Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007989.1 Hibiscus syriacus cultivar Beakdansim tig00110437_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: 510264
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 2 of 2
Found at i:214141 original size:35 final size:35
Alignment explanation
Indices: 214095--214168 Score: 148
Period size: 35 Copynumber: 2.1 Consensus size: 35
214085 AGAACCTAGG
214095 GATAATTAGTTCCACGATCCAACAGAAATCTTAAA
1 GATAATTAGTTCCACGATCCAACAGAAATCTTAAA
214130 GATAATTAGTTCCACGATCCAACAGAAATCTTAAA
1 GATAATTAGTTCCACGATCCAACAGAAATCTTAAA
214165 GATA
1 GATA
214169 TAAGGTGACG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.43, C:0.19, G:0.12, T:0.26
Consensus pattern (35 bp):
GATAATTAGTTCCACGATCCAACAGAAATCTTAAA
Found at i:214799 original size:37 final size:38
Alignment explanation
Indices: 214729--214802 Score: 114
Period size: 38 Copynumber: 2.0 Consensus size: 38
214719 AACCTGAACC
*
214729 CGACCCGAATATAACATTTAAAAAAACCCGACCCGACT
1 CGACCCGAATATAACACTTAAAAAAACCCGACCCGACT
* *
214767 CGACCCGAATATTACACTT-AAAAAACCTGACCCGAC
1 CGACCCGAATATAACACTTAAAAAAACCCGACCCGAC
214803 CCGAAAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
37 16 0.48
38 17 0.52
ACGTcount: A:0.41, C:0.32, G:0.11, T:0.16
Consensus pattern (38 bp):
CGACCCGAATATAACACTTAAAAAAACCCGACCCGACT
Found at i:215754 original size:2 final size:2
Alignment explanation
Indices: 215747--215774 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
215737 ATGCACATTA
215747 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
215775 TAAAAAATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:228328 original size:3 final size:3
Alignment explanation
Indices: 228320--228381 Score: 90
Period size: 3 Copynumber: 20.7 Consensus size: 3
228310 GGCCCGTTTG
* *
228320 TAA TAA TAA -AA TAA TAA TAA AAA TAA TAA TAA TCA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
228367 TAAA TAA TAA TAA TA
1 T-AA TAA TAA TAA TA
228382 GTAAATGGAA
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 48 0.91
4 3 0.06
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:228344 original size:12 final size:13
Alignment explanation
Indices: 228320--228381 Score: 90
Period size: 13 Copynumber: 4.6 Consensus size: 13
228310 GGCCCGTTTG
228320 TAATAATAAAATAA
1 TAATAAT-AAATAA
228334 TAATAA-AAATAA
1 TAATAATAAATAA
228346 TAATAATCATAATAA
1 TAATAAT-A-AATAA
228361 TAATAATAAATAA
1 TAATAATAAATAA
228374 TAATAATA
1 TAATAATA
228382 GTAAATGGAA
Statistics
Matches: 45, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
12 12 0.27
13 13 0.29
14 8 0.18
15 12 0.27
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.31
Consensus pattern (13 bp):
TAATAATAAATAA
Found at i:228841 original size:42 final size:42
Alignment explanation
Indices: 228789--228932 Score: 207
Period size: 42 Copynumber: 3.4 Consensus size: 42
228779 AATATTGCAG
* * * * *
228789 TTGTGGGGATGAGTTGCAACGTCTTTCAGTAAAGGATTGCAG
1 TTGTGGGGATGAATTGCAACGACTTTCACTAAAGGATTGAAA
*
228831 TTGTGGGGATGAATTGCAATGACTTTCACTAAAGGATTGAAA
1 TTGTGGGGATGAATTGCAACGACTTTCACTAAAGGATTGAAA
* *
228873 TTGTGGGGATGAATTGCAACAACTTTCACTGAAGGATTGAAA
1 TTGTGGGGATGAATTGCAACGACTTTCACTAAAGGATTGAAA
*
228915 CTGTGGGGATGAATTGCA
1 TTGTGGGGATGAATTGCA
228933 GTACGTGATC
Statistics
Matches: 92, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 92 1.00
ACGTcount: A:0.29, C:0.11, G:0.30, T:0.30
Consensus pattern (42 bp):
TTGTGGGGATGAATTGCAACGACTTTCACTAAAGGATTGAAA
Found at i:235110 original size:15 final size:14
Alignment explanation
Indices: 235075--235112 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
235065 CTTGGATAAC
235075 AATAAAAACTAAAA
1 AATAAAAACTAAAA
235089 AATTAAAAACTAAAA
1 AA-TAAAAACTAAAA
235104 ACATAAAAA
1 A-ATAAAAA
235113 AAACCTTGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 2 0.09
15 19 0.86
16 1 0.05
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (14 bp):
AATAAAAACTAAAA
Found at i:240414 original size:22 final size:22
Alignment explanation
Indices: 240375--240439 Score: 103
Period size: 22 Copynumber: 2.9 Consensus size: 22
240365 CTCGTAAATG
240375 CACCGAAGTGCCCCGTAGAATTA
1 CACCGAAGTG-CCCGTAGAATTA
*
240398 CACCGAAGTGCCCGTAGAATTG
1 CACCGAAGTGCCCGTAGAATTA
*
240420 CACCGTAGTGCCCGTAGAAT
1 CACCGAAGTGCCCGTAGAAT
240440 GATGTCCATA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
22 30 0.75
23 10 0.25
ACGTcount: A:0.28, C:0.29, G:0.25, T:0.18
Consensus pattern (22 bp):
CACCGAAGTGCCCGTAGAATTA
Found at i:241188 original size:2 final size:2
Alignment explanation
Indices: 241176--241224 Score: 89
Period size: 2 Copynumber: 24.0 Consensus size: 2
241166 CATTTATTTC
241176 AT AT CAT 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
241219 AT AT AT
1 AT AT AT
241225 CCTCAAGATT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 44 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:242155 original size:21 final size:21
Alignment explanation
Indices: 242131--242175 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
242121 TCTTGTTCGT
* *
242131 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
242152 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
242173 TTG
1 TTG
242176 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:245293 original size:22 final size:22
Alignment explanation
Indices: 245266--245331 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
245256 CTCGTATAAA
245266 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
245289 T-CACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
245310 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
245332 GATGTCCATA
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
21 11 0.27
22 29 0.71
23 1 0.02
ACGTcount: A:0.26, C:0.29, G:0.26, T:0.20
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:246987 original size:21 final size:21
Alignment explanation
Indices: 246963--247007 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
246953 TCTTGTTCGT
* *
246963 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
246984 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
247005 TTG
1 TTG
247008 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:252963 original size:2 final size:2
Alignment explanation
Indices: 252956--252988 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
252946 AAACACAAGC
252956 AT AT AT AT -T 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
252989 TAGTTTTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:253548 original size:36 final size:36
Alignment explanation
Indices: 253489--253590 Score: 125
Period size: 36 Copynumber: 2.8 Consensus size: 36
253479 ACACTTTTCT
** *
253489 AAATCCCACAAAATCAAATGATTGCG-TCTACAAAGTC
1 AAATCCCAC-AAATCAAGGGATTGCGAT-TACAAAATC
* *
253526 AAATCCCACAAATCAAGGGATTGTGATTACAAAATT
1 AAATCCCACAAATCAAGGGATTGCGATTACAAAATC
*
253562 AAATCCCACAAATCAAGGGATTGTGATTA
1 AAATCCCACAAATCAAGGGATTGCGATTA
253591 TAAAGTCTTC
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
36 49 0.83
37 10 0.17
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.24
Consensus pattern (36 bp):
AAATCCCACAAATCAAGGGATTGCGATTACAAAATC
Found at i:257290 original size:28 final size:28
Alignment explanation
Indices: 257250--257326 Score: 111
Period size: 28 Copynumber: 2.8 Consensus size: 28
257240 TCGAGGGTTC
*
257250 TACGTGATCCTTCGGGACATATGTGTTA
1 TACGTGGTCCTTCGGGACATATGTGTTA
*
257278 TACGTGGTCCTTCGGGACATATGTGTTC
1 TACGTGGTCCTTCGGGACATATGTGTTA
*
257306 TATGTGGTCCTTCAGGG-CATA
1 TACGTGGTCCTTC-GGGACATA
257327 GTGGTCCTTC
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
28 42 0.93
29 3 0.07
ACGTcount: A:0.18, C:0.19, G:0.27, T:0.35
Consensus pattern (28 bp):
TACGTGGTCCTTCGGGACATATGTGTTA
Found at i:264182 original size:33 final size:34
Alignment explanation
Indices: 264119--264184 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 34
264109 AAATTTTGGG
* *
264119 GTCGGGTCTGGTTTTTTTTAAGCTTGATATTCGA
1 GTCGGGTCTGGGTTTTTTTAAGCTTAATATTCGA
264153 GTCGGGTC-GGGTTTTTTTAAG-TGTAATATTCG
1 GTCGGGTCTGGGTTTTTTTAAGCT-TAATATTCG
264185 GGTAGGGCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 1 0.03
33 20 0.69
34 8 0.28
ACGTcount: A:0.15, C:0.11, G:0.29, T:0.45
Consensus pattern (34 bp):
GTCGGGTCTGGGTTTTTTTAAGCTTAATATTCGA
Found at i:264795 original size:18 final size:17
Alignment explanation
Indices: 264753--264800 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
264743 GTTTCAGATT
264753 CAGATTCTAATT-CGTA
1 CAGATTCTAATTCCGTA
* *
264769 CATATTCTAATTCCTTCA
1 CAGATTCTAATTCCGT-A
264787 CAGATTCTAATTCC
1 CAGATTCTAATTCC
264801 CTTATAAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 11 0.41
17 2 0.07
18 14 0.52
ACGTcount: A:0.29, C:0.25, G:0.06, T:0.40
Consensus pattern (17 bp):
CAGATTCTAATTCCGTA
Found at i:265064 original size:16 final size:18
Alignment explanation
Indices: 265043--265090 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
265033 GTTTCAGATT
*
265043 CAGATTATAATTCC-T-A
1 CAGATTCTAATTCCTTCA
265059 CAGATTCTAATTCCTTCA
1 CAGATTCTAATTCCTTCA
265077 CAGATTCTAATTCC
1 CAGATTCTAATTCC
265091 CTCATAACTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
16 13 0.45
17 1 0.03
18 15 0.52
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.38
Consensus pattern (18 bp):
CAGATTCTAATTCCTTCA
Found at i:265170 original size:290 final size:288
Alignment explanation
Indices: 264604--265184 Score: 986
Period size: 290 Copynumber: 2.0 Consensus size: 288
264594 TGTAAGTTAT
264604 AAAACAAACTAAAATTAAGAAAAAAATAAGAAAGGCAATTTGTCATTTTACATTACTGAAATCAA
1 AAAACAAACTAAAATTAAGAAAAAAATAAGAAAGGCAATTTGTCATTTTACATTACTGAAATCAA
*
264669 ATTCATCTGACATGTCTGCGAACCAAACAAAATATGAAATTGGATTCCAATTCAATTTCCTGCCA
66 ATTCATCTGACATGTCTGCGAACCAAACAAAATATGAAATTGGATTCCAATTCAATTTCCTACCA
* * *
264734 ACCAAACAGGTTTCAGATTCAGATTCTAATTCGTACATATTCTAATTCCTTCACAGATTCTAATT
131 ACCAAACAGGTTTCAGATTCAGATTATAATTCCTACAGATTCTAATTCCTTCACAGATTCTAATT
* * * *
264799 CCCTTATAAACATTCTAGCGAATCAAACACCACGTTAAGGTTAGGCGTGGACTGTGAATTGAATG
196 CCCTCATAAACATTCTAACAAATCAAACACCACGTTAAAGTTAGGCGTGGACTGTGAATTGAATG
*
264864 TGCCCACGATTTTAAAAATATTACCATA
261 TGCCCACGACTTTAAAAATATTACCATA
*
264892 AAAACAAACTAAAATTAAGAAAAAAAATAAGAAGGGCAATTCTGTCATTTTACATTACTGAAATC
1 AAAACAAACTAAAATTAAG-AAAAAAATAAGAAAGGCAATT-TGTCATTTTACATTACTGAAATC
*
264957 AAATTCATCTGACATGTCTGCGATCCAAACAAAATATGAAATTGGATTCCAATTCAATTTCCTAC
64 AAATTCATCTGACATGTCTGCGAACCAAACAAAATATGAAATTGGATTCCAATTCAATTTCCTAC
265022 CAACCAAACAGGTTTCAGATTCAGATTATAATTCCTACAGATTCTAATTCCTTCACAGATTCTAA
129 CAACCAAACAGGTTTCAGATTCAGATTATAATTCCTACAGATTCTAATTCCTTCACAGATTCTAA
*
265087 TTCCCTCAT-AACTATT-TCAACAAATCAAACACCACGTTAAAGTTAGGTGTGGACTGTGAATTG
194 TTCCCTCATAAAC-ATTCT-AACAAATCAAACACCACGTTAAAGTTAGGCGTGGACTGTGAATTG
* *
265150 AATGTGCCTACGGCTTTAAAAATATTACCATA
257 AATGTGCCCACGACTTTAAAAATATTACCATA
265182 AAA
1 AAA
265185 TTAAAACAGT
Statistics
Matches: 275, Mismatches: 14, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
288 19 0.07
289 24 0.09
290 232 0.84
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.29
Consensus pattern (288 bp):
AAAACAAACTAAAATTAAGAAAAAAATAAGAAAGGCAATTTGTCATTTTACATTACTGAAATCAA
ATTCATCTGACATGTCTGCGAACCAAACAAAATATGAAATTGGATTCCAATTCAATTTCCTACCA
ACCAAACAGGTTTCAGATTCAGATTATAATTCCTACAGATTCTAATTCCTTCACAGATTCTAATT
CCCTCATAAACATTCTAACAAATCAAACACCACGTTAAAGTTAGGCGTGGACTGTGAATTGAATG
TGCCCACGACTTTAAAAATATTACCATA
Found at i:270068 original size:29 final size:29
Alignment explanation
Indices: 270029--270138 Score: 186
Period size: 29 Copynumber: 3.8 Consensus size: 29
270019 TATGTGATAT
270029 GAGAACATGACATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
270059 GAGAAATGACATGAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
* *
270088 GAGAAATGACATGAACTACATAATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
270117 GAGAAATGACATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
270139 ACATATGAAA
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
28 6 0.08
29 65 0.86
30 5 0.07
ACGTcount: A:0.46, C:0.16, G:0.20, T:0.17
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:270241 original size:15 final size:15
Alignment explanation
Indices: 270223--270256 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
270213 GAGTGTATAA
270223 TAGTCATTCGGGACG
1 TAGTCATTCGGGACG
* *
270238 TAGTCCTTCGGGATG
1 TAGTCATTCGGGACG
270253 TAGT
1 TAGT
270257 GGTTCTACGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.32, T:0.32
Consensus pattern (15 bp):
TAGTCATTCGGGACG
Found at i:276506 original size:64 final size:64
Alignment explanation
Indices: 276437--276593 Score: 153
Period size: 64 Copynumber: 2.5 Consensus size: 64
276427 TTGAAGGTGT
** *
276437 ATCGATGCACTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAAAGATCGAATGCA-ATTAGT
1 ATCGATGCACTGGTAGTGCATCGATGCATC-CCATTAATAAT-AAAACATCGAATGCATATTA-T
276499 GC
63 GC
* *
276501 ATCGATGCA-TAAGGCA-TGCATCGATGCATCCCATTAATAATAAAACATCGAATGCATTTTATG
1 ATCGATGCACT--GGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCATATTATG
276564 C
64 C
* * **
276565 ACCAATGCACAAGTAGTGCATCGATGCAT
1 ATCGATGCACTGGTAGTGCATCGATGCAT
276594 ACCTTCATTA
Statistics
Matches: 76, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
63 3 0.04
64 63 0.83
65 10 0.13
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (64 bp):
ATCGATGCACTGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCATATTATGC
Found at i:277024 original size:29 final size:29
Alignment explanation
Indices: 276970--277072 Score: 127
Period size: 29 Copynumber: 3.5 Consensus size: 29
276960 TATGTGATAT
276970 GAGAACATGACATGAG-ATACATGATCACAA
1 GAGAA-ATGACATGAGCA-ACATGATCACAA
* *
277000 GAGAAATAACATGAGCAACACGATCACAA
1 GAGAAATGACATGAGCAACATGATCACAA
* * *
277029 GGGAAATGACATGAACTACATGATCACAA
1 GAGAAATGACATGAGCAACATGATCACAA
*
277058 GATAAATGACATGAG
1 GAGAAATGACATGAG
277073 TACATGAACA
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
29 56 0.90
30 6 0.10
ACGTcount: A:0.48, C:0.17, G:0.20, T:0.16
Consensus pattern (29 bp):
GAGAAATGACATGAGCAACATGATCACAA
Found at i:277196 original size:15 final size:15
Alignment explanation
Indices: 277164--277197 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
277154 GAGGGTATAA
*
277164 TAGTCCTTCGGTACG
1 TAGTCCTTCGGGACG
*
277179 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGACG
277194 TAGT
1 TAGT
277198 GGTCCTACGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.21, G:0.29, T:0.35
Consensus pattern (15 bp):
TAGTCCTTCGGGACG
Found at i:289292 original size:43 final size:42
Alignment explanation
Indices: 289217--289402 Score: 232
Period size: 43 Copynumber: 4.3 Consensus size: 42
289207 TTAATTACCG
*
289217 TTACAATTTCCCCCAAGTCCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTT-CCCCAAGT-CCTTTGCTGTGTGCAAGGGTAAGCC
* * *
289261 TTACAGTTTCCCCAGGTCCATTTGCTATGTGCAAGGATAAGCC
1 TTACAGTTTCCCCAAGTCC-TTTGCTGTGTGCAAGGGTAAGCC
* * *
289304 TTACAG-TTCTCCCAATTTCTTTTGTTGTGTGCAAGGGTAAGCC
1 TTACAGTTTC-CCCAA-GTCCTTTGCTGTGTGCAAGGGTAAGCC
*
289347 TTACAGTTT-CCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTTCCCCAAG-TCCTTTGCTGTGTGCAAGGGTAAGCC
289389 TTACAGTTTCCCCA
1 TTACAGTTTCCCCA
289403 TGCTCTTTTG
Statistics
Matches: 122, Mismatches: 14, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
42 42 0.34
43 68 0.56
44 12 0.10
ACGTcount: A:0.20, C:0.26, G:0.21, T:0.33
Consensus pattern (42 bp):
TTACAGTTTCCCCAAGTCCTTTGCTGTGTGCAAGGGTAAGCC
Found at i:289376 original size:42 final size:42
Alignment explanation
Indices: 289236--289400 Score: 242
Period size: 43 Copynumber: 3.9 Consensus size: 42
289226 CCCCCAAGTC
289236 CCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGG-T
1 CCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTT-CCCAGGTT
* * **
289278 CCATTTGCTATGTGCAAGGATAAGCCTTACAGTTCTCCCAATTT
1 CC-TTTGCTGTGTGCAAGGGTAAGCCTTACAGTT-TCCCAGGTT
* *
289322 CTTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTT
1 CCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTT
289364 CCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
1 CCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
289401 CATGCTCTTT
Statistics
Matches: 108, Mismatches: 12, Indels: 6
0.86 0.10 0.05
Matches are distributed among these distances:
42 44 0.41
43 61 0.56
44 3 0.03
ACGTcount: A:0.19, C:0.24, G:0.23, T:0.34
Consensus pattern (42 bp):
CCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTT
Found at i:289410 original size:85 final size:86
Alignment explanation
Indices: 289238--289423 Score: 270
Period size: 85 Copynumber: 2.2 Consensus size: 86
289228 CCCAAGTCCC
289238 TTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTCCATTTGCTATGTGCAAGGATAAGC
1 TTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTCCATTTGCTATGTGCAAGGATAAGC
*
289303 CTTACAGTTCTCCCAATTTCT
66 CTTACAGTTCTCCCAATCTCT
* * *
289324 TTTGTTGTGTGCAAGGGTAAGCCTTACAGTTT-CCCAGGTTCC-TTTGCTGTGTGCAAGGGTAAG
1 TTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGG-TCCATTTGCTATGTGCAAGGATAAG
*
289387 CCTTACAGTT-TCCCCATGCTCT
65 CCTTACAGTTCTCCCAAT-CTCT
* *
289409 TTTGCTATATGCAAG
1 TTTGCTGTGTGCAAG
289424 TATAAAACCT
Statistics
Matches: 90, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
84 6 0.07
85 50 0.56
86 34 0.38
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.35
Consensus pattern (86 bp):
TTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTCCATTTGCTATGTGCAAGGATAAGC
CTTACAGTTCTCCCAATCTCT
Found at i:293089 original size:12 final size:12
Alignment explanation
Indices: 293072--293096 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
293062 AAATATTCTT
293072 TTTATCTATCTA
1 TTTATCTATCTA
293084 TTTATCTATCTA
1 TTTATCTATCTA
293096 T
1 T
293097 CTATTAGTAG
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:0.24, C:0.16, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTATCTATCTA
Found at i:306483 original size:62 final size:63
Alignment explanation
Indices: 306407--306537 Score: 228
Period size: 66 Copynumber: 2.0 Consensus size: 63
306397 ATTTTGACAG
306407 CAAAACGACACTTGTC-ATATATATAAGAGATAATTATAATATTATATTGGGTCAGGTCATGT
1 CAAAACGACACTTGTCAATATATATAAGAGATAATTATAATATTATATTGGGTCAGGTCATGT
306469 CAAAACGACACTTGTCATATATATATATAAGAGATAATTATAATATTATATTGGGTCAGGTCATG
1 CAAAACGACACTTGTC--A-ATATATATAAGAGATAATTATAATATTATATTGGGTCAGGTCATG
306534 T
63 T
306535 CAA
1 CAA
306538 TTTTTCACCA
Statistics
Matches: 65, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
62 16 0.25
66 49 0.75
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (63 bp):
CAAAACGACACTTGTCAATATATATAAGAGATAATTATAATATTATATTGGGTCAGGTCATGT
Found at i:308468 original size:23 final size:22
Alignment explanation
Indices: 308418--308471 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
308408 CAATATTTAT
308418 TTATT-ATATATTAATAAAATA
1 TTATTAATATATTAATAAAATA
308439 TTATTAATATATTAAATATAAAT-
1 TTATTAATATATT-AATA-AAATA
*
308462 TTTTTAATAT
1 TTATTAATAT
308472 GATAGAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 5 0.17
22 7 0.24
23 13 0.45
24 4 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTATTAATATATTAATAAAATA
Found at i:309574 original size:20 final size:20
Alignment explanation
Indices: 309549--309587 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
309539 GAATAAAATG
*
309549 TTTATTTGTTTGTGTTTGTA
1 TTTATTTGTTTATGTTTGTA
*
309569 TTTATTTTTTTATGTTTGT
1 TTTATTTGTTTATGTTTGT
309588 TTGTTTAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.10, C:0.00, G:0.15, T:0.74
Consensus pattern (20 bp):
TTTATTTGTTTATGTTTGTA
Found at i:322544 original size:21 final size:21
Alignment explanation
Indices: 322520--322561 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
322510 CGATAGGGAC
322520 GAAAATGATAAATTGAGTCTA
1 GAAAATGATAAATTGAGTCTA
322541 GAAAATGATAAATTGAGTCTA
1 GAAAATGATAAATTGAGTCTA
322562 CTACAGGACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.05, G:0.19, T:0.29
Consensus pattern (21 bp):
GAAAATGATAAATTGAGTCTA
Found at i:329698 original size:261 final size:255
Alignment explanation
Indices: 329213--329729 Score: 980
Period size: 261 Copynumber: 2.0 Consensus size: 255
329203 TTTCGAAACA
329213 ACTTTTAAATGTTGAACACCCGCACTTAATGAGAGTGGAAGCAACATTCTAACAGTTTACAACTT
1 ACTTTTAAATGTTGAACACCCGCACTTAATGAGAGTGGAAGCAACATTCTAACAGTTTACAACTT
329278 GTTTCGTATTTGAATAGTAACAAATTGATGAGCCACTCATGGTTTATAGTATGGACCAGATCCAC
66 GTTTCGTATTTGAATAGTAACAAATTGATGAGCCACTCATGGTTTATAGTATGGACCAGATCCAC
329343 CATCATGCAGCACATGGAGTAGCTTAGTTCATGAATGGAATGTAAGCACTCCACAAAAGGAGACA
131 CATCATGCAGCACATGGAGTAGCTTAGTTCATGAATGGAATGTAAGCACTCCACAAAAGGAGACA
329408 AAACAATACATCTAAAGTAAAATTAGATTAGAACTTTGAGCTAGTCTAAATATTCACAAC
196 AAACAATACATCTAAAGTAAAATTAGATTAGAACTTTGAGCTAGTCTAAATATTCACAAC
329468 ACTTTTAAATGTTGAACACCCGCACTTAATGAGAGTGGAAGCAACCATTCTAACAGTTTACAACT
1 ACTTTTAAATGTTGAACACCCGCACTTAATGAGAGTGGAAGCAA-CATTCTAACAGTTTACAACT
329533 TGTTTTCGTATTTGCAATAGTAACAAATTGATGAGCCACTCATGGTTTCATAGTATGGACCAGAT
65 TG-TTTCGTATTTG-AATAGTAACAAATTGATGAGCCACTCATGGTTT-ATAGTATGGACCAGAT
329598 CCAACCATCATGCAGCACATGGAGTAGCTTAGTTCATGAATGGAATGTAAGCCACTCCACAAAAG
127 CC-ACCATCATGCAGCACATGGAGTAGCTTAGTTCATGAATGGAATGTAAG-CACTCCACAAAAG
329663 GAGACAAAACAATACATCTAAAGTAAAATTAGATTAGAACTTTGAGCTAGTCTAAATATTCACAA
190 GAGACAAAACAATACATCTAAAGTAAAATTAGATTAGAACTTTGAGCTAGTCTAAATATTCACAA
329728 C
255 C
329729 A
1 A
329730 AGAGTAACTA
Statistics
Matches: 256, Mismatches: 0, Indels: 6
0.98 0.00 0.02
Matches are distributed among these distances:
255 44 0.17
256 22 0.09
257 11 0.04
258 33 0.13
259 18 0.07
260 48 0.19
261 80 0.31
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (255 bp):
ACTTTTAAATGTTGAACACCCGCACTTAATGAGAGTGGAAGCAACATTCTAACAGTTTACAACTT
GTTTCGTATTTGAATAGTAACAAATTGATGAGCCACTCATGGTTTATAGTATGGACCAGATCCAC
CATCATGCAGCACATGGAGTAGCTTAGTTCATGAATGGAATGTAAGCACTCCACAAAAGGAGACA
AAACAATACATCTAAAGTAAAATTAGATTAGAACTTTGAGCTAGTCTAAATATTCACAAC
Found at i:336770 original size:20 final size:20
Alignment explanation
Indices: 336666--336811 Score: 81
Period size: 20 Copynumber: 7.1 Consensus size: 20
336656 AATGACCAAC
336666 AAATCGCAACGCGATATC--A
1 AAATCGCAACGCGAT-TCAGA
*
336685 AAA-CGCAACGCGATTTAGA
1 AAATCGCAACGCGATTCAGA
* * *
336704 AAAGCGCAACGTTGA--AAGA
1 AAATCGCAACG-CGATTCAGA
*
336723 AGATCGCAAC-CGATCTTCCA-A
1 AAATCGCAACGCGA--TT-CAGA
*
336744 GAATCGCAACGCGATTCAGAAA
1 AAATCGCAACGCGATTCAG--A
*
336766 ATCGCAATCGCAACGCGATTAAGA
1 A----AATCGCAACGCGATTCAGA
336790 AAATCGCAACGCGATTCAGA
1 AAATCGCAACGCGATTCAGA
336810 AA
1 AA
336812 TGAGTAAATT
Statistics
Matches: 98, Mismatches: 12, Indels: 33
0.69 0.08 0.23
Matches are distributed among these distances:
17 3 0.03
18 11 0.11
19 20 0.20
20 29 0.30
21 11 0.11
22 5 0.05
24 2 0.02
26 17 0.17
ACGTcount: A:0.41, C:0.24, G:0.20, T:0.15
Consensus pattern (20 bp):
AAATCGCAACGCGATTCAGA
Found at i:336781 original size:26 final size:26
Alignment explanation
Indices: 336745--336798 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
336735 ATCTTCCAAG
*
336745 AATCGCAACGCGATTCAGAAAATCGC
1 AATCGCAACGCGATTAAGAAAATCGC
336771 AATCGCAACGCGATTAAGAAAATCGC
1 AATCGCAACGCGATTAAGAAAATCGC
336797 AA
1 AA
336799 CGCGATTCAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.43, C:0.24, G:0.19, T:0.15
Consensus pattern (26 bp):
AATCGCAACGCGATTAAGAAAATCGC
Found at i:336904 original size:6 final size:6
Alignment explanation
Indices: 336893--337009 Score: 167
Period size: 6 Copynumber: 20.3 Consensus size: 6
336883 GACACGTATT
336893 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
336941 ACCACGG ACCACG A-CA-G ACCACG ACCACG ACCACG ACC-CG ACCACG
1 ACCAC-G ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
336987 AACC-CG ACC-CG ACC-CG ACC-CG AC
1 -ACCACG ACCACG ACCACG ACCACG AC
337010 GAGACGGACG
Statistics
Matches: 106, Mismatches: 0, Indels: 11
0.91 0.00 0.09
Matches are distributed among these distances:
4 2 0.02
5 26 0.25
6 69 0.65
7 9 0.08
ACGTcount: A:0.32, C:0.50, G:0.18, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:337448 original size:20 final size:20
Alignment explanation
Indices: 337340--337491 Score: 78
Period size: 20 Copynumber: 7.2 Consensus size: 20
337330 AATGACCAAC
337340 AAAATCGCAACGCGATATC--
1 AAAATCGCAACGCGAT-TCAG
* * *
337359 AAAACCGCAACGTGATTTAG
1 AAAATCGCAACGCGATTCAG
* * **
337379 AAAAGCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTCAG
* *
337399 AAGATCGCAACACGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
*
337421 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
*
337441 AAAATCGCAATCGCAACGCGATTAAG
1 --AA----AATCGCAACGCGATTCAG
337467 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
337487 AAAAT
1 AAAAT
337492 GAGTAAATTC
Statistics
Matches: 101, Mismatches: 18, Indels: 27
0.69 0.12 0.18
Matches are distributed among these distances:
18 1 0.01
19 18 0.18
20 46 0.46
21 3 0.03
22 13 0.13
23 1 0.01
24 2 0.02
26 17 0.17
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTCAG
Found at i:337459 original size:26 final size:26
Alignment explanation
Indices: 337423--337476 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
337413 ATCTTCCAAG
*
337423 AATCGCAACGCGATTCAGAAAATCGC
1 AATCGCAACGCGATTAAGAAAATCGC
337449 AATCGCAACGCGATTAAGAAAATCGC
1 AATCGCAACGCGATTAAGAAAATCGC
337475 AA
1 AA
337477 CGCGATTCAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.43, C:0.24, G:0.19, T:0.15
Consensus pattern (26 bp):
AATCGCAACGCGATTAAGAAAATCGC
Found at i:337586 original size:6 final size:6
Alignment explanation
Indices: 337575--337614 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
337565 CACGTATTAC
337575 CGACCA CGACCA CGACCA CGACCA CGACCA CGACC- CGACC
1 CGACCA CGACCA CGACCA CGACCA CGACCA CGACCA CGACC
337615 CGAGACGAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.15
6 29 0.85
ACGTcount: A:0.30, C:0.53, G:0.17, T:0.00
Consensus pattern (6 bp):
CGACCA
Found at i:338122 original size:6 final size:6
Alignment explanation
Indices: 338107--338199 Score: 177
Period size: 6 Copynumber: 15.5 Consensus size: 6
338097 CGGGTCGGTC
*
338107 GGTCGG GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
338155 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
338200 AATAGTAATA
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 86 1.00
ACGTcount: A:0.00, C:0.16, G:0.52, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:338301 original size:22 final size:21
Alignment explanation
Indices: 338263--338775 Score: 465
Period size: 20 Copynumber: 25.0 Consensus size: 21
338253 CTCATTTTCT
* *
338263 GAATCGCG-TGCGTTTCTTTCT
1 GAATCGCGTTGCGATTC-TTCG
*
338284 TAATCGCGTTGCGATTCTT-G
1 GAATCGCGTTGCGATTCTTCG
338304 GAAGATCGCGTTGCGATTCTT-G
1 G-A-ATCGCGTTGCGATTCTTCG
338326 GAAGATCGCGTTGCGATT-TTC-
1 G-A-ATCGCGTTGCGATTCTTCG
**
338347 TTATCGCGTTGCGATTCTT-G
1 GAATCGCGTTGCGATTCTTCG
*
338367 GAAGATCGCGTTGCGATT-TTCT
1 G-A-ATCGCGTTGCGATTCTTCG
*
338389 TAATCGCGTTGCGATTCTT-G
1 GAATCGCGTTGCGATTCTTCG
338409 GAAGATCGCGTTGCGATTCTT-G
1 G-A-ATCGCGTTGCGATTCTTCG
338431 GAAGATCGCGTTGCGATTCTT--
1 G-A-ATCGCGTTGCGATTCTTCG
338452 GAATCGCGTTGCGATTCTT-G
1 GAATCGCGTTGCGATTCTTCG
*
338472 GAATCGCGTTGCGATT-TTCT
1 GAATCGCGTTGCGATTCTTCG
*
338492 TAATCGCGTTGCGATTCTT-G
1 GAATCGCGTTGCGATTCTTCG
*
338512 GAA--GCGTTGCGATT-TTCT
1 GAATCGCGTTGCGATTCTTCG
*
338530 TAATCGCGTTGCGATT-TTC-
1 GAATCGCGTTGCGATTCTTCG
**
338549 TTATCGCGTTGCGATTCTT-G
1 GAATCGCGTTGCGATTCTTCG
338569 GAAGATCGCGTTGCGATTCTT-G
1 G-A-ATCGCGTTGCGATTCTTCG
*
338591 GAATCGCGTTGCGATT-TTCT
1 GAATCGCGTTGCGATTCTTCG
338611 GAATCGCGTTGCGATTCTT-G
1 GAATCGCGTTGCGATTCTTCG
*
338631 GAATCGCGTTGCGATT-TTCT
1 GAATCGCGTTGCGATTCTTCG
*
338651 TAATCGCGTTGCGATTCTT-G
1 GAATCGCGTTGCGATTCTTCG
*
338671 GAAGATCGCGTTGCGATT-TTCT
1 G-A-ATCGCGTTGCGATTCTTCG
338693 GAATCGCGTTGCGATTCTT-G
1 GAATCGCGTTGCGATTCTTCG
**
338713 GAAGATCGCGTTGCGATT-TTAT
1 G-A-ATCGCGTTGCGATTCTTCG
*
338735 GAATCGCATTGCGATTCTT-G
1 GAATCGCGTTGCGATTCTTCG
338755 GAAGATCGCGTTGCGA-TCTTC
1 G-A-ATCGCGTTGCGATTCTTC
338776 TTTTCAACGT
Statistics
Matches: 422, Mismatches: 33, Indels: 73
0.80 0.06 0.14
Matches are distributed among these distances:
17 2 0.00
18 13 0.03
19 52 0.12
20 156 0.37
21 43 0.10
22 156 0.37
ACGTcount: A:0.16, C:0.19, G:0.27, T:0.37
Consensus pattern (21 bp):
GAATCGCGTTGCGATTCTTCG
Found at i:338396 original size:20 final size:20
Alignment explanation
Indices: 338256--338833 Score: 389
Period size: 20 Copynumber: 28.2 Consensus size: 20
338246 GAATTTACTC
*
338256 ATTTTCTGAATCGCG-TGCG
1 ATTTTCTTAATCGCGTTGCG
*
338275 TTTCTTTCTTAATCGCGTTGCG
1 -AT-TTTCTTAATCGCGTTGCG
***
338297 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTTA-ATCGCGTTGCG
***
338319 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTTA-ATCGCGTTGCG
338341 ATTTTCTT-ATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
***
338360 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTTA-ATCGCGTTGCG
338382 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
***
338402 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTTA-ATCGCGTTGCG
***
338424 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTTA-ATCGCGTTGCG
338446 A--TTCTTGAATCGCGTTGCG
1 ATTTTCTT-AATCGCGTTGCG
338465 A--TTCTTGGAATCGCGTTGCG
1 ATTTTCTT--AATCGCGTTGCG
338485 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
338505 A--TTCTTGGAA--GCGTTGCG
1 ATTTTCTT--AATCGCGTTGCG
338523 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
338543 ATTTTCTT-ATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
***
338562 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTTA-ATCGCGTTGCG
338584 A--TTCTTGGAATCGCGTTGCG
1 ATTTTCTT--AATCGCGTTGCG
*
338604 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
338624 A--TTCTTGGAATCGCGTTGCG
1 ATTTTCTT--AATCGCGTTGCG
338644 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
***
338664 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTTA-ATCGCGTTGCG
*
338686 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
***
338706 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTTA-ATCGCGTTGCG
* * *
338728 ATTTTATGAATCGCATTGCG
1 ATTTTCTTAATCGCGTTGCG
***
338748 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTTA-ATCGCGTTGCG
* * *
338770 ATCTTCTT-TTCAACGTTGCG
1 ATTTTCTTAATC-GCGTTGCG
* *
338790 CTTTTCTAAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
* **
338810 GTTTTGAT-ATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
338829 ATTTT
1 ATTTT
338834 GTTGGTCATT
Statistics
Matches: 458, Mismatches: 62, Indels: 77
0.77 0.10 0.13
Matches are distributed among these distances:
18 20 0.04
19 66 0.14
20 174 0.38
21 44 0.10
22 154 0.34
ACGTcount: A:0.16, C:0.19, G:0.26, T:0.38
Consensus pattern (20 bp):
ATTTTCTTAATCGCGTTGCG
Found at i:338692 original size:42 final size:41
Alignment explanation
Indices: 338279--338831 Score: 544
Period size: 42 Copynumber: 13.5 Consensus size: 41
338269 CGTGCGTTTC
338279 TTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGAT
1 TTTCTTAATCGCGTTGCGATTCTTGGAA-ATCGCGTTGCGAT
*** ***
338321 TCTTGGAAGATCGCGTTGCGATT-TT-CTTATCGCGTTGCGAT
1 T-TTCTTA-ATCGCGTTGCGATTCTTGGAAATCGCGTTGCGAT
*** ***
338362 TCTTGGAAGATCGCGTTGCGATT-TTCTTAATCGCGTTGCGAT
1 T-TTCTTA-ATCGCGTTGCGATTCTTGGAAATCGCGTTGCGAT
***
338404 TCTTGGAAGATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGA-
1 T-TTCTTA-ATCGCGTTGCGATTCTTGGAA-ATCGCGTTGCGAT
338447 -TTCTTGAATCGCGTTGCGATTCTTGG-AATCGCGTTGCGAT
1 TTTCTT-AATCGCGTTGCGATTCTTGGAAATCGCGTTGCGAT
338487 TTTCTTAATCGCGTTGCGATTCTTGG-AA--GCGTTGCGAT
1 TTTCTTAATCGCGTTGCGATTCTTGGAAATCGCGTTGCGAT
***
338525 TTTCTTAATCGCGTTGCGATT-TT-CTTATCGCGTTGCGAT
1 TTTCTTAATCGCGTTGCGATTCTTGGAAATCGCGTTGCGAT
***
338564 TCTTGGAAGATCGCGTTGCGATTCTTGG-AATCGCGTTGCGAT
1 T-TTCTTA-ATCGCGTTGCGATTCTTGGAAATCGCGTTGCGAT
*
338606 TTTCTGAATCGCGTTGCGATTCTTGG-AATCGCGTTGCGAT
1 TTTCTTAATCGCGTTGCGATTCTTGGAAATCGCGTTGCGAT
338646 TTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGAT
1 TTTCTTAATCGCGTTGCGATTCTTGGAA-ATCGCGTTGCGAT
*
338688 TTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGAT
1 TTTCTTAATCGCGTTGCGATTCTTGGAA-ATCGCGTTGCGAT
* * *
338730 TTTATGAATCGCATTGCGATTCTTGGAAGATCGCGTTGCGAT
1 TTTCTTAATCGCGTTGCGATTCTTGGAA-ATCGCGTTGCGAT
* * * * ** *
338772 CTTCTT-TTCAACGTTGCGCTT-TTCTAAATCGCGTTGCGGT
1 TTTCTTAATC-GCGTTGCGATTCTTGGAAATCGCGTTGCGAT
**
338812 TTTGAT-ATCGCGTTGCGATT
1 TTTCTTAATCGCGTTGCGATT
338832 TTGTTGGTCA
Statistics
Matches: 449, Mismatches: 44, Indels: 39
0.84 0.08 0.07
Matches are distributed among these distances:
37 3 0.01
38 31 0.07
39 32 0.07
40 101 0.22
41 88 0.20
42 160 0.36
43 8 0.02
44 26 0.06
ACGTcount: A:0.16, C:0.19, G:0.27, T:0.38
Consensus pattern (41 bp):
TTTCTTAATCGCGTTGCGATTCTTGGAAATCGCGTTGCGAT
Found at i:352421 original size:291 final size:289
Alignment explanation
Indices: 351913--352465 Score: 788
Period size: 291 Copynumber: 1.9 Consensus size: 289
351903 GTGAAATCAC
* *
351913 GCATAAGACTCCTCCAAGCAAGGAAACTAGGAGGAAGAGATCACAACCATCATGTTCTAAACCTC
1 GCATAAGACTCCTCCAAGCAAGGAAACTAGGAAGAAGAGATCACAACAATCATGTTCTAAACCTC
* *
351978 GGAAGAAACAGCAAACCAATAAAAAAGACAAAAGTAAGTACAGTTCTTATGTTACTAAATCTGGC
66 GGAAGAAACAGAAAACCAATAAAAAAGACAAAAGTAAGTACAGTTCTTATATTACTAAATCTGGC
* * *
352043 TATTTTATGATCCTTCATTGTGTTGATCTTCTGTGGGAGAACACTTTCAGATGAAAACATTTGTG
131 TATTTTATGATCCTTCATTGCGCTGATCTTCTGTGGGAGAACACTTTCAGATGAAAACAGTTGTG
* * *
352108 AAGATTTTTCTATCGCTGAAGAAGACATGCACACCGAGGTTTCTGGAGATGCACTTGCATTTGGA
196 AAGATTTGTCTATCGCTGAAGAAGACATGCACACCAAGGTTCCTGGAGATGCACTTGCATTTGGA
352173 GCTAAAGATGATCCTAGGGATGAACTCTT
261 GCTAAAGATGATCCTAGGGATGAACTCTT
* * * *
352202 GCATAAGCCTCCTCCATGCAAGGAAACTAGGAAGAAGCA-ATCACGAGAATCATGTTCTAAACCT
1 GCATAAGACTCCTCCAAGCAAGGAAACTAGGAAGAAG-AGATCACAACAATCATGTTCTAAACCT
* * * * * * *
352266 CGGAAGAAACAGAAAACCAGTAAATACGATAAAAGTATGTGCAGAGTTTTTATATTACTAAATCT
65 CGGAAGAAACAGAAAACCAATAAAAAAGACAAAAGTAAGT--ACAGTTCTTATATTACTAAATCT
* ***
352331 GGCTATTTTATGATCCTTCATTGCGCTGATCTTCTGT-GGATGAACTCTTTCAGATGAAAGTGGT
128 GGCTATTTTATGATCCTTCATTGCGCTGATCTTCTGTGGGA-GAACACTTTCAGATGAAAACAGT
* * *
352395 TGTGAAGATTTGTCTAAT-GGTGAAGAAGACCTGCATACCAAGGTTCCTGGAGATGCACTTGCAT
192 TGTGAAGATTTGTCT-ATCGCTGAAGAAGACATGCACACCAAGGTTCCTGGAGATGCACTTGCAT
352459 TTGGAGC
256 TTGGAGC
352466 CAGCGAATTA
Statistics
Matches: 231, Mismatches: 28, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
289 90 0.39
290 4 0.02
291 135 0.58
292 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.27
Consensus pattern (289 bp):
GCATAAGACTCCTCCAAGCAAGGAAACTAGGAAGAAGAGATCACAACAATCATGTTCTAAACCTC
GGAAGAAACAGAAAACCAATAAAAAAGACAAAAGTAAGTACAGTTCTTATATTACTAAATCTGGC
TATTTTATGATCCTTCATTGCGCTGATCTTCTGTGGGAGAACACTTTCAGATGAAAACAGTTGTG
AAGATTTGTCTATCGCTGAAGAAGACATGCACACCAAGGTTCCTGGAGATGCACTTGCATTTGGA
GCTAAAGATGATCCTAGGGATGAACTCTT
Found at i:355838 original size:338 final size:342
Alignment explanation
Indices: 355284--356452 Score: 890
Period size: 339 Copynumber: 3.5 Consensus size: 342
355274 ATTCTGAAGC
*
355284 CAGTCAAGTTGCATCTAAAGGTTGCTTGGTACC--AATTGAAGCTGATGGTGATTTTGGCAATTG
1 CAGTCAAGTTGCATCAAAAGGTTGCTTGGTACCAAAATTGAAGCTGA---TGATTTTGGC-A-TG
** * * *
355347 TTCTGCT-GAAAAGCATAGTCCTGCTGCCCAACTTACTACAATAGTG-TATCAAGAAAATCAAGG
61 TTCTGCTGGAAATTC-TAGTCCTGCTGCCCAACTCACTACCATAG-GATATCAAGAAAATCAAGA
* *
355410 GGAAGTCAATCCTAGTAAGTATATCTGCTATG--TCCTTTAAAGCTGACAATACTAGATACAACA
124 GGAAGTCAATCCTAGTAAGTATATCTGCAATGCCTCCTTTAAACCTGACAATACTAGATACAACA
* * *
355473 CGAACAAAATATGAAAAATAAAACTAACAAT-AGGATACAAAACACAATGA-GACAAGAAAAATA
189 CGAACAAAATATGAAAAATAAAACTAACAATAAGG-TACAAAACACAA-CACAACAAGAAAAAGA
* ** * *
355536 AGCACGGGCATGATTCAAATACATTAATATGTCAAAA-TCTGTATTGCTTA-G-TA-TA-TTTGT
252 AGCACGAGCATGATTCAAATACACGAACATGTCAAAATTCT-TATTGATTACGATATTATTTTGT
*
355596 -CG-ATATTAAGCTGACGCTGCTAAAGG
316 CCGAATATTAAGCTGACGATGCTAAA-G
* *
355622 CAGTCAAGTTGCATCCAAAGGTTGCTTGGTACCGAAAATTGAAGCTGATGATTTTGGC-GGTTCT
1 CAGTCAAGTTGCATCAAAAGGTTGCTTGGTACC-AAAATTGAAGCTGATGATTTTGGCATGTTCT
** * * *
355686 GCTGGAAATTCTACCCCTGCTGCCCAAGTCACCACCATAGGATATCAAGAAAATCAAGAGGAAAT
65 GCTGGAAATTCTAGTCCTGCTGCCCAACTCACTACCATAGGATATCAAGAAAATCAAGAGGAAGT
* *
355751 CAGTCCTAGTAAGTACATCTGCAATGACCTCACTTTAAACCTGACAATACTAGATACAACA-G-A
130 CAATCCTAGTAAGTATATCTGCAATG-CCTC-CTTTAAACCTGACAATACTAGATACAACACGAA
* * * * * *
355814 GAATATTTAGAAAAA-AATAACTAACAATAAGGTGCAAAACTCAACACAACAAGAAAAAGAAGCT
193 CAAAATAT-GAAAAATAA-AACTAACAATAAGGTACAAAACACAACACAACAAGAAAAAGAAGCA
* * *
355878 TGAGCATGATTCAAATATACGAACATGTCAAAATTCTTATTGATTACGATATTATTTTTTCCGAT
256 CGAGCATGATTCAAATACACGAACATGTCAAAATTCTTATTGATTACGATATTATTTTGTCCGA-
* **
355943 ATATTCAGCTGATTATGCTAAAG
320 ATATTAAGCTGACGATGCTAAAG
* * *
355966 C---C-AG-T-CA--AAAAGGTCGCTTGGTACCAAAAATTGAAGATGGTGATTTTGGCAATTGTT
1 CAGTCAAGTTGCATCAAAAGGTTGCTTGGTACC-AAAATTGAAGCTGATGATTTTGGC-A-TGTT
* * * * ** *
356023 CTGCTGGAAATTCTAGTCCTACTGCCCAACTCACTGCCACAGGATACCAAGAAAATCGGGAGCAA
63 CTGCTGGAAATTCTAGTCCTGCTGCCCAACTCACTACCATAGGATATCAAGAAAATCAAGAGGAA
* * * ***
356088 GTCAATCCTAGTAAGTATATCTGCAATTTCCTCTCTTTAAATCTTG-CAATATTAGAT--GTGAC
128 GTCAATCCTAGTAAGTATATCTGCAA-TGCCTC-CTTTAAA-CCTGACAATACTAGATACAACAC
* * * * * * * *
356150 GTATATAA-A--ACAAAT--AACAAACAACAAGATAC---A-A-AACACGACAAGAAAAAGAAGC
190 GAACAAAATATGAAAAATAAAACTAACAATAAGGTACAAAACACAACACAACAAGAAAAAGAAGC
* * * *
356205 ACAAACACT-ATTCAAATACACAAACATGT-AAAATTCTTTATTGATT-CG-TA-TA-TTTCT-C
255 ACGAGCA-TGATTCAAATACACGAACATGTCAAAATTC-TTATTGATTACGATATTATTTTGTCC
* * ** * **
356263 AAATTATTCAGCTGTTGATGATGGAG
318 GAA-TATTAAGCTGACGATGCTAAAG
* * * *
356289 CCAGTCAAGTTTCATCTAAAGATTGCTTGGTACCAAAAATTGAAGCT-ACTGCTGTTATTGGCA-
1 -CAGTCAAGTTGCATCAAAAGGTTGCTTGGTACC-AAAATTGAAGCTGA-TG--ATT-TTGGCAT
* * * * * * *
356352 ATTGTGCTGTAAATTCTA-TACCTGCTGCCCAATTCACTGCCATAGGATATCAAGAAACTGAAGA
60 GTTCTGCTGGAAATTCTAGT-CCTGCTGCCCAACTCACTACCATAGGATATCAAGAAAATCAAGA
* * * *
356416 GGAAGTCAAACGTAGTAAGTTTATCTCCAATGTCCTC
124 GGAAGTCAATCCTAGTAAGTATATCTGCAATG-CCTC
356453 AAAACACAAT
Statistics
Matches: 673, Mismatches: 111, Indels: 100
0.76 0.13 0.11
Matches are distributed among these distances:
322 1 0.00
323 19 0.03
324 5 0.01
325 2 0.00
326 2 0.00
327 10 0.01
328 52 0.08
329 2 0.00
330 3 0.00
331 2 0.00
332 109 0.16
333 13 0.02
334 4 0.01
335 84 0.12
336 43 0.06
337 10 0.01
338 123 0.18
339 140 0.21
340 8 0.01
341 15 0.02
342 4 0.01
343 2 0.00
344 2 0.00
345 18 0.03
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.27
Consensus pattern (342 bp):
CAGTCAAGTTGCATCAAAAGGTTGCTTGGTACCAAAATTGAAGCTGATGATTTTGGCATGTTCTG
CTGGAAATTCTAGTCCTGCTGCCCAACTCACTACCATAGGATATCAAGAAAATCAAGAGGAAGTC
AATCCTAGTAAGTATATCTGCAATGCCTCCTTTAAACCTGACAATACTAGATACAACACGAACAA
AATATGAAAAATAAAACTAACAATAAGGTACAAAACACAACACAACAAGAAAAAGAAGCACGAGC
ATGATTCAAATACACGAACATGTCAAAATTCTTATTGATTACGATATTATTTTGTCCGAATATTA
AGCTGACGATGCTAAAG
Found at i:356036 original size:339 final size:337
Alignment explanation
Indices: 355101--356452 Score: 878
Period size: 338 Copynumber: 4.0 Consensus size: 337
355091 TTTCTACAGT
* * * **
355101 CCTCACTTTAAACCTGACAATACTAGATACAACATGAACAAGATATTAAAAA-AATAACCGAC--
1 CCTC-CTTTAAACCTGACAATACTAGATACAACACGAACAAAATATGAAAAATAA-AACTAACAA
* * ** * *
355163 TA-GAAATAAAACACAATGC-AATTAGAAAAAAGAAGCACAAGCATGATTCAAATTA-ACAAACA
64 TAGGATACAAAACACAAT-CAAACAAG-AAAAAGAAGCACGAGCATGATTCAAA-TACACGAACA
* * * * * * * * * * *
355225 TATTAAATTGTGTATTGATTAGTA-ACTTT-TCTTTTATATTCAGCTAATGATTCTGAAGCCAGT
126 TGTCAAAATCTGTATTGATTAGTATA-TTTGTC---GATATTAAGCTGACGATGCTAAAGGCA--
* *
355288 CAAGTTGCATCTAAAGGTTGCTTGGTACC---AATTGAAGCTGATGGTGATTTTGGCAATTGTTC
185 CAAGTTGCA-CAAAAGGTCGCTTGGTACCAAAAATTGAA---GATGGTGATTTTGGCAATTGTTC
** * * *
355350 TGCT-GAAAAGCATAGTCCTGCTGCCCAACTTACTACAATAGTG-TATCAAGAAAATCAAGGGGA
246 TGCTGGAAATTC-TAGTCCTGCTGCCCAACTCACTACCATAG-GATATCAAGAAAATCAAGAGGA
*
355413 AGTCAATCCTAGTAAGTATATCTGCTATG
309 AGTCAATCCTAGTAAGTATATCTGCAATG
*
355442 --TCCTTTAAAGCTGACAATACTAGATACAACACGAACAAAATATGAAAAATAAAACTAACAATA
1 CCTCCTTTAAACCTGACAATACTAGATACAACACGAACAAAATATGAAAAATAAAACTAACAATA
* * * * ** *
355505 GGATACAAAACACAATGAGACAAGAAAAATAAGCACGGGCATGATTCAAATACATTAATATGTCA
66 GGATACAAAACACAATCAAACAAGAAAAAGAAGCACGAGCATGATTCAAATACACGAACATGTCA
* *
355570 AAATCTGTATTGCTTAGTATATTTGTCGATATTAAGCTGACGCTGCTAAAGGCAGTCAAGTTGCA
131 AAATCTGTATTGATTAGTATATTTGTCGATATTAAGCTGACGATGCTAAAGGCA--CAAGTTGCA
* * * * * *
355635 TCCAAAGGTTGCTTGGTACCGAAAATTGAAGCTGATGATTTTGGC---GGTTCTGCTGGAAATTC
194 -CAAAAGGTCGCTTGGTACCAAAAATTGAAGATGGTGATTTTGGCAATTGTTCTGCTGGAAATTC
** * * * *
355697 TACCCCTGCTGCCCAAGTCACCACCATAGGATATCAAGAAAATCAAGAGGAAATCAGTCCTAGTA
258 TAGTCCTGCTGCCCAACTCACTACCATAGGATATCAAGAAAATCAAGAGGAAGTCAATCCTAGTA
*
355762 AGTACATCTGCAATG
323 AGTATATCTGCAATG
* * *
355777 ACCTCACTTTAAACCTGACAATACTAGATACAACA-G-AGAATATTTAGAAAAA-AATAACTAAC
1 -CCTC-CTTTAAACCTGACAATACTAGATACAACACGAACAAAATAT-GAAAAATAA-AACTAAC
* * ** *
355839 AATAAGG-TGCAAAACTCAA-CACAACAAGAAAAAGAAGCTTGAGCATGATTCAAATATACGAAC
62 AAT-AGGATACAAAACACAATCA-AACAAGAAAAAGAAGCACGAGCATGATTCAAATACACGAAC
* * **
355902 ATGTCAAAATTCT-TATTGATTACGATATTATTTTTTCCGATATATTCAGCTGATTATGCTAAA-
125 ATGTCAAAA-TCTGTATTGATTA-G-TA-TA-TTTGT-CG--ATATTAAGCTGACGATGCTAAAG
355965 GC-C-AG-T-CA-AAAAGGTCGCTTGGTACCAAAAATTGAAGATGGTGATTTTGGCAATTGTTCT
182 GCACAAGTTGCACAAAAGGTCGCTTGGTACCAAAAATTGAAGATGGTGATTTTGGCAATTGTTCT
* * * * ** *
356025 GCTGGAAATTCTAGTCCTACTGCCCAACTCACTGCCACAGGATACCAAGAAAATCGGGAGCAAGT
247 GCTGGAAATTCTAGTCCTGCTGCCCAACTCACTACCATAGGATATCAAGAAAATCAAGAGGAAGT
*
356090 CAATCCTAGTAAGTATATCTGCAATTT
312 CAATCCTAGTAAGTATATCTGCAA-TG
* * *** * * * * *
356117 CCTCTCTTTAAATCTTG-CAATATTAGAT--GTGACGTATATAA-A--ACAAAT--AACAAACAA
1 CCTC-CTTTAAA-CCTGACAATACTAGATACAACACGAACAAAATATGAAAAATAAAACTAACAA
* * * * * *
356174 CAAGATAC-AAA-AC-A-C-GACAAGAAAAAGAAGCACAAACACT-ATTCAAATACACAAACATG
64 TAGGATACAAAACACAATCAAACAAGAAAAAGAAGCACGAGCA-TGATTCAAATACACGAACATG
* * * * * ** * ** *
356233 T-AAAATTCTTTATTGATTCGTATATTTCTCAAATTATTCAGCTGTTGATGATGGAGCCAGTCAA
128 TCAAAA-TCTGTATTGATTAGTATATTTGTC-GA-TATTAAGCTGACGATGCTAAAGGCA--CAA
* * * * *
356297 GTTTCATCTAAAGATTGCTTGGTACCAAAAATTGAAGCTACTGCTG-TTATTGGCAATTG---TG
188 GTTGCA-CAAAAGGTCGCTTGGTACCAAAAATTGAAG--A-TGGTGATT-TTGGCAATTGTTCTG
* * * * *
356358 CTGTAAATTCTA-TACCTGCTGCCCAATTCACTGCCATAGGATATCAAGAAACTGAAGAGGAAGT
248 CTGGAAATTCTAGT-CCTGCTGCCCAACTCACTACCATAGGATATCAAGAAAATCAAGAGGAAGT
* * * *
356422 CAAACGTAGTAAGTTTATCTCCAATG
312 CAATCCTAGTAAGTATATCTGCAATG
356448 TCCTC
1 -CCTC
356453 AAAACACAAT
Statistics
Matches: 812, Mismatches: 142, Indels: 123
0.75 0.13 0.11
Matches are distributed among these distances:
322 1 0.00
323 17 0.02
324 5 0.01
325 2 0.00
326 2 0.00
327 10 0.01
328 46 0.06
329 2 0.00
330 4 0.00
331 3 0.00
332 109 0.13
333 10 0.01
334 4 0.00
335 93 0.11
336 43 0.05
337 10 0.01
338 191 0.24
339 146 0.18
340 59 0.07
341 29 0.04
342 4 0.00
343 2 0.00
344 2 0.00
345 18 0.02
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.27
Consensus pattern (337 bp):
CCTCCTTTAAACCTGACAATACTAGATACAACACGAACAAAATATGAAAAATAAAACTAACAATA
GGATACAAAACACAATCAAACAAGAAAAAGAAGCACGAGCATGATTCAAATACACGAACATGTCA
AAATCTGTATTGATTAGTATATTTGTCGATATTAAGCTGACGATGCTAAAGGCACAAGTTGCACA
AAAGGTCGCTTGGTACCAAAAATTGAAGATGGTGATTTTGGCAATTGTTCTGCTGGAAATTCTAG
TCCTGCTGCCCAACTCACTACCATAGGATATCAAGAAAATCAAGAGGAAGTCAATCCTAGTAAGT
ATATCTGCAATG
Found at i:368294 original size:19 final size:19
Alignment explanation
Indices: 368270--368311 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
368260 CTATGAGTTG
368270 CATTCGATCATTTTCATTA
1 CATTCGATCATTTTCATTA
* *
368289 CATTCGATTATTTTTATTA
1 CATTCGATCATTTTCATTA
368308 CATT
1 CATT
368312 TTTATTTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.26, C:0.17, G:0.05, T:0.52
Consensus pattern (19 bp):
CATTCGATCATTTTCATTA
Found at i:369642 original size:21 final size:23
Alignment explanation
Indices: 369618--369662 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
369608 CTGAACACAA
369618 AAAT-AACTTTTAAGAAAA-AAT
1 AAATAAACTTTTAAGAAAAGAAT
* *
369639 AAATAAAGTTTTAATAAAAGAAT
1 AAATAAACTTTTAAGAAAAGAAT
369662 A
1 A
369663 TTTAAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 4 0.20
22 12 0.60
23 4 0.20
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29
Consensus pattern (23 bp):
AAATAAACTTTTAAGAAAAGAAT
Found at i:371661 original size:19 final size:19
Alignment explanation
Indices: 371637--371680 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
371627 AGCCCAAACT
371637 ATTTAAAACCCAATTAATA
1 ATTTAAAACCCAATTAATA
*
371656 ATTTAAAATCCAATTAATA
1 ATTTAAAACCCAATTAATA
371675 ATTTAA
1 ATTTAA
371681 GATCTAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.36
Consensus pattern (19 bp):
ATTTAAAACCCAATTAATA
Found at i:371938 original size:29 final size:31
Alignment explanation
Indices: 371883--371941 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 31
371873 ATATTTTCGA
*
371883 AAAAAAAAATTCGGTTCGATTAACGGTTAAAG
1 AAAAAAAAATTCGGTTCAATT-ACGGTTAAAG
371915 AAAAAAAAATTCGGTT-AATT-CGGTTAA
1 AAAAAAAAATTCGGTTCAATTACGGTTAA
371942 TGGTAGTTCG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 7 0.27
31 3 0.12
32 16 0.62
ACGTcount: A:0.47, C:0.08, G:0.17, T:0.27
Consensus pattern (31 bp):
AAAAAAAAATTCGGTTCAATTACGGTTAAAG
Found at i:372047 original size:2 final size:2
Alignment explanation
Indices: 372040--372066 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
372030 TTAATTTTTA
372040 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
372067 ATACCTAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:374132 original size:20 final size:20
Alignment explanation
Indices: 374088--374535 Score: 494
Period size: 20 Copynumber: 22.2 Consensus size: 20
374078 AATGACCAAC
*
374088 AAAATCGCAACGCGA--AATA
1 AAAATCGCAACGCGATTAA-G
*
374107 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTAAG
* *
374127 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTAAG
*
374147 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TAAG
***
374167 AAAATCGCAACGCGATATTCC
1 AAAATCGCAACGCGAT-TAAG
*
374188 AAGAATCGCAATGCGATTAAG
1 AA-AATCGCAACGCGATTAAG
* ***
374209 AGAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TAAG
374230 AAGAATCGCAACGCGATTAAG
1 AA-AATCGCAACGCGATTAAG
*
374251 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTAAG
374271 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
374291 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
374311 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
374333 --AATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
*
374353 --AATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTAAG
374371 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
374391 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
374413 --AATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
374431 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
374453 --AATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
374471 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
374493 --AATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
374511 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
374531 AAAAT
1 AAAAT
374536 GAGTAAATTC
Statistics
Matches: 376, Mismatches: 26, Indels: 53
0.83 0.06 0.12
Matches are distributed among these distances:
18 12 0.03
19 15 0.04
20 295 0.78
21 14 0.04
22 40 0.11
ACGTcount: A:0.42, C:0.23, G:0.20, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACGCGATTAAG
Found at i:374642 original size:6 final size:6
Alignment explanation
Indices: 374631--374657 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
374621 GACACGTATT
374631 ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
374658 CGAGACGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:375174 original size:6 final size:6
Alignment explanation
Indices: 375163--375309 Score: 294
Period size: 6 Copynumber: 24.5 Consensus size: 6
375153 TCTCGTCTCG
375163 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
375211 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
375259 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
375307 GGT
1 GGT
375310 AATACGTGTC
Statistics
Matches: 141, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 141 1.00
ACGTcount: A:0.00, C:0.16, G:0.50, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:375430 original size:20 final size:20
Alignment explanation
Indices: 375405--375658 Score: 203
Period size: 20 Copynumber: 12.2 Consensus size: 20
375395 GAATTTACTC
375405 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
375425 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
*
375445 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
*
375465 ATTGCGATTCTTGGAATCGCATTGCG
1 ATT----TTCTT--AATCGCGTTGCG
*
375491 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
***
375511 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTTA-ATCGCGTTGCG
* *
375533 ATTCTCTTAATCGCATTGCG
1 ATTTTCTTAATCGCGTTGCG
***
375553 ATTCTTGGAATATCGCGTTGCG
1 ATT-TTCTTA-ATCGCGTTGCG
*
375575 ATTTTCTT--TTGACCGTTGCG
1 ATTTTCTTAATCG--CGTTGCG
* *
375595 ATTTTCTT-TTCAACGTTGCG
1 ATTTTCTTAATC-GCGTTGCG
*
375615 ATTTTCTAAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
*
375635 A-TTT-TTATTTCGCGTTGCG
1 ATTTTCTTA-ATCGCGTTGCG
375654 ATTTT
1 ATTTT
375659 GTTGGTCATT
Statistics
Matches: 188, Mismatches: 29, Indels: 34
0.75 0.12 0.14
Matches are distributed among these distances:
18 4 0.02
19 14 0.07
20 109 0.58
21 12 0.06
22 31 0.16
24 4 0.02
26 14 0.07
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.43
Consensus pattern (20 bp):
ATTTTCTTAATCGCGTTGCG
Found at i:375460 original size:40 final size:42
Alignment explanation
Indices: 375405--375658 Score: 208
Period size: 42 Copynumber: 6.1 Consensus size: 42
375395 GAATTTACTC
*
375405 ATTTTCTTAATCGCGTTGCGATT-TTCTTA-ATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTCTTATATCGCGTTGCG
*
375445 ATTTTCTGAATCGCGTTGCGATTGCGATTCTTGGA-ATCGCATTGCG
1 ATTTTCTGAATCGCGTTGCGATT-C--TTCTT--ATATCGCGTTGCG
*** *
375491 ATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTCTTATATCGCGTTGCG
* * * ***
375533 ATTCTCTTAATCGCATTGCGATTCTTGGAATATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTCTTATATCGCGTTGCG
*
375575 ATTTTCTTTTG-A-C-CGTTGCGATT-TTCTT-T-TCAACGTTGCG
1 ATTTTC---TGAATCGCGTTGCGATTCTTCTTATATC-GCGTTGCG
* *
375615 ATTTTCTAAATCGCGTTGCGA-T-TT-TTATTTCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTCTTATATCGCGTTGCG
375654 ATTTT
1 ATTTT
375659 GTTGGTCATT
Statistics
Matches: 179, Mismatches: 19, Indels: 33
0.77 0.08 0.14
Matches are distributed among these distances:
37 1 0.01
38 3 0.02
39 19 0.11
40 46 0.26
41 3 0.02
42 62 0.35
43 3 0.02
44 6 0.03
45 2 0.01
46 34 0.19
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.43
Consensus pattern (42 bp):
ATTTTCTGAATCGCGTTGCGATTCTTCTTATATCGCGTTGCG
Found at i:377408 original size:13 final size:13
Alignment explanation
Indices: 377390--377438 Score: 71
Period size: 13 Copynumber: 3.8 Consensus size: 13
377380 TCATAACCCG
377390 ACCCGACCCGTTT
1 ACCCGACCCGTTT
377403 ACCCGACCCGTTT
1 ACCCGACCCGTTT
** *
377416 ACCCGACCAATTG
1 ACCCGACCCGTTT
377429 ACCCGACCCG
1 ACCCGACCCG
377439 ACCCGTTGAC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.20, C:0.47, G:0.16, T:0.16
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:377439 original size:18 final size:18
Alignment explanation
Indices: 377416--377451 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
377406 CGACCCGTTT
377416 ACCCGACCAATTGACCCG
1 ACCCGACCAATTGACCCG
**
377434 ACCCGACCCGTTGACCCG
1 ACCCGACCAATTGACCCG
377452 TTGACCGTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.47, G:0.19, T:0.11
Consensus pattern (18 bp):
ACCCGACCAATTGACCCG
Found at i:377449 original size:8 final size:8
Alignment explanation
Indices: 377438--377484 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 8
377428 GACCCGACCC
377438 GACCCGTT
1 GACCCGTT
377446 GACCCGTT
1 GACCCGTT
377454 GA-CCGTT
1 GACCCGTT
377461 GACCCACGTT
1 GA-CC-CGTT
377471 GACCACTGTT
1 GACC-C-GTT
377481 GACC
1 GACC
377485 AAAACTTTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
7 7 0.20
8 10 0.29
9 5 0.14
10 13 0.37
ACGTcount: A:0.17, C:0.36, G:0.23, T:0.23
Consensus pattern (8 bp):
GACCCGTT
Found at i:390006 original size:42 final size:42
Alignment explanation
Indices: 389966--390098 Score: 207
Period size: 42 Copynumber: 3.2 Consensus size: 42
389956 ACACTTCATA
*
389966 CCTTTTACTTGGGGC-A-TCTACTGGTGTTTTTAACCTTTCATC
1 CCTTTTACTT-GGGCTATTC-ACTGGTGTTTTTAACCTTTCAAC
* *
390008 ACTTTTACTTGGGCTATTCACAGGTGTTTTTAACCTTTCAAC
1 CCTTTTACTTGGGCTATTCACTGGTGTTTTTAACCTTTCAAC
390050 CCTTTTACTTGGGCTATTCACTGGTGTTTTTAACCTTTCAAC
1 CCTTTTACTTGGGCTATTCACTGGTGTTTTTAACCTTTCAAC
390092 CCTTTTA
1 CCTTTTA
390099 GATGGTGAAA
Statistics
Matches: 84, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
41 4 0.05
42 78 0.93
43 2 0.02
ACGTcount: A:0.17, C:0.23, G:0.14, T:0.45
Consensus pattern (42 bp):
CCTTTTACTTGGGCTATTCACTGGTGTTTTTAACCTTTCAAC
Found at i:393068 original size:2 final size:2
Alignment explanation
Indices: 393063--393095 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
393053 ATGTTTAAAT
393063 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
393096 TATTTTAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:397485 original size:24 final size:24
Alignment explanation
Indices: 397453--397508 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
397443 TCCTGCTGTT
397453 TCAATTGACATAAACAAATGAGCA
1 TCAATTGACATAAACAAATGAGCA
397477 TCAATTGACATAAACAAATGAGCA
1 TCAATTGACATAAACAAATGAGCA
397501 TCAATTGA
1 TCAATTGA
397509 AGTAAGATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.48, C:0.16, G:0.12, T:0.23
Consensus pattern (24 bp):
TCAATTGACATAAACAAATGAGCA
Found at i:401065 original size:19 final size:19
Alignment explanation
Indices: 401041--401080 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
401031 TTGTGGGTCA
401041 AGGTAGTATTTCTAGTTTT
1 AGGTAGTATTTCTAGTTTT
401060 AGGTAGTATTTCTAGTTTT
1 AGGTAGTATTTCTAGTTTT
401079 AG
1 AG
401081 TCATGAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.23, C:0.05, G:0.23, T:0.50
Consensus pattern (19 bp):
AGGTAGTATTTCTAGTTTT
Found at i:419267 original size:18 final size:19
Alignment explanation
Indices: 419230--419266 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
419220 TTTTTTTATA
*
419230 TGGGGGAATCGGTTCCCCC
1 TGGGGGAATCGATTCCCCC
*
419249 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
419267 TCTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.11, C:0.30, G:0.35, T:0.24
Consensus pattern (19 bp):
TGGGGGAATCGATTCCCCC
Found at i:419317 original size:21 final size:21
Alignment explanation
Indices: 419293--419335 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
419283 TTCATATTCG
* *
419293 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
419314 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
419335 T
1 T
419336 AGCCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:422719 original size:5 final size:5
Alignment explanation
Indices: 422709--422734 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
422699 TTTATTTTGT
422709 TCGGG TCGGG TCGGG TCGGG TCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG T
422735 TTTTAAAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.58, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:422762 original size:27 final size:28
Alignment explanation
Indices: 422724--422789 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
422714 TCGGGTCGGG
422724 TCGGGTCGGG-TTTTTAAAGTGTGATAT
1 TCGGGTCGGGTTTTTTAAAGTGTGATAT
* *
422751 TCGGGTCTGGTTTTTTTAAGTGTGATAT
1 TCGGGTCGGGTTTTTTAAAGTGTGATAT
422779 TCGGGTCGGGT
1 TCGGGTCGGGT
422790 CGGGTTAGGG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
27 9 0.26
28 26 0.74
ACGTcount: A:0.14, C:0.09, G:0.35, T:0.42
Consensus pattern (28 bp):
TCGGGTCGGGTTTTTTAAAGTGTGATAT
Found at i:434170 original size:18 final size:20
Alignment explanation
Indices: 434130--434172 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
434120 TTTTTTATTC
* *
434130 CTTTTTTTTTTACACTTATT
1 CTTTTTCTTTTACACTTACT
434150 CTTTTTCTTTT-CA-TTACT
1 CTTTTTCTTTTACACTTACT
434168 CTTTT
1 CTTTT
434173 ATAAAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 9 0.43
19 2 0.10
20 10 0.48
ACGTcount: A:0.12, C:0.19, G:0.00, T:0.70
Consensus pattern (20 bp):
CTTTTTCTTTTACACTTACT
Found at i:438868 original size:107 final size:108
Alignment explanation
Indices: 438681--438885 Score: 394
Period size: 107 Copynumber: 1.9 Consensus size: 108
438671 GTGTGGCCGA
438681 TGCCACGTGGGAACGGTGGTCCATGCAGACATCAAAGAGTTTAAAAGTAACACGTGTTAGATAAA
1 TGCCACGTGGGAACGGTGGTCCATGCAGACATCAAAGAGTTTAAAAGTAACACGTGTTAGATAAA
*
438746 GAGAGGTGACAGGCTGTTTATTAAGACGCATATGTGATTTCGG
66 GAGAGGTGACAGGCTGTTTATCAAGACGCATATGTGATTTCGG
438789 TGCCACGTGGGAACGGTGGTCCATGC-GACATCAAAGAGTTTAAAAGTAACACGTGTTAGATAAA
1 TGCCACGTGGGAACGGTGGTCCATGCAGACATCAAAGAGTTTAAAAGTAACACGTGTTAGATAAA
438853 GAGAGGTGACAGGCTGTTTATCAAGACGCATAT
66 GAGAGGTGACAGGCTGTTTATCAAGACGCATAT
438886 AAAATTTAAA
Statistics
Matches: 96, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
107 70 0.73
108 26 0.27
ACGTcount: A:0.32, C:0.16, G:0.28, T:0.24
Consensus pattern (108 bp):
TGCCACGTGGGAACGGTGGTCCATGCAGACATCAAAGAGTTTAAAAGTAACACGTGTTAGATAAA
GAGAGGTGACAGGCTGTTTATCAAGACGCATATGTGATTTCGG
Found at i:439491 original size:20 final size:21
Alignment explanation
Indices: 439481--439668 Score: 217
Period size: 20 Copynumber: 9.2 Consensus size: 21
439471 ATTCTGACTA
* **
439481 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTACGTAAT
* * *
439502 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGTAAT
439523 TCGCATTGCGATTTACGTAA-
1 TCGCATTGCGATTTACGTAAT
439543 TCGCATTGCGATTTACGT-AT
1 TCGCATTGCGATTTACGTAAT
* *
439563 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGTAAT
439584 TCGCATTGCGATTTACGTAA-
1 TCGCATTGCGATTTACGTAAT
439604 TCGCATTGCGATTTACGT-AT
1 TCGCATTGCGATTTACGTAAT
* * *
439624 TTGTATTGCGATTTATGT-AT
1 TCGCATTGCGATTTACGTAAT
* *
439644 TCGTATTGCGATTTA-GTAAA
1 TCGCATTGCGATTTACGTAAT
439664 TCGCA
1 TCGCA
439669 ACGAGATTCT
Statistics
Matches: 147, Mismatches: 16, Indels: 9
0.85 0.09 0.05
Matches are distributed among these distances:
19 4 0.03
20 88 0.60
21 55 0.37
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTACGTAAT
Found at i:439510 original size:21 final size:21
Alignment explanation
Indices: 439481--439617 Score: 172
Period size: 21 Copynumber: 6.7 Consensus size: 21
439471 ATTCTGACTA
* *
439481 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTTCCTAAT
*
439502 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCTAAT
* *
439523 TCGCATTGCGATTTACGTAA-
1 TCGCATTGCGATTTTCCTAAT
* *
439543 TCGCATTGCGATTTACGT-AT
1 TCGCATTGCGATTTTCCTAAT
439563 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCTAAT
* *
439584 TCGCATTGCGATTTACGTAA-
1 TCGCATTGCGATTTTCCTAAT
439604 TCGCATTGCGATTT
1 TCGCATTGCGATTT
439618 ACGTATTTGT
Statistics
Matches: 104, Mismatches: 10, Indels: 5
0.87 0.08 0.04
Matches are distributed among these distances:
19 1 0.01
20 48 0.46
21 55 0.53
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.39
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCTAAT
Found at i:439589 original size:61 final size:61
Alignment explanation
Indices: 439480--439668 Score: 258
Period size: 61 Copynumber: 3.1 Consensus size: 61
439470 GATTCTGACT
* ** *
439480 ATCGCATTGCGATTTCCCAAATTCGCGTTGCGATTTTCCTAATTCGCATTGCGATTTACGTA
1 ATCGCATTGCGATTT-ACGTATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGTA
439542 ATCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGTA
1 ATCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGTA
* * * *
439603 ATCGCATTGCGATTTACGTATTTGTATTGCGATTTAT-GT-ATTCGTATTGCGATTTA-GTAA
1 ATCGCATTGCGATTTACGTATTCGCATTGCGATTT-TCCTAATTCGCATTGCGATTTACGT-A
439663 ATCGCA
1 ATCGCA
439669 ACGAGATTCT
Statistics
Matches: 117, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
59 2 0.02
60 23 0.20
61 76 0.65
62 16 0.14
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.40
Consensus pattern (61 bp):
ATCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGTA
Found at i:440576 original size:24 final size:24
Alignment explanation
Indices: 440516--440583 Score: 91
Period size: 24 Copynumber: 2.8 Consensus size: 24
440506 GTGAGTACTA
* *
440516 GTCAATATTCGAAATTTGATCTTG
1 GTCAATACTCGGAATTTGATCTTG
* *
440540 GTCAATACCCGGACTTTGATCTTG
1 GTCAATACTCGGAATTTGATCTTG
*
440564 GTCAATACTCGGATTTTGAT
1 GTCAATACTCGGAATTTGAT
440584 GATTTTTCAG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (24 bp):
GTCAATACTCGGAATTTGATCTTG
Found at i:442500 original size:20 final size:19
Alignment explanation
Indices: 442472--442515 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
442462 CAATCATCTT
* *
442472 AATGTCTATTGCAACGCGGA
1 AATGACTATCGCAACGC-GA
*
442492 AATGACTATCGCAATGCGA
1 AATGACTATCGCAACGCGA
442511 AATGA
1 AATGA
442516 AAATCACAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (19 bp):
AATGACTATCGCAACGCGA
Found at i:442544 original size:33 final size:33
Alignment explanation
Indices: 442499--442610 Score: 172
Period size: 33 Copynumber: 3.4 Consensus size: 33
442489 GGAAATGACT
442499 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
*
442532 ATTGCAATGCGAAATGAAAATCGA-AACGAGAGA
1 ATCGCAATGCGAAATGAAAATC-ACAACGAGAGA
* *
442565 ATCGCAATGCGAAATGAAAATCGCAACGGGAGA
1 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
*
442598 ATCGCAACGCGAA
1 ATCGCAATGCGAA
442611 TTTAGTTTCG
Statistics
Matches: 72, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
33 71 0.99
34 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCACAACGAGAGA
Found at i:444721 original size:19 final size:19
Alignment explanation
Indices: 444675--444820 Score: 131
Period size: 19 Copynumber: 7.8 Consensus size: 19
444665 TCTGGAACTT
*
444675 AAAATCGCAACGTGAAAAATG
1 AAAATCGCAACGCG--AAATG
** * *
444696 ACTATCGCAACGTGAAATT
1 AAAATCGCAACGCGAAATG
* *
444715 AAAATCGTAACGAGAGAATG
1 AAAATCGCAACGCGA-AATG
*
444735 AAAATCGCAACGCGAAACG
1 AAAATCGCAACGCGAAATG
*
444754 AAAATCGCAA--TG--A-G
1 AAAATCGCAACGCGAAATG
*
444768 AGAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
*
444787 AAAATCGCAATGCGAAATG
1 AAAATCGCAACGCGAAATG
444806 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
444821 TTATAGTTTC
Statistics
Matches: 102, Mismatches: 17, Indels: 14
0.77 0.13 0.11
Matches are distributed among these distances:
14 10 0.10
15 1 0.01
16 1 0.01
17 1 0.01
18 1 0.01
19 60 0.59
20 16 0.16
21 12 0.12
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:444855 original size:20 final size:20
Alignment explanation
Indices: 444826--444863 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
444816 CGCGATTATA
* *
444826 GTTTCGCGTTGCGATTTTTG
1 GTTTCACGTTACGATTTTTG
444846 GTTTCACGTTACGATTTT
1 GTTTCACGTTACGATTTT
444864 GTCGTTGCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.16, G:0.24, T:0.50
Consensus pattern (20 bp):
GTTTCACGTTACGATTTTTG
Found at i:444890 original size:19 final size:19
Alignment explanation
Indices: 444866--444955 Score: 91
Period size: 19 Copynumber: 4.9 Consensus size: 19
444856 ACGATTTTGT
444866 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
444885 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
* *
444899 CGTTGCGATTTTCGTCTCG
1 CGTTGCGATTTTCATTTCG
*
444918 CGTTGCGATTTTCATTCTCT
1 CGTTGCGATTTTCATT-TCG
*
444938 CGTTGTGATTTTCATTTC
1 CGTTGCGATTTTCATTTC
444956 AACCAAAAGA
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
14 10 0.17
16 3 0.05
17 3 0.05
19 26 0.44
20 17 0.29
ACGTcount: A:0.09, C:0.23, G:0.20, T:0.48
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:444902 original size:33 final size:33
Alignment explanation
Indices: 444832--444927 Score: 120
Period size: 33 Copynumber: 2.9 Consensus size: 33
444822 TATAGTTTCG
* * * * *
444832 CGTTGCGATTTTTGGTTTCACGTTACGATTTTGT
1 CGTTGCGA-TTTTCGTTTCGCGTTGCGATTCTCT
*
444866 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCGTTTCGCGTTGCGATTCTCT
*
444899 CGTTGCGATTTTCGTCTCGCGTTGCGATT
1 CGTTGCGATTTTCGTTTCGCGTTGCGATT
444928 TTCATTCTCT
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
33 46 0.85
34 8 0.15
ACGTcount: A:0.09, C:0.21, G:0.24, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCGTTTCGCGTTGCGATTCTCT
Found at i:445162 original size:94 final size:94
Alignment explanation
Indices: 445046--445513 Score: 779
Period size: 94 Copynumber: 5.1 Consensus size: 94
445036 ATGGATTGCA
* *
445046 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
445110 TTAGCAGAATTGGCAGCAAACGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
445139 TTACTTTCAACCAAAAGATAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
445204 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
445233 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
445298 TTAGCAGAATTGGCAGCAACCGAAGAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* *
445327 TTACTTTCAACCAAAAGTCAAAACAAAGACAAATACTAACTTCAGAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
445392 TTAGCAGAATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* *
445421 TTAC-TTCAACCAAAAGACAACA-AAAGACAAATACTAACTTCACAGTGTT----AATAAACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
445480 TTAGCAGTATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
445509 TTACT
1 TTACT
445514 AAGTAATCTA
Statistics
Matches: 359, Mismatches: 14, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
88 41 0.11
92 26 0.07
93 20 0.06
94 272 0.76
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:447261 original size:19 final size:19
Alignment explanation
Indices: 447197--447309 Score: 110
Period size: 20 Copynumber: 6.1 Consensus size: 19
447187 TCTTTTGGTT
*
447197 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
447216 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
447236 GGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
*
447256 GAAATGAAAATCGTAA---
1 GAAATGAAAATCGCAACGC
* *
447272 -AGA-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
447289 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
447308 GA
1 GA
447310 TTTTGGTTTC
Statistics
Matches: 75, Mismatches: 12, Indels: 14
0.74 0.12 0.14
Matches are distributed among these distances:
14 9 0.12
15 2 0.03
18 2 0.03
19 29 0.39
20 31 0.41
21 2 0.03
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:447353 original size:33 final size:33
Alignment explanation
Indices: 447305--447396 Score: 148
Period size: 33 Copynumber: 2.8 Consensus size: 33
447295 AAAATCGCAA
**
447305 TGCGATTTTGGTTTCGCGTTGCGATTATATCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATATCGT
* *
447338 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATATCGT
447371 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTCATTTCGCGTTGCGATT
447397 TTAAGTTTAA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.11, C:0.20, G:0.24, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTATATCGT
Found at i:447359 original size:19 final size:19
Alignment explanation
Indices: 447335--447398 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 19
447325 GCGATTATAT
447335 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
447354 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
447368 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
447387 CGTTGCGATTTT
1 CGTTGCGATTTT
447399 AAGTTTAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 10 0.26
16 3 0.08
17 3 0.08
19 22 0.58
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:447975 original size:20 final size:20
Alignment explanation
Indices: 447952--448013 Score: 97
Period size: 20 Copynumber: 3.0 Consensus size: 20
447942 CGATAGTCAG
447952 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
447972 ATTCGCATTGCGATTTTCTT
1 ATTCGCATTGCGATTTACGT
447992 AATTCGCATTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGT
448013 A
1 A
448014 ATTGCGTTGC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
20 19 0.51
21 18 0.49
ACGTcount: A:0.21, C:0.19, G:0.18, T:0.42
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:448004 original size:41 final size:41
Alignment explanation
Indices: 447952--448033 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 41
447942 CGATAGTCAG
*
447952 ATTCGCATTGCGATTTACGT-ATTCGCATTGCGATTTTCTTA
1 ATTCGCATTGCGATTTACGTAATT-GCATTGCAATTTTCTTA
*
447993 ATTCGCATTGCGATTTACGTAATTGCGTTGCAATTTTCTTA
1 ATTCGCATTGCGATTTACGTAATTGCATTGCAATTTTCTTA
448034 CGTATTCGCT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
41 35 0.92
42 3 0.08
ACGTcount: A:0.21, C:0.18, G:0.17, T:0.44
Consensus pattern (41 bp):
ATTCGCATTGCGATTTACGTAATTGCATTGCAATTTTCTTA
Found at i:448028 original size:20 final size:21
Alignment explanation
Indices: 447952--448016 Score: 105
Period size: 21 Copynumber: 3.1 Consensus size: 21
447942 CGATAGTCAG
447952 ATTCGCATTGCGATTTACGT-
1 ATTCGCATTGCGATTTACGTA
* *
447972 ATTCGCATTGCGATTTTCTTA
1 ATTCGCATTGCGATTTACGTA
447993 ATTCGCATTGCGATTTACGTA
1 ATTCGCATTGCGATTTACGTA
448014 ATT
1 ATT
448017 GCGTTGCAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 18 0.45
21 22 0.55
ACGTcount: A:0.22, C:0.18, G:0.17, T:0.43
Consensus pattern (21 bp):
ATTCGCATTGCGATTTACGTA
Found at i:448063 original size:21 final size:21
Alignment explanation
Indices: 448046--448112 Score: 107
Period size: 21 Copynumber: 3.2 Consensus size: 21
448036 TATTCGCTTT
448046 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
*
448067 GCGAATTAGGAAAATCACAAC
1 GCGAATTAGGAAAATCGCAAC
* *
448088 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
448109 GCGA
1 GCGA
448113 TAGTCAGAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.16
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:450511 original size:35 final size:35
Alignment explanation
Indices: 450458--450533 Score: 89
Period size: 35 Copynumber: 2.2 Consensus size: 35
450448 TTACATTTAT
* * * *
450458 TAAACTATTATAATATAATCACTACAATCTTATAA
1 TAAATTATCATAAAATAATCACTACAATATTATAA
* * *
450493 TAAATTATCATAAAATAATTATTATAATATTATAA
1 TAAATTATCATAAAATAATCACTACAATATTATAA
450528 TAAATT
1 TAAATT
450534 TTAAAAGTTC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (35 bp):
TAAATTATCATAAAATAATCACTACAATATTATAA
Found at i:451117 original size:14 final size:14
Alignment explanation
Indices: 451098--451126 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
451088 CTAGAAAACT
451098 AAAAATCATTATAA
1 AAAAATCATTATAA
451112 AAAAATCATTATAA
1 AAAAATCATTATAA
451126 A
1 A
451127 CCGACCCTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAAATCATTATAA
Found at i:454667 original size:21 final size:21
Alignment explanation
Indices: 454643--454683 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
454633 TTCAACTTAG
454643 TTTCCAAATTCGCAACGCGAA
1 TTTCCAAATTCGCAACGCGAA
* *
454664 TTTCCAGATTCGCAATGCGA
1 TTTCCAAATTCGCAACGCGA
454684 TTTTGAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (21 bp):
TTTCCAAATTCGCAACGCGAA
Found at i:454762 original size:44 final size:41
Alignment explanation
Indices: 454685--454766 Score: 119
Period size: 44 Copynumber: 1.9 Consensus size: 41
454675 GCAATGCGAT
* *
454685 TTTGAAAAATGTGTTGCGATAGTTAAAATGTGTTGCGAGAG
1 TTTGAAAAATGTGTTGCGATAGTGAAAAAGTGTTGCGAGAG
454726 TTTGAAAAACGTGTTGTTGCGATAGTGAAAAAGTGTTGCGA
1 TTTGAAAAA--TG-TGTTGCGATAGTGAAAAAGTGTTGCGA
454767 TAGTGAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
41 9 0.25
43 2 0.06
44 25 0.69
ACGTcount: A:0.32, C:0.06, G:0.29, T:0.33
Consensus pattern (41 bp):
TTTGAAAAATGTGTTGCGATAGTGAAAAAGTGTTGCGAGAG
Found at i:454776 original size:19 final size:20
Alignment explanation
Indices: 454687--454777 Score: 105
Period size: 19 Copynumber: 4.4 Consensus size: 20
454677 AATGCGATTT
454687 TGAAAAATGTGTTGCGATAG
1 TGAAAAATGTGTTGCGATAG
* *
454707 T-TAAAATGTGTTGCGAGAG
1 TGAAAAATGTGTTGCGATAG
454726 TTTGAAAAACGTGTTGTTGCGATAG
1 --TGAAAAA--TG-TGTTGCGATAG
454751 TGAAAAA-GTGTTGCGATAG
1 TGAAAAATGTGTTGCGATAG
454770 TGAAAAAT
1 TGAAAAAT
454778 CCAAAATAAG
Statistics
Matches: 60, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
19 34 0.57
20 2 0.03
21 1 0.02
22 4 0.07
23 7 0.12
24 2 0.03
25 10 0.17
ACGTcount: A:0.35, C:0.05, G:0.29, T:0.31
Consensus pattern (20 bp):
TGAAAAATGTGTTGCGATAG
Found at i:455236 original size:21 final size:21
Alignment explanation
Indices: 455212--455419 Score: 178
Period size: 21 Copynumber: 10.2 Consensus size: 21
455202 TTGGAAAATT
* *
455212 GCAATGCGAACTTCGACTATC
1 GCAACGCGAACTTGGACTATC
* *
455233 GCAACGTGAACTTGGATTATC
1 GCAACGCGAACTTGGACTATC
* **
455254 GCAA--CGAATTTGGAAAATC
1 GCAACGCGAACTTGGACTATC
*
455273 GCAACGCGAACTTCGACTA-C
1 GCAACGCGAACTTGGACTATC
** **
455293 TGCAA--CGAGTTTGGAAAATC
1 -GCAACGCGAACTTGGACTATC
*
455313 GCAACGCGAACTTCGACTATC
1 GCAACGCGAACTTGGACTATC
*
455334 GCAACGTGAACTTGGACTATC
1 GCAACGCGAACTTGGACTATC
* * **
455355 GCAA--CGAATTTTGAAAATC
1 GCAACGCGAACTTGGACTATC
* *
455374 GCAACGCGAACTTCGATTATC
1 GCAACGCGAACTTGGACTATC
455395 GCAACGCGAACTTGGACTATC
1 GCAACGCGAACTTGGACTATC
455416 GCAA
1 GCAA
455420 AATCGCGTTG
Statistics
Matches: 144, Mismatches: 35, Indels: 16
0.74 0.18 0.08
Matches are distributed among these distances:
19 41 0.28
20 2 0.01
21 101 0.70
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (21 bp):
GCAACGCGAACTTGGACTATC
Found at i:455274 original size:40 final size:40
Alignment explanation
Indices: 455230--455419 Score: 170
Period size: 40 Copynumber: 4.7 Consensus size: 40
455220 AACTTCGACT
* * *
455230 ATCGCAACGTGAACTTGGATTATCGCAACGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAA
*
455270 ATCGCAACGCGAACTTCGACTA-CTGCAACGAGTTTGGAAA
1 ATCGCAACGCGAACTTCGACTATC-GCAACGAATTTGGAAA
* **
455310 ATCGCAACGCGAACTTCGACTATCGCAACGTGAACTTGGACT
1 ATCGCAACGCGAACTTCGACTATCGCAAC--GAATTTGGAAA
* * ** * * **
455352 ATCGCAA--CGAATTTTGAAAATCGCAACGCGAACTTCGATT
1 ATCGCAACGCGAACTTCGACTATCGCAA--CGAATTTGGAAA
*
455392 ATCGCAACGCGAACTTGGACTATCGCAA
1 ATCGCAACGCGAACTTCGACTATCGCAA
455420 AATCGCGTTG
Statistics
Matches: 124, Mismatches: 18, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
39 1 0.01
40 92 0.74
41 1 0.01
42 30 0.24
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (40 bp):
ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAA
Found at i:455335 original size:61 final size:61
Alignment explanation
Indices: 455212--455419 Score: 242
Period size: 61 Copynumber: 3.4 Consensus size: 61
455202 TTGGAAAATT
* * * ** * * **
455212 GCAATGCGAACTTCGACTATCGCAACGTGAACTTGGATTATCGCAA--CGAATTTGGAAAATC
1 GCAACGCGAACTTGGACTATCGCAAC--GAATTTGGAAAATCGCAACGCGAACTTCGACTATC
* *
455273 GCAACGCGAACTTCGACTA-CTGCAACGAGTTTGGAAAATCGCAACGCGAACTTCGACTATC
1 GCAACGCGAACTTGGACTATC-GCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATC
* * *
455334 GCAACGTGAACTTGGACTATCGCAACGAATTTTGAAAATCGCAACGCGAACTTCGATTATC
1 GCAACGCGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATC
455395 GCAACGCGAACTTGGACTATCGCAA
1 GCAACGCGAACTTGGACTATCGCAA
455420 AATCGCGTTG
Statistics
Matches: 128, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
59 14 0.11
60 1 0.01
61 112 0.88
62 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (61 bp):
GCAACGCGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATC
Found at i:455371 original size:101 final size:101
Alignment explanation
Indices: 455195--455389 Score: 345
Period size: 101 Copynumber: 1.9 Consensus size: 101
455185 GGAAAATCGT
* * *
455195 AACGAATTTGGAAAATTGCAATGCGAACTTCGACTATCGCAACGTGAACTTGGATTATCGCAACG
1 AACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGTGAACTTGGACTATCGCAACG
455260 AATTTGGAAAATCGCAACGCGAACTTCGACTACTGC
66 AATTTGGAAAATCGCAACGCGAACTTCGACTACTGC
*
455296 AACGAGTTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGTGAACTTGGACTATCGCAACG
1 AACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGTGAACTTGGACTATCGCAACG
*
455361 AATTTTGAAAATCGCAACGCGAACTTCGA
66 AATTTGGAAAATCGCAACGCGAACTTCGA
455390 TTATCGCAAC
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
101 89 1.00
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.23
Consensus pattern (101 bp):
AACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGTGAACTTGGACTATCGCAACG
AATTTGGAAAATCGCAACGCGAACTTCGACTACTGC
Found at i:457008 original size:15 final size:15
Alignment explanation
Indices: 456988--457021 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
456978 AGTGATGCAG
456988 CTTCATCTTCATCCT
1 CTTCATCTTCATCCT
*
457003 CTTCATCTTCGTCCT
1 CTTCATCTTCATCCT
457018 CTTC
1 CTTC
457022 GCCATCATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.09, C:0.41, G:0.03, T:0.47
Consensus pattern (15 bp):
CTTCATCTTCATCCT
Found at i:458937 original size:12 final size:12
Alignment explanation
Indices: 458922--458955 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
458912 AATGATGAAT
*
458922 ATGAAGATGACG
1 ATGAGGATGACG
458934 ATGAGGATGACG
1 ATGAGGATGACG
458946 ATGAGGATGA
1 ATGAGGATGA
458956 TAATGTGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.38, C:0.06, G:0.38, T:0.18
Consensus pattern (12 bp):
ATGAGGATGACG
Found at i:473548 original size:20 final size:19
Alignment explanation
Indices: 473479--473557 Score: 54
Period size: 23 Copynumber: 3.9 Consensus size: 19
473469 TTTTGGTGCG
*
473479 AGGGAATCGA-TCCCCCCA
1 AGGGAACCGATTCCCCCCA
*
473497 TGAGGGAACCGATTCCCCCTTTGA
1 --AGGGAACCGATTCCCCC---CA
473521 AGGGGAACCGATTCCCCCCA
1 A-GGGAACCGATTCCCCCCA
*
473541 CAGGGAA-CGATACCCCC
1 -AGGGAACCGATTCCCCC
473558 TTGGGGTTCT
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
19 9 0.18
20 15 0.31
21 7 0.14
22 1 0.02
23 16 0.33
24 1 0.02
ACGTcount: A:0.25, C:0.37, G:0.24, T:0.14
Consensus pattern (19 bp):
AGGGAACCGATTCCCCCCA
Found at i:474036 original size:17 final size:18
Alignment explanation
Indices: 474003--474037 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
473993 GAAAACTATA
474003 CATATTTGTTCTCAAAAC
1 CATATTTGTTCTCAAAAC
*
474021 CATATTT-TTTTCAAAAC
1 CATATTTGTTCTCAAAAC
474038 TTTTTCAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.34, C:0.20, G:0.03, T:0.43
Consensus pattern (18 bp):
CATATTTGTTCTCAAAAC
Found at i:477300 original size:23 final size:23
Alignment explanation
Indices: 477247--477349 Score: 75
Period size: 23 Copynumber: 4.5 Consensus size: 23
477237 AGAGTCAAGG
*
477247 TTTCTACGTGGTCATTC-ATGACA
1 TTTCTACGTGGTCCTTCGA-GACA
* *
477270 GTTATACGTGGTCCTTCGAGACA
1 TTTCTACGTGGTCCTTCGAGACA
* *
477293 TTTCTACGCT-GTCCTTTGGGACA
1 TTTCTACG-TGGTCCTTCGAGACA
* ** **
477316 TATCTATTTGGTCCTTCTTGACA
1 TTTCTACGTGGTCCTTCGAGACA
*
477339 TTTCTATGTGG
1 TTTCTACGTGG
477350 CACTTCGGTG
Statistics
Matches: 62, Mismatches: 15, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
22 1 0.02
23 59 0.95
24 2 0.03
ACGTcount: A:0.17, C:0.21, G:0.20, T:0.41
Consensus pattern (23 bp):
TTTCTACGTGGTCCTTCGAGACA
Found at i:482071 original size:18 final size:18
Alignment explanation
Indices: 482027--482073 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
482017 GACCTAATTC
482027 GACCCGTTGACACAACTT
1 GACCCGTTGACACAACTT
* * *
482045 GATCTGTTGACTCGAAC-T
1 GACCCGTTGACAC-AACTT
482063 GACCCGTTGAC
1 GACCCGTTGAC
482074 CGTTAACTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
18 20 0.87
19 3 0.13
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.26
Consensus pattern (18 bp):
GACCCGTTGACACAACTT
Found at i:482841 original size:32 final size:31
Alignment explanation
Indices: 482769--482842 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
482759 CTAATGTGAC
* *
482769 TCTTAGGTAGGCTCTACAGCCTTAAGATCAT
1 TCTTAGGTAGGCCCTACAGCCATAAGATCAT
* * **
482800 TCTTGGGTAGGCCCTACGGCCATAAGATGTGT
1 TCTTAGGTAGGCCCTACAGCCATAAGAT-CAT
482832 TCTTAGGTAGG
1 TCTTAGGTAGG
482843 TCCCGTGACC
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
31 24 0.69
32 11 0.31
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTACAGCCATAAGATCAT
Found at i:489119 original size:127 final size:129
Alignment explanation
Indices: 488864--489120 Score: 308
Period size: 127 Copynumber: 2.0 Consensus size: 129
488854 GACCCGACCT
* * *
488864 GTTGACTGTTTACCAAAAAGTCAATTTTTTCGAAAAGTCATATTATATGTTTTTCAACGTCATGA
1 GTTGACTGTTGACCAAAAAGTCAATTTTTTCGAAAAGACATATTATATATTTTTCAACGTCATGA
* * * **
488929 GTTTGAATTTGAAGTTCGTTTTCCAAATTCGAACCCGAAAGCCTCTAAATCATTAGTCAAACCC
66 GTTTGAATTCGAAGTCCGTTTTCCAAATTCGAACCCGAAAGCCTCCAAATCAGCAGTCAAACCC
** *
488993 GTTGACT-TTGACCAAAAAGTCAAATTTTTT-GAAAAGACAT-TT-TATATTTTTGGACGTCCTG
1 GTTGACTGTTGACCAAAAAGTC-AATTTTTTCGAAAAGACATATTATATATTTTTCAACGTCATG
* * * **
489054 AGTTTG-ATTCCGCAGTCCGTTTTGCCAAATTCGAAGCTGAAAGCCTCCAAATTGGCAGTCAAAC
65 AGTTTGAATT-CGAAGTCCGTTTT-CCAAATTCGAACCCGAAAGCCTCCAAATCAGCAGTCAAAC
489118 CC
128 CC
489120 G
1 G
489121 GAAAATGCAT
Statistics
Matches: 109, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
125 3 0.03
126 31 0.28
127 38 0.35
128 22 0.20
129 15 0.14
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.34
Consensus pattern (129 bp):
GTTGACTGTTGACCAAAAAGTCAATTTTTTCGAAAAGACATATTATATATTTTTCAACGTCATGA
GTTTGAATTCGAAGTCCGTTTTCCAAATTCGAACCCGAAAGCCTCCAAATCAGCAGTCAAACCC
Found at i:494563 original size:39 final size:39
Alignment explanation
Indices: 494450--494567 Score: 182
Period size: 39 Copynumber: 3.0 Consensus size: 39
494440 ACATCAAGTG
*
494450 GTCTTCCCAAGGAATTTTGACAAGACTAGATATTGCGTT
1 GTCTTCCCAAGGAATTTTGACAAGACTAGATATTGGGTT
* * *
494489 CTATTCCCAAGGAATTTTGACAAGACTATATATTGGGTT
1 GTCTTCCCAAGGAATTTTGACAAGACTAGATATTGGGTT
* *
494528 GTCTTCCCAAGGAGTTTTGACAATACTAGATATTGGGTT
1 GTCTTCCCAAGGAATTTTGACAAGACTAGATATTGGGTT
494567 G
1 G
494568 AAATGGTATC
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 70 1.00
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (39 bp):
GTCTTCCCAAGGAATTTTGACAAGACTAGATATTGGGTT
Found at i:497228 original size:8 final size:8
Alignment explanation
Indices: 497213--497252 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
497203 ATGTTTATAC
497213 ATATACAT
1 ATATACAT
*
497221 AAATACAT
1 ATATACAT
*
497229 ATATATAT
1 ATATACAT
*
497237 ATATATAT
1 ATATACAT
497245 ATATACAT
1 ATATACAT
497253 GCGCGCACGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (8 bp):
ATATACAT
Found at i:497431 original size:15 final size:15
Alignment explanation
Indices: 497401--497430 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
497391 TGTGTATATA
497401 TATATACTATTATTT
1 TATATACTATTATTT
497416 TATATAC-ATTATTT
1 TATATACTATTATTT
497430 T
1 T
497431 TTTCCTTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (15 bp):
TATATACTATTATTT
Found at i:499143 original size:17 final size:17
Alignment explanation
Indices: 499121--499158 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
499111 ATGTTGGATA
*
499121 TTTTATGGATATTATAT
1 TTTTATGCATATTATAT
*
499138 TTTTATGCATCTTATAT
1 TTTTATGCATATTATAT
499155 TTTT
1 TTTT
499159 GAGACATTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.63
Consensus pattern (17 bp):
TTTTATGCATATTATAT
Found at i:500711 original size:21 final size:20
Alignment explanation
Indices: 500686--500753 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
500676 TTTCAGATTT
500686 TTTAACTTTGACTCATTATTA
1 TTTAACTTTGA-TCATTATTA
* * *
500707 TTTAAATTAT-ATTATTGATTT
1 TTTAACTT-TGATCATT-ATTA
500728 TTTAACTTTGATTCATTATTA
1 TTTAACTTTGA-TCATTATTA
500749 TTTAA
1 TTTAA
500754 ATTATATTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
20 5 0.14
21 27 0.73
22 5 0.14
ACGTcount: A:0.31, C:0.07, G:0.04, T:0.57
Consensus pattern (20 bp):
TTTAACTTTGATCATTATTA
Found at i:500744 original size:42 final size:42
Alignment explanation
Indices: 500681--500767 Score: 165
Period size: 42 Copynumber: 2.1 Consensus size: 42
500671 ATTTTTTTCA
500681 GATTTTTTAACTTTGACTCATTATTATTTAAATTATATTATT
1 GATTTTTTAACTTTGACTCATTATTATTTAAATTATATTATT
*
500723 GATTTTTTAACTTTGATTCATTATTATTTAAATTATATTATT
1 GATTTTTTAACTTTGACTCATTATTATTTAAATTATATTATT
500765 GAT
1 GAT
500768 GAAAACATGA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (42 bp):
GATTTTTTAACTTTGACTCATTATTATTTAAATTATATTATT
Found at i:504158 original size:129 final size:130
Alignment explanation
Indices: 503985--504222 Score: 338
Period size: 129 Copynumber: 1.8 Consensus size: 130
503975 GACCTGACCT
* * * *
503985 GTTGATTTTGACCGAAAAAGTTAAAATTTTCGAAAAGTCATATTTTATGTTATTTGATGTCCTGA
1 GTTGACTTTGACCGAAAAAGTCAAAATTTTCAAAAAGTCATATTTTATGTTATTTGACGTCCTGA
* * * *
504050 GTCTGAATTCGAAGT-TCGTTTTTCTAAATTC-GAACCCGAAAGCCTCGAAATAGTCAGTCAAAC
66 ATCTGAATCCGAAGTCT-GTTTTGCAAAATTCTG-ACCCGAAAGCCTCGAAATAGTCAGTCAAAC
504113 TC
129 TC
* **
504115 GTTGACTTTGACC-AAAAAGTCAAAATTTTCAAAAAGTCATATTTTATGTTTTTTGACGTTTTGA
1 GTTGACTTTGACCGAAAAAGTCAAAATTTTCAAAAAGTCATATTTTATGTTATTTGACGTCCTGA
504179 ATCTGAATCCGAAGTCTGTTTTGCAAAATTCTGACCCGAAAGCC
66 ATCTGAATCCGAAGTCTGTTTTGCAAAATTCTGACCCGAAAGCC
504223 CTGAATCGAG
Statistics
Matches: 95, Mismatches: 11, Indels: 5
0.86 0.10 0.05
Matches are distributed among these distances:
129 81 0.85
130 14 0.15
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (130 bp):
GTTGACTTTGACCGAAAAAGTCAAAATTTTCAAAAAGTCATATTTTATGTTATTTGACGTCCTGA
ATCTGAATCCGAAGTCTGTTTTGCAAAATTCTGACCCGAAAGCCTCGAAATAGTCAGTCAAACTC
Done.