Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008229.1 Hibiscus syriacus cultivar Beakdansim tig00110865_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: 3634043
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 17
Found at i:3219125 original size:35 final size:34
Alignment explanation
Indices: 3219068--3219299 Score: 187
Period size: 35 Copynumber: 6.7 Consensus size: 34
3219058 CTTATGTACA
3219068 ATATATA-AGTTTTAAAAACATTTTGAAAATTAT
1 ATATATATAGTTTTAAAAACATTTTGAAAATTAT
* *
3219101 ATAGTATATAGTTTTGAAATCATTTTGAAAA-TAT
1 ATA-TATATAGTTTTAAAAACATTTTGAAAATTAT
3219135 A-ATATATAGTTTTTAAAAAAACATTTTTTTGAAAATTTAT
1 ATATATATAG-TTTT--AAAAACA---TTTTGAAAA-TTAT
3219175 ATAATATATAG-TTTAAAAACATTTTGGAAAACTTAT
1 AT-ATATATAGTTTTAAAAACATTTT-GAAAA-TTAT
* *
3219211 ATA-ACAT--TTTTAAAATCATTTTTGAAAATTAT
1 ATATATATAGTTTTAAAAACA-TTTTGAAAATTAT
* * *
3219243 ATAATATATAGTTTTGAAAACGTTTT-TAAA-TA-
1 AT-ATATATAGTTTTAAAAACATTTTGAAAATTAT
* * *
3219275 AAATATATAGTTTAAAAAATATTTT
1 ATATATATAGTTTTAAAAACATTTT
3219300 TTTTGAAACA
Statistics
Matches: 163, Mismatches: 17, Indels: 40
0.74 0.08 0.18
Matches are distributed among these distances:
31 19 0.12
32 14 0.09
33 25 0.15
34 21 0.13
35 34 0.21
36 19 0.12
38 16 0.10
40 7 0.04
42 8 0.05
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (34 bp):
ATATATATAGTTTTAAAAACATTTTGAAAATTAT
Found at i:3219150 original size:68 final size:69
Alignment explanation
Indices: 3219067--3219300 Score: 241
Period size: 68 Copynumber: 3.4 Consensus size: 69
3219057 ACTTATGTAC
* *
3219067 AATATATAAG-TTTTAAAAACA-TTTTGAAAATTATATAGTATATAGTTTTGAAATCATTTTGAA
1 AATATAT-AGTTTTTAAAAACATTTTTGAAAATTATATAATATATAGTTTTGAAAACATTTTGAA
3219130 AATAT
65 AATAT
*
3219135 AATATATAGTTTTTAAAAAAACATTTTTTTGAAAATTTATATAATATATAG-TTTAAAAACATTT
1 AATATATAGTTTTT--AAAAACA--TTTTTGAAAA-TTATATAATATATAGTTTTGAAAACATTT
3219199 TGGAAAACT-T
61 T-GAAAA-TAT
* * * *
3219209 -ATATA-ACATTTTTAAAATCATTTTTGAAAATTATATAATATATAGTTTTGAAAACGTTTT-TA
1 AATATATA-GTTTTTAAAAACATTTTTGAAAATTATATAATATATAGTTTTGAAAACATTTTGAA
*
3219271 AATAA
65 AATAT
* *
3219276 AATATATAG-TTTAAAAAATATTTTT
1 AATATATAGTTTTTAAAAACATTTTT
3219301 TTTGAAACAT
Statistics
Matches: 139, Mismatches: 13, Indels: 29
0.77 0.07 0.16
Matches are distributed among these distances:
66 1 0.01
67 18 0.13
68 31 0.22
69 23 0.17
70 7 0.05
71 6 0.04
72 1 0.01
73 31 0.22
74 20 0.14
75 1 0.01
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (69 bp):
AATATATAGTTTTTAAAAACATTTTTGAAAATTATATAATATATAGTTTTGAAAACATTTTGAAA
ATAT
Found at i:3219190 original size:108 final size:113
Alignment explanation
Indices: 3219048--3219262 Score: 277
Period size: 110 Copynumber: 1.9 Consensus size: 113
3219038 TTTTGAAACG
* *
3219048 TTTTTGAAAACTTATGTACAATATATAAGTTTTAAAAACATTTT-GAAAA-TTATATAGTATATA
1 TTTTTGAAAACTTATATACAATATATAAGTTTTAAAAACATTTTGGAAAACTTATATA--ACAT-
* *
3219111 GTTTTGAAATCA-TTTTG-AAA-ATATAATATATAGTTTTTAAAAAAACATT
63 -TTTTAAAATCATTTTTGAAAATATATAATATATAGTTTTGAAAAAAACATT
*
3219160 TTTTTGAAAA-TT-TATATAATATAT-AG-TTTAAAAACATTTTGGAAAACTTATATAACATTTT
1 TTTTTGAAAACTTATATACAATATATAAGTTTTAAAAACATTTTGGAAAACTTATATAACATTTT
3219221 TAAAATCATTTTTGAAAATTATATAATATATAGTTTTGAAAA
66 TAAAATCATTTTTGAAAA-TATATAATATATAGTTTTGAAAA
3219263 CGTTTTTAAA
Statistics
Matches: 92, Mismatches: 5, Indels: 14
0.83 0.05 0.13
Matches are distributed among these distances:
106 10 0.11
107 5 0.05
108 20 0.22
109 7 0.08
110 38 0.41
111 2 0.02
112 10 0.11
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (113 bp):
TTTTTGAAAACTTATATACAATATATAAGTTTTAAAAACATTTTGGAAAACTTATATAACATTTT
TAAAATCATTTTTGAAAATATATAATATATAGTTTTGAAAAAAACATT
Found at i:3219213 original size:73 final size:68
Alignment explanation
Indices: 3219077--3219256 Score: 206
Period size: 73 Copynumber: 2.6 Consensus size: 68
3219067 AATATATAAG
* * *
3219077 TTTTAAAAACA-TTTTGAAAATTATATAGTATATAGTTTTGAAATCATTTTGAAAATATAATATA
1 TTTTAAAAACATTTTTGAAAATTATATAATATATAG-TTTAAAAACATTTTGAAAATATAATATA
*
3219141 TA-GT
65 -ACAT
3219145 TTTTAAAAAAACATTTTTTTGAAAATTTATATAATATATAGTTTAAAAACATTTTGGAAAACT-T
1 TTTT--AAAAACA--TTTTTGAAAA-TTATATAATATATAGTTTAAAAACATTTT-GAAAA-TAT
3219209 -ATATAACAT
59 AATATAACAT
*
3219218 TTTTAAAATCATTTTTGAAAATTATATAATATATAGTTT
1 TTTTAAAAACATTTTTGAAAATTATATAATATATAGTTT
3219257 TGAAAACGTT
Statistics
Matches: 98, Mismatches: 5, Indels: 18
0.81 0.04 0.15
Matches are distributed among these distances:
68 22 0.22
69 10 0.10
70 7 0.07
71 6 0.06
72 1 0.01
73 31 0.32
74 20 0.20
75 1 0.01
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (68 bp):
TTTTAAAAACATTTTTGAAAATTATATAATATATAGTTTAAAAACATTTTGAAAATATAATATAA
CAT
Found at i:3219301 original size:68 final size:68
Alignment explanation
Indices: 3219067--3219300 Score: 217
Period size: 69 Copynumber: 3.4 Consensus size: 68
3219057 ACTTATGTAC
* * *
3219067 AATATATAAGTTTTAAAAACA-TTTTGAAAATTATATAGTATATAGTTTTGAAATCATTTTGAAA
1 AATATATAAGTTTAAAAAACATTTTTGAAAATTATATAATATATAGTTTTGAAAACATTTT-AAA
*
3219131 ATAT
65 ATAA
*
3219135 AATATAT-AGTTTTTAAAAAAACATTTTTTTGAAAATTTATATAATATATAG-TTTAAAAACATT
1 AATATATAAG--TTT-AAAAAACA--TTTTTGAAAA-TTATATAATATATAGTTTTGAAAACATT
**
3219198 TTGGAA-AA
60 TTAAAATAA
** * * * * *
3219206 CTTATATAACATTTTTAAAATCATTTTTGAAAATTATATAATATATAGTTTTGAAAACGTTTTTA
1 AATATAT-A-AGTTTAAAAAACATTTTTGAAAATTATATAATATATAGTTTTGAAAACATTTTAA
3219271 AATAA
64 AATAA
*
3219276 AATATAT-AGTTTAAAAAATATTTTT
1 AATATATAAGTTTAAAAAACATTTTT
3219301 TTTGAAACAT
Statistics
Matches: 132, Mismatches: 22, Indels: 25
0.74 0.12 0.14
Matches are distributed among these distances:
67 16 0.12
68 22 0.17
69 27 0.20
70 14 0.11
71 12 0.09
72 5 0.04
73 21 0.16
74 15 0.11
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (68 bp):
AATATATAAGTTTAAAAAACATTTTTGAAAATTATATAATATATAGTTTTGAAAACATTTTAAAA
TAA
Found at i:3219332 original size:17 final size:16
Alignment explanation
Indices: 3219310--3219341 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
3219300 TTTTGAAACA
3219310 TATATTATTATATAATC
1 TATATTATTAT-TAATC
3219327 TATATTATTATTAAT
1 TATATTATTATTAAT
3219342 ATTTATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
TATATTATTATTAATC
Found at i:3220089 original size:22 final size:23
Alignment explanation
Indices: 3220064--3220117 Score: 63
Period size: 28 Copynumber: 2.1 Consensus size: 23
3220054 TTCGGGGTAG
3220064 TTTTAGGTGACTTAGGCTTTGATTT
1 TTTTAGGTGACTTAGGCTTTGA--T
3220089 TGCGTTTAGGTGACTTAGGCTTTGAT
1 T---TTTAGGTGACTTAGGCTTTGAT
3220115 TTT
1 TTT
3220118 CGATAGAGGC
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
23 2 0.08
25 1 0.04
26 2 0.08
28 21 0.81
ACGTcount: A:0.15, C:0.09, G:0.26, T:0.50
Consensus pattern (23 bp):
TTTTAGGTGACTTAGGCTTTGAT
Found at i:3220561 original size:19 final size:20
Alignment explanation
Indices: 3220526--3220566 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
3220516 TTAATACTTC
*
3220526 TTTATTTTTATTTATTTAAT
1 TTTAATTTTATTTATTTAAT
3220546 TTTAATTTTA-TTATTTAAT
1 TTTAATTTTATTTATTTAAT
3220565 TT
1 TT
3220567 CTTTGGTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTAATTTTATTTATTTAAT
Found at i:3220741 original size:13 final size:13
Alignment explanation
Indices: 3220723--3220752 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3220713 CGAACCAAAT
3220723 TTTTAAATTTCAA
1 TTTTAAATTTCAA
*
3220736 TTTTAAATTTTAA
1 TTTTAAATTTCAA
3220749 TTTT
1 TTTT
3220753 CACAATTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTTAAATTTCAA
Found at i:3226008 original size:82 final size:84
Alignment explanation
Indices: 3225921--3226076 Score: 280
Period size: 84 Copynumber: 1.9 Consensus size: 84
3225911 GCTCAAGGCC
*
3225921 AGAAGGGTTATCTGCC-ACC-AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATT
1 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
*
3225984 TATAGCATAACCTATGTCG
66 TACAGCATAACCTATGTCG
3226003 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
3226068 TACAGCATA
66 TACAGCATA
3226077 GAGTTCGATT
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
82 16 0.23
83 3 0.04
84 51 0.73
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (84 bp):
AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
TACAGCATAACCTATGTCG
Found at i:3226009 original size:227 final size:227
Alignment explanation
Indices: 3225614--3226069 Score: 876
Period size: 227 Copynumber: 2.0 Consensus size: 227
3225604 AGGAACCTCC
* *
3225614 TAAAGAACTATGACCGGCTTAGACCTGTGAAGGGAAGCCATTTTTTTAAAAGGACATTATTTGCA
1 TAAAGAACTATGACCGGCTTAGACCTATGAAGGGAAGCCATTTTTTTAAAAGGACATCATTTGCA
3225679 GCATAGCTCAAGGCCAGAAGGGTTATCTGCCACCAAGACCTTCGAGTTCGACTACGCTCAGCTCC
66 GCATAGCTCAAGGCCAGAAGGGTTATCTGCCACCAAGACCTTCGAGTTCGACTACGCTCAGCTCC
*
3225744 AAGGCATATCATTTATAGCATAACCTATGTCGAGAAGGGTTATGTGCCAACCAAAGACCTTCGAG
131 AAGGCATATCATTTATAGCATAACCTATGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAG
3225809 TTCGACTACGCTCAACTCCAAGGCACATCATT
196 TTCGACTACGCTCAACTCCAAGGCACATCATT
3225841 TAAAGAACTATGACCGGCTTAGACCTATGAAGGGAAGCCATTTTTTTAAAAGGACATCATTTGCA
1 TAAAGAACTATGACCGGCTTAGACCTATGAAGGGAAGCCATTTTTTTAAAAGGACATCATTTGCA
3225906 GCATAGCTCAAGGCCAGAAGGGTTATCTGCCACCAAGACCTTCGAGTTCGACTACGCTCAGCTCC
66 GCATAGCTCAAGGCCAGAAGGGTTATCTGCCACCAAGACCTTCGAGTTCGACTACGCTCAGCTCC
3225971 AAGGCATATCATTTATAGCATAACCTATGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAG
131 AAGGCATATCATTTATAGCATAACCTATGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAG
*
3226036 TTCGACTACGCTCAGCTCCAAGGCACATCATT
196 TTCGACTACGCTCAACTCCAAGGCACATCATT
3226068 TA
1 TA
3226070 CAGCATAGAG
Statistics
Matches: 225, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
227 225 1.00
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (227 bp):
TAAAGAACTATGACCGGCTTAGACCTATGAAGGGAAGCCATTTTTTTAAAAGGACATCATTTGCA
GCATAGCTCAAGGCCAGAAGGGTTATCTGCCACCAAGACCTTCGAGTTCGACTACGCTCAGCTCC
AAGGCATATCATTTATAGCATAACCTATGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAG
TTCGACTACGCTCAACTCCAAGGCACATCATT
Found at i:3226096 original size:44 final size:45
Alignment explanation
Indices: 3226033--3226121 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 45
3226023 AAAGACCTTC
*
3226033 GAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTACAGCATA
1 GAGTTCGACTACACTCAGCTTCCAAGGCACATCATTTACAGCATA
* * * *
3226077 GAGTTCGATTACACTCAGCTTCGAGGGTACATCATTTACAGCATA
1 GAGTTCGACTACACTCAGCTTCCAAGGCACATCATTTACAGCATA
3226122 ACCTAAGTCA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 17 0.44
45 22 0.56
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (45 bp):
GAGTTCGACTACACTCAGCTTCCAAGGCACATCATTTACAGCATA
Found at i:3226387 original size:164 final size:164
Alignment explanation
Indices: 3226077--3226562 Score: 749
Period size: 164 Copynumber: 3.0 Consensus size: 164
3226067 TTACAGCATA
* *
3226077 GAGTTCGATTACACTCAGCTTCGAGGGTACATCATTTACAGCATAAC-CTAAGTCAAGAAGGGTT
1 GAGTTCGATTACACTCAGCTTCGAGGGTACATCATTTACAGCATAACTC-AAGGCTAGAAGGGTT
*
3226141 ATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATA
65 ATCTGCC-ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCGCATCATTTGCAGCATA
3226206 GCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCC
129 GCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCC
*
3226242 GAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTA
1 GAGTTCGATTACACTCAGCTTCGAGGGTACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTA
* * * ** *
3226307 TCTGCCATCAAAGACCTTTGAGTTCGACTACGTTCAGCTCCAAGGCGCATCGCTTGCAGCATAGT
66 TCTGCCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCGCATCATTTGCAGCATAGC
*
3226372 TTAAGTCGAGAAGGGCTATCTTCCAAAGACCCCC
131 TTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCC
*
3226406 GAGTTCGATTACACTCAGCTTCAAGGGTACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTA
1 GAGTTCGATTACACTCAGCTTCGAGGGTACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTA
* * * ** *
3226471 TATGTCACCAAAAGACCTTCGAGTTCGACTACACTCAGCTTGAAGGCGCATCATTTGCAGTATAG
66 TCTGCCACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCGCATCATTTGCAGCATAG
* * *
3226536 CTTAAGTTGAGAAGGGTTGTCTGCCAA
130 CTTAAGTCGAGAAGGGCTATCTGCCAA
3226563 TCAAAGACCT
Statistics
Matches: 290, Mismatches: 29, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
164 154 0.53
165 135 0.47
166 1 0.00
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (164 bp):
GAGTTCGATTACACTCAGCTTCGAGGGTACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTA
TCTGCCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCGCATCATTTGCAGCATAGC
TTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCC
Found at i:3226424 original size:80 final size:80
Alignment explanation
Indices: 3226077--3226551 Score: 383
Period size: 84 Copynumber: 5.8 Consensus size: 80
3226067 TTACAGCATA
* * * * * * * * *
3226077 GAGTTCGATTACACTCAGCTTCGAGGGTACATCATTTACAGCATAACCTAAGTCAAGAAGGGTTA
1 GAGTTCGACTACACTCAGC-TCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTA
**
3226142 TCTGCCAACCAAAGACCTTC
65 TCT--C--CCAAAGACCCCC
*
3226162 GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTAT
1 GAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTAT
*
3226227 CTGCCAAAGACCCCC
66 CTCCCAAAGACCCCC
* * * * * * * * *
3226242 GAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTA
1 GAGTTCGACTACACTCAGC-TCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTA
***
3226307 TCTGCCATCAAAGACCTTT
65 TCT-CC--CAAAGACCCCC
** * ** *
3226326 GAGTTCGACTACGTTCAGCTCCAAGGCGCATCGCTTGCAGCATAGTTTAAGTCGAGAAGGGCTAT
1 GAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTAT
*
3226391 CTTCCAAAGACCCCC
66 CTCCCAAAGACCCCC
* * * * * * * * *
3226406 GAGTTCGATTACACTCAGCTTCAAGGGTACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTA
1 GAGTTCGACTACACTCAGCTCCAA-GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGG--C
* **
3226471 TATGTCACCAAAAGACCTTC
63 TATCTC-CC-AAAGACCCCC
** * * *
3226491 GAGTTCGACTACACTCAGCTTGAAGGCGCATCATTTGCAGTATAGCTTAAGTTGAGAAGGG
1 GAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGG
3226552 TTGTCTGCCA
Statistics
Matches: 305, Mismatches: 76, Indels: 19
0.76 0.19 0.05
Matches are distributed among these distances:
80 55 0.18
81 67 0.22
82 2 0.01
83 40 0.13
84 94 0.31
85 47 0.15
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (80 bp):
GAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTAT
CTCCCAAAGACCCCC
Found at i:3226581 original size:14 final size:14
Alignment explanation
Indices: 3226559--3226588 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3226549 GGGTTGTCTG
*
3226559 CCAATCAAAGACCT
1 CCAACCAAAGACCT
3226573 CCAACCAAAGACCT
1 CCAACCAAAGACCT
3226587 CC
1 CC
3226589 GAGTTCAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.43, G:0.07, T:0.10
Consensus pattern (14 bp):
CCAACCAAAGACCT
Found at i:3227402 original size:35 final size:34
Alignment explanation
Indices: 3227345--3227535 Score: 169
Period size: 35 Copynumber: 5.4 Consensus size: 34
3227335 CTTATGTACA
3227345 ATATATA-AGTTTTAAAAACATTTTGAAAATTAT
1 ATATATATAGTTTTAAAAACATTTTGAAAATTAT
* *
3227378 ATAGTATATAGTTTTGAAATCATTTTGAAAA-TAT
1 ATA-TATATAGTTTTAAAAACATTTTGAAAATTAT
3227412 A-ATATATAGTTTTTAGAAAAACATTTTTTGAAAATTTAT
1 ATATATATAG-TTTT--AAAAACA--TTTTGAAAA-TTAT
*
3227451 ATAATATATAGTTTAAAAAAACATTTTGGAAAACTTAT
1 AT-ATATATAGTTT-TAAAAACATTTT-GAAAA-TTAT
* * *
3227489 ATA-ACAT--TTTTAAAATCATATTTGAAAATTAC
1 ATATATATAGTTTTAAAAACAT-TTTGAAAATTAT
3227521 ATAATATATAGTTTT
1 AT-ATATATAGTTTT
3227536 GAAACGTTTT
Statistics
Matches: 129, Mismatches: 11, Indels: 33
0.75 0.06 0.19
Matches are distributed among these distances:
32 12 0.09
33 21 0.16
34 17 0.13
35 25 0.19
36 7 0.05
37 14 0.11
38 11 0.09
39 11 0.09
40 3 0.02
41 8 0.06
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (34 bp):
ATATATATAGTTTTAAAAACATTTTGAAAATTAT
Found at i:3227460 original size:109 final size:106
Alignment explanation
Indices: 3227291--3227546 Score: 265
Period size: 109 Copynumber: 2.4 Consensus size: 106
3227281 AAAAATATTT
* * * *
3227291 TTTTGAAATATATATTATATAATTTTTTGAAACGTTTTTGAAAACTTATGTACAATATATAAGTT
1 TTTTGAAA-ATATAATATATAGTTTTTAGAAACGTTTTTGAAAACTTATATACAATATAT-AGTT
* * *
3227356 T-TAAAAACATTTT-GAAAA-TTATATAGTATATAGTTTTGAAATCA
64 TAAAAAAACATTTTGGAAAACTTATATA--ACAT--TTTTAAAATCA
* *
3227400 TTTTGAAAATATAATATATAGTTTTTAGAAAAACATTTTTTGAAAA-TT-TATATAATATATAGT
1 TTTTGAAAATATAATATATAGTTTTTAG--AAAC-GTTTTTGAAAACTTATATACAATATATAGT
3227463 TTAAAAAAACATTTTGGAAAACTTATATAACATTTTTAAAATCA
63 TTAAAAAAACATTTTGGAAAACTTATATAACATTTTTAAAATCA
3227507 TATTTGAAAATTACATAATATATAG-TTTT-GAAACGTTTTT
1 T-TTTGAAAA-T--ATAATATATAGTTTTTAGAAACGTTTTT
3227547 AAATAAAATA
Statistics
Matches: 127, Mismatches: 10, Indels: 23
0.79 0.06 0.14
Matches are distributed among these distances:
106 5 0.04
107 15 0.12
108 30 0.24
109 34 0.27
110 15 0.12
111 28 0.22
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44
Consensus pattern (106 bp):
TTTTGAAAATATAATATATAGTTTTTAGAAACGTTTTTGAAAACTTATATACAATATATAGTTTA
AAAAAACATTTTGGAAAACTTATATAACATTTTTAAAATCA
Found at i:3227637 original size:18 final size:18
Alignment explanation
Indices: 3227598--3227653 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
3227588 ATAATCTATA
*
3227598 TTATTAT-TAATATTTATT
1 TTATTATCTAAT-TTAATT
*
3227616 TTATT-TC--ATTTCATT
1 TTATTATCTAATTTAATT
3227631 TTATTATCTAATTTAATT
1 TTATTATCTAATTTAATT
3227649 TTATT
1 TTATT
3227654 CATTATTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
15 10 0.31
16 4 0.12
17 1 0.03
18 17 0.53
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (18 bp):
TTATTATCTAATTTAATT
Found at i:3228895 original size:20 final size:20
Alignment explanation
Indices: 3228865--3228905 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
3228855 TTAATACTTC
3228865 TTTATTTTTATTTATTTAATT
1 TTTATTTTTA-TTATTTAATT
*
3228886 TTTA-TTTTATTATTTTATT
1 TTTATTTTTATTATTTAATT
3228905 T
1 T
3228906 CTTTTGTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 10 0.53
20 5 0.26
21 4 0.21
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTATTTTTATTATTTAATT
Found at i:3229076 original size:13 final size:13
Alignment explanation
Indices: 3229058--3229087 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3229048 CGAACCGAAT
3229058 TTTTAAATTTCAA
1 TTTTAAATTTCAA
*
3229071 TTTTAAATTTTAA
1 TTTTAAATTTCAA
3229084 TTTT
1 TTTT
3229088 CGCAATTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTTAAATTTCAA
Found at i:3230084 original size:23 final size:23
Alignment explanation
Indices: 3230035--3230085 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
3230025 GTGTTATATT
**
3230035 ATATTTTAAAAATATTAATTATT
1 ATATTTTAAAAATATTAATTAAA
* * *
3230058 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
3230081 ATATT
1 ATATT
3230086 ATTAGATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:3230141 original size:19 final size:19
Alignment explanation
Indices: 3230073--3230153 Score: 64
Period size: 19 Copynumber: 4.3 Consensus size: 19
3230063 TTAAATATCT
3230073 TTATTAA-AATATTATTAGA
1 TTATTAATAATATTATTA-A
3230092 TTATTATATTAATATTA--AA
1 TTATTA-A-TAATATTATTAA
* *
3230111 TATATAAATAATATTATTCA
1 T-TATTAATAATATTATTAA
*
3230131 TTATTAATAAT-TTAATAA
1 TTATTAATAATATTATTAA
3230149 -TATTA
1 TTATTA
3230154 TTTCTATGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
17 5 0.10
18 13 0.25
19 18 0.35
20 8 0.16
22 7 0.14
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (19 bp):
TTATTAATAATATTATTAA
Found at i:3230269 original size:8 final size:8
Alignment explanation
Indices: 3230230--3230292 Score: 51
Period size: 8 Copynumber: 8.2 Consensus size: 8
3230220 TAAAATATCG
*
3230230 TATATTAT
1 TATAATAT
3230238 TATAATAT
1 TATAATAT
* *
3230246 AAT-TTAT
1 TATAATAT
**
3230253 TATTTTAT
1 TATAATAT
3230261 TATAATAT
1 TATAATAT
3230269 TA-AA-AT
1 TATAATAT
3230275 TATAATAT
1 TATAATAT
*
3230283 TATATTAT
1 TATAATAT
3230291 TA
1 TA
3230293 GAAATATTAA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
6 4 0.09
7 9 0.20
8 32 0.71
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (8 bp):
TATAATAT
Found at i:3231560 original size:20 final size:20
Alignment explanation
Indices: 3231535--3231578 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
3231525 AAAATTGATG
3231535 GAGTAAAAGAGCTTCTAATA
1 GAGTAAAAGAGCTTCTAATA
3231555 GAGTAAAAGAGCTTCTAATA
1 GAGTAAAAGAGCTTCTAATA
3231575 GAGT
1 GAGT
3231579 TTAACTTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.43, C:0.09, G:0.23, T:0.25
Consensus pattern (20 bp):
GAGTAAAAGAGCTTCTAATA
Found at i:3234573 original size:20 final size:20
Alignment explanation
Indices: 3234548--3234591 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
3234538 AAAATTGATG
3234548 GAGTAAAAGAGCTTCTAATA
1 GAGTAAAAGAGCTTCTAATA
3234568 GAGTAAAAGAGCTTCTAATA
1 GAGTAAAAGAGCTTCTAATA
3234588 GAGT
1 GAGT
3234592 TTAACTTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.43, C:0.09, G:0.23, T:0.25
Consensus pattern (20 bp):
GAGTAAAAGAGCTTCTAATA
Found at i:3236816 original size:11 final size:11
Alignment explanation
Indices: 3236775--3236817 Score: 59
Period size: 12 Copynumber: 3.7 Consensus size: 11
3236765 ATTTAAACGA
*
3236775 GTATTGGGCCAG
1 GTATTGGGTC-G
3236787 GTATTGGGTCG
1 GTATTGGGTCG
3236798 GTTATTGGGTCG
1 G-TATTGGGTCG
3236810 GTATTGGG
1 GTATTGGG
3236818 CTGGGAATCG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 9 0.31
12 20 0.69
ACGTcount: A:0.12, C:0.09, G:0.44, T:0.35
Consensus pattern (11 bp):
GTATTGGGTCG
Found at i:3236953 original size:12 final size:13
Alignment explanation
Indices: 3236936--3236964 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3236926 TTTATTGGGT
3236936 CGGGT-ATCGGGG
1 CGGGTAATCGGGG
3236948 CGGGTAATCGGGG
1 CGGGTAATCGGGG
3236961 CGGG
1 CGGG
3236965 GATTACCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.10, C:0.17, G:0.59, T:0.14
Consensus pattern (13 bp):
CGGGTAATCGGGG
Found at i:3238416 original size:24 final size:24
Alignment explanation
Indices: 3238397--3238528 Score: 99
Period size: 24 Copynumber: 5.3 Consensus size: 24
3238387 AAAATATATT
3238397 TATTA-AAATTTATAATAATATAA
1 TATTATAAATTTATAATAATATAA
** *
3238420 TATTATATTTTTATAATAATAAAA
1 TATTATAAATTTATAATAATATAA
*
3238444 TAATA-AATTATATTATAATAATATAA
1 TATTATAA--AT-TTATAATAATATAA
** *
3238470 TATTATATTTTTATAATAATAAAA
1 TATTATAAATTTATAATAATATAA
*
3238494 TAATA-AATTATATTATAATAATATAAGA
1 TATTATAA--AT-TTATAATAATAT-A-A
3238522 TATTATA
1 TATTATA
3238529 TTTTTATTTT
Statistics
Matches: 82, Mismatches: 16, Indels: 16
0.72 0.14 0.14
Matches are distributed among these distances:
23 7 0.09
24 36 0.44
25 3 0.04
26 28 0.34
27 2 0.02
28 5 0.06
29 1 0.01
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (24 bp):
TATTATAAATTTATAATAATATAA
Found at i:3238420 original size:8 final size:8
Alignment explanation
Indices: 3238407--3238519 Score: 68
Period size: 8 Copynumber: 13.6 Consensus size: 8
3238397 TATTAAAATT
3238407 TATAATAA
1 TATAATAA
*
3238415 TATAATAT
1 TATAATAA
* **
3238423 TATATTTT
1 TATAATAA
3238431 TATAATAA
1 TATAATAA
*
3238439 TAAAATAA
1 TATAATAA
3238447 TA-AATTATA
1 TATAA-TA-A
3238456 TTATAATAA
1 -TATAATAA
*
3238465 TATAATAT
1 TATAATAA
* **
3238473 TATATTTT
1 TATAATAA
3238481 TATAATAA
1 TATAATAA
*
3238489 TAAAATAA
1 TATAATAA
3238497 TA-AATTATA
1 TATAA-TA-A
3238506 TTATAATAA
1 -TATAATAA
3238515 TATAA
1 TATAA
3238520 GATATTATAT
Statistics
Matches: 83, Mismatches: 14, Indels: 16
0.73 0.12 0.14
Matches are distributed among these distances:
7 4 0.05
8 63 0.76
9 4 0.05
10 8 0.10
11 4 0.05
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (8 bp):
TATAATAA
Found at i:3238475 original size:50 final size:50
Alignment explanation
Indices: 3238406--3238557 Score: 243
Period size: 50 Copynumber: 3.0 Consensus size: 50
3238396 TTATTAAAAT
3238406 TTATAATAATATAATATTATATTTTTATAATAATAAAATAATAAATTATA
1 TTATAATAATATAATATTATATTTTTATAATAATAAAATAATAAATTATA
3238456 TTATAATAATATAATATTATATTTTTATAATAATAAAATAATAAATTATA
1 TTATAATAATATAATATTATATTTTTATAATAATAAAATAATAAATTATA
**
3238506 TTATAATAATATAAGATATTATATTTTTATTTTAA-AATATATAATAAATTAT
1 TTATAATAATAT-A-ATATTATATTTTTATAATAATAA-A-ATAATAAATTAT
3238558 TAATAAAATT
Statistics
Matches: 96, Mismatches: 2, Indels: 5
0.93 0.02 0.05
Matches are distributed among these distances:
50 62 0.65
51 3 0.03
52 19 0.20
53 12 0.12
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (50 bp):
TTATAATAATATAATATTATATTTTTATAATAATAAAATAATAAATTATA
Found at i:3238630 original size:19 final size:18
Alignment explanation
Indices: 3238606--3238674 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 18
3238596 ATATTATTAA
3238606 ATTATTAATAATGAATAAT
1 ATTATTAATAAT-AATAAT
* *
3238625 ATTATTTAT-ATATTTAAT
1 ATTATTAATAATA-ATAAT
3238643 ATTAATATAATAATCTAATAAT
1 ATT-AT-TAATAA--TAATAAT
3238665 ATT-TTAATAA
1 ATTATTAATAA
3238675 AGATATTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
17 1 0.03
18 9 0.22
19 16 0.40
20 4 0.10
21 1 0.03
22 7 0.17
23 2 0.05
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (18 bp):
ATTATTAATAATAATAAT
Found at i:3238695 original size:23 final size:23
Alignment explanation
Indices: 3238669--3238713 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3238659 AATAATATTT
3238669 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
3238692 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
3238714 ATATAACAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:3240495 original size:26 final size:26
Alignment explanation
Indices: 3240449--3240500 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
3240439 ATAAATTATG
* *
3240449 AAAATGCCCTTATATTGAAAATGACC
1 AAAATGCCCTTAAAGTGAAAATGACC
3240475 AAAATGCCC-TAAAGTGTAAAATGACC
1 AAAATGCCCTTAAAGTG-AAAATGACC
3240501 TAATTTAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.44, C:0.19, G:0.13, T:0.23
Consensus pattern (26 bp):
AAAATGCCCTTAAAGTGAAAATGACC
Found at i:3241886 original size:20 final size:20
Alignment explanation
Indices: 3241861--3241912 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
3241851 TTTCAAAAAT
3241861 TGGTACCGATACTGATCTTA
1 TGGTACCGATACTGATCTTA
*
3241881 TGGTACTGATACTGATCTTA
1 TGGTACCGATACTGATCTTA
*
3241901 TGGTATCGATAC
1 TGGTACCGATAC
3241913 CCTTGGTATC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37
Consensus pattern (20 bp):
TGGTACCGATACTGATCTTA
Found at i:3242760 original size:29 final size:29
Alignment explanation
Indices: 3242726--3242795 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
3242716 ATTTATCTAT
*
3242726 TTTAGTCACTAAATTCTAAAGATTTACAA
1 TTTAGTCACTAAATTATAAAGATTTACAA
* *
3242755 TTTAGTCACTAAATTATGAAGTTTTACAA
1 TTTAGTCACTAAATTATAAAGATTTACAA
*
3242784 TTTGGTCACTAA
1 TTTAGTCACTAA
3242796 CCCGATATTG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (29 bp):
TTTAGTCACTAAATTATAAAGATTTACAA
Found at i:3248154 original size:22 final size:22
Alignment explanation
Indices: 3248126--3248170 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
3248116 GGCATGCGAA
3248126 ATATGTCCCGAAGGACCTATGT
1 ATATGTCCCGAAGGACCTATGT
3248148 ATATGTCCCGAAGGACCTATGT
1 ATATGTCCCGAAGGACCTATGT
3248170 A
1 A
3248171 ACCCTCGACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (22 bp):
ATATGTCCCGAAGGACCTATGT
Found at i:3248902 original size:18 final size:19
Alignment explanation
Indices: 3248879--3248916 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
3248869 ATGGTATCGG
3248879 TACCCTT-GGTATCGATAC
1 TACCCTTAGGTATCGATAC
3248897 TACCCTTCAGGTATCGATAC
1 TACCCTT-AGGTATCGATAC
3248917 CCCATGAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
20 11 0.61
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.32
Consensus pattern (19 bp):
TACCCTTAGGTATCGATAC
Found at i:3257966 original size:20 final size:20
Alignment explanation
Indices: 3257938--3257980 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
3257928 TAAAAAATTA
3257938 TTTTAATTTTAAAT-TGTTGT
1 TTTTAA-TTTAAATATGTTGT
* *
3257958 TTTTGATTTAATTATGTTGT
1 TTTTAATTTAAATATGTTGT
3257978 TTT
1 TTT
3257981 CATGAAAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.21, C:0.00, G:0.12, T:0.67
Consensus pattern (20 bp):
TTTTAATTTAAATATGTTGT
Found at i:3258034 original size:12 final size:13
Alignment explanation
Indices: 3258005--3258037 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
3257995 ATATTATGAT
*
3258005 TTTTCAAACATTG
1 TTTTCAAACATAG
3258018 TTTTCAAA-ATAG
1 TTTTCAAACATAG
3258030 TTTTCAAA
1 TTTTCAAA
3258038 TTTTTCCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.45
Consensus pattern (13 bp):
TTTTCAAACATAG
Found at i:3258224 original size:12 final size:12
Alignment explanation
Indices: 3258207--3258231 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3258197 TCTAGTCGGT
3258207 CAAACCAACCTC
1 CAAACCAACCTC
3258219 CAAACCAACCTC
1 CAAACCAACCTC
3258231 C
1 C
3258232 TATTCTACCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.52, G:0.00, T:0.08
Consensus pattern (12 bp):
CAAACCAACCTC
Found at i:3259846 original size:13 final size:13
Alignment explanation
Indices: 3259817--3259851 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
3259807 GGGGAGTAAT
*
3259817 TTTTCAAAATTGA
1 TTTTCAAAAATGA
3259830 -TTTCAAAAATGA
1 TTTTCAAAAATGA
3259842 TTTTCAAAAA
1 TTTTCAAAAA
3259852 AGAAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.40
Consensus pattern (13 bp):
TTTTCAAAAATGA
Found at i:3263834 original size:2 final size:2
Alignment explanation
Indices: 3263827--3263860 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3263817 ATGATTTCAA
3263827 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
3263861 GTTCACTTTT
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:3264116 original size:3 final size:3
Alignment explanation
Indices: 3264110--3264169 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
3264100 CTTCTTCTTC
3264110 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3264158 TTA TTA TTA TTA
1 TTA TTA TTA TTA
3264170 GGATTTTAAG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3274105 original size:64 final size:65
Alignment explanation
Indices: 3273948--3274110 Score: 190
Period size: 65 Copynumber: 2.5 Consensus size: 65
3273938 TCTTTAACAT
* * * * *
3273948 GTGCATCGATGCACTACCCATGCATCGATACAC-AATTTACCTTCGATGTTTTCATTTTAAGGGG
1 GTGCATCGATGCACTTCCTATGCATCGATACACTAATCTACATTCGATGTTTCCATTTTAA-GGG
3274012 G
65 G
* * *
3274013 GTGCATCGATGCAC-TCCTAATGCATCGATGCACTAA-CTGCATTCGATGTTTCCATTTTTAA-T
1 GTGCATCGATGCACTTCCT-ATGCATCGATACACTAATCTACATTCGATGTTTCCA-TTTTAAGG
3274075 GG
64 GG
*
3274077 GTGCATCGATGCACTTCCTGTGCATCGATACACT
1 GTGCATCGATGCACTTCCTATGCATCGATACACT
3274111 CTGAACAATT
Statistics
Matches: 84, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
64 31 0.37
65 45 0.54
66 8 0.10
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.33
Consensus pattern (65 bp):
GTGCATCGATGCACTTCCTATGCATCGATACACTAATCTACATTCGATGTTTCCATTTTAAGGGG
Found at i:3285671 original size:29 final size:29
Alignment explanation
Indices: 3285636--3285715 Score: 151
Period size: 29 Copynumber: 2.8 Consensus size: 29
3285626 AAAATAAAAA
*
3285636 TGGTTCTTTAGATAATTTTTTTTAAAAGG
1 TGGTTCTTTTGATAATTTTTTTTAAAAGG
3285665 TGGTTCTTTTGATAATTTTTTTTAAAAGG
1 TGGTTCTTTTGATAATTTTTTTTAAAAGG
3285694 TGGTTCTTTTGATAATTTTTTT
1 TGGTTCTTTTGATAATTTTTTT
3285716 CCTAGTATAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.23, C:0.04, G:0.16, T:0.57
Consensus pattern (29 bp):
TGGTTCTTTTGATAATTTTTTTTAAAAGG
Found at i:3286453 original size:16 final size:16
Alignment explanation
Indices: 3286432--3286464 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3286422 AAAAAAAATT
3286432 TGTTCGTTTATCTTCG
1 TGTTCGTTTATCTTCG
*
3286448 TGTTCGTTTATGTTCG
1 TGTTCGTTTATCTTCG
3286464 T
1 T
3286465 TTATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.15, G:0.21, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATCTTCG
Found at i:3295753 original size:15 final size:14
Alignment explanation
Indices: 3295721--3295755 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
3295711 GTCATGTTAT
*
3295721 TTTATGGTTAAATA
1 TTTATTGTTAAATA
3295735 TTTATTGTTAATATA
1 TTTATTGTTAA-ATA
3295750 TTTATT
1 TTTATT
3295756 TTTACTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.60
Consensus pattern (14 bp):
TTTATTGTTAAATA
Found at i:3296663 original size:29 final size:29
Alignment explanation
Indices: 3296617--3296673 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
3296607 AAATGGTTAC
* *
3296617 TGTAATCAAAGTTGTATAACTTTTTAAAT
1 TGTAATCAAAGTTATATAACCTTTTAAAT
* *
3296646 TGTAATCGAATTTATATAACCTTTTAAA
1 TGTAATCAAAGTTATATAACCTTTTAAA
3296674 ATAGACATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.44
Consensus pattern (29 bp):
TGTAATCAAAGTTATATAACCTTTTAAAT
Found at i:3301300 original size:15 final size:15
Alignment explanation
Indices: 3301280--3301326 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
3301270 CCTCTTGACT
3301280 TTCTTCAGCCTTCTC
1 TTCTTCAGCCTTCTC
*
3301295 TTCTTCA-TC-T-TC
1 TTCTTCAGCCTTCTC
3301307 TTCTTCAGCCTTCTC
1 TTCTTCAGCCTTCTC
3301322 TTCTT
1 TTCTT
3301327 GTTCCTCTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
12 9 0.33
13 2 0.07
14 2 0.07
15 14 0.52
ACGTcount: A:0.06, C:0.36, G:0.04, T:0.53
Consensus pattern (15 bp):
TTCTTCAGCCTTCTC
Found at i:3301357 original size:45 final size:45
Alignment explanation
Indices: 3301305--3301441 Score: 220
Period size: 45 Copynumber: 3.0 Consensus size: 45
3301295 TTCTTCATCT
**
3301305 TCTTCTTCAGCCTTCTCTTCTTGTTCCTCTGCATCTTCTTTTGAC
1 TCTTCTTCAGCCTTCTCTTCTTGTTCCTCTGCATCTTCTTTCAAC
**
3301350 TCTTCTTCAGCCTTCTCTTCTTGTTCCTCTGTGTCTTCTTTCAAC
1 TCTTCTTCAGCCTTCTCTTCTTGTTCCTCTGCATCTTCTTTCAAC
* *
3301395 TCTTCTTCAGCCTTCACTTCTTTTTCCTCTGCATCTTCTTTCAAC
1 TCTTCTTCAGCCTTCTCTTCTTGTTCCTCTGCATCTTCTTTCAAC
3301440 TC
1 TC
3301442 AACTTTCTCA
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 84 1.00
ACGTcount: A:0.08, C:0.34, G:0.07, T:0.50
Consensus pattern (45 bp):
TCTTCTTCAGCCTTCTCTTCTTGTTCCTCTGCATCTTCTTTCAAC
Found at i:3307039 original size:12 final size:12
Alignment explanation
Indices: 3307024--3307050 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3307014 ACTAATGATT
3307024 AAAATAATAATA
1 AAAATAATAATA
3307036 AAAATAATAATA
1 AAAATAATAATA
3307048 AAA
1 AAA
3307051 TATAGACTAA
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:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (12 bp):
AAAATAATAATA
Found at i:3311367 original size:23 final size:23
Alignment explanation
Indices: 3311337--3311382 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
3311327 GATCAGAGAT
3311337 GGAGCTAGAATTAAATATTGGCA
1 GGAGCTAGAATTAAATATTGGCA
3311360 GGAGCTAGAATTAAATATTGGCA
1 GGAGCTAGAATTAAATATTGGCA
3311383 AGGGCTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.26, T:0.26
Consensus pattern (23 bp):
GGAGCTAGAATTAAATATTGGCA
Found at i:3311784 original size:65 final size:63
Alignment explanation
Indices: 3311712--3311871 Score: 223
Period size: 65 Copynumber: 2.5 Consensus size: 63
3311702 AATTAAATTG
* *
3311712 AACATCGAATGCATTTCATGCATCGATGCACATACCATGCACCGATGCACTGAGGAT-TTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACA-ACCATGCACCGATGCACTCAGGATATTT-TG-
3311776 A
63 A
* * *
3311777 AACATCGAATGCATTTGATGCATCGATGCACCAACCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCA-CAACCATGCACCGATGCACTCAGGATATTTTGA
*
3311841 AACATCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
3311872 TCTTAGTGCA
Statistics
Matches: 87, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
63 1 0.01
64 30 0.34
65 51 0.59
66 5 0.06
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACAACCATGCACCGATGCACTCAGGATATTTTGA
Found at i:3311871 original size:17 final size:19
Alignment explanation
Indices: 3311843--3311891 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
3311833 TATTTTGAAA
3311843 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
3311861 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
3311880 CACCGATGCACT
1 CATCGATGCACT
3311892 ATGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:3317686 original size:24 final size:24
Alignment explanation
Indices: 3317659--3317739 Score: 75
Period size: 24 Copynumber: 3.5 Consensus size: 24
3317649 TTTGTGCTTA
3317659 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCATCCCTTTGAAT
* *
3317683 GTGCATCGATTCAT-CATGTTG-A-
1 GTGCATCGATGCATCCCT-TTGAAT
*
3317705 -TGCACCGATGCA-CTCC-TTGAAT
1 GTGCATCGATGCATC-CCTTTGAAT
3317727 GTGCATCGATGCA
1 GTGCATCGATGCA
3317740 CATGGTCATG
Statistics
Matches: 45, Mismatches: 6, Indels: 13
0.70 0.09 0.20
Matches are distributed among these distances:
20 3 0.07
21 11 0.24
22 1 0.02
23 14 0.31
24 16 0.36
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (24 bp):
GTGCATCGATGCATCCCTTTGAAT
Found at i:3317729 original size:44 final size:44
Alignment explanation
Indices: 3317660--3317762 Score: 138
Period size: 44 Copynumber: 2.3 Consensus size: 44
3317650 TTGTGCTTAG
* * *
3317660 TGCATCGATGCATCCCTTTGAATGTGCATCGATTCATCATGTTGA
1 TGCATCGATGCATCCCTTTGAATGTGCATCGATGCA-CATGGTCA
*
3317705 TGCACCGATGCA-CTCC-TTGAATGTGCATCGATGCACATGGTCA
1 TGCATCGATGCATC-CCTTTGAATGTGCATCGATGCACATGGTCA
3317748 TGCATCGATGCATCC
1 TGCATCGATGCATCC
3317763 GTCGGGTTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
43 18 0.35
44 20 0.39
45 13 0.25
ACGTcount: A:0.22, C:0.26, G:0.21, T:0.30
Consensus pattern (44 bp):
TGCATCGATGCATCCCTTTGAATGTGCATCGATGCACATGGTCA
Found at i:3320453 original size:46 final size:45
Alignment explanation
Indices: 3320402--3320502 Score: 141
Period size: 45 Copynumber: 2.2 Consensus size: 45
3320392 TACCATGCTC
* *
3320402 CGATGCACTGAGGAT-TTTATGAAAACATCGAATGCATTTGATGCAT
1 CGATGCACTCAGGATATTT-TG-AAACATCGAATGCACTTGATGCAT
* *
3320448 CGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTGATGCAT
1 CGATGCACTCAGGATATTTTGAAACATCGAATGCACTTGATGCAT
3320493 CGATGCACTC
1 CGATGCACTC
3320503 TTAGTGCACC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
45 33 0.66
46 14 0.28
47 3 0.06
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.30
Consensus pattern (45 bp):
CGATGCACTCAGGATATTTTGAAACATCGAATGCACTTGATGCAT
Found at i:3320500 original size:17 final size:19
Alignment explanation
Indices: 3320472--3320520 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
3320462 TATTTTGAAA
3320472 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
3320490 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
3320509 CACCGATGCACT
1 CATCGATGCACT
3320521 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:3327089 original size:103 final size:103
Alignment explanation
Indices: 3326864--3327081 Score: 373
Period size: 103 Copynumber: 2.1 Consensus size: 103
3326854 GTCGAGGGTC
* *
3326864 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTAAAGTCTGGTGAGACACATAC
* *
3326929 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
* *
3326967 TATATGGTACTTCGGGACATATATGTATTCTTTGGAACATGTGTAAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTAAAGTCTGGTGAGACACATAC
*
3327032 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
3327070 TATGTGGTCCTT
1 TATGTGGTCCTT
3327082 ATGGACATTA
Statistics
Matches: 106, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
103 106 1.00
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTAAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:3327142 original size:47 final size:47
Alignment explanation
Indices: 3327088--3327207 Score: 215
Period size: 47 Copynumber: 2.6 Consensus size: 47
3327078 CCTTATGGAC
3327088 ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCGGTGCA
1 ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCGGTGCA
3327135 ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCGGTGCA
1 ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCGGTGCA
* *
3327182 ATTA-TATGTGGCACTTCGGTGCAATT
1 ATTATTATATGGCACTACGGTGCAATT
3327208 ATATGAGCTG
Statistics
Matches: 71, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
46 20 0.28
47 51 0.72
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.30
Consensus pattern (47 bp):
ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCGGTGCA
Found at i:3327208 original size:23 final size:23
Alignment explanation
Indices: 3327088--3327212 Score: 133
Period size: 23 Copynumber: 5.3 Consensus size: 23
3327078 CCTTATGGAC
*
3327088 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * * *
3327112 ATTCTACGCGGCACTCCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
3327135 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * * *
3327159 ATTCTACGCGGCACTCCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
3327182 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
3327205 ATTATATG
1 ATTATATG
3327213 AGCTGTGGTA
Statistics
Matches: 81, Mismatches: 19, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
23 60 0.74
24 21 0.26
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.30
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:3330402 original size:41 final size:41
Alignment explanation
Indices: 3330345--3330432 Score: 167
Period size: 41 Copynumber: 2.1 Consensus size: 41
3330335 TTACAATCAC
*
3330345 TAATGTATAAAATTAAAAGGGTAAACTACATAAATGGTCAT
1 TAATGTATAAAATTAAAAGGGTAAACTACACAAATGGTCAT
3330386 TAATGTATAAAATTAAAAGGGTAAACTACACAAATGGTCAT
1 TAATGTATAAAATTAAAAGGGTAAACTACACAAATGGTCAT
3330427 TAATGT
1 TAATGT
3330433 TTGAGTAAGC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.48, C:0.08, G:0.15, T:0.30
Consensus pattern (41 bp):
TAATGTATAAAATTAAAAGGGTAAACTACACAAATGGTCAT
Found at i:3330733 original size:42 final size:42
Alignment explanation
Indices: 3330633--3330841 Score: 199
Period size: 42 Copynumber: 5.0 Consensus size: 42
3330623 TAAAATGATT
* * * * *
3330633 AAATTAGGGGCTTAAATTTTAAAAGTAAAAAGT-ATGATGGAAA
1 AAATTAGGGGCCTCAATTATAAAGGTAAAAAGTGA-GAT-TAAA
** * * * *
3330676 AAATTATCGACCTCAATTATAAAGGTAAATAGTTATATTAAA
1 AAATTAGGGGCCTCAATTATAAAGGTAAAAAGTGAGATTAAA
* *
3330718 AAATTAGGGGTCTCAATTATAAAAGTAAAAAGTGAGATTAAA
1 AAATTAGGGGCCTCAATTATAAAGGTAAAAAGTGAGATTAAA
*
3330760 AAATTAGGGGCCTCAATTATAAAGG-AAGAAAGCGAGATTGAAA
1 AAATTAGGGGCCTCAATTATAAAGGTAA-AAAGTGAGATT-AAA
** * *
3330803 AAATTAGGAACAT-AATTATAAAGGTACAAAGTGAGATTA
1 AAATTAGGGGCCTCAATTATAAAGGTAAAAAGTGAGATTA
3330842 TAAAGATAAA
Statistics
Matches: 136, Mismatches: 26, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
41 3 0.02
42 91 0.67
43 41 0.30
44 1 0.01
ACGTcount: A:0.49, C:0.06, G:0.19, T:0.26
Consensus pattern (42 bp):
AAATTAGGGGCCTCAATTATAAAGGTAAAAAGTGAGATTAAA
Found at i:3330843 original size:21 final size:20
Alignment explanation
Indices: 3330817--3330900 Score: 59
Period size: 21 Copynumber: 4.2 Consensus size: 20
3330807 TAGGAACATA
3330817 ATTATAAAGGTACAAAGTGAG
1 ATTATAAA-GTACAAAGTGAG
*
3330838 ATTATAAAGATAAAAAGT-ATG
1 ATTATAAAG-TACAAAGTGA-G
* * * *
3330859 ACTACAAA--A-AAATTAAG
1 ATTATAAAGTACAAAGTGAG
3330876 ATTATAAAGTTACAAAGTGAG
1 ATTATAAAG-TACAAAGTGAG
3330897 ATTA
1 ATTA
3330901 AAAAAATTAG
Statistics
Matches: 48, Mismatches: 8, Indels: 14
0.69 0.11 0.20
Matches are distributed among these distances:
17 11 0.23
18 2 0.04
20 3 0.06
21 32 0.67
ACGTcount: A:0.54, C:0.05, G:0.15, T:0.26
Consensus pattern (20 bp):
ATTATAAAGTACAAAGTGAG
Found at i:3336709 original size:15 final size:16
Alignment explanation
Indices: 3336679--3336714 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
3336669 ATCTGAGTCT
3336679 TTATT-TATTTATATA
1 TTATTATATTTATATA
3336694 TTATTATATTTA-ATA
1 TTATTATATTTATATA
3336709 TTATTA
1 TTATTA
3336715 GTGTTATCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTATTATATTTATATA
Found at i:3364385 original size:14 final size:13
Alignment explanation
Indices: 3364342--3364386 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
3364332 GTTTGTGTGT
3364342 TGTTCGTTTAT-G
1 TGTTCGTTTATGG
*
3364354 T-TT-GTTTATTG
1 TGTTCGTTTATGG
3364365 TGTTCGTTTATGG
1 TGTTCGTTTATGG
3364378 TCGTTCGTT
1 T-GTTCGTT
3364387 CGTGTTCGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 6 0.21
11 4 0.14
12 3 0.11
13 8 0.29
14 7 0.25
ACGTcount: A:0.07, C:0.09, G:0.24, T:0.60
Consensus pattern (13 bp):
TGTTCGTTTATGG
Found at i:3374189 original size:39 final size:39
Alignment explanation
Indices: 3374149--3374317 Score: 162
Period size: 39 Copynumber: 4.3 Consensus size: 39
3374139 AATGACATGT
* * *
3374149 GGTAAGGACTTACCATGTGCACAAAGCAGAGGAGCTTGT
1 GGTAAGGACTTACCATGAGCACAAAGCAGAGGAGCCTGC
* * ** *
3374188 GGTAAGGACTTA-CATTGACCATAATCCCA-AGGAGCATGC
1 GGTAAGGACTTACCA-TGAGCACAA-AGCAGAGGAGCCTGC
* * * * *
3374227 GGTAAGAACTTACCTTGAGCAAAAAGCCGAGGAGCCTAC
1 GGTAAGGACTTACCATGAGCACAAAGCAGAGGAGCCTGC
* * *
3374266 GGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTAC
1 GGTAAGGACTTACCATGAGCACAAAGCAGAGGAGCCTGC
3374305 GGTAAGGACTTAC
1 GGTAAGGACTTAC
3374318 AAGTCATAGA
Statistics
Matches: 107, Mismatches: 19, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
38 3 0.03
39 101 0.94
40 3 0.03
ACGTcount: A:0.33, C:0.22, G:0.27, T:0.18
Consensus pattern (39 bp):
GGTAAGGACTTACCATGAGCACAAAGCAGAGGAGCCTGC
Found at i:3374299 original size:78 final size:78
Alignment explanation
Indices: 3374144--3374317 Score: 186
Period size: 78 Copynumber: 2.2 Consensus size: 78
3374134 AACATAATGA
* * * * ** *
3374144 CATGTGGTAAGGACTTACCATGTGCACAAAGCAGAGGAGCTTGTGGTAAGGACTTACATTGACCA
1 CATGCGGTAAGGACTTACCATGAGCAAAAAGCAGAGGAGCCTACGGTAAGGACTTACACTGACCA
* *
3374209 TAATCCCAAGGAG
66 CAAACCCAAGGAG
* * * * *
3374222 CATGCGGTAAGAACTTACCTTGAGCAAAAAGCCGAGGAGCCTACGGTAAGGACTTACCCTGAGCA
1 CATGCGGTAAGGACTTACCATGAGCAAAAAGCAGAGGAGCCTACGGTAAGGACTTACACTGACCA
* *
3374287 CAAAGCCGAGGAG
66 CAAACCCAAGGAG
* *
3374300 CCTACGGTAAGGACTTAC
1 CATGCGGTAAGGACTTAC
3374318 AAGTCATAGA
Statistics
Matches: 77, Mismatches: 19, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
78 77 1.00
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.18
Consensus pattern (78 bp):
CATGCGGTAAGGACTTACCATGAGCAAAAAGCAGAGGAGCCTACGGTAAGGACTTACACTGACCA
CAAACCCAAGGAG
Found at i:3379630 original size:12 final size:12
Alignment explanation
Indices: 3379613--3379638 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3379603 GCCTTTTGAA
3379613 TCGGTCTCGATC
1 TCGGTCTCGATC
3379625 TCGGTCTCGATC
1 TCGGTCTCGATC
3379637 TC
1 TC
3379639 TCATGCACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.35, G:0.23, T:0.35
Consensus pattern (12 bp):
TCGGTCTCGATC
Found at i:3382037 original size:18 final size:18
Alignment explanation
Indices: 3382008--3382070 Score: 74
Period size: 18 Copynumber: 3.6 Consensus size: 18
3381998 TTAAAAAAAA
*
3382008 GTCAAC-GTCGGTCAATG
1 GTCAACGGTCGGTTAATG
**
3382025 GTCAACGGTCGGTTAACA
1 GTCAACGGTCGGTTAATG
* *
3382043 GTTAACGGTCGATTAATG
1 GTCAACGGTCGGTTAATG
3382061 GTCAACGGTC
1 GTCAACGGTC
3382071 AACTATTGAC
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
17 6 0.16
18 31 0.84
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (18 bp):
GTCAACGGTCGGTTAATG
Found at i:3383601 original size:17 final size:17
Alignment explanation
Indices: 3383579--3383620 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
3383569 TCTGATGAGA
3383579 GAGAAGAAGTTCCTAAT
1 GAGAAGAAGTTCCTAAT
3383596 GAGAAGAAGTTCCTAAT
1 GAGAAGAAGTTCCTAAT
3383613 GAGAAGAA
1 GAGAAGAA
3383621 CTTACTGAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.45, C:0.10, G:0.26, T:0.19
Consensus pattern (17 bp):
GAGAAGAAGTTCCTAAT
Found at i:3383691 original size:44 final size:44
Alignment explanation
Indices: 3383628--3383975 Score: 374
Period size: 44 Copynumber: 7.9 Consensus size: 44
3383618 GAACTTACTG
* * *
3383628 AACATTTCGCTTGAGTCCATCACATAAGGAGTTGGA-CTAACATC
1 AACATTTCGCTCGAATCCATCACAGAAGGAGTTGGATC-AACATC
*
3383672 AACATTTCGCTCAAATCCATCACAGAAGGAGTTGGATCAACATC
1 AACATTTCGCTCGAATCCATCACAGAAGGAGTTGGATCAACATC
* * * *
3383716 AATATTTCGTTCGAATCCATCACAGAAGTAGTTGGATAAAGCATC
1 AACATTTCGCTCGAATCCATCACAGAAGGAGTTGGATCAA-CATC
* * *
3383761 AACATTTCGCTCGAATCCATCGCAGAGGGAGTTGAATCAACATC
1 AACATTTCGCTCGAATCCATCACAGAAGGAGTTGGATCAACATC
* * * * *
3383805 AATATTTCACTCGAATCCATCATAGAAGGAGTTGGATTAGCATC
1 AACATTTCGCTCGAATCCATCACAGAAGGAGTTGGATCAACATC
* * *
3383849 AACATTTTGTTTGAATCCATCACAGAAGGAGTTGGATCAACATC
1 AACATTTCGCTCGAATCCATCACAGAAGGAGTTGGATCAACATC
* ** * * * * *
3383893 AATATTTATCTCGAGTCAATCACATAAGGAGTTGGACCAGCATC
1 AACATTTCGCTCGAATCCATCACAGAAGGAGTTGGATCAACATC
* * * * * *
3383937 AAAATTTCGCTTGATTCCATCACATAGGGAATTGGATCA
1 AACATTTCGCTCGAATCCATCACAGAAGGAGTTGGATCA
3383976 GCACAATTAA
Statistics
Matches: 251, Mismatches: 51, Indels: 4
0.82 0.17 0.01
Matches are distributed among these distances:
44 213 0.85
45 38 0.15
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (44 bp):
AACATTTCGCTCGAATCCATCACAGAAGGAGTTGGATCAACATC
Found at i:3383866 original size:133 final size:132
Alignment explanation
Indices: 3383628--3383944 Score: 366
Period size: 133 Copynumber: 2.4 Consensus size: 132
3383618 GAACTTACTG
* * * * *
3383628 AACATTTCGCTTGAGTCCATCACATAAGGAGTTGGACTAACATCAACATTTCGCTCAAATCCATC
1 AACATTTCGCTCGAATCCATCACAGAAGGAGTTGAACTAACATCAACATTTCACTCAAATCCATC
* *
3383693 ACAGAAGGAGTTGGATCAACATCAATATTTCGTTCGAATCCATCACAGAAGTAGTTGGATAAAGC
66 ACAGAAGGAGTTGGATCAACATCAACATTTCGTTCGAATCCATCACAGAAGGAGTTGGATAAA-C
3383758 ATC
130 ATC
* * * *
3383761 AACATTTCGCTCGAATCCATCGCAGAGGGAGTTGAA-TCAACATCAATATTTCACTCGAATCCAT
1 AACATTTCGCTCGAATCCATCACAGAAGGAGTTGAACT-AACATCAACATTTCACTCAAATCCAT
* * * * * *
3383825 CATAGAAGGAGTTGGATTAGCATCAACATTTTGTTTGAATCCATCACAGAAGGAGTTGGATCAAC
65 CACAGAAGGAGTTGGATCAACATCAACATTTCGTTCGAATCCATCACAGAAGGAGTTGGATAAAC
3383890 ATC
130 ATC
* ** * * * * * * *
3383893 AATATTTATCTCGAGTCAATCACATAAGGAGTTGGACCAGCATCAAAATTTC
1 AACATTTCGCTCGAATCCATCACAGAAGGAGTTGAACTAACATCAACATTTC
3383945 GCTTGATTCC
Statistics
Matches: 153, Mismatches: 29, Indels: 5
0.82 0.16 0.03
Matches are distributed among these distances:
132 44 0.29
133 109 0.71
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (132 bp):
AACATTTCGCTCGAATCCATCACAGAAGGAGTTGAACTAACATCAACATTTCACTCAAATCCATC
ACAGAAGGAGTTGGATCAACATCAACATTTCGTTCGAATCCATCACAGAAGGAGTTGGATAAACA
TC
Found at i:3383896 original size:88 final size:88
Alignment explanation
Indices: 3383643--3384016 Score: 412
Period size: 88 Copynumber: 4.2 Consensus size: 88
3383633 TTCGCTTGAG
* * *
3383643 TCCATCACATAAGGAGTTGGACTAACATCAACATTTCGCTCAAATCCATCACAGAAGGAGTTGGA
1 TCCATCACAGAAGGAGTTGGACTAGCATCAACATTTCGCTCGAATCCATCACAGAAGGAGTTGGA
**
3383708 TCAACATCAATATTTCGTTCGAA
66 TCAACATCAATATTTCACTCGAA
* * *
3383731 TCCATCACAGAAGTAGTTGGA-TAAAGCATCAACATTTCGCTCGAATCCATCGCAGAGGGAGTTG
1 TCCATCACAGAAGGAGTTGGACT--AGCATCAACATTTCGCTCGAATCCATCACAGAAGGAGTTG
*
3383795 AATCAACATCAATATTTCACTCGAA
64 GATCAACATCAATATTTCACTCGAA
* * * * *
3383820 TCCATCATAGAAGGAGTTGGATTAGCATCAACATTTTGTTTGAATCCATCACAGAAGGAGTTGGA
1 TCCATCACAGAAGGAGTTGGACTAGCATCAACATTTCGCTCGAATCCATCACAGAAGGAGTTGGA
*
3383885 TCAACATCAATATTT-ATCTCGAG
66 TCAACATCAATATTTCA-CTCGAA
* * * * * * * * *
3383908 TCAATCACATAAGGAGTTGGACCAGCATCAAAATTTCGCTTGATTCCATCACATAGGGAATTGGA
1 TCCATCACAGAAGGAGTTGGACTAGCATCAACATTTCGCTCGAATCCATCACAGAAGGAGTTGGA
* * * *
3383973 TCAGCA-CAATTAATTCACTTGAT
66 TCAACATCAA-TATTTCACTCGAA
* * *
3383996 TCTATCGCATAAGGAGTTGGA
1 TCCATCACAGAAGGAGTTGGA
3384017 TAAACTTGGT
Statistics
Matches: 244, Mismatches: 36, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
87 5 0.02
88 160 0.66
89 78 0.32
90 1 0.00
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (88 bp):
TCCATCACAGAAGGAGTTGGACTAGCATCAACATTTCGCTCGAATCCATCACAGAAGGAGTTGGA
TCAACATCAATATTTCACTCGAA
Found at i:3383994 original size:44 final size:44
Alignment explanation
Indices: 3383631--3384017 Score: 253
Period size: 44 Copynumber: 8.8 Consensus size: 44
3383621 CTTACTGAAC
* * * *
3383631 ATTTCGCTTGAGTCCATCACATAAGGAGTTGGA-CTAACATCAAC
1 ATTTCACTTGATTCCATCACATAAGGAGTTGGATC-AGCATCAAA
* ** * * * *
3383675 ATTTCGCTCAAATCCATCACAGAAGGAGTTGGATCAACATCAAT
1 ATTTCACTTGATTCCATCACATAAGGAGTTGGATCAGCATCAAA
* * * * * *
3383719 ATTTC-GTTCGAATCCATCACAGAAGTAGTTGGATAAAGCATCAAC
1 ATTTCACTT-GATTCCATCACATAAGGAGTTGGAT-CAGCATCAAA
* * * * * * * * *
3383764 ATTTCGCTCGAATCCATCGCAGAGGGAGTTGAATCAACATCAAT
1 ATTTCACTTGATTCCATCACATAAGGAGTTGGATCAGCATCAAA
* * * * * *
3383808 ATTTCACTCGAATCCATCATAGAAGGAGTTGGATTAGCATCAAC
1 ATTTCACTTGATTCCATCACATAAGGAGTTGGATCAGCATCAAA
*** * * * *
3383852 ATTTTGTTTGAATCCATCACAGAAGGAGTTGGATCAACATCAAT
1 ATTTCACTTGATTCCATCACATAAGGAGTTGGATCAGCATCAAA
* * * *
3383896 ATTT-ATCTCGAGTCAATCACATAAGGAGTTGGACCAGCATCAAA
1 ATTTCA-CTTGATTCCATCACATAAGGAGTTGGATCAGCATCAAA
* * *
3383940 ATTTCGCTTGATTCCATCACATAGGGAATTGGATCAGCA-CAATTA
1 ATTTCACTTGATTCCATCACATAAGGAGTTGGATCAGCATCAA--A
* *
3383985 A-TTCACTTGATTCTATCGCATAAGGAGTTGGAT
1 ATTTCACTTGATTCCATCACATAAGGAGTTGGAT
3384018 AAACTTGGTA
Statistics
Matches: 277, Mismatches: 58, Indels: 16
0.79 0.17 0.05
Matches are distributed among these distances:
43 4 0.01
44 236 0.85
45 36 0.13
46 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.28
Consensus pattern (44 bp):
ATTTCACTTGATTCCATCACATAAGGAGTTGGATCAGCATCAAA
Found at i:3384377 original size:46 final size:47
Alignment explanation
Indices: 3384282--3384378 Score: 117
Period size: 46 Copynumber: 2.1 Consensus size: 47
3384272 ATTTTCTTTG
* * *
3384282 AAATAATATGTAGTTTTGTAAAGGATAATATAATATTATATGATTTTA
1 AAATAATATATAG-TTTGTAAAGAATAATATAATATTATATGATCTTA
* *
3384330 AAATAATATATAG-TTGTAAATAATAATATTATATTATAT-AGTCTTA
1 AAATAATATATAGTTTGTAAAGAATAATATAATATTATATGA-TCTTA
3384376 AAA
1 AAA
3384379 ATGTTATACT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
45 1 0.02
46 30 0.70
48 12 0.28
ACGTcount: A:0.47, C:0.01, G:0.09, T:0.42
Consensus pattern (47 bp):
AAATAATATATAGTTTGTAAAGAATAATATAATATTATATGATCTTA
Found at i:3384435 original size:2 final size:2
Alignment explanation
Indices: 3384430--3384456 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3384420 TAGTTTAAAA
3384430 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 A
3384457 GTTTGTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3384501 original size:13 final size:13
Alignment explanation
Indices: 3384483--3384510 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3384473 CATATGCAGC
3384483 TTTGAAATAAATA
1 TTTGAAATAAATA
3384496 TTTGAAATAAATA
1 TTTGAAATAAATA
3384509 TT
1 TT
3384511 AGCATGTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (13 bp):
TTTGAAATAAATA
Found at i:3386170 original size:21 final size:22
Alignment explanation
Indices: 3386144--3386197 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
3386134 TAATTGTTTT
3386144 ATTAATTAATTCTAATTT-TAA
1 ATTAATTAATTCTAATTTGTAA
* * *
3386165 TTTAATTTAATCCTCATTTGTAA
1 ATTAA-TTAATTCTAATTTGTAA
3386188 ATT-ATTAATT
1 ATTAATTAATT
3386198 AGTCTGTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
21 9 0.35
22 12 0.46
23 5 0.19
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54
Consensus pattern (22 bp):
ATTAATTAATTCTAATTTGTAA
Found at i:3388108 original size:138 final size:137
Alignment explanation
Indices: 3387830--3388111 Score: 415
Period size: 138 Copynumber: 2.1 Consensus size: 137
3387820 GTCATAGGTG
* *
3387830 CATTTCGACATAAATTGTATATAAAAGTTATCGATCAATTTTGTTTAATGCATAATGGTGCATTT
1 CATTTCGACATAAATTATATATAAAAGTTATCGATCAATTTTGTTTAATGCATAATGATGCATTT
* *
3387895 TCGTATCAGTACTATGTGTACTTTCGGCACTAAATGTACAATCATGATATTCATAATGAGTTTAT
66 TCGTATCAGTACTATATGTACTTTCGACACTAAATGTACAATCATGATATTCATAATGAGTTTAT
3387960 AAATTAC
131 AAATTAC
* * *
3387967 CATTTCGATATACAATTATGTATAAAAGTTATCGATCGATTTTGTTTAATGCATAATGATGCATT
1 CATTTCGACATA-AATTATATATAAAAGTTATCGATCAATTTTGTTTAATGCATAATGATGCATT
* *
3388032 TTCGTATCAGTACTATATGTACTTTCGACACTATATGTGC-ATCCATGGA-ATTCATAATGAGTT
65 TTCGTATCAGTACTATATGTACTTTCGACACTAAATGTACAAT-CAT-GATATTCATAATGAGTT
* * *
3388095 TGTGAATTTC
128 TATAAATTAC
3388105 CATTTCG
1 CATTTCG
3388112 GGACTTCGGT
Statistics
Matches: 130, Mismatches: 12, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
137 13 0.10
138 115 0.88
139 2 0.02
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.40
Consensus pattern (137 bp):
CATTTCGACATAAATTATATATAAAAGTTATCGATCAATTTTGTTTAATGCATAATGATGCATTT
TCGTATCAGTACTATATGTACTTTCGACACTAAATGTACAATCATGATATTCATAATGAGTTTAT
AAATTAC
Found at i:3395149 original size:20 final size:20
Alignment explanation
Indices: 3395124--3395164 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
3395114 TACACTTGAG
3395124 TAAGGATTTAAAATGAACTT
1 TAAGGATTTAAAATGAACTT
3395144 TAAGGATTTAAAATGAACTT
1 TAAGGATTTAAAATGAACTT
3395164 T
1 T
3395165 GAAATACTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.37
Consensus pattern (20 bp):
TAAGGATTTAAAATGAACTT
Found at i:3401573 original size:22 final size:21
Alignment explanation
Indices: 3401531--3401570 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3401521 GAGTTTATTT
*
3401531 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
3401552 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
3401571 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:3403535 original size:18 final size:19
Alignment explanation
Indices: 3403498--3403536 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
3403488 CGTTGAACAG
3403498 TGGGGGGAATCGGTACTCCC
1 TGGGGGGAATCGGTA-TCCC
3403518 TGGGGGGAATCGGT-TCCC
1 TGGGGGGAATCGGTATCCC
3403536 T
1 T
3403537 CCGAGCATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.26
20 14 0.74
ACGTcount: A:0.13, C:0.23, G:0.41, T:0.23
Consensus pattern (19 bp):
TGGGGGGAATCGGTATCCC
Found at i:3414680 original size:20 final size:19
Alignment explanation
Indices: 3414617--3414690 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 19
3414607 TAATGTTTAA
* *
3414617 AAGTATCGATACTTATATA
1 AAGTATCGATACTTTTATG
*
3414636 AAGTATCGAAACTTTTGCA-G
1 AAGTATCGATACTTTT--ATG
*
3414656 GAGTATCGATACTTTTAATG
1 AAGTATCGATACTTTT-ATG
*
3414676 TAGTATCGATACTTT
1 AAGTATCGATACTTT
3414691 CAGTCTGTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
19 15 0.33
20 29 0.64
21 1 0.02
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (19 bp):
AAGTATCGATACTTTTATG
Found at i:3421898 original size:19 final size:20
Alignment explanation
Indices: 3421874--3421921 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
3421864 ACAATGTTTA
3421874 AAAGTAAT-GATACTTATAT
1 AAAGTAATCGATACTTATAT
3421893 AAAGT-ATCGATACTTATAT
1 AAAGTAATCGATACTTATAT
3421912 AAAGT-ATCGA
1 AAAGTAATCGA
3421922 AATTTTGCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 2 0.07
19 26 0.93
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.33
Consensus pattern (20 bp):
AAAGTAATCGATACTTATAT
Found at i:3424475 original size:9 final size:9
Alignment explanation
Indices: 3424461--3424490 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
3424451 GTTTTTTGCA
3424461 TTTCTTCTT
1 TTTCTTCTT
3424470 TTTCTTCTT
1 TTTCTTCTT
3424479 TTTCTTCTT
1 TTTCTTCTT
3424488 TTT
1 TTT
3424491 AATAGGGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTCTTCTT
Found at i:3426842 original size:2 final size:2
Alignment explanation
Indices: 3426835--3426887 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
3426825 TCTTGGAATC
3426835 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3426877 AT AT AT AT AT A
1 AT AT AT AT AT A
3426888 CACGAAACAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3438906 original size:32 final size:32
Alignment explanation
Indices: 3438865--3438930 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
3438855 CTTGCGTAGG
*
3438865 AGTCTCTTGTATCTATCCCAGCATTGAAACAT
1 AGTCTCTTGTATCTATCCCAGCACTGAAACAT
*
3438897 AGTCTCTTGTATCTATCCCAGTACTGAAACAT
1 AGTCTCTTGTATCTATCCCAGCACTGAAACAT
3438929 AG
1 AG
3438931 ACTCGTCATC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (32 bp):
AGTCTCTTGTATCTATCCCAGCACTGAAACAT
Found at i:3444531 original size:21 final size:22
Alignment explanation
Indices: 3444492--3444532 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3444482 TACTCGTTTC
*
3444492 TAAAATAAAGAAGAGAATTGAA
1 TAAAAAAAAGAAGAGAATTGAA
*
3444514 TAAAAAAAATAAG-GAATTG
1 TAAAAAAAAGAAGAGAATTG
3444533 GTGATTCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.63, C:0.00, G:0.17, T:0.20
Consensus pattern (22 bp):
TAAAAAAAAGAAGAGAATTGAA
Found at i:3446427 original size:3 final size:3
Alignment explanation
Indices: 3446419--3446449 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
3446409 TGTCCGGGTA
3446419 ATT ATT ATT ATT ATT ATT ATT ATT AATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT
3446450 TTAATTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:3446453 original size:9 final size:10
Alignment explanation
Indices: 3446419--3446457 Score: 57
Period size: 9 Copynumber: 4.2 Consensus size: 10
3446409 TGTCCGGGTA
3446419 ATTATT-ATT
1 ATTATTAATT
3446428 ATTATT-ATT
1 ATTATTAATT
3446437 ATTATTAATT
1 ATTATTAATT
3446447 ATT-TTAATT
1 ATTATTAATT
3446456 AT
1 AT
3446458 ATTGTTTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
9 23 0.79
10 6 0.21
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
ATTATTAATT
Found at i:3456082 original size:26 final size:26
Alignment explanation
Indices: 3456046--3456127 Score: 79
Period size: 26 Copynumber: 3.4 Consensus size: 26
3456036 CCTTAATGCA
3456046 TCCTTTCATGCATATTATTTATGGTG
1 TCCTTTCATGCATATTATTTATGGTG
* *
3456072 TCCTTTCATGC--CTTA---AT-GTA
1 TCCTTTCATGCATATTATTTATGGTG
* *
3456092 TCC-TTCATGCATTTTATTTATGGCG
1 TCCTTTCATGCATATTATTTATGGTG
3456117 TCCTTTCATGC
1 TCCTTTCATGC
3456128 CTTAATACAT
Statistics
Matches: 44, Mismatches: 5, Indels: 14
0.70 0.08 0.22
Matches are distributed among these distances:
19 7 0.16
20 5 0.11
21 5 0.11
24 5 0.11
25 4 0.09
26 18 0.41
ACGTcount: A:0.17, C:0.22, G:0.13, T:0.48
Consensus pattern (26 bp):
TCCTTTCATGCATATTATTTATGGTG
Found at i:3456106 original size:91 final size:91
Alignment explanation
Indices: 3456011--3456276 Score: 408
Period size: 91 Copynumber: 2.9 Consensus size: 91
3456001 GTTAAATTTT
**
3456011 ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATATTATTTATGGTGTCCT
1 ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCAT-TTATTTATGGCATCCT
*
3456076 TTCATGCCTTAATGTATCC-TTCATGC
65 TTCATGCCTTAATGCATCCTTTCATGC
* * *
3456102 ATTTTATTTATGGCGTCCTTTCATGCCTTAATACATCCTTTCATGCATTTAATTTATCGCATCCT
1 ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTT-ATTTATGGCATCCT
3456167 TTCATGCCTTAATGCATCCTTTCATGC
65 TTCATGCCTTAATGCATCCTTTCATGC
*
3456194 ATTTTATTTATGGCATCCTTTTATGCCTTAATGCATCCTTTCATGCATTTTTATTTATGGCATCC
1 ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCA--TTTATTTATGGCATCC
*
3456259 TTTCATGCCAATAATGCA
64 TTTCATGCC-TTAATGCA
3456277 CCCATATGCA
Statistics
Matches: 159, Mismatches: 11, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
90 2 0.01
91 75 0.47
92 51 0.32
93 21 0.13
94 10 0.06
ACGTcount: A:0.21, C:0.23, G:0.11, T:0.45
Consensus pattern (91 bp):
ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTATTTATGGCATCCTT
TCATGCCTTAATGCATCCTTTCATGC
Found at i:3456165 original size:137 final size:139
Alignment explanation
Indices: 3456011--3456267 Score: 428
Period size: 137 Copynumber: 1.9 Consensus size: 139
3456001 GTTAAATTTT
* * **
3456011 ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATATTATTTATGGTGTCCT
1 ATTTAATTTATCGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATATTATTTATGGCATCCT
* *
3456076 TTCATGCCTTAATGTATCC-TTCATGCA-TTTTATTTATGGCGTCCTTTCATGCCTTAATACATC
66 TTCATGCCTTAATGCATCCTTTCATGCATTTTTATTTATGGCATCCTTTCATGCCTTAATACATC
3456139 CTTTCATGC
131 CTTTCATGC
*
3456148 ATTTAATTTATCGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTATTTATGGCATCCT
1 ATTTAATTTATCGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATATTATTTATGGCATCCT
*
3456213 TTTATGCCTTAATGCATCCTTTCATGCATTTTTATTTATGGCATCCTTTCATGCC
66 TTCATGCCTTAATGCATCCTTTCATGCATTTTTATTTATGGCATCCTTTCATGCC
3456268 AATAATGCAC
Statistics
Matches: 110, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
137 77 0.70
138 8 0.07
139 25 0.23
ACGTcount: A:0.20, C:0.23, G:0.11, T:0.46
Consensus pattern (139 bp):
ATTTAATTTATCGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATATTATTTATGGCATCCT
TTCATGCCTTAATGCATCCTTTCATGCATTTTTATTTATGGCATCCTTTCATGCCTTAATACATC
CTTTCATGC
Found at i:3456288 original size:46 final size:46
Alignment explanation
Indices: 3456011--3456276 Score: 417
Period size: 46 Copynumber: 5.8 Consensus size: 46
3456001 GTTAAATTTT
3456011 ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* ** *
3456057 ATATTATTTATGGTGTCCTTTCATGCCTTAATGTATCC-TTCATGC
1 ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* *
3456102 ATTTTATTTATGGCGTCCTTTCATGCCTTAATACATCCTTTCATGC
1 ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* *
3456148 ATTTAATTTATCGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
*
3456194 ATTTTATTTATGGCATCCTTTTATGCCTTAATGCATCCTTTCATGC
1 ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
*
3456240 ATTTTTATTTATGGCATCCTTTCATGCCAATAATGCA
1 A-TTTTATTTATGGCATCCTTTCATGCC-TTAATGCA
3456277 CCCATATGCA
Statistics
Matches: 200, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
45 41 0.20
46 127 0.63
47 25 0.12
48 7 0.04
ACGTcount: A:0.21, C:0.23, G:0.11, T:0.45
Consensus pattern (46 bp):
ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
Found at i:3456349 original size:79 final size:79
Alignment explanation
Indices: 3456249--3456455 Score: 319
Period size: 79 Copynumber: 2.6 Consensus size: 79
3456239 CATTTTTATT
3456249 TATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATATCGATAATGCACCC
1 TATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATATCGATAATGCACCC
3456314 ATATGCATTT-AAGC
66 ATATGCATTTCAA-C
* * * * *
3456328 TATGACATCTTTTCATGCCAATAATGAACCCATATGCATTATTCTTTTATGTCGATAATGCATCC
1 TATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATATCGATAATGCACCC
*
3456393 ATATGTATTTCAAC
66 ATATGCATTTCAAC
* *
3456407 TATGGCATCCTTTCATGTCAAT-ATGCACCCATATGCAATATTCTTTTAT
1 TATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTAT
3456456 TAATTTGTTC
Statistics
Matches: 116, Mismatches: 11, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
78 25 0.22
79 89 0.77
80 2 0.02
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.38
Consensus pattern (79 bp):
TATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATATCGATAATGCACCC
ATATGCATTTCAAC
Found at i:3458169 original size:36 final size:36
Alignment explanation
Indices: 3458110--3458209 Score: 112
Period size: 36 Copynumber: 2.8 Consensus size: 36
3458100 TGTTTTTCTC
*
3458110 AAAACAAAATTTTGTCTCACTTGAGACAAGTTT-TATA
1 AAAAC-AAATTTTGACTCACTTGAGACAA-TTTCTATA
* * *
3458147 AAAACAAATTTTGACTCGCTTGAGACAATTTCTCTC
1 AAAACAAATTTTGACTCACTTGAGACAATTTCTATA
* * *
3458183 AAAACAAATTTCGTCTTACTTGAGACA
1 AAAACAAATTTTGACTCACTTGAGACA
3458210 TTTTTCCTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
35 3 0.06
36 46 0.85
37 5 0.09
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (36 bp):
AAAACAAATTTTGACTCACTTGAGACAATTTCTATA
Found at i:3458334 original size:37 final size:36
Alignment explanation
Indices: 3458250--3458334 Score: 91
Period size: 36 Copynumber: 2.3 Consensus size: 36
3458240 GTTTCACTTG
* * ** *
3458250 AAACAAAGTTTATCTCACTTGAGATTGTTTTCTTCA
1 AAACAAACTTTGTCTCACTTGAGACAGTCTTCTTCA
3458286 AAACAAACTTTGTCTCACTTGAGACAGTCCTTCTT-A
1 AAACAAACTTTGTCTCACTTGAGACAGT-CTTCTTCA
*
3458322 AGACAAATCTTTG
1 AAACAAA-CTTTG
3458335 AGTCTGTTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
36 31 0.76
37 10 0.24
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (36 bp):
AAACAAACTTTGTCTCACTTGAGACAGTCTTCTTCA
Found at i:3458419 original size:66 final size:65
Alignment explanation
Indices: 3458339--3458551 Score: 209
Period size: 66 Copynumber: 3.3 Consensus size: 65
3458329 TCTTTGAGTC
* * *
3458339 TGTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGAAAAATTCTATTGAAACATCAGCTTTAGGA
1 TGTTTCCCTTGAAACAAAATTTT-TCTCTCTTGAGACAGATTCTATTGAAACATCATCTTTAGGA
3458404 T
65 T
** * * * *
3458405 TGTTTCCCTTGAAACAAGTTTTTTCTCCCTTGAGACAGTTTCTTTTGAAACAACCATCTTT-GAG
1 TGTTTCCCTTGAAACAAAATTTTTCTCTCTTGAGACAGATTCTATTGAAAC-ATCATCTTTAG-G
3458469 AT
64 AT
* ** * * * *
3458471 CGTTTCCCTTGAAA-TGAA-TTTTCTCTCTTGAGACAGCTTCTCTTGAAGCATCATCTTTGAGTA
1 TGTTTCCCTTGAAACAAAATTTTTCTCTCTTGAGACAGATTCTATTGAAACATCATCTTT-AGGA
3458534 -
65 T
*
3458534 TGTTTCACTTGAAACAAA
1 TGTTTCCCTTGAAACAAA
3458552 TCCCTAAAGA
Statistics
Matches: 118, Mismatches: 24, Indels: 12
0.77 0.16 0.08
Matches are distributed among these distances:
63 20 0.17
64 29 0.25
65 25 0.21
66 44 0.37
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (65 bp):
TGTTTCCCTTGAAACAAAATTTTTCTCTCTTGAGACAGATTCTATTGAAACATCATCTTTAGGAT
Found at i:3458861 original size:134 final size:130
Alignment explanation
Indices: 3458572--3458907 Score: 370
Period size: 134 Copynumber: 2.6 Consensus size: 130
3458562 TGACCTACTA
* * * * *
3458572 TCCTCATCACATAGGAACCGTGTCATCCCCTGACTATACCTCCTCATCACGTAGGAGTCGTGTCA
1 TCCTCATCACGTAGGAACCGTGTCATCCCCTGACCAGACCTCCTCATCACATAGGAGCCGTGTCA
* * * * * * **
3458637 -ACCTAGATAACAGTCGTCCTCATAACGTAGGAGCCGTGATATCATCCCTAAAGATGGTATGTCG
66 CCCCTAGATAACAGCCGTCCTCATAACGTAGGAACCGTGATACCATCCCTAAAGATAGCATCCCG
* * * *
3458701 TCCTCATCACGTAGAAACTGTATCATCCACC-GACCAGACCTCCTCATCACTTAGGAGCCGTGTC
1 TCCTCATCACGTAGGAACCGTGTCATCC-CCTGACCAGACCTCCTCATCACATAGGAGCCGTGTC
** * *
3458765 ACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAATCGTGTTATCACCATCCCTAAAGATAGCC
65 ACCCCTAGATAA-CAGCCGTCCTCATAACGTAGGAACCGTG--AT-ACCATCCCTAAAGATAGCA
*
3458830 TCCCT
126 TCCCG
* * * *
3458835 TCTTCATCGCGTAGGAACCGTGTCATCCCCTGACCAGATCTCCTCATCACATAGGAACCGTGTCA
1 TCCTCATCACGTAGGAACCGTGTCATCCCCTGACCAGACCTCCTCATCACATAGGAGCCGTGTCA
*
3458900 CCCTTAGA
66 CCCCTAGA
3458908 CGACTAGAAC
Statistics
Matches: 170, Mismatches: 30, Indels: 9
0.81 0.14 0.04
Matches are distributed among these distances:
129 54 0.32
130 11 0.06
131 23 0.14
133 4 0.02
134 78 0.46
ACGTcount: A:0.25, C:0.33, G:0.18, T:0.24
Consensus pattern (130 bp):
TCCTCATCACGTAGGAACCGTGTCATCCCCTGACCAGACCTCCTCATCACATAGGAGCCGTGTCA
CCCCTAGATAACAGCCGTCCTCATAACGTAGGAACCGTGATACCATCCCTAAAGATAGCATCCCG
Found at i:3459136 original size:25 final size:26
Alignment explanation
Indices: 3459095--3459148 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 26
3459085 GGGTCACAAA
3459095 TATTATTTATTAATAATTATTGTT-AT
1 TATTATTTATTAATAATTATT-TTAAT
*
3459121 TATTA-TTATTATTAATTATTTTAAT
1 TATTATTTATTAATAATTATTTTAAT
3459146 TAT
1 TAT
3459149 ATTGTTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 2 0.08
25 19 0.73
26 5 0.19
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (26 bp):
TATTATTTATTAATAATTATTTTAAT
Found at i:3459144 original size:9 final size:10
Alignment explanation
Indices: 3459096--3459148 Score: 58
Period size: 9 Copynumber: 5.5 Consensus size: 10
3459086 GGTCACAAAT
3459096 ATTATTTATTA
1 ATTA-TTATTA
*
3459107 ATAATTATT-
1 ATTATTATTA
*
3459116 GTTATTATT-
1 ATTATTATTA
3459125 ATTATTATTA
1 ATTATTATTA
3459135 ATTATT-TTA
1 ATTATTATTA
3459144 ATTAT
1 ATTAT
3459149 ATTGTTTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
9 23 0.62
10 11 0.30
11 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (10 bp):
ATTATTATTA
Found at i:3460301 original size:14 final size:14
Alignment explanation
Indices: 3460251--3460312 Score: 70
Period size: 14 Copynumber: 4.2 Consensus size: 14
3460241 CATATTATGT
*
3460251 TTTATTTTATTTTG
1 TTTATTTTATTTTA
* *
3460265 GTCATTTCTATGTTTA
1 TTTATTT-TAT-TTTA
3460281 TTTTATTTTATTTTA
1 -TTTATTTTATTTTA
3460296 TTTATTTTATTTTA
1 TTTATTTTATTTTA
3460310 TTT
1 TTT
3460313 GCATTTATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
14 22 0.55
15 7 0.17
16 6 0.15
17 5 0.12
ACGTcount: A:0.18, C:0.03, G:0.05, T:0.74
Consensus pattern (14 bp):
TTTATTTTATTTTA
Found at i:3460301 original size:19 final size:20
Alignment explanation
Indices: 3460277--3460329 Score: 81
Period size: 19 Copynumber: 2.7 Consensus size: 20
3460267 CATTTCTATG
*
3460277 TTTATTTTATTTTATTT-TA
1 TTTATTTTATTTTATTTGCA
3460296 TTTATTTTATTTTATTTGCA
1 TTTATTTTATTTTATTTGCA
*
3460316 TTTATTTTAATTTA
1 TTTATTTTATTTTA
3460330 GCCACCATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.74
Consensus pattern (20 bp):
TTTATTTTATTTTATTTGCA
Found at i:3460324 original size:5 final size:5
Alignment explanation
Indices: 3460250--3460312 Score: 67
Period size: 5 Copynumber: 12.6 Consensus size: 5
3460240 CCATATTATG
** *
3460250 TTTTA TTTTA TTTT- GGTCA TTTCTA TGTTTA TTTTA TTTTA TTTTA -TTTA
1 TTTTA TTTTA TTTTA TTTTA TTT-TA T-TTTA TTTTA TTTTA TTTTA TTTTA
3460300 TTTTA TTTTA TTT
1 TTTTA TTTTA TTT
3460313 GCATTTATTT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
4 5 0.10
5 36 0.75
6 5 0.10
7 2 0.04
ACGTcount: A:0.17, C:0.03, G:0.05, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:3460328 original size:10 final size:10
Alignment explanation
Indices: 3460277--3460329 Score: 63
Period size: 10 Copynumber: 5.4 Consensus size: 10
3460267 CATTTCTATG
*
3460277 TTTATTTTAT
1 TTTATTTTAA
3460287 TTTATTTT-A
1 TTTATTTTAA
*
3460296 TTTATTTTAT
1 TTTATTTTAA
**
3460306 TTTATTTGCA
1 TTTATTTTAA
3460316 TTTATTTTAA
1 TTTATTTTAA
3460326 TTTA
1 TTTA
3460330 GCCACCATTT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
9 8 0.23
10 27 0.77
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.74
Consensus pattern (10 bp):
TTTATTTTAA
Found at i:3462233 original size:20 final size:20
Alignment explanation
Indices: 3462208--3462248 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
3462198 TGCATTTCAA
3462208 ACATTCCACACACAAAATGG
1 ACATTCCACACACAAAATGG
3462228 ACATTCCACACACAAAATGG
1 ACATTCCACACACAAAATGG
3462248 A
1 A
3462249 AGCATGCAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.46, C:0.29, G:0.10, T:0.15
Consensus pattern (20 bp):
ACATTCCACACACAAAATGG
Found at i:3463755 original size:6 final size:6
Alignment explanation
Indices: 3463748--3463794 Score: 58
Period size: 6 Copynumber: 7.8 Consensus size: 6
3463738 TTATTTATTT
* * * *
3463748 ATTATT ATTATA ATTATA ATTATA ATAATA ATAATA ATAATA ATTAT
1 ATTATA ATTATA ATTATA ATTATA ATTATA ATTATA ATTATA ATTAT
3463795 TAATATATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
ATTATA
Found at i:3463775 original size:3 final size:3
Alignment explanation
Indices: 3463757--3463825 Score: 66
Period size: 3 Copynumber: 21.3 Consensus size: 3
3463747 TATTATTATT
* * *
3463757 ATA ATT ATA ATT ATA ATA ATA ATA ATA ATA ATA ATTA TTA ATA TATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA -ATA
3463804 TATA TATAA ATA ATA ATA ATA A
1 -ATA -AT-A ATA ATA ATA ATA A
3463826 AAATTACAAG
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
3 42 0.74
4 14 0.25
5 1 0.02
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
ATA
Found at i:3465129 original size:21 final size:18
Alignment explanation
Indices: 3465076--3465135 Score: 59
Period size: 21 Copynumber: 3.1 Consensus size: 18
3465066 TATATTGTTC
3465076 TAATTGTATTTTTATT-TT
1 TAATT-TATTTTTATTATT
3465094 TAATTTACTTGTTTATATATT
1 TAATTTA-TT-TTTAT-TATT
3465115 TAAATATTATTTTTATTATT
1 T-AAT-TTATTTTTATTATT
3465135 T
1 T
3465136 TATATAGTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
17 2 0.06
18 7 0.19
19 5 0.14
20 6 0.17
21 8 0.22
22 5 0.14
23 3 0.08
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.67
Consensus pattern (18 bp):
TAATTTATTTTTATTATT
Found at i:3465190 original size:18 final size:17
Alignment explanation
Indices: 3465169--3465216 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 17
3465159 ATAATAAATA
3465169 ATAATTTATTTATTTTAC
1 ATAATTTATTTATTTT-C
* *
3465187 ATAAATTATTT-TTATC
1 ATAATTTATTTATTTTC
3465203 AT-ATTTATTTATTT
1 ATAATTTATTTATTT
3465217 ATTTTTCAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 7 0.28
16 5 0.20
17 3 0.12
18 10 0.40
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (17 bp):
ATAATTTATTTATTTTC
Found at i:3465418 original size:23 final size:26
Alignment explanation
Indices: 3465386--3465435 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 26
3465376 CATTTTCTGA
*
3465386 TATTTCTAAATA-A-ATAAAT-ATTT
1 TATTTATAAATATATATAAATGATTT
3465409 TATTTATAAATATATATAAATGATTT
1 TATTTATAAATATATATAAATGATTT
3465435 T
1 T
3465436 TTTCTGATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 1 0.04
25 6 0.26
26 5 0.22
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (26 bp):
TATTTATAAATATATATAAATGATTT
Found at i:3473121 original size:18 final size:19
Alignment explanation
Indices: 3473093--3473129 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
3473083 AGATGGCAAT
*
3473093 CATTCTTTACATTTTTTTA
1 CATTCTTTACATTTATTTA
3473112 CATT-TTTACATTTATTTA
1 CATTCTTTACATTTATTTA
3473130 TTTCATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.24, C:0.14, G:0.00, T:0.62
Consensus pattern (19 bp):
CATTCTTTACATTTATTTA
Found at i:3476678 original size:7 final size:7
Alignment explanation
Indices: 3476663--3476715 Score: 58
Period size: 7 Copynumber: 8.0 Consensus size: 7
3476653 AAAAAAGAAC
3476663 AAAAAAG
1 AAAAAAG
*
3476670 AACAAAG
1 AAAAAAG
*
3476677 -AAAGA-
1 AAAAAAG
3476682 AAAAAAG
1 AAAAAAG
*
3476689 AACAAA-
1 AAAAAAG
3476695 AAAAAAG
1 AAAAAAG
3476702 AAAAAAG
1 AAAAAAG
3476709 AAAAAAG
1 AAAAAAG
3476716 GGGGTCAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
6 12 0.32
7 25 0.68
ACGTcount: A:0.83, C:0.04, G:0.13, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:3476685 original size:19 final size:20
Alignment explanation
Indices: 3476663--3476715 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
3476653 AAAAAAGAAC
*
3476663 AAAAAAGAACAAAGAAAGA-
1 AAAAAAGAACAAAGAAAAAG
*
3476682 AAAAAAGAACAAAAAAAAAG
1 AAAAAAGAACAAAGAAAAAG
*
3476702 AAAAAAGAAAAAAG
1 AAAAAAGAACAAAG
3476716 GGGGTCAAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.83, C:0.04, G:0.13, T:0.00
Consensus pattern (20 bp):
AAAAAAGAACAAAGAAAAAG
Found at i:3476690 original size:29 final size:28
Alignment explanation
Indices: 3476652--3476714 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 28
3476642 TGCTTGAAGA
*
3476652 AAAAAAAGAACAAAAAAGAACAAAGAAAG
1 AAAAAAAGAACAAAAAAAAACAAA-AAAG
*
3476681 AAAAAAAGAACAAAAAAAAAGAAAAAAG
1 AAAAAAAGAACAAAAAAAAACAAAAAAG
3476709 AAAAAA
1 AAAAAA
3476715 GGGGGTCAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 10 0.31
29 22 0.69
ACGTcount: A:0.84, C:0.05, G:0.11, T:0.00
Consensus pattern (28 bp):
AAAAAAAGAACAAAAAAAAACAAAAAAG
Found at i:3478316 original size:115 final size:115
Alignment explanation
Indices: 3477944--3478291 Score: 608
Period size: 115 Copynumber: 3.0 Consensus size: 115
3477934 TTGGAGCAAG
3477944 TGAATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATTTTCTGGAAGTGTTCTTTGAGTTAT
1 TGAATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATTTTCTGGAAGTGTTCTTTGAGTTAT
3478009 CTGATCTGGTTTGGTATGAACCCCAAAAACCAATTATTGGATTTGAAAGA
66 CTGATCTGGTTTGGTATGAACCCCAAAAACCAATTATTGGATTTGAAAGA
3478059 TGAATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATTTTCTGGAAGTGTTCTTTGAGTTAT
1 TGAATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATTTTCTGGAAGTGTTCTTTGAGTTAT
3478124 CTGATCTGGTTTGGTATGAACCCCAAAAACCAATTATTGGATTTGAAAGA
66 CTGATCTGGTTTGGTATGAACCCCAAAAACCAATTATTGGATTTGAAAGA
* *
3478174 TGAATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGATAT
1 TGAATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATTTTCTGGAAGTGTTCTTTGAGTTAT
* * * * * * *
3478239 CTGATCTGGTTCGGTAGGAACCAC-ATAACCAATCATTGGAATTAAAAGA
66 CTGATCTGGTTTGGTATGAACCCCAAAAACCAATTATTGGATTTGAAAGA
3478288 TGAA
1 TGAA
3478292 CTGCATGATC
Statistics
Matches: 224, Mismatches: 9, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
114 25 0.11
115 199 0.89
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (115 bp):
TGAATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATTTTCTGGAAGTGTTCTTTGAGTTAT
CTGATCTGGTTTGGTATGAACCCCAAAAACCAATTATTGGATTTGAAAGA
Found at i:3479222 original size:73 final size:73
Alignment explanation
Indices: 3479074--3479237 Score: 186
Period size: 73 Copynumber: 2.2 Consensus size: 73
3479064 GAAAAAGAAA
* * ** * ** *
3479074 TTCATAATGAGAAGAATTTGTTCCACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCC
1 TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATCAGATGGAACAGCAGTACC
3479139 AGAAAAAG
66 AGAAAAAG
* * *
3479147 TTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCAG-TGGAACAGCAGTAC
1 TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCA-TCAGATGGAACAGCAGTAC
** *
3479211 CAGTTAGAG
65 CAGAAAAAG
3479220 TTCATAATGAGAAGAACT
1 TTCATAATGAGAAGAACT
3479238 CACCTAAAGA
Statistics
Matches: 76, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
73 74 0.97
74 2 0.03
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (73 bp):
TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATCAGATGGAACAGCAGTACC
AGAAAAAG
Found at i:3479346 original size:113 final size:112
Alignment explanation
Indices: 3479139--3479728 Score: 699
Period size: 113 Copynumber: 5.2 Consensus size: 112
3479129 CAGCTTTTCC
* * * *
3479139 AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCAGTGGAACA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTGA-TGGATCA
* * * *
3479204 GCAGTACCAGTTAGAGTTCATAATGAGAAGAACTCACCTAAAGAAGGA
65 GCATTACCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * *
3479252 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTTCTTGAATTCATCATTCAATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATT-GATGGATCA
* *
3479317 GCATTACCAATTCGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGA
65 GCATTACCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * * * *
3479365 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATTATTTGATGGATTA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCA-TTGATGGATCA
* * * *
3479430 ACATTACCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAACGA
65 GCATTACCAGTTCGAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGA
* * * * *
3479481 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCA-TTGATGGATCA
* **
3479546 GCTTTTTCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
65 GCATTACCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * * *
3479594 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAAATTTTTGCTCAAATCCATCACTTGATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCA-TTGATGGATCA
** *
3479659 G-ATTTTTC--TACAGAAGTTCATAATGAGAAGAACTCATCT---GAA-GA
65 GCA-TTACCAGTTC-G-AGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
3479703 AGAAGAAGTTCATAATGAGAAGAACT
1 AGAAGAAGTTCATAATGAGAAGAACT
3479729 CATCTGAAGA
Statistics
Matches: 423, Mismatches: 46, Indels: 20
0.87 0.09 0.04
Matches are distributed among these distances:
109 27 0.06
110 3 0.01
111 2 0.00
112 1 0.00
113 287 0.68
114 4 0.01
115 1 0.00
116 98 0.23
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.29
Consensus pattern (112 bp):
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTGATGGATCAG
CATTACCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
Found at i:3479582 original size:229 final size:226
Alignment explanation
Indices: 3479139--3479728 Score: 718
Period size: 229 Copynumber: 2.6 Consensus size: 226
3479129 CAGCTTTTCC
* * * * *
3479139 AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCAGTGGAACA
1 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTTAAATTCATCATTGA-TGGATCA
* * * *
3479204 GCAGTACCAGTTAGAGTTCATAATGAGAAGAACTCA-C--CTAAAGAAGGAAGAAGAAGTTCATA
65 ACATTACCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAA-GAAGAAGAA-TTCATA
* * ** *
3479266 ATGAGAAGAACTTGTTCAACTTTTTTCTTGAATTCATCATTCAATGGATCAGCATTACCAATTCG
128 ATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATCAGCATTACCAATTCG
3479331 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGA
193 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGA
* * * *
3479365 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATTATTTGATGGATTA
1 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTTAAATTCATCA-TTGATGGATCA
3479430 ACATTACCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAACGAAGAAGAAATTCATA
65 ACATTACCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAA-GAAGAAG-AATTCATA
* * * ** *
3479495 ATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTT-GATGGATCAGCTTTTTCAGTTC
128 ATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCA-TTCAATGGATCAGCATTACCAATTC
*
3479559 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
192 GAGTTCATAATAAGAAGAACTCATCTGAAGAAGGA
* * *
3479594 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAAATTTTTGCTCAAATCCATCACTTGATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTTAAATTCATCA-TTGATGGATCA
** *
3479659 GATTTTTCTACA-G-A-AGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGAAGAAG--TTCAT
65 -ACATTAC--CAGGTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGAAGAAGAATTCAT
3479716 AATGAGAAGAACT
127 AATGAGAAGAACT
3479729 CATCTGAAGA
Statistics
Matches: 317, Mismatches: 38, Indels: 22
0.84 0.10 0.06
Matches are distributed among these distances:
222 17 0.05
225 7 0.02
226 98 0.31
227 4 0.01
229 179 0.56
230 9 0.03
231 1 0.00
232 2 0.01
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.29
Consensus pattern (226 bp):
AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTTAAATTCATCATTGATGGATCAA
CATTACCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGAAGAAGAATTCATAATG
AGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCAATGGATCAGCATTACCAATTCGAGT
TCATAATAAGAAGAACTCATCTGAAGAAGGA
Done.