Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004578.1 Hibiscus syriacus cultivar Beakdansim tig00010204_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: 1248949
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 7
Found at i:552327 original size:23 final size:24
Alignment explanation
Indices: 552276--552328 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
552266 TTTTTTATTG
**
552276 ATTTAATTTTTTTAGTATTTTTAT
1 ATTTAATTTTTTTAGTATTTGAAT
552300 ATTTAA-TTTTTTA-TATTTGAAT
1 ATTTAATTTTTTTAGTATTTGAAT
552322 AGTTTAA
1 A-TTTAA
552329 ATTTAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 8 0.31
23 12 0.46
24 6 0.23
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (24 bp):
ATTTAATTTTTTTAGTATTTGAAT
Found at i:553282 original size:16 final size:16
Alignment explanation
Indices: 553261--553291 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
553251 GTCGAGCGTG
*
553261 GATGAGCACCCTTAAC
1 GATGAGCACCATTAAC
553277 GATGAGCACCATTAA
1 GATGAGCACCATTAA
553292 ATTAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (16 bp):
GATGAGCACCATTAAC
Found at i:555680 original size:20 final size:20
Alignment explanation
Indices: 555655--555714 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
555645 CTGGAAATCA
*
555655 AATTTTAGGTTGCAACCTAG
1 AATTTTAGGTTGCAAACTAG
* *
555675 AATTTTAAGTTGGAAACTA-
1 AATTTTAGGTTGCAAACTAG
*
555694 AATTTTAGGTTGCAATCTAG
1 AATTTTAGGTTGCAAACTAG
555714 A
1 A
555715 TTCTATATTA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (20 bp):
AATTTTAGGTTGCAAACTAG
Found at i:556187 original size:19 final size:21
Alignment explanation
Indices: 556141--556181 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
556131 CTCCACACGT
*
556141 CAAGCTATGGTGAGTCACCAC
1 CAAGCTATGGTGACTCACCAC
556162 CATAGCTATGGTGACTCACC
1 CA-AGCTATGGTGACTCACC
556182 GAAGCTTCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (21 bp):
CAAGCTATGGTGACTCACCAC
Found at i:557331 original size:43 final size:42
Alignment explanation
Indices: 557214--557334 Score: 104
Period size: 44 Copynumber: 2.8 Consensus size: 42
557204 TATATAATGA
*
557214 ATAATATTTATTTACTTTTTTATATATTAA-ATAAAAATTCTATT
1 ATAATATTTATTTA-TTTTTTA-ATATTAAGA-AAAAAATCTATT
** * *
557258 ATAA-ATTTAATTTATATAAATTACTTTTAAGAAAAATAATCATATT
1 ATAATATTT-ATTTAT-T-TTTTAATATTAAGAAAAA-AATC-TATT
557304 -TAATATTTATTTATTTTTTAATATTAAGAAA
1 ATAATATTTATTTATTTTTTAATATTAAGAAA
557335 TATGTTGTCT
Statistics
Matches: 61, Mismatches: 9, Indels: 15
0.72 0.11 0.18
Matches are distributed among these distances:
43 17 0.28
44 20 0.33
45 16 0.26
46 8 0.13
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (42 bp):
ATAATATTTATTTATTTTTTAATATTAAGAAAAAAATCTATT
Found at i:557417 original size:149 final size:146
Alignment explanation
Indices: 557255--557536 Score: 388
Period size: 146 Copynumber: 1.9 Consensus size: 146
557245 TAAAAATTCT
557255 ATTATAAATTTAATTTATATAAATTACTTTTAAGAAAAATAATCATATTTAATATTTATTTATTT
1 ATTATAAATTTAATTTATATAAATTA-TTTTAAGAAAAAT-ATCATA-TTAATATTTATTTATTT
* *
557320 TTTAATATTAAGAAATATGTTGTCTTAAAGCACCTAGAAGTCCTTTTATGATATTAT-TAAATAA
63 TTTAATATTAAGAAATAGGTTGTCTTAAAGCA-CTAGAAGTCATTTTATGATATT-TCTAAATAA
557384 ATAAATATCATATTTTTATAA
126 ATAAATATCATATTTTTATAA
* * * * * * **
557405 ATTATATA-TTAATTTATTTTAATTATTTTTAGAGAAATGTTTTATTAATATTTATTTATTTTTT
1 ATTATAAATTTAATTTATATAAATTATTTTAAGAAAAATATCATATTAATATTTATTTATTTTTT
* * *
557469 AATATTAAGAAATGGGTTGTCTTAAAGCACTAGAAGTCATTTTCTGATATTTCTAAGTAAATAAA
66 AATATTAAGAAATAGGTTGTCTTAAAGCACTAGAAGTCATTTTATGATATTTCTAAATAAATAAA
557534 TAT
131 TAT
557537 TTATTTATAA
Statistics
Matches: 118, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
144 1 0.01
145 34 0.29
146 47 0.40
147 3 0.03
148 11 0.09
149 15 0.13
150 7 0.06
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.48
Consensus pattern (146 bp):
ATTATAAATTTAATTTATATAAATTATTTTAAGAAAAATATCATATTAATATTTATTTATTTTTT
AATATTAAGAAATAGGTTGTCTTAAAGCACTAGAAGTCATTTTATGATATTTCTAAATAAATAAA
TATCATATTTTTATAA
Found at i:557588 original size:146 final size:146
Alignment explanation
Indices: 557303--557580 Score: 352
Period size: 146 Copynumber: 1.9 Consensus size: 146
557293 ATAATCATAT
* *
557303 TTAATATTTATTTATTTTTTAATATTAAGAAATATGTTGTCTTAAAGCACCTAGAAGTCCTTTTA
1 TTAATATTTATTTATTTTTTAATATTAAGAAATAGGTTGTCTTAAAGCACCTAGAAGTCATTTTA
* * * ** *
557368 TGATATTATTAAATAAATAAATATCATATTTTTATAAATTATATATTAATTTATTTTAATTATTT
66 TGATATTATTAAATAAATAAATATCATATTTATATAAAATATATAATAATTTATTAAAATTATTA
* *
557433 TTAGAGAAATGTTTTA
131 ATAAAGAAATGTTTTA
* *
557449 TTAATATTTATTTATTTTTTAATATTAAGAAATGGGTTGTCTTAAAGCA-CTAGAAGTCATTTTC
1 TTAATATTTATTTATTTTTTAATATTAAGAAATAGGTTGTCTTAAAGCACCTAGAAGTCATTTTA
* * *
557513 TGATATT-TCTAAGTAAATAAATAT-TTATTTATA-AAAATATA-AAT-ATTTCTTAAAATTATA
66 TGATATTAT-TAAATAAATAAATATCATATTTATATAAAATATATAATAATTTATTAAAATTAT-
557573 CTAATAAA
129 -TAATAAA
557581 TTTGAAATAA
Statistics
Matches: 114, Mismatches: 15, Indels: 9
0.83 0.11 0.07
Matches are distributed among these distances:
141 12 0.11
142 2 0.02
143 11 0.10
144 8 0.07
145 34 0.30
146 47 0.41
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.47
Consensus pattern (146 bp):
TTAATATTTATTTATTTTTTAATATTAAGAAATAGGTTGTCTTAAAGCACCTAGAAGTCATTTTA
TGATATTATTAAATAAATAAATATCATATTTATATAAAATATATAATAATTTATTAAAATTATTA
ATAAAGAAATGTTTTA
Found at i:558684 original size:46 final size:46
Alignment explanation
Indices: 558615--558702 Score: 124
Period size: 46 Copynumber: 1.9 Consensus size: 46
558605 TGATTTCATT
* *
558615 TTTTTCTAAACAAAGCATAGAACTAGAAATCATGCA-GTTAGGTTAA
1 TTTTTCCAAACAAAGCATAGAACTAGAAAGCATG-AGGTTAGGTTAA
* *
558661 TTTTTCCAAGCAAAGCATGGAACTAGAAAGCATGAGGTTAGG
1 TTTTTCCAAACAAAGCATAGAACTAGAAAGCATGAGGTTAGG
558703 ATTTATACAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
45 1 0.03
46 36 0.97
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (46 bp):
TTTTTCCAAACAAAGCATAGAACTAGAAAGCATGAGGTTAGGTTAA
Found at i:565662 original size:75 final size:75
Alignment explanation
Indices: 565583--565723 Score: 230
Period size: 75 Copynumber: 1.9 Consensus size: 75
565573 ATTAACAAGA
* * *
565583 AGCAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAAGTT-GGAATATTAATGCATTTTGA
1 AGCAAATGCTGGGGCATGCTGAAAGCCCATTTCAATCAGAA-TTAGAAATATTAACGCATTTTGA
565647 ACATTTGTATC
65 ACATTTGTATC
*
565658 AGCAAATGCTGGGGCATGCTGAAAGCCCATTTCAATCAGAATTAGAAATGTTAACGCATTTTGAA
1 AGCAAATGCTGGGGCATGCTGAAAGCCCATTTCAATCAGAATTAGAAATATTAACGCATTTTGAA
565723 C
66 C
565724 GTTGGAGCAT
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
74 2 0.03
75 59 0.97
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.29
Consensus pattern (75 bp):
AGCAAATGCTGGGGCATGCTGAAAGCCCATTTCAATCAGAATTAGAAATATTAACGCATTTTGAA
CATTTGTATC
Found at i:566783 original size:54 final size:54
Alignment explanation
Indices: 566658--566791 Score: 146
Period size: 54 Copynumber: 2.5 Consensus size: 54
566648 TCCCTGACCA
* * * *
566658 AAAATCTGTGCAGAAACCACAGAAAAATATAAATGTGTTGTCAAATGCTTTACG
1 AAAATCTGAGCAGAAGCCACAGAAAAATATAAATGTGTTATCAAAAGCTTTACG
* * * * *
566712 AACATCT-AGCTATAAGCCATA-ATAAATGATGAATGTGTTATCAAAAGCTTTACG
1 AAAATCTGAGC-AGAAGCCACAGAAAAAT-ATAAATGTGTTATCAAAAGCTTTACG
566766 AAAATCTGAGCAGAAGCCACGAGAAA
1 AAAATCTGAGCAGAAGCCAC-AGAAA
566792 GGATGAATGT
Statistics
Matches: 62, Mismatches: 13, Indels: 8
0.75 0.16 0.10
Matches are distributed among these distances:
53 7 0.11
54 49 0.79
55 4 0.06
56 2 0.03
ACGTcount: A:0.43, C:0.16, G:0.17, T:0.24
Consensus pattern (54 bp):
AAAATCTGAGCAGAAGCCACAGAAAAATATAAATGTGTTATCAAAAGCTTTACG
Found at i:567214 original size:22 final size:22
Alignment explanation
Indices: 567189--567243 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
567179 ACATCTATAT
**
567189 TCTTCAAAGATGACAGATTTTC
1 TCTTCAAAGATGACAGATTCAC
*
567211 TCTTCAAAGATGATAGATTCAC
1 TCTTCAAAGATGACAGATTCAC
*
567233 TTTTCAAAGAT
1 TCTTCAAAGAT
567244 AAGCTTTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (22 bp):
TCTTCAAAGATGACAGATTCAC
Found at i:568015 original size:22 final size:21
Alignment explanation
Indices: 567987--568042 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
567977 GGGTCATCTG
567987 TAAGACCTACAGTGCAAGATGA
1 TAAGACCTACAGTGCAAGAT-A
* * **
568009 TAAGACCT-CAGGGCCATCTA
1 TAAGACCTACAGTGCAAGATA
568029 TAAGACCTACAGTG
1 TAAGACCTACAGTG
568043 TAGGATGTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 9 0.32
21 11 0.39
22 8 0.29
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.20
Consensus pattern (21 bp):
TAAGACCTACAGTGCAAGATA
Found at i:568118 original size:118 final size:118
Alignment explanation
Indices: 567909--568409 Score: 763
Period size: 118 Copynumber: 4.3 Consensus size: 118
567899 TTCCCACATT
* * **
567909 CATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTTGAAAGCTTTTTGATATTTTCAAAGCC
1 CATAAGACCTACAGTGTAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGCC
567974 TTCGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATC
66 TTCGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATC
*
568027 TATAAGACCTACAGTGTAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGCC
1 CATAAGACCTACAGTGTAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGCC
* * * *
568092 TTCAGGTCATCTGTAATACCTACAGTGTAAGATGATAAGACCTCAGGGTCATC
66 TTCGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATC
* * *
568145 CATAAGACCTACAGTGTAGGATATTTTCAAAAAGCATTTGGGAGCTTTTTGATATTTTCAAAGCC
1 CATAAGACCTACAGTGTAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGCC
* * *
568210 TCCGGGTCATTTGTAAGACATACAGTGCAAGATGATAAGACCTCAGGGCCATC
66 TTCGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATC
* * *
568263 CATAATACCTATAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGCC
1 CATAAGACCTACAGTGTAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGCC
* * *
568328 -TCTGGGTCATCTGTAAGACCTACAGTGCAAGATAATAAGACCTTAGGGCCATT
66 TTC-GGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATC
* * *
568381 CATAAGACCT-CTGGGTAGAATGTTTTCAA
1 CATAAGACCTACAGTGTAGGATGTTTTCAA
568410 CATTTCCATC
Statistics
Matches: 344, Mismatches: 38, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
117 15 0.04
118 329 0.96
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (118 bp):
CATAAGACCTACAGTGTAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGCC
TTCGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATC
Found at i:569750 original size:19 final size:20
Alignment explanation
Indices: 569726--569766 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
569716 GTTATTTAAT
569726 TTTAATTA-TAT-GTTATATA
1 TTTAATTATTATAGTTAT-TA
569745 TTTAATTATTATAGTTATTA
1 TTTAATTATTATAGTTATTA
569765 TT
1 TT
569767 ATTTTACAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 8 0.40
20 7 0.35
21 5 0.25
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (20 bp):
TTTAATTATTATAGTTATTA
Found at i:569840 original size:14 final size:14
Alignment explanation
Indices: 569823--569851 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
569813 ATATTTAGTC
569823 ATTTTTAATTATTT
1 ATTTTTAATTATTT
569837 ATTTTTAATTATTT
1 ATTTTTAATTATTT
569851 A
1 A
569852 ATATTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
ATTTTTAATTATTT
Found at i:569850 original size:24 final size:23
Alignment explanation
Indices: 569809--569869 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
569799 TATTATTTTC
* * *
569809 ATTTATATTTAGTCATTTTTAATT
1 ATTTATTTTTAATTATTTTTAA-T
569833 ATTTATTTTTAATTA--TTTAAT
1 ATTTATTTTTAATTATTTTTAAT
569854 ATTTA-TTTTAATTATT
1 ATTTATTTTTAATTATT
569870 ATAGTTAGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
20 9 0.28
21 6 0.19
22 5 0.16
24 12 0.38
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (23 bp):
ATTTATTTTTAATTATTTTTAAT
Found at i:570065 original size:135 final size:142
Alignment explanation
Indices: 569940--570248 Score: 357
Period size: 146 Copynumber: 2.2 Consensus size: 142
569930 TTATATATTA
*
569940 AATAAAAATCCTA-TTTATAAATT-TA-ATT-TTGTA-TAAATTATTTTTA-AGAAAATAATCAT
1 AATAAATATCCTATTTTATAAATTATATATTATT-TATTAAATTATTTTTAGAG-AAAT-AT--T
*
569999 ATT-TTAATATTTATTTATTTTTTAATATTAAGAAATGAGCTGTCTTAAAGCACCTAGAAGTCTT
61 -TTATTAATATTTATTTATCTTTTAATATTAAGAAATGAGCTGTCTTAAAGCACCTAGAAGTCTT
*
570063 TTTCTAATATTCTTAAAT
125 TTTCTAATATTATTAAAT
*
570081 AAATAAATATCCTATTTTTATAAATTATATATTAATTTATTTTAATTATTTTTAGAGAAATATTT
1 -AATAAATATCCTA-TTTTATAAATTATATATT-ATTTA-TTAAATTATTTTTAGAGAAATATTT
* * *
570146 TATTAATATTTATTTATCTTTTAATATTAAGAAATGGGCTGTCTTAAATCACCTAGAAGTCCTTT
62 TATTAATATTTATTTATCTTTTAATATTAAGAAATGAGCTGTCTTAAAGCACCTAGAAGTCTTTT
* *
570211 TCTGATATT-TCTAACT
127 TCTAATATTAT-TAAAT
*
570227 AAATAAATATCTTA-TTTATAAA
1 -AATAAATATCCTATTTTATAAA
570249 AATATAAATA
Statistics
Matches: 147, Mismatches: 9, Indels: 20
0.84 0.05 0.11
Matches are distributed among these distances:
142 12 0.08
144 18 0.12
145 5 0.03
146 88 0.60
147 2 0.01
148 4 0.03
149 16 0.11
150 2 0.01
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.47
Consensus pattern (142 bp):
AATAAATATCCTATTTTATAAATTATATATTATTTATTAAATTATTTTTAGAGAAATATTTTATT
AATATTTATTTATCTTTTAATATTAAGAAATGAGCTGTCTTAAAGCACCTAGAAGTCTTTTTCTA
ATATTATTAAAT
Found at i:572007 original size:20 final size:21
Alignment explanation
Indices: 571969--572007 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
571959 AAAAAGTTAA
*
571969 ATATATTGGCTTTACAAAATC
1 ATATATTGGCTTTAAAAAATC
*
571990 ATATA-TGGGTTTAAAAAA
1 ATATATTGGCTTTAAAAAA
572008 CTGACTGGCC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.36
Consensus pattern (21 bp):
ATATATTGGCTTTAAAAAATC
Found at i:575922 original size:32 final size:31
Alignment explanation
Indices: 575849--575924 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
575839 CTAATGTGAC
* *
575849 TCTTAGGTAGGCTCTGCAGCCCTGAGATCAT
1 TCTTAGGTAGGCCCTGCAGCCCTAAGATCAT
** * **
575880 TCTCGGGTAGGCCCTGCGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTGCAGCCCTAAGAT-CAT
575912 TCTTAGGTAGGCC
1 TCTTAGGTAGGCC
575925 TCGTGGCCCC
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.66
32 12 0.34
ACGTcount: A:0.16, C:0.26, G:0.30, T:0.28
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGCAGCCCTAAGATCAT
Found at i:581159 original size:30 final size:30
Alignment explanation
Indices: 581133--581207 Score: 150
Period size: 30 Copynumber: 2.5 Consensus size: 30
581123 AGGATTAAAT
581133 TGAAATTTTAATTAAATTCAGAGATTATAG
1 TGAAATTTTAATTAAATTCAGAGATTATAG
581163 TGAAATTTTAATTAAATTCAGAGATTATAG
1 TGAAATTTTAATTAAATTCAGAGATTATAG
581193 TGAAATTTTAATTAA
1 TGAAATTTTAATTAA
581208 TTTTAGATCC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.44, C:0.03, G:0.12, T:0.41
Consensus pattern (30 bp):
TGAAATTTTAATTAAATTCAGAGATTATAG
Found at i:587294 original size:18 final size:18
Alignment explanation
Indices: 587271--587306 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
587261 GTAGAACACA
587271 TATGTCCCAG-AGGACCAC
1 TATGTCCC-GTAGGACCAC
587289 TATGTCCCGTAGGACCAC
1 TATGTCCCGTAGGACCAC
587307 GTAGAACCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 1 0.06
18 16 0.94
ACGTcount: A:0.25, C:0.33, G:0.22, T:0.19
Consensus pattern (18 bp):
TATGTCCCGTAGGACCAC
Found at i:587377 original size:19 final size:19
Alignment explanation
Indices: 587353--587392 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
587343 ATAGCTCTCA
587353 TAACACATTACATGGGTGT
1 TAACACATTACATGGGTGT
587372 TAACACATTACATGGGTGT
1 TAACACATTACATGGGTGT
587391 TA
1 TA
587393 CCTTTTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.33
Consensus pattern (19 bp):
TAACACATTACATGGGTGT
Found at i:587834 original size:25 final size:25
Alignment explanation
Indices: 587806--587855 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
587796 TTTAGCACCA
587806 TATCACTACATATTTATGCTTCAGT
1 TATCACTACATATTTATGCTTCAGT
* *
587831 TATCCCTACATGTTTATGCTTCAGT
1 TATCACTACATATTTATGCTTCAGT
587856 ACCCCTAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.44
Consensus pattern (25 bp):
TATCACTACATATTTATGCTTCAGT
Found at i:591431 original size:18 final size:18
Alignment explanation
Indices: 591387--591432 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
591377 CGAATTGGTG
*
591387 AACTATTGATCGACCGTT
1 AACTATTGACCGACCGTT
* *
591405 AAATGTTGACCGACCGTT
1 AACTATTGACCGACCGTT
*
591423 GACTATTGAC
1 AACTATTGAC
591433 TTCTATTGAT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (18 bp):
AACTATTGACCGACCGTT
Found at i:593328 original size:15 final size:15
Alignment explanation
Indices: 593310--593340 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
593300 AAATTCTAAA
593310 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
593325 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
593340 T
1 T
593341 CTATTTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:593572 original size:12 final size:13
Alignment explanation
Indices: 593552--593580 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
593542 ATAATATATA
593552 TTATAACAATAAT
1 TTATAACAATAAT
593565 TTAT-ACAATAAT
1 TTATAACAATAAT
593577 TTAT
1 TTAT
593581 TTATTTATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (13 bp):
TTATAACAATAAT
Found at i:597214 original size:16 final size:16
Alignment explanation
Indices: 597167--597215 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
597157 ACCTAAGGTC
597167 AATATTAGTTCAAGTCA
1 AATATTAGTTCAAGT-A
* *
597184 AATATGAACTT-AAGTA
1 AATAT-TAGTTCAAGTA
597200 AATATTAGTTCAAGTA
1 AATATTAGTTCAAGTA
597216 GGTTGGGCTA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
15 3 0.12
16 11 0.42
17 9 0.35
18 3 0.12
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.35
Consensus pattern (16 bp):
AATATTAGTTCAAGTA
Found at i:598338 original size:93 final size:93
Alignment explanation
Indices: 598240--598627 Score: 410
Period size: 93 Copynumber: 4.2 Consensus size: 93
598230 CATCCCTTGT
* *
598240 ATCCTCCGGCTCCATGGGGACATTATGTTCCAGAGGTGAACTGGGCTAATCCTAGCC-CAAACCC
1 ATCCTCCGGCTCCATGGGGACATTATGTTCCAGAGGTGAAATGGGCTCATCCT-GCCTCAAACCC
* *
598304 TCCTCTTCCATGAGCACATCATCACCCGG
65 TCCTCTCCCATGAGCTCATCATCACCCGG
** * * *
598333 ATCCTCATGCTCCTTGGGGACATTATGTTCTAGAGGTGAAATGGGTTCATCCTGCCTCAGAA-CC
1 ATCCTCCGGCTCCATGGGGACATTATGTTCCAGAGGTGAAATGGGCTCATCCTGCCTCA-AACCC
* * *
598397 TCCTCCCCCATGAGCTCATCATCCCCCGA
65 TCCTCTCCCATGAGCTCATCATCACCCGG
* ** * ** * * * *
598426 ACCCTCTTGCTCAATGGTAACATCAAG-TCTCAGAGGTGAAATGGGCTTATCCTGCCTCAGACCC
1 ATCCTCCGGCTCCATGGGGACATTATGTTC-CAGAGGTGAAATGGGCTCATCCTGCCTCAAACCC
*
598490 TCCTCTCCCATGAGCTCATCATCACCTGG
65 TCCTCTCCCATGAGCTCATCATCACCCGG
* * * *
598519 ATCCTCCCGCTCCTTGGGGACATTATGTTCCAGAGGTGAAATGGGCTCATCCAGCC-CTAGACCC
1 ATCCTCCGGCTCCATGGGGACATTATGTTCCAGAGGTGAAATGGGCTCATCCTGCCTC-AAACCC
*
598583 TCCTC-CCCTATGAGCTCATCATC-CCCTAG
65 TCCTCTCCC-ATGAGCTCATCATCACCC-GG
* *
598612 ATCGTTCGGCTCCATG
1 ATCCTCCGGCTCCATG
598628 TGGATATCAT
Statistics
Matches: 242, Mismatches: 45, Indels: 16
0.80 0.15 0.05
Matches are distributed among these distances:
92 12 0.05
93 226 0.93
94 4 0.02
ACGTcount: A:0.21, C:0.34, G:0.20, T:0.25
Consensus pattern (93 bp):
ATCCTCCGGCTCCATGGGGACATTATGTTCCAGAGGTGAAATGGGCTCATCCTGCCTCAAACCCT
CCTCTCCCATGAGCTCATCATCACCCGG
Found at i:598523 original size:186 final size:186
Alignment explanation
Indices: 598270--598608 Score: 529
Period size: 186 Copynumber: 1.8 Consensus size: 186
598260 CATTATGTTC
* *
598270 CAGAGGTGAACTGGGCTAATCCTAGCCCAAACCCTCCTCTTCCATGAGCACATCATCACCCGGAT
1 CAGAGGTGAAATGGGCTAATCCTAGCCCAAACCCTCCTCTCCCATGAGCACATCATCACCCGGAT
* * * *
598335 CCTCATGCTCCTTGGGGACATTATGTTCTAGAGGTGAAATGGGTTCATCCTG-CCTCAGAACCTC
66 CCTCACGCTCCTTGGGGACATTATGTTCCAGAGGTGAAATGGGCTCATCCAGCCCT-AGAACCTC
598399 CTCCCCCATGAGCTCATCATCCCCCGAACCCTCTTGCTCAATGGTAACATCAAGTCT
130 CTCCCCCATGAGCTCATCATCCCCCGAACCCTCTTGCTCAATGGTAACATCAAGTCT
* * * *
598456 CAGAGGTGAAATGGGCTTATCCT-GCCTCAGACCCTCCTCTCCCATGAGCTCATCATCACCTGGA
1 CAGAGGTGAAATGGGCTAATCCTAGCC-CAAACCCTCCTCTCCCATGAGCACATCATCACCCGGA
* *
598520 TCCTCCCGCTCCTTGGGGACATTATGTTCCAGAGGTGAAATGGGCTCATCCAGCCCTAGACCCTC
65 TCCTCACGCTCCTTGGGGACATTATGTTCCAGAGGTGAAATGGGCTCATCCAGCCCTAGAACCTC
*
598585 CTCCCCTATGAGCTCATCATCCCC
130 CTCCCCCATGAGCTCATCATCCCC
598609 TAGATCGTTC
Statistics
Matches: 138, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
185 3 0.02
186 132 0.96
187 3 0.02
ACGTcount: A:0.22, C:0.35, G:0.19, T:0.24
Consensus pattern (186 bp):
CAGAGGTGAAATGGGCTAATCCTAGCCCAAACCCTCCTCTCCCATGAGCACATCATCACCCGGAT
CCTCACGCTCCTTGGGGACATTATGTTCCAGAGGTGAAATGGGCTCATCCAGCCCTAGAACCTCC
TCCCCCATGAGCTCATCATCCCCCGAACCCTCTTGCTCAATGGTAACATCAAGTCT
Found at i:602953 original size:14 final size:14
Alignment explanation
Indices: 602936--602975 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
602926 AGATTTAGGT
602936 TTTAGGGTTTATAA
1 TTTAGGGTTTATAA
* * *
602950 TTTATGGTTTGTGA
1 TTTAGGGTTTATAA
602964 TTTAGGGTTTAT
1 TTTAGGGTTTAT
602976 TATAAAGACA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.20, C:0.00, G:0.25, T:0.55
Consensus pattern (14 bp):
TTTAGGGTTTATAA
Found at i:605796 original size:14 final size:14
Alignment explanation
Indices: 605777--605809 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
605767 TATAGAATTT
605777 GAAAAT-AATATTCA
1 GAAAATGAAT-TTCA
605791 GAAAATGAATTTCA
1 GAAAATGAATTTCA
605805 GAAAA
1 GAAAA
605810 CAACCCTACC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 15 0.83
15 3 0.17
ACGTcount: A:0.58, C:0.06, G:0.12, T:0.24
Consensus pattern (14 bp):
GAAAATGAATTTCA
Found at i:606990 original size:30 final size:30
Alignment explanation
Indices: 606956--607022 Score: 93
Period size: 30 Copynumber: 2.2 Consensus size: 30
606946 TACAAAAACA
606956 TTTTATTA-TATT-ATATATATATTTATTTAT
1 TTTTATTATTATTAATATAT-TATTTATTT-T
*
606986 TTTTATTATTATTAATATATTTTTTATTTT
1 TTTTATTATTATTAATATATTATTTATTTT
607016 TTTTATT
1 TTTTATT
607023 TTTGCATGCC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
30 16 0.47
31 12 0.35
32 6 0.18
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (30 bp):
TTTTATTATTATTAATATATTATTTATTTT
Found at i:606994 original size:9 final size:9
Alignment explanation
Indices: 606956--607025 Score: 52
Period size: 9 Copynumber: 7.4 Consensus size: 9
606946 TACAAAAACA
606956 TTTTATTAT
1 TTTTATTAT
*
606965 ATTATATATAT
1 -TTTTAT-TAT
*
606976 ATTTATTTAT
1 TTTTA-TTAT
606986 TTTTATTAT
1 TTTTATTAT
* *
606995 TATTAATAT
1 TTTTATTAT
607004 ATTTT-TTAT
1 -TTTTATTAT
*
607013 TTTTTTTAT
1 TTTTATTAT
607022 TTTT
1 TTTT
607026 GCATGCCCCA
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
8 4 0.08
9 22 0.46
10 18 0.38
11 4 0.08
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (9 bp):
TTTTATTAT
Found at i:607003 original size:28 final size:27
Alignment explanation
Indices: 606964--607022 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 27
606954 CATTTTATTA
606964 TATTATATATATATTTATTTATTTTTAT
1 TATTATATATATATTT-TTTATTTTTAT
*
606992 TATTAT-TAATATATTTTTTATTTTTTT
1 TATTATAT-ATATATTTTTTATTTTTAT
607019 TATT
1 TATT
607023 TTTGCATGCC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 15 0.52
28 14 0.48
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (27 bp):
TATTATATATATATTTTTTATTTTTAT
Found at i:610496 original size:26 final size:26
Alignment explanation
Indices: 610436--610496 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
610426 AACTAAGGTT
* *
610436 GACCAAGATTTTTAAATCGAGAAGAA
1 GACCAAGGTCTTTAAATCGAGAAGAA
*
610462 CACTC-AGGTCTTTAAATCGAGAAGAA
1 GAC-CAAGGTCTTTAAATCGAGAAGAA
610488 GACCAAGGT
1 GACCAAGGT
610497 TGACCAAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
25 1 0.03
26 27 0.93
27 1 0.03
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.21
Consensus pattern (26 bp):
GACCAAGGTCTTTAAATCGAGAAGAA
Found at i:610778 original size:22 final size:22
Alignment explanation
Indices: 610745--610789 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 22
610735 TATTTTATTA
610745 TATTATATATATATATATTTAT
1 TATTATATATATATATATTTAT
610767 TATTAT-TA-ATATATATTT-T
1 TATTATATATATATATATTTAT
610786 TATT
1 TATT
610790 TTTTTATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 5 0.22
20 10 0.43
21 2 0.09
22 6 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTATATATATATATATTTAT
Found at i:610796 original size:24 final size:23
Alignment explanation
Indices: 610734--610797 Score: 65
Period size: 26 Copynumber: 2.6 Consensus size: 23
610724 GTCTACAAAA
610734 ATATTTTATTATATTATATATATAT
1 ATATTTT-TT-TATTATATATATAT
*
610759 ATATTTATTATTATTAATATATATTT
1 ATATTT-TT-TTATT-ATATATATAT
*
610785 TTATTTTTTTATT
1 ATATTTTTTTATT
610798 TTTGCAGGCC
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
24 5 0.15
25 13 0.38
26 16 0.47
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
ATATTTTTTTATTATATATATAT
Found at i:613075 original size:16 final size:16
Alignment explanation
Indices: 613054--613086 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
613044 TTTATTTTTT
613054 GATGGTCAAACTGAAA
1 GATGGTCAAACTGAAA
*
613070 GATGGTTAAACTGAAA
1 GATGGTCAAACTGAAA
613086 G
1 G
613087 GGTAAACCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.09, G:0.27, T:0.21
Consensus pattern (16 bp):
GATGGTCAAACTGAAA
Found at i:613829 original size:19 final size:20
Alignment explanation
Indices: 613794--613831 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
613784 TAGTTTGATC
613794 CTTGGGGACAAGGATTGTTT
1 CTTGGGGACAAGGATTGTTT
*
613814 CTTGGGG-CAAGTATTGTT
1 CTTGGGGACAAGGATTGTT
613832 ACAATCGGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.18, C:0.11, G:0.34, T:0.37
Consensus pattern (20 bp):
CTTGGGGACAAGGATTGTTT
Found at i:613889 original size:34 final size:34
Alignment explanation
Indices: 613851--613916 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
613841 GGAGGAGAAG
* *
613851 AAGAAAGTCACGAGGAAGAGGAAATTGAGAATTC
1 AAGAAAGTCACGAGAAAAAGGAAATTGAGAATTC
* *
613885 AAGAAAGTCACGAGAAAAAGGAATTTGGGAAT
1 AAGAAAGTCACGAGAAAAAGGAAATTGAGAAT
613917 CCATATGAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.48, C:0.08, G:0.29, T:0.15
Consensus pattern (34 bp):
AAGAAAGTCACGAGAAAAAGGAAATTGAGAATTC
Found at i:614063 original size:40 final size:40
Alignment explanation
Indices: 614013--614160 Score: 122
Period size: 40 Copynumber: 3.7 Consensus size: 40
614003 AATAGAAAAT
*
614013 TAGAA-AATAAAATTCATAAGTA-AAT-AACAATATTAACTC
1 TAGAACAATAAAATCCATAA--ACAATCAACAATATTAACTC
* * *
614052 TAGAACAATAAAATCCATAAACAATCCATAATATTAAGTC
1 TAGAACAATAAAATCCATAAACAATCAACAATATTAACTC
* * * * * * * *
614092 TAAAACAATAAAATCTATAAACAAACCATAATATTTAGTA
1 TAGAACAATAAAATCCATAAACAATCAACAATATTAACTC
* *
614132 TAAAACAATAAAATTCATAAACAAATCAA
1 TAGAACAATAAAATCCATAAAC-AATCAA
614161 TTGAGTTCAA
Statistics
Matches: 92, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
38 1 0.01
39 8 0.09
40 79 0.86
41 4 0.04
ACGTcount: A:0.57, C:0.14, G:0.03, T:0.26
Consensus pattern (40 bp):
TAGAACAATAAAATCCATAAACAATCAACAATATTAACTC
Found at i:614117 original size:20 final size:19
Alignment explanation
Indices: 614094--614161 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 19
614084 ATTAAGTCTA
614094 AAACAATAAAATCTATAAAC
1 AAACAATAAAAT-TATAAAC
* * *
614114 AAACCATAATATTTAGTATA-
1 AAACAATAA-AATTA-TAAAC
614134 AAACAATAAAATTCATAAAC
1 AAACAATAAAATT-ATAAAC
614154 AAATCAAT
1 AAA-CAAT
614162 TGAGTTCAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
19 6 0.16
20 22 0.59
21 9 0.24
ACGTcount: A:0.60, C:0.13, G:0.01, T:0.25
Consensus pattern (19 bp):
AAACAATAAAATTATAAAC
Found at i:617735 original size:12 final size:12
Alignment explanation
Indices: 617718--617743 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
617708 AAATTTTAAG
617718 ATTTTCTTGAAA
1 ATTTTCTTGAAA
617730 ATTTTCTTGAAA
1 ATTTTCTTGAAA
617742 AT
1 AT
617744 ACTCCCCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.50
Consensus pattern (12 bp):
ATTTTCTTGAAA
Found at i:620077 original size:20 final size:21
Alignment explanation
Indices: 620052--620110 Score: 66
Period size: 23 Copynumber: 2.8 Consensus size: 21
620042 GAGGTTGCAT
*
620052 GAACAATATCGGTACT-TAAA
1 GAACAATATCGGTACTAAAAA
*
620072 GAACAATATCGATACTGAAAAAA
1 GAACAATATCGGTACT--AAAAA
*
620095 GAACAATATTGGTACT
1 GAACAATATCGGTACT
620111 GGAGGAACAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 15 0.47
23 17 0.53
ACGTcount: A:0.47, C:0.14, G:0.15, T:0.24
Consensus pattern (21 bp):
GAACAATATCGGTACTAAAAA
Found at i:625085 original size:15 final size:15
Alignment explanation
Indices: 625067--625097 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
625057 AAAGAAGAAG
625067 AAGATCAAGAAAATA
1 AAGATCAAGAAAATA
*
625082 AAGATGAAGAAAATA
1 AAGATCAAGAAAATA
625097 A
1 A
625098 GGAAATGGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.68, C:0.03, G:0.16, T:0.13
Consensus pattern (15 bp):
AAGATCAAGAAAATA
Found at i:625102 original size:24 final size:24
Alignment explanation
Indices: 625057--625103 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
625047 AATGATGGTA
*
625057 AAAGAAGAAGAAGATCAAGAAAAT
1 AAAGAAGAAGAAAATCAAGAAAAT
* *
625081 AAAGATGAAGAAAAT-AAGGAAAT
1 AAAGAAGAAGAAAATCAAGAAAAT
625104 GGAAAAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.66, C:0.02, G:0.21, T:0.11
Consensus pattern (24 bp):
AAAGAAGAAGAAAATCAAGAAAAT
Found at i:629828 original size:20 final size:21
Alignment explanation
Indices: 629805--629866 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 21
629795 TTTGTGCACT
629805 TAGTATCGATATTGTTCAT-A
1 TAGTATCGATATTGTTCATCA
* * * *
629825 TAGTATTGATACTGTTCTTGCT
1 TAGTATCGATATTGTTCAT-CA
*
629847 TAGTTTCGATATTGTTCATC
1 TAGTATCGATATTGTTCATC
629867 CAATACCGAT
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
20 16 0.50
21 1 0.03
22 15 0.47
ACGTcount: A:0.23, C:0.13, G:0.16, T:0.48
Consensus pattern (21 bp):
TAGTATCGATATTGTTCATCA
Found at i:630408 original size:23 final size:23
Alignment explanation
Indices: 630382--630428 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
630372 ATTATATATG
* *
630382 TATATTATTGTTTTTCACAAAAT
1 TATACTATTATTTTTCACAAAAT
*
630405 TATACTATTATTTTTCATAAAAT
1 TATACTATTATTTTTCACAAAAT
630428 T
1 T
630429 GTTTTCACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.53
Consensus pattern (23 bp):
TATACTATTATTTTTCACAAAAT
Found at i:634914 original size:15 final size:15
Alignment explanation
Indices: 634894--634923 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
634884 CTTCATGAGT
634894 AACTTCAAGTTTATC
1 AACTTCAAGTTTATC
634909 AACTTCAAGTTTATC
1 AACTTCAAGTTTATC
634924 TCATATCTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (15 bp):
AACTTCAAGTTTATC
Found at i:638774 original size:23 final size:22
Alignment explanation
Indices: 638719--638774 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
638709 TATGGTCCGA
* *
638719 TAAAATTTTAACTTCTAGCCGC
1 TAAATTTTTAACTTCTAACCGC
* * *
638741 TAACTTATTAATTTACTAACCGC
1 TAAATTTTTAACTT-CTAACCGC
638764 TAAATTTTTAA
1 TAAATTTTTAA
638775 AATATATTCA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
22 10 0.38
23 16 0.62
ACGTcount: A:0.36, C:0.18, G:0.05, T:0.41
Consensus pattern (22 bp):
TAAATTTTTAACTTCTAACCGC
Found at i:638939 original size:16 final size:16
Alignment explanation
Indices: 638897--638941 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
638887 ATTAATTTAT
638897 TTTTTGTCA-TTTAAA
1 TTTTTGTCATTTTAAA
*
638912 TTTTTG-CCTTTTAAA
1 TTTTTGTCATTTTAAA
*
638927 TTTTTGTTATTTTAA
1 TTTTTGTCATTTTAA
638942 GTTCCGTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 1 0.04
15 18 0.72
16 6 0.24
ACGTcount: A:0.22, C:0.07, G:0.07, T:0.64
Consensus pattern (16 bp):
TTTTTGTCATTTTAAA
Found at i:640424 original size:33 final size:33
Alignment explanation
Indices: 640382--640450 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
640372 TAGAACTATC
* * * *
640382 TTAGGTTGATACTTACAAGTGTAATCATGAGAA
1 TTAGGTTGATAATTAAAAGAGTAAGCATGAGAA
640415 TTAGGTTGATAATTAAAAGAGTAAGCATGAGAA
1 TTAGGTTGATAATTAAAAGAGTAAGCATGAGAA
640448 TTA
1 TTA
640451 AGCGTTTTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.41, C:0.06, G:0.22, T:0.32
Consensus pattern (33 bp):
TTAGGTTGATAATTAAAAGAGTAAGCATGAGAA
Found at i:642056 original size:33 final size:33
Alignment explanation
Indices: 642011--642077 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
642001 TTGGACTATC
* *
642011 TTAGGTTGATACTTACAAGTGTAATCATGGGAA
1 TTAGGTTGATACTTAAAAGTGTAAGCATGGGAA
*
642044 TTAGGTTTATACTTAAAAGTGTAAGCATGGGAA
1 TTAGGTTGATACTTAAAAGTGTAAGCATGGGAA
642077 T
1 T
642078 CAAGAGTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.34, C:0.07, G:0.24, T:0.34
Consensus pattern (33 bp):
TTAGGTTGATACTTAAAAGTGTAAGCATGGGAA
Found at i:642251 original size:451 final size:455
Alignment explanation
Indices: 641397--643197 Score: 1509
Period size: 477 Copynumber: 3.9 Consensus size: 455
641387 ATAAAACATA
* * * ** * ** *
641397 TAAATCTTCACTTCACTTTTTTCCTTGTTTCTTCACCAGACTGTGCTCCTCTTAAATCGGCCACG
1 TAAATCTTCACTTCACTTTTTGCCTTGTTTC-TCACGAGACTCTATTCCTCTTAAATAGATCATG
* * * * * * *
641462 ACGTGACAATAAGGGGATACTTAGCGAGTTCC-ATTGGAGTTCCTTATA--T---TCAGAT--TG
65 ATGTGACAATAAGGGGATACTTAGTGGGTTCCGA-TGGGGTGCCTTATATTTAGGTCGGGTGGTG
* *
641519 GGTAAAAA-C-GAACCCAACCCAT-T-CTAATCCCTAGGACTATCTTAGGTTGATATTTACAAGT
129 GGTAAAAATCAG-ACCCAA-CCATGTGC--ATCCCTTGGACTATCTTAGGTTGATACTTACAAGT
* * * * *
641580 TTAATCATGGGAATTAGGTTGATACATAAAAGTGTAAGCATGAGAGTTAAGAGTTTTC-TTCTTT
190 GTAATCATGGGAATTAGGTTTATACTTAAAAGTGTAAGCATGAGAATCAAGAGTTTTCTTTC-TT
** * * * * *
641644 ATACTAAAGCTCAAAACTAAGGGTCACGAGATTTTATTTGAACGCTTAGGTTCATAGTTGTTTCT
254 ATACTAAAGCTCAGGACTAAAGGTCA-AAGCTTTTATTTGAACGCTTAGGCTCATACTTGTTTCT
* * * * * **
641709 CCCTCGGAATCTAAACCTCTT-TATGGTGACGTAATTAATGC-AAAA-AT--ATGGAATATATCA
318 CCATCAGAATATAAACCTCTTATATGGTGGCGTCATTAATGCGAAAAGATGGA-GGAATCCATCA
* * * *
641769 ACAAGTCTGAACCATATAAAATA-ATTAATTCTAC-TG-GTAAT-A-TT-A-TA-CCTTT-CA-G
382 ACTAGTCCGAACCATATAAAACACA-TAATTCTACATGAATAATCATTTAACTATCCTTTACATG
*
641824 GAATTATGCG
446 GAATTATGTG
*
641834 TAAATCTTCACTTCACTTTTTTGCCTTGTTTCTACACCGA-ACTCTATTCCTCTTAAATAGGTCA
1 TAAATCTTCACTTCAC-TTTTTGCCTTGTTTCT-CA-CGAGACTCTATTCCTCTTAAATAGATCA
* * * * * *
641898 CGATGTAACAATAAGGGGATATTTAGCGAGTTCCGATGGCAGTGCCTTATATTTAGGTCGGGGTC
63 TGATGTGACAATAAGGGGATACTTAGTGGGTTCCGATGG-GGTGCCTTATATTTAGGTC-GGGT-
* *
641963 GAGTGAGGTAAAAATCAGACTCAATCCATGTGCATTCCTTGGACTATCTTAGGTTGATACTTACA
125 G-GTG-GGTAAAAATCAGACCCAA-CCATGTGCATCCCTTGGACTATCTTAGGTTGATACTTACA
*
642028 AGTGTAATCATGGGAATTAGGTTTATACTTAAAAGTGTAAGCATGGGAATCAAGAGTTTTCTTTC
187 AGTGTAATCATGGGAATTAGGTTTATACTTAAAAGTGTAAGCATGAGAATCAAGAGTTTTCTTTC
* * * *
642093 ATATACTAAAGCTCAGGACTAAAGG-C-CAGCTTTTATTTTAACACTTAGGCTCATACTTGTTTC
252 TTATACTAAAGCTCAGGACTAAAGGTCAAAGCTTTTATTTGAACGCTTAGGCTCATACTTGTTTC
* * * *
642156 TCCATCAGAATATAACCCTCTTATATGGTGGCG-CATTGATGCGAAAATATGGAGGAATGCATCA
317 TCCATCAGAATATAAACCTCTTATATGGTGGCGTCATTAATGCGAAAAGATGGAGGAATCCATCA
*
642220 ACTGGTCCGAACCATATAAAACACATAATTCTACATGCAAAATAATACATTTCAGACGTATCCAT
382 ACTAGTCCGAACCATATAAAACACATAATTCTACATG---AATAAT-CATTT-A-AC-TATCC--
*
642285 TTTATAGGTTTGG-ATTAATGTG
438 TTTACA----TGGAATT-ATGTG
* * * * * ** *
642307 TAAATCTTCTCTTCACTTATTACCTTGTTTATCCACGAGACTCTTTTCCTCTTAAATTCATCATA
1 TAAATCTTCACTTCACTTTTTGCCTTGTTTCT-CACGAGACTCTATTCCTCTTAAATAGATCATG
*
642372 ATGTGACAATAAGGGGATACTTAGTGGGTT-CTAGTGGGGATGCCTTATA--T---TCGGGT-G-
65 ATGTGACAATAAGGGGATACTTAGTGGGTTCCGA-TGGGG-TGCCTTATATTTAGGTCGGGTGGT
* ** * * * *
642429 GGGTAAAAGTCAGACCCAACTCATGCACATCCCTAGGACTATCATAGGTTAATAGTTACAAGTGT
128 GGGTAAAAATCAGACCCAAC-CATGTGCATCCCTTGGACTATCTTAGGTTGATACTTACAAGTGT
* * * ** * * *
642494 GATTATGGGAATTAGGTTTATACTTAAAAGTGAAAATATGAGAATCAAGAATTTTCCTCCTTATA
192 AATCATGGGAATTAGGTTTATACTTAAAAGTGTAAGCATGAGAATCAAGAGTTTTCTTTCTTATA
* ** * * *
642559 CCAAAGCTTGGGACT-AAGGATCATAAGCTTTTATTTCAACGCTTAGGGTCATACTTATTTCTCC
257 CTAAAGCTCAGGACTAAAGG-TCA-AAGCTTTTATTTGAACGCTTAGGCTCATACTTGTTTCTCC
* * * * * * *
642623 ATCAGAATCTAAACCTCTTCTACGGTGGCGTTATTGATGCGAACAGATAGAGGAATCCATCAACT
320 ATCAGAATATAAACCTCTTATATGGTGGCGTCATTAATGCGAAAAGATGGAGGAATCCATCAACT
* * * *
642688 GGTCCAAACCATATAAAACACATAATTTTACATGTAAAATAATGCATTTAAGACGTATTCATTTT
385 AGTCCGAACCATATAAAACACATAATTCTACATG---AATAAT-CATTT-A-AC-TA-TC--CTT
*
642753 TACATGTTTGGAATTATGTT
440 TACA----TGGAATTATGTG
* *
642773 TAAATCTTCACTTCACTTTTTGCCTTGTTTCTCTACTAGACTCTATTCCTCTTAAATCGATCATG
1 TAAATCTTCACTTCACTTTTTGCCTTGTTTCTC-ACGAGACTCTATTCCTCTTAAATAGATCATG
* * * * *
642838 ATGTGACAATAAAGGGATACTTAATGGGTTCCGATGGTGGTGCCTTATATTCAGGTTAAGGTTGG
65 ATGTGACAATAAGGGGATACTTAGTGGGTTCCGATGG-GGTGCCTTATATTTAGG-T-CGGGT-G
* * * * *
642903 GTGGTGTAAAAATTAAACCCAACCCATGTGTATCCCTAT-AACTATCTTAGGTTGATACTTACAT
126 GTGG-GTAAAAATCAGACCCAA-CCATGTGCATCCCT-TGGACTATCTTAGGTTGATACTTACAA
* * * *
642967 GTGTGAT-ACTGGGAATTAGGTTTATA-TGCAAAAGTTTAAGCATGAGAGTCAAGAGTTTTCTTT
188 GTGTAATCA-TGGGAATTAGGTTTATACT-TAAAAGTGTAAGCATGAGAATCAAGAGTTTTCTTT
* * *
643030 CTTATACTAAAGCTCGGGACTAAGGGTTGC-AAGCTTTTATTTGAACTCTTAGGCTCATACTTGT
251 CTTATACTAAAGCTCAGGACTAAAGG-T-CAAAGCTTTTATTTGAACGCTTAGGCTCATACTTGT
* * * * *
643094 TTCTCCATCAGAATATAAACATCTTATATGGTAGCATCGTTAATGCGGAAAGATGGAGGAATCCA
314 TTCTCCATCAGAATATAAACCTCTTATATGGTGGCGTCATTAATGCGAAAAGATGGAGGAATCC-
* *
643159 AT-AACTAGTCTGAACCATATAAAACACATTATTCTACAT
378 ATCAACTAGTCCGAACCATATAAAACACATAATTCTACAT
643198 ATAAAATTTT
Statistics
Matches: 1107, Mismatches: 173, Indels: 128
0.79 0.12 0.09
Matches are distributed among these distances:
437 17 0.02
438 69 0.06
439 13 0.01
441 1 0.00
444 2 0.00
445 2 0.00
448 56 0.05
449 15 0.01
450 11 0.01
451 152 0.14
452 9 0.01
453 1 0.00
456 4 0.00
458 1 0.00
459 2 0.00
460 5 0.00
461 120 0.11
462 3 0.00
463 1 0.00
464 63 0.06
465 84 0.08
466 115 0.10
467 12 0.01
468 1 0.00
470 1 0.00
471 6 0.01
472 77 0.07
473 24 0.02
475 1 0.00
476 4 0.00
477 227 0.21
478 7 0.01
479 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Consensus pattern (455 bp):
TAAATCTTCACTTCACTTTTTGCCTTGTTTCTCACGAGACTCTATTCCTCTTAAATAGATCATGA
TGTGACAATAAGGGGATACTTAGTGGGTTCCGATGGGGTGCCTTATATTTAGGTCGGGTGGTGGG
TAAAAATCAGACCCAACCATGTGCATCCCTTGGACTATCTTAGGTTGATACTTACAAGTGTAATC
ATGGGAATTAGGTTTATACTTAAAAGTGTAAGCATGAGAATCAAGAGTTTTCTTTCTTATACTAA
AGCTCAGGACTAAAGGTCAAAGCTTTTATTTGAACGCTTAGGCTCATACTTGTTTCTCCATCAGA
ATATAAACCTCTTATATGGTGGCGTCATTAATGCGAAAAGATGGAGGAATCCATCAACTAGTCCG
AACCATATAAAACACATAATTCTACATGAATAATCATTTAACTATCCTTTACATGGAATTATGTG
Found at i:643155 original size:477 final size:466
Alignment explanation
Indices: 641823--643428 Score: 1573
Period size: 477 Copynumber: 3.4 Consensus size: 466
641813 ATACCTTTCA
*
641823 GGAATTATGCGTAAATCTTCACTTCACTTTTTTGCCTTGTTTCTACACCGAACTCTATTCCTCTT
1 GGAATTATGCGTAAATCTTCACTTCAC-TTTTTGCCTTGTTTCT-CACAG-ACTCTATTCCTCTT
* * * * * * * * *
641888 AAATAGGTCACGATGTAACAATAAGGGGATATTTAGCGAGTTCCGATGGCAGTGCCTTATATTTA
63 AAATCGATCATGATGTGACAATAAGGGGATACTTAGTGGGTTCCGATGG-GGTGCCTTATATTCA
* * * *
641953 GGTCGGGGTCGAGTGAGGTAAAAATCAGACTCAATCCATGTGCATTCCT-TGGACTATCTTAGGT
127 GGT---GGTTG-GTG-GGTAAAAATCAGACCCAACCCATGTGCATCCCTAT-GACTATCTTAGGT
* *
642017 TGATACTTACAAGTGTAAT-CATGGGAATTAGGTTTATACTTAAAAGTGTAAGCATGGGAATCAA
186 TGATACTTACAAGTGTGATAC-TGGGAATTAGGTTTATACTTAAAAGTGTAAGCATGAGAATCAA
* * * * *
642081 GAGTTTTCTTTCATATACTAAAGCTCAGGACTAA-AG-GCCAGCTTTTATTTTAACACTTAGGCT
250 GAGTTTTCTTTCTTATACTAAAGCTCGGGACTAAGGGTGCAAGCTTTTATTTCAACACTTAGGCT
* * * *
642144 CATACTTGTTTCTCCATCAGAATATAACCCTCTTATATGGTGGCGCATTGATGCGAAAATATGGA
315 CATACTTGTTTCTCCATCAGAATATAAACCTCTTATATGGTGGCTCATTGATGCGGAAAGATGGA
* *
642209 GGAATGCATCAACTGGTCCGAACCATATAAAACACATAATTCTACATGCAAAATAATACATTTCA
380 GGAATCCATCAACTGGTCCGAACCATATAAAACACATAATTCTACATGTAAAATAATACATTT-A
* * *
642274 GACGTATCCA-TTTTATAGGTTT
444 GACGTATTCATTTTTACAAGTTT
* * * * * *
642296 GG-ATTAATGTGTAAATCTTCTCTTCACTTATTACCTTGTTTATCCACGAGACTCTTTTCCTCTT
1 GGAATT-ATGCGTAAATCTTCACTTCACTTTTTGCCTTGTTTCT-CAC-AGACTCTATTCCTCTT
* *
642360 AAATTC-ATCATAATGTGACAATAAGGGGATACTTAGTGGGTT-CTAGTGGGGATGCCTTATATT
63 AAA-TCGATCATGATGTGACAATAAGGGGATACTTAGTGGGTTCCGA-TGGGG-TGCCTTATATT
* * ** * * *
642423 C--G-GG-T-G-GGGTAAAAGTCAGACCCAACTCATGCACATCCCTAGGACTATCATAGGTTAAT
125 CAGGTGGTTGGTGGGTAAAAATCAGACCCAACCCATGTGCATCCCTATGACTATCTTAGGTTGAT
* * ** *
642482 AGTTACAAGTGTGATTA-TGGGAATTAGGTTTATACTTAAAAGTGAAAATATGAGAATCAAGAAT
190 ACTTACAAGTGTGA-TACTGGGAATTAGGTTTATACTTAAAAGTGTAAGCATGAGAATCAAGAGT
* * * * * * *
642546 TTTCCTCCTTATACCAAAGCTTGGGACTAAGGAT-CATAAGCTTTTATTTCAACGCTTAGGGTCA
254 TTTCTTTCTTATACTAAAGCTCGGGACTAAGGGTGC--AAGCTTTTATTTCAACACTTAGGCTCA
* * * * * *
642610 TACTTATTTCTCCATCAGAATCTAAACCTCTTCTACGGTGGCGTTATTGATGC-GAACAGATAGA
317 TACTTGTTTCTCCATCAGAATATAAACCTCTTATATGGTGGC-TCATTGATGCGGAA-AGATGGA
* * *
642674 GGAATCCATCAACTGGTCCAAACCATATAAAACACATAATTTTACATGTAAAATAATGCATTTAA
380 GGAATCCATCAACTGGTCCGAACCATATAAAACACATAATTCTACATGTAAAATAATACATTT-A
*
642739 GACGTATTCATTTTTACATGTTT
444 GACGTATTCATTTTTACAAGTTT
**
642762 GGAATTATGTTTAAATCTTCACTTCACTTTTTGCCTTGTTTCTCTACTAGACTCTATTCCTCTTA
1 GGAATTATGCGTAAATCTTCACTTCACTTTTTGCCTTGTTTCTC-AC-AGACTCTATTCCTCTTA
* *
642827 AATCGATCATGATGTGACAATAAAGGGATACTTAATGGGTTCCGATGGTGGTGCCTTATATTCAG
64 AATCGATCATGATGTGACAATAAGGGGATACTTAGTGGGTTCCGATGG-GGTGCCTTATATTCAG
* * * *
642892 GTTAAGGTTGGGTGGTGTAAAAATTAAACCCAACCCATGTGTATCCCTATAACTATCTTAGGTTG
128 G-T--GGTT-GGTGG-GTAAAAATCAGACCCAACCCATGTGCATCCCTATGACTATCTTAGGTTG
* * * *
642957 ATACTTACATGTGTGATACTGGGAATTAGGTTTATA-TGCAAAAGTTTAAGCATGAGAGTCAAGA
188 ATACTTACAAGTGTGATACTGGGAATTAGGTTTATACT-TAAAAGTGTAAGCATGAGAATCAAGA
* *
643021 GTTTTCTTTCTTATACTAAAGCTCGGGACTAAGGGTTGCAAGCTTTTATTTGAACTCTTAGGCTC
252 GTTTTCTTTCTTATACTAAAGCTCGGGACTAAGGG-TGCAAGCTTTTATTTCAACACTTAGGCTC
* * * *
643086 ATACTTGTTTCTCCATCAGAATATAAACATCTTATATGGTAGCATCGTTAATGCGGAAAGATGGA
316 ATACTTGTTTCTCCATCAGAATATAAACCTCTTATATGGTGGC-TCATTGATGCGGAAAGATGGA
* * * * ** *
643151 GGAATCCAAT-AACTAGTCTGAACCATATAAAACACATTATTCTACATATAAAATTTTTCATTCT
380 GGAATCC-ATCAACTGGTCCGAACCATATAAAACACATAATTCTACATGTAAAATAATACATT-T
* * *
643215 AGACCTA-TCTATTTTTGCAAGTGT
443 AGACGTATTC-ATTTTTACAAGTTT
* * * * * * * **
643239 GGAATTAAGCGTAAATCTTCACTTCATTTTTTGCTTTATTTCTCGACCAGAATGTATTTCGGTTA
1 GGAATTATGCGTAAATCTTCACTTCACTTTTTGCCTTGTTTCTC-A-CAGACTCTATTCCTCTTA
* * * * *
643304 AATTTG-TCACGATGTGACAATAA-TGGATACTTA-TCGGGTT-CTAGTGGGGCTACCTTATATT
64 AA-TCGATCATGATGTGACAATAAGGGGATACTTAGT-GGGTTCCGA-TGGGG-TGCCTTATATT
* * * *
643365 CA---GG-T--TGGCTAAAAATCAGTCCCAACCCATGCGCATCCCT-TGGACTATCTTAGGTTGG
125 CAGGTGGTTGGTGGGTAAAAATCAGACCCAACCCATGTGCATCCCTAT-GACTATCTTAGGTTGA
643423 TACTTA
189 TACTTA
643429 AAAATGTAAG
Statistics
Matches: 932, Mismatches: 156, Indels: 98
0.79 0.13 0.08
Matches are distributed among these distances:
461 119 0.13
462 3 0.00
463 1 0.00
464 63 0.07
465 130 0.14
466 117 0.13
467 7 0.01
468 1 0.00
469 1 0.00
470 3 0.00
471 3 0.00
472 80 0.09
473 24 0.03
475 6 0.01
476 36 0.04
477 327 0.35
478 10 0.01
479 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (466 bp):
GGAATTATGCGTAAATCTTCACTTCACTTTTTGCCTTGTTTCTCACAGACTCTATTCCTCTTAAA
TCGATCATGATGTGACAATAAGGGGATACTTAGTGGGTTCCGATGGGGTGCCTTATATTCAGGTG
GTTGGTGGGTAAAAATCAGACCCAACCCATGTGCATCCCTATGACTATCTTAGGTTGATACTTAC
AAGTGTGATACTGGGAATTAGGTTTATACTTAAAAGTGTAAGCATGAGAATCAAGAGTTTTCTTT
CTTATACTAAAGCTCGGGACTAAGGGTGCAAGCTTTTATTTCAACACTTAGGCTCATACTTGTTT
CTCCATCAGAATATAAACCTCTTATATGGTGGCTCATTGATGCGGAAAGATGGAGGAATCCATCA
ACTGGTCCGAACCATATAAAACACATAATTCTACATGTAAAATAATACATTTAGACGTATTCATT
TTTACAAGTTT
Found at i:643850 original size:430 final size:429
Alignment explanation
Indices: 643030--643867 Score: 1030
Period size: 430 Copynumber: 1.9 Consensus size: 429
643020 AGTTTTCTTT
* * *
643030 CTTATACTAAAGCTCGGGACTAAGGGTTGCAAGCTTTTATTTGAACTCTTAGGCTCATACTTGTT
1 CTTATACTAAAGCTCGGCACTAAGGGTTGCAAGATTTTATTTGAACACTTAGGCTCATACTTGTT
* *
643095 TCTCCATCAGAATATAAACATCTTATATGGTAGCATCGTTAATGCGGAAAGATGGAGGAATCCAA
66 TCTCCATCAGAATATAAACATC-TATATGGTAGCATCATTAATGCGGAAAGATGAAGGAATCCAA
* *
643160 TAACTAGTCTGAACCATATAAAACACATTATTCTACATATAAAATTTTTCATTCTAGACCTATCT
130 TAACTAGTCTGAACCATATAAAACACATTATTCTACATATAAAATTTTGCATTCTAGACATATCT
* * * * *
643225 ATTTTTGCAAGTGTGGAATTAAGCGTAAATCTTCACTTCATTTTTTGCTTTATTTCTCGACCAGA
195 ATATTTACAAGTGTGGAATTAAGCGTAAATCTTCACTTCACTTTTTGCCTTATTTCTCCACCAGA
* * * ** * * *
643290 ATGTATTTCGGTTAAATTTGTCACGATGTGACAATAATGGATACTTATCGGGTTCTAGTGGGGCT
260 ATCTATTCCGCTTAAATGGGTCACGATGTGACAATAAAGGATACTTAACGGGTTCCAGTGGGGCT
* * * * * * *
643355 ACCTTATATTCAGGTTGGCTAAAAATCAGTCCCAACCCATGCGCATCCCTTGGACTATCTTAGGT
325 ACCTTATATTCAGGTGGGATAAAAATCAGACCCAACCCATGCACATCCCTAGGACAATATTAGGT
*
643420 TGGTACTTAAAAATGTAAGCATGTGAATCAAAAAATTTTC
390 TGATACTTAAAAATGTAAGCATGTGAATCAAAAAATTTTC
* * * *
643460 CTTATACTAAAGCTTGGCATTAAGGGTTGCCATATTTTATTTGAACACTTAGGCTCATACTTGTT
1 CTTATACTAAAGCTCGGCACTAAGGGTTGCAAGATTTTATTTGAACACTTAGGCTCATACTTGTT
* * * * *
643525 TCTCTATCAGAATCTAAACCCATC-CTATGGTGGCATCATTGATGCGGAAAGATGAAGGAATCCA
66 TCTCCATCAGAATATAAA--CATCTATATGGTAGCATCATTAATGCGGAAAGATGAAGGAATCCA
* * *
643589 TTAACTGGT-TGGAACCATATAAAACAC-TTAATTCTACAT-TTAAATTTATGCATT-TCAGACA
129 ATAACTAGTCT-GAACCATATAAAACACATT-ATTCTACATATAAAATTT-TGCATTCT-AGACA
* * *
643650 TATGCT-TATTTACAAGTTTGGAA-TAATGTGTAAATCTTCACTTTACTTTTTGCCTTATTTCTC
190 TAT-CTATATTTACAAGTGTGGAATTAA-GCGTAAATCTTCACTTCACTTTTTGCCTTATTTCTC
** * * *
643713 CA-GTGGATCTATTCCTCTTAAATGGGTCATGATGTGACAATAAGAGGATACTTAACGGGTTCCA
253 CACCAGAATCTATTCCGCTTAAATGGGTCACGATGTGACAATAA-AGGATACTTAACGGGTTCCA
* *
643777 GTAGGGG-TGCCTTATATTCTA-GTGGGATAAAAATCAGACCCAACCCATGCACATTCCTAGGAC
317 GT-GGGGCTACCTTATATTC-AGGTGGGATAAAAATCAGACCCAACCCATGCACATCCCTAGGAC
* *
643840 AATATTAGGTTGATACTTACAAGTGTAA
380 AATATTAGGTTGATACTTAAAAATGTAA
643868 TCCTGAAAAT
Statistics
Matches: 345, Mismatches: 52, Indels: 22
0.82 0.12 0.05
Matches are distributed among these distances:
429 45 0.13
430 289 0.84
431 7 0.02
432 4 0.01
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (429 bp):
CTTATACTAAAGCTCGGCACTAAGGGTTGCAAGATTTTATTTGAACACTTAGGCTCATACTTGTT
TCTCCATCAGAATATAAACATCTATATGGTAGCATCATTAATGCGGAAAGATGAAGGAATCCAAT
AACTAGTCTGAACCATATAAAACACATTATTCTACATATAAAATTTTGCATTCTAGACATATCTA
TATTTACAAGTGTGGAATTAAGCGTAAATCTTCACTTCACTTTTTGCCTTATTTCTCCACCAGAA
TCTATTCCGCTTAAATGGGTCACGATGTGACAATAAAGGATACTTAACGGGTTCCAGTGGGGCTA
CCTTATATTCAGGTGGGATAAAAATCAGACCCAACCCATGCACATCCCTAGGACAATATTAGGTT
GATACTTAAAAATGTAAGCATGTGAATCAAAAAATTTTC
Found at i:645167 original size:48 final size:48
Alignment explanation
Indices: 645113--645363 Score: 170
Period size: 49 Copynumber: 5.2 Consensus size: 48
645103 CATAAGTAAT
* * * *
645113 GTCAGACGTGCTAGGTACCACTGATAGTAGCATCACCGTCACTCAAAC
1 GTCAGACGTGCTAGGTACCACTAATAGTAGCACCACCATCACACAAAC
* * * *
645161 GTCAGACATGCTAGGTACCATTCATAATAG-ACCACCATCACACAAAC
1 GTCAGACGTGCTAGGTACCACTAATAGTAGCACCACCATCACACAAAC
** *
645208 GTCAGACGTGCTAATTATCACTAATAGTAGCACCACCATCACA-AATAC
1 GTCAGACGTGCTAGGTACCACTAATAGTAGCACCACCATCACACAA-AC
* * ** * ** *
645256 -TCCAAACATGCTAAATCATCGTTAATAGTAGCACCACCCTCACA-AAGAC
1 GT-CAGACGTGCTAGGT-ACCACTAATAGTAGCACCACCATCACACAA-AC
* * * * * * * *
645305 GTCAGACGTGGTAAGTCATCATTAATAGTAACATCACCGTCACA-AAGAT
1 GTCAGACGTGCTAGGT-ACCACTAATAGTAGCACCACCATCACACAA-AC
645354 GTCAGACGTG
1 GTCAGACGTG
645364 TTAAATGCTC
Statistics
Matches: 168, Mismatches: 30, Indels: 9
0.81 0.14 0.04
Matches are distributed among these distances:
47 40 0.24
48 51 0.30
49 76 0.45
50 1 0.01
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (48 bp):
GTCAGACGTGCTAGGTACCACTAATAGTAGCACCACCATCACACAAAC
Found at i:645220 original size:47 final size:48
Alignment explanation
Indices: 645113--645250 Score: 161
Period size: 48 Copynumber: 2.9 Consensus size: 48
645103 CATAAGTAAT
* * * * *
645113 GTCAGACGTGCTAGGTACCACTGATAGTAGCATCACCGTCACTCAAAC
1 GTCAGACGTGCTAGGTACCACTCATAATAGCACCACCATCACACAAAC
* *
645161 GTCAGACATGCTAGGTACCATTCATAATAG-ACCACCATCACACAAAC
1 GTCAGACGTGCTAGGTACCACTCATAATAGCACCACCATCACACAAAC
** * * *
645208 GTCAGACGTGCTAATTATCACTAATAGTAGCACCACCATCACA
1 GTCAGACGTGCTAGGTACCACTCATAATAGCACCACCATCACA
645251 AATACTCCAA
Statistics
Matches: 75, Mismatches: 14, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
47 37 0.49
48 38 0.51
ACGTcount: A:0.34, C:0.29, G:0.16, T:0.21
Consensus pattern (48 bp):
GTCAGACGTGCTAGGTACCACTCATAATAGCACCACCATCACACAAAC
Found at i:645265 original size:95 final size:96
Alignment explanation
Indices: 645113--645350 Score: 232
Period size: 95 Copynumber: 2.5 Consensus size: 96
645103 CATAAGTAAT
** * * * * **
645113 GTCAGACGTGCTAGGTACCACTGATAGTAGCATCACCGTCACTCAAACGTCAGACATGCTAGGT-
1 GTCAGACGTGCTAATTATCACTAATAGTAGCATCACCGTCAC-AAAACGTCAAACATGCTAAATC
*
645177 ACCATTCATAATAG-ACCACCATCACACAA-AC
65 ACCATTAATAATAGCACCACCATCACA-AAGAC
* *
645208 GTCAGACGTGCTAATTATCACTAATAGTAGCACCACCATCACAAATAC-TCCAAACATGCTAAAT
1 GTCAGACGTGCTAATTATCACTAATAGTAGCATCACCGTCACAAA-ACGT-CAAACATGCTAAAT
* * * *
645272 CATCGTTAATAGTAGCACCACCCTCACAAAGAC
64 CACCATTAATAATAGCACCACCATCACAAAGAC
* * * *
645305 GTCAGACGTGGTAAGTCATCATTAATAGTAACATCACCGTCACAAA
1 GTCAGACGTGCTAA-TTATCACTAATAGTAGCATCACCGTCACAAA
645351 GATGTCAGAC
Statistics
Matches: 116, Mismatches: 21, Indels: 9
0.79 0.14 0.06
Matches are distributed among these distances:
94 3 0.03
95 49 0.42
96 12 0.10
97 26 0.22
98 26 0.22
ACGTcount: A:0.36, C:0.28, G:0.15, T:0.21
Consensus pattern (96 bp):
GTCAGACGTGCTAATTATCACTAATAGTAGCATCACCGTCACAAAACGTCAAACATGCTAAATCA
CCATTAATAATAGCACCACCATCACAAAGAC
Found at i:646055 original size:11 final size:11
Alignment explanation
Indices: 646039--646068 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
646029 GCATTAAAAT
646039 GAATTCTTTTA
1 GAATTCTTTTA
646050 GAATTCTTTTA
1 GAATTCTTTTA
*
646061 AAATTCTT
1 GAATTCTT
646069 CTCAACATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (11 bp):
GAATTCTTTTA
Found at i:648754 original size:2 final size:2
Alignment explanation
Indices: 648747--648776 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
648737 AATATTAAGA
648747 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
648777 CAAATATTAT
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:656020 original size:38 final size:37
Alignment explanation
Indices: 655962--656044 Score: 98
Period size: 38 Copynumber: 2.2 Consensus size: 37
655952 ATATAAATCC
**
655962 TTAAATAATATAATAGTATCCTATTAATATTTAAA-AT
1 TTAAATAATATAATAGTATCCTATTAAT-TCGAAATAT
*
655999 TTAAATAAT-TCACATAGTATCCTTTTAATTCGAAATAT
1 TTAAATAATAT-A-ATAGTATCCTATTAATTCGAAATAT
656037 TTAAATAA
1 TTAAATAA
656045 ATATGTCACC
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
36 1 0.03
37 14 0.35
38 25 0.62
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (37 bp):
TTAAATAATATAATAGTATCCTATTAATTCGAAATAT
Found at i:656598 original size:429 final size:430
Alignment explanation
Indices: 655754--656610 Score: 1201
Period size: 429 Copynumber: 2.0 Consensus size: 430
655744 AAAATACAAA
* *
655754 AAAAATTATTTGTAAACACTTTAAATAGAGAAAAAAATTATGATTGTTGTCAAAGATCATTAGAG
1 AAAAATTATTTGTAAACACTTTAAATAGAGAAAAAAATTATGATCGTTGTCAAAGATAATTAGAG
** * *
655819 AAATCATTATGTGAAAGTTATTATTACGCAAAAACTATTCTCACAGTCTTAATACATAAGTACAC
66 AAATCATTATGTGAAAGTTATTACAACACAAAAACTATTCTCACAATCTTAATACATAAGTACAC
*** * *
655884 CAGAGAAAATACTATGTTTCGATTTCAATGAAATATAAATTCGTAAATAAATATTCTAATTTAAT
131 CAGAGAAAATAC-AAAATTCGATTTCAATGAAATATAAATTCGTAAATAAATATTCGAATTCAAT
* * * *
655949 TGAATATAAATCCTTAAATAATATAATAGTATCCTATTAATATTTAAAATTTAAATAATTCACAT
195 TGAATATAAATCCTTAAATAATATAACAGTATCCTATTAATAATCAAAATTTAAAGAATTCACAT
* * ** *
656014 AGTATCCTTTTAATTCGAAATATTTAAATAAATATGTCACCTTTAACAAAAATTCAATTAGCAAA
260 AATATCCTTTTAATTCGAAATATTTAAATAAATATGTAAAATTTAACAAAAATTCAATTACCAAA
* * * *
656079 TTCATCCATGAATTCACAAAATTTTCCAGCAAGCCTGACCAATTCCCCTTTAGATTGCATGCCTA
325 TTCAACAATGAATTCACAAAATTTTCCAACAAGCCTGACCAATTCCCCTTTAGATTACATGCCTA
* ** * *
656144 AAATAGATAAAGAAACTAGGAAATAATATAATGAAAAATAC
390 AAATAAATAAAGAAAAGACGAAATAATATAATAAAAAATAC
656185 AAAAA-TATTTGTAAACACTTTAAATAGAG-AAAAAATTATGATCGTTGTCAAAGATAATTAGAG
1 AAAAATTATTTGTAAACACTTTAAATAGAGAAAAAAATTATGATCGTTGTCAAAGATAATTAGAG
*
656248 AAATCATTATGTGGAAA-TTATTACAACACAAAAACTATTCTCACAATCTTATTACATAAGTACA
66 AAATCATTATGT-GAAAGTTATTACAACACAAAAACTATTCTCACAATCTTAATACATAAGTACA
*
656312 CCAGAGAAAA-A-AAAATTCTATTTCAA-GAGAATATAAATTCGTAAATAACATATTCGAATATC
130 CCAGAGAAAATACAAAATTCGATTTCAATGA-AATATAAATTCGTAAATAA-ATATTCGAAT-TC
* *
656374 AATTGAATATAAATCTTTAAATAATATAACA-TGATCTTATTAATAATCAAAATTTAAAGAATTC
192 AATTGAATATAAATCCTTAAATAATATAACAGT-ATCCTATTAATAATCAAAATTTAAAGAATTC
* * * **
656438 ACATAATATCTTTTTTAATTTGAAATATTTAAATAGATATGTAAAATTTAAGGAAAATTCAATTA
256 ACATAATATC-CTTTTAATTCGAAATATTTAAATAAATATGTAAAATTTAACAAAAATTCAATTA
* *
656503 CCAAATTGAACAATGAATTCAC-ACATTTTCCCAACACA-CCTGACCAATTCCCCTTTAGATTAC
320 CCAAATTCAACAATGAATTCACAAAATTTT-CCAACA-AGCCTGACCAATTCCCCTTTAGATTAC
*
656566 ATGCCTAAAATAAATAAATAAAAGACGAAATAATATAATAAAAAA
383 ATGCCTAAAATAAATAAAGAAAAGACGAAATAATATAATAAAAAA
656611 ATTTTGTAAA
Statistics
Matches: 377, Mismatches: 41, Indels: 18
0.86 0.09 0.04
Matches are distributed among these distances:
425 2 0.01
426 30 0.08
427 10 0.03
428 73 0.19
429 228 0.60
430 29 0.08
431 5 0.01
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.32
Consensus pattern (430 bp):
AAAAATTATTTGTAAACACTTTAAATAGAGAAAAAAATTATGATCGTTGTCAAAGATAATTAGAG
AAATCATTATGTGAAAGTTATTACAACACAAAAACTATTCTCACAATCTTAATACATAAGTACAC
CAGAGAAAATACAAAATTCGATTTCAATGAAATATAAATTCGTAAATAAATATTCGAATTCAATT
GAATATAAATCCTTAAATAATATAACAGTATCCTATTAATAATCAAAATTTAAAGAATTCACATA
ATATCCTTTTAATTCGAAATATTTAAATAAATATGTAAAATTTAACAAAAATTCAATTACCAAAT
TCAACAATGAATTCACAAAATTTTCCAACAAGCCTGACCAATTCCCCTTTAGATTACATGCCTAA
AATAAATAAAGAAAAGACGAAATAATATAATAAAAAATAC
Found at i:657990 original size:47 final size:47
Alignment explanation
Indices: 657920--658057 Score: 183
Period size: 47 Copynumber: 3.0 Consensus size: 47
657910 CCAACCTAAA
* *
657920 AAATAA-TTTTAGATCCATCATTGTTTCTAGTAAGACAATTTGAATG
1 AAATAATTTTTGGATCCGTCATTGTTTCTAGTAAGACAATTTGAATG
*
657966 AGAA-AATTTTTGGA-CCTGTCATTGTTTCTAATAAGACAATTTGAATG
1 A-AATAATTTTTGGATCC-GTCATTGTTTCTAGTAAGACAATTTGAATG
* * *
658013 AAATAATTTTTTGATCCGTCACTGTTTCAAGTAAGACAATTTGAA
1 AAATAATTTTTGGATCCGTCATTGTTTCTAGTAAGACAATTTGAA
658058 CGAGGCAGGT
Statistics
Matches: 80, Mismatches: 7, Indels: 9
0.83 0.07 0.09
Matches are distributed among these distances:
46 7 0.09
47 71 0.89
48 2 0.03
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (47 bp):
AAATAATTTTTGGATCCGTCATTGTTTCTAGTAAGACAATTTGAATG
Found at i:662798 original size:2 final size:2
Alignment explanation
Indices: 662786--662980 Score: 205
Period size: 2 Copynumber: 101.5 Consensus size: 2
662776 ATTGAAACAA
662786 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * **
662825 AT AT AT AT AT AT -T AT AT GT AT GA- AT GT -T A- AT -T AG GT GC
1 AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT
* * *
662863 AT GT AT AT AT AC AT CT AT AT ACT AT ACT AT AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT A-T AT AT AT AT AT AT AT AT
662906 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
662948 -T AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
662981 AGTGGCAAGG
Statistics
Matches: 164, Mismatches: 15, Indels: 28
0.79 0.07 0.14
Matches are distributed among these distances:
1 11 0.07
2 148 0.90
3 5 0.03
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:672559 original size:21 final size:22
Alignment explanation
Indices: 672512--672567 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 22
672502 ATAATATATA
672512 TATATAATATGTACGATGAATG
1 TATATAATATGTACGATGAATG
* * *
672534 T-TATAATAT-TATGGTGCATG
1 TATATAATATGTACGATGAATG
672554 TATAT-ATAATGTAC
1 TATATAAT-ATGTAC
672568 ACTATACTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
20 11 0.41
21 13 0.48
22 3 0.11
ACGTcount: A:0.38, C:0.05, G:0.16, T:0.41
Consensus pattern (22 bp):
TATATAATATGTACGATGAATG
Found at i:672632 original size:10 final size:10
Alignment explanation
Indices: 672619--672664 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 10
672609 TATATACTTT
672619 TATATATATA
1 TATATATATA
672629 TATATA-ATA
1 TATATATATA
672638 TA-ATATA-A
1 TATATATATA
672646 TATA-ATATA
1 TATATATATA
672655 -ATATA-ATA
1 TATATATATA
672663 TA
1 TA
672665 AGTGACAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
8 15 0.48
9 10 0.32
10 6 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
TATATATATA
Found at i:672640 original size:5 final size:5
Alignment explanation
Indices: 672619--672665 Score: 76
Period size: 5 Copynumber: 9.0 Consensus size: 5
672609 TATATACTTT
672619 TATATA TATATA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATA-A TATA-A TATAA TATAA TATAA TATAA TATAA TATAA TATAA
672666 GTGACAAAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 31 0.76
6 10 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
TATAA
Found at i:672862 original size:15 final size:15
Alignment explanation
Indices: 672796--672863 Score: 52
Period size: 15 Copynumber: 4.7 Consensus size: 15
672786 TTCCAATTTT
672796 TATAAGTATAAAGTA
1 TATAAGTATAAAGTA
* *
672811 TATATA-TATAAACTT
1 TATA-AGTATAAAGTA
* **
672826 TAAAAAAATAAA-TA
1 TATAAGTATAAAGTA
672840 T-TAAGTATAAAGTA
1 TATAAGTATAAAGTA
*
672854 TATATGTATA
1 TATAAGTATA
672864 TAATATAAGT
Statistics
Matches: 40, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
13 7 0.17
14 6 0.15
15 26 0.65
16 1 0.03
ACGTcount: A:0.54, C:0.01, G:0.07, T:0.37
Consensus pattern (15 bp):
TATAAGTATAAAGTA
Found at i:673658 original size:50 final size:50
Alignment explanation
Indices: 673604--673707 Score: 208
Period size: 50 Copynumber: 2.1 Consensus size: 50
673594 TAATTAAAAT
673604 TTATAATATAAGGATTATAATTAATATAGAAAGTAAATTTATTACTTTAG
1 TTATAATATAAGGATTATAATTAATATAGAAAGTAAATTTATTACTTTAG
673654 TTATAATATAAGGATTATAATTAATATAGAAAGTAAATTTATTACTTTAG
1 TTATAATATAAGGATTATAATTAATATAGAAAGTAAATTTATTACTTTAG
673704 TTAT
1 TTAT
673708 CATAACTAAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 54 1.00
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.43
Consensus pattern (50 bp):
TTATAATATAAGGATTATAATTAATATAGAAAGTAAATTTATTACTTTAG
Found at i:673907 original size:16 final size:16
Alignment explanation
Indices: 673888--673918 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
673878 TAAATTATAG
673888 GTCAGGTTCATAACAA
1 GTCAGGTTCATAACAA
*
673904 GTCAGGTTGATAACA
1 GTCAGGTTCATAACA
673919 GGTCGGGTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (16 bp):
GTCAGGTTCATAACAA
Found at i:682930 original size:29 final size:30
Alignment explanation
Indices: 682875--682931 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
682865 TTGAGTAACA
*
682875 AAATGAAACGTTAGGCACGAAACTGGAACG
1 AAATGAAACATTAGGCACGAAACTGGAACG
* *
682905 AAAT-AAACATTAGGCACTAAATTGGAA
1 AAATGAAACATTAGGCACGAAACTGGAA
682932 AAACGGGCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 20 0.83
30 4 0.17
ACGTcount: A:0.47, C:0.14, G:0.21, T:0.18
Consensus pattern (30 bp):
AAATGAAACATTAGGCACGAAACTGGAACG
Found at i:684187 original size:9 final size:9
Alignment explanation
Indices: 684173--684206 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
684163 TAAAAGGGAA
684173 AAATAAAAT
1 AAATAAAAT
684182 AAATAAAAT
1 AAATAAAAT
684191 AAAT-AAAT
1 AAATAAAAT
684199 AAGATAAA
1 AA-ATAAA
684207 GAAAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 6 0.26
9 15 0.65
10 2 0.09
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (9 bp):
AAATAAAAT
Found at i:684194 original size:13 final size:13
Alignment explanation
Indices: 684172--684206 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
684162 GTAAAAGGGA
684172 AAAATAAAATAAAT
1 AAAAT-AAATAAAT
684186 AAAATAAATAAAT
1 AAAATAAATAAAT
*
684199 AAGATAAA
1 AAAATAAA
684207 GAAAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 15 0.75
14 5 0.25
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:684266 original size:2 final size:2
Alignment explanation
Indices: 684259--684303 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
684249 GAAAAAGGAA
684259 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
684301 AT A
1 AT A
684304 CATCAAAGTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:684701 original size:2 final size:2
Alignment explanation
Indices: 684694--684750 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
684684 TATTAAAGAA
684694 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
*
684736 AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT A
684751 ATAATAATAC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:684770 original size:17 final size:17
Alignment explanation
Indices: 684748--684789 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
684738 ATATATACAT
*
684748 ATAATAATAATACATGA
1 ATAATAATAATAAATGA
*
684765 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
684782 ATAA-AATA
1 ATAATAATA
684790 TCCATATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 3 0.14
17 19 0.86
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:686485 original size:22 final size:21
Alignment explanation
Indices: 686459--686510 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
686449 TTTTTTATTA
686459 TTTTTCTTATCTCACTAAC-TTT
1 TTTTTCTT-TCTC-CTAACATTT
**
686481 TTTTTCTTTCTCCTTTCATTT
1 TTTTTCTTTCTCCTAACATTT
686502 TTTTTCTTT
1 TTTTTCTTT
686511 TGCATTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 3 0.11
21 16 0.59
22 8 0.30
ACGTcount: A:0.10, C:0.21, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTTTCTTTCTCCTAACATTT
Found at i:686520 original size:18 final size:18
Alignment explanation
Indices: 686499--686533 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
686489 TCTCCTTTCA
*
686499 TTTTTTT-TCTTTTGCAT
1 TTTTTTTATCATTTGCAT
686516 TTTTTTTATCATTTGCAT
1 TTTTTTTATCATTTGCAT
686534 CATTTAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.11, C:0.11, G:0.06, T:0.71
Consensus pattern (18 bp):
TTTTTTTATCATTTGCAT
Found at i:689356 original size:106 final size:106
Alignment explanation
Indices: 689171--690283 Score: 1596
Period size: 106 Copynumber: 10.5 Consensus size: 106
689161 GAGTAAATTT
** *
689171 CAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGGCAACGCA
1 CAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
689236 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA
66 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA
* * *
689277 CAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGACATTGGACTCCAGGCAACGCA
1 CAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
689342 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA
66 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA
*
689383 CAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCA
1 CAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
*
689448 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAAAAA
66 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC--AACAAA
* *
689491 CAACTTCTCAATTTCGGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
1 CAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
*
689556 AGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAA
66 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA
** * * * *
689597 TGATTTCTCAATTTCAGAGGCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGATAACGCA
1 CAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
*
689662 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAAAAA
66 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC--AACAAA
* *
689705 CAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
1 CAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
* *
689770 AGTTCAACTTCACGACGAAAGGACCGCTGGTTGTCAATAAA
66 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA
* * *
689811 TAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
1 CAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
*
689876 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAA
66 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA
* * ** * * *
689917 CAACTTCCCAATTTCAGAGCCGATTTTGACTTCTCAGCGAAGGATCTTGGAC-CCAAGACAACAC
1 CAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC-AGACAACGC
* * *
689981 AAGCTCAACTTCACGACGAATGGG-CGGCTGATTGTCAAC-AA
65 AAGTTCAACTTCACGACGAA-GGGACCGCTGGTTGTCAACAAA
* * * *
690022 -AA-TT-TC-ATTT-AGAGCCAATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAGCACA
1 CAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
* *
690082 AGTTCAACTTCACAAACGAAGGGACGGCTGGTTGTCAACAAA
66 AGTTCAACTTCAC-GACGAAGGGACCGCTGGTTGTCAACAAA
* * * * *
690124 CAACTTCCCAATTTCAGAGCCAATTTCAATTTCACAGCGAAAGATATTGGACTCGAGACAACACA
1 CAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
*
690189 AGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAA
66 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA
* * ** * * *
690230 CAATTTCCCGGTTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGTACTC
1 CAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGGACTC
690284 GGAACAATGC
Statistics
Matches: 921, Mismatches: 70, Indels: 32
0.90 0.07 0.03
Matches are distributed among these distances:
100 55 0.06
101 24 0.03
102 3 0.00
103 4 0.00
104 4 0.00
105 6 0.01
106 564 0.61
107 62 0.07
108 199 0.22
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.23
Consensus pattern (106 bp):
CAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA
Found at i:689587 original size:214 final size:212
Alignment explanation
Indices: 689175--690283 Score: 1615
Period size: 214 Copynumber: 5.2 Consensus size: 212
689165 AAATTTCAAC
** * *
689175 TTCTCAATTTCAGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGGCAACGCAAGTT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTT
* *
689240 CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCA
66 CAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAAACAACTTCCCAATTTCAGAGCCAATTTCA
* * *
689305 ACTTCACAACGAAGGACATTGGACTCCAGGCAACGCAAGTTCAACTTCACGACGAAGGGACCGCT
131 ACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCT
*
689370 GGTTGTCAACAAACAAC
196 GGTTGTCAACAAACAAT
689387 TTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTT
* *
689452 CAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAAAAACAACTTCTCAATTTCGGAGCCAATTT
66 CAACTTCACGACGAAGGGACCGCTGGTTGTC--AAAAAACAACTTCCCAATTTCAGAGCCAATTT
* *
689517 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCG
129 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
**
689582 CTGGTTGTCAACAAATGAT
194 CTGGTTGTCAACAAACAAT
* *
689601 TTCTCAATTTCAGAGGCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGATAACGCAAGTT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTT
*
689666 CAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAAAAACAATTTCCCAATTTCAGAGCCAATTT
66 CAACTTCACGACGAAGGGACCGCTGGTTGTC--AAAAAACAACTTCCCAATTTCAGAGCCAATTT
*
689731 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAAGGACCG
129 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
* *
689796 CTGGTTGTCAATAAATAAT
194 CTGGTTGTCAACAAACAAT
* *
689815 TTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTT
* * **
689880 CAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCGATTTTG
66 CAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAAACAACTTCCCAATTTCAGAGCCAATTTCA
* * * * *
689945 ACTTCTCAGCGAAGGATCTTGGAC-CCAAGACAACACAAGCTCAACTTCACGACGAATGGG-CGG
131 ACTTCACAGCGAAGGATATTGGACTCC-AGACAACGCAAGTTCAACTTCACGACGAA-GGGACCG
*
690008 CTGATTGTCAAC-AA-AA-
194 CTGGTTGTCAACAAACAAT
* * * *
690024 TT-TC-ATTT-AGAGCCAATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAGCACAAGTT
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTT
* * *
690086 CAACTTCACAAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTC
66 CAACTTCAC-GACGAAGGGACCGCTGGTTGTCAAAAAACAACTTCCCAATTTCAGAGCCAATTTC
* * * * *
690151 AATTTCACAGCGAAAGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACCGC
130 AACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
690216 TGGTTGTCAACAAACAAT
195 TGGTTGTCAACAAACAAT
* ** * * *
690234 TTCCCGGTTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGTACTC
1 TTCTCAATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGGACTC
690284 GGAACAATGC
Statistics
Matches: 818, Mismatches: 65, Indels: 27
0.90 0.07 0.03
Matches are distributed among these distances:
206 62 0.08
207 114 0.14
208 4 0.00
209 4 0.00
210 4 0.00
211 5 0.01
212 185 0.23
213 36 0.04
214 404 0.49
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.23
Consensus pattern (212 bp):
TTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTT
CAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAAACAACTTCCCAATTTCAGAGCCAATTTCA
ACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCT
GGTTGTCAACAAACAAT
Found at i:689825 original size:320 final size:317
Alignment explanation
Indices: 689171--690283 Score: 1592
Period size: 320 Copynumber: 3.5 Consensus size: 317
689161 GAGTAAATTT
* * *
689171 CAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGGCAACGCA
1 CAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
* *
689236 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAAT
66 AGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAAT
* * * *
689301 TTCAACTTCACAACGAAGGACATTGGACTCCAGGCAACGCAAGTTCAACTTCACGACGAAGGGAC
131 TTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
* *
689366 CGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATT
196 CGCTGGTTGTCAAAAAACAATTTC-CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATT
689431 GGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAAAAA
260 GGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC--AAAAAA
* *
689491 CAACTTCTCAATTTCGGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
1 CAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
** * * *
689556 AGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAATGATTTCTCAATTTCAGAGGCAAT
66 AGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAAT
*
689621 TTCAACTTCACAGCGAAGGATATTGGACTCAAGATAACGCAAGTTCAACTTCACGACGAAGGGAC
131 TTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
689686 CGCTGGTTGTCAAAAAAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATA
196 CGCTGGTTGTC--AAAAAACAATTT-CCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATA
* * *
689751 TTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAAGGACCGCTGGTTGTCAATAAA
258 TTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAAA
* * *
689811 TAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCA
1 CAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
* * *
689876 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCGAT
66 AGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAAT
** * * * * *
689941 TTTGACTTCTCAGCGAAGGATCTTGGACCCAAGACAACACAAGCTCAACTTCACGACGAATGGG-
131 TTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAA-GGGA
* * *
690005 CGGCTGATTGTC-AACAA-AATTT-C-ATTT-AGAGCCAATTTCAACTTCACAGCGAAGGATATT
195 CCGCTGGTTGTCAAAAAACAATTTCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATT
* * * * * * *
690065 AGACTCGAGACAGCACAAGTTCAACTTCACAAACGAAGGGACGGCTGGTTGTCAACAAA
260 GGACTCAAGACAACGCAAGTTCAACTTCAC-GACGAAGGGACCGCTGGTTGTCAAAAAA
* * * * *
690124 CAACTTCCCAATTTCAGAGCCAATTTCAATTTCACAGCGAAAGATATTGGACTCGAGACAACACA
1 CAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
* ** *
690189 AGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCAAT
66 AGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAAT
* *
690254 TTCAACTTCAC-GACGGAGGATATTGTACTC
131 TTCAACTTCACAG-CGAAGGATATTGGACTC
690284 GGAACAATGC
Statistics
Matches: 717, Mismatches: 70, Indels: 19
0.89 0.09 0.02
Matches are distributed among these distances:
312 60 0.08
313 166 0.23
314 1 0.00
316 5 0.01
317 4 0.01
320 377 0.53
321 3 0.00
322 100 0.14
323 1 0.00
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.23
Consensus pattern (317 bp):
CAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
AGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAAT
TTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
CGCTGGTTGTCAAAAAACAATTTCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTG
GACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAAA
Found at i:690593 original size:84 final size:84
Alignment explanation
Indices: 690461--690615 Score: 229
Period size: 84 Copynumber: 1.8 Consensus size: 84
690451 AAGATCTTCG
* * * * *
690461 AGTTCGACTACGCTCAGCTCTAAGGTATATCATTTGCAGCATAACTTAAGAAGAGAAAGGTTATC
1 AGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAACTTAAGAAGAGAAAGGCTATC
690526 TGCCAACCAAAGACCTCCT
66 TGCCAACCAAAGACCTCCT
* ** *
690545 AGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAGCTTAAGTCGAGAAGGGCTATC
1 AGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAACTTAAGAAGAGAAAGGCTATC
690610 TGCCAA
66 TGCCAA
690616 AGGCCCCCGT
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
84 62 1.00
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (84 bp):
AGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAACTTAAGAAGAGAAAGGCTATC
TGCCAACCAAAGACCTCCT
Found at i:690808 original size:37 final size:37
Alignment explanation
Indices: 690764--690867 Score: 174
Period size: 37 Copynumber: 2.8 Consensus size: 37
690754 TCTCTTGAAA
* *
690764 AAAACCTTTGAAATCGTTTCTCTT-AGAACACAAAAAG
1 AAAACCTTTGAAATTGTTTCTCTTGA-AACAAAAAAAG
690801 AAAACCTTTGAAATTGTTTCTCTTGAAACAAAAAAAG
1 AAAACCTTTGAAATTGTTTCTCTTGAAACAAAAAAAG
690838 AAAACCTTTGAAATTGTTTCTCTTGAAACA
1 AAAACCTTTGAAATTGTTTCTCTTGAAACA
690868 CCAAACCTTT
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
37 63 0.98
38 1 0.02
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.31
Consensus pattern (37 bp):
AAAACCTTTGAAATTGTTTCTCTTGAAACAAAAAAAG
Found at i:692362 original size:12 final size:13
Alignment explanation
Indices: 692335--692370 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
692325 TATTTTATAT
692335 TTTCATTTTTTCC
1 TTTCATTTTTTCC
*
692348 TTTCATTTTTTCT
1 TTTCATTTTTTCC
*
692361 TTTCGTTTTT
1 TTTCATTTTT
692371 GTTTCATGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.06, C:0.17, G:0.03, T:0.75
Consensus pattern (13 bp):
TTTCATTTTTTCC
Found at i:692431 original size:23 final size:23
Alignment explanation
Indices: 692405--692452 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
692395 TTTTCTTCAC
692405 TTTATTTTTTC-TCTTTTTTAATT
1 TTTATTTTTTCAT-TTTTTTAATT
*
692428 TTTATTTTTTCATTTTTTTCATT
1 TTTATTTTTTCATTTTTTTAATT
692451 TT
1 TT
692453 CTTTATCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 22 0.96
24 1 0.04
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.79
Consensus pattern (23 bp):
TTTATTTTTTCATTTTTTTAATT
Found at i:692502 original size:30 final size:29
Alignment explanation
Indices: 692428--692505 Score: 81
Period size: 30 Copynumber: 2.6 Consensus size: 29
692418 TTTTTTAATT
692428 TTTATTTTTTCATTTTTTTCATTTTCTTTA
1 TTTA-TTTTTCATTTTTTTCATTTTCTTTA
*
692458 TCTT-TACTTT-ATTTTTATTC-TATTTCTTTA
1 T-TTAT-TTTTCATTTTT-TTCAT-TTTCTTTA
692488 TTTATTTTTCATTTTTTT
1 TTTATTTTTCATTTTTTT
692506 TATTACCTAC
Statistics
Matches: 40, Mismatches: 2, Indels: 13
0.73 0.04 0.24
Matches are distributed among these distances:
29 15 0.38
30 23 0.57
31 2 0.05
ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (29 bp):
TTTATTTTTCATTTTTTTCATTTTCTTTA
Found at i:692567 original size:2 final size:2
Alignment explanation
Indices: 692560--692592 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
692550 ATATTACTAT
692560 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
692593 TATTTACTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:699690 original size:31 final size:30
Alignment explanation
Indices: 699651--699714 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 30
699641 GTAAGTGTGG
699651 TTGCTGTTGATGCGCATGGAGGGGCTGCTT
1 TTGCTGTTGATGCGCATGGAGGGGCTGCTT
*
699681 TTGCTTGTTGATGCGCATGGAGGGGTTGCTT
1 TTGC-TGTTGATGCGCATGGAGGGGCTGCTT
699712 TTG
1 TTG
699715 TGGGTGAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 4 0.12
31 28 0.88
ACGTcount: A:0.09, C:0.14, G:0.39, T:0.38
Consensus pattern (30 bp):
TTGCTGTTGATGCGCATGGAGGGGCTGCTT
Found at i:700473 original size:47 final size:47
Alignment explanation
Indices: 700404--700545 Score: 232
Period size: 47 Copynumber: 3.0 Consensus size: 47
700394 TTGAACCTTA
*
700404 TTTGAAAACATCCTGCACTGAAGGTCTTATGGATGACGCGAAGGCTT
1 TTTGAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGAAGGCTT
* *
700451 TTTGAAAACATCATGCACTGAAGGTCTTATGGATGACTCGAAGGCTT
1 TTTGAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGAAGGCTT
* *
700498 TTTGAAAAAATCCTGCACTCAAGGTCTTATGGATGACCCGAAGG-TT
1 TTTGAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGAAGGCTT
700544 TT
1 TT
700546 ACAAATTACC
Statistics
Matches: 89, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
46 4 0.04
47 85 0.96
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (47 bp):
TTTGAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGAAGGCTT
Found at i:701007 original size:249 final size:249
Alignment explanation
Indices: 700567--701816 Score: 2112
Period size: 249 Copynumber: 5.0 Consensus size: 249
700557 GGAGGTTTTA
** * * *
700567 ATTTTCTAGAACATTAAATGAGAAACTTTGGTAATCGTTTTCTCATTTT-ATGTGAAAATCATAT
1 ATTTTCTAGAACATTAAATGAGAAACTTTGAAAATCGCTATCTCATTTTCATGCGAAAATCATAT
* *
700631 GTGAACAT-CTACCCAAAGGCTTTACGAATGGCCCTAAGGACTTATCATCTTGCTCGAAAGACTG
66 GTGAACATCCTACCCAAAGGCTTTACGGATGGCCCTAAGGACTTATCATCTTGCTTGAAAGACTG
* * *
700695 ACAGATGACCC-AGAGGTTTTAAGCATCATGATCGAAAGACTAACAGATGACCTGAAAGATTTAC
131 ACAGATGACCCGA-AGGTTTTAAGCATCATGCTCGAAAGACTAACAGATGACCCGAAGGATTTAC
700759 AAATTTGTGGGAAATACTTTACTAGGTAAGAAACTTCTTACTTTTCAAGAATTTG
195 AAATTTGTGGGAAATACTTTACTAGGTAAGAAACTTCTTACTTTTCAAGAATTTG
*
700814 ATTTTCTAGAACATTAAATGAGAAACTTTGAAAATTGCTATCTCATTTTCATGCGAAAATCATAT
1 ATTTTCTAGAACATTAAATGAGAAACTTTGAAAATCGCTATCTCATTTTCATGCGAAAATCATAT
* *
700879 GTGAACATCCTACCCAAAGGCTTTACAGATGGCCCTAAGCACTTATCATCTTGCTTGAAAGACTG
66 GTGAACATCCTACCCAAAGGCTTTACGGATGGCCCTAAGGACTTATCATCTTGCTTGAAAGACTG
* *
700944 ACAGATGACCCGAAGGTTTTAAGCATCATGCTCAAAAGACTAACAGATAACCCGAAGGATTTACA
131 ACAGATGACCCGAAGGTTTTAAGCATCATGCTCGAAAGACTAACAGATGACCCGAAGGATTTACA
*
701009 AATTTATGGGAAATACTTTACTAGGTAAGAAACTTCTTACTTTTCAAGAATTTG
196 AATTTGTGGGAAATACTTTACTAGGTAAGAAACTTCTTACTTTTCAAGAATTTG
* * *
701063 ATTTTCTAGAATATTAAATAAGAAACTTTGAAAATCGCTATCTCATTTTCATGCAAAAATCATAT
1 ATTTTCTAGAACATTAAATGAGAAACTTTGAAAATCGCTATCTCATTTTCATGCGAAAATCATAT
* * * *
701128 GTGAACATCCTACCCAAAGGCTTTACGGATTGCCCTAAAGACTTGTCATCTTGCTTAAAAGACTG
66 GTGAACATCCTACCCAAAGGCTTTACGGATGGCCCTAAGGACTTATCATCTTGCTTGAAAGACTG
* * *
701193 AAAGATGACCTGAAGGTTTTAAGCATCATGCTCGAAAGACTAACAGATGACCCGAAAGATTTACA
131 ACAGATGACCCGAAGGTTTTAAGCATCATGCTCGAAAGACTAACAGATGACCCGAAGGATTTACA
*
701258 AATTTGTGGGAAATACTTTACTAGGTAAGAAACTTCTTACTTTTTAAGAATTTG
196 AATTTGTGGGAAATACTTTACTAGGTAAGAAACTTCTTACTTTTCAAGAATTTG
701312 ATTTTCTAGAACATTAAATGAGAAACTTTGAAAATCGCTATCTCATTTTCATGCGAAAATCATAT
1 ATTTTCTAGAACATTAAATGAGAAACTTTGAAAATCGCTATCTCATTTTCATGCGAAAATCATAT
701377 GTGAACATCCTACCCAAAGGCTTTACGGATGGCCCTAAGGACTTATCATCTTGCTTGAAAGACTG
66 GTGAACATCCTACCCAAAGGCTTTACGGATGGCCCTAAGGACTTATCATCTTGCTTGAAAGACTG
*
701442 ACAGATGACCCGAAGGTTTTAAGCATCATGCTCAAAAGACTAACAGATGACCCGAAGGATTTACA
131 ACAGATGACCCGAAGGTTTTAAGCATCATGCTCGAAAGACTAACAGATGACCCGAAGGATTTACA
* *
701507 AATTTATGGGAAATACTTTACTAGGTAAGAAACTTCTTACTTTTCAAGAATTCG
196 AATTTGTGGGAAATACTTTACTAGGTAAGAAACTTCTTACTTTTCAAGAATTTG
*
701561 ATTTTCTAGAACATTAAATGAGAAACTTTGAAAATCGCTATCTCATTTTCATGCGAAAATGATAT
1 ATTTTCTAGAACATTAAATGAGAAACTTTGAAAATCGCTATCTCATTTTCATGCGAAAATCATAT
**
701626 GTGAACATCCTACCCAAAGGCTTTACGGATGGCCCTAAGGACTTATCATCTTGCTCAAAAGACTG
66 GTGAACATCCTACCCAAAGGCTTTACGGATGGCCCTAAGGACTTATCATCTTGCTTGAAAGACTG
* * * * *
701691 ACAGATAACCCGAAGGTTTAAAGCATCATGCTCGAAAGACTAAAAGATGTCCCGAAGGATTTATA
131 ACAGATGACCCGAAGGTTTTAAGCATCATGCTCGAAAGACTAACAGATGACCCGAAGGATTTACA
*
701756 AATTTGTGGGAAATACTTTACT-GGTAAGAAACTTCTTACTTTTCAAGAATTTC
196 AATTTGTGGGAAATACTTTACTAGGTAAGAAACTTCTTACTTTTCAAGAATTTG
701809 ATTTTCTA
1 ATTTTCTA
701817 AAAAAGACTA
Statistics
Matches: 941, Mismatches: 59, Indels: 5
0.94 0.06 0.00
Matches are distributed among these distances:
247 44 0.05
248 59 0.06
249 837 0.89
250 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (249 bp):
ATTTTCTAGAACATTAAATGAGAAACTTTGAAAATCGCTATCTCATTTTCATGCGAAAATCATAT
GTGAACATCCTACCCAAAGGCTTTACGGATGGCCCTAAGGACTTATCATCTTGCTTGAAAGACTG
ACAGATGACCCGAAGGTTTTAAGCATCATGCTCGAAAGACTAACAGATGACCCGAAGGATTTACA
AATTTGTGGGAAATACTTTACTAGGTAAGAAACTTCTTACTTTTCAAGAATTTG
Found at i:701745 original size:42 final size:43
Alignment explanation
Indices: 701672--701753 Score: 103
Period size: 42 Copynumber: 1.9 Consensus size: 43
701662 AAGGACTTAT
* * *
701672 CATCTTGCTCAAAAGACTGACAGATAACCCGAAGG-TTTAAAG
1 CATCATGCTCAAAAGACTAAAAGATAACCCGAAGGATTTAAAG
* **
701714 CATCATGCTCGAAAGACTAAAAGATGTCCCGAAGGATTTA
1 CATCATGCTCAAAAGACTAAAAGATAACCCGAAGGATTTA
701754 TAAATTTGTG
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
42 29 0.88
43 4 0.12
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.22
Consensus pattern (43 bp):
CATCATGCTCAAAAGACTAAAAGATAACCCGAAGGATTTAAAG
Found at i:704995 original size:7 final size:7
Alignment explanation
Indices: 704983--705048 Score: 61
Period size: 7 Copynumber: 9.9 Consensus size: 7
704973 ATTTCTTTTT
704983 TTCTTTA
1 TTCTTTA
704990 TTCTTT-
1 TTCTTTA
*
704996 TTAC-TTC
1 TT-CTTTA
705003 TTCTTTA
1 TTCTTTA
705010 TTCTTTA
1 TTCTTTA
705017 TTCTTT-
1 TTCTTTA
*
705023 TTAC-TTC
1 TT-CTTTA
705030 TTCTTTA
1 TTCTTTA
705037 TTCTTT-
1 TTCTTTA
705043 TTCTTT
1 TTCTTT
705049 CTTTGAGTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
6 16 0.31
7 35 0.69
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (7 bp):
TTCTTTA
Found at i:705015 original size:27 final size:27
Alignment explanation
Indices: 704975--705048 Score: 127
Period size: 27 Copynumber: 2.9 Consensus size: 27
704965 CTAAATCAAT
704975 TTCTT-TTT-TTCTTTATTCTTTTTAC
1 TTCTTCTTTATTCTTTATTCTTTTTAC
705000 TTCTTCTTTATTCTTTATTCTTTTTAC
1 TTCTTCTTTATTCTTTATTCTTTTTAC
705027 TTCTTCTTTATTCTTT-TTCTTT
1 TTCTTCTTTATTCTTTATTCTTT
705049 CTTTGAGTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
25 5 0.11
26 9 0.19
27 33 0.70
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (27 bp):
TTCTTCTTTATTCTTTATTCTTTTTAC
Found at i:705051 original size:20 final size:20
Alignment explanation
Indices: 704980--705048 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
704970 TCAATTTCTT
704980 TTTTTCTTTATTCTTT-TTAC
1 TTTTTCTTTATTCTTTATT-C
*
705000 TTCTTCTTTATTCTTTATTC
1 TTTTTCTTTATTCTTTATTC
*
705020 TTTTTAC-TTCTTCTTTATTC
1 TTTTT-CTTTATTCTTTATTC
705040 TTTTTCTTT
1 TTTTTCTTT
705049 CTTTGAGTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
19 1 0.02
20 39 0.91
21 3 0.07
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTTCTTTATTCTTTATTC
Found at i:708856 original size:15 final size:15
Alignment explanation
Indices: 708836--708865 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
708826 TATAGTTTAT
708836 TTTTTTCTTTCTCTG
1 TTTTTTCTTTCTCTG
*
708851 TTTTTTTTTTCTCTG
1 TTTTTTCTTTCTCTG
708866 GTTTCTGTCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.17, G:0.07, T:0.77
Consensus pattern (15 bp):
TTTTTTCTTTCTCTG
Found at i:709342 original size:3 final size:3
Alignment explanation
Indices: 709334--709448 Score: 173
Period size: 3 Copynumber: 39.3 Consensus size: 3
709324 TTAATATATT
709334 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA -AA -AA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
709379 TAT TAA TAA TGA TAA TAA TAA TAT TAA TAA TAA TAA TAA TAA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
709427 TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA T
709449 TTGGATAAAA
Statistics
Matches: 102, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
2 6 0.06
3 96 0.94
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:709772 original size:61 final size:61
Alignment explanation
Indices: 709698--709855 Score: 289
Period size: 61 Copynumber: 2.6 Consensus size: 61
709688 CTTGATGAGT
* * *
709698 TCTTCTCATTATGAACTTTTTCTGCCTTCTTCAGATAATATCAAACAAAGGTTGAATAAGC
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAATATCAAACAAAGGTTGAACAAGC
709759 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAATATCAAACAAAGGTTGAACAAGC
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAATATCAAACAAAGGTTGAACAAGC
709820 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT
709856 GAGTTCTTTT
Statistics
Matches: 94, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 94 1.00
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (61 bp):
TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAATATCAAACAAAGGTTGAACAAGC
Found at i:710056 original size:113 final size:113
Alignment explanation
Indices: 709805--710364 Score: 960
Period size: 113 Copynumber: 4.9 Consensus size: 113
709795 AATATCAAAC
** *
709805 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTTTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * * * ***
709870 CATGAACTTTCTCTGGCAATA-TTGATCCATCAAATGATGAATTTAAACA
66 -ATGAACTTTCTCTGG-AAAAGATGATCCACCAAATGATGGATTCAGGTA
* *
709919 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
709984 ATGAACTTTCTCTGGAAAAGATGATCGACCAAATGATGGATTCAGGTA
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGTA
*
710032 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
710097 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGTA
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGTA
710145 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
710210 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGTA
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGTA
710258 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
710323 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATT
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATT
710365 TGAATCTTTG
Statistics
Matches: 428, Mismatches: 17, Indels: 3
0.96 0.04 0.01
Matches are distributed among these distances:
112 3 0.01
113 363 0.85
114 62 0.14
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.37
Consensus pattern (113 bp):
AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGTA
Found at i:711148 original size:84 final size:83
Alignment explanation
Indices: 710942--711158 Score: 362
Period size: 85 Copynumber: 2.6 Consensus size: 83
710932 GTTCTGTAAA
* * *
710942 TTCTGCCAAACCAGATCAGAGAACTCAATGAACACTTCCAGAAGATGCTATTGGCACATTCATCT
1 TTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCACATTCATCT
711007 TCTAAATTCAATGATTGG
66 TCTAAATTCAATGATTGG
* *
711025 TTCTACCAAACCAGATCAGATACCTCAAAGAAACACTTCCAGAAGATGCTATTAAGCACATTCAT
1 TTCTGCCAAACCAGATCAGATAACTCAAAG-AACACTTCCAGAAGATGCTATT-AGCACATTCAT
*
711090 CTTCTAAATTCAATGTTTGG
64 CTTCTAAATTCAATGATTGG
711110 TTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
1 TTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
711159 TGGTTCTGTC
Statistics
Matches: 124, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
83 26 0.21
84 41 0.33
85 57 0.46
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (83 bp):
TTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCACATTCATCT
TCTAAATTCAATGATTGG
Found at i:711174 original size:52 final size:52
Alignment explanation
Indices: 711109--712314 Score: 2215
Period size: 52 Copynumber: 23.2 Consensus size: 52
711099 TCAATGTTTG
711109 GTTCTG-CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT-T
1 GTTCTGTCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
*
711160 GGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 -GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
* *
711213 GTTCTGTCCAACCAGATTAGATAACTCAAAGAACACTTCCAGAAGATGTTAT
1 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
*
711265 GTTCTGTCCAACCAAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
711317 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
711369 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
711421 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
* *
711473 GTTTTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTAT
1 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
*
711525 GTTCTGTCCAACCAAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
711577 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
711629 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
711681 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
*
711733 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTAT
1 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
*
711785 GTTCTGTCCAACCAAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
711837 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
711889 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
711941 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
711993 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT-T
1 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
*
712044 GCTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 G-TTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
712097 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
712149 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT-T
1 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
*
712200 GGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT-T
1 -GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
* *
712252 GGTTCTGTCTAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 -GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
712305 GTTCTGTCCA
1 GTTCTGTCCA
712315 TTATTTTGTT
Statistics
Matches: 1125, Mismatches: 23, Indels: 12
0.97 0.02 0.01
Matches are distributed among these distances:
51 3 0.00
52 1117 0.99
53 5 0.00
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.24
Consensus pattern (52 bp):
GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
Found at i:713126 original size:16 final size:16
Alignment explanation
Indices: 713105--713141 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
713095 GAATTTCCAA
713105 AAATAAATTGAATCTT-
1 AAATAAATTGAA-CTTG
713121 AAATAAATTGAACTTG
1 AAATAAATTGAACTTG
713137 AAATA
1 AAATA
713142 GATATAATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 3 0.15
16 17 0.85
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.32
Consensus pattern (16 bp):
AAATAAATTGAACTTG
Found at i:726026 original size:3 final size:3
Alignment explanation
Indices: 726018--726138 Score: 190
Period size: 3 Copynumber: 40.7 Consensus size: 3
726008 TTAATATATT
*
726018 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA AAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
726065 TAA TAT TAA TAA TGA TAA TAA TAA TAT TAA TAA TAA TAA TAA TAA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
726113 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
726139 TGGATAAAAA
Statistics
Matches: 107, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
2 2 0.02
3 105 0.98
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:729281 original size:22 final size:23
Alignment explanation
Indices: 729242--729299 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 23
729232 TTAAAATTGC
729242 ATAAAATAAAATAATT-AATATTAA
1 ATAAAATAAAA-AATTAAATA-TAA
*
729266 A-AAAATAAAAACTTAAATATAA
1 ATAAAATAAAAAATTAAATATAA
*
729288 ATAAAACAAAAA
1 ATAAAATAAAAA
729300 GGGCATAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
22 7 0.23
23 22 0.73
24 1 0.03
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.24
Consensus pattern (23 bp):
ATAAAATAAAAAATTAAATATAA
Found at i:735104 original size:3 final size:3
Alignment explanation
Indices: 735096--735212 Score: 86
Period size: 3 Copynumber: 39.7 Consensus size: 3
735086 TAATCACTAT
* **
735096 TTA TTA TTA TTA TTA TTA -TA TTTA ATA TT- TT- TTA ACA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
*
735139 TTA TTTA TTA TTA -TA TTA TTA GTA CTT- TT- TCTA TTA TTA TTA TTTA
1 TTA -TTA TTA TTA TTA TTA TTA TTA -TTA TTA T-TA TTA TTA TTA -TTA
* *
735185 TTA TTA TTA CTA ATA -TA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
735213 TCAAAATATA
Statistics
Matches: 94, Mismatches: 10, Indels: 20
0.76 0.08 0.16
Matches are distributed among these distances:
2 13 0.14
3 71 0.76
4 10 0.11
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:737900 original size:138 final size:136
Alignment explanation
Indices: 737725--738396 Score: 697
Period size: 138 Copynumber: 4.8 Consensus size: 136
737715 GACTTGAATC
* ** * * *
737725 ATAATTGATTAAAATAAATTAGGATTAATA-TTAGAGCCTTC-ACTTTAAGCCTAATTTCAAACT
1 ATAATTGGTTAAAATTGACTAGG-TTAATATTTAGAGCC-TCAATTTTAAGCTTAATTTCAAA-T
* * *
737788 TAGTCATTAAATCAGGGTAATTTTTAATTTGGTCCTCGCTTTTGCTCGAGGTTCCATTTTAATTA
63 TAGTCCTTAAATTAGGG-AATTTTTAATTTGGTCATCGCTTTTGCTCGAGGTTCCATTTTAATTA
**
737853 TTTGAATCAA
127 TTCAAATCAA
* * * * *
737863 ATAACTGGATAAAATTGACTAGGTTAATATTTAGAGCCTCAATTTTTAGATAAATTTCAAATTAG
1 ATAATTGGTTAAAATTGACTAGGTTAATATTTAGAGCCTCAATTTTAAGCTTAATTTCAAATTA-
* *
737928 GTCCTTAAATTAGGAGAATTTTTAATTTGGTCATCGTTTTTGCTCGAGGTTTCATTTTAATTATT
65 GTCCTTAAATTAGG-GAATTTTTAATTTGGTCATCGCTTTTGCTCGAGGTTCCATTTTAATTATT
737993 CAAATCAA
129 CAAATCAA
* * * * * **
738001 TTAATTGGTTAAAATTGACTAGGTTATTAATTAGAGCCTCTATTTTAGGCTTAGCTTCAAATTAG
1 ATAATTGGTTAAAATTGACTAGGTTAATATTTAGAGCCTCAATTTTAAGCTTAATTTCAAATTAG
*
738066 TTCCTTAAATTAGAGGATTTTTTAATTTGGTCATCGCTTTTGCTCGAGGTTCCATTTTAATTATT
66 -TCCTTAAATTAG-GGAATTTTTAATTTGGTCATCGCTTTTGCTCGAGGTTCCATTTTAATTATT
738131 CAAATCAA
129 CAAATCAA
* * * * * *
738139 ATAATTAGTTAAAATTGACTAGATTAATTTTTAGAGCCTCCATTTT-AGTCTTAATTTCTCACTT
1 ATAATTGGTTAAAATTGACTAGGTTAATATTTAGAGCCTCAATTTTAAG-CTTAATTTC-AAATT
* *
738203 AG-CCTTTAAATTTAGGGGAATTTTTAATTTGGTCATCGCTTTTGCTCGATGATCCATTTTAATT
64 AGTCC-TTAAA-TTA-GGGAATTTTTAATTTGGTCATCGCTTTTGCTCGAGGTTCCATTTTAATT
*
738267 ATTCGAATCAA
126 ATTCAAATCAA
* * * * * * *
738278 TTAATTGGTTAAAATT-AATAAGGATAATTTTTAAGAGCCTCCATATTTAGGTTTAATTTCATAA
1 ATAATTGGTTAAAATTGACT-AGGTTAATATTT-AGAGCCTCAAT-TTTAAGCTTAATTTCA-AA
** * * * * *
738342 CCAGTCCTTAAATATAGGACAACTTTTGATTTGGTCATCGGTTATGCTCGAGGTT
62 TTAGTCCTTAAAT-TAGG-GAATTTTTAATTTGGTCATCGCTTTTGCTCGAGGTT
738397 TCACTTTGAC
Statistics
Matches: 448, Mismatches: 67, Indels: 35
0.81 0.12 0.06
Matches are distributed among these distances:
137 15 0.03
138 276 0.62
139 89 0.20
140 15 0.03
141 50 0.11
142 3 0.01
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.42
Consensus pattern (136 bp):
ATAATTGGTTAAAATTGACTAGGTTAATATTTAGAGCCTCAATTTTAAGCTTAATTTCAAATTAG
TCCTTAAATTAGGGAATTTTTAATTTGGTCATCGCTTTTGCTCGAGGTTCCATTTTAATTATTCA
AATCAA
Found at i:738492 original size:277 final size:276
Alignment explanation
Indices: 737809--738462 Score: 616
Period size: 276 Copynumber: 2.4 Consensus size: 276
737799 TCAGGGTAAT
* * * * ** * * *
737809 TTTTAATTTGGTCCTCGCTTTTGCTCGAGGTTCCATTTTAATTATTTGAATCAAATAACTGGATA
1 TTTTAATTTGGTCATCGCTTATGCTCGAGGTTCCACTTTAACTATTCAAATCAAATAATTAGCTA
* * * * **
737874 AAATTGACTAGGTTAA-TATTTAGAGCCT-CAATTTTTAG-ATAAATT-TCAAATTAGGTCC-TT
66 AAATTAACTAGATTAATTA-TTAGAGCCTAC-A-TTTTAGTCTTAATTCTC-ACCTA-G-CCTTT
* * *
737934 AAA-TTAGGAGAATTTTTAATTTGGTCATCGTTTTTGCTCGAGGTTTCATTTTAATTATTCAAAT
125 AAATTTAGGAGAATTTTTAATTTGGTCATCGCTTTTGCTCGAGGATCCATTTTAATTATTCAAAT
* * * * *
737998 CAATTAATTGGTTAAAATTGACTAGGTTATTAATTAGAGCCTCTATTTTAGGCTTAGCTTCAAAT
190 CAATTAATTGGTTAAAATTGAATAGGTAATTAATTAGAGCCTCCATTTTAGGCTTAACTTCAAAC
* * **
738063 TAGTTCCTTAAATTAGAGGATT
255 CAGTTCCTTAAATTAGAGCAAC
* * * *
738085 TTTTAATTTGGTCATCGCTTTTGCTCGAGGTTCCATTTTAATTATTCAAATCAAATAATTAGTTA
1 TTTTAATTTGGTCATCGCTTATGCTCGAGGTTCCACTTTAACTATTCAAATCAAATAATTAGCTA
* * * *
738150 AAATTGACTAGATTAATTTTTAGAGCCTCCATTTTAGTCTTAATTTCTCACTTAGCCTTTAAATT
66 AAATTAACTAGATTAATTATTAGAGCCTACATTTTAGTCTTAA-TTCTCACCTAGCCTTTAAATT
* * *
738215 TAGGGGAATTTTTAATTTGGTCATCGCTTTTGCTCGATGATCCATTTTAATTATTCGAATCAATT
130 TAGGAGAATTTTTAATTTGGTCATCGCTTTTGCTCGAGGATCCATTTTAATTATTCAAATCAATT
* * *
738280 AATTGGTTAAAATT-AATAAGGATAATT-TTTAAGAGCCTCCATATTTAGGTTTAATTTCATAAC
195 AATTGGTTAAAATTGAAT-AGG-TAATTAATT-AGAGCCTCCAT-TTTAGGCTTAACTTCA-AAC
738343 CAG-TCCTTAAATATAG-GACAAC
255 CAGTTCCTTAAAT-TAGAG-CAAC
* * * * * *
738365 TTTTGATTTGGTCATCGGTTATGCTCGAGGTTTCACTTTGACTATTCGATTC-AATAATTTA-CT
1 TTTTAATTTGGTCATCGCTTATGCTCGAGGTTCCACTTTAACTATTCAAATCAAATAA-TTAGCT
* * *
738428 AAAATTAATTAGGA-TAA-TATTAGAGCTTATATTTT
65 AAAATTAACTA-GATTAATTATTAGAGCCTACATTTT
738463 CAGGTTTAAT
Statistics
Matches: 317, Mismatches: 45, Indels: 30
0.81 0.11 0.08
Matches are distributed among these distances:
275 8 0.03
276 95 0.30
277 87 0.27
278 30 0.09
279 41 0.13
280 56 0.18
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.43
Consensus pattern (276 bp):
TTTTAATTTGGTCATCGCTTATGCTCGAGGTTCCACTTTAACTATTCAAATCAAATAATTAGCTA
AAATTAACTAGATTAATTATTAGAGCCTACATTTTAGTCTTAATTCTCACCTAGCCTTTAAATTT
AGGAGAATTTTTAATTTGGTCATCGCTTTTGCTCGAGGATCCATTTTAATTATTCAAATCAATTA
ATTGGTTAAAATTGAATAGGTAATTAATTAGAGCCTCCATTTTAGGCTTAACTTCAAACCAGTTC
CTTAAATTAGAGCAAC
Found at i:746929 original size:23 final size:23
Alignment explanation
Indices: 746896--746963 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
746886 CATCTTATGT
* *
746896 GGCACTACGGTGTATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* *
746919 GGCACTTCGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
*
746942 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
746964 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.18, C:0.25, G:0.26, T:0.31
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:753805 original size:23 final size:23
Alignment explanation
Indices: 753775--753844 Score: 113
Period size: 23 Copynumber: 3.0 Consensus size: 23
753765 GACATCTTAT
*
753775 GTGGCACTACGGTGCATTTCTAC
1 GTGGCACTTCGGTGCATTTCTAC
*
753798 GTGGCACTTCGGTGCAATTCTAC
1 GTGGCACTTCGGTGCATTTCTAC
*
753821 GTGGCACTTCGGTGCATTTATAC
1 GTGGCACTTCGGTGCATTTCTAC
753844 G
1 G
753845 AGCTATGGTG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.17, C:0.24, G:0.27, T:0.31
Consensus pattern (23 bp):
GTGGCACTTCGGTGCATTTCTAC
Found at i:754999 original size:9 final size:9
Alignment explanation
Indices: 754974--755024 Score: 58
Period size: 9 Copynumber: 6.2 Consensus size: 9
754964 ATGGCAATCG
754974 TTCTTTACA
1 TTCTTTACA
754983 TT-TTTACA
1 TTCTTTACA
754991 TTCTTTACA
1 TTCTTTACA
*
755000 TTCGTT--A
1 TTCTTTACA
755007 TT-TTT-CA
1 TTCTTTACA
755014 TTCTTTACA
1 TTCTTTACA
755023 TT
1 TT
755025 TATTTCATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
6 2 0.06
7 6 0.17
8 11 0.31
9 17 0.47
ACGTcount: A:0.20, C:0.18, G:0.02, T:0.61
Consensus pattern (9 bp):
TTCTTTACA
Found at i:757896 original size:6 final size:6
Alignment explanation
Indices: 757885--757947 Score: 51
Period size: 6 Copynumber: 10.2 Consensus size: 6
757875 AGAAAAATAG
*
757885 AAGAAA AAGAAA TA-AAA AAG-AA AAGAAA AA-ATAA CAAGAAAA AAGAAAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGA-AA -AAG-AAA AAG-AAA
757934 AATGAAA AAGAAA A
1 AA-GAAA AAGAAA A
757948 TTAAAATGGG
Statistics
Matches: 48, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
5 10 0.21
6 18 0.38
7 16 0.33
8 3 0.06
9 1 0.02
ACGTcount: A:0.81, C:0.02, G:0.13, T:0.05
Consensus pattern (6 bp):
AAGAAA
Found at i:757906 original size:20 final size:18
Alignment explanation
Indices: 757877--757947 Score: 63
Period size: 20 Copynumber: 3.6 Consensus size: 18
757867 TTAAAGGAAG
757877 AAAAATAGAAGAAAAAGAAAT
1 AAAAA-AGAA-AAAAA-AAAT
757898 AAAAAAGAAAAGAAAAAAT
1 AAAAAAGAAAA-AAAAAAT
757917 AACAAGAA-AAAAGAAAAAAT
1 AA-AA-AAGAAAA-AAAAAAT
*
757937 GAAAAAGAAAA
1 AAAAAAGAAAA
757948 TTAAAATGGG
Statistics
Matches: 45, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
18 2 0.04
19 14 0.31
20 22 0.49
21 7 0.16
ACGTcount: A:0.80, C:0.01, G:0.13, T:0.06
Consensus pattern (18 bp):
AAAAAAGAAAAAAAAAAT
Found at i:757913 original size:11 final size:11
Alignment explanation
Indices: 757874--757947 Score: 51
Period size: 11 Copynumber: 6.2 Consensus size: 11
757864 CGCTTAAAGG
* *
757874 AAGAAAAATAG
1 AAGAAAAAGAA
757885 AAGAAAAAGAA
1 AAGAAAAAGAA
757896 ATA-AAAAAGAA
1 A-AGAAAAAGAA
*
757907 AAGAAAAAATAA
1 AAG-AAAAAGAA
757919 CAAGAAAAAAGAAAA
1 -AAG-AAAAAG--AA
757934 AATGAAAAAGAA
1 AA-GAAAAAGAA
757946 AA
1 AA
757948 TTAAAATGGG
Statistics
Matches: 52, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
10 1 0.02
11 19 0.37
12 12 0.23
13 9 0.17
14 8 0.15
15 3 0.06
ACGTcount: A:0.80, C:0.01, G:0.14, T:0.05
Consensus pattern (11 bp):
AAGAAAAAGAA
Found at i:757923 original size:13 final size:12
Alignment explanation
Indices: 757888--757947 Score: 59
Period size: 12 Copynumber: 4.8 Consensus size: 12
757878 AAAATAGAAG
*
757888 AAAAAG-AAATA
1 AAAAAGAAAAGA
757899 AAAAAGAAAAGA
1 AAAAAGAAAAGA
*
757911 AAAAATAACAAGA
1 AAAAAGAA-AAGA
*
757924 AAAAAGAAAAAA
1 AAAAAGAAAAGA
757936 TGAAAAAGAAAA
1 --AAAAAGAAAA
757948 TTAAAATGGG
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
11 6 0.15
12 14 0.34
13 11 0.27
14 10 0.24
ACGTcount: A:0.82, C:0.02, G:0.12, T:0.05
Consensus pattern (12 bp):
AAAAAGAAAAGA
Found at i:757940 original size:8 final size:7
Alignment explanation
Indices: 757874--757947 Score: 53
Period size: 7 Copynumber: 10.0 Consensus size: 7
757864 CGCTTAAAGG
757874 AAGAAAA
1 AAGAAAA
757881 ATAGAAGAAA
1 A-AG-A-AAA
757891 AAGAAATA
1 AAGAAA-A
*
757899 AAAAAGAA
1 AAGAA-AA
757907 AAGAAAA
1 AAGAAAA
* *
757914 AA-TAAC
1 AAGAAAA
757920 AAGAAAA
1 AAGAAAA
757927 AAGAAAA
1 AAGAAAA
757934 AATG-AAA
1 AA-GAAAA
757941 AAGAAAA
1 AAGAAAA
757948 TTAAAATGGG
Statistics
Matches: 53, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
6 5 0.09
7 26 0.49
8 14 0.26
9 4 0.08
10 4 0.08
ACGTcount: A:0.80, C:0.01, G:0.14, T:0.05
Consensus pattern (7 bp):
AAGAAAA
Found at i:759417 original size:54 final size:54
Alignment explanation
Indices: 759335--760000 Score: 951
Period size: 54 Copynumber: 12.3 Consensus size: 54
759325 ATTACCAAAT
*
759335 AGGCACTAAGTGTGCATTCCACGTAATTCATCATGAGTTGATGAATAACTGTAC
1 AGGCACTAAGTGTGCATTCCACGGAATTCATCATGAGTTGATGAATAACTGTAC
* *
759389 AGGCACTAAGTGTGCATTTCACGGAATTCATCATGAGTTGATGAATAACCGTAC
1 AGGCACTAAGTGTGCATTCCACGGAATTCATCATGAGTTGATGAATAACTGTAC
* * * *
759443 ATGCACTAAGTGTGCATTCCACGGAATTCACCATGAGTTGGTGAATAACCGTAC
1 AGGCACTAAGTGTGCATTCCACGGAATTCATCATGAGTTGATGAATAACTGTAC
* * *
759497 ATGTACTAAGTGTGCATTCCACAGAATTCATCATGAGTTGATGAATAA-TCGTAC
1 AGGCACTAAGTGTGCATTCCACGGAATTCATCATGAGTTGATGAATAACT-GTAC
* *
759551 ATGCACTAAGTGTGCATTTCACGGAATTCATCATGAGTTGATGAATAACTGTAC
1 AGGCACTAAGTGTGCATTCCACGGAATTCATCATGAGTTGATGAATAACTGTAC
*
759605 AGGCACTAAGTGTGCATTTCACGGAATTCATCATGAGTTGATGAATAACTGTAC
1 AGGCACTAAGTGTGCATTCCACGGAATTCATCATGAGTTGATGAATAACTGTAC
* * * *
759659 ATGTACTAAGTGTGCTTTCCACGGAATTCATCATGAGTTGATGAATAACCGTAC
1 AGGCACTAAGTGTGCATTCCACGGAATTCATCATGAGTTGATGAATAACTGTAC
* * * *
759713 AGACACTAAGTGTGCATTCCATGGAAATCATCATGAGTCGATGAATAAGC-GTAC
1 AGGCACTAAGTGTGCATTCCACGGAATTCATCATGAGTTGATGAATAA-CTGTAC
* * *
759767 ATGCACTAAGTGTGCATTCCACTGAATTCATCATGAGTTGATGAATAACCGTAC
1 AGGCACTAAGTGTGCATTCCACGGAATTCATCATGAGTTGATGAATAACTGTAC
759821 AGGCACTAAGTGTGCATTCCACGGAATTCATCATGAGTTGATGAATAACTGTAC
1 AGGCACTAAGTGTGCATTCCACGGAATTCATCATGAGTTGATGAATAACTGTAC
* * * * *
759875 ATGTACCAAGTGTGCATTTCACGGAATTCATCATGAGTTGATGAATAACCGTAC
1 AGGCACTAAGTGTGCATTCCACGGAATTCATCATGAGTTGATGAATAACTGTAC
* * * * * *
759929 AAGCACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAACT-ATTGTAT
1 AGGCACTAAGTGTGC-ATTCCACGGAATTCATCATGAGTTGATGAA-TAACTGTAC
*
759984 AGGCACTACGTGTGCAT
1 AGGCACTAAGTGTGCAT
760001 CTTAATAAAT
Statistics
Matches: 551, Mismatches: 55, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
53 1 0.00
54 503 0.91
55 46 0.08
56 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (54 bp):
AGGCACTAAGTGTGCATTCCACGGAATTCATCATGAGTTGATGAATAACTGTAC
Found at i:760239 original size:81 final size:81
Alignment explanation
Indices: 760138--760387 Score: 385
Period size: 81 Copynumber: 3.1 Consensus size: 81
760128 TAGTCCAAAA
760138 TAAAAGAATAATGGCCTAATTGTGCAATTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACG
1 TAAAAGAATAATGGCCTAATTGTGCAATTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACG
*
760203 ATTAAAGACCGTCAAG
66 GTTAAAGACCGTCAAG
* * * * * *
760219 TAAAAGAATGATGGCATAATTGTGTAATTGGCATAAAGGTGTCAATTATGCCAATTAGATAAACG
1 TAAAAGAATAATGGCCTAATTGTGCAATTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACG
**
760284 GTTAAAGACCGTTGAG
66 GTTAAAGACCGTCAAG
* *
760300 TAAAAGAATAATGGCCTAATTGTGCAATTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAATG
1 TAAAAGAATAATGGCCTAATTGTGCAATTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACG
760365 GTTAAAGACCG-CTAAG
66 GTTAAAGACCGTC-AAG
760381 TAAAAGA
1 TAAAAGA
760388 TGAAAAGTCA
Statistics
Matches: 149, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
81 149 1.00
ACGTcount: A:0.39, C:0.12, G:0.23, T:0.26
Consensus pattern (81 bp):
TAAAAGAATAATGGCCTAATTGTGCAATTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACG
GTTAAAGACCGTCAAG
Found at i:761799 original size:104 final size:104
Alignment explanation
Indices: 761613--761801 Score: 254
Period size: 104 Copynumber: 1.8 Consensus size: 104
761603 TTGCAATAAT
** * * * *
761613 AAGAACTTGTTTGACCTTTTCCTCAAATTCACCACAGAATGAGGTAGATTATCATTTCTAATAGA
1 AAGAACTTGTTCAACATTTTCCTCAAATTCACCACAAAAAGAGGTAGATCATCATTTCTAATAGA
*
761678 ATAGTTCATAATAAAAACTCATAATAAACTCTTAATGAG
66 ATAGTTCAAAATAAAAACTCATAATAAACTCTTAATGAG
* * *
761717 AAGAACTTGTTCAACATTTTTCTTAAATTCATCACAAAAAGAGGTTA-ATCATCATTTCTAATAG
1 AAGAACTTGTTCAACATTTTCCTCAAATTCACCACAAAAAGAGG-TAGATCATCATTTCTAATAG
* *
761781 AATGGTTCAAAATGAAAACTC
65 AATAGTTCAAAATAAAAACTC
761802 GTTCGAAAAG
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
104 70 0.97
105 2 0.03
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (104 bp):
AAGAACTTGTTCAACATTTTCCTCAAATTCACCACAAAAAGAGGTAGATCATCATTTCTAATAGA
ATAGTTCAAAATAAAAACTCATAATAAACTCTTAATGAG
Found at i:762052 original size:3 final size:3
Alignment explanation
Indices: 762044--762094 Score: 59
Period size: 3 Copynumber: 16.7 Consensus size: 3
762034 TAATCACTAT
* *
762044 TTA TTA TTA TTA TTAA TAA TTA TTA TTA TTA CTT- TTG TTA TTA TTA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
762090 TTA TT
1 TTA TT
762095 TCAATATATA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
2 2 0.05
3 36 0.86
4 4 0.10
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:764525 original size:139 final size:137
Alignment explanation
Indices: 764234--765390 Score: 1128
Period size: 140 Copynumber: 8.4 Consensus size: 137
764224 TTTAATTTAG
* * * * * * * *
764234 ATTCGAATC--ATAATTGATTAAAATTAATTAAGATTAAT-ATTAAAGCCTTCACTTTAGGCCTA
1 ATTCGAATCAAATAATTGGTTAAAATTGACT-AGGTTAATAATTAGAGCCTCCATTTTAGGCTTA
* * *
764296 ATTTCAAACTTAGTCATTAAATCAGGGGAATTTTTAATTTGGTCATCGCTTTTGCTTGAGGTTCC
65 ATTTCAAA-TTAGTCCTTAAATTAGGGGAATTTTTAATTTGGTCATCGCTTTTGCTCGAGGTTCC
764361 ATTTTAATT
129 ATTTTAATT
* *
764370 ATTTGAATCAAATAATTGGATAAAATTGACTAGGTTAATAATTAGAGCCTCCATTTTAGGCTTAA
1 ATTCGAATCAAATAATTGGTTAAAATTGACTAGGTTAATAATTAGAGCCTCCATTTTAGGCTTAA
* * *
764435 TTTCAAATTAAGTCCTTAAATTAGGGGAATTTTTTAATTTGTTCATCGCTTTTGATCGAAGTTCC
66 TTTCAAATT-AGTCCTTAAATTAGGGGAA-TTTTTAATTTGGTCATCGCTTTTGCTCGAGGTTCC
764500 ATTTTAATT
129 ATTTTAATT
* ** *
764509 ATTCGAATCAAATAATTGGTTAAAATTGACTAGATTAATTTTTTAGAGCCTCCATTTTATGCTTA
1 ATTCGAATCAAATAATTGGTTAAAATTGACTAGGTTAA-TAATTAGAGCCTCCATTTTAGGCTTA
* * * * *
764574 ATTT-AACACTTAGTCCTTAAATTTATGGAAAATTTTAATTTGGTCATCGCTTTTGTTTGAGGTT
65 ATTTCAA-A-TTAGTCCTTAAA-TTAGGGGAATTTTTAATTTGGTCATCGCTTTTGCTCGAGGTT
*
764638 CCATTTTTATT
127 CCATTTTAATT
* * *
764649 ATTCGAATCAAATAATTGGTTAAAATTGATTAGGTTAATAATTAGAGCCTCTATTTGAGGCTTAA
1 ATTCGAATCAAATAATTGGTTAAAATTGACTAGGTTAATAATTAGAGCCTCCATTTTAGGCTTAA
* * * ** ** * *
764714 TTTCAAATTAAGTCCTTCAATTAGGGGAATTTTTAATTTAGTCCTCATTTTTATTCTAGGTTTCA
66 TTTCAAATT-AGTCCTTAAATTAGGGGAATTTTTAATTTGGTCATCGCTTTTGCTCGAGGTTCCA
764779 TTTTAATT
130 TTTTAATT
* * * ** * *
764787 ATTTGAATCAAATAGTTGGTAAAAATTGACTAGGTTAATTTTTTAGAGCCTCAATTTTAGGTTTA
1 ATTCGAATCAAATAATTGGTTAAAATTGACTAGGTTAA-TAATTAGAGCCTCCATTTTAGGCTTA
* * * * ** * *
764852 ATTTCACACTTAGTCCTTAAATTTAGGGTAATTTTTAATTTGATCCTCAATTTTGCTCGAGATTT
65 ATTTCA-AATTAGTCCTTAAA-TTAGGGGAATTTTTAATTTGGTCATCGCTTTTGCTCGAGGTTC
764917 CATTTTAATT
128 CATTTTAATT
* * * *
764927 ATTCGAATCAAATAATCGTTTAAAATTGACTAGGTTAATAATTAGAGCCTCTATTTTAGGTTTAA
1 ATTCGAATCAAATAATTGGTTAAAATTGACTAGGTTAATAATTAGAGCCTCCATTTTAGGCTTAA
* * * ** * *
764992 TTTTAAGATTAGGTCCTTAAATTAAGGGAATTTTTAA-TTGGTCCTCATTTTTTCTCGAGATTCC
66 TTTCAA-ATTA-GTCCTTAAATTAGGGGAATTTTTAATTTGGTCATCGCTTTTGCTCGAGGTTCC
765056 ATTTTAATT
129 ATTTTAATT
* ** *
765065 ATTCGAATCAAATAATTGGTTAAAATTGACTAGGTTATTTTTTTAGAGCTTCCATTTTAGGC-T-
1 ATTCGAATCAAATAATTGGTTAAAATTGACTAGGTTA-ATAATTAGAGCCTCCATTTTAGGCTTA
* * * *
765128 -TTTCAAATTAGATTCTTAAATTTAGGGGAATTTTGAATTTTGTCTTCGCTTTTGCTCGAGGTTC
65 ATTTCAAATTAG-TCCTTAAA-TTAGGGGAATTTTTAATTTGGTCATCGCTTTTGCTCGAGGTTC
765192 CATTTTAATT
128 CATTTTAATT
* * * * ** * * *
765202 ATTCGAATCAAATAATTTGTTAAAATTAATTAGGATAAATTTTTAAAGCCTCAATTTTTAGGTTT
1 ATTCGAATCAAATAATTGGTTAAAATTGACTAGG-TTAATAATTAGAGCCTCCA-TTTTAGGCTT
* ** * * * ** * * * *
765267 AATTTTATAACCAGTCCTTAAATCTTGGAGAAATTTCGATTTGTTCTTCGCTTATGCTCGAGGTA
64 AATTTCA-AATTAGTCCTTAAAT-TAGGGGAATTTTTAATTTGGTCATCGCTTTTGCTCGAGGTT
* * *
765332 CCACTTTGACT
127 CCATTTTAATT
* *** * * *
765343 ATTCGATTC-AATAATTTACTAAAATTAATTAGGATAAT-ATTAGAGCCT
1 ATTCGAATCAAATAATTGGTTAAAATTGACTAGGTTAATAATTAGAGCCT
765391 AAATTTTTAG
Statistics
Matches: 859, Mismatches: 135, Indels: 52
0.82 0.13 0.05
Matches are distributed among these distances:
134 1 0.00
135 11 0.01
136 27 0.03
137 82 0.10
138 224 0.26
139 215 0.25
140 227 0.26
141 68 0.08
142 4 0.00
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (137 bp):
ATTCGAATCAAATAATTGGTTAAAATTGACTAGGTTAATAATTAGAGCCTCCATTTTAGGCTTAA
TTTCAAATTAGTCCTTAAATTAGGGGAATTTTTAATTTGGTCATCGCTTTTGCTCGAGGTTCCAT
TTTAATT
Done.