Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000520.1 Hibiscus syriacus cultivar Beakdansim tig00000991_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: 1956684
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 11
Found at i:198874 original size:94 final size:93
Alignment explanation
Indices: 198664--199037 Score: 587
Period size: 94 Copynumber: 4.1 Consensus size: 93
198654 TAGATTGCTT
* * *
198664 AGTAAATTTATTCGGTTGATGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
* *
198725 ATTTATCTTT-TGTTGTCTTTTGGTTGA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
*
198752 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAATTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
198817 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* *
198846 AGTAAATTTGTTCGGTTGCTGTCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
198911 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * * *
198940 AGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
199005 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
199033 AGTAA
1 AGTAA
199038 TGCAATCCAT
Statistics
Matches: 267, Mismatches: 13, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
88 33 0.12
90 3 0.01
91 2 0.01
92 28 0.10
93 21 0.08
94 180 0.67
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:199177 original size:20 final size:20
Alignment explanation
Indices: 199154--199191 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
199144 CGAGAGAATG
199154 AAAATCGCAACGCGAAACCA
1 AAAATCGCAACGCGAAACCA
199174 AAAATCGCAACGCGAAAC
1 AAAATCGCAACGCGAAAC
199192 TATAATCGCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.29, G:0.16, T:0.05
Consensus pattern (20 bp):
AAAATCGCAACGCGAAACCA
Found at i:199219 original size:19 final size:19
Alignment explanation
Indices: 199197--199317 Score: 91
Period size: 19 Copynumber: 6.8 Consensus size: 19
199187 GAAACTATAA
199197 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
199216 TCGCATTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
199230 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
199249 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
199263 TCTCGTTGCGATTTTCGTT
1 TCGCGTTGCGATTTTCATT
**
199282 TCGCGTTGCGATAGTCATTTT
1 TCGCGTTGCGATTTTCA--TT
*
199303 TCACGTTGCGATTTT
1 TCGCGTTGCGATTTT
199318 AAGTTCCAGA
Statistics
Matches: 78, Mismatches: 12, Indels: 22
0.70 0.11 0.20
Matches are distributed among these distances:
14 19 0.24
16 6 0.08
17 6 0.08
19 33 0.42
21 14 0.18
ACGTcount: A:0.11, C:0.22, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:199240 original size:14 final size:14
Alignment explanation
Indices: 199221--199275 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
199211 TCATTTCGCA
199221 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
199235 TTGCGATTTTCATTTCGCG
1 TTGCGA--TTC---TCTCG
199254 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
199268 TTGCGATT
1 TTGCGATT
199276 TTCGTTTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.24, G:0.22, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:199242 original size:33 final size:33
Alignment explanation
Indices: 199200--199293 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
199190 ACTATAATCG
*
199200 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
199233 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
*
199266 CGTTGCGATTTTCGTTTCGCGTTGCGAT
1 CGTTGCGATTTTCATTTCGCGTTGCGAT
199294 AGTCATTTTT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:201200 original size:14 final size:14
Alignment explanation
Indices: 201181--201216 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
201171 ATTGTTTAAT
201181 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
201195 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
201209 TGATTTGT
1 TGATTTGT
201217 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:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:201339 original size:19 final size:19
Alignment explanation
Indices: 201323--201407 Score: 83
Period size: 19 Copynumber: 4.7 Consensus size: 19
201313 AAAAATGACT
* *
201323 ATCGCAATGTGAAATGAAA
1 ATCGCAACGCGAAATGAAA
201342 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
* *
201361 TTCGCAA--CG--A-CAAA
1 ATCGCAACGCGAAATGAAA
201375 ATCGCAACGCGAAACT-AAA
1 ATCGCAACGCGAAA-TGAAA
201394 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
201408 CTAATTTCGC
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
14 9 0.16
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 40 0.73
ACGTcount: A:0.46, C:0.22, G:0.19, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:201381 original size:33 final size:33
Alignment explanation
Indices: 201339--201402 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 33
201329 ATGTGAAATG
*
201339 AAAATCGCAACGCGAAA-TGAAATTCGCAACGAC
1 AAAATCGCAACGCGAAACT-AAAATCGCAACGAC
201372 AAAATCGCAACGCGAAACTAAAATCGCAACG
1 AAAATCGCAACGCGAAACTAAAATCGCAACG
201403 CGAAACTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.47, C:0.25, G:0.17, T:0.11
Consensus pattern (33 bp):
AAAATCGCAACGCGAAACTAAAATCGCAACGAC
Found at i:201417 original size:19 final size:19
Alignment explanation
Indices: 201339--201411 Score: 86
Period size: 19 Copynumber: 4.1 Consensus size: 19
201329 ATGTGAAATG
201339 AAAATCGCAACGCGAAA-T
1 AAAATCGCAACGCGAAACT
*
201357 GAAATTCGCAA--CG--AC-
1 -AAAATCGCAACGCGAAACT
201372 AAAATCGCAACGCGAAACT
1 AAAATCGCAACGCGAAACT
201391 AAAATCGCAACGCGAAACT
1 AAAATCGCAACGCGAAACT
201410 AA
1 AA
201412 TTTCGCGTTG
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
14 9 0.20
15 1 0.02
16 2 0.04
17 2 0.04
18 2 0.04
19 30 0.65
ACGTcount: A:0.48, C:0.25, G:0.16, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACT
Found at i:201445 original size:19 final size:18
Alignment explanation
Indices: 201411--201530 Score: 76
Period size: 19 Copynumber: 6.8 Consensus size: 18
201401 CGCGAAACTA
*
201411 ATTTCGCGTTGTGATTTTC
1 ATTTCGC-TTGCGATTTTC
201430 ATTTCGCTTTGCGA--TTC
1 ATTTCGC-TTGCGATTTTC
**
201447 -CCTCG-TTGCGATTTTC
1 ATTTCGCTTGCGATTTTC
201463 ATTTCGCATTGCGA--TTC
1 ATTTCGC-TTGCGATTTTC
*
201480 -TCTCG-TTGCGATTTTC
1 ATTTCGCTTGCGATTTTC
**
201496 ATTTCGCATTGCGATAGTC
1 ATTTCGC-TTGCGATTTTC
201515 ATTTCCGCGTTGCGAT
1 ATTT-CGC-TTGCGAT
201531 AGACATTAAG
Statistics
Matches: 79, Mismatches: 11, Indels: 21
0.71 0.10 0.19
Matches are distributed among these distances:
14 12 0.15
16 13 0.16
17 13 0.16
19 31 0.39
20 10 0.13
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.44
Consensus pattern (18 bp):
ATTTCGCTTGCGATTTTC
Found at i:201460 original size:33 final size:33
Alignment explanation
Indices: 201417--201510 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
201407 ACTAATTTCG
* *
201417 CGTTGTGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
201450 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
201483 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
201511 AGTCATTTCC
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.12, C:0.23, G:0.19, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:201529 original size:20 final size:19
Alignment explanation
Indices: 201483--201537 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
201473 GCGATTCTCT
**
201483 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
201502 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
*
201522 CGTTGCGATAGACATT
1 CGTTGCGATAGTCATT
201538 AAGATGATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:204038 original size:24 final size:24
Alignment explanation
Indices: 203987--204038 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
203977 ATCCAAGTAT
** *
203987 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
204011 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
204035 TGAC
1 TGAC
204039 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:204895 original size:20 final size:21
Alignment explanation
Indices: 204871--204981 Score: 149
Period size: 20 Copynumber: 5.5 Consensus size: 21
204861 CAGAATCTCG
204871 TTGCGA-TTACGTAAATCGCA
1 TTGCGATTTACGTAAATCGCA
* * * *
204891 ATGCGATTTTCCTAATTCGCA
1 TTGCGATTTACGTAAATCGCA
204912 TTGCGATTTACGT-AATCGCA
1 TTGCGATTTACGTAAATCGCA
204932 TTGCGATTTACGT-AATCGCA
1 TTGCGATTTACGTAAATCGCA
*
204952 TTGCGATTTACGT-ATTCGCA
1 TTGCGATTTACGTAAATCGCA
204972 TTGCGATTTA
1 TTGCGATTTA
204982 GGAAATTCGC
Statistics
Matches: 81, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
20 60 0.74
21 21 0.26
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (21 bp):
TTGCGATTTACGTAAATCGCA
Found at i:204991 original size:21 final size:20
Alignment explanation
Indices: 204871--205020 Score: 131
Period size: 20 Copynumber: 7.3 Consensus size: 20
204861 CAGAATCTCG
204871 TTGCGA-TTACGTAAATCGCA
1 TTGCGATTTACG-AAATCGCA
* * * *
204891 ATGCGATTTTCCTAATTCGCA
1 TTGCGA-TTTACGAAATCGCA
*
204912 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGAAATCGCA
*
204932 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGAAATCGCA
* *
204952 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGAAATCGCA
*
204972 TTGCGATTTAGGAAATTCGCA
1 TTGCGATTTACGAAA-TCGCA
** **
204993 ACGCGAATTTGGGAAATCGCA
1 TTGCG-ATTTACGAAATCGCA
*
205014 ATGCGAT
1 TTGCGAT
205021 AGTCAGAATC
Statistics
Matches: 109, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
20 68 0.62
21 29 0.27
22 12 0.11
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (20 bp):
TTGCGATTTACGAAATCGCA
Found at i:205007 original size:22 final size:21
Alignment explanation
Indices: 204977--205019 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
204967 TCGCATTGCG
204977 ATTTAGGAAATTCGCAACGCGA
1 ATTTAGGAAA-TCGCAACGCGA
* *
204999 ATTTGGGAAATCGCAATGCGA
1 ATTTAGGAAATCGCAACGCGA
205020 TAGTCAGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.23
Consensus pattern (21 bp):
ATTTAGGAAATCGCAACGCGA
Found at i:205256 original size:16 final size:16
Alignment explanation
Indices: 205235--205289 Score: 76
Period size: 16 Copynumber: 3.5 Consensus size: 16
205225 GGGAGGATGT
205235 GGGGCGGGCAGATGCG
1 GGGGCGGGCAGATGCG
*
205251 GGGGCGGGCAGATACG
1 GGGGCGGGCAGATGCG
* *
205267 GGGGCGGGCGGATG-T
1 GGGGCGGGCAGATGCG
205282 GGGGCGGG
1 GGGGCGGG
205290 TAAGGTCTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
15 8 0.23
16 27 0.77
ACGTcount: A:0.11, C:0.16, G:0.65, T:0.07
Consensus pattern (16 bp):
GGGGCGGGCAGATGCG
Found at i:207298 original size:17 final size:17
Alignment explanation
Indices: 207251--207300 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 17
207241 GATTTGTGAT
* * *
207251 AAATTATATTTAATTTC
1 AAATAATATTTAATATA
*
207268 AAATCAT-TTT-ATATA
1 AAATAATATTTAATATA
207283 AAATAATATTTAATATA
1 AAATAATATTTAATATA
207300 A
1 A
207301 TAGAATTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 9 0.33
16 6 0.22
17 12 0.44
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (17 bp):
AAATAATATTTAATATA
Found at i:210849 original size:24 final size:24
Alignment explanation
Indices: 210795--210852 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
210785 GCTCCAAATC
210795 ATTTTGTCCACTAGAGTCTCCATT
1 ATTTTGTCCACTAGAGTCTCCATT
** * *
210819 AACTTGTCCAC-CGAGCTCTTCATT
1 ATTTTGTCCACTAGAG-TCTCCATT
210843 ATTTTGTCCA
1 ATTTTGTCCA
210853 TTGGGATCAC
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
23 3 0.11
24 24 0.89
ACGTcount: A:0.21, C:0.28, G:0.12, T:0.40
Consensus pattern (24 bp):
ATTTTGTCCACTAGAGTCTCCATT
Found at i:216155 original size:19 final size:19
Alignment explanation
Indices: 216133--216185 Score: 54
Period size: 21 Copynumber: 2.7 Consensus size: 19
216123 AAAGTTTAAA
*
216133 TCGAATTGTAAAATATAAT
1 TCGAATTGTAAAATATAAC
216152 TCGAATAACT-TAAAATATAAC
1 TCGAAT---TGTAAAATATAAC
*
216173 TCGAGTTGTAAAA
1 TCGAATTGTAAAA
216186 ATTTAAAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
18 1 0.04
19 11 0.39
21 15 0.54
22 1 0.04
ACGTcount: A:0.47, C:0.09, G:0.11, T:0.32
Consensus pattern (19 bp):
TCGAATTGTAAAATATAAC
Found at i:216987 original size:60 final size:61
Alignment explanation
Indices: 216851--216967 Score: 168
Period size: 61 Copynumber: 1.9 Consensus size: 61
216841 GTTGTGTGAC
* *
216851 CATTTTGTAACTTTTAATAGTCGAGATACTCAACAAAAGCAACACTCTATAGTCGAAAGAT
1 CATTTTATAATTTTTAATAGTCGAGATACTCAACAAAAGCAACACTCTATAGTCGAAAGAT
*
216912 CATTTTATAATTTTTAATAGTCTG-GATACTCAACAAAA-CAACA-TCCTATATTCGAA
1 CATTTTATAATTTTTAATAGTC-GAGATACTCAACAAAAGCAACACT-CTATAGTCGAA
216968 GGACGTTTGT
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
59 1 0.02
60 15 0.29
61 34 0.67
62 1 0.02
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.32
Consensus pattern (61 bp):
CATTTTATAATTTTTAATAGTCGAGATACTCAACAAAAGCAACACTCTATAGTCGAAAGAT
Found at i:217755 original size:12 final size:11
Alignment explanation
Indices: 217731--217764 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
217721 TATTATTCTA
*
217731 TTAATCTAAAT
1 TTAATTTAAAT
217742 TTAATTTGAAAT
1 TTAATTT-AAAT
217754 TTAATTTAAAT
1 TTAATTTAAAT
217765 ATACAATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (11 bp):
TTAATTTAAAT
Found at i:226360 original size:22 final size:21
Alignment explanation
Indices: 226326--226366 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
226316 ATAATTATTT
226326 AAAAAATTAAATAAAAATACC
1 AAAAAATTAAATAAAAATACC
*
226347 AAAAATATTTAATAAAAATA
1 AAAAA-ATTAAATAAAAATA
226367 ATTTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATACC
Found at i:232069 original size:23 final size:23
Alignment explanation
Indices: 232038--232091 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
232028 TTTTAATCAA
232038 AAAAT-TATTTATTAAAATATTT
1 AAAATATATTTATTAAAATATTT
* *
232060 AAAATATATTTATTAATATTTTT
1 AAAATATATTTATTAAAATATTT
232083 AATAATATA
1 AA-AATATA
232092 ATATTCTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 5 0.18
23 17 0.61
24 6 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
AAAATATATTTATTAAAATATTT
Found at i:232077 original size:12 final size:12
Alignment explanation
Indices: 232043--232091 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
232033 ATCAAAAAAT
*
232043 TATTTATTAAAA
1 TATTTATTAATA
*
232055 TATTTA-AAATA
1 TATTTATTAATA
232066 TATTTATTAATA
1 TATTTATTAATA
* *
232078 TTTTTAATAATA
1 TATTTATTAATA
232090 TA
1 TA
232092 ATATTCTATT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
11 9 0.30
12 21 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TATTTATTAATA
Found at i:232096 original size:23 final size:24
Alignment explanation
Indices: 232047--232108 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 24
232037 AAAAATTATT
* * *
232047 TATTAAAATATTTAA-AATATATT
1 TATTAATATTTTTAATAATATATA
232070 TATTAATATTTTTAATAATATA-A
1 TATTAATATTTTTAATAATATATA
*
232093 TATT-CTATTTTTAATA
1 TATTAATATTTTTAATA
232109 TTTTAATAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
22 11 0.32
23 17 0.50
24 6 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (24 bp):
TATTAATATTTTTAATAATATATA
Found at i:232929 original size:15 final size:16
Alignment explanation
Indices: 232910--232955 Score: 60
Period size: 15 Copynumber: 2.9 Consensus size: 16
232900 TAAATATTAT
232910 TAATTTAATTTATAAA
1 TAATTTAATTTATAAA
232926 -AATTTAAATTTA-AAA
1 TAATTT-AATTTATAAA
*
232941 TAATTTAATATATAA
1 TAATTTAATTTATAA
232956 TTATAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TAATTTAATTTATAAA
Found at i:232937 original size:16 final size:16
Alignment explanation
Indices: 232910--232948 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
232900 TAAATATTAT
232910 TAATTT-AATTTATAAA
1 TAATTTAAATTTA-AAA
232926 -AATTTAAATTTAAAA
1 TAATTTAAATTTAAAA
232941 TAATTTAA
1 TAATTTAA
232949 TATATAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TAATTTAAATTTAAAA
Found at i:234759 original size:18 final size:18
Alignment explanation
Indices: 234738--234775 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
234728 GTTTGTTTGT
*
234738 TTAGATTTGTGTTTGAGC
1 TTAGATGTGTGTTTGAGC
234756 TTAGATGTGTGTTTGAGC
1 TTAGATGTGTGTTTGAGC
234774 TT
1 TT
234776 TATTGATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.05, G:0.29, T:0.50
Consensus pattern (18 bp):
TTAGATGTGTGTTTGAGC
Found at i:238138 original size:30 final size:30
Alignment explanation
Indices: 238090--238148 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
238080 AAGTTAGCAA
**
238090 GTGACCGAAAATATAATTTTTAAAAGTTTG
1 GTGACCGAAAATATAATTTAGAAAAGTTTG
*
238120 GTGACC-AAAGTATAAATTTAGAAAAGTTT
1 GTGACCGAAAATAT-AATTTAGAAAAGTTT
238149 AAGGAATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 6 0.24
30 19 0.76
ACGTcount: A:0.42, C:0.07, G:0.17, T:0.34
Consensus pattern (30 bp):
GTGACCGAAAATATAATTTAGAAAAGTTTG
Found at i:239285 original size:21 final size:19
Alignment explanation
Indices: 239261--239304 Score: 56
Period size: 17 Copynumber: 2.3 Consensus size: 19
239251 GTCCTATTTT
239261 GAAAATATTATGTGAATGGTG
1 GAAAATA-T-TGTGAATGGTG
239282 G-AAA-ATTGTGAATGGTG
1 GAAAATATTGTGAATGGTG
239299 GAAAAT
1 GAAAAT
239305 GATGATTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
17 12 0.57
18 4 0.19
19 1 0.05
20 3 0.14
21 1 0.05
ACGTcount: A:0.41, C:0.00, G:0.30, T:0.30
Consensus pattern (19 bp):
GAAAATATTGTGAATGGTG
Found at i:239293 original size:17 final size:17
Alignment explanation
Indices: 239271--239304 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
239261 GAAAATATTA
239271 TGTGAATGGTGGAAAAT
1 TGTGAATGGTGGAAAAT
239288 TGTGAATGGTGGAAAAT
1 TGTGAATGGTGGAAAAT
239305 GATGATTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.29
Consensus pattern (17 bp):
TGTGAATGGTGGAAAAT
Found at i:239848 original size:28 final size:28
Alignment explanation
Indices: 239811--239867 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
239801 TATTATTACA
* *
239811 AGACCGGAA-GACCTATGTTACAACAAAC
1 AGACCCGAAGGACC-ATATTACAACAAAC
*
239839 AGACCCGAAGGTCCATATTACAACAAAC
1 AGACCCGAAGGACCATATTACAACAAAC
239867 A
1 A
239868 TGTCCATACT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 22 0.88
29 3 0.12
ACGTcount: A:0.44, C:0.26, G:0.16, T:0.14
Consensus pattern (28 bp):
AGACCCGAAGGACCATATTACAACAAAC
Found at i:241954 original size:18 final size:18
Alignment explanation
Indices: 241927--241976 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
241917 GTCTACGCGA
*
241927 TCCTTTGGGACATAGTGG
1 TCCTTCGGGACATAGTGG
241945 TCCTTCGGGACATAGTGG
1 TCCTTCGGGACATAGTGG
**
241963 TTATTCGGGACATA
1 TCCTTCGGGACATA
241977 TGTGTTATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.20, C:0.18, G:0.30, T:0.32
Consensus pattern (18 bp):
TCCTTCGGGACATAGTGG
Found at i:242022 original size:21 final size:21
Alignment explanation
Indices: 241984--242023 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
241974 ATATGTGTTA
**
241984 TATGTAGTCCTTTGGGACATC
1 TATGTAGTCCTTCAGGACATC
*
242005 TATGTGGTCCTTCAGGACA
1 TATGTAGTCCTTCAGGACA
242024 AATTATACAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (21 bp):
TATGTAGTCCTTCAGGACATC
Found at i:245122 original size:24 final size:22
Alignment explanation
Indices: 245083--245159 Score: 67
Period size: 24 Copynumber: 3.6 Consensus size: 22
245073 ATGCAATTAC
245083 TGCATCGATGCA---TAAGGAG
1 TGCATCGATGCACTGTAAGGAG
245102 TGCATCGATGCACATGTTAAGG-G
1 TGCATCGATGCAC-TG-TAAGGAG
* *
245125 ATGCATCGATACACTGT-A-GAA
1 -TGCATCGATGCACTGTAAGGAG
245146 TGCATCGATGCACT
1 TGCATCGATGCACT
245160 TCAAGGGGAA
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
19 12 0.25
20 14 0.29
21 1 0.02
22 1 0.02
23 3 0.06
24 17 0.35
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (22 bp):
TGCATCGATGCACTGTAAGGAG
Found at i:256979 original size:18 final size:18
Alignment explanation
Indices: 256958--256994 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
256948 GAAAGTATCT
256958 CCTTAGAAGAAGGTATTA
1 CCTTAGAAGAAGGTATTA
256976 CCTTAGAAGAAGGTATTA
1 CCTTAGAAGAAGGTATTA
256994 C
1 C
256995 GTTTTGGGCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.27
Consensus pattern (18 bp):
CCTTAGAAGAAGGTATTA
Found at i:258375 original size:20 final size:20
Alignment explanation
Indices: 258350--258387 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
258340 ACCATAGCAT
*
258350 AGGGTATCAATACCATGGTG
1 AGGGTATCAATAACATGGTG
*
258370 AGGGTATCGATAACATGG
1 AGGGTATCAATAACATGG
258388 CTGCATCGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.13, G:0.32, T:0.24
Consensus pattern (20 bp):
AGGGTATCAATAACATGGTG
Found at i:258416 original size:95 final size:95
Alignment explanation
Indices: 258237--258431 Score: 227
Period size: 95 Copynumber: 2.1 Consensus size: 95
258227 GATTTAACCA
* * * *
258237 GTATCAGTACCCAAGCAATATGGTATCGATACCATGGTAAGGGTATCGATACCAGTAAACATCGA
1 GTATCAGTACCCAAGCAATAGGGTATCAATACCATGGTAAGGGTATCGATAACAGGAAACATCGA
* * *
258302 ATTTAATTTGGGTATCGATACCT-AGAGGGG
66 ACTAAATTTGGGTATCGATACATGA-AGGGG
* ***
258332 GTATCAGTA-CCATAGC-ATAGGGTATCAATACCATGGTGAGGGTATCGATAACATGGCTGCATC
1 GTATCAGTACCCA-AGCAATAGGGTATCAATACCATGGTAAGGGTATCGATAACA-GGAAACATC
258395 GAAGCTAAATTT-GGTATCGATACATGAAGGGG
64 GAA-CTAAATTTGGGTATCGATACATGAAGGGG
258427 GTATC
1 GTATC
258432 GATACCCTAA
Statistics
Matches: 85, Mismatches: 11, Indels: 8
0.82 0.11 0.08
Matches are distributed among these distances:
94 36 0.42
95 42 0.49
96 7 0.08
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (95 bp):
GTATCAGTACCCAAGCAATAGGGTATCAATACCATGGTAAGGGTATCGATAACAGGAAACATCGA
ACTAAATTTGGGTATCGATACATGAAGGGG
Found at i:258457 original size:22 final size:23
Alignment explanation
Indices: 258427--258471 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
258417 CATGAAGGGG
*
258427 GTATCGATACCCTAA-TAGGGTA
1 GTATCGATACCATAAGTAGGGTA
*
258449 GTATTGATACCATAAGTAGGGTA
1 GTATCGATACCATAAGTAGGGTA
258472 TTGATACCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.29
Consensus pattern (23 bp):
GTATCGATACCATAAGTAGGGTA
Found at i:260704 original size:45 final size:45
Alignment explanation
Indices: 260655--260776 Score: 172
Period size: 45 Copynumber: 2.7 Consensus size: 45
260645 ATGCACTATC
*
260655 TATGCATCGGTGCACAAATCCCATTCGATGTTTGTATTTTAATCA
1 TATGCATCGGTGCACAAATCCCATTCGATGTTTGTATTTTAAGCA
*
260700 TATGCATCGGTGTACAAATCCCATTCGATGTTTGTATTTTAAGCA
1 TATGCATCGGTGCACAAATCCCATTCGATGTTTGTATTTTAAGCA
** * * **
260745 GGTGCATCGATGCACTAATTGCATTCGATGTT
1 TATGCATCGGTGCACAAATCCCATTCGATGTT
260777 CATTTATTTA
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 68 1.00
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (45 bp):
TATGCATCGGTGCACAAATCCCATTCGATGTTTGTATTTTAAGCA
Found at i:261649 original size:45 final size:45
Alignment explanation
Indices: 261600--261818 Score: 246
Period size: 45 Copynumber: 4.9 Consensus size: 45
261590 AAAGGATGCC
261600 AGAGTTGAAATGCATATGGGTGCATTATCAACTGAAAAGTATACT
1 AGAGTTGAAATGCATATGGGTGCATTATCAACTGAAAAGTATACT
* * * * *
261645 AGAGTTGAAATGCATATGGATGCATTATGAACAGAAAAATATGCT
1 AGAGTTGAAATGCATATGGGTGCATTATCAACTGAAAAGTATACT
* * *
261690 AGAGTTGAAATGTATATGGGTACATTATCAA-TAGAAAAGTATAAT
1 AGAGTTGAAATGCATATGGGTGCATTATCAACT-GAAAAGTATACT
* * * * *
261735 -GTGGTTGAGATGTATATAGGTACATTATCAACAT-AAAAGTATACT
1 AG-AGTTGAAATGCATATGGGTGCATTATCAAC-TGAAAAGTATACT
* * *
261780 ATAGTTGAAATGCACATGGGTGCATTATCAACAGAAAAG
1 AGAGTTGAAATGCATATGGGTGCATTATCAACTGAAAAG
261819 ATGTTATGGT
Statistics
Matches: 143, Mismatches: 25, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
44 1 0.01
45 141 0.99
47 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.21, T:0.29
Consensus pattern (45 bp):
AGAGTTGAAATGCATATGGGTGCATTATCAACTGAAAAGTATACT
Found at i:261852 original size:90 final size:89
Alignment explanation
Indices: 261600--261861 Score: 244
Period size: 90 Copynumber: 2.9 Consensus size: 89
261590 AAAGGATGCC
* *
261600 AGAGTTGAAATGCATATGGGTGCATTATCAACTGAAAAGTATACTA-GAGTTGAAATGCATATGG
1 AGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAG-ATATTATGAGTTGAAATGCATAT-G
* * * *
261664 ATGCATTATGAACAGAAAAATATGCT
64 ATGTATTATAAACATAAAAATATACT
* * * * * * *
261690 AGAGTTGAAATGTATATGGGTACATTATCAATAGAAAAG-TATAATGTGGTTGAGATGTATAT-A
1 AGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGATATTATG-AGTTGAAATGCATATGA
* * *
261753 GGTACATTATCAACATAAAAGTATACT
65 TGT--ATTATAAACATAAAAATATACT
* * * *
261780 ATAGTTGAAATGCACATGGGTGCATTATCAACAGAAAAGATGTTATG-GTTTAAAATGCATAATG
1 AGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGATATTATGAG-TTGAAATGCAT-ATG
*
261844 ATGTATTATAAAAATAAA
64 ATGTATTATAAACATAAA
261862 TGAAGGTGTT
Statistics
Matches: 136, Mismatches: 28, Indels: 16
0.76 0.16 0.09
Matches are distributed among these distances:
88 5 0.04
89 2 0.01
90 119 0.88
91 7 0.05
92 3 0.02
ACGTcount: A:0.42, C:0.08, G:0.20, T:0.30
Consensus pattern (89 bp):
AGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGATATTATGAGTTGAAATGCATATGAT
GTATTATAAACATAAAAATATACT
Found at i:267859 original size:24 final size:24
Alignment explanation
Indices: 267814--267859 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
267804 GTAATAAAAT
**
267814 AAAGAAAAGAAAAAATTGAACTCA
1 AAAGAAAAGAAAAAATAAAACTCA
* *
267838 AAAGAAATGAAACAATAAAACT
1 AAAGAAAAGAAAAAATAAAACT
267860 GTCTGTCATG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.67, C:0.09, G:0.11, T:0.13
Consensus pattern (24 bp):
AAAGAAAAGAAAAAATAAAACTCA
Found at i:274706 original size:12 final size:13
Alignment explanation
Indices: 274688--274756 Score: 54
Period size: 13 Copynumber: 5.2 Consensus size: 13
274678 TAATAATAAT
*
274688 AATAAAAATAAAA
1 AATAAAAACAAAA
*
274701 AAAAAAAAC-AAA
1 AATAAAAACAAAA
274713 AATAAAAACAAAA
1 AATAAAAACAAAA
274726 CCAA-AACAAA-AACCAA
1 --AATAA-AAACAA--AA
274742 AATAAAAACAAAA
1 AATAAAAACAAAA
274755 AA
1 AA
274757 ATAATATATA
Statistics
Matches: 45, Mismatches: 3, Indels: 16
0.70 0.05 0.25
Matches are distributed among these distances:
12 11 0.24
13 14 0.31
14 9 0.20
15 9 0.20
16 2 0.04
ACGTcount: A:0.83, C:0.12, G:0.00, T:0.06
Consensus pattern (13 bp):
AATAAAAACAAAA
Found at i:274737 original size:18 final size:18
Alignment explanation
Indices: 274692--274756 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 18
274682 AATAATAATA
* *
274692 AAAATAAAAAAAAAAAAC
1 AAAACAAAAAACAAAAAC
*
274710 AAAA-ATAAAAACAAAACC
1 AAAACA-AAAAACAAAAAC
*
274728 AAAACAAAAACCAAAATA-
1 AAAACAAAAAACAAAA-AC
274746 AAAACAAAAAA
1 AAAACAAAAAA
274757 ATAATATATA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
17 1 0.03
18 37 0.95
19 1 0.03
ACGTcount: A:0.83, C:0.12, G:0.00, T:0.05
Consensus pattern (18 bp):
AAAACAAAAAACAAAAAC
Found at i:274743 original size:29 final size:29
Alignment explanation
Indices: 274699--274754 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
274689 ATAAAAATAA
274699 AAAAAAAAAACAAAAATAAAAACAAAACC
1 AAAAAAAAAACAAAAATAAAAACAAAACC
* *
274728 AAAACAAAAACCAAAATAAAAACAAAA
1 AAAAAAAAAACAAAAATAAAAACAAAA
274755 AAATAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.82, C:0.14, G:0.00, T:0.04
Consensus pattern (29 bp):
AAAAAAAAAACAAAAATAAAAACAAAACC
Found at i:274749 original size:6 final size:6
Alignment explanation
Indices: 274698--274755 Score: 64
Period size: 6 Copynumber: 9.8 Consensus size: 6
274688 AATAAAAATA
* * * * *
274698 AAAAAA AAAAAC AAAAAT AAAAAC -AAAAC CAAAAC AAAAAC CAAAAT
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC
274745 AAAAAC AAAAA
1 AAAAAC AAAAA
274756 AATAATATAT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
5 5 0.12
6 38 0.88
ACGTcount: A:0.83, C:0.14, G:0.00, T:0.03
Consensus pattern (6 bp):
AAAAAC
Found at i:280178 original size:135 final size:133
Alignment explanation
Indices: 279921--280181 Score: 504
Period size: 135 Copynumber: 1.9 Consensus size: 133
279911 GAGGCACTTC
279921 TGTCACACAAAACTCCGTAGCGGCCCTTCACTTTAGTCTCCCGCCTTTATACGGTGTAACGTCAT
1 TGTCACACAAAACTCCGTAGCGGCCCTTCACTTTAGTCTCCCGCCTTTATACGGTGTAACGTCAT
279986 CATCTACACCCCCATCTTTATGTATCATAGATCCTAGGTACTTGAAACAATCCTTTGAGGGGAGA
66 CATCTACACCCCCATCTTTATGTATCATAGATCCTAGGTACTTGAAACAATCCTTTGAGGGGAGA
280051 TCT
131 TCT
280054 TGTCACACAAAACTCCAGTAGCGGCCCTTCACTTTAGTCATCCCGCCTTTATACGGTGTAACGTC
1 TGTCACACAAAACTCC-GTAGCGGCCCTTCACTTTAGTC-TCCCGCCTTTATACGGTGTAACGTC
280119 ATCATCTACACCCCCATCTTTATGTATCATAGATCCTAGGTACTTGAAACAATCCTTTGAGGG
64 ATCATCTACACCCCCATCTTTATGTATCATAGATCCTAGGTACTTGAAACAATCCTTTGAGGG
280182 AGAACGTGTC
Statistics
Matches: 126, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
133 16 0.13
134 22 0.17
135 88 0.70
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.30
Consensus pattern (133 bp):
TGTCACACAAAACTCCGTAGCGGCCCTTCACTTTAGTCTCCCGCCTTTATACGGTGTAACGTCAT
CATCTACACCCCCATCTTTATGTATCATAGATCCTAGGTACTTGAAACAATCCTTTGAGGGGAGA
TCT
Found at i:282612 original size:37 final size:37
Alignment explanation
Indices: 282560--282632 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
282550 AATCAACCAC
*
282560 AAAGATTAAATTATAACTCCTCAACTTTATTACACAG
1 AAAGATTAAAATATAACTCCTCAACTTTATTACACAG
282597 AAAGATTAAAATATAACTCCTCAACTTTATTACACA
1 AAAGATTAAAATATAACTCCTCAACTTTATTACACA
282633 ATGAACTGTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.45, C:0.19, G:0.04, T:0.32
Consensus pattern (37 bp):
AAAGATTAAAATATAACTCCTCAACTTTATTACACAG
Found at i:286509 original size:3 final size:3
Alignment explanation
Indices: 286501--286547 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
286491 AATAAAAATG
*
286501 TAA TAA TAA -AA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
286548 ACCCTGGGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:291163 original size:59 final size:59
Alignment explanation
Indices: 291089--291207 Score: 204
Period size: 59 Copynumber: 2.0 Consensus size: 59
291079 GCAGAATCCA
291089 TGGAGATCGATCTAAATTCCTACAAATTTTCAATTACATAACAATTCCAATCCCATGGT
1 TGGAGATCGATCTAAATTCCTACAAATTTTCAATTACATAACAATTCCAATCCCATGGT
* *
291148 TGGAGATTC-ATCTAAATTCCTACAAATTTTCAATTATATATCAATTCCAATCCCATGGT
1 TGGAGA-TCGATCTAAATTCCTACAAATTTTCAATTACATAACAATTCCAATCCCATGGT
291207 T
1 T
291208 AGTTTTCTCA
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
59 55 0.96
60 2 0.04
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.35
Consensus pattern (59 bp):
TGGAGATCGATCTAAATTCCTACAAATTTTCAATTACATAACAATTCCAATCCCATGGT
Found at i:293699 original size:23 final size:23
Alignment explanation
Indices: 293671--293725 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
293661 TGGCTTCAGA
293671 GGCGGCTGGAAACCCTTGGAATC
1 GGCGGCTGGAAACCCTTGGAATC
*
293694 GGCGGCTGGAAACCCTTGGAGTC
1 GGCGGCTGGAAACCCTTGGAATC
*
293717 AGCGGCTGG
1 GGCGGCTGG
293726 GGCTAGGGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.18, C:0.25, G:0.40, T:0.16
Consensus pattern (23 bp):
GGCGGCTGGAAACCCTTGGAATC
Found at i:293860 original size:3 final size:3
Alignment explanation
Indices: 293852--293910 Score: 73
Period size: 3 Copynumber: 18.7 Consensus size: 3
293842 TTTCTTTATT
**
293852 TAA TAA TAA TAA TATA TATA TATA TAA TAA TAA TAA TAA TTT TAA TAA
1 TAA TAA TAA TAA TA-A TA-A TA-A TAA TAA TAA TAA TAA TAA TAA TAA
293900 TAA TAA TAA TA
1 TAA TAA TAA TA
293911 TGAAAAAATT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
3 40 0.78
4 11 0.22
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:293897 original size:18 final size:19
Alignment explanation
Indices: 293854--293911 Score: 82
Period size: 18 Copynumber: 3.0 Consensus size: 19
293844 TCTTTATTTA
293854 ATAATAATAATATATATATAT
1 ATAATAATAATA-ATA-ATAT
293875 ATAATAATAATAATAAT-T
1 ATAATAATAATAATAATAT
*
293893 TTAATAATAATAATAATAT
1 ATAATAATAATAATAATAT
293912 GAAAAAATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
18 17 0.49
19 3 0.09
20 3 0.09
21 12 0.34
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
ATAATAATAATAATAATAT
Found at i:294244 original size:73 final size:73
Alignment explanation
Indices: 294093--294496 Score: 639
Period size: 73 Copynumber: 5.5 Consensus size: 73
294083 GATCCAAAGG
* ** * * * * *
294093 TTTTGAAAACATCATGCACTAAAGGCCTTAAAGATGACCC-GAAGGTTTTGAAAATATCGAAAAG
1 TTTTGAGAACATCATGCACTGTAGGTCTTACAGATGACCCTG-AGGCTTT---AAGATCAAAAAG
294157 CTCCCGAAGGCT
62 CTCCCGAAGGCT
* *
294169 TTTTGAGAACATCATACACTGTAGGTCTTACAGGTGACCCTGAGGCTTTAAGATCAAAAAGCTCC
1 TTTTGAGAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCC
294234 CGAAGGCT
66 CGAAGGCT
* * *
294242 TTTTGAGAACATTATGCACTGTAGGTCTTACAGATGACCCTCAAGCTTTAAGATCAAAAAGCTCC
1 TTTTGAGAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCC
*
294307 CGAAGGTT
66 CGAAGGCT
294315 TTTTGAGAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCC
1 TTTTGAGAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCC
294380 CGAAGGCT
66 CGAAGGCT
294388 TTTTGAGAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCC
1 TTTTGAGAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCC
294453 CGAAGGCT
66 CGAAGGCT
294461 TTTTGAGAACATCATGCACTGTAGGTCTTACAGATG
1 TTTTGAGAACATCATGCACTGTAGGTCTTACAGATG
294497 TGGGAAATAA
Statistics
Matches: 307, Mismatches: 20, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
73 267 0.87
76 39 0.13
77 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (73 bp):
TTTTGAGAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCC
CGAAGGCT
Found at i:295014 original size:20 final size:20
Alignment explanation
Indices: 294977--295032 Score: 85
Period size: 20 Copynumber: 2.7 Consensus size: 20
294967 AATAAAGCTT
294977 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTG--AAGAGAATCTA
*
294999 TCATCTTTGGAGAGAATCTA
1 TCATCTTTGAAGAGAATCTA
295019 TCATCTTTGAAGAG
1 TCATCTTTGAAGAG
295033 TGCAGATGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 23 0.72
22 9 0.28
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (20 bp):
TCATCTTTGAAGAGAATCTA
Found at i:296454 original size:75 final size:75
Alignment explanation
Indices: 296314--296461 Score: 181
Period size: 75 Copynumber: 2.0 Consensus size: 75
296304 GTAAGATGAT
* * *
296314 ATGGGGTTTCAGCATACCCCAGCATTTGCTAATACAGACGTTCAAAATGCGCCAACATTCTTGAT
1 ATGGGCTTTCAGCATACCCCAGCATTTGCTAATACAGACGTTCAAAAAGCGCCAACATTCCTGAT
*
296379 TCTGATTGAA
66 TATGATTGAA
* * * *** *
296389 ATGGGCTTTCAGCATGCCCCAGTATTTGCTGATACA-ATCGTTCAAAAAGTTTCAATATTCCTGA
1 ATGGGCTTTCAGCATACCCCAGCATTTGCTAATACAGA-CGTTCAAAAAGCGCCAACATTCCTGA
296453 TTATGATTG
65 TTATGATTG
296462 GAATAGACTT
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
74 1 0.02
75 60 0.98
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.32
Consensus pattern (75 bp):
ATGGGCTTTCAGCATACCCCAGCATTTGCTAATACAGACGTTCAAAAAGCGCCAACATTCCTGAT
TATGATTGAA
Found at i:299306 original size:9 final size:9
Alignment explanation
Indices: 299292--299348 Score: 60
Period size: 9 Copynumber: 6.1 Consensus size: 9
299282 TTTGATTCAA
299292 TTTTTTCCTT
1 TTTTTTCC-T
*
299302 TTTTTTTCT
1 TTTTTTCCT
**
299311 TTTTTTTTT
1 TTTTTTCCT
*
299320 TCTTTTTTCT
1 T-TTTTTCCT
299330 TTTTTTCCT
1 TTTTTTCCT
299339 TTTTTTCCT
1 TTTTTTCCT
299348 T
1 T
299349 CTTCAAGTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
9 27 0.64
10 15 0.36
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTTCCT
Found at i:299313 original size:7 final size:7
Alignment explanation
Indices: 299303--299334 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
299293 TTTTTCCTTT
299303 TTTTTTC
1 TTTTTTC
299310 -TTTTT-
1 TTTTTTC
299315 TTTTTTC
1 TTTTTTC
299322 TTTTTTC
1 TTTTTTC
299329 TTTTTT
1 TTTTTT
299335 TCCTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
6 10 0.43
7 13 0.57
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (7 bp):
TTTTTTC
Found at i:302075 original size:7 final size:8
Alignment explanation
Indices: 302051--302075 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
302041 GCAAAGATGC
302051 AAATGAAA
1 AAATGAAA
302059 AAATGAAA
1 AAATGAAA
302067 AAATGAAA
1 AAATGAAA
302075 A
1 A
302076 TGTAAATGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
AAATGAAA
Found at i:303825 original size:20 final size:20
Alignment explanation
Indices: 303802--303848 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
303792 TTTAATTTTC
303802 AATTGATAGAGACAATTTAT
1 AATTGATAGAGACAATTTAT
**
303822 AATTGATTTAGACAATTTAT
1 AATTGATAGAGACAATTTAT
303842 AATTGAT
1 AATTGAT
303849 TTTAAAGCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.43, C:0.04, G:0.13, T:0.40
Consensus pattern (20 bp):
AATTGATAGAGACAATTTAT
Found at i:303849 original size:20 final size:20
Alignment explanation
Indices: 303811--303850 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
303801 CAATTGATAG
303811 AGACAATTTATAATTGATTT
1 AGACAATTTATAATTGATTT
303831 AGACAATTTATAATTGATTT
1 AGACAATTTATAATTGATTT
303851 TAAAGCTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (20 bp):
AGACAATTTATAATTGATTT
Found at i:304621 original size:159 final size:147
Alignment explanation
Indices: 304290--304693 Score: 406
Period size: 145 Copynumber: 2.7 Consensus size: 147
304280 AATTTATATA
*
304290 TATATAAATAAGATATTTATTTATTT-AGAAATATCAGAAAATGACTTCTAGGTACTTTAAGACA
1 TATATAAATAAGATATTTATTTATTTAAG-AATATCAGAAAATGACTTCTAGGTGCTTTAAGACA
* *
304354 ACT-TTTCTTAATATT-AAAAATAAATAAATATTAATAAAACATTTTTCTAAAAATAATTAAAAT
65 GCTCTTTCTTAATATTAAAAAATAAATAAATATTAATAAAACATTTTTCTAAAAATAATTAAAAA
*
304417 AAATTAGTATATATAATT
130 AAAATAGTATATATAATT
* *
304435 TATAAAAATAGGATATTTATTTATTTAAGAATATCAGAAAATGACTTCTAGGTGCTTTAAGACAG
1 TATATAAATAAGATATTTATTTATTTAAGAATATCAGAAAATGACTTCTAGGTGCTTTAAGACAG
* *
304500 CTCATTTCTTAATATTAAAAAATATATAAATATTAA-AATATGATTATTTTTCTAAAAAAAATAA
66 CTC-TTTCTTAATATTAAAAAATAAATAAATATTAATAA-A--A-CATTTTTCT---AAAAATAA
* * **
304564 TTGAAATAAAACAATATGTATTTTCTGGTT
123 TT-AAA-AAAA-AATA-GTA-TATATAATT
* * * * * * *
304594 TTTATAAGTAAGATATTTATTTATTTAA-AATA-CAAGAATAGGACATCTAGTTGCTTTAAGACT
1 TATATAAATAAGATATTTATTTATTTAAGAATATC-AGAAAATGACTTCTAGGTGCTTTAAGACA
* ** *
304657 GCCCTTTTCTTTGGTATTAAAAAATAAATAAACATTA
65 GCTC-TTTC-TTAATATTAAAAAATAAATAAATATTA
304694 TTATCTAAAC
Statistics
Matches: 214, Mismatches: 27, Indels: 22
0.81 0.10 0.08
Matches are distributed among these distances:
145 60 0.28
146 2 0.01
147 14 0.07
148 19 0.09
150 1 0.00
151 8 0.04
154 10 0.05
155 3 0.01
156 3 0.01
157 4 0.02
158 38 0.18
159 52 0.24
ACGTcount: A:0.45, C:0.07, G:0.08, T:0.39
Consensus pattern (147 bp):
TATATAAATAAGATATTTATTTATTTAAGAATATCAGAAAATGACTTCTAGGTGCTTTAAGACAG
CTCTTTCTTAATATTAAAAAATAAATAAATATTAATAAAACATTTTTCTAAAAATAATTAAAAAA
AAATAGTATATATAATT
Found at i:305179 original size:148 final size:148
Alignment explanation
Indices: 304894--305180 Score: 361
Period size: 148 Copynumber: 1.9 Consensus size: 148
304884 TCATATTTAT
* *
304894 ATATTTATATATTTTTTAATATTAAGAAATGGGCTGTCTTAAAGCACCTAGAAGTTCTTTTCTGA
1 ATATTTATATATTTTTTAATATTAAGAAATGAGCTGTCTTAAAGCACCTAGAAGTCCTTTTCTGA
* * * * *
304959 TATTCTTAAATAAATAAATATCCTATTTTTATAAATTATATATACTAATTTATTTTAATTATTTT
66 TATTCTTAAATAAATAAATATCCTATTTATATAAATTAAATATAATAATTTATTTAAATTATTAT
305024 TAGATAAATGTTTTATTA
131 TAGATAAATGTTTTATTA
* * * *
305042 ATATTTATTTATTTTTTAATATTAATTAAA-GAGTTGTCTTAAAGTACCTAGAAGTCCTTTTCTG
1 ATATTTATATATTTTTTAATATTAA-GAAATGAGCTGTCTTAAAGCACCTAGAAGTCCTTTTCTG
* *
305106 ATATT-TCTAAATAAATAAATATCTTATTTATATATATATAAAT-TAATAGATTT-TCTTAAAAT
65 ATATTCT-TAAATAAATAAATATCCTATTTATATAAAT-TAAATATAATA-ATTTAT-TT-AAAT
305168 TA-TATTA-ATAAAT
125 TATTATTAGATAAAT
305181 TTAAAATAAC
Statistics
Matches: 120, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
147 1 0.01
148 97 0.81
149 17 0.14
150 5 0.04
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.48
Consensus pattern (148 bp):
ATATTTATATATTTTTTAATATTAAGAAATGAGCTGTCTTAAAGCACCTAGAAGTCCTTTTCTGA
TATTCTTAAATAAATAAATATCCTATTTATATAAATTAAATATAATAATTTATTTAAATTATTAT
TAGATAAATGTTTTATTA
Found at i:305599 original size:20 final size:19
Alignment explanation
Indices: 305576--305617 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
305566 TTATTTAAAA
*
305576 AATAAAATATTTAAAATTAT
1 AATAAAA-ATTTAAAAATAT
*
305596 AATAAGAATTTAAAAATAT
1 AATAAAAATTTAAAAATAT
305615 AAT
1 AAT
305618 TGTAAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (19 bp):
AATAAAAATTTAAAAATAT
Found at i:308681 original size:2 final size:2
Alignment explanation
Indices: 308674--308709 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
308664 GATATGTTTA
308674 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
308710 TGAATTCATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:310817 original size:22 final size:21
Alignment explanation
Indices: 310788--310834 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
310778 GGTGATTTTG
310788 AAATTTATT-T-TTTAATATTAA
1 AAATTTATTATATTT-ATA-TAA
310809 AAATATTATTATATTTATATAA
1 AAAT-TTATTATATTTATATAA
310831 AAAT
1 AAAT
310835 GACTTAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
21 4 0.17
22 12 0.52
23 4 0.17
24 3 0.13
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AAATTTATTATATTTATATAA
Found at i:315340 original size:2 final size:2
Alignment explanation
Indices: 315333--315380 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
315323 CGACAAAGTC
315333 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
315375 AT AT AT
1 AT AT AT
315381 TGGAAAACAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:317047 original size:17 final size:18
Alignment explanation
Indices: 317025--317059 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
317015 GTAAGCTGCA
317025 CAAATA-TTTTTTAATTG
1 CAAATATTTTTTTAATTG
317042 CAAATATTTTTTTAATTG
1 CAAATATTTTTTTAATTG
317060 GTACAATCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.54
Consensus pattern (18 bp):
CAAATATTTTTTTAATTG
Found at i:328942 original size:13 final size:14
Alignment explanation
Indices: 328924--328955 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
328914 TTAGTGAGAC
328924 ATAATAATAATA-T
1 ATAATAATAATACT
328937 ATAATAATAATACT
1 ATAATAATAATACT
328951 ATAAT
1 ATAAT
328956 GAGATGGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (14 bp):
ATAATAATAATACT
Found at i:329168 original size:23 final size:23
Alignment explanation
Indices: 329142--329210 Score: 111
Period size: 23 Copynumber: 3.0 Consensus size: 23
329132 CACCACAGCT
*
329142 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
329165 CGTAGAATTGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
329188 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
329211 TATAAAATGT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.32, C:0.26, G:0.26, T:0.16
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:329232 original size:22 final size:23
Alignment explanation
Indices: 329207--329250 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
329197 GCACCGAAGT
* *
329207 GCCATATA-AAATGTCCACAAGG
1 GCCACATAGAAATCTCCACAAGG
*
329229 GCCACATAGAAATCTCCTCAAG
1 GCCACATAGAAATCTCCACAAG
329251 AACTATATAC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.39, C:0.27, G:0.16, T:0.18
Consensus pattern (23 bp):
GCCACATAGAAATCTCCACAAGG
Found at i:331234 original size:19 final size:19
Alignment explanation
Indices: 331207--331245 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
331197 GATAAGAGAA
*
331207 AAAATATATAAACCATATG
1 AAAAGATATAAACCATATG
* *
331226 AAAAGATATGAGCCATATG
1 AAAAGATATAAACCATATG
331245 A
1 A
331246 TATGATCTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.54, C:0.10, G:0.13, T:0.23
Consensus pattern (19 bp):
AAAAGATATAAACCATATG
Found at i:331776 original size:6 final size:6
Alignment explanation
Indices: 331767--331792 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
331757 TAATGAAATG
331767 ATATGT ATATGT ATATGT ATATGT AT
1 ATATGT ATATGT ATATGT ATATGT AT
331793 GTATTTATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (6 bp):
ATATGT
Found at i:345465 original size:20 final size:20
Alignment explanation
Indices: 345371--345699 Score: 396
Period size: 20 Copynumber: 16.4 Consensus size: 20
345361 GATTTTCCAT
* ** *
345371 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
345391 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
345411 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
345431 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
345451 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
345471 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
345491 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
345511 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
345531 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
345551 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
345571 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
345591 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
345611 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
345631 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
345651 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
345671 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
345691 AATCACAAC
1 AATCGCAAC
345700 ACTTAAATTT
Statistics
Matches: 269, Mismatches: 32, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
19 3 0.01
20 263 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:346419 original size:24 final size:24
Alignment explanation
Indices: 346380--346426 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
346370 AAATTTGGTC
346380 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
346404 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
346427 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:348930 original size:19 final size:19
Alignment explanation
Indices: 348908--349328 Score: 595
Period size: 19 Copynumber: 23.4 Consensus size: 19
348898 CGGAAAATAC
*
348908 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
348927 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
348941 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
348961 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
348975 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
348994 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
349013 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
349027 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
349046 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
349065 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
349084 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
349103 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
349122 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
349141 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
**
349160 AATCGCAA--CGGCA-G--
1 AATCGCAATGCGAAATGAA
*
349174 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
349193 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
349212 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
349231 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
349250 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
349269 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
349283 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
349302 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
349321 AATCGCAA
1 AATCGCAA
349329 CGAGATAATC
Statistics
Matches: 364, Mismatches: 12, Indels: 52
0.85 0.03 0.12
Matches are distributed among these distances:
14 46 0.13
15 1 0.00
16 18 0.05
17 16 0.04
18 2 0.01
19 268 0.74
20 13 0.04
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:349110 original size:109 final size:107
Alignment explanation
Indices: 348975--349328 Score: 570
Period size: 109 Copynumber: 3.3 Consensus size: 107
348965 GCAACGAGAG
*
348975 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGACA-G-AATCGCAATG
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGAAATCGCAATG
349037 CGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
66 CGAAATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAA
349084 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-AAATCGCAA
** *
349149 TGCGAAATGAAAATCGCAACGGCAGAATCGCAATGCGAAATTAA
64 TGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAA
349193 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-AAATCGCAA
349258 TGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAA
64 TGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAA
349302 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
349329 CGAGATAATC
Statistics
Matches: 233, Mismatches: 7, Indels: 10
0.93 0.03 0.04
Matches are distributed among these distances:
109 197 0.85
111 5 0.02
112 4 0.02
114 27 0.12
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (107 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGAAATCGCAATG
CGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAA
Found at i:349466 original size:19 final size:19
Alignment explanation
Indices: 349357--349458 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
349347 AAATTATAAA
349357 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
349376 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
349396 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
349412 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
349429 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
349448 CGCATTGCGAT
1 CGCATTGCGAT
349459 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:349584 original size:14 final size:14
Alignment explanation
Indices: 349565--349601 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
349555 CATCAATTAC
349565 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
349579 ACAAATCATCTTTT
1 ACAAATCAACTTTT
349593 ACAAATCAA
1 ACAAATCAA
349602 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:351540 original size:19 final size:19
Alignment explanation
Indices: 351500--351634 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
351490 TAGTTTACTT
* *
351500 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
351520 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
351539 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
351558 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
351572 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
351591 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
351605 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
351624 TCGCAATGCGA
1 TCGCAACGCGA
351635 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:351575 original size:14 final size:14
Alignment explanation
Indices: 351556--351612 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
351546 GCGAAATGAA
*
351556 AATCGCAACGACAG
1 AATCGCAACGAAAG
351570 AATCGCAACGCGAAATG
1 AATCGCAA--CGAAA-G
351587 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
351603 AATCGCAACG
1 AATCGCAACG
351613 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.25, G:0.21, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:351579 original size:33 final size:33
Alignment explanation
Indices: 351537--351629 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
351527 GCGAAACCAA
*
351537 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
351570 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
351603 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
351630 TGCGATTTTG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:351626 original size:52 final size:54
Alignment explanation
Indices: 351500--351634 Score: 131
Period size: 52 Copynumber: 2.5 Consensus size: 54
351490 TAGTTTACTT
*
351500 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAA
1 TCGCAAC-CGAAA-TGAAAATCGCAACGCGAAACCAAAATCGCAAC-CGAAATG-AAA
* **
351558 TCGCAA-CGACA-G--AATCGCAACGCGAAATGAAAATCGCAA-CGAAA-G-AA
1 TCGCAACCGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACCGAAATGAAA
*
351605 TCGCAACGCGAAATGAAAATCGCAATGCGA
1 TCGCAAC-CGAAATGAAAATCGCAACGCGA
351635 TTTTGGTTTC
Statistics
Matches: 66, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
47 8 0.12
49 5 0.08
50 6 0.09
52 37 0.56
56 4 0.06
58 6 0.09
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (54 bp):
TCGCAACCGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACCGAAATGAAA
Found at i:351652 original size:19 final size:19
Alignment explanation
Indices: 351630--351758 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
351620 AAAATCGCAA
351630 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
351649 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
351663 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
351682 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
351696 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
351715 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
351734 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
351754 TGCGA
1 TGCGA
351759 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:351672 original size:33 final size:33
Alignment explanation
Indices: 351630--351721 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
351620 AAAATCGCAA
351630 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
351663 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
351696 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
351722 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:352093 original size:93 final size:93
Alignment explanation
Indices: 351802--352458 Score: 1275
Period size: 93 Copynumber: 7.1 Consensus size: 93
351792 TTGAATGGAT
351802 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
351867 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
351895 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
351959 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
351987 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
352052 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
352080 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
352144 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
352172 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
352237 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
352265 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATATAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
352329 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
352357 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
352422 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
352450 AAATTTACT
1 AAATTTACT
352459 AAGCAATCTA
Statistics
Matches: 558, Mismatches: 3, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
92 275 0.49
93 283 0.51
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:352114 original size:185 final size:185
Alignment explanation
Indices: 351802--352458 Score: 1296
Period size: 185 Copynumber: 3.6 Consensus size: 185
351792 TTGAATGGAT
351802 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
351867 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
351932 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
351987 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
352052 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
352117 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
352172 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
352237 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
352302 TATATTTCACAGTGTTAAAGAATATACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
352357 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
352422 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
352459 AAGCAATCTA
Statistics
Matches: 470, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
185 470 1.00
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (185 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:354183 original size:14 final size:14
Alignment explanation
Indices: 354164--354253 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
354154 TTGAAATGAA
354164 AATCGCAACGAGAG
1 AATCGCAACGAGAG
354178 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
354195 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
354211 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
354230 AATCGCAACGAGAG
1 AATCGCAACGAGAG
354244 AATCGCAACG
1 AATCGCAACG
354254 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:354201 original size:33 final size:33
Alignment explanation
Indices: 354156--354270 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
354146 TCTTTTGGTT
354156 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
354189 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
354222 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
354255 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
354271 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:354202 original size:19 final size:18
Alignment explanation
Indices: 354163--354275 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
354153 GTTGAAATGA
354163 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
354178 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
354195 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
354211 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
354228 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
354244 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
354261 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
354276 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:354306 original size:14 final size:14
Alignment explanation
Indices: 354287--354343 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
354277 TTTGGTTTCG
354287 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
354301 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
*
354320 CGTTGCGATTCTTT
1 CGTTGCGATTCTCT
354334 CGTTGCGATT
1 CGTTGCGATT
354344 GTCATTCTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.23, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:354319 original size:33 final size:33
Alignment explanation
Indices: 354271--354363 Score: 132
Period size: 33 Copynumber: 2.8 Consensus size: 33
354261 AAAATCGCAA
**
354271 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
354304 TGCGATTTTCATTTCGCGTTGCGATTCTTTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
* *
354337 TGCGATTGTCATTCTCTCGTTGCGATT
1 TGCGATTTTCATT-TCGCGTTGCGATT
354364 TTCATTTATC
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 42 0.78
34 12 0.22
ACGTcount: A:0.09, C:0.22, G:0.24, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:354356 original size:20 final size:19
Alignment explanation
Indices: 354298--354382 Score: 90
Period size: 20 Copynumber: 4.6 Consensus size: 19
354288 GTTGCGATTC
354298 TCTCGTTGCGATTTTCATT
1 TCTCGTTGCGATTTTCATT
*
354317 TCGCGTTGCGA--TTC--T
1 TCTCGTTGCGATTTTCATT
*
354332 T-TCGTTGCGATTGTCATT
1 TCTCGTTGCGATTTTCATT
354350 CTCTCGTTGCGATTTTCATTT
1 -TCTCGTTGCGATTTTCA-TT
354371 ATCTCGTTGCGA
1 -TCTCGTTGCGA
354383 CTCTTCTGCA
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
14 8 0.15
15 2 0.04
16 2 0.04
17 3 0.06
18 1 0.02
19 11 0.20
20 14 0.26
21 13 0.24
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.47
Consensus pattern (19 bp):
TCTCGTTGCGATTTTCATT
Found at i:354504 original size:33 final size:33
Alignment explanation
Indices: 354462--354532 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
354452 AATACTAACT
*
354462 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
354495 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
354528 TGAAA
1 TGAAA
354533 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:354766 original size:22 final size:22
Alignment explanation
Indices: 354714--354768 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
354704 TGGTTGTGAG
**
354714 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
354736 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
354758 GGATTTCTTCG
1 GGATTTCTTCG
354769 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:354939 original size:20 final size:20
Alignment explanation
Indices: 354914--355106 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
354904 CTTTAAATAT
354914 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
354934 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
354956 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
354975 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
354995 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
355015 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
355035 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
355055 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
355075 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
355095 CGCGTTGCGATT
1 CGCGTTGCGATT
355107 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:355101 original size:60 final size:60
Alignment explanation
Indices: 354914--355106 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
354904 CTTTAAATAT
**
354914 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
354975 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
355035 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
355095 CGCGTTGCGATT
1 CGCGTTGCGATT
355107 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:355187 original size:20 final size:20
Alignment explanation
Indices: 355162--355213 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
355152 AAGAATCGCG
*
355162 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
355182 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
355202 TTGCGATTCTGG
1 TTGCGATTCTGG
355214 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:358640 original size:3 final size:3
Alignment explanation
Indices: 358632--358749 Score: 236
Period size: 3 Copynumber: 39.3 Consensus size: 3
358622 CGGGTTTTAA
358632 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
358680 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
358728 ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT A
358750 CCCTATCCAC
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 115 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:358820 original size:20 final size:20
Alignment explanation
Indices: 358795--358839 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
358785 CCACTCAACT
358795 TTCCACCATTCCATGTTTTA
1 TTCCACCATTCCATGTTTTA
*
358815 TTCCACCATTCCATGTTTTC
1 TTCCACCATTCCATGTTTTA
358835 TTCCA
1 TTCCA
358840 TGTTTTATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.18, C:0.33, G:0.04, T:0.44
Consensus pattern (20 bp):
TTCCACCATTCCATGTTTTA
Found at i:358885 original size:2 final size:2
Alignment explanation
Indices: 358878--358926 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
358868 TTTTCTTATG
358878 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
358920 AT AT AT A
1 AT AT AT A
358927 ATAGGCTATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:362369 original size:29 final size:28
Alignment explanation
Indices: 362337--362411 Score: 68
Period size: 29 Copynumber: 2.7 Consensus size: 28
362327 CCAATCAGAG
362337 CAAAAAG-AAAAGAGAATAAAA-AAGAGAAA
1 CAAAAAGTAAAA-AGAA-AAAACAAGA-AAA
*
362366 CAAAGAGTAAAAAGAAAAAACAAGAAAA
1 CAAAAAGTAAAAAGAAAAAACAAGAAAA
*
362394 -AAAAA-CAAAGAAGAAAAA
1 CAAAAAGTAAA-AAGAAAAA
362412 GAAAAAGCAA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
26 3 0.08
27 12 0.30
28 7 0.17
29 14 0.35
30 4 0.10
ACGTcount: A:0.77, C:0.05, G:0.15, T:0.03
Consensus pattern (28 bp):
CAAAAAGTAAAAAGAAAAAACAAGAAAA
Found at i:362394 original size:17 final size:17
Alignment explanation
Indices: 362338--362429 Score: 64
Period size: 17 Copynumber: 5.4 Consensus size: 17
362328 CAATCAGAGC
* * *
362338 AAAAAGAAAAGAGAATA
1 AAAAAGAAAAAACAAGA
*
362355 AAAAAGAGAAACAA-AGAGT
1 AAAAAGA-AAA-AACA-AGA
362374 AAAAAGAAAAAACAAGA
1 AAAAAGAAAAAACAAGA
*
362391 AAAAA-AAACAAAGAAG-
1 AAAAAGAAA-AAACAAGA
* *
362407 AAAAAGAAAAAGCAAGC
1 AAAAAGAAAAAACAAGA
362424 AAAAAG
1 AAAAAG
362430 GGACGATAAT
Statistics
Matches: 61, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
16 13 0.21
17 31 0.51
18 8 0.13
19 9 0.15
ACGTcount: A:0.76, C:0.05, G:0.16, T:0.02
Consensus pattern (17 bp):
AAAAAGAAAAAACAAGA
Found at i:362398 original size:13 final size:15
Alignment explanation
Indices: 362380--362411 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
362370 GAGTAAAAAG
362380 AAAAAAC-AAGAA-A
1 AAAAAACAAAGAAGA
362393 AAAAAACAAAGAAGA
1 AAAAAACAAAGAAGA
362408 AAAA
1 AAAA
362412 GAAAAAGCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 5 0.29
15 5 0.29
ACGTcount: A:0.84, C:0.06, G:0.09, T:0.00
Consensus pattern (15 bp):
AAAAAACAAAGAAGA
Found at i:362411 original size:33 final size:33
Alignment explanation
Indices: 362363--362428 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
362353 TAAAAAAGAG
362363 AAACAAAGAGTAAAAAGAAAAAACAAGAAAAAA
1 AAACAAAGAGTAAAAAGAAAAAACAAGAAAAAA
* *
362396 AAACAAAGAAG-AAAAAGAAAAAGCAAGCAAAAA
1 AAACAAAG-AGTAAAAAGAAAAAACAAGAAAAAA
362429 GGGACGATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.93
34 2 0.07
ACGTcount: A:0.77, C:0.08, G:0.14, T:0.02
Consensus pattern (33 bp):
AAACAAAGAGTAAAAAGAAAAAACAAGAAAAAA
Found at i:363831 original size:120 final size:120
Alignment explanation
Indices: 363668--364426 Score: 887
Period size: 120 Copynumber: 6.3 Consensus size: 120
363658 AAAACAATTC
* ** *
363668 TTGGATTTCAACTTCATGATGAAGGATATTTAATTCGATGCTCAACTTCACGACGAAGGGGCCAT
1 TTGGATTTCAACTTCACGATGAAGGATATCCAATTCGAGGCTCAACTTCACGACGAAGGGGCCAT
* * ** * * *
363733 CCACGATTTCAACTTCATGATGAATAATATCGTGTCTATCGGCAACATCCTTATA
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGTCCATCAGCAACATCCTTAGA
* **
363788 TTGGATTTCAACTTCACGATAAAGGATATCCAATTCGAGGCTCAACTTCACGACGAATAGGCCAT
1 TTGGATTTCAACTTCACGATGAAGGATATCCAATTCGAGGCTCAACTTCACGACGAAGGGGCCAT
* * *
363853 CCACAATTTCAACTTCACGACGAATGATATCGTGTCCATCACCAACATCCTTAGA
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGTCCATCAGCAACATCCTTAGA
* *
363908 TTGGATTTTAACTTCACGATGAAGGATATCCAATTCGAGGCTCAACTTCACAACGAAGGGGCCAT
1 TTGGATTTCAACTTCACGATGAAGGATATCCAATTCGAGGCTCAACTTCACGACGAAGGGGCCAT
* * * *
363973 CCATGATTTCAACTTCACGACGAAGGATATTGTGTCAATCAGCAACATCGTTAGA
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGTCCATCAGCAACATCCTTAGA
* * *
364028 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCGAGGCTCAACTTCATGACGAAGGGGCTAT
1 TTGGATTTCAACTTCACGATGAAGGATATCCAATTCGAGGCTCAACTTCACGACGAAGGGGCCAT
* ** *
364093 CCACAATTTCAACTTCACGACGAAGGATATCGTGTCCATCAATAACATCCTGAGA
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGTCCATCAGCAACATCCTTAGA
* * *
364148 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCAT
1 TTGGATTTCAACTTCACGATGAAGGATATCCAATTCGAGGCTCAACTTCACGACGAAGGGGCCAT
* * * * * * * **
364213 CCACGATTTCAACTACACAACGAAGGATATCATGCCCA-CAAGCAGCAATGC-AATCC
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGTCCATC-AGCAAC-ATCCTTA-GA
* * * * * * * *
364269 TTGGGTTTCAACTTCATGACGAAGGATATCCAATTCAAAGCTCAACATCACAACGAATGAGG-CA
1 TTGGATTTCAACTTCACGATGAAGGATATCCAATTCGAGGCTCAACTTCACGACGAA-GGGGCCA
* * * * *
364333 TCCATGATTTCAACTTCACGACGAAGGATATCGTGCCCA-CAAGTAGCAATACAACTCGAGA
65 TCCACGATTTCAACTTCACGACGAAGGATATCGTGTCCATC-AGCAAC-AT-C--CT-TAGA
* *
364394 TTGGATTTCAACTTCACGACGAATGATATCCAA
1 TTGGATTTCAACTTCACGATGAAGGATATCCAA
364427 CCCGACATGA
Statistics
Matches: 557, Mismatches: 73, Indels: 13
0.87 0.11 0.02
Matches are distributed among these distances:
119 1 0.00
120 418 0.75
121 103 0.18
122 3 0.01
124 1 0.00
125 30 0.05
126 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (120 bp):
TTGGATTTCAACTTCACGATGAAGGATATCCAATTCGAGGCTCAACTTCACGACGAAGGGGCCAT
CCACGATTTCAACTTCACGACGAAGGATATCGTGTCCATCAGCAACATCCTTAGA
Found at i:364574 original size:40 final size:41
Alignment explanation
Indices: 364435--364723 Score: 144
Period size: 46 Copynumber: 6.7 Consensus size: 41
364425 AACCCGACAT
* * *
364435 GATCTCCCTCATCACGTAGGAGCCGTGTCAAACTCTA-GATAACCA
1 GATCT-CCTCATCACGTAGGAACCGTGTC--A-TC-ACCATGACCA
* *
364480 G-TCGTCCTCATCACGTAGGAACCGTGTTATCATCCTTAAATG-GCA
1 GATC-TCCTCATCACGTAGGAACCGTGTCATCA-CC----ATGACCA
* *
364525 TG-TCGTCCTCACCACGTAGGAACTGTGTCATCACC-TGACCA
1 -GATC-TCCTCATCACGTAGGAACCGTGTCATCACCATGACCA
* * * *
364566 GATCTCCTCATCACGTAGGAGCCGTGTCAACCCCAGATAACCA
1 GATCTCCTCATCACGTAGGAACCGTGTCATCACC--ATGACCA
* * * *
364609 GCA-GTCCTCATCACGTAGGAACCGTGTTATCACCCTTAGACGACCT
1 G-ATCTCCTCATCACGTAGGAACCGTGTCATCA-CC----ATGACCA
* *
364655 G-TCATCCTCATCACGTAGGAACCGTGTCATCACC-CGACCT
1 GATC-TCCTCATCACGTAGGAACCGTGTCATCACCATGACCA
* **
364695 GATCTGCTCATCACGTAGGAGTCGTGTCA
1 GATCTCCTCATCACGTAGGAACCGTGTCA
364724 ACCCTTAGAT
Statistics
Matches: 196, Mismatches: 28, Indels: 45
0.73 0.10 0.17
Matches are distributed among these distances:
40 58 0.30
41 8 0.04
42 1 0.01
43 30 0.15
44 26 0.13
45 8 0.04
46 65 0.33
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.24
Consensus pattern (41 bp):
GATCTCCTCATCACGTAGGAACCGTGTCATCACCATGACCA
Found at i:364671 original size:46 final size:45
Alignment explanation
Indices: 364441--364689 Score: 214
Period size: 46 Copynumber: 5.7 Consensus size: 45
364431 ACATGATCTC
* * * * *
364441 CCTCATCACGTAGGAGCCGTGTCA-AACTCTAGATAACCAGTCGT
1 CCTCATCACGTAGGAACCGTGTCATCACCCTAGATGACCAGTCAT
* * * * *
364485 CCTCATCACGTAGGAACCGTGTTATCATCCTTAAATG-GCATGTCGT
1 CCTCATCACGTAGGAACCGTGTCATCA-CCCTAGATGACCA-GTCAT
* *
364531 CCTCACCACGTAGGAACTGTGTCATCA-CC----TGACCAGATC-T
1 CCTCATCACGTAGGAACCGTGTCATCACCCTAGATGACCAG-TCAT
* * *
364571 CCTCATCACGTAGGAGCCGTGTCA--ACCCCAGATAACCAG-CAGT
1 CCTCATCACGTAGGAACCGTGTCATCACCCTAGATGACCAGTCA-T
* * *
364614 CCTCATCACGTAGGAACCGTGTTATCACCCTTAGACGACCTGTCAT
1 CCTCATCACGTAGGAACCGTGTCATCACCC-TAGATGACCAGTCAT
364660 CCTCATCACGTAGGAACCGTGTCATCACCC
1 CCTCATCACGTAGGAACCGTGTCATCACCC
364690 GACCTGATCT
Statistics
Matches: 165, Mismatches: 24, Indels: 30
0.75 0.11 0.14
Matches are distributed among these distances:
38 1 0.01
39 2 0.01
40 25 0.15
41 5 0.03
43 29 0.18
44 23 0.14
45 7 0.04
46 71 0.43
47 2 0.01
ACGTcount: A:0.25, C:0.33, G:0.19, T:0.23
Consensus pattern (45 bp):
CCTCATCACGTAGGAACCGTGTCATCACCCTAGATGACCAGTCAT
Found at i:364672 original size:129 final size:129
Alignment explanation
Indices: 364426--364727 Score: 428
Period size: 129 Copynumber: 2.3 Consensus size: 129
364416 ATGATATCCA
* *
364426 ACCCGA-CATGATCTCCCTCATCACGTAGGAGCCGTGTCAAACTCTAGATAACCAGTCGTCCTCA
1 ACCCGACCA-GATCT-CCTCATCACGTAGGAGCCGTGTC-AACCCCAGATAACCAGTCGTCCTCA
* * * * *
364490 TCACGTAGGAACCGTGTTATCATCCTTAAATGGCATGTCGTCCTCACCACGTAGGAACTGTGTCA
63 TCACGTAGGAACCGTGTTATCACCCTTAAACGACATGTCATCCTCACCACGTAGGAACCGTGTCA
364555 TC
128 TC
*
364557 ACCTGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCCCAGATAACCAG-CAGTCCTCATC
1 ACCCGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCCCAGATAACCAGTC-GTCCTCATC
* * *
364621 ACGTAGGAACCGTGTTATCACCCTTAGACGACCTGTCATCCTCATCACGTAGGAACCGTGTCATC
65 ACGTAGGAACCGTGTTATCACCCTTAAACGACATGTCATCCTCACCACGTAGGAACCGTGTCATC
* * *
364686 ACCCGACCTGATCTGCTCATCACGTAGGAGTCGTGTCAACCC
1 ACCCGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCC
364728 TTAGATGACC
Statistics
Matches: 154, Mismatches: 15, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
128 1 0.01
129 118 0.77
130 23 0.15
131 10 0.06
132 2 0.01
ACGTcount: A:0.25, C:0.33, G:0.19, T:0.23
Consensus pattern (129 bp):
ACCCGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCCCAGATAACCAGTCGTCCTCATCA
CGTAGGAACCGTGTTATCACCCTTAAACGACATGTCATCCTCACCACGTAGGAACCGTGTCATC
Found at i:364683 original size:25 final size:25
Alignment explanation
Indices: 364613--364685 Score: 66
Period size: 25 Copynumber: 3.1 Consensus size: 25
364603 TAACCAGCAG
*
364613 TCCTCATCACGTAGGAACCGTGTTA
1 TCCTCATCACGTAGGAACCGTGTCA
* * *
364638 TCAC-CCTTA-G-ACG-ACC-TGTCA
1 TC-CTCATCACGTAGGAACCGTGTCA
364659 TCCTCATCACGTAGGAACCGTGTCA
1 TCCTCATCACGTAGGAACCGTGTCA
364684 TC
1 TC
364686 ACCCGACCTG
Statistics
Matches: 35, Mismatches: 7, Indels: 12
0.65 0.13 0.22
Matches are distributed among these distances:
20 1 0.03
21 9 0.26
22 4 0.11
23 4 0.11
24 4 0.11
25 12 0.34
26 1 0.03
ACGTcount: A:0.23, C:0.33, G:0.18, T:0.26
Consensus pattern (25 bp):
TCCTCATCACGTAGGAACCGTGTCA
Found at i:364930 original size:3 final size:3
Alignment explanation
Indices: 364924--364949 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
364914 TTTAAAAAAA
364924 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
364950 CCCTACCCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:365402 original size:146 final size:146
Alignment explanation
Indices: 365134--365421 Score: 342
Period size: 146 Copynumber: 2.0 Consensus size: 146
365124 TTCGTCGGTG
* * * *
365134 ATCGGGATCTCCAATCAACGTTCTGAACGCTGAAAATTTGCGCAAGGCCAACACGAACAACATAC
1 ATCGGGATCTACAATCAACGTTCCGAACGCTGAAAAGTTGCACAAGGCCAACACGAACAACATAC
* * ** * * **
365199 TAAAAAATCAGGACGATAAGACAGTGGACGACGGTGGATTGGAGAAAATAAATCCGAATGGTTTT
66 TAAAAAATCAGGACGAGAAGACAGTGGACGACGGCGGATCAGAGAAAAGAAAGCCGAACAGTTTT
*
365264 TGGCCTTTTTACAATA
131 TGGCCTTCTTACAATA
* * * *
365280 ATCGGGATCTACGATCAACGTTCCGAACGGTGAAAAGTTGTACAAGGCCAACACGGACAACATAC
1 ATCGGGATCTACAATCAACGTTCCGAACGCTGAAAAGTTGCACAAGGCCAACACGAACAACATAC
* ** ** ** *
365345 TGAAAAATCAGGACGAGCGGATGGTGGACGGTGGCGGATCAGAGAATAGAAAGCCGAACAGTTTT
66 TAAAAAATCAGGACGAGAAGACAGTGGACGACGGCGGATCAGAGAAAAGAAAGCCGAACAGTTTT
*
365410 TTGCCTTCTTAC
131 TGGCCTTCTTAC
365422 TACAAACGAA
Statistics
Matches: 116, Mismatches: 26, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
146 116 1.00
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.21
Consensus pattern (146 bp):
ATCGGGATCTACAATCAACGTTCCGAACGCTGAAAAGTTGCACAAGGCCAACACGAACAACATAC
TAAAAAATCAGGACGAGAAGACAGTGGACGACGGCGGATCAGAGAAAAGAAAGCCGAACAGTTTT
TGGCCTTCTTACAATA
Found at i:365686 original size:29 final size:28
Alignment explanation
Indices: 365654--365720 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 28
365644 CCTGAATCTC
*
365654 TGTGTTTTTCTGATTTT-GACACTTTAGTT
1 TGTGTTTTT-T-ATTTTAGACACTTAAGTT
*
365683 TGTGTTATTTTATTTTAGTCACTTAAGTT
1 TGTGTT-TTTTATTTTAGACACTTAAGTT
*
365712 TCTGTTTTT
1 TGTGTTTTT
365721 GTTATTTACG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
28 8 0.24
29 22 0.67
30 3 0.09
ACGTcount: A:0.15, C:0.09, G:0.15, T:0.61
Consensus pattern (28 bp):
TGTGTTTTTTATTTTAGACACTTAAGTT
Found at i:365728 original size:29 final size:29
Alignment explanation
Indices: 365673--365777 Score: 79
Period size: 30 Copynumber: 3.6 Consensus size: 29
365663 CTGATTTTGA
* * *
365673 CACTTTAGTTTGTGTTATT-TTATTTTAGT
1 CACTTAAGTTTCTGTTTTTGTTA-TTTAGT
365702 CACTTAAGTTTCTGTTTTTGTTATTTACGT
1 CACTTAAGTTTCTGTTTTTGTTATTTA-GT
* ** *
365732 C-CATTAAATTTCTGTTTAAGTTGTTTTAGT
1 CAC-TTAAGTTTCTGTTTTTGTT-ATTTAGT
**
365762 CTTTTAAGTTTCTGTT
1 CACTTAAGTTTCTGTT
365778 CTTACCATTT
Statistics
Matches: 62, Mismatches: 9, Indels: 9
0.77 0.11 0.11
Matches are distributed among these distances:
29 21 0.34
30 37 0.60
31 4 0.06
ACGTcount: A:0.18, C:0.10, G:0.13, T:0.58
Consensus pattern (29 bp):
CACTTAAGTTTCTGTTTTTGTTATTTAGT
Found at i:366456 original size:179 final size:178
Alignment explanation
Indices: 366148--366503 Score: 694
Period size: 179 Copynumber: 2.0 Consensus size: 178
366138 ACTCTATCCA
366148 ATTTTTTTCAAATTAATCTAAAACCCTAAATTTTCTAAAATTAAAAATCGTAACTGTTTTTAAAA
1 ATTTTTTTCAAATTAATCTAAAACCCTAAATTTTCTAAAATTAAAAATCGTAACTGTTTTTAAAA
366213 CAATAAATAATTGTTCAACCTAAAAACGGTTATGACAAATTGTACATTTTCTATTTTCACCATAT
66 CAATAAATAATTGTTCAACCTAAAAACGGTTATGACAAATTGTACATTTTCTATTTTCACCATAT
366278 AGTTCATTTTCTTTTGATTTTCTAATCTTTGAAGATTCCTAATTTTCC
131 AGTTCATTTTCTTTTGATTTTCTAATCTTTGAAGATTCCTAATTTTCC
366326 ATTTTTTTCCAAATTAATCTAAAACCCTAAATTTTCTAAAATTAAAAATCGTAACTGTTTTTAAA
1 ATTTTTTT-CAAATTAATCTAAAACCCTAAATTTTCTAAAATTAAAAATCGTAACTGTTTTTAAA
*
366391 ACAATAAATAATTGTTCCACCTAAAAACGGTTATGACAAATTGTACATTTTCTATTTTCACCATA
65 ACAATAAATAATTGTTCAACCTAAAAACGGTTATGACAAATTGTACATTTTCTATTTTCACCATA
366456 TAGTTCATTTTCTTTTGATTTTCTAATCTTTGAAGATTCCTAATTTTC
130 TAGTTCATTTTCTTTTGATTTTCTAATCTTTGAAGATTCCTAATTTTC
366504 TTATGAACAT
Statistics
Matches: 176, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
178 8 0.05
179 168 0.95
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.43
Consensus pattern (178 bp):
ATTTTTTTCAAATTAATCTAAAACCCTAAATTTTCTAAAATTAAAAATCGTAACTGTTTTTAAAA
CAATAAATAATTGTTCAACCTAAAAACGGTTATGACAAATTGTACATTTTCTATTTTCACCATAT
AGTTCATTTTCTTTTGATTTTCTAATCTTTGAAGATTCCTAATTTTCC
Found at i:370814 original size:96 final size:91
Alignment explanation
Indices: 370705--370884 Score: 234
Period size: 96 Copynumber: 1.9 Consensus size: 91
370695 AAAAAATAGA
* * *
370705 AAAAACTTGGTTAAATTTAATTCAAAATTAAATGAATAAATAAGAGGAATGAGAAAAGATGGTAA
1 AAAAACTTGGTTAAATTTAATTCAAAAATAAATGAATAAATAAGA-GAA--ACAAAAAAT-GTAA
*
370770 AAAACTAAGCATTTTATGAAATTATAAATAT
62 AAAACTAA-AATTTTATGAAATTATAAATAT
* * * * *
370801 AAAAAGTTTGTTAAATTTAATTCAAAAATGAATGAATTAATAAGAGAAACAAAAAATGTCAAAAA
1 AAAAACTTGGTTAAATTTAATTCAAAAATAAATGAATAAATAAGAGAAACAAAAAATGTAAAAAA
370866 CTAAAATTTTATGAAATTA
66 CTAAAATTTTATGAAATTA
370885 CAAAAATTAG
Statistics
Matches: 75, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
91 14 0.19
92 11 0.15
93 7 0.09
95 3 0.04
96 40 0.53
ACGTcount: A:0.54, C:0.04, G:0.12, T:0.29
Consensus pattern (91 bp):
AAAAACTTGGTTAAATTTAATTCAAAAATAAATGAATAAATAAGAGAAACAAAAAATGTAAAAAA
CTAAAATTTTATGAAATTATAAATAT
Found at i:370917 original size:28 final size:29
Alignment explanation
Indices: 370886--370952 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
370876 ATGAAATTAC
* *
370886 AAAAATTAGGA-CCCTAATTATAAATATA
1 AAAAATTAGGAGCCCTAATTACAAATACA
* *
370914 AAAAATTAAGAGTCCTAATTACAAATACA
1 AAAAATTAGGAGCCCTAATTACAAATACA
*
370943 AAAAAATAGG
1 AAAAATTAGG
370953 GGCCTGAGCA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 10 0.31
29 22 0.69
ACGTcount: A:0.57, C:0.10, G:0.09, T:0.24
Consensus pattern (29 bp):
AAAAATTAGGAGCCCTAATTACAAATACA
Found at i:373023 original size:17 final size:17
Alignment explanation
Indices: 373001--373039 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
372991 ACCCTAAAAA
*
373001 AAATAAACA-AAATGAAT
1 AAATAAA-ATAAATAAAT
373018 AAATAAAATAAATAAAT
1 AAATAAAATAAATAAAT
373035 AAATA
1 AAATA
373040 CAATGTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (17 bp):
AAATAAAATAAATAAAT
Done.