Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008311.1 Hibiscus syriacus cultivar Beakdansim tig00111002_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: 1790494
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 8
Found at i:1059565 original size:24 final size:24
Alignment explanation
Indices: 1059530--1059576 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1059520 ATTGGGATAA
* * *
1059530 ACATAAATGAACACACATAAATGG
1 ACATAAACGAACAAAAATAAATGG
1059554 ACATAAACGAACAAAAATAAATG
1 ACATAAACGAACAAAAATAAATG
1059577 AACTTAAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.60, C:0.15, G:0.11, T:0.15
Consensus pattern (24 bp):
ACATAAACGAACAAAAATAAATGG
Found at i:1068512 original size:35 final size:34
Alignment explanation
Indices: 1068473--1068539 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 34
1068463 ATGATTCCAT
1068473 AAATCAAGAAAA-ATCATAATTTTCAATGAAAACTG
1 AAATC-AGAAAATA-CATAATTTTCAATGAAAACTG
* *
1068508 AAATCAGAGAATACATATTTTTCAATGAAAAC
1 AAATCAGAAAATACATAATTTTCAATGAAAAC
1068540 CATAATCAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 23 0.79
35 6 0.21
ACGTcount: A:0.52, C:0.12, G:0.09, T:0.27
Consensus pattern (34 bp):
AAATCAGAAAATACATAATTTTCAATGAAAACTG
Found at i:1068531 original size:34 final size:34
Alignment explanation
Indices: 1068487--1068552 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
1068477 CAAGAAAAAT
*
1068487 CATAATTTTCAATGAAAACTGA-AATCAGAGAATA
1 CATAATTTTCAATGAAAAC-CATAATCAGAGAATA
*
1068521 CATATTTTTCAATGAAAACCATAATCAGAGAA
1 CATAATTTTCAATGAAAACCATAATCAGAGAA
1068553 CATGTGCCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 1 0.03
34 28 0.97
ACGTcount: A:0.48, C:0.14, G:0.11, T:0.27
Consensus pattern (34 bp):
CATAATTTTCAATGAAAACCATAATCAGAGAATA
Found at i:1089692 original size:19 final size:20
Alignment explanation
Indices: 1089627--1089698 Score: 67
Period size: 19 Copynumber: 3.7 Consensus size: 20
1089617 AAATGACCAA
* *
1089627 CAAATTCGCAACACGATCT-
1 CAAATTCGCAACGCGAACTC
* *
1089646 CGAGTTCGCAACGCGAACTC
1 CAAATTCGCAACGCGAACTC
* * *
1089666 CAATTTCGCAACTC-AATTC
1 CAAATTCGCAACGCGAACTC
1089685 CAAATTCGCAACGC
1 CAAATTCGCAACGC
1089699 AAATATGTAA
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
19 31 0.74
20 11 0.26
ACGTcount: A:0.32, C:0.33, G:0.14, T:0.21
Consensus pattern (20 bp):
CAAATTCGCAACGCGAACTC
Found at i:1089715 original size:20 final size:20
Alignment explanation
Indices: 1089690--1089761 Score: 108
Period size: 20 Copynumber: 3.6 Consensus size: 20
1089680 AATTCCAAAT
1089690 TCGCAACGCAAATATGTAAA
1 TCGCAACGCAAATATGTAAA
*
1089710 TCGCAATGCAAATATGTAAA
1 TCGCAACGCAAATATGTAAA
* *
1089730 TCGCAACGCGAATCTGTAAA
1 TCGCAACGCAAATATGTAAA
*
1089750 TCGCAACACAAA
1 TCGCAACGCAAA
1089762 AGTCAAATTC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.43, C:0.22, G:0.15, T:0.19
Consensus pattern (20 bp):
TCGCAACGCAAATATGTAAA
Found at i:1089774 original size:40 final size:42
Alignment explanation
Indices: 1089685--1089780 Score: 119
Period size: 40 Copynumber: 2.4 Consensus size: 42
1089675 AACTCAATTC
* **
1089685 CAAATTCGCAACGCAAATATGTAAATCGCAATGCAAATATGT
1 CAAATTCGCAACGCGAATATGTAAATCGCAACACAAATATGT
*
1089727 -AAA-TCGCAACGCGAATCTGTAAATCGCAACACAAA-A-GT
1 CAAATTCGCAACGCGAATATGTAAATCGCAACACAAATATGT
*
1089765 CAAATTCGCAATGCGA
1 CAAATTCGCAACGCGA
1089781 TTTCCAAATT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
38 2 0.04
39 4 0.09
40 38 0.81
41 3 0.06
ACGTcount: A:0.43, C:0.22, G:0.16, T:0.20
Consensus pattern (42 bp):
CAAATTCGCAACGCGAATATGTAAATCGCAACACAAATATGT
Found at i:1089788 original size:20 final size:20
Alignment explanation
Indices: 1089765--1089901 Score: 124
Period size: 20 Copynumber: 7.0 Consensus size: 20
1089755 ACACAAAAGT
1089765 CAAATTCGCAATGCGATTTC
1 CAAATTCGCAATGCGATTTC
1089785 CAAATTCGCAA--CGATTTC
1 CAAATTCGCAATGCGATTTC
* *
1089803 CAAATTCGCAACGTGATTT-
1 CAAATTCGCAATGCGATTTC
* *
1089822 -AAATTCGCCATGCGATTTA
1 CAAATTCGCAATGCGATTTC
* * *
1089841 CAATTTCGCCATGCGATTTA
1 CAAATTCGCAATGCGATTTC
**
1089861 CAAATTCGCAACACTGAATTT-
1 CAAATTCGCAATGC-G-ATTTC
1089882 CAAATTCGCAACT-CGATTTC
1 CAAATTCGCAA-TGCGATTTC
1089902 TGAATTCACA
Statistics
Matches: 99, Mismatches: 10, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
18 33 0.33
19 4 0.04
20 45 0.45
21 13 0.13
22 4 0.04
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.31
Consensus pattern (20 bp):
CAAATTCGCAATGCGATTTC
Found at i:1089821 original size:38 final size:37
Alignment explanation
Indices: 1089765--1089872 Score: 119
Period size: 38 Copynumber: 2.8 Consensus size: 37
1089755 ACACAAAAGT
*
1089765 CAAATTCGCAATGCGATTTCCAAATTCGCAACGATTTC
1 CAAATTCGCAATGCGATTT-CAAATTCGCAACGATTTA
* * *
1089803 CAAATTCGCAACGTGATTT-AAATTCGCCATGCGATTTA
1 CAAATTCGCAATGCGATTTCAAATTCG-CA-ACGATTTA
* *
1089841 CAATTTCGCCATGCGATTTACAAATTCGCAAC
1 CAAATTCGCAATGCGATTT-CAAATTCGCAAC
1089873 ACTGAATTTC
Statistics
Matches: 57, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
36 7 0.12
37 2 0.04
38 39 0.68
39 2 0.04
40 7 0.12
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (37 bp):
CAAATTCGCAATGCGATTTCAAATTCGCAACGATTTA
Found at i:1089933 original size:20 final size:20
Alignment explanation
Indices: 1089884--1089953 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
1089874 CTGAATTTCA
*
1089884 AATTCGCAACTCGATTTCTG
1 AATTCGCAACTCGATTTTTG
*
1089904 AATTCACAACTCGATTTTTG
1 AATTCGCAACTCGATTTTTG
* * *
1089924 AATTTGCAACACGAATTTT-
1 AATTCGCAACTCGATTTTTG
1089943 AATTTCGCAAC
1 AA-TTCGCAAC
1089954 AGGTTTTATT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
19 2 0.05
20 40 0.95
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.36
Consensus pattern (20 bp):
AATTCGCAACTCGATTTTTG
Found at i:1089954 original size:20 final size:20
Alignment explanation
Indices: 1089865--1089973 Score: 75
Period size: 20 Copynumber: 5.5 Consensus size: 20
1089855 GATTTACAAA
* *
1089865 TTCGCAACACTGAATTTCAAA
1 TTCGCAACAC-GAATTTTAAT
*
1089886 TTCGCAACTCG-ATTTCTGAA-
1 TTCGCAACACGAATTT-T-AAT
* * *
1089906 TTCACAACTCGATTTTTGAAT
1 TTCGCAACACGAATTTT-AAT
1089927 TT-GCAACACGAATTTTAAT
1 TTCGCAACACGAATTTTAAT
* *
1089946 TTCGCAACA-G-GTTTTATT
1 TTCGCAACACGAATTTTAAT
1089964 TTCGCAACAC
1 TTCGCAACAC
1089974 AAATGTTTTG
Statistics
Matches: 73, Mismatches: 9, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
18 15 0.21
19 10 0.14
20 32 0.44
21 16 0.22
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (20 bp):
TTCGCAACACGAATTTTAAT
Found at i:1090762 original size:12 final size:12
Alignment explanation
Indices: 1090741--1090774 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1090731 ACCAAATTTC
*
1090741 CAATACCAAACA
1 CAATATCAAACA
1090753 CAATATCAAACA
1 CAATATCAAACA
*
1090765 CAATCTCAAA
1 CAATATCAAA
1090775 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:1090927 original size:24 final size:24
Alignment explanation
Indices: 1090900--1090946 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1090890 GTATTCGAAA
1090900 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1090924 TTTGATCTTGGTTAATACTCGGA
1 TTTGATCTTGGTCAATACCCGGA
1090947 TTTTTATGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1093703 original size:25 final size:25
Alignment explanation
Indices: 1093667--1093714 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
1093657 ATCAATTAAA
*
1093667 CATTGTTGTGGGTACATTATTTGAG
1 CATTGTTATGGGTACATTATTTGAG
1093692 CATTGTTATGGGTACATTATTTG
1 CATTGTTATGGGTACATTATTTG
1093715 GAAAATAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.21, C:0.08, G:0.25, T:0.46
Consensus pattern (25 bp):
CATTGTTATGGGTACATTATTTGAG
Found at i:1094121 original size:18 final size:18
Alignment explanation
Indices: 1094100--1094136 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1094090 GTAATTGGAG
1094100 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
1094118 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
1094136 T
1 T
1094137 ATAAATTTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:1094143 original size:24 final size:24
Alignment explanation
Indices: 1094092--1094144 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
1094082 TTTCATATGT
* * *
1094092 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
1094116 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
1094140 AATTT
1 AATTT
1094145 CAGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:1096792 original size:111 final size:111
Alignment explanation
Indices: 1096589--1096792 Score: 338
Period size: 111 Copynumber: 1.8 Consensus size: 111
1096579 GCCACTAATT
*
1096589 AAAGTTATCGATCGATATTGTTAAATGCATAACGATGCATTATAGGCATAAAAGGTGCCACTCAT
1 AAAGCTATCGATCGATATTGTTAAATGCATAACGATGCATTATAGGCATAAAAGGTGCCACTCAT
*
1096654 GGTATTCATAAAAGGTGAATTACCATTTCGACATACTTCGTGTATG
66 GGTATTCATAAAAGGTGAATGACCATTTCGACATACTTCGTGTATG
* * *
1096700 AAAGCTATCGATTGATATTGTTTAATGCATAACGGTGCATTATAGGCATAAAAGGTGCCACTTC-
1 AAAGCTATCGATCGATATTGTTAAATGCATAACGATGCATTATAGGCATAAAAGGTGCCAC-TCA
*
1096764 TGGTATTCATAAAAGGTGAATGAGCATTT
65 TGGTATTCATAAAAGGTGAATGACCATTT
1096793 TTTCACTTCG
Statistics
Matches: 86, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
111 84 0.98
112 2 0.02
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (111 bp):
AAAGCTATCGATCGATATTGTTAAATGCATAACGATGCATTATAGGCATAAAAGGTGCCACTCAT
GGTATTCATAAAAGGTGAATGACCATTTCGACATACTTCGTGTATG
Found at i:1107407 original size:25 final size:25
Alignment explanation
Indices: 1107372--1107434 Score: 108
Period size: 25 Copynumber: 2.5 Consensus size: 25
1107362 TGGGTTGGGA
1107372 TGTGTGCTTATGCAAGATGGAAAAGT
1 TGTGT-CTTATGCAAGATGGAAAAGT
1107398 TGTGTCTTATGCAAGATGGAAAAGT
1 TGTGTCTTATGCAAGATGGAAAAGT
*
1107423 TGTGGCTTATGC
1 TGTGTCTTATGC
1107435 CTCATGACAG
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
25 31 0.86
26 5 0.14
ACGTcount: A:0.27, C:0.10, G:0.30, T:0.33
Consensus pattern (25 bp):
TGTGTCTTATGCAAGATGGAAAAGT
Found at i:1116864 original size:10 final size:10
Alignment explanation
Indices: 1116851--1116926 Score: 64
Period size: 10 Copynumber: 7.3 Consensus size: 10
1116841 TTTTTTGAAA
1116851 TTTTTGTTTT
1 TTTTTGTTTT
1116861 TTTTTGTTTT
1 TTTTTGTTTT
**
1116871 TTGCCT-TTTT
1 TT-TTTGTTTT
*
1116881 TCTTTGCCTTTTT
1 TTTTTG---TTTT
**
1116894 TTTTTGCCTT
1 TTTTTGTTTT
1116904 TTTTTGTTTT
1 TTTTTGTTTT
1116914 TTTTTGTTTT
1 TTTTTGTTTT
1116924 TTT
1 TTT
1116927 GAAAAAAAAA
Statistics
Matches: 51, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
9 1 0.02
10 40 0.78
11 1 0.02
13 9 0.18
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.82
Consensus pattern (10 bp):
TTTTTGTTTT
Found at i:1116908 original size:13 final size:13
Alignment explanation
Indices: 1116862--1116908 Score: 76
Period size: 13 Copynumber: 3.5 Consensus size: 13
1116852 TTTTGTTTTT
1116862 TTTTGTTTTTTGCC
1 TTTT-TTTTTTGCC
*
1116876 TTTTTTCTTTGCC
1 TTTTTTTTTTGCC
1116889 TTTTTTTTTTGCC
1 TTTTTTTTTTGCC
1116902 TTTTTTT
1 TTTTTTT
1116909 GTTTTTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
13 27 0.87
14 4 0.13
ACGTcount: A:0.00, C:0.15, G:0.09, T:0.77
Consensus pattern (13 bp):
TTTTTTTTTTGCC
Found at i:1116915 original size:20 final size:18
Alignment explanation
Indices: 1116851--1116927 Score: 61
Period size: 17 Copynumber: 4.3 Consensus size: 18
1116841 TTTTTTGAAA
1116851 TTTTTGTTTTTTTTTG-T
1 TTTTTGTTTTTTTTTGTT
** *
1116868 TTTTTG-CCTTTTTTCTT
1 TTTTTGTTTTTTTTTGTT
***
1116885 TGCCT-TTTTTTTTTGCCTT
1 TTTTTGTTTTTTTTTG--TT
1116904 TTTTTGTTTTTTTTTGTT
1 TTTTTGTTTTTTTTTGTT
1116922 TTTTTG
1 TTTTTG
1116928 AAAAAAAAAA
Statistics
Matches: 43, Mismatches: 12, Indels: 9
0.67 0.19 0.14
Matches are distributed among these distances:
16 6 0.14
17 15 0.35
18 8 0.19
19 4 0.09
20 10 0.23
ACGTcount: A:0.00, C:0.09, G:0.10, T:0.81
Consensus pattern (18 bp):
TTTTTGTTTTTTTTTGTT
Found at i:1118693 original size:110 final size:111
Alignment explanation
Indices: 1118544--1118748 Score: 317
Period size: 110 Copynumber: 1.9 Consensus size: 111
1118534 GCCACTAATT
*
1118544 AAAGTTATCGATCGATATTGTTAATTGCATAACAATGCATTATAGGCATAAAAGGTGCCAC-TCA
1 AAAGCTATCGATCGATATTGTTAATTGCATAACAATGCATTATAGGCATAAAAGGTGCCACTTC-
* *
1118608 TGATATTCATAAAAGGTGAATTACCTTTTCGACATACTTCGTGTATG
65 TGATATTCATAAAAGGTGAATGACCATTTCGACATACTTCGTGTATG
**
1118655 AAAGCTAT-GATCGATATTGTTTAA-TGCATAACGGTGCATTATAGGCATAAAAGGTGCCACTTC
1 AAAGCTATCGATCGATATTG-TTAATTGCATAACAATGCATTATAGGCATAAAAGGTGCCACTTC
*
1118718 TGGTATTCATAAAAGGTGAATGACCATTTCG
65 TGATATTCATAAAAGGTGAATGACCATTTCG
1118749 GCACTTCGGT
Statistics
Matches: 86, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
110 73 0.85
111 13 0.15
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (111 bp):
AAAGCTATCGATCGATATTGTTAATTGCATAACAATGCATTATAGGCATAAAAGGTGCCACTTCT
GATATTCATAAAAGGTGAATGACCATTTCGACATACTTCGTGTATG
Found at i:1121348 original size:21 final size:21
Alignment explanation
Indices: 1121322--1121366 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
1121312 ATCAAAATGC
1121322 ATGTTGCCACCTATGCTAACT
1 ATGTTGCCACCTATGCTAACT
*
1121343 ATGTTGTCACCTATGCTAACT
1 ATGTTGCCACCTATGCTAACT
1121364 ATG
1 ATG
1121367 CAAATGAGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (21 bp):
ATGTTGCCACCTATGCTAACT
Found at i:1129608 original size:5 final size:5
Alignment explanation
Indices: 1129598--1129631 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
1129588 ATCAAAGATA
*
1129598 AAAAT AAAAT AAAAT AAAAC AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1129632 ATGGAACGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:1130166 original size:17 final size:17
Alignment explanation
Indices: 1130137--1130171 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1130127 TACATAAAAT
1130137 AAAATACTGGAAATAAA
1 AAAATACTGGAAATAAA
1130154 AAAATGACT-GAAATAAA
1 AAAAT-ACTGGAAATAAA
1130171 A
1 A
1130172 TGCAGCAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.82
18 3 0.18
ACGTcount: A:0.66, C:0.06, G:0.11, T:0.17
Consensus pattern (17 bp):
AAAATACTGGAAATAAA
Found at i:1130441 original size:34 final size:32
Alignment explanation
Indices: 1130389--1130474 Score: 109
Period size: 34 Copynumber: 2.6 Consensus size: 32
1130379 TTAGTTTGTG
1130389 CAATAAAATAAAATGTTAGTAAGTTAGTAAGAA
1 CAATAAAATAAAA-GTTAGTAAGTTAGTAAGAA
* * *
1130422 CAATAAAAATATAAAGTTAGTATGTTTGTATGAA
1 CAAT-AAAATA-AAAGTTAGTAAGTTAGTAAGAA
1130456 CAAGTAAAATAAAAGTTAG
1 CAA-TAAAATAAAAGTTAG
1130475 GGGGTTTTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
33 12 0.26
34 31 0.66
35 4 0.09
ACGTcount: A:0.52, C:0.03, G:0.15, T:0.29
Consensus pattern (32 bp):
CAATAAAATAAAAGTTAGTAAGTTAGTAAGAA
Found at i:1130539 original size:201 final size:201
Alignment explanation
Indices: 1130263--1130674 Score: 587
Period size: 201 Copynumber: 2.0 Consensus size: 201
1130253 TGCATAAATT
* * * *
1130263 TAAAAGTTATGGGGTTGTTTCTAACCGTTTAACCCGGACCATAAATAATCTGGATCATCCCCTAG
1 TAAAAGTTAGGGGGTTGTTTCTAACCGTATAACCCGAACCATAAATAATCTGGATCATCCCCCAG
** * * * *
1130328 GGCAGGTCACCGCAAGGTCGTTGAATATT-TGAATGTTAGAAAGTTAGCGGGTTAGTTTGTGCAA
66 AACAGGTCACCGCAAGGTCGTTAAATATTCT-AAAGTTAGAAAATTAGCGGGTTAGTCTGTGCAA
* ** *
1130392 TAAAATAAAATGTTAGTAAGTTAGTAAGAACAATAAAAATATAAAGTTAGTATGTTTGTATGAAC
130 TAAAATAAAACGTTAGTAAGTTAGTAAGAACAATAAAAATA-AAAGTTAGTATGTTAATATAAAC
*
1130457 AAGTAAAA
194 AAATAAAA
* * *
1130465 TAAAAGTTAGGGGGTT-TTTTTAACTGTATAACTCGAACCATAAATAATGC-GGATCATCCCCCA
1 TAAAAGTTAGGGGGTTGTTTCTAACCGTATAACCCGAACCATAAATAAT-CTGGATCATCCCCCA
* *
1130528 GAACGGGTCACCGCAAGGTCGTTAAATATTCTAAAGTTAGAAAATTAGTGGGTTAGTCTGTGCAA
65 GAACAGGTCACCGCAAGGTCGTTAAATATTCTAAAGTTAGAAAATTAGCGGGTTAGTCTGTGCAA
*
1130593 TAAAATAAAACGTTAGTAAGTTAGTAAGAACAATAAAAATACAAGTTAGTATGTTAATATAAACA
130 TAAAATAAAACGTTAGTAAGTTAGTAAGAACAATAAAAATAAAAGTTAGTATGTTAATATAAACA
1130658 AATAAAA
195 AATAAAA
1130665 TAAAAGTTAG
1 TAAAAGTTAG
1130675 AATGTTAGTA
Statistics
Matches: 187, Mismatches: 21, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
200 36 0.19
201 134 0.72
202 17 0.09
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (201 bp):
TAAAAGTTAGGGGGTTGTTTCTAACCGTATAACCCGAACCATAAATAATCTGGATCATCCCCCAG
AACAGGTCACCGCAAGGTCGTTAAATATTCTAAAGTTAGAAAATTAGCGGGTTAGTCTGTGCAAT
AAAATAAAACGTTAGTAAGTTAGTAAGAACAATAAAAATAAAAGTTAGTATGTTAATATAAACAA
ATAAAA
Found at i:1130627 original size:33 final size:32
Alignment explanation
Indices: 1130590--1130686 Score: 108
Period size: 33 Copynumber: 2.9 Consensus size: 32
1130580 TTAGTCTGTG
1130590 CAATAAAATAAAACGTTAGTAAGTTAGTAAGAA
1 CAATAAAATAAAA-GTTAGTAAGTTAGTAAGAA
* * *
1130623 CAATAAAAATACAAGTTAGTATGTTAATATA-AA
1 CAAT-AAAATAAAAGTTAGTAAGTTAGTA-AGAA
1130656 CAAATAAAATAAAAGTTAG-AATGTTAGTAAG
1 C-AATAAAATAAAAGTTAGTAA-GTTAGTAAG
1130687 TTAGTAAGTT
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
32 2 0.04
33 39 0.74
34 12 0.23
ACGTcount: A:0.55, C:0.05, G:0.13, T:0.27
Consensus pattern (32 bp):
CAATAAAATAAAAGTTAGTAAGTTAGTAAGAA
Found at i:1139828 original size:2 final size:2
Alignment explanation
Indices: 1139816--1139845 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1139806 TTTGTTAAAC
1139816 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1139846 GTCAATTTCG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1154577 original size:105 final size:107
Alignment explanation
Indices: 1154380--1154579 Score: 296
Period size: 111 Copynumber: 1.9 Consensus size: 107
1154370 GCCACTAATT
*
1154380 AAAGTTATCGATCGATATTGTTAAATGCATAACGATGCATTATAGGCATAAAAGGTGCCACTAAT
1 AAAGCTATCGATCGATATTGTTAAATGCATAACGATGC----TAGGCATAAAAGGTGCCACTAAT
*
1154445 GGTATTCATAAAAGGTGAATTACCATTTCGACATACTTCGTGTATG
62 GGTATTCATAAAAGGTGAATGACCATTTCGACATACTTCGTGTATG
* * **
1154491 AAAGCTATCGATCGATATTGTTTAATGCATAACGGTGC-AGGCATAAAAGGTG-CACTTTTGGTA
1 AAAGCTATCGATCGATATTGTTAAATGCATAACGATGCTAGGCATAAAAGGTGCCACTAATGGTA
1154554 TTCATAAAAGGTGAATGACCATTTCG
66 TTCATAAAAGGTGAATGACCATTTCG
1154580 GCACTTTGGT
Statistics
Matches: 83, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
105 34 0.41
106 14 0.17
111 35 0.42
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.31
Consensus pattern (107 bp):
AAAGCTATCGATCGATATTGTTAAATGCATAACGATGCTAGGCATAAAAGGTGCCACTAATGGTA
TTCATAAAAGGTGAATGACCATTTCGACATACTTCGTGTATG
Found at i:1158351 original size:21 final size:21
Alignment explanation
Indices: 1158325--1158369 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1158315 ATCAAAATGC
*
1158325 ATGTTGCCACCTATGTTAACT
1 ATGTTGCCACCTATGCTAACT
*
1158346 ATGTTGTCACCTATGCTAACT
1 ATGTTGCCACCTATGCTAACT
1158367 ATG
1 ATG
1158370 CAAATGAGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (21 bp):
ATGTTGCCACCTATGCTAACT
Found at i:1165811 original size:18 final size:18
Alignment explanation
Indices: 1165788--1165831 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
1165778 AGTAGTTAAG
1165788 CTAACTACTGTAACTACA
1 CTAACTACTGTAACTACA
1165806 CTAACTACTGTAACTACA
1 CTAACTACTGTAACTACA
1165824 CTAACTAC
1 CTAACTAC
1165832 CTTAAGCAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.39, C:0.30, G:0.05, T:0.27
Consensus pattern (18 bp):
CTAACTACTGTAACTACA
Found at i:1165828 original size:9 final size:9
Alignment explanation
Indices: 1165788--1165831 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
1165778 AGTAGTTAAG
*
1165788 CTAACTACT
1 CTAACTACA
*
1165797 GTAACTACA
1 CTAACTACA
*
1165806 CTAACTACT
1 CTAACTACA
*
1165815 GTAACTACA
1 CTAACTACA
1165824 CTAACTAC
1 CTAACTAC
1165832 CTTAAGCAAC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.39, C:0.30, G:0.05, T:0.27
Consensus pattern (9 bp):
CTAACTACA
Found at i:1167219 original size:18 final size:19
Alignment explanation
Indices: 1167177--1167219 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
1167167 ATGCAAATAC
1167177 ATAAAATAAAATACTGGAA
1 ATAAAATAAAATACTGGAA
*
1167196 AT-AAATAAATTACT-GAA
1 ATAAAATAAAATACTGGAA
1167213 ATAAAAT
1 ATAAAAT
1167220 GCAGCAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 5 0.23
18 15 0.68
19 2 0.09
ACGTcount: A:0.63, C:0.05, G:0.07, T:0.26
Consensus pattern (19 bp):
ATAAAATAAAATACTGGAA
Found at i:1167499 original size:34 final size:33
Alignment explanation
Indices: 1167450--1167532 Score: 96
Period size: 34 Copynumber: 2.5 Consensus size: 33
1167440 GTTTGTGCAA
*
1167450 TAAAATAAAATGTTAGTAAGTTAGTAAGAACGA-
1 TAAAATAAAA-GTTAGTAAGTTAGTAAGAACAAG
* * *
1167483 TAAAAATATAAAGTTAGTATGTTTGTATGAACAAG
1 T-AAAATA-AAAGTTAGTAAGTTAGTAAGAACAAG
1167518 TAAAATAAAAGTTAG
1 TAAAATAAAAGTTAG
1167533 GGGTTGTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
33 9 0.21
34 30 0.70
35 4 0.09
ACGTcount: A:0.51, C:0.02, G:0.17, T:0.30
Consensus pattern (33 bp):
TAAAATAAAAGTTAGTAAGTTAGTAAGAACAAG
Found at i:1167676 original size:201 final size:201
Alignment explanation
Indices: 1167331--1167733 Score: 603
Period size: 201 Copynumber: 2.0 Consensus size: 201
1167321 TAAAATTCGT
* * *
1167331 GGGGTTGTATCTAACCGTTTAACCCGGACCATAAATAATCTGGATCGTCCCCCAGGGCAGGTCAC
1 GGGGTTGTATCTAACCGTATAACCCGAACCATAAATAATCTGGATCATCCCCCAGGGCAGGTCAC
* * * *
1167396 CGCAAGGTCGTTGAATATTCGAATGTTAGAAAGTTATCGGGTTAGTTTGTGCAATAAAATAAAAT
66 CGCAAGGTCGTTGAATATTCGAAAGTTAGAAAATTAGCGAGTTAGTTTGTGCAATAAAATAAAAT
* ** * *
1167461 GTTAGTAAGTTAGTAAGAACGAT-AAAAATATAAAGTTAGTATGTTTGTATGAACAAGTAAAATA
131 GTTAGTAAGTTAGTAAGAACAATAAAAAATA-AAAGTTAGTATGTTAATATAAACAAATAAAATA
1167525 AAAGTTA
195 AAAGTTA
* * * *
1167532 GGGGTTGTTTTTAACTGTATAACCCGAACCATAAATAATGC-GGATCATCCCCCAGGGCGGGTCA
1 GGGGTTGTATCTAACCGTATAACCCGAACCATAAATAAT-CTGGATCATCCCCCAGGGCAGGTCA
* *
1167596 CCGCAAGGTCGTTGAATATTCTAAAGTTAGAAAATTAGCGAGTTAGTTTGTGCAATAAAATAAAG
65 CCGCAAGGTCGTTGAATATTCGAAAGTTAGAAAATTAGCGAGTTAGTTTGTGCAATAAAATAAAA
*
1167661 TGTTCGTAAGTTAGTAAGAACAATAAAAAATAAAAGTTAGTATGTTAATATAAACAAATAAAATA
130 TGTTAGTAAGTTAGTAAGAACAATAAAAAATAAAAGTTAGTATGTTAATATAAACAAATAAAATA
1167726 AAAGTTA
195 AAAGTTA
1167733 G
1 G
1167734 AATGTTAGTA
Statistics
Matches: 181, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
201 173 0.96
202 8 0.04
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (201 bp):
GGGGTTGTATCTAACCGTATAACCCGAACCATAAATAATCTGGATCATCCCCCAGGGCAGGTCAC
CGCAAGGTCGTTGAATATTCGAAAGTTAGAAAATTAGCGAGTTAGTTTGTGCAATAAAATAAAAT
GTTAGTAAGTTAGTAAGAACAATAAAAAATAAAAGTTAGTATGTTAATATAAACAAATAAAATAA
AAGTTA
Found at i:1169307 original size:120 final size:122
Alignment explanation
Indices: 1169083--1169339 Score: 358
Period size: 120 Copynumber: 2.1 Consensus size: 122
1169073 CAATTTAGAT
* *
1169083 ATAACTTGGTGTTGAAGATAACACTGCTCATCCATATTGAAGAGATATGGCCGCTTTCAGATAAA
1 ATAATTTGGTGTTGAAGACAACACTGCTCATCCATATTGAAGAGATATGGCCGCTTTCAGATAAA
* * *
1169148 TTATTTGTTGAAGATGACATTGTTCCTTCTCGTTGAGGAAATCAGGA-CAATCTGGAG
66 TTATTTATTGAAGATGACAATGTTCCTTCTCGTTAAGGAAATCA-GATCAATCTGGAG
* * * * * *
1169205 ATAATTTGGTGTTGAAGACAACTCTGCTCATCCGTGTTG-A-AGATCTGGTCGCTTTTAGATAAA
1 ATAATTTGGTGTTGAAGACAACACTGCTCATCCATATTGAAGAGATATGGCCGCTTTCAGATAAA
* *
1169268 TTGTTTATTGAAGATGACAATGTTCCTTCTTGTTAAGGAAATCAGATCAATCTGGAG
66 TTATTTATTGAAGATGACAATGTTCCTTCTCGTTAAGGAAATCAGATCAATCTGGAG
*
1169325 GTAATTTGGTGTTGA
1 ATAATTTGGTGTTGA
1169340 TGTTCTGGAA
Statistics
Matches: 120, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
119 2 0.02
120 83 0.69
121 1 0.01
122 34 0.28
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.35
Consensus pattern (122 bp):
ATAATTTGGTGTTGAAGACAACACTGCTCATCCATATTGAAGAGATATGGCCGCTTTCAGATAAA
TTATTTATTGAAGATGACAATGTTCCTTCTCGTTAAGGAAATCAGATCAATCTGGAG
Found at i:1169648 original size:139 final size:138
Alignment explanation
Indices: 1169429--1169856 Score: 378
Period size: 139 Copynumber: 3.1 Consensus size: 138
1169419 TGCTCCTTCA
* * * * *
1169429 CATTGAGGAGATCTGATCTGTGGACGACATTGTTCCTTCATGTTGAGGAAGTCTAGTC-TTTTTA
1 CATTGAGGAGATCTGGTCGGTGGACGACATTGTTCCTTCGTGTTGAGGATGTCTAGTCGTCTTTA
* ** * * * *
1169493 GAAGATAATTTCGAGACAACACGGTTCATTTGCGTTGAGGATGTATGGTTGTC-TGAGGATGGA-
66 G--GATAATTTGGAGACAACACGGTTCATACGCGATGAGAAAGTATGATTG-CATGAGGAT-GAC
*
1169556 ATTGATCCT-TCG
127 ACTGATCCTAT-G
** * * *
1169568 TGTTGAGGAGATTTGGTCGGTGGATGACATTTTTCCTTCGTGTTGAGGATGTCTAGTCGTCTTTA
1 CATTGAGGAGATCTGGTCGGTGGACGACATTGTTCCTTCGTGTTGAGGATGTCTAGTCGTCTTTA
* * * * *
1169633 GGCCTACTTTGGAGACAACACGCTTCCTACGCGATGAGAAAGTCTGATTGCATGAGGATGACACT
66 GG-ATAATTTGGAGACAACACGGTTCATACGCGATGAGAAAGTATGATTGCATGAGGATGACACT
*
1169698 GCTCCTATG
130 GATCCTATG
* * * *
1169707 CATTGAGGAGATCTGGTTGGTGGACGACATTGTTCCTACGTGATGAGGATGTCTAGCCGTCTTTA
1 CATTGAGGAGATCTGGTCGGTGGACGACATTGTTCCTTCGTGTTGAGGATGTCTAGTCGTCTTTA
* * * *** * * * * **
1169772 GGGATAATTTGTAGACAACACAGTTCCTACATAATGAGGAAGTCTGATTGCCTGAGAATGACGTT
66 -GGATAATTTGGAGACAACACGGTTCATACGCGATGAGAAAGTATGATTGCATGAGGATGACACT
*
1169837 GCTCCTATG
130 GATCCTATG
* *
1169846 CGTTGAAGAGA
1 CATTGAGGAGA
1169857 GCTAGTCATA
Statistics
Matches: 235, Mismatches: 48, Indels: 12
0.80 0.16 0.04
Matches are distributed among these distances:
138 4 0.02
139 222 0.94
140 9 0.04
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.32
Consensus pattern (138 bp):
CATTGAGGAGATCTGGTCGGTGGACGACATTGTTCCTTCGTGTTGAGGATGTCTAGTCGTCTTTA
GGATAATTTGGAGACAACACGGTTCATACGCGATGAGAAAGTATGATTGCATGAGGATGACACTG
ATCCTATG
Found at i:1170200 original size:104 final size:102
Alignment explanation
Indices: 1170022--1170259 Score: 279
Period size: 104 Copynumber: 2.3 Consensus size: 102
1170012 GGTGAGATAA
* *
1170022 AATTTTGTTTCAAGTGAAAC-ATTT-CAAATTTGTGTTTCATGGGAAAATTATCTCAATCAAGAA
1 AATTTTGTTTCAAGTGAAACAATTTCCAAATTTGTGTTTCATGGGAAAACTATCTCAAGCAAGAA
* *
1170085 GAAATTTGTTTTTAAGAAAAACAATCTCAA-ATGTTATC
66 GAAATTAGTTTTTAAGAAAAACAATCTCAACAAG--ATC
* * *
1170123 AATTTTGTTTCAAGTGAAACAATTTCCAATTTTTGTGTTTTGA-GGGAAAACTCTCTCAAGCAAG
1 AATTTTGTTTCAAGTGAAACAATTTCCAA-ATTTGTG-TTTCATGGGAAAACTATCTCAAGCAAG
* * * * *
1170187 ATGAAATTAGTTTTTTAGGAAAACTATTTCAAGCAAGATC
64 AAGAAATTAGTTTTTAAGAAAAACAATCTCAA-CAAGATC
*
1170227 AA-TTTGTTTCAAGTGAAACAATTTCAAAATTTG
1 AATTTTGTTTCAAGTGAAACAATTTCCAAATTTG
1170260 GGGAAAATTG
Statistics
Matches: 117, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
101 20 0.17
102 8 0.07
103 28 0.24
104 55 0.47
105 4 0.03
106 2 0.02
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.37
Consensus pattern (102 bp):
AATTTTGTTTCAAGTGAAACAATTTCCAAATTTGTGTTTCATGGGAAAACTATCTCAAGCAAGAA
GAAATTAGTTTTTAAGAAAAACAATCTCAACAAGATC
Found at i:1170662 original size:24 final size:23
Alignment explanation
Indices: 1170620--1170667 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
1170610 CAATGATGCA
*
1170620 TTTATGAATGACTACATGAATGTT
1 TTTATGAATGACAACATGAA-GTT
* *
1170644 TTTATGAATGTCAAGATGAAGTT
1 TTTATGAATGACAACATGAAGTT
1170667 T
1 T
1170668 ATTTTATGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.33, C:0.06, G:0.19, T:0.42
Consensus pattern (23 bp):
TTTATGAATGACAACATGAAGTT
Found at i:1173430 original size:13 final size:13
Alignment explanation
Indices: 1173412--1173454 Score: 70
Period size: 13 Copynumber: 3.4 Consensus size: 13
1173402 ACTTTCTTAT
1173412 TTTTTTTCTTTGC
1 TTTTTTTCTTTGC
1173425 TTTTTTTCTTTGC
1 TTTTTTTCTTTGC
*
1173438 -TTTTTTCTTTCC
1 TTTTTTTCTTTGC
1173450 TTTTT
1 TTTTT
1173455 GCCCCTTGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
12 11 0.39
13 17 0.61
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.79
Consensus pattern (13 bp):
TTTTTTTCTTTGC
Found at i:1178927 original size:34 final size:33
Alignment explanation
Indices: 1178867--1178936 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 33
1178857 TTAGTTTGTG
1178867 CAATAAAATAAAATGTTAGTAAGTTAGTAAGAA
1 CAATAAAATAAAATGTTAGTAAGTTAGTAAGAA
* * *
1178900 CAATAAAAATATAAA-GTTATTATGTTAGTATGAA
1 CAAT-AAAATA-AAATGTTAGTAAGTTAGTAAGAA
1178934 CAA
1 CAA
1178937 GTTTAGGGGG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 4 0.12
34 25 0.78
35 3 0.09
ACGTcount: A:0.53, C:0.04, G:0.13, T:0.30
Consensus pattern (33 bp):
CAATAAAATAAAATGTTAGTAAGTTAGTAAGAA
Found at i:1179078 original size:33 final size:32
Alignment explanation
Indices: 1179041--1179143 Score: 102
Period size: 33 Copynumber: 3.1 Consensus size: 32
1179031 AATTAGAAAA
* **
1179041 TTAGTTGGTTAGTTTGTGCAATAAAATAAAATG
1 TTAGTT-GTTAGTATGAACAATAAAATAAAATG
* *
1179074 TTAGTAAGTTAGTAAGAACAATAAATATAAAA-G
1 TTAGT-TGTTAGTATGAACAATAAA-ATAAAATG
1179107 TTAGTATGTTAGTATGAACAAATAAAATAAAAT-
1 TTAGT-TGTTAGTATGAAC-AATAAAATAAAATG
1179140 TTAG
1 TTAG
1179144 AATGTTATTA
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
33 47 0.80
34 12 0.20
ACGTcount: A:0.47, C:0.03, G:0.17, T:0.34
Consensus pattern (32 bp):
TTAGTTGTTAGTATGAACAATAAAATAAAATG
Found at i:1179086 original size:192 final size:190
Alignment explanation
Indices: 1178748--1179127 Score: 573
Period size: 192 Copynumber: 2.0 Consensus size: 190
1178738 AATTTAAAAG
* * * *
1178748 TTAGGGGGTTATTTTAACCGTTTAACCCGGACCATAAATAATGCAGATCGTCCCCCAGGGCGGGT
1 TTAGGGGGTTATTTTAACCATTTAACCCAGACCATAAATAATGCAGATCATCCCCCAGGGCAGGT
* *
1178813 CATCGCAAGGTCGTTGAATATTCAAATGTTAGAAAGTTAGCTGGTTAGTTTGTGCAATAAAATAA
66 CATCGCAAGGTCGTTGAATATTCAAATATTAGAAAATTAGCTGGTTAGTTTGTGCAATAAAATAA
*
1178878 AATGTTAGTAAGTTAGTAAGAACAATAAAAATATAAAGTTATTATGTTAGTATGAACAAGT
131 AATGTTAGTAAGTTAGTAAGAACAATAAAAATA-AAAGTTAGTATGTTAGTATGAACAAGT
* * ** * *
1178939 TTAGGGGGTTGTTTTTAACCATTTAACTCAGACCATAAATAATGTGGATCATCCCCCAGGGTATG
1 TTAGGGGGTT-ATTTTAACCATTTAACCCAGACCATAAATAATGCAGATCATCCCCCAGGGCAGG
* * *
1179004 TCATTGCAAGGTCGTTGAATATTTGAAA-ATTAGAAAATTAGTTGGTTAGTTTGTGCAATAAAAT
65 TCATCGCAAGGTCGTTGAATA-TTCAAATATTAGAAAATTAGCTGGTTAGTTTGTGCAATAAAAT
*
1179068 AAAATGTTAGTAAGTTAGTAAGAACAATAAATATAAAAGTTAGTATGTTAGTATGAACAA
129 AAAATGTTAGTAAGTTAGTAAGAACAATAAAAATAAAAGTTAGTATGTTAGTATGAACAA
1179128 ATAAAATAAA
Statistics
Matches: 170, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
191 34 0.20
192 131 0.77
193 5 0.03
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.32
Consensus pattern (190 bp):
TTAGGGGGTTATTTTAACCATTTAACCCAGACCATAAATAATGCAGATCATCCCCCAGGGCAGGT
CATCGCAAGGTCGTTGAATATTCAAATATTAGAAAATTAGCTGGTTAGTTTGTGCAATAAAATAA
AATGTTAGTAAGTTAGTAAGAACAATAAAAATAAAAGTTAGTATGTTAGTATGAACAAGT
Found at i:1179149 original size:33 final size:32
Alignment explanation
Indices: 1179059--1179155 Score: 115
Period size: 33 Copynumber: 2.9 Consensus size: 32
1179049 TTAGTTTGTG
1179059 CAATAAAATAAAATGTTAGTAA-GTTAGTAAGAA
1 CAATAAAATAAAAT-TTAG-AATGTTAGTAAGAA
* * *
1179092 CAATAAATATAAAAGTTAGTATGTTAGTATGAA
1 CAATAAA-ATAAAATTTAGAATGTTAGTAAGAA
*
1179125 CAAATAAAATAAAATTTAGAATGTTATTAAG
1 C-AATAAAATAAAATTTAGAATGTTAGTAAG
1179156 TTAGAAAAGT
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
32 1 0.02
33 41 0.76
34 12 0.22
ACGTcount: A:0.53, C:0.03, G:0.13, T:0.31
Consensus pattern (32 bp):
CAATAAAATAAAATTTAGAATGTTAGTAAGAA
Found at i:1180371 original size:2 final size:2
Alignment explanation
Indices: 1180364--1180430 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
1180354 AACACCTAAC
1180364 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
1180406 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1180431 GTTTGTGTGA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1181214 original size:59 final size:60
Alignment explanation
Indices: 1181148--1181284 Score: 136
Period size: 59 Copynumber: 2.3 Consensus size: 60
1181138 TAAAGTATAC
*
1181148 AAATGATCCCCTGACTATATAACACTGCTTTGTTGAGT-CATCG-CTTATTAAAAATTACA
1 AAATGATCCCCTGACTATATAACACTGCTTTGTTAAGTCCATCGAC-TATTAAAAATTACA
*** * *** * *
1181207 AAATGATCTATTGACTATATGATGTTGCTTTGTTAAGTCCTTCGACTATTAAAAGTTACA
1 AAATGATCCCCTGACTATATAACACTGCTTTGTTAAGTCCATCGACTATTAAAAATTACA
*
1181267 AAATGGTCACCC-GACTAT
1 AAATGATC-CCCTGACTAT
1181285 TCATTATATT
Statistics
Matches: 61, Mismatches: 14, Indels: 5
0.76 0.17 0.06
Matches are distributed among these distances:
59 30 0.49
60 30 0.49
61 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (60 bp):
AAATGATCCCCTGACTATATAACACTGCTTTGTTAAGTCCATCGACTATTAAAAATTACA
Found at i:1181617 original size:60 final size:60
Alignment explanation
Indices: 1181490--1181626 Score: 168
Period size: 60 Copynumber: 2.3 Consensus size: 60
1181480 ATAACCAGGT
* * * * * *
1181490 GACCATTTTGTAACTTTTAATAGTCGAGAGACTTAACAAAACAACATCCTATAGTCGATG
1 GACCATTTTGTAACTTTTAACAATCGAGAAACTCAACAAAACAACATCCTATAATCGAGG
* * * *
1181550 GATCATTTTGTAACTTTTAACAATCGAGAAACTCAACAAAGCATCATCCTATAATTGAGG
1 GACCATTTTGTAACTTTTAACAATCGAGAAACTCAACAAAACAACATCCTATAATCGAGG
1181610 GACCATTTGTGT-ACTTT
1 GACCATTT-TGTAACTTT
1181627 ATCCTAATTT
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
60 62 0.95
61 3 0.05
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (60 bp):
GACCATTTTGTAACTTTTAACAATCGAGAAACTCAACAAAACAACATCCTATAATCGAGG
Found at i:1185914 original size:108 final size:109
Alignment explanation
Indices: 1185711--1185932 Score: 317
Period size: 108 Copynumber: 2.0 Consensus size: 109
1185701 GTAACACCTT
1185711 TTTAATACTGATGGAGCCTTAGAAATCTAACGATAACAAAATAGGTTAATTACTTAATTTGTTAT
1 TTTAATACTGATGGAGCCTTAGAAATCTAACGATAACAAAATAGGTTAATTACTTAATTTGTTAT
* *
1185776 CAATATTATCAACATATTATGTAGAGCCTAAAATGTTATCAAAG
66 CAATATTATCAACATATTAGGTAGAACCTAAAATGTTATCAAAG
* * * *
1185820 TTTAA-ACTGATGG-GACCTTAGAAATCTGACGATTACAAAATATGTTAATTACTTATTTTGTTA
1 TTTAATACTGATGGAG-CCTTAGAAATCTAACGATAACAAAATAGGTTAATTACTTAATTTGTTA
* *
1185883 TTAATATTTTCAAC-TAATTAGGTA-ACACCTAAAATGTTATCAAAG
65 TCAATATTATCAACAT-ATTAGGTAGA-ACCTAAAATGTTATCAAAG
1185928 TTTAA
1 TTTAA
1185933 GTTGATAGAG
Statistics
Matches: 102, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
107 3 0.03
108 94 0.92
109 5 0.05
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (109 bp):
TTTAATACTGATGGAGCCTTAGAAATCTAACGATAACAAAATAGGTTAATTACTTAATTTGTTAT
CAATATTATCAACATATTAGGTAGAACCTAAAATGTTATCAAAG
Found at i:1185952 original size:108 final size:107
Alignment explanation
Indices: 1185711--1186010 Score: 304
Period size: 108 Copynumber: 2.8 Consensus size: 107
1185701 GTAACACCTT
* * *
1185711 TTTAATACTGATGGAGCCTTAGAAATCTAACGATAACAAAATAGGTTAATTACTTAATTTGTTAT
1 TTTAA-ACTGATGG-GACTTAGAAATCTAACGATAACAAAATATGTTAATTACTTATTTTGTTAT
* * *
1185776 CAATATTATCAACATATTATGTAGAGCCTAAAATGTTATCAAAG
64 AAATATTATCAACATATTAGGTAGAACCTAAAATGTTATCAAAG
* * *
1185820 TTTAAACTGATGGGACCTTAGAAATCTGACGATTACAAAATATGTTAATTACTTATTTTGTTATT
1 TTTAAACTGATGGGA-CTTAGAAATCTAACGATAACAAAATATGTTAATTACTTATTTTGTTATA
*
1185885 AATATTTTCAAC-TAATTAGGTA-ACACCTAAAATGTTATCAAAG
65 AATATTATCAACAT-ATTAGGTAGA-ACCTAAAATGTTATCAAAG
** * * * * *
1185928 TTTAAGTTGATAGAGTA-TTTGAAATTCCATA--ATAACAAAATATGTTACTTTCTTATTTTGTT
1 TTTAAACTGAT-G-GGACTTAGAAA-TCTA-ACGATAACAAAATATGTTAATTACTTATTTTGTT
* *
1185990 ATAAATAAATATTAACATATT
62 ATAAAT-ATTATCAACATATT
1186011 GTGTTGCGCC
Statistics
Matches: 160, Mismatches: 22, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
107 3 0.02
108 136 0.85
109 17 0.11
110 4 0.03
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (107 bp):
TTTAAACTGATGGGACTTAGAAATCTAACGATAACAAAATATGTTAATTACTTATTTTGTTATAA
ATATTATCAACATATTAGGTAGAACCTAAAATGTTATCAAAG
Found at i:1186652 original size:75 final size:75
Alignment explanation
Indices: 1186565--1186896 Score: 423
Period size: 75 Copynumber: 4.4 Consensus size: 75
1186555 GTAACGCCTA
* * * *
1186565 TTTAATATAATAGGTAGTGCCTATTTTATTTTACCGTTTACATTATTATTAACCTTTAAACAAAC
1 TTTAACATAATAGGTAGCGCTTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAAC
*
1186630 CGATAGTTAG
66 CGATAGGTAG
* * * **
1186640 TTTAACATAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAATAATCTTTAAACAAGT
1 TTTAACATAATAGGTAGCGCTTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAAC
*
1186705 CGGTAGGTAG
66 CGATAGGTAG
* * * *
1186715 TTTAACGTAATAGGTAGTGCTTATTTTATTTTACCTTTTACATTATTAGTAACCTTTAAATAAAC
1 TTTAACATAATAGGTAGCGCTTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAAC
* * *
1186780 TGATGGGTAT
66 CGATAGGTAG
* * ** * *
1186790 TTTAACGTAATAAGTAGCGCTTATTTTA-TTTATTGTTTACATTATTAGTAACCTTCAAACAAGC
1 TTTAACATAATAGGTAGCGCTTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAAC
*
1186854 CGATAGATAG
66 CGATAGGTAG
*
1186864 TTTAACATAATAGGTAGCGTTTATTTTATTTTA
1 TTTAACATAATAGGTAGCGCTTATTTTATTTTA
1186897 ACCGGTTAAG
Statistics
Matches: 220, Mismatches: 36, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
74 61 0.28
75 159 0.72
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (75 bp):
TTTAACATAATAGGTAGCGCTTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAAC
CGATAGGTAG
Found at i:1187762 original size:3 final size:3
Alignment explanation
Indices: 1187754--1187788 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
1187744 TTGACTTTTC
*
1187754 TTA TTA TTA TTT TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1187789 CTTAAGTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:1193937 original size:17 final size:16
Alignment explanation
Indices: 1193917--1193966 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 16
1193907 CGAGTGACGT
1193917 TTATATATATATATATA
1 TTAT-TATATATATATA
*
1193934 TTATTATTATATTTATA
1 TTATTA-TATATATATA
1193951 TTATTAT-TACTATATA
1 TTATTATATA-TATATA
1193967 CATAATAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
15 2 0.07
16 8 0.28
17 19 0.66
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (16 bp):
TTATTATATATATATA
Found at i:1204525 original size:34 final size:35
Alignment explanation
Indices: 1204459--1204559 Score: 129
Period size: 34 Copynumber: 3.0 Consensus size: 35
1204449 CCTTACAAAC
* * * *
1204459 TCCTTAG-TTTTTC-CGGGCTAAACTATAACCTTT
1 TCCTTAGCTTTTACACGGGATAAGCTAGAACCTTT
1204492 TCC-TAGCTTTTACACGGGATAAGCTAGAACC-TT
1 TCCTTAGCTTTTACACGGGATAAGCTAGAACCTTT
*
1204525 TCCTTAGCTTTTACACTGGATAAGCTAGAACCTTT
1 TCCTTAGCTTTTACACGGGATAAGCTAGAACCTTT
1204560 CCCCTTTACA
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
32 3 0.05
33 13 0.22
34 41 0.69
35 2 0.03
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.37
Consensus pattern (35 bp):
TCCTTAGCTTTTACACGGGATAAGCTAGAACCTTT
Found at i:1206444 original size:19 final size:20
Alignment explanation
Indices: 1206401--1206448 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1206391 CTAAATCCTT
*
1206401 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
1206421 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
1206440 TTTTCAAAA
1 TTTTCAAAA
1206449 GAAAATTGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:1207384 original size:16 final size:16
Alignment explanation
Indices: 1207363--1207399 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1207353 AACCTTTCCC
1207363 TAGCTTTTACACGGGA
1 TAGCTTTTACACGGGA
* *
1207379 TAGCTTTTTCACTGGA
1 TAGCTTTTACACGGGA
1207395 TAGCT
1 TAGCT
1207400 AAAACCTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.38
Consensus pattern (16 bp):
TAGCTTTTACACGGGA
Found at i:1218875 original size:15 final size:15
Alignment explanation
Indices: 1218857--1218909 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
1218847 TATATATATA
1218857 TATATTTTATATTTT
1 TATATTTTATATTTT
* *
1218872 TATATTAATTATATATA
1 TATATT--TTATATTTT
1218889 TA-ATATTTATATTTT
1 TATAT-TTTATATTTT
1218904 TATATT
1 TATATT
1218910 AATTATATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
15 16 0.53
16 4 0.13
17 10 0.33
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TATATTTTATATTTT
Found at i:1218886 original size:32 final size:33
Alignment explanation
Indices: 1218847--1218923 Score: 131
Period size: 32 Copynumber: 2.4 Consensus size: 33
1218837 CGATTATATA
1218847 TATATATATATATATTTTATATTTTTATATTAAT
1 TATATATATATATA-TTTATATTTTTATATTAAT
1218881 TATATATATA-ATATTTATATTTTTATATTAAT
1 TATATATATATATATTTATATTTTTATATTAAT
1218913 TATATA-ATATA
1 TATATATATATA
1218924 AACCCTAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
31 3 0.07
32 26 0.62
33 3 0.07
34 10 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (33 bp):
TATATATATATATATTTATATTTTTATATTAAT
Found at i:1218915 original size:17 final size:17
Alignment explanation
Indices: 1218863--1218917 Score: 69
Period size: 17 Copynumber: 3.4 Consensus size: 17
1218853 TATATATATT
1218863 TTATATTTTTATATTAA
1 TTATATTTTTATATTAA
* * *
1218880 TTATA--TATATAATAT
1 TTATATTTTTATATTAA
1218895 TTATATTTTTATATTAA
1 TTATATTTTTATATTAA
1218912 TTATAT
1 TTATAT
1218918 AATATAAACC
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
15 12 0.40
17 18 0.60
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTATATTTTTATATTAA
Found at i:1221453 original size:63 final size:63
Alignment explanation
Indices: 1221374--1221498 Score: 241
Period size: 63 Copynumber: 2.0 Consensus size: 63
1221364 AGCCTAGATC
*
1221374 AAGTCCTGTTGAGATGTGTGGATACTAAAGAAGCTAAATTGATTCTTGAAGAAGTACATGAGA
1 AAGTCCTGTTGAGATGTGTGGATACTAAAGAAGCTAAATCGATTCTTGAAGAAGTACATGAGA
1221437 AAGTCCTGTTGAGATGTGTGGATACTAAAGAAGCTAAATCGATTCTTGAAGAAGTACATGAG
1 AAGTCCTGTTGAGATGTGTGGATACTAAAGAAGCTAAATCGATTCTTGAAGAAGTACATGAG
1221499 GGAATATGTG
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.36, C:0.10, G:0.26, T:0.28
Consensus pattern (63 bp):
AAGTCCTGTTGAGATGTGTGGATACTAAAGAAGCTAAATCGATTCTTGAAGAAGTACATGAGA
Found at i:1223110 original size:3 final size:3
Alignment explanation
Indices: 1223102--1223190 Score: 60
Period size: 3 Copynumber: 30.3 Consensus size: 3
1223092 TTTATATATA
* * *
1223102 TAT TAT TAT TA- TAT T-T ATAT TAT TAT TA- TAT ATAT AAT AAA TAT
1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT -TAT TAT TAT TAT
* * * * *
1223146 AAT GAA TAA TAT TA- TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1223191 CTTAATCATT
Statistics
Matches: 69, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
2 7 0.10
3 58 0.84
4 4 0.06
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (3 bp):
TAT
Found at i:1224218 original size:15 final size:15
Alignment explanation
Indices: 1224198--1224233 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
1224188 AAAAGCATGT
1224198 TTTAGTATATTTTAA
1 TTTAGTATATTTTAA
1224213 TTTAGTATATTTTAA
1 TTTAGTATATTTTAA
1224228 TTTAGT
1 TTTAGT
1224234 TTTCAAGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (15 bp):
TTTAGTATATTTTAA
Found at i:1225208 original size:13 final size:13
Alignment explanation
Indices: 1225177--1225201 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1225167 AAGAGGGAGT
1225177 AATTTTTTAAAAC
1 AATTTTTTAAAAC
1225190 AATTTTTTAAAA
1 AATTTTTTAAAA
1225202 TATTTTTATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
AATTTTTTAAAAC
Found at i:1225569 original size:21 final size:20
Alignment explanation
Indices: 1225514--1225573 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 20
1225504 TTATGGATCA
*
1225514 ATCCCTTCACAAAAAGATTG
1 ATCCCTTCACAAAAGGATTG
*
1225534 ATCCC-TCGAGGAAAAGGATTG
1 ATCCCTTC-A-CAAAAGGATTG
1225555 ATCCCTTCACCAAAAGGAT
1 ATCCCTTCA-CAAAAGGAT
1225574 CAATCCCTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
19 2 0.06
20 6 0.18
21 23 0.70
22 2 0.06
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.22
Consensus pattern (20 bp):
ATCCCTTCACAAAAGGATTG
Found at i:1225579 original size:21 final size:20
Alignment explanation
Indices: 1225508--1225581 Score: 60
Period size: 21 Copynumber: 3.6 Consensus size: 20
1225498 AGCAAGTTAT
1225508 GGATCAATCCCTTCACAAAA
1 GGATCAATCCCTTCACAAAA
* ** *
1225528 AGATTGATCCC-TCGAGGAAAA
1 GGATCAATCCCTTC-A-CAAAA
**
1225549 GGATTGATCCCTTCACCAAAA
1 GGATCAATCCCTTCA-CAAAA
1225570 GGATCAATCCCT
1 GGATCAATCCCT
1225582 CAATGAAAAG
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
19 2 0.05
20 9 0.21
21 29 0.69
22 2 0.05
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (20 bp):
GGATCAATCCCTTCACAAAA
Found at i:1225582 original size:42 final size:41
Alignment explanation
Indices: 1225514--1225600 Score: 102
Period size: 42 Copynumber: 2.1 Consensus size: 41
1225504 TTATGGATCA
** * * *
1225514 ATCCCTTCACAAAAAGATTGATCCCTCGAGGAAAAGGATTG
1 ATCCCTTCACAAAAAGATCAATCCCTCAAGGAAAAGAATCG
* *
1225555 ATCCCTTCACCAAAAGGATCAATCCCTCAATGAAAAGAATCG
1 ATCCCTTCA-CAAAAAGATCAATCCCTCAAGGAAAAGAATCG
1225597 ATCC
1 ATCC
1225601 ATTTCCCTAA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 9 0.24
42 29 0.76
ACGTcount: A:0.38, C:0.26, G:0.15, T:0.21
Consensus pattern (41 bp):
ATCCCTTCACAAAAAGATCAATCCCTCAAGGAAAAGAATCG
Found at i:1227740 original size:20 final size:20
Alignment explanation
Indices: 1227702--1227740 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1227692 AATTAAATAT
* *
1227702 CAATTAGACACCTAAATTAC
1 CAATTAGAAAACTAAATTAC
*
1227722 CAATTAGAAAACTATATTA
1 CAATTAGAAAACTAAATTA
1227741 ATTTGTTGCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.49, C:0.18, G:0.05, T:0.28
Consensus pattern (20 bp):
CAATTAGAAAACTAAATTAC
Found at i:1228304 original size:15 final size:15
Alignment explanation
Indices: 1228270--1228313 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
1228260 TACAAAATTC
1228270 TAATT-TTTTAAAAA
1 TAATTATTTTAAAAA
*
1228284 TAAATTATTTTAATAA
1 T-AATTATTTTAAAAA
1228300 TAATTATTTATAAA
1 TAATTATTT-TAAA
1228314 TTTTATCTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 1 0.04
15 12 0.48
16 12 0.48
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATTATTTTAAAAA
Found at i:1237373 original size:23 final size:24
Alignment explanation
Indices: 1237342--1237386 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
1237332 AAGTGACTAA
1237342 AAAATAAAAGAA-AAAATTTAAAAG
1 AAAATAAAA-AACAAAATTTAAAAG
*
1237366 AAAA-AAAAAACATAATTTAAA
1 AAAATAAAAAACAAAATTTAAA
1237387 GAAGGCATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 2 0.11
23 13 0.68
24 4 0.21
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.18
Consensus pattern (24 bp):
AAAATAAAAAACAAAATTTAAAAG
Found at i:1238797 original size:147 final size:144
Alignment explanation
Indices: 1238592--1238882 Score: 494
Period size: 147 Copynumber: 2.0 Consensus size: 144
1238582 AAAATAATTA
1238592 AAAAACCTATTTTTTTCAAATCTTAAAAAAACAAAACTTGTAAAAATTTCATTTTAATCCC-TTG
1 AAAAACCTATTTTTTTCAAATCTTAAAAAAACAAAACTTGTAAAAATTTCATTTTAATCCCTTTG
** *
1238656 TCACACCAGTTGCCACCAACACAGTCAATCGGCCGAACACCCAATGAATTGTGATTAGCTAACTA
66 TCACACCA-TTGCCACCAACACAGTCAATCGGCCGAACACCCAACAAATTGTGATCAGCTAACTA
1238721 CCCACAACCAAAACC
130 CCCACAACCAAAACC
*
1238736 AAAAACCTATTTTTTTCAAATCTTAAAAAAAACCAAAAACTTTTAAAAATTTCATTTTAATCCCT
1 AAAAACCTATTTTTTTCAAATCTT-AAAAAAA-C-AAAACTTGTAAAAATTTCATTTTAATCCCT
*
1238801 TTGTCACACCATTGCCACCAACACCGTCAATCGGCCGAACACCCAACAAATTGTGATCAGCTAAC
63 TTGTCACACCATTGCCACCAACACAGTCAATCGGCCGAACACCCAACAAATTGTGATCAGCTAAC
1238866 TACCCACAACCAAAACC
128 TACCCACAACCAAAACC
1238883 CCATACTTTC
Statistics
Matches: 138, Mismatches: 5, Indels: 5
0.93 0.03 0.03
Matches are distributed among these distances:
144 24 0.17
145 7 0.05
146 1 0.01
147 95 0.69
148 11 0.08
ACGTcount: A:0.40, C:0.27, G:0.07, T:0.25
Consensus pattern (144 bp):
AAAAACCTATTTTTTTCAAATCTTAAAAAAACAAAACTTGTAAAAATTTCATTTTAATCCCTTTG
TCACACCATTGCCACCAACACAGTCAATCGGCCGAACACCCAACAAATTGTGATCAGCTAACTAC
CCACAACCAAAACC
Found at i:1239317 original size:19 final size:18
Alignment explanation
Indices: 1239293--1239368 Score: 64
Period size: 18 Copynumber: 3.9 Consensus size: 18
1239283 CGAGACATAA
*
1239293 TTTAAATACTTATTTTTAT
1 TTTAAAT-CTAATTTTTAT
1239312 TTTAAATCTAATTTTT-T
1 TTTAAATCTAATTTTTAT
*
1239329 TAACGGTTAAATACTTATTTTTAT
1 T-----TTAAAT-CTAATTTTTAT
1239353 TTTAAATCTAATTTTT
1 TTTAAATCTAATTTTT
1239369 TTAACGGTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 15
0.72 0.05 0.23
Matches are distributed among these distances:
17 2 0.04
18 16 0.34
19 13 0.28
22 6 0.13
23 8 0.17
24 2 0.04
ACGTcount: A:0.32, C:0.07, G:0.03, T:0.59
Consensus pattern (18 bp):
TTTAAATCTAATTTTTAT
Found at i:1239330 original size:20 final size:20
Alignment explanation
Indices: 1239305--1239371 Score: 66
Period size: 20 Copynumber: 3.3 Consensus size: 20
1239295 TAAATACTTA
1239305 TTTTTATTTTAAATCTAATT
1 TTTTTATTTTAAATCTAATT
** *
1239325 TTTTTAACGGTTAAATACT--TA
1 TTTTT-A-TTTTAAAT-CTAATT
1239346 TTTTTATTTTAAATCTAATT
1 TTTTTATTTTAAATCTAATT
1239366 TTTTTA
1 TTTTTA
1239372 ACGGTTATGA
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
18 2 0.06
19 6 0.17
20 13 0.36
21 7 0.19
22 6 0.17
23 2 0.06
ACGTcount: A:0.30, C:0.06, G:0.03, T:0.61
Consensus pattern (20 bp):
TTTTTATTTTAAATCTAATT
Found at i:1239340 original size:22 final size:22
Alignment explanation
Indices: 1239313--1239378 Score: 70
Period size: 22 Copynumber: 3.1 Consensus size: 22
1239303 TATTTTTATT
1239313 TTAAATCTAATTTTTTTAACGG
1 TTAAATCTAATTTTTTTAACGG
*
1239335 TTAAATACTTATTTTTATT-----
1 TTAAAT-CTAATTTTT-TTAACGG
1239354 TTAAATCTAATTTTTTTAACGG
1 TTAAATCTAATTTTTTTAACGG
1239376 TTA
1 TTA
1239379 TGACATCGTG
Statistics
Matches: 35, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
17 2 0.06
18 8 0.23
19 6 0.17
22 9 0.26
23 8 0.23
24 2 0.06
ACGTcount: A:0.32, C:0.08, G:0.06, T:0.55
Consensus pattern (22 bp):
TTAAATCTAATTTTTTTAACGG
Found at i:1239346 original size:41 final size:41
Alignment explanation
Indices: 1239294--1239378 Score: 170
Period size: 41 Copynumber: 2.1 Consensus size: 41
1239284 GAGACATAAT
1239294 TTAAATACTTATTTTTATTTTAAATCTAATTTTTTTAACGG
1 TTAAATACTTATTTTTATTTTAAATCTAATTTTTTTAACGG
1239335 TTAAATACTTATTTTTATTTTAAATCTAATTTTTTTAACGG
1 TTAAATACTTATTTTTATTTTAAATCTAATTTTTTTAACGG
1239376 TTA
1 TTA
1239379 TGACATCGTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.56
Consensus pattern (41 bp):
TTAAATACTTATTTTTATTTTAAATCTAATTTTTTTAACGG
Found at i:1239369 original size:19 final size:19
Alignment explanation
Indices: 1239305--1239369 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
1239295 TAAATACTTA
1239305 TTTTTATTTTAAATCTAATT
1 TTTTTATTTTAAATCTAA-T
** *
1239325 TTTTTAACGGTTAAATACTTA-
1 TTTTT-A-TTTTAAAT-CTAAT
1239346 TTTTTATTTTAAATCTAAT
1 TTTTTATTTTAAATCTAAT
1239365 TTTTT
1 TTTTT
1239370 TAACGGTTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 9
0.70 0.12 0.18
Matches are distributed among these distances:
18 3 0.09
19 11 0.31
20 6 0.17
21 6 0.17
22 6 0.17
23 3 0.09
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (19 bp):
TTTTTATTTTAAATCTAAT
Found at i:1252106 original size:17 final size:18
Alignment explanation
Indices: 1252075--1252119 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
1252065 TAACAATTCT
*
1252075 TTAACTTCA-TTCCTTTA
1 TTAATTTCATTTCCTTTA
*
1252092 TT-ATTTCATTTCCTTTC
1 TTAATTTCATTTCCTTTA
1252109 TTAATTTCATT
1 TTAATTTCATT
1252120 ATTCTATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 5 0.21
17 11 0.46
18 8 0.33
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (18 bp):
TTAATTTCATTTCCTTTA
Found at i:1257502 original size:23 final size:23
Alignment explanation
Indices: 1257472--1257516 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1257462 TCAATGGAAG
* *
1257472 ATGGATGATGGTGTTGAAGTTGA
1 ATGGATGACGGTGATGAAGTTGA
1257495 ATGGATGACGGTGATGAAGTTG
1 ATGGATGACGGTGATGAAGTTG
1257517 TTTCTCAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.02, G:0.40, T:0.31
Consensus pattern (23 bp):
ATGGATGACGGTGATGAAGTTGA
Found at i:1260771 original size:13 final size:13
Alignment explanation
Indices: 1260753--1260778 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1260743 AGTCTTGTGC
1260753 ATGTGCTAGGTGT
1 ATGTGCTAGGTGT
1260766 ATGTGCTAGGTGT
1 ATGTGCTAGGTGT
1260779 GTCCCATGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.38, T:0.38
Consensus pattern (13 bp):
ATGTGCTAGGTGT
Found at i:1275700 original size:11 final size:11
Alignment explanation
Indices: 1275684--1275711 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1275674 AAAAATGGCT
1275684 AAGAAAGGATG
1 AAGAAAGGATG
1275695 AAGAAAGGATG
1 AAGAAAGGATG
1275706 AAGAAA
1 AAGAAA
1275712 AGAAGGAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.32, T:0.07
Consensus pattern (11 bp):
AAGAAAGGATG
Found at i:1276490 original size:20 final size:21
Alignment explanation
Indices: 1276462--1276509 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
1276452 TAGACTTGTT
* * *
1276462 AGCTTAAATTGAGCTAATG-G
1 AGCTGAAATGGAGCTAAGGTG
1276482 AGCTGAAATGGAGCTAAGGTG
1 AGCTGAAATGGAGCTAAGGTG
1276503 AGCTGAA
1 AGCTGAA
1276510 TTCACCTAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.35, C:0.10, G:0.31, T:0.23
Consensus pattern (21 bp):
AGCTGAAATGGAGCTAAGGTG
Found at i:1278186 original size:31 final size:31
Alignment explanation
Indices: 1278151--1278214 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
1278141 TGCCTTGGGG
1278151 CCTATGGGCCTACCCAAGGGTATCCTTAGGC
1 CCTATGGGCCTACCCAAGGGTATCCTTAGGC
*
1278182 CCTATGGGCCTACCTAAGGGTATCCTTAGGC
1 CCTATGGGCCTACCCAAGGGTATCCTTAGGC
1278213 CC
1 CC
1278215 GTAAGGTCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.19, C:0.33, G:0.25, T:0.23
Consensus pattern (31 bp):
CCTATGGGCCTACCCAAGGGTATCCTTAGGC
Found at i:1301765 original size:41 final size:40
Alignment explanation
Indices: 1301590--1302044 Score: 394
Period size: 41 Copynumber: 11.2 Consensus size: 40
1301580 TAGCGGCATT
* * *
1301590 TTTAGCGGCGTTTTTAGAACAAACGCCGCTAAATACTTGTAC
1 TTTAGTGGCGTTTTTA-TACAAACGCCGCTAAAGAC-TGTAC
* *
1301632 TTTAGTGTCGTTTTT-TACAAATGCCGCTAAAGACTGT-C
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTGTAC
* * * * *
1301670 TTTAGTGGCATATTTAGAACAAACGCCGCTAAATACTCATAC
1 TTTAGTGGCGTTTTTA-TACAAACGCCGCTAAAGACT-GTAC
* *
1301712 TTTAATGGCGTTTTTAATACAAACGCCGATAAAGACTGTAC
1 TTTAGTGGCGTTTTT-ATACAAACGCCGCTAAAGACTGTAC
* * * *
1301753 TTTAGCGACGTTTTTATACAAACGCCGTTATAGACTCGTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACT-GTAC
* *
1301794 TTTAGTGGTGTTTTTATACAAACGCCGCTAAAGACTTATAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGAC-TGTAC
* * * * *
1301835 TTTAGTGGC-TTTTTATATAAATGTCGCTAAAGACTCATAT
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACT-GTAC
* * * *
1301875 TTTAGTGGCGTTTTAATACAAACGTCGCTATAGACTAGTCC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACT-GTAC
* * * *
1301916 TTTAGTGGAGTTTTTATATAAACGCCGCTATAGACTCTAAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTGT-AC
* * * ** * * *
1301957 TTTAGTGGCATTTTTTTACAAACACCGCTGTACACTCATGC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACT-GTAC
* * * *
1301998 TTTAGTGGCATTTTTATACAAACGCCGTTATAGACTCGTGC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACT-GTAC
1302039 TTTAGT
1 TTTAGT
1302045 TGGAGCCCCT
Statistics
Matches: 338, Mismatches: 64, Indels: 23
0.80 0.15 0.05
Matches are distributed among these distances:
38 13 0.04
39 4 0.01
40 87 0.26
41 188 0.56
42 45 0.13
43 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (40 bp):
TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTGTAC
Found at i:1301865 original size:163 final size:162
Alignment explanation
Indices: 1301590--1302034 Score: 481
Period size: 163 Copynumber: 2.7 Consensus size: 162
1301580 TAGCGGCATT
* * * * * *
1301590 TTTAGCGGCGTTTTTAGAACAAACGCCGCTAAATACTTGTACTTTAGT-GTCGTTTTTTACAAAT
1 TTTAGCGACGTTTTTA-TACAAACGCCGCTATAGACTCGTACTTTAGTGGT-GTTTTTTACAAAC
* * * *
1301654 GCCGCTAAAGAC-TGTCTTTAGTGGCATATTTAGAACAAACGCCGCTAAATACTCATACTTTAAT
64 GCCGCTAAAGACTTATCTTTAGTGGCATTTTTA-TACAAACGCCGCTAAAGACTCATACTTTAAT
1301718 GGCGTTTTTAATACAAACGCCGATAAAGACT-GTAC
128 GGCG-TTTTAATACAAACGCCGATAAAGACTAGTAC
*
1301753 TTTAGCGACGTTTTTATACAAACGCCGTTATAGACTCGTACTTTAGTGGTGTTTTTATACAAACG
1 TTTAGCGACGTTTTTATACAAACGCCGCTATAGACTCGTACTTTAGTGGTGTTTTT-TACAAACG
* * * * *
1301818 CCGCTAAAGACTTATACTTTAGTGGC-TTTTTATATAAATGTCGCTAAAGACTCATATTTTAGTG
65 CCGCTAAAGACTTAT-CTTTAGTGGCATTTTTATACAAACGCCGCTAAAGACTCATACTTTAATG
* * * *
1301882 GCGTTTTAATACAAACGTCGCTATAGACTAGTCC
129 GCGTTTTAATACAAACGCCGATAAAGACTAGTAC
* *
1301916 TTTAGTGGA-GTTTTTATATAAACGCCGCTATAGACTC-TAACTTTAGTGGCAT-TTTTTTACAA
1 TTTAG-CGACGTTTTTATACAAACGCCGCTATAGACTCGT-ACTTTAGTGG--TGTTTTTTACAA
* ** * * * *
1301978 ACACCGCTGTACACTCATGCTTTAGTGGCATTTTTATACAAACGCCGTTATAGACTC
62 ACGCCGCTAAAGACTTAT-CTTTAGTGGCATTTTTATACAAACGCCGCTAAAGACTC
1302035 GTGCTTTAGT
Statistics
Matches: 238, Mismatches: 34, Indels: 19
0.82 0.12 0.07
Matches are distributed among these distances:
162 56 0.24
163 135 0.57
164 36 0.15
165 11 0.05
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (162 bp):
TTTAGCGACGTTTTTATACAAACGCCGCTATAGACTCGTACTTTAGTGGTGTTTTTTACAAACGC
CGCTAAAGACTTATCTTTAGTGGCATTTTTATACAAACGCCGCTAAAGACTCATACTTTAATGGC
GTTTTAATACAAACGCCGATAAAGACTAGTAC
Found at i:1305559 original size:65 final size:65
Alignment explanation
Indices: 1305455--1305584 Score: 251
Period size: 65 Copynumber: 2.0 Consensus size: 65
1305445 AGATACTTGT
*
1305455 TTCGAAAAGGTTCCTACAATCCCAACCAATTAAGGAGGAACTCCAAAGGAGCAATATCTTTCACA
1 TTCGAAAAGGTGCCTACAATCCCAACCAATTAAGGAGGAACTCCAAAGGAGCAATATCTTTCACA
1305520 TTCGAAAAGGTGCCTACAATCCCAACCAATTAAGGAGGAACTCCAAAGGAGCAATATCTTTCACA
1 TTCGAAAAGGTGCCTACAATCCCAACCAATTAAGGAGGAACTCCAAAGGAGCAATATCTTTCACA
1305585 CAAGGTGCCA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.38, C:0.25, G:0.16, T:0.21
Consensus pattern (65 bp):
TTCGAAAAGGTGCCTACAATCCCAACCAATTAAGGAGGAACTCCAAAGGAGCAATATCTTTCACA
Found at i:1311403 original size:24 final size:25
Alignment explanation
Indices: 1311351--1311411 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 25
1311341 TTTGTGAATA
*
1311351 CCAAAAGTCATGACTATTGGTTCTT
1 CCAAAAGTCATGACTATTAGTTCTT
*
1311376 -CAAAAGTCAT-ATCTTTTAGTT-TT
1 CCAAAAGTCATGA-CTATTAGTTCTT
*
1311399 CCAAAAGCCATGA
1 CCAAAAGTCATGA
1311412 TTTTTGATTC
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
23 3 0.10
24 26 0.87
25 1 0.03
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34
Consensus pattern (25 bp):
CCAAAAGTCATGACTATTAGTTCTT
Found at i:1311727 original size:85 final size:86
Alignment explanation
Indices: 1311627--1311791 Score: 224
Period size: 85 Copynumber: 1.9 Consensus size: 86
1311617 TGGTAACAAA
* *
1311627 AAACGCCGCAATAGGTAACGATATATAACGGCGTTTGTCCAAAAAACGCCGCAATAGGTGTTGAT
1 AAACGCCGCAATAGGTAACGAGATATAACGGCGTTTGTCCAAAAAACGCCGCAATAGGTGTTGAG
*
1311692 ATTTGGCGGCGTTTTTCCTAC
66 ATTTAGCGGCGTTTTTCCTAC
*** * * * * *
1311713 AAACG-CGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCTATAAACGCCGCAATAGGTGTTGAG
1 AAACGCCGCAATAGGTAACGAGATATAACGGCGTTTGTCCAAAAAACGCCGCAATAGGTGTTGAG
1311777 ATTTAGCGGCGTTTT
66 ATTTAGCGGCGTTTT
1311792 CCCCAAAAAT
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
85 63 0.93
86 5 0.07
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (86 bp):
AAACGCCGCAATAGGTAACGAGATATAACGGCGTTTGTCCAAAAAACGCCGCAATAGGTGTTGAG
ATTTAGCGGCGTTTTTCCTAC
Found at i:1311743 original size:42 final size:43
Alignment explanation
Indices: 1311625--1311851 Score: 258
Period size: 43 Copynumber: 5.3 Consensus size: 43
1311615 TTTGGTAACA
*** * * * * *
1311625 AAAAACGCCGCAATAGGTAACGATATATAACGGCGTTTGTCCA
1 AAAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCC
* * *
1311668 AAAAACGCCGCAATAGGTGTTGATATTTGGCGGCGTTTTTCCT
1 AAAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCC
* *
1311711 ACAAACG-CGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCT
1 AAAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCC
* *
1311753 ATAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTCCCC
1 AAAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCC
* * * *
1311796 AAAAATGCCGTAATAGGTGTTGAGATTGAGCGGCATTTTTCCC
1 AAAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCC
* *
1311839 ACAAACACCGCAA
1 AAAAACGCCGCAA
1311852 AAGATCTGGT
Statistics
Matches: 159, Mismatches: 24, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
42 39 0.25
43 120 0.75
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.27
Consensus pattern (43 bp):
AAAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCC
Found at i:1311850 original size:86 final size:85
Alignment explanation
Indices: 1311670--1311851 Score: 247
Period size: 85 Copynumber: 2.1 Consensus size: 85
1311660 TTTGTCCAAA
* * * * *
1311670 AAACGCCGCAATAGGTGTTGATATTTGGCGGCGTTTTTCCTACAAACGCGCAATAGGTGTTGAGA
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTCCCCAAAAACGCGCAATAGGTGTTGAGA
* * * *
1311735 TTTAGCGGCGTTTTTCCTAT
66 TTGAGCGGCATTTTTCCCAC
* *
1311755 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTCCCCAAAAATGCCGTAATAGGTGTTGAG
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTCCCCAAAAACG-CGCAATAGGTGTTGAG
1311820 ATTGAGCGGCATTTTTCCCAC
65 ATTGAGCGGCATTTTTCCCAC
*
1311841 AAACACCGCAA
1 AAACGCCGCAA
1311852 AAGATCTGGT
Statistics
Matches: 84, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
85 42 0.50
86 42 0.50
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.29
Consensus pattern (85 bp):
AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTCCCCAAAAACGCGCAATAGGTGTTGAGA
TTGAGCGGCATTTTTCCCAC
Found at i:1311869 original size:128 final size:128
Alignment explanation
Indices: 1311627--1311877 Score: 276
Period size: 128 Copynumber: 2.0 Consensus size: 128
1311617 TGGTAACAAA
* *
1311627 AAACGCCGCAATAGGTAACGATATATAACGGCGTTTGTCCAAAAAACGCCGCAATAGGTGTTGAT
1 AAACGCCGCAATAGGTAACGAGATATAACGGCGTTTGTCCAAAAAACGCCGCAATAGGTGTTGAG
* * * * * * * *
1311692 ATTTGGCGGCGTTTTTCCTACAAACGCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCTAT
66 ATTTGGCGGCATTTTTCCCACAAACCCGCAAAAGATGCTGAGATATAGCGGCATTTTTCCTAT
*** * * * * *
1311755 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTT-TCCCCAAAAATGCCGTAATAGGTGTTGA
1 AAACGCCGCAATAGGTAACGAGATATAACGGCGTTTGT-CCAAAAAACGCCGCAATAGGTGTTGA
1311819 GA-TTGAGCGGCATTTTTCCCACAAACACCGCAAAAGAT-CTG-GTATATAGCGGCATTTTT
65 GATTTG-GCGGCATTTTTCCCACAAAC-CCGCAAAAGATGCTGAG-ATATAGCGGCATTTTT
1311878 AGAACAAACG
Statistics
Matches: 101, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
127 5 0.05
128 88 0.87
129 8 0.08
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (128 bp):
AAACGCCGCAATAGGTAACGAGATATAACGGCGTTTGTCCAAAAAACGCCGCAATAGGTGTTGAG
ATTTGGCGGCATTTTTCCCACAAACCCGCAAAAGATGCTGAGATATAGCGGCATTTTTCCTAT
Found at i:1312072 original size:21 final size:21
Alignment explanation
Indices: 1312046--1312104 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
1312036 ATTTTCCAAT
*
1312046 AAACTTGACATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
* *
1312067 AAACTTAAAATCCATAACAAG
1 AAACTTGAAATCCATAACAAC
**
1312088 AAAAATGAAATCCATAA
1 AAACTTGAAATCCATAA
1312105 TAATAAATCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.56, C:0.20, G:0.05, T:0.19
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:1314104 original size:41 final size:41
Alignment explanation
Indices: 1314037--1314357 Score: 351
Period size: 41 Copynumber: 7.8 Consensus size: 41
1314027 TTGTAAACTT
* * *
1314037 GCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATA
1 GCGGCGTTTGTATA-A-AAACGCCACTAAAGTACAAGTCTATA
* * *
1314080 GCGGCGTTTGAATAAAAACGCCACTAAAGTACGAGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACAAGTCTATA
* * ** *
1314121 GC-GCGTTTTTATAAAAATGCCACTAAAGTATGAGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACAAGTCTATA
* * ** *
1314161 GCGGCGTTTGTATAAAAATGCCACTAAATTATGAGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACAAGTCTATA
* * * *
1314202 GCGGCGTTTATAAACACAAACGCCACTATAGTACATA-TGTATA
1 GCGGCGTTTGTATA-A-AAACGCCACTAAAGTACA-AGTCTATA
* *
1314245 ACGGCGTTTGTATAAAAACGCCACTAAAGTACAATTCTATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACAAGTCTATA
** *
1314286 GCGGCGTTTGTATAAAAATTCCACTAAATTACAAGTCT-TA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACAAGTCTATA
1314326 GCGGCGTTTGTATAAAAACGCCACTAAAGTAC
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTAC
1314358 TACTCTTTTG
Statistics
Matches: 239, Mismatches: 34, Indels: 13
0.84 0.12 0.05
Matches are distributed among these distances:
40 68 0.28
41 127 0.53
42 3 0.01
43 40 0.17
44 1 0.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (41 bp):
GCGGCGTTTGTATAAAAACGCCACTAAAGTACAAGTCTATA
Found at i:1314288 original size:125 final size:122
Alignment explanation
Indices: 1314037--1314357 Score: 353
Period size: 125 Copynumber: 2.6 Consensus size: 122
1314027 TTGTAAACTT
* * * * * *
1314037 GCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAGCGGCGTTTGA-ATAAAAACGC
1 GCGGCGTTTGTATA-A-AAATGCCACTAAATTACAAGTCT-TAGCGGCGTTT-ATAAAAAAACGC
* * * * ** *
1314101 CACTAAAGTACGAGTCT-T-TAGC-GCGTTTTTATAAAAATGCCACTAAAGTATGAGTCTTTA
62 CACTAAAGTAC-A-TATGTATAACGGCGTTTGTATAAAAACGCCACTAAAGTACAAGTCTATA
**
1314161 GCGGCGTTTGTATAAAAATGCCACTAAATTATGAGTCTTTAGCGGCGTTTATAAACACAAACGCC
1 GCGGCGTTTGTATAAAAATGCCACTAAATTACAAGTC-TTAGCGGCGTTTATAAA-A-AAACGCC
* *
1314226 ACTATAGTACATATGTATAACGGCGTTTGTATAAAAACGCCACTAAAGTACAATTCTATA
63 ACTAAAGTACATATGTATAACGGCGTTTGTATAAAAACGCCACTAAAGTACAAGTCTATA
* * *
1314286 GCGGCGTTTGTATAAAAATTCCACTAAATTACAAGTCTTAGCGGCGTTTGTATAAAAACGCCACT
1 GCGGCGTTTGTATAAAAATGCCACTAAATTACAAGTCTTAGCGGCGTTTATAAAAAAACGCCACT
1314351 AAAGTAC
66 AAAGTAC
1314358 TACTCTTTTG
Statistics
Matches: 167, Mismatches: 23, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
121 1 0.01
122 47 0.28
123 6 0.04
124 47 0.28
125 66 0.40
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (122 bp):
GCGGCGTTTGTATAAAAATGCCACTAAATTACAAGTCTTAGCGGCGTTTATAAAAAAACGCCACT
AAAGTACATATGTATAACGGCGTTTGTATAAAAACGCCACTAAAGTACAAGTCTATA
Found at i:1314329 original size:165 final size:165
Alignment explanation
Indices: 1314037--1314353 Score: 494
Period size: 165 Copynumber: 1.9 Consensus size: 165
1314027 TTGTAAACTT
* *
1314037 GCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAGCGGCGTTTGAATAAAAACGCC
1 GCGGCGTTTATAAACACAAACGCCACTATAGTACAAGTGTATAACGGCGTTTGAATAAAAACGCC
* * * **
1314102 ACTAAAGTACGAGTCTTTAGCGCGTTTTTATAAAAATGCCACTAAAGTATGAGTCTTTAGCGGCG
66 ACTAAAGTACAAGTCTATAGCGCGTTTGTATAAAAATGCCACTAAAGTACAAGTCTTTAGCGGCG
*
1314167 TTTGTATAAAAATGCCACTAAATTATGAGTCTTTA
131 TTTGTATAAAAACGCCACTAAATTATGAGTCTTTA
*
1314202 GCGGCGTTTATAAACACAAACGCCACTATAGTACATA-TGTATAACGGCGTTTGTATAAAAACGC
1 GCGGCGTTTATAAACACAAACGCCACTATAGTACA-AGTGTATAACGGCGTTTGAATAAAAACGC
* * *
1314266 CACTAAAGTACAATTCTATAGCGGCGTTTGTATAAAAATTCCACTAAATTACAAGTC-TTAGCGG
65 CACTAAAGTACAAGTCTATAGC-GCGTTTGTATAAAAATGCCACTAAAGTACAAGTCTTTAGCGG
1314330 CGTTTGTATAAAAACGCCACTAAA
129 CGTTTGTATAAAAACGCCACTAAA
1314354 GTACTACTCT
Statistics
Matches: 138, Mismatches: 12, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
165 108 0.78
166 30 0.22
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (165 bp):
GCGGCGTTTATAAACACAAACGCCACTATAGTACAAGTGTATAACGGCGTTTGAATAAAAACGCC
ACTAAAGTACAAGTCTATAGCGCGTTTGTATAAAAATGCCACTAAAGTACAAGTCTTTAGCGGCG
TTTGTATAAAAACGCCACTAAATTATGAGTCTTTA
Found at i:1314377 original size:81 final size:81
Alignment explanation
Indices: 1314037--1314365 Score: 349
Period size: 81 Copynumber: 4.0 Consensus size: 81
1314027 TTGTAAACTT
* * * * *
1314037 GCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAGCGGCGTTTGAATAAAAACGCC
1 GCGGCGTTTGTATA-A-AAATGCCACTAAAGTACAAGTCT-TAGCGGCGTTTGTATAAAAACGCC
*
1314102 ACTAAAGTACGAGTCTTTA
63 ACTAAAGTACTAGTCTTTA
* ** *
1314121 GC-GCGTTTTTATAAAAATGCCACTAAAGTATGAGTCTTTAGCGGCGTTTGTATAAAAATGCCAC
1 GCGGCGTTTGTATAAAAATGCCACTAAAGTACAAGTC-TTAGCGGCGTTTGTATAAAAACGCCAC
*
1314185 TAAATTA-TGAGTCTTTA
65 TAAAGTACT-AGTCTTTA
* * * * * *
1314202 GCGGCGTTTATAAACACAAACGCCACTATAGTACATATGT-ATAACGGCGTTTGTATAAAAACGC
1 GCGGCGTTTGTATA-A-AAATGCCACTAAAGTACA-A-GTCTTAGCGGCGTTTGTATAAAAACGC
* * *
1314266 CACTAAAGTACAATTCTATA
62 CACTAAAGTACTAGTCTTTA
* *
1314286 GCGGCGTTTGTATAAAAATTCCACTAAATTACAAGTCTTAGCGGCGTTTGTATAAAAACGCCACT
1 GCGGCGTTTGTATAAAAATGCCACTAAAGTACAAGTCTTAGCGGCGTTTGTATAAAAACGCCACT
*
1314351 AAAGTACTACTCTTT
66 AAAGTACTAGTCTTT
1314366 TGCGACATTT
Statistics
Matches: 201, Mismatches: 35, Indels: 21
0.78 0.14 0.08
Matches are distributed among these distances:
80 2 0.01
81 96 0.48
82 25 0.12
83 11 0.05
84 64 0.32
85 1 0.00
86 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (81 bp):
GCGGCGTTTGTATAAAAATGCCACTAAAGTACAAGTCTTAGCGGCGTTTGTATAAAAACGCCACT
AAAGTACTAGTCTTTA
Found at i:1323765 original size:44 final size:44
Alignment explanation
Indices: 1323702--1323788 Score: 138
Period size: 44 Copynumber: 2.0 Consensus size: 44
1323692 GGCTAGAATA
1323702 GATGAACAACTCCCTTGGTCGAATAGTCTTATGATGATTCATTG
1 GATGAACAACTCCCTTGGTCGAATAGTCTTATGATGATTCATTG
* * * *
1323746 GATGAACATCTCTCTTGGTCGAATGGTCTTGTGATGATTCATT
1 GATGAACAACTCCCTTGGTCGAATAGTCTTATGATGATTCATT
1323789 TTGGCGCCTA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (44 bp):
GATGAACAACTCCCTTGGTCGAATAGTCTTATGATGATTCATTG
Found at i:1326106 original size:29 final size:28
Alignment explanation
Indices: 1326074--1326132 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
1326064 ATTGTTTCCT
1326074 TTATTACACAT-TTATATCTTTGTCTTTAA
1 TTATTACA-ATGTTATATC-TTGTCTTTAA
* *
1326103 TTATTACATTGTTTTATCTTGTCTTTAA
1 TTATTACAATGTTATATCTTGTCTTTAA
1326131 TT
1 TT
1326133 CTCTTTAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 13 0.48
29 14 0.52
ACGTcount: A:0.24, C:0.12, G:0.05, T:0.59
Consensus pattern (28 bp):
TTATTACAATGTTATATCTTGTCTTTAA
Found at i:1328687 original size:34 final size:34
Alignment explanation
Indices: 1328649--1328718 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 34
1328639 TTCATGCATT
* *
1328649 TAGTTCATT-AATAAAGTTAGTTCATTAATCAAAC
1 TAGTTCATTCAATAAA-CTAGTGCATTAATCAAAC
**
1328683 TAGTTCATTCGTTAAACTAGTGCATTAATCAAAC
1 TAGTTCATTCAATAAACTAGTGCATTAATCAAAC
1328717 TA
1 TA
1328719 ACTCTTAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 27 0.87
35 4 0.13
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (34 bp):
TAGTTCATTCAATAAACTAGTGCATTAATCAAAC
Found at i:1328716 original size:17 final size:17
Alignment explanation
Indices: 1328649--1328718 Score: 79
Period size: 17 Copynumber: 4.1 Consensus size: 17
1328639 TTCATGCATT
*
1328649 TAGTTCATTAAT-AAAGT
1 TAGTTCATTAATCAAA-C
1328666 TAGTTCATTAATCAAAC
1 TAGTTCATTAATCAAAC
** *
1328683 TAGTTCATTCGTTAAAC
1 TAGTTCATTAATCAAAC
*
1328700 TAGTGCATTAATCAAAC
1 TAGTTCATTAATCAAAC
1328717 TA
1 TA
1328719 ACTCTTAATT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
17 41 0.93
18 3 0.07
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (17 bp):
TAGTTCATTAATCAAAC
Found at i:1332500 original size:34 final size:34
Alignment explanation
Indices: 1332462--1332531 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 34
1332452 TTCATGCATT
* *
1332462 TAGTTCATT-AATAAAGTTAGTTCATTAATCAAAC
1 TAGTTCATTCAATAAA-CTAGTGCATTAATCAAAC
**
1332496 TAGTTCATTCGTTAAACTAGTGCATTAATCAAAC
1 TAGTTCATTCAATAAACTAGTGCATTAATCAAAC
1332530 TA
1 TA
1332532 ACTCTTAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 27 0.87
35 4 0.13
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (34 bp):
TAGTTCATTCAATAAACTAGTGCATTAATCAAAC
Found at i:1332529 original size:17 final size:17
Alignment explanation
Indices: 1332462--1332531 Score: 79
Period size: 17 Copynumber: 4.1 Consensus size: 17
1332452 TTCATGCATT
*
1332462 TAGTTCATTAAT-AAAGT
1 TAGTTCATTAATCAAA-C
1332479 TAGTTCATTAATCAAAC
1 TAGTTCATTAATCAAAC
** *
1332496 TAGTTCATTCGTTAAAC
1 TAGTTCATTAATCAAAC
*
1332513 TAGTGCATTAATCAAAC
1 TAGTTCATTAATCAAAC
1332530 TA
1 TA
1332532 ACTCTTAATT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
17 41 0.93
18 3 0.07
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (17 bp):
TAGTTCATTAATCAAAC
Found at i:1333024 original size:16 final size:16
Alignment explanation
Indices: 1333000--1333039 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
1332990 AAGGGTGTCT
*
1333000 ATATACATTCAAGTCC
1 ATATTCATTCAAGTCC
1333016 ATATTCATTC-AGTCC
1 ATATTCATTCAAGTCC
1333031 -T-TTCATTCA
1 ATATTCATTCA
1333040 TATGAAGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 7 0.32
14 1 0.05
15 5 0.23
16 9 0.41
ACGTcount: A:0.30, C:0.25, G:0.05, T:0.40
Consensus pattern (16 bp):
ATATTCATTCAAGTCC
Found at i:1335920 original size:20 final size:20
Alignment explanation
Indices: 1335884--1335922 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1335874 CCATGATATG
*
1335884 TAAATGATATACGAACATAA
1 TAAATGATATACAAACATAA
1335904 TAAATGAATATA-AAACATA
1 TAAATG-ATATACAAACATA
1335923 TGTAAAACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.59, C:0.08, G:0.08, T:0.26
Consensus pattern (20 bp):
TAAATGATATACAAACATAA
Found at i:1336601 original size:20 final size:19
Alignment explanation
Indices: 1336576--1336626 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1336566 GAAATCCCTT
*
1336576 TGAAAATACATGATTTTTAA
1 TGAAAATACATGA-CTTTAA
* *
1336596 TGAAAATATAAGACTTTAA
1 TGAAAATACATGACTTTAA
*
1336615 TGAAGATACATG
1 TGAAAATACATG
1336627 CTCTTGGCCA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.47, C:0.06, G:0.14, T:0.33
Consensus pattern (19 bp):
TGAAAATACATGACTTTAA
Found at i:1340699 original size:19 final size:20
Alignment explanation
Indices: 1340660--1340715 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 20
1340650 GAAATCCCTT
*
1340660 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATCTTTAA
1340680 TGAAAATACATGA-CTTTAA
1 TGAAAATACATGATCTTTAA
*
1340699 TGAAAATACATGCTCTT
1 TGAAAATACATGATCTT
1340716 AGATGAATGA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.36
Consensus pattern (20 bp):
TGAAAATACATGATCTTTAA
Found at i:1341589 original size:45 final size:45
Alignment explanation
Indices: 1341524--1341671 Score: 260
Period size: 45 Copynumber: 3.3 Consensus size: 45
1341514 ATTATTCATT
1341524 ATTTCCATTTATGACATCCTTTCATGCCTTTAATGCACCGTTATGC
1 ATTT-CATTTATGACATCCTTTCATGCCTTTAATGCACCGTTATGC
* *
1341570 ATTTCATTTTTGTCATCCTTTCATGCCTTTAATGCACCGTTATGC
1 ATTTCATTTATGACATCCTTTCATGCCTTTAATGCACCGTTATGC
*
1341615 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
1 ATTTCATTTATGACATCCTTTCATGCCTTTAATGCACCGTTATGC
1341660 ATTTCATTTATG
1 ATTTCATTTATG
1341672 TAATGAAAAC
Statistics
Matches: 98, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
45 94 0.96
46 4 0.04
ACGTcount: A:0.20, C:0.24, G:0.11, T:0.45
Consensus pattern (45 bp):
ATTTCATTTATGACATCCTTTCATGCCTTTAATGCACCGTTATGC
Found at i:1342203 original size:95 final size:94
Alignment explanation
Indices: 1342034--1342216 Score: 235
Period size: 95 Copynumber: 1.9 Consensus size: 94
1342024 CCTACCATGG
* * * *
1342034 TATCGATACTTATATACTATGGTACCGATACCCCCTTTCATTATCGATACCATTTCTACATTCTG
1 TATCGATACTTATATACTACGGTACCGATACCCCCTTTCAGTATCGATACCATTTCTACATTATA
* *
1342099 TAATTCATGGTATCGATACCTTTCTCTCAC
66 CAATCCATGGTATCGATA-CTTTCTCTCAC
* * *
1342129 TATCGATAC-TACTATACTACGGTACCGATACTCCCTTTTAGTATCGATACCATTT-TAGCCTTA
1 TATCGATACTTA-TATACTACGGTACCGATACCCCCTTTCAGTATCGATACCATTTCTA-CATTA
*
1342192 TACAATCCATGGTATCGGTACTTTC
64 TACAATCCATGGTATCGATACTTTC
1342217 CTTTTAGTAT
Statistics
Matches: 76, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
94 9 0.12
95 67 0.88
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.38
Consensus pattern (94 bp):
TATCGATACTTATATACTACGGTACCGATACCCCCTTTCAGTATCGATACCATTTCTACATTATA
CAATCCATGGTATCGATACTTTCTCTCAC
Found at i:1345499 original size:29 final size:29
Alignment explanation
Indices: 1345453--1345511 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
1345443 GAATATCATT
*** *
1345453 TACTCTAACTTTTGATATTCTAGTGTCTA
1 TACTCTAACTTCCAATATTCGAGTGTCTA
1345482 TACTCTAACTTCCAATATTCGAGTGTCTA
1 TACTCTAACTTCCAATATTCGAGTGTCTA
1345511 T
1 T
1345512 CACATTAACT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.25, C:0.20, G:0.10, T:0.44
Consensus pattern (29 bp):
TACTCTAACTTCCAATATTCGAGTGTCTA
Found at i:1347983 original size:45 final size:45
Alignment explanation
Indices: 1347914--1348017 Score: 145
Period size: 45 Copynumber: 2.3 Consensus size: 45
1347904 CTTTAATCAT
*
1347914 TATTTCCATTTATAGCATCCTTTCATGCCTTTAATCCACCGTTATG
1 TATTT-CATTTATGGCATCCTTTCATGCCTTTAATCCACCGTTATG
* * **
1347960 TATTTCATTTATGGCATCTTTTCATGCCTTTAATGCATTGTTATG
1 TATTTCATTTATGGCATCCTTTCATGCCTTTAATCCACCGTTATG
*
1348005 CATTTCATTTATG
1 TATTTCATTTATG
1348018 TAATGAAAAC
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
45 47 0.90
46 5 0.10
ACGTcount: A:0.21, C:0.20, G:0.11, T:0.48
Consensus pattern (45 bp):
TATTTCATTTATGGCATCCTTTCATGCCTTTAATCCACCGTTATG
Found at i:1352134 original size:45 final size:45
Alignment explanation
Indices: 1352080--1352227 Score: 242
Period size: 45 Copynumber: 3.3 Consensus size: 45
1352070 ATTATTCATT
1352080 ATTTCCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
1 ATTT-CATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
*
1352126 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGT
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* * *
1352171 ATTTCATTTATGGCATCATTTCATTCCTTTAATGCACCGTTAAGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
*
1352216 GTTTCATTTATG
1 ATTTCATTTATG
1352228 TAATGAAGAC
Statistics
Matches: 96, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
45 92 0.96
46 4 0.04
ACGTcount: A:0.21, C:0.22, G:0.13, T:0.44
Consensus pattern (45 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
Found at i:1352750 original size:94 final size:94
Alignment explanation
Indices: 1352593--1352774 Score: 251
Period size: 94 Copynumber: 1.9 Consensus size: 94
1352583 CCTACCATGG
* *
1352593 TATCGATACTTCTATACTATGGTACCAATACCCCCTTTCAGTATCGATACCATTTCTATATTCTA
1 TATCGATACTACTATACTATGGTACCAATACCCCCTTTCAGTATCGATACCATTTCTACATTCTA
* *
1352658 TAATTCATGGTATCGATACCTTTCTCTCAT
66 GAATCCATGGTATCGATA-CTTTCTCTCAT
* * *
1352688 TATCGATACTAC-ATACTATGGTACCGATACTCCCTTTCAGTATCGATACCATTT-TGGCATTCT
1 TATCGATACTACTATACTATGGTACCAATACCCCCTTTCAGTATCGATACCATTTCT-ACATTCT
* *
1352751 GGAATCCGTGGTATCGATACTTTC
65 AGAATCCATGGTATCGATACTTTC
1352775 CTTTTAGTAT
Statistics
Matches: 77, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
93 6 0.08
94 60 0.78
95 11 0.14
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (94 bp):
TATCGATACTACTATACTATGGTACCAATACCCCCTTTCAGTATCGATACCATTTCTACATTCTA
GAATCCATGGTATCGATACTTTCTCTCAT
Found at i:1356961 original size:2 final size:2
Alignment explanation
Indices: 1356954--1356995 Score: 75
Period size: 2 Copynumber: 20.5 Consensus size: 2
1356944 GTACCACATG
1356954 TA TA TA TA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1356996 CAAAGTAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1378068 original size:19 final size:20
Alignment explanation
Indices: 1378026--1378081 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 20
1378016 GTAATCCCTT
* *
1378026 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATCTTCAA
1378046 TGAAAATACATGA-CTTCAA
1 TGAAAATACATGATCTTCAA
*
1378065 TGAAAATACATGCTCTT
1 TGAAAATACATGATCTT
1378082 GACCGAATAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.34
Consensus pattern (20 bp):
TGAAAATACATGATCTTCAA
Found at i:1388722 original size:19 final size:19
Alignment explanation
Indices: 1388683--1388752 Score: 104
Period size: 19 Copynumber: 3.6 Consensus size: 19
1388673 CACCCCTTTT
* *
1388683 AAAATACATTATTTTTTATG
1 AAAATACATGA-TTTTAATG
1388703 AAAATACATGATTTTAATG
1 AAAATACATGATTTTAATG
*
1388722 AAAATACAAGATTTTAATG
1 AAAATACATGATTTTAATG
1388741 AAAATACATGAT
1 AAAATACATGAT
1388753 CTTGACCGAA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
19 36 0.78
20 10 0.22
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.37
Consensus pattern (19 bp):
AAAATACATGATTTTAATG
Found at i:1392269 original size:19 final size:20
Alignment explanation
Indices: 1392231--1392281 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
1392221 GAAAACCCTT
1392231 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATTTTTAA
*
1392251 TGAACATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
1392270 TGAATATACATG
1 TGAAAATACATG
1392282 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:1393237 original size:19 final size:20
Alignment explanation
Indices: 1393199--1393249 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
1393189 GAAACCCCAT
*
1393199 TGAAAGTACATGATTTTTAA
1 TGAAAATACATGATTTTTAA
1393219 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
1393238 TGAATATACATG
1 TGAAAATACATG
1393250 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:1397065 original size:16 final size:16
Alignment explanation
Indices: 1397044--1397091 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
1397034 TTGATAACAA
*
1397044 CTTTATCCCTTAATTT
1 CTTTATCACTTAATTT
*
1397060 CTTTATCACTTTATTT
1 CTTTATCACTTAATTT
1397076 C-TT-TCA-TTAATTT
1 CTTTATCACTTAATTT
1397089 CTT
1 CTT
1397092 ATTCCATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
13 7 0.25
14 4 0.14
15 2 0.07
16 15 0.54
ACGTcount: A:0.19, C:0.21, G:0.00, T:0.60
Consensus pattern (16 bp):
CTTTATCACTTAATTT
Found at i:1405978 original size:26 final size:26
Alignment explanation
Indices: 1405925--1405974 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
1405915 ATAAATGGTT
*
1405925 AATGGAATAATGAAATTAAGAAAGGA
1 AATGGAATAATGAAATAAAGAAAGGA
* *
1405951 AATGGAATGAT-AAATAAATAAAGG
1 AATGGAATAATGAAATAAAGAAAGG
1405975 GAAAAATTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.58, C:0.00, G:0.22, T:0.20
Consensus pattern (26 bp):
AATGGAATAATGAAATAAAGAAAGGA
Found at i:1406756 original size:26 final size:25
Alignment explanation
Indices: 1406727--1406802 Score: 72
Period size: 26 Copynumber: 3.2 Consensus size: 25
1406717 ATGCACTCAT
1406727 ATGCATTTTAATAATGGCATCCTTTC
1 ATGCATTTT-ATAATGGCATCCTTTC
* *
1406753 ATGC---CT-TAAT-GCATCATTTC
1 ATGCATTTTATAATGGCATCCTTTC
*
1406773 ATGCATTTTATTTATGGCATCCTTTC
1 ATGCATTTTA-TAATGGCATCCTTTC
1406799 ATGC
1 ATGC
1406803 CTTAATGCTT
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
20 13 0.33
21 4 0.10
23 2 0.05
25 3 0.08
26 17 0.44
ACGTcount: A:0.24, C:0.21, G:0.12, T:0.43
Consensus pattern (25 bp):
ATGCATTTTATAATGGCATCCTTTC
Found at i:1406791 original size:46 final size:44
Alignment explanation
Indices: 1406670--1406810 Score: 176
Period size: 46 Copynumber: 3.1 Consensus size: 44
1406660 TTCATACTTG
* * * *
1406670 TAATGCACCATTATGCATTTTCATTTATGACATTCTTTCATGCCA
1 TAATGCATCATTATGCATTTT-ATTTATGGCATCCTTTCATGCCT
* * *
1406715 AAATGCACTCA-TATGCATTTTAATAATGGCATCCTTTCATGCCT
1 TAATGCA-TCATTATGCATTTTATTTATGGCATCCTTTCATGCCT
1406759 TAATGCATCATTTCATGCATTTTATTTATGGCATCCTTTCATGCCT
1 TAATGCATCA-TT-ATGCATTTTATTTATGGCATCCTTTCATGCCT
1406805 TAATGC
1 TAATGC
1406811 TTCCTTTAAA
Statistics
Matches: 82, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
43 3 0.04
44 24 0.29
45 17 0.21
46 38 0.46
ACGTcount: A:0.26, C:0.22, G:0.11, T:0.41
Consensus pattern (44 bp):
TAATGCATCATTATGCATTTTATTTATGGCATCCTTTCATGCCT
Found at i:1406817 original size:20 final size:20
Alignment explanation
Indices: 1406738--1406817 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 20
1406728 TGCATTTTAA
1406738 TAATGGCATCCTTTCATGCCT
1 TAAT-GCATCCTTTCATGCCT
* *
1406759 TAATGCATCATTTCATGCATTT
1 TAATGCATCCTTTCATGC--CT
1406781 TATTTATGGCATCCTTTCATGCCT
1 TA---AT-GCATCCTTTCATGCCT
*
1406805 TAATGCTTCCTTT
1 TAATGCATCCTTT
1406818 AAAATTGAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 13
0.73 0.08 0.20
Matches are distributed among these distances:
20 21 0.44
21 6 0.12
22 3 0.06
24 3 0.06
25 2 0.04
26 13 0.27
ACGTcount: A:0.20, C:0.24, G:0.11, T:0.45
Consensus pattern (20 bp):
TAATGCATCCTTTCATGCCT
Found at i:1413914 original size:22 final size:22
Alignment explanation
Indices: 1413886--1413933 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
1413876 AGGTCCAGAA
1413886 ACATCAAGTGCTTTGGAAAAAG
1 ACATCAAGTGCTTTGGAAAAAG
*
1413908 ACATCAAGTGCTTTGGAAAAGG
1 ACATCAAGTGCTTTGGAAAAAG
1413930 ACAT
1 ACAT
1413934 TTTGCAAGCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.23
Consensus pattern (22 bp):
ACATCAAGTGCTTTGGAAAAAG
Done.