Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007703.1 Hibiscus syriacus cultivar Beakdansim tig00109916_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: 1017536
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 6
Found at i:194891 original size:21 final size:21
Alignment explanation
Indices: 194867--194906 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
194857 CAATTTATTC
194867 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
*
194888 ATTGATGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
194907 CCTTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:202321 original size:25 final size:25
Alignment explanation
Indices: 202285--202333 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
202275 TATTAAGTAC
*
202285 AAAAATTGAACAAACTAAATAATAA
1 AAAAATTCAACAAACTAAATAATAA
* *
202310 AAAAATTCAACAAATTAATTAATA
1 AAAAATTCAACAAACTAAATAATA
202334 GACACAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.65, C:0.08, G:0.02, T:0.24
Consensus pattern (25 bp):
AAAAATTCAACAAACTAAATAATAA
Found at i:202844 original size:22 final size:23
Alignment explanation
Indices: 202796--202844 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 23
202786 AGAGGGGTCA
*
202796 TAAAACCATGCAGTGATGGTATC
1 TAAAACCATGCAGTGATGGCATC
* *
202819 -AAAACC-TGCTGTGGTGGCATC
1 TAAAACCATGCAGTGATGGCATC
202840 TAAAA
1 TAAAA
202845 TGGAGGCGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.24
Consensus pattern (23 bp):
TAAAACCATGCAGTGATGGCATC
Found at i:205258 original size:81 final size:81
Alignment explanation
Indices: 205121--205278 Score: 208
Period size: 81 Copynumber: 2.0 Consensus size: 81
205111 GGGAAGATGA
* * * * ***
205121 CATTTTCGTAGATGAAAATGGCGTTGGACGAACGTAAGACGTGACTGGTGGCCGATGTGGCTGTT
1 CATTTTCGTAGATGAAAATGACGGTAGACGAACGTAAGACGTCACTGGAAACCGATGTGGCTGTT
* *
205186 ATGTGCTTAATTATGG
66 ATCTCCTTAATTATGG
* * *
205202 CATTTTTGTAGATGAAAATGACGGTAGACGAACGTAAGATGTCACTGGAAATCGATGTGGCTGTT
1 CATTTTCGTAGATGAAAATGACGGTAGACGAACGTAAGACGTCACTGGAAACCGATGTGGCTGTT
205267 ATCTCCTTAATT
66 ATCTCCTTAATT
205279 TCTTATTGGT
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
81 65 1.00
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.32
Consensus pattern (81 bp):
CATTTTCGTAGATGAAAATGACGGTAGACGAACGTAAGACGTCACTGGAAACCGATGTGGCTGTT
ATCTCCTTAATTATGG
Found at i:209430 original size:23 final size:22
Alignment explanation
Indices: 209404--209459 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 22
209394 AATTCATATT
209404 GTTAT-ATATAAACTCAAATTTTA
1 GTTATAAT-TAAA-TCAAATTTTA
*
209427 GTTATAATTAAATTAAATTTTA
1 GTTATAATTAAATCAAATTTTA
209449 GTGGTATAATT
1 GT--TATAATT
209460 GAAGATTAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 11 0.38
23 9 0.31
24 9 0.31
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (22 bp):
GTTATAATTAAATCAAATTTTA
Found at i:209447 original size:22 final size:25
Alignment explanation
Indices: 209419--209468 Score: 70
Period size: 22 Copynumber: 2.1 Consensus size: 25
209409 ATATAAACTC
209419 AAATTTTAGT-TATAATT-AA-ATT
1 AAATTTTAGTGTATAATTGAAGATT
209441 AAATTTTAGTGGTATAATTGAAGATT
1 AAATTTTAGT-GTATAATTGAAGATT
209467 AA
1 AA
209469 GTTTATTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 10 0.42
24 7 0.29
25 2 0.08
26 5 0.21
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (25 bp):
AAATTTTAGTGTATAATTGAAGATT
Found at i:214697 original size:15 final size:16
Alignment explanation
Indices: 214667--214700 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
214657 TTTGATTTTT
*
214667 TTAATTTATCTTATAA
1 TTAATATATCTTATAA
214683 TTAATATAT-TTATAA
1 TTAATATATCTTATAA
214698 TTA
1 TTA
214701 TTTTGATCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
TTAATATATCTTATAA
Found at i:220702 original size:64 final size:63
Alignment explanation
Indices: 220593--220712 Score: 177
Period size: 64 Copynumber: 1.9 Consensus size: 63
220583 CATAAATCAT
* * *
220593 ATTCGATGTTTGCATTTAAGGGGGTGCATCGATGCACTACTTGTGCATCGATACACTGATGGC
1 ATTCGATGTTTGCATTTAAAGGAGTGCATCGATGCACTACATGTGCATCGATACACTGATGGC
** *
220656 ATTCGATGTTTTTATTTTAAAGGAGTGCATCGATGCACTTCATGTGCATCGATACAC
1 ATTCGATGTTTGCA-TTTAAAGGAGTGCATCGATGCACTACATGTGCATCGATACAC
220713 CTTGAACAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
63 12 0.24
64 38 0.76
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.34
Consensus pattern (63 bp):
ATTCGATGTTTGCATTTAAAGGAGTGCATCGATGCACTACATGTGCATCGATACACTGATGGC
Found at i:223906 original size:18 final size:19
Alignment explanation
Indices: 223872--223911 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
223862 CAAAAATCCT
223872 AAAAGATACATTTAAAATTA
1 AAAAGATACATTTAAAA-TA
223892 AAAAGATA-A-TTAAAATA
1 AAAAGATACATTTAAAATA
223909 AAA
1 AAA
223912 TTAAAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 6 0.30
19 1 0.05
20 8 0.40
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.25
Consensus pattern (19 bp):
AAAAGATACATTTAAAATA
Found at i:223919 original size:12 final size:12
Alignment explanation
Indices: 223884--223924 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
223874 AAGATACATT
223884 TAAAATTAAAAA
1 TAAAATTAAAAA
* *
223896 GATAATT-AAAA
1 TAAAATTAAAAA
223907 TAAAATTAAAAA
1 TAAAATTAAAAA
223919 TAAAAT
1 TAAAAT
223925 AAATACTAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (12 bp):
TAAAATTAAAAA
Found at i:225366 original size:20 final size:20
Alignment explanation
Indices: 225341--225379 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
225331 TATTAATATG
225341 ATCGCGAACTAATTTTTTGA
1 ATCGCGAACTAATTTTTTGA
225361 ATCGCGAACTAATTTTTTG
1 ATCGCGAACTAATTTTTTG
225380 TCATAGTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.41
Consensus pattern (20 bp):
ATCGCGAACTAATTTTTTGA
Found at i:225868 original size:21 final size:21
Alignment explanation
Indices: 225844--225883 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
225834 TAAAAAAATT
225844 TAAAAATATAAAAATAAAAAG
1 TAAAAATATAAAAATAAAAAG
* *
225865 TAAAATTATAAAATTAAAA
1 TAAAAATATAAAAATAAAA
225884 TTAAATTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (21 bp):
TAAAAATATAAAAATAAAAAG
Found at i:225877 original size:20 final size:19
Alignment explanation
Indices: 225844--225898 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
225834 TAAAAAAATT
*
225844 TAAAAATATAAAAATAAAAA
1 TAAAATTAT-AAAATAAAAA
*
225864 GTAAAATTATAAAATTAAAA
1 -TAAAATTATAAAATAAAAA
*
225884 TTAAATT-TAAAATAA
1 TAAAATTATAAAATAA
225899 TTTAAGATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 7 0.23
19 6 0.20
20 9 0.30
21 8 0.27
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (19 bp):
TAAAATTATAAAATAAAAA
Found at i:225884 original size:14 final size:13
Alignment explanation
Indices: 225838--225888 Score: 57
Period size: 14 Copynumber: 3.7 Consensus size: 13
225828 ATAATCTAAA
225838 AAAATTTAAAAATAT
1 AAAA-TTAAAAAT-T
* *
225853 AAAAATAAAAAGT
1 AAAATTAAAAATT
225866 AAAATTATAAAATT
1 AAAATTA-AAAATT
225880 AAAATTAAA
1 AAAATTAAA
225889 TTTAAAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
13 9 0.29
14 18 0.58
15 4 0.13
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (13 bp):
AAAATTAAAAATT
Found at i:225915 original size:21 final size:19
Alignment explanation
Indices: 225893--225951 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 19
225883 ATTAAATTTA
225893 AAATAATTTAAGATTAAAAT
1 AAATAATTTAA-ATTAAAAT
* **
225913 AAAGAATTTAAATATTAAGGT
1 AAATAATTT-AA-ATTAAAAT
225934 GAAATAATTTAAATTAAA
1 -AAATAATTTAAATTAAA
225952 GAGTGAGTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
20 13 0.42
21 10 0.32
22 8 0.26
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (19 bp):
AAATAATTTAAATTAAAAT
Found at i:225957 original size:22 final size:22
Alignment explanation
Indices: 225893--225957 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 22
225883 ATTAAATTTA
225893 AAATAATTTAAGATTAAA-A-T-
1 AAATAATTTAA-ATTAAAGAGTG
* *
225913 AAAGAATTTAAATATTAAG-GTG
1 AAATAATTTAAAT-TAAAGAGTG
225935 AAATAATTTAAATTAAAGAGTG
1 AAATAATTTAAATTAAAGAGTG
225957 A
1 A
225958 GTTAGAATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
19 2 0.06
20 13 0.36
21 5 0.14
22 16 0.44
ACGTcount: A:0.55, C:0.00, G:0.12, T:0.32
Consensus pattern (22 bp):
AAATAATTTAAATTAAAGAGTG
Found at i:226009 original size:13 final size:14
Alignment explanation
Indices: 225977--226014 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
225967 TTAGAGTAAA
225977 ATAATTAAAAAATT
1 ATAATTAAAAAATT
*
225991 AAAATTAAAAAATT
1 ATAATTAAAAAATT
226005 -TAATTAAAAA
1 ATAATTAAAAA
226015 TGAAAATAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
ATAATTAAAAAATT
Found at i:234224 original size:15 final size:15
Alignment explanation
Indices: 234204--234237 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
234194 GGTCAACTCC
234204 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
234219 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
234234 GGTC
1 GGTC
234238 GGGTAAACGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.24, C:0.26, G:0.35, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:234237 original size:8 final size:7
Alignment explanation
Indices: 234203--234234 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
234193 TGGTCAACTC
234203 CGGTCAA
1 CGGTCAA
234210 CGGTCAA
1 CGGTCAA
234217 CGGGTCAA
1 C-GGTCAA
234225 CGGTCAA
1 CGGTCAA
234232 CGG
1 CGG
234235 GTCGGGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:234255 original size:18 final size:18
Alignment explanation
Indices: 234232--234277 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
234222 CAACGGTCAA
234232 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
*
234250 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTAAACGGGT
234268 CGGGTCGGGT
1 CGGGTCGGGT
234278 TGTGACCGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.11, C:0.20, G:0.52, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTAAACGGGT
Found at i:234273 original size:13 final size:13
Alignment explanation
Indices: 234211--234255 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
234201 TCCGGTCAAC
*
234211 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
234226 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
234239 GGTAAACGGGTCG
1 GGTCAACGGGTCG
234252 GGTC
1 GGTC
234256 GGGTCAACGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 15 0.56
15 12 0.44
ACGTcount: A:0.20, C:0.22, G:0.42, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:238065 original size:18 final size:18
Alignment explanation
Indices: 238042--238076 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
238032 TTCCATCCGG
*
238042 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
238060 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
238077 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:239419 original size:18 final size:18
Alignment explanation
Indices: 239398--239443 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
239388 GTCGGGTCAA
239398 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
*
239416 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTAAACGGGT
239434 CGGGTCGGGT
1 CGGGTCGGGT
239444 TGTGACCGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.11, C:0.20, G:0.52, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTAAACGGGT
Found at i:239439 original size:13 final size:13
Alignment explanation
Indices: 239379--239421 Score: 77
Period size: 13 Copynumber: 3.3 Consensus size: 13
239369 AACGGTCAAC
239379 GGTCAACGGGTCG
1 GGTCAACGGGTCG
239392 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
239405 GGTAAACGGGTCG
1 GGTCAACGGGTCG
239418 GGTC
1 GGTC
239422 GGGTCAACGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.16, C:0.21, G:0.47, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:241309 original size:22 final size:22
Alignment explanation
Indices: 241283--241325 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
241273 AAGTAAACAG
241283 TAATATCAGGATTGTGATCCAA
1 TAATATCAGGATTGTGATCCAA
241305 TAATATCAGGATTGTGATCCA
1 TAATATCAGGATTGTGATCCA
241326 GTAAAATCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (22 bp):
TAATATCAGGATTGTGATCCAA
Found at i:248156 original size:4 final size:4
Alignment explanation
Indices: 248149--248185 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
248139 CATACAAAAT
* *
248149 TATG TATG TATG AATG TATG TATG CATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG T
248186 CACTCATCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.27, C:0.03, G:0.24, T:0.46
Consensus pattern (4 bp):
TATG
Found at i:252288 original size:3 final size:3
Alignment explanation
Indices: 252259--252337 Score: 95
Period size: 3 Copynumber: 25.7 Consensus size: 3
252249 TTGGGTTTTG
* * * *
252259 TAA TAT TAA TAAA TAA TATA TAT TAA TAA TAA TAA TTA TAA TTA TAA
1 TAA TAA TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
252306 TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
252338 TAAATAACAT
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
3 58 0.91
4 6 0.09
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:253219 original size:113 final size:113
Alignment explanation
Indices: 252569--253238 Score: 929
Period size: 113 Copynumber: 6.0 Consensus size: 113
252559 TAGAGTCATT
* ** *
252569 CAAAAGGTTGAATAAGCTCTTCTTATTATGAAC-T-TTC-T-CTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
**** * * * * * **
252630 TTATGAACTTTCTCTGTAAAGGTTGATCCATTATGTGATGAATTCAAG
66 TTATGAACTCGAACTGGAAAAGTTGATCCATCAAGTGATGGATTTGAG
* * *
252678 CAAAA-GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*** * * * * * **
252742 TTATGAACTCTTTCTAGAAAAGCTAATCCATCAAATGATGAATTCAAG
66 TTATGAACTCGAACTGGAAAAGTTGATCCATCAAGTGATGGATTTGAG
** *
252790 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTGATTCTTTAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
252855 TTATGAACTCGAACTGGAAAAGTTGATCCATCAAGTGATGGATTTGAG
66 TTATGAACTCGAACTGGAAAAGTTGATCCATCAAGTGATGGATTTGAG
* * *
252903 TAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCCGATGAGTTATTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
252968 TTATGAACTCGAACTGGAAAAGTTGATCCATCAAGTGATAGATTTGAG
66 TTATGAACTCGAACTGGAAAAGTTGATCCATCAAGTGATGGATTTGAG
253016 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
253081 TTATGAACTCGAACTGGAAAAGTTGATCCATCAAGTGATGGATTTGAG
66 TTATGAACTCGAACTGGAAAAGTTGATCCATCAAGTGATGGATTTGAG
*
253129 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCCGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
** * *
253194 TTATGAACTCGAACT-GACACTGTTGATCCATTAAATGATGGATTT
66 TTATGAACTCGAACTGGA-AAAGTTGATCCATCAAGTGATGGATTT
253239 AAATCTTTGC
Statistics
Matches: 510, Mismatches: 45, Indels: 8
0.91 0.08 0.01
Matches are distributed among these distances:
108 25 0.05
109 6 0.01
110 3 0.01
111 1 0.00
112 67 0.13
113 408 0.80
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.37
Consensus pattern (113 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTCGAACTGGAAAAGTTGATCCATCAAGTGATGGATTTGAG
Found at i:254321 original size:83 final size:83
Alignment explanation
Indices: 254173--255047 Score: 1498
Period size: 83 Copynumber: 10.7 Consensus size: 83
254163 GGTTTCATAT
* * *
254173 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCACATTCCTCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
* *
254238 TTCAATAACTGGTTTTAC
66 TTCAATGATTGGTTTTAC
*
254256 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGATCACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
254321 TTCAATGATTGGTTTTAC
66 TTCAATGATTGGTTTTAC
*
254339 CAAACCAGATCAGATAACTCAAATAACACTTCC--AAGATGCTATGAGCACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
254402 TTCAATGATTGGTTTTAC
66 TTCAATGATTGGTTTTAC
* * *
254420 CAAACCAGATCAGATAAATCAAAGAACACTTCCAGAAGATGCTATGATCACATTTATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
254485 TTCAATGATTGGTTTTAC
66 TTCAATGATTGGTTTTAC
254503 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT--G-----TCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
254561 TTCAATGATTGGTTTTAC
66 TTCAATGATTGGTTTTAC
*
254579 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGGACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
254644 TTCAATGATTGGTTTTAC
66 TTCAATGATTGGTTTTAC
*
254662 CAAACCAGATCAGATAACTCAAATAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
254727 TTCAATGATTGGTTTTAC
66 TTCAATGATTGGTTTTAC
* * *
254745 CAAACCAGATCAGATAAATCAAAGAACACTTCCAGAAGATGCTATGATCACATTTATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
254810 TTCAATGATTGGTTTTAC
66 TTCAATGATTGGTTTTAC
* *
254828 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGATCACATTCATCTTTTAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
254893 TTCAATGATTGGTTTTAC
66 TTCAATGATTGGTTTTAC
* *
254911 CAAACTAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGGACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
254976 TTCAATGATTGGTTTTAC
66 TTCAATGATTGGTTTTAC
* *
254994 CAAACCAGATCAGATAACTCAAATAACACTTCCAGAAGATGCTATGAGTACATT
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT
255048 GCATTTGTTC
Statistics
Matches: 752, Mismatches: 31, Indels: 18
0.94 0.04 0.02
Matches are distributed among these distances:
76 74 0.10
78 1 0.00
81 78 0.10
83 599 0.80
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (83 bp):
CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
TTCAATGATTGGTTTTAC
Found at i:256222 original size:25 final size:27
Alignment explanation
Indices: 256194--256260 Score: 113
Period size: 25 Copynumber: 2.6 Consensus size: 27
256184 TTGACCCCCC
256194 TTTTTCTTTTTCT-TTTTTCTC-TTTT
1 TTTTTCTTTTTCTCTTTTTCTCTTTTT
256219 TTTTTCTTTTT-TCTTTTTCTCTTTTT
1 TTTTTCTTTTTCTCTTTTTCTCTTTTT
256245 TTTTTCTTTTTCTCTT
1 TTTTTCTTTTTCTCTT
256261 CAAGCATAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
24 1 0.03
25 19 0.49
26 15 0.38
27 4 0.10
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (27 bp):
TTTTTCTTTTTCTCTTTTTCTCTTTTT
Found at i:256230 original size:26 final size:27
Alignment explanation
Indices: 256194--256260 Score: 104
Period size: 26 Copynumber: 2.6 Consensus size: 27
256184 TTGACCCCCC
256194 TTTTTC-TTTTTCTTTTTTCTC-TTTT
1 TTTTTCTTTTTTCTTTTTTCTCTTTTT
256219 TTTTTCTTTTTTC-TTTTTCTCTTTTT
1 TTTTTCTTTTTTCTTTTTTCTCTTTTT
256245 TTTTTCTTTTTCTCTT
1 TTTTTCTTTTT-TCTT
256261 CAAGCATAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
25 14 0.37
26 21 0.55
27 2 0.05
28 1 0.03
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (27 bp):
TTTTTCTTTTTTCTTTTTTCTCTTTTT
Found at i:256260 original size:19 final size:19
Alignment explanation
Indices: 256193--256257 Score: 98
Period size: 19 Copynumber: 3.4 Consensus size: 19
256183 CTTGACCCCC
256193 CTTTTTCTTTTTCTTTTTT
1 CTTTTTCTTTTTCTTTTTT
256212 CTCTTTT-TTTTTCTTTTTT
1 CT-TTTTCTTTTTCTTTTTT
256231 CTTTTTCTCTTTT-TTTTTT
1 CTTTTTCT-TTTTCTTTTTT
256250 CTTTTTCT
1 CTTTTTCT
256258 CTTCAAGCAT
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
18 4 0.09
19 31 0.72
20 8 0.19
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (19 bp):
CTTTTTCTTTTTCTTTTTT
Found at i:263592 original size:15 final size:15
Alignment explanation
Indices: 263569--263600 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
263559 TGAAATGAAT
263569 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
263584 AATGCATGTATGCAA
1 AATGAATGTATGCAA
263599 AA
1 AA
263601 AGGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:269060 original size:3 final size:3
Alignment explanation
Indices: 269031--269121 Score: 130
Period size: 3 Copynumber: 29.7 Consensus size: 3
269021 TTGGGTTTTG
* *
269031 TAA TAT TAA TAAA TAA TATA TAT TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
269078 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TA
269122 TAAATAACAT
Statistics
Matches: 80, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
2 2 0.03
3 70 0.88
4 8 0.10
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:271734 original size:2 final size:2
Alignment explanation
Indices: 271727--271768 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
271717 TTTACAAAAC
271727 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
271769 CAAAGTACAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:279408 original size:2 final size:2
Alignment explanation
Indices: 279403--279433 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
279393 ACACACACAA
*
279403 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
279434 CACAAAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:297809 original size:17 final size:16
Alignment explanation
Indices: 297776--297814 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
297766 TATGGTATCT
*
297776 ACACTTTAGTTCCATG
1 ACACTTTAGTCCCATG
*
297792 ATACTTTAGTACCCATG
1 ACACTTTAGT-CCCATG
297809 ACACTT
1 ACACTT
297815 ATAACATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.28, C:0.26, G:0.10, T:0.36
Consensus pattern (16 bp):
ACACTTTAGTCCCATG
Found at i:298914 original size:3 final size:3
Alignment explanation
Indices: 298906--298932 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
298896 CAAACTGATG
298906 CAA CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA
298933 AACCCAATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:304707 original size:16 final size:15
Alignment explanation
Indices: 304666--304707 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
304656 ATATTTATTT
304666 TTATATAAACTAAAA
1 TTATATAAACTAAAA
304681 -TACTATTAAACTAAAA
1 TTA-TA-TAAACTAAAA
304697 TTATATCAAAC
1 TTATAT-AAAC
304708 ATATAAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
14 2 0.09
15 3 0.13
16 16 0.70
17 2 0.09
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (15 bp):
TTATATAAACTAAAA
Found at i:308803 original size:13 final size:13
Alignment explanation
Indices: 308785--308814 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
308775 ACCATTCAAC
308785 ATTGCTTTCTATA
1 ATTGCTTTCTATA
308798 ATTGCTTTCTATA
1 ATTGCTTTCTATA
308811 ATTG
1 ATTG
308815 AAGCCTGAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.23, C:0.13, G:0.10, T:0.53
Consensus pattern (13 bp):
ATTGCTTTCTATA
Found at i:312027 original size:44 final size:44
Alignment explanation
Indices: 311959--312049 Score: 148
Period size: 44 Copynumber: 2.1 Consensus size: 44
311949 ATAACATTTA
311959 TAACATTTCTTGTTAATTGGGTAAGTTTACATAAA-TTAAATAGT
1 TAACATTTCTTGTTAATTGGGTAAGTTTACATAAATTTAAATA-T
* *
312003 TAACGTTTCTTGTTAGTTGGGTAAGTTTACATAAATTTAAATAT
1 TAACATTTCTTGTTAATTGGGTAAGTTTACATAAATTTAAATAT
312047 TAA
1 TAA
312050 TGTGACATAT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 37 0.84
45 7 0.16
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.44
Consensus pattern (44 bp):
TAACATTTCTTGTTAATTGGGTAAGTTTACATAAATTTAAATAT
Found at i:318316 original size:125 final size:125
Alignment explanation
Indices: 318129--318375 Score: 345
Period size: 125 Copynumber: 2.0 Consensus size: 125
318119 TTATTTCAAA
* *
318129 GTTAACTATTGACTTTTATTTTATTGCACTTTAACAATTGTTATTTATTTATTGTTTCTAATATT
1 GTTAACTACTGAC-TTTATTTTATTGCACTTTAACAATTGTTATTTATTTATTGTTTATAATATT
* * * *
318194 TGATTCGATCTTGTGATGAC-CAGATCTGGGATATGATCTACATTATTATGATTCAGACTCT
65 TGAATCGATCTTGTGATAACTC-GATCCGGGATATGATCCACATTATTATGATTCAGACTCT
* **
318255 GTTAACTACTGAC-TTATTTTATTGCATTTTAACTGTTGCTTATTTATTTATTGTTTATAATATT
1 GTTAACTACTGACTTTATTTTATTGCACTTTAACAATTG-TTATTTATTTATTGTTTATAATATT
* * *
318319 TGAATCGATCTTGTGGTAACTCGATCCGGGGTATGATCCACATTATTATGGTTCAGA
65 TGAATCGATCTTGTGATAACTCGATCCGGGATATGATCCACATTATTATGATTCAGA
318376 TTCAGCTAAC
Statistics
Matches: 107, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
124 22 0.21
125 72 0.67
126 13 0.12
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.47
Consensus pattern (125 bp):
GTTAACTACTGACTTTATTTTATTGCACTTTAACAATTGTTATTTATTTATTGTTTATAATATTT
GAATCGATCTTGTGATAACTCGATCCGGGATATGATCCACATTATTATGATTCAGACTCT
Found at i:319102 original size:20 final size:20
Alignment explanation
Indices: 319077--319150 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
319067 TTTTCCCAAT
*
319077 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
** *
319097 TCGCAACGCGAATTGGGAAA
1 TCGCAACGCGAATAAGTAAA
*
319117 TTCGCAATGCGAATAAGTAAA
1 -TCGCAACGCGAATAAGTAAA
319138 TCGCAACGCGAAT
1 TCGCAACGCGAAT
319151 TGGGAAAATC
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGAATAAGTAAA
Found at i:319119 original size:41 final size:41
Alignment explanation
Indices: 319074--319164 Score: 173
Period size: 41 Copynumber: 2.2 Consensus size: 41
319064 CGATTTTCCC
319074 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
319115 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
319156 AAATCGCAA
1 AATTCGCAA
319165 CGATACTGAC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:319123 original size:21 final size:20
Alignment explanation
Indices: 319077--319166 Score: 90
Period size: 20 Copynumber: 4.4 Consensus size: 20
319067 TTTTCCCAAT
* *
319077 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGGAAA
**
319097 TCGCAACGCGAATTGGGAAA
1 TCGCAACGCGAATAAGGAAA
* *
319117 TTCGCAATGCGAATAAGTAAA
1 -TCGCAACGCGAATAAGGAAA
**
319138 TCGCAACGCGAATTGGGAAAA
1 TCGCAACGCGAATAAGG-AAA
319159 TCGCAACG
1 TCGCAACG
319167 ATACTGACTA
Statistics
Matches: 56, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
20 29 0.52
21 27 0.48
ACGTcount: A:0.39, C:0.19, G:0.24, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAATAAGGAAA
Found at i:319223 original size:20 final size:21
Alignment explanation
Indices: 319198--319249 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
319188 TAATAAAAAA
*
319198 TCGCAACGA-GATACTTACTT
1 TCGCAACGACGATACTGACTT
319218 TCGCAAC-ACGATACTGACTT
1 TCGCAACGACGATACTGACTT
319238 TCGCAACG-CGAT
1 TCGCAACGACGAT
319250 TTACTTAGCG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (21 bp):
TCGCAACGACGATACTGACTT
Found at i:319822 original size:19 final size:19
Alignment explanation
Indices: 319798--319842 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
319788 GCAACGAGAT
*
319798 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
319817 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
319836 AATCGCA
1 AATCGCA
319843 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:319860 original size:19 final size:19
Alignment explanation
Indices: 319838--320022 Score: 174
Period size: 19 Copynumber: 10.1 Consensus size: 19
319828 GAAACCAAAA
*
319838 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
319857 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
319876 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
319895 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
319915 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
319931 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
319948 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
319962 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
319981 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
320001 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
320021 TC
1 TC
320023 AACCAAAAGA
Statistics
Matches: 138, Mismatches: 15, Indels: 26
0.77 0.08 0.15
Matches are distributed among these distances:
14 20 0.14
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 60 0.43
20 49 0.36
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:319915 original size:39 final size:38
Alignment explanation
Indices: 319838--319927 Score: 153
Period size: 39 Copynumber: 2.3 Consensus size: 38
319828 GAAACCAAAA
* *
319838 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATTTCGCGTTGCGATTTTCATT
319876 TCGCGTTGCGATTTTAATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATTTCGC-GTTGCGATTTTCATT
319915 TCGCGTTGCGATT
1 TCGCGTTGCGATT
319928 GTCTGGTCGC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 21 0.43
39 28 0.57
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (38 bp):
TCGCGTTGCGATTTTAATTTCGCGTTGCGATTTTCATT
Found at i:319947 original size:33 final size:33
Alignment explanation
Indices: 319910--319997 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
319900 GTTGCGATTT
* *
319910 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
319943 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
319976 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
319998 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:319999 original size:20 final size:20
Alignment explanation
Indices: 319965--320022 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
319955 GCGATTCTCT
**
319965 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
319985 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
320005 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
320023 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:322099 original size:21 final size:21
Alignment explanation
Indices: 322075--322141 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
322065 TCATTCCTCG
322075 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
322096 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
322117 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
322138 AGAG
1 AGAG
322142 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:323513 original size:14 final size:14
Alignment explanation
Indices: 323494--323529 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
323484 ATTGTTTAAT
323494 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
323508 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
323522 TGATTTGT
1 TGATTTGT
323530 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:323730 original size:19 final size:19
Alignment explanation
Indices: 323708--323804 Score: 79
Period size: 19 Copynumber: 5.6 Consensus size: 19
323698 CGAAATTAAA
*
323708 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
* *
323727 TTCGCATTGTGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
323743 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
323760 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
323776 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
323793 TTCGCATTGCGA
1 TTCGCATTGCGA
323805 AAGTTATTTC
Statistics
Matches: 59, Mismatches: 9, Indels: 20
0.67 0.10 0.23
Matches are distributed among these distances:
14 11 0.19
16 13 0.22
17 13 0.22
19 22 0.37
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.44
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:323754 original size:33 final size:33
Alignment explanation
Indices: 323712--323804 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
323702 ATTAAATTCG
*
323712 CGTTGCGATTTTCATTTCGCATTGTGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
323745 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
323778 CGTTGCGATTTTCATTTCGCATTGCGA
1 CGTTGCGATTTTCATTTCGCATTGCGA
323805 AAGTTATTTC
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:325691 original size:21 final size:20
Alignment explanation
Indices: 325666--325720 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
325656 TTCATGTCCC
*
325666 CGAAAGGCATTCATCTCGTTG
1 CGAAAGGCA-TCATCGCGTTG
* **
325687 CGAAAGTCAGAATCGCGTTG
1 CGAAAGGCATCATCGCGTTG
325707 CGAAAGGCAATCAT
1 CGAAAGGC-ATCAT
325721 TTGACCATCG
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.22
Consensus pattern (20 bp):
CGAAAGGCATCATCGCGTTG
Found at i:326213 original size:14 final size:14
Alignment explanation
Indices: 326194--326230 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
326184 CATCAATTAA
326194 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
326208 ACAAATCATCTTTT
1 ACAAATCAACATTT
326222 ACAAATCAA
1 ACAAATCAA
326231 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:326614 original size:20 final size:20
Alignment explanation
Indices: 326589--326639 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
326579 ATTCATTTGA
*
326589 CTATCGCAACGTGAAAATGG
1 CTATCGCAACGCGAAAATGG
326609 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
326629 TTATCGCAACG
1 CTATCGCAACG
326640 AGAATATCGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.20
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:326688 original size:14 final size:15
Alignment explanation
Indices: 326668--326740 Score: 60
Period size: 14 Copynumber: 4.5 Consensus size: 15
326658 ATGAAATCGC
326668 ATTGCGATTTTCTCG
1 ATTGCGATTTTCTCG
326683 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC---TCG
*
326700 CATTGCGATTTCATTTCG
1 -ATTGCGATTT--TCTCG
326718 CATTGCGATTTTCTCG
1 -ATTGCGATTTTCTCG
326734 -TTGCGAT
1 ATTGCGAT
326741 AGCCATTTCG
Statistics
Matches: 49, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
14 18 0.37
16 4 0.08
17 3 0.06
18 14 0.29
19 9 0.18
21 1 0.02
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.47
Consensus pattern (15 bp):
ATTGCGATTTTCTCG
Found at i:326705 original size:19 final size:19
Alignment explanation
Indices: 326664--326730 Score: 92
Period size: 18 Copynumber: 3.8 Consensus size: 19
326654 CGAAATGAAA
326664 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
326680 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
326697 TCGCATTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
326715 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
326731 TCGTTGCGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
14 11 0.24
16 3 0.07
17 3 0.07
18 18 0.40
19 10 0.22
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:326866 original size:14 final size:14
Alignment explanation
Indices: 326847--326883 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
326837 CATCAATTAA
326847 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
326861 ACAAATCATCTTTT
1 ACAAATCAACATTT
326875 ACAAATCAA
1 ACAAATCAA
326884 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:326912 original size:40 final size:41
Alignment explanation
Indices: 326833--326912 Score: 92
Period size: 40 Copynumber: 2.0 Consensus size: 41
326823 ACAAATTATG
* * ** *
326833 TACACATCAATTAAACAAATCAACATTTACAAATCATCTTT
1 TACAAATCAATTAAACAAATCAAAAAATACAAATAATCTTT
326874 TACAAATCAATTAAAC-AATCAAAAAATA-ATAATAATCTT
1 TACAAATCAATTAAACAAATCAAAAAATACA-AATAATCTT
326913 ATTTCTTCAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
39 1 0.03
40 17 0.52
41 15 0.45
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (41 bp):
TACAAATCAATTAAACAAATCAAAAAATACAAATAATCTTT
Found at i:328773 original size:20 final size:19
Alignment explanation
Indices: 328738--328804 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
328728 GAAACTTAAA
328738 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
328757 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* * **
328777 ATCGCAATGCAAAATGAAA
1 ATCGCAACGCGAAATGACT
328796 ATCGCAACG
1 ATCGCAACG
328805 ACAAAATCGC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
19 23 0.57
20 17 0.43
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:328842 original size:13 final size:13
Alignment explanation
Indices: 328793--328849 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
328783 ATGCAAAATG
328793 AAAATCGCAACGA
1 AAAATCGCAACGA
328806 CAAAATCGCAACGCGAA
1 -AAAATCGCAA--CG-A
328823 ATGAAATCGCAACGA
1 A--AAATCGCAACGA
328838 AAAATCGCAACG
1 AAAATCGCAACG
328850 CGAAACACAA
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.29
14 10 0.26
15 2 0.05
16 5 0.13
17 1 0.03
18 9 0.24
ACGTcount: A:0.49, C:0.25, G:0.18, T:0.09
Consensus pattern (13 bp):
AAAATCGCAACGA
Found at i:328845 original size:31 final size:33
Alignment explanation
Indices: 328777--328854 Score: 124
Period size: 31 Copynumber: 2.4 Consensus size: 33
328767 GGAAATGGCT
* *
328777 ATCGCAATGCAAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
328810 ATCGCAACGCGAAATG-AAATCGCAACGA-AAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
328841 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
328855 CACAAATCGC
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
31 17 0.40
32 12 0.28
33 14 0.33
ACGTcount: A:0.49, C:0.23, G:0.18, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:328862 original size:32 final size:32
Alignment explanation
Indices: 328794--328865 Score: 110
Period size: 32 Copynumber: 2.2 Consensus size: 32
328784 TGCAAAATGA
**
328794 AAATCGCAACGACAAAATCGCAACGCGAAATG
1 AAATCGCAACGACAAAATCGCAACGCGAAAAC
328826 AAATCGCAACGA-AAAATCGCAACGCGAAACAC
1 AAATCGCAACGACAAAATCGCAACGCGAAA-AC
328858 AAATCGCA
1 AAATCGCA
328866 TTGCGATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 17 0.46
32 20 0.54
ACGTcount: A:0.49, C:0.26, G:0.17, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGACAAAATCGCAACGCGAAAAC
Found at i:328883 original size:19 final size:18
Alignment explanation
Indices: 328861--328994 Score: 104
Period size: 20 Copynumber: 7.6 Consensus size: 18
328851 GAAACACAAA
*
328861 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATT
*
328880 TCGCGTTGCGATTT--TG
1 TCGCGTTGCGATTTCATT
328896 T--CGTTGCGATTTCATT
1 TCGCGTTGCGATTTCATT
*
328912 TCGCGTTGCGATTT--TG
1 TCGCGTTGCGATTTCATT
328928 T--CGTTGCGATTTCATT
1 TCGCGTTGCGATTTCATT
**
328944 TCGCGTTGCGATAGCCATTT
1 TCGCGTTGCGAT-TTCA-TT
*
328964 TCGCGTTGCGATAGTCATTT
1 TCGCGTTGCGAT-TTCA-TT
*
328984 TCGTGTTGCGA
1 TCGCGTTGCGA
328995 AAATAAACTA
Statistics
Matches: 96, Mismatches: 9, Indels: 19
0.77 0.07 0.15
Matches are distributed among these distances:
14 22 0.23
16 8 0.08
18 23 0.24
19 12 0.12
20 31 0.32
ACGTcount: A:0.12, C:0.20, G:0.25, T:0.43
Consensus pattern (18 bp):
TCGCGTTGCGATTTCATT
Found at i:328902 original size:14 final size:14
Alignment explanation
Indices: 328883--328939 Score: 69
Period size: 14 Copynumber: 3.8 Consensus size: 14
328873 TTTCATTTCG
328883 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
328897 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
328913 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
328929 CGTTGCGATTT
1 CGTTGCGATTT
328940 CATTTCGCGT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 22 0.59
16 4 0.11
18 11 0.30
ACGTcount: A:0.09, C:0.18, G:0.26, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:328913 original size:32 final size:32
Alignment explanation
Indices: 328866--328955 Score: 171
Period size: 32 Copynumber: 2.8 Consensus size: 32
328856 ACAAATCGCA
328866 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
328899 TTGCGATTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTCATTTCGCGTTGCGATTTTGTCG
328931 TTGCGATTTCATTTCGCGTTGCGAT
1 TTGCGATTTCATTTCGCGTTGCGAT
328956 AGCCATTTTC
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
32 51 0.89
33 6 0.11
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (32 bp):
TTGCGATTTCATTTCGCGTTGCGATTTTGTCG
Found at i:329490 original size:18 final size:18
Alignment explanation
Indices: 329464--329508 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
329454 GTCGATCAGA
*
329464 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
329482 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
329500 TGATGGCTC
1 TGATGGCTC
329509 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:330852 original size:20 final size:20
Alignment explanation
Indices: 330827--330864 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
330817 AATAGTTTCT
330827 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
330847 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
330865 GAGAGAATCG
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:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:331138 original size:22 final size:22
Alignment explanation
Indices: 331113--331156 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
331103 GATTTAGATA
331113 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
331135 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
331157 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:331373 original size:20 final size:20
Alignment explanation
Indices: 331344--331397 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
331334 GATTATGTAT
* *
331344 TATCGCGTTGCGAAAGTCAG
1 TATCGTGTTGCGAAAGTAAG
331364 TATCGTGTTGCGAAAGTAAG
1 TATCGTGTTGCGAAAGTAAG
331384 TATC-TCGTTGCGAA
1 TATCGT-GTTGCGAA
331398 TTTTTATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (20 bp):
TATCGTGTTGCGAAAGTAAG
Found at i:331454 original size:21 final size:21
Alignment explanation
Indices: 331428--331500 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 21
331418 TAGTCAGTAT
331428 CGTTGCGATTTTCCCAATTCG
1 CGTTGCGATTTTCCCAATTCG
* **
331449 CGTTGCGA-TTTACTTATTCG
1 CGTTGCGATTTTCCCAATTCG
* *
331469 CATTGCGAATTTCCCAATTCG
1 CGTTGCGATTTTCCCAATTCG
331490 CGTTGCGATTT
1 CGTTGCGATTT
331501 ACTTATTCGC
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 16 0.38
21 26 0.62
ACGTcount: A:0.16, C:0.25, G:0.19, T:0.40
Consensus pattern (21 bp):
CGTTGCGATTTTCCCAATTCG
Found at i:331469 original size:20 final size:20
Alignment explanation
Indices: 331444--331517 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
331434 GATTTTCCCA
*
331444 ATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCGATTTACTT
* **
331464 ATTCGCATTGCGAATTTCCCA
1 ATTCGCATTGCG-ATTTACTT
*
331485 ATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCGATTTACTT
331505 ATTCGCATTGCGA
1 ATTCGCATTGCGA
331518 ATTGGGAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACTT
Found at i:331482 original size:41 final size:41
Alignment explanation
Indices: 331430--331520 Score: 173
Period size: 41 Copynumber: 2.2 Consensus size: 41
331420 GTCAGTATCG
*
331430 TTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCGCA
1 TTGCGAATTTCCCAATTCGCGTTGCGATTTACTTATTCGCA
331471 TTGCGAATTTCCCAATTCGCGTTGCGATTTACTTATTCGCA
1 TTGCGAATTTCCCAATTCGCGTTGCGATTTACTTATTCGCA
331512 TTGCGAATT
1 TTGCGAATT
331521 GGGAAAATCG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.41
Consensus pattern (41 bp):
TTGCGAATTTCCCAATTCGCGTTGCGATTTACTTATTCGCA
Found at i:331890 original size:2 final size:2
Alignment explanation
Indices: 331748--331871 Score: 248
Period size: 2 Copynumber: 62.0 Consensus size: 2
331738 TATGCATAAT
331748 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
331790 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
331832 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
331872 CGTATGCATA
Statistics
Matches: 122, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 122 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:331986 original size:2 final size:2
Alignment explanation
Indices: 331979--332009 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
331969 ATTCATTTGT
331979 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 T
332010 TCAAGAACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:335353 original size:18 final size:18
Alignment explanation
Indices: 335330--335366 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
335320 AAAATAAACC
335330 AGAATCAACTGGTTAATA
1 AGAATCAACTGGTTAATA
335348 AGAATCAACTGGTTAATA
1 AGAATCAACTGGTTAATA
335366 A
1 A
335367 CAAACTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.11, G:0.16, T:0.27
Consensus pattern (18 bp):
AGAATCAACTGGTTAATA
Found at i:340433 original size:14 final size:14
Alignment explanation
Indices: 340414--340443 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
340404 AAATATTTTG
340414 GTGTTCTCTTTTAT
1 GTGTTCTCTTTTAT
340428 GTGTTCTCTTTTAT
1 GTGTTCTCTTTTAT
340442 GT
1 GT
340444 CTATTTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.07, C:0.13, G:0.17, T:0.63
Consensus pattern (14 bp):
GTGTTCTCTTTTAT
Found at i:342696 original size:35 final size:34
Alignment explanation
Indices: 342616--342737 Score: 136
Period size: 35 Copynumber: 3.5 Consensus size: 34
342606 TTAAAACTTA
*
342616 CAAAATAATCTTCAATTTCATTCTAAACCCATATTC
1 CAAAATAA--TTCAATTTCATTCTAAACCCAAATTC
* * *
342652 CGAAGTAATTCAATTTCATTCTAAACCTTAAATTC
1 CAAAATAATTCAATTTCATTCTAAACC-CAAATTC
*
342687 CAAAATAATTCAATTACATTCTAAACCCCAAATTC
1 CAAAATAATTCAATTTCATTCTAAA-CCCAAATTC
* * *
342722 TAAAATACTTTAATTT
1 CAAAATAATTCAATTT
342738 AAGGAGGAAT
Statistics
Matches: 72, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
34 19 0.26
35 45 0.62
36 8 0.11
ACGTcount: A:0.41, C:0.21, G:0.02, T:0.36
Consensus pattern (34 bp):
CAAAATAATTCAATTTCATTCTAAACCCAAATTC
Found at i:343847 original size:35 final size:34
Alignment explanation
Indices: 343798--343910 Score: 138
Period size: 35 Copynumber: 3.2 Consensus size: 34
343788 AAAAAAGACA
*
343798 GAAATTGAAGTATTTTAGAATTTGGGTTTTAGAAT
1 GAAATTGAATTATTTTAGAATTTGGG-TTTAGAAT
*
343833 -ATAATTGAATTATTTTAGAATTTAAGGTTTAGAAT
1 GA-AATTGAATTATTTTAGAATTT-GGGTTTAGAAT
* * *
343868 GAAATCGAATTATTTTGGAATTTGGGGTTTAAAAT
1 GAAATTGAATTATTTTAGAATTT-GGGTTTAGAAT
343903 GAAATTGA
1 GAAATTGA
343911 GGACTAATTT
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
34 1 0.01
35 63 0.94
36 3 0.04
ACGTcount: A:0.37, C:0.01, G:0.20, T:0.42
Consensus pattern (34 bp):
GAAATTGAATTATTTTAGAATTTGGGTTTAGAAT
Found at i:348059 original size:13 final size:13
Alignment explanation
Indices: 348041--348103 Score: 62
Period size: 13 Copynumber: 5.2 Consensus size: 13
348031 TTGTGGGTGT
348041 ATGGGGGCACCGA
1 ATGGGGGCACCGA
* *
348054 ATGGGGGGA--GC
1 ATGGGGGCACCGA
348065 ATGGGGGCACCGA
1 ATGGGGGCACCGA
* *
348078 ATGGGGGGA--GC
1 ATGGGGGCACCGA
348089 ATGGGGGCACCGA
1 ATGGGGGCACCGA
348102 AT
1 AT
348104 TCCACCGAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
11 18 0.47
13 20 0.53
ACGTcount: A:0.22, C:0.17, G:0.51, T:0.10
Consensus pattern (13 bp):
ATGGGGGCACCGA
Found at i:348068 original size:24 final size:24
Alignment explanation
Indices: 348041--348103 Score: 126
Period size: 24 Copynumber: 2.6 Consensus size: 24
348031 TTGTGGGTGT
348041 ATGGGGGCACCGAATGGGGGGAGC
1 ATGGGGGCACCGAATGGGGGGAGC
348065 ATGGGGGCACCGAATGGGGGGAGC
1 ATGGGGGCACCGAATGGGGGGAGC
348089 ATGGGGGCACCGAAT
1 ATGGGGGCACCGAAT
348104 TCCACCGAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.22, C:0.17, G:0.51, T:0.10
Consensus pattern (24 bp):
ATGGGGGCACCGAATGGGGGGAGC
Found at i:357596 original size:18 final size:17
Alignment explanation
Indices: 357573--357627 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 17
357563 TAACAATATA
357573 ATAATATAAATAACTTAT
1 ATAATAT-AATAACTTAT
357591 ATAATAT-AT-AC-TAT
1 ATAATATAATAACTTAT
357605 ATAATATATATATACTATAT
1 ATAATATA-ATA-ACT-TAT
357625 ATA
1 ATA
357628 TTTTAAAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
14 10 0.32
15 2 0.06
16 4 0.13
18 9 0.29
20 6 0.19
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (17 bp):
ATAATATAATAACTTAT
Found at i:357600 original size:9 final size:9
Alignment explanation
Indices: 357567--357627 Score: 51
Period size: 9 Copynumber: 7.1 Consensus size: 9
357557 AAATATTAAC
357567 AATATA-AT
1 AATATATAT
*
357575 AATATAAAT
1 AATATATAT
357584 AACT-TATAT
1 AA-TATATAT
357593 AATATATACT
1 AATATATA-T
357603 -ATATA-AT
1 AATATATAT
357610 -ATATATAT
1 AATATATAT
*
357618 ACTATATAT
1 AATATATAT
357627 A
1 A
357628 TTTTAAAAAG
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
7 6 0.13
8 10 0.22
9 27 0.60
10 2 0.04
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (9 bp):
AATATATAT
Found at i:357643 original size:20 final size:21
Alignment explanation
Indices: 357620--357669 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
357610 ATATATATAC
357620 TATATATATTTT-AAAAAGT-A
1 TATATATATTTTCAAAAA-TAA
* *
357640 TATATTTATTTTCAAATATAA
1 TATATATATTTTCAAAAATAA
357661 TATATATAT
1 TATATATAT
357670 ACTATAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (21 bp):
TATATATATTTTCAAAAATAA
Found at i:357644 original size:2 final size:2
Alignment explanation
Indices: 357588--357628 Score: 50
Period size: 2 Copynumber: 20.5 Consensus size: 2
357578 ATAAATAACT
357588 TA TA TA -A TA TA TA CTA TA TA -A TA TA TA TA TA CTA TA TA TA T
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA T
357629 TTTAAAAAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
1 2 0.06
2 29 0.83
3 4 0.11
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:358418 original size:225 final size:225
Alignment explanation
Indices: 357993--358841 Score: 885
Period size: 225 Copynumber: 3.8 Consensus size: 225
357983 TTTAAGACGG
* * * * * *
357993 ATATCCTCCGTTGTGGAGTTAAAATCTGACTTCGAAAATATTTCACCAGAAGATGG-TTCCTTGC
1 ATATCCTCCATTGTGGAGTTGAAAT-TGACTTCGAAAAGATTTGACTAGAAGATGGCTT-CTCGC
***
358057 CGCTGAGTTAAGCCAAATTGCAGTCAATTCTGAATG-CAATTCTG-GGTCAAGTATCCTTCA-CA
64 CGCTGAGTTAAGCCAAATTGCAGTCAATTCTGAATGTGTTTTC-GAGGTCAAGTATCCTTCATC-
* * * * * * * *
358119 ATGCAGTTGAAAATTCGCCTGAAAAATTCAACTGAAAATTAGCTCATCATCGTGGAGTTAAGCTA
127 GTGAAGTTGAAACTTGGCCTGAAAACTTCAACTGAAAACTAGCTCCTCATCCT-GAGTTAAGCTA
*
358184 GATCGCAGTCGGTTCTGAATTGGCTTTCAAACCCA
191 GATCGCAGTCGATTCTGAATTGGCTTTCAAACCCA
* *
358219 ATATCCTTCATTGTGGAGTTGAAATTGACTTC-AAAATGCTTTGACTAGAAGATGGCTTCTCGCC
1 ATATCCTCCATTGTGGAGTTGAAATTGACTTCGAAAA-GATTTGACTAGAAGATGGCTTCTCGCC
* * *
358283 ACTGAGTTAAGCCAAATTGCATTCAGTTCTGAATGTGTTTTC-AGGTCAAGTATCCTTCATCGTG
65 GCTGAGTTAAGCCAAATTGCAGTCAATTCTGAATGTGTTTTCGAGGTCAAGTATCCTTCATCGTG
* * * * * *
358347 AAGTTGAAACTTAGCCT-AAATACTTCAACTGAAAACTAGTTCCTCGTCACTAAGTTATGTTAGA
130 AAGTTGAAACTTGGCCTGAAA-ACTTCAACTGAAAACTAGCTCCTCATC-CTGAGTTAAGCTAGA
* * *
358411 CCGCAGTCGATTCTGAATTGGATTTCGAACCCA
193 TCGCAGTCGATTCTGAATTGGCTTTCAAACCCA
* ** * *
358444 ATATCCTCTATTGTGGAGTTGAAATTGACTTCGAAAAGATTTGACTAGAAGATGAATCCTCGCTG
1 ATATCCTCCATTGTGGAGTTGAAATTGACTTCGAAAAGATTTGACTAGAAGATGGCTTCTCGCCG
* * * * * * * * * **
358509 TTGAGTTAAGCCAGATGGCGGTCAGTTCTAAATGTG-CTTCGGGGTCAAGTATTCTTTGTCGTGA
66 CTGAGTTAAGCCAAATTGCAGTCAATTCTGAATGTGTTTTCGAGGTCAAGTATCCTTCATCGTGA
* * * * * * *
358573 AGTTGAAACTTGGTCTGAAAACTCCAACTGAAAACTAGCTCTTCATCGTTGAGTTAAACAAGATT
131 AGTTGAAACTTGGCCTGAAAACTTCAACTGAAAACTAGCTCCTCATC-CTGAGTTAAGCTAGATC
*
358638 GCAGTCGATTCTGAATTGACTTTCAAACCCA
195 GCAGTCGATTCTGAATTGGCTTTCAAACCCA
* * **
358669 ATATCCTCCATTGTGGAGTTGAAATTAACTTCGAAAAGATTTAACTAGAAGATGGC-TCATCATC
1 ATATCCTCCATTGTGGAGTTGAAATTGACTTCGAAAAGATTTGACTAGAAGATGGCTTC-TCGCC
** * * * * *
358733 GCTGAGTTAAGCCAAATTGCAACCAATTTTGAATTTGGTTTT-GA-GTGAAGTATCATTCGTCGT
65 GCTGAGTTAAGCCAAATTGCAGTCAATTCTGAATGT-GTTTTCGAGGTCAAGTATCCTTCATCGT
* *
358796 GAAGTTAAAACTTGGTCTGAAAACTTCAACTTG-AAACTAGCTCCTC
129 GAAGTTGAAACTTGGCCTGAAAACTTCAAC-TGAAAACTAGCTCCTC
358842 GCTGTTGAGT
Statistics
Matches: 513, Mismatches: 96, Indels: 29
0.80 0.15 0.05
Matches are distributed among these distances:
224 11 0.02
225 460 0.90
226 40 0.08
227 2 0.00
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.32
Consensus pattern (225 bp):
ATATCCTCCATTGTGGAGTTGAAATTGACTTCGAAAAGATTTGACTAGAAGATGGCTTCTCGCCG
CTGAGTTAAGCCAAATTGCAGTCAATTCTGAATGTGTTTTCGAGGTCAAGTATCCTTCATCGTGA
AGTTGAAACTTGGCCTGAAAACTTCAACTGAAAACTAGCTCCTCATCCTGAGTTAAGCTAGATCG
CAGTCGATTCTGAATTGGCTTTCAAACCCA
Found at i:363407 original size:30 final size:31
Alignment explanation
Indices: 363352--363414 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 31
363342 AAAAAAATAT
363352 AATAAAAGTAAAATAAAAAGGATTAAATTGA
1 AATAAAAGTAAAATAAAAAGGATTAAATTGA
* * *
363383 AATAAAATTAAAAT-TAATGGATTAAATTGA
1 AATAAAAGTAAAATAAAAAGGATTAAATTGA
363413 AA
1 AA
363415 AATGAGACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 16 0.55
31 13 0.45
ACGTcount: A:0.62, C:0.00, G:0.11, T:0.27
Consensus pattern (31 bp):
AATAAAAGTAAAATAAAAAGGATTAAATTGA
Found at i:364238 original size:14 final size:13
Alignment explanation
Indices: 364193--364244 Score: 54
Period size: 14 Copynumber: 4.0 Consensus size: 13
364183 AAATAAAAAT
364193 ATTA-ATAATATA
1 ATTATATAATATA
**
364205 ACAATATAA-ATA
1 ATTATATAATATA
364217 ACTTATATAATATA
1 A-TTATATAATATA
364231 TATTATATAATATA
1 -ATTATATAATATA
364245 CAATATAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
12 6 0.19
13 10 0.31
14 15 0.47
15 1 0.03
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (13 bp):
ATTATATAATATA
Found at i:364251 original size:14 final size:14
Alignment explanation
Indices: 364197--364251 Score: 53
Period size: 14 Copynumber: 4.1 Consensus size: 14
364187 AAAAATATTA
364197 ATAATATAACAATAT
1 ATAATAT-ACAATAT
*
364212 A-AATA-AC-TTAT
1 ATAATATACAATAT
* *
364223 ATAATATATATTAT
1 ATAATATACAATAT
364237 ATAATATACAATAT
1 ATAATATACAATAT
364251 A
1 A
364252 ATAGTGTGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
11 4 0.12
12 6 0.18
13 1 0.03
14 21 0.64
15 1 0.03
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (14 bp):
ATAATATACAATAT
Found at i:364317 original size:2 final size:2
Alignment explanation
Indices: 364305--364407 Score: 55
Period size: 2 Copynumber: 55.0 Consensus size: 2
364295 AAGTATAACC
*
364305 TA TA T- TA TA TA TA TA -A TA TA TA -A TA CA -A 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
* * *
364343 TA T- TA -A TA -A CTA TA TA T- TT TA T- TT TCA AA TA -A TA TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA
* *
364381 TA TA TA TA TA TA AA CTA TA TA TG TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA
364408 AAATGTATTA
Statistics
Matches: 79, Mismatches: 9, Indels: 26
0.69 0.08 0.23
Matches are distributed among these distances:
1 10 0.13
2 67 0.85
3 2 0.03
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.47
Consensus pattern (2 bp):
TA
Found at i:370876 original size:83 final size:83
Alignment explanation
Indices: 370786--370945 Score: 295
Period size: 83 Copynumber: 1.9 Consensus size: 83
370776 AAAATGGTGT
*
370786 TATATATCTCATCTTAAAAATATTCCTAATTA-AGAGATCATAACACTTATAACCTCTAAGTCAT
1 TATATATCTCATCTTAAAAATATTCCTAATTATA-AAATCATAACACTTATAACCTCTAAGTCAT
370850 GCAGAATAATCAATGATGG
65 GCAGAATAATCAATGATGG
370869 TATATATCTCATCTTAAAAATATTCCTAATTATAAAATCATAACACTTATAACCTCTAAGTCATG
1 TATATATCTCATCTTAAAAATATTCCTAATTATAAAATCATAACACTTATAACCTCTAAGTCATG
370934 CAGAATAATCAA
66 CAGAATAATCAA
370946 AGTAGTTGCT
Statistics
Matches: 75, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
83 74 0.99
84 1 0.01
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (83 bp):
TATATATCTCATCTTAAAAATATTCCTAATTATAAAATCATAACACTTATAACCTCTAAGTCATG
CAGAATAATCAATGATGG
Found at i:371198 original size:31 final size:31
Alignment explanation
Indices: 371163--371227 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
371153 CATACAATGA
371163 AAATGAGCTCATTTAGCTCTTTTAGTTAATT
1 AAATGAGCTCATTTAGCTCTTTTAGTTAATT
**
371194 AAATGAGCTCATTTCTCTCTTTTAGTTAATT
1 AAATGAGCTCATTTAGCTCTTTTAGTTAATT
371225 AAA
1 AAA
371228 ATTTATTGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.45
Consensus pattern (31 bp):
AAATGAGCTCATTTAGCTCTTTTAGTTAATT
Found at i:372122 original size:26 final size:26
Alignment explanation
Indices: 372063--372126 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 26
372053 GAAAAACGAG
* * *
372063 AAAATAAAGAAAAGAAAATTTAAATA
1 AAAATAAATAAAAGAAAAATAAAATA
** *
372089 AATTTAAATATAAGAAAAATAAAATA
1 AAAATAAATAAAAGAAAAATAAAATA
372115 AAAATAAATAAA
1 AAAATAAATAAA
372127 TCAAAGACAA
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (26 bp):
AAAATAAATAAAAGAAAAATAAAATA
Found at i:373762 original size:85 final size:85
Alignment explanation
Indices: 373666--374560 Score: 610
Period size: 80 Copynumber: 10.9 Consensus size: 85
373656 TTTGCCTCTG
* *
373666 AGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACTCTTATAGCCTTGAGTTATGC
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGC
* * **
373731 TACAAATGATATGCCCCCGA
66 TGCAAATGATGTGCCCTTGA
* * * * * * * * *
373751 AGCTGAGTGTAACCGAACTTGAAGGTCTTTGGTTGGCATATAGCCCTTCTCGACTTAAGCTATGC
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGC
* *
373816 TGCAAATGTTGTGCCTTTG-
66 TGCAAATGATGTGCCCTTGA
* *
373835 AGCTGAGTGTAATCTAACTCGAAGGTC-TTTGTTGGCAGATAACCTTTCTAGCCTTGAGTTATGC
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGC
*
373899 TGCAAATGATGTG-CCTTGG
66 TGCAAATGATGTGCCCTTGA
* ** * * * * * * *
373918 AGTTGAACGTAGTCGAACTCGAAGG-----TGATTGGCATATAGCCCTTCTCGACTTAAGTTATA
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTTTG-TTGGCAGATAACCCTTCTAGCCTTGAGTTATG
* *
373978 CTGCAAACGATGTG-CCTTGG
65 CTGCAAATGATGTGCCCTTGA
** * * * ** *
373998 AGCTGAACGTAGTCAAACTCGAAGGTCTTTTGGTCACAGACAACCCTTCTAGCCTTGAGTTATGC
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGC
* * *
374063 TGTAAATGTTGTGCCCTCGA
66 TGCAAATGATGTGCCCTTGA
* * * * * * * **
374083 AGTTGAGTGTAGTCGAACTCGAGGGTC---T-TTGGCAGATAGCCCTTCTCGACTTAAACTACT-
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTA-TG
* * *
374143 CTGCAAATAATATG-CCTTGG
65 CTGCAAATGATGTGCCCTTGA
* * * * **
374163 AGCTGAGCGTAGTCGAACTTGAAGGTCTTTTGGTAACAGATAACCCTTCTAGCCTTGAGTTATGC
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGC
* * *
374228 TGTAAATGTTGTGCCCTCGA
66 TGCAAATGATGTGCCCTTGA
* * * * * * * * *
374248 AGCTGAGTGTAATCGAACTTGCAGG---TAT-TTGGCAGATAGCCCTTCTCGACTTAAGCTATTC
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGC
* * * *
374309 TGCAAATGATATG-CATAGG
66 TGCAAATGATGTGCCCTTGA
* * * * * ** * * * *
374328 AGCTGAGCGTAGTCGAACTCAAAAGTCTTTTGGTCACATATAACCCTTATAGCATTGAGTTATGT
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGC
*
374393 TG----TGATGTGCCCTCGA
66 TGCAAATGATGTGCCCTTGA
* * * * * * * **
374409 AGCTGAATGTAATCGAACTCGAGGGTC---T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATTA
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGC
374470 TGCAAATGATGTG-CCTT-A
66 TGCAAATGATGTGCCCTTGA
** * * * *
374488 GAGCTGAACGTAGTCGAACTCAAAGGTC-TTTGTTGGCATATAACCCTTCTAGCCTTGAGTTAAG
1 -AGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATG
374552 CTGCAAATG
65 CTGCAAATG
374561 TTGTTGTTTT
Statistics
Matches: 606, Mismatches: 176, Indels: 58
0.72 0.21 0.07
Matches are distributed among these distances:
77 22 0.04
78 1 0.00
79 3 0.00
80 148 0.24
81 95 0.16
82 9 0.01
83 97 0.16
84 110 0.18
85 121 0.20
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (85 bp):
AGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGC
TGCAAATGATGTGCCCTTGA
Found at i:374149 original size:165 final size:164
Alignment explanation
Indices: 373665--374560 Score: 1032
Period size: 165 Copynumber: 5.5 Consensus size: 164
373655 GTTTGCCTCT
* * * * * *
373665 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACTCTTATAGCCTTGAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATG
* * * * * *
373730 CTACAAATGATATGCCCCCGAAGCTGAGTGTAACCGAACTTGAAGGTCTTTGGTTGGCATATAGC
66 CTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTC--T--TTGGCAGATAGC
* *
373795 CCTTCTCGACTTAAGCTATGCTGCAAATGTTGTGCCTTT
127 CCTTCTCGACTTAAGCTAT-CTGCAAATGATGTGCCTTG
* * * * * *
373834 GAGCTGAGTGTAATCTAACTCGAAGGTC-TTTGTTGGCAGATAACCTTTCTAGCCTTGAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATG
* * * ** * ** *
373898 CTGCAAATGATGTG-CCTTGGAGTTGAACGTAGTCGAACTCGAAGGTGATTGGCATATAGCCCTT
66 CTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTT
* *
373962 CTCGACTTAAGTTATACTGCAAACGATGTGCCTTG
131 CTCGACTTAAGCTAT-CTGCAAATGATGTGCCTTG
* * * *
373997 GAGCTGAACGTAGTCAAACTCGAAGGTCTTTTGGTCACAGACAACCCTTCTAGCCTTGAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATG
* * * * *
374062 CTGTAAATGTTGTGCCCTCGAAGTTGAGTGTAGTCGAACTCGAGGGTCTTTGGCAGATAGCCCTT
66 CTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTT
* * *
374127 CTCGACTTAAACTACTCTGCAAATAATATGCCTTG
131 CTCGACTTAAGCTA-TCTGCAAATGATGTGCCTTG
* *
374162 GAGCTGAGCGTAGTCGAACTTGAAGGTCTTTTGGTAACAGATAACCCTTCTAGCCTTGAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATG
* * * * *
374227 CTGTAAATGTTGTGCCCTCGAAGCTGAGTGTAATCGAACTTGCAGGTATTTGGCAGATAGCCCTT
66 CTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTT
* * *
374292 CTCGACTTAAGCTATTCTGCAAATGATATGCATAG
131 CTCGACTTAAGCTA-TCTGCAAATGATGTGCCTTG
* * * * * *
374327 GAGCTGAGCGTAGTCGAACTCAAAAGTCTTTTGGTCACATATAACCCTTATAGCATTGAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATG
* * *
374392 TTG----TGATGTGCCCTCGAAGCTGAATGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTT
66 CTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTT
* *
374453 CTCGACTTAAGCTATTATGCAAATGATGTGCCTTA
131 CTCGACTTAAGCTA-TCTGCAAATGATGTGCCTTG
* * * * * *
374488 GAGCTGAACGTAGTCGAACTCAAAGGTC-TTTGTTGGCATATAACCCTTCTAGCCTTGAGTTAAG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATG
374552 CTGCAAATG
66 CTGCAAATG
374561 TTGTTGTTTT
Statistics
Matches: 630, Mismatches: 90, Indels: 19
0.85 0.12 0.03
Matches are distributed among these distances:
160 32 0.05
161 108 0.17
163 70 0.11
164 45 0.07
165 279 0.44
166 1 0.00
167 23 0.04
168 45 0.07
169 27 0.04
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (164 bp):
GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATG
CTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTT
CTCGACTTAAGCTATCTGCAAATGATGTGCCTTG
Found at i:378716 original size:50 final size:50
Alignment explanation
Indices: 378693--378799 Score: 139
Period size: 50 Copynumber: 2.1 Consensus size: 50
378683 AAAAATAAGA
378693 AAAATAAAATAAATCAAAGAAAGAAAAAATAAAATAAATAAAAATATAATG
1 AAAA-AAAATAAATCAAAGAAAGAAAAAATAAAATAAATAAAAATATAATG
378744 AAAAAAAATAAATCAAAGACAACGAAAAAATGAAGAATAAA-AAACAAT-TAAT-
1 AAAAAAAATAAATCAAAGA-AA-GAAAAAAT-AA-AATAAATAAA-AATATAATG
378796 AAAA
1 AAAA
378800 TTAATAAAAG
Statistics
Matches: 51, Mismatches: 0, Indels: 9
0.85 0.00 0.15
Matches are distributed among these distances:
50 15 0.29
51 6 0.12
52 12 0.24
53 9 0.18
54 9 0.18
ACGTcount: A:0.74, C:0.05, G:0.07, T:0.15
Consensus pattern (50 bp):
AAAAAAAATAAATCAAAGAAAGAAAAAATAAAATAAATAAAAATATAATG
Found at i:378720 original size:25 final size:25
Alignment explanation
Indices: 378692--378784 Score: 93
Period size: 25 Copynumber: 3.6 Consensus size: 25
378682 GAAAAATAAG
378692 AAAAATAAAATAAATCAAAGAAAGA
1 AAAAATAAAATAAATCAAAGAAAGA
*
378717 AAAAATAAAATAAAT-AAA-AATATA
1 AAAAATAAAATAAATCAAAGAA-AGA
378741 ATGAAAA-AAAATAAATCAAAGACAACGA
1 A--AAAATAAAATAAATCAAAGA-AA-GA
378769 AAAAATGAAGAATAAA
1 AAAAAT-AA-AATAAA
378785 AAACAATTAA
Statistics
Matches: 56, Mismatches: 2, Indels: 16
0.76 0.03 0.22
Matches are distributed among these distances:
23 2 0.04
24 6 0.11
25 24 0.43
26 11 0.20
27 2 0.04
28 5 0.09
29 6 0.11
ACGTcount: A:0.74, C:0.04, G:0.08, T:0.14
Consensus pattern (25 bp):
AAAAATAAAATAAATCAAAGAAAGA
Found at i:378737 original size:15 final size:15
Alignment explanation
Indices: 378673--378755 Score: 57
Period size: 15 Copynumber: 5.5 Consensus size: 15
378663 AAGAAATTTT
*
378673 AAATAAATTGAAAAA
1 AAATAAAATGAAAAA
*
378688 TAAGA-AAAAT-AAAAT
1 -AA-ATAAAATGAAAAA
*
378703 AAATCAAA-GAAAGAAA
1 AAATAAAATG-AA-AAA
378719 AAATAAAAT-AAATAA
1 AAATAAAATGAAA-AA
*
378734 AAATATAATGAAAAA
1 AAATAAAATGAAAAA
378749 AAATAAA
1 AAATAAA
378756 TCAAAGACAA
Statistics
Matches: 52, Mismatches: 7, Indels: 17
0.68 0.09 0.22
Matches are distributed among these distances:
13 1 0.02
14 6 0.12
15 26 0.50
16 18 0.35
17 1 0.02
ACGTcount: A:0.76, C:0.01, G:0.06, T:0.17
Consensus pattern (15 bp):
AAATAAAATGAAAAA
Found at i:381764 original size:21 final size:21
Alignment explanation
Indices: 381717--381765 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
381707 GTTGACATGG
*
381717 TCGTTGACTTTGACCCATTGA
1 TCGTTGACTTTGACACATTGA
**
381738 -CTGTTGACTTTGACATGTTGA
1 TC-GTTGACTTTGACACATTGA
381759 TCGTTGA
1 TCGTTGA
381766 TTTTAAAGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 1 0.04
21 21 0.91
22 1 0.04
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.41
Consensus pattern (21 bp):
TCGTTGACTTTGACACATTGA
Found at i:383243 original size:14 final size:14
Alignment explanation
Indices: 383224--383253 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
383214 ATATAAAGTA
383224 TGGTTTCTGATATC
1 TGGTTTCTGATATC
*
383238 TGGTTTCTGATTTC
1 TGGTTTCTGATATC
383252 TG
1 TG
383254 ACACAAGGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.10, C:0.13, G:0.23, T:0.53
Consensus pattern (14 bp):
TGGTTTCTGATATC
Found at i:384091 original size:6 final size:6
Alignment explanation
Indices: 384080--384105 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
384070 ATTTACAATT
384080 ATCAAC ATCAAC ATCAAC ATCAAC AT
1 ATCAAC ATCAAC ATCAAC ATCAAC AT
384106 TGGGAGTTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.31, G:0.00, T:0.19
Consensus pattern (6 bp):
ATCAAC
Found at i:384753 original size:29 final size:29
Alignment explanation
Indices: 384694--384754 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
384684 AAATGCCCAA
*
384694 TTTTTCAATACTTATTATTAGGGCTCAAT
1 TTTTTCAATACTTATTATTAGGGCGCAAT
* *
384723 TTTTTTAATATTTATTATTAGGG-GCATAT
1 TTTTTCAATACTTATTATTAGGGCGCA-AT
384752 TTT
1 TTT
384755 AATATTCAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 2 0.07
29 26 0.93
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.54
Consensus pattern (29 bp):
TTTTTCAATACTTATTATTAGGGCGCAAT
Found at i:387246 original size:2 final size:2
Alignment explanation
Indices: 387239--387264 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
387229 TGAGGTTTCA
387239 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
387265 CGTCTAAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:392654 original size:34 final size:34
Alignment explanation
Indices: 392611--392677 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
392601 CATCCATCAA
392611 AATGATCAGTTTAATTTAGCCAATTTATGTTATT
1 AATGATCAGTTTAATTTAGCCAATTTATGTTATT
392645 AATGATCAGTTTAATTTAGCCAATTTATGTTAT
1 AATGATCAGTTTAATTTAGCCAATTTATGTTAT
392678 CTTACTAGGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (34 bp):
AATGATCAGTTTAATTTAGCCAATTTATGTTATT
Found at i:394973 original size:16 final size:16
Alignment explanation
Indices: 394952--394982 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
394942 AACCGGAACA
394952 CGAAAATGCCTTTCAG
1 CGAAAATGCCTTTCAG
*
394968 CGAAAATGTCTTTCA
1 CGAAAATGCCTTTCA
394983 ACGGTGAAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (16 bp):
CGAAAATGCCTTTCAG
Found at i:398625 original size:23 final size:22
Alignment explanation
Indices: 398554--398625 Score: 58
Period size: 23 Copynumber: 3.3 Consensus size: 22
398544 GATAGACATG
*
398554 TAAA-AGTTTAATTTATATTTTT
1 TAAATAGTCTAATTTAT-TTTTT
* * ** *
398576 TTAATAGTTTAATTTA-CATAT
1 TAAATAGTCTAATTTATTTTTT
398597 TAAATAGCTCTAATTTATTTTTT
1 TAAATAG-TCTAATTTATTTTTT
398620 TAAATA
1 TAAATA
398626 TCTTTTACAA
Statistics
Matches: 38, Mismatches: 9, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
21 8 0.21
22 11 0.29
23 19 0.50
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (22 bp):
TAAATAGTCTAATTTATTTTTT
Found at i:398949 original size:31 final size:31
Alignment explanation
Indices: 398914--398989 Score: 125
Period size: 31 Copynumber: 2.5 Consensus size: 31
398904 TTTAAAACAC
*
398914 AAGTTTTGGTCACTTATGTTATTGTTTTATT
1 AAGTTTTGGTCACTTATGTTATCGTTTTATT
* *
398945 AAGTTTTGATCATTTATGTTATCGTTTTATT
1 AAGTTTTGGTCACTTATGTTATCGTTTTATT
398976 AAGTTTTGGTCACT
1 AAGTTTTGGTCACT
398990 AAGACGTTGA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.21, C:0.08, G:0.16, T:0.55
Consensus pattern (31 bp):
AAGTTTTGGTCACTTATGTTATCGTTTTATT
Found at i:399260 original size:31 final size:31
Alignment explanation
Indices: 399225--399300 Score: 116
Period size: 31 Copynumber: 2.5 Consensus size: 31
399215 TTTAAAACAC
*
399225 AAGTTTTGGTCACTTATGTTATTGTTTTATT
1 AAGTTTTGGTCACTTATGTTATCGTTTTATT
** *
399256 AAGTTTTAATCATTTATGTTATCGTTTTATT
1 AAGTTTTGGTCACTTATGTTATCGTTTTATT
399287 AAGTTTTGGTCACT
1 AAGTTTTGGTCACT
399301 AAGACATTGA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.22, C:0.08, G:0.14, T:0.55
Consensus pattern (31 bp):
AAGTTTTGGTCACTTATGTTATCGTTTTATT
Found at i:399456 original size:311 final size:311
Alignment explanation
Indices: 398893--399519 Score: 1209
Period size: 311 Copynumber: 2.0 Consensus size: 311
398883 TGTACATTTT
*
398893 TGCTCACCAAATTTAAAACACAAGTTTTGGTCACTTATGTTATTGTTTTATTAAGTTTTGATCAT
1 TGCTCACCAAATTTAAAACACAAGTTTTGGTCACTTATGTTATTGTTTTATTAAGTTTTAATCAT
*
398958 TTATGTTATCGTTTTATTAAGTTTTGGTCACTAAGACGTTGAATGTCATTAGTTTAATGATGTGA
66 TTATGTTATCGTTTTATTAAGTTTTGGTCACTAAGACATTGAATGTCATTAGTTTAATGATGTGA
399023 CCCATTAATAAAATTGTCTAATTTTATTTTAACCCCTAAACTTTAGACAAAATATTGATTATGGG
131 CCCATTAATAAAATTGTCTAATTTTATTTTAACCCCTAAACTTTAGACAAAATATTGATTATGGG
399088 TCCTTTTGTAAATTCAAATTCGCTTAGGGAAAACATTTCAATTTATCCATTTTAATAGGTTTTCT
196 TCCTTTTGTAAATTCAAATTCGCTTAGGGAAAACATTTCAATTTATCCATTTTAATAGGTTTTCT
*
399153 TCCCAACCCTATTATTGTTCATCTTGTCTCTGATTCTTCTTTAGACATATC
261 TCCCAACCCTATTATTGTTCATCTTATCTCTGATTCTTCTTTAGACATATC
399204 TGCTCACCAAATTTAAAACACAAGTTTTGGTCACTTATGTTATTGTTTTATTAAGTTTTAATCAT
1 TGCTCACCAAATTTAAAACACAAGTTTTGGTCACTTATGTTATTGTTTTATTAAGTTTTAATCAT
399269 TTATGTTATCGTTTTATTAAGTTTTGGTCACTAAGACATTGAATGTCATTAGTTTAATGATGTGA
66 TTATGTTATCGTTTTATTAAGTTTTGGTCACTAAGACATTGAATGTCATTAGTTTAATGATGTGA
399334 CCCATTAATAAAATTGTCTAATTTTATTTTAACCCCTAAACTTTAGACAAAATATTGATTATGGG
131 CCCATTAATAAAATTGTCTAATTTTATTTTAACCCCTAAACTTTAGACAAAATATTGATTATGGG
*
399399 TCCTTTTGTAAATTCAAATTCGTTTAGGGAAAACATTTCAATTTATCCATTTTAATAGGTTTTCT
196 TCCTTTTGTAAATTCAAATTCGCTTAGGGAAAACATTTCAATTTATCCATTTTAATAGGTTTTCT
*
399464 TCCCAACCCTATTATTGTTCATCTTATCTCTGATTCTTCTTTAGACATCTC
261 TCCCAACCCTATTATTGTTCATCTTATCTCTGATTCTTCTTTAGACATATC
399515 TGCTC
1 TGCTC
399520 CATTGCTTTA
Statistics
Matches: 311, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
311 311 1.00
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.44
Consensus pattern (311 bp):
TGCTCACCAAATTTAAAACACAAGTTTTGGTCACTTATGTTATTGTTTTATTAAGTTTTAATCAT
TTATGTTATCGTTTTATTAAGTTTTGGTCACTAAGACATTGAATGTCATTAGTTTAATGATGTGA
CCCATTAATAAAATTGTCTAATTTTATTTTAACCCCTAAACTTTAGACAAAATATTGATTATGGG
TCCTTTTGTAAATTCAAATTCGCTTAGGGAAAACATTTCAATTTATCCATTTTAATAGGTTTTCT
TCCCAACCCTATTATTGTTCATCTTATCTCTGATTCTTCTTTAGACATATC
Found at i:400609 original size:28 final size:28
Alignment explanation
Indices: 400570--400623 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
400560 ATTTAGTAAA
400570 ACAATAACATAAGTGACCAAAACTTAAT
1 ACAATAACATAAGTGACCAAAACTTAAT
*
400598 ACAATAACATAAGTGACCAAAGCTTA
1 ACAATAACATAAGTGACCAAAACTTA
400624 TGTTTTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.52, C:0.19, G:0.09, T:0.20
Consensus pattern (28 bp):
ACAATAACATAAGTGACCAAAACTTAAT
Found at i:404960 original size:27 final size:27
Alignment explanation
Indices: 404922--404987 Score: 123
Period size: 27 Copynumber: 2.4 Consensus size: 27
404912 GATAATGACT
*
404922 CTGAATCATTCAGAATGTACTTTTGTG
1 CTGAATCATTCAGAATGTACTTCTGTG
404949 CTGAATCATTCAGAATGTACTTCTGTG
1 CTGAATCATTCAGAATGTACTTCTGTG
404976 CTGAATCATTCA
1 CTGAATCATTCA
404988 ACACTGTTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (27 bp):
CTGAATCATTCAGAATGTACTTCTGTG
Found at i:405764 original size:2 final size:2
Alignment explanation
Indices: 405757--405787 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
405747 TTTAAATAAG
405757 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
405788 ACGATCTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:408467 original size:18 final size:19
Alignment explanation
Indices: 408433--408468 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
408423 TCTAAACTTT
*
408433 TTATTGGATTCATTAAGAA
1 TTATTCGATTCATTAAGAA
408452 TTATTCGATT-ATTAAGA
1 TTATTCGATTCATTAAGA
408469 TTGTTAAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.36, C:0.06, G:0.14, T:0.44
Consensus pattern (19 bp):
TTATTCGATTCATTAAGAA
Found at i:412414 original size:578 final size:578
Alignment explanation
Indices: 411319--412483 Score: 2321
Period size: 578 Copynumber: 2.0 Consensus size: 578
411309 TCACTTCAAA
411319 AAAAAATTTAATGACAAGATTTTTTTTTTGCAATTGTGTTCCATTCCATAACTTATTTCTACACC
1 AAAAAATTTAATGACAAGATTTTTTTTTTGCAATTGTGTTCCATTCCATAACTTATTTCTACACC
411384 ACTTTCAACATGAAGATCAAGAAAATGAATTGTATGGTTTGATTTCAATGAAGCTTAAAAAATAT
66 ACTTTCAACATGAAGATCAAGAAAATGAATTGTATGGTTTGATTTCAATGAAGCTTAAAAAATAT
411449 ACAACACAACAAATGGCTTTTTTGCAAGTATAAGTTTCTTTTGATGAGCCCGACCCTGAAGCCAA
131 ACAACACAACAAATGGCTTTTTTGCAAGTATAAGTTTCTTTTGATGAGCCCGACCCTGAAGCCAA
411514 CCCTGAAACTTACCAAATAGGAAGTACCTTCGAAAGATGTTTAGGGATTACACAAACATGTCAGT
196 CCCTGAAACTTACCAAATAGGAAGTACCTTCGAAAGATGTTTAGGGATTACACAAACATGTCAGT
411579 GGTATGAACATCGAGTTGACTGTAAAACTTGAGGAATAAGCATCTTCATCAAGTAATGTAAAAGC
261 GGTATGAACATCGAGTTGACTGTAAAACTTGAGGAATAAGCATCTTCATCAAGTAATGTAAAAGC
411644 AACTCAATTGTCCCAAGACCAAGAGGATGAAGCACGAGATATGCTATGAAAAACATTTTCGTCTT
326 AACTCAATTGTCCCAAGACCAAGAGGATGAAGCACGAGATATGCTATGAAAAACATTTTCGTCTT
411709 CATTAGACATTTCTACAGAATACGAAAAACATCTTCTAGCTCCTTTTATATTCATTTCAACTAAC
391 CATTAGACATTTCTACAGAATACGAAAAACATCTTCTAGCTCCTTTTATATTCATTTCAACTAAC
411774 TATAACTTCATGTAGTTCTTTTTTTATGTTTATAAACTAGTGTTTAAATAAATTATCATTTTGAA
456 TATAACTTCATGTAGTTCTTTTTTTATGTTTATAAACTAGTGTTTAAATAAATTATCATTTTGAA
411839 GTATAATTTGATTGATATTTTAAATATGTGATCTAACAAAACTTAATTAATAAATTTT
521 GTATAATTTGATTGATATTTTAAATATGTGATCTAACAAAACTTAATTAATAAATTTT
411897 AAAAAATTTAATGACAAGATTTTTTTTTTGCAATTGTGTTCCATTCCATAACTTATTTCTACACC
1 AAAAAATTTAATGACAAGATTTTTTTTTTGCAATTGTGTTCCATTCCATAACTTATTTCTACACC
411962 ACTTTCAACATGAAGATCAAGAAAATGAATTGTATGGTTTGATTTCAATGAAGCTTAAAAAATAT
66 ACTTTCAACATGAAGATCAAGAAAATGAATTGTATGGTTTGATTTCAATGAAGCTTAAAAAATAT
412027 ACAACACAACAAATGGCTTTTTTGCAAGTATAAGTTTCTTTTGATGAGCCCGACCCTGAAGCCAA
131 ACAACACAACAAATGGCTTTTTTGCAAGTATAAGTTTCTTTTGATGAGCCCGACCCTGAAGCCAA
412092 CCCTGAAACTTACCAAATAGGAAGTACCTTCGAAAGATGTTTAGGGATTACACAAACATGTCAGT
196 CCCTGAAACTTACCAAATAGGAAGTACCTTCGAAAGATGTTTAGGGATTACACAAACATGTCAGT
412157 GGTATGAACATCGAGTTGACTGTAAAACTTGAGGAATAAGCATCTTCATCAAGTAATGTAAAAGC
261 GGTATGAACATCGAGTTGACTGTAAAACTTGAGGAATAAGCATCTTCATCAAGTAATGTAAAAGC
412222 AACTCAATTGTCCCAAGACCAAGAGGATGAAGCACGAGATATGCTATGAAAAACATTTTCGTCTT
326 AACTCAATTGTCCCAAGACCAAGAGGATGAAGCACGAGATATGCTATGAAAAACATTTTCGTCTT
412287 CATTAGACATTTCTACAGAATACGAAAAACATCTTCTAGCTCCTTTTATATTCATTTCAACTAAC
391 CATTAGACATTTCTACAGAATACGAAAAACATCTTCTAGCTCCTTTTATATTCATTTCAACTAAC
412352 TATAACTTCATGTAGTTCTTTTTTTATGTTTATAAACTAGTGTTTAAATAAATTATCATTTTGAA
456 TATAACTTCATGTAGTTCTTTTTTTATGTTTATAAACTAGTGTTTAAATAAATTATCATTTTGAA
*
412417 GTATAATTTTATTGATATTTTAAATATGTGATCTAACAAAACTTAATTAATAAATTTT
521 GTATAATTTGATTGATATTTTAAATATGTGATCTAACAAAACTTAATTAATAAATTTT
412475 AAAAAATTT
1 AAAAAATTT
412484 GAACATTATA
Statistics
Matches: 586, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
578 586 1.00
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.34
Consensus pattern (578 bp):
AAAAAATTTAATGACAAGATTTTTTTTTTGCAATTGTGTTCCATTCCATAACTTATTTCTACACC
ACTTTCAACATGAAGATCAAGAAAATGAATTGTATGGTTTGATTTCAATGAAGCTTAAAAAATAT
ACAACACAACAAATGGCTTTTTTGCAAGTATAAGTTTCTTTTGATGAGCCCGACCCTGAAGCCAA
CCCTGAAACTTACCAAATAGGAAGTACCTTCGAAAGATGTTTAGGGATTACACAAACATGTCAGT
GGTATGAACATCGAGTTGACTGTAAAACTTGAGGAATAAGCATCTTCATCAAGTAATGTAAAAGC
AACTCAATTGTCCCAAGACCAAGAGGATGAAGCACGAGATATGCTATGAAAAACATTTTCGTCTT
CATTAGACATTTCTACAGAATACGAAAAACATCTTCTAGCTCCTTTTATATTCATTTCAACTAAC
TATAACTTCATGTAGTTCTTTTTTTATGTTTATAAACTAGTGTTTAAATAAATTATCATTTTGAA
GTATAATTTGATTGATATTTTAAATATGTGATCTAACAAAACTTAATTAATAAATTTT
Found at i:414200 original size:26 final size:25
Alignment explanation
Indices: 414157--414206 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
414147 ATTATTGTAA
414157 AAAATTACAATAACATAAACTAAAAT
1 AAAATTACAATAACATAAA-TAAAAT
* **
414183 AAAATTTCAATATTATAAATAAAA
1 AAAATTACAATAACATAAATAAAA
414207 AATCAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (25 bp):
AAAATTACAATAACATAAATAAAAT
Found at i:423183 original size:19 final size:19
Alignment explanation
Indices: 423161--423199 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
423151 CTATCCTATG
423161 TAGATGTTTCTTATTGGCT
1 TAGATGTTTCTTATTGGCT
423180 TAGATGTTTCTTATTGGCT
1 TAGATGTTTCTTATTGGCT
423199 T
1 T
423200 CGGTTCGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.10, G:0.21, T:0.54
Consensus pattern (19 bp):
TAGATGTTTCTTATTGGCT
Found at i:429072 original size:2 final size:2
Alignment explanation
Indices: 429065--429095 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
429055 AACCAGAGCT
429065 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 T
429096 GTGCGCGCGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.