Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008935.1 Hibiscus syriacus cultivar Beakdansim tig00112253_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: 1775090
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 9
Found at i:1717939 original size:22 final size:23
Alignment explanation
Indices: 1717892--1717954 Score: 92
Period size: 22 Copynumber: 2.8 Consensus size: 23
1717882 TAAAAATATG
*
1717892 ATGTAATAAGTAGCGCTTGTATA
1 ATGTAATAGGTAGCGCTTGTATA
*
1717915 ATGTAATAGGTAGCG-TTTTATA
1 ATGTAATAGGTAGCGCTTGTATA
*
1717937 ATGTAATAGGTAGTGCTT
1 ATGTAATAGGTAGCGCTT
1717955 ATATTGTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
22 20 0.56
23 16 0.44
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.38
Consensus pattern (23 bp):
ATGTAATAGGTAGCGCTTGTATA
Found at i:1718396 original size:21 final size:20
Alignment explanation
Indices: 1718370--1718434 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 20
1718360 AAAAATATGA
1718370 TAATAGGTAGCGCTTATAATG
1 TAATAGGTAGCG-TTATAATG
*
1718391 TAATAGGTAGCGTT-TATATAA
1 TAATAGGTAGCGTTATA-AT-G
* *
1718412 TAATAGGTAGTGTTATATTG
1 TAATAGGTAGCGTTATAATG
1718432 TAA
1 TAA
1718435 AGTATCTATC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
19 2 0.05
20 7 0.19
21 26 0.70
22 2 0.05
ACGTcount: A:0.35, C:0.05, G:0.22, T:0.38
Consensus pattern (20 bp):
TAATAGGTAGCGTTATAATG
Found at i:1718822 original size:20 final size:21
Alignment explanation
Indices: 1718782--1718825 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1718772 TACATAACTT
* *
1718782 TAAAAAGTATCGATCCTTTTA
1 TAAAAAGGATCGATACTTTTA
1718803 TAAAAAGGATCGATAC-TTTA
1 TAAAAAGGATCGATACTTTTA
1718823 TAA
1 TAA
1718826 TATATTAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (21 bp):
TAAAAAGGATCGATACTTTTA
Found at i:1718871 original size:23 final size:23
Alignment explanation
Indices: 1718840--1718912 Score: 128
Period size: 23 Copynumber: 3.2 Consensus size: 23
1718830 TTAAGTAAAA
*
1718840 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
1718863 ATATAATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
1718886 ATATAATGTAATATGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
1718909 ATAT
1 ATAT
1718913 TGTAAAGTAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.34, C:0.08, G:0.21, T:0.37
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1723126 original size:3 final size:3
Alignment explanation
Indices: 1723118--1723144 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1723108 GAATTGGGTT
1723118 TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG
1723145 CCCAATATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:1724271 original size:29 final size:31
Alignment explanation
Indices: 1724218--1724293 Score: 81
Period size: 30 Copynumber: 2.5 Consensus size: 31
1724208 TTCCAAACCC
* *
1724218 CTGTTTTTGCT-GTTTGATACTTTAAA-TTT
1 CTGTTTTTGCTATTTTAATACTTTAAACTTT
1724247 CTGTTTTTGCTATTTTAATAC-TTAAAGCTTT
1 CTGTTTTTGCTATTTTAATACTTTAAA-CTTT
1724278 -TGTTTTCT-CTATTTTA
1 CTGTTTT-TGCTATTTTA
1724294 GTCTTTATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
29 16 0.39
30 21 0.51
31 4 0.10
ACGTcount: A:0.18, C:0.12, G:0.11, T:0.59
Consensus pattern (31 bp):
CTGTTTTTGCTATTTTAATACTTTAAACTTT
Found at i:1726913 original size:8 final size:7
Alignment explanation
Indices: 1726887--1726976 Score: 68
Period size: 6 Copynumber: 13.4 Consensus size: 7
1726877 AGATCAACAT
1726887 TTTTGCA
1 TTTTGCA
*
1726894 -TCTGCA
1 TTTTGCA
1726900 -TTTGCA
1 TTTTGCA
1726906 TCTTTGCA
1 T-TTTGCA
1726914 TTTTGCA
1 TTTTGCA
*
1726921 -TCTGCA
1 TTTTGCA
1726927 -TTTGCA
1 TTTTGCA
1726933 TATTTGCA
1 T-TTTGCA
1726941 TTTTGCA
1 TTTTGCA
* *
1726948 -TCTACA
1 TTTTGCA
1726954 -TTTGCA
1 TTTTGCA
1726960 TCTTTGCA
1 T-TTTGCA
1726968 TTTT-CA
1 TTTTGCA
1726974 TTT
1 TTT
1726977 ATTTTTAAAC
Statistics
Matches: 69, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
6 33 0.48
7 15 0.22
8 21 0.30
ACGTcount: A:0.17, C:0.20, G:0.12, T:0.51
Consensus pattern (7 bp):
TTTTGCA
Found at i:1726923 original size:27 final size:27
Alignment explanation
Indices: 1726887--1726971 Score: 152
Period size: 27 Copynumber: 3.1 Consensus size: 27
1726877 AGATCAACAT
1726887 TTTTGCATCTGCATTTGCATCTTTGCA
1 TTTTGCATCTGCATTTGCATCTTTGCA
*
1726914 TTTTGCATCTGCATTTGCATATTTGCA
1 TTTTGCATCTGCATTTGCATCTTTGCA
*
1726941 TTTTGCATCTACATTTGCATCTTTGCA
1 TTTTGCATCTGCATTTGCATCTTTGCA
1726968 TTTT
1 TTTT
1726972 CATTTATTTT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 55 1.00
ACGTcount: A:0.16, C:0.20, G:0.13, T:0.51
Consensus pattern (27 bp):
TTTTGCATCTGCATTTGCATCTTTGCA
Found at i:1727326 original size:175 final size:176
Alignment explanation
Indices: 1727035--1727384 Score: 693
Period size: 175 Copynumber: 2.0 Consensus size: 176
1727025 TATAAAATGG
1727035 TCCTAACCATGTGACACCACATAGAAGCAAGAAGTTGAAATCAATACAGTGGGAGCTTGTTCAGC
1 TCCTAACCATGTGACACCACATAGAAGCAAGAAGTTGAAATCAATACAGTGGGAGCTTGTTCAGC
1727100 TGATTGTAGGATTGAGCCTTCCAGAGTGATCTGAGAAAAGAATCCCCATATCCCGAGGGTTACGA
66 TGATTGTAGGATTGAGCCTTCCAGAGTGATCTGAGAAAAGAATCCCCATATCCCGAGGGTTACGA
1727165 TGTTGATATCATGCACAATTACCACATAGGAAGTTCA-GACATTCT
131 TGTTGATATCATGCACAATTACCACATAGGAAGTTCATGACATTCT
1727210 TCCTAACCATGTGACACCACATAGAAGCAAGAAGTTGAAATCAATACAGTGGGAGCTTGTTCAGC
1 TCCTAACCATGTGACACCACATAGAAGCAAGAAGTTGAAATCAATACAGTGGGAGCTTGTTCAGC
1727275 TGATTGTAGGATTGAGCCTTCCAGAGTGATCTGAGAAAAGAATCCCCATATCCCGAGGGTTACGA
66 TGATTGTAGGATTGAGCCTTCCAGAGTGATCTGAGAAAAGAATCCCCATATCCCGAGGGTTACGA
1727340 TGTTGATATCATGCACAATTACCACATAGGAAGTTCATGACATTC
131 TGTTGATATCATGCACAATTACCACATAGGAAGTTCATGACATTC
1727385 CTCTGAGAAT
Statistics
Matches: 174, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
175 167 0.96
176 7 0.04
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.25
Consensus pattern (176 bp):
TCCTAACCATGTGACACCACATAGAAGCAAGAAGTTGAAATCAATACAGTGGGAGCTTGTTCAGC
TGATTGTAGGATTGAGCCTTCCAGAGTGATCTGAGAAAAGAATCCCCATATCCCGAGGGTTACGA
TGTTGATATCATGCACAATTACCACATAGGAAGTTCATGACATTCT
Found at i:1729439 original size:15 final size:15
Alignment explanation
Indices: 1729420--1729449 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1729410 AGAAGCAAAA
1729420 AAAAAAAAACAAAAGC
1 AAAAAAAAA-AAAAGC
1729436 AAAAAAAAAAAAAG
1 AAAAAAAAAAAAAG
1729450 ATCAGATGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.87, C:0.07, G:0.07, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAGC
Found at i:1731145 original size:24 final size:24
Alignment explanation
Indices: 1731110--1731177 Score: 79
Period size: 24 Copynumber: 2.9 Consensus size: 24
1731100 AGAGAGGGGC
1731110 AATA-TTTTCAAAACTTTTGACTA
1 AATATTTTTCAAAACTTTTGACTA
*
1731133 AATATTTTTCAAAACTCTT--CTA
1 AATATTTTTCAAAACTTTTGACTA
*
1731155 ATTGATATTTTCAAAACTTTTGA
1 AAT-AT-TTTTCAAAACTTTTGA
1731178 AAATAAAAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
22 5 0.14
23 6 0.16
24 26 0.70
ACGTcount: A:0.37, C:0.13, G:0.04, T:0.46
Consensus pattern (24 bp):
AATATTTTTCAAAACTTTTGACTA
Found at i:1731366 original size:32 final size:32
Alignment explanation
Indices: 1731299--1731410 Score: 160
Period size: 32 Copynumber: 3.6 Consensus size: 32
1731289 AGCAATAGAG
* *
1731299 GGCATCTTTGAAGATTCAACATC-AATGTTGG
1 GGCATCTTTGGAGATTCAACATCAAATGTTGT
*
1731330 GGCATCTTTAGAGATTCAACATCAAATGTTGT
1 GGCATCTTTGGAGATTCAACATCAAATGTTGT
1731362 GGCATCTTTGGAGATTCAACATCAAAATG-T-T
1 GGCATCTTTGGAGATTCAACATC-AAATGTTGT
1731393 -GCATCTTTGGAGATTCAA
1 GGCATCTTTGGAGATTCAA
1731411 TATCGAATAT
Statistics
Matches: 75, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
30 18 0.24
31 22 0.29
32 30 0.40
33 5 0.07
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (32 bp):
GGCATCTTTGGAGATTCAACATCAAATGTTGT
Found at i:1731428 original size:62 final size:60
Alignment explanation
Indices: 1731292--1731428 Score: 150
Period size: 62 Copynumber: 2.2 Consensus size: 60
1731282 GTGCTGAAGC
*
1731292 AATAGAGGGCATCTTTGAAGATTCAACATCAATGTTGGGGCATCTTTAGAGATTCAACATCA
1 AATATAGGGCATCTTTGAAGATTCAACATCAATGTT--GGCATCTTTAGAGATTCAACATCA
* * * * * *
1731354 AATGTTGTGGCATCTTTGGAGATTCAACATCAAAATGTT-GCATCTTTGGAGATTCAATATCG
1 AATATAG-GGCATCTTTGAAGATTCAACATC--AATGTTGGCATCTTTAGAGATTCAACATCA
1731416 AATATAAGGGCAT
1 AATAT-AGGGCAT
1731429 TCGATATCCT
Statistics
Matches: 62, Mismatches: 9, Indels: 8
0.78 0.11 0.10
Matches are distributed among these distances:
62 33 0.53
63 23 0.37
65 6 0.10
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (60 bp):
AATATAGGGCATCTTTGAAGATTCAACATCAATGTTGGCATCTTTAGAGATTCAACATCA
Found at i:1731577 original size:34 final size:34
Alignment explanation
Indices: 1731537--1731640 Score: 181
Period size: 34 Copynumber: 3.1 Consensus size: 34
1731527 AAAAAAAATT
1731537 TTTTGTCTCACTTGAGATAATTTCTCAAAACAAA
1 TTTTGTCTCACTTGAGATAATTTCTCAAAACAAA
* *
1731571 TTTTGTCTCACTTGAGACACTTTCTCAAAACAAA
1 TTTTGTCTCACTTGAGATAATTTCTCAAAACAAA
*
1731605 TTTCGTCTCACTTGAGATAATTTCTCAAAACAAA
1 TTTTGTCTCACTTGAGATAATTTCTCAAAACAAA
1731639 TT
1 TT
1731641 CCGTCTCGTT
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 65 1.00
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.38
Consensus pattern (34 bp):
TTTTGTCTCACTTGAGATAATTTCTCAAAACAAA
Found at i:1731646 original size:34 final size:34
Alignment explanation
Indices: 1731541--1731661 Score: 179
Period size: 34 Copynumber: 3.6 Consensus size: 34
1731531 AAAATTTTTT
* *
1731541 GTCTCACTTGAGATAATTTCTCAAAACAAATTTT
1 GTCTCACTTGAGACAATTTCTCAAAACAAATTTC
*
1731575 GTCTCACTTGAGACACTTTCTCAAAACAAATTTC
1 GTCTCACTTGAGACAATTTCTCAAAACAAATTTC
* *
1731609 GTCTCACTTGAGATAATTTCTCAAAACAAATTCC
1 GTCTCACTTGAGACAATTTCTCAAAACAAATTTC
**
1731643 GTCTCGTTTGAGACAATTT
1 GTCTCACTTGAGACAATTT
1731662 TTCTCTGAGA
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 78 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (34 bp):
GTCTCACTTGAGACAATTTCTCAAAACAAATTTC
Found at i:1731947 original size:76 final size:74
Alignment explanation
Indices: 1731826--1731969 Score: 180
Period size: 76 Copynumber: 1.9 Consensus size: 74
1731816 GTTTCATTTG
* * * * * *
1731826 AAACAAAGTTGTCTCACTTGAGACTGTTTTACTTGAAAGAAGACATTTCATTTGACTCAAGATTG
1 AAACAAAGTTGTCTCACTGGAGACTATTTTACTTAAAACAAGACATTTCATTTCACTCAAGATAG
1731891 TTTTTCTCA
66 TTTTTCTCA
* * * *
1731900 AAACAAGATTTGTCTCGCTGGAGACATATTTTATTTAAAACAAGACATTTTATTTCACTCAAGAT
1 AAACAA-AGTTGTCTCACTGGAGAC-TATTTTACTTAAAACAAGACATTTCATTTCACTCAAGAT
1731965 AGTTT
64 AGTTT
1731970 CCCTCGAAAC
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
74 6 0.10
75 15 0.26
76 37 0.64
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (74 bp):
AAACAAAGTTGTCTCACTGGAGACTATTTTACTTAAAACAAGACATTTCATTTCACTCAAGATAG
TTTTTCTCA
Found at i:1732029 original size:36 final size:36
Alignment explanation
Indices: 1731984--1732200 Score: 355
Period size: 36 Copynumber: 6.0 Consensus size: 36
1731974 CGAAACAGAA
1731984 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGGAAA-
1 AAATTTTGTCTCCCTTGAGACAGTTTCCCTT-GAAAC
1732020 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
1 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
*
1732056 AAATTTTGTCTCCCTTGAGACGGTTTCCCTTGAAAC
1 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
1732092 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
1 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
* * * *
1732128 ATATTTTGTCTCTCTTGAGACGGTTTCACTTGAAAC
1 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
* *
1732164 AAATTTTGTCTCCCTTGAGACAATTTCACTTGAAAC
1 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
1732200 A
1 A
1732201 GAAGATTGTA
Statistics
Matches: 170, Mismatches: 10, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
35 4 0.02
36 166 0.98
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (36 bp):
AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
Found at i:1732071 original size:21 final size:21
Alignment explanation
Indices: 1732045--1732109 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
1732035 TGAGACAGTT
1732045 TCCCTTGAAACAAATTTTGTC
1 TCCCTTGAAACAAATTTTGTC
* * *
1732066 TCCCTTGAGAC------GGTT
1 TCCCTTGAAACAAATTTTGTC
1732081 TCCCTTGAAACAAATTTTGTC
1 TCCCTTGAAACAAATTTTGTC
1732102 TCCCTTGA
1 TCCCTTGA
1732110 GACAGTTTCC
Statistics
Matches: 32, Mismatches: 6, Indels: 12
0.64 0.12 0.24
Matches are distributed among these distances:
15 12 0.38
21 20 0.62
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.37
Consensus pattern (21 bp):
TCCCTTGAAACAAATTTTGTC
Found at i:1732231 original size:39 final size:39
Alignment explanation
Indices: 1731965--1732287 Score: 235
Period size: 36 Copynumber: 8.6 Consensus size: 39
1731955 CACTCAAGAT
* * * * *
1731965 AGTTTCCCTCGAAACAGAAAAATTTTGTCTCCCTTGAGAC
1 AGTTTCACTTGAAACAG-AAGATTTTATCTCGCTTGAGAC
* * * *
1732005 AGTTTCCCTTGGAA-A-AA-ATTTTGTCTCCCTTGAGAC
1 AGTTTCACTTGAAACAGAAGATTTTATCTCGCTTGAGAC
* * *
1732041 AGTTTCCCTTGAAAC--AA-ATTTTGTCTCCCTTGAGAC
1 AGTTTCACTTGAAACAGAAGATTTTATCTCGCTTGAGAC
* * * *
1732077 GGTTTCCCTTGAAAC--AA-ATTTTGTCTCCCTTGAGAC
1 AGTTTCACTTGAAACAGAAGATTTTATCTCGCTTGAGAC
* * * *
1732113 AGTTTCCCTTGAAAC---ATATTTTGTCTCTCTTGAGAC
1 AGTTTCACTTGAAACAGAAGATTTTATCTCGCTTGAGAC
* * *
1732149 GGTTTCACTTGAAAC--AA-ATTTTGTCTCCCTTGAGAC
1 AGTTTCACTTGAAACAGAAGATTTTATCTCGCTTGAGAC
* * *
1732185 AATTTCACTTGAAACAGAAGATTGTATCTCGCTTGAGAT
1 AGTTTCACTTGAAACAGAAGATTTTATCTCGCTTGAGAC
* * *
1732224 TGTTTCACTTGAAACAGAAGATTTTAGCTCGCTTGAGAT
1 AGTTTCACTTGAAACAGAAGATTTTATCTCGCTTGAGAC
* * * *
1732263 AGTTTCGCTCGAAACACAATATTTT
1 AGTTTCACTTGAAACAGAAGATTTT
1732288 TAGAAACTAA
Statistics
Matches: 253, Mismatches: 24, Indels: 13
0.87 0.08 0.04
Matches are distributed among these distances:
35 1 0.00
36 164 0.65
37 3 0.01
38 2 0.01
39 71 0.28
40 12 0.05
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (39 bp):
AGTTTCACTTGAAACAGAAGATTTTATCTCGCTTGAGAC
Found at i:1732376 original size:43 final size:43
Alignment explanation
Indices: 1732309--1732646 Score: 369
Period size: 43 Copynumber: 7.6 Consensus size: 43
1732299 CCTGATTTTC
* * *
1732309 AGGGGTTTCTTGAAGAAAATCTTGAGAGACCATCGTGATATGT
1 AGGGGTTTCTTGATGACAAGCTTGAGAGACCATCGTGATATGT
*
1732352 AGGGGTTTCTTGAGGACAAGCTTGA-AGGACCATCGTGATATGT
1 AGGGGTTTCTTGATGACAAGCTTGAGA-GACCATCGTGATATGT
*
1732395 AGGGGTTCCTTGATGACAAGCTTGA-AGGACCATCGTGATATGT
1 AGGGGTTTCTTGATGACAAGCTTGAGA-GACCATCGTGATATGT
*
1732438 AGGGG-TTCTTTGATGACAAGCTTGAGAAACCATCGTGATATGT
1 AGGGGTTTC-TTGATGACAAGCTTGAGAGACCATCGTGATATGT
* *
1732481 AGGGGTTTCTTGATGAAAAGCTTGAGGGACCATCGTGATATGT
1 AGGGGTTTCTTGATGACAAGCTTGAGAGACCATCGTGATATGT
* * *
1732524 AGGGGTTCCTTGATGACAAACTTGATTACACACTTGAAGGACCATCGTAATATGT
1 AGGGGTTTCTTGATGACAAGCTTG-------A---G-A-GACCATCGTGATATGT
*
1732579 AGGGG-TTCTTCGATGACAAGCTTGAGAAACCATCGTGATATGT
1 AGGGGTTTCTT-GATGACAAGCTTGAGAGACCATCGTGATATGT
* * *
1732622 AGGGGTTTCTTAATGAAAAACTTGA
1 AGGGGTTTCTTGATGACAAGCTTGA
1732647 TGAACACTTA
Statistics
Matches: 255, Mismatches: 22, Indels: 36
0.81 0.07 0.12
Matches are distributed among these distances:
42 3 0.01
43 202 0.79
44 10 0.04
45 1 0.00
48 1 0.00
50 1 0.00
53 1 0.00
54 4 0.02
55 32 0.13
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.29
Consensus pattern (43 bp):
AGGGGTTTCTTGATGACAAGCTTGAGAGACCATCGTGATATGT
Found at i:1732577 original size:55 final size:53
Alignment explanation
Indices: 1732501--1732694 Score: 196
Period size: 55 Copynumber: 3.8 Consensus size: 53
1732491 TGATGAAAAG
*
1732501 CTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAACTTGATTACACA
1 CTTGAAGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAACTTGA-TA-ACA
* *
1732556 CTTGAAGGACCATCGTAATATGTAGGGGTT-CTTCGATGACAAGCTTG-----A
1 CTTGAAGGACCATCGTGATATGTAGGGGTTCCTT-GATGACAAACTTGATAACA
* * *
1732604 ---GAA--ACCATCGTGATATGTAGGGGTTTCTTAATGAAAAACTTGATGAACA
1 CTTGAAGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAACTTGAT-AACA
*
1732653 CTT-AAGGGACCATCGTGATATGTAGGGGTTCCTTGGTGACAA
1 CTTGAA-GGACCATCGTGATATGTAGGGGTTCCTTGATGACAA
1732695 TTAAGAAACT
Statistics
Matches: 114, Mismatches: 11, Indels: 29
0.74 0.07 0.19
Matches are distributed among these distances:
43 31 0.27
44 3 0.03
45 3 0.03
48 1 0.01
49 1 0.01
51 2 0.02
54 33 0.29
55 40 0.35
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (53 bp):
CTTGAAGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAACTTGATAACA
Found at i:1732594 original size:98 final size:96
Alignment explanation
Indices: 1732466--1732683 Score: 321
Period size: 98 Copynumber: 2.2 Consensus size: 96
1732456 AGCTTGAGAA
**
1732466 ACCATCGTGATATGTAGGGGTTTCTTGATGAAAAGCTTGAGGGACCATCGTGATATGTAGGGGTT
1 ACCATCGTGATATGTAGGGG-TTCTTGATGAAAAGCTTGAGAAACCATCGTGATATGTAGGGGTT
* * *
1732531 CCTTGATGACAAACTTGATTACACACTTGAA-GG
65 CCTTAATGAAAAACTTGATGA-ACACTT-AAGGG
* *
1732564 ACCATCGTAATATGTAGGGGTTCTTCGATGACAAGCTTGAGAAACCATCGTGATATGTAGGGGTT
1 ACCATCGTGATATGTAGGGGTTCTT-GATGAAAAGCTTGAGAAACCATCGTGATATGTAGGGGTT
*
1732629 TCTTAATGAAAAACTTGATGAACACTTAAGGG
65 CCTTAATGAAAAACTTGATGAACACTTAAGGG
1732661 ACCATCGTGATATGTAGGGGTTC
1 ACCATCGTGATATGTAGGGGTTC
1732684 CTTGGTGACA
Statistics
Matches: 109, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
96 2 0.02
97 35 0.32
98 72 0.66
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (96 bp):
ACCATCGTGATATGTAGGGGTTCTTGATGAAAAGCTTGAGAAACCATCGTGATATGTAGGGGTTC
CTTAATGAAAAACTTGATGAACACTTAAGGG
Found at i:1732855 original size:91 final size:90
Alignment explanation
Indices: 1732696--1733014 Score: 521
Period size: 90 Copynumber: 3.5 Consensus size: 90
1732686 TGGTGACAAT
*
1732696 TAAGAAACTGAGCCTTCGGGGGTTTCTTGATTTTTATGTCCTTCGGGCCATCCATAAGACCTTCA
1 TAAGAAACTGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCA
*
1732761 GTGCAGAATGTTTTCAAATGAGATC
66 GTGCAGGATGTTTTCAAATGAGATC
* * *
1732786 TAAGAAACTAAGTCTTCGGGGGTTTCTTGATTTTTTAAGTCCTTCGGGCCATCCATAAGACCTTT
1 TAAGAAACTGAGCCTTCGGGGGTTTCTTGA-TTTTTAAGTCCTTCGGGCCATCCATAAGACCTTC
* *
1732851 AGTGCAGGATGTTTTTAAATGAAATC
65 AGTGCAGGATGTTTTCAAATGAGATC
* * * *
1732877 TAAGAAACTCAGCCTTCGGGAGCTTCTTGATTTTTAAGTCCTTCGGGTCATCCATAAGACCTTCA
1 TAAGAAACTGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCA
1732942 GTGCAGGATGTTTTCAAATGAGATC
66 GTGCAGGATGTTTTCAAATGAGATC
*
1732967 TAAGAAATTGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCGGGC
1 TAAGAAACTGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCGGGC
1733015 AGAATGTTTT
Statistics
Matches: 208, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
90 127 0.61
91 81 0.39
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.34
Consensus pattern (90 bp):
TAAGAAACTGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCA
GTGCAGGATGTTTTCAAATGAGATC
Found at i:1733314 original size:6 final size:6
Alignment explanation
Indices: 1733303--1733329 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1733293 GCCCACCAAT
1733303 CCAGAC CCAGAC CCAGAC CCAGAC CCA
1 CCAGAC CCAGAC CCAGAC CCAGAC CCA
1733330 ATTGCAGCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
CCAGAC
Found at i:1734723 original size:14 final size:15
Alignment explanation
Indices: 1734689--1734729 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
1734679 ACGCAGATCA
1734689 ATTTGTCTTAAAAATG
1 ATTT-TCTTAAAAATG
*
1734705 ATTTTCTTAAAATTG
1 ATTTTCTTAAAAATG
1734720 -TTTT-TTAAAA
1 ATTTTCTTAAAA
1734730 GACGTTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 6 0.25
14 4 0.17
15 10 0.42
16 4 0.17
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (15 bp):
ATTTTCTTAAAAATG
Found at i:1734956 original size:18 final size:18
Alignment explanation
Indices: 1734917--1734950 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1734907 AAATAATGTC
1734917 AAAA-AAATAAAATAAAA
1 AAAAGAAATAAAATAAAA
*
1734934 AAAAGAAATAAATTAAA
1 AAAAGAAATAAAATAAA
1734951 TTAAAGGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (18 bp):
AAAAGAAATAAAATAAAA
Found at i:1735725 original size:9 final size:9
Alignment explanation
Indices: 1735711--1735751 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
1735701 ACCGTGGTTC
1735711 GATGTTGTT
1 GATGTTGTT
1735720 GATGTTGTT
1 GATGTTGTT
*
1735729 AATGTTGTT
1 GATGTTGTT
1735738 G-TGTT-TGT
1 GATGTTGT-T
1735746 GATGTT
1 GATGTT
1735752 CTCTCGGTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
7 1 0.04
8 6 0.21
9 21 0.75
ACGTcount: A:0.12, C:0.00, G:0.32, T:0.56
Consensus pattern (9 bp):
GATGTTGTT
Found at i:1736249 original size:20 final size:21
Alignment explanation
Indices: 1736204--1736255 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
1736194 CCAAACTGAA
1736204 AAATAAAAA-ATAAAAAGGAAT
1 AAATAAAAATATAAAAA-GAAT
* *
1736225 TAATAAAAATATAAACA-AAT
1 AAATAAAAATATAAAAAGAAT
*
1736245 AAATAATAATA
1 AAATAAAAATA
1736256 ATAATAATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 12 0.46
21 8 0.31
22 6 0.23
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.21
Consensus pattern (21 bp):
AAATAAAAATATAAAAAGAAT
Found at i:1736438 original size:36 final size:36
Alignment explanation
Indices: 1736279--1736648 Score: 253
Period size: 36 Copynumber: 10.6 Consensus size: 36
1736269 AAAAAAGAAA
* *
1736279 TTTAAAACTATATATTGTATATAATTTTTTTAAAA-G-T
1 TTTAAAACTATATA-T-TATATAA-ATTTTCAAAATGTT
* * *
1736316 TTTCAAAC--TATATTATA-AACTTTTCAAAACG-T
1 TTTAAAACTATATATTATATAAATTTTCAAAATGTT
** *
1736348 TTTAAAAAAATCATATATATATACATTTTCAAAATGCTTT
1 TTTAAAACTAT-ATAT-TATATAAATTTTCAAAATG--TT
* *
1736388 TTTAAAACTATATATTATATAAATTTTTAAAATGAT
1 TTTAAAACTATATATTATATAAATTTTCAAAATGTT
* * *
1736424 TTCAAAACAATATA-T-TATAAGTTTTCCAAAATGTT
1 TTTAAAACTATATATTATATAAATTTT-CAAAATGTT
* *
1736459 TTAAAAAC--TATA-TATGT---TTTT-AAAATG-T
1 TTTAAAACTATATATTATATAAATTTTCAAAATGTT
*
1736487 TTTAAAACTATATATTATAT--ATTTTCAAAATATT
1 TTTAAAACTATATATTATATAAATTTTCAAAATGTT
*
1736521 TTTAAAAAC-ATATA-TATAT-AATTTTTAAATAT-TT
1 TTT-AAAACTATATATTATATAAATTTTCAAA-ATGTT
* * *
1736555 TTAAAAACTATATATTATATATAGTTTCAAAATGTT
1 TTTAAAACTATATATTATATAAATTTTCAAAATGTT
* **
1736591 TTAAAAACTATATATTATATATGTTTTCAAAATGCTT
1 TTTAAAACTATATATTATATAAATTTTCAAAATG-TT
** *
1736628 TCAAAAACTATACATTATATA
1 TTTAAAACTATATATTATATA
1736649 TGTTAAAAAT
Statistics
Matches: 276, Mismatches: 32, Indels: 50
0.77 0.09 0.14
Matches are distributed among these distances:
28 8 0.03
29 6 0.02
30 4 0.01
31 16 0.06
32 14 0.05
33 24 0.09
34 39 0.14
35 37 0.13
36 58 0.21
37 39 0.14
38 17 0.06
39 4 0.01
40 10 0.04
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (36 bp):
TTTAAAACTATATATTATATAAATTTTCAAAATGTT
Found at i:1736466 original size:35 final size:33
Alignment explanation
Indices: 1736324--1736646 Score: 273
Period size: 36 Copynumber: 9.3 Consensus size: 33
1736314 GTTTTCAAAC
* *
1736324 TATATTATAAACTTTTCAAAACGTTTTAAAAAAATCA
1 TATATTAT-AA-TTTTCAAAATGTTTT-AAAAACT-A
*
1736361 TATATATATACATTTTCAAAATGCTTTTTTAAAACTA
1 TATAT-TATA-ATTTTCAAAATG--TTTTAAAAACTA
* * * *
1736398 TATATTATATAAATTTTTAAAATGATTTCAAAACAA
1 TATA-T-TAT-AATTTTCAAAATGTTTTAAAAACTA
1736434 TATATTATAAGTTTTCCAAAATGTTTTAAAAACTA
1 TATATTATAA-TTTT-CAAAATGTTTTAAAAACTA
*
1736469 TATA-TGT--TTTT-AAAATGTTTT-AAAACTA
1 TATATTATAATTTTCAAAATGTTTTAAAAACTA
*
1736497 TATATTATATATTTTCAAAATATTTTTAAAAAC-A
1 TATATTATA-ATTTTCAAAAT-GTTTTAAAAACTA
*
1736531 TATATATATAATTTTTAAATAT-TTTTAAAAACTA
1 TATAT-TATAATTTTCAAA-ATGTTTTAAAAACTA
1736565 TATATTATATATAGTTTCAAAATGTTTTAAAAACTA
1 TATATTATA-AT--TTTCAAAATGTTTTAAAAACTA
*
1736601 TATATTATATATGTTTTCAAAATGCTTTCAAAAACTA
1 TATATTATA-A--TTTTCAAAATG-TTTTAAAAACTA
*
1736638 TACATTATA
1 TATATTATA
1736647 TATGTTAAAA
Statistics
Matches: 243, Mismatches: 18, Indels: 50
0.78 0.06 0.16
Matches are distributed among these distances:
28 11 0.05
29 12 0.05
31 4 0.02
32 4 0.02
33 21 0.09
34 35 0.14
35 33 0.14
36 52 0.21
37 40 0.16
38 26 0.11
39 5 0.02
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (33 bp):
TATATTATAATTTTCAAAATGTTTTAAAAACTA
Found at i:1736478 original size:30 final size:28
Alignment explanation
Indices: 1736439--1736501 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
1736429 AACAATATAT
*
1736439 TATAAGTTTTCCAAAATGTTTTAAAAACTA
1 TATATGTTTT-CAAAATGTTTT-AAAACTA
*
1736469 TATATGTTTTTAAAATGTTTTAAAACTA
1 TATATGTTTTCAAAATGTTTTAAAACTA
1736497 TATAT
1 TATAT
1736502 TATATATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 12 0.39
29 10 0.32
30 9 0.29
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.46
Consensus pattern (28 bp):
TATATGTTTTCAAAATGTTTTAAAACTA
Found at i:1736597 original size:132 final size:136
Alignment explanation
Indices: 1736360--1736605 Score: 346
Period size: 132 Copynumber: 1.8 Consensus size: 136
1736350 TAAAAAAATC
* *
1736360 ATATATATATACATTTTCAAAATGCTTTTTTAAAACTATATATTATATAAATTTTTAAAATGATT
1 ATATATATATACATTTTCAAAATGATTTTTAAAAACTATATATTATATAAATTTTTAAAATGATT
*
1736425 TCAAAACAATATATTATAAGTTTTCCAAAATGTTTTAAAAACTATATATGTTTTTAAAATGTTTT
66 TAAAAACAATATATTATAAGTTTTCCAAAATGTTTTAAAAACTATATATGTTTTTAAAATGTTTT
1736490 AAAACT
131 AAAACT
* *
1736496 ATATAT-TATATATTTTCAAAAT-ATTTTTAAAAAC-ATATA-TATAT-AATTTTTAAATAT-TT
1 ATATATATATACATTTTCAAAATGATTTTTAAAAACTATATATTATATAAATTTTTAAA-ATGAT
*
1736555 TTAAAAACTATATATTATATA-TAGTTT-CAAAATGTTTTAAAAACTATATAT
65 TTAAAAACAATATATTATA-AGT--TTTCCAAAATGTTTTAAAAACTATATAT
1736606 TATATATGTT
Statistics
Matches: 100, Mismatches: 6, Indels: 12
0.85 0.05 0.10
Matches are distributed among these distances:
131 29 0.29
132 32 0.32
133 8 0.08
134 10 0.10
135 15 0.15
136 6 0.06
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (136 bp):
ATATATATATACATTTTCAAAATGATTTTTAAAAACTATATATTATATAAATTTTTAAAATGATT
TAAAAACAATATATTATAAGTTTTCCAAAATGTTTTAAAAACTATATATGTTTTTAAAATGTTTT
AAAACT
Found at i:1736675 original size:2 final size:2
Alignment explanation
Indices: 1736668--1736698 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1736658 TCATTTGCAA
1736668 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1736699 AAAAAATACG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1737437 original size:84 final size:84
Alignment explanation
Indices: 1737235--1738403 Score: 1574
Period size: 84 Copynumber: 13.9 Consensus size: 84
1737225 TTCTTGACAT
* * * * * * * *
1737235 ATAACCCTTCTTGCCTTGAGCTATACTGTAAATTTGATTTGCCTCTGAGTTAAATGTAATTGAAC
1 ATAACCCTTCTTGCCTTGAGCTATGCTGCAAA--TGATGTGCCTTTGAGCTGAGTGTAATCGAAC
* ** *
1737300 TCGAAGTTC-TTTCATGACAG
64 TCGAAGGTCTTTTGTTGGCAG
* *
1737320 ATAACCCTTCTCGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
1 ATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
*
1737385 GAAGGTCTTTTGTTGACAG
66 GAAGGTCTTTTGTTGGCAG
* * ** * * *
1737404 ATAACCCTT-TTCGCCTTAAGCTATGTTATAAATGATGTGCATTTGAGCTGAGTGTAATTGAAAT
1 ATAACCCTTCTT-GCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACT
1737468 CGAAGGTCTTTTGTTGGCAG
65 CGAAGGTCTTTTGTTGGCAG
* * * *
1737488 ATAACCCTTCTTGCCTTGAGTTATGCTGTAAATGATGTGCCTTTGAGCTAAGTGCAATCGAACTC
1 ATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
*
1737553 GAAGGTATTTTGTTGGCAG
66 GAAGGTCTTTTGTTGGCAG
* *
1737572 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGTCTTTGAGCTGAGTGTAATCGAACTC
1 ATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
1737637 GAAGGTCTTTTGTTGGCAG
66 GAAGGTCTTTTGTTGGCAG
* * * * *
1737656 ATAACCCTTCTTG-CTTGAGCTATGCTAC-AATAATGTGCCTTTGAGCTGAATATTATCGAACTC
1 ATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
*
1737719 GAAGGGCTTTTGTTGGCAG
66 GAAGGTCTTTTGTTGGCAG
* *
1737738 ATAACCCTTCTTGCCTTGGGCTATACTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
1 ATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
* * *
1737803 GAAGATCTTTTATTGGTAG
66 GAAGGTCTTTTGTTGGCAG
* * * *
1737822 ATAACCCTTCTTGCCTTGAGCTATTCTACAAATAATGTGCCTTTGAGCTGAGTGTAATCGAACTT
1 ATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
*
1737887 GAAGGTCTTTTGTTGGAAG
66 GAAGGTCTTTTGTTGGCAG
* * * *
1737906 ATAGCCCTTCTTGCCTTGAGTTATGCTACAAATGATGTTCCTTTGAGCTGAGTGTAATCGAACTC
1 ATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
* * *
1737971 TAAGGTCTTTTGGTGGTAG
66 GAAGGTCTTTTGTTGGCAG
* * * *
1737990 ATATCCCTTCTTGCCTTGAGCTATGCTACAAATGACGTGCCTTTGAACTGAGTGTAATCGAACTC
1 ATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
* * *
1738055 AAAAGTCTTTTTTTGGCAG
66 GAAGGTCTTTTGTTGGCAG
* * *
1738074 ATAACCCTTCTTGCCTTGAGCTATACTGCAAATGATATGCCTTTGACCTGAGTGTAATCGAACTC
1 ATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
* * *
1738139 GAAGGACTTTTGATGGAAG
66 GAAGGTCTTTTGTTGGCAG
* ** *
1738158 ATAGCCCTTCTTTTCTTGAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGTGTAATCGAACTC
1 ATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
*
1738223 AAAGGTCTTTTGTTGGCAG
66 GAAGGTCTTTTGTTGGCAG
* *
1738242 ATAACCCTTCTTGCCTTGAGCTAT-ATGCAAATGATGTGCCTTTGGGCTGAGTGTAATCGAACTC
1 ATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
1738306 GAAGGTCTTTTGTTGGCAG
66 GAAGGTCTTTTGTTGGCAG
* * * * * *
1738325 ATAATCATTCTTTCCTTGAGCTATACTGCAAATGATGTTCCTTTGAGCTGAGTATAATCGAACTC
1 ATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
1738390 GAAGGTCTTTTGTT
66 GAAGGTCTTTTGTT
1738404 AAAAGTGCTT
Statistics
Matches: 955, Mismatches: 123, Indels: 13
0.88 0.11 0.01
Matches are distributed among these distances:
82 61 0.06
83 136 0.14
84 728 0.76
85 30 0.03
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (84 bp):
ATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
GAAGGTCTTTTGTTGGCAG
Found at i:1741914 original size:14 final size:14
Alignment explanation
Indices: 1741895--1741941 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 14
1741885 TGAATGATGC
*
1741895 AAATGATAAAAATA
1 AAATGAAAAAAATA
1741909 AAATGAAAAAAATAA
1 AAATGAAAAAAAT-A
*
1741924 AAATGAAAGAAAACA
1 AAATGAAA-AAAATA
1741939 AAA
1 AAA
1741942 AATGAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 12 0.41
15 13 0.45
16 4 0.14
ACGTcount: A:0.77, C:0.02, G:0.09, T:0.13
Consensus pattern (14 bp):
AAATGAAAAAAATA
Found at i:1741942 original size:17 final size:16
Alignment explanation
Indices: 1741902--1741955 Score: 74
Period size: 17 Copynumber: 3.4 Consensus size: 16
1741892 TGCAAATGAT
*
1741902 AAAAATAAAATGAAA-
1 AAAAAAAAAATGAAAG
*
1741917 AAAATAAAAATGAAAG
1 AAAAAAAAAATGAAAG
1741933 AAAACAAAAAATGAAAG
1 AAAA-AAAAAATGAAAG
1741950 AAAAAA
1 AAAAAA
1741956 GTTAGTGAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
15 13 0.38
16 6 0.18
17 15 0.44
ACGTcount: A:0.80, C:0.02, G:0.09, T:0.09
Consensus pattern (16 bp):
AAAAAAAAAATGAAAG
Found at i:1742903 original size:6 final size:6
Alignment explanation
Indices: 1742892--1742938 Score: 85
Period size: 6 Copynumber: 7.7 Consensus size: 6
1742882 TTTATTTGCG
1742892 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAATTT AAAA
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAA-TT AAAA
1742939 ACCCGATTCG
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
6 34 0.85
7 6 0.15
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAAATT
Found at i:1745576 original size:30 final size:30
Alignment explanation
Indices: 1745502--1745590 Score: 133
Period size: 30 Copynumber: 3.0 Consensus size: 30
1745492 GGCAGCAACA
* * *
1745502 TTTTCTTCTTCCTCCTCATTTCTTCCTTCT
1 TTTTCTCCTTCCTCTTTATTTCTTCCTTCT
1745532 TTTTCTCCTTCCTCTTTATTTCTTCCTTCT
1 TTTTCTCCTTCCTCTTTATTTCTTCCTTCT
* *
1745562 TTTTCTCCTTCCTCTTTCTTCCTTCCTTC
1 TTTTCTCCTTCCTCTTTATTTCTTCCTTC
1745591 ATTCCTTCTT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 54 1.00
ACGTcount: A:0.02, C:0.37, G:0.00, T:0.61
Consensus pattern (30 bp):
TTTTCTCCTTCCTCTTTATTTCTTCCTTCT
Found at i:1751652 original size:3 final size:3
Alignment explanation
Indices: 1751621--1751680 Score: 57
Period size: 3 Copynumber: 18.3 Consensus size: 3
1751611 CATATTTGTG
* *
1751621 AGA AGA ATGA AGGA AGGA ACA AGGA AGA AGA AGA AGG AGA AGA AGGA
1 AGA AGA A-GA A-GA A-GA AGA A-GA AGA AGA AGA AGA AGA AGA A-GA
1751668 AGA AGA AGA AGA A
1 AGA AGA AGA AGA A
1751681 ATTGTTGCTA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
3 34 0.69
4 15 0.31
ACGTcount: A:0.60, C:0.02, G:0.37, T:0.02
Consensus pattern (3 bp):
AGA
Found at i:1751666 original size:22 final size:24
Alignment explanation
Indices: 1751621--1751678 Score: 84
Period size: 22 Copynumber: 2.5 Consensus size: 24
1751611 CATATTTGTG
1751621 AGAAGAATGAAGGAAGGAACAAGGA
1 AGAAGAA-GAAGGAAGGAACAAGGA
*
1751646 AGAAGAAGAAGG-A-GAAGAAGGA
1 AGAAGAAGAAGGAAGGAACAAGGA
1751668 AGAAGAAGAAG
1 AGAAGAAGAAG
1751679 AAATTGTTGC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
22 19 0.59
23 1 0.03
24 5 0.16
25 7 0.22
ACGTcount: A:0.59, C:0.02, G:0.38, T:0.02
Consensus pattern (24 bp):
AGAAGAAGAAGGAAGGAACAAGGA
Found at i:1753419 original size:23 final size:23
Alignment explanation
Indices: 1753376--1753420 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1753366 TAATATTTTA
*
1753376 TTTTAAATAATTTACTTTTATAT
1 TTTTAAATAATTTACTATTATAT
*
1753399 TTTTAACTAATTTA-TAATTATA
1 TTTTAAATAATTTACT-ATTATA
1753421 CGTTCAGTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 1 0.05
23 18 0.95
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (23 bp):
TTTTAAATAATTTACTATTATAT
Found at i:1759466 original size:25 final size:24
Alignment explanation
Indices: 1759434--1759505 Score: 71
Period size: 25 Copynumber: 3.1 Consensus size: 24
1759424 ATTATTACAG
1759434 TTGT-ATATTATTGTTGTTTTAAT
1 TTGTAATATTATTGTTGTTTTAAT
* * *
1759457 TTGATAATATTATTATTATTATAA-
1 TTG-TAATATTATTGTTGTTTTAAT
*
1759481 -TGTTATATTATTGTTG-TTTAAT
1 TTGTAATATTATTGTTGTTTTAAT
1759503 TTG
1 TTG
1759506 GTGTACTATT
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
21 4 0.11
22 11 0.29
23 7 0.18
24 1 0.03
25 15 0.39
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.61
Consensus pattern (24 bp):
TTGTAATATTATTGTTGTTTTAAT
Found at i:1759592 original size:15 final size:15
Alignment explanation
Indices: 1759572--1759604 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1759562 TCAATTATTA
1759572 ATATTTTTA-AAATAT
1 ATATTTTTATAAA-AT
1759587 ATATTTTTATAAAAT
1 ATATTTTTATAAAAT
1759602 ATA
1 ATA
1759605 ATTATATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 14 0.82
16 3 0.18
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATATTTTTATAAAAT
Found at i:1759601 original size:17 final size:16
Alignment explanation
Indices: 1759570--1759617 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
1759560 AATCAATTAT
1759570 TAATATTTT-TAAAATA
1 TAAT-TTTTATAAAATA
1759586 TATATTTTTATAAAATA
1 TA-ATTTTTATAAAATA
*
1759603 TAATTATATATAAAA
1 TAATT-TTTATAAAA
1759618 AATTAACCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 9 0.32
17 19 0.68
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TAATTTTTATAAAATA
Found at i:1759647 original size:17 final size:17
Alignment explanation
Indices: 1759627--1759661 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1759617 AAATTAACCT
*
1759627 TTAAAAAATATTGAATA
1 TTAAAAAATATTCAATA
*
1759644 TTAAAACATATTCAATA
1 TTAAAAAATATTCAATA
1759661 T
1 T
1759662 GTACAACTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.37
Consensus pattern (17 bp):
TTAAAAAATATTCAATA
Found at i:1761637 original size:2 final size:2
Alignment explanation
Indices: 1761612--1761715 Score: 50
Period size: 2 Copynumber: 56.5 Consensus size: 2
1761602 GTATACAATG
* * *
1761612 TA TA TG TA T- TA TA T- TA TA TA -A TA TA TA CA TA T- TA TG T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
1761649 TG TA TA CTA TA -A T- TA TA TA -A CA TA AA TA TA TA TA T- TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1761688 TA TA T- TA TA TA TCA T- TA TA TA TA CA TA T
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA T
1761716 TCATTTTTTA
Statistics
Matches: 78, Mismatches: 11, Indels: 26
0.68 0.10 0.23
Matches are distributed among these distances:
1 11 0.14
2 63 0.81
3 4 0.05
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1761638 original size:23 final size:22
Alignment explanation
Indices: 1761603--1761710 Score: 64
Period size: 23 Copynumber: 5.0 Consensus size: 22
1761593 CTATTTACAG
* *
1761603 TATACAATGTATATGTATTATAT
1 TATATAATATATAT-TATTATAT
* *
1761626 TATATAATATATACATATTATGT
1 TATATAATATATA-TTATTATAT
* * *
1761649 TGTATACTATA-ATTA-TATAA
1 TATATAATATATATTATTATAT
*
1761669 CATA-AATATATA-TATTATA-
1 TATATAATATATATTATTATAT
*
1761688 TATATTATATATCATTATATATA
1 TATATAATATAT-ATTAT-TATA
1761711 CATATTCATT
Statistics
Matches: 64, Mismatches: 14, Indels: 14
0.70 0.15 0.15
Matches are distributed among these distances:
19 10 0.16
20 16 0.25
21 3 0.05
22 4 0.06
23 31 0.48
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (22 bp):
TATATAATATATATTATTATAT
Found at i:1761689 original size:9 final size:9
Alignment explanation
Indices: 1761675--1761710 Score: 63
Period size: 9 Copynumber: 3.9 Consensus size: 9
1761665 ATAACATAAA
1761675 TATATATAT
1 TATATATAT
1761684 TATATATAT
1 TATATATAT
1761693 TATATATCAT
1 TATATAT-AT
1761703 TATATATA
1 TATATATA
1761711 CATATTCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 17 0.65
10 9 0.35
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (9 bp):
TATATATAT
Found at i:1761710 original size:30 final size:31
Alignment explanation
Indices: 1761612--1761710 Score: 80
Period size: 30 Copynumber: 3.2 Consensus size: 31
1761602 GTATACAATG
* * *
1761612 TATATGTATTATATTATATAATATATACA-TA
1 TATATATATTATACTATATTATATAT-CATTA
* * *
1761643 T-TATGT-TGTATACTATAATTATATAACATAAA
1 TATATATAT-TATACTAT-ATTATATATCAT-TA
1761675 TATATATATTATA-TATATTATATATCATTA
1 TATATATATTATACTATATTATATATCATTA
1761705 TATATA
1 TATATA
1761711 CATATTCATT
Statistics
Matches: 55, Mismatches: 7, Indels: 13
0.73 0.09 0.17
Matches are distributed among these distances:
29 1 0.02
30 21 0.38
31 19 0.35
32 5 0.09
33 8 0.15
34 1 0.02
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.48
Consensus pattern (31 bp):
TATATATATTATACTATATTATATATCATTA
Found at i:1761719 original size:17 final size:19
Alignment explanation
Indices: 1761676--1761720 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
1761666 TAACATAAAT
*
1761676 ATATAT-ATTATATATATT
1 ATATATCATTATATATATC
1761694 ATATATCATTATATATA-C
1 ATATATCATTATATATATC
1761712 ATAT-TCATT
1 ATATATCATT
1761721 TTTTATTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 5 0.20
18 10 0.40
19 10 0.40
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (19 bp):
ATATATCATTATATATATC
Found at i:1762835 original size:21 final size:22
Alignment explanation
Indices: 1762796--1762839 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1762786 GATTTTTATA
* *
1762796 TTTATTTTGTTGTTGTTTATTT
1 TTTATTTTATTGTTATTTATTT
1762818 TTTATTTTATT-TTATTTATTT
1 TTTATTTTATTGTTATTTATTT
1762839 T
1 T
1762840 CCTTTTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.80
Consensus pattern (22 bp):
TTTATTTTATTGTTATTTATTT
Found at i:1766930 original size:21 final size:21
Alignment explanation
Indices: 1766906--1766949 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1766896 GCGAAGAAGA
*
1766906 TGGAAGAGAAAATGAAGCTGG
1 TGGAAGACAAAATGAAGCTGG
* *
1766927 TGGAAGACCAAATGAAGGTGG
1 TGGAAGACAAAATGAAGCTGG
1766948 TG
1 TG
1766950 AAGGGGGACC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.07, G:0.39, T:0.16
Consensus pattern (21 bp):
TGGAAGACAAAATGAAGCTGG
Found at i:1769063 original size:25 final size:20
Alignment explanation
Indices: 1769012--1769049 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1769002 TTTTTTGTTG
1769012 TTTAATTTTTATTTTATTAT
1 TTTAATTTTTATTTTATTAT
1769032 TTT-ATTTTTCATTTTATT
1 TTTAATTTTT-ATTTTATT
1769050 TAGTTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTAATTTTTATTTTATTAT
Found at i:1769353 original size:22 final size:22
Alignment explanation
Indices: 1769319--1769363 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1769309 GCATGGTTTG
* *
1769319 TTTTCTTTGTTCTATTTATTTC
1 TTTTCTTTATTCTATTAATTTC
* *
1769341 TTTTTTTTATTCTGTTAATTTC
1 TTTTCTTTATTCTATTAATTTC
1769363 T
1 T
1769364 CGGCATGTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.11, C:0.11, G:0.04, T:0.73
Consensus pattern (22 bp):
TTTTCTTTATTCTATTAATTTC
Found at i:1773306 original size:18 final size:18
Alignment explanation
Indices: 1773270--1773309 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
1773260 ATAAATTTTA
1773270 TTTTTTTATTTATAAATG
1 TTTTTTTATTTATAAATG
*
1773288 TTTTTATTATTT-TACATG
1 TTTTT-TTATTTATAAATG
1773306 TTTT
1 TTTT
1773310 AATAAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.70
Consensus pattern (18 bp):
TTTTTTTATTTATAAATG
Done.