Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001978.1 Hibiscus syriacus cultivar Beakdansim tig00004013_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: 2594977
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 10
Found at i:2188837 original size:2 final size:2
Alignment explanation
Indices: 2188830--2188867 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2188820 ATACTACATC
2188830 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2188868 CGAAAAATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2189388 original size:21 final size:21
Alignment explanation
Indices: 2189364--2189412 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
2189354 GCATGGCATG
*
2189364 GCCCTGCACCGACCTAGCCCT
1 GCCCTGCACCCACCTAGCCCT
*
2189385 GCCCTACACCCACCTAGCCCT
1 GCCCTGCACCCACCTAGCCCT
2189406 GCCCTGC
1 GCCCTGC
2189413 CCTGCCCTGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.14, C:0.55, G:0.16, T:0.14
Consensus pattern (21 bp):
GCCCTGCACCCACCTAGCCCT
Found at i:2189763 original size:42 final size:42
Alignment explanation
Indices: 2189708--2189824 Score: 189
Period size: 42 Copynumber: 2.8 Consensus size: 42
2189698 TCCCGAATTT
* *
2189708 CCGTGTTTTTTTCACGTAATTCGTTTTCCGGAAAATATTTTC
1 CCGTGTTTATTTCACGTAATTCGTTTTCCGGAAAACATTTTC
* *
2189750 CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTTTTC
1 CCGTGTTTATTTCACGTAATTCGTTTTCCGGAAAACATTTTC
*
2189792 CCGTGTTTATTTCACATAATTCGTTTTCCGGAA
1 CCGTGTTTATTTCACGTAATTCGTTTTCCGGAA
2189825 TGTAATTCAT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.19, C:0.21, G:0.16, T:0.44
Consensus pattern (42 bp):
CCGTGTTTATTTCACGTAATTCGTTTTCCGGAAAACATTTTC
Found at i:2190055 original size:29 final size:28
Alignment explanation
Indices: 2190022--2190183 Score: 91
Period size: 27 Copynumber: 6.0 Consensus size: 28
2190012 AAATATTTAA
2190022 AATATATTTATTAATATTTATAATAATAT
1 AATATATTTATT-ATATTTATAATAATAT
2190051 AATATATATT-TTA-ATATTAT-ATAA-AT
1 AATATAT-TTATTATAT-TTATAATAATAT
* * *
2190077 AATCA-ATTATATTATAATAAT-ATAAGAT
1 AAT-ATATT-TATTATATTTATAATAATAT
*
2190105 ATTATA-TT-TT-TATTT-TAATAATAT
1 AATATATTTATTATATTTATAATAATAT
* *
2190129 AATA-ATTTTTTTATATTTAATAATGA-AT
1 AATATA-TTTATTATATTT-ATAATAATAT
*
2190157 AATATTATTTA-TATATTT-CAATAATAT
1 AATA-TATTTATTATATTTATAATAATAT
2190184 TTTAGTAAAG
Statistics
Matches: 104, Mismatches: 11, Indels: 38
0.68 0.07 0.25
Matches are distributed among these distances:
23 2 0.02
24 12 0.12
25 5 0.05
26 15 0.14
27 26 0.25
28 24 0.23
29 17 0.16
30 3 0.03
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (28 bp):
AATATATTTATTATATTTATAATAATAT
Found at i:2190098 original size:52 final size:52
Alignment explanation
Indices: 2190040--2190183 Score: 120
Period size: 52 Copynumber: 2.7 Consensus size: 52
2190030 TATTAATATT
2190040 TATAATAATATAATATATATTTTAATATTATATAA-ATAATCAATTATATTATA
1 TATAATAATATAATATATATTTTAATATTA-ATAATATAAT-AATTATATTATA
* * * *
2190093 -ATAAT-ATA-AGATATTATATTTTTATTTTAATAATATAATAATTTTTTTATA
1 TATAATAATATA-ATA-TATATTTTAATATTAATAATATAATAATTATATTATA
*
2190144 TTTAATAATGAATAATAT-TA-TTTATATATTTCAATAATAT
1 TATAATAAT--ATAATATATATTTTA-ATA-TT-AATAATAT
2190184 TTTAGTAAAG
Statistics
Matches: 73, Mismatches: 7, Indels: 20
0.73 0.07 0.20
Matches are distributed among these distances:
50 1 0.01
51 20 0.27
52 30 0.41
53 6 0.08
54 3 0.04
55 12 0.16
56 1 0.01
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (52 bp):
TATAATAATATAATATATATTTTAATATTAATAATATAATAATTATATTATA
Found at i:2190140 original size:26 final size:27
Alignment explanation
Indices: 2190086--2190183 Score: 85
Period size: 29 Copynumber: 3.5 Consensus size: 27
2190076 TAATCAATTA
* *
2190086 TATTATAATAATATAAGATATTATATTTT
1 TATTTTAATAATATAATA-ATTAT-TTTT
2190115 TATTTTAATAATATAATAA-T-TTTTT
1 TATTTTAATAATATAATAATTATTTTT
*
2190140 TATATTTAATAATGAATAAT-ATTATTTATA
1 TAT-TTTAATAAT--ATAATAATTATTT-TT
*
2190170 TATTTCAATAATAT
1 TATTTTAATAATAT
2190184 TTTAGTAAAG
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
25 7 0.12
26 10 0.17
27 4 0.07
28 7 0.12
29 27 0.46
30 4 0.07
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (27 bp):
TATTTTAATAATATAATAATTATTTTT
Found at i:2190393 original size:20 final size:20
Alignment explanation
Indices: 2190344--2190412 Score: 113
Period size: 20 Copynumber: 3.5 Consensus size: 20
2190334 TTTCCAGATG
2190344 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
2190364 -TTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
* *
2190383 TTTTACAGAAATATAATTCA
1 TTTTCCAGAAATGTAATTCA
2190403 TTTTCCAGAA
1 TTTTCCAGAA
2190413 TTCAAATTCC
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
19 19 0.42
20 26 0.58
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:2190431 original size:15 final size:15
Alignment explanation
Indices: 2190405--2190461 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
2190395 ATAATTCATT
2190405 TTCCAG-AATTCAAA
1 TTCCAGTAATTCAAA
**
2190419 TTCCAGTAATTCATT
1 TTCCAGTAATTCAAA
2190434 TTCCAGTAATTCAAA
1 TTCCAGTAATTCAAA
2190449 TTCCAGTAATTCA
1 TTCCAGTAATTCA
2190462 TTTTCTGGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
14 6 0.16
15 32 0.84
ACGTcount: A:0.35, C:0.21, G:0.07, T:0.37
Consensus pattern (15 bp):
TTCCAGTAATTCAAA
Found at i:2190438 original size:29 final size:30
Alignment explanation
Indices: 2190396--2190466 Score: 135
Period size: 30 Copynumber: 2.4 Consensus size: 30
2190386 TACAGAAATA
2190396 TAATTCATTTTCCAG-AATTCAAATTCCAG
1 TAATTCATTTTCCAGTAATTCAAATTCCAG
2190425 TAATTCATTTTCCAGTAATTCAAATTCCAG
1 TAATTCATTTTCCAGTAATTCAAATTCCAG
2190455 TAATTCATTTTC
1 TAATTCATTTTC
2190467 TGGAAAACCA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 15 0.37
30 26 0.63
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.42
Consensus pattern (30 bp):
TAATTCATTTTCCAGTAATTCAAATTCCAG
Found at i:2191185 original size:26 final size:24
Alignment explanation
Indices: 2191135--2191185 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 24
2191125 AGTTCTATTT
*
2191135 AATATATATATAATTTTTTGAAAA
1 AATATATATATAATGTTTTGAAAA
2191159 AATATATATAATATATAGTTTTGAAAA
1 AATATATAT-ATA-AT-GTTTTGAAAA
2191186 CATTTTGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 9 0.39
25 3 0.13
26 2 0.09
27 9 0.39
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (24 bp):
AATATATATATAATGTTTTGAAAA
Found at i:2191227 original size:37 final size:37
Alignment explanation
Indices: 2191157--2191687 Score: 636
Period size: 37 Copynumber: 14.4 Consensus size: 37
2191147 ATTTTTTGAA
2191157 AAAATATATATAATATATAG-TTTTGAAAACATTTTG
1 AAAATATATATAATATATAGTTTTTGAAAACATTTTG
* * *
2191193 AAAACATATATAATATATAATTTTTGAAAACATTTCG
1 AAAATATATATAATATATAGTTTTTGAAAACATTTTG
* *
2191230 AAAATATATATAATATATAGTTTCTGAAAACATTTCG
1 AAAATATATATAATATATAGTTTTTGAAAACATTTTG
* *
2191267 AAAATATATATAATATATAGTTTCTGAAAACATTTCG
1 AAAATATATATAATATATAGTTTTTGAAAACATTTTG
*
2191304 AAAATATATATAATATATAGTTTCTGAAAACA-TTT-
1 AAAATATATATAATATATAGTTTTTGAAAACATTTTG
* * *
2191339 CAAATATATATAATATATAGTTTCTGAAAACATTTCG
1 AAAATATATATAATATATAGTTTTTGAAAACATTTTG
* *
2191376 AAAATATATATAATATATAGTTTCTGAAAATATTTTG
1 AAAATATATATAATATATAGTTTTTGAAAACATTTTG
* *
2191413 AAAAAATATATTTAATATATAATTTTTGAAAACATTTTG
1 --AAAATATATATAATATATAGTTTTTGAAAACATTTTG
*
2191452 AAAATATATATATAATATATAATTTTT---AAC---TTG
1 -AAA-ATATATATAATATATAGTTTTTGAAAACATTTTG
* *
2191485 AATATATGTATAATATATATAGTTTTTGAAAACATTTTG
1 AAAATATATAT-A-ATATATAGTTTTTGAAAACATTTTG
* *
2191524 AAAATATATATAATATATAGTTTTTAAAAACATTTTT
1 AAAATATATATAATATATAGTTTTTGAAAACATTTTG
2191561 AAAATATATATAATATATAGTTTTTGAAAACATTTTG
1 AAAATATATATAATATATAGTTTTTGAAAACATTTTG
*
2191598 AAAATATAT-TTATAATATAGTTTTTGAAAACATTTT-
1 AAAATATATATAAT-ATATAGTTTTTGAAAACATTTTG
** * * * ***
2191634 TTAACATATATAATAT-TTGGTTTTGAATGTATTTTTCG
1 AAAATATATATAATATATAGTTTTTGAAAACA-TTTT-G
2191672 AAAATATATATAATAT
1 AAAATATATATAATAT
2191688 CATTTTTTTT
Statistics
Matches: 437, Mismatches: 39, Indels: 36
0.85 0.08 0.07
Matches are distributed among these distances:
31 7 0.02
32 3 0.01
33 15 0.03
35 41 0.09
36 43 0.10
37 244 0.56
38 18 0.04
39 66 0.15
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.43
Consensus pattern (37 bp):
AAAATATATATAATATATAGTTTTTGAAAACATTTTG
Found at i:2191236 original size:26 final size:26
Alignment explanation
Indices: 2191188--2191237 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
2191178 TTTGAAAACA
* *
2191188 TTTTGAAAACATATATAATATATAAT
1 TTTTGAAAACATATAGAAAATATAAT
* *
2191214 TTTTGAAAACATTTCGAAAATATA
1 TTTTGAAAACATATAGAAAATATA
2191238 TATAATATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.40
Consensus pattern (26 bp):
TTTTGAAAACATATAGAAAATATAAT
Found at i:2191739 original size:23 final size:22
Alignment explanation
Indices: 2191713--2191760 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 22
2191703 TATAATGCCA
*
2191713 TTTTATTTATTTATTTTCATTTT
1 TTTTATTTATCTATTTTC-TTTT
2191736 TTTTATTTATCTATTTTCTTTT
1 TTTTATTTATCTATTTTCTTTT
2191758 TTT
1 TTT
2191761 CTTTTTTAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTTATTTATCTATTTTCTTTT
Found at i:2191742 original size:15 final size:15
Alignment explanation
Indices: 2191722--2191767 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
2191712 ATTTTATTTA
2191722 TTTATTTTCATTTTT
1 TTTATTTTCATTTTT
*
2191737 TTTATTTATCTATTTTC
1 TTTATTT-TC-ATTTTT
2191754 TTT-TTTTC-TTTTT
1 TTTATTTTCATTTTT
2191767 T
1 T
2191768 AGGGATCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
13 5 0.19
15 9 0.33
16 5 0.19
17 8 0.30
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTATTTTCATTTTT
Found at i:2193965 original size:22 final size:22
Alignment explanation
Indices: 2193937--2194080 Score: 252
Period size: 22 Copynumber: 6.5 Consensus size: 22
2193927 CAAGAATCGA
*
2193937 GGGACATATACAGTGGTTATTC
1 GGGACATATACAGTGGTCATTC
2193959 GGGACATATACAGTGGTCATTC
1 GGGACATATACAGTGGTCATTC
2193981 GGGACATATACAGTGGTCATTC
1 GGGACATATACAGTGGTCATTC
*
2194003 GGGACATATACAGTGGTCCTTC
1 GGGACATATACAGTGGTCATTC
* *
2194025 GAGACATATACAATGGTCATTC
1 GGGACATATACAGTGGTCATTC
2194047 GGGACATATACAGTGGTCATTC
1 GGGACATATACAGTGGTCATTC
2194069 GGGACATATACA
1 GGGACATATACA
2194081 TAAATTTCAC
Statistics
Matches: 115, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 115 1.00
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (22 bp):
GGGACATATACAGTGGTCATTC
Found at i:2203120 original size:2 final size:2
Alignment explanation
Indices: 2203113--2203163 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
2203103 TGTACATTAG
2203113 AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2203154 AT AT AT AT AT
1 AT AT AT AT AT
2203164 CATCCCTTCA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2203800 original size:45 final size:45
Alignment explanation
Indices: 2203770--2203984 Score: 270
Period size: 45 Copynumber: 4.8 Consensus size: 45
2203760 ACTCTAACGT
* *
2203770 CTTTTTTGTTGATAATGCACCCATATGCATTTCAACTATAGTATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATA
* * * * *
2203815 CTTTTATGTTGATAATGTACCCATATACATCTCAAC-CATAATATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTC-TAGTATA
* ** * *
2203860 ATTTTCTGTTGATAATATACCCATATACATTTCAACTCTAGCATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATA
* **
2203905 CTTTTCTATTGATAATGCATACATATGCATTTCAACTCTAGTATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATA
*
2203950 CTTTTCTGTTGATAATGCACCCATATGCATCTCAA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAA
2203985 ATCTGGCATC
Statistics
Matches: 144, Mismatches: 24, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
45 143 0.99
46 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (45 bp):
CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATA
Found at i:2204020 original size:90 final size:87
Alignment explanation
Indices: 2203770--2204025 Score: 235
Period size: 90 Copynumber: 2.8 Consensus size: 87
2203760 ACTCTAACGT
* * * * *
2203770 CTTTTTTGTTGATAATGCACCCATATGCATTTCAACTATAGTATACTTTTATGTTGATAATGTAC
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGCATCCTTTCA---TGATAATGTAC
* *
2203835 CCATATACATCTCAACCATAATATA
63 CCATATGCATTTCAACCATAATATA
* ** * * * *
2203860 ATTTTCTGTTGATAATATACCCATATACATTTCAACTCTAGCATACTTTTCTATTGATAATGCAT
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGCAT-CCTTTC-A-TGATAATGTAC
* *
2203925 ACATATGCATTTCAACTC-TAGTATA
63 CCATATGCATTTCAAC-CATAATATA
* * * *
2203950 CTTTTCTGTTGATAATGCACCCATATGCATCTCAAATCTGGCATCCTTTCATGCCAATAATTTAC
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGCATCCTTTCATG---ATAATGTAC
2204015 CCATATGCATT
63 CCATATGCATT
2204026 ATTCTGTTAT
Statistics
Matches: 132, Mismatches: 28, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
87 2 0.02
88 1 0.01
89 5 0.04
90 119 0.90
91 4 0.03
92 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.39
Consensus pattern (87 bp):
CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGCATCCTTTCATGATAATGTACCCA
TATGCATTTCAACCATAATATA
Found at i:2207608 original size:99 final size:99
Alignment explanation
Indices: 2207424--2207613 Score: 256
Period size: 99 Copynumber: 1.9 Consensus size: 99
2207414 TTATAATATT
* * *
2207424 ATATGTATACAATAAAGCTTGAGCTGTCCCTCCAGAGCAATTGGTTAATCGCCCCGTCTTTATGG
1 ATATATATACAATAAAGCTTGAGCTGTCCCTCCAGAGCAATTGGTTAAACGCCCAGTCTTTATGG
2207489 ATAAGATTCAGCTAGACTGATAAAGGTGATTATA
66 ATAAGATTCAGCTAGACTGATAAAGGTGATTATA
* * * ** * *
2207523 ATATATATGCAATAAATCTTTAGCTGTGTCTCTAGAGCAATTGGTTAAACATCCCAG-CTTTATG
1 ATATATATACAATAAAGCTTGAGCTGTCCCTCCAGAGCAATTGGTTAAAC-GCCCAGTCTTTATG
* *
2207587 GATAAGATTTAGCTAGCCTGATAAAGG
65 GATAAGATTCAGCTAGACTGATAAAGG
2207614 CAAATTACAA
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
99 74 0.95
100 4 0.05
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (99 bp):
ATATATATACAATAAAGCTTGAGCTGTCCCTCCAGAGCAATTGGTTAAACGCCCAGTCTTTATGG
ATAAGATTCAGCTAGACTGATAAAGGTGATTATA
Found at i:2216211 original size:36 final size:37
Alignment explanation
Indices: 2216163--2216358 Score: 221
Period size: 37 Copynumber: 5.4 Consensus size: 37
2216153 TCGAATATAT
2216163 ATATATATATATATATAG--TTTGAAACA-TTTTGAAA
1 ATATATATA-ATATATAGTTTTTGAAACATTTTTGAAA
**
2216198 ATATATATAATATATAGTTTTTGAAA-ACTTTTCAAAA
1 ATATATATAATATATAGTTTTTGAAACA-TTTTTGAAA
2216235 ATATATATAATATATAGTTTTTTGAAAACA-TTTTGAAA
1 ATATATATAATATATAG-TTTTTG-AAACATTTTTGAAA
2216273 ATATATATAA-ATATAGTTTTTGTAAACATTTTTG--A
1 ATATATATAATATATAGTTTTTG-AAACATTTTTGAAA
* * *
2216308 ACACATATAATATAT-GGTTTTGAAAGCATTTTTTGAAA
1 ATATATATAATATATAGTTTTTGAAA-CA-TTTTTGAAA
2216346 ATATATATAATAT
1 ATATATATAATAT
2216359 CATTTTAAAA
Statistics
Matches: 138, Mismatches: 10, Indels: 23
0.81 0.06 0.13
Matches are distributed among these distances:
34 11 0.08
35 27 0.20
36 28 0.20
37 34 0.25
38 34 0.25
39 3 0.02
40 1 0.01
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (37 bp):
ATATATATAATATATAGTTTTTGAAACATTTTTGAAA
Found at i:2216236 original size:37 final size:37
Alignment explanation
Indices: 2216163--2216358 Score: 228
Period size: 38 Copynumber: 5.4 Consensus size: 37
2216153 TCGAATATAT
2216163 ATATATATATATATATAG--TTTG-AAACATTTTGAAA
1 ATATATATA-ATATATAGTTTTTGAAAACATTTTGAAA
*
2216198 ATATATATAATATATAGTTTTTGAAAAC-TTTTCAAAA
1 ATATATATAATATATAGTTTTTGAAAACATTTT-GAAA
2216235 ATATATATAATATATAGTTTTTTGAAAACATTTTGAAA
1 ATATATATAATATATAG-TTTTTGAAAACATTTTGAAA
*
2216273 ATATATATAA-ATATAGTTTTTGTAAACATTTTTG--A
1 ATATATATAATATATAGTTTTTGAAAACA-TTTTGAAA
* * * *
2216308 ACACATATAATATAT-GGTTTTGAAAGCATTTTTTGAAA
1 ATATATATAATATATAGTTTTTGAAAACA--TTTTGAAA
2216346 ATATATATAATAT
1 ATATATATAATAT
2216359 CATTTTAAAA
Statistics
Matches: 140, Mismatches: 10, Indels: 19
0.83 0.06 0.11
Matches are distributed among these distances:
34 8 0.06
35 28 0.20
36 29 0.21
37 35 0.25
38 36 0.26
39 4 0.03
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (37 bp):
ATATATATAATATATAGTTTTTGAAAACATTTTGAAA
Found at i:2216389 original size:4 final size:4
Alignment explanation
Indices: 2216380--2216424 Score: 63
Period size: 4 Copynumber: 10.8 Consensus size: 4
2216370 ATATATACAT
*
2216380 TTTA TTTA TTTA TTTTCA TTTA TTTA TTTA TTTA TTTA TTCA TTT
1 TTTA TTTA TTTA -TTT-A TTTA TTTA TTTA TTTA TTTA TTTA TTT
2216425 TTATTTTTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
4 30 0.81
5 6 0.16
6 1 0.03
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:2216427 original size:22 final size:21
Alignment explanation
Indices: 2216379--2216438 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 21
2216369 AATATATACA
2216379 TTTTATTTATTTATTTTCATT
1 TTTTATTTATTTATTTTCATT
2216400 TATTTATTTATTTATTTATTCA-T
1 T-TTTATTTATTTA-TT-TTCATT
*
2216423 TTTTATTT-TTTCTTTT
1 TTTTATTTATTTATTTT
2216439 TTTAAGGGTC
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
19 2 0.06
20 2 0.06
21 4 0.11
22 19 0.54
23 4 0.11
24 4 0.11
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTTATTTATTTATTTTCATT
Found at i:2217770 original size:5 final size:5
Alignment explanation
Indices: 2217762--2217807 Score: 74
Period size: 5 Copynumber: 9.2 Consensus size: 5
2217752 ATTTCAACTC
* *
2217762 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT CTTAT TTTAT TCTAT T
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT T
2217808 CTTTAACCCT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 38 1.00
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTAT
Found at i:2217782 original size:15 final size:15
Alignment explanation
Indices: 2217711--2217807 Score: 79
Period size: 15 Copynumber: 6.2 Consensus size: 15
2217701 ATTTATCCAA
*
2217711 ATTTTATTTAATTTT
1 ATTTTATTTTATTTT
* *
2217726 ACTTTATTTT-TTGT
1 ATTTTATTTTATTTT
* *
2217740 CTTTAATATTTTATTTCA
1 ATTT--TATTTTATTT-T
2217758 ACTCTTTATTTTATTTT
1 A-T-TTTATTTTATTTT
2217775 ATTTTATTTTATTTT
1 ATTTTATTTTATTTT
* *
2217790 ATCTTATTTTATTCT
1 ATTTTATTTTATTTT
2217805 ATT
1 ATT
2217808 CTTTAACCCT
Statistics
Matches: 64, Mismatches: 12, Indels: 12
0.73 0.14 0.14
Matches are distributed among these distances:
14 5 0.08
15 36 0.56
16 7 0.11
17 3 0.05
18 10 0.16
19 1 0.02
20 2 0.03
ACGTcount: A:0.22, C:0.07, G:0.01, T:0.70
Consensus pattern (15 bp):
ATTTTATTTTATTTT
Found at i:2217799 original size:10 final size:10
Alignment explanation
Indices: 2217711--2217807 Score: 79
Period size: 10 Copynumber: 9.3 Consensus size: 10
2217701 ATTTATCCAA
*
2217711 ATTTTATTTA
1 ATTTTATTTT
*
2217721 ATTTTACTTT
1 ATTTTATTTT
*
2217731 ATTTT-TTGT
1 ATTTTATTTT
*
2217740 CTTTAATATTTT
1 ATTT--TATTTT
*
2217752 ATTTCAACTCTTT
1 ATTT-TA-T-TTT
2217765 ATTTTATTTT
1 ATTTTATTTT
2217775 ATTTTATTTT
1 ATTTTATTTT
*
2217785 ATTTTATCTT
1 ATTTTATTTT
*
2217795 ATTTTATTCT
1 ATTTTATTTT
2217805 ATT
1 ATT
2217808 CTTTAACCCT
Statistics
Matches: 69, Mismatches: 13, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
9 5 0.07
10 46 0.67
11 3 0.04
12 8 0.12
13 7 0.10
ACGTcount: A:0.22, C:0.07, G:0.01, T:0.70
Consensus pattern (10 bp):
ATTTTATTTT
Found at i:2219357 original size:21 final size:21
Alignment explanation
Indices: 2219323--2219362 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2219313 GCCCCTTCTC
*
2219323 CCTCCCAGCTGCCTGCTCCTT
1 CCTCCCAGCTGCCTCCTCCTT
2219344 CCTCCCACGC-GCCTCCTCC
1 CCTCCCA-GCTGCCTCCTCC
2219363 GCCTTCCCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.05, C:0.60, G:0.12, T:0.23
Consensus pattern (21 bp):
CCTCCCAGCTGCCTCCTCCTT
Found at i:2220583 original size:29 final size:25
Alignment explanation
Indices: 2220525--2220577 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
2220515 TTAAAAGAGA
2220525 AAAATATATATATAATGAAATAAAAT
1 AAAATATA-ATATAATGAAATAAAAT
*
2220551 AAAATATAATATAATGAAA-AAACT
1 AAAATATAATATAATGAAATAAAAT
2220575 AAA
1 AAA
2220578 TTAAAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 7 0.27
25 11 0.42
26 8 0.31
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (25 bp):
AAAATATAATATAATGAAATAAAAT
Found at i:2221812 original size:4 final size:4
Alignment explanation
Indices: 2221794--2221843 Score: 52
Period size: 4 Copynumber: 12.8 Consensus size: 4
2221784 ACCTGTTCCA
*
2221794 AAAT AAA- AAAA AAAT AAAT AAAT -AAT GAAAT AAAT -AAT AAAT AAAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT -AAAT
2221841 AAA
1 AAA
2221844 ATAATAAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
3 9 0.22
4 24 0.60
5 7 0.17
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:2221826 original size:12 final size:11
Alignment explanation
Indices: 2221795--2221838 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
2221785 CCTGTTCCAA
* *
2221795 AATAAAAAAAA
1 AATAAATAAAT
2221806 AATAAATAAAT
1 AATAAATAAAT
2221817 AATGAAATAAAT
1 AAT-AAATAAAT
2221829 AATAAATAAA
1 AATAAATAAA
2221839 ATAAAATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 19 0.63
12 11 0.37
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.20
Consensus pattern (11 bp):
AATAAATAAAT
Found at i:2221826 original size:16 final size:16
Alignment explanation
Indices: 2221794--2221851 Score: 66
Period size: 16 Copynumber: 3.6 Consensus size: 16
2221784 ACCTGTTCCA
*
2221794 AAATAA-AAAAAAAAT
1 AAATAATAAATAAAAT
*
2221809 AAATAA-ATAATGAAAT
1 AAATAATA-AATAAAAT
2221825 AAATAATAAATAAAAT
1 AAATAATAAATAAAAT
2221841 AAAATAATAAA
1 -AAATAATAAA
2221852 ATGTAATAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
15 7 0.19
16 19 0.51
17 11 0.30
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.21
Consensus pattern (16 bp):
AAATAATAAATAAAAT
Found at i:2221840 original size:12 final size:12
Alignment explanation
Indices: 2221795--2221853 Score: 61
Period size: 12 Copynumber: 5.0 Consensus size: 12
2221785 CCTGTTCCAA
*
2221795 AATAAA-AAAAA
1 AATAAATAAAAT
2221806 AATAAAT-AAAT
1 AATAAATAAAAT
2221817 AATGAAAT-AAAT
1 AAT-AAATAAAAT
2221829 AATAAATAAAAT
1 AATAAATAAAAT
*
2221841 AAAATAATAAAAT
1 AATA-AATAAAAT
2221854 GTAATAATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
11 16 0.38
12 18 0.43
13 8 0.19
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (12 bp):
AATAAATAAAAT
Found at i:2221914 original size:33 final size:32
Alignment explanation
Indices: 2221877--2222260 Score: 123
Period size: 35 Copynumber: 11.3 Consensus size: 32
2221867 CTATATAGAT
*
2221877 TATTATATGTTTTCGAAAAATTTTTTAAATATA
1 TATTATACGTTTTC-AAAAATTTTTTAAATATA
** * *
2221910 TATTATACGTTTTC-AAAATCATTTAAAAACA
1 TATTATACGTTTTCAAAAATTTTTTAAATATA
* ** *
2221941 TATTATACATTTTCAAAACCGTTTTGAAA-ACTA
1 TATTATACGTTTTCAAAA-ATTTTTTAAATA-TA
* * **
2221974 TATTATATGTTTTCAAAACCGTTTTAAAAAACTATA
1 TATTATACGTTTTCAAAA--ATTTT-TTAAA-TATA
* * *
2222010 TATTATATGTTTTCAAAACTATTTTAAA-ACCTA
1 TATTATACGTTTTCAAAAATTTTTTAAATA--TA
* ***
2222043 TATATATACGTTTTCCAAACTATTTAAAAAACTATA
1 TAT-TATACGTTTT-CAAA-AATTTTTTAAA-TATA
* * *** **
2222079 TACTATATGTTTTCGAACCGTTTTAAAAACTATA
1 TATTATACGTTTTC-AAAAATTTTTTAAA-TATA
*
2222113 TATTATACGTTTTCAAAAACTATTTTTAAAAACTA
1 TATTATACGTTTTCAAAAA-T-TTTTTAAATA-TA
* ** **
2222148 TA-TATTACATTTTCCAACTATTTTGAAAAACTATA
1 TATTA-TACGTTTT-CAAAAATTTT-TTAAA-TATA
* * * *
2222183 TACTATATGTTTTC-AAAATCGTTTTAAAAACTA
1 TATTATACGTTTTCAAAAAT-TTTTTAAATA-TA
**
2222216 TATTATACG-TTTCTAAAACTATTTTAAAAACTATA
1 TATTATACGTTTTC-AAAA--ATTTTTTAAA-TATA
2222251 TATTATACGT
1 TATTATACGT
2222261 GTTTTTGCAA
Statistics
Matches: 257, Mismatches: 63, Indels: 59
0.68 0.17 0.16
Matches are distributed among these distances:
31 27 0.11
32 9 0.04
33 60 0.23
34 55 0.21
35 65 0.25
36 39 0.15
37 1 0.00
38 1 0.00
ACGTcount: A:0.41, C:0.12, G:0.05, T:0.43
Consensus pattern (32 bp):
TATTATACGTTTTCAAAAATTTTTTAAATATA
Found at i:2221935 original size:31 final size:30
Alignment explanation
Indices: 2221900--2222130 Score: 113
Period size: 33 Copynumber: 6.9 Consensus size: 30
2221890 CGAAAAATTT
2221900 TTTAAATATATATTATACGTTTTCAAAATC-A
1 TTTAAA-ATATATTATACGTTTTCAAAA-CGA
* * *
2221931 TTTAAAAACATATTATACATTTTCAAAACCGT
1 TTT-AAAATATATTATACGTTTTCAAAA-CGA
* *
2221963 TTTGAAAACTATATTATATGTTTTCAAAACCGT
1 TTT-AAAA-TATATTATACGTTTTCAAAA-CGA
* *
2221996 TTTAAAAAACTATATATTATATGTTTTCAAAACTA
1 TTT---AAA--ATATATTATACGTTTTCAAAACGA
* *
2222031 TTTTAAAACCTATATATATACGTTTTCCAAACTA
1 -TTTAAAA--TATAT-TATACGTTTTCAAAACGA
* * * *
2222065 TTTAAAAAACTATATACTATATGTTTTCGAACCGT
1 TTT--AAAA-TATAT--TATACGTTTTCAAAACGA
2222100 TTTAAAAACTATATATTATACGTTTTCAAAA
1 TTT--AAA--ATATATTATACGTTTTCAAAA
2222131 ACTATTTTTA
Statistics
Matches: 162, Mismatches: 22, Indels: 29
0.76 0.10 0.14
Matches are distributed among these distances:
31 24 0.15
32 10 0.06
33 35 0.22
34 34 0.21
35 29 0.18
36 28 0.17
37 2 0.01
ACGTcount: A:0.41, C:0.13, G:0.05, T:0.42
Consensus pattern (30 bp):
TTTAAAATATATTATACGTTTTCAAAACGA
Found at i:2222024 original size:69 final size:67
Alignment explanation
Indices: 2221877--2222260 Score: 315
Period size: 69 Copynumber: 5.6 Consensus size: 67
2221867 CTATATAGAT
* * * * *
2221877 TATTATATGTTTTCGAAAAATTTTTTAAATA-TATATTATACGTTTTCAAAATCATTTAAAAAC-
1 TATTATATGTTTTC-AAAACTATTTTAAAAACTATATTATACGTTTTCAAAACCTTTTAAAAACT
2221940 --A
65 ATA
** ** * *
2221941 TATTATACATTTTCAAAACCGTTTTGAAAACTATATTATATGTTTTCAAAACCGTTTTAAAAAAC
1 TATTATATGTTTTCAAAACTATTTTAAAAACTATATTATACGTTTTCAAAACC-TTTT-AAAAAC
2222006 TATA
64 TATA
* *
2222010 TATTATATGTTTTCAAAACTATTTTAAAACCTATATATATACGTTTTCCAAA-CTATTTAAAAAA
1 TATTATATGTTTTCAAAACTATTTTAAAAACTATAT-TATACGTTTTCAAAACCT-TTT-AAAAA
2222074 CTATA
63 CTATA
* * ** *
2222079 TACTATATGTTTTC-GAACCGTTTTAAAAACTATATATTATACGTTTTCAAAAACTATTTTTAAA
1 TATTATATGTTTTCAAAACTATTTTAAAAAC--TATATTATACGTTTTC-AAAAC--CTTTTAAA
2222143 AACTATA
61 AACTATA
* * * *
2222150 TATTACA--TTTTC-CAACTATTTTGAAAAACTATATACTATATGTTTTCAAAATCGTTTTAAAA
1 TATTATATGTTTTCAAAACTATTTT-AAAAACTATAT--TATACGTTTTCAAAA-CCTTTTAAAA
2222212 AC--TA
62 ACTATA
*
2222216 TATTATACG-TTTCTAAAACTATTTTAAAAACTATATATTATACGT
1 TATTATATGTTTTC-AAAACTATTTTAAAAAC--TATATTATACGT
2222261 GTTTTTGCAA
Statistics
Matches: 261, Mismatches: 35, Indels: 44
0.77 0.10 0.13
Matches are distributed among these distances:
63 11 0.04
64 32 0.12
65 3 0.01
66 14 0.05
67 4 0.02
68 40 0.15
69 95 0.36
70 43 0.16
71 15 0.06
72 3 0.01
73 1 0.00
ACGTcount: A:0.41, C:0.12, G:0.05, T:0.43
Consensus pattern (67 bp):
TATTATATGTTTTCAAAACTATTTTAAAAACTATATTATACGTTTTCAAAACCTTTTAAAAACTA
TA
Found at i:2222108 original size:103 final size:105
Alignment explanation
Indices: 2221906--2222258 Score: 462
Period size: 103 Copynumber: 3.4 Consensus size: 105
2221896 ATTTTTTAAA
* * ** **
2221906 TATATATTATACGTTTTCAAAATC-A-TTTAAAAAC-ATAT-TATACATTTTCAAAACCGTTTTG
1 TATATATTATACGTTTTCAAAAACTATTTTAAAAACTATATATATACATTTTCCAAACTATTTAA
2221967 AAAACTATAT--TATATGTTTTCAAAACCGTTTTAAAAAAC
66 AAAACTATATACTATATGTTTTCAAAACCGTTTT-AAAAAC
* * *
2222006 TATATATTATATGTTTTC-AAAACTATTTTAAAACCTATATATATACGTTTTCCAAACTATTTAA
1 TATATATTATACGTTTTCAAAAACTATTTTAAAAACTATATATATACATTTTCCAAACTATTTAA
*
2222070 AAAACTATATACTATATGTTTTC-GAACCGTTTTAAAAAC
66 AAAACTATATACTATATGTTTTCAAAACCGTTTTAAAAAC
2222109 TATATATTATACGTTTTCAAAAACTATTTTTAAAAACTATATAT-TACATTTTCC-AACTATTTT
1 TATATATTATACGTTTTCAAAAACTA-TTTTAAAAACTATATATATACATTTTCCAAACTA-TTT
* *
2222172 GAAAAACTATATACTATATGTTTTCAAAATCGTTTTAAAAAC
64 AAAAAACTATATACTATATGTTTTCAAAACCGTTTTAAAAAC
*
2222214 --TATATTATACG-TTTCTAAAACTATTTTAAAAACTATATATTATAC
1 TATATATTATACGTTTTCAAAAACTATTTTAAAAACTATATA-TATAC
2222259 GTGTTTTTGC
Statistics
Matches: 224, Mismatches: 17, Indels: 21
0.85 0.06 0.08
Matches are distributed among these distances:
99 4 0.02
100 18 0.08
101 24 0.11
102 16 0.07
103 69 0.31
104 52 0.23
105 41 0.18
ACGTcount: A:0.41, C:0.13, G:0.04, T:0.42
Consensus pattern (105 bp):
TATATATTATACGTTTTCAAAAACTATTTTAAAAACTATATATATACATTTTCCAAACTATTTAA
AAAACTATATACTATATGTTTTCAAAACCGTTTTAAAAAC
Found at i:2233863 original size:19 final size:18
Alignment explanation
Indices: 2233826--2233863 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2233816 AAACTAAATT
2233826 AAAAAAGAAAAAATGAAG
1 AAAAAAGAAAAAATGAAG
2233844 AAAAAAGTAATAAAAT-AAG
1 AAAAAAG-AA-AAAATGAAG
2233863 A
1 A
2233864 GAATTTTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 6 0.33
20 5 0.28
ACGTcount: A:0.76, C:0.00, G:0.13, T:0.11
Consensus pattern (18 bp):
AAAAAAGAAAAAATGAAG
Found at i:2234691 original size:27 final size:29
Alignment explanation
Indices: 2234634--2234692 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
2234624 AGGATTTTTC
* *
2234634 TTGGTATTTTTTGTGGTGTTCGATTGCTG
1 TTGGTATTTTTTGTGGTGTTCCAATGCTG
*
2234663 TTGGTATTTTTTG-GGTTTTCCAATG-TG
1 TTGGTATTTTTTGTGGTGTTCCAATGCTG
2234690 TTG
1 TTG
2234693 TGTTTGTGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 5 0.19
28 9 0.33
29 13 0.48
ACGTcount: A:0.08, C:0.07, G:0.29, T:0.56
Consensus pattern (29 bp):
TTGGTATTTTTTGTGGTGTTCCAATGCTG
Found at i:2235054 original size:7 final size:7
Alignment explanation
Indices: 2235032--2235081 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 7
2235022 ACCTTGACCG
2235032 AAATAA-
1 AAATAAT
2235038 AAATAA-
1 AAATAAT
2235044 AAATAAT
1 AAATAAT
2235051 AAATAAAT
1 AAAT-AAT
2235059 AAATAAT
1 AAATAAT
2235066 -AATAAAT
1 AAAT-AAT
*
2235073 AAAAAAT
1 AAATAAT
2235080 AA
1 AA
2235082 TATGTAATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
6 15 0.38
7 15 0.38
8 9 0.23
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (7 bp):
AAATAAT
Found at i:2235064 original size:21 final size:21
Alignment explanation
Indices: 2235038--2235081 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2235028 ACCGAAATAA
2235038 AAATAAAAAT-AATAAATAAAT
1 AAATAAAAATAAATAAA-AAAT
*
2235059 AAATAATAATAAATAAAAAAT
1 AAATAAAAATAAATAAAAAAT
2235080 AA
1 AA
2235082 TATGTAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (21 bp):
AAATAAAAATAAATAAAAAAT
Found at i:2235231 original size:103 final size:103
Alignment explanation
Indices: 2235109--2235471 Score: 351
Period size: 103 Copynumber: 3.5 Consensus size: 103
2235099 TATATAGTAT
* * *
2235109 TATATTATATGTTTTCAAAAAAGTTTTTAAAATATATATTATACGTTTTCAAAATCCTTTAAAAA
1 TATACTATATGTTTTCAAAACAGTTTTTAAAATATATATTATACGTTTTCAAAATCTTTTAAAAA
* * * *
2235174 ATGTATATTATACGTTTTTAAAACCATTTCGAAAACTA
66 CTATATATTATACGTTTTCAAAACCATTTCAAAAACTA
*
2235212 TATTA-TATATGTTTTCAAAACTGTTTTTAAAA-ACTATATTATACGTTTTCAAAA-CTTTTTAA
1 TA-TACTATATGTTTTCAAAACAGTTTTTAAAATA-TATATTATACGTTTTCAAAATC-TTTTAA
* * * *
2235274 AAACTATATATTATACATTTTCCAAACTATTTTAAAAACTA
63 AAACTATATATTATACGTTTTCAAAACCATTTCAAAAACTA
* * * *
2235315 TATACCATATGTTTTCAAAACCA-TTTTAAAAATTATATATTATACATTTTCAAAACTATTTTTA
1 TATACTATATGTTTTCAAAA-CAGTTTTTAAAA-TATATATTATACGTTTTCAAAA-T-CTTTTA
* * * * *
2235379 AAAACTATATATTATACGCTTTCCAAACTATTTTGAAAAACTC
62 AAAACTATATATTATACGTTTTCAAAACCA-TTTCAAAAACTA
* * * * *
2235422 TATATTATACGCTTTT-AAAATTA-TTTTAAAAACTATATATTAAACGTTTT
1 TATACTATATG-TTTTCAAAA-CAGTTTTTAAAA-TATATATTATACGTTTT
2235472 TTTTAAAACA
Statistics
Matches: 220, Mismatches: 28, Indels: 20
0.82 0.10 0.07
Matches are distributed among these distances:
102 4 0.02
103 109 0.50
104 22 0.10
105 1 0.00
106 33 0.15
107 47 0.21
108 4 0.02
ACGTcount: A:0.41, C:0.12, G:0.04, T:0.44
Consensus pattern (103 bp):
TATACTATATGTTTTCAAAACAGTTTTTAAAATATATATTATACGTTTTCAAAATCTTTTAAAAA
CTATATATTATACGTTTTCAAAACCATTTCAAAAACTA
Found at i:2235250 original size:36 final size:35
Alignment explanation
Indices: 2235109--2235471 Score: 348
Period size: 35 Copynumber: 10.4 Consensus size: 35
2235099 TATATAGTAT
* **
2235109 TATATTATATGTTTTCAAAAAAGTTTTT-AAAA-TA
1 TATATTATACGTTTTC-AAAACTTTTTTAAAAACTA
** * *
2235143 TATATTATACGTTTTCAAAA-TCCTTTAAAAAATG
1 TATATTATACGTTTTCAAAACTTTTTTAAAAACTA
* ** **
2235177 TATATTATACGTTTTTAAAACCATTTCGAAAACTA
1 TATATTATACGTTTTCAAAACTTTTTTAAAAACTA
*
2235212 TAT-TATATATGTTTTCAAAACTGTTTTTAAAAAC--
1 TATAT-TATACGTTTTCAAAACT-TTTTTAAAAACTA
2235246 TATATTATACGTTTTCAAAAC-TTTTTAAAAACTA
1 TATATTATACGTTTTCAAAACTTTTTTAAAAACTA
* * *
2235280 TATATTATACATTTTCCAAACTATTTTAAAAACTA
1 TATATTATACGTTTTCAAAACTTTTTTAAAAACTA
** * ** *
2235315 TATACCATATGTTTTCAAAACCATTTTAAAAATTA
1 TATATTATACGTTTTCAAAACTTTTTTAAAAACTA
*
2235350 TATATTATACATTTTCAAAACTATTTTTAAAAACTA
1 TATATTATACGTTTTCAAAACT-TTTTTAAAAACTA
* * * *
2235386 TATATTATACGCTTTCCAAACTATTTTGAAAAACTC
1 TATATTATACGTTTTCAAAACT-TTTTTAAAAACTA
2235422 TATATTATACGCTTTT-AAAA-TTATTTTAAAAACTA
1 TATATTATACG-TTTTCAAAACTT-TTTTAAAAACTA
*
2235457 TATATTAAACGTTTT
1 TATATTATACGTTTT
2235472 TTTTAAAACA
Statistics
Matches: 270, Mismatches: 47, Indels: 24
0.79 0.14 0.07
Matches are distributed among these distances:
32 14 0.05
33 8 0.03
34 78 0.29
35 103 0.38
36 64 0.24
37 3 0.01
ACGTcount: A:0.41, C:0.12, G:0.04, T:0.44
Consensus pattern (35 bp):
TATATTATACGTTTTCAAAACTTTTTTAAAAACTA
Found at i:2238057 original size:28 final size:28
Alignment explanation
Indices: 2238017--2238073 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
2238007 TTGATATTGG
*
2238017 AGATACTGAAGCTAACTGTCAGTAAACC
1 AGATACTGAAGCTAACCGTCAGTAAACC
2238045 AGATACTGAAGCTAACCGTCAGTAAACC
1 AGATACTGAAGCTAACCGTCAGTAAACC
2238073 A
1 A
2238074 ACTTTTTCGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.40, C:0.23, G:0.18, T:0.19
Consensus pattern (28 bp):
AGATACTGAAGCTAACCGTCAGTAAACC
Found at i:2245115 original size:43 final size:43
Alignment explanation
Indices: 2245055--2245139 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
2245045 CTGTGTATTT
*
2245055 TTTTTTCATAGGATTTAAAAGTTTGGAAGAAGAGTGGTTGTAC
1 TTTTTTCATAGGATTTAAAAGTTTGGAAGAAGAGTAGTTGTAC
* *
2245098 TTTTTTCGA-AGGGTTTAAAGGTTTGGAAGAAGAGTAGTTGTA
1 TTTTTTC-ATAGGATTTAAAAGTTTGGAAGAAGAGTAGTTGTA
2245140 TTCTTTTGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 37 0.97
44 1 0.03
ACGTcount: A:0.29, C:0.04, G:0.28, T:0.39
Consensus pattern (43 bp):
TTTTTTCATAGGATTTAAAAGTTTGGAAGAAGAGTAGTTGTAC
Found at i:2246146 original size:76 final size:74
Alignment explanation
Indices: 2245925--2246164 Score: 239
Period size: 76 Copynumber: 3.1 Consensus size: 74
2245915 TTTTAGGCTC
* * **
2245925 AACCCATTTTATTAATAAAAATATTAACATTTCAGATTAAAACTTATTTCTTAGTGAATTATTAT
1 AACCTATTTTATTAATAAAAATATTAACATTTCAGA-TAAAAC-TATTTTTTAGTGAACCA-TAT
* **
2245990 ATTCTTGGGTGT
63 ATTTTTGGGCAT
* * * * *
2246002 AACCTATTTTATTAA-AAAAATATTAACATTCCAAATAGTAACCTATTTTTGAGTCAACCATGAT
1 AACCTATTTTATTAATAAAAATATTAACATTTCAGATA--AAACTATTTTTTAGTGAACCAT-AT
2246066 ATTTTTGGGCAT
63 ATTTTTGGGCAT
* * *
2246078 AACCTATTTTATTAATAAAAATATTAATATTTCAGATCACAAACTATTTTTTAGTGAGCCATACA
1 AACCTATTTTATTAATAAAAATATTAACATTTCAGAT-A-AAACTATTTTTTAGTGAACCATATA
* *
2246143 TTTTTAGGCAC
64 TTTTTGGGCAT
2246154 AACCATATTTT
1 AACC-TATTTT
2246165 TATATACATT
Statistics
Matches: 134, Mismatches: 23, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
75 3 0.02
76 71 0.53
77 59 0.44
78 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (74 bp):
AACCTATTTTATTAATAAAAATATTAACATTTCAGATAAAACTATTTTTTAGTGAACCATATATT
TTTGGGCAT
Found at i:2251633 original size:17 final size:18
Alignment explanation
Indices: 2251595--2251635 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
2251585 TTGTCACTTG
2251595 TTTTA-TCCTTTTTTACGA
1 TTTTAGTCCTTTTTTAC-A
2251613 -TTTAGTCCTTTTTTA-A
1 TTTTAGTCCTTTTTTACA
2251629 TTTTAGT
1 TTTTAGT
2251636 TTTACTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 1 0.05
17 10 0.48
18 10 0.48
ACGTcount: A:0.17, C:0.12, G:0.07, T:0.63
Consensus pattern (18 bp):
TTTTAGTCCTTTTTTACA
Found at i:2251864 original size:8 final size:8
Alignment explanation
Indices: 2251836--2251908 Score: 51
Period size: 8 Copynumber: 9.0 Consensus size: 8
2251826 ATACCATTTG
*
2251836 TATTTGTT
1 TATTTTTT
*
2251844 T-TTTTCT
1 TATTTTTT
2251851 TA-TTTTT
1 TATTTTTT
2251858 TATTTTTT
1 TATTTTTT
2251866 TATTTTTT
1 TATTTTTT
*
2251874 TCTTTTTAT
1 TATTTTT-T
* *
2251883 CTCTTGATTT
1 -TATT-TTTT
*
2251893 TATTTATT
1 TATTTTTT
2251901 TATTTTTT
1 TATTTTTT
2251909 CCTTAAGTGT
Statistics
Matches: 51, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
7 11 0.22
8 29 0.57
9 4 0.08
10 5 0.10
11 2 0.04
ACGTcount: A:0.12, C:0.05, G:0.03, T:0.79
Consensus pattern (8 bp):
TATTTTTT
Found at i:2251879 original size:15 final size:14
Alignment explanation
Indices: 2251836--2251882 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 14
2251826 ATACCATTTG
*
2251836 TATTTGTTTTTTTCT
1 TATTT-TTTTTTTTT
2251851 TATTTTTTATTTTTT
1 TATTTTTT-TTTTTT
*
2251866 TATTTTTTTCTTTT
1 TATTTTTTTTTTTT
2251880 TAT
1 TAT
2251883 CTCTTGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 11 0.38
15 18 0.62
ACGTcount: A:0.11, C:0.04, G:0.02, T:0.83
Consensus pattern (14 bp):
TATTTTTTTTTTTT
Found at i:2255782 original size:95 final size:95
Alignment explanation
Indices: 2255672--2255853 Score: 285
Period size: 95 Copynumber: 1.9 Consensus size: 95
2255662 ATATTATTTA
*
2255672 TATACAATAAAGCTTGAGTTGTCCCTAT-AGAGCAATTGGTTAAACACCCCGACTTTATGGATAA
1 TATACAATAAAGCTTGAGCTGTCCCTATAAG-GCAATTGGTTAAACACCCCGACTTTATGGATAA
* *
2255736 TATTCAGCTAGCCTGATAAAGGTGATTATAC
65 GATTCAGCTAACCTGATAAAGGTGATTATAC
* ** *
2255767 TATACAATAAAGCTTGAGCTGTCCCTCTAAGGCAATTGGTTAAATGCCCCGGCTTTATGGATAAG
1 TATACAATAAAGCTTGAGCTGTCCCTATAAGGCAATTGGTTAAACACCCCGACTTTATGGATAAG
2255832 ATTCAGCTAACCTGATAAAGGT
66 ATTCAGCTAACCTGATAAAGGT
2255854 ATTTACATAT
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
95 77 0.97
96 2 0.03
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (95 bp):
TATACAATAAAGCTTGAGCTGTCCCTATAAGGCAATTGGTTAAACACCCCGACTTTATGGATAAG
ATTCAGCTAACCTGATAAAGGTGATTATAC
Found at i:2257252 original size:106 final size:108
Alignment explanation
Indices: 2257109--2257402 Score: 398
Period size: 106 Copynumber: 2.7 Consensus size: 108
2257099 TAATTTACTC
* **
2257109 AAAA-AAAGTTTTGTCTCTCTTGAGACGGTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAG
1 AAAACAAA-TTTTGTCTCTATTGAGACATTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAG
2257173 TTTCTCGTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCGT
65 TTTCTCGTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCGT
* *
2257217 AAAA-TAATTTTGTCT-TTTTGAGACATTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAGT
1 AAAACAAATTTTGTCTCTATTGAGACATTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAGT
* * * * *
2257280 TTCTTGTAAAACAATTTTTTTCTCTCTTGAGACATTTTCTCTT
66 TTCTCGTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCGT
* ** *
2257323 AAAACAAATTTTGTCTCTATTGAGACAGTTTTC-ATTGGATCAAATTTTGTCTCTCTTGAGACAG
1 AAAACAAATTTTGTCTCTATTGAGACA-TTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAG
* *
2257387 TTTCCCTTAAAACAAA
65 TTTCTCGTAAAACAAA
2257403 ATCTTTAAAT
Statistics
Matches: 164, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
106 87 0.53
107 18 0.11
108 54 0.33
109 5 0.03
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.42
Consensus pattern (108 bp):
AAAACAAATTTTGTCTCTATTGAGACATTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAGT
TTCTCGTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCGT
Found at i:2257355 original size:37 final size:36
Alignment explanation
Indices: 2257109--2257402 Score: 400
Period size: 36 Copynumber: 8.2 Consensus size: 36
2257099 TAATTTACTC
*
2257109 AAAA-AAAGTTTTGTCTCTCTTGAGACGGTTTCTCTT
1 AAAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCTT
*
2257145 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCGT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
*
2257181 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCGT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
* * *
2257217 AAAA-TAATTTTGTCT-TTTTGAGACATTTTCTCTT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
2257251 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCT-TGT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCT-T
* * *
2257287 AAAACAATTTTTTTCTCTCTTGAGACATTTTCTCTT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
*
2257323 AAAACAAATTTTGTCTCTATTGAGACAGTTT-TCATT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTC-TT
** * *
2257359 GGATCAAATTTTGTCTCTCTTGAGACAGTTTCCCTT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
2257395 AAAACAAA
1 AAAACAAA
2257403 ATCTTTAAAT
Statistics
Matches: 227, Mismatches: 24, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
34 20 0.09
35 23 0.10
36 179 0.79
37 5 0.02
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.42
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
Found at i:2257506 original size:101 final size:101
Alignment explanation
Indices: 2257314--2257605 Score: 356
Period size: 101 Copynumber: 2.9 Consensus size: 101
2257304 TCTTGAGACA
* * * * *
2257314 TTTTCTCTTAAAACAAATTTTGTCTCTATTGAGACAGTTT-TCATTGGATCAAATTTTGTCTCTC
1 TTTTC-CTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCT-TTTGAATTAAGTTTTGTCTCTC
*
2257378 TTGAGACAGTTTCCCTTAAAACAAAATCTTTAAATCTG
64 TTGAGACAGTTTCCCTTGAAACAAAATCTTTAAATCTG
* * *
2257416 TTTTCCTTTAAACAAATTTTGTCTCTCTCGAGACAGTTTCTTTTGAAATTAAGTTTTATCTCTCT
1 TTTTCCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCTTTTG-AATTAAGTTTTGTCTCTCT
* * *
2257481 TGAAACAGTTTCCCTTGAAA-TAAATCTTTGAATCTG
65 TGAGACAGTTTCCCTTGAAACAAAATCTTTAAATCTG
* * * * *
2257517 TTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAATTTCTTTTGGAACT-AGATTTTGTCTCTC
1 TTTTCCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCTTTT-GAATTAAG-TTTTGTCTCTC
*
2257581 TTGAGACAGTTTCCCTTGAATCAAA
64 TTGAGACAGTTTCCCTTGAAACAAA
2257606 TTTTGTCTCT
Statistics
Matches: 163, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
100 2 0.01
101 119 0.73
102 42 0.26
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (101 bp):
TTTTCCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCTTTTGAATTAAGTTTTGTCTCTCTT
GAGACAGTTTCCCTTGAAACAAAATCTTTAAATCTG
Found at i:2257615 original size:36 final size:36
Alignment explanation
Indices: 2257516--2257805 Score: 281
Period size: 37 Copynumber: 8.1 Consensus size: 36
2257506 CTTTGAATCT
* * *
2257516 GTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* ** * *
2257552 ATTTCTTTTGGAACTAGATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACA
*
2257589 GTTTCCCTTGAATCAAATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* *
2257625 GTTTCCCTTGAAACAAA----AT-T-T-TTGA-ATCT
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGA-CA
* * *
2257654 GTTTTCCTTTAAACAAATTTTCGTCTCTCTCGAGACA
1 GTTTCCCTTGAAACAAATTTT-GTCTCTCTTGAGACA
** * *
2257691 GTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACA
** *
2257728 GTTTATCTTGAAATAAATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
*
2257764 GTTTCCCTTGAAACAAAGTTTTGCCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGACA
2257801 GTTTC
1 GTTTC
2257806 TATTGAAGCA
Statistics
Matches: 203, Mismatches: 38, Indels: 25
0.76 0.14 0.09
Matches are distributed among these distances:
28 1 0.00
29 20 0.10
30 1 0.00
31 1 0.00
32 1 0.00
34 1 0.00
35 1 0.00
36 82 0.40
37 88 0.43
38 7 0.03
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.42
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
Found at i:2257646 original size:73 final size:73
Alignment explanation
Indices: 2257516--2257805 Score: 283
Period size: 73 Copynumber: 4.1 Consensus size: 73
2257506 CTTTGAATCT
* * * * ** * * *
2257516 GTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAATTTCTTTTGGAACTAGATTTTGTCTCTC
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTC
2257581 TTGAGACA
66 TTGAGACA
*
2257589 GTTTCCCTTGAATCAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAA-----T-T-T-
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTC
*
2257646 TTGA-ATCT
66 TTGAGA-CA
* * * ** * * *
2257654 GTTTTCCTTTAAACAAATTTTCGTCTCTCTCGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCT
1 GTTTCCCTTGAAACAAATTTT-GTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCT
2257719 CTTGAGACA
65 CTTGAGACA
** * * *
2257728 GTTTATCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGCCTCTC
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTC
2257793 TTGAGACA
66 TTGAGACA
2257801 GTTTC
1 GTTTC
2257806 TATTGAAGCA
Statistics
Matches: 174, Mismatches: 32, Indels: 22
0.76 0.14 0.10
Matches are distributed among these distances:
64 1 0.01
65 23 0.13
66 28 0.16
67 1 0.01
68 1 0.01
71 1 0.01
72 1 0.01
73 95 0.55
74 22 0.13
75 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.42
Consensus pattern (73 bp):
GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTC
TTGAGACA
Found at i:2257719 original size:139 final size:138
Alignment explanation
Indices: 2257431--2257785 Score: 527
Period size: 139 Copynumber: 2.6 Consensus size: 138
2257421 CTTTAAACAA
* * * * *
2257431 ATTTTGTCTCTCTCGAGACAGTTTCTTTTGAAATTAAGTTTTATCTCTCTTGAAACAGTTTCCCT
1 ATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA-TAAATTTTGTCTCTCTTGAGACAGTTTCCCT
* * *
2257496 TGAAA-TAAATCTTTGAATCTGTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAATTTCTTT
65 TGAAACAAAATTTTTGAATCTGTTTTCCTTGAAACAAATTTCGTCTCCCTCGAGACAATTTCTTT
2257560 TGGAACTAG
130 TGGAACTAG
*
2257569 ATTTTGTCTCTCTTGAGACAGTTTCCCTTG-AATCAAATTTTGTCTCTCTTGAGACAGTTTCCCT
1 ATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAT-AAATTTTGTCTCTCTTGAGACAGTTTCCCT
* * *
2257633 TGAAACAAAATTTTTGAATCTGTTTTCCTTTAAACAAATTTTCGTCTCTCTCGAGACAGTTTCTT
65 TGAAACAAAATTTTTGAATCTGTTTTCCTTGAAACAAA-TTTCGTCTCCCTCGAGACAATTTCTT
2257698 TTGGAACTA-
129 TTGGAACTAG
*
2257707 AGTTTTGTCTCTCTTGAGACAGTTTATCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCT
1 A-TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCT
*
2257772 TGAAACAAAGTTTT
65 TGAAACAAAATTTT
2257786 GCCTCTCTTG
Statistics
Matches: 197, Mismatches: 15, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
136 1 0.01
137 34 0.17
138 57 0.29
139 102 0.52
140 3 0.02
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.43
Consensus pattern (138 bp):
ATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTT
GAAACAAAATTTTTGAATCTGTTTTCCTTGAAACAAATTTCGTCTCCCTCGAGACAATTTCTTTT
GGAACTAG
Found at i:2257887 original size:36 final size:36
Alignment explanation
Indices: 2257821--2257952 Score: 162
Period size: 36 Copynumber: 3.7 Consensus size: 36
2257811 AAGCACCAAT
**
2257821 CTTTGAAATTGTTTCTCTTGAAACAC--AAAAAAAC
1 CTTTGAAACAGTTTCTCTTGAAACACAAAAAAAAAC
*
2257855 CTTTGAAACAGTTTTTCTTGAAACACAAAAAAAAAAC
1 CTTTGAAACAGTTTCTCTTGAAACAC-AAAAAAAAAC
* *
2257892 C-TTGAGACATTTTCTCTTGAAACACAAAAAAAAAC
1 CTTTGAAACAGTTTCTCTTGAAACACAAAAAAAAAC
** *
2257927 CTTTGAAATTGTTTCTCTTAAAACAC
1 CTTTGAAACAGTTTCTCTTGAAACAC
2257953 CAAACCTTCG
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
34 23 0.28
35 11 0.13
36 40 0.48
37 9 0.11
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.31
Consensus pattern (36 bp):
CTTTGAAACAGTTTCTCTTGAAACACAAAAAAAAAC
Found at i:2258491 original size:2 final size:2
Alignment explanation
Indices: 2258484--2258512 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2258474 ATTTATATGT
2258484 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2258513 TTACATGTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2259749 original size:16 final size:16
Alignment explanation
Indices: 2259725--2259755 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2259715 TATTATATTT
*
2259725 TTATTTATATACCATA
1 TTATATATATACCATA
2259741 TTATATATATACCAT
1 TTATATATATACCAT
2259756 TTCTATTTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (16 bp):
TTATATATATACCATA
Found at i:2259924 original size:35 final size:36
Alignment explanation
Indices: 2259867--2259934 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 36
2259857 ACTTTATTTG
2259867 TTTTTTATGTTTTACTTATTTTATTATTATTTTTTC
1 TTTTTTATGTTTTACTTATTTTATTATTATTTTTTC
* * *
2259903 TTTTTTCT-TTTTCCTTGTTTTATTATTATTTT
1 TTTTTTATGTTTTACTTATTTTATTATTATTTT
2259935 CATGTTTGCA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 22 0.76
36 7 0.24
ACGTcount: A:0.13, C:0.07, G:0.03, T:0.76
Consensus pattern (36 bp):
TTTTTTATGTTTTACTTATTTTATTATTATTTTTTC
Found at i:2268947 original size:65 final size:64
Alignment explanation
Indices: 2268818--2268967 Score: 171
Period size: 65 Copynumber: 2.3 Consensus size: 64
2268808 TATTTTGAAA
* * * *
2268818 GCATTTTGTGTACCGATGCACATCCATACATCGATGCACTCTTGAATTTATTGAAACATTGAAT
1 GCATTTTATGTACCGATGCACAACCATACATCGATGCACTCTAGAATTTATTGAAACATCGAAT
* *
2268882 GCATTTTATGTACCGATGCACAGACCATGCATCGATGCACTCCTAG-CTCTT-TTGAAACATCGA
1 GCATTTTATGTACCGATGCACA-ACCATACATCGATGCACT-CTAGAAT-TTATTGAAACATCGA
2268945 AT
63 AT
* *
2268947 GTA-ATTAGTGTACCGATGCAC
1 GCATTTTA-TGTACCGATGCAC
2268968 CCCTAGTGTA
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
64 24 0.32
65 45 0.61
66 5 0.07
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (64 bp):
GCATTTTATGTACCGATGCACAACCATACATCGATGCACTCTAGAATTTATTGAAACATCGAAT
Found at i:2282596 original size:12 final size:12
Alignment explanation
Indices: 2282581--2282608 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
2282571 ACAAGGGCAA
2282581 AAAAATAAAATC
1 AAAAATAAAATC
2282593 AAAAATAAAATC
1 AAAAATAAAATC
2282605 AAAA
1 AAAA
2282609 TGTAGTTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (12 bp):
AAAAATAAAATC
Found at i:2285524 original size:16 final size:16
Alignment explanation
Indices: 2285503--2285535 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2285493 ACCATCCAAG
2285503 AACCAAAGTGTTATTC
1 AACCAAAGTGTTATTC
2285519 AACCAAAGTGTTATTC
1 AACCAAAGTGTTATTC
2285535 A
1 A
2285536 GAGAGTTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.30
Consensus pattern (16 bp):
AACCAAAGTGTTATTC
Found at i:2285627 original size:26 final size:26
Alignment explanation
Indices: 2285610--2285661 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
2285600 AAATTTTAGT
2285610 AGATAATAAATTTATAAAATTTCAAG
1 AGATAATAAATTTATAAAATTTCAAG
2285636 AGATAATAAATTTATAAAATTTCAAG
1 AGATAATAAATTTATAAAATTTCAAG
2285662 CATTAAAGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.54, C:0.04, G:0.08, T:0.35
Consensus pattern (26 bp):
AGATAATAAATTTATAAAATTTCAAG
Found at i:2286080 original size:18 final size:18
Alignment explanation
Indices: 2286049--2286085 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2286039 TGATTAAATT
2286049 ATTAGTTATTTTATTAAA
1 ATTAGTTATTTTATTAAA
2286067 ATTA-TTATTATTATTAAA
1 ATTAGTTATT-TTATTAAA
2286085 A
1 A
2286086 GAAGTATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
ATTAGTTATTTTATTAAA
Found at i:2286806 original size:19 final size:19
Alignment explanation
Indices: 2286773--2286809 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2286763 TAATTAGCAG
2286773 TAATATTAATATTTTATTT
1 TAATATTAATATTTTATTT
2286792 TAATCATTAAT-TTTTATT
1 TAAT-ATTAATATTTTATT
2286810 AGTATTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
TAATATTAATATTTTATTT
Found at i:2286855 original size:31 final size:29
Alignment explanation
Indices: 2286797--2286855 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
2286787 TATTTTAATC
*
2286797 ATTAATTTTTATTAGTATTAATTTTGACT
1 ATTAATTTTTATTAGTATTAATCTTGACT
2286826 ATTAATTTTTATT-GATCCATTAATCTTGAC
1 ATTAATTTTTATTAG-T--ATTAATCTTGAC
2286856 AATTTCATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 1 0.04
29 14 0.54
31 11 0.42
ACGTcount: A:0.31, C:0.08, G:0.07, T:0.54
Consensus pattern (29 bp):
ATTAATTTTTATTAGTATTAATCTTGACT
Found at i:2297863 original size:20 final size:18
Alignment explanation
Indices: 2297820--2297859 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
2297810 AAAACATTGG
2297820 GGAA-CTCTCTGACTATA
1 GGAATCTCTCTGACTATA
2297837 GGAATCTCTCTGACTATA
1 GGAATCTCTCTGACTATA
2297855 GGAAT
1 GGAAT
2297860 ATCTTTTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (18 bp):
GGAATCTCTCTGACTATA
Found at i:2300355 original size:21 final size:21
Alignment explanation
Indices: 2300329--2300409 Score: 108
Period size: 21 Copynumber: 3.9 Consensus size: 21
2300319 ATATGAAATT
*
2300329 TGTCCCGAATGACCTCATGTA
1 TGTCCCGAAGGACCTCATGTA
2300350 TGTCCCGAAGGACCTCATGTA
1 TGTCCCGAAGGACCTCATGTA
* * * *
2300371 TGTCCTGAAAGACCTCGTATA
1 TGTCCCGAAGGACCTCATGTA
*
2300392 TGTCCCGAAGGACATCAT
1 TGTCCCGAAGGACCTCAT
2300410 ATAACCCTCG
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (21 bp):
TGTCCCGAAGGACCTCATGTA
Found at i:2318660 original size:3 final size:3
Alignment explanation
Indices: 2318652--2318677 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2318642 TAAAGGAATT
2318652 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
2318678 TTGTTCCCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2320170 original size:28 final size:27
Alignment explanation
Indices: 2320122--2320179 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
2320112 AGGGGTGCAT
2320122 AAAAAATCCGAATATCCGATTTTGCGAA
1 AAAAAATCCGAATATCCGA-TTTGCGAA
* * *
2320150 AAAAATATTCGAA-ATCGGATTTGGGAA
1 AAAAA-ATCCGAATATCCGATTTGCGAA
2320177 AAA
1 AAA
2320180 CCGATTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 10 0.38
28 10 0.38
29 6 0.23
ACGTcount: A:0.47, C:0.12, G:0.17, T:0.24
Consensus pattern (27 bp):
AAAAAATCCGAATATCCGATTTGCGAA
Found at i:2322431 original size:45 final size:45
Alignment explanation
Indices: 2322345--2322729 Score: 521
Period size: 45 Copynumber: 8.6 Consensus size: 45
2322335 CCTCCATTCA
* *
2322345 TGTTTATAATGCA-TCATTATGCATTTTCAACTATAGCATACTTTTAC
1 TGTTGATAATGCACCCA-TATGCA-TTTCAACTATAGCATACTTTT-C
* *
2322392 -GTTGATAATGCACCTATATGCATTTCAACTTTAGCATACTTTTC
1 TGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTTC
*
2322436 TGTTGATAATGCACCCATATGCATTTCAACTATAACATACTTTT-
1 TGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTTC
* * * *
2322480 T-TTTATAATGCACCCATATACATTCCAACTATAGCATAATTTTC
1 TGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTTC
*
2322524 TTGTTGATAATGCACCCATATGCATTTCAACTATAACATACTTTTC
1 -TGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTTC
2322570 TGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTTC
1 TGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTTC
* * *
2322615 TGTTGATAATGCACCCATATGCATTTTAACTATATCATATTTTTC
1 TGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTTC
*
2322660 TGTTGATAATGCACCCATATGCATTTCAACTAT-GACAT-CCTTTC
1 TGTTGATAATGCACCCATATGCATTTCAACTATAG-CATACTTTTC
** *
2322704 ATGCCGATAATGTACCCATATGCATT
1 -TGTTGATAATGCACCCATATGCATT
2322730 ATTAATTTCA
Statistics
Matches: 303, Mismatches: 28, Indels: 16
0.87 0.08 0.05
Matches are distributed among these distances:
43 37 0.12
44 6 0.02
45 204 0.67
46 55 0.18
47 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.39
Consensus pattern (45 bp):
TGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTTC
Found at i:2325926 original size:17 final size:19
Alignment explanation
Indices: 2325904--2325947 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
2325894 ATAATTATAT
2325904 AAATATTAT-TTTA-ATAA
1 AAATATTATATTTACATAA
*
2325921 AAATATAATATTTACATAA
1 AAATATTATATTTACATAA
*
2325940 ATATATTA
1 AAATATTA
2325948 ATATAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 8 0.36
18 4 0.18
19 10 0.45
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
AAATATTATATTTACATAA
Found at i:2325939 original size:19 final size:18
Alignment explanation
Indices: 2325891--2325951 Score: 54
Period size: 17 Copynumber: 3.4 Consensus size: 18
2325881 TTCTAAATAA
* *
2325891 ATAATAATT-ATATAAAT
1 ATAATATTTAATAAAAAT
*
2325908 ATTAT-TTTAATAAAAAT
1 ATAATATTTAATAAAAAT
*
2325925 ATAATATTTACATAAATAT
1 ATAATATTTA-ATAAAAAT
2325944 ATTAATAT
1 A-TAATAT
2325952 AAAAAATAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
16 2 0.06
17 15 0.43
18 4 0.11
19 8 0.23
20 6 0.17
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
ATAATATTTAATAAAAAT
Found at i:2325989 original size:32 final size:34
Alignment explanation
Indices: 2325917--2325992 Score: 88
Period size: 33 Copynumber: 2.3 Consensus size: 34
2325907 TATTATTTTA
* *
2325917 ATAAAAAT-ATAATATTTACATAAATATATTAAT
1 ATAAAAATAATAATATTTACATAAATATACTAAC
2325950 ATAAAAAATAATAACTATTTA-A-AAA-ATACTAAC
1 AT-AAAAATAATAA-TATTTACATAAATATACTAAC
2325983 ATAAAAATAA
1 ATAAAAATAA
2325993 ATTTCTTACC
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
32 8 0.21
33 10 0.26
34 9 0.24
35 5 0.13
36 6 0.16
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (34 bp):
ATAAAAATAATAATATTTACATAAATATACTAAC
Found at i:2326993 original size:3 final size:3
Alignment explanation
Indices: 2326982--2327014 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
2326972 ATTATTACTA
2326982 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2327015 CAAGCCCAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:2328283 original size:26 final size:27
Alignment explanation
Indices: 2328254--2328324 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 27
2328244 ATATATATGG
2328254 TTTTATTCATATTATTATATTTCTCT-
1 TTTTATTCATATTATTATATTTCTCTA
* *
2328280 TTTTCTTC--ATT-TTATATTTCTTTAA
1 TTTTATTCATATTATTATATTTCTCT-A
* *
2328305 TTTTAGTCATATTAATATAT
1 TTTTATTCATATTATTATAT
2328325 ATTATTTGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
23 11 0.31
24 3 0.09
25 6 0.17
26 7 0.20
27 3 0.09
28 5 0.14
ACGTcount: A:0.25, C:0.10, G:0.01, T:0.63
Consensus pattern (27 bp):
TTTTATTCATATTATTATATTTCTCTA
Found at i:2328361 original size:31 final size:33
Alignment explanation
Indices: 2328301--2328362 Score: 85
Period size: 31 Copynumber: 1.9 Consensus size: 33
2328291 TTATATTTCT
*
2328301 TTAATTTTAGTCATATTAATATATATTATTTGA
1 TTAATTTTAGTCAAATTAATATATATTATTTGA
2328334 TTAATTTT-GT-AAATTAATA-ATATTTATTT
1 TTAATTTTAGTCAAATTAATATATA-TTATTT
2328363 ATTTTTCAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 3 0.11
31 14 0.52
32 2 0.07
33 8 0.30
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (33 bp):
TTAATTTTAGTCAAATTAATATATATTATTTGA
Found at i:2337539 original size:2 final size:2
Alignment explanation
Indices: 2337532--2337565 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2337522 GGTTGGGTCC
2337532 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2337566 GTACGTTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2337593 original size:18 final size:18
Alignment explanation
Indices: 2337570--2337605 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2337560 ATATATGTAC
2337570 GTTTAATATCTTAATGAT
1 GTTTAATATCTTAATGAT
2337588 GTTTAATATCTTAATGAT
1 GTTTAATATCTTAATGAT
2337606 TACTTTTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.11, T:0.50
Consensus pattern (18 bp):
GTTTAATATCTTAATGAT
Found at i:2337666 original size:2 final size:2
Alignment explanation
Indices: 2337659--2337702 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2337649 AATTTAATCT
2337659 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2337701 TA
1 TA
2337703 AAGTTATAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2352877 original size:2 final size:2
Alignment explanation
Indices: 2352866--2352894 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2352856 CATTTAATGC
2352866 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2352895 AATACTCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2361509 original size:93 final size:93
Alignment explanation
Indices: 2361234--2361509 Score: 453
Period size: 93 Copynumber: 3.0 Consensus size: 93
2361224 TAAGTCATTT
2361234 GGGCCATCAGTAAGGCTTTCGAGCATGATGATTAAGTCTTTCAGGTAATTTGTAAGCCTTCACGG
1 GGGCCATCAGTAAGGCTTTCGAGCATGATGATTAAGTCTTTCAGGTAATTTGTAAGCCTTCACGG
* **
2361299 AAGAGTAGCGAAGCAAACCCATCAATTC
66 AAGAGTAGTGAAGCAAACCCATCAGCTC
**
2361327 GGGCCATCAGTAAGGCTTTCGAGCATGATGATTAAGTCTTTCAGGTAATTCATAAGCCTTCACGG
1 GGGCCATCAGTAAGGCTTTCGAGCATGATGATTAAGTCTTTCAGGTAATTTGTAAGCCTTCACGG
*
2361392 AAGAGTAGTAAAGCAAACCCATCAGCTC
66 AAGAGTAGTGAAGCAAACCCATCAGCTC
* * * *
2361420 GGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCAGGTAATTTGTAAGCCTTCACAG
1 GGGCCATCAGTAAGGCTTTCGAGCATGATGATTAAGTCTTTCAGGTAATTTGTAAGCCTTCACGG
*
2361485 AAGAGTAGTGAAGCAAATCCATCAG
66 AAGAGTAGTGAAGCAAACCCATCAG
2361510 TAAGTCTTTC
Statistics
Matches: 169, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 169 1.00
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (93 bp):
GGGCCATCAGTAAGGCTTTCGAGCATGATGATTAAGTCTTTCAGGTAATTTGTAAGCCTTCACGG
AAGAGTAGTGAAGCAAACCCATCAGCTC
Found at i:2361550 original size:42 final size:42
Alignment explanation
Indices: 2361503--2361591 Score: 142
Period size: 42 Copynumber: 2.1 Consensus size: 42
2361493 TGAAGCAAAT
2361503 CCATCAGTAAGTCTTTCCAGCATGATAATAAAATCCTTCGGG
1 CCATCAGTAAGTCTTTCCAGCATGATAATAAAATCCTTCGGG
* * * *
2361545 CCATCAGTAAGTCTTTCGAGCATGATGATTAAGTCCTTCGGG
1 CCATCAGTAAGTCTTTCCAGCATGATAATAAAATCCTTCGGG
2361587 CCATC
1 CCATC
2361592 TTAAGCCTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (42 bp):
CCATCAGTAAGTCTTTCCAGCATGATAATAAAATCCTTCGGG
Found at i:2361639 original size:36 final size:36
Alignment explanation
Indices: 2361587--2361662 Score: 134
Period size: 36 Copynumber: 2.1 Consensus size: 36
2361577 GTCCTTCGGG
* *
2361587 CCATCTTAAGCCTTCACGGAAGAGTAGTGAAGTAAA
1 CCATATTAAGCCTTCACGGAAGAGTAGTGAAGCAAA
2361623 CCATATTAAGCCTTCACGGAAGAGTAGTGAAGCAAA
1 CCATATTAAGCCTTCACGGAAGAGTAGTGAAGCAAA
2361659 CCAT
1 CCAT
2361663 CAACAAGCCT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (36 bp):
CCATATTAAGCCTTCACGGAAGAGTAGTGAAGCAAA
Found at i:2361693 original size:114 final size:114
Alignment explanation
Indices: 2361561--2361778 Score: 330
Period size: 114 Copynumber: 1.9 Consensus size: 114
2361551 GTAAGTCTTT
* * * * * *
2361561 CGAGCATGATGATTAAGTCCTTCGGGCCATCTTAAGCCTTCACGGAAGAGTAGTGAAGTAAACCA
1 CGAGCATGATGATTAAGTCCTCCAGGCCATCTTAAGCATTCACGGAAAAGTAATGAAGCAAACCA
*
2361626 TATTAAGCCTTCACGGAAGAGTAGTGA-AGCAAACCATCAACAAGCCTTC
66 TATTAAGCCTTCACGGAAGAGT-GTGAGAGCAAACAATCAACAAGCCTTC
2361675 CGAGCATGATGATTAAGTCCTCCAGGCCATCTTAAGCATTCACGGAAAAGTAATGAAGCAAACCA
1 CGAGCATGATGATTAAGTCCTCCAGGCCATCTTAAGCATTCACGGAAAAGTAATGAAGCAAACCA
* * *
2361740 TTTTAAGCCTTCTCGGAAGAGTGTTAGAGCAAACAATCA
66 TATTAAGCCTTCACGGAAGAGTGTGAGAGCAAACAATCA
2361779 GATCATCAGA
Statistics
Matches: 93, Mismatches: 10, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
113 3 0.03
114 90 0.97
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.22
Consensus pattern (114 bp):
CGAGCATGATGATTAAGTCCTCCAGGCCATCTTAAGCATTCACGGAAAAGTAATGAAGCAAACCA
TATTAAGCCTTCACGGAAGAGTGTGAGAGCAAACAATCAACAAGCCTTC
Found at i:2362234 original size:53 final size:53
Alignment explanation
Indices: 2362100--2362349 Score: 333
Period size: 53 Copynumber: 4.7 Consensus size: 53
2362090 CACACCAAAC
*
2362100 GATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAGGTA-AA
1 GATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAGGCAGAA
* * *
2362152 GCTTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGAGAACCCGTAGGCAGAA
1 GATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAGGCAGAA
* * *
2362205 GATTGTTCGAGTTCTACTCCTTGAAGCAAGAGAGAGCGAACCCATAAGCAGAA
1 GATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAGGCAGAA
* * ****
2362258 TATTGTTCGAGTTCTACTCCCTGAAGCAATAGGGAGCGAACCCATTTTTAGAA
1 GATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAGGCAGAA
* *
2362311 GATTGTTCGAGTTCCTTAATCCCTTAA-CAAGAGGGAGCG
1 GATTGTTCGAGTT-C-TACTCCCTGAAGCAAGAGGGAGCG
2362350 GACACGTCAT
Statistics
Matches: 173, Mismatches: 22, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
52 46 0.27
53 106 0.61
54 12 0.07
55 9 0.05
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.24
Consensus pattern (53 bp):
GATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAGGCAGAA
Found at i:2363926 original size:2 final size:2
Alignment explanation
Indices: 2363919--2363952 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2363909 GCTTTGAAAG
2363919 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2363953 AATACTCATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2376584 original size:25 final size:25
Alignment explanation
Indices: 2376517--2376598 Score: 139
Period size: 25 Copynumber: 3.3 Consensus size: 25
2376507 TCCTTGTAGG
*
2376517 TGGCTCCCTAGCCCTTTTCCAACCT
1 TGGCTCCCTAGCCCTTTTCCAGCCT
2376542 TGGCTCCC-AGCCCTTTTCCAGCCT
1 TGGCTCCCTAGCCCTTTTCCAGCCT
*
2376566 TGGCTCCCTAGCCCTTTTCCAGCAT
1 TGGCTCCCTAGCCCTTTTCCAGCCT
2376591 TGGCTCCC
1 TGGCTCCC
2376599 CTCTCTAAGG
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
24 23 0.43
25 31 0.57
ACGTcount: A:0.10, C:0.44, G:0.16, T:0.30
Consensus pattern (25 bp):
TGGCTCCCTAGCCCTTTTCCAGCCT
Found at i:2384657 original size:22 final size:23
Alignment explanation
Indices: 2384632--2384679 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
2384622 TTGCTAAATG
*
2384632 CTCTTCC-TAACGTTCTCTCAAT
1 CTCTTCCATAACGTTCTCGCAAT
*
2384654 CTC-TCCATACCGTTCTCGCAAT
1 CTCTTCCATAACGTTCTCGCAAT
2384676 CTCT
1 CTCT
2384680 CCCCTCTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 3 0.14
22 19 0.86
ACGTcount: A:0.17, C:0.40, G:0.06, T:0.38
Consensus pattern (23 bp):
CTCTTCCATAACGTTCTCGCAAT
Found at i:2391224 original size:20 final size:20
Alignment explanation
Indices: 2391196--2391234 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2391186 ATAGTGCTAC
*
2391196 AGTATACGAAGTATTACTAT
1 AGTACACGAAGTATTACTAT
2391216 AGTACACGAAGTATTACTA
1 AGTACACGAAGTATTACTA
2391235 CAATACCACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (20 bp):
AGTACACGAAGTATTACTAT
Found at i:2393242 original size:25 final size:25
Alignment explanation
Indices: 2393214--2393268 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
2393204 ACTAAACTTT
2393214 CAAAACTTAAATTTTGGCCACTAAC
1 CAAAACTTAAATTTTGGCCACTAAC
*
2393239 CAAAACTTAAATTTTGGCTACTAAC
1 CAAAACTTAAATTTTGGCCACTAAC
2393264 CAAAA
1 CAAAA
2393269 TTTAGGATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.44, C:0.22, G:0.07, T:0.27
Consensus pattern (25 bp):
CAAAACTTAAATTTTGGCCACTAAC
Found at i:2398682 original size:47 final size:48
Alignment explanation
Indices: 2398631--2398747 Score: 146
Period size: 49 Copynumber: 2.4 Consensus size: 48
2398621 ACGAAGAGAT
*
2398631 GAGGAAGCACATCAACAA-TTTTTCAAATTTGATCTTCATAAAAAGAC
1 GAGGAAGCAAATCAACAAGTTTTTCAAATTTGATCTTCATAAAAAGAC
* * *
2398678 GAGGAAGCAAATCAACAATGTTTTTCAGATTTGATCTTCATTAAGAGAC
1 GAGGAAGCAAATCAACAA-GTTTTTCAAATTTGATCTTCATAAAAAGAC
** *
2398727 GACAAAGCAAAACAACCAAGT
1 GAGGAAGCAAATCAA-CAAGT
2398748 GAAGATAAAC
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
47 17 0.28
49 40 0.67
50 3 0.05
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.25
Consensus pattern (48 bp):
GAGGAAGCAAATCAACAAGTTTTTCAAATTTGATCTTCATAAAAAGAC
Found at i:2399187 original size:23 final size:22
Alignment explanation
Indices: 2399137--2399187 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 22
2399127 CGAGAATTCT
2399137 AGTTTATTAAGAATTTTAAATA
1 AGTTTATTAAGAATTTTAAATA
* * * *
2399159 ATTTTATTGAATATTTTTAATTA
1 AGTTTATT-AAGAATTTTAAATA
2399182 AGTTTA
1 AGTTTA
2399188 CCTTTATACT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (22 bp):
AGTTTATTAAGAATTTTAAATA
Found at i:2399747 original size:16 final size:17
Alignment explanation
Indices: 2399709--2399759 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 17
2399699 TTAATTAACG
2399709 TTTATTATTTATTATTTTCC
1 TTTATTA-TT-TTA-TTTCC
2399729 TTTATTATTTTATTT-C
1 TTTATTATTTTATTTCC
2399745 TTTATT-TCTTTATTT
1 TTTATTAT-TTTATTT
2399760 GCTATTTAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 1 0.03
16 14 0.47
17 3 0.10
18 3 0.10
19 2 0.07
20 7 0.23
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTATTATTTTATTTCC
Found at i:2399942 original size:13 final size:14
Alignment explanation
Indices: 2399924--2399953 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
2399914 ATTAATTAAA
2399924 TTGATTCTTTGA-T
1 TTGATTCTTTGACT
2399937 TTGATTCTTTGACT
1 TTGATTCTTTGACT
2399951 TTG
1 TTG
2399954 TAATTAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.13, C:0.10, G:0.17, T:0.60
Consensus pattern (14 bp):
TTGATTCTTTGACT
Found at i:2407748 original size:21 final size:22
Alignment explanation
Indices: 2407722--2407790 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 22
2407712 AGCTGAAAAT
* *
2407722 GAAGCAAG-GGAAGCAGAGAGA
1 GAAGCAAGCGAAAGCACAGAGA
*
2407743 GCAGC-AGCGAAAGCACAGAGA
1 GAAGCAAGCGAAAGCACAGAGA
* * *
2407764 GAAGCAA-CGACAGTATAGAGA
1 GAAGCAAGCGAAAGCACAGAGA
2407785 GAAGCA
1 GAAGCA
2407791 CATATCAGCA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
20 2 0.05
21 36 0.92
22 1 0.03
ACGTcount: A:0.46, C:0.16, G:0.35, T:0.03
Consensus pattern (22 bp):
GAAGCAAGCGAAAGCACAGAGA
Found at i:2408373 original size:43 final size:44
Alignment explanation
Indices: 2408326--2408449 Score: 153
Period size: 44 Copynumber: 2.8 Consensus size: 44
2408316 TTTCGCGGCG
2408326 TTTATGGGAAAAACGCCGGTTAATCTCAACACCTATT-GCAGCA
1 TTTATGGGAAAAACGCCGGTTAATCTCAACACCTATTGGCAGCA
* * * *
2408369 TTTATGGGAAAAACACC-GCTAAGTCTCAACACCTATTGGCGGCG
1 TTTATGGGAAAAACGCCGGTTAA-TCTCAACACCTATTGGCAGCA
* * * *
2408413 TTTGTGGGGAAAACGCCGCTAAATCTCAACACCTATT
1 TTTATGGGAAAAACGCCGGTTAATCTCAACACCTATT
2408450 ATGGATATCT
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
42 4 0.06
43 30 0.44
44 32 0.47
45 2 0.03
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (44 bp):
TTTATGGGAAAAACGCCGGTTAATCTCAACACCTATTGGCAGCA
Found at i:2408440 original size:44 final size:43
Alignment explanation
Indices: 2408320--2408449 Score: 179
Period size: 43 Copynumber: 3.0 Consensus size: 43
2408310 TATGCATTTC
* *
2408320 GCGGCGTTTATGGGAAAAACGCCGGTTAATCTCAACACCTATT
1 GCGGCGTTTATGGGAAAAACGCCGCTAAATCTCAACACCTATT
* * * *
2408363 GCAGCATTTATGGGAAAAACACCGCTAAGTCTCAACACCTATT
1 GCGGCGTTTATGGGAAAAACGCCGCTAAATCTCAACACCTATT
* *
2408406 GGCGGCGTTTGTGGGGAAAACGCCGCTAAATCTCAACACCTATT
1 -GCGGCGTTTATGGGAAAAACGCCGCTAAATCTCAACACCTATT
2408450 ATGGATATCT
Statistics
Matches: 74, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
43 37 0.50
44 37 0.50
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (43 bp):
GCGGCGTTTATGGGAAAAACGCCGCTAAATCTCAACACCTATT
Found at i:2414922 original size:45 final size:45
Alignment explanation
Indices: 2414845--2415083 Score: 255
Period size: 45 Copynumber: 5.3 Consensus size: 45
2414835 AATACATCAT
* * * *
2414845 TATGCATTTTAAACTATAATAT-CTTTTTTGTTGATAATGCACCTA
1 TATGCA-TTTCAACTATAGTATACTTTTCTGTTGATAATGCACCCA
* * * *
2414890 TATGCATTTCAACTATAGTATACTGTTATGTTGATAATGTACACA
1 TATGCATTTCAACTATAGTATACTTTTCTGTTGATAATGCACCCA
* * * * *
2414935 TATACATCTCAACCATAGTATACTTTTCTGCTGATAATGTACCCA
1 TATGCATTTCAACTATAGTATACTTTTCTGTTGATAATGCACCCA
* * * * * *
2414980 TATACATTTCAATTCTAGCATTCTTTTCTGTCGATAATGCACCCA
1 TATGCATTTCAACTATAGTATACTTTTCTGTTGATAATGCACCCA
* * *
2415025 TATGCATTTCAACTCTAGCATACTTTTCTGTTGATAATACACCCA
1 TATGCATTTCAACTATAGTATACTTTTCTGTTGATAATGCACCCA
*
2415070 TATGCATTTTAACT
1 TATGCATTTCAACT
2415084 TTGGCATCCT
Statistics
Matches: 164, Mismatches: 29, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
44 13 0.08
45 151 0.92
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.41
Consensus pattern (45 bp):
TATGCATTTCAACTATAGTATACTTTTCTGTTGATAATGCACCCA
Found at i:2415107 original size:45 final size:45
Alignment explanation
Indices: 2414975--2415107 Score: 113
Period size: 45 Copynumber: 3.0 Consensus size: 45
2414965 CTGATAATGT
* * * ** * * *
2414975 ACCCATATACATTTCAATTCTAGCATTCTTTTCTGTCGATAATGC
1 ACCCATATGCATTTCAACTCTAGCATACTTTAATGCCAATAATAC
** ***
2415020 ACCCATATGCATTTCAACTCTAGCATACTTTTCTGTTGATAATAC
1 ACCCATATGCATTTCAACTCTAGCATACTTTAATGCCAATAATAC
* * * *
2415065 ACCCATATGCATTTTAACTTTGGCATCCTTTAATGCCAATAAT
1 ACCCATATGCATTTCAACTCTAGCATACTTTAATGCCAATAAT
2415108 GCATTATTAT
Statistics
Matches: 74, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 74 1.00
ACGTcount: A:0.29, C:0.24, G:0.09, T:0.38
Consensus pattern (45 bp):
ACCCATATGCATTTCAACTCTAGCATACTTTAATGCCAATAATAC
Found at i:2415107 original size:90 final size:90
Alignment explanation
Indices: 2414923--2415110 Score: 200
Period size: 90 Copynumber: 2.1 Consensus size: 90
2414913 TGTTATGTTG
* * **
2414923 ATAATGTACACATATACATCTCAACCATAGTATACTTTTCTGCTGATAATGTACCCATATACATT
1 ATAATGCACACATATACATCTCAACCATAGCATACTTTTCTGCTGATAATACACCCATATACATT
* ** * *
2414988 TCAATTCTAGCATTCTTTTCTGTCG
66 TCAATTCTAGCATCCTTTAATGCCA
* * * * *
2415013 ATAATGCACCCATATGCATTTCAACTC-TAGCATACTTTTCTGTTGATAATACACCCATATGCAT
1 ATAATGCACACATATACATCTCAAC-CATAGCATACTTTTCTGCTGATAATACACCCATATACAT
* *
2415077 TTTAACTT-TGGCATCCTTTAATGCCA
65 TTCAA-TTCTAGCATCCTTTAATGCCA
2415103 ATAATGCA
1 ATAATGCA
2415111 TTATTATTTT
Statistics
Matches: 80, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
90 77 0.96
91 3 0.04
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (90 bp):
ATAATGCACACATATACATCTCAACCATAGCATACTTTTCTGCTGATAATACACCCATATACATT
TCAATTCTAGCATCCTTTAATGCCA
Found at i:2415107 original size:135 final size:135
Alignment explanation
Indices: 2414866--2415108 Score: 288
Period size: 135 Copynumber: 1.8 Consensus size: 135
2414856 AACTATAATA
* * * * **
2414866 TCTTTTTTGTTGATAATGCACCTATATGCATTTCAACTATAGTATACTGTTATGTTGATAATGTA
1 TCTTTTCTGTCGATAATGCACCCATATGCATTTCAACTATAGCATACTGTTATGTTGATAATACA
* ** **
2414931 CACATATACATCTCAACCATAGTATACTTTTCTGCTGATAATGTACCCATATACATTTCAATTCT
66 CACATATACATCTCAACCATAGCATACTTTAATGCCAATAATGTACCCATATACATTTCAATTCT
2414996 AGCAT
131 AGCAT
* * *
2415001 TCTTTTCTGTCGATAATGCACCCATATGCATTTCAACTCTAGCATACTTTTCTGTTGATAATACA
1 TCTTTTCTGTCGATAATGCACCCATATGCATTTCAACTATAGCATACTGTTATGTTGATAATACA
* * * * ** * *
2415066 CCCATATGCATTTTAACTTTGGCATCCTTTAATGCCAATAATG
66 CACATATACATCTCAACCATAGCATACTTTAATGCCAATAATG
2415109 CATTATTATT
Statistics
Matches: 86, Mismatches: 22, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
135 86 1.00
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.40
Consensus pattern (135 bp):
TCTTTTCTGTCGATAATGCACCCATATGCATTTCAACTATAGCATACTGTTATGTTGATAATACA
CACATATACATCTCAACCATAGCATACTTTAATGCCAATAATGTACCCATATACATTTCAATTCT
AGCAT
Found at i:2415661 original size:20 final size:20
Alignment explanation
Indices: 2415604--2415661 Score: 82
Period size: 22 Copynumber: 2.8 Consensus size: 20
2415594 TGGCCCTTCA
2415604 GTATCGATACCCCTACTATG
1 GTATCGATACCCCTACTATG
2415624 GTAAT-GATACTACCCTACTATG
1 GT-ATCGATAC--CCCTACTATG
2415646 GTATCGATACCCCTAC
1 GTATCGATACCCCTAC
2415662 CAGTATCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
20 13 0.38
21 4 0.12
22 17 0.50
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.29
Consensus pattern (20 bp):
GTATCGATACCCCTACTATG
Found at i:2415738 original size:95 final size:93
Alignment explanation
Indices: 2415604--2415827 Score: 213
Period size: 95 Copynumber: 2.4 Consensus size: 93
2415594 TGGCCCTTCA
* * ** * * *
2415604 GTATCGATACCC-CTACTATGGTAAT-GATACTACCCTACTATGGTATCGATACCCCTACCA-GT
1 GTATCGATACCCTC-ACCATGGT-ATCGATACCACTATACTATGATACCAATACCCCTA-CAGGT
*
2415666 ATCAATACCAAAATTAGATTCGATATGG-CCCT
63 ATCAATACCAAAATTAGATTCG--ATGGACCCG
* * * * *
2415698 GTATCGATACTCTTACCATAGGTATCGATACCACTATACTATTATACCAATACTCCTATATGGTA
1 GTATCGATACCCTCACCAT-GGTATCGATACCACTATACTATGATACCAATACCCCTACA-GGTA
* *
2415763 TCGATACCAAAATTAGGTTCGATGGTACCCG
64 TCAATACCAAAATTAGATTCGATGG-ACCCG
2415794 GTATCGATACCCTCACCATGGTATCGATACCACT
1 GTATCGATACCCTCACCATGGTATCGATACCACT
2415828 TCATTAGGTA
Statistics
Matches: 106, Mismatches: 17, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
94 22 0.21
95 42 0.40
96 42 0.40
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.29
Consensus pattern (93 bp):
GTATCGATACCCTCACCATGGTATCGATACCACTATACTATGATACCAATACCCCTACAGGTATC
AATACCAAAATTAGATTCGATGGACCCG
Found at i:2421834 original size:45 final size:45
Alignment explanation
Indices: 2421767--2421989 Score: 196
Period size: 45 Copynumber: 5.1 Consensus size: 45
2421757 ATTCATTTTA
* *
2421767 AACTATAACAT-CTTTTACGTTGATAATGCTCCCATATGAATTTC
1 AACTATAGCATACTTTTATGTTGATAATGCTCCCATATGAATTTC
* * *
2421811 AACTATTGTATACTTTTATGTTGATAATG-TACCCATAT-ACATCTC
1 AACTATAGCATACTTTTATGTTGATAATGCT-CCCATATGA-ATTTC
* *
2421856 AACCATAGTATAC---T-T-TTGATAATG-TACCCATAT-ACATTTC
1 AACTATAGCATACTTTTATGTTGATAATGCT-CCCATATGA-ATTTC
* * * * *
2421896 AACTCTAGCATACTTTTCTGTTGATAATGCACCCATATGCATTTT
1 AACTATAGCATACTTTTATGTTGATAATGCTCCCATATGAATTTC
* * * *
2421941 AACTCTAGCATACTTTTCTGTTGATAATGCACCCATATGCATTTC
1 AACTATAGCATACTTTTATGTTGATAATGCTCCCATATGAATTTC
2421986 AACT
1 AACT
2421990 TTGGCATCCT
Statistics
Matches: 154, Mismatches: 15, Indels: 19
0.82 0.08 0.10
Matches are distributed among these distances:
40 34 0.22
41 1 0.01
42 1 0.01
43 1 0.01
44 11 0.07
45 106 0.69
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.39
Consensus pattern (45 bp):
AACTATAGCATACTTTTATGTTGATAATGCTCCCATATGAATTTC
Found at i:2421886 original size:40 final size:40
Alignment explanation
Indices: 2421831--2421957 Score: 139
Period size: 40 Copynumber: 3.0 Consensus size: 40
2421821 TACTTTTATG
*
2421831 TTGATAATGTACCCATATACATCTCAAC-CATAGTATACTT
1 TTGATAATGTACCCATATACATCTCAACTC-TAGCATACTT
*
2421871 TTGATAATGTACCCATATACATTTCAACTCTAGCATACTTTTCT
1 TTGATAATGTACCCATATACATCTCAACTCTAGCATAC---T-T
* * * *
2421915 GTTGATAATGCACCCATATGCATTTTAACTCTAGCATACTT
1 -TTGATAATGTACCCATATACATCTCAACTCTAGCATACTT
2421956 TT
1 TT
2421958 CTGTTGATAA
Statistics
Matches: 76, Mismatches: 5, Indels: 12
0.82 0.05 0.13
Matches are distributed among these distances:
40 36 0.47
41 2 0.03
42 1 0.01
43 1 0.01
44 1 0.01
45 35 0.46
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.39
Consensus pattern (40 bp):
TTGATAATGTACCCATATACATCTCAACTCTAGCATACTT
Found at i:2421954 original size:85 final size:88
Alignment explanation
Indices: 2421785--2422028 Score: 232
Period size: 85 Copynumber: 2.8 Consensus size: 88
2421775 CATCTTTTAC
* * * *
2421785 GTTGATAATGCT-CCCATATGA-ATTTCAACTATTGTATACTTTTATGTTGATAATGTACCCATA
1 GTTGATAATG-TACCCATAT-ACATTTCAACTATAGCATACTTTTCTGTTGATAATGCACCCATA
* * *
2421848 TACATCTCAACCATAGTATAC-T-T
64 TGCATTTCAACCATAGCATACTTCT
*
2421871 -TTGATAATGTACCCATATACATTTCAACTCTAGCATACTTTTCTGTTGATAATGCACCCATATG
1 GTTGATAATGTACCCATATACATTTCAACTATAGCATACTTTTCTGTTGATAATGCACCCATATG
*
2421935 CATTTTAACTC-TAGCATACTTTTCT
66 CATTTCAAC-CATAGCATAC--TTCT
* * * * * ***
2421960 GTTGATAATGCACCCATATGCATTTCAACTTTGGCAT-CCTTTCATGCCAATAATGCACCCATAT
1 GTTGATAATGTACCCATATACATTTCAACTATAGCATACTTTTC-TGTTGATAATGCACCCATAT
2422024 GCATT
65 GCATT
2422029 CTTCTTTTAT
Statistics
Matches: 132, Mismatches: 17, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
84 2 0.02
85 68 0.52
86 1 0.01
88 1 0.01
89 6 0.05
90 54 0.41
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.38
Consensus pattern (88 bp):
GTTGATAATGTACCCATATACATTTCAACTATAGCATACTTTTCTGTTGATAATGCACCCATATG
CATTTCAACCATAGCATACTTCT
Found at i:2422013 original size:45 final size:45
Alignment explanation
Indices: 2421874--2422107 Score: 197
Period size: 45 Copynumber: 5.4 Consensus size: 45
2421864 TATACTTTTG
* * * * *
2421874 ATAATGTACCCATATACATTTCAACTCTAGCATACTTTTC-TGTTG
1 ATAATGCACCCATATGCATTTCAACTCTAGCAT-CCTTTCATGCTA
* * * *
2421919 ATAATGCACCCATATGCATTTTAACTCTAGCATACTTTTC-TGTTG
1 ATAATGCACCCATATGCATTTCAACTCTAGCAT-CCTTTCATGCTA
* * *
2421964 ATAATGCACCCATATGCATTTCAACTTTGGCATCCTTTCATGCCA
1 ATAATGCACCCATATGCATTTCAACTCTAGCATCCTTTCATGCTA
2422009 ATAATGCACCCATATGCA-TT---CT-T--C-T--TTT-ATGCTA
1 ATAATGCACCCATATGCATTTCAACTCTAGCATCCTTTCATGCTA
* * * * * *
2422043 ATAATGTACCCATATACATTTCAGCTATGGCATCCTTTCATGCCA
1 ATAATGCACCCATATGCATTTCAACTCTAGCATCCTTTCATGCTA
2422088 ATAATGCACCCATATGCATT
1 ATAATGCACCCATATGCATT
2422108 ATTCTTTTAC
Statistics
Matches: 161, Mismatches: 16, Indels: 24
0.80 0.08 0.12
Matches are distributed among these distances:
34 21 0.13
35 5 0.03
37 1 0.01
38 3 0.02
39 1 0.01
40 1 0.01
41 3 0.02
42 1 0.01
44 10 0.06
45 115 0.71
ACGTcount: A:0.28, C:0.25, G:0.10, T:0.37
Consensus pattern (45 bp):
ATAATGCACCCATATGCATTTCAACTCTAGCATCCTTTCATGCTA
Found at i:2422046 original size:34 final size:34
Alignment explanation
Indices: 2421998--2422062 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
2421988 CTTTGGCATC
*
2421998 CTTTCATGCCAATAATGCACCCATATGCATTCTT
1 CTTTCATGCCAATAATGCACCCATATACATTCTT
* * *
2422032 CTTTTATGCTAATAATGTACCCATATACATT
1 CTTTCATGCCAATAATGCACCCATATACATT
2422063 TCAGCTATGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.29, C:0.25, G:0.08, T:0.38
Consensus pattern (34 bp):
CTTTCATGCCAATAATGCACCCATATACATTCTT
Found at i:2422056 original size:79 final size:79
Alignment explanation
Indices: 2421964--2422116 Score: 261
Period size: 79 Copynumber: 1.9 Consensus size: 79
2421954 TTTTCTGTTG
* *
2421964 ATAATGCACCCATATGCATTTCAACTTTGGCATCCTTTCATGCCAATAATGCACCCATATGCATT
1 ATAATGCACCCATATACATTTCAACTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATT
*
2422029 CTTCTTTTATGCTA
66 ATTCTTTTATGCTA
* *
2422043 ATAATGTACCCATATACATTTCAGCTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATT
1 ATAATGCACCCATATACATTTCAACTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATT
2422108 ATTCTTTTA
66 ATTCTTTTA
2422117 CATTCATTTC
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
79 69 1.00
ACGTcount: A:0.28, C:0.25, G:0.10, T:0.37
Consensus pattern (79 bp):
ATAATGCACCCATATACATTTCAACTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATT
ATTCTTTTATGCTA
Found at i:2422542 original size:15 final size:16
Alignment explanation
Indices: 2422522--2422556 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
2422512 GGCCCTTCAG
2422522 TATCGATAC-CCCTAC
1 TATCGATACACCCTAC
2422537 TATCGATACTACCCTAC
1 TATCGATAC-ACCCTAC
2422554 TAT
1 TAT
2422557 GGTATCGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
17 9 0.50
ACGTcount: A:0.29, C:0.34, G:0.06, T:0.31
Consensus pattern (16 bp):
TATCGATACACCCTAC
Found at i:2422580 original size:19 final size:19
Alignment explanation
Indices: 2422514--2422587 Score: 52
Period size: 19 Copynumber: 4.0 Consensus size: 19
2422504 CAATTTATGG
2422514 CCCT-TCAGTATCGATA-C
1 CCCTATCAGTATCGATACC
2422531 CCCTA-C--TATCGATACTAC
1 CCCTATCAGTATCGATAC--C
*
2422549 CCTACTAT-GGTATCGATACC
1 CC--CTATCAGTATCGATACC
*
2422569 CCCTATCAGTATCAATACC
1 CCCTATCAGTATCGATACC
2422588 AAAATTAGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 18
0.69 0.03 0.28
Matches are distributed among these distances:
15 8 0.18
17 5 0.11
18 7 0.16
19 10 0.22
20 6 0.13
22 9 0.20
ACGTcount: A:0.27, C:0.35, G:0.09, T:0.28
Consensus pattern (19 bp):
CCCTATCAGTATCGATACC
Found at i:2422637 original size:21 final size:22
Alignment explanation
Indices: 2422611--2422706 Score: 87
Period size: 22 Copynumber: 4.5 Consensus size: 22
2422601 ATATGGCCCC
2422611 GTATCGATACC-CT-TACCATAG
1 GTATCGATACCACTATACCAT-G
*
2422632 GTATCGATACCACTATACTATG
1 GTATCGATACCACTATACCATG
* **
2422654 GTACCGATACCACTATATTATG
1 GTATCGATACCACTATACCATG
*
2422676 GTA-CTGATACCCCTAT---ATG
1 GTATC-GATACCACTATACCATG
2422695 GTATCGATACCA
1 GTATCGATACCA
2422707 AAATTAGGTT
Statistics
Matches: 66, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
19 12 0.18
20 1 0.02
21 12 0.18
22 36 0.55
23 5 0.08
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (22 bp):
GTATCGATACCACTATACCATG
Found at i:2422661 original size:22 final size:22
Alignment explanation
Indices: 2422615--2422692 Score: 88
Period size: 22 Copynumber: 3.6 Consensus size: 22
2422605 GGCCCCGTAT
* *
2422615 CGATACC-CT-TACCATAGGTAT
1 CGATACCACTATACTAT-GGTAC
2422636 CGATACCACTATACTATGGTAC
1 CGATACCACTATACTATGGTAC
*
2422658 CGATACCACTATATTATGGTAC
1 CGATACCACTATACTATGGTAC
* *
2422680 TGATACCCCTATA
1 CGATACCACTATA
2422693 TGGTATCGAT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.14
22 38 0.76
23 5 0.10
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (22 bp):
CGATACCACTATACTATGGTAC
Found at i:2422693 original size:22 final size:22
Alignment explanation
Indices: 2422631--2422693 Score: 90
Period size: 22 Copynumber: 2.9 Consensus size: 22
2422621 CCTTACCATA
* *
2422631 GGTATCGATACCACTATACTAT
1 GGTACCGATACCACTATATTAT
2422653 GGTACCGATACCACTATATTAT
1 GGTACCGATACCACTATATTAT
* *
2422675 GGTACTGATACCCCTATAT
1 GGTACCGATACCACTATAT
2422694 GGTATCGATA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (22 bp):
GGTACCGATACCACTATATTAT
Found at i:2426488 original size:22 final size:22
Alignment explanation
Indices: 2426408--2426490 Score: 78
Period size: 22 Copynumber: 3.8 Consensus size: 22
2426398 TTTATCACGG
*
2426408 AAGTGCCTTAGCACTAATACTA
1 AAGTGCCTTAACACTAATACTA
* * **
2426430 AAGTGTCTCAACACTGGTAC-A
1 AAGTGCCTTAACACTAATACTA
* **
2426451 GAAGTGCATTCGCACTAATACTA
1 -AAGTGCCTTAACACTAATACTA
2426474 AAGTGCCTTAACACTAA
1 AAGTGCCTTAACACTAA
2426491 GGGAGAGAAT
Statistics
Matches: 44, Mismatches: 15, Indels: 4
0.70 0.24 0.06
Matches are distributed among these distances:
21 1 0.02
22 42 0.95
23 1 0.02
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25
Consensus pattern (22 bp):
AAGTGCCTTAACACTAATACTA
Found at i:2426791 original size:20 final size:21
Alignment explanation
Indices: 2426752--2426800 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
2426742 ACGATGGTAC
2426752 CGATACTAGGCCTGGCAGTAT
1 CGATACTAGGCCTGGCAGTAT
* *
2426773 CGATACTA-GCCTTGTAGTAT
1 CGATACTAGGCCTGGCAGTAT
2426793 CGATACTA
1 CGATACTA
2426801 CCCCGAGTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (21 bp):
CGATACTAGGCCTGGCAGTAT
Found at i:2429565 original size:22 final size:22
Alignment explanation
Indices: 2429525--2429567 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2429515 TTTAATATTT
*
2429525 TTATTTTAATATTACAATAATC
1 TTATTTTAATAGTACAATAATC
2429547 TTATTTTAATAAGTA-AATAAT
1 TTATTTTAAT-AGTACAATAAT
2429568 AAAATTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (22 bp):
TTATTTTAATAGTACAATAATC
Found at i:2431794 original size:21 final size:21
Alignment explanation
Indices: 2431768--2431812 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
2431758 TGTTGCTCAA
*
2431768 CTCGACTCGTTGCTCGTTAAG
1 CTCGACTCGTTGCTCGCTAAG
2431789 CTCGACTCGTTGCTCGCTAAG
1 CTCGACTCGTTGCTCGCTAAG
2431810 CTC
1 CTC
2431813 ACTAAAAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.13, C:0.33, G:0.22, T:0.31
Consensus pattern (21 bp):
CTCGACTCGTTGCTCGCTAAG
Found at i:2433686 original size:12 final size:12
Alignment explanation
Indices: 2433669--2433695 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2433659 AATAAATAAA
2433669 AAATATAACTTT
1 AAATATAACTTT
2433681 AAATATAACTTT
1 AAATATAACTTT
2433693 AAA
1 AAA
2433696 AAAGTGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (12 bp):
AAATATAACTTT
Done.