Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 52 of 120
Found at i:15047382 original size:24 final size:24
Alignment explanation
Indices: 15047350--15047525 Score: 156
Period size: 24 Copynumber: 7.3 Consensus size: 24
15047340 GGTTAAATTC
*
15047350 TATCTGGGCTCGTAAGAGCTTACT
1 TATCTGGGCTCGTAAGAGCTAACT
* * * *
15047374 TATCTGGGCTTGTAAGGGCTTACC
1 TATCTGGGCTCGTAAGAGCTAACT
* * *
15047398 TATCTAGGCTTGTAAGAGCTAATT
1 TATCTGGGCTCGTAAGAGCTAACT
* * *
15047422 CTATTTGGGCTCGTTAGAGCTAACC
1 -TATCTGGGCTCGTAAGAGCTAACT
* *
15047447 TATCTAGGCTTGTAAGAGCTAACT
1 TATCTGGGCTCGTAAGAGCTAACT
* *
15047471 TATTTGGGCTCGTAAGAGCTAATT
1 TATCTGGGCTCGTAAGAGCTAACT
* * * *
15047495 CTGTCTGGGCTCGAAAAAGCTAA-A
1 -TATCTGGGCTCGTAAGAGCTAACT
15047519 TATCTGG
1 TATCTGG
15047526 AAGACCTAAA
Statistics
Matches: 121, Mismatches: 29, Indels: 5
0.78 0.19 0.03
Matches are distributed among these distances:
23 6 0.05
24 79 0.65
25 36 0.30
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (24 bp):
TATCTGGGCTCGTAAGAGCTAACT
Found at i:15047450 original size:49 final size:48
Alignment explanation
Indices: 15047349--15047492 Score: 198
Period size: 48 Copynumber: 3.0 Consensus size: 48
15047339 TGGTTAAATT
* * * * * * *
15047349 CTATCTGGGCTCGTAAGAGCTTACTTATCTGGGCTTGTAAGGGCTTAC
1 CTATCTAGGCTTGTAAGAGCTAACTTATTTGGGCTCGTAAGAGCTAAC
* *
15047397 CTATCTAGGCTTGTAAGAGCTAATTCTATTTGGGCTCGTTAGAGCTAAC
1 CTATCTAGGCTTGTAAGAGCTAACT-TATTTGGGCTCGTAAGAGCTAAC
15047446 CTATCTAGGCTTGTAAGAGCTAACTTATTTGGGCTCGTAAGAGCTAA
1 CTATCTAGGCTTGTAAGAGCTAACTTATTTGGGCTCGTAAGAGCTAA
15047493 TTCTGTCTGG
Statistics
Matches: 84, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
48 42 0.50
49 42 0.50
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (48 bp):
CTATCTAGGCTTGTAAGAGCTAACTTATTTGGGCTCGTAAGAGCTAAC
Found at i:15047486 original size:73 final size:73
Alignment explanation
Indices: 15047345--15047517 Score: 220
Period size: 73 Copynumber: 2.4 Consensus size: 73
15047335 ATACTGGTTA
* * * * * *
15047345 AATTCTATCTGGGCTCGTAAGAGCTTACTTATCTGGGCTTGTAAGGGCTTACCTATCTAGGCTTG
1 AATTCTATCTGGGCTCGTAAGAGCTAACCTATCTAGGCTTGTAAGAGCTAACCTATCTAGGCTCG
15047410 TAAGAGCT
66 TAAGAGCT
* * * * *
15047418 AATTCTATTTGGGCTCGTTAGAGCTAACCTATCTAGGCTTGTAAGAGCTAACTTATTTGGGCTCG
1 AATTCTATCTGGGCTCGTAAGAGCTAACCTATCTAGGCTTGTAAGAGCTAACCTATCTAGGCTCG
15047483 TAAGAGCT
66 TAAGAGCT
* * *
15047491 AATTCTGTCTGGGCTCGAAAAAGCTAA
1 AATTCTATCTGGGCTCGTAAGAGCTAA
15047518 ATATCTGGAA
Statistics
Matches: 84, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
73 84 1.00
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (73 bp):
AATTCTATCTGGGCTCGTAAGAGCTAACCTATCTAGGCTTGTAAGAGCTAACCTATCTAGGCTCG
TAAGAGCT
Found at i:15058978 original size:81 final size:76
Alignment explanation
Indices: 15058869--15059127 Score: 335
Period size: 75 Copynumber: 3.4 Consensus size: 76
15058859 TCAAAATTCT
* *
15058869 GAAAAAAAATCAAAATCAATTCTGTTGAATGGTAGGAATAAATCCTGAAACAGAATTATTTAATT
1 GAAAAAAAAT-AGAATAAATTCTGTTGAATGGTAGGAATAAATCCTGAAACAGAATTATTTAATT
*
15058934 AATTCTTGTTTG
65 AATTCTTATTTG
* * *
15058946 GAAACAAAAAAAAATAGAATAAATTCTGTTGAAAGGTATGAATAAATCCTAAAACAGAATTATTT
1 G-----AAAAAAAATAGAATAAATTCTGTTGAATGGTAGGAATAAATCCTGAAACAGAATTATTT
*
15059011 AATTAATTCTTATTTT
61 AATTAATTCTTATTTG
** *
15059027 G-AAAAAAATAGAATAAATTCTGTTGAATGACAGGAATAAATCCTGAAACAAAATTATTTAATTA
1 GAAAAAAAATAGAATAAATTCTGTTGAATGGTAGGAATAAATCCTGAAACAGAATTATTTAATTA
*
15059091 ATTCTTATCT-
66 ATTCTTATTTG
*
15059101 -AAAAAAAATCGAATAAATTCTGTTGAA
1 GAAAAAAAATAGAATAAATTCTGTTGAA
15059128 CAGCATGAAT
Statistics
Matches: 161, Mismatches: 15, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
74 25 0.16
75 66 0.41
77 1 0.01
81 60 0.37
82 9 0.06
ACGTcount: A:0.47, C:0.08, G:0.12, T:0.32
Consensus pattern (76 bp):
GAAAAAAAATAGAATAAATTCTGTTGAATGGTAGGAATAAATCCTGAAACAGAATTATTTAATTA
ATTCTTATTTG
Found at i:15059149 original size:74 final size:74
Alignment explanation
Indices: 15058864--15059155 Score: 309
Period size: 75 Copynumber: 3.8 Consensus size: 74
15058854 TAGAATCAAA
* * * * * *
15058864 ATTCTGAAAAAAAATCAAAATCAATTCTGTTGAATGGTAGGAATAAATCCTGAAACAGAATTATT
1 ATTCT-AAAAAAAAT-AGAATAAATTCTGTTGAA-AGCATGAATAAATCCTGAAACAAAATTATT
15058929 TAATTAATTCTT
63 TAATTAATTCTT
* * * * *
15058941 GTTTGGAAACAAAAAAAAATAGAATAAATTCTGTTGAAAGGTATGAATAAATCCTAAAACAGAAT
1 -ATT-----CTAAAAAAAATAGAATAAATTCTGTTGAAA-GCATGAATAAATCCTGAAACAAAAT
15059006 TATTTAATTAATTCTT
59 TATTTAATTAATTCTT
* * * *
15059022 ATTTTGAAAAAAATAGAATAAATTCTGTTGAATGACAGGAATAAATCCTGAAACAAAATTATTTA
1 ATTCTAAAAAAAATAGAATAAATTCTGTTGAAAG-CATGAATAAATCCTGAAACAAAATTATTTA
15059087 ATTAATTCTT
65 ATTAATTCTT
*
15059097 A-TCTAAAAAAAATCGAATAAATTCTGTTGAACAGCATGAATAAAT-CTCGAAACAAAATT
1 ATTCTAAAAAAAATAGAATAAATTCTGTTGAA-AGCATGAATAAATCCT-GAAACAAAATT
15059156 TCAATTTTAA
Statistics
Matches: 184, Mismatches: 21, Indels: 22
0.81 0.09 0.10
Matches are distributed among these distances:
73 2 0.01
74 49 0.27
75 64 0.35
78 2 0.01
80 2 0.01
81 55 0.30
82 9 0.05
83 1 0.01
ACGTcount: A:0.47, C:0.10, G:0.11, T:0.32
Consensus pattern (74 bp):
ATTCTAAAAAAAATAGAATAAATTCTGTTGAAAGCATGAATAAATCCTGAAACAAAATTATTTAA
TTAATTCTT
Found at i:15064605 original size:51 final size:50
Alignment explanation
Indices: 15064526--15064707 Score: 199
Period size: 51 Copynumber: 3.6 Consensus size: 50
15064516 TTTCATTTAA
* ** * *
15064526 TACTCACGATGATAGATAGTCATTGGACCTCTTATTCCGTATAGGAATTCA-
1 TACTCACGATGACACTTAGTCATCGGACCT-TTAATCCGTATAGG-ATTCAT
* * *
15064577 TACTCACAATGACA-TTGAGTTATCGGACCTTTAATCCATCAT-GGATTCATT
1 TACTCACGATGACACTT-AGTCATCGGACCTTTAATCCGT-ATAGGATTCA-T
* *
15064628 TACTCACGATGATACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTATAGGATTCA-T
15064679 TACTCACGATGACACTTAGTCATCGGACC
1 TACTCACGATGACACTTAGTCATCGGACC
15064708 CTTTCGTTTA
Statistics
Matches: 112, Mismatches: 13, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
49 5 0.04
50 11 0.10
51 94 0.84
52 2 0.02
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (50 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTATAGGATTCAT
Found at i:15066525 original size:150 final size:147
Alignment explanation
Indices: 15066360--15066700 Score: 454
Period size: 150 Copynumber: 2.3 Consensus size: 147
15066350 TGATTAAAAC
* *
15066360 AAAATCACTACTTTACTTCAAAATCAAAACTTTTATTTCGAAATAACTACAAAAAATCAAAACTT
1 AAAATCACTATTTTACTTAAAAATCAAAACTTTTATTTCGAAATAACTACAAAAAATCAAAACTT
* *
15066425 TATTTAAAAA-TTAAACTTTTTCTTTAAAATCATTAAAAAA-ATAGATTTT-TTAAAAAAATATA
66 TATTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACATA-ATTTTATTAAAAAAA-ATA
15066487 TAAACTTTCTCTTTTTTTTAAA
129 TAAACTTTCTC---TTTTTAAA
* ** ** *
15066509 GAAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTTTAAAAAATTAAAACT
1 -AAAATCACTATTTTACTTAAAAATCAAAACTTTTATTTCGAAATAACTACAAAAAATCAAAACT
* * ***
15066574 TTGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACATATTTTTATTTTTAAAAATAT
65 TTATTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACATAATTTTATTAAAAAAAATAT
15066639 AAACTTTCTCTTTTTAAA
130 AAACTTTCTCTTTTTAAA
* *
15066657 AAAATCACTATTTTATTTTAAAATCAAAACTTTTATTTCGAAAT
1 AAAATCACTATTTTACTTAAAAATCAAAACTTTTATTTCGAAAT
15066701 TATTTAAAAA
Statistics
Matches: 170, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
147 41 0.24
148 8 0.05
150 66 0.39
151 46 0.27
152 9 0.05
ACGTcount: A:0.45, C:0.11, G:0.02, T:0.42
Consensus pattern (147 bp):
AAAATCACTATTTTACTTAAAAATCAAAACTTTTATTTCGAAATAACTACAAAAAATCAAAACTT
TATTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACATAATTTTATTAAAAAAAATATA
AACTTTCTCTTTTTAAA
Found at i:15066675 original size:23 final size:23
Alignment explanation
Indices: 15066620--15066679 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
15066610 AAAAAACATA
*
15066620 TTTTTATTTTTAAAAATATAAAC
1 TTTTTATTTTTAAAAAAATAAAC
* * *
15066643 TTTCTCTTTTTAAAAAAAT-CAC
1 TTTTTATTTTTAAAAAAATAAAC
15066665 TATTTTA-TTTTAAAA
1 T-TTTTATTTTTAAAA
15066680 TCAAAACTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
22 11 0.37
23 19 0.63
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTTTATTTTTAAAAAAATAAAC
Found at i:15067140 original size:3 final size:3
Alignment explanation
Indices: 15067132--15067161 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
15067122 CATGAAACCC
15067132 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
15067162 AGACGATGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:15071950 original size:51 final size:51
Alignment explanation
Indices: 15071829--15072167 Score: 491
Period size: 51 Copynumber: 6.6 Consensus size: 51
15071819 TTCATTTAAC
* ** * * * *
15071829 ACTCACGATGATA-TATAGTCATCGGACCTCTTGTTTCATATAGGAATTCATAT
1 ACTCACGATGACACT-TAGTCATCGGACCT-TTAATCCGTAAAGG-ATTCATTT
* *
15071882 ACTCACGATAACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATTT
1 ACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATTT
* *
15071933 ACTCACGATGACTCTTAGTCATCGGACCTTTAATCCGTAAAAGATTCATTT
1 ACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATTT
* *
15071984 ACTCACGATGACACTTAATCATCGGTCCTTTAATCCGTAAAGGATTCATTT
1 ACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATTT
* * *
15072035 ACTCATGATGAAACTTAGTCATCGAACCTTTAATCCGTAAAGGATTCATTT
1 ACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATTT
*
15072086 ACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAAGATTCATTT
1 ACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATTT
15072137 ACTCACGATGACACTTAGTCATCGGACCTTT
1 ACTCACGATGACACTTAGTCATCGGACCTTT
15072168 TCATGTAAAG
Statistics
Matches: 261, Mismatches: 24, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
51 225 0.86
52 10 0.04
53 25 0.10
54 1 0.00
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.33
Consensus pattern (51 bp):
ACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATTT
Found at i:15087338 original size:24 final size:24
Alignment explanation
Indices: 15087293--15087342 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
15087283 AGAGTTTGAC
*
15087293 TGAAAAAAATAAATAGAATTTAAT
1 TGAAAAAAATAAACAGAATTTAAT
* **
15087317 TGAAACAAATAAACAGGGTTTAAT
1 TGAAAAAAATAAACAGAATTTAAT
15087341 TG
1 TG
15087343 GAAGATTATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.54, C:0.04, G:0.14, T:0.28
Consensus pattern (24 bp):
TGAAAAAAATAAACAGAATTTAAT
Found at i:15087597 original size:17 final size:17
Alignment explanation
Indices: 15087575--15087678 Score: 118
Period size: 17 Copynumber: 6.1 Consensus size: 17
15087565 AACTTTTAAT
*
15087575 TTTTAAATTTTAATTTA
1 TTTTAAATTTAAATTTA
*
15087592 TTTTAAATTTTAATTTA
1 TTTTAAATTTAAATTTA
*
15087609 TTTTAAATTTAAATTCA
1 TTTTAAATTTAAATTTA
* * *
15087626 TGTTGAGTTTAAATTTA
1 TTTTAAATTTAAATTTA
*
15087643 TTTTAAATTTGAATTTA
1 TTTTAAATTTAAATTTA
* * *
15087660 TTTTGAATTAAAAATTA
1 TTTTAAATTTAAATTTA
15087677 TT
1 TT
15087679 AATATTAAAA
Statistics
Matches: 73, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 73 1.00
ACGTcount: A:0.37, C:0.01, G:0.05, T:0.58
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:15088386 original size:3 final size:3
Alignment explanation
Indices: 15088378--15088430 Score: 52
Period size: 3 Copynumber: 17.0 Consensus size: 3
15088368 AATGAATCAG
* * *
15088378 TAA TAA TAA CAC TTAA TAA TAA TAA TAA TAT TAA TAAA TAA TAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
*
15088425 AAA TAA
1 TAA TAA
15088431 AAAAATAGAA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
3 35 0.88
4 5 0.12
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:15088402 original size:19 final size:19
Alignment explanation
Indices: 15088378--15088424 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
15088368 AATGAATCAG
15088378 TAATAATAACACTTAAT-AA
1 TAATAATAACA-TTAATAAA
*
15088397 TAATAATAATATTAATAAA
1 TAATAATAACATTAATAAA
15088416 TAATAATAA
1 TAATAATAA
15088425 AAATAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 5 0.19
19 21 0.81
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (19 bp):
TAATAATAACATTAATAAA
Found at i:15088406 original size:22 final size:22
Alignment explanation
Indices: 15088378--15088437 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
15088368 AATGAATCAG
* *
15088378 TAATAATAACACTTAATAATAA
1 TAATAATAACAATAAATAATAA
**
15088400 TAATAATATTAATAAATAATAA
1 TAATAATAACAATAAATAATAA
*
15088422 TAAAAATAA-AA-AAATA
1 TAATAATAACAATAAATA
15088438 GAAAACGAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 5 0.16
21 2 0.06
22 25 0.78
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (22 bp):
TAATAATAACAATAAATAATAA
Found at i:15088429 original size:16 final size:16
Alignment explanation
Indices: 15088398--15088431 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
15088388 ACTTAATAAT
**
15088398 AATAATAATATTAATA
1 AATAATAATAAAAATA
15088414 AATAATAATAAAAATA
1 AATAATAATAAAAATA
15088430 AA
1 AA
15088432 AAAATAGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AATAATAATAAAAATA
Found at i:15089576 original size:30 final size:29
Alignment explanation
Indices: 15089540--15089624 Score: 116
Period size: 30 Copynumber: 2.9 Consensus size: 29
15089530 AGAGGTCTCG
*
15089540 AAACTTCCAAAAATTACATTTTTACCACCC
1 AAACTTCCAAAAATTACATTTTTACC-CCA
* * *
15089570 AAACTTCCAAAAACTCCATTTTTGACCTCA
1 AAACTTCCAAAAATTACATTTTT-ACCCCA
15089600 AAACTTCCAAAAATTACATTTTTAC
1 AAACTTCCAAAAATTACATTTTTAC
15089625 TCCCGAATAT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
29 2 0.04
30 43 0.90
31 3 0.06
ACGTcount: A:0.40, C:0.27, G:0.01, T:0.32
Consensus pattern (29 bp):
AAACTTCCAAAAATTACATTTTTACCCCA
Found at i:15089807 original size:27 final size:27
Alignment explanation
Indices: 15089723--15089822 Score: 148
Period size: 27 Copynumber: 3.7 Consensus size: 27
15089713 CAAATTTTCC
* * *
15089723 CAAAATTACCATTTTTCCCCAAAGAGTC
1 CAAAATTACCATTTTGCCCC-GAGAGTT
*
15089751 CAAAATTACCATTTTG-CTCGAGAGTT
1 CAAAATTACCATTTTGCCCCGAGAGTT
15089777 CAAAATTACCATTTTGCCCCGAGAGTT
1 CAAAATTACCATTTTGCCCCGAGAGTT
15089804 CAAAATTACCATTTTGCCC
1 CAAAATTACCATTTTGCCC
15089823 TCGGGTATCC
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
26 21 0.32
27 30 0.45
28 15 0.23
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.31
Consensus pattern (27 bp):
CAAAATTACCATTTTGCCCCGAGAGTT
Found at i:15097301 original size:21 final size:21
Alignment explanation
Indices: 15097275--15097314 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
15097265 TTCACATCTT
*
15097275 CAACAAGGACTTCCTCCTTTC
1 CAACAAGAACTTCCTCCTTTC
*
15097296 CAACAATAACTTCCTCCTT
1 CAACAAGAACTTCCTCCTT
15097315 AACAGTAGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.38, G:0.05, T:0.30
Consensus pattern (21 bp):
CAACAAGAACTTCCTCCTTTC
Found at i:15103244 original size:18 final size:18
Alignment explanation
Indices: 15103221--15103263 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
15103211 TTGAACCAAT
*
15103221 CTTTTTTTCTTTTTCTTC
1 CTTTTTTTCATTTTCTTC
* * *
15103239 CTTTTTCTCATTTTGTTT
1 CTTTTTTTCATTTTCTTC
15103257 CTTTTTT
1 CTTTTTT
15103264 AAATGACTGA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.77
Consensus pattern (18 bp):
CTTTTTTTCATTTTCTTC
Found at i:15115205 original size:80 final size:80
Alignment explanation
Indices: 15115069--15115231 Score: 317
Period size: 80 Copynumber: 2.0 Consensus size: 80
15115059 ATACCTTTGC
15115069 AGTGTTCTTTCCCCCTCGGATTGGGATTTTTCGTGTCACTAGGTAGTGTGCCCGGTGGTCGAGTA
1 AGTGTTCTTTCCCCCTCGGATTGGGATTTTTCGTGTCACTAGGTAGTGTGCCCGGTGGTCGAGTA
15115134 TTCAGATTCGAAGCA
66 TTCAGATTCGAAGCA
*
15115149 AGTGTTCTTTCCCCCTCGGATTGGGATTTTTCGTGTCACTAGGTAGTGTGCTCGGTGGTCGAGTA
1 AGTGTTCTTTCCCCCTCGGATTGGGATTTTTCGTGTCACTAGGTAGTGTGCCCGGTGGTCGAGTA
15115214 TTCAGATTCGAAGCA
66 TTCAGATTCGAAGCA
15115229 AGT
1 AGT
15115232 TGTCCTAATT
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 82 1.00
ACGTcount: A:0.17, C:0.20, G:0.29, T:0.34
Consensus pattern (80 bp):
AGTGTTCTTTCCCCCTCGGATTGGGATTTTTCGTGTCACTAGGTAGTGTGCCCGGTGGTCGAGTA
TTCAGATTCGAAGCA
Found at i:15115437 original size:21 final size:20
Alignment explanation
Indices: 15115412--15115468 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
15115402 TGAAGAGTGT
* *
15115412 TGTGGTTGCGTCTGATTCTGG
1 TGTGGATGCATCTGATT-TGG
*
15115433 TGTGGATGCATCTAGATTTGT
1 TGTGGATGCATCT-GATTTGG
15115454 TGTGGATGCATCTGA
1 TGTGGATGCATCTGA
15115469 GTATGTTGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.06
21 26 0.81
22 4 0.12
ACGTcount: A:0.14, C:0.12, G:0.33, T:0.40
Consensus pattern (20 bp):
TGTGGATGCATCTGATTTGG
Found at i:15115475 original size:21 final size:21
Alignment explanation
Indices: 15115409--15115476 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
15115399 CATTGAAGAG
* * * *
15115409 TGTTGTGGTTGCGTCTGATTC
1 TGTTGTGGATGCATCTGAGTA
* *
15115430 TGGTGTGGATGCATCT-AGATT
1 TGTTGTGGATGCATCTGAG-TA
15115451 TGTTGTGGATGCATCTGAGTA
1 TGTTGTGGATGCATCTGAGTA
15115472 TGTTG
1 TGTTG
15115477 ATTGTAGTTC
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
20 1 0.03
21 35 0.92
22 2 0.05
ACGTcount: A:0.13, C:0.10, G:0.34, T:0.43
Consensus pattern (21 bp):
TGTTGTGGATGCATCTGAGTA
Found at i:15123676 original size:29 final size:31
Alignment explanation
Indices: 15123635--15123695 Score: 72
Period size: 30 Copynumber: 2.0 Consensus size: 31
15123625 TTATTCTATT
*
15123635 AATAATATTATTTTAAAT-TTAAAAATTTTAA
1 AATAATA-TATTTCAAATATTAAAAATTTTAA
* *
15123666 AATAATA-ATTTCAAATATTATAATTTTTAA
1 AATAATATATTTCAAATATTAAAAATTTTAA
15123696 TATTATTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
29 8 0.31
30 11 0.42
31 7 0.27
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (31 bp):
AATAATATATTTCAAATATTAAAAATTTTAA
Found at i:15132525 original size:30 final size:30
Alignment explanation
Indices: 15132484--15132541 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
15132474 AAAACTGCCA
15132484 CATAATTGTCATAAATGGCCACATAGTCTG
1 CATAATTGTCATAAATGGCCACATAGTCTG
*
15132514 CATATTTGTCATAAATGGCCACATAGTC
1 CATAATTGTCATAAATGGCCACATAGTC
15132542 ACTTTATAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.31
Consensus pattern (30 bp):
CATAATTGTCATAAATGGCCACATAGTCTG
Found at i:15132569 original size:48 final size:48
Alignment explanation
Indices: 15132514--15132681 Score: 214
Period size: 48 Copynumber: 3.5 Consensus size: 48
15132504 ACATAGTCTG
* * **
15132514 CATATTTGTCATAAATGGCCACATAGTCACTTTATAGATGAACTGCTA
1 CATATTTGTCAAAAATGACCACATAGTCACTTTGCAGATGAACTGCTA
*
15132562 CATATTTG-CAAAAAATGACCACATAGTCACTTTGCAGATGAGCTGCTA
1 CATATTTGTC-AAAAATGACCACATAGTCACTTTGCAGATGAACTGCTA
* *
15132610 CATATTT-TCCAAAAATGATCACACAGTCACTTTGCAGATGAACTGCTA
1 CATATTTGT-CAAAAATGACCACATAGTCACTTTGCAGATGAACTGCTA
* * *
15132658 CATATTTGCCATAAATGGCCACAT
1 CATATTTGTCAAAAATGACCACAT
15132682 CTTCCTTCTT
Statistics
Matches: 103, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
47 1 0.01
48 101 0.98
49 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (48 bp):
CATATTTGTCAAAAATGACCACATAGTCACTTTGCAGATGAACTGCTA
Found at i:15139752 original size:48 final size:48
Alignment explanation
Indices: 15139679--15139896 Score: 240
Period size: 48 Copynumber: 4.5 Consensus size: 48
15139669 ACAAGCCACC
* * * * * * *
15139679 ACATATTTACCGTAAAATTGCCACATAATCATTTTGC-GGTAAAACTGCC
1 ACATATTTGCCAT-AAATGGCCACATAGTCACTTTGCAGAT-AAACTGCT
* * * * *
15139728 ACATAATTGCCATAAATGGCCACATATTCACTTTGTAGATGAACTACT
1 ACATATTTGCCATAAATGGCCACATAGTCACTTTGCAGATAAACTGCT
** * * *
15139776 ACATATTTTTCATAAATGGCCACATTGTCACTTTGTAGATGAACTGCT
1 ACATATTTGCCATAAATGGCCACATAGTCACTTTGCAGATAAACTGCT
* *
15139824 ACATATTTGCCATAAATGGCCACATAGTCACTTTGCAAATGAACTGCT
1 ACATATTTGCCATAAATGGCCACATAGTCACTTTGCAGATAAACTGCT
15139872 ACATATTTGCCATAAATGGCCACAT
1 ACATATTTGCCATAAATGGCCACAT
15139897 CTTCCTCCTT
Statistics
Matches: 146, Mismatches: 22, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
48 134 0.92
49 12 0.08
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.32
Consensus pattern (48 bp):
ACATATTTGCCATAAATGGCCACATAGTCACTTTGCAGATAAACTGCT
Found at i:15139866 original size:96 final size:96
Alignment explanation
Indices: 15139721--15139896 Score: 280
Period size: 96 Copynumber: 1.8 Consensus size: 96
15139711 TTTGCGGTAA
* * * **
15139721 AACTGCCACATAATTGCCATAAATGGCCACATATTCACTTTGTAGATGAACTACTACATATTTTT
1 AACTGCCACATAATTGCCATAAATGGCCACATAGTCACTTTGCAAATGAACTACTACATATTTGC
15139786 CATAAATGGCCACATTGTCACTTTGTAGATG
66 CATAAATGGCCACATTGTCACTTTGTAGATG
* * *
15139817 AACTGCTACATATTTGCCATAAATGGCCACATAGTCACTTTGCAAATGAACTGCTACATATTTGC
1 AACTGCCACATAATTGCCATAAATGGCCACATAGTCACTTTGCAAATGAACTACTACATATTTGC
15139882 CATAAATGGCCACAT
66 CATAAATGGCCACAT
15139897 CTTCCTCCTT
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
96 72 1.00
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (96 bp):
AACTGCCACATAATTGCCATAAATGGCCACATAGTCACTTTGCAAATGAACTACTACATATTTGC
CATAAATGGCCACATTGTCACTTTGTAGATG
Found at i:15140072 original size:8 final size:8
Alignment explanation
Indices: 15140057--15140101 Score: 54
Period size: 8 Copynumber: 5.5 Consensus size: 8
15140047 GATCTCGATG
15140057 TTCACATA
1 TTCACATA
*
15140065 TCCACATA
1 TTCACATA
15140073 TTCACATA
1 TTCACATA
*
15140081 TTCACATTT
1 TTCACA-TA
*
15140090 TTCACATG
1 TTCACATA
15140098 TTCA
1 TTCA
15140102 TATCACATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
8 25 0.78
9 7 0.22
ACGTcount: A:0.31, C:0.27, G:0.02, T:0.40
Consensus pattern (8 bp):
TTCACATA
Found at i:15151092 original size:14 final size:16
Alignment explanation
Indices: 15151059--15151099 Score: 59
Period size: 14 Copynumber: 2.7 Consensus size: 16
15151049 CTTGAAAAAC
*
15151059 AAAGAAAAAATGAGAA
1 AAAGAATAAATGAGAA
15151075 AAAGAATAAA-GA-AA
1 AAAGAATAAATGAGAA
15151089 AAAGAATAAAT
1 AAAGAATAAAT
15151100 TGCTTAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 12 0.52
15 2 0.09
16 9 0.39
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.10
Consensus pattern (16 bp):
AAAGAATAAATGAGAA
Found at i:15160440 original size:20 final size:20
Alignment explanation
Indices: 15160415--15160455 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
15160405 AGAGATTGCT
*
15160415 TGCAAGTCAAGTAAAATATA
1 TGCAAGTCAAGCAAAATATA
15160435 TGCAAGTCAAGCAAAATATA
1 TGCAAGTCAAGCAAAATATA
15160455 T
1 T
15160456 TTTCTTTCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.12, G:0.15, T:0.24
Consensus pattern (20 bp):
TGCAAGTCAAGCAAAATATA
Found at i:15164376 original size:18 final size:19
Alignment explanation
Indices: 15164346--15164383 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
15164336 TTGGTATCAT
15164346 TTTGTGCGTGATATTATTG
1 TTTGTGCGTGATATTATTG
*
15164365 TTTGTG-GTGATATTCTTG
1 TTTGTGCGTGATATTATTG
15164383 T
1 T
15164384 GAGCAAAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.13, C:0.05, G:0.26, T:0.55
Consensus pattern (19 bp):
TTTGTGCGTGATATTATTG
Found at i:15164557 original size:29 final size:29
Alignment explanation
Indices: 15164517--15164572 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
15164507 TCGTGGAAGA
* * *
15164517 GGTGGAGAACTTGTTCGTTGAGAATTCGT
1 GGTGAAGAACTTGTTCATTAAGAATTCGT
15164546 GGTGAAGAACTTGTTCATTAAGAATTC
1 GGTGAAGAACTTGTTCATTAAGAATTC
15164573 ATGTCAAGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.27, C:0.11, G:0.29, T:0.34
Consensus pattern (29 bp):
GGTGAAGAACTTGTTCATTAAGAATTCGT
Found at i:15172243 original size:3 final size:3
Alignment explanation
Indices: 15172235--15172303 Score: 138
Period size: 3 Copynumber: 23.0 Consensus size: 3
15172225 ACCCGACTAT
15172235 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
15172283 GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA
15172304 ATGACAGAAA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:15181595 original size:26 final size:25
Alignment explanation
Indices: 15181546--15181603 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
15181536 AGTTAATTCA
15181546 TCAAATCGAATAATTTTTTATTTTT
1 TCAAATCGAATAATTTTTTATTTTT
*
15181571 TCAAATTC-AATAATTTTTTAATTTT
1 TCAAA-TCGAATAATTTTTTATTTTT
15181596 T-AAATCGA
1 TCAAATCGA
15181604 GTGTTCCTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
23 2 0.07
24 4 0.13
25 22 0.73
26 2 0.07
ACGTcount: A:0.36, C:0.09, G:0.03, T:0.52
Consensus pattern (25 bp):
TCAAATCGAATAATTTTTTATTTTT
Found at i:15182321 original size:16 final size:17
Alignment explanation
Indices: 15182290--15182325 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
15182280 AACACATGTT
15182290 TTTGTTGTTTTATTTTG
1 TTTGTTGTTTTATTTTG
*
15182307 TTTGTT-TTTTGTTTTG
1 TTTGTTGTTTTATTTTG
15182323 TTT
1 TTT
15182326 AGATTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.03, C:0.00, G:0.17, T:0.81
Consensus pattern (17 bp):
TTTGTTGTTTTATTTTG
Found at i:15182662 original size:17 final size:18
Alignment explanation
Indices: 15182619--15182657 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
15182609 TTAAAAATAC
15182619 TTTGAAAAGGTCAAATTT
1 TTTGAAAAGGTCAAATTT
15182637 TTTGAAAAGGTCAAATTT
1 TTTGAAAAGGTCAAATTT
15182655 TTT
1 TTT
15182658 CAAAGTGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.36, C:0.05, G:0.15, T:0.44
Consensus pattern (18 bp):
TTTGAAAAGGTCAAATTT
Found at i:15188559 original size:24 final size:25
Alignment explanation
Indices: 15188508--15188569 Score: 81
Period size: 24 Copynumber: 2.5 Consensus size: 25
15188498 TTTTCAATAT
*
15188508 TTTCCCAATTAAACACCGTTTTTAG
1 TTTCCCACTTAAACACCGTTTTTAG
* *
15188533 TTTCCCACTTAAACTCTG-TTTTAG
1 TTTCCCACTTAAACACCGTTTTTAG
*
15188557 TTTCACACTTAAA
1 TTTCCCACTTAAA
15188570 TTCTAATTAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
24 18 0.55
25 15 0.45
ACGTcount: A:0.27, C:0.24, G:0.06, T:0.42
Consensus pattern (25 bp):
TTTCCCACTTAAACACCGTTTTTAG
Found at i:15190543 original size:135 final size:134
Alignment explanation
Indices: 15190334--15190603 Score: 310
Period size: 135 Copynumber: 2.0 Consensus size: 134
15190324 ATTATTTCCA
* * * * * **
15190334 TTTTCTTTTTTTTCTTATTTCGTTTTTTTCCATTATTCCTTTCTTCTTCATTCTTTCTCTTTTCA
1 TTTTCTTTTTTTCCTTATTTCATTTTTTTCAAGTATTCCTTTCTTCTTCATTCTTCCTCTCGTCA
* ** * * * *
15190399 GTTCGTCTTTTTATTTTTTGGGTTTATTTAATC-TTTTTGGGTTTCTATG-AAATGAAATTTAAG
66 GTTCATCTTTTTATTTTTTGAATTCATTCAA-CATTTATGGGTTTCT-TGTAAAAGAAATTTAAG
15190462 AACATT
129 AACATT
* * * *
15190468 TTTTGTTTTTTTCCTTATTTTATTCTTTTTCAAGTGTTCCTTTCTTCTTCTTTCTTCCTCTCGTC
1 TTTTCTTTTTTTCCTTATTTCATT-TTTTTCAAGTATTCCTTTCTTCTTCATTCTTCCTCTCGTC
* * *
15190533 ATTTTATCTTTTTCTTTTTTGAATTCATTCAACATTTATGGGTTTCTTGTAAAAGAAATTTAAGA
65 AGTTCATCTTTTTATTTTTTGAATTCATTCAACATTTATGGGTTTCTTGTAAAAGAAATTTAAGA
15190598 ACATT
130 ACATT
15190603 T
1 T
15190604 CTAAGTCACG
Statistics
Matches: 112, Mismatches: 21, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
134 23 0.21
135 89 0.79
ACGTcount: A:0.17, C:0.15, G:0.09, T:0.59
Consensus pattern (134 bp):
TTTTCTTTTTTTCCTTATTTCATTTTTTTCAAGTATTCCTTTCTTCTTCATTCTTCCTCTCGTCA
GTTCATCTTTTTATTTTTTGAATTCATTCAACATTTATGGGTTTCTTGTAAAAGAAATTTAAGAA
CATT
Found at i:15191472 original size:6 final size:6
Alignment explanation
Indices: 15191451--15191491 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
15191441 GAGAAATAAT
* *
15191451 AAAAGA AAAGGA AAAAGGA AAAAGA AAAAGA AAAATA AAAA
1 AAAAGA AAAAGA AAAA-GA AAAAGA AAAAGA AAAAGA AAAA
15191492 AAGAGATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (6 bp):
AAAAGA
Found at i:15191491 original size:19 final size:19
Alignment explanation
Indices: 15191444--15191492 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
15191434 TGGGAACGAG
*
15191444 AAATAATAAAAGAAAAGGAA
1 AAATAA-AAAAGAAAAAGAA
**
15191464 AAAGGAAAAAGAAAAAGAA
1 AAATAAAAAAGAAAAAGAA
15191483 AAATAAAAAA
1 AAATAAAAAA
15191493 AGAGATTATG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 20 0.83
20 4 0.17
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.06
Consensus pattern (19 bp):
AAATAAAAAAGAAAAAGAA
Found at i:15191715 original size:6 final size:6
Alignment explanation
Indices: 15191704--15191743 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
15191694 CTAAAATAAA
*
15191704 ATATTT ATATTT ATATTT ATATTT GTATTT ATATTT ATAT
1 ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT ATAT
15191744 ATTTTATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (6 bp):
ATATTT
Found at i:15192349 original size:6 final size:6
Alignment explanation
Indices: 15192338--15192385 Score: 60
Period size: 6 Copynumber: 7.7 Consensus size: 6
15192328 ATAATCTCTT
* *
15192338 TTTTTC TTTTTC TTTTTC TTTTTC ATTTTTTC ATTTTC CTTTTC TTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC --TTTTTC TTTTTC TTTTTC TTTT
15192386 ATTATTTCCC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
6 31 0.84
8 6 0.16
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTTC
Found at i:15192359 original size:20 final size:20
Alignment explanation
Indices: 15192334--15192385 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
15192324 CGTCATAATC
*
15192334 TCTTTTT-TTCTTTTTCTTTT
1 TCTTTTTCTT-TTTTTCATTT
*
15192354 TCTTTTTCATTTTTTCATTT
1 TCTTTTTCTTTTTTTCATTT
*
15192374 TCCTTTTCTTTT
1 TCTTTTTCTTTT
15192386 ATTATTTCCC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 26 0.96
21 1 0.04
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (20 bp):
TCTTTTTCTTTTTTTCATTT
Found at i:15192469 original size:27 final size:27
Alignment explanation
Indices: 15192439--15192493 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
15192429 CTCCTCATCC
* *
15192439 TTTTCCCAACCCTAACCACCTCCAACA
1 TTTTCCAAACCCTAACCACCACCAACA
* *
15192466 TTTTTCAAACCCTAGCCACCACCAACA
1 TTTTCCAAACCCTAACCACCACCAACA
15192493 T
1 T
15192494 ACACAATAGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.31, C:0.44, G:0.02, T:0.24
Consensus pattern (27 bp):
TTTTCCAAACCCTAACCACCACCAACA
Found at i:15193406 original size:15 final size:15
Alignment explanation
Indices: 15193386--15193415 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
15193376 AAGAAAATGG
*
15193386 AAATAATTTTTTTAA
1 AAATAATTTTATTAA
15193401 AAATAATTTTATTAA
1 AAATAATTTTATTAA
15193416 TTTTTAATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AAATAATTTTATTAA
Found at i:15208748 original size:16 final size:17
Alignment explanation
Indices: 15208727--15208765 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
15208717 CATGCATATT
15208727 ATTTTA-TTATCATTGC
1 ATTTTAGTTATCATTGC
* *
15208743 ATTTTAGTTGTCGTTGC
1 ATTTTAGTTATCATTGC
15208760 ATTTTA
1 ATTTTA
15208766 CTTGTTAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.21, C:0.10, G:0.13, T:0.56
Consensus pattern (17 bp):
ATTTTAGTTATCATTGC
Found at i:15213899 original size:8 final size:8
Alignment explanation
Indices: 15213886--15213944 Score: 59
Period size: 8 Copynumber: 7.2 Consensus size: 8
15213876 TATTCTATAA
15213886 TATAAAAT
1 TATAAAAT
15213894 TATAAAAT
1 TATAAAAT
*
15213902 AATCAAAA-
1 TAT-AAAAT
15213910 TATTAATAAT
1 TA-TAA-AAT
15213920 TATAAAAT
1 TATAAAAT
15213928 TATAAAA-
1 TATAAAAT
*
15213935 TATAATAT
1 TATAAAAT
15213943 TA
1 TA
15213945 CATTCAACTA
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
7 6 0.14
8 25 0.58
9 10 0.23
10 2 0.05
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (8 bp):
TATAAAAT
Found at i:15213938 original size:15 final size:15
Alignment explanation
Indices: 15213884--15213944 Score: 61
Period size: 17 Copynumber: 3.8 Consensus size: 15
15213874 ACTATTCTAT
15213884 AATATAAAATTATAA
1 AATATAAAATTATAA
15213899 AATAATCAAAA-TATTAA
1 AAT-AT-AAAATTA-TAA
15213916 TAATTATAAAATTATAA
1 -AA-TATAAAATTATAA
*
15213933 AATATAATATTA
1 AATATAAAATTA
15213945 CATTCAACTA
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
15 12 0.31
16 6 0.15
17 14 0.36
18 6 0.15
19 1 0.03
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (15 bp):
AATATAAAATTATAA
Found at i:15223196 original size:19 final size:19
Alignment explanation
Indices: 15223172--15223211 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
15223162 GCCACTTTAG
*
15223172 TAAATTATTTTAAAATTAT
1 TAAATTATTTTAAAATCAT
15223191 TAAATTATTTTAAAATCAT
1 TAAATTATTTTAAAATCAT
15223210 TA
1 TA
15223212 TCATCCTCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (19 bp):
TAAATTATTTTAAAATCAT
Found at i:15233328 original size:34 final size:35
Alignment explanation
Indices: 15233276--15233346 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 35
15233266 CTAGTTGTAA
* *
15233276 TTTAATTGTCACCACATTC-CCTTTGTCATTTCAT
1 TTTAATTGTCACCACATTCACATTTGTCATTGCAT
** *
15233310 TTTAATTGTCACTGCATTCACATTTTTCATTGCAT
1 TTTAATTGTCACCACATTCACATTTGTCATTGCAT
15233345 TT
1 TT
15233347 CCATTTGTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
34 17 0.55
35 14 0.45
ACGTcount: A:0.21, C:0.23, G:0.07, T:0.49
Consensus pattern (35 bp):
TTTAATTGTCACCACATTCACATTTGTCATTGCAT
Found at i:15233345 original size:18 final size:18
Alignment explanation
Indices: 15233292--15233359 Score: 59
Period size: 18 Copynumber: 3.8 Consensus size: 18
15233282 TGTCACCACA
* *
15233292 TTCCCTTTGTCATTTCAT
1 TTCCATTTGTCATTGCAT
* * *
15233310 TT-TAATTGTCACTGCA-
1 TTCCATTTGTCATTGCAT
*
15233326 TTCACATTTTTCATTGCAT
1 TTC-CATTTGTCATTGCAT
15233345 TTCCATTTGTCATTG
1 TTCCATTTGTCATTG
15233360 TAAATTAATG
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
16 2 0.05
17 9 0.24
18 23 0.62
19 3 0.08
ACGTcount: A:0.18, C:0.22, G:0.09, T:0.51
Consensus pattern (18 bp):
TTCCATTTGTCATTGCAT
Found at i:15237441 original size:16 final size:17
Alignment explanation
Indices: 15237408--15237442 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
15237398 CAAAAAATTA
15237408 TCGACGCAACTACTGATG
1 TCGACGCAAC-ACTGATG
15237426 TCGACGCAAC-CTGATG
1 TCGACGCAACACTGATG
15237442 T
1 T
15237443 ATCCATACCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
18 10 0.59
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.23
Consensus pattern (17 bp):
TCGACGCAACACTGATG
Found at i:15241955 original size:24 final size:24
Alignment explanation
Indices: 15241927--15241978 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
15241917 AGCATTAAAC
15241927 AAACACTAGGCCTGAAAACCCTAA
1 AAACACTAGGCCTGAAAACCCTAA
15241951 AAACACTAGGCCTGAAAACCCTAA
1 AAACACTAGGCCTGAAAACCCTAA
15241975 AAAC
1 AAAC
15241979 TCATCTAGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.48, C:0.29, G:0.12, T:0.12
Consensus pattern (24 bp):
AAACACTAGGCCTGAAAACCCTAA
Found at i:15265362 original size:15 final size:15
Alignment explanation
Indices: 15265326--15265372 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
15265316 TGGGCTTTTA
* *
15265326 TATTTATTTTTCGTA
1 TATTTATTTTTGGTT
15265341 T-TTTATTTCTT-GTT
1 TATTTATTT-TTGGTT
15265355 TATTTATTTTTGGTT
1 TATTTATTTTTGGTT
15265370 TAT
1 TAT
15265373 GACTCGAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
14 12 0.43
15 16 0.57
ACGTcount: A:0.15, C:0.04, G:0.09, T:0.72
Consensus pattern (15 bp):
TATTTATTTTTGGTT
Found at i:15281186 original size:14 final size:16
Alignment explanation
Indices: 15281156--15281188 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
15281146 TATCGAAGAG
15281156 GAGAAGGAAGAAGAAA
1 GAGAAGGAAGAAGAAA
15281172 GAGAA-GAAG-AGAAA
1 GAGAAGGAAGAAGAAA
15281186 GAG
1 GAG
15281189 GAAGTTCCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 4 0.24
16 5 0.29
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (16 bp):
GAGAAGGAAGAAGAAA
Found at i:15290483 original size:21 final size:21
Alignment explanation
Indices: 15290454--15290496 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
15290444 TATCTTCTTC
*
15290454 TTCATTTTTCTAGTGTTTAGT
1 TTCACTTTTCTAGTGTTTAGT
*
15290475 TTCACTTTTCTAGTTTTTAGT
1 TTCACTTTTCTAGTGTTTAGT
15290496 T
1 T
15290497 GTGTTAGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.14, C:0.12, G:0.12, T:0.63
Consensus pattern (21 bp):
TTCACTTTTCTAGTGTTTAGT
Found at i:15292931 original size:37 final size:38
Alignment explanation
Indices: 15292881--15292973 Score: 100
Period size: 37 Copynumber: 2.4 Consensus size: 38
15292871 CGGATAGATT
*
15292881 CGATGAGGTACTGGGTACCACTTTA-CTTCG-ACTAGGC
1 CGATGAGGCACTGGGTACCACTTTATCTTCGAACTA-GC
* ** *
15292918 CGATGAGACACTGGGTGTCACTTTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTACCACTTTA-T-CTTCGAACTAGC
15292958 CGATGAGGCACTGGGT
1 CGATGAGGCACTGGGT
15292974 GCCATTATGG
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
37 21 0.46
40 21 0.46
41 4 0.09
ACGTcount: A:0.22, C:0.23, G:0.28, T:0.28
Consensus pattern (38 bp):
CGATGAGGCACTGGGTACCACTTTATCTTCGAACTAGC
Found at i:15299054 original size:37 final size:38
Alignment explanation
Indices: 15299004--15299096 Score: 100
Period size: 37 Copynumber: 2.4 Consensus size: 38
15298994 CGGATAGATT
*
15299004 CGATGAGGTACTGGGTACCACTTTA-CTTCG-ACTAGGC
1 CGATGAGGCACTGGGTACCACTTTATCTTCGAACTA-GC
* ** *
15299041 CGATGAGACACTGGGTGTCACTTTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTACCACTTTA-T-CTTCGAACTAGC
15299081 CGATGAGGCACTGGGT
1 CGATGAGGCACTGGGT
15299097 GCCATTATGG
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
37 21 0.46
40 21 0.46
41 4 0.09
ACGTcount: A:0.22, C:0.23, G:0.28, T:0.28
Consensus pattern (38 bp):
CGATGAGGCACTGGGTACCACTTTATCTTCGAACTAGC
Found at i:15302240 original size:22 final size:22
Alignment explanation
Indices: 15302192--15302271 Score: 97
Period size: 22 Copynumber: 3.6 Consensus size: 22
15302182 TTTCGCACCT
* * *
15302192 TGTGTGCCTACTGATTTGCGCTA
1 TGTGCGCCTACTGA-TTGCACTG
15302215 TGTGCGCCTACTGATTGCACTG
1 TGTGCGCCTACTGATTGCACTG
*
15302237 TGTGCCCCTACTGATTGCACTG
1 TGTGCGCCTACTGATTGCACTG
* *
15302259 TGTGTGCTTACTG
1 TGTGCGCCTACTG
15302272 TTTCCCCAGC
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
22 37 0.74
23 13 0.26
ACGTcount: A:0.12, C:0.25, G:0.26, T:0.36
Consensus pattern (22 bp):
TGTGCGCCTACTGATTGCACTG
Found at i:15322827 original size:20 final size:19
Alignment explanation
Indices: 15322787--15322833 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
15322777 AAGTTCATTT
*
15322787 ACAAAAATAATTATTACAA
1 ACAAAAATAAATATTACAA
15322806 ACAAATAATAAATATGTA-AA
1 ACAAA-AATAAATAT-TACAA
15322826 ACTAAAAA
1 AC-AAAAA
15322834 AAGTTTACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 5 0.21
20 14 0.58
21 5 0.21
ACGTcount: A:0.66, C:0.09, G:0.02, T:0.23
Consensus pattern (19 bp):
ACAAAAATAAATATTACAA
Found at i:15326475 original size:16 final size:17
Alignment explanation
Indices: 15326430--15326477 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
15326420 TTTTATTTTT
* *
15326430 ATATAAAAAATTAAAAA
1 ATATTAAAAATAAAAAA
* *
15326447 ATATTACACATAAAAAA
1 ATATTAAAAATAAAAAA
15326464 AT-TTAAAAATAAAA
1 ATATTAAAAATAAAA
15326478 GTAAATGTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
16 10 0.40
17 15 0.60
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (17 bp):
ATATTAAAAATAAAAAA
Found at i:15326950 original size:19 final size:16
Alignment explanation
Indices: 15326928--15326968 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 16
15326918 TTTTATTGAG
15326928 ATTTTTCAATTTTTGATTT
1 ATTTTTC-ATTTTT--TTT
15326947 ATTTTTCATTTTTTTT
1 ATTTTTCATTTTTTTT
15326963 ATTTTT
1 ATTTTT
15326969 TGGTAAAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.41
18 6 0.27
19 7 0.32
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.76
Consensus pattern (16 bp):
ATTTTTCATTTTTTTT
Found at i:15327067 original size:20 final size:20
Alignment explanation
Indices: 15327032--15327080 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
15327022 TCCCTTATAT
*
15327032 TTTTGGTACT-TCTCATAA-
1 TTTTGGTATTATCTCATAAC
15327050 TTCTTGGTATTATCTCATAAC
1 TT-TTGGTATTATCTCATAAC
15327071 TTTTGGTATT
1 TTTTGGTATT
15327081 GTTTCAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 2 0.07
19 7 0.26
20 16 0.59
21 2 0.07
ACGTcount: A:0.20, C:0.14, G:0.12, T:0.53
Consensus pattern (20 bp):
TTTTGGTATTATCTCATAAC
Found at i:15327552 original size:20 final size:21
Alignment explanation
Indices: 15327506--15327544 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
15327496 ATTTTTTTAT
*
15327506 ATTTTTTGATATTTCCTCAAA
1 ATTTTTTGATACTTCCTCAAA
*
15327527 AATTTTT-ATACTTCCTCA
1 ATTTTTTGATACTTCCTCA
15327545 TCATTTTTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.28, C:0.18, G:0.03, T:0.51
Consensus pattern (21 bp):
ATTTTTTGATACTTCCTCAAA
Found at i:15327912 original size:22 final size:21
Alignment explanation
Indices: 15327886--15327929 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
15327876 AAACGAGATA
15327886 TAATTTTGAAGTAA-AAATATAT
1 TAATTTTGAA-TAATAAA-ATAT
15327908 TAATTTTGAATAATAAAATAT
1 TAATTTTGAATAATAAAATAT
15327929 T
1 T
15327930 TCATTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (21 bp):
TAATTTTGAATAATAAAATAT
Found at i:15328106 original size:21 final size:20
Alignment explanation
Indices: 15328082--15328120 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
15328072 AACAATATAT
*
15328082 GAGAGATTACAAAATAATTAC
1 GAGAAATTACAAAA-AATTAC
*
15328103 GAGAAATTATAAAAAATT
1 GAGAAATTACAAAAAATT
15328121 TGGAGGGACC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.56, C:0.05, G:0.13, T:0.26
Consensus pattern (20 bp):
GAGAAATTACAAAAAATTAC
Found at i:15328446 original size:21 final size:20
Alignment explanation
Indices: 15328422--15328474 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
15328412 AAACATAAAA
*
15328422 GAGTACTAAAAATTATAAAGT
1 GAGTACAAAAAATTAT-AAGT
* * *
15328443 GAGTGCCAAAAATTATGAGT
1 GAGTACAAAAAATTATAAGT
15328463 GAGTACAAAAAA
1 GAGTACAAAAAA
15328475 CACGAGAGAG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 13 0.48
21 14 0.52
ACGTcount: A:0.51, C:0.08, G:0.19, T:0.23
Consensus pattern (20 bp):
GAGTACAAAAAATTATAAGT
Found at i:15328463 original size:20 final size:20
Alignment explanation
Indices: 15328429--15328494 Score: 62
Period size: 19 Copynumber: 3.3 Consensus size: 20
15328419 AAAGAGTACT
*
15328429 AAAAATTATAAAGTGAGTGCC
1 AAAAATTAT-GAGTGAGTGCC
*
15328450 AAAAATTATGAGTGAGT-AC
1 AAAAATTATGAGTGAGTGCC
** * *
15328469 AAAAAACACGAGAGAGTGCC
1 AAAAATTATGAGTGAGTGCC
15328489 AAAAAT
1 AAAAAT
15328495 ATTGGTTTGT
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
19 14 0.39
20 13 0.36
21 9 0.25
ACGTcount: A:0.52, C:0.11, G:0.20, T:0.18
Consensus pattern (20 bp):
AAAAATTATGAGTGAGTGCC
Found at i:15329773 original size:2 final size:2
Alignment explanation
Indices: 15329766--15329807 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
15329756 TTATTTACTC
15329766 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
15329808 ACAATGCATG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:15337085 original size:9 final size:9
Alignment explanation
Indices: 15337071--15337104 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
15337061 CATTTGATCA
15337071 AATTAACCG
1 AATTAACCG
* *
15337080 AATTAATCA
1 AATTAACCG
15337089 AATTAACCG
1 AATTAACCG
15337098 AATTAAC
1 AATTAAC
15337105 TAAATAGCAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.50, C:0.18, G:0.06, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:15337109 original size:18 final size:18
Alignment explanation
Indices: 15337067--15337103 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
15337057 TATTCATTTG
15337067 ATCAAATTAACCGAATTA
1 ATCAAATTAACCGAATTA
15337085 ATCAAATTAACCGAATTA
1 ATCAAATTAACCGAATTA
15337103 A
1 A
15337104 CTAAATAGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.16, G:0.05, T:0.27
Consensus pattern (18 bp):
ATCAAATTAACCGAATTA
Found at i:15337715 original size:29 final size:29
Alignment explanation
Indices: 15337680--15337745 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
15337670 TAAATCATTT
*
15337680 AAAAATTTTAAT-TTTTTA-AAAAATATGA
1 AAAAATTTAAATATTTTTATAAAAATAT-A
*
15337708 AAATAATTTAAATATTTTTATAAAATTATA
1 AAA-AATTTAAATATTTTTATAAAAATATA
15337738 AAAAATTT
1 AAAAATTT
15337746 CAGAAAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
28 3 0.09
29 13 0.39
30 10 0.30
31 7 0.21
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (29 bp):
AAAAATTTAAATATTTTTATAAAAATATA
Found at i:15338316 original size:198 final size:198
Alignment explanation
Indices: 15337978--15338362 Score: 592
Period size: 198 Copynumber: 1.9 Consensus size: 198
15337968 TCCCCAACTC
** * * *
15337978 ATAAATAGGAGGATAATACACTTCATTGCATTCGAACTCACATCCTCCTGCATTGGCAACAATGT
1 ATAAATAGGAGGATAATACACTTCAGCGCATTCAAACTCACATCCTCCTACATTGGCAACAATAT
** * *
15338043 CCATGTCAATCGAGTTAAGACTTAATCGACTTAAAAAACATTTTTTTATTAATATTCATTTACCT
66 CCATACCAATCGAGCTAAGACTTAATCGACTTAAAAAACATTTTTTAATTAATATTCATTTACCT
* *
15338108 TTCCTTTTTAACTTTATTCATTTCTTTCTTTTCTTTTCATTTT-TTAAACCTAAAACCCGATAGT
131 TTCCTTTTTAACTTTATTCATTTCTTTCTTTTCCTTCCATTTTCTT-AACCTAAAACCCGATAGT
15338172 TTTT
195 TTTT
* * ** *
15338176 ATAAATAGGAGGATAATACGCTTGAGCGCATTCAAACTCATGTCCTCTTACATTGGCAACAATAT
1 ATAAATAGGAGGATAATACACTTCAGCGCATTCAAACTCACATCCTCCTACATTGGCAACAATAT
*
15338241 TCATACCAATCGAGCTAAGACTTAATCGACTTAAAAAACATTTTTTAATTAATATTCATTTACCT
66 CCATACCAATCGAGCTAAGACTTAATCGACTTAAAAAACATTTTTTAATTAATATTCATTTACCT
*
15338306 TTCCTTTTTAACTTTATTCGTTTCTTTCTTTTCCTTCCATTTTCTTAACCTAAAACC
131 TTCCTTTTTAACTTTATTCATTTCTTTCTTTTCCTTCCATTTTCTTAACCTAAAACC
15338363 TAATAATTTC
Statistics
Matches: 168, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
198 166 0.99
199 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.41
Consensus pattern (198 bp):
ATAAATAGGAGGATAATACACTTCAGCGCATTCAAACTCACATCCTCCTACATTGGCAACAATAT
CCATACCAATCGAGCTAAGACTTAATCGACTTAAAAAACATTTTTTAATTAATATTCATTTACCT
TTCCTTTTTAACTTTATTCATTTCTTTCTTTTCCTTCCATTTTCTTAACCTAAAACCCGATAGTT
TTT
Found at i:15340999 original size:16 final size:16
Alignment explanation
Indices: 15340978--15341024 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
15340968 TAGTTATTCT
15340978 TAAACAACAGTTGTTC
1 TAAACAACAGTTGTTC
** *
15340994 TAAACAACAAATATTC
1 TAAACAACAGTTGTTC
*
15341010 TAAACAAGAGTTGTT
1 TAAACAACAGTTGTT
15341025 GCTCTGGAAG
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.30
Consensus pattern (16 bp):
TAAACAACAGTTGTTC
Found at i:15341157 original size:4 final size:4
Alignment explanation
Indices: 15341148--15341174 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
15341138 AGTGTAGTAA
15341148 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
15341175 ATAATTATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:15352685 original size:18 final size:18
Alignment explanation
Indices: 15352662--15352711 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
15352652 TGGTAAGAGT
*
15352662 TTATTTCATTTTTTAATA
1 TTATTTAATTTTTTAATA
15352680 TTATTTAATTTTTTAAT-
1 TTATTTAATTTTTTAATA
*
15352697 TTAATTAATATTTTT
1 TTATTTAAT-TTTTT
15352712 TTATAATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.28
18 21 0.72
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (18 bp):
TTATTTAATTTTTTAATA
Found at i:15357588 original size:16 final size:17
Alignment explanation
Indices: 15357555--15357588 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
15357545 ATGAGTTAGA
*
15357555 ATAATGTTTAGATATTT
1 ATAATGGTTAGATATTT
15357572 ATAATGGTTAG-TATTT
1 ATAATGGTTAGATATTT
15357588 A
1 A
15357589 GGGTTTTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (17 bp):
ATAATGGTTAGATATTT
Found at i:15362996 original size:18 final size:18
Alignment explanation
Indices: 15362973--15363018 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
15362963 TGCCCAGCAA
*
15362973 AATTCCCATTG-CAACCTC
1 AATTCCCATCGTC-ACCTC
*
15362991 AATTCCTATCGTCACCTC
1 AATTCCCATCGTCACCTC
15363009 AATTCCCATC
1 AATTCCCATC
15363019 ACCTTATGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 23 0.96
19 1 0.04
ACGTcount: A:0.26, C:0.39, G:0.04, T:0.30
Consensus pattern (18 bp):
AATTCCCATCGTCACCTC
Found at i:15363391 original size:59 final size:59
Alignment explanation
Indices: 15363298--15363521 Score: 243
Period size: 59 Copynumber: 3.7 Consensus size: 59
15363288 ATTTATTTCA
15363298 AATATTTTTGTAAACATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTCTTTTG
1 AATATTTTTGTAAACATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTCTTTTG
* *
15363357 AATATTTTTGTAAACATTATTTTTATATTTTTTCATTTAATAAAATAGAAGTTCTGTTG
1 AATATTTTTGTAAACATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTCTTTTG
* * * * ** * * * * *
15363416 AATAATTGTGTACACATTAGTTTTGGCATATTGTAACATTTAATGAAATACAAATTCTTATA
1 AATATTTTTGTAAACATTA-TTTT--TATATTGTTTCATTTAATAAAATAGAAGTTCTTTTG
* *
15363478 AATATTTTT-CAACACATTATTTTTGGCATATTATTTCATTTAAT
1 AATATTTTTGTAA-ACATTATTTTT---ATATTGTTTCATTTAAT
15363522 TGAGAACCAA
Statistics
Matches: 135, Mismatches: 23, Indels: 11
0.80 0.14 0.07
Matches are distributed among these distances:
59 73 0.54
60 4 0.03
61 5 0.04
62 53 0.39
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.49
Consensus pattern (59 bp):
AATATTTTTGTAAACATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTCTTTTG
Found at i:15367772 original size:24 final size:24
Alignment explanation
Indices: 15367736--15368059 Score: 194
Period size: 24 Copynumber: 13.7 Consensus size: 24
15367726 ATAAGCTGAT
* *
15367736 TGACGAGCATAAACATGTGCAAAC
1 TGACGAGCGTAAACATGTGCAAGC
* *
15367760 TGACGAGCTTAAACGTGTGCAAGC
1 TGACGAGCGTAAACATGTGCAAGC
*
15367784 TGACGA--GTATAACATGTGCAAGT
1 TGACGAGCGTA-AACATGTGCAAGC
* *
15367807 TGACGAGCGTAAACGTGTTCAAGC
1 TGACGAGCGTAAACATGTGCAAGC
15367831 TGACGAGCGTAAACATGTGCAA--
1 TGACGAGCGTAAACATGTGCAAGC
* * *
15367853 -GACAAGCGTAAA-AGTGTGCCAGA
1 TGACGAGCGTAAACA-TGTGCAAGC
** * ** *
15367876 TGACGAGCGTAAATGTATATAAGA
1 TGACGAGCGTAAACATGTGCAAGC
* * * * *
15367900 TGACGAGCATAAACGTATACAAGT
1 TGACGAGCGTAAACATGTGCAAGC
* * ** *
15367924 TGATGAGTGTAAAGGTGTGTAAGC
1 TGACGAGCGTAAACATGTGCAAGC
* * * **
15367948 TTATGAGCGTAAA-AGTATATAAGC
1 TGACGAGCGTAAACA-TGTGCAAGC
* * **
15367972 TGATGAGCGTAAACATATATAAGC
1 TGACGAGCGTAAACATGTGCAAGC
* *
15367996 TGACGAGCATAAACATGTGCAAGA
1 TGACGAGCGTAAACATGTGCAAGC
* * * **
15368020 TGACGAGCATAAACGTATATAAGC
1 TGACGAGCGTAAACATGTGCAAGC
15368044 TGACGAGCGTAAACAT
1 TGACGAGCGTAAACAT
15368060 ATAAAATCTG
Statistics
Matches: 240, Mismatches: 50, Indels: 20
0.77 0.16 0.06
Matches are distributed among these distances:
20 1 0.00
21 17 0.07
22 2 0.01
23 17 0.07
24 199 0.83
25 4 0.02
ACGTcount: A:0.38, C:0.15, G:0.26, T:0.22
Consensus pattern (24 bp):
TGACGAGCGTAAACATGTGCAAGC
Found at i:15367811 original size:47 final size:47
Alignment explanation
Indices: 15367736--15367882 Score: 158
Period size: 47 Copynumber: 3.1 Consensus size: 47
15367726 ATAAGCTGAT
* * *
15367736 TGACGAGCATAAACATGTGCAAACTGACGAGCTTAAACGTGTGCAAGC
1 TGACGAGTAT-AACATGTGCAAGCTGACGAGCGTAAACGTGTGCAAGC
* *
15367784 TGACGAGTATAACATGTGCAAGTTGACGAGCGTAAACGTGTTCAAGC
1 TGACGAGTATAACATGTGCAAGCTGACGAGCGTAAACGTGTGCAAGC
* * * *
15367831 TGACGAGCGTA-AACATGTGCAA---GACAAGCGTAAAAGTGTGCCAGA
1 TGACGA--GTATAACATGTGCAAGCTGACGAGCGTAAACGTGTGCAAGC
15367876 TGACGAG
1 TGACGAG
15367883 CGTAAATGTA
Statistics
Matches: 87, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
43 1 0.01
45 24 0.28
47 39 0.45
48 20 0.23
49 3 0.03
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (47 bp):
TGACGAGTATAACATGTGCAAGCTGACGAGCGTAAACGTGTGCAAGC
Found at i:15367957 original size:72 final size:72
Alignment explanation
Indices: 15367759--15368062 Score: 269
Period size: 72 Copynumber: 4.3 Consensus size: 72
15367749 CATGTGCAAA
* * * * * * *
15367759 CTGACGAGCTTAAACGTGTGCAAGCTGACGAGTAT-AACATGTGCAAGTTGACGAGCGTAAACGT
1 CTGACGAGCGTAAACATATACAAGCTGACGAGCATAAACATGTGCAAGATGACGAGCGTAAAAGT
*
15367823 GT-TCAAG
66 ATAT-AAG
* * * * * *
15367830 CTGACGAGCGTAAACATGTGCAA---GACAAGCGTAAA-AGTGTGCCAGATGACGAGCGTAAATG
1 CTGACGAGCGTAAACATATACAAGCTGACGAGCATAAACA-TGTGCAAGATGACGAGCGTAAAAG
15367891 TATATAAG
65 TATATAAG
* * * * * ** ** * * * *
15367899 ATGACGAGCATAAACGTATACAAGTTGATGAGTGTAAAGGTGTGTAAGCTTATGAGCGTAAAAGT
1 CTGACGAGCGTAAACATATACAAGCTGACGAGCATAAACATGTGCAAGATGACGAGCGTAAAAGT
15367964 ATATAAG
66 ATATAAG
* * * *
15367971 CTGATGAGCGTAAACATATATAAGCTGACGAGCATAAACATGTGCAAGATGACGAGCATAAACGT
1 CTGACGAGCGTAAACATATACAAGCTGACGAGCATAAACATGTGCAAGATGACGAGCGTAAAAGT
15368036 ATATAAG
66 ATATAAG
15368043 CTGACGAGCGTAAACATATA
1 CTGACGAGCGTAAACATATA
15368063 AAATCTGGCA
Statistics
Matches: 184, Mismatches: 42, Indels: 13
0.77 0.18 0.05
Matches are distributed among these distances:
68 7 0.04
69 46 0.25
70 1 0.01
71 21 0.11
72 109 0.59
ACGTcount: A:0.38, C:0.15, G:0.26, T:0.22
Consensus pattern (72 bp):
CTGACGAGCGTAAACATATACAAGCTGACGAGCATAAACATGTGCAAGATGACGAGCGTAAAAGT
ATATAAG
Found at i:15368062 original size:24 final size:24
Alignment explanation
Indices: 15367876--15368081 Score: 153
Period size: 24 Copynumber: 8.6 Consensus size: 24
15367866 GTGTGCCAGA
** *
15367876 TGACGAGCGTAAATGTATATAAGA
1 TGACGAGCGTAAACATATATAAGC
* * * *
15367900 TGACGAGCATAAACGTATACAAGT
1 TGACGAGCGTAAACATATATAAGC
* * ** * *
15367924 TGATGAGTGTAAAGGTGTGTAAGC
1 TGACGAGCGTAAACATATATAAGC
* *
15367948 TTATGAGCGTAAA-AGTATATAAGC
1 TGACGAGCGTAAACA-TATATAAGC
*
15367972 TGATGAGCGTAAACATATATAAGC
1 TGACGAGCGTAAACATATATAAGC
* * ** *
15367996 TGACGAGCATAAACATGTGCAAGA
1 TGACGAGCGTAAACATATATAAGC
* *
15368020 TGACGAGCATAAACGTATATAAGC
1 TGACGAGCGTAAACATATATAAGC
* *
15368044 TGACGAGCGTAAACATATAAAATC
1 TGACGAGCGTAAACATATATAAGC
* *
15368068 TGGCAAGCGTAAAC
1 TGACGAGCGTAAAC
15368082 GTAGTGAATT
Statistics
Matches: 145, Mismatches: 35, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
24 144 0.99
25 1 0.01
ACGTcount: A:0.40, C:0.13, G:0.24, T:0.23
Consensus pattern (24 bp):
TGACGAGCGTAAACATATATAAGC
Found at i:15369028 original size:8 final size:8
Alignment explanation
Indices: 15369015--15369050 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
15369005 TCCTAAGTAT
15369015 TATACATA
1 TATACATA
15369023 TATACATA
1 TATACATA
*
15369031 CATACATA
1 TATACATA
*
15369039 CATACATA
1 TATACATA
15369047 TATA
1 TATA
15369051 TATGTATGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (8 bp):
TATACATA
Found at i:15369033 original size:12 final size:12
Alignment explanation
Indices: 15369016--15369050 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
15369006 CCTAAGTATT
15369016 ATACATATATAC
1 ATACATATATAC
*
15369028 ATACATACATAC
1 ATACATATATAC
15369040 ATACATATATA
1 ATACATATATA
15369051 TATGTATGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.31
Consensus pattern (12 bp):
ATACATATATAC
Found at i:15369053 original size:4 final size:4
Alignment explanation
Indices: 15369016--15369046 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
15369006 CCTAAGTATT
*
15369016 ATAC ATAT ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
15369047 TATATATGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.19, G:0.00, T:0.29
Consensus pattern (4 bp):
ATAC
Found at i:15371769 original size:3 final size:3
Alignment explanation
Indices: 15371761--15371792 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
15371751 AATTTTGTAA
15371761 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
15371793 ACAATGAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:15377929 original size:29 final size:29
Alignment explanation
Indices: 15377885--15377965 Score: 117
Period size: 29 Copynumber: 2.8 Consensus size: 29
15377875 AGTTACACTG
*
15377885 AAGTACTTTACCATAACAGAGTGGCACCA
1 AAGTACTTTATCATAACAGAGTGGCACCA
* * *
15377914 AAGTACTTTATTATAACAGAGTAGCACCG
1 AAGTACTTTATCATAACAGAGTGGCACCA
*
15377943 AAGTACTTTATCATAACAAAGTG
1 AAGTACTTTATCATAACAGAGTG
15377966 CATTAATAGA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.26
Consensus pattern (29 bp):
AAGTACTTTATCATAACAGAGTGGCACCA
Found at i:15386684 original size:45 final size:45
Alignment explanation
Indices: 15386620--15386830 Score: 180
Period size: 45 Copynumber: 4.7 Consensus size: 45
15386610 CCTGAATGTA
* *
15386620 TAAGACCATAGTTGAAAGATACTATGGCATTAACCTAGGATTGTG
1 TAAGACCATAGTTGAAAGATACTATGGCATCAATCTAGGATTGTG
* * * *
15386665 TAAGACCATAGTTGAAAGATAATATGACACCAAAT-TA-GATATGTA
1 TAAGACCATAGTTGAAAGATACTATGGCATC-AATCTAGGAT-TGTG
* * * **
15386710 TAAGACCTTAGTTGAAAGATACTACGGCATCATATC-GGGAATAAT-
1 TAAGACCATAGTTGAAAGATACTATGGCATCA-ATCTAGG-ATTGTG
* * * *
15386755 CAAGACCATAGTTGAACGATACTATGGCATC-ATTTCGGGATTGTG
1 TAAGACCATAGTTGAAAGATACTATGGCATCAATCT-AGGATTGTG
* * *
15386800 TAAGACCTTGGTTGAAAGATACCATGGCATC
1 TAAGACCATAGTTGAAAGATACTATGGCATC
15386831 CCGGAATAAT
Statistics
Matches: 131, Mismatches: 26, Indels: 18
0.75 0.15 0.10
Matches are distributed among these distances:
43 2 0.02
44 7 0.05
45 116 0.89
46 4 0.03
47 2 0.02
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.27
Consensus pattern (45 bp):
TAAGACCATAGTTGAAAGATACTATGGCATCAATCTAGGATTGTG
Found at i:15390233 original size:3 final size:3
Alignment explanation
Indices: 15390221--15390286 Score: 59
Period size: 3 Copynumber: 23.3 Consensus size: 3
15390211 GCTAGACAAT
* * *
15390221 AGA A-A AGA AGA AG- AGA AAA AGA AGA AGA AGA AGA AGA AG- AGG CGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* *
15390266 ATA AGA AGC AGA AG- AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA A
15390287 ATGGAGATAC
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
2 8 0.16
3 42 0.84
ACGTcount: A:0.64, C:0.03, G:0.32, T:0.02
Consensus pattern (3 bp):
AGA
Found at i:15390403 original size:11 final size:11
Alignment explanation
Indices: 15390371--15390414 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
15390361 ATCTTTGTCC
15390371 CTTTTTCTTCT
1 CTTTTTCTTCT
*
15390382 CTTCTTCTCTTGT
1 CTT-TT-TCTTCT
*
15390395 CTTTTTCTTTT
1 CTTTTTCTTCT
15390406 CTTTTTCTT
1 CTTTTTCTT
15390415 AACTCTAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 17 0.59
12 4 0.14
13 8 0.28
ACGTcount: A:0.00, C:0.25, G:0.02, T:0.73
Consensus pattern (11 bp):
CTTTTTCTTCT
Found at i:15394464 original size:15 final size:15
Alignment explanation
Indices: 15394425--15394468 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
15394415 AAGGAGAGGG
15394425 AAAGGAAAGAGAAAGT
1 AAAGGAAAG-GAAAGT
*
15394441 AAAGCAAAGGAAAGT
1 AAAGGAAAGGAAAGT
*
15394456 AAGGGAAA-GAAAG
1 AAAGGAAAGGAAAG
15394469 AATCTTCCCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 5 0.20
15 12 0.48
16 8 0.32
ACGTcount: A:0.61, C:0.02, G:0.32, T:0.05
Consensus pattern (15 bp):
AAAGGAAAGGAAAGT
Found at i:15401747 original size:42 final size:42
Alignment explanation
Indices: 15401661--15401749 Score: 101
Period size: 42 Copynumber: 2.1 Consensus size: 42
15401651 GGTTCGAAAC
* * *
15401661 TTTTGAAAATCATGTTTTCATTTGTTTTACTTTTTATTTCTA
1 TTTTTAAAATCATGTTTTCATATGTTTTACTTTTCATTTCTA
* *
15401703 TTTTTAAAATC-TGTTTT-ATATGTTTTATCATTTTCCTTTTTA
1 TTTTTAAAATCATGTTTTCATATGTTTTA-C-TTTTCATTTCTA
15401745 TTTTT
1 TTTTT
15401750 TTTAAAAACT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
40 9 0.22
41 7 0.17
42 24 0.60
ACGTcount: A:0.20, C:0.09, G:0.06, T:0.65
Consensus pattern (42 bp):
TTTTTAAAATCATGTTTTCATATGTTTTACTTTTCATTTCTA
Found at i:15403134 original size:46 final size:44
Alignment explanation
Indices: 15403052--15403152 Score: 123
Period size: 47 Copynumber: 2.2 Consensus size: 44
15403042 TGAGATGGTA
* *
15403052 GCTTCAATCTGCCACTCTTGATTTTAGGAGTAAAAGATTGGATAGTG
1 GCTTCAATCTGCCACTCTTGATCTTAGGAGTAAAAGATT--AGA-TG
* * *
15403099 GCTTCAATCTGCCCCTTTTGA-CTTAGGGGTAAAAGATTAGATG
1 GCTTCAATCTGCCACTCTTGATCTTAGGAGTAAAAGATTAGATG
15403142 GCTTCAATCTG
1 GCTTCAATCTG
15403153 TCCCATGATC
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
43 13 0.27
44 2 0.04
46 15 0.31
47 19 0.39
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.34
Consensus pattern (44 bp):
GCTTCAATCTGCCACTCTTGATCTTAGGAGTAAAAGATTAGATG
Found at i:15403195 original size:42 final size:41
Alignment explanation
Indices: 15403126--15403263 Score: 158
Period size: 42 Copynumber: 3.4 Consensus size: 41
15403116 TTGACTTAGG
* *
15403126 GGTAAAAGATTAGATG-G-CTTCAATCTGTCCCATGATCGA
1 GGTAAGAGATTGGATGAGACTTCAATCTGTCCCATGATCGA
* *
15403165 GGTAAGAGATTGGATGATATCTTCAATCTGTCCCATGATCGG
1 GGTAAGAGATTGGATGAGA-CTTCAATCTGTCCCATGATCGA
* * * *
15403207 GGTAAGAGATTGGATG-GACCTCAGTCT-ACCCTATGACCGA
1 GGTAAGAGATTGGATGAGACTTCAATCTGTCCC-ATGATCGA
15403247 GGTAAGAGATTGGATGA
1 GGTAAGAGATTGGATGA
15403264 CATTACCACA
Statistics
Matches: 84, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
39 17 0.20
40 29 0.35
41 1 0.01
42 37 0.44
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.27
Consensus pattern (41 bp):
GGTAAGAGATTGGATGAGACTTCAATCTGTCCCATGATCGA
Found at i:15403374 original size:50 final size:49
Alignment explanation
Indices: 15403316--15403575 Score: 209
Period size: 50 Copynumber: 5.2 Consensus size: 49
15403306 TATAAAGGGA
* * * *
15403316 AAGGTTGAGGCCACAATGGCGAACCCGGTACCTTAAAAGATGTGATGGG
1 AAGGTTGAGGCCACAACGGTGAACCCGATACCTTAGAAGATGTGATGGG
* * ** * * *
15403365 AAGGATTGAGGCTACAACGGCGAATTCGATACCAT-GAAGATATGAAGGG
1 AAGG-TTGAGGCCACAACGGTGAACCCGATACCTTAGAAGATGTGATGGG
* * * * *
15403414 AAAGGTTAAGGCCGCAACGGTAAACCCGGTACCTTAGAAGATGTGATAGG
1 -AAGGTTGAGGCCACAACGGTGAACCCGATACCTTAGAAGATGTGATGGG
* * * * * *
15403464 AAGGATTGAGGTCACAACAGTGAATCCAATACCTTA-AAGATATGAAGGG
1 AAGG-TTGAGGCCACAACGGTGAACCCGATACCTTAGAAGATGTGATGGG
* * * * *
15403513 AAAGGTTGAGGCCGCAACAGTGTACCCAATACCTTAGAAGATGTGATAGG
1 -AAGGTTGAGGCCACAACGGTGAACCCGATACCTTAGAAGATGTGATGGG
*
15403563 AATGATTGAGGCC
1 AA-GGTTGAGGCC
15403576 GCATCAGCGA
Statistics
Matches: 164, Mismatches: 40, Indels: 13
0.76 0.18 0.06
Matches are distributed among these distances:
49 79 0.48
50 85 0.52
ACGTcount: A:0.35, C:0.17, G:0.29, T:0.19
Consensus pattern (49 bp):
AAGGTTGAGGCCACAACGGTGAACCCGATACCTTAGAAGATGTGATGGG
Found at i:15403474 original size:99 final size:99
Alignment explanation
Indices: 15403303--15403672 Score: 370
Period size: 99 Copynumber: 3.7 Consensus size: 99
15403293 GGAAACATAG
* * * * * *
15403303 AGATATAAAGGGAAAGGTTGAGGCCACAATGGCGAACCCGGTACCTTAAAAGATGTGATGGGAAG
1 AGATATGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTAGAAGATGTGATAGGAAG
*
15403368 GATTGAGGCTACAACGGCGAATTCGATACCATGA
66 GATTGAGGCTACAACAGCGAATTCGATACCATGA
* *
15403402 AGATATGAAGGGAAAGGTTAAGGCCGCAACGGTAAACCCGGTACCTTAGAAGATGTGATAGGAAG
1 AGATATGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTAGAAGATGTGATAGGAAG
* * * * *
15403467 GATTGAGG-TCACAACAGTGAATCCAATACCTTAA
66 GATTGAGGCT-ACAACAGCGAATTCGATACCATGA
* * ** *
15403501 AGATATGAAGGGAAAGGTTGAGGCCGCAACAGTGTACCCAATACCTTAGAAGATGTGATAGGAAT
1 AGATATGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTAGAAGATGTGATAGGAAG
** * * * *
15403566 GATTGAGGCCGCATCAGCGAATCTTG-TACCACGG
66 GATTGAGGCTACAACAGCGAAT-TCGATACCATGA
* ** * * *** *
15403600 AGATATGGAGGGAAAGGTTGAAACTGCAATGGTGAACCTTATACCTTAG-AGATATGA-AGGGAA
1 AGATATGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTAGAAGATGTGATA-GGAA
*
15403663 AGATTGAGGC
65 GGATTGAGGC
15403673 CCTAATGGCA
Statistics
Matches: 224, Mismatches: 43, Indels: 9
0.81 0.16 0.03
Matches are distributed among these distances:
97 1 0.00
98 21 0.09
99 202 0.90
ACGTcount: A:0.35, C:0.15, G:0.29, T:0.20
Consensus pattern (99 bp):
AGATATGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTAGAAGATGTGATAGGAAG
GATTGAGGCTACAACAGCGAATTCGATACCATGA
Found at i:15403577 original size:50 final size:50
Alignment explanation
Indices: 15403344--15403578 Score: 190
Period size: 49 Copynumber: 4.7 Consensus size: 50
15403334 GCGAACCCGG
* * * ** * * ** *
15403344 TACCTTAAAAGATGTGATGGGAAGGATTGAGGCTACAACGGCGAATTCGA
1 TACCTTAGAAGATGTGATAGGAAAGATTGAGGCCGCAACAGTGAACCCAA
* * * * * * **
15403394 TACCAT-GAAGATATGA-AGGGAAAGGTTAAGGCCGCAACGGTAAACCCGG
1 TACCTTAGAAGATGTGATA-GGAAAGATTGAGGCCGCAACAGTGAACCCAA
* * * *
15403443 TACCTTAGAAGATGTGATAGGAAGGATTGAGGTCACAACAGTGAATCCAA
1 TACCTTAGAAGATGTGATAGGAAAGATTGAGGCCGCAACAGTGAACCCAA
* * *
15403493 TACCTTA-AAGATATGA-AGGGAAAGGTTGAGGCCGCAACAGTGTACCCAA
1 TACCTTAGAAGATGTGATA-GGAAAGATTGAGGCCGCAACAGTGAACCCAA
*
15403542 TACCTTAGAAGATGTGATAGGAATGATTGAGGCCGCA
1 TACCTTAGAAGATGTGATAGGAAAGATTGAGGCCGCA
15403579 TCAGCGAATC
Statistics
Matches: 143, Mismatches: 36, Indels: 12
0.75 0.19 0.06
Matches are distributed among these distances:
48 1 0.01
49 74 0.52
50 66 0.46
51 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.29, T:0.20
Consensus pattern (50 bp):
TACCTTAGAAGATGTGATAGGAAAGATTGAGGCCGCAACAGTGAACCCAA
Found at i:15403648 original size:198 final size:197
Alignment explanation
Indices: 15403303--15403671 Score: 429
Period size: 198 Copynumber: 1.9 Consensus size: 197
15403293 GGAAACATAG
** ** *
15403303 AGATATAAAGGGAAAGGTTGAGGCCACAATGGCGAACCCGGTACCTTAAAAGATGTGATGGGAAG
1 AGATATAAAGGGAAAGGTTGAGGCCACAACAGCGAACCCAATACCTTAAAAGATGTGATAGGAAG
* * * *
15403368 GATTGAGGCTACAACGGCGAATTCGATACCATGAAGATATGAAGGGAAAGGTTAAGGCCGCAACG
66 GATTGAGGCCACAACAGCGAATTCGATACCACGAAGATATGAAGGGAAAGGTTAAGACCGCAACG
* * *
15403433 GTAAACCCGGTACCTTAGAAGATGTGATA-GGAAGGATTGAGGTCACAACAGTGAATCCAATACC
131 GTAAACCCGATACCTTAG-AGATATGA-AGGGAAAGATTGAGGTCACAACAGTGAATCCAATACC
15403497 TTAA
194 TTAA
* * * * * *
15403501 AGATATGAAGGGAAAGGTTGAGGCCGCAACAGTGTACCCAATACCTTAGAAGATGTGATAGGAAT
1 AGATATAAAGGGAAAGGTTGAGGCCACAACAGCGAACCCAATACCTTAAAAGATGTGATAGGAAG
* * * * * *
15403566 GATTGAGGCCGCATCAGCGAATCTTG-TACCACGGAGATATGGAGGGAAAGGTTGAA-ACTGCAA
66 GATTGAGGCCACAACAGCGAAT-TCGATACCACGAAGATATGAAGGGAAAGGTT-AAGACCGCAA
* * **
15403629 TGGTGAACCTTATACCTTAGAGATATGAAGGGAAAGATTGAGG
129 CGGTAAACCCGATACCTTAGAGATATGAAGGGAAAGATTGAGG
15403672 CCCTAATGGC
Statistics
Matches: 140, Mismatches: 28, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
196 1 0.01
197 19 0.14
198 116 0.83
199 4 0.03
ACGTcount: A:0.36, C:0.15, G:0.30, T:0.20
Consensus pattern (197 bp):
AGATATAAAGGGAAAGGTTGAGGCCACAACAGCGAACCCAATACCTTAAAAGATGTGATAGGAAG
GATTGAGGCCACAACAGCGAATTCGATACCACGAAGATATGAAGGGAAAGGTTAAGACCGCAACG
GTAAACCCGATACCTTAGAGATATGAAGGGAAAGATTGAGGTCACAACAGTGAATCCAATACCTT
AA
Found at i:15403965 original size:39 final size:39
Alignment explanation
Indices: 15403911--15404347 Score: 445
Period size: 39 Copynumber: 11.0 Consensus size: 39
15403901 AAGCAAAACA
15403911 AAGTCATCCAATCTCTTACCCCGATCATGAGGCAGATTG
1 AAGTCATCCAATCTCTTACCCCGATCATGAGGCAGATTG
* *
15403950 AAGTCATCCAATCTCTTACCCTGATCATGAGACAGATTG
1 AAGTCATCCAATCTCTTACCCCGATCATGAGGCAGATTG
* *
15403989 AAGCCATCCAATCTCTTACCCCGATCATGA-GAAGGATTG
1 AAGTCATCCAATCTCTTACCCCGATCATGAGGCA-GATTG
* * * * * *
15404028 AAGACACACCAATC-CTTTA-CCCGATCATGCGACGGATTAA
1 AAGTCA-TCCAATCTC-TTACCCCGATCATGAGGCAGATT-G
* **
15404068 AAATACA-CCAATCTCTTACCATGATCATGAGGCAGATTG
1 AAGT-CATCCAATCTCTTACCCCGATCATGAGGCAGATTG
* * *
15404107 AAG-AATCCAATCCCTTACCCCGATCATGAGGCGGATTG
1 AAGTCATCCAATCTCTTACCCCGATCATGAGGCAGATTG
* * * *
15404145 AAGACATACCAATCTCTTACCCCAATCATGGGGCAAATTG
1 AAGTCAT-CCAATCTCTTACCCCGATCATGAGGCAGATTG
* * * *
15404185 AAGCCATCCAATCTCTTAACCCGATCATAAGGTAGATTG
1 AAGTCATCCAATCTCTTACCCCGATCATGAGGCAGATTG
*
15404224 AAGACATCATCCAATCTCTTACCCCCGATCAT-ACGGTAGATTG
1 AAG---TCATCCAATCTCTTA-CCCCGATCATGA-GGCAGATTG
* *
15404267 AGGATCATCCAATCTCTTACCCCGATCATGAGGCAAATTG
1 AAG-TCATCCAATCTCTTACCCCGATCATGAGGCAGATTG
*
15404307 AAGACATCATCCAATCTCTTACCCCGATCATGAGGTAGATT
1 AAG---TCATCCAATCTCTTACCCCGATCATGAGGCAGATT
15404348 AAACCTCAAA
Statistics
Matches: 331, Mismatches: 48, Indels: 35
0.80 0.12 0.08
Matches are distributed among these distances:
37 1 0.00
38 32 0.10
39 132 0.40
40 78 0.24
41 19 0.06
42 49 0.15
43 20 0.06
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (39 bp):
AAGTCATCCAATCTCTTACCCCGATCATGAGGCAGATTG
Found at i:15405255 original size:6 final size:6
Alignment explanation
Indices: 15405246--15405301 Score: 58
Period size: 6 Copynumber: 8.7 Consensus size: 6
15405236 TCGACCTCTC
* *
15405246 CTTTTT CTTTTT CTTCTCTT CTCTTCT CTTTTT CTTTTT CTTTTT TTTCTTT
1 CTTTTT CTTTTT CTT-T-TT CT-TTTT CTTTTT CTTTTT CTTTTT CTT-TTT
15405298 CTTT
1 CTTT
15405302 CCCTTTTTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
6 27 0.64
7 9 0.21
8 5 0.12
9 1 0.02
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (6 bp):
CTTTTT
Found at i:15405317 original size:33 final size:33
Alignment explanation
Indices: 15405246--15405309 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
15405236 TCGACCTCTC
*
15405246 CTTTTTCTTTTTCTTCTCTTCTCTTCTCTTTTT
1 CTTTTTCTTTTTCTTCTCTTCTCTTCCCTTTTT
*
15405279 CTTTTTCTTTTTTTTCT-TTCT-TTCCCTTTTT
1 CTTTTTCTTTTTCTTCTCTTCTCTTCCCTTTTT
15405310 TATTTTTTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 9 0.31
32 4 0.14
33 16 0.55
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (33 bp):
CTTTTTCTTTTTCTTCTCTTCTCTTCCCTTTTT
Found at i:15406178 original size:21 final size:19
Alignment explanation
Indices: 15406154--15406192 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
15406144 GGGTTTTCAT
15406154 TTTGACTTTTTCCTTCTTTTC
1 TTTGA-TTTTT-CTTCTTTTC
*
15406175 TTTGATTTTTTTTCTTTT
1 TTTGATTTTTCTTCTTTT
15406193 TGTCCCTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 5 0.29
21 5 0.29
ACGTcount: A:0.05, C:0.15, G:0.05, T:0.74
Consensus pattern (19 bp):
TTTGATTTTTCTTCTTTTC
Found at i:15410312 original size:25 final size:25
Alignment explanation
Indices: 15410284--15410335 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
15410274 GTCATGCATG
15410284 ATTAAATTAAATAATAAAATATAAA
1 ATTAAATTAAATAATAAAATATAAA
* * **
15410309 ATTATATTTAATAATTTAATATAAA
1 ATTAAATTAAATAATAAAATATAAA
15410334 AT
1 AT
15410336 ATTTCATTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
ATTAAATTAAATAATAAAATATAAA
Found at i:15417656 original size:20 final size:20
Alignment explanation
Indices: 15417606--15417658 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
15417596 CAAGGATAAT
15417606 GTATTAATACTTTGTGAAAA
1 GTATTAATACTTTGTGAAAA
* * **
15417626 GTATCAGTACTTTG-GTAAGG
1 GTATTAATACTTTGTG-AAAA
15417646 GTATTAATACTTT
1 GTATTAATACTTT
15417659 TGATTTTTGC
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 1 0.04
20 25 0.96
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.42
Consensus pattern (20 bp):
GTATTAATACTTTGTGAAAA
Found at i:15418365 original size:60 final size:59
Alignment explanation
Indices: 15418297--15418462 Score: 167
Period size: 60 Copynumber: 2.8 Consensus size: 59
15418287 TTATTTTTAA
* * * *
15418297 AATTTTTAGAATTAGACTAAATTGATAAATTTTGTACATATTG-AGGGCTAAATTTATTG
1 AATTTTTAGAATTAGACTAAATTGATAAATTTTGTAAACATTGAAAGGC-AAATTTACTG
* * *
15418356 AAGTTTTTAGAATTCAAACTAAAATGA-AAAGTTTTGTAAACATTGAAAGGCAAATTTCCTG
1 AA-TTTTTAGAATT-AGACTAAATTGATAAA-TTTTGTAAACATTGAAAGGCAAATTTACTG
* * *
15418417 AATTTTTAGAGTTTAGA-TAAAATTGATAAAATTTGTAAACAATGAA
1 AATTTTTAGA-ATTAGACT-AAATTGATAAATTTTGTAAACATTGAA
15418463 GGGTTAAAGG
Statistics
Matches: 88, Mismatches: 12, Indels: 13
0.78 0.11 0.12
Matches are distributed among these distances:
59 3 0.03
60 44 0.50
61 37 0.42
62 4 0.05
ACGTcount: A:0.42, C:0.06, G:0.14, T:0.37
Consensus pattern (59 bp):
AATTTTTAGAATTAGACTAAATTGATAAATTTTGTAAACATTGAAAGGCAAATTTACTG
Found at i:15421273 original size:21 final size:22
Alignment explanation
Indices: 15421220--15421275 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
15421210 AAATCAATTT
* *
15421220 AATTATAATCGAATGACTATAT
1 AATTATAATTGAATGACTATAA
*
15421242 AATGTAT-ATTGAAT-TCTATAA
1 AAT-TATAATTGAATGACTATAA
15421263 AATTATAATTGAA
1 AATTATAATTGAA
15421276 ACCCTAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 3 0.10
21 14 0.48
22 9 0.31
23 3 0.10
ACGTcount: A:0.46, C:0.05, G:0.09, T:0.39
Consensus pattern (22 bp):
AATTATAATTGAATGACTATAA
Found at i:15423675 original size:21 final size:22
Alignment explanation
Indices: 15423622--15423677 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
15423612 AAATCAATTT
* *
15423622 AATTATAATCGAATGACTATAT
1 AATTATAATTGAATGACTATAA
*
15423644 AATGTAT-ATTGAAT-TCTATAA
1 AAT-TATAATTGAATGACTATAA
15423665 AATTATAATTGAA
1 AATTATAATTGAA
15423678 ACCCTAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 3 0.10
21 14 0.48
22 9 0.31
23 3 0.10
ACGTcount: A:0.46, C:0.05, G:0.09, T:0.39
Consensus pattern (22 bp):
AATTATAATTGAATGACTATAA
Found at i:15424774 original size:22 final size:22
Alignment explanation
Indices: 15424746--15424787 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
15424736 TGGATAAACC
* *
15424746 AAATAAACTTTATTTTTGTAGA
1 AAATAAACTTAATATTTGTAGA
15424768 AAATAAACTTAATATTTGTA
1 AAATAAACTTAATATTTGTA
15424788 AACTGAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (22 bp):
AAATAAACTTAATATTTGTAGA
Found at i:15430772 original size:30 final size:30
Alignment explanation
Indices: 15430738--15430805 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
15430728 TCATGTTGAA
*
15430738 AACACTGGAGC-TGCGAACACTTATGTTGCG
1 AACACTGGA-CATGCGAACACTGATGTTGCG
**
15430768 AACAC-ACACAATGCGAACACTGATGTTGCG
1 AACACTGGAC-ATGCGAACACTGATGTTGCG
15430798 AACACTGG
1 AACACTGG
15430806 TGTTGCGCGC
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
28 1 0.03
29 1 0.03
30 28 0.93
ACGTcount: A:0.32, C:0.25, G:0.24, T:0.19
Consensus pattern (30 bp):
AACACTGGACATGCGAACACTGATGTTGCG
Found at i:15430804 original size:15 final size:15
Alignment explanation
Indices: 15430749--15430812 Score: 65
Period size: 15 Copynumber: 4.3 Consensus size: 15
15430739 ACACTGGAGC
*
15430749 TGCGAACACTTATGT
1 TGCGAACACTGATGT
** ***
15430764 TGCGAACACACACAA
1 TGCGAACACTGATGT
15430779 TGCGAACACTGATGT
1 TGCGAACACTGATGT
*
15430794 TGCGAACACTGGTGT
1 TGCGAACACTGATGT
15430809 TGCG
1 TGCG
15430813 CGCACGGATG
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.23
Consensus pattern (15 bp):
TGCGAACACTGATGT
Found at i:15431935 original size:112 final size:112
Alignment explanation
Indices: 15431738--15431962 Score: 342
Period size: 112 Copynumber: 2.0 Consensus size: 112
15431728 GTAACCCTTG
*
15431738 TGGCGTCAATCTGATTCATTCGAACCTATCACTTCTTTGAAGTGTGGCGTTCACCCTTATACCGA
1 TGGCGTCAATCTGATTCATTCGAACCTATCACTTCTTTGAAGTGTGGCGTTCACCCCTATACCGA
* * * * *
15431803 TTGGTTCTTATCTCGCTAGATAGAGGGTCGCGGTCCTTACTTGTAAT
66 TTGGTTCCTATCTCGCTAGATAGAAGGCCACGATCCTTACTTGTAAT
* * * *
15431850 TGGCGTCAATCTGATTCATTTGAACTTATCACTTCTTTGAAGTGTGGTGTTCACCCCTATATCGA
1 TGGCGTCAATCTGATTCATTCGAACCTATCACTTCTTTGAAGTGTGGCGTTCACCCCTATACCGA
* *
15431915 TTGGTTCCTATCTTGCTAGATAGAAGGCCACGATCGTTACTTGTAAT
66 TTGGTTCCTATCTCGCTAGATAGAAGGCCACGATCCTTACTTGTAAT
15431962 T
1 T
15431963 CATTTTAAGT
Statistics
Matches: 101, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
112 101 1.00
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.37
Consensus pattern (112 bp):
TGGCGTCAATCTGATTCATTCGAACCTATCACTTCTTTGAAGTGTGGCGTTCACCCCTATACCGA
TTGGTTCCTATCTCGCTAGATAGAAGGCCACGATCCTTACTTGTAAT
Found at i:15436780 original size:17 final size:17
Alignment explanation
Indices: 15436758--15436805 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
15436748 AGAATTCGTC
15436758 GTTTGGCAGACTCT-AG
1 GTTTGGCAGACTCTAAG
*
15436774 AGTTTGGCAGATTCTAAG
1 -GTTTGGCAGACTCTAAG
*
15436792 GTTTGGCGGACTCT
1 GTTTGGCAGACTCT
15436806 TTTGTGTGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 25 0.93
18 2 0.07
ACGTcount: A:0.19, C:0.17, G:0.31, T:0.33
Consensus pattern (17 bp):
GTTTGGCAGACTCTAAG
Found at i:15438257 original size:27 final size:27
Alignment explanation
Indices: 15438203--15438263 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
15438193 CACATCAGGA
* *
15438203 AAAGAAATGCCTTTGTGGTGCAATATG
1 AAAGAAATGCCTTTGTGGTACAAAATG
* *
15438230 AAGGAAATGCCTTTGTGGTATAAAATG
1 AAAGAAATGCCTTTGTGGTACAAAATG
15438257 AAAGAAA
1 AAAGAAA
15438264 ACTCATCTAG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.41, C:0.08, G:0.25, T:0.26
Consensus pattern (27 bp):
AAAGAAATGCCTTTGTGGTACAAAATG
Found at i:15440481 original size:3 final size:3
Alignment explanation
Indices: 15440475--15440513 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
15440465 AATAATAATA
*
15440475 ATT ATT ATT ATT -TT ATT ACT ATT ATT AATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT
15440514 TTTAGGGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.84
4 3 0.09
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:15441036 original size:45 final size:47
Alignment explanation
Indices: 15440958--15441069 Score: 117
Period size: 47 Copynumber: 2.4 Consensus size: 47
15440948 ATTTTGAAAT
* *
15440958 AAAAGTTTAGAA-TTTTAAGAAAAATAATGA-TTT-TC-TTTAAAAAA
1 AAAAGTTTA-AATTTTTAAAAAAAAAAATGATTTTGTCATTTAAAAAA
* *
15441002 AGAAAGTTTAAATTTTTAAAAATAAAAAAT-ATTTTGTCATTTTAAAGA
1 A-AAAGTTTAAATTTTTAAAAA-AAAAAATGATTTTGTCATTTAAAAAA
*
15441050 AAAATTTTAAATTTTTAAAA
1 AAAAGTTTAAATTTTTAAAA
15441070 TTTTTTTTGA
Statistics
Matches: 57, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
44 3 0.05
45 17 0.30
46 9 0.16
47 20 0.35
48 8 0.14
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39
Consensus pattern (47 bp):
AAAAGTTTAAATTTTTAAAAAAAAAAATGATTTTGTCATTTAAAAAA
Found at i:15441121 original size:144 final size:136
Alignment explanation
Indices: 15440925--15441438 Score: 415
Period size: 148 Copynumber: 3.6 Consensus size: 136
15440915 TTGATCTTGG
* * * *
15440925 AAAAAGTTTTAATTTTTTTAA-TAATTTTGAAATAAAAGTTTAGAATTTTAAGAAAAATAATGAT
1 AAAAAATTTTAATTTTTTTAACT-ATTTCGAAATAAAAGTTT-GGATTTTAAGAAAAATAGTGAT
* **
15440989 TTTCTTTAAAAAAAGAAAGTTTAAATTTTTAAAAATAAAAA-ATATTTTGTCATTTTAAAGAAAA
64 TTTCTTTAAAAAAAGAAAGTTTAGATTTTTAAAAATAAAAATATATTTT-T--TAGT-AA-AAAA
*
15441053 ATTTTAAATTTTT
124 AGTTTAAATTTTT
** * *
15441066 AAAATTTTTTTTGAATTTTTTAAACTATTTCGAACTAAAAGTTTGGAGTTTTAAGAAAAATAGTG
1 AAAA--AATTTT-AATTTTTTTAACTATTTCGAAATAAAAGTTTGGA-TTTTAAGAAAAATAGTG
* ** * *
15441131 TTTTTCATAAAAAAAAAAAGAAAGTTTAGATTTTTAAAAATAAAAATCTATTTTTTAGTCAAAAA
62 ATTTTC-T--TTAAAAAAAGAAAGTTTAGATTTTTAAAAATAAAAATATATTTTTTAGTAAAAAA
*
15441196 GGTTTAAATTTTT
124 AGTTTAAATTTTT
* * * *
15441209 AAAAAAGTTTAATTTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTCAGTAAAGTAGTGAAC
1 AAAAAATTTTAA-TTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTAAGAAAAATAGTG-A-
** *
15441274 TTTT-TTTAAAAAAAGAAAGTTTAGATTTTTTTTAAA-AAAAATCTATTTTTTTAGGCATTTAAA
63 TTTTCTTTAAAAAAAGAAAGTTTAGA-TTTTTAAAAATAAAAATATA-TTTTTTA-G----T--A
*
15441337 AGAGAAAAGTTTAATTTTTT
119 A-A-AAAAGTTTAAATTTTT
* * * * * *
15441357 AAACAAAATTTGATTTTTTTAACTATTTCAAAATAAAATTTTTGATTTTTAAGAAAAGTAGTGAT
1 AAA-AAATTTTAATTTTTTTAACTATTTCGAAATAAAAGTTTGGA-TTTTAAGAAAAATAGTGAT
* *
15441422 TTTAGTCTAAAAAAAGA
64 TTT-CTTTAAAAAAAGA
15441439 TAACTTTTTA
Statistics
Matches: 305, Mismatches: 41, Indels: 46
0.78 0.10 0.12
Matches are distributed among these distances:
138 27 0.09
139 15 0.05
140 18 0.06
141 37 0.12
142 4 0.01
143 25 0.08
144 49 0.16
145 4 0.01
146 1 0.00
147 39 0.13
148 53 0.17
149 33 0.11
ACGTcount: A:0.44, C:0.04, G:0.10, T:0.43
Consensus pattern (136 bp):
AAAAAATTTTAATTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTAAGAAAAATAGTGATTT
TCTTTAAAAAAAGAAAGTTTAGATTTTTAAAAATAAAAATATATTTTTTAGTAAAAAAAGTTTAA
ATTTTT
Found at i:15441227 original size:19 final size:18
Alignment explanation
Indices: 15441191--15441225 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
15441181 TTTTTTAGTC
*
15441191 AAAAAGGTTTAAATTTTT
1 AAAAAAGTTTAAATTTTT
15441209 AAAAAAGTTT-AATTTTT
1 AAAAAAGTTTAAATTTTT
15441226 TTTAACTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.46
Consensus pattern (18 bp):
AAAAAAGTTTAAATTTTT
Found at i:15442021 original size:16 final size:16
Alignment explanation
Indices: 15442000--15442030 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
15441990 TTATTCTTAC
15442000 TTCATCTTTATTTATT
1 TTCATCTTTATTTATT
15442016 TTCATCTTTATTTAT
1 TTCATCTTTATTTAT
15442031 ATTTATGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.13, G:0.00, T:0.68
Consensus pattern (16 bp):
TTCATCTTTATTTATT
Done.