Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003208.1 Hibiscus syriacus cultivar Beakdansim tig00006753_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: 1278004
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 7
Found at i:176099 original size:26 final size:23
Alignment explanation
Indices: 176040--176088 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
176030 AGTTAAATGT
176040 CTATTTTATTATATAAGCGCTAC
1 CTATTTTATTATATAAGCGCTAC
**
176063 CTATTACATTATATAAGCGCTAC
1 CTATTTTATTATATAAGCGCTAC
176086 CTA
1 CTA
176089 ATATGTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (23 bp):
CTATTTTATTATATAAGCGCTAC
Found at i:176109 original size:87 final size:87
Alignment explanation
Indices: 175963--176125 Score: 263
Period size: 87 Copynumber: 1.9 Consensus size: 87
175953 AAATAGGTCA
* * * *
175963 ATATAAGCGTTATCTATTACATTATATAAGAGCTGCCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGAGCTACCTAATATGTTATTATACTTGATAATATTT
176028 CCAGTTAAATGTCTATTTTATT
66 CCAGTTAAATGTCTATTTTATT
*
176050 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTATACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGAGCTACCTAATATGTTATTATACTTGATAATATTT
* *
176115 TCGGTTAAATG
66 CCAGTTAAATG
176126 ATATAACATT
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 69 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGAGCTACCTAATATGTTATTATACTTGATAATATTT
CCAGTTAAATGTCTATTTTATT
Found at i:176493 original size:48 final size:48
Alignment explanation
Indices: 176437--176531 Score: 163
Period size: 48 Copynumber: 2.0 Consensus size: 48
176427 TAGATATCTT
*
176437 AAACAAGATTATGAGTTTGAATCCTAGGCTGCTAGCGTTTTCGAGTGG
1 AAACAAGATTATGAGTTTGAATCCTAGGCTGCTAGCGTTTCCGAGTGG
* *
176485 AAACAAGATTATGAGTTTGAATCCTAGGTTGTTAGCGTTTCCGAGTG
1 AAACAAGATTATGAGTTTGAATCCTAGGCTGCTAGCGTTTCCGAGTG
176532 AAGCAATCTA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.33
Consensus pattern (48 bp):
AAACAAGATTATGAGTTTGAATCCTAGGCTGCTAGCGTTTCCGAGTGG
Found at i:177815 original size:28 final size:28
Alignment explanation
Indices: 177772--177826 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
177762 CTCTGTTTAT
* *
177772 ATTATGTCATCAAGCCATTGCTTAAAAC
1 ATTATGTCATCAAGCCAGTGCTGAAAAC
*
177800 ATTATGTCATCGAGCCAGTGCTGAAAA
1 ATTATGTCATCAAGCCAGTGCTGAAAA
177827 GCAACGAAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (28 bp):
ATTATGTCATCAAGCCAGTGCTGAAAAC
Found at i:185158 original size:16 final size:16
Alignment explanation
Indices: 185139--185187 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
185129 AAATATTATT
185139 TTATTAAATTTATTAA
1 TTATTAAATTTATTAA
185155 TTATTAAAATTTA-TAA
1 TTATT-AAATTTATTAA
*
185171 --AAT-AATTTATTAA
1 TTATTAAATTTATTAA
185184 TTAT
1 TTAT
185188 AAGATTTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 9
0.71 0.05 0.24
Matches are distributed among these distances:
12 6 0.22
13 3 0.11
14 2 0.07
15 1 0.04
16 8 0.30
17 7 0.26
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTATTAAATTTATTAA
Found at i:185164 original size:17 final size:15
Alignment explanation
Indices: 185127--185168 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
185117 GTGAATGTTG
185127 TAAAATATTATTTTAT
1 TAAAAT-TTATTTTAT
185143 T-AAATTTATTAATTAT
1 TAAAATTTATT--TTAT
185159 TAAAATTTAT
1 TAAAATTTAT
185169 AAAATAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 5 0.22
15 4 0.17
16 6 0.26
17 8 0.35
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TAAAATTTATTTTAT
Found at i:190062 original size:25 final size:25
Alignment explanation
Indices: 190034--190083 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
190024 ATACCTTCCA
190034 AGACCATCAAATAATTCACCTTCTT
1 AGACCATCAAATAATTCACCTTCTT
*
190059 AGACCATCAAATAATTCGCCTTCTT
1 AGACCATCAAATAATTCACCTTCTT
190084 TGGTTAACTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.34, C:0.28, G:0.06, T:0.32
Consensus pattern (25 bp):
AGACCATCAAATAATTCACCTTCTT
Found at i:199039 original size:20 final size:21
Alignment explanation
Indices: 199004--199043 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
198994 ATTCATCGAT
*
199004 AATATATTATTTTATTATTTA
1 AATATATCATTTTATTATTTA
199025 AATATATCA-TTTATTATTT
1 AATATATCATTTTATTATTT
199044 TAATTAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
AATATATCATTTTATTATTTA
Found at i:202996 original size:35 final size:34
Alignment explanation
Indices: 202957--203029 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 34
202947 AAAATTGAAT
202957 AATAAAACAAATT-AAAATATCAACGCCAAGAAACA
1 AATAAAA-AAATTGAAAATATCAACGCC-AGAAACA
** *
202992 AATAAAAATGTTGAAAATATCAACGCCAGAAGCA
1 AATAAAAAAATTGAAAATATCAACGCCAGAAACA
203026 AATA
1 AATA
203030 CCTAAAAGGG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
34 13 0.38
35 21 0.62
ACGTcount: A:0.59, C:0.15, G:0.10, T:0.16
Consensus pattern (34 bp):
AATAAAAAAATTGAAAATATCAACGCCAGAAACA
Found at i:207034 original size:60 final size:61
Alignment explanation
Indices: 206933--207059 Score: 152
Period size: 60 Copynumber: 2.1 Consensus size: 61
206923 TTAGGTAAAA
* *
206933 TACACAAATGGTCCTCCGACTATAGGAAATGTTTTTGTTGAGTTC-CCCGACTATT-AAAAGT
1 TACA-AAATGATCCTCCGACTATAGGAAATGTTTCTGTTGAG-TCACCCGACTATTAAAAAGT
* * * *
206994 TACAAAATGATCCTCTGACTATATGATATTGTTTCT-TTGAGTCACTCGACTATTAAAAAGT
1 TACAAAATGATCCTCCGACTATAGGA-AATGTTTCTGTTGAGTCACCCGACTATTAAAAAGT
207055 TACAA
1 TACAA
207060 TATGGTCACC
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
59 2 0.04
60 33 0.58
61 22 0.39
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (61 bp):
TACAAAATGATCCTCCGACTATAGGAAATGTTTCTGTTGAGTCACCCGACTATTAAAAAGT
Found at i:209566 original size:30 final size:31
Alignment explanation
Indices: 209501--209589 Score: 103
Period size: 31 Copynumber: 2.9 Consensus size: 31
209491 AAATTGACAT
*
209501 TTTATCTAAAATTTAATGGCTAAATTAATAC
1 TTTATCTAAAATTTAATGGCTAAACTAATAC
* *
209532 TTTATCTAAATTTTAATGG-TCAAACTGATA-
1 TTTATCTAAAATTTAATGGCT-AAACTAATAC
*
209562 TTTATCTAAAATTT-ATAGGTTAAACTAA
1 TTTATCTAAAATTTAAT-GGCTAAACTAA
209590 AAATTAACCC
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
29 2 0.04
30 22 0.44
31 26 0.52
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.43
Consensus pattern (31 bp):
TTTATCTAAAATTTAATGGCTAAACTAATAC
Found at i:210169 original size:22 final size:23
Alignment explanation
Indices: 210136--210183 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
210126 TTAATTTATA
210136 AAACGTTAAATTATAAAATA-TT
1 AAACGTTAAATTATAAAATAGTT
*
210158 AAACG-TATAATTATAAATTAGTT
1 AAACGTTA-AATTATAAAATAGTT
210181 AAA
1 AAA
210184 AATCTAAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 2 0.09
22 16 0.70
23 5 0.22
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.35
Consensus pattern (23 bp):
AAACGTTAAATTATAAAATAGTT
Found at i:215980 original size:22 final size:21
Alignment explanation
Indices: 215939--215978 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
215929 AAATAATTAA
215939 TTTAGACATCAATGTTTATAAT
1 TTTAGACA-CAATGTTTATAAT
*
215961 TTTAGACA-AATGTATATA
1 TTTAGACACAATGTTTATA
215979 TATATTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
22 8 0.47
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.42
Consensus pattern (21 bp):
TTTAGACACAATGTTTATAAT
Found at i:216314 original size:35 final size:35
Alignment explanation
Indices: 216274--216351 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 35
216264 TCATCAATTC
* * **
216274 ATTCTAAACCCCAATTTCCAAAGTAATTCAATTTT
1 ATTCTAAACCCCAAATTCCAAAATAATTCAATTAA
* * *
216309 ATTCTAAACCCTAAATTCTAAAATACTTCAATTAA
1 ATTCTAAACCCCAAATTCCAAAATAATTCAATTAA
216344 ATTCTAAA
1 ATTCTAAA
216352 ATACTTCAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.42, C:0.21, G:0.01, T:0.36
Consensus pattern (35 bp):
ATTCTAAACCCCAAATTCCAAAATAATTCAATTAA
Found at i:216345 original size:21 final size:21
Alignment explanation
Indices: 216320--216362 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
216310 TTCTAAACCC
216320 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
216341 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
216362 T
1 T
216363 TAAGGTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTCTAAAATACTTCAAT
Found at i:216511 original size:16 final size:18
Alignment explanation
Indices: 216478--216511 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
216468 TATATTAATG
216478 TTGAATCATTTATATTTT
1 TTGAATCATTTATATTTT
216496 TTGAAT-ATTT-TATTTT
1 TTGAATCATTTATATTTT
216512 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 4 0.25
18 6 0.38
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TTGAATCATTTATATTTT
Found at i:220728 original size:16 final size:16
Alignment explanation
Indices: 220709--220739 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
220699 TTTTTAATTT
*
220709 ATTTGATTTTTTCTTA
1 ATTTGATTTTCTCTTA
220725 ATTTGATTTTCTCTT
1 ATTTGATTTTCTCTT
220740 TTAATTTTGG
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:0.16, C:0.10, G:0.06, T:0.68
Consensus pattern (16 bp):
ATTTGATTTTCTCTTA
Found at i:224490 original size:33 final size:33
Alignment explanation
Indices: 224453--224521 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
224443 GAGCGTTGTC
224453 AAAGAGATTTAGTCGTCGTCCATAAAAGGAAAT
1 AAAGAGATTTAGTCGTCGTCCATAAAAGGAAAT
*
224486 AAAGAGATTTAGTCGTTGTCCATAAAAGGAAAT
1 AAAGAGATTTAGTCGTCGTCCATAAAAGGAAAT
224519 AAA
1 AAA
224522 AATAATGCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.25
Consensus pattern (33 bp):
AAAGAGATTTAGTCGTCGTCCATAAAAGGAAAT
Found at i:227459 original size:111 final size:111
Alignment explanation
Indices: 227336--227535 Score: 310
Period size: 111 Copynumber: 1.8 Consensus size: 111
227326 CAAGTTAGTG
* * * *
227336 GTTAGTTGTTAACAAAGTCCGAATCATAATAATATAGATCATATCCTGGATCGAGTCACCACAAG
1 GTTAGATGTTAACAAAGTCCGAACCATAATAATATAGATCATACCCCGGATCGAGTCACCACAAG
227401 GTCGGTTCGAATAATAACAATAAATTTTTAGCAGTTGTGGTTAGCA
66 GTCGGTTCGAATAATAACAATAAATTTTTAGCAGTTGTGGTTAGCA
* * * * *
227447 GTTAGATGTTAACAAAGTCTGGACCATAATAATATGGATCATACCCCGGATCGGGTCACCATAAG
1 GTTAGATGTTAACAAAGTCCGAACCATAATAATATAGATCATACCCCGGATCGAGTCACCACAAG
*
227512 GTCGGTTCGAATAATATCAATAAA
66 GTCGGTTCGAATAATAACAATAAA
227536 CAGAAAATAG
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
111 79 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (111 bp):
GTTAGATGTTAACAAAGTCCGAACCATAATAATATAGATCATACCCCGGATCGAGTCACCACAAG
GTCGGTTCGAATAATAACAATAAATTTTTAGCAGTTGTGGTTAGCA
Found at i:229725 original size:102 final size:103
Alignment explanation
Indices: 229592--229828 Score: 280
Period size: 102 Copynumber: 2.3 Consensus size: 103
229582 TTTGTATTCT
* * * *
229592 AAGGGAAAACTGTCTCAAGCGAGAAAAAAATTGATTTTAAGAAAAACAATCTCAAGTGAGATAAA
1 AAGGGAAAATTGTCTCAAGCGAG-AAAAAATTGATTCTAAGAAAAACAATATCAAGTAAGATAAA
* *
229657 TCTTGTTTTAAGTGAAACAATTCCAAAAGTTGTGCTT-C
65 TCTTGTTTTAAGAGAAACAATTCCAAAAGTTGTGCTTAA
** * * *
229695 AAGGGAAAATTGTCTCAAGCGAGATGAAATTGGTTCTAAGAAAAATAATATCAAGTAAGATCAAT
1 AAGGGAAAATTGTCTCAAGCGAGAAAAAATTGATTCTAAGAAAAACAATATCAAGTAAGATAAAT
* * * * * *
229760 TTTGTTTTGAGAGAAACAATTTCAATATTTGTGTTTAA
66 CTTGTTTTAAGAGAAACAATTCCAAAAGTTGTGCTTAA
*
229798 AAGGG-AAATTGTCTCAAGTGAGACAAAAATT
1 AAGGGAAAATTGTCTCAAGCGAGA-AAAAATT
229829 ATGAATGAAA
Statistics
Matches: 112, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
102 80 0.71
103 32 0.29
ACGTcount: A:0.42, C:0.10, G:0.19, T:0.29
Consensus pattern (103 bp):
AAGGGAAAATTGTCTCAAGCGAGAAAAAATTGATTCTAAGAAAAACAATATCAAGTAAGATAAAT
CTTGTTTTAAGAGAAACAATTCCAAAAGTTGTGCTTAA
Found at i:231349 original size:41 final size:43
Alignment explanation
Indices: 231292--231377 Score: 158
Period size: 41 Copynumber: 2.0 Consensus size: 43
231282 TTCCCCACAC
231292 TTTAAAAGATTAGCTCAAAGTAATACC-AAG-AATCTTTTGTT
1 TTTAAAAGATTAGCTCAAAGTAATACCAAAGAAATCTTTTGTT
231333 TTTAAAAGATTAGCTCAAAGTAATACCAAAGAAATCTTTTGTT
1 TTTAAAAGATTAGCTCAAAGTAATACCAAAGAAATCTTTTGTT
231376 TT
1 TT
231378 CTTTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
41 27 0.63
42 3 0.07
43 13 0.30
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.37
Consensus pattern (43 bp):
TTTAAAAGATTAGCTCAAAGTAATACCAAAGAAATCTTTTGTT
Found at i:231925 original size:25 final size:24
Alignment explanation
Indices: 231887--232025 Score: 78
Period size: 25 Copynumber: 5.9 Consensus size: 24
231877 CTCATTCAAT
* *
231887 TTTTTTTTTTTTTTTATTTCTCTCA
1 TTTTTTCTTATTTTTATTTCTCT-A
*
231912 TTTTTTCTTATTTTTATTTTTCTA
1 TTTTTTCTTATTTTTATTTCTCTA
* * *
231936 TCTTTTTCTT-TTCTTGTTTATC-A
1 T-TTTTTCTTATTTTTATTTCTCTA
* *
231959 TTATTTCTT-TTTTCATTT-T-TA
1 TTTTTTCTTATTTTTATTTCTCTA
* *
231980 CTTTTTTCTT-TTCTTT-TTTCTTTT
1 -TTTTTTCTTATT-TTTATTTCTCTA
232004 TTTTCTCTCTTATTTTT-TTTCT
1 TTTT-T-TCTTATTTTTATTTCT
232026 TTTCTTTTCT
Statistics
Matches: 92, Mismatches: 13, Indels: 18
0.75 0.11 0.15
Matches are distributed among these distances:
21 2 0.02
22 26 0.28
23 9 0.10
24 13 0.14
25 40 0.43
26 2 0.02
ACGTcount: A:0.08, C:0.14, G:0.01, T:0.78
Consensus pattern (24 bp):
TTTTTTCTTATTTTTATTTCTCTA
Found at i:231925 original size:27 final size:26
Alignment explanation
Indices: 231885--231942 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
231875 CCCTCATTCA
* *
231885 ATTTTTTTT-TTTTTTTTATTTCTCTC
1 ATTTTTTTTATTTTTATT-TTTCTATC
231911 ATTTTTTCTTATTTTTATTTTTCTATC
1 ATTTTTT-TTATTTTTATTTTTCTATC
231938 -TTTTT
1 ATTTTT
231943 CTTTTCTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 12 0.43
27 9 0.32
28 7 0.25
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.79
Consensus pattern (26 bp):
ATTTTTTTTATTTTTATTTTTCTATC
Found at i:231931 original size:15 final size:15
Alignment explanation
Indices: 231913--232004 Score: 56
Period size: 15 Copynumber: 6.3 Consensus size: 15
231903 TTTCTCTCAT
*
231913 TTTTTCTTATTTTTA
1 TTTTTCTTATTTTCA
*
231928 TTTTTC-TATCTTT-T
1 TTTTTCTTAT-TTTCA
*
231942 TCTTTTCTTGTTTATCA
1 T-TTTTCTTATTT-TCA
231959 TTATTTCTT-TTTTCA
1 TT-TTTCTTATTTTCA
231974 TTTTTACTT-TTTTC-
1 TTTTT-CTTATTTTCA
231988 -TTTTCTT-TTTTC-
1 TTTTTCTTATTTTCA
232000 TTTTT
1 TTTTT
232005 TTTCTCTCTT
Statistics
Matches: 66, Mismatches: 3, Indels: 18
0.76 0.03 0.21
Matches are distributed among these distances:
12 8 0.12
13 8 0.12
14 7 0.11
15 29 0.44
16 7 0.11
17 7 0.11
ACGTcount: A:0.09, C:0.13, G:0.01, T:0.77
Consensus pattern (15 bp):
TTTTTCTTATTTTCA
Found at i:231977 original size:7 final size:7
Alignment explanation
Indices: 231886--232005 Score: 63
Period size: 7 Copynumber: 16.6 Consensus size: 7
231876 CCTCATTCAA
231886 TTTT-TT
1 TTTTCTT
231892 TTTT-TT
1 TTTTCTT
*
231898 TTTTATT
1 TTTTCTT
*
231905 TCTCTCATT
1 T-TTTC-TT
231914 TTTTCTT
1 TTTTCTT
231921 ATTTT-TAT
1 -TTTTCT-T
231929 TTTTCTAT
1 TTTTCT-T
*
231937 CTTTT-TC
1 -TTTTCTT
231944 TTTTCTT
1 TTTTCTT
231951 GTTTATCATT
1 -TTT-TC-TT
*
231961 ATTTCTT
1 TTTTCTT
231968 TTTTCATT
1 TTTTC-TT
*
231976 TTTACTT
1 TTTTCTT
231983 TTTTC--
1 TTTTCTT
231988 TTTTCTT
1 TTTTCTT
231995 TTTTCTT
1 TTTTCTT
232002 TTTT
1 TTTT
232006 TTCTCTCTTA
Statistics
Matches: 91, Mismatches: 9, Indels: 27
0.72 0.07 0.21
Matches are distributed among these distances:
5 5 0.05
6 14 0.15
7 34 0.37
8 25 0.27
9 11 0.12
10 2 0.02
ACGTcount: A:0.08, C:0.12, G:0.01, T:0.78
Consensus pattern (7 bp):
TTTTCTT
Found at i:233494 original size:18 final size:19
Alignment explanation
Indices: 233460--233500 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
233450 TAAAAGATTG
*
233460 TAAAGAATGTAAGAATG-A
1 TAAAGAATATAAGAATGTA
233478 TAAAGAATATGAA-AATGTA
1 TAAAGAATAT-AAGAATGTA
233497 TAAA
1 TAAA
233501 ATGATTGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.59, C:0.00, G:0.17, T:0.24
Consensus pattern (19 bp):
TAAAGAATATAAGAATGTA
Found at i:237544 original size:43 final size:43
Alignment explanation
Indices: 237490--237579 Score: 105
Period size: 43 Copynumber: 2.1 Consensus size: 43
237480 AATAAAAGAT
* *
237490 TAAAAATTAAAGCAAATAAAATTT-AAGG-GTA-AAATTAAATAAA
1 TAAAAAATAAAG-AAAT-AAATTTAAAGGTGCATAAA-TAAATAAA
*
237533 TAAAAAATAAAGGAATAAATTTAAAGGTGCATAAATAAATAAA
1 TAAAAAATAAAGAAATAAATTTAAAGGTGCATAAATAAATAAA
237576 TAAA
1 TAAA
237580 CGAGCAATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
41 6 0.15
42 7 0.17
43 25 0.61
44 3 0.07
ACGTcount: A:0.63, C:0.02, G:0.10, T:0.24
Consensus pattern (43 bp):
TAAAAAATAAAGAAATAAATTTAAAGGTGCATAAATAAATAAA
Found at i:237545 original size:28 final size:28
Alignment explanation
Indices: 237492--237545 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
237482 TAAAAGATTA
* *
237492 AAAATTAAAGCAAATAAAATTTAAGGGT
1 AAAATTAAAGCAAATAAAAATAAAGGGT
*
237520 AAAATTAAA-TAAATAAAAAATAAAGG
1 AAAATTAAAGCAAAT-AAAAATAAAGG
237546 AATAAATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 4 0.18
28 18 0.82
ACGTcount: A:0.65, C:0.02, G:0.11, T:0.22
Consensus pattern (28 bp):
AAAATTAAAGCAAATAAAAATAAAGGGT
Found at i:237671 original size:4 final size:4
Alignment explanation
Indices: 237662--237693 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
237652 TGGTTCAAAC
237662 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
237694 CAAGTTAGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAA
Found at i:239397 original size:44 final size:44
Alignment explanation
Indices: 239305--239419 Score: 144
Period size: 44 Copynumber: 2.6 Consensus size: 44
239295 TATTCATGCT
* * *
239305 ATGT-ATATTGATCT-CTGTGATTACATGAATATGTTATACAAGCT
1 ATGTGATA-TGATCTAC-GTGATTACATGAATATGTGATACAAACC
*
239349 ATGTGATATGATCTACGTGATTACATGAATATGTGATATAAACC
1 ATGTGATATGATCTACGTGATTACATGAATATGTGATACAAACC
* *
239393 ATGTGACATGACCTACGTGATTACATG
1 ATGTGATATGATCTACGTGATTACATG
239420 TCTATGTGTT
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
44 59 0.94
45 4 0.06
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (44 bp):
ATGTGATATGATCTACGTGATTACATGAATATGTGATACAAACC
Found at i:239612 original size:23 final size:23
Alignment explanation
Indices: 239586--239632 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
239576 ATTTCTACAC
239586 GATCATTCGAGACAATACTATGT
1 GATCATTCGAGACAATACTATGT
* * * *
239609 GATCTTTCGGGACATTTCTATGT
1 GATCATTCGAGACAATACTATGT
239632 G
1 G
239633 GCGCTTCAGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (23 bp):
GATCATTCGAGACAATACTATGT
Found at i:246195 original size:20 final size:20
Alignment explanation
Indices: 246170--246213 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
246160 TCCAATTTCA
246170 CAACGCGAATATGTAAATCG
1 CAACGCGAATATGTAAATCG
*
246190 CAACGCGAATTTGTAAATCG
1 CAACGCGAATATGTAAATCG
246210 CAAC
1 CAAC
246214 ACAGAAGTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (20 bp):
CAACGCGAATATGTAAATCG
Found at i:246235 original size:20 final size:20
Alignment explanation
Indices: 246207--246313 Score: 162
Period size: 20 Copynumber: 5.3 Consensus size: 20
246197 AATTTGTAAA
246207 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
* * *
246227 TCACAACACAAAACTCAAAT
1 TCGCAACACAGAAGTCAAAT
246247 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
246267 TCGCAACAC-GATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
*
246287 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
246307 TCGCAAC
1 TCGCAAC
246314 GCGAAATTTC
Statistics
Matches: 78, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
19 2 0.03
20 75 0.96
21 1 0.01
ACGTcount: A:0.46, C:0.27, G:0.11, T:0.16
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:246251 original size:60 final size:59
Alignment explanation
Indices: 246207--246334 Score: 177
Period size: 60 Copynumber: 2.1 Consensus size: 59
246197 AATTTGTAAA
*
246207 TCGCAACACAGA-AGTCAAATTCACAACACAAAACTCAAATTCGCAACACAGAAGTCAAAT
1 TCGCAACAC-GATAGTCAAATTCACAACACAAAACTCAAATTCGCAACGC-GAAGTCAAAT
* * *
246267 TCGCAACACGATAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAAATTTCAAAT
1 TCGCAACACGATAGTCAAATTCACAACACAAAACTCAAATTCGCAACGCG-AA-GTCAAAT
246328 TCGCAAC
1 TCGCAAC
246335 TGAATTTCAA
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
59 3 0.05
60 45 0.74
61 13 0.21
ACGTcount: A:0.45, C:0.27, G:0.12, T:0.17
Consensus pattern (59 bp):
TCGCAACACGATAGTCAAATTCACAACACAAAACTCAAATTCGCAACGCGAAGTCAAAT
Found at i:246262 original size:40 final size:40
Alignment explanation
Indices: 246207--246334 Score: 175
Period size: 40 Copynumber: 3.2 Consensus size: 40
246197 AATTTGTAAA
*
246207 TCGCAACACAGAAGTCAAATTCACAACACAAAACTCAAAT
1 TCGCAACACAGAAGTCAAATTCGCAACACAAAACTCAAAT
* * *
246247 TCGCAACACAGAAGTCAAATTCGCAACACGATAGTCAAAT
1 TCGCAACACAGAAGTCAAATTCGCAACACAAAACTCAAAT
* * **
246287 TCGCAACACAAAAGTCAAATTCGCAACGCGAAATTTCAAAT
1 TCGCAACACAGAAGTCAAATTCGCAACAC-AAAACTCAAAT
246328 TCGCAAC
1 TCGCAAC
246335 TGAATTTCAA
Statistics
Matches: 77, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
40 63 0.82
41 14 0.18
ACGTcount: A:0.45, C:0.27, G:0.12, T:0.17
Consensus pattern (40 bp):
TCGCAACACAGAAGTCAAATTCGCAACACAAAACTCAAAT
Found at i:246342 original size:19 final size:19
Alignment explanation
Indices: 246301--246430 Score: 154
Period size: 19 Copynumber: 6.7 Consensus size: 19
246291 AACACAAAAG
*
246301 TCAAATTCGCAACGCGAAATT
1 TCAAATTCGCAAC-TG-AATT
246322 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
*
246341 TCAAATTTGCAACTGAATT
1 TCAAATTCGCAACTGAATT
*
246360 TTAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
*
246379 TCAAATTCGCAACTAGATTT
1 TCAAATTCGCAACT-GAATT
* *
246399 TCGAATTCGCAACACGAATT
1 TCAAATTCGCAAC-TGAATT
*
246419 T-AATTTCGCAAC
1 TCAAATTCGCAAC
246431 AGGTTTTAGT
Statistics
Matches: 96, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
19 61 0.64
20 22 0.23
21 13 0.14
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.32
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:246431 original size:19 final size:19
Alignment explanation
Indices: 246183--246431 Score: 132
Period size: 20 Copynumber: 12.7 Consensus size: 19
246173 CGCGAATATG
*
246183 TAAA-TCGCAACGCGAATTT
1 TAAATTCGCAACACGAA-TT
*
246202 GTAAA-TCGCAACACAGAAGT
1 -TAAATTCGCAACAC-GAATT
* * * *
246222 CAAATTCACAACACAAAACT
1 TAAATTCGCAACAC-GAATT
* *
246242 CAAATTCGCAACACAGAAGT
1 TAAATTCGCAACAC-GAATT
* *
246262 CAAATTCGCAACACGATAGT
1 TAAATTCGCAACACGA-ATT
* * *
246282 CAAATTCGCAACACAAAAGT
1 TAAATTCGCAACAC-GAATT
* *
246302 CAAATTCGCAACGCGAAATT
1 TAAATTCGCAACACG-AATT
*
246322 TCAAATTCGCAAC-TGAATT
1 T-AAATTCGCAACACGAATT
* *
246341 TCAAATTTGCAAC-TGAATTT
1 T-AAATTCGCAACACGAA-TT
*
246361 TAAATTCGCAAC-TGAATT
1 TAAATTCGCAACACGAATT
*
246379 TCAAATTCGCAACTA-GATTT
1 T-AAATTCGCAAC-ACGAATT
*
246399 TCGAATTCGCAACACGAATT
1 T-AAATTCGCAACACGAATT
*
246419 TAATTTCGCAACA
1 TAAATTCGCAACA
246432 GGTTTTAGTT
Statistics
Matches: 196, Mismatches: 22, Indels: 23
0.81 0.09 0.10
Matches are distributed among these distances:
18 3 0.02
19 61 0.31
20 117 0.60
21 15 0.08
ACGTcount: A:0.41, C:0.22, G:0.12, T:0.24
Consensus pattern (19 bp):
TAAATTCGCAACACGAATT
Found at i:246606 original size:14 final size:15
Alignment explanation
Indices: 246587--246624 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
246577 TCCCCATCTC
246587 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
246601 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
246617 TAATTTTT
1 TAATTTTT
246625 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:247240 original size:12 final size:12
Alignment explanation
Indices: 247219--247252 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
247209 ACCACATTTC
*
247219 CAATACCAAACA
1 CAATATCAAACA
247231 CAATATCAAACA
1 CAATATCAAACA
*
247243 CAATCTCAAA
1 CAATATCAAA
247253 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:247434 original size:24 final size:24
Alignment explanation
Indices: 247378--247454 Score: 120
Period size: 24 Copynumber: 3.2 Consensus size: 24
247368 GTATTCAAAA
*
247378 TTTGATCTTGGTCAATAC-CCGAC
1 TTTGATCTTGGTCAATACTCGGAC
*
247401 CTTGATCTTGGTCAATACTCGGAC
1 TTTGATCTTGGTCAATACTCGGAC
*
247425 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACTCGGAC
247449 TTTGAT
1 TTTGAT
247455 GATGTGATGG
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
23 17 0.35
24 32 0.65
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.39
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACTCGGAC
Found at i:249735 original size:18 final size:18
Alignment explanation
Indices: 249712--249747 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
249702 AAGCAAAAGG
*
249712 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
249730 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
249748 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:250260 original size:25 final size:25
Alignment explanation
Indices: 250232--250281 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
250222 AAATCAATTA
*
250232 AACATTATTGTGGGTACATTATTTG
1 AACATTATTATGGGTACATTATTTG
* *
250257 AACATTGTTATGGGTATATTATTTG
1 AACATTATTATGGGTACATTATTTG
250282 GAAAATAATG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.28, C:0.06, G:0.20, T:0.46
Consensus pattern (25 bp):
AACATTATTATGGGTACATTATTTG
Found at i:250696 original size:18 final size:18
Alignment explanation
Indices: 250665--250701 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
250655 TGTAATTGAG
250665 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
250683 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
250701 T
1 T
250702 ATAAATTTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:250708 original size:24 final size:24
Alignment explanation
Indices: 250660--250710 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
250650 TCATATGTAA
* *
250660 TTGAGTTTGAATTTAAATTTCAAT
1 TTGAGTTTGAATTTAAATATAAAT
*
250684 TTGAGTTTGAATTTCAATATAAAT
1 TTGAGTTTGAATTTAAATATAAAT
250708 TTG
1 TTG
250711 GCTCCACTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.04, G:0.14, T:0.49
Consensus pattern (24 bp):
TTGAGTTTGAATTTAAATATAAAT
Found at i:251678 original size:18 final size:18
Alignment explanation
Indices: 251655--251690 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
251645 AAACAAAAGG
*
251655 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
251673 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
251691 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:252001 original size:20 final size:20
Alignment explanation
Indices: 251976--252025 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
251966 ATGTTGCGAT
*
251976 CAACGCGAAAGTCAAATTCG
1 CAACGCAAAAGTCAAATTCG
*
251996 CAACGCAAAAGTCAAGTTCG
1 CAACGCAAAAGTCAAATTCG
252016 CAACGCAAAA
1 CAACGCAAAA
252026 TAAGCATTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.44, C:0.26, G:0.18, T:0.12
Consensus pattern (20 bp):
CAACGCAAAAGTCAAATTCG
Found at i:252245 original size:66 final size:65
Alignment explanation
Indices: 252163--252337 Score: 246
Period size: 66 Copynumber: 2.6 Consensus size: 65
252153 AATTTAAAAC
*
252163 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATT
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAACAATTCTTATTTACACATC-AATT
252228 A
65 A
* *
252229 AACAAATCAACTTTTACAAATCAATTAAACAAGC-AAAAAACAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAACAATTCTTATTTACACATCAATTA
252293 AACAAATCAACTTTCAATGTA-AAATTCAATTAAACAAGCAAAAAA
1 AACAAATCAAC-TT---T-TACAAA-TCAATTAAACAAGCAAAAAA
252338 GTGTACCCCA
Statistics
Matches: 99, Mismatches: 3, Indels: 10
0.88 0.03 0.09
Matches are distributed among these distances:
64 16 0.16
65 24 0.24
66 34 0.34
68 4 0.04
69 16 0.16
70 5 0.05
ACGTcount: A:0.53, C:0.18, G:0.02, T:0.27
Consensus pattern (65 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAACAATTCTTATTTACACATCAATTA
Found at i:253710 original size:21 final size:21
Alignment explanation
Indices: 253686--253763 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 21
253676 GCCGGCGGGA
*
253686 CCTCTTGAGCGATGACAGGGG
1 CCTCTTGAACGATGACAGGGG
* *
253707 CCTCTTGAACGGTGATAGGGG
1 CCTCTTGAACGATGACAGGGG
* * * *
253728 CCTTTTCAACGAT-AGGAGGCG
1 CCTCTTGAACGATGA-CAGGGG
*
253749 CCTCTTGAATGATGA
1 CCTCTTGAACGATGA
253764 TAGGTTCACC
Statistics
Matches: 44, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
20 1 0.02
21 42 0.95
22 1 0.02
ACGTcount: A:0.22, C:0.22, G:0.32, T:0.24
Consensus pattern (21 bp):
CCTCTTGAACGATGACAGGGG
Found at i:253936 original size:4 final size:4
Alignment explanation
Indices: 253906--253946 Score: 55
Period size: 4 Copynumber: 10.2 Consensus size: 4
253896 GGCCCGTTGA
* * *
253906 AAAT AAAT TAAT ACAT AAAT CAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
253947 GTGCCGAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (4 bp):
AAAT
Found at i:255987 original size:14 final size:14
Alignment explanation
Indices: 255942--255987 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
255932 ACACGAAAAT
*
255942 GAAAATCGCAACAC
1 GAAAATCGCAACGC
* *
255956 CAAAATCGCAACGA
1 GAAAATCGCAACGC
255970 GAAAATCGCAACGC
1 GAAAATCGCAACGC
255984 GAAA
1 GAAA
255988 CTAAAATTGC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.50, C:0.26, G:0.17, T:0.07
Consensus pattern (14 bp):
GAAAATCGCAACGC
Found at i:256049 original size:20 final size:20
Alignment explanation
Indices: 256011--256049 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
256001 GCAATTTTGG
* * *
256011 TGTTGCGATTTTCATTTTCT
1 TGTTGCGAATTTAAGTTTCT
256031 TGTTGCGAATTTAAGTTTC
1 TGTTGCGAATTTAAGTTTC
256050 AAAAACTATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.15, C:0.13, G:0.18, T:0.54
Consensus pattern (20 bp):
TGTTGCGAATTTAAGTTTCT
Found at i:256552 original size:20 final size:20
Alignment explanation
Indices: 256524--256704 Score: 168
Period size: 20 Copynumber: 8.9 Consensus size: 20
256514 ATATTGTGTT
*
256524 TCGCTTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
* *
256544 TCGCATTGCGAATTTGA-AA
1 TCGCGTTGCGAATTTGACTA
*
256563 TTCAGTGTTGCGAATTTGACTA
1 -TC-GCGTTGCGAATTTGACTA
* *
256585 TCGCGTTGCGAATTTAACTT
1 TCGCGTTGCGAATTTGACTA
* * *
256605 TTGTGTTGCGAATTTGA-AA
1 TCGCGTTGCGAATTTGACTA
**
256624 TTCAGTATTGCGAATTTGACTA
1 -TC-GCGTTGCGAATTTGACTA
* *
256646 TCGCGTTGCGAAGTTGACTT
1 TCGCGTTGCGAATTTGACTA
* * *
256666 TTGTGTTGCGGATTTGACTA
1 TCGCGTTGCGAATTTGACTA
256686 TCGCGTTGCGAATTTGACT
1 TCGCGTTGCGAATTTGACT
256705 TCTGTGTTGC
Statistics
Matches: 127, Mismatches: 28, Indels: 12
0.76 0.17 0.07
Matches are distributed among these distances:
19 1 0.01
20 93 0.73
21 31 0.24
22 2 0.02
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGACTA
Found at i:256574 original size:41 final size:40
Alignment explanation
Indices: 256529--256621 Score: 141
Period size: 41 Copynumber: 2.3 Consensus size: 40
256519 GTGTTTCGCT
256529 TTGCGAATTTGACTATCGCATTGCGAATTTGAAATTCAGTG
1 TTGCGAATTTGACTATCGCATTGCGAATTT-AAATTCAGTG
* * **
256570 TTGCGAATTTGACTATCGCGTTGCGAATTTAACTTTTGTG
1 TTGCGAATTTGACTATCGCATTGCGAATTTAAATTCAGTG
256610 TTGCGAATTTGA
1 TTGCGAATTTGA
256622 AATTCAGTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
40 19 0.40
41 29 0.60
ACGTcount: A:0.24, C:0.14, G:0.23, T:0.40
Consensus pattern (40 bp):
TTGCGAATTTGACTATCGCATTGCGAATTTAAATTCAGTG
Found at i:256575 original size:21 final size:21
Alignment explanation
Indices: 256549--256642 Score: 104
Period size: 21 Copynumber: 4.6 Consensus size: 21
256539 GACTATCGCA
256549 TTGCGAATTTGAAATTCAGTG
1 TTGCGAATTTGAAATTCAGTG
* *
256570 TTGCGAATTTG-ACTATC-GCG
1 TTGCGAATTTGAAAT-TCAGTG
* **
256590 TTGCGAATTT-AACTTTTGTG
1 TTGCGAATTTGAAATTCAGTG
*
256610 TTGCGAATTTGAAATTCAGTA
1 TTGCGAATTTGAAATTCAGTG
256631 TTGCGAATTTGA
1 TTGCGAATTTGA
256643 CTATCGCGTT
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
19 1 0.02
20 29 0.48
21 31 0.51
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.40
Consensus pattern (21 bp):
TTGCGAATTTGAAATTCAGTG
Found at i:256614 original size:61 final size:61
Alignment explanation
Indices: 256549--256720 Score: 235
Period size: 61 Copynumber: 2.9 Consensus size: 61
256539 GACTATCGCA
256549 TTGCGAATTTGAAATTCAGTGTTGCGAATTTGACTATCGCGTTGCGAATTTAACTTTTGTG
1 TTGCGAATTTGAAATTCAGTGTTGCGAATTTGACTATCGCGTTGCGAATTTAACTTTTGTG
* * *
256610 TTGCGAATTTGAAATTCAGTATTGCGAATTTGACTATCGCGTTGCGAAGTTGACTTTTGTG
1 TTGCGAATTTGAAATTCAGTGTTGCGAATTTGACTATCGCGTTGCGAATTTAACTTTTGTG
* * * *
256671 TTGCGGATTTG-ACTATC-GCGTTGCGAATTTGACT-TCTGTGTTGCG-ATTTA
1 TTGCGAATTTGAAAT-TCAGTGTTGCGAATTTGACTATC-GCGTTGCGAATTTA
256721 CAAATTCGCG
Statistics
Matches: 99, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
59 5 0.05
60 24 0.24
61 70 0.71
ACGTcount: A:0.21, C:0.14, G:0.24, T:0.41
Consensus pattern (61 bp):
TTGCGAATTTGAAATTCAGTGTTGCGAATTTGACTATCGCGTTGCGAATTTAACTTTTGTG
Found at i:256681 original size:40 final size:40
Alignment explanation
Indices: 256569--256736 Score: 144
Period size: 40 Copynumber: 4.2 Consensus size: 40
256559 GAAATTCAGT
* * * * * * *
256569 GTTGCGAATTTGACTATC-GCGTTGCGAATTTAACTTTTGT
1 GTTGCGAAGTTGACT-TCTGTGTTGCGGATTTGACTATCGC
* * * * *
256609 GTTGCGAATTTGAAATTCAGTATTGCGAATTTGACTATCGC
1 GTTGCGAAGTTG-ACTTCTGTGTTGCGGATTTGACTATCGC
*
256650 GTTGCGAAGTTGACTTTTGTGTTGCGGATTTGACTATCGC
1 GTTGCGAAGTTGACTTCTGTGTTGCGGATTTGACTATCGC
* *
256690 GTTGCGAATTTGACTTCTGTGTTGC-GATTT-ACAAATTCGC
1 GTTGCGAAGTTGACTTCTGTGTTGCGGATTTGAC-TA-TCGC
256730 GTTGCGA
1 GTTGCGA
256737 TATTGGAAAC
Statistics
Matches: 108, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
38 2 0.02
39 6 0.06
40 71 0.66
41 29 0.27
ACGTcount: A:0.20, C:0.15, G:0.25, T:0.39
Consensus pattern (40 bp):
GTTGCGAAGTTGACTTCTGTGTTGCGGATTTGACTATCGC
Found at i:257189 original size:18 final size:17
Alignment explanation
Indices: 257155--257210 Score: 55
Period size: 16 Copynumber: 3.3 Consensus size: 17
257145 TTTTTAAAAC
*
257155 ATATTTTTTCAA-ATTT
1 ATATTTTTTAAATATTT
257171 ATATTCTTTTATAAT-TTT
1 ATATT-TTTTA-AATATTT
257189 A-ATTTTTTAAATATTT
1 ATATTTTTTAAATATTT
257205 GATATT
1 -ATATT
257211 ATTAGAAAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
15 3 0.09
16 13 0.39
17 8 0.24
18 9 0.27
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (17 bp):
ATATTTTTTAAATATTT
Found at i:258661 original size:3 final size:3
Alignment explanation
Indices: 258655--258679 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
258645 AAAATAATAT
258655 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
258680 CTCGGATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:263480 original size:14 final size:14
Alignment explanation
Indices: 263461--263490 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
263451 TTTTCAAAAC
*
263461 TTAAATTGTCAATA
1 TTAAATTGTAAATA
263475 TTAAATTGTAAATA
1 TTAAATTGTAAATA
263489 TT
1 TT
263491 TTTATAAAAA
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:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (14 bp):
TTAAATTGTAAATA
Found at i:266717 original size:18 final size:18
Alignment explanation
Indices: 266694--266761 Score: 118
Period size: 18 Copynumber: 3.8 Consensus size: 18
266684 AGGGATTATC
266694 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
266712 AGTGGTCCTTTGGGACAT
1 AGTGGTCCTTCGGGACAT
*
266730 AGTGGTCCTTTGGGACAT
1 AGTGGTCCTTCGGGACAT
266748 AGTGGTCCTTCGGG
1 AGTGGTCCTTCGGG
266762 CAAATATTCA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 48 1.00
ACGTcount: A:0.15, C:0.19, G:0.35, T:0.31
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:283362 original size:18 final size:18
Alignment explanation
Indices: 283339--283377 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
283329 AATACATAGC
*
283339 AACTGAATTTACATT-AGA
1 AACTGAACTTA-ATTGAGA
283357 AACTGAACTTAATTGAGA
1 AACTGAACTTAATTGAGA
283375 AAC
1 AAC
283378 CAATTTGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (18 bp):
AACTGAACTTAATTGAGA
Found at i:283609 original size:20 final size:20
Alignment explanation
Indices: 283572--283623 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
283562 AGTCAACGAG
*
283572 TCGGGTCGGGTC-GGTTGAC
1 TCGGTTCGGGTCAGGTTGAC
* *
283591 TTGTTTCGGGTCAGGTTGAC
1 TCGGTTCGGGTCAGGTTGAC
283611 TCGGTTCGGGTCA
1 TCGGTTCGGGTCA
283624 ACAGACCCAG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 9 0.33
20 18 0.67
ACGTcount: A:0.08, C:0.19, G:0.40, T:0.33
Consensus pattern (20 bp):
TCGGTTCGGGTCAGGTTGAC
Found at i:285501 original size:51 final size:51
Alignment explanation
Indices: 285436--285563 Score: 229
Period size: 51 Copynumber: 2.5 Consensus size: 51
285426 TGAGTCTTTT
*
285436 GACTATTAAAAGTTACAAAATCATCATCGGTGTTGCTGTGTTGAGTCCCTC
1 GACTCTTAAAAGTTACAAAATCATCATCGGTGTTGCTGTGTTGAGTCCCTC
*
285487 GACTCTTAAAAGTTACAAAATCATCATCGGTGTTGCTTTGTTGAGTCCCTC
1 GACTCTTAAAAGTTACAAAATCATCATCGGTGTTGCTGTGTTGAGTCCCTC
*
285538 GACTCTTAAAAGTTACAAAATGATCA
1 GACTCTTAAAAGTTACAAAATCATCA
285564 CTTGACTATT
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 74 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (51 bp):
GACTCTTAAAAGTTACAAAATCATCATCGGTGTTGCTGTGTTGAGTCCCTC
Found at i:290539 original size:29 final size:30
Alignment explanation
Indices: 290468--290540 Score: 94
Period size: 29 Copynumber: 2.4 Consensus size: 30
290458 GATTTAACGA
*
290468 TTCAGTGGTATAATTGAAACGAAAATCAAAG
1 TTCAGTGGTATAATTGAAAC-AAAATAAAAG
* *
290499 TTCAGTGCTATAATTGAAA-AAATTAAAAG
1 TTCAGTGGTATAATTGAAACAAAATAAAAG
*
290528 TTTAGTGGTATAA
1 TTCAGTGGTATAA
290541 ACAATACAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 19 0.51
31 18 0.49
ACGTcount: A:0.44, C:0.07, G:0.18, T:0.32
Consensus pattern (30 bp):
TTCAGTGGTATAATTGAAACAAAATAAAAG
Found at i:294561 original size:2 final size:2
Alignment explanation
Indices: 294556--294589 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
294546 ACACACACAC
294556 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
294590 ATCAGCATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:294640 original size:18 final size:18
Alignment explanation
Indices: 294599--294662 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 18
294589 AATCAGCATC
* * *
294599 ATCATCATCATCATCAAT
1 ATCATTATCAACATCATT
294617 ATCATTATCAACATCATT
1 ATCATTATCAACATCATT
* *
294635 ATCATTGT-AACTATAATT
1 ATCATTATCAAC-ATCATT
*
294653 ATAATTATCA
1 ATCATTATCA
294663 CAGTTTATTA
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
17 3 0.08
18 33 0.89
19 1 0.03
ACGTcount: A:0.41, C:0.19, G:0.02, T:0.39
Consensus pattern (18 bp):
ATCATTATCAACATCATT
Found at i:294842 original size:46 final size:46
Alignment explanation
Indices: 294790--294886 Score: 131
Period size: 46 Copynumber: 2.1 Consensus size: 46
294780 AAGTGCCACA
* * * * * *
294790 TAGAAATGTCTCGAAGGACCACATAGTATTGTCCTGAAGGATCGTG
1 TAGAAATGTCCCGAAAGACCACATAGTATTATCCCGAAGGACCGCG
*
294836 TAGAAATGTCCCGAAAGACCACGTAGTATTATCCCGAAGGACCGCG
1 TAGAAATGTCCCGAAAGACCACATAGTATTATCCCGAAGGACCGCG
294882 TAGAA
1 TAGAA
294887 CCCTCGACTC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.22
Consensus pattern (46 bp):
TAGAAATGTCCCGAAAGACCACATAGTATTATCCCGAAGGACCGCG
Found at i:294861 original size:23 final size:23
Alignment explanation
Indices: 294777--294886 Score: 78
Period size: 23 Copynumber: 4.8 Consensus size: 23
294767 ATAAATTGCA
*
294777 CCGAAGTG-CCACATAGAAATGTC
1 CCGAAG-GACCACGTAGAAATGTC
* * * *
294800 TCGAAGGACCACATAGTATTGTC
1 CCGAAGGACCACGTAGAAATGTC
* * **
294823 CTGAAGGATCGTGTAGAAATGTC
1 CCGAAGGACCACGTAGAAATGTC
* * * *
294846 CCGAAAGACCACGTAGTATTATC
1 CCGAAGGACCACGTAGAAATGTC
*
294869 CCGAAGGACCGCGTAGAA
1 CCGAAGGACCACGTAGAA
294887 CCCTCGACTC
Statistics
Matches: 64, Mismatches: 22, Indels: 2
0.73 0.25 0.02
Matches are distributed among these distances:
22 1 0.02
23 63 0.98
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.20
Consensus pattern (23 bp):
CCGAAGGACCACGTAGAAATGTC
Found at i:295026 original size:31 final size:32
Alignment explanation
Indices: 294991--295130 Score: 78
Period size: 31 Copynumber: 4.3 Consensus size: 32
294981 CTTAGTTCAA
294991 TATCACATAGACATATAAGCACATAGATC-CT
1 TATCACATAGACATATAAGCACATAGATCACT
* *
295022 TATCATATAG-CTTATATCACATGTTCATATA-ATCACT
1 TATCACATAGAC--ATAT-A-A-G--CACATAGATCACT
* * * * *
295059 TATGTCA-ATA-CCATATAACCACTTAGTTCAAT
1 TA--TCACATAGACATATAAGCACATAGATCACT
295091 T-TCACATAGACATATAAGCACATAGATC-CT
1 TATCACATAGACATATAAGCACATAGATCACT
*
295121 TATCATATAG
1 TATCACATAG
295131 CTTATATCAC
Statistics
Matches: 81, Mismatches: 13, Indels: 30
0.65 0.10 0.24
Matches are distributed among these distances:
29 3 0.04
30 6 0.07
31 35 0.43
32 9 0.11
33 1 0.01
34 2 0.02
35 2 0.02
36 7 0.09
37 9 0.11
38 4 0.05
39 3 0.04
ACGTcount: A:0.39, C:0.21, G:0.08, T:0.33
Consensus pattern (32 bp):
TATCACATAGACATATAAGCACATAGATCACT
Found at i:295040 original size:45 final size:45
Alignment explanation
Indices: 294990--295142 Score: 132
Period size: 45 Copynumber: 3.2 Consensus size: 45
294980 ACTTAGTTCA
294990 ATATCACATAGACATATAAGCACATAGATCCTTATCATATAGCTT
1 ATATCACATAGACATATAAGCACATAGATCCTTATCATATAGCTT
* * * *
295035 ATATCACAT-GTTCATATAATCACTTATGTCAATACCATATAACCACT-TAG-TT
1 ATATCACATAG-ACATATAAGCACATA-G---AT-CC-T-T-ATCA-TATAGCTT
*
295087 CAATTTCACATAGACATATAAGCACATAGATCCTTATCATATAGCTT
1 --ATATCACATAGACATATAAGCACATAGATCCTTATCATATAGCTT
295134 ATATCACAT
1 ATATCACAT
295143 GTTCATATAA
Statistics
Matches: 83, Mismatches: 10, Indels: 30
0.67 0.08 0.24
Matches are distributed among these distances:
44 1 0.01
45 30 0.36
46 7 0.08
47 3 0.04
48 1 0.01
49 4 0.05
50 4 0.05
51 1 0.01
52 3 0.04
53 7 0.08
54 21 0.25
55 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.07, T:0.33
Consensus pattern (45 bp):
ATATCACATAGACATATAAGCACATAGATCCTTATCATATAGCTT
Found at i:295143 original size:99 final size:99
Alignment explanation
Indices: 294972--295174 Score: 379
Period size: 99 Copynumber: 2.1 Consensus size: 99
294962 TCACATATTT
294972 ATATAACCACTTAGTTCAATATCACATAGACATATAAGCACATAGATCCTTATCATATAGCTTAT
1 ATATAACCACTTAGTTCAATATCACATAGACATATAAGCACATAGATCCTTATCATATAGCTTAT
*
295037 ATCACATGTTCATATAATCACTTATGTCAATACC
66 ATCACATGTTCATATAATCACTTATGTCAATACA
*
295071 ATATAACCACTTAGTTCAATTTCACATAGACATATAAGCACATAGATCCTTATCATATAGCTTAT
1 ATATAACCACTTAGTTCAATATCACATAGACATATAAGCACATAGATCCTTATCATATAGCTTAT
*
295136 ATCACATGTTCATATAATCACTTGTGTCAATACA
66 ATCACATGTTCATATAATCACTTATGTCAATACA
295170 ATATA
1 ATATA
295175 GCTTATATCA
Statistics
Matches: 101, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
99 101 1.00
ACGTcount: A:0.38, C:0.20, G:0.07, T:0.34
Consensus pattern (99 bp):
ATATAACCACTTAGTTCAATATCACATAGACATATAAGCACATAGATCCTTATCATATAGCTTAT
ATCACATGTTCATATAATCACTTATGTCAATACA
Found at i:297408 original size:19 final size:18
Alignment explanation
Indices: 297360--297420 Score: 90
Period size: 17 Copynumber: 3.4 Consensus size: 18
297350 GGAAGTCAAC
297360 GGTCA-ACGGTCGGGTCG
1 GGTCAGACGGTCGGGTCG
297377 GGTCA-ACGGTCGGGTCG
1 GGTCAGACGGTCGGGTCG
*
297394 GGTCAGTAGGGTCGGGTCG
1 GGTCAG-ACGGTCGGGTCG
297413 GGTCAGAC
1 GGTCAGAC
297421 CGGTTAAACC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
17 22 0.55
18 1 0.03
19 17 0.43
ACGTcount: A:0.13, C:0.21, G:0.48, T:0.18
Consensus pattern (18 bp):
GGTCAGACGGTCGGGTCG
Found at i:297460 original size:19 final size:19
Alignment explanation
Indices: 297419--297463 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
297409 GTCGGGTCAG
*
297419 ACCGGTTAAACCGGTTCAT
1 ACCGGTCAAACCGGTTCAT
*
297438 ACCGGTCAAACTGGTTCGA-
1 ACCGGTCAAACCGGTTC-AT
297457 ACCGGTC
1 ACCGGTC
297464 GGAACCGGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 22 0.96
20 1 0.04
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.22
Consensus pattern (19 bp):
ACCGGTCAAACCGGTTCAT
Found at i:299855 original size:14 final size:14
Alignment explanation
Indices: 299823--299863 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
299813 ATAGGCATGA
* *
299823 ATGGTGATAGAGA-
1 ATGGTGATGGAAAG
299836 ATGGTGATGGAAAG
1 ATGGTGATGGAAAG
299850 ATGGTGATGGAAAG
1 ATGGTGATGGAAAG
299864 GTAGTATCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.37, C:0.00, G:0.41, T:0.22
Consensus pattern (14 bp):
ATGGTGATGGAAAG
Found at i:300262 original size:78 final size:78
Alignment explanation
Indices: 300164--300325 Score: 279
Period size: 78 Copynumber: 2.1 Consensus size: 78
300154 TAGGCCGAAT
*
300164 AGATACTTATGGTTCAGCCAAGGTTGAAACCCCTTTGAAAATACATGATTTTTTTATGAAAATAC
1 AGATACTTATGGTTCAGCCAAGGTTGAAACCCCTTTGAAAATACATGATTTTTTGATGAAAATAC
300229 ATGATTTAAATAA
66 ATGATTTAAATAA
* * *
300242 AGATACTTATGGTTCGGCCAATGTTGAAACCCCTTTGAAAATACATGATTTTTTGATGAAATTAC
1 AGATACTTATGGTTCAGCCAAGGTTGAAACCCCTTTGAAAATACATGATTTTTTGATGAAAATAC
*
300307 ATGATTTAAATGA
66 ATGATTTAAATAA
300320 AGATAC
1 AGATAC
300326 ATGCTCTTGG
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
78 79 1.00
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (78 bp):
AGATACTTATGGTTCAGCCAAGGTTGAAACCCCTTTGAAAATACATGATTTTTTGATGAAAATAC
ATGATTTAAATAA
Found at i:303277 original size:15 final size:15
Alignment explanation
Indices: 303257--303295 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
303247 AGGATAAGGT
*
303257 AATGAAATAAGAAAG
1 AATGAAATAAGAAAA
* *
303272 AATGAAAGAATAAAA
1 AATGAAATAAGAAAA
303287 AATGAAATA
1 AATGAAATA
303296 GTAAGAAAGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (15 bp):
AATGAAATAAGAAAA
Found at i:307884 original size:6 final size:6
Alignment explanation
Indices: 307884--307946 Score: 63
Period size: 6 Copynumber: 10.5 Consensus size: 6
307874 CATCATTATC
* * ** * *
307884 ATCATC ATCAAT ATCATT ATCATT ATCAAC ATCATT ATCATT GTCACT
1 ATCATT ATCATT ATCATT ATCATT ATCATT ATCATT ATCATT ATCATT
*
307932 ATAATT ATCATT ATC
1 ATCATT ATCATT ATC
307947 TTAATTTATT
Statistics
Matches: 44, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.37, C:0.21, G:0.02, T:0.41
Consensus pattern (6 bp):
ATCATT
Found at i:307889 original size:12 final size:12
Alignment explanation
Indices: 307871--307924 Score: 63
Period size: 12 Copynumber: 4.5 Consensus size: 12
307861 TATATATATA
*
307871 TATCATCATTAT
1 TATCATCATCAT
* *
307883 CATCATCATCAA
1 TATCATCATCAT
*
307895 TATCATTATCAT
1 TATCATCATCAT
*
307907 TATCAACATCAT
1 TATCATCATCAT
307919 TATCAT
1 TATCAT
307925 TGTCACTATA
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.37, C:0.22, G:0.00, T:0.41
Consensus pattern (12 bp):
TATCATCATCAT
Found at i:307925 original size:18 final size:18
Alignment explanation
Indices: 307874--307946 Score: 76
Period size: 18 Copynumber: 3.9 Consensus size: 18
307864 ATATATATAT
307874 CATCATTATCATCATCATCAA
1 CATCATTATCAT--T-ATCAA
*
307895 TATCATTATCATTATCAA
1 CATCATTATCATTATCAA
*
307913 CATCATTATCATTGTC-A
1 CATCATTATCATTATCAA
*
307930 CTATAATTATCATTATC
1 C-ATCATTATCATTATC
307947 TTAATTTATT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
17 2 0.04
18 32 0.70
19 1 0.02
21 11 0.24
ACGTcount: A:0.36, C:0.22, G:0.01, T:0.41
Consensus pattern (18 bp):
CATCATTATCATTATCAA
Found at i:312014 original size:46 final size:46
Alignment explanation
Indices: 311947--312043 Score: 124
Period size: 46 Copynumber: 2.1 Consensus size: 46
311937 TGTGACAACA
* * * *
311947 TAGAAATACCTCGAAGGACCACATAGTATTGTCTCGAATGATCGCG
1 TAGAAATACCTCGAAGGACCACATAGTATTATCCCGAAGGACCGCG
* *
311993 TAGAAATATCC-CGAAGTACCACGTAGTATTATCCCGAAGGACCGCG
1 TAGAAATA-CCTCGAAGGACCACATAGTATTATCCCGAAGGACCGCG
312039 TAGAA
1 TAGAA
312044 CCCTCGACTC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
46 42 0.95
47 2 0.05
ACGTcount: A:0.34, C:0.23, G:0.22, T:0.22
Consensus pattern (46 bp):
TAGAAATACCTCGAAGGACCACATAGTATTATCCCGAAGGACCGCG
Found at i:312017 original size:23 final size:23
Alignment explanation
Indices: 311947--312043 Score: 70
Period size: 23 Copynumber: 4.2 Consensus size: 23
311937 TGTGACAACA
*
311947 TAGAAATA-CCTCGAAGGACCACA
1 TAGAAATATCC-CGAAGGACCACG
* * * * * * *
311970 TAGTATTGTCTCGAATGATCGCG
1 TAGAAATATCCCGAAGGACCACG
*
311993 TAGAAATATCCCGAAGTACCACG
1 TAGAAATATCCCGAAGGACCACG
* * *
312016 TAGTATTATCCCGAAGGACCGCG
1 TAGAAATATCCCGAAGGACCACG
312039 TAGAA
1 TAGAA
312044 CCCTCGACTC
Statistics
Matches: 52, Mismatches: 21, Indels: 2
0.69 0.28 0.03
Matches are distributed among these distances:
23 51 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.23, G:0.22, T:0.22
Consensus pattern (23 bp):
TAGAAATATCCCGAAGGACCACG
Found at i:319592 original size:15 final size:16
Alignment explanation
Indices: 319563--319594 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
319553 GCACTAGTTA
319563 TCTGTTTTACTTTATT
1 TCTGTTTTACTTTATT
319579 TCTGTTTT-CTTTATT
1 TCTGTTTTACTTTATT
319594 T
1 T
319595 ATTGTAGGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.09, C:0.12, G:0.06, T:0.72
Consensus pattern (16 bp):
TCTGTTTTACTTTATT
Found at i:329744 original size:155 final size:155
Alignment explanation
Indices: 329462--329771 Score: 620
Period size: 155 Copynumber: 2.0 Consensus size: 155
329452 TATATATATA
329462 TATATTAAGGTACATGTCAGAGTTACATCATAGGTTCAAACCAATATGAACTTGTTGGAAAAATG
1 TATATTAAGGTACATGTCAGAGTTACATCATAGGTTCAAACCAATATGAACTTGTTGGAAAAATG
329527 AACTGATAACTATTTGGTGGTTTCCTGTGATTATTGTTCTCATAAAGTGCAAATCCTTAACTGCA
66 AACTGATAACTATTTGGTGGTTTCCTGTGATTATTGTTCTCATAAAGTGCAAATCCTTAACTGCA
329592 GTTTGGAGATATTAATATCAGATTG
131 GTTTGGAGATATTAATATCAGATTG
329617 TATATTAAGGTACATGTCAGAGTTACATCATAGGTTCAAACCAATATGAACTTGTTGGAAAAATG
1 TATATTAAGGTACATGTCAGAGTTACATCATAGGTTCAAACCAATATGAACTTGTTGGAAAAATG
329682 AACTGATAACTATTTGGTGGTTTCCTGTGATTATTGTTCTCATAAAGTGCAAATCCTTAACTGCA
66 AACTGATAACTATTTGGTGGTTTCCTGTGATTATTGTTCTCATAAAGTGCAAATCCTTAACTGCA
329747 GTTTGGAGATATTAATATCAGATTG
131 GTTTGGAGATATTAATATCAGATTG
329772 CAGCAGATAG
Statistics
Matches: 155, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
155 155 1.00
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (155 bp):
TATATTAAGGTACATGTCAGAGTTACATCATAGGTTCAAACCAATATGAACTTGTTGGAAAAATG
AACTGATAACTATTTGGTGGTTTCCTGTGATTATTGTTCTCATAAAGTGCAAATCCTTAACTGCA
GTTTGGAGATATTAATATCAGATTG
Found at i:334605 original size:210 final size:210
Alignment explanation
Indices: 334243--334667 Score: 787
Period size: 210 Copynumber: 2.0 Consensus size: 210
334233 AGGATTAGGC
*
334243 TAAGATTATGGTTTTTTATATGTTATAAAGAGTTATTCACTGCTAGGTCTAGGTGAAAAAAATTT
1 TAAGATTATGGTTTTTTATATGTTATAAAGAGTTATTCACTGCTAGGACTAGGTGAAAAAAATTT
*
334308 AAAAGTCACTCTTAGAAGCATATATTTGTTGGTGCTACATTATATATATTTATATATAAATTATG
66 AAAAGTCACTCTTAGAAGCATATATTTGTTGGTGATACATTATATATATTTATATATAAATTATG
334373 CTCAATGATGTGGTTTATCTTCGATAATCTTTGGAAATGAAAAAGGTGCGATCAAATGCTAGACG
131 CTCAATGATGTGGTTTATCTTCGATAATCTTTGGAAATGAAAAAGGTGCGATCAAATGCTAGACG
334438 TTGCTACAAATTGTT
196 TTGCTACAAATTGTT
*
334453 TAAGATTATGGTTTTTTATATGTTATAAAGAGTTATTCACTTCTAGGACTAGGTGAAAAAAATTT
1 TAAGATTATGGTTTTTTATATGTTATAAAGAGTTATTCACTGCTAGGACTAGGTGAAAAAAATTT
* * *
334518 AAAAGTCACTCTTAGAAGTATATATTTGTTGGTTATGCATTATATATATTTATATATAAATTATG
66 AAAAGTCACTCTTAGAAGCATATATTTGTTGGTGATACATTATATATATTTATATATAAATTATG
334583 CTCAATGATGTGGTTTATCTTCGATAATCTTTGGAAATGAAAAAGGTGCGATCAAATGCTAGACG
131 CTCAATGATGTGGTTTATCTTCGATAATCTTTGGAAATGAAAAAGGTGCGATCAAATGCTAGACG
334648 TTGCTACAAATTGTT
196 TTGCTACAAATTGTT
*
334663 CAAGA
1 TAAGA
334668 AAACTTGGCC
Statistics
Matches: 208, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
210 208 1.00
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (210 bp):
TAAGATTATGGTTTTTTATATGTTATAAAGAGTTATTCACTGCTAGGACTAGGTGAAAAAAATTT
AAAAGTCACTCTTAGAAGCATATATTTGTTGGTGATACATTATATATATTTATATATAAATTATG
CTCAATGATGTGGTTTATCTTCGATAATCTTTGGAAATGAAAAAGGTGCGATCAAATGCTAGACG
TTGCTACAAATTGTT
Found at i:339984 original size:64 final size:63
Alignment explanation
Indices: 339899--340059 Score: 207
Period size: 64 Copynumber: 2.5 Consensus size: 63
339889 TTGTTTAAGG
* * * *
339899 TGCATCGATGCACATGCAGTGCATCGATGCAT-GAATTTAAATAGAAAACATCGAATATGATTTA
1 TGCATCGATGCATATGTAGTGCATCGATGCATCCAA-TTAAATA-AAAACATCGAATAGGATTTA
* * *
339963 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATATGTAGTGCATCGATGCAT-CCAATTAAATAAAAACATCGAATAGGATTTA
*
340027 TGCATCGATGCATGGTGTAGTGCATCGATGCAT
1 TGCATCGATGCAT-ATGTAGTGCATCGATGCAT
340060 ACCTTCATTA
Statistics
Matches: 85, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 60 0.71
65 24 0.28
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (63 bp):
TGCATCGATGCATATGTAGTGCATCGATGCATCCAATTAAATAAAAACATCGAATAGGATTTA
Found at i:341124 original size:21 final size:21
Alignment explanation
Indices: 341098--341160 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
341088 GTCGAGGGTT
341098 TCATAGGTCCTTCGGGACAAC
1 TCATAGGTCCTTCGGGACAAC
* *
341119 TCATAGGTCATTCGGGACAAAT
1 TCATAGGTCCTTCGGGAC-AAC
*
341141 TCACAGGTCCTTCGGGACAA
1 TCATAGGTCCTTCGGGACAA
341161 ATTTCATATG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
21 19 0.51
22 18 0.49
ACGTcount: A:0.27, C:0.25, G:0.24, T:0.24
Consensus pattern (21 bp):
TCATAGGTCCTTCGGGACAAC
Found at i:341154 original size:22 final size:22
Alignment explanation
Indices: 341097--341168 Score: 101
Period size: 22 Copynumber: 3.3 Consensus size: 22
341087 AGTCGAGGGT
341097 TTCATAGGTCCTTCGGGAC-AA
1 TTCATAGGTCCTTCGGGACAAA
* *
341118 CTCATAGGTCATTCGGGACAAA
1 TTCATAGGTCCTTCGGGACAAA
*
341140 TTCACAGGTCCTTCGGGACAAA
1 TTCATAGGTCCTTCGGGACAAA
341162 TTTCATA
1 -TTCATA
341169 TGCCACTCTG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.40
22 21 0.49
23 5 0.12
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.28
Consensus pattern (22 bp):
TTCATAGGTCCTTCGGGACAAA
Found at i:352886 original size:3 final size:3
Alignment explanation
Indices: 352878--352909 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
352868 GAATAGGGTT
352878 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
352910 TTTATGCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:353005 original size:3 final size:3
Alignment explanation
Indices: 352997--353056 Score: 111
Period size: 3 Copynumber: 19.7 Consensus size: 3
352987 TGAGTTTACG
352997 TAA TAA TAA TAA TAA TAA TAA TAAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
353043 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
353057 TTATTATTAT
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 53 0.95
4 3 0.05
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:353061 original size:3 final size:3
Alignment explanation
Indices: 353055--353090 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
353045 ATAATAATAA
353055 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
353091 AACAAATAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:359807 original size:24 final size:24
Alignment explanation
Indices: 359783--359862 Score: 133
Period size: 24 Copynumber: 3.3 Consensus size: 24
359773 AACTCTATTG
* * *
359783 AAGCTAGAAACTCAAGCTCGATTG
1 AAGCTCGAAACTCGAGCTCGATTC
359807 AAGCTCGAAACTCGAGCTCGATTC
1 AAGCTCGAAACTCGAGCTCGATTC
359831 AAGCTCGAAACTCGAGCTCGATTC
1 AAGCTCGAAACTCGAGCTCGATTC
359855 AAGCTCGA
1 AAGCTCGA
359863 GTCACTGCTA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.20
Consensus pattern (24 bp):
AAGCTCGAAACTCGAGCTCGATTC
Found at i:359826 original size:13 final size:13
Alignment explanation
Indices: 359808--359851 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
359798 GCTCGATTGA
359808 AGCTCGAAACTCG
1 AGCTCGAAACTCG
* *
359821 AGCTCG--ATTCA
1 AGCTCGAAACTCG
359832 AGCTCGAAACTCG
1 AGCTCGAAACTCG
359845 AGCTCGA
1 AGCTCGA
359852 TTCAAGCTCG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 9 0.36
13 16 0.64
ACGTcount: A:0.30, C:0.30, G:0.23, T:0.18
Consensus pattern (13 bp):
AGCTCGAAACTCG
Found at i:359837 original size:11 final size:11
Alignment explanation
Indices: 359794--359862 Score: 57
Period size: 11 Copynumber: 5.9 Consensus size: 11
359784 AGCTAGAAAC
359794 TCAAGCTCGAT
1 TCAAGCTCGAT
* *
359805 TGAAGCTCGAAAC
1 TCAAGCTCG--AT
*
359818 TCGAGCTCGAT
1 TCAAGCTCGAT
*
359829 TCAAGCTCGAAAC
1 TCAAGCTCG--AT
*
359842 TCGAGCTCGAT
1 TCAAGCTCGAT
359853 TCAAGCTCGA
1 TCAAGCTCGA
359863 GTCACTGCTA
Statistics
Matches: 44, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
11 27 0.61
13 17 0.39
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.22
Consensus pattern (11 bp):
TCAAGCTCGAT
Found at i:361028 original size:18 final size:19
Alignment explanation
Indices: 361005--361040 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
360995 ACAGTCCCTC
*
361005 ATTTG-TTTAAATTTTCTT
1 ATTTGTTTTAAATGTTCTT
361023 ATTTGTTTTAAATGTTCT
1 ATTTGTTTTAAATGTTCT
361041 GGTGTCATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.22, C:0.06, G:0.08, T:0.64
Consensus pattern (19 bp):
ATTTGTTTTAAATGTTCTT
Found at i:365971 original size:42 final size:41
Alignment explanation
Indices: 365910--366016 Score: 117
Period size: 42 Copynumber: 2.6 Consensus size: 41
365900 CCCAAATTTG
* * * *
365910 TAAATCCTTCA-GGTTATCTGTCAGTCTTTCGGGCATGATGCT
1 TAAATCCTT-AGGGTCATCTGTCAGTCTTTCGAGCAAGATG-A
*
365952 TAAATCCTTAGGGTCATCTGTCAGTCTTTTGAGCAAGATGA
1 TAAATCCTTAGGGTCATCTGTCAGTCTTTCGAGCAAGATGA
* * *
365993 TAAGTCCTTAGGGCCATCCGTCAG
1 TAAATCCTTAGGGTCATCTGTCAG
366017 ACCTTTGGGT
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
41 22 0.39
42 34 0.61
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.34
Consensus pattern (41 bp):
TAAATCCTTAGGGTCATCTGTCAGTCTTTCGAGCAAGATGA
Found at i:366016 original size:41 final size:42
Alignment explanation
Indices: 365929--366016 Score: 106
Period size: 41 Copynumber: 2.1 Consensus size: 42
365919 CAGGTTATCT
* * * * *
365929 GTCAGTCTTTCGGGCATGATGCTTAAATCCTTAGGGTCATCT
1 GTCAGTCTTTCGAGCAAGATGCATAAATCCTTAGGGCCATCC
* *
365971 GTCAGTCTTTTGAGCAAGATG-ATAAGTCCTTAGGGCCATCC
1 GTCAGTCTTTCGAGCAAGATGCATAAATCCTTAGGGCCATCC
366012 GTCAG
1 GTCAG
366017 ACCTTTGGGT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 21 0.54
42 18 0.46
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.32
Consensus pattern (42 bp):
GTCAGTCTTTCGAGCAAGATGCATAAATCCTTAGGGCCATCC
Found at i:366265 original size:247 final size:251
Alignment explanation
Indices: 365798--366524 Score: 1124
Period size: 247 Copynumber: 2.9 Consensus size: 251
365788 GTAGACGACT
* * *
365798 TGAGGAAGTGATTTTCAAAGTTTCACATTTAATGTTCAAGAAAATGAAATTCTTAAAAAGT-ATG
1 TGAGGAAGCGATTTTCAAAGTTT--CATTTAATGTTAAAGAAAATGAAATTCTTGAAAAGTAAT-
* * * **
365862 AAAACAATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTTGTAAATCCTTCAGGTTAT
63 AAAGCAATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTTCTAAATCCTTCGGGTCGT
*
365927 CTGTCAGTCTTTCGGGCATGATGCTTAAATCCTTAGGGTCATCTGTCAGTCTTTTGAGCAAGATG
128 CTGTCAGTCTTTCGAGCATGATGCTTAAATCCTTAGGGTCATCTGTCAGTCTTTTGAGCAAGATG
365992 ATAAGTCCTTAGGGCCATCCGTCAGACCTTTGGGTA-G-G-ATG-TTTACACATGAAAA
193 ATAAGTCCTTAGGGCCATCCGTCAGACCTTTGGGTATGAGTATGATTTACACATGAAAA
*
366047 TGAGAAAGCGATTTTCAAAGTTTCATTTAATGTTAAAGAAAATGAAATTCTTGAAAAGTAATAAA
1 TGAGGAAGCGATTTTCAAAGTTTCATTTAATGTTAAAGAAAATGAAATTCTTGAAAAGTAATAAA
366112 GCAATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTTCTAAATCCTTCGGGTCGTCTG
66 GCAATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTTCTAAATCCTTCGGGTCGTCTG
* * *
366177 TCAGTCTTTCGAGCATGATGCTTAAATCCTTAGGGTCATCTTTCAGTCTTTTAAGCAAGATGATG
131 TCAGTCTTTCGAGCATGATGCTTAAATCCTTAGGGTCATCTGTCAGTCTTTTGAGCAAGATGATA
* * *
366242 AGTCCTTAGGGCTATCTGTCAGACCTTTGGGTATGATGTTTACACATGATTTTCACATGAAAA
196 AGTCCTTAGGGCCATCCGTCAGACCTTTGGGTATGA-G--T----ATGATTTACACATGAAAA
* *
366305 TAAGGAAGCGATTTTCAAAGTTTCTCATTTAATGTTTAAGAAAATGAAATTCTTGAAAAGTAATA
1 TGAGGAAGCGATTTTCAAAG-TT-TCATTTAATGTTAAAGAAAATGAAATTCTTGAAAAGTAATA
366370 AAGCAATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTTCTAAATCCTTCGGGTCGTC
64 AAGCAATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTTCTAAATCCTTCGGGTCGTC
*
366435 TGTCAGTCTTTCGAGCATGATGCTTAAATCCTTA-GGTCATCTGTCAGTCTTTTGAGCAAAATGA
129 TGTCAGTCTTTCGAGCATGATGCTTAAATCCTTAGGGTCATCTGTCAGTCTTTTGAGCAAGATGA
*
366499 TAAGTCCTTAGGGCCATCCGTAAGAC
194 TAAGTCCTTAGGGCCATCCGTCAGAC
366525 ATTCACGCAG
Statistics
Matches: 438, Mismatches: 26, Indels: 18
0.91 0.05 0.04
Matches are distributed among these distances:
247 189 0.43
248 3 0.01
249 21 0.05
250 1 0.00
257 3 0.01
258 31 0.07
259 51 0.12
260 139 0.32
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (251 bp):
TGAGGAAGCGATTTTCAAAGTTTCATTTAATGTTAAAGAAAATGAAATTCTTGAAAAGTAATAAA
GCAATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTTCTAAATCCTTCGGGTCGTCTG
TCAGTCTTTCGAGCATGATGCTTAAATCCTTAGGGTCATCTGTCAGTCTTTTGAGCAAGATGATA
AGTCCTTAGGGCCATCCGTCAGACCTTTGGGTATGAGTATGATTTACACATGAAAA
Found at i:367965 original size:10 final size:10
Alignment explanation
Indices: 367950--367982 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
367940 ATTGCCTATG
367950 TATTTATATA
1 TATTTATATA
367960 TATTTATATTA
1 TATTTATA-TA
367971 TATTT-TATA
1 TATTTATATA
367980 TAT
1 TAT
367983 GTATTCTGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 5 0.23
10 10 0.45
11 7 0.32
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
TATTTATATA
Found at i:368977 original size:21 final size:21
Alignment explanation
Indices: 368953--369022 Score: 54
Period size: 21 Copynumber: 3.4 Consensus size: 21
368943 ACCCCACCAG
368953 AAATAATATATTTATTTAAAA
1 AAATAATATATTTATTTAAAA
* * *
368974 AAAT-ATTTTTTTATTTTATAA
1 AAATAATATATTTA-TTTAAAA
** *
368995 AAATAA-GGATTTAATTAAAA
1 AAATAATATATTTATTTAAAA
*
369015 TAATAATA
1 AAATAATA
369023 AATAGAGGGA
Statistics
Matches: 36, Mismatches: 10, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
20 17 0.47
21 18 0.50
22 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (21 bp):
AAATAATATATTTATTTAAAA
Found at i:369935 original size:22 final size:22
Alignment explanation
Indices: 369910--369966 Score: 114
Period size: 22 Copynumber: 2.6 Consensus size: 22
369900 AGAGGTACTG
369910 ATACCCCTATGAATGGGTATCT
1 ATACCCCTATGAATGGGTATCT
369932 ATACCCCTATGAATGGGTATCT
1 ATACCCCTATGAATGGGTATCT
369954 ATACCCCTATGAA
1 ATACCCCTATGAA
369967 GGCTCAAACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.30
Consensus pattern (22 bp):
ATACCCCTATGAATGGGTATCT
Found at i:370012 original size:19 final size:19
Alignment explanation
Indices: 369988--370040 Score: 106
Period size: 19 Copynumber: 2.8 Consensus size: 19
369978 CGAATGCAAA
369988 AAGGGTATCGATACCGTGC
1 AAGGGTATCGATACCGTGC
370007 AAGGGTATCGATACCGTGC
1 AAGGGTATCGATACCGTGC
370026 AAGGGTATCGATACC
1 AAGGGTATCGATACC
370041 ATAGTGCAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.28, C:0.21, G:0.30, T:0.21
Consensus pattern (19 bp):
AAGGGTATCGATACCGTGC
Found at i:373156 original size:44 final size:44
Alignment explanation
Indices: 373089--373173 Score: 161
Period size: 44 Copynumber: 1.9 Consensus size: 44
373079 CACAAATATC
*
373089 TGATCCATACTATGAAGTCTATGAACCATCCTGGTAGTATTATT
1 TGATCCATACTATGAAGTATATGAACCATCCTGGTAGTATTATT
373133 TGATCCATACTATGAAGTATATGAACCATCCTGGTAGTATT
1 TGATCCATACTATGAAGTATATGAACCATCCTGGTAGTATT
373174 GATACTTTTG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (44 bp):
TGATCCATACTATGAAGTATATGAACCATCCTGGTAGTATTATT
Found at i:374276 original size:19 final size:20
Alignment explanation
Indices: 374232--374277 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
374222 AATAGGCTTT
*
374232 TAAG-AAAAATATTTTTCGA
1 TAAGTAAAAATATGTTTCGA
*
374251 TCA-TAAAAATA-GTTTCGA
1 TAAGTAAAAATATGTTTCGA
374269 TAAGTAAAA
1 TAAGTAAAA
374278 TAATTATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.50, C:0.07, G:0.11, T:0.33
Consensus pattern (20 bp):
TAAGTAAAAATATGTTTCGA
Found at i:379118 original size:29 final size:29
Alignment explanation
Indices: 379076--379180 Score: 86
Period size: 29 Copynumber: 3.4 Consensus size: 29
379066 ACTTGAACTA
379076 TAATAATTTT-AAATATACATTTTAGGGTT
1 TAAT-ATTTTAAAATATACATTTTAGGGTT
** **
379105 TAATATTTTAAAATATACATTCAAGAATTTTTAT
1 TAATATTTTAAAATATACATTTTAG----GGT-T
379139 TATACTATTTTAAAATATACATTTTAGGGTT
1 TA-A-TATTTTAAAATATACATTTTAGGGTT
*
379170 TAATTTTTTAA
1 TAATATTTTAA
379181 TAGTTAATTA
Statistics
Matches: 59, Mismatches: 9, Indels: 16
0.70 0.11 0.19
Matches are distributed among these distances:
28 5 0.08
29 24 0.41
30 1 0.02
31 3 0.05
32 1 0.02
33 1 0.02
34 3 0.05
35 1 0.02
36 20 0.34
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.50
Consensus pattern (29 bp):
TAATATTTTAAAATATACATTTTAGGGTT
Found at i:379739 original size:22 final size:22
Alignment explanation
Indices: 379714--379760 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
379704 ATATTTATTC
*
379714 ATATTTTTAATAATATAATATA
1 ATATTTTTAATAATATAATAAA
* *
379736 ATATTTTTATTATTATAATAAA
1 ATATTTTTAATAATATAATAAA
379758 ATA
1 ATA
379761 ATCAATTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
ATATTTTTAATAATATAATAAA
Found at i:379794 original size:23 final size:23
Alignment explanation
Indices: 379746--379794 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
379736 ATATTTTTAT
**
379746 TATTATAATAAAATAATCAATTA
1 TATTATAATAAAATAATCAAAGA
*
379769 TATTATAATAATATAAT-ATAAGA
1 TATTATAATAAAATAATCA-AAGA
379792 TAT
1 TAT
379795 CATATTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 1 0.05
23 21 0.95
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (23 bp):
TATTATAATAAAATAATCAAAGA
Found at i:379920 original size:27 final size:27
Alignment explanation
Indices: 379840--379925 Score: 70
Period size: 27 Copynumber: 3.1 Consensus size: 27
379830 AATAAATTTT
* *
379840 ATATTATTTAT-TAATTTCATAGAAATA
1 ATATTATTTATAT-ATTTAATATAAATA
* *
379867 ATATTA-TTAAAT-TATTAATAATGAATA
1 ATATTATTTATATAT-TTAAT-ATAAATA
379894 ATATTATTTATATATTTAATATTAATATA
1 ATATTATTTATATATTTAATA-TAA-ATA
379923 ATA
1 ATA
379926 ATATAATAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
25 1 0.02
26 7 0.15
27 19 0.41
28 12 0.26
29 7 0.15
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (27 bp):
ATATTATTTATATATTTAATATAAATA
Found at i:379949 original size:34 final size:35
Alignment explanation
Indices: 379911--379990 Score: 87
Period size: 35 Copynumber: 2.3 Consensus size: 35
379901 TTATATATTT
*
379911 AATATTAATATAATA-ATA-TAA-TAATATTTTAATA
1 AATA-TAATATAAAATATACTAATTAATATTTTAA-A
* *
379945 AATAT-ATTTAAAATATACTAATTAATATTTTTAA
1 AATATAATATAAAATATACTAATTAATATTTTAAA
379979 AATATAATATAA
1 AATATAATATAA
379991 CACTATTGCT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
32 6 0.16
33 4 0.11
34 13 0.34
35 15 0.39
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (35 bp):
AATATAATATAAAATATACTAATTAATATTTTAAA
Found at i:379952 original size:54 final size:52
Alignment explanation
Indices: 379810--379952 Score: 123
Period size: 59 Copynumber: 2.6 Consensus size: 52
379800 TTTTATTTTA
* *
379810 ATAAT-ATATAATAAATCTTTAATAAAT-T-TTATATTATTTATTAATTTCAT
1 ATAATAATATAATAAAT-TTTAATAAATATATTATATTATATATTAATTTAAT
* *
379860 AGAAATAATATTATTAAATTATTAATAATGAATAATATTAT-TTATATATTTAATATTAAT
1 A-TAATAATA-TAATAAATT-TTAAT-A--AAT-ATATTATATTATATA-TTAAT-TTAAT
379920 ATAATAATATAATAATATTTTAATAAATATATT
1 ATAATAATATAATAA-ATTTTAATAAATATATT
379953 TAAAATATAC
Statistics
Matches: 74, Mismatches: 6, Indels: 22
0.73 0.06 0.22
Matches are distributed among these distances:
50 1 0.01
51 3 0.04
52 4 0.05
53 12 0.16
54 6 0.08
55 3 0.04
56 3 0.04
57 1 0.01
58 17 0.23
59 19 0.26
60 5 0.07
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (52 bp):
ATAATAATATAATAAATTTTAATAAATATATTATATTATATATTAATTTAAT
Found at i:379959 original size:23 final size:23
Alignment explanation
Indices: 379912--379984 Score: 76
Period size: 23 Copynumber: 3.1 Consensus size: 23
379902 TATATATTTA
*
379912 ATATTAATATAATA-ATATAATAAT
1 ATATTAATA-AATATATTTAA-AAT
*
379936 ATTTTAATAAATATATTTAAAAT
1 ATATTAATAAATATATTTAAAAT
* * *
379959 ATACTAATTAATATTTTTAAAAT
1 ATATTAATAAATATATTTAAAAT
379982 ATA
1 ATA
379985 ATATAACACT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
23 29 0.69
24 13 0.31
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (23 bp):
ATATTAATAAATATATTTAAAAT
Found at i:380092 original size:31 final size:32
Alignment explanation
Indices: 380014--380095 Score: 91
Period size: 31 Copynumber: 2.6 Consensus size: 32
380004 ACAAATAATT
*
380014 AATATAAT-TTATAATATTTTTATTTCAATAA
1 AATATAATATTTTAATATTTTTATTTCAATAA
*
380045 AATATACCA-ATATTAATATTTTTA-TT-AATAA
1 AATATA--ATATTTTAATATTTTTATTTCAATAA
380076 AATTATAATATTTTAATATT
1 AA-TATAATATTTTAATATT
380096 AAATAAATTA
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
30 1 0.02
31 23 0.53
32 6 0.14
33 13 0.30
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (32 bp):
AATATAATATTTTAATATTTTTATTTCAATAA
Found at i:380103 original size:25 final size:23
Alignment explanation
Indices: 380058--380117 Score: 66
Period size: 28 Copynumber: 2.4 Consensus size: 23
380048 ATACCAATAT
380058 TAATATTTTTATTAATAAAATTA
1 TAATATTTTTATTAATAAAATTA
*
380081 TAATATTTTAATATTAAATAAATTATTT
1 TAATATTTT--TATT-AATAAA--ATTA
380109 TAATATTTT
1 TAATATTTT
380118 AAAAATAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
23 9 0.29
25 4 0.13
26 6 0.19
28 12 0.39
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TAATATTTTTATTAATAAAATTA
Found at i:380558 original size:60 final size:61
Alignment explanation
Indices: 380403--380576 Score: 203
Period size: 60 Copynumber: 2.8 Consensus size: 61
380393 TGTATATAAG
* *
380403 TATAGCTTGGGAT-AAATTAGAATGTTCAAAAAGTTTAAGGACCAATTTAAAATGAAGGACAT
1 TATAGTTTGGGATGAAATTAGAATGTTC-AAAAGTTTAAGGACTAATTTAAAATGAAGGA-AT
* * * * *
380465 AATAGTTTGGAGATGAAATT-GAAATGTTTAAAAGTTTGAGGACTAATTTATAATG-AGG-GT
1 TATAGTTTGG-GATGAAATTAG-AATGTTCAAAAGTTTAAGGACTAATTTAAAATGAAGGAAT
*
380525 TATAGTTTAGGGATGAAATTAGAATGTTCAAAAGTTTAAGGATTAATTTAAA
1 TATAGTTT-GGGATGAAATTAGAATGTTCAAAAGTTTAAGGACTAATTTAAA
380577 GTGACGGACA
Statistics
Matches: 95, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
60 43 0.45
61 3 0.03
62 11 0.12
63 27 0.28
64 11 0.12
ACGTcount: A:0.41, C:0.04, G:0.21, T:0.33
Consensus pattern (61 bp):
TATAGTTTGGGATGAAATTAGAATGTTCAAAAGTTTAAGGACTAATTTAAAATGAAGGAAT
Found at i:383111 original size:2 final size:2
Alignment explanation
Indices: 383104--383130 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
383094 AGTCCCATGA
383104 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
383131 CATGCTTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:383394 original size:27 final size:26
Alignment explanation
Indices: 383336--383394 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
383326 GTTAAACCTC
*
383336 TTAATTTAGATTTTTAATATTTTAGT
1 TTAATATAGATTTTTAATATTTTAGT
*
383362 TCTAATATAGATTATTT-TTATTTTAGGT
1 T-TAATATAGATT-TTTAATATTTTA-GT
383390 TTAAT
1 TTAAT
383395 CCTTAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
26 1 0.04
27 21 0.75
28 6 0.21
ACGTcount: A:0.31, C:0.02, G:0.08, T:0.59
Consensus pattern (26 bp):
TTAATATAGATTTTTAATATTTTAGT
Found at i:386973 original size:32 final size:31
Alignment explanation
Indices: 386935--387035 Score: 100
Period size: 32 Copynumber: 3.2 Consensus size: 31
386925 GAGAACACAT
386935 AGAAAAAGAAAAGAAAAAATATAGCA-AAAAGA
1 AGAAAAAGAAAAGAAAAAA-ATAG-AGAAAAGA
*
386967 AGAAAAAGAAAACATAAAAAATAGAGAAAAGA
1 AGAAAAAGAAAAGA-AAAAAATAGAGAAAAGA
* * * *
386999 A-AGAAAGAAAAGAAAGTAAACA-AAAAAAGA
1 AGAAAAAGAAAAGAAA-AAAATAGAGAAAAGA
387029 AGAAAAA
1 AGAAAAA
387036 AGAGAGATAA
Statistics
Matches: 58, Mismatches: 7, Indels: 9
0.78 0.09 0.12
Matches are distributed among these distances:
30 10 0.17
31 19 0.33
32 24 0.41
33 5 0.09
ACGTcount: A:0.76, C:0.03, G:0.16, T:0.05
Consensus pattern (31 bp):
AGAAAAAGAAAAGAAAAAAATAGAGAAAAGA
Found at i:386986 original size:23 final size:24
Alignment explanation
Indices: 386926--387000 Score: 68
Period size: 23 Copynumber: 3.2 Consensus size: 24
386916 AATCGAGTTG
* *
386926 AGAACACATAGAAAAAGAA-AAGA
1 AGAAAACATAGAAAAAGAAGAAAA
*
386949 A-AAAATATAGCAAAAAGAAGAAAA
1 AGAAAACATAG-AAAAAGAAGAAAA
*
386973 AGAAAACATA-AAAAA-TAGAGAAA
1 AGAAAACATAGAAAAAGAAGA-AAA
386996 AGAAA
1 AGAAA
387001 GAAAGAAAAG
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
22 10 0.23
23 22 0.51
24 4 0.09
25 7 0.16
ACGTcount: A:0.73, C:0.05, G:0.15, T:0.07
Consensus pattern (24 bp):
AGAAAACATAGAAAAAGAAGAAAA
Found at i:387007 original size:40 final size:40
Alignment explanation
Indices: 386962--387052 Score: 98
Period size: 40 Copynumber: 2.3 Consensus size: 40
386952 AATATAGCAA
* *
386962 AAAGAAGAAAAAGAAAACATAAAAAA-TAGAGAAAAGAAAG
1 AAAGAAGAAAAAGAAAACA-AAAAAAGAAGAAAAAAGAAAG
* *
387002 AAAGAA-AAGAAAGTAAACAAAAAAAGAAGAAAAAAGAGAG
1 AAAGAAGAA-AAAGAAAACAAAAAAAGAAGAAAAAAGAAAG
387042 ATAA-AAGAAAA
1 A-AAGAAGAAAA
387053 CAAAAAAGGA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
39 8 0.19
40 31 0.72
41 4 0.09
ACGTcount: A:0.76, C:0.02, G:0.18, T:0.04
Consensus pattern (40 bp):
AAAGAAGAAAAAGAAAACAAAAAAAGAAGAAAAAAGAAAG
Found at i:387009 original size:13 final size:13
Alignment explanation
Indices: 386991--387034 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
386981 TAAAAAATAG
386991 AGAAAAGAAAGAA
1 AGAAAAGAAAGAA
387004 AGAAAAGAAAGTAA
1 AGAAAAGAAAG-AA
*
387018 ACAAAA-AAAG-A
1 AGAAAAGAAAGAA
387029 AGAAAA
1 AGAAAA
387035 AAGAGAGATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 6 0.21
13 15 0.54
14 7 0.25
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.02
Consensus pattern (13 bp):
AGAAAAGAAAGAA
Found at i:387762 original size:28 final size:28
Alignment explanation
Indices: 387697--387763 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
387687 CAAAGAAGCC
* *
387697 AACCTGAAACATATTACCTCCCCAAATT
1 AACCTGAAACACATTACCTCCCAAAATT
* **
387725 AACCTCAAACACATTACCTCTTAAAATT
1 AACCTGAAACACATTACCTCCCAAAATT
*
387753 AACTTGAAACA
1 AACCTGAAACA
387764 TTACCTTTCC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.43, C:0.28, G:0.03, T:0.25
Consensus pattern (28 bp):
AACCTGAAACACATTACCTCCCAAAATT
Done.