Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007984.1 Hibiscus syriacus cultivar Beakdansim tig00110429_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: 12923621
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 26 of 65
Found at i:5187651 original size:17 final size:17
Alignment explanation
Indices: 5187627--5187676 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
5187617 AACAAATAAC
*
5187627 AAAT-AAATAATAAATA
1 AAATAAAATAAAAAATA
*
5187643 CAATAAAATAAAAAATA
1 AAATAAAATAAAAAATA
5187660 AAATAAAGA-AAAAAATA
1 AAATAAA-ATAAAAAATA
5187677 TTTTTTTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
16 3 0.10
17 25 0.86
18 1 0.03
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.18
Consensus pattern (17 bp):
AAATAAAATAAAAAATA
Found at i:5187659 original size:12 final size:13
Alignment explanation
Indices: 5187644--5187676 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
5187634 TAATAAATAC
5187644 AATAAAATAAA-A
1 AATAAAATAAAGA
5187656 AATAAAATAAAGA
1 AATAAAATAAAGA
5187669 AA-AAAATA
1 AATAAAATA
5187677 TTTTTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 17 0.85
13 3 0.15
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (13 bp):
AATAAAATAAAGA
Found at i:5187671 original size:21 final size:21
Alignment explanation
Indices: 5187627--5187671 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
5187617 AACAAATAAC
* *
5187627 AAATAAATAATAAATACAATA
1 AAATAAAAAATAAATACAAGA
5187648 AAATAAAAAATAAAATA-AAGA
1 AAATAAAAAAT-AAATACAAGA
5187669 AAA
1 AAA
5187672 AAATATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.18
Consensus pattern (21 bp):
AAATAAAAAATAAATACAAGA
Found at i:5187748 original size:39 final size:38
Alignment explanation
Indices: 5187674--5187748 Score: 89
Period size: 39 Copynumber: 1.9 Consensus size: 38
5187664 AAAGAAAAAA
* * **
5187674 ATATTTTTTTTAAAACTATATTTTATATATGATTTTTT
1 ATATTTTTTTCAAAACCATATACTATATATGATTTTTT
5187712 ATATGTTTTTTCAAAACCATATACTATAATAT-ATTTT
1 ATAT-TTTTTTCAAAACCATATACTAT-ATATGATTTT
5187749 CAAAAAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
38 4 0.13
39 23 0.74
40 4 0.13
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.56
Consensus pattern (38 bp):
ATATTTTTTTCAAAACCATATACTATATATGATTTTTT
Found at i:5187814 original size:37 final size:36
Alignment explanation
Indices: 5187756--5188034 Score: 185
Period size: 37 Copynumber: 7.8 Consensus size: 36
5187746 TTTCAAAAAA
* *
5187756 AAATATTTT-AAAATTATATATTATATATATTTTCC
1 AAATGTTTTAAAAACTATATATTATATATATTTTCC
* *
5187791 GAAATGTTTTAAAAATTATATATTATATA-AGTTTTCAA
1 -AAATGTTTTAAAAACTATATATTATATATA-TTTTC-C
* * * *
5187829 AAATATTTTTAAAAAACTATACAATATATATATTTTTTC
1 AAAT-GTTTT-AAAAACTATATATTATATATA-TTTTCC
* *
5187868 -AATTTTTTAAAAAAAACTATATA-T-TATATATTTTCAAA
1 AAATGTTTT---AAAAACTATATATTATATATATTTTC--C
*
5187906 ATAATTTTTTAAAAAC--TATA-TA-ATATA---T--
1 A-AATGTTTTAAAAACTATATATTATATATATTTTCC
*
5187934 AAATGTTTTCAAAACTATATATTATATA-AGTTTT-C
1 AAATGTTTTAAAAACTATATATTATATATA-TTTTCC
*
5187969 AAATGATTTTAAAAACTATATATTATATATATTTTCTA
1 AAATG-TTTTAAAAACTATATATTATATATATTTTC-C
*
5188007 AAATGTTTTAAAAACTCTATATTATATA
1 AAATGTTTTAAAAACTATATATTATATA
5188035 GTTTTAAAAA
Statistics
Matches: 200, Mismatches: 17, Indels: 51
0.75 0.06 0.19
Matches are distributed among these distances:
27 12 0.06
28 1 0.00
29 4 0.02
30 3 0.01
31 3 0.01
32 1 0.00
34 1 0.00
35 15 0.08
36 39 0.19
37 67 0.34
38 13 0.06
39 28 0.14
40 13 0.06
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.46
Consensus pattern (36 bp):
AAATGTTTTAAAAACTATATATTATATATATTTTCC
Found at i:5187881 original size:76 final size:74
Alignment explanation
Indices: 5187797--5187945 Score: 194
Period size: 76 Copynumber: 2.0 Consensus size: 74
5187787 TTCCGAAATG
* *
5187797 TTTT-AAAAATTATATATTATATAAGTTTTCAAAA-ATATTTTTAAAAAACTATACAATATATAT
1 TTTTAAAAAACTATATATTATAT-A-TTTTCAAAATA-ATTTTTAAAAAACTATACAATATATAA
*
5187860 ATTTTTTCAATT
63 ATGTTTTCAATT
* *
5187872 TTTTAAAAAAAACTATATATTATATATTTTCAAAATAATTTTTTAAAAACTATATAATATATAAA
1 TTTT--AAAAAACTATATATTATATATTTTCAAAATAATTTTTAAAAAACTATACAATATATAAA
5187937 TGTTTTCAA
64 TGTTTTCAA
5187946 AACTATATAT
Statistics
Matches: 65, Mismatches: 5, Indels: 7
0.84 0.06 0.09
Matches are distributed among these distances:
75 4 0.06
76 42 0.65
77 2 0.03
78 17 0.26
ACGTcount: A:0.47, C:0.05, G:0.01, T:0.46
Consensus pattern (74 bp):
TTTTAAAAAACTATATATTATATATTTTCAAAATAATTTTTAAAAAACTATACAATATATAAATG
TTTTCAATT
Found at i:5187950 original size:27 final size:25
Alignment explanation
Indices: 5187912--5187971 Score: 84
Period size: 27 Copynumber: 2.3 Consensus size: 25
5187902 CAAAATAATT
*
5187912 TTTTAAAAACTATATAATATATAAATG
1 TTTTCAAAACTATATAATATAT-AA-G
*
5187939 TTTTCAAAACTATATATTATATAAG
1 TTTTCAAAACTATATAATATATAAG
5187964 TTTTCAAA
1 TTTTCAAA
5187972 TGATTTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
25 9 0.29
26 2 0.06
27 20 0.65
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (25 bp):
TTTTCAAAACTATATAATATATAAG
Found at i:5188043 original size:24 final size:24
Alignment explanation
Indices: 5188011--5188058 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
5188001 TTTCTAAAAT
5188011 GTTTTAAAAACTCTATATTATATA
1 GTTTTAAAAACTCTATATTATATA
*
5188035 GTTTTAAAAACTGTATATTATATA
1 GTTTTAAAAACTCTATATTATATA
5188059 TATTTTCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (24 bp):
GTTTTAAAAACTCTATATTATATA
Found at i:5188069 original size:26 final size:24
Alignment explanation
Indices: 5188012--5188069 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
5188002 TTCTAAAATG
*
5188012 TTTTAAAAACTCTATATTATATAG
1 TTTTAAAAACTCTATATTATATAA
*
5188036 TTTTAAAAACTGTATATTATATATA
1 TTTTAAAAACTCTATATTATATA-A
*
5188061 TTTTCAAAA
1 TTTTAAAAA
5188070 TGTTTTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 22 0.73
25 8 0.27
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (24 bp):
TTTTAAAAACTCTATATTATATAA
Found at i:5188107 original size:61 final size:61
Alignment explanation
Indices: 5187976--5188124 Score: 167
Period size: 61 Copynumber: 2.4 Consensus size: 61
5187966 TTCAAATGAT
* * **
5187976 TTTAAAAACTATATATTATATATATTTTCTAAAATGTTTTAAAAACTCTATATTATATAGT
1 TTTAAAAACTATATATTATATATATTTTCTAAAATGTTTTAAAAACTCTATATTAAAAACA
* * *
5188037 TTTAAAAACTGTATATTATATATATTTTC-AAAATGTTTTAAAAA-TGTATTTTCAAAAACCA
1 TTTAAAAACTATATATTATATATATTTTCTAAAATGTTTTAAAAACTCTATATT-AAAAA-CA
**
5188098 TTTGCAAACTATAATATATATATATAT
1 TTTAAAAACTAT-ATAT-TATATATAT
5188125 ATATATATAT
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
59 6 0.08
60 18 0.24
61 37 0.50
62 4 0.05
63 9 0.12
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (61 bp):
TTTAAAAACTATATATTATATATATTTTCTAAAATGTTTTAAAAACTCTATATTAAAAACA
Found at i:5188848 original size:84 final size:84
Alignment explanation
Indices: 5188708--5190173 Score: 1698
Period size: 84 Copynumber: 17.5 Consensus size: 84
5188698 ACTCGACACC
* ** * * * * * *
5188708 TTTGTTGACAGATAGCCCTTCTTAACTTGAGCCATGTTGTAAATTTAATATGCCTTTGAGCTGAA
1 TTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAA--TGATGTGCCTTTGAGCTGAG
5188773 TGTAATCGAACTCGAAGGTCT
64 TGTAATCGAACTCGAAGGTCT
* *
5188794 TTTCTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTTGAGCTGAGTG
1 TTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTG
5188859 TAATCGAACTCGAAGGTC-
66 TAATCGAACTCGAAGGTCT
* **
5188877 --T-TTGGCAGATAGCCCTTCTTTCCTTGAGCTATGCTGCAAATGATGCACCTTTGAGCTGAGTG
1 TTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTG
* *
5188939 TAATCGAACTTGAAGGCCT
66 TAATCGAACTCGAAGGTCT
* * * * * * ** ** * *
5188958 TTTGATGACAGATAACCCTTCTAGACTTGAGTTATGCTATAAATGATGCACCTCTT-AGCTAAAT
1 TTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCT-TTGAGCTGAGT
* *
5189022 GTAATCAAACTCGAAGGTTT
65 GTAATCGAACTCGAAGGTCT
* ** **
5189042 TTTGTTGGAAGATAGATCTTCTTGCCTTGAGCTATGCTGCAAATGACATGCCTTTGAGCTGAGTG
1 TTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTG
5189107 TAATCGAACTCGAAGGTC-
66 TAATCGAACTCGAAGGTCT
* * * * *
5189125 --T-TTGGCAGATAACCCTTTTTGCCTTGAGCTATTCTACAAATGATGCGCCTTTGAGCTGAGTG
1 TTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTG
* *
5189187 TAATCAAACTCAAAGGTCT
66 TAATCGAACTCGAAGGTCT
* * * * * * * * *
5189206 TTTGATGACATATAACCCTTATAGCCTTGAGTTATGCTGTAAATGATGTGCCTCTGAGCTGAGTG
1 TTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTG
* *
5189271 CAATCAAACTCGAAGGTC-
66 TAATCGAACTCGAAGGTCT
* * * * **
5189289 TTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATATTGTC-AATGATGTGCCTTTGAGCTGAGT
1 TTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTG-CAAATGATGTGCCTTTGAGCTGAGT
*
5189353 GTAATCGAACTTGAAGGTC-
65 GTAATCGAACTCGAAGGTCT
* *
5189372 TTTATTGGCAGATAGCCCCTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTG
1 TTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTG
5189437 TAATCGAACTCGAAGGTCT
66 TAATCGAACTCGAAGGTCT
* * * * * ** *
5189456 TTGGTTAGCATATAGCCCTTCTTGCATTAAGCTATGCTGCAAATGATGCACCTTTGAGCTGATTG
1 TTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTG
* *
5189521 TAATTGAACTCGATGGTCT
66 TAATCGAACTCGAAGGTCT
* * *
5189540 TTTGTTGGCAGATAGTCATTCTTGCCTTGAGCTATACTGCAAATGATGTGCCTTTGAGCTGAGTG
1 TTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTG
**
5189605 TAATTAAACTCGAAGGTCT
66 TAATCGAACTCGAAGGTCT
* * * *
5189624 TTTGTTGGCAGATAGCCCTTATTTCCTTGAGCTATGCTGCAAATGATGTACCTTTGAGCTAAGTG
1 TTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTG
*
5189689 TAATCGAACTCAAAGGTCT
66 TAATCGAACTCGAAGGTCT
* * * * * *
5189708 TGTGTTGGCATATAACCCTTCTAGCCTTGAGTTATACTGCAAATGATGTGCCTTTGAGCTGAGTG
1 TTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTG
5189773 TAATCGAACTCGAAGGTCT
66 TAATCGAACTCGAAGGTCT
* * * * * * * * *
5189792 TGTGTTGGAATATAACCCTTCTAT-CTTTGTGTTATGTTGCAAATGATATGCCTTTGAGCTGAGT
1 TTTGTTGGCAGATAGCCCTTCT-TGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
* *
5189856 GTAATAGATCTCGAAGGTCT
65 GTAATCGAACTCGAAGGTCT
* * * *
5189876 TTTGTTGGCAGATAGCCCTTCTTTCCTTGAGCTATGCTGTAAATTATGCGCCTTTGAGCTGAGTG
1 TTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTG
* *
5189941 TAATCGAACTCAAACGTCT
66 TAATCGAACTCGAAGGTCT
* * * * ** *
5189960 TGTGTTGGCAGATAACTCTTCTAGCCTTGATTTATGCTGTAAATGATGTGCCTTTGAGCTGAGTG
1 TTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTG
5190025 TAATCGAACTCGAAGGTCT
66 TAATCGAACTCGAAGGTCT
* * ** *
5190044 TTTTTTGGCAGATAGACCTTCTCACCTTGAGCTATGTTGCAAATGATGTGCCTTTGAGCTGAGTG
1 TTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTG
5190109 TAATCGAACTCGAAGGTCT
66 TAATCGAACTCGAAGGTCT
* * * * *
5190128 TGTGTTGGCAAATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGA
1 TTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGA
5190174 AAAAAATAGA
Statistics
Matches: 1170, Mismatches: 195, Indels: 32
0.84 0.14 0.02
Matches are distributed among these distances:
80 140 0.12
81 2 0.00
82 1 0.00
83 149 0.13
84 839 0.72
85 2 0.00
86 37 0.03
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (84 bp):
TTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTG
TAATCGAACTCGAAGGTCT
Found at i:5191487 original size:93 final size:93
Alignment explanation
Indices: 5191308--5191563 Score: 309
Period size: 93 Copynumber: 2.7 Consensus size: 93
5191298 AGCTAGCTGG
* * * * *
5191308 ATCCATAAAGCCGAGACATTTAA-CAGTTGCTCTAGAGGGACATCTCAATATCATTGTATATATA
1 ATCCATAAAGCCGAGGCGTTTAACCAATTGCTCTAGAGGGACAACTC-A-AGC-TT-TAT-TATA
* * *
5191372 TTATAATCGCCTTTATCAGGCTATCTGAATATT
61 TTATAATCACCTTTATCAGGCTAGCTAAATATT
5191405 ATCCATAAAGCCGAGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTATATTATA
1 ATCCATAAAGCCGAGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTATATTATA
*
5191470 ATCACCTTTATCAGGCTAGCTAAATCTT
66 ATCACCTTTATCAGGCTAGCTAAATATT
* * * * *
5191498 ATCCATAAAGCC-AGAGAGTTTAACTAATTACTTTAGAGGGACAACTCAAGCTTTATTGTATATA
1 ATCCATAAAGCCGAG-GCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTATAT-TA
5191562 TA
64 TA
5191564 TAATATTATA
Statistics
Matches: 142, Mismatches: 14, Indels: 9
0.86 0.08 0.05
Matches are distributed among these distances:
92 2 0.01
93 86 0.61
94 7 0.05
95 2 0.01
96 2 0.01
97 22 0.15
98 21 0.15
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (93 bp):
ATCCATAAAGCCGAGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTATATTATA
ATCACCTTTATCAGGCTAGCTAAATATT
Found at i:5193286 original size:16 final size:16
Alignment explanation
Indices: 5193258--5193302 Score: 67
Period size: 15 Copynumber: 2.9 Consensus size: 16
5193248 TAATATAATT
5193258 CCTAAAC-AAATTAAA
1 CCTAAACTAAATTAAA
5193273 CCTAAACTAAATTAAA
1 CCTAAACTAAATTAAA
*
5193289 CATAAA-TAAATTAA
1 CCTAAACTAAATTAA
5193303 GCCTCACGCG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 15 0.54
16 13 0.46
ACGTcount: A:0.60, C:0.16, G:0.00, T:0.24
Consensus pattern (16 bp):
CCTAAACTAAATTAAA
Found at i:5194484 original size:55 final size:54
Alignment explanation
Indices: 5194410--5194599 Score: 208
Period size: 55 Copynumber: 3.5 Consensus size: 54
5194400 CGAATGATGG
* * *
5194410 GTCCGCTCCCTATTCCTTCAGGGAGTATAAGACTCGAATAATCTTCAACAAATAT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAAGACTCG-ATAATCTTCAACAAATGT
* * * * *
5194465 GTCCGTTCACTATTTC-TTCAGAGAGTATAGGACT---TGATCTTCAACAAACGT
1 GTCCGCTCCCTA-TTCATTCAGAGAGTATAAGACTCGATAATCTTCAACAAATGT
* * *
5194516 GTCCGCTCCCTATTCATTCAGAGAGTATAAGACTCGATCAATCTTTAATAAATGG
1 GTCCGCTCCCTATTCATTCAGAGAGTATAAGACTCGAT-AATCTTCAACAAATGT
* *
5194571 GTCCGCTCCCTATTCGTTCAGGGAGTATA
1 GTCCGCTCCCTATTCATTCAGAGAGTATA
5194600 GAACCCCTAT
Statistics
Matches: 112, Mismatches: 17, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
50 3 0.03
51 41 0.37
54 1 0.01
55 64 0.57
56 3 0.03
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (54 bp):
GTCCGCTCCCTATTCATTCAGAGAGTATAAGACTCGATAATCTTCAACAAATGT
Found at i:5194529 original size:51 final size:51
Alignment explanation
Indices: 5194410--5194554 Score: 157
Period size: 51 Copynumber: 2.8 Consensus size: 51
5194400 CGAATGATGG
* * * *
5194410 GTCCGCTCCCTATTCCTTCAGGGAGTATAAGACTCGAATAATCTTCAACAAATAT
1 GTCCGCTCCCTATTTCTTCAGAGAGTATAAGACT----TGATCTTCAACAAACAT
* * * *
5194465 GTCCGTTCACTATTTCTTCAGAGAGTATAGGACTTGATCTTCAACAAACGT
1 GTCCGCTCCCTATTTCTTCAGAGAGTATAAGACTTGATCTTCAACAAACAT
*
5194516 GTCCGCTCCCTA-TTCATTCAGAGAGTATAAGACTCGATC
1 GTCCGCTCCCTATTTC-TTCAGAGAGTATAAGACTTGATC
5194555 AATCTTTAAT
Statistics
Matches: 77, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
50 3 0.04
51 45 0.58
55 29 0.38
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (51 bp):
GTCCGCTCCCTATTTCTTCAGAGAGTATAAGACTTGATCTTCAACAAACAT
Found at i:5194597 original size:106 final size:106
Alignment explanation
Indices: 5194410--5194600 Score: 269
Period size: 106 Copynumber: 1.8 Consensus size: 106
5194400 CGAATGATGG
* * * *
5194410 GTCCGCTCCCTATTCCTTCAGGGAGTATAAGACTCGAATAATCTTCAACAAATATGTCCGTTCAC
1 GTCCGCTCCCTATTCATTCAGAGAGTATAAGACTCGAATAATCTTCAACAAATAGGTCCGCTCAC
5194475 TATTTCTTCAGAGAGTATAGGACTTGATCTTCAACAAACGT
66 TATTTCTTCAGAGAGTATAGGACTTGATCTTCAACAAACGT
* * * *
5194516 GTCCGCTCCCTATTCATTCAGAGAGTATAAGACTCG-ATCAATCTTTAATAAATGGGTCCGCTCC
1 GTCCGCTCCCTATTCATTCAGAGAGTATAAGACTCGAAT-AATCTTCAACAAATAGGTCCGCTCA
*
5194580 CTA-TTCGTTCAGGGAGTATAG
65 CTATTTC-TTCAGAGAGTATAG
5194601 AACCCCTATT
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
105 5 0.07
106 69 0.93
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.31
Consensus pattern (106 bp):
GTCCGCTCCCTATTCATTCAGAGAGTATAAGACTCGAATAATCTTCAACAAATAGGTCCGCTCAC
TATTTCTTCAGAGAGTATAGGACTTGATCTTCAACAAACGT
Found at i:5194614 original size:26 final size:26
Alignment explanation
Indices: 5194578--5194629 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
5194568 TGGGTCCGCT
*
5194578 CCCTATTCGTTCAGGGAGTATAGAAC
1 CCCTATTCGTTCAGGGAGTAAAGAAC
5194604 CCCTATTCGTTCAGGGAGTAAAGAAC
1 CCCTATTCGTTCAGGGAGTAAAGAAC
5194630 TCGAACAATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (26 bp):
CCCTATTCGTTCAGGGAGTAAAGAAC
Found at i:5194697 original size:55 final size:55
Alignment explanation
Indices: 5194613--5194798 Score: 275
Period size: 55 Copynumber: 3.4 Consensus size: 55
5194603 CCCCTATTCG
* *
5194613 TTCAGGGAGTAAAGAACTCGAACAATCTTCTTCGAATGAGTTTGCTCCCTCTTGC
1 TTCAGGAAGTATAGAACTCGAACAATCTTCTTCGAATGAGTTTGCTCCCTCTTGC
* *
5194668 TTCAGGAAGTATAGAACTCGAACAATCTTCTTCGAATGAGTTCGCTCCCTTTTGC
1 TTCAGGAAGTATAGAACTCGAACAATCTTCTTCGAATGAGTTTGCTCCCTCTTGC
* * *
5194723 TTCAGTAAGTATAGAACTCGAACAATCTTCTTCCAACGAGTTTGCTCCCTCTTGC
1 TTCAGGAAGTATAGAACTCGAACAATCTTCTTCGAATGAGTTTGCTCCCTCTTGC
* *
5194778 TACAAGG-AGTATATAACTCGA
1 TTC-AGGAAGTATAGAACTCGA
5194799 TCTTCATAAA
Statistics
Matches: 118, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
55 116 0.98
56 2 0.02
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (55 bp):
TTCAGGAAGTATAGAACTCGAACAATCTTCTTCGAATGAGTTTGCTCCCTCTTGC
Found at i:5194855 original size:37 final size:38
Alignment explanation
Indices: 5194807--5194917 Score: 129
Period size: 37 Copynumber: 3.0 Consensus size: 38
5194797 GATCTTCATA
* *
5194807 AAATGAATTTGCTTCACTATTCTTCTGTGAAGGCTTAT
1 AAATGAATTTGCTTCACTACTCTTCCGTGAAGGCTTAT
5194845 AAATG-ATTTGCTTCACTACTCTTCCGTGAAGGCTTA-
1 AAATGAATTTGCTTCACTACTCTTCCGTGAAGGCTTAT
* * * * *
5194881 AGATTGAA-TTGCTTCAATGCTTTTTCGTGAAGGCTTA
1 A-AATGAATTTGCTTCACTACTCTTCCGTGAAGGCTTA
5194918 AGATTGAATT
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
36 1 0.02
37 57 0.89
38 6 0.09
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.40
Consensus pattern (38 bp):
AAATGAATTTGCTTCACTACTCTTCCGTGAAGGCTTAT
Found at i:5194918 original size:37 final size:37
Alignment explanation
Indices: 5194827--5194937 Score: 134
Period size: 37 Copynumber: 3.0 Consensus size: 37
5194817 GCTTCACTAT
* * * * *
5194827 TCTTCTGTGAAGGCTTATA-AATGATTTGCTTCACTAC
1 TCTTCCGTGAAGGCTTA-AGATTGAATTGCTTCAATGC
5194864 TCTTCCGTGAAGGCTTAAGATTGAATTGCTTCAATGC
1 TCTTCCGTGAAGGCTTAAGATTGAATTGCTTCAATGC
* *
5194901 TTTTTCGTGAAGGCTTAAGATTGAATTGCTTCGAATG
1 TCTTCCGTGAAGGCTTAAGATTGAATTGCTTC-AATG
5194938 TCAAACCTAA
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
36 1 0.02
37 60 0.92
38 4 0.06
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (37 bp):
TCTTCCGTGAAGGCTTAAGATTGAATTGCTTCAATGC
Found at i:5196219 original size:19 final size:19
Alignment explanation
Indices: 5196203--5196242 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
5196193 CCCCTTTTTA
5196203 TTTTTC-TCTATTTTTTTCT
1 TTTTTCATC-ATTTTTTTCT
5196222 TTTTTCATCA-TTTTTTCT
1 TTTTTCATCATTTTTTTCT
5196240 TTT
1 TTT
5196243 CTTTTTTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 11 0.55
19 7 0.35
20 2 0.10
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTTCATCATTTTTTTCT
Found at i:5196224 original size:7 final size:7
Alignment explanation
Indices: 5196214--5196332 Score: 66
Period size: 7 Copynumber: 16.9 Consensus size: 7
5196204 TTTTCTCTAT
5196214 TTTTTTC
1 TTTTTTC
5196221 TTTTTTC
1 TTTTTTC
5196228 ATCATTTTT-
1 -T--TTTTTC
*
5196237 TCTTTTC
1 TTTTTTC
5196244 TTTTTTC
1 TTTTTTC
*
5196251 TTCTATT-
1 TT-TTTTC
* *
5196258 TTCTAT-
1 TTTTTTC
5196264 TTTTTTC
1 TTTTTTC
*
5196271 TATTTTC
1 TTTTTTC
*
5196278 TATTTTC
1 TTTTTTC
*
5196285 TATTTTC
1 TTTTTTC
*
5196292 TATTTTCC
1 T-TTTTTC
*
5196300 TTTTTCC
1 TTTTTTC
5196307 TTTTTT-
1 TTTTTTC
* *
5196313 TCTTTTA
1 TTTTTTC
5196320 TTTTTTC
1 TTTTTTC
5196327 TTTTTT
1 TTTTTT
5196333 TTCATTTCTT
Statistics
Matches: 89, Mismatches: 15, Indels: 16
0.74 0.12 0.13
Matches are distributed among these distances:
6 14 0.16
7 60 0.67
8 10 0.11
10 5 0.06
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTTC
Found at i:5196224 original size:17 final size:16
Alignment explanation
Indices: 5196204--5196318 Score: 77
Period size: 17 Copynumber: 7.2 Consensus size: 16
5196194 CCCTTTTTAT
5196204 TTTTCTCTATTTTTTTC
1 TTTT-TCTATTTTTTTC
5196221 TTTTT-TCATCATTTTTTC
1 TTTTTCT-AT--TTTTTTC
5196239 -TTTTCT-TTTTTCTTC
1 TTTTTCTATTTTT-TTC
5196254 TATTTTCTATTTTTTTC
1 T-TTTTCTATTTTTTTC
5196271 TATTTTCTA---TTTTC
1 T-TTTTCTATTTTTTTC
*
5196285 TATTTTCTA--TTTTCC
1 T-TTTTCTATTTTTTTC
*
5196300 TTTTTC-CTTTTTTTC
1 TTTTTCTATTTTTTTC
5196315 TTTT
1 TTTT
5196319 ATTTTTTCTT
Statistics
Matches: 84, Mismatches: 3, Indels: 24
0.76 0.03 0.22
Matches are distributed among these distances:
14 23 0.27
15 18 0.21
16 4 0.05
17 26 0.31
18 13 0.15
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTCTATTTTTTTC
Found at i:5196254 original size:10 final size:10
Alignment explanation
Indices: 5196203--5196271 Score: 54
Period size: 10 Copynumber: 6.7 Consensus size: 10
5196193 CCCCTTTTTA
5196203 TTTTTC-TCT
1 TTTTTCTTCT
5196212 ATTTTT-TTCT
1 -TTTTTCTTCT
*
5196222 TTTTTCATCAT
1 TTTTTCTTC-T
5196233 TTTTTCTTTTCT
1 TTTTTC--TTCT
5196245 TTTTTCTTCT
1 TTTTTCTTCT
*
5196255 ATTTTCTAT-T
1 TTTTTCT-TCT
5196265 TTTTTCT
1 TTTTTCT
5196272 ATTTTCTATT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
9 5 0.10
10 27 0.55
11 8 0.16
12 7 0.14
13 2 0.04
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTTTCTTCT
Found at i:5196266 original size:50 final size:45
Alignment explanation
Indices: 5196204--5196318 Score: 124
Period size: 50 Copynumber: 2.4 Consensus size: 45
5196194 CCCTTTTTAT
* * *
5196204 TTTTCTCTATTTTTTTCTTTTTTCATCATTTTTTCTTTTCTTTTTTCTTC
1 TTTT-TCTATTTTTTTCTTTTTTC-T-ATTTTCTATTTTCTATTTTC--C
*
5196254 TATTTTCTATTTTTTTCTATTTTCTATTTTCTATTTTCTATTTTCC
1 T-TTTTCTATTTTTTTCTTTTTTCTATTTTCTATTTTCTATTTTCC
*
5196300 TTTTTC-CTTTTTTTCTTTT
1 TTTTTCTATTTTTTTCTTTT
5196319 ATTTTTTCTT
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
44 11 0.19
45 5 0.09
46 2 0.03
48 17 0.29
49 1 0.02
50 19 0.33
51 3 0.05
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.76
Consensus pattern (45 bp):
TTTTTCTATTTTTTTCTTTTTTCTATTTTCTATTTTCTATTTTCC
Found at i:5196272 original size:10 final size:10
Alignment explanation
Indices: 5196197--5196276 Score: 53
Period size: 10 Copynumber: 8.1 Consensus size: 10
5196187 TGAACCCCCC
5196197 TTTT-TATTT
1 TTTTCTATTT
*
5196206 TTCTCTATTT
1 TTTTCTATTT
5196216 TTTTCT-TTT
1 TTTTCTATTT
*
5196225 TTCATC-A-TT
1 TT-TTCTATTT
*
5196234 TTTTCTTTTCTT
1 TTTTC-TAT-TT
*
5196246 TTTTCT-TCTA
1 TTTTCTAT-TT
5196256 TTTTCTATTT
1 TTTTCTATTT
5196266 TTTTCTATTT
1 TTTTCTATTT
5196276 T
1 T
5196277 CTATTTTCTA
Statistics
Matches: 56, Mismatches: 7, Indels: 15
0.72 0.09 0.19
Matches are distributed among these distances:
8 2 0.04
9 12 0.21
10 33 0.59
11 2 0.04
12 7 0.12
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTCTATTT
Found at i:5196318 original size:21 final size:21
Alignment explanation
Indices: 5196263--5196340 Score: 59
Period size: 21 Copynumber: 3.6 Consensus size: 21
5196253 CTATTTTCTA
*
5196263 TTTTTTTCTATTTTCTATTTT-C
1 TTTTTTTCT-TTTCCT-TTTTCC
* *
5196285 TATTTTCTATTTTCCTTTTTCC
1 T-TTTTTTCTTTTCCTTTTTCC
** *
5196307 TTTTTTTCTTTTATTTTTTCT
1 TTTTTTTCTTTTCCTTTTTCC
*
5196328 TTTTTTTCATTTC
1 TTTTTTTCTTTTC
5196341 TTCTTCAAGC
Statistics
Matches: 44, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
21 30 0.68
22 8 0.18
23 6 0.14
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTTTTTCTTTTCCTTTTTCC
Found at i:5196332 original size:14 final size:14
Alignment explanation
Indices: 5196231--5196332 Score: 57
Period size: 13 Copynumber: 7.0 Consensus size: 14
5196221 TTTTTTCATC
5196231 ATTTTTTCTTTTCTT
1 ATTTTTTCTTTT-TT
5196246 -TTTTCTTCTATTTTCT
1 ATTTT-TTCT-TTTT-T
5196262 ATTTTTTTCTATTTTCT
1 A-TTTTTTCT-TTTT-T
* * *
5196279 ATTTTCTATTTTCT
1 ATTTTTTCTTTTTT
* *
5196293 A-TTTTCCTTTTTC
1 ATTTTTTCTTTTTT
* *
5196306 CTTTTTT-TCTTTT
1 ATTTTTTCTTTTTT
5196319 ATTTTTTCTTTTTT
1 ATTTTTTCTTTTTT
5196333 TTCATTTCTT
Statistics
Matches: 66, Mismatches: 14, Indels: 15
0.69 0.15 0.16
Matches are distributed among these distances:
13 17 0.26
14 15 0.23
15 8 0.12
16 10 0.15
17 12 0.18
18 4 0.06
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (14 bp):
ATTTTTTCTTTTTT
Found at i:5206095 original size:47 final size:47
Alignment explanation
Indices: 5205988--5206101 Score: 113
Period size: 47 Copynumber: 2.4 Consensus size: 47
5205978 CAATGCTTTG
* * *
5205988 TTATTCACAAAAAGAAATCCTAACCGCGTGATATCTAATTCGCATGC
1 TTATTCACAAAAAGAAATCCTAACCGCGTGATATCTAACTCACAAGC
* * * *
5206035 TTGTTCGAGAAAAATAAA-CCTAACCGCGTGATATCTAGCTCACAAGC
1 TTATTC-ACAAAAAGAAATCCTAACCGCGTGATATCTAACTCACAAGC
*
5206082 ATTTATTCAAAAAAATGAAA
1 --TTATTCACAAAAA-GAAA
5206102 ATAAATGACT
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
47 30 0.57
48 15 0.28
49 8 0.15
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.26
Consensus pattern (47 bp):
TTATTCACAAAAAGAAATCCTAACCGCGTGATATCTAACTCACAAGC
Found at i:5208123 original size:15 final size:15
Alignment explanation
Indices: 5208103--5208147 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
5208093 TAATATAATT
*
5208103 CCTAAACAAATTAAA
1 CCTAAATAAATTAAA
5208118 CCTAAATTAAATTAAA
1 CCTAAA-TAAATTAAA
*
5208134 CATAAATAAATTAA
1 CCTAAATAAATTAA
5208148 GCCTCACGCG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 14 0.52
16 13 0.48
ACGTcount: A:0.60, C:0.13, G:0.00, T:0.27
Consensus pattern (15 bp):
CCTAAATAAATTAAA
Found at i:5208131 original size:16 final size:15
Alignment explanation
Indices: 5208105--5208147 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
5208095 ATATAATTCC
* *
5208105 TAAACAAATTAAACC
1 TAAATAAATTAAACA
5208120 TAAATTAAATTAAACA
1 TAAA-TAAATTAAACA
5208136 TAAATAAATTAA
1 TAAATAAATTAA
5208148 GCCTCACGCG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.63, C:0.09, G:0.00, T:0.28
Consensus pattern (15 bp):
TAAATAAATTAAACA
Found at i:5210325 original size:15 final size:17
Alignment explanation
Indices: 5210292--5210338 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
5210282 TGAATGATGC
* *
5210292 AAAAGATGAAAATAAAAT
1 AAAA-ATGAAAAGAGAAT
5210310 -AAAAT-AAAAGAGAAT
1 AAAAATGAAAAGAGAAT
5210325 AAAAATGAAAAGAG
1 AAAAATGAAAAGAG
5210339 TTAGTGAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
15 8 0.32
16 7 0.28
17 10 0.40
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.13
Consensus pattern (17 bp):
AAAAATGAAAAGAGAAT
Found at i:5211517 original size:18 final size:17
Alignment explanation
Indices: 5211493--5211608 Score: 75
Period size: 17 Copynumber: 6.8 Consensus size: 17
5211483 CGAAAGCTAG
5211493 TAAAAA-AAGTAAAGATAA
1 TAAAAATAA-TAAA-ATAA
5211511 TAGAAAATAATAAAATAA
1 TA-AAAATAATAAAATAA
**
5211529 TAAAAAGGTTGGTAAAA-AA
1 TAAAAA---TAATAAAATAA
* *
5211548 TAAACA-AA-CAAATAA
1 TAAAAATAATAAAATAA
5211563 TAAAAATAATAAAATAA
1 TAAAAATAATAAAATAA
5211580 TAAAAA-AAGTAATAA-AA
1 TAAAAATAA-TAA-AATAA
5211597 T-AAAATAATAAA
1 TAAAAATAATAAA
5211609 CTAAATAAAC
Statistics
Matches: 79, Mismatches: 8, Indels: 25
0.71 0.07 0.22
Matches are distributed among these distances:
14 3 0.04
15 8 0.10
16 11 0.14
17 24 0.30
18 10 0.13
19 15 0.19
20 8 0.10
ACGTcount: A:0.72, C:0.02, G:0.07, T:0.20
Consensus pattern (17 bp):
TAAAAATAATAAAATAA
Found at i:5211578 original size:8 final size:8
Alignment explanation
Indices: 5211557--5211608 Score: 61
Period size: 8 Copynumber: 6.2 Consensus size: 8
5211547 ATAAACAAAC
5211557 AAATAATAA
1 AAATAAT-A
5211566 AAATAATA
1 AAATAATA
5211574 AAATAATA
1 AAATAATA
*
5211582 AAAAAAGTA
1 AAATAA-TA
5211591 ATAA-AATA
1 A-AATAATA
5211599 AAATAATA
1 AAATAATA
5211607 AA
1 AA
5211609 CTAAATAAAC
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
7 2 0.05
8 23 0.59
9 12 0.31
10 2 0.05
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (8 bp):
AAATAATA
Found at i:5211581 original size:20 final size:21
Alignment explanation
Indices: 5211558--5211604 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
5211548 TAAACAAACA
5211558 AATAATAAAAA-TAATAAAAT
1 AATAATAAAAAGTAATAAAAT
5211578 AATAA-AAAAAGTAATAAAAT
1 AATAATAAAAAGTAATAAAAT
5211598 AA-AATAA
1 AATAATAA
5211605 TAAACTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (21 bp):
AATAATAAAAAGTAATAAAAT
Found at i:5212769 original size:25 final size:23
Alignment explanation
Indices: 5212734--5212788 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 23
5212724 ATATAATGAA
*
5212734 AATAAATAAATAGTATAAATAAAAT
1 AATAAAAAAATA-TATAAA-AAAAT
*
5212759 AATAAAAAAATATATATAAAAAT
1 AATAAAAAAATATATAAAAAAAT
5212782 -ATAAAAA
1 AATAAAAA
5212789 TGTATGTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 7 0.25
23 5 0.18
24 5 0.18
25 11 0.39
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (23 bp):
AATAAAAAAATATATAAAAAAAT
Found at i:5212769 original size:44 final size:44
Alignment explanation
Indices: 5212720--5212809 Score: 112
Period size: 44 Copynumber: 2.0 Consensus size: 44
5212710 GCAAAAAACT
*
5212720 AAAAATATA-ATGAAAATA-AATAAATAGTATAAATAAAATAATAA
1 AAAAATATATATAAAAATATAA-AAAT-GTATAAATAAAATAATAA
** *
5212764 AAAAATATATATAAAAATATAAAAATGTATGTATAATATAATAA
1 AAAAATATATATAAAAATATAAAAATGTATAAATAAAATAATAA
5212808 AA
1 AA
5212810 TACTAAATAG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
44 26 0.65
45 12 0.30
46 2 0.05
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (44 bp):
AAAAATATATATAAAAATATAAAAATGTATAAATAAAATAATAA
Found at i:5212772 original size:22 final size:22
Alignment explanation
Indices: 5212720--5212861 Score: 64
Period size: 22 Copynumber: 6.4 Consensus size: 22
5212710 GCAAAAAACT
5212720 AAAAATAT-AATGAAAATAA-ATA
1 AAAAATATAAAT-AAAATAATA-A
* *
5212742 AATAGTATAAATAAAATAATAA
1 AAAAATATAAATAAAATAATAA
* *
5212764 AAAAATATATAT-AAA-AATAT
1 AAAAATATAAATAAAATAATAA
* ** *
5212784 AAAAATGTATGTATAAT-ATAA
1 AAAAATATAAATAAAATAATAA
* *
5212805 TAAAATACTAAATAGTAATAATAA
1 AAAAATA-TAAATA-AAATAATAA
5212829 TAATAAATA-AAA-AAAATAAATATA
1 -AA-AAATATAAATAAAAT-AATA-A
*
5212853 ATAAATATA
1 AAAAATATA
5212862 GTAATCATAG
Statistics
Matches: 91, Mismatches: 17, Indels: 23
0.69 0.13 0.18
Matches are distributed among these distances:
20 14 0.15
21 13 0.14
22 35 0.38
23 15 0.16
24 8 0.09
25 1 0.01
26 5 0.05
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.28
Consensus pattern (22 bp):
AAAAATATAAATAAAATAATAA
Found at i:5212858 original size:13 final size:13
Alignment explanation
Indices: 5212734--5212859 Score: 77
Period size: 13 Copynumber: 9.6 Consensus size: 13
5212724 ATATAATGAA
5212734 AATAAATAAATAGT
1 AATAAATAAATA-T
5212748 -ATAAATAAA-AT
1 AATAAATAAATAT
*
5212759 AATAAAAAAATAT
1 AATAAATAAATAT
5212772 -ATATAA-AAATAT
1 AATA-AATAAATAT
**
5212784 AA-AAATGTATGTAT
1 AATAAA--TAAATAT
5212798 AATATAATAAA-AT
1 AATA-AATAAATAT
*
5212811 ACTAAATAGTAATAAT
1 AATAAATA--AAT-AT
*
5212827 AAT-AATAAATAA
1 AATAAATAAATAT
*
5212839 AAAAAATAAATAT
1 AATAAATAAATAT
5212852 AATAAATA
1 AATAAATA
5212860 TAGTAATCAT
Statistics
Matches: 87, Mismatches: 11, Indels: 29
0.69 0.09 0.23
Matches are distributed among these distances:
11 3 0.03
12 26 0.30
13 37 0.43
14 10 0.11
15 5 0.06
16 6 0.07
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (13 bp):
AATAAATAAATAT
Found at i:5212864 original size:43 final size:46
Alignment explanation
Indices: 5212816--5212907 Score: 111
Period size: 43 Copynumber: 2.1 Consensus size: 46
5212806 AAAATACTAA
5212816 ATAGTAATAATA-ATAATAAATAAAA-AAAATAA-ATATA-ATAAAT
1 ATAGTAATAATAGA-AATAAATAAAATAAAATAATATATATATAAAT
* * * *
5212859 ATAGTAATCATAGAAATATATAAAATATAATAATATATATATATAT
1 ATAGTAATAATAGAAATAAATAAAATAAAATAATATATATATAAAT
5212905 ATA
1 ATA
5212908 TATATATATA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
43 21 0.51
44 7 0.17
45 5 0.12
46 8 0.20
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (46 bp):
ATAGTAATAATAGAAATAAATAAAATAAAATAATATATATATAAAT
Found at i:5212896 original size:2 final size:2
Alignment explanation
Indices: 5212874--5213079 Score: 164
Period size: 2 Copynumber: 106.5 Consensus size: 2
5212864 AATCATAGAA
*
5212874 AT AT AT A- AA AT AT A- AT A- AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
5212913 AT AT AT AT AT AT AT AT AT AT AT AT A- AC GT -T AGG A- AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
* * * * * * * * * *
5212953 AGT AA AA AA AC AT AGT AA AT A- AGT AA AC AT AG AT A- AA AA AT
1 A-T AT AT AT AT AT A-T AT AT AT A-T AT AT AT AT AT AT AT AT AT
5212994 A- AT A- AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5213033 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5213075 AT AT A
1 AT AT A
5213080 ATAGGAAAAT
Statistics
Matches: 173, Mismatches: 16, Indels: 30
0.79 0.07 0.14
Matches are distributed among these distances:
1 11 0.06
2 156 0.90
3 6 0.03
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.40
Consensus pattern (2 bp):
AT
Found at i:5212896 original size:10 final size:10
Alignment explanation
Indices: 5212770--5213082 Score: 70
Period size: 12 Copynumber: 30.0 Consensus size: 10
5212760 ATAAAAAAAT
5212770 ATATATAA-A
1 ATATATAATA
*
5212779 A-ATATAAAA
1 ATATATAATA
* *
5212788 ATGTATGTATA
1 ATATAT-AATA
5212799 ATATAATAA-A
1 ATAT-ATAATA
5212809 ATACTA-AATA
1 ATA-TATAATA
*
5212819 GTA-ATAATA
1 ATATATAATA
5212828 ATA-ATAAATA
1 ATATAT-AATA
* *
5212838 A-AAAAAATA
1 ATATATAATA
5212847 A-ATATAATA
1 ATATATAATA
*
5212856 A-ATATAGTA
1 ATATATAATA
*
5212865 ATCATA-GA-A
1 AT-ATATAATA
5212874 ATATAT-A-A
1 ATATATAATA
5212882 A-ATATAATA
1 ATATATAATA
5212891 ATATATATATA
1 ATATATA-ATA
5212902 TATATATATATA
1 -ATATATA-ATA
5212914 TATATATATATA
1 -ATATATA-ATA
5212926 TATATATATATA
1 -ATATATA-ATA
*
5212938 ACGT-TAGGAA-A
1 A--TATA-TAATA
*
5212949 ATATAGTAAAA
1 ATATA-TAATA
* * *
5212960 AAACATAGTA
1 ATATATAATA
5212970 A-ATAAGTAA-A
1 ATAT-A-TAATA
*
5212980 CATAGATAA-A
1 -ATATATAATA
*
5212990 AAATAATAATA
1 ATAT-ATAATA
5213001 ATATATATATA
1 ATATATA-ATA
5213012 TATATATATATA
1 -ATATATA-ATA
5213024 TATATATATATA
1 -ATATATA-ATA
5213036 TATATATATATA
1 -ATATATA-ATA
5213048 TATATATATATA
1 -ATATATA-ATA
5213060 TATATATATATA
1 -ATATATA-ATA
5213072 TATATATAATA
1 -ATATATAATA
5213083 GGAAAATAAT
Statistics
Matches: 249, Mismatches: 25, Indels: 58
0.75 0.08 0.17
Matches are distributed among these distances:
7 4 0.02
8 14 0.06
9 43 0.17
10 44 0.18
11 34 0.14
12 108 0.43
13 2 0.01
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (10 bp):
ATATATAATA
Found at i:5213624 original size:37 final size:37
Alignment explanation
Indices: 5213583--5213667 Score: 116
Period size: 37 Copynumber: 2.3 Consensus size: 37
5213573 GGATCTTATC
* *
5213583 TTTAGGAGTTTAAATAATAGTAGAACTCTATCCTATT
1 TTTAGGAGTTTAAATAATAGCAAAACTCTATCCTATT
* ** *
5213620 TTTAGGAGTTTGAATCCTAGCAAAATTCTATCCTATT
1 TTTAGGAGTTTAAATAATAGCAAAACTCTATCCTATT
5213657 TTTAGGAGTTT
1 TTTAGGAGTTT
5213668 GAATCCTAGT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (37 bp):
TTTAGGAGTTTAAATAATAGCAAAACTCTATCCTATT
Found at i:5214522 original size:106 final size:106
Alignment explanation
Indices: 5214332--5216030 Score: 2731
Period size: 106 Copynumber: 16.0 Consensus size: 106
5214322 GCATTGTTTC
* * **
5214332 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAATCAGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
** * *
5214397 CCAATGGTCCCTTCATCGTGAAGATGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
5214438 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCT-TCGAAATTGGGAAATTGTTTGTTGAAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-GAAATTGGGAAGTTGTTTGTTGACA
*
5214502 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
5214544 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
5214609 CCAGCGGT-CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
5214649 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
** *
5214714 CCAATGGTCCCTTCGTCGTGAAGATGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
5214755 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCT-TCGAAATTGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-GAAATTGGGAAGTTGTTTGTTGACA
5214819 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** * * *
5214861 GAGTCCAATATATTTCACTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
5214926 CCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
5214967 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
5215032 CCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
5215073 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
** *
5215138 CCAATGGTCCCTTCGTCGTGAAGATGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
5215179 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCT-TCGAAATTGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-GAAATTGGGAAGTTGTTTGTTGACA
5215243 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** * * *
5215285 GAGTCCAATATATTTCCCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
5215350 CCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
5215391 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
5215456 CCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
5215497 GAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
5215562 CCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
5215603 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
5215668 CCAGCGGTCCTTTCGTCATGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
5215709 AAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
5215774 CCAGCGGTCCCTTCTTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* ** * *
5215815 AAGTCCAATATCCTTCATTGTGAAGTTGAAATTAGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
5215880 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
5215921 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATTTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
5215986 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
5216027 GAGT
1 GAGT
5216031 GGCACGATAT
Statistics
Matches: 1480, Mismatches: 106, Indels: 14
0.93 0.07 0.01
Matches are distributed among these distances:
105 103 0.07
106 1376 0.93
107 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:5221985 original size:20 final size:19
Alignment explanation
Indices: 5221934--5221990 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
5221924 AACCAATAAT
5221934 AATAAACATAAAAT-AATTG
1 AATAAA-ATAAAATAAATTG
* *
5221953 GATGAAAAAAAAATGAAATTG
1 AAT-AAAATAAAAT-AAATTG
5221974 AATAAAATAAAATAAAT
1 AATAAAATAAAATAAAT
5221991 GAAGATAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
19 12 0.39
20 12 0.39
21 7 0.23
ACGTcount: A:0.67, C:0.02, G:0.09, T:0.23
Consensus pattern (19 bp):
AATAAAATAAAATAAATTG
Found at i:5222137 original size:23 final size:23
Alignment explanation
Indices: 5222093--5222168 Score: 75
Period size: 21 Copynumber: 3.3 Consensus size: 23
5222083 ATATAATGAA
*
5222093 AATAAATAAATAGTATAAATAAAAT
1 AATAAA-AAATA-TATATATAAAAT
5222118 AATAAAAAATATATATAT-AAA-
1 AATAAAAAATATATATATAAAAT
* * * *
5222139 AATATAAAATGTATGTATAATAT
1 AATAAAAAATATATATATAAAAT
5222162 AATAAAA
1 AATAAAA
5222169 TACTAAATAG
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
21 15 0.35
22 5 0.12
23 12 0.28
24 5 0.12
25 6 0.14
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (23 bp):
AATAAAAAATATATATATAAAAT
Found at i:5222318 original size:14 final size:14
Alignment explanation
Indices: 5222296--5222343 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 14
5222286 TAACGTTAGG
*
5222296 AAAATATAGTAAAA
1 AAAACATAGTAAAA
5222310 AAAACATAGTAAATA
1 AAAACATAGTAAA-A
5222325 AGTAAACATAGATAAAA
1 A--AAACATAG-TAAAA
5222342 AA
1 AA
5222344 TAATAATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
14 12 0.41
15 3 0.10
17 10 0.34
18 4 0.14
ACGTcount: A:0.69, C:0.04, G:0.08, T:0.19
Consensus pattern (14 bp):
AAAACATAGTAAAA
Found at i:5222436 original size:22 final size:21
Alignment explanation
Indices: 5222411--5222467 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
5222401 AAAAAAAAAT
5222411 TATAATAAATAAATAAATTATA
1 TATAATAAATAAATAAA-TATA
* *
5222433 TATAATTAAATATATACATATA
1 TATAA-TAAATAAATAAATATA
5222455 TATATATAAATAA
1 TATA-ATAAATAA
5222468 TAAGGGTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 19 0.63
23 11 0.37
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
TATAATAAATAAATAAATATA
Found at i:5222955 original size:37 final size:37
Alignment explanation
Indices: 5222862--5222963 Score: 123
Period size: 37 Copynumber: 2.8 Consensus size: 37
5222852 ATGCTTGTGG
* * ** * *
5222862 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCC
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCC
* * *
5222899 ATCATATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCC
5222936 ATCCTATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
5222964 TAGGACGAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCC
Found at i:5223550 original size:14 final size:14
Alignment explanation
Indices: 5223533--5223591 Score: 50
Period size: 13 Copynumber: 4.3 Consensus size: 14
5223523 ATAAATAAAG
5223533 AAAAATATTTTTTT
1 AAAAATATTTTTTT
* *
5223547 AAAACTA-TATTTT
1 AAAAATATTTTTTT
*
5223560 ATAAATGATTTTTTT
1 AAAAAT-ATTTTTTT
* *
5223575 -AAAATGTTTTTTC
1 AAAAATATTTTTTT
5223588 AAAA
1 AAAA
5223592 CCATATACTA
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
13 15 0.44
14 14 0.41
15 5 0.15
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.51
Consensus pattern (14 bp):
AAAAATATTTTTTT
Found at i:5223604 original size:41 final size:41
Alignment explanation
Indices: 5223534--5223612 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 41
5223524 TAAATAAAGA
* * **
5223534 AAAATATTTTTTTAAAACTATATTTTATAA-ATGATTTTTTT
1 AAAATATTTTTTCAAAACCATATACTATAATAT-ATTTTTTT
*
5223575 AAAATGTTTTTTCAAAACCATATACTATAATATATTTT
1 AAAATATTTTTTCAAAACCATATACTATAATATATTTT
5223613 CCAAAAAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
41 30 0.94
42 2 0.06
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.51
Consensus pattern (41 bp):
AAAATATTTTTTCAAAACCATATACTATAATATATTTTTTT
Found at i:5223677 original size:37 final size:36
Alignment explanation
Indices: 5223594--5223880 Score: 236
Period size: 37 Copynumber: 7.9 Consensus size: 36
5223584 TTTCAAAACC
* *
5223594 ATATACTATAATATATTTTCCAAAAAATATTTT-AAAATT
1 ATATATTAT-ATATATTTT-C--AAAATGTTTTAAAAATT
5223633 ATATATTATATATATTTTCCAAAATGTTTTAAAAATT
1 ATATATTATATATATTTT-CAAAATGTTTTAAAAATT
* * * *
5223670 ATATATTATACAAATTTTCAAAAATATTTTTAAAAAACT
1 ATATATTATATATATTTTC-AAAAT-GTTTT-AAAAATT
* *
5223709 ATACAATATATATATTTTCAAAAATGTTTTAAAAA--
1 ATATATTATATATATTTTC-AAAATGTTTTAAAAATT
*
5223744 ACTATATAATATATATTTTCAAAATGTTTT-----TT
1 A-TATATTATATATATTTTCAAAATGTTTTAAAAATT
* * * * * *
5223776 TTAAACTATATA-A-TAT-ATAAATGTTTTCAAAACT
1 ATATATTATATATATTTTCA-AAATGTTTTAAAAATT
* *
5223810 ATATAATATATAAATTTTCAAAATGATTTTAAAAATT
1 ATATATTATATATATTTTCAAAATG-TTTTAAAAATT
5223847 ATATATTATATATATTTTCAAAATGTTTTAAAAA
1 ATATATTATATATATTTTCAAAATGTTTTAAAAA
5223881 CGTATTTTCA
Statistics
Matches: 203, Mismatches: 28, Indels: 37
0.76 0.10 0.14
Matches are distributed among these distances:
28 1 0.00
29 11 0.05
30 1 0.00
31 8 0.04
34 10 0.05
35 12 0.06
36 41 0.20
37 65 0.32
38 19 0.09
39 35 0.17
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (36 bp):
ATATATTATATATATTTTCAAAATGTTTTAAAAATT
Found at i:5223782 original size:36 final size:36
Alignment explanation
Indices: 5223600--5223880 Score: 173
Period size: 36 Copynumber: 7.9 Consensus size: 36
5223590 AACCATATAC
* * *
5223600 TATAATATAT-TTTCCAAAAAATATTTTAAAATTA-TA
1 TATAATATATATTTTC-AAAAATGTTTTAAAA-AACTA
* *
5223636 TATTATATATATTTTCCAAAATGTTTTAAAAATTA-TA
1 TATAATATATATTTTCAAAAATGTTTTAAAAA--ACTA
* * * *
5223673 TATTATACAAATTTTCAAAAATATTTTTAAAAAACTA
1 TATAATATATATTTTCAAAAAT-GTTTTAAAAAACTA
*
5223710 TACAATATATATATTTTCAAAAATGTTTTAAAAAACTA
1 TA-TA-ATATATATTTTCAAAAATGTTTTAAAAAACTA
***
5223748 TATAATATATATTTTC-AAAATGTTTTTTTTAAACTA
1 TATAATATATATTTTCAAAAATG-TTTTAAAAAACTA
*
5223784 TAT-A-ATATA---T---AAATGTTTTCAAAACTA-TA
1 TATAATATATATTTTCAAAAATGTTTT-AAAA-AACTA
*
5223813 TA-ATATATAAATTTTC-AAAATGATTTTAAAAATTA-TA
1 TATA-ATATATATTTTCAAAAATG-TTTTAAAAA--ACTA
*
5223850 TATTATATATATTTTC-AAAATGTTTTAAAAA
1 TATAATATATATTTTCAAAAATGTTTTAAAAA
5223881 CGTATTTTCA
Statistics
Matches: 197, Mismatches: 26, Indels: 44
0.74 0.10 0.16
Matches are distributed among these distances:
28 4 0.02
29 10 0.05
30 2 0.01
31 5 0.03
34 6 0.03
35 7 0.04
36 66 0.34
37 57 0.29
38 24 0.12
39 16 0.08
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (36 bp):
TATAATATATATTTTCAAAAATGTTTTAAAAAACTA
Found at i:5223802 original size:27 final size:27
Alignment explanation
Indices: 5223778--5223832 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
5223768 TGTTTTTTTT
5223778 AAACTATATAATATATAAATGTTTTCA
1 AAACTATATAATATATAAATGTTTTCA
5223805 AAACTATATAATATATAAA--TTTTCA
1 AAACTATATAATATATAAATGTTTTCA
5223830 AAA
1 AAA
5223833 TGATTTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 9 0.32
27 19 0.68
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.38
Consensus pattern (27 bp):
AAACTATATAATATATAAATGTTTTCA
Found at i:5223857 original size:64 final size:64
Alignment explanation
Indices: 5223730--5223858 Score: 172
Period size: 64 Copynumber: 2.0 Consensus size: 64
5223720 ATATTTTCAA
* **
5223730 AAATGTTTTAAAAAACTATATAATATATATTTTCAAAATGTTTTTTTTAAACTATATAATATAT
1 AAATGTTTTAAAAAACTATATAATATATATTTTCAAAATGTATTTTAAAAACTATATAATATAT
* * *
5223794 AAATGTTTT-CAAAACTATATAATATATAAATTTTCAAAATG-ATTTTAAAAATTATATATTATA
1 AAATGTTTTAAAAAACTATATAATATAT--ATTTTCAAAATGTATTTTAAAAACTATATAATATA
5223857 T
64 T
5223858 A
1 A
5223859 TATTTTCAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
63 17 0.30
64 28 0.49
65 12 0.21
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (64 bp):
AAATGTTTTAAAAAACTATATAATATATATTTTCAAAATGTATTTTAAAAACTATATAATATAT
Found at i:5223889 original size:24 final size:24
Alignment explanation
Indices: 5223859--5223917 Score: 118
Period size: 24 Copynumber: 2.5 Consensus size: 24
5223849 ATATTATATA
5223859 TATTTTCAAAATGTTTTAAAAACG
1 TATTTTCAAAATGTTTTAAAAACG
5223883 TATTTTCAAAATGTTTTAAAAACG
1 TATTTTCAAAATGTTTTAAAAACG
5223907 TATTTTCAAAA
1 TATTTTCAAAA
5223918 ACCATTTACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.42
Consensus pattern (24 bp):
TATTTTCAAAATGTTTTAAAAACG
Found at i:5223944 original size:2 final size:2
Alignment explanation
Indices: 5223931--5223990 Score: 111
Period size: 2 Copynumber: 30.0 Consensus size: 2
5223921 ATTTACAAAC
*
5223931 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5223973 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
5223991 CGAACGAAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5226201 original size:145 final size:143
Alignment explanation
Indices: 5225938--5226226 Score: 542
Period size: 145 Copynumber: 2.0 Consensus size: 143
5225928 ATCAATGTGT
*
5225938 TTTACTGTCTGCAATTCATATTTAGAAAAGGGTATTGTATAAAATTCTTTCAACTTTTGGTTCCC
1 TTTACTGTCTGCAATTCATATTTAGAAAAGGGTATTGTATAAAATTCTTTCAACTTTTGGTTACC
*
5226003 CGTGGATTGGGATTTGATATCTCTACTTATGGTAGAAATTGTCAAAATAGAACATGTCTGTGTGT
66 CGTGGATTGGGATTTGATATCTCTACTTATGGTAGAAATTGTCAAAATAGAACA--TCTGTGTAT
5226068 AACTTTAATGGAGTA
129 AACTTTAATGGAGTA
5226083 TTTACTGTCTGCAATTCATATTTAGAAAAGGGTATTGTATAAAATTCTTTCAACTTTTGGTTACC
1 TTTACTGTCTGCAATTCATATTTAGAAAAGGGTATTGTATAAAATTCTTTCAACTTTTGGTTACC
5226148 CGTGGATTGGGATTTGATATCTCTACTTATGGTAGAAATTGTCAAAATAGAACATCTGTGTATAA
66 CGTGGATTGGGATTTGATATCTCTACTTATGGTAGAAATTGTCAAAATAGAACATCTGTGTATAA
5226213 CTTTAATGGAGTA
131 CTTTAATGGAGTA
5226226 T
1 T
5226227 ATCATCCTAG
Statistics
Matches: 142, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
143 24 0.17
145 118 0.83
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (143 bp):
TTTACTGTCTGCAATTCATATTTAGAAAAGGGTATTGTATAAAATTCTTTCAACTTTTGGTTACC
CGTGGATTGGGATTTGATATCTCTACTTATGGTAGAAATTGTCAAAATAGAACATCTGTGTATAA
CTTTAATGGAGTA
Found at i:5228071 original size:30 final size:30
Alignment explanation
Indices: 5228010--5228259 Score: 102
Period size: 30 Copynumber: 8.4 Consensus size: 30
5228000 ATATTTAAAA
*
5228010 GGACCAAAATAGCAAAAA-AGGAAACCTAAG
1 GGACTAAAATAGCAAAAATA-GAAACCTAAG
* *
5228040 GGACTGAAATAGCAAAAATAGAAA-TTGAAG
1 GGACTAAAATAGCAAAAATAGAAACCT-AAG
* * *
5228070 GGACTAAAATCA-CAAAAATAGAATCTTAAA
1 GGACTAAAAT-AGCAAAAATAGAAACCTAAG
* * * ** *
5228100 GGACTAAAAAAG-AAAAAGAAAAATTTAAA
1 GGACTAAAATAGCAAAAATAGAAACCTAAG
* * * *
5228129 GGAATAAAAT-GAAAAAATCGAAAACTTAAAG
1 GGACTAAAATAGCAAAAATAG-AAACCT-AAG
* * ** * **
5228160 GG-CTATAACAATAAAAATTGAAAGTTAAG
1 GGACTAAAATAGCAAAAATAGAAACCTAAG
* ** ** *
5228189 GGTCT-AAATAATAAAAATAGAAAATTAAA
1 GGACTAAAATAGCAAAAATAGAAACCTAAG
* * *
5228218 GGAATAAAATAGAAAAAATAGAAACTTAAAG
1 GGACTAAAATAGCAAAAATAGAAACCT-AAG
5228249 GG-CTAAAATAG
1 GGACTAAAATAG
5228260 TAATTACAAA
Statistics
Matches: 171, Mismatches: 37, Indels: 24
0.74 0.16 0.10
Matches are distributed among these distances:
28 1 0.01
29 55 0.32
30 96 0.56
31 19 0.11
ACGTcount: A:0.59, C:0.08, G:0.16, T:0.17
Consensus pattern (30 bp):
GGACTAAAATAGCAAAAATAGAAACCTAAG
Found at i:5228225 original size:29 final size:28
Alignment explanation
Indices: 5228053--5228255 Score: 124
Period size: 30 Copynumber: 6.9 Consensus size: 28
5228043 CTGAAATAGC
* *
5228053 AAAAATAG-AAATTGAAGGGACTAAAATCAC
1 AAAAATAGAAAATT-AAAGGACT-AAAT-AA
**
5228083 AAAAATAGAATCTTAAAGGACTAAA-AA
1 AAAAATAGAAAATTAAAGGACTAAATAA
* *
5228110 AGAAAA-AGAAAAATTTAAAGGAATAAAATGA
1 A-AAAATAG-AAAA-TTAAAGGACT-AAATAA
* * *
5228141 AAAAATCGAAAACTTAAAGGGCTATAACAA
1 AAAAATAGAAAA-TTAAAGGACTA-AATAA
* * * *
5228171 TAAAAATTGAAAGTTAAGGGTCTAAATAA
1 -AAAAATAGAAAATTAAAGGACTAAATAA
*
5228200 TAAAAATAGAAAATTAAAGGAATAAAATAGA
1 -AAAAATAGAAAATTAAAGGACT-AAATA-A
* *
5228231 AAAAATAGAAACTTAAAGGGCTAAA
1 AAAAATAGAAAATTAAAGGACTAAA
5228256 ATAGTAATTA
Statistics
Matches: 135, Mismatches: 27, Indels: 23
0.73 0.15 0.12
Matches are distributed among these distances:
27 4 0.03
28 6 0.04
29 38 0.28
30 70 0.52
31 17 0.13
ACGTcount: A:0.61, C:0.06, G:0.15, T:0.19
Consensus pattern (28 bp):
AAAAATAGAAAATTAAAGGACTAAATAA
Found at i:5228867 original size:10 final size:10
Alignment explanation
Indices: 5228852--5228876 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5228842 CTACGCCGTG
5228852 AAGAGATTCT
1 AAGAGATTCT
5228862 AAGAGATTCT
1 AAGAGATTCT
5228872 AAGAG
1 AAGAG
5228877 CCTCAGCCGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.08, G:0.24, T:0.24
Consensus pattern (10 bp):
AAGAGATTCT
Found at i:5229347 original size:32 final size:32
Alignment explanation
Indices: 5229306--5229366 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
5229296 TAGTTGCTGG
5229306 AATCATTAGATCTAGAAATAGGATATGAATTA
1 AATCATTAGATCTAGAAATAGGATATGAATTA
*
5229338 AATCATTAGATCTAGAAATATGATATGAA
1 AATCATTAGATCTAGAAATAGGATATGAA
5229367 ATATTATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.48, C:0.07, G:0.15, T:0.31
Consensus pattern (32 bp):
AATCATTAGATCTAGAAATAGGATATGAATTA
Found at i:5229718 original size:24 final size:22
Alignment explanation
Indices: 5229686--5229729 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
5229676 AAAATTTGTA
5229686 AACAATATAATTAATAATAATAAT
1 AACAATATAA-TAA-AATAATAAT
*
5229710 AACATTATAATAAAATAATA
1 AACAATATAATAAAATAATA
5229730 TTTTTTTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 3 0.16
24 9 0.47
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (22 bp):
AACAATATAATAAAATAATAAT
Found at i:5230243 original size:130 final size:131
Alignment explanation
Indices: 5230037--5230273 Score: 307
Period size: 130 Copynumber: 1.8 Consensus size: 131
5230027 ATTCCTATGC
* * * *
5230037 GATGAGGACGACTGGTTATCTAGGGGTGACACAGCTCTTACGTGATGAGGAGGTCTGGTCGATGG
1 GATGAGGACGACTGGTTATCTAGGGGTGACACAGCTCCTACGTAATAAGGAGGTCTGGTCGAGGG
* * * *
5230102 ATGACACGGTTCCTACGTGATGAGGTCGGCATACCATCTTTAGGAATGATAACTCGGTTCCTACA
66 ATGACACGGTTCCTACGCGATGAGGACGACAAACCATCTTTAGGAATGATAACTCGGTTCCTACA
5230167 T
131 T
* * * * *
5230168 GATGAGGATGACTGGTTATC-AGGGGTGACA-TGACTCCTATGTAATAAGGAGGTCTGGTTGGGG
1 GATGAGGACGACTGGTTATCTAGGGGTGACACAG-CTCCTACGTAATAAGGAGGTCTGGTCGAGG
* * *
5230231 GATGACATGGTTCTTATGCGATGAGGACGACAAACCATCTTTA
65 GATGACACGGTTCCTACGCGATGAGGACGACAAACCATCTTTA
5230274 AGGAGAATGA
Statistics
Matches: 89, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
129 1 0.01
130 69 0.78
131 19 0.21
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (131 bp):
GATGAGGACGACTGGTTATCTAGGGGTGACACAGCTCCTACGTAATAAGGAGGTCTGGTCGAGGG
ATGACACGGTTCCTACGCGATGAGGACGACAAACCATCTTTAGGAATGATAACTCGGTTCCTACA
T
Found at i:5230403 original size:67 final size:64
Alignment explanation
Indices: 5230283--5230459 Score: 176
Period size: 64 Copynumber: 2.7 Consensus size: 64
5230273 AAGGAGAATG
* * * * *
5230283 ATTTCAAGGGAAACCGACTCAAATATGATTTTGTTTTAAGAGAAACTGTCTCAAGAAAGAAAAAA
1 ATTTAAAGGGAAA-TGACTCAAAGATGATTTTGTTTCAAGAGAAACTGACTC---AAAGAAAAAA
5230348 TTC
62 TTC
* * *
5230351 GTTTAAAGGGAAATGACTCAAAGATGGTTTTGTTTCAAGAGAAACAT-ACTCAAAGATAAAATTC
1 ATTTAAAGGGAAATGACTCAAAGATGATTTTGTTTCAAGAGAAAC-TGACTCAAAGAAAAAATTC
* * * *
5230415 ATTTCAAGGGAAATAACTTAAAGATGATTTGTTGTTTCATGAGAA
1 ATTTAAAGGGAAATGACTCAAAGATGA-TT-TTGTTTCAAGAGAA
5230460 GAGGTCTCAA
Statistics
Matches: 92, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
64 34 0.37
65 2 0.02
66 13 0.14
67 31 0.34
68 12 0.13
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.30
Consensus pattern (64 bp):
ATTTAAAGGGAAATGACTCAAAGATGATTTTGTTTCAAGAGAAACTGACTCAAAGAAAAAATTC
Found at i:5230795 original size:91 final size:88
Alignment explanation
Indices: 5230653--5230815 Score: 247
Period size: 91 Copynumber: 1.8 Consensus size: 88
5230643 GTCTCAGAGA
* * * *
5230653 AAAAATGTCTCAAGCGAGACGAATTTTTTTTGAGAGAAATTGTCTCAAGCGA-GATAAAATTTAT
1 AAAAATATCTCAAACGAGACGAATTTTTTTTAAGAGAAATTGTCTCAAGCGATG-CAAAATTTAT
5230717 TTTTAAGATTTTCAAAATTTGTGG
65 TTTTAAGATTTTCAAAATTTGTGG
5230741 AAAAATATCTCAAACGAGACAGAATTTGTTTTTAAGAGAAAGTTGTCTCAAGCGATGCAAAATTT
1 AAAAATATCTCAAACGAGAC-GAATTT-TTTTTAAGAGAAA-TTGTCTCAAGCGATGCAAAATTT
5230806 ATTTTTAAGA
63 ATTTTTAAGA
5230816 AGACTGTCTC
Statistics
Matches: 67, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
88 18 0.27
89 6 0.09
90 12 0.18
91 30 0.45
92 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (88 bp):
AAAAATATCTCAAACGAGACGAATTTTTTTTAAGAGAAATTGTCTCAAGCGATGCAAAATTTATT
TTTAAGATTTTCAAAATTTGTGG
Found at i:5232247 original size:2 final size:2
Alignment explanation
Indices: 5232240--5232408 Score: 320
Period size: 2 Copynumber: 84.5 Consensus size: 2
5232230 AGCTTTATTG
5232240 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
5232282 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
5232324 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5232366 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5232408 T
1 T
5232409 TTCTGGGTAT
Statistics
Matches: 163, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 163 1.00
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5236569 original size:30 final size:30
Alignment explanation
Indices: 5236350--5236583 Score: 124
Period size: 30 Copynumber: 7.9 Consensus size: 30
5236340 TAAAAGGACC
* * *
5236350 AAAATAGCAAAAAA-GGAAACTTAAGGGACT
1 AAAATAG-AAAAAATAGAAACTTAAAGGAAT
* * * *
5236380 GAAATAGAAAAAATAGATA-TTGAAGGGAT
1 AAAATAGAAAAAATAGAAACTTAAAGGAAT
* * *
5236409 GAAAATCA-CAAAAATAGAATCTTAAAGGACT
1 -AAAAT-AGAAAAAATAGAAACTTAAAGGAAT
* * ** *
5236440 AACACA-ACAAAACCA-AAATTTAAAGGAAT
1 AAAATAGA-AAAAATAGAAACTTAAAGGAAT
* **
5236469 AAAAT-GAAAAAA-CGAAAACTTAAAGGGTT
1 AAAATAGAAAAAATAG-AAACTTAAAGGAAT
* * * ** * **
5236498 ATAACAGTAAAAACCGAAAGTTAAAGGTCT
1 AAAATAGAAAAAATAGAAACTTAAAGGAAT
*
5236528 -AAATAGCAAAAATAGAAACTTAAAGGAAT
1 AAAATAGAAAAAATAGAAACTTAAAGGAAT
5236557 AAAATAGAAAAAATAGAAACTTAAAGG
1 AAAATAGAAAAAATAGAAACTTAAAGG
5236584 GCTAGAAAAG
Statistics
Matches: 149, Mismatches: 44, Indels: 22
0.69 0.20 0.10
Matches are distributed among these distances:
28 4 0.03
29 63 0.42
30 72 0.48
31 10 0.07
ACGTcount: A:0.58, C:0.09, G:0.16, T:0.17
Consensus pattern (30 bp):
AAAATAGAAAAAATAGAAACTTAAAGGAAT
Found at i:5238002 original size:3 final size:3
Alignment explanation
Indices: 5237994--5238030 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
5237984 AATATAGTTG
*
5237994 ATA ATA ATA ATA ATA ATA ATA A-C ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5238031 TATTTTTTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
2 3 0.10
3 27 0.90
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:5239986 original size:3 final size:3
Alignment explanation
Indices: 5239978--5240045 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
5239968 TATACATCAA
5239978 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5240026 AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
5240046 GAACAACTAA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5241138 original size:3 final size:3
Alignment explanation
Indices: 5241130--5241181 Score: 68
Period size: 3 Copynumber: 17.0 Consensus size: 3
5241120 ATTTATTTAT
* * *
5241130 TTA TTA TTA TTA TAA ATA TTA TTA TTA TTA TTA TTA TTA TTAA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA
5241176 TTA TTA
1 TTA TTA
5241182 CAAGCCCAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
3 40 0.95
4 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:5244791 original size:6 final size:6
Alignment explanation
Indices: 5244782--5244858 Score: 50
Period size: 6 Copynumber: 12.7 Consensus size: 6
5244772 ACATTCACAT
* * * *
5244782 ATTTAC ATTTGC ATTTAC ATTTTTC ATTTAC ATTTGC ATTT-- TTTTAC
1 ATTTAC ATTTAC ATTTAC A-TTTAC ATTTAC ATTTAC ATTTAC ATTTAC
* * *
5244829 GTTTAT ATTTAC ATTTTC ATAATTAC ATTT
1 ATTTAC ATTTAC ATTTAC AT--TTAC ATTT
5244859 TATTTCAAAC
Statistics
Matches: 54, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
4 3 0.06
6 41 0.76
7 5 0.09
8 5 0.09
ACGTcount: A:0.26, C:0.13, G:0.04, T:0.57
Consensus pattern (6 bp):
ATTTAC
Found at i:5244799 original size:12 final size:12
Alignment explanation
Indices: 5244782--5244822 Score: 64
Period size: 12 Copynumber: 3.3 Consensus size: 12
5244772 ACATTCACAT
5244782 ATTTACATTTGC
1 ATTTACATTTGC
*
5244794 ATTTACATTTTTC
1 ATTTACA-TTTGC
5244807 ATTTACATTTGC
1 ATTTACATTTGC
5244819 ATTT
1 ATTT
5244823 TTTTACGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 15 0.58
13 11 0.42
ACGTcount: A:0.24, C:0.15, G:0.05, T:0.56
Consensus pattern (12 bp):
ATTTACATTTGC
Found at i:5244815 original size:19 final size:19
Alignment explanation
Indices: 5244770--5244824 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
5244760 ATTTTTATTG
* *
5244770 TTACATTCACATATTTACAT
1 TTACATTTACAT-TTTTCAT
*
5244790 TTGCATTTACATTTTTCAT
1 TTACATTTACATTTTTCAT
*
5244809 TTACATTTGCATTTTT
1 TTACATTTACATTTTT
5244825 TTACGTTTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 20 0.67
20 10 0.33
ACGTcount: A:0.25, C:0.16, G:0.04, T:0.55
Consensus pattern (19 bp):
TTACATTTACATTTTTCAT
Found at i:5249989 original size:114 final size:114
Alignment explanation
Indices: 5249788--5250007 Score: 350
Period size: 114 Copynumber: 1.9 Consensus size: 114
5249778 CATGTTCTCG
* * *
5249788 TAGTAGAAATAAGGAGCCCCAATAGCATCTTCTCGAAGTGTTCTTTGAGTTATCTGATCTGATTT
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGATTC
* * *
5249853 GGTATGAACCCCAAAACTAATCATTAGATTTGAAAGATGAATTTGCTCA
66 GGTAGGAACCCCAAAACCAATCATTAGAATTGAAAGATGAATTTGCTCA
* *
5249902 TAGTAGAAATAAGGAGATCCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTC
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGATTC
* *
5249967 GGTAGGAACCCCAGAACCAATCATTGGAATTGAAAGATGAA
66 GGTAGGAACCCCAAAACCAATCATTAGAATTGAAAGATGAA
5250008 CTGCATGATC
Statistics
Matches: 96, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
114 96 1.00
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.30
Consensus pattern (114 bp):
TAGTAGAAATAAGGAGACCCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGATTC
GGTAGGAACCCCAAAACCAATCATTAGAATTGAAAGATGAATTTGCTCA
Found at i:5252216 original size:50 final size:54
Alignment explanation
Indices: 5252084--5252241 Score: 218
Period size: 54 Copynumber: 3.0 Consensus size: 54
5252074 TAATTGAGAA
*
5252084 ATCTGAGCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAATGCTTTACGAAC
1 ATCTGAGCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
* * *
5252138 ATCTGAGCAGAAGCCACAGAAAAGGATGAAGGTGTTGTCAAGTGTTTTAC-ATC
1 ATCTGAGCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
* *
5252191 -TC-GA-CAGAAACCACAGGAAAA-GATGAATGTATTGTCAAATGTTTTACGAAC
1 ATCTGAGCAGAAGCCACA-GAAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
5252242 CAGTGATTAT
Statistics
Matches: 93, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
50 33 0.35
51 9 0.10
52 2 0.02
53 2 0.02
54 47 0.51
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.23
Consensus pattern (54 bp):
ATCTGAGCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
Found at i:5253809 original size:113 final size:113
Alignment explanation
Indices: 5253006--5253796 Score: 1235
Period size: 113 Copynumber: 7.0 Consensus size: 113
5252996 TAGCAAAGAT
* *
5253006 TCAAATCCATCACTTGATGGATCAGCTTTTCTAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
5253071 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * *
5253119 TCAAATCCATCATTTGATGGATCAACCTTTCTAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
5253184 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* *
5253232 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAATAACTGATCTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
5253297 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
5253345 TCAAATCCATCATTTGATGGATTAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
5253410 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
5253458 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTAAAT-TG
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACT-CATCTG
* *
5253522 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCGC
65 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTT-GC
** * * * * ****
5253571 TTGAATTCATCATTCGATGGATCAGCATTGCCAGGGCGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
* * *
5253636 AGAAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * * * * *
5253684 TCGAATTCATCACTCGATGGATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
* * **
5253749 AGAAAGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
5253797 ATGACTCTAT
Statistics
Matches: 635, Mismatches: 39, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
112 7 0.01
113 622 0.98
114 6 0.01
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (113 bp):
TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:5254035 original size:3 final size:3
Alignment explanation
Indices: 5254027--5254088 Score: 88
Period size: 3 Copynumber: 20.0 Consensus size: 3
5254017 ATTTATTTAT
*
5254027 TTA TTA TTA TTAA ATA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
5254073 TTA TTA CATA TTA TTA
1 TTA TTA -TTA TTA TTA
5254089 CAAGCCCAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
3 49 0.92
4 4 0.08
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:5260624 original size:16 final size:16
Alignment explanation
Indices: 5260603--5260637 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
5260593 TTAGCTAATA
5260603 GGGGTGACGATTTAGT
1 GGGGTGACGATTTAGT
5260619 GGGGTGACGATTTAGT
1 GGGGTGACGATTTAGT
5260635 GGG
1 GGG
5260638 ATGGAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.17, C:0.06, G:0.49, T:0.29
Consensus pattern (16 bp):
GGGGTGACGATTTAGT
Found at i:5264999 original size:3 final size:3
Alignment explanation
Indices: 5264985--5265039 Score: 69
Period size: 3 Copynumber: 19.0 Consensus size: 3
5264975 TATCCCGATT
* * *
5264985 TTA TTA TT- TTA TTA TTA TAA TAA TTA TTA TTA TAA TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5265031 TTA TTA TTA
1 TTA TTA TTA
5265040 ATAAATAATT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
2 4 0.09
3 42 0.91
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:5265010 original size:20 final size:21
Alignment explanation
Indices: 5264987--5265049 Score: 78
Period size: 20 Copynumber: 3.1 Consensus size: 21
5264977 TCCCGATTTT
5264987 ATTATT-TTATTATTATAATA
1 ATTATTATTATTATTATAATA
* *
5265007 ATTATTATTATAATTAT-ATT
1 ATTATTATTATTATTATAATA
*
5265027 ATTATTATTATTAATA-AATA
1 ATTATTATTATTATTATAATA
5265047 ATT
1 ATT
5265050 TTTACAGGCC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 27 0.75
21 9 0.25
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTATTATTATTATTATAATA
Found at i:5265014 original size:23 final size:23
Alignment explanation
Indices: 5264985--5265039 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
5264975 TATCCCGATT
*
5264985 TTATTATT-TTATTATTATAATAA
1 TTATTATTATAATTA-TATAATAA
* *
5265008 TTATTATTATAATTATATTATTA
1 TTATTATTATAATTATATAATAA
5265031 TTATTATTA
1 TTATTATTA
5265040 ATAAATAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 23 0.82
24 5 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TTATTATTATAATTATATAATAA
Found at i:5266913 original size:135 final size:138
Alignment explanation
Indices: 5266764--5267013 Score: 318
Period size: 135 Copynumber: 1.8 Consensus size: 138
5266754 GTTTAAATAA
* *
5266764 TAATGTTTATTTA-TTTTTAATATCAAAGAAAATGA-CAGTCTTAAAGCAACTAGATGTCC-TAT
1 TAATATTTATTTATTTTTTAATAT-AAAGAAAA-GAGCAGTCTTAAAGCAACTAGAAG-CCATAT
*
5266826 TCTGATATTT-TAAAAATAAAT-AAATATCCTATA-A-AT-TATTAATCTATTTTAATTATTTTT
63 TCTGATATTTCT--AAATAAATAAAATATCCTATATATATATATTAATATATTTTAATTATTTTT
5266886 TAGATAAATGTTT
126 TAGATAAATGTTT
* * * * *
5266899 TAATATTTATTTATTTTTTAATATTAAGGAAAGAGCTGTCTTAAAGCACCTAGAAGCCATTTTCT
1 TAATATTTATTTATTTTTTAATATAAAGAAAAGAGCAGTCTTAAAGCAACTAGAAGCCATATTCT
*
5266964 GATATTTCTAAATAAATAAAATATCTTATATATATATATTAATATATTTT
66 GATATTTCTAAATAAATAAAATATCCTATATATATATATTAATATATTTT
5267014 CATAAAATTA
Statistics
Matches: 98, Mismatches: 9, Indels: 13
0.82 0.08 0.11
Matches are distributed among these distances:
134 12 0.12
135 59 0.60
136 12 0.12
137 2 0.02
138 13 0.13
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (138 bp):
TAATATTTATTTATTTTTTAATATAAAGAAAAGAGCAGTCTTAAAGCAACTAGAAGCCATATTCT
GATATTTCTAAATAAATAAAATATCCTATATATATATATTAATATATTTTAATTATTTTTTAGAT
AAATGTTT
Found at i:5267539 original size:28 final size:27
Alignment explanation
Indices: 5267507--5267560 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
5267497 TAATTATTTC
*
5267507 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCAAAATATTTATATATA-TTATTA
*
5267535 TTTTCATAATATTTATATATATTATT
1 TTTTCAAAATATTTATATATATTATT
5267561 TTATTAATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (27 bp):
TTTTCAAAATATTTATATATATTATTA
Found at i:5267556 original size:30 final size:30
Alignment explanation
Indices: 5267485--5267556 Score: 78
Period size: 28 Copynumber: 2.5 Consensus size: 30
5267475 AAAAATCCAT
* *
5267485 ATATTTA-ATTTATAATTATTTCTTTTCAA
1 ATATTTATATATATAATTATTTATTTTCAA
* *
5267514 A-ATTTTTATATATACTTA-TTATTTTCATA
1 ATATTTATATATATAATTATTTATTTTCA-A
5267543 ATATTTATATATAT
1 ATATTTATATATAT
5267557 TATTTTATTA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
28 12 0.34
29 12 0.34
30 11 0.31
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (30 bp):
ATATTTATATATATAATTATTTATTTTCAA
Found at i:5278213 original size:17 final size:18
Alignment explanation
Indices: 5278193--5278236 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
5278183 ATATTATGAT
*
5278193 TGAAGAAAAAATG-AAAA
1 TGAAGAAAAAAAGAAAAA
5278210 TGAA-AAAAAAAGAAAAA
1 TGAAGAAAAAAAGAAAAA
*
5278227 TGATGAAAAA
1 TGAAGAAAAA
5278237 TATATATGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 7 0.30
17 11 0.48
18 5 0.22
ACGTcount: A:0.73, C:0.00, G:0.16, T:0.11
Consensus pattern (18 bp):
TGAAGAAAAAAAGAAAAA
Found at i:5279874 original size:24 final size:23
Alignment explanation
Indices: 5279831--5279875 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
5279821 GTTCATAATG
*
5279831 AGAAGAACTCATCTGAAGAAGGA
1 AGAAGAACTCATATGAAGAAGGA
5279854 AGAAGAAACTCATAATG-AGAAG
1 AGAAG-AACTCAT-ATGAAGAAG
5279876 AATTTGTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.26
24 12 0.63
25 2 0.11
ACGTcount: A:0.51, C:0.11, G:0.24, T:0.13
Consensus pattern (23 bp):
AGAAGAACTCATATGAAGAAGGA
Found at i:5280027 original size:112 final size:113
Alignment explanation
Indices: 5279814--5280100 Score: 400
Period size: 112 Copynumber: 2.6 Consensus size: 113
5279804 CAATATTTGA
**
5279814 AGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAACTCATAATGAGAAGAAT
1 AGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
* * ** *
5279879 TTGTTCAACCTTTTGCTTTAATACATCACTTGATGGATCAACAATGCC
66 TTGTTCAACCATTCGCTCGAATACATCACTCGATGGATCAACAATGCC
* *
5279927 AGGTAGAGTTCATAATGAGAAGAACTCGTATGAAGAAGG-AGAAGAAGTTCATAATGAGAAGAAT
1 AGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
* ** *
5279991 TTGTTCAACCATTCGCTCGAATTCATCACTCGATGGATCAACTTTTCC
66 TTGTTCAACCATTCGCTCGAATACATCACTCGATGGATCAACAATGCC
* * *
5280039 AGAG-AAAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAAAAGAAGTTCATAATGAGAAGA
1 AG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
5280101 GCTTGTTTAA
Statistics
Matches: 154, Mismatches: 18, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
111 3 0.02
112 113 0.73
113 38 0.25
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (113 bp):
AGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
TTGTTCAACCATTCGCTCGAATACATCACTCGATGGATCAACAATGCC
Found at i:5280178 original size:121 final size:119
Alignment explanation
Indices: 5280027--5280350 Score: 463
Period size: 121 Copynumber: 2.7 Consensus size: 119
5280017 CACTCGATGG
* *
5280027 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAAAAGAAGTTCATA
1 ATCAACATTTCC--AGAAAGTTCATAATGAGAAGAACTCATCTGAAGA-GAAAAAGAAGTTCATA
* * ***
5280092 ATGAGAAGAGCTTGTTTAACCTTTTTTTGACTCTATCACAGAAGGAGATAGATCAAC
63 ATGAGAAGAACTTGTTCAACCTTTGCATGACTCTATCACAGAAGGAGATAGATCAAC
*
5280149 ATCAACATTTCCAGAAATGTTCATAATGAGAAGAACTCATCTGAAGAGAAAGAAAAAGTTCATAA
1 ATCAACATTTCCAGAAA-GTTCATAATGAGAAGAACTCATCTGAAGAGAAA-AAGAAGTTCATAA
* *
5280214 TGAGAAGAACTTGTTCAACCTTTGCATGACTCTATCGCAGAAGGAGATAGATCAGC
64 TGAGAAGAACTTGTTCAACCTTTGCATGACTCTATCACAGAAGGAGATAGATCAAC
* *
5280270 ATCAACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTG-A-CGAAGAAGAAGTTCATAA
1 ATCAACATTTCCAGAA--AGTTCATAATGAGAAGAACTCATCTGAAGAGAAAAAGAAGTTCATAA
5280333 TGAGAAGAACTTGTTCAA
64 TGAGAAGAACTTGTTCAA
5280351 ACATTTCGCT
Statistics
Matches: 185, Mismatches: 13, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
119 30 0.16
120 12 0.06
121 106 0.57
122 36 0.19
123 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.25
Consensus pattern (119 bp):
ATCAACATTTCCAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGAAAAAGAAGTTCATAATG
AGAAGAACTTGTTCAACCTTTGCATGACTCTATCACAGAAGGAGATAGATCAAC
Found at i:5280575 original size:3 final size:3
Alignment explanation
Indices: 5280561--5280615 Score: 69
Period size: 3 Copynumber: 19.0 Consensus size: 3
5280551 TATCCTGATT
* * *
5280561 TTA TTA TT- TTA TTA TTA TAA TAA TTA TTA TTA TAA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5280607 TTA TTA TTA
1 TTA TTA TTA
5280616 AATAATTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
2 4 0.09
3 42 0.91
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:5282558 original size:2 final size:2
Alignment explanation
Indices: 5282546--5282584 Score: 55
Period size: 2 Copynumber: 20.0 Consensus size: 2
5282536 AATAAATAAA
5282546 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT -T A- AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5282585 TTTCATAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 2 0.06
2 30 0.88
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5283009 original size:3 final size:3
Alignment explanation
Indices: 5283001--5283063 Score: 117
Period size: 3 Copynumber: 21.0 Consensus size: 3
5282991 TATGTATTCA
5283001 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
5283049 AAT AGT AAT AAT AAT
1 AAT AAT AAT AAT AAT
5283064 GGGAGGAATC
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5285603 original size:87 final size:87
Alignment explanation
Indices: 5285457--5285619 Score: 254
Period size: 87 Copynumber: 1.9 Consensus size: 87
5285447 TATGTTATAT
* * *
5285457 CATTTTACCGAAAATATTATCAAATACAATAATATATTAAGTAGCGTTTATATAATGTAATAGGT
1 CATTTAACCGAAAATATTATCAAATACAATAACATATTAAGTAGCGCTTATATAATGTAATAGGT
5285522 AACGCTTATATAATAAAATAGA
66 AACGCTTATATAATAAAATAGA
* * *
5285544 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
1 CATTTAACCGAAAATATTATCAAATACAATAACATATTAAGTAGCGCTTATATAATGTAATAGGT
* *
5285609 AGCGTTTATAT
66 AACGCTTATAT
5285620 TGACATATTT
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
87 68 1.00
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.34
Consensus pattern (87 bp):
CATTTAACCGAAAATATTATCAAATACAATAACATATTAAGTAGCGCTTATATAATGTAATAGGT
AACGCTTATATAATAAAATAGA
Found at i:5286068 original size:200 final size:198
Alignment explanation
Indices: 5285637--5286071 Score: 584
Period size: 200 Copynumber: 2.2 Consensus size: 198
5285627 TTTTCTAACT
* * * *
5285637 AAACCGGTATATTTATACTGGTAACATTGCAAATTTACATATTACATTATAATTATAGGTTTTGA
1 AAACCGGTATATTTATACCGGTTACATTGTAAATTTACATATTACATTATAATTATAGGTTTCGA
* * * *
5285702 TGTTTTTGGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTC
66 AGTTTTTGAGATCGATACAATTTTAAATGTATCGACACTTTATGAGTGCACCTCGTTGGACATTC
* * * * *
5285767 ATTCTGGAAAAAAGTATCGACACAAACTTAAAATGTGTCGATACATTATGTAGACATATTTTTTC
131 ATTCTAGAAAAAAGTATCGACACAAACTTAAAAAGTGTCAATACATTATGTAGACATATTCTCTC
5285832 ATA
196 ATA
* * * * * *
5285835 AAACCGGTATATTTCTACCGGCTATATTGTAAATTTACTTATTACATTGTAATTATCGGTTTCGA
1 AAACCGGTATATTTATACCGGTTACATTGTAAATTTACATATTACATTATAATTATAGGTTTCGA
* *
5285900 AGTTTTTGAGATCGATAC-TTTTAATAAATGTATCGACACTTTATGAGTGCACCTCGTTTGACAT
66 AGTTTTTGAGATCGATACAATTT--TAAATGTATCGACACTTTATGAGTGCACCTCGTTGGACAT
* * * * ** *
5285964 TCATTCTAGACAAAATGTATTGACACAAATTTAAAAAGTGTCAATATATTATGTTTACCTATTCT
129 TCATTCTAGA-AAAAAGTATCGACACAAACTTAAAAAGTGTCAATACATTATGTAGACATATTCT
5286029 CTCATA
193 CTCATA
5286035 AAACCGGTATATTTATACCGGTTACATTGTAAATTTA
1 AAACCGGTATATTTATACCGGTTACATTGTAAATTTA
5286072 TGTCAGGTGT
Statistics
Matches: 203, Mismatches: 31, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
197 3 0.01
198 71 0.35
199 46 0.23
200 83 0.41
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (198 bp):
AAACCGGTATATTTATACCGGTTACATTGTAAATTTACATATTACATTATAATTATAGGTTTCGA
AGTTTTTGAGATCGATACAATTTTAAATGTATCGACACTTTATGAGTGCACCTCGTTGGACATTC
ATTCTAGAAAAAAGTATCGACACAAACTTAAAAAGTGTCAATACATTATGTAGACATATTCTCTC
ATA
Found at i:5286453 original size:182 final size:182
Alignment explanation
Indices: 5286145--5286988 Score: 1099
Period size: 182 Copynumber: 4.6 Consensus size: 182
5286135 TATGCGTACT
* * * *
5286145 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGTTTTACCCGTTTTTTCATTTTGAGACAG
1 TATTAAAGTATCGACACTTTCAACATATCCGATAGCGTTTTACCCGTTTTGTCATTTCGAGACCG
* * * *
5286210 ATTTTTTCATATTTTGACATGTTATATTGTTATAG-ATCGATACACTTTTATAAAGTATCGACAC
66 ATTTTGTCATATTTTTACATGTTATATTGTTAT-GCATCGATACATTTTTATAAAATATCGACAC
5286274 TTTATAGGAGGTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
130 TTTATAGGAGGTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
*
5286327 TATTAAAGTATCGACACTTTCAACATATCTGATAGCGTTTTACCCGTTTTGTCATTTCGAGACCG
1 TATTAAAGTATCGACACTTTCAACATATCCGATAGCGTTTTACCCGTTTTGTCATTTCGAGACCG
** *
5286392 ATTTTGTCATATTTTTATTTGTTATATTGTTATGCATCGCTACATTTTTATAAAATATCGACACT
66 ATTTTGTCATATTTTTACATGTTATATTGTTATGCATCGATACATTTTTATAAAATATCGACACT
* * * *
5286457 TTATACGCGGTATTAATGCTTCTCTTTTAAATTCCAAAAGTTTCGATACTTA
131 TTATAGGAGGTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* * *
5286509 TATTAAAGTATCGACACTTTCAACATATCTGATAGCGTTTTACCTGTTTTGTCATTTCGAGAACG
1 TATTAAAGTATCGACACTTTCAACATATCCGATAGCGTTTTACCCGTTTTGTCATTTCGAGACCG
* *
5286574 ATTTTGTCATATTTTTACATGTTATATTGTTAT-CGATAGATACATTTTTATAAAGTATCGACAC
66 ATTTTGTCATATTTTTACATGTTATATTGTTATGC-ATCGATACATTTTTATAAAATATCGACAC
* *
5286638 TTTATA-GACTGTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCTATACTTA
130 TTTATAGGA-GGTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* **
5286691 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGTTTTACCAATTTTGTCATTTCGAGACCG
1 TATTAAAGTATCGACACTTTCAACATATCCGATAGCGTTTTACCCGTTTTGTCATTTCGAGACCG
* * * * * *
5286756 GTTTTGTCATATTTTTACCTGTTATATTCTTATGGATCAATACATTTTTTTAAAATTATCGACAC
66 ATTTTGTCATATTTTTACATGTTATATTGTTATGCATCGATACATTTTTATAAAA-TATCGACAC
*** * *
5286821 TTTATAGGCTTTATTATTGCTTCTCTTTTAAATTCCAAAAGTGTCGATATTTA
130 TTTATAGGAGGTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
** * * * * * *
5286874 T-TTCAATCTAATCGATACTTTCAACATATCC-AGTATCGCTTTA-CCGATTATGTCATAAT-AA
1 TATT-AAAGT-ATCGACACTTTCAACATATCCGA-TAGCGTTTTACCCG-TTTTGTCAT-TTCGA
* * * * * *
5286935 AACCGGTTTTATCATATTTTAACATGTTATATTGCTATGGATCGATACATTTTT
61 GACCGATTTTGTCATATTTTTACATGTTATATTGTTATGCATCGATACATTTTT
5286989 TATTTGTATT
Statistics
Matches: 587, Mismatches: 64, Indels: 20
0.87 0.10 0.03
Matches are distributed among these distances:
181 3 0.01
182 438 0.75
183 60 0.10
184 85 0.14
185 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.43
Consensus pattern (182 bp):
TATTAAAGTATCGACACTTTCAACATATCCGATAGCGTTTTACCCGTTTTGTCATTTCGAGACCG
ATTTTGTCATATTTTTACATGTTATATTGTTATGCATCGATACATTTTTATAAAATATCGACACT
TTATAGGAGGTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
Found at i:5287441 original size:31 final size:30
Alignment explanation
Indices: 5287374--5287441 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 30
5287364 CTCACAAGCT
* *
5287374 AAAAATTATCAAACTCAGCTCGAACTCGAT
1 AAAAATTATCAAACTCAGCTCGAACTCAAA
* *
5287404 ATAAATTATTGAAACTC-GACTCGAACTCAAA
1 AAAAATTA-TCAAACTCAG-CTCGAACTCAAA
5287435 AAAAATT
1 AAAAATT
5287442 TAAGAGCTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
30 8 0.26
31 23 0.74
ACGTcount: A:0.47, C:0.19, G:0.09, T:0.25
Consensus pattern (30 bp):
AAAAATTATCAAACTCAGCTCGAACTCAAA
Found at i:5288954 original size:7 final size:7
Alignment explanation
Indices: 5288942--5288993 Score: 59
Period size: 7 Copynumber: 7.4 Consensus size: 7
5288932 ACATAATAGA
5288942 GTTTAGG
1 GTTTAGG
5288949 GTTTAGG
1 GTTTAGG
*
5288956 GTTTATG
1 GTTTAGG
**
5288963 GTTTAAA
1 GTTTAGG
5288970 GTTTAGG
1 GTTTAGG
*
5288977 GGTTAGG
1 GTTTAGG
*
5288984 GATTAGG
1 GTTTAGG
5288991 GTT
1 GTT
5288994 CATTGCAAAG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.19, C:0.00, G:0.38, T:0.42
Consensus pattern (7 bp):
GTTTAGG
Found at i:5295454 original size:14 final size:14
Alignment explanation
Indices: 5295435--5295467 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
5295425 ATGATTGGTG
5295435 CAGCCGCTATCAAT
1 CAGCCGCTATCAAT
5295449 CAGCCGCTATCAAT
1 CAGCCGCTATCAAT
5295463 CAGCC
1 CAGCC
5295468 AACTCTCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.27, C:0.39, G:0.15, T:0.18
Consensus pattern (14 bp):
CAGCCGCTATCAAT
Found at i:5298753 original size:6 final size:6
Alignment explanation
Indices: 5298742--5298766 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5298732 AGGATGATAA
5298742 ACGGGG ACGGGG ACGGGG ACGGGG A
1 ACGGGG ACGGGG ACGGGG ACGGGG A
5298767 AAATCCATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.16, G:0.64, T:0.00
Consensus pattern (6 bp):
ACGGGG
Found at i:5298874 original size:12 final size:13
Alignment explanation
Indices: 5298829--5298873 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
5298819 CGCCCCGATT
5298829 ACCCGATTACCCG
1 ACCCGATTACCCG
*
5298842 CCCCGATTACCCG
1 ACCCGATTACCCG
*
5298855 TCCCGA-TACCCG
1 ACCCGATTACCCG
5298867 ACCCGAT
1 ACCCGAT
5298874 AAATATTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 11 0.39
13 17 0.61
ACGTcount: A:0.20, C:0.49, G:0.16, T:0.16
Consensus pattern (13 bp):
ACCCGATTACCCG
Found at i:5298951 original size:24 final size:25
Alignment explanation
Indices: 5298924--5298974 Score: 86
Period size: 24 Copynumber: 2.1 Consensus size: 25
5298914 ATATTAATAA
5298924 ATTTAATTTAAATAAA-AAATATAT
1 ATTTAATTTAAATAAATAAATATAT
*
5298948 ATTTAATTTAAATAAATATATATAT
1 ATTTAATTTAAATAAATAAATATAT
5298973 AT
1 AT
5298975 ACCCGGCCCG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 16 0.64
25 9 0.36
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
ATTTAATTTAAATAAATAAATATAT
Found at i:5298953 original size:19 final size:21
Alignment explanation
Indices: 5298894--5298970 Score: 79
Period size: 21 Copynumber: 3.8 Consensus size: 21
5298884 AATAATTATT
* * *
5298894 TATATATATATATATATATAA
1 TATAAATAAATATATATTTAA
* *
5298915 TATTAATAAATTTA-ATTTAA
1 TATAAATAAATATATATTTAA
5298935 -ATAAA-AAATATATATTTAA
1 TATAAATAAATATATATTTAA
*
5298954 TTTAAATAAATATATAT
1 TATAAATAAATATATAT
5298971 ATATACCCGG
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
18 6 0.13
19 10 0.22
20 9 0.20
21 20 0.44
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TATAAATAAATATATATTTAA
Found at i:5299037 original size:12 final size:12
Alignment explanation
Indices: 5298993--5299038 Score: 67
Period size: 12 Copynumber: 3.9 Consensus size: 12
5298983 CGATTCCCAG
5298993 CCCAATACC-GA
1 CCCAATACCTGA
*
5299004 CCCAATACCCGA
1 CCCAATACCTGA
*
5299016 CCCAATACCTGG
1 CCCAATACCTGA
5299028 CCCAATACCTG
1 CCCAATACCTG
5299039 TTTAAATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 9 0.28
12 23 0.72
ACGTcount: A:0.30, C:0.46, G:0.11, T:0.13
Consensus pattern (12 bp):
CCCAATACCTGA
Found at i:5302335 original size:25 final size:25
Alignment explanation
Indices: 5302301--5302358 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
5302291 GTCTTAAATC
5302301 TGTGTAAGACTAAAAAGTTTTACAT
1 TGTGTAAGACTAAAAAGTTTTACAT
*
5302326 TGTGTAAGACTAAAGAGTTTTACAT
1 TGTGTAAGACTAAAAAGTTTTACAT
5302351 TGTGTAAG
1 TGTGTAAG
5302359 TGGATCCTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (25 bp):
TGTGTAAGACTAAAAAGTTTTACAT
Found at i:5302379 original size:2 final size:2
Alignment explanation
Indices: 5302372--5302404 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5302362 ATCCTAACCC
5302372 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5302405 AGTCGTTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5307509 original size:17 final size:17
Alignment explanation
Indices: 5307487--5307520 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5307477 CTATCATGTT
5307487 ACCGGTTAGCGAACCGG
1 ACCGGTTAGCGAACCGG
5307504 ACCGGTTAGCGAACCGG
1 ACCGGTTAGCGAACCGG
5307521 TCATGTTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.29, G:0.35, T:0.12
Consensus pattern (17 bp):
ACCGGTTAGCGAACCGG
Found at i:5311436 original size:15 final size:15
Alignment explanation
Indices: 5311412--5311443 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
5311402 TGGAAGATCG
*
5311412 AAATCCAGAATGGGA
1 AAATCAAGAATGGGA
5311427 AAATCAAGAATGGGA
1 AAATCAAGAATGGGA
5311442 AA
1 AA
5311444 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.09, G:0.25, T:0.12
Consensus pattern (15 bp):
AAATCAAGAATGGGA
Found at i:5325664 original size:18 final size:18
Alignment explanation
Indices: 5325641--5325681 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
5325631 TTCTTCAGAT
5325641 CTCTATAATGCATCATAG
1 CTCTATAATGCATCATAG
5325659 CTCTATAATGCATCATAG
1 CTCTATAATGCATCATAG
5325677 CTCTA
1 CTCTA
5325682 CGACTAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.32, C:0.24, G:0.10, T:0.34
Consensus pattern (18 bp):
CTCTATAATGCATCATAG
Found at i:5338212 original size:83 final size:83
Alignment explanation
Indices: 5338064--5338219 Score: 186
Period size: 83 Copynumber: 1.9 Consensus size: 83
5338054 AGCAACATTT
* * * * *** *
5338064 TTATATAAACTCCGTAATAGGGTTAATCTATAGTGACATTTTTTCAACAAACGCCGTAACCGAGT
1 TTATACAAACACCGTAATAGGGTTAATATATAATGACATTTTTTCAACAAACGCAACAACAGAGT
*
5338129 AGTACTTTTACGGTGTTG
66 AGGACTTTTACGGTGTTG
*** * *
5338147 TTATACAAACACCGTAATAGGGTTAATATATAATGGTGTTTTTTCAACAAATGCAACAATAGAGT
1 TTATACAAACACCGTAATAGGGTTAATATATAATGACATTTTTTCAACAAACGCAACAACAGAGT
5338212 AGGACTTT
66 AGGACTTT
5338220 AGTTGTGCTT
Statistics
Matches: 59, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
83 59 1.00
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (83 bp):
TTATACAAACACCGTAATAGGGTTAATATATAATGACATTTTTTCAACAAACGCAACAACAGAGT
AGGACTTTTACGGTGTTG
Found at i:5338500 original size:41 final size:41
Alignment explanation
Indices: 5338452--5338621 Score: 162
Period size: 41 Copynumber: 4.1 Consensus size: 41
5338442 AAAAGATTCT
* *
5338452 TACTTTAGTGGTGTTTGTATACAAACACCGCTACAGACTCA
1 TACTTTAGTGGTGTTTGTATACAAACACCGCTATAAACTCA
* * * * *
5338493 CATTTTAGGGGCGTTTGTAAACAAACACCGCTATAAACTCA
1 TACTTTAGTGGTGTTTGTATACAAACACCGCTATAAACTCA
* ** * ** * *
5338534 TACGTTAGTGGAATTTTTATACAAATGCCACTATAAACTCG
1 TACTTTAGTGGTGTTTGTATACAAACACCGCTATAAACTCA
* * *
5338575 TACTTTAGTGGTGTTTTTATACAAACGCCGCTA-AAGACTCG
1 TACTTTAGTGGTGTTTGTATACAAACACCGCTATAA-ACTCA
5338616 TACTTT
1 TACTTT
5338622 TGGAAACACA
Statistics
Matches: 104, Mismatches: 24, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
40 2 0.02
41 102 0.98
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (41 bp):
TACTTTAGTGGTGTTTGTATACAAACACCGCTATAAACTCA
Found at i:5343425 original size:44 final size:44
Alignment explanation
Indices: 5343343--5343426 Score: 107
Period size: 44 Copynumber: 1.9 Consensus size: 44
5343333 TTTTAAATTT
* * * *
5343343 ACAAATGTCGCTATATGTCATGACTTTTACCGGTGTTTTTGGGA
1 ACAAATGCCACTATATGTCATGAATTTTACCGGCGTTTTTGGGA
*
5343387 ACAAATGCCACTATATGTCAT-AATATTTAGCGGCGTTTTT
1 ACAAATGCCACTATATGTCATGAAT-TTTACCGGCGTTTTT
5343427 TTACAAACAC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 2 0.06
44 32 0.94
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (44 bp):
ACAAATGCCACTATATGTCATGAATTTTACCGGCGTTTTTGGGA
Found at i:5347770 original size:20 final size:19
Alignment explanation
Indices: 5347728--5347797 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 19
5347718 TAACACTAGG
* *
5347728 GTATCGATACCTTGAGTGGA
1 GTATCGATA-CTTAAGAGGA
5347748 GTATCGATACTTAAGAGGTA
1 GTATCGATACTTAAGAGG-A
* *
5347768 GTATCGACACTGAA-AGGACA
1 GTATCGATACTTAAGAGG--A
5347788 GTATCGATAC
1 GTATCGATAC
5347798 CAAGGTACTT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
19 10 0.24
20 32 0.76
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.26
Consensus pattern (19 bp):
GTATCGATACTTAAGAGGA
Found at i:5350929 original size:3 final size:3
Alignment explanation
Indices: 5350923--5351091 Score: 241
Period size: 3 Copynumber: 56.0 Consensus size: 3
5350913 GATGATATGA
*
5350923 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATG
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * *
5350971 ATT ATT ATT ATT ATC ATT ATC ATT ATC ATT ATC ATC ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5351019 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
5351067 A-T ATTT ATCT ATT TTT ATT AAT ATT
1 ATT A-TT AT-T ATT ATT ATT ATT ATT
5351092 TTTAATACCA
Statistics
Matches: 149, Mismatches: 14, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
2 2 0.01
3 142 0.95
4 5 0.03
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:5351815 original size:29 final size:29
Alignment explanation
Indices: 5351782--5351863 Score: 78
Period size: 31 Copynumber: 2.8 Consensus size: 29
5351772 TTTCAATTTG
*
5351782 GTCCTTAAACTTTTGAACATTTTAATTTCA
1 GTCCTTAAACTTTTGAACATTTTAAATT-A
* *
5351812 -TCCTTAAA-TTGTGACAATCATTCTAAATTA
1 GTCCTTAAACTTTTG--AA-CATTTTAAATTA
*
5351842 GTCCTCAAACTTTTGAACATTT
1 GTCCTTAAACTTTTGAACATTT
5351864 CATTCTCATG
Statistics
Matches: 41, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
28 4 0.10
29 12 0.29
30 5 0.12
31 16 0.39
32 4 0.10
ACGTcount: A:0.32, C:0.18, G:0.07, T:0.43
Consensus pattern (29 bp):
GTCCTTAAACTTTTGAACATTTTAAATTA
Found at i:5351862 original size:60 final size:60
Alignment explanation
Indices: 5351782--5351900 Score: 161
Period size: 60 Copynumber: 2.0 Consensus size: 60
5351772 TTTCAATTTG
* *
5351782 GTCCTTAAACTTTTGAACATTTTAATT-TCATCCTTAAATTGTGA-CAATCATTCTAAATTA
1 GTCCTCAAACTTTTGAACA-TTTAATTCTCATCCTTAAATTATGATC-ATCATTCTAAATTA
* * *
5351842 GTCCTCAAACTTTTGAACATTTCATTCTCATGCTTAAATTATGATCTTCATTCTAAATT
1 GTCCTCAAACTTTTGAACATTTAATTCTCATCCTTAAATTATGATCATCATTCTAAATT
5351901 GATCCTAAGA
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
59 6 0.12
60 45 0.87
61 1 0.02
ACGTcount: A:0.31, C:0.18, G:0.07, T:0.44
Consensus pattern (60 bp):
GTCCTCAAACTTTTGAACATTTAATTCTCATCCTTAAATTATGATCATCATTCTAAATTA
Found at i:5351914 original size:60 final size:59
Alignment explanation
Indices: 5351782--5351930 Score: 160
Period size: 60 Copynumber: 2.5 Consensus size: 59
5351772 TTTCAATTTG
* * *
5351782 GTCCTTAAACTTTTGAACATTTTAATTTCATCCTTAAATTGTGACAATCATTCTAAATTA
1 GTCCTCAAACTTTTGAACA-TTTCATTTCATCCTTAAATTATGACAATCATTCTAAATTA
* *
5351842 GTCCTCAAACTTTTGAACATTTCATTCTCATGCTTAAATTATGATC-TTCATTCTAAATT-
1 GTCCTCAAACTTTTGAACATTTCATT-TCATCCTTAAATTATGA-CAATCATTCTAAATTA
*
5351901 GATCCT-AAGACTTTTTGAATATTTCGATTT
1 G-TCCTCAA-AC-TTTTGAACATTTC-ATTT
5351931 ATCGTAAATT
Statistics
Matches: 77, Mismatches: 6, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
59 9 0.12
60 51 0.66
61 14 0.18
62 3 0.04
ACGTcount: A:0.30, C:0.17, G:0.08, T:0.44
Consensus pattern (59 bp):
GTCCTCAAACTTTTGAACATTTCATTTCATCCTTAAATTATGACAATCATTCTAAATTA
Found at i:5352204 original size:59 final size:59
Alignment explanation
Indices: 5352097--5352242 Score: 163
Period size: 59 Copynumber: 2.4 Consensus size: 59
5352087 AAAAGTTTTG
* ** *
5352097 AGGACCAATTTAGAATGGGATTCATAGTTTGGAGATGAAATTGAAATGTTCAAAAGTTCA
1 AGGACTAATTTAGAATAAGA-TCATAGGTTGGAGATGAAATTGAAATGTTCAAAAGTTCA
* *
5352157 AGGA-TGAATTTAGAATAAGAGTCATAGGTT-GAGATGAAATT-AGAATGTTTAAAAGTTTA
1 AGGACT-AATTTAGAATAAGA-TCATAGGTTGGAGATGAAATTGA-AATGTTCAAAAGTTCA
*
5352216 AGGACTAATTTAAAATGAAGATCATAG
1 AGGACTAATTTAGAAT-AAGATCATAG
5352243 TTTAAGGACA
Statistics
Matches: 74, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
58 1 0.01
59 44 0.59
60 29 0.39
ACGTcount: A:0.42, C:0.05, G:0.23, T:0.30
Consensus pattern (59 bp):
AGGACTAATTTAGAATAAGATCATAGGTTGGAGATGAAATTGAAATGTTCAAAAGTTCA
Found at i:5355340 original size:2 final size:2
Alignment explanation
Indices: 5355294--5355324 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
5355284 TTATCTAACC
5355294 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5355325 TCTTTCATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5355829 original size:158 final size:158
Alignment explanation
Indices: 5355614--5355943 Score: 482
Period size: 158 Copynumber: 2.1 Consensus size: 158
5355604 CATGTAGTTT
* * * *
5355614 AAATTTGGTAAAAAACGAACTTAAAATAAATGAAAAATTGAAGGAACAAGGAGATTATGAAAACT
1 AAATTTTGTAAAAAACGAACTTAAAATAAATGAAAAATTGAAGGAACAAGAACATTATGAAAAAT
* *
5355679 TGAAGGACTAAATAAAAAAATAAAAAAATTATTATCAAAAAGAGGAATTGAAAGTACACATGTAT
66 TGAAAGACTAAATAAAAAAATAAAAAAATTATTATCAAAAAGAGGAATTGAAAATACACATGTAT
5355744 TCTACTATGGTTTAGGAGCATGAGGATC
131 TCTACTATGGTTTAGGAGCATGAGGATC
* ** * * *
5355772 AAATTTTGTAAAAAACGGACTTAAAATAAATGACGAGTTGAAGTAAGAAGAACATTATGAAAAAT
1 AAATTTTGTAAAAAACGAACTTAAAATAAATGAAAAATTGAAGGAACAAGAACATTATGAAAAAT
** * * *
5355837 TGAAAGACTAAATTGAAAAATAAAAAATTTGTTATTAAAAAGAGGAATTGAAAATACACATGTAT
66 TGAAAGACTAAATAAAAAAATAAAAAAATTATTATCAAAAAGAGGAATTGAAAATACACATGTAT
* *
5355902 TCTACTATGGTTTAGGAGCATGTGGTTC
131 TCTACTATGGTTTAGGAGCATGAGGATC
5355930 -AATTTTGTAAAAAA
1 AAATTTTGTAAAAAA
5355944 ATAGACTTAA
Statistics
Matches: 153, Mismatches: 19, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
157 14 0.09
158 139 0.91
ACGTcount: A:0.49, C:0.07, G:0.17, T:0.27
Consensus pattern (158 bp):
AAATTTTGTAAAAAACGAACTTAAAATAAATGAAAAATTGAAGGAACAAGAACATTATGAAAAAT
TGAAAGACTAAATAAAAAAATAAAAAAATTATTATCAAAAAGAGGAATTGAAAATACACATGTAT
TCTACTATGGTTTAGGAGCATGAGGATC
Found at i:5356737 original size:37 final size:37
Alignment explanation
Indices: 5356683--5356767 Score: 161
Period size: 37 Copynumber: 2.3 Consensus size: 37
5356673 ACCCTTGGAG
5356683 TTCTATGGCTTCCCGTGGAGTTGATGAAGAAGCCATC
1 TTCTATGGCTTCCCGTGGAGTTGATGAAGAAGCCATC
*
5356720 TTCTATGGCTTCTCGTGGAGTTGATGAAGAAGCCATC
1 TTCTATGGCTTCCCGTGGAGTTGATGAAGAAGCCATC
5356757 TTCTATGGCTT
1 TTCTATGGCTT
5356768 ACCTGCTGAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 47 1.00
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (37 bp):
TTCTATGGCTTCCCGTGGAGTTGATGAAGAAGCCATC
Done.