Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007418.1 Hibiscus syriacus cultivar Beakdansim tig00020063_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: 1198774
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 6
Found at i:454093 original size:265 final size:264
Alignment explanation
Indices: 453327--454494 Score: 1619
Period size: 265 Copynumber: 4.4 Consensus size: 264
453317 TCCCGAATTT
* * * *
453327 GTAAGTCATTCGGGCCATCTGTAAGTCTTTCTAGCATGATGTTTAAATCATTTGGGTCATCTGTA
1 GTAAGTCATTCGGGCCATCTGTAAGACTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTA
* * *
453392 AGCCTTTCGATCAAGATGATAAATCCTTCAGGTCATTCATAAGACCTTCAGTGCTGG-ATGTTTT
66 AGCCTTTCGAGCAAGATGATAAAGCCTTCTGGTCATTCATAAGACCTTCAGTGCTGGTA-GTTTT
* * *
453456 CAAATGAGATTTT--AGAAACTAAGCC-TTTCAGGGGTTTCCTAATTATCTCAAAAGAGTTGTTA
130 CAAATGAGATTTTAAAAAAACTAAGCCATTTAAGGGGTTTCCTAATTATCTCAAAAGAGTTATTA
* * * *
453518 AAGGATA-ATAAGCCTAGCAAAGGGGTTCCTTGACAACTAAGAAACTAAGTTTTCAAGGGTTTCT
195 AAGGA-AGCTAAGCCTAACAAAGGGGTTCCTTGACAACTAAGAAACTAAGCTTTCGAGGGTTTCT
453582 TGATTC
259 TGATTC
* ** * *
453588 ATAAGTCATTCGGGCCATCTGTAAGACTTTTAAGCATGATGTTTAAATCCTTCGCGTCATCTATA
1 GTAAGTCATTCGGGCCATCTGTAAGACTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTA
* * *
453653 AGCCTTTCGAGCAAGATGATAAAGCCTTCTTGTCATCCATAAGACCTTCAGTGCT-GAATGTTTT
66 AGCCTTTCGAGCAAGATGATAAAGCCTTCTGGTCATTCATAAGACCTTCAGTGCTGGTA-GTTTT
* *
453717 GAGATGAGATTTTAAAAAAACTAAGCCTAATTTAAAGGGGTTTCCTAATTATCTCAAAAGAGTTA
130 CAAATGAGATTTTAAAAAAACTAAGCC--ATTT-AAGGGGTTTCCTAATTATCTCAAAAGAGTTA
453782 TTAAAGGAAGCTAAGCCTAACAAAGGGGTTCCTTGACAACTAAGAAACTAAGCTTTCGAGGGTTT
192 TTAAAGGAAGCTAAGCCTAACAAAGGGGTTCCTTGACAACTAAGAAACTAAGCTTTCGAGGGTTT
453847 CTTGATTC
257 CTTGATTC
* *
453855 GTAAGTCATTCGGGCCATCTGTAAGTCTTTCGAGCAAGATGTTTAAAT-CTTCGGGTCATCTGTA
1 GTAAGTCATTCGGGCCATCTGTAAGACTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTA
* * *
453919 AGCCTTTCGAGCAATATGATAAAGCCTTCTGGTCATTCATAAGACCTTCAGTTCTAG-A-TTTTC
66 AGCCTTTCGAGCAAGATGATAAAGCCTTCTGGTCATTCATAAGACCTTCAGTGCTGGTAGTTTTC
* *
453982 AAATGAGATTTTAAAAAAAACTAAGCCTAATTTTAAGGGGTTTCCTAATTATCTTAAAAGAATTA
131 AAATGAGATTTT-AAAAAAACTAAGCC--A-TTTAAGGGGTTTCCTAATTATCTCAAAAGAGTTA
* * *
454047 TTAAAGGAAGCTAAGCCTAACAAAGGGGCTACTTAACAACTAAGAAACTAAGCTTTCGAGGGTTT
192 TTAAAGGAAGCTAAGCCTAACAAAGGGGTTCCTTGACAACTAAGAAACTAAGCTTTCGAGGGTTT
454112 CTTGATTC
257 CTTGATTC
* * * *
454120 GTAAGTCCGTT-GTGCCATCTGTAAGCCTTTCGAGCATGATGTTTAAATCCATCGGGTCATCTGT
1 GTAAGT-CATTCGGGCCATCTGTAAGACTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGT
* * * * *
454184 AAGCCTTTCGAGCAAGATGATAAAGTCTTCTGGTCATCCATAAGACCTTTAGTGTTGGTTGTTTT
65 AAGCCTTTCGAGCAAGATGATAAAGCCTTCTGGTCATTCATAAGACCTTCAGTGCTGGTAGTTTT
* * *
454249 CAAATGAGATTTAAAAAAAACTAAGCCA-TTAAGGGGTTTCCTGATTATCTCAAAAGAGTTGTTA
130 CAAATGAGATTTTAAAAAAACTAAGCCATTTAAGGGGTTTCCTAATTATCTCAAAAGAGTTATTA
* * *
454313 AAGGAAGCTAAGCCTAACAAAGGGGTTCCTTGACAACTAAGAAACTAAGATTTTGAGGGGTTCTT
195 AAGGAAGCTAAGCCTAACAAAGGGGTTCCTTGACAACTAAGAAACTAAGCTTTCGAGGGTTTCTT
454378 GATTC
260 GATTC
* *
454383 GTAAGTCCTTCGGGCCATCTGTAAGACTTTCGAGCATGA---TTAAATCCTTCGGGTCATCTATA
1 GTAAGTCATTCGGGCCATCTGTAAGACTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTA
* * * *
454445 AGCCTTTTGAGCAAGATGTTTAAATCCTT-TAGGCCATTCATAAGACCTTC
66 AGCCTTTCGAGCAAGATG-ATAAAGCCTTCT-GGTCATTCATAAGACCTTC
454495 GGATAGAATG
Statistics
Matches: 813, Mismatches: 76, Indels: 36
0.88 0.08 0.04
Matches are distributed among these distances:
260 40 0.05
261 148 0.18
262 3 0.00
263 139 0.17
264 15 0.02
265 157 0.19
266 141 0.17
267 154 0.19
268 16 0.02
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.32
Consensus pattern (264 bp):
GTAAGTCATTCGGGCCATCTGTAAGACTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTA
AGCCTTTCGAGCAAGATGATAAAGCCTTCTGGTCATTCATAAGACCTTCAGTGCTGGTAGTTTTC
AAATGAGATTTTAAAAAAACTAAGCCATTTAAGGGGTTTCCTAATTATCTCAAAAGAGTTATTAA
AGGAAGCTAAGCCTAACAAAGGGGTTCCTTGACAACTAAGAAACTAAGCTTTCGAGGGTTTCTTG
ATTC
Found at i:454912 original size:3 final size:3
Alignment explanation
Indices: 454884--454969 Score: 106
Period size: 3 Copynumber: 29.3 Consensus size: 3
454874 TTTGTTCATT
*
454884 TTA TT- TTA CTA TTA TCTA TT- TTA TTA TTA TTA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
454927 TTA CTA TTA TCA TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
454970 ATAATAAATA
Statistics
Matches: 71, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
2 6 0.08
3 62 0.87
4 3 0.04
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:455343 original size:21 final size:21
Alignment explanation
Indices: 455318--455364 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
455308 AAAACACAAC
455318 CGACATGGAGCAAGCAATGGA
1 CGACATGGAGCAAGCAATGGA
455339 CGACATGGAGCAAGCAATGGA
1 CGACATGGAGCAAGCAATGGA
455360 CGACA
1 CGACA
455365 AAGATAAAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.38, C:0.21, G:0.32, T:0.09
Consensus pattern (21 bp):
CGACATGGAGCAAGCAATGGA
Found at i:455374 original size:21 final size:21
Alignment explanation
Indices: 455329--455375 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
455319 GACATGGAGC
** *
455329 AAGCAATGGACGACATGGAGC
1 AAGCAATGGACGACAAAGAGA
*
455350 AAGCAATGGACGACAAAGATA
1 AAGCAATGGACGACAAAGAGA
455371 AAGCA
1 AAGCA
455376 TCAAGAGGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.17, G:0.28, T:0.09
Consensus pattern (21 bp):
AAGCAATGGACGACAAAGAGA
Found at i:456959 original size:2 final size:2
Alignment explanation
Indices: 456952--456998 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
456942 GACAGATACA
456952 AT AT 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 AT AT
456993 AT AT AT
1 AT AT AT
456999 CGATAATTGT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:457149 original size:60 final size:58
Alignment explanation
Indices: 457071--457207 Score: 148
Period size: 58 Copynumber: 2.3 Consensus size: 58
457061 GCCCTCTAAG
* * * **
457071 TTTTTGAATATTCTAATTTTATCCTCAAACTATGATACTCATTCTAAATTAGTTCTTAAAC
1 TTTTT-AATATTCCAATTTTATCCTCAAAC--TGACACTCATTCTAAATTAGTCCCAAAAC
* ** * * *
457132 TTTTTAACATTCCAATTTTATCCTTGAACTGACCCTCATTTTAAATTGGTCCCAAAAC
1 TTTTTAATATTCCAATTTTATCCTCAAACTGACACTCATTCTAAATTAGTCCCAAAAC
457190 TTTTTAATATTCCAATTT
1 TTTTTAATATTCCAATTT
457208 CACCCCAAAT
Statistics
Matches: 64, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
58 39 0.61
60 20 0.31
61 5 0.08
ACGTcount: A:0.31, C:0.19, G:0.05, T:0.45
Consensus pattern (58 bp):
TTTTTAATATTCCAATTTTATCCTCAAACTGACACTCATTCTAAATTAGTCCCAAAAC
Found at i:457898 original size:3 final size:3
Alignment explanation
Indices: 457890--457929 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
457880 ACAAGTTGCA
*
457890 ATT ATT ATT ATT ATT ATT ATT ATT ATT TTT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
457930 ATTTGGATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:459450 original size:60 final size:60
Alignment explanation
Indices: 459341--459453 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 60
459331 TCGGGTAATC
* * *
459341 ATTTTGTTACTTTTAATAGTTTGCGGACTCAACAAAGTAACACCCTATAGTTGAAGAACT
1 ATTTTGTAACTTTTAATAGTTTGCGGACTCAACAAAATAACACCATATAGTTGAAGAACT
* * * * *
459401 ATTTTGTAACTTTTAATAG-TTGGGAGATTTAACAAAATAATATCATATAGTTG
1 ATTTTGTAACTTTTAATAGTTTGCG-GACTCAACAAAATAACACCATATAGTTG
459454 GGAACCAATT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
59 4 0.09
60 40 0.91
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (60 bp):
ATTTTGTAACTTTTAATAGTTTGCGGACTCAACAAAATAACACCATATAGTTGAAGAACT
Found at i:461950 original size:16 final size:16
Alignment explanation
Indices: 461929--462033 Score: 87
Period size: 16 Copynumber: 6.6 Consensus size: 16
461919 TTCCTTCACA
461929 TTTTATTATTATTATT
1 TTTTATTATTATTATT
461945 TTTTA-T-TTATTATT
1 TTTTATTATTATTATT
* *
461959 TTTTATT-TAAATAATGT
1 TTTTATTAT-TATTAT-T
*
461976 TTTTATTATTATCTATA
1 TTTTATTATTAT-TATT
*
461993 TTTAATTA-TA-TATAT
1 TTTTATTATTATTAT-T
462008 TTTTATTACTTATTA-T
1 TTTTATTA-TTATTATT
462024 TTTTATTATT
1 TTTTATTATT
462034 TTTTCATTCT
Statistics
Matches: 72, Mismatches: 8, Indels: 19
0.73 0.08 0.19
Matches are distributed among these distances:
14 16 0.22
15 12 0.17
16 20 0.28
17 19 0.26
18 5 0.07
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.69
Consensus pattern (16 bp):
TTTTATTATTATTATT
Found at i:461954 original size:14 final size:13
Alignment explanation
Indices: 461928--462061 Score: 90
Period size: 14 Copynumber: 9.2 Consensus size: 13
461918 GTTCCTTCAC
461928 ATTTTATTATTATT
1 ATTTT-TTATTATT
461942 ATTTTTTATTTATT
1 ATTTTTTA-TTATT
*
461956 ATTTTTTATTTAAATA
1 ATTTTTTA-TT--ATT
461972 ATGTTTTTATTATT
1 AT-TTTTTATTATT
461986 ATCTATATTTAATTATAT
1 AT-T-T-TTT-ATTAT-T
462004 ATATTTTTATTACTT
1 AT-TTTTTATTA-TT
*
462019 ATTATTT-TTATT
1 ATTTTTTATTATT
*
462031 ATTTTTTCATTCTT
1 ATTTTTT-ATTATT
*
462045 CTTTATTTATTATT
1 ATTT-TTTATTATT
462059 ATT
1 ATT
462062 GCTTCCTTTA
Statistics
Matches: 98, Mismatches: 10, Indels: 24
0.74 0.08 0.18
Matches are distributed among these distances:
12 8 0.08
13 6 0.06
14 44 0.45
15 11 0.11
16 13 0.13
17 12 0.12
18 4 0.04
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.69
Consensus pattern (13 bp):
ATTTTTTATTATT
Found at i:462255 original size:15 final size:15
Alignment explanation
Indices: 462227--462259 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
462217 AATTTTTTAG
462227 TTTATTTTTCATTTT
1 TTTATTTTTCATTTT
462242 TTTATCTTTT-ATTTT
1 TTTAT-TTTTCATTTT
462257 TTT
1 TTT
462260 GATGTTCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTATTTTTCATTTT
Found at i:462343 original size:6 final size:6
Alignment explanation
Indices: 462332--462370 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
462322 TTTTATGTTT
*
462332 TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTTTA TTT
1 TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTT
462371 CTATTTATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (6 bp):
TTTTCA
Found at i:462376 original size:18 final size:18
Alignment explanation
Indices: 462320--462390 Score: 60
Period size: 18 Copynumber: 3.9 Consensus size: 18
462310 ACTATTTTAT
462320 TATTTT-ATGTTTT-TTTC
1 TATTTTCAT-TTTTATTTC
*
462337 -ATTTTCATTTTCATTT-
1 TATTTTCATTTTTATTTC
462353 TCATTTTCATTTTTATTTC
1 T-ATTTTCATTTTTATTTC
*
462372 TATTTATTTATTTTTATTT
1 TA-TT-TTCATTTTTATTT
462391 TCTTTATCTT
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
16 8 0.18
17 5 0.11
18 16 0.36
19 3 0.07
20 12 0.27
ACGTcount: A:0.17, C:0.08, G:0.01, T:0.73
Consensus pattern (18 bp):
TATTTTCATTTTTATTTC
Found at i:462387 original size:6 final size:6
Alignment explanation
Indices: 462322--462391 Score: 52
Period size: 6 Copynumber: 11.5 Consensus size: 6
462312 TATTTTATTA
* * * * * *
462322 TTTTAT GTTT-T TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
*
462369 TTCTATT TATTTAT TTTTAT TTT
1 TTTTA-T T-TTTAT TTTTAT TTT
462392 CTTTATCTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
5 3 0.05
6 45 0.82
7 4 0.07
8 3 0.05
ACGTcount: A:0.16, C:0.09, G:0.01, T:0.74
Consensus pattern (6 bp):
TTTTAT
Found at i:464942 original size:111 final size:109
Alignment explanation
Indices: 464728--464947 Score: 422
Period size: 111 Copynumber: 2.0 Consensus size: 109
464718 TATACTTTTT
464728 ATTTAAGAGTTCAGTGATGACATGATCTTTACAGATGGAATAGTCGAGTACGTGAGTCTAGTTTA
1 ATTTAAGAGTTCAGTGATGACATGATCTTTACAGATGGAATAGTCGAGTACGTGAGTCTAGTTTA
464793 GGTCAGTTGCTTGGAAATTGAACTCTAAAGATGAGATTCCTTGA
66 GGTCAGTTGCTTGGAAATTGAACTCTAAAGATGAGATTCCTTGA
464837 ATTTAAGACGTTCAGTGATGATCATGATCTTTACAGATGGAATAGTCGAGTACGTGAGTCTAGTT
1 ATTTAAGA-GTTCAGTGATGA-CATGATCTTTACAGATGGAATAGTCGAGTACGTGAGTCTAGTT
464902 TAGGTCAGTTGCTTGGAAATTGAACTCTAAAGATGAGATTCCTTGA
64 TAGGTCAGTTGCTTGGAAATTGAACTCTAAAGATGAGATTCCTTGA
464948 CTTTCAAAAA
Statistics
Matches: 109, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
109 8 0.07
110 12 0.11
111 89 0.82
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (109 bp):
ATTTAAGAGTTCAGTGATGACATGATCTTTACAGATGGAATAGTCGAGTACGTGAGTCTAGTTTA
GGTCAGTTGCTTGGAAATTGAACTCTAAAGATGAGATTCCTTGA
Found at i:465277 original size:94 final size:94
Alignment explanation
Indices: 465029--465283 Score: 275
Period size: 95 Copynumber: 2.7 Consensus size: 94
465019 TATAATATTA
* * * * *
465029 TATA-TATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAACTGGTTAAATACCCCGACTTTTTGG
1 TATACTATACAATAAAGATTGAGCTGTCCCTCTAGAGCAATTGGTTAAATA-CCCTACTTTATGG
* * *
465093 ATAATATTCAGCTAGCCTGATAAAGGTGAT
65 ATAAGATTCAGCTAACCTAATAAAGGTGAT
* * * *
465123 TATACTATACAATAAAGCTTAAACTGTCCCTCTA-AGGCAATTGGTTAAATGCCCCTACTTTATG
1 TATACTATACAATAAAGATTGAGCTGTCCCTCTAGA-GCAATTGGTTAAAT-ACCCTACTTTATG
465187 GATAAGATTCAGCTAACCTAATAAAGGTG-T
64 GATAAGATTCAGCTAACCTAATAAAGGTGAT
**** * *
465217 T-TACATATTGTTTACATATTGAGCTGTCCCTCTAGAGCAATTGGTTAAATACCCTAACTTTATG
1 TATAC-TATACAATAAAGATTGAGCTGTCCCTCTAGAGCAATTGGTTAAATACCCT-ACTTTATG
465281 GAT
64 GAT
465284 TCAGCTAGCC
Statistics
Matches: 135, Mismatches: 20, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
93 7 0.05
94 52 0.39
95 76 0.56
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Consensus pattern (94 bp):
TATACTATACAATAAAGATTGAGCTGTCCCTCTAGAGCAATTGGTTAAATACCCTACTTTATGGA
TAAGATTCAGCTAACCTAATAAAGGTGAT
Found at i:466803 original size:2 final size:2
Alignment explanation
Indices: 466796--466825 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
466786 AAGTATGTGA
466796 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
466826 GAACATATGT
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:467164 original size:21 final size:21
Alignment explanation
Indices: 467138--467236 Score: 180
Period size: 21 Copynumber: 4.7 Consensus size: 21
467128 GGGTTTCATA
467138 GGTCCTTCGGGACAATACAGT
1 GGTCCTTCGGGACAATACAGT
467159 GGTCCTTCGGGACAATACAGT
1 GGTCCTTCGGGACAATACAGT
*
467180 GATCCTTCGGGACAATACAGT
1 GGTCCTTCGGGACAATACAGT
467201 GGTCCTTCGGGACAATACAGT
1 GGTCCTTCGGGACAATACAGT
*
467222 GATCCTTCGGGACAA
1 GGTCCTTCGGGACAA
467237 ATTTCATATG
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 75 1.00
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.23
Consensus pattern (21 bp):
GGTCCTTCGGGACAATACAGT
Found at i:469252 original size:12 final size:12
Alignment explanation
Indices: 469222--469256 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
469212 TATCTTTTAT
469222 TTATCTTGTTT-
1 TTATCTTGTTTC
*
469233 TAATCTTGTTTC
1 TTATCTTGTTTC
469245 TTATCTTGTTTC
1 TTATCTTGTTTC
469257 CAGCACCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.11, C:0.14, G:0.09, T:0.66
Consensus pattern (12 bp):
TTATCTTGTTTC
Found at i:474792 original size:22 final size:23
Alignment explanation
Indices: 474767--474809 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
474757 CAATTCCTTT
474767 ATCTTTTAT-TTATCTTGTTTTA
1 ATCTTTTATCTTATCTTGTTTTA
*
474789 ATCTTTTTTCTTATCTTGTTT
1 ATCTTTTATCTTATCTTGTTT
474810 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.70
Consensus pattern (23 bp):
ATCTTTTATCTTATCTTGTTTTA
Found at i:476019 original size:84 final size:82
Alignment explanation
Indices: 475866--476669 Score: 750
Period size: 84 Copynumber: 9.6 Consensus size: 82
475856 CTATCGACAA
* * * * * * * * *
475866 CATAACTCAAGGCGATAAAGGTTATCTGTCAGCCAAGACCTTCGAGTTCGATTACACTCA-ATAC
1 CATAACTCAAGG-TAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACGCTCAGCT-C
475930 AAAGGCACATCATTTGCAG
64 AAAGGCACATCATTTGCAG
* *
475949 CATAACTCAAGGTAAGAAGGGTTATCTGCCACCAAAAGACCTTCGAGTTCGACTACGCTCATCTC
1 CATAACTCAAGGT-AGAAGGGTTATCTGCCAAC-AAAGACCTTCGAGTTCGACTACGCTCAGCTC
* * *
476014 TAAGGCATATCATTTGTAG
64 AAAGGCACATCATTTGCAG
* * * * *
476033 CATAACTCAAGGCTATAAGGGATATATTCCAATCAAAGACCTTCGAGTTCGACTACGCTCGGCTC
1 CATAACTCAAGG-TAGAAGGGTTATCTGCCAA-CAAAGACCTTCGAGTTCGACTACGCTCAGCTC
* * * *
476098 CAAGGTACATCATTTACAA
64 AAAGGCACATCATTTGCAG
* * * * *
476117 CATAGCTCAAGGCAAGAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTTGACTATGCTCAGCTC
1 CATAACTCAAGG-TAGAAGGGTTATCTGCCAAC-AAAGACCTTCGAGTTCGACTACGCTCAGCTC
** * *
476182 AAATACAAATCATTTGCAA
64 AAAGGCACATCATTTGCAG
* * *
476201 CATAACTCAAGGCTAGAAGGGTTATCTGCCACCAAAAGACCTTCGAGTTCGACTAAGCTTAGCTC
1 CATAACTCAAGG-TAGAAGGGTTATCTGCCAAC-AAAGACCTTCGAGTTCGACTACGCTCAGCTC
*
476266 CAAGGCACATCATTTGCAG
64 AAAGGCACATCATTTGCAG
* *
476285 CGTAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTACGCTCAGCTC
1 CATAACTCAAGG-TAGAAGGGTTATCTGCCAA-CAAAGACCTTCGAGTTCGACTACGCTCAGCTC
* *
476350 TAAGGCACATCATTTGCAA
64 AAAGGCACATCATTTGCAG
* * * * * * * *
476369 CATAGCTCAAGGAAAAAAGGGCTATTTACCAAAAAAAGTCCTTCGAGTTCGACTACGCTCAGCTC
1 CATAACTCAAGG-TAGAAGGGTTATCTGCC-AACAAAGACCTTCGAGTTCGACTACGCTCAGCTC
*
476434 AAAGGCACATCATTTGTAG
64 AAAGGCACATCATTTGCAG
* * * * * * * * *
476453 CTTAGCTTAAGGCAAGAAGGGTTATCTGCCAACAAATACCATCGAGTCCGATTACACTCAGCTTC
1 CATAACTCAAGG-TAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACGCTCAGC-TC
* **
476518 -GAGGCCACATCATTTATAG
64 AAAGG-CACATCATTTGCAG
* ** * *
476537 CATAACTCAAGGCTATAAGGGTTATCTGTAAACAAAGACCTTCGAGTTCGATTACACTCAGCTCA
1 CATAACTCAAGG-TAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCA
476602 AAGGCACATCATTTGCAG
65 AAGGCACATCATTTGCAG
* * * * * *
476620 GATAGCTTAAGGCGAGAA-GGTCTATCTACCAACAAAATACCTTCGAGTTC
1 CATAACTCAAGG-TAGAAGGGT-TATCTGCCAAC-AAAGACCTTCGAGTTC
476670 AATTCCATTC
Statistics
Matches: 597, Mismatches: 111, Indels: 25
0.81 0.15 0.03
Matches are distributed among these distances:
82 3 0.01
83 91 0.15
84 497 0.83
85 6 0.01
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (82 bp):
CATAACTCAAGGTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCAA
AGGCACATCATTTGCAG
Found at i:476196 original size:168 final size:167
Alignment explanation
Indices: 475900--476669 Score: 845
Period size: 168 Copynumber: 4.6 Consensus size: 167
475890 TCTGTCAGCC
* * * * *
475900 AAGACCTTCGAGTTCGATTACACTCA-ATACAAAGGCACATCATTTGCAGCATAACTCAAGGTAA
1 AAGACCTTCGAGTTCGACTACGCTCAGCT-CAAAGGCACATCATTTGCAGCATAGCTCAAGGCAA
* * *
475964 GAAGGGTTATCTGCCACCAAAAGACCTTCGAGTTCGACTACGCTCATCTCTAAGGCATATCATTT
65 GAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTT
* * *
476029 GTAGCATAACTCAAGGCTATAAGGGATATATTCCAATCA
130 GCAACATAACTCAAGGCTATAAGGG-TATATTCCAAACA
* * * * *
476068 AAGACCTTCGAGTTCGACTACGCTCGGCTCCAAGGTACATCATTTACAACATAGCTCAAGGCAAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAG
* * * * ** *
476133 AAGGGTTATTTGCCAACAAAAGACCTTCGAGTTTGACTATGCTCAGCTCAAATACAAATCATTTG
66 AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTG
* *
476198 CAACATAACTCAAGGCTAGAAGGGT-TATCTGCC-ACCAA
131 CAACATAACTCAAGGCTATAAGGGTATAT-T-CCAAAC-A
* * * * * *
476236 AAGACCTTCGAGTTCGACTAAGCTTAGCTCCAAGGCACATCATTTGCAGCGTAACTCAAGGCTAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAG
* *
476301 AAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCTAAGGCACATCATTTG
66 AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTG
* ** * *
476366 CAACATAGCTCAAGGAAAAAAGGGCTAT-TTACCAAAAA
131 CAACATAACTCAAGGCTATAAGGG-TATATT-CCAAACA
* * * *
476404 AAGTCCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGTAGCTTAGCTTAAGGCAAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAG
* * * * * *
476469 AAGGGTTATCTGCCAAC-AAATACCATCGAGTCCGATTACACTCAGCT-TCGAGGCCACATCATT
66 AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCT-AAGG-CACATCATT
** * **
476532 TATAGCATAACTCAAGGCTATAAGGGT-TATCTGTAAACA
129 TGCAACATAACTCAAGGCTATAAGGGTATAT-TCCAAACA
* * * * *
476571 AAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGGATAGCTTAAGGCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAG
* *
476636 AA-GGTCTATCTACCAACAAAATACCTTCGAGTTC
66 AAGGGT-TATCTGCCAACAAAAGACCTTCGAGTTC
476670 AATTCCATTC
Statistics
Matches: 507, Mismatches: 82, Indels: 26
0.82 0.13 0.04
Matches are distributed among these distances:
166 8 0.02
167 107 0.21
168 387 0.76
169 4 0.01
170 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (167 bp):
AAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAG
AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTG
CAACATAACTCAAGGCTATAAGGGTATATTCCAAACA
Found at i:476362 original size:252 final size:252
Alignment explanation
Indices: 475900--476669 Score: 931
Period size: 252 Copynumber: 3.1 Consensus size: 252
475890 TCTGTCAGCC
* * * * *
475900 AAGACCTTCGAGTTCGATTACACTCA-ATACAAAGGCACATCATTTGCAGCATAACTCAAGG-TA
1 AAGACCTTCGAGTTCGACTACGCTCAGCT-CAAAGACAAATCATTTGCAGCATAACTCAAGGCT-
* * * *
475963 AGAAGGGTTATCTGCCACCAAAAGACCTTCGAGTTCGACTACGCTCATCTCTAAGGCATATCATT
64 AGAAGGGTTATCTGCCACCAAAAGACCTTCGAGTTCGACTAAGCTCAGCTCCAAGGCACATCATT
* * * *
476028 TGTAGCATAACTCAAGGCTATAAGGGATATATTCCAATCAAAGACCTTCGAGTTCGACTACGCTC
129 TGTAGCATAACTCAAGGCTATAAGGGTTATCTGCCAAACAAAGACCTTCGAGTTCGACTACGCTC
* * * * *
476093 GGCTCCAAGGTACATCATTTACAACATAGCTCAAGGCAAGAAGGGTTATTTGCCAACAA
194 AGCTCAAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAAGGGTTATTTACCAACAA
* * * *
476152 AAGACCTTCGAGTTTGACTATGCTCAGCTCAAATACAAATCATTTGCAACATAACTCAAGGCTAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGACAAATCATTTGCAGCATAACTCAAGGCTAG
*
476217 AAGGGTTATCTGCCACCAAAAGACCTTCGAGTTCGACTAAGCTTAGCTCCAAGGCACATCATTTG
66 AAGGGTTATCTGCCACCAAAAGACCTTCGAGTTCGACTAAGCTCAGCTCCAAGGCACATCATTTG
* * * * *
476282 CAGCGTAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTACGCTCAG
131 TAGCATAACTCAAGGCTATAAGGGTTATCTGCCAAACAAAGACCTTCGAGTTCGACTACGCTCAG
* * * * *
476347 CTCTAAGGCACATCATTTGCAACATAGCTCAAGGAAAAAAGGGCTATTTACCAAAAA
196 CTCAAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAAGGGTTATTTACCAACAA
* * * * * * * *
476404 AAGTCCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGTAGCTTAGCTTAAGGCAAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGACAAATCATTTGCAGCATAACTCAAGGCTAG
* * * * * * *
476469 AAGGGTTATCTGCCAAC-AAATACCATCGAGTCCGATTACA-CTCAGCTTCGAGGCCACATCATT
66 AAGGGTTATCTGCCACCAAAAGACCTTCGAGTTCGACTA-AGCTCAGCTCCAAGG-CACATCATT
* * * *
476532 TATAGCATAACTCAAGGCTATAAGGGTTATCTG-TAAACAAAGACCTTCGAGTTCGATTACACTC
129 TGTAGCATAACTCAAGGCTATAAGGGTTATCTGCCAAACAAAGACCTTCGAGTTCGACTACGCTC
** * * *
476596 AGCTCAAAGGCACATCATTTGCAGGATAGCTTAAGGCGAGAA-GGTCTATCTACCAACAA
194 AGCTCAAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAAGGGT-TATTTACCAACAA
*
476655 AATACCTTCGAGTTC
1 AAGACCTTCGAGTTC
476670 AATTCCATTC
Statistics
Matches: 441, Mismatches: 72, Indels: 11
0.84 0.14 0.02
Matches are distributed among these distances:
250 2 0.00
251 112 0.25
252 325 0.74
253 2 0.00
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (252 bp):
AAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGACAAATCATTTGCAGCATAACTCAAGGCTAG
AAGGGTTATCTGCCACCAAAAGACCTTCGAGTTCGACTAAGCTCAGCTCCAAGGCACATCATTTG
TAGCATAACTCAAGGCTATAAGGGTTATCTGCCAAACAAAGACCTTCGAGTTCGACTACGCTCAG
CTCAAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAAGGGTTATTTACCAACAA
Found at i:478601 original size:32 final size:32
Alignment explanation
Indices: 478565--478625 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
478555 ATTATATATA
* * *
478565 TATTTATTACTTATTA-TTTTTTCATTATTCTT
1 TATTTA-TAATTATTACTTCTTTCAATATTCTT
478597 TATTTATAATTATTACTTCTTTCAATATT
1 TATTTATAATTATTACTTCTTTCAATATT
478626 TTAATCTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 8 0.32
32 17 0.68
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.64
Consensus pattern (32 bp):
TATTTATAATTATTACTTCTTTCAATATTCTT
Found at i:478933 original size:6 final size:6
Alignment explanation
Indices: 478877--478937 Score: 56
Period size: 6 Copynumber: 10.5 Consensus size: 6
478867 TATTTTATTA
* * * *
478877 TTTTAT GTTTT-T TTTCAT TTTCAT TTTTAT TTCTAT TTCTAT TTTTA-
1 TTTTAT -TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
478924 -TTTAT TTTTAT TTT
1 TTTTAT TTTTAT TTT
478938 CTTTATCTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
4 4 0.09
5 3 0.06
6 36 0.77
7 4 0.09
ACGTcount: A:0.15, C:0.07, G:0.02, T:0.77
Consensus pattern (6 bp):
TTTTAT
Found at i:486879 original size:12 final size:12
Alignment explanation
Indices: 486862--486898 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
486852 AGAAACCATA
486862 TCTCTC-CCTCTC
1 TCTCTCTCC-CTC
486874 TCTCTCTCCCTC
1 TCTCTCTCCCTC
486886 TCTCTCTCCCTC
1 TCTCTCTCCCTC
486898 T
1 T
486899 TCTAATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 22 0.92
13 2 0.08
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (12 bp):
TCTCTCTCCCTC
Found at i:486881 original size:14 final size:14
Alignment explanation
Indices: 486862--486893 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
486852 AGAAACCATA
486862 TCTCTCCCTCTCTC
1 TCTCTCCCTCTCTC
486876 TCTCTCCCTCTCTC
1 TCTCTCCCTCTCTC
486890 TCTC
1 TCTC
486894 CCTCTTCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (14 bp):
TCTCTCCCTCTCTC
Found at i:489548 original size:22 final size:22
Alignment explanation
Indices: 489520--489588 Score: 120
Period size: 22 Copynumber: 3.1 Consensus size: 22
489510 GGGAACATGA
489520 CCATCAAAGGATGATCCAATGC
1 CCATCAAAGGATGATCCAATGC
489542 CCATCAAAGGATGATCCAATGC
1 CCATCAAAGGATGATCCAATGC
* *
489564 CCATCAAATGATGATCTAATGC
1 CCATCAAAGGATGATCCAATGC
489586 CCA
1 CCA
489589 ATTGTCTTGC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.36, C:0.28, G:0.16, T:0.20
Consensus pattern (22 bp):
CCATCAAAGGATGATCCAATGC
Found at i:493819 original size:39 final size:39
Alignment explanation
Indices: 493774--493853 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
493764 ACATGGTTAG
493774 ATCAATGAGAATGTACAGGGTGAATACAATTGGTTGTGA
1 ATCAATGAGAATGTACAGGGTGAATACAATTGGTTGTGA
*
493813 ATCAATGAGAATGTGCAGGGTGAATACAATTGGTTGTGA
1 ATCAATGAGAATGTACAGGGTGAATACAATTGGTTGTGA
493852 AT
1 AT
493854 GCAAATATTA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.35, C:0.07, G:0.29, T:0.29
Consensus pattern (39 bp):
ATCAATGAGAATGTACAGGGTGAATACAATTGGTTGTGA
Found at i:496500 original size:121 final size:122
Alignment explanation
Indices: 496285--496518 Score: 373
Period size: 121 Copynumber: 1.9 Consensus size: 122
496275 ATGGTACATT
* ***
496285 TGGAGATTATGGTACCAAACTACCAATGGCCATACAATAAATGTAGCCCTCCGGTATTCTGCTAA
1 TGGAGATTATGGTACCAAACTACCAATGGCCATACAATAAACGTAGCCCTCCAACATTCTGCTAA
496350 ATCCAACTCGTGACTTTCACATAGTTCAATATGAGACTTCCAAGTTGGCCATATATA
66 ATCCAACTCGTGACTTTCACATAGTTCAATATGAGACTTCCAAGTTGGCCATATATA
* *
496407 TGGAGATTATGGTACCAAACTACCAGTGG-CATACAATGAACGTAGCCCTCCAACATTCTGCTAA
1 TGGAGATTATGGTACCAAACTACCAATGGCCATACAATAAACGTAGCCCTCCAACATTCTGCTAA
* *
496471 ATCTAACTCGCT-ACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGG
66 ATCCAACTCG-TGACTTTCACATAGTTCAATATGAGACTTCCAAGTTGG
496519 ACTCTTTTAA
Statistics
Matches: 103, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
121 74 0.72
122 29 0.28
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (122 bp):
TGGAGATTATGGTACCAAACTACCAATGGCCATACAATAAACGTAGCCCTCCAACATTCTGCTAA
ATCCAACTCGTGACTTTCACATAGTTCAATATGAGACTTCCAAGTTGGCCATATATA
Found at i:498010 original size:24 final size:24
Alignment explanation
Indices: 497983--498092 Score: 141
Period size: 24 Copynumber: 4.6 Consensus size: 24
497973 CATAATTCAT
*
497983 GTCAAGTATCATATCAAAATCCAA
1 GTCAAGTATCAGATCAAAATCCAA
*
498007 GTCAAGTAGCAGATCAAAATCCAA
1 GTCAAGTATCAGATCAAAATCCAA
* * *
498031 GTCAAGCATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAAAATCCAA
* *
498055 GTC-AGATATTAGATCAAAATCCAT
1 GTCAAG-TATCAGATCAAAATCCAA
498079 GTCAAGTATCAGAT
1 GTCAAGTATCAGAT
498093 TAGAATTCAA
Statistics
Matches: 74, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
23 2 0.03
24 70 0.95
25 2 0.03
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.24
Consensus pattern (24 bp):
GTCAAGTATCAGATCAAAATCCAA
Found at i:500396 original size:17 final size:17
Alignment explanation
Indices: 500374--500416 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
500364 TGGTCAACAG
* *
500374 TGGTCAACGCCGGTCAA
1 TGGTCAACACAGGTCAA
500391 TGGTCAACACAGGTCAA
1 TGGTCAACACAGGTCAA
*
500408 CGGTCAACA
1 TGGTCAACA
500417 GTCGACCGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (17 bp):
TGGTCAACACAGGTCAA
Found at i:505574 original size:3 final size:3
Alignment explanation
Indices: 505566--505598 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
505556 ACATAACAAC
*
505566 TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
505599 ATGTACTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:508304 original size:30 final size:29
Alignment explanation
Indices: 508257--508407 Score: 223
Period size: 29 Copynumber: 5.2 Consensus size: 29
508247 AATATTTACT
* *
508257 AAAATAGCA-CCTTTTCGAATTAAATTCAC
1 AAAATAGCACCCATTTCGAATT-AATTCCC
* **
508286 AAAATAACACCTTTTTCGAATTAAATTCCC
1 AAAATAGCACCCATTTCGAATT-AATTCCC
*
508316 AAAATAACACCCATTTCGAATTAATTCCC
1 AAAATAGCACCCATTTCGAATTAATTCCC
508345 AAAATAGCACCCATTTCGAATTAATTCCC
1 AAAATAGCACCCATTTCGAATTAATTCCC
508374 AAAATAGCACCCATTTCGAATTAATTCCC
1 AAAATAGCACCCATTTCGAATTAATTCCC
508403 AAAAT
1 AAAAT
508408 GTCACCCGGT
Statistics
Matches: 115, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
29 77 0.67
30 38 0.33
ACGTcount: A:0.41, C:0.25, G:0.05, T:0.29
Consensus pattern (29 bp):
AAAATAGCACCCATTTCGAATTAATTCCC
Found at i:514702 original size:14 final size:15
Alignment explanation
Indices: 514667--514699 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
514657 CCGAAATACA
514667 GAAATCAGATATCAG
1 GAAATCAGATATCAG
514682 GAAATCA-ATATTCAG
1 GAAATCAGATA-TCAG
514697 GAA
1 GAA
514700 TCACGTATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.18
15 14 0.82
ACGTcount: A:0.48, C:0.12, G:0.18, T:0.21
Consensus pattern (15 bp):
GAAATCAGATATCAG
Found at i:515486 original size:29 final size:29
Alignment explanation
Indices: 515450--515626 Score: 243
Period size: 29 Copynumber: 6.1 Consensus size: 29
515440 CATTTTACAG
* * * * *
515450 AAATAGCACCCTTTTTTAAATAATTACTA
1 AAATAGCACCCATTTTGAATTAATTCCCA
515479 AAATAGCA-CC-TTTTCGAATTAAATTCCCA
1 AAATAGCACCCATTTT-GAATT-AATTCCCA
* *
515508 AAATAGCA-CCATTTCGAATTAAATCCCA
1 AAATAGCACCCATTTTGAATTAATTCCCA
515536 AAATAGCACCCATTTTGAATTAATTCCCA
1 AAATAGCACCCATTTTGAATTAATTCCCA
515565 AAATAGCACCCATTTTGAATTAATTCCCA
1 AAATAGCACCCATTTTGAATTAATTCCCA
*
515594 AAATAGCACCCATTTCGAATTAATTCCCA
1 AAATAGCACCCATTTTGAATTAATTCCCA
515623 AAAT
1 AAAT
515627 GTCACCCGGT
Statistics
Matches: 135, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
27 4 0.03
28 20 0.15
29 108 0.80
30 3 0.02
ACGTcount: A:0.40, C:0.23, G:0.06, T:0.31
Consensus pattern (29 bp):
AAATAGCACCCATTTTGAATTAATTCCCA
Found at i:515595 original size:86 final size:87
Alignment explanation
Indices: 515450--515626 Score: 261
Period size: 86 Copynumber: 2.0 Consensus size: 87
515440 CATTTTACAG
* * *
515450 AAATAGCACCCTTTTTTAAATAATTACTAAAATAGCACCTTTTCGAATTAAATTCCCAAAATAGC
1 AAATAGCACCCATTTTGAAATAATTACCAAAATAGCACCTTTTCGAATTAAATTCCCAAAATAGC
515515 A-CCATTTCGAATTAAATCCCA
66 ACCCATTTCGAATTAAATCCCA
* *
515536 AAATAGCACCCATTTTGAATTAATTCCCAAAATAGCACCCATTTT-GAATT-AATTCCCAAAATA
1 AAATAGCACCCATTTTGAAATAATTACCAAAATAGCA-CC-TTTTCGAATTAAATTCCCAAAATA
*
515599 GCACCCATTTCGAATTAATTCCCA
64 GCACCCATTTCGAATTAAATCCCA
515623 AAAT
1 AAAT
515627 GTCACCCGGT
Statistics
Matches: 82, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
86 48 0.59
87 30 0.37
88 4 0.05
ACGTcount: A:0.40, C:0.23, G:0.06, T:0.31
Consensus pattern (87 bp):
AAATAGCACCCATTTTGAAATAATTACCAAAATAGCACCTTTTCGAATTAAATTCCCAAAATAGC
ACCCATTTCGAATTAAATCCCA
Found at i:515674 original size:17 final size:17
Alignment explanation
Indices: 515633--515685 Score: 88
Period size: 17 Copynumber: 3.1 Consensus size: 17
515623 AAATGTCACC
515633 CGGTCAACGGGTCGGGT
1 CGGTCAACGGGTCGGGT
515650 CGGGTCAACGGGTCGGGT
1 C-GGTCAACGGGTCGGGT
*
515668 CGGTCAACGGGTCAGGT
1 CGGTCAACGGGTCGGGT
515685 C
1 C
515686 ATAACCGGTC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
17 17 0.50
18 17 0.50
ACGTcount: A:0.13, C:0.25, G:0.45, T:0.17
Consensus pattern (17 bp):
CGGTCAACGGGTCGGGT
Found at i:523590 original size:21 final size:21
Alignment explanation
Indices: 523566--523648 Score: 69
Period size: 21 Copynumber: 3.9 Consensus size: 21
523556 TTGGTGCAGA
*
523566 GGGAATCAATACCCCCTGAAG
1 GGGAACCAATACCCCCTGAAG
*
523587 GGGAACCAATTCCCCCTTTGAAG
1 GGGAACCAATACCCCC--TGAAG
* * *
523610 GGGAACCGATTCCCCC-CATAG
1 GGGAACCAATACCCCCTGA-AG
* *
523631 GGGAATCGATACCCCCTG
1 GGGAACCAATACCCCCTG
523649 GGGGTTCTGG
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
20 1 0.02
21 30 0.59
23 20 0.39
ACGTcount: A:0.27, C:0.33, G:0.24, T:0.17
Consensus pattern (21 bp):
GGGAACCAATACCCCCTGAAG
Found at i:523612 original size:23 final size:21
Alignment explanation
Indices: 523566--523625 Score: 75
Period size: 23 Copynumber: 2.8 Consensus size: 21
523556 TTGGTGCAGA
* *
523566 GGGAATCAATACCCCCTGAAG
1 GGGAACCAATTCCCCCTGAAG
523587 GGGAACCAATTCCCCCTTTGAAG
1 GGGAACCAATTCCCCC--TGAAG
*
523610 GGGAACCGATTCCCCC
1 GGGAACCAATTCCCCC
523626 CATAGGGGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 14 0.41
23 20 0.59
ACGTcount: A:0.27, C:0.33, G:0.23, T:0.17
Consensus pattern (21 bp):
GGGAACCAATTCCCCCTGAAG
Found at i:534989 original size:13 final size:13
Alignment explanation
Indices: 534971--535018 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
534961 TGTTTAATAC
*
534971 ATATAAGATACTT
1 ATATAAGATAATT
* *
534984 ATATAAGTTAAAT
1 ATATAAGATAATT
534997 ACTAATAAGATAATT
1 A-T-ATAAGATAATT
535012 ATATAAG
1 ATATAAG
535019 TCGAGCCCCA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
13 16 0.57
14 2 0.07
15 10 0.36
ACGTcount: A:0.52, C:0.04, G:0.08, T:0.35
Consensus pattern (13 bp):
ATATAAGATAATT
Found at i:542609 original size:18 final size:18
Alignment explanation
Indices: 542588--542629 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
542578 TAAATGCAAC
542588 TTAAACGTCAAA-TAAATT
1 TTAAACG-CAAACTAAATT
*
542606 TTAAAACGGAAACTAAATT
1 TT-AAACGCAAACTAAATT
542625 TTAAA
1 TTAAA
542630 ATTTATAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.52, C:0.10, G:0.07, T:0.31
Consensus pattern (18 bp):
TTAAACGCAAACTAAATT
Found at i:543160 original size:15 final size:16
Alignment explanation
Indices: 543140--543173 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
543130 GAGTCATTGT
*
543140 GGATTTAGGTATT-TA
1 GGATTTAGGGATTCTA
543155 GGATTTAGGGATTCTA
1 GGATTTAGGGATTCTA
543171 GGA
1 GGA
543174 GATTTAAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.26, C:0.03, G:0.32, T:0.38
Consensus pattern (16 bp):
GGATTTAGGGATTCTA
Found at i:545268 original size:131 final size:131
Alignment explanation
Indices: 545026--545390 Score: 541
Period size: 131 Copynumber: 2.8 Consensus size: 131
545016 ATTTTAAGAA
* * * *
545026 AAAAAGATAATATCTATTTATTTCCAATCGAGAATAAATGACCTCTTATGCTTTAAAGCAGTAAT
1 AAAAAGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAGTCAT
* * *
545091 TTATTACTCCGATCAAAATGAAGAGATATCACTATTTCATCCTAAAATTCAATATTGATTCGAGA
66 TTATTACTCCAATCAAAATGAAAAGATATCACTATTTTATCCTAAAATTCAATATTGATTCGAGA
545156 G
131 G
* **
545157 AAAATGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAATAGTCAT
1 AAAAAGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAGTCAT
* * *
545222 TTATTACTCCAATCGAAATGAAAAGATATCACTATTTTGTCTTAAAATTCAATATTGATTCGAGA
66 TTATTACTCCAATCAAAATGAAAAGATATCACTATTTTATCCTAAAATTCAATATTGATTCGAGA
545287 G
131 G
** * * * *
545288 AAAACCATAATATTTAATTATTTCCAATCGAGAATAAATGACCTATCATGCCTTTAAGCAATCAT
1 AAAAAGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAGTCAT
* *
545353 TTATTGCTCCAATCAAAATGAAAAGATATTACTATTTT
66 TTATTACTCCAATCAAAATGAAAAGATATCACTATTTT
545391 CAATATTAAT
Statistics
Matches: 210, Mismatches: 24, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
131 210 1.00
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (131 bp):
AAAAAGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAGTCAT
TTATTACTCCAATCAAAATGAAAAGATATCACTATTTTATCCTAAAATTCAATATTGATTCGAGA
G
Found at i:550982 original size:22 final size:22
Alignment explanation
Indices: 550940--550985 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
550930 TATTATTTTA
*
550940 TTTTATTTTTAATGAAATATTT
1 TTTTATTTTTAATAAAATATTT
*
550962 TTTTA-TTTTCATAAAAGTATTT
1 TTTTATTTTTAATAAAA-TATTT
550984 TT
1 TT
550986 AGTTTTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.63
Consensus pattern (22 bp):
TTTTATTTTTAATAAAATATTT
Found at i:551128 original size:28 final size:29
Alignment explanation
Indices: 551096--551152 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
551086 TCAATACATT
* *
551096 TTTAACATTTATATTATA-ATATTATATA
1 TTTAACATTTATATGATATAGATTATATA
**
551124 TTTAATTTTTATATGATATAGATTATATA
1 TTTAACATTTATATGATATAGATTATATA
551153 ATATATTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 15 0.62
29 9 0.38
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (29 bp):
TTTAACATTTATATGATATAGATTATATA
Found at i:552373 original size:13 final size:14
Alignment explanation
Indices: 552355--552385 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
552345 TAGGAAGACA
552355 ACAAAAAGTTTG-T
1 ACAAAAAGTTTGTT
552368 ACAAAAAGTTTGTT
1 ACAAAAAGTTTGTT
552382 ACAA
1 ACAA
552386 CAATAAGTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.48, C:0.10, G:0.13, T:0.29
Consensus pattern (14 bp):
ACAAAAAGTTTGTT
Found at i:557263 original size:17 final size:17
Alignment explanation
Indices: 557241--557276 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
557231 TTTATAAAGA
557241 GTTTGGCTTTTAATTGG
1 GTTTGGCTTTTAATTGG
*
557258 GTTTGGGTTTTAATTGG
1 GTTTGGCTTTTAATTGG
557275 GT
1 GT
557277 ATGGGGTCCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.11, C:0.03, G:0.33, T:0.53
Consensus pattern (17 bp):
GTTTGGCTTTTAATTGG
Found at i:557281 original size:17 final size:17
Alignment explanation
Indices: 557248--557281 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
557238 AGAGTTTGGC
*
557248 TTTTAATTGGGTTTGGG
1 TTTTAATTGGGTATGGG
557265 TTTTAATTGGGTATGGG
1 TTTTAATTGGGTATGGG
557282 GTCCGGTTAA
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:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (17 bp):
TTTTAATTGGGTATGGG
Found at i:557768 original size:119 final size:119
Alignment explanation
Indices: 557545--557772 Score: 332
Period size: 119 Copynumber: 1.9 Consensus size: 119
557535 CCTCTGTTGG
* * * * * *
557545 ATGAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAGCGAGGCGTTTCTTAT
1 ATGAGTTCTTCTCATTATGAACTCTCAATTGGAAATGTCAAACCCTCAAGCGAGGCATTGCTGAT
* *
557610 TCAAAGTGCTGTGAACCGAGCAATAGGTTGAATAAGTTCTTCTCTCCCTATCGT
66 TCAAAGTGCTGTGAACCGAGCAATAGGTTCAAAAAGTTCTTCTCTCCCTATCGT
*
557664 ATGAGTTCTTCTCATTATGAACTCTTAATTGGAAATGTCAAACCCTCAAGCGAGGCATTGCTGAT
1 ATGAGTTCTTCTCATTATGAACTCTCAATTGGAAATGTCAAACCCTCAAGCGAGGCATTGCTGAT
* * *
557729 TCGAAGTGTTGTGAATCGAGCAATAGG-TCAAAAACGTTCTTCTC
66 TCAAAGTGCTGTGAACCGAGCAATAGGTTCAAAAA-GTTCTTCTC
557773 ATAATAAACT
Statistics
Matches: 96, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
118 5 0.05
119 91 0.95
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (119 bp):
ATGAGTTCTTCTCATTATGAACTCTCAATTGGAAATGTCAAACCCTCAAGCGAGGCATTGCTGAT
TCAAAGTGCTGTGAACCGAGCAATAGGTTCAAAAAGTTCTTCTCTCCCTATCGT
Found at i:558065 original size:135 final size:135
Alignment explanation
Indices: 557646--558108 Score: 581
Period size: 136 Copynumber: 3.4 Consensus size: 135
557636 GTTGAATAAG
* * * * **
557646 TTCTTCTCTCC-CTATCGTATGAGTTCTTCTCATTATGAACTCTTAATTGGAAATGTCAA-ACCC
1 TTCTTCTC-CCTCTGTCGGATGAGTTATTCTCATTAGGAACTCTCCATTGGAAATGTCAATA-CC
* *
557709 TCAAGCGAGGCATTGCTGATTCGAAGTGTTGTGAATCGAGCAATAGGT-CAAAAACGTTCTTCTC
64 TCAAGCGAGGCATTGCTGATT-GAAGTGTTGTGAATCTAGCAATAGGTCCAACAA-GTTCTTCTC
* *
557773 ATAATAAAC
127 ATTATGAAC
* * * * * *
557782 TTTTTCTCACTTTGTCGGATGAGTTATTCTCATTAGGAACTCTCCATTAGAAATATCAATCCCTC
1 TTCTTCTCCCTCTGTCGGATGAGTTATTCTCATTAGGAACTCTCCATTGGAAATGTCAATACCTC
* * * *
557847 AAGCGAGGCATTGCTAATTTGAAGTTTTGTGAATCTAGCAATAGGTCGAACAAGTTCTTCTCAAT
66 AAGCGAGGCATTGCTGA-TTGAAGTGTTGTGAATCTAGCAATAGGTCCAACAAGTTCTTCTCATT
557912 ATGAAC
130 ATGAAC
* *
557918 TTATTCTCCCTCTGTCGGATGAGTTATTCTCATTAGGAACTATCCATTGGAAATGTCAATACCTC
1 TTCTTCTCCCTCTGTCGGATGAGTTATTCTCATTAGGAACTCTCCATTGGAAATGTCAATACCTC
* * * **
557983 AAGAGAGGCATTACTGGTTGAAGTGTTGTGAATCTAATAATAGGTCCAACAAGTTCTTCTCATTA
66 AAGCGAGGCATTGCTGATTGAAGTGTTGTGAATCTAGCAATAGGTCCAACAAGTTCTTCTCATTA
558048 TGAAC
131 TGAAC
** * *
558053 TTCTTCTCCCTCTGTTAGATGAGTTCTTCTCATTAGGAACTCTTCATTGGAAATGT
1 TTCTTCTCCCTCTGTCGGATGAGTTATTCTCATTAGGAACTCTCCATTGGAAATGT
558109 TGATCAATTC
Statistics
Matches: 281, Mismatches: 42, Indels: 9
0.85 0.13 0.03
Matches are distributed among these distances:
135 99 0.35
136 176 0.63
137 6 0.02
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (135 bp):
TTCTTCTCCCTCTGTCGGATGAGTTATTCTCATTAGGAACTCTCCATTGGAAATGTCAATACCTC
AAGCGAGGCATTGCTGATTGAAGTGTTGTGAATCTAGCAATAGGTCCAACAAGTTCTTCTCATTA
TGAAC
Found at i:559069 original size:25 final size:24
Alignment explanation
Indices: 559041--559099 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
559031 CTTGAACCTC
*
559041 TCATTTTCTTTTTCTTTTTTCATTT
1 TCATTTTCTTTTTC-CTTTTCATTT
* *
559066 TCATTTTCCTTTTCCTTTTCCTTT
1 TCATTTTCTTTTTCCTTTTCATTT
559090 T--TTTTCTTTT
1 TCATTTTCTTTT
559100 ATTTTTAGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 8 0.27
24 9 0.30
25 13 0.43
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (24 bp):
TCATTTTCTTTTTCCTTTTCATTT
Found at i:559072 original size:12 final size:12
Alignment explanation
Indices: 559041--559090 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
559031 CTTGAACCTC
*
559041 TCATTTTCTTTT
1 TCATTTTCCTTT
* *
559053 TCTTTTTTCATTT
1 TC-ATTTTCCTTT
559066 TCATTTTCCTTT
1 TCATTTTCCTTT
*
559078 TCCTTTTCCTTT
1 TCATTTTCCTTT
559090 T
1 T
559091 TTTTCTTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
12 22 0.69
13 10 0.31
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (12 bp):
TCATTTTCCTTT
Found at i:569621 original size:20 final size:22
Alignment explanation
Indices: 569598--569644 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
569588 AATTAAAATA
569598 ATAAATAAT-AATAA-AAAAAC
1 ATAAATAATAAATAACAAAAAC
*
569618 AT-AA-AATAAATAACATAAAC
1 ATAAATAATAAATAACAAAAAC
569638 ATAAATA
1 ATAAATA
569645 CAAGGACCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
18 3 0.14
19 7 0.32
20 9 0.41
21 2 0.09
22 1 0.05
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.21
Consensus pattern (22 bp):
ATAAATAATAAATAACAAAAAC
Found at i:572303 original size:3 final size:3
Alignment explanation
Indices: 572295--572347 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
572285 AATTTAATCC
572295 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
572343 ATT AT
1 ATT AT
572348 ATACAACAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:573086 original size:19 final size:21
Alignment explanation
Indices: 573056--573099 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
573046 GCCCATATCA
*
573056 TTTTATTCTTAATATAA-TAT
1 TTTTATTCTTAATAAAAGTAT
573076 TTTTATT-TTAATAAAAGTAT
1 TTTTATTCTTAATAAAAGTAT
573096 TTTT
1 TTTT
573100 TTTATTTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (21 bp):
TTTTATTCTTAATAAAAGTAT
Found at i:573718 original size:2 final size:2
Alignment explanation
Indices: 573711--573768 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
573701 GAAAAACAGA
573711 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
573753 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
573769 GGATAGGTTC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:574728 original size:24 final size:24
Alignment explanation
Indices: 574715--574833 Score: 159
Period size: 24 Copynumber: 5.0 Consensus size: 24
574705 AAACATAATT
* *
574715 CATGTCAAGTATCATATCAAAATC
1 CATGTCAAGTATCAGATCAGAATC
* *
574739 AAGGTCAAGTATCAGATCAGAATC
1 CATGTCAAGTATCAGATCAGAATC
*
574763 CAAGTCAAGTATCAGATCAGAATC
1 CATGTCAAGTATCAGATCAGAATC
*
574787 CATGTC-AGATATCATATCAGAATC
1 CATGTCAAG-TATCAGATCAGAATC
*
574811 CATGTCAAGTATCATATCAGAAT
1 CATGTCAAGTATCAGATCAGAAT
574834 TCAAATTGAA
Statistics
Matches: 85, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
23 2 0.02
24 81 0.95
25 2 0.02
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.26
Consensus pattern (24 bp):
CATGTCAAGTATCAGATCAGAATC
Found at i:574849 original size:72 final size:72
Alignment explanation
Indices: 574715--574851 Score: 170
Period size: 72 Copynumber: 1.9 Consensus size: 72
574705 AAACATAATT
* *
574715 CATGTCAAGTATCATATCAAAATCAAGGTCAAGTATCAGATCAGAATCCAAGTCAAGTATCAGAT
1 CATGTCAAGTATCATATCAAAATCAAGGTCAAGTATCAGATCAGAATCAAAGTCAAGAATCAGAT
574780 CAGAATC
66 CAGAATC
* * * * * *
574787 CATGTC-AGATATCATATCAGAATCCATGTCAAGTATCATATCAGAATTCAAATTGAA-AATCAG
1 CATGTCAAG-TATCATATCAAAATCAAGGTCAAGTATCAGATCAGAA-TCAAAGTCAAGAATCAG
574850 AT
64 AT
574852 AAAATATTCA
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
71 2 0.04
72 46 0.84
73 7 0.13
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (72 bp):
CATGTCAAGTATCATATCAAAATCAAGGTCAAGTATCAGATCAGAATCAAAGTCAAGAATCAGAT
CAGAATC
Found at i:579770 original size:13 final size:12
Alignment explanation
Indices: 579752--579792 Score: 57
Period size: 13 Copynumber: 3.3 Consensus size: 12
579742 AAAAAATGAA
579752 AAAAATGAAGAAT
1 AAAAAT-AAGAAT
579765 AAAAATAAGTAAT
1 AAAAATAAG-AAT
579778 AAAAATAA-AAT
1 AAAAATAAGAAT
579789 AAAA
1 AAAA
579793 TTAAAGGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 7 0.26
12 3 0.11
13 17 0.63
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (12 bp):
AAAAATAAGAAT
Found at i:579791 original size:11 final size:11
Alignment explanation
Indices: 579752--579812 Score: 52
Period size: 13 Copynumber: 5.3 Consensus size: 11
579742 AAAAAATGAA
579752 AAAAATGAAGAAT
1 AAAAAT-AA-AAT
579765 AAAAATAAGTAAT
1 AAAAATAA--AAT
579778 AAAAATAAAAT
1 AAAAATAAAAT
* **
579789 AAAATTAAAGG
1 AAAAATAAAAT
579800 AAAAAT-AAAT
1 AAAAATAAAAT
579810 AAA
1 AAA
579813 TAAATAAATG
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
10 5 0.12
11 16 0.40
12 2 0.05
13 17 0.43
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.18
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:579932 original size:34 final size:35
Alignment explanation
Indices: 579894--579959 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
579884 TAGTAATATG
*
579894 AAAATATAATATA-ATATAAA-CAAATAAAAAAACA
1 AAAATA-AATAAATATATAAACCAAATAAAAAAACA
*
579928 AAAATAAATAAATATATAAACCAAATATAAAA
1 AAAATAAATAAATATATAAACCAAATAAAAAA
579960 GTATACATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 5 0.18
34 13 0.46
35 10 0.36
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.21
Consensus pattern (35 bp):
AAAATAAATAAATATATAAACCAAATAAAAAAACA
Found at i:579948 original size:22 final size:23
Alignment explanation
Indices: 579909--579958 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
579899 ATAATATAAT
579909 ATAAACAAATAAAAAAA-CAAAA
1 ATAAACAAATAAAAAAACCAAAA
* * * *
579931 ATAAATAAATATATAAACCAAAT
1 ATAAACAAATAAAAAAACCAAAA
579954 ATAAA
1 ATAAA
579959 AGTATACATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.74, C:0.08, G:0.00, T:0.18
Consensus pattern (23 bp):
ATAAACAAATAAAAAAACCAAAA
Found at i:581157 original size:106 final size:106
Alignment explanation
Indices: 581019--582246 Score: 1919
Period size: 106 Copynumber: 11.6 Consensus size: 106
581009 CTCTGGAACC
* * * * * *
581019 GGGAAATTGTTTGTTGAAAACCAGTC-GTCCCTTCGTTGTGAAGTTAAACTTGTGTTGTCTCGAG
1 GGGAAATTGTTTATTGACAACCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
581083 TCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT
65 TCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT
* *
581125 GGGAAATTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGATCTTGC----TCTGGAGT
1 GGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* *
581186 CCAATATCCTTCACTGTGAAGTTGAAATTGGCTTTGAAATT
66 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT
* * * * *
581227 GGGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTTTGTGAAGTTGAACTTCCGTTGTCTGGAG
1 GGGAAATTGTTTATTGACAACCAGCGGTCCCTTCG-TCGTGAAGTTGAACTTGCGTTGTCTGGAG
* * *
581292 TCCAATATCCTTCGTTGTGAAGTTGAAATTGGATTTGAAATT
65 TCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT
* * * * *
581334 GAGAAGTTATTTGTTAACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
1 GGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
581399 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT
66 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT
* *
581440 GGGAAGTTGTTTATTGACAACCAGCGATCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
1 GGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* *
581505 CCAATATCCTTCACTGTGAAGTTGAAATTGGATCTGAAATT
66 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT
* * *
581546 GAGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCTTGAAGTTGAACTTGTGTTGTCTGGAGT
1 GGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
581611 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT
66 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT
581652 GGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
1 GGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
581717 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT
66 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT
* * *
581758 GGAAAATTGTTTATTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGAGTTGTCTGGAGT
1 GGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* *
581823 CCAATATCCTTCGTTGTGAAGTTTAAATTGGCTCTGAAATT
66 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT
*
581864 GGAAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
1 GGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
581929 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT
66 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT
* * * *
581970 GGGAAGTTGTTTATTGACAACCTGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAAT
1 GGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
582035 CCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCTGAAATT
66 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT
* * *
582076 GGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTTGTGAAGTCGAACTTGCGTTGTCTAGAGT
1 GGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
582141 CCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATT
66 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT
* * * * * *
582182 GGGAAGTTGTTTGTTGACAACCAGTC-GTCCCTTCATCATGAAGTTGAACTTGTGTTGTCTCGAG
1 GGGAAATTGTTTATTGACAACCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
582246 T
65 T
582247 GGCACGATAT
Statistics
Matches: 1035, Mismatches: 80, Indels: 14
0.92 0.07 0.01
Matches are distributed among these distances:
102 77 0.07
103 15 0.01
105 1 0.00
106 864 0.83
107 78 0.08
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (106 bp):
GGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT
Found at i:586951 original size:10 final size:10
Alignment explanation
Indices: 586934--586989 Score: 55
Period size: 10 Copynumber: 5.7 Consensus size: 10
586924 AAAAATGAAG
586934 AATAAAAATA
1 AATAAAAATA
*
586944 AGTAAAAATA
1 AATAAAAATA
586954 AAT-AAAATAA
1 AATAAAAAT-A
*
586964 AAGGAAAAATA
1 AA-TAAAAATA
586975 AAT--AAATA
1 AATAAAAATA
586983 AATAAAA
1 AATAAAA
586990 TATTAATATA
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
8 8 0.22
9 5 0.14
10 16 0.43
11 3 0.08
12 5 0.14
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (10 bp):
AATAAAAATA
Found at i:586973 original size:21 final size:21
Alignment explanation
Indices: 586934--586984 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
586924 AAAAATGAAG
* *
586934 AATAAAA-ATAAGTAAAAATA
1 AATAAAATAAAAGGAAAAATA
586954 AATAAAATAAAAGGAAAAATA
1 AATAAAATAAAAGGAAAAATA
586975 AAT-AAATAAA
1 AATAAAATAAA
586985 TAAAATATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (21 bp):
AATAAAATAAAAGGAAAAATA
Found at i:587104 original size:33 final size:34
Alignment explanation
Indices: 587066--587130 Score: 89
Period size: 33 Copynumber: 1.9 Consensus size: 34
587056 TAGTAATATG
*
587066 AAAATATAATATA-ATATAAA-CAAATAAAAAACA
1 AAAATA-AATAAATATATAAACCAAATAAAAAACA
*
587099 AAAATAAATAAATATATAAACCAAATATAAAA
1 AAAATAAATAAATATATAAACCAAATAAAAAA
587131 GTATACATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 5 0.18
33 13 0.46
34 10 0.36
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (34 bp):
AAAATAAATAAATATATAAACCAAATAAAAAACA
Found at i:587949 original size:37 final size:37
Alignment explanation
Indices: 587851--587951 Score: 130
Period size: 37 Copynumber: 2.7 Consensus size: 37
587841 ATGCTTGTGG
* * * * *
587851 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGAAAAACTCT
* * *
587888 ATCCTATTTTTAGGTGTTTGAATCCTAGAAAAAGTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGAAAAACTCT
587925 ATCCTATTTTTAGGAGTTTGAATCCTA
1 ATCCTATTTTTAGGAGTTTGAATCCTA
587952 TTAGGACGAA
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGAAAAACTCT
Found at i:588064 original size:24 final size:24
Alignment explanation
Indices: 588030--588148 Score: 159
Period size: 24 Copynumber: 5.0 Consensus size: 24
588020 AAACATAATT
* *
588030 CATGTCCAGTATCATATCAAAATC
1 CATGTCAAGTATCATATCAGAATC
* *
588054 CAGGTCAAGTATCAGATCAGAATC
1 CATGTCAAGTATCATATCAGAATC
* * *
588078 CAAGTCAATTATCAGATCAGAATC
1 CATGTCAAGTATCATATCAGAATC
588102 CATGTC-AGATATCATATCAGAATC
1 CATGTCAAG-TATCATATCAGAATC
588126 CATGTCAAGTATCATATCAGAAT
1 CATGTCAAGTATCATATCAGAAT
588149 TCAAATCGAA
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
23 1 0.01
24 81 0.96
25 2 0.02
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.27
Consensus pattern (24 bp):
CATGTCAAGTATCATATCAGAATC
Found at i:593195 original size:21 final size:21
Alignment explanation
Indices: 593128--593195 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 21
593118 AGTTTGTTAC
* *
593128 AACAATAAGCACATGATAAAA
1 AACAATAAGCAAATGAGAAAA
** *
593149 AAC-ATAAAGACAAAAT-AGCTAC
1 AACAAT-AAG-C-AAATGAGAAAA
593171 AACAATAAGCAAATGAGAAAA
1 AACAATAAGCAAATGAGAAAA
593192 AACA
1 AACA
593196 TGTTGATTAG
Statistics
Matches: 34, Mismatches: 8, Indels: 10
0.65 0.15 0.19
Matches are distributed among these distances:
20 6 0.18
21 14 0.41
22 9 0.26
23 5 0.15
ACGTcount: A:0.63, C:0.15, G:0.10, T:0.12
Consensus pattern (21 bp):
AACAATAAGCAAATGAGAAAA
Found at i:594957 original size:3 final size:3
Alignment explanation
Indices: 594949--594992 Score: 61
Period size: 3 Copynumber: 14.0 Consensus size: 3
594939 TTTGTCTGGG
*
594949 TTA TTA TTA ATA TTA TATA TTTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA T-TA -TTA TTA TTA TTA TTA TTA TTA TTA
594993 AATTTCTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
3 32 0.86
4 4 0.11
5 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:595110 original size:23 final size:23
Alignment explanation
Indices: 595084--595129 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
595074 ATACCTAATT
595084 CAAGCAACCCGTACCC-AACCCAA
1 CAAGCAACCCG-ACCCAAACCCAA
595107 CAAGCAACCCGACCCAAACCCAA
1 CAAGCAACCCGACCCAAACCCAA
595130 ATTTTGTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.41, C:0.48, G:0.09, T:0.02
Consensus pattern (23 bp):
CAAGCAACCCGACCCAAACCCAA
Found at i:597958 original size:12 final size:12
Alignment explanation
Indices: 597937--597966 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
597927 CCTTTCCTCA
*
597937 TATTTATTTATT
1 TATTTTTTTATT
597949 TATTTTTTTATT
1 TATTTTTTTATT
597961 TATTTT
1 TATTTT
597967 GCATAAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (12 bp):
TATTTTTTTATT
Found at i:602052 original size:41 final size:42
Alignment explanation
Indices: 601987--602066 Score: 108
Period size: 41 Copynumber: 1.9 Consensus size: 42
601977 ATCAGTAAGC
* *
601987 TTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAAATA
1 TTTCGAGCAAGATGATTAAATCCTTCGGGCCATCTGTAAATA
* * *
602029 TTTCGAGCAAGATGA-TAAGTCCTTTGGGCCATTTGTAA
1 TTTCGAGCAAGATGATTAAATCCTTCGGGCCATCTGTAA
602067 GACCTTTAGG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
41 19 0.58
42 14 0.42
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (42 bp):
TTTCGAGCAAGATGATTAAATCCTTCGGGCCATCTGTAAATA
Found at i:602295 original size:257 final size:257
Alignment explanation
Indices: 601837--602792 Score: 1165
Period size: 255 Copynumber: 3.7 Consensus size: 257
601827 CCATTAAGTT
* * *
601837 ATTTTGAAAATTGAGAAAACAATTTCCAAAGTTTCTCATTTAAATCTTTTCAGAAAATGAAATTT
1 ATTTTGAAAAATGAGAAAACAATTTCCAAAGTTTCTCATTT-AATGTTTTCAAAAAATGAAATTT
* ** * ** * *
601902 TTGAAAAGTAATAAAGCAATTTCCAAAGTTTCTTACCTAGTAAACCATTTCCCAAATTGGTAAGT
65 TTGAAAAGTAAGAAAGTGATTTCTAAAGTTTCTTACCTAGTAAATTATTTCCAAAATTTGTAAGT
* * * * *
601967 CCTTCGGACCATCAGTAAG-CTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAAATATT
130 CCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGAGTAAATCCTTCGGGTCATCTGTCAGTCTT
* * *
602031 TCGAGCAAGATGATAAGTCCTTTGGGCCATTTGTAAGACCTTTAGGTAGGATGTTTTCACATG
195 TCGAGCAAGATGATAAGTCCTTTGGGCCATCTGTAAGACCTTTAGGCAGGATGTTTCCACATG
* * * * * *
602094 AATTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAGTATTTTCAAAAAATAAAATTTT
1 ATTTTGAAAAATGAGAAAACAATTTCCAAAGTTTCTCATTTAATGTTTTCAAAAAATGAAATTTT
* *
602159 TGAAAAGTAAAAAAATGATTTCTAAAGTTTCTTACCTAGTAAATTATTTCCAAAATTTGTAAGTC
66 TGAAAAGTAAGAAAGTGATTTCTAAAGTTTCTTACCTAGTAAATTATTTCCAAAATTTGTAAGTC
* * * *
602224 ATTCGGGCCATTAGTAAGTCTTTCGAGCATGATGCGTAAATCCTTCGGGTCATTTGTCAGTCTTT
131 CTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGAGTAAATCCTTCGGGTCATCTGTCAGTCTTT
* * ** **
602289 CGAGCAAGATGATAAGTCCTTTGGACTATCCATAAGACCTTCGGGCAGGATGTTTCCACATG
196 CGAGCAAGATGATAAGTCCTTTGGGCCATCTGTAAGACCTTTAGGCAGGATGTTTCCACATG
* * *
602351 ATTTTCAAAAGATGAGAAAACAATTTCCAAAGTTACCCATTTAATGTTTTCAAAAAATGAAATTT
1 ATTTTGAAAA-ATGAGAAAACAATTTCCAAAGTTTCTCATTTAATGTTTTCAAAAAATGAAATTT
* * * *
602416 TTGAAAAGTAAGAAAGTGATTTCCAAAAG----TTACCCAATAAATTATTTCAAAAATTTGTAAG
65 TTGAAAAGTAAGAAAGTGATTT-CTAAAGTTTCTTACCTAGTAAATTATTTCCAAAATTTGTAAG
* * * * *
602477 TCCTTTGGGCCATCAGTAAGTCTTCCGAGCATGATGTGTTAATCCTTTGGGTCATCTGTCAGTCT
129 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGAGTAAATCCTTCGGGTCATCTGTCAGTCT
* * * * * *
602542 TTCGAACAAGATGATAAGT-CTTTCGGGGCATCTGTAAGACC-TTCGAACAGAATATTTCCACAT
194 TTCGAGCAAGATGATAAGTCCTTT-GGGCCATCTGTAAGACCTTTAG-GCAGGATGTTTCCACAT
602605 G
257 G
* *
602606 ATTTTTGAAAAATGAGAAAGCATTTTCCAAAGTTTCTCATTTAATGTTTTCAAAAAAATGAAATT
1 A-TTTTGAAAAATGAGAAAACAATTTCCAAAGTTTCTCATTTAATGTTTTC-AAAAAATGAAATT
* *
602671 TTTGAATAGTAAGAAAGTGATTT-TCAAAGTTTCTTACAC-AGTAAATTATTTCCAAAATTAGTA
64 TTTGAAAAGTAAGAAAGTGATTTCT-AAAGTTTCTTAC-CTAGTAAATTATTTCCAAAATTTGTA
* * * * ** * *
602734 AGTCGTTCCGTCCATCAATAAGTCTTTCGAGGGTGATGATTAAATCCTTCGGGTTATCT
127 AGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGAGTAAATCCTTCGGGTCATCT
602793 ATCTATCTCA
Statistics
Matches: 594, Mismatches: 92, Indels: 24
0.84 0.13 0.03
Matches are distributed among these distances:
254 6 0.01
255 172 0.29
256 134 0.23
257 138 0.23
258 67 0.11
259 76 0.13
260 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Consensus pattern (257 bp):
ATTTTGAAAAATGAGAAAACAATTTCCAAAGTTTCTCATTTAATGTTTTCAAAAAATGAAATTTT
TGAAAAGTAAGAAAGTGATTTCTAAAGTTTCTTACCTAGTAAATTATTTCCAAAATTTGTAAGTC
CTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGAGTAAATCCTTCGGGTCATCTGTCAGTCTTT
CGAGCAAGATGATAAGTCCTTTGGGCCATCTGTAAGACCTTTAGGCAGGATGTTTCCACATG
Found at i:602930 original size:3 final size:3
Alignment explanation
Indices: 602922--602968 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
602912 TTTGTCTGGG
* *
602922 TTA TTA TTA ATA TTA TT- TTA TTTA TTA TTA ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
602967 TT
1 TT
602969 CTTAATAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:602948 original size:21 final size:20
Alignment explanation
Indices: 602922--602982 Score: 86
Period size: 21 Copynumber: 3.0 Consensus size: 20
602912 TTTGTCTGGG
602922 TTATTATTAATATTATTTTA
1 TTATTATTAATATTATTTTA
602942 TTTATTATTAATATTATTATTA
1 -TTATTATTAATATTATT-TTA
* *
602964 TTATTCTTAATAATATTTT
1 TTATTATTAATATTATTTT
602983 TAATTAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 2 0.05
21 32 0.86
22 3 0.08
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (20 bp):
TTATTATTAATATTATTTTA
Found at i:606101 original size:37 final size:37
Alignment explanation
Indices: 606024--606546 Score: 624
Period size: 37 Copynumber: 13.8 Consensus size: 37
606014 TACATATAAC
*
606024 ATATATAATATATA-TTGTTGAAAACATTTTTTTAAA-
1 ATATATAATATATAGTT-TTGAAAACATTTTTTGAAAT
* *
606060 ATATATAATATATAGTTCTGGAAACATTTTTTTGAATATAT
1 ATATATAATATATAGTTTTGAAAACA-TTTTTTG-A-A-AT
* *
606101 ATATATAATTTATAGTTTTGAAAACATTTTTCGAAAAT
1 ATATATAATATATAGTTTTGAAAACATTTTTTG-AAAT
* * *
606139 ATATATAATTTATAGTTTTGAAATCATTTTTCGAAAAT
1 ATATATAATATATAGTTTTGAAAACATTTTTTG-AAAT
* *
606177 ATATAAAATATATAATTTTGAAAACA-TTTTTGAATAT
1 ATATATAATATATAGTTTTGAAAACATTTTTTGAA-AT
606214 ATATATAATATATAGTTTTGAAAACATTTTTTTGAAAAT
1 ATATATAATATATAGTTTTGAAAACA-TTTTTTG-AAAT
*
606253 ATATATAATATATAGTTTTGAAAACATTTTTTGAAAA
1 ATATATAATATATAGTTTTGAAAACATTTTTTGAAAT
606290 ATATATAATATATAGTTTTGAAAACATTTTTTGAAAAT
1 ATATATAATATATAGTTTTGAAAACATTTTTTG-AAAT
* * ** ** *
606328 ATATATAGTATATAGTTTTGAAAAAAAATCATAAAAT
1 ATATATAATATATAGTTTTGAAAACATTTTTTGAAAT
* *
606365 ATATATAGTATATAGTTTTGTAAACA-TTTTTGAAAAT
1 ATATATAATATATAGTTTTGAAAACATTTTTTG-AAAT
*
606402 ATATATAATATATAGTTTTGTAAACA-TTTTTGAAAAT
1 ATATATAATATATAGTTTTGAAAACATTTTTTG-AAAT
**
606439 ATATATAATATATAGTTTTGAAAACATTTTTCAAAAAT
1 ATATATAATATATAGTTTTGAAAACATTTTT-TGAAAT
* *
606477 ATATATAATATATAGTTTTGAAATCATTTTTCGAAAAAT
1 ATATATAATATATAGTTTTGAAAACATTTTTTG--AAAT
* *
606516 ATATATAATATATAATTTTTAAAACATTTTT
1 ATATATAATATATAGTTTTGAAAACATTTTT
606547 GAGAAGCGTA
Statistics
Matches: 431, Mismatches: 40, Indels: 29
0.86 0.08 0.06
Matches are distributed among these distances:
36 25 0.06
37 168 0.39
38 136 0.32
39 68 0.16
40 11 0.03
41 23 0.05
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (37 bp):
ATATATAATATATAGTTTTGAAAACATTTTTTGAAAT
Found at i:606235 original size:75 final size:75
Alignment explanation
Indices: 606024--606546 Score: 705
Period size: 75 Copynumber: 6.9 Consensus size: 75
606014 TACATATAAC
** * *
606024 ATATATAATATATA-TTGTTGAAAACATTTTTTTAAA-ATATATAATATATAGTTCTGGAAACAT
1 ATATATAATATATAGTT-TTGAAAACATTTTTGAAAATATATATAATATATAGTTTTGAAAACA-
606087 TTTTTTGAATATAT
64 TTTTTTGAA-A-AT
* * *
606101 ATATATAATTTATAGTTTTGAAAACATTTTTCGAAAATATATATAATTTATAGTTTTGAAATCAT
1 ATATATAATATATAGTTTTGAAAACATTTTT-GAAAATATATATAATATATAGTTTTGAAAACAT
*
606166 TTTTCGAAAAT
65 TTTTTGAAAAT
* * *
606177 ATATAAAATATATAATTTTGAAAACATTTTTGAATATATATATAATATATAGTTTTGAAAACATT
1 ATATATAATATATAGTTTTGAAAACATTTTTGAAAATATATATAATATATAGTTTTGAAAACA-T
606242 TTTTTGAAAAT
65 TTTTTGAAAAT
606253 ATATATAATATATAGTTTTGAAAACATTTTTTGAAAA-ATATATAATATATAGTTTTGAAAACAT
1 ATATATAATATATAGTTTTGAAAACA-TTTTTGAAAATATATATAATATATAGTTTTGAAAACAT
606317 TTTTTGAAAAT
65 TTTTTGAAAAT
* * * ** * *
606328 ATATATAGTATATAGTTTTGAAAAAAAATCAT-AAAATATATATAGTATATAGTTTTGTAAACA-
1 ATATATAATATATAGTTTTG-AAAACATTTTTGAAAATATATATAATATATAGTTTTGAAAACAT
606391 TTTTTGAAAAT
65 TTTTTGAAAAT
*
606402 ATATATAATATATAGTTTTGTAAACATTTTTGAAAATATATATAATATATAGTTTTGAAAACATT
1 ATATATAATATATAGTTTTGAAAACATTTTTGAAAATATATATAATATATAGTTTTGAAAACATT
**
606467 TTTCAAAAAT
66 TTTTGAAAAT
* * *
606477 ATATATAATATATAGTTTTGAAATCATTTTTCGAAAAATATATATAATATATAATTTTTAAAACA
1 ATATATAATATATAGTTTTGAAAACATTTTT-G-AAAATATATATAATATATAGTTTTGAAAACA
606542 TTTTT
64 TTTTT
606547 GAGAAGCGTA
Statistics
Matches: 396, Mismatches: 39, Indels: 22
0.87 0.09 0.05
Matches are distributed among these distances:
73 6 0.02
74 63 0.16
75 124 0.31
76 97 0.24
77 71 0.18
78 13 0.03
79 22 0.06
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (75 bp):
ATATATAATATATAGTTTTGAAAACATTTTTGAAAATATATATAATATATAGTTTTGAAAACATT
TTTTGAAAAT
Found at i:606622 original size:27 final size:27
Alignment explanation
Indices: 606597--606646 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
606587 AGAACACATT
606597 TTATA-TTATATAATT-TTTATTTACA
1 TTATATTTATATAATTATTTATTTACA
* *
606622 TTATATTTATTTATTTATTTATTTA
1 TTATATTTATATAATTATTTATTTA
606647 TTTTATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 5 0.24
26 8 0.38
27 8 0.38
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (27 bp):
TTATATTTATATAATTATTTATTTACA
Found at i:606632 original size:4 final size:4
Alignment explanation
Indices: 606625--606654 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
606615 ATTTACATTA
606625 TATT TATT TATT TATT TATT TATTT TATT T
1 TATT TATT TATT TATT TATT TA-TT TATT T
606655 TTATTTTAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TATT
Found at i:606642 original size:12 final size:13
Alignment explanation
Indices: 606625--606662 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 13
606615 ATTTACATTA
606625 TATTTATTTA-TT
1 TATTTATTTATTT
606637 TATTTATTTATTT
1 TATTTATTTATTT
606650 TA-TT-TTTATTT
1 TATTTATTTATTT
606661 TA
1 TA
606663 GTCCCAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 9 0.36
12 12 0.48
13 4 0.16
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TATTTATTTATTT
Found at i:606652 original size:27 final size:26
Alignment explanation
Indices: 606594--606660 Score: 73
Period size: 27 Copynumber: 2.6 Consensus size: 26
606584 TTGAGAACAC
*
606594 ATTTTATA-TTATATAATTTTTATTT
1 ATTTTATATTTATTTAATTTTTATTT
** *
606619 ACATTATATTTATTTATTTATTTATTT
1 ATTTTATATTTATTTAATT-TTTATTT
*
606646 ATTTTATTTTTATTT
1 ATTTTATATTTATTT
606661 TAGTCCCAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
25 6 0.18
26 8 0.24
27 19 0.58
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.70
Consensus pattern (26 bp):
ATTTTATATTTATTTAATTTTTATTT
Found at i:610583 original size:26 final size:26
Alignment explanation
Indices: 610554--610607 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
610544 CCTGAAAAGG
610554 AAGTTCAAAGAACTAAATGAAAAACA
1 AAGTTCAAAGAACTAAATGAAAAACA
610580 AAGTTCAAAGAACTAAATGAAAAACA
1 AAGTTCAAAGAACTAAATGAAAAACA
610606 AA
1 AA
610608 CATTGAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.63, C:0.11, G:0.11, T:0.15
Consensus pattern (26 bp):
AAGTTCAAAGAACTAAATGAAAAACA
Found at i:614778 original size:22 final size:21
Alignment explanation
Indices: 614749--614815 Score: 62
Period size: 22 Copynumber: 3.1 Consensus size: 21
614739 TTCATTTCAT
614749 TTTCTTTTGAATTTAATTTTC
1 TTTCTTTTGAATTTAATTTTC
* * **
614770 TTTCATTTTGTATTTTATTTAA
1 TTTC-TTTTGAATTTAATTTTC
* *
614792 TTTCCTTTTAAATTTAATATTC
1 TTT-CTTTTGAATTTAATTTTC
614814 TT
1 TT
614816 CCAGTATGTG
Statistics
Matches: 34, Mismatches: 10, Indels: 3
0.72 0.21 0.06
Matches are distributed among these distances:
21 4 0.12
22 29 0.85
23 1 0.03
ACGTcount: A:0.22, C:0.09, G:0.03, T:0.66
Consensus pattern (21 bp):
TTTCTTTTGAATTTAATTTTC
Found at i:620080 original size:23 final size:24
Alignment explanation
Indices: 620053--620114 Score: 90
Period size: 25 Copynumber: 2.6 Consensus size: 24
620043 CCCCCTTACT
620053 CTAACACTTCTCCCTTT-AAAACG
1 CTAACACTTCTCCCTTTAAAAACG
*
620076 CTAACACTTCTCCCTTTAAAAAACT
1 CTAACACTTCTCCCTTT-AAAAACG
*
620101 TTAACACTTCTCCC
1 CTAACACTTCTCCC
620115 CCTTTTTGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 17 0.49
25 18 0.51
ACGTcount: A:0.31, C:0.35, G:0.02, T:0.32
Consensus pattern (24 bp):
CTAACACTTCTCCCTTTAAAAACG
Found at i:622010 original size:21 final size:22
Alignment explanation
Indices: 621928--622009 Score: 103
Period size: 23 Copynumber: 3.7 Consensus size: 22
621918 AGAACCCCAG
* *
621928 GGGGGTATCGATTCCCCTAC-A
1 GGGGGAATCGATTCCCCTTCAA
*
621949 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGATTCCCCTTC-AA
*
621972 GGGGGAATCGGTTCCCCTTCAA
1 GGGGGAATCGATTCCCCTTCAA
*
621994 GGGGGTATCGATTCCC
1 GGGGGAATCGATTCCC
622010 TCTCCACCAA
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
21 17 0.31
22 16 0.30
23 21 0.39
ACGTcount: A:0.18, C:0.27, G:0.32, T:0.23
Consensus pattern (22 bp):
GGGGGAATCGATTCCCCTTCAA
Found at i:628739 original size:36 final size:37
Alignment explanation
Indices: 628667--629118 Score: 328
Period size: 38 Copynumber: 11.6 Consensus size: 37
628657 ACTTATAACG
* *
628667 TATATAATATATAGTGTTGAAAATATTTTTT--TAA-A
1 TATATAATATATAGTTTTGAAAAT-TTTTTTGAAAATA
* *
628702 TATATAATATTTAGTTTTGAAAATAATTTTTGAAAATA
1 TATATAATATATAGTTTTGAAAAT-TTTTTTGAAAATA
**
628740 TATATAATATATAGTTTTG-ATTTTTTTTTGAAAATA
1 TATATAATATATAGTTTTGAAAATTTTTTTGAAAATA
* *
628776 TATATAATATATAATTTTG-GAATTTTTTTGAAAATA
1 TATATAATATATAGTTTTGAAAATTTTTTTGAAAATA
* *
628812 TATATAATATATAGTTTTGAAAACATTTTTTAATAAATA
1 TATATAATATATAGTTTTGAAAA-TTTTTTTGA-AAATA
***
628851 TATATATATATATA-TATATAT-AATATATAGGTTTGAAAACATTTTTTGAAAA
1 TATATA-ATATATAGT-T-T-TGAA-A-ATTTTTTTG-AAA-A-----T----A
*
628903 TATATAAAATATATAGTTTTGAAAATATTTTTCGAAAATA
1 TATAT--AATATATAGTTTTGAAAAT-TTTTTTGAAAATA
628943 TATATAATATATAGTTTTGAAAACATTTTTTT-AAAATA
1 TATATAATATATAGTTTTG-AAA-ATTTTTTTGAAAATA
* * * *
628981 TATGTAATATGTAGTTTTGAAAACATTTTTCGAAAATA
1 TATATAATATATAGTTTTGAAAA-TTTTTTTGAAAATA
* *** *
629019 TATATAATACATAGTTTTGAAAAACAATTATGAAAAATA
1 TATATAATATATAGTTTTG-AAAATTTTTTTG-AAAATA
* *
629058 TATATAATATATAGTTTTGAAAACTTTTTTGAAAAGA
1 TATATAATATATAGTTTTGAAAATTTTTTTGAAAATA
*
629095 GTATATAATAT-TAGATTTTAAAAA
1 -TATATAATATATAG-TTTTGAAAA
629119 AAATATTTTT
Statistics
Matches: 337, Mismatches: 44, Indels: 69
0.75 0.10 0.15
Matches are distributed among these distances:
35 28 0.08
36 63 0.19
37 22 0.07
38 115 0.34
39 48 0.14
40 16 0.05
41 3 0.01
42 7 0.02
43 3 0.01
44 1 0.00
48 1 0.00
49 1 0.00
50 5 0.01
51 5 0.01
52 9 0.03
53 8 0.02
54 2 0.01
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (37 bp):
TATATAATATATAGTTTTGAAAATTTTTTTGAAAATA
Found at i:628853 original size:2 final size:2
Alignment explanation
Indices: 628848--628879 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
628838 TTTTTAATAA
628848 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
628880 GGTTTGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:628889 original size:55 final size:53
Alignment explanation
Indices: 628809--628917 Score: 173
Period size: 55 Copynumber: 2.0 Consensus size: 53
628799 TTTTTTGAAA
* *
628809 ATATATATAATATATAGTTTTGAAAACATTTTTTAATAAATATATATATATATAT
1 ATATATATAATATATAGGTTTGAAAACATTTTTTAA-AAATATATA-AAATATAT
*
628864 ATATATATAATATATAGGTTTGAAAACATTTTTTGAAAATATATAAAATATAT
1 ATATATATAATATATAGGTTTGAAAACATTTTTTAAAAATATATAAAATATAT
628917 A
1 A
628918 GTTTTGAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
53 8 0.16
54 9 0.18
55 34 0.67
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.44
Consensus pattern (53 bp):
ATATATATAATATATAGGTTTGAAAACATTTTTTAAAAATATATAAAATATAT
Found at i:628900 original size:93 final size:89
Alignment explanation
Indices: 628773--628955 Score: 258
Period size: 93 Copynumber: 2.0 Consensus size: 89
628763 TTTTTTGAAA
* * * *
628773 ATATATATAATATATAATTTTGGAATTTTTTTGAAAATATATATAATATATAGTTTTGAAAACAT
1 ATATATATAATATATAAGTTTGAAAATTTTTTGAAAATATATAAAATATATAGTTTTGAAAACAT
*
628838 TTTTTAATAAATATATATATATATAT
66 TTTTCAA-AAATATATATA-ATATAT
* *
628864 ATATATATAATATATAGGTTTGAAAACATTTTTTGAAAATATATAAAATATATAGTTTTGAAAAT
1 ATATATATAATATATAAGTTTG-AAA-ATTTTTTGAAAATATATAAAATATATAGTTTTGAAAAC
*
628929 ATTTTTCGAAAATATATATAATATAT
64 ATTTTTCAAAAATATATATAATATAT
628955 A
1 A
628956 GTTTTGAAAA
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
91 27 0.33
92 13 0.16
93 42 0.51
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.45
Consensus pattern (89 bp):
ATATATATAATATATAAGTTTGAAAATTTTTTGAAAATATATAAAATATATAGTTTTGAAAACAT
TTTTCAAAAATATATATAATATAT
Found at i:628956 original size:76 final size:76
Alignment explanation
Indices: 628864--629155 Score: 340
Period size: 76 Copynumber: 3.8 Consensus size: 76
628854 ATATATATAT
* *
628864 ATATATATAATATATAGGTTTGAAAACATTTTTTGAAAATATATAAAATATATAGTTTTGAAAAT
1 ATATATATAATATATAGTTTTGAAAACATTTTTTGAAAATATATATAATATATAGTTTTGAAAAT
628929 ATTTTTCGAAA
66 ATTTTTCGAAA
* * * *
628940 ATATATATAATATATAGTTTTGAAAACATTTTTTTAAAATATATGTAATATGTAGTTTTGAAAAC
1 ATATATATAATATATAGTTTTGAAAACATTTTTTGAAAATATATATAATATATAGTTTTGAAAAT
629005 ATTTTTCGAAA
66 ATTTTTCGAAA
* * *
629016 ATATATATAATACATAGTTTTGAAAAACA-ATTATGAAAAATATATATAATATATAGTTTTGAAA
1 ATATATATAATATATAGTTTTG-AAAACATTTTTTG-AAAATATATATAATATATAGTTTTGAAA
629080 ACT-TTTTT-GAAA
64 A-TATTTTTCGAAA
* * * * * *
629092 AGAGTATATAATAT-TAGATTTTAAAAAAAATATTTTTGAGAACACATTTATATTATATAGTTTT
1 ATA-TATATAATATATAG-TTTT-GAAAACAT-TTTTTGA-AA-ATATATATAATATATAGTTTT
629156 TATTTACATT
Statistics
Matches: 184, Mismatches: 22, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
76 103 0.56
77 56 0.30
78 1 0.01
79 6 0.03
80 18 0.10
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.42
Consensus pattern (76 bp):
ATATATATAATATATAGTTTTGAAAACATTTTTTGAAAATATATATAATATATAGTTTTGAAAAT
ATTTTTCGAAA
Found at i:629172 original size:4 final size:4
Alignment explanation
Indices: 629165--629213 Score: 53
Period size: 4 Copynumber: 11.8 Consensus size: 4
629155 TTATTTACAT
* * *
629165 TTTA TTTA TTTA TTTA TTTTG TTTA TTTG TTTA TTTTA TTTT TTTA TTT
1 TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTT
629214 TAGGCCCAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
4 30 0.81
5 7 0.19
ACGTcount: A:0.16, C:0.00, G:0.04, T:0.80
Consensus pattern (4 bp):
TTTA
Found at i:629214 original size:13 final size:13
Alignment explanation
Indices: 629152--629215 Score: 60
Period size: 13 Copynumber: 4.8 Consensus size: 13
629142 TATTATATAG
*
629152 TTTTTATTTACATT
1 TTTTTATTT-TATT
629166 TTATTTA-TTTATT
1 TT-TTTATTTTATT
*
629179 TATTTT-GTTTATT
1 T-TTTTATTTTATT
*
629192 TGTTTATTTTATT
1 TTTTTATTTTATT
629205 TTTTTATTTTA
1 TTTTTATTTTA
629216 GGCCCAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
12 3 0.07
13 30 0.71
14 5 0.12
15 4 0.10
ACGTcount: A:0.19, C:0.02, G:0.03, T:0.77
Consensus pattern (13 bp):
TTTTTATTTTATT
Found at i:634376 original size:3 final size:3
Alignment explanation
Indices: 634370--634408 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
634360 ACATTATTAT
634370 TAA TAA TAA -AA TAA T-A TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
634409 TCCCGAACAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.12
3 30 0.88
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:634697 original size:54 final size:54
Alignment explanation
Indices: 634589--637011 Score: 1671
Period size: 54 Copynumber: 44.8 Consensus size: 54
634579 CAGAAAATAT
* * * * **
634589 GTTCACTCCCTATTCCTTCAGGGAGTAGA-AACTCGAACAATCTT-TTGCCTACGG
1 GTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAA-AATCTTCTT-CAAACGG
* * *
634643 GTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTTGAAAATATTCTGCAAACGG
1 GTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAAATCTTCTTCAAACGG
* * * *
634697 GTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAAATATT-TTGAAAATGT
1 GTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAAATCTTCTT-CAAACGG
* * * ** * *
634751 GTAT-GCTCCCTATTCCTTCAGAGAGTAT-GAGACTCGAACAATCTTCAACAATCGT
1 GT-TCGCTCCCTCTTTCTTCAGGGAGTATAGA-ACTCGAA-AATCTTCTTCAAACGG
* * * * ** * *
634806 G-TCTGCTCCCTATTCCTTCAGAGAGTAT-GAGACTTGAACAATCTTCAACAATCGT
1 GTTC-GCTCCCTCTTTCTTCAGGGAGTATAGA-ACTCGAA-AATCTTCTTCAAACGG
* * * * * * **
634861 G-TCTGTTCCCTATTCCTTCA--GAG---AG---T--ACAATCTTCAAT-AATCAT
1 GTTC-GCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAAATCTTC-TTCAAACGG
* * * * *
634905 G-TCTGCT--ATCTATTCGTTCAGAGAGTATA-AGACTGGAACAATCTTC--AATAAC-C
1 GTTC-GCTCCCTCT-TTC-TTCAGGGAGTATAGA-ACTCGAA-AATCTTCTTCA-AACGG
* * * * *
634958 GTATCTGCTCCCTATTCCTTCAGAGAGTATA-AGACTCGAATAATCTTCTGCAAACAG
1 GT-TC-GCTCCCTCTTTCTTCAGGGAGTATAGA-ACTCGAA-AATCTTCTTCAAACGG
* * * * ** *
635015 GTTCGCTCCCTATTCTTTTCAGGGAGTATAAAACTTGAGAAATCTTCTAAAAATGG
1 GTTCGCTCCCTCTT-TCTTCAGGGAGTATAGAACTCGA-AAATCTTCTTCAAACGG
* * ** ** *
635071 GTTCGCTCCCTATTCCTTTTGGGGAGTATAGAACTCGAACAATC-TCATGAAAATGG
1 GTTCGCTCCCTCTTTC-TTCAGGGAGTATAGAACTCGAA-AATCTTC-TTCAAACGG
* * * * * **
635127 GTTCGCTCCCTATTCCTTTCAAGAAGTATAGAACTCGAGAAATCTTC-TGAAA-TA
1 GTTCGCTCCCTCTTTC-TTCAGGGAGTATAGAACTCGA-AAATCTTCTTCAAACGG
* * * * * ** * *
635181 ATGTCTGCTCTCTATTTGTTCAGAGAGTATA-AGACTCGAACAATCTTCAACAATCGT
1 GT-TC-GCTCCCTCTTTCTTCAGGGAGTATAGA-ACTCGAA-AATCTTCTTCAAACGG
* * * ** * *
635238 GTGT-G-TACCCTATTCCTTCAGAGAGTATA-AGACTCGAACAATCTTCAACAATCGT
1 GT-TCGCT-CCCTCTTTCTTCAGGGAGTATAGA-ACTCGAA-AATCTTCTTCAAACGG
635293 G-TCTGCTCCCTCTTTC-TCTAGGGAGTATAGAACTCGAACAA--TT-TTCAAACGG
1 GTTC-GCTCCCTCTTTCTTC-AGGGAGTATAGAACTCGAA-AATCTTCTTCAAACGG
* * *
635345 GTTCGCTCCCTCTTTC-TCTAGGGAGTATAGAACTCGGACATTTTCTTCAAACGG
1 GTTCGCTCCCTCTTTCTTC-AGGGAGTATAGAACTCGAAAATCTTCTTCAAACGG
* * * *
635399 GTTCGCTCCCTCTTTC-TCTATGGATTATGGAACTCGGAAATCTTCTTCAAACGG
1 GTTCGCTCCCTCTTTCTTC-AGGGAGTATAGAACTCGAAAATCTTCTTCAAACGG
* * *
635453 GTTCGCTCCCTCTTTC-TCTAGGGAGTATGGAACTCGGATATCTTCTTCAAACGG
1 GTTCGCTCCCTCTTTCTTC-AGGGAGTATAGAACTCGAAAATCTTCTTCAAACGG
* *
635507 GTTCGCTCCCTCTTT-TTCTAGGGAGTATGGAACTC-AGACATCTTCTTCAAACGG
1 GTTCGCTCCCTCTTTCTTC-AGGGAGTATAGAACTCGA-AAATCTTCTTCAAACGG
* *
635561 GTTCGCTTCCTCTTTCTAT-AGGGAGTATAGAACTCGAACATCTTCTTCAAACGG
1 GTTCGCTCCCTCTTTCT-TCAGGGAGTATAGAACTCGAAAATCTTCTTCAAACGG
* * * * *
635615 GTTCGCTCCCTCTTTC-TCTAGGGGGTATGGAACTCGGACATCTTCTTCAAATGG
1 GTTCGCTCCCTCTTTCTTC-AGGGAGTATAGAACTCGAAAATCTTCTTCAAACGG
* * *
635669 GTTGGCTCCCTCTTTC-TCTAGGGAGTATGGAACTC-AGACATCTTCTTCAAACGG
1 GTTCGCTCCCTCTTTCTTC-AGGGAGTATAGAACTCGA-AAATCTTCTTCAAACGG
* * * *
635723 GTTCGCTCCCTCTTTC-TCTAGGGATTATGGAACTAGAAAA-ATT-TTCAAACGG
1 GTTCGCTCCCTCTTTCTTC-AGGGAGTATAGAACTCGAAAATCTTCTTCAAACGG
* * * * *
635775 GTTTGTTCCCTCTTTC-TCTAGGGAGTATAGAACTCGAACATTTTATTCAAACGG
1 GTTCGCTCCCTCTTTCTTC-AGGGAGTATAGAACTCGAAAATCTTCTTCAAACGG
* * * * *
635829 GCTCGCTCCCTCTTTC-TCTAAGGAGTATGGAACTCGGACATCTTCTTCAAACGG
1 GTTCGCTCCCTCTTTCTTC-AGGGAGTATAGAACTCGAAAATCTTCTTCAAACGG
* *
635883 GTTCGCTCCCTCTTTC-TCTAGGGAGTAT-GAAACTCGAACATCTTCTTCAAACGA
1 GTTCGCTCCCTCTTTCTTC-AGGGAGTATAG-AACTCGAAAATCTTCTTCAAACGG
* * *
635937 GTTCGCTCCCTCTTTCTAT-AGGGAGTATGGAACTCGGACATCTTCTTCAAACGG
1 GTTCGCTCCCTCTTTCT-TCAGGGAGTATAGAACTCGAAAATCTTCTTCAAACGG
* * *
635991 GTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATCTTCTTCAAACGG
1 GTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAAATCTTCTTCAAACGG
* * *
636045 GTTCGCTCCCTCTTTC-TCTAGGGAGTATGGAACTCGAACATATTCTTCAAACGG
1 GTTCGCTCCCTCTTTCTTC-AGGGAGTATAGAACTCGAAAATCTTCTTCAAACGG
* *
636099 GTTCGCTCCCTCTTTC-TCTAGGGAGTATGGAACTCGGAAATCTTCTTCAAACGG
1 GTTCGCTCCCTCTTTCTTC-AGGGAGTATAGAACTCGAAAATCTTCTTCAAACGG
* * * *
636153 GTTCACTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATCTTCTTCAAACGG
1 GTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAAATCTTCTTCAAACGG
* * * * **
636207 ATTCACTCCCTCTTTC-TCTAGGGAGTATAGAACTCGGACATCTTCTTCAAACAT
1 GTTCGCTCCCTCTTTCTTC-AGGGAGTATAGAACTCGAAAATCTTCTTCAAACGG
* * * **
636261 GTTCGCTCCCTTTTTC-TCTGGGGAGTATGGAACTC-AAACATCTTCTTCTTACGG
1 GTTCGCTCCCTCTTTCTTC-AGGGAGTATAGAACTCGAAA-ATCTTCTTCAAACGG
* * * * * *
636315 GTTCGCTCCCTTTTTCTTCAGGGAGTATAGTACTTGGACATATTCTTCAAACGG
1 GTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAAATCTTCTTCAAACGG
* * * *
636369 GCTCGCTCCCTCTTTATTCAGGGAGTATAGAACTCGAAAATCTTCTACAAACAG
1 GTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAAATCTTCTTCAAACGG
* * *
636423 GTTTGCTCCCTCTTTCTTCAGGGAGTATAGAACTCAAAAATCTTCTGCAAACGG
1 GTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAAATCTTCTTCAAACGG
* * * * * *
636477 GTTCACTCCCTATTTCTTTAGGGAGTATAGAAATCGACTAATCTT-TTGCAAACAG
1 GTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGA-AAATCTTCTT-CAAACGG
* * * * * * *
636532 GTTCGCTCCCTATTTATTTAGGAAGTATAGAACTCGAATGATCTTTTTGCAAATGG
1 GTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAA-AATCTTCTT-CAAACGG
* * * * **
636588 GCTT-GCTCCCTCTTTCTTTAGGGAGTA-GGAACTCGAACGATCTTCTACTTACGG
1 G-TTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAA-AATCTTCTTCAAACGG
* * *
636642 GTTCGCTCCCTCTTTCTTTAGGGAGTA-GGAACTCGAACGATCTTCTATC-AACGG
1 GTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAA-AATCTTCT-TCAAACGG
* * * * * ***
636696 GTTCGCTTCCTCTTTCTTTAGGGAGTA-GGAACTTGAACAATCTTCTGCTTTCGG
1 GTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAA-AATCTTCTTCAAACGG
* * * * *
636750 GTTCGCTCCCTCTTTCTTTAGGGAGTA-GGAACTCAAACAATCTTCTGTC-AATGA
1 GTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAA-AATCTTCT-TCAAACGG
* * * * * **
636804 GTTCACTCCCTCTTTCTTTAGGGAGTA-GGAACTCGAACGATCTTCTGCTTACGG
1 GTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAA-AATCTTCTTCAAACGG
* * * * * **
636858 GTTCACTCCCTCTTTCTTTAGGGAGTA-GGAACTCGAACGATCTTCTGCTTACGG
1 GTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAA-AATCTTCTTCAAACGG
* * * * ** **
636912 GTTCGCTCCCTCTTTCTTTAGGGAGTA-GGAACTC-AAACGATCTTATGCTTATAG
1 GTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAA--ATCTTCTTCAAACGG
* * * *
636966 GTTCACTCCCTCTTTCTTTAGGGAGTATGGAACTCAAACAATCTTC
1 GTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAA-AATCTTC
637012 ACTTGCTTCA
Statistics
Matches: 2028, Mismatches: 246, Indels: 189
0.82 0.10 0.08
Matches are distributed among these distances:
42 2 0.00
43 2 0.00
44 22 0.01
45 2 0.00
46 3 0.00
47 1 0.00
49 1 0.00
51 2 0.00
52 84 0.04
53 31 0.02
54 1367 0.67
55 332 0.16
56 163 0.08
57 16 0.01
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (54 bp):
GTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAAATCTTCTTCAAACGG
Found at i:634825 original size:55 final size:55
Alignment explanation
Indices: 634701--635340 Score: 467
Period size: 55 Copynumber: 11.8 Consensus size: 55
634691 AAACGGGTTC
* * * * * * *
634701 GCTCCCTCTTTCTTCAGGGAGTAT-AGAACTCGAAAATATTTTGAA-AAT-GTGTAT
1 GCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACA-ATCTTCAACAATCGTGTCT
*
634755 GCTCCCTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCT
* *
634810 GCTCCCTATTCCTTCAGAGAGTATGAGACTTGAACAATCTTCAACAATCGTGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCT
* * *
634865 GTTCCCTATTCCTTC--AGAG----AG--T---ACAATCTTCAATAATCATGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCT
** * * * * *
634909 GCTATCTATTCGTTCAGAGAGTATAAGACTGGAACAATCTTCAATAACCGTATCT
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCT
* ** *
634964 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAATAATCTTCTGCAAACAG-GT-T
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATC-GTGTCT
* * * * * *
635018 CGCTCCCTATTCTTTTCAGGGAGTATAAAACTTGAGA-AATCTTCTAAAAAT-GGGT-T
1 -GCTCCCTATTC-CTTCAGAGAGTATAAGACTCGA-ACAATCTTC-AACAATCGTGTCT
** * * *
635074 CGCTCCCTATTCCTTTTGGGGAGTAT-AGAACTCGAACAATC-TCATGAAAAT-GGGT-T
1 -GCTCCCTATTCC-TTCAGAGAGTATAAG-ACTCGAACAATCTTCA--ACAATCGTGTCT
* **
635130 CGCTCCCTATTCCTTTCA-AGAAGTAT-AGAACTCGAGA-AATCTTCTGA-AATAATGTCT
1 -GCTCCCTATTCC-TTCAGAG-AGTATAAG-ACTCGA-ACAATCTTC-AACAATCGTGTCT
* ** *
635187 GCTCTCTATTTGTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTGT
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCT
635242 G-TACCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCT
1 GCT-CCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCT
* * * *
635297 GCTCCCTCTTTC-TCTAGGGAGTAT-AGAACTCGAACAATTTTCAA
1 GCTCCCTATTCCTTC-AGAGAGTATAAG-ACTCGAACAATCTTCAA
635341 ACGGGTTCGC
Statistics
Matches: 485, Mismatches: 62, Indels: 77
0.78 0.10 0.12
Matches are distributed among these distances:
44 31 0.06
46 4 0.01
47 1 0.00
49 2 0.00
50 2 0.00
52 1 0.00
53 10 0.02
54 41 0.08
55 265 0.55
56 121 0.25
57 7 0.01
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.32
Consensus pattern (55 bp):
GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCT
Found at i:634908 original size:44 final size:44
Alignment explanation
Indices: 634843--634931 Score: 124
Period size: 44 Copynumber: 2.0 Consensus size: 44
634833 TGAGACTTGA
* * *
634843 ACAATCTTCAACAATCGTGTCTGTTCCCTATTCCTTCAGAGAGT
1 ACAATCTTCAACAATCATGTCTGCTACCTATTCCTTCAGAGAGT
* * *
634887 ACAATCTTCAATAATCATGTCTGCTATCTATTCGTTCAGAGAGT
1 ACAATCTTCAACAATCATGTCTGCTACCTATTCCTTCAGAGAGT
634931 A
1 A
634932 TAAGACTGGA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (44 bp):
ACAATCTTCAACAATCATGTCTGCTACCTATTCCTTCAGAGAGT
Found at i:634970 original size:99 final size:99
Alignment explanation
Indices: 634788--634986 Score: 299
Period size: 99 Copynumber: 2.0 Consensus size: 99
634778 TGAGACTCGA
* * * *
634788 ACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATGAGACTTGAACAATCTTCA
1 ACAATCTTCAACAATCATGTCTGCTACCTATTCCTTCAGAGAGTATAAGACTGGAACAATCTTCA
* * *
634853 ACAATCGTGTCTGTTCCCTATTCCTTCAGAGAGT
66 ACAACCGTATCTGCTCCCTATTCCTTCAGAGAGT
* * *
634887 ACAATCTTCAATAATCATGTCTGCTATCTATTCGTTCAGAGAGTATAAGACTGGAACAATCTTCA
1 ACAATCTTCAACAATCATGTCTGCTACCTATTCCTTCAGAGAGTATAAGACTGGAACAATCTTCA
*
634952 ATAACCGTATCTGCTCCCTATTCCTTCAGAGAGT
66 ACAACCGTATCTGCTCCCTATTCCTTCAGAGAGT
634986 A
1 A
634987 TAAGACTCGA
Statistics
Matches: 89, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
99 89 1.00
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.32
Consensus pattern (99 bp):
ACAATCTTCAACAATCATGTCTGCTACCTATTCCTTCAGAGAGTATAAGACTGGAACAATCTTCA
ACAACCGTATCTGCTCCCTATTCCTTCAGAGAGT
Found at i:635529 original size:162 final size:162
Alignment explanation
Indices: 635297--637000 Score: 2046
Period size: 162 Copynumber: 10.5 Consensus size: 162
635287 AATCGTGTCT
* *
635297 GCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACA-ATT-TTCAAACGGGTTCGCTCCCTCTTT
1 GCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTT
* * * * *
635360 CTCTAGGGAGTATAGAACTCGGACATTTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTATGGATT
66 CTTTAGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGT
635425 ATGGAACTCGGAA-ATCTTCTTCAAACGGGTTC
131 ATGGAACTC-GAACATCTTCTTCAAACGGGTTC
* *
635457 GCTCCCTCTTTCTCTAGGGAGTATGGAACTCGGATATCTTCTTCAAACGGGTTCGCTCCCTCTTT
1 GCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTT
* * *
635522 -TTCTAGGGAGTATGGAACTCAGACATCTTCTTCAAACGGGTTCGCTTCCTCTTTCTATAGGGAG
66 CTT-TAGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAG
*
635586 TATAGAACTCGAACATCTTCTTCAAACGGGTTC
130 TATGGAACTCGAACATCTTCTTCAAACGGGTTC
* * * *
635619 GCTCCCTCTTTCTCTAGGGGGTATGGAACTCGGACATCTTCTTCAAATGGGTTGGCTCCCTCTTT
1 GCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTT
* * *
635684 CTCTAGGGAGTATGGAACTCAGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGATT
66 CTTTAGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGT
* ** *
635749 ATGGAACTAGAA-AAATT-TTCAAACGGGTTT
131 ATGGAACTCGAACATCTTCTTCAAACGGGTTC
* * * * *
635779 GTTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATTTTATTCAAACGGGCTCGCTCCCTCTTT
1 GCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTT
* *
635844 CTCTAAGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGT
66 CTTTAGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGT
* *
635909 ATGAAACTCGAACATCTTCTTCAAACGAGTTC
131 ATGGAACTCGAACATCTTCTTCAAACGGGTTC
* *
635941 GCTCCCTCTTTCTATAGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTT
1 GCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTT
*
636006 CTTTAGGGAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGT
66 CTTTAGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGT
*
636071 ATGGAACTCGAACATATTCTTCAAACGGGTTC
131 ATGGAACTCGAACATCTTCTTCAAACGGGTTC
*
636103 GCTCCCTCTTTCTCTAGGGAGTATGGAACTCGGAA-ATCTTCTTCAAACGGGTTCACTCCCTCTT
1 GCTCCCTCTTTCTCTAGGGAGTATGGAACTC-GAACATCTTCTTCAAACGGGTTCGCTCCCTCTT
* * *
636167 TCTTTAGGGAGTATGGAACTCGAACATCTTCTTCAAACGGATTCACTCCCTCTTTCTCTAGGGAG
65 TCTTTAGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAG
* * **
636232 TATAGAACTCGGACATCTTCTTCAAACATGTTC
130 TATGGAACTCGAACATCTTCTTCAAACGGGTTC
* * * ** *
636265 GCTCCCTTTTTCTCTGGGGAGTATGGAACTCAAACATCTTCTTCTTACGGGTTCGCTCCCTTTTT
1 GCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTT
* * * * * * *
636330 CTTCAGGGAGTATAGTACTTGGACATATTCTTCAAACGGGCTCGCTCCCTCTTTAT-TCAGGGAG
66 CTTTAGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGGAG
* * * * *
636394 TATAGAACTCGAAAATCTTCTACAAACAGGTTT
130 TATGGAACTCGAACATCTTCTTCAAACGGGTTC
* * * * * *
636427 GCTCCCTCTTTCT-TCAGGGAGTATAGAACTCAAAAATCTTCTGCAAACGGGTTCACTCCCTATT
1 GCTCCCTCTTTCTCT-AGGGAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTT
* * * * * *
636491 TCTTTAGGGAGTATAGAAATC-GACTAATCTT-TTGCAAACAGGTTCGCTCCCTATTTATTTAGG
65 TCTTTAGGGAGTATGGAACTCGGAC--ATCTTCTT-CAAACGGGTTCGCTCCCTCTTTCTCTAGG
* * * * *
636554 AAGTATAGAACTCGAATGATCTTTTTGCAAATGGGCTT-
127 GAGTATGGAACTCGAA-CATCTTCTT-CAAACGGG-TTC
* * **
636592 GCTCCCTCTTTCTTTAGGGAGTA-GGAACTCGAACGATCTTCTACTTACGGGTTCGCTCCCTCTT
1 GCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAC-ATCTTCTTCAAACGGGTTCGCTCCCTCTT
* * *
636656 TCTTTAGGGAGTA-GGAACTCGAACGATCTTCTATC-AACGGGTTCGCTTCCTCTTTCTTTAGGG
65 TCTTTAGGGAGTATGGAACTCGGAC-ATCTTCT-TCAAACGGGTTCGCTCCCTCTTTCTCTAGGG
* * ***
636719 AGTA-GGAACTTGAACAATCTTCTGCTTTCGGGTTC
128 AGTATGGAACTCGAAC-ATCTTCTTCAAACGGGTTC
* * * * *
636754 GCTCCCTCTTTCTTTAGGGAGTA-GGAACTCAAACAATCTTCTGTC-AATGAGTTCACTCCCTCT
1 GCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAC-ATCTTCT-TCAAACGGGTTCGCTCCCTCT
* * ** * *
636817 TTCTTTAGGGAGTA-GGAACTCGAACGATCTTCTGCTTACGGGTTCACTCCCTCTTTCTTTAGGG
64 TTCTTTAGGGAGTATGGAACTCGGAC-ATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGG
* **
636881 AGTA-GGAACTCGAACGATCTTCTGCTTACGGGTTC
128 AGTATGGAACTCGAAC-ATCTTCTTCAAACGGGTTC
* * * * ** ** *
636916 GCTCCCTCTTTCTTTAGGGAGTA-GGAACTCAAACGATCTTATGCTTATAGGTTCACTCCCTCTT
1 GCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAC-ATCTTCTTCAAACGGGTTCGCTCCCTCTT
636980 TCTTTAGGGAGTATGGAACTC
65 TCTTTAGGGAGTATGGAACTC
637001 AAACAATCTT
Statistics
Matches: 1357, Mismatches: 158, Indels: 55
0.86 0.10 0.04
Matches are distributed among these distances:
160 173 0.13
161 23 0.02
162 969 0.71
163 68 0.05
164 52 0.04
165 68 0.05
166 4 0.00
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.33
Consensus pattern (162 bp):
GCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTT
CTTTAGGGAGTATGGAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGT
ATGGAACTCGAACATCTTCTTCAAACGGGTTC
Found at i:647072 original size:3 final size:3
Alignment explanation
Indices: 647066--647101 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
647056 ACATTATTAT
647066 TAA TAA TAA -AA TAA T-A TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
647102 TCCCGGACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:651870 original size:16 final size:17
Alignment explanation
Indices: 651839--651873 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
651829 CGATAATAAG
651839 AGATTTAAATTTTTTTA
1 AGATTTAAATTTTTTTA
651856 AGATTTAAATTTTTTTA
1 AGATTTAAATTTTTTTA
651873 A
1 A
651874 TAAAAAATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (17 bp):
AGATTTAAATTTTTTTA
Found at i:654912 original size:20 final size:20
Alignment explanation
Indices: 654887--654936 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
654877 ATGACAATAT
654887 AACCGGTAAAAATATGACAA
1 AACCGGTAAAAATATGACAA
***
654907 AACCGGTTTCAATATGACAA
1 AACCGGTAAAAATATGACAA
*
654927 AATCGGTAAA
1 AACCGGTAAA
654937 GAGCTACCGG
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.20
Consensus pattern (20 bp):
AACCGGTAAAAATATGACAA
Found at i:655061 original size:194 final size:194
Alignment explanation
Indices: 654764--655196 Score: 559
Period size: 194 Copynumber: 2.2 Consensus size: 194
654754 ATTGAAATTT
* * * * * * *
654764 GTATCGATACTTTTCTAAGTATATGCACCAAATTATAGATACGTTATGAATTTAAAAAAATTGCA
1 GTATCGATACTTTTATAAGTATATGTATCATATTATCGATACTTTAGGAATTTAAAAAAATTGCA
* * **
654829 ATAATAAAGCATATAAAATATCGATACTTTATAAACATGTATCGATACATGACAATATAACCGGT
66 ATAATAAAGCATATAAAATATCAATACTTTAGAAACATGTATCGATACATGACAATATAACAAGT
* * * *
654894 AAAAATATGACAAAACCGGTTTCAATATGACAAAATC-GGTAAAG-AGCTACCGGATATGTTGAA
131 AAAAATATGACAAAACCGATTTCAATATGACAAAA-CAGATAAAGCA-CTACAGAATATGTTGAA
654957 G
194 G
*
654958 GTATCGATACTTTTATAAGTATATGTATCATATTATCGATACTTTAGGAATTTAAAAGAATTAG-
1 GTATCGATACTTTTATAAGTATATGTATCATATTATCGATACTTTAGGAATTTAAAAAAATT-GC
*** * *
655022 AATAATGGCGCCTATAAAGTATCAATACTTTAGAAACATGTATCGATACATGACAATATAACAAG
65 AATAATAAAGCATATAAAATATCAATACTTTAGAAACATGTATCGATACATGACAATATAACAAG
* * * *
655087 TTAAAATATGACAAAACCGATTTTAATATGACAAAACAGATAAAGCATTATAGAATATGTTGAAG
130 TAAAAATATGACAAAACCGATTTCAATATGACAAAACAGATAAAGCACTACAGAATATGTTGAAG
* *
655152 GTATCAATA-TTTTAATAAGTATATGTATCATATTATCGAAACTTT
1 GTATCGATACTTTT-ATAAGTATATGTATCATATTATCGATACTTT
655197 TAAAAGAAGA
Statistics
Matches: 208, Mismatches: 27, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
193 5 0.02
194 201 0.97
195 2 0.01
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.32
Consensus pattern (194 bp):
GTATCGATACTTTTATAAGTATATGTATCATATTATCGATACTTTAGGAATTTAAAAAAATTGCA
ATAATAAAGCATATAAAATATCAATACTTTAGAAACATGTATCGATACATGACAATATAACAAGT
AAAAATATGACAAAACCGATTTCAATATGACAAAACAGATAAAGCACTACAGAATATGTTGAAG
Found at i:658879 original size:6 final size:6
Alignment explanation
Indices: 658850--658914 Score: 67
Period size: 6 Copynumber: 10.8 Consensus size: 6
658840 TTTCATTTTC
* * * * *
658850 AATTTC AATTTT AATTCG AGTTTG AATTTG AATTTG AATTTT AATTTG
1 AATTTG AATTTG AATTTG AATTTG AATTTG AATTTG AATTTG AATTTG
* *
658898 AGTTTG AATTTC AATTT
1 AATTTG AATTTG AATTT
658915 CGTCTCCAAT
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 48 1.00
ACGTcount: A:0.31, C:0.05, G:0.12, T:0.52
Consensus pattern (6 bp):
AATTTG
Found at i:658895 original size:18 final size:18
Alignment explanation
Indices: 658850--658914 Score: 76
Period size: 18 Copynumber: 3.6 Consensus size: 18
658840 TTTCATTTTC
* *
658850 AATTTCAATTTTAATTCG
1 AATTTCAATTTGAATTTG
* *
658868 AGTTTGAATTTGAATTTG
1 AATTTCAATTTGAATTTG
* *
658886 AATTTTAATTTGAGTTTG
1 AATTTCAATTTGAATTTG
658904 AATTTCAATTT
1 AATTTCAATTT
658915 CGTCTCCAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.31, C:0.05, G:0.12, T:0.52
Consensus pattern (18 bp):
AATTTCAATTTGAATTTG
Found at i:658915 original size:6 final size:6
Alignment explanation
Indices: 658816--658915 Score: 51
Period size: 6 Copynumber: 16.7 Consensus size: 6
658806 TTTATGCAGT
* * * * *
658816 TTTCAT TTTCAA TTTTAGA ATT-AA TTTCAT TTTCAA TTTCAA TTTTAA
1 TTTCAA TTTCAA TTTCA-A TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA
* * * * * * * *
658864 -TTCGAG TTTGAA TTTGAA TTTGAA TTTTAA TTTGAG TTTGAA TTTCAA
1 TTTC-AA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA
658912 TTTC
1 TTTC
658916 GTCTCCAATA
Statistics
Matches: 74, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
5 5 0.07
6 64 0.86
7 5 0.07
ACGTcount: A:0.29, C:0.08, G:0.09, T:0.54
Consensus pattern (6 bp):
TTTCAA
Found at i:661870 original size:227 final size:225
Alignment explanation
Indices: 661409--661892 Score: 664
Period size: 227 Copynumber: 2.1 Consensus size: 225
661399 ATTACTTTAA
** * *
661409 AGTAATTAACCGGTTATGTTATCGTCGGATTCCTAAGGCTCTATCAACTTAAATTTTGTTAACAT
1 AGTAATTAACCGGTTATGTTATCGTCGGATTTATAAGGCTATATCAACTTAAATTTTGGTAACAT
* * * *
661474 TTAGGTGTTACCTAATATGTTGATAATACTGATAACAAATTAGGTAATTAACCTATTTTGTTATT
66 TTAGGCGTTACCTAATATGTTGATAATACTAATAACAAATTAAGTAATTAACCTATTTTGTTATC
* * * * * * * * * *
661539 TTCAGATTTCTAAGGCCCCATCAGCTTTAATAATGCTCTACTTATTATGTTACGTAAGTGCTACC
131 GTCAGATTTCAAAAGCCCCATCAGCTTAAAAAAGGCTCTACATATTACGTTACATAAGCGCTACC
* *
661604 TAATATGTTATTATTCTTGATAATGTTTCT
196 TAATATGTTATTATGCTTGATAATGTTTCC
* ** *
661634 AGTAATTAACCGGTTATGTTATCGTCGAATTTATAAGGCTATATCAGTTTACAA-TTTGGTAATA
1 AGTAATTAACCGGTTATGTTATCGTCGGATTTATAAGGCTATATCAACTTA-AATTTTGGTAACA
661698 TTTTAGGCGTTACCTAATATGTTGATAATACTAATAACAAATTAAGTAATTAACCTATTTTGTTA
65 -TTTAGGCGTTACCTAATATGTTGATAATACTAATAACAAATTAAGTAATTAACCTATTTTGTTA
* * * *
661763 TCGTCGGATTTGCAAAATCCCCATCAGCTTAAAAAAGGTTCTACATATTACGTTATATAAGCGCT
129 TCGTCAGATTT-CAAAAGCCCCATCAGCTTAAAAAAGGCTCTACATATTACGTTACATAAGCGCT
661828 ACCTAATATGTTATTATGCTTGATAATGTTTCC
193 ACCTAATATGTTATTATGCTTGATAATGTTTCC
* *
661861 AGTAATTAACCGATTATATTATCGTCGGATTT
1 AGTAATTAACCGGTTATGTTATCGTCGGATTT
661893 CCAAAGCCCC
Statistics
Matches: 225, Mismatches: 31, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
225 53 0.24
226 71 0.32
227 101 0.45
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (225 bp):
AGTAATTAACCGGTTATGTTATCGTCGGATTTATAAGGCTATATCAACTTAAATTTTGGTAACAT
TTAGGCGTTACCTAATATGTTGATAATACTAATAACAAATTAAGTAATTAACCTATTTTGTTATC
GTCAGATTTCAAAAGCCCCATCAGCTTAAAAAAGGCTCTACATATTACGTTACATAAGCGCTACC
TAATATGTTATTATGCTTGATAATGTTTCC
Found at i:661957 original size:118 final size:119
Alignment explanation
Indices: 661742--662001 Score: 387
Period size: 118 Copynumber: 2.2 Consensus size: 119
661732 TAACAAATTA
* * * **
661742 AGTAATTAACCTATTTTGTTATCGTCGGATTTGCAAAATCCCCATCAGCTTAAAAAAGGTTCTAC
1 AGTAATTAACCGATTATGTTATCGTCGGATTTGCAAAAGCCCCATCAGCTTAAAAAAGGCACTAC
* *
661807 ATATTACGTTATATAAGCGCTACCTAATATGTTATTATGCTTGATAATGTTTCC
66 ATATTACGTTATATAAGAGCTACCTAATATGTTATTATGCTTAATAATGTTTCC
* * *
661861 AGTAATTAACCGATTATATTATCGTCGGATTT-CCAAAGCCCCATCAGCTTTAAAAAGGCACTAC
1 AGTAATTAACCGATTATGTTATCGTCGGATTTGCAAAAGCCCCATCAGCTTAAAAAAGGCACTAC
* * *
661925 CTATTTCGTTATATAAGAGCTACCTAATATGTTATTATGCTTAATAATGTTTCT
66 ATATTACGTTATATAAGAGCTACCTAATATGTTATTATGCTTAATAATGTTTCC
*
661979 AGTAATTAACCGGTTATGTTATC
1 AGTAATTAACCGATTATGTTATC
662002 ATCTATATTT
Statistics
Matches: 126, Mismatches: 15, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
118 97 0.77
119 29 0.23
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (119 bp):
AGTAATTAACCGATTATGTTATCGTCGGATTTGCAAAAGCCCCATCAGCTTAAAAAAGGCACTAC
ATATTACGTTATATAAGAGCTACCTAATATGTTATTATGCTTAATAATGTTTCC
Found at i:665779 original size:20 final size:20
Alignment explanation
Indices: 665751--665793 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
665741 TATATTGGGC
* *
665751 TATTGTCTATTGTTTATGGT
1 TATTGTCTATGGTATATGGT
*
665771 TATTTTCTATGGTATATGGT
1 TATTGTCTATGGTATATGGT
665791 TAT
1 TAT
665794 GGAATAATGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.19, C:0.05, G:0.19, T:0.58
Consensus pattern (20 bp):
TATTGTCTATGGTATATGGT
Found at i:667410 original size:26 final size:28
Alignment explanation
Indices: 667359--667416 Score: 77
Period size: 26 Copynumber: 2.1 Consensus size: 28
667349 AATTGTTTTG
*
667359 TCCTCCTAAAATTTATATAAGTTCACTT
1 TCCTCCTAAAATTTATATAAGTTCACTC
667387 TCCT-CTAAAATGTTATA-AA-TTCACTC
1 TCCTCCTAAAAT-TTATATAAGTTCACTC
667413 TCCT
1 TCCT
667417 AGTATAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 10 0.36
27 9 0.32
28 9 0.32
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (28 bp):
TCCTCCTAAAATTTATATAAGTTCACTC
Found at i:669620 original size:156 final size:155
Alignment explanation
Indices: 669320--669627 Score: 386
Period size: 156 Copynumber: 2.0 Consensus size: 155
669310 TTATTTTTAA
* * * *
669320 AAAAACCATAGTAATCCCTCCAACCGAACACATCAAAATGTGTAGGTTCCCCATAACCATACACC
1 AAAAACCATAGCAATCCCTCCAACCCAACACATCAAAATGTGTAGGATCCCCAGAACCATACACC
**** * *
669385 TGTTGTACATCTAGTAAGACCCTGAGCACAAAGCCAAGGAGCCTACGAAAAGACTTCCTCCAACA
66 CACCGTACATCTAGTAAGACCATGAGCACAAAGCCAAGGAGCCTACGAAAAGACTTCATCCAACA
*
669450 ATACCCCCAAATAAAATATTTTATC
131 ATACCCCCAAATAAAACATTTTATC
* * *
669475 AAAAACCATAGCAATCCCTTCAGCCCAACACATCATAATGTGTAGGATCCCCAGAACCATACACC
1 AAAAACCATAGCAATCCCTCCAACCCAACACATCAAAATGTGTAGGATCCCCAGAACCATACACC
* * * * * *
669540 CACCGTCACATC-AGGTAAGGCCATGAGCACAAAGCCGAGGAGCTTGC-AAGTATACTTCATCCA
66 CACCGT-ACATCTA-GTAAGACCATGAGCACAAAGCCAAGGAGCCTACGAA-AAGACTTCATCCA
*
669603 ACATTACCCCCAAATAAAACATTTT
128 ACAATACCCCCAAATAAAACATTTT
669628 TCTTCATTAA
Statistics
Matches: 129, Mismatches: 21, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
155 63 0.49
156 66 0.51
ACGTcount: A:0.38, C:0.30, G:0.13, T:0.20
Consensus pattern (155 bp):
AAAAACCATAGCAATCCCTCCAACCCAACACATCAAAATGTGTAGGATCCCCAGAACCATACACC
CACCGTACATCTAGTAAGACCATGAGCACAAAGCCAAGGAGCCTACGAAAAGACTTCATCCAACA
ATACCCCCAAATAAAACATTTTATC
Found at i:669721 original size:24 final size:24
Alignment explanation
Indices: 669671--669733 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
669661 ATAATTCAGA
*
669671 TCAGATATCATAACAAAATCTAGG
1 TCAGGTATCATAACAAAATCTAGG
* *
669695 TCAGGTATCAGAACAAAATAC-ATG
1 TCAGGTATCATAACAAAAT-CTAGG
*
669719 TCAAGTATCATAACA
1 TCAGGTATCATAACA
669734 GAATTCAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
24 32 0.97
25 1 0.03
ACGTcount: A:0.46, C:0.17, G:0.13, T:0.24
Consensus pattern (24 bp):
TCAGGTATCATAACAAAATCTAGG
Found at i:673818 original size:2 final size:2
Alignment explanation
Indices: 673811--673842 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
673801 TATTTAAATA
673811 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
673843 TATGTTCGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:674302 original size:17 final size:17
Alignment explanation
Indices: 674271--674304 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
674261 GATTAAAACC
674271 ATTAGATTCAATTTTTT
1 ATTAGATTCAATTTTTT
*
674288 ATTAG-TTCAAGTTTTT
1 ATTAGATTCAATTTTTT
674304 A
1 A
674305 ATTTTGTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.29, C:0.06, G:0.09, T:0.56
Consensus pattern (17 bp):
ATTAGATTCAATTTTTT
Found at i:682345 original size:26 final size:27
Alignment explanation
Indices: 682308--682366 Score: 93
Period size: 26 Copynumber: 2.2 Consensus size: 27
682298 AAGGGATCGA
*
682308 AAAAACACAGAGATCATTCATAAACAT
1 AAAAACACAGAGAGCATTCATAAACAT
*
682335 AAAAA-ACAGAGAGCATTCATCAACAT
1 AAAAACACAGAGAGCATTCATAAACAT
682361 AAAAAC
1 AAAAAC
682367 CAAATAGAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 24 0.83
27 5 0.17
ACGTcount: A:0.58, C:0.19, G:0.08, T:0.15
Consensus pattern (27 bp):
AAAAACACAGAGAGCATTCATAAACAT
Found at i:682469 original size:18 final size:19
Alignment explanation
Indices: 682428--682473 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
682418 ATAAAAACCA
*
682428 AAAAAATACCATAGGAAAC
1 AAAAAATACCAGAGGAAAC
*
682447 AAAAAATACCAGATGAAAC
1 AAAAAATACCAGAGGAAAC
682466 AAAAAATA
1 AAAAAATA
682474 GAGAAAATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.67, C:0.13, G:0.09, T:0.11
Consensus pattern (19 bp):
AAAAAATACCAGAGGAAAC
Found at i:688072 original size:174 final size:175
Alignment explanation
Indices: 687778--688141 Score: 525
Period size: 174 Copynumber: 2.1 Consensus size: 175
687768 AAGATGATAT
** *
687778 GTCCTTCGGGCCATCTATATGACCTTTGGGCATGATGTTTCCACATGAATTTTAAAAATGAAAAA
1 GTCCTTCGGGCCATCTATATGACCTTCAGGCAGGATGTTTCCACATGAATTTTAAAAATGAAAAA
** * *
687843 TGTTATTTTCAAAGTTTCTCATTTAGTATTTTTAGAAAGTGAAATTTTTGAAAAGTGAGAAAGCT
66 TGCAATTTTCAAAGTTTCTCATTTAGTATTTTCAGAAAGTGAAATTTTTGAAAAGTAAGAAAG-T
* *
687908 -ATTTCCAAAGTTTCTTACCCAGTAAACCAATTCCAAATTCAGTAA
130 GATTTCCAAAGTTTCTTACCCAATAAACCAATTCCAAAATCAGTAA
* * *
687953 GTCCTTCGGGCCATCTATATGACCTTCAGGCAGGATGTTTTCATATGAATTTTAAAAATGAGAAA
1 GTCCTTCGGGCCATCTATATGACCTTCAGGCAGGATGTTTCCACATGAATTTTAAAAATGAAAAA
* *
688018 -GCAATTTTCAAAGTTTCTCATTTAGTATTTTCAGAAAGTGGAATTTTTGAAAAGTAAGAATGTG
66 TGCAATTTTCAAAGTTTCTCATTTAGTATTTTCAGAAAGTGAAATTTTTGAAAAGTAAGAAAGTG
** * *
688082 ATTTCCAAAGTTTCTTACCCAATAAATTATTTCCAAAATCGGTAA
131 ATTTCCAAAGTTTCTTACCCAATAAACCAATTCCAAAATCAGTAA
* *
688127 GTCATTCGGGTCATC
1 GTCCTTCGGGCCATC
688142 AGTAAGTCTT
Statistics
Matches: 168, Mismatches: 20, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
173 1 0.01
174 108 0.64
175 59 0.35
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (175 bp):
GTCCTTCGGGCCATCTATATGACCTTCAGGCAGGATGTTTCCACATGAATTTTAAAAATGAAAAA
TGCAATTTTCAAAGTTTCTCATTTAGTATTTTCAGAAAGTGAAATTTTTGAAAAGTAAGAAAGTG
ATTTCCAAAGTTTCTTACCCAATAAACCAATTCCAAAATCAGTAA
Found at i:688498 original size:20 final size:20
Alignment explanation
Indices: 688475--688513 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
688465 AGTCTTTCAG
*
688475 GCCATCTATAAGGCCTTCGA
1 GCCATCTATAAGACCTTCGA
688495 GCCATCTATAAGACCTTCG
1 GCCATCTATAAGACCTTCG
688514 GGTAGGATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.26
Consensus pattern (20 bp):
GCCATCTATAAGACCTTCGA
Found at i:688796 original size:260 final size:260
Alignment explanation
Indices: 687950--688801 Score: 645
Period size: 258 Copynumber: 3.3 Consensus size: 260
687940 CCAAATTCAG
* * * * * *
687950 TAAGTCCTTCGGGCCATCTATATGACCTTCAGGCAGGATGTTTTCATATGAATTTTAAAAATGAG
1 TAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAA-TTTGAAAATGAG
** *** * * ** * * **
688015 AAAGCAATTTTC----AAAGTTTCTCATTT--AGTATTTTCAGAAAGTGGAATTTTTGAAAAGTA
65 AAAGTGATTTTCAAAAAAAGAAGCTCATTTGCA-AAGTTTCTCAAAGAGAAATTTTCAAAAAGT-
* * * * *
688074 AGAATGTGATTTCCAAAGTTTCTTACCCAATAAATTATTTCCAAAATCGGTAAGTCATTCGGGTC
128 AGAAAGTGATTTCCAAAGTTTCTTACCCAATAAACTATTTCCAAAATCAGTAAGTCATTTGGGCC
* * * *
688139 ATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTTGGGTCATATGTCAGTCTTTCGATCAAGA
193 ATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTTGGGTCATATGTAAGTCTTTTGAGCAAGA
688204 TGA
258 TGA
* *
688207 TAAGTCCTTCGGGCCATTCATAAGACCTTCGGGTAGGATGTTTTCAGATGAATTTGAAAAATGAG
1 TAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAATTTG-AAAATGAG
* * * *** ** ** * **
688272 GAAGCGA-TTTC---CAAAGTTTCTCATTTGGTATTTTTCTGAAAGAGAAATTTTTGAAAAGTAA
65 AAAGTGATTTTCAAAAAAAGAAGCTCATTTGCAAAGTTTCTCAAAGAGAAATTTTCAAAAAGT-A
* * * * *
688333 GAAAGTGATTTCGAAAGTTTCTTACCCAATAAACTATTTCCAAAAT-TGGAAGTCA-TTCGGCTA
129 GAAAGTGATTTCCAAAGTTTCTTACCCAATAAACTATTTCCAAAATCAGTAAGTCATTTGGGCCA
* * * * *
688396 TCATTAAGTCTTTC-AGGCATGACGATTAAATCCTATGGGTCATCTGTTAGGT-TTTTGAGCAAG
194 TCAATAAGTCTTTCGA-GCATGATGATTAAATCCTTTGGGTCATATG-TAAGTCTTTTGAGCAAG
688459 ATGA
257 ATGA
* * * * * * * * * **
688463 TAAGTCTTTCAGGCCATCTATAAGGCCTTC--G-AGCCAT-CTAT-A-A-GACCTTCGGGTAGGA
1 TAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAG-GATGTTTTCACATGA-ATT--TG-AAAA
*** * * *** *
688521 TGTTTTCACGTGATTTTCAAAAAATGAGAAAGC-CATTTTCAAAGTTTCTCATTTAG-TATTTTC
61 TG--AGAAAGTGATTTTCAAAAAA--AG-AAGCTCATTTGCAAAGTTTCTCAAAGAGAAATTTTC
* * *
688584 AAAAAGT-GAAAGTGATTTCCAAAGTTTCTTACTCAATAGACTATTTCTAAAATCAGTAAGTCAT
121 AAAAAGTAGAAAGTGATTTCCAAAGTTTCTTACCCAATAAACTATTTCCAAAATCAGTAAGTCAT
* * *
688648 TTGGGCCATCAATAAGCCTTTCGAGCATGATAATTAAAACCTTTGGGTCATATGTAAGTCTTTTG
186 TTGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTTGGGTCATATGTAAGTCTTTTG
*
688713 AGCGAGATGA
251 AGCAAGATGA
* *
688723 TAAGTCCTTCGGGCCATCCGTAAGACCTTCGGGTAGGATGTTTTCACATGAATTTGAAACTGAGA
1 TAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAATGAGA
688788 AAGTGATTTTCAAA
66 AAGTGATTTTCAAA
688802 GTTTCTCATT
Statistics
Matches: 465, Mismatches: 100, Indels: 57
0.75 0.16 0.09
Matches are distributed among these distances:
250 2 0.00
251 3 0.01
252 1 0.00
253 9 0.02
254 3 0.01
255 5 0.01
256 93 0.20
257 83 0.18
258 112 0.24
259 13 0.03
260 106 0.23
261 17 0.04
262 7 0.02
263 5 0.01
264 1 0.00
265 3 0.01
266 2 0.00
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (260 bp):
TAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAATGAGA
AAGTGATTTTCAAAAAAAGAAGCTCATTTGCAAAGTTTCTCAAAGAGAAATTTTCAAAAAGTAGA
AAGTGATTTCCAAAGTTTCTTACCCAATAAACTATTTCCAAAATCAGTAAGTCATTTGGGCCATC
AATAAGTCTTTCGAGCATGATGATTAAATCCTTTGGGTCATATGTAAGTCTTTTGAGCAAGATGA
Done.