Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006564.1 Hibiscus syriacus cultivar Beakdansim tig00016065_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: 1886890
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 8
Found at i:1199044 original size:207 final size:207
Alignment explanation
Indices: 1198611--1199052 Score: 552
Period size: 207 Copynumber: 2.1 Consensus size: 207
1198601 ATTGGAAATG
* * *
1198611 TTGATCCACCTCCTTTTGTGATAGAATCGAACAAAATATTGACGCTGATCTACCTCATTCTATGA
1 TTGATCCACCTCCTTCTGTGATAGAATCGAACAAAATATTAACGCTGATCTACCTCATTCTACGA
* * *
1198676 TAGAATCGAGCAAAAAGGTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTTTCGGACGAG
66 TAGAATCGAGCAAAAAGGTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTTAGGACAAG
* *
1198741 TTCTTCTCATTATGAACCCTCCATTGGAAATGACGATCCACCTCCTTTTGTGATGGAATCGAGAA
131 TTCTTCTCATTATGAACCCTCCATTGGAAATGACGATCCACCTCCTTCTGCGATGGAATCGAGAA
*
1198806 AGAATGACAATA
196 AAAATGACAATA
* * * * * *
1198818 TTGATCCACCTCTTTCTGTGA-AGGAATCGAACAAAATGTTAATGCTGATCTATCTCCTTCTGCG
1 TTGATCCACCTCCTTCTGTGATA-GAATCGAACAAAATATTAACGCTGATCTACCTCATTCTACG
* * * * *
1198882 ATAGAATCTAGC-AATAGTGTGAACAAGTTCTTCTCATTGTGAACTTTTTCTCCCTCTTAGGATA
65 ATAGAATCGAGCAAAAAG-GTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTTAGGACA
* *
1198946 AGTTCTTCTCATTATGAACTCTCCATTGTAAATG-CTGATCCACCTCCTTCTGCGATGGAATC-A
129 AGTTCTTCTCATTATGAACCCTCCATTGGAAATGAC-GATCCACCTCCTTCTGCGATGGAATCGA
*** *
1199009 -AACAAAATGTTGATGC
193 GAA-AAAATGACAAT-A
* *
1199025 TTGATCTATCTCCTTCTGTGATAGAATC
1 TTGATCCACCTCCTTCTGTGATAGAATC
1199053 TAGCATAAGG
Statistics
Matches: 200, Mismatches: 29, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
205 2 0.01
206 14 0.07
207 183 0.92
208 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (207 bp):
TTGATCCACCTCCTTCTGTGATAGAATCGAACAAAATATTAACGCTGATCTACCTCATTCTACGA
TAGAATCGAGCAAAAAGGTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTTAGGACAAG
TTCTTCTCATTATGAACCCTCCATTGGAAATGACGATCCACCTCCTTCTGCGATGGAATCGAGAA
AAAATGACAATA
Found at i:1199074 original size:162 final size:162
Alignment explanation
Indices: 1198819--1199321 Score: 573
Period size: 162 Copynumber: 3.1 Consensus size: 162
1198809 ATGACAATAT
* * * *
1198819 TGATCCACCTCTTTCTGTGAAGGAATCGAACAAAATGTTAATGC-TGATCTATCTCCTTCTGCGA
1 TGATCCACCTCATTCTGTGATGGAATCGAACAAAATGTTGATGCTTGATCTATCTCCTTCTGTGA
* * *
1198883 TAGAATCTAGCAATAGTGTGAACAAGTTCTTCTCATTGTGAACTTTTTCTCCCTCTTAGGATAAG
66 TAGAATCTAGCAA-AGGGTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTTAGGATAAG
* * *
1198948 TTCTTCTCATTATGAACTCTCCATTGTAAATGC
130 TTCTTATCATTATGAACTCTCCATTGGAAATGA
* * *
1198981 TGATCCACCTCCTTCTGCGATGGAATCAAACAAAATGTTGATGCTTGATCTATCTCCTTCTGTGA
1 TGATCCACCTCATTCTGTGATGGAATCGAACAAAATGTTGATGCTTGATCTATCTCCTTCTGTGA
* * * *
1199046 TAGAATCTAGCATAAGGGTG-ACAAGTTCTTCTCATTATGAACTTCCTCTCCTTCTTTGGATGAG
66 TAGAATCTAGCA-AAGGGTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTTAGGATAAG
1199110 TTCTTATCATTATGAACTCTCCATTGGAAATGA
130 TTCTTATCATTATGAACTCTCCATTGGAAATGA
* * * * * * ** * *
1199143 AGATCCACCTCATTTTGTGATGGATTTGAGCAAAATGTTGATG-TTGGTCTATCTTATTTTATGA
1 TGATCCACCTCATTCTGTGATGGAATCGAACAAAATGTTGATGCTTGATCTATCTCCTTCTGTGA
* * * * * * *
1199207 TAGAGTCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCTCTTTTGTGGATGA
66 TAGAATCTAGC-AAAGGGTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTT-AGGATAA
* * ** *
1199272 TTTCTTTAT-GTTATGAACTCTCTTTTGGAAATGT
129 GTTC-TTATCATTATGAACTCTCCATTGGAAATGA
*
1199306 TGATCCACCTCTTTCT
1 TGATCCACCTCATTCT
1199322 ATAATAGATT
Statistics
Matches: 291, Mismatches: 44, Indels: 11
0.84 0.13 0.03
Matches are distributed among these distances:
161 31 0.11
162 175 0.60
163 80 0.27
164 5 0.02
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (162 bp):
TGATCCACCTCATTCTGTGATGGAATCGAACAAAATGTTGATGCTTGATCTATCTCCTTCTGTGA
TAGAATCTAGCAAAGGGTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTTAGGATAAGT
TCTTATCATTATGAACTCTCCATTGGAAATGA
Found at i:1199672 original size:36 final size:36
Alignment explanation
Indices: 1199639--1199716 Score: 102
Period size: 36 Copynumber: 2.2 Consensus size: 36
1199629 GGGAAAACTG
*
1199639 TCTCAAGCAAGATGAAATTGGTTTTGAGAAAAACAA
1 TCTCAAGCAAGATCAAATTGGTTTTGAGAAAAACAA
* * **
1199675 TCTCAAGCAAGATCAATTTTGTTTTGAGTGAAACAA
1 TCTCAAGCAAGATCAAATTGGTTTTGAGAAAAACAA
*
1199711 TTTCAA
1 TCTCAA
1199717 AATTTGTGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.31
Consensus pattern (36 bp):
TCTCAAGCAAGATCAAATTGGTTTTGAGAAAAACAA
Found at i:1199732 original size:102 final size:102
Alignment explanation
Indices: 1199582--1199838 Score: 356
Period size: 102 Copynumber: 2.5 Consensus size: 102
1199572 ATCTCATGTG
* * * * * *
1199582 AGATAAATTTTGGTTTCGAGCG-AACAATTTCAAATTTTGTATTCCAAGGGAAAACTGTCTCAAG
1 AGATCAATTTT-GTTTTGAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAAACTGTCTCAAG
1199646 CAAGATGAAATTGGTTTTGAGAAAAACAATCTCAAGCA
65 CAAGATGAAATTGGTTTTGAGAAAAACAATCTCAAGCA
* *
1199684 AGATCAATTTTGTTTTGAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAAATTGTCTCAGGC
1 AGATCAATTTTGTTTTGAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAAACTGTCTCAAGC
* * *
1199749 GAGATGAAATTGGTTTTGAGAAAAACAATCTCTAGTA
66 AAGATGAAATTGGTTTTGAGAAAAACAATCTCAAGCA
* *
1199786 AGATCAATTTTGTTTCT-AGTGAAACAATTTCAAAATTTTTGTTTGAAAGGGAA
1 AGATCAATTTTGTTT-TGAGTGAAACAATTTCAAAATTTGTGTTT-CAAGGGAA
1199839 CTTGTCTCAA
Statistics
Matches: 139, Mismatches: 13, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
101 8 0.06
102 123 0.88
103 8 0.06
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (102 bp):
AGATCAATTTTGTTTTGAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAAACTGTCTCAAGC
AAGATGAAATTGGTTTTGAGAAAAACAATCTCAAGCA
Found at i:1199960 original size:66 final size:64
Alignment explanation
Indices: 1199794--1199982 Score: 170
Period size: 66 Copynumber: 2.9 Consensus size: 64
1199784 TAAGATCAAT
* * * * * *
1199794 TTTGTTTCTAGTGAAACAATTTCAAAATTTTTGTTTGAAAGGGAACTTGTCTCAAGTGAGATAAC
1 TTTGATTC-AGTGAAACAATTTC-AAATTTGTGTTT-CAAGAGAAATTGTCTCAAGTGAGATAAA
1199859 AA
63 AA
* * * * *
1199861 TTCTGA---A-TGAAATAATTTCACAATTCGTATTTCAAGAGAAAATATCTCAAGTGAGATAAAA
1 TT-TGATTCAGTGAAACAATTTCA-AATTTGTGTTTCAAGAGAAATTGTCTCAAGTGAGATAAAA
1199922 A
64 A
* *
1199923 TTTGATTCGAGTGAAACAATTTCAAACTTTGTGTTTCAAGCGAAATTGTCTCAAGCGAGA
1 TTTGATTC-AGTGAAACAATTTCAAA-TTTGTGTTTCAAGAGAAATTGTCTCAAGTGAGA
1199983 CGAAATTTGT
Statistics
Matches: 96, Mismatches: 18, Indels: 17
0.73 0.14 0.13
Matches are distributed among these distances:
61 3 0.03
62 27 0.28
63 19 0.20
64 1 0.01
65 3 0.03
66 39 0.41
67 2 0.02
68 2 0.02
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (64 bp):
TTTGATTCAGTGAAACAATTTCAAATTTGTGTTTCAAGAGAAATTGTCTCAAGTGAGATAAAAA
Found at i:1201989 original size:34 final size:33
Alignment explanation
Indices: 1201946--1202062 Score: 98
Period size: 34 Copynumber: 3.5 Consensus size: 33
1201936 TGAACCCTCC
*
1201946 TTTCATTTTTATTTTTTTTCT-TTTTCTTCATTGT
1 TTTCTTTTTTATTTTTTTTCTATTTTCTTC-TT-T
* * *
1201980 TTTCTTTTTTCTTTTTTTT-TCTTTTC-CCTTT
1 TTTCTTTTTTATTTTTTTTCTATTTTCTTCTTT
1202011 TTTCTGTTTTCT-TTTTTTTTCTTATTTTCTTTCTTAT
1 TTTCT-TTTT-TATTTTTTTTC-TATTTTC-TTCTT-T
*
1202048 TTTCTTTCTTATTTT
1 TTTCTTTTTTATTTT
1202063 CTCTCTCTTT
Statistics
Matches: 68, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
31 6 0.09
32 14 0.21
33 3 0.04
34 28 0.41
35 1 0.01
36 10 0.15
37 6 0.09
ACGTcount: A:0.05, C:0.15, G:0.02, T:0.79
Consensus pattern (33 bp):
TTTCTTTTTTATTTTTTTTCTATTTTCTTCTTT
Found at i:1201994 original size:12 final size:12
Alignment explanation
Indices: 1201959--1202108 Score: 84
Period size: 12 Copynumber: 12.4 Consensus size: 12
1201949 CATTTTTATT
1201959 TTTTTTCTTTTTC
1 TTTTTTC-TTTTC
** *
1201972 TTCATTGTTTTC
1 TTTTTTCTTTTC
1201984 TTTTTTC-TTT-
1 TTTTTTCTTTTC
1201994 TTTTTTCTTTTCCC
1 TTTTTTCTTTT--C
1202008 TTTTTTCTGTTT-
1 TTTTTTCT-TTTC
1202020 TCTTTTT-TTTTC
1 T-TTTTTCTTTTC
1202032 TTATTTTC-TTTC
1 TT-TTTTCTTTTC
1202044 TTATTTTC-TTTC
1 TT-TTTTCTTTTC
*
1202056 TTATTTTC-TCTC
1 TT-TTTTCTTTTC
*
1202068 TCTTTT-TTTTC
1 TTTTTTCTTTTC
*
1202079 TTATTTTC-CTTC
1 TT-TTTTCTTTTC
*
1202091 TTTTTCCTTATTC
1 TTTTTTCTT-TTC
1202104 TTTTT
1 TTTTT
1202109 CATCATTCTC
Statistics
Matches: 110, Mismatches: 13, Indels: 28
0.73 0.09 0.19
Matches are distributed among these distances:
10 7 0.06
11 22 0.20
12 53 0.48
13 17 0.15
14 8 0.07
15 3 0.03
ACGTcount: A:0.04, C:0.18, G:0.01, T:0.77
Consensus pattern (12 bp):
TTTTTTCTTTTC
Found at i:1202010 original size:24 final size:24
Alignment explanation
Indices: 1201959--1202054 Score: 81
Period size: 25 Copynumber: 3.9 Consensus size: 24
1201949 CATTTTTATT
* *
1201959 TTTTTTCTTTTTCTTCATTGTTTT-C
1 TTTTTTCTTTTTATT--TTCTTTTCC
1201984 TTTTTTCTTTTT-TTTTCTTTTCCC
1 TTTTTTCTTTTTATTTTCTTTT-CC
* *
1202008 TTTTTTCTGTTTTCTTTT-TTTTTC
1 TTTTTTCT-TTTTATTTTCTTTTCC
1202032 TTATTTTCTTTCTTATTTTCTTT
1 TT-TTTTCTTT-TTATTTTCTTT
1202055 CTTATTTTCT
Statistics
Matches: 61, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
22 6 0.10
24 16 0.26
25 32 0.52
26 7 0.11
ACGTcount: A:0.03, C:0.16, G:0.02, T:0.79
Consensus pattern (24 bp):
TTTTTTCTTTTTATTTTCTTTTCC
Found at i:1202081 original size:35 final size:34
Alignment explanation
Indices: 1202018--1202092 Score: 96
Period size: 35 Copynumber: 2.2 Consensus size: 34
1202008 TTTTTTCTGT
* *
1202018 TTTCTTTTTTTTTCTTATTTTCTTTCTTATTTTC
1 TTTCTTATTTTCTCTTATTTTCTTTCTTATTTTC
* *
1202052 TTTCTTATTTTCTCTCTCTTTTTTTTCTTATTTTC
1 TTTCTTATTTTCTCT-TATTTTCTTTCTTATTTTC
*
1202087 CTTCTT
1 TTTCTT
1202093 TTTCCTTATT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
34 13 0.37
35 22 0.63
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (34 bp):
TTTCTTATTTTCTCTTATTTTCTTTCTTATTTTC
Found at i:1204902 original size:21 final size:21
Alignment explanation
Indices: 1204876--1204920 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1204866 AAAAGTAAAG
* *
1204876 ATGAAAGTGCGAATGCAAAAA
1 ATGAAAATGCAAATGCAAAAA
*
1204897 ATGAAAATGCAAATGCAACAA
1 ATGAAAATGCAAATGCAAAAA
1204918 ATG
1 ATG
1204921 TATTAATTCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.53, C:0.11, G:0.20, T:0.16
Consensus pattern (21 bp):
ATGAAAATGCAAATGCAAAAA
Found at i:1212168 original size:22 final size:24
Alignment explanation
Indices: 1212143--1212197 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 24
1212133 AAAATTGACT
1212143 GAAAACGTATCA-AAAGATAGA-A
1 GAAAACGTATCATAAAGATAGAGA
* ** *
1212165 GAAAATGCGTCATAAAGATAGAGG
1 GAAAACGTATCATAAAGATAGAGA
1212189 GAAAACGTA
1 GAAAACGTA
1212198 CCTTAAAAAC
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
22 9 0.38
23 9 0.38
24 6 0.25
ACGTcount: A:0.53, C:0.09, G:0.24, T:0.15
Consensus pattern (24 bp):
GAAAACGTATCATAAAGATAGAGA
Found at i:1213089 original size:59 final size:58
Alignment explanation
Indices: 1212948--1213108 Score: 153
Period size: 59 Copynumber: 2.7 Consensus size: 58
1212938 ATAGTTTGAG
* * *
1212948 GATAAAATTGAAGTGTTCAAAAGTTTGAAGACCAATTTAGAATAAGAATAATAGTTCAAG
1 GATAAAATTGAA-TGTTAAAAAGTTTG-AGACCAATTTAGAATAAGAATAATAATTCAAA
* * * * ** * *
1213008 GAAAAAATTGAAATATTTAAAAGTTTGAGACCAATTTTA-AATGAGGGTCATAATTTAAA
1 GATAAAATTG-AATGTTAAAAAGTTTGAGACCAA-TTTAGAATAAGAATAATAATTCAAA
*
1213067 GATAAAATTAGAATGTTAAAAAGTTTGAGAACTAATTTAGAA
1 GATAAAATT-GAATGTTAAAAAGTTTGAG-ACCAATTTAGAA
1213109 AGAAGATACT
Statistics
Matches: 82, Mismatches: 14, Indels: 10
0.77 0.13 0.09
Matches are distributed among these distances:
59 48 0.59
60 32 0.39
61 2 0.02
ACGTcount: A:0.48, C:0.05, G:0.17, T:0.30
Consensus pattern (58 bp):
GATAAAATTGAATGTTAAAAAGTTTGAGACCAATTTAGAATAAGAATAATAATTCAAA
Found at i:1213467 original size:31 final size:32
Alignment explanation
Indices: 1213344--1213467 Score: 89
Period size: 31 Copynumber: 3.9 Consensus size: 32
1213334 AAAGATAAAT
* * * *
1213344 TTTGTTAAGTTTAA-GGATCATTTTTTAA-TAG
1 TTTGATAAGTTTAATGAAT-ATTTTGTAACTAA
*
1213375 TTTGATAAGTTTAATAAAT-TTTTGATAA-TAA
1 TTTGATAAGTTTAATGAATATTTTG-TAACTAA
* * *
1213406 TTTGATAAAATTTAATG-ATAATTCTATAACT-A
1 TTTGAT-AAGTTTAATGAAT-ATTTTGTAACTAA
*
1213438 TTTGATCAGTTTAATGAATATTTTGTAACT
1 TTTGATAAGTTTAATGAATATTTTGTAACT
1213468 TGTAAAATTT
Statistics
Matches: 73, Mismatches: 13, Indels: 14
0.73 0.13 0.14
Matches are distributed among these distances:
30 4 0.05
31 43 0.59
32 22 0.30
33 4 0.05
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.48
Consensus pattern (32 bp):
TTTGATAAGTTTAATGAATATTTTGTAACTAA
Found at i:1219434 original size:37 final size:37
Alignment explanation
Indices: 1219381--1219485 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
1219371 CATTTTCGTC
*
1219381 CTACTAGGATTCAAACTCTTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
1219418 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * *
1219455 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
1219486 CTACAAGCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:1224757 original size:9 final size:8
Alignment explanation
Indices: 1224730--1224807 Score: 53
Period size: 7 Copynumber: 10.2 Consensus size: 8
1224720 ATATCCAATC
*
1224730 AAGAACAA
1 AAGAAGAA
1224738 AA-AAGAA
1 AAGAAGAA
1224745 AAGAAGCAA
1 AAGAAG-AA
1224754 AAGAAG-A
1 AAGAAGAA
1224761 AA-AA-AA
1 AAGAAGAA
1224767 AAGAA-AA
1 AAGAAGAA
1224774 AAGAA-AA
1 AAGAAGAA
*
1224781 ACAAAAGAA
1 A-AGAAGAA
*
1224790 AAAAAG-A
1 AAGAAGAA
1224797 AAGAACGAA
1 AAGAA-GAA
1224806 AA
1 AA
1224808 TCAAAAAGAA
Statistics
Matches: 59, Mismatches: 3, Indels: 15
0.77 0.04 0.19
Matches are distributed among these distances:
6 5 0.08
7 26 0.44
8 14 0.24
9 14 0.24
ACGTcount: A:0.79, C:0.05, G:0.15, T:0.00
Consensus pattern (8 bp):
AAGAAGAA
Found at i:1224762 original size:17 final size:15
Alignment explanation
Indices: 1224730--1224791 Score: 58
Period size: 16 Copynumber: 4.1 Consensus size: 15
1224720 ATATCCAATC
1224730 AAGAACAAAAAAGAA
1 AAGAACAAAAAAGAA
1224745 AAGAAGCAAAAGAAGAA
1 AAGAA-CAAAA-AAGAA
*
1224762 AA-AA-AAAGAA-AA
1 AAGAACAAAAAAGAA
*
1224774 AAGAAAAACAAAAGAA
1 AAGAACAA-AAAAGAA
1224790 AA
1 AA
1224792 AAAGAAAGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
12 4 0.10
13 4 0.10
14 5 0.13
15 8 0.21
16 11 0.28
17 7 0.18
ACGTcount: A:0.81, C:0.05, G:0.15, T:0.00
Consensus pattern (15 bp):
AAGAACAAAAAAGAA
Found at i:1224773 original size:18 final size:18
Alignment explanation
Indices: 1224752--1224820 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 18
1224742 GAAAAGAAGC
1224752 AAAAGAAGAAAAA-AAAAG
1 AAAA-AAGAAAAACAAAAG
1224770 AAAAAAGAAAAACAAAAG
1 AAAAAAGAAAAACAAAAG
*
1224788 AAAAAAAGAAAGAACGAAAAT
1 -AAAAAAGAAA-AAC-AAAAG
*
1224809 CAAAAAGAAAAA
1 AAAAAAGAAAAA
1224821 TGGACAAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
17 8 0.18
18 9 0.20
19 12 0.27
20 12 0.27
21 4 0.09
ACGTcount: A:0.81, C:0.04, G:0.13, T:0.01
Consensus pattern (18 bp):
AAAAAAGAAAAACAAAAG
Found at i:1224781 original size:26 final size:26
Alignment explanation
Indices: 1224729--1224820 Score: 89
Period size: 27 Copynumber: 3.5 Consensus size: 26
1224719 AATATCCAAT
* *
1224729 CAAGAACAAAAAAGAAAAGAAGCAAAA
1 CAAGAAAAAAAAAGAAAA-AAGAAAAA
*
1224756 GAAGAAAAAAAAAGAAAAAAGAAAAA
1 CAAGAAAAAAAAAGAAAAAAGAAAAA
* *
1224782 CAA-AAGAAAAAAAGAAAGAACGAAAAT
1 CAAGAA-AAAAAAAGAAA-AAAGAAAAA
*
1224809 CAA-AAAGAAAAA
1 CAAGAAAAAAAAA
1224821 TGGACAAAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
25 2 0.04
26 26 0.46
27 28 0.50
ACGTcount: A:0.78, C:0.07, G:0.14, T:0.01
Consensus pattern (26 bp):
CAAGAAAAAAAAAGAAAAAAGAAAAA
Found at i:1226243 original size:37 final size:35
Alignment explanation
Indices: 1226200--1226331 Score: 124
Period size: 37 Copynumber: 3.7 Consensus size: 35
1226190 TTTCTAATAT
* *
1226200 AAATTTTGTCTCGCTTGAGACAGTCTCATTTAAAAC
1 AAATTTTGTCTCCCTTGAGACAGTCTC-TTTGAAAC
* ** * *
1226236 AAGATTTTATCTCGTTTGAGATAGTTTTTCTTTGAAAC
1 AA-ATTTTGTCTCCCTTGAGACAG--TCTCTTTGAAAC
* *
1226274 AAATTTCGTCTCCCTTGAGACAGTCTTCCTTGAAAC
1 AAATTTTGTCTCCCTTGAGACAGTC-TCTTTGAAAC
1226310 AAA--TTGTCTCCCTTGAGACAGT
1 AAATTTTGTCTCCCTTGAGACAGT
1226332 TTCTCTCCAG
Statistics
Matches: 79, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
34 18 0.23
35 1 0.01
36 14 0.18
37 34 0.43
38 9 0.11
39 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (35 bp):
AAATTTTGTCTCCCTTGAGACAGTCTCTTTGAAAC
Found at i:1226338 original size:19 final size:19
Alignment explanation
Indices: 1226277--1226339 Score: 53
Period size: 19 Copynumber: 3.5 Consensus size: 19
1226267 TTGAAACAAA
1226277 TTTCGTCTCCCTTGAGACAG
1 TTTC-TCTCCCTTGAGACAG
* *
1226297 --TCT-T-CCTTGAAACAA
1 TTTCTCTCCCTTGAGACAG
* *
1226312 ATTGTCTCCCTTGAGACAG
1 TTTCTCTCCCTTGAGACAG
1226331 TTTCTCTCC
1 TTTCTCTCC
1226340 AGACAACACA
Statistics
Matches: 32, Mismatches: 7, Indels: 9
0.67 0.15 0.19
Matches are distributed among these distances:
15 9 0.28
16 1 0.03
17 3 0.09
18 3 0.09
19 16 0.50
ACGTcount: A:0.19, C:0.30, G:0.14, T:0.37
Consensus pattern (19 bp):
TTTCTCTCCCTTGAGACAG
Found at i:1226525 original size:106 final size:106
Alignment explanation
Indices: 1226336--1227089 Score: 1123
Period size: 106 Copynumber: 7.0 Consensus size: 106
1226326 GACAGTTTCT
* * * *
1226336 CTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAATAATTTCCCA
1 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCA
*
1226401 ATTTCAAAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
* * * * * * ** **
1226442 CTCAAGACAGCACAAGCTCAACTTCAC-AGCGAAGGGGCGGCTGACTGTCAACAAACAGCTTCTC
1 CTCCAGACAACGCAAGTTCAACTTCACGA-CGAAGGGACCGCTGGTTGTCAACAAACAATTTCTC
1226506 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
65 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
*
1226548 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCA
1 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCA
*
1226613 ATTTCAGAGCCAATTTCAACTTCACAGCGAAAGATATTGGA
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
*
1226654 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGATCGCTGGTTGTCAACAAACAATTTCTCA
1 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCA
* * *
1226719 ATTTCGGAGCCAATTTCAACTTCACATCGAAGGATATTTGA
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
*
1226760 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCA
1 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCA
*
1226825 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGA
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
* * * * *
1226866 CTCAATACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACAATTTCTCAA
1 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC-A-AA-----CAA
* *
1226931 TTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAAGATATTGGA
59 TTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
* * *
1226979 CTCCAGACAACGCAAGTTCAACTTTACGACGAATGGACCGCTGGTTGTCAATAAACAATTTCTCA
1 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCA
*
1227044 ATTTCAGAGCAAATTTCAACTTCACAGCGAAGGATATTGGA
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
1227085 CTCCA
1 CTCCA
1227090 AAAAAACGCA
Statistics
Matches: 587, Mismatches: 52, Indels: 18
0.89 0.08 0.03
Matches are distributed among these distances:
105 1 0.00
106 486 0.83
107 2 0.00
108 2 0.00
111 2 0.00
112 1 0.00
113 93 0.16
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCA
ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
Found at i:1237619 original size:22 final size:22
Alignment explanation
Indices: 1237593--1237635 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1237583 TAATAAATTA
1237593 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
1237615 TTTAAAATAAATTAATCCATA
1 TTTAAAATAAATCAATCCATA
1237636 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:1237644 original size:22 final size:22
Alignment explanation
Indices: 1237595--1237643 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1237585 ATAAATTATT
**
1237595 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
1237617 TAAAATAAATTAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
1237640 TAAA
1 TAAA
1237644 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:1237647 original size:54 final size:54
Alignment explanation
Indices: 1237583--1238140 Score: 485
Period size: 54 Copynumber: 10.4 Consensus size: 54
1237573 ACAACTACAA
*
1237583 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATTAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* **
1237637 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATA-
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATAC
** * ** ** *
1237694 TTTTAAA--A-TAAACCAATCCATACAAATAAAT-TATTTAAAATAAATCAATCCATAA
1 TAATAAATTATTTAA--AATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATAC
*
1237749 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* *** * * *
1237803 TAATAAATTATTTAAAATAAATCAATCTATACAACTACAAT-AATAAATCAAT-C
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAATCAATCCATAC
* ** * *
1237856 -CAT--A-T-TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT-CA-AT
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAA--A--T-AAATCAATCCATAC
* * ** *
1237909 TCATACAACTA-CAAAAATAAATCAATCTATATTTTAAAATAAATCAAT-C-TA-
1 TAATA-AATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* * *
1237960 T-AT-AACTA--CAATAATAAATCAATTCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAA-AATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1238011 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* *
1238065 TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCTATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1238119 TAATAAATTATTTAAAATAAAT
1 TAATAAATTATTTAAAATAAAT
1238141 TATTTTAAAA
Statistics
Matches: 415, Mismatches: 52, Indels: 74
0.77 0.10 0.14
Matches are distributed among these distances:
47 2 0.00
48 61 0.15
49 2 0.00
50 6 0.01
51 2 0.00
52 14 0.03
53 7 0.02
54 234 0.56
55 19 0.05
56 10 0.02
57 17 0.04
58 41 0.10
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
Found at i:1237655 original size:32 final size:32
Alignment explanation
Indices: 1237615--1238140 Score: 239
Period size: 32 Copynumber: 18.4 Consensus size: 32
1237605 CAATCCATAT
*
1237615 TTTAAAATAAATTAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
1237647 TTTAAAATAAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
1237677 --T--AATAAATCAATCC--A-T-AT------
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
1237695 TTTAAAATAAACCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
1237727 TTTAAAATAAATCAATCCATAATAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1237759 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
1237781 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
1237813 TTTAAAATAAATCAATCTATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
1237843 --T--AATAAATCAATCC--A-T-AT------
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1237861 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
1237893 TTTAAAATAAATCAATTCATAC-AACT--A-CA
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
* * *
1237922 ---AAAATAAATCAATCTATATTTTAAAATAAATCAA
1 TTTAAAATAAATCAATCCATA--CT--AATAAAT-TA
* * * * *
1237956 TCT-ATATAACTACAAT-AATA--AATCAATTCATA
1 TTTAAAATAAAT-CAATCCATACTAAT-AAAT--TA
1237988 TTTTAAAATAAATCAATCCATACTAATAAATTA
1 -TTTAAAATAAATCAATCCATACTAATAAATTA
1238021 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1238043 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1238075 TTTAAAATAAATC-A---AT-CT-AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
1238097 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1238129 TTTAAAATAAAT
1 TTTAAAATAAAT
1238141 TATTTTAAAA
Statistics
Matches: 382, Mismatches: 29, Indels: 166
0.66 0.05 0.29
Matches are distributed among these distances:
20 2 0.01
22 72 0.19
23 8 0.02
24 7 0.02
25 1 0.00
26 55 0.14
27 4 0.01
28 11 0.03
29 1 0.00
30 10 0.03
31 17 0.04
32 157 0.41
33 8 0.02
34 10 0.03
35 3 0.01
36 12 0.03
37 4 0.01
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:1237685 original size:80 final size:80
Alignment explanation
Indices: 1237598--1237957 Score: 560
Period size: 80 Copynumber: 4.4 Consensus size: 80
1237588 AATTATTTAA
*
1237598 AATAAATCAATCCATATTTTAAAATAAATTAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1237663 CCATACAACTACAAT
66 CCATACAACTACAAT
* *
1237678 AATAAATCAATCCATATTTTAAAATAAACCAATCCATACAAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
* *
1237743 CCATA-ATAATAAATTATTT
66 CCATACA-ACTACA--A--T
*
1237762 AAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCA
1 --AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
*
1237827 ATCTATACAACTACAAT
64 ATCCATACAACTACAAT
1237844 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
* *
1237909 TCATACAACTACAAA
66 CCATACAACTACAAT
*
1237924 AATAAATCAATCTATATTTTAAAATAAATCAATC
1 AATAAATCAATCCATATTTTAAAATAAATCAATC
1237958 TATATAACTA
Statistics
Matches: 256, Mismatches: 16, Indels: 16
0.89 0.06 0.06
Matches are distributed among these distances:
79 1 0.00
80 180 0.70
82 2 0.01
84 2 0.01
86 70 0.27
87 1 0.00
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (80 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
CCATACAACTACAAT
Found at i:1237736 original size:14 final size:14
Alignment explanation
Indices: 1237717--1237770 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
1237707 CAATCCATAC
1237717 AAATAAATTATTTA
1 AAATAAATTATTTA
* *
1237731 AAATAAATCAATCCATA
1 AAATAAAT-TAT--TTA
1237748 ATAATAAATTATTTA
1 A-AATAAATTATTTA
1237763 AAATAAAT
1 AAATAAAT
1237771 CAATCCATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 15 0.47
15 5 0.16
17 5 0.16
18 7 0.22
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATAAATTATTTA
Found at i:1237785 original size:22 final size:22
Alignment explanation
Indices: 1237759--1237801 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1237749 TAATAAATTA
1237759 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
1237781 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
1237802 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:1237810 original size:22 final size:22
Alignment explanation
Indices: 1237761--1237809 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1237751 ATAAATTATT
**
1237761 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
1237783 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
1237806 TAAA
1 TAAA
1237810 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:1237890 original size:22 final size:22
Alignment explanation
Indices: 1237815--1237889 Score: 69
Period size: 22 Copynumber: 3.2 Consensus size: 22
1237805 ATAAATTATT
* *
1237815 TAAAATAAATCAATCTATACAA
1 TAAAATAAATCAATCCATATAA
**
1237837 CTACAATAATAAATCAATCCATATTT
1 -T--AA-AATAAATCAATCCATATAA
1237863 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
1237886 TAAA
1 TAAA
1237890 TTATTTAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
22 16 0.38
23 8 0.19
25 3 0.07
26 15 0.36
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:1237994 original size:128 final size:133
Alignment explanation
Indices: 1237727--1238095 Score: 529
Period size: 128 Copynumber: 2.8 Consensus size: 133
1237717 AAATAAATTA
* ***
1237727 TTTAAAATAAATCAATCCATAATAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAAACTAAAATAAA
*
1237792 TCAATTCATACTAATAAATTATTTAAAATAAATCAATCTATACAACTACAATAATAAATCAATCC
66 TCAAATCATACTAAT-AATTATTTAAAATAAATCAATCTATACAACTACAATAATAAATCAATCC
1237857 ATAT
130 ATAT
* *
1237861 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATTCATACAACTACAA-AA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA-AACTAAAATAA
* *
1237925 AT-AAATCA-ATCT-AT-A-T-TTTAAAATAAATCAATCTATATAACTACAATAATAAATCAATT
65 ATCAAATCATA-CTAATAATTATTTAAAATAAATCAATCTATACAACTACAATAATAAATCAATC
1237984 CATAT
129 CATAT
***
1237989 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAAACTAAAATAAA
1238054 TC-AATCCATACTAATAAATTATTTAAAATAAATCAATCTATA
66 TCAAAT-CATACTAAT-AATTATTTAAAATAAATCAATCTATA
1238096 TTTTAAAATA
Statistics
Matches: 210, Mismatches: 14, Indels: 22
0.85 0.06 0.09
Matches are distributed among these distances:
127 4 0.02
128 105 0.50
129 5 0.02
130 4 0.02
132 4 0.02
133 8 0.04
134 76 0.36
135 4 0.02
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (133 bp):
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAAACTAAAATAAA
TCAAATCATACTAATAATTATTTAAAATAAATCAATCTATACAACTACAATAATAAATCAATCCA
TAT
Found at i:1238047 original size:22 final size:22
Alignment explanation
Indices: 1238021--1238063 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1238011 TAATAAATTA
1238021 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
1238043 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
1238064 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:1238072 original size:22 final size:22
Alignment explanation
Indices: 1238023--1238071 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1238013 ATAAATTATT
**
1238023 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
1238045 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
1238068 TAAA
1 TAAA
1238072 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:1238117 original size:22 final size:22
Alignment explanation
Indices: 1237922--1238005 Score: 98
Period size: 22 Copynumber: 3.6 Consensus size: 22
1237912 TACAACTACA
1237922 AAAATAAATCAATCTATATTTT
1 AAAATAAATCAATCTATATTTT
**
1237944 AAAATAAATCAATCTATATAACTAC
1 AAAATAAATCAATCTATAT---TTT
1237969 AATAATAAATCAAT-TCATATTTT
1 AA-AATAAATCAATCT-ATATTTT
1237992 AAAATAAATCAATC
1 AAAATAAATCAATC
1238006 CATACTAATA
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
22 30 0.58
23 3 0.06
25 4 0.08
26 15 0.29
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.35
Consensus pattern (22 bp):
AAAATAAATCAATCTATATTTT
Found at i:1238126 original size:22 final size:22
Alignment explanation
Indices: 1238077--1238125 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1238067 ATAAATTATT
**
1238077 TAAAATAAATCAATCTATATTT
1 TAAAATAAATCAATCTATATAA
1238099 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCTATA-TAA
1238122 TAAA
1 TAAA
1238126 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (22 bp):
TAAAATAAATCAATCTATATAA
Found at i:1238149 original size:15 final size:15
Alignment explanation
Indices: 1238120--1238262 Score: 146
Period size: 15 Copynumber: 9.5 Consensus size: 15
1238110 AATCTATACT
1238120 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
1238134 AATAAATTATTTTAA
1 AATAAATTATTTTAA
* ** *
1238149 AATAAATCAATCCATAT
1 AATAAAT-TAT-TTTAA
** * *
1238166 TTTATAA-TAATTTAT
1 AATA-AATTATTTTAA
* *
1238181 TATAAATTATTTTAT
1 AATAAATTATTTTAA
1238196 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
1238211 AATAAATTATTTTAT
1 AATAAATTATTTTAA
1238226 AATAAATTATTTTAA
1 AATAAATTATTTTAA
1238241 AATAAATTATTTTAA
1 AATAAATTATTTTAA
1238256 AATAAAT
1 AATAAAT
1238263 AACCTTATTA
Statistics
Matches: 108, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
14 11 0.10
15 88 0.81
16 3 0.03
17 4 0.04
18 2 0.02
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:1238179 original size:47 final size:47
Alignment explanation
Indices: 1237884--1238247 Score: 223
Period size: 54 Copynumber: 7.5 Consensus size: 47
1237874 AATCCATACT
* *
1237884 AATAAATTA-TTTAAAATAAATCAATTCATAC-AACTACAA-AA-AT-A
1 AATAAATTATTTTAAAATAAATCAATCCATACTAA-TA-AATAATTTAA
* *
1237928 AATCAATCTATATTTTAAAATAAATCAATCTATA-TAACTACAATAA--T-A
1 AAT-AA-AT-TATTTTAAAATAAATCAATCCATACTAA-TA-AATAATTTAA
* *
1237976 AATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AAT-AAAT--TATTTTAAAATAAATCAATCCATACTAATAAATAATTTAA
*
1238026 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AAT--A--AAT---TATTTTAAAATAAATCAATCCATACTAATAAATAATTTAA
* *
1238080 AATAAATCAATCTATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAA
1 AAT--A--AA--T-TATTTTAAAATAAATCAATCCATACTAATAAATAATTTAA
** *
1238134 AATAAATTATTTTAAAATAAATCAATCCATA-TTTTATAATAATTTAT
1 AATAAATTATTTTAAAATAAATCAATCCATACTAATA-AATAATTTAA
* * * ** * * *
1238181 TATAAATTATTTTATAATAAAT-TAT-TTTA-AAATAAATTATTTTAT
1 AATAAATTATTTTAAAATAAATCAATCCATACTAATAAA-TAATTTAA
1238226 AATAAATTATTTTAAAATAAAT
1 AATAAATTATTTTAAAATAAAT
1238248 TATTTTAAAA
Statistics
Matches: 276, Mismatches: 25, Indels: 37
0.82 0.07 0.11
Matches are distributed among these distances:
44 5 0.02
45 33 0.12
46 6 0.02
47 58 0.21
48 62 0.22
49 6 0.02
50 6 0.02
51 1 0.00
52 1 0.00
53 2 0.01
54 95 0.34
56 1 0.00
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (47 bp):
AATAAATTATTTTAAAATAAATCAATCCATACTAATAAATAATTTAA
Found at i:1240932 original size:24 final size:23
Alignment explanation
Indices: 1240888--1240933 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 23
1240878 GAATTTAATA
1240888 TTAATAAAATATTTTAATATTATT
1 TTAATAAAATA-TTTAATATTATT
1240912 TTAATCAAAATA-TTAATTATTA
1 TTAAT-AAAATATTTAA-TATTA
1240934 AAATATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 4 0.20
24 10 0.50
25 6 0.30
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
TTAATAAAATATTTAATATTATT
Found at i:1241289 original size:22 final size:22
Alignment explanation
Indices: 1241232--1241290 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
1241222 ACGCGATTCT
*
1241232 GACTATCGCATTACGATTTTCC
1 GACTATCGCATTGCGATTTTCC
* * *
1241254 AAAT-TCGCGTTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
*
1241275 GACTATCGCAATGCGA
1 GACTATCGCATTGCGA
1241291 ATATGTAAAT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (22 bp):
GACTATCGCATTGCGATTTTCC
Found at i:1241322 original size:20 final size:20
Alignment explanation
Indices: 1241275--1241345 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
1241265 GCGATTTTCC
1241275 GACTATCGCAATGCGAATAT
1 GACTATCGCAATGCGAATAT
* *
1241295 GTA-AATCGCAATGCGAGTAT
1 G-ACTATCGCAATGCGAATAT
* *
1241315 GACTATCGCAACGC-AATTCT
1 GACTATCGCAATGCGAA-TAT
1241335 GACTATCGCAA
1 GACTATCGCAA
1241346 CACGATTCTG
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 2 0.05
20 39 0.93
21 1 0.02
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.24
Consensus pattern (20 bp):
GACTATCGCAATGCGAATAT
Found at i:1241346 original size:20 final size:20
Alignment explanation
Indices: 1241299--1241385 Score: 102
Period size: 20 Copynumber: 4.3 Consensus size: 20
1241289 GAATATGTAA
* * *
1241299 ATCGCAATGCGAGTATGACT
1 ATCGCAACGCGATTCTGACT
*
1241319 ATCGCAACGCAATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
1241339 ATCGCAACACGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* * *
1241359 GTCGCAACGTGATGCTGACT
1 ATCGCAACGCGATTCTGACT
1241379 ATCGCAA
1 ATCGCAA
1241386 TACGATTTTC
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:1241391 original size:40 final size:40
Alignment explanation
Indices: 1241299--1241392 Score: 116
Period size: 40 Copynumber: 2.4 Consensus size: 40
1241289 GAATATGTAA
* * *
1241299 ATCGCAATGCGAGTATGACTATCGCAACGCAATTCTGACT
1 ATCGCAATACGATTATGACTATCGCAACGCAATGCTGACT
* * * **
1241339 ATCGCAACACGATTCTGACTGTCGCAACGTGATGCTGACT
1 ATCGCAATACGATTATGACTATCGCAACGCAATGCTGACT
1241379 ATCGCAATACGATT
1 ATCGCAATACGATT
1241393 TTCAAAGCGC
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.26
Consensus pattern (40 bp):
ATCGCAATACGATTATGACTATCGCAACGCAATGCTGACT
Found at i:1242035 original size:20 final size:20
Alignment explanation
Indices: 1241974--1242060 Score: 115
Period size: 20 Copynumber: 4.5 Consensus size: 20
1241964 AGAATCGCAA
*
1241974 TGCGATTTT-AGTTTCGCGT
1 TGCGATTTTCATTTTCGCGT
1241993 TGCGATTTTCATTTT-GCGT
1 TGCGATTTTCATTTTCGCGT
** *
1242012 TGCGATAGTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
*
1242032 TGCGATTTTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
1242052 TGCGATTTT
1 TGCGATTTT
1242061 AAGTTTCAGA
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
19 26 0.43
20 34 0.57
ACGTcount: A:0.11, C:0.15, G:0.23, T:0.51
Consensus pattern (20 bp):
TGCGATTTTCATTTTCGCGT
Found at i:1243033 original size:20 final size:20
Alignment explanation
Indices: 1242990--1243150 Score: 112
Period size: 20 Copynumber: 8.0 Consensus size: 20
1242980 AAATTCAGTG
* * *
1242990 TTGCGACAGTCAGAATTGCG
1 TTGCGATAGTCAGAATCGCA
*
1243010 TTGCGATAGTCAGAATCACA
1 TTGCGATAGTCAGAATCGCA
*
1243030 TTGCGATAGTCATAATCGCA
1 TTGCGATAGTCAGAATCGCA
* * *
1243050 TTGCGAT-TTACATATTCGCA
1 TTGCGATAGT-CAGAATCGCA
* * *
1243070 TTGCGAT-TTACATATTCGCA
1 TTGCGATAGT-CAGAATCGCA
* * *
1243090 TTGCGAT-TTACATATTCGCA
1 TTGCGATAGT-CAGAATCGCA
*
1243110 TTGCGATAGTCGGAAAATCGCA
1 TTGCGATAGTC--AGAATCGCA
*
1243132 ATGCGATAGTCAGAATCGC
1 TTGCGATAGTCAGAATCGC
1243151 GTTACGAATA
Statistics
Matches: 124, Mismatches: 13, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
19 1 0.01
20 105 0.85
21 1 0.01
22 17 0.14
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCA
Found at i:1243072 original size:40 final size:40
Alignment explanation
Indices: 1243028--1243138 Score: 152
Period size: 40 Copynumber: 2.7 Consensus size: 40
1243018 GTCAGAATCA
1243028 CATTGCGATAGTCATAATCGCATTGCGATTTACATATTCG
1 CATTGCGATAGTCATAATCGCATTGCGATTTACATATTCG
* *
1243068 CATTGCGAT-TTACATATTCGCATTGCGATTTACATATTCG
1 CATTGCGATAGT-CATAATCGCATTGCGATTTACATATTCG
* *
1243108 CATTGCGATAGTCGGAAAATCGCAATGCGAT
1 CATTGCGATAGTC--ATAATCGCATTGCGAT
1243139 AGTCAGAATC
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
39 1 0.02
40 46 0.75
41 1 0.02
42 13 0.21
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (40 bp):
CATTGCGATAGTCATAATCGCATTGCGATTTACATATTCG
Found at i:1243587 original size:4 final size:4
Alignment explanation
Indices: 1243578--1243605 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
1243568 AGGTGTGTAA
1243578 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1243606 GGGGTAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:1246292 original size:25 final size:24
Alignment explanation
Indices: 1246239--1246294 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
1246229 CAAAAATTTA
*
1246239 TTTATAAAATTTATTTAACAAACT
1 TTTATAAAAATTATTTAACAAACT
* *
1246263 ATTATAAGAAATTATTTAA-ATAATT
1 TTTATAA-AAATTATTTAACA-AACT
1246288 TTTATAA
1 TTTATAA
1246295 TAATAATAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 7 0.27
25 19 0.73
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (24 bp):
TTTATAAAAATTATTTAACAAACT
Found at i:1247124 original size:64 final size:64
Alignment explanation
Indices: 1247022--1247210 Score: 337
Period size: 64 Copynumber: 3.0 Consensus size: 64
1247012 CTTTAAAAAT
*
1247022 GATTTATGCAATTTATAAT--ATTTTTATATTTTAACAATTAAAATAATATATTTCATAACAAA
1 GATTTATGCAATTTATAATCGTTTTTTATATTTTAACAATTAAAATAATATATTTCATAACAAA
* *
1247084 GATTTATGCAATTTATAATCGTTTTTTATATTTTAACAATTGAAATAATATATCTCATAACAAA
1 GATTTATGCAATTTATAATCGTTTTTTATATTTTAACAATTAAAATAATATATTTCATAACAAA
1247148 GATTTATGCAATTTATAATCGTTTTTTATATTTTAACAATTAAAATAATATATTTCATAACAA
1 GATTTATGCAATTTATAATCGTTTTTTATATTTTAACAATTAAAATAATATATTTCATAACAA
1247211 TTTATTACAT
Statistics
Matches: 120, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
62 19 0.16
64 101 0.84
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (64 bp):
GATTTATGCAATTTATAATCGTTTTTTATATTTTAACAATTAAAATAATATATTTCATAACAAA
Found at i:1247577 original size:28 final size:28
Alignment explanation
Indices: 1247545--1247601 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
1247535 CTCTTCGTTT
* * *
1247545 ACATTATGTTGTCGAGCTAGTACTTGAA
1 ACATTATATCGTCGAGCCAGTACTTGAA
*
1247573 ACATTATATCGTCGAGCCAGTGCTTGAA
1 ACATTATATCGTCGAGCCAGTACTTGAA
1247601 A
1 A
1247602 GCCACAACGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.32
Consensus pattern (28 bp):
ACATTATATCGTCGAGCCAGTACTTGAA
Found at i:1251402 original size:21 final size:21
Alignment explanation
Indices: 1251358--1251410 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
1251348 TAGCAATTAC
* * * *
1251358 TATAATATATATATATATATA
1 TATAATATTTAAATATAAAAA
1251379 TATAATATTTAAATATAAAAA
1 TATAATATTTAAATATAAAAA
1251400 TATGAA-ATTTA
1 TAT-AATATTTA
1251411 TTTCAACAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 25 0.93
22 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
TATAATATTTAAATATAAAAA
Found at i:1251593 original size:19 final size:19
Alignment explanation
Indices: 1251569--1251619 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
1251559 ACCAATAAAA
*
1251569 TCGCAATGCGATCGCTAAT
1 TCGCAACGCGATCGCTAAT
1251588 TCGCAACGCGATCGCTAAT
1 TCGCAACGCGATCGCTAAT
1251607 TCGCAACGCGATC
1 TCGCAACGCGATC
1251620 TCCATTATCG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.25, C:0.31, G:0.22, T:0.22
Consensus pattern (19 bp):
TCGCAACGCGATCGCTAAT
Found at i:1251736 original size:20 final size:20
Alignment explanation
Indices: 1251711--1251803 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
1251701 TTTTCCCAAT
1251711 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
1251731 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
1251751 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
1251772 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
1251793 TCGCAATGCGA
1 TCGCAATGCGA
1251804 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:1251753 original size:41 final size:41
Alignment explanation
Indices: 1251708--1251803 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
1251698 CGATTTTCCC
1251708 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1251749 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
1251790 AAATCGCAATGCGA
1 AATTCGCAATGCGA
1251804 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:1251757 original size:21 final size:20
Alignment explanation
Indices: 1251711--1251803 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
1251701 TTTTCCCAAT
*
1251711 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
1251731 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
1251751 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
1251772 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
1251793 TCGCAATGCGA
1 TCGCAATGCGA
1251804 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:1251816 original size:41 final size:41
Alignment explanation
Indices: 1251730--1251864 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
1251720 GAATAAGTAA
* * *
1251730 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
1251771 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
1251812 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
1251853 TTCGCAACGCGA
1 ATCGCAACGCGA
1251865 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:1251817 original size:20 final size:20
Alignment explanation
Indices: 1251792--1251886 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
1251782 AATTGGGAAA
*
1251792 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
1251812 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
1251833 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
1251853 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
1251873 TTCGCAACGCGATA
1 ATCGCAACGCGATA
1251887 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1252102 original size:22 final size:22
Alignment explanation
Indices: 1252074--1252117 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1252064 CACTCTCTCA
1252074 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1252096 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1252118 TATCTAAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.45, G:0.14, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1252406 original size:20 final size:20
Alignment explanation
Indices: 1252381--1252418 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1252371 CGATTCTCTC
1252381 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
1252401 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
1252419 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:1253761 original size:18 final size:18
Alignment explanation
Indices: 1253740--1253784 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
1253730 TCCACTTCGG
* *
1253740 GAGCCATCACCTCGCCCA
1 GAGCAATCACCTCACCCA
* *
1253758 GAGCTATCACCTCACCTA
1 GAGCAATCACCTCACCCA
1253776 GAGCAATCA
1 GAGCAATCA
1253785 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.29, C:0.40, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCAATCACCTCACCCA
Found at i:1254282 original size:20 final size:20
Alignment explanation
Indices: 1254257--1254302 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1254247 TAGTTTACTT
1254257 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
1254277 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
1254297 TCGCAA
1 TCGCAA
1254303 TGCGAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:1254318 original size:19 final size:18
Alignment explanation
Indices: 1254296--1254391 Score: 66
Period size: 19 Copynumber: 5.6 Consensus size: 18
1254286 GGAAATGGCT
*
1254296 ATCGCAATGCGAAATAAAA
1 ATCGCAA-GCGAAATCAAA
1254315 ATCGCAA-CG--A-CAAA
1 ATCGCAAGCGAAATCAAA
*
1254329 ATCGCAACGCGAAAT-GAA
1 ATCGCAA-GCGAAATCAAA
1254347 ATCGCAA-CG--A-CAAA
1 ATCGCAAGCGAAATCAAA
*
1254361 ATCGCAACGCGAAATGAAA
1 ATCGCAA-GCGAAATCAAA
1254380 ATCGCAATGCGA
1 ATCGCAA-GCGA
1254392 TTTGTGTTTC
Statistics
Matches: 61, Mismatches: 5, Indels: 22
0.69 0.06 0.25
Matches are distributed among these distances:
14 20 0.33
15 1 0.02
16 6 0.10
17 2 0.03
18 11 0.18
19 21 0.34
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (18 bp):
ATCGCAAGCGAAATCAAA
Found at i:1254331 original size:14 final size:14
Alignment explanation
Indices: 1254312--1254369 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1254302 ATGCGAAATA
1254312 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1254326 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
1254342 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1254358 AAAATCGCAACG
1 AAAATCGCAACG
1254370 CGAAATGAAA
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:1254354 original size:32 final size:32
Alignment explanation
Indices: 1254296--1254386 Score: 146
Period size: 32 Copynumber: 2.8 Consensus size: 32
1254286 GGAAATGGCT
* *
1254296 ATCGCAATGCGAAATAAAAATCGCAACGACAAA
1 ATCGCAACGCGAAAT-GAAATCGCAACGACAAA
1254329 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1254361 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATG-AAATCGCAA
1254387 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 32 0.58
33 23 0.42
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.11
Consensus pattern (32 bp):
ATCGCAACGCGAAATGAAATCGCAACGACAAA
Found at i:1254422 original size:14 final size:14
Alignment explanation
Indices: 1254403--1254460 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1254393 TTGTGTTTCG
1254403 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1254417 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1254433 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
1254449 CGTTGCGATTTT
1 CGTTGCGATTTT
1254461 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1254437 original size:32 final size:33
Alignment explanation
Indices: 1254398--1254476 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
1254388 GCGATTTGTG
1254398 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1254430 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
1254463 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
1254477 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:1254475 original size:19 final size:19
Alignment explanation
Indices: 1254417--1254534 Score: 95
Period size: 20 Copynumber: 6.4 Consensus size: 19
1254407 GCGATTTTGT
1254417 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
1254435 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
1254449 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
1254468 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
1254488 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
1254507 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
1254527 TGTTGCGA
1 CGTTGCGA
1254535 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 11 0.14
19 26 0.32
20 29 0.36
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:1256556 original size:19 final size:19
Alignment explanation
Indices: 1256534--1256620 Score: 139
Period size: 19 Copynumber: 4.8 Consensus size: 19
1256524 ATCACAACGA
1256534 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1256553 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1256572 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1256591 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
1256605 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
1256621 TTTTCATTTC
Statistics
Matches: 65, Mismatches: 0, Indels: 8
0.89 0.00 0.11
Matches are distributed among these distances:
14 11 0.17
15 1 0.02
16 2 0.03
17 2 0.03
19 49 0.75
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:1256585 original size:38 final size:33
Alignment explanation
Indices: 1256505--1256620 Score: 142
Period size: 33 Copynumber: 3.4 Consensus size: 33
1256495 AAAACAGACT
* *** *
1256505 ATCGCAACGCGAAATGGCTATCACAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1256538 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAA
1256576 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1256609 ATCGCAATGCGA
1 ATCGCAATGCGA
1256621 TTTTCATTTC
Statistics
Matches: 73, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
33 37 0.51
34 1 0.01
35 2 0.03
36 2 0.03
37 1 0.01
38 30 0.41
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:1256696 original size:20 final size:20
Alignment explanation
Indices: 1256639--1256696 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
1256629 TCGCATTGCG
* *
1256639 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
1256659 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
1256679 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
1256697 TCAAATGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:1257783 original size:24 final size:24
Alignment explanation
Indices: 1257756--1257809 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1257746 GTATTCGAAA
* *
1257756 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
1257780 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
1257804 TTTGAT
1 TTTGAT
1257810 GATGTTTCAG
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:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:1258001 original size:12 final size:12
Alignment explanation
Indices: 1257984--1258008 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1257974 ATATAATCCT
1257984 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1257996 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1258008 G
1 G
1258009 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1260343 original size:33 final size:33
Alignment explanation
Indices: 1260301--1260493 Score: 273
Period size: 33 Copynumber: 5.8 Consensus size: 33
1260291 GGAAATTACT
1260301 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * **
1260334 ATCGCAATGCGAAAAGAAAATCGCAATGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
1260366 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1260400 ATCGCAATGCGAAATGAAAATCGCAACGCGA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
1260432 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1260466 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1260494 CGAATTTAAT
Statistics
Matches: 139, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
32 2 0.01
33 135 0.97
34 2 0.01
ACGTcount: A:0.42, C:0.19, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1260408 original size:66 final size:66
Alignment explanation
Indices: 1260302--1260500 Score: 362
Period size: 66 Copynumber: 3.0 Consensus size: 66
1260292 GAAATTACTA
* * * *
1260302 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAAGAAAATCGCAATGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1260367 T
66 T
1260368 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1260433 T
66 T
1260434 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1260499 T
66 T
1260500 T
1 T
1260501 AATTTCGCGT
Statistics
Matches: 129, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 129 1.00
ACGTcount: A:0.42, C:0.19, G:0.23, T:0.16
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:1260515 original size:19 final size:19
Alignment explanation
Indices: 1260493--1260555 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 19
1260483 AAATCGCAAC
*
1260493 GCGAATTTAATTTCGCGTT
1 GCGATTTTAATTTCGCGTT
*
1260512 GCGATTTTCATTTTCGCGTT
1 GCGATTTT-AATTTCGCGTT
* *
1260532 GCGATTTTCATTTCGCATT
1 GCGATTTTAATTTCGCGTT
1260551 GCGAT
1 GCGAT
1260556 AGTACTTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
19 20 0.53
20 18 0.47
ACGTcount: A:0.16, C:0.19, G:0.21, T:0.44
Consensus pattern (19 bp):
GCGATTTTAATTTCGCGTT
Found at i:1260528 original size:20 final size:19
Alignment explanation
Indices: 1260502--1260555 Score: 90
Period size: 20 Copynumber: 2.8 Consensus size: 19
1260492 CGCGAATTTA
1260502 ATTTCGCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
1260521 ATTTTCGCGTTGCGATTTTC
1 A-TTTCGCGTTGCGATTTTC
*
1260541 ATTTCGCATTGCGAT
1 ATTTCGCGTTGCGAT
1260556 AGTACTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
19 14 0.42
20 19 0.58
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.46
Consensus pattern (19 bp):
ATTTCGCGTTGCGATTTTC
Found at i:1260681 original size:14 final size:14
Alignment explanation
Indices: 1260662--1260698 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1260652 CATCAATTAA
1260662 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1260676 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1260690 ACAAATCAA
1 ACAAATCAA
1260699 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1262100 original size:21 final size:21
Alignment explanation
Indices: 1262070--1262156 Score: 68
Period size: 21 Copynumber: 4.1 Consensus size: 21
1262060 TGAATGGTGG
*
1262070 GAGGGACCTCTTCAACGATGA
1 GAGGGGCCTCTTCAACGATGA
* * * *
1262091 GAGTGGCCTCTTGAACGGTGG
1 GAGGGGCCTCTTCAACGATGA
* * *
1262112 GAGGGGACTC-TCGAGGAATGA
1 GAGGGGCCTCTTCAACG-ATGA
* *
1262133 TAGGGGCCTCTTCAACGATAA
1 GAGGGGCCTCTTCAACGATGA
1262154 GAG
1 GAG
1262157 TGGAATCTTG
Statistics
Matches: 46, Mismatches: 18, Indels: 4
0.68 0.26 0.06
Matches are distributed among these distances:
20 3 0.07
21 39 0.85
22 4 0.09
ACGTcount: A:0.25, C:0.20, G:0.36, T:0.20
Consensus pattern (21 bp):
GAGGGGCCTCTTCAACGATGA
Found at i:1264262 original size:33 final size:33
Alignment explanation
Indices: 1264205--1264303 Score: 135
Period size: 33 Copynumber: 3.0 Consensus size: 33
1264195 ACGAGATAAT
* *
1264205 GAGAATCGCAATGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
1264239 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
1264272 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
1264304 GCGAATAAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
33 45 0.78
34 13 0.22
ACGTcount: A:0.39, C:0.25, G:0.23, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:1264297 original size:19 final size:19
Alignment explanation
Indices: 1264180--1264363 Score: 156
Period size: 19 Copynumber: 10.1 Consensus size: 19
1264170 TCTTTTGGTT
*
1264180 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
* *
1264199 GATAATGAGAATCGCAATGC
1 GA-AATGAAAATCGCAACGC
**
1264219 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
1264237 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
1264253 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
1264271 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1264286 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
1264306 G-AATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1264324 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1264343 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1264362 GA
1 GA
1264364 TTTTGGTTTC
Statistics
Matches: 135, Mismatches: 16, Indels: 28
0.75 0.09 0.16
Matches are distributed among these distances:
14 19 0.14
15 3 0.02
16 2 0.01
17 1 0.01
18 8 0.06
19 70 0.52
20 30 0.22
21 2 0.01
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1264392 original size:19 final size:19
Alignment explanation
Indices: 1264359--1264425 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
1264349 AAAATCGCAA
**
1264359 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
1264378 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
1264397 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
1264417 TGCGATTTT
1 TGCGATTTT
1264426 CATTCTCGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 29 0.71
20 12 0.29
ACGTcount: A:0.10, C:0.16, G:0.25, T:0.48
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:1265012 original size:21 final size:21
Alignment explanation
Indices: 1264979--1265058 Score: 65
Period size: 21 Copynumber: 3.9 Consensus size: 21
1264969 TGCGAAAGTA
* * *
1264979 AGTATCTCGTTGCGATTTTTT
1 AGTATCGCATTGCGATTTTTC
* **
1265000 ATTATCGCATTGCGA-TAGTC
1 AGTATCGCATTGCGATTTTTC
1265020 AGTATCGCATTGCGATTTTCTC
1 AGTATCGCATTGCGATTTT-TC
* *
1265042 AAT-TCGCGTTGCGATTT
1 AGTATCGCATTGCGATTT
1265059 ACTTATTCGC
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
20 16 0.35
21 26 0.57
22 4 0.09
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.42
Consensus pattern (21 bp):
AGTATCGCATTGCGATTTTTC
Found at i:1265035 original size:20 final size:20
Alignment explanation
Indices: 1264942--1265035 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
1264932 CGCTATGTAA
*
1264942 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* *
1264962 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
1264982 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
1265003 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
1265023 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
1265036 TTTCTCAATT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:1265054 original size:41 final size:41
Alignment explanation
Indices: 1264963--1265097 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
1264953 AAAGTCAGTA
* * * * *
1264963 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCTCAAT
* *
1265003 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCTCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCTCAAT
* ** * *
1265045 TCGCGTTGCGAT-TTACTTATTCGCATTGCGAATTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCTCAAT
1265086 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1265098 TTACTTATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.04
41 72 0.92
42 3 0.04
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCTCAAT
Found at i:1265068 original size:20 final size:20
Alignment explanation
Indices: 1265024--1265116 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 20
1265014 ATAGTCAGTA
*
1265024 TCGCATTGCGATTTTCTCAAT
1 TCGCATTGCGATTTACT-AAT
* *
1265045 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
* *
1265065 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTAAT
* *
1265086 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
1265106 TCGCATTGCGA
1 TCGCATTGCGA
1265117 ATTGGGAAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.47
21 31 0.53
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTAAT
Found at i:1265098 original size:41 final size:41
Alignment explanation
Indices: 1265024--1265119 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
1265014 ATAGTCAGTA
* *
1265024 TCGCATTGCGATTTTCTCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1265065 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1265106 TCGCATTGCGAATT
1 TCGCATTGCGAATT
1265120 GGGAAAATCG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:1286613 original size:23 final size:23
Alignment explanation
Indices: 1286557--1286605 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
1286547 ATTATATGGA
*
1286557 ACTACGGTGCAATTCTACGTGGC
1 ACTACGGTGCAATTCTACGCGGC
1286580 ACTACGGTGCAATTCTACGCGGC
1 ACTACGGTGCAATTCTACGCGGC
1286603 ACT
1 ACT
1286606 TCTGTGCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.24
Consensus pattern (23 bp):
ACTACGGTGCAATTCTACGCGGC
Found at i:1291518 original size:23 final size:23
Alignment explanation
Indices: 1291487--1291548 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
1291477 ACATTATTAT
1291487 ATGGCACTACGGTGCAATTCTAC
1 ATGGCACTACGGTGCAATTCTAC
*
1291510 GTGGCACTACGGTGCAATTCTAC
1 ATGGCACTACGGTGCAATTCTAC
* *
1291533 ACGGCACTTCGGTGCA
1 ATGGCACTACGGTGCA
1291549 TTTATACGAG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.23, C:0.27, G:0.26, T:0.24
Consensus pattern (23 bp):
ATGGCACTACGGTGCAATTCTAC
Found at i:1291842 original size:15 final size:13
Alignment explanation
Indices: 1291807--1291844 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 13
1291797 TAATTTGATG
1291807 ATAATGAT-ATAA
1 ATAATGATAATAA
1291819 ATAATGATAATAA
1 ATAATGATAATAA
1291832 TATATATGATAAT
1 -ATA-ATGATAAT
1291845 GCTAAGAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 8 0.35
13 4 0.17
14 3 0.13
15 8 0.35
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (13 bp):
ATAATGATAATAA
Found at i:1295457 original size:24 final size:23
Alignment explanation
Indices: 1295430--1295476 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
1295420 ATACCATAAT
*
1295430 ATCAAGTAAAACAAAATGATTTAA
1 ATCAACTAAAACAAAAT-ATTTAA
* *
1295454 ATCAACTATAACATAATATTTAA
1 ATCAACTAAAACAAAATATTTAA
1295477 GGTCAATACC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.55, C:0.11, G:0.04, T:0.30
Consensus pattern (23 bp):
ATCAACTAAAACAAAATATTTAA
Found at i:1297623 original size:31 final size:31
Alignment explanation
Indices: 1297588--1297671 Score: 82
Period size: 31 Copynumber: 2.7 Consensus size: 31
1297578 GGAGCACCGT
**
1297588 GGGGCCTGAGAGCCTACCCAAGAAAGTTCTC
1 GGGGCCTGAGAGCCTACCCAAGAAAAATCTC
* * *
1297619 GGGGCCACG-GAACCTACTCAAGAAAAATCTC
1 GGGGCC-TGAGAGCCTACCCAAGAAAAATCTC
*
1297650 GGGG-CTACAGAGCCTACCCAAG
1 GGGGCCT-GAGAGCCTACCCAAG
1297672 GGTCACCTTA
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
30 1 0.02
31 39 0.95
32 1 0.02
ACGTcount: A:0.30, C:0.30, G:0.27, T:0.13
Consensus pattern (31 bp):
GGGGCCTGAGAGCCTACCCAAGAAAAATCTC
Found at i:1298749 original size:19 final size:19
Alignment explanation
Indices: 1298725--1298763 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1298715 CAACTCTGAC
* *
1298725 CAAAGTCAATGGTTTGGGT
1 CAAAGTCAACGGTTCGGGT
*
1298744 CAAAGTTAACGGTTCGGGT
1 CAAAGTCAACGGTTCGGGT
1298763 C
1 C
1298764 GGGTCAACAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (19 bp):
CAAAGTCAACGGTTCGGGT
Found at i:1303037 original size:19 final size:19
Alignment explanation
Indices: 1303013--1303049 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1303003 AACTCAAACC
1303013 AAAGTCAACGGGTTGGGTA
1 AAAGTCAACGGGTTGGGTA
*
1303032 AAAGTCAACGGTTTGGGT
1 AAAGTCAACGGGTTGGGT
1303050 CGGGTCAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.11, G:0.35, T:0.24
Consensus pattern (19 bp):
AAAGTCAACGGGTTGGGTA
Found at i:1303056 original size:18 final size:18
Alignment explanation
Indices: 1303035--1303071 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1303025 TTGGGTAAAA
* *
1303035 GTCAACGGTTTGGGTCGG
1 GTCAACAGTTCGGGTCGG
1303053 GTCAACAGTTCGGGTCGG
1 GTCAACAGTTCGGGTCGG
1303071 G
1 G
1303072 CAGAAGGGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.19, G:0.43, T:0.24
Consensus pattern (18 bp):
GTCAACAGTTCGGGTCGG
Found at i:1308277 original size:21 final size:20
Alignment explanation
Indices: 1308253--1308294 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1308243 TCCGATTTCC
1308253 TATATAAATCATCAACAAAGT
1 TATATAAATCATCAA-AAAGT
**
1308274 TATATTCATCATCAAAAAGT
1 TATATAAATCATCAAAAAGT
1308294 T
1 T
1308295 CAATAACGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.33
Consensus pattern (20 bp):
TATATAAATCATCAAAAAGT
Found at i:1310805 original size:64 final size:62
Alignment explanation
Indices: 1310720--1310880 Score: 189
Period size: 64 Copynumber: 2.5 Consensus size: 62
1310710 TTGTTTAAGG
* * *
1310720 TGCATCGATGCACATGCAGTGCATCGATGCAT-TAATTTAAAAAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCA-AAGGAGTGCATCGATGCATCCAA-TTAAAAA-AAAACATCGAATAGGATTTA
* * *
1310784 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCA-AAGGAGTGCATCGATGCAT-CCAATTAAAAAAAAACATCGAATAGGATTTA
*
1310848 TGCATCGATGCAAGGTGTAGTGCATCGATGCAT
1 TGCATCGATGCAAAG-G-AGTGCATCGATGCAT
1310881 ACCTCCATTA
Statistics
Matches: 85, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
63 2 0.02
64 61 0.72
65 21 0.25
66 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (62 bp):
TGCATCGATGCAAAGGAGTGCATCGATGCATCCAATTAAAAAAAAACATCGAATAGGATTTA
Found at i:1311566 original size:103 final size:103
Alignment explanation
Indices: 1311341--1311558 Score: 418
Period size: 103 Copynumber: 2.1 Consensus size: 103
1311331 GTAGAGGGTC
*
1311341 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTAGTGAGACACATAC
1311406 TTGATCCTTGGCATATGTATATGATTATTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTATTAAGGAATGA
*
1311444 TATTTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTAGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTAGTGAGACACATAC
1311509 TTGATCCTTGGCATATGTATATGATTATTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTATTAAGGAATGA
1311547 TATGTGGTCCTT
1 TATGTGGTCCTT
1311559 ATGGACATTA
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTAGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTATTAAGGAATGA
Found at i:1311608 original size:23 final size:23
Alignment explanation
Indices: 1311576--1311626 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
1311566 TTATTATATG
*
1311576 GCACTACGGTGTAATTCTACGTA
1 GCACTACGGTGCAATTCTACGTA
* *
1311599 GCACTCCGGTGCAATTCTACGTG
1 GCACTACGGTGCAATTCTACGTA
1311622 GCACT
1 GCACT
1311627 TAGGTACAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (23 bp):
GCACTACGGTGCAATTCTACGTA
Found at i:1311636 original size:23 final size:23
Alignment explanation
Indices: 1311588--1311637 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
1311578 ACTACGGTGT
* *
1311588 AATTCTACGTAGCACTCCGGTGC
1 AATTCTACGTAGCACTCAGGTAC
* *
1311611 AATTCTACGTGGCACTTAGGTAC
1 AATTCTACGTAGCACTCAGGTAC
1311634 AATT
1 AATT
1311638 ATATGAGTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (23 bp):
AATTCTACGTAGCACTCAGGTAC
Found at i:1317824 original size:64 final size:63
Alignment explanation
Indices: 1317739--1317899 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 63
1317729 TTGTTTAAGG
* * * *
1317739 TGCATCGATGCACATGCAGTGCATCGATGCAT-TAATTTAAAAAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCAA-TTAAAAA-AAAACATCGAATAGGATTTA
* * *
1317803 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCAT-CCAATTAAAAAAAAACATCGAATAGGATTTA
*
1317867 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
1317900 ACCTCCATTA
Statistics
Matches: 85, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
63 1 0.01
64 62 0.73
65 21 0.25
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (63 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCAATTAAAAAAAAACATCGAATAGGATTTA
Found at i:1318585 original size:103 final size:103
Alignment explanation
Indices: 1318360--1318574 Score: 412
Period size: 103 Copynumber: 2.1 Consensus size: 103
1318350 GTAGAGGGTC
* *
1318360 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGCCTAGTGAGACACATAC
1318425 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
1318463 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGCCTAGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGCCTAGTGAGACACATAC
1318528 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
1318566 TATGTGGTC
1 TATGTGGTC
1318575 TTTATGGACA
Statistics
Matches: 110, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGCCTAGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:1318643 original size:23 final size:23
Alignment explanation
Indices: 1318589--1318645 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
1318579 TGGACATTAT
1318589 TATATGGCACTATGATGCAATTC
1 TATATGGCACTATGATGCAATTC
*** * *
1318612 TACGCGGCACTCTGGTGCAATTC
1 TATATGGCACTATGATGCAATTC
1318635 TATATGGCACT
1 TATATGGCACT
1318646 TAGGTGTAAT
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.32
Consensus pattern (23 bp):
TATATGGCACTATGATGCAATTC
Found at i:1318651 original size:23 final size:23
Alignment explanation
Indices: 1318589--1318656 Score: 59
Period size: 23 Copynumber: 3.0 Consensus size: 23
1318579 TGGACATTAT
*
1318589 TATATGGCAC-TATGATGCAATTC
1 TATATGGCACTTA-GGTGCAATTC
***
1318612 TACGCGGCACTCT-GGTGCAATTC
1 TATATGGCACT-TAGGTGCAATTC
*
1318635 TATATGGCACTTAGGTGTAATT
1 TATATGGCACTTAGGTGCAATT
1318657 ATATGAGTTG
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
22 1 0.03
23 32 0.94
25 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (23 bp):
TATATGGCACTTAGGTGCAATTC
Found at i:1324398 original size:22 final size:22
Alignment explanation
Indices: 1324373--1324414 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1324363 AAGAGTTATT
* *
1324373 TGATTTAATTCCAGGGGTTACA
1 TGATATAATTCCAGGAGTTACA
*
1324395 TGATATAATTTCAGGAGTTA
1 TGATATAATTCCAGGAGTTA
1324415 TAACAGCTGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (22 bp):
TGATATAATTCCAGGAGTTACA
Found at i:1330287 original size:22 final size:22
Alignment explanation
Indices: 1330262--1330316 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
1330252 TCAGGAGTTA
* *
1330262 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
1330284 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
1330306 CGGGAGTTATA
1 CAGGAGTTATA
1330317 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:1333549 original size:15 final size:15
Alignment explanation
Indices: 1333529--1333559 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1333519 TTATTTGTTC
1333529 ATGATCCTTTCTCAA
1 ATGATCCTTTCTCAA
1333544 ATGATCCTTTCTCAA
1 ATGATCCTTTCTCAA
1333559 A
1 A
1333560 GACACTTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.26, G:0.06, T:0.39
Consensus pattern (15 bp):
ATGATCCTTTCTCAA
Found at i:1336921 original size:19 final size:19
Alignment explanation
Indices: 1336880--1336922 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1336870 TCAAATATTT
* *
1336880 TATTAATAATATAATTATG
1 TATTTATAATATAATTATA
1336899 TATTTATAA-ATAATTATAA
1 TATTTATAATATAATTAT-A
1336918 TATTT
1 TATTT
1336923 TAGAAAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
TATTTATAATATAATTATA
Found at i:1337446 original size:21 final size:19
Alignment explanation
Indices: 1337414--1337457 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
1337404 ACGTTTTACG
*
1337414 AACAATAAAATACGGTATA
1 AACAATAAAATACCGTATA
*
1337433 AACAATGAACAATACCGTATG
1 AACAAT-AA-AATACCGTATA
1337454 AACA
1 AACA
1337458 GTTTTGTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.29
20 2 0.10
21 13 0.62
ACGTcount: A:0.55, C:0.16, G:0.11, T:0.18
Consensus pattern (19 bp):
AACAATAAAATACCGTATA
Found at i:1338451 original size:31 final size:32
Alignment explanation
Indices: 1338363--1338458 Score: 117
Period size: 31 Copynumber: 3.1 Consensus size: 32
1338353 GAACCTCGGC
* *
1338363 AACTGTCCATAGGTC-CCAAAGAACCTAGGTA
1 AACTGTCCATATGTCTCCAAAGAACATAGGTA
* **
1338394 AACTATCCATATGT-TCCTTAGAACATAGGTA
1 AACTGTCCATATGTCTCCAAAGAACATAGGTA
*
1338425 AACTGTCCATATGTCTCGAAAG-ACATAGGTA
1 AACTGTCCATATGTCTCCAAAGAACATAGGTA
1338456 AAC
1 AAC
1338459 CCTCGACTCT
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
31 50 0.93
32 4 0.07
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (32 bp):
AACTGTCCATATGTCTCCAAAGAACATAGGTA
Found at i:1341582 original size:14 final size:14
Alignment explanation
Indices: 1341563--1341611 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
1341553 CGACTGAATG
1341563 AAAATAAAAATAAA
1 AAAATAAAAATAAA
1341577 AAAAT--AAATAAA
1 AAAATAAAAATAAA
*
1341589 ATAAATAAAAACAAA
1 A-AAATAAAAATAAA
*
1341604 TAAATAAA
1 AAAATAAA
1341612 TAAAAAAGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
12 8 0.27
13 4 0.13
14 12 0.40
15 6 0.20
ACGTcount: A:0.82, C:0.02, G:0.00, T:0.16
Consensus pattern (14 bp):
AAAATAAAAATAAA
Found at i:1341587 original size:4 final size:4
Alignment explanation
Indices: 1341570--1341615 Score: 51
Period size: 4 Copynumber: 11.8 Consensus size: 4
1341560 ATGAAAATAA
* *
1341570 AAAT AAAA AAAT AAAT AAAAT AAAT -AA- AAAC AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1341616 AAAGTATATT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
3 4 0.11
4 28 0.78
5 4 0.11
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.17
Consensus pattern (4 bp):
AAAT
Found at i:1341587 original size:18 final size:18
Alignment explanation
Indices: 1341568--1341617 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
1341558 GAATGAAAAT
1341568 AAAAATAAA-AAAATA-AA
1 AAAAATAAATAAAA-ACAA
*
1341585 TAAAATAAATAAAAACAA
1 AAAAATAAATAAAAACAA
*
1341603 ATAAATAAATAAAAA
1 AAAAATAAATAAAAA
1341618 AGTATATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 9 0.32
18 19 0.68
ACGTcount: A:0.82, C:0.02, G:0.00, T:0.16
Consensus pattern (18 bp):
AAAAATAAATAAAAACAA
Found at i:1341608 original size:27 final size:27
Alignment explanation
Indices: 1341564--1341616 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
1341554 GACTGAATGA
*
1341564 AAATAAAAATAAAAAAATAAATAAAAT
1 AAATAAAAACAAAAAAATAAATAAAAT
*
1341591 AAATAAAAACAAATAAATAAATAAAA
1 AAATAAAAACAAAAAAATAAATAAAA
1341617 AAGTATATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.17
Consensus pattern (27 bp):
AAATAAAAACAAAAAAATAAATAAAAT
Found at i:1341681 original size:38 final size:36
Alignment explanation
Indices: 1341631--1341717 Score: 97
Period size: 36 Copynumber: 2.4 Consensus size: 36
1341621 ATATTATAAA
* **
1341631 ATATA-TTTCAAAAACGTTTTGGAAGCCTATACA-TAT
1 ATATATTTTCAAAAACATTTT--AAAACTATACATTAT
*
1341667 GATATATTTTCAAAAACATTTTAAAACTATATATTAT
1 -ATATATTTTCAAAAACATTTTAAAACTATACATTAT
1341704 ATATATTTTCAAAA
1 ATATATTTTCAAAA
1341718 CTATATATTA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
36 22 0.50
37 8 0.18
38 14 0.32
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (36 bp):
ATATATTTTCAAAAACATTTTAAAACTATACATTAT
Found at i:1341717 original size:25 final size:25
Alignment explanation
Indices: 1341684--1341742 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
1341674 TTTCAAAAAC
*
1341684 ATTTT-AAAACTATATATTATATAT
1 ATTTTCAAAACTATATATTAGATAT
*
1341708 ATTTTCAAAACTATATATTAGGTAT
1 ATTTTCAAAACTATATATTAGATAT
1341733 ATTTTCAAAA
1 ATTTTCAAAA
1341743 TGTTTTCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 5 0.16
25 27 0.84
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (25 bp):
ATTTTCAAAACTATATATTAGATAT
Found at i:1341768 original size:2 final size:2
Alignment explanation
Indices: 1341756--1341787 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1341746 TTTCAAAAAC
1341756 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1341788 TCAAAATGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1341830 original size:39 final size:39
Alignment explanation
Indices: 1341767--1341853 Score: 129
Period size: 39 Copynumber: 2.2 Consensus size: 39
1341757 ATATTATATA
* * *
1341767 TATATATATATATATATATATTCAAAATGTTTTTAGAAAT
1 TATATAT-TATATATATATATTCAAAATGTTTTCAAAAAC
*
1341807 TATATATTATATATATATTTTCAAAATGTTTTCAAAAAC
1 TATATATTATATATATATATTCAAAATGTTTTCAAAAAC
1341846 TATATATT
1 TATATATT
1341854 TTCAAAACTA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
39 36 0.84
40 7 0.16
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (39 bp):
TATATATTATATATATATATTCAAAATGTTTTCAAAAAC
Found at i:1341849 original size:28 final size:28
Alignment explanation
Indices: 1341818--1341908 Score: 91
Period size: 28 Copynumber: 3.3 Consensus size: 28
1341808 ATATATTATA
1341818 TATATATTTTCAAAATGTTTTCAAAAAC
1 TATATATTTTCAAAATGTTTTCAAAAAC
* * *
1341846 TATATATTTTCAAAACTATATATT-ATATA-
1 TATATATTTTCAAAA-TGT-T-TTCAAAAAC
*
1341875 TATATA-TTT-GAAATGTTTTCAAAAAC
1 TATATATTTTCAAAATGTTTTCAAAAAC
1341901 TATATATT
1 TATATATT
1341909 ATATATATTT
Statistics
Matches: 50, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
24 2 0.04
25 4 0.08
26 8 0.16
27 4 0.08
28 18 0.36
29 8 0.16
30 4 0.08
31 2 0.04
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (28 bp):
TATATATTTTCAAAATGTTTTCAAAAAC
Found at i:1341862 original size:16 final size:17
Alignment explanation
Indices: 1341835--1341869 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
1341825 TTTCAAAATG
1341835 TTTTCAAAAACTATATA
1 TTTTCAAAAACTATATA
1341852 TTTTC-AAAACTATATA
1 TTTTCAAAAACTATATA
1341868 TT
1 TT
1341870 ATATATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (17 bp):
TTTTCAAAAACTATATA
Found at i:1341925 original size:94 final size:94
Alignment explanation
Indices: 1341709--1341956 Score: 307
Period size: 94 Copynumber: 2.7 Consensus size: 94
1341699 ATTATATATA
** * *
1341709 TTTTC-AAAACTATATATTAGGTATA-TTTTCAAAATGTTTTCAAAAAC--TATATTAT--ATA-
1 TTTTCAAAAACTATATATTATATATATTTTTCAAAATGTTTTCAAAAACTATATATTTTCAAAAC
1341767 TATATATATATATATATATATTCAAAATG
66 TATATATATATATATATATATTCAAAATG
* * *
1341796 TTTTTAGAAATTATATATTATATATATATTTTCAAAATGTTTTCAAAAACTATATATTTTCAAAA
1 TTTTCAAAAACTATATATTATATATAT-TTTTCAAAATGTTTTCAAAAACTATATATTTTCAAAA
**
1341861 CTATATAT-TATATATATATATTTGAAATG
65 CTATATATATATATATATATATTCAAAATG
*
1341890 TTTTCAAAAACTATATATTATATATATTTTTTCAAAATATTTTCAAAAGTA-TATATATTTTCAA
1 TTTTCAAAAACTATATATTATATATA-TTTTTCAAAATGTTTTCAAAA--ACTATATATTTTCAA
1341954 AAC
63 AAC
1341957 GTCTTCAAAA
Statistics
Matches: 137, Mismatches: 13, Indels: 14
0.84 0.08 0.09
Matches are distributed among these distances:
87 4 0.03
88 16 0.12
90 22 0.16
92 7 0.05
94 63 0.46
95 24 0.18
96 1 0.01
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (94 bp):
TTTTCAAAAACTATATATTATATATATTTTTCAAAATGTTTTCAAAAACTATATATTTTCAAAAC
TATATATATATATATATATATTCAAAATG
Found at i:1341933 original size:39 final size:38
Alignment explanation
Indices: 1341849--1341945 Score: 133
Period size: 39 Copynumber: 2.5 Consensus size: 38
1341839 CAAAAACTAT
*
1341849 ATATTTTCAAAACTATATATTATATATATATATTTGAA
1 ATATTTTCAAAACTATATATTATATATATATATTTAAA
* *
1341887 ATGTTTTCAAAAACTATATATTATATATAT-TTTTTCAAA
1 ATATTTTC-AAAACTATATATTATATATATATATTT-AAA
*
1341926 ATATTTTCAAAAGTATATAT
1 ATATTTTCAAAACTATATAT
1341946 ATTTTCAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
38 22 0.42
39 30 0.58
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.47
Consensus pattern (38 bp):
ATATTTTCAAAACTATATATTATATATATATATTTAAA
Done.