Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006743.1 Hibiscus syriacus cultivar Beakdansim tig00016935_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: 431342
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 2 of 3
Found at i:189899 original size:34 final size:37
Alignment explanation
Indices: 189855--189956 Score: 167
Period size: 34 Copynumber: 2.8 Consensus size: 37
189845 TTTCGTCCTA
189855 CTAGGATTCAAACTCCTAAAAATAGGATAGA-A-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
189890 -TAGGATTCAAACTCCTAAAAATAGGATA-ACATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
189925 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
189957 GTTCTATTAA
Statistics
Matches: 62, Mismatches: 0, Indels: 7
0.90 0.00 0.10
Matches are distributed among these distances:
33 1 0.02
34 29 0.47
35 3 0.05
37 28 0.45
38 1 0.02
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (37 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
Found at i:189980 original size:37 final size:34
Alignment explanation
Indices: 189856--189990 Score: 162
Period size: 37 Copynumber: 3.8 Consensus size: 34
189846 TTCGTCCTAC
*
189856 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGATTTT
*
189890 TAGGATTCAAACTCCTAAAAATAGGATAACATTTT
1 TAGGATTCAAACTCCTAAAAATAGGAT-AGATTTT
189925 GCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTCTAT
1 --TAGGATTCAAACTCCTAAAAATAGGATAGA-TT-T-T
* * * *
189964 TAAGATTTAAATTCCTAAAGATAGGAT
1 TAGGATTCAAACTCCTAAAAATAGGAT
189991 CCACAAGCAC
Statistics
Matches: 88, Mismatches: 7, Indels: 9
0.85 0.07 0.09
Matches are distributed among these distances:
34 27 0.31
35 5 0.06
36 2 0.02
37 52 0.59
38 1 0.01
39 1 0.01
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (34 bp):
TAGGATTCAAACTCCTAAAAATAGGATAGATTTT
Found at i:190385 original size:18 final size:17
Alignment explanation
Indices: 190346--190388 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
190336 ATTATATAGA
190346 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
190362 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
190380 TATTATTAT
1 TATTATTAT
190389 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:199046 original size:119 final size:116
Alignment explanation
Indices: 198806--199030 Score: 380
Period size: 119 Copynumber: 1.9 Consensus size: 116
198796 AAGACCACAC
*
198806 TAAAACCACCGTATGAATAAATCACAACATATCATTCAATCCAATTAGCCATAATAGTAAATACA
1 TAAAACCACCGTATGAATAAATCACAACATATCATTCAATCCAATTAGCCAAAATAGTAAATACA
*
198871 TTTTTAGGGTGGTATAATCGTAAAAGGATGATGCCTTCTGACTAATCGTAATGG
66 TTTTTAGGGTGGTATAATC---AAAGGATGATGCCTTCTGACTAATCGGAATGG
*
198925 TAAAACCACCTTATGAATAAATCACAACATATCATTCAATCCAATTAGCCAAAATAGTAAATACA
1 TAAAACCACCGTATGAATAAATCACAACATATCATTCAATCCAATTAGCCAAAATAGTAAATACA
*
198990 TTTTTAGGGTGGTATAATC-AAGGATTATGCCTTCTGACTAA
66 TTTTTAGGGTGGTATAATCAAAGGATGATGCCTTCTGACTAA
199031 GAATTGGATT
Statistics
Matches: 103, Mismatches: 3, Indels: 4
0.94 0.03 0.04
Matches are distributed among these distances:
115 21 0.20
119 82 0.80
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (116 bp):
TAAAACCACCGTATGAATAAATCACAACATATCATTCAATCCAATTAGCCAAAATAGTAAATACA
TTTTTAGGGTGGTATAATCAAAGGATGATGCCTTCTGACTAATCGGAATGG
Found at i:200984 original size:16 final size:16
Alignment explanation
Indices: 200963--200998 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
200953 TTAGAGTGAC
200963 AACAATATTAGTTTAT
1 AACAATATTAGTTTAT
200979 AACAATATTAGTTTAT
1 AACAATATTAGTTTAT
200995 AACA
1 AACA
200999 TCTACGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.39
Consensus pattern (16 bp):
AACAATATTAGTTTAT
Found at i:204390 original size:11 final size:11
Alignment explanation
Indices: 204374--204405 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
204364 TAGAAAGATA
204374 GGAGAGGAGGC
1 GGAGAGGAGGC
204385 GGAGAGGAGGC
1 GGAGAGGAGGC
204396 GGAGAGGAGG
1 GGAGAGGAGG
204406 GTTTTTGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.28, C:0.06, G:0.66, T:0.00
Consensus pattern (11 bp):
GGAGAGGAGGC
Found at i:207780 original size:16 final size:17
Alignment explanation
Indices: 207759--207790 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
207749 AGTTTAGTAT
207759 TTCTTCTTTT-TTCTTC
1 TTCTTCTTTTCTTCTTC
207775 TTCTTCTTTTCTTCTT
1 TTCTTCTTTTCTTCTT
207791 TTTTTTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (17 bp):
TTCTTCTTTTCTTCTTC
Found at i:207888 original size:21 final size:21
Alignment explanation
Indices: 207864--207906 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
207854 TTCATATTCG
* *
207864 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
207885 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
207906 T
1 T
207907 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:210690 original size:13 final size:13
Alignment explanation
Indices: 210672--210712 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
210662 CCGAAGTGCC
210672 CCGTAGAATTGCA
1 CCGTAGAATTGCA
210685 CCGTAG---TGC-
1 CCGTAGAATTGCA
210694 CCGTAGAATTGCA
1 CCGTAGAATTGCA
210707 CCGTAG
1 CCGTAG
210713 TGCCCGTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
9 6 0.25
10 3 0.12
12 3 0.12
13 12 0.50
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (13 bp):
CCGTAGAATTGCA
Found at i:210699 original size:22 final size:22
Alignment explanation
Indices: 210658--210724 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
210648 CTCGTATAAA
*
210658 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGTAGTG-CCCGTAGAAT
210681 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGTAGTGCCCGTAGAAT
210703 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGTAGTGCCCGTAGAAT
210725 GATGTCCCTA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 32 0.74
23 11 0.26
ACGTcount: A:0.24, C:0.28, G:0.27, T:0.21
Consensus pattern (22 bp):
TGCACCGTAGTGCCCGTAGAAT
Found at i:212497 original size:22 final size:21
Alignment explanation
Indices: 212451--212493 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
212441 TTCATATTCG
* *
212451 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
212472 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
212493 C
1 C
212494 CTTGCCCATA
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:0.28, G:0.28, T:0.28
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:217828 original size:14 final size:13
Alignment explanation
Indices: 217803--217841 Score: 69
Period size: 14 Copynumber: 2.9 Consensus size: 13
217793 AGTTTAGTCT
217803 TTCTTCTTTTTTC
1 TTCTTCTTTTTTC
217816 TTCTTCTTCTTTTC
1 TTCTTCTT-TTTTC
217830 TTCTTCTTTTTT
1 TTCTTCTTTTTT
217842 TATATAGGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 12 0.48
14 13 0.52
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TTCTTCTTTTTTC
Found at i:221819 original size:13 final size:13
Alignment explanation
Indices: 221797--221847 Score: 66
Period size: 13 Copynumber: 3.9 Consensus size: 13
221787 TTTATATAAA
221797 TAATTAATCAAAT
1 TAATTAATCAAAT
*
221810 TAATTTATCAAAT
1 TAATTAATCAAAT
* * *
221823 AAACTAATTAAAT
1 TAATTAATCAAAT
221836 TAATTAATCAAA
1 TAATTAATCAAA
221848 CCAACTATTA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (13 bp):
TAATTAATCAAAT
Found at i:221853 original size:26 final size:26
Alignment explanation
Indices: 221801--221864 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
221791 TATAAATAAT
* * *
221801 TAATCAAATTAATTTATCAAATAAAC
1 TAATTAAATTAATTAATCAAACAAAC
*
221827 TAATTAAATTAATTAATCAAACCAAC
1 TAATTAAATTAATTAATCAAACAAAC
221853 T-ATTAAAATTAA
1 TAATT-AAATTAA
221865 CTATAAGCTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 3 0.09
26 30 0.91
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (26 bp):
TAATTAAATTAATTAATCAAACAAAC
Found at i:232182 original size:12 final size:12
Alignment explanation
Indices: 232165--232241 Score: 54
Period size: 12 Copynumber: 6.5 Consensus size: 12
232155 TATATAACTT
232165 AATAATAATAAA
1 AATAATAATAAA
*
232177 AATAATCATAAA
1 AATAATAATAAA
*
232189 GATAATAATTTAAA
1 AATAATAA--TAAA
*
232203 CAT-AT-ATCAAA
1 AATAATAAT-AAA
*
232214 AGTAATAAT-AA
1 AATAATAATAAA
*
232225 AATAA-AATAAT
1 AATAATAATAAA
232236 AATAAT
1 AATAAT
232242 TAAAATGAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 14
0.69 0.11 0.19
Matches are distributed among these distances:
10 4 0.08
11 16 0.32
12 20 0.40
13 4 0.08
14 6 0.12
ACGTcount: A:0.65, C:0.04, G:0.03, T:0.29
Consensus pattern (12 bp):
AATAATAATAAA
Found at i:232237 original size:16 final size:17
Alignment explanation
Indices: 232211--232270 Score: 65
Period size: 15 Copynumber: 3.8 Consensus size: 17
232201 AACATATATC
232211 AAAAGTAATAATAAAAT
1 AAAAGTAATAATAAAAT
*
232228 AAAA-TAATAAT-AATT
1 AAAAGTAATAATAAAAT
* *
232243 AAAA-TGA-AAGAAAAT
1 AAAAGTAATAATAAAAT
232258 AAAAGTAATAATA
1 AAAAGTAATAATA
232271 TTAAAACTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
14 2 0.06
15 16 0.47
16 9 0.26
17 7 0.21
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (17 bp):
AAAAGTAATAATAAAAT
Found at i:232258 original size:19 final size:19
Alignment explanation
Indices: 232216--232259 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
232206 ATATCAAAAG
*
232216 TAATAATAAAATAAAATAA
1 TAATAATAAAATAAAAGAA
*
232235 TAATAATTAAAATGAAAGAA
1 TAATAA-TAAAATAAAAGAA
232255 -AATAA
1 TAATAA
232260 AAGTAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (19 bp):
TAATAATAAAATAAAAGAA
Found at i:233607 original size:3 final size:3
Alignment explanation
Indices: 233599--233674 Score: 89
Period size: 3 Copynumber: 24.7 Consensus size: 3
233589 TTATTTATTA
* * *
233599 AAT AAT AAT AAT ATAT AAT ATT AAT ATT AAT AAT AAAT AAT AAT ACT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
**
233646 AAT AAT AAT AAT TTT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
233675 ATTTAAATGA
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
3 55 0.90
4 6 0.10
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:234220 original size:113 final size:113
Alignment explanation
Indices: 234023--238112 Score: 7446
Period size: 113 Copynumber: 36.3 Consensus size: 113
234013 GAATTATGCG
* ** * *
234023 AAAGGTTGAATAAGCTCTTCTCATTGTGAACTTT-TTCTT-CTCCTTCAGATGAGTTCTTCTCAT
1 AAAGGTTGAACAAATTCTTCTCATTATGAA-TTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
234086 TATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
65 TATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
234135 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
234200 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
66 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
*
234248 AAAGGTTGAACAAATTCTTCTCATTATGAATTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
234313 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
66 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
234361 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
234426 ATGAACTTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
66 ATGAAC-TTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
*
234475 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCATATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
234540 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
66 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
234588 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
234653 ATGAACTTTTTCTGAAAAAGCTGATCCATCAGATGATGGATTTGAGAA
66 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
234701 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
234766 ATGAACTTTTTCTGG-AAAGCTGATCCATCAGATGATGGATTTGAGCA
66 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
234813 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
234878 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
66 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
* *
234926 AAAGGTTGAACAAATTCTTCTCATTATGAATTTATTCTTCATTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
234991 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAACA
66 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
*
235039 AAAGGTTGAACAAATTCTTCTCATTATGAATTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
235104 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
66 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
235152 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
235217 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAACA
66 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
* *
235265 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCATCCTTCTTCAGATTAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
235330 ATGAACTTTTTCTAGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
66 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
*
235378 AAATGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
235443 ATGAGCTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
66 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
*
235491 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTAATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
235556 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATAGATTTGAGCA
66 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
235604 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
235669 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
66 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
* * * *
235717 AAAGGTTGAACAAATTATTCTCATTATGAATTTATTCTTCATTCTTCAGATGAATTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* **
235782 ATGAACTTTTTCTGGAAAAGTTGATCCATCAGATGATGGATTTGAATA
66 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
* * *
235830 AAAGGTTGAATAAATTCTTCTCATTATGAATTTCTTATTTCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
235895 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATAATGGATTTGAGCA
66 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
235943 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
236008 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGAATTTGAACA
66 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
236056 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
236121 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGA--T-----
66 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
236162 -----TTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
236222 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
66 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
*
236270 AAAGGTTGAACAAATTCTTCTCA-TATGAATTTCTTCTTCCTTCTTCAGATGAGTTATTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
236334 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAACA
66 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
236382 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
236447 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
66 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
236495 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
236560 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
66 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
*
236608 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTACCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
236673 ATGAACTTTTTCTGGAAAAGCTGGTCCATCAGATGATGGATTTGAGCA
66 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
236721 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
236786 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAACA
66 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
*
236834 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
236899 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
66 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
236947 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
237012 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
66 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
*
237060 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
237125 ATGAACTTTTTCTGGAAAAGCTGGTCCATCAGATGATGGATTTGAGCA
66 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
237173 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
237238 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAACA
66 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
*
237286 AAAGGTTGAATAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAG-T-TTCTTCAT
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTC-TCAT
* *
237349 TATGAACTTTTTCTTGAAAAGCTGGTCCATCAGATGATGGATTTGAGCA
65 TATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
237398 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
237463 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAACA
66 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
*
237511 AAAGGTTGAATAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
237576 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
66 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
* *
237624 AAAGATTGAACAAATTCTTCTCATTATGAATTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
237689 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAACA
66 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
237737 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
237802 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAACA
66 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
237850 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
237915 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
66 ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
* *
237963 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTATTCCTTATTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
238028 ATGAACTTTTTCTGGAAATA-TTGATCC-TCAAATGATAGATTTGAGCA
66 ATGAACTTTTTCTGGAAA-AGCTGATCCATCAGATGATGGATTTGAGCA
* ** * *
238075 AAATGTTGAACAAGCTCTTCTCATTATAAACTTCTTCT
1 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCT
238113 GAAAATGCTG
Statistics
Matches: 3851, Mismatches: 106, Indels: 42
0.96 0.03 0.01
Matches are distributed among these distances:
101 100 0.03
103 1 0.00
111 7 0.00
112 406 0.11
113 3221 0.84
114 116 0.03
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.39
Consensus pattern (113 bp):
AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCA
Found at i:234526 original size:24 final size:23
Alignment explanation
Indices: 234491--234535 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
234481 TGAACAAATT
*
234491 CTTCTCATTATGAATTTCTTCTTC
1 CTTCTCATTATG-AGTTCTTCTTC
234515 CTTCTTCA-TATGAGTTCTTCT
1 CTTC-TCATTATGAGTTCTTCT
234536 CATTATGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 8 0.42
24 8 0.42
25 3 0.16
ACGTcount: A:0.16, C:0.24, G:0.07, T:0.53
Consensus pattern (23 bp):
CTTCTCATTATGAGTTCTTCTTC
Found at i:238362 original size:112 final size:113
Alignment explanation
Indices: 238162--238597 Score: 639
Period size: 113 Copynumber: 3.9 Consensus size: 113
238152 TCAAACAAAG
* * *
238162 GTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCATTCTTCATATGAGTTCTTCTCATTATGA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
* * * *
238227 ACTTTCTATGGAAAAGTTAATCCATC-AAGTGATGAATTCAGGC-AAAA
66 ACTTTCTCTGGAAATGTTGATCCATCGAA-TGATGAATTCAAGCGAAAA
* * * *
238274 GGTTAAACAAATTCTTCTCATTATGAATTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTATG
1 -GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATG
*
238338 AACTTTCTCTGGAAATGTTGATCCATCGAATGATAAATTCAAGCGAAAA
65 AACTTTCTCTGGAAATGTTGATCCATCGAATGATGAATTCAAGCGAAAA
238387 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
** *
238452 ACTCGAC-CTGGCAATGTTGATCCATCGAATGATGAATTCAAGCGAAAA
66 ACT-TTCTCTGGAAATGTTGATCCATCGAATGATGAATTCAAGCGAAAA
*
238500 GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
* * *
238565 ACTCT-TCTAGAAATGTTGATCCATTGAATGATG
66 ACTTTCTCTGGAAATGTTGATCCATCGAATGATG
238598 GATTTGAACT
Statistics
Matches: 292, Mismatches: 26, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
112 118 0.40
113 173 0.59
114 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.38
Consensus pattern (113 bp):
GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
ACTTTCTCTGGAAATGTTGATCCATCGAATGATGAATTCAAGCGAAAA
Found at i:238430 original size:225 final size:224
Alignment explanation
Indices: 238162--238596 Score: 644
Period size: 225 Copynumber: 1.9 Consensus size: 224
238152 TCAAACAAAG
*
238162 GTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCATTCTTCATATGAGTTCTTCTCATTATGA
1 GTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGA
* *
238227 ACTTTCTA-TGGAAAAGTTAATCCATC-AAGTGATGAATTCAGGC-AAAAGGTTAAACAAATTCT
66 AC--TCGACTGGAAAAGTTAATCCATCGAA-TGATGAATTCAAGCGAAAA-GTTAAACAAATTCT
* * *
238289 TCTCATTATGAATTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAA
127 TCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTCT-TCTAGAAA
238353 TGTTGATCCATCGAATGATAAATTCAAGCGAAAA
191 TGTTGATCCATCGAATGATAAATTCAAGCGAAAA
* *
238387 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGA
* * * * *
238452 ACTCGACCTGGCAATGTTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCT
66 ACTCGA-CTGGAAAAGTTAATCCATCGAATGATGAATTCAAGCGAAAAGTTAAACAAATTCTTCT
* *
238517 TATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTAGAAATGTT
130 CATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTCTTCTAGAAATGTT
*
238582 GATCCATTGAATGAT
195 GATCCATCGAATGAT
238597 GGATTTGAAC
Statistics
Matches: 189, Mismatches: 16, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
223 3 0.02
225 150 0.79
226 36 0.19
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (224 bp):
GTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGA
ACTCGACTGGAAAAGTTAATCCATCGAATGATGAATTCAAGCGAAAAGTTAAACAAATTCTTCTC
ATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTCTTCTAGAAATGTTG
ATCCATCGAATGATAAATTCAAGCGAAAA
Found at i:239029 original size:22 final size:22
Alignment explanation
Indices: 239004--239061 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
238994 GATAAAGCTT
*
239004 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* *
239026 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
239048 TCATCTTTGAAAAG
1 TCATCTTTGAAAAG
239062 TGTAAATGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:247650 original size:14 final size:14
Alignment explanation
Indices: 247616--247669 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
247606 TTGTGCAATA
* *
247616 CAAATGAAAAGATG
1 CAAATGTAAATATG
247630 CCAAATGTAAATATG
1 -CAAATGTAAATATG
*
247645 CAAATGTAAAAATG
1 CAAATGTAAATATG
*
247659 TAAATGTAAAT
1 CAAATGTAAAT
247670 TATTTAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.54, C:0.07, G:0.15, T:0.24
Consensus pattern (14 bp):
CAAATGTAAATATG
Found at i:249267 original size:18 final size:19
Alignment explanation
Indices: 249230--249267 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
249220 AAAAATAAAT
*
249230 AATGAAATAAAATAATAAA
1 AATGAAATAAAATAAGAAA
*
249249 AATG-AATATAATAAGAAA
1 AATGAAATAAAATAAGAAA
249267 A
1 A
249268 TAATACTATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.21
Consensus pattern (19 bp):
AATGAAATAAAATAAGAAA
Found at i:251409 original size:3 final size:3
Alignment explanation
Indices: 251401--251479 Score: 95
Period size: 3 Copynumber: 25.7 Consensus size: 3
251391 TTATTTATTA
* * *
251401 AAT AAT AAT AAT ATAT AAT ATT AAT ATT AAT AAAT AAT AAT ACT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT
**
251448 AAT AAT AAT TTT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
251480 ATTTAAATGA
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:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:251536 original size:2 final size:2
Alignment explanation
Indices: 251525--251667 Score: 272
Period size: 2 Copynumber: 72.5 Consensus size: 2
251515 ATTGTGTATT
251525 GA GA -A GA GA GA GA GA GA G- GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
251565 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
251607 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
251649 GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA G
251668 GAACAACTGG
Statistics
Matches: 139, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
1 2 0.01
2 137 0.99
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:252939 original size:22 final size:21
Alignment explanation
Indices: 252895--252963 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
252885 TTAATAATTT
*
252895 TATT-TTTATATTGTTAAAATA
1 TATTATTTA-ATTATTAAAATA
252916 TATTATTTAATTATTAAAAT-
1 TATTATTTAATTATTAAAATA
* * *
252936 TA-TAATAAATAATTATAAATA
1 TATTATTTAATTATTA-AAATA
252957 TATTATT
1 TATTATT
252964 ATAAAATGTA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
19 10 0.26
20 6 0.15
21 16 0.41
22 7 0.18
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (21 bp):
TATTATTTAATTATTAAAATA
Found at i:252975 original size:15 final size:14
Alignment explanation
Indices: 252901--252978 Score: 54
Period size: 13 Copynumber: 5.6 Consensus size: 14
252891 ATTTTATTTT
*
252901 TATATTGTTA-AAA
1 TATATTATTATAAA
*
252914 TATATTATT-TAAT
1 TATATTATTATAAA
**
252927 TATTAAAATTAT-AA
1 TA-TATTATTATAAA
* *
252941 TAAATAATTATAAA
1 TATATTATTATAAA
252955 TATATTATTATAAAA
1 TATATTATTAT-AAA
*
252970 TGTATTATT
1 TATATTATT
252979 TTAATTATTT
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
13 19 0.38
14 19 0.38
15 12 0.24
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (14 bp):
TATATTATTATAAA
Found at i:254032 original size:26 final size:26
Alignment explanation
Indices: 253983--254032 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
253973 TCAGTATCAA
* *
253983 TTATATCGCTAAACTTTGATTTTTAT
1 TTATATCACTAAACTTTGAATTTTAT
* *
254009 TTATATCATTAAACTTTTAATTTT
1 TTATATCACTAAACTTTGAATTTT
254033 TTTCAATTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.30, C:0.10, G:0.04, T:0.56
Consensus pattern (26 bp):
TTATATCACTAAACTTTGAATTTTAT
Found at i:257600 original size:18 final size:19
Alignment explanation
Indices: 257565--257607 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
257555 TTTAAATAAT
257565 AATTTATTTGTAATCCTAAA
1 AATTTATTTGTAATCCT-AA
257585 AATTTATTT-T-ATCCTAA
1 AATTTATTTGTAATCCTAA
257602 AATTTA
1 AATTTA
257608 GAACATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.35
18 5 0.22
19 1 0.04
20 9 0.39
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (19 bp):
AATTTATTTGTAATCCTAA
Found at i:258731 original size:41 final size:41
Alignment explanation
Indices: 258674--258756 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 41
258664 TCCATCCTTG
* * *
258674 GGATGTGACCTAGTTAAACGGATGATGCAGCTGATAATTTA
1 GGATGTGACCTAGTTAAACGCACGATGCAGCTGATAAATTA
* *
258715 GGATGTGTCCTAGTTAAATGCACGATGCAGCTGATAAATTA
1 GGATGTGACCTAGTTAAACGCACGATGCAGCTGATAAATTA
258756 G
1 G
258757 TGGCATGTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (41 bp):
GGATGTGACCTAGTTAAACGCACGATGCAGCTGATAAATTA
Found at i:260598 original size:22 final size:23
Alignment explanation
Indices: 260554--260601 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
260544 ATCTGATTAA
* *
260554 TAAAATTAAAAGAAATCAGTAGT
1 TAAAATAAAAAGAAATCAATAGT
260577 TAAAATAAAAAGAAA-CAATAGT
1 TAAAATAAAAAGAAATCAATAGT
260599 TAA
1 TAA
260602 GTAAATGATC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.62, C:0.04, G:0.10, T:0.23
Consensus pattern (23 bp):
TAAAATAAAAAGAAATCAATAGT
Found at i:261465 original size:23 final size:22
Alignment explanation
Indices: 261421--261465 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
261411 TCAGGAGTTA
261421 CAGGAGTTATCTGATTTAATTT
1 CAGGAGTTATCTGATTTAATTT
261443 CAGGAGTTATAACTG-TTTAATTT
1 CAGGAGTTAT--CTGATTTAATTT
261466 TTATGCAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 10 0.48
23 8 0.38
24 3 0.14
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.44
Consensus pattern (22 bp):
CAGGAGTTATCTGATTTAATTT
Found at i:264527 original size:14 final size:14
Alignment explanation
Indices: 264508--264537 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
264498 CATTTTTGAA
264508 AGGAGATCTAGATG
1 AGGAGATCTAGATG
*
264522 AGGAGATCTATATG
1 AGGAGATCTAGATG
264536 AG
1 AG
264538 AACAATGGTA
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:0.37, C:0.07, G:0.33, T:0.23
Consensus pattern (14 bp):
AGGAGATCTAGATG
Found at i:265951 original size:31 final size:31
Alignment explanation
Indices: 265913--265975 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
265903 CCCAAGAGTT
*
265913 TGGGAGTTCCTAGTGTGAAGGACATATTGAA
1 TGGGAGTTCCTAGTGAGAAGGACATATTGAA
265944 TGGGAGTTCCTAGTGAGAAGGACATATTGAA
1 TGGGAGTTCCTAGTGAGAAGGACATATTGAA
265975 T
1 T
265976 TCACCAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.30, C:0.10, G:0.32, T:0.29
Consensus pattern (31 bp):
TGGGAGTTCCTAGTGAGAAGGACATATTGAA
Found at i:266929 original size:22 final size:23
Alignment explanation
Indices: 266899--266948 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
266889 TAATATCAGG
266899 ATTTACAGGAGTTAT-CTGATTTA
1 ATTTACAGGAGTTATACTG-TTTA
266922 ATTT-CAGGAGTTATAACTGTTTA
1 ATTTACAGGAGTTAT-ACTGTTTA
266945 ATTT
1 ATTT
266949 TTATGTAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 10 0.40
23 12 0.48
24 3 0.12
ACGTcount: A:0.30, C:0.08, G:0.16, T:0.46
Consensus pattern (23 bp):
ATTTACAGGAGTTATACTGTTTA
Found at i:283954 original size:144 final size:144
Alignment explanation
Indices: 283694--283981 Score: 558
Period size: 144 Copynumber: 2.0 Consensus size: 144
283684 AGAAGCATCA
*
283694 GAACGTATAGATGTCGTAGCAGGCAAATAGGCCACGCCATTTGTCGTACGATTTACGTAAACTAC
1 GAACGTATAGATGTCGTAGCAGGCAAATAGGCCACGCCATTTGTCGTAAGATTTACGTAAACTAC
283759 TTAACAATAGGTAAACTTAATACAGCCCGACTGAAAGGGATCCATATGTACTCCAAGAGTGGATA
66 TTAACAATAGGTAAACTTAATACAGCCCGACTGAAAGGGATCCATATGTACTCCAAGAGTGGATA
283824 CATCCGAGTCCTCC
131 CATCCGAGTCCTCC
283838 GAACGTATAGATGTCGTAGCAGGCAAATAGGCCACGCCATTTGTCGTAAGATTTACGTAAACTAC
1 GAACGTATAGATGTCGTAGCAGGCAAATAGGCCACGCCATTTGTCGTAAGATTTACGTAAACTAC
*
283903 TTAACAATAGGTAAACTTAATACAGCCCGACTGAATGGGATCCATATGTACTCCAAGAGTGGATA
66 TTAACAATAGGTAAACTTAATACAGCCCGACTGAAAGGGATCCATATGTACTCCAAGAGTGGATA
283968 CATCCGAGTCCTCC
131 CATCCGAGTCCTCC
283982 CTTTTGAATT
Statistics
Matches: 142, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
144 142 1.00
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.24
Consensus pattern (144 bp):
GAACGTATAGATGTCGTAGCAGGCAAATAGGCCACGCCATTTGTCGTAAGATTTACGTAAACTAC
TTAACAATAGGTAAACTTAATACAGCCCGACTGAAAGGGATCCATATGTACTCCAAGAGTGGATA
CATCCGAGTCCTCC
Found at i:286960 original size:15 final size:15
Alignment explanation
Indices: 286937--286966 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
286927 TTTTATTTAA
*
286937 AAAATATAAAAATAT
1 AAAAGATAAAAATAT
286952 AAAAGATAAAAATAT
1 AAAAGATAAAAATAT
286967 TTTTTATAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (15 bp):
AAAAGATAAAAATAT
Found at i:290846 original size:6 final size:6
Alignment explanation
Indices: 290777--290845 Score: 129
Period size: 6 Copynumber: 11.5 Consensus size: 6
290767 GACACGTATT
290777 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
*
290825 ACCACG ACCACG ACCCCG ACC
1 ACCACG ACCACG ACCACG ACC
290846 CGAGACGAGA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 62 1.00
ACGTcount: A:0.32, C:0.52, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:291611 original size:6 final size:6
Alignment explanation
Indices: 291600--291638 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
291590 TCTCGTCTCG
291600 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
291639 AATACGTGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.00, C:0.15, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:291743 original size:20 final size:20
Alignment explanation
Indices: 291718--291877 Score: 162
Period size: 20 Copynumber: 7.8 Consensus size: 20
291708 TACGAACTAA
291718 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
291738 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
* *
291758 GAATCGCGTTACGATT-TTCT
1 GAATCGCGTTGCGATTCTT-G
* *
291778 CAATCGCGTTGCGATTATTG
1 GAATCGCGTTGCGATTCTTG
* *
291798 GAATCGCGTTGCGATTTTCTC
1 GAATCGCGTTGCGATTCT-TG
* *
291819 G-ATCACATTGCGATTCTTCG
1 GAATCGCGTTGCGATTCTT-G
* *
291839 AAGATCGCATTGCGATTCTTG
1 GA-ATCGCGTTGCGATTCTTG
291860 GAAGATCGCGTTGCGATT
1 G-A-ATCGCGTTGCGATT
291878 TTCTTTTGAC
Statistics
Matches: 117, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
19 3 0.03
20 78 0.67
21 5 0.04
22 31 0.26
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.35
Consensus pattern (20 bp):
GAATCGCGTTGCGATTCTTG
Found at i:291833 original size:60 final size:62
Alignment explanation
Indices: 291719--291881 Score: 197
Period size: 60 Copynumber: 2.6 Consensus size: 62
291709 ACGAACTAAG
* * * * **
291719 AATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTCT-TGGAATCGCGTTACGATT-TTCTC
1 AATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTCGAATCACATTACGATTCTTCGA
* *
291779 AATCGCGTTGCGATTATTGGAATCGCGTTGCGATTTTCTCG-ATCACATTGCGATTCTTCGA
1 AATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTCGAATCACATTACGATTCTTCGA
*
291840 AGATCGCATTGCGATTCTTGGAAGATCGCGTTGCGATTTTCT
1 A-ATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCGATTTTCT
291882 TTTGACCGTT
Statistics
Matches: 88, Mismatches: 10, Indels: 6
0.85 0.10 0.06
Matches are distributed among these distances:
60 46 0.52
61 6 0.07
62 17 0.19
63 1 0.01
64 18 0.20
ACGTcount: A:0.18, C:0.21, G:0.25, T:0.36
Consensus pattern (62 bp):
AATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTTTCTCGAATCACATTACGATTCTTCGA
Found at i:291893 original size:20 final size:20
Alignment explanation
Indices: 291868--291921 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
291858 TGGAAGATCG
* *
291868 CGTTGCGATTTTCTTTTGAC
1 CGTTGCGATTTTCTTTTCAA
291888 CGTTGCGATTTTCTTTTCAA
1 CGTTGCGATTTTCTTTTCAA
291908 CGTTGCGATTTTCT
1 CGTTGCGATTTTCT
291922 AAATCGCGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.11, C:0.20, G:0.19, T:0.50
Consensus pattern (20 bp):
CGTTGCGATTTTCTTTTCAA
Found at i:291931 original size:20 final size:20
Alignment explanation
Indices: 291908--291958 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
291898 TTCTTTTCAA
*
291908 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
291928 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
291947 CGTTGCGATTTT
1 CGTTGCGATTTT
291959 GTTGGTAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:292151 original size:31 final size:30
Alignment explanation
Indices: 292110--292169 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
292100 TGTTTTCTTA
* * *
292110 AATTTTTATATAATACTTTAATTTCCAAAAT
1 AATTTATATATAATAATCTAATTT-CAAAAT
*
292141 AATTTATATATATTAATCTAATTTCAAAA
1 AATTTATATATAATAATCTAATTTCAAAA
292170 CATTATATAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 5 0.20
31 20 0.80
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (30 bp):
AATTTATATATAATAATCTAATTTCAAAAT
Found at i:298834 original size:14 final size:14
Alignment explanation
Indices: 298815--298901 Score: 66
Period size: 14 Copynumber: 5.5 Consensus size: 14
298805 TCATTTCGCA
298815 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
298829 TTGCGATTTTCATTTCGCG
1 TTGCGA--TTC---TCTCG
298848 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
298862 TTGCGATAGTCATTTCGCG
1 TTGCGAT--TC---TCTCG
298881 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
298895 TTGCGAT
1 TTGCGAT
298902 AGTCATTTTC
Statistics
Matches: 59, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
14 28 0.47
16 5 0.08
17 5 0.08
19 21 0.36
ACGTcount: A:0.10, C:0.24, G:0.23, T:0.43
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:298838 original size:33 final size:33
Alignment explanation
Indices: 298796--298925 Score: 206
Period size: 33 Copynumber: 3.9 Consensus size: 33
298786 CAAAATCGCA
** *
298796 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
**
298829 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
298862 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
298895 TTGCGATAGTCATTTTCGCGTTGCGATTCTC
1 TTGCGATAGTCA-TTTCGCGTTGCGATTCTC
298926 ATTATCTCGT
Statistics
Matches: 93, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
33 75 0.81
34 18 0.19
ACGTcount: A:0.12, C:0.24, G:0.22, T:0.43
Consensus pattern (33 bp):
TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
Found at i:298918 original size:20 final size:19
Alignment explanation
Indices: 298827--298941 Score: 79
Period size: 20 Copynumber: 6.5 Consensus size: 19
298817 GCGATTCTCT
**
298827 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
298846 CGTTGCGAT--TC---TCT
1 CGTTGCGATAGTCATTTCG
298860 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
298879 CGTTGCGAT--TC---TCT
1 CGTTGCGATAGTCATTTCG
298893 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA-TTTCG
** *
298913 CGTTGCGATTCTCATTATCT
1 CGTTGCGATAGTCATT-TCG
298933 CGTTGCGAT
1 CGTTGCGAT
298942 TTTCATTTCA
Statistics
Matches: 77, Mismatches: 7, Indels: 23
0.72 0.07 0.21
Matches are distributed among these distances:
14 22 0.29
16 4 0.05
17 4 0.05
19 22 0.29
20 25 0.32
ACGTcount: A:0.12, C:0.23, G:0.23, T:0.42
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:298942 original size:20 final size:20
Alignment explanation
Indices: 298890--298948 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
298880 GTTGCGATTC
** *
298890 TCTCGTTGCGATAGTCATTT
1 TCTCGTTGCGATTCTCATTA
*
298910 TCGCGTTGCGATTCTCATTA
1 TCTCGTTGCGATTCTCATTA
*
298930 TCTCGTTGCGATTTTCATT
1 TCTCGTTGCGATTCTCATT
298949 TCAACCAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (20 bp):
TCTCGTTGCGATTCTCATTA
Found at i:301119 original size:21 final size:21
Alignment explanation
Indices: 301095--301161 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
301085 TCATTCCTTG
301095 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
301116 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
301137 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
301158 AGAG
1 AGAG
301162 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:301119 original size:42 final size:42
Alignment explanation
Indices: 301068--301161 Score: 111
Period size: 42 Copynumber: 2.2 Consensus size: 42
301058 CTACTCCTAT
* *
301068 CGTTGAAGAGGCCCCTATCATTCCTTG-AGA-GTCCCCTCCCAC
1 CGTTCAAGAGGCCACTATCA-TCCTTGAAGAGGT-CCCTCCCAC
* *
301110 CGTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCAC
1 CGTTCAAGAGGCCACTATCATCCTTGAAGAGGTCCCTCCCAC
*
301152 CATTCAAGAG
1 CGTTCAAGAG
301162 CCCGATTCAC
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
41 5 0.11
42 38 0.84
43 2 0.04
ACGTcount: A:0.22, C:0.34, G:0.21, T:0.22
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCATCCTTGAAGAGGTCCCTCCCAC
Found at i:302538 original size:14 final size:14
Alignment explanation
Indices: 302519--302554 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
302509 ATTGTTTAAT
302519 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
302533 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
302547 TGATTTGT
1 TGATTTGT
302555 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:302706 original size:33 final size:33
Alignment explanation
Indices: 302661--302724 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
302651 AAAAAGTACT
*
302661 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
302694 ATCGCAACGCGAAATGAAAATCGCAACGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGA
302725 AATTAAATTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:302736 original size:19 final size:19
Alignment explanation
Indices: 302661--302727 Score: 72
Period size: 19 Copynumber: 3.8 Consensus size: 19
302651 AAAAAGTACT
* *
302661 ATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAAATGAAA
302680 ATCGCAACGAG--A-G--A
1 ATCGCAACGAGAAATGAAA
*
302694 ATCGCAACGCGAAATGAAA
1 ATCGCAACGAGAAATGAAA
302713 ATCGCAACGAGAAAT
1 ATCGCAACGAGAAAT
302728 TAAATTCGCG
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
14 11 0.28
16 2 0.05
17 2 0.05
19 24 0.62
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.12
Consensus pattern (19 bp):
ATCGCAACGAGAAATGAAA
Found at i:302754 original size:19 final size:19
Alignment explanation
Indices: 302732--302881 Score: 87
Period size: 19 Copynumber: 8.7 Consensus size: 19
302722 AGAAATTAAA
302732 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
302751 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
302766 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
302784 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
302798 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
302817 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
302832 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
302850 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
302869 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
302882 AGACATTAAG
Statistics
Matches: 95, Mismatches: 21, Indels: 30
0.65 0.14 0.21
Matches are distributed among these distances:
14 28 0.29
16 6 0.06
17 6 0.06
19 55 0.58
ACGTcount: A:0.15, C:0.22, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:302778 original size:33 final size:32
Alignment explanation
Indices: 302736--302862 Score: 193
Period size: 33 Copynumber: 3.9 Consensus size: 32
302726 ATTAAATTCG
302736 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
302769 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
302802 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
302835 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
302863 AGTAATTTCG
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
31 3 0.03
33 80 0.93
35 3 0.03
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:302814 original size:66 final size:66
Alignment explanation
Indices: 302729--302861 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
302719 ACGAGAAATT
*
302729 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
302794 G
66 G
*
302795 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
302860 G
66 G
302861 A
1 A
302862 TAGTAATTTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:305140 original size:12 final size:12
Alignment explanation
Indices: 305123--305147 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
305113 TCTTCGGGGA
305123 CTTTTTCTTCTT
1 CTTTTTCTTCTT
305135 CTTTTTCTTCTT
1 CTTTTTCTTCTT
305147 C
1 C
305148 AGGATTATGA
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:305356 original size:24 final size:24
Alignment explanation
Indices: 305324--305370 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
305314 TCATCAAAAA
*
305324 TCCGAGTATTGACCAATATCAAAG
1 TCCGAGTATTGACCAAGATCAAAG
*
305348 TCCGGGTATTGACCAAGATCAAA
1 TCCGAGTATTGACCAAGATCAAA
305371 TTTTGAATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TCCGAGTATTGACCAAGATCAAAG
Found at i:306161 original size:20 final size:21
Alignment explanation
Indices: 306136--306187 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
306126 TTTTCCTAAT
*
306136 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
306156 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
306177 TCGCAATGCGA
1 TCGCAATGCGA
306188 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:306209 original size:20 final size:20
Alignment explanation
Indices: 306176--306254 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 20
306166 AATTTGGAAA
* *
306176 ATCGCAATGCGATACTGACT
1 ATCGCAACGAGATACTGACT
* *
306196 ATCGCAACGAGATAAT-ACAAA
1 ATCGCAACGAGATACTGAC--T
*
306217 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATACTGACT
* *
306237 TTCGCAACGAGATTCTGA
1 ATCGCAACGAGATACTGA
306255 AAATCACAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
19 2 0.04
20 30 0.62
21 14 0.29
22 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGAGATACTGACT
Found at i:306571 original size:20 final size:20
Alignment explanation
Indices: 306476--306563 Score: 88
Period size: 20 Copynumber: 4.4 Consensus size: 20
306466 CAACGGGGAA
306476 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
*
306496 ATCGCAACGCGAAACTGGCT
1 ATCGCAACGCGAAAATGGCT
* ** ***
306516 ATTGCAATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
*
306536 ATCGCAACGCAAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
306556 ATCGCAAC
1 ATCGCAAC
306564 TAGAAAATCG
Statistics
Matches: 51, Mismatches: 15, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
19 4 0.08
20 42 0.82
21 5 0.10
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:306617 original size:14 final size:16
Alignment explanation
Indices: 306598--306667 Score: 58
Period size: 19 Copynumber: 4.2 Consensus size: 16
306588 AATCGCATTA
306598 CGATTTTC-TCG-TTG
1 CGATTTTCTTCGATTG
306612 CGATTTTCATTTCGCATTG
1 CGATTTTC--TTCG-ATTG
306631 CGATTTTCATTTCGCATTG
1 CGATTTTC--TTCG-ATTG
306650 CGATTTTC-TCG-TTG
1 CGATTTTCTTCGATTG
306664 CGAT
1 CGAT
306668 AGTCAGTTTC
Statistics
Matches: 51, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
14 15 0.29
16 3 0.06
17 3 0.06
19 30 0.59
ACGTcount: A:0.13, C:0.21, G:0.19, T:0.47
Consensus pattern (16 bp):
CGATTTTCTTCGATTG
Found at i:306631 original size:19 final size:19
Alignment explanation
Indices: 306609--306657 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
306599 GATTTTCTCG
306609 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
306628 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
306647 TTGCGATTTTC
1 TTGCGATTTTC
306658 TCGTTGCGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.14, C:0.20, G:0.16, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:306813 original size:14 final size:14
Alignment explanation
Indices: 306794--306830 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
306784 CATCAATTAA
306794 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
306808 ACAAATCACCTTTT
1 ACAAATCAACATTT
306822 ACAAATCAA
1 ACAAATCAA
306831 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:0.24, G:0.00, T:0.27
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:308552 original size:20 final size:20
Alignment explanation
Indices: 308529--308580 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
308519 AACTTAAAAT
308529 CGCAACGCGAAAATGACTAC
1 CGCAACGCGAAAATGACTAC
* * *
308549 CGCAACGCGGAAATGGCTAT
1 CGCAACGCGAAAATGACTAC
*
308569 CGCAATGCGAAA
1 CGCAACGCGAAA
308581 TGAAAATCGT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.37, C:0.27, G:0.25, T:0.12
Consensus pattern (20 bp):
CGCAACGCGAAAATGACTAC
Found at i:308589 original size:19 final size:19
Alignment explanation
Indices: 308567--308627 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
308557 GGAAATGGCT
308567 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
308586 ATCGTAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
308600 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
308619 ATCGCAATG
1 ATCGCAATG
308628 ACAAAATCGC
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
14 9 0.27
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 18 0.55
ACGTcount: A:0.46, C:0.18, G:0.20, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:308609 original size:33 final size:33
Alignment explanation
Indices: 308567--308671 Score: 167
Period size: 33 Copynumber: 3.2 Consensus size: 33
308557 GGAAATGGCT
* *
308567 ATCGCAATGCGAAATGAAAATCGTAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAAAGACAAA
*
308600 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAAAGACAAA
*
308633 ATCGCAATGCAAAATG-AAATCGCAAAGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAAAGACAAA
308665 ATCGCAA
1 ATCGCAA
308672 CGCAAAACAC
Statistics
Matches: 68, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
32 22 0.32
33 46 0.68
ACGTcount: A:0.50, C:0.19, G:0.17, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAAAGACAAA
Found at i:308635 original size:14 final size:14
Alignment explanation
Indices: 308616--308671 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 14
308606 ATGCGAAATG
308616 AAAATCGCAATGAC
1 AAAATCGCAATGAC
*
308630 AAAATCGCAATGCAAA
1 AAAATCGCAATG--AC
*
308646 ATGAAATCGCAAAGAC
1 A--AAATCGCAATGAC
308662 AAAATCGCAA
1 AAAATCGCAA
308672 CGCAAAACAC
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
14 21 0.60
16 4 0.11
18 10 0.29
ACGTcount: A:0.54, C:0.20, G:0.14, T:0.12
Consensus pattern (14 bp):
AAAATCGCAATGAC
Found at i:308647 original size:13 final size:13
Alignment explanation
Indices: 308612--308647 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
308602 CGCAATGCGA
308612 AATG-AAAATCGC
1 AATGCAAAATCGC
308624 AATGACAAAATCGC
1 AATG-CAAAATCGC
308638 AATGCAAAAT
1 AATGCAAAAT
308648 GAAATCGCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.18
13 6 0.27
14 12 0.55
ACGTcount: A:0.53, C:0.17, G:0.14, T:0.17
Consensus pattern (13 bp):
AATGCAAAATCGC
Found at i:308675 original size:19 final size:19
Alignment explanation
Indices: 308653--308689 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
308643 AAAATGAAAT
308653 CGCAAAGACA-AAATCGCAA
1 CGCAAA-ACACAAATCGCAA
308672 CGCAAAACACAAATCGCA
1 CGCAAAACACAAATCGCA
308690 TTGCGATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.51, C:0.30, G:0.14, T:0.05
Consensus pattern (19 bp):
CGCAAAACACAAATCGCAA
Found at i:308686 original size:65 final size:66
Alignment explanation
Indices: 308567--308689 Score: 169
Period size: 65 Copynumber: 1.9 Consensus size: 66
308557 GGAAATGGCT
* * * * **
308567 ATCGCAATGCGAAATGAAAATCGTAACGACAAAATCGCAATGCGAAATGAAAATCGCAATGACAA
1 ATCGCAATGCAAAATGAAAATCGCAAAGACAAAATCGCAACGCGAAAACAAAATCGCAATGACAA
308632 A
66 A
308633 ATCGCAATGCAAAATG-AAATCGCAAAGACAAAATCGCAACGC-AAAACACAAATCGCA
1 ATCGCAATGCAAAATGAAAATCGCAAAGACAAAATCGCAACGCGAAAACA-AAATCGCA
308690 TTGCGATTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
64 4 0.08
65 31 0.62
66 15 0.30
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (66 bp):
ATCGCAATGCAAAATGAAAATCGCAAAGACAAAATCGCAACGCGAAAACAAAATCGCAATGACAA
A
Found at i:308707 original size:19 final size:18
Alignment explanation
Indices: 308685--308781 Score: 84
Period size: 19 Copynumber: 5.7 Consensus size: 18
308675 AAAACACAAA
308685 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTT-ATT
* *
308704 TCGCGTTGCGA-TTT-TG
1 TCGCATTGCGATTTTATT
308720 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTT-ATT
*
308737 TCGCATTGCGA-TTT-TG
1 TCGCATTGCGATTTTATT
308753 TCG--TTGCGATTTTTATT
1 TCGCATTGCGA-TTTTATT
308770 TCGCATTGCGAT
1 TCGCATTGCGAT
308782 AGTCATTTTC
Statistics
Matches: 63, Mismatches: 5, Indels: 21
0.71 0.06 0.24
Matches are distributed among these distances:
14 12 0.19
15 3 0.05
16 11 0.17
17 8 0.13
18 7 0.11
19 22 0.35
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (18 bp):
TCGCATTGCGATTTTATT
Found at i:308726 original size:14 final size:14
Alignment explanation
Indices: 308707--308765 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
308697 TTTCATTTCG
308707 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
308721 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
308738 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
308754 CGTTGCGATTTT
1 CGTTGCGATTTT
308766 TATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 18 0.47
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:308732 original size:33 final size:33
Alignment explanation
Indices: 308690--308781 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
308680 ACAAATCGCA
*
308690 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
308723 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
308756 TTGCGATTTTTATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
308782 AGTCATTTTC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:309302 original size:18 final size:18
Alignment explanation
Indices: 309276--309321 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
309266 GTCGATCAGA
*
309276 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
309294 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
309312 TGATGGCTCT
1 TGATGGCTCT
309322 CGAAGTGGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.13, C:0.15, G:0.43, T:0.28
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:310585 original size:20 final size:20
Alignment explanation
Indices: 310537--310595 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
310527 AATAGTTTCT
** *
310537 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
310557 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
310577 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
310596 AGAGAATTGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:310886 original size:22 final size:22
Alignment explanation
Indices: 310859--310902 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
310849 GATGGAGATA
310859 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
310881 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
310903 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:311120 original size:20 final size:20
Alignment explanation
Indices: 311091--311142 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
311081 ATTATGTATT
311091 ATCGCATTGCGAAAGTCAGA
1 ATCGCATTGCGAAAGTCAGA
* *
311111 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGAAAGTCAGA
311131 ATCGCATTGCGA
1 ATCGCATTGCGA
311143 TTTTCCCAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (20 bp):
ATCGCATTGCGAAAGTCAGA
Found at i:311254 original size:21 final size:21
Alignment explanation
Indices: 311214--311254 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
311204 ACTGTATACC
** *
311214 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
311235 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
311255 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:315609 original size:29 final size:29
Alignment explanation
Indices: 315576--315632 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
315566 CTAAATTAAT
315576 TTGATGTCATTGCTTACATCAATTTAGTA
1 TTGATGTCATTGCTTACATCAATTTAGTA
315605 TTGATGTCATTGCTTACATCAATTTAGT
1 TTGATGTCATTGCTTACATCAATTTAGT
315633 TAGGTGAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.46
Consensus pattern (29 bp):
TTGATGTCATTGCTTACATCAATTTAGTA
Found at i:320300 original size:29 final size:29
Alignment explanation
Indices: 320267--320350 Score: 168
Period size: 29 Copynumber: 2.9 Consensus size: 29
320257 CTAAATTAAT
320267 TTGATGTCATTGCTTACATCAATTTAGTA
1 TTGATGTCATTGCTTACATCAATTTAGTA
320296 TTGATGTCATTGCTTACATCAATTTAGTA
1 TTGATGTCATTGCTTACATCAATTTAGTA
320325 TTGATGTCATTGCTTACATCAATTTA
1 TTGATGTCATTGCTTACATCAATTTA
320351 ATTAGGTGAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 55 1.00
ACGTcount: A:0.27, C:0.14, G:0.13, T:0.45
Consensus pattern (29 bp):
TTGATGTCATTGCTTACATCAATTTAGTA
Found at i:321575 original size:35 final size:34
Alignment explanation
Indices: 321536--321603 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
321526 AATATATATA
* *
321536 TTATGAGGTATATTTATTTTTTATAATTTAAAATT
1 TTATG-GGTATAATTATATTTTATAATTTAAAATT
* *
321571 TTATGTGTATAATTATATTTTGTAATTTAAAAT
1 TTATGGGTATAATTATATTTTATAATTTAAAAT
321604 CATATATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 24 0.83
35 5 0.17
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (34 bp):
TTATGGGTATAATTATATTTTATAATTTAAAATT
Found at i:327894 original size:31 final size:31
Alignment explanation
Indices: 327856--328071 Score: 362
Period size: 31 Copynumber: 7.0 Consensus size: 31
327846 GGGTCGAGGG
*
327856 TTACCTATGTTCTTCGGGACATATAGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
327887 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
327918 TTACCTATGTTCTTCAGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
327949 TTATCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
327980 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
328011 TTACCTATGTTCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
328042 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
328072 GTCCTTCGGG
Statistics
Matches: 176, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
31 175 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:332320 original size:31 final size:31
Alignment explanation
Indices: 332282--332497 Score: 380
Period size: 31 Copynumber: 7.0 Consensus size: 31
332272 GGGTCGAGGG
*
332282 TTACCTATGTTCTTCGGGACATATAGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
332313 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
332344 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
332375 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
332406 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
332437 TTACCTATGTTCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
332468 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
332498 GTCCTTCGGG
Statistics
Matches: 180, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
31 179 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:337091 original size:20 final size:21
Alignment explanation
Indices: 337054--337095 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
337044 GTCATGCAAC
337054 TAATAATAGTTGCATAATGCA
1 TAATAATAGTTGCATAATGCA
*
337075 TAATAATGGTT-CATAATGCA
1 TAATAATAGTTGCATAATGCA
337095 T
1 T
337096 TGTAAGTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (21 bp):
TAATAATAGTTGCATAATGCA
Found at i:337618 original size:20 final size:21
Alignment explanation
Indices: 337593--337634 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
337583 CCAACTTACA
337593 ATGCATTATG-AACCATTATT
1 ATGCATTATGCAACCATTATT
*
337613 ATGCATTATGCAACTATTATT
1 ATGCATTATGCAACCATTATT
337634 A
1 A
337635 GTTGTGTGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (21 bp):
ATGCATTATGCAACCATTATT
Found at i:346154 original size:23 final size:23
Alignment explanation
Indices: 346128--346172 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
346118 CACCATAGCT
* *
346128 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATACACCGAAGTGCCG
* *
346151 CGTAGAATTACACCGTAGTGCC
1 CGTAGAAATACACCGAAGTGCC
346173 ATATAATGAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.29, C:0.27, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATACACCGAAGTGCCG
Found at i:347636 original size:16 final size:16
Alignment explanation
Indices: 347615--347645 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
347605 TGTAATACAG
*
347615 ATAACCACATATAATT
1 ATAACCACACATAATT
347631 ATAACCACACATAAT
1 ATAACCACACATAAT
347646 CATGTCCATG
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:0.52, C:0.23, G:0.00, T:0.26
Consensus pattern (16 bp):
ATAACCACACATAATT
Found at i:348022 original size:21 final size:21
Alignment explanation
Indices: 347998--348042 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
347988 TTTTGTTCGT
* *
347998 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
348019 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
348040 TTG
1 TTG
348043 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:351197 original size:23 final size:23
Alignment explanation
Indices: 351171--351215 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
351161 CACCACAGCT
*
351171 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* * *
351194 CGTAGAATTGCATCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
351216 ATATAATGAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:351358 original size:25 final size:25
Alignment explanation
Indices: 351330--351398 Score: 138
Period size: 25 Copynumber: 2.8 Consensus size: 25
351320 TATATATATA
351330 TCCCGAAGGACCGCGTAGAATATTG
1 TCCCGAAGGACCGCGTAGAATATTG
351355 TCCCGAAGGACCGCGTAGAATATTG
1 TCCCGAAGGACCGCGTAGAATATTG
351380 TCCCGAAGGACCGCGTAGA
1 TCCCGAAGGACCGCGTAGA
351399 CCCTCTACTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.28, C:0.26, G:0.29, T:0.17
Consensus pattern (25 bp):
TCCCGAAGGACCGCGTAGAATATTG
Found at i:352703 original size:16 final size:16
Alignment explanation
Indices: 352682--352712 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
352672 TGTAATACAG
*
352682 ATAACCACATATAATT
1 ATAACCACACATAATT
352698 ATAACCACACATAAT
1 ATAACCACACATAAT
352713 CATGTCCATG
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:0.52, C:0.23, G:0.00, T:0.26
Consensus pattern (16 bp):
ATAACCACACATAATT
Found at i:353089 original size:21 final size:21
Alignment explanation
Indices: 353065--353109 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
353055 TTTTGTTCGT
* *
353065 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
353086 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
353107 TTG
1 TTG
353110 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:356046 original size:2 final size:2
Alignment explanation
Indices: 356037--356075 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
356027 TATATGTTTA
* *
356037 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
356076 GTACCTATGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
AT
Found at i:358425 original size:4 final size:4
Alignment explanation
Indices: 358416--358447 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
358406 GGTTTCACCG
*
358416 ATAA ATAA ATAA ATAA ATAA ATAC ATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
358448 CTTCGAGAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAA
Found at i:364941 original size:2 final size:2
Alignment explanation
Indices: 364934--364959 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
364924 GATATTAATC
364934 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
364960 TAATTTTAAC
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:370450 original size:22 final size:22
Alignment explanation
Indices: 370433--370499 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
370423 CTCGTATAAA
370433 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
370455 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
370477 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
370499 T
1 T
370500 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:371534 original size:18 final size:18
Alignment explanation
Indices: 371513--371549 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
371503 TTTCCCCTCT
371513 ATCTTATC-TTATATGTTC
1 ATCTTATCATT-TATGTTC
371531 ATCTTATCATTTATGTTC
1 ATCTTATCATTTATGTTC
371549 A
1 A
371550 AATCTCCTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.24, C:0.16, G:0.05, T:0.54
Consensus pattern (18 bp):
ATCTTATCATTTATGTTC
Found at i:372179 original size:22 final size:21
Alignment explanation
Indices: 372133--372175 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
372123 TTCATATTCG
* *
372133 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
372154 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
372175 C
1 C
372176 CTTGCCCAGA
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:0.28, G:0.28, T:0.28
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:375324 original size:22 final size:22
Alignment explanation
Indices: 375307--375373 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
375297 CTCGTATAAA
375307 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
375329 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
375351 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
375373 T
1 T
375374 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:376415 original size:18 final size:18
Alignment explanation
Indices: 376394--376428 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
376384 TCCCCTCTAG
376394 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
376412 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
376429 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:377058 original size:22 final size:21
Alignment explanation
Indices: 377012--377054 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
377002 TTCATATTCG
* *
377012 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
377033 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
377054 C
1 C
377055 CTTGCCCAGA
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:0.28, G:0.28, T:0.28
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:380155 original size:19 final size:19
Alignment explanation
Indices: 380131--380176 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
380121 TTTCGACAAC
* *
380131 ATATTATATTTTAAATTTT
1 ATATTATATTTAAAAGTTT
380150 ATATTAT-TTTAAAAGTTT
1 ATATTATATTTAAAAGTTT
380168 A-ATTATATT
1 ATATTATATT
380177 GAATAATTCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 5 0.21
18 12 0.50
19 7 0.29
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (19 bp):
ATATTATATTTAAAAGTTT
Found at i:387041 original size:28 final size:28
Alignment explanation
Indices: 387001--387064 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
386991 CCCGAACTCG
*
387001 ACCCGACCCGAATATCACATTTAAAAAA
1 ACCCGACCCGAATATCACACTTAAAAAA
*
387029 ACCCGACCTGAATATCACACTT-AAAAA
1 ACCCGACCCGAATATCACACTTAAAAAA
*
387056 ACACGACCC
1 ACCCGACCC
387065 AAACAACATA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 12 0.38
28 20 0.62
ACGTcount: A:0.44, C:0.33, G:0.08, T:0.16
Consensus pattern (28 bp):
ACCCGACCCGAATATCACACTTAAAAAA
Found at i:392409 original size:483 final size:483
Alignment explanation
Indices: 391503--392469 Score: 1862
Period size: 483 Copynumber: 2.0 Consensus size: 483
391493 ACAATGATTC
*
391503 TAAATTTTAAGTATTTAAAACAGTGAATGAAAAGTGGATCAAAATATTTGTGAGAAATGGAATTA
1 TAAATTTCAAGTATTTAAAACAGTGAATGAAAAGTGGATCAAAATATTTGTGAGAAATGGAATTA
*
391568 TATAAGTTATAGCCTGTACTCCACCACCACCAGGATTGATTTCACTTACAGAGAGCCTCATTTGA
66 TATAAATTATAGCCTGTACTCCACCACCACCAGGATTGATTTCACTTACAGAGAGCCTCATTTGA
391633 TTCAGCATCTTCTCTTCATCTCTTTCTTCAGAGATCAATAGAGTTGCCTGAACTGAATCACTTGA
131 TTCAGCATCTTCTCTTCATCTCTTTCTTCAGAGATCAATAGAGTTGCCTGAACTGAATCACTTGA
*
391698 ACATCTCTCTTCCTTTCTTCGATTCCTGCCTCGAAGTTGTTCCGTTTAAGCGCTCTCTATCGCTT
196 ACATCTCTCTTCCTTTCTTCGATTCCTGCCTCAAAGTTGTTCCGTTTAAGCGCTCTCTATCGCTT
*
391763 TCATCATCTTAGGTGAGTTACGAAGCTTCAATTCCCCCATATTTCGGTTTGTTATGCTTTCAGTT
261 TCATCATCTTAGGTGAGTTACGAAGCTTCAATTCCCCCATATTTCGATTTGTTATGCTTTCAGTT
391828 ATTGTATCTTCATGTGATTAACTATTTGAATTTGAATTTTTTTAGGTACCCATTTTTTCCTTCTG
326 ATTGTATCTTCATGTGATTAACTATTTGAATTTGAATTTTTTTAGGTACCCATTTTTTCCTTCTG
391893 GTTTCCAAGAAAAACCCAGAAAATTTTAGACTCAAAATCTGATACTTTTCCATTCTTTTTCTGAC
391 GTTTCCAAGAAAAACCCAGAAAATTTTAGACTCAAAATCTGATACTTTTCCATTCTTTTTCTGAC
*
391958 TTTTCGCGATTCCTACTCTTTGGGGTTT
456 TTTCCGCGATTCCTACTCTTTGGGGTTT
391986 TAAATTTCAAGTATTTAAAACAGTGAATGAAAAGTGGATCAAAATATTTGTGAGAAATGGAATTA
1 TAAATTTCAAGTATTTAAAACAGTGAATGAAAAGTGGATCAAAATATTTGTGAGAAATGGAATTA
*
392051 TATAAATTATAGCCTGTACTCCACCACCATCAGGATTGATTTCACTTACAGAGAGCCTCATTTGA
66 TATAAATTATAGCCTGTACTCCACCACCACCAGGATTGATTTCACTTACAGAGAGCCTCATTTGA
392116 TTCAGCATCTTCTCTTCATCTCTTTCTTCAGAGATCAATAGAGTTGCCTGAACTGAATCACTTGA
131 TTCAGCATCTTCTCTTCATCTCTTTCTTCAGAGATCAATAGAGTTGCCTGAACTGAATCACTTGA
392181 ACATCTCTCTTCCTTTCTTCGATTCCTGCCTCAAAGTTGTTCCGTTTAAGCGCTCTCTATCGCTT
196 ACATCTCTCTTCCTTTCTTCGATTCCTGCCTCAAAGTTGTTCCGTTTAAGCGCTCTCTATCGCTT
392246 TCATCATCTTAGGTGAGTTACGAAGCTTCAATTCCCCCATATTTCGATTTGTTATGCTTTCAGTT
261 TCATCATCTTAGGTGAGTTACGAAGCTTCAATTCCCCCATATTTCGATTTGTTATGCTTTCAGTT
*
392311 ATTGTATCTTCATGTGATTAACTATTTGAATTTGAATTTTTTTAGGTACTCATTTTTTCCTTCTG
326 ATTGTATCTTCATGTGATTAACTATTTGAATTTGAATTTTTTTAGGTACCCATTTTTTCCTTCTG
*
392376 GTTTCCAAGAAAAACCCAGAAAATTTTAGACTCAAAATCTGTTACTTTTCCATTCTTTTTCTGAC
391 GTTTCCAAGAAAAACCCAGAAAATTTTAGACTCAAAATCTGATACTTTTCCATTCTTTTTCTGAC
392441 TTTCCGCGATTCCTACTCTTTGGGGTTT
456 TTTCCGCGATTCCTACTCTTTGGGGTTT
392469 T
1 T
392470 TCTGCTTCTG
Statistics
Matches: 476, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
483 476 1.00
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.39
Consensus pattern (483 bp):
TAAATTTCAAGTATTTAAAACAGTGAATGAAAAGTGGATCAAAATATTTGTGAGAAATGGAATTA
TATAAATTATAGCCTGTACTCCACCACCACCAGGATTGATTTCACTTACAGAGAGCCTCATTTGA
TTCAGCATCTTCTCTTCATCTCTTTCTTCAGAGATCAATAGAGTTGCCTGAACTGAATCACTTGA
ACATCTCTCTTCCTTTCTTCGATTCCTGCCTCAAAGTTGTTCCGTTTAAGCGCTCTCTATCGCTT
TCATCATCTTAGGTGAGTTACGAAGCTTCAATTCCCCCATATTTCGATTTGTTATGCTTTCAGTT
ATTGTATCTTCATGTGATTAACTATTTGAATTTGAATTTTTTTAGGTACCCATTTTTTCCTTCTG
GTTTCCAAGAAAAACCCAGAAAATTTTAGACTCAAAATCTGATACTTTTCCATTCTTTTTCTGAC
TTTCCGCGATTCCTACTCTTTGGGGTTT
Found at i:394630 original size:43 final size:42
Alignment explanation
Indices: 394543--394630 Score: 99
Period size: 43 Copynumber: 2.1 Consensus size: 42
394533 AATCGAATCT
* * *
394543 AACCCTAAACCCTAAACCTTTAACATTTATCTATAAATTCTA
1 AACCCTAAACCCTAAACCATAAACATTTATCTATAAATCCTA
*
394585 AACCCTAAAACCCTTAACCATAAACATTTAATC-ATAAA-CCATA
1 AACCCT-AAACCCTAAACCATAAACATTT-ATCTATAAATCC-TA
394628 AAC
1 AAC
394631 ACTTGACCTT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
42 7 0.18
43 29 0.74
44 3 0.08
ACGTcount: A:0.45, C:0.27, G:0.00, T:0.27
Consensus pattern (42 bp):
AACCCTAAACCCTAAACCATAAACATTTATCTATAAATCCTA
Found at i:394643 original size:21 final size:21
Alignment explanation
Indices: 394596--394643 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
394586 ACCCTAAAAC
*
394596 CCTT-AACCATAAACATTTAA
1 CCTTAAACCATAAACACTTAA
* * *
394616 TCATAAACCATAAACACTTGA
1 CCTTAAACCATAAACACTTAA
394637 CCTTAAA
1 CCTTAAA
394644 TGTTAAACCA
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.46, C:0.25, G:0.02, T:0.27
Consensus pattern (21 bp):
CCTTAAACCATAAACACTTAA
Found at i:395181 original size:185 final size:186
Alignment explanation
Indices: 394851--395240 Score: 653
Period size: 185 Copynumber: 2.1 Consensus size: 186
394841 TTTTCTAATT
* * *
394851 TATATAA-AAATTAAATA-TTTTTAATTCAAAAAAAAAGTTTATAATTAATTTAAATAATATATA
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAAAAGTTTACAATTAATTTAAATAATATATA
394914 ATTATAAAATAAAAATTTTAGATAAAATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
66 ATTATAAAATAAAAATTTTAGATAAAATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
394979 TTGGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTA
131 TTGGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTA
395035 TATATAATATATTTAATATTTTTTAATTCAAAAAAACAA-TTTACAATTAATTTAAATAATATAT
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAA-AAGTTTACAATTAATTTAAATAATATAT
* ** * *
395099 AATTATAAAATAAAAATTTTATATAATTTTTTTAATTAATT-ATTTTTATTTAGGTTTAAAAGTT
65 AATTATAAAATAAAAATTTTAGATAAAATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTT
*
395163 ATTGGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGTTGAGCCCATATGTTA
130 ATTGGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTA
*
395220 TATATAATATATTTAAAATTT
1 TATATAATATATTTAATATTT
395241 AAAATTTAAT
Statistics
Matches: 193, Mismatches: 10, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
184 7 0.04
185 105 0.54
186 79 0.41
187 2 0.01
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (186 bp):
TATATAATATATTTAATATTTTTTAATTCAAAAAAAAAGTTTACAATTAATTTAAATAATATATA
ATTATAAAATAAAAATTTTAGATAAAATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
TTGGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTA
Found at i:400250 original size:18 final size:18
Alignment explanation
Indices: 400227--400262 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
400217 ACTGGGATCA
400227 ATACGATGAAGCTTCAAC
1 ATACGATGAAGCTTCAAC
400245 ATACGATGAAGCTTCAAC
1 ATACGATGAAGCTTCAAC
400263 TTACAGCTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (18 bp):
ATACGATGAAGCTTCAAC
Found at i:405407 original size:24 final size:24
Alignment explanation
Indices: 405355--405408 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
405345 TAGTATATTC
405355 TTAT-AATATTTTATAGTTTATAG
1 TTATAAATATTTTATAGTTTATAG
* *
405378 TT-TAAATATTATTATTG-TTATAT
1 TTATAAATATT-TTATAGTTTATAG
405401 TTATAAAT
1 TTATAAAT
405409 TATATAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 1 0.04
23 15 0.58
24 10 0.38
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (24 bp):
TTATAAATATTTTATAGTTTATAG
Found at i:407061 original size:21 final size:21
Alignment explanation
Indices: 407035--407077 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
407025 CTATATAAAC
407035 AATTTAA-TTTAAGAATAAATT
1 AATTTAATTTTAA-AATAAATT
407056 AATTTAATTTTAAAATAAATT
1 AATTTAATTTTAAAATAAATT
407077 A
1 A
407078 TATAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
AATTTAATTTTAAAATAAATT
Found at i:407098 original size:11 final size:11
Alignment explanation
Indices: 407084--407108 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
407074 ATTATATAAA
407084 AATATTGTAAT
1 AATATTGTAAT
407095 AATATTGTAAT
1 AATATTGTAAT
407106 AAT
1 AAT
407109 TTAAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (11 bp):
AATATTGTAAT
Found at i:407459 original size:19 final size:20
Alignment explanation
Indices: 407431--407474 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
407421 AATTTAAGAA
*
407431 TAAATTATATAAAAAT-ATT
1 TAAATAATATAAAAATAATT
* *
407450 TAAATAATATTATAATAATT
1 TAAATAATATAAAAATAATT
407470 TAAAT
1 TAAAT
407475 CAATTTAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TAAATAATATAAAAATAATT
Found at i:407483 original size:26 final size:26
Alignment explanation
Indices: 407454--407516 Score: 60
Period size: 26 Copynumber: 2.4 Consensus size: 26
407444 AATATTTAAA
407454 TAATATTATAATA-ATTTAA-ATCAATT
1 TAATATTATAATATA-TTAATAT-AATT
*
407480 TAAT-TTAAGAATATATTAATATAATT
1 TAATATT-ATAATATATTAATATAATT
*
407506 TAAAATTATAA
1 TAATATTATAA
407517 ATGATCTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
25 2 0.07
26 23 0.77
27 5 0.17
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (26 bp):
TAATATTATAATATATTAATATAATT
Found at i:411905 original size:15 final size:16
Alignment explanation
Indices: 411882--411915 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
411872 AATCTGATCC
*
411882 AAATGTAAAAAT-ATT
1 AAATATAAAAATAATT
411897 AAATATAAAAATAATT
1 AAATATAAAAATAATT
411913 AAA
1 AAA
411916 ATCCATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (16 bp):
AAATATAAAAATAATT
Found at i:416010 original size:12 final size:12
Alignment explanation
Indices: 415993--416022 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
415983 TTATACAAAT
415993 CACATCATCTAA
1 CACATCATCTAA
416005 CACATCATCTAA
1 CACATCATCTAA
416017 CACATC
1 CACATC
416023 GTGTCTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.40, C:0.37, G:0.00, T:0.23
Consensus pattern (12 bp):
CACATCATCTAA
Found at i:416174 original size:26 final size:26
Alignment explanation
Indices: 416144--416194 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
416134 TTAAGAATAA
416144 ATTATCCAAATCAAACAATGATAATC
1 ATTATCCAAATCAAACAATGATAATC
416170 ATTATCCAAATCAAACAATGATAAT
1 ATTATCCAAATCAAACAATGATAAT
416195 TTAAATTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.51, C:0.18, G:0.04, T:0.27
Consensus pattern (26 bp):
ATTATCCAAATCAAACAATGATAATC
Found at i:420766 original size:21 final size:21
Alignment explanation
Indices: 420741--420783 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
420731 CTATATAAAC
420741 AATTTAA-TTTAAGAATAAATT
1 AATTTAATTTTAA-AATAAATT
420762 AATTTAATTTTAAAATAAATT
1 AATTTAATTTTAAAATAAATT
420783 A
1 A
420784 TATAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
AATTTAATTTTAAAATAAATT
Done.