Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008209.1 Hibiscus syriacus cultivar Beakdansim tig00110831_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: 6561538
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 27 of 30
Found at i:5906103 original size:33 final size:33
Alignment explanation
Indices: 5906060--5906171 Score: 147
Period size: 33 Copynumber: 3.4 Consensus size: 33
5906050 CGAAATTAAA
* *
5906060 TTCGCGTTGCGATTCCCTCGTTGCGATTTTCAT
1 TTCGCATTGCGATTCACTCGTTGCGATTTTCAT
*
5906093 TTCGCATTGCGAAATT-AGT-GTTGCGATTTTCAT
1 TTCGCATTGCG--ATTCACTCGTTGCGATTTTCAT
* *
5906126 TTCGCATTGTGATTCTCTCGTTGCGATTTTCAT
1 TTCGCATTGCGATTCACTCGTTGCGATTTTCAT
5906159 TTCGCATTGCGAT
1 TTCGCATTGCGAT
5906172 AGTAATTTCC
Statistics
Matches: 68, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
31 3 0.04
32 1 0.01
33 60 0.88
34 1 0.01
35 3 0.04
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.44
Consensus pattern (33 bp):
TTCGCATTGCGATTCACTCGTTGCGATTTTCAT
Found at i:5906104 original size:19 final size:19
Alignment explanation
Indices: 5906080--5906171 Score: 69
Period size: 19 Copynumber: 5.4 Consensus size: 19
5906070 GATTCCCTCG
5906080 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
** *
5906099 TTGCGAAATT-A-GT-G--
1 TTGCGATTTTCATTTCGCA
5906113 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
5906132 TTGTGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
5906146 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5906165 TTGCGAT
1 TTGCGAT
5906172 AGTAATTTCC
Statistics
Matches: 53, Mismatches: 10, Indels: 20
0.64 0.12 0.24
Matches are distributed among these distances:
14 13 0.25
15 1 0.02
16 9 0.17
17 9 0.17
18 1 0.02
19 20 0.38
ACGTcount: A:0.16, C:0.18, G:0.20, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:5908481 original size:12 final size:12
Alignment explanation
Indices: 5908464--5908488 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5908454 TCTTCGGGGA
5908464 CTTTTTCTTCTT
1 CTTTTTCTTCTT
5908476 CTTTTTCTTCTT
1 CTTTTTCTTCTT
5908488 C
1 C
5908489 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:5908697 original size:24 final size:24
Alignment explanation
Indices: 5908663--5908716 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
5908653 CTGAAACATC
* *
5908663 ATCAAAATCCATGTATTGACCAAT
1 ATCAAAATCCAGGTATTGACCAAG
*
5908687 ATCAAAGTCCAGGTATTGACCAAG
1 ATCAAAATCCAGGTATTGACCAAG
5908711 ATCAAA
1 ATCAAA
5908717 TTTTGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.43, C:0.20, G:0.13, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCAGGTATTGACCAAG
Found at i:5909796 original size:20 final size:20
Alignment explanation
Indices: 5909771--5909828 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
5909761 ATTCATTTGA
5909771 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
5909791 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
5909811 CTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
5909829 CGCAATGCGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:5909871 original size:14 final size:16
Alignment explanation
Indices: 5909851--5909924 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
5909841 TGAAAATCGC
5909851 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
5909866 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
5909883 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
5909902 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
5909918 -TTGCGAT
1 ATTGCGAT
5909925 AGCCATTTCG
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 18 0.33
16 3 0.06
17 3 0.06
19 30 0.56
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:5909888 original size:19 final size:19
Alignment explanation
Indices: 5909847--5909914 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
5909837 GAAATGAAAA
5909847 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
5909863 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
5909880 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
5909899 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
5909915 TCGTTGCGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.23
16 3 0.06
17 3 0.06
19 30 0.64
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:5910050 original size:14 final size:14
Alignment explanation
Indices: 5910031--5910067 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
5910021 CATCAATTAA
5910031 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
5910045 ACAAATCATCTTTT
1 ACAAATCAACATTT
5910059 ACAAATCAA
1 ACAAATCAA
5910068 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:5911967 original size:20 final size:19
Alignment explanation
Indices: 5911932--5911998 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
5911922 GAAACTTAAA
5911932 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
5911951 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* * **
5911971 ATCACAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
5911990 ATCGCAACG
1 ATCGCAACG
5911999 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 23 0.59
20 16 0.41
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:5912006 original size:14 final size:14
Alignment explanation
Indices: 5911987--5912044 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
5911977 ATGCGAAATG
5911987 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
5912001 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
*
5912017 ATGAAATCGTAACGAC
1 A--AAATCGCAACGAC
5912033 AAAATCGCAACG
1 AAAATCGCAACG
5912045 TGAAACACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 8 0.22
18 8 0.22
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:5912031 original size:32 final size:33
Alignment explanation
Indices: 5911979--5912049 Score: 117
Period size: 32 Copynumber: 2.2 Consensus size: 33
5911969 CTATCACAAT
5911979 GCGAAATGAAAATCGCAACGACAAAATCGCAAC
1 GCGAAATGAAAATCGCAACGACAAAATCGCAAC
*
5912012 GCGAAATG-AAATCGTAACGACAAAATCGCAAC
1 GCGAAATGAAAATCGCAACGACAAAATCGCAAC
*
5912044 GTGAAA
1 GCGAAA
5912050 CACAAATCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 28 0.78
33 8 0.22
ACGTcount: A:0.48, C:0.21, G:0.20, T:0.11
Consensus pattern (33 bp):
GCGAAATGAAAATCGCAACGACAAAATCGCAAC
Found at i:5912078 original size:19 final size:17
Alignment explanation
Indices: 5912056--5912151 Score: 78
Period size: 19 Copynumber: 5.6 Consensus size: 17
5912046 GAAACACAAA
5912056 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGA-TTTCATT
*
5912075 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
5912091 TCG-TTGCGATTTCATT
1 TCGCTTGCGATTTCATT
*
5912107 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
5912123 TCG-TTGCGATTTTCATT
1 TCGCTTGCGA-TTTCATT
5912140 TCGCATTGCGAT
1 TCGC-TTGCGAT
5912152 AGCCATTTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
14 15 0.24
15 3 0.05
16 12 0.19
17 4 0.06
18 13 0.21
19 16 0.25
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (17 bp):
TCGCTTGCGATTTCATT
Found at i:5912097 original size:14 final size:14
Alignment explanation
Indices: 5912078--5912135 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
5912068 TTTCATTTCG
5912078 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
5912092 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
5912108 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
5912124 CGTTGCGATTTT
1 CGTTGCGATTTT
5912136 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:5912142 original size:33 final size:33
Alignment explanation
Indices: 5912061--5912151 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
5912051 ACAAATCGCA
5912061 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
5912094 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
5912126 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
5912152 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:5912170 original size:20 final size:19
Alignment explanation
Indices: 5912136--5912190 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
5912126 TTGCGATTTT
*
5912136 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
5912155 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
5912175 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
5912191 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:5912698 original size:18 final size:18
Alignment explanation
Indices: 5912672--5912716 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
5912662 GTCGATCAGA
*
5912672 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
5912690 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
5912708 TGATGGCTC
1 TGATGGCTC
5912717 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:5914061 original size:20 final size:20
Alignment explanation
Indices: 5914036--5914109 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
5914026 AATAGTTTCT
5914036 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
*
5914056 GAAAATGAAAATCGCAACGC
1 GAAAATGAAAATCGCAACAC
* **
5914076 G-AATTCGACTATCGCAACAC
1 GAAAAT-GAAAATCGCAACAC
*
5914096 GAAACT-AAAATCGC
1 GAAAATGAAAATCGC
5914110 GTTTCGATTT
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
19 9 0.20
20 32 0.73
21 3 0.07
ACGTcount: A:0.47, C:0.23, G:0.16, T:0.14
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:5914370 original size:22 final size:22
Alignment explanation
Indices: 5914343--5914386 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
5914333 GATGGAGATA
5914343 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
5914365 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
5914387 TGAGAGAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.14, G:0.45, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:5914599 original size:20 final size:20
Alignment explanation
Indices: 5914574--5914667 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
5914564 GATTATGTAT
5914574 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
5914594 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
5914614 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
5914635 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
5914655 TATCGCATTGCGA
1 TATCGCGTTGCGA
5914668 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:5914668 original size:20 final size:20
Alignment explanation
Indices: 5914554--5914668 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
5914544 CGCTTTGAAA
*
5914554 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
5914575 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
5914595 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
5914615 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
5914636 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
5914656 ATCGCATTGCGAT
1 ATCGCATTGCGAT
5914669 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:5914686 original size:21 final size:21
Alignment explanation
Indices: 5914657--5914749 Score: 91
Period size: 20 Copynumber: 4.5 Consensus size: 21
5914647 ATAGTCAGTA
5914657 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
5914678 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
5914698 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * * **
5914719 TTGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
5914739 TCGCATTGCGA
1 TCGCATTGCGA
5914750 ATTGGGAAAA
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 31 0.55
21 25 0.45
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:5914687 original size:41 final size:41
Alignment explanation
Indices: 5914596--5914730 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
5914586 AAAGTCAGTA
* * * ** *
5914596 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
5914636 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
5914678 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
*
5914719 TTGCGTTGCGAT
1 TCGCGTTGCGAT
5914731 TTACTTATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.04
41 73 0.94
42 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:5914731 original size:41 final size:41
Alignment explanation
Indices: 5914657--5914749 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
5914647 ATAGTCAGTA
5914657 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
*
5914698 TCGCATTGCGATTTTCCCAATTTGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
5914739 TCGCATTGCGA
1 TCGCATTGCGA
5914750 ATTGGGAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:5918798 original size:60 final size:59
Alignment explanation
Indices: 5918711--5918824 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 59
5918701 ATTATTACTA
* * **
5918711 TCATTCTAAATTAGTCCTAAAACTTTTGAATATTTTAATTTCATCACCAAACTATGACCT
1 TCATTCTAAATTAGCCCTAAAACTTTTGAACATTCCAATTTCATC-CCAAACTATGACCT
* *
5918771 TCATTCTAAATTGGCCCT-GAACTTTTTGAACATTCCAATTTCATCCCAAACTAT
1 TCATTCTAAATTAGCCCTAAAAC-TTTTGAACATTCCAATTTCATCCCAAACTAT
5918825 ACACTTTGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
59 12 0.26
60 35 0.74
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.39
Consensus pattern (59 bp):
TCATTCTAAATTAGCCCTAAAACTTTTGAACATTCCAATTTCATCCCAAACTATGACCT
Found at i:5919045 original size:59 final size:60
Alignment explanation
Indices: 5918894--5919053 Score: 171
Period size: 60 Copynumber: 2.7 Consensus size: 60
5918884 GATGAATTTG
* ** * ****
5918894 GGGATAAAATTGGAATATTCAAAAGTTTGGGGACTAATGTAGAAATATGGTGATAGTTTA
1 GGGATAAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAAATATACCCATAGTTTA
* * * * *
5918954 AGGATGAAATTAGAATGTTCAACAGTTCAAGGACTAATTTAG-AATGATACCCATAGTTT-
1 GGGATAAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAAAT-ATACCCATAGTTTA
*
5919013 GGGATAAAATTAGAATATTCAAAAGTTTAAGGACCAATTTA
1 GGGATAAAATTAGAATATTCAAAAGTTTAAGGACTAATTTA
5919054 AAAGAAGGGT
Statistics
Matches: 80, Mismatches: 19, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
59 38 0.47
60 42 0.52
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.31
Consensus pattern (60 bp):
GGGATAAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAAATATACCCATAGTTTA
Found at i:5919069 original size:59 final size:60
Alignment explanation
Indices: 5918894--5919072 Score: 166
Period size: 60 Copynumber: 3.0 Consensus size: 60
5918884 GATGAATTTG
* ** * * * *
5918894 GGGATAAAATTGGAATATTCAAAAGTTTGGGGACTAATGTAGAAATATGGTGATAGTTTA
1 GGGATAAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAAAGAAGGTCATAGTTTA
* * * * * * **
5918954 AGGATGAAATTAGAATGTTCAACAGTTCAAGGACTAATTTAGAATGATA-CCCATAGTTT-
1 GGGATAAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAAAGA-AGGTCATAGTTTA
* *
5919013 GGGATAAAATTAGAATATTCAAAAGTTTAAGGACCAATTTA-AAAGAAGGGTTATAGTTTA
1 GGGATAAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAAAGAA-GGTCATAGTTTA
5919073 TAGACATATT
Statistics
Matches: 90, Mismatches: 25, Indels: 8
0.73 0.20 0.07
Matches are distributed among these distances:
57 1 0.01
58 4 0.04
59 42 0.47
60 43 0.48
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.31
Consensus pattern (60 bp):
GGGATAAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAAAGAAGGTCATAGTTTA
Found at i:5924505 original size:2 final size:2
Alignment explanation
Indices: 5924498--5924528 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5924488 TGATTAAGTA
5924498 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5924529 AAATAAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5926013 original size:21 final size:21
Alignment explanation
Indices: 5925972--5926013 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
5925962 TTCGGTCCTT
* *
5925972 TTTTATAATATATCAGTATAA
1 TTTTATAATAAATCAGCATAA
5925993 TTTTATAATAAACTCA-CATAA
1 TTTTATAATAAA-TCAGCATAA
5926014 AATAAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.43
Consensus pattern (21 bp):
TTTTATAATAAATCAGCATAA
Found at i:5926463 original size:2 final size:2
Alignment explanation
Indices: 5926456--5926486 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5926446 TTTAAATTTA
5926456 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5926487 ATTAAATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5929843 original size:3 final size:3
Alignment explanation
Indices: 5929828--5929882 Score: 67
Period size: 3 Copynumber: 18.0 Consensus size: 3
5929818 ATTTATTTAT
*
5929828 TAA TAA TATA TAA TAA TATA TAA TAA TAA TAA TAA TAA TTA -AA TAA
1 TAA TAA TA-A TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
5929874 TAA AAA TAA
1 TAA TAA TAA
5929883 AAGTAAACTG
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 1 0.02
3 38 0.84
4 6 0.13
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:5929843 original size:10 final size:10
Alignment explanation
Indices: 5929828--5929864 Score: 67
Period size: 10 Copynumber: 3.8 Consensus size: 10
5929818 ATTTATTTAT
5929828 TAATAATATA
1 TAATAATATA
5929838 TAATAATATA
1 TAATAATATA
5929848 TAATAATA-A
1 TAATAATATA
5929857 TAATAATA
1 TAATAATA
5929865 ATTAAATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 9 0.33
10 18 0.67
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
TAATAATATA
Found at i:5929852 original size:17 final size:16
Alignment explanation
Indices: 5929828--5929881 Score: 69
Period size: 14 Copynumber: 3.5 Consensus size: 16
5929818 ATTTATTTAT
5929828 TAATAATATATAATAA
1 TAATAATATATAATAA
5929844 TATATAATA-ATAATAA
1 TA-ATAATATATAATAA
5929860 TAATAAT-TA-AATAA
1 TAATAATATATAATAA
*
5929874 TAAAAATA
1 TAATAATA
5929882 AAAGTAAACT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 11 0.32
15 6 0.18
16 11 0.32
17 6 0.18
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TAATAATATATAATAA
Found at i:5929872 original size:20 final size:22
Alignment explanation
Indices: 5929828--5929882 Score: 78
Period size: 20 Copynumber: 2.5 Consensus size: 22
5929818 ATTTATTTAT
5929828 TAATAATATATAATAATATATAA
1 TAATAATA-ATAATAATATATAA
5929851 TAATAATAATAATAAT-TA-AA
1 TAATAATAATAATAATATATAA
*
5929871 TAATAAAAATAA
1 TAATAATAATAA
5929883 AAGTAAACTG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
20 13 0.42
21 2 0.06
22 8 0.26
23 8 0.26
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
TAATAATAATAATAATATATAA
Found at i:5930088 original size:17 final size:18
Alignment explanation
Indices: 5930064--5930116 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 18
5930054 TATTAAAATG
5930064 TTTAATTTAATACATATA
1 TTTAATTTAATACATATA
* * *
5930082 TTT-ATTTATTA-AAATG
1 TTTAATTTAATACATATA
5930098 TTTAATTTAATACATATA
1 TTTAATTTAATACATATA
5930116 T
1 T
5930117 ATTGATCGAA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
16 6 0.22
17 14 0.52
18 7 0.26
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (18 bp):
TTTAATTTAATACATATA
Found at i:5930089 original size:34 final size:34
Alignment explanation
Indices: 5930048--5930116 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
5930038 GCAATGATAC
5930048 TTTATTTATTAAAATGTTTAATTTAATACATATA
1 TTTATTTATTAAAATGTTTAATTTAATACATATA
5930082 TTTATTTATTAAAATGTTTAATTTAATACATATA
1 TTTATTTATTAAAATGTTTAATTTAATACATATA
5930116 T
1 T
5930117 ATTGATCGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (34 bp):
TTTATTTATTAAAATGTTTAATTTAATACATATA
Found at i:5931812 original size:37 final size:36
Alignment explanation
Indices: 5931753--5931872 Score: 181
Period size: 35 Copynumber: 3.3 Consensus size: 36
5931743 ATCTCATTAT
* *
5931753 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
5931789 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
5931825 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
5931860 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
5931873 TTGGTTACCA
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
35 35 0.45
36 13 0.17
37 29 0.38
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.32
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:5931828 original size:21 final size:21
Alignment explanation
Indices: 5931804--5931864 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
5931794 TTCAAAGAAA
5931804 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
5931825 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
5931839 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
5931860 CATTT
1 CATTT
5931865 TTTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:5931881 original size:35 final size:36
Alignment explanation
Indices: 5931755--5931899 Score: 142
Period size: 35 Copynumber: 4.1 Consensus size: 36
5931745 CTCATTATCA
*
5931755 TTTTTCAACA-AACA-TCTACCAAACTTTGAAAAAC-T
1 TTTTTCAA-AGAACAGT-TACCAAACTTTGAAAACCAT
*
5931790 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA-
1 -TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
*
5931827 -TTTTCAAAGAAACATTTACCAAACTTTGAAAACCAT
1 TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
***
5931863 TTTTTCAAAG-TTGGTTACCAAAC-TTGAAAACCAT
1 TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
5931897 TTT
1 TTT
5931900 AATACTTTCA
Statistics
Matches: 98, Mismatches: 5, Indels: 14
0.84 0.04 0.12
Matches are distributed among these distances:
34 14 0.14
35 45 0.46
36 8 0.08
37 30 0.31
38 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.33
Consensus pattern (36 bp):
TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
Found at i:5936435 original size:38 final size:38
Alignment explanation
Indices: 5936375--5936495 Score: 155
Period size: 35 Copynumber: 3.3 Consensus size: 38
5936365 ATCTCATTAT
* *
5936375 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAAAC
*
5936412 TATTTTTCAAAGAAACATTTACCAAACTTTG--AAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAAAC
*
5936448 CA-TTTTCAAAGAACCATTTACCAAACTTTG--AAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAAAC
5936483 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
5936496 TTGGTTACCA
Statistics
Matches: 76, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
35 34 0.45
36 6 0.08
37 16 0.21
38 20 0.26
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (38 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAAAC
Found at i:5936451 original size:21 final size:21
Alignment explanation
Indices: 5936427--5936487 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
5936417 TTCAAAGAAA
5936427 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
5936448 CATTT-TCAAA----G--AAC
1 CATTTACCAAACTTTGAAAAC
5936462 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
5936483 CATTT
1 CATTT
5936488 TTTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 8 0.26
15 4 0.13
16 1 0.03
19 1 0.03
20 4 0.13
21 13 0.42
ACGTcount: A:0.41, C:0.23, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:5936504 original size:35 final size:36
Alignment explanation
Indices: 5936393--5936522 Score: 117
Period size: 35 Copynumber: 3.6 Consensus size: 36
5936383 AACAAACATC
* * *
5936393 TACCAAACTTTGAAAA-AACTATTTTTCAAAGAAACATT
1 TACCAAACTTTGAAAACCA-T-TTTTTCAAAG-ACCAGT
*
5936431 TACCAAACTTTGAAAACCA--TTTTCAAAGAACCATT
1 TACCAAACTTTGAAAACCATTTTTTCAAAG-ACCAGT
***
5936466 TACCAAACTTTGAAAACCATTTTTTCAAAG-TTGGT
1 TACCAAACTTTGAAAACCATTTTTTCAAAGACCAGT
*
5936501 TACCAAAC-TTGAAAATCATTTT
1 TACCAAACTTTGAAAACCATTTT
5936523 AATACTTTCA
Statistics
Matches: 82, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
34 13 0.16
35 43 0.52
37 9 0.11
38 16 0.20
39 1 0.01
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.33
Consensus pattern (36 bp):
TACCAAACTTTGAAAACCATTTTTTCAAAGACCAGT
Found at i:5938503 original size:18 final size:18
Alignment explanation
Indices: 5938480--5938514 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5938470 ATTTTTACTA
5938480 AATAAAAATAATATTTTT
1 AATAAAAATAATATTTTT
* *
5938498 AATAAATATATTATTTT
1 AATAAAAATAATATTTT
5938515 GGGTCGATGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AATAAAAATAATATTTTT
Found at i:5940581 original size:32 final size:32
Alignment explanation
Indices: 5940454--5940573 Score: 152
Period size: 32 Copynumber: 3.8 Consensus size: 32
5940444 TAATCAACAT
5940454 TGCATTCAGATAATGCACAATAGAATCAGTAG
1 TGCATTCAGATAATGCACAATAGAATCAGTAG
* *
5940486 TGCATTCAGATAATGTACAATAGAATCAATAG
1 TGCATTCAGATAATGCACAATAGAATCAGTAG
* * * *
5940518 TGTATTCAGATAATGCACAGTAGAGTTAGTA-
1 TGCATTCAGATAATGCACAATAGAATCAGTAG
* *
5940549 TGGCATTCAAATAATGCACAGTAGA
1 T-GCATTCAGATAATGCACAATAGA
5940574 GCCAGTATCG
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
31 1 0.01
32 76 0.99
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (32 bp):
TGCATTCAGATAATGCACAATAGAATCAGTAG
Found at i:5940587 original size:64 final size:64
Alignment explanation
Indices: 5940457--5940597 Score: 160
Period size: 64 Copynumber: 2.2 Consensus size: 64
5940447 TCAACATTGC
* * *
5940457 ATTCAGATAATGCACAATAGAATCAGTAGTGCATTCAGATAATGTACAATAGAATCAATAGTGT
1 ATTCAGATAATGCACAATAGAATCAGTAGTGCATTCAAATAATGCACAATAGAACCAATAGTGT
* * * * * *
5940521 ATTCAGATAATGCACAGTAGAGTTAGTA-TGGCATTCAAATAATGCACAGTAGAGCCAGTA-TCG
1 ATTCAGATAATGCACAATAGAATCAGTAGT-GCATTCAAATAATGCACAATAGAACCAATAGT-G
5940584 T
64 T
*
5940585 ATTTAGATAATGC
1 ATTCAGATAATGC
5940598 GTAGCGGATT
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
63 2 0.03
64 63 0.97
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.28
Consensus pattern (64 bp):
ATTCAGATAATGCACAATAGAATCAGTAGTGCATTCAAATAATGCACAATAGAACCAATAGTGT
Found at i:5940595 original size:32 final size:32
Alignment explanation
Indices: 5940457--5940597 Score: 115
Period size: 32 Copynumber: 4.4 Consensus size: 32
5940447 TCAACATTGC
* ** *
5940457 ATTCAGATAATGCACAATAGAATCAGTAGT-GC
1 ATTCAGATAATGCACAGTAGAGCCAGTA-TCGT
* * ** *
5940489 ATTCAGATAATGTACAATAGAATCAATAGT-GT
1 ATTCAGATAATGCACAGTAGAGCCAGTA-TCGT
** * *
5940521 ATTCAGATAATGCACAGTAGAGTTAGTATGGC
1 ATTCAGATAATGCACAGTAGAGCCAGTATCGT
*
5940553 ATTCAAATAATGCACAGTAGAGCCAGTATCGT
1 ATTCAGATAATGCACAGTAGAGCCAGTATCGT
*
5940585 ATTTAGATAATGC
1 ATTCAGATAATGC
5940598 GTAGCGGATT
Statistics
Matches: 92, Mismatches: 16, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
31 1 0.01
32 91 0.99
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.28
Consensus pattern (32 bp):
ATTCAGATAATGCACAGTAGAGCCAGTATCGT
Found at i:5941993 original size:15 final size:15
Alignment explanation
Indices: 5941969--5942010 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
5941959 GTGAAACTTT
5941969 AATA-TTAAATTATA
1 AATATTTAAATTATA
*
5941983 AATATTTAAA-TAAA
1 AATATTTAAATTATA
*
5941997 AATATTTTAATTAT
1 AATATTTAAATTAT
5942011 TACCCTATCC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 16 0.70
15 7 0.30
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATATTTAAATTATA
Found at i:5945633 original size:143 final size:142
Alignment explanation
Indices: 5945319--5945622 Score: 385
Period size: 143 Copynumber: 2.1 Consensus size: 142
5945309 GAATCTAAGT
* *
5945319 GTGCCAAATTAATCATCTTTAGCAACGTTTCAGTGATATATCAACTCATTTTAGAAAACTTTCAC
1 GTGCCCAATTAATCATCTTTAGCAACTTTTCAGTGATATATCAACTCATTTTAGAAAACTTTCAC
* * * * * ***
5945384 TAATGATATATCAATTCATATTAGAAAAATGTGCATTTTTCATAGGCAAAATAATGAACCATTTC
66 TAATGATATATCAATTCATATAAGAAAAACGTGCATTTCTCACAGGCAAAATAATGAACAATGAA
*
5945449 AGTAAATTTTTA
131 AGTAAATTTTCA
*
5945461 GTGCCCAATTAATCATCTTTAGCATCTTTTCAGTGATATATCAACTCATTTTAGAAAACTTTTCA
1 GTGCCCAATTAATCATCTTTAGCAACTTTTCAGTGATATATCAACTCATTTTAGAAAAC-TTTCA
* * * * ** * * *
5945526 GTGATGATATATCACTTTATATAAGAAAAACGTTTATTTCTCACATGCAAAATAATGCAGAATGA
65 CTAATGATATATCAATTCATATAAGAAAAACGTGCATTTCTCACAGGCAAAATAATGAACAATGA
*
5945591 AAG-AAACTTTTCG
130 AAGTAAA-TTTTCA
5945604 GTGCCCAATTAATCATCTT
1 GTGCCCAATTAATCATCTT
5945623 CAATAACTTT
Statistics
Matches: 138, Mismatches: 22, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
142 59 0.43
143 79 0.57
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (142 bp):
GTGCCCAATTAATCATCTTTAGCAACTTTTCAGTGATATATCAACTCATTTTAGAAAACTTTCAC
TAATGATATATCAATTCATATAAGAAAAACGTGCATTTCTCACAGGCAAAATAATGAACAATGAA
AGTAAATTTTCA
Found at i:5945663 original size:32 final size:32
Alignment explanation
Indices: 5945595--5945666 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
5945585 GAATGAAAGA
*
5945595 AACTTTTCGGTGCCCAATTAATCATCTTCAAT
1 AACTTTTCGGTGCCCAATTAATCATCTTCAAC
** * *
5945627 AACTTTTTTGTGCCCAATTAATCATCTTTAGC
1 AACTTTTCGGTGCCCAATTAATCATCTTCAAC
5945659 AACTTTTC
1 AACTTTTC
5945667 AGTGATATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.26, C:0.24, G:0.08, T:0.42
Consensus pattern (32 bp):
AACTTTTCGGTGCCCAATTAATCATCTTCAAC
Found at i:5945667 original size:175 final size:175
Alignment explanation
Indices: 5945446--5945808 Score: 548
Period size: 175 Copynumber: 2.1 Consensus size: 175
5945436 AATGAACCAT
* *
5945446 TTCAGTAAATTTTTAGTGCCCAATTAATCATCTTTAGCATCTTTTCAGTGATATATCAACTCATT
1 TTCAGTAACTTTTTAGTGCCCAATTAATCATCTTTAGCAACTTTTCAGTGATATATCAACTCATT
* * *
5945511 TTAGAAAACTTTTCAGTGATGATATATCACTTT-ATATAAGAAAAACGTTTATTTCTCACATGCA
66 TCAGAAAACTTTTCAGTGATGATATATCA-TTTCATATAAGAAAAACGTGTATTTCTCACAGGCA
* **
5945575 AAATAATGCAGAATGAAAGAAACTTTTCGGTGCCCAATTAATCATC
130 AAATAATGCACAATGAAAGAAACTTTTCAATGCCCAATTAATCATC
* *
5945621 TTCAATAACTTTTTTGTGCCCAATTAATCATCTTTAGCAACTTTTCAGTGATATATCAACTCATT
1 TTCAGTAACTTTTTAGTGCCCAATTAATCATCTTTAGCAACTTTTCAGTGATATATCAACTCATT
* * *
5945686 TCATAAAACTTTTCAGTGGTGATATATCATTTCATATAAGAAAAACGTGTATTTCTCATAGGCAA
66 TCAGAAAACTTTTCAGTGATGATATATCATTTCATATAAGAAAAACGTGTATTTCTCACAGGCAA
* * **
5945751 AATAATGTACCATGGCAGAAACTTTTCAATGCCCAATTAATCATC
131 AATAATGCACAATGAAAGAAACTTTTCAATGCCCAATTAATCATC
*
5945796 TTCAGTTACTTTT
1 TTCAGTAACTTTT
5945809 CAATGATATA
Statistics
Matches: 168, Mismatches: 19, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
174 3 0.02
175 165 0.98
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.37
Consensus pattern (175 bp):
TTCAGTAACTTTTTAGTGCCCAATTAATCATCTTTAGCAACTTTTCAGTGATATATCAACTCATT
TCAGAAAACTTTTCAGTGATGATATATCATTTCATATAAGAAAAACGTGTATTTCTCACAGGCAA
AATAATGCACAATGAAAGAAACTTTTCAATGCCCAATTAATCATC
Found at i:5945719 original size:31 final size:32
Alignment explanation
Indices: 5945659--5945721 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 32
5945649 CATCTTTAGC
5945659 AACTTTTCAGTGATATATCAACTCATTTCATAA
1 AACTTTTCAGTGATATAT-AACTCATTTCATAA
*
5945692 AACTTTTCAGTGGTGATAT-A-TCATTTCATA
1 AACTTTTCAGTGAT-ATATAACTCATTTCATA
5945722 TAAGAAAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 10 0.36
32 1 0.04
33 13 0.46
34 4 0.14
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (32 bp):
AACTTTTCAGTGATATATAACTCATTTCATAA
Found at i:5945808 original size:143 final size:143
Alignment explanation
Indices: 5945637--5946066 Score: 560
Period size: 144 Copynumber: 3.0 Consensus size: 143
5945627 AACTTTTTTG
* *
5945637 TGCCCAATTAATCATCTTTAGCAACTTTTCAGTGATATATCAACTCATTTCATAAAACTTTTCAG
1 TGCCCAATTAATCATCTTCAGCAACTTTTCAGTGATATATCAACTCATTTCAGAAAACTTTTCAG
* * *
5945702 TGGTGATATATCATTTCATATAAGAAAAACGTGTATTTCTCATAGGCAAAATAATGTACCATGGC
66 TGGTGATATATCACTTCATATAAGAAAAACGTGTATTTCTCATAGGCAAAATAATGCACCATGAC
5945767 AGAAACTTTTCAA
131 AGAAACTTTTCAA
** * * * *
5945780 TGCCCAATTAATCATCTTCAGTTACTTTTCAATGATATATTAACTCATTTCAGAAAACTTTTTAA
1 TGCCCAATTAATCATCTTCAGCAACTTTTCAGTGATATATCAACTCATTTCAGAAAACTTTTCAG
* ** *
5945845 TAGTGATATATCACTTCATATAAGAAAAAATATGTATTTCTCATAGGCAAAATAATGCACCGTGA
66 TGGTGATATATCACTTCATATAAG-AAAAACGTGTATTTCTCATAGGCAAAATAATGCACCATGA
* *
5945910 CAGAAA-TATTTTAG
130 CAGAAACT-TTTCAA
* * *
5945924 TGCCCAATTAATCATCTTCAACAACTTTT-ATGCGATATATCAACTCATTTCAGAAAACTTTCCA
1 TGCCCAATTAATCATCTTCAGCAACTTTTCA-GTGATATATCAACTCATTTCAGAAAACTTTTCA
* * * **
5945988 GTGGTGATATATCACTTCATATCAACAAAAACGTGCAATTC-CTATATACAAAATAATGCACCAT
65 GTGGTGATATATCACTTCATAT-AAGAAAAACGTGTATTTCTC-ATAGGCAAAATAATGCACCAT
*
5946052 GACATAAACTTTTCA
128 GACAGAAACTTTTCA
5946067 GTCCACAAAC
Statistics
Matches: 244, Mismatches: 37, Indels: 11
0.84 0.13 0.04
Matches are distributed among these distances:
143 82 0.34
144 159 0.65
145 3 0.01
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.34
Consensus pattern (143 bp):
TGCCCAATTAATCATCTTCAGCAACTTTTCAGTGATATATCAACTCATTTCAGAAAACTTTTCAG
TGGTGATATATCACTTCATATAAGAAAAACGTGTATTTCTCATAGGCAAAATAATGCACCATGAC
AGAAACTTTTCAA
Found at i:5951624 original size:38 final size:38
Alignment explanation
Indices: 5951573--5951649 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
5951563 AAAAAATTAC
*
5951573 TCTCTTGTCAGATGAAATGTGTGTCTCACTTCAATTTG
1 TCTCTTGTCAGATGAAACGTGTGTCTCACTTCAATTTG
5951611 TCTCTTGTCAGATGAAACGTGTGTCTCACTTCAATTTG
1 TCTCTTGTCAGATGAAACGTGTGTCTCACTTCAATTTG
5951649 T
1 T
5951650 TAACTATCTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.21, C:0.19, G:0.18, T:0.42
Consensus pattern (38 bp):
TCTCTTGTCAGATGAAACGTGTGTCTCACTTCAATTTG
Found at i:5957047 original size:17 final size:17
Alignment explanation
Indices: 5956995--5957035 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
5956985 TACAGAACCT
5956995 TTGAATCATTCAACTCA
1 TTGAATCATTCAACTCA
*
5957012 TTGAATCATTCAGCTCA
1 TTGAATCATTCAACTCA
5957029 TTGAATC
1 TTGAATC
5957036 CATTAAATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.37
Consensus pattern (17 bp):
TTGAATCATTCAACTCA
Found at i:5964664 original size:26 final size:26
Alignment explanation
Indices: 5964628--5964706 Score: 158
Period size: 26 Copynumber: 3.0 Consensus size: 26
5964618 TATTGTACAT
5964628 CAACTTAATATAAGATTAAGAAAAAA
1 CAACTTAATATAAGATTAAGAAAAAA
5964654 CAACTTAATATAAGATTAAGAAAAAA
1 CAACTTAATATAAGATTAAGAAAAAA
5964680 CAACTTAATATAAGATTAAGAAAAAA
1 CAACTTAATATAAGATTAAGAAAAAA
5964706 C
1 C
5964707 GTGACTAAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.61, C:0.09, G:0.08, T:0.23
Consensus pattern (26 bp):
CAACTTAATATAAGATTAAGAAAAAA
Found at i:5964891 original size:14 final size:14
Alignment explanation
Indices: 5964872--5964899 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5964862 TTTCGATCGT
5964872 GCCTTTCCTTAACC
1 GCCTTTCCTTAACC
5964886 GCCTTTCCTTAACC
1 GCCTTTCCTTAACC
5964900 TTACATTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.43, G:0.07, T:0.36
Consensus pattern (14 bp):
GCCTTTCCTTAACC
Found at i:5969153 original size:23 final size:24
Alignment explanation
Indices: 5969109--5969154 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
5969099 ATTTAAAATT
* * *
5969109 AAAAAAATAAAATTATATATTTTA
1 AAAAAAAGAAAATTACAAATTTTA
5969133 AAAAAAAGAAAA-TACAAATTTT
1 AAAAAAAGAAAATTACAAATTTT
5969155 GAAATAAACC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (24 bp):
AAAAAAAGAAAATTACAAATTTTA
Found at i:5976251 original size:19 final size:21
Alignment explanation
Indices: 5976202--5976249 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
5976192 ATTAATAAAA
* *
5976202 TATTATTTACAATATTATTATT
1 TATT-TTTAAAATATTAATATT
5976224 TATTTTTAAAATATTAATATT
1 TATTTTTAAAATATTAATATT
5976245 T-TTTT
1 TATTTT
5976250 AATATTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 4 0.17
21 16 0.67
22 4 0.17
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTTTTAAAATATTAATATT
Found at i:5980753 original size:2 final size:2
Alignment explanation
Indices: 5980746--5980773 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5980736 ATAATTGTTA
5980746 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
5980774 GCACCTCACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5980854 original size:2 final size:2
Alignment explanation
Indices: 5980849--5980911 Score: 60
Period size: 2 Copynumber: 32.0 Consensus size: 2
5980839 AATACAATAG
* * *
5980849 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TC CA TA CA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5980889 TA TCA TA T- TA CTA TA TA TA TA TA
1 TA T-A TA TA TA -TA TA TA TA TA TA
5980912 ATACTAATTA
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
1 3 0.06
2 44 0.86
3 4 0.08
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5985049 original size:74 final size:67
Alignment explanation
Indices: 5984964--5985180 Score: 240
Period size: 74 Copynumber: 3.1 Consensus size: 67
5984954 TTCCATGCCG
* * *
5984964 TTTTTTCCAAATTTGTTTAAAATTTTCTAAATGTTTGATATTATTTTTAACTTCGAAATTTTTAA
1 TTTTTTTCAAATTTG-TTAAAAATTTCTAAAAGTTTGATATTATTTTTAACTTCGAAATTTTT--
5985029 AAAAATAAT
63 ---AAT-AT
* **
5985038 TTTTTTTCAAATTTGTTAAACAAATTCTAAAAGTTTGATATTATTTTTAACTTC-AAAAATTTAA
1 TTTTTTTCAAATTTGTTAAA-AATTTCTAAAAGTTTGATATTATTTTTAACTTCGAAATTTTTAA
5985102 TAT
65 TAT
* * *
5985105 TTTTAAAATTCAAATTTGATAAAAATTTCTAAAAGTTTGATATTATTTTTAACTTAGAAA-TTTT
1 TTTT---TTTCAAATTTGTTAAAAATTTCTAAAAGTTTGATATTATTTTTAACTTCGAAATTTTT
5985169 AATAT
63 AATAT
5985174 TTTTTTT
1 TTTTTTT
5985181 GATTTTATTA
Statistics
Matches: 126, Mismatches: 12, Indels: 18
0.81 0.08 0.12
Matches are distributed among these distances:
66 2 0.02
67 6 0.05
68 3 0.02
69 43 0.34
70 17 0.13
73 11 0.09
74 44 0.35
ACGTcount: A:0.38, C:0.06, G:0.05, T:0.51
Consensus pattern (67 bp):
TTTTTTTCAAATTTGTTAAAAATTTCTAAAAGTTTGATATTATTTTTAACTTCGAAATTTTTAAT
AT
Found at i:5985152 original size:69 final size:70
Alignment explanation
Indices: 5985043--5985177 Score: 220
Period size: 69 Copynumber: 1.9 Consensus size: 70
5985033 ATAATTTTTT
*
5985043 TTCAAATTTGTTAAACAAATTCTAAAAGTTTGATATTATTTTTAACTTCA-AAAATTTAATATTT
1 TTCAAATTTGATAAACAAATTCTAAAAGTTTGATATTATTTTTAACTT-AGAAAATTTAATATTT
5985107 TTAAAA
65 TTAAAA
* *
5985113 TTCAAATTTGATAAA-AATTTCTAAAAGTTTGATATTATTTTTAACTTAGAAATTTTAATATTTT
1 TTCAAATTTGATAAACAAATTCTAAAAGTTTGATATTATTTTTAACTTAGAAAATTTAATATTTT
5985177 T
66 T
5985178 TTTGATTTTA
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
68 1 0.02
69 46 0.75
70 14 0.23
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.48
Consensus pattern (70 bp):
TTCAAATTTGATAAACAAATTCTAAAAGTTTGATATTATTTTTAACTTAGAAAATTTAATATTTT
TAAAA
Found at i:5991967 original size:3 final size:3
Alignment explanation
Indices: 5991954--5991984 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
5991944 AGCATAAATT
5991954 TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
5991985 GTAGGAAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:5996605 original size:3 final size:3
Alignment explanation
Indices: 5996599--5996642 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
5996589 ATATTATTTG
* * *
5996599 TAA TAA TAA T-A TAA TTA TTA TAA TAA TAA TAG TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5996643 ATATAATTAG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:5996884 original size:42 final size:42
Alignment explanation
Indices: 5996837--5996920 Score: 109
Period size: 42 Copynumber: 2.0 Consensus size: 42
5996827 TATTCATCTT
*
5996837 GCTCGAAAGACTAATAAATGA-CCATAAGGATTTA-AACATTTG
1 GCTCGAAAGACTAACAAATGACCCA-AAGGATTTACAA-ATTTG
* *
5996879 GCTCGAAAGACTGACAGATGACCCAAAGGATTTACAAATTTG
1 GCTCGAAAGACTAACAAATGACCCAAAGGATTTACAAATTTG
5996921 TGGGAAATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
42 32 0.86
43 5 0.14
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (42 bp):
GCTCGAAAGACTAACAAATGACCCAAAGGATTTACAAATTTG
Found at i:5997351 original size:248 final size:249
Alignment explanation
Indices: 5996811--5997411 Score: 886
Period size: 248 Copynumber: 2.4 Consensus size: 249
5996801 AGGTCTTACA
* * * * * * ** *
5996811 GATGGCCCAAAGGACTTATTCATCTTGCTCGAAAGACTAATAAATGACCATAAGGATTTAAACAT
1 GATGGCCCTAAGGACTTA-TCATCTAGCTCGAAAGGCTTACAGATGACCCGAAGGATTTAAGCAT
* * * * *
5996876 -TTGGCTCGAAAGACTGACAGATGACCCAAAGGATTTACAAATTTGTGGGAAATAATTTACTAGG
65 CAT-GCTCGAAAGACTTACTGATGACCCGAAGGATTTACAAATTTGTGCGAAATAATTTACTAGG
**
5996940 TAAAAAAACTTCTTACTTTTCAAAAATTTCATTTTCTTGAACATTAAATGAGAAACTTTGAAATT
129 TAAAAAAACTTCTTACTTTTCAAAAATTTCATTTTCTTGAACATTAAATGAGAAACTTTGAAACC
* *
5997005 TTCTTTCTCATTTTATGCGAAAATCATATGTAAACATCCTACCCAAAGGTTTGACG
194 GTCTTTCTCATTTTATGCGAAAATCATAGGTAAACATCCTACCCAAAGGTTTGACG
* * * *
5997061 GATGGACCTAAGGACTTATTATCTATCGCGAAAGGCTTACAGATGACCCGAAGGATTTAAGCATC
1 GATGGCCCTAAGGACTTATCATCTAGCTCGAAAGGCTTACAGATGACCCGAAGGATTTAAGCATC
*
5997126 ATGCTCAAAAGACTTACTGATGACCCGAAGGATTTACAAATTTGTGCGAAATAATTTACT-GGT-
66 ATGCTCGAAAGACTTACTGATGACCCGAAGGATTTACAAATTTGTGCGAAATAATTTACTAGGTA
*
5997189 AAGAAACTTCTTACTTTTCAAAAATTTCATTTTCTTGAACATTAAATGAGAAACTTTGAAAACCG
131 AAAAAACTTCTTACTTTTCAAAAATTTCATTTTCTTGAACATTAAATGAGAAACTTTG-AAACCG
*
5997254 T-TTTCTCATTTTCATGTGAAAATCATAGGTAAACATCCTACCCAAAGGTTTGACG
195 TCTTTCTCATTTT-ATGCGAAAATCATAGGTAAACATCCTACCCAAAGGTTTGACG
* *
5997309 GATGGCCCTAAGGACTTATCATCTGGCTTGAAAGGCTTACAGATGACCCGAAGGATTTAAGCATC
1 GATGGCCCTAAGGACTTATCATCTAGCTCGAAAGGCTTACAGATGACCCGAAGGATTTAAGCATC
*
5997374 ATGCTCGAAAGACTTATTGATGACCCGAAGGATTTACA
66 ATGCTCGAAAGACTTACTGATGACCCGAAGGATTTACA
5997412 TATCAAGAAA
Statistics
Matches: 315, Mismatches: 33, Indels: 8
0.88 0.09 0.02
Matches are distributed among these distances:
247 68 0.22
248 142 0.45
249 88 0.28
250 17 0.05
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (249 bp):
GATGGCCCTAAGGACTTATCATCTAGCTCGAAAGGCTTACAGATGACCCGAAGGATTTAAGCATC
ATGCTCGAAAGACTTACTGATGACCCGAAGGATTTACAAATTTGTGCGAAATAATTTACTAGGTA
AAAAAACTTCTTACTTTTCAAAAATTTCATTTTCTTGAACATTAAATGAGAAACTTTGAAACCGT
CTTTCTCATTTTATGCGAAAATCATAGGTAAACATCCTACCCAAAGGTTTGACG
Found at i:5997634 original size:41 final size:42
Alignment explanation
Indices: 5997584--5997665 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
5997574 AGGTCTTATG
* * * *
5997584 GATGGCCCGAAGGACTT-ATCATCTTGCTCAAAAGGCTTACA
1 GATGACCCGAAGGACTTAAGCATCATGCTCAAAAGACTTACA
* *
5997625 GATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTAC
1 GATGACCCGAAGGACTTAAGCATCATGCTCAAAAGACTTAC
5997666 TAATGGCTCG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 15 0.44
42 19 0.56
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (42 bp):
GATGACCCGAAGGACTTAAGCATCATGCTCAAAAGACTTACA
Found at i:6000736 original size:14 final size:12
Alignment explanation
Indices: 6000701--6000784 Score: 73
Period size: 11 Copynumber: 6.8 Consensus size: 12
6000691 TAATTCAATT
*
6000701 TCTTTTTTTAT-
1 TCTTTTTTTTTC
**
6000712 TCTTTCATTTTC
1 TCTTTTTTTTTC
6000724 TCTTTTCTCTTTTC
1 TCTTTT-T-TTTTC
6000738 TCTTTTTTTTT-
1 TCTTTTTTTTTC
6000749 TCTTTTTTTTTC
1 TCTTTTTTTTTC
*
6000761 TTTTTCCTTTTTTTC
1 -TCTT--TTTTTTTC
6000776 TCTTTTTTT
1 TCTTTTTTT
6000785 CTGATGAATG
Statistics
Matches: 59, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
11 19 0.32
12 14 0.24
13 4 0.07
14 14 0.24
15 8 0.14
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (12 bp):
TCTTTTTTTTTC
Found at i:6000746 original size:17 final size:16
Alignment explanation
Indices: 6000714--6000781 Score: 58
Period size: 15 Copynumber: 4.6 Consensus size: 16
6000704 TTTTTTATTC
*
6000714 TTTCATTTTCTC-TTT
1 TTTCTTTTTCTCTTTT
*
6000729 TCTC-TTTTCTC--TT
1 TTTCTTTTTCTCTTTT
*
6000742 TTT-TTTTTCTTTTTT
1 TTTCTTTTTCTCTTTT
6000757 TTTCTTTTTC-CTTTT
1 TTTCTTTTTCTCTTTT
6000772 TTTCTCTTTT
1 TTTCT-TTTT
6000782 TTTCTGATGA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
13 10 0.23
14 7 0.16
15 17 0.39
16 10 0.23
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTCTTTTTCTCTTTT
Found at i:6000749 original size:27 final size:25
Alignment explanation
Indices: 6000719--6000784 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 25
6000709 TATTCTTTCA
6000719 TTTTCTCTTTTCTCTTTTCTCTT-TTT
1 TTTTCTCTTTT-T-TTTTCTCTTCTTT
*
6000745 TTTT-TCTTTTTTTTTCTTTTTCCTTT
1 TTTTCTCTTTTTTTTTC-TCTT-CTTT
6000771 TTTTCTCTTTTTTT
1 TTTTCTCTTTTTTT
6000785 CTGATGAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
23 5 0.14
24 4 0.11
25 6 0.17
26 11 0.31
27 9 0.26
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (25 bp):
TTTTCTCTTTTTTTTTCTCTTCTTT
Found at i:6000752 original size:37 final size:38
Alignment explanation
Indices: 6000701--6000784 Score: 109
Period size: 37 Copynumber: 2.2 Consensus size: 38
6000691 TAATTCAATT
6000701 TCTTTTTTTATTCTTTCATTTTCTCTTTT-C-TCTTTTC
1 TCTTTTTTTATTCTTTCATTTTCT-TTTTCCTTCTTTTC
* ** *
6000738 TCTTTTTTTTTTCTTTTTTTTTCTTTTTCCTTTTTTTC
1 TCTTTTTTTATTCTTTCATTTTCTTTTTCCTTCTTTTC
6000776 TCTTTTTTT
1 TCTTTTTTT
6000785 CTGATGAATG
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
36 4 0.10
37 22 0.54
38 15 0.37
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (38 bp):
TCTTTTTTTATTCTTTCATTTTCTTTTTCCTTCTTTTC
Found at i:6000757 original size:28 final size:27
Alignment explanation
Indices: 6000726--6000786 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
6000716 TCATTTTCTC
* * *
6000726 TTTTCTCTTTTCTCTTTTTTTTTTCTTT
1 TTTTCTC-TTTTTCCTTTTTTTCTCTTT
*
6000754 TTTTTTCTTTTTCCTTTTTTTCTCTTT
1 TTTTCTCTTTTTCCTTTTTTTCTCTTT
6000781 TTTTCT
1 TTTTCT
6000787 GATGAATGAG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 22 0.79
28 6 0.21
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (27 bp):
TTTTCTCTTTTTCCTTTTTTTCTCTTT
Found at i:6000781 original size:7 final size:7
Alignment explanation
Indices: 6000719--6000771 Score: 57
Period size: 7 Copynumber: 8.6 Consensus size: 7
6000709 TATTCTTTCA
6000719 TTTTCTC
1 TTTTCTC
6000726 TTTTCTC
1 TTTTCTC
6000733 TTTTCTC
1 TTTTCTC
6000740 TTTT-T-
1 TTTTCTC
6000745 TTTT-TC
1 TTTTCTC
6000751 TTTT-T-
1 TTTTCTC
6000756 TTTTCT-
1 TTTTCTC
6000762 TTTTC-C
1 TTTTCTC
6000768 TTTT
1 TTTT
6000772 TTTCTCTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
5 9 0.21
6 16 0.37
7 18 0.42
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTTCTC
Found at i:6000782 original size:17 final size:17
Alignment explanation
Indices: 6000744--6000782 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
6000734 TTTCTCTTTT
* *
6000744 TTTTTTCTTTTTTTTTC
1 TTTTTCCTTTTTTTCTC
6000761 TTTTTCCTTTTTTTCTC
1 TTTTTCCTTTTTTTCTC
6000778 TTTTT
1 TTTTT
6000783 TTCTGATGAA
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:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTTCCTTTTTTTCTC
Found at i:6000785 original size:10 final size:10
Alignment explanation
Indices: 6000733--6000786 Score: 60
Period size: 10 Copynumber: 5.6 Consensus size: 10
6000723 CTCTTTTCTC
6000733 TTTTCTCTTTT
1 TTTTCTC-TTT
*
6000744 TTTTTTCTTT
1 TTTTCTCTTT
*
6000754 TTTT-T-TCT
1 TTTTCTCTTT
6000762 TTTTC-CTTT
1 TTTTCTCTTT
6000771 TTTTCTCTTT
1 TTTTCTCTTT
6000781 TTTTCT
1 TTTTCT
6000787 GATGAATGAG
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
8 6 0.16
9 8 0.22
10 17 0.46
11 6 0.16
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTCTCTTT
Found at i:6001526 original size:17 final size:17
Alignment explanation
Indices: 6001504--6001537 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
6001494 GTGTTAAGAA
6001504 TTGGTTTTTGTAAGGAT
1 TTGGTTTTTGTAAGGAT
6001521 TTGGTTTTTGTAAGGAT
1 TTGGTTTTTGTAAGGAT
6001538 CAAATAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.00, G:0.29, T:0.53
Consensus pattern (17 bp):
TTGGTTTTTGTAAGGAT
Found at i:6002463 original size:21 final size:21
Alignment explanation
Indices: 6002437--6002512 Score: 75
Period size: 21 Copynumber: 3.6 Consensus size: 21
6002427 AGGGTGTCAA
6002437 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
6002458 AGTGCATCCATGCACCTGCC-AC
1 AGTGCATCCATGCACC--CCTGC
* *
6002480 TAGTGCATCGATGCA-CCATGC
1 -AGTGCATCCATGCACCCCTGC
*
6002501 ATTGCATCCATG
1 AGTGCATCCATG
6002513 ATGCACTCAA
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
20 11 0.24
21 17 0.38
22 2 0.04
23 15 0.33
ACGTcount: A:0.22, C:0.36, G:0.20, T:0.22
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:6002488 original size:23 final size:21
Alignment explanation
Indices: 6002437--6002496 Score: 68
Period size: 23 Copynumber: 2.8 Consensus size: 21
6002427 AGGGTGTCAA
*
6002437 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTAC
6002458 AGTGCATCCATGCACCTGCC-AC
1 AGTGCATCCATGCACC--CCTAC
*
6002480 TAGTGCATCGATGCACC
1 -AGTGCATCCATGCACC
6002497 ATGCATTGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.47
22 1 0.03
23 17 0.50
ACGTcount: A:0.22, C:0.38, G:0.20, T:0.20
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTAC
Found at i:6008410 original size:4 final size:4
Alignment explanation
Indices: 6008403--6008428 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
6008393 AATCCAAAAA
6008403 AAAG AAAG AAAG AAAG AAAG AAAG AA
1 AAAG AAAG AAAG AAAG AAAG AAAG AA
6008429 CAAGGATAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:6008493 original size:21 final size:21
Alignment explanation
Indices: 6008469--6008508 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
6008459 TATTTTCTTT
6008469 ATTGACATCGAGATTCTCAGA
1 ATTGACATCGAGATTCTCAGA
6008490 ATTGACATCGAGATTCTCA
1 ATTGACATCGAGATTCTCA
6008509 TAGTAGACCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (21 bp):
ATTGACATCGAGATTCTCAGA
Found at i:6014585 original size:20 final size:21
Alignment explanation
Indices: 6014506--6014593 Score: 99
Period size: 21 Copynumber: 4.2 Consensus size: 21
6014496 TACCAAGGAT
* *
6014506 GAGAAGAGCATTCATAAAGAC
1 GAGAAGACCCTTCATAAAGAC
* * *
6014527 GAG-AGTGCCATTCATCAAGAC
1 GAGAAG-ACCCTTCATAAAGAC
6014548 GAGAAGACCCTTCATAAAGAC
1 GAGAAGACCCTTCATAAAGAC
*
6014569 GAGAAGA-CCTTCGTAAAGAC
1 GAGAAGACCCTTCATAAAGAC
6014589 GAGAA
1 GAGAA
6014594 TTCCACATCG
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
20 19 0.33
21 37 0.64
22 2 0.03
ACGTcount: A:0.42, C:0.19, G:0.24, T:0.15
Consensus pattern (21 bp):
GAGAAGACCCTTCATAAAGAC
Found at i:6020759 original size:11 final size:10
Alignment explanation
Indices: 6020743--6020825 Score: 57
Period size: 11 Copynumber: 7.9 Consensus size: 10
6020733 ATATTTTGCT
6020743 TGAAAAAATAA
1 TGAAAAAA-AA
6020754 TG--AAAAAA
1 TGAAAAAAAA
6020762 TGAAATAAAAA
1 TGAAA-AAAAA
*
6020773 AGAAAAAAAAA
1 TG-AAAAAAAA
6020784 TGAAAAAGAAA
1 TGAAAAA-AAA
6020795 --AAAGAAAAA
1 TGAAA-AAAAA
6020804 TGAATGAAAAAA
1 TGAA--AAAAAA
6020816 TGGAAAAAAA
1 T-GAAAAAAA
6020826 GAAGGGTTCA
Statistics
Matches: 59, Mismatches: 2, Indels: 22
0.71 0.02 0.27
Matches are distributed among these distances:
8 4 0.07
9 10 0.17
10 8 0.14
11 24 0.41
12 9 0.15
13 4 0.07
ACGTcount: A:0.76, C:0.00, G:0.13, T:0.11
Consensus pattern (10 bp):
TGAAAAAAAA
Found at i:6020784 original size:17 final size:17
Alignment explanation
Indices: 6020764--6020797 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
6020754 TGAAAAAATG
6020764 AAATAAAAAAGAAAAAA
1 AAATAAAAAAGAAAAAA
*
6020781 AAATGAAAAAGAAAAAA
1 AAATAAAAAAGAAAAAA
6020798 GAAAAATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.85, C:0.00, G:0.09, T:0.06
Consensus pattern (17 bp):
AAATAAAAAAGAAAAAA
Found at i:6020795 original size:24 final size:24
Alignment explanation
Indices: 6020756--6020814 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
6020746 AAAAATAATG
*
6020756 AAAAAATG--AAATAAAAAAGAAA
1 AAAAAATGAAAAAGAAAAAAGAAA
6020778 AAAAAATGAAAAAGAAAAAAGAAA
1 AAAAAATGAAAAAGAAAAAAGAAA
**
6020802 AATGAATGAAAAA
1 AAAAAATGAAAAA
6020815 ATGGAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
22 8 0.25
24 24 0.75
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (24 bp):
AAAAAATGAAAAAGAAAAAAGAAA
Found at i:6020814 original size:17 final size:18
Alignment explanation
Indices: 6020764--6020802 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
6020754 TGAAAAAATG
6020764 AAATAAAAAAG-AAAAAA
1 AAATAAAAAAGAAAAAAA
*
6020781 AAATGAAAAAGAAAAAAGA
1 AAATAAAAAAGAAAAAA-A
6020800 AAA
1 AAA
6020803 ATGAATGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
18 5 0.26
19 4 0.21
ACGTcount: A:0.85, C:0.00, G:0.10, T:0.05
Consensus pattern (18 bp):
AAATAAAAAAGAAAAAAA
Found at i:6022279 original size:54 final size:53
Alignment explanation
Indices: 6022133--6023014 Score: 1412
Period size: 54 Copynumber: 16.5 Consensus size: 53
6022123 GCAACAGAAG
6022133 ATTGTTCGAGTTCTACTCCCTGAAGAAATAG-G-GCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
* *
6022184 ATTGTTCGAGTTCTACTCCGTGTAGAAATAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
*
6022237 ATTGTTCGAGTTCTTACTCCCTGAAGAAATAGAGAGCGGACCCATAGGAAGATT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
* *
6022291 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAAAAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
*
6022345 ATTGTTCGAGTTCTTACTCCCTGAAGAAATAGAGAGCGGACCTGTAGGAAGATT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
* * *
6022399 ATTGTTCGAGTTCTACTCCTTGAAGGAAA-AGAGAGCAGACCCGTAAGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAA-GAAATAGAGAGCGGACCCGTAGGAAGATT
*
6022452 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
6022506 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
* * *
6022559 ATTGTTCAAGTTCTACTCCCTAAAGAAATAGAGAGCGGACCCGTAAGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
*
6022612 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
* *
6022666 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGCAGAAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
*
6022719 ATTGTTCGAGTTCTTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGAAAGATT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
6022773 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
* *
6022826 TTTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
*
6022880 ATTGTTTGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
* **
6022933 ATTGTTCGAGTTCTACTCCCTGAAGAAA-AGAGAGAGTGAGCCCGTAGGAAGAAG
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCG-GA-CCCGTAGGAAGATT
* * *
6022987 AATGTTTGAGTTCTACTCCCTAAAGAAA
1 ATTGTTCGAGTTCTACTCCCTGAAGAAA
6023015 GAGAAAGTGA
Statistics
Matches: 777, Mismatches: 43, Indels: 19
0.93 0.05 0.02
Matches are distributed among these distances:
51 29 0.04
52 8 0.01
53 350 0.45
54 390 0.50
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.25
Consensus pattern (53 bp):
ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
Found at i:6022491 original size:107 final size:106
Alignment explanation
Indices: 6022133--6023014 Score: 1407
Period size: 107 Copynumber: 8.3 Consensus size: 106
6022123 GCAACAGAAG
6022133 ATTGTTCGAGTTCTACTCCCTGAAGAAATAG-G-GCGGACCCGTAGGAAGATTATTGTTCGAGTT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
* *
6022196 C-TACTCCGTGTAGAAATAGAGAGCGGACCCGTAGGAAGATT
66 CTTACTCCCTGAAGAAA-AGAGAGCGGACCCGTAGGAAGATT
*
6022237 ATTGTTCGAGTTCTTACTCCCTGAAGAAATAGAGAGCGGACCCATAGGAAGATTATTGTTCGAGT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGT
*
6022302 TCTTACTCCCTGAAGAAAAAAAGAGCGGACCCGTAGGAAGATT
65 TCTTACTCCCTGAAG-AAAAGAGAGCGGACCCGTAGGAAGATT
*
6022345 ATTGTTCGAGTTCTTACTCCCTGAAGAAATAGAGAGCGGACCTGTAGGAAGATTATTGTTCGAGT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGT
* * *
6022410 TC-TACTCCTTGAAGGAAAAGAGAGCAGACCCGTAAGAAGATT
65 TCTTACTCCCTGAA-GAAAAGAGAGCGGACCCGTAGGAAGATT
*
6022452 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGT
6022517 TC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
65 TCTTACTCCCTGAAGAAA-AGAGAGCGGACCCGTAGGAAGATT
* * *
6022559 ATTGTTCAAGTTCTACTCCCTAAAGAAATAGAGAGCGGACCCGTAAGAAGATTATTGTTCGAGTT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
6022624 CTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATT
66 CTTACTCCCTGAAG-AAAAGAGAGCGGACCCGTAGGAAGATT
* *
6022666 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGCAGAAAGATTATTGTTCGAGTT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
*
6022731 CTTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGAAAGATT
66 CTTACTCCCTGAAGAAA-AGAGAGCGGACCCGTAGGAAGATT
*
6022773 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTTTTGTTCGAGTT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
6022838 CTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATT
66 CTTACTCCCTGAAG-AAAAGAGAGCGGACCCGTAGGAAGATT
*
6022880 ATTGTTTGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
* **
6022945 C-TACTCCCTGAAGAAAAGAGAGAGTGAGCCCGTAGGAAGAAG
66 CTTACTCCCTGAAGAAAAGAGAGCG-GA-CCCGTAGGAAGATT
* * *
6022987 AATGTTTGAGTTCTACTCCCTAAAGAAA
1 ATTGTTCGAGTTCTACTCCCTGAAGAAA
6023015 GAGAAAGTGA
Statistics
Matches: 729, Mismatches: 36, Indels: 23
0.93 0.05 0.03
Matches are distributed among these distances:
104 13 0.02
105 28 0.04
106 72 0.10
107 508 0.70
108 105 0.14
109 3 0.00
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.25
Consensus pattern (106 bp):
ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
CTTACTCCCTGAAGAAAAGAGAGCGGACCCGTAGGAAGATT
Found at i:6037885 original size:17 final size:17
Alignment explanation
Indices: 6037860--6037892 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
6037850 TTGTTGAAGG
6037860 ATAACTTAAACAAATTA
1 ATAACTTAAACAAATTA
*
6037877 ATAATTTAAACAAATT
1 ATAACTTAAACAAATT
6037893 TTAACATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (17 bp):
ATAACTTAAACAAATTA
Found at i:6041213 original size:29 final size:29
Alignment explanation
Indices: 6041171--6041259 Score: 178
Period size: 29 Copynumber: 3.1 Consensus size: 29
6041161 CTACAGTGGT
6041171 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
6041200 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
6041229 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
6041258 CT
1 CT
6041260 GTGTGTATTA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 60 1.00
ACGTcount: A:0.13, C:0.31, G:0.37, T:0.18
Consensus pattern (29 bp):
CTTGGAGGTCGCCATGGCATCCGGGCGAC
Found at i:6041304 original size:18 final size:18
Alignment explanation
Indices: 6041281--6041322 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
6041271 AGAATAGGGC
6041281 CATGCAATCAACATGGGA
1 CATGCAATCAACATGGGA
6041299 CATGCAATCAACATGGGA
1 CATGCAATCAACATGGGA
*
6041317 CGTGCA
1 CATGCA
6041323 TGGGGGAGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.17
Consensus pattern (18 bp):
CATGCAATCAACATGGGA
Found at i:6041352 original size:15 final size:15
Alignment explanation
Indices: 6041319--6041491 Score: 123
Period size: 15 Copynumber: 10.6 Consensus size: 15
6041309 ACATGGGACG
* *
6041319 TGCATGGGGGAGGGGA
1 TGCAT-GGGGTGGGAA
6041335 TGCATGGGGTGGGAA
1 TGCATGGGGTGGGAA
*
6041350 TGCATGGGG-GAGGGA
1 TGCATGGGGTG-GGAA
*
6041365 TCAACATGGGATGTGGGAA
1 T--GCATGGG--GTGGGAA
* *
6041384 TGCATGGGGGAGGGGA
1 TGCAT-GGGGTGGGAA
6041400 TGCATGGGACGTGGGAA
1 TGCATGGG--GTGGGAA
6041417 TGCATGGGGTGGGAA
1 TGCATGGGGTGGGAA
* *
6041432 TGCATGGGGGAGGGGATGG
1 TGCAT-GGGG-TGGGA--A
*
6041451 TGCATTGGACGTGGGAA
1 TGCA-TGG-GGTGGGAA
6041468 TGCATGGGGTGGGAA
1 TGCATGGGGTGGGAA
6041483 TGCATGGGG
1 TGCATGGGG
6041492 AGGGGATGGT
Statistics
Matches: 126, Mismatches: 16, Indels: 31
0.73 0.09 0.18
Matches are distributed among these distances:
14 1 0.01
15 52 0.41
16 22 0.17
17 30 0.24
18 3 0.02
19 15 0.12
20 3 0.02
ACGTcount: A:0.21, C:0.08, G:0.53, T:0.18
Consensus pattern (15 bp):
TGCATGGGGTGGGAA
Found at i:6041427 original size:82 final size:83
Alignment explanation
Indices: 6041334--6041490 Score: 228
Period size: 82 Copynumber: 1.9 Consensus size: 83
6041324 GGGGGAGGGG
*
6041334 ATGCATGGGGTGGGAATGCATGGGGGA-GGGAT-CAACATGGGATGTGGGAATGCATGGGGGAGG
1 ATGCATGGGGTGGGAATGCATGGGGGAGGGGATGCAACATGGGACGTGGGAATGCAT-GGGGAGG
*
6041397 GGATGCATGGGACGTGGGA
65 GAATGCATGGGACGTGGGA
*** * *
6041416 ATGCATGGGGTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAATGCATGGGGTGGG
1 ATGCATGGGGTGGGAATGCATGGGGGAGGGGATGCAACATGGGACGTGGGAATGCATGGGGAGGG
6041481 AATGCATGGG
66 AATGCATGGG
6041491 GAGGGGATGG
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
82 27 0.41
83 21 0.32
84 18 0.27
ACGTcount: A:0.22, C:0.08, G:0.52, T:0.18
Consensus pattern (83 bp):
ATGCATGGGGTGGGAATGCATGGGGGAGGGGATGCAACATGGGACGTGGGAATGCATGGGGAGGG
AATGCATGGGACGTGGGA
Found at i:6041476 original size:51 final size:51
Alignment explanation
Indices: 6041377--6041501 Score: 213
Period size: 51 Copynumber: 2.5 Consensus size: 51
6041367 AACATGGGAT
6041377 GTGGGAATGCATGGGGGAGGGGA---TGCATGGGACGTGGGAATGCATGGG
1 GTGGGAATGCATGGGGGAGGGGATGGTGCATGGGACGTGGGAATGCATGGG
*
6041425 GTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAATGCATGGG
1 GTGGGAATGCATGGGGGAGGGGATGGTGCATGGGACGTGGGAATGCATGGG
6041476 GTGGGAATGCAT-GGGGAGGGGATGGT
1 GTGGGAATGCATGGGGGAGGGGATGGT
6041502 CACGGTGGTC
Statistics
Matches: 73, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
48 23 0.32
50 14 0.19
51 36 0.49
ACGTcount: A:0.20, C:0.07, G:0.54, T:0.18
Consensus pattern (51 bp):
GTGGGAATGCATGGGGGAGGGGATGGTGCATGGGACGTGGGAATGCATGGG
Found at i:6041956 original size:21 final size:21
Alignment explanation
Indices: 6041908--6041956 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
6041898 ACTAAAATCT
*
6041908 AGTTAATTAGTTTGTTAGTATA
1 AGTT-ATTAGTTTGTAAGTATA
* *
6041930 AATTATTAGTTTGTAAGTTTA
1 AGTTATTAGTTTGTAAGTATA
6041951 AGTTAT
1 AGTTAT
6041957 ATTATATTAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (21 bp):
AGTTATTAGTTTGTAAGTATA
Found at i:6041966 original size:28 final size:30
Alignment explanation
Indices: 6041933--6041995 Score: 94
Period size: 28 Copynumber: 2.2 Consensus size: 30
6041923 TAGTATAAAT
*
6041933 TATTAGTTTGTAAGTTTAAG-T-TATATTA
1 TATTAGTTTATAAGTTTAAGTTATATATTA
*
6041961 TATTAGTTTATTAGTTTAAGTTATATATTA
1 TATTAGTTTATAAGTTTAAGTTATATATTA
6041991 TATTA
1 TATTA
6041996 TATAAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 18 0.58
29 1 0.03
30 12 0.39
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (30 bp):
TATTAGTTTATAAGTTTAAGTTATATATTA
Found at i:6042506 original size:16 final size:16
Alignment explanation
Indices: 6042485--6042541 Score: 60
Period size: 16 Copynumber: 3.3 Consensus size: 16
6042475 TAATTTCCGT
6042485 TTTAAAAAATATTGTG
1 TTTAAAAAATATTGTG
*
6042501 TTTAAAAATATTTAGTGTTG
1 TTTAAAAA-A--TATTG-TG
*
6042521 TTTAAAAAATATTTTG
1 TTTAAAAAATATTGTG
6042537 TTTAA
1 TTTAA
6042542 TTTACATTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
16 15 0.44
17 4 0.12
19 5 0.15
20 10 0.29
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (16 bp):
TTTAAAAAATATTGTG
Found at i:6042831 original size:26 final size:25
Alignment explanation
Indices: 6042802--6042860 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
6042792 AAATCATATT
*
6042802 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AGTAAATATCAAATC
*
6042828 ATTAGATT-AATAGTAATTATCAAATC
1 ATT--ATTAAATAGTAAATATCAAATC
6042854 ATTATTA
1 ATTATTA
6042861 GGTTTATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
24 3 0.11
26 19 0.68
27 3 0.11
28 3 0.11
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (25 bp):
ATTATTAAATAGTAAATATCAAATC
Found at i:6045773 original size:26 final size:26
Alignment explanation
Indices: 6045744--6046233 Score: 384
Period size: 26 Copynumber: 19.8 Consensus size: 26
6045734 TTTGATGATT
6045744 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
6045770 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
* *
6045796 TAATAATGA-TT--TAATAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* *
6045818 TA--AAT-ATTTAATGAACAAAT-ATT-
1 TAGTAATGATTTGAT-AA-TAATCATTA
6045841 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
6045867 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
*
6045893 TAATAATGATTT-ATTAATAATCATTA
1 TAGTAATGATTTGA-TAATAATCATTA
** * * *
6045919 TAAAAATGATTTAATAATGAATTA-AA
1 TAGTAATGATTTGATAAT-AATCATTA
* *
6045945 TATTTAATGATTTG------ATGATT-
1 TA-GTAATGATTTGATAATAATCATTA
6045965 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
6045991 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
* *
6046017 TAATAATGA-TT--TAATAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* * * *
6046039 TA--AAT-ATTTAATGATTTGATGATT-
1 TAGTAATGATTTGAT-A-ATAATCATTA
*
6046063 TAGTAATTATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
6046089 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
*
6046115 TAATAATGATTT-AGTAATAATCATTA
1 TAGTAATGATTTGA-TAATAATCATTA
** *
6046141 TAAAAATGA-TT--TAATAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* * * *
6046163 TA--AAT-ATTTAATGATTTGATGATT-
1 TAGTAATGATTTGAT-A-ATAATCATTA
6046187 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
* *
6046213 TAATAATGATTTTATAATAAT
1 TAGTAATGATTTGATAATAAT
6046234 TATTTAGAAT
Statistics
Matches: 387, Mismatches: 36, Indels: 82
0.77 0.07 0.16
Matches are distributed among these distances:
19 13 0.03
20 20 0.05
22 9 0.02
23 39 0.10
24 24 0.06
25 33 0.09
26 224 0.58
27 25 0.06
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (26 bp):
TAGTAATGATTTGATAATAATCATTA
Found at i:6045881 original size:97 final size:98
Alignment explanation
Indices: 6045689--6045910 Score: 383
Period size: 97 Copynumber: 2.3 Consensus size: 98
6045679 ATGTATTTAT
* ****
6045689 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAATAATGATTTAATAATGATTTAAATATTTAATGAACAAATGATTTAGTAATGAT
6045754 TTGATAATAATCATTATAGTAATGATTTGATAA
66 TTGATAATAATCATTATAGTAATGATTTGATAA
6045787 TAATCATTATAATAATGATTTAATAATGATTTAAATATTTAATGAACAAAT-ATTTAGTAATGAT
1 TAATCATTATAATAATGATTTAATAATGATTTAAATATTTAATGAACAAATGATTTAGTAATGAT
6045851 TTGATAATAATCATTATAGTAATGATTTGATAA
66 TTGATAATAATCATTATAGTAATGATTTGATAA
*
6045884 TAATCATTATAATAATGATTTATTAAT
1 TAATCATTATAATAATGATTTAATAAT
6045911 AATCATTATA
Statistics
Matches: 118, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
97 72 0.61
98 46 0.39
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44
Consensus pattern (98 bp):
TAATCATTATAATAATGATTTAATAATGATTTAAATATTTAATGAACAAATGATTTAGTAATGAT
TTGATAATAATCATTATAGTAATGATTTGATAA
Found at i:6046036 original size:98 final size:97
Alignment explanation
Indices: 6045867--6046235 Score: 480
Period size: 98 Copynumber: 3.8 Consensus size: 97
6045857 ATAATCATTA
* *
6045867 TAGTAATGATTTGATAATAATCATTATAATAATGATTT-ATTAATAATCATTATAAAAATGATTT
1 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGA-TAATAATCATTATAATAATGATTT
6045931 AATAATGAATTAAATATTTAATGATTTGATGATT
65 AATAAT-AATTAAATATTTAATGATTTGATGATT
6045965 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
*
6046030 ATAATGATTTAAATATTTAATGATTTGATGATT
66 ATAAT-AATTAAATATTTAATGATTTGATGATT
*
6046063 TAGTAATTATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
* * * ** *
6046128 GTAATAA-TCATTATAAAAATGATTTAATAATGATT
66 ATAATAATTAAATAT-TTAATGA-TT--TGATGATT
* * * *
6046163 TA--AAT-ATTTAATGATTTGATGATT-TAGTAATGATTTGATAATAATCATTATAATAATGATT
1 TAGTAATGATTTGAT-A-ATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATT
*
6046224 TTATAATAATTA
64 TAATAATAATTA
6046236 TTTAGAATAC
Statistics
Matches: 245, Mismatches: 18, Indels: 15
0.88 0.06 0.05
Matches are distributed among these distances:
96 5 0.02
97 12 0.05
98 211 0.86
99 8 0.03
100 9 0.04
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (97 bp):
TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
ATAATAATTAAATATTTAATGATTTGATGATT
Found at i:6046185 original size:124 final size:124
Alignment explanation
Indices: 6045744--6046233 Score: 549
Period size: 124 Copynumber: 4.0 Consensus size: 124
6045734 TTTGATGATT
* * * *
6045744 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATT--ATA-ATAATGAT
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTTAATAATGAT--TTAAATATTTAATGA-
* * *
6045806 TTAATAATGATTTA--AA-TATTTAATGAACAAAT-ATT-TAGTAATGATTTGATAATAATCATT
63 TT--TGATGATTTAGTAATTATTTGAT-AA-TAATCATTATAGTAATGATTTGATAATAATCATT
6045866 A
124 A
* *
6045867 TAGTAATGATTTGATAATAATCATTATAATAATGATTTATTAATAATCATTATAA-A---AATGA
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTTAATAATGAT--TTA-AATATTTAATGA
* * ** * * * * * *
6045928 TTTAATAATGAATTAAATATTTAATGATTTGATGATT-TAGTAATGATTTGATAATAATCATTA
63 TTTGATGATTTAGTAATTATTTGAT-A-ATAATCATTATAGTAATGATTTGATAATAATCATTA
6045991 TAGTAATGATTTGATAATAATCATTATAATAATGATTTAATAATGATTTAAATATTTAATGATTT
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTTAATAATGATTTAAATATTTAATGATTT
6046056 GATGATTTAGTAATTATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTA
66 GATGATTTAGTAATTATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTA
* *
6046115 TAATAATGATTT-AGTAATAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATT
1 TAGTAATGATTTGA-TAATAATCATTATAATAATGATTTAATAATGATTTAAATATTTAATGATT
* * *
6046179 TGATGATTTAGTAATGATTTGATAATAATCATTATAATAATGATTTTATAATAAT
65 TGATGATTTAGTAATTATTTGATAATAATCATTATAGTAATGATTTGATAATAAT
6046234 TATTTAGAAT
Statistics
Matches: 327, Mismatches: 26, Indels: 27
0.86 0.07 0.07
Matches are distributed among these distances:
120 7 0.02
121 2 0.01
122 8 0.02
123 72 0.22
124 213 0.65
125 24 0.07
126 1 0.00
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (124 bp):
TAGTAATGATTTGATAATAATCATTATAATAATGATTTAATAATGATTTAAATATTTAATGATTT
GATGATTTAGTAATTATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTA
Found at i:6046455 original size:17 final size:17
Alignment explanation
Indices: 6046430--6046462 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
6046420 ACTAAATATC
*
6046430 TAATTATTTGATACTAG
1 TAATGATTTGATACTAG
6046447 TAATGATTTGATACTA
1 TAATGATTTGATACTA
6046463 AAAATCATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (17 bp):
TAATGATTTGATACTAG
Found at i:6048925 original size:47 final size:46
Alignment explanation
Indices: 6048825--6048915 Score: 134
Period size: 44 Copynumber: 2.0 Consensus size: 46
6048815 CAACAAACAA
6048825 ATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTTT
1 ATATAAC-TAACTATTTAACTAACACAAACTAATTAAATAATTTTTT
* *
6048872 ATATAACTAACTA-TTAAC-AATACAAACTAATT-AATTATTTTTT
1 ATATAACTAACTATTTAACTAACACAAACTAATTAAATAATTTTTT
6048915 A
1 A
6048916 ACTATATAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
43 11 0.26
44 13 0.31
45 5 0.12
46 6 0.14
47 7 0.17
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (46 bp):
ATATAACTAACTATTTAACTAACACAAACTAATTAAATAATTTTTT
Found at i:6048983 original size:41 final size:40
Alignment explanation
Indices: 6048846--6048983 Score: 111
Period size: 41 Copynumber: 3.3 Consensus size: 40
6048836 CTATTTAACT
* *
6048846 AACACAAACTAATTAAATAATTTTTT-A-TATAACTAACTATT
1 AACATAAACTAATTAAAT-ATTTTTTAACTAT-A-TAACTATA
*
6048887 AACAATACAAACTAATTAATTATTTTTTAACTATATAACTATCA
1 AAC-AT--AAACTAATTAAATATTTTTTAACTATATAACTAT-A
* * *
6048931 AACATATACTAATTAAATATTTTTTAATTTATGTATACTAT-
1 AACATAAACTAATTAAATATTTTTTAA-CTATATA-ACTATA
*
6048972 AACTTAAACTAA
1 AACATAAACTAA
6048984 CAATCATATA
Statistics
Matches: 80, Mismatches: 9, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
41 33 0.41
42 6 0.08
43 21 0.26
44 17 0.21
45 3 0.04
ACGTcount: A:0.47, C:0.12, G:0.01, T:0.41
Consensus pattern (40 bp):
AACATAAACTAATTAAATATTTTTTAACTATATAACTATA
Found at i:6049146 original size:17 final size:16
Alignment explanation
Indices: 6049147--6049178 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
6049137 CCCTTTCTTT
6049147 CTTTCTTTCCTTTCTCC
1 CTTTCTTT-CTTTCTCC
6049164 CTTTCTTTCTTTCTC
1 CTTTCTTTCTTTCTC
6049179 GGCTGCAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (16 bp):
CTTTCTTTCTTTCTCC
Found at i:6049148 original size:4 final size:4
Alignment explanation
Indices: 6049120--6049177 Score: 53
Period size: 4 Copynumber: 14.0 Consensus size: 4
6049110 TTTCGAATTC
* ** **
6049120 TTCT TACT TTCCT TTCT CCCT TTCT TTCT TTCT TTCCT TTCT CCCT TTCT
1 TTCT TTCT TT-CT TTCT TTCT TTCT TTCT TTCT TT-CT TTCT TTCT TTCT
6049170 TTCT TTCT
1 TTCT TTCT
6049178 CGGCTGCAAT
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
4 34 0.81
5 8 0.19
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.64
Consensus pattern (4 bp):
TTCT
Found at i:6049154 original size:25 final size:25
Alignment explanation
Indices: 6049120--6049177 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
6049110 TTTCGAATTC
*
6049120 TTCTTACTTTCCTTTCTCCCTTTCT
1 TTCTTTCTTTCCTTTCTCCCTTTCT
6049145 TTCTTTCTTTCCTTTCTCCCTTTCT
1 TTCTTTCTTTCCTTTCTCCCTTTCT
6049170 TTCTTTCT
1 TTCTTTCT
6049178 CGGCTGCAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.64
Consensus pattern (25 bp):
TTCTTTCTTTCCTTTCTCCCTTTCT
Found at i:6049267 original size:25 final size:25
Alignment explanation
Indices: 6049239--6049290 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
6049229 TTTCTTTTAT
*
6049239 AACCGGCTGCCTCAATTATTTCACC
1 AACCGACTGCCTCAATTATTTCACC
*
6049264 AACCGACTGCCTTAATTATTTCACC
1 AACCGACTGCCTCAATTATTTCACC
6049289 AA
1 AA
6049291 TAATTGTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.33, G:0.10, T:0.29
Consensus pattern (25 bp):
AACCGACTGCCTCAATTATTTCACC
Found at i:6049458 original size:26 final size:23
Alignment explanation
Indices: 6049401--6049460 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
6049391 ACACGTGAAG
6049401 GAATGGATGATGGGGCTGCATGT
1 GAATGGATGATGGGGCTGCATGT
6049424 GAATGGATGATGGGGCTGCATGT
1 GAATGGATGATGGGGCTGCATGT
*
6049447 GAATGGACGATGGG
1 GAATGGATGATGGG
6049461 AATGGCGCCG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.23, C:0.08, G:0.45, T:0.23
Consensus pattern (23 bp):
GAATGGATGATGGGGCTGCATGT
Found at i:6049499 original size:29 final size:29
Alignment explanation
Indices: 6049466--6049603 Score: 233
Period size: 29 Copynumber: 4.8 Consensus size: 29
6049456 ATGGGAATGG
6049466 CGCCGGGACTACATGGCGACCTATAAGGT
1 CGCCGGGACTACATGGCGACCTATAAGGT
6049495 CGCCGGGACTACATGGCGACCTATAAGGT
1 CGCCGGGACTACATGGCGACCTATAAGGT
6049524 CGCCGGGACTACATGGCGACCTATAAGGT
1 CGCCGGGACTACATGGCGACCTATAAGGT
*
6049553 CGCCGGGACTACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTATAAGGT
* *
6049582 CGCCTAGG-CTGCATGGCGACCT
1 CGCC-GGGACTACATGGCGACCT
6049604 CTCTCCTATT
Statistics
Matches: 105, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
29 103 0.98
30 2 0.02
ACGTcount: A:0.22, C:0.30, G:0.31, T:0.17
Consensus pattern (29 bp):
CGCCGGGACTACATGGCGACCTATAAGGT
Found at i:6049635 original size:19 final size:19
Alignment explanation
Indices: 6049611--6049648 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
6049601 CCTCTCTCCT
6049611 ATTCCACTGCATGGCCACC
1 ATTCCACTGCATGGCCACC
6049630 ATTCCACTGCATGGCCACC
1 ATTCCACTGCATGGCCACC
6049649 TCGCATGGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.42, G:0.16, T:0.21
Consensus pattern (19 bp):
ATTCCACTGCATGGCCACC
Found at i:6049671 original size:15 final size:15
Alignment explanation
Indices: 6049648--6049677 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6049638 GCATGGCCAC
6049648 CTCGCATGGCTCGTA
1 CTCGCATGGCTCGTA
*
6049663 CTCGTATGGCTCGTA
1 CTCGCATGGCTCGTA
6049678 TGCATGGGGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.30, G:0.27, T:0.30
Consensus pattern (15 bp):
CTCGCATGGCTCGTA
Found at i:6049776 original size:55 final size:55
Alignment explanation
Indices: 6049711--6049821 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
6049701 GAACGACCTC
6049711 TCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCA
1 TCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCA
6049766 TCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCA
1 TCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCA
6049821 T
1 T
6049822 GGGGACCTCG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.16, C:0.34, G:0.22, T:0.28
Consensus pattern (55 bp):
TCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCA
Found at i:6049798 original size:139 final size:139
Alignment explanation
Indices: 6049630--6049905 Score: 543
Period size: 139 Copynumber: 2.0 Consensus size: 139
6049620 CATGGCCACC
*
6049630 ATTCCACTGCATGGCCACCTCGCATGGCTCGTACTCGTATGGCTCGTATGCATGGGGACCTCGCA
1 ATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCATGGGGACCTCGCA
6049695 TGGGGAGAACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCG
66 TGGGGAGAACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCG
6049760 TATGCATCT
131 TATGCATCT
6049769 ATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCATGGGGACCTCGCA
1 ATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCATGGGGACCTCGCA
6049834 TGGGGAGAACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCG
66 TGGGGAGAACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCG
6049899 TATGCAT
131 TATGCAT
6049906 GGGGAGAACC
Statistics
Matches: 136, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
139 136 1.00
ACGTcount: A:0.17, C:0.33, G:0.25, T:0.25
Consensus pattern (139 bp):
ATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCATGGGGACCTCGCA
TGGGGAGAACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCG
TATGCATCT
Found at i:6049803 original size:27 final size:27
Alignment explanation
Indices: 6049718--6049803 Score: 68
Period size: 27 Copynumber: 3.1 Consensus size: 27
6049708 CTCTCTATTC
6049718 CACTGCATGGCCACCTCGCATGGCTCG
1 CACTGCATGGCCACCTCGCATGGCTCG
* * * * ***
6049745 CACTCGTATGG-CTCGTATGCATCTATTC-
1 CACT-GCATGGCCACCT-CGCAT-GGCTCG
6049773 CACTGCATGGCCACCTCGCATGGCTCG
1 CACTGCATGGCCACCTCGCATGGCTCG
6049800 CACT
1 CACT
6049804 CGTATGGCTC
Statistics
Matches: 40, Mismatches: 14, Indels: 10
0.62 0.22 0.16
Matches are distributed among these distances:
26 2 0.05
27 20 0.50
28 16 0.40
29 2 0.05
ACGTcount: A:0.16, C:0.37, G:0.22, T:0.24
Consensus pattern (27 bp):
CACTGCATGGCCACCTCGCATGGCTCG
Found at i:6049830 original size:41 final size:41
Alignment explanation
Indices: 6049776--6049907 Score: 119
Period size: 41 Copynumber: 3.2 Consensus size: 41
6049766 TCTATTCCAC
6049776 TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
1 TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
** *** * *
6049817 TGCATGGGGACCTCGCATGGGGAGAACGACCTCTCTAT---TC-CA
1 TGCATGGCCACCTCGCATGGCTCG--C-A-CTC-GTATGGCTCGTA
6049859 CTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
1 -TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
6049901 TGCATGG
1 TGCATGG
6049908 GGAGAACCAG
Statistics
Matches: 67, Mismatches: 14, Indels: 20
0.66 0.14 0.20
Matches are distributed among these distances:
38 3 0.04
39 3 0.04
40 1 0.01
41 29 0.43
42 2 0.03
43 22 0.33
44 1 0.01
45 3 0.04
46 3 0.04
ACGTcount: A:0.17, C:0.32, G:0.28, T:0.23
Consensus pattern (41 bp):
TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
Found at i:6052240 original size:9 final size:9
Alignment explanation
Indices: 6052208--6052232 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
6052198 AAAAGGGAAA
6052208 AAATAAAAT
1 AAATAAAAT
6052217 AAATAAAAT
1 AAATAAAAT
6052226 AAATAAA
1 AAATAAA
6052233 TAAGATAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAATAAAAT
Found at i:6052367 original size:40 final size:42
Alignment explanation
Indices: 6052297--6052377 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
6052287 ATGAAAAAAA
*
6052297 ATATATATATACATCAAATTATTAATAAAATA-AATAAGCTAT
1 ATATATATATACAACAAATTATTAATAAAATAGAA-AAGCTAT
*
6052339 ATATATATATACAACAAA-TATTTA-AAAATAGAAAAGCTA
1 ATATATATATACAACAAATTATTAATAAAATAGAAAAGCTA
6052378 CCCTCTCACT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
40 12 0.33
41 7 0.19
42 17 0.47
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.32
Consensus pattern (42 bp):
ATATATATATACAACAAATTATTAATAAAATAGAAAAGCTAT
Found at i:6052879 original size:18 final size:17
Alignment explanation
Indices: 6052858--6052899 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
6052848 ATATATACGT
*
6052858 ATAATAATAATAACATGA
1 ATAATAATAA-AAAATGA
6052876 ATAATAA-AAAAAATGA
1 ATAATAATAAAAAATGA
6052892 ATAA-AATA
1 ATAATAATA
6052900 TCCATATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 2 0.09
16 11 0.50
17 2 0.09
18 7 0.32
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.24
Consensus pattern (17 bp):
ATAATAATAAAAAATGA
Found at i:6054754 original size:3 final size:3
Alignment explanation
Indices: 6054746--6054781 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
6054736 AGTAAATTTG
6054746 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
6054782 CTGTAAAGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:6055166 original size:12 final size:12
Alignment explanation
Indices: 6055149--6055175 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
6055139 AATATTATTA
6055149 TTCTTTTAATAT
1 TTCTTTTAATAT
6055161 TTCTTTTAATAT
1 TTCTTTTAATAT
6055173 TTC
1 TTC
6055176 CGGTAAAGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.11, G:0.00, T:0.67
Consensus pattern (12 bp):
TTCTTTTAATAT
Done.