Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008341.1 Hibiscus syriacus cultivar Beakdansim tig00111067_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: 1248125
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 6
Found at i:986505 original size:20 final size:20
Alignment explanation
Indices: 986480--986518 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
986470 TAAACAGTCA
986480 ACATTTGCAAAACAACCAAC
1 ACATTTGCAAAACAACCAAC
*
986500 ACATTTTCAAAACAACCAA
1 ACATTTGCAAAACAACCAA
986519 TAACAACCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.28, G:0.03, T:0.18
Consensus pattern (20 bp):
ACATTTGCAAAACAACCAAC
Found at i:997666 original size:20 final size:20
Alignment explanation
Indices: 997602--997669 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
997592 CTGGACAATC
*
997602 AGTACCGATATTGTTCTTAT
1 AGTACCGATATTGTTCATAT
* *
997622 AATATCGATA-T-TTCATGAAT
1 AGTACCGATATTGTTCAT--AT
997642 AGTACCGATATTGTTCATAT
1 AGTACCGATATTGTTCATAT
*
997662 GGTACCGA
1 AGTACCGA
997670 AACCAAAGGT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
18 4 0.11
19 1 0.03
20 27 0.71
21 1 0.03
22 5 0.13
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (20 bp):
AGTACCGATATTGTTCATAT
Found at i:1005148 original size:9 final size:11
Alignment explanation
Indices: 1005123--1005148 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1005113 GTTGTAAAAA
1005123 GCGCGCCTGAG
1 GCGCGCCTGAG
1005134 GCGCGCCTGAG
1 GCGCGCCTGAG
1005145 GCGC
1 GCGC
1005149 AAAAGCGCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.38, G:0.46, T:0.08
Consensus pattern (11 bp):
GCGCGCCTGAG
Found at i:1005690 original size:21 final size:21
Alignment explanation
Indices: 1005666--1005705 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1005656 AAAATAATTA
* *
1005666 AATTTATTTATTTTGAAATCT
1 AATTTAATTATTCTGAAATCT
1005687 AATTTAATTATTCTGAAAT
1 AATTTAATTATTCTGAAAT
1005706 TTACATTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.53
Consensus pattern (21 bp):
AATTTAATTATTCTGAAATCT
Found at i:1006234 original size:57 final size:57
Alignment explanation
Indices: 1006122--1006256 Score: 166
Period size: 57 Copynumber: 2.4 Consensus size: 57
1006112 CCACAATTCG
* *
1006122 TGCGTATGTGTTTGTTCTTGTTTTTTTCTTTTCTTTTCTAAGTATACAGTTATTCGTAAT
1 TGCGTATGTGTCTGTTCTTG-TTTTTTCTTTCCTTTTCTAAGTATACAGTTATTCGT--T
* * * *
1006182 TTCGTATGTGTCTATTCTTG-TTTTT-TTTCCTTTTTTAAGTATGCAGTTATTCGTT
1 TGCGTATGTGTCTGTTCTTGTTTTTTCTTTCCTTTTCTAAGTATACAGTTATTCGTT
*
1006237 TGCTTATGTGTCTGTTCTTG
1 TGCGTATGTGTCTGTTCTTG
1006257 ATAATCACAG
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
55 18 0.27
57 26 0.39
58 5 0.08
60 17 0.26
ACGTcount: A:0.13, C:0.13, G:0.16, T:0.59
Consensus pattern (57 bp):
TGCGTATGTGTCTGTTCTTGTTTTTTCTTTCCTTTTCTAAGTATACAGTTATTCGTT
Found at i:1008304 original size:45 final size:45
Alignment explanation
Indices: 1008240--1008331 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
1008230 TTCATGAATC
1008240 CGCGCCTTTCATGCGCCTCACGCCTCAAGGCTCCAGGACACTTTG
1 CGCGCCTTTCATGCGCCTCACGCCTCAAGGCTCCAGGACACTTTG
1008285 CGCGCCTTTCATGCGCCTCACGCCTCAAGGCTCCAGGACACTTTG
1 CGCGCCTTTCATGCGCCTCACGCCTCAAGGCTCCAGGACACTTTG
1008330 CG
1 CG
1008332 TCTCGATGCG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.15, C:0.40, G:0.23, T:0.22
Consensus pattern (45 bp):
CGCGCCTTTCATGCGCCTCACGCCTCAAGGCTCCAGGACACTTTG
Found at i:1009833 original size:25 final size:25
Alignment explanation
Indices: 1009799--1009853 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
1009789 TCTAGGTCTA
1009799 CCTCTTGGTGCAACACGAAATTCTT
1 CCTCTTGGTGCAACACGAAATTCTT
1009824 CCTCTTGGTGCAACACGAAATTCTT
1 CCTCTTGGTGCAACACGAAATTCTT
1009849 CCTCT
1 CCTCT
1009854 CTTTGGGATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.22, C:0.31, G:0.15, T:0.33
Consensus pattern (25 bp):
CCTCTTGGTGCAACACGAAATTCTT
Found at i:1014732 original size:15 final size:16
Alignment explanation
Indices: 1014707--1014739 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1014697 GACATATATA
1014707 TTTTATATTTTCAATT
1 TTTTATATTTTCAATT
*
1014723 TTTTAT-TTTTTAATT
1 TTTTATATTTTCAATT
1014738 TT
1 TT
1014740 GTTTTGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTATATTTTCAATT
Found at i:1015515 original size:10 final size:11
Alignment explanation
Indices: 1015482--1015515 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 11
1015472 TAAACTGTTT
1015482 AAAAATTATTA
1 AAAAATTATTA
1015493 AAAATATTATTA
1 AAAA-ATTATTA
1015505 AAAAATT-TTA
1 AAAAATTATTA
1015515 A
1 A
1015516 CGGCAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 4 0.18
11 7 0.32
12 11 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAAATTATTA
Found at i:1017097 original size:41 final size:41
Alignment explanation
Indices: 1016946--1017112 Score: 171
Period size: 41 Copynumber: 4.1 Consensus size: 41
1016936 TTTTAAGCAA
* * *
1016946 AAACACCGCTAAATAC-CTGTACTTTAGTGCCAA-TTTTATAT
1 AAACACCGCTAAAGACTC-GTACTTTAGTG-GAATTTTTATAC
* *
1016987 AAACGCCGCTAAAGA-TTGTACTTTAGT-GACATTTTTATAC
1 AAACACCGCTAAAGACTCGTACTTTAGTGGA-ATTTTTATAC
* * *
1017027 AAACACCGCTATAGGCTCGTACTTTAGTGGAATATTTATAC
1 AAACACCGCTAAAGACTCGTACTTTAGTGGAATTTTTATAC
* * **
1017068 AAACACCACTAAAGACTCATACTTTAGTGGTGTTTTTATAC
1 AAACACCGCTAAAGACTCGTACTTTAGTGGAATTTTTATAC
1017109 AAAC
1 AAAC
1017113 GACGTAATAG
Statistics
Matches: 104, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
38 1 0.01
39 1 0.01
40 29 0.28
41 71 0.68
42 2 0.02
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.33
Consensus pattern (41 bp):
AAACACCGCTAAAGACTCGTACTTTAGTGGAATTTTTATAC
Found at i:1021200 original size:20 final size:20
Alignment explanation
Indices: 1021172--1021219 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
1021162 TAAATTGTGT
*
1021172 TCCATTACTTTTAAAGGTAA
1 TCCAATACTTTTAAAGGTAA
*
1021192 TCCAATACTTTTAAAGGTAG
1 TCCAATACTTTTAAAGGTAA
1021212 TCCAATAC
1 TCCAATAC
1021220 CTATGCTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.35
Consensus pattern (20 bp):
TCCAATACTTTTAAAGGTAA
Found at i:1025541 original size:27 final size:25
Alignment explanation
Indices: 1025487--1025541 Score: 58
Period size: 25 Copynumber: 2.1 Consensus size: 25
1025477 GTAACCATAA
*
1025487 TTCATAAACCAGTAAATTCAATTAT
1 TTCATAAACCAGTAAATTCAACTAT
*
1025512 TTCATAAATCATGTACAATTCATACT-T
1 TTCATAAACCA-GTA-AATTCA-ACTAT
1025539 TTC
1 TTC
1025542 GAAAACCGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
25 10 0.40
26 3 0.12
27 10 0.40
28 2 0.08
ACGTcount: A:0.38, C:0.18, G:0.04, T:0.40
Consensus pattern (25 bp):
TTCATAAACCAGTAAATTCAACTAT
Found at i:1026485 original size:20 final size:20
Alignment explanation
Indices: 1026457--1026504 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
1026447 TAAATTGTGT
*
1026457 TCCATTACTTTTAAAGGTAA
1 TCCAATACTTTTAAAGGTAA
*
1026477 TCCAATACTTTTAAAGGTAG
1 TCCAATACTTTTAAAGGTAA
1026497 TCCAATAC
1 TCCAATAC
1026505 CTATTCTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.35
Consensus pattern (20 bp):
TCCAATACTTTTAAAGGTAA
Found at i:1030773 original size:27 final size:25
Alignment explanation
Indices: 1030719--1030773 Score: 58
Period size: 27 Copynumber: 2.1 Consensus size: 25
1030709 GTAACCATAA
*
1030719 TTCATAAACCAGTAAATTCAATTAT
1 TTCATAAACCAGTAAATTCAACTAT
*
1030744 TTCATAAATCATGTAAAATTCATACT-T
1 TTCATAAACCA-GT-AAATTCA-ACTAT
1030771 TTC
1 TTC
1030774 GATGAAAACC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
25 10 0.40
26 2 0.08
27 11 0.44
28 2 0.08
ACGTcount: A:0.40, C:0.16, G:0.04, T:0.40
Consensus pattern (25 bp):
TTCATAAACCAGTAAATTCAACTAT
Found at i:1031996 original size:131 final size:132
Alignment explanation
Indices: 1031841--1032104 Score: 503
Period size: 131 Copynumber: 2.0 Consensus size: 132
1031831 ATTTTATTCC
1031841 ATTCATTTTAGAGCTCGAGGATATCCAATCATTCCTGAGCTTGGTGATATTCTTGGGTCATTTTC
1 ATTCATTTTAGAGCTCGAGGATATCCAATCATTCCTGAGCTTGGTGATATTCTTGGGTCATTTTC
1031906 ATTACAGGGGTATTTTGGTCATTTTACAGATTCAGTGTATTTTAATCATTTTCGTCCGTCCGATC
66 ATTACAGGGGTATTTTGGTCATTTTACAGATTCAGTGTATTTTAATCATTTTCGTCCGTCCGATC
1031971 TT
131 TT
1031973 ATTCA-TTTAGAGCTCGAGGATATCCAATCATTCCTGAGCTTGGTGATATTCTTGGGTCATTTTC
1 ATTCATTTTAGAGCTCGAGGATATCCAATCATTCCTGAGCTTGGTGATATTCTTGGGTCATTTTC
* *
1032037 ATTACAGTGGTATTTTGGTCATTTTACAGATTCAGTGTATTTTAATCATTTTCTTCCGTCCGATC
66 ATTACAGGGGTATTTTGGTCATTTTACAGATTCAGTGTATTTTAATCATTTTCGTCCGTCCGATC
1032102 TT
131 TT
1032104 A
1 A
1032105 CTATTAAATC
Statistics
Matches: 130, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
131 125 0.96
132 5 0.04
ACGTcount: A:0.22, C:0.17, G:0.18, T:0.43
Consensus pattern (132 bp):
ATTCATTTTAGAGCTCGAGGATATCCAATCATTCCTGAGCTTGGTGATATTCTTGGGTCATTTTC
ATTACAGGGGTATTTTGGTCATTTTACAGATTCAGTGTATTTTAATCATTTTCGTCCGTCCGATC
TT
Found at i:1046601 original size:137 final size:136
Alignment explanation
Indices: 1046350--1046622 Score: 501
Period size: 137 Copynumber: 2.0 Consensus size: 136
1046340 ATTTAAAAGT
*
1046350 AAATCAAACATCAGTAAATCTGTAATTTTGGAAAATCATGCTTTAAAACAGGTAAAACATATACA
1 AAATCAAACATCAGTAAATCTGTAATTTTGGAAAATCACGCTTTAAAACAGGTAAAACATATACA
1046415 CGTCACATAAGGAACACACTAAAGGATCCAGTTATTCTTCAAAGATACTTGGTATTTATCAGGTA
66 CGTCACATAAGGAACACACTAAAGGATCCAGTTATTCTTCAAAGATACTTGGTATTTATCAGGTA
*
1046480 GGGTAC
131 AGGTAC
*
1046486 AAATCAAAACATTAGTAAATCTGTAATTTTGGAAAATCACGCTTTAAAACAGGTAAAACATATAC
1 AAATC-AAACATCAGTAAATCTGTAATTTTGGAAAATCACGCTTTAAAACAGGTAAAACATATAC
*
1046551 ATGTCACATAAGGAACACACTAAAGGATCCAGTTATTCTTCAAAGATACTTGGTATTTATCAGGT
65 ACGTCACATAAGGAACACACTAAAGGATCCAGTTATTCTTCAAAGATACTTGGTATTTATCAGGT
1046616 AAGGTAC
130 AAGGTAC
1046623 TATAAAACTT
Statistics
Matches: 132, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
136 5 0.04
137 127 0.96
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.28
Consensus pattern (136 bp):
AAATCAAACATCAGTAAATCTGTAATTTTGGAAAATCACGCTTTAAAACAGGTAAAACATATACA
CGTCACATAAGGAACACACTAAAGGATCCAGTTATTCTTCAAAGATACTTGGTATTTATCAGGTA
AGGTAC
Found at i:1047570 original size:28 final size:28
Alignment explanation
Indices: 1047539--1047598 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
1047529 AGGGCTTAGA
*
1047539 GGTACTTTGGGTCATTTTACACTTGAAG
1 GGTACTTTGGGTCATTTTACACTTCAAG
* *
1047567 GGTATTTTTGGTCATTTTACACTTCAAG
1 GGTACTTTGGGTCATTTTACACTTCAAG
1047595 GGTA
1 GGTA
1047599 ATTCTATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.22, C:0.13, G:0.23, T:0.42
Consensus pattern (28 bp):
GGTACTTTGGGTCATTTTACACTTCAAG
Found at i:1048413 original size:22 final size:22
Alignment explanation
Indices: 1048388--1048433 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
1048378 TCAATTAACC
*
1048388 AATTGCAATCAATATTTAGCCA
1 AATTACAATCAATATTTAGCCA
1048410 AATTACAATCAATATTTAGCCA
1 AATTACAATCAATATTTAGCCA
1048432 AA
1 AA
1048434 ACCATCCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.30
Consensus pattern (22 bp):
AATTACAATCAATATTTAGCCA
Found at i:1052945 original size:19 final size:19
Alignment explanation
Indices: 1052920--1052969 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
1052910 CAACTATAGC
*
1052920 CAAAGTCAATGGGTTGGGT
1 CAAAGTCAATGGGTTGAGT
* *
1052939 TAAAGTCATTGGGTTGAGT
1 CAAAGTCAATGGGTTGAGT
1052958 CAAAGTCAATGG
1 CAAAGTCAATGG
1052970 TCGGTCAAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.30, C:0.10, G:0.32, T:0.28
Consensus pattern (19 bp):
CAAAGTCAATGGGTTGAGT
Found at i:1057825 original size:19 final size:19
Alignment explanation
Indices: 1057784--1057826 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
1057774 AACTATTGCC
* *
1057784 AAAGTCAACGAGTCGGGTC
1 AAAGTCAACGAGTCGAGTA
*
1057803 AAAGTCAACGGGTCGAGTA
1 AAAGTCAACGAGTCGAGTA
1057822 AAAGT
1 AAAGT
1057827 TAATGGGTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.37, C:0.16, G:0.30, T:0.16
Consensus pattern (19 bp):
AAAGTCAACGAGTCGAGTA
Found at i:1058403 original size:18 final size:18
Alignment explanation
Indices: 1058364--1058404 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1058354 AACTATTGCC
* *
1058364 AAAGTCACGGGTCGGGTC
1 AAAGTCACGGGTCGAGTA
1058382 AAAGTCACGGGTCGAGTA
1 AAAGTCACGGGTCGAGTA
1058400 AAAGT
1 AAAGT
1058405 TAATGGGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.32, C:0.17, G:0.34, T:0.17
Consensus pattern (18 bp):
AAAGTCACGGGTCGAGTA
Found at i:1063298 original size:235 final size:238
Alignment explanation
Indices: 1063001--1063478 Score: 660
Period size: 235 Copynumber: 2.0 Consensus size: 238
1062991 ATTAAGTTAT
*
1063001 TTTGAAAAATGAGAAAGCAATTTCCAAAGTTTCTCATTTAAATCTTTTCTGAAAATGAAATTTTT
1 TTTGAAAAATGAGAAAGCAATTTCCAAAGTTTCTCATTTAAATCTTTTCTGAAAATGAAATTTTC
* * *
1063066 GAAAAGTAAGAAAATGATTTCCAAAATTTCTTATTTAGTAAGTCCTTCGGGCCATCAGCAAGTCT
66 GAAAAGTAAGAAAATGATTTCCAAAATGTCTTACTTAGTAAGTCCTTCGGGCCATCAGCAACTCT
* * * *** * * *
1063131 TTTGAGCATGATGATTAAATCCTTTGGGTCATCTATAAGTCTTTTGAGCAAAATGATAAGTCATT
131 TTGGAGCATGACGATTAAATCATCCAGGTCACCTATAACTCTTTCGAGCAAAATGATAAGTCATT
* * * * *
1063196 TGGGCTATCTGTAATACCTTTGGGTAAGG-TG-TTTCACATGAA
196 TGGGCCATCCGTAAGACCTTCGAGT-AGGATGTTTTCACATGAA
* *
1063238 TTTGAAAAATGGGAAAGCGATTT-CAAAGTTT-TCCATTT-AATCTTTTCTGAAAATGAAATTTT
1 TTTGAAAAATGAGAAAGCAATTTCCAAAGTTTCT-CATTTAAATCTTTTCTGAAAATGAAATTTT
* * * *
1063300 CGAGAAGTAAGAAAATGATTTCCAAAGTGTCTTCCTTAGTAAGTCCTTCGGGCCATCAGTAACTC
65 CGAAAAGTAAGAAAATGATTTCCAAAATGTCTTACTTAGTAAGTCCTTCGGGCCATCAGCAACTC
* * *
1063365 TTTGGAGCATGACGATTAAATCATCCAGGTCACCTGTAACTCTTTCGAGCAAGATGATAAGTCCT
130 TTTGGAGCATGACGATTAAATCATCCAGGTCACCTATAACTCTTTCGAGCAAAATGATAAGTCAT
1063430 TTGGGCCATCCGTAAGACCTTCGAGTAGGATGTTTTCACATGAA
195 TTGGGCCATCCGTAAGACCTTCGAGTAGGATGTTTTCACATGAA
1063474 TTTGA
1 TTTGA
1063479 TTAAATCATC
Statistics
Matches: 211, Mismatches: 27, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
234 3 0.01
235 158 0.75
236 29 0.14
237 21 0.10
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (238 bp):
TTTGAAAAATGAGAAAGCAATTTCCAAAGTTTCTCATTTAAATCTTTTCTGAAAATGAAATTTTC
GAAAAGTAAGAAAATGATTTCCAAAATGTCTTACTTAGTAAGTCCTTCGGGCCATCAGCAACTCT
TTGGAGCATGACGATTAAATCATCCAGGTCACCTATAACTCTTTCGAGCAAAATGATAAGTCATT
TGGGCCATCCGTAAGACCTTCGAGTAGGATGTTTTCACATGAA
Found at i:1063536 original size:98 final size:99
Alignment explanation
Indices: 1063378--1063576 Score: 391
Period size: 98 Copynumber: 2.0 Consensus size: 99
1063368 GGAGCATGAC
1063378 GATTAAATCATCCAGGTCACCTGTAACTCTTTCGAGCAAGATGATAAGTCCTTTGGGCCATCCGT
1 GATTAAATCATCCAGGTCACCTGTAACTCTTTCGAGCAAGATGATAAGTCCTTTGGGCCATCCGT
1063443 AAGACCTTCGAGTAGGATGTTTTCACATGAATTT
66 AAGACCTTCGAGTAGGATGTTTTCACATGAATTT
1063477 GATTAAATCATCCAGGTCACCTGTAACTC-TTCGAGCAAGATGATAAGTCCTTTGGGCCATCCGT
1 GATTAAATCATCCAGGTCACCTGTAACTCTTTCGAGCAAGATGATAAGTCCTTTGGGCCATCCGT
1063541 AAGACCTTCGAGTAGGATGTTTTCACATGAATTT
66 AAGACCTTCGAGTAGGATGTTTTCACATGAATTT
1063575 GA
1 GA
1063577 AAAAATGGGA
Statistics
Matches: 100, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
98 71 0.71
99 29 0.29
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (99 bp):
GATTAAATCATCCAGGTCACCTGTAACTCTTTCGAGCAAGATGATAAGTCCTTTGGGCCATCCGT
AAGACCTTCGAGTAGGATGTTTTCACATGAATTT
Found at i:1063896 original size:237 final size:236
Alignment explanation
Indices: 1063491--1064245 Score: 1172
Period size: 237 Copynumber: 3.2 Consensus size: 236
1063481 AAATCATCCA
* * * *
1063491 GGTCACCTGTAACTC-TTCGAGCAAGATGATAAGTCCTTTGGGCCATCCGTAAGACCTTCGAGTA
1 GGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCATTCGGGCCATCCGTAAGACCTTCG-GTA
* *
1063555 GGATGTTTTCACATGAATTTGAAAAAATGGGAAAGCAATTTTCAAAGTTTCCCATTTAGTCTTTT
65 GGGTGTTTTCACATGAATTTG-AAAAATGGGAAAGCAATTTTCAAAGTTTCCCATTTAATCTTTT
* * *
1063620 CTGACAATAAAATTTTTGAAAAGTAAGAAAATTATTTCCAAAGTTTCATACTTAGTAAGTTCTTC
129 CTGAAAAGAAAATTTTTGAAAAGTAAGAAAATAATTTCCAAAGTTTCATACTTAGTAAGTTCTTC
*
1063685 GGGCCATCAGCAAGTTTTTCGAGAATGATGATTAAATCCTTTG
194 GGGCCATCAGCAAGTCTTTCGAGAATGATGATTAAATCCTTTG
* * * * *
1063728 GGTTATTTGTAAGTCTTTCGAGTAAGATGATAAGTCATTCAGGCCATCTGTAAGACCTTCAGGTA
1 GGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCATTCGGGCCATCCGTAAGACCTTC-GGTA
*
1063793 GGGTGTTTTCACATGAATTTGAAAAATGGGAAAGCGATTTTCAAAGTTTCCCATTTAATCTTTTC
65 GGGTGTTTTCACATGAATTTGAAAAATGGGAAAGCAATTTTCAAAGTTTCCCATTTAATCTTTTC
* *
1063858 TGAAAAGAAAATTTTTGAAAAGTAAGAAAATGATTTCCAAAGTTTCGTACTTAGTAAGTTCTTCG
130 TGAAAAGAAAATTTTTGAAAAGTAAGAAAATAATTTCCAAAGTTTCATACTTAGTAAGTTCTTCG
1063923 GGCCATCAGCAAGTCTTTCGAGAATGATGATTAAATCCTTTG
195 GGCCATCAGCAAGTCTTTCGAGAATGATGATTAAATCCTTTG
*
1063965 GGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCGTAAGACCTTCGGGTA
1 GGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCATTCGGGCCATCCGTAAGACCTTC-GGTA
* *
1064030 TGGTGTTTTCACATGAATTTGAAAAATGGGAAAGCAATTTTCAAAGTTTCCCATTTAATCTTTTA
65 GGGTGTTTTCACATGAATTTGAAAAATGGGAAAGCAATTTTCAAAGTTTCCCATTTAATCTTTTC
* * * *
1064095 TGAAAATG-AAATTTTTGAAAAGTAAGAAAACAATTTCCAAAGTTTCTTACTTAGTATGTCCTTC
130 TGAAAA-GAAAATTTTTGAAAAGTAAGAAAATAATTTCCAAAGTTTCATACTTAGTAAGTTCTTC
* * * * *
1064159 GGGCCATTAGTAAGTCTTTCAAGCATGATGATTAAATCCTTCG
194 GGGCCATCAGCAAGTCTTTCGAGAATGATGATTAAATCCTTTG
*
1064202 GGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCATTCGGGC
1 GGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCATTCGGGC
1064246 AGGATGTTTT
Statistics
Matches: 476, Mismatches: 39, Indels: 6
0.91 0.07 0.01
Matches are distributed among these distances:
237 412 0.87
238 63 0.13
239 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (236 bp):
GGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCATTCGGGCCATCCGTAAGACCTTCGGTAG
GGTGTTTTCACATGAATTTGAAAAATGGGAAAGCAATTTTCAAAGTTTCCCATTTAATCTTTTCT
GAAAAGAAAATTTTTGAAAAGTAAGAAAATAATTTCCAAAGTTTCATACTTAGTAAGTTCTTCGG
GCCATCAGCAAGTCTTTCGAGAATGATGATTAAATCCTTTG
Found at i:1064018 original size:41 final size:42
Alignment explanation
Indices: 1063912--1064018 Score: 128
Period size: 42 Copynumber: 2.6 Consensus size: 42
1063902 TCGTACTTAG
* *
1063912 TAAGTTCTTCGGGCCATCAGCAAGTCTTTCGAGAATGATGAT
1 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGAATGATGAT
* * * *
1063954 TAAATCCTTTGGGTCATCTGTAAGTCTTTCGAGCAA-GATGA-
1 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAG-AATGATGAT
*
1063995 TAAGTCCTTCGGGCCATCCGTAAG
1 TAAGTCCTTCGGGCCATCAGTAAG
1064019 ACCTTCGGGT
Statistics
Matches: 54, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
41 20 0.37
42 32 0.59
43 2 0.04
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (42 bp):
TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGAATGATGAT
Found at i:1064217 original size:42 final size:42
Alignment explanation
Indices: 1064153--1064245 Score: 109
Period size: 42 Copynumber: 2.2 Consensus size: 42
1064143 ACTTAGTATG
*
1064153 TCCTTCGGGCCATTAGTAAGTCTTTCAAGCATGATGATTAAA
1 TCCTTCGGGCCATTAGTAAGTCTTTCAAGCAAGATGATTAAA
* * * *
1064195 TCCTTCGGGTCATCT-GTCAGTCTTTCGAGCAAGATGA-TAAG
1 TCCTTCGGGCCAT-TAGTAAGTCTTTCAAGCAAGATGATTAAA
*
1064236 TCATTCGGGC
1 TCCTTCGGGC
1064246 AGGATGTTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
41 11 0.26
42 31 0.72
43 1 0.02
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.32
Consensus pattern (42 bp):
TCCTTCGGGCCATTAGTAAGTCTTTCAAGCAAGATGATTAAA
Found at i:1064687 original size:239 final size:235
Alignment explanation
Indices: 1064152--1064913 Score: 879
Period size: 231 Copynumber: 3.2 Consensus size: 235
1064142 TACTTAGTAT
*
1064152 GTCCTTCGGGCCATTAGTAAGTCTTTCAAGCATGATGATTAAATCCTTCGGGTCATCTGTCAGTC
1 GTCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTCGGGTCATCTGTCAGTC
* * * *
1064217 TTTCGAGCAAGATGATAAGTCATTCGGGCAGGATGTTTTCGCATGATTTATGAAAAATGAGAAAA
66 TTTCGAGCAAGATGATAAGTCATTCGGGTAGGATGTTTTCACATGATTT-TAAAAAATGAGAAAG
* * *
1064282 CGATTTCCAAAGTTTCTCAATTAATATTTTC--AAAATAAAATCTTTGAAAA-TAA-AATTGATT
130 CAATTTCCAAAGTTTCTCAATTAATATTTTCAGAAAATGAAATCTTTGAAAAGTAAGAA-AGATT
* * *
1064343 TCCAAAG-TTTCT-CCTAGTAAACTATTTCCAAAATTGGTAA
194 TCCAAAGTTTTTTACCTAGTAAACTTTTTCAAAAATTGGTAA
* * **
1064383 GTCCTTTGGGCCATCAGTAAGTCTTTCAATCATGATGATTAAATCCTTCCAGTCATCTGTCAGTC
1 GTCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTCGGGTCATCTGTCAGTC
* * *
1064448 TTTCGAGAAATATGATAAGTCATTCGGGTAGGATATTTTCACATGATTTTCAAAAAATGAGAAAG
66 TTTCGAGCAAGATGATAAGTCATTCGGGTAGGATGTTTTCACATGATTTT-AAAAAATGAGAAAG
* *
1064513 CAATTTCCAAAATTTCTCAATAAATATTTTCAGAAAATGAAATCTTTGAAAAAGTAAGAAAGAAA
130 CAATTTCCAAAGTTTCTCAATTAATATTTTCAGAAAATGAAATCTTTG-AAAAGTAAGAAAG--A
*
1064578 TTTCCAAAGTTTTTTACCTAGTAAACTTTTTCAAAAATTTGTAA
192 TTTCCAAAGTTTTTTACCTAGTAAACTTTTTCAAAAATTGGTAA
* ** *
1064622 GTCCTTCGAGCCATCAGTAAGTCTTTTGAGCATGATAATTAAATCCTTCGGGTCATCTGTCAGTC
1 GTCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTCGGGTCATCTGTCAGTC
* * * * * *
1064687 TTCCGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGATGCTTTCATACGATGTTTGAGAAAA
66 TTTCGAGCAAGATGATAAGTCATTCGGG-------TAGGATGTTTTCACATGAT-TTT-A-AAAA
* * * * * *
1064752 ATGAGAAAAGCAATTTTCAAAGTTTTTCATTTAATATTTTCAGAAAATGAAATTTTTTAAAAGGA
121 ATGAG-AAAGCAATTTCCAAAGTTTCTCAATTAATATTTTCAGAAAATGAAATCTTTGAAAAGTA
* * * *
1064817 AGAAAGTGATTTCCAAAGTTTCTTACCAAGTAAACTATTTCCCAAAAATTGGAAA
185 AGAAA--GATTTCCAAAGTTTTTTACCTAGTAAACT-TTT-TCAAAAATTGGTAA
* * * **
1064872 ATCCTTCGGGCAATTAGTAAGTCTTTTGAGCATGATGATTAA
1 GTCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGATGATTAA
1064914 GTCATTCGAG
Statistics
Matches: 450, Mismatches: 57, Indels: 29
0.84 0.11 0.05
Matches are distributed among these distances:
230 1 0.00
231 144 0.32
233 14 0.03
234 4 0.01
235 4 0.01
236 2 0.00
237 10 0.02
238 4 0.01
239 106 0.24
246 14 0.03
247 4 0.01
248 46 0.10
249 48 0.11
250 49 0.11
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (235 bp):
GTCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTCGGGTCATCTGTCAGTC
TTTCGAGCAAGATGATAAGTCATTCGGGTAGGATGTTTTCACATGATTTTAAAAAATGAGAAAGC
AATTTCCAAAGTTTCTCAATTAATATTTTCAGAAAATGAAATCTTTGAAAAGTAAGAAAGATTTC
CAAAGTTTTTTACCTAGTAAACTTTTTCAAAAATTGGTAA
Found at i:1064720 original size:41 final size:42
Alignment explanation
Indices: 1064619--1064725 Score: 117
Period size: 42 Copynumber: 2.6 Consensus size: 42
1064609 CAAAAATTTG
* * ** *
1064619 TAAGTCCTTCGAGCCATCAGTAAGTCTTTTGAGCATGATAAT
1 TAAGTCCTTCGGGCCATCTGTAAGTCTTCCGAGCAAGATAAT
* * * *
1064661 TAAATCCTTCGGGTCATCTGTCAGTCTTCCGAGCAAGATGA-
1 TAAGTCCTTCGGGCCATCTGTAAGTCTTCCGAGCAAGATAAT
*
1064702 TAAGTCCTTCGGGCCATCTATAAG
1 TAAGTCCTTCGGGCCATCTGTAAG
1064726 ATGCTTTCAT
Statistics
Matches: 52, Mismatches: 13, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
41 20 0.38
42 32 0.62
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (42 bp):
TAAGTCCTTCGGGCCATCTGTAAGTCTTCCGAGCAAGATAAT
Found at i:1065066 original size:3 final size:3
Alignment explanation
Indices: 1065058--1065105 Score: 69
Period size: 3 Copynumber: 15.7 Consensus size: 3
1065048 TTTGTTTGGG
* *
1065058 TTA TTA TTA TTA TTA ATA TTA TTA TTA TTTA ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
1065104 TT
1 TT
1065106 TTGTTATTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1065555 original size:36 final size:36
Alignment explanation
Indices: 1065501--1065594 Score: 125
Period size: 36 Copynumber: 2.6 Consensus size: 36
1065491 GTCCTACTAG
*
1065501 GATTGAAACTCTCAAAAATAGGATAGAATTCTGCTAT
1 GATTTAAACTCT-AAAAATAGGATAGAATTCTGCTAT
* *
1065538 GATTTCAACTCTAAAAATAGGATAGAATTTTGCTAT
1 GATTTAAACTCTAAAAATAGGATAGAATTCTGCTAT
* *
1065574 GTTTTAAACTCCTAAAGATAG
1 GATTTAAACT-CTAAAAATAG
1065595 ATCCACAAGC
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
36 31 0.62
37 19 0.38
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (36 bp):
GATTTAAACTCTAAAAATAGGATAGAATTCTGCTAT
Found at i:1069443 original size:11 final size:10
Alignment explanation
Indices: 1069426--1069478 Score: 52
Period size: 11 Copynumber: 4.9 Consensus size: 10
1069416 ACAAAAGGGC
1069426 AAAAAGAAAA
1 AAAAAGAAAA
1069436 AGAAAAGAAGCAA
1 A-AAAAGAA--AA
*
1069449 AAAAGGAAAA
1 AAAAAGAAAA
*
1069459 AAACAAGAACA
1 AAA-AAGAAAA
1069470 AAAAAGAAA
1 AAAAAGAAA
1069479 GAACAAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
10 11 0.31
11 15 0.43
12 6 0.17
13 3 0.09
ACGTcount: A:0.79, C:0.06, G:0.15, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:1069449 original size:21 final size:22
Alignment explanation
Indices: 1069426--1069478 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 22
1069416 ACAAAAGGGC
1069426 AAAAAGAAAAAGAA-AAGAAGCA
1 AAAAAGAAAAA-AACAAGAAGCA
1069448 AAAAAGGAAAAAAACAAGAA-CA
1 AAAAA-GAAAAAAACAAGAAGCA
1069470 AAAAAGAAA
1 AAAAAGAAA
1069479 GAACAAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
21 4 0.14
22 14 0.48
23 11 0.38
ACGTcount: A:0.79, C:0.06, G:0.15, T:0.00
Consensus pattern (22 bp):
AAAAAGAAAAAAACAAGAAGCA
Found at i:1069483 original size:20 final size:22
Alignment explanation
Indices: 1069426--1069499 Score: 73
Period size: 22 Copynumber: 3.4 Consensus size: 22
1069416 ACAAAAGGGC
*
1069426 AAAAAGAAAAAGAA-AAGAAGCA
1 AAAAAGGAAAAGAACAAGAA-CA
*
1069448 AAAAAGGAAAAAAACAAGAACA
1 AAAAAGGAAAAGAACAAGAACA
* *
1069470 AAAAA-G-AAAGAACAAAAATA
1 AAAAAGGAAAAGAACAAGAACA
1069490 AAAAATGGAA
1 AAAAA-GGAA
1069500 CAAAAGCACA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
20 16 0.37
21 1 0.02
22 20 0.47
23 6 0.14
ACGTcount: A:0.77, C:0.05, G:0.15, T:0.03
Consensus pattern (22 bp):
AAAAAGGAAAAGAACAAGAACA
Found at i:1071020 original size:36 final size:36
Alignment explanation
Indices: 1070977--1071076 Score: 146
Period size: 37 Copynumber: 2.8 Consensus size: 36
1070967 CTCACCATTG
1070977 TCTCTTGAGACAGTTTCCCTTGAAACAAACTTTGTC
1 TCTCTTGAGACAGTTTCCCTTGAAACAAACTTTGTC
* *
1071013 TCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTTTC
1 TCTCTTGAGACAGTTTCCCTTGAAAC-AAACTTTGTC
* * *
1071050 TCCCTTGAGTCAGTTTCTCTTGAAACA
1 TCTCTTGAGACAGTTTCCCTTGAAACA
1071077 TAAACATTGA
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
36 27 0.47
37 31 0.53
ACGTcount: A:0.25, C:0.24, G:0.13, T:0.38
Consensus pattern (36 bp):
TCTCTTGAGACAGTTTCCCTTGAAACAAACTTTGTC
Found at i:1071139 original size:36 final size:37
Alignment explanation
Indices: 1071092--1071178 Score: 104
Period size: 37 Copynumber: 2.4 Consensus size: 37
1071082 ATTGAAAACA
** * *
1071092 TTTCCCTTGAAA-ATGAGTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAAGTTTGTCTCCCTTGAGACAG
* *
1071128 TTTCCCTTGAAACAAAATTTTTTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAAGTTTGTCTCCCTTGAGACAG
*
1071165 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
1071179 TAAACATTGG
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
36 12 0.28
37 31 0.72
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAAGTTTGTCTCCCTTGAGACAG
Found at i:1071166 original size:102 final size:101
Alignment explanation
Indices: 1070990--1071381 Score: 624
Period size: 102 Copynumber: 3.9 Consensus size: 101
1070980 CTTGAGACAG
** * *
1070990 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTTTCTCCCT
1 TTTCCCTTGAAATGAA-TTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
*
1071055 TGAGTCAGTTTCTCTTGAAACATAAACATTGAAAACA
65 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* *
1071092 TTTCCCTTGAAAATGAGTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTTTCTCCCT
1 TTTCCCTTG-AAATGAATTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
*
1071157 TGAGACAGTTTCTCTTGAAACATAAACATTGGAAACA
65 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
1071194 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
1 TTTCCCTTGAAATGAA-TTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
** *
1071259 TTTGACAGTTTCTCCTGAAACATAAACATTGAAAACA
65 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
*
1071296 TTTCCCTTGAAATGAATTTCGTCTCTCTTGAGATAATTTCCCTTGAAAC-AAATTTTGTCTCCCT
1 TTTCCCTTGAAATGAATTT-GTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
*
1071360 TGCGACAGTTTCTCTTGAAACA
65 TGAGACAGTTTCTCTTGAAACA
1071382 CAAAACCTTT
Statistics
Matches: 271, Mismatches: 16, Indels: 7
0.92 0.05 0.02
Matches are distributed among these distances:
101 43 0.16
102 224 0.83
103 4 0.01
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (101 bp):
TTTCCCTTGAAATGAATTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTT
GAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:1071269 original size:37 final size:37
Alignment explanation
Indices: 1071194--1071280 Score: 97
Period size: 37 Copynumber: 2.4 Consensus size: 37
1071184 ATTGGAAACA
** * *
1071194 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
**
1071230 TTTCCCTTGAAACAAAATTTTGTCTCCCTTTTGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1071267 TTTCTCC-TGAAACA
1 TTTC-CCTTGAAACA
1071281 TAAACATTGA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
36 12 0.28
37 29 0.67
38 2 0.05
ACGTcount: A:0.24, C:0.22, G:0.13, T:0.41
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:1071340 original size:204 final size:203
Alignment explanation
Indices: 1070990--1071448 Score: 659
Period size: 204 Copynumber: 2.2 Consensus size: 203
1070980 CTTGAGACAG
*
1070990 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTTTCTCCCT
1 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
* * *
1071055 TGAGTCAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAATGAGTTTGTCTCTCT
66 TGAGACAGTTTCTCCTGAAACATAAACATTGAAAACATTTCCCTTGAAAATGAATTTGTCTCTCT
* *
1071120 TGAGATAGTTTCCCTTGAAACAAAATTTTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
131 TGAGATAATTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
1071185 TTGGAAACA
195 TTGGAAACA
** * *
1071194 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
1 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
**
1071259 TTTGACAGTTTCTCCTGAAACATAAACATTGAAAACATTTCCCTTG-AAATGAATTTCGTCTCTC
66 TGAGACAGTTTCTCCTGAAACATAAACATTGAAAACATTTCCCTTGAAAATGAATTT-GTCTCTC
* *
1071323 TTGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTTGCGACAGTTTCTCTTGAAACACAAAAC
130 TTGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA-TAAAC
* * ***
1071388 CTTTGAGATTG
194 ATTGGA-AACA
* * * * *
1071399 TTTCCCTCGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACA
1 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
1071449 CAAAATCTTT
Statistics
Matches: 226, Mismatches: 26, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
203 44 0.19
204 138 0.61
205 44 0.19
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (203 bp):
TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
TGAGACAGTTTCTCCTGAAACATAAACATTGAAAACATTTCCCTTGAAAATGAATTTGTCTCTCT
TGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACAT
TGGAAACA
Found at i:1071342 original size:36 final size:36
Alignment explanation
Indices: 1071295--1071381 Score: 102
Period size: 36 Copynumber: 2.4 Consensus size: 36
1071285 CATTGAAAAC
** * *
1071295 ATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGATA
1 ATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACA
* *
1071331 ATTTCCCTTGAAACAAATTTTGTCTCCCTTGCGACA
1 ATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACA
* *
1071367 GTTTCTCTTGAAACA
1 ATTTCCCTTGAAACA
1071382 CAAAACCTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.25, C:0.23, G:0.13, T:0.39
Consensus pattern (36 bp):
ATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACA
Found at i:1071472 original size:67 final size:67
Alignment explanation
Indices: 1071323--1071481 Score: 223
Period size: 67 Copynumber: 2.4 Consensus size: 67
1071313 TTCGTCTCTC
** * *
1071323 TTGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTTGCGACAGTTTCTCTTGAAACACAAAAC
1 TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAAC
1071388 CT
66 CT
* *
1071390 TTGAGATTGTTTCCCTCGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAAT
1 TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAAC
1071455 CT
66 CT
*
1071457 TTGA-ATT-TATCTCCCTTAAAACAAA
1 TTGAGATTGT-T-TCCCTTGAAACAAA
1071482 ATTCCGTTTC
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
65 1 0.01
66 4 0.05
67 77 0.94
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.35
Consensus pattern (67 bp):
TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAAC
CT
Found at i:1072288 original size:109 final size:108
Alignment explanation
Indices: 1072055--1072396 Score: 421
Period size: 109 Copynumber: 3.2 Consensus size: 108
1072045 AGCTAGAGTC
* * * *
1072055 AGTTCAACTTCACAACGAAGGGACGGTGGTTGCCAAC-AACAATTTCCCAATTTCGGAACCGA--
1 AGTTCAACTTCACAACGAAGGGACGCTGGTTGTCAACGAACAACTTCCCAATTTCAGAACCGATT
*
1072117 TTCACTCCACGACGGAGG-TATCGTGCTACCCG-GACAA-ACA
66 TTAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACACA
*
1072157 AGTTCAACTTCACAACGAAGGGACAGCTGGTTGTCAACGAACAACTTCCCAATTCCAGAACCGAT
1 AGTTCAACTTCACAACGAAGGGAC-GCTGGTTGTCAACGAACAACTTCCCAATTTCAGAACCGAT
* *
1072222 TTTAACTCCACTACGGAGGATATCGTGCTACCCGAGAAAACACA
65 TTTAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACACA
* * * ** * **
1072266 AGTCCAACTTCACAACGAAGGGACGGCTGGTTGTCAATGAATAACTTTTCAGTTTCA-TCCGCGA
1 AGTTCAACTTCACAACGAAGGGAC-GCTGGTTGTCAACGAACAACTTCCCAATTTCAGAAC-CGA
* * *
1072330 TTTCAACTCCACGACGGAGGA-ATCGTGCCACTCGAGACAACACA
64 TTTTAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACACA
*
1072374 AGTTCAACTTCACAATGAAGGGA
1 AGTTCAACTTCACAACGAAGGGA
1072397 GAGCCAATTT
Statistics
Matches: 207, Mismatches: 25, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
102 24 0.12
103 11 0.05
104 22 0.11
106 16 0.08
107 14 0.07
108 46 0.22
109 74 0.36
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.21
Consensus pattern (108 bp):
AGTTCAACTTCACAACGAAGGGACGCTGGTTGTCAACGAACAACTTCCCAATTTCAGAACCGATT
TTAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACACA
Found at i:1072576 original size:98 final size:102
Alignment explanation
Indices: 1072396--1072636 Score: 307
Period size: 98 Copynumber: 2.4 Consensus size: 102
1072386 CAATGAAGGG
1072396 AGAGCCAATTTCAACTTCA-AGCGAAGGATATTGGACTCGAGACAACACAAGTCAACTTCACAAC
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTCAACTTCACAAC
* *
1072460 GAGGGACAACTGATTGTCAAC-AA-GATTT-C-GTT-C
66 GAGGGA-AACTGACTGTCAACAAACAATTTCCGGTTCC
* * * *
1072493 AGAGTCAATTTCAACTTCACAACGAAGGATATTAGACTCGAGACAGCACAAGCTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAG-TCAACTTCACAA
**
1072558 CGAAGGG-GGCTGACTGTCAACAAACAATTTCCCGGTTCC
65 CG-AGGGAAACTGACTGTCAACAAACAATTT-CCGGTTCC
* *
1072597 AGAACCAATTTCAACTTCACAGCGGAGGATATTGGACTCG
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCG
1072637 GAACAATATT
Statistics
Matches: 122, Mismatches: 13, Indels: 11
0.84 0.09 0.08
Matches are distributed among these distances:
97 18 0.15
98 40 0.33
99 16 0.13
100 8 0.07
102 1 0.01
103 3 0.02
104 36 0.30
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (102 bp):
AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTCAACTTCACAAC
GAGGGAAACTGACTGTCAACAAACAATTTCCGGTTCC
Found at i:1073187 original size:37 final size:36
Alignment explanation
Indices: 1073093--1073189 Score: 115
Period size: 36 Copynumber: 2.6 Consensus size: 36
1073083 CGCCTACTAG
1073093 GATTCAAACT-CTCAAAAATAGGATAGAATTCTGCTAC
1 GATT-AAACTCCT-AAAAATAGGATAGAATTCTGCTAC
* * *
1073130 GATTCAACTCCTAAAAATAGGATAGAATTTTGCTAT
1 GATTAAACTCCTAAAAATAGGATAGAATTCTGCTAC
* *
1073166 GTTTTAAACTCCTAAAGATAGGAT
1 G-ATTAAACTCCTAAAAATAGGAT
1073190 CCACAAGCAC
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
36 27 0.52
37 25 0.48
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.31
Consensus pattern (36 bp):
GATTAAACTCCTAAAAATAGGATAGAATTCTGCTAC
Found at i:1073875 original size:16 final size:16
Alignment explanation
Indices: 1073854--1073897 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
1073844 TGTTTTCATG
1073854 TATTATATTATTACAT
1 TATTATATTATTACAT
*
1073870 TATTATTATT-TTACTT
1 TATTA-TATTATTACAT
*
1073886 TATTAAATTATT
1 TATTATATTATT
1073898 TTTTCGTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 3 0.12
16 17 0.71
17 4 0.17
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (16 bp):
TATTATATTATTACAT
Found at i:1073907 original size:19 final size:21
Alignment explanation
Indices: 1073871--1073919 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
1073861 TTATTACATT
*
1073871 ATTATTATTTTACTTTATTAA
1 ATTATTATTTTACGTTATTAA
1073892 ATTATT-TTTT-CGTTATTATA
1 ATTATTATTTTACGTTATTA-A
*
1073912 TTTATTAT
1 ATTATTAT
1073920 ATATATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 7 0.29
20 10 0.42
21 7 0.29
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (21 bp):
ATTATTATTTTACGTTATTAA
Found at i:1076787 original size:16 final size:16
Alignment explanation
Indices: 1076763--1076802 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
1076753 TTATCCCCCT
* *
1076763 TTTTTTTCCCGTCGTC
1 TTTTCTTCCCATCGTC
1076779 TTTTCTTCCCATCGTC
1 TTTTCTTCCCATCGTC
*
1076795 TCTTCTTC
1 TTTTCTTC
1076803 TTCTTTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.03, C:0.35, G:0.07, T:0.55
Consensus pattern (16 bp):
TTTTCTTCCCATCGTC
Found at i:1077278 original size:23 final size:23
Alignment explanation
Indices: 1077252--1077331 Score: 115
Period size: 23 Copynumber: 3.5 Consensus size: 23
1077242 TTGGTTCCTG
*
1077252 TTGGTCTTCCAGGTTTGGGTGTA
1 TTGGGCTTCCAGGTTTGGGTGTA
*
1077275 TTGGGCTTCCGGGTTTGGGTGTA
1 TTGGGCTTCCAGGTTTGGGTGTA
** *
1077298 TTGGGCTTCTGGGTTTAGGTGTA
1 TTGGGCTTCCAGGTTTGGGTGTA
1077321 TTGGGCTTCCA
1 TTGGGCTTCCA
1077332 TGTTAACTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.07, C:0.14, G:0.38, T:0.41
Consensus pattern (23 bp):
TTGGGCTTCCAGGTTTGGGTGTA
Found at i:1077383 original size:3 final size:3
Alignment explanation
Indices: 1077377--1077426 Score: 75
Period size: 3 Copynumber: 17.0 Consensus size: 3
1077367 AATTATTATT
* *
1077377 TAA TAA TAA TAA TAA TAA TAA TAG TAT TAA TAA TAA TAA TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1077424 TAA
1 TAA
1077427 GGATATATGG
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1079734 original size:78 final size:80
Alignment explanation
Indices: 1079580--1079727 Score: 205
Period size: 78 Copynumber: 1.9 Consensus size: 80
1079570 ATATAGTAAG
*
1079580 TAAACATTAAAAGAATGTAATTTAGATTATAACTCTTTTAATTGATATATAATTCGGAATAATTA
1 TAAACATTAAAAGAATGTAATTCAGATTATAACTCTTTTAATTGATATATAATTCGGAATAATTA
1079645 AATAACTTTTTAAAA
66 AATAACTTTTTAAAA
* * * *
1079660 TAAACATT-AAAGATTGTAATTCAGATTATAAGTC-TTTAA-TGTATATTTAATT-TGAATTAAT
1 TAAACATTAAAAGAATGTAATTCAGATTATAACTCTTTTAATTG-ATATATAATTCGGAA-TAAT
1079721 TAAATAA
64 TAAATAA
1079728 TATTTTATTT
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
77 5 0.08
78 25 0.41
79 23 0.38
80 8 0.13
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.41
Consensus pattern (80 bp):
TAAACATTAAAAGAATGTAATTCAGATTATAACTCTTTTAATTGATATATAATTCGGAATAATTA
AATAACTTTTTAAAA
Found at i:1081504 original size:49 final size:49
Alignment explanation
Indices: 1081450--1081548 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
1081440 AAATAGCGGG
1081450 AGTAATTTGTAAATAAAGACCTATTTATAAATTTTAATTCGGTAAATTT
1 AGTAATTTGTAAATAAAGACCTATTTATAAATTTTAATTCGGTAAATTT
1081499 AGTAATTTGTAAATAAAGACCTATTTATAAATTTTAATTCGGTAAATTT
1 AGTAATTTGTAAATAAAGACCTATTTATAAATTTTAATTCGGTAAATTT
1081548 A
1 A
1081549 CTTACTTTAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.42
Consensus pattern (49 bp):
AGTAATTTGTAAATAAAGACCTATTTATAAATTTTAATTCGGTAAATTT
Found at i:1086610 original size:77 final size:79
Alignment explanation
Indices: 1086462--1086614 Score: 179
Period size: 77 Copynumber: 2.0 Consensus size: 79
1086452 ATACAAATGA
* * * *
1086462 TTTTAATTAAACATTAAAAGAATGTAATTTAGATTACAACTCTTTTAATTGATATATAATTCAGA
1 TTTTAAATAAACATTAAAAGAATATAATTCAGACTACAACTCTTTTAATTGATATATAATTCAGA
1086527 ATAATTAAATAAGT
66 ATAATTAAATAAGT
* * * * *
1086541 TTTTAAATAAACATT-AAAGATTATAATTCAGACTATAAGTC-TTTAA-TGTATATTTAATT-TG
1 TTTTAAATAAACATTAAAAGAATATAATTCAGACTACAACTCTTTTAATTG-ATATATAATTCAG
1086602 AATTAATTAAATA
65 AA-TAATTAAATA
1086615 CTATTTTATT
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
76 5 0.08
77 24 0.38
78 20 0.32
79 14 0.22
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.42
Consensus pattern (79 bp):
TTTTAAATAAACATTAAAAGAATATAATTCAGACTACAACTCTTTTAATTGATATATAATTCAGA
ATAATTAAATAAGT
Found at i:1087882 original size:60 final size:60
Alignment explanation
Indices: 1087809--1087946 Score: 188
Period size: 60 Copynumber: 2.3 Consensus size: 60
1087799 ACTTAAGAGT
* *
1087809 AAAG-TACACAAATGGTCCCCCGACTATAGGGTGTTACTTTGTTGAGTCACTTGACTATTA
1 AAAGTTACA-AAATGGTCCCCCAACTATAGGGTGTTACTTTGTTGAGTCACTTGAATATTA
* * * * *
1087869 AAAGTTACAAAATGGTCCCCTAACTATAGTGTGTTGCTTTGTTTAGTCCCTTGAATATTA
1 AAAGTTACAAAATGGTCCCCCAACTATAGGGTGTTACTTTGTTGAGTCACTTGAATATTA
1087929 AAAGTTACAAAAATGGTC
1 AAAGTTAC-AAAATGGTC
1087947 ATCTGACTAT
Statistics
Matches: 69, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
60 56 0.81
61 13 0.19
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Consensus pattern (60 bp):
AAAGTTACAAAATGGTCCCCCAACTATAGGGTGTTACTTTGTTGAGTCACTTGAATATTA
Found at i:1088045 original size:84 final size:84
Alignment explanation
Indices: 1087906--1088161 Score: 388
Period size: 84 Copynumber: 3.0 Consensus size: 84
1087896 AGTGTGTTGC
* * * *
1087906 TTTGTTTAGTCCCTTGAATATTAAAAGTTACAAAAATGGTCATCTGACTATTTATATGTTTCAAA
1 TTTGTTGAGTCTCTCGACTATTAAAAGTTAC-AAAATGGTCATCTGACTATTTATATGTTTCAAA
* *
1087971 CTCTTTCTTTTTCGTTAAAA
65 CTCGTCCTTTTTCGTTAAAA
*
1087991 TTTGTTGAGTCTCTCGACTATTAAAAGTTACAAAATGGTCGTCTGACTATTTATATGTTTCAAAC
1 TTTGTTGAGTCTCTCGACTATTAAAAGTTACAAAATGGTCATCTGACTATTTATATGTTTCAAAC
1088056 TCGTCCTTTTTCGTTAAAA
66 TCGTCCTTTTTCGTTAAAA
* * *
1088075 TTTATTGAGTCTCTCGACTATTAAAAATTACAAAATGGTCATATGACTATTTATATGTTTCAAAC
1 TTTGTTGAGTCTCTCGACTATTAAAAGTTACAAAATGGTCATCTGACTATTTATATGTTTCAAAC
* *
1088140 TCGTCATTTTTTGTT-AAA
66 TCGTCCTTTTTCGTTAAAA
1088158 TTTG
1 TTTG
1088162 ATGACAATCT
Statistics
Matches: 157, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
83 6 0.04
84 124 0.79
85 27 0.17
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (84 bp):
TTTGTTGAGTCTCTCGACTATTAAAAGTTACAAAATGGTCATCTGACTATTTATATGTTTCAAAC
TCGTCCTTTTTCGTTAAAA
Found at i:1090660 original size:17 final size:18
Alignment explanation
Indices: 1090623--1090660 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
1090613 TAACATCTAA
1090623 TATAATATGTAATACTATT
1 TATAATATGTAATA-TATT
1090642 TATAATATGTAAT-TATT
1 TATAATATGTAATATATT
1090659 TA
1 TA
1090661 ATATGAAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.32
19 13 0.68
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (18 bp):
TATAATATGTAATATATT
Found at i:1091024 original size:41 final size:41
Alignment explanation
Indices: 1090967--1091050 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 41
1090957 TTCTGCGTTC
*
1090967 TACGGGATTATAAAAACTTTTAAATTGAAGGTTATTGTATT
1 TACGGGATTATAAAAACTTTTAAATTAAAGGTTATTGTATT
1091008 TACGGGATTATAAAAACTTTTAAATTAAAGGTTATTGTATT
1 TACGGGATTATAAAAACTTTTAAATTAAAGGTTATTGTATT
1091049 TA
1 TA
1091051 TTTTTAATTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.42
Consensus pattern (41 bp):
TACGGGATTATAAAAACTTTTAAATTAAAGGTTATTGTATT
Found at i:1091438 original size:127 final size:127
Alignment explanation
Indices: 1091212--1091459 Score: 424
Period size: 127 Copynumber: 2.0 Consensus size: 127
1091202 ACTCGAGTCT
*
1091212 TTCCTTTTGAGCTGTCTACTGTGGATGGACCACAGTAATTCTACACATTCCTCCCTCAAATTACG
1 TTCCTTTTGAGCTGTCTACTGTGGATGGACCACAATAATTCTACACATTCCTCCCTCAAATTACG
*
1091277 GGAATGGTTTTTTTTCAAATATACAATCTGTGAGTGGAGTAGGAAACTTTAAGACTTGTGAC
66 GGAATGATTTTTTTTCAAATATACAATCTGTGAGTGGAGTAGGAAACTTTAAGACTTGTGAC
* * * *
1091339 TTCCTTTTGAGCTGTGTACTGTGGATGGACCACAATAATTCTACATATTCCTCGCTCAAATTATG
1 TTCCTTTTGAGCTGTCTACTGTGGATGGACCACAATAATTCTACACATTCCTCCCTCAAATTACG
* *
1091404 GGTATGATTTTTTTTCAAATATACAATCTGTGAGTGGAGTAGGAAACTTTACGACT
66 GGAATGATTTTTTTTCAAATATACAATCTGTGAGTGGAGTAGGAAACTTTAAGACT
1091460 AGTAAGGACT
Statistics
Matches: 113, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
127 113 1.00
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (127 bp):
TTCCTTTTGAGCTGTCTACTGTGGATGGACCACAATAATTCTACACATTCCTCCCTCAAATTACG
GGAATGATTTTTTTTCAAATATACAATCTGTGAGTGGAGTAGGAAACTTTAAGACTTGTGAC
Found at i:1100481 original size:23 final size:22
Alignment explanation
Indices: 1100448--1100554 Score: 90
Period size: 23 Copynumber: 4.5 Consensus size: 22
1100438 ATATGAAGAA
*
1100448 ATAATGATATAGTAAATTGTATAT
1 ATAAT-ATATA-TAAATTATATAT
*
1100472 ATAATATATATTATATTATATAT
1 ATAATATATA-TAAATTATATAT
*
1100495 A-AACTATATATAAACTATATTAT
1 ATAA-TATATATAAATTATA-TAT
* *
1100518 ATTATATATTATAAATATATTTAT
1 ATAATATA-TATAAAT-TATATAT
1100542 ATAAATATATATA
1 AT-AATATATATA
1100555 TATATGTAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 12
0.76 0.10 0.13
Matches are distributed among these distances:
22 9 0.13
23 30 0.44
24 21 0.31
25 8 0.12
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.46
Consensus pattern (22 bp):
ATAATATATATAAATTATATAT
Found at i:1100506 original size:32 final size:32
Alignment explanation
Indices: 1100467--1100573 Score: 119
Period size: 32 Copynumber: 3.2 Consensus size: 32
1100457 TAGTAAATTG
1100467 TATATATAATATATATTATATTATATATAAAC
1 TATATATAATATATATTATATTATATATAAAC
*
1100499 TATATATAA-ACTATATTATATTATATATTATAAA
1 TATATATAATA-TATATTATATTATATA-TA-AAC
* * *
1100533 TATAT-TTATATAAATATATATATATATGTAAAC
1 TATATATAATATATAT-TATAT-TATATATAAAC
1100566 TATATATA
1 TATATATA
1100574 TGTGAACTAT
Statistics
Matches: 62, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
31 1 0.02
32 25 0.40
33 15 0.24
34 16 0.26
35 5 0.08
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.47
Consensus pattern (32 bp):
TATATATAATATATATTATATTATATATAAAC
Found at i:1100571 original size:15 final size:15
Alignment explanation
Indices: 1100551--1100599 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
1100541 TATAAATATA
1100551 TATATATATGTAAAC
1 TATATATATGTAAAC
*
1100566 TATATATATGTGAAC
1 TATATATATGTAAAC
* *
1100581 TATATATGTATAAAC
1 TATATATATGTAAAC
1100596 TATA
1 TATA
1100600 GAAAGTATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (15 bp):
TATATATATGTAAAC
Found at i:1100587 original size:2 final size:2
Alignment explanation
Indices: 1100467--1100574 Score: 84
Period size: 2 Copynumber: 55.5 Consensus size: 2
1100457 TAGTAAATTG
*
1100467 TA TA TA TA -A TA TA TA T- TA TA T- TA TA TA TA AA CTA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
* * * *
1100507 AA CTA TA T- TA TA T- TA TA TA T- TA TA AA TA TA TT TA TA TA AA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
1100547 TA TA TA TA TA TA TG TA AA CTA TA TA TA T
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA T
1100575 GTGAACTATA
Statistics
Matches: 83, Mismatches: 14, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
1 6 0.07
2 74 0.89
3 3 0.04
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1101017 original size:7 final size:7
Alignment explanation
Indices: 1101007--1101061 Score: 67
Period size: 7 Copynumber: 8.0 Consensus size: 7
1100997 TAGTTTATAG
1101007 AAACCCT
1 AAACCCT
**
1101014 AAACTTT
1 AAACCCT
1101021 AAACCCT
1 AAACCCT
*
1101028 AAACTCT
1 AAACCCT
1101035 AAACCCT
1 AAACCCT
1101042 AAACCCT
1 AAACCCT
*
1101049 AAA-CAT
1 AAACCCT
1101055 AAACCCT
1 AAACCCT
1101062 TATATATGTA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
6 5 0.13
7 34 0.87
ACGTcount: A:0.45, C:0.35, G:0.00, T:0.20
Consensus pattern (7 bp):
AAACCCT
Found at i:1101026 original size:14 final size:14
Alignment explanation
Indices: 1101007--1101052 Score: 74
Period size: 14 Copynumber: 3.3 Consensus size: 14
1100997 TAGTTTATAG
*
1101007 AAACCCTAAACTTT
1 AAACCCTAAACTCT
1101021 AAACCCTAAACTCT
1 AAACCCTAAACTCT
*
1101035 AAACCCTAAACCCT
1 AAACCCTAAACTCT
1101049 AAAC
1 AAAC
1101053 ATAAACCCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.46, C:0.35, G:0.00, T:0.20
Consensus pattern (14 bp):
AAACCCTAAACTCT
Found at i:1101102 original size:15 final size:16
Alignment explanation
Indices: 1101063--1101108 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
1101053 ATAAACCCTT
1101063 ATATATGTAT-TACATGC
1 ATATATGTATGT--ATGC
1101080 ATATATGTATGTATGC
1 ATATATGTATGTATGC
*
1101096 ATA-ATGTGTGTAT
1 ATATATGTATGTAT
1101109 TAATGTATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 9 0.33
16 7 0.26
17 10 0.37
18 1 0.04
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (16 bp):
ATATATGTATGTATGC
Found at i:1101633 original size:23 final size:23
Alignment explanation
Indices: 1101601--1101652 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
1101591 GTATGATACA
*
1101601 TATGT-TATATGCATATATTATG
1 TATGTATATATGCATATATGATG
* *
1101623 TATGTATATATGTATGTATGATG
1 TATGTATATATGCATATATGATG
*
1101646 CATGTAT
1 TATGTAT
1101653 TAAAATTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 5 0.20
23 20 0.80
ACGTcount: A:0.31, C:0.04, G:0.17, T:0.48
Consensus pattern (23 bp):
TATGTATATATGCATATATGATG
Found at i:1101647 original size:34 final size:35
Alignment explanation
Indices: 1101577--1101654 Score: 88
Period size: 34 Copynumber: 2.2 Consensus size: 35
1101567 TATTATAAAA
*
1101577 ATATATTGATGTGTGTATGATACATATGTTATATGC
1 ATATATT-ATGTATGTATGATACATATGTTATATGC
**
1101613 ATATATTATGTATGTAT-ATATGTATG-TATGATGC
1 ATATATTATGTATGTATGATACATATGTTAT-ATGC
*
1101647 ATGTATTA
1 ATATATTA
1101655 AAATTTTAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
33 3 0.08
34 18 0.49
35 9 0.24
36 7 0.19
ACGTcount: A:0.32, C:0.04, G:0.18, T:0.46
Consensus pattern (35 bp):
ATATATTATGTATGTATGATACATATGTTATATGC
Found at i:1101940 original size:16 final size:16
Alignment explanation
Indices: 1101898--1101934 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
1101888 CAATGGTGAT
1101898 ATAT-AAGTCAGGTAA
1 ATATCAAGTCAGGTAA
*
1101913 ATGTCAAGTCAGGTAA
1 ATATCAAGTCAGGTAA
1101929 ATATCA
1 ATATCA
1101935 GATCAGATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
15 3 0.16
16 16 0.84
ACGTcount: A:0.43, C:0.11, G:0.19, T:0.27
Consensus pattern (16 bp):
ATATCAAGTCAGGTAA
Found at i:1102780 original size:60 final size:60
Alignment explanation
Indices: 1102635--1102780 Score: 197
Period size: 60 Copynumber: 2.5 Consensus size: 60
1102625 ACTTAAGAGT
* * * * *
1102635 AAAG-TACACAAATGGTCCCC-GACTATAGGGTGTTGTTTTGTTGAGTCCCTTGACTATTA
1 AAAGTTACA-AAATGGTCCCCTGACTATAGCGTGTTGCTTTGTTGAATCCCTCGAATATTA
*
1102694 AAAGTTACAAAATGGTCCCCTAACTATAGCGTGTTGCTTTGTTGAATCCCTCGAATATTA
1 AAAGTTACAAAATGGTCCCCTGACTATAGCGTGTTGCTTTGTTGAATCCCTCGAATATTA
**
1102754 AAAGTTACAAAATGGTCGTCTGACTAT
1 AAAGTTACAAAATGGTCCCCTGACTAT
1102781 TTATATATTT
Statistics
Matches: 76, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
59 15 0.20
60 61 0.80
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.33
Consensus pattern (60 bp):
AAAGTTACAAAATGGTCCCCTGACTATAGCGTGTTGCTTTGTTGAATCCCTCGAATATTA
Found at i:1102841 original size:84 final size:84
Alignment explanation
Indices: 1102731--1102898 Score: 275
Period size: 84 Copynumber: 2.0 Consensus size: 84
1102721 AGCGTGTTGC
1102731 TTTGTTGAATCCCTCGAATATTAAAAGTTACAAAATGGTCGTCTGACTATTTATATATTTCAAAC
1 TTTGTTGAATCCCTCGAATATTAAAAGTTACAAAATGGTCGTCTGACTATTTATATATTTCAAAC
*
1102796 TCATCCTTTTTCGTTAAAA
66 TCATCATTTTTCGTTAAAA
* * *
1102815 TTTGTT-AAGTCCCTCGACTATTAAAAGTTACAAAATGGTCGTTTGACTATTTATATGTTTCAAA
1 TTTGTTGAA-TCCCTCGAATATTAAAAGTTACAAAATGGTCGTCTGACTATTTATATATTTCAAA
*
1102879 CTCGTCATTTTTCGTTAAAA
65 CTCATCATTTTTCGTTAAAA
1102899 ATTGATGACA
Statistics
Matches: 78, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
83 2 0.03
84 76 0.97
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (84 bp):
TTTGTTGAATCCCTCGAATATTAAAAGTTACAAAATGGTCGTCTGACTATTTATATATTTCAAAC
TCATCATTTTTCGTTAAAA
Found at i:1103189 original size:60 final size:60
Alignment explanation
Indices: 1103081--1103194 Score: 156
Period size: 60 Copynumber: 1.9 Consensus size: 60
1103071 GATTTGTAAG
* * *
1103081 TTTTAATAGTCAGTGGACTCAACAAAATAATACCCTATAGTTAAGGGACCATTTCATAAT
1 TTTTAATAATCAGAGGACTCAACAAAATAATACCCTATAGTCAAGGGACCATTTCATAAT
* * * * *
1103141 TTTTAATAATTAGAGGACTCAATAAAATAATATCCTATAGTCAGGGGACTATTT
1 TTTTAATAATCAGAGGACTCAACAAAATAATACCCTATAGTCAAGGGACCATTT
1103195 GTGTACTTTA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (60 bp):
TTTTAATAATCAGAGGACTCAACAAAATAATACCCTATAGTCAAGGGACCATTTCATAAT
Found at i:1106823 original size:13 final size:13
Alignment explanation
Indices: 1106805--1106834 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1106795 GATAATTATG
1106805 TTTAAATTATGCC
1 TTTAAATTATGCC
*
1106818 TTTAAATTATGTC
1 TTTAAATTATGCC
1106831 TTTA
1 TTTA
1106835 GGAAAGTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (13 bp):
TTTAAATTATGCC
Found at i:1112013 original size:54 final size:54
Alignment explanation
Indices: 1111952--1112059 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
1111942 ATGTCCATCA
1111952 CTGATTGTAATTATATTTAAAAGATAACGTAAACTACCCCATTGTTATTAAATT
1 CTGATTGTAATTATATTTAAAAGATAACGTAAACTACCCCATTGTTATTAAATT
1112006 CTGATTGTAATTATATTTAAAAGATAACGTAAACTACCCCATTGTTATTAAATT
1 CTGATTGTAATTATATTTAAAAGATAACGTAAACTACCCCATTGTTATTAAATT
1112060 TTAAATTTAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (54 bp):
CTGATTGTAATTATATTTAAAAGATAACGTAAACTACCCCATTGTTATTAAATT
Found at i:1114160 original size:36 final size:36
Alignment explanation
Indices: 1114120--1114508 Score: 192
Period size: 39 Copynumber: 10.7 Consensus size: 36
1114110 GATACATTTC
* *
1114120 TTGTTTCAAGGGAAACTGTTTCAAGAGAGACAAAAT
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAT
* * **
1114156 TTGTTTCAAGGGAAACAGTCTC-A-A-AG--ATTA-
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAT
* *
1114186 TTGTTTCAAGAGAAACTGTCTCATGCGAGACAAAAT
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAT
** * **
1114222 TTGTTTCATTAGAAACATAT-TC-A-A-AG---ATTT
1 TTGTTTCAAGAGAAAC-TGTCTCAAGAGAGACAAAAT
*
1114252 TGTGTTTCAAGAGAAACTGTCTCAAAAGAGACAAAAT
1 T-TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAT
* * *
1114289 TTGTTTTAAGGGAAACTGTCTCAAGCGAGACAAAATCT
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA--T
** * * *
1114327 TCTGTTTTGAGAGAAACTATCTTAAGCGAGACAAAATCT
1 T-TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA--T
* * * * *
1114366 TCTGTTTCGAGAGAAACTATCTCAAGCGGGATAAAATCT
1 T-TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA--T
* * * *
1114405 TCTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTT
1 T-TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA---T
* * * *
1114445 TTGTTTCGAGAGAAACTATCTCAAGCGAGATAAAATCT
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA--T
* * *
1114483 TCTGTTTCTAGGGAAACTATCTCAAG
1 T-TGTTTCAAGAGAAACTGTCTCAAG
1114509 CGAGTTAAAA
Statistics
Matches: 288, Mismatches: 45, Indels: 37
0.78 0.12 0.10
Matches are distributed among these distances:
30 25 0.09
31 17 0.06
32 1 0.00
33 7 0.02
34 3 0.01
35 3 0.01
36 66 0.23
37 5 0.02
38 4 0.01
39 155 0.54
40 2 0.01
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (36 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAT
Found at i:1114226 original size:66 final size:66
Alignment explanation
Indices: 1114120--1114312 Score: 253
Period size: 66 Copynumber: 2.9 Consensus size: 66
1114110 GATACATTTC
* *
1114120 TTGTTTCAAGGGAAACTGTTTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAGTCTCAAAGATT
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAGTCTCAAAGATT
1114185 A
66 A
* * *** *
1114186 TTGTTTCAAGAGAAACTGTCTCATGCGAGACAAAATTTGTTTCATTAGAAACA-TATTCAAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAGT-CTCAAAGAT
*
1114250 TT
65 TA
* * *
1114252 TGTGTTTCAAGAGAAACTGTCTCAAAAGAGACAAAATTTGTTTTAAGGGAAACTGTCTCAA
1 T-TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAGTCTCAA
1114313 GCGAGACAAA
Statistics
Matches: 106, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
65 1 0.01
66 56 0.53
67 48 0.45
68 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (66 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAGTCTCAAAGATT
A
Found at i:1114344 original size:39 final size:39
Alignment explanation
Indices: 1114297--1114621 Score: 497
Period size: 39 Copynumber: 8.3 Consensus size: 39
1114287 ATTTGTTTTA
* * *
1114297 AGGGAAACTGTCTCAAGCGAGACAAAATCTTCTGTTTTG
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
* * *
1114336 AGAGAAACTATCTTAAGCGAGACAAAATCTTCTGTTTCG
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
* * *
1114375 AGAGAAACTATCTCAAGCGGGATAAAATCTTCTGTTTCA
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
*
1114414 AGGGAAACTATCTCAAGCGAGATAAAATCTTTTGTTTCG
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
* *
1114453 AGAGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCT
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
*
1114492 AGGGAAACTATCTCAAGCGAGTTAAAATCTTCTGTTTCG
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
* *
1114531 AGGGAAAATATCTCAAGCGAGTTAAAATCTTCTGTTTCG
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
* *
1114570 AGGGAAACTATCTCAATCGAGTTAAAATCTTCTGTTTCG
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
1114609 AGGGAAACTATCT
1 AGGGAAACTATCT
1114622 TAGGTGAGAC
Statistics
Matches: 265, Mismatches: 21, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 265 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (39 bp):
AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
Found at i:1114387 original size:22 final size:22
Alignment explanation
Indices: 1114323--1114387 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 22
1114313 GCGAGACAAA
*
1114323 ATCTTCTGTTTTGAGAGAAACT
1 ATCTTCTGTTTCGAGAGAAACT
** *
1114345 ATCTTAAG---CGAGACAAA--
1 ATCTTCTGTTTCGAGAGAAACT
1114362 ATCTTCTGTTTCGAGAGAAACT
1 ATCTTCTGTTTCGAGAGAAACT
1114384 ATCT
1 ATCT
1114388 CAAGCGGGAT
Statistics
Matches: 31, Mismatches: 7, Indels: 10
0.65 0.15 0.21
Matches are distributed among these distances:
17 6 0.19
19 7 0.23
20 8 0.26
22 10 0.32
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (22 bp):
ATCTTCTGTTTCGAGAGAAACT
Found at i:1114538 original size:20 final size:20
Alignment explanation
Indices: 1114515--1114615 Score: 64
Period size: 20 Copynumber: 5.2 Consensus size: 20
1114505 CAAGCGAGTT
1114515 AAAATCTTCTGTTTCGAGGG
1 AAAATCTTCTGTTTCGAGGG
* **** **
1114535 AAAAT-ATCTCAAGCGAGTT
1 AAAATCTTCTGTTTCGAGGG
1114554 AAAATCTTCTGTTTCGAGGG
1 AAAATCTTCTGTTTCGAGGG
*** **
1114574 -AAA-CTATCTCAATCGAGTT
1 AAAATCT-TCTGTTTCGAGGG
1114593 AAAATCTTCTGTTTCGAGGG
1 AAAATCTTCTGTTTCGAGGG
1114613 AAA
1 AAA
1114616 CTATCTTAGG
Statistics
Matches: 53, Mismatches: 24, Indels: 8
0.62 0.28 0.09
Matches are distributed among these distances:
18 2 0.04
19 23 0.43
20 26 0.49
21 2 0.04
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.32
Consensus pattern (20 bp):
AAAATCTTCTGTTTCGAGGG
Found at i:1114791 original size:13 final size:13
Alignment explanation
Indices: 1114773--1114802 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1114763 TCTTGTTCCC
1114773 TTCTATTGGAAAT
1 TTCTATTGGAAAT
1114786 TTCTATTGGAAAT
1 TTCTATTGGAAAT
1114799 TTCT
1 TTCT
1114803 CCTGAAAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.27, C:0.10, G:0.13, T:0.50
Consensus pattern (13 bp):
TTCTATTGGAAAT
Found at i:1119775 original size:20 final size:18
Alignment explanation
Indices: 1119724--1119776 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 18
1119714 GATAATTATA
1119724 TTAT-TTAAAGTTAAAATT
1 TTATATTAAA-TTAAAATT
*
1119742 TTATATTAGTATTAAATATT
1 TTATATTA-AATTAAA-ATT
1119762 TTATAATTAAATTAA
1 TTAT-ATTAAATTAA
1119777 GGGTAAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 4 0.14
19 8 0.28
20 13 0.45
21 4 0.14
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (18 bp):
TTATATTAAATTAAAATT
Found at i:1124200 original size:3 final size:3
Alignment explanation
Indices: 1124192--1124258 Score: 95
Period size: 3 Copynumber: 23.3 Consensus size: 3
1124182 ATATTACAAA
1124192 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
1124238 TA- TAT TAT AAA TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT T
1124259 TAACAAACCA
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
2 6 0.11
3 51 0.89
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1128693 original size:20 final size:20
Alignment explanation
Indices: 1128670--1128708 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1128660 AAGGTGATCC
1128670 AAGAAAACTTAAGGAGCCCT
1 AAGAAAACTTAAGGAGCCCT
1128690 AAGAAAACTTAAGGAGCCC
1 AAGAAAACTTAAGGAGCCC
1128709 CATACAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.13
Consensus pattern (20 bp):
AAGAAAACTTAAGGAGCCCT
Found at i:1134172 original size:28 final size:27
Alignment explanation
Indices: 1134141--1134193 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
1134131 AGGGCTTGGA
1134141 GGTACTTTGGGTCATTTTACACTTCAAG
1 GGTA-TTTGGGTCATTTTACACTTCAAG
* *
1134169 GGTATTTTGGTTATTTTACACTTCA
1 GGTATTTGGGTCATTTTACACTTCA
1134194 GGTGCAATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.21, C:0.15, G:0.19, T:0.45
Consensus pattern (27 bp):
GGTATTTGGGTCATTTTACACTTCAAG
Found at i:1134807 original size:19 final size:19
Alignment explanation
Indices: 1134783--1134848 Score: 87
Period size: 19 Copynumber: 3.5 Consensus size: 19
1134773 CAATTATAGC
*
1134783 CAAAGTCAATGTGTCAGGT
1 CAAAGTCAATGAGTCAGGT
* *
1134802 CAAAGTCAATGGGTCGGGT
1 CAAAGTCAATGAGTCAGGT
* *
1134821 CAAAGTAAACGAGTCAGGT
1 CAAAGTCAATGAGTCAGGT
1134840 CAAAGTCAA
1 CAAAGTCAA
1134849 CGGGTTGGGT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.36, C:0.17, G:0.27, T:0.20
Consensus pattern (19 bp):
CAAAGTCAATGAGTCAGGT
Found at i:1134859 original size:19 final size:19
Alignment explanation
Indices: 1134783--1134859 Score: 82
Period size: 19 Copynumber: 4.1 Consensus size: 19
1134773 CAATTATAGC
* * *
1134783 CAAAGTCAATGTGTCAGGT
1 CAAAGTCAACGGGTCGGGT
*
1134802 CAAAGTCAATGGGTCGGGT
1 CAAAGTCAACGGGTCGGGT
* * *
1134821 CAAAGTAAACGAGTCAGGT
1 CAAAGTCAACGGGTCGGGT
*
1134840 CAAAGTCAACGGGTTGGGT
1 CAAAGTCAACGGGTCGGGT
1134859 C
1 C
1134860 GGGTTGACTT
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 48 1.00
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.21
Consensus pattern (19 bp):
CAAAGTCAACGGGTCGGGT
Found at i:1136165 original size:12 final size:12
Alignment explanation
Indices: 1136145--1136174 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1136135 TAATAATCAT
*
1136145 TATTATTATTAA
1 TATTTTTATTAA
1136157 TATTTTTATTAA
1 TATTTTTATTAA
1136169 TATTTT
1 TATTTT
1136175 GTTTGCATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TATTTTTATTAA
Found at i:1142205 original size:15 final size:15
Alignment explanation
Indices: 1142185--1142221 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1142175 ATCCATGAAT
1142185 TTTAATTCTTTTTAA
1 TTTAATTCTTTTTAA
*
1142200 TTTAATCCTTTTTAA
1 TTTAATTCTTTTTAA
*
1142215 TTGAATT
1 TTTAATT
1142222 TTCTTTCATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.27, C:0.08, G:0.03, T:0.62
Consensus pattern (15 bp):
TTTAATTCTTTTTAA
Found at i:1145724 original size:3 final size:3
Alignment explanation
Indices: 1145716--1145740 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1145706 AATATGGCTA
1145716 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
1145741 TTTAAATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1146108 original size:21 final size:21
Alignment explanation
Indices: 1146051--1146102 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
1146041 GGACTAAATA
1146051 TGTTATTTTACTTAAAATATC
1 TGTTATTTTACTTAAAATATC
1146072 TGTTATTTTACTTAAAATATC
1 TGTTATTTTACTTAAAATATC
1146093 TGTTATTTTA
1 TGTTATTTTA
1146103 TGTAAAGGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.31, C:0.08, G:0.06, T:0.56
Consensus pattern (21 bp):
TGTTATTTTACTTAAAATATC
Found at i:1147328 original size:18 final size:18
Alignment explanation
Indices: 1147275--1147331 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
1147265 TAATTTAATT
*
1147275 AATAATGATAATAGTAAAA
1 AATAATAATAATA-TAAAA
* *
1147294 AAT-ATAAATTATGTAAAA
1 AATAAT-AATAATATAAAA
1147312 AATAATAATAATATAAAA
1 AATAATAATAATATAAAA
1147330 AA
1 AA
1147332 AACCCAAATG
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
18 22 0.71
19 9 0.29
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (18 bp):
AATAATAATAATATAAAA
Found at i:1148497 original size:32 final size:32
Alignment explanation
Indices: 1148436--1148498 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
1148426 TGGGGGCACC
*
1148436 TTTGAAGATTCAACATCAAATGTTGGGGCATT
1 TTTGAAGATTCAACATCAAATATTGGGGCATT
* ** *
1148468 TTTGGAGATTCAACATTGAATATTTGGGCAT
1 TTTGAAGATTCAACATCAAATATTGGGGCAT
1148499 CTTCAGGGAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.37
Consensus pattern (32 bp):
TTTGAAGATTCAACATCAAATATTGGGGCATT
Found at i:1149280 original size:156 final size:151
Alignment explanation
Indices: 1149074--1149357 Score: 415
Period size: 156 Copynumber: 1.8 Consensus size: 151
1149064 AAAACCTGTG
* *
1149074 TGTCAACAAACAAATTTTCAGTTTCATTCAAAGTTAATTTCAACTTCACAGTGAAGGATATTGGA
1 TGTCAACAAACAAATTTTCAGTTTCATTCAAAGTCAATTTCAACTTCACAGCGAAGGATATT-GA
* * *
1149139 CTCGAAACAATGCAACTTACACAAGATTAGATTTCAACTTCACAACGAAAGATATCCAATTCAAA
65 -ACGAAAC---GAAACTTACACAAGATTAGATTTCAACTTCACAACGAAAGATATCCAACTCAAA
1149204 GCTCAACTTCACAGCGAAGGAGAGTC
126 GCTCAACTTCACAGCGAAGGAGAGTC
*
1149230 TGTCAACAAACAACTTTTCAGTTTCATTCAAAGTCAATTTCAACTTCACAGCGAAGGATATTGAA
1 TGTCAACAAACAAATTTTCAGTTTCATTCAAAGTCAATTTCAACTTCACAGCGAAGGATATTGAA
* * * ** *
1149295 CGAAGCGAAACTTACTCAAGATTGGATTTCAACTTCATGACGAAGGATATCCAACTCAAAGCT
66 CGAAACGAAACTTACACAAGATTAGATTTCAACTTCACAACGAAAGATATCCAACTCAAAGCT
1149358 AATTTTGGTG
Statistics
Matches: 116, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
151 50 0.43
154 5 0.04
155 2 0.02
156 59 0.51
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (151 bp):
TGTCAACAAACAAATTTTCAGTTTCATTCAAAGTCAATTTCAACTTCACAGCGAAGGATATTGAA
CGAAACGAAACTTACACAAGATTAGATTTCAACTTCACAACGAAAGATATCCAACTCAAAGCTCA
ACTTCACAGCGAAGGAGAGTC
Found at i:1149549 original size:65 final size:65
Alignment explanation
Indices: 1149301--1149541 Score: 358
Period size: 65 Copynumber: 3.7 Consensus size: 65
1149291 TGAACGAAGC
* *
1149301 GAAACTTACTCAAGATTGGATTTCAACTTCATGACGAAGGATATCCAACTCAAAGCTAATTTTGG
1 GAAACTTACTCAAGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGCCAA-TTTGG
1149366 T
65 T
* *
1149367 GAAACTTACTCAAGATTGGATTTCAACTTCACTACGAACGATATCCAACTCAAAGCCAATTTGGT
1 GAAACTTACTCAAGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGCCAATTTGGT
* * * *
1149432 GAAACTTACT-AGAGATTGGATTTCAATTTCACGACGAAGGTTATCTAATTCAAAGCCAATTTGG
1 GAAACTTACTCA-AGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGCCAATTTGG
1149496 T
65 T
* * *
1149497 GAAACTTACTCAATATTGGATTTCAACTTCACAATGAAGGATATC
1 GAAACTTACTCAAGATTGGATTTCAACTTCACGACGAAGGATATC
1149542 AAATTCAAGG
Statistics
Matches: 158, Mismatches: 15, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
64 1 0.01
65 101 0.64
66 56 0.35
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (65 bp):
GAAACTTACTCAAGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGCCAATTTGGT
Found at i:1149744 original size:124 final size:122
Alignment explanation
Indices: 1149516--1149862 Score: 439
Period size: 124 Copynumber: 2.8 Consensus size: 122
1149506 TCAATATTGG
* *
1149516 ATTTCAACTTCACAATGAAGGATATCAAATTCAAGG-TTCAACTTCACAACGAAAGAGCCATCCA
1 ATTTCAACTTCATAA-AAAGGATATC-AATTCAAGGCTT-AACTTCACAACGAAAGAGCCATCCA
* * * * * *
1149580 TGATTACAACTTCACGATGAATGATATCGAT-CCCATAAGCAGCATCCATCTCTAGATTAA
63 CGATTTCAACTTCACGACGAAGGATATTG-TGCCCACAAGCAGCATCCATCTCTAGATTAA
* *
1149640 ATTTCAACTTCATAACAAAGGATATACAATTCAAGGCTTAACTTCACAACGAAGGAGTCATCCAC
1 ATTTCAACTTCATAA-AAAGGATAT-CAATTCAAGGCTTAACTTCACAACGAAAGAGCCATCCAC
**
1149705 GATTTCAA-TGTCACGACGAAGGATATTGTGCCCACAAGCAGCATCCATCTCTAGATTGG
64 GATTTCAACT-TCACGACGAAGGATATTGTGCCCACAAGCAGCATCCATCTCTAGATTAA
* * *
1149764 ATTTCAACTTCATAAAGAAGGATAGCCAATTCAAGGCTCAACTTCACAACGAATGAGCCATCCAC
1 ATTTCAACTTCATAAA-AAGGATA-TCAATTCAAGGCTTAACTTCACAACGAAAGAGCCATCCAC
* *
1149829 GAATTAAACTTCACGACGAAGGATATTGTGCCCA
64 GATTTCAACTTCACGACGAAGGATATTGTGCCCA
1149863 ACGGATCGAC
Statistics
Matches: 197, Mismatches: 19, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
123 3 0.02
124 190 0.96
125 4 0.02
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (122 bp):
ATTTCAACTTCATAAAAAGGATATCAATTCAAGGCTTAACTTCACAACGAAAGAGCCATCCACGA
TTTCAACTTCACGACGAAGGATATTGTGCCCACAAGCAGCATCCATCTCTAGATTAA
Found at i:1150532 original size:3 final size:3
Alignment explanation
Indices: 1150514--1150545 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
1150504 AAAAAAGTTA
1150514 TAT TA- TAT TA- TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1150546 TTTTTACAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.15
3 23 0.85
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1154744 original size:20 final size:20
Alignment explanation
Indices: 1154699--1154750 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
1154689 CCGATTCAAG
* *
1154699 TGGTATCGATACCAAGAGGG
1 TGGTATCGATACCAAGACGA
* *
1154719 TAGTATCGATACCATGACGA
1 TGGTATCGATACCAAGACGA
*
1154739 TGGTATCAATAC
1 TGGTATCGATAC
1154751 AATTGATCAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (20 bp):
TGGTATCGATACCAAGACGA
Found at i:1155293 original size:54 final size:53
Alignment explanation
Indices: 1155184--1155320 Score: 152
Period size: 54 Copynumber: 2.5 Consensus size: 53
1155174 TACAAAAAGT
* ** *
1155184 TAAGAAATTCATACTAAGTGTATAAATTTACGTATGGCACTTTGTGTGCAAAAC
1 TAAGAAATTCATACTAAGTGTATGAATTTACGTATGAAACTATGTGT-CAAAAC
* *
1155238 TAAGAAATTCATACTAAGTGTATGAATTTTCGTATGAAAACTATGTGT-ATGAAC
1 TAAGAAATTCATACTAAGTGTATGAATTTACGTATG-AAACTATGTGTCA-AAAC
* *
1155292 TAATAAA-TCTATAATAAGTGTATGAATTT
1 TAAGAAATTC-ATACTAAGTGTATGAATTT
1155321 CCATATGGGA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
53 3 0.04
54 61 0.85
55 8 0.11
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.36
Consensus pattern (53 bp):
TAAGAAATTCATACTAAGTGTATGAATTTACGTATGAAACTATGTGTCAAAAC
Found at i:1155623 original size:68 final size:68
Alignment explanation
Indices: 1155542--1155795 Score: 384
Period size: 68 Copynumber: 3.7 Consensus size: 68
1155532 AATATAAATA
* * * *
1155542 GCCTAATTGTGCATTTGACAGAAAGGTTTCAATTATGCCAGTTAGATGAAAGGTTAAGTACCTTT
1 GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
1155607 GAG
66 GAG
* * * * *
1155610 GTCTAACTGTGCATTTGACCGAAAGATGTCAATTTTTCCAGTTAGATGAAAGGCTAAGTGCCTTT
1 GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
1155675 GAG
66 GAG
*
1155678 ACCTAACTGTGCATTTGACCA-AAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
1 GCCTAACTGTGCATTTGA-CAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
1155742 TGAG
65 TGAG
* *
1155746 GCCTAACTGTGCATTTGGCAGAAAGGTGTCAATTATGACAGTTAGATGAA
1 GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
1155796 CGGTTAAAGA
Statistics
Matches: 166, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
67 2 0.01
68 163 0.98
69 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.30
Consensus pattern (68 bp):
GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
GAG
Found at i:1155884 original size:81 final size:81
Alignment explanation
Indices: 1155745--1156599 Score: 1170
Period size: 81 Copynumber: 10.6 Consensus size: 81
1155735 GTGCCTTTGA
* * * *
1155745 GGCCTAACTGTGCATTTGGCAGAAAGGTGTCAATTATGACAGTTAGATGAACGGTTAAAGACCAT
1 GGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
1155810 TGAGTAAAAGATAAAT
66 TGAGTAAAAGATAAAT
* ** * * * * **
1155826 GGCCTAGCCGTATATTTGGTAGAAATGTGTCAATTATGCTAGTTAAATGAACGATTAAAGACTAT
1 GGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
1155891 TGAGTAAAAGATAAAT
66 TGAGTAAAAGATAAAT
* * *
1155907 AGCCTAGTTGTGCATTTGGCATAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
1 GGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
1155972 TGAGTAAAAGATAAAT
66 TGAGTAAAAGATAAAT
* * *
1155988 GGCCTAGTTGTGTATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCAT
1 GGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
* *
1156053 TGACTAAAAGATAACT
66 TGAGTAAAAGATAAAT
* * * * * *
1156069 GACCTAGCTATGCATTTGGTAAAAATGTGTCAATTATGCAAGTTAGATGAACGGTTAAAGACTGT
1 GGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
*
1156134 TGAGTAAAAAATAAAT
66 TGAGTAAAAGATAAAT
* * * * * * * *
1156150 GGCCTAGTTGTACATTTGGTATAAAGGTGTCAATTATGCCAGTTAAATGGACGGTTAAAAACCGT
1 GGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
1156215 TGAGTAAAAGATAAAT
66 TGAGTAAAAGATAAAT
* * * * * * * *
1156231 GACCTAGCTATACATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATAAATGATTAAAGACTGT
1 GGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
1156296 TGAGTAAAAGATAAAT
66 TGAGTAAAAGATAAAT
* * * *
1156312 GGCCTAGCTGTGTATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACAGTTAAATATCGT
1 GGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
1156377 TGAGTAAAAGATAAAT
66 TGAGTAAAAGATAAAT
* *
1156393 GGCCTAGCTGTGCATTTGGCAAAAATGTGTCAATTATGCCAGTTAGATGAACAGTTAAAGACCGT
1 GGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
1156458 TGAGTAAAAGATAAAT
66 TGAGTAAAAGATAAAT
* * * * *
1156474 GGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGTCAGTTAGATGAATGGTTAAAGACTGT
1 GGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
1156539 TGAGTAAAAGATAAAT
66 TGAGTAAAAGATAAAT
* * * * *
1156555 GGCCTAGCTATGCATTAGGCAGAAAAGTGTCAATCATGCAAGTTA
1 GGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTA
1156600 TGCATAAGTG
Statistics
Matches: 679, Mismatches: 95, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 679 1.00
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (81 bp):
GGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
TGAGTAAAAGATAAAT
Found at i:1164813 original size:30 final size:30
Alignment explanation
Indices: 1164777--1164842 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
1164767 AATGAACCGG
* *
1164777 CGGTTCAAACCGATTTTGCTGGTTTTCAGC
1 CGGTTCAAACCGATTTTCCCGGTTTTCAGC
** *
1164807 CGGTTCACCCCGGTTTTCCCGGTTTTCAGC
1 CGGTTCAAACCGATTTTCCCGGTTTTCAGC
1164837 CGGTTC
1 CGGTTC
1164843 TTTACCGGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.11, C:0.30, G:0.24, T:0.35
Consensus pattern (30 bp):
CGGTTCAAACCGATTTTCCCGGTTTTCAGC
Found at i:1166791 original size:15 final size:16
Alignment explanation
Indices: 1166761--1166791 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1166751 GAAACATTTC
1166761 TTTTACAAAATCGAGT
1 TTTTACAAAATCGAGT
1166777 TTTTACAAAAT-GAGT
1 TTTTACAAAATCGAGT
1166792 CGAGACTCGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.39
Consensus pattern (16 bp):
TTTTACAAAATCGAGT
Found at i:1172210 original size:38 final size:36
Alignment explanation
Indices: 1172168--1172243 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 36
1172158 TTGGGTGTTG
*
1172168 TTTCTCTCGAAACAAAATGTCGTCTCACTTGAGATATT
1 TTTCTCT-GAAA-AAAATGTCGTCTCACTTGAGACATT
* * * *
1172206 TTTCTCTTAAAAAAATTTTGTTTCACTTGAGACATT
1 TTTCTCTGAAAAAAATGTCGTCTCACTTGAGACATT
1172242 TT
1 TT
1172244 CCTTCGGAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
36 23 0.70
37 3 0.09
38 7 0.21
ACGTcount: A:0.29, C:0.17, G:0.11, T:0.43
Consensus pattern (36 bp):
TTTCTCTGAAAAAAATGTCGTCTCACTTGAGACATT
Found at i:1172328 original size:37 final size:37
Alignment explanation
Indices: 1172270--1172359 Score: 119
Period size: 37 Copynumber: 2.5 Consensus size: 37
1172260 TTCAAAGTTG
*
1172270 TTTTTCT-TAAAAACAAATTTTGTCTCGCTTGAGACA
1 TTTTTCTCTAAAAACAAATTTTGTCTCACTTGAGACA
* * * *
1172306 TTTTTCTCTTAAAATAAATTTTGTTTCACTTGAGATA
1 TTTTTCTCTAAAAACAAATTTTGTCTCACTTGAGACA
*
1172343 TTTTTCTCTCAAAACAA
1 TTTTTCTCTAAAAACAA
1172360 GCATCGTCTC
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
36 7 0.15
37 39 0.85
ACGTcount: A:0.31, C:0.16, G:0.08, T:0.46
Consensus pattern (37 bp):
TTTTTCTCTAAAAACAAATTTTGTCTCACTTGAGACA
Found at i:1172543 original size:36 final size:36
Alignment explanation
Indices: 1172487--1172579 Score: 113
Period size: 35 Copynumber: 2.6 Consensus size: 36
1172477 AACAAAATCT
*
1172487 TTGA-ATATGTTTCCCTTGAAATAAAATTTTGTCTCCC
1 TTGAGATA-GTTTCCCTTGAAA-AAAATTTTATCTCCC
*
1172524 TTGAGA-AGTTTCTCC-TGAAACAAATTTTATCTCCC
1 TTGAGATAGTTTC-CCTTGAAAAAAATTTTATCTCCC
1172559 TTGAGATAGTTTCCCTT-AAAA
1 TTGAGATAGTTTCCCTTGAAAA
1172580 TAGACTTTGT
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
35 24 0.49
36 17 0.35
37 7 0.14
38 1 0.02
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (36 bp):
TTGAGATAGTTTCCCTTGAAAAAAATTTTATCTCCC
Found at i:1172598 original size:36 final size:35
Alignment explanation
Indices: 1172487--1172600 Score: 108
Period size: 36 Copynumber: 3.2 Consensus size: 35
1172477 AACAAAATCT
*
1172487 TTGA-ATATGTTTCCCTTGAAATAAAATTTTGTCTCCC
1 TTGAGATA-GTTTCCCTT-AAA-ATAATTTTGTCTCCC
* *
1172524 TTGAGA-AGTTTCTCCTGAAACA-AATTTTATCTCCC
1 TTGAGATAGTTTC-CCTTAAA-ATAATTTTGTCTCCC
* *
1172559 TTGAGATAGTTTCCCTTAAAATAGACTTTGTCTCAC
1 TTGAGATAGTTTCCCTTAAAATA-ATTTTGTCTCCC
1172595 TTGAGA
1 TTGAGA
1172601 CATTTTTTTC
Statistics
Matches: 65, Mismatches: 7, Indels: 11
0.78 0.08 0.13
Matches are distributed among these distances:
34 1 0.02
35 25 0.38
36 30 0.46
37 8 0.12
38 1 0.02
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.39
Consensus pattern (35 bp):
TTGAGATAGTTTCCCTTAAAATAATTTTGTCTCCC
Found at i:1172662 original size:75 final size:77
Alignment explanation
Indices: 1172573--1172731 Score: 216
Period size: 75 Copynumber: 2.1 Consensus size: 77
1172563 GATAGTTTCC
* * *
1172573 CTTAAAATAGACTTTGTCTCACTTGAGACATTTTTTT-CTCACAACAAGACAT-TTCGTTTCA-T
1 CTTAAAACAGACTTTGTCTCACTTGAGACATTTTTTTACTCAAAACAAGA-ATATTCATTTCACT
* *
1172635 TACAATTATTTTT
65 CAAAATTATTTTT
* *
1172648 CTTAAAACATACTTTGTCTCGCTTGAGACATTTTTTTACTCAAAACAAGAATATTCATTTCACTC
1 CTTAAAACAGACTTTGTCTCACTTGAGACATTTTTTTACTCAAAACAAGAATATTCATTTCACTC
*
1172713 AAAATTGTTTTT
66 AAAATTATTTTT
1172725 CTTAAAA
1 CTTAAAA
1172732 AACAAAATTT
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
75 36 0.49
76 19 0.26
77 18 0.25
ACGTcount: A:0.32, C:0.18, G:0.08, T:0.42
Consensus pattern (77 bp):
CTTAAAACAGACTTTGTCTCACTTGAGACATTTTTTTACTCAAAACAAGAATATTCATTTCACTC
AAAATTATTTTT
Found at i:1172694 original size:38 final size:36
Alignment explanation
Indices: 1172576--1172694 Score: 98
Period size: 38 Copynumber: 3.2 Consensus size: 36
1172566 AGTTTCCCTT
*
1172576 AAAATAGACTTTGTCTCACTTGAGACATTTTTTTCTC
1 AAAACAGACTTTGTCTC-CTTGAGACATTTTTTTCTC
* * * * *
1172613 ACAACAAGACATTTCGTTTCATT-ACA-ATTATTTTTCTT
1 AAAAC-AGAC-TTT-GTCTCCTTGAGACATT-TTTTTCTC
*
1172651 AAAACATACTTTGTCTCGCTTGAGACATTTTTTTACTC
1 AAAACAGACTTTGTCTC-CTTGAGACATTTTTTT-CTC
1172689 AAAACA
1 AAAACA
1172695 AGAATATTCA
Statistics
Matches: 62, Mismatches: 12, Indels: 15
0.70 0.13 0.17
Matches are distributed among these distances:
35 4 0.06
36 5 0.08
37 16 0.26
38 28 0.45
39 5 0.08
40 4 0.06
ACGTcount: A:0.31, C:0.19, G:0.08, T:0.41
Consensus pattern (36 bp):
AAAACAGACTTTGTCTCCTTGAGACATTTTTTTCTC
Found at i:1172754 original size:79 final size:75
Alignment explanation
Indices: 1172589--1172754 Score: 199
Period size: 75 Copynumber: 2.2 Consensus size: 75
1172579 ATAGACTTTG
* * * * *
1172589 TCTCACTTGAGACATTTTTTTCTCACAACAAGACATTTCGTTTCATTACAATTATTTTTCTTAAA
1 TCTCGCTTGAGACATTTTTTTCTCAAAACAAGACATTTCATTTCATCAAAATTATTTTTCTTAAA
* * *
1172654 ACATACTTTG
66 ACAAAATTTA
*
1172664 TCTCGCTTGAGACATTTTTTTACTCAAAACAAGA-ATATTCATTTCACTCAAAATTGTTTTTCTT
1 TCTCGCTTGAGACATTTTTTT-CTCAAAACAAGACAT-TTCATTTCA-TCAAAATTATTTTTCTT
1172728 AAAAAACAAAATTTA
63 --AAAACAAAATTTA
1172743 TCTCGCTTGAGA
1 TCTCGCTTGAGA
1172755 TAGTTTCCCT
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
75 22 0.29
76 19 0.25
77 14 0.18
79 22 0.29
ACGTcount: A:0.33, C:0.19, G:0.08, T:0.41
Consensus pattern (75 bp):
TCTCGCTTGAGACATTTTTTTCTCAAAACAAGACATTTCATTTCATCAAAATTATTTTTCTTAAA
ACAAAATTTA
Found at i:1172918 original size:52 final size:52
Alignment explanation
Indices: 1172850--1173279 Score: 402
Period size: 52 Copynumber: 8.1 Consensus size: 52
1172840 CCTGGCTTTA
** * * *
1172850 AGGGGTTTCTCGATGTTTTCAAATGAACTTGAAAGAAGCTAAGCTTAATTTT
1 AGGGGTTTCTTAATGTTTTCAAATGAACTTCAAAGAAACTAAGCCTAATTTT
* * * *
1172902 AGGGGTTTTTTAATGTTTT-AAATGAATTTCAAAGAAATTAAGCCTGATTTT
1 AGGGGTTTCTTAATGTTTTCAAATGAACTTCAAAGAAACTAAGCCTAATTTT
** * * *
1172953 AAGGGGTTTCTCGATGTTTTCAAATGAACTTGAAAGAAGCTAAGCTTAATTTT
1 -AGGGGTTTCTTAATGTTTTCAAATGAACTTCAAAGAAACTAAGCCTAATTTT
* * *
1173006 AGGGGTTTCTTAATGTTTT-AAATGAATTTCAAAGAAATTAAGCCTGATTTT
1 AGGGGTTTCTTAATGTTTTCAAATGAACTTCAAAGAAACTAAGCCTAATTTT
** * * *
1173057 AAGGGGTTTCTCGATGTTTTCAAATGAACTTGAAAGAAGCTAAGCTTAATTTT
1 -AGGGGTTTCTTAATGTTTTCAAATGAACTTCAAAGAAACTAAGCCTAATTTT
* *
1173110 AGGGGTTTCTTAATGTTTT-AAATGAATTTCAAAGAAATTAAGCCTAATTTTT
1 AGGGGTTTCTTAATGTTTTCAAATGAACTTCAAAGAAACTAAGCCTAA-TTTT
* * * * *** *
1173162 AGGGATTTCTTGATATTTTCAAATG-AGTTTTTAGAAACTAAGCCTGATTTTT
1 AGGGGTTTCTTAATGTTTTCAAATGAACTTCAAAGAAACTAAGCCT-AATTTT
** *
1173214 AGGGGTTTCTTGATGATGATTTTC-AATGAGTTTTTAAAAGGAAACTAAGCCTAATTCTT
1 AGGGGTTTCTT-A--ATG-TTTTCAAATGA--ACTTCAAA-GAAACTAAGCCTAATT-TT
1173273 AGGGGTT
1 AGGGGTT
1173280 CCTTGACAAC
Statistics
Matches: 303, Mismatches: 59, Indels: 25
0.78 0.15 0.06
Matches are distributed among these distances:
51 75 0.25
52 132 0.44
53 58 0.19
55 6 0.02
56 5 0.02
58 6 0.02
59 21 0.07
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.40
Consensus pattern (52 bp):
AGGGGTTTCTTAATGTTTTCAAATGAACTTCAAAGAAACTAAGCCTAATTTT
Found at i:1173224 original size:104 final size:104
Alignment explanation
Indices: 1172830--1173187 Score: 644
Period size: 104 Copynumber: 3.4 Consensus size: 104
1172820 GAAGATTTTT
**
1172830 AGAAATTAAGCCTGGCTTTAAGGGGTTTCTCGATGTTTTCAAATGAACTTGAAAGAAGCTAAGCT
1 AGAAATTAAGCCTGATTTTAAGGGGTTTCTCGATGTTTTCAAATGAACTTGAAAGAAGCTAAGCT
*
1172895 TAATTTTAGGGGTTTTTTAATGTTTTAAATGAATTTCAA
66 TAATTTTAGGGGTTTCTTAATGTTTTAAATGAATTTCAA
1172934 AGAAATTAAGCCTGATTTTAAGGGGTTTCTCGATGTTTTCAAATGAACTTGAAAGAAGCTAAGCT
1 AGAAATTAAGCCTGATTTTAAGGGGTTTCTCGATGTTTTCAAATGAACTTGAAAGAAGCTAAGCT
1172999 TAATTTTAGGGGTTTCTTAATGTTTTAAATGAATTTCAA
66 TAATTTTAGGGGTTTCTTAATGTTTTAAATGAATTTCAA
1173038 AGAAATTAAGCCTGATTTTAAGGGGTTTCTCGATGTTTTCAAATGAACTTGAAAGAAGCTAAGCT
1 AGAAATTAAGCCTGATTTTAAGGGGTTTCTCGATGTTTTCAAATGAACTTGAAAGAAGCTAAGCT
1173103 TAATTTTAGGGGTTTCTTAATGTTTTAAATGAATTTCAA
66 TAATTTTAGGGGTTTCTTAATGTTTTAAATGAATTTCAA
* * * * *
1173142 AGAAATTAAGCCTAATTTTTAGGGATTTCTTGATATTTTCAAATGA
1 AGAAATTAAGCCTGATTTTAAGGGGTTTCTCGATGTTTTCAAATGA
1173188 GTTTTTAGAA
Statistics
Matches: 246, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
104 246 1.00
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.39
Consensus pattern (104 bp):
AGAAATTAAGCCTGATTTTAAGGGGTTTCTCGATGTTTTCAAATGAACTTGAAAGAAGCTAAGCT
TAATTTTAGGGGTTTCTTAATGTTTTAAATGAATTTCAA
Found at i:1174447 original size:105 final size:105
Alignment explanation
Indices: 1174265--1174516 Score: 452
Period size: 105 Copynumber: 2.4 Consensus size: 105
1174255 GGATAAACCG
1174265 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAGGTTCGTAATGAG
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAGGTTCGTAATGAG
* *
1174330 AAGAGCATGTTCCTTTCAAATCCACCGCAGAAAGAGGTGA
66 AAGAACATGTTCCTTTCAAATCCACCCCAGAAAGAGGTGA
1174370 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAGGTTCGTAATGAG
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAGGTTCGTAATGAG
* *
1174435 AAGAAC-TCGTTCCTTTCAAATTCACCCCAGAAGGAGGTGA
66 AAGAACAT-GTTCCTTTCAAATCCACCCCAGAAAGAGGTGA
1174475 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCC
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCC
1174517 AACAAAAGGA
Statistics
Matches: 142, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
104 1 0.01
105 141 0.99
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (105 bp):
ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAGGTTCGTAATGAG
AAGAACATGTTCCTTTCAAATCCACCCCAGAAAGAGGTGA
Found at i:1178779 original size:38 final size:39
Alignment explanation
Indices: 1178737--1178815 Score: 124
Period size: 38 Copynumber: 2.1 Consensus size: 39
1178727 TTTAAATCTA
* *
1178737 AACTAAATATTAGATATGATTTTAAAATTATAAAAT-AT
1 AACTAAATATTAGATATGATTTTAAAAATAAAAAATGAT
*
1178775 AACTAAATATTATATATGATTTTAAAAATAAAAAATGAT
1 AACTAAATATTAGATATGATTTTAAAAATAAAAAATGAT
1178814 AA
1 AA
1178816 TTTAGATATT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
38 33 0.89
39 4 0.11
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.37
Consensus pattern (39 bp):
AACTAAATATTAGATATGATTTTAAAAATAAAAAATGAT
Found at i:1181934 original size:30 final size:31
Alignment explanation
Indices: 1181900--1181962 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 31
1181890 AACTAATTAT
1181900 TTTCTGTCAAAAACTT-AATGACCATCTGAG
1 TTTCTGTCAAAAACTTAAATGACCATCTGAG
1181930 TTTCTGTCAAAAACTTAAATGACCATCTGAG
1 TTTCTGTCAAAAACTTAAATGACCATCTGAG
1181961 TT
1 TT
1181963 AAATGTTAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 16 0.50
31 16 0.50
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (31 bp):
TTTCTGTCAAAAACTTAAATGACCATCTGAG
Found at i:1184873 original size:31 final size:31
Alignment explanation
Indices: 1184838--1184902 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
1184828 CAAAAAAGTA
*
1184838 TAATATTTGATCACTTTCATTTTTATTTAAT
1 TAATATTGGATCACTTTCATTTTTATTTAAT
* * *
1184869 TAATATTGGGTCATTTTTATTTTTATTTAAT
1 TAATATTGGATCACTTTCATTTTTATTTAAT
1184900 TAA
1 TAA
1184903 GATGTGGTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.58
Consensus pattern (31 bp):
TAATATTGGATCACTTTCATTTTTATTTAAT
Found at i:1184912 original size:31 final size:31
Alignment explanation
Indices: 1184856--1184914 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
1184846 GATCACTTTC
*
1184856 ATTTTTATTTAATTAATATTGGGTCATTTTT
1 ATTTTTATTTAATTAAGATTGGGTCATTTTT
1184887 ATTTTTATTTAATTAAGA-TGTGGTCATT
1 ATTTTTATTTAATTAAGATTG-GGTCATT
1184915 AAGAGTTAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 2 0.08
31 24 0.92
ACGTcount: A:0.27, C:0.03, G:0.12, T:0.58
Consensus pattern (31 bp):
ATTTTTATTTAATTAAGATTGGGTCATTTTT
Found at i:1185912 original size:37 final size:39
Alignment explanation
Indices: 1185868--1185953 Score: 122
Period size: 39 Copynumber: 2.3 Consensus size: 39
1185858 TGAAATTAAA
* *
1185868 AAAATAATTTAAG-AACTAA-TATTTAGAATATTATGGT
1 AAAATAATTTAAGAAACTAAGTATTTAGAATATTAGGGC
* *
1185905 GAAATAATTTAAGAAACTAAGTATTTAGAATGTTAGGGC
1 AAAATAATTTAAGAAACTAAGTATTTAGAATATTAGGGC
1185944 AAAATAATTT
1 AAAATAATTT
1185954 TGGAATTAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
37 12 0.29
38 6 0.14
39 24 0.57
ACGTcount: A:0.48, C:0.03, G:0.14, T:0.35
Consensus pattern (39 bp):
AAAATAATTTAAGAAACTAAGTATTTAGAATATTAGGGC
Found at i:1188377 original size:59 final size:59
Alignment explanation
Indices: 1188310--1188480 Score: 184
Period size: 60 Copynumber: 2.9 Consensus size: 59
1188300 TAAAACTTTT
*
1188310 ATTTTAAATTAATTCTTAAACTTTTAAATATTTTAATTTCATCCCAAATTAT-AACTCTC
1 ATTTTAAATTAATTCTTAAACTTTTGAATATTTTAATTTCATCCCAAATTATGAA-TCTC
* * * * *
1188369 ATTTTAAA-TCATCTCTTAAGCTTTTGAACATTTTAATTTCATCGCTAAACTATGAATCTC
1 ATTTTAAATTAAT-TCTTAAACTTTTGAATATTTTAATTTCATC-CCAAATTATGAATCTC
* * * * **
1188429 TTTTTAAATTGATCCCTAAACTTTTGAATATTCCAATTTCATCCTCAAATTA
1 ATTTTAAATTAATTCTTAAACTTTTGAATATTTTAATTTCATCC-CAAATTA
1188481 ATCCAACTAT
Statistics
Matches: 91, Mismatches: 16, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
58 3 0.03
59 36 0.40
60 47 0.52
61 5 0.05
ACGTcount: A:0.34, C:0.18, G:0.04, T:0.45
Consensus pattern (59 bp):
ATTTTAAATTAATTCTTAAACTTTTGAATATTTTAATTTCATCCCAAATTATGAATCTC
Found at i:1188454 original size:60 final size:59
Alignment explanation
Indices: 1188295--1188477 Score: 181
Period size: 59 Copynumber: 3.1 Consensus size: 59
1188285 TCACAATTCT
* * * * *
1188295 CAAACTAAAACTTTTATTTTAAATTAATTCTTAAACTTTTAAATATTTTAATTTCATCC
1 CAAACTATAACTCTCATTTTAAATTAATCCTTAAACTTTTGAATATTTTAATTTCATCC
* * * *
1188354 CAAATTATAACTCTCATTTTAAA-TCATCTCTTAAGCTTTTGAACATTTTAATTTCATCGC
1 CAAACTATAACTCTCATTTTAAATTAATC-CTTAAACTTTTGAATATTTTAATTTCATC-C
* * * * **
1188414 TAAACTATGAA-TCTCTTTTTAAATTGATCCCTAAACTTTTGAATATTCCAATTTCATCC
1 CAAACTAT-AACTCTCATTTTAAATTAATCCTTAAACTTTTGAATATTTTAATTTCATCC
1188473 TCAAA
1 -CAAA
1188478 TTAATCCAAC
Statistics
Matches: 100, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
58 3 0.03
59 46 0.46
60 45 0.45
61 6 0.06
ACGTcount: A:0.35, C:0.18, G:0.03, T:0.44
Consensus pattern (59 bp):
CAAACTATAACTCTCATTTTAAATTAATCCTTAAACTTTTGAATATTTTAATTTCATCC
Found at i:1188589 original size:2 final size:2
Alignment explanation
Indices: 1188582--1188611 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1188572 AAGGGATGTA
1188582 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
1188612 TGGGATAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1188710 original size:60 final size:60
Alignment explanation
Indices: 1188632--1188789 Score: 166
Period size: 60 Copynumber: 2.7 Consensus size: 60
1188622 TTAGTGTTAA
* * * * * *
1188632 AAAAGTTTGGGGAATAATTTAGAATGATG-GTCATAGTTTGGGGATGAAATTGAAATGTCT
1 AAAAGTTTGAGGAATAATTTAAAAT-AAGAGTCATACTTTGAGGATGAAATTAAAATGTCT
* * * *
1188692 AAAAGTTTGAGGACTAATTTAAAATAAGAGTCATACTTTGAGGATTAAATTAAAATATTT
1 AAAAGTTTGAGGAATAATTTAAAATAAGAGTCATACTTTGAGGATGAAATTAAAATGTCT
*
1188752 AAAA---T-A-GACTAATTTAAAATAAGAGTCATACTTTGAGG
1 AAAAGTTTGAGGAATAATTTAAAATAAGAGTCATACTTTGAGG
1188790 TCATGTGATA
Statistics
Matches: 87, Mismatches: 10, Indels: 7
0.84 0.10 0.07
Matches are distributed among these distances:
55 32 0.37
56 1 0.01
57 1 0.01
59 2 0.02
60 51 0.59
ACGTcount: A:0.42, C:0.05, G:0.20, T:0.33
Consensus pattern (60 bp):
AAAAGTTTGAGGAATAATTTAAAATAAGAGTCATACTTTGAGGATGAAATTAAAATGTCT
Found at i:1194506 original size:24 final size:24
Alignment explanation
Indices: 1194474--1194529 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
1194464 CTATTCTTTC
1194474 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
1194498 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
*
1194522 GTTTCAAT
1 GCTTCAAT
1194530 CGAACTTCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (24 bp):
GCTTCAATTGAGCTCAAATTTTAG
Found at i:1196983 original size:12 final size:14
Alignment explanation
Indices: 1196966--1196998 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1196956 TAGATTTATT
1196966 TAATATTA-TT-AA
1 TAATATTATTTAAA
1196978 TAATATTATTTAAA
1 TAATATTATTTAAA
1196992 TAATATT
1 TAATATT
1196999 GTATTTTAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.42
13 2 0.11
14 9 0.47
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TAATATTATTTAAA
Done.