Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002637.1 Hibiscus syriacus cultivar Beakdansim tig00005377_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: 3156206
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 14
Found at i:226650 original size:2 final size:2
Alignment explanation
Indices: 226643--226709 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
226633 TCAATCTACA
226643 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
226685 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 A
226710 ATTTACGACA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:226877 original size:85 final size:85
Alignment explanation
Indices: 226729--226918 Score: 256
Period size: 85 Copynumber: 2.2 Consensus size: 85
226719 ATACAATCAC
* * *
226729 GACACACGAATGTGTGTCATCTTCATTTATGACGTGTGCTTCAATGACACGCAATGTAAGTCATA
1 GACACACAAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATGACACGCAATGTAAGTCATA
***
226794 AATGCTTGTCATAAATTTAT
66 AATGCGCATCATAAATTTAT
* * *
226814 GACACACAAATGTGTGTCATCTTCATTTATGATGGGGGCTTCAATGACGCGCAATG-AGCGTCAT
1 GACACACAAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATGACACGCAATGTA-AGTCAT
*
226878 AAATGCGCATCATAGATTTAT
65 AAATGCGCATCATAAATTTAT
* *
226899 GACACACAATTGCGTGTCAT
1 GACACACAAATGTGTGTCAT
226919 ATGAGATTCA
Statistics
Matches: 92, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
84 1 0.01
85 91 0.99
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (85 bp):
GACACACAAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATGACACGCAATGTAAGTCATA
AATGCGCATCATAAATTTAT
Found at i:227162 original size:22 final size:22
Alignment explanation
Indices: 227107--227152 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
227097 GGTCAGCTTG
* * *
227107 GTCGATACGACCGAGCGACTCA
1 GTCGACACGATCGAGCAACTCA
227129 GTCGACACGATCGAGCAACTCA
1 GTCGACACGATCGAGCAACTCA
227151 GT
1 GT
227153 TGTCTCGATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.15
Consensus pattern (22 bp):
GTCGACACGATCGAGCAACTCA
Found at i:227193 original size:13 final size:13
Alignment explanation
Indices: 227177--227232 Score: 66
Period size: 13 Copynumber: 4.6 Consensus size: 13
227167 GAATCGATCC
227177 GCTCGGTCATACG
1 GCTCGGTCATACG
227190 GCTCGG---T-CG
1 GCTCGGTCATACG
227199 GCTCGGTCATACG
1 GCTCGGTCATACG
* *
227212 GCTCGGTTAGACG
1 GCTCGGTCATACG
227225 GCTCGGTC
1 GCTCGGTC
227233 GGCTCGGTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
9 8 0.22
10 1 0.03
12 1 0.03
13 26 0.72
ACGTcount: A:0.11, C:0.30, G:0.36, T:0.23
Consensus pattern (13 bp):
GCTCGGTCATACG
Found at i:227202 original size:22 final size:22
Alignment explanation
Indices: 227177--227218 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
227167 GAATCGATCC
227177 GCTCGGTCATACGGCTCGGTCG
1 GCTCGGTCATACGGCTCGGTCG
227199 GCTCGGTCATACGGCTCGGT
1 GCTCGGTCATACGGCTCGGT
227219 TAGACGGCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.10, C:0.31, G:0.36, T:0.24
Consensus pattern (22 bp):
GCTCGGTCATACGGCTCGGTCG
Found at i:227226 original size:35 final size:35
Alignment explanation
Indices: 227177--227254 Score: 120
Period size: 35 Copynumber: 2.2 Consensus size: 35
227167 GAATCGATCC
* *
227177 GCTCGGTCATACGGCTCGGTCGGCTCGGTCATACG
1 GCTCGGTCAGACGGCTCGGTCGGCTCGGTCAGACG
* *
227212 GCTCGGTTAGACGGCTCGGTCGGCTCGGTTAGACG
1 GCTCGGTCAGACGGCTCGGTCGGCTCGGTCAGACG
227247 GCTCGGTC
1 GCTCGGTC
227255 GGCTTAGTCA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.10, C:0.29, G:0.37, T:0.23
Consensus pattern (35 bp):
GCTCGGTCAGACGGCTCGGTCGGCTCGGTCAGACG
Found at i:227235 original size:22 final size:22
Alignment explanation
Indices: 227210--227276 Score: 98
Period size: 22 Copynumber: 3.0 Consensus size: 22
227200 CTCGGTCATA
227210 CGGCTCGGTTAGACGGCTCGGT
1 CGGCTCGGTTAGACGGCTCGGT
227232 CGGCTCGGTTAGACGGCTCGGT
1 CGGCTCGGTTAGACGGCTCGGT
** * *
227254 CGGCTTAGTCAGACGACTCGGT
1 CGGCTCGGTTAGACGGCTCGGT
227276 C
1 C
227277 CAATCGGTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.12, C:0.28, G:0.37, T:0.22
Consensus pattern (22 bp):
CGGCTCGGTTAGACGGCTCGGT
Found at i:227248 original size:13 final size:13
Alignment explanation
Indices: 227197--227253 Score: 68
Period size: 13 Copynumber: 4.7 Consensus size: 13
227187 ACGGCTCGGT
* *
227197 CGGCTCGGTCATA
1 CGGCTCGGTTAGA
227210 CGGCTCGGTTAGA
1 CGGCTCGGTTAGA
227223 CGGCTCGG-T---
1 CGGCTCGGTTAGA
227232 CGGCTCGGTTAGA
1 CGGCTCGGTTAGA
227245 CGGCTCGGT
1 CGGCTCGGT
227254 CGGCTTAGTC
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
9 8 0.21
10 1 0.03
12 1 0.03
13 28 0.74
ACGTcount: A:0.11, C:0.28, G:0.39, T:0.23
Consensus pattern (13 bp):
CGGCTCGGTTAGA
Found at i:243826 original size:2 final size:2
Alignment explanation
Indices: 243821--243850 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
243811 GAAAAAATTA
243821 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
243851 TGGCAAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:244972 original size:31 final size:28
Alignment explanation
Indices: 244911--244983 Score: 92
Period size: 28 Copynumber: 2.5 Consensus size: 28
244901 CAAAATTGAT
*
244911 CATTTTGGCCCCCAATCTTTTTTTAGAA
1 CATTTTGGCCCCCAATCTTTTTTTAAAA
*
244939 CATTTTGGCCCCTAATCTTTTTTTTAAAAAA
1 CATTTTGGCCCCCAATC-TTTTTTT--AAAA
*
244970 CATTTTGGCTCCCA
1 CATTTTGGCCCCCA
244984 GCATTTCAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 16 0.42
29 7 0.18
31 15 0.39
ACGTcount: A:0.23, C:0.25, G:0.10, T:0.42
Consensus pattern (28 bp):
CATTTTGGCCCCCAATCTTTTTTTAAAA
Found at i:252034 original size:2 final size:2
Alignment explanation
Indices: 252002--252060 Score: 61
Period size: 2 Copynumber: 30.0 Consensus size: 2
251992 CAAGGGTTTC
* *
252002 TA TA TT TA TA T- TA TA TA GTA TT TA TA T- TA TA TA TA GTA TA -A
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA
252043 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
252061 CACACAGATA
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
1 3 0.06
2 41 0.85
3 4 0.08
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:252098 original size:22 final size:22
Alignment explanation
Indices: 252073--252148 Score: 98
Period size: 24 Copynumber: 3.2 Consensus size: 22
252063 CACAGATAAA
252073 ATATAGTCTTTGAAAATATATAAT
1 ATATAGT-TTTGAAAATATAT-AT
252097 ATATAGTTTTGAAACATATATAT
1 ATATAGTTTTGAAA-ATATATAT
*
252120 ATAATAGTTTTTGAATATATATAT
1 AT-ATAG-TTTTGAAAATATATAT
252144 ATATA
1 ATATA
252149 TATATATATA
Statistics
Matches: 48, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
23 14 0.29
24 27 0.56
25 7 0.15
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.45
Consensus pattern (22 bp):
ATATAGTTTTGAAAATATATAT
Found at i:252139 original size:2 final size:2
Alignment explanation
Indices: 252134--252163 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
252124 TAGTTTTTGA
252134 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
252164 TTGGAAGGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:253697 original size:14 final size:15
Alignment explanation
Indices: 253678--253709 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
253668 TTGGAACGAA
253678 TTTTA-TTTTTATTT
1 TTTTATTTTTTATTT
253692 TTTTATTTTTTATTT
1 TTTTATTTTTTATTT
253707 TTT
1 TTT
253710 ACGATTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (15 bp):
TTTTATTTTTTATTT
Found at i:253700 original size:7 final size:7
Alignment explanation
Indices: 253678--253710 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
253668 TTGGAACGAA
253678 TTTTA-T
1 TTTTATT
253684 TTTTATTT
1 TTTTA-TT
253692 TTTTATT
1 TTTTATT
253699 TTTTATT
1 TTTTATT
253706 TTTTA
1 TTTTA
253711 CGATTAAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 5 0.20
7 14 0.56
8 6 0.24
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTATT
Found at i:270184 original size:20 final size:21
Alignment explanation
Indices: 270146--270184 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
270136 CATCAAGGTC
*
270146 TTTGTTGAGGCCATGAAATCT
1 TTTGTCGAGGCCATGAAATCT
270167 TTTGTCGAGGCCAT-AAAT
1 TTTGTCGAGGCCATGAAAT
270185 TCCTGCTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (21 bp):
TTTGTCGAGGCCATGAAATCT
Found at i:280164 original size:46 final size:46
Alignment explanation
Indices: 280091--280347 Score: 415
Period size: 46 Copynumber: 5.6 Consensus size: 46
280081 TAAAACGAAT
280091 TCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
1 TCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
**
280137 TCATAACTAAAATGCATGAAAATATGCATTAAGGCATGAAAGGATG
1 TCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * *
280183 CCATAACTAAAATGCATGAAAGGGTGCATTAAGGCATGAAAGGGTG
1 TCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
** *
280229 TCATAACTAAAATGCATGAAAGGAAACATTAAGGCATGAAAGAATG
1 TCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * *
280275 CCATAAATAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATA
1 TCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
280321 TCATAACTAAAATGCATGAAAGGATGC
1 TCATAACTAAAATGCATGAAAGGATGC
280348 CATAACTAAA
Statistics
Matches: 190, Mismatches: 21, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 190 1.00
ACGTcount: A:0.45, C:0.12, G:0.22, T:0.21
Consensus pattern (46 bp):
TCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
Found at i:280338 original size:118 final size:118
Alignment explanation
Indices: 280216--280463 Score: 399
Period size: 118 Copynumber: 2.1 Consensus size: 118
280206 GTGCATTAAG
* *
280216 GCATGAAAGGGTGTCATAACTAAAATGCATGAAAGGAAACATTAAGGCATGAAAGAATGCCATAA
1 GCATGAAAGGATGCCATAACTAAAATGCATGAAAGGAAACATTAAGGCATGAAAGAATGCCATAA
*
280281 ATAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT-ATCATAACTAAAAT
66 ATAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCT-ATAACTAAAAT
** * *
280334 GCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATTCCATAA
1 GCATGAAAGGATGCCATAACTAAAATGCATGAAAGGAAACATTAAGGCATGAAAGAATGCCATAA
*
280399 CTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCTATAACTAAAAT
66 ATAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCTATAACTAAAAT
*
280452 GTATGAAAGGAT
1 GCATGAAAGGAT
280464 ACATTAAGGC
Statistics
Matches: 120, Mismatches: 9, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
118 119 0.99
119 1 0.01
ACGTcount: A:0.46, C:0.11, G:0.22, T:0.21
Consensus pattern (118 bp):
GCATGAAAGGATGCCATAACTAAAATGCATGAAAGGAAACATTAAGGCATGAAAGAATGCCATAA
ATAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCTATAACTAAAAT
Found at i:280369 original size:164 final size:164
Alignment explanation
Indices: 280170--280483 Score: 531
Period size: 164 Copynumber: 1.9 Consensus size: 164
280160 ATGCATTAAG
* *
280170 GCATGAAAGGATGCCATAACTAAAATGCATGAAAGGGTGCATTAAGGCATGAAAGGGTGT-CATA
1 GCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT-TCCATA
280234 ACTAAAATGCATGAAAGGAAACATTAAGGCATGAAAGAATGCCATAAATAAAATGCATGAAAGGA
65 ACTAAAATGCATGAAAGGAAACATTAAGGCATGAAAGAATGCCATAAATAAAATGCATGAAAGGA
*
280299 TGCATTAAGGCATGAAAGGATATCATAACTAAAAT
130 TACATTAAGGCATGAAAGGATATCATAACTAAAAT
280334 GCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATTCCATAA
1 GCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATTCCATAA
** * * * *
280399 CTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCTATAACTAAAATGTATGAAAGGAT
66 CTAAAATGCATGAAAGGAAACATTAAGGCATGAAAGAATGCCATAAATAAAATGCATGAAAGGAT
280464 ACATTAAGGCATGAAAGGAT
131 ACATTAAGGCATGAAAGGAT
280484 GCCATAAATG
Statistics
Matches: 140, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
163 1 0.01
164 139 0.99
ACGTcount: A:0.45, C:0.11, G:0.23, T:0.21
Consensus pattern (164 bp):
GCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATTCCATAA
CTAAAATGCATGAAAGGAAACATTAAGGCATGAAAGAATGCCATAAATAAAATGCATGAAAGGAT
ACATTAAGGCATGAAAGGATATCATAACTAAAAT
Found at i:280384 original size:92 final size:90
Alignment explanation
Indices: 280104--280391 Score: 343
Period size: 92 Copynumber: 3.1 Consensus size: 90
280094 TAACTAAAAT
**
280104 GCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAACTAAAATGCATGAAAATATG-CATTA
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAACTAAAATGCATGAAAGGATGCCATTA
*
280168 AGGCATGAAAGGATGCCATAACTAAAAT
66 AGGCATGAAAGGATGCCAT-A-T-AAAG
* * **
280196 GCATGAAAGGGTGCATTAAGGCATGAAAGGGTGTCATAACTAAAATGCATGAAAGGA-AACATTA
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAACTAAAATGCATGAAAGGATGCCATTA
* *
280260 AGGCATGAAAGAATGCCATAAATAAAAT
66 AGGCATGAAAGGATGCCAT--AT-AAAG
*
280288 GCATGAAAGGATGCATTAAGGCATGAAAGGATATCATAACTAAAATGCATGAAAGGATGCCATAA
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAACTAAAATGCATGAAAGGATGCCAT--
*
280353 CTAAAATGCATGAAAGGATG-CAT-T-AAG
64 -T--AAGGCATGAAAGGATGCCATATAAAG
280380 GCATGAAAGGAT
1 GCATGAAAGGAT
280392 TCCATAACTA
Statistics
Matches: 174, Mismatches: 14, Indels: 16
0.85 0.07 0.08
Matches are distributed among these distances:
92 150 0.86
93 5 0.03
94 1 0.01
96 1 0.01
97 3 0.02
98 14 0.08
ACGTcount: A:0.45, C:0.11, G:0.23, T:0.20
Consensus pattern (90 bp):
GCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAACTAAAATGCATGAAAGGATGCCATTA
AGGCATGAAAGGATGCCATATAAAG
Found at i:280384 original size:138 final size:135
Alignment explanation
Indices: 280104--280390 Score: 355
Period size: 138 Copynumber: 2.1 Consensus size: 135
280094 TAACTAAAAT
** * * * *
280104 GCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAACTAAAATGCATGAAAATATGCATTAA
1 GCATGAAAGGAAACATTAAGGCATGAAAGAATGCCATAAATAAAATGCATGAAAAGATGCATTAA
* * *
280169 GGCATGAAAGGATGCCATAACTAAAATGCATGAAAGGGTGCATTAAGGCATGAAAGGGTGTCATA
66 GGCATGAAAGGATACCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGTCAT-
*
280234 ACTAAAAT
130 A-T-AAAG
*
280242 GCATGAAAGGAAACATTAAGGCATGAAAGAATGCCATAAATAAAATGCATGAAAGGATGCATTAA
1 GCATGAAAGGAAACATTAAGGCATGAAAGAATGCCATAAATAAAATGCATGAAAAGATGCATTAA
* *
280307 GGCATGAAAGGATATCATAACTAAAATGCATGAAAGGATGCCATAACTAAAATGCATGAAAGGAT
66 GGCATGAAAGGATACCATAACTAAAATGCATGAAAGGATG-CAT---T--AAGGCATGAAAGGAT
280372 G-CAT-T-AAG
125 GTCATATAAAG
280380 GCATGAAAGGA
1 GCATGAAAGGA
280391 TTCCATAACT
Statistics
Matches: 130, Mismatches: 13, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
138 108 0.83
139 3 0.02
140 1 0.01
142 1 0.01
143 3 0.02
144 14 0.11
ACGTcount: A:0.45, C:0.11, G:0.23, T:0.20
Consensus pattern (135 bp):
GCATGAAAGGAAACATTAAGGCATGAAAGAATGCCATAAATAAAATGCATGAAAAGATGCATTAA
GGCATGAAAGGATACCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATA
TAAAG
Found at i:280504 original size:46 final size:46
Alignment explanation
Indices: 280334--280490 Score: 278
Period size: 46 Copynumber: 3.4 Consensus size: 46
280324 TAACTAAAAT
280334 GCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAG
*
280380 GCATGAAAGGATTCCATAACTAAAATGCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAG
* * *
280426 GCATGAAAGGATGCTATAACTAAAATGTATGAAAGGATACATTAAG
1 GCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAG
280472 GCATGAAAGGATGCCATAA
1 GCATGAAAGGATGCCATAA
280491 ATGAAATTAA
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 105 1.00
ACGTcount: A:0.44, C:0.12, G:0.23, T:0.21
Consensus pattern (46 bp):
GCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAG
Found at i:282121 original size:20 final size:21
Alignment explanation
Indices: 282088--282128 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
282078 TTTGTAATTT
282088 TTTTCCTTTTTTTTTG-TGAA
1 TTTTCCTTTTTTTTTGATGAA
282108 TTTT-CTTTTCTTTTTGATGAA
1 TTTTCCTTTT-TTTTTGATGAA
282129 AATCAGCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.26
20 10 0.53
21 4 0.21
ACGTcount: A:0.12, C:0.10, G:0.10, T:0.68
Consensus pattern (21 bp):
TTTTCCTTTTTTTTTGATGAA
Found at i:282121 original size:23 final size:22
Alignment explanation
Indices: 282078--282122 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 22
282068 TTGTTTATGA
282078 TTTGTAATTTTTTTCCTTTTTT
1 TTTGTAATTTTTTTCCTTTTTT
*
282100 TTTGTGAATTTTCTTTTCTTTTT
1 TTTGT-AATTTT-TTTCCTTTTT
282123 GATGAAAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 5 0.25
23 6 0.30
24 9 0.45
ACGTcount: A:0.09, C:0.09, G:0.07, T:0.76
Consensus pattern (22 bp):
TTTGTAATTTTTTTCCTTTTTT
Found at i:284785 original size:22 final size:22
Alignment explanation
Indices: 284756--284807 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
284746 CCCCTTTTCT
284756 CTTTTTTTA-ATATAAAACTCC
1 CTTTTTTTAGATATAAAACTCC
*
284777 CATTTTTTTAGATTTAAAACTCC
1 C-TTTTTTTAGATATAAAACTCC
284800 CTTTTTTT
1 CTTTTTTT
284808 CTCTCTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 1 0.04
22 15 0.54
23 12 0.43
ACGTcount: A:0.27, C:0.17, G:0.02, T:0.54
Consensus pattern (22 bp):
CTTTTTTTAGATATAAAACTCC
Found at i:285083 original size:13 final size:13
Alignment explanation
Indices: 285065--285090 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
285055 AGTGACGCGG
285065 GAGTGATCGACGA
1 GAGTGATCGACGA
285078 GAGTGATCGACGA
1 GAGTGATCGACGA
285091 TGGGGACTCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.38, T:0.15
Consensus pattern (13 bp):
GAGTGATCGACGA
Found at i:285234 original size:15 final size:14
Alignment explanation
Indices: 285206--285245 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
285196 TTGGGAATGC
285206 AAAAATAA-AATAA
1 AAAAATAATAATAA
285219 AATAAATAATAATAA
1 AA-AAATAATAATAA
285234 AAATAATAATAA
1 AAA-AATAATAA
285246 ATTCAGACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 2 0.08
14 7 0.29
15 15 0.62
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
AAAAATAATAATAA
Found at i:285237 original size:12 final size:12
Alignment explanation
Indices: 285222--285246 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
285212 AAAATAAAAT
285222 AAATAATAATAA
1 AAATAATAATAA
285234 AAATAATAATAA
1 AAATAATAATAA
285246 A
1 A
285247 TTCAGACAAA
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAATAATAATAA
Found at i:285963 original size:22 final size:21
Alignment explanation
Indices: 285934--285975 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
285924 TTTTATTTTC
285934 TAAAAAATAGA-AAAAATAAAA
1 TAAAAAATA-ATAAAAATAAAA
285955 TAAATAAATAATAAAAATAAA
1 TAAA-AAATAATAAAAATAAA
285976 TGTATAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (21 bp):
TAAAAAATAATAAAAATAAAA
Found at i:292991 original size:29 final size:30
Alignment explanation
Indices: 292959--293020 Score: 108
Period size: 29 Copynumber: 2.1 Consensus size: 30
292949 GTTTAATCGA
*
292959 TTTCTAATTTGTATTTTGTATTTATTT-AG
1 TTTCTAATTTGTATGTTGTATTTATTTCAG
292988 TTTCTAATTTGTATGTTGTATTTATTTCAG
1 TTTCTAATTTGTATGTTGTATTTATTTCAG
293018 TTT
1 TTT
293021 ATTGGAGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 26 0.84
30 5 0.16
ACGTcount: A:0.19, C:0.05, G:0.11, T:0.65
Consensus pattern (30 bp):
TTTCTAATTTGTATGTTGTATTTATTTCAG
Found at i:294262 original size:20 final size:20
Alignment explanation
Indices: 294237--294274 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
294227 CTATATGAGT
294237 TTGTTTTATTTATCTTTTGA
1 TTGTTTTATTTATCTTTTGA
*
294257 TTGTTTTATTTATGTTTT
1 TTGTTTTATTTATCTTTT
294275 AAATGTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.03, G:0.11, T:0.74
Consensus pattern (20 bp):
TTGTTTTATTTATCTTTTGA
Found at i:295599 original size:25 final size:25
Alignment explanation
Indices: 295564--295633 Score: 86
Period size: 25 Copynumber: 2.8 Consensus size: 25
295554 AATCCCCGCA
* *
295564 GTTTTTCAAGCGGGGACGGGTATGG
1 GTTTTTTAAGCGGGGACGGGTATAG
*
295589 GTTTTTTAAGCGGGGATGGGTATAG
1 GTTTTTTAAGCGGGGACGGGTATAG
* * *
295614 ATTTTTTAAACAGGGACGGG
1 GTTTTTTAAGCGGGGACGGG
295634 GACGGGGGGA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.21, C:0.09, G:0.39, T:0.31
Consensus pattern (25 bp):
GTTTTTTAAGCGGGGACGGGTATAG
Found at i:296235 original size:2 final size:2
Alignment explanation
Indices: 296219--296262 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
296209 TTTTAAAAAC
*
296219 AT AT -T AT AC 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
296260 AT A
1 AT A
296263 GTCATATCAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:296806 original size:8 final size:7
Alignment explanation
Indices: 296754--296791 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
296744 TATTTAGTAA
296754 TTTAATT
1 TTTAATT
296761 TTT-ATT
1 TTTAATT
296767 TTTAATAT
1 TTTAAT-T
*
296775 TTTAATA
1 TTTAATT
296782 TTTAATT
1 TTTAATT
296789 TTT
1 TTT
296792 TTGTTTTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
6 6 0.22
7 14 0.52
8 7 0.26
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTAATT
Found at i:297995 original size:96 final size:95
Alignment explanation
Indices: 297847--298028 Score: 267
Period size: 96 Copynumber: 1.9 Consensus size: 95
297837 AGCAATGTAG
* *
297847 TATCGATACCATGGTAAGGGTATCGATACCAGGAAACATCGAATCTAGTTTTGGTACCGATACTG
1 TATCGATACCATGGTAAGGGTATCGATACCAGGAAACATCGAAGCTAATTTTGGTACCGATACTG
*
297912 AAAGGGGGGTATCGGTACCATAGCATAGTGC
66 AAA-GGGGGTATCGATACCATAGCATAGTGC
* * **
297943 TATCGATACCATGGTGAGGGTATCGATACC-GGACTACATCGAAGCTAATTTTGGTATTGATACT
1 TATCGATACCATGGTAAGGGTATCGATACCAGGA-AACATCGAAGCTAATTTTGGTACCGATACT
*
298007 GGAAGGGGGTATCGATACCATA
65 GAAAGGGGGTATCGATACCATA
298029 ATAGGGTAGT
Statistics
Matches: 77, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
95 20 0.26
96 57 0.74
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.26
Consensus pattern (95 bp):
TATCGATACCATGGTAAGGGTATCGATACCAGGAAACATCGAAGCTAATTTTGGTACCGATACTG
AAAGGGGGTATCGATACCATAGCATAGTGC
Found at i:298057 original size:39 final size:38
Alignment explanation
Indices: 298014--298101 Score: 115
Period size: 39 Copynumber: 2.3 Consensus size: 38
298004 ACTGGAAGGG
298014 GGTATCGATACCATAATAGGGTAGT-ATCACCATAGTAGA
1 GGTATCGATACCATAATAGGGTA-TCAT-ACCATAGTAGA
* * *
298053 GGTATCGATACCATAGTAGGGTATCGATACTATAGTAGG
1 GGTATCGATACCATAATAGGGTATC-ATACCATAGTAGA
298092 GGTATCGATA
1 GGTATCGATA
298102 TTGAAGGGCC
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 41 0.93
40 2 0.05
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (38 bp):
GGTATCGATACCATAATAGGGTATCATACCATAGTAGA
Found at i:298065 original size:20 final size:19
Alignment explanation
Indices: 298013--298101 Score: 110
Period size: 19 Copynumber: 4.6 Consensus size: 19
298003 TACTGGAAGG
*
298013 GGGTATCGATACCATAATA
1 GGGTATCGATACCATAGTA
298032 GGGTA--GTATCACCATAGTA
1 GGGTATCG-AT-ACCATAGTA
298051 GAGGTATCGATACCATAGTA
1 G-GGTATCGATACCATAGTA
*
298071 GGGTATCGATACTATAGTA
1 GGGTATCGATACCATAGTA
298090 GGGGTATCGATA
1 -GGGTATCGATA
298102 TTGAAGGGCC
Statistics
Matches: 62, Mismatches: 2, Indels: 11
0.83 0.03 0.15
Matches are distributed among these distances:
17 1 0.02
18 2 0.03
19 31 0.50
20 25 0.40
21 2 0.03
22 1 0.02
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.27
Consensus pattern (19 bp):
GGGTATCGATACCATAGTA
Found at i:298601 original size:45 final size:45
Alignment explanation
Indices: 298552--298857 Score: 398
Period size: 45 Copynumber: 6.8 Consensus size: 45
298542 GGATGCTATG
* ** * **
298552 GTTGAAATGTATATGGGTACATTATCAATAGAAAAACATATTTTA
1 GTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTAGA
* *
298597 GTTGAAATGTATATGAGTACATTATCAACAGAAAAATATACTAGA
1 GTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTAGA
* * *
298642 GTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATGCTAGA
1 GTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTAGA
* ** * * * *
298687 GTTGAAATGCATATGGGTGTATTCTCAACAGAAGAGCATGCTAGA
1 GTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTAGA
298732 GTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATG-
1 GTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTA-GA
* *
298777 GTTGAAATGTATAGGGGTACATTATCAACAGAAAAGTATACTATA
1 GTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTAGA
* *
298822 GTTGAAATGCATATGGGTGCATTATCAACAGAAAAG
1 GTTGAAATGTATATGGGTACATTATCAACAGAAAAG
298858 ATGTTATAGT
Statistics
Matches: 232, Mismatches: 27, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
45 231 1.00
46 1 0.00
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (45 bp):
GTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTAGA
Found at i:298891 original size:45 final size:45
Alignment explanation
Indices: 298547--298900 Score: 325
Period size: 45 Copynumber: 7.9 Consensus size: 45
298537 TGAAAGGATG
* * * * * **
298547 CTATGGTTGAAATGTATATGGGTACATTATCAATAGAAAAACATA
1 CTATAGTTGAAATGCAAATGGGTGCATTATCAACAGAAAAGTATA
* * * * * * *
298592 TTTTAGTTGAAATGTATATGAGTACATTATCAACAGAAAAATATA
1 CTATAGTTGAAATGCAAATGGGTGCATTATCAACAGAAAAGTATA
* * *
298637 CTAGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATG
1 CTATAGTTGAAATGCAAATGGGTGCATTATCAACAGAAAAGTATA
* * * * * * *
298682 CTAGAGTTGAAATGCATATGGGTGTATTCTCAACAGAAGAGCATG
1 CTATAGTTGAAATGCAAATGGGTGCATTATCAACAGAAAAGTATA
* * * *
298727 CTAGAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATA
1 CTATAGTTGAAATGCAAATGGGTGCATTATCAACAGAAAAGTATA
* * * * *
298772 CTATGGTTGAAATGTATAGGGGTACATTATCAACAGAAAAGTATA
1 CTATAGTTGAAATGCAAATGGGTGCATTATCAACAGAAAAGTATA
* *
298817 CTATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAG-ATG
1 CTATAGTTGAAATGCAAATGGGTGCATTATCAACAGAAAAGTATA
* * * *
298861 TTATAGTTTAAAGTGCACAAT-GGTGTATTATAAACAGAAA
1 CTATAGTTGAAA-TGCA-AATGGGTGCATTATCAACAGAAA
298901 TGGAGGTTAT
Statistics
Matches: 269, Mismatches: 38, Indels: 4
0.86 0.12 0.01
Matches are distributed among these distances:
44 12 0.04
45 255 0.95
46 2 0.01
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.30
Consensus pattern (45 bp):
CTATAGTTGAAATGCAAATGGGTGCATTATCAACAGAAAAGTATA
Found at i:298891 original size:90 final size:89
Alignment explanation
Indices: 298552--298900 Score: 358
Period size: 90 Copynumber: 3.9 Consensus size: 89
298542 GGATGCTATG
* * ** * * * *
298552 GTTGAAATGTATATGGGTACATTATCAATAGAAAAACATATTTTAGTTGAAATGTATATGAGTAC
1 GTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACTATAGTTGAAATGCAAATG-GTAC
*
298617 ATTATCAACAGAAAAATATACTAGA
65 ATTATCAACAGAAAAGTATACTAGA
* * * * **
298642 GTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATGCTAGAGTTGAAATGCATATGGGTGT
1 GTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACTATAGTTGAAATGCAAAT-GGTAC
* * * *
298707 ATTCTCAACAGAAGAGCATGCTAGA
65 ATTATCAACAGAAAAGTATACTAGA
* * * **
298732 GTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATGGTTGAAATGTATAGGGGTAC
1 GTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACTATAGTTGAAATGCA-AATGGTAC
*
298797 ATTATCAACAGAAAAGTATACTATA
65 ATTATCAACAGAAAAGTATACTAGA
* ** * *
298822 GTTGAAATGCATATGGGTGCATTATCAACAGAAAAG-ATGTTATAGTTTAAAGTGCACAATGGTG
1 GTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACTATAGTTGAAA-TGCA-AATGGTA
* *
298886 TATTATAAACAGAAA
64 CATTATCAACAGAAA
298901 TGGAGGTTAT
Statistics
Matches: 210, Mismatches: 46, Indels: 6
0.80 0.18 0.02
Matches are distributed among these distances:
89 11 0.05
90 198 0.94
91 1 0.00
ACGTcount: A:0.40, C:0.09, G:0.21, T:0.30
Consensus pattern (89 bp):
GTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACTATAGTTGAAATGCAAATGGTACA
TTATCAACAGAAAAGTATACTAGA
Found at i:298891 original size:135 final size:133
Alignment explanation
Indices: 298547--298900 Score: 406
Period size: 135 Copynumber: 2.6 Consensus size: 133
298537 TGAAAGGATG
* * * * * * *
298547 CTATGGTTGAAATGTATATGGGTACATTATCAATAGAAAAACATATTTTAGTTGAAATGTATATG
1 CTATAGTTGAAATGCATATGGGTGCATTATCAACAG-AAAAGATGTTATAGTTGAAATGTATATG
** * *
298612 AGTACATTATCAACAGAAAAATATACTAGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAA
65 -GTGTATTATCAACAGAAAAATATACTAGAGTTGAAATGCATAGGGGTACATTATCAACAGAAAA
*
298677 GTATG
129 GTATA
* * * * * *
298682 CTAGAGTTGAAATGCATATGGGTGTATTCTCAACAGAAGAGCATGCTAGAGTTGAAATGTATATG
1 CTATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAG-ATGTTATAGTTGAAATGTATATG
* *
298747 G-GTACATTATCAACAGAAAAGTATACTATG-GTTGAAATGTATAGGGGTACATTATCAACAGAA
65 GTGT--ATTATCAACAGAAAAATATACTA-GAGTTGAAATGCATAGGGGTACATTATCAACAGAA
298810 AAGTATA
127 AAGTATA
* * *
298817 CTATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGATGTTATAGTTTAAAGTGCACAAT
1 CTATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGATGTTATAGTTGAAA-TGTA-TAT
*
298882 GGTGTATTATAAACAGAAA
64 GGTGTATTATCAACAGAAA
298901 TGGAGGTTAT
Statistics
Matches: 182, Mismatches: 30, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
134 16 0.09
135 159 0.87
136 5 0.03
137 2 0.01
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.30
Consensus pattern (133 bp):
CTATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGATGTTATAGTTGAAATGTATATGG
TGTATTATCAACAGAAAAATATACTAGAGTTGAAATGCATAGGGGTACATTATCAACAGAAAAGT
ATA
Found at i:300022 original size:44 final size:44
Alignment explanation
Indices: 299974--300374 Score: 462
Period size: 44 Copynumber: 9.0 Consensus size: 44
299964 CCATAAGTGG
* * *
299974 CACCTTTCTGCCAATAATGTACCTTTATACATTTTCATTTATGA
1 CACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGA
* *
300018 CACCTTTATGCCAATAATGCACTGTTATGCATTTTCATTTATGA
1 CACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGA
* * *
300062 CACATTTCTGCCAAAAATACACCGTTATGCATTTTCATTTATGA
1 CACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGA
* * * *
300106 CACTTTTCTGCCAATAATACACCTTTATGCATTTTCATTTATGG
1 CACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGA
* * * *
300150 CATCTTTCTACCAGTAATGCACCATTATGCATTTTCATTTATGGAA
1 CACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTAT-G-A
* * * *
300196 CATTTCTTTTTCTACCAATAATGCACCGTTATACATTTTCATTTATGG
1 CA---C-CTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGA
* * * *
300244 CACCTTTTTTCCAATAATGCACCGTTATGCATTTTGATTTATGG
1 CACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGA
* * * *
300288 CACCTTTCTGCTAAAAATGCACTGTTATGCATTTTCATTTATGG
1 CACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGA
*
300332 CACCTTT-TAGCCAATAATGCACCGTTATACATTTTTCATTTAT
1 CACCTTTCT-GCCAATAATGCACCGTTATGCA-TTTTCATTTAT
300375 TTTGGTAACA
Statistics
Matches: 307, Mismatches: 42, Indels: 15
0.84 0.12 0.04
Matches are distributed among these distances:
43 1 0.00
44 253 0.82
45 13 0.04
46 2 0.01
48 2 0.01
49 1 0.00
50 35 0.11
ACGTcount: A:0.27, C:0.22, G:0.10, T:0.42
Consensus pattern (44 bp):
CACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGA
Found at i:300247 original size:25 final size:24
Alignment explanation
Indices: 300218--300291 Score: 59
Period size: 20 Copynumber: 3.2 Consensus size: 24
300208 TACCAATAAT
300218 GCACCGTTATACATTTTCATTTATG
1 GCACCGTTAT-CATTTTCATTTATG
* * *
300243 GCACC-TT-T--TTTCCAATAAT-
1 GCACCGTTATCATTTTCATTTATG
*
300262 GCACCGTTATGCATTTTGATTTATG
1 GCACCGTTAT-CATTTTCATTTATG
300287 GCACC
1 GCACC
300292 TTTCTGCTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 12
0.65 0.13 0.22
Matches are distributed among these distances:
19 5 0.14
20 10 0.28
21 1 0.03
23 1 0.03
24 9 0.25
25 10 0.28
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.41
Consensus pattern (24 bp):
GCACCGTTATCATTTTCATTTATG
Found at i:300269 original size:182 final size:183
Alignment explanation
Indices: 299971--300374 Score: 497
Period size: 182 Copynumber: 2.3 Consensus size: 183
299961 ATACCATAAG
* * * * *
299971 TGGCACCTTTCT-GCCAATAATGTACCTTTATACA-TTTTCATTTAT-G-ACA---C-CTTTATG
1 TGGCACCTTT-TAGCCAATAATGCACCATTATACATTTTTCATTTATGGAACATTTCTTTTTCTA
* *
300028 CCAATAATGCACTGTTATGCATTTTCATTTATGACACATTTCTGCCAAAAATACACCGTTATGCA
65 CCAATAATGCACCGTTATACATTTTCATTTATGACACATTTCTGCCAAAAATACACCGTTATGCA
* *
300093 TTTTCATTTATGACACTTTTCTGCCAATAATACACCT-TTATGCATTTTCATTTA
130 TTTTCATTTATGACACCTTTCTGCCAAAAATACA-CTGTTATGCATTTTCATTTA
* * *
300147 TGGCATCTTTCTA-CCAGTAATGCACCATTATGCA-TTTTCATTTATGGAACATTTCTTTTTCTA
1 TGGCACCTTT-TAGCCAATAATGCACCATTATACATTTTTCATTTATGGAACATTTCTTTTTCTA
* * * * * *
300210 CCAATAATGCACCGTTATACATTTTCATTTATGGCACCTTTTTTCCAATAATGCACCGTTATGCA
65 CCAATAATGCACCGTTATACATTTTCATTTATGACACATTTCTGCCAAAAATACACCGTTATGCA
* * * *
300275 TTTTGATTTATGGCACCTTTCTGCTAAAAATGCACTGTTATGCATTTTCATTTA
130 TTTTCATTTATGACACCTTTCTGCCAAAAATACACTGTTATGCATTTTCATTTA
*
300329 TGGCACCTTTTAGCCAATAATGCACCGTTATACATTTTTCATTTAT
1 TGGCACCTTTTAGCCAATAATGCACCATTATACATTTTTCATTTAT
300375 TTTGGTAACA
Statistics
Matches: 192, Mismatches: 26, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
176 39 0.20
177 1 0.01
178 3 0.02
181 5 0.03
182 133 0.69
183 11 0.06
ACGTcount: A:0.26, C:0.22, G:0.10, T:0.42
Consensus pattern (183 bp):
TGGCACCTTTTAGCCAATAATGCACCATTATACATTTTTCATTTATGGAACATTTCTTTTTCTAC
CAATAATGCACCGTTATACATTTTCATTTATGACACATTTCTGCCAAAAATACACCGTTATGCAT
TTTCATTTATGACACCTTTCTGCCAAAAATACACTGTTATGCATTTTCATTTA
Found at i:300509 original size:2 final size:2
Alignment explanation
Indices: 300502--300548 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
300492 AAATGTTGTA
300502 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
300544 AT AT A
1 AT AT A
300549 CAAAACATTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:307301 original size:44 final size:44
Alignment explanation
Indices: 307234--307542 Score: 305
Period size: 44 Copynumber: 7.0 Consensus size: 44
307224 CCATGAGTGG
* * *
307234 CACCTTTCTGCCAATAATGCACCGTCATGTATTTTCATTTATGA
1 CACCTTTCTGCAAATAATGCACCGTTATGCATTTTCATTTATGA
* ** * *
307278 CACATTTCTGTTAATAATGCACCGTTATGTATTTTCATTTATGG
1 CACCTTTCTGCAAATAATGCACCGTTATGCATTTTCATTTATGA
* ** *
307322 CACCTTTCTGCTAAAAAAAACAACGTTATGCATTTTCATTTATGA
1 CACCTTTCTGC-AAATAATGCACCGTTATGCATTTTCATTTATGA
* * * ** * *
307367 CACATTTCTGCCAATAATTCACTATTATACATTTTCATTTATGG
1 CACCTTTCTGCAAATAATGCACCGTTATGCATTTTCATTTATGA
* * ** * *
307411 CACCCTTCTTCCGATAATGCACCGTTATGCAATTTCATTTATGG
1 CACCTTTCTGCAAATAATGCACCGTTATGCATTTTCATTTATGA
* * *
307455 CATCGTTT-TACAAATAATGCATCGTTATGCATTTTTCATTTATGA
1 CA-CCTTTCTGCAAATAATGCACCGTTATGCA-TTTTCATTTATGA
* *
307500 CACCTTTCTGCAAATAATACACCGTTATGTATTTTTCATTTAT
1 CACCTTTCTGCAAATAATGCACCGTTATGCA-TTTTCATTTAT
307543 TTTGGTAACA
Statistics
Matches: 215, Mismatches: 46, Indels: 7
0.80 0.17 0.03
Matches are distributed among these distances:
44 132 0.61
45 83 0.39
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41
Consensus pattern (44 bp):
CACCTTTCTGCAAATAATGCACCGTTATGCATTTTCATTTATGA
Found at i:307383 original size:89 final size:88
Alignment explanation
Indices: 307231--307542 Score: 338
Period size: 89 Copynumber: 3.5 Consensus size: 88
307221 ATACCATGAG
* * * * **
307231 TGGCACCTTTCTGCCAATAATGCACCGTCATGTATTTTCATTTATGACACATTTCTGTTAATAAT
1 TGGCACCTTTCTGCAAATAATACACCGTTATGCATTTTCATTTATGACACATTTCTGCAAATAAT
*
307296 GCACCGTTATGTATTTTCATTTA
66 GCACCGTTATGCATTTTCATTTA
* * * *
307319 TGGCACCTTTCTGCTAAAAAAAACAACGTTATGCATTTTCATTTATGACACATTTCTGCCAATAA
1 TGGCACCTTTCTGC-AAATAATACACCGTTATGCATTTTCATTTATGACACATTTCTGCAAATAA
* ** *
307384 TTCACTATTATACATTTTCATTTA
65 TGCACCGTTATGCATTTTCATTTA
* * ** * * * * *
307408 TGGCACCCTTCTTCCGATAATGCACCGTTATGCAATTTCATTTATGGCATCGTTT-TACAAATAA
1 TGGCACCTTTCTGCAAATAATACACCGTTATGCATTTTCATTTATGACA-CATTTCTGCAAATAA
*
307472 TGCATCGTTATGCATTTTTCATTTA
65 TGCACCGTTATGCA-TTTTCATTTA
* *
307497 TGACACCTTTCTGCAAATAATACACCGTTATGTATTTTTCATTTAT
1 TGGCACCTTTCTGCAAATAATACACCGTTATGCA-TTTTCATTTAT
307543 TTTGGTAACA
Statistics
Matches: 180, Mismatches: 40, Indels: 6
0.80 0.18 0.03
Matches are distributed among these distances:
88 57 0.32
89 113 0.63
90 10 0.06
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.41
Consensus pattern (88 bp):
TGGCACCTTTCTGCAAATAATACACCGTTATGCATTTTCATTTATGACACATTTCTGCAAATAAT
GCACCGTTATGCATTTTCATTTA
Found at i:307534 original size:133 final size:133
Alignment explanation
Indices: 307234--307542 Score: 363
Period size: 133 Copynumber: 2.3 Consensus size: 133
307224 CCATGAGTGG
* * * *
307234 CACCTTTCTGCCAATAATGCACCGTCATGTATTTTCATTTATGACACATTTCTGTTAATAATGCA
1 CACCTTTCTGCCAATAATACACCGTTATGTATTTTCATTTATGACACACTTCTGTCAATAATGCA
* * *
307299 CCGTTATGTATTTTCATTTATGGCACCTTTCTGCTAAAAAAAACAACGTTATGCATTTTCATTTA
66 CCGTTATGCAATTTCATTTATGGCACCTTTCTACTAAAAAAAACAACGTTATGCATTTTCATTTA
307364 TGA
131 TGA
* * ** ** * * *
307367 CACATTTCTGCCAATAATTCACTATTATACATTTTCATTTATGGCACCCTTCT-TCCGATAATGC
1 CACCTTTCTGCCAATAATACACCGTTATGTATTTTCATTTATGACACACTTCTGT-CAATAATGC
* * ** *
307431 ACCGTTATGCAATTTCATTTATGGCATCGTTT-TAC-AAATAATGCATCGTTATGCATTTTTCAT
65 ACCGTTATGCAATTTCATTTATGGCA-CCTTTCTACTAAAAAAAACAACGTTATGCA-TTTTCAT
307494 TTATGA
128 TTATGA
*
307500 CACCTTTCTGCAAATAATACACCGTTATGTATTTTTCATTTAT
1 CACCTTTCTGCCAATAATACACCGTTATGTA-TTTTCATTTAT
307543 TTTGGTAACA
Statistics
Matches: 145, Mismatches: 27, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
132 17 0.12
133 113 0.78
134 15 0.10
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41
Consensus pattern (133 bp):
CACCTTTCTGCCAATAATACACCGTTATGTATTTTCATTTATGACACACTTCTGTCAATAATGCA
CCGTTATGCAATTTCATTTATGGCACCTTTCTACTAAAAAAAACAACGTTATGCATTTTCATTTA
TGA
Found at i:309885 original size:36 final size:36
Alignment explanation
Indices: 309806--309889 Score: 98
Period size: 36 Copynumber: 2.3 Consensus size: 36
309796 ATTAGATAAG
* *
309806 TTTACAAAAGATTTTGACCAAACTAAACTAAGTTCA
1 TTTACAAAATAATTTGACCAAACTAAACTAAGTTCA
* * * *
309842 TTCACAAAATAATTTGCCCAAACTAAACTAGGTT-T
1 TTTACAAAATAATTTGACCAAACTAAACTAAGTTCA
309877 TGTTACAAAATAA
1 T-TTACAAAATAA
309890 ACATGATTAG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
35 1 0.03
36 39 0.98
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.31
Consensus pattern (36 bp):
TTTACAAAATAATTTGACCAAACTAAACTAAGTTCA
Found at i:317822 original size:48 final size:48
Alignment explanation
Indices: 317766--317916 Score: 151
Period size: 48 Copynumber: 3.1 Consensus size: 48
317756 TTTGATCTTA
* *
317766 TATTAGTGCAATTAAGCATTCCTGAATTAGTGCAATCATGCACTCATG
1 TATTAGTGCAATTAAGCATTCCTGTATTAGTGCAATCATGCACTCCTG
* * * ** * *
317814 TATTAGTGCAAATATGCATTCTTGTATTAGTGCCTTCTTGCACCCCTG
1 TATTAGTGCAATTAAGCATTCCTGTATTAGTGCAATCATGCACTCCTG
* * * ** *
317862 AATCAGTGCCATTGGGCACTCCTGTATTAGTGCGAAT-ATGCACTCCTG
1 TATTAGTGCAATTAAGCATTCCTGTATTAGTGC-AATCATGCACTCCTG
317910 TATTAGT
1 TATTAGT
317917 AAAATTGTGC
Statistics
Matches: 79, Mismatches: 23, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
48 78 0.99
49 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (48 bp):
TATTAGTGCAATTAAGCATTCCTGTATTAGTGCAATCATGCACTCCTG
Found at i:317904 original size:24 final size:23
Alignment explanation
Indices: 317766--317916 Score: 115
Period size: 24 Copynumber: 6.3 Consensus size: 23
317756 TTTGATCTTA
* *
317766 TATTAGTGCAATTAAGCATTCCTG
1 TATTAGTGCAA-TATGCACTCCTG
* *
317790 AATTAGTGCAATCATGCACTCATG
1 TATTAGTGCAAT-ATGCACTCCTG
* *
317814 TATTAGTGCAAATATGCATTCTTG
1 TATTAGTGC-AATATGCACTCCTG
** * *
317838 TATTAGTGCCTTCTTGCACCCCTG
1 TATTAGTGCAAT-ATGCACTCCTG
* * *
317862 AATCAGTGCCAT-TGGGCACTCCTG
1 TATTAGTGCAATAT--GCACTCCTG
317886 TATTAGTGCGAATATGCACTCCTG
1 TATTAGTGC-AATATGCACTCCTG
317910 TATTAGT
1 TATTAGT
317917 AAAATTGTGC
Statistics
Matches: 100, Mismatches: 20, Indels: 14
0.75 0.15 0.10
Matches are distributed among these distances:
22 1 0.01
23 2 0.02
24 91 0.91
25 5 0.05
26 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (23 bp):
TATTAGTGCAATATGCACTCCTG
Found at i:317927 original size:24 final size:23
Alignment explanation
Indices: 317874--317964 Score: 74
Period size: 24 Copynumber: 3.8 Consensus size: 23
317864 TCAGTGCCAT
**
317874 TGGGCACTCCTGTATTAGTGCGAA
1 TGGGCACTCCTGTATTAGT-AAAA
**
317898 TATGCACTCCTGTATTAGTAAAA
1 TGGGCACTCCTGTATTAGTAAAA
* **
317921 TTGTGCACTCCCATATTAGTACAAA
1 -TGGGCACTCCTGTATTAGTA-AAA
* *
317946 TGGGTACTCCTCTATTAGT
1 TGGGCACTCCTGTATTAGT
317965 GCATCTGTGT
Statistics
Matches: 54, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
23 2 0.04
24 49 0.91
25 3 0.06
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (23 bp):
TGGGCACTCCTGTATTAGTAAAA
Found at i:320240 original size:81 final size:83
Alignment explanation
Indices: 320137--320346 Score: 232
Period size: 81 Copynumber: 2.6 Consensus size: 83
320127 AATCAAAGTT
* * ** * *
320137 GATCATGGCAGCATGCACTAATTCACAATTTGACTCAATTTTATCTTGAAAACATGC-AGTAATT
1 GATCATGGAAGCATGCAATAATTCACAATTCAACTCAATTTAATCATGAAAACATGCAAG-AATT
320201 CACCATTTGACTCAATT-A
65 CACCATTTGACTCAATTCA
* ** *
320219 GATCAT-GAAGCATGCAATAATTCACAATTCAATTCAATTTAATCATGGTAGCATGCAAGAATTC
1 GATCATGGAAGCATGCAATAATTCACAATTCAACTCAATTTAATCATGAAAACATGCAAGAATTC
*
320283 ACCATTTGATTCAATTCA
66 ACCATTTGACTCAATTCA
* * * * *
320301 -ATCATGGTAGCATG-TATAATTCACAATCCAACTTAATTCAATCATG
1 GATCATGGAAGCATGCAATAATTCACAATTCAACTCAATTTAATCATG
320347 GCAACATTTA
Statistics
Matches: 108, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
81 92 0.85
82 16 0.15
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (83 bp):
GATCATGGAAGCATGCAATAATTCACAATTCAACTCAATTTAATCATGAAAACATGCAAGAATTC
ACCATTTGACTCAATTCA
Found at i:320307 original size:41 final size:41
Alignment explanation
Indices: 320138--320327 Score: 163
Period size: 41 Copynumber: 4.7 Consensus size: 41
320128 ATCAAAGTTG
* ** *
320138 ATCATGGCAGCATGCACTAATTCACAATTTGACTCAATTTT
1 ATCATGGAAGCATGCAAGAATTCACAATTTGACTCAATTTA
* * * *
320179 ATCTTGAAAACATGC-AGTAATTCACCATTTGACTCAA-TTA
1 ATCATGGAAGCATGCAAG-AATTCACAATTTGACTCAATTTA
* ** *
320219 GATCAT-GAAGCATGCAATAATTCACAATTCAATTCAATTTA
1 -ATCATGGAAGCATGCAAGAATTCACAATTTGACTCAATTTA
* * * *
320260 ATCATGGTAGCATGCAAGAATTCACCATTTGATTCAATTCA
1 ATCATGGAAGCATGCAAGAATTCACAATTTGACTCAATTTA
* * *
320301 ATCATGGTAGCATG-TATAATTCACAAT
1 ATCATGGAAGCATGCAAGAATTCACAAT
320328 CCAACTTAAT
Statistics
Matches: 119, Mismatches: 25, Indels: 11
0.77 0.16 0.07
Matches are distributed among these distances:
40 39 0.33
41 80 0.67
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (41 bp):
ATCATGGAAGCATGCAAGAATTCACAATTTGACTCAATTTA
Found at i:320380 original size:41 final size:41
Alignment explanation
Indices: 320229--320552 Score: 242
Period size: 41 Copynumber: 7.9 Consensus size: 41
320219 GATCATGAAG
* * * * *
320229 CATGCAATAATTCACAATTCAATTCAATTTAATCATGGTAG
1 CATGTAATAATTCACAATCCAATTCAATTCAATCATGGCAA
* * * *** * *
320270 CATGCAAGAATTCACCATTTGATTCAATTCAATCATGGTAG
1 CATGTAATAATTCACAATCCAATTCAATTCAATCATGGCAA
320311 CATGT-ATAATTCACAATCCAACTT-AATTCAATCATGGCAA
1 CATGTAATAATTCACAATCCAA-TTCAATTCAATCATGGCAA
* ** * *
320351 CATTTAATAATTCTTAATTCAATTCAATTCAGTCATGGCAA
1 CATGTAATAATTCACAATCCAATTCAATTCAATCATGGCAA
* * * * *
320392 CATGCATTTATTCACAAACCAATTCAATT-AGATCATGGCAG
1 CATGTAATAATTCACAATCCAATTCAATTCA-ATCATGGCAA
** * **
320433 CATGTAATAATTCTTAATTCAATTCAATTCGGTCATGGCAA
1 CATGTAATAATTCACAATCCAATTCAATTCAATCATGGCAA
* * * * * *
320474 CATGCATTTATTCGCAAACCAATTCAATT-AGATCATGGTAA
1 CATGTAATAATTCACAATCCAATTCAATTCA-ATCATGGCAA
* * * *
320515 CATGTATTAATTCATAACCCAATTCAATTTAAATCATG
1 CATGTAATAATTCACAATCCAATTCAA-TTCAATCATG
320553 TAAACAATCA
Statistics
Matches: 222, Mismatches: 53, Indels: 15
0.77 0.18 0.05
Matches are distributed among these distances:
40 32 0.14
41 181 0.82
42 8 0.04
43 1 0.00
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (41 bp):
CATGTAATAATTCACAATCCAATTCAATTCAATCATGGCAA
Found at i:320405 original size:122 final size:123
Alignment explanation
Indices: 320234--320552 Score: 268
Period size: 123 Copynumber: 2.6 Consensus size: 123
320224 TGAAGCATGC
* * * * ****
320234 AATAATTCACAATTCAATTCAATTTAATCATGGTAGCATGCAAGAATTCACCATTTGATTCAATT
1 AATAATTCACAATTCAATTCAATTCAATCATGGCAACATGCAAGAATTCACAAACCAATTCAATT
*
320299 CA-ATCATGGTAGCATGT-ATAATTCACAATCCAACTT-AATTCAATCATGGCAACATTT
66 -AGATCATGGCAGCATGTAATAATTCACAATCCAA-TTCAATTCAATCATGGCAACATTT
** * ***
320356 AATAATTCTTAATTCAATTCAATTCAGTCATGGCAACATGCATTTATTCACAAACCAATTCAATT
1 AATAATTCACAATTCAATTCAATTCAATCATGGCAACATGCAAGAATTCACAAACCAATTCAATT
** * ** **
320421 AGATCATGGCAGCATGTAATAATTCTTAATTCAATTCAATTCGGTCATGGCAACATGC
66 AGATCATGGCAGCATGTAATAATTCACAATCCAATTCAATTCAATCATGGCAACATTT
* * * ** * * ** * *
320479 ATTTATTCGCAAACCAATTCAATT-AGATCATGGTAACATGTATTAATTCATAACCCAATTCAAT
1 AATAATTCACAATTCAATTCAATTCA-ATCATGGCAACATGCAAGAATTCACAAACCAATTCAA-
*
320543 TTAAATCATG
64 TTAGATCATG
320553 TAAACAATCA
Statistics
Matches: 157, Mismatches: 35, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
121 1 0.01
122 68 0.43
123 79 0.50
124 9 0.06
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (123 bp):
AATAATTCACAATTCAATTCAATTCAATCATGGCAACATGCAAGAATTCACAAACCAATTCAATT
AGATCATGGCAGCATGTAATAATTCACAATCCAATTCAATTCAATCATGGCAACATTT
Found at i:320441 original size:82 final size:81
Alignment explanation
Indices: 320229--320543 Score: 319
Period size: 82 Copynumber: 3.9 Consensus size: 81
320219 GATCATGAAG
* ** * * * * ** **
320229 CATGCAATAATTCACAATTCAATTCAATTTAATCATGGTAGCATGCAAGAATTCACCATTTGATT
1 CATGCATTAATTCACAAACCAATTCAA-TTAATCATGGCAACATGTAATAATTCATAATTCAATT
* * *
320294 CAATTCAATCATGGTAG
65 CAATTCAGTCATGGCAA
* * * *
320311 CATGTA-TAATTCACAATCCAACTT-AATTCAATCATGGCAACATTTAATAATTCTTAATTCAAT
1 CATGCATTAATTCACAAACCAA-TTCAATT-AATCATGGCAACATGTAATAATTCATAATTCAAT
320374 TCAATTCAGTCATGGCAA
64 TCAATTCAGTCATGGCAA
* * *
320392 CATGCATTTATTCACAAACCAATTCAATTAGATCATGGCAGCATGTAATAATTCTTAATTCAATT
1 CATGCATTAATTCACAAACCAATTCAATTA-ATCATGGCAACATGTAATAATTCATAATTCAATT
*
320457 CAATTCGGTCATGGCAA
65 CAATTCAGTCATGGCAA
* * * * **
320474 CATGCATTTATTCGCAAACCAATTCAATTAGATCATGGTAACATGTATTAATTCATAACCCAATT
1 CATGCATTAATTCACAAACCAATTCAATTA-ATCATGGCAACATGTAATAATTCATAATTCAATT
320539 CAATT
65 CAATT
320544 TAAATCATGT
Statistics
Matches: 200, Mismatches: 28, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
80 2 0.01
81 63 0.31
82 135 0.68
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (81 bp):
CATGCATTAATTCACAAACCAATTCAATTAATCATGGCAACATGTAATAATTCATAATTCAATTC
AATTCAGTCATGGCAA
Found at i:321601 original size:17 final size:18
Alignment explanation
Indices: 321570--321603 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
321560 TTTAAAGCTT
*
321570 AAATATTCAATAAATTTC
1 AAATATTCAACAAATTTC
321588 AAAT-TTCAACAAATTT
1 AAATATTCAACAAATTT
321604 ATCCTACATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (18 bp):
AAATATTCAACAAATTTC
Found at i:325363 original size:78 final size:79
Alignment explanation
Indices: 325228--325383 Score: 251
Period size: 78 Copynumber: 2.0 Consensus size: 79
325218 TTCGGGCTTT
* * *
325228 ATTTTCAATTTTTCTATTAAGTTTGAGTATACAAATGAATGAGAAGATCATGAGTCTATTAAAGC
1 ATTTTCAATTTTTCTATTAAGTTTAAGCATACAAATGAATGAGAAGATCATAAGTCTATTAAAGC
325293 ATAAACATGTATTA
66 ATAAACATGTATTA
* *
325307 ATTTT-AATTTTTCTATTAAGTTTAAGCATACAAATGAATGAGTAGATCCTAAGTCTATTAAAGC
1 ATTTTCAATTTTTCTATTAAGTTTAAGCATACAAATGAATGAGAAGATCATAAGTCTATTAAAGC
*
325371 ATAAATATGTATT
66 ATAAACATGTATT
325384 GAGTTTAACT
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
78 66 0.93
79 5 0.07
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (79 bp):
ATTTTCAATTTTTCTATTAAGTTTAAGCATACAAATGAATGAGAAGATCATAAGTCTATTAAAGC
ATAAACATGTATTA
Found at i:326479 original size:45 final size:45
Alignment explanation
Indices: 326403--327082 Score: 848
Period size: 45 Copynumber: 15.1 Consensus size: 45
326393 TTATTCGTTA
* * *
326403 ATTTCATTTATGGTATCCTTTCATGCCGATAATGCACCGTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCTGATAATGCACCGTTATGC
* * * *
326448 ATATT-ATTTATGACATCCTTTCATACTGATAATGCACCATTACGC
1 AT-TTCATTTATGGCATCCTTTCATGCTGATAATGCACCGTTATGC
* * * *
326493 ATTTCATTTATGGCATTCTTT-ATTG-TCAGTAATACACTGTTATGC
1 ATTTCATTTATGGCATCCTTTCA-TGCTGA-TAATGCACCGTTATGC
* * * * **
326538 ATTTCATTTATGGAATCATTTCATGCCGACAATGCAATGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCTGATAATGCACCGTTATGC
*
326583 ATTTCATTTATGCCATCCTTTCATG-TCGATAATGCACCGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCT-GATAATGCACCGTTATGC
* * * * *
326628 ATTTCATTTATGACATCATTTCATGCTGGTAATACACTGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCTGATAATGCACCGTTATGC
* * * *
326673 ATTTCATTTATGTCATCCTTTCATGCCGATAATGCGCCGTTATTC
1 ATTTCATTTATGGCATCCTTTCATGCTGATAATGCACCGTTATGC
* *
326718 ATTTCATTTATGGCATCCTTTCATGTTGATAATGCACTGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCTGATAATGCACCGTTATGC
* * *
326763 ATTTCATTTATGACATCATTTCATTC-GATAATGCACCGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCTGATAATGCACCGTTATGC
*
326807 ATTTCATTTATGGCATCATTTCATGCTGATAATGCACCGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCTGATAATGCACCGTTATGC
*
326852 ATTTCATTTATGGCATCATTTCATGCTGATAATGCACCGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCTGATAATGCACCGTTATGC
* ** * *
326897 ATTTCATTTATGGCTTCCTTTTTTGCTGGTAATACACCGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCTGATAATGCACCGTTATGC
*** * * * **
326942 ATTTCATTTACAACATCATTTCATTCCGATAATGCACCGAAATGC
1 ATTTCATTTATGGCATCCTTTCATGCTGATAATGCACCGTTATGC
326987 ATTTCATTTATGGCATCCTTTCATGCTGATAATGCACCGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCTGATAATGCACCGTTATGC
* *
327032 ATTTCATTTATGGCATCCTTTCATGTTGGTAATGCACCGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCTGATAATGCACCGTTATGC
327077 ATTTCA
1 ATTTCA
327083 CTTTTCATCC
Statistics
Matches: 541, Mismatches: 85, Indels: 18
0.84 0.13 0.03
Matches are distributed among these distances:
44 46 0.09
45 490 0.91
46 5 0.01
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.41
Consensus pattern (45 bp):
ATTTCATTTATGGCATCCTTTCATGCTGATAATGCACCGTTATGC
Found at i:327244 original size:81 final size:81
Alignment explanation
Indices: 327062--327245 Score: 244
Period size: 81 Copynumber: 2.3 Consensus size: 81
327052 TCATGTTGGT
* * * *
327062 AATGCACCGTTATGCATTTCACT-TTTCATCCAAAGGCATTTAACCTTTCATCTAACTTGCATTA
1 AATGCACAGTTAGGCATTT-AGTATTTCATCCAAAGGCATTTAACCTTTCATCTAACTTGCATCA
*
327126 TTGGAACCTTTCTGGAA
65 TTGGAACCTTTCTGCAA
**
327143 AATGCACAGTTAGGCATTTAGTATTTCATCTGAAGGCATTTAACCTTTCATCTAACTTGCATCAT
1 AATGCACAGTTAGGCATTTAGTATTTCATCCAAAGGCATTTAACCTTTCATCTAACTTGCATCAT
* * *
327208 TGGCACCTTTCTTCCA
66 TGGAACCTTTCTGCAA
* *
327224 AATGCATAGTTGGGCATTTAGT
1 AATGCACAGTTAGGCATTTAGT
327246 CTTTTATTTT
Statistics
Matches: 90, Mismatches: 12, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
80 2 0.02
81 88 0.98
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.37
Consensus pattern (81 bp):
AATGCACAGTTAGGCATTTAGTATTTCATCCAAAGGCATTTAACCTTTCATCTAACTTGCATCAT
TGGAACCTTTCTGCAA
Found at i:330646 original size:2 final size:2
Alignment explanation
Indices: 330639--330689 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
330629 CCATAAAATC
330639 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
330681 TA TA TA TA T
1 TA TA TA TA T
330690 CTTTCTGACA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:332482 original size:45 final size:45
Alignment explanation
Indices: 332424--332967 Score: 784
Period size: 45 Copynumber: 12.1 Consensus size: 45
332414 TATTCGTTAT
* ** *
332424 TTTCATTTATGACATCCTTTCATATTGATAATGCATCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCTGATAATGCACCGTTATGCA
* * * *
332469 TTTTATTTATGACATCCTTTCATGCTGATAATGCACTGTTATTCA
1 TTTCATTTATGGCATCCTTTCATGCTGATAATGCACCGTTATGCA
*
332514 TTTCATTTATGGCATCCTTTCATGTTGATAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCTGATAATGCACCGTTATGCA
* * * * * *
332559 TTTCATTTTTGACATCCTTTCATTCTGGTAATGCATCGTTATACA
1 TTTCATTTATGGCATCCTTTCATGCTGATAATGCACCGTTATGCA
**
332604 TTTCATTTATGGCATCAGTTCATGCTGATAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCTGATAATGCACCGTTATGCA
* *
332649 TTTCATTTATGGCATACTTTCATGCCG-TAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCTGATAATGCACCGTTATGCA
* * **
332693 TTTCATTTATGGTATCCTTTTATGCCCATAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCTGATAATGCACCGTTATGCA
* *
332738 TTTCATTTATGGCATCCTTTCATTCCGATAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCTGATAATGCACCGTTATGCA
*
332783 TTTCATTTATGGCATCCTTTCATGCTGGTAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCTGATAATGCACCGTTATGCA
* * *
332828 TTTTATTTATGGCATCCTTTCATTCCGATAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCTGATAATGCACCGTTATGCA
*
332873 TTTCATTTATGGCATCCTTTCATGCTGATAATGCACCGTTATGAA
1 TTTCATTTATGGCATCCTTTCATGCTGATAATGCACCGTTATGCA
* * *
332918 TTTTATTTATGGCATCCTTTCATGCCGGTAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCTGATAATGCACCGTTATGCA
332963 TTTCA
1 TTTCA
332968 CTTTTAATCC
Statistics
Matches: 444, Mismatches: 54, Indels: 2
0.89 0.11 0.00
Matches are distributed among these distances:
44 40 0.09
45 404 0.91
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.42
Consensus pattern (45 bp):
TTTCATTTATGGCATCCTTTCATGCTGATAATGCACCGTTATGCA
Found at i:333082 original size:81 final size:81
Alignment explanation
Indices: 332974--333134 Score: 252
Period size: 81 Copynumber: 2.0 Consensus size: 81
332964 TTCACTTTTA
* * *
332974 ATCCAAAGGCATTTAACCTTTCATCTAACTTTCATTTTTGGCACATTTTTGCCAAATGC-TCAAT
1 ATCCAAAGGCATTTAACCTTTCATCTAACTTGCATTATTGGCACATTTCTGCCAAATGCAT-AAT
*
333038 TAGGCATTTAGTCTTTC
65 TAGGCATTTAGCCTTTC
* *
333055 ATCCAAAGGCATTTAACCTTTCATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCATAGTT
1 ATCCAAAGGCATTTAACCTTTCATCTAACTTGCATTATTGGCACATTTCTGCCAAATGCATAATT
333120 AGGCATTTAGCCTTT
66 AGGCATTTAGCCTTT
333135 TATTTTAAAA
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
81 72 0.99
82 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.12, T:0.39
Consensus pattern (81 bp):
ATCCAAAGGCATTTAACCTTTCATCTAACTTGCATTATTGGCACATTTCTGCCAAATGCATAATT
AGGCATTTAGCCTTTC
Found at i:335538 original size:41 final size:41
Alignment explanation
Indices: 335493--335824 Score: 272
Period size: 41 Copynumber: 8.1 Consensus size: 41
335483 AATTTAATCA
*
335493 AATTCGATCATGGCAGCATGCACTAATTCACAATTCAACTC
1 AATTCGATCATGGCAGCATGCAATAATTCACAATTCAACTC
* * * *
335534 AATTCTATCATGGAAACATGCAATAATTCACCATTCAACTC
1 AATTCGATCATGGCAGCATGCAATAATTCACAATTCAACTC
* * * * * *
335575 AATTCCATCATGGAAACATGTAATAATTCACAATTCGATTC
1 AATTCGATCATGGCAGCATGCAATAATTCACAATTCAACTC
* * * * * *
335616 GATTCAATCATGGCAGCATGTAATAATTCACCATTCGATTC
1 AATTCGATCATGGCAGCATGCAATAATTCACAATTCAACTC
* * *
335657 AATTCAATCATGGCAGCGTGCAATAATTCACAA-TCTAACTT
1 AATTCGATCATGGCAGCATGCAATAATTCACAATTC-AACTC
* * * *
335698 AATTCGATCATGGCAGCATGGAATAATCCATAATTCAATTC
1 AATTCGATCATGGCAGCATGCAATAATTCACAATTCAACTC
* * * * * * ** *
335739 AATTTGGTCATGGAAACATGCATTTATTCACAAACCAATTC
1 AATTCGATCATGGCAGCATGCAATAATTCACAATTCAACTC
* * * * * * *
335780 AAATAGATCATGGTTA-CATGTATTAATTCGCAATCCAACTC
1 AATTCGATCATGG-CAGCATGCAATAATTCACAATTCAACTC
335821 AATT
1 AATT
335825 TAAATCAAAG
Statistics
Matches: 238, Mismatches: 50, Indels: 6
0.81 0.17 0.02
Matches are distributed among these distances:
40 2 0.01
41 233 0.98
42 3 0.01
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.30
Consensus pattern (41 bp):
AATTCGATCATGGCAGCATGCAATAATTCACAATTCAACTC
Found at i:335769 original size:123 final size:123
Alignment explanation
Indices: 335493--335742 Score: 304
Period size: 123 Copynumber: 2.0 Consensus size: 123
335483 AATTTAATCA
* * *
335493 AATTCGATCATGGCAGCATGCACTAATTCACAATTCAACTCAATTCTATCATGGAAACATGCAAT
1 AATTCAATCATGGCAGCATGCAATAATTCACAATTCAACTCAATTCAATCATGGAAACATGCAAT
* * * *
335558 AATTCACCATTCAACTCAATTCCATCATGGAAACATGTAATAATTCACAATTCGATTC
66 AATTCACAATTCAACTCAATTCCATCATGGAAACATGGAATAATCCACAATTCAATTC
* * * * * * * *
335616 GATTCAATCATGGCAGCATGTAATAATTCACCATTCGATTCAATTCAATCATGGCAGCGTGCAAT
1 AATTCAATCATGGCAGCATGCAATAATTCACAATTCAACTCAATTCAATCATGGAAACATGCAAT
* * * * *
335681 AATTCACAA-TCTAACTTAATTCGATCATGGCAGCATGGAATAATCCATAATTCAATTC
66 AATTCACAATTC-AACTCAATTCCATCATGGAAACATGGAATAATCCACAATTCAATTC
335739 AATT
1 AATT
335743 TGGTCATGGA
Statistics
Matches: 105, Mismatches: 21, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
122 2 0.02
123 103 0.98
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.30
Consensus pattern (123 bp):
AATTCAATCATGGCAGCATGCAATAATTCACAATTCAACTCAATTCAATCATGGAAACATGCAAT
AATTCACAATTCAACTCAATTCCATCATGGAAACATGGAATAATCCACAATTCAATTC
Found at i:338473 original size:15 final size:15
Alignment explanation
Indices: 338453--338481 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
338443 ATTATATATG
338453 AATAGTATTTTATTA
1 AATAGTATTTTATTA
338468 AATAGTATTTTATT
1 AATAGTATTTTATT
338482 TTTGTGTAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (15 bp):
AATAGTATTTTATTA
Found at i:342368 original size:36 final size:38
Alignment explanation
Indices: 342303--342378 Score: 95
Period size: 36 Copynumber: 2.1 Consensus size: 38
342293 AAAATATATA
* *
342303 TATATATATACATCAAAGTATTAATAAAATA-AATAAGC
1 TATATATATACATAAAAATATTAATAAAATAGAA-AAGC
*
342341 TATATATATACA-AAAAATATTTA-AAAATAGAAAAGC
1 TATATATATACATAAAAATATTAATAAAATAGAAAAGC
342377 TA
1 TA
342379 CCCTCTCACT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 12 0.35
37 10 0.29
38 12 0.35
ACGTcount: A:0.58, C:0.07, G:0.05, T:0.30
Consensus pattern (38 bp):
TATATATATACATAAAAATATTAATAAAATAGAAAAGC
Found at i:342455 original size:41 final size:39
Alignment explanation
Indices: 342394--342470 Score: 118
Period size: 41 Copynumber: 1.9 Consensus size: 39
342384 TCACTTCACC
* *
342394 GAAAGTGGGGGGCTTTAGTTAGAAATAAGACAAAAAGAG
1 GAAAGTGGGGGACTTTAGTTAGAAATAAAACAAAAAGAG
342433 GAAAGTGGGAGAGACTTTAGTTAGAAATAAAACAAAAA
1 GAAAGTGGG-G-GACTTTAGTTAGAAATAAAACAAAAA
342471 AATGGGTCCT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
39 9 0.26
40 1 0.03
41 24 0.71
ACGTcount: A:0.48, C:0.05, G:0.29, T:0.18
Consensus pattern (39 bp):
GAAAGTGGGGGACTTTAGTTAGAAATAAAACAAAAAGAG
Found at i:342665 original size:2 final size:2
Alignment explanation
Indices: 342587--342649 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
342577 AATAATAAAA
342587 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
342629 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
342650 AAGTTATAAG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:343287 original size:35 final size:35
Alignment explanation
Indices: 343248--343319 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
343238 CTAAAAAACC
343248 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
343283 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
343318 CT
1 CT
343320 TCGGTTGGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.40
Consensus pattern (35 bp):
CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
Found at i:343964 original size:106 final size:105
Alignment explanation
Indices: 343777--344314 Score: 686
Period size: 106 Copynumber: 5.1 Consensus size: 105
343767 TTGTATTGTT
* * * * * **
343777 TCGAGTCTAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGGAACTGAAAAATTGTTTGTTGAC
1 TCGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGAC
* * * *
343842 AGCCAACCGTCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTC
66 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTG-TGTC
* * * * * *
343883 TTGAGTCTAATATCCTTCGATGTGAAGTTGAAATTGACCCTGAATTTGGGAAATTGTTTATTGAC
1 TCGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGAC
*
343948 AACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTCGTC
66 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGT-GTC
*
343989 TCGAGTCCAATATCCTTC-ACTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGA
1 TCGAGTCCAATATCCTTCGA-TGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGA
344053 CAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTG-GTC
65 CAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTGTC
* *
344093 TCGATTCCAACATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGAC
1 TCGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGAC
*
344158 AACCAGCCGTCCCTTTGTTGTGAAGTTGAACTTGTGTTGTC
66 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTG-TGTC
* * * * * *
344199 CCGAGTCCAATATTCTTCGTTGTGAAGTTGAAATTGGCTCTGAATGAAACT-GAAAAGTGGTTTG
1 TCGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTC----TGAAATTGGGAAA-TTGTTTG
** *
344263 TTGACAACCAGTTGTCCCTTTGTTGTGAAGTTGAACTTGTGTTGTC
61 TTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTG-TGTC
344309 TCGAGT
1 TCGAGT
344315 GGCGCGCTAT
Statistics
Matches: 383, Mismatches: 39, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
104 98 0.26
105 3 0.01
106 217 0.57
109 4 0.01
110 61 0.16
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (105 bp):
TCGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGAC
AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTGTC
Found at i:344184 original size:210 final size:211
Alignment explanation
Indices: 343777--344314 Score: 729
Period size: 210 Copynumber: 2.5 Consensus size: 211
343767 TTGTATTGTT
* * * *
343777 TCGAGTCTAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGGAACTGAAAAATTGTTTGTTGAC
1 TCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAACTGGAAAATTGTTTGTTGAC
* * * * * * *
343842 AGCCAACCGTCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGAGTCTAATATCCTTCGATGTG
66 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTG-TGTCTCGAGTCCAACATCCTTCGATGTG
* *
343907 AAGTTGAAATTGACCCTGAATTTGGGAAATTGTTTATTGACAACCAGTCGTCCCTTCGTTGTGAA
130 AAGTTGAAATTGACCCTGAAATTGGGAAATTGTTTATTGACAACCAGCCGTCCCTTCGTTGTGAA
343972 GTTGAACTTGTGTCGTC
195 GTTGAACTTGTGTCGTC
** * * *
343989 TCGAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGAC
1 TCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAACTGGAAAATTGTTTGTTGAC
*
344054 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTG-GTCTCGATTCCAACATCCTTCGATGTGA
66 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTGTCTCGAGTCCAACATCCTTCGATGTGA
* * * *
344118 AGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCCGTCCCTTTGTTGTGAAG
131 AGTTGAAATTGACCCTGAAATTGGGAAATTGTTTATTGACAACCAGCCGTCCCTTCGTTGTGAAG
*
344183 TTGAACTTGTGTTGTC
196 TTGAACTTGTGTCGTC
* * *
344199 CCGAGTCCAATATTCTTCGTTGTGAAGTTGAAATTGGCTCTGAATGAAACT-GAAAAGTGGTTTG
1 TCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC----TGAAACTGGAAAA-TTGTTTG
** *
344263 TTGACAACCAGTTGTCCCTTTGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT
61 TTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTG-TGTCTCGAGT
344315 GGCGCGCTAT
Statistics
Matches: 283, Mismatches: 36, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
210 134 0.47
212 88 0.31
213 4 0.01
214 49 0.17
216 8 0.03
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (211 bp):
TCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAACTGGAAAATTGTTTGTTGAC
AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTGTCTCGAGTCCAACATCCTTCGATGTGA
AGTTGAAATTGACCCTGAAATTGGGAAATTGTTTATTGACAACCAGCCGTCCCTTCGTTGTGAAG
TTGAACTTGTGTCGTC
Found at i:345024 original size:37 final size:37
Alignment explanation
Indices: 344942--345054 Score: 104
Period size: 37 Copynumber: 3.1 Consensus size: 37
344932 GTTTCATGAG
* * * * **
344942 AAACGGTCTCAAAAGAGACAAAATTTTGTTTTAAGAA
1 AAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAGAA
344979 AAACTGTCTCAAGAGAGACAAAACTTAGTTCCAA-AA
1 AAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAGAA
* * **
345015 GAAATTGTCTCAAGGGGAGATGAAA-TTAGTTCCAAGAA
1 -AAACTGTCTCAA-GAGAGACAAAACTTAGTTCCAAGAA
345053 AA
1 AA
345055 CCATATTCAA
Statistics
Matches: 63, Mismatches: 10, Indels: 6
0.80 0.13 0.08
Matches are distributed among these distances:
36 2 0.03
37 51 0.81
38 10 0.16
ACGTcount: A:0.45, C:0.13, G:0.19, T:0.23
Consensus pattern (37 bp):
AAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAGAA
Found at i:345229 original size:36 final size:37
Alignment explanation
Indices: 345175--345249 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 37
345165 AACAATTTCA
* *
345175 AAAGTTTTTTTCCAAGGGAAACTGTCTCAAGAGAGAC
1 AAAGTTTGTTTCCAAGGGAAACTATCTCAAGAGAGAC
345212 AAAGTTTGTTT-CAAGGGAAACTATCTCAAGAGAGAC
1 AAAGTTTGTTTCCAAGGGAAACTATCTCAAGAGAGAC
345248 AA
1 AA
345250 TGGTGAGCAC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
36 26 0.72
37 10 0.28
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (37 bp):
AAAGTTTGTTTCCAAGGGAAACTATCTCAAGAGAGAC
Found at i:346855 original size:10 final size:10
Alignment explanation
Indices: 346842--346876 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
346832 TTTGCTTCTT
346842 TTCTTTTTTG
1 TTCTTTTTTG
346852 TTCTTGTTTT-
1 TTCTT-TTTTG
346862 TTCTTTTTTG
1 TTCTTTTTTG
346872 TTCTT
1 TTCTT
346877 GATTGAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 4 0.17
10 15 0.65
11 4 0.17
ACGTcount: A:0.00, C:0.11, G:0.09, T:0.80
Consensus pattern (10 bp):
TTCTTTTTTG
Found at i:346865 original size:20 final size:20
Alignment explanation
Indices: 346840--346877 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
346830 TTTTTGCTTC
346840 TTTTCTTTTTTGTTCTTGTT
1 TTTTCTTTTTTGTTCTTGTT
346860 TTTTCTTTTTTGTTCTTG
1 TTTTCTTTTTTGTTCTTG
346878 ATTGAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.00, C:0.11, G:0.11, T:0.79
Consensus pattern (20 bp):
TTTTCTTTTTTGTTCTTGTT
Found at i:350901 original size:10 final size:10
Alignment explanation
Indices: 350882--350914 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
350872 ACATTTAGTA
350882 AAATAAAAAT
1 AAATAAAAAT
*
350892 AAATAGAAAT
1 AAATAAAAAT
350902 AAA-AAAAAT
1 AAATAAAAAT
350911 AAAT
1 AAAT
350915 GGCAAGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:350903 original size:16 final size:15
Alignment explanation
Indices: 350882--350911 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
350872 ACATTTAGTA
350882 AAATAAAAATAAATAG
1 AAATAAAAA-AAATAG
350898 AAATAAAAAAAATA
1 AAATAAAAAAAATA
350912 AATGGCAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (15 bp):
AAATAAAAAAAATAG
Found at i:350924 original size:19 final size:19
Alignment explanation
Indices: 350886--350932 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
350876 TTAGTAAAAT
*
350886 AAAAATAAATAGAAATAAA
1 AAAAATAAATAGAAAGAAA
* *
350905 AAAAATAAATGGCAAGAAA
1 AAAAATAAATAGAAAGAAA
350924 AAAACATAA
1 AAAA-ATAA
350933 GAGAAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 20 0.83
20 4 0.17
ACGTcount: A:0.74, C:0.04, G:0.09, T:0.13
Consensus pattern (19 bp):
AAAAATAAATAGAAAGAAA
Found at i:350925 original size:20 final size:18
Alignment explanation
Indices: 350881--350943 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 18
350871 AACATTTAGT
*
350881 AAAATAAAAATAAATAGA
1 AAAAAAAAAATAAATAGA
*
350899 AATAAAAAAAATAAATGGCA
1 AA-AAAAAAAATAAATAG-A
* *
350919 AGAAAAAAACAT-AAGAGA
1 A-AAAAAAAAATAAATAGA
350937 AAAAAAA
1 AAAAAAA
350944 CATGGTTAGG
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
17 6 0.16
18 4 0.11
19 16 0.43
20 10 0.27
21 1 0.03
ACGTcount: A:0.76, C:0.03, G:0.10, T:0.11
Consensus pattern (18 bp):
AAAAAAAAAATAAATAGA
Found at i:352013 original size:38 final size:37
Alignment explanation
Indices: 351922--352024 Score: 116
Period size: 40 Copynumber: 2.6 Consensus size: 37
351912 TATATATAGT
** *
351922 AATATTTGAAAAATGAAAAATATATATATATATATATCA
1 AATATTT-AAAAAT-AAAAAGCTATATATATATATAACA
*
351961 AAGTATTAATAAAATAAATAAGCTATATATATATATAACA
1 AA-TATTTA-AAAATAAA-AAGCTATATATATATATAACA
352001 AATATTTAAAAATAGAAAAGCTAT
1 AATATTTAAAAATA-AAAAGCTAT
352025 CCTCTCACTT
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
38 13 0.24
39 13 0.24
40 29 0.53
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.33
Consensus pattern (37 bp):
AATATTTAAAAATAAAAAGCTATATATATATATAACA
Found at i:352527 original size:18 final size:17
Alignment explanation
Indices: 352504--352546 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
352494 ATATATACGT
352504 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
352522 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
352539 ATAA-AATA
1 ATAATAATA
352547 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:352958 original size:35 final size:35
Alignment explanation
Indices: 352919--352990 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
352909 ATAAAAAACC
352919 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
352954 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
352989 CT
1 CT
352991 TCTTTTTTGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.40
Consensus pattern (35 bp):
CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
Found at i:362257 original size:2 final size:2
Alignment explanation
Indices: 362252--362283 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
362242 TGTCCTAAAA
362252 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
362284 CTTGAAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:362428 original size:33 final size:32
Alignment explanation
Indices: 362355--362430 Score: 82
Period size: 33 Copynumber: 2.2 Consensus size: 32
362345 TTACATCATA
*
362355 TATATATATATTACTTAAAAATATATTTTATAG
1 TATATAT-TATTACTTAAAAATATATTGTATAG
*
362388 TGGATATATTA-TATTTAAAAATATATATGTATTAG
1 T--ATATATTATTACTTAAAAATATAT-TGTA-TAG
362423 TATATATT
1 TATATATT
362431 CTATATATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
33 22 0.59
34 5 0.14
35 10 0.27
ACGTcount: A:0.43, C:0.01, G:0.07, T:0.49
Consensus pattern (32 bp):
TATATATTATTACTTAAAAATATATTGTATAG
Found at i:368506 original size:399 final size:399
Alignment explanation
Indices: 367766--368568 Score: 1318
Period size: 399 Copynumber: 2.0 Consensus size: 399
367756 TTTCGCACAC
**
367766 AAATGTGTGAAGAGTCATGGTGGGAAATAAGAAGATAGTAGAATAGACTTGGTGGCATAAGGGTG
1 AAATGTGTGAAGAGTCATGGTGGGAAATAAGAAGATAGTAGAATAGACTTGGTGGCATAAAAGTG
* * *
367831 TCTCGACTGAGGATGCCATGGTGAGTTTGCAAGAAAGCCTTGAAGTAGTGAAAGCACGATAAAAG
66 TCTCGACTGAGGATGCCATGGTGAGTTTGCAAGAAAGCCTTAAAGCAGTAAAAGCACGATAAAAG
367896 GAGCTAAATCTCGTGGAAGAGAAGCATGATCGAGCGAGTGTTGAATGTTTTGGAAAAGAGGAAAG
131 GAGCTAAATCTCGTGGAAGAGAAGCATGATCGAGCGAGTGTTGAATGTTTTGGAAAAGAGGAAAG
* * * *
367961 AGATATCGACATCGTTAGAGAAGAGGGTCACAAGACTTGAGAAATCCGACGAGAAACTAATGAGA
196 AGATATCGACATCGCTAGAGAAGAGGGTCACAAGACTTAAGAAATCCGACGAGAAACCAAGGAGA
* *
368026 CACAGAGAGTTGTGAAGTCTCGTCTTAATAGATTGAAGTCCATAGAATACAAGTTCAATGATGAG
261 CACAGAGAGTTGTGAAGTCCCGTCTTAATAGATTGAAGTCCATAGAATAAAAGTTCAATGATGAG
* *
368091 CTACAACGAATTATCAATGAGTTAGAGATAGTTTAAGAGAGTAATGTCCGTGAAGCTGAGGTGAA
326 CTACAACGAATTATCAATGAGTTAGAGATAGTTTAAGAGAGTAATGTCCATGAAGCCGAGGTGAA
368156 AAGTTTGAG
391 AAGTTTGAG
* *
368165 AAATGTGTGAAGAGTCATGGTGGGAAATAAGAGGATAGTATAATAGACTTGGTGGCATAAAAGTG
1 AAATGTGTGAAGAGTCATGGTGGGAAATAAGAAGATAGTAGAATAGACTTGGTGGCATAAAAGTG
* * * *
368230 TCTCTACTGAGGATGCTATGGTGAGTTTGCAAGAAAGCCTTAAAGCAGTAAAAGCATGTTAAAAG
66 TCTCGACTGAGGATGCCATGGTGAGTTTGCAAGAAAGCCTTAAAGCAGTAAAAGCACGATAAAAG
* * *
368295 GAGCTAAATCTCGTGGGAGAGAAGCATGATCGAGTGAGTGTTGAATGTTTTGGAAAAGAGGTAAG
131 GAGCTAAATCTCGTGGAAGAGAAGCATGATCGAGCGAGTGTTGAATGTTTTGGAAAAGAGGAAAG
* * *
368360 AGATATCGATATCGCTAGAGAAGAGGGTCATAAGACTTAAGAAATCCGAGGAGAAACCAAGGAGA
196 AGATATCGACATCGCTAGAGAAGAGGGTCACAAGACTTAAGAAATCCGACGAGAAACCAAGGAGA
* * * * *
368425 CACAGGGAGTTGTGGAGTCCCGTCTTGATAGATTGAAGTCCATAGAGTAAAATTTCAATGATGAG
261 CACAGAGAGTTGTGAAGTCCCGTCTTAATAGATTGAAGTCCATAGAATAAAAGTTCAATGATGAG
* *
368490 CTACAACGAGTTATCAATGAGTTAGAGGTAGTTTAAGAGAGTAATGTCCATGAAGCCGAGGTGAA
326 CTACAACGAATTATCAATGAGTTAGAGATAGTTTAAGAGAGTAATGTCCATGAAGCCGAGGTGAA
368555 AAGTTTGAG
391 AAGTTTGAG
368564 AAATG
1 AAATG
368569 AGATGAATAA
Statistics
Matches: 372, Mismatches: 32, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
399 372 1.00
ACGTcount: A:0.36, C:0.11, G:0.29, T:0.24
Consensus pattern (399 bp):
AAATGTGTGAAGAGTCATGGTGGGAAATAAGAAGATAGTAGAATAGACTTGGTGGCATAAAAGTG
TCTCGACTGAGGATGCCATGGTGAGTTTGCAAGAAAGCCTTAAAGCAGTAAAAGCACGATAAAAG
GAGCTAAATCTCGTGGAAGAGAAGCATGATCGAGCGAGTGTTGAATGTTTTGGAAAAGAGGAAAG
AGATATCGACATCGCTAGAGAAGAGGGTCACAAGACTTAAGAAATCCGACGAGAAACCAAGGAGA
CACAGAGAGTTGTGAAGTCCCGTCTTAATAGATTGAAGTCCATAGAATAAAAGTTCAATGATGAG
CTACAACGAATTATCAATGAGTTAGAGATAGTTTAAGAGAGTAATGTCCATGAAGCCGAGGTGAA
AAGTTTGAG
Found at i:371798 original size:16 final size:16
Alignment explanation
Indices: 371777--371808 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
371767 CATTATTCCT
371777 CACTGATGTGTGTGTA
1 CACTGATGTGTGTGTA
371793 CACTGATGTGTGTGTA
1 CACTGATGTGTGTGTA
371809 TACACCATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.12, G:0.31, T:0.38
Consensus pattern (16 bp):
CACTGATGTGTGTGTA
Found at i:371834 original size:28 final size:28
Alignment explanation
Indices: 371794--371848 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
371784 GTGTGTGTAC
371794 ACTGATGTGTGTGTATACACCATTCCTT
1 ACTGATGTGTGTGTATACACCATTCCTT
*
371822 ACTGATGTGTGTGTGTACACCATTCCT
1 ACTGATGTGTGTGTATACACCATTCCT
371849 CATTGAACTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.38
Consensus pattern (28 bp):
ACTGATGTGTGTGTATACACCATTCCTT
Found at i:372385 original size:226 final size:224
Alignment explanation
Indices: 371854--372979 Score: 874
Period size: 226 Copynumber: 5.0 Consensus size: 224
371844 TTCCTCATTG
* * * * * * ** *
371854 AACTAGAAAG--TTGCATTAATTTAGGATTGTTGGACGAGTAAAAATAGACGGTTGAGATGAATA
1 AACTAGAAAGTTTTACATTGATTTAAGATCGTTGGATGAGTAAAAATAGATGACTGAGATTAATA
* ** * * * *
371917 ATATAAAATGAGAAGGTATTTACT-GAAAAACAAGGAGATAATCTCAATTGTCCATTTTCATTCA
66 GTAGGAAATGAGAAGATATTAACTGGAAAAACAAGGAGATAATCTCAATCGTCCATTTTCACTCA
* * * * * * *
371981 CCCAACGATCATAAATCAGTGTAAAACTAAAAGTTTTTAACATTGTGTAAATGGATCCTAACTCA
131 TCCAACGATCCTAAATGAGTGTAAAACTAAAAGTTTTTTACATTGTGTAAGTGGATTCTAACCCA
* ** *
372046 TATAG-GGTAGGTTTTA-ATTACATAATGTAA
196 TATAGAGGTAAG-TCCAGA-TACAT-GTGTAA
* * * * *
372076 AAATAGAAAGTTTTACAATGGTTTAAGATCATTGGATGAGTAAAAATAGATGGA-TGAGATTATT
1 AACTAGAAAGTTTTACATTGATTTAAGATCGTTGGATGAGTAAAAATAGAT-GACTGAGATTAAT
* * * * *
372140 AGTTGAAAATGATAAGATATTAACTGGAAAAACAAGGAGATAGTATCAATCGTCCATTTTCACTC
65 AGTAGGAAATGAGAAGATATTAACTGGAAAAACAAGGAGATAATCTCAATCGTCCATTTTCACTC
*** *
372205 ATCCAACGATCCTAAATGAGTGTAAAACTATACTTTTTTTTACATTATGTAAGTGGATTCTAACC
130 ATCCAACGATCCTAAATGAGTGTAAAACTA-AAAGTTTTTTACATTGTGTAAGTGGATTCTAACC
* *
372270 CATATAGTGGTAAGTCCCAGATATATGTTGTAA
194 CATATAGAGGTAAGT-CCAGATACATG-TGTAA
* * * * *
372303 AACTA-TAAGTTTTACTTTGATTTATGATTGTTGGATGAGTAAAAATAGATGACTGAGATTAAAA
1 AACTAGAAAGTTTTACATTGATTTAAGATCGTTGGATGAGTAAAAATAGATGACTGAGATTAATA
* ** * * *
372367 ATAGGAAATGAGAAGATATTCAGTTGAAGAAAAA-AAGGAGATAATCTCAA-CTATCTATTTCCA
66 GTAGGAAATGAGAAGATATT-AACTG--GAAAAACAAGGAGATAATCTCAATC-GTCCATTTTCA
* * * * * *
372430 CTCATCCAACGATCCTCAATTAGTGTAGAA-TTAAAGTTTTTTACATTGTGTAAGTGAATCCTAA
127 CTCATCCAACGATCCTAAATGAGTGTAAAACTAAAAGTTTTTTACATTGTGTAAGTGGATTCTAA
* * *
372494 TCCATATAGAGAT-AG----GAT-CA-GTGAAA
192 CCCATATAGAGGTAAGTCCAGATACATGTGTAA
* * * * * ** *
372520 AACTATAAAATTTTACATTGATTTAAGATCATTGGATAAGTGAAAATAGAAAAATGAGATTAATA
1 AACTAGAAAGTTTTACATTGATTTAAGATCGTTGGATGAGTAAAAATAGATGACTGAGATTAATA
* * * * * * *
372585 GTAGGAAATTAGAAGATATTCACTGGAAAAAAAACAAGGAGATAATATTAGTTGTCCA-TTTCCC
66 GTAGGAAATGAGAAGATATTAACTGG---AAAAACAAGGAGATAATCTCAATCGTCCATTTTCAC
* ** * *
372649 TTCATCCAATGATATTAAATCGA-TGTAAAACTAAAAGTTTTTTGCATTGTGTAAGTGAATTCTA
128 -TCATCCAACGATCCTAAAT-GAGTGTAAAACTAAAAGTTTTTTACATTGTGTAAGTGGATTCTA
* * ** *
372713 ACCCATATAAAGGTAGGATCCATTTATATGGTGTAA
191 ACCCATATAGAGGTAAG-TCCAGATACAT-GTGTAA
* * * * * *
372749 AGCTAGAAAGTTTTACATTGATTT-AGAATCGTTAGATGAGTGAAAATAAATGACTAAGATTAAC
1 AACTAGAAAGTTTTACATTGATTTAAG-ATCGTTGGATGAGTAAAAATAGATGACTGAGATTAAT
* * * * * * *
372813 AGTATGAAATAAAAAGATATTCACT-GAAAAATAAGGAGATAATCTCAACCGACCATTTTCACTC
65 AGTAGGAAATGAGAAGATATTAACTGGAAAAACAAGGAGATAATCTCAATCGTCCATTTTCACTC
* * * * * * *
372877 ATCTAATGATCCTTAATTAGCGTAAAACTAAAAGGTTTTTTTGTAACATTGTGTAAATAGATTCT
130 ATCCAACGATCCTAAATGAGTGTAAAACTAAAA-G--TTTTT-T-ACATTGTGTAAGTGGATTCT
*
372942 AACCCATATAGAGGTAGGATCCA-ATTACATAGTGTAA
190 AACCCATATAGAGGTAAG-TCCAGA-TACAT-GTGTAA
372979 A
1 A
372980 TTATAAAGTC
Statistics
Matches: 709, Mismatches: 154, Indels: 74
0.76 0.16 0.08
Matches are distributed among these distances:
215 1 0.00
217 11 0.02
218 75 0.11
219 38 0.05
220 45 0.06
221 1 0.00
222 9 0.01
224 58 0.08
225 116 0.16
226 140 0.20
227 25 0.04
228 58 0.08
229 83 0.12
230 49 0.07
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (224 bp):
AACTAGAAAGTTTTACATTGATTTAAGATCGTTGGATGAGTAAAAATAGATGACTGAGATTAATA
GTAGGAAATGAGAAGATATTAACTGGAAAAACAAGGAGATAATCTCAATCGTCCATTTTCACTCA
TCCAACGATCCTAAATGAGTGTAAAACTAAAAGTTTTTTACATTGTGTAAGTGGATTCTAACCCA
TATAGAGGTAAGTCCAGATACATGTGTAA
Found at i:372878 original size:444 final size:444
Alignment explanation
Indices: 371933--372952 Score: 1022
Period size: 444 Copynumber: 2.3 Consensus size: 444
371923 AATGAGAAGG
* * * * * * * *
371933 TATTTACTGAAAAACAAGGAGATAATCTCAATTGTCCATTTTCATTCACCCAACGATCATAAATC
1 TATTCACTGAAAAAAAAGGAGATAATCTCAA-CGACCATTTTCACTCATCCAACGATCCTAAATT
* *
371998 AGTGTAAAACTAAAAGTTTTTAACATTGTGTAAATGGATCCTAACTCATATAGGGTAGGTTTTAA
65 AGTGTAAAACTAAAAGTTTTTAACATTGTGTAAATGAATCCTAACTCATATAGGATAGG---T-A
* * * **
372063 TTACATAATGTAAAAATAGAAAGTTTTACAATGGTTTAAGATCATTGGATGAGTAAAAATAGATG
126 TTACA-AATGTAAAAATAGAAAATTTTACAATGATTTAAGATCATTGGATAAGTAAAAATAGAAA
* * * * *
372128 GATGAGATTATTAGTTGAAAATGATAAGATATTAACTGGAAAAACAAGGAGATAGTATCAATCGT
190 AATGAGATTAATAGTAGAAAATGAGAAGATATTAACTGGAAAAACAAGGAGATAATATCAATCGT
* ***
372193 CCATTTTCACTCATCCAACGATCCTAAATGAGTGTAAAACTATACTTTTTTTTACATTATGTAAG
255 CCATTTTCACTCATCCAACGATACTAAATGAGTGTAAAACTATAAAGTTTTTTACATTATGTAAG
* ** * * *
372258 TGGATTCTAACCCATATAGTGGTAAGTCCCAGATATATGTTGTAAAACTATAAGTTTTACTTTGA
320 TGAATTCTAACCCATATAAAGGTAAGTCCCAGATATATGGTGTAAAACTAAAAGTTTTACATTGA
* * * * * *
372323 TTTATGATTGTTGGATGAGTAAAAATAGATGACTGAGATTAAAAATAGGAAATGAGAAGA
385 TTTATGATCGTTAGATGAGTAAAAATAAATGACTAAGATTAAAAATAGGAAATAAAAAGA
* * * * *
372383 TATTCAGTTGAAGAAAAAAAGGAGATAATCTCAACTATCTATTTCCACTCATCCAACGATCCTCA
1 TATTCA-CTG-A-AAAAAAAGGAGATAATCTCAACGA-CCATTTTCACTCATCCAACGATCCTAA
* * * *
372448 ATTAGTGTAGAA-TTAAAGTTTTTTACATTGTGTAAGTGAATCCTAA-TCCATATAGAGATAGG-
62 ATTAGTGTAAAACTAAAAGTTTTTAACATTGTGTAAATGAATCCTAACT-CATATAG-GATAGGT
* * * *
372510 A-T-C-AGTG-AAAAACTATAAAATTTTACATTGATTTAAGATCATTGGATAAGTGAAAATAGAA
125 ATTACAAATGTAAAAA-TAGAAAATTTTACAATGATTTAAGATCATTGGATAAGTAAAAATAGAA
* * * * *
372571 AAATGAGATTAATAGTAGGAAATTAGAAGATATTCACTGGAAAAAAAACAAGGAGATAATATTAG
189 AAATGAGATTAATAGTAGAAAATGAGAAGATATTAACTGG---AAAAACAAGGAGATAATATCAA
* * * * * *
372636 TTGTCCA-TTTCCCTTCATCCAATGATATTAAATCGA-TGTAAAACTA-AAAGTTTTTTGCATTG
251 TCGTCCATTTTCAC-TCATCCAACGATACTAAAT-GAGTGTAAAACTATAAAGTTTTTTACATTA
* ** *
372698 TGTAAGTGAATTCTAACCCATATAAAGGTAGGAT-CCATTTATATGGTGTAAAGCTAGAAAGTTT
314 TGTAAGTGAATTCTAACCCATATAAAGGTAAG-TCCCAGATATATGGTGTAAAACTA-AAAGTTT
* * * *
372762 TACATTGATTTA-GAATCGTTAGATGAGTGAAAATAAATGACTAAGATTAACAGTATGAAATAAA
377 TACATTGATTTATG-ATCGTTAGATGAGTAAAAATAAATGACTAAGATTAAAAATAGGAAATAAA
372826 AAGA
441 AAGA
* * * *
372830 TATTCACTGAAAAATAAGGAGATAATCTCAACCGACCATTTTCACTCATCTAATGATCCTTAATT
1 TATTCACTGAAAAAAAAGGAGATAATCTCAA-CGACCATTTTCACTCATCCAACGATCCTAAATT
* * *
372895 AGCGTAAAACTAAAAGGTTTTTTTGTAACATTGTGTAAAT-AGATTCTAACCCATATAG
65 AGTGTAAAACTAAAA-G---TTTT-TAACATTGTGTAAATGA-ATCCTAACTCATATAG
372953 AGGTAGGATC
Statistics
Matches: 463, Mismatches: 83, Indels: 48
0.78 0.14 0.08
Matches are distributed among these distances:
443 5 0.01
444 128 0.28
445 7 0.02
446 67 0.14
447 120 0.26
448 3 0.01
449 5 0.01
450 31 0.07
451 3 0.01
452 38 0.08
453 56 0.12
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (444 bp):
TATTCACTGAAAAAAAAGGAGATAATCTCAACGACCATTTTCACTCATCCAACGATCCTAAATTA
GTGTAAAACTAAAAGTTTTTAACATTGTGTAAATGAATCCTAACTCATATAGGATAGGTATTACA
AATGTAAAAATAGAAAATTTTACAATGATTTAAGATCATTGGATAAGTAAAAATAGAAAAATGAG
ATTAATAGTAGAAAATGAGAAGATATTAACTGGAAAAACAAGGAGATAATATCAATCGTCCATTT
TCACTCATCCAACGATACTAAATGAGTGTAAAACTATAAAGTTTTTTACATTATGTAAGTGAATT
CTAACCCATATAAAGGTAAGTCCCAGATATATGGTGTAAAACTAAAAGTTTTACATTGATTTATG
ATCGTTAGATGAGTAAAAATAAATGACTAAGATTAAAAATAGGAAATAAAAAGA
Found at i:373161 original size:26 final size:26
Alignment explanation
Indices: 373132--373193 Score: 124
Period size: 26 Copynumber: 2.4 Consensus size: 26
373122 AAGTTAATTT
373132 GAGTCAAGTCAAAAGAATAGTTTCTC
1 GAGTCAAGTCAAAAGAATAGTTTCTC
373158 GAGTCAAGTCAAAAGAATAGTTTCTC
1 GAGTCAAGTCAAAAGAATAGTTTCTC
373184 GAGTCAAGTC
1 GAGTCAAGTC
373194 GAGTTTTGCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (26 bp):
GAGTCAAGTCAAAAGAATAGTTTCTC
Found at i:377672 original size:9 final size:9
Alignment explanation
Indices: 377658--377720 Score: 56
Period size: 9 Copynumber: 6.8 Consensus size: 9
377648 ATAAACAAGT
377658 AAATAAAAA
1 AAATAAAAA
377667 AAATAAAAA
1 AAATAAAAA
*
377676 AAATACAAAT
1 AAATA-AAAA
377686 AAATAAAACA
1 AAATAAAA-A
* *
377696 AATGTAAAGA
1 AA-ATAAAAA
*
377706 AGAT-AAAA
1 AAATAAAAA
377714 AAATAAA
1 AAATAAA
377721 GATAAGGAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
8 6 0.14
9 20 0.48
10 12 0.29
11 4 0.10
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.14
Consensus pattern (9 bp):
AAATAAAAA
Found at i:377807 original size:12 final size:12
Alignment explanation
Indices: 377790--377820 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
377780 AATAAAATAG
377790 AATAATATTAAT
1 AATAATATTAAT
377802 AATAATATTAAT
1 AATAATATTAAT
377814 AATAATA
1 AATAATA
377821 AAAAATGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
AATAATATTAAT
Found at i:378574 original size:37 final size:37
Alignment explanation
Indices: 378524--378598 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
378514 ATGCTTGTAG
*
378524 ATCCTATTTTTAGGAGTTTGAATCTTAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
378561 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
378598 A
1 A
378599 ACATTATGCT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
Found at i:379269 original size:78 final size:79
Alignment explanation
Indices: 379170--379376 Score: 238
Period size: 84 Copynumber: 2.6 Consensus size: 79
379160 AAATTTGATT
* * * * *
379170 TGCCTCTGAGTTGAATGTAATCGAACTCGAAGGTCTTTATTGACATATAACCCTTCTCGCCTTGA
1 TGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACATATAACCCTTCTCGACTTAA
*
379235 GTTATGCTG-GATA
66 GCTATGCTGAGATA
* * *
379248 TGCCTTTGAGCTGAATGTAATCGAACTCGATGGTTTTTGGTT-AGCATATAGCCCTTCTCGACTT
1 TGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTT-GTTGA-CATATAACCCTTCTCGACTT
*
379312 AAGCTATGCTGCAAATGATG
64 AAGCTATGCTG---A-GATA
* *
379332 TGCATTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACA
1 TGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACA
379377 GATAGTTTTT
Statistics
Matches: 107, Mismatches: 14, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
78 35 0.33
79 29 0.27
83 5 0.05
84 38 0.36
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (79 bp):
TGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACATATAACCCTTCTCGACTTAA
GCTATGCTGAGATA
Found at i:379503 original size:37 final size:36
Alignment explanation
Indices: 379462--379758 Score: 301
Period size: 37 Copynumber: 8.4 Consensus size: 36
379452 TTTTTTTTTG
* *
379462 TGTTTCAAGAGAAATTGTCTCAATAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
379499 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * * * * *
379536 AGTTCCAAAAGAAATTGTCTCAAGGGAGGCGAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
379572 TGTTTCAAG-GAAAACATAT-TC-A-A-AG----ATTT
1 TGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAATT
*
379601 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
379637 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
379673 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * * *
379710 AGTTCCGAA-AGAAACTATCTCAAGGGAGACGAAATT
1 TGTTTC-AAGAGAAACTGTCTCAAGAGAGACAAAATT
379746 TGTTTCAA-AGAAA
1 TGTTTCAAGAGAAA
379759 ACATATTTAA
Statistics
Matches: 221, Mismatches: 26, Indels: 28
0.80 0.09 0.10
Matches are distributed among these distances:
28 2 0.01
29 18 0.08
30 2 0.01
31 1 0.00
32 2 0.01
33 2 0.01
35 9 0.04
36 91 0.41
37 92 0.42
38 2 0.01
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:379646 original size:36 final size:36
Alignment explanation
Indices: 379599--379758 Score: 225
Period size: 36 Copynumber: 4.4 Consensus size: 36
379589 ATTCAAAGAT
*
379599 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
379635 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
379671 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * *
379707 CTTAGTTCCGAA-AGAAACTATCTCAAGGGAGACGAAA
1 -TTTGTTTC-AAGAGAAACTGTCTCAAGAGAGACAAAA
379744 TTTGTTTCAA-AGAAA
1 TTTGTTTCAAGAGAAA
379759 ACATATTTAA
Statistics
Matches: 114, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
35 7 0.06
36 77 0.68
37 28 0.25
38 2 0.02
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:379682 original size:21 final size:21
Alignment explanation
Indices: 379620--379684 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
379610 GGAAACTGTC
379620 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
* *
379641 TCAAG-G-G---AAA-CTGTC
1 TCAAGAGAGACAAAATTTGTT
379656 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
379677 TCAAGAGA
1 TCAAGAGA
379685 AACTGTCTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
15 8 0.24
16 4 0.12
17 1 0.03
19 1 0.03
20 4 0.12
21 16 0.47
ACGTcount: A:0.42, C:0.12, G:0.22, T:0.25
Consensus pattern (21 bp):
TCAAGAGAGACAAAATTTGTT
Found at i:379753 original size:174 final size:176
Alignment explanation
Indices: 379462--379816 Score: 606
Period size: 174 Copynumber: 2.0 Consensus size: 176
379452 TTTTTTTTTG
* *
379462 TGTTTCAAGAGAAATTGTCTCAATAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAG
* * * *
379527 ACAAAACTTAGTTCCAAAAGAAATTGTCTCAAGGGAGGCGAAATTTGTTTCAAGGAAAACATATT
66 ACAAAACTTAGTTCCAAAAGAAACTATCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACATATT
379592 CAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TT
131 CAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
*
379637 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGAGAAACTGTCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAG
*
379701 ACAAAACTTAGTTCCGAAAGAAACTATCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACATATT
66 ACAAAACTTAGTTCCAAAAGAAACTATCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACATATT
* *
379766 TAAAGATTTTGTTTCAAGGGAAACTGTTTCAAGAGAGACAAAATTT
131 CAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
379812 TGTTT
1 TGTTT
379817 TGAGCAAATT
Statistics
Matches: 169, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
174 131 0.78
175 38 0.22
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (176 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAG
ACAAAACTTAGTTCCAAAAGAAACTATCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACATATT
CAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:380073 original size:34 final size:34
Alignment explanation
Indices: 380035--380118 Score: 132
Period size: 34 Copynumber: 2.5 Consensus size: 34
380025 GGATGGCTTA
* *
380035 TTCGCTGTGAAATTGAGCTTTTAATTTGACGTCC
1 TTCGCTGTGAAATTGAGCATTTAATTGGACGTCC
380069 TTCGCTGTGAAATTGAGCATTTAATTGGACGTCC
1 TTCGCTGTGAAATTGAGCATTTAATTGGACGTCC
* *
380103 TTCGTTGTGAAGTTGA
1 TTCGCTGTGAAATTGA
380119 AATTGATTCT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.21, C:0.15, G:0.24, T:0.39
Consensus pattern (34 bp):
TTCGCTGTGAAATTGAGCATTTAATTGGACGTCC
Found at i:381570 original size:22 final size:22
Alignment explanation
Indices: 381542--381583 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
381532 TTTCTCTTTT
381542 TTATTTTCTCT-TTTCTTTCTCC
1 TTATTTTCTCTCTTT-TTTCTCC
*
381564 TTATTTTTTCTCTTTTTTCT
1 TTATTTTCTCTCTTTTTTCT
381584 TTTTGTTCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (22 bp):
TTATTTTCTCTCTTTTTTCTCC
Found at i:381577 original size:24 final size:25
Alignment explanation
Indices: 381527--381579 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
381517 TTTCCTTTGT
* * *
381527 TTTTGTTTCTCTTTTTTATTTTCTC
1 TTTTCTTTCTCCTTATTATTTTCTC
381552 TTTTCTTTCTCCTTATT-TTTTCTC
1 TTTTCTTTCTCCTTATTATTTTCTC
381576 TTTT
1 TTTT
381580 TTCTTTTTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 11 0.44
25 14 0.56
ACGTcount: A:0.04, C:0.19, G:0.02, T:0.75
Consensus pattern (25 bp):
TTTTCTTTCTCCTTATTATTTTCTC
Found at i:384518 original size:33 final size:32
Alignment explanation
Indices: 384460--384525 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 32
384450 AACGTGTTAG
384460 ATAAAAAAATGAAAAATAAATAGAATAAAAAA
1 ATAAAAAAATGAAAAATAAATAGAATAAAAAA
*
384492 ATAAAAAAATGACCGAAATAAA-AGAATAAAAAA
1 ATAAAAAAATGA--AAAATAAATAGAATAAAAAA
384525 A
1 A
384526 GAGTGAAGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
32 12 0.39
33 12 0.39
34 7 0.23
ACGTcount: A:0.76, C:0.03, G:0.08, T:0.14
Consensus pattern (32 bp):
ATAAAAAAATGAAAAATAAATAGAATAAAAAA
Found at i:384723 original size:6 final size:6
Alignment explanation
Indices: 384713--384773 Score: 70
Period size: 6 Copynumber: 9.8 Consensus size: 6
384703 AAAAAGGGTA
*
384713 AATAAA AATAAAT AA-AAT AGAATAAT AATAAT AATAAT AATAAT AATAAT
1 AATAAT AAT-AAT AATAAT A-A-TAAT AATAAT AATAAT AATAAT AATAAT
*
384763 ACTAAT AATAA
1 AATAAT AATAA
384774 AAACAGGAAG
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
5 4 0.08
6 35 0.73
7 5 0.10
8 4 0.08
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (6 bp):
AATAAT
Found at i:384729 original size:9 final size:10
Alignment explanation
Indices: 384711--384774 Score: 71
Period size: 9 Copynumber: 6.4 Consensus size: 10
384701 ATAAAAAGGG
*
384711 TAAATAAAAA
1 TAAATAATAA
384721 TAAATAA-AA
1 TAAATAATAA
384730 TAGAATAATAA
1 TA-AATAATAA
384741 T-AATAATAA
1 TAAATAATAA
384750 T-AATAATAA
1 TAAATAATAA
384759 TAATACTAATAA
1 TAA-A-TAATAA
384771 TAAA
1 TAAA
384775 AACAGGAAGT
Statistics
Matches: 49, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
9 22 0.45
10 13 0.27
11 5 0.10
12 9 0.18
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (10 bp):
TAAATAATAA
Found at i:384741 original size:3 final size:3
Alignment explanation
Indices: 384733--384773 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
384723 AATAAAATAG
*
384733 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ACT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
384774 AAACAGGAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:385097 original size:26 final size:25
Alignment explanation
Indices: 385063--385134 Score: 72
Period size: 29 Copynumber: 2.7 Consensus size: 25
385053 AAAACAAAAT
* *
385063 AAAACATATAAAATATAATAATAAT
1 AAAAAATATAAAATATAATAATAAG
*
385088 AATGAAATATATATAATAATAATAATAAG
1 AA--AAA-ATATAAAAT-ATAATAATAAG
*
385117 AAAAAAAATAAAATATAA
1 AAAAAATATAAAATATAA
385135 AAAATTGAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
25 6 0.16
26 7 0.18
27 5 0.13
28 8 0.21
29 12 0.32
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.26
Consensus pattern (25 bp):
AAAAAATATAAAATATAATAATAAG
Found at i:385105 original size:20 final size:19
Alignment explanation
Indices: 385073--385110 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
385063 AAAACATATA
385073 AAATATAATAATAATAATG
1 AAATATAATAATAATAATG
385092 AAATATATATAATAATAAT
1 AAATATA-ATAATAATAAT
385111 AATAAGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (19 bp):
AAATATAATAATAATAATG
Found at i:387925 original size:2 final size:2
Alignment explanation
Indices: 387918--387960 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
387908 GGCTATGATG
387918 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
387960 T
1 T
387961 TATTTAATAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:388485 original size:159 final size:161
Alignment explanation
Indices: 388189--388502 Score: 438
Period size: 159 Copynumber: 2.0 Consensus size: 161
388179 TATATAATCT
* * *
388189 AATAAAAATTAATTAAAATATAAATAATTTATATATGTTATTTTTTTAATAAAAATTTAAATTTT
1 AATAAAAATTAATTAAAATATAAATAATTTATATATGTTA-TTTTTTAATAAAAAGTAAAATTAT
* *
388254 TAATTAAGTTAAAAGATATCAATTTTTACATTATATCTATAATCATTAAATTATAAATACAAAAA
65 CAATTAAGTTAAAAGATATCAATTTGTACATTATATCTATAATCATTAAATTATAAATACAAAAA
*
388319 AAATATTAAATTTAATTTCAAATATCCAACCC
130 AAATATTAAATTTAATTTAAAATATCCAACCC
* *
388351 AATAAAAATTAATTAAAATATAAATGATTTGTATACT-TTA-TTTTTAATAAAAAGTAAAATTAT
1 AATAAAAATTAATTAAAATATAAATAATTTATATA-TGTTATTTTTTAATAAAAAGTAAAATTAT
* * * * *
388414 CAATTGAA-TTAAAAG-TATCCATTTGTAGATTATATTTATAATCATTAAATTATAACTATAAAA
65 CAATT-AAGTTAAAAGATATCAATTTGTACATTATATCTATAATCATTAAATTATAAATACAAAA
**
388477 AACGTATTAAATTTAATTTAAAATAT
129 AAAATATTAAATTTAATTTAAAATAT
388503 ACAAAATGTA
Statistics
Matches: 135, Mismatches: 15, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
159 65 0.48
160 31 0.23
161 2 0.01
162 36 0.27
163 1 0.01
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.41
Consensus pattern (161 bp):
AATAAAAATTAATTAAAATATAAATAATTTATATATGTTATTTTTTAATAAAAAGTAAAATTATC
AATTAAGTTAAAAGATATCAATTTGTACATTATATCTATAATCATTAAATTATAAATACAAAAAA
AATATTAAATTTAATTTAAAATATCCAACCC
Found at i:388539 original size:30 final size:29
Alignment explanation
Indices: 388474--388539 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 29
388464 TATAACTATA
*
388474 AAAAACGTATTAAATTTAATTTAAAATAT
1 AAAAATGTATTAAATTTAATTTAAAATAT
*
388503 ACAAAATGTATTAAATTTAGATGTTTAAAT-T
1 A-AAAATGTATTAAATTTA-AT-TTAAAATAT
388534 AAAAAT
1 AAAAAT
388540 TTCTAAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 1 0.03
30 21 0.66
31 4 0.12
32 6 0.19
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.38
Consensus pattern (29 bp):
AAAAATGTATTAAATTTAATTTAAAATAT
Found at i:395031 original size:21 final size:21
Alignment explanation
Indices: 395007--395069 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
394997 TAATTAAGAA
* *
395007 TCAAGGAGCTTTACTTCAAAG
1 TCAAGGCGCCTTACTTCAAAG
395028 TCAAGGCGCCTTACTTCAAAG
1 TCAAGGCGCCTTACTTCAAAG
*
395049 TCAATGCGCCTTACTTCAAAG
1 TCAAGGCGCCTTACTTCAAAG
395070 CCATAGCTCG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.27
Consensus pattern (21 bp):
TCAAGGCGCCTTACTTCAAAG
Found at i:399616 original size:27 final size:28
Alignment explanation
Indices: 399586--399639 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
399576 TCTCATTTTT
* *
399586 TTAACTTTTTC-TTTTTCTCTTTCATTC
1 TTAACTTTTACTTTTTTCTCTCTCATTC
399613 TTAACTTTTACTTTTTTCTCTCTCATT
1 TTAACTTTTACTTTTTTCTCTCTCATT
399640 TCTTCATCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 10 0.42
28 14 0.58
ACGTcount: A:0.13, C:0.22, G:0.00, T:0.65
Consensus pattern (28 bp):
TTAACTTTTACTTTTTTCTCTCTCATTC
Found at i:405794 original size:45 final size:45
Alignment explanation
Indices: 405730--405819 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
405720 GATGTTTCTT
*
405730 AGGTACAACTGACGAAGAAGGTGCAGATGAAAAACTATTTAACAG
1 AGGTACAACTGACGAAGAAGGTGCAGATGAAAAACTATATAACAG
*
405775 AGGTACAACTGACGAAGAAGGTGCAGATGACAAACTATATAACAG
1 AGGTACAACTGACGAAGAAGGTGCAGATGAAAAACTATATAACAG
405820 GGAAAACATT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.44, C:0.14, G:0.24, T:0.17
Consensus pattern (45 bp):
AGGTACAACTGACGAAGAAGGTGCAGATGAAAAACTATATAACAG
Found at i:406384 original size:18 final size:18
Alignment explanation
Indices: 406361--406407 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
406351 CTCTACCCCT
406361 AGTATCGATACTCCCATG
1 AGTATCGATACTCCCATG
406379 AGTATCGATACTCCCATG
1 AGTATCGATACTCCCATG
*
406397 AGTATTGATAC
1 AGTATCGATAC
406408 CAAAAATGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (18 bp):
AGTATCGATACTCCCATG
Found at i:406391 original size:38 final size:39
Alignment explanation
Indices: 406314--406391 Score: 106
Period size: 41 Copynumber: 2.0 Consensus size: 39
406304 AGTTTTGCTC
*
406314 ACCCCTAGTATCGATACCCCGGTTGGGAGTATCGATACTCT
1 ACCCCTAGTATCGATACCCC-GAT-GGAGTATCGATACTCT
406355 ACCCCTAGTATCGATACTCCC-AT-GAGTATCGATACTC
1 ACCCCTAGTATCGATAC-CCCGATGGAGTATCGATACTC
406392 CCATGAGTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
38 14 0.40
40 1 0.03
41 17 0.49
42 3 0.09
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (39 bp):
ACCCCTAGTATCGATACCCCGATGGAGTATCGATACTCT
Found at i:408228 original size:22 final size:22
Alignment explanation
Indices: 408193--408273 Score: 67
Period size: 22 Copynumber: 3.7 Consensus size: 22
408183 ATATCCCCAG
408193 CAGTGCTAAGGCACTT-TAGTAT
1 CAGTGCTAAGGCACTTCTA-TAT
* *
408215 CAGTGGTAATGCACTTCTATAT
1 CAGTGCTAAGGCACTTCTATAT
* * * *
408237 CAGTACTGAGGAACTT-TAGTAC
1 CAGTGCTAAGGCACTTCTA-TAT
*
408259 CAATGCTAAGGCACT
1 CAGTGCTAAGGCACT
408274 CCTGTTATTC
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
21 2 0.04
22 41 0.91
23 2 0.04
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.30
Consensus pattern (22 bp):
CAGTGCTAAGGCACTTCTATAT
Found at i:423527 original size:10 final size:9
Alignment explanation
Indices: 423514--423666 Score: 70
Period size: 10 Copynumber: 16.4 Consensus size: 9
423504 TTTGGATTTA
423514 TTTTCTTCT
1 TTTTCTTCT
*
423523 ATTTTACTTTTT
1 -TTTT-C-TTCT
423535 TTTTCTTCGT
1 TTTTCTTC-T
423545 TTTTCTTTCT
1 TTTTC-TTCT
423555 TTTTCTT-T
1 TTTTCTTCT
*
423563 TTCTTTTTCT
1 TT-TTCTTCT
423573 TTTTCTT-T
1 TTTTCTTCT
*
423581 TTCTTTTTCT
1 TT-TTCTTCT
423591 TTTTC-TCT
1 TTTTCTTCT
*
423599 TTCTC-T-T
1 TTTTCTTCT
423606 TTTTCTTTCT
1 TTTTC-TTCT
*
423616 TTTCATTTTCAT
1 TTT--TCTTC-T
*
423628 TTTCTTTTCT
1 TTT-TCTTCT
423638 TCTTTCTTC-
1 T-TTTCTTCT
423647 TTTTCTT-T
1 TTTTCTTCT
*
423655 ATTT-TTCT
1 TTTTCTTCT
423663 TTTT
1 TTTT
423667 TCATTAGCAA
Statistics
Matches: 113, Mismatches: 13, Indels: 36
0.70 0.08 0.22
Matches are distributed among these distances:
7 7 0.06
8 27 0.24
9 20 0.18
10 33 0.29
11 18 0.16
12 8 0.07
ACGTcount: A:0.03, C:0.18, G:0.01, T:0.78
Consensus pattern (9 bp):
TTTTCTTCT
Found at i:423561 original size:6 final size:6
Alignment explanation
Indices: 423519--423666 Score: 128
Period size: 6 Copynumber: 24.3 Consensus size: 6
423509 ATTTATTTTC
*
423519 TTCTATT TTACTTT TTTTTT CTTCGTTT TTC--T TTCTTT TTCTTT TTCTTT
1 TTCT-TT TT-CTTT TTCTTT -TTC-TTT TTCTTT TTCTTT TTCTTT TTCTTT
*
423569 TTCTTT TTCTTT TTCTTT TTCTTT TTCTCTT TCTCTTT TT-TCT TTC-TT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCT-TT T-TCTTT TTCTTT TTCTTT
* * * *
423617 TTCATT TTCATT TTC-TT TTCTTCT TTCTTCT TT-TCT TTATTT TTCTTT
1 TTCTTT TTCTTT TTCTTT TTCTT-T TTCTT-T TTCTTT TTCTTT TTCTTT
423665 TT
1 TT
423667 TCATTAGCAA
Statistics
Matches: 122, Mismatches: 7, Indels: 25
0.79 0.05 0.16
Matches are distributed among these distances:
4 4 0.03
5 16 0.13
6 67 0.55
7 27 0.22
8 8 0.07
ACGTcount: A:0.03, C:0.18, G:0.01, T:0.78
Consensus pattern (6 bp):
TTCTTT
Done.