Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 162 of 163
Found at i:46496056 original size:23 final size:23
Alignment explanation
Indices: 46495907--46496044 Score: 120
Period size: 23 Copynumber: 5.9 Consensus size: 23
46495897 CGAAGTACTT
46495907 AACAGTAAGCACAC-AAGTGCTGGGGA
1 AACAGTAAGCACACAAAGTGC----GA
*
46495933 AACAGTAAGCACACACAGTGC-A
1 AACAGTAAGCACACAAAGTGCGA
* * * * *
46495955 ATCAGTAGGCGCACATAGCGC-A
1 AACAGTAAGCACACAAAGTGCGA
* *
46495977 AATCAGTAGGCACACGAAGTGCGA
1 AA-CAGTAAGCACACAAAGTGCGA
*
46496001 AACAGTAGGCACACAAAGTGCGA
1 AACAGTAAGCACACAAAGTGCGA
*
46496024 AACAGTAAGCACACACAGTGC
1 AACAGTAAGCACACAAAGTGC
46496045 TGAACGGTAA
Statistics
Matches: 95, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
22 19 0.20
23 54 0.57
24 3 0.03
26 14 0.15
27 5 0.05
ACGTcount: A:0.40, C:0.24, G:0.25, T:0.11
Consensus pattern (23 bp):
AACAGTAAGCACACAAAGTGCGA
Found at i:46504653 original size:43 final size:43
Alignment explanation
Indices: 46504581--46504707 Score: 168
Period size: 43 Copynumber: 2.9 Consensus size: 43
46504571 AGGAAGGGAC
* *
46504581 CAAGAAGTGAGCATATTATAAAGTAGATTAAATTAAAATGAAA
1 CAAGTAGTGAGCATATTATAAAGTTGATTAAATTAAAATGAAA
*
46504624 CAAGTAGTGAGAATATT-TAAAGTTTGATTAAATTGAAAA-GAAA
1 CAAGTAGTGAGCATATTATAAAG-TTGATTAAATT-AAAATGAAA
* *
46504667 CAATTAAGTGAGCATATTATAAAGGTGATTAAATTAAAATG
1 CAAGT-AGTGAGCATATTATAAAGTTGATTAAATTAAAATG
46504708 GAGGAGGATA
Statistics
Matches: 73, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
42 5 0.07
43 37 0.51
44 26 0.36
45 5 0.07
ACGTcount: A:0.50, C:0.04, G:0.17, T:0.29
Consensus pattern (43 bp):
CAAGTAGTGAGCATATTATAAAGTTGATTAAATTAAAATGAAA
Found at i:46509165 original size:2 final size:2
Alignment explanation
Indices: 46509158--46509182 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
46509148 CCAATTGAAC
46509158 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 T
46509183 TAATTATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:46520971 original size:20 final size:20
Alignment explanation
Indices: 46520941--46520992 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
46520931 ATGTTTTAGT
46520941 ATTTGAAATTTTA-GAT-TAA
1 ATTT-AAATTTTAGGATATAA
46520960 GATTTAAGA-TTTAGGATATAA
1 -ATTTAA-ATTTTAGGATATAA
46520981 ATTTAAATTTTA
1 ATTTAAATTTTA
46520993 TTTTTTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
19 7 0.25
20 18 0.64
21 3 0.11
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (20 bp):
ATTTAAATTTTAGGATATAA
Found at i:46521151 original size:23 final size:24
Alignment explanation
Indices: 46521103--46521151 Score: 57
Period size: 23 Copynumber: 2.0 Consensus size: 24
46521093 ATAAATTTTC
*
46521103 AAAATTATATCGATAATAAATTATA
1 AAAATTATA-CGATAATAAATAATA
46521128 AAAATTATA-GATAA-AAATCAATA
1 AAAATTATACGATAATAAAT-AATA
46521151 A
1 A
46521152 TGTTCATCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
22 4 0.18
23 9 0.41
25 9 0.41
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.31
Consensus pattern (24 bp):
AAAATTATACGATAATAAATAATA
Found at i:46523551 original size:18 final size:18
Alignment explanation
Indices: 46523528--46523568 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
46523518 ATAGGTTTTC
*
46523528 AATTAAATAATTT-TAATT
1 AATTAAA-AATTTAAAATT
46523546 AATTAAAAATTTAAAATT
1 AATTAAAAATTTAAAATT
46523564 AATTA
1 AATTA
46523569 CACCTTGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AATTAAAAATTTAAAATT
Found at i:46525371 original size:30 final size:30
Alignment explanation
Indices: 46525337--46525393 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
46525327 TAAAATTAAA
*
46525337 ATTAAA-TTAAATTATTATTATTATTAAGTG
1 ATTAAAGTGAAATT-TTATTATTATTAAGTG
*
46525367 ATTAAAGTGAAATTTTATTTTTATTAA
1 ATTAAAGTGAAATTTTATTATTATTAA
46525394 TTTAAAATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 18 0.75
31 6 0.25
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (30 bp):
ATTAAAGTGAAATTTTATTATTATTAAGTG
Found at i:46530539 original size:29 final size:29
Alignment explanation
Indices: 46530507--46530563 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
46530497 TAGTGATAGA
46530507 TTTATATTATAAT-CTTAATTTATTTATAT
1 TTTATATTATAATACTT-ATTTATTTATAT
* * *
46530536 TTTATTTTTTAGTACTTATTTATTTATA
1 TTTATATTATAATACTTATTTATTTATA
46530564 CTTCATAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 21 0.88
30 3 0.12
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.65
Consensus pattern (29 bp):
TTTATATTATAATACTTATTTATTTATAT
Found at i:46530554 original size:14 final size:14
Alignment explanation
Indices: 46530524--46530566 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
46530514 TATAATCTTA
*
46530524 ATTTATTTATATTTT
1 ATTTATTTATA-CTT
46530539 ATTT-TTTAGTACTT
1 ATTTATTTA-TACTT
46530553 ATTTATTTATACTT
1 ATTTATTTATACTT
46530567 CATAATCTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 15 0.60
15 10 0.40
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (14 bp):
ATTTATTTATACTT
Found at i:46544000 original size:13 final size:13
Alignment explanation
Indices: 46543973--46544011 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 13
46543963 AATAATTCAG
*
46543973 AAATTCTTA-GAA
1 AAATACTTATGAA
46543985 AAATACTTATGAA
1 AAATACTTATGAA
46543998 AAATACTT-TGAA
1 AAATACTTATGAA
46544010 AA
1 AA
46544012 TTTGTCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 14 0.56
13 11 0.44
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (13 bp):
AAATACTTATGAA
Found at i:46564880 original size:28 final size:32
Alignment explanation
Indices: 46564838--46564905 Score: 83
Period size: 30 Copynumber: 2.2 Consensus size: 32
46564828 TAATAATATA
46564838 TTTTTATAATTTTTA-AAAGATT-AAAT-TAAT
1 TTTTTATAATTTTTAGAAAG-TTAAAATGTAAT
46564868 TTTTTAT-A-TTTTAGAAAGTTAAAATGTAAT
1 TTTTTATAATTTTTAGAAAGTTAAAATGTAAT
46564898 TTTATTAT
1 TTT-TTAT
46564906 TATTAATTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
28 7 0.21
29 9 0.26
30 14 0.41
31 4 0.12
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (32 bp):
TTTTTATAATTTTTAGAAAGTTAAAATGTAAT
Found at i:46564906 original size:29 final size:27
Alignment explanation
Indices: 46564839--46564911 Score: 67
Period size: 29 Copynumber: 2.5 Consensus size: 27
46564829 AATAATATAT
*
46564839 TTTTATAATTTTTAAAAGATTAAATTAA
1 TTTTATTA-TTTTAAAAGATTAAATTAA
*
46564867 TTTTTTATATTTTAGAAAG-TTAAAATGTAA
1 TTTTAT-TATTTTA-AAAGATT-AAAT-TAA
46564897 TTTTATTATTATTAA
1 TTTTATTATT-TTAA
46564912 TTTAAAATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
28 12 0.32
29 14 0.38
30 11 0.30
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.53
Consensus pattern (27 bp):
TTTTATTATTTTAAAAGATTAAATTAA
Found at i:46567460 original size:116 final size:118
Alignment explanation
Indices: 46567340--46567593 Score: 415
Period size: 118 Copynumber: 2.2 Consensus size: 118
46567330 TAATCAAAAT
46567340 GTAAATTTATTAATAATTTAA-AAACTTTTTAAATATAACTTACCTTAAAAATAATTTAAAAAAT
1 GTAAATTTATTAATAATTTAATAAA-TTTTTAAATATAACTTACCTTAAAAATAATTTAAAAAAT
*
46567404 -T-AGAAAAGATATTTAAATTATCCGATTTAGTAACCTTTAAGTGTAATATTAC
65 GTAAAAAAAGATATTTAAATTATCCGATTTAGTAACCTTTAAGTGTAATATTAC
* **
46567456 GTAAATTTATTAATAATTTAATAAATTTTTAAATATAATTTACCTTAAAAATAATTTAGGAAATG
1 GTAAATTTATTAATAATTTAATAAATTTTTAAATATAACTTACCTTAAAAATAATTTAAAAAATG
*
46567521 TAAAAAAAGATATTTAAATTATCCGATTTAGTAACCTTTAAGTGTAATTTTAC
66 TAAAAAAAGATATTTAAATTATCCGATTTAGTAACCTTTAAGTGTAATATTAC
* *
46567574 GTAAATTTGTTAATAGTTTA
1 GTAAATTTATTAATAATTTA
46567594 CCAATTTTTT
Statistics
Matches: 128, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
116 57 0.45
117 4 0.03
118 67 0.52
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.41
Consensus pattern (118 bp):
GTAAATTTATTAATAATTTAATAAATTTTTAAATATAACTTACCTTAAAAATAATTTAAAAAATG
TAAAAAAAGATATTTAAATTATCCGATTTAGTAACCTTTAAGTGTAATATTAC
Found at i:46574485 original size:4 final size:4
Alignment explanation
Indices: 46574478--46574507 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
46574468 ACACACACGG
46574478 ATAA AT-A ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
46574508 TATATACACA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAA
Found at i:46575393 original size:28 final size:29
Alignment explanation
Indices: 46575327--46575394 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
46575317 CAATTGGAAC
*
46575327 TAAATTTT-AAAATCTAAAGGGTAGAGAT
1 TAAATTTTGAAAATCAAAAGGGTAGAGAT
* *
46575355 TAAAATCTTGAAAAT-AAAAGTGTA-AGGAT
1 T-AAATTTTGAAAATCAAAAGGGTAGA-GAT
46575384 TAAATTTTGAA
1 TAAATTTTGAA
46575395 TTTGTGAAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
28 11 0.33
29 17 0.52
30 5 0.15
ACGTcount: A:0.49, C:0.03, G:0.16, T:0.32
Consensus pattern (29 bp):
TAAATTTTGAAAATCAAAAGGGTAGAGAT
Found at i:46576778 original size:51 final size:51
Alignment explanation
Indices: 46576693--46576879 Score: 261
Period size: 51 Copynumber: 3.6 Consensus size: 51
46576683 GTTATAAACG
46576693 AAAGAGTCCGATGACTAAGTGTCATCATGAGTAAATGAATCATTTACGGATT
1 AAAG-GTCCGATGACTAAGTGTCATCATGAGTAAATGAATCATTTACGGATT
* * * *
46576745 AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACAGATT
1 AAAGGTCCGATGACTAAGTGTCATCATGAGTAAATGAATCATTTACGGATT
* *
46576796 AAAGGTCCGATGACTAAGTGTCATCATGAGTAAATGAATTCA-TGACGAATT
1 AAAGGTCCGATGACTAAGTGTCATCATGAGTAAATGAA-TCATTTACGGATT
*
46576847 AAATGGTCCGATGAC-AATATGTCATCATGAGTA
1 AAA-GGTCCGATGACTAA-GTGTCATCATGAGTA
46576880 TTAAATGAAA
Statistics
Matches: 121, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
51 90 0.74
52 31 0.26
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCATGAGTAAATGAATCATTTACGGATT
Found at i:46581418 original size:15 final size:16
Alignment explanation
Indices: 46581388--46581426 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
46581378 ATAATAAAAT
46581388 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
*
46581405 ATAATTTA-TATTTTT
1 ATAATTTATTATTTTA
46581420 ATAATTT
1 ATAATTT
46581427 TTAAATGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Found at i:46584228 original size:4 final size:4
Alignment explanation
Indices: 46584221--46584256 Score: 56
Period size: 4 Copynumber: 9.0 Consensus size: 4
46584211 CATATTTATT
46584221 TTAG TTAG TTAG TTAG TTA- TTAG TATAG TTAG TTAG
1 TTAG TTAG TTAG TTAG TTAG TTAG T-TAG TTAG TTAG
46584257 AGTTGAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 3 0.10
4 23 0.77
5 4 0.13
ACGTcount: A:0.28, C:0.00, G:0.22, T:0.50
Consensus pattern (4 bp):
TTAG
Found at i:46591257 original size:182 final size:181
Alignment explanation
Indices: 46590946--46591663 Score: 810
Period size: 182 Copynumber: 4.0 Consensus size: 181
46590936 ACTATGAATT
** * * * *
46590946 AAGTATCACGTGTTGTAATCAGGCTTCGGTTAGTTTAGTTTCTTTTTAGGAAGCAATTTGAAATT
1 AAGTATCAAATGTTGTAATCAGGCTTCAGTCAGTTTAGTTTCTTTTTA-GAAGCAA-TTGCAAGT
* ** * ** * *
46591011 C-ATCAAGAAGATGCAAATTACAGCTAATATTAAGCTTGGTGGAGTGTTAGAAAT-TGAGTTAAA
64 CAATCAAGAAGCTGTGAATTGCAGCTAATATTAAGCTTAATGGAGTGTTAAAAATCAGA-TTAAA
** ** * *
46591074 TTGACAAAAATAATCTGTTTATGTATATATTTGTCTTAGAAAGGGAGAAAGTTG
128 TTGATGAAAATAATCCATTTATGTATATATTTGTCTCAGAAAAGGAGAAAGTTG
46591128 AAGTATCAAATGTTGTAATCAGGCTTCAGTCAGTTTAGTTTCTTTCTTAGAAGCAACTTGCAA-T
1 AAGTATCAAATGTTGTAATCAGGCTTCAGTCAGTTTAGTTTCTTT-TTAGAAGCAA-TTGCAAGT
46591192 CAATCAAGAAGCTGTGAATTGCAGCTAATATTAAGCTTAATGGAGTGTTAAAAATCAGATTAAAT
64 CAATCAAGAAGCTGTGAATTGCAGCTAATATTAAGCTTAATGGAGTGTTAAAAATCAGATTAAAT
* * * * *
46591257 TGATGAAAATAGTCCATTTATGTTTACATTTGTCTCAG--AA-GAG-GA-TTC
129 TGATGAAAATAATCCATTTATGTATATATTTGTCTCAGAAAAGGAGAAAGTTG
* ** * * *
46591305 AAGTATCAAATGTTGTAACCAGGCTTGGGTCAGTTTAGTTTCTTTTTCTGTAACCAATTGCTA-T
1 AAGTATCAAATGTTGTAATCAGGCTTCAGTCAGTTTAGTTTCTTTTT-AG-AAGCAATTGCAAGT
* * * ** * * *
46591369 TAATCAAGAAGCTCTGAATTGCAGCT-ATATTAAGCTTAATGGAGGGTTAAATGTCGGGTTAATT
64 CAATCAAGAAGCTGTGAATTGCAGCTAATATTAAGCTTAATGGAGTGTTAAAAATCAGATTAAAT
* * *
46591433 TGATGAAAATAGTCCATTCATGTATATATGTGTCTCAGAAAAGGAGAAAGTTG
129 TGATGAAAATAATCCATTTATGTATATATTTGTCTCAGAAAAGGAGAAAGTTG
* * * *
46591486 AAATATTACATGTTGTAATCAGGCTTCAGTCAGTTAAGTTTCTATTTTAGAAGCATATTGCAAGT
1 AAGTATCAAATGTTGTAATCAGGCTTCAGTCAGTTTAGTTTCT-TTTTAGAAGCA-ATTGCAAGT
* *
46591551 -AATCAAGAAGCTGTGAATTGCAGCTAATATTAAGCTTAATGGAGTGTTAAAAATCAGGTTAAGT
64 CAATCAAGAAGCTGTGAATTGCAGCTAATATTAAGCTTAATGGAGTGTTAAAAATCAGATTAAAT
* * * *
46591615 TGATGAAAGTAATCCATTTATGTATTTGTTTGTGTCAGAAAAGGAGAAA
129 TGATGAAAATAATCCATTTATGTATATATTTGTCTCAGAAAAGGAGAAA
46591664 AGTAACGGAA
Statistics
Matches: 454, Mismatches: 68, Indels: 28
0.83 0.12 0.05
Matches are distributed among these distances:
176 68 0.15
177 75 0.17
178 8 0.02
179 6 0.01
180 6 0.01
181 71 0.16
182 215 0.47
183 5 0.01
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.35
Consensus pattern (181 bp):
AAGTATCAAATGTTGTAATCAGGCTTCAGTCAGTTTAGTTTCTTTTTAGAAGCAATTGCAAGTCA
ATCAAGAAGCTGTGAATTGCAGCTAATATTAAGCTTAATGGAGTGTTAAAAATCAGATTAAATTG
ATGAAAATAATCCATTTATGTATATATTTGTCTCAGAAAAGGAGAAAGTTG
Found at i:46599467 original size:2 final size:2
Alignment explanation
Indices: 46599460--46599495 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
46599450 ATCCACTATC
46599460 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
46599496 TTAAATTCAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46600622 original size:133 final size:130
Alignment explanation
Indices: 46600385--46600623 Score: 293
Period size: 131 Copynumber: 1.8 Consensus size: 130
46600375 TGTTAAAAAA
* * * **
46600385 TGTTCAAATTAATCTTTGTACCTTAGATAAAAAAGCAATTAAAGGTGTGTGAATATATATATGCC
1 TGTTCAAATTAATCATTGTACATTAGATAAAAAAGCAACTAAAAATGTGTGAATATATATA-GCC
* *
46600450 ACTAGTTTGTAAAAGTACCATAGATGCTCTTAGATTAGGAGTAGGATTTTGTTTTGGCCTATCTA
65 ACTAATTGGTAAAAGTACCATAGATGCTCTTAGATTAGGAGTAGGATTTTGTTTTGGCCTATCTA
46600515 T
130 T
** * *
46600516 TGTTCAAATTTGTCATTGTACATTAGATCAAAAAGTAACTAAAAATGTGTGAATATATATA-CAC
1 TGTTCAAATTAATCATTGTACATTAGATAAAAAAGCAACTAAAAATGTGTGAATATATATAGC-C
* *
46600580 ACCTTTAATTGGTAAAAGTACTATGGATGC-CTTTAGATTAGGAG
65 A-C--TAATTGGTAAAAGTACCATAGATGCTC-TTAGATTAGGAG
46600624 CAAGATTACA
Statistics
Matches: 90, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
129 1 0.01
130 2 0.02
131 53 0.59
132 1 0.01
133 33 0.37
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (130 bp):
TGTTCAAATTAATCATTGTACATTAGATAAAAAAGCAACTAAAAATGTGTGAATATATATAGCCA
CTAATTGGTAAAAGTACCATAGATGCTCTTAGATTAGGAGTAGGATTTTGTTTTGGCCTATCTAT
Found at i:46630123 original size:6 final size:6
Alignment explanation
Indices: 46630114--46630140 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
46630104 GCCAACGACT
46630114 GAGTCC GAGTCC GAGTCC GAGTCC GAG
1 GAGTCC GAGTCC GAGTCC GAGTCC GAG
46630141 CTTGAGACTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.30, G:0.37, T:0.15
Consensus pattern (6 bp):
GAGTCC
Found at i:46635000 original size:11 final size:11
Alignment explanation
Indices: 46634986--46635013 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
46634976 TTTTTAATTA
46634986 TTTAATAATAT
1 TTTAATAATAT
46634997 TTTAATAATAT
1 TTTAATAATAT
46635008 TTTAAT
1 TTTAAT
46635014 GTATTGATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTAATAATAT
Found at i:46639428 original size:37 final size:34
Alignment explanation
Indices: 46639387--46639458 Score: 99
Period size: 34 Copynumber: 2.0 Consensus size: 34
46639377 AATTGTAATG
*
46639387 AAGTTAACATTTTCTCCATAAAAGATATCTTGAAACA
1 AAGTTAACAATTTCTCC-T--AAGATATCTTGAAACA
*
46639424 AAGTTAACAATTTCTCCTTAGATATCTTGAAACA
1 AAGTTAACAATTTCTCCTAAGATATCTTGAAACA
46639458 A
1 A
46639459 TAACAATTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
34 16 0.48
36 1 0.03
37 16 0.48
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.33
Consensus pattern (34 bp):
AAGTTAACAATTTCTCCTAAGATATCTTGAAACA
Found at i:46648062 original size:387 final size:387
Alignment explanation
Indices: 46647068--46648229 Score: 2026
Period size: 387 Copynumber: 3.0 Consensus size: 387
46647058 ATTGTAATTT
* * *
46647068 TGAACAGGCTCAAGCTAAGAGGAGGGCACCTGACAAGTCCATTAGAGAAGACCAGGACAAGATAG
1 TGAACAGGCTCAAGCTAAGAGGAGGGCACGTGACAAGTCCATCAGAGAAGACCAGGACAAGATGG
* * *
46647133 ACAGGAGTGTTCCTGCTTTGTCCGTTGATCATAGTGCAGAACCCTCTCAAGCTAAGGAGGGGAAT
66 ACAGGAGTGTTCCTGCTTCGTCTGTTGATCATAGTGCAGAACCCTCTCAAGCTAAGGAGGGGGAT
* *
46647198 GAAGCTTTCATTAGACCCAAGAAAGTGCACAAGCCCATCTCAATTGAGAGGAATGACACTGCTCG
131 GAAGCTTTCATTAGACCCAAGAAAGTGCGCAAGCCCAACTCAATTGAGAGGAATGACACTGCTCG
* *
46647263 CACTCATGAGGTGTGTTTTTGGATGTTGTTTTCTGAAATCTTGGAATTTTCTTTTACCATGAAGT
196 CACTCATGAGGTGTGTATTTGGATGTTGTTTTGTGAAATCTTGGAATTTTCTTTTACCATGAAGT
*
46647328 TTAAGGCTTATCCTTTCATTACACTGCATGCTTTAACTTGTAATTGTAATCTCCTGCTAGATTTT
261 TTAAGGCTTATCCTTTCATTACACTGCATGCTTTAACTTGTAATTGTAATCTCCTGCTAAATTTT
*
46647393 CTCCTTCGTACGCTTCATTGTTATTACCATTTTAAGTCCTGCCTGACTTTGCCTTATTTTTA
326 CTCCTTCGTACGCTTCATTGTTATAACCATTTTAAGTCCTGCCTGACTTTGCCTTATTTTTA
46647455 TGAACAGGCTCAAGCT-A-A-GAGGGCACGTGACAAGTCCATCAGAGAAGACCAGGACAAGATGG
1 TGAACAGGCTCAAGCTAAGAGGAGGGCACGTGACAAGTCCATCAGAGAAGACCAGGACAAGATGG
46647517 ACAGGAGTGTTCCTGCTTCGTCTGTTGATCATAGTGCAGAACCCTCTCAAGCTAAGGAGGGGGAT
66 ACAGGAGTGTTCCTGCTTCGTCTGTTGATCATAGTGCAGAACCCTCTCAAGCTAAGGAGGGGGAT
*
46647582 GAAGCTTTCATTAGACCCAAGAAAGTGTGCAAGCCCAACTCAATTGAGAGGAATGACACTGCTCG
131 GAAGCTTTCATTAGACCCAAGAAAGTGCGCAAGCCCAACTCAATTGAGAGGAATGACACTGCTCG
*
46647647 GACTCATGAGGTGTGTATTTGGATGTTGTTTTGTGAAATCTTGGAATTTTCTTTTACCATGAAGT
196 CACTCATGAGGTGTGTATTTGGATGTTGTTTTGTGAAATCTTGGAATTTTCTTTTACCATGAAGT
* *
46647712 TTAAGGTTTATCCTTTCATTACACTGCATGCTTTAACTTGTAATTGTAATCACCTGCTAAATTTT
261 TTAAGGCTTATCCTTTCATTACACTGCATGCTTTAACTTGTAATTGTAATCTCCTGCTAAATTTT
* *
46647777 CTCCTTTGTACGCTTCATTGTTATAACCATTTTAAGTCCTACCTGACTTTGCCTTATTTTTA
326 CTCCTTCGTACGCTTCATTGTTATAACCATTTTAAGTCCTGCCTGACTTTGCCTTATTTTTA
*
46647839 TGAACAGGCTCAAGCTAAGAGGAGGGCATGTGACAAGTCCATCAGAGAAGACCAGGACAAGATGG
1 TGAACAGGCTCAAGCTAAGAGGAGGGCACGTGACAAGTCCATCAGAGAAGACCAGGACAAGATGG
*
46647904 ACAGGAGTGTTGCTGCTTCGTCTGTTGATCATAGTGCAGAACCCTCTCAAGCTAAGGAGGGGGAT
66 ACAGGAGTGTTCCTGCTTCGTCTGTTGATCATAGTGCAGAACCCTCTCAAGCTAAGGAGGGGGAT
* ** * *
46647969 GAAGCTTTCATTAGATCCAAGAAAGTGCGCAAGCCCAACTCAGCTGAGAGGAATGACACTGTTCA
131 GAAGCTTTCATTAGACCCAAGAAAGTGCGCAAGCCCAACTCAATTGAGAGGAATGACACTGCTCG
** *
46648034 CACTCATGAGGTGTGTGCTTAGATGTTGTTTTGTGAAATCTTGGAATTTTCTTTTACCATGAAGT
196 CACTCATGAGGTGTGTATTTGGATGTTGTTTTGTGAAATCTTGGAATTTTCTTTTACCATGAAGT
46648099 TTAAGGCTTATCCTTTCATTACACTGCATGCTTTAACTTGTAATTGTAATCTCCTGCTAAATTTT
261 TTAAGGCTTATCCTTTCATTACACTGCATGCTTTAACTTGTAATTGTAATCTCCTGCTAAATTTT
*
46648164 CTCCTTCATACG-TGTCATTGTTATAACCATTTTAAGTCCTGCCTGACTTTGCCTTATTTTTA
326 CTCCTTCGTACGCT-TCATTGTTATAACCATTTTAAGTCCTGCCTGACTTTGCCTTATTTTTA
46648226 TGAA
1 TGAA
46648230 ATCTTGGGAG
Statistics
Matches: 736, Mismatches: 35, Indels: 8
0.94 0.04 0.01
Matches are distributed among these distances:
384 364 0.49
385 2 0.00
386 3 0.00
387 367 0.50
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (387 bp):
TGAACAGGCTCAAGCTAAGAGGAGGGCACGTGACAAGTCCATCAGAGAAGACCAGGACAAGATGG
ACAGGAGTGTTCCTGCTTCGTCTGTTGATCATAGTGCAGAACCCTCTCAAGCTAAGGAGGGGGAT
GAAGCTTTCATTAGACCCAAGAAAGTGCGCAAGCCCAACTCAATTGAGAGGAATGACACTGCTCG
CACTCATGAGGTGTGTATTTGGATGTTGTTTTGTGAAATCTTGGAATTTTCTTTTACCATGAAGT
TTAAGGCTTATCCTTTCATTACACTGCATGCTTTAACTTGTAATTGTAATCTCCTGCTAAATTTT
CTCCTTCGTACGCTTCATTGTTATAACCATTTTAAGTCCTGCCTGACTTTGCCTTATTTTTA
Found at i:46654143 original size:30 final size:30
Alignment explanation
Indices: 46654109--46654260 Score: 191
Period size: 30 Copynumber: 5.1 Consensus size: 30
46654099 CCTCTTTAGG
46654109 CTTCTCAGCTTCTTTGGGTTTCTCCGGTTT
1 CTTCTCAGCTTCTTTGGGTTTCTCCGGTTT
* *
46654139 CTTCTCACCGTCTTTGGGCTTT-TCCGGTTT
1 CTTCTCAGCTTCTTTGGG-TTTCTCCGGTTT
* * *
46654169 CTTCTCCGCTTCCTTGGGTTTTTCCGGTTT
1 CTTCTCAGCTTCTTTGGGTTTCTCCGGTTT
* *
46654199 CTTCTCGGCTTCTTTGGGTTTTTCCGGTTT
1 CTTCTCAGCTTCTTTGGGTTTCTCCGGTTT
* * *
46654229 CTTCTCAGCTTCTTTCGGCTTCT-CGGCTT
1 CTTCTCAGCTTCTTTGGGTTTCTCCGGTTT
46654258 CTT
1 CTT
46654261 TAGGTTTGTC
Statistics
Matches: 107, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
29 11 0.10
30 93 0.87
31 3 0.03
ACGTcount: A:0.02, C:0.29, G:0.20, T:0.49
Consensus pattern (30 bp):
CTTCTCAGCTTCTTTGGGTTTCTCCGGTTT
Found at i:46654272 original size:18 final size:18
Alignment explanation
Indices: 46654229--46654264 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
46654219 TTTCCGGTTT
* *
46654229 CTTCTCAGCTTCTTTCGG
1 CTTCTCGGCTTCTTTAGG
46654247 CTTCTCGGCTTCTTTAGG
1 CTTCTCGGCTTCTTTAGG
46654265 TTTGTCGGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.06, C:0.31, G:0.19, T:0.44
Consensus pattern (18 bp):
CTTCTCGGCTTCTTTAGG
Found at i:46655567 original size:31 final size:31
Alignment explanation
Indices: 46655532--46655667 Score: 100
Period size: 31 Copynumber: 4.5 Consensus size: 31
46655522 ATCCCAAAAT
*
46655532 GTTTAAGTACCAACTTAAAAAAAAGTACCAA
1 GTTTAAGTACCAAATTAAAAAAAAGTACCAA
* * **
46655563 GTTTAGGTACCAAATTAGAAAAAAGTGTCAA
1 GTTTAAGTACCAAATTAAAAAAAAGTACCAA
* * * *
46655594 GCTTGAGTACCAAATTGGACAAAAA--A--AA
1 GTTTAAGTACCAAATT-AAAAAAAAGTACCAA
* * * ***
46655622 GTTTAGGTATCAAATTAGAAAAAAGTGTGAA
1 GTTTAAGTACCAAATTAAAAAAAAGTACCAA
46655653 GTTTAAGTACCAAAT
1 GTTTAAGTACCAAAT
46655668 GTTATATTAA
Statistics
Matches: 78, Mismatches: 22, Indels: 10
0.71 0.20 0.09
Matches are distributed among these distances:
27 5 0.06
28 14 0.18
31 54 0.69
32 5 0.06
ACGTcount: A:0.47, C:0.11, G:0.17, T:0.25
Consensus pattern (31 bp):
GTTTAAGTACCAAATTAAAAAAAAGTACCAA
Found at i:46655644 original size:90 final size:90
Alignment explanation
Indices: 46655475--46655667 Score: 203
Period size: 90 Copynumber: 2.1 Consensus size: 90
46655465 TTAAAAAAAA
* * * ** *
46655475 TTAGGTATCAAATTAGGAAAAATAGTCAAGTTCAGGTGCCAAATTGGATCCCAAAATGTTTAAGT
1 TTAGGTACCAAATTAGAAAAAATAGTCAAGTTCAGGTACCAAATTGGATCAAAAAAAGTTTAAGT
*
46655540 ACCAACTTAAAAAAAAGTACCAAGT
66 ACCAAATTAAAAAAAAGTACCAAGT
*
46655565 TTAGGTACCAAATTAGAAAAAAGT-GTCAAGCTTGA-GTACCAAATTGGA-CAAAAAAAAGTTTA
1 TTAGGTACCAAATTAGAAAAAA-TAGTCAAG-TTCAGGTACCAAATTGGATC-AAAAAAAGTTTA
* * * ***
46655627 GGTATCAAATTAGAAAAAAGTGTGAAGT
63 AGTACCAAATTAAAAAAAAGTACCAAGT
*
46655655 TTAAGTACCAAAT
1 TTAGGTACCAAAT
46655668 GTTATATTAA
Statistics
Matches: 85, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
89 1 0.01
90 80 0.94
91 4 0.05
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.25
Consensus pattern (90 bp):
TTAGGTACCAAATTAGAAAAAATAGTCAAGTTCAGGTACCAAATTGGATCAAAAAAAGTTTAAGT
ACCAAATTAAAAAAAAGTACCAAGT
Found at i:46661927 original size:31 final size:30
Alignment explanation
Indices: 46661892--46661975 Score: 105
Period size: 30 Copynumber: 2.8 Consensus size: 30
46661882 TAAAATTATA
46661892 TACAATTAAATCAAAATCAAAGTTTCATATG
1 TACAATTAAATC-AAATCAAAGTTTCATATG
* *
46661923 TACAATTTAATCAAATCAAAGTTTCATATA
1 TACAATTAAATCAAATCAAAGTTTCATATG
* * * *
46661953 CATAATTATATTAAATCAAAGTT
1 TACAATTAAATCAAATCAAAGTT
46661976 AATATATCCA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
30 35 0.76
31 11 0.24
ACGTcount: A:0.48, C:0.12, G:0.05, T:0.36
Consensus pattern (30 bp):
TACAATTAAATCAAATCAAAGTTTCATATG
Found at i:46662196 original size:4 final size:4
Alignment explanation
Indices: 46662189--46662213 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
46662179 ATACATACAC
46662189 GCAT GCAT GCAT GCAT GCAT GCAT G
1 GCAT GCAT GCAT GCAT GCAT GCAT G
46662214 GGGAAATGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (4 bp):
GCAT
Found at i:46664138 original size:60 final size:58
Alignment explanation
Indices: 46664052--46664218 Score: 203
Period size: 60 Copynumber: 2.8 Consensus size: 58
46664042 TTTGACAATT
*
46664052 TTTTTCTAATTTGGTACTTAAA-TTTTTTTTGACCTAATTTGGTACCTGAACTTGACA
1 TTTTTCTAATTTGGTACCTAAACTTTTTTTTGACCTAATTTGGTACCTGAACTTGACA
* ** * * *
46664109 CTTTTTCTTAATTTGATACCTAAACTTTTTTTAAACCAAAATTGGTACCTGAACTTGGCA
1 -TTTTTC-TAATTTGGTACCTAAACTTTTTTTTGACCTAATTTGGTACCTGAACTTGACA
*
46664169 TTTTTCCTAATTTGGTACCTAAACTTTTTTTTAGA-TTCAATTTGGTACCT
1 TTTTT-CTAATTTGGTACCTAAACTTTTTTTT-GACCT-AATTTGGTACCT
46664219 AAAATTATTA
Statistics
Matches: 91, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
58 6 0.07
59 42 0.46
60 43 0.47
ACGTcount: A:0.26, C:0.16, G:0.11, T:0.47
Consensus pattern (58 bp):
TTTTTCTAATTTGGTACCTAAACTTTTTTTTGACCTAATTTGGTACCTGAACTTGACA
Found at i:46664173 original size:59 final size:59
Alignment explanation
Indices: 46664052--46664199 Score: 201
Period size: 59 Copynumber: 2.5 Consensus size: 59
46664042 TTTGACAATT
* ** * *
46664052 TTTTTCTAATTTGGTACTTAAA-TTTTTTTTGACCTAATTTGGTACCTGAACTTGACAC
1 TTTTTCTAATTTGGTACCTAAACTTTTTTTAAACCAAAATTGGTACCTGAACTTGACAC
* *
46664110 TTTTTCTTAATTTGATACCTAAACTTTTTTTAAACCAAAATTGGTACCTGAACTTGGCA-
1 TTTTTC-TAATTTGGTACCTAAACTTTTTTTAAACCAAAATTGGTACCTGAACTTGACAC
46664169 TTTTTCCTAATTTGGTACCTAAACTTTTTTT
1 TTTTT-CTAATTTGGTACCTAAACTTTTTTT
46664200 TAGATTCAAT
Statistics
Matches: 79, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
58 6 0.08
59 42 0.53
60 31 0.39
ACGTcount: A:0.26, C:0.16, G:0.10, T:0.48
Consensus pattern (59 bp):
TTTTTCTAATTTGGTACCTAAACTTTTTTTAAACCAAAATTGGTACCTGAACTTGACAC
Found at i:46665172 original size:36 final size:36
Alignment explanation
Indices: 46665132--46665208 Score: 127
Period size: 36 Copynumber: 2.1 Consensus size: 36
46665122 CGCTAAAGGA
46665132 GCAGCTACAGCAAGTTGCGCAACCTTCTGAGGCGGC
1 GCAGCTACAGCAAGTTGCGCAACCTTCTGAGGCGGC
* * *
46665168 GCAGCTGCAGCAGGTTGCGCAACCTTCTGAGGTGGC
1 GCAGCTACAGCAAGTTGCGCAACCTTCTGAGGCGGC
46665204 GCAGC
1 GCAGC
46665209 CGCTTCCTCT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.19, C:0.30, G:0.34, T:0.17
Consensus pattern (36 bp):
GCAGCTACAGCAAGTTGCGCAACCTTCTGAGGCGGC
Found at i:46665200 original size:18 final size:18
Alignment explanation
Indices: 46665148--46665206 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
46665138 ACAGCAAGTT
*
46665148 GCGCAACCTTCTGAGGCG
1 GCGCAACCTTCTGAGGTG
* * * *
46665166 GCGC-AGCTGCAGCAGGTT
1 GCGCAACCTTCTG-AGGTG
46665184 GCGCAACCTTCTGAGGTG
1 GCGCAACCTTCTGAGGTG
46665202 GCGCA
1 GCGCA
46665207 GCCGCTTCCT
Statistics
Matches: 30, Mismatches: 9, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
17 5 0.17
18 20 0.67
19 5 0.17
ACGTcount: A:0.17, C:0.31, G:0.36, T:0.17
Consensus pattern (18 bp):
GCGCAACCTTCTGAGGTG
Found at i:46666344 original size:22 final size:22
Alignment explanation
Indices: 46666297--46666344 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
46666287 AATAGATATT
* *
46666297 AATATAAATAATATCTTATATC
1 AATATAAATAATATCTTACATA
*
46666319 AATATAAATTAA-ATTTTACATA
1 AATATAAA-TAATATCTTACATA
46666341 AATA
1 AATA
46666345 ATAATTATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (22 bp):
AATATAAATAATATCTTACATA
Found at i:46670731 original size:36 final size:36
Alignment explanation
Indices: 46670680--46670779 Score: 191
Period size: 36 Copynumber: 2.8 Consensus size: 36
46670670 CGATATTCGA
*
46670680 TTTACTCCCTGTTGACCCAAAGGTCATGATGCTTGT
1 TTTACTCCCTATTGACCCAAAGGTCATGATGCTTGT
46670716 TTTACTCCCTATTGACCCAAAGGTCATGATGCTTGT
1 TTTACTCCCTATTGACCCAAAGGTCATGATGCTTGT
46670752 TTTACTCCCTATTGACCCAAAGGTCATG
1 TTTACTCCCTATTGACCCAAAGGTCATG
46670780 CCTGTTACCA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 63 1.00
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.35
Consensus pattern (36 bp):
TTTACTCCCTATTGACCCAAAGGTCATGATGCTTGT
Found at i:46673078 original size:23 final size:23
Alignment explanation
Indices: 46673037--46673095 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 23
46673027 ACTAGTGTTG
*
46673037 AATTTTTCAGATATTTTTA-TAATT
1 AATTTTT-A-ATAATTTTAGTAATT
*
46673061 AATATTTTAATAATTTTAGTATTT
1 AAT-TTTTAATAATTTTAGTAATT
46673085 AATTTTTAATA
1 AATTTTTAATA
46673096 TAATTATACT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 16 0.52
24 11 0.35
25 4 0.13
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (23 bp):
AATTTTTAATAATTTTAGTAATT
Found at i:46675623 original size:4 final size:4
Alignment explanation
Indices: 46675616--46675640 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
46675606 ATACATACAC
46675616 GCAT GCAT GCAT GCAT GCAT GCAT G
1 GCAT GCAT GCAT GCAT GCAT GCAT G
46675641 GGGAAATGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (4 bp):
GCAT
Found at i:46685125 original size:2 final size:2
Alignment explanation
Indices: 46685118--46685152 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
46685108 AAAAATGGTA
46685118 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
46685153 AGTTAATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:46686663 original size:8 final size:8
Alignment explanation
Indices: 46686640--46686683 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
46686630 TTTTAATTCC
*
46686640 ATATACAT
1 ATATATAT
*
46686648 ATACATAT
1 ATATATAT
46686656 ATATATAT
1 ATATATAT
*
46686664 ATATATAA
1 ATATATAT
*
46686672 ATATATTT
1 ATATATAT
46686680 ATAT
1 ATAT
46686684 GAAAAATTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (8 bp):
ATATATAT
Found at i:46686669 original size:6 final size:6
Alignment explanation
Indices: 46686640--46686683 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
46686630 TTTTAATTCC
* * * *
46686640 ATATAC ATATAC ATATAT ATATAT ATATAT AAATAT ATTTAT AT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT AT
46686684 GAAAAATTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (6 bp):
ATATAT
Found at i:46697992 original size:63 final size:63
Alignment explanation
Indices: 46697906--46698063 Score: 203
Period size: 63 Copynumber: 2.5 Consensus size: 63
46697896 GTTAATATGG
* * *
46697906 TACCTATACTTT-A-AAAATATTCAATGTGGTATTTAAACTATCAGTATATATTTTATTAGGA
1 TACCTTTACTTTCATAAAATATTCAATATGGTATTTAAACTATCAATATATATTTTATTAGGA
* * * * *
46697967 TACTTTTATTTTCATAAAATATTCAATATGATATTTGAATTATCAATATATATTTTATTAGGA
1 TACCTTTACTTTCATAAAATATTCAATATGGTATTTAAACTATCAATATATATTTTATTAGGA
* * *
46698030 TACCTTTACTTTCATAAAATGTCCAATTTGGTAT
1 TACCTTTACTTTCATAAAATATTCAATATGGTAT
46698064 CTGTACTTTG
Statistics
Matches: 81, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
61 9 0.11
62 1 0.01
63 71 0.88
ACGTcount: A:0.36, C:0.10, G:0.08, T:0.46
Consensus pattern (63 bp):
TACCTTTACTTTCATAAAATATTCAATATGGTATTTAAACTATCAATATATATTTTATTAGGA
Found at i:46702675 original size:22 final size:19
Alignment explanation
Indices: 46702640--46702679 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 19
46702630 AAAAACATTT
46702640 AAAAATAAAAAATTACAAAA
1 AAAAATAAAAAATT-CAAAA
46702660 AAAAATCATAAAAATTCAAA
1 AAAAAT-A-AAAAATTCAAA
46702680 GAATTAGCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 5 0.28
22 7 0.39
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.17
Consensus pattern (19 bp):
AAAAATAAAAAATTCAAAA
Found at i:46706226 original size:84 final size:81
Alignment explanation
Indices: 46706135--46706473 Score: 389
Period size: 84 Copynumber: 4.0 Consensus size: 81
46706125 AGAAGAGAAA
* ***
46706135 AAGAAGGCAGTTGAAGAAAGAAAACTTG-TCGATTTGGAGATGGCTAAAGCAAGCGAGTTGAGGA
1 AAGAAGGCTGTTGAAGAAAGAAAAC-TGCT-GATTTGGAGATGGCTAAAGC-AG-GAGCAAAGGA
46706199 AGATTGCAGAAGAAACTAAG
62 AGATTGCAGAAGAAACTAAG
* * * *
46706219 AAAAAGGCTGTTGATGAAAGAAAATGTGCTGATTTGGAGATGGCTAAAGCGGAGAAGCAAAGGAA
1 AAGAAGGCTGTTGAAGAAAGAAAA-CTGCTGATTTGGAGATGGCTAAAGC--AGGAGCAAAGGAA
46706284 GATTGCTA-AAGAAACTAAG
63 GATTGC-AGAAGAAACTAAG
* *
46706303 AAGAAGGCTGTTGAAGAAAGAAAACGTGCTGATTTAGAGATGGCTGAAGCAGTGAAGCAAAGGAA
1 AAGAAGGCTGTTGAAGAAAGAAAAC-TGCTGATTTGGAGATGGCTAAAGCAG-G-AGCAAAGGAA
*
46706368 GATTGCAGAAGAAAAC-ATG
63 GATTGCAGAAG-AAACTAAG
* *
46706387 AAGAAGGCTGTTGAAGTAAGAAAACAAGCTGATATT-GAGATGGCTAAAGCAGAAGAGCAAAGGA
1 AAGAAGGCTGTTGAAGAAAGAAAAC-TGCTGAT-TTGGAGATGGCTAAAGCAG--GAGCAAAGGA
46706451 AGATTGCAGAAGAAACTAAG
62 AGATTGCAGAAGAAACTAAG
46706471 AAG
1 AAG
46706474 GCTGTTGAAG
Statistics
Matches: 221, Mismatches: 22, Indels: 24
0.83 0.08 0.09
Matches are distributed among these distances:
82 2 0.01
83 5 0.02
84 203 0.92
85 11 0.05
ACGTcount: A:0.44, C:0.09, G:0.30, T:0.17
Consensus pattern (81 bp):
AAGAAGGCTGTTGAAGAAAGAAAACTGCTGATTTGGAGATGGCTAAAGCAGGAGCAAAGGAAGAT
TGCAGAAGAAACTAAG
Found at i:46706429 original size:168 final size:168
Alignment explanation
Indices: 46706135--46706473 Score: 438
Period size: 168 Copynumber: 2.0 Consensus size: 168
46706125 AGAAGAGAAA
* * ***
46706135 AAGAAGGCAGTTGAAGAAAGAAAACTTGTCGATTTGGAGATGGCTAAAGCAAGCGAGTTGAGGAA
1 AAGAAGGCAGTTGAAGAAAGAAAACGTGTCGATTTAGAGATGGCTAAAGCAAGCGAGCAAAGGAA
* ***
46706200 GATTGCAGAAGAAACTAAGAAAAAGGCTGTTGATGAAAGAAAATGTGCTGATTTGGAGATGGCTA
66 GATTGCAGAAGAAACTAAGAAAAAGGCTGTTGAAGAAAGAAAACAAGCTGATTTGGAGATGGCTA
*
46706265 AAGC-GGAGAAGCAAAGGAAGATTGCTA-AAGAAACTAAG
131 AAGCAGAAG-AGCAAAGGAAGATTGC-AGAAGAAACTAAG
* * *
46706303 AAGAAGGCTGTTGAAGAAAGAAAACGTG-CTGATTTAGAGATGGCTGAAGC-AGTGAAGCAAAGG
1 AAGAAGGCAGTTGAAGAAAGAAAACGTGTC-GATTTAGAGATGGCTAAAGCAAGCG-AGCAAAGG
* * *
46706366 AAGATTGCAGAAGAAAAC-ATGAAGAAGGCTGTTGAAGTAAGAAAACAAGCTGATATT-GAGATG
64 AAGATTGCAGAAG-AAACTAAGAAAAAGGCTGTTGAAGAAAGAAAACAAGCTGAT-TTGGAGATG
46706429 GCTAAAGCAGAAGAGCAAAGGAAGATTGCAGAAGAAACTAAG
127 GCTAAAGCAGAAGAGCAAAGGAAGATTGCAGAAGAAACTAAG
46706471 AAG
1 AAG
46706474 GCTGTTGAAG
Statistics
Matches: 149, Mismatches: 16, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
167 5 0.03
168 135 0.91
169 9 0.06
ACGTcount: A:0.44, C:0.09, G:0.30, T:0.17
Consensus pattern (168 bp):
AAGAAGGCAGTTGAAGAAAGAAAACGTGTCGATTTAGAGATGGCTAAAGCAAGCGAGCAAAGGAA
GATTGCAGAAGAAACTAAGAAAAAGGCTGTTGAAGAAAGAAAACAAGCTGATTTGGAGATGGCTA
AAGCAGAAGAGCAAAGGAAGATTGCAGAAGAAACTAAG
Found at i:46713485 original size:58 final size:56
Alignment explanation
Indices: 46713423--46713531 Score: 146
Period size: 58 Copynumber: 1.9 Consensus size: 56
46713413 ATTGAATTTA
*
46713423 ACAATTATTCTCATCTTAAGGTTTAAATTTTTTTAATCCAATTTAATCCTTAAACTTG
1 ACAATTATTCTCATATTAAGGTTTAAATTTTTTT--TCCAATTTAATCCTTAAACTTG
* * ** *
46713481 ACAATTATTTTTATATTGGGGTTTGAATTTTTTTTCCAATTTAATCCTTAA
1 ACAATTATTCTCATATTAAGGTTTAAATTTTTTTTCCAATTTAATCCTTAA
46713532 TATTTCTGTA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
56 17 0.38
58 28 0.62
ACGTcount: A:0.30, C:0.13, G:0.07, T:0.50
Consensus pattern (56 bp):
ACAATTATTCTCATATTAAGGTTTAAATTTTTTTTCCAATTTAATCCTTAAACTTG
Found at i:46713705 original size:22 final size:22
Alignment explanation
Indices: 46713677--46713722 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
46713667 CAAAAATGAA
*
46713677 AACAATAGTAAAATGGGTTTGG
1 AACAATAGGAAAATGGGTTTGG
46713699 AACAATAGGAAAATGGGTTTGG
1 AACAATAGGAAAATGGGTTTGG
46713721 AA
1 AA
46713723 TAGAAGTAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.43, C:0.04, G:0.28, T:0.24
Consensus pattern (22 bp):
AACAATAGGAAAATGGGTTTGG
Found at i:46718498 original size:29 final size:27
Alignment explanation
Indices: 46718449--46718507 Score: 64
Period size: 29 Copynumber: 2.1 Consensus size: 27
46718439 TTAAAAATTC
** *
46718449 AAAAAATAAAATATTTTAAATATGTTT
1 AAAAAATAAAATATAATAAATATGGTT
*
46718476 AAAAAATCAAAATATAAATAAATTTGGTT
1 AAAAAAT-AAAATAT-AATAAATATGGTT
46718505 AAA
1 AAA
46718508 GTTTTAGAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 7 0.27
29 12 0.46
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (27 bp):
AAAAAATAAAATATAATAAATATGGTT
Found at i:46721575 original size:23 final size:23
Alignment explanation
Indices: 46721531--46721576 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
46721521 ACATTGTTCG
* *
46721531 TGAACATGTTCGATTAAGTTAAA
1 TGAACATGTTCGATGAAATTAAA
46721554 TGAACATGTTCG-TGAACATTAAA
1 TGAACATGTTCGATGAA-ATTAAA
46721577 CAAATGAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (23 bp):
TGAACATGTTCGATGAAATTAAA
Found at i:46725767 original size:2 final size:2
Alignment explanation
Indices: 46725760--46725905 Score: 82
Period size: 2 Copynumber: 78.5 Consensus size: 2
46725750 TTAATAAAAT
46725760 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A T- TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * * * *
46725799 T- TCA -A T- TA TA CA TA TT TA AA GA AA TA AA TA CA TA GA TT TA
1 TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
46725839 TT TT TA TA T- TA GA T- TA -A TA -A AA T- TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
46725876 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
46725906 CCAACATAAA
Statistics
Matches: 110, Mismatches: 21, Indels: 26
0.70 0.13 0.17
Matches are distributed among these distances:
1 12 0.11
2 98 0.89
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:46725873 original size:102 final size:104
Alignment explanation
Indices: 46725697--46725903 Score: 400
Period size: 102 Copynumber: 2.0 Consensus size: 104
46725687 TTTTATTTAT
46725697 TTCAATTATACATATTTAAAGAAATAAATACATAGATTTATTTTTATATTAGATTAATAAAATTA
1 TTCAATTATACATATTTAAAGAAATAAATACATAGATTTATTTTTATATTAGATTAATAAAATTA
46725762 TATATATATATATATATATATATATATA-AT-TATATAA
66 TATATATATATATATATATATATATATATATATATATAA
46725799 TTCAATTATACATATTTAAAGAAATAAATACATAGATTTATTTTTATATTAGATTAATAAAATTA
1 TTCAATTATACATATTTAAAGAAATAAATACATAGATTTATTTTTATATTAGATTAATAAAATTA
46725864 TATATATATATATATATATATATATATATATATATATAA
66 TATATATATATATATATATATATATATATATATATATAA
46725903 T
1 T
46725904 ATCCAACATA
Statistics
Matches: 103, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
102 93 0.90
103 2 0.02
104 8 0.08
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (104 bp):
TTCAATTATACATATTTAAAGAAATAAATACATAGATTTATTTTTATATTAGATTAATAAAATTA
TATATATATATATATATATATATATATATATATATATAA
Found at i:46725987 original size:30 final size:29
Alignment explanation
Indices: 46725952--46726012 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 29
46725942 GTGATTTTTA
*
46725952 AAAATTGAATC-AAATCAAGATTTTATATAT
1 AAAATTGAA-CAAAATCAA-AGTTTATATAT
*
46725982 AAAATTGTACAAAATCAAAGTTTATATAT
1 AAAATTGAACAAAATCAAAGTTTATATAT
46726011 AA
1 AA
46726013 CGTTGCATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 13 0.46
30 15 0.54
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.34
Consensus pattern (29 bp):
AAAATTGAACAAAATCAAAGTTTATATAT
Found at i:46726301 original size:20 final size:18
Alignment explanation
Indices: 46726256--46726303 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 18
46726246 AAGATTAATT
46726256 GATTTCAAATATAAAATA
1 GATTTCAAATATAAAATA
*
46726274 -ATTATCAACTATATTAAATA
1 GATT-TCAA--ATATAAAATA
46726294 GATTTCAAAT
1 GATTTCAAAT
46726304 TGGAATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
17 3 0.12
18 6 0.24
20 13 0.52
21 3 0.12
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (18 bp):
GATTTCAAATATAAAATA
Found at i:46726748 original size:31 final size:31
Alignment explanation
Indices: 46726687--46726749 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
46726677 GATTTGATGT
* *
46726687 AATTATACACATGTAATTTAATTGTGATTCA
1 AATTATACACATGCAATTTAATTGTAATTCA
* *
46726718 AATTA-ACACATGCAACTTTGATTTTAATTCA
1 AATTATACACATGCAA-TTTAATTGTAATTCA
46726749 A
1 A
46726750 TCATGCACAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 9 0.33
31 18 0.67
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.40
Consensus pattern (31 bp):
AATTATACACATGCAATTTAATTGTAATTCA
Found at i:46728839 original size:39 final size:39
Alignment explanation
Indices: 46728780--46728858 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
46728770 CAACATGCAA
*
46728780 TACCGCTTTTTTTAAACATATTTTAATTACTCTATCAAC
1 TACCACTTTTTTTAAACATATTTTAATTACTCTATCAAC
46728819 TACCACTTTTTTTAAACATATTTTAATTACTCTATCAAC
1 TACCACTTTTTTTAAACATATTTTAATTACTCTATCAAC
46728858 T
1 T
46728859 TTTTTATATT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.32, C:0.20, G:0.01, T:0.47
Consensus pattern (39 bp):
TACCACTTTTTTTAAACATATTTTAATTACTCTATCAAC
Found at i:46730914 original size:7 final size:7
Alignment explanation
Indices: 46730902--46730931 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
46730892 TATCATCTTC
46730902 GATTGCT
1 GATTGCT
46730909 GATTGCT
1 GATTGCT
46730916 GATTGCT
1 GATTGCT
46730923 GATTGCT
1 GATTGCT
46730930 GA
1 GA
46730932 GTCAGTGCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.17, C:0.13, G:0.30, T:0.40
Consensus pattern (7 bp):
GATTGCT
Found at i:46732353 original size:23 final size:23
Alignment explanation
Indices: 46732283--46732476 Score: 180
Period size: 23 Copynumber: 8.3 Consensus size: 23
46732273 ACGGAACAAG
* *
46732283 CAGAGAGTAC-CAAAGTACT-AA
1 CAGAGAGCACACAAAGTGCTAAA
* *
46732304 CAGAGAGCACA-TAAGTGCTGGGCAA
1 CAGAGAGCACACAAAGTGCT---AAA
*
46732329 CAGAGAGCACACACAGTGCTAAA
1 CAGAGAGCACACAAAGTGCTAAA
* * *
46732352 CAGAGAGTACACAAAGTACTAAT
1 CAGAGAGCACACAAAGTGCTAAA
*
46732375 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAA
*
46732398 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAA
* *
46732421 CAGAGAGCTCACACAGTGCTAATAA
1 CAGAGAGCACACAAAGTGCT-A-AA
* *
46732446 CAGAGAGCACGA-GACGTGCTAAA
1 CAGAGAGCAC-ACAAAGTGCTAAA
46732469 CAGAGAGC
1 CAGAGAGC
46732477 GCGCTAGTGT
Statistics
Matches: 145, Mismatches: 19, Indels: 16
0.81 0.11 0.09
Matches are distributed among these distances:
21 15 0.10
23 93 0.64
24 2 0.01
25 28 0.19
26 7 0.05
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.12
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAA
Found at i:46732402 original size:69 final size:68
Alignment explanation
Indices: 46732283--46732476 Score: 207
Period size: 69 Copynumber: 2.8 Consensus size: 68
46732273 ACGGAACAAG
* *
46732283 CAGAGAGTAC-CAAAGTACTAA-CAGAGAGCACATAAGTGCTGGGCAACAGAGAGCACACACAGT
1 CAGAGAGTACACAAAGTACTAATCAGAGAGCACAAAAGTGCT--G-AACAGAGAGCACACAAAGT
46732346 GCTAAA
63 GCTAAA
46732352 CAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT-AATCAGAGAGCACACAAAGTG
1 CAGAGAGTACACAAAGTACTAATCAGAGAGCACA-AAAGTGCTGAA-CAGAGAGCACACAAAGTG
*
46732416 CTAAT
64 CTAAA
* * * * *
46732421 CAGAGAGCT-CACACAGTGCTAATAACAGAGAGCACGAGACGTGCTAAACAGAGAGC
1 CAGAGAG-TACACAAAGTACTAAT--CAGAGAGCAC-AAAAGTGCTGAACAGAGAGC
46732477 GCGCTAGTGT
Statistics
Matches: 109, Mismatches: 7, Indels: 16
0.83 0.05 0.12
Matches are distributed among these distances:
68 2 0.02
69 50 0.46
70 12 0.11
71 35 0.32
72 10 0.09
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.12
Consensus pattern (68 bp):
CAGAGAGTACACAAAGTACTAATCAGAGAGCACAAAAGTGCTGAACAGAGAGCACACAAAGTGCT
AAA
Found at i:46739738 original size:23 final size:23
Alignment explanation
Indices: 46739668--46739861 Score: 180
Period size: 23 Copynumber: 8.3 Consensus size: 23
46739658 ACGGAACAAG
* *
46739668 CAGAGAGTAC-CAAAGTACT-AA
1 CAGAGAGCACACAAAGTGCTAAA
* *
46739689 CAGAGAGCACA-TAAGTGCTGGGCAA
1 CAGAGAGCACACAAAGTGCT---AAA
*
46739714 CAGAGAGCACACACAGTGCTAAA
1 CAGAGAGCACACAAAGTGCTAAA
* * *
46739737 CAGAGAGTACACAAAGTACTAAT
1 CAGAGAGCACACAAAGTGCTAAA
*
46739760 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAA
*
46739783 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAA
* *
46739806 CAGAGAGCTCACACAGTGCTAATAA
1 CAGAGAGCACACAAAGTGCT-A-AA
* *
46739831 CAGAGAGCACGA-GACGTGCTAAA
1 CAGAGAGCAC-ACAAAGTGCTAAA
46739854 CAGAGAGC
1 CAGAGAGC
46739862 GCGCTAGTGT
Statistics
Matches: 145, Mismatches: 19, Indels: 16
0.81 0.11 0.09
Matches are distributed among these distances:
21 15 0.10
23 93 0.64
24 2 0.01
25 28 0.19
26 7 0.05
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.12
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAA
Found at i:46739787 original size:69 final size:68
Alignment explanation
Indices: 46739668--46739861 Score: 207
Period size: 69 Copynumber: 2.8 Consensus size: 68
46739658 ACGGAACAAG
* *
46739668 CAGAGAGTAC-CAAAGTACTAA-CAGAGAGCACATAAGTGCTGGGCAACAGAGAGCACACACAGT
1 CAGAGAGTACACAAAGTACTAATCAGAGAGCACAAAAGTGCT--G-AACAGAGAGCACACAAAGT
46739731 GCTAAA
63 GCTAAA
46739737 CAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT-AATCAGAGAGCACACAAAGTG
1 CAGAGAGTACACAAAGTACTAATCAGAGAGCACA-AAAGTGCTGAA-CAGAGAGCACACAAAGTG
*
46739801 CTAAT
64 CTAAA
* * * * *
46739806 CAGAGAGCT-CACACAGTGCTAATAACAGAGAGCACGAGACGTGCTAAACAGAGAGC
1 CAGAGAG-TACACAAAGTACTAAT--CAGAGAGCAC-AAAAGTGCTGAACAGAGAGC
46739862 GCGCTAGTGT
Statistics
Matches: 109, Mismatches: 7, Indels: 16
0.83 0.05 0.12
Matches are distributed among these distances:
68 2 0.02
69 50 0.46
70 12 0.11
71 35 0.32
72 10 0.09
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.12
Consensus pattern (68 bp):
CAGAGAGTACACAAAGTACTAATCAGAGAGCACAAAAGTGCTGAACAGAGAGCACACAAAGTGCT
AAA
Found at i:46743861 original size:29 final size:30
Alignment explanation
Indices: 46743827--46743901 Score: 93
Period size: 29 Copynumber: 2.5 Consensus size: 30
46743817 TTGTACCTAC
46743827 ATATTATTTTAATAAA-TAATTTATAAC-CT
1 ATATTATTTTAATAAATTAATTT-TAACTCT
* *
46743856 ATATTATTTTAA-AAATTAATTTTATCTTTT
1 ATATTATTTTAATAAATTAATTTTAAC-TCT
46743886 ATATTATTTTAATAAA
1 ATATTATTTTAATAAA
46743902 ATCCCAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
28 6 0.15
29 18 0.45
30 13 0.32
31 3 0.08
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (30 bp):
ATATTATTTTAATAAATTAATTTTAACTCT
Found at i:46745183 original size:2 final size:2
Alignment explanation
Indices: 46745173--46745206 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
46745163 AAAAAAAGAA
*
46745173 AC AC GC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
46745207 TTGAAAATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.50, G:0.03, T:0.00
Consensus pattern (2 bp):
AC
Found at i:46745668 original size:6 final size:6
Alignment explanation
Indices: 46745627--46745710 Score: 75
Period size: 6 Copynumber: 14.5 Consensus size: 6
46745617 GAGATAGGAA
* * * * *
46745627 GGATAA GGATAA GGATAA GGATAA GGATAG GGATAG GGATAG AGATA-
1 GGATAG GGATAG GGATAG GGATAG GGATAG GGATAG GGATAG GGATAG
* * *
46745674 GG--AG GGACAG GGATAG GGATAG AGATAG AGATAG GGA
1 GGATAG GGATAG GGATAG GGATAG GGATAG GGATAG GGA
46745711 CGGAGATAGG
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
3 1 0.01
4 2 0.03
5 1 0.01
6 65 0.94
ACGTcount: A:0.42, C:0.01, G:0.43, T:0.14
Consensus pattern (6 bp):
GGATAG
Found at i:46745673 original size:18 final size:18
Alignment explanation
Indices: 46745627--46745737 Score: 73
Period size: 18 Copynumber: 6.0 Consensus size: 18
46745617 GAGATAGGAA
* *
46745627 GGATAAGGATA-AGGATAA
1 GGATAGGGATAGA-GATAG
* *
46745645 GGATAAGGATAGGGATAG
1 GGATAGGGATAGAGATAG
* *
46745663 GGATAGAGATAGGAGGGACAG
1 GGATAGGGATA-GA--GATAG
46745684 GGATAGGGATAGAGATAG
1 GGATAGGGATAGAGATAG
* **
46745702 AGATAGGGACGGAGATA-
1 GGATAGGGATAGAGATAG
*
46745719 GGAGTAGGCATAGAGATAG
1 GGA-TAGGGATAGAGATAG
46745738 ATATAAGGAG
Statistics
Matches: 72, Mismatches: 15, Indels: 11
0.73 0.15 0.11
Matches are distributed among these distances:
17 2 0.03
18 53 0.74
19 1 0.01
20 2 0.03
21 14 0.19
ACGTcount: A:0.41, C:0.03, G:0.42, T:0.14
Consensus pattern (18 bp):
GGATAGGGATAGAGATAG
Found at i:46745685 original size:21 final size:21
Alignment explanation
Indices: 46745655--46745695 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
46745645 GGATAAGGAT
*
46745655 AGGGATAGGGATAGAGATAGG
1 AGGGACAGGGATAGAGATAGG
*
46745676 AGGGACAGGGATAGGGATAG
1 AGGGACAGGGATAGAGATAG
46745696 AGATAGAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.02, G:0.49, T:0.12
Consensus pattern (21 bp):
AGGGACAGGGATAGAGATAGG
Found at i:46752072 original size:20 final size:22
Alignment explanation
Indices: 46752044--46752089 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
46752034 GTTTTAAATG
*
46752044 TTTACTTTG-TATTT-AATTTT
1 TTTAATTTGATATTTGAATTTT
*
46752064 TTTAATTTGATATTTGAGTTTT
1 TTTAATTTGATATTTGAATTTT
46752086 TTTA
1 TTTA
46752090 TCAATTTAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 8 0.36
21 5 0.23
22 9 0.41
ACGTcount: A:0.22, C:0.02, G:0.09, T:0.67
Consensus pattern (22 bp):
TTTAATTTGATATTTGAATTTT
Found at i:46752085 original size:21 final size:20
Alignment explanation
Indices: 46752044--46752087 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
46752034 GTTTTAAATG
* *
46752044 TTTACTTTGTATTTAATTTT
1 TTTAATTTGTATTTAAGTTT
*
46752064 TTTAATTTGATATTTGAGTTT
1 TTTAATTTG-TATTTAAGTTT
46752085 TTT
1 TTT
46752088 TATCAATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.20, C:0.02, G:0.09, T:0.68
Consensus pattern (20 bp):
TTTAATTTGTATTTAAGTTT
Found at i:46752095 original size:25 final size:23
Alignment explanation
Indices: 46752044--46752112 Score: 65
Period size: 25 Copynumber: 3.0 Consensus size: 23
46752034 GTTTTAAATG
*
46752044 TTTACTTT-GTATTT-A-ATTTT
1 TTTAATTTAGTATTTGAGATTTT
*
46752064 TTTAATTT-GATATTTGAGTTTTT
1 TTTAATTTAG-TATTTGAGATTTT
46752087 TTATCAATTTAGTATTTGAGATTTT
1 TT-T-AATTTAGTATTTGAGATTTT
46752112 T
1 T
46752113 ATTTATCTCA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
20 8 0.20
21 5 0.12
22 1 0.03
23 6 0.15
24 1 0.03
25 18 0.45
26 1 0.03
ACGTcount: A:0.23, C:0.03, G:0.10, T:0.64
Consensus pattern (23 bp):
TTTAATTTAGTATTTGAGATTTT
Found at i:46753714 original size:14 final size:14
Alignment explanation
Indices: 46753695--46753751 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
46753685 ATATTAATAA
46753695 ATAATATAAAATTT
1 ATAATATAAAATTT
46753709 ATAATATAAAATTTT
1 ATAATATAAAA-TTT
*
46753724 AAAAATTATAATAATTAT
1 -ATAA-TATAA-AATT-T
46753742 ATAATATAAA
1 ATAATATAAA
46753752 TATCTCATTG
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
14 11 0.31
15 4 0.11
16 8 0.22
17 10 0.28
18 3 0.08
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
ATAATATAAAATTT
Found at i:46757883 original size:18 final size:18
Alignment explanation
Indices: 46757860--46757902 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
46757850 AAATAGGTTT
46757860 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
46757878 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
46757896 TTAATTA
1 TTAATTA
46757903 CATTTTGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:46765888 original size:25 final size:25
Alignment explanation
Indices: 46765860--46765912 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
46765850 ATACATCAAT
* *
46765860 TTATTTTTATATTGAATAAATATAA
1 TTATTTTTATATTCAATAAATAAAA
* *
46765885 TTATTTTTGTATTCAATATATAAAA
1 TTATTTTTATATTCAATAAATAAAA
46765910 TTA
1 TTA
46765913 AAATGATGCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (25 bp):
TTATTTTTATATTCAATAAATAAAA
Found at i:46766015 original size:29 final size:30
Alignment explanation
Indices: 46765978--46766042 Score: 78
Period size: 31 Copynumber: 2.2 Consensus size: 30
46765968 AAATTTTATG
46765978 TATAAAATTGTACA-AAATCAAAATTCATA
1 TATAAAATTGTACATAAATCAAAATTCATA
* * * *
46766007 TATACAATTGTATATTAAATCAAAGTTCATG
1 TATAAAATTGTACA-TAAATCAAAATTCATA
46766038 TATAA
1 TATAA
46766043 TTTTAATATT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
29 12 0.41
31 17 0.59
ACGTcount: A:0.49, C:0.09, G:0.06, T:0.35
Consensus pattern (30 bp):
TATAAAATTGTACATAAATCAAAATTCATA
Found at i:46766564 original size:29 final size:30
Alignment explanation
Indices: 46766495--46766564 Score: 70
Period size: 31 Copynumber: 2.3 Consensus size: 30
46766485 ATCTCAAAAG
*
46766495 TATATATGAACTTTGGTTTAATACTTAATTA
1 TATATATGAACTTTGATTTAATAC-TAATTA
** ** *
46766526 TATGCATGAACTTTGATTTTGTAC-AATTT
1 TATATATGAACTTTGATTTAATACTAATTA
46766555 TATATATGAA
1 TATATATGAA
46766565 ATTTTAATTT
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
29 12 0.39
31 19 0.61
ACGTcount: A:0.34, C:0.07, G:0.11, T:0.47
Consensus pattern (30 bp):
TATATATGAACTTTGATTTAATACTAATTA
Found at i:46798984 original size:20 final size:18
Alignment explanation
Indices: 46798959--46798997 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
46798949 AAAAAATAAA
46798959 TTCTTTATAATTTTTAATAT
1 TTCTTTAT-ATTTTT-ATAT
*
46798979 TTCTTTGTATTTTTATAT
1 TTCTTTATATTTTTATAT
46798997 T
1 T
46798998 ACATAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 6 0.33
20 7 0.39
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.69
Consensus pattern (18 bp):
TTCTTTATATTTTTATAT
Found at i:46804170 original size:30 final size:30
Alignment explanation
Indices: 46804129--46804190 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
46804119 GAGAGGACCT
*
46804129 CCTGGTCCACCACCACCACGCCCTGGAATG
1 CCTGCTCCACCACCACCACGCCCTGGAATG
46804159 CCTGCTCCACCACCACCACGCCCTGGAATG
1 CCTGCTCCACCACCACCACGCCCTGGAATG
46804189 CC
1 CC
46804191 GCCTCCCCCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.19, C:0.50, G:0.18, T:0.13
Consensus pattern (30 bp):
CCTGCTCCACCACCACCACGCCCTGGAATG
Found at i:46812904 original size:13 final size:14
Alignment explanation
Indices: 46812878--46812908 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
46812868 ATAAATTGTA
46812878 ATTATAAAAGAATT
1 ATTATAAAAGAATT
46812892 ATTATAAAA-AATT
1 ATTATAAAAGAATT
46812905 ATTA
1 ATTA
46812909 GTATGATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (14 bp):
ATTATAAAAGAATT
Found at i:46815683 original size:18 final size:18
Alignment explanation
Indices: 46815656--46815698 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
46815646 TAATATATTT
*
46815656 TTAATTTTATTAATAATAA
1 TTAATATTATTAATAA-AA
*
46815675 -TAATATTATTATTAAAA
1 TTAATATTATTAATAAAA
46815692 TTAATAT
1 TTAATAT
46815699 AACTTTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTAATATTATTAATAAAA
Found at i:46833167 original size:3 final size:3
Alignment explanation
Indices: 46833159--46833183 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
46833149 TACTCTACTA
46833159 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
46833184 TTAACGAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:46836385 original size:25 final size:25
Alignment explanation
Indices: 46836357--46836407 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
46836347 TAAAAAGCGA
46836357 CATTTCTATTTATCACGTAAATGTT
1 CATTTCTATTTATCACGTAAATGTT
46836382 CATTTCTATTTATCACGTAAATGTT
1 CATTTCTATTTATCACGTAAATGTT
46836407 C
1 C
46836408 CAAGTTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.18, G:0.08, T:0.47
Consensus pattern (25 bp):
CATTTCTATTTATCACGTAAATGTT
Found at i:46843259 original size:20 final size:20
Alignment explanation
Indices: 46843234--46843282 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
46843224 TTTATATATC
46843234 AATTAATTTAATAAAATAAA
1 AATTAATTTAATAAAATAAA
*** *
46843254 AATTAAAAAAATAAATTAAA
1 AATTAATTTAATAAAATAAA
*
46843274 ATTTAATTT
1 AATTAATTT
46843283 CGACCCCTAA
Statistics
Matches: 21, Mismatches: 8, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AATTAATTTAATAAAATAAA
Found at i:46849706 original size:13 final size:13
Alignment explanation
Indices: 46849688--46849721 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
46849678 TTCTTTTTTT
*
46849688 TTTTCTTTCTTAC
1 TTTTCTTTATTAC
*
46849701 TTTTCTTTATTAT
1 TTTTCTTTATTAC
46849714 TTTTCTTT
1 TTTTCTTT
46849722 TTAATAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTCTTTATTAC
Found at i:46849706 original size:25 final size:26
Alignment explanation
Indices: 46849668--46849721 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
46849658 GAAGATCGAG
*
46849668 TTTCTTCTTCTTCTTT-TTTTTTTTC
1 TTTCTTCTTCTTCTTTATTATTTTTC
46849693 TTTCTTACTT-TTCTTTATTATTTTTC
1 TTTCTT-CTTCTTCTTTATTATTTTTC
46849719 TTT
1 TTT
46849722 TTAATAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 12 0.46
26 14 0.54
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.78
Consensus pattern (26 bp):
TTTCTTCTTCTTCTTTATTATTTTTC
Found at i:46854027 original size:172 final size:172
Alignment explanation
Indices: 46853741--46854086 Score: 638
Period size: 172 Copynumber: 2.0 Consensus size: 172
46853731 TGACAGAATT
46853741 TGATGACATAAAGCTAATTCGATTGGTTATCACCATAAACACCGTCAAAATGTTTACACCCAAAA
1 TGATGACATAAAGCTAATTCGATTGGTTATCACCATAAACACCGTCAAAATGTTTACACCCAAAA
* *
46853806 CTTGAGCTTTTTAAATGTTATAAATCATAGAATAAGCTGGTTCTTATGCCATGCTCATTGAACTA
66 CTTGAGCATTTTAAATGTTATAAATCATAGAATAAGCTGGTTCTTATGCCATGCTCATTGAAATA
* *
46853871 TAGCACATGCAAGCAAATCCATCATTCAAAGAAACTAAAATG
131 TAGCACATGAAAGCAAATCCATCATGCAAAGAAACTAAAATG
46853913 TGATGACATAAAGCTAATTCGATTGGTTATCACCATAAACACCGTCAAAATGTTTACACCCAAAA
1 TGATGACATAAAGCTAATTCGATTGGTTATCACCATAAACACCGTCAAAATGTTTACACCCAAAA
46853978 CTTGAGCATTTTAAATGTTATAAATCATAGAATAAGCTGGTTCTTATGCCATGCTCATTGAAATA
66 CTTGAGCATTTTAAATGTTATAAATCATAGAATAAGCTGGTTCTTATGCCATGCTCATTGAAATA
* *
46854043 TAGCACATGAAAGCAAATCCATCATGCTAAGAAATTAAAATG
131 TAGCACATGAAAGCAAATCCATCATGCAAAGAAACTAAAATG
46854085 TG
1 TG
46854087 TTGTTCTTAT
Statistics
Matches: 168, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
172 168 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (172 bp):
TGATGACATAAAGCTAATTCGATTGGTTATCACCATAAACACCGTCAAAATGTTTACACCCAAAA
CTTGAGCATTTTAAATGTTATAAATCATAGAATAAGCTGGTTCTTATGCCATGCTCATTGAAATA
TAGCACATGAAAGCAAATCCATCATGCAAAGAAACTAAAATG
Found at i:46869222 original size:24 final size:23
Alignment explanation
Indices: 46869181--46869232 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
46869171 TCAAAGCATA
*
46869181 AATTGATTTTTTTATTAAAAATT
1 AATTTATTTTTTTATTAAAAATT
* *
46869204 TATTTATTTTTATTGTTAAAAATT
1 AATTTATTTTT-TTATTAAAAATT
46869228 AATTT
1 AATTT
46869233 TTGTATGTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (23 bp):
AATTTATTTTTTTATTAAAAATT
Found at i:46869587 original size:25 final size:25
Alignment explanation
Indices: 46869559--46869617 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
46869549 ATCGGTTCTA
**
46869559 TTAAAAATTTTATTGAA-TTTTATTG
1 TTAAAAATTTTA-ACAATTTTTATTG
*
46869584 TTAAAAGTTTTAACAATTTTTATTG
1 TTAAAAATTTTAACAATTTTTATTG
46869609 TTAAAAATT
1 TTAAAAATT
46869618 GATCTCTGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 2 0.07
25 27 0.93
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.53
Consensus pattern (25 bp):
TTAAAAATTTTAACAATTTTTATTG
Found at i:46890549 original size:15 final size:14
Alignment explanation
Indices: 46890530--46890617 Score: 54
Period size: 15 Copynumber: 6.0 Consensus size: 14
46890520 TAATTCATAT
46890530 TTTAATAATAATTA
1 TTTAATAATAATTA
*
46890544 TATTAAAAAT-ATTA
1 T-TTAATAATAATTA
* *
46890558 TTAAATTATATATTA
1 TTTAATAATA-ATTA
* *
46890573 TTTTATTAA-ATTGTA
1 -TTTAATAATAAT-TA
46890588 TTTAATAATAATTA
1 TTTAATAATAATTA
*
46890602 TGTTAAAATATAATTA
1 T-TTAATA-ATAATTA
46890618 AATAAATTAA
Statistics
Matches: 55, Mismatches: 11, Indels: 14
0.69 0.14 0.17
Matches are distributed among these distances:
13 5 0.09
14 17 0.31
15 21 0.38
16 12 0.22
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (14 bp):
TTTAATAATAATTA
Found at i:46894286 original size:58 final size:58
Alignment explanation
Indices: 46894198--46894343 Score: 174
Period size: 58 Copynumber: 2.5 Consensus size: 58
46894188 ATATATTATA
* *
46894198 ATTTTTACT-AATTCATATTTTAATAATAATTATATTAAAA-AT-ATT-ATTAAATTACAT
1 ATTTTTATTAAATT-ATA-TTTAATAATAATTATATTAAAATATAATTAAATAAATTA-AT
* *
46894255 ATTATTTTATTAAATTGTATTTAATAATAATTATGTTAAAATATAATTAAATAAATTAAT
1 A-T-TTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATAAATTAAT
*
46894315 ATTTTTATTCAATTATATTTAATAATAAT
1 ATTTTTATTAAATTATATTTAATAATAAT
46894344 CATTAAAATT
Statistics
Matches: 77, Mismatches: 6, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
57 1 0.01
58 47 0.61
59 11 0.14
60 10 0.13
61 8 0.10
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (58 bp):
ATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATAAATTAAT
Found at i:46894534 original size:16 final size:16
Alignment explanation
Indices: 46894513--46894566 Score: 90
Period size: 16 Copynumber: 3.4 Consensus size: 16
46894503 TGAATTACTG
* *
46894513 ATTACAGCTCTATTTC
1 ATTACACCTCTATTCC
46894529 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
46894545 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
46894561 ATTACA
1 ATTACA
46894567 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.28, C:0.31, G:0.02, T:0.39
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:46908430 original size:29 final size:31
Alignment explanation
Indices: 46908379--46908439 Score: 72
Period size: 29 Copynumber: 2.0 Consensus size: 31
46908369 AAATTGTTAG
* * * *
46908379 TTAGTCCTTATATTTTAATAAAATTTGAAAT
1 TTAGTCCATATATCTTAATAAAAATTAAAAT
46908410 TTAGTCCATATA-CTTAA-AAAAATTAAAAT
1 TTAGTCCATATATCTTAATAAAAATTAAAAT
46908439 T
1 T
46908440 AAATCCTCAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
29 11 0.42
30 4 0.15
31 11 0.42
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.43
Consensus pattern (31 bp):
TTAGTCCATATATCTTAATAAAAATTAAAAT
Found at i:46924766 original size:20 final size:20
Alignment explanation
Indices: 46924743--46924780 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
46924733 ATTTTTTTCC
*
46924743 TAATTTTAATTATTTTTACA
1 TAATATTAATTATTTTTACA
*
46924763 TAATATTAATTTTTTTTA
1 TAATATTAATTATTTTTA
46924781 AAAGTGATGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (20 bp):
TAATATTAATTATTTTTACA
Found at i:46924909 original size:2 final size:2
Alignment explanation
Indices: 46924902--46924946 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
46924892 GGAAATTCTT
46924902 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
46924944 TA T
1 TA T
46924947 TTAATAATTG
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:46926662 original size:31 final size:32
Alignment explanation
Indices: 46926596--46926665 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
46926586 TTTATTCTTT
* **
46926596 AAAATAATAAAAAAAATTAATTTAATTATTTA
1 AAAATAATAAAAAAAATCAATTTAATTATCCA
*
46926628 AAAATAAT-AAAAATATACAATTTAATT-TCCA
1 AAAATAATAAAAAAAAT-CAATTTAATTATCCA
46926659 AAAATAA
1 AAAATAA
46926666 AATTCTGACT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
31 16 0.48
32 17 0.52
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (32 bp):
AAAATAATAAAAAAAATCAATTTAATTATCCA
Found at i:46927733 original size:17 final size:18
Alignment explanation
Indices: 46927700--46927733 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
46927690 ATATTAAAAC
*
46927700 AATAAAATATTAAAATTA
1 AATAAAATATAAAAATTA
46927718 AATAAAA-ATAAAAATT
1 AATAAAATATAAAAATT
46927734 GATGTTTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AATAAAATATAAAAATTA
Found at i:46928506 original size:18 final size:18
Alignment explanation
Indices: 46928464--46928511 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
46928454 CATTCATGAT
*
46928464 AATTCAATTTATTTTAAA
1 AATTCAATTTATTTCAAA
*
46928482 AAATCAA-TTATTTCATAA
1 AATTCAATTTATTTCA-AA
46928500 AATTCAAATTTA
1 AATTC-AATTTA
46928512 AAATCAACAC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 7 0.29
18 12 0.50
19 2 0.08
20 3 0.12
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (18 bp):
AATTCAATTTATTTCAAA
Found at i:46936225 original size:58 final size:58
Alignment explanation
Indices: 46936148--46936314 Score: 230
Period size: 58 Copynumber: 2.9 Consensus size: 58
46936138 GATTATTGTT
* *
46936148 ATTAAATTTTAATAAAATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTA
1 ATTATATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTA
* * *
46936206 ATTATATTTTAACATAATTATTATTAAATACAATTTAAT-AAAATAATATATAATTTA
1 ATTATATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTA
* *
46936263 ATAATATTTTTAATATAATTATTATTAAAATATGAA-TTAATAAAAATTATAA
1 ATTATA-TTTTAATATAATTATTATT-AAATAT-AATTTAATAAAAATAATAA
46936315 TATATAATAT
Statistics
Matches: 95, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
57 22 0.23
58 53 0.56
59 10 0.11
60 10 0.11
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (58 bp):
ATTATATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTA
Found at i:46936311 original size:25 final size:24
Alignment explanation
Indices: 46936283--46936333 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
46936273 TAATATAATT
*
46936283 ATTATTAAAATATGA-ATTAATAAAA
1 ATTA-TAAAATATAATATTAA-AAAA
*
46936308 ATTATAATATATAATATTAAAAAA
1 ATTATAAAATATAATATTAAAAAA
46936332 AT
1 AT
46936334 AATATATAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (24 bp):
ATTATAAAATATAATATTAAAAAA
Found at i:46939453 original size:20 final size:20
Alignment explanation
Indices: 46939428--46939465 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
46939418 ATAATTTTTT
*
46939428 TATAATTGAATAAATAATAA
1 TATAATTGAAAAAATAATAA
*
46939448 TATAATTTAAAAAATAAT
1 TATAATTGAAAAAATAAT
46939466 TAAAATGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (20 bp):
TATAATTGAAAAAATAATAA
Found at i:46940488 original size:20 final size:20
Alignment explanation
Indices: 46940449--46940492 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
46940439 CTCAAACTCA
46940449 TTTTAAATCCATTCATATTAAT
1 TTTTAAAT-CATTCATATT-AT
*
46940471 TTTTAAAT-ATTTATATTAT
1 TTTTAAATCATTCATATTAT
46940490 TTT
1 TTT
46940493 AATTTAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 5 0.24
20 8 0.38
22 8 0.38
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTAAATCATTCATATTAT
Found at i:46940506 original size:30 final size:30
Alignment explanation
Indices: 46940466--46940522 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
46940456 TCCATTCATA
* *
46940466 TTAATTTTTAAATATTTATAT-TATTTTAAT
1 TTAATATTT-AATAATTATATATATTTTAAT
46940496 TTAATATTTAATAATTATATATATTTT
1 TTAATATTTAATAATTATATATATTTT
46940523 TTATTTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 10 0.42
30 14 0.58
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (30 bp):
TTAATATTTAATAATTATATATATTTTAAT
Found at i:46943622 original size:16 final size:15
Alignment explanation
Indices: 46943595--46943647 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 15
46943585 ATCATTGAAA
46943595 TCTCTTTCTCTTTCCC
1 TCTC-TTCTCTTTCCC
*
46943611 TTTCTCTCTCTTTTTCCC
1 --TCTCT-TCTCTTTCCC
46943629 TCTCTTCTCTTTCCC
1 TCTCTTCTCTTTCCC
46943644 TCTC
1 TCTC
46943648 CCTTTCCTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 13 0.41
16 5 0.16
17 1 0.03
18 13 0.41
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (15 bp):
TCTCTTCTCTTTCCC
Found at i:46943626 original size:18 final size:18
Alignment explanation
Indices: 46943595--46943640 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
46943585 ATCATTGAAA
* * *
46943595 TCTCTTTCTCTTTCCCTT
1 TCTCTCTCTTTTTCCCTC
46943613 TCTCTCTCTTTTTCCCTC
1 TCTCTCTCTTTTTCCCTC
46943631 TCT-TCTCTTT
1 TCTCTCTCTTT
46943641 CCCTCTCCCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 7 0.28
18 18 0.72
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (18 bp):
TCTCTCTCTTTTTCCCTC
Found at i:46943664 original size:15 final size:14
Alignment explanation
Indices: 46943598--46943665 Score: 51
Period size: 12 Copynumber: 5.1 Consensus size: 14
46943588 ATTGAAATCT
46943598 CTTT-CTCT-TTCC
1 CTTTCCTCTCTTCC
46943610 CTTTCTCTCTCTT--
1 CTTTC-CTCTCTTCC
*
46943623 -TTTCCCTCTCTTCT
1 CTTT-CCTCTCTTCC
46943637 CTTTCC-CTC-TCC
1 CTTTCCTCTCTTCC
46943649 CTTTCCTCTTCTTCC
1 CTTTCCTC-TCTTCC
46943664 CT
1 CT
46943666 CCGCCTTCTC
Statistics
Matches: 45, Mismatches: 1, Indels: 17
0.71 0.02 0.27
Matches are distributed among these distances:
12 22 0.49
13 5 0.11
14 8 0.18
15 10 0.22
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (14 bp):
CTTTCCTCTCTTCC
Found at i:46944762 original size:51 final size:51
Alignment explanation
Indices: 46944703--46944803 Score: 193
Period size: 51 Copynumber: 2.0 Consensus size: 51
46944693 TTTATTTATG
*
46944703 TCTTCTACATCATTAATAATTAATTGGATGAATCTTTTATTAAAACCATAA
1 TCTTCTACATCATTAATAATTAATTGGATGAATCTTTTATTAAAAACATAA
46944754 TCTTCTACATCATTAATAATTAATTGGATGAATCTTTTATTAAAAACATA
1 TCTTCTACATCATTAATAATTAATTGGATGAATCTTTTATTAAAAACATA
46944804 TTTAGTTAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.40, C:0.13, G:0.06, T:0.42
Consensus pattern (51 bp):
TCTTCTACATCATTAATAATTAATTGGATGAATCTTTTATTAAAAACATAA
Found at i:46961361 original size:53 final size:52
Alignment explanation
Indices: 46961299--46961415 Score: 189
Period size: 53 Copynumber: 2.2 Consensus size: 52
46961289 ATAATAACTT
* * *
46961299 TAACCCTCAATATTTATGTATTGTTTCAATTTAGTATTGATTCTAAAAAAATC
1 TAACCCTCAATATTTATATATTGTTTAAATTTAGCATTGATTCT-AAAAAATC
46961352 TAACCCTCAATATTTATATATTGTTTAAATTTAGCATTGATTCTAAAAAATC
1 TAACCCTCAATATTTATATATTGTTTAAATTTAGCATTGATTCTAAAAAATC
*
46961404 TAACCCTTAATA
1 TAACCCTCAATA
46961416 AATTACACAT
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
52 19 0.32
53 41 0.68
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.42
Consensus pattern (52 bp):
TAACCCTCAATATTTATATATTGTTTAAATTTAGCATTGATTCTAAAAAATC
Found at i:46961435 original size:52 final size:53
Alignment explanation
Indices: 46961299--46961432 Score: 144
Period size: 53 Copynumber: 2.5 Consensus size: 53
46961289 ATAATAACTT
* *** * * *
46961299 TAACCCTCAATATTTATGTATTGTTTCAATTTAGTATTGATTCTAAAAAAATC
1 TAACCCTCAATAATTACACATTGTGTAAATTTAGCATTGATTCTAAAAAAATC
* * * *
46961352 TAACCCTCAATATTTATATATTGTTTAAATTTAGCATTGATTCT-AAAAAATC
1 TAACCCTCAATAATTACACATTGTGTAAATTTAGCATTGATTCTAAAAAAATC
*
46961404 TAACCCTTAATAAATTACACATTGTGTAA
1 TAACCCTCAAT-AATTACACATTGTGTAA
46961433 TTTGGTTAGT
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
52 18 0.25
53 54 0.75
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (53 bp):
TAACCCTCAATAATTACACATTGTGTAAATTTAGCATTGATTCTAAAAAAATC
Found at i:46980185 original size:3 final size:3
Alignment explanation
Indices: 46980179--46980220 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
46980169 AGAAATGATG
46980179 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
46980221 TCGCTAAGCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:46981044 original size:50 final size:45
Alignment explanation
Indices: 46980986--46981076 Score: 112
Period size: 45 Copynumber: 1.9 Consensus size: 45
46980976 TTTTTAAAAT
46980986 GAGTAATATTACTCGAAGGTATCATAAT-TTTTTCACTTTAAAAAAAAAGA
1 GAGTAATATTACTC-AA-GT-T--TAATCTTTTT-ACTTTAAAAAAAAAGA
*
46981036 GAGTAATATTATTCAAGTTTAATCTTTTTACTTTAAAAAAA
1 GAGTAATATTACTCAAGTTTAATCTTTTTACTTTAAAAAAA
46981077 TAAAAAAATA
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
45 16 0.41
46 5 0.13
47 1 0.03
48 2 0.05
49 2 0.05
50 13 0.33
ACGTcount: A:0.43, C:0.09, G:0.10, T:0.38
Consensus pattern (45 bp):
GAGTAATATTACTCAAGTTTAATCTTTTTACTTTAAAAAAAAAGA
Found at i:46987739 original size:35 final size:35
Alignment explanation
Indices: 46987698--46987770 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
46987688 AATTGATCAA
46987698 ATTCAGAGATTAAATGTGATTTGTTCTATCAATAT
1 ATTCAGAGATTAAATGTGATTTGTTCTATCAATAT
46987733 ATTCAGAGATTAAATGTGATTTGTTCTATCAATAT
1 ATTCAGAGATTAAATGTGATTTGTTCTATCAATAT
46987768 ATT
1 ATT
46987771 ATAAGAGCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.44
Consensus pattern (35 bp):
ATTCAGAGATTAAATGTGATTTGTTCTATCAATAT
Found at i:46995125 original size:45 final size:45
Alignment explanation
Indices: 46995061--46995147 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
46995051 CCACAATCAA
* *
46995061 ATGCTTGACAAACATATAAGAAAAAAGGAGACAGTAGGTTGAAAG
1 ATGCTTAACAAACATATAAGAAAAAAGGAAACAGTAGGTTGAAAG
*
46995106 ATGCTTAACAAACATATAAGAAAAAGGGAAACAGTAGGTTGA
1 ATGCTTAACAAACATATAAGAAAAAAGGAAACAGTAGGTTGA
46995148 GGAAAGGAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.49, C:0.09, G:0.23, T:0.18
Consensus pattern (45 bp):
ATGCTTAACAAACATATAAGAAAAAAGGAAACAGTAGGTTGAAAG
Found at i:47000686 original size:79 final size:80
Alignment explanation
Indices: 47000594--47000758 Score: 246
Period size: 79 Copynumber: 2.1 Consensus size: 80
47000584 TAAATATACA
* *
47000594 AAAATA-ACACAAATGTACTAAGTATCCGATATCAAACTTTATAC-AAATGCAAACCACCATT-A
1 AAAATATACACAAATGTACTAAGTATCCAATATCAAACTTTATACAAAATGCAAAACACC-TTCA
47000656 ACACTACTATCACATG
65 ACACTACTATCACATG
* * *
47000672 AAAATATACACAAATGTACTAATTATCCAATATCAAGCTTTATACAAAATGTAAAACACCTTCAA
1 AAAATATACACAAATGTACTAAGTATCCAATATCAAACTTTATACAAAATGCAAAACACCTTCAA
*
47000737 CATTACTATCACATG
66 CACTACTATCACATG
47000752 AAAATAT
1 AAAATAT
47000759 GCAAAAATAA
Statistics
Matches: 78, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
78 6 0.08
79 37 0.47
80 35 0.45
ACGTcount: A:0.47, C:0.21, G:0.05, T:0.27
Consensus pattern (80 bp):
AAAATATACACAAATGTACTAAGTATCCAATATCAAACTTTATACAAAATGCAAAACACCTTCAA
CACTACTATCACATG
Found at i:47011555 original size:31 final size:31
Alignment explanation
Indices: 47011517--47011575 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
47011507 AACTTAAAAA
47011517 AAAAAGTGACAAATTT-AGGTACCAAATTAGG
1 AAAAAGTGACAAATTTGA-GTACCAAATTAGG
* *
47011548 AAAAAGTGTCAAGTTTGAGTACCAAATT
1 AAAAAGTGACAAATTTGAGTACCAAATT
47011576 GGACCAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 24 0.96
32 1 0.04
ACGTcount: A:0.46, C:0.10, G:0.19, T:0.25
Consensus pattern (31 bp):
AAAAAGTGACAAATTTGAGTACCAAATTAGG
Found at i:47011612 original size:92 final size:92
Alignment explanation
Indices: 47011439--47011612 Score: 242
Period size: 92 Copynumber: 1.9 Consensus size: 92
47011429 TTAAAAAAGA
* * **
47011439 TTAGGTACTAAATTAGGAAAAAGAGTCAAGTTCAGGTACTAAATTGGACCCCAAAAAGTTTAAGT
1 TTAGGTACCAAATTAGGAAAAAGAGTCAAGTTCAGGTACCAAATTGGACCAAAAAAAGTTTAAGT
* *
47011504 ATCAACTTAAAAAAAAAAGTGACAAAT
66 ACCAAATTAAAAAAAAAAGTGACAAAT
* *
47011531 TTAGGTACCAAATTAGGAAAAAGTGTCAAGTT-TGAGTACCAAATTGGACCAAAAAAAAGTTTAA
1 TTAGGTACCAAATTAGGAAAAAGAGTCAAGTTCAG-GTACCAAATTGGACC-AAAAAAAGTTTAA
*
47011595 GTACCAAATTAAGAAAAA
64 GTACCAAATTAAAAAAAA
47011613 TGTCAAGTTC
Statistics
Matches: 71, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
91 1 0.01
92 44 0.62
93 26 0.37
ACGTcount: A:0.48, C:0.11, G:0.17, T:0.24
Consensus pattern (92 bp):
TTAGGTACCAAATTAGGAAAAAGAGTCAAGTTCAGGTACCAAATTGGACCAAAAAAAGTTTAAGT
ACCAAATTAAAAAAAAAAGTGACAAAT
Found at i:47011627 original size:30 final size:30
Alignment explanation
Indices: 47011530--47011633 Score: 106
Period size: 30 Copynumber: 3.5 Consensus size: 30
47011520 AAGTGACAAA
*
47011530 TTTAGGTACCAAATTAGGAAAAAGTGTCAAG
1 TTTAAGTACCAAATTAGGAAAAA-TGTCAAG
* **
47011561 TTTGAGTACCAAATT-GGACCAAAA--AAAAG
1 TTTAAGTACCAAATTAGGA--AAAATGTCAAG
*
47011590 TTTAAGTACCAAATTAAGAAAAATGTCAAG
1 TTTAAGTACCAAATTAGGAAAAATGTCAAG
*
47011620 TTCAAGTACCAAAT
1 TTTAAGTACCAAAT
47011634 ATTGATAAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
28 4 0.07
29 17 0.29
30 21 0.36
31 13 0.22
32 4 0.07
ACGTcount: A:0.46, C:0.12, G:0.16, T:0.25
Consensus pattern (30 bp):
TTTAAGTACCAAATTAGGAAAAATGTCAAG
Found at i:47016161 original size:18 final size:18
Alignment explanation
Indices: 47016138--47016175 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
47016128 AAACTTTATT
47016138 TTAA-TTTATTTATACATA
1 TTAATTTTA-TTATACATA
47016156 TTAATTTTATTATACATA
1 TTAATTTTATTATACATA
47016174 TT
1 TT
47016176 TTATTACTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (18 bp):
TTAATTTTATTATACATA
Found at i:47019480 original size:188 final size:190
Alignment explanation
Indices: 47019141--47019484 Score: 453
Period size: 188 Copynumber: 1.8 Consensus size: 190
47019131 TTTTGGTTAT
* * * * * *
47019141 TCATGTATTCTTTTCTTATTTGTGTATCTTCTCGTATTATAGCCGTGCTTAAAATTATTTTATAT
1 TCATGTATTCTTTTCGTATTTGTGTATCTTCTCGTACTATAACCGCGCTTAAAAGTATTCTATAT
* ** *
47019206 TTATATAGAACTTATGATAAGTTAAAAGTGGATTGGATTTGTTTGGTTATATGTGTATTCTTTTT
66 TTATATACAACTTATGATAAGTTAAAAGTGGATTGGATTTACTTGGTTATATATGTATTCTTTTT
* *
47019271 GTGCTTGTGTAACTTCTCGTATTATAGTCATGCTGAATGCATTTATATTTATTTAACTTA
131 GTACTTGTGTAACTGCTCGTATTATAGTCATGCTGAATGCATTTATATTTATTTAACTTA
* ** *
47019331 TCATGTATTCTTTTTCGTATTTGTGTATCTTCTCGTACTGTAATTGCGCTT-AAGGTATTCTATA
1 TCATGTATTC-TTTTCGTATTTGTGTATCTTCTCGTACTATAACCGCGCTTAAAAGTATTCTATA
* * *
47019395 -TT-T-TACAACTTTTGATAAGTTAACAGTGGATTGGATTTACTTGGTTTGTATATGTATTCTTT
65 TTTATATACAACTTATGATAAGTTAAAAGTGGATTGGATTTACTTGG-TTATATATGTATTCTTT
* *
47019457 TTGTATTTGTGTATCTGCTCGTATTATA
129 TTGTACTTGTGTAACTGCTCGTATTATA
47019485 ATTGTACTCA
Statistics
Matches: 131, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
187 36 0.27
188 40 0.31
189 2 0.02
190 20 0.15
191 33 0.25
ACGTcount: A:0.23, C:0.11, G:0.16, T:0.50
Consensus pattern (190 bp):
TCATGTATTCTTTTCGTATTTGTGTATCTTCTCGTACTATAACCGCGCTTAAAAGTATTCTATAT
TTATATACAACTTATGATAAGTTAAAAGTGGATTGGATTTACTTGGTTATATATGTATTCTTTTT
GTACTTGTGTAACTGCTCGTATTATAGTCATGCTGAATGCATTTATATTTATTTAACTTA
Found at i:47019562 original size:112 final size:112
Alignment explanation
Indices: 47019328--47019642 Score: 438
Period size: 112 Copynumber: 2.8 Consensus size: 112
47019318 TTTATTTAAC
* * *
47019328 TTAT-CATGTATTCTTTTTCGTATTTGTGTATCTTCTCGTACTGTAATTGCGCTTAAGGTATTCT
1 TTATACATGTATTCTTTTT-GTATTTGTGTATCTTCTCGTAATATAATTGTGCTTAAGGTATT-T
*
47019392 ATATTT-TACAACTTTTGATAAGTTAACAGTGGATTGGATTTACTTGGT
64 ATATTTATAGAACTTTTGATAAGTTAACAGTGGATTGGATTTACTTGGT
* * * * * *
47019440 TTGTATATGTATTCTTTTTGTATTTGTGTATCTGCTCGTATTATAATTGTACTCAAGGTATGTTA
1 TTATACATGTATTCTTTTTGTATTTGTGTATCTTCTCGTAATATAATTGTGCTTAAGGTAT-TTA
* *
47019505 TATTTATAGAACTTTTGATAAGTTAACAGTGGATTTGATTTATTTGG-
65 TATTTATAGAACTTTTGATAAGTTAACAGTGGATTGGATTTACTTGGT
* *
47019552 TTATACATGTATTCTTTTCGTGTTTGTGTATCTTCTCGTAATATAATTGTGCTTAAGGTATTTTA
1 TTATACATGTATTCTTTTTGTATTTGTGTATCTTCTCGTAATATAATTGTGCTTAAGGTA-TTTA
*
47019617 TATTTATAGAACTTTGGATAAGTTAA
65 TATTTATAGAACTTTTGATAAGTTAA
47019643 TGAATCGTGT
Statistics
Matches: 179, Mismatches: 20, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
112 126 0.70
113 53 0.30
ACGTcount: A:0.24, C:0.10, G:0.17, T:0.49
Consensus pattern (112 bp):
TTATACATGTATTCTTTTTGTATTTGTGTATCTTCTCGTAATATAATTGTGCTTAAGGTATTTAT
ATTTATAGAACTTTTGATAAGTTAACAGTGGATTGGATTTACTTGGT
Found at i:47022958 original size:16 final size:18
Alignment explanation
Indices: 47022926--47022960 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
47022916 AAGGTTATGG
47022926 ATAAAAAATGAACATTAT
1 ATAAAAAATGAACATTAT
47022944 ATAAAAAAT-AA-ATTAT
1 ATAAAAAATGAACATTAT
47022960 A
1 A
47022961 CTGAGAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 2 0.12
18 9 0.53
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (18 bp):
ATAAAAAATGAACATTAT
Found at i:47026585 original size:33 final size:33
Alignment explanation
Indices: 47026541--47026603 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
47026531 AAGAAACACA
47026541 TGCTTGAATGGGCGAGAATAGAACACATCCTTG
1 TGCTTGAATGGGCGAGAATAGAACACATCCTTG
*
47026574 TGCTTGCATGGGCGAGAATAGAACACATCC
1 TGCTTGAATGGGCGAGAATAGAACACATCC
47026604 CGCCATGGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.22
Consensus pattern (33 bp):
TGCTTGAATGGGCGAGAATAGAACACATCCTTG
Found at i:47026610 original size:27 final size:29
Alignment explanation
Indices: 47026548--47026612 Score: 71
Period size: 33 Copynumber: 2.2 Consensus size: 29
47026538 ACATGCTTGA
*
47026548 ATGGGCGAGAATAGAACACATCCTTGTGCTTGC
1 ATGGGCGAGAATAGAACACATCC-T-CGC-T-C
47026581 ATGGGCGAGAATAGAACACATCC-CGC-C
1 ATGGGCGAGAATAGAACACATCCTCGCTC
47026608 ATGGG
1 ATGGG
47026613 GCAGGAGCGC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
27 6 0.19
30 2 0.06
33 23 0.74
ACGTcount: A:0.29, C:0.23, G:0.29, T:0.18
Consensus pattern (29 bp):
ATGGGCGAGAATAGAACACATCCTCGCTC
Done.