Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008821.1 Hibiscus syriacus cultivar Beakdansim tig00111989_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: 1271541
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 7
Found at i:155901 original size:33 final size:32
Alignment explanation
Indices: 155859--155985 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
155849 ATTAAATTCG
155859 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
155892 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
*
155925 CGTTGCGATTTTCATTTCGCATTGTGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
155958 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
155986 AGTAATTTCC
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
31 3 0.04
33 78 0.93
35 3 0.04
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:155960 original size:66 final size:66
Alignment explanation
Indices: 155852--155984 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
155842 ACGCGAAATT
*
155852 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
155917 G
66 G
* *
155918 AAATTAGCGTTGCGATTTTCATTTCGCATTGTGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
155983 G
66 G
155984 A
1 A
155985 TAGTAATTTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:158501 original size:24 final size:24
Alignment explanation
Indices: 158467--158520 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
158457 CTGAAACATC
* *
158467 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
158491 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
158515 ATCAAA
1 ATCAAA
158521 TTTCGAATAC
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:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:159576 original size:20 final size:20
Alignment explanation
Indices: 159551--159628 Score: 138
Period size: 20 Copynumber: 3.9 Consensus size: 20
159541 ATTCATTTGA
159551 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
159571 CTATCGCAACGTGAAAATGG
1 CTATCGCAACGCGAAAATGG
159591 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
159611 CTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
159629 CGCAATGCGA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:159671 original size:14 final size:16
Alignment explanation
Indices: 159651--159724 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
159641 TAAAAATCGC
159651 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
159666 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
159683 TATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
159702 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
159718 -TTGCGAT
1 ATTGCGAT
159725 AGCCATTTCG
Statistics
Matches: 53, Mismatches: 1, Indels: 11
0.82 0.02 0.17
Matches are distributed among these distances:
14 18 0.34
16 3 0.06
17 3 0.06
19 29 0.55
ACGTcount: A:0.14, C:0.19, G:0.19, T:0.49
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:159688 original size:19 final size:19
Alignment explanation
Indices: 159647--159714 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
159637 GAAATAAAAA
159647 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
159663 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
159680 TCGTATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
159699 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
159715 TCGTTGCGAT
Statistics
Matches: 46, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
14 11 0.24
16 3 0.07
17 3 0.07
19 29 0.63
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.49
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:161763 original size:20 final size:19
Alignment explanation
Indices: 161728--161794 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
161718 GAAACTTAAA
161728 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
161747 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
161767 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
161786 ATCGCAACG
1 ATCGCAACG
161795 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:161802 original size:14 final size:14
Alignment explanation
Indices: 161783--161840 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
161773 ATGCGAAATG
161783 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
161797 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
161813 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
161829 AAAATCGCAACG
1 AAAATCGCAACG
161841 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:161825 original size:32 final size:33
Alignment explanation
Indices: 161767--161845 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
161757 GGAAATGGCT
*
161767 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
161800 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
161832 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
161846 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:161893 original size:14 final size:14
Alignment explanation
Indices: 161874--161931 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
161864 TTTCATTTCG
161874 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
161888 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
161904 CACGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
161920 CGTTGCGATTTT
1 CGTTGCGATTTT
161932 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:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:161904 original size:32 final size:33
Alignment explanation
Indices: 161857--161947 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
161847 ACAAATCGCA
161857 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
161890 TTGCGA-TTTCATTTCACGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
161922 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
161948 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 31 0.57
33 23 0.43
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:161966 original size:20 final size:19
Alignment explanation
Indices: 161932--161986 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
161922 TTGCGATTTT
*
161932 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
161951 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
161971 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
161987 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:162492 original size:18 final size:18
Alignment explanation
Indices: 162466--162510 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
162456 GTCGATCAGA
*
162466 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
162484 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
162502 TGATGGCTC
1 TGATGGCTC
162511 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:163848 original size:20 final size:20
Alignment explanation
Indices: 163823--163896 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
163813 AATAGTTTCT
*
163823 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACGC
**
163843 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACGC
** **
163863 GAATTTGACTATCGCAACGC
1 GAAAATGAAAATCGCAACGC
*
163883 GAAACT-AAAATCGC
1 GAAAATGAAAATCGC
163897 GTTGCGATTT
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 6 0.13
20 39 0.87
ACGTcount: A:0.43, C:0.23, G:0.18, T:0.16
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACGC
Found at i:164154 original size:21 final size:21
Alignment explanation
Indices: 164128--164170 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
164118 GATGGAGATA
164128 GACGGATTTCGCCGGAGATGG
1 GACGGATTTCGCCGGAGATGG
*
164149 GACGGATTTCGTCGGAGATGG
1 GACGGATTTCGCCGGAGATGG
164170 G
1 G
164171 TGAGAGTGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.16, G:0.44, T:0.21
Consensus pattern (21 bp):
GACGGATTTCGCCGGAGATGG
Found at i:164378 original size:20 final size:20
Alignment explanation
Indices: 164352--164424 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
164342 GATTATGTAT
164352 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
164372 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
164392 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
*
164412 TATCTCGTTGCGA
1 TATCGCGTTGCGA
164425 TTTTGTATTA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:164462 original size:20 final size:20
Alignment explanation
Indices: 164352--164466 Score: 106
Period size: 20 Copynumber: 5.7 Consensus size: 20
164342 GATTATGTAT
*
164352 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
164372 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
164392 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGATAGTCAG
* * *
164412 TATCTCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
* *
164433 TATTGCATTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
164453 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
164467 TTTCCCAATT
Statistics
Matches: 79, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
19 3 0.04
20 63 0.80
21 11 0.14
22 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:164469 original size:41 final size:41
Alignment explanation
Indices: 164332--164467 Score: 150
Period size: 41 Copynumber: 3.3 Consensus size: 41
164322 CGCTTTGAAA
*
164332 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
* * * *
164373 ATCGCGTTGCGA--AAGTCAGTATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATTATGT-ATTATCGCGTTGCGAAAGTCAGT
* * * * * *
164413 ATCTCGTTGCGATTTTGTATTATTGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
164454 ATCGCATTGCGATT
1 ATCGCATTGCGATT
164468 TTCCCAATTC
Statistics
Matches: 77, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
39 3 0.04
40 31 0.40
41 41 0.53
42 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (41 bp):
ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
Found at i:164484 original size:21 final size:21
Alignment explanation
Indices: 164455--164548 Score: 84
Period size: 20 Copynumber: 4.5 Consensus size: 21
164445 ATAGTCAGTA
164455 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
164476 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
*
164496 TCGTATTGCGATTTTCCCCAAT
1 TCGCATTGCGATTTT-CCCAAT
* * **
164518 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
164538 TCGCATTGCGA
1 TCGCATTGCGA
164549 ATTGGGAAAA
Statistics
Matches: 56, Mismatches: 15, Indels: 5
0.74 0.20 0.07
Matches are distributed among these distances:
20 28 0.50
21 16 0.29
22 12 0.21
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:164528 original size:42 final size:41
Alignment explanation
Indices: 164455--164548 Score: 170
Period size: 42 Copynumber: 2.3 Consensus size: 41
164445 ATAGTCAGTA
164455 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
*
164496 TCGTATTGCGATTTTCCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTT-CCCAATTCGCGTTGCGATTTACTTAT
164538 TCGCATTGCGA
1 TCGCATTGCGA
164549 ATTGGGAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
41 14 0.28
42 36 0.72
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:170150 original size:31 final size:31
Alignment explanation
Indices: 170113--170175 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
170103 CCCCAAAATT
170113 TTTTGGGTAAACCAACATTCAGTAGCATGCA
1 TTTTGGGTAAACCAACATTCAGTAGCATGCA
170144 TTTTGGGTAAACCAACATTCAGTAGCATGCA
1 TTTTGGGTAAACCAACATTCAGTAGCATGCA
170175 T
1 T
170176 CTCACTCTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (31 bp):
TTTTGGGTAAACCAACATTCAGTAGCATGCA
Found at i:170961 original size:155 final size:157
Alignment explanation
Indices: 170679--170990 Score: 610
Period size: 155 Copynumber: 2.0 Consensus size: 157
170669 TTACATGTCC
170679 CAATCTCATGTGCCATAGTCTAGCTTTGTCAGTTTCAGATTGAACTACATTTAACGAGTTACCAA
1 CAATCTCATGTGCCATAGTCTAGCTTTGTCAGTTTCAGATTGAACTACATTTAACGAGTTACCAA
170744 TCACAGTTCTTCCAATTAGTGATTATAGACCATTACTTATAAGTCCTTTCATGGCAATT-AA-AG
66 TCACAGTTCTTCCAATTAGTGATTATAGACCATTACTTATAAGTCCTTTCATGGCAATTAAAGAG
170807 CCTTTAGTTACTCGTATACAACCATTT
131 CCTTTAGTTACTCGTATACAACCATTT
170834 CAATCTCATGTGCCATAGTCTAGCTTTGTCAGTTTCAGATTGAACTACATTTAACGAGTTACCAA
1 CAATCTCATGTGCCATAGTCTAGCTTTGTCAGTTTCAGATTGAACTACATTTAACGAGTTACCAA
170899 TCACAGTTCTTCCAATTAGTGATTATAGACCATTACTTATAAGTCCTTTCATGGCAATTAAAGAG
66 TCACAGTTCTTCCAATTAGTGATTATAGACCATTACTTATAAGTCCTTTCATGGCAATTAAAGAG
170964 CCTTTAGTTACTCGTATACAACCATTT
131 CCTTTAGTTACTCGTATACAACCATTT
170991 TCTGCCTTAA
Statistics
Matches: 155, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
155 124 0.80
156 2 0.01
157 29 0.19
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (157 bp):
CAATCTCATGTGCCATAGTCTAGCTTTGTCAGTTTCAGATTGAACTACATTTAACGAGTTACCAA
TCACAGTTCTTCCAATTAGTGATTATAGACCATTACTTATAAGTCCTTTCATGGCAATTAAAGAG
CCTTTAGTTACTCGTATACAACCATTT
Found at i:173371 original size:13 final size:16
Alignment explanation
Indices: 173341--173370 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
173331 AATTTATCAA
173341 TTAATTATTATTTGTG
1 TTAATTATTATTTGTG
173357 TTAATTA-TATTTGT
1 TTAATTATTATTTGT
173371 TTGTCTACCG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (16 bp):
TTAATTATTATTTGTG
Found at i:174391 original size:17 final size:17
Alignment explanation
Indices: 174369--174404 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
174359 GCTTGATATA
174369 ATTAGAA-TATTATATTT
1 ATTAGAATTA-TATATTT
174386 ATTAGAATTATATATTT
1 ATTAGAATTATATATTT
174403 AT
1 AT
174405 GTTTCAGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 16 0.89
18 2 0.11
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
ATTAGAATTATATATTT
Found at i:175066 original size:42 final size:42
Alignment explanation
Indices: 174964--175055 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 42
174954 AATGCCACAG
*
174964 GGGTACATGCCCAGCCCACCAGTTCAGATGCCATCTCCGCAA
1 GGGTACATGCCAAGCCCACCAGTTCAGATGCCATCTCCGCAA
* * **
175006 GGGTATATGCCAAGCCCACCAGTTCATATTTCATCTCCGC-A
1 GGGTACATGCCAAGCCCACCAGTTCAGATGCCATCTCCGCAA
175047 GGGTTACAT
1 GGG-TACAT
175056 TCCTAACCCA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 4 0.09
42 39 0.91
ACGTcount: A:0.24, C:0.33, G:0.21, T:0.23
Consensus pattern (42 bp):
GGGTACATGCCAAGCCCACCAGTTCAGATGCCATCTCCGCAA
Found at i:175096 original size:21 final size:21
Alignment explanation
Indices: 175072--175114 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
175062 CCCACAGGGG
175072 TACATACCCAGCCCGCAAGGT
1 TACATACCCAGCCCGCAAGGT
* *
175093 TACATGCCCATCCCGCAAGGT
1 TACATACCCAGCCCGCAAGGT
175114 T
1 T
175115 TTATGACACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.37, G:0.19, T:0.19
Consensus pattern (21 bp):
TACATACCCAGCCCGCAAGGT
Found at i:176853 original size:137 final size:137
Alignment explanation
Indices: 176131--177570 Score: 1365
Period size: 136 Copynumber: 10.6 Consensus size: 137
176121 TGCCATTTTA
* *
176131 GGGG-CATCACACATAATACGACAATTATAACATATTCTCTGACAAAAAAATGGAAGGCGCGCCC
1 GGGGACATCACACATAATAGGGCAATTATAACATATTCTCTGAC-AAAAAA-GGAAGGCGCGCCC
* * * ** *
176195 CCTAAAACGCGCTTTAACCACATTGA-TACATCCCCTC-TCCAATGATAGGTACTGACATAAATA
64 CCTGAAACGCGCTTTAACCACATT-ATTGCGTCCCCTCAAAC-ATGATAGGTACTGACATGAATA
*
176258 GTGCCCC-GTCG
127 GTGCCCCACT-G
* * ** * **
176269 GGGGACATCACACATAATAGGGCAATTATAACCTATTCTCTGATAAAAAAAAAAGGAAAGATACC
1 GGGGACATCACACATAATAGGGCAATTATAACATATTCTCTGACAAAAAAGGAAGG--CG-CGCC
* * * * * * * *
176334 CCTTGAAACACACTTTAACCATATTGTTGCATCCCTTCTC-CA-ATGATAGGTACTGATATGAAT
63 CCCTGAAACGCGCTTTAACCACATTATTGCGTCCC--CTCAAACATGATAGGTACTGACATGAAT
*
176397 AGTGCCCCACCG
126 AGTGCCCCACTG
* **
176409 GGGGACATCACACATAATAGGGCAATTATAATC-TATTCTCTGACAAAAAATGGAAGACGCG-TA
1 GGGGACATCACACATAATAGGGCAATTATAA-CATATTCTCTGACAAAAAA-GGAAGGCGCGCCC
* * * *
176472 CCTGAAACGCACTTTAACCACATTATTGCGTCCCCT-AAAAATGATAGGTATTAACATGAATAGT
64 CCTGAAACGCGCTTTAACCACATTATTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAGT
** *
176536 G--TTATTTCG
129 GCCCCA-CT-G
* * *
176545 GGGGACATCACACATAATAAGGCAATTATAACATATTCTCT-AAAAAAAAGGAA-G-GTGCCCCC
1 GGGGACATCACACATAATAGGGCAATTATAACATATTCTCTGACAAAAAAGGAAGGCGCGCCCCC
* * * * *
176607 TGAAACGCACTTTAA-C-CA--ATTGTGT---CACAATCATGATAGGTACTGACATGAATAGTAC
66 TGAAACGCGCTTTAACCACATTATTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAGTGC
** **
176665 ATCGTTG
131 CCCACTG
* *
176672 GGGG-CATCA-ACATAATAGGGCAATTATAACATATTCTCTGACAAAAAAGGTAAGGTGTGCCCC
1 GGGGACATCACACATAATAGGGCAATTATAACATATTCTCTGACAAAAAAGG-AAGGCGCGCCCC
* * *
176735 CTGAAACGCGCTTTAACCACATTACTG-GTCCCCTCAAACATGATAGGTACTAACATAAATAGTG
65 CTGAAACGCGCTTTAACCACATTATTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAGTG
176799 CCCCACTG
130 CCCCACTG
* * * ***
176807 GGGGACATCACACAAAATAGGGCAATTATAACTTATTCTCTAACAAAAAAAGGAAGGCGCATTCC
1 GGGGACATCACACATAATAGGGCAATTATAACATATTCTCTGAC-AAAAAAGGAAGGCGCGCCCC
* * *
176872 CTGAAACGCGCTTTAACCACATTGTTACGTTCCCCCCAAACATGATAGGTACTGACATGAATAGT
65 CTGAAACGCGCTTTAACCACATTATTGCG-TCCCCTCAAACATGATAGGTACTGACATGAATAGT
* ****
176937 GTCATTTTG
129 GCCCCACTG
* * *
176946 GGGGACATCACACATAATAGGGCAATTATAACATATTCTATG-GAAAAAAGAGAAGGCACGCCCC
1 GGGGACATCACACATAATAGGGCAATTATAACATATTCTCTGACAAAAAAG-GAAGGCGCGCCCC
* * *
177010 CTGAAACGTGTTTTAACCACATTGA-TGCGTCCCCTCTAACATGATAGGTACTGACATGAATAGT
65 CTGAAACGCGCTTTAACCACATT-ATTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAGT
* **
177074 GCCTCACCA
129 GCCCCACTG
*** * *
177083 GGGGACATCA-ACATAATATATCAATTATAACATATTTTCTGACAAAAAAGGGAAGGTGC-CCCC
1 GGGGACATCACACATAATAGGGCAATTATAACATATTCTCTGACAAAAAA-GGAAGGCGCGCCCC
* * *
177146 CTTAAACGCGCTTTAACCACATTGA-TGCGTCCCCTCAAACATGATAGGTACTTACATAAATAGT
65 CTGAAACGCGCTTTAACCACATT-ATTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAGT
*
177210 GCCCCGCTG
129 GCCCCACTG
* * * * * *
177219 GGGGACATCA-ACATAATAGGGCAATTACAACATATTCTATTACAAAAAAAAAGGGAATGTGTGC
1 GGGGACATCACACATAATAGGGCAATTATAACATATTCTCTGAC---AAAAAA-GGAAGGCGCGC
* * * *
177283 CCCCTGAAACGTGTTTTAA-C-CATTGTTGTGT-CCCTCAAACATGATAGGTACTGACAT-AATA
62 CCCCTGAAACGCGCTTTAACCACATTATTGCGTCCCCTCAAACATGATAGGTACTGACATGAATA
177344 GTGCCCCAC--
127 GTGCCCCACTG
* * * *
177353 AGGAACATCA-ACATAATAGGGCAATTATAACATATTATCTGACAAAAAAAGAGAAGG-ACGCCC
1 GGGGACATCACACATAATAGGGCAATTATAACATATTCTCTGAC-AAAAAAG-GAAGGCGCGCCC
*
177416 CCTGAAACGTGCTTTAACCACATTATTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAGT
64 CCTGAAACGCGCTTTAACCACATTATTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAGT
* **
177481 -ACCCTGTCG
129 GCCCCACT-G
** * *
177490 GGGGACATCACACATAATAGGAAAATTATAACATATTATCTGACAAAGAAAAGGGAAGGCGCACC
1 GGGGACATCACACATAATAGGGCAATTATAACATATTCTCTGAC-AA-AAAA-GGAAGGCGCGCC
*
177555 CCCTGAAACGCACTTT
63 CCCTGAAACGCGCTTT
177571 CATATGAATA
Statistics
Matches: 1076, Mismatches: 170, Indels: 110
0.79 0.13 0.08
Matches are distributed among these distances:
125 29 0.03
126 15 0.01
127 31 0.03
128 3 0.00
129 29 0.03
130 1 0.00
131 25 0.02
132 17 0.02
133 29 0.03
134 71 0.07
135 52 0.05
136 207 0.19
137 191 0.18
138 95 0.09
139 135 0.13
140 139 0.13
141 4 0.00
142 3 0.00
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.24
Consensus pattern (137 bp):
GGGGACATCACACATAATAGGGCAATTATAACATATTCTCTGACAAAAAAGGAAGGCGCGCCCCC
TGAAACGCGCTTTAACCACATTATTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAGTGC
CCCACTG
Found at i:177271 original size:276 final size:276
Alignment explanation
Indices: 176131--177570 Score: 1439
Period size: 276 Copynumber: 5.3 Consensus size: 276
176121 TGCCATTTTA
* * *
176131 GGGG-CATCACACATAATACGACAATTATAACATATTCTCTGACAAAAAAATGGAAGGCGCGCCC
1 GGGGACATCACACATAATAGGGCAATTATAACATATTCTCTGACAAAAAAAAGGAAGGCGCGCCC
* * * **
176195 CCTAAAACGCGCTTTAACCACATTGATACATCCCCTC-TCCAATGATAGGTACTGACATAAATAG
66 CCTGAAACGCGCTTTAACCACATTGATGCGTCCCCTCAAAC-ATGATAGGTACTGACATAAATAG
** * *
176259 TGCCCCGTCGGGGGACATCACACATAATAGGGCAATTATAACCTATTCTCTGATAAAAAAAAAAG
130 TGCCCCACCGGGGGACATCACACATAATAGGGCAATTATAACATATTCTCTG----ACAAAAAAG
* * * * * * * * * *
176324 GAAAGAT-ACCCCTTGAAACACACTTTAACCATATTGTTGCATCCCTTCTC-CA-ATGATAGGTA
191 GGAAGGTGCCCCCCTGAAACGCGCTTTAACCACATTGATGCGTCCC--CTCAAACATGATAGGTA
* * *
176386 CTGATATGAATAGTGCCCCACCG
254 CTGACATGAATAGTGCCCCGCTG
* * *
176409 GGGGACATCACACATAATAGGGCAATTATAATC-TATTCTCTGAC-AAAAAATGGAAGACGCG-T
1 GGGGACATCACACATAATAGGGCAATTATAA-CATATTCTCTGACAAAAAAAAGGAAGGCGCGCC
* * * * * *
176471 ACCTGAAACGCACTTTAACCACATT-ATTGCGTCCCCT-AAAAATGATAGGTATTAACATGAATA
65 CCCTGAAACGCGCTTTAACCACATTGA-TGCGTCCCCTCAAACATGATAGGTACTGACATAAATA
****** * *
176534 GTGTTATTTCGGGGGACATCACACATAATAAGGCAATTATAACATATTCTCT-A-AAAAAAAGGA
129 GTGCCCCACCGGGGGACATCACACATAATAGGGCAATTATAACATATTCTCTGACAAAAAAGGGA
* * *
176597 AGGTG-CCCCCTGAAACGCACTTTAACCA-ATTG-T--GT---CACAATCATGATAGGTACTGAC
194 AGGTGCCCCCCTGAAACGCGCTTTAACCACATTGATGCGTCCCCTCAAACATGATAGGTACTGAC
* ** *
176654 ATGAATAGTACATCGTTG
259 ATGAATAGTGCCCCGCTG
* *
176672 GGGG-CATCA-ACATAATAGGGCAATTATAACATATTCTCTGAC--AAAAAAGGTAAGGTGTGCC
1 GGGGACATCACACATAATAGGGCAATTATAACATATTCTCTGACAAAAAAAAGG-AAGGCGCGCC
*
176733 CCCTGAAACGCGCTTTAACCACATT-ACTG-GTCCCCTCAAACATGATAGGTACTAACATAAATA
65 CCCTGAAACGCGCTTTAACCACATTGA-TGCGTCCCCTCAAACATGATAGGTACTGACATAAATA
* * * * *
176796 GTGCCCCACTGGGGGACATCACACAAAATAGGGCAATTATAACTTATTCTCTAACAAAAAAAGGA
129 GTGCCCCACCGGGGGACATCACACATAATAGGGCAATTATAACATATTCTCTGACAAAAAAGGGA
* ** * * *
176861 AGGCGCATTCCCTGAAACGCGCTTTAACCACATTGTTACGTTCCCCCCAAACATGATAGGTACTG
194 AGGTGC-CCCCCTGAAACGCGCTTTAACCACATTGATGCG-TCCCCTCAAACATGATAGGTACTG
* ****
176926 ACATGAATAGTGTCATTTTG
257 ACATGAATAGTGCCCCGCTG
* * * *
176946 GGGGACATCACACATAATAGGGCAATTATAACATATTCTATG-GAAAAAAGA-GAAGGCACGCCC
1 GGGGACATCACACATAATAGGGCAATTATAACATATTCTCTGACAAAAAAAAGGAAGGCGCGCCC
* * * *
177009 CCTGAAACGTGTTTTAACCACATTGATGCGTCCCCTCTAACATGATAGGTACTGACATGAATAGT
66 CCTGAAACGCGCTTTAACCACATTGATGCGTCCCCTCAAACATGATAGGTACTGACATAAATAGT
* * *** *
177074 GCCTCACCAGGGGACATCA-ACATAATATATCAATTATAACATATTTTCTGACAAAAAAGGGAAG
131 GCCCCACCGGGGGACATCACACATAATAGGGCAATTATAACATATTCTCTGACAAAAAAGGGAAG
* *
177138 GTGCCCCCCTTAAACGCGCTTTAACCACATTGATGCGTCCCCTCAAACATGATAGGTACTTACAT
196 GTGCCCCCCTGAAACGCGCTTTAACCACATTGATGCGTCCCCTCAAACATGATAGGTACTGACAT
*
177203 AAATAGTGCCCCGCTG
261 GAATAGTGCCCCGCTG
* * * * * *
177219 GGGGACATCA-ACATAATAGGGCAATTACAACATATTCTATTACAAAAAAAAAGGGAATGTGTGC
1 GGGGACATCACACATAATAGGGCAATTATAACATATTCTCTGAC-AAAAAAAA-GGAAGGCGCGC
* * * *
177283 CCCCTGAAACGTGTTTTAA-C-CATTGTTGTGT-CCCTCAAACATGATAGGTACTGACAT-AATA
64 CCCCTGAAACGCGCTTTAACCACATTGATGCGTCCCCTCAAACATGATAGGTACTGACATAAATA
* * * *
177344 GTGCCCCA-C-AGGAACATCA-ACATAATAGGGCAATTATAACATATTATCTGACAAAAAAAGAG
129 GTGCCCCACCGGGGGACATCACACATAATAGGGCAATTATAACATATTCTCTGAC-AAAAAAGGG
* *
177406 AAGG-ACGCCCCCTGAAACGTGCTTTAACCACATT-ATTGCGTCCCCTCAAACATGATAGGTACT
193 AAGGTGC-CCCCCTGAAACGCGCTTTAACCACATTGA-TGCGTCCCCTCAAACATGATAGGTACT
* *
177469 GACATGAATAGTACCCTG-TCG
256 GACATGAATAGTGCCCCGCT-G
** * * *
177490 GGGGACATCACACATAATAGGAAAATTATAACATATTATCTGACAAAGAAAAGGGAAGGCGCACC
1 GGGGACATCACACATAATAGGGCAATTATAACATATTCTCTGACAAA-AAAAAGGAAGGCGCGCC
*
177555 CCCTGAAACGCACTTT
65 CCCTGAAACGCGCTTT
177571 CATATGAATA
Statistics
Matches: 976, Mismatches: 147, Indels: 85
0.81 0.12 0.07
Matches are distributed among these distances:
260 8 0.01
261 45 0.05
262 96 0.10
263 31 0.03
264 14 0.01
266 21 0.02
267 4 0.00
268 2 0.00
269 4 0.00
270 73 0.07
271 116 0.12
272 71 0.07
273 71 0.07
274 80 0.08
275 78 0.08
276 171 0.18
277 35 0.04
278 20 0.02
279 35 0.04
280 1 0.00
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.24
Consensus pattern (276 bp):
GGGGACATCACACATAATAGGGCAATTATAACATATTCTCTGACAAAAAAAAGGAAGGCGCGCCC
CCTGAAACGCGCTTTAACCACATTGATGCGTCCCCTCAAACATGATAGGTACTGACATAAATAGT
GCCCCACCGGGGGACATCACACATAATAGGGCAATTATAACATATTCTCTGACAAAAAAGGGAAG
GTGCCCCCCTGAAACGCGCTTTAACCACATTGATGCGTCCCCTCAAACATGATAGGTACTGACAT
GAATAGTGCCCCGCTG
Found at i:183405 original size:16 final size:16
Alignment explanation
Indices: 183384--183415 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
183374 GCAAGCATGC
183384 TTATAAACATATGCAT
1 TTATAAACATATGCAT
183400 TTATAAACATATGCAT
1 TTATAAACATATGCAT
183416 GAAAACGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (16 bp):
TTATAAACATATGCAT
Found at i:188207 original size:25 final size:24
Alignment explanation
Indices: 188133--188209 Score: 84
Period size: 24 Copynumber: 3.2 Consensus size: 24
188123 CTAAAATTCG
188133 ATTTGATTTTAAAATAAAAAAATA
1 ATTTGATTTTAAAATAAAAAAATA
* * * * *
188157 TTTTTAATTT-AAATAATATACATA
1 ATTTGATTTTAAAATAA-AAAAATA
188181 ATTTGATTTTAAAATAAAAAAATTA
1 ATTTGATTTTAAAATAAAAAAA-TA
188206 ATTT
1 ATTT
188210 AAATAATATA
Statistics
Matches: 40, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
23 6 0.15
24 22 0.55
25 12 0.30
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (24 bp):
ATTTGATTTTAAAATAAAAAAATA
Found at i:188208 original size:43 final size:46
Alignment explanation
Indices: 188133--188222 Score: 141
Period size: 43 Copynumber: 2.0 Consensus size: 46
188123 CTAAAATTCG
188133 ATTTGATTTTAAAATAAAAAAATATTTTTAATTTAAATAATATACATA
1 ATTTGATTTTAAAATAAAAAAATA--TTTAATTTAAATAATATACATA
188181 ATTTGATTTTAAAAT-AAAAAA-A-TTAATTTAAATAATATACAT
1 ATTTGATTTTAAAATAAAAAAATATTTAATTTAAATAATATACAT
188223 TGTGTCTTCT
Statistics
Matches: 42, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
43 20 0.48
46 1 0.02
47 6 0.14
48 15 0.36
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (46 bp):
ATTTGATTTTAAAATAAAAAAATATTTAATTTAAATAATATACATA
Found at i:188360 original size:19 final size:17
Alignment explanation
Indices: 188320--188355 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
188310 TAATATATTA
188320 TATATAAAATTATTTTT
1 TATATAAAATTATTTTT
188337 TATATAAAATTATTTTT
1 TATATAAAATTATTTTT
188354 TA
1 TA
188356 AATATTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATATAAAATTATTTTT
Found at i:189906 original size:11 final size:11
Alignment explanation
Indices: 189892--189917 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
189882 AAATATATAA
189892 TATATATTATT
1 TATATATTATT
189903 TATATATTATT
1 TATATATTATT
189914 TATA
1 TATA
189918 AATTTTGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TATATATTATT
Found at i:205758 original size:156 final size:157
Alignment explanation
Indices: 205473--205786 Score: 621
Period size: 156 Copynumber: 2.0 Consensus size: 157
205463 AAGAGTCTTT
205473 AAAACAAATATTACCACTTATAATAATCCTAGATTAATAAAAACAAATACTTAAAATGCATAAAA
1 AAAACAAATATTACCACTTATAATAATCCTAGATTAATAAAAACAAATACTTAAAATGCATAAAA
205538 TGATAGTTTTATGAGCATATTTTATATGGTAAATAAGAAAAACAACTTTCTAAAATAGTGTAATT
66 TGATAGTTTTATGAGCATATTTTATATGGTAAATAAGAAAAACAACTTTCTAAAATAGTGTAATT
205603 ACTTAACATATATGAAAATGGCTTAAA
131 ACTTAACATATATGAAAATGGCTTAAA
205630 AAAACAAATATTACCACTTATAATAATCCTAGATTAATAAAAA-AAATACTTAAAATGCATAAAA
1 AAAACAAATATTACCACTTATAATAATCCTAGATTAATAAAAACAAATACTTAAAATGCATAAAA
205694 TGATAGTTTTATGAGCATATTTTATATGGTAAATAAGAAAAACAACTTTCTAAAATAGTGTAATT
66 TGATAGTTTTATGAGCATATTTTATATGGTAAATAAGAAAAACAACTTTCTAAAATAGTGTAATT
205759 ACTTAACATATATGAAAATGGCTTAAA
131 ACTTAACATATATGAAAATGGCTTAAA
205786 A
1 A
205787 TAACCATACG
Statistics
Matches: 157, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
156 114 0.73
157 43 0.27
ACGTcount: A:0.49, C:0.10, G:0.09, T:0.32
Consensus pattern (157 bp):
AAAACAAATATTACCACTTATAATAATCCTAGATTAATAAAAACAAATACTTAAAATGCATAAAA
TGATAGTTTTATGAGCATATTTTATATGGTAAATAAGAAAAACAACTTTCTAAAATAGTGTAATT
ACTTAACATATATGAAAATGGCTTAAA
Found at i:206244 original size:9 final size:11
Alignment explanation
Indices: 206222--206270 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
206212 ATCAATATTC
206222 TTTTATATTAA
1 TTTTATATTAA
206233 TTTTAT-TT-A
1 TTTTATATTAA
* *
206242 TTTTA-AATAT
1 TTTTATATTAA
206252 TTTTATATTAA
1 TTTTATATTAA
*
206263 ATTTATAT
1 TTTTATAT
206271 ATAAAAAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
9 7 0.23
10 7 0.23
11 16 0.53
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TTTTATATTAA
Found at i:206273 original size:15 final size:15
Alignment explanation
Indices: 206223--206273 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
206213 TCAATATTCT
*
206223 TTTATATTAATTTTA
1 TTTATATTAAATTTA
*
206238 TTTATTTTAAATATT-
1 TTTATATTAAAT-TTA
206253 TTTATATTAAATTTA
1 TTTATATTAAATTTA
*
206268 TATATA
1 TTTATA
206274 AAAAAATTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
14 2 0.07
15 26 0.87
16 2 0.07
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTATATTAAATTTA
Found at i:206433 original size:26 final size:29
Alignment explanation
Indices: 206394--206447 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
206384 TTAATTTCAT
*
206394 AATTAAGTAAT-AAA-T-TTGAAGGTTTG
1 AATTAAATAATAAAAGTATTGAAGGTTTG
*
206420 AATTAAATACTAAAAGTATTGAAGGTTT
1 AATTAAATAATAAAAGTATTGAAGGTTT
206448 TTAATCTAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 9 0.39
27 3 0.13
28 1 0.04
29 10 0.43
ACGTcount: A:0.44, C:0.02, G:0.17, T:0.37
Consensus pattern (29 bp):
AATTAAATAATAAAAGTATTGAAGGTTTG
Found at i:209678 original size:2 final size:2
Alignment explanation
Indices: 209671--209697 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
209661 ATAAATAAAT
209671 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 T
209698 TGAAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:212755 original size:38 final size:37
Alignment explanation
Indices: 212703--212784 Score: 128
Period size: 38 Copynumber: 2.2 Consensus size: 37
212693 TTACATGCAT
212703 GAGATTGATTATGAAGAAATGAGGGCACCTGAATTCCCG
1 GAGA-TGATTATGAAGAAATGAGGGCACCTGAATT-CCG
* *
212742 GAGATGATTATGAAGCAATGAGGGCACTTGAATTCCG
1 GAGATGATTATGAAGAAATGAGGGCACCTGAATTCCG
212779 GAGATG
1 GAGATG
212785 TCACATTTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
37 9 0.22
38 28 0.68
39 4 0.10
ACGTcount: A:0.33, C:0.13, G:0.30, T:0.23
Consensus pattern (37 bp):
GAGATGATTATGAAGAAATGAGGGCACCTGAATTCCG
Found at i:213936 original size:64 final size:62
Alignment explanation
Indices: 213852--213990 Score: 149
Period size: 64 Copynumber: 2.2 Consensus size: 62
213842 CACATTCAGT
* *
213852 GTGTACCGATGCACTCTT-AAATA-ATGAACATCGAATGCCATTAATGCATCGATGCATAAGG-A
1 GTGTATCGATGCACTCTTAAAATACA--AACATCGAATGCCATTAATGCACCGATGCAT-AGGTA
** *
213914 GTGTATCGATGCACTCTTTTAAAATACAAACATCGAATGGGATTTATGCACCGATGCATAGGTA
1 GTGTATCGATGCACTC--TTAAAATACAAACATCGAATGCCATTAATGCACCGATGCATAGGTA
* *
213978 GTGCATCAATGCA
1 GTGTATCGATGCA
213991 TCTGTCAAGG
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
62 15 0.23
63 3 0.05
64 41 0.63
65 5 0.08
66 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (62 bp):
GTGTATCGATGCACTCTTAAAATACAAACATCGAATGCCATTAATGCACCGATGCATAGGTA
Found at i:214566 original size:18 final size:18
Alignment explanation
Indices: 214543--214613 Score: 79
Period size: 18 Copynumber: 3.8 Consensus size: 18
214533 AGGGATCATC
214543 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* * *
214561 AGTGGTTCTTTGGAACAATT
1 AGTGGTCCTTCGGGAC-A-T
214581 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
214599 AGTGATCATTCGGGA
1 AGTGGTCCTTCGGGA
214614 TAAATATTCA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
18 27 0.63
19 2 0.05
20 14 0.33
ACGTcount: A:0.21, C:0.17, G:0.31, T:0.31
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:220786 original size:64 final size:62
Alignment explanation
Indices: 220708--220841 Score: 166
Period size: 64 Copynumber: 2.1 Consensus size: 62
220698 CAATGTGTAC
* *
220708 CGATGCACTCTT-AAATA-ATGAACATCGAATGCCATTAATGCATCGATGCATAAGG-AGTGCAT
1 CGATGCACTCTTAAAATACA--AACATCGAATGACATTAATGCACCGATGCAT-AGGTAGTGCAT
* *
220770 CGATGCACTCTTTTAAAATACAAACATCGAATGAGATTTATGCACCGATGCATAGGTAGTGCAT
1 CGATGCACTC--TTAAAATACAAACATCGAATGACATTAATGCACCGATGCATAGGTAGTGCAT
220834 CGATGCAC
1 CGATGCAC
220842 CTGTCAAGGG
Statistics
Matches: 63, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
62 10 0.16
63 3 0.05
64 44 0.70
65 5 0.08
66 1 0.02
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.26
Consensus pattern (62 bp):
CGATGCACTCTTAAAATACAAACATCGAATGACATTAATGCACCGATGCATAGGTAGTGCAT
Found at i:221421 original size:18 final size:18
Alignment explanation
Indices: 221398--221470 Score: 110
Period size: 18 Copynumber: 3.9 Consensus size: 18
221388 AGGGATTATC
221398 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
221416 AGTGGTTCTTCGGAACAATT
1 AGTGGTCCTTCGGGAC-A-T
221436 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
221454 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
221471 AATATTTAGT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
18 32 0.65
19 2 0.04
20 15 0.31
ACGTcount: A:0.19, C:0.21, G:0.32, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:221449 original size:38 final size:38
Alignment explanation
Indices: 221398--221471 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
221388 AGGGATTATC
*
221398 AGTGGTCCTTCGGGACATAGTGGTTCTTCGGAACAATT
1 AGTGGTCCTTCGGGACATAGTGGTCCTTCGGAACAATT
*
221436 AGTGGTCCTTCGGGACATAGTGGTCCTTCGGGACAA
1 AGTGGTCCTTCGGGACATAGTGGTCCTTCGGAACAA
221472 ATATTTAGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.28
Consensus pattern (38 bp):
AGTGGTCCTTCGGGACATAGTGGTCCTTCGGAACAATT
Found at i:223877 original size:22 final size:21
Alignment explanation
Indices: 223852--223924 Score: 58
Period size: 22 Copynumber: 3.3 Consensus size: 21
223842 TAGTAATGAT
223852 ATGATTTATTAAAAATGATTTA
1 ATGATTTA-TAAAAATGATTTA
** * *
223874 ATGATTTA-ATGATTTACTATTA
1 ATGATTTATAAAAATGA-T-TTA
*
223896 ATGATTTAATAATAATGATTTA
1 ATGATTT-ATAAAAATGATTTA
223918 ATGATTT
1 ATGATTT
223925 TTGTGGCTAA
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
20 4 0.10
21 1 0.03
22 28 0.72
23 2 0.05
24 4 0.10
ACGTcount: A:0.41, C:0.01, G:0.10, T:0.48
Consensus pattern (21 bp):
ATGATTTATAAAAATGATTTA
Found at i:223898 original size:14 final size:14
Alignment explanation
Indices: 223865--223919 Score: 74
Period size: 14 Copynumber: 3.8 Consensus size: 14
223855 ATTTATTAAA
223865 AATGATTTAATGATTT
1 AATGATTTAAT-A-TT
*
223881 AATGATTTACTATT
1 AATGATTTAATATT
*
223895 AATGATTTAATAAT
1 AATGATTTAATATT
223909 AATGATTTAAT
1 AATGATTTAAT
223920 GATTTTTGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
14 25 0.69
15 1 0.03
16 10 0.28
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (14 bp):
AATGATTTAATATT
Found at i:223943 original size:8 final size:8
Alignment explanation
Indices: 223865--223924 Score: 74
Period size: 8 Copynumber: 8.0 Consensus size: 8
223855 ATTTATTAAA
223865 AATGATTT
1 AATGATTT
223873 AATGATTT
1 AATGATTT
223881 AATGATTT
1 AATGATTT
*
223889 ACT-A-TT
1 AATGATTT
223895 AATGATTT
1 AATGATTT
*
223903 AAT-A-AT
1 AATGATTT
223909 AATGATTT
1 AATGATTT
223917 AATGATTT
1 AATGATTT
223925 TTGTGGCTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
6 8 0.18
7 4 0.09
8 32 0.73
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (8 bp):
AATGATTT
Found at i:223951 original size:14 final size:14
Alignment explanation
Indices: 223932--224022 Score: 63
Period size: 11 Copynumber: 6.9 Consensus size: 14
223922 TTTTTGTGGC
223932 TAATGATTTAATAA
1 TAATGATTTAATAA
223946 TAATGA-TT--TAA
1 TAATGATTTAATAA
*
223957 TAATGATTTGATAA
1 TAATGATTTAATAA
* *
223971 TAA-CAATT--TAA
1 TAATGATTTAATAA
*
223982 TAATGA-TTACTAA
1 TAATGATTTAATAA
*
223995 TAATGATTTGAACT-T
1 TAATGATTT-AA-TAA
224010 TAATGATTTAATA
1 TAATGATTTAATA
224023 TGATTACTAC
Statistics
Matches: 62, Mismatches: 5, Indels: 20
0.71 0.06 0.23
Matches are distributed among these distances:
11 17 0.27
12 3 0.05
13 15 0.24
14 16 0.26
15 10 0.16
16 1 0.02
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.43
Consensus pattern (14 bp):
TAATGATTTAATAA
Found at i:223957 original size:11 final size:11
Alignment explanation
Indices: 223943--224027 Score: 64
Period size: 11 Copynumber: 7.0 Consensus size: 11
223933 AATGATTTAA
223943 TAATAATGATT
1 TAATAATGATT
223954 TAATAATGATTT
1 TAATAATGA-TT
**
223966 GATAATAACAATT
1 --TAATAATGATT
223979 TAATAATGATT
1 TAATAATGATT
223990 ACTAATAATGATT
1 --TAATAATGATT
224003 TGAACTTTAATGATT
1 T-AA---TAATGATT
224018 TAAT-ATGATT
1 TAATAATGATT
224028 ACTACTAATT
Statistics
Matches: 61, Mismatches: 4, Indels: 19
0.73 0.05 0.23
Matches are distributed among these distances:
10 6 0.10
11 20 0.33
12 4 0.07
13 13 0.21
14 9 0.15
15 9 0.15
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.44
Consensus pattern (11 bp):
TAATAATGATT
Found at i:223970 original size:25 final size:24
Alignment explanation
Indices: 223932--224003 Score: 92
Period size: 25 Copynumber: 2.9 Consensus size: 24
223922 TTTTTGTGGC
223932 TAATGATTTAATAATAATGATTTAA
1 TAATGATTT-ATAATAATGATTTAA
**
223957 TAATGATTTGATAATAACAATTTAA
1 TAATGATTT-ATAATAATGATTTAA
223982 TAATGA-TTACTAATAATGATTT
1 TAATGATTTA-TAATAATGATTT
224004 GAACTTTAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
23 1 0.02
24 12 0.29
25 28 0.68
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (24 bp):
TAATGATTTATAATAATGATTTAA
Found at i:224270 original size:14 final size:14
Alignment explanation
Indices: 224251--224370 Score: 81
Period size: 14 Copynumber: 8.5 Consensus size: 14
224241 TAGTAATGAT
224251 ATGATTTATTAATA
1 ATGATTTATTAATA
* *
224265 ATGATTTACTACTA
1 ATGATTTATTAATA
*
224279 ATGATTTAATAATA
1 ATGATTTATTAATA
*
224293 ATGATTTAATGATTTGATA
1 ATGA-TT--T-A-TTAATA
* *
224312 CTAATGTT-TTAATA
1 ATGAT-TTATTAATA
224326 ATGATTTGA-TAATA
1 ATGATTT-ATTAATA
224340 ATGA--T-TTAATA
1 ATGATTTATTAATA
224351 ATGA-TTATTAATA
1 ATGATTTATTAATA
224364 ATGATTT
1 ATGATTT
224371 GAACTTTAAT
Statistics
Matches: 83, Mismatches: 11, Indels: 24
0.70 0.09 0.20
Matches are distributed among these distances:
11 9 0.11
12 2 0.02
13 12 0.14
14 47 0.57
15 2 0.02
17 2 0.02
18 2 0.02
19 7 0.08
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.47
Consensus pattern (14 bp):
ATGATTTATTAATA
Found at i:224287 original size:25 final size:24
Alignment explanation
Indices: 224259--224395 Score: 81
Period size: 25 Copynumber: 5.5 Consensus size: 24
224249 ATATGATTTA
224259 TTAATAATGATTTACTACTAATGAT
1 TTAATAATGATTTA-TACTAATGAT
* * *
224284 TTAATAAT-AATGAT-TTAATGAT
1 TTAATAATGATTTATACTAATGAT
*
224306 TTGATACTAATG-TTT-TAATAATGATT
1 TT-A-A-TAATGATTTATACTAATGA-T
224332 TGATAATAATGATTTA-A-TAATGATT
1 T--TAATAATGATTTATACTAATGA-T
224357 ATTAATAATGATTTGA-ACTTTAATGAT
1 -TTAATAATGATTT-ATAC--TAATGAT
224384 TTAATAATGATT
1 TTAATAATGATT
224396 ACTACTTATT
Statistics
Matches: 91, Mismatches: 6, Indels: 29
0.72 0.05 0.23
Matches are distributed among these distances:
22 9 0.10
23 2 0.02
24 17 0.19
25 34 0.37
26 20 0.22
27 2 0.02
28 7 0.08
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.46
Consensus pattern (24 bp):
TTAATAATGATTTATACTAATGAT
Found at i:224305 original size:36 final size:35
Alignment explanation
Indices: 224263--224370 Score: 114
Period size: 36 Copynumber: 3.0 Consensus size: 35
224253 GATTTATTAA
224263 TAATGATTTACTACTAATGATTTAATAATAATGATT
1 TAATGATTTA-TACTAATGATTTAATAATAATGATT
* * *
224299 TAATGATTTGATACTAATGTTTTAATAATGATTTGATAA
1 TAATGATTT-ATACTAATGATTTAATAAT-A-ATGAT-T
*
224338 TAATGATTTA-A-TAATGA-TTATTAATAATGATT
1 TAATGATTTATACTAATGATTTAATAATAATGATT
224370 T
1 T
224371 GAACTTTAAT
Statistics
Matches: 61, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
32 1 0.02
33 4 0.07
34 1 0.02
35 7 0.11
36 31 0.51
37 3 0.05
38 5 0.08
39 9 0.15
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.46
Consensus pattern (35 bp):
TAATGATTTATACTAATGATTTAATAATAATGATT
Found at i:224355 original size:367 final size:366
Alignment explanation
Indices: 223932--224805 Score: 1325
Period size: 367 Copynumber: 2.4 Consensus size: 366
223922 TTTTTGTGGC
* * **
223932 TAATGATTTAATAATAATGATTTAATAATGATTTGATAATAACAATTTAATAATGATTACTAATA
1 TAATGATTTGATACTAATGATTTAATAATGATTTGATAATAATGATTTAATAATGATTA-TAATA
*
223997 ATGATTTGAACTTTAATGATTTAAT-ATGATTACTACTAATTATATAACATTTTTTATTTTTTAA
65 ATGATTTGAACTTTAATGATTTAATAATGATTACTACT-ATTTTATAACATTTTTTATTTTTTAA
* * *
224061 ATGCCAAACAAATTTGTTAATTAATTTTTATAAATTTTTAA-ATTATATTATATTCAATTATTTG
129 ATGCCAAACAAATTTGTTAATTAATTTTTATAAA-TTTGAAGATTATATTACATTCAATTACTTG
* *
224125 AATATATATATATATATATATATTACTTAAAGTTTAAAACATCAATTTTAACTCCTTATTGAAAT
193 -A-ATATATATACATAT-T-TATTACTTAAAGTTTAAAACATCAATTTTAACTCCTTACTGAAAT
224190 GAAAAATTTAACTAAAGGTTTCGAACTTTAATAGTAAAAAACTCAATTTAA-TAGTAATGATATG
254 GAAAAATTTAACTAAAGGTTTCGAACTTTAATAGTAAAAAACTCAATTTAAGT-GTAATGATATG
224254 ATTTATTAATAATGA-TT-T-A-CTACTAATGATTTAATAATAATGATT
318 ATTTATTAATAATGATTTATGATCTACTAATGATTTAATAATAATGATT
*
224299 TAATGATTTGATACTAATGTTTTAATAATGATTTGATAATAATGATTTAATAATGATTATTAATA
1 TAATGATTTGATACTAATGATTTAATAATGATTTGATAATAATGATTTAATAATGATTA-TAATA
224364 ATGATTTGAACTTTAATGATTTAATAATGATTACTACTTATTTTATAACA-TTTTTATTTTTTAA
65 ATGATTTGAACTTTAATGATTTAATAATGATTACTAC-TATTTTATAACATTTTTTATTTTTTAA
* *
224428 ATGCCAAAAAAATTTGTTAATTAATTTTTATAAATTTGAAGATTATATTCCATTCAATTACTTGA
129 ATGCCAAACAAATTTGTTAATTAATTTTTATAAATTTGAAGATTATATTACATTCAATTACTTGA
* *
224493 ATATATATACATATTTATTACTTAAAGTTTAAAACGTCAATTTTAACTCCTTACTGAAATGAAAT
194 ATATATATACATATTTATTACTTAAAGTTTAAAACATCAATTTTAACTCCTTACTGAAATGAAAA
* *
224558 TTTTTACTAAAGGTTTCGAACTTTAATAGTAAAAAACTCAATTTAAGTGTAATGATATGATTTAT
259 ATTTAACTAAAGGTTTCGAACTTTAATAGTAAAAAACTCAATTTAAGTGTAATGATATGATTTAT
224623 TAATAATGATTTAATGATTTTCTACTAATGATTTAATAATAATGATT
324 TAATAATGATTT-ATGA---TCTACTAATGATTTAATAATAATGATT
224670 TAATGATTTGATACTAATGATTTAATAATGATTTGATAATAATGA--T--T--T-A-T-TAATAA
1 TAATGATTTGATACTAATGATTTAATAATGATTTGATAATAATGATTTAATAATGATTATAATAA
* *
224726 TGATTTGAACTTTAATGATTTAATAATTATTACTACTATTTTATAACATTTTTGA-TTTTTAAAT
66 TGATTTGAACTTTAATGATTTAATAATGATTACTACTATTTTATAACATTTTTTATTTTTTAAAT
224790 GCCAAACAAATTTGTT
131 GCCAAACAAATTTGTT
224806 TATGATATTC
Statistics
Matches: 472, Mismatches: 22, Indels: 33
0.90 0.04 0.06
Matches are distributed among these distances:
360 36 0.08
361 46 0.10
363 118 0.25
364 5 0.01
365 14 0.03
366 7 0.01
367 153 0.32
368 21 0.04
369 2 0.00
371 70 0.15
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.45
Consensus pattern (366 bp):
TAATGATTTGATACTAATGATTTAATAATGATTTGATAATAATGATTTAATAATGATTATAATAA
TGATTTGAACTTTAATGATTTAATAATGATTACTACTATTTTATAACATTTTTTATTTTTTAAAT
GCCAAACAAATTTGTTAATTAATTTTTATAAATTTGAAGATTATATTACATTCAATTACTTGAAT
ATATATACATATTTATTACTTAAAGTTTAAAACATCAATTTTAACTCCTTACTGAAATGAAAAAT
TTAACTAAAGGTTTCGAACTTTAATAGTAAAAAACTCAATTTAAGTGTAATGATATGATTTATTA
ATAATGATTTATGATCTACTAATGATTTAATAATAATGATT
Found at i:224381 original size:39 final size:37
Alignment explanation
Indices: 224294--224396 Score: 129
Period size: 39 Copynumber: 2.7 Consensus size: 37
224284 TTAATAATAA
224294 TGATTTAATGATTTGATACTAATG-TT-TTAATAATGATT
1 TGATTTAATGATTT-A-A-TAATGATTATTAATAATGATT
*
224332 TGATAATAATGATTTAATAATGATTATTAATAATGATT
1 TGAT-TTAATGATTTAATAATGATTATTAATAATGATT
224370 TGAACTTTAATGATTTAATAATGATTA
1 TG-A-TTTAATGATTTAATAATGATTA
224397 CTACTTATTT
Statistics
Matches: 58, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
36 5 0.09
37 3 0.05
38 19 0.33
39 30 0.52
40 1 0.02
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.47
Consensus pattern (37 bp):
TGATTTAATGATTTAATAATGATTATTAATAATGATT
Found at i:224402 original size:26 final size:28
Alignment explanation
Indices: 224349--224402 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 28
224339 AATGATTTAA
**
224349 TAATGATTATTAATAATGATTTGAACTT
1 TAATGATTATTAATAATGATTACAACTT
*
224377 TAATGA-T-TTAATAATGATTACTACTT
1 TAATGATTATTAATAATGATTACAACTT
224403 ATTTTATAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 16 0.70
27 1 0.04
28 6 0.26
ACGTcount: A:0.39, C:0.06, G:0.09, T:0.46
Consensus pattern (28 bp):
TAATGATTATTAATAATGATTACAACTT
Found at i:224639 original size:22 final size:22
Alignment explanation
Indices: 224614--224731 Score: 67
Period size: 25 Copynumber: 5.0 Consensus size: 22
224604 GTGTAATGAT
224614 ATGATTTATTAATAATGATTTA
1 ATGATTTATTAATAATGATTTA
*
224636 ATGATTT-TCTACTAATGATTTA
1 ATGATTTAT-TAATAATGATTTA
* * * *
224658 ATAATAATGATTTAATGATTTGATACTA
1 ATGAT--TTA-TTAAT-A-ATGAT-TTA
* * *
224686 ATGATTTAATAATGATTTGATAATA
1 ATGATTTATTAAT-A-ATGAT-TTA
224711 ATGATTTATTAATAATGATTT
1 ATGATTTATTAATAATGATTT
224732 GAACTTTAAT
Statistics
Matches: 75, Mismatches: 13, Indels: 16
0.72 0.12 0.15
Matches are distributed among these distances:
21 1 0.01
22 24 0.32
23 4 0.05
24 2 0.03
25 30 0.40
26 4 0.05
27 4 0.05
28 6 0.08
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (22 bp):
ATGATTTATTAATAATGATTTA
Found at i:224651 original size:14 final size:14
Alignment explanation
Indices: 224634--224752 Score: 78
Period size: 14 Copynumber: 9.1 Consensus size: 14
224624 AATAATGATT
** *
224634 TAATGATTTTCTAC
1 TAATGATTTAATAA
224648 TAATGATTTAATAA
1 TAATGATTTAATAA
224662 TAATGA--T--T--
1 TAATGATTTAATAA
* *
224670 TAATGATTTGATAC
1 TAATGATTTAATAA
224684 TAATGA-TT--TAA
1 TAATGATTTAATAA
*
224695 TAATGATTTGATAA
1 TAATGATTTAATAA
*
224709 TAATGATTTATTAA
1 TAATGATTTAATAA
*
224723 TAATGATTTGAACT-T
1 TAATGATTT-AA-TAA
224738 TAATGATTTAATAA
1 TAATGATTTAATAA
224752 T
1 T
224753 TATTACTACT
Statistics
Matches: 84, Mismatches: 9, Indels: 24
0.72 0.08 0.21
Matches are distributed among these distances:
8 6 0.07
10 2 0.02
11 8 0.10
12 4 0.05
13 3 0.04
14 50 0.60
15 10 0.12
16 1 0.01
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.46
Consensus pattern (14 bp):
TAATGATTTAATAA
Found at i:224655 original size:36 final size:36
Alignment explanation
Indices: 224614--224698 Score: 143
Period size: 36 Copynumber: 2.4 Consensus size: 36
224604 GTGTAATGAT
* **
224614 ATGATTTATTAATAATGATTTAATGATTTTCTACTA
1 ATGATTTAATAATAATGATTTAATGATTTGATACTA
224650 ATGATTTAATAATAATGATTTAATGATTTGATACTA
1 ATGATTTAATAATAATGATTTAATGATTTGATACTA
224686 ATGATTTAATAAT
1 ATGATTTAATAAT
224699 GATTTGATAA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (36 bp):
ATGATTTAATAATAATGATTTAATGATTTGATACTA
Found at i:224698 original size:25 final size:25
Alignment explanation
Indices: 224648--224752 Score: 110
Period size: 25 Copynumber: 4.2 Consensus size: 25
224638 GATTTTCTAC
*
224648 TAATGATTTAATAATAATGA-TT--
1 TAATGATTTGATAATAATGATTTAA
*
224670 TAATGATTTGATACTAATGATTTAA
1 TAATGATTTGATAATAATGATTTAA
224695 TAATGATTTGATAATAATGATTTATTAA
1 TAATGATTTGATAATAATGA--T-TTAA
*
224723 TAATGATTTGA-ACTTTAATGATTTAA
1 TAATGATTTGATA--ATAATGATTTAA
224749 TAAT
1 TAAT
224753 TATTACTACT
Statistics
Matches: 71, Mismatches: 4, Indels: 12
0.82 0.05 0.14
Matches are distributed among these distances:
22 18 0.25
23 2 0.03
25 19 0.27
26 8 0.11
27 3 0.04
28 15 0.21
29 6 0.08
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.46
Consensus pattern (25 bp):
TAATGATTTGATAATAATGATTTAA
Found at i:224917 original size:13 final size:13
Alignment explanation
Indices: 224897--224932 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
224887 TACTAATGAA
224897 TAAT-ATGATTAG
1 TAATAATGATTAG
*
224909 TAATAATGATTAT
1 TAATAATGATTAG
224922 TAATAATGATT
1 TAATAATGATT
224933 TAATTATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 4 0.18
13 18 0.82
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (13 bp):
TAATAATGATTAG
Found at i:224941 original size:21 final size:22
Alignment explanation
Indices: 224912--224960 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 22
224902 TGATTAGTAA
*
224912 TAATGATTATTAA-TAATGATT
1 TAATTATTATTAATTAATGATT
224933 TAATTATTATTAATTTAATGATT
1 TAATTATTATTAA-TTAATGATT
224956 TAATT
1 TAATT
224961 TTTAATGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 12 0.48
23 13 0.52
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (22 bp):
TAATTATTATTAATTAATGATT
Found at i:224944 original size:24 final size:24
Alignment explanation
Indices: 224847--225106 Score: 115
Period size: 24 Copynumber: 10.7 Consensus size: 24
224837 TACTAATAAT
*
224847 TTAATAATGA-TTACTATAATGATTA
1 TTAATAATGATTTA--ATAATTATTA
** * * * *
224872 TTAATTTTTATTTAATACTAATGA
1 TTAATAATGATTTAATAATTATTA
* *
224896 ATAAT-ATGATTAGTAATAATGATTA
1 TTAATAATGATT--TAATAATTATTA
*
224921 TTAATAATGATTTAATTATTATTAA
1 TTAATAATGATTTAATAATTATT-A
** *
224946 TT--TAATGATTTAATTTTTAATGA
1 TTAATAATGATTTAATAATT-ATTA
* *
224969 TTTAGTAATGATTACTAATAATGTTTTA
1 -TTAATAATGATT--TAATAAT-TATTA
* *
224997 TTATTAAT-ATTTAA-AGATT-TGA
1 TTAATAATGATTTAATA-ATTATTA
* ** *
225019 -TACTAATGATTTAGGAATGATTA
1 TTAATAATGATTTAATAATTATTA
* * *
225042 CTAATAATGAAATT-ATAATAATTA
1 TTAATAATG-ATTTAATAATTATTA
*
225066 CTAATAATGATTTAATAATTATTA
1 TTAATAATGATTTAATAATTATTA
*
225090 CTAATAATGATTTAATA
1 TTAATAATGATTTAATA
225107 GTGATTTAAT
Statistics
Matches: 182, Mismatches: 34, Indels: 39
0.71 0.13 0.15
Matches are distributed among these distances:
21 6 0.03
22 9 0.05
23 28 0.15
24 78 0.43
25 26 0.14
26 20 0.11
27 7 0.04
28 7 0.04
29 1 0.01
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.47
Consensus pattern (24 bp):
TTAATAATGATTTAATAATTATTA
Found at i:224971 original size:23 final size:23
Alignment explanation
Indices: 224925--224972 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
224915 TGATTATTAA
*
224925 TAATGATTTAATTATTATTAATT
1 TAATGATTTAATTATTAATAATT
* *
224948 TAATGATTTAATTTTTAATGATT
1 TAATGATTTAATTATTAATAATT
224971 TA
1 TA
224973 GTAATGATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (23 bp):
TAATGATTTAATTATTAATAATT
Found at i:225039 original size:59 final size:62
Alignment explanation
Indices: 224913--225051 Score: 185
Period size: 59 Copynumber: 2.3 Consensus size: 62
224903 GATTAGTAAT
* * * ** *
224913 AATGATTATTAATAATGATTTAATTATTATTAATTTAATGATTTAATTTTTAATGATTTAGT
1 AATGATTACTAATAATGATTTAATTATTAATAATTTAAAGATTTAATTACTAATGATTTAGG
* *
224975 AATGATTACTAATAATG-TTTTATTATTAAT-ATTTAAAGATTTGA-TACTAATGATTTAGG
1 AATGATTACTAATAATGATTTAATTATTAATAATTTAAAGATTTAATTACTAATGATTTAGG
225034 AATGATTACTAATAATGA
1 AATGATTACTAATAATGA
225052 AATTATAATA
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
59 29 0.43
60 12 0.18
61 11 0.16
62 16 0.24
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.47
Consensus pattern (62 bp):
AATGATTACTAATAATGATTTAATTATTAATAATTTAAAGATTTAATTACTAATGATTTAGG
Found at i:225171 original size:27 final size:27
Alignment explanation
Indices: 225116--225177 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
225106 AGTGATTTAA
**
225116 TAATA-TTAAATATTTAAATTTTATCT
1 TAATATTTAAATATTTAAATTAAATCT
225142 TAATATTTAAATATTTAAA-TAAATCTT
1 TAATATTTAAATATTTAAATTAAATC-T
*
225169 TAATTTTTA
1 TAATATTTA
225178 TTTAAATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 9 0.29
27 22 0.71
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (27 bp):
TAATATTTAAATATTTAAATTAAATCT
Found at i:229139 original size:11 final size:11
Alignment explanation
Indices: 229123--229168 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
229113 CATCCTTTTC
229123 GAAAAAAGAGA
1 GAAAAAAGAGA
*
229134 GAAAAAACAGA
1 GAAAAAAGAGA
229145 GAACAAAA-A-A
1 GAA-AAAAGAGA
*
229155 GGAAAAAGAGA
1 GAAAAAAGAGA
229166 GAA
1 GAA
229169 GAGAGGAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
9 4 0.14
10 4 0.14
11 17 0.59
12 4 0.14
ACGTcount: A:0.72, C:0.04, G:0.24, T:0.00
Consensus pattern (11 bp):
GAAAAAAGAGA
Found at i:229453 original size:16 final size:16
Alignment explanation
Indices: 229432--229464 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
229422 GAGTTTGGCA
229432 AACTCTCTCTTCCCTC
1 AACTCTCTCTTCCCTC
229448 AACTCTCTCTTCCCTC
1 AACTCTCTCTTCCCTC
229464 A
1 A
229465 GTTGAGTAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.15, C:0.48, G:0.00, T:0.36
Consensus pattern (16 bp):
AACTCTCTCTTCCCTC
Found at i:230079 original size:19 final size:19
Alignment explanation
Indices: 230055--230092 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
230045 TTTGGGTCTG
230055 CCATGTTTGATGTTTGTTC
1 CCATGTTTGATGTTTGTTC
230074 CCATGTTTGATGTTTGTTC
1 CCATGTTTGATGTTTGTTC
230093 ATTTAAGCCA
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:0.11, C:0.16, G:0.21, T:0.53
Consensus pattern (19 bp):
CCATGTTTGATGTTTGTTC
Found at i:230225 original size:2 final size:2
Alignment explanation
Indices: 230218--230270 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
230208 CATGTTTTCC
230218 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
230260 AT AT AT AT AT A
1 AT AT AT AT AT A
230271 AATAAATGTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:230382 original size:21 final size:22
Alignment explanation
Indices: 230353--230404 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
230343 ATTTGGAATT
*
230353 TGTT-TTTTTTATGTATATAAG
1 TGTTATTTTTAATGTATATAAG
*
230374 TGTTATTTTTAAATGTATTTAAG
1 TGTTATTTTT-AATGTATATAAG
230397 TG-TATTTT
1 TGTTATTTT
230405 GTGTAGAGCC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 4 0.15
22 11 0.41
23 12 0.44
ACGTcount: A:0.25, C:0.00, G:0.13, T:0.62
Consensus pattern (22 bp):
TGTTATTTTTAATGTATATAAG
Found at i:231193 original size:18 final size:19
Alignment explanation
Indices: 231159--231197 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
231149 TGGTAAACGC
*
231159 AAACCAATTTTTGTCTTAA
1 AAACAAATTTTTGTCTTAA
231178 AAACAAATTTTT-TCTTAA
1 AAACAAATTTTTGTCTTAA
231196 AA
1 AA
231198 TTATTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.44, C:0.13, G:0.03, T:0.41
Consensus pattern (19 bp):
AAACAAATTTTTGTCTTAA
Found at i:231396 original size:10 final size:10
Alignment explanation
Indices: 231365--231420 Score: 58
Period size: 10 Copynumber: 5.5 Consensus size: 10
231355 TATATTACTT
*
231365 ATATATACTA
1 ATATATAATA
*
231375 AAATACTAATA
1 ATATA-TAATA
231386 ATATATAATA
1 ATATATAATA
*
231396 ATATATTATA
1 ATATATAATA
* *
231406 ATATGTACTA
1 ATATATAATA
231416 ATATA
1 ATATA
231421 ATATATGTTG
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
10 29 0.78
11 8 0.22
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (10 bp):
ATATATAATA
Found at i:232940 original size:47 final size:48
Alignment explanation
Indices: 232845--232942 Score: 153
Period size: 47 Copynumber: 2.0 Consensus size: 48
232835 CATGTTTATC
* *
232845 TCAATATAAACCACCCAAACTAGCATGCTATGAAATAATTAATAGCTTTT
1 TCAATATAAACCACCCAAACTAG-A-GCTATGAAAAAATTAAGAGCTTTT
232895 TCAATATAAACCACCCAAACTAG-GCTATGAAAAAATTAAGAGCTTTT
1 TCAATATAAACCACCCAAACTAGAGCTATGAAAAAATTAAGAGCTTTT
232942 T
1 T
232943 TAATGGCTCA
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
47 23 0.50
50 23 0.50
ACGTcount: A:0.43, C:0.19, G:0.09, T:0.29
Consensus pattern (48 bp):
TCAATATAAACCACCCAAACTAGAGCTATGAAAAAATTAAGAGCTTTT
Found at i:236686 original size:31 final size:31
Alignment explanation
Indices: 236641--236717 Score: 95
Period size: 30 Copynumber: 2.5 Consensus size: 31
236631 CTTTTAAAAC
** *
236641 TTGCAATACAGTCCCCCAACATTTAGT-TCGT
1 TTGCAATATGGTCCCCCAACATTTAGTCT-AT
*
236672 TTGTAATATGGT-CCCCAACATTTAGTCTAT
1 TTGCAATATGGTCCCCCAACATTTAGTCTAT
236702 TTGCAATATGGTCCCC
1 TTGCAATATGGTCCCC
236718 GACTGTTTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
30 26 0.67
31 13 0.33
ACGTcount: A:0.25, C:0.26, G:0.14, T:0.35
Consensus pattern (31 bp):
TTGCAATATGGTCCCCCAACATTTAGTCTAT
Found at i:236843 original size:12 final size:12
Alignment explanation
Indices: 236826--236858 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
236816 CAACAAAGTC
*
236826 CTAAATTTCATT
1 CTAAATTCCATT
236838 CTAAATTCCATT
1 CTAAATTCCATT
236850 CTAAATTCC
1 CTAAATTCC
236859 TTTTTCGATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.33, C:0.24, G:0.00, T:0.42
Consensus pattern (12 bp):
CTAAATTCCATT
Found at i:238677 original size:31 final size:31
Alignment explanation
Indices: 238639--238716 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
238629 TCAAACGGTC
* *
238639 GGGGACCATATTGCAAACAGACTTAATGTTG
1 GGGGACCATATTGCAAACAGACTAAATGTTA
** *
238670 GGGGACCATATAACAAACGGACTAAATGTTA
1 GGGGACCATATTGCAAACAGACTAAATGTTA
*
238701 GGGGACTATATTGCAA
1 GGGGACCATATTGCAA
238717 GTTTTAAAAG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.23
Consensus pattern (31 bp):
GGGGACCATATTGCAAACAGACTAAATGTTA
Found at i:246623 original size:52 final size:52
Alignment explanation
Indices: 246545--246647 Score: 197
Period size: 52 Copynumber: 2.0 Consensus size: 52
246535 TTATAATATT
246545 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
*
246597 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTTTCCTATTTCTATG
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATG
246648 TGTCCAATTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (52 bp):
CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
Found at i:250936 original size:26 final size:27
Alignment explanation
Indices: 250907--250960 Score: 92
Period size: 26 Copynumber: 2.0 Consensus size: 27
250897 ACAGAATAAC
250907 CGGCCTGTATGTCGAAAA-ATTCCCTA
1 CGGCCTGTATGTCGAAAACATTCCCTA
250933 CGGCCTGTATGTCGAAAACCATTCCCTA
1 CGGCCTGTATGTCGAAAA-CATTCCCTA
250961 TTTGGCGTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 18 0.69
28 8 0.31
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.26
Consensus pattern (27 bp):
CGGCCTGTATGTCGAAAACATTCCCTA
Found at i:256835 original size:446 final size:446
Alignment explanation
Indices: 256045--256864 Score: 1290
Period size: 446 Copynumber: 1.8 Consensus size: 446
256035 AGTATACTGG
*
256045 ACAAAAAGTATCGATACTTTATGTTAACATATTTTGTCATTAAATTGGTATATTTTTACCGCTTA
1 ACAAAAAGTATCGATACTTTATGTTAACATATTTTGTCATTAAACTGGTATATTTTTACCGCTTA
*
256110 CGTTGTAAATTTACATATTACTTTAAAGTAATCCATTTCAAAGTTTTAAGAATTGATACTTTTCG
66 CATTGTAAATTTACATATTACTTTAAAGTAATCCATTTCAAAGTTTTAAGAATTGATACTTTTCG
* *
256175 TACGTGTATTGATACTTTATAGGTGCAATTATGAAAATCAGTTTTGTTAATTTTGAACGTGTTAA
131 TACGTGTATTGATACTTTATAGGTGCAATTATGAAAACCAGTTTTGTTAATTTTGAACCTGTTAA
* * * * * *
256240 GTTATTTATATTTAATCGATAGCATTACCTTTACTTAAGTATCAATACTTTTTTTGTATGGTATT
196 GTTATTTATATTTAATCGATACCATTACCCTTACCTAAGTATCAATACTTTTTTTATAAGGTATC
* * * * *
256305 GATACTTTCGAGACGTTTTATTTTTTTGTAAACCAGTATCTTTTTACATGTTTTGCATATTGAAA
261 AATACTTTCGAGACATTTCATTTTTTTGTAAACCAGTATCTCTTTACATGTTTGGCATATTGAAA
** * *
256370 CCGGTTTTATCAATTTCAACCTGTTATATTGTCATGTATCGATACATGTGTATTTAGTATCGATA
326 CCAATTTTATAAATTTCAACATGTTATATTGTCATGTATCGATACATGTGTATTTAGTATCGATA
256435 CTTTCTGCGTGCATCTAGTTTGGGAAGCATACTGGACAAAAAGTATCGATACATAT
391 CTTTCTGCGTGCATCTAGTTTGGGAAGCATACTGGACAAAAAGTATCGATACATAT
256491 ACAAAAAGTATCGATACTTTATGTTAACATATTTTGTCATTAAACTGGTATATTTTTACCGCTTA
1 ACAAAAAGTATCGATACTTTATGTTAACATATTTTGTCATTAAACTGGTATATTTTTACCGCTTA
* * **
256556 CATTGTAAATTTACCTATTACTTTAAAGTAATCCGTTTTGAAGTTTTAAGAATTGATA-TTTCTC
66 CATTGTAAATTTACATATTACTTTAAAGTAATCCATTTCAAAGTTTTAAGAATTGATACTTT-TC
* *
256620 GTACGTGTATTGATACTTTATAGGTGCAATTATGGAAACC-GATTTTG-TCATTTTGAACCTGTT
130 GTACGTGTATTGATACTTTATAGGTGCAATTATGAAAACCAG-TTTTGTTAATTTTGAACCTGTT
*
256683 AAGTTATTTATATTTAATCGATACCATTACCCTTACCTAAGTATCGATAC-TTTTTTATAAGGTA
194 AAGTTATTTATATTTAATCGATACCATTACCCTTACCTAAGTATCAATACTTTTTTTATAAGGTA
* * *
256747 TCAATATTTTCGAGACATTTCGTTTTTTTGTAAACCGGTATCTCTTTAC-TGGTATTGGCATATT
259 TCAATACTTTCGAGACATTTCATTTTTTTGTAAACCAGTATCTCTTTACAT-GT-TTGGCATATT
*
256811 GAAACCAATTTTCTAAATTTTCAACATGTTATATTGTCATGTATCGATACATGT
322 GAAACCAATTTTATAAA-TTTCAACATGTTATATTGTCATGTATCGATACATGT
256865 TTCTTAGGTA
Statistics
Matches: 339, Mismatches: 30, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
443 1 0.00
444 55 0.16
445 86 0.25
446 197 0.58
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.43
Consensus pattern (446 bp):
ACAAAAAGTATCGATACTTTATGTTAACATATTTTGTCATTAAACTGGTATATTTTTACCGCTTA
CATTGTAAATTTACATATTACTTTAAAGTAATCCATTTCAAAGTTTTAAGAATTGATACTTTTCG
TACGTGTATTGATACTTTATAGGTGCAATTATGAAAACCAGTTTTGTTAATTTTGAACCTGTTAA
GTTATTTATATTTAATCGATACCATTACCCTTACCTAAGTATCAATACTTTTTTTATAAGGTATC
AATACTTTCGAGACATTTCATTTTTTTGTAAACCAGTATCTCTTTACATGTTTGGCATATTGAAA
CCAATTTTATAAATTTCAACATGTTATATTGTCATGTATCGATACATGTGTATTTAGTATCGATA
CTTTCTGCGTGCATCTAGTTTGGGAAGCATACTGGACAAAAAGTATCGATACATAT
Found at i:256966 original size:18 final size:18
Alignment explanation
Indices: 256943--256978 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
256933 TTCAATCAAT
256943 TTTGTCAAATTTTAATCG
1 TTTGTCAAATTTTAATCG
256961 TTTGTCAAATTTTAATCG
1 TTTGTCAAATTTTAATCG
256979 GTTTAGAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.50
Consensus pattern (18 bp):
TTTGTCAAATTTTAATCG
Found at i:258353 original size:6 final size:6
Alignment explanation
Indices: 258342--258465 Score: 124
Period size: 6 Copynumber: 20.5 Consensus size: 6
258332 TAATGGAGCC
* * * * *
258342 GAAATT GAAATT GAAATT CAAACT CAAATT AAAATT GATATT GAAATT
1 GAAATT GAAATT GAAATT GAAATT GAAATT GAAATT GAAATT GAAATT
* * * * * *
258390 GAAACT CAAATT AAAATT GAAATT GAAAAT GAAATT -CAGTCT GAAATT
1 GAAATT GAAATT GAAATT GAAATT GAAATT GAAATT GAAAT-T GAAATT
258438 GAAATT GAAATT GAAATT GAAAATT GAA
1 GAAATT GAAATT GAAATT G-AAATT GAA
258466 TAAATGATTC
Statistics
Matches: 97, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
5 2 0.02
6 87 0.90
7 8 0.08
ACGTcount: A:0.51, C:0.06, G:0.13, T:0.31
Consensus pattern (6 bp):
GAAATT
Found at i:258392 original size:36 final size:36
Alignment explanation
Indices: 258342--258459 Score: 140
Period size: 36 Copynumber: 3.4 Consensus size: 36
258332 TAATGGAGCC
258342 GAAATTGAAATTGAAATTCAAACTCAAATTAAAATT
1 GAAATTGAAATTGAAATTCAAACTCAAATTAAAATT
*
258378 G--A-T---ATTGAAATTGAAACTCAAATTAAAATT
1 GAAATTGAAATTGAAATTCAAACTCAAATTAAAATT
* ** * *
258408 GAAATTGAAAATGAAATTCAGTCTGAAATTGAAATT
1 GAAATTGAAATTGAAATTCAAACTCAAATTAAAATT
258444 GAAATTGAAATTGAAA
1 GAAATTGAAATTGAAA
258460 ATTGAATAAA
Statistics
Matches: 68, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
30 27 0.40
32 1 0.01
33 2 0.03
34 1 0.01
36 37 0.54
ACGTcount: A:0.51, C:0.06, G:0.13, T:0.31
Consensus pattern (36 bp):
GAAATTGAAATTGAAATTCAAACTCAAATTAAAATT
Found at i:258455 original size:30 final size:30
Alignment explanation
Indices: 258343--258453 Score: 152
Period size: 30 Copynumber: 3.7 Consensus size: 30
258333 AATGGAGCCG
*
258343 AAATTGAAATTGAAATTCAAACTCAAATTA
1 AAATTGAAATTGAAATTGAAACTCAAATTA
*
258373 AAATTGATATTGAAATTGAAACTCAAATTA
1 AAATTGAAATTGAAATTGAAACTCAAATTA
* * * *
258403 AAATTGAAATTGAAAATGAAATTC-AGTCTG
1 AAATTGAAATTGAAATTGAAACTCAAAT-TA
258433 AAATTGAAATTGAAATTGAAA
1 AAATTGAAATTGAAATTGAAA
258454 TTGAAAATTG
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
29 2 0.03
30 70 0.97
ACGTcount: A:0.51, C:0.06, G:0.12, T:0.31
Consensus pattern (30 bp):
AAATTGAAATTGAAATTGAAACTCAAATTA
Found at i:258736 original size:15 final size:15
Alignment explanation
Indices: 258712--258741 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
258702 CCAAACATAC
258712 ATACAAAACAATGTT
1 ATACAAAACAATGTT
*
258727 ATACATAACAATGTT
1 ATACAAAACAATGTT
258742 TTCTTCTTTT
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:0.50, C:0.13, G:0.07, T:0.30
Consensus pattern (15 bp):
ATACAAAACAATGTT
Found at i:260712 original size:2 final size:2
Alignment explanation
Indices: 260705--260730 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
260695 GAATCCGGAG
260705 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
260731 CCTTCCCCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:261945 original size:200 final size:199
Alignment explanation
Indices: 261507--263096 Score: 1590
Period size: 200 Copynumber: 8.1 Consensus size: 199
261497 TCAATGCTTT
* * * * *
261507 CATACTGGATAAAAAGTATTGATACACATACAAAAAGTATCGATACTTTGTGTTTACTTATTTTG
1 CATACTGGACAAAAAGTATCGATACAAATACAAAAAGTATCGATACTTTATGTTTACATATTTTG
* ** * ** * *
261572 TCATTTAACTGGTATATTTTAACAACTTACATTGTAAATTTATCTATTACTTTATACTAATCGGT
66 TCATTAAACCAGTATATTTTTACCGCTAACATTGTAAATTTACCTATTACTTTATACTAATCGGT
* * *
261637 TTTGAAGTTTTAAGAATC--T--TCTCGTACGTGTATCGATACTTTATGTGTGCATCTAGTTTGG
131 TTCGAAGTTTTAAGAATCGATACTCTCATACGTGTATCGATACTTTCTGTGTGCATCTAGTTTGG
261698 AAAG
196 AAAG
* * *
261702 CTTACTGGACAAAAAGTATCGATACATATACAAAAAGTATCGATACTTTATGTTTACATATATTG
1 CATACTGGACAAAAAGTATCGATACAAATACAAAAAGTATCGATACTTTATGTTTACATATTTTG
* ** *
261767 TCACTAAACCAGTATATTTTTACCGCTTTCATTGTAAATTTACCTATTACTTTATACTAATTGGT
66 TCATTAAACCAGTATATTTTTACCGCTAACATTGTAAATTTACCTATTACTTTATACTAATCGGT
* * * * * *
261832 TTCAAAGTTTCAAGAATCGATACATCTCGTACATGTATCGATATTTTCTGTGTGCGTCTAGTTTG
131 TTCGAAGTTTTAAGAATCGATAC-TCTCATACGTGTATCGATACTTTCTGTGTGCATCTAGTTTG
261897 GAAAG
195 GAAAG
* * * *
261902 CATATTGGACAAAAAGTATCGATACAAATATAAAAAGTATCGATACTTTATATTTACGTATTTTG
1 CATACTGGACAAAAAGTATCGATACAAATACAAAAAGTATCGATACTTTATGTTTACATATTTTG
* * * * * * *
261967 TCATTAAATCGGTATATTTTTACCTCTAACCTTGTAAATTTACCTATTACCTTAAATTAATCGGT
66 TCATTAAACCAGTATATTTTTACCGCTAACATTGTAAATTTACCTATTACTTTATACTAATCGGT
* * * * * *
262032 TTCGAAGTTTTAAGAATCGATACTTTACATAAGTGTATCGATACGTTATGCGTGCATCTCGTTTG
131 TTCGAAGTTTTAAGAATCGATACTCT-CATACGTGTATCGATACTTTCTGTGTGCATCTAGTTTG
*
262097 CG-ATG
195 -GAAAG
* * * *
262102 CATACTGGACAAAAAGTATCGGTACACATACAAAAAGTATCAATACTTTATGTTTACATATCTTG
1 CATACTGGACAAAAAGTATCGATACAAATACAAAAAGTATCGATACTTTATGTTTACATATTTTG
*
262167 TCATTAAACCAGTATATTGTTACCGCTAACATTGTAAATTTACCTATTACTTTATACTAATCGGT
66 TCATTAAACCAGTATATTTTTACCGCTAACATTGTAAATTTACCTATTACTTTATACTAATCGGT
* * *
262232 TTCGAAGTTTTAAGAATCGATACTTTTAATTCGTGTATCGATACTTTCTGTGTGCATCTAGTTTG
131 TTCGAAGTTTTAAGAATCGATAC-TCTCATACGTGTATCGATACTTTCTGTGTGCATCTAGTTTG
262297 GAAAG
195 GAAAG
** * * * *
262302 CATACTGGACAATTAGTAACGATACAAATACGAAAAGTATCGATACTTTGTGTTTACATATTTTA
1 CATACTGGACAAAAAGTATCGATACAAATACAAAAAGTATCGATACTTTATGTTTACATATTTTG
* * * *
262367 TCATTAAACCAATATATTTTTATCGCTTACATTGTAAATTTACCTATTACTTTATACTAATCAGT
66 TCATTAAACCAGTATATTTTTACCGCTAACATTGTAAATTTACCTATTACTTTATACTAATCGGT
* * *
262432 TTC-ACAGTTTTAAGAATCGATACTTCTCATACGTTTATCGATACTTTCTGCGTGGATCTAGTTT
131 TTCGA-AGTTTTAAGAATCGATAC-TCTCATACGTGTATCGATACTTTCTGTGTGCATCTAGTTT
262496 GGAAAG
194 GGAAAG
* ** * * *
262502 CATACTTGACAATTAGTATCGATACAAATACAAAAAGTATCGATACTTTGTGTTTACGTATTTTT
1 CATACTGGACAAAAAGTATCGATACAAATACAAAAAGTATCGATACTTTATGTTTACATATTTTG
** * * * * * *
262567 TCATTAAACTGGTATATTTTTACCTCTAACCTAGTAAATTTACCTATTACCTTAAATTAATCGGT
66 TCATTAAACCAGTATATTTTTACCGCTAACATTGTAAATTTACCTATTACTTTATACTAATCGGT
* * * *
262632 TTTGAAGTTTTAAGAATCGATACT-TTATGCGTG---C-AT-C---C--CGT---T-T-G---GG
131 TTCGAAGTTTTAAGAATCGATACTCTCATACGTGTATCGATACTTTCTGTGTGCATCTAGTTTGG
*
262678 ATA-
196 AAAG
* * * * *
262681 CATACTGGA-AAAAAGTATCGATACATATACAAAGAGTAGCGATACTTTATGTTTACGTATATTG
1 CATACTGGACAAAAAGTATCGATACAAATACAAAAAGTATCGATACTTTATGTTTACATATTTTG
* * * *
262745 TCATTAAATCAATATATTTTTACCGCTAACATTGTAAATTTACCTATTACCTTTA-AATAATTGG
66 TCATTAAACCAGTATATTTTTACCGCTAACATTGTAAATTTACCTATTA-CTTTATACTAATCGG
** * * * * * * *
262809 TTTTAAAGTTTTAAGAATCAATACTTTTCATACTTGTATCGATACTTGT-TTTTTACTTACTTAA
130 TTTCGAAGTTTTAAGAATCGATAC-TCTCATACGTGTATCGATACTT-TCTGTGTGCAT-C-T-A
* *
262873 GTTTGGGATG
190 GTTTGGAAAG
* * * * * * * * * * *
262883 CATACTGTA-AAGAAGTATAGATGCACATATAAAAAGTATTGATACTTTATGTTAACGTGTTTTA
1 CATACTGGACAAAAAGTATCGATACAAATACAAAAAGTATCGATACTTTATGTTTACATATTTTG
** * * * * *
262947 TCA-TAAACTGGTATCTTTTTACCTCTAACATTGTAAAATTACATATTACTTTA-AGTTAATCGG
66 TCATTAAACCAGTATATTTTTACCGCTAACATTGTAAATTTACCTATTACTTTATA-CTAATCGG
* * * * * * * * * *
263010 TTTCAAATTTTTAAGAATCGATTCTTTTCATATC-TGTATCGATACTTTCTTTTTACTTCCAATT
130 TTTCGAAGTTTTAAGAATCGATAC-TCTCATA-CGTGTATCGATACTTTCTGTGTGCATCTAGTT
*
263074 TGGGAAG
193 TGGAAAG
263081 CATACTGGACAAAAAG
1 CATACTGGACAAAAAG
263097 GATTAAAACT
Statistics
Matches: 1171, Mismatches: 183, Indels: 78
0.82 0.13 0.05
Matches are distributed among these distances:
178 118 0.10
179 13 0.01
180 10 0.01
183 2 0.00
184 3 0.00
185 2 0.00
188 3 0.00
190 2 0.00
193 2 0.00
194 2 0.00
195 129 0.11
196 1 0.00
197 1 0.00
198 24 0.02
199 10 0.01
200 694 0.59
201 100 0.09
202 55 0.05
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.39
Consensus pattern (199 bp):
CATACTGGACAAAAAGTATCGATACAAATACAAAAAGTATCGATACTTTATGTTTACATATTTTG
TCATTAAACCAGTATATTTTTACCGCTAACATTGTAAATTTACCTATTACTTTATACTAATCGGT
TTCGAAGTTTTAAGAATCGATACTCTCATACGTGTATCGATACTTTCTGTGTGCATCTAGTTTGG
AAAG
Found at i:262642 original size:600 final size:574
Alignment explanation
Indices: 261507--263059 Score: 1789
Period size: 600 Copynumber: 2.7 Consensus size: 574
261497 TCAATGCTTT
* * * *
261507 CATACTGGATAAAAAGTATTGATACACATACAAAAAGTATCGATACTTTGTGTTTACTTATTTTG
1 CATACTGGA-AAAAAGTATCGATACACATACAAAAAGTATCGATACTTTATGTTTACATATATTG
* ** ** * *
261572 TCATTTAACTGGTATATTTTAACAACTTACATTGTAAATTTATCTATTACTTTATACTAATCGGT
65 TCATTAAACCAGTATATTTT-ACCGCTAACATTGTAAATTTACCTATTACTTTATACTAATCGGT
* **
261637 TTTGAAGTTTTAAGAATC-TTCTCGTA-CGTGTATCGATACTTTATGTGTGCATCTAGTTTGGAA
129 TTTGAAGTTTTAAGAATCATACTTTTATCGTGTATCGATACTTTATGTGTGCATCTAGTTTGGAA
* * *
261700 AGCTTACTGGACAAAAAGTATCGATACATATACAAAAAGTATCGATACTTTATGTTTACATATAT
194 AGCATACTGGACAAAAAGTAACGATACAAATACAAAAAGTATCGATACTTTATGTTTACATATAT
* * * **
261765 TGTCACTAAACCAGTATATTTTTACCGCTTTCATTGTAAATTTACCTATTACTTTATACTAATTG
259 TATCACTAAACCAATATATTTTTACCGCTTACATTGTAAATTTACCTATTACTTTATACTAATCA
* * *
261830 GTTTCAAAGTTTCAAGAATCGATACATCTCGTACATGTATCGATATTTTCTGTGTGCGTCTAGTT
324 GTTTCAAAGTTTCAAGAATCGATACATCTCATACATGTATCGATACTTTCTGCGTGCGTCTAGTT
*
261895 TGGAAAGCATATTGGACAAAAAGTATCGATACAAATATAAAAAGTATCGATACTTTATATTTACG
389 TGGAAAGCATATTGGACAAAAAGTATCGATACAAATACAAAAAGTATCGATACTTTATATTTACG
*
261960 TATTTTGTCATTAAATCGGTATATTTTTACCTCTAACCTTGTAAATTTACCTATTACCTTAAATT
454 TATTTTGTCATTAAATCGGTATATTTTTACCTCTAACCTAGTAAATTTACCTATTACCTTAAATT
262025 AATCGGTTTCGAAGTTTTAAGAATCGATACTTTACATAAGTGTATCGATACGTTATGCGTGCATC
519 AATCGGTTTCGAAGTTTTAAGAATCG------------A---TA-C--T---TTATGCGTGCATC
* *
262090 TCGTTTGCGATG
563 CCGTTTGCGATA
* * *
262102 CATACTGGACAAAAAGTATCGGTACACATACAAAAAGTATCAATACTTTATGTTTACATATCTTG
1 CATACTGGA-AAAAAGTATCGATACACATACAAAAAGTATCGATACTTTATGTTTACATATATTG
262167 TCATTAAACCAGTATATTGTTACCGCTAACATTGTAAATTTACCTATTACTTTATACTAATCGGT
65 TCATTAAACCAGTATATT-TTACCGCTAACATTGTAAATTTACCTATTACTTTATACTAATCGGT
* *
262232 TTCGAAGTTTTAAGAATCGATACTTTTAATTCGTGTATCGATACTTTCTGTGTGCATCTAGTTTG
129 TTTGAAGTTTTAAGAATC-ATACTTTT-A-TCGTGTATCGATACTTTATGTGTGCATCTAGTTTG
** * *
262297 GAAAGCATACTGGACAATTAGTAACGATACAAATACGAAAAGTATCGATACTTTGTGTTTACATA
191 GAAAGCATACTGGACAAAAAGTAACGATACAAATACAAAAAGTATCGATACTTTATGTTTACATA
* * *
262362 TTTTATCATTAAACCAATATATTTTTATCGCTTACATTGTAAATTTACCTATTACTTTATACTAA
256 TATTATCACTAAACCAATATATTTTTACCGCTTACATTGTAAATTTACCTATTACTTTATACTAA
* * * * *
262427 TCAGTTTCACAGTTTTAAGAATCGATACTTCTCATACGTTTATCGATACTTTCTGCGTG-GATCT
321 TCAGTTTCAAAGTTTCAAGAATCGATACATCTCATACATGTATCGATACTTTCTGCGTGCG-TCT
** * *
262491 AGTTTGGAAAGCATACTT-GACAATTAGTATCGATACAAATACAAAAAGTATCGATACTTTGTGT
385 AGTTTGGAAAGCATA-TTGGACAAAAAGTATCGATACAAATACAAAAAGTATCGATACTTTATAT
*
262555 TTACGTATTTTTTCATTAAA-CTGGTATATTTTTACCTCTAACCTAGTAAATTTACCTATTACCT
449 TTACGTATTTTGTCATTAAATC-GGTATATTTTTACCTCTAACCTAGTAAATTTACCTATTACCT
* *
262619 TAAATTAATCGGTTTTGAAGTTTTAAGAATCGATACTTTATGCGTGCATCCCGTTTGGGATA
513 TAAATTAATCGGTTTCGAAGTTTTAAGAATCGATACTTTATGCGTGCATCCCGTTTGCGATA
* * * *
262681 CATACTGGAAAAAAGTATCGATACATATACAAAGAGTAGCGATACTTTATGTTTACGTATATTGT
1 CATACTGGAAAAAAGTATCGATACACATACAAAAAGTATCGATACTTTATGTTTACATATATTGT
* * * *
262746 CATTAAATCAATATATTTTTACCGCTAACATTGTAAATTTACCTATTACCTTTA-AATAATTGGT
66 CATTAAACCAGTATA-TTTTACCGCTAACATTGTAAATTTACCTATTA-CTTTATACTAATCGGT
* * * * * *
262810 TTTAAAGTTTTAAGAATCAATACTTTTCATACTTGTATCGATACTTGT-TTTTTACTTACTTAAG
129 TTTGAAGTTTTAAGAATC-ATACTTTT-AT-CGTGTATCGATACTT-TATGTGTGCAT-C-T-AG
* * * * * * * * *
262874 TTTGGGATGCATACTGTA-AAGAAGTATA-GATGCACATATAAAAAGTATTGATACTTTATGTTA
187 TTTGGAAAGCATACTGGACAAAAAGTA-ACGATACAAATACAAAAAGTATCGATACTTTATGTTT
* * * *** * * * * *
262937 ACGTGTTTTATCA-TAAACTGGTATCTTTTTACCTCTAACATTGTAAAATTACATATTACTTTA-
251 ACATATATTATCACTAAACCAATATATTTTTACCGCTTACATTGTAAATTTACCTATTACTTTAT
* * * * * * *
263000 AGTTAATCGGTTTCAAATTTTTAAGAATCGATTCTTTTCATATC-TGTATCGATACTTTCT
316 A-CTAATCAGTTTCAAAGTTTCAAGAATCGATACATCTCATA-CATGTATCGATACTTTCT
263060 TTTTACTTCC
Statistics
Matches: 836, Mismatches: 103, Indels: 54
0.84 0.10 0.05
Matches are distributed among these distances:
577 1 0.00
578 145 0.17
579 130 0.16
580 47 0.06
581 18 0.02
582 1 0.00
584 1 0.00
585 2 0.00
588 1 0.00
595 130 0.16
596 2 0.00
597 4 0.00
598 1 0.00
599 2 0.00
600 349 0.42
601 2 0.00
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (574 bp):
CATACTGGAAAAAAGTATCGATACACATACAAAAAGTATCGATACTTTATGTTTACATATATTGT
CATTAAACCAGTATATTTTACCGCTAACATTGTAAATTTACCTATTACTTTATACTAATCGGTTT
TGAAGTTTTAAGAATCATACTTTTATCGTGTATCGATACTTTATGTGTGCATCTAGTTTGGAAAG
CATACTGGACAAAAAGTAACGATACAAATACAAAAAGTATCGATACTTTATGTTTACATATATTA
TCACTAAACCAATATATTTTTACCGCTTACATTGTAAATTTACCTATTACTTTATACTAATCAGT
TTCAAAGTTTCAAGAATCGATACATCTCATACATGTATCGATACTTTCTGCGTGCGTCTAGTTTG
GAAAGCATATTGGACAAAAAGTATCGATACAAATACAAAAAGTATCGATACTTTATATTTACGTA
TTTTGTCATTAAATCGGTATATTTTTACCTCTAACCTAGTAAATTTACCTATTACCTTAAATTAA
TCGGTTTCGAAGTTTTAAGAATCGATACTTTATGCGTGCATCCCGTTTGCGATA
Found at i:263025 original size:201 final size:200
Alignment explanation
Indices: 262671--263096 Score: 499
Period size: 201 Copynumber: 2.1 Consensus size: 200
262661 CGTGCATCCC
* * *
262671 GTTTGGGATACATACTGGAAAAAAGTATCGATACATATACAAAGAGTAGCGATACTTTATGTTTA
1 GTTTGGGATGCATACTGGAAAAAAGTATAGATACATATACAAAGAGTAGCGATACTTTATGTTAA
* * *
262736 CGTATATTGTCATTAAATCAATATATTTTTACCGCTAACATTGTAAATTTACCTATTACCTTTAA
66 CGTATATTATCATTAAATCAATATATTTTTACCGCTAACATTGTAAAATTACATATTACCTTTAA
* *
262801 ATAATTGGTTTTAAAGTTTTAAGAATCAATACTTTTCATA-CTTGTATCGATACTTGT-TTTTTA
131 ATAATCGGTTTCAAAGTTTTAAGAATCAATACTTTTCATATC-TGTATCGATACTT-TCTTTTTA
*
262864 CTTACTTAA
194 CTT-C-CAA
* * **
262873 GTTTGGGATGCATACTGTAAAGAAGTATAGATGCACATATA-AAA-AGTATTGATACTTTATGTT
1 GTTTGGGATGCATACTGGAAAAAAGTATAGAT--ACATATACAAAGAGTAGCGATACTTTATGTT
* * ** * *
262936 AACGTGTTTTATCA-TAAA-CTGGTATCTTTTTACCTCTAACATTGTAAAATTACATATTA-CTT
64 AACGTATATTATCATTAAATC-AATATATTTTTACCGCTAACATTGTAAAATTACATATTACCTT
* * * *
262998 TAAGTTAATCGGTTTCAAATTTTTAAGAATCGATTCTTTTCATATCTGTATCGATACTTTCTTTT
128 TAA-ATAATCGGTTTCAAAGTTTTAAGAATCAATACTTTTCATATCTGTATCGATACTTTCTTTT
263063 TACTTCCAA
192 TACTTCCAA
*
263072 -TTTGGGAAGCATACTGGACAAAAAG
1 GTTTGGGATGCATACTGGA-AAAAAG
263097 GATTAAAACT
Statistics
Matches: 191, Mismatches: 26, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
198 16 0.08
199 7 0.04
200 9 0.05
201 93 0.49
202 56 0.29
203 3 0.02
204 7 0.04
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (200 bp):
GTTTGGGATGCATACTGGAAAAAAGTATAGATACATATACAAAGAGTAGCGATACTTTATGTTAA
CGTATATTATCATTAAATCAATATATTTTTACCGCTAACATTGTAAAATTACATATTACCTTTAA
ATAATCGGTTTCAAAGTTTTAAGAATCAATACTTTTCATATCTGTATCGATACTTTCTTTTTACT
TCCAA
Found at i:265839 original size:19 final size:18
Alignment explanation
Indices: 265798--265845 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
265788 TTGTTAATCT
* *
265798 TATACATAATTACATTCA
1 TATACAAAATTAAATTCA
*
265816 CATACAAAATTATAATTCA
1 TATACAAAATTA-AATTCA
265835 TATACAAAATT
1 TATACAAAATT
265846 TTTCTTACAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (18 bp):
TATACAAAATTAAATTCA
Found at i:270279 original size:20 final size:20
Alignment explanation
Indices: 270220--270271 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
270210 TATTTCTACT
270220 GGTTTTGTCAAATTGAAACC
1 GGTTTTGTCAAATTGAAACC
270240 GGTTTTGTCAAATTGAAACC
1 GGTTTTGTCAAATTGAAACC
270260 GGTTTTGTCAAA
1 GGTTTTGTCAAA
270272 CTTCAACCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (20 bp):
GGTTTTGTCAAATTGAAACC
Found at i:276915 original size:12 final size:12
Alignment explanation
Indices: 276898--276931 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
276888 AATTTAAATC
276898 AATTATAATGAT
1 AATTATAATGAT
276910 AATTATAATGAT
1 AATTATAATGAT
276922 AATTA-AATGA
1 AATTATAATGA
276932 ATTTAATAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 5 0.23
12 17 0.77
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (12 bp):
AATTATAATGAT
Found at i:278568 original size:82 final size:82
Alignment explanation
Indices: 278464--278879 Score: 487
Period size: 82 Copynumber: 5.0 Consensus size: 82
278454 ACCACTATTT
** * **
278464 CACTATTTCACATGTTTTCTGAAAAGTTTTTTAAATTATGCATTGAATGACCTCTGAAAAGTTAT
1 CACTATTTCACCCGTTTTCTGAAAAGTTGTTTAAATTATGCATTGAATGACCTCTGAAAAGTTGC
*
278529 TGAAGATGATAATGCAC
66 AGAAGATGATAATGCAC
* *
278546 CACTATTTCACCCGTTTTCTGAAAAGTTGTTTAAA-TATGCATTGAATGACATCTGAAAAGTTGT
1 CACTATTTCACCCGTTTTCTGAAAAGTTGTTTAAATTATGCATTGAATGACCTCTGAAAAGTTGC
*
278610 AGAAGATGATAATACAC
66 AGAAGATGATAATGCAC
* * * * * * *
278627 CATTATTTCACCCGTTTTTTTGAAAATTTGTTTAAATTATACATTGAATGACATTTGAAAAGTTA
1 CACTATTTCACCCG-TTTTCTGAAAAGTTGTTTAAATTATGCATTGAATGACCTCTGAAAAGTTG
* * *
278692 CAGAAGATTATAATGTAT
65 CAGAAGATGATAATGCAC
* * * * *
278710 TATTATTTCA-TCGTTTTCTGGAAAGTTGTTTAAATTATGCATTGAATGAATGACCTTTGAAACA
1 CACTATTTCACCCGTTTTCTGAAAAGTTGTTTAAATTATGCA-T---TGAATGACCTCTGAAA-A
* *
278774 -TTGCAGAAGATTATAACGCAC
61 GTTGCAGAAGATGATAATGCAC
* * * *
278795 CACTATTTCACCTGTTTTCTGAAATGTTGTTTAAATTATGCATTGAATGACCTCAGAAAACTTGC
1 CACTATTTCACCCGTTTTCTGAAAAGTTGTTTAAATTATGCATTGAATGACCTCTGAAAAGTTGC
278860 AGAAGATGATAATGCAC
66 AGAAGATGATAATGCAC
278877 CAC
1 CAC
278880 AATTATTTGG
Statistics
Matches: 286, Mismatches: 39, Indels: 18
0.83 0.11 0.05
Matches are distributed among these distances:
81 80 0.28
82 90 0.31
83 47 0.16
85 41 0.14
86 28 0.10
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (82 bp):
CACTATTTCACCCGTTTTCTGAAAAGTTGTTTAAATTATGCATTGAATGACCTCTGAAAAGTTGC
AGAAGATGATAATGCAC
Found at i:278617 original size:81 final size:82
Alignment explanation
Indices: 278464--278879 Score: 480
Period size: 81 Copynumber: 5.0 Consensus size: 82
278454 ACCACTATTT
** * * **
278464 CACTATTTCACATGTTTTCTGAAAAGTTTTTTAAATTATGCATTGAATGACCTCTGAAAAGTTAT
1 CACTATTTCACCCGTTTTCTGAAAAGTTGTTTAAATTATGCATTGAATGACATCTGAAAAGTTGC
*
278529 TGAAGATGATAATGCAC
66 AGAAGATGATAATGCAC
*
278546 CACTATTTCACCCGTTTTCTGAAAAGTTGTTTAAA-TATGCATTGAATGACATCTGAAAAGTTGT
1 CACTATTTCACCCGTTTTCTGAAAAGTTGTTTAAATTATGCATTGAATGACATCTGAAAAGTTGC
*
278610 AGAAGATGATAATACAC
66 AGAAGATGATAATGCAC
* * * * * *
278627 CATTATTTCACCCGTTTTTTTGAAAATTTGTTTAAATTATACATTGAATGACATTTGAAAAGTTA
1 CACTATTTCACCCG-TTTTCTGAAAAGTTGTTTAAATTATGCATTGAATGACATCTGAAAAGTTG
* * *
278692 CAGAAGATTATAATGTAT
65 CAGAAGATGATAATGCAC
* * * *
278710 TATTATTTCA-TCGTTTTCTGGAAAGTTGTTTAAATTATGCATTGAATGA-ATGACCTTTGAAAC
1 CACTATTTCACCCGTTTTCTGAAAAGTTGTTTAAATTATGCATTGAATGACAT---C--TGAAA-
* *
278773 A-TTGCAGAAGATTATAACGCAC
60 AGTTGCAGAAGATGATAATGCAC
* * * * *
278795 CACTATTTCACCTGTTTTCTGAAATGTTGTTTAAATTATGCATTGAATGACCTCAGAAAACTTGC
1 CACTATTTCACCCGTTTTCTGAAAAGTTGTTTAAATTATGCATTGAATGACATCTGAAAAGTTGC
278860 AGAAGATGATAATGCAC
66 AGAAGATGATAATGCAC
278877 CAC
1 CAC
278880 AATTATTTGG
Statistics
Matches: 284, Mismatches: 39, Indels: 22
0.82 0.11 0.06
Matches are distributed among these distances:
80 2 0.01
81 88 0.31
82 79 0.28
83 47 0.17
84 1 0.00
85 30 0.11
86 36 0.13
87 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (82 bp):
CACTATTTCACCCGTTTTCTGAAAAGTTGTTTAAATTATGCATTGAATGACATCTGAAAAGTTGC
AGAAGATGATAATGCAC
Found at i:280385 original size:35 final size:34
Alignment explanation
Indices: 280320--280388 Score: 84
Period size: 35 Copynumber: 2.0 Consensus size: 34
280310 ATTAAGATAG
*
280320 AAATAAAAAAATAAAAGGAATGAAAAAAAATTCA
1 AAATAAAAAAATAAAAGGAAAGAAAAAAAATTCA
* * **
280354 AAATAAAAAATTAAATTGGAAAGAATTAAAATTCA
1 AAATAAAAAAATAAA-AGGAAAGAAAAAAAATTCA
280389 TGGATCAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
34 14 0.48
35 15 0.52
ACGTcount: A:0.68, C:0.03, G:0.09, T:0.20
Consensus pattern (34 bp):
AAATAAAAAAATAAAAGGAAAGAAAAAAAATTCA
Found at i:280506 original size:30 final size:27
Alignment explanation
Indices: 280427--280508 Score: 69
Period size: 30 Copynumber: 3.0 Consensus size: 27
280417 GCAAGAGAAA
* *
280427 AAACATAAACTTAAGGGATT-AAATAGC
1 AAACA-AAAATTAAAGGATTAAAATAGC
* **
280454 AAA-AAAAATTAAAGTACCAAAATAGCAC
1 AAACAAAAATTAAAGGATTAAAATAG--C
280482 AAACAGAAAATTAAAGGATTAAAATAG
1 AAACA-AAAATTAAAGGATTAAAATAG
280509 TATTAACAGA
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
25 9 0.21
26 7 0.17
27 3 0.07
28 4 0.10
29 1 0.02
30 18 0.43
ACGTcount: A:0.60, C:0.10, G:0.12, T:0.18
Consensus pattern (27 bp):
AAACAAAAATTAAAGGATTAAAATAGC
Found at i:282495 original size:3 final size:3
Alignment explanation
Indices: 282487--282539 Score: 70
Period size: 3 Copynumber: 17.0 Consensus size: 3
282477 AAATTTAAAT
*
282487 TTA TTA TTA TTA TTA TTA TTA TTA TTA GTA TTA TATA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA -TTA TTA
*
282534 ATA TTA
1 TTA TTA
282540 CAAAACCCAA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
3 38 0.86
4 6 0.14
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:283799 original size:22 final size:21
Alignment explanation
Indices: 283764--283806 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
283754 TTAGTCACTA
*
283764 TTTTCAATTTTTATTTATTTT
1 TTTTCAAATTTTATTTATTTT
*
283785 TTTTACAAATTTTATTTGTTTT
1 TTTT-CAAATTTTATTTATTTT
283807 AAATATATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.72
Consensus pattern (21 bp):
TTTTCAAATTTTATTTATTTT
Found at i:284110 original size:119 final size:118
Alignment explanation
Indices: 283978--284208 Score: 304
Period size: 120 Copynumber: 1.9 Consensus size: 118
283968 CATTTTTAAT
* * * *
283978 ATTTATTTATTTTTCAATAT-TAAGAAATGA-CAGTCTTAAAACAACTGGATGTTCATTTTCTGA
1 ATTTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTTC-TTTTCTGA
* *
284041 TATTTTTAAATAAATAAATATCCTATTTTATAAATTATATATTAATTAATTTATTA
65 TATTTCTAAATAAATAAATATCCTA-TTTATAAA-TATATATAAATTAATTTATTA
* * ** *
284097 ATTTATTTATTTTTTAATATCGAAGAAAAGAGCTGTCTTAAGGCATCTAGAAGTTCTTTTCTGAT
1 ATTTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTTCTTTTCTGAT
**
284162 ATTTCTAAATAAATAAATATTTTATTTATAAATATATATAAATTAAT
66 ATTTCTAAATAAATAAATATCCTATTTATAAATATATATAAATTAAT
284209 ATTTTTTCCA
Statistics
Matches: 97, Mismatches: 13, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
118 14 0.14
119 27 0.28
120 38 0.39
121 18 0.19
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (118 bp):
ATTTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTTCTTTTCTGAT
ATTTCTAAATAAATAAATATCCTATTTATAAATATATATAAATTAATTTATTA
Found at i:284221 original size:29 final size:29
Alignment explanation
Indices: 284170--284226 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
284160 ATATTTCTAA
*
284170 ATAAATAAATATTTTATTTATAAATATAT
1 ATAAATAAATATTTTATTCATAAATATAT
* *
284199 ATAAATTAATATTTT-TTCCATAATTATA
1 ATAAATAAATATTTTATT-CATAAATATA
284227 ATTTTGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (29 bp):
ATAAATAAATATTTTATTCATAAATATAT
Found at i:286851 original size:22 final size:22
Alignment explanation
Indices: 286819--286880 Score: 117
Period size: 22 Copynumber: 2.9 Consensus size: 22
286809 TTTTCATATA
286819 TGCA-TTTTCATTTTGCATCTT
1 TGCATTTTTCATTTTGCATCTT
286840 TGCATTTTTCATTTTGCATCTT
1 TGCATTTTTCATTTTGCATCTT
286862 TGCATTTTTCATTTTGCAT
1 TGCATTTTTCATTTTGCAT
286881 TCATACTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
21 4 0.10
22 36 0.90
ACGTcount: A:0.15, C:0.18, G:0.10, T:0.58
Consensus pattern (22 bp):
TGCATTTTTCATTTTGCATCTT
Found at i:286854 original size:7 final size:7
Alignment explanation
Indices: 286819--286881 Score: 83
Period size: 7 Copynumber: 8.9 Consensus size: 7
286809 TTTTCATATA
286819 TGCATTT
1 TGCATTT
286826 T-CATTT
1 TGCATTT
286832 TGCATCTT
1 TGCAT-TT
286840 TGCATTT
1 TGCATTT
*
286847 TTCATTT
1 TGCATTT
286854 TGCATCTT
1 TGCAT-TT
286862 TGCATTT
1 TGCATTT
*
286869 TTCATTT
1 TGCATTT
286876 TGCATT
1 TGCATT
286882 CATACTTTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
6 6 0.12
7 29 0.59
8 14 0.29
ACGTcount: A:0.14, C:0.17, G:0.10, T:0.59
Consensus pattern (7 bp):
TGCATTT
Found at i:286857 original size:14 final size:14
Alignment explanation
Indices: 286809--286881 Score: 76
Period size: 15 Copynumber: 5.1 Consensus size: 14
286799 AGTAAACACC
*
286809 TTTTCATATATGCA-
1 TTTTCAT-TTTGCAT
286823 TTTTCATTTTGCAT
1 TTTTCATTTTGCAT
* *
286837 CTTTGCATTTTTCAT
1 -TTTTCATTTTGCAT
*
286852 TTTGCATCTTTGCAT
1 TTTTCAT-TTTGCAT
286867 TTTTCATTTTGCAT
1 TTTTCATTTTGCAT
286881 T
1 T
286882 CATACTTTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
13 5 0.10
14 22 0.43
15 24 0.47
ACGTcount: A:0.16, C:0.16, G:0.08, T:0.59
Consensus pattern (14 bp):
TTTTCATTTTGCAT
Found at i:292252 original size:35 final size:35
Alignment explanation
Indices: 292208--292274 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 35
292198 TTCAACTAGA
292208 AATAGAATA-TTGAGGCATT-TTGAAGGCTCATAAC
1 AATAGAATATTTG-GGCATTCTTGAAGGCTCATAAC
*
292242 AATATGAATATTTGGGCATTCTTGGAGGCTCAT
1 AATA-GAATATTTGGGCATTCTTGAAGGCTCAT
292275 CTCAACAAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 4 0.14
35 11 0.38
36 14 0.48
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.33
Consensus pattern (35 bp):
AATAGAATATTTGGGCATTCTTGAAGGCTCATAAC
Found at i:293883 original size:23 final size:22
Alignment explanation
Indices: 293832--293909 Score: 120
Period size: 22 Copynumber: 3.5 Consensus size: 22
293822 ATCTACACTC
293832 TTCAAAGATGATAAATTCTCTT
1 TTCAAAGATGATAAATTCTCTT
*
293854 TTCAAAGATGATAGATTCTCTTT
1 TTCAAAGATGATAAATTCTC-TT
* *
293877 TTAAAAGATGATATATTCTCTT
1 TTCAAAGATGATAAATTCTCTT
293899 TTCAAAGATGA
1 TTCAAAGATGA
293910 AAGCTTTATT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
22 31 0.61
23 20 0.39
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.41
Consensus pattern (22 bp):
TTCAAAGATGATAAATTCTCTT
Found at i:294698 original size:166 final size:168
Alignment explanation
Indices: 294424--294750 Score: 525
Period size: 166 Copynumber: 2.0 Consensus size: 168
294414 AAAATGAGCA
*
294424 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAACAGAATGAGAAAATG
1 TTATCTTGAGATTGGGGCATCTTACCCAATCAACATGTTATTTCAAAAAACAGAATGAGAAAATG
* * * *
294489 ATTTTCATAGTTTCTCATTTTATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAATGATTTT
66 ATTTCCATAGTTTCTCATTTAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTC
*
294554 CTTAG-TTTTTTACTT-AGTAAACTATTTCCAACAGCC
131 CTTAGTTTTTTTACTTAAATAAACTATTTCCAACAGCC
* *** *
294590 TTATCTTGAGATTGGGGCATCTTATCCAATCAACATGTTATTTTTGAAAA-ATAATGAGAAAATG
1 TTATCTTGAGATTGGGGCATCTTACCCAATCAACATGTTATTTCAAAAAACAGAATGAGAAAATG
294654 ATTTCCATAGTTTCTCATTTAATCTTTTCTAAAAATGAAATTGTTGAAAAGTAAGAAAACGATTT
66 ATTTCCATAGTTTCTCATTTAATCTTTTCT-AAAATGAAATTGTTGAAAAGTAAGAAAACGATTT
294719 CCTTAGTTTTTTTACTTAAATAAACTATTTCC
130 CCTTAGTTTTTTTACTTAAATAAACTATTTCC
294751 CACATCTGTA
Statistics
Matches: 147, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
165 41 0.28
166 83 0.56
167 10 0.07
168 13 0.09
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (168 bp):
TTATCTTGAGATTGGGGCATCTTACCCAATCAACATGTTATTTCAAAAAACAGAATGAGAAAATG
ATTTCCATAGTTTCTCATTTAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTC
CTTAGTTTTTTTACTTAAATAAACTATTTCCAACAGCC
Found at i:294857 original size:76 final size:76
Alignment explanation
Indices: 294753--295542 Score: 1391
Period size: 76 Copynumber: 10.4 Consensus size: 76
294743 CTATTTCCCA
* *
294753 CATCTGTAAGTCCTGCAGTGCATAATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
294818 AGCCTTAGGGT
66 AGCCTTAGGGT
*
294829 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
294894 AGCCTTAGGGT
66 AGCCTTAGGGT
*
294905 CATCTATAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
294970 AGCCTTAGGGT
66 AGCCTTAGGGT
*
294981 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
295046 AGTCTTATGGT
66 AGCCTTAGGGT
* *
295057 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
295122 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
295133 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGGTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
295198 AGCCTTAGGGT
66 AGCCTTAGGGT
295209 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
295274 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
295285 CATCTGTAAGTCCTGTAGTGCATGATATTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
295350 AGCCTTTGGGT
66 AGCCTTAGGGT
* *
295361 CATCTGTAAGCCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
295426 AGCCTTAGGGT
66 AGCCTTAGGGT
*
295437 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
295502 AACCTTCGGGT
66 AGCCTTAGGGT
* *
295513 CATCTGTAAGCCCTTCAGTGCATGATGTTT
1 CATCTGTAAGTCCTGCAGTGCATGATGTTT
295543 TCAACATTTC
Statistics
Matches: 681, Mismatches: 33, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 681 1.00
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:295688 original size:3 final size:3
Alignment explanation
Indices: 295680--295744 Score: 85
Period size: 3 Copynumber: 21.0 Consensus size: 3
295670 AAATTTAAAT
* *
295680 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA ATA TTA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
*
295729 TTA TTTA TTA ATA TTA
1 TTA -TTA TTA TTA TTA
295745 CAAAGCCCAA
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
3 48 0.89
4 6 0.11
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:296813 original size:21 final size:21
Alignment explanation
Indices: 296789--296829 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
296779 AATAACAAAT
* *
296789 TTAATCCTTTAATTTTAATAA
1 TTAATACTTTAATTTGAATAA
*
296810 TTAATATTTTAATTTGAATA
1 TTAATACTTTAATTTGAATA
296830 GCATGTTTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (21 bp):
TTAATACTTTAATTTGAATAA
Found at i:297026 original size:22 final size:21
Alignment explanation
Indices: 296991--297033 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
296981 TTAGTCAATA
*
296991 TTTTCAATTTTTATTTATTTT
1 TTTTCAAATTTTATTTATTTT
297012 TTTTACAAATTTTATTTATTTT
1 TTTT-CAAATTTTATTTATTTT
297034 AAATATATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTTCAAATTTTATTTATTTT
Found at i:297320 original size:111 final size:110
Alignment explanation
Indices: 297205--297425 Score: 268
Period size: 111 Copynumber: 2.0 Consensus size: 110
297195 CATGTTTTAA
* * *
297205 TATTTATTTATTTTTCAATATT-AAGAAATGA-CAGTCTTAAAACAACTGGATGTCCATGTTCTG
1 TATTTATTTATTTTT-AATATTGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCC-TGTTCTG
* *
297268 ATATTTTTAAATAAATAAATATCCTAT-TTTATAAATTATATATTAATT
64 ATATTTCTAAATAAATAAATAT-CTATATTTATAAA-TATATATAAATT
* *** * *
297316 TATTTATTTATTTTTAATATTGAAGAAAAGAGCTGTCTTAAGGTACCTAGAAGTCCTTTTCTGAT
1 TATTTATTTATTTTTAATATTGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCCTGTTCTGAT
* *
297381 ATTTCTAAATAAATAAATATTTTTATTTATAAATATATATAAATT
66 ATTTCTAAATAAATAAATATCTATATTTATAAATATATATAAATT
297426 AATATTTTTT
Statistics
Matches: 94, Mismatches: 13, Indels: 7
0.82 0.11 0.06
Matches are distributed among these distances:
110 19 0.20
111 58 0.62
112 17 0.18
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.45
Consensus pattern (110 bp):
TATTTATTTATTTTTAATATTGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCCTGTTCTGAT
ATTTCTAAATAAATAAATATCTATATTTATAAATATATATAAATT
Found at i:297423 original size:30 final size:30
Alignment explanation
Indices: 297389--297447 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
297379 ATATTTCTAA
297389 ATAAATAAATATTTTTATTT-ATAAATATAT
1 ATAAATAAATATTTTT-TTTCATAAATATAT
* *
297419 ATAAATTAATATTTTTTTTCATAATTATA
1 ATAAATAAATATTTTTTTTCATAAATATA
297448 ATTTTGAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 23 0.88
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (30 bp):
ATAAATAAATATTTTTTTTCATAAATATAT
Found at i:298714 original size:2 final size:2
Alignment explanation
Indices: 298707--298769 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
298697 CTAAAGCGTG
298707 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
298749 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
298770 TACATGTAAG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:299571 original size:20 final size:20
Alignment explanation
Indices: 299519--299572 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
299509 AACTTAATAT
*
299519 TATTATTTTTAAAATATTAAAA
1 TATTATTTTT--ATTATTAAAA
*
299541 TAATT-TATTTATTATTAAAA
1 T-ATTATTTTTATTATTAAAA
299561 TATTATTTTTAT
1 TATTATTTTTAT
299573 AATTTTATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
19 3 0.11
20 16 0.59
22 5 0.19
23 3 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TATTATTTTTATTATTAAAA
Found at i:299697 original size:23 final size:23
Alignment explanation
Indices: 299668--299712 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
299658 AGTGTTATAT
299668 TATATTTTTAAA-ATATTAATTAG
1 TATA-TTTTAAATATATTAATTAG
*
299691 TATATTTTAAATATATTTATTA
1 TATATTTTAAATATATTAATTA
299713 AAATATTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
TATATTTTAAATATATTAATTAG
Found at i:299718 original size:23 final size:22
Alignment explanation
Indices: 299673--299719 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
299663 TATATTATAT
**
299673 TTTTAAAATATTAATTAGTATA
1 TTTTAAAATATTAATTAAAATA
*
299695 TTTTAAATATATTTATTAAAATA
1 TTTTAAA-ATATTAATTAAAATA
299718 TT
1 TT
299720 ATTTGATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
TTTTAAAATATTAATTAAAATA
Found at i:299741 original size:34 final size:34
Alignment explanation
Indices: 299662--299741 Score: 78
Period size: 34 Copynumber: 2.4 Consensus size: 34
299652 AATAATAGTG
299662 TTATATT-ATATTTTTAAAATATTAATTAGTATA
1 TTATATTAATATTTTTAAAATATTAATTAGTATA
* * *
299695 TTTTA-AATATATTTATTAAAATATT-ATTTG-ATTA
1 TTATATTA-ATATTT-TTAAAATATTAATTAGTA-TA
299729 TTATATTAATATT
1 TTATATTAATATT
299742 AAATATATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
33 5 0.14
34 21 0.57
35 11 0.30
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (34 bp):
TTATATTAATATTTTTAAAATATTAATTAGTATA
Found at i:304852 original size:15 final size:15
Alignment explanation
Indices: 304832--304862 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
304822 ATAATAAATT
*
304832 AGAAAATTAAGAGAA
1 AGAAAATTAAAAGAA
304847 AGAAAATTAAAAGAA
1 AGAAAATTAAAAGAA
304862 A
1 A
304863 CCGTGCGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.16, T:0.13
Consensus pattern (15 bp):
AGAAAATTAAAAGAA
Found at i:310538 original size:18 final size:18
Alignment explanation
Indices: 310515--310552 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
310505 TATTGCAGTG
310515 TTGATTGTATTGATAGCC
1 TTGATTGTATTGATAGCC
310533 TTGATTGTATTGATAGCC
1 TTGATTGTATTGATAGCC
310551 TT
1 TT
310553 CTAACCAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.11, G:0.21, T:0.47
Consensus pattern (18 bp):
TTGATTGTATTGATAGCC
Found at i:311187 original size:10 final size:9
Alignment explanation
Indices: 311157--311190 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
311147 GTTTTGTTAA
311157 GAAAAATTT
1 GAAAAATTT
311166 GAAAAATTT
1 GAAAAATTT
*
311175 GAAAATTTCT
1 GAAAAATT-T
311185 GAAAAA
1 GAAAAA
311191 ATGTCCACCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 16 0.73
10 6 0.27
ACGTcount: A:0.56, C:0.03, G:0.12, T:0.29
Consensus pattern (9 bp):
GAAAAATTT
Done.