Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold321
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: 1060354
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
File 2 of 6
Found at i:179717 original size:64 final size:66
Alignment explanation
Indices: 179584--179709 Score: 211
Period size: 66 Copynumber: 1.9 Consensus size: 66
179574 ATTAAAAACA
*
179584 TAAAAAGATATAGATATTTTTATTTAATATTTTTTATAATTATTTTTATTTATTTTGTATAAAAT
1 TAAAAAGATATAGATATTTTTATTCAATATTTTTTATAATTATTTTTATTTATTTTGTATAAAAT
179649 T
66 T
* *
179650 TAAAAATATATAGATATTTTTATTCGATATTTTTTATAATT-TTTTTATTTATTTT-TATAA
1 TAAAAAGATATAGATATTTTTATTCAATATTTTTTATAATTATTTTTATTTATTTTGTATAA
179710 TTTTTAAATT
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
64 5 0.09
65 14 0.25
66 38 0.67
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.59
Consensus pattern (66 bp):
TAAAAAGATATAGATATTTTTATTCAATATTTTTTATAATTATTTTTATTTATTTTGTATAAAAT
T
Found at i:179860 original size:2 final size:2
Alignment explanation
Indices: 179853--179882 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
179843 TTAAAGTAAC
179853 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
179883 CATGTTGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:180174 original size:30 final size:27
Alignment explanation
Indices: 180131--180222 Score: 73
Period size: 28 Copynumber: 3.4 Consensus size: 27
180121 TTTAACTTAG
*
180131 TAATT-TATATTAAAAATAATATTATT
1 TAATTATAAATTAAAAATAATATTATT
*
180157 TAATTAAATTAAATTAAATAT-ATATTA-T
1 TAATT--A-TAAATTAAAAATAATATTATT
* * *
180185 AAATTATAAATTATAATTAATATTTATT
1 TAATTATAAATTAAAAATAATA-TTATT
*
180213 TAATTTTAAA
1 TAATTATAAA
180223 ATTATTTTTT
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
25 9 0.18
26 9 0.18
27 3 0.06
28 14 0.27
29 6 0.12
30 10 0.20
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
TAATTATAAATTAAAAATAATATTATT
Found at i:181689 original size:77 final size:77
Alignment explanation
Indices: 181562--181716 Score: 310
Period size: 77 Copynumber: 2.0 Consensus size: 77
181552 TGAGCAGAGT
181562 GAAACTGAATTGCTTTCACACTCGAGCAGACCTCCTGCTGAAGTTGCATCCGTGGAAGGTGGAGA
1 GAAACTGAATTGCTTTCACACTCGAGCAGACCTCCTGCTGAAGTTGCATCCGTGGAAGGTGGAGA
181627 AGAGGTTGCGCA
66 AGAGGTTGCGCA
181639 GAAACTGAATTGCTTTCACACTCGAGCAGACCTCCTGCTGAAGTTGCATCCGTGGAAGGTGGAGA
1 GAAACTGAATTGCTTTCACACTCGAGCAGACCTCCTGCTGAAGTTGCATCCGTGGAAGGTGGAGA
181704 AGAGGTTGCGCA
66 AGAGGTTGCGCA
181716 G
1 G
181717 GTGGCTGGAA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 78 1.00
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.22
Consensus pattern (77 bp):
GAAACTGAATTGCTTTCACACTCGAGCAGACCTCCTGCTGAAGTTGCATCCGTGGAAGGTGGAGA
AGAGGTTGCGCA
Found at i:183988 original size:63 final size:62
Alignment explanation
Indices: 183905--184150 Score: 237
Period size: 63 Copynumber: 3.9 Consensus size: 62
183895 AGTAATCAGA
* ** * *
183905 ATAATAGAGTAACTAAAGAATTGCGACA-CTGCATTCAACTTATGACATGAAAGGAAAGACAGC
1 ATAATAGAGTAACTAAAGAATCGC-A-AGCTGTGTTCATCTTATGACATGTAAGGAAAGACAGC
* * * *
183968 ATAATAAAGTAGCTAAAGAATCGCAAAGTTGTGTTCATCTTTTGACATGTAAGGAAAGACAGC
1 ATAATAGAGTAACTAAAGAATCGC-AAGCTGTGTTCATCTTATGACATGTAAGGAAAGACAGC
* * * * *
184031 GTAATAGAGAAACTAAGGAATCGCTAAGCTGTGTTCATCTTCTGACATGTAAGGAAAGACCGC
1 ATAATAGAGTAACTAAAGAATCGC-AAGCTGTGTTCATCTTATGACATGTAAGGAAAGACAGC
* * * * * * *
184094 ATAAT--AGTCACTAAGGAATTGCCAAGCTATGATCATCTTATGAAACGTAAGGAAAGA
1 ATAATAGAGTAACTAAAGAATCG-CAAGCTGTGTTCATCTTATGACATGTAAGGAAAGA
184151 TTGTGCATAC
Statistics
Matches: 153, Mismatches: 28, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
61 42 0.27
62 2 0.01
63 109 0.71
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.24
Consensus pattern (62 bp):
ATAATAGAGTAACTAAAGAATCGCAAGCTGTGTTCATCTTATGACATGTAAGGAAAGACAGC
Found at i:186264 original size:18 final size:17
Alignment explanation
Indices: 186230--186272 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
186220 TATATGATCG
*
186230 ATATAAAAAATTATAAA
1 ATATAATAAATTATAAA
186247 ATATAATAAATATATAAA
1 ATATAATAAAT-TATAAA
*
186265 TTATAATA
1 ATATAATA
186273 TATAATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
ATATAATAAATTATAAA
Found at i:186290 original size:12 final size:13
Alignment explanation
Indices: 186253--186292 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
186243 TAAAATATAA
*
186253 TAAATATATAAAT
1 TAAATATATAATT
186266 TATAATATATAATT
1 TA-AATATATAATT
186280 TAAATAT-TAATT
1 TAAATATATAATT
186292 T
1 T
186293 TTATTTATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 6 0.24
13 7 0.28
14 12 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TAAATATATAATT
Found at i:187087 original size:2 final size:2
Alignment explanation
Indices: 187080--187105 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
187070 CAGAAGATAC
187080 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
187106 CAAAATAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:189720 original size:26 final size:28
Alignment explanation
Indices: 189691--189762 Score: 78
Period size: 26 Copynumber: 2.7 Consensus size: 28
189681 ACAAGTCATT
189691 TTAAAATTAATTTAATTTATTT-AAA-G
1 TTAAAATTAATTTAATTTATTTAAAATG
* * * * *
189717 TTAAATTTAAATTAAATAATTTAAAATT
1 TTAAAATTAATTTAATTTATTTAAAATG
189745 TTAAAA-TAATTTAATTTA
1 TTAAAATTAATTTAATTTA
189763 AATTAAATTT
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
26 18 0.51
27 12 0.34
28 5 0.14
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (28 bp):
TTAAAATTAATTTAATTTATTTAAAATG
Found at i:191427 original size:3 final size:3
Alignment explanation
Indices: 191421--191455 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
191411 AAAAAAAAAA
191421 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
191456 CTTAGAACCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:191909 original size:2 final size:2
Alignment explanation
Indices: 191902--191940 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
191892 AAATCACAAA
191902 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
191941 TATATATATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:194901 original size:5 final size:5
Alignment explanation
Indices: 194880--194914 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
194870 ACCTTATTTA
*
194880 AAAAT AACAAA AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AA-AAT AAAAT AAAAT AAAAT AAAAT AAAA
194915 AGTATGCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 23 0.85
6 4 0.15
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.14
Consensus pattern (5 bp):
AAAAT
Found at i:196654 original size:4 final size:4
Alignment explanation
Indices: 196645--196669 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
196635 ATATATGGTA
196645 ATGG ATGG ATGG ATGG ATGG ATGG A
1 ATGG ATGG ATGG ATGG ATGG ATGG A
196670 ATTGGTGCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.48, T:0.24
Consensus pattern (4 bp):
ATGG
Found at i:197143 original size:17 final size:16
Alignment explanation
Indices: 197110--197180 Score: 58
Period size: 17 Copynumber: 4.4 Consensus size: 16
197100 TGTATTATAA
*
197110 TTATATTTAAATTATT
1 TTATATTTAAATAATT
197126 TTATATTTAAATAAATT
1 TTATATTTAAAT-AATT
* *
197143 TAATAAATT-AATAA-T
1 TTAT-ATTTAAATAATT
197158 TTATATTATATAA-AATT
1 TTATATT-TA-AATAATT
197175 TTATAT
1 TTATAT
197181 ATTTATATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
14 2 0.05
15 5 0.11
16 16 0.36
17 18 0.41
18 3 0.07
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTATATTTAAATAATT
Found at i:197144 original size:16 final size:16
Alignment explanation
Indices: 197110--197144 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
197100 TGTATTATAA
* *
197110 TTATATTTAAATTATT
1 TTATATTTAAATAAAT
197126 TTATATTTAAATAAAT
1 TTATATTTAAATAAAT
197142 TTA
1 TTA
197145 ATAAATTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTATATTTAAATAAAT
Found at i:201317 original size:19 final size:17
Alignment explanation
Indices: 201287--201351 Score: 53
Period size: 18 Copynumber: 3.6 Consensus size: 17
201277 TTTAAAAAAA
*
201287 TTTAATAAAAATAATAT
1 TTTAATATAAATAATAT
*
201304 ATTTAAATATAAATACT-T
1 -TTT-AATATAAATAATAT
201322 TTTAATAATTAAATAA-AT
1 TTTAAT-A-TAAATAATAT
201340 TTTAAATATAAA
1 TTT-AATATAAA
201352 ACTTTTAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
16 3 0.08
17 8 0.21
18 15 0.38
19 13 0.33
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
TTTAATATAAATAATAT
Found at i:201363 original size:33 final size:36
Alignment explanation
Indices: 201287--201376 Score: 120
Period size: 35 Copynumber: 2.6 Consensus size: 36
201277 TTTAAAAAAA
201287 TTTAATAA-AAATAATATATTTAAATATAAATACTT
1 TTTAATAATAAATAATATATTTAAATATAAATACTT
201322 TTTAATAATTAAATAA-AT-TTTAAATATAAA-AC-T
1 TTTAATAA-TAAATAATATATTTAAATATAAATACTT
201355 TTTAATAATAATATAATA-ATTT
1 TTTAATAATAA-ATAATATATTT
201377 TTATTTAATA
Statistics
Matches: 50, Mismatches: 0, Indels: 11
0.82 0.00 0.18
Matches are distributed among these distances:
32 3 0.06
33 13 0.26
34 6 0.12
35 20 0.40
36 2 0.04
37 6 0.12
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (36 bp):
TTTAATAATAAATAATATATTTAAATATAAATACTT
Found at i:201373 original size:36 final size:37
Alignment explanation
Indices: 201287--201379 Score: 110
Period size: 36 Copynumber: 2.7 Consensus size: 37
201277 TTTAAAAAAA
*
201287 TTTAATAA-AA-ATAATATA-TTTAAATATAAATACT
1 TTTAATAATAATATAATAAATTTTAAATATAAATACT
201321 TTT--TAATAAT-TAAATAAATTTTAAATATAAA-ACT
1 TTTAATAATAATAT-AATAAATTTTAAATATAAATACT
*
201355 TTTAATAATAATATAATAATTTTTA
1 TTTAATAATAATATAATAAATTTTA
201380 TTTAATAGTT
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
32 3 0.06
33 3 0.06
34 14 0.28
35 12 0.24
36 17 0.34
37 1 0.02
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (37 bp):
TTTAATAATAATATAATAAATTTTAAATATAAATACT
Found at i:201644 original size:2 final size:2
Alignment explanation
Indices: 201637--201662 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
201627 CCACTCTCCA
201637 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
201663 GAAAATCTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:203526 original size:18 final size:18
Alignment explanation
Indices: 203503--203550 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
203493 ACAGGGAGTC
*
203503 TTTTCTCTTTAGTTATTT
1 TTTTCTCTTTAGTGATTT
203521 TTTTCTCTTTCAGTGATTT
1 TTTTCTCTTT-AGTGATTT
* *
203540 CTTTCCCTTTA
1 TTTTCTCTTTA
203551 ACTTTAGCAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 11 0.42
19 15 0.58
ACGTcount: A:0.10, C:0.19, G:0.06, T:0.65
Consensus pattern (18 bp):
TTTTCTCTTTAGTGATTT
Found at i:205520 original size:16 final size:16
Alignment explanation
Indices: 205499--205545 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
205489 TTTTAGTATA
205499 TAATATTTATATAATT
1 TAATATTTATATAATT
205515 TAATATGTTA-ATAATT
1 TAATAT-TTATATAATT
*
205531 T-ATA-TTATATTATT
1 TAATATTTATATAATT
205545 T
1 T
205546 TTAAAATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
13 3 0.11
14 6 0.21
15 3 0.11
16 13 0.46
17 3 0.11
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (16 bp):
TAATATTTATATAATT
Found at i:205951 original size:15 final size:17
Alignment explanation
Indices: 205915--205955 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
205905 TTTTCACTAA
205915 TTAAAAATTTTTATATTT
1 TTAAAAA-TTTTATATTT
205933 TTAAAAATTTTA-A-TT
1 TTAAAAATTTTATATTT
205948 TTAAAAAT
1 TTAAAAAT
205956 ATATAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 10 0.43
16 1 0.04
17 5 0.22
18 7 0.30
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTAAAAATTTTATATTT
Found at i:207161 original size:20 final size:20
Alignment explanation
Indices: 207117--207154 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
207107 GAATTGAAAA
207117 AAAATTTAAATATAAATAAT
1 AAAATTTAAATATAAATAAT
*
207137 TAAATTTGAAAT-TAAATA
1 AAAATTT-AAATATAAATA
207155 TGAAAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (20 bp):
AAAATTTAAATATAAATAAT
Found at i:207622 original size:34 final size:34
Alignment explanation
Indices: 207558--207740 Score: 251
Period size: 34 Copynumber: 5.4 Consensus size: 34
207548 TTATCAAATC
* *
207558 TGTTGATTAAAT-GGTGATTTGGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
207591 TGTTGACTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
207625 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * * *
207659 TATTGATTAAATTGGTGATTTGGTGGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
207693 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
207727 TGTTGATTAAATGG
1 TGTTGATTAAATGG
207741 TGGTTTTTAC
Statistics
Matches: 130, Mismatches: 19, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
33 11 0.08
34 119 0.92
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:212218 original size:34 final size:34
Alignment explanation
Indices: 212152--212336 Score: 264
Period size: 34 Copynumber: 5.5 Consensus size: 34
212142 AAGTGGGAGA
* *
212152 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
212185 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
212219 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
212253 ATTATTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
212287 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
212321 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
212337 TGGTTTTTAC
Statistics
Matches: 134, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 13 0.10
34 121 0.90
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:213202 original size:2 final size:2
Alignment explanation
Indices: 213148--213184 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
213138 TTATATTTAC
213148 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
213185 GATTCATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:215323 original size:13 final size:13
Alignment explanation
Indices: 215301--215350 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
215291 CTTAAGTTTG
* *
215301 TATATGATATAAT
1 TATATTATATAAA
215314 TATATTATATAAA
1 TATATTATATAAA
*
215327 TATAATATATAAA
1 TATATTATATAAA
*
215340 AATA-TATATAA
1 TATATTATATAA
215351 TATTATATGA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
12 7 0.21
13 26 0.79
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (13 bp):
TATATTATATAAA
Found at i:215331 original size:19 final size:19
Alignment explanation
Indices: 215307--215358 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 19
215297 TTTGTATATG
215307 ATATAATTATATTATATAA
1 ATATAATTATATTATATAA
215326 ATATAA-TATA-TA-A-AA
1 ATATAATTATATTATATAA
*
215341 ATATATATAATATTATAT
1 ATATA-ATTATATTATAT
215359 GAAAAAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 9
0.73 0.03 0.24
Matches are distributed among these distances:
15 7 0.26
16 2 0.07
17 5 0.19
18 6 0.22
19 7 0.26
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATATAATTATATTATATAA
Found at i:215365 original size:25 final size:23
Alignment explanation
Indices: 215319--215377 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 23
215309 ATAATTATAT
*
215319 TATATA-AATATAATATATAAAAA
1 TATATATAATATTATATA-AAAAA
215342 TATATATAATATTATATGAAAAAA
1 TATATATAATATTATAT-AAAAAA
215366 TA-ATATAA-ATTA
1 TATATATAATATTA
215378 AATGCATATA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
22 4 0.12
23 12 0.36
24 16 0.48
25 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (23 bp):
TATATATAATATTATATAAAAAA
Found at i:216134 original size:15 final size:15
Alignment explanation
Indices: 216117--216261 Score: 83
Period size: 15 Copynumber: 9.7 Consensus size: 15
216107 CCCGTTAGCT
*
216117 CTCCACCACCGGCTT
1 CTCCACCACCGGCTA
* *
216132 CTCCTCCCCCGGCTA
1 CTCCACCACCGGCTA
* * *
216147 CTCCTCCTCCAGCTA
1 CTCCACCACCGGCTA
* * *
216162 CTCCACCTCCCGCCA
1 CTCCACCACCGGCTA
* *
216177 CTCCTCCACCGGCTT
1 CTCCACCACCGGCTA
* * *
216192 CTCCACCTCCCGCCA
1 CTCCACCACCGGCTA
* * *
216207 CCCCACCTCCTGCTA
1 CTCCACCACCGGCTA
* *
216222 CTCCTCCACCGGCAA
1 CTCCACCACCGGCTA
* * *
216237 CTCCTCCTCCAGCTA
1 CTCCACCACCGGCTA
*
216252 CCCCACCACC
1 CTCCACCACC
216262 TGCTCCTTTG
Statistics
Matches: 98, Mismatches: 32, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
15 98 1.00
ACGTcount: A:0.13, C:0.59, G:0.09, T:0.19
Consensus pattern (15 bp):
CTCCACCACCGGCTA
Found at i:216182 original size:30 final size:30
Alignment explanation
Indices: 216146--216258 Score: 127
Period size: 30 Copynumber: 3.8 Consensus size: 30
216136 TCCCCCGGCT
216146 ACTCCTCCTCCAGCTACTCCACCTCCCGCC
1 ACTCCTCCTCCAGCTACTCCACCTCCCGCC
* * *
216176 ACTCCTCCACCGGCTTCTCCACCTCCCGCC
1 ACTCCTCCTCCAGCTACTCCACCTCCCGCC
* * * * * * *
216206 ACCCCACCTCCTGCTACTCCTCCACCGGCA
1 ACTCCTCCTCCAGCTACTCCACCTCCCGCC
*
216236 ACTCCTCCTCCAGCTACCCCACC
1 ACTCCTCCTCCAGCTACTCCACC
216259 ACCTGCTCCT
Statistics
Matches: 66, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 66 1.00
ACGTcount: A:0.14, C:0.59, G:0.08, T:0.19
Consensus pattern (30 bp):
ACTCCTCCTCCAGCTACTCCACCTCCCGCC
Found at i:216264 original size:45 final size:45
Alignment explanation
Indices: 216119--216265 Score: 177
Period size: 45 Copynumber: 3.3 Consensus size: 45
216109 CGTTAGCTCT
* * * *
216119 CCACCACCGGCTTCTCCTCCCCCGGCTACTCCTCCTCCAGCTACT
1 CCACCACCTGCTACTCCTCCACCGGCTACTCCTCCTCCAGCTACC
* * * * * * *
216164 CCACCTCCCGCCACTCCTCCACCGGCTTCTCCACCTCCCGCCACC
1 CCACCACCTGCTACTCCTCCACCGGCTACTCCTCCTCCAGCTACC
* *
216209 CCACCTCCTGCTACTCCTCCACCGGCAACTCCTCCTCCAGCTACC
1 CCACCACCTGCTACTCCTCCACCGGCTACTCCTCCTCCAGCTACC
216254 CCACCACCTGCT
1 CCACCACCTGCT
216266 CCTTTGGCTT
Statistics
Matches: 84, Mismatches: 18, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 84 1.00
ACGTcount: A:0.13, C:0.59, G:0.10, T:0.19
Consensus pattern (45 bp):
CCACCACCTGCTACTCCTCCACCGGCTACTCCTCCTCCAGCTACC
Found at i:232956 original size:2 final size:2
Alignment explanation
Indices: 232949--232985 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
232939 GCACTCCCAG
232949 AT AT AT AT AT AT AT AT AT AT AT A- 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
232986 CTAAATTCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:237126 original size:2 final size:2
Alignment explanation
Indices: 237119--237155 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
237109 CCATGCCAGA
*
237119 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
237156 GATTACCTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:242459 original size:14 final size:14
Alignment explanation
Indices: 242440--242487 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
242430 TAAATTTATT
242440 TATTTTTATATAAA
1 TATTTTTATATAAA
242454 TATTTTTA-ATAAA
1 TATTTTTATATAAA
*
242467 -A--TTTAAATAAA
1 TATTTTTATATAAA
242478 TATATTTTAT
1 TAT-TTTTAT
242488 TATTTAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
10 4 0.14
11 5 0.18
12 2 0.07
13 5 0.18
14 8 0.29
15 4 0.14
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TATTTTTATATAAA
Found at i:242461 original size:24 final size:23
Alignment explanation
Indices: 242421--242492 Score: 63
Period size: 24 Copynumber: 3.0 Consensus size: 23
242411 TAAAGGAAAA
**
242421 TTAAATAAATAAATTTATTTATTT
1 TTAAATAAATATTTTTA-TTATTT
* * **
242445 TTATATAAATATTTTTAATAAAAT
1 TTAAATAAATATTTTT-ATTATTT
242469 TTAAATAAATATATTTTATTATTT
1 TTAAATAAATAT-TTTTATTATTT
242493 AAATAATAAT
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
24 31 0.86
25 5 0.14
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TTAAATAAATATTTTTATTATTT
Found at i:244414 original size:16 final size:16
Alignment explanation
Indices: 244393--244444 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
244383 TTTTATTAGT
244393 TATTTATTAAATTTAA
1 TATTTATTAAATTTAA
*
244409 TATTTATTAAATATAA
1 TATTTATTAAATTTAA
*
244425 TA-TTA-TATATTTAA
1 TATTTATTAAATTTAA
244439 TATTTA
1 TATTTA
244445 ATTTTTTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
14 9 0.28
15 6 0.19
16 17 0.53
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TATTTATTAAATTTAA
Found at i:245811 original size:21 final size:19
Alignment explanation
Indices: 245749--245818 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 19
245739 ATAATAAAAT
* * *
245749 TTAAACATATATAATTATA
1 TTAAAAATATATTATTAAA
*
245768 TTAAAAATTCTATTATTAAA
1 TTAAAAA-TATATTATTAAA
*
245788 TTAAATATATATTATTTAAAA
1 TTAAAAATATATTA-TT-AAA
245809 TTAAAAATAT
1 TTAAAAATAT
245819 TTAAATAAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
19 12 0.29
20 17 0.41
21 12 0.29
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (19 bp):
TTAAAAATATATTATTAAA
Found at i:245819 original size:19 final size:20
Alignment explanation
Indices: 245767--245819 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
245757 ATATAATTAT
*
245767 ATTAAAAAT-TCTATTATTAA
1 ATTAAAAATAT-TATTATAAA
245787 ATTAAATATATATTATT-TAAA
1 ATTAAA-A-ATATTATTATAAA
245808 ATTAAAAATATT
1 ATTAAAAATATT
245820 TAAATAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
19 5 0.17
20 7 0.24
21 10 0.34
22 6 0.21
23 1 0.03
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTAAAAATATTATTATAAA
Found at i:246379 original size:21 final size:21
Alignment explanation
Indices: 246355--246404 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
246345 TCATCAATAA
*
246355 TCATCATTATC-ATTGTCATCT
1 TCATCATTATCGATT-TCATAT
246376 TCATCATTATCGATTTCATAT
1 TCATCATTATCGATTTCATAT
*
246397 TGATCATT
1 TCATCATT
246405 GTCAAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.26, C:0.20, G:0.06, T:0.48
Consensus pattern (21 bp):
TCATCATTATCGATTTCATAT
Found at i:246698 original size:2 final size:2
Alignment explanation
Indices: 246681--246748 Score: 59
Period size: 2 Copynumber: 34.5 Consensus size: 2
246671 AAAGTCGTTT
* * * ** *
246681 TA TA TGA TA AA TA TA TA TG T- TG TA TA TA TA TA CG TA TG TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
246723 TA TA -A TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
246749 TTATGTTGAT
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
1 2 0.04
2 49 0.92
3 2 0.04
ACGTcount: A:0.44, C:0.01, G:0.07, T:0.47
Consensus pattern (2 bp):
TA
Found at i:246732 original size:21 final size:21
Alignment explanation
Indices: 246706--246747 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
246696 TATGTTGTAT
* *
246706 ATATATACGTATGTATATATA
1 ATATATACATATATATATATA
*
246727 ATATATATATATATATATATA
1 ATATATACATATATATATATA
246748 TTTATGTTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (21 bp):
ATATATACATATATATATATA
Found at i:250964 original size:14 final size:13
Alignment explanation
Indices: 250903--250965 Score: 51
Period size: 14 Copynumber: 4.8 Consensus size: 13
250893 CCTCGTCCAC
250903 TATTGTTTAATT-T
1 TATT-TTTAATTAT
*
250916 TA-TTTTAA-TGT
1 TATTTTTAATTAT
250927 TATTTTTATATTAT
1 TATTTTTA-ATTAT
*
250941 ATAATTTTAATTAT
1 -TATTTTTAATTAT
250955 TATTTATTAAT
1 TATTT-TTAAT
250966 AAAAATATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
10 1 0.02
11 8 0.20
12 6 0.15
13 7 0.17
14 12 0.29
15 7 0.17
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (13 bp):
TATTTTTAATTAT
Found at i:251001 original size:25 final size:25
Alignment explanation
Indices: 250939--251021 Score: 62
Period size: 25 Copynumber: 3.3 Consensus size: 25
250929 TTTTTATATT
*
250939 ATATAATTTTAATTATTATTTATTA
1 ATATAATTTTAATTATTATTTATCA
* * *
250964 ATAAAAATATAATT-TT-TTGTCATCA
1 ATATAATTTTAATTATTATT-T-ATCA
* * *
250989 ATATAATTTTAATAATTAATTTTTTA
1 ATATAATTTTAATTATT-ATTTATCA
251015 ATATAAT
1 ATATAAT
251022 ATAATTTTGA
Statistics
Matches: 43, Mismatches: 10, Indels: 9
0.69 0.16 0.15
Matches are distributed among these distances:
23 2 0.05
24 3 0.07
25 24 0.56
26 11 0.26
27 1 0.02
28 2 0.05
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.53
Consensus pattern (25 bp):
ATATAATTTTAATTATTATTTATCA
Found at i:251071 original size:29 final size:29
Alignment explanation
Indices: 250988--251071 Score: 82
Period size: 28 Copynumber: 2.9 Consensus size: 29
250978 TTTTGTCATC
* * *
250988 AATATAATTTTAATAATTAATTTTTTAATAT
1 AATATAATTTT--TAATTTATATTTTAACAT
* *
251019 AATATAATTTTGAATTTTTA-TTTAACAT
1 AATATAATTTTTAATTTATATTTTAACAT
251047 AA-ATATATTTTTAATTTATATTTTA
1 AATATA-ATTTTTAATTTATATTTTA
251072 TTATTTAATA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
27 3 0.07
28 21 0.48
29 9 0.20
31 11 0.25
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (29 bp):
AATATAATTTTTAATTTATATTTTAACAT
Found at i:252836 original size:2 final size:2
Alignment explanation
Indices: 252829--252856 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
252819 GATTCCTATG
252829 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
252857 GTAAGTCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:260740 original size:2 final size:2
Alignment explanation
Indices: 260733--260777 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
260723 ACACGCATTA
260733 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
260775 AG A
1 AG A
260778 TTGAAAGTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:262908 original size:18 final size:17
Alignment explanation
Indices: 262887--262928 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
262877 TTTAGATACT
*
262887 AATAAATATTTTATTTAA
1 AATAAATAATTTA-TTAA
262905 AATAAA-AATTTATTAA
1 AATAAATAATTTATTAA
262921 ATATAAAT
1 A-ATAAAT
262929 TAAAAGTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 5 0.24
17 10 0.48
18 6 0.29
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AATAAATAATTTATTAA
Found at i:264811 original size:18 final size:17
Alignment explanation
Indices: 264790--264831 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
264780 TTTAGATACT
*
264790 AATAAATATTTTATTTAA
1 AATAAATAATTTA-TTAA
264808 AATAAA-AATTTATTAA
1 AATAAATAATTTATTAA
264824 ATATAAAT
1 A-ATAAAT
264832 TAAAAGTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 5 0.24
17 10 0.48
18 6 0.29
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AATAAATAATTTATTAA
Found at i:269165 original size:20 final size:20
Alignment explanation
Indices: 269137--269175 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
269127 TCTGTTGTAC
*
269137 TTTATTGAC-TATAAGAAAAT
1 TTTAATGACATATAA-AAAAT
269157 TTTAATGACATATAAAAAA
1 TTTAATGACATATAAAAAA
269176 CAAAGAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.51, C:0.05, G:0.08, T:0.36
Consensus pattern (20 bp):
TTTAATGACATATAAAAAAT
Found at i:277535 original size:6 final size:6
Alignment explanation
Indices: 277503--277533 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
277493 TGATCCAATC
*
277503 CGAAGT CGAAGT CGAAGT CGAAGT CAAAGT C
1 CGAAGT CGAAGT CGAAGT CGAAGT CGAAGT C
277534 AATCAGGGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.35, C:0.19, G:0.29, T:0.16
Consensus pattern (6 bp):
CGAAGT
Found at i:280021 original size:222 final size:221
Alignment explanation
Indices: 279636--280074 Score: 797
Period size: 222 Copynumber: 2.0 Consensus size: 221
279626 TAGTAACAGC
279636 TGAGAACAAGATAACCTGTAAAAAATATATAGCAGTAAGCTAGCAGAGATCAAGAGCAGCAAATT
1 TGAGAACAAGATAACCTGTAAAAAATATATAGCAGTAAGCTAGCAGAGATCAAGAGCAGCAAATT
* *
279701 GCCCAAGATCACATTCAGAATAACCTAAGCATTCAAATTGTAATCGTGCTTTACAATGACCGGAA
66 GCCCAAGATCACATTCAGAATAACCTAAGCATTAAAATTGTAATCGTGCTTTACAATGACAGGAA
*
279766 CCTTTTTTCTTAAACTCACAGTCCCAGACCAGCAGGCCTCTTAGAGGAGCATGAAAACTTTATTA
131 ACTTTTTTCTTAAACTCACAGTCCCAGACCAGCAGGCCTCTTAGAGGAGCATGAAAACTTTATTA
279831 AACTACAGACACGTACATCTATCTAT
196 AACTACAGACACGTACATCTATCTAT
*
279857 TGAGAACAAGATAACCTGTAAAAAATATATAGCAGTAAGCTAGCAGAGATCAAGAGCATCAAATT
1 TGAGAACAAGATAACCTGTAAAAAATATATAGCAGTAAGCTAGCAGAGATCAAGAGCAGCAAATT
* *
279922 GCCCAAGGGTCACATTCAGAATAACCTAGGCATTAAAATTGTAATCGTGCTTTACAATGACAGGA
66 GCCCAA-GATCACATTCAGAATAACCTAAGCATTAAAATTGTAATCGTGCTTTACAATGACAGGA
279987 AACTTTTTTCTTAAACTCACAGTCCCAGACCAGCAGGCCTCTTAGAGGAGCATGAAAACTTTATT
130 AACTTTTTTCTTAAACTCACAGTCCCAGACCAGCAGGCCTCTTAGAGGAGCATGAAAACTTTATT
**
280052 AAACTACAGTTACGTACATCTAT
195 AAACTACAGACACGTACATCTAT
280075 TTACCACAAA
Statistics
Matches: 209, Mismatches: 8, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
221 70 0.33
222 139 0.67
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.25
Consensus pattern (221 bp):
TGAGAACAAGATAACCTGTAAAAAATATATAGCAGTAAGCTAGCAGAGATCAAGAGCAGCAAATT
GCCCAAGATCACATTCAGAATAACCTAAGCATTAAAATTGTAATCGTGCTTTACAATGACAGGAA
ACTTTTTTCTTAAACTCACAGTCCCAGACCAGCAGGCCTCTTAGAGGAGCATGAAAACTTTATTA
AACTACAGACACGTACATCTATCTAT
Found at i:283782 original size:18 final size:20
Alignment explanation
Indices: 283756--283796 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
283746 ATTTAAACAT
*
283756 AAATATAATGAGAT-AAATA
1 AAATATAATGAAATAAAATA
*
283775 AAAT-TAATTAAATAAAATA
1 AAATATAATGAAATAAAATA
283794 AAA
1 AAA
283797 CATATTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (20 bp):
AAATATAATGAAATAAAATA
Found at i:283807 original size:20 final size:21
Alignment explanation
Indices: 283782--283822 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
283772 ATAAAATTAA
*
283782 TTAAATA-AAATAAAACATAT
1 TTAAATATAAAGAAAACATAT
*
283802 TTAAATATAAAGAATACATAT
1 TTAAATATAAAGAAAACATAT
283823 AAAGTGATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (21 bp):
TTAAATATAAAGAAAACATAT
Found at i:291096 original size:25 final size:24
Alignment explanation
Indices: 291042--291100 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
291032 TAAATTTAGA
*
291042 ATTTATATAAATTATAGTTGATGT
1 ATTTATATAAATTATAATTGATGT
291066 ATTTATAATAAATTA-AATT-ATGAT
1 ATTTAT-ATAAATTATAATTGATG-T
291090 ATCTTAT-TAAA
1 AT-TTATATAAA
291101 AATAATTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
23 7 0.23
24 12 0.39
25 12 0.39
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (24 bp):
ATTTATATAAATTATAATTGATGT
Found at i:300561 original size:16 final size:16
Alignment explanation
Indices: 300530--300570 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
300520 TGTGATTAAA
300530 AAAT-TTTA-AATATT
1 AAATATTTATAATATT
*
300544 AAATATTTATAATTTT
1 AAATATTTATAATATT
*
300560 AAAAATTTATA
1 AAATATTTATA
300571 TTTAAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 4 0.17
15 4 0.17
16 15 0.65
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AAATATTTATAATATT
Found at i:304433 original size:17 final size:17
Alignment explanation
Indices: 304413--304446 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
304403 TAATAAAAAA
304413 TTTAAAAAAATAATTTT
1 TTTAAAAAAATAATTTT
*
304430 TTTAAAAAAATTATTTT
1 TTTAAAAAAATAATTTT
304447 ATTTTAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTAAAAAAATAATTTT
Found at i:304439 original size:18 final size:19
Alignment explanation
Indices: 304416--304453 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
304406 TAAAAAATTT
304416 AAAAAAATAATTT-TTTTA
1 AAAAAAATAATTTATTTTA
* *
304434 AAAAAATTATTTTATTTTA
1 AAAAAAATAATTTATTTTA
304453 A
1 A
304454 TTTTTTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AAAAAAATAATTTATTTTA
Found at i:304482 original size:14 final size:14
Alignment explanation
Indices: 304420--304483 Score: 51
Period size: 14 Copynumber: 4.7 Consensus size: 14
304410 AAATTTAAAA
*
304420 AAAT-AATTTTTTT
1 AAATAAATTATTTT
*
304433 AAAAAAATTATTTT
1 AAATAAATTATTTT
** * *
304447 ATTTTAATTTTTTT
1 AAATAAATTATTTT
304461 AAAT-AATTATTTT
1 AAATAAATTATTTT
*
304474 AACTAAATTA
1 AAATAAATTA
304484 ATATTATTTA
Statistics
Matches: 38, Mismatches: 11, Indels: 3
0.73 0.21 0.06
Matches are distributed among these distances:
13 14 0.37
14 24 0.63
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (14 bp):
AAATAAATTATTTT
Found at i:304482 original size:27 final size:28
Alignment explanation
Indices: 304424--304482 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
304414 TTAAAAAAAT
** *
304424 AATTTTTTTAAAAAAATTATTTTATTTT
1 AATTTTTTTAAAAAAATTATTTTAACTA
*
304452 AATTTTTTT-AAATAATTATTTTAACTA
1 AATTTTTTTAAAAAAATTATTTTAACTA
304479 AATT
1 AATT
304483 AATATTATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 18 0.67
28 9 0.33
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (28 bp):
AATTTTTTTAAAAAAATTATTTTAACTA
Found at i:308695 original size:13 final size:13
Alignment explanation
Indices: 308679--308704 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
308669 ATATTTTTAA
308679 TTTGGATACAAAT
1 TTTGGATACAAAT
308692 TTTGGATACAAAT
1 TTTGGATACAAAT
308705 ATTTTAAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (13 bp):
TTTGGATACAAAT
Found at i:310830 original size:25 final size:25
Alignment explanation
Indices: 310799--310857 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
310789 TCAAATCCTT
310799 CTTTGATTTTCTCTTAATCCTTTTC
1 CTTTGATTTTCTCTTAATCCTTTTC
310824 CTTTGATTTTCTCTTAATCCTTTTC
1 CTTTGATTTTCTCTTAATCCTTTTC
310849 CTTTGATTT
1 CTTTGATTT
310858 CCATAACGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.12, C:0.22, G:0.05, T:0.61
Consensus pattern (25 bp):
CTTTGATTTTCTCTTAATCCTTTTC
Found at i:312315 original size:23 final size:24
Alignment explanation
Indices: 312257--312330 Score: 82
Period size: 23 Copynumber: 3.1 Consensus size: 24
312247 ATTTAATGTA
312257 TTATTAAAAGATAAATT-TATATAT
1 TTATTAAAA-ATAAATTATATATAT
* * *
312281 TAATTTATAATAAATTATAT-TAT
1 TTATTAAAAATAAATTATATATAT
312304 TTATTAAAAAT-AATTAATATATAT
1 TTATTAAAAATAAATT-ATATATAT
312328 TTA
1 TTA
312331 AAATTTTATT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
22 4 0.10
23 22 0.54
24 15 0.37
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (24 bp):
TTATTAAAAATAAATTATATATAT
Found at i:314847 original size:17 final size:17
Alignment explanation
Indices: 314817--314852 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
314807 ATAATTTAAT
* *
314817 TTTATGAATTAATATAA
1 TTTATAAATAAATATAA
314834 TTTATAAATAAATATAA
1 TTTATAAATAAATATAA
314851 TT
1 TT
314853 ATTAATTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
TTTATAAATAAATATAA
Found at i:323052 original size:4 final size:4
Alignment explanation
Indices: 323043--323068 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
323033 GTAATGGTAA
323043 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
323069 TGGTGTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:324736 original size:20 final size:20
Alignment explanation
Indices: 324713--324756 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
324703 TTAATAATAA
*
324713 TTAAATATATTAAGATATAT
1 TTAAATATATCAAGATATAT
324733 TTAAATATATCAAGATATAT
1 TTAAATATATCAAGATATAT
324753 TTAA
1 TTAA
324757 TTTTAATTTA
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:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (20 bp):
TTAAATATATCAAGATATAT
Found at i:326463 original size:6 final size:6
Alignment explanation
Indices: 326454--326487 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
326444 GTATTTTCTT
326454 TTTTTA -TTTTA TTTTTA TTTTTA TTTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
326488 TTTACTGCGG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:326468 original size:18 final size:18
Alignment explanation
Indices: 326445--326490 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
326435 TAACCCCATG
326445 TATTTTCTTTTTTTA-TTT
1 TATTTT-TTTTTTTATTTT
*
326463 TATTTTTATTTTTATTTT
1 TATTTTTTTTTTTATTTT
326481 TATTTTTTTT
1 TATTTTTTTT
326491 ACTGCGGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 7 0.28
18 18 0.72
ACGTcount: A:0.13, C:0.02, G:0.00, T:0.85
Consensus pattern (18 bp):
TATTTTTTTTTTTATTTT
Found at i:327039 original size:19 final size:20
Alignment explanation
Indices: 327017--327085 Score: 77
Period size: 20 Copynumber: 3.3 Consensus size: 20
327007 ATTGATAATT
* *
327017 TAAAATATAATA-TATAAAA
1 TAAAATAAAATATTAAAAAA
327036 TAAAATAAAATATTAAAAAA
1 TAAAATAAAATATTAAAAAA
327056 TAAAATAAAAGTATTTAAATAAA
1 TAAAATAAAA-TA-TTAAA-AAA
327079 TTAAAAT
1 -TAAAAT
327086 TTATATAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
19 11 0.26
20 16 0.37
21 2 0.05
22 5 0.12
23 3 0.07
24 6 0.14
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.30
Consensus pattern (20 bp):
TAAAATAAAATATTAAAAAA
Found at i:327096 original size:20 final size:20
Alignment explanation
Indices: 327017--327096 Score: 76
Period size: 20 Copynumber: 4.1 Consensus size: 20
327007 ATTGATAATT
* *
327017 TAAAATATAATATATA-AAA
1 TAAAATAAAATTTATATAAA
*
327036 TAAAATAAAATATTA-AAAAA
1 TAAAATAAAAT-TTATATAAA
* *
327056 TAAAATAAAA-GTATTTAAA
1 TAAAATAAAATTTATATAAA
*
327075 TAAATTAAAATTTATATAAA
1 TAAAATAAAATTTATATAAA
327095 TA
1 TA
327097 TATAATAAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
18 2 0.04
19 23 0.47
20 24 0.49
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (20 bp):
TAAAATAAAATTTATATAAA
Found at i:327234 original size:8 final size:8
Alignment explanation
Indices: 327223--327252 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
327213 TCCTTTTTCC
327223 TTTTTTAT
1 TTTTTTAT
327231 TTTTTTAT
1 TTTTTTAT
*
327239 TTTTTAAT
1 TTTTTTAT
327247 TTTTTT
1 TTTTTT
327253 TATTACTCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTTAT
Found at i:332604 original size:11 final size:11
Alignment explanation
Indices: 332589--332627 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
332579 TTTAATATAA
*
332589 ATTATAATTAT
1 ATTATATTTAT
*
332600 TTTAT-TTTAT
1 ATTATATTTAT
332610 ATTATATTTAT
1 ATTATATTTAT
332621 ATTATAT
1 ATTATAT
332628 GATTGAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 8 0.33
11 16 0.67
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
ATTATATTTAT
Found at i:332619 original size:16 final size:15
Alignment explanation
Indices: 332589--332627 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
332579 TTTAATATAA
332589 ATTATAATTATTTTAT
1 ATTAT-ATTATTTTAT
*
332605 TTTATATTATATTTAT
1 ATTATATTAT-TTTAT
332621 ATTATAT
1 ATTATAT
332628 GATTGAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
ATTATATTATTTTAT
Found at i:333345 original size:22 final size:23
Alignment explanation
Indices: 333288--333354 Score: 73
Period size: 22 Copynumber: 2.9 Consensus size: 23
333278 AAATTTATAT
*
333288 ATATATATATTTTAATTTTTTAAAA
1 ATATTTATA-TTTAA-TTTTTAAAA
* *
333313 ATATTTTTATTTAATTTTTAATA
1 ATATTTATATTTAATTTTTAAAA
*
333336 AT-TTTATATTAAATTTTTA
1 ATATTTATATTTAATTTTTA
333355 TATGATATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
22 15 0.41
23 10 0.27
24 5 0.14
25 7 0.19
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
ATATTTATATTTAATTTTTAAAA
Found at i:333347 original size:21 final size:21
Alignment explanation
Indices: 333312--333354 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
333302 ATTTTTTAAA
*
333312 AATATTTTTATTT-AATTTTT
1 AATAATTTTATTTAAATTTTT
333332 AATAATTTTATATTAAATTTTT
1 AATAATTTTAT-TTAAATTTTT
333354 A
1 A
333355 TATGATATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 2 0.10
22 8 0.40
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
AATAATTTTATTTAAATTTTT
Found at i:334574 original size:15 final size:16
Alignment explanation
Indices: 334556--334596 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
334546 TAAATAGTTA
334556 TAAATATTAAAATT-T
1 TAAATATTAAAATTAT
*
334571 TAAA-ATTTAAATTTAT
1 TAAATA-TTAAAATTAT
334587 TAAATATTAA
1 TAAATATTAA
334597 GTAATTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
14 1 0.05
15 11 0.50
16 9 0.41
17 1 0.05
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TAAATATTAAAATTAT
Found at i:334693 original size:22 final size:23
Alignment explanation
Indices: 334659--334727 Score: 54
Period size: 22 Copynumber: 3.0 Consensus size: 23
334649 TTAAAAATAC
334659 TAAAATATTATTTTATATTAATAAT
1 TAAAATA--ATTTTATATTAATAAT
*
334684 T-AAATAA-TTTATAATTAA-ATT
1 TAAAATAATTTTAT-ATTAATAAT
* *
334705 TAAAATTATTTTTTATTTAATAA
1 TAAAATAATTTTATA-TTAATAA
334728 ATAGTGCTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 11
0.70 0.08 0.22
Matches are distributed among these distances:
21 8 0.23
22 12 0.34
23 8 0.23
24 6 0.17
25 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TAAAATAATTTTATATTAATAAT
Found at i:337204 original size:24 final size:24
Alignment explanation
Indices: 337177--337223 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
337167 TGGATATGTA
*
337177 GGTGGAGGATACGCTGAAGGTGGG
1 GGTGGAGGATACGCAGAAGGTGGG
* *
337201 GGTGGAGGGTATGCAGAAGGTGG
1 GGTGGAGGATACGCAGAAGGTGG
337224 AGGAGGATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.21, C:0.06, G:0.55, T:0.17
Consensus pattern (24 bp):
GGTGGAGGATACGCAGAAGGTGGG
Found at i:337234 original size:21 final size:21
Alignment explanation
Indices: 337204--337255 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
337194 AGGTGGGGGT
*
337204 GGAGGGTATGCAGAAGGTGGA
1 GGAGGATATGCAGAAGGTGGA
**
337225 GGAGGATATGCAGCTGGTGGA
1 GGAGGATATGCAGAAGGTGGA
337246 GGAGGATATG
1 GGAGGATATG
337256 TAGATGAAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.27, C:0.06, G:0.50, T:0.17
Consensus pattern (21 bp):
GGAGGATATGCAGAAGGTGGA
Found at i:338641 original size:53 final size:53
Alignment explanation
Indices: 338560--338665 Score: 176
Period size: 53 Copynumber: 2.0 Consensus size: 53
338550 GGAGAAATTA
**
338560 GAAACAACAGAGATTCCATAATTGTATGGAGAAATAAAAGCAGGGCTTCACAG
1 GAAACAACAGAGATTCCATAATCATATGGAGAAATAAAAGCAGGGCTTCACAG
**
338613 GAAACAACAGAGATTCCATGGTCATATGGAGAAATAAAAGCAGGGCTTCACAG
1 GAAACAACAGAGATTCCATAATCATATGGAGAAATAAAAGCAGGGCTTCACAG
338666 CCAATATTGC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.42, C:0.16, G:0.24, T:0.18
Consensus pattern (53 bp):
GAAACAACAGAGATTCCATAATCATATGGAGAAATAAAAGCAGGGCTTCACAG
Found at i:339369 original size:14 final size:13
Alignment explanation
Indices: 339344--339368 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
339334 CCATAGCCAA
339344 AAATTAAAAAAAT
1 AAATTAAAAAAAT
339357 AAATTAAAAAAA
1 AAATTAAAAAAA
339369 AAACGAACCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAATTAAAAAAAT
Found at i:340152 original size:26 final size:28
Alignment explanation
Indices: 340108--340165 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
340098 AATACCTGTA
340108 ATATAAAAAATAATAAATTTAAATAT-AT
1 ATATAAAAAATAATAAA-TTAAATATGAT
* *
340136 ATATAAAAAGT-AT-AATTAAATTTGAT
1 ATATAAAAAATAATAAATTAAATATGAT
340162 ATAT
1 ATAT
340166 TAATACATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 7 0.26
26 8 0.30
27 2 0.07
28 10 0.37
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (28 bp):
ATATAAAAAATAATAAATTAAATATGAT
Found at i:341579 original size:2 final size:2
Alignment explanation
Indices: 341572--341598 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
341562 AGACCAAAAG
341572 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
341599 GACATTAAGC
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:344735 original size:2 final size:2
Alignment explanation
Indices: 344728--344766 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
344718 TGCCTTTGAG
*
344728 AT AT AT AT AT AT AT AT AT AT CT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
344767 AGCTGCACTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:351912 original size:200 final size:200
Alignment explanation
Indices: 351569--351935 Score: 734
Period size: 200 Copynumber: 1.8 Consensus size: 200
351559 AGGAACGGAA
351569 GGAAGAACACGTGAAACTGAGGAATTACACTATCCATATCCCCTCCTTCAAAGATTAGAGATCAA
1 GGAAGAACACGTGAAACTGAGGAATTACACTATCCATATCCCCTCCTTCAAAGATTAGAGATCAA
351634 CTAAGTGCTCAACGAAAAAAATTGAAGAAATCGAGGATGAAAGCAATGATTATTGATATAAATAT
66 CTAAGTGCTCAACGAAAAAAATTGAAGAAATCGAGGATGAAAGCAATGATTATTGATATAAATAT
351699 AAGAAATAAGAATCTTAGGCTGATGTTTTCTAAGGTTAGAAAACATATCCCCTCCTTCAAACTGA
131 AAGAAATAAGAATCTTAGGCTGATGTTTTCTAAGGTTAGAAAACATATCCCCTCCTTCAAACTGA
351764 GGGAG
196 GGGAG
351769 GGAAGAACACGTGAAACTGAGGAATTACACTATCCATATCCCCTCCTTCAAAGATTAGAGATCAA
1 GGAAGAACACGTGAAACTGAGGAATTACACTATCCATATCCCCTCCTTCAAAGATTAGAGATCAA
351834 CTAAGTGCTCAACGAAAAAAATTGAAGAAATCGAGGATGAAAGCAATGATTATTGATATAAATAT
66 CTAAGTGCTCAACGAAAAAAATTGAAGAAATCGAGGATGAAAGCAATGATTATTGATATAAATAT
351899 AAGAAATAAGAATCTTAGGCTGATGTTTTCTAAGGTT
131 AAGAAATAAGAATCTTAGGCTGATGTTTTCTAAGGTT
351936 GGTTGAAATG
Statistics
Matches: 167, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
200 167 1.00
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.25
Consensus pattern (200 bp):
GGAAGAACACGTGAAACTGAGGAATTACACTATCCATATCCCCTCCTTCAAAGATTAGAGATCAA
CTAAGTGCTCAACGAAAAAAATTGAAGAAATCGAGGATGAAAGCAATGATTATTGATATAAATAT
AAGAAATAAGAATCTTAGGCTGATGTTTTCTAAGGTTAGAAAACATATCCCCTCCTTCAAACTGA
GGGAG
Found at i:353207 original size:36 final size:35
Alignment explanation
Indices: 353167--353244 Score: 99
Period size: 34 Copynumber: 2.3 Consensus size: 35
353157 ATTATTATAA
*
353167 TTTAAATTATTATTTATTAAATA-AAAATATATATTT
1 TTTAAATTATTAATTATTAAATATAAAA-ATA-ATTT
*
353203 TTTAAA-T-TTAATTATTTAATATAAAAATAATTT
1 TTTAAATTATTAATTATTAAATATAAAAATAATTT
353236 TTTAAATTA
1 TTTAAATTA
353245 AAATAATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
33 10 0.27
34 16 0.43
35 5 0.14
36 6 0.16
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (35 bp):
TTTAAATTATTAATTATTAAATATAAAAATAATTT
Found at i:353241 original size:33 final size:34
Alignment explanation
Indices: 353180--353243 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
353170 AAATTATTAT
353180 TTATTAAATAAAAATATATATTTTTTAAATTTAA
1 TTATTAAATAAAAATATATATTTTTTAAATTTAA
*
353214 TTATTTAATATAAAA-ATA-ATTTTTTAAATT
1 TTATTAAATA-AAAATATATATTTTTTAAATT
353244 AAAATAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 12 0.43
34 12 0.43
35 4 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (34 bp):
TTATTAAATAAAAATATATATTTTTTAAATTTAA
Found at i:353249 original size:18 final size:19
Alignment explanation
Indices: 353211--353255 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
353201 TTTTTAAATT
*
353211 TAATTATTTAATATAAAAA
1 TAATTTTTTAATATAAAAA
*
353230 TAATTTTTTAA-ATTAAAA
1 TAATTTTTTAATATAAAAA
353248 TAATTTTT
1 TAATTTTT
353256 GAATTCAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TAATTTTTTAATATAAAAA
Found at i:356905 original size:10 final size:11
Alignment explanation
Indices: 356878--356910 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
356868 TTTTCTTATA
*
356878 ATTATAATTTT
1 ATTAAAATTTT
356889 ATTAAAATTTT
1 ATTAAAATTTT
356900 -TTAAAATTTT
1 ATTAAAATTTT
356910 A
1 A
356911 AATTATATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
ATTAAAATTTT
Found at i:357228 original size:23 final size:24
Alignment explanation
Indices: 357200--357253 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 24
357190 AAAATTAAAA
*
357200 AATTAAAAATATTTTTAT-ATTA-
1 AATTAAAAATAATTTTATAATTAT
*
357222 ATATT-AATATAATTTTATAATTAT
1 A-ATTAAAAATAATTTTATAATTAT
357246 AATTAAAA
1 AATTAAAA
357254 TTAAAATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
22 12 0.48
23 10 0.40
24 3 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
AATTAAAAATAATTTTATAATTAT
Found at i:365282 original size:1 final size:1
Alignment explanation
Indices: 365272--365366 Score: 64
Period size: 1 Copynumber: 95.0 Consensus size: 1
365262 TGGCAATTGG
* * * * ** * * * *
365272 AAAAAGAAAAAAACAAAACAAGAAAAAAGGAAAAAGAAAAAAAGAAAAAAACAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
** * *
365337 GGAAAAAGAAAAAAAAAACAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
365367 GTGAAGATTT
Statistics
Matches: 70, Mismatches: 24, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 70 1.00
ACGTcount: A:0.85, C:0.05, G:0.09, T:0.00
Consensus pattern (1 bp):
A
Found at i:365296 original size:22 final size:21
Alignment explanation
Indices: 365271--365366 Score: 85
Period size: 21 Copynumber: 4.5 Consensus size: 21
365261 ATGGCAATTG
365271 GAAAAAGAAAAAAACAAAACAA
1 GAAAAAGAAAAAAA-AAAACAA
*
365293 GAAAAAAGGAAAAAGAAAAA-AA
1 G-AAAAA-GAAAAAAAAAAACAA
*
365315 GAAAAA-AACAAAACAAAAAAAA
1 GAAAAAGAA-AAAA-AAAAACAA
365337 GGAAAAAG-AAAAAAAAAACAA
1 -GAAAAAGAAAAAAAAAAACAA
365358 -AAAAA-AAAA
1 GAAAAAGAAAA
365367 GTGAAGATTT
Statistics
Matches: 63, Mismatches: 3, Indels: 19
0.74 0.04 0.22
Matches are distributed among these distances:
19 10 0.16
20 3 0.05
21 17 0.27
22 10 0.16
23 16 0.25
24 7 0.11
ACGTcount: A:0.84, C:0.05, G:0.10, T:0.00
Consensus pattern (21 bp):
GAAAAAGAAAAAAAAAAACAA
Found at i:365321 original size:37 final size:37
Alignment explanation
Indices: 365272--365365 Score: 152
Period size: 38 Copynumber: 2.5 Consensus size: 37
365262 TGGCAATTGG
365272 AAAAAGAAAAAAACAAAACAAGAAAAAAGGAAAAAGAA
1 AAAAAGAAAAAAACAAAACAA-AAAAAAGGAAAAAGAA
365310 AAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAGAA
1 AAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAGAA
* *
365347 AAAAAAAACAAAAAAAAAA
1 AAAAAGAA-AAAAACAAAA
365366 AGTGAAGATT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
37 23 0.43
38 30 0.57
ACGTcount: A:0.85, C:0.05, G:0.10, T:0.00
Consensus pattern (37 bp):
AAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAGAA
Found at i:365336 original size:30 final size:29
Alignment explanation
Indices: 365272--365366 Score: 109
Period size: 30 Copynumber: 3.1 Consensus size: 29
365262 TGGCAATTGG
* * * *
365272 AAAAAGAAAAAAACAAAACAAGAAAAAAGG
1 AAAAAGAAAAAAAAAAAAAAACAAAAAA-A
*
365302 AAAAAGAAAAAAAGAAAAAAACAAAACAAA
1 AAAAAGAAAAAAAAAAAAAAACAAAA-AAA
365332 AAAAAGGAAAAAGAAAAAAAAAACAAAAAAA
1 AAAAA-GAAAAA-AAAAAAAAAACAAAAAAA
365363 AAAA
1 AAAA
365367 GTGAAGATTT
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
30 28 0.49
31 15 0.26
32 14 0.25
ACGTcount: A:0.85, C:0.05, G:0.09, T:0.00
Consensus pattern (29 bp):
AAAAAGAAAAAAAAAAAAAAACAAAAAAA
Found at i:365367 original size:30 final size:31
Alignment explanation
Indices: 365270--365366 Score: 115
Period size: 31 Copynumber: 3.0 Consensus size: 31
365260 CATGGCAATT
365270 GGAAAAAGAAAAAAACAAAACAAGAAAAAAGGAAAA
1 GGAAAAAG-AAAAAA-AAAACAA-AAAAAA--AAAA
* *
365306 AGAAAAA-AAGAAAAAAACAAAACAAAAAAAA
1 GGAAAAAGAAAAAAAAAACAAAA-AAAAAAAA
365337 GGAAAAAGAAAAAAAAAACAAAAAAAAAAA
1 GGAAAAAGAAAAAAAAAACAAAAAAAAAAA
365367 GTGAAGATTT
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
31 17 0.31
32 16 0.29
33 11 0.20
34 5 0.09
36 6 0.11
ACGTcount: A:0.84, C:0.05, G:0.11, T:0.00
Consensus pattern (31 bp):
GGAAAAAGAAAAAAAAAACAAAAAAAAAAAA
Found at i:365373 original size:28 final size:27
Alignment explanation
Indices: 365272--365363 Score: 80
Period size: 27 Copynumber: 3.2 Consensus size: 27
365262 TGGCAATTGG
*
365272 AAAAAGAAAAA-AACAAAACAAGAAAAAA
1 AAAAAGAAAAAGAA-AAAACAA-AACAAA
365300 GGAAAAAGAAAAAAAGAAAAAAACAAAACAAA
1 --AAAAAG--AAAAAG-AAAAAACAAAACAAA
*
365332 AAAAAGGAAAAAGAAAAAA-AAAACAAA
1 AAAAAGAAAAA-GAAAAAACAAAACAAA
365359 AAAAA
1 AAAAA
365364 AAAGTGAAGA
Statistics
Matches: 55, Mismatches: 2, Indels: 13
0.79 0.03 0.19
Matches are distributed among these distances:
27 13 0.24
28 10 0.18
29 1 0.02
30 12 0.22
32 10 0.18
33 7 0.13
34 2 0.04
ACGTcount: A:0.85, C:0.05, G:0.10, T:0.00
Consensus pattern (27 bp):
AAAAAGAAAAAGAAAAAACAAAACAAA
Found at i:367787 original size:37 final size:37
Alignment explanation
Indices: 367710--367788 Score: 86
Period size: 37 Copynumber: 2.1 Consensus size: 37
367700 GATAGTTTGA
* * * *
367710 TCAATTTATTATAATTATTAATATTTAGGTGACAATG
1 TCAATATATTATAATTATTAAAATTTAAGTGACAACG
* * * *
367747 TCAATATATTATGATTGTTAAAATTTAAGTGGCAGCG
1 TCAATATATTATAATTATTAAAATTTAAGTGACAACG
367784 TCAAT
1 TCAAT
367789 CCACGAAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.42
Consensus pattern (37 bp):
TCAATATATTATAATTATTAAAATTTAAGTGACAACG
Found at i:372497 original size:37 final size:37
Alignment explanation
Indices: 372451--372528 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
372441 CTTGGTCAAT
* * * *
372451 CCACTATGATCGTTAGTATTTGGGTGGCAGTGCCAAC
1 CCACAATGATCGTTAGAATTTGAGTGGCAGCGCCAAC
* *
372488 CCACAATGATTGTTAGAATTTGAGTGGCAGCGCCAAT
1 CCACAATGATCGTTAGAATTTGAGTGGCAGCGCCAAC
372525 CCAC
1 CCAC
372529 GAAAAATAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (37 bp):
CCACAATGATCGTTAGAATTTGAGTGGCAGCGCCAAC
Found at i:377754 original size:2 final size:2
Alignment explanation
Indices: 377747--377772 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
377737 TTGAATCTGA
377747 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
377773 CAATAAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:378160 original size:24 final size:24
Alignment explanation
Indices: 378108--378151 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
378098 AAGTTGAGAT
378108 ATTTTCTTATTACATTATTTTTGA
1 ATTTTCTTATTACATTATTTTTGA
378132 ATTTTCTT-TTA-ATTATTTTT
1 ATTTTCTTATTACATTATTTTT
378152 TACGATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 9 0.45
23 3 0.15
24 8 0.40
ACGTcount: A:0.23, C:0.07, G:0.02, T:0.68
Consensus pattern (24 bp):
ATTTTCTTATTACATTATTTTTGA
Found at i:381075 original size:31 final size:31
Alignment explanation
Indices: 381022--381106 Score: 116
Period size: 31 Copynumber: 2.7 Consensus size: 31
381012 TATAATGATG
* * * *
381022 TAATATCATGTTTGTTTATTAATTTTTTAAAT
1 TAATTTCAT-TTTGCTTATTAATATTTTAAAA
381054 TAATTTCATTTTGCTTATTAATATTTTAAAA
1 TAATTTCATTTTGCTTATTAATATTTTAAAA
*
381085 CAATTTCATTTTGCTTATTAAT
1 TAATTTCATTTTGCTTATTAAT
381107 GATGTGATAT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
31 40 0.83
32 8 0.17
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.56
Consensus pattern (31 bp):
TAATTTCATTTTGCTTATTAATATTTTAAAA
Found at i:381708 original size:18 final size:18
Alignment explanation
Indices: 381687--381721 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
381677 TTTTAAAATA
381687 TAAAAATAATTTATATTT
1 TAAAAATAATTTATATTT
* *
381705 TAAAAATTATTTTTATT
1 TAAAAATAATTTATATT
381722 ATTTAAATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TAAAAATAATTTATATTT
Found at i:383081 original size:20 final size:20
Alignment explanation
Indices: 383045--383083 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
383035 GGGGTGAATC
*
383045 TGAAAAAAAATGGAAAAATA
1 TGAAAAAAAATGAAAAAATA
383065 TGAAAGAAAAAT-AAAAAAT
1 TGAAA-AAAAATGAAAAAAT
383084 CCTGCCAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.72, C:0.00, G:0.13, T:0.15
Consensus pattern (20 bp):
TGAAAAAAAATGAAAAAATA
Found at i:393206 original size:24 final size:24
Alignment explanation
Indices: 393159--393203 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
393149 AAGTTGAGAT
393159 ATTTTCTTATTAAATTATTTTTTA
1 ATTTTCTTATTAAATTATTTTTTA
*
393183 ATTTTCTT-TT-AATTCTTTTTT
1 ATTTTCTTATTAAATTATTTTTT
393204 TTATGATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 10 0.50
23 2 0.10
24 8 0.40
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.71
Consensus pattern (24 bp):
ATTTTCTTATTAAATTATTTTTTA
Found at i:395191 original size:2 final size:2
Alignment explanation
Indices: 395184--395214 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
395174 TAGGATTTCA
395184 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
395215 GTTCTTTTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:399431 original size:13 final size:13
Alignment explanation
Indices: 399413--399441 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
399403 AAAAATAATT
399413 TAATTTTTATTAA
1 TAATTTTTATTAA
399426 TAATTTTTATTAA
1 TAATTTTTATTAA
399439 TAA
1 TAA
399442 GTTATCGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TAATTTTTATTAA
Found at i:402217 original size:2 final size:2
Alignment explanation
Indices: 402210--402242 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
402200 TGATTTGATA
402210 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
402243 CTATACATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:402254 original size:2 final size:2
Alignment explanation
Indices: 402244--402278 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
402234 TGTGTGTGTC
* *
402244 TA TA CA TA TA TA TG TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
402279 TTCCTATTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:402815 original size:24 final size:24
Alignment explanation
Indices: 402783--402843 Score: 97
Period size: 24 Copynumber: 2.5 Consensus size: 24
402773 CTTATGATAA
*
402783 GTAGTCTACATACTGA-AATGTTCT
1 GTAGTCTACATACT-ATAATGTTCC
402807 GTAGTCTACATACTATAATGTTCC
1 GTAGTCTACATACTATAATGTTCC
402831 GTAGTCTACATAC
1 GTAGTCTACATAC
402844 CATTTGGTGC
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
23 1 0.03
24 34 0.97
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.36
Consensus pattern (24 bp):
GTAGTCTACATACTATAATGTTCC
Found at i:413343 original size:15 final size:15
Alignment explanation
Indices: 413325--413372 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
413315 TCTTTTCATC
413325 AGCACCATTTTAATT
1 AGCACCATTTTAATT
* *
413340 AGCA-C-TTTTCATC
1 AGCACCATTTTAATT
413353 AGCACCATTTTAATT
1 AGCACCATTTTAATT
413368 AGCAC
1 AGCAC
413373 GCCTTAGTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
13 10 0.37
14 2 0.07
15 15 0.56
ACGTcount: A:0.31, C:0.25, G:0.08, T:0.35
Consensus pattern (15 bp):
AGCACCATTTTAATT
Found at i:413356 original size:28 final size:28
Alignment explanation
Indices: 413316--413372 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
413306 TTCCCAACAT
413316 CTTTTCATCAGCACCATTTTAATTAGCA
1 CTTTTCATCAGCACCATTTTAATTAGCA
413344 CTTTTCATCAGCACCATTTTAATTAGCA
1 CTTTTCATCAGCACCATTTTAATTAGCA
413372 C
1 C
413373 GCCTTAGTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.28, C:0.26, G:0.07, T:0.39
Consensus pattern (28 bp):
CTTTTCATCAGCACCATTTTAATTAGCA
Found at i:417946 original size:2 final size:2
Alignment explanation
Indices: 417939--417971 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
417929 TAAATAAACA
*
417939 AG AG AG AG AG AG AG AG AG AG AG AG AG AG GG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
417972 ATCACATGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:419715 original size:27 final size:27
Alignment explanation
Indices: 419685--419738 Score: 65
Period size: 30 Copynumber: 1.9 Consensus size: 27
419675 TTTGAAATAA
419685 TATTT-TTTAATTAAAATAATATATATT
1 TATTTATTTAATTAAAA-AATATATATT
*
419712 TATTTAAATTTAATTATAAAATATATA
1 TATTT--ATTTAATTAAAAAATATATA
419739 AATAATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 5 0.22
29 8 0.35
30 10 0.43
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
TATTTATTTAATTAAAAAATATATATT
Found at i:419718 original size:20 final size:19
Alignment explanation
Indices: 419674--419719 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
419664 TTTTGAATCG
* *
419674 ATTTGAAATAATATTTTTT
1 ATTTAAAATAATATTATTT
*
419693 AATTAAAATAATATATATTT
1 ATTTAAAATAATAT-TATTT
419713 ATTTAAA
1 ATTTAAA
419720 TTTAATTATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (19 bp):
ATTTAAAATAATATTATTT
Found at i:419749 original size:29 final size:30
Alignment explanation
Indices: 419690--419749 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 30
419680 AATAATATTT
** * *
419690 TTTAATTAAAATAATATATATTTATTTAAA
1 TTTAATTAAAATAATATATAAATAATAAAA
*
419720 TTTAATTATAA-AATATATAAATAATAAAA
1 TTTAATTAAAATAATATATAAATAATAAAA
419749 T
1 T
419750 ATTTTTTAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (30 bp):
TTTAATTAAAATAATATATAAATAATAAAA
Found at i:419815 original size:11 final size:11
Alignment explanation
Indices: 419799--419850 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
419789 AGAGTTCAAG
419799 TTAAATTAAAT
1 TTAAATTAAAT
419810 TTAAATTAAATT
1 TTAAATTAAA-T
419822 TTAAATTTAAA-
1 TTAAA-TTAAAT
** *
419833 AAAAATTATAT
1 TTAAATTAAAT
419844 TTAAATT
1 TTAAATT
419851 GTCCTTTGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
10 4 0.12
11 18 0.55
12 6 0.18
13 5 0.15
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
TTAAATTAAAT
Found at i:419838 original size:18 final size:18
Alignment explanation
Indices: 419804--419839 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
419794 TCAAGTTAAA
**
419804 TTAAATTTAAATTAAATT
1 TTAAATTTAAAAAAAATT
419822 TTAAATTTAAAAAAAATT
1 TTAAATTTAAAAAAAATT
419840 ATATTTAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TTAAATTTAAAAAAAATT
Found at i:430289 original size:2 final size:2
Alignment explanation
Indices: 430282--430315 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
430272 AACTACGACC
430282 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
430316 GCATATACTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:430439 original size:26 final size:26
Alignment explanation
Indices: 430400--430451 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
430390 TTATAAAAAT
*
430400 TTTAAAATTGAAT-AAATTAATTGAA
1 TTTAAAATTGAATAAAATCAATTGAA
*
430425 TTTAAAATTTTAATAAAATCAATTGAA
1 TTTAAAA-TTGAATAAAATCAATTGAA
430452 ATATATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 7 0.30
26 5 0.22
27 11 0.48
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (26 bp):
TTTAAAATTGAATAAAATCAATTGAA
Found at i:431295 original size:41 final size:42
Alignment explanation
Indices: 431237--431318 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 42
431227 TTTGGGATAA
* * *
431237 AATTAAATATAATAATAAATATTATATAATTATA-TAATATT
1 AATTAAATATAAAAATAAATATGATATAAATATATTAATATT
* *
431278 AATTTAATATAAAAATAAATATGATGTAAATATATTAATAT
1 AATTAAATATAAAAATAAATATGATATAAATATATTAATAT
431319 ATTAAAATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
41 29 0.83
42 6 0.17
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (42 bp):
AATTAAATATAAAAATAAATATGATATAAATATATTAATATT
Done.