Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009462.1 Hibiscus syriacus cultivar Beakdansim tig00113725_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: 20687664
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 91
Found at i:1093162 original size:34 final size:34
Alignment explanation
Indices: 1093124--1093223 Score: 130
Period size: 33 Copynumber: 3.0 Consensus size: 34
1093114 AAATTTAATG
*
1093124 TTAAATTTTGAATACTATAATTTATATTTTAAAT
1 TTAAATTTTGAATAATATAATTTATATTTTAAAT
* * * *
1093158 TTAAA-TTTGAATAATATTATTTTTATTTTTATT
1 TTAAATTTTGAATAATATAATTTATATTTTAAAT
* *
1093191 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTTGAATAATATAATTTATATTTTAAA
1093224 AACATTTATC
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (34 bp):
TTAAATTTTGAATAATATAATTTATATTTTAAAT
Found at i:1093831 original size:21 final size:21
Alignment explanation
Indices: 1093743--1093836 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
1093733 TATGGTATAA
*
1093743 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
1093764 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
1093785 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
1093806 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
1093827 AACCCTGCGG
1 AACCCTGCGG
1093837 AGATGGCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 3 0.04
21 63 0.91
22 3 0.04
ACGTcount: A:0.20, C:0.27, G:0.35, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:1093866 original size:21 final size:21
Alignment explanation
Indices: 1093840--1093887 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1093830 CCTGCGGAGA
*
1093840 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
1093861 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
1093882 GGGCAT
1 TGGCAT
1093888 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:1095654 original size:34 final size:31
Alignment explanation
Indices: 1095611--1095698 Score: 95
Period size: 31 Copynumber: 2.7 Consensus size: 31
1095601 TTAATAATTC
*
1095611 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATAATTATATAAATA-TA--TTAA
* *
1095645 TAAAAAAATAATATTTACATAAATATATTAA
1 TAAAAAAATAATAATTATATAAATATATTAA
* * *
1095676 TATAAAAATAATAACTATTTAAA
1 TAAAAAAATAATAATTATATAAA
1095699 AAATACTAAC
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
31 22 0.48
33 2 0.04
34 22 0.48
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (31 bp):
TAAAAAAATAATAATTATATAAATATATTAA
Found at i:1095688 original size:31 final size:33
Alignment explanation
Indices: 1095611--1095689 Score: 99
Period size: 34 Copynumber: 2.4 Consensus size: 33
1095601 TTAATAATTC
* *
1095611 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATAATTACATAAATATTA-TTTAA
*
1095645 TAAAAAAATAATATTTACATAAATA-TA-TTAA
1 TAAAAAAATAATAATTACATAAATATTATTTAA
*
1095676 TATAAAAATAATAA
1 TAAAAAAATAATAA
1095690 CTATTTAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
31 16 0.40
33 2 0.05
34 22 0.55
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (33 bp):
TAAAAAAATAATAATTACATAAATATTATTTAA
Found at i:1095713 original size:32 final size:34
Alignment explanation
Indices: 1095644--1095718 Score: 95
Period size: 32 Copynumber: 2.3 Consensus size: 34
1095634 TATTATTTTA
* *
1095644 ATAAAAA-AATAATATTTACATAAATATATTAAT
1 ATAAAAATAATAATATTTACATAAATATACTAAC
1095677 ATAAAAATAATAACTATTTA-A-AAA-ATACTAAC
1 ATAAAAATAATAA-TATTTACATAAATATACTAAC
1095709 ATAAAAATAA
1 ATAAAAATAA
1095719 ATTTCTTACC
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
32 16 0.42
33 10 0.26
34 6 0.16
35 6 0.16
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (34 bp):
ATAAAAATAATAATATTTACATAAATATACTAAC
Found at i:1101465 original size:15 final size:14
Alignment explanation
Indices: 1101445--1101479 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
1101435 ATATTTTTTA
1101445 ATTTTTTTAAAATAT
1 ATTTTTTT-AAATAT
1101460 ATTTTTTTAAATAT
1 ATTTTTTTAAATAT
*
1101474 GTTTTT
1 ATTTTT
1101480 AAGGAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (14 bp):
ATTTTTTTAAATAT
Found at i:1101466 original size:25 final size:27
Alignment explanation
Indices: 1101431--1101481 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
1101421 ATTGGTCCAT
*
1101431 ATATATATTTTTTAAT-T-TTTTTAAA
1 ATATATATTTTTAAATATGTTTTTAAA
*
1101456 ATATATTTTTTTAAATATGTTTTTAA
1 ATATATATTTTTAAATATGTTTTTAA
1101482 GGAATTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 14 0.64
26 1 0.05
27 7 0.32
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (27 bp):
ATATATATTTTTAAATATGTTTTTAAA
Found at i:1107928 original size:21 final size:21
Alignment explanation
Indices: 1107880--1107928 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
1107870 ACTAAAATCT
* *
1107880 AGTTAATTAGTTTGTTAGTATA
1 AGTT-ATTAGTTTGCTAATATA
* *
1107902 AATTATTAGTTTGCTAATTTA
1 AGTTATTAGTTTGCTAATATA
1107923 AGTTAT
1 AGTTAT
1107929 ATTATATTAG
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.33, C:0.02, G:0.14, T:0.51
Consensus pattern (21 bp):
AGTTATTAGTTTGCTAATATA
Found at i:1107929 original size:28 final size:28
Alignment explanation
Indices: 1107898--1107963 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
1107888 AGTTTGTTAG
1107898 TATAAATTATTAGTTTGCTAATTTAAGT
1 TATAAATTATTAGTTTGCTAATTTAAGT
* * *
1107926 TAT-ATTATATTAGTTTGTTAGTTTAAGT
1 TATAAAT-TATTAGTTTGCTAATTTAAGT
*
1107954 TATATATTAT
1 TATAAATTAT
1107964 ATTATATAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
27 2 0.06
28 28 0.90
29 1 0.03
ACGTcount: A:0.33, C:0.02, G:0.11, T:0.55
Consensus pattern (28 bp):
TATAAATTATTAGTTTGCTAATTTAAGT
Found at i:1107989 original size:8 final size:8
Alignment explanation
Indices: 1107976--1108000 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1107966 TATATAAAAA
1107976 ATTAGTTT
1 ATTAGTTT
1107984 ATTAGTTT
1 ATTAGTTT
1107992 ATTAGTTT
1 ATTAGTTT
1108000 A
1 A
1108001 AGTTATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (8 bp):
ATTAGTTT
Found at i:1108330 original size:22 final size:21
Alignment explanation
Indices: 1108293--1108333 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
1108283 GATTGATTCG
1108293 AAGAAAGAAACAAAGAAGGAA
1 AAGAAAGAAACAAAGAAGGAA
1108314 AAGAAAGGAAA-AGAAGAAGG
1 AAGAAA-GAAACA-AAGAAGG
1108334 CATAAATACG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.68, C:0.02, G:0.29, T:0.00
Consensus pattern (21 bp):
AAGAAAGAAACAAAGAAGGAA
Found at i:1108507 original size:23 final size:24
Alignment explanation
Indices: 1108463--1108507 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
1108453 AATTGTGTTT
**
1108463 AAAAATATTTAGTGTTGTTTTAAA
1 AAAAATATTTAGTGTTAATTTAAA
*
1108487 AAAAATATTTTGT-TTAATTTA
1 AAAAATATTTAGTGTTAATTTA
1108508 TATTGTATGT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 6 0.33
24 12 0.67
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (24 bp):
AAAAATATTTAGTGTTAATTTAAA
Found at i:1111799 original size:22 final size:22
Alignment explanation
Indices: 1111774--1111850 Score: 59
Period size: 22 Copynumber: 3.3 Consensus size: 22
1111764 TGATTAGTAA
1111774 TAATGAAATTATTATTAATATT
1 TAATGAAATTATTATTAATATT
* *
1111796 TAATG-ATTTGA-TAGTAATGATTAGT
1 TAATGAAATT-ATTATTAAT-A-T--T
1111821 AATAATGAAATTATTATTAATATT
1 --TAATGAAATTATTATTAATATT
1111845 TAATGA
1 TAATGA
1111851 TTTGATAGTA
Statistics
Matches: 42, Mismatches: 4, Indels: 18
0.66 0.06 0.28
Matches are distributed among these distances:
21 9 0.21
22 13 0.31
23 1 0.02
24 1 0.02
25 1 0.02
26 1 0.02
27 7 0.17
28 9 0.21
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.45
Consensus pattern (22 bp):
TAATGAAATTATTATTAATATT
Found at i:1111804 original size:49 final size:49
Alignment explanation
Indices: 1111734--1111921 Score: 331
Period size: 49 Copynumber: 3.8 Consensus size: 49
1111724 GGCACCCATC
*
1111734 TATTATTAATATTTAATGATTTAATAGTAATGATTAGTAATAATGAAAT
1 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
1111783 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
1 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
* *
1111832 TATTATTAATATTTAATGATTTGATAGTAATAATTAGTAATAATAAAAT
1 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
* *
1111881 TATTATTAATATTTAATTATTTGATAGTAATGATAAGTAAT
1 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAAT
1111922 TATTAATAAT
Statistics
Matches: 133, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 133 1.00
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (49 bp):
TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
Found at i:1111870 original size:59 final size:57
Alignment explanation
Indices: 1111807--1111942 Score: 153
Period size: 49 Copynumber: 2.5 Consensus size: 57
1111797 AATGATTTGA
1111807 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATAAT
1 TAGTAAT-ATTA-TAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATAAT
* *
1111866 TAG---TA--ATAAT-A--AAATTATTATTAATATTTAATTATTTGATAGTAATGAT
1 TAGTAATATTATAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATAAT
*
1111915 AAGTAATTATTAATAATAATGAAATTAT
1 TAGTAA-TATT-ATAATAATGAAATTAT
1111943 AATAATAATG
Statistics
Matches: 64, Mismatches: 3, Indels: 20
0.74 0.03 0.23
Matches are distributed among these distances:
49 38 0.59
51 1 0.02
52 4 0.06
53 3 0.05
55 1 0.02
56 6 0.09
57 1 0.02
59 10 0.16
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (57 bp):
TAGTAATATTATAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATAAT
Found at i:1111933 original size:17 final size:17
Alignment explanation
Indices: 1111919--1111953 Score: 61
Period size: 17 Copynumber: 2.0 Consensus size: 17
1111909 AATGATAAGT
1111919 AATTATTAATAATAATGA
1 AATTA-TAATAATAATGA
1111937 AATTATAATAATAATGA
1 AATTATAATAATAATGA
1111954 TTTACTCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (17 bp):
AATTATAATAATAATGA
Found at i:1112153 original size:12 final size:11
Alignment explanation
Indices: 1112132--1112174 Score: 68
Period size: 12 Copynumber: 3.7 Consensus size: 11
1112122 CATAAAAATG
1112132 ATTTAATAATA
1 ATTTAATAATA
1112143 ATTTAAATAATA
1 ATTT-AATAATA
1112155 ATTTAATAATGA
1 ATTTAATAAT-A
1112167 ATTTAATA
1 ATTTAATA
1112175 TTTAATGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.33
12 20 0.67
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (11 bp):
ATTTAATAATA
Found at i:1112158 original size:23 final size:23
Alignment explanation
Indices: 1112124--1112172 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
1112114 CAATTAACCA
*
1112124 TAAAAATGATTTAATAAT-AATT
1 TAAAAATAATTTAATAATGAATT
1112146 TAAATAATAATTTAATAATGAATT
1 TAAA-AATAATTTAATAATGAATT
1112170 TAA
1 TAA
1112173 TATTTAATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 4 0.17
23 13 0.54
24 7 0.29
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (23 bp):
TAAAAATAATTTAATAATGAATT
Found at i:1112222 original size:26 final size:25
Alignment explanation
Indices: 1112196--1112428 Score: 201
Period size: 26 Copynumber: 9.3 Consensus size: 25
1112186 GATGATTTAG
* *
1112196 TAATGATTCGATAATAATTATTATAG
1 TAATGATT-GATAATAATCATTATAA
1112222 TAATGATTCGATAATAATCATTATAA
1 TAATGATT-GATAATAATCATTATAA
*
1112248 TAATGATTTAGTAATAATCATTATAA
1 TAATGATTGA-TAATAATCATTATAA
*
1112274 TAATGATTTAGTAATAATCATTATAA
1 TAATGATTGA-TAATAATCATTATAA
*
1112300 TAATGATT--TAATAATGATT-TAAA
1 TAATGATTGATAATAATCATTAT-AA
* * * * * *
1112323 TATTTATTGAT-TTGATGATT-TAG
1 TAATGATTGATAATAATCATTATAA
1112346 TAATGATTTGATAATAATCATTATAA
1 TAATGA-TTGATAATAATCATTATAA
* *
1112372 TAATGATT--TAATAATAATGATAA
1 TAATGATTGATAATAATCATTATAA
* * * *
1112395 TAATGATTTAATAATAGTAATGATAA
1 TAATGA-TTGATAATAATCATTATAA
1112421 TAATGATT
1 TAATGATT
1112429 TAATAGTAAT
Statistics
Matches: 179, Mismatches: 18, Indels: 21
0.82 0.08 0.10
Matches are distributed among these distances:
22 1 0.01
23 42 0.23
24 15 0.08
25 12 0.07
26 109 0.61
ACGTcount: A:0.45, C:0.03, G:0.10, T:0.43
Consensus pattern (25 bp):
TAATGATTGATAATAATCATTATAA
Found at i:1112311 original size:23 final size:23
Alignment explanation
Indices: 1112207--1112483 Score: 164
Period size: 26 Copynumber: 11.2 Consensus size: 23
1112197 AATGATTCGA
* *
1112207 TAATAATTATTATAGTAATGATT
1 TAATAATCATTATAATAATGATT
1112230 CGATAATAATCATTATAATAATGATTT
1 ---TAATAATCATTATAATAATGA-TT
1112257 AGTAATAATCATTATAATAATGATTT
1 --TAATAATCATTATAATAATGA-TT
1112283 AGTAATAATCATTATAATAATGATT
1 --TAATAATCATTATAATAATGATT
* * *
1112308 TAATAATGATT-TAAATATTTATT
1 TAATAATCATTAT-AATAATGATT
* * * * *
1112331 GATTTGATGATT-TAGTAATGATTT
1 TA-ATAATCATTATAATAATGA-TT
1112355 GATAATAATCATTATAATAATGATT
1 --TAATAATCATTATAATAATGATT
* *
1112380 TAATAATAATGATAATAATGATT
1 TAATAATCATTATAATAATGATT
1112403 TAATAAT-AGTAATGATAATAATGATT
1 TAATAATCA-T--T-ATAATAATGATT
* * * *
1112429 TAATAGTAATTATTTAGTAATTATT
1 TAATAATCATTA--TAATAATGATT
* * *
1112454 TAGTAATGATTTTATAATAATAATT
1 TAATAATCA--TTATAATAATGATT
1112479 TAATA
1 TAATA
1112484 TTAATGATTT
Statistics
Matches: 205, Mismatches: 30, Indels: 33
0.76 0.11 0.12
Matches are distributed among these distances:
22 2 0.01
23 54 0.26
24 11 0.05
25 38 0.19
26 94 0.46
27 6 0.03
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.44
Consensus pattern (23 bp):
TAATAATCATTATAATAATGATT
Found at i:1112363 original size:14 final size:13
Alignment explanation
Indices: 1112346--1112499 Score: 78
Period size: 14 Copynumber: 12.1 Consensus size: 13
1112336 GATGATTTAG
1112346 TAATGATTTGATAA
1 TAATGATTT-ATAA
*
1112360 TAATCA-TTATAA
1 TAATGATTTATAA
1112372 TAATGATTTAATAA
1 TAATGATTT-ATAA
1112386 TAATG----ATAA
1 TAATGATTTATAA
1112395 TAATGATTTAATAA
1 TAATGATTT-ATAA
* * *
1112409 TAGT-AATGATAA
1 TAATGATTTATAA
*
1112421 TAATGATTTAATAG
1 TAATGATTT-ATAA
*
1112435 TAATTATTTAGTAA
1 TAATGATTTA-TAA
*
1112449 T--T-A-TT-TAG
1 TAATGATTTATAA
1112457 TAATGATTTTATAA
1 TAATGA-TTTATAA
* *
1112471 TAATAATTTAATAT
1 TAATGATTT-ATAA
1112485 TAATGATTTAATAA
1 TAATGATTT-ATAA
1112499 T
1 T
1112500 TATTACTTAT
Statistics
Matches: 106, Mismatches: 17, Indels: 34
0.68 0.11 0.22
Matches are distributed among these distances:
8 3 0.03
9 9 0.08
10 3 0.03
11 2 0.02
12 17 0.16
13 14 0.13
14 58 0.55
ACGTcount: A:0.46, C:0.01, G:0.08, T:0.45
Consensus pattern (13 bp):
TAATGATTTATAA
Found at i:1112396 original size:9 final size:9
Alignment explanation
Indices: 1112382--1112427 Score: 58
Period size: 9 Copynumber: 5.2 Consensus size: 9
1112372 TAATGATTTA
1112382 ATAATAATG
1 ATAATAATG
1112391 ATAATAATG
1 ATAATAATG
* *
1112400 AT-TTAATA
1 ATAATAATG
*
1112408 ATAGTAATG
1 ATAATAATG
1112417 ATAATAATG
1 ATAATAATG
1112426 AT
1 AT
1112428 TTAATAGTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
8 6 0.19
9 25 0.81
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (9 bp):
ATAATAATG
Found at i:1112398 original size:150 final size:145
Alignment explanation
Indices: 1112123--1112465 Score: 440
Period size: 150 Copynumber: 2.3 Consensus size: 145
1112113 TCAATTAACC
*
1112123 ATAAAAATGATTTAATAATAAT-TTA-AATAATAATTTAATAATGAATTTAATATTTAATGATTT
1 ATAATAATGATTTAATAATAATATTATAATAATAATTTAATAATG-ATTTAATATTTAATGATTT
* * *
1112186 GATGATTTAGTAATGATTCGATAATAATTATTATAGTAATGATTCGATAATAATCATTATAATAA
65 GATGATTTAGTAATGATTCGATAATAATCATTATAATAATGATTCAATAATAATC---ATAATAA
* * *
1112251 TGATTTAGTAATAATCATT
127 TGATTTAATAATAATAATG
* * *
1112270 ATAATAATGATTTAGTAATAATCATTATAATAATGATTTAATAATGATTTAAATATTTATTGATT
1 ATAATAATGATTTAATAATAAT-ATTATAATAATAATTTAATAATGATTT-AATATTTAATGATT
* * *
1112335 TGATGATTTAGTAATGATTTGATAATAATCATTATAATAATGATTTAATAATAATGATAATAATG
64 TGATGATTTAGTAATGATTCGATAATAATCATTATAATAATGATTCAATAATAATCATAATAATG
*
1112400 ATTTAATAATAGTAATG
129 ATTTAATAATAATAATG
* * * *
1112417 ATAATAATGATTTAATAGTAATTATT-TAGTAATTATTTAGTAATGATTT
1 ATAATAATGATTTAATAATAA-TATTATAATAATAATTTAATAATGATTT
1112466 TATAATAATA
Statistics
Matches: 172, Mismatches: 19, Indels: 11
0.85 0.09 0.05
Matches are distributed among these distances:
146 20 0.12
147 64 0.37
148 1 0.01
149 7 0.04
150 80 0.47
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.44
Consensus pattern (145 bp):
ATAATAATGATTTAATAATAATATTATAATAATAATTTAATAATGATTTAATATTTAATGATTTG
ATGATTTAGTAATGATTCGATAATAATCATTATAATAATGATTCAATAATAATCATAATAATGAT
TTAATAATAATAATG
Found at i:1112491 original size:150 final size:149
Alignment explanation
Indices: 1112123--1112499 Score: 414
Period size: 147 Copynumber: 2.5 Consensus size: 149
1112113 TCAATTAACC
* * *
1112123 ATAAAAATGATTTAATAATAAT--TTA-AATAATAATTTAATAATGAATT---TAATATTTAATG
1 ATAATAATGATTTAATAATAATCATTATAATAATGATTTAATAATGATTTAAATAATATTTAAT-
* * * *
1112182 ATTTGATGATTTAGTAATGATTCGATAATAATTATTATAGTAATGATTCGATAATAATCATTATA
65 A-TTGATGATTTAGTAATGATTCGATAATAATCATTATAATAATGATT--ATAATAATAATGATA
* * *
1112247 ATAATGATTTAGTAATAATCATT
127 ATAATGATTTAATAATAATAATG
* * *
1112270 ATAATAATGATTTAGTAATAATCATTATAATAATGATTTAATAATGATTTAAAT-ATTTATTGAT
1 ATAATAATGATTTAATAATAATCATTATAATAATGATTTAATAATGATTTAAATAATAT-TTAAT
*
1112334 -TTGATGATTTAGTAATGATTTGATAATAATCATTATAATAATGATT-TAATAATAATGATAATA
65 ATTGATGATTTAGTAATGATTCGATAATAATCATTATAATAATGATTATAATAATAATGATAATA
*
1112397 ATGATTTAATAATAGTAATG
130 ATGATTTAATAATAATAATG
* * * * *
1112417 ATAATAATGATTTAATAGTAATTATT-TAGTAATTATTTAGTAATGATTTTATAATAATAATTTA
1 ATAATAATGATTTAATAATAATCATTATAATAATGATTTAATAATGA-TTTA-AATAAT-ATTTA
* *
1112481 ATATTAATGATTTAATAAT
63 ATATTGATGATTTAGTAAT
1112500 TATTACTTAT
Statistics
Matches: 193, Mismatches: 25, Indels: 21
0.81 0.10 0.09
Matches are distributed among these distances:
146 17 0.09
147 78 0.40
148 3 0.02
149 9 0.05
150 78 0.40
152 3 0.02
153 5 0.03
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.44
Consensus pattern (149 bp):
ATAATAATGATTTAATAATAATCATTATAATAATGATTTAATAATGATTTAAATAATATTTAATA
TTGATGATTTAGTAATGATTCGATAATAATCATTATAATAATGATTATAATAATAATGATAATAA
TGATTTAATAATAATAATG
Found at i:1112667 original size:17 final size:16
Alignment explanation
Indices: 1112627--1112668 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
1112617 AATGATTTAC
1112627 TAATTATTATTAATAA
1 TAATTATTATTAATAA
*
1112643 TAATTTATTATTAATATT
1 TAA-TTATTATTAATA-A
1112661 TAATTATT
1 TAATTATT
1112669 TGATACTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 3 0.13
17 17 0.74
18 3 0.13
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TAATTATTATTAATAA
Found at i:1115041 original size:22 final size:22
Alignment explanation
Indices: 1115016--1115064 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
1115006 ACAACTAATA
*
1115016 AACTATTCTTTAATATAACTTT
1 AACTATTCTTTAATATAACGTT
1115038 AACTATTCTTTAATATAACGTT
1 AACTATTCTTTAATATAACGTT
1115060 AACTA
1 AACTA
1115065 ATAAACTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.39, C:0.14, G:0.02, T:0.45
Consensus pattern (22 bp):
AACTATTCTTTAATATAACGTT
Found at i:1115042 original size:30 final size:30
Alignment explanation
Indices: 1115008--1115133 Score: 103
Period size: 30 Copynumber: 4.4 Consensus size: 30
1114998 TCCCTTAAAC
1115008 AACTAATAAACTATTCTTTAATATAAC--T
1 AACTAATAAACTATTCTTTAATATAACTTT
*
1115036 ---T--T-AACTATTCTTTAATATAACGTT
1 AACTAATAAACTATTCTTTAATATAACTTT
* *
1115060 AACTAATAAACTATTTTTTAATATAACTTA
1 AACTAATAAACTATTCTTTAATATAACTTT
1115090 AACTAATAAA-TGATT-TTTAATTATAA-TTT
1 AACTAATAAACT-ATTCTTTAA-TATAACTTT
*
1115119 ATTACTAAAAAACTA
1 A--ACTAATAAACTA
1115134 ATTAACTAAT
Statistics
Matches: 80, Mismatches: 5, Indels: 23
0.74 0.05 0.21
Matches are distributed among these distances:
22 19 0.24
23 1 0.01
24 1 0.01
25 1 0.01
27 1 0.01
29 10 0.12
30 37 0.46
31 9 0.11
32 1 0.01
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.43
Consensus pattern (30 bp):
AACTAATAAACTATTCTTTAATATAACTTT
Found at i:1115092 original size:22 final size:22
Alignment explanation
Indices: 1115014--1115094 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 22
1115004 AAACAACTAA
*
1115014 TAAACTATTCTTTAATATAACT
1 TAAACTATTTTTTAATATAACT
* *
1115036 TTAACTATTCTTTAATATAACGTTAACT
1 TAAACTATT-TTTTA-AT-A---TAACT
1115064 AATAAACTATTTTTTAATATAACT
1 --TAAACTATTTTTTAATATAACT
1115088 TAAACTA
1 TAAACTA
1115095 ATAAATGATT
Statistics
Matches: 46, Mismatches: 5, Indels: 16
0.69 0.07 0.24
Matches are distributed among these distances:
22 15 0.33
23 3 0.07
24 7 0.15
25 1 0.02
27 1 0.02
28 7 0.15
29 4 0.09
30 8 0.17
ACGTcount: A:0.42, C:0.12, G:0.01, T:0.44
Consensus pattern (22 bp):
TAAACTATTTTTTAATATAACT
Found at i:1115413 original size:29 final size:29
Alignment explanation
Indices: 1115380--1115473 Score: 98
Period size: 29 Copynumber: 3.0 Consensus size: 29
1115370 TGTTTTACCC
1115380 TAATTTATAATAATAAACTAATTAACTAA
1 TAATTTATAATAATAAACTAATTAACTAA
* *
1115409 TAATTTATAACAATAAACTAATTTAAATAA
1 TAATTTATAATAATAAACTAA-TTAACTAA
* *
1115439 TTATTCTTTTATATAACTTAAACTAATTAACTAA
1 -TAAT-TTATA-ATAA--TAAACTAATTAACTAA
1115473 T
1 T
1115474 TTTTTTATAT
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
29 20 0.38
30 7 0.13
31 3 0.06
32 4 0.08
33 4 0.08
34 7 0.13
35 8 0.15
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (29 bp):
TAATTTATAATAATAAACTAATTAACTAA
Found at i:1115432 original size:18 final size:18
Alignment explanation
Indices: 1115379--1115433 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
1115369 TTGTTTTACC
*
1115379 CTAATTTATAATAATAAA
1 CTAATTTATAACAATAAA
1115397 CTAA--T-TAAC--T-AA
1 CTAATTTATAACAATAAA
1115409 -TAATTTATAACAATAAA
1 CTAATTTATAACAATAAA
1115426 CTAATTTA
1 CTAATTTA
1115434 AATAATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 14
0.66 0.02 0.32
Matches are distributed among these distances:
11 3 0.10
12 2 0.07
13 2 0.07
14 4 0.14
15 3 0.10
16 2 0.07
17 2 0.07
18 11 0.38
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (18 bp):
CTAATTTATAACAATAAA
Found at i:1115462 original size:35 final size:31
Alignment explanation
Indices: 1115422--1115485 Score: 83
Period size: 31 Copynumber: 1.9 Consensus size: 31
1115412 TTTATAACAA
1115422 TAAACTAATTTAAATAATTATTCTTTTATATAACT
1 TAAACTAA-TTAAATAA-T-TT-TTTTATATAACT
*
1115457 TAAACTAATTAACTAATTTTTTTATATAA
1 TAAACTAATTAAATAATTTTTTTATATAA
1115486 TATAAATTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 10 0.36
32 2 0.07
33 1 0.04
34 7 0.25
35 8 0.29
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (31 bp):
TAAACTAATTAAATAATTTTTTTATATAACT
Found at i:1115840 original size:11 final size:11
Alignment explanation
Indices: 1115824--1115859 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
1115814 TTGAAGGACT
1115824 GCAATAATGCA
1 GCAATAATGCA
*
1115835 GCAATAAGTGCT
1 GCAATAA-TGCA
1115847 GCAATAATGCA
1 GCAATAATGCA
1115858 GC
1 GC
1115860 TGAATTCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.39, C:0.19, G:0.22, T:0.19
Consensus pattern (11 bp):
GCAATAATGCA
Found at i:1116052 original size:29 final size:28
Alignment explanation
Indices: 1116010--1116117 Score: 129
Period size: 29 Copynumber: 4.0 Consensus size: 28
1116000 CGAGAACGTT
*
1116010 GGACGCCGGGCGTGCATGGCGTCCTTATA
1 GGACGCCGGGCGTGCATGGCGACC-TATA
*
1116039 GGACGTCGGGCGTGCATGGCGACCTATA
1 GGACGCCGGGCGTGCATGGCGACCTATA
1116067 --A----GGGCGTGCATGGCGACCTATAA
1 GGACGCCGGGCGTGCATGGCGACCTAT-A
*
1116090 GGACGCCGGGCGTGCATGTCGACCTATA
1 GGACGCCGGGCGTGCATGGCGACCTATA
1116118 CTGGTTCGTC
Statistics
Matches: 69, Mismatches: 3, Indels: 15
0.79 0.03 0.17
Matches are distributed among these distances:
22 20 0.29
23 1 0.01
25 1 0.01
26 1 0.01
28 5 0.07
29 41 0.59
ACGTcount: A:0.19, C:0.26, G:0.37, T:0.19
Consensus pattern (28 bp):
GGACGCCGGGCGTGCATGGCGACCTATA
Found at i:1116074 original size:22 final size:22
Alignment explanation
Indices: 1116046--1116091 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
1116036 ATAGGACGTC
1116046 GGGCGTGCATGGCGACCTATAA
1 GGGCGTGCATGGCGACCTATAA
1116068 GGGCGTGCATGGCGACCTATAA
1 GGGCGTGCATGGCGACCTATAA
1116090 GG
1 GG
1116092 ACGCCGGGCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.22, C:0.22, G:0.39, T:0.17
Consensus pattern (22 bp):
GGGCGTGCATGGCGACCTATAA
Found at i:1116093 original size:51 final size:51
Alignment explanation
Indices: 1116017--1116117 Score: 159
Period size: 51 Copynumber: 2.0 Consensus size: 51
1116007 GTTGGACGCC
* *
1116017 GGGCGTGCATGGCGTCCTTATAGGACGTCGGGCGTGCATGGCGACCTATAA
1 GGGCGTGCATGGCGACCTTATAGGACGCCGGGCGTGCATGGCGACCTATAA
*
1116068 GGGCGTGCATGGCGACC-TATAAGGACGCCGGGCGTGCATGTCGACCTATA
1 GGGCGTGCATGGCGACCTTAT-AGGACGCCGGGCGTGCATGGCGACCTATA
1116118 CTGGTTCGTC
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
50 3 0.07
51 43 0.93
ACGTcount: A:0.19, C:0.25, G:0.37, T:0.20
Consensus pattern (51 bp):
GGGCGTGCATGGCGACCTTATAGGACGCCGGGCGTGCATGGCGACCTATAA
Found at i:1117396 original size:22 final size:22
Alignment explanation
Indices: 1117370--1117453 Score: 138
Period size: 22 Copynumber: 3.9 Consensus size: 22
1117360 TACGAAAACA
1117370 AGGGAGAGAGAGAGGGAGGGAGG
1 AGGGAGAGAGAGAGGGAGGG-GG
1117393 -GGGAGAGAGAGAGGGAGGGGG
1 AGGGAGAGAGAGAGGGAGGGGG
1117414 AGGGAGAGAGAGAGGGAGGGGG
1 AGGGAGAGAGAGAGGGAGGGGG
1117436 AGGGAG-G-GAGAGGGAGGG
1 AGGGAGAGAGAGAGGGAGGG
1117454 AGAGTTTTTG
Statistics
Matches: 60, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
20 11 0.18
21 3 0.05
22 46 0.77
ACGTcount: A:0.31, C:0.00, G:0.69, T:0.00
Consensus pattern (22 bp):
AGGGAGAGAGAGAGGGAGGGGG
Found at i:1117400 original size:18 final size:18
Alignment explanation
Indices: 1117377--1117445 Score: 84
Period size: 18 Copynumber: 3.6 Consensus size: 18
1117367 ACAAGGGAGA
1117377 GAGAGAGGGAGGGAGGGG
1 GAGAGAGGGAGGGAGGGG
*
1117395 GAGAGAGAGAGGGAGGGG
1 GAGAGAGGGAGGGAGGGG
1117413 GAGGGAGAGAGAGAGGGAGGGG
1 GA--GAGAG-G-GAGGGAGGGG
*
1117435 GAGGGAGGGAG
1 GAGAGAGGGAG
1117446 AGGGAGGGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
18 22 0.50
19 1 0.02
20 9 0.20
22 12 0.27
ACGTcount: A:0.30, C:0.00, G:0.70, T:0.00
Consensus pattern (18 bp):
GAGAGAGGGAGGGAGGGG
Found at i:1117432 original size:4 final size:4
Alignment explanation
Indices: 1117370--1117455 Score: 62
Period size: 4 Copynumber: 23.5 Consensus size: 4
1117360 TACGAAAACA
* * * *
1117370 AGGG AGAG AGAG AGGG AGGG A-GG -GGG AGAG AGAG AGGG A-GG -GGG
1 AGGG AGGG AGGG AGGG AGGG AGGG AGGG AGGG AGGG AGGG AGGG AGGG
* *
1117414 AGGG AGAG AGAG AGGG A-GG -GGG AGGG AGGG A--G AGGG AGGG AG
1 AGGG AGGG AGGG AGGG AGGG AGGG AGGG AGGG AGGG AGGG AGGG AG
1117456 AGTTTTTGGC
Statistics
Matches: 68, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
2 2 0.03
3 12 0.18
4 54 0.79
ACGTcount: A:0.31, C:0.00, G:0.69, T:0.00
Consensus pattern (4 bp):
AGGG
Found at i:1117454 original size:18 final size:18
Alignment explanation
Indices: 1117370--1117457 Score: 79
Period size: 18 Copynumber: 4.8 Consensus size: 18
1117360 TACGAAAACA
*
1117370 AGGGAGAGAGAGAGGGAGGG
1 AGGGAGAG-G-GAGAGAGGG
* *
1117390 AGGGGGAGAGAGAGAGGG
1 AGGGAGAGGGAGAGAGGG
* *
1117408 AGGGGGAGGGAGAGAGAG
1 AGGGAGAGGGAGAGAGGG
* *
1117426 AGGGAGGGGGAGGGAGGG
1 AGGGAGAGGGAGAGAGGG
1117444 AGAGG-GAGGGAGAG
1 AG-GGAGAGGGAGAG
1117458 TTTTTGGCCT
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
18 47 0.84
19 2 0.04
20 7 0.12
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (18 bp):
AGGGAGAGGGAGAGAGGG
Found at i:1117912 original size:12 final size:12
Alignment explanation
Indices: 1117895--1117924 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
1117885 ATTATATAGT
1117895 AAAAAAAAGAAA
1 AAAAAAAAGAAA
1117907 AAAAAAAAGAAA
1 AAAAAAAAGAAA
1117919 AAAAAA
1 AAAAAA
1117925 TGCAGAGCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGAAA
Found at i:1121912 original size:46 final size:45
Alignment explanation
Indices: 1121823--1121916 Score: 145
Period size: 46 Copynumber: 2.1 Consensus size: 45
1121813 GATATCAACT
1121823 TTTTACGATTCTAAAGAAAGCAAAATTATATTAAAATATTAAAATA
1 TTTTACGATTCTAAAGAAAGCAAAATTATATTAAAATATTAAAA-A
* *
1121869 TTTTACGATTCTAAAGAAAGTAAAATTATATTAATCATA-TAAAAA
1 TTTTACGATTCTAAAGAAAGCAAAATTATATTAA-AATATTAAAAA
1121914 TTT
1 TTT
1121917 AAAATATTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
45 4 0.09
46 38 0.84
47 3 0.07
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.37
Consensus pattern (45 bp):
TTTTACGATTCTAAAGAAAGCAAAATTATATTAAAATATTAAAAA
Found at i:1128552 original size:22 final size:22
Alignment explanation
Indices: 1128524--1128576 Score: 90
Period size: 22 Copynumber: 2.4 Consensus size: 22
1128514 TCACAAACAT
1128524 AATTTTAGA-AACTAACAGTTCA
1 AATTTTA-ATAACTAACAGTTCA
1128546 AATTTTAATAACTAACAGTTCA
1 AATTTTAATAACTAACAGTTCA
1128568 AATTTTAAT
1 AATTTTAAT
1128577 TTTTCAGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 1 0.03
22 29 0.97
ACGTcount: A:0.45, C:0.11, G:0.06, T:0.38
Consensus pattern (22 bp):
AATTTTAATAACTAACAGTTCA
Found at i:1132465 original size:16 final size:16
Alignment explanation
Indices: 1132444--1132476 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1132434 GGATAATTAC
1132444 CATGATACCATTCTTT
1 CATGATACCATTCTTT
1132460 CATGATACCATTCTTT
1 CATGATACCATTCTTT
1132476 C
1 C
1132477 TATAATTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.06, T:0.42
Consensus pattern (16 bp):
CATGATACCATTCTTT
Found at i:1138839 original size:29 final size:30
Alignment explanation
Indices: 1138792--1138875 Score: 98
Period size: 29 Copynumber: 2.8 Consensus size: 30
1138782 AGTTGTTTAA
* * *
1138792 AAAATCAAAAGTTTAGGTATTAAAATGGACC
1 AAAA-CAATAGTTTAGGTACTAAAACGGACC
*
1138823 AAAA-AATAGTTTAGGTACTAAAACGGGCC
1 AAAACAATAGTTTAGGTACTAAAACGGACC
*
1138852 AAAACCAATAATTTAGGTACTAAA
1 AAAA-CAATAGTTTAGGTACTAAA
1138876 TGCGTTAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
29 25 0.54
31 21 0.46
ACGTcount: A:0.49, C:0.12, G:0.15, T:0.24
Consensus pattern (30 bp):
AAAACAATAGTTTAGGTACTAAAACGGACC
Found at i:1143189 original size:28 final size:28
Alignment explanation
Indices: 1143149--1143202 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
1143139 TACAAAACGC
*
1143149 GAGGTGTACGAGAAATTGAATTTATCGT
1 GAGGTGCACGAGAAATTGAATTTATCGT
1143177 GAGGTGCACGAGAAATTGAATTTATC
1 GAGGTGCACGAGAAATTGAATTTATC
1143203 ATGTGCAGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.33, C:0.09, G:0.28, T:0.30
Consensus pattern (28 bp):
GAGGTGCACGAGAAATTGAATTTATCGT
Found at i:1144151 original size:23 final size:23
Alignment explanation
Indices: 1144121--1144168 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
1144111 AAATAGATAG
1144121 TTTACTCTTGAGATTGGGTTTTA
1 TTTACTCTTGAGATTGGGTTTTA
1144144 TTTACTCTTGAGATTGGGTTTTA
1 TTTACTCTTGAGATTGGGTTTTA
1144167 TT
1 TT
1144169 GAAACTAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.17, C:0.08, G:0.21, T:0.54
Consensus pattern (23 bp):
TTTACTCTTGAGATTGGGTTTTA
Found at i:1145331 original size:19 final size:19
Alignment explanation
Indices: 1145288--1145332 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
1145278 GTACTATGCT
* *
1145288 TGAAATTAATGTTTGAGTA
1 TGAAATTAATGTTAGAATA
* *
1145307 TTAAATTAATGTTAGAATG
1 TGAAATTAATGTTAGAATA
1145326 TGAAATT
1 TGAAATT
1145333 TGATTATTTT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.18, T:0.42
Consensus pattern (19 bp):
TGAAATTAATGTTAGAATA
Found at i:1153785 original size:3 final size:3
Alignment explanation
Indices: 1153752--1153841 Score: 63
Period size: 3 Copynumber: 28.0 Consensus size: 3
1153742 ATAGTAATTG
* * * * *
1153752 TTA TTA GTA TTA GTA TTAA TTA TTA TGA TTA TTAA ATA CTAA TTA TTA
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TT-A TTA -TTA TTA TTA
* *
1153800 TTA TTTA TTA ATA TTTA TTA TTA TTA TTG TTAA TTA TTA TTA
1 TTA -TTA TTA TTA -TTA TTA TTA TTA TTA TT-A TTA TTA TTA
1153842 AATATTAAAT
Statistics
Matches: 67, Mismatches: 14, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
3 54 0.81
4 13 0.19
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:1153837 original size:23 final size:22
Alignment explanation
Indices: 1153730--1153838 Score: 110
Period size: 23 Copynumber: 4.8 Consensus size: 22
1153720 CAATTTTACA
* *
1153730 TATTATTAATTAATAGTAATTGT
1 TATTATT-ATTAATATTAATTAT
* *
1153753 TATTAGTATTAGTATTAATTAT
1 TATTATTATTAATATTAATTAT
* *
1153775 TATGATTATTAAATACTAATTAT
1 TATTATTATT-AATATTAATTAT
*
1153798 TATTATTTATTAATATTTATTAT
1 TATTA-TTATTAATATTAATTAT
*
1153821 TATTATTGTTAATTATTA
1 TATTATTATTAA-TATTA
1153839 TTAAATATTA
Statistics
Matches: 70, Mismatches: 13, Indels: 6
0.79 0.15 0.07
Matches are distributed among these distances:
22 26 0.37
23 39 0.56
24 5 0.07
ACGTcount: A:0.38, C:0.01, G:0.06, T:0.56
Consensus pattern (22 bp):
TATTATTATTAATATTAATTAT
Found at i:1153842 original size:10 final size:10
Alignment explanation
Indices: 1153730--1153848 Score: 80
Period size: 10 Copynumber: 11.5 Consensus size: 10
1153720 CAATTTTACA
1153730 TATTATTAAT
1 TATTATTAAT
* *
1153740 TAATAGTAAT
1 TATTATTAAT
*
1153750 TGTTATTAGTAT
1 TATTATTA--AT
*
1153762 TAGTATTAAT
1 TATTATTAAT
*
1153772 TATTA-TGAT
1 TATTATTAAT
1153781 TATTAAATACTAAT
1 TATT--AT--TAAT
*
1153795 TATTATTATT
1 TATTATTAAT
* *
1153805 TATTAATATT
1 TATTATTAAT
1153815 TATTATT-AT
1 TATTATTAAT
*
1153824 TATTGTTAAT
1 TATTATTAAT
*
1153834 TATTATTAAA
1 TATTATTAAT
1153844 TATTA
1 TATTA
1153849 AATATCTATG
Statistics
Matches: 84, Mismatches: 17, Indels: 16
0.72 0.15 0.14
Matches are distributed among these distances:
9 14 0.17
10 52 0.62
11 1 0.01
12 10 0.12
14 7 0.08
ACGTcount: A:0.39, C:0.01, G:0.05, T:0.55
Consensus pattern (10 bp):
TATTATTAAT
Found at i:1158576 original size:31 final size:31
Alignment explanation
Indices: 1158538--1158599 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
1158528 GCGTATTGAT
* *
1158538 GTTTTTAACTAGTACACTGGGTAACATATGG
1 GTTTTTAACCAGTACACTGGGTAACACATGG
1158569 GTTTTTAACCAGTACACTGGGTAACACATGG
1 GTTTTTAACCAGTACACTGGGTAACACATGG
1158600 CCCTTACTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (31 bp):
GTTTTTAACCAGTACACTGGGTAACACATGG
Found at i:1166497 original size:15 final size:15
Alignment explanation
Indices: 1166477--1166507 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1166467 CAACAGTTAG
1166477 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
1166492 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
1166507 A
1 A
1166508 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:1166698 original size:19 final size:18
Alignment explanation
Indices: 1166656--1166698 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
1166646 CAGTAATCCT
**
1166656 ATTCCCTGGTAATCTTTT
1 ATTCCCTGGTAATCTTAC
1166674 ATTTCCACTGGTAATCTTAC
1 A-TTCC-CTGGTAATCTTAC
1166694 ATTCC
1 ATTCC
1166699 GTGAACCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 8 0.38
20 12 0.57
ACGTcount: A:0.21, C:0.26, G:0.09, T:0.44
Consensus pattern (18 bp):
ATTCCCTGGTAATCTTAC
Found at i:1167063 original size:20 final size:20
Alignment explanation
Indices: 1167038--1167082 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
1167028 TTATCCGAAA
*
1167038 AAAAATCCGGTCTGGGGTTT
1 AAAAATCCGGTCTGAGGTTT
1167058 AAAAATCCGGTCTGAGGTTT
1 AAAAATCCGGTCTGAGGTTT
1167078 AAAAA
1 AAAAA
1167083 ATTGGATGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (20 bp):
AAAAATCCGGTCTGAGGTTT
Found at i:1167275 original size:21 final size:21
Alignment explanation
Indices: 1167249--1167296 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
1167239 GAAAAAACCG
1167249 GATCGGTTTTTATCCGATCCA
1 GATCGGTTTTTATCCGATCCA
*
1167270 GATCGGTTTTTATCCGATCCG
1 GATCGGTTTTTATCCGATCCA
1167291 GATCGG
1 GATCGG
1167297 ATTTAAATCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.17, C:0.23, G:0.25, T:0.35
Consensus pattern (21 bp):
GATCGGTTTTTATCCGATCCA
Found at i:1169534 original size:175 final size:175
Alignment explanation
Indices: 1169243--1169594 Score: 704
Period size: 175 Copynumber: 2.0 Consensus size: 175
1169233 TATTCACCAG
1169243 TCCCACAGAACCTCTTGATAGAGCTAGGTCAATTAGTAATTACCGCATCTAAACTAATAACATGT
1 TCCCACAGAACCTCTTGATAGAGCTAGGTCAATTAGTAATTACCGCATCTAAACTAATAACATGT
1169308 CAATAACCATATGCAAAGTTGGCAACAGGTTGCACACAAGAAATCACTTCCTTCTCCATCTTCAA
66 CAATAACCATATGCAAAGTTGGCAACAGGTTGCACACAAGAAATCACTTCCTTCTCCATCTTCAA
1169373 GTAAGATACAAGGAATACTTACAGAATACAAATATTCAACAGCTC
131 GTAAGATACAAGGAATACTTACAGAATACAAATATTCAACAGCTC
1169418 TCCCACAGAACCTCTTGATAGAGCTAGGTCAATTAGTAATTACCGCATCTAAACTAATAACATGT
1 TCCCACAGAACCTCTTGATAGAGCTAGGTCAATTAGTAATTACCGCATCTAAACTAATAACATGT
1169483 CAATAACCATATGCAAAGTTGGCAACAGGTTGCACACAAGAAATCACTTCCTTCTCCATCTTCAA
66 CAATAACCATATGCAAAGTTGGCAACAGGTTGCACACAAGAAATCACTTCCTTCTCCATCTTCAA
1169548 GTAAGATACAAGGAATACTTACAGAATACAAATATTCAACAGCTC
131 GTAAGATACAAGGAATACTTACAGAATACAAATATTCAACAGCTC
1169593 TC
1 TC
1169595 TCTGGGTTGT
Statistics
Matches: 177, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
175 177 1.00
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (175 bp):
TCCCACAGAACCTCTTGATAGAGCTAGGTCAATTAGTAATTACCGCATCTAAACTAATAACATGT
CAATAACCATATGCAAAGTTGGCAACAGGTTGCACACAAGAAATCACTTCCTTCTCCATCTTCAA
GTAAGATACAAGGAATACTTACAGAATACAAATATTCAACAGCTC
Found at i:1170102 original size:6 final size:6
Alignment explanation
Indices: 1170093--1170121 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1170083 TCGAGCCGGA
1170093 GCTGGT GCTGGT GCTGGT GCTGGT GCTGG
1 GCTGGT GCTGGT GCTGGT GCTGGT GCTGG
1170122 AGCCAGAGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.17, G:0.52, T:0.31
Consensus pattern (6 bp):
GCTGGT
Found at i:1170132 original size:18 final size:18
Alignment explanation
Indices: 1170080--1170136 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 18
1170070 AAGAAACTGT
*
1170080 TGCTCGAGCCGGAGCTGG
1 TGCTGGAGCCGGAGCTGG
* * *
1170098 TGCTGGTGCTGGTGCTGG
1 TGCTGGAGCCGGAGCTGG
*
1170116 TGCTGGAGCCAGAGCTGG
1 TGCTGGAGCCGGAGCTGG
1170134 TGC
1 TGC
1170137 CGGTGCACTT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.09, C:0.23, G:0.46, T:0.23
Consensus pattern (18 bp):
TGCTGGAGCCGGAGCTGG
Found at i:1176839 original size:15 final size:15
Alignment explanation
Indices: 1176805--1176845 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
1176795 AAATCATTAA
*
1176805 ATTAATAATT-AATC
1 ATTAATTATTAAATC
*
1176819 AATAATTATTAAATC
1 ATTAATTATTAAATC
1176834 ATTAATTATTAA
1 ATTAATTATTAA
1176846 TAAATCATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
14 8 0.35
15 15 0.65
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (15 bp):
ATTAATTATTAAATC
Found at i:1176855 original size:29 final size:28
Alignment explanation
Indices: 1176805--1176864 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
1176795 AAATCATTAA
* *
1176805 ATTAATAATTAATCAATAATTATTAAATC
1 ATTAATAATTAATAAATAATTAGT-AATC
* *
1176834 ATTAATTATTAATAAATCATTAGTAATC
1 ATTAATAATTAATAAATAATTAGTAATC
1176862 ATT
1 ATT
1176865 TGTATCAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 7 0.26
29 20 0.74
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (28 bp):
ATTAATAATTAATAAATAATTAGTAATC
Found at i:1176867 original size:76 final size:73
Alignment explanation
Indices: 1176727--1176878 Score: 191
Period size: 76 Copynumber: 2.0 Consensus size: 73
1176717 GTTTTTTACT
* * * * *
1176727 ATTAAATTATTATTAGTAATAATTATTATAATTTCATTATTAGTAATCATTAATAAATCTTTTGT
1 ATTAAATTATAATTAATAATAATTATTATAATTTAATTATTAATAATCATTAATAAATCATTTGT
1176792 ATCAAATC
66 ATCAAATC
*
1176800 ATTAAATTAATAATTAATCAATAATTATTA-AATCATTAATTATTAATAAATCATTAGT-AATCA
1 ATTAAATT-ATAATTAAT-AATAATTATTATAAT--TTAATTATTAAT-AATCATTAATAAATCA
1176863 TTTGTATCAAATC
61 TTTGTATCAAATC
1176876 ATT
1 ATT
1176879 TTAGTTTTTT
Statistics
Matches: 68, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
73 8 0.12
74 10 0.15
75 11 0.16
76 30 0.44
77 9 0.13
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.45
Consensus pattern (73 bp):
ATTAAATTATAATTAATAATAATTATTATAATTTAATTATTAATAATCATTAATAAATCATTTGT
ATCAAATC
Found at i:1177173 original size:27 final size:27
Alignment explanation
Indices: 1177143--1177198 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
1177133 ATCGAATATA
1177143 ATATAATCTACAAATTTATTATAAATC
1 ATATAATCTACAAATTTATTATAAATC
1177170 ATATAATCTACAAATTTATTATAAATC
1 ATATAATCTACAAATTTATTATAAATC
1177197 AT
1 AT
1177199 TATTATCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (27 bp):
ATATAATCTACAAATTTATTATAAATC
Found at i:1177219 original size:25 final size:25
Alignment explanation
Indices: 1177187--1177352 Score: 96
Period size: 25 Copynumber: 6.6 Consensus size: 25
1177177 CTACAAATTT
1177187 ATTA-TAAATCATTATTATCAAATC
1 ATTATTAAATCATTATTATCAAATC
* *
1177211 ATTATTAAATTATTAGTATCAAATC
1 ATTATTAAATCATTATTATCAAATC
1177236 ---ATTAAATCATTATTAAT-AAATC
1 ATTATTAAATCATTATT-ATCAAATC
* * * *
1177258 ATATGATTACAT-A-AATCATTAAATC
1 AT-T-ATTAAATCATTATTATCAAATC
**
1177283 ATTATTACTAATCATTAAAATTCAAATC
1 ATTATTA--AATCATTATTA-TCAAATC
* * *
1177311 ATTATT-AATAATTATTATTAAATT
1 ATTATTAAATCATTATTATCAAATC
1177335 ATTAGTATCAAATCATTA
1 ATTA-T-T-AAATCATTA
1177353 AATCATTGAA
Statistics
Matches: 107, Mismatches: 18, Indels: 30
0.69 0.12 0.19
Matches are distributed among these distances:
22 17 0.16
23 6 0.06
24 16 0.15
25 38 0.36
26 3 0.03
27 8 0.07
28 19 0.18
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.42
Consensus pattern (25 bp):
ATTATTAAATCATTATTATCAAATC
Found at i:1177237 original size:39 final size:39
Alignment explanation
Indices: 1177192--1177352 Score: 97
Period size: 36 Copynumber: 4.2 Consensus size: 39
1177182 AATTTATTAT
*
1177192 AAATCATTATTATCAAATCATTATTAAATTATTAGTATC
1 AAATCATTATTATCAAATCATTATTAAATCATTAGTATC
* * * *
1177231 AAATCATTA-AATC--ATTATTAATAAATCA-TA-TGATT
1 AAATCATTATTATCAAATCATTATTAAATCATTAGT-ATC
* * * * **
1177266 ACAT-A-AATCATTAAATCATTATTACTAATCATTAAAATTC
1 AAATCATTATTATCAAATCATTATTA--AATCATTAGTA-TC
* *
1177306 AAATCATTATTA--ATAATTATTATTAAATTATTAGTATC
1 AAATCATTATTATCA-AATCATTATTAAATCATTAGTATC
1177344 AAATCATTA
1 AAATCATTA
1177353 AATCATTGAA
Statistics
Matches: 90, Mismatches: 20, Indels: 25
0.67 0.15 0.19
Matches are distributed among these distances:
33 1 0.01
34 4 0.04
35 7 0.08
36 20 0.22
38 19 0.21
39 20 0.22
40 5 0.06
41 11 0.12
42 3 0.03
ACGTcount: A:0.47, C:0.10, G:0.02, T:0.42
Consensus pattern (39 bp):
AAATCATTATTATCAAATCATTATTAAATCATTAGTATC
Found at i:1177273 original size:17 final size:14
Alignment explanation
Indices: 1177238--1178317 Score: 175
Period size: 14 Copynumber: 78.0 Consensus size: 14
1177228 ATCAAATCAT
1177238 TAAATCATTATTAA
1 TAAATCATTATTAA
1177252 TAAATCATATGATTACA
1 TAAATCAT-T-ATTA-A
1177269 TAAATC---A-T--
1 TAAATCATTATTAA
*
1177277 TAAATCATTATTAC
1 TAAATCATTATTAA
*
1177291 T-AATCATTA-AAA
1 TAAATCATTATTAA
1177303 TTCAAATCATTATTAA
1 -T-AAATCATTATTAA
*
1177319 T--A--ATTATTAT
1 TAAATCATTATTAA
* *
1177329 TAAATTATTAGT-A
1 TAAATCATTATTAA
* *
1177342 TCAAATCATTAAATCAT
1 T-AAATCATT--ATTAA
* *
1177359 TGAATTATTATTAA
1 TAAATCATTATTAA
1177373 TAAATCATATGATTACA
1 TAAATCAT-T-ATTA-A
* *
1177390 CTTAAATCATTAAATCAT
1 --TAAATCATT--ATTAA
1177408 TAAATCATTATTAA
1 TAAATCATTATTAA
1177422 TAAATCATATGATTACA
1 TAAATCAT-T-ATTA-A
1177439 TAAATC---A-T--
1 TAAATCATTATTAA
*
1177447 TAAATCATTATTAT
1 TAAATCATTATTAA
* *
1177461 TAAACCATTA-AAA
1 TAAATCATTATTAA
1177474 TTCAAATCATTATTAA
1 -T-AAATCATTATTAA
1177490 T-AATCATTATT-A
1 TAAATCATTATTAA
1177502 TCAAATCATTA-T--
1 T-AAATCATTATTAA
* *
1177514 TAAATTATTAGT-A
1 TAAATCATTATTAA
* *
1177527 TCAAATCATTAAATCAT
1 T-AAATCATT--ATTAA
*
1177544 TGAATCATTATTAA
1 TAAATCATTATTAA
* *
1177558 TAAATCA-TATGAT
1 TAAATCATTATTAA
* * *
1177571 TACA-C-TTAAATCAT
1 TAAATCATT--ATTAA
1177585 TAAATCATTATTAA
1 TAAATCATTATTAA
1177599 TAAATCATATAATTACA
1 TAAATCAT-T-ATTA-A
1177616 TAAATC---A-T--
1 TAAATCATTATTAA
*
1177624 TAAATCATTATTAC
1 TAAATCATTATTAA
*
1177638 T-AATCATTA-AAA
1 TAAATCATTATTAA
1177650 TTCAAATCATTATTAA
1 -T-AAATCATTATTAA
1177666 T-AATCATTA-T--
1 TAAATCATTATTAA
* *
1177676 TAAATTATTAGT-A
1 TAAATCATTATTAA
1177689 TCAAATCATTAAATCATTGAA
1 T-AAATCA-T---T-ATT-AA
1177710 TAAATCATATGATTACA
1 TAAATCAT-T-ATTA-A
* *
1177727 CTTAAATCATTAAATCAT
1 --TAAATCATT--ATTAA
1177745 TAAATCATTATTAA
1 TAAATCATTATTAA
*
1177759 TAAATAATATGATTACA
1 TAAATCAT-T-ATTA-A
1177776 TAAATC---A-T--
1 TAAATCATTATTAA
*
1177784 TAAATCATTATTAT
1 TAAATCATTATTAA
*
1177798 TAAATCATTA-AAA
1 TAAATCATTATTAA
1177811 TTCAAATCATTATTAA
1 -T-AAATCATTATTAA
1177827 T-AATCATTATT-A
1 TAAATCATTATTAA
1177839 TCAAATCATTA-T--
1 T-AAATCATTATTAA
* *
1177851 TAAATTATTAGT-A
1 TAAATCATTATTAA
* *
1177864 TCAAATCATTAAATCAT
1 T-AAATCATT--ATTAA
*
1177881 TGAATCATTATTAA
1 TAAATCATTATTAA
* *
1177895 TAAATCA-TATGAT
1 TAAATCATTATTAA
* * *
1177908 TACA-C-TTAAATCAT
1 TAAATCATT--ATTAA
1177922 TAAATCATTATTAA
1 TAAATCATTATTAA
1177936 TAAATCATATAATTACA
1 TAAATCAT-T-ATTA-A
1177953 TAAATC---A-T--
1 TAAATCATTATTAA
*
1177961 TAAATCATTATTAT
1 TAAATCATTATTAA
*
1177975 TAAATCATTA-AAA
1 TAAATCATTATTAA
1177988 TTCAAATCATTATTAA
1 -T-AAATCATTATTAA
1178004 T-AATCATTATT-A
1 TAAATCATTATTAA
1178016 TCAAATCATTA-T--
1 T-AAATCATTATTAA
* *
1178028 TAAATTATTAGT-A
1 TAAATCATTATTAA
* *
1178041 TCAAATCATTAAATCAT
1 T-AAATCATT--ATTAA
1178058 TAAATCATTATTAA
1 TAAATCATTATTAA
1178072 TAAATCATATAATTACA
1 TAAATCAT-T-ATTA-A
1178089 TAAATCATTA--AA
1 TAAATCATTATTAA
* * *
1178101 T-CATTATTACTAA
1 TAAATCATTATTAA
* * *
1178114 T-AGTTA-AATT--
1 TAAATCATTATTAA
*
1178124 TCAAATCATTATTAG
1 T-AAATCATTATTAA
1178139 T-AATCATTATT-A
1 TAAATCATTATTAA
1178151 TCAAATCATTA-T--
1 T-AAATCATTATTAA
* *
1178163 TAAATTATTAGT-A
1 TAAATCATTATTAA
* *
1178176 TCAAATCATTAAATCAT
1 T-AAATCATT--ATTAA
* *
1178193 TGAATCATTATTTA
1 TAAATCATTATTAA
1178207 TAAATCATATGATTACA
1 TAAATCAT-T-ATTA-A
* *
1178224 CTTAAATCATTAGTAC
1 --TAAATCATTATTAA
1178240 TAAATC---A-T--
1 TAAATCATTATTAA
*
1178248 TAAATCATTATTAT
1 TAAATCATTATTAA
*
1178262 TAAATCATTA-AAA
1 TAAATCATTATTAA
1178275 TTTAAATCATTATTAA
1 --TAAATCATTATTAA
*
1178291 T-AATCATTATTAC
1 TAAATCATTATTAA
* *
1178304 CAAATTATTATTAA
1 TAAATCATTATTAA
1178318 ATTATTAATA
Statistics
Matches: 793, Mismatches: 115, Indels: 316
0.65 0.09 0.26
Matches are distributed among these distances:
8 36 0.05
10 11 0.01
11 57 0.07
12 43 0.05
13 115 0.15
14 250 0.32
15 70 0.09
16 107 0.13
17 59 0.07
18 4 0.01
19 33 0.04
20 6 0.01
21 2 0.00
ACGTcount: A:0.47, C:0.11, G:0.02, T:0.41
Consensus pattern (14 bp):
TAAATCATTATTAA
Found at i:1177404 original size:49 final size:46
Alignment explanation
Indices: 1177344--1177462 Score: 186
Period size: 49 Copynumber: 2.5 Consensus size: 46
1177334 TATTAGTATC
1177344 AAATCATTAAATCATTGAATTATTATTAATAAATCATATGATTACACTT
1 AAATCATTAAATCATT-AATTATTATTAATAAATCATATGATTACA--T
*
1177393 AAATCATTAAATCATTAAATCATTATTAATAAATCATATGATTACAT
1 AAATCATTAAATCATT-AATTATTATTAATAAATCATATGATTACAT
1177440 AAATCATTAAATCATT-ATTATTA
1 AAATCATTAAATCATTAATTATTA
1177463 AACCATTAAA
Statistics
Matches: 67, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
45 6 0.09
47 17 0.25
49 44 0.66
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (46 bp):
AAATCATTAAATCATTAATTATTATTAATAAATCATATGATTACAT
Found at i:1177528 original size:25 final size:27
Alignment explanation
Indices: 1177448--1177537 Score: 94
Period size: 25 Copynumber: 3.3 Consensus size: 27
1177438 ATAAATCATT
* * **
1177448 AAATCATTATTATTAAACCATTAAAATTC
1 AAATCATTATTAAT-AATCATTAGTA-TC
*
1177477 AAATCATTATTAATAATCATTATTATC
1 AAATCATTATTAATAATCATTAGTATC
*
1177504 AAATCATTATT-A-AATTATTAGTATC
1 AAATCATTATTAATAATCATTAGTATC
1177529 AAATCATTA
1 AAATCATTA
1177538 AATCATTGAA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
25 20 0.36
26 1 0.02
27 13 0.24
28 8 0.15
29 13 0.24
ACGTcount: A:0.47, C:0.11, G:0.01, T:0.41
Consensus pattern (27 bp):
AAATCATTATTAATAATCATTAGTATC
Found at i:1177628 original size:177 final size:177
Alignment explanation
Indices: 1177307--1178109 Score: 1135
Period size: 177 Copynumber: 4.6 Consensus size: 177
1177297 TTAAAATTCA
* *
1177307 AATCATTATTA--ATAATTATTATTAAATTATTAGTATCAAATCATTAAATCATTGAATTATTAT
1 AATCATTATTATCA-AATCATTATTAAATTATTAGTATCAAATCATTAAATCATTGAATCATTAT
*
1177370 TAATAAATCATATGATTACACTTAAATCATTAAATCATTAAATCATTATTAATAAATCATATGAT
65 TAATAAATCATATGATT--AC----A-C-TTAAATCATTAAATCATTATTAATAAATCATATAAT
*
1177435 TACATAAATCATTAAATCATTATTATTAAACCATTAAAATTCAAATCATTATTAAT
122 TACATAAATCATTAAATCATTATTATTAAATCATTAAAATTCAAATCATTATTAAT
1177491 AATCATTATTATCAAATCATTATTAAATTATTAGTATCAAATCATTAAATCATTGAATCATTATT
1 AATCATTATTATCAAATCATTATTAAATTATTAGTATCAAATCATTAAATCATTGAATCATTATT
1177556 AATAAATCATATGATTACACTTAAATCATTAAATCATTATTAATAAATCATATAATTACATAAAT
66 AATAAATCATATGATTACACTTAAATCATTAAATCATTATTAATAAATCATATAATTACATAAAT
*
1177621 CATTAAATCATTATTACT-AATCATTAAAATTCAAATC-------AT
131 CATTAAATCATTATTATTAAATCATTAAAATTCAAATCATTATTAAT
1177660 --T-ATTA--AT--AATCATTATTAAATTATTAGTATCAAATCATTAAATCATTGAATAAATCAT
1 AATCATTATTATCAAATCATTATTAAATTATTAGTATCAAATCATTAAATCATTG----AATCAT
* * * *
1177718 ATGATTACACTTAAATCAT-TAAAT-CA-TTAAATCA-T---T-A---TTAATAAATAATATGAT
62 -T-ATTA-A--TAAATCATATGATTACACTTAAATCATTAAATCATTATTAATAAATCATATAAT
1177772 TACATAAATCATTAAATCATTATTATTAAATCATTAAAATTCAAATCATTATTAAT
122 TACATAAATCATTAAATCATTATTATTAAATCATTAAAATTCAAATCATTATTAAT
1177828 AATCATTATTATCAAATCATTATTAAATTATTAGTATCAAATCATTAAATCATTGAATCATTATT
1 AATCATTATTATCAAATCATTATTAAATTATTAGTATCAAATCATTAAATCATTGAATCATTATT
1177893 AATAAATCATATGATTACACTTAAATCATTAAATCATTATTAATAAATCATATAATTACATAAAT
66 AATAAATCATATGATTACACTTAAATCATTAAATCATTATTAATAAATCATATAATTACATAAAT
1177958 CATTAAATCATTATTATTAAATCATTAAAATTCAAATCATTATTAAT
131 CATTAAATCATTATTATTAAATCATTAAAATTCAAATCATTATTAAT
*
1178005 AATCATTATTATCAAATCATTATTAAATTATTAGTATCAAATCATTAAATCATTAAATCATTATT
1 AATCATTATTATCAAATCATTATTAAATTATTAGTATCAAATCATTAAATCATTGAATCATTATT
*
1178070 AATAAATCATATAATTACA--TAAATCATTAAATCATTATTA
66 AATAAATCATATGATTACACTTAAATCATTAAATCATTATTA
1178110 CTAATAGTTA
Statistics
Matches: 566, Mismatches: 16, Indels: 83
0.85 0.02 0.12
Matches are distributed among these distances:
160 41 0.07
161 19 0.03
162 41 0.07
163 1 0.00
164 3 0.01
166 18 0.03
167 6 0.01
168 17 0.03
169 17 0.03
170 6 0.01
171 18 0.03
173 3 0.01
174 1 0.00
175 62 0.11
176 18 0.03
177 214 0.38
178 1 0.00
179 1 0.00
183 2 0.00
184 11 0.02
185 65 0.11
186 1 0.00
ACGTcount: A:0.47, C:0.10, G:0.02, T:0.41
Consensus pattern (177 bp):
AATCATTATTATCAAATCATTATTAAATTATTAGTATCAAATCATTAAATCATTGAATCATTATT
AATAAATCATATGATTACACTTAAATCATTAAATCATTATTAATAAATCATATAATTACATAAAT
CATTAAATCATTATTATTAAATCATTAAAATTCAAATCATTATTAAT
Found at i:1177631 original size:39 final size:39
Alignment explanation
Indices: 1177536--1177805 Score: 209
Period size: 39 Copynumber: 6.8 Consensus size: 39
1177526 ATCAAATCAT
* *
1177536 TAAATCATTGAATCATTATTAATAAATCATATGATTACA
1 TAAATCATTAAATCATTATTAATAAATCATATAATTACA
1177575 CTTAAATCATTAAATCATTATTAATAAATCATATAATTACA
1 --TAAATCATTAAATCATTATTAATAAATCATATAATTACA
* *
1177616 TAAATCATTAAATCATTATTACT-AATCATTAAAATT-C-
1 TAAATCATTAAATCATTATTAATAAATCA-TATAATTACA
* * * * *
1177653 -AAATCATTATTAATAATCATTATTAAAT--TATTAGT--A
1 TAAATCATTA--AATCATTATTAATAAATCATATAATTACA
*
1177689 TCAAATCATTAAATCA-T-TGAATAAATCATATGATTACACTTAAATCA
1 T-AAATCATTAAATCATTATTAATAAATC--AT-A-TA-A-TT--A-CA
* *
1177736 TTAAATCATTAAATCATTATTAATAAATAATATGATTACA
1 -TAAATCATTAAATCATTATTAATAAATCATATAATTACA
*
1177776 TAAATCATTAAATCATTATTATTAAATCAT
1 TAAATCATTAAATCATTATTAATAAATCAT
1177806 TAAAATTCAA
Statistics
Matches: 185, Mismatches: 21, Indels: 48
0.73 0.08 0.19
Matches are distributed among these distances:
34 7 0.04
36 17 0.09
38 26 0.14
39 60 0.32
40 3 0.02
41 39 0.21
42 1 0.01
43 2 0.01
44 1 0.01
45 1 0.01
46 1 0.01
47 17 0.09
48 2 0.01
49 8 0.04
ACGTcount: A:0.47, C:0.11, G:0.02, T:0.40
Consensus pattern (39 bp):
TAAATCATTAAATCATTATTAATAAATCATATAATTACA
Found at i:1177809 original size:337 final size:336
Alignment explanation
Indices: 1177231--1178235 Score: 1567
Period size: 337 Copynumber: 3.0 Consensus size: 336
1177221 TATTAGTATC
*
1177231 AAATCATTAAATCATTATTAATAAATCATATGATTACATAAATCATTAAATCATTATTACTAATC
1 AAATCATTAAATCATTATTAATAAATCATATAATTACATAAATCATTAAATCATTATTACTAATC
*
1177296 ATTAAAATTCAAATCATTATTAATAATTATTATTAAATTATTAGTATCAAATCATTAAATCATTG
66 ATTAAAATTCAAATCATTATTAATAATCATTATTAAATTATTAGTATCAAATCATTAAATCATTG
1177361 AATTATTATTAATAAATCATATGATTACACTTAAATCATTAAATCATTAAATCATTATTAATAAA
131 ----------AATAAATCATATGATTACACTTAAATCATTAAATCATTAAATCATTATTAATAAA
*
1177426 TCATATGATTACATAAATCATTAAATCATTATTATTAAACCATTAAAATTCAAATCATTATTAAT
186 T-ATATGATTACATAAATCATTAAATCATTATTATTAAATCATTAAAATTCAAATCATTATTAAT
1177491 AATCATTATTATCAAATCATTATTAAATTATTAGTATCAAATCATTAAATCATTGAATCATTATT
250 AATCATTATTATCAAATCATTATTAAATTATTAGTATCAAATCATTAAATCATTGAATCATTATT
1177556 AATAAATCATATGATTACACTT
315 AATAAATCATATGATTACACTT
1177578 AAATCATTAAATCATTATTAATAAATCATATAATTACATAAATCATTAAATCATTATTACTAATC
1 AAATCATTAAATCATTATTAATAAATCATATAATTACATAAATCATTAAATCATTATTACTAATC
1177643 ATTAAAATTCAAATCATTATTAATAATCATTATTAAATTATTAGTATCAAATCATTAAATCATTG
66 ATTAAAATTCAAATCATTATTAATAATCATTATTAAATTATTAGTATCAAATCATTAAATCATTG
1177708 AATAAATCATATGATTACACTTAAATCATTAAATCATTAAATCATTATTAATAAATAATATGATT
131 AATAAATCATATGATTACACTTAAATCATTAAATCATTAAATCATTATTAATAAAT-ATATGATT
1177773 ACATAAATCATTAAATCATTATTATTAAATCATTAAAATTCAAATCATTATTAATAATCATTATT
195 ACATAAATCATTAAATCATTATTATTAAATCATTAAAATTCAAATCATTATTAATAATCATTATT
1177838 ATCAAATCATTATTAAATTATTAGTATCAAATCATTAAATCATTGAATCATTATTAATAAATCAT
260 ATCAAATCATTATTAAATTATTAGTATCAAATCATTAAATCATTGAATCATTATTAATAAATCAT
1177903 ATGATTACACTT
325 ATGATTACACTT
*
1177915 AAATCATTAAATCATTATTAATAAATCATATAATTACATAAATCATTAAATCATTATTATTAAAT
1 AAATCATTAAATCATTATTAATAAATCATATAATTACATAAATCATTAAATCATTATTACT-AAT
* * *
1177980 CATTAAAATTCAAATCATTATTAATAATCATTATT--ATCA--A--ATC--ATTATTAAATTATT
65 CATTAAAATTCAAATCATTATTAATAATCATTATTAAATTATTAGTATCAAATCATTAAATCATT
* * * *
1178037 -AGT--ATCA-A--A-T-CA-TTAAATCATTAAATCATT--AT--TAATAAAT-CATATA--ATT
130 GAATAAATCATATGATTACACTTAAATCATTAAATCATTAAATCATTATTAATAAATATATGATT
* * *
1178086 ACATAAATCATTAAATCATTATTACT-AAT-AGTTAAATTTCAAATCATTATTAGTAATCATTAT
195 ACATAAATCATTAAATCATTATTATTAAATCA-TTAAAATTCAAATCATTATTAATAATCATTAT
*
1178149 TATCAAATCATTATTAAATTATTAGTATCAAATCATTAAATCATTGAATCATTATTTATAAATCA
259 TATCAAATCATTATTAAATTATTAGTATCAAATCATTAAATCATTGAATCATTATTAATAAATCA
1178214 TATGATTACACTT
324 TATGATTACACTT
1178227 AAATCATTA
1 AAATCATTA
1178236 GTACTAAATC
Statistics
Matches: 640, Mismatches: 16, Indels: 39
0.92 0.02 0.06
Matches are distributed among these distances:
311 1 0.00
312 119 0.19
313 28 0.04
315 3 0.00
316 2 0.00
317 6 0.01
319 2 0.00
321 18 0.03
322 2 0.00
323 1 0.00
324 1 0.00
326 1 0.00
327 4 0.01
329 2 0.00
330 12 0.02
332 3 0.00
334 1 0.00
336 3 0.00
337 265 0.41
338 38 0.06
347 128 0.20
ACGTcount: A:0.47, C:0.11, G:0.02, T:0.41
Consensus pattern (336 bp):
AAATCATTAAATCATTATTAATAAATCATATAATTACATAAATCATTAAATCATTATTACTAATC
ATTAAAATTCAAATCATTATTAATAATCATTATTAAATTATTAGTATCAAATCATTAAATCATTG
AATAAATCATATGATTACACTTAAATCATTAAATCATTAAATCATTATTAATAAATATATGATTA
CATAAATCATTAAATCATTATTATTAAATCATTAAAATTCAAATCATTATTAATAATCATTATTA
TCAAATCATTATTAAATTATTAGTATCAAATCATTAAATCATTGAATCATTATTAATAAATCATA
TGATTACACTT
Found at i:1177836 original size:39 final size:39
Alignment explanation
Indices: 1177626--1177838 Score: 104
Period size: 39 Copynumber: 5.3 Consensus size: 39
1177616 TAAATCATTA
1177626 AATCATTATTACTAATCATTAAAATTCAAATCATTATTAAT
1 AATCATTATTA--AATCATTAAAATTCAAATCATTATTAAT
* **
1177667 AATCATTATTAAATTATTAGTA-TCAAATC---ATT-A-
1 AATCATTATTAAATCATTAAAATTCAAATCATTATTAAT
* * * *
1177700 AATCATTGAATAAATCATATGATTACACTT-AAATCATTAAATCATT
1 AATCATT-ATTAAATCAT-T-A--A-AATTCAAATCATT--ATTAAT
* *
1177746 AAATCATTATT-AATAAATAATATGATTACATAAATCATTA--AAT
1 -AATCATTATTAAATCATTAA-A--ATT-C--AAATCATTATTAAT
* *
1177789 CATTATTATTAAATCATTAAAATTCAAATCATTATTAAT
1 AATCATTATTAAATCATTAAAATTCAAATCATTATTAAT
1177828 AATCATTATTA
1 AATCATTATTA
1177839 TCAAATCATT
Statistics
Matches: 126, Mismatches: 22, Indels: 50
0.64 0.11 0.25
Matches are distributed among these distances:
33 7 0.06
34 9 0.07
35 4 0.03
36 1 0.01
37 9 0.07
38 7 0.06
39 26 0.21
40 4 0.03
41 13 0.10
42 9 0.07
43 12 0.10
44 3 0.02
45 5 0.04
46 2 0.02
47 15 0.12
ACGTcount: A:0.47, C:0.10, G:0.02, T:0.40
Consensus pattern (39 bp):
AATCATTATTAAATCATTAAAATTCAAATCATTATTAAT
Found at i:1177865 original size:25 final size:25
Alignment explanation
Indices: 1177776--1178338 Score: 141
Period size: 25 Copynumber: 22.0 Consensus size: 25
1177766 TATGATTACA
*
1177776 TAAATCATTAA-ATC--ATTATTAT
1 TAAATCATTAATATCAAATCATTAT
*
1177798 TAAATCATTAAAATTCAAATCATTAT
1 TAAATCATTAATA-TCAAATCATTAT
*
1177824 TAATAATCATTATTATCAAATCATTAT
1 T-A-AATCATTAATATCAAATCATTAT
* *
1177851 TAAATTATTAGTATCAAATC---AT
1 TAAATCATTAATATCAAATCATTAT
* * *
1177873 TAAATCATTGA-ATC--ATTATTAA
1 TAAATCATTAATATCAAATCATTAT
* *
1177895 TAAATCATATGATTACACTTAAATCATTA-
1 TAAATCAT-T-A--ATA-TCAAATCATTAT
* * * *
1177924 -AATCATTATTAATAAATCATATAATTACA
1 TAA--ATCATTAAT--ATCAAATCATTA-T
*
1177953 TAAATCATTAA-ATC--ATTATTAT
1 TAAATCATTAATATCAAATCATTAT
*
1177975 TAAATCATTAAAATTCAAATCATTAT
1 TAAATCATTAATA-TCAAATCATTAT
*
1178001 TAATAATCATTATTATCAAATCATTAT
1 T-A-AATCATTAATATCAAATCATTAT
* *
1178028 TAAATTATTAGTATCAAATC---AT
1 TAAATCATTAATATCAAATCATTAT
* *
1178050 TAAATCATTAA-ATC--ATTATTAA
1 TAAATCATTAATATCAAATCATTAT
*
1178072 TAAATCATATAAT-TACATAA--ATCAT
1 TAAATCAT-TAATAT-CA-AATCATTAT
* *
1178097 TAAATCATTATTA-CTAAT-AGTTAAATT
1 TAAATCATTAATATCAAATCA-TT--A-T
*
1178124 TCAAATCATTATTAGT--AATCATTATT
1 T-AAATCATTAATA-TCAAATCATTA-T
*
1178150 ATCAAATCATT-AT-T-AAATTATTAGT
1 -T-AAATCATTAATATCAAATCATTA-T
1178175 ATCAAATCATTAA-ATCATTGAATCATTATTT
1 -T-AAATCATTAATATCA---AATCATTA--T
* *
1178206 ATAAATCATATGATTACACTTAAATCATTAGT
1 -TAAATCAT-T-A--ATA-TCAAATCATTA-T
*
1178238 ACTAAATCATTAA-ATC--ATTATTAT
1 --TAAATCATTAATATCAAATCATTAT
* *
1178262 TAAATCATTAAAATTTAAATCATTAT
1 TAAATCATTAATA-TCAAATCATTAT
* * *
1178288 TAATAATCATTATTACCAAATTATTAT
1 T-A-AATCATTAATATCAAATCATTAT
*
1178315 TAAATTATTAATATCAAATCATTA
1 TAAATCATTAATATCAAATCATTA
1178339 AATCATTAAA
Statistics
Matches: 414, Mismatches: 56, Indels: 139
0.68 0.09 0.23
Matches are distributed among these distances:
19 4 0.01
21 6 0.01
22 74 0.18
23 16 0.04
24 12 0.03
25 89 0.21
26 36 0.09
27 63 0.15
28 57 0.14
29 3 0.01
30 26 0.06
31 5 0.01
32 3 0.01
33 16 0.04
34 1 0.00
35 1 0.00
36 2 0.00
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.42
Consensus pattern (25 bp):
TAAATCATTAATATCAAATCATTAT
Found at i:1177917 original size:41 final size:40
Alignment explanation
Indices: 1177870--1177982 Score: 183
Period size: 41 Copynumber: 2.8 Consensus size: 40
1177860 AGTATCAAAT
* *
1177870 CATTAAATCATTGAATCATTATTAATAAATCATATGATTA
1 CATTAAATCATTAAATCATTATTAATAAATCATATAATTA
1177910 CACTTAAATCATTAAATCATTATTAATAAATCATATAATTA
1 CA-TTAAATCATTAAATCATTATTAATAAATCATATAATTA
*
1177951 CA-TAAATCATTAAATCATTATTATTAAATCAT
1 CATTAAATCATTAAATCATTATTAATAAATCAT
1177983 TAAAATTCAA
Statistics
Matches: 69, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
39 29 0.42
40 2 0.03
41 38 0.55
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.40
Consensus pattern (40 bp):
CATTAAATCATTAAATCATTATTAATAAATCATATAATTA
Found at i:1178146 original size:177 final size:178
Alignment explanation
Indices: 1177654--1178161 Score: 527
Period size: 177 Copynumber: 2.9 Consensus size: 178
1177644 TTAAAATTCA
*
1177654 AATCATTATTA--ATAATCATTATTAAATTATTAGTATCAAATCATTAAATCATTGAATAAATCA
1 AATCATTATTATCATAATCATTATTAAATAATTA-TATCAAATCATTAAATCA-T---TAAATCA
* * * * * * * **
1177717 -TATGATTACA-C-T-TAAAT-CATTAAATCATTAAATCATTATTAATAAAT-AATATGATTACA
61 TTATTAATAAATCATATGATTACA-TAAATCATTAAATCATTATTATTAAATCATTAAAATT-CA
* *
1177776 TAA--ATCATT-A-AATCATTATTATTAAATCATTAAAATTCAAATCATTATTAAT
124 -AATCATTATTAATAATCATTATTATCAAATCATTAAAATTCAAATCATTATTAAT
* *
1177828 AATCATTATTATCA-AATCATTATTAAATTATTAGTATCAAATCATTAAATCATTGAATCATTAT
1 AATCATTATTATCATAATCATTATTAAATAATTA-TATCAAATCATTAAATCATTAAATCATTAT
* *
1177892 TAATAAATCATATGATTACACTTAAATCATTAAATCATTATTAATAAATCA-TATAATTACATAA
65 TAATAAATCATATGATTACA--TAAATCATTAAATCATTATTATTAAATCATTAAAATT-CA-AA
* *
1177956 --ATCATT-A-AATCATTATTATTAAATCATTAAAATTCAAATCATTATTAAT
126 TCATTATTAATAATCATTATTATCAAATCATTAAAATTCAAATCATTATTAAT
*
1178005 AATCATTATTATCA-AATCATTATTAAATTATTAGTATCAAATCATTAAATCATTAAATCATTAT
1 AATCATTATTATCATAATCATTATTAAATAATTA-TATCAAATCATTAAATCATTAAATCATTAT
* * *
1178069 TAATAAATCATATAATTACATAAATCATTAAATCATTATTACT-AAT-AGTTAAATTTCAAATCA
65 TAATAAATCATATGATTACATAAATCATTAAATCATTATTATTAAATCA-TTAAAATTCAAATCA
*
1178132 TTATTAGTAATCATTATTATCAAATCATTA
129 TTATTAATAATCATTATTATCAAATCATTA
1178162 TTAAATTATT
Statistics
Matches: 304, Mismatches: 15, Indels: 27
0.88 0.04 0.08
Matches are distributed among these distances:
171 6 0.02
172 7 0.02
173 4 0.01
174 18 0.06
175 73 0.24
176 3 0.01
177 192 0.63
178 1 0.00
ACGTcount: A:0.47, C:0.10, G:0.02, T:0.41
Consensus pattern (178 bp):
AATCATTATTATCATAATCATTATTAAATAATTATATCAAATCATTAAATCATTAAATCATTATT
AATAAATCATATGATTACATAAATCATTAAATCATTATTATTAAATCATTAAAATTCAAATCATT
ATTAATAATCATTATTATCAAATCATTAAAATTCAAATCATTATTAAT
Found at i:1178189 original size:8 final size:8
Alignment explanation
Indices: 1178178--1178286 Score: 54
Period size: 8 Copynumber: 14.1 Consensus size: 8
1178168 TATTAGTATC
1178178 AAATCATT
1 AAATCATT
1178186 AAATCATT
1 AAATCATT
*
1178194 GAATCATT
1 AAATCATT
* *
1178202 -ATTTA-T
1 AAATCATT
1178208 AAATCATAT
1 AAATCAT-T
* *
1178217 GATTACACTT
1 AAAT-CA-TT
1178227 AAATCATT
1 AAATCATT
* *
1178235 -AGT-ACT
1 AAATCATT
1178241 AAATCATT
1 AAATCATT
1178249 AAATCATT
1 AAATCATT
*
1178257 --ATTATT
1 AAATCATT
1178263 AAATCATT
1 AAATCATT
1178271 AAA--ATTT
1 AAATCA-TT
1178278 AAATCATT
1 AAATCATT
1178286 A
1 A
1178287 TTAATAATCA
Statistics
Matches: 74, Mismatches: 15, Indels: 24
0.65 0.13 0.21
Matches are distributed among these distances:
6 9 0.12
7 15 0.20
8 38 0.51
9 6 0.08
10 5 0.07
11 1 0.01
ACGTcount: A:0.46, C:0.11, G:0.03, T:0.40
Consensus pattern (8 bp):
AAATCATT
Found at i:1178253 original size:22 final size:22
Alignment explanation
Indices: 1178225--1178273 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
1178215 ATGATTACAC
1178225 TTAAATCATTAGTACTAAATCA
1 TTAAATCATTAGTACTAAATCA
* *
1178247 TTAAATCATTATTATTAAATCA
1 TTAAATCATTAGTACTAAATCA
1178269 TTAAA
1 TTAAA
1178274 ATTTAAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.47, C:0.10, G:0.02, T:0.41
Consensus pattern (22 bp):
TTAAATCATTAGTACTAAATCA
Found at i:1178313 original size:514 final size:519
Alignment explanation
Indices: 1177236--1178340 Score: 1374
Period size: 514 Copynumber: 2.1 Consensus size: 519
1177226 GTATCAAATC
* * *
1177236 ATTAAATCATTATTAATAAATCATATGATTACATAAATCATTAAATCATTATTACTAATCATTAA
1 ATTAAATCATTATTAAT-AATCAT-T-ATTAC-CAAATTATTAAATCATTATTACAAATCATTAA
* *
1177301 AATTCAAATCATTATTAATAATTATTATTAAATTATTAGTATCAAATCATTAAATCATTGAATTA
62 AATT-AAATCATTATTAATAATCATTATTAAATTATTAGTATCAAATCATTAAATCATTGAATCA
1177366 TTATTAATAAATCATATGATTACACTTAAATCATTAAATCATTAAATCATTATTAATAAATCATA
126 TTATTAATAAATCATATGATTA-AC---AATCATTAAATCATTAAATCATTATTAATAAATCATA
*
1177431 TGATTACATAAATCATTAAATCATTATTATTAAACCATTAAAATTCAAATCATTATTAATAATCA
187 TAATTACATAAATCATTAAATCATTATTATTAAACCATTAAAATTCAAATCATTATTAATAATCA
*
1177496 TTATTATCAAATCATTATTAAATTATTAGTATCAAATCATTAAATCATTGAATCATTATTAATAA
252 TTATTATCAAATCATTATTAAATTATTAGTATCAAATCATTAAATCATTAAATCATTATTAATAA
* *
1177561 ATCATATGATTACACTTAAATCATTAAATCATTATTAATAAATCATATAATTACATAAATCATTA
317 ATCATATAATTACAC-TAAATCATTAAATCATTATTAATAAATCATATAA-TACAT--AT-ATCA
*
1177626 AATCATTATTACTAATCATTAAAATTCAAATCATTATTAATAATCATTATTAAATTATTAGTATC
377 AATCATTATTACTAATCATTAAAATTCAAATCATTATTAATAATCATTATTAAA-TATCAGTATC
1177691 AAATCATTAAATCATTGAATAAATCATATGATTACACTTAAATCATTAAATCATTAAATCATTAT
441 AAATCATTAAATCATTGAATAAATCATATGATTACACTTAAATCATTAAATCATTAAATCATTAT
**
1177756 TAATAAATAATATG
506 TAATAAATAATAAA
* * * ** * *
1177770 ATTACATAAATCATT-A-AATCATTATTATTAAATCATT-AA--A--ATT-CAAATCATTATTAA
1 ATTAAAT-CATTATTAATAATCATTATTACCAAATTATTAAATCATTATTACAAATCATTA-AAA
1177827 -T-AATCATTATT-ATCAAATCATTATTAAATTATTAGTATCAAATCATTAAATCATTGAATCAT
64 TTAAATCATTATTAAT--AATCATTATTAAATTATTAGTATCAAATCATTAAATCATTGAATCAT
1177889 TATTAATAAATCATATGATT-AC-A-C-TTAAATCATTAAATCATTATTAATAAATCATATAATT
127 TATTAATAAATCATATGATTAACAATCATTAAATCATTAAATCATTATTAATAAATCATATAATT
*
1177950 ACATAAATCATTAAATCATTATTATTAAATCATTAAAATTCAAATCATTATTAATAATCATTATT
192 ACATAAATCATTAAATCATTATTATTAAACCATTAAAATTCAAATCATTATTAATAATCATTATT
1178015 ATCAAATCATTATTAAATTATTAGTATCAAATCATTAAATCATTAAATCATTATTAATAAATCAT
257 ATCAAATCATTATTAAATTATTAGTATCAAATCATTAAATCATTAAATCATTATTAATAAATCAT
*
1178080 ATAATTACA-TAAATCATTAAATCATTATTACT-AAT-AGT-T-A-A-AT-T-TCAAATCATTAT
322 ATAATTACACTAAATCATTAAATCATTATTAATAAATCA-TATAATACATATATCAAATCATTAT
* ** * *
1178136 TAGTAATCATTATTA-TCAAATCATTATT-A-AATTATTAGTATCAA-ATCA-T-T-AAATCATT
386 TACTAATCATTAAAATTCAAATCATTATTAATAATCATTA-T-TAAATATCAGTATCAAATCATT
*
1178194 GAATCATT-ATTTATAAATCATATGATTACACTTAAATCATTAGTACTAAATCATTAAATCATTA
449 AAATCATTGA---ATAAATCATATGATTACACTTAAATC---A-T--TAAATCATTAAATCATTA
* *
1178258 TTATTAAATCATTAAA
505 TTAATAAAT-AATAAA
* *
1178274 ATTTAAATCATTATTAATAATCATTATTACCAAATTATTATTAAATTATTAATATCAAATCATTA
1 A-TTAAATCATTATTAATAATCATTATTACC-AA--ATTATTAAATCATTATTA-CAAATCATTA
1178339 AA
61 AA
1178341 TCATTAAACC
Statistics
Matches: 508, Mismatches: 33, Indels: 79
0.82 0.05 0.13
Matches are distributed among these distances:
494 1 0.00
495 15 0.03
496 1 0.00
497 27 0.05
498 10 0.02
499 2 0.00
500 17 0.03
501 24 0.05
503 27 0.05
504 9 0.02
505 6 0.01
506 13 0.03
507 3 0.01
509 6 0.01
510 4 0.01
511 4 0.01
512 23 0.05
514 174 0.34
515 2 0.00
516 11 0.02
520 4 0.01
521 10 0.02
522 65 0.13
523 10 0.02
524 5 0.01
526 1 0.00
528 2 0.00
529 9 0.02
530 4 0.01
531 1 0.00
532 6 0.01
534 7 0.01
535 5 0.01
ACGTcount: A:0.47, C:0.10, G:0.02, T:0.41
Consensus pattern (519 bp):
ATTAAATCATTATTAATAATCATTATTACCAAATTATTAAATCATTATTACAAATCATTAAAATT
AAATCATTATTAATAATCATTATTAAATTATTAGTATCAAATCATTAAATCATTGAATCATTATT
AATAAATCATATGATTAACAATCATTAAATCATTAAATCATTATTAATAAATCATATAATTACAT
AAATCATTAAATCATTATTATTAAACCATTAAAATTCAAATCATTATTAATAATCATTATTATCA
AATCATTATTAAATTATTAGTATCAAATCATTAAATCATTAAATCATTATTAATAAATCATATAA
TTACACTAAATCATTAAATCATTATTAATAAATCATATAATACATATATCAAATCATTATTACTA
ATCATTAAAATTCAAATCATTATTAATAATCATTATTAAATATCAGTATCAAATCATTAAATCAT
TGAATAAATCATATGATTACACTTAAATCATTAAATCATTAAATCATTATTAATAAATAATAAA
Found at i:1178359 original size:16 final size:16
Alignment explanation
Indices: 1178327--1178373 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
1178317 AATTATTAAT
1178327 ATCAAATCATTAAATC
1 ATCAAATCATTAAATC
* * *
1178343 ATTAAACCATCAAATC
1 ATCAAATCATTAAATC
1178359 ATCAAATCATTAAAT
1 ATCAAATCATTAAAT
1178374 TAATAATTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.51, C:0.19, G:0.00, T:0.30
Consensus pattern (16 bp):
ATCAAATCATTAAATC
Found at i:1178359 original size:24 final size:24
Alignment explanation
Indices: 1178327--1178372 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
1178317 AATTATTAAT
*
1178327 ATCAAATCATTAAATCATTAAACC
1 ATCAAATCATCAAATCATTAAACC
1178351 ATCAAATCATCAAATCATTAAA
1 ATCAAATCATCAAATCATTAAA
1178373 TTAATAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.52, C:0.20, G:0.00, T:0.28
Consensus pattern (24 bp):
ATCAAATCATCAAATCATTAAACC
Found at i:1178361 original size:8 final size:8
Alignment explanation
Indices: 1178327--1178373 Score: 58
Period size: 8 Copynumber: 5.9 Consensus size: 8
1178317 AATTATTAAT
1178327 ATCAAATC
1 ATCAAATC
*
1178335 ATTAAATC
1 ATCAAATC
* *
1178343 ATTAAACC
1 ATCAAATC
1178351 ATCAAATC
1 ATCAAATC
1178359 ATCAAATC
1 ATCAAATC
*
1178367 ATTAAAT
1 ATCAAAT
1178374 TAATAATTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
8 34 1.00
ACGTcount: A:0.51, C:0.19, G:0.00, T:0.30
Consensus pattern (8 bp):
ATCAAATC
Found at i:1178407 original size:13 final size:13
Alignment explanation
Indices: 1178389--1178424 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1178379 ATTTTTAGTA
1178389 AATCATTATTACT
1 AATCATTATTACT
*
1178402 AATCATTAGTACT
1 AATCATTATTACT
1178415 AATCA-TATTA
1 AATCATTATTA
1178425 TTCATTACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 4 0.19
13 17 0.81
ACGTcount: A:0.42, C:0.14, G:0.03, T:0.42
Consensus pattern (13 bp):
AATCATTATTACT
Found at i:1178451 original size:22 final size:20
Alignment explanation
Indices: 1178415--1178466 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
1178405 CATTAGTACT
1178415 AATCA-TATTATTCATTACA
1 AATCATTATTATTCATTACA
**
1178434 AATCATTATTAGTGTCATTAGT
1 AATCATTATTA-T-TCATTACA
1178456 AATCATTATTA
1 AATCATTATTA
1178467 AATTAATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 5 0.18
20 5 0.18
21 1 0.04
22 17 0.61
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (20 bp):
AATCATTATTATTCATTACA
Found at i:1183520 original size:30 final size:30
Alignment explanation
Indices: 1183457--1183522 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
1183447 AGAACTGGAA
* * * *
1183457 GAACCGGCTGAAAATCGGGAAAATCGGGGT
1 GAACCGACTGAAAACCGGCAAAACCGGGGT
**
1183487 GAACCGACTGAAAACCGGCAAAACCGGTTT
1 GAACCGACTGAAAACCGGCAAAACCGGGGT
1183517 GAACCG
1 GAACCG
1183523 TCGGTTCACT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.35, C:0.23, G:0.30, T:0.12
Consensus pattern (30 bp):
GAACCGACTGAAAACCGGCAAAACCGGGGT
Found at i:1189916 original size:12 final size:12
Alignment explanation
Indices: 1189893--1189938 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
1189883 TAAATAATAA
*
1189893 AAAAATTACAAT
1 AAAAAGTACAAT
*
1189905 AAAAAGTCCAAT
1 AAAAAGTACAAT
*
1189917 AAACAACTACAAT
1 AAA-AAGTACAAT
1189930 AAAAAGTAC
1 AAAAAGTAC
1189939 TAAATACAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
12 18 0.64
13 10 0.36
ACGTcount: A:0.63, C:0.15, G:0.04, T:0.17
Consensus pattern (12 bp):
AAAAAGTACAAT
Found at i:1189947 original size:25 final size:25
Alignment explanation
Indices: 1189888--1189959 Score: 74
Period size: 25 Copynumber: 2.8 Consensus size: 25
1189878 AATGATAAAT
*
1189888 AATAAAAAAATTACAATAAAAAGTCC
1 AATAAACAAA-TACAATAAAAAGTCC
* *
1189914 AATAAACAACTACAATAAAAAGTACT
1 AATAAACAAATACAATAAAAAGT-CC
* *
1189940 AA-ATACAAATATAATAAAAA
1 AATAAACAAATACAATAAAAA
1189960 ACAAAATCTA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
25 28 0.72
26 11 0.28
ACGTcount: A:0.67, C:0.11, G:0.03, T:0.19
Consensus pattern (25 bp):
AATAAACAAATACAATAAAAAGTCC
Found at i:1194016 original size:17 final size:17
Alignment explanation
Indices: 1193994--1194026 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1193984 CGTTAAGAAT
1193994 TCGAG-TCGAGCTCGAGC
1 TCGAGTTCGAG-TCGAGC
1194011 TCGAGTTCGAGTCGAG
1 TCGAGTTCGAGTCGAG
1194027 TCCATTCGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.18, C:0.24, G:0.36, T:0.21
Consensus pattern (17 bp):
TCGAGTTCGAGTCGAGC
Found at i:1195359 original size:23 final size:23
Alignment explanation
Indices: 1195333--1195392 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
1195323 TTTTCTTCCT
1195333 TTTTCCTTTTTCTTAAATTTTT-A
1 TTTTCCTTTTT-TTAAATTTTTCA
** **
1195356 TTTTTATTTTTTTTCATTTTTCA
1 TTTTCCTTTTTTTAAATTTTTCA
1195379 TTTTCCTCTTTTTT
1 TTTTCCT-TTTTTT
1195393 TTTTGAATTA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
22 8 0.28
23 15 0.52
24 6 0.21
ACGTcount: A:0.12, C:0.13, G:0.00, T:0.75
Consensus pattern (23 bp):
TTTTCCTTTTTTTAAATTTTTCA
Found at i:1195369 original size:16 final size:17
Alignment explanation
Indices: 1195350--1195382 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1195340 TTTTCTTAAA
1195350 TTTTT-ATTTTT-ATTT
1 TTTTTCATTTTTCATTT
1195365 TTTTTCATTTTTCATTT
1 TTTTTCATTTTTCATTT
1195382 T
1 T
1195383 CCTCTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 6 0.38
17 5 0.31
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTCATTTTTCATTT
Found at i:1196328 original size:14 final size:11
Alignment explanation
Indices: 1196297--1196321 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1196287 GAAATTTGAT
1196297 TAAAAATATAA
1 TAAAAATATAA
1196308 TAAAAATATAA
1 TAAAAATATAA
1196319 TAA
1 TAA
1196322 TTTAAATTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
TAAAAATATAA
Found at i:1196445 original size:41 final size:39
Alignment explanation
Indices: 1196383--1196461 Score: 104
Period size: 41 Copynumber: 2.0 Consensus size: 39
1196373 TAACCTAAGA
* * * *
1196383 TATTATAAAAATATAATATTTTTAATTATCAATCAAAAATT
1 TATTAAAAAAACATAACATTTTAAATTAT-AAT-AAAAATT
1196424 TATTAAAAAAACATAACATTTTAAATTATAATAAAAAT
1 TATTAAAAAAACATAACATTTTAAATTATAATAAAAAT
1196462 ACTATAGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 6 0.18
40 3 0.09
41 25 0.74
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (39 bp):
TATTAAAAAAACATAACATTTTAAATTATAATAAAAATT
Found at i:1196473 original size:39 final size:41
Alignment explanation
Indices: 1196383--1196490 Score: 114
Period size: 39 Copynumber: 2.7 Consensus size: 41
1196373 TAACCTAAGA
* * * *
1196383 TATTATAAAAATATAATATTTTTAATTATCAATCAAAAATT
1 TATTAAAAAAATATAACATTTTAAATTATCAATCAAAAATC
*
1196424 TATTAAAAAAACATAACATTTTAAATTAT-AAT-AAAAATAC
1 TATTAAAAAAATATAACATTTTAAATTATCAATCAAAAAT-C
* * *
1196464 TA-TAGAAAAATATAAGATTTTATATTA
1 TATTAAAAAAATATAACATTTTAAATTA
1196491 CATCTAATCT
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
39 27 0.47
40 5 0.09
41 25 0.44
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.39
Consensus pattern (41 bp):
TATTAAAAAAATATAACATTTTAAATTATCAATCAAAAATC
Found at i:1196738 original size:14 final size:14
Alignment explanation
Indices: 1196719--1196752 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
1196709 AGTCACTCAA
1196719 CTATTTTCATGATT
1 CTATTTTCATGATT
1196733 CTATTTTCATGATT
1 CTATTTTCATGATT
1196747 CTATTT
1 CTATTT
1196753 CGCCACCCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.21, C:0.15, G:0.06, T:0.59
Consensus pattern (14 bp):
CTATTTTCATGATT
Found at i:1202673 original size:32 final size:32
Alignment explanation
Indices: 1202632--1202696 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
1202622 TGATTTACAA
1202632 TAAAAATGATTCTAAAGTTTTCTTCTCCTCTT
1 TAAAAATGATTCTAAAGTTTTCTTCTCCTCTT
1202664 TAAAAATGATTCTAAAGTTTTCTTCTCCTCTT
1 TAAAAATGATTCTAAAGTTTTCTTCTCCTCTT
1202696 T
1 T
1202697 CTTTTGTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.28, C:0.18, G:0.06, T:0.48
Consensus pattern (32 bp):
TAAAAATGATTCTAAAGTTTTCTTCTCCTCTT
Found at i:1203647 original size:2 final size:2
Alignment explanation
Indices: 1203640--1203664 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1203630 TTAACCAAGA
1203640 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
1203665 TGCATATTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1205159 original size:12 final size:13
Alignment explanation
Indices: 1205142--1205175 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
1205132 AATATAAATA
1205142 TAATTTATATTTT
1 TAATTTATATTTT
*
1205155 T-ATTTTTATTTT
1 TAATTTATATTTT
1205167 TAATTTATA
1 TAATTTATA
1205176 ATATAATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TAATTTATATTTT
Found at i:1205842 original size:80 final size:83
Alignment explanation
Indices: 1205708--1205874 Score: 232
Period size: 80 Copynumber: 2.0 Consensus size: 83
1205698 CTATTTGAAT
* ** * *
1205708 TTAAAAAAAATTACAAAAAATCAAAACAAATTATAAACTAATTAATATATTTATTTATTTAATTT
1 TTAAAAAAAATTAC-AAAAATCAAAACAAATTACAAAAAAATTAATATAATTATTTATCTAATTT
1205773 CAATATATTTTTATATATA
65 CAATATATTTTTATATATA
*
1205792 TTAAAAAAAA-TAC-AAAATCAAAA-AAATTACAAAAAAATTAATATAATTATTTATCTAATTTT
1 TTAAAAAAAATTACAAAAATCAAAACAAATTACAAAAAAATTAATATAATTATTTATCTAATTTC
* *
1205854 AATATGTTTTTATCTATA
66 AATATATTTTTATATATA
1205872 TTA
1 TTA
1205875 TAATTTAATA
Statistics
Matches: 75, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
80 52 0.69
81 10 0.13
83 3 0.04
84 10 0.13
ACGTcount: A:0.53, C:0.06, G:0.01, T:0.41
Consensus pattern (83 bp):
TTAAAAAAAATTACAAAAATCAAAACAAATTACAAAAAAATTAATATAATTATTTATCTAATTTC
AATATATTTTTATATATA
Found at i:1211841 original size:23 final size:22
Alignment explanation
Indices: 1211811--1211864 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
1211801 TACATGTATA
1211811 ACACATTTTCATCT-ATCTTTATG
1 ACACATTTTC-TCTAATCTTT-TG
*
1211834 ACACATTTTCTTTAATCTTTTG
1 ACACATTTTCTCTAATCTTTTG
*
1211856 ACATATTTT
1 ACACATTTT
1211865 TCGATTGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 12 0.43
23 16 0.57
ACGTcount: A:0.26, C:0.19, G:0.04, T:0.52
Consensus pattern (22 bp):
ACACATTTTCTCTAATCTTTTG
Found at i:1213524 original size:41 final size:42
Alignment explanation
Indices: 1213461--1213553 Score: 125
Period size: 41 Copynumber: 2.2 Consensus size: 42
1213451 AATATATCAA
** * * *
1213461 TTTTTTATTAAATTTATTAAAAATTTGACGTAATGATTATAT
1 TTTTTTATTAAATACATCAAAAAATTAACGTAATGATTATAT
*
1213503 TTTTTTATTAAA-ACATCAAAAAATTAATGTAATGATTATAT
1 TTTTTTATTAAATACATCAAAAAATTAACGTAATGATTATAT
1213544 TTTTTTATTA
1 TTTTTTATTA
1213554 GATTTTTTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
41 33 0.73
42 12 0.27
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (42 bp):
TTTTTTATTAAATACATCAAAAAATTAACGTAATGATTATAT
Found at i:1213606 original size:20 final size:22
Alignment explanation
Indices: 1213581--1213627 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
1213571 AATAATGTGT
1213581 TTTTAT-TTTTT-TTATTAAAG
1 TTTTATCTTTTTATTATTAAAG
1213601 TTTTATCTTTTTCATTATTAAAG
1 TTTTATCTTTTT-ATTATTAAAG
1213624 TTTT
1 TTTT
1213628 CAATTAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 6 0.25
21 5 0.21
23 13 0.54
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.68
Consensus pattern (22 bp):
TTTTATCTTTTTATTATTAAAG
Found at i:1215101 original size:64 final size:64
Alignment explanation
Indices: 1215000--1215127 Score: 238
Period size: 64 Copynumber: 2.0 Consensus size: 64
1214990 TTGCTAAAAG
*
1215000 GGGTAAACTTCATTTTGACTCCCTCTGTTTTTAAAAAACATTTAATTTGGTCCCCAAATCGGTT
1 GGGTAAACTTCATTTTGACTCCCTCTGTTTTAAAAAAACATTTAATTTGGTCCCCAAATCGGTT
*
1215064 GGGTAAACTTCATTTTGGCTCCCTCTGTTTTAAAAAAACATTTAATTTGGTCCCCAAATCGGTT
1 GGGTAAACTTCATTTTGACTCCCTCTGTTTTAAAAAAACATTTAATTTGGTCCCCAAATCGGTT
1215128 TAATTCCCTT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (64 bp):
GGGTAAACTTCATTTTGACTCCCTCTGTTTTAAAAAAACATTTAATTTGGTCCCCAAATCGGTT
Found at i:1215382 original size:17 final size:17
Alignment explanation
Indices: 1215360--1215392 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1215350 ATTACTCATA
*
1215360 TTTGTTTTTTTATTTTC
1 TTTGTTTTTATATTTTC
1215377 TTTGTTTTTATATTTT
1 TTTGTTTTTATATTTT
1215393 TTATTCATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.09, C:0.03, G:0.06, T:0.82
Consensus pattern (17 bp):
TTTGTTTTTATATTTTC
Found at i:1225920 original size:1 final size:1
Alignment explanation
Indices: 1225914--1225987 Score: 67
Period size: 1 Copynumber: 74.0 Consensus size: 1
1225904 GTCCTAAGTT
* * * * * * * *
1225914 AAAAAAAAAAACAAAAAAAAAACAAAAAACAAAAAGAAACAAAAACAAAAAAACAAAAAAACAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
1225979 AAACAAAAA
1 AAAAAAAAA
1225988 GAGAAGAACG
Statistics
Matches: 55, Mismatches: 18, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.88, C:0.11, G:0.01, T:0.00
Consensus pattern (1 bp):
A
Found at i:1225929 original size:7 final size:7
Alignment explanation
Indices: 1225914--1225987 Score: 75
Period size: 7 Copynumber: 10.6 Consensus size: 7
1225904 GTCCTAAGTT
1225914 AAAAA-A
1 AAAAACA
1225920 AAAAAC-
1 AAAAACA
1225926 -AAAA-A
1 AAAAACA
1225931 AAAAACA
1 AAAAACA
1225938 AAAAACA
1 AAAAACA
*
1225945 AAAAGAAA
1 AAAA-ACA
1225953 CAAAAACAA
1 -AAAAAC-A
1225962 AAAAACAA
1 AAAAAC-A
1225970 AAAAACA
1 AAAAACA
1225977 AAAAACA
1 AAAAACA
1225984 AAAA
1 AAAA
1225988 GAGAAGAACG
Statistics
Matches: 59, Mismatches: 2, Indels: 13
0.80 0.03 0.18
Matches are distributed among these distances:
5 4 0.07
6 9 0.15
7 24 0.41
8 17 0.29
9 5 0.08
ACGTcount: A:0.88, C:0.11, G:0.01, T:0.00
Consensus pattern (7 bp):
AAAAACA
Found at i:1225940 original size:23 final size:22
Alignment explanation
Indices: 1225914--1225987 Score: 94
Period size: 23 Copynumber: 3.2 Consensus size: 22
1225904 GTCCTAAGTT
1225914 AAAAAAAAAAACAAAAAAAAAAC
1 AAAAAAAAAAA-AAAAAAAAAAC
* *
1225937 AAAAAACAAAAAGAAACAAAAAC
1 AAAAAA-AAAAAAAAAAAAAAAC
*
1225960 AAAAAAACAAAAAAACAAAAAAC
1 AAAAAAA-AAAAAAAAAAAAAAC
1225983 AAAAA
1 AAAAA
1225988 GAGAAGAACG
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
22 1 0.02
23 38 0.86
24 5 0.11
ACGTcount: A:0.88, C:0.11, G:0.01, T:0.00
Consensus pattern (22 bp):
AAAAAAAAAAAAAAAAAAAAAC
Found at i:1225958 original size:39 final size:39
Alignment explanation
Indices: 1225914--1225989 Score: 125
Period size: 39 Copynumber: 1.9 Consensus size: 39
1225904 GTCCTAAGTT
*
1225914 AAAAAAAAAAACAAAAAAAAAACAAAAAACAAAAAGAAAC
1 AAAAACAAAAA-AAAAAAAAAACAAAAAACAAAAAGAAAC
*
1225954 AAAAACAAAAAAACAAAAAAACAAAAAACAAAAAGA
1 AAAAACAAAAAAAAAAAAAAACAAAAAACAAAAAGA
1225990 GAAGAACGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 24 0.71
40 10 0.29
ACGTcount: A:0.87, C:0.11, G:0.03, T:0.00
Consensus pattern (39 bp):
AAAAACAAAAAAAAAAAAAAACAAAAAACAAAAAGAAAC
Found at i:1227005 original size:105 final size:105
Alignment explanation
Indices: 1226823--1227852 Score: 1721
Period size: 105 Copynumber: 9.9 Consensus size: 105
1226813 AGGTTTTACC
* *
1226823 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCATG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1226888 ATGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
1226928 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
1226993 ATGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAAAT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
1227033 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
1227098 ATGAA-GGACCGCTGGTTGTCAACAAACATTTCTCAAAAT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
1227137 CA-AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1227201 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
1227241 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1227306 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
1227346 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTC-ACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1227410 ACGAAGGGACCGCTGGTTGTCAAC-AACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
1227449 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1227514 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
1227554 CAGAGCCAATTTTAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * * *
1227619 GCGAAGGGACCGCTGGTTGTCAACAACCAACTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAAATT
* * *
1227660 CATAGCCAATTTCAACGTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
1227725 ACGAAGGGACCGCTGGTTTTCAA-TAA-A-----CAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
* * ***
1227758 C----CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGATAGTACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1227819 ACGAAGGGACCGCTGGTTGTCAACAAACAATTTC
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTC
1227853 CCAGTCCCAG
Statistics
Matches: 886, Mismatches: 27, Indels: 28
0.94 0.03 0.03
Matches are distributed among these distances:
94 77 0.09
95 2 0.00
97 1 0.00
98 7 0.01
103 137 0.15
104 135 0.15
105 435 0.49
106 92 0.10
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
Found at i:1227209 original size:208 final size:210
Alignment explanation
Indices: 1226823--1227852 Score: 1721
Period size: 208 Copynumber: 5.0 Consensus size: 210
1226813 AGGTTTTACC
* *
1226823 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCATG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1226888 ATGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACG
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACG
*
1226953 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACA
131 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
*
1227018 AACATTTCTCAAAAT
196 AACATTTCTCAAATT
1227033 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
1227098 ATGAA-GGACCGCTGGTTGTCAACAAACATTTCTCAAAATCA-AGCCAATTTCAACTTCACAACG
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACG
1227161 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
131 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
1227226 AACATTTCTCAAATT
196 AACATTTCTCAAATT
1227241 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1227306 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACG
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACG
1227371 AAGGATATTGGACTCCAGACAACGCAAGTTC-ACTTCACGACGAAGGGACCGCTGGTTGTCAAC-
131 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
1227434 AACATTTCTCAAATT
196 AACATTTCTCAAATT
*
1227449 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
1227514 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTTAACTTCACAACG
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACG
*
1227579 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGGCGAAGGGACCGCTGGTTGTCAACA
131 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
* * *
1227644 ACCAACTTCTCAATTT
196 AAC-ATTTCTCAAATT
* * *
1227660 CATAGCCAATTTCAACGTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
1227725 ACGAAGGGACCGCTGGTTTTCAA-TAA-A-----CAATTTC----CCAATTTCAACTTCACAACG
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACG
* * ***
1227779 AAGGATATTGGACTCAAGATAGTACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
131 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
1227844 AACAATTTC
196 AAC-ATTTC
1227853 CCAGTCCCAG
Statistics
Matches: 786, Mismatches: 29, Indels: 20
0.94 0.03 0.02
Matches are distributed among these distances:
200 85 0.11
204 6 0.01
208 343 0.44
209 134 0.17
210 125 0.16
211 93 0.12
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (210 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACG
AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
AACATTTCTCAAATT
Found at i:1227394 original size:313 final size:313
Alignment explanation
Indices: 1226826--1227852 Score: 1718
Period size: 313 Copynumber: 3.3 Consensus size: 313
1226816 TTTTACCCAG
* * *
1226826 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCATGATG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1226891 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAG
*
1226956 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAAC
131 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
*
1227021 ATTTCTCAAAATCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
196 ATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
*
1227086 TTCAACTTCACGATGAA-GGACCGCTGGTTGTCAACAAACATTTCTCAAAATCA
261 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTC-AAATCA
1227139 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1227204 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAG
1227269 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
131 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
1227334 ATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
196 ATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1227399 TTC-ACTTCACGACGAAGGGACCGCTGGTTGTCAAC-AACATTTCTCAAATTCA
261 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAA-TCA
*
1227451 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGAC
1 -AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAC
*
1227516 GAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTTAACTTCACAACGAA
65 GAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAA
* *
1227581 GGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGGCGAAGGGACCGCTGGTTGTCAACAAC
130 GGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA
* * * * *
1227646 CAACTTCTCAATTTCATAGCCAATTTCAACGTCACAACGAAGGATATTGGACTCCAGACAACACA
195 C-ATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
* * *
1227711 AGTTCAACTTCACGACGAAGGGACCGCTGGTTTTCAATAAACA-AT-T----TC-
259 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATCA
* * ***
1227759 --CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGATAGTACAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1227822 AAGGGACCGCTGGTTGTCAACAAACAATTTC
66 AAGGGACCGCTGGTTGTCAACAAAC-ATTTC
1227853 CCAGTCCCAG
Statistics
Matches: 683, Mismatches: 24, Indels: 21
0.94 0.03 0.03
Matches are distributed among these distances:
305 82 0.12
306 5 0.01
309 2 0.00
311 3 0.00
312 25 0.04
313 467 0.68
314 64 0.09
315 31 0.05
316 4 0.01
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (313 bp):
AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAG
GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
ATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATCA
Found at i:1227826 original size:94 final size:94
Alignment explanation
Indices: 1227559--1227855 Score: 378
Period size: 94 Copynumber: 3.0 Consensus size: 94
1227549 AAATTCAGAG
* * * * *
1227559 CCAATTTTAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGGCGAA
1 CCAATTTCAACGTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACGACGAA
1227624 GGGACCGCTGGTTGTCAACAACCAACTTCTCAATTTC
66 GGGACCGCTGGTTGTCAAC-A--AA-----CAATTTC
*
1227661 ATAGCCAATTTCAACGTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGA
1 ----CCAATTTCAACGTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACGA
* *
1227726 CGAAGGGACCGCTGGTTTTCAATAAACAATTTC
62 CGAAGGGACCGCTGGTTGTCAACAAACAATTTC
* * **
1227759 CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGATAGTACAAGTTCAACTTCACGACGAA
1 CCAATTTCAACGTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACGACGAA
1227824 GGGACCGCTGGTTGTCAACAAACAATTTC
66 GGGACCGCTGGTTGTCAACAAACAATTTC
1227853 CCA
1 CCA
1227856 GTCCCAGAAT
Statistics
Matches: 178, Mismatches: 13, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
94 90 0.51
98 7 0.04
103 2 0.01
105 1 0.01
106 78 0.44
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (94 bp):
CCAATTTCAACGTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACGACGAA
GGGACCGCTGGTTGTCAACAAACAATTTC
Found at i:1229478 original size:64 final size:64
Alignment explanation
Indices: 1229377--1229504 Score: 229
Period size: 64 Copynumber: 2.0 Consensus size: 64
1229367 TTGCTAAAAG
* *
1229377 GGGTAAACTTCATTTTGACTCCCTCTGTTTTTAAAAAACATTTAATTTGGTCCCCAAATCGGTT
1 GGGTAAACTTCATTTTGACTCCCCCTGTTTTAAAAAAACATTTAATTTGGTCCCCAAATCGGTT
*
1229441 GGGTAAACTTCATTTTGGCTCCCCCTGTTTTAAAAAAACATTTAATTTGGTCCCCAAATCGGTT
1 GGGTAAACTTCATTTTGACTCCCCCTGTTTTAAAAAAACATTTAATTTGGTCCCCAAATCGGTT
1229505 TAATTCCCTT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.38
Consensus pattern (64 bp):
GGGTAAACTTCATTTTGACTCCCCCTGTTTTAAAAAAACATTTAATTTGGTCCCCAAATCGGTT
Found at i:1229759 original size:17 final size:17
Alignment explanation
Indices: 1229737--1229769 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1229727 ATTACTCATA
*
1229737 TTTGTTTTTTTATTTTC
1 TTTGTTTTTATATTTTC
1229754 TTTGTTTTTATATTTT
1 TTTGTTTTTATATTTT
1229770 TTATTCATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.09, C:0.03, G:0.06, T:0.82
Consensus pattern (17 bp):
TTTGTTTTTATATTTTC
Found at i:1233086 original size:5 final size:5
Alignment explanation
Indices: 1233076--1233146 Score: 63
Period size: 5 Copynumber: 14.4 Consensus size: 5
1233066 AGATTCCTGC
* * * * * *
1233076 AATAA AATAA AA-AA GATAG AATAA AATAC AATTA TATAA AATAA AATTA
1 AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA
* *
1233125 AATTA TATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AA
1233147 AATCAGACCC
Statistics
Matches: 51, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
4 3 0.06
5 48 0.94
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.25
Consensus pattern (5 bp):
AATAA
Found at i:1233120 original size:20 final size:19
Alignment explanation
Indices: 1233076--1233145 Score: 86
Period size: 20 Copynumber: 3.6 Consensus size: 19
1233066 AGATTCCTGC
** * *
1233076 AATAAAATAAAAAAGATAG
1 AATAAAATAAATTATATAA
1233095 AATAAAATACAATTATATAA
1 AATAAAATA-AATTATATAA
1233115 AATAAAATTAAATTATATAA
1 AATAAAA-TAAATTATATAA
1233135 AATAAAATAAA
1 AATAAAATAAA
1233146 AAATCAGACC
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
19 13 0.29
20 30 0.67
21 2 0.04
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.26
Consensus pattern (19 bp):
AATAAAATAAATTATATAA
Found at i:1233976 original size:25 final size:26
Alignment explanation
Indices: 1233928--1233979 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
1233918 GCAAAAAAAA
*
1233928 TATTGTTTCCAATATGTTTAATTAAT
1 TATTGTTTCCAACATGTTTAATTAAT
*
1233954 TATTGTTT-CAACATGTTTGATTAAT
1 TATTGTTTCCAACATGTTTAATTAAT
1233979 T
1 T
1233980 TTTTTTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 16 0.67
26 8 0.33
ACGTcount: A:0.29, C:0.08, G:0.10, T:0.54
Consensus pattern (26 bp):
TATTGTTTCCAACATGTTTAATTAAT
Found at i:1236397 original size:3 final size:3
Alignment explanation
Indices: 1236389--1236417 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1236379 TTCCGTACTT
1236389 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1236418 TATTCCTAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1238581 original size:21 final size:23
Alignment explanation
Indices: 1238542--1238584 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
1238532 TGCAGACCTA
1238542 AATTTGTTGTTTTAATTAAAATT
1 AATTTGTTGTTTTAATTAAAATT
*
1238565 AATTT-TT-TTTTATTTAAAAT
1 AATTTGTTGTTTTAATTAAAAT
1238585 GGCAAAACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
22 2 0.11
23 5 0.26
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (23 bp):
AATTTGTTGTTTTAATTAAAATT
Found at i:1239512 original size:44 final size:42
Alignment explanation
Indices: 1239462--1239580 Score: 141
Period size: 44 Copynumber: 2.7 Consensus size: 42
1239452 TTGAATAAGT
1239462 ATGCGAACTAGAA-ATGCGGTTAGGTATATTTTCTCGAACAAAGC
1 ATGCGAACTAGAACATGCGGTTAGGT-T-TTTTCTCGAAC-AAGC
*
1239506 ATGCGAACTAGAAATCATGCGGTTATGTTTTTTCTCGAACAAGC
1 ATGCGAACTAG-AA-CATGCGGTTAGGTTTTTTCTCGAACAAGC
* *
1239550 ATGCGAATTAGATATCATGCGATTAGGTTTT
1 ATGCGAACTAGA-A-CATGCGGTTAGGTTTT
1239581 CTTTTTGTGA
Statistics
Matches: 67, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
43 1 0.01
44 41 0.61
45 13 0.19
46 1 0.01
47 11 0.16
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (42 bp):
ATGCGAACTAGAACATGCGGTTAGGTTTTTTCTCGAACAAGC
Found at i:1245320 original size:36 final size:36
Alignment explanation
Indices: 1245278--1245354 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
1245268 AGCAAAGTCA
* * * * *
1245278 ATCTTAAGCCTTCACTAAAGAGTAGTGAAGCAAACC
1 ATCTTAAGCATGCACCAAAGAATAATGAAGCAAACC
*
1245314 GTCTTAAGCATGCACCAAAGAATAATGAAGCAAACC
1 ATCTTAAGCATGCACCAAAGAATAATGAAGCAAACC
1245350 ATCTT
1 ATCTT
1245355 GTGTCTTCAT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (36 bp):
ATCTTAAGCATGCACCAAAGAATAATGAAGCAAACC
Found at i:1245841 original size:52 final size:50
Alignment explanation
Indices: 1245767--1246436 Score: 588
Period size: 50 Copynumber: 13.5 Consensus size: 50
1245757 TGAAGCAAAA
*
1245767 GAAGAT-TTCGAGTTCCATACTCCCTAGAGAAAAAAGGGAGCGAACCCGTT
1 GAAGATGTTCGAGTTCCATACTCCCTAGAG-AAAGAGGGAGCGAACCCGTT
*
1245817 GAAGATGTTCGAGTTTTCATACT-CCT-GAAGAAAGAGGGAGCGAACCCGTTT
1 GAAGATGTTCGAG-TTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCG-TT
* * * ** * * *
1245868 GAAGAAGAGGTAGAGTTTTATACTCCTTAAAGAAAGAGGGAGCGAACCAGTTT
1 GAAG-A-TGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCG-TT
* * * *
1245921 GAAGAAGATCCGAGTTCTATACTCCCTAGAGAAAGAGGAAGCGAACCCGTTT
1 GAAGATG-TTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCG-TT
* * *
1245973 GAAGAAAATATCCGAGTTCCATACTCCCTAGAG-AA-A--GAG-G-----TTT
1 GAAG---ATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTT
** *
1246016 GAAGAAATACGAGTTCCATACT-CCTAGAGAAAGAGGGAGCGAACCCGTTT
1 GAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCG-TT
* *
1246066 GAAGAAGATGTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTT
1 GAAGATG-T-TCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTT
* *
1246118 GAAGAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGA-GGAGCGAACCCGTTT
1 ---GAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCG-TT
* *
1246171 GAAGAAGATTCCAGTTCCATACT-CCTAGAGAAAGA-GGAGCGAACCCGTT
1 GAAGATG-TTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTT
* *
1246220 GAAGA--ATCCAGTTCCATACT-CCTA-AG-AAGA-GGAGCGAACCCGTT
1 GAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTT
*
1246264 GAAGATGTTTGAGTTCCATACT-CCTA-AGAAAGA-GGAGCGAACCCGTTT
1 GAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCG-TT
* * *
1246312 GAAAAGAT-TTTGAGTTCCATACT-CCTAGAGAAAGAGGGAGTGAACCCGTAA
1 G--AAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGT-T
* * *
1246363 GAAGATTTTCGAGTTCTATACTGCCT-GAGAAAGAGGGAGCGAACCCGTT
1 GAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTT
*
1246412 GAAGATTGTTCGAGTTCTATACTCC
1 GAAGA-TGTTCGAGTTCCATACTCC
1246437 TGAAGAAATA
Statistics
Matches: 531, Mismatches: 46, Indels: 86
0.80 0.07 0.13
Matches are distributed among these distances:
39 7 0.01
40 18 0.03
41 1 0.00
43 9 0.02
44 24 0.05
45 2 0.00
46 36 0.07
47 16 0.03
48 3 0.01
49 37 0.07
50 128 0.24
51 47 0.09
52 85 0.16
53 88 0.17
54 23 0.04
55 7 0.01
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.22
Consensus pattern (50 bp):
GAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTT
Done.