAAAC-AAAGGTTGAACAAGCTCTTCTCATTATGAA--TAT
* *
3594867 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGAT-C----C-AT
1 TCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTC-CTGGAAATGTTGATACTGATCTAT
* * * * * *
3594926 C-GA--AT--GAT-GAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCT
65 CTCATTCTGGGATAGAA-TCAAAC-AAAGGTTGAACAAGCTCTTCTCATTATGAA--TAT
* ** *
3594980 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGTAATGTTGATAC
1 TCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACT-TTCCTGGAAATGTTGATAC
3595037 ATTGAATGAT
Statistics
Matches: 356, Mismatches: 34, Indels: 35
0.84 0.08 0.08
Matches are distributed among these distances:
108 2 0.01
109 36 0.10
111 1 0.00
112 9 0.03
113 148 0.42
114 5 0.01
120 42 0.12
121 9 0.03
122 3 0.01
123 73 0.21
124 28 0.08
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (120 bp):
TCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCCTGGAAATGTTGATACTGATCTATC
TCATTCTGGGATAGAATCAAACAAAGGTTGAACAAGCTCTTCTCATTATGAATAT
Found at i:3594920 original size:113 final size:113
Alignment explanation
Indices: 3594719--3595047 Score: 497
Period size: 113 Copynumber: 2.9 Consensus size: 113
3594709 GATAGAGTCG
* * * *
3594719 AGCAAAAGGTTTAACAAGTTCTTCTTATTATGAA---ATTCTTCC-TCTTCAGATGAGTTCTTCT
1 AGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* *
3594780 CATTATGAACTCTACCTGGCAATGTTGATCCATCGAATGATGAATTCA
66 CATTATGAACTCTACCTGGAAAAGTTGATCCATCGAATGATGAATTCA
3594828 AGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 AGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
*
3594893 CATTATGAACT-TTCTCTGGAAAAGTTGATCCATCGAATGATGAATTCA
66 CATTATGAACTCTAC-CTGGAAAAGTTGATCCATCGAATGATGAATTCA
*
3594941 AGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 AGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * * * *
3595006 CATTATGAACTCGACCTGGTAATGTTGATACATTGAATGATG
66 CATTATGAACTCTACCTGGAAAAGTTGATCCATCGAATGATG
3595048 GATTTAAATC
Statistics
Matches: 200, Mismatches: 14, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
109 31 0.16
112 9 0.05
113 159 0.80
114 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (113 bp):
AGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
CATTATGAACTCTACCTGGAAAAGTTGATCCATCGAATGATGAATTCA
Found at i:3595533 original size:22 final size:22
Alignment explanation
Indices: 3595455--3595531 Score: 118
Period size: 22 Copynumber: 3.5 Consensus size: 22
3595445 GATAAAGCTT
*
3595455 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* *
3595477 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
3595499 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
3595521 TCATCTTTGAA
1 TCATCTTTGAA
3595532 GAATATAGAT
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:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:3595973 original size:54 final size:54
Alignment explanation
Indices: 3595891--3596056 Score: 269
Period size: 54 Copynumber: 3.1 Consensus size: 54
3595881 AGAATAGCAG
** ** *
3595891 GTTCGTAAAATATTTGACGGCGTATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAATATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGCTCAGAT
*
3595945 GTTCGTAAAATATTTGACAACACATTCATCCTTTCCTGTAGTTTCTGCTCAGAT
1 GTTCGTAAAATATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGCTCAGAT
*
3595999 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGCTCAGAT
1 GTTCGTAAAATATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGCTCAGAT
3596053 GTTC
1 GTTC
3596057 TCAATCATTG
Statistics
Matches: 104, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 104 1.00
ACGTcount: A:0.22, C:0.23, G:0.16, T:0.39
Consensus pattern (54 bp):
GTTCGTAAAATATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGCTCAGAT
Found at i:3598333 original size:113 final size:114
Alignment explanation
Indices: 3598117--3598453 Score: 577
Period size: 113 Copynumber: 3.0 Consensus size: 114
3598107 TCATGCAGTT
* * * * * * *
3598117 CATCTTTTAATTCCAATGATTGGTTCTGGGGTTCCTACCGAACCAGATCAGATAACTCAAAGAAC
1 CATCTTTCAAATCTAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGAAC
* *
3598182 ACTTCCAGAAGATGCTATTAGGTCTCCTTATTTCTACTATGAGCAAATC
66 ACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAATC
3598231 CATCTTTCAAATCTAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTC-AAGAAC
1 CATCTTTCAAATCTAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGAAC
*
3598295 ACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAATT
66 ACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAATC
3598344 CATCTTTCAAATCTAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGAAC
1 CATCTTTCAAATCTAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGAAC
3598409 ACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCA
66 ACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCA
3598454 CATGGCACTT
Statistics
Matches: 212, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
113 110 0.52
114 102 0.48
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (114 bp):
CATCTTTCAAATCTAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGAAC
ACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAATC
Found at i:3603907 original size:14 final size:14
Alignment explanation
Indices: 3603869--3603922 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
3603859 CATAAAAATA
* *
3603869 CAAATGCAAAGATG
1 CAAATGTAAATATG
3603883 CCAAATGTAAATATG
1 -CAAATGTAAATATG
* *
3603898 CAATTGTAAAAATG
1 CAAATGTAAATATG
*
3603912 TAAATGTAAAT
1 CAAATGTAAAT
3603923 TATTTAAAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
14 20 0.62
15 12 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (14 bp):
CAAATGTAAATATG
Found at i:3606143 original size:28 final size:29
Alignment explanation
Indices: 3606112--3606166 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
3606102 ATTTCAAAAT
*
3606112 TATAATTATGAA-AAAATATTAATTTACA
1 TATAATTATAAATAAAATATTAATTTACA
* *
3606140 TATATTTATAAATAAAATATTTATTTA
1 TATAATTATAAATAAAATATTAATTTA
3606167 TTTAGAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 10 0.43
29 13 0.57
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (29 bp):
TATAATTATAAATAAAATATTAATTTACA
Found at i:3606433 original size:86 final size:88
Alignment explanation
Indices: 3606270--3606447 Score: 220
Period size: 86 Copynumber: 2.0 Consensus size: 88
3606260 AAATAGATAT
* * * *
3606270 AATTTATAAAAGTAAGATATTTATTTATTTAAGAATATCAGAAAAGGACTTCTAGGTGCTTTAAG
1 AATTTAT-AAAGTAAGAAATTTATTTATTTAAGAATACCAGAAAAGGACATCTAGGTACTTTAAG
3606335 ACAGCCCATTTC-TTAATATTAAGA
65 ACAGCCCATTTCTTTAATATTAA-A
* * *
3606359 AATTTAT-AAGTAAGAAATTTATTTATTTAA-AATACCAGAATAGGGCATCTAGTTACTTTAAGA
1 AATTTATAAAGTAAGAAATTTATTTATTTAAGAATACCAGAAAAGGACATCTAGGTACTTTAAGA
* *
3606422 CTA-CCCTTTTCTTTGATATTAAA
66 C-AGCCCATTTCTTTAATATTAAA
3606445 AAT
1 AAT
3606448 AAATACATAT
Statistics
Matches: 78, Mismatches: 9, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
86 39 0.50
87 32 0.41
89 7 0.09
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.38
Consensus pattern (88 bp):
AATTTATAAAGTAAGAAATTTATTTATTTAAGAATACCAGAAAAGGACATCTAGGTACTTTAAGA
CAGCCCATTTCTTTAATATTAAA
Found at i:3606518 original size:11 final size:11
Alignment explanation
Indices: 3606504--3606607 Score: 113
Period size: 11 Copynumber: 9.2 Consensus size: 11
3606494 GACTAAGATA
3606504 AAAATAATAAT
1 AAAATAATAAT
3606515 AAAATAATAAT
1 AAAATAATAAT
3606526 AAAATAATAATT
1 AAAATAATAA-T
*
3606538 AAAGTAATAATT
1 AAAATAATAA-T
*
3606550 AAAAT-ATATT
1 AAAATAATAAT
3606560 AAAAATAATAAT
1 -AAAATAATAAT
*
3606572 AAAATAATATT
1 AAAATAATAAT
3606583 ACAAATAAATAAT
1 A-AAAT-AATAAT
*
3606596 GAAATAA-AAT
1 AAAATAATAAT
3606606 AA
1 AA
3606608 CTAAATAAAA
Statistics
Matches: 80, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
10 5 0.06
11 42 0.52
12 28 0.35
13 5 0.06
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.29
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:3606527 original size:23 final size:22
Alignment explanation
Indices: 3606504--3606607 Score: 113
Period size: 23 Copynumber: 4.6 Consensus size: 22
3606494 GACTAAGATA
3606504 AAAATAATAATAAAATAATAAT
1 AAAATAATAATAAAATAATAAT
*
3606526 AAAATAATAATTAAAGTAATAATT
1 AAAATAATAA-TAAAATAATAA-T
*
3606550 AAAAT-ATATTAAAAATAATAAT
1 AAAATAATAAT-AAAATAATAAT
*
3606572 AAAATAATATTACAAATAAATAAT
1 AAAATAATAATA-AAAT-AATAAT
*
3606596 GAAATAA-AATAA
1 AAAATAATAATAA
3606608 CTAAATAAAA
Statistics
Matches: 71, Mismatches: 5, Indels: 12
0.81 0.06 0.14
Matches are distributed among these distances:
22 19 0.27
23 34 0.48
24 18 0.25
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.29
Consensus pattern (22 bp):
AAAATAATAATAAAATAATAAT
Found at i:3610294 original size:3 final size:3
Alignment explanation
Indices: 3610286--3610361 Score: 73
Period size: 3 Copynumber: 25.0 Consensus size: 3
3610276 ATGTTATTTA
* * * *
3610286 TAT TAT TAT AAT TAT AAT TAT TAT TAT AAT TA- TAA TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
3610333 TAT TAA TAT ATAT TATT TAT TAA TAT TAT
1 TAT TAT TAT -TAT TA-T TAT TAT TAT TAT
3610362 AAAACTCAAA
Statistics
Matches: 59, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
2 2 0.03
3 51 0.86
4 6 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:3615791 original size:15 final size:15
Alignment explanation
Indices: 3615773--3615804 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3615763 ATCAATACTT
3615773 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
3615788 TTTTGCATACATTCA
1 TTTTGCATACATGCA
3615803 TT
1 TT
3615805 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:3622953 original size:140 final size:141
Alignment explanation
Indices: 3622701--3622981 Score: 555
Period size: 140 Copynumber: 2.0 Consensus size: 141
3622691 AGCAGTCTTA
3622701 TCAATTGAAGTTGAGATTCCATCGCTTCGAATTTTGAGAGAAACAAAATTGGATGAATCTGAATG
1 TCAATTGAAGTTGAGATTCCATCGCTTCGAATTTTGAGAGAAACAAAATTGGATGAATCTGAATG
3622766 GATCCAAGCTAGATTTGATCAATTGAACCTTATTGAGGAGAAAAGATTG-AAGCTATTTGCCATG
66 GATCCAAGCTAGATTTGATCAATTGAACCTTATTGAGGAGAAAAGATTGAAAGCTATTTGCCATG
3622830 GACAGATGTAT
131 GACAGATGTAT
3622841 TCAATTGAAGTTGAGATTCCATCGCTTCGAATTTTGAGAGAAACAAAATTGGATGAATCTGAATG
1 TCAATTGAAGTTGAGATTCCATCGCTTCGAATTTTGAGAGAAACAAAATTGGATGAATCTGAATG
3622906 GATCCAAGCTAGATTTGATCAATTGAACCTTATTGAGGAGAAAAGATTGAAAGCTATTTGCCATG
66 GATCCAAGCTAGATTTGATCAATTGAACCTTATTGAGGAGAAAAGATTGAAAGCTATTTGCCATG
3622971 GACAGATGTAT
131 GACAGATGTAT
3622982 CAGAAACGGA
Statistics
Matches: 140, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
140 114 0.81
141 26 0.19
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (141 bp):
TCAATTGAAGTTGAGATTCCATCGCTTCGAATTTTGAGAGAAACAAAATTGGATGAATCTGAATG
GATCCAAGCTAGATTTGATCAATTGAACCTTATTGAGGAGAAAAGATTGAAAGCTATTTGCCATG
GACAGATGTAT
Found at i:3623268 original size:10 final size:11
Alignment explanation
Indices: 3623237--3623267 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
3623227 AAAAAATTGA
3623237 AAAAAAAAAAG
1 AAAAAAAAAAG
3623248 AAAAAAAAAAG
1 AAAAAAAAAAG
3623259 AAAAAAAAA
1 AAAAAAAAA
3623268 GGGGTCAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:3624929 original size:93 final size:92
Alignment explanation
Indices: 3624631--3625268 Score: 643
Period size: 83 Copynumber: 6.9 Consensus size: 92
3624621 GAACAAATGC
3624631 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG--T-------
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCAC
3624687 AAAACCAATCATTGAATTTGAAAGATG
66 AAAACCAATCATTGAATTTGAAAGATG
3624714 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT-TGGGTTTGG--T------
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT-GGTTTGGTATGAACCA
3624770 -AAAACCAATCATTGAATTTGAAAGATG
65 CAAAACCAATCATTGAATTTGAAAGATG
3624797 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACC-C
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCAC
*
3624861 TAAAAACCAATCATTAAATTTGAAAGATG
66 --AAAACCAATCATTGAATTTGAAAGATG
*
3624890 AATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCA
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATG-AACCA
* *
3624955 CAGAACCAATCATTGGATATTGAAAGATG
65 CAAAACCAATCATTGAAT-TTGAAAGATG
* * ** *** * *
3624984 AATTTGCTCATAGTAGAAATAAGGAGACCCAAGAGCATCTTCTGGAAGTGTTCTTTGAGTTATCT
1 AATGTGCTCATAG--CATCTTCTG-G----AAGTG-TTCTT-T-G-AGT-----------TATCT
* * *
3625049 GATCTGGTTTGGTATGAACCACAGAACCAGTTATTGAATTTGAAAGATG
44 GATCTGGTTTGGTATGAACCACAAAACCAATCATTGAATTTGAAAGATG
*
3625098 AATGTGCTCATAGCAACTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCAC
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCAC
* * * * *
3625163 AGAACCAGTTATTGAATTTGGAAGAAG
66 AAAACCAATCATTGAATTTGAAAGATG
* * *
3625190 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTGGTTTGATATAAAACC-
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAT-GAACCA
*
3625254 CAGAACCAATCATTG
65 CAAAACCAATCATTG
3625269 GAATAAAAAG
Statistics
Matches: 483, Mismatches: 34, Indels: 67
0.83 0.06 0.11
Matches are distributed among these distances:
82 1 0.00
83 134 0.28
84 1 0.00
85 1 0.00
92 120 0.25
93 102 0.21
94 25 0.05
95 1 0.00
96 3 0.01
97 1 0.00
101 4 0.01
102 4 0.01
103 4 0.01
104 2 0.00
105 4 0.01
106 4 0.01
107 4 0.01
111 1 0.00
112 4 0.01
114 22 0.05
115 20 0.04
116 21 0.04
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (92 bp):
AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCAC
AAAACCAATCATTGAATTTGAAAGATG
Found at i:3625179 original size:92 final size:92
Alignment explanation
Indices: 3625017--3625261 Score: 420
Period size: 92 Copynumber: 2.7 Consensus size: 92
3625007 GAGACCCAAG
3625017 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAGTTA
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAGTTA
*
3625082 TTGAATTTGAAAGATGAATGTGCTCAT
66 TTGAATTTGAAAGAAGAATGTGCTCAT
*
3625109 AGCAACTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAGTTA
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAGTTA
*
3625174 TTGAATTTGGAAGAAGAATGTGCTCAT
66 TTGAATTTGAAAGAAGAATGTGCTCAT
* * *
3625201 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTGGTTTGATATAAAACC-CAGAACCA
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAT-GAACCACAGAACCA
3625262 ATCATTGGAA
Statistics
Matches: 145, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
92 141 0.97
93 4 0.03
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (92 bp):
AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAGTTA
TTGAATTTGAAAGAAGAATGTGCTCAT
Found at i:3626252 original size:113 final size:113
Alignment explanation
Indices: 3626000--3626753 Score: 1182
Period size: 113 Copynumber: 6.7 Consensus size: 113
3625990 TCAACAGTGT
* * *
3626000 CAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAG-AGAGAAGAAGAATTTCATAATAAGAAGA
1 CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAG-GAAGAAGAAGTTCATAATGAGAAGA
*
3626064 ACTTGTTCAA-CTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTC
65 ATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTC
* *
3626112 CAGTTTGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAA
1 CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
*
3626177 TTTGTTCAACCTTTTGCTCAAATCCATCA-TTCAATGGATCAGCTTTTC
66 TTTGTTCAACCTTTTGCTCAAATCCATCACTT-GATGGATCAGCTTTTC
3626225 CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
1 CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
3626290 TTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTC
66 TTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTC
3626338 CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
1 CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
3626403 TTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTC
66 TTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTC
3626451 CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
1 CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
* *
3626516 TTTGTTCAACATTTTGCTCAAATCCATCACTTGATGGATCAGATTTTC
66 TTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTC
*
3626564 CAGTTTGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
1 CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
* * * * * * * *
3626629 CTTGTTTAACCCTTTGTTCAAATTCATCACTTAATGGATCAAC-CTTC
66 TTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTC
* **** *
3626676 AAAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA-G-AG-A-AAGTTCATAATAAGAAGA
1 -CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
** *
3626737 GCTTATTCAACCTTTTG
65 ATTTGTTCAACCTTTTG
3626754 AATGACTCTA
Statistics
Matches: 605, Mismatches: 32, Indels: 13
0.93 0.05 0.02
Matches are distributed among these distances:
109 30 0.05
110 1 0.00
111 2 0.00
112 72 0.12
113 498 0.82
114 2 0.00
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.29
Consensus pattern (113 bp):
CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
TTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTC
Found at i:3626990 original size:3 final size:3
Alignment explanation
Indices: 3626982--3627051 Score: 77
Period size: 3 Copynumber: 22.7 Consensus size: 3
3626972 ATGTTATTTA
* * * *
3626982 TAT TAT TAT AAT TAT TAT TAT TAT TAT AAT AAT TAT TAT TAT TAT TAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
3627030 TAT ATAT TATT TAT TAA TAT TA
1 TAT -TAT TA-T TAT TAT TAT TA
3627052 CAAAACCCAA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
3 51 0.89
4 6 0.11
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:3634662 original size:21 final size:21
Alignment explanation
Indices: 3634637--3634676 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
3634627 AGTATGTTCA
3634637 GGGGGTATCGATTCCCCCTTG
1 GGGGGTATCGATTCCCCCTTG
3634658 GGGGGTATCGATTCCCCCT
1 GGGGGTATCGATTCCCCCT
3634677 AAATGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.10, C:0.30, G:0.33, T:0.28
Consensus pattern (21 bp):
GGGGGTATCGATTCCCCCTTG
Found at i:3634877 original size:21 final size:21
Alignment explanation
Indices: 3634852--3634891 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
3634842 AGTATGTTCA
3634852 GGGGGTATCGATTCCCCCTTG
1 GGGGGTATCGATTCCCCCTTG
3634873 GGGGGTATCGATTCCCCCT
1 GGGGGTATCGATTCCCCCT
3634892 AAATGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.10, C:0.30, G:0.33, T:0.28
Consensus pattern (21 bp):
GGGGGTATCGATTCCCCCTTG
Found at i:3634950 original size:215 final size:220
Alignment explanation
Indices: 3634579--3635013 Score: 835
Period size: 215 Copynumber: 2.0 Consensus size: 220
3634569 GAGGGAACCG
3634579 ATACCCTATGAATGGGTATCGATTCCCCCCTCTTGAACGAAAAATTCCAGTATGTTCAGGGGGTA
1 ATACCCTATGAATGGGTATCGATTCCCCCCTCTTGAACGAAAAATTCCAGTATGTTCAGGGGGTA
3634644 TCGATTCCCCCTTGGGGGGTATCGATTCCCCCTAAATGAAAAATGGAATTTGGTTCTTTAATTTG
66 TCGATTCCCCCTTGGGGGGTATCGATTCCCCCTAAATGAAAAATGGAATTTGGTTCTTTAATTTG
3634709 GTTTAAGTTATTAACATCAAGTTTAAGGTTTAGGCTTTTGATAGTTGTTTTG-AATGTTA-ATTT
131 GTTTAAGTTATTAACATCAAGTTTAAGGTTTAGGCTTTTGATAGTTGTTTTGAAATGTTATATTT
3634772 AT-TAGATATTAA-TCT-AACAAGT
196 ATGTAGATATTAAGTCTAAACAAGT
3634794 ATACCCTATGAATGGGTATCGATTCCCCCCTCTTGAACGAAAAATTCCAGTATGTTCAGGGGGTA
1 ATACCCTATGAATGGGTATCGATTCCCCCCTCTTGAACGAAAAATTCCAGTATGTTCAGGGGGTA
3634859 TCGATTCCCCCTTGGGGGGTATCGATTCCCCCTAAATGAAAAATGGAATTTGGTTCTTTAATTTG
66 TCGATTCCCCCTTGGGGGGTATCGATTCCCCCTAAATGAAAAATGGAATTTGGTTCTTTAATTTG
3634924 GTTTAAGTTATTAACATCAAGTTTAAGGTTTAGGCTTTTGATAGTTGTTTTGAAATGTTATATTT
131 GTTTAAGTTATTAACATCAAGTTTAAGGTTTAGGCTTTTGATAGTTGTTTTGAAATGTTATATTT
3634989 ATGTAGATATTAAGTCTAAACAAGT
196 ATGTAGATATTAAGTCTAAACAAGT
3635014 TCCGGAATAA
Statistics
Matches: 215, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
215 182 0.85
216 7 0.03
217 6 0.03
218 10 0.05
219 3 0.01
220 7 0.03
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (220 bp):
ATACCCTATGAATGGGTATCGATTCCCCCCTCTTGAACGAAAAATTCCAGTATGTTCAGGGGGTA
TCGATTCCCCCTTGGGGGGTATCGATTCCCCCTAAATGAAAAATGGAATTTGGTTCTTTAATTTG
GTTTAAGTTATTAACATCAAGTTTAAGGTTTAGGCTTTTGATAGTTGTTTTGAAATGTTATATTT
ATGTAGATATTAAGTCTAAACAAGT
Found at i:3642578 original size:18 final size:19
Alignment explanation
Indices: 3642555--3642596 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
3642545 ATGACTGGGT
3642555 TATAT-ATGTCATA-TGAAA
1 TATATAATG-CATATTGAAA
3642573 TATATACATGCATATTGAAA
1 TATATA-ATGCATATTGAAA
3642593 TATA
1 TATA
3642597 ATGATCAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
18 5 0.24
19 4 0.19
20 12 0.57
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (19 bp):
TATATAATGCATATTGAAA
Found at i:3655543 original size:83 final size:81
Alignment explanation
Indices: 3655437--3655607 Score: 207
Period size: 83 Copynumber: 2.1 Consensus size: 81
3655427 CAAAATGGTA
* * * ** *
3655437 ACTTTAGCGGCGTTTTTATACAAATGCTGCAATAAGATTAATTTATAGTGGCGTTATTTTAACAA
1 ACTTTAGCGGCGCTGTTATACAAATGCCGCAATAAGATTAATAAATAGTGGCATT-TTTT-ACAA
**
3655502 ACTTCGCAACATAGTAGT
64 ACGCCGCAACATAGTAGT
* * * *
3655520 ATTTTAGCGGCGCTGTTATACAAATGCCGCAATAGGTTTCATAAATAGTGGCATTTTTTACAAAC
1 ACTTTAGCGGCGCTGTTATACAAATGCCGCAATAAGATTAATAAATAGTGGCATTTTTTACAAAC
*
3655585 GCCGCACCATAGTAGT
66 GCCGCAACATAGTAGT
3655601 ACTTTAG
1 ACTTTAG
3655608 TGGTTTTTTA
Statistics
Matches: 74, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
81 25 0.34
82 4 0.05
83 45 0.61
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (81 bp):
ACTTTAGCGGCGCTGTTATACAAATGCCGCAATAAGATTAATAAATAGTGGCATTTTTTACAAAC
GCCGCAACATAGTAGT
Found at i:3655633 original size:80 final size:81
Alignment explanation
Indices: 3655437--3655670 Score: 204
Period size: 83 Copynumber: 2.9 Consensus size: 81
3655427 CAAAATGGTA
* * ** ** **
3655437 ACTTTAGCGGCGTTTTTATACAAATGCTGCAATAAGATTA-ATTTATAGTGGCGTTATTTTAACA
1 ACTTTAGCGGCGCTGTTATACAAATGCCACAAT-AGGGTACATAAATAGTGGC-TT-TTTTAACA
**
3655501 AACTTCGCAACATAGTAGT
63 AACGCCGCAACATAGTAGT
* * * *
3655520 ATTTTAGCGGCGCTGTTATACAAATGCCGCAATAGGTTTCATAAATAGTGGCATTTTTT-ACAAA
1 ACTTTAGCGGCGCTGTTATACAAATGCCACAATAGGGTACATAAATAGTGGC-TTTTTTAACAAA
*
3655584 CGCCGCACCATAGTAGT
65 CGCCGCAACATAGTAGT
* ** * * * *
3655601 ACTTTAGTGG-TTTTTTATATAAATGCCACAATAGGGTACGTATATAGTGGCTTTTTTCAACAAA
1 ACTTTAGCGGCGCTGTTATACAAATGCCACAATAGGGTACATAAATAGTGGCTTTTTT-AACAAA
3655665 CGCCGC
65 CGCCGC
3655671 TATATGACTA
Statistics
Matches: 125, Mismatches: 23, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
79 6 0.05
80 32 0.26
81 38 0.30
82 8 0.06
83 41 0.33
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Consensus pattern (81 bp):
ACTTTAGCGGCGCTGTTATACAAATGCCACAATAGGGTACATAAATAGTGGCTTTTTTAACAAAC
GCCGCAACATAGTAGT
Found at i:3655954 original size:42 final size:42
Alignment explanation
Indices: 3655866--3656012 Score: 163
Period size: 42 Copynumber: 3.5 Consensus size: 42
3655856 GACCCCTACG
** * *
3655866 TTAGTGGCGTTTTTATAA-AAATGGCGTAATAGTCTTGTACT
1 TTAGTGGCGTTTTTATAATAAATACCGCAATAGTCATGTACT
* * * *
3655907 TTAGTGGTGTTTGTATAATAAATACCGCAATAATCATGTAAT
1 TTAGTGGCGTTTTTATAATAAATACCGCAATAGTCATGTACT
* * *
3655949 TTAGTGGCTTTTTTGTAATAAA-AGCCGCAATAGTCATGTACC
1 TTAGTGGCGTTTTTATAATAAATA-CCGCAATAGTCATGTACT
*
3655991 TTAGTGGCGTTTTTATTATAAA
1 TTAGTGGCGTTTTTATAATAAA
3656013 CATCGTGATT
Statistics
Matches: 86, Mismatches: 18, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
41 17 0.20
42 69 0.80
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.40
Consensus pattern (42 bp):
TTAGTGGCGTTTTTATAATAAATACCGCAATAGTCATGTACT
Found at i:3659905 original size:18 final size:18
Alignment explanation
Indices: 3659882--3659920 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
3659872 AAGGTGATGA
3659882 CGGCATCATATATGGCTG
1 CGGCATCATATATGGCTG
3659900 CGGCATCATATATGGCTG
1 CGGCATCATATATGGCTG
3659918 CGG
1 CGG
3659921 TGGCTGCTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.21, C:0.23, G:0.31, T:0.26
Consensus pattern (18 bp):
CGGCATCATATATGGCTG
Found at i:3661621 original size:110 final size:110
Alignment explanation
Indices: 3661427--3661646 Score: 352
Period size: 110 Copynumber: 2.0 Consensus size: 110
3661417 ATTACAAAAA
* * * *
3661427 TTAATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTAATAATAATTTAAATTA
1 TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTA
** *
3661492 AATTAAAACGTTAAAATGTTATTGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGC-AAGTGTAGAGATAT
*
3661538 TTAATTATTAATATAATAATCATGCATTAAATAAAT-AACTAAATATTACTAATAATTTAAATTA
1 TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTA
3661602 AATTAAAACGTTAAAATGTTACCGTATCAGCAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAGTGTAGAGATAT
3661647 ATGATTTCCA
Statistics
Matches: 101, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
109 13 0.13
110 55 0.54
111 33 0.33
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.37
Consensus pattern (110 bp):
TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAGTGTAGAGATAT
Found at i:3661784 original size:12 final size:10
Alignment explanation
Indices: 3661770--3661810 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
3661760 ACCTTAAAAA
*
3661770 GAGAGTATTT
1 GAGAGAATTT
3661780 GAGAGAAATTT
1 GAGAG-AATTT
3661791 -AGAGAATTT
1 GAGAGAATTT
3661800 GAGAGAATTT
1 GAGAGAATTT
3661810 G
1 G
3661811 GTGTGATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 5 0.18
10 19 0.68
11 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:3662033 original size:51 final size:50
Alignment explanation
Indices: 3661941--3662049 Score: 173
Period size: 51 Copynumber: 2.2 Consensus size: 50
3661931 TATAGCACAC
**
3661941 GCAGGGGGCGCGCTATACCCACGTGGCGCCAGCTCACCGTATAGCGCGGT
1 GCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCACCGTATAGCGCGGT
*
3661991 GCAGGGGGCGCGCTATATCCCACGTGGCGCCAAATCATCGTATAGCGCGGT
1 GCAGGGGGCGCGCTATA-CCCACGTGGCGCCAAATCACCGTATAGCGCGGT
*
3662042 GTAGGGGG
1 GCAGGGGG
3662050 TGCACTTTAC
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
50 17 0.31
51 37 0.69
ACGTcount: A:0.17, C:0.29, G:0.38, T:0.16
Consensus pattern (50 bp):
GCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCACCGTATAGCGCGGT
Found at i:3662669 original size:21 final size:21
Alignment explanation
Indices: 3662643--3662692 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
3662633 TCCATATTCG
3662643 CAACGCGAACTTCGACTATCA
1 CAACGCGAACTTCGACTATCA
*
3662664 CAACGCGAACTTCGACTATCG
1 CAACGCGAACTTCGACTATCA
*
3662685 CAATGCGA
1 CAACGCGA
3662693 TTTTCCAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.32, C:0.32, G:0.18, T:0.18
Consensus pattern (21 bp):
CAACGCGAACTTCGACTATCA
Found at i:3662734 original size:21 final size:20
Alignment explanation
Indices: 3662704--3662903 Score: 174
Period size: 21 Copynumber: 9.7 Consensus size: 20
3662694 TTTCCAAATT
3662704 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCGAAGTT-G
* *
3662725 CGTTGTGATAGTCCAAGTT-
1 CGTTGCGATAGTCGAAGTTG
*
3662744 TGTTGCGATAGTCGAAGTTTG
1 CGTTGCGATAGTCGAAG-TTG
* *
3662765 CGTTGCGATTTATTCCAAGTT-
1 CGTTGCGA--TAGTCGAAGTTG
3662786 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCGAAGTT-G
* *
3662807 CGTTGCGATTTATTCCAAGTT-
1 CGTTGCGA--TAGTCGAAGTTG
*
3662828 CGTTGCTATAGTCGAAGTTCG
1 CGTTGCGATAGTCGAAGTT-G
* *
3662849 CGTTGCGATTTATTCCAAGTT-
1 CGTTGCGA--TAGTCGAAGTTG
*
3662870 CGTTGCGATGGTCGAAGTTCG
1 CGTTGCGATAGTCGAAGTT-G
3662891 CGTTGCGATAGTC
1 CGTTGCGATAGTC
3662904 CAAAATCGCA
Statistics
Matches: 143, Mismatches: 22, Indels: 28
0.74 0.11 0.15
Matches are distributed among these distances:
19 40 0.28
20 2 0.01
21 74 0.52
22 2 0.01
23 25 0.17
ACGTcount: A:0.18, C:0.18, G:0.28, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCGAAGTTG
Found at i:3662795 original size:42 final size:42
Alignment explanation
Indices: 3662688--3662899 Score: 333
Period size: 42 Copynumber: 5.1 Consensus size: 42
3662678 ACTATCGCAA
*
3662688 TGCGA-TT-TTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
* * * *
3662728 TGTGA--TAGTCCAAGTTTGTTGCGATAGTCGAAGTTTGCGT
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
3662768 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
*
3662810 TGCGATTTATTCCAAGTTCGTTGCTATAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
*
3662852 TGCGATTTATTCCAAGTTCGTTGCGATGGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
3662894 TGCGAT
1 TGCGAT
3662900 AGTCCAAAAT
Statistics
Matches: 157, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
39 1 0.01
40 37 0.24
42 119 0.76
ACGTcount: A:0.19, C:0.18, G:0.27, T:0.36
Consensus pattern (42 bp):
TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
Found at i:3662912 original size:21 final size:21
Alignment explanation
Indices: 3662870--3662912 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3662860 ATTCCAAGTT
* * **
3662870 CGTTGCGATGGTCGAAGTTCG
1 CGTTGCGATAGTCCAAAATCG
3662891 CGTTGCGATAGTCCAAAATCG
1 CGTTGCGATAGTCCAAAATCG
3662912 C
1 C
3662913 AACGATTGGT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.23, G:0.30, T:0.26
Consensus pattern (21 bp):
CGTTGCGATAGTCCAAAATCG
Found at i:3663818 original size:42 final size:42
Alignment explanation
Indices: 3663756--3664057 Score: 401
Period size: 42 Copynumber: 7.2 Consensus size: 42
3663746 ATACCACCAG
3663756 TCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTA
1 TCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTA
** * * *
3663798 TTACAACGAATTTGTAATAAATCGCAACACGAACTTAGACTA
1 TCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTA
* *
3663840 TCGCAACGAATTTGTAATAAATCGCAACGCGAACTTGGACTA
1 TCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTA
* *
3663882 TCGCAATGAATTTGG-A-AAATCGCAACGCGAACTTGGACTA
1 TCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTA
* *
3663922 TCGCAACAAATTTGGAATAAATCGCAATGCGAACTTCGACTA
1 TCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTA
* * *
3663964 TCGCAGCGAATTTGTAATAAATCGCAACGCGAACTTGGACTA
1 TCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTA
* * **
3664006 TTGCGAACTTAATTTGGAATAAATTACAACGCGAACTTCGACTA
1 TCGC-AAC-GAATTTGGAATAAATCGCAACGCGAACTTCGACTA
*
3664050 TTGCAACG
1 TCGCAACG
3664058 CGAACTTGGA
Statistics
Matches: 228, Mismatches: 28, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
40 37 0.16
41 2 0.01
42 150 0.66
43 5 0.02
44 34 0.15
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (42 bp):
TCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTA
Found at i:3663829 original size:23 final size:23
Alignment explanation
Indices: 3663803--3663872 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 23
3663793 GACTATTACA
3663803 ACGAATTTGTAATAAATCGCAAC
1 ACGAATTTGTAATAAATCGCAAC
* *
3663826 ACGAACTTAG-ACT--ATCGC-A-
1 ACGAA-TTTGTAATAAATCGCAAC
3663845 ACGAATTTGTAATAAATCGCAAC
1 ACGAATTTGTAATAAATCGCAAC
*
3663868 GCGAA
1 ACGAA
3663873 CTTGGACTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 12
0.68 0.09 0.23
Matches are distributed among these distances:
18 3 0.08
19 7 0.19
20 1 0.03
21 10 0.28
22 1 0.03
23 11 0.31
24 3 0.08
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.23
Consensus pattern (23 bp):
ACGAATTTGTAATAAATCGCAAC
Found at i:3663994 original size:124 final size:126
Alignment explanation
Indices: 3663756--3664056 Score: 444
Period size: 124 Copynumber: 2.4 Consensus size: 126
3663746 ATACCACCAG
* * * *
3663756 TCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATTACAACGAATTTGTAATAAATC
1 TCGCAATGAATTTGGAATAAATCGCAACGCGAACTTCGACTATTGCAACAAATTTGGAATAAATC
3663821 GCAACACGAACTTAGACTATCGCAACGAATTTGTAATAAATCGCAACGCGAACTTGGACTA
66 GCAACACGAACTTAGACTATCGCAACGAATTTGTAATAAATCGCAACGCGAACTTGGACTA
* *
3663882 TCGCAATGAATTTGG-A-AAATCGCAACGCGAACTTGGACTATCGCAACAAATTTGGAATAAATC
1 TCGCAATGAATTTGGAATAAATCGCAACGCGAACTTCGACTATTGCAACAAATTTGGAATAAATC
** * *
3663945 GCAATGCGAACTTCGACTATCGCAGCGAATTTGTAATAAATCGCAACGCGAACTTGGACTA
66 GCAACACGAACTTAGACTATCGCAACGAATTTGTAATAAATCGCAACGCGAACTTGGACTA
* * **
3664006 TTGCGAACTTAATTTGGAATAAATTACAACGCGAACTTCGACTATTGCAAC
1 TCGC-AA-TGAATTTGGAATAAATCGCAACGCGAACTTCGACTATTGCAAC
3664057 GCGAACTTGG
Statistics
Matches: 155, Mismatches: 16, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
124 102 0.66
125 3 0.02
126 22 0.14
127 1 0.01
128 27 0.17
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.25
Consensus pattern (126 bp):
TCGCAATGAATTTGGAATAAATCGCAACGCGAACTTCGACTATTGCAACAAATTTGGAATAAATC
GCAACACGAACTTAGACTATCGCAACGAATTTGTAATAAATCGCAACGCGAACTTGGACTA
Found at i:3664058 original size:21 final size:21
Alignment explanation
Indices: 3664032--3664081 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
3664022 GAATAAATTA
*
3664032 CAACGCGAACTTCGACTATTG
1 CAACGCGAACTTCGACTATCG
*
3664053 CAACGCGAACTTGGACTATCG
1 CAACGCGAACTTCGACTATCG
*
3664074 CAATGCGA
1 CAACGCGA
3664082 TAGTCGAAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.30, C:0.28, G:0.22, T:0.20
Consensus pattern (21 bp):
CAACGCGAACTTCGACTATCG
Found at i:3678150 original size:153 final size:153
Alignment explanation
Indices: 3677845--3678138 Score: 389
Period size: 153 Copynumber: 1.9 Consensus size: 153
3677835 AAATGATTCA
* *
3677845 ATTGCCAACAGTCGGCCTCTCTATTTGAAGAAGCCTTCCCATCAGCACACCCATCATCCTTTGAA
1 ATTGCCAACAATCGGCATCTCTATTTGAAGAAGCCTTCCCATCAGCACACCCATCATCCTTTGAA
* * * * *
3677910 TCCCTAATTTTGACAGAATCTCCATCAACCTTATCCTCCACGATTGCCTCTTGTTTTCTAGTGAG
66 TCCCTAATTTTAACAGAATCTCCATCAACCTTATCCTCAACAACTGCCTCTTGTTTTCCAGTGAG
3677975 ACTATCTTTTAAAGACGGGTAAT
131 ACTATCTTTTAAAGACGGGTAAT
* * * *
3677998 ATTGCCAACAATCGAG-ATCTCTATTTGAAGAAGTCTTCCCATCAGCACGA-GCATCGTCTTTTG
1 ATTGCCAACAATCG-GCATCTCTATTTGAAGAAGCCTTCCCATCAGCAC-ACCCATCATCCTTTG
* * *
3678061 AATCCCTAATTTTAACAGAATC-CCTGTCAACTTTCTCCTCAACAACTGCCTCTTGTTTTCCAGT
64 AATCCCTAATTTTAACAGAATCTCC-ATCAACCTTATCCTCAACAACTGCCTCTTGTTTTCCAGT
*
3678125 -AGGGCTATCTTTTA
128 GA-GACTATCTTTTA
3678139 GAGATGTGTA
Statistics
Matches: 122, Mismatches: 15, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
152 3 0.02
153 117 0.96
154 2 0.02
ACGTcount: A:0.26, C:0.28, G:0.14, T:0.33
Consensus pattern (153 bp):
ATTGCCAACAATCGGCATCTCTATTTGAAGAAGCCTTCCCATCAGCACACCCATCATCCTTTGAA
TCCCTAATTTTAACAGAATCTCCATCAACCTTATCCTCAACAACTGCCTCTTGTTTTCCAGTGAG
ACTATCTTTTAAAGACGGGTAAT
Found at i:3691426 original size:22 final size:22
Alignment explanation
Indices: 3691398--3691450 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
3691388 GTATGAACAA
3691398 TATCGATACCATATG-GAAAAGG
1 TATCGATACCATATGTG-AAAGG
* *
3691420 TATCGATA-CATATGTGGAGGG
1 TATCGATACCATATGTGAAAGG
3691441 TATCGATACC
1 TATCGATACC
3691451 CAGGGAACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 17 0.63
22 10 0.37
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.26
Consensus pattern (22 bp):
TATCGATACCATATGTGAAAGG
Found at i:3691672 original size:79 final size:79
Alignment explanation
Indices: 3691541--3691694 Score: 308
Period size: 79 Copynumber: 1.9 Consensus size: 79
3691531 TTGTAGTACC
3691541 GATACCCTTTAAGTTGGAAAGTTGAATTGGAGTTTTATTTAGTTGTATTGATATGAATCGTATCT
1 GATACCCTTTAAGTTGGAAAGTTGAATTGGAGTTTTATTTAGTTGTATTGATATGAATCGTATCT
3691606 AGTAATTCGAATCT
66 AGTAATTCGAATCT
3691620 GATACCCTTTAAGTTGGAAAGTTGAATTGGAGTTTTATTTAGTTGTATTGATATGAATCGTATCT
1 GATACCCTTTAAGTTGGAAAGTTGAATTGGAGTTTTATTTAGTTGTATTGATATGAATCGTATCT
3691685 AGTAATTCGA
66 AGTAATTCGA
3691695 GTCTCGACAT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 75 1.00
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.42
Consensus pattern (79 bp):
GATACCCTTTAAGTTGGAAAGTTGAATTGGAGTTTTATTTAGTTGTATTGATATGAATCGTATCT
AGTAATTCGAATCT
Found at i:3705375 original size:24 final size:25
Alignment explanation
Indices: 3705328--3705376 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
3705318 TGTGGCTAAT
*
3705328 TTTAAATTATTAATGAATTGTTAAA
1 TTTAAATTATTAATGAATTATTAAA
3705353 TTTAAA-TATTAA-GAATTTATTAAA
1 TTTAAATTATTAATGAA-TTATTAAA
3705377 ATATTTATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 3 0.14
24 13 0.59
25 6 0.27
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (25 bp):
TTTAAATTATTAATGAATTATTAAA
Found at i:3705850 original size:20 final size:20
Alignment explanation
Indices: 3705825--3705863 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3705815 AATGAACCGG
*
3705825 CTGAAAACCGGTAGAATCGA
1 CTGAAAACCGGTAAAATCGA
*
3705845 CTGAAAACTGGTAAAATCG
1 CTGAAAACCGGTAAAATCG
3705864 GGGTGAATCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.18
Consensus pattern (20 bp):
CTGAAAACCGGTAAAATCGA
Found at i:3708445 original size:16 final size:17
Alignment explanation
Indices: 3708419--3708453 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
3708409 TTGCTTTTGG
3708419 ATTTCTTAATTCTCCAT
1 ATTTCTTAATTCTCCAT
*
3708436 ATTT-TTAATTTTCCAT
1 ATTTCTTAATTCTCCAT
3708452 AT
1 AT
3708454 ATATATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.26, C:0.17, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTTCTTAATTCTCCAT
Found at i:3709020 original size:14 final size:14
Alignment explanation
Indices: 3709001--3709034 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3708991 TTTTTGTATT
*
3709001 TACATATACATACA
1 TACATACACATACA
3709015 TACATACACATACA
1 TACATACACATACA
*
3709029 CACATA
1 TACATA
3709035 GTTGAAGTGG
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:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (14 bp):
TACATACACATACA
Found at i:3712940 original size:12 final size:12
Alignment explanation
Indices: 3712923--3712956 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3712913 AACAACACAC
3712923 ATGTATGTATAA
1 ATGTATGTATAA
* *
3712935 ATGTATGTACAT
1 ATGTATGTATAA
3712947 ATGTATGTAT
1 ATGTATGTAT
3712957 GTTTGCCATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.35, C:0.03, G:0.18, T:0.44
Consensus pattern (12 bp):
ATGTATGTATAA
Found at i:3713773 original size:18 final size:18
Alignment explanation
Indices: 3713734--3713775 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
3713724 GTCATAACCC
*
3713734 GACCCGACCCGCTGACCC
1 GACCCGACCCGCTGACCA
* *
3713752 GACCCGACCCGTTTACCA
1 GACCCGACCCGCTGACCA
3713770 GACCCG
1 GACCCG
3713776 TTGACCATTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.19, C:0.50, G:0.21, T:0.10
Consensus pattern (18 bp):
GACCCGACCCGCTGACCA
Found at i:3716199 original size:24 final size:24
Alignment explanation
Indices: 3716172--3716293 Score: 156
Period size: 24 Copynumber: 5.1 Consensus size: 24
3716162 TCAATTTGAT
3716172 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
*
3716196 TTCTGATCGGATA-TCTGACATGGA
1 TTCTGATCTGATACT-TGACATGGA
*
3716220 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
** *
3716244 TTCTGATCAAATACTTGACCTGGA
1 TTCTGATCTGATACTTGACATGGA
* * *
3716268 TTTTGATATGATACTTGACCTGGA
1 TTCTGATCTGATACTTGACATGGA
3716292 TT
1 TT
3716294 ATGTTTTGAT
Statistics
Matches: 86, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
23 1 0.01
24 84 0.98
25 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:3716937 original size:26 final size:28
Alignment explanation
Indices: 3716898--3716951 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 28
3716888 AATTGTATTT
*
3716898 TGTTTTAATATTTG-ATTCTGA-AAATC
1 TGTTTTAATATTTGTATACTGATAAATC
* *
3716924 TGTTTTATTTTTTGTATACTGATAAATC
1 TGTTTTAATATTTGTATACTGATAAATC
3716952 ATTTTGTTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 12 0.52
27 6 0.26
28 5 0.22
ACGTcount: A:0.28, C:0.07, G:0.11, T:0.54
Consensus pattern (28 bp):
TGTTTTAATATTTGTATACTGATAAATC
Found at i:3719973 original size:39 final size:39
Alignment explanation
Indices: 3719929--3720009 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
3719919 CTATCTGTAA
3719929 ATTCTGGTGTGCTCCCTACTCACATGAATATTTTACCTG
1 ATTCTGGTGTGCTCCCTACTCACATGAATATTTTACCTG
3719968 ATTCTGGTGTGCTCCCTACTCACATGAATATTTTACCTG
1 ATTCTGGTGTGCTCCCTACTCACATGAATATTTTACCTG
3720007 ATT
1 ATT
3720010 TTCAATTTGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.40
Consensus pattern (39 bp):
ATTCTGGTGTGCTCCCTACTCACATGAATATTTTACCTG
Found at i:3720073 original size:12 final size:12
Alignment explanation
Indices: 3720036--3720098 Score: 58
Period size: 12 Copynumber: 5.2 Consensus size: 12
3720026 ATCTGATACT
3720036 TGACATGGATTC
1 TGACATGGATTC
*
3720048 TGATAT-GATATC
1 TGACATGGAT-TC
3720060 TGACATGGATTC
1 TGACATGGATTC
* *
3720072 TGATAT-GATAC
1 TGACATGGATTC
*
3720083 TTGACTTGGATTC
1 -TGACATGGATTC
3720096 TGA
1 TGA
3720099 TCGAATACTT
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
11 7 0.17
12 26 0.65
13 7 0.17
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (12 bp):
TGACATGGATTC
Found at i:3720152 original size:24 final size:24
Alignment explanation
Indices: 3720021--3720142 Score: 158
Period size: 24 Copynumber: 5.1 Consensus size: 24
3720011 TCAATTTGAT
*
3720021 TTCTGATCTGATACTTGACATGGA
1 TTCTGATATGATACTTGACATGGA
3720045 TTCTGATATGATA-TCTGACATGGA
1 TTCTGATATGATACT-TGACATGGA
*
3720069 TTCTGATATGATACTTGACTTGGA
1 TTCTGATATGATACTTGACATGGA
* *
3720093 TTCTGAT-CGAATACTTGACCTGGA
1 TTCTGATATG-ATACTTGACATGGA
* *
3720117 TTTTGATATGATACTTGACTTGGA
1 TTCTGATATGATACTTGACATGGA
3720141 TT
1 TT
3720143 ATGTTTTGAT
Statistics
Matches: 87, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
23 2 0.02
24 83 0.95
25 2 0.02
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.40
Consensus pattern (24 bp):
TTCTGATATGATACTTGACATGGA
Found at i:3720786 original size:26 final size:28
Alignment explanation
Indices: 3720747--3720800 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 28
3720737 AATTGTATTT
*
3720747 TGTTTTAATATTTG-ATTCTGA-AAATC
1 TGTTTTAATATTTGTATACTGATAAATC
* *
3720773 TGTTTTATTTTTTGTATACTGATAAATC
1 TGTTTTAATATTTGTATACTGATAAATC
3720801 ATTTTGTTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 12 0.52
27 6 0.26
28 5 0.22
ACGTcount: A:0.28, C:0.07, G:0.11, T:0.54
Consensus pattern (28 bp):
TGTTTTAATATTTGTATACTGATAAATC
Found at i:3723825 original size:39 final size:39
Alignment explanation
Indices: 3723781--3723861 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
3723771 CTATCTGTAA
3723781 ATTCTGGTGTGCTCCCTACTCACATGAATATTTTACCTG
1 ATTCTGGTGTGCTCCCTACTCACATGAATATTTTACCTG
3723820 ATTCTGGTGTGCTCCCTACTCACATGAATATTTTACCTG
1 ATTCTGGTGTGCTCCCTACTCACATGAATATTTTACCTG
3723859 ATT
1 ATT
3723862 TTCAATTTGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.40
Consensus pattern (39 bp):
ATTCTGGTGTGCTCCCTACTCACATGAATATTTTACCTG
Found at i:3723900 original size:24 final size:24
Alignment explanation
Indices: 3723873--3723994 Score: 149
Period size: 24 Copynumber: 5.1 Consensus size: 24
3723863 TCAATTTGAT
*
3723873 TTCTGATCTGATACTTGACATGGA
1 TTCTGATATGATACTTGACATGGA
*
3723897 TTCTGATATGGTA-TCTGACATGGA
1 TTCTGATATGATACT-TGACATGGA
*
3723921 TTCTGATATGATACTTGACTTGGA
1 TTCTGATATGATACTTGACATGGA
* *
3723945 TTCTGAT-CGAATACTTGACCTGGA
1 TTCTGATATG-ATACTTGACATGGA
* *
3723969 TTTTGATATGATACTTGACTTGGA
1 TTCTGATATGATACTTGACATGGA
3723993 TT
1 TT
3723995 ATGTTTTGAT
Statistics
Matches: 85, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
23 2 0.02
24 81 0.95
25 2 0.02
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.40
Consensus pattern (24 bp):
TTCTGATATGATACTTGACATGGA
Found at i:3723913 original size:12 final size:12
Alignment explanation
Indices: 3723892--3723951 Score: 54
Period size: 12 Copynumber: 5.0 Consensus size: 12
3723882 GATACTTGAC
3723892 ATGGATTCTGAT
1 ATGGATTCTGAT
*
3723904 ATGG-TATCTGAC
1 ATGGAT-TCTGAT
3723916 ATGGATTCTGAT
1 ATGGATTCTGAT
*
3723928 AT-GATACTTGACT
1 ATGGATTC-TGA-T
3723941 -TGGATTCTGAT
1 ATGGATTCTGAT
3723952 CGAATACTTG
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
11 6 0.15
12 27 0.69
13 6 0.15
ACGTcount: A:0.25, C:0.12, G:0.23, T:0.40
Consensus pattern (12 bp):
ATGGATTCTGAT
Found at i:3726129 original size:18 final size:18
Alignment explanation
Indices: 3726103--3726141 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
3726093 ACCAGTCATA
* *
3726103 ACCCGACCCAACCTGTTG
1 ACCCAACCCAACCCGTTG
*
3726121 ACCCAACCCGACCCGTTG
1 ACCCAACCCAACCCGTTG
3726139 ACC
1 ACC
3726142 ATTGACCGGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.23, C:0.49, G:0.15, T:0.13
Consensus pattern (18 bp):
ACCCAACCCAACCCGTTG
Found at i:3728627 original size:24 final size:24
Alignment explanation
Indices: 3728597--3728718 Score: 140
Period size: 24 Copynumber: 5.1 Consensus size: 24
3728587 TCAATTTGAT
3728597 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
*
3728621 TTCTGATATGATA-TCTGACATGGA
1 TTCTGATCTGATACT-TGACATGGA
* *
3728645 TTCTAATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
*
3728669 TTCTGATC-GAATACTTGACCTGGA
1 TTCTGATCTG-ATACTTGACATGGA
* * * *
3728693 TTTTGATATGATACTTAACCTGGA
1 TTCTGATCTGATACTTGACATGGA
3728717 TT
1 TT
3728719 ATGTTTTGAT
Statistics
Matches: 85, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
23 2 0.02
24 81 0.95
25 2 0.02
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:3739779 original size:127 final size:127
Alignment explanation
Indices: 3739549--3740292 Score: 1157
Period size: 127 Copynumber: 6.0 Consensus size: 127
3739539 GTACTATTCA
* * *
3739549 CGTGAAGGTGCGTTACCGGGGGCGCGCCTTCCATTATTTTATCAGAGAATATGTTATCATTGCCC
1 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
3739614 TATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACATATTATTCCTTAGGGGAC
66 TATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACATATTATTCCTTAGGGGAC
* *
3739676 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCTATTATTTTGTCAGATAATATGTTATCATTGCCC
1 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
* *
3739741 TATTATGTCACTTATGTCCCCCGGGAACTATTCGTGTCAATACCTATTATTCCTTAGGGGAC
66 TATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACATATTATTCCTTAGGGGAC
* *
3739803 CGTGAAGGCGTGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATATTATCATTGCCC
1 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
*
3739868 TATTATGTCACTTATGTCCCCCAGGAACTATTCATGTCAATACATATTATTCCTTAGGGGAC
66 TATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACATATTATTCCTTAGGGGAC
* **
3739930 CGTGAAGGCACGTTCCCAGGGGG-GCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTTTC
1 CGTGAAGGCGCGTTCCC-GGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCC
* *
3739994 CTATTATGTCACTTATGTCCCCCGGGAACTATTCGTGT-AATACCTATTATTCCTTAGGGGAC
65 CTATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACATATTATTCCTTAGGGGAC
*
3740056 CGTGAA---------------G-GCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCC
1 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
* **
3740105 TATTATGTCAGTTATGTCCCCCATGAACTATTCATGTCAATACATATTATTCCTTAGGGGAC
66 TATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACATATTATTCCTTAGGGGAC
*
3740167 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTTCATTATTTTGTCAGAGAATATGTTATCATTGCCC
1 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
*
3740232 TATTATGTCACTTATGT-CCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
66 TATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACATATTATTCCTTAGGGGAC
3740293 TTTAAAGTGC
Statistics
Matches: 564, Mismatches: 35, Indels: 37
0.89 0.06 0.06
Matches are distributed among these distances:
110 74 0.13
111 29 0.05
126 71 0.13
127 385 0.68
128 5 0.01
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34
Consensus pattern (127 bp):
CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
TATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACATATTATTCCTTAGGGGAC
Found at i:3740090 original size:110 final size:111
Alignment explanation
Indices: 3739952--3740182 Score: 383
Period size: 110 Copynumber: 2.1 Consensus size: 111
3739942 TTCCCAGGGG
**
3739952 GGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTTTCCTATTATGTCACTTATGTCCCCC
1 GGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTATGTCACTTATGTCCCCC
* * *
3740017 GGGAACTATTCGTGT-AATACCTATTATTCCTTAGGGGACCGTGAA
66 AGGAACTATTCATGTCAATACATATTATTCCTTAGGGGACCGTGAA
*
3740062 GGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTATGTCAGTTATGTCCCCC
1 GGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTATGTCACTTATGTCCCCC
*
3740127 ATGAACTATTCATGTCAATACATATTATTCCTTAGGGGACCGTGAA
66 AGGAACTATTCATGTCAATACATATTATTCCTTAGGGGACCGTGAA
*
3740173 GGCGCGTTCC
1 GGCGCCTTCC
3740183 CGGGGGCGCG
Statistics
Matches: 112, Mismatches: 8, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
110 74 0.66
111 38 0.34
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (111 bp):
GGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTATGTCACTTATGTCCCCC
AGGAACTATTCATGTCAATACATATTATTCCTTAGGGGACCGTGAA
Found at i:3740241 original size:237 final size:240
Alignment explanation
Indices: 3739569--3740292 Score: 1154
Period size: 237 Copynumber: 3.0 Consensus size: 240
3739559 CGTTACCGGG
*
3739569 GGCGCGCCTTCCATTATTTTATCAGAGAATATGTTATCATTGCCCTATTATGTCACTTATGTCCC
1 GGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTTATGTCCC
*
3739634 CCGGGAACTATTCATGTCAATACATATTATTCCTTAGGGGACCGTGAAGGCGCGTTCCCGGGGGC
66 CCAGGAACTATTCATGTCAATACATATTATTCCTTAGGGGACCGTGAAGGCGCGTTCCCGGGGGC
*
3739699 GCGCC-TTCTATTATTTTGTCAGATAATATGTTATCATTGCCCTATTATGTCACTTATGTCCCCC
131 GCGCCTTTC-ATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTTATGTCCCCC
3739763 GGGAACTATTCGTGTCAATACCTATTATTCCTTAGGGGACCGTGAA
195 GGGAACTATTCGTGTCAATACCTATTATTCCTTAGGGGACCGTGAA
*
3739809 GGCGTGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATATTATCATTGCCCTATTAT
1 --------------GGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTAT
3739874 GTCACTTATGTCCCCCAGGAACTATTCATGTCAATACATATTATTCCTTAGGGGACCGTGAAGGC
52 GTCACTTATGTCCCCCAGGAACTATTCATGTCAATACATATTATTCCTTAGGGGACCGTGAAGGC
* * **
3739939 ACGTTCCCAGGGGG-GCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTTTCCTATTATGT
117 GCGTTCCC-GGGGGCGCGCCTTTCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGT
3740003 CACTTATGTCCCCCGGGAACTATTCGTGT-AATACCTATTATTCCTTAGGGGACCGTGAA
181 CACTTATGTCCCCCGGGAACTATTCGTGTCAATACCTATTATTCCTTAGGGGACCGTGAA
* *
3740062 -G-GCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTATGTCAGTTATGTCCC
1 GGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTTATGTCCC
*
3740125 CCATGAACTATTCATGTCAATACATATTATTCCTTAGGGGACCGTGAAGGCGCGTTCCCGGGGGC
66 CCAGGAACTATTCATGTCAATACATATTATTCCTTAGGGGACCGTGAAGGCGCGTTCCCGGGGGC
3740190 GCGCCTTTCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTTATGT-CCCCG
131 GCGCCTTTCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTTATGTCCCCCG
*
3740254 GGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
196 GGAACTATTCGTGTCAATACCTATTATTCCTTAGGGGAC
3740293 TTTAAAGTGC
Statistics
Matches: 449, Mismatches: 17, Indels: 25
0.91 0.03 0.05
Matches are distributed among these distances:
236 23 0.05
237 196 0.44
238 1 0.00
253 30 0.07
254 192 0.43
255 7 0.02
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.34
Consensus pattern (240 bp):
GGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTTATGTCCC
CCAGGAACTATTCATGTCAATACATATTATTCCTTAGGGGACCGTGAAGGCGCGTTCCCGGGGGC
GCGCCTTTCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTTATGTCCCCCG
GGAACTATTCGTGTCAATACCTATTATTCCTTAGGGGACCGTGAA
Found at i:3740760 original size:34 final size:34
Alignment explanation
Indices: 3740722--3740822 Score: 148
Period size: 34 Copynumber: 3.0 Consensus size: 34
3740712 GAATTTAATG
* *
3740722 TTAAATTTTGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATACTATAATTTGTATTTTAAAT
* * *
3740756 TTAAATTTCGAATAATATTATTTGTATTTTAATT
1 TTAAATTTCGAATACTATAATTTGTATTTTAAAT
*
3740790 TTAAATTTCAAATACTATAATTTGTATTTTAAA
1 TTAAATTTCGAATACTATAATTTGTATTTTAAA
3740823 AACATTTATT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 58 1.00
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (34 bp):
TTAAATTTCGAATACTATAATTTGTATTTTAAAT
Found at i:3741393 original size:21 final size:21
Alignment explanation
Indices: 3741342--3741393 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
3741332 TATGGTATAA
* * *
3741342 AACCCTACGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATAT
3741363 AA-CCTAGCGGGCTAGGAATAT
1 AACCCT-GCGGGCTAGGAATAT
3741384 AACCCTGCGG
1 AACCCTGCGG
3741394 AGATGACATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 3 0.12
21 20 0.77
22 3 0.12
ACGTcount: A:0.27, C:0.27, G:0.29, T:0.17
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATAT
Found at i:3741417 original size:42 final size:42
Alignment explanation
Indices: 3741366--3741449 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 42
3741356 GGCATGTAAC
*
3741366 CTAGCGGGCTAGGA-ATATAACCCTGCGGAGATGACATATGAA
1 CTAGCGGGCT-GGACATATAACCCTGAGGAGATGACATATGAA
* * * * *
3741408 CTAGTGGGCTTGACATATACCCCTGAGGAGATGGCATCTGAA
1 CTAGCGGGCTGGACATATAACCCTGAGGAGATGACATATGAA
3741450 GTGGAGGGAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
41 2 0.06
42 33 0.94
ACGTcount: A:0.30, C:0.20, G:0.29, T:0.21
Consensus pattern (42 bp):
CTAGCGGGCTGGACATATAACCCTGAGGAGATGACATATGAA
Found at i:3743213 original size:19 final size:18
Alignment explanation
Indices: 3743184--3743220 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
3743174 AAAAATAATT
*
3743184 AATTAATAAATTTAAATA
1 AATTAATAAATATAAATA
3743202 AATTATATAAATATAAATA
1 AATTA-ATAAATATAAATA
3743221 TTATTTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTAATAAATATAAATA
Found at i:3745877 original size:37 final size:36
Alignment explanation
Indices: 3745818--3745937 Score: 181
Period size: 35 Copynumber: 3.3 Consensus size: 36
3745808 ATCCCATTAT
* *
3745818 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
3745854 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
3745890 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
3745925 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
3745938 TTGGTTACCA
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
35 35 0.45
36 13 0.17
37 29 0.38
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.32
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:3745893 original size:21 final size:21
Alignment explanation
Indices: 3745869--3745929 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
3745859 TTCAAAGAAA
3745869 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
3745890 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
3745904 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
3745925 CATTT
1 CATTT
3745930 TTTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:3745946 original size:35 final size:36
Alignment explanation
Indices: 3745820--3745964 Score: 142
Period size: 35 Copynumber: 4.1 Consensus size: 36
3745810 CCCATTATCA
*
3745820 TTTTTCAACA-AACA-TCTACCAAACTTTGAAAAAC-T
1 TTTTTCAA-AGAACAGT-TACCAAACTTTGAAAACCAT
*
3745855 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA-
1 -TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
*
3745892 -TTTTCAAAGAAACATTTACCAAACTTTGAAAACCAT
1 TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
***
3745928 TTTTTCAAAG-TTGGTTACCAAAC-TTGAAAACCAT
1 TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
3745962 TTT
1 TTT
3745965 AATACTTTCA
Statistics
Matches: 98, Mismatches: 5, Indels: 14
0.84 0.04 0.12
Matches are distributed among these distances:
34 14 0.14
35 45 0.46
36 8 0.08
37 30 0.31
38 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.33
Consensus pattern (36 bp):
TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
Found at i:3750494 original size:37 final size:36
Alignment explanation
Indices: 3750435--3750553 Score: 179
Period size: 35 Copynumber: 3.3 Consensus size: 36
3750425 ATCCCATTAT
* *
3750435 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
3750471 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
3750507 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
3750542 CATTTTTTCAAA
1 CA-TTTTTCAAA
3750554 ATTGGTTACC
Statistics
Matches: 76, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
35 35 0.46
36 13 0.17
37 28 0.37
ACGTcount: A:0.44, C:0.20, G:0.04, T:0.32
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:3750510 original size:21 final size:21
Alignment explanation
Indices: 3750486--3750546 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
3750476 TTCAAAGAAA
3750486 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
3750507 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
3750521 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
3750542 CATTT
1 CATTT
3750547 TTTCAAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:3761430 original size:25 final size:25
Alignment explanation
Indices: 3761402--3761451 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
3761392 TTGAAATGTA
*
3761402 CCAATTTTTTATGATTATTAGATTT
1 CCAATTCTTTATGATTATTAGATTT
3761427 CCAATTCTTTATGATTATTAGATTT
1 CCAATTCTTTATGATTATTAGATTT
3761452 AGGGTTGGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.28, C:0.10, G:0.08, T:0.54
Consensus pattern (25 bp):
CCAATTCTTTATGATTATTAGATTT
Found at i:3761674 original size:41 final size:40
Alignment explanation
Indices: 3761590--3761696 Score: 117
Period size: 41 Copynumber: 2.6 Consensus size: 40
3761580 TTTTAATTTT
* * * * * *
3761590 ATGTAATAACAATATTAAGAAAATATTACTAATAGATGTC
1 ATGTCATAAAAATATTAATAAAATAATACCAATAGATGCC
3761630 ATGTCATAAAAAATATTAATAAAATAATACCAACT-GATGCC
1 ATGTCAT-AAAAATATTAATAAAATAATACCAA-TAGATGCC
* *
3761671 ATGTTATAAAAATATTATTAAAATAA
1 ATGTCATAAAAATATTAATAAAATAA
3761697 AATTAAGTTA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
40 24 0.42
41 32 0.56
42 1 0.02
ACGTcount: A:0.52, C:0.08, G:0.07, T:0.32
Consensus pattern (40 bp):
ATGTCATAAAAATATTAATAAAATAATACCAATAGATGCC
Found at i:3762342 original size:18 final size:18
Alignment explanation
Indices: 3762299--3762343 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
3762289 AGGAAGATGG
*
3762299 AGAAGAAGAGGATCACGA
1 AGAAGAAGAGGATAACGA
* * *
3762317 GGAGGAAGATGATAACGA
1 AGAAGAAGAGGATAACGA
3762335 AGAAGAAGA
1 AGAAGAAGA
3762344 AGACGAAGAA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.51, C:0.07, G:0.36, T:0.07
Consensus pattern (18 bp):
AGAAGAAGAGGATAACGA
Found at i:3762351 original size:12 final size:12
Alignment explanation
Indices: 3762333--3762377 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
3762323 AGATGATAAC
*
3762333 GAAGAAGAAGAA
1 GAAGAAGAAGAG
*
3762345 GACGAAGAAGAG
1 GAAGAAGAAGAG
3762357 GAAGAAGGAA-AG
1 GAAGAA-GAAGAG
3762369 GAAGAAGAA
1 GAAGAAGAA
3762378 AATGGTGAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
11 3 0.10
12 23 0.79
13 3 0.10
ACGTcount: A:0.60, C:0.02, G:0.38, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAGAG
Found at i:3765620 original size:16 final size:16
Alignment explanation
Indices: 3765586--3765620 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3765576 TAAATAAATG
*
3765586 AACATAAACGAATACA
1 AACATAAACGAACACA
*
3765602 AACATAAACGAACATA
1 AACATAAACGAACACA
3765618 AAC
1 AAC
3765621 GAACAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.63, C:0.20, G:0.06, T:0.11
Consensus pattern (16 bp):
AACATAAACGAACACA
Found at i:3766625 original size:14 final size:14
Alignment explanation
Indices: 3766608--3766662 Score: 83
Period size: 14 Copynumber: 3.9 Consensus size: 14
3766598 GATTGGGTTA
*
3766608 AACATAAATGAACG
1 AACATAAACGAACG
*
3766622 AACATAACCGAACG
1 AACATAAACGAACG
*
3766636 AACATAAACGAACA
1 AACATAAACGAACG
3766650 AACATAAACGAAC
1 AACATAAACGAAC
3766663 ATAACCTAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 37 1.00
ACGTcount: A:0.58, C:0.22, G:0.11, T:0.09
Consensus pattern (14 bp):
AACATAAACGAACG
Found at i:3773193 original size:86 final size:86
Alignment explanation
Indices: 3773048--3773216 Score: 329
Period size: 86 Copynumber: 2.0 Consensus size: 86
3773038 CGGCCCAAGA
3773048 GCCTGTTGCTTCCATCGGAGGAAACCCATTCGCGTAGACACTACCGCCAGCAGTAGCTTTTTAGT
1 GCCTGTTGCTTCCATCGGAGGAAACCCATTCGCGTAGACACTACCGCCAGCAGTAGCTTTTTAGT
3773113 CTTTTTTCAGTCTAGTAGAGG
66 CTTTTTTCAGTCTAGTAGAGG
*
3773134 GCCTGTTGCTTCCATCGGAGGAAACCCGTTCGCGTAGACACTACCGCCAGCAGTAGCTTTTTAGT
1 GCCTGTTGCTTCCATCGGAGGAAACCCATTCGCGTAGACACTACCGCCAGCAGTAGCTTTTTAGT
3773199 CTTTTTTCAGTCTAGTAG
66 CTTTTTTCAGTCTAGTAG
3773217 TTGCCTGGTA
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 82 1.00
ACGTcount: A:0.20, C:0.26, G:0.23, T:0.31
Consensus pattern (86 bp):
GCCTGTTGCTTCCATCGGAGGAAACCCATTCGCGTAGACACTACCGCCAGCAGTAGCTTTTTAGT
CTTTTTTCAGTCTAGTAGAGG
Found at i:3775239 original size:31 final size:31
Alignment explanation
Indices: 3775204--3775268 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
3775194 TAATAATTTG
*
3775204 ATAACT-GATAAATTTTAATTATCATTTTAAA
1 ATAACTCGATAAA-TTTAATGATCATTTTAAA
*
3775235 ATAACTCGATAAATTTAATGATCATTTTATA
1 ATAACTCGATAAATTTAATGATCATTTTAAA
3775266 ATA
1 ATA
3775269 TTTTATTCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 25 0.81
32 6 0.19
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.43
Consensus pattern (31 bp):
ATAACTCGATAAATTTAATGATCATTTTAAA
Found at i:3776126 original size:71 final size:71
Alignment explanation
Indices: 3776034--3776176 Score: 207
Period size: 71 Copynumber: 2.0 Consensus size: 71
3776024 AAATTGTCCC
* * * *
3776034 TTGACTATATGATATTATTTTGTTGAGTCA-CTGACTATTAAAAGTAATAAAATGGTCCGACTAT
1 TTGACTATAGGATAATATTTTGTTGACTCATC-GACTATTAAAAGTAATAAAATGATCCGACTAT
3776098 AGGGAGA
65 AGGGAGA
* * *
3776105 TTGACTATAGGATAATGTTTTGTTGACTCATCGACTATTAAAAGTTATAAAATGATCTGACTATA
1 TTGACTATAGGATAATATTTTGTTGACTCATCGACTATTAAAAGTAATAAAATGATCCGACTATA
3776170 GGGAGA
66 GGGAGA
3776176 T
1 T
3776177 GTTTTGTTGA
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
71 63 0.98
72 1 0.02
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.36
Consensus pattern (71 bp):
TTGACTATAGGATAATATTTTGTTGACTCATCGACTATTAAAAGTAATAAAATGATCCGACTATA
GGGAGA
Found at i:3777603 original size:21 final size:20
Alignment explanation
Indices: 3777577--3777621 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
3777567 TATTTGTAAA
*
3777577 ATAAAATATTAAATAATTATT
1 ATAAAAAATTAAATAA-TATT
*
3777598 ATAAAAAATTAATTAATATT
1 ATAAAAAATTAAATAATATT
3777618 -TAAA
1 ATAAA
3777622 CTAATAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 4 0.18
20 4 0.18
21 14 0.64
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
ATAAAAAATTAAATAATATT
Found at i:3779301 original size:76 final size:76
Alignment explanation
Indices: 3779209--3779351 Score: 234
Period size: 76 Copynumber: 1.9 Consensus size: 76
3779199 ATTAATGAAT
* *
3779209 GTGTGCTAACCTAAAAAATATGTATGAATCCGCCACTACTC-TCGTCTCAATTTTTTCAATTCAT
1 GTGTGCTAAACTAAAAAATATGTATGAATCCACCACTA-TCATCGTCTCAATTTTTTCAATTCAT
3779273 AATATCATAATG
65 AATATCATAATG
* *
3779285 GTGTGCTAAACTAAAAAATATTTATGAATTCACCACTATCATCGTCTCAATTTTTTCAATTCATA
1 GTGTGCTAAACTAAAAAATATGTATGAATCCACCACTATCATCGTCTCAATTTTTTCAATTCATA
3779350 AT
66 AT
3779352 GTTAAAATTA
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
75 2 0.03
76 60 0.97
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.37
Consensus pattern (76 bp):
GTGTGCTAAACTAAAAAATATGTATGAATCCACCACTATCATCGTCTCAATTTTTTCAATTCATA
ATATCATAATG
Found at i:3784649 original size:2 final size:2
Alignment explanation
Indices: 3784632--3784708 Score: 131
Period size: 2 Copynumber: 39.0 Consensus size: 2
3784622 GAATTATGTA
3784632 AT AT AT -T A- AT AGT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3784673 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
3784709 GTGTGTGTGT
Statistics
Matches: 72, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.03
2 68 0.94
3 2 0.03
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3786097 original size:88 final size:90
Alignment explanation
Indices: 3785960--3786128 Score: 236
Period size: 88 Copynumber: 1.9 Consensus size: 90
3785950 CTTCTTCATA
* * *
3785960 AACAAACGAAGGCTTACTAGATTCTTCACCTATCTAACTAACATCTGAAATTGACTTTACATATA
1 AACAAACGAAGGCTTACAAGATTCTTCAAC-ATCTAACTAACATCTGAAATTGACTTTACACATA
*
3786025 TTTCTTCAATTTTACATATGAAGGCT
65 CTTCTTCAATTTTACATATGAAGGCT
* * *
3786051 AACAAATGAAGGCTTACAAGATT-TTTAAC-TCTAACTAACAAT-TGAAATTGATTTTACACATA
1 AACAAACGAAGGCTTACAAGATTCTTCAACATCTAACTAAC-ATCTGAAATTGACTTTACACATA
3786113 CTTCTTCAATTTTACA
65 CTTCTTCAATTTTACA
3786129 CATATTACAC
Statistics
Matches: 70, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
88 43 0.61
89 2 0.03
90 4 0.06
91 21 0.30
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (90 bp):
AACAAACGAAGGCTTACAAGATTCTTCAACATCTAACTAACATCTGAAATTGACTTTACACATAC
TTCTTCAATTTTACATATGAAGGCT
Found at i:3798396 original size:37 final size:37
Alignment explanation
Indices: 3798307--3798410 Score: 127
Period size: 37 Copynumber: 2.8 Consensus size: 37
3798297 ATTTTCGTCC
*
3798307 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTA
* * **
3798344 TGCTAGGATTCAAACTCCTAAAAATATGATAGGGTTA
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTA
** * *
3798381 TACTATTATTTAAACTCCTAAAGATAGGAT
1 TACTAGGATTCAAACTCCTAAAAATAGGAT
3798411 CCACAAGCAT
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.32
Consensus pattern (37 bp):
TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTA
Found at i:3798843 original size:11 final size:11
Alignment explanation
Indices: 3798827--3798868 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
3798817 TATATATGTA
3798827 TATATTTTTAT
1 TATATTTTTAT
3798838 TATA-TTTTAT
1 TATATTTTTAT
3798848 T-TATTTTTTAT
1 TATA-TTTTTAT
3798859 TATAATTTTT
1 TAT-ATTTTT
3798869 TTCATTTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
9 2 0.07
10 7 0.26
11 11 0.41
12 6 0.22
13 1 0.04
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TATATTTTTAT
Found at i:3798855 original size:21 final size:22
Alignment explanation
Indices: 3798831--3798877 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
3798821 TATGTATATA
3798831 TTTTTATTAT-ATTTTATTT-AT
1 TTTTTATTATAATTTT-TTTCAT
3798852 TTTTTATTATAATTTTTTTCAT
1 TTTTTATTATAATTTTTTTCAT
3798874 TTTT
1 TTTT
3798878 CTTTACGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (22 bp):
TTTTTATTATAATTTTTTTCAT
Found at i:3798917 original size:2 final size:2
Alignment explanation
Indices: 3798910--3798941 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3798900 TTCCTATTAT
3798910 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3798942 TATTATTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3799181 original size:25 final size:25
Alignment explanation
Indices: 3799099--3799201 Score: 77
Period size: 25 Copynumber: 3.9 Consensus size: 25
3799089 CATTCATTTA
** *
3799099 TTTATTATTATTACTATTTAGTATTTTT
1 TTTA-TATTA-TACTATTTTTTA-TTAT
*
3799127 TTTATATTATACATACATTTTTA-TATT
1 TTTATATTATAC-TA-TTTTTTATTA-T
3799154 TTTATATATATA-TATTTTTTATTAT
1 TTTATAT-TATACTATTTTTTATTAT
3799179 TTTAT-TTATACTATTTATTTATT
1 TTTATATTATACTATTT-TTTATT
3799202 TTCATTATAT
Statistics
Matches: 63, Mismatches: 5, Indels: 17
0.74 0.06 0.20
Matches are distributed among these distances:
23 4 0.06
24 6 0.10
25 18 0.29
26 8 0.13
27 15 0.24
28 12 0.19
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (25 bp):
TTTATATTATACTATTTTTTATTAT
Found at i:3799331 original size:20 final size:18
Alignment explanation
Indices: 3799308--3799358 Score: 50
Period size: 20 Copynumber: 2.7 Consensus size: 18
3799298 CTTCATTTAT
3799308 TTTTATTTTATTCAATTTCA
1 TTTTATTTTATTCAA-TT-A
*
3799328 TTTT-TTTTCATCCAATTA
1 TTTTATTTT-ATTCAATTA
3799346 TTTTATGTTTATT
1 TTTTAT-TTTATT
3799359 ATTATTGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
18 5 0.19
19 9 0.35
20 12 0.46
ACGTcount: A:0.22, C:0.10, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTTATTTTATTCAATTA
Found at i:3800195 original size:20 final size:20
Alignment explanation
Indices: 3800170--3800211 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
3800160 GGGTCTGGCT
3800170 AGCCCAAGGGGGCACCAGCA
1 AGCCCAAGGGGGCACCAGCA
*
3800190 AGCCCAAGGGGGCACCGGCA
1 AGCCCAAGGGGGCACCAGCA
3800210 AG
1 AG
3800212 GAGAACTCGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.33, G:0.38, T:0.00
Consensus pattern (20 bp):
AGCCCAAGGGGGCACCAGCA
Found at i:3800349 original size:4 final size:4
Alignment explanation
Indices: 3800340--3800367 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
3800330 TACTTTCGTC
3800340 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
3800368 TACTAACATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:3803703 original size:16 final size:15
Alignment explanation
Indices: 3803678--3803724 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
3803668 AATAAGGGCA
3803678 AAAACAAAAAAGAA-
1 AAAACAAAAAAGAAG
3803692 AAGAAGCAAAAAAGAAG
1 AA-AA-CAAAAAAGAAG
3803709 AAAACAAAAAA-AAG
1 AAAACAAAAAAGAAG
3803723 AA
1 AA
3803725 CAAAAATCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
14 7 0.23
15 9 0.30
16 12 0.40
17 2 0.07
ACGTcount: A:0.81, C:0.06, G:0.13, T:0.00
Consensus pattern (15 bp):
AAAACAAAAAAGAAG
Found at i:3803730 original size:18 final size:18
Alignment explanation
Indices: 3803699--3803737 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
3803689 GAAAAGAAGC
*
3803699 AAAAAAGAAGAAAA-CAA
1 AAAAAAGAAAAAAATCAA
3803716 AAAAAAGAACAAAAATCAA
1 AAAAAAGAA-AAAAATCAA
3803735 AAA
1 AAA
3803738 GAAAAAGGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 9 0.47
18 4 0.21
19 6 0.32
ACGTcount: A:0.82, C:0.08, G:0.08, T:0.03
Consensus pattern (18 bp):
AAAAAAGAAAAAAATCAA
Found at i:3804376 original size:22 final size:22
Alignment explanation
Indices: 3804348--3804402 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
3804338 GCTACCCCAT
3804348 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
*
3804370 CAAACCTTTGAGCATTAAATGC
1 CAAACCTTTGAGCATCAAATGC
3804392 CAAACCTTTGA
1 CAAACCTTTGA
3804403 CCAAACACAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.25
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:3806607 original size:106 final size:106
Alignment explanation
Indices: 3805338--3806607 Score: 1817
Period size: 106 Copynumber: 12.0 Consensus size: 106
3805328 ATATCGTGCC
* * * * * *
3805338 ACTCGAGACAACACAAGTTCAACTTCACAACGAATGGACGGCTGGTTGTCAACAAATAACTTCCC
1 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* * *
3805403 AAATTCAAAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
3805444 ACTCCAGACAACAG-AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT---C-AAC---TTCT
1 ACTCGAGACAAC-GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCC
3805501 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
3805543 ACTCTAGACAATGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
3805608 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * * * *
3805649 ACTCAAGATAACACAAGTTCAACTTCATGACGAAGGGATCGCTGGTTGTCAATAAACAACTTCCT
1 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
*
3805714 AATTTCAGAGCCAATTTCAACTTCACAACGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
3805755 ACTCCAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* *
3805820 AATTTTAGAGCCAATTTCAACTTCACAACGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
3805861 ACTCAAGACAACGCAAGTTCAACTTCACGAAGAAGGGACCGCTGGTTGTCAACAAATAATTTCCC
1 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
** *
3805926 AATTTCAGAGCCAATTTCAACTTCACAGTGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
3805967 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
** **
3806032 AATTTTGGAGCCAATTTCAACTTCACAACGAAATATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
3806073 ACTTC-AGACAACGCAAGTTTAACTTCATGACGAAGGGACGGCTGGTTGTCAACAAACAATTTCC
1 AC-TCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCC
* *
3806137 CAATTTCGGAGCCAATTTCAACTTCACATCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * *
3806179 ACTCCAGACAACGCAAGTTTAACTTCACGAAGAAGGGA-CGACTGGTTGTCAACAAACAACTTCT
1 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAATTTCC
3806243 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
3806285 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACTGCTGGTTGTCAACAAACAACTTCCC
1 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
*
3806350 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
3806391 ACTCGAGACAACGCAAATTCAACTTCAC-AGCGAAGGGACCACTGGTTGTCAACAAACAATTTCC
1 ACTCGAGACAACGCAAGTTCAACTTCACGA-CGAAGGGACCGCTGGTTGTCAACAAACAATTTCC
* *
3806455 CAATTTCGGAGCCAATTTCAACTTCACAACAAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* **
3806497 ACTCGAGACAACACAAGTTCAACTTCATAACGAAGGGA-CGACTGGTTGTCAACAAACAATTTCC
1 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAATTTCC
* * * * *
3806561 CGATTCCAGAGCCAATTTCAACTTCACGACGGATGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
3806603 ACTCG
1 ACTCG
3806608 TAATAATGAT
Statistics
Matches: 1059, Mismatches: 89, Indels: 32
0.90 0.08 0.03
Matches are distributed among these distances:
98 1 0.00
99 86 0.08
102 2 0.00
103 4 0.00
105 5 0.00
106 957 0.90
107 4 0.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (106 bp):
ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:3807409 original size:37 final size:37
Alignment explanation
Indices: 3807357--3807460 Score: 136
Period size: 37 Copynumber: 2.8 Consensus size: 37
3807347 ATTTTCATCC
*
3807357 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTA
* * *
3807394 TGCTAGGATTCAAACTCCTAAAAATATGATAGAGTTA
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTA
** * *
3807431 TACTATTATTTAAACTCCTAAAGATAGGAT
1 TACTAGGATTCAAACTCCTAAAAATAGGAT
3807461 CCACAAGCAT
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.32
Consensus pattern (37 bp):
TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTA
Found at i:3808214 original size:21 final size:20
Alignment explanation
Indices: 3808183--3808249 Score: 62
Period size: 23 Copynumber: 3.0 Consensus size: 20
3808173 TTATACATGC
3808183 ATTTTTATATTTTTATATATAT
1 ATTTTT-TATTTTTAT-TATAT
3808205 ATTTTTTATTATTTTATTTATACT
1 ATTTTTTA-T-TTTTA-TTATA-T
*
3808229 ATTTATTTATTTTCATTATAT
1 ATTT-TTTATTTTTATTATAT
3808250 TTTCAGTTTC
Statistics
Matches: 39, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
21 3 0.08
22 12 0.31
23 13 0.33
24 7 0.18
25 4 0.10
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (20 bp):
ATTTTTTATTTTTATTATAT
Found at i:3808219 original size:23 final size:25
Alignment explanation
Indices: 3808184--3808239 Score: 73
Period size: 23 Copynumber: 2.3 Consensus size: 25
3808174 TATACATGCA
3808184 TTTTTA-TATTTTTATATATA-TAT
1 TTTTTATTATTTTTATATATACTAT
*
3808207 TTTTTATTA-TTTTATTTATACTAT
1 TTTTTATTATTTTTATATATACTAT
3808231 TTATTTATT
1 TT-TTTATT
3808240 TTCATTATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 16 0.55
24 7 0.24
25 6 0.21
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (25 bp):
TTTTTATTATTTTTATATATACTAT
Found at i:3808250 original size:28 final size:27
Alignment explanation
Indices: 3808194--3808251 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
3808184 TTTTTATATT
* *
3808194 TTTATATATATATTTTTTATTATTTTA
1 TTTATATATATATTTTTTATCATTATA
*
3808221 TTTATACTATTTATTTATTT-TCATTATA
1 TTTATA-TATATATTT-TTTATCATTATA
3808249 TTT
1 TTT
3808252 TCAGTTTCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 6 0.23
28 17 0.65
29 3 0.12
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (27 bp):
TTTATATATATATTTTTTATCATTATA
Found at i:3809083 original size:31 final size:31
Alignment explanation
Indices: 3809045--3809154 Score: 175
Period size: 31 Copynumber: 3.5 Consensus size: 31
3809035 AGGGTCGAGG
3809045 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
3809076 GTTTACCTATGTTCTTCGGGACATATGAACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
3809107 GTTTATCTATGTTCTTCGGGACCTATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
3809138 GATTACCTAGGTTCTTC
1 GTTTACCTATGTTCTTC
3809155 AGAATCTATG
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 72 1.00
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:3809164 original size:31 final size:30
Alignment explanation
Indices: 3809045--3809169 Score: 160
Period size: 31 Copynumber: 4.0 Consensus size: 30
3809035 AGGGTCGAGG
3809045 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGAC-TATGGACT
*
3809076 GTTTACCTATGTTCTTCGGGACATATGAACT
1 GTTTACCTATGTTCTTCGGGAC-TATGGACT
*
3809107 GTTTATCTATGTTCTTCGGGACCTATGGACT
1 GTTTACCTATGTTCTTCGGGA-CTATGGACT
* * * *
3809138 GATTACCTAGGTTCTTCAGAATCTATGGACT
1 GTTTACCTATGTTCTTCGGGA-CTATGGACT
3809169 G
1 G
3809170 GTTCTTCGGG
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
31 83 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (30 bp):
GTTTACCTATGTTCTTCGGGACTATGGACT
Found at i:3810503 original size:20 final size:21
Alignment explanation
Indices: 3810478--3810570 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
3810468 TTTTCCCAAT
*
3810478 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
3810498 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
3810519 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
3810539 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
3810560 TCGCAATGCGA
1 TCGCAATGCGA
3810571 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:3810584 original size:20 final size:20
Alignment explanation
Indices: 3810559--3810673 Score: 106
Period size: 20 Copynumber: 5.7 Consensus size: 20
3810549 AATTGGGAAA
*
3810559 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
3810579 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* * *
3810600 ATTGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
3810620 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
3810640 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
3810660 TTCGCAACGCGATA
1 ATCGCAACGCGATA
3810674 ATACATAATC
Statistics
Matches: 79, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.03
20 63 0.80
21 12 0.15
22 2 0.03
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:3810585 original size:41 final size:41
Alignment explanation
Indices: 3810478--3810570 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
3810468 TTTTCCCAAT
3810478 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
3810519 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
3810560 TCGCAATGCGA
1 TCGCAATGCGA
3810571 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:3810889 original size:22 final size:22
Alignment explanation
Indices: 3810861--3810904 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
3810851 CACTCTCTCA
3810861 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
3810883 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
3810905 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:3811221 original size:20 final size:20
Alignment explanation
Indices: 3811167--3811225 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
3811157 GCGATTATCT
**
3811167 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
3811187 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
3811207 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
3811226 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:3812565 original size:18 final size:18
Alignment explanation
Indices: 3812544--3812588 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
3812534 TCCACTTCGG
*
3812544 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
3812562 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
3812580 GAGCCATCA
1 GAGCCATCA
3812589 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:3813120 original size:20 final size:20
Alignment explanation
Indices: 3813070--3813122 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
3813060 TAGTTTACTT
*
3813070 TCGCAACACGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
*
3813090 TCGCAACGCGAAAATGGCTA
1 TCGCAACGCGAAAATGACTA
*
3813110 TCGCAATGCGAAA
1 TCGCAACGCGAAA
3813123 TGAAAATCAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.40, C:0.25, G:0.21, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Done.