Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009175.1 Hibiscus syriacus cultivar Beakdansim tig00112738_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: 10629029
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 51
Found at i:1205596 original size:20 final size:20
Alignment explanation
Indices: 1205571--1205646 Score: 116
Period size: 20 Copynumber: 3.8 Consensus size: 20
1205561 TGAAACCGAG
1205571 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
*
1205591 AATGACTATCGCAATGCGAA
1 AATGACTATCGCAACGCGAA
*
1205611 AATGACTATCGCAATGCGAA
1 AATGACTATCGCAACGCGAA
**
1205631 TTTGACTATCGCAACG
1 AATGACTATCGCAACG
1205647 AGAGAATCGC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:1205713 original size:20 final size:20
Alignment explanation
Indices: 1205688--1205737 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1205678 TGCGATTCTT
1205688 GCGTTGCGATAGTCAAATTC
1 GCGTTGCGATAGTCAAATTC
**
1205708 GCGTTGCGATAGTCATTTTC
1 GCGTTGCGATAGTCAAATTC
*
1205728 GTGTTGCGAT
1 GCGTTGCGAT
1205738 TTTCATTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.18, C:0.18, G:0.28, T:0.36
Consensus pattern (20 bp):
GCGTTGCGATAGTCAAATTC
Found at i:1205743 original size:20 final size:20
Alignment explanation
Indices: 1205705--1205759 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
1205695 GATAGTCAAA
* **
1205705 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
1205725 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
1205745 TTCGTGTTGCGATTT
1 TTCGTGTTGCGATTT
1205760 AAAGTTTCAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.11, C:0.16, G:0.24, T:0.49
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:1205767 original size:20 final size:20
Alignment explanation
Indices: 1205724--1205767 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1205714 CGATAGTCAT
** *
1205724 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTAAAG
1205744 TTTCGTGTTGCGATTTAAAG
1 TTTCGTGTTGCGATTTAAAG
1205764 TTTC
1 TTTC
1205768 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAG
Found at i:1207231 original size:6 final size:6
Alignment explanation
Indices: 1207220--1207249 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1207210 TCTCCCTGTT
*
1207220 CTCCAC CTCCAC CTCTAC CTCCAC CTCCAC
1 CTCCAC CTCCAC CTCCAC CTCCAC CTCCAC
1207250 GGGGAGTTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.17, C:0.63, G:0.00, T:0.20
Consensus pattern (6 bp):
CTCCAC
Found at i:1207645 original size:20 final size:20
Alignment explanation
Indices: 1207620--1207817 Score: 267
Period size: 20 Copynumber: 10.5 Consensus size: 20
1207610 AGAATAGTTT
*
1207620 ACTATCGCAATACGAAAATG
1 ACTATCGCAATGCGAAAATG
*
1207640 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
1207660 ACTATCGCAAT--G-AGA-G
1 ACTATCGCAATGCGAAAATG
1207676 A--ATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
1207694 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
1207714 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
1207734 ACTATCGCAATGCAAAAATG
1 ACTATCGCAATGCGAAAATG
*
1207754 ACTATCGCAAT--G-AGA-G
1 ACTATCGCAATGCGAAAATG
1207770 A--ATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
1207788 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
1207808 ACTATCGCAA
1 ACTATCGCAA
1207818 CGAAAGAATC
Statistics
Matches: 157, Mismatches: 9, Indels: 24
0.83 0.05 0.13
Matches are distributed among these distances:
14 16 0.10
16 6 0.04
17 8 0.05
18 5 0.03
20 122 0.78
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.19
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:1207681 original size:34 final size:37
Alignment explanation
Indices: 1207620--1207838 Score: 201
Period size: 34 Copynumber: 5.9 Consensus size: 37
1207610 AGAATAGTTT
*
1207620 ACTATCGCAATACGAAAATGACTATCGCAACGCGAAAATG
1 ACTATCGCAAT--GAAAATGAC-ATCGCAATGCGAAAATG
*
1207660 ACTATCGCAATG-AGA-GA-ATCGCAATGCGAAAATG
1 ACTATCGCAATGAAAATGACATCGCAATGCGAAAATG
1207694 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
1 ACTATCGCAAT--GAAAATGAC-ATCGCAATGCGAAAATG
*
1207734 ACTATCGCAATGCAAAAATGACTATCGCAAT--G-AGA-G
1 ACTATCGCAATG--AAAATGAC-ATCGCAATGCGAAAATG
1207770 A--ATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
1 ACTATCGCAAT--GAAAATGAC-ATCGCAATGCGAAAATG
* *
1207808 ACTATCGCAACG-AAA-GA-ATCGCAATACGAAA
1 ACTATCGCAATGAAAATGACATCGCAATGCGAAA
1207839 TGAAAATCGC
Statistics
Matches: 156, Mismatches: 7, Indels: 38
0.78 0.03 0.19
Matches are distributed among these distances:
34 65 0.42
36 9 0.06
37 11 0.07
38 8 0.05
40 63 0.40
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.18
Consensus pattern (37 bp):
ACTATCGCAATGAAAATGACATCGCAATGCGAAAATG
Found at i:1207781 original size:94 final size:94
Alignment explanation
Indices: 1207620--1207817 Score: 369
Period size: 94 Copynumber: 2.1 Consensus size: 94
1207610 AGAATAGTTT
*
1207620 ACTATCGCAATACGAAAATGACTATCGCAACGCGAAAATGACTATCGCAATGAGAGAATCGCAAT
1 ACTATCGCAATACGAAAATGACTATCGCAACGCAAAAATGACTATCGCAATGAGAGAATCGCAAT
1207685 GCGAAAATGACTATCGCAATGCGAAAATG
66 GCGAAAATGACTATCGCAATGCGAAAATG
* *
1207714 ACTATCGCAATGCGAAAATGACTATCGCAATGCAAAAATGACTATCGCAATGAGAGAATCGCAAT
1 ACTATCGCAATACGAAAATGACTATCGCAACGCAAAAATGACTATCGCAATGAGAGAATCGCAAT
1207779 GCGAAAATGACTATCGCAATGCGAAAATG
66 GCGAAAATGACTATCGCAATGCGAAAATG
1207808 ACTATCGCAA
1 ACTATCGCAA
1207818 CGAAAGAATC
Statistics
Matches: 101, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
94 101 1.00
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.19
Consensus pattern (94 bp):
ACTATCGCAATACGAAAATGACTATCGCAACGCAAAAATGACTATCGCAATGAGAGAATCGCAAT
GCGAAAATGACTATCGCAATGCGAAAATG
Found at i:1207826 original size:54 final size:57
Alignment explanation
Indices: 1207620--1207855 Score: 246
Period size: 54 Copynumber: 4.3 Consensus size: 57
1207610 AGAATAGTTT
* *
1207620 ACTATCGCAATACGAAAATGACTATCGCAACGCGAAAATGACTATCGCAAT--GAGA-G
1 ACTATCGCAATGCGAAAATGACTATCGCAA-GCGAAAATGAC-ATCGCAATGCGAAATG
1207676 A--ATCGCAATGCGAAAATGACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAA-GCGAAAATGAC-ATCGCAATGCG-AAATG
* * *
1207734 ACTATCGCAATGCAAAAATGACTATCGCAA-TG-AGA-GA-ATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAAGCGAAAATGACATCGCAATGCG-AAATG
*
1207788 ACTATCGCAATGCGAAAATGACTATCGCAA-CG-AAA-GA-ATCGCAATACGAAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAAGCGAAAATGACATCGCAATGCGAAATG
** *
1207841 AAAATCGCATTGCGA
1 ACTATCGCAATGCGA
1207856 TTCTCTCGTT
Statistics
Matches: 161, Mismatches: 13, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
53 17 0.11
54 107 0.66
56 4 0.02
57 4 0.02
58 3 0.02
60 26 0.16
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.18
Consensus pattern (57 bp):
ACTATCGCAATGCGAAAATGACTATCGCAAGCGAAAATGACATCGCAATGCGAAATG
Found at i:1207892 original size:20 final size:20
Alignment explanation
Indices: 1207864--1207970 Score: 178
Period size: 20 Copynumber: 5.3 Consensus size: 20
1207854 GATTCTCTCG
**
1207864 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
1207884 TTACGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
1207904 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
1207924 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
1207944 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
1207964 TTGCGAT
1 TTGCGAT
1207971 TTTAAGTTTC
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 82 1.00
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:1208545 original size:21 final size:20
Alignment explanation
Indices: 1208454--1208558 Score: 68
Period size: 21 Copynumber: 5.0 Consensus size: 20
1208444 GACTCACCTG
1208454 TCATCGTTCAAGAGG-CCTCC
1 TCATCGTTCAAGAGGCCCT-C
* *
1208474 CCTATCGTTCAAGAGGCCCCTA
1 TC-ATCGTTCAAGAGG-CCCTC
** *
1208496 TCATCCCTCAAGAGTCCCATC
1 TCATCGTTCAAGAGGCCC-TC
* * *
1208517 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCC-CTC
*
1208538 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGG-CCCTC
1208559 CCAACATTCT
Statistics
Matches: 62, Mismatches: 17, Indels: 11
0.69 0.19 0.12
Matches are distributed among these distances:
20 4 0.06
21 51 0.82
22 4 0.06
23 3 0.05
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.23
Consensus pattern (20 bp):
TCATCGTTCAAGAGGCCCTC
Found at i:1208551 original size:42 final size:42
Alignment explanation
Indices: 1208479--1208561 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
1208469 CCTCCCCTAT
*
1208479 CGTTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCATCCCAC
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCC-TCCCAC
* ** *
1208521 CGTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCA
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCA
1208562 ACATTCTAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 30 0.86
43 5 0.14
ACGTcount: A:0.23, C:0.37, G:0.19, T:0.20
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCAC
Found at i:1209932 original size:14 final size:14
Alignment explanation
Indices: 1209913--1209948 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1209903 ATTGTTTAAT
1209913 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1209927 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1209941 TGATTTGT
1 TGATTTGT
1209949 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1210138 original size:34 final size:33
Alignment explanation
Indices: 1210050--1210145 Score: 138
Period size: 33 Copynumber: 2.8 Consensus size: 33
1210040 AAAACAGACT
* **
1210050 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
1210084 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1210117 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
1210146 CGAAACTAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 31 0.54
34 26 0.46
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1210141 original size:20 final size:19
Alignment explanation
Indices: 1210083--1210150 Score: 74
Period size: 19 Copynumber: 3.8 Consensus size: 19
1210073 GCAACGAGAG
1210083 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1210102 AATCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
1210116 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
1210136 AATCGCAACGCGAAA
1 AATCGCAATGCGAAA
1210151 CTAAATTCAC
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
14 8 0.20
16 5 0.12
17 2 0.05
18 3 0.08
19 11 0.28
20 11 0.28
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1210188 original size:19 final size:19
Alignment explanation
Indices: 1210164--1210209 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
1210154 AATTCACTCG
1210164 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1210183 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1210202 TTGCGATT
1 TTGCGATT
1210210 CTCTCGTTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.15, C:0.20, G:0.17, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1210239 original size:20 final size:20
Alignment explanation
Indices: 1210214--1210307 Score: 127
Period size: 20 Copynumber: 4.7 Consensus size: 20
1210204 GCGATTCTCT
1210214 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
1210234 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
**
1210254 TATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
1210274 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
*
1210294 CGTTGAGATAGTCA
1 CGTTGCGATAGTCA
1210308 AATGAATGTC
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
20 64 0.97
21 2 0.03
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:1210843 original size:20 final size:20
Alignment explanation
Indices: 1210819--1210902 Score: 98
Period size: 20 Copynumber: 4.2 Consensus size: 20
1210809 CAGAATCTCG
1210819 TTGCGATTTACAG-ATTCGCA
1 TTGCGATTTAC-GTATTCGCA
*
1210839 ATGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
* ** *
1210859 TTGCGATTTTCCAAATTCGCG
1 TTGCGA-TTTACGTATTCGCA
1210880 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
1210900 TTG
1 TTG
1210903 TGAATTAGGA
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
19 1 0.02
20 35 0.67
21 16 0.31
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.38
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:1210928 original size:21 final size:21
Alignment explanation
Indices: 1210904--1210947 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1210894 TTCGCATTGT
1210904 GAATTAGGAAAATCGCAACGC
1 GAATTAGGAAAATCGCAACGC
* * *
1210925 GAATTTGGGAAATCGCAATGC
1 GAATTAGGAAAATCGCAACGC
1210946 GA
1 GA
1210948 TGGTCAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.16, G:0.27, T:0.18
Consensus pattern (21 bp):
GAATTAGGAAAATCGCAACGC
Found at i:1215415 original size:39 final size:39
Alignment explanation
Indices: 1215356--1215436 Score: 126
Period size: 39 Copynumber: 2.1 Consensus size: 39
1215346 TAAGTTTTAA
* * *
1215356 TAACCTGAAATTCATATGAAGTTATGTTATGAACATAAT
1 TAACATGAAATTCATATGAAGTTATGTAATGAAAATAAT
*
1215395 TAACATGAAATTCATTTGAAGTTATGTAATGAAAATAAT
1 TAACATGAAATTCATATGAAGTTATGTAATGAAAATAAT
1215434 TAA
1 TAA
1215437 ACTTGAAGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.36
Consensus pattern (39 bp):
TAACATGAAATTCATATGAAGTTATGTAATGAAAATAAT
Found at i:1216534 original size:14 final size:14
Alignment explanation
Indices: 1216510--1216569 Score: 57
Period size: 14 Copynumber: 4.3 Consensus size: 14
1216500 AGTATCAGAT
*
1216510 ACCAGAGATCAAAA
1 ACCAGATATCAAAA
* * *
1216524 ATCATATATCAGAA
1 ACCAGATATCAAAA
* * *
1216538 TCTAGAGATCAAAA
1 ACCAGATATCAAAA
1216552 ACCAGATATCAAAA
1 ACCAGATATCAAAA
1216566 ACCA
1 ACCA
1216570 TATTTTTATT
Statistics
Matches: 33, Mismatches: 13, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.53, C:0.20, G:0.10, T:0.17
Consensus pattern (14 bp):
ACCAGATATCAAAA
Found at i:1219732 original size:32 final size:33
Alignment explanation
Indices: 1219690--1219756 Score: 109
Period size: 32 Copynumber: 2.1 Consensus size: 33
1219680 AATCTAAAAT
*
1219690 AAATATCATTTAGGATAC-AAGAATCAGTAAAC
1 AAATATCATTTAGGATACAAAGAATCAATAAAC
*
1219722 AAATGTCATTTAGGATACAAAGAATCAATAAAC
1 AAATATCATTTAGGATACAAAGAATCAATAAAC
1219755 AA
1 AA
1219757 GTGAACAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.53
33 15 0.47
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.24
Consensus pattern (33 bp):
AAATATCATTTAGGATACAAAGAATCAATAAAC
Found at i:1227320 original size:3 final size:3
Alignment explanation
Indices: 1227305--1227368 Score: 76
Period size: 3 Copynumber: 21.3 Consensus size: 3
1227295 ATATTTAATT
*
1227305 TAA TAA TAT TAA TAA T-A TATA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
** *
1227350 TAA TTT TAA AAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA T
1227369 TTAAATAATT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
2 2 0.04
3 46 0.90
4 3 0.06
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:1227688 original size:76 final size:76
Alignment explanation
Indices: 1227533--1228169 Score: 1141
Period size: 76 Copynumber: 8.4 Consensus size: 76
1227523 AGGTCCTAAA
* *
1227533 AAACATCATGCACTGAAGGGCTTACAGATGACCCTAAGG-TTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1227597 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
1227608 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGTTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1227673 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
1227684 AAACATCGTGCACTGTAGGACTTACAGAAGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1227749 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
1227760 AAACATCTTGCACTATAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
1227825 AGGCTTTCTGG
66 AGGCTTTTTGG
* *
1227836 AAACATCATGCACTGCAGGACTTACAGATGAACCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1227901 AGGCTTTTTGG
66 AGGCTTTTTGG
*
1227912 AAACATCAGGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1227977 AGGCTTTTTGG
66 AGGCTTTTTGG
*
1227988 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1228053 AGGCTTTTTGG
66 AGGCTTTTTGG
*
1228064 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1228129 AGGCTTTTTGG
66 AGGCTTTTTGG
1228140 AAACATCATGCACTGTAGGACTTACAGATG
1 AAACATCATGCACTGTAGGACTTACAGATG
1228170 TGGGAAATAG
Statistics
Matches: 538, Mismatches: 23, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
75 37 0.07
76 501 0.93
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (76 bp):
AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:1228871 original size:22 final size:22
Alignment explanation
Indices: 1228843--1228897 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
1228833 CATAAAGCTT
1228843 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
1228865 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
1228887 TCATCTTTGAA
1 TCATCTTTGAA
1228898 GAGTGTAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:1229393 original size:54 final size:54
Alignment explanation
Indices: 1229318--1229472 Score: 231
Period size: 54 Copynumber: 2.9 Consensus size: 54
1229308 CTGCTCAAAT
* * * * * *
1229318 GTAAAACACTTGACAACACATTTATCTTTTTCTTTGGTTTCTGCTCAGATGTTC
1 GTAAAGCATTTGAAAACACATTCATCCTTTTCTTTGGCTTCTGCTCAGATGTTC
1229372 GTAAAGCATTTGAAAACACATTCATCCTTTTCTTTGGCTTCTGCTCAGATGTTC
1 GTAAAGCATTTGAAAACACATTCATCCTTTTCTTTGGCTTCTGCTCAGATGTTC
*
1229426 GTAAAGCATTT-AACAACACATTCATCCTTTTCTGTGGCTTCTGCTCA
1 GTAAAGCATTTGAA-AACACATTCATCCTTTTCTTTGGCTTCTGCTCA
1229473 TATTTCTCAA
Statistics
Matches: 93, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
53 2 0.02
54 91 0.98
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.39
Consensus pattern (54 bp):
GTAAAGCATTTGAAAACACATTCATCCTTTTCTTTGGCTTCTGCTCAGATGTTC
Found at i:1233380 original size:32 final size:32
Alignment explanation
Indices: 1233339--1233400 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
1233329 TGAAGAAATG
*
1233339 GTTGTTATGCTCATCTTGTAGAGATACTTCTC
1 GTTGTTATGCTCATCTGGTAGAGATACTTCTC
1233371 GTTGTTATGCTCATCTGGTAGAGATACTTC
1 GTTGTTATGCTCATCTGGTAGAGATACTTC
1233401 ATGTGTCTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.42
Consensus pattern (32 bp):
GTTGTTATGCTCATCTGGTAGAGATACTTCTC
Found at i:1233935 original size:15 final size:15
Alignment explanation
Indices: 1233917--1233953 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
1233907 TTGTTTTTCC
1233917 CTTTTTTTCCTTT-TT
1 CTTTTTTT-CTTTCTT
1233932 CTTTTTTTCTTTCTT
1 CTTTTTTTCTTTCTT
1233947 -TTTTTTT
1 CTTTTTTT
1233954 GCTGGATGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (15 bp):
CTTTTTTTCTTTCTT
Found at i:1233943 original size:23 final size:24
Alignment explanation
Indices: 1233903--1233948 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
1233893 AATTTCTCCT
*
1233903 CTTTTTGTTTTTCCCTTT-TTTTC
1 CTTTTTCTTTTTCCCTTTCTTTTC
**
1233926 CTTTTTCTTTTTTTCTTTCTTTT
1 CTTTTTCTTTTTCCCTTTCTTTT
1233949 TTTTTGCTGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (24 bp):
CTTTTTCTTTTTCCCTTTCTTTTC
Found at i:1236799 original size:28 final size:28
Alignment explanation
Indices: 1236767--1236824 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
1236757 GTAATTATGT
1236767 AAAAATGAAAAATGTAAATACAAACGTAA
1 AAAAAT-AAAAATGTAAATACAAACGTAA
* * *
1236796 AAAAATACAAATGTAAATGCAAATGTAA
1 AAAAATAAAAATGTAAATACAAACGTAA
1236824 A
1 A
1236825 TATGTGAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 20 0.77
29 6 0.23
ACGTcount: A:0.64, C:0.07, G:0.10, T:0.19
Consensus pattern (28 bp):
AAAAATAAAAATGTAAATACAAACGTAA
Found at i:1236803 original size:16 final size:16
Alignment explanation
Indices: 1236782--1236812 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1236772 TGAAAAATGT
1236782 AAATACAAACGTAAAA
1 AAATACAAACGTAAAA
*
1236798 AAATACAAATGTAAA
1 AAATACAAACGTAAA
1236813 TGCAAATGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.10, G:0.06, T:0.16
Consensus pattern (16 bp):
AAATACAAACGTAAAA
Found at i:1236913 original size:8 final size:7
Alignment explanation
Indices: 1236884--1236925 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
1236874 ATAAAAGTAT
1236884 AAATGCA
1 AAATGCA
* *
1236891 CAATGAA
1 AAATGCA
1236898 AAATGCA
1 AAATGCA
1236905 AAGATGCA
1 AA-ATGCA
1236913 AAATG-A
1 AAATGCA
1236919 AAATGCA
1 AAATGCA
1236926 TGTATGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
6 6 0.21
7 16 0.55
8 7 0.24
ACGTcount: A:0.57, C:0.12, G:0.17, T:0.14
Consensus pattern (7 bp):
AAATGCA
Found at i:1239298 original size:147 final size:147
Alignment explanation
Indices: 1238998--1239266 Score: 371
Period size: 147 Copynumber: 1.8 Consensus size: 147
1238988 AAATATAAGA
* * *
1238998 GATATTTACTTATTTAGAAATATCAGAAAAGGGCTTCTAGGTGCTTTAAGACAGCTCTTTTCTTT
1 GATATTTACTTATTTAGAAATATAAGAAAAGGACTTCTAGGTGCTTTAAGACAGCTCATTTCTTT
* * * * *
1239063 GATATTAAAAAATAAATAAATATCAATAAAACATTTTTCTAAAAACATTAAAATAAATTAATATA
66 AATATTAAAAAATAAAAAAATATCAATAAAACATTTTTATAAAAAAACTAAAATAAATTAATATA
*
1239128 TAATTTAAAAAAAATAG
131 TAATATAAAAAAAATAG
* *
1239145 GATATTTATTTATTTA-AGAATATAAGAAAATGACTTCTAGGTGCTTTAAGACAGCTCATTTC-T
1 GATATTTACTTATTTAGA-AATATAAGAAAAGGACTTCTAGGTGCTTTAAGACAGCTCATTTCTT
* *
1239208 TAATATTAAAAAATAAAAAAAATATTAATAAAATATGTTTTATAAAAATAACTAAAATA
65 TAATATTAAAAAAT-AAAAAAATATCAATAAAACAT-TTTTATAAAAA-AACTAAAATA
1239267 TATAGATTAA
Statistics
Matches: 106, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
146 15 0.14
147 73 0.69
148 10 0.09
149 8 0.08
ACGTcount: A:0.48, C:0.08, G:0.09, T:0.36
Consensus pattern (147 bp):
GATATTTACTTATTTAGAAATATAAGAAAAGGACTTCTAGGTGCTTTAAGACAGCTCATTTCTTT
AATATTAAAAAATAAAAAAATATCAATAAAACATTTTTATAAAAAAACTAAAATAAATTAATATA
TAATATAAAAAAAATAG
Found at i:1239433 original size:11 final size:12
Alignment explanation
Indices: 1239421--1239462 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
1239411 ATGATTAAAA
1239421 TAAAATAATAA-
1 TAAAATAATAAT
*
1239432 TAAATTAATAAT
1 TAAAATAATAAT
**
1239444 TAAAGCAATAAT
1 TAAAATAATAAT
1239456 TAAAATA
1 TAAAATA
1239463 TAAAAGTAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (12 bp):
TAAAATAATAAT
Found at i:1240832 original size:3 final size:3
Alignment explanation
Indices: 1240817--1240877 Score: 70
Period size: 3 Copynumber: 20.3 Consensus size: 3
1240807 ATATTTAATT
*
1240817 TAA TAA TAT TAA TAA T-A TATA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
** *
1240862 TTT TAA AAA TAA TAA T
1 TAA TAA TAA TAA TAA T
1240878 TTAAATAATT
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
2 2 0.04
3 43 0.90
4 3 0.06
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:1242465 original size:15 final size:15
Alignment explanation
Indices: 1242436--1242470 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1242426 GGTCTTTTAA
1242436 TTCTT-ACTTTAGAG
1 TTCTTAACTTTAGAG
*
1242450 TTCTTAACTTTTGAG
1 TTCTTAACTTTAGAG
1242465 TTCTTA
1 TTCTTA
1242471 TTTTTATCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.20, C:0.14, G:0.11, T:0.54
Consensus pattern (15 bp):
TTCTTAACTTTAGAG
Found at i:1242539 original size:11 final size:11
Alignment explanation
Indices: 1242523--1242551 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1242513 GGATGGCAAC
1242523 GGATCGGATTA
1 GGATCGGATTA
1242534 GGATCGGATTA
1 GGATCGGATTA
1242545 GGATCGG
1 GGATCGG
1242552 GCTTTGATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.24, C:0.10, G:0.41, T:0.24
Consensus pattern (11 bp):
GGATCGGATTA
Found at i:1242999 original size:10 final size:10
Alignment explanation
Indices: 1242986--1243026 Score: 55
Period size: 10 Copynumber: 3.8 Consensus size: 10
1242976 AACACGAATG
1242986 AACGAACATA
1 AACGAACATA
1242996 AACGAACACAATA
1 AACG-A-AC-ATA
1243009 AACGAACATA
1 AACGAACATA
1243019 AACGAACA
1 AACGAACA
1243027 ACACAAACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 15 0.54
11 3 0.11
12 3 0.11
13 7 0.25
ACGTcount: A:0.61, C:0.22, G:0.10, T:0.07
Consensus pattern (10 bp):
AACGAACATA
Found at i:1243016 original size:23 final size:24
Alignment explanation
Indices: 1242969--1243026 Score: 100
Period size: 23 Copynumber: 2.5 Consensus size: 24
1242959 CATTTAATAA
*
1242969 ATAAACGAACACGAATGAACGAAC
1 ATAAACGAACACGAATAAACGAAC
1242993 ATAAACGAACAC-AATAAACGAAC
1 ATAAACGAACACGAATAAACGAAC
1243016 ATAAACGAACA
1 ATAAACGAACA
1243027 ACACAAACAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 21 0.64
24 12 0.36
ACGTcount: A:0.59, C:0.21, G:0.12, T:0.09
Consensus pattern (24 bp):
ATAAACGAACACGAATAAACGAAC
Found at i:1243034 original size:23 final size:23
Alignment explanation
Indices: 1242969--1243034 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 23
1242959 CATTTAATAA
**
1242969 ATAAACGAACACGAATGAACGAAC
1 ATAAACGAACAC-AACAAACGAAC
*
1242993 ATAAACGAACACAATAAACGAAC
1 ATAAACGAACACAACAAACGAAC
1243016 ATAAACGAACA-ACACAAAC
1 ATAAACGAACACA-ACAAAC
1243035 AAAAAAAACT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
22 1 0.03
23 26 0.67
24 12 0.31
ACGTcount: A:0.59, C:0.23, G:0.11, T:0.08
Consensus pattern (23 bp):
ATAAACGAACACAACAAACGAAC
Found at i:1243324 original size:24 final size:24
Alignment explanation
Indices: 1243285--1243359 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
1243275 GCCCTCTGTT
**
1243285 CGAACATAAATTAACATAAATGAA
1 CGAACATAAACAAACATAAATGAA
*
1243309 CGAACATAAACGAACAT--AT-AA
1 CGAACATAAACAAACATAAATGAA
** *
1243330 TCGAACATTCACAAACGTAAATGAA
1 -CGAACATAAACAAACATAAATGAA
1243355 CGAAC
1 CGAAC
1243360 GAGCCCTTTG
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
21 2 0.05
22 15 0.37
24 22 0.54
25 2 0.05
ACGTcount: A:0.53, C:0.19, G:0.11, T:0.17
Consensus pattern (24 bp):
CGAACATAAACAAACATAAATGAA
Found at i:1244952 original size:27 final size:27
Alignment explanation
Indices: 1244912--1244965 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
1244902 AATAGAGATA
*
1244912 GAGATTAAGTTCTTATTTAAAATTAAC
1 GAGATTAAGTTCTTATGTAAAATTAAC
1244939 GAGATTGAAG-TCTTATGTAAAATTAAC
1 GAGATT-AAGTTCTTATGTAAAATTAAC
1244966 TCTAAAATGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 22 0.88
28 3 0.12
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (27 bp):
GAGATTAAGTTCTTATGTAAAATTAAC
Found at i:1245064 original size:29 final size:28
Alignment explanation
Indices: 1245012--1245066 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
1245002 ATAAAACAAA
*
1245012 TAAATAATATAAAATAAACTAATATTAC
1 TAAATAATATAAAATAAACAAATATTAC
1245040 TAAACTAATATAAAATAATA-AAATATT
1 TAAA-TAATATAAAATAA-ACAAATATT
1245067 TTTAGAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 4 0.17
29 19 0.79
30 1 0.04
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (28 bp):
TAAATAATATAAAATAAACAAATATTAC
Found at i:1245085 original size:19 final size:19
Alignment explanation
Indices: 1245061--1245118 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
1245051 AAAATAATAA
1245061 AATATTTTTAGAAATAAAT
1 AATATTTTTAGAAATAAAT
1245080 AATA---TT---AATAAACT
1 AATATTTTTAGAAATAAA-T
1245094 AATATTTTTAGAAATAAAT
1 AATATTTTTAGAAATAAAT
1245113 AATATT
1 AATATT
1245119 AATAAACTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 14
0.70 0.00 0.30
Matches are distributed among these distances:
13 6 0.19
14 5 0.16
16 2 0.06
17 2 0.06
19 11 0.34
20 6 0.19
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.41
Consensus pattern (19 bp):
AATATTTTTAGAAATAAAT
Found at i:1245098 original size:33 final size:33
Alignment explanation
Indices: 1245009--1245131 Score: 148
Period size: 33 Copynumber: 3.8 Consensus size: 33
1244999 AAAATAAAAC
* **
1245009 AAATAAATAATATAAAATAAACTAATATTACTA-
1 AAATAAATAATAT-TAATAAACTAATATTTTTAG
* *
1245042 AACTAATATAA-AATAAT-AA--AATATTTTTAG
1 AAATAA-ATAATATTAATAAACTAATATTTTTAG
1245072 AAATAAATAATATTAATAAACTAATATTTTTAG
1 AAATAAATAATATTAATAAACTAATATTTTTAG
1245105 AAATAAATAATATTAATAAACTAATAT
1 AAATAAATAATATTAATAAACTAATAT
1245132 AATAATAAAT
Statistics
Matches: 77, Mismatches: 7, Indels: 12
0.80 0.07 0.12
Matches are distributed among these distances:
29 12 0.16
30 10 0.13
31 4 0.05
32 3 0.04
33 44 0.57
34 4 0.05
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (33 bp):
AAATAAATAATATTAATAAACTAATATTTTTAG
Found at i:1245133 original size:19 final size:19
Alignment explanation
Indices: 1245078--1245135 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
1245068 TTAGAAATAA
1245078 ATAATATTAATAAACTAAT
1 ATAATATTAATAAACTAAT
* *
1245097 AT--T-TTTAGAAA-TAA-
1 ATAATATTAATAAACTAAT
1245111 ATAATATTAATAAACTAAT
1 ATAATATTAATAAACTAAT
1245130 ATAATA
1 ATAATA
1245136 ATAAATAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
14 2 0.07
15 3 0.10
16 7 0.23
17 7 0.23
18 3 0.10
19 8 0.27
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (19 bp):
ATAATATTAATAAACTAAT
Found at i:1245142 original size:33 final size:33
Alignment explanation
Indices: 1245070--1245156 Score: 120
Period size: 33 Copynumber: 2.6 Consensus size: 33
1245060 AAATATTTTT
** *
1245070 AGAAATAAATAATATTAATAAACTAATATTTTT
1 AGAAATAAATAATATTAATAAACTAATATAATA
1245103 AGAAATAAATAATATTAATAAACTAATATAATA
1 AGAAATAAATAATATTAATAAACTAATATAATA
*
1245136 ATAAATAAATAAAATATTAAT
1 AGAAATAAAT--AATATTAAT
1245157 TAATACCTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
33 39 0.81
35 9 0.19
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (33 bp):
AGAAATAAATAATATTAATAAACTAATATAATA
Found at i:1247474 original size:21 final size:21
Alignment explanation
Indices: 1247444--1247483 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1247434 CGAGGGAGAA
1247444 GGAGAAAAAGAAGGA-GAAAAG
1 GGAGAAAAAG-AGGATGAAAAG
*
1247465 GGAGATAAAGAGGATGAAA
1 GGAGAAAAAGAGGATGAAA
1247484 GCAAATCTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.57, C:0.00, G:0.38, T:0.05
Consensus pattern (21 bp):
GGAGAAAAAGAGGATGAAAAG
Found at i:1256451 original size:29 final size:29
Alignment explanation
Indices: 1256413--1256473 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
1256403 CAGAAAAACA
1256413 TTAGACACTTATTTTTAATGAAATATACT
1 TTAGACACTTATTTTTAATGAAATATACT
* *
1256442 TTAGATACTTATTTTTAATGAAATATATT
1 TTAGACACTTATTTTTAATGAAATATACT
1256471 TTA
1 TTA
1256474 AGCACCTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.49
Consensus pattern (29 bp):
TTAGACACTTATTTTTAATGAAATATACT
Found at i:1256474 original size:15 final size:15
Alignment explanation
Indices: 1256425--1256474 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
1256415 AGACACTTAT
1256425 TTTTAATGAAATATA
1 TTTTAATGAAATATA
* **
1256440 CTTTAGAT-ACTTAT-
1 TTTTA-ATGAAATATA
1256454 TTTTAATGAAATATA
1 TTTTAATGAAATATA
1256469 TTTTAA
1 TTTTAA
1256475 GCACCTAAAG
Statistics
Matches: 26, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
13 2 0.08
14 8 0.31
15 14 0.54
16 2 0.08
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (15 bp):
TTTTAATGAAATATA
Found at i:1259574 original size:117 final size:117
Alignment explanation
Indices: 1259368--1259593 Score: 317
Period size: 117 Copynumber: 1.9 Consensus size: 117
1259358 CATCATTGTG
* *
1259368 AGGCATAAGGAGGAAGATTTGACATGTGAAGAATGTCTTTCTTCCAACACATGACTCCAACCTAT
1 AGGCATAAGGAGGAAGATTAGACATGTGAAGAATGTCTTTCTTCCAACACATGACTCCAACCCAT
* ***
1259433 TCAACTAGTTCGGATAAAATTGAGAAGATGCAAACAATAAATGTGTTTTTTT
66 TCAACTAGTTCAGATAAAATTGAGAAGACAAAAACAATAAATGTGTTTTTTT
* * * ** *
1259485 AGGCATAAGGTGGAAGATTAGATATGTGAAGAATGTTTTTCTTCCAATGCATGACTCCAACCCGT
1 AGGCATAAGGAGGAAGATTAGACATGTGAAGAATGTCTTTCTTCCAACACATGACTCCAACCCAT
* * *
1259550 TCATCTCGTTCAGATATAATTGAGAAGACAAAAACAATAAATGT
66 TCAACTAGTTCAGATAAAATTGAGAAGACAAAAACAATAAATGT
1259594 AAATAAAACA
Statistics
Matches: 94, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
117 94 1.00
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.29
Consensus pattern (117 bp):
AGGCATAAGGAGGAAGATTAGACATGTGAAGAATGTCTTTCTTCCAACACATGACTCCAACCCAT
TCAACTAGTTCAGATAAAATTGAGAAGACAAAAACAATAAATGTGTTTTTTT
Found at i:1260787 original size:32 final size:31
Alignment explanation
Indices: 1260721--1260788 Score: 75
Period size: 32 Copynumber: 2.2 Consensus size: 31
1260711 AAATCTAAAA
* *
1260721 ATTGACCCAAATCAAAATTAATCAATTCAAT
1 ATTGACCCAAATAAAAATTAATCAATCCAAT
* *
1260752 ATTGACCCAACCTAAAAATTGAAT-AATCCAGT
1 ATTGACCCAA-ATAAAAATT-AATCAATCCAAT
1260784 ATTGA
1 ATTGA
1260789 TCGATCTGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
31 10 0.32
32 18 0.58
33 3 0.10
ACGTcount: A:0.46, C:0.19, G:0.07, T:0.28
Consensus pattern (31 bp):
ATTGACCCAAATAAAAATTAATCAATCCAAT
Found at i:1260836 original size:32 final size:32
Alignment explanation
Indices: 1260749--1260917 Score: 110
Period size: 32 Copynumber: 5.3 Consensus size: 32
1260739 TAATCAATTC
* * * *
1260749 AATATTGACCCAACCTAAAAATTGAA-TAATCC
1 AATATTGACTCAACCTGAAAA-TCAACTAATCT
* * * *
1260781 AGTATTGA-TCGATCTG-AAATCAACTGATCT
1 AATATTGACTCAACCTGAAAATCAACTAATCT
* *
1260811 AGTATTGACTCAACCTGAAAATCAACTAATCC
1 AATATTGACTCAACCTGAAAATCAACTAATCT
* * * ** *
1260843 AATATTGACACGACCCTAGAAAGTCAACCGATTT
1 AATATTGACTC-AACCT-GAAAATCAACTAATCT
* * * *
1260877 TATATTGATTCGACCTGAAAACCAACTAATCT
1 AATATTGACTCAACCTGAAAATCAACTAATCT
1260909 AATATTGAC
1 AATATTGAC
1260918 CGATCCGAAA
Statistics
Matches: 100, Mismatches: 32, Indels: 10
0.70 0.23 0.07
Matches are distributed among these distances:
29 3 0.03
30 15 0.15
31 10 0.10
32 46 0.46
33 7 0.07
34 19 0.19
ACGTcount: A:0.40, C:0.21, G:0.11, T:0.28
Consensus pattern (32 bp):
AATATTGACTCAACCTGAAAATCAACTAATCT
Found at i:1260894 original size:66 final size:62
Alignment explanation
Indices: 1260775--1260936 Score: 173
Period size: 66 Copynumber: 2.5 Consensus size: 62
1260765 AAAAATTGAA
* * * * * * *
1260775 TAATCCAGTATTGATCGATCTGAAATCAACTGA-TCTAGTATTGACTCAACCTGAAAATCAAC
1 TAATCCAATATTGACCGACCCGAAATCAACCGATTTTA-TATTGACTCAACCTGAAAACCAAC
* *
1260837 TAATCCAATATTGACACGACCCTAGAAAGTCAACCGATTTTATATTGATTCGACCTGAAAACCAA
1 TAATCCAATATTGAC-CGACCC--GAAA-TCAACCGATTTTATATTGACTCAACCTGAAAACCAA
1260902 C
62 C
* *
1260903 TAATCTAATATTGACCGATCCGAAATCAACCGAT
1 TAATCCAATATTGACCGACCCGAAATCAACCGAT
1260937 GTGTATTCCC
Statistics
Matches: 84, Mismatches: 11, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
62 22 0.26
63 8 0.10
65 9 0.11
66 42 0.50
67 3 0.04
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (62 bp):
TAATCCAATATTGACCGACCCGAAATCAACCGATTTTATATTGACTCAACCTGAAAACCAAC
Found at i:1262237 original size:20 final size:19
Alignment explanation
Indices: 1262198--1262249 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
1262188 TTTCTTCAAT
1262198 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
1262217 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
*
1262237 ATTTATAAAATAA
1 A-TTAAAAAATAA
1262250 GATATTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 7 0.26
20 15 0.56
21 5 0.19
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:1262255 original size:120 final size:118
Alignment explanation
Indices: 1262107--1262343 Score: 305
Period size: 121 Copynumber: 2.0 Consensus size: 118
1262097 AAAATATATT
* * * * * *
1262107 AATTTATATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAA-GGACTTCTAGG
1 AATTAATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAAAAAATGAACATCCAGG
*
1262171 TACCTTAAGACAGCTCTTTTCTTCAATATTAAAAAATAAATAAATAATTAAAAC
66 TACCTTAAGACAGCCCTTTTCTTCAATATTAAAAAATAAATAAAT-ATTAAAAC
*
1262225 AATTAATATATAATTTATAAAATAAGATATTTATTTATTTAAAAATATCAAAAAATGAACATCCA
1 AATTAATATAT-ATTTAT-AAATAAAATATTTATTTATTTAAAAATATCAAAAAATGAACATCCA
* *** * * *
1262290 GTTGTTTTAAGACTGCCCTTTTCTTCGATATTGAAAAATAAATAAATATTAAAA
64 GGTACCTTAAGACAGCCCTTTTCTTCAATATTAAAAAATAAATAAATATTAAAA
1262344 TATGATAAAA
Statistics
Matches: 101, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
118 10 0.10
119 6 0.06
120 40 0.40
121 45 0.45
ACGTcount: A:0.47, C:0.09, G:0.07, T:0.38
Consensus pattern (118 bp):
AATTAATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAAAAAATGAACATCCAGG
TACCTTAAGACAGCCCTTTTCTTCAATATTAAAAAATAAATAAATATTAAAAC
Found at i:1262442 original size:28 final size:28
Alignment explanation
Indices: 1262410--1262485 Score: 66
Period size: 29 Copynumber: 2.7 Consensus size: 28
1262400 TTATATGACT
* **
1262410 ATATAATAATAATAAAAATAATATTTAA
1 ATATAATAATAATAAAAATAAAACATAA
* *
1262438 ATAT-ATAAACAAGTAAAATTAAAACATAA
1 ATATAAT-AATAA-TAAAAATAAAACATAA
*
1262467 ATA-AACAATAATAAAAATA
1 ATATAATAATAATAAAAATA
1262486 CAATTAGAAC
Statistics
Matches: 37, Mismatches: 8, Indels: 7
0.71 0.15 0.13
Matches are distributed among these distances:
27 9 0.24
28 12 0.32
29 16 0.43
ACGTcount: A:0.67, C:0.04, G:0.01, T:0.28
Consensus pattern (28 bp):
ATATAATAATAATAAAAATAAAACATAA
Found at i:1263444 original size:23 final size:23
Alignment explanation
Indices: 1263400--1263444 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
1263390 TTTTGTTGGT
* *
1263400 TGTCTTCTCTCGTTCTTGCTCTG
1 TGTCTCCTCTCGTTCTTCCTCTG
* *
1263423 TGTCTCCTCTCTTTTTTCCTCT
1 TGTCTCCTCTCGTTCTTCCTCT
1263445 CATTTTCTTC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.00, C:0.33, G:0.11, T:0.56
Consensus pattern (23 bp):
TGTCTCCTCTCGTTCTTCCTCTG
Found at i:1264244 original size:139 final size:139
Alignment explanation
Indices: 1263933--1264278 Score: 482
Period size: 139 Copynumber: 2.5 Consensus size: 139
1263923 CTAGCAAAAA
* *
1263933 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTTTCAGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
* * * * * *
1263998 C-TCCTTCTGGAAATGCTGATCTTCAAAAGAGGGATTTGTTGATTCAACTCCATATGTGATGAAT
66 CTTCCTTCTGAAAATACTGATCCTCAAAAGAGGGATTTGTTCATTCAACTCCATAGGAGATGAAT
* *
1264062 TAAGGTAAG
131 CAAGGCAAG
*
1264071 GTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
* * * * *
1264136 CTTCC-TCTGAAAATATTGATCCTCAAATGA-GGTTCTTCTTTCATTCAATTCCATAGGAGATGA
66 CTTCCTTCTGAAAATACTGATCCTCAAAAGAGGGAT-TT-GTTCATTCAACTCCATAGGAGATGA
*
1264199 ATCAATGCAAG
129 ATCAAGGCAAG
* *
1264210 GTTGAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
1264275 CTTC
66 CTTC
1264279 ACCTGGAAAT
Statistics
Matches: 185, Mismatches: 20, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
137 3 0.02
138 85 0.46
139 97 0.52
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (139 bp):
GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
CTTCCTTCTGAAAATACTGATCCTCAAAAGAGGGATTTGTTCATTCAACTCCATAGGAGATGAAT
CAAGGCAAG
Found at i:1264561 original size:123 final size:123
Alignment explanation
Indices: 1264207--1265227 Score: 749
Period size: 113 Copynumber: 8.7 Consensus size: 123
1264197 GAATCAATGC
*
1264207 AAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* * * * * * * *
1264272 GAAC-TTCACCTGGAAATAGCT-CTGCTGCTCTATCTCTTTTTG-GAAGTGGAGTCAAGTAA
66 GAACTTTC-TCTGGAAA-AGTTGATGCTGATCTATCTCCTTCTGTG-A-TAGAGTCAAGCAA
*
1264331 AATGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT--T-TTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
** * * * * * *
1264393 GAACACT-TCTGGAAATGTTGATGTTGATCTATCTGCTTCTATGATAGAGTTAAACAA
66 GAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCAAGCAA
* * * *
1264450 AAGGTTAAATAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
*
1264515 GAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCATGCAA
66 GAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCAAGCAA
* *
1264573 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATTA
* ** *
1264638 TGAACTTTCTCTGG-AAA--TG-T--TGATCCA--T-C-GAT-TGAT-GAATTCAAGCAA
65 TGAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAG-AGTCAAGCAA
* *
1264686 AAAGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATTA
** * * * *** *
1264751 TGAACTCGCCCTGG-TAA--TG-T--TGATCCA--T-C--GAATGAT-GAATTCAAGCGAA
65 TGAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAG-AGTCAAGC-AA
*
1264800 AA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATTA
** * * * *** *
1264864 TGAACTCTT-TC---ACTAG-GGATACTGATCCA--T-C--AAATGAT-GAATTCAAGCGAA
65 TGAACT-TTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAG-AGTCAAGC-AA
*
1264915 AA-GTTGAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATTA
* * * *** * * **
1264979 TGAA----CTCT----AA-CTGATACTG-T-TGATC-CATTAAATGATGGATTTGAGCAA
65 TGAACTTTCTCTGGAAAAGTTGATGCTGATCT-ATCTCCTTCTGTGATAGAGTCAAGCAA
* *
1265027 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATTA
* ** *
1265092 TGAACTTTCTCTGGAAAAGTT-A-----ATCCA--T-C--AAGTGAT-GAATTCAAGCAA
65 TGAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAG-AGTCAAGCAA
* * *
1265140 AAGGTTGAACAAATTCTTCTCATTATGAA-TTCCTTCTTCCTCTTCAGATAAGTTCTTCTCATTT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTT-CTTCTTCCTCTTCAGATGAGTTCTTCTCATTA
* *
1265204 TGAACTTTTTCTGGAAATGTTGAT
65 TGAACTTTCTCTGGAAAAGTTGAT
1265228 CCATTGAATG
Statistics
Matches: 772, Mismatches: 81, Indels: 98
0.81 0.09 0.10
Matches are distributed among these distances:
109 2 0.00
110 8 0.01
111 3 0.00
112 49 0.06
113 308 0.40
114 6 0.01
115 95 0.12
116 1 0.00
117 6 0.01
118 6 0.01
119 45 0.06
120 23 0.03
121 34 0.04
122 30 0.04
123 83 0.11
124 73 0.09
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (123 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
GAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCAAGCAA
Found at i:1264770 original size:113 final size:113
Alignment explanation
Indices: 1264569--1265240 Score: 893
Period size: 113 Copynumber: 5.9 Consensus size: 113
1264559 ATAGAGTCAT
* * *
1264569 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * *
1264634 ATTATGAACTTTCTCTGGAAATGTTGATCCATCGATTGATGAATTCAA
66 ATTATGAACTCTCACTGGAAATGTTGATCCATCAAATGATGAATTCAA
*
1264682 GCAAAAAGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * *
1264747 ATTATGAACTCGCCCTGGTAATGTTGATCCATCGAATGATGAATTCAA
66 ATTATGAACTCTCACTGGAAATGTTGATCCATCAAATGATGAATTCAA
* *
1264795 GCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTT
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* **
1264860 ATTATGAACTCTTTCACTAGG-GATACTGATCCATCAAATGATGAATTCAA
66 ATTATGAACTC--TCACT-GGAAATGTTGATCCATCAAATGATGAATTCAA
* *
1264910 GCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * **
1264975 ATTATGAACTCTAACT-GATACTGTTGATCCATTAAATGATGGATTTGA
66 ATTATGAACTCTCACTGGA-AATGTTGATCCATCAAATGATGAATTCAA
* * *
1265023 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTT
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * *
1265088 ATTATGAACTTTCTCTGGAAAAGTTAATCCATCAAGTGATGAATTCAA
66 ATTATGAACTCTCACTGGAAATGTTGATCCATCAAATGATGAATTCAA
* * *
1265136 GCAAAAGGTTGAACAAATTCTTCTCATTATGAA-TTCCTTCTTCC-TCTTCAGATAAGTTCTTCT
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTT-CTTCTTCCTTCTTCAGATGAGTTCTTCT
* * ** **
1265199 CATTTTGAACTTTTTCTGGAAATGTTGATCCATTGAATGATG
65 CATTATGAACTCTCACTGGAAATGTTGATCCATCAAATGATG
1265241 GATTTAAATC
Statistics
Matches: 498, Mismatches: 54, Indels: 15
0.88 0.10 0.03
Matches are distributed among these distances:
111 1 0.00
112 54 0.11
113 337 0.68
114 2 0.00
115 102 0.20
116 2 0.00
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (113 bp):
GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTCTCACTGGAAATGTTGATCCATCAAATGATGAATTCAA
Found at i:1264956 original size:228 final size:224
Alignment explanation
Indices: 1264569--1265240 Score: 945
Period size: 228 Copynumber: 3.0 Consensus size: 224
1264559 ATAGAGTCAT
* * *
1264569 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTT
* * * *
1264634 ATTATGAACTTTCTCTGGAAATGTTGATCCATCGATTGATGAATTCAAGCAAAAAGTTAAACAAG
66 ATTATGAACTTTCTCTGG-AATATTGATCCATCAAATGATGAATTCAAGC-AAAAGTTGAACAAG
***
1264699 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGCCCTG
129 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTG
*
1264764 GTAATGTTGATCCATCGAATGATGAATTCAA
194 GTAATGTTGATCCATTGAATGATGAATTCAA
1264795 GCGAAAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 GC-AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * *
1264859 TATTATGAACTCTTTCACTAGGGATACTGATCCATCAAATGATGAATTCAAGCGAAAAGTTGAAC
65 TATTATGAA--CTTTCTCT-GGAATATTGATCCATCAAATGATGAATTCAAGC-AAAAGTTGAAC
*
1264924 AAGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAA
126 AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAA
* * * * **
1264989 CTGATACTGTTGATCCATTAAATGATGGATTTGA
191 CTGGTAATGTTGATCCATTGAATGATGAATTCAA
*
1265023 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTT
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTT
* * * *
1265088 ATTATGAACTTTCTCTGGAAAAGTTAATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAA
66 ATTATGAACTTTCTCTGGAATA-TTGATCCATCAAATGATGAATTCAAGCAAAA-GTTGAACAAG
* * * **
1265153 TTCTTCTCATTATGAA-TTCCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTTTGAACTTTTTCT
129 TTCTTCTCATTATGAACTT-CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACT
*
1265216 GGAAATGTTGATCCATTGAATGATG
193 GGTAATGTTGATCCATTGAATGATG
1265241 GATTTAAATC
Statistics
Matches: 398, Mismatches: 40, Indels: 17
0.87 0.09 0.04
Matches are distributed among these distances:
225 62 0.16
226 128 0.32
227 8 0.02
228 198 0.50
229 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (224 bp):
GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTT
ATTATGAACTTTCTCTGGAATATTGATCCATCAAATGATGAATTCAAGCAAAAGTTGAACAAGTT
CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGGT
AATGTTGATCCATTGAATGATGAATTCAA
Found at i:1265711 original size:44 final size:44
Alignment explanation
Indices: 1265648--1265793 Score: 247
Period size: 44 Copynumber: 3.3 Consensus size: 44
1265638 CATAAAGCTT
*
1265648 TCATCTTTGAAAAGAGAATCTATCATCTTTAAAAAGAGAATTTA
1 TCATCTTTGAAGAGAGAATCTATCATCTTTAAAAAGAGAATTTA
1265692 TCATCTTTGAAGAGAGAATCTATCATCTTTAAAAAGAGAATTTA
1 TCATCTTTGAAGAGAGAATCTATCATCTTTAAAAAGAGAATTTA
* * * *
1265736 TCATCTTTGAAGAGAGAATTTATCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTATCATCTTTAAAAAGAGAATTTA
1265780 TCATCTTTGAAGAG
1 TCATCTTTGAAGAG
1265794 TGTAGATATA
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 97 1.00
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (44 bp):
TCATCTTTGAAGAGAGAATCTATCATCTTTAAAAAGAGAATTTA
Found at i:1265731 original size:66 final size:66
Alignment explanation
Indices: 1265648--1265787 Score: 244
Period size: 66 Copynumber: 2.1 Consensus size: 66
1265638 CATAAAGCTT
*
1265648 TCATCTTTGAAAAGAGAATCTATCATCTTTAAAAAGAGAATTTATCATCTTTGAAGAGAGAATCT
1 TCATCTTTAAAAAGAGAATCTATCATCTTTAAAAAGAGAATTTATCATCTTTGAAGAGAGAATCT
1265713 A
66 A
* * *
1265714 TCATCTTTAAAAAGAGAATTTATCATCTTTGAAGAGAGAATTTATCATCTTTGAAGAGAGAATCT
1 TCATCTTTAAAAAGAGAATCTATCATCTTTAAAAAGAGAATTTATCATCTTTGAAGAGAGAATCT
1265779 A
66 A
1265780 TCATCTTT
1 TCATCTTT
1265788 GAAGAGTGTA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 70 1.00
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.36
Consensus pattern (66 bp):
TCATCTTTAAAAAGAGAATCTATCATCTTTAAAAAGAGAATTTATCATCTTTGAAGAGAGAATCT
A
Found at i:1265791 original size:22 final size:22
Alignment explanation
Indices: 1265648--1265793 Score: 220
Period size: 22 Copynumber: 6.6 Consensus size: 22
1265638 CATAAAGCTT
*
1265648 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
* * *
1265670 TCATCTTTAAAAAGAGAATTTA
1 TCATCTTTGAAGAGAGAATCTA
1265692 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
* * *
1265714 TCATCTTTAAAAAGAGAATTTA
1 TCATCTTTGAAGAGAGAATCTA
*
1265736 TCATCTTTGAAGAGAGAATTTA
1 TCATCTTTGAAGAGAGAATCTA
1265758 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
1265780 TCATCTTTGAAGAG
1 TCATCTTTGAAGAG
1265794 TGTAGATATA
Statistics
Matches: 113, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 113 1.00
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:1268481 original size:115 final size:114
Alignment explanation
Indices: 1268315--1268646 Score: 495
Period size: 114 Copynumber: 2.9 Consensus size: 114
1268305 AATCATGCAG
* * * * * **
1268315 TTCATCTTTTAATTCCAATGATTGGTTCTGTGGTTCCTACTGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* * *
1268380 ACACTTCCAGAAGATGCTATTGGG-CCTCTTTATTTCTACCATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTTC-TTATTTCTACCATAAACAAA
**
1268429 TTCATCTTTCAAATTTAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGG-TTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
* *
1268494 AACACTTCCAGAAGATGTTATTGGGTCTTCTTATTTCTACTATAAACAAA
65 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACCATAAACAAA
*
1268544 TTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
1268609 ACACTTCTAGAAGATGCTATTGGGTCTTCTTATTTCTA
66 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTA
1268647 TTATGAGCGC
Statistics
Matches: 197, Mismatches: 19, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
114 97 0.49
115 97 0.49
116 3 0.02
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.35
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACCATAAACAAA
Found at i:1268630 original size:114 final size:114
Alignment explanation
Indices: 1268315--1268646 Score: 486
Period size: 115 Copynumber: 2.9 Consensus size: 114
1268305 AATCATGCAG
* * * * * * **
1268315 TTCATCTTTTAATTCCAATGATTGGTTCTGTGGTTCCTACTGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* * *
1268380 ACACTTCCAGAAGATGCTATTGGG-CCTCTTTATTTCTACCATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTTC-TTATTTCTACCATAAACAAA
** *
1268429 TTCATCTTTCAAATTTAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATT-GATTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
* *
1268494 AACACTTCCAGAAGATGTTATTGGGTCTTCTTATTTCTACTATAAACAAA
65 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACCATAAACAAA
1268544 TTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
1268609 ACACTTCTAGAAGATGCTATTGGGTCTTCTTATTTCTA
66 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTA
1268647 TTATGAGCGC
Statistics
Matches: 196, Mismatches: 20, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
114 96 0.49
115 97 0.49
116 3 0.02
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.35
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACCATAAACAAA
Found at i:1270806 original size:26 final size:26
Alignment explanation
Indices: 1270760--1270816 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
1270750 TTCTCCCTTT
* *
1270760 TTTTTCCTTTTTTTTTCTTTTTATCA
1 TTTTTCCTTTTTATCTCTTTTTATCA
* *
1270786 TTTTTCCTTTTTCATCT-TTTTTTTCT
1 TTTTTCCTTTTT-ATCTCTTTTTATCA
1270812 TTTTT
1 TTTTT
1270817 TTCATTCTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 24 0.92
27 2 0.08
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (26 bp):
TTTTTCCTTTTTATCTCTTTTTATCA
Found at i:1270841 original size:23 final size:23
Alignment explanation
Indices: 1270811--1270856 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
1270801 CTTTTTTTTC
1270811 TTTTTTTTCATTCTTTGCTGGAT
1 TTTTTTTTCATTCTTTGCTGGAT
*
1270834 TTTTTTTTCTTTCTTTGCTGGAT
1 TTTTTTTTCATTCTTTGCTGGAT
1270857 GAGTATAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.07, C:0.13, G:0.13, T:0.67
Consensus pattern (23 bp):
TTTTTTTTCATTCTTTGCTGGAT
Found at i:1276128 original size:16 final size:16
Alignment explanation
Indices: 1276109--1276156 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
1276099 ATAATGAATA
1276109 AATAAAATAAAAAAAT
1 AATAAAATAAAAAAAT
* *
1276125 AATAATATATAAAAAT
1 AATAAAATAAAAAAAT
1276141 AATAAGTAATAAAAAA
1 AATAA--AATAAAAAA
1276157 TTTGAAAGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
16 19 0.73
18 7 0.27
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (16 bp):
AATAAAATAAAAAAAT
Found at i:1276136 original size:18 final size:20
Alignment explanation
Indices: 1276115--1276151 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
1276105 AATAAATAAA
1276115 ATAAAAA-AATAA-TAATAT
1 ATAAAAATAATAAGTAATAT
1276133 ATAAAAATAATAAGTAATA
1 ATAAAAATAATAAGTAATA
1276152 AAAAATTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 5 0.29
20 5 0.29
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (20 bp):
ATAAAAATAATAAGTAATAT
Found at i:1276786 original size:20 final size:19
Alignment explanation
Indices: 1276747--1276798 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
1276737 TTTCTTCAAT
1276747 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
1276766 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
*
1276786 ATTTATAAAATAA
1 A-TTAAAAAATAA
1276799 GATATTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 7 0.26
20 15 0.56
21 5 0.19
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:1276804 original size:120 final size:118
Alignment explanation
Indices: 1276656--1276892 Score: 314
Period size: 121 Copynumber: 2.0 Consensus size: 118
1276646 AAAATATATT
* * * * *
1276656 AATTTATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAA-GGACTTCTAGG
1 AATTAATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAAAAAATGAACATCCAGG
*
1276720 TACCTTAAGACAGCTCTTTTCTTCAATATTAAAAAATAAATAAATAATTAAAAC
66 TACCTTAAGACAGCCCTTTTCTTCAATATTAAAAAATAAATAAAT-ATTAAAAC
*
1276774 AATTAATATATAATTTATAAAATAAGATATTTATTTATTTAAAAATATCAAAAAATGAACATCCA
1 AATTAATATAT-ATTTAT-AAATAAAATATTTATTTATTTAAAAATATCAAAAAATGAACATCCA
* *** * * *
1276839 GTTGTTTTAAGACTGCCCTTTTCTTCGATATTGAAAAATAAATAAATATTAAAA
64 GGTACCTTAAGACAGCCCTTTTCTTCAATATTAAAAAATAAATAAATATTAAAA
1276893 TATGATAAAA
Statistics
Matches: 102, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
118 10 0.10
119 6 0.06
120 41 0.40
121 45 0.44
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (118 bp):
AATTAATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAAAAAATGAACATCCAGG
TACCTTAAGACAGCCCTTTTCTTCAATATTAAAAAATAAATAAATATTAAAAC
Found at i:1276991 original size:28 final size:28
Alignment explanation
Indices: 1276959--1277034 Score: 66
Period size: 29 Copynumber: 2.7 Consensus size: 28
1276949 TTATATGACT
* **
1276959 ATATAATAATAATAAAAATAATATTTAA
1 ATATAATAATAATAAAAATAAAACATAA
* *
1276987 ATAT-ATAAACAAGTAAAATTAAAACATAA
1 ATATAAT-AATAA-TAAAAATAAAACATAA
*
1277016 ATA-AAAAATAATAAAAATA
1 ATATAATAATAATAAAAATA
1277035 CAAGTAGAAC
Statistics
Matches: 37, Mismatches: 8, Indels: 7
0.71 0.15 0.13
Matches are distributed among these distances:
27 9 0.24
28 12 0.32
29 16 0.43
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.28
Consensus pattern (28 bp):
ATATAATAATAATAAAAATAAAACATAA
Found at i:1278872 original size:9 final size:9
Alignment explanation
Indices: 1278858--1278885 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
1278848 TCCAGCCTCA
1278858 CTTCTTCCT
1 CTTCTTCCT
1278867 CTTCTTCCT
1 CTTCTTCCT
1278876 CTTCTTCCT
1 CTTCTTCCT
1278885 C
1 C
1278886 GTACTCTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (9 bp):
CTTCTTCCT
Found at i:1286991 original size:55 final size:55
Alignment explanation
Indices: 1286916--1287103 Score: 170
Period size: 55 Copynumber: 3.4 Consensus size: 55
1286906 AAACGGGCTC
* *
1286916 GCTCCCTATTTCTTTCAGGGAGTATAGAACTCGCACAATCTTCAACAAATGTCTCT
1 GCTCCCTA-TTCTTTCAGGGAGTATAGAACTCGAACAATCTTCAACAAACGTCTCT
* * * * *
1286972 GCTCTCTATTCTTTCAGGGAGTTTA-AGACTCGAACAATCTTCAGCAAACGTGTTT
1 GCTCCCTATTCTTTCAGGGAGTATAGA-ACTCGAACAATCTTCAACAAACGTCTCT
* * * * *
1287027 GTTCCCTATTCTTTCAAGGAGTATAGGACTC-AAGAAATCTTCTGAA-AACAGGT-T-T
1 GCTCCCTATTCTTTCAGGGAGTATAGAACTCGAA-CAATCTTC--AACAA-ACGTCTCT
1287082 GCTCCCTATTCCTTTCAGGGAG
1 GCTCCCTATT-CTTTCAGGGAG
1287104 GCTTAAAATG
Statistics
Matches: 108, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
54 3 0.03
55 81 0.75
56 20 0.19
57 4 0.04
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (55 bp):
GCTCCCTATTCTTTCAGGGAGTATAGAACTCGAACAATCTTCAACAAACGTCTCT
Found at i:1287415 original size:42 final size:41
Alignment explanation
Indices: 1287323--1287423 Score: 103
Period size: 42 Copynumber: 2.4 Consensus size: 41
1287313 AGGTTTTATG
* * * * *
1287323 GATGGCCCGAAGGACTTATCATCTTTCTCTAAAGGCTTACA
1 GATGGCCCGAAGGACTTAACATCATACTCGAAAGACTTACA
* * * *
1287364 AATGACCCGAAGGATTTAAACATCATACTCGAAAGACTTACT
1 GATGGCCCGAAGGACTT-AACATCATACTCGAAAGACTTACA
*
1287406 GATGGCCCGAATGACTTA
1 GATGGCCCGAAGGACTTA
1287424 TAAATCGTGA
Statistics
Matches: 46, Mismatches: 13, Indels: 2
0.75 0.21 0.03
Matches are distributed among these distances:
41 15 0.33
42 31 0.67
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.26
Consensus pattern (41 bp):
GATGGCCCGAAGGACTTAACATCATACTCGAAAGACTTACA
Found at i:1287593 original size:34 final size:34
Alignment explanation
Indices: 1287548--1288103 Score: 643
Period size: 34 Copynumber: 15.9 Consensus size: 34
1287538 TGGATGGATT
* *
1287548 TGCTTCACTACTCTTATGTGAAGGCTTAAGATAG
1 TGCTTCACTACTCTTCTGTGAAGGCTTAAGATGG
* *
1287582 TACTTCACTACTCCTCTGTGAAGGCTTAAGATGG
1 TGCTTCACTACTCTTCTGTGAAGGCTTAAGATGG
* *
1287616 TGTTTCACTACTCTTCTGTGAAGGCTTAAGATGAT
1 TGCTTCACTACTCTTCTGTGAAGGCTTAAGATG-G
* * *
1287651 TGCTTTACTACTCTCCGGTGAAGGCTTAAGATGG
1 TGCTTCACTACTCTTCTGTGAAGGCTTAAGATGG
* * *
1287685 TGCTTCACTACTCTTTTGTGAAGGCTTAATATGAT
1 TGCTTCACTACTCTTCTGTGAAGGCTTAAGATG-G
* *
1287720 TGCTTCACTACTCTCCGGTGAAGGCTTAAGATGG
1 TGCTTCACTACTCTTCTGTGAAGGCTTAAGATGG
*
1287754 TTTGCTTCACTCCTCTT-TGGTGAAGGCTTAAGATGG
1 --TGCTTCACTACTCTTCT-GTGAAGGCTTAAGATGG
* *
1287790 TTTACTTCACTCCTCTT-TGGTGAAGGCTTAAGATGG
1 --TGCTTCACTACTCTTCT-GTGAAGGCTTAAGATGG
* *
1287826 TGCTTCACTACTCTTCTGCGAATGCTTAAGATGG
1 TGCTTCACTACTCTTCTGTGAAGGCTTAAGATGG
*
1287860 TTTGCTTCACTCCTCTT-TGGTGAAGGCTTAAGATGG
1 --TGCTTCACTACTCTTCT-GTGAAGGCTTAAGATGG
*
1287896 TTTGCTTCACTCCTCTTC-GATGAAGGCTTAAGATGG
1 --TGCTTCACTACTCTTCTG-TGAAGGCTTAAGATGG
* * *
1287932 TTTGCTTCACTCCTCTTCGGTAAAGGCTTAAGATGG
1 --TGCTTCACTACTCTTCTGTGAAGGCTTAAGATGG
*
1287968 TGCTTCACTACTCCTCTGTGAAGGCTTAAGATGG
1 TGCTTCACTACTCTTCTGTGAAGGCTTAAGATGG
* *
1288002 TACTTCACTACTCTTCTGTGAAGGCTTAAGATGAT
1 TGCTTCACTACTCTTCTGTGAAGGCTTAAGATG-G
*
1288037 TGCTTCACTACTCTTCTGTGAAGGCTTAAGATGAT
1 TGCTTCACTACTCTTCTGTGAAGGCTTAAGATG-G
* * *
1288072 TACTTCACTACTCTCCGGTGAAGGCTTAAGAT
1 TGCTTCACTACTCTTCTGTGAAGGCTTAAGAT
1288104 TGACTTACCC
Statistics
Matches: 462, Mismatches: 47, Indels: 25
0.87 0.09 0.05
Matches are distributed among these distances:
34 177 0.38
35 124 0.27
36 160 0.35
37 1 0.00
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (34 bp):
TGCTTCACTACTCTTCTGTGAAGGCTTAAGATGG
Found at i:1287859 original size:106 final size:103
Alignment explanation
Indices: 1287540--1288103 Score: 681
Period size: 106 Copynumber: 5.4 Consensus size: 103
1287530 AGGCTTTATG
* * *
1287540 GATGGATTTGCTTCACTACTCT-TATGTGAAGGCTTAAGATAGTACTTCACTACTCCTCTGTGAA
1 GATGG-TTTGCTTCACTACTCTCT-GGTGAAGGCTTAAGATGGTACTTCACTACT-CTTTGTGAA
*
1287604 GGCTTAAGATGGTGTTTCACTACTCTTCTGTGAAGGCTTAA
63 GGCTTAAGATGGTGCTTCACTACTCTTCTGTGAAGGCTTAA
* * * *
1287645 GAT-GATTGCTTTACTACTCTCCGGTGAAGGCTTAAGATGGTGCTTCACTACTCTTTTGTGAAGG
1 GATGGTTTGCTTCACTACTCTCTGGTGAAGGCTTAAGATGGTACTTCACTACTC-TTTGTGAAGG
* * * *
1287709 CTTAATATGATTGCTTCACTACTCTCCGGTGAAGGCTTAA
65 CTTAAGATG-GTGCTTCACTACTCTTCTGTGAAGGCTTAA
* * *
1287749 GATGGTTTGCTTCACTCCTCTTTGGTGAAGGCTTAAGATGGTTTACTTCACTCCTCTTTGGTGAA
1 GATGGTTTGCTTCACTACTCTCTGGTGAAGGCTTAAGATGG--TACTTCACTACTCTTT-GTGAA
* *
1287814 GGCTTAAGATGGTGCTTCACTACTCTTCTGCGAATGCTTAA
63 GGCTTAAGATGGTGCTTCACTACTCTTCTGTGAAGGCTTAA
* * * * *
1287855 GATGGTTTGCTTCACTCCTCTTTGGTGAAGGCTTAAGATGGTTTGCTTCACTCCTCTTCGATGAA
1 GATGGTTTGCTTCACTACTCTCTGGTGAAGGCTTAAGATGG--TACTTCACTACTCTTTG-TGAA
* * *
1287920 GGCTTAAGATGGTTTGCTTCACTCCTCTTCGGTAAAGGCTTAA
63 GGCTTAAGATGG--TGCTTCACTACTCTTCTGTGAAGGCTTAA
1287963 GATGG--TGCTTCACTACTCCTCT-GTGAAGGCTTAAGATGGTACTTCACTACTCTTCTGTGAAG
1 GATGGTTTGCTTCACTACT-CTCTGGTGAAGGCTTAAGATGGTACTTCACTACTCTT-TGTGAAG
*
1288025 GCTTAAGATGATTGCTTCACTACTCTTCTGTGAAGGCTTAA
64 GCTTAAGATG-GTGCTTCACTACTCTTCTGTGAAGGCTTAA
* * *
1288066 GAT-GATTACTTCACTACTCTCCGGTGAAGGCTTAAGAT
1 GATGGTTTGCTTCACTACTCTCTGGTGAAGGCTTAAGAT
1288104 TGACTTACCC
Statistics
Matches: 400, Mismatches: 43, Indels: 33
0.84 0.09 0.07
Matches are distributed among these distances:
102 2 0.00
103 90 0.22
104 84 0.21
105 37 0.09
106 129 0.32
107 29 0.07
108 29 0.07
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (103 bp):
GATGGTTTGCTTCACTACTCTCTGGTGAAGGCTTAAGATGGTACTTCACTACTCTTTGTGAAGGC
TTAAGATGGTGCTTCACTACTCTTCTGTGAAGGCTTAA
Found at i:1290950 original size:2 final size:2
Alignment explanation
Indices: 1290939--1290981 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1290929 TTGTATACAC
1290939 AT AT -T 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
1290980 AT
1 AT
1290982 TGGGTACACG
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1293104 original size:6 final size:6
Alignment explanation
Indices: 1293093--1293125 Score: 57
Period size: 6 Copynumber: 5.3 Consensus size: 6
1293083 ACGTACATAC
1293093 AATGCA AATGCA AATGCCA AATGCA AATGCA AA
1 AATGCA AATGCA AATG-CA AATGCA AATGCA AA
1293126 AGGTGTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.52, C:0.18, G:0.15, T:0.15
Consensus pattern (6 bp):
AATGCA
Found at i:1293115 original size:13 final size:13
Alignment explanation
Indices: 1293093--1293122 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1293083 ACGTACATAC
1293093 AATG-CAAATGCA
1 AATGCCAAATGCA
1293105 AATGCCAAATGCA
1 AATGCCAAATGCA
1293118 AATGC
1 AATGC
1293123 AAAAGGTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.47, C:0.20, G:0.17, T:0.17
Consensus pattern (13 bp):
AATGCCAAATGCA
Found at i:1296952 original size:24 final size:24
Alignment explanation
Indices: 1296908--1296957 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1296898 ATAAAGAACC
*
1296908 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
1296932 AAAATAAAGTTCAAACA-ACCATTA
1 AAAATAAACTT-AAACATACCATTA
1296956 AA
1 AA
1296958 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:1303463 original size:40 final size:40
Alignment explanation
Indices: 1303408--1303490 Score: 148
Period size: 40 Copynumber: 2.1 Consensus size: 40
1303398 CTATTATCGA
* *
1303408 AAACAAGTATGGTGAAAGGAGTGTCAGAGATCAACTCTCC
1 AAACAAGTATGGTGAAAGGAGTGCCAGAGATCAACCCTCC
1303448 AAACAAGTATGGTGAAAGGAGTGCCAGAGATCAACCCTCC
1 AAACAAGTATGGTGAAAGGAGTGCCAGAGATCAACCCTCC
1303488 AAA
1 AAA
1303491 TTAATTATGT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.40, C:0.19, G:0.24, T:0.17
Consensus pattern (40 bp):
AAACAAGTATGGTGAAAGGAGTGCCAGAGATCAACCCTCC
Found at i:1311239 original size:29 final size:29
Alignment explanation
Indices: 1311197--1311253 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
1311187 TGTTTTTCCA
*
1311197 ATAAACCATTATCAAACGATGATTTGTTC
1 ATAAAACATTATCAAACGATGATTTGTTC
1311226 ATAAAACATTATCAAACGATGATTTGTT
1 ATAAAACATTATCAAACGATGATTTGTT
1311254 ACTATTTGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35
Consensus pattern (29 bp):
ATAAAACATTATCAAACGATGATTTGTTC
Found at i:1312038 original size:23 final size:22
Alignment explanation
Indices: 1311995--1312073 Score: 72
Period size: 23 Copynumber: 3.5 Consensus size: 22
1311985 AAAATATTTT
*
1311995 AAAATATGTATTTAATT-TTTAA
1 AAAATAT-TATTTATTTATTTAA
*
1312017 AATTATATTATTTATTTATTTAA
1 AA-AATATTATTTATTTATTTAA
* *
1312040 AAAAGTATTAATTATTTATTT-G
1 AAAA-TATTATTTATTTATTTAA
*
1312062 ATAATATTATTT
1 AAAATATTATTT
1312074 TTAAATTATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
21 7 0.15
22 14 0.30
23 26 0.55
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (22 bp):
AAAATATTATTTATTTATTTAA
Found at i:1312363 original size:11 final size:11
Alignment explanation
Indices: 1312347--1312371 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1312337 TATTTTAATT
1312347 TAATAATGATA
1 TAATAATGATA
1312358 TAATAATGATA
1 TAATAATGATA
1312369 TAA
1 TAA
1312372 ATATGTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (11 bp):
TAATAATGATA
Found at i:1317966 original size:17 final size:17
Alignment explanation
Indices: 1317944--1317982 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
1317934 TAAAAATATG
1317944 AATAAAAATATAATTAT
1 AATAAAAATATAATTAT
* *
1317961 AATAAAAATATATTTTT
1 AATAAAAATATAATTAT
1317978 AATAA
1 AATAA
1317983 CTCACCATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AATAAAAATATAATTAT
Found at i:1322171 original size:30 final size:30
Alignment explanation
Indices: 1322136--1322192 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
1322126 TAAAAGTGGT
*
1322136 ATAATTATATATTTGGTCCTTAATATTGGC
1 ATAATTATACATTTGGTCCTTAATATTGGC
1322166 ATAATTATACATTTGGTCCTTAATATT
1 ATAATTATACATTTGGTCCTTAATATT
1322193 TACATACTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47
Consensus pattern (30 bp):
ATAATTATACATTTGGTCCTTAATATTGGC
Found at i:1322562 original size:43 final size:42
Alignment explanation
Indices: 1322499--1322850 Score: 407
Period size: 44 Copynumber: 8.1 Consensus size: 42
1322489 AACCAAAAAT
* *
1322499 GCCGCAATAGGACAAGATCTATAGCGGCGTTTTTGGAACAAAC
1 GCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGAACAAAC
* * * *
1322542 ACCGCAAAAGGTTGATATCTATAGCGGTGTTTTTGGAACAAAC
1 GCCGCAAAAGG-TCAGATCTATAGCGGCGTTTTTGGAACAAAC
* ** *
1322585 GCCGCAATAGGTCAGATCTATAGCGGTATTTTTTTGAACAAAC
1 GCCGCAAAAGGTCAGATCTATAGCGG-CGTTTTTGGAACAAAC
* **
1322628 GCCGCAAAAGGTCAGATCTATAGCGGCATTTTTTTTAAACAAAC
1 GCCGCAAAAGGTCAGATCTATAGCGGC--GTTTTTGGAACAAAC
* * *
1322672 GCCTCAAAAGATCAGATATATAGCGGCGTTTTTTTGGAACAAAC
1 GCCGCAAAAGGTCAGATCTATAGCGGCG--TTTTTGGAACAAAC
*
1322716 GCCGCAAAAGGTCAAATCTATAGCGGCGTTTTTGGAACAAAC
1 GCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAACAAAC
* * * *
1322758 GCCGCAAAAGATTAGATATATAGCGGTGTTTTTTTGGAACAAAC
1 GCCGCAAAAGGTCAGATCTATAGCGGCG--TTTTTGGAACAAAC
*
1322802 TCACGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATACAAAC
1 GC-CGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGA-ACAAAC
1322846 GCCGC
1 GCCGC
1322851 TAATTTCCTT
Statistics
Matches: 262, Mismatches: 37, Indels: 20
0.82 0.12 0.06
Matches are distributed among these distances:
42 50 0.19
43 94 0.36
44 96 0.37
45 22 0.08
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.26
Consensus pattern (42 bp):
GCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAACAAAC
Found at i:1322661 original size:86 final size:86
Alignment explanation
Indices: 1322528--1322850 Score: 450
Period size: 87 Copynumber: 3.7 Consensus size: 86
1322518 TATAGCGGCG
* * * * *
1322528 TTTTTGGAACAAACACCGCAAAAGGTTGATATCTATAGCGGTGTTTTTGGAACAAACGCCGCAAT
1 TTTTTGGAACAAACGCCGCAAAAGG-TCAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAA
* * *
1322593 AGGTCAGATCTATAGCGGTATT
65 AGATCAGATATATAGCGGTGTT
* ** *
1322615 TTTTT-GAACAAACGCCGCAAAAGGTCAGATCTATAGCGGCATTTTTTTTAAACAAACGCCTCAA
1 TTTTTGGAACAAACGCCGCAAAAGGTCAGATCTATAGCGGC--GTTTTTGGAACAAACGCCGCAA
*
1322679 AAGATCAGATATATAGCGGCGTT
64 AAGATCAGATATATAGCGGTGTT
*
1322702 TTTTTGGAACAAACGCCGCAAAAGGTCAAATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAA
1 TTTTTGGAACAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAA
*
1322767 GATTAGATATATAGCGGTGTT
66 GATCAGATATATAGCGGTGTT
*
1322788 TTTTTGGAACAAACTCACGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATACAAACGCCGC
1 TTTTTGGAACAAACGC-CGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGA-ACAAACGCCGC
1322851 TAATTTCCTT
Statistics
Matches: 209, Mismatches: 22, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
85 13 0.06
86 72 0.34
87 79 0.38
88 45 0.22
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.27
Consensus pattern (86 bp):
TTTTTGGAACAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAA
GATCAGATATATAGCGGTGTT
Found at i:1322720 original size:131 final size:129
Alignment explanation
Indices: 1322561--1322850 Score: 384
Period size: 130 Copynumber: 2.2 Consensus size: 129
1322551 GGTTGATATC
* * * * *
1322561 TATAGCGGTGTTTTTGGAACAAACGCCGCAATAGGTCAGATCTATAGCGGTATTTTTTTGAACAA
1 TATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCAAATCTATAGCGG-AGTTTTTGGAACAA
* * * *
1322626 ACGCCGCAAAAGGTCAGATCTATAGCGGCATTTTTTTTAAACAAACGC-CTCAAAAGATCAGATA
65 ACGCCGCAAAAGATCAGATATATAGCGGCATTTTTTTGAAACAAACGCACGCAAAAGATCAGATA
*
1322690 TATAGCGGCGTTTTTTTGGAACAAACGCCGCAAAAGGTCAAATCTATAGCGGCGTTTTTGGAACA
1 TATAGCGGCG--TTTTTGGAACAAACGCCGCAAAAGGTCAAATCTATAGCGGAGTTTTTGGAACA
* ** * * *
1322755 AACGCCGCAAAAGATTAGATATATAGCGGTGTTTTTTTGGAACAAACTCACGCAAAAGGTCAGAT
64 AACGCCGCAAAAGATCAGATATATAGCGGCATTTTTTTGAAACAAACGCACGCAAAAGATCAGAT
*
1322820 C
129 A
1322821 TATAGCGGCGTTTTTGGATACAAACGCCGC
1 TATAGCGGCGTTTTTGGA-ACAAACGCCGC
1322851 TAATTTCCTT
Statistics
Matches: 140, Mismatches: 17, Indels: 7
0.85 0.10 0.04
Matches are distributed among these distances:
129 17 0.12
130 62 0.44
131 61 0.44
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (129 bp):
TATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCAAATCTATAGCGGAGTTTTTGGAACAAA
CGCCGCAAAAGATCAGATATATAGCGGCATTTTTTTGAAACAAACGCACGCAAAAGATCAGATA
Found at i:1324652 original size:16 final size:17
Alignment explanation
Indices: 1324633--1324664 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1324623 GATAAAAAAA
1324633 TTTAAA-AAATTATTTG
1 TTTAAATAAATTATTTG
1324649 TTTAAATAAATTATTT
1 TTTAAATAAATTATTT
1324665 TTTCTTTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTAAATAAATTATTTG
Found at i:1324786 original size:93 final size:95
Alignment explanation
Indices: 1324677--1324903 Score: 386
Period size: 95 Copynumber: 2.4 Consensus size: 95
1324667 TCTTTAACCA
** *
1324677 TTAATCGAATTGAAATTTATTTGAAAATTATTAACCGAACCAAATTAACTG-ATT-TTTTTCTTT
1 TTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCGAATTATTTTTCTTT
*
1324740 AACATTAATCGAACCGAAATTATTTGACCG
66 AACATTAATCCAACCGAAATTATTTGACCG
*
1324770 TTAATCGAACCGAAATTTATTTGAAAATTATTAACTGAACCAAATTAACCGAATTATTTTTCTTT
1 TTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCGAATTATTTTTCTTT
1324835 AACATTAATCCAACCGAAATTATTTGACCG
66 AACATTAATCCAACCGAAATTATTTGACCG
*
1324865 TTAATCGAACCGAAATTTATTTGAAAATTTTTAACCGAA
1 TTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAA
1324904 TTTTTTCCTT
Statistics
Matches: 125, Mismatches: 7, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
93 47 0.38
94 3 0.02
95 75 0.60
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (95 bp):
TTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCGAATTATTTTTCTTT
AACATTAATCCAACCGAAATTATTTGACCG
Found at i:1324936 original size:81 final size:81
Alignment explanation
Indices: 1324813--1324987 Score: 244
Period size: 81 Copynumber: 2.2 Consensus size: 81
1324803 ACTGAACCAA
* * * * *
1324813 ATTAACCGAATTATTTTTCTTTAACATTAATCCAACCGAAATTATTTGACCGTTAATCGAACCGA
1 ATTAACCGAATTATTTTCCTTTAACACTAATACAACCAAAATTATTTGACCGTTAATCGAACCCA
*
1324878 AATTTATTTGAAAATT
66 AATTTATTTAAAAATT
* * *
1324894 TTTAACCGAATT-TTTTCCTTTAGCCACTAATAGAACCAAAATTATTTGACCGTTAATCGAACCC
1 ATTAACCGAATTATTTTCCTTTA-ACACTAATACAACCAAAATTATTTGACCGTTAATCGAACCC
1324958 AAATTTATTTAAAAATT
65 AAATTTATTTAAAAATT
*
1324975 ATTAACTGAATTA
1 ATTAACCGAATTA
1324988 ACCGAATAAA
Statistics
Matches: 81, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
80 9 0.11
81 72 0.89
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.38
Consensus pattern (81 bp):
ATTAACCGAATTATTTTCCTTTAACACTAATACAACCAAAATTATTTGACCGTTAATCGAACCCA
AATTTATTTAAAAATT
Found at i:1325079 original size:68 final size:71
Alignment explanation
Indices: 1324942--1325110 Score: 193
Period size: 74 Copynumber: 2.4 Consensus size: 71
1324932 AAATTATTTG
* * * *
1324942 ACCGTTAATCGAACCCAAATTTATTTAAAAATTATTAACTGAATTAACCGAATAAAATAAATTAT
1 ACCGTTAATCGAACCAAAATTTATTTGAAAATTATTAACTG-A--AACCAAATAAAACAAATTAT
1325007 TTTTCTTTA
63 TTTTCTTTA
* * **
1325016 ACCGTTAATCGAATCAAAATTTATTTGAAAATTATTAACTG-AACCAAAT-CAACCGATT-TTTT
1 ACCGTTAATCGAACCAAAATTTATTTGAAAATTATTAACTGAAACCAAATAAAACAAATTATTTT
1325078 TCTTTA
66 TCTTTA
* *
1325084 ACCATTAATCGAACCAACA-TTATTTGA
1 ACCGTTAATCGAACCAAAATTTATTTGA
1325111 CCGTTAATCG
Statistics
Matches: 84, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
67 8 0.10
68 26 0.31
69 5 0.06
70 7 0.08
74 38 0.45
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.37
Consensus pattern (71 bp):
ACCGTTAATCGAACCAAAATTTATTTGAAAATTATTAACTGAAACCAAATAAAACAAATTATTTT
TCTTTA
Found at i:1325132 original size:168 final size:166
Alignment explanation
Indices: 1324652--1325222 Score: 627
Period size: 168 Copynumber: 3.4 Consensus size: 166
1324642 TTATTTGTTT
*** *
1324652 AAATAAATTATTTTTTCTTTAACCATTAATCGAATTGAAATTTATTTGAAAATTATTAACCGAAC
1 AAATAAATTA-TTTTTCTTTAACCATTAATCGAACCAAAATTTATTTGAAAATTATTAACTGAAC
*
1324717 CAAATTAACTGATTTTTTTCTTTAA-CATTAATCGAACCGAAATTATTTGACCGTTAATCGAACC
65 CAAATTAACCGATTTTTTTCTTTAACCATTAATCGAACC-AAATTATTTGACCGTTAATCGAACC
* *
1324781 GAAATTTATTTGAAAATTATTAACTG---AACCAAATT
129 GAAATTTATTTGAAAATTATTAACTGATTAACCGAATA
*** * *
1324816 AACCGAATTATTTTTCTTTAA-CATTAATCCAACCGAAATTATTTGACCGTTAATCGAACCGAAA
1 AAATAAATTATTTTTCTTTAACCATTAATCGAACC-AAA--ATTT-A---TT--T-GAA---AAT
** * * * * *
1324880 T-TTATTTGAA--AATTTTTAACCGAATTTTTTCCTTTAGCCACTAATAGAACCAAAATTATTTG
53 TATTAACTGAACCAA--ATTAACCG-ATTTTTTTCTTTAACCATTAATCGAACC-AAATTATTTG
* *
1324942 ACCGTTAATCGAACCCAAATTTATTTAAAAATTATTAACTGAATTAACCGAATA
114 ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACTG-ATTAACCGAATA
* *
1324996 AAATAAATTATTTTTCTTTAACCGTTAATCGAATCAAAATTTATTTGAAAATTATTAACTGAACC
1 AAATAAATTATTTTTCTTTAACCATTAATCGAACCAAAATTTATTTGAAAATTATTAACTGAACC
* *
1325061 AAATCAACCGATTTTTTTCTTTAACCATTAATCGAACCAACATTATTTGACCGTTAATCGAATCG
66 AAATTAACCGATTTTTTTCTTTAACCATTAATCGAACCAA-ATTATTTGACCGTTAATCGAACCG
*
1325126 AAATTTATTTGAAAATTATTAACCGGATTAACCGAATA
130 AAATTTATTTGAAAATTATTAA-CTGATTAACCGAATA
* * *
1325164 AAATAAATTATTTTTCCTTAACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAAC
1 AAATAAATTATTTTTCTTTAACCATTAATCGAACCAAAATTTATTTGAAAATTATTAAC
1325223 CAATCTTTAA
Statistics
Matches: 336, Mismatches: 44, Indels: 50
0.78 0.10 0.12
Matches are distributed among these distances:
162 10 0.03
163 13 0.04
164 7 0.02
165 4 0.01
166 1 0.00
167 2 0.01
168 138 0.41
169 17 0.05
171 6 0.02
172 6 0.02
174 14 0.04
175 15 0.04
176 60 0.18
177 1 0.00
178 4 0.01
180 28 0.08
181 10 0.03
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.37
Consensus pattern (166 bp):
AAATAAATTATTTTTCTTTAACCATTAATCGAACCAAAATTTATTTGAAAATTATTAACTGAACC
AAATTAACCGATTTTTTTCTTTAACCATTAATCGAACCAAATTATTTGACCGTTAATCGAACCGA
AATTTATTTGAAAATTATTAACTGATTAACCGAATA
Found at i:1325222 original size:37 final size:36
Alignment explanation
Indices: 1325110--1325223 Score: 88
Period size: 37 Copynumber: 3.1 Consensus size: 36
1325100 ACATTATTTG
1325110 ACCGTTAATCGAATCGAAATTTATTTGAAAATTATTA
1 ACCGTTAATCGAA-CGAAATTTATTTGAAAATTATTA
* * * * * *** *
1325147 ACCGGATTAACCGAA-TAAAATAAATT-ATTTTTCCTTA
1 ACC-G-TTAATCGAACGAAATTTATTTGAAAATT-ATTA
1325184 ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTA
1 ACCGTTAATCGAA-CGAAATTTATTTGAAAATTATTA
1325221 ACC
1 ACC
1325224 AATCTTTAAC
Statistics
Matches: 53, Mismatches: 18, Indels: 12
0.64 0.22 0.14
Matches are distributed among these distances:
35 8 0.15
36 4 0.08
37 29 0.55
38 4 0.08
39 8 0.15
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (36 bp):
ACCGTTAATCGAACGAAATTTATTTGAAAATTATTA
Found at i:1325265 original size:74 final size:75
Alignment explanation
Indices: 1325078--1325379 Score: 303
Period size: 74 Copynumber: 4.0 Consensus size: 75
1325068 CCGATTTTTT
* *
1325078 TCTTTAACCATTAATCGAACC-AACATTATTTGACCGTTAATCGAATCGAAATTTATTTGAAAAT
1 TCTTTAACCATTAATCGAACCGAA-ATTATTTGACCGTTAATCAAACCGAAATTTATTTGAAAAT
*
1325142 TATTAACCGGA
65 TATTAACCGAA
* *** *** * * * *
1325153 ---TTAACCGAATAAAATAA-ATTATTTTTCCTTAACCGTTAATCGAACCGAAATTTATTTGAAA
1 TCTTTAACC-ATTAATCGAACCGAAATTAT--TTGACCGTTAATCAAACCGAAATTTATTTGAAA
1325214 ATTATTAACC-AA
63 ATTATTAACCGAA
*
1325226 TCTTTAACCATTAATCGAACCGAAATTATTTGACTGTTAATCAAACCGAAATTTATTTGAAAATT
1 TCTTTAACCATTAATCGAACCGAAATTATTTGACCGTTAATCAAACCGAAATTTATTTGAAAATT
1325291 ATTAACCGAA
66 ATTAACCGAA
* * *
1325301 TTTTTTTCTTTAACCA-TAATCGAACCGAAATTATTTAATCGTTAATCAAACCAAAATTTATTTG
1 ------TCTTTAACCATTAATCGAACCGAAATTATTTGACCGTTAATCAAACCGAAATTTATTTG
1325365 AAAATTATTAACCGA
60 AAAATTATTAACCGA
1325380 TTAATGATTA
Statistics
Matches: 185, Mismatches: 27, Indels: 25
0.78 0.11 0.11
Matches are distributed among these distances:
72 9 0.05
73 8 0.04
74 81 0.44
75 8 0.04
76 10 0.05
80 59 0.32
81 10 0.05
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (75 bp):
TCTTTAACCATTAATCGAACCGAAATTATTTGACCGTTAATCAAACCGAAATTTATTTGAAAATT
ATTAACCGAA
Found at i:1325349 original size:80 final size:81
Alignment explanation
Indices: 1325226--1325379 Score: 267
Period size: 80 Copynumber: 1.9 Consensus size: 81
1325216 TATTAACCAA
* *
1325226 TCTTTAACCATTAATCGAACCGAAATTATTTGACTGTTAATCAAACCGAAATTTATTTGAAAATT
1 TCTTTAACCATTAATCGAACCGAAATTATTTAACTGTTAATCAAACCAAAATTTATTTGAAAATT
1325291 ATTAACCGAATTTTTT
66 ATTAACCGAATTTTTT
1325307 TCTTTAACCA-TAATCGAACCGAAATTATTTAA-TCGTTAATCAAACCAAAATTTATTTGAAAAT
1 TCTTTAACCATTAATCGAACCGAAATTATTTAACT-GTTAATCAAACCAAAATTTATTTGAAAAT
1325370 TATTAACCGA
65 TATTAACCGA
1325380 TTAATGATTA
Statistics
Matches: 70, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
79 1 0.01
80 59 0.84
81 10 0.14
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.37
Consensus pattern (81 bp):
TCTTTAACCATTAATCGAACCGAAATTATTTAACTGTTAATCAAACCAAAATTTATTTGAAAATT
ATTAACCGAATTTTTT
Found at i:1328032 original size:21 final size:20
Alignment explanation
Indices: 1328008--1328052 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
1327998 TCAGGATGAG
*
1328008 AGTATCAATAGTGAACCCTTC
1 AGTATCAATACTG-ACCCTTC
* *
1328029 AGTATCGATACTGACCCTTG
1 AGTATCAATACTGACCCTTC
1328049 AGTA
1 AGTA
1328053 CCGATATTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (20 bp):
AGTATCAATACTGACCCTTC
Found at i:1328047 original size:20 final size:21
Alignment explanation
Indices: 1328008--1328058 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
1327998 TCAGGATGAG
* *
1328008 AGTATCAATAGTGAACCCTTC
1 AGTATCGATACTGAACCCTTC
*
1328029 AGTATCGATACTG-ACCCTTG
1 AGTATCGATACTGAACCCTTC
*
1328049 AGTACCGATA
1 AGTATCGATA
1328059 TTCACCCTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (21 bp):
AGTATCGATACTGAACCCTTC
Found at i:1328065 original size:20 final size:20
Alignment explanation
Indices: 1328022--1328068 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
1328012 TCAATAGTGA
* * *
1328022 ACCCTTCAGTATCGATACTG
1 ACCCTTGAGTACCGATACTC
*
1328042 ACCCTTGAGTACCGATATTC
1 ACCCTTGAGTACCGATACTC
1328062 ACCCTTG
1 ACCCTTG
1328069 GTATCAATAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.32, G:0.15, T:0.30
Consensus pattern (20 bp):
ACCCTTGAGTACCGATACTC
Found at i:1330062 original size:25 final size:24
Alignment explanation
Indices: 1330041--1330096 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
1330031 TTTATATTAA
1330041 TTATATAT-ATAATATATAATATT
1 TTATATATAATAATATATAATATT
*
1330064 TT-TCATATTAATTATATATAATATT
1 TTAT-ATA-TAATAATATATAATATT
1330089 TTATATAT
1 TTATATAT
1330097 TTTATATTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
22 1 0.04
23 5 0.18
24 2 0.07
25 19 0.68
26 1 0.04
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (24 bp):
TTATATATAATAATATATAATATT
Found at i:1330080 original size:32 final size:32
Alignment explanation
Indices: 1330027--1330136 Score: 150
Period size: 32 Copynumber: 3.4 Consensus size: 32
1330017 ATTTTTTTTA
*
1330027 ATTTTTTATATTAATTATATATATAATATATAAT
1 ATTTTTTATATTAA-T-TATATATAATATATTAT
* *
1330061 ATTTTTCATATTAATTATATATAATATTTTAT
1 ATTTTTTATATTAATTATATATAATATATTAT
*
1330093 ATATTTTATATTAATTATATATAATA-ATTTAT
1 ATTTTTTATATTAATTATATATAATATA-TTAT
1330125 ATTTTTTATATT
1 ATTTTTTATATT
1330137 TTTATATTTT
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
32 54 0.79
33 1 0.01
34 13 0.19
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (32 bp):
ATTTTTTATATTAATTATATATAATATATTAT
Found at i:1330094 original size:14 final size:14
Alignment explanation
Indices: 1330075--1330126 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
1330065 TTCATATTAA
1330075 TTATATATAATATT
1 TTATATATAATATT
*
1330089 TTATATATTTTATATT
1 TTATATA--TAATATT
*
1330105 AATTATATATAATAAT
1 --TTATATATAATATT
1330121 TTATAT
1 TTATAT
1330127 TTTTTATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
14 13 0.42
16 11 0.35
18 7 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTATATATAATATT
Found at i:1330134 original size:9 final size:9
Alignment explanation
Indices: 1330120--1330166 Score: 71
Period size: 9 Copynumber: 5.4 Consensus size: 9
1330110 TATATAATAA
1330120 TTTATATTT
1 TTTATATTT
1330129 TTTATA-TT
1 TTTATATTT
1330137 TTTATA-TT
1 TTTATATTT
1330145 TTTATATTT
1 TTTATATTT
*
1330154 TTTCTATTT
1 TTTATATTT
1330163 TTTA
1 TTTA
1330167 AATGAAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
8 16 0.46
9 19 0.54
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTATATTT
Found at i:1330142 original size:17 final size:18
Alignment explanation
Indices: 1330120--1330166 Score: 71
Period size: 17 Copynumber: 2.7 Consensus size: 18
1330110 TATATAATAA
1330120 TTTATATTTTTTATA-TT
1 TTTATATTTTTTATATTT
1330137 TTTATA-TTTTTATATTT
1 TTTATATTTTTTATATTT
*
1330154 TTTCTATTTTTTA
1 TTTATATTTTTTA
1330167 AATGAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 8 0.30
17 13 0.48
18 6 0.22
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTATATTTTTTATATTT
Found at i:1330164 original size:8 final size:8
Alignment explanation
Indices: 1330120--1330155 Score: 63
Period size: 8 Copynumber: 4.4 Consensus size: 8
1330110 TATATAATAA
1330120 TTTATATTT
1 TTTATA-TT
1330129 TTTATATT
1 TTTATATT
1330137 TTTATATT
1 TTTATATT
1330145 TTTATATT
1 TTTATATT
1330153 TTT
1 TTT
1330156 TCTATTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 21 0.78
9 6 0.22
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTATATT
Found at i:1335469 original size:36 final size:36
Alignment explanation
Indices: 1335427--1335499 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
1335417 TCAACTTGTC
1335427 TAGTTGAATATTTTTTTCGAAACACATGGTTAAAGA
1 TAGTTGAATATTTTTTTCGAAACACATGGTTAAAGA
1335463 TAGTTGAATATTTTTTTCGAAACACATGGTTAAAGA
1 TAGTTGAATATTTTTTTCGAAACACATGGTTAAAGA
1335499 T
1 T
1335500 TTTCAATAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (36 bp):
TAGTTGAATATTTTTTTCGAAACACATGGTTAAAGA
Found at i:1335787 original size:117 final size:117
Alignment explanation
Indices: 1335620--1335849 Score: 345
Period size: 117 Copynumber: 2.0 Consensus size: 117
1335610 ACTGAAAACT
* * * * *
1335620 TTCTGTCATGGTGCATTATTTTTCATGTGAGAAATGTATGTTTCTCTGATATGAACTGATATATC
1 TTCTGCCATGGTGCATTATTTTGCATATGAGAAATGTACGTTTCTCTGATATGAACTGACATATC
* *
1335685 ACCACTGAAAAGTTTGTTGAAATGAGTTGATATATCACTGAAAAGTTGTTGA
66 ACCACTAAAAAGTTTGCTGAAATGAGTTGATATATCACTGAAAAGTTGTTGA
* * *
1335737 TTCTGCCATGGTGCATTATTTTGCCTATGAGAAATGTACGTTT-TATTGATATGAAGTGACATAT
1 TTCTGCCATGGTGCATTATTTTGCATATGAGAAATGTACGTTTCT-CTGATATGAACTGACATAT
*
1335801 CACCATTAAAAAGTTTGCTGAAATGAGTTGATATATCACTGAAAAGTTG
65 CACCACTAAAAAGTTTGCTGAAATGAGTTGATATATCACTGAAAAGTTG
1335850 CTTAAGATAA
Statistics
Matches: 101, Mismatches: 11, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
116 1 0.01
117 100 0.99
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.38
Consensus pattern (117 bp):
TTCTGCCATGGTGCATTATTTTGCATATGAGAAATGTACGTTTCTCTGATATGAACTGACATATC
ACCACTAAAAAGTTTGCTGAAATGAGTTGATATATCACTGAAAAGTTGTTGA
Found at i:1336000 original size:143 final size:144
Alignment explanation
Indices: 1335740--1336304 Score: 766
Period size: 143 Copynumber: 4.0 Consensus size: 144
1335730 TTGTTGATTC
* *
1335740 TGCCATGGTGCATTATTTTGCCTATGAGAAATGTACG-TTTTATTGATATGAAGTGACATATCAC
1 TGCCATGGTGCATTATTTTGCCTATGAGAAATGCACGTTTTTA-TGATATGAAGTGATATATCAC
*
1335804 CA-TTAAAAAGTTTGCTGAAATGAGTTGATATATCACTGAAAAGTTGCTTAAGATAATTAATTGA
65 CACTTAAAAAGTTTGCTGAAATGAGTTGATATATCACTGAAAAGTTGCTTAAGATAATTAATTGG
*
1335868 GTACTGAAAAGTTTT
130 GCACTGAAAAGTTTT
*
1335883 TGCCATGGTGCATTATTTTGCCTATGAGAAATGCACGTTTTTATGATATTAAGTGATATATCACC
1 TGCCATGGTGCATTATTTTGCCTATGAGAAATGCACGTTTTTATGATATGAAGTGATATATCACC
* **
1335948 ACTT-AAAAGTTTGTTGAAATGAGTTGATATATCACTGAAAAGTTGCAGAAGATAATTAATTGGG
66 ACTTAAAAAGTTTGCTGAAATGAGTTGATATATCACTGAAAAGTTGCTTAAGATAATTAATTGGG
* *
1336012 CACTAAAAAGTTTC
131 CACTGAAAAGTTTT
* * * * * *
1336026 TACTATGGTACATTATTTTGTCTATGAGAAATGCACGTTTTT-TTATACGAAGTGATATATCACC
1 TGCCATGGTGCATTATTTTGCCTATGAGAAATGCACGTTTTTATGATATGAAGTGATATATCACC
* * * * *
1336090 -GTTGAAAA-TTTAGCTGAAATGAGTTCATATATCACCGAAAAGTTTCTTAAGATAATTAATTGG
66 ACTTAAAAAGTTT-GCTGAAATGAGTTGATATATCACTGAAAAGTTGCTTAAGATAATTAATTGG
1336153 GCACTGAAAAGTTTT
130 GCACTGAAAAGTTTT
* * * * * * **
1336168 TGACATGGTGCATTATTTTGCCTATGAGAAATGCATGTTTTTCTGATATTAAGTGATGTGTCTTC
1 TGCCATGGTGCATTATTTTGCCTATGAGAAATGCACGTTTTTATGATATGAAGTGATATATCACC
* * * *
1336233 ACCT-AAAAGTTTGCTTAAATGAGTTGATATATTACTGAAAAGTTGTTTAAGATAATTAATTGGG
66 ACTTAAAAAGTTTGCTGAAATGAGTTGATATATCACTGAAAAGTTGCTTAAGATAATTAATTGGG
1336297 CACTGAAA
131 CACTGAAA
1336305 GTTGATTTTT
Statistics
Matches: 368, Mismatches: 47, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
141 5 0.01
142 117 0.32
143 235 0.64
144 11 0.03
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (144 bp):
TGCCATGGTGCATTATTTTGCCTATGAGAAATGCACGTTTTTATGATATGAAGTGATATATCACC
ACTTAAAAAGTTTGCTGAAATGAGTTGATATATCACTGAAAAGTTGCTTAAGATAATTAATTGGG
CACTGAAAAGTTTT
Found at i:1336299 original size:285 final size:286
Alignment explanation
Indices: 1335744--1336300 Score: 850
Period size: 285 Copynumber: 2.0 Consensus size: 286
1335734 TGATTCTGCC
* * *
1335744 ATGGTGCATTATTTTGCCTATGAGAAATGTACGTTTTATTGATATGAAGTGACATATCACCATTA
1 ATGGTACATTATTTTGCCTATGAGAAATGCACGTTTTATTGATACGAAGTGACATATCACCATTA
* * *
1335809 AAAAGTTTGCTGAAATGAGTTGATATATCACTGAAAAGTTGCTTAAGATAATTAATTGAGTACTG
66 AAAAGTTTGCTGAAATGAGTTCATATATCACCGAAAAGTTGCTTAAGATAATTAATTGAGCACTG
*
1335874 AAAAGTTTTTGCCATGGTGCATTATTTTGCCTATGAGAAATGCACGTTTTTATGATATTAAGTGA
131 AAAAGTTTTTGACATGGTGCATTATTTTGCCTATGAGAAATGCACGTTTTTATGATATTAAGTGA
*
1335939 TATATCACCACTTAAAAGTTTGTTGAAATGAGTTGATATATCACTGAAAAGTTGCAGAAGATAAT
196 TATATCACCACCTAAAAGTTTGTTGAAATGAGTTGATATATCACTGAAAAGTTGCAGAAGATAAT
1336004 TAATTGGGCACTAAAAAGTTTCTACT
261 TAATTGGGCACTAAAAAGTTTCTACT
* * * * *
1336030 ATGGTACATTATTTTGTCTATGAGAAATGCACGTTTT-TTTATACGAAGTGATATATCACCGTTG
1 ATGGTACATTATTTTGCCTATGAGAAATGCACGTTTTATTGATACGAAGTGACATATCACCATTA
* *
1336094 AAAA-TTTAGCTGAAATGAGTTCATATATCACCGAAAAGTTTCTTAAGATAATTAATTGGGCACT
66 AAAAGTTT-GCTGAAATGAGTTCATATATCACCGAAAAGTTGCTTAAGATAATTAATTGAGCACT
* *
1336158 GAAAAGTTTTTGACATGGTGCATTATTTTGCCTATGAGAAATGCATGTTTTTCTGATATTAAGTG
130 GAAAAGTTTTTGACATGGTGCATTATTTTGCCTATGAGAAATGCACGTTTTTATGATATTAAGTG
* * ** * ***
1336223 ATGTGTCTTCACCTAAAAGTTTGCTT-AAATGAGTTGATATATTACTGAAAAGTTGTTTAAGATA
195 ATATATCACCACCTAAAAGTTTG-TTGAAATGAGTTGATATATCACTGAAAAGTTGCAGAAGATA
1336287 ATTAATTGGGCACT
259 ATTAATTGGGCACT
1336301 GAAAGTTGAT
Statistics
Matches: 244, Mismatches: 25, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
284 3 0.01
285 205 0.84
286 36 0.15
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.37
Consensus pattern (286 bp):
ATGGTACATTATTTTGCCTATGAGAAATGCACGTTTTATTGATACGAAGTGACATATCACCATTA
AAAAGTTTGCTGAAATGAGTTCATATATCACCGAAAAGTTGCTTAAGATAATTAATTGAGCACTG
AAAAGTTTTTGACATGGTGCATTATTTTGCCTATGAGAAATGCACGTTTTTATGATATTAAGTGA
TATATCACCACCTAAAAGTTTGTTGAAATGAGTTGATATATCACTGAAAAGTTGCAGAAGATAAT
TAATTGGGCACTAAAAAGTTTCTACT
Found at i:1341065 original size:11 final size:11
Alignment explanation
Indices: 1341051--1341075 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1341041 TATTAATAAC
1341051 ATAAAAGTTTA
1 ATAAAAGTTTA
1341062 ATAAAAGTTTA
1 ATAAAAGTTTA
1341073 ATA
1 ATA
1341076 CACATGATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (11 bp):
ATAAAAGTTTA
Found at i:1342281 original size:2 final size:2
Alignment explanation
Indices: 1342270--1342305 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1342260 TTTATATCAT
1342270 TA TA -A TA TA TA 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 TA TA TA T
1342306 CATCCTTTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1356756 original size:103 final size:106
Alignment explanation
Indices: 1356573--1356778 Score: 267
Period size: 103 Copynumber: 2.0 Consensus size: 106
1356563 TCATCGCCTT
* * *
1356573 CTTCTTTATCCCATCATCTTCTTCCCTAATCTTAAATCATTAAATCTCCATGTTTTGCTATACTC
1 CTTCTTTATCCCATCATCTTCTTCCCCAATCTTAAAGCATTAAATCTCCATGTTTTGCTATACTA
*
1356638 TTTCTTTAATCCACCATTATATTCTAA-ATTAAAAATCATAA
66 TTTCTTTAATCCACCATTATAATC-AAGATTAAAAATCATAA
* * * *
1356679 CTTCTTTATCTCATCATTTTC-TCCCCAATC-TCAAGCATTAAATCT-CATGTTTTGCTATGCTA
1 CTTCTTTATCCCATCATCTTCTTCCCCAATCTTAAAGCATTAAATCTCCATGTTTTGCTATACTA
** * *
1356741 TTTCTTTGGTTCACCATTATAATCAAGATTTAAAATCA
66 TTTCTTTAATCCACCATTATAATCAAGATTAAAAATCA
1356779 ATACACAATT
Statistics
Matches: 87, Mismatches: 12, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
102 2 0.02
103 45 0.52
104 13 0.15
105 8 0.09
106 19 0.22
ACGTcount: A:0.29, C:0.24, G:0.04, T:0.43
Consensus pattern (106 bp):
CTTCTTTATCCCATCATCTTCTTCCCCAATCTTAAAGCATTAAATCTCCATGTTTTGCTATACTA
TTTCTTTAATCCACCATTATAATCAAGATTAAAAATCATAA
Found at i:1363673 original size:6 final size:6
Alignment explanation
Indices: 1363662--1363688 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1363652 TGAAAATTAG
1363662 CAAATA CAAATA CAAATA CAAATA CAA
1 CAAATA CAAATA CAAATA CAAATA CAA
1363689 GAACAAGTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.67, C:0.19, G:0.00, T:0.15
Consensus pattern (6 bp):
CAAATA
Found at i:1364940 original size:21 final size:21
Alignment explanation
Indices: 1364916--1364965 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
1364906 TTAAGAACAT
1364916 TAATGTTTTAGGTAGAAATAA
1 TAATGTTTTAGGTAGAAATAA
1364937 TAATGTTTTAGGTAGAAATAA
1 TAATGTTTTAGGTAGAAATAA
1364958 TAATGTTT
1 TAATGTTT
1364966 CCCGTAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.40, C:0.00, G:0.18, T:0.42
Consensus pattern (21 bp):
TAATGTTTTAGGTAGAAATAA
Found at i:1366970 original size:63 final size:63
Alignment explanation
Indices: 1366871--1366996 Score: 252
Period size: 63 Copynumber: 2.0 Consensus size: 63
1366861 AATTTTGATC
1366871 AGGAGATTGGAGATTGTGTAAAAAGCTATGAAGAGATAAAGTCCGGTAAAATATTCGGATAAT
1 AGGAGATTGGAGATTGTGTAAAAAGCTATGAAGAGATAAAGTCCGGTAAAATATTCGGATAAT
1366934 AGGAGATTGGAGATTGTGTAAAAAGCTATGAAGAGATAAAGTCCGGTAAAATATTCGGATAAT
1 AGGAGATTGGAGATTGTGTAAAAAGCTATGAAGAGATAAAGTCCGGTAAAATATTCGGATAAT
1366997 CACATTAAAT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.41, C:0.06, G:0.27, T:0.25
Consensus pattern (63 bp):
AGGAGATTGGAGATTGTGTAAAAAGCTATGAAGAGATAAAGTCCGGTAAAATATTCGGATAAT
Found at i:1368450 original size:31 final size:31
Alignment explanation
Indices: 1368415--1368473 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
1368405 ATTAGGCACT
*
1368415 AAATTACAAATTTATATAAATT-ATGAGTTTG
1 AAATT-CAAATTGATATAAATTGATGAGTTTG
* *
1368446 AAATTGAAATTGGTATAAATTGATGAGT
1 AAATTCAAATTGATATAAATTGATGAGT
1368474 AGACATTGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 13 0.54
31 11 0.46
ACGTcount: A:0.44, C:0.02, G:0.15, T:0.39
Consensus pattern (31 bp):
AAATTCAAATTGATATAAATTGATGAGTTTG
Done.