Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 22 of 190
Found at i:6155085 original size:25 final size:26
Alignment explanation
Indices: 6155033--6155085 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
6155023 TATTATTATA
*
6155033 ATATATAAATGTTATAATAAGTATATT
1 ATATATAAATGTTATAATAAG-ACATT
6155060 ATAT-TAATATGTTATAATAA-ACATT
1 ATATATAA-ATGTTATAATAAGACATT
6155085 A
1 A
6155086 AAAGAAAGCC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 5 0.21
26 3 0.12
27 16 0.67
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (26 bp):
ATATATAAATGTTATAATAAGACATT
Found at i:6156032 original size:43 final size:44
Alignment explanation
Indices: 6155969--6156079 Score: 140
Period size: 43 Copynumber: 2.6 Consensus size: 44
6155959 AGGACTCTGA
*
6155969 TATGTGTTTTCGTGTAAGACCAC-GTCTGGGAC-GTCGGCATCGAC
1 TATGTGTTTACGTGTAAGACCACTGTCTGGGACAGT-GGCATC-AC
*
6156013 T-TGTGTTTACGTGTAAGACC-CTGTCTGGGACAGTGGCATCAG
1 TATGTGTTTACGTGTAAGACCACTGTCTGGGACAGTGGCATCAC
* *
6156055 TATGTGATTACATGTAAGACCACTG
1 TATGTGTTTACGTGTAAGACCACTG
6156080 ATTATCCGTG
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
42 3 0.05
43 50 0.85
44 6 0.10
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.31
Consensus pattern (44 bp):
TATGTGTTTACGTGTAAGACCACTGTCTGGGACAGTGGCATCAC
Found at i:6160793 original size:31 final size:31
Alignment explanation
Indices: 6160755--6160817 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
6160745 TCAGAGGTTC
6160755 GACAGTATTGGCGCAACATTGCAGCAAATCT
1 GACAGTATTGGCGCAACATTGCAGCAAATCT
6160786 GACAGTATTGGCGCAACATTGCAGCAAATCT
1 GACAGTATTGGCGCAACATTGCAGCAAATCT
6160817 G
1 G
6160818 TCAGCATCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.22
Consensus pattern (31 bp):
GACAGTATTGGCGCAACATTGCAGCAAATCT
Found at i:6164999 original size:13 final size:13
Alignment explanation
Indices: 6164961--6165038 Score: 60
Period size: 13 Copynumber: 6.3 Consensus size: 13
6164951 AGCACTTAAA
*
6164961 ATTTATGCATTTT
1 ATTTATACATTTT
*
6164974 ATTT-T-TA-TTT
1 ATTTATACATTTT
6164984 ATTTATACATTTT
1 ATTTATACATTTT
*
6164997 ATTT-TATCAATTT
1 ATTTATA-CATTTT
*
6165010 A-CTATATCA-TTT
1 ATTTATA-CATTTT
6165022 ATTTATACATTTT
1 ATTTATACATTTT
6165035 ATTT
1 ATTT
6165039 TTATTTTATC
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
10 7 0.13
11 2 0.04
12 11 0.21
13 33 0.62
ACGTcount: A:0.28, C:0.08, G:0.01, T:0.63
Consensus pattern (13 bp):
ATTTATACATTTT
Found at i:6165009 original size:22 final size:23
Alignment explanation
Indices: 6164960--6165010 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
6164950 TAGCACTTAA
* *
6164960 AATTTATGCATTTTATTTTTATT
1 AATTTATACATTTTATTTTTATC
*
6164983 TATTTATACATTTTA-TTTTATC
1 AATTTATACATTTTATTTTTATC
6165005 AATTTA
1 AATTTA
6165011 CTATATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.63
Consensus pattern (23 bp):
AATTTATACATTTTATTTTTATC
Found at i:6165243 original size:16 final size:15
Alignment explanation
Indices: 6165224--6165253 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
6165214 TCTTCATCTA
6165224 TTTATTTATTCATTTG
1 TTTATTTA-TCATTTG
6165240 TTTATTTATCATTT
1 TTTATTTATCATTT
6165254 TAACGTCATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.20, C:0.07, G:0.03, T:0.70
Consensus pattern (15 bp):
TTTATTTATCATTTG
Found at i:6171260 original size:29 final size:29
Alignment explanation
Indices: 6171218--6171302 Score: 115
Period size: 29 Copynumber: 3.0 Consensus size: 29
6171208 CATTGAACCA
*
6171218 ACAGGCTCACTCTTGACACAGATTAACGC
1 ACAGGCTCATTCTTGACACAGATTAACGC
6171247 ACAGGCTCATTCTTGACACAG---AAC-C
1 ACAGGCTCATTCTTGACACAGATTAACGC
*
6171272 AACAGACTCATTCTTGACACAGATTAACGC
1 -ACAGGCTCATTCTTGACACAGATTAACGC
6171302 A
1 A
6171303 TAAATAAACT
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
25 1 0.02
26 23 0.47
29 24 0.49
30 1 0.02
ACGTcount: A:0.34, C:0.29, G:0.15, T:0.21
Consensus pattern (29 bp):
ACAGGCTCATTCTTGACACAGATTAACGC
Found at i:6171283 original size:26 final size:26
Alignment explanation
Indices: 6171212--6171294 Score: 105
Period size: 26 Copynumber: 3.1 Consensus size: 26
6171202 CTTATCCATT
*
6171212 GAACCAACAGGCTCACTCTTGACACA
1 GAACCAACAGGCTCATTCTTGACACA
6171238 GATTAACGC-ACAGGCTCATTCTTGACACA
1 G---AAC-CAACAGGCTCATTCTTGACACA
*
6171267 GAACCAACAGACTCATTCTTGACACA
1 GAACCAACAGGCTCATTCTTGACACA
6171293 GA
1 GA
6171295 TTAACGCATA
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
25 1 0.02
26 25 0.50
29 23 0.46
30 1 0.02
ACGTcount: A:0.35, C:0.30, G:0.16, T:0.19
Consensus pattern (26 bp):
GAACCAACAGGCTCATTCTTGACACA
Found at i:6171711 original size:22 final size:22
Alignment explanation
Indices: 6171686--6171739 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
6171676 CTCAAATCGA
* *
6171686 GCATTTGACCCAAAAAATTAGG
1 GCATTCGAACCAAAAAATTAGG
*
6171708 GCATTCGAACCAAAACATTAGG
1 GCATTCGAACCAAAAAATTAGG
6171730 GCATTC-AACC
1 GCATTCGAACC
6171740 CTTGCATATC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 4 0.14
22 25 0.86
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (22 bp):
GCATTCGAACCAAAAAATTAGG
Found at i:6184343 original size:19 final size:18
Alignment explanation
Indices: 6184320--6184365 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
6184310 TAATTTAGCC
*
6184320 ATTTTTATTTCTATTATA
1 ATTTTTATTTCTAGTATA
6184338 ATTTTTATTTCTAGTATA
1 ATTTTTATTTCTAGTATA
*
6184356 AATTTTATTT
1 ATTTTTATTT
6184366 TGTTTTTAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.65
Consensus pattern (18 bp):
ATTTTTATTTCTAGTATA
Found at i:6184375 original size:23 final size:23
Alignment explanation
Indices: 6184340--6184385 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
6184330 CTATTATAAT
6184340 TTTTATTTCTAGTATAAATTTTA
1 TTTTATTTCTAGTATAAATTTTA
* * * *
6184363 TTTTGTTTTTAGTTTAATTTTTA
1 TTTTATTTCTAGTATAAATTTTA
6184386 CATTCTAATC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.67
Consensus pattern (23 bp):
TTTTATTTCTAGTATAAATTTTA
Found at i:6188323 original size:6 final size:6
Alignment explanation
Indices: 6188314--6188380 Score: 59
Period size: 6 Copynumber: 11.3 Consensus size: 6
6188304 TTTGTTTTCT
* * * *
6188314 TTTTAG TTTTAG TTTTA- TTTTA- TGTCTA- TGATTAT TTTTAT TTTTAG
1 TTTTAG TTTTAG TTTTAG TTTTAG T-TTTAG T-TTTAG TTTTAG TTTTAG
6188361 TTTTAG TTTTAG TTTTAG TT
1 TTTTAG TTTTAG TTTTAG TT
6188381 GTTTTATTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
5 6 0.11
6 47 0.87
7 1 0.02
ACGTcount: A:0.18, C:0.01, G:0.12, T:0.69
Consensus pattern (6 bp):
TTTTAG
Found at i:6188391 original size:6 final size:6
Alignment explanation
Indices: 6188308--6188396 Score: 54
Period size: 6 Copynumber: 14.5 Consensus size: 6
6188298 ATTTTATTTG
* * * * * **
6188308 TTTTCT TTTTAG TTTTAG TTTTA- TTTTAT GTCTAT GATTAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
* * *
6188355 TTTTAG TTTTAG TTTTAG TTTTAGTT GTTTTAT TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTA--T -TTTTAT TTTTAT TTT
6188397 CTTAGACTTA
Statistics
Matches: 69, Mismatches: 10, Indels: 8
0.79 0.11 0.09
Matches are distributed among these distances:
5 5 0.07
6 58 0.84
7 1 0.01
9 5 0.07
ACGTcount: A:0.16, C:0.02, G:0.10, T:0.72
Consensus pattern (6 bp):
TTTTAT
Found at i:6189996 original size:22 final size:23
Alignment explanation
Indices: 6189970--6190016 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
6189960 TTCCTAATGA
* *
6189970 ATGGCTCTC-CGAGCTTCCCGAT
1 ATGGCTCGCTCGAACTTCCCGAT
*
6189992 ATGGCTCGCTTGAACTTCCCGAT
1 ATGGCTCGCTCGAACTTCCCGAT
6190015 AT
1 AT
6190017 ATGGCTATCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.17, C:0.32, G:0.21, T:0.30
Consensus pattern (23 bp):
ATGGCTCGCTCGAACTTCCCGAT
Found at i:6190034 original size:25 final size:23
Alignment explanation
Indices: 6189980--6190035 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
6189970 ATGGCTCTCC
* *
6189980 GAGCTTCCCGATATGGCTCGCTT
1 GAGCTTCCCGATATGGCTAGCTG
* *
6190003 GAACTTCCCGATATATGGCTATCTG
1 GAGCTTCCCG--ATATGGCTAGCTG
6190028 GAGCTTCC
1 GAGCTTCC
6190036 TGATTAATGG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 9 0.35
25 17 0.65
ACGTcount: A:0.18, C:0.29, G:0.23, T:0.30
Consensus pattern (23 bp):
GAGCTTCCCGATATGGCTAGCTG
Found at i:6193328 original size:30 final size:30
Alignment explanation
Indices: 6193292--6193380 Score: 142
Period size: 30 Copynumber: 3.0 Consensus size: 30
6193282 AGCTTCAGGG
* *
6193292 GCCACACGGGTTGGGCACATGCCCATGTGA
1 GCCACACGGGCTGGCCACATGCCCATGTGA
* *
6193322 GCCACACGGGCTGGCCATACGCCCATGTGA
1 GCCACACGGGCTGGCCACATGCCCATGTGA
6193352 GCCACACGGGCTGGCCACATGCCCATGTG
1 GCCACACGGGCTGGCCACATGCCCATGTG
6193381 CTAGCCCGTT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.19, C:0.35, G:0.31, T:0.15
Consensus pattern (30 bp):
GCCACACGGGCTGGCCACATGCCCATGTGA
Found at i:6204988 original size:14 final size:14
Alignment explanation
Indices: 6204955--6204991 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
6204945 GCATGGTATG
*
6204955 GGTTTATGGGTTTT
1 GGTTTATAGGTTTT
6204969 GG-TTATAGGTTTT
1 GGTTTATAGGTTTT
6204982 GGTTTATAGG
1 GGTTTATAGG
6204992 CAAATGATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.14, C:0.00, G:0.35, T:0.51
Consensus pattern (14 bp):
GGTTTATAGGTTTT
Found at i:6212685 original size:2 final size:2
Alignment explanation
Indices: 6212678--6212702 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6212668 GAGTAAAATT
6212678 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
6212703 GGTTTTTAGA
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:6214835 original size:23 final size:25
Alignment explanation
Indices: 6214800--6214851 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 25
6214790 AAAAGGTAGC
6214800 AAAATAGTGAAAAAAAATAACAA-G
1 AAAATAGTGAAAAAAAATAACAAGG
*
6214824 AAAATAGT-AAAAAAAATAGCAAGG
1 AAAATAGTGAAAAAAAATAACAAGG
6214848 AAAA
1 AAAA
6214852 GCAGCAGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 13 0.50
24 13 0.50
ACGTcount: A:0.71, C:0.04, G:0.13, T:0.12
Consensus pattern (25 bp):
AAAATAGTGAAAAAAAATAACAAGG
Found at i:6215207 original size:19 final size:20
Alignment explanation
Indices: 6215183--6215242 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 20
6215173 ATTCTTTACA
6215183 TTTTATAATTTTTTAC-AAT
1 TTTTATAATTTTTTACTAAT
* *
6215202 TTTTAT-GTTTTTTTCTAAT
1 TTTTATAATTTTTTACTAAT
* *
6215221 TTTTAATAACTTTTTAATAAT
1 TTTT-ATAATTTTTTACTAAT
6215242 T
1 T
6215243 GAATTTTTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
18 7 0.22
19 13 0.41
20 2 0.06
21 10 0.31
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (20 bp):
TTTTATAATTTTTTACTAAT
Found at i:6215543 original size:92 final size:90
Alignment explanation
Indices: 6215322--6215554 Score: 274
Period size: 92 Copynumber: 2.5 Consensus size: 90
6215312 AATTTTTAAT
*
6215322 AAAAGTAGGGGCTTAATTGCTTTTTTTGAAAAGGTTTGAGGGTCTTTTTGATGCATTTTGAAAGA
1 AAAAG-AGGGGCTTAATTGCTTTTTTTGAAAA-GTTTGAGAG-CTTTTTGATGCATTTTGAAAGA
* * *
6215387 TCAAGTGCCTAATTTGAGTGCAAAAAAA
63 TCAAGTACCCAATATGAGTGCAAAAAAA
* * **
6215415 AATA-A-GGGCTTAATTTCTTTTTTTTTTTTAAAGTTTGAGAGCCTTTTTGATGCATTTTGAAAG
1 AAAAGAGGGGCTTAATTGC---TTTTTTTGAAAAGTTTGAGAG-CTTTTTGATGCATTTTGAAAG
*
6215478 TTCAAGTACCCAA-ATGAGTGCAAAAAAA
62 ATCAAGTACCCAATATGAGTGCAAAAAAA
*
6215506 AAAAGCAGGGGCTTAATTGCTTTTTTTGAAAATGTTTGAGTGCTTTTTG
1 AAAAG-AGGGGCTTAATTGCTTTTTTTGAAAA-GTTTGAGAGCTTTTTG
6215555 CACCCTTAAG
Statistics
Matches: 118, Mismatches: 15, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
90 11 0.09
91 35 0.30
92 47 0.40
93 14 0.12
94 11 0.09
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.39
Consensus pattern (90 bp):
AAAAGAGGGGCTTAATTGCTTTTTTTGAAAAGTTTGAGAGCTTTTTGATGCATTTTGAAAGATCA
AGTACCCAATATGAGTGCAAAAAAA
Found at i:6218594 original size:27 final size:26
Alignment explanation
Indices: 6218564--6218619 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
6218554 AGGCTATCCC
6218564 TTCATAATT-CACCACAAAGGCATTCAT
1 TTCAT-ATTGCACCACAAAGGCATTC-T
* *
6218591 TTCATATTGCGCCACAAAGGCTTTCT
1 TTCATATTGCACCACAAAGGCATTCT
6218617 TTC
1 TTC
6218620 TTTCCTGACG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 7 0.27
27 19 0.73
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.34
Consensus pattern (26 bp):
TTCATATTGCACCACAAAGGCATTCT
Found at i:6220700 original size:34 final size:35
Alignment explanation
Indices: 6220568--6220699 Score: 101
Period size: 34 Copynumber: 3.8 Consensus size: 35
6220558 AATATGACGC
* *
6220568 ATTGGCGTTGTGGTGGGATATTGATT-AATGAAGT
1 ATTGGCGTTGTGGCGGGATATTAATTGAATGAAGT
** * * *
6220602 -TCTGGCGTTGTGGCAAGATGTTGATTGAATGATGT
1 AT-TGGCGTTGTGGCGGGATATTAATTGAATGAAGT
** * * *
6220637 ATCAGTGTTGTGGTGGAATGA-TAATTGAA-GAAGT
1 ATTGGCGTTGTGGCGGGAT-ATTAATTGAATGAAGT
*
6220671 ATTGGTGTTGTGGCGGGATATTAATTGAA
1 ATTGGCGTTGTGGCGGGATATTAATTGAA
6220700 GGAGGACTAG
Statistics
Matches: 74, Mismatches: 19, Indels: 10
0.72 0.18 0.10
Matches are distributed among these distances:
33 2 0.03
34 47 0.64
35 24 0.32
36 1 0.01
ACGTcount: A:0.25, C:0.05, G:0.34, T:0.36
Consensus pattern (35 bp):
ATTGGCGTTGTGGCGGGATATTAATTGAATGAAGT
Found at i:6222855 original size:116 final size:123
Alignment explanation
Indices: 6222725--6222965 Score: 363
Period size: 129 Copynumber: 2.0 Consensus size: 123
6222715 ATCATGTGTC
6222725 ATAATTAATTTAATTAAGAGATTCA-T-T-AATAAAA-A-T-AAA-ATAATATTAAGTAAATTAA
1 ATAATTAATTTAATTAAGAGATTCATTATAAATAAAATACTAAAAGATAATATTAAGTAAATTAA
6222783 TAAGAGATAATTAAAATTATTTTGTTGAAGAGAAGATTGATT-AAAAAAAGTGAAATT
66 TAAGAGATAATTAAAATTATTTTGTTGAAGAGAAGATTGATTAAAAAAAAGTGAAATT
6222840 ATAATTTAATTTAATTAAGAGATTCATTAATAAAAATAAAATACTTAAAAGTGATAATATTAAGT
1 ATAA-TTAATTTAATTAAGAGATTCATT-AT--AAATAAAATAC-TAAAA--GATAATATTAAGT
6222905 AAATTAATAAGAGATAATTAAAATTATTTTGTTGAAGAGAAGATTGATTAAAAAAAAGTGA
59 AAATTAATAAGAGATAATTAAAATTATTTTGTTGAAGAGAAGATTGATTAAAAAAAAGTGA
6222966 GAATAATACA
Statistics
Matches: 111, Mismatches: 0, Indels: 15
0.88 0.00 0.12
Matches are distributed among these distances:
115 4 0.04
116 21 0.19
117 1 0.01
119 1 0.01
122 7 0.06
123 1 0.01
125 1 0.01
126 3 0.03
129 61 0.55
130 11 0.10
ACGTcount: A:0.53, C:0.01, G:0.12, T:0.34
Consensus pattern (123 bp):
ATAATTAATTTAATTAAGAGATTCATTATAAATAAAATACTAAAAGATAATATTAAGTAAATTAA
TAAGAGATAATTAAAATTATTTTGTTGAAGAGAAGATTGATTAAAAAAAAGTGAAATT
Found at i:6226208 original size:12 final size:12
Alignment explanation
Indices: 6226191--6226233 Score: 77
Period size: 12 Copynumber: 3.6 Consensus size: 12
6226181 TAAGGGAAGA
6226191 GAGCCCAAGCAT
1 GAGCCCAAGCAT
*
6226203 GAGCCCAAGTAT
1 GAGCCCAAGCAT
6226215 GAGCCCAAGCAT
1 GAGCCCAAGCAT
6226227 GAGCCCA
1 GAGCCCA
6226234 GGTATGTCGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.33, C:0.33, G:0.26, T:0.09
Consensus pattern (12 bp):
GAGCCCAAGCAT
Found at i:6226223 original size:24 final size:24
Alignment explanation
Indices: 6226191--6226239 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
6226181 TAAGGGAAGA
6226191 GAGCCCAAGCATGAGCCCAAGTAT
1 GAGCCCAAGCATGAGCCCAAGTAT
*
6226215 GAGCCCAAGCATGAGCCCAGGTAT
1 GAGCCCAAGCATGAGCCCAAGTAT
6226239 G
1 G
6226240 TCGCCTTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.31, C:0.29, G:0.29, T:0.12
Consensus pattern (24 bp):
GAGCCCAAGCATGAGCCCAAGTAT
Found at i:6232812 original size:19 final size:19
Alignment explanation
Indices: 6232774--6232812 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
6232764 AAATAGTGAG
*
6232774 AATTTATTTTCTAAGTATA
1 AATTTATTTTCTAAGAATA
6232793 AATTCTATTTTCT-AGAATA
1 AATT-TATTTTCTAAGAATA
6232812 A
1 A
6232813 CAATTCTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.49
Consensus pattern (19 bp):
AATTTATTTTCTAAGAATA
Found at i:6235387 original size:13 final size:13
Alignment explanation
Indices: 6235369--6235403 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
6235359 TTTAATTGGG
*
6235369 TAATTAATTTAGT
1 TAATTAATTTAAT
*
6235382 TAATTAAATTAAT
1 TAATTAATTTAAT
6235395 TAATTAATT
1 TAATTAATT
6235404 AATATTTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (13 bp):
TAATTAATTTAAT
Found at i:6237399 original size:43 final size:43
Alignment explanation
Indices: 6237330--6237446 Score: 139
Period size: 43 Copynumber: 2.7 Consensus size: 43
6237320 TTACAAACAA
* **
6237330 AAACGCCGCTAAAGATCATGTTCTTTAGCGACGCTTT-TCCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGACG-TTTCTCCCAC
* **
6237373 AAACGCCGCTAAAGAACATGACCTTTAGCGATGTTTCTTTCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGACGTTTCTCCCAC
* *
6237416 AAACGCCGCAAAAGAACA-AACCTTTAGCGAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGAC
6237447 ACTTGTAGCA
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
42 14 0.22
43 50 0.78
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.23
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGACCTTTAGCGACGTTTCTCCCAC
Found at i:6240262 original size:25 final size:25
Alignment explanation
Indices: 6240234--6240292 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
6240224 ATCTCCCAAC
6240234 AATTGATAAACCAATA-ATATGATCA
1 AATT-ATAAACCAATACATATGATCA
* **
6240259 AATTATAACCCCTTACATATGATCA
1 AATTATAAACCAATACATATGATCA
6240284 AATTATAAA
1 AATTATAAA
6240293 TCACTATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 8 0.28
25 21 0.72
ACGTcount: A:0.49, C:0.15, G:0.05, T:0.31
Consensus pattern (25 bp):
AATTATAAACCAATACATATGATCA
Found at i:6249569 original size:9 final size:9
Alignment explanation
Indices: 6249555--6249579 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
6249545 GAAAACTAAC
6249555 AACTAACTT
1 AACTAACTT
6249564 AACTAACTT
1 AACTAACTT
6249573 AACTAAC
1 AACTAAC
6249580 AACTATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (9 bp):
AACTAACTT
Found at i:6253766 original size:26 final size:27
Alignment explanation
Indices: 6253701--6253763 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
6253691 ATACGTCAGG
*
6253701 AAAGGAAGCCTTTGTGGATAACTCTAA
1 AAAGGAAGCCTTTGTGGACAACTCTAA
* * *
6253728 AAAGAAAGCCTTTGTGGCCAACTTTAA
1 AAAGGAAGCCTTTGTGGACAACTCTAA
6253755 AAAGGAAGC
1 AAAGGAAGC
6253764 TTTCATGGCG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.22
Consensus pattern (27 bp):
AAAGGAAGCCTTTGTGGACAACTCTAA
Found at i:6253772 original size:27 final size:27
Alignment explanation
Indices: 6253701--6253778 Score: 68
Period size: 27 Copynumber: 2.9 Consensus size: 27
6253691 ATACGTCAGG
* * **
6253701 AAAGGAAGCCTTTGTGGATAACTCTAA
1 AAAGAAAGCCTTTATGGCCAACTCTAA
* *
6253728 AAAGAAAGCCTTTGTGGCCAACTTTAA
1 AAAGAAAGCCTTTATGGCCAACTCTAA
* *
6253755 AAAGGAAG-CTTTCATGGCGAACTC
1 AAAGAAAGCCTTT-ATGGCCAACTC
6253779 CAAAGGAATA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
26 4 0.10
27 38 0.90
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (27 bp):
AAAGAAAGCCTTTATGGCCAACTCTAA
Found at i:6264560 original size:15 final size:15
Alignment explanation
Indices: 6264540--6264571 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
6264530 AATTTCACTA
*
6264540 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
6264555 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
6264570 TT
1 TT
6264572 TGCATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:6268061 original size:5 final size:5
Alignment explanation
Indices: 6268047--6268101 Score: 92
Period size: 5 Copynumber: 11.0 Consensus size: 5
6268037 AATATATATA
* *
6268047 TCAAT TCAAT CCAAT TCAAT TCAAT CCAAT TCAAT TCAAT TCAAT TCAAT
1 TCAAT TCAAT TCAAT TCAAT TCAAT TCAAT TCAAT TCAAT TCAAT TCAAT
6268097 TCAAT
1 TCAAT
6268102 AATCAATACA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 46 1.00
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (5 bp):
TCAAT
Found at i:6269413 original size:37 final size:37
Alignment explanation
Indices: 6269372--6269715 Score: 329
Period size: 37 Copynumber: 9.2 Consensus size: 37
6269362 TTGAACAACT
* * *
6269372 TTCAGTATATTTAGTAGACATTGCTCTTTTGAGCATG
1 TTCAGTATAATCAGTAGATATTGCTCTTTTGAGCATG
*
6269409 TTCAGTATAATTAGTAGATATTGCT-TGTTTGAGCAACT-
1 TTCAGTATAATCAGTAGATATTGCTCT-TTTGAGC-A-TG
* * * *
6269447 TTCAATATAATCAGTAGACATTGCTCTTTTAAGCACG
1 TTCAGTATAATCAGTAGATATTGCTCTTTTGAGCATG
*
6269484 TTTAGTATAATCAGTAGATATTGCT-TATTTGAGCAACT-
1 TTCAGTATAATCAGTAGATATTGCTCT-TTTGAGC-A-TG
* * ** *
6269522 TTCAGTATAATCAATAGACATTATTCTTTTGAGCACG
1 TTCAGTATAATCAGTAGATATTGCTCTTTTGAGCATG
* *
6269559 TTCAATATAATCAGTAGATATTGCTCGTTTGAGCAACT-
1 TTCAGTATAATCAGTAGATATTGCTCTTTTGAGC-A-TG
* *
6269597 TTCAGTATAATCAGTAGACATTGCTCTTTTGAGCACG
1 TTCAGTATAATCAGTAGATATTGCTCTTTTGAGCATG
* * * * **
6269634 TCCAGTATAATTAGAAGATATTGCTCGTTTGAGCACA
1 TTCAGTATAATCAGTAGATATTGCTCTTTTGAGCATG
* * * *
6269671 TTCAGTATAATAAGTAGATACTGCTCATTTGAGCATA
1 TTCAGTATAATCAGTAGATATTGCTCTTTTGAGCATG
6269708 TTCAGTAT
1 TTCAGTAT
6269716 TTAATCGATT
Statistics
Matches: 253, Mismatches: 41, Indels: 26
0.79 0.13 0.08
Matches are distributed among these distances:
36 2 0.01
37 159 0.63
38 89 0.35
39 3 0.01
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.38
Consensus pattern (37 bp):
TTCAGTATAATCAGTAGATATTGCTCTTTTGAGCATG
Found at i:6269491 original size:75 final size:75
Alignment explanation
Indices: 6269358--6269715 Score: 484
Period size: 75 Copynumber: 4.8 Consensus size: 75
6269348 ACAATATCGT
* * * * *
6269358 TCGTTTGAACAACTTTCAGTATATTTAGTAGACATTGCTCTTTTGAGCATGTTCAGTATAATTAG
1 TCGTTTGAGCAACTTTCAGTATAATCAGTAGACATTGCTCTTTTGAGCACGTTCAGTATAATCAG
6269423 TAGATATTGC
66 TAGATATTGC
* * * *
6269433 TTGTTTGAGCAACTTTCAATATAATCAGTAGACATTGCTCTTTTAAGCACGTTTAGTATAATCAG
1 TCGTTTGAGCAACTTTCAGTATAATCAGTAGACATTGCTCTTTTGAGCACGTTCAGTATAATCAG
6269498 TAGATATTGC
66 TAGATATTGC
** * ** *
6269508 TTATTTGAGCAACTTTCAGTATAATCAATAGACATTATTCTTTTGAGCACGTTCAATATAATCAG
1 TCGTTTGAGCAACTTTCAGTATAATCAGTAGACATTGCTCTTTTGAGCACGTTCAGTATAATCAG
6269573 TAGATATTGC
66 TAGATATTGC
* *
6269583 TCGTTTGAGCAACTTTCAGTATAATCAGTAGACATTGCTCTTTTGAGCACGTCCAGTATAATTAG
1 TCGTTTGAGCAACTTTCAGTATAATCAGTAGACATTGCTCTTTTGAGCACGTTCAGTATAATCAG
*
6269648 AAGATATTGC
66 TAGATATTGC
* * * * * **
6269658 TCGTTTGAGC-ACATTCAGTATAATAAGTAGATACTGCTCATTTGAGCATATTCAGTAT
1 TCGTTTGAGCAACTTTCAGTATAATCAGTAGACATTGCTCTTTTGAGCACGTTCAGTAT
6269716 TTAATCGATT
Statistics
Matches: 249, Mismatches: 34, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
74 40 0.16
75 209 0.84
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.38
Consensus pattern (75 bp):
TCGTTTGAGCAACTTTCAGTATAATCAGTAGACATTGCTCTTTTGAGCACGTTCAGTATAATCAG
TAGATATTGC
Found at i:6273481 original size:37 final size:39
Alignment explanation
Indices: 6273440--6273535 Score: 98
Period size: 37 Copynumber: 2.6 Consensus size: 39
6273430 ATATTATTTT
6273440 AATAGTTTAATATTAAATTTAAT-TT-AA-T-ACTTATCTA
1 AATAGTTTAATATT-AATTTAATATTAAAGTGA-TTATCTA
* *
6273477 AATAGTATT-CTATTAATTTAATATTAAAGTGATTATCTT
1 AATAGT-TTAATATTAATTTAATATTAAAGTGATTATCTA
6273516 AATA-TTTAAT-TTAATTTAAT
1 AATAGTTTAATATTAATTTAAT
6273536 GTTTATCTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
36 8 0.16
37 24 0.48
38 6 0.12
39 11 0.22
40 1 0.02
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (39 bp):
AATAGTTTAATATTAATTTAATATTAAAGTGATTATCTA
Found at i:6273589 original size:62 final size:59
Alignment explanation
Indices: 6273514--6273630 Score: 153
Period size: 62 Copynumber: 1.9 Consensus size: 59
6273504 AGTGATTATC
* * * * * *
6273514 TTAATATTTAATTTAATTTAATGTTTATCTTGTAGATAAATATTCTATTATTTTAATAAGAT
1 TTAATATTAAATTTAATCTAATATTTATC-T-TA-ATAAACATTATATTAATTTAATAAGAT
6273576 TTAATATTAAATTTAATCTAATATTTATCTTAATAAACATTATATTAATTTAATA
1 TTAATATTAAATTTAATCTAATATTTATCTTAATAAACATTATATTAATTTAATA
6273631 TTAAAGTCAT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
59 20 0.41
60 2 0.04
61 1 0.02
62 26 0.53
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.51
Consensus pattern (59 bp):
TTAATATTAAATTTAATCTAATATTTATCTTAATAAACATTATATTAATTTAATAAGAT
Found at i:6277043 original size:45 final size:45
Alignment explanation
Indices: 6276974--6277074 Score: 148
Period size: 45 Copynumber: 2.2 Consensus size: 45
6276964 GATGTGTTCG
* * *
6276974 TATAACAGGTTTGGATATCGTAAATGAGCTTACACACGTCCAACC
1 TATAACAGATCTGGATATCATAAATGAGCTTACACACGTCCAACC
* * *
6277019 TATAACAGATCTGGATATCATAAATGGGCTTGCACATGTCCAACC
1 TATAACAGATCTGGATATCATAAATGAGCTTACACACGTCCAACC
6277064 TATAACAGATC
1 TATAACAGATC
6277075 ACTCTTATTT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.27
Consensus pattern (45 bp):
TATAACAGATCTGGATATCATAAATGAGCTTACACACGTCCAACC
Found at i:6277690 original size:25 final size:25
Alignment explanation
Indices: 6277651--6277707 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
6277641 TGCAAATTTT
6277651 TTAAGAATTACAAAAAGTTAT-AAAAA
1 TTAA-AATTAC-AAAAGTTATCAAAAA
* *
6277677 TTAAAATTATAAAATTTATCAAAAA
1 TTAAAATTACAAAAGTTATCAAAAA
*
6277702 TAAAAA
1 TTAAAA
6277708 ATGTTTATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 8 0.30
25 15 0.56
26 4 0.15
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.30
Consensus pattern (25 bp):
TTAAAATTACAAAAGTTATCAAAAA
Found at i:6285075 original size:22 final size:22
Alignment explanation
Indices: 6285041--6285110 Score: 104
Period size: 22 Copynumber: 3.2 Consensus size: 22
6285031 AAATTCAATA
*
6285041 TCAATTTCATTAAAAAATTCTC
1 TCAATTTCCTTAAAAAATTCTC
*
6285063 TCAATTCCCTTAAAAAATTCTC
1 TCAATTTCCTTAAAAAATTCTC
**
6285085 TCAATTTCCTTCCAAAATTCTC
1 TCAATTTCCTTAAAAAATTCTC
6285107 TCAA
1 TCAA
6285111 ACTCTCAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.36, C:0.26, G:0.00, T:0.39
Consensus pattern (22 bp):
TCAATTTCCTTAAAAAATTCTC
Found at i:6285116 original size:30 final size:30
Alignment explanation
Indices: 6285082--6285141 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
6285072 TTAAAAAATT
* *
6285082 CTCTCAATTTCCTTCCAAAATTCTCTCAAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAAA
*
6285112 CTCTCAAATTCCTTCCAAAATCCTTTCAAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAAA
6285142 TTCCTTCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.32, C:0.33, G:0.00, T:0.35
Consensus pattern (30 bp):
CTCTCAAATTCCTTCCAAAATCCTCTCAAA
Found at i:6285378 original size:14 final size:15
Alignment explanation
Indices: 6285349--6285382 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
6285339 AAATTTTAAA
6285349 TTTTATTTAAGATAT
1 TTTTATTTAAGATAT
*
6285364 TTTTATTTATG-TAT
1 TTTTATTTAAGATAT
6285378 TTTTA
1 TTTTA
6285383 GATATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TTTTATTTAAGATAT
Found at i:6287568 original size:23 final size:23
Alignment explanation
Indices: 6287542--6287682 Score: 183
Period size: 23 Copynumber: 5.7 Consensus size: 23
6287532 AACCCTAACT
6287542 CTAACCTAATTTAATTAAAAACC
1 CTAACCTAATTTAATTAAAAACC
6287565 CTAACCTAATTTAATTTAATTAAAAACC
1 CTAACC-----TAATTTAATTAAAAACC
6287593 CTAACCTAACTTAATTTAATTAAAAACC
1 CTAA-C---C-TAATTTAATTAAAAACC
6287621 CTAACCTAATTTAATTAAAAACC
1 CTAACCTAATTTAATTAAAAACC
*
6287644 CTAACCTAACTTAATTAAAAACC
1 CTAACCTAATTTAATTAAAAACC
6287667 CTAACCTAATTTAATT
1 CTAACCTAATTTAATT
6287683 TAATTAAAAA
Statistics
Matches: 107, Mismatches: 2, Indels: 18
0.84 0.02 0.14
Matches are distributed among these distances:
23 60 0.56
24 1 0.01
27 1 0.01
28 43 0.40
29 1 0.01
32 1 0.01
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (23 bp):
CTAACCTAATTTAATTAAAAACC
Found at i:6287601 original size:33 final size:28
Alignment explanation
Indices: 6287521--6287711 Score: 249
Period size: 28 Copynumber: 7.1 Consensus size: 28
6287511 TTTTGACATT
* *
6287521 ATTTGATTAAAAACCCTAACTCTAACCTA
1 ATTTAATTAAAAACCCTAAC-CTAACTTA
*
6287550 ATTTAATTAAAAACCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
6287578 ATTTAATTAAAAACCCTAACCTAACTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
6287606 ATTTAATTAAAAACCCTAA-C---C-TA
1 ATTTAATTAAAAACCCTAACCTAACTTA
6287629 ATTTAATTAAAAACCCTAACCTAAC---
1 ATTTAATTAAAAACCCTAACCTAACTTA
*
6287654 --TTAATTAAAAACCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
*
6287680 ATTTAATTAAAAACCCTAACCCTAACCTA
1 ATTTAATTAAAAACCCTAA-CCTAACTTA
6287709 ATT
1 ATT
6287712 GACTGGCTGT
Statistics
Matches: 145, Mismatches: 7, Indels: 20
0.84 0.04 0.12
Matches are distributed among these distances:
23 43 0.30
24 2 0.01
27 2 0.01
28 69 0.48
29 29 0.20
ACGTcount: A:0.46, C:0.22, G:0.01, T:0.32
Consensus pattern (28 bp):
ATTTAATTAAAAACCCTAACCTAACTTA
Found at i:6287624 original size:51 final size:51
Alignment explanation
Indices: 6287521--6287711 Score: 210
Period size: 51 Copynumber: 3.6 Consensus size: 51
6287511 TTTTGACATT
*
6287521 ATTTGATTAAAAACCCTAACTCTAACCTAATTTAATTAAAAACCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAAC-CTAACCTAATTTAATTAAAAA--C---CCTAATTTA
* **
6287578 ATTTAATTAAAAACCCTAACCTAACTTAATTTAATTAAAAACCCTAACCTA
1 ATTTAATTAAAAACCCTAACCTAACCTAATTTAATTAAAAACCCTAATTTA
*
6287629 ATTTAATTAAAAACCCTAACCTAACTTAA-TTAA--AAACCCTAA-CCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAACCTAATTTAATTAAA----AACCCTAATTTA
6287680 ATTTAATTAAAAACCCTAACCCTAACCTAATT
1 ATTTAATTAAAAACCCTAA-CCTAACCTAATT
6287712 GACTGGCTGT
Statistics
Matches: 121, Mismatches: 7, Indels: 16
0.84 0.05 0.11
Matches are distributed among these distances:
48 3 0.02
50 4 0.03
51 62 0.51
52 11 0.09
53 1 0.01
54 1 0.01
56 20 0.17
57 19 0.16
ACGTcount: A:0.46, C:0.22, G:0.01, T:0.32
Consensus pattern (51 bp):
ATTTAATTAAAAACCCTAACCTAACCTAATTTAATTAAAAACCCTAATTTA
Found at i:6287697 original size:23 final size:23
Alignment explanation
Indices: 6287569--6287698 Score: 125
Period size: 23 Copynumber: 5.2 Consensus size: 23
6287559 AAAACCCTAA
6287569 CCTAATTTAATTTAATTAAAAAC
1 CCTAATTTAATTTAATTAAAAAC
6287592 CCTAACCTAACTTAATTTAATTAAAAAC
1 CCTAA--T---TTAATTTAATTAAAAAC
**
6287620 CCTAACCTAATTTAATTAAAAAC
1 CCTAATTTAATTTAATTAAAAAC
** *
6287643 CCTAACCTAACTTAATTAAAAACCC
1 CCTAATTTAATTTAATTAAAAA--C
6287668 TAACCTAATTTAATTTAATTAAAAAC
1 ---CCTAATTTAATTTAATTAAAAAC
6287694 CCTAA
1 CCTAA
6287699 CCCTAACCTA
Statistics
Matches: 91, Mismatches: 6, Indels: 20
0.78 0.05 0.17
Matches are distributed among these distances:
23 47 0.52
25 2 0.02
26 1 0.01
28 41 0.45
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (23 bp):
CCTAATTTAATTTAATTAAAAAC
Found at i:6290876 original size:125 final size:124
Alignment explanation
Indices: 6290655--6290899 Score: 375
Period size: 125 Copynumber: 2.0 Consensus size: 124
6290645 CTCGAGGGCA
*
6290655 CGATTTGACACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCCTACATGACCAACTGTAGCGA
1 CGATTTGACACTATTTGCTCAGAAAAGTCAAAAAAAATTATTTCCTACATGACCAACTGTAGCGA
* * * *
6290720 TATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCATATAGCATCCTGGTATCAG
66 AATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTATCAG
* * *
6290779 CGATTTTATACTATTTGCTCAGTAAAAGTCAAAAAAAAATTATTTCTTACATGACC-ACTGTAGC
1 CGATTTGACACTATTTGCTCAG-AAAAGTC-AAAAAAAATTATTTCCTACATGACCAACTGTAGC
* *
6290843 GAAATCGCGTCCACGAGGCCACTATTTCACAATTTTTTCTCAAATAGCATCCTGGTA
64 GAAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTA
6290900 GAAGCGGTTT
Statistics
Matches: 109, Mismatches: 10, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
124 20 0.18
125 65 0.60
126 24 0.22
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (124 bp):
CGATTTGACACTATTTGCTCAGAAAAGTCAAAAAAAATTATTTCCTACATGACCAACTGTAGCGA
AATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTATCAG
Found at i:6299357 original size:6 final size:6
Alignment explanation
Indices: 6299346--6299373 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
6299336 ACAGTGGAGG
6299346 TTTGAC TTTGAC TTTGAC TTTGAC TTTG
1 TTTGAC TTTGAC TTTGAC TTTGAC TTTG
6299374 GTCTCCGCGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.18, T:0.54
Consensus pattern (6 bp):
TTTGAC
Found at i:6303732 original size:22 final size:21
Alignment explanation
Indices: 6303683--6303737 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
6303673 AAATAATAAA
** *
6303683 ATATTAAAAATATATTATTTT
1 ATATTAAATTTATATTATTTG
6303704 ATATTAATATTTATA-TATTTG
1 ATATTAA-ATTTATATTATTTG
6303725 ATATTTAAATTTA
1 ATA-TTAAATTTA
6303738 AAATAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 20 0.69
22 9 0.31
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
ATATTAAATTTATATTATTTG
Found at i:6303939 original size:29 final size:30
Alignment explanation
Indices: 6303898--6303976 Score: 97
Period size: 29 Copynumber: 2.6 Consensus size: 30
6303888 AATTAAATCA
* * *
6303898 AATCAAAATTTCAAGTATAAATTTATACA-T
1 AATC-AAATTTCATGTATAAAATTACACATT
*
6303928 AATCAAAGTTCATGTATAAAATTACACATT
1 AATCAAATTTCATGTATAAAATTACACATT
6303958 AGATCAAATTTCATGTATA
1 A-ATCAAATTTCATGTATA
6303977 TTTTTGAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 20 0.48
30 6 0.14
31 16 0.38
ACGTcount: A:0.47, C:0.11, G:0.06, T:0.35
Consensus pattern (30 bp):
AATCAAATTTCATGTATAAAATTACACATT
Found at i:6304058 original size:20 final size:21
Alignment explanation
Indices: 6304016--6304059 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
6304006 GTATGTTTTA
*
6304016 ATATTTACATTGTAATACTAT
1 ATATTTACATTGTAATACAAT
* *
6304037 ATATTTA-ATTTTTATACAAT
1 ATATTTACATTGTAATACAAT
6304057 ATA
1 ATA
6304060 AAATACATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (21 bp):
ATATTTACATTGTAATACAAT
Found at i:6305795 original size:11 final size:11
Alignment explanation
Indices: 6305779--6305803 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
6305769 GTCACCAGCG
6305779 GGTTGGATAAA
1 GGTTGGATAAA
6305790 GGTTGGATAAA
1 GGTTGGATAAA
6305801 GGT
1 GGT
6305804 AAACACTAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.40, T:0.28
Consensus pattern (11 bp):
GGTTGGATAAA
Found at i:6314125 original size:33 final size:33
Alignment explanation
Indices: 6314065--6314147 Score: 98
Period size: 33 Copynumber: 2.5 Consensus size: 33
6314055 GCTCATTTTT
*
6314065 AAAATAAATATTAAAAAATTATTTTAAAAAT-A
1 AAAATAAATATTAAAAAAGTATTTTAAAAATAA
** *
6314097 AAAATAAATTATTTTAAAAGTATTTTAAAATTAA
1 AAAATAAA-TATTAAAAAAGTATTTTAAAAATAA
*
6314131 AAAATAAA-AATAAAAAA
1 AAAATAAATATTAAAAAA
6314148 TATATATTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
32 14 0.33
33 19 0.45
34 9 0.21
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (33 bp):
AAAATAAATATTAAAAAAGTATTTTAAAAATAA
Found at i:6316161 original size:14 final size:14
Alignment explanation
Indices: 6316142--6316169 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6316132 AGCATAACAA
6316142 CTGGATTATATAAT
1 CTGGATTATATAAT
6316156 CTGGATTATATAAT
1 CTGGATTATATAAT
6316170 TTTCTTTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (14 bp):
CTGGATTATATAAT
Found at i:6318043 original size:15 final size:15
Alignment explanation
Indices: 6318025--6318056 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
6318015 TCAATGTCAC
6318025 TACTGCTTTTATGTT
1 TACTGCTTTTATGTT
6318040 TACTGCTTTTATGTT
1 TACTGCTTTTATGTT
6318055 TA
1 TA
6318057 AGTGTTGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.16, C:0.12, G:0.12, T:0.59
Consensus pattern (15 bp):
TACTGCTTTTATGTT
Found at i:6324449 original size:11 final size:11
Alignment explanation
Indices: 6324426--6324463 Score: 53
Period size: 10 Copynumber: 3.6 Consensus size: 11
6324416 GTAAGATGGC
6324426 TTTTCTT-TCT
1 TTTTCTTCTCT
6324436 TTTTCTTCTCT
1 TTTTCTTCTCT
*
6324447 TTTTTTTCT-T
1 TTTTCTTCTCT
6324457 TTTTCTT
1 TTTTCTT
6324464 TTTTCTGTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 14 0.56
11 11 0.44
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTCTTCTCT
Found at i:6324454 original size:14 final size:13
Alignment explanation
Indices: 6324427--6324469 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
6324417 TAAGATGGCT
6324427 TTTCTTTCTTTTTC
1 TTTCTTT-TTTTTC
6324441 TTCTCTTTTTTTTC
1 TT-TCTTTTTTTTC
*
6324455 TTTTTTCTTTTTTC
1 TTTCTT-TTTTTTC
6324469 T
1 T
6324470 GTAGTTGACA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
13 3 0.12
14 18 0.69
15 5 0.19
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTCTTTTTTTTC
Found at i:6326571 original size:12 final size:12
Alignment explanation
Indices: 6326554--6326583 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
6326544 ACAAAATTCG
6326554 AATTTAATTTCC
1 AATTTAATTTCC
*
6326566 AATTTAATTTCT
1 AATTTAATTTCC
6326578 AATTTA
1 AATTTA
6326584 TTTATGCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (12 bp):
AATTTAATTTCC
Found at i:6331654 original size:12 final size:12
Alignment explanation
Indices: 6331637--6331669 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
6331627 ACAAAATCCG
6331637 AATTTAATTTCC
1 AATTTAATTTCC
*
6331649 AATTTAATTTCT
1 AATTTAATTTCC
6331661 AATTTAATT
1 AATTTAATT
6331670 ATTTATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (12 bp):
AATTTAATTTCC
Found at i:6332092 original size:6 final size:6
Alignment explanation
Indices: 6332081--6332105 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
6332071 GCTTTTTTAT
6332081 TTAATA TTAATA TTAATA TTAATA T
1 TTAATA TTAATA TTAATA TTAATA T
6332106 AAAATTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTAATA
Found at i:6332419 original size:30 final size:29
Alignment explanation
Indices: 6332356--6332433 Score: 75
Period size: 30 Copynumber: 2.6 Consensus size: 29
6332346 TAATCTTGTT
* * *
6332356 TAGTTGGATGACCAATTTAAAAAAATTCA
1 TAGTTGGGTGACAAATTTAAAAAAATCCA
* *
6332385 TAGTTGGGTGACAAATTTGAGACAAATCCA
1 TAGTTGGGTGACAAATTT-AAAAAAATCCA
* *
6332415 TAGTTAGGTAATCAAATTT
1 TAGTTGGGTGA-CAAATTT
6332434 TTTTTCTAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 16 0.40
30 17 0.43
31 7 0.17
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.32
Consensus pattern (29 bp):
TAGTTGGGTGACAAATTTAAAAAAATCCA
Found at i:6333872 original size:18 final size:18
Alignment explanation
Indices: 6333845--6333879 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6333835 AGCACCAAAG
6333845 CTTTCATCCTCCTCCTCA
1 CTTTCATCCTCCTCCTCA
* *
6333863 CTTTCTTCCTCTTCCTC
1 CTTTCATCCTCCTCCTC
6333880 TTCTTCATTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.06, C:0.49, G:0.00, T:0.46
Consensus pattern (18 bp):
CTTTCATCCTCCTCCTCA
Found at i:6339388 original size:34 final size:33
Alignment explanation
Indices: 6339283--6339388 Score: 133
Period size: 34 Copynumber: 3.2 Consensus size: 33
6339273 TTTAGTGTTC
* *
6339283 TTTTTT-AAAAATTAATTAAATTAGGGTTTAGG
1 TTTTTTAAAAAATTAATTAAATTTGGGTTTAGT
** *
6339315 AGTTTTAAATTAATTAATTAAATTTGGGTTTAGT
1 TTTTTTAAA-AAATTAATTAAATTTGGGTTTAGT
*
6339349 GTTTTTAAGAAAATTAATTAAATTTGGGTTTAGT
1 TTTTTTAA-AAAATTAATTAAATTTGGGTTTAGT
6339383 TTTTTT
1 TTTTTT
6339389 TAAAGGCATA
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
32 4 0.06
33 2 0.03
34 55 0.89
35 1 0.02
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (33 bp):
TTTTTTAAAAAATTAATTAAATTTGGGTTTAGT
Found at i:6341122 original size:40 final size:40
Alignment explanation
Indices: 6341078--6341157 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
6341068 GTCAACGTAG
6341078 TTGACCGTTAAAAATGGGCTGATTTTTAAAAAAACTGTAA
1 TTGACCGTTAAAAATGGGCTGATTTTTAAAAAAACTGTAA
**
6341118 TTGACCGTTAAAAATGGTTTGATTTTTAAAAAAACTGTAA
1 TTGACCGTTAAAAATGGGCTGATTTTTAAAAAAACTGTAA
6341158 CGTTGAGGGT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (40 bp):
TTGACCGTTAAAAATGGGCTGATTTTTAAAAAAACTGTAA
Found at i:6341745 original size:126 final size:125
Alignment explanation
Indices: 6341319--6341836 Score: 665
Period size: 126 Copynumber: 4.2 Consensus size: 125
6341309 GATTTTGGTT
* * * * ** * *
6341319 TTTTTCTACGGTAGTTCCTGAAAAAATAATTTTAAGAAGATGGTTCCCAACAAATAGTCTTAAAA
1 TTTTTCTACAGTAGTTCATGAAAAAATAATTTTAAGAAGACGTTTCTGAACAAATAGTGTCAAAA
* *
6341384 ATGCTTCAAGCAGGATGCACTGTCAGCAAAATTACT-AAAAAAACTCCCACGTGGA-AGCTC
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTA-TGAAAAAAGCTCCCACGTGGACA-CTC
** * *
6341444 ---TTCTACAACAGTTCTTGAAAAAATAATTTTAAGAAGACAG-TTCTAAACAAATAGTGTCAAA
1 TTTTTCTACAGTAGTTCATGAAAAAATAATTTTAAGAAGAC-GTTTCTGAACAAATAGTGTCAAA
* *
6341505 AACGCTTCAAGCA-GATGCACTGTCAACAAAATTGATGAAAAAAGCTCCTACGTGGACACT-
65 AACGCTTCAAGCAGGATGCACTGTCAGCAAAATT-ATGAAAAAAGCTCCCACGTGGACACTC
* * * *
6341565 TTTTTTTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGTTTCTGAATAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCATGAAAAAATAATTTTAAGAAGACGTTTCTGAACAAATAGTGTCAAAA
* *
6341630 ACGCTTCAAGTAGGATGCACTGTCAGCAAAATTGAAGAAAAAAGCTCCCACGTGGACACTC
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATT-ATGAAAAAAGCTCCCACGTGGACACTC
* * * *
6341691 TTTTTCTATAGTAGTTCATGAAAAAATAATTTTGAGAAAACGTTTCTGAATAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCATGAAAAAATAATTTTAAGAAGACGTTTCTGAACAAATAGTGTCAAAA
* * *
6341756 ACACTTCAAGTAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTC
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTA-TGAAAAAAGCTCCCACGTGGACACTC
6341817 TTTTTCTACAGTAGTTCATG
1 TTTTTCTACAGTAGTTCATG
6341837 TTTGGCCTTA
Statistics
Matches: 350, Mismatches: 32, Indels: 21
0.87 0.08 0.05
Matches are distributed among these distances:
121 20 0.06
122 82 0.23
123 3 0.01
124 64 0.18
125 45 0.13
126 136 0.39
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (125 bp):
TTTTTCTACAGTAGTTCATGAAAAAATAATTTTAAGAAGACGTTTCTGAACAAATAGTGTCAAAA
ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTATGAAAAAAGCTCCCACGTGGACACTC
Found at i:6342033 original size:28 final size:28
Alignment explanation
Indices: 6342002--6342063 Score: 115
Period size: 28 Copynumber: 2.2 Consensus size: 28
6341992 CGGCGTTATT
6342002 TTTTTATCGGAGAACACAACGCGAATAA
1 TTTTTATCGGAGAACACAACGCGAATAA
*
6342030 TTTTTATCGGAGAACACAACGCGAATTA
1 TTTTTATCGGAGAACACAACGCGAATAA
6342058 TTTTTA
1 TTTTTA
6342064 ACTAGACTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (28 bp):
TTTTTATCGGAGAACACAACGCGAATAA
Found at i:6344979 original size:24 final size:23
Alignment explanation
Indices: 6344923--6344979 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 23
6344913 AAGAACTTCT
*
6344923 ATTTTATTAAAAATATAAAAATA
1 ATTTTATTAAAAATATAAAAACA
6344946 ATTTACTATT-AAAATATTAAAAACA
1 ATTT--TATTAAAAATA-TAAAAACA
6344971 ACTTTTATT
1 A-TTTTATT
6344980 TTATTAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
23 4 0.14
24 10 0.34
25 12 0.41
26 3 0.10
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (23 bp):
ATTTTATTAAAAATATAAAAACA
Found at i:6345383 original size:18 final size:18
Alignment explanation
Indices: 6345360--6345396 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
6345350 GGGAAAAGGA
* *
6345360 ATATAAGGGTTATGATAC
1 ATATAAGGGCTAGGATAC
6345378 ATATAAGGGCTAGGATAC
1 ATATAAGGGCTAGGATAC
6345396 A
1 A
6345397 CACCTGGCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.41, C:0.08, G:0.24, T:0.27
Consensus pattern (18 bp):
ATATAAGGGCTAGGATAC
Found at i:6347174 original size:30 final size:30
Alignment explanation
Indices: 6347140--6347208 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
6347130 ATTAATTAAA
6347140 GAGAGTTTTGAGAAATTTA-AGGAGAAATTT
1 GAGAGTTTTGAGAAATTTAGA-GAGAAATTT
*
6347170 GAGAGCTTTGAGAAATTTAGAGAGAAATTT
1 GAGAGTTTTGAGAAATTTAGAGAGAAATTT
*
6347200 GAAAGTTTT
1 GAGAGTTTT
6347209 TTTTGCTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
30 34 0.97
31 1 0.03
ACGTcount: A:0.39, C:0.01, G:0.26, T:0.33
Consensus pattern (30 bp):
GAGAGTTTTGAGAAATTTAGAGAGAAATTT
Found at i:6348298 original size:38 final size:38
Alignment explanation
Indices: 6348247--6348322 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
6348237 ATTATATGTG
6348247 CTTATTTTTCTAGATTAGTTCAGATTTAAATTGATTTT
1 CTTATTTTTCTAGATTAGTTCAGATTTAAATTGATTTT
*
6348285 CTTATTTTTCTAGATTAGTTCATATTTAAATTGATTTT
1 CTTATTTTTCTAGATTAGTTCAGATTTAAATTGATTTT
6348323 TATACATTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.26, C:0.08, G:0.09, T:0.57
Consensus pattern (38 bp):
CTTATTTTTCTAGATTAGTTCAGATTTAAATTGATTTT
Found at i:6348320 original size:20 final size:20
Alignment explanation
Indices: 6348259--6348320 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 20
6348249 TATTTTTCTA
*
6348259 GATTAGTTCAGATTTAAATT
1 GATTAGTTCATATTTAAATT
* *** *
6348279 GATT--TTCTTATTTTTCTA
1 GATTAGTTCATATTTAAATT
6348297 GATTAGTTCATATTTAAATT
1 GATTAGTTCATATTTAAATT
6348317 GATT
1 GATT
6348321 TTTATACATT
Statistics
Matches: 29, Mismatches: 11, Indels: 4
0.66 0.25 0.09
Matches are distributed among these distances:
18 12 0.41
20 17 0.59
ACGTcount: A:0.29, C:0.06, G:0.11, T:0.53
Consensus pattern (20 bp):
GATTAGTTCATATTTAAATT
Found at i:6371776 original size:14 final size:14
Alignment explanation
Indices: 6371757--6371784 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6371747 ACCCTAGTAG
6371757 TAATTAACAAGAAA
1 TAATTAACAAGAAA
6371771 TAATTAACAAGAAA
1 TAATTAACAAGAAA
6371785 GTCGCTAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.07, G:0.07, T:0.21
Consensus pattern (14 bp):
TAATTAACAAGAAA
Found at i:6375539 original size:23 final size:24
Alignment explanation
Indices: 6375513--6375558 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
6375503 TACAAGTCTA
6375513 GTTTAGTAA-TATATTGAATTATG
1 GTTTAGTAATTATATTGAATTATG
*
6375536 GTTTAGTAATTTTATTGAATTAT
1 GTTTAGTAATTATATTGAATTAT
6375559 AATTAATTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (24 bp):
GTTTAGTAATTATATTGAATTATG
Found at i:6377426 original size:17 final size:17
Alignment explanation
Indices: 6377401--6377448 Score: 78
Period size: 17 Copynumber: 2.8 Consensus size: 17
6377391 TGATGTGTTC
*
6377401 TTCAGTAAAAGAAAGAA
1 TTCAATAAAAGAAAGAA
6377418 TTCAATAAAAGAAAGAA
1 TTCAATAAAAGAAAGAA
*
6377435 TTCGATAAAAGAAA
1 TTCAATAAAAGAAA
6377449 AGTAGGCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.60, C:0.06, G:0.15, T:0.19
Consensus pattern (17 bp):
TTCAATAAAAGAAAGAA
Found at i:6383980 original size:38 final size:38
Alignment explanation
Indices: 6383927--6384003 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
6383917 AAATACTAAG
6383927 TGATAAATTCATTTAGCATGCTTACTTTTAACTCTTAT
1 TGATAAATTCATTTAGCATGCTTACTTTTAACTCTTAT
** **
6383965 TGATAAATTTGTTTAGCATGCTTGTTTTTAACTCTTAT
1 TGATAAATTCATTTAGCATGCTTACTTTTAACTCTTAT
6384003 T
1 T
6384004 TTTGTGATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.26, C:0.13, G:0.10, T:0.51
Consensus pattern (38 bp):
TGATAAATTCATTTAGCATGCTTACTTTTAACTCTTAT
Found at i:6385950 original size:17 final size:18
Alignment explanation
Indices: 6385928--6385964 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
6385918 CAAAACTAAG
6385928 GTTCATTTGGTGTT-CAT
1 GTTCATTTGGTGTTCCAT
6385945 GTTCATTTGGTGTTCCAT
1 GTTCATTTGGTGTTCCAT
6385963 GT
1 GT
6385965 CAGGATGCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.11, C:0.14, G:0.24, T:0.51
Consensus pattern (18 bp):
GTTCATTTGGTGTTCCAT
Found at i:6396897 original size:77 final size:76
Alignment explanation
Indices: 6396770--6396992 Score: 247
Period size: 77 Copynumber: 2.9 Consensus size: 76
6396760 CAATTCTCCA
* *
6396770 CATGGTATCAAATGTTTTTGGTTCTTTCCTTATAAGTGTTTTTTTTCTGGTCGAACTCTTGCTTC
1 CATGGTATCAGATGTTTTTGGTTCTTT-CTTATAAGTGTTTTTTTTCTGGTCGAAATCTTGCTTC
*
6396835 TCATGTTTATTC
65 TCATGTTCATTC
* *
6396847 CATGGTATCAGATGTTTTTGGTT-TTT-TTCCTAAGTGTTTTCTTTTCCTGGTTGAAATCTTGCT
1 CATGGTATCAGATGTTTTTGGTTCTTTCTT-ATAAGTGTTTT-TTTT-CTGGTCGAAATCTTGCT
*
6396910 TCTCTTGTTCATTC
63 TCTCATGTTCATTC
* * * *
6396924 CATGGTATCAGAT-TTTTCTGGTTCCTTAC-TATGAAGAGTTTTTTTTTCTTGGTCGAATTATTG
1 CATGGTATCAGATGTTTT-TGGTT-CTTTCTTAT-AAGTG-TTTTTTTTC-TGGTCGAAATCTTG
6396987 CTTCTC
61 CTTCTC
6396993 CTATTCTATT
Statistics
Matches: 124, Mismatches: 12, Indels: 18
0.81 0.08 0.12
Matches are distributed among these distances:
74 2 0.02
75 10 0.08
76 11 0.09
77 67 0.54
78 2 0.02
79 28 0.23
80 4 0.03
ACGTcount: A:0.15, C:0.17, G:0.17, T:0.52
Consensus pattern (76 bp):
CATGGTATCAGATGTTTTTGGTTCTTTCTTATAAGTGTTTTTTTTCTGGTCGAAATCTTGCTTCT
CATGTTCATTC
Found at i:6409323 original size:6 final size:7
Alignment explanation
Indices: 6409308--6409333 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
6409298 CTTCCGTTAA
6409308 TTTTATT
1 TTTTATT
6409315 TTTTATT
1 TTTTATT
6409322 TTTTATT
1 TTTTATT
6409329 TTTTA
1 TTTTA
6409334 AAATTTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTATT
Found at i:6410518 original size:36 final size:30
Alignment explanation
Indices: 6410450--6410509 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
6410440 GCTCGATAAG
6410450 AATCTTAAATATTAATATTGATACTAAGTT
1 AATCTTAAATATTAATATTGATACTAAGTT
*
6410480 AATCTTAAATATTAATATTGATATTAAGTT
1 AATCTTAAATATTAATATTGATACTAAGTT
6410510 TAAATTAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (30 bp):
AATCTTAAATATTAATATTGATACTAAGTT
Found at i:6410589 original size:31 final size:27
Alignment explanation
Indices: 6410551--6410612 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 27
6410541 AAATAATCAT
6410551 TCAACTATGATAGTGTTTTTATTTTAGTCA
1 TCAACTAT-A-AGTGTTTTTA-TTTAGTCA
* *
6410581 CTCAACTATAATTTTTTTTATTTAGTCA
1 -TCAACTATAAGTGTTTTTATTTAGTCA
6410609 TCAA
1 TCAA
6410613 AGTTTTCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 4 0.14
28 8 0.28
29 8 0.28
30 1 0.03
31 8 0.28
ACGTcount: A:0.29, C:0.13, G:0.08, T:0.50
Consensus pattern (27 bp):
TCAACTATAAGTGTTTTTATTTAGTCA
Found at i:6415117 original size:2 final size:2
Alignment explanation
Indices: 6415112--6415155 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
6415102 ACACACACAG
6415112 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
6415154 AT
1 AT
6415156 GCTTAGATTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6416853 original size:20 final size:21
Alignment explanation
Indices: 6416812--6416854 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
6416802 ACCAATAGAT
*
6416812 AATTGTGGACAATGCCACCAG
1 AATTGTAGACAATGCCACCAG
*
6416833 AATTGTAGACAA-GCTACCAG
1 AATTGTAGACAATGCCACCAG
6416853 AA
1 AA
6416855 CAAATATGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.19
Consensus pattern (21 bp):
AATTGTAGACAATGCCACCAG
Found at i:6417369 original size:71 final size:71
Alignment explanation
Indices: 6417288--6417432 Score: 281
Period size: 71 Copynumber: 2.0 Consensus size: 71
6417278 CACGAGATAA
6417288 AACACACACCTTAAACCAACGATCCAAAATCACCAATCTAAAATGTATCAGCTTTTCGTCTCAAA
1 AACACACACCTTAAACCAACGATCCAAAATCACCAATCTAAAATGTATCAGCTTTTCGTCTCAAA
6417353 TACTTG
66 TACTTG
*
6417359 AACACACACCTTAAACCAACGATCCAAAATCAGCAATCTAAAATGTATCAGCTTTTCGTCTCAAA
1 AACACACACCTTAAACCAACGATCCAAAATCACCAATCTAAAATGTATCAGCTTTTCGTCTCAAA
6417424 TACTTG
66 TACTTG
6417430 AAC
1 AAC
6417433 CACTTATTAA
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 73 1.00
ACGTcount: A:0.40, C:0.28, G:0.08, T:0.25
Consensus pattern (71 bp):
AACACACACCTTAAACCAACGATCCAAAATCACCAATCTAAAATGTATCAGCTTTTCGTCTCAAA
TACTTG
Found at i:6417752 original size:56 final size:56
Alignment explanation
Indices: 6417689--6417802 Score: 219
Period size: 56 Copynumber: 2.0 Consensus size: 56
6417679 GACAAAAAGG
*
6417689 AAAAGAATAAGGGTTGTTAACAAAAATATGGATAGATGAAAACAAAAGAAAAGGGA
1 AAAAGAATAAGGGTTGTTAACAAAAATATGGATAGACGAAAACAAAAGAAAAGGGA
6417745 AAAAGAATAAGGGTTGTTAACAAAAATATGGATAGACGAAAACAAAAGAAAAGGGA
1 AAAAGAATAAGGGTTGTTAACAAAAATATGGATAGACGAAAACAAAAGAAAAGGGA
6417801 AA
1 AA
6417803 GAAGCATAGA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.58, C:0.04, G:0.23, T:0.15
Consensus pattern (56 bp):
AAAAGAATAAGGGTTGTTAACAAAAATATGGATAGACGAAAACAAAAGAAAAGGGA
Found at i:6420017 original size:16 final size:16
Alignment explanation
Indices: 6419965--6420027 Score: 65
Period size: 16 Copynumber: 3.9 Consensus size: 16
6419955 GTTTAGTTCA
6419965 CTGTAATGGAATAG-G
1 CTGTAATGGAATAGAG
* * *
6419980 ACTATAATGTAATAGAA
1 -CTGTAATGGAATAGAG
*
6419997 TTGTAATGGAATAGAG
1 CTGTAATGGAATAGAG
*
6420013 CTGTAATAGAATAGA
1 CTGTAATGGAATAGA
6420028 ACTTTAATAA
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.43, C:0.05, G:0.24, T:0.29
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:6420035 original size:16 final size:16
Alignment explanation
Indices: 6419968--6420036 Score: 52
Period size: 16 Copynumber: 4.3 Consensus size: 16
6419958 TAGTTCACTG
* * *
6419968 TAATGGAATAGGACTA
1 TAATAGAATAGAACTT
6419984 TAAT-GTAATAGAA-TT
1 TAATAG-AATAGAACTT
* * *
6419999 GTAATGGAATAGAGCTG
1 -TAATAGAATAGAACTT
6420016 TAATAGAATAGAACTT
1 TAATAGAATAGAACTT
6420032 TAATA
1 TAATA
6420037 AGTAATCCAA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
15 2 0.05
16 38 0.90
17 2 0.05
ACGTcount: A:0.45, C:0.04, G:0.20, T:0.30
Consensus pattern (16 bp):
TAATAGAATAGAACTT
Found at i:6420231 original size:26 final size:24
Alignment explanation
Indices: 6420188--6420251 Score: 78
Period size: 26 Copynumber: 2.7 Consensus size: 24
6420178 TAATTATTGT
* *
6420188 TATTAAAT--TTTAATAAAATTAT
1 TATTAAATAATTTAATAAAAATAA
6420210 TATTAAATATAATTTAATAAAAATAA
1 TATT-AA-ATAATTTAATAAAAATAA
6420236 TATTAAATAATTTAAT
1 TATTAAATAATTTAAT
6420252 CATGTTTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.11
23 2 0.06
24 12 0.33
25 2 0.06
26 16 0.44
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TATTAAATAATTTAATAAAAATAA
Found at i:6420353 original size:21 final size:22
Alignment explanation
Indices: 6420301--6420353 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 22
6420291 TATACTACTC
6420301 TAATAAA--ATAGTAAAATATT
1 TAATAAATTATAGTAAAATATT
6420321 TAATAAATTATAGT-AAAT-TT
1 TAATAAATTATAGTAAAATATT
*
6420341 TAATTAATATATA
1 TAATAAAT-TATA
6420354 AGCTATTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 16 0.55
21 8 0.28
22 5 0.17
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (22 bp):
TAATAAATTATAGTAAAATATT
Found at i:6422498 original size:3 final size:3
Alignment explanation
Indices: 6422490--6422515 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
6422480 AAATTAGTTA
6422490 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
6422516 AAGAATAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:6422883 original size:31 final size:32
Alignment explanation
Indices: 6422820--6422884 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
6422810 GGCAAATTAT
6422820 AAGAGTAATTGAATCCTAATAAAATCTCTTTA
1 AAGAGTAATTGAATCCTAATAAAATCTCTTTA
6422852 AAGAGTAATTGAATCCTAATAAAA-CTCTTTA
1 AAGAGTAATTGAATCCTAATAAAATCTCTTTA
6422883 AA
1 AA
6422885 ATTATTTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 9 0.27
32 24 0.73
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.32
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAATCTCTTTA
Found at i:6428970 original size:32 final size:32
Alignment explanation
Indices: 6428929--6429025 Score: 187
Period size: 32 Copynumber: 3.1 Consensus size: 32
6428919 GGCAAATTAT
6428929 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
6428961 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
6428993 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
6429024 AA
1 AA
6429026 ATTATCTAAG
Statistics
Matches: 65, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
31 13 0.20
32 52 0.80
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.31
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACTCTTTA
Found at i:6429631 original size:29 final size:25
Alignment explanation
Indices: 6429580--6429632 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
6429570 AAGATTACTT
6429580 ATTTGAATTTAATTACAAACAATTA
1 ATTTGAATTTAATTACAAACAATTA
*
6429605 ATTTGAATTTAATTACAAACAATCA
1 ATTTGAATTTAATTACAAACAATTA
6429630 ATT
1 ATT
6429633 CTTAAAAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (25 bp):
ATTTGAATTTAATTACAAACAATTA
Found at i:6432536 original size:21 final size:21
Alignment explanation
Indices: 6432510--6432557 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
6432500 ATTAGGTGGA
*
6432510 TCAGCTCTTACGAGCTTTTGT
1 TCAGCTCTTACGAGCTTCTGT
6432531 TCAGCTCTTACGAGCTTCTGT
1 TCAGCTCTTACGAGCTTCTGT
*
6432552 TTAGCT
1 TCAGCT
6432558 TTTGAGCTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.15, C:0.25, G:0.19, T:0.42
Consensus pattern (21 bp):
TCAGCTCTTACGAGCTTCTGT
Found at i:6442965 original size:42 final size:43
Alignment explanation
Indices: 6442863--6442967 Score: 124
Period size: 42 Copynumber: 2.5 Consensus size: 43
6442853 AATGCCAACG
* * * * *
6442863 TCCCAGACGTGGTCTTACATGTAATTAATTATCGATGCCACTG
1 TCCCAGACATGGTCTTACACGTAATTAATTATCGACGCCAATA
* *
6442906 TCCCAAACAGGGTCTTACACGTAATT-ATATAT-GACGCCAATA
1 TCCCAGACATGGTCTTACACGTAATTAAT-TATCGACGCCAATA
6442948 TCCCAGACATGGTCTTACAC
1 TCCCAGACATGGTCTTACAC
6442968 ATAAATCTCA
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
42 27 0.52
43 25 0.48
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.29
Consensus pattern (43 bp):
TCCCAGACATGGTCTTACACGTAATTAATTATCGACGCCAATA
Found at i:6443970 original size:15 final size:15
Alignment explanation
Indices: 6443950--6443980 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
6443940 ATAAATTAAA
6443950 AGGTATAATTTCAAC
1 AGGTATAATTTCAAC
6443965 AGGTATAATTTCAAC
1 AGGTATAATTTCAAC
6443980 A
1 A
6443981 TAAGGCCCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (15 bp):
AGGTATAATTTCAAC
Found at i:6455218 original size:9 final size:9
Alignment explanation
Indices: 6455204--6455244 Score: 73
Period size: 9 Copynumber: 4.6 Consensus size: 9
6455194 AACTTGGTGC
6455204 ATTTTGTTT
1 ATTTTGTTT
6455213 ATTTTGTTT
1 ATTTTGTTT
*
6455222 ATTTTATTT
1 ATTTTGTTT
6455231 ATTTTGTTT
1 ATTTTGTTT
6455240 ATTTT
1 ATTTT
6455245 TAATATTTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (9 bp):
ATTTTGTTT
Found at i:6455325 original size:23 final size:23
Alignment explanation
Indices: 6455295--6455346 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
6455285 TGCAACTTGG
6455295 TTTCATAATAATAGCTA-ATATGC
1 TTTCATAATAATAGCTATA-ATGC
*
6455318 TTTCATAATGATAGCTATAATGC
1 TTTCATAATAATAGCTATAATGC
6455341 TTTCAT
1 TTTCAT
6455347 CTTTTGCTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (23 bp):
TTTCATAATAATAGCTATAATGC
Found at i:6455358 original size:59 final size:59
Alignment explanation
Indices: 6455295--6455410 Score: 196
Period size: 59 Copynumber: 2.0 Consensus size: 59
6455285 TGCAACTTGG
*
6455295 TTTCATAATAATAGCTAATATGCTTTCATAATGATAGCTATAATGCTTTCATCTTTTGC
1 TTTCATAATAATAGCTAATATGCTTTCATAATGATAGCTACAATGCTTTCATCTTTTGC
* * *
6455354 TTTCATAATGATAGCTAATATGCTTTCATAATGGTAGTTACAATGCTTTCATCTTTT
1 TTTCATAATAATAGCTAATATGCTTTCATAATGATAGCTACAATGCTTTCATCTTTT
6455411 TAATTATTAA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.29, C:0.15, G:0.11, T:0.45
Consensus pattern (59 bp):
TTTCATAATAATAGCTAATATGCTTTCATAATGATAGCTACAATGCTTTCATCTTTTGC
Found at i:6455379 original size:23 final size:23
Alignment explanation
Indices: 6455351--6455405 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
6455341 TTTCATCTTT
6455351 TGCTTTCATAATGATAGCTA-ATA
1 TGCTTTCATAATGATAGCTACA-A
* *
6455374 TGCTTTCATAATGGTAGTTACAA
1 TGCTTTCATAATGATAGCTACAA
6455397 TGCTTTCAT
1 TGCTTTCAT
6455406 CTTTTTAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 28 0.97
24 1 0.03
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.42
Consensus pattern (23 bp):
TGCTTTCATAATGATAGCTACAA
Found at i:6460396 original size:13 final size:13
Alignment explanation
Indices: 6460378--6460402 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6460368 ATTTCTGGTC
6460378 TTTACTCAAGTTT
1 TTTACTCAAGTTT
6460391 TTTACTCAAGTT
1 TTTACTCAAGTT
6460403 CTTAAGCTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.52
Consensus pattern (13 bp):
TTTACTCAAGTTT
Found at i:6464876 original size:13 final size:13
Alignment explanation
Indices: 6464858--6464882 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6464848 ATTTCTGGTC
6464858 TTTACTCAAGTTT
1 TTTACTCAAGTTT
6464871 TTTACTCAAGTT
1 TTTACTCAAGTT
6464883 CTTAAGCTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.52
Consensus pattern (13 bp):
TTTACTCAAGTTT
Found at i:6470878 original size:46 final size:46
Alignment explanation
Indices: 6470811--6470903 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
6470801 AAGATACAAG
6470811 ACAAAGTCAAAAATAGATGTAGCGACAATCATACATTAAAAAAATT
1 ACAAAGTCAAAAATAGATGTAGCGACAATCATACATTAAAAAAATT
6470857 ACAAAGTCAAAAATAGATGTAGCGACAATCATACATTAAAAAAATT
1 ACAAAGTCAAAAATAGATGTAGCGACAATCATACATTAAAAAAATT
6470903 A
1 A
6470904 ATGCTCCAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.55, C:0.13, G:0.11, T:0.22
Consensus pattern (46 bp):
ACAAAGTCAAAAATAGATGTAGCGACAATCATACATTAAAAAAATT
Found at i:6471612 original size:22 final size:22
Alignment explanation
Indices: 6471587--6471640 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
6471577 TTGTTTTTAA
* *
6471587 AAAATTAT-TTAATTTTAATTAT
1 AAAATTATATAAATATTAA-TAT
*
6471609 AAAAGTATATAAATATTAATAT
1 AAAATTATATAAATATTAATAT
*
6471631 AACATTATAT
1 AAAATTATAT
6471641 TTTTTAAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 18 0.69
23 8 0.31
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (22 bp):
AAAATTATATAAATATTAATAT
Found at i:6471758 original size:29 final size:28
Alignment explanation
Indices: 6471700--6471758 Score: 64
Period size: 29 Copynumber: 2.1 Consensus size: 28
6471690 TATGTAAAAT
* * **
6471700 ATATTAATATTAATCTTTTATTATGTTA
1 ATATTAAAATTAATATTTTATTATACTA
*
6471728 ATATTAAAATTATATATTTTATTTTACTA
1 ATATTAAAATTA-ATATTTTATTATACTA
6471757 AT
1 AT
6471759 TATCATATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 11 0.44
29 14 0.56
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (28 bp):
ATATTAAAATTAATATTTTATTATACTA
Found at i:6476079 original size:18 final size:20
Alignment explanation
Indices: 6476022--6476084 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 20
6476012 AAAAAAATTA
6476022 ATTTTC-CTATTATTATTATTT
1 ATTTTCACTATT-TTATT-TTT
*
6476043 ATTTTTACTATTTTA-TTTT
1 ATTTTCACTATTTTATTTTT
6476062 ATTTTCA-T-TTTTATTTTT
1 ATTTTCACTATTTTATTTTT
6476080 ATTTT
1 ATTTT
6476085 TGCAGGAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
17 5 0.13
18 10 0.26
19 9 0.24
20 1 0.03
21 8 0.21
22 5 0.13
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (20 bp):
ATTTTCACTATTTTATTTTT
Found at i:6476083 original size:6 final size:6
Alignment explanation
Indices: 6476029--6476085 Score: 62
Period size: 6 Copynumber: 9.2 Consensus size: 6
6476019 TTAATTTTCC
* *
6476029 TATTAT TATTATT TATTTT TACTATTT TA-TTT TATTTT CATTTT TATTTT
1 TATTTT TATT-TT TATTTT TA-T-TTT TATTTT TATTTT TATTTT TATTTT
6476079 TATTTT T
1 TATTTT T
6476086 GCAGGAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
5 5 0.11
6 28 0.64
7 6 0.14
8 5 0.11
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (6 bp):
TATTTT
Found at i:6506014 original size:4 final size:4
Alignment explanation
Indices: 6506005--6506030 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
6505995 ACATGCTTCA
6506005 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
6506031 TTGTAGTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:6507579 original size:7 final size:7
Alignment explanation
Indices: 6507499--6507596 Score: 81
Period size: 7 Copynumber: 14.0 Consensus size: 7
6507489 TCCTTTTCAA
*
6507499 CTCAATA
1 CTCAATT
**
6507506 CTCAACC
1 CTCAATT
6507513 CTCAATT
1 CTCAATT
*
6507520 CTAAATT
1 CTCAATT
* *
6507527 CTCACTC
1 CTCAATT
6507534 CTCAATT
1 CTCAATT
*
6507541 TTC-ATT
1 CTCAATT
6507547 CCTCAATT
1 -CTCAATT
* *
6507555 TTCAATC
1 CTCAATT
* *
6507562 CTGAATC
1 CTCAATT
6507569 CTCAATT
1 CTCAATT
6507576 CTCAATT
1 CTCAATT
6507583 CTCAATT
1 CTCAATT
6507590 CTCAATT
1 CTCAATT
6507597 ATTATTTTTA
Statistics
Matches: 71, Mismatches: 18, Indels: 4
0.76 0.19 0.04
Matches are distributed among these distances:
6 3 0.04
7 65 0.92
8 3 0.04
ACGTcount: A:0.29, C:0.32, G:0.01, T:0.39
Consensus pattern (7 bp):
CTCAATT
Found at i:6512181 original size:42 final size:41
Alignment explanation
Indices: 6512050--6512190 Score: 147
Period size: 42 Copynumber: 3.4 Consensus size: 41
6512040 GAAGCCCGAA
* * *
6512050 GGTTGAACAGAAGCTCATGAGAGCTAAACAAAAACTCATAAG
1 GGTTAAACAGAAGCTCATAAGAGCTGAAC-AAAACTCATAAG
* * * * *
6512092 GGTTGAACGGAAGCTCGTAAGAGATGAACAGAAACCCATAAG
1 GGTTAAACAGAAGCTCATAAGAGCTGAACA-AAACTCATAAG
* *
6512134 GGTTAAACAGAAGCTCAAAAGAGCTGAACGAAAACTCATATG
1 GGTTAAACAGAAGCTCATAAGAGCTGAAC-AAAACTCATAAG
* *
6512176 AGTTAAAGAGAAGCT
1 GGTTAAACAGAAGCT
6512191 TGTGAGAGCT
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
41 1 0.01
42 80 0.98
43 1 0.01
ACGTcount: A:0.44, C:0.16, G:0.24, T:0.16
Consensus pattern (41 bp):
GGTTAAACAGAAGCTCATAAGAGCTGAACAAAACTCATAAG
Found at i:6518714 original size:11 final size:12
Alignment explanation
Indices: 6518700--6518728 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
6518690 TTAATTAATA
6518700 ATATTATTATT-
1 ATATTATTATTG
6518711 ATATTATTATTG
1 ATATTATTATTG
6518723 ATATTA
1 ATATTA
6518729 CAATCAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (12 bp):
ATATTATTATTG
Found at i:6520526 original size:21 final size:21
Alignment explanation
Indices: 6520502--6520571 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
6520492 AGATTATTTG
6520502 CACCGTTGAGTGGTTTATCCA
1 CACCGTTGAGTGGTTTATCCA
*** *
6520523 CACCGTTTGAGCAATTTATCTA
1 CACCG-TTGAGTGGTTTATCCA
** *
6520545 CATTGTTTAGTGGTTTATCCA
1 CACCGTTGAGTGGTTTATCCA
6520566 CACCGT
1 CACCGT
6520572 ATTAGCAGTT
Statistics
Matches: 35, Mismatches: 13, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
21 20 0.57
22 15 0.43
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (21 bp):
CACCGTTGAGTGGTTTATCCA
Found at i:6520582 original size:22 final size:21
Alignment explanation
Indices: 6520514--6520582 Score: 66
Period size: 22 Copynumber: 3.2 Consensus size: 21
6520504 CCGTTGAGTG
6520514 GTTTATCCACACCGTTTGAGCA
1 GTTTATCCACACCGTTT-AGCA
* * ** **
6520536 ATTTATCTACATTGTTTAGTG
1 GTTTATCCACACCGTTTAGCA
6520557 GTTTATCCACACCGTATTAGCA
1 GTTTATCCACACCGT-TTAGCA
6520579 GTTT
1 GTTT
6520583 TAATCTACAA
Statistics
Matches: 34, Mismatches: 12, Indels: 2
0.71 0.25 0.04
Matches are distributed among these distances:
21 13 0.38
22 21 0.62
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.41
Consensus pattern (21 bp):
GTTTATCCACACCGTTTAGCA
Found at i:6525539 original size:13 final size:14
Alignment explanation
Indices: 6525521--6525549 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
6525511 TAAAGACTTG
6525521 ATATG-ATTAACCA
1 ATATGAATTAACCA
6525534 ATATGAATTAACCA
1 ATATGAATTAACCA
6525548 AT
1 AT
6525550 GTCACCAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.48, C:0.14, G:0.07, T:0.31
Consensus pattern (14 bp):
ATATGAATTAACCA
Found at i:6537705 original size:5 final size:5
Alignment explanation
Indices: 6537695--6537721 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
6537685 AATTAATCTA
6537695 AAAAT AAAAT AAAAT AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AA
6537722 TATTATTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:6539697 original size:18 final size:18
Alignment explanation
Indices: 6539661--6539705 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
6539651 ACAAATGCCT
6539661 TTAA-AATAGTAACAAAA
1 TTAACAATAGTAACAAAA
6539678 TTAACAATAG-AACAATAA
1 TTAACAATAGTAACAA-AA
6539696 TTATACAATA
1 TTA-ACAATA
6539706 TCCAAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 9 0.36
18 10 0.40
19 6 0.24
ACGTcount: A:0.60, C:0.09, G:0.04, T:0.27
Consensus pattern (18 bp):
TTAACAATAGTAACAAAA
Found at i:6539807 original size:20 final size:21
Alignment explanation
Indices: 6539755--6539810 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
6539745 TAGTGAAAAA
*
6539755 AAAACAACAATAAAATAGCAAG
1 AAAACAATAA-AAAATAGCAAG
*
6539777 AAAATAATAAAAAATAGCAAG
1 AAAACAATAAAAAATAGCAAG
*
6539798 -AAACAGTAAAAAA
1 AAAACAATAAAAAA
6539811 AAAGTAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 11 0.37
21 11 0.37
22 8 0.27
ACGTcount: A:0.71, C:0.09, G:0.09, T:0.11
Consensus pattern (21 bp):
AAAACAATAAAAAATAGCAAG
Found at i:6540215 original size:31 final size:31
Alignment explanation
Indices: 6540157--6540222 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 31
6540147 CGTGTAATTA
* **
6540157 TATACATGAAACTTTAATTGTGGTTCAAATG
1 TATACATGAAACATTAATTGTAATTCAAATG
* *
6540188 TATATATGAAACATTAATTTTAATTC-AAT-
1 TATACATGAAACATTAATTGTAATTCAAATG
6540217 TATACA
1 TATACA
6540223 CATTTAAATA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
29 5 0.17
30 3 0.10
31 21 0.72
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (31 bp):
TATACATGAAACATTAATTGTAATTCAAATG
Found at i:6546520 original size:46 final size:45
Alignment explanation
Indices: 6546453--6546860 Score: 417
Period size: 46 Copynumber: 9.6 Consensus size: 45
6546443 TTTGAGTACT
*
6546453 TCTGATCAAG-AAATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGAA-AAAGTGATAAGTGGTAGC-TTAGCTACACTTA
6546499 TCTGATCAAGTGAAAAAGTGAT-A-----AG--T-GCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* *
6546535 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
6546581 TCTGATCAAGTGAAAAAGTGAT-A-----AG--T-GCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* * * *
6546617 TCTGATCAAGAGACAAAGTGATAAGTTGTAGCTTTAACTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
6546663 TCTGATCAAGTGAAAAAGTGATAA---GT-GC-TA--T--ACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* *
6546699 TCTGAGCAAGTGAAAAAGTGATAAGTGTTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
*
6546745 TCTGATCAAGTGAGAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
* * *
6546791 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGTTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* *
6546836 TCTGATC-AG-GGACAAGTGATAAGTG
1 TCTGATCAAGTGAAAAAGTGATAAGTG
6546861 ATCATACGTA
Statistics
Matches: 310, Mismatches: 21, Indels: 65
0.78 0.05 0.16
Matches are distributed among these distances:
36 88 0.28
37 4 0.01
38 1 0.00
39 1 0.00
40 7 0.02
41 1 0.00
42 8 0.03
43 15 0.05
44 3 0.01
45 23 0.07
46 157 0.51
47 2 0.01
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (45 bp):
TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
Done.