Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr8
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: 56894857
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1173888 characters in sequence are not A, C, G, or T
File 5 of 185
Found at i:1188181 original size:24 final size:24
Alignment explanation
Indices: 1188149--1188196 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1188139 AACAAAGAGC
1188149 AAATTTCAAAAGAGCTCTTAGTAA
1 AAATTTCAAAAGAGCTCTTAGTAA
1188173 AAATTTCAAAAGAGCTCTTAGTAA
1 AAATTTCAAAAGAGCTCTTAGTAA
1188197 GCTTTCGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.29
Consensus pattern (24 bp):
AAATTTCAAAAGAGCTCTTAGTAA
Found at i:1195979 original size:18 final size:18
Alignment explanation
Indices: 1195956--1195990 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1195946 TTATAAAAAA
*
1195956 TTTTATTTTTTGAATTTC
1 TTTTATTTCTTGAATTTC
1195974 TTTTATTTCTTGAATTT
1 TTTTATTTCTTGAATTT
1195991 GTTGTTGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.71
Consensus pattern (18 bp):
TTTTATTTCTTGAATTTC
Found at i:1207795 original size:69 final size:69
Alignment explanation
Indices: 1207684--1207815 Score: 230
Period size: 69 Copynumber: 1.9 Consensus size: 69
1207674 TTTCTTATAC
* *
1207684 TTTGAACTCAAGACCATGTTTCAATTCTTGAAAGTCTATCTTTGATCTTCAAATTAAAAAGTACA
1 TTTGAACTCAAGACCAGGTTACAATTCTTGAAAGTCTATCTTTGATCTTCAAATTAAAAAGTACA
1207749 GCAG
66 GCAG
1207753 TTTGAACTCAAGACCAGGTTACAACTT-TTGAAAGTCTATCTTTGATCTTCAAATTAAAAAGTA
1 TTTGAACTCAAGACCAGGTTACAA-TTCTTGAAAGTCTATCTTTGATCTTCAAATTAAAAAGTA
1207816 AAGCTTTCAA
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
69 58 0.97
70 2 0.03
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.35
Consensus pattern (69 bp):
TTTGAACTCAAGACCAGGTTACAATTCTTGAAAGTCTATCTTTGATCTTCAAATTAAAAAGTACA
GCAG
Found at i:1209716 original size:10 final size:9
Alignment explanation
Indices: 1209701--1209819 Score: 75
Period size: 10 Copynumber: 12.3 Consensus size: 9
1209691 GAAGGAGAGG
1209701 GAAAGAAGAA
1 GAAAGAA-AA
1209711 GAAAG-AAA
1 GAAAGAAAA
1209719 GAAAG-AAA
1 GAAAGAAAA
1209727 GAAAGAAAA
1 GAAAGAAAA
1209736 GGAAAGAAAA
1 -GAAAGAAAA
* *
1209746 GGAAAGGAGAG
1 -GAAA-GAAAA
1209757 GAAAG-AAA
1 GAAAGAAAA
1209765 GAAA-AAGAA
1 GAAAGAA-AA
1209774 GGAAAGAAAA
1 -GAAAGAAAA
1209784 GGAAAGGAGAAGA
1 -GAAA-GA-AA-A
*
1209797 GAAAAAAAAA
1 G-AAAGAAAA
1209807 GAAAGAAGAA
1 GAAAGAA-AA
1209817 GAA
1 GAA
1209820 GATGGAAGAA
Statistics
Matches: 91, Mismatches: 6, Indels: 24
0.75 0.05 0.20
Matches are distributed among these distances:
8 21 0.23
9 12 0.13
10 41 0.45
11 9 0.10
12 4 0.04
13 4 0.04
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (9 bp):
GAAAGAAAA
Found at i:1209718 original size:4 final size:4
Alignment explanation
Indices: 1209701--1209852 Score: 76
Period size: 4 Copynumber: 38.2 Consensus size: 4
1209691 GAAGGAGAGG
1209701 GAAA G-AA G-AA GAAA GAAA GAAA GAAA GAAA GAAAA GGAAA GAAAA GGAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA G-AAA -GAAA G-AAA -GAAA
* * *
1209751 GGAGAG GAAA GAAA G-AA -AAA GAAG GAAA GAAAA GGAAA G-GA GAAGA
1 -GA-AA GAAA GAAA GAAA GAAA GAAA GAAA G-AAA -GAAA GAAA GAA-A
* *
1209797 GAAA -AAA -AAA GAAA G-AA G-AA GAAGA TGGAA GAAG GAAA -AAA -AAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAA-A -GAAA GAAA GAAA GAAA GAAA
1209841 GAAA GAAA -AAA G
1 GAAA GAAA GAAA G
1209853 GTAATTTTTA
Statistics
Matches: 120, Mismatches: 10, Indels: 36
0.72 0.06 0.22
Matches are distributed among these distances:
3 33 0.28
4 52 0.43
5 29 0.24
6 6 0.05
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.01
Consensus pattern (4 bp):
GAAA
Found at i:1209776 original size:38 final size:37
Alignment explanation
Indices: 1209700--1209809 Score: 138
Period size: 38 Copynumber: 3.0 Consensus size: 37
1209690 AGAAGGAGAG
*
1209700 GGAAAGAAGAA-GAAA-GAAAGAAAGAAAGAAAGAA-AA
1 GGAAAGAA-AAGGAAAGGAGAGAAAGAAAGAAA-AAGAA
1209736 GGAAAGAAAAGGAAAGGAGAGGAAAGAAAGAAAAAGAA
1 GGAAAGAAAAGGAAAGGAGA-GAAAGAAAGAAAAAGAA
* *
1209774 GGAAAGAAAAGGAAAGGAGA-AGAGAAAAAAAAAGAA
1 GGAAAGAAAAGGAAAGGAGAGAAAGAAAGAAAAAGAA
1209810 AGAAGAAGAA
Statistics
Matches: 67, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
35 2 0.03
36 26 0.39
37 5 0.07
38 34 0.51
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (37 bp):
GGAAAGAAAAGGAAAGGAGAGAAAGAAAGAAAAAGAA
Found at i:1209819 original size:38 final size:39
Alignment explanation
Indices: 1209714--1209852 Score: 127
Period size: 38 Copynumber: 3.7 Consensus size: 39
1209704 AGAAGAAGAA
* *
1209714 AGAAAGAAAGAAAGAAAGAAA-AGGAAAGAAAAGGAAAGG
1 AGAAGGAAAGAAA-AAAGAAAGAAGAAAGAAAAGGAAAGG
*
1209753 AG-AGGAAAGAAAGAA-AAAGAAGGAAAGAAAAGGAAAGG
1 AGAAGGAAAGAAAAAAGAAAGAA-GAAAGAAAAGGAAAGG
*
1209791 AGAAGAGAAA-AAAAAAGAAAGAAG-AAG--AA-G-ATGG
1 AGAAG-GAAAGAAAAAAGAAAGAAGAAAGAAAAGGAAAGG
*
1209825 AAGAAGGAAA-AAAAAAGAAAGAAAAAAG
1 -AGAAGGAAAGAAAAAAGAAAGAAGAAAG
1209853 GTAATTTTTA
Statistics
Matches: 87, Mismatches: 6, Indels: 18
0.78 0.05 0.16
Matches are distributed among these distances:
34 20 0.23
35 9 0.10
36 5 0.06
37 3 0.03
38 30 0.34
39 10 0.11
40 10 0.11
ACGTcount: A:0.70, C:0.00, G:0.29, T:0.01
Consensus pattern (39 bp):
AGAAGGAAAGAAAAAAGAAAGAAGAAAGAAAAGGAAAGG
Found at i:1210353 original size:158 final size:156
Alignment explanation
Indices: 1210188--1210705 Score: 547
Period size: 158 Copynumber: 3.3 Consensus size: 156
1210178 TATTTAATAA
* * * *
1210188 ATTTCAAACATAATGCACTAAAATAATGTAAAATGATAAAATTAAAAATTACGATATTTTTTAAA
1 ATTTCAAACAAAATGCACTGAAATAATATAAAATAATAAAATTAAAAATTACGATATTTTTTAAA
*
1210253 ATAATATAATGCGGATAAAAAAATACGAACAACTGGCCGAAGTAAGAGTGTATTACTAACTTTTT
66 ATAATATAATGCGGATAAAAAAATACGAACAAATGGCCGAAGTAAGAGTGTATTACTAACTTTTT
1210318 TAAAAACTCAGAAATAATTAATACAAAT
131 TAAAAA-TCA-AAATAATTAATACAAAT
**
1210346 ATTTCAAACAAAATGCACTGAAATAATATAAAATAATAAAA-TACGAAAA-TAAAATATTTTTAT
1 ATTTCAAACAAAATGCACTGAAATAATATAAAATAATAAAATTA--AAAATTACGATA-TTTT-T
* * * * * * * *
1210409 TGAAAGTAATAAAAAT-CGG-GAAAATAATACGAGCAAATGG-C-AAGGATAAGGGT-TTTTTCT
62 T-AAAATAAT-ATAATGCGGATAAAAAAATACGAACAAATGGCCGAA-G-TAAGAGTGTATTAC-
* * * *
1210469 TACACCAAATTAATTTAAAAAACACACTAAATTAAT--AAAT
122 TA-A-C---TT-TTTTAAAAATCAAAAT-AATTAATACAAAT
** * * *
1210509 -TTT-AAACATTATGCACTGAAATAATGTAAAATGATAAAATTAGAAATTACGATATTTTTTAAA
1 ATTTCAAACAAAATGCACTGAAATAATATAAAATAATAAAATTAAAAATTACGATATTTTTTAAA
1210572 ATAATATAATGCGGATAAAAAAA-ACGAACAAATGGCCGAAGTAAGAGTGTATTACTAACTTTTT
66 ATAATATAATGCGGATAAAAAAATACGAACAAATGGCCGAAGTAAGAGTGTATTACTAACTTTTT
1210636 TAAAAATTCATAAATAATTAATACAAAT
131 TAAAAA-TCA-AAATAATTAATACAAAT
*
1210664 ATTTTAAACAAAATGCACTGAAATAATATAAAATAATAAAAT
1 ATTTCAAACAAAATGCACTGAAATAATATAAAATAATAAAAT
1210706 ACGAAAATAA
Statistics
Matches: 289, Mismatches: 42, Indels: 59
0.74 0.11 0.15
Matches are distributed among these distances:
152 8 0.03
153 11 0.04
154 2 0.01
155 4 0.01
156 4 0.01
157 40 0.14
158 73 0.25
159 28 0.10
160 36 0.12
161 48 0.17
162 10 0.03
163 4 0.01
164 2 0.01
165 11 0.04
166 8 0.03
ACGTcount: A:0.51, C:0.09, G:0.10, T:0.30
Consensus pattern (156 bp):
ATTTCAAACAAAATGCACTGAAATAATATAAAATAATAAAATTAAAAATTACGATATTTTTTAAA
ATAATATAATGCGGATAAAAAAATACGAACAAATGGCCGAAGTAAGAGTGTATTACTAACTTTTT
TAAAAATCAAAATAATTAATACAAAT
Found at i:1210759 original size:318 final size:318
Alignment explanation
Indices: 1210181--1210940 Score: 1192
Period size: 318 Copynumber: 2.4 Consensus size: 318
1210171 AATTATATAT
* *
1210181 TTAATAAATTTCAAACATAATGCACTAAAATAATGTAAAATGATAAAATTAAAAATTACGATATT
1 TTAATAAATTTTAAACAT-ATGCACT-AAATAATGTAAAATGATAAAATTAGAAATTACGATATT
*
1210246 TTTTAAAATAATATAATGCGGATAAAAAAATACGAACAACTGGCCGAAGTAAGAGTGTATTACTA
64 TTTTAAAATAATATAATGCGGATAAAAAAATACGAACAAATGGCCGAAGTAAGAGTGTATTACTA
1210311 ACTTTTTTAAAAACTCAGAAATAATTAATACAAATATTTCAAACAAAATGCACTGAAATAATATA
129 ACTTTTTTAAAAACTCAGAAATAATTAATACAAATATTTCAAACAAAATGCACTGAAATAATATA
1210376 AAATAATAAAATACGAAAATAAAATATTTTTATTGAAAGTAATAAAAATCGGGAAAATAATACGA
194 AAATAATAAAATACGAAAATAAAATATTTTTATTGAAAGTAATAAAAATCGGGAAAATAATACGA
*
1210441 GCAAATGGCAAGGAT-AAGGGTTTTTTCTTACACCAAATTAATTTAAAAAACACACTAAA
259 GCAAAGGGCAAGGATAAAGGGTTTTTTCTTACACCAAATTAATTTAAAAAACACACTAAA
1210500 TTAATAAATTTTAAACATTATGCACTGAAATAATGTAAAATGATAAAATTAGAAATTACGATATT
1 TTAATAAATTTTAAACA-TATGCACT-AAATAATGTAAAATGATAAAATTAGAAATTACGATATT
1210565 TTTTAAAATAATATAATGCGGATAAAAAAA-ACGAACAAATGGCCGAAGTAAGAGTGTATTACTA
64 TTTTAAAATAATATAATGCGGATAAAAAAATACGAACAAATGGCCGAAGTAAGAGTGTATTACTA
* * *
1210629 ACTTTTTTAAAAATTCATAAATAATTAATACAAATATTTTAAACAAAATGCACTGAAATAATATA
129 ACTTTTTTAAAAACTCAGAAATAATTAATACAAATATTTCAAACAAAATGCACTGAAATAATATA
1210694 AAATAATAAAATACGAAAATAAAATATTTTTATTGAAAGTAATAAAAATCGGGAAAATAATACGA
194 AAATAATAAAATACGAAAATAAAATATTTTTATTGAAAGTAATAAAAATCGGGAAAATAATACGA
* * * * *
1210759 GCAAAGGGCAGGGATAAAGGTTTTTTTCTTATACCAATTTAATTTAAAAAACAGACTAAA
259 GCAAAGGGCAAGGATAAAGGGTTTTTTCTTACACCAAATTAATTTAAAAAACACACTAAA
* *
1210819 TTAATAAA-TTT---CA-A---AC-----AATGTAAAATTATAAAATTAGAAATTAAGATA-TTT
1 TTAATAAATTTTAAACATATGCACTAAATAATGTAAAATGATAAAATTAGAAATTACGATATTTT
* * * * * *
1210870 TTAAAGTAATAAAATGCGGAGAAAAAAATACGAACAAATGGCCGAAGTAAGAGTTTTTTATTAAC
66 TTAAAATAATATAATGCGGATAAAAAAATACGAACAAATGGCCGAAGTAAGAGTGTATTACTAAC
1210935 TTTTTT
131 TTTTTT
1210941 TTCAACTTGC
Statistics
Matches: 417, Mismatches: 21, Indels: 21
0.91 0.05 0.05
Matches are distributed among these distances:
303 28 0.07
304 69 0.17
310 2 0.00
313 1 0.00
315 2 0.00
318 176 0.42
319 138 0.33
320 1 0.00
ACGTcount: A:0.50, C:0.09, G:0.11, T:0.30
Consensus pattern (318 bp):
TTAATAAATTTTAAACATATGCACTAAATAATGTAAAATGATAAAATTAGAAATTACGATATTTT
TTAAAATAATATAATGCGGATAAAAAAATACGAACAAATGGCCGAAGTAAGAGTGTATTACTAAC
TTTTTTAAAAACTCAGAAATAATTAATACAAATATTTCAAACAAAATGCACTGAAATAATATAAA
ATAATAAAATACGAAAATAAAATATTTTTATTGAAAGTAATAAAAATCGGGAAAATAATACGAGC
AAAGGGCAAGGATAAAGGGTTTTTTCTTACACCAAATTAATTTAAAAAACACACTAAA
Found at i:1215459 original size:18 final size:18
Alignment explanation
Indices: 1215432--1215476 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1215422 ATCCCAATGA
*
1215432 TCGCCGCCACCTTCTTCT
1 TCGCCACCACCTTCTTCT
1215450 TCGCCACCACCTTCTTCT
1 TCGCCACCACCTTCTTCT
*
1215468 TCACCACCA
1 TCGCCACCA
1215477 ACCATATCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.13, C:0.51, G:0.07, T:0.29
Consensus pattern (18 bp):
TCGCCACCACCTTCTTCT
Found at i:1218118 original size:35 final size:36
Alignment explanation
Indices: 1218035--1218122 Score: 92
Period size: 35 Copynumber: 2.4 Consensus size: 36
1218025 TAATTTTTTA
* *
1218035 TTTTAGACTTT-AATATCCTTAGATTTAATTTATGT
1 TTTTAGATTTTAAATATCCTTAGATTTAACTTATGT
*
1218070 TTGATATAAATTTTAAATATTCCTTAGATTT-ACTTAT-T
1 TT--T-TAGATTTTAAATA-TCCTTAGATTTAACTTATGT
1218108 TTTTAGATTTTAAAT
1 TTTTAGATTTTAAAT
1218123 TTTTGGTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
35 13 0.30
36 1 0.02
37 1 0.02
38 9 0.20
39 9 0.20
40 11 0.25
ACGTcount: A:0.32, C:0.07, G:0.07, T:0.55
Consensus pattern (36 bp):
TTTTAGATTTTAAATATCCTTAGATTTAACTTATGT
Found at i:1223743 original size:18 final size:18
Alignment explanation
Indices: 1223720--1223764 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
1223710 CTCAAGGGAT
1223720 TTACAAGAT-TTCCTAAGA
1 TTACAAGATCTT-CTAAGA
*
1223738 TTACAAAATCTTCTAAGA
1 TTACAAGATCTTCTAAGA
1223756 TTACAAGAT
1 TTACAAGAT
1223765 ATTGGTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 22 0.92
19 2 0.08
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (18 bp):
TTACAAGATCTTCTAAGA
Found at i:1226245 original size:27 final size:27
Alignment explanation
Indices: 1226209--1226262 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
1226199 AAGGGTTCTA
1226209 AAACAAGAGCCCCCAACAGAGTAGGCT
1 AAACAAGAGCCCCCAACAGAGTAGGCT
1226236 AAACAAGAGCCCCCAACAGAGTAGGCT
1 AAACAAGAGCCCCCAACAGAGTAGGCT
1226263 CGGTTTTGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.30, G:0.22, T:0.07
Consensus pattern (27 bp):
AAACAAGAGCCCCCAACAGAGTAGGCT
Found at i:1226627 original size:49 final size:48
Alignment explanation
Indices: 1226524--1226628 Score: 122
Period size: 49 Copynumber: 2.2 Consensus size: 48
1226514 TGCCACACGG
* * ** *
1226524 CCGTGTGGTAGGCTGTGTGTGGCACATGGCCGTGTGAAACTCTGTAGA
1 CCGTGTGGTAGGCTATGTGTGGCACATGACCGTGTGAAACTCTACAAA
* *
1226572 CTGTGTGGCTAGGCTATGTGTGGCACATGACTGTGTGAAACT-TCACAAA
1 CCGTGTGG-TAGGCTATGTGTGGCACATGACCGTGTGAAACTCT-ACAAA
1226621 CCGTGTGG
1 CCGTGTGG
1226629 GTAGATAGTG
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
48 8 0.17
49 39 0.83
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.28
Consensus pattern (48 bp):
CCGTGTGGTAGGCTATGTGTGGCACATGACCGTGTGAAACTCTACAAA
Found at i:1229951 original size:49 final size:49
Alignment explanation
Indices: 1229822--1229957 Score: 148
Period size: 49 Copynumber: 2.8 Consensus size: 49
1229812 TATAATGATT
* ** * *
1229822 TAAAA-CCATCATTGTCTGGCCAATCAAGATGATAGAATATGCAAAGAG
1 TAAAAGCCATCATTGTCGGGCCACCCGAGATGGTAGAATATGCAAAGAG
* ** *
1229870 TAAAAGCCGTCATTGTCGGGCCACTTGAGATGGTAGAATATGCAAATAG
1 TAAAAGCCATCATTGTCGGGCCACCCGAGATGGTAGAATATGCAAAGAG
* * * *
1229919 TGAAAGTCATCATTGTTGGGCCACCCGGGATGGTAGAAT
1 TAAAAGCCATCATTGTCGGGCCACCCGAGATGGTAGAAT
1229958 GTACAAGTTC
Statistics
Matches: 73, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
48 5 0.07
49 68 0.93
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (49 bp):
TAAAAGCCATCATTGTCGGGCCACCCGAGATGGTAGAATATGCAAAGAG
Found at i:1231051 original size:19 final size:18
Alignment explanation
Indices: 1231004--1231057 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 18
1230994 ATACTAAAAA
1231004 TAAACTTTAATTAATTATAAT
1 TAAA-TTTAATTAA-T-TAAT
1231025 TAAA-TTAATTAATTAAT
1 TAAATTTAATTAATTAAT
*
1231042 TAATATTTAACTAATT
1 TAA-ATTTAATTAATT
1231058 TTAACCTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
17 7 0.23
18 2 0.07
19 17 0.57
21 4 0.13
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (18 bp):
TAAATTTAATTAATTAAT
Found at i:1231056 original size:23 final size:23
Alignment explanation
Indices: 1231010--1231057 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1231000 AAAATAAACT
*
1231010 TTAATTAATTATAATTAAATTAA
1 TTAATTAATTATAATTAAACTAA
*
1231033 TTAATTAATTA-ATATTTAACTAA
1 TTAATTAATTATA-ATTAAACTAA
1231056 TT
1 TT
1231058 TTAACCTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 21 0.95
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
TTAATTAATTATAATTAAACTAA
Found at i:1231382 original size:19 final size:20
Alignment explanation
Indices: 1231358--1231397 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
1231348 AGATTAAACT
1231358 TTAATTAATT-ATAATTAAC
1 TTAATTAATTAATAATTAAC
1231377 TTAATTAATTAATAATTAAC
1 TTAATTAATTAATAATTAAC
1231397 T
1 T
1231398 AATGTTAACC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (20 bp):
TTAATTAATTAATAATTAAC
Found at i:1232349 original size:49 final size:49
Alignment explanation
Indices: 1232225--1232365 Score: 149
Period size: 49 Copynumber: 2.9 Consensus size: 49
1232215 ATAATGATTC
* * ** * *
1232225 AAAA-CCATCATTGTTAGGCCACTCAAGATGATAGAATATGCAAATAGT
1 AAAAGCCATCATCGTTGGGCCACTCGGGATGGTAGAATATACAAATAGT
* *
1232273 CAAAGCCATCATCGTTGTGCCACTCGGGATGGTAGAATATACAAATAGT
1 AAAAGCCATCATCGTTGGGCCACTCGGGATGGTAGAATATACAAATAGT
* * * * * *
1232322 AAAAGTCATCATTGTTGGGTCATTCGGGATGGTTGAATGTACAA
1 AAAAGCCATCATCGTTGGGCCACTCGGGATGGTAGAATATACAA
1232366 GTTCTACATG
Statistics
Matches: 76, Mismatches: 16, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
48 3 0.04
49 73 0.96
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (49 bp):
AAAAGCCATCATCGTTGGGCCACTCGGGATGGTAGAATATACAAATAGT
Found at i:1233524 original size:4 final size:4
Alignment explanation
Indices: 1233508--1233554 Score: 76
Period size: 4 Copynumber: 11.8 Consensus size: 4
1233498 ATTTCATTTA
* *
1233508 TATG TATG CATG TATG TATG TATG TATG TATG TATA TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1233555 ATTTGATTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.28, C:0.02, G:0.21, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:1234275 original size:20 final size:20
Alignment explanation
Indices: 1234250--1234294 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
1234240 TTCAGCTCTT
1234250 ATGCAGCAGGCAAGGTGGCC
1 ATGCAGCAGGCAAGGTGGCC
* *
1234270 ATGCAGGAGTCAAGGTGGCC
1 ATGCAGCAGGCAAGGTGGCC
1234290 ATGCA
1 ATGCA
1234295 AGGAACGTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.27, C:0.22, G:0.38, T:0.13
Consensus pattern (20 bp):
ATGCAGCAGGCAAGGTGGCC
Found at i:1238357 original size:20 final size:20
Alignment explanation
Indices: 1238332--1238376 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
1238322 GTCAGCTCCT
1238332 ATGCAGCAGTCAAGGTGGCC
1 ATGCAGCAGTCAAGGTGGCC
*
1238352 ATGCAGGAGTCAAGGTGGCC
1 ATGCAGCAGTCAAGGTGGCC
1238372 ATGCA
1 ATGCA
1238377 AGGAACGTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.27, C:0.22, G:0.36, T:0.16
Consensus pattern (20 bp):
ATGCAGCAGTCAAGGTGGCC
Found at i:1250288 original size:33 final size:33
Alignment explanation
Indices: 1250251--1250346 Score: 174
Period size: 33 Copynumber: 2.9 Consensus size: 33
1250241 TTTATTTTAT
1250251 TTTAGTTTGTTTACTTATATGTTTTAGTTTTTG
1 TTTAGTTTGTTTACTTATATGTTTTAGTTTTTG
*
1250284 TTTAGTTTGTTTACTTATATGTTGTAGTTTTTG
1 TTTAGTTTGTTTACTTATATGTTTTAGTTTTTG
*
1250317 TTTAGTTTGTTTACTTATGTGTTTTAGTTT
1 TTTAGTTTGTTTACTTATATGTTTTAGTTT
1250347 AGTACTATGT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.15, C:0.03, G:0.17, T:0.66
Consensus pattern (33 bp):
TTTAGTTTGTTTACTTATATGTTTTAGTTTTTG
Found at i:1266371 original size:19 final size:21
Alignment explanation
Indices: 1266336--1266376 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
1266326 GTGTGCATAG
1266336 CTTTTTGCATTTAATTG-CAT
1 CTTTTTGCATTTAATTGTCAT
1266356 CTTTTTG-ATATT-ATTGTCAT
1 CTTTTTGCAT-TTAATTGTCAT
1266376 C
1 C
1266377 CCATTCACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.56
Consensus pattern (21 bp):
CTTTTTGCATTTAATTGTCAT
Found at i:1271942 original size:71 final size:71
Alignment explanation
Indices: 1271804--1271952 Score: 203
Period size: 71 Copynumber: 2.1 Consensus size: 71
1271794 AGAATATTGG
* * * **
1271804 TAGAAGTGCAGGGAATGTTGAACTTTGGCTACTGACTTGACTTGTTTCGTTAGAAGTCCTCAAGG
1 TAGAAGTGCAGGGAATGCTAAACTTTGGCTACTGACTTGACTTGTTTCGGTAGAAGGACTCAAGG
1271869 TATCAA
66 TATCAA
*
1271875 TAGAAGTGCA-GGAGATGCTAAACTTTGGCTACTGACTTGACTTGTTTCGGTAGAAGGGAC-CAG
1 TAGAAGTGCAGGGA-ATGCTAAACTTTGGCTACTGACTTGACTTGTTTCGGTAGAA-GGACTCAA
*
1271938 GGTATCGA
64 GGTATCAA
1271946 TAGAAGT
1 TAGAAGT
1271953 CTCAGGCCAA
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
70 3 0.04
71 64 0.93
72 2 0.03
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (71 bp):
TAGAAGTGCAGGGAATGCTAAACTTTGGCTACTGACTTGACTTGTTTCGGTAGAAGGACTCAAGG
TATCAA
Found at i:1273974 original size:4 final size:4
Alignment explanation
Indices: 1273965--1274003 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
1273955 ATTTCATTTA
1273965 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1274004 ATTTGATTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:1299796 original size:122 final size:122
Alignment explanation
Indices: 1299632--1299939 Score: 485
Period size: 122 Copynumber: 2.5 Consensus size: 122
1299622 AATTATTCAC
* *
1299632 AATATTAACTCAAAAATCAAGGCT-TGACCACTCTTGGTTCCACTAACCCAATCCTTCTAGCCCA
1 AATATTAACTCAAAAATC-AGGGTGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCC-
*
1299696 GTTTTTG-GGATGTGACAATAAGGATTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
64 GGTTTTGAGGATGTGACAATAAGGATTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
* **
1299754 AATATTAACTCAAAAATCAGGGTGTGACCACTCTTGGCTCCACTAACCCAATCCTTCTAATTCGG
1 AATATTAACTCAAAAATCAGGGTGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCGG
* *
1299819 TTTTGAGGATGTGACAATAGGGGTTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
66 TTTTGAGGATGTGACAATAAGGATTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
* * *
1299876 AATATTAACTCAAAAATCATGGTGTGACCGCTGTTGGTTCCACTAACCCAATCCTTCTAACCCG
1 AATATTAACTCAAAAATCAGGGTGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCG
1299940 ATTTAGGGTT
Statistics
Matches: 170, Mismatches: 14, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
121 10 0.06
122 160 0.94
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.30
Consensus pattern (122 bp):
AATATTAACTCAAAAATCAGGGTGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCGG
TTTTGAGGATGTGACAATAAGGATTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
Found at i:1300237 original size:15 final size:15
Alignment explanation
Indices: 1300219--1300266 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
1300209 AAATTAAATT
1300219 AATTAACTAGATGCA
1 AATTAACTAGATGCA
*
1300234 AATTAACCTAAATGCA
1 AATTAA-CTAGATGCA
* *
1300250 AATAAAATGAGATGCA
1 AATTAACT-AGATGCA
1300266 A
1 A
1300267 GGTGATGGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 7 0.26
16 20 0.74
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.23
Consensus pattern (15 bp):
AATTAACTAGATGCA
Found at i:1301004 original size:49 final size:49
Alignment explanation
Indices: 1300885--1301020 Score: 150
Period size: 49 Copynumber: 2.8 Consensus size: 49
1300875 TCAAACATGT
** * * *
1300885 TAAAA-CCATCATTGTCAGGCCACTCAGGATGATAGAATATGCAAATAT
1 TAAAAGCCATCATTGTTTGGCCACTCGGGATGGTAGAATATGCAAATAG
* *
1300933 TGAAAGCCATCATTGTTTGGCCATTCGGGATGGTAGAATATGCAAATAG
1 TAAAAGCCATCATTGTTTGGCCACTCGGGATGGTAGAATATGCAAATAG
* * * *
1300982 TAAAAGTCATC-TTTTTTGGGCCACCCGAGATGGTAGAAT
1 TAAAAGCCATCATTGTTT-GGCCACTCGGGATGGTAGAAT
1301021 GTACAAGTTC
Statistics
Matches: 73, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
48 9 0.12
49 64 0.88
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (49 bp):
TAAAAGCCATCATTGTTTGGCCACTCGGGATGGTAGAATATGCAAATAG
Found at i:1303186 original size:45 final size:45
Alignment explanation
Indices: 1303136--1303257 Score: 244
Period size: 45 Copynumber: 2.7 Consensus size: 45
1303126 AGCTTTTGTC
1303136 GTATGGAAATGGAAAAGAGTATTTCATTTATATGTATGTATGTAT
1 GTATGGAAATGGAAAAGAGTATTTCATTTATATGTATGTATGTAT
1303181 GTATGGAAATGGAAAAGAGTATTTCATTTATATGTATGTATGTAT
1 GTATGGAAATGGAAAAGAGTATTTCATTTATATGTATGTATGTAT
1303226 GTATGGAAATGGAAAAGAGTATTTCATTTATA
1 GTATGGAAATGGAAAAGAGTATTTCATTTATA
1303258 ATTTGCTGAG
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 77 1.00
ACGTcount: A:0.37, C:0.02, G:0.22, T:0.39
Consensus pattern (45 bp):
GTATGGAAATGGAAAAGAGTATTTCATTTATATGTATGTATGTAT
Found at i:1303701 original size:24 final size:23
Alignment explanation
Indices: 1303656--1303703 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
1303646 GGCGATTTAT
*
1303656 TGCATTTTTACTAGCAACTTTTC
1 TGCATTTTTACTAGCAAATTTTC
*
1303679 TGCATTTTTACTGGCATAATTTTC
1 TGCATTTTTACTAGCA-AATTTTC
1303703 T
1 T
1303704 CCATATTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.21, C:0.19, G:0.10, T:0.50
Consensus pattern (23 bp):
TGCATTTTTACTAGCAAATTTTC
Found at i:1304858 original size:71 final size:71
Alignment explanation
Indices: 1304742--1304882 Score: 214
Period size: 71 Copynumber: 2.0 Consensus size: 71
1304732 AGAGTATTGG
* *
1304742 TAGAAGTGCAGGGAATGTTAAACTTTGGCTACTGACTTGACTTGTTTC-GATAGAAGTCCTTAAG
1 TAGAAGTGCAGGGAATGCTAAACTTTGGCTACTGACTTGACTTGTTTCAG-TAGAAGTCCTCAAG
1304806 GTATCGA
65 GTATCGA
* *
1304813 TAGAAGTGCA-GGAGATGCTAAATTTTGGCTACTGACTTGACTTGTTTCAGTAGAAGTCCTCCAG
1 TAGAAGTGCAGGGA-ATGCTAAACTTTGGCTACTGACTTGACTTGTTTCAGTAGAAGTCCTCAAG
1304877 GTATCG
65 GTATCG
1304883 GTAACACTTT
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
70 3 0.05
71 60 0.94
72 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.32
Consensus pattern (71 bp):
TAGAAGTGCAGGGAATGCTAAACTTTGGCTACTGACTTGACTTGTTTCAGTAGAAGTCCTCAAGG
TATCGA
Found at i:1305008 original size:20 final size:21
Alignment explanation
Indices: 1304975--1305013 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1304965 GTTCTATAGA
* *
1304975 TAGAAGTCCGAGTT-TACCGG
1 TAGAACTCCCAGTTCTACCGG
1304995 TAGAACTCCCAGTTCTACC
1 TAGAACTCCCAGTTCTACC
1305014 AGCAGAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (21 bp):
TAGAACTCCCAGTTCTACCGG
Found at i:1308228 original size:21 final size:21
Alignment explanation
Indices: 1308196--1308236 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1308186 AGGCTCGAGG
1308196 GGCCTGTTTTAGGCC-ATACAA
1 GGCCTGTTTTA-GCCTATACAA
1308217 GGCCT-TTCTTAGCCTATACA
1 GGCCTGTT-TTAGCCTATACA
1308237 CCAAATGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.32
Consensus pattern (21 bp):
GGCCTGTTTTAGCCTATACAA
Found at i:1310752 original size:73 final size:73
Alignment explanation
Indices: 1310633--1310891 Score: 500
Period size: 73 Copynumber: 3.5 Consensus size: 73
1310623 ACAACTTGAC
*
1310633 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1310698 CACTAACA
66 CACTAACA
*
1310706 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1310771 CACTAACA
66 CACTAACA
1310779 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1310844 CACTAACA
66 CACTAACA
1310852 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCA
1 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCA
1310892 AATAATAATA
Statistics
Matches: 185, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 185 1.00
ACGTcount: A:0.41, C:0.25, G:0.06, T:0.27
Consensus pattern (73 bp):
AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
CACTAACA
Found at i:1310900 original size:3 final size:3
Alignment explanation
Indices: 1310892--1310926 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1310882 ATTACATCCA
1310892 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1310927 AACATGTGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1318518 original size:13 final size:13
Alignment explanation
Indices: 1318502--1318527 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1318492 CTTTGCATAT
1318502 TGTCTTCAACAGG
1 TGTCTTCAACAGG
1318515 TGTCTTCAACAGG
1 TGTCTTCAACAGG
1318528 CTCGCACTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (13 bp):
TGTCTTCAACAGG
Found at i:1337134 original size:121 final size:120
Alignment explanation
Indices: 1336867--1337232 Score: 570
Period size: 122 Copynumber: 3.0 Consensus size: 120
1336857 AAATATTCAC
* * *
1336867 AATATTAACTCAAAAATCAAGGCTTAACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCTAG
1 AATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCTAG
*
1336932 TTTTTGCGATGTGACAATAAGGATTTTAATTAGAAAGAAAGTTTAATTAATCAACCT
66 TTTTTG-GATGTGACAATAAGG-TTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
* *
1336989 AATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCTCTAACCCAATCCTTCTAAACTAG
1 AATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCTAG
*
1337054 TTTTTAGGATGTGACAATAAGGTTTTAATTAGAAAGAAAGTTCAATTAATTAACCT
66 TTTTT-GGATGTGACAATAAGGTTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
* * *
1337110 AATATTAACTCAAAAATCAGGGCGTGACCGCTCTTGGTTCCACTAACCCAATCCTTCTAACCCAA
1 AATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCTAG
* * *
1337175 TTTTTCGGATGTGATAATAGGAGTTTTAATTAGAAAGAAAGTTGAATTAATCAACCT
66 TTTTT-GGATGTGACAATAAG-GTTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
1337232 A
1 A
1337233 GAGTCTGTTG
Statistics
Matches: 225, Mismatches: 17, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
121 110 0.49
122 114 0.51
123 1 0.00
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (120 bp):
AATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCTAG
TTTTTGGATGTGACAATAAGGTTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
Found at i:1346379 original size:21 final size:21
Alignment explanation
Indices: 1346347--1346387 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1346337 GAACATTTGG
1346347 TGTATAGGCTAAGAA-AGGCCT
1 TGTATAGGCTAA-AACAGGCCT
1346368 TGTAT-GGCCTAAAACAGGCC
1 TGTATAGG-CTAAAACAGGCC
1346388 CCTCGAGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.22
Consensus pattern (21 bp):
TGTATAGGCTAAAACAGGCCT
Found at i:1352750 original size:19 final size:19
Alignment explanation
Indices: 1352726--1352763 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
1352716 AACGTAAGGG
1352726 TAAAATAGTAAA-TAAATAA
1 TAAAAT-GTAAATTAAATAA
1352745 TAAAATGTAAATTAAATAA
1 TAAAATGTAAATTAAATAA
1352764 AACTTTAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (19 bp):
TAAAATGTAAATTAAATAA
Found at i:1360342 original size:122 final size:120
Alignment explanation
Indices: 1360125--1360492 Score: 565
Period size: 122 Copynumber: 3.0 Consensus size: 120
1360115 AAAATATTCA
* * *
1360125 TAATATTAACACAAAAATCAAGGCTTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCA
1 TAATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCA
* **
1360190 GTTTTTGCGATGTGACAATAAGAATTTTAATTAGAAAGAAAGTTCAATTAATCAACC
66 ATTTTTG-GATGTGACAAT-AGGGTTTTAATTAGAAAGAAAGTTCAATTAATCAACC
*
1360247 TAATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCTAATCCTTCTAACCCA
1 TAATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCA
1360312 ATTTTTAGGATGTGACAATATGGGTTTTAATTAGAAAGAAAGTTCAATTAATCAACC
66 ATTTTT-GGATGTGACAATA-GGGTTTTAATTAGAAAGAAAGTTCAATTAATCAACC
* **
1360369 TAATATTAACTCAAAATTCAGGGCGTGACTGCTCTTGGTTCCACTAACCCAATCCTTCTAACCCA
1 TAATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCA
* * *
1360434 ATTTTTTGGATGTGATAATAGGAGTTTTAATTAGAAATAAAGTTGAATTAATCAACC
66 A-TTTTTGGATGTGACAATAGG-GTTTTAATTAGAAAGAAAGTTCAATTAATCAACC
1360491 TA
1 TA
1360493 GAGTCAGTTG
Statistics
Matches: 228, Mismatches: 14, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
121 3 0.01
122 219 0.96
123 6 0.03
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.32
Consensus pattern (120 bp):
TAATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCA
ATTTTTGGATGTGACAATAGGGTTTTAATTAGAAAGAAAGTTCAATTAATCAACC
Found at i:1360795 original size:34 final size:34
Alignment explanation
Indices: 1360757--1360821 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
1360747 ATAGATTTTA
* *
1360757 AAATTGAATTAATTAACTAGATGCAAATTAACCG
1 AAATTAAATTAATTAACTAGATGAAAATTAACCG
1360791 AAATTAAATTAATTAACTAGATGAAAATTAA
1 AAATTAAATTAATTAACTAGATGAAAATTAA
1360822 TCAGCTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.52, C:0.08, G:0.09, T:0.31
Consensus pattern (34 bp):
AAATTAAATTAATTAACTAGATGAAAATTAACCG
Found at i:1363786 original size:122 final size:122
Alignment explanation
Indices: 1363569--1363932 Score: 568
Period size: 122 Copynumber: 3.0 Consensus size: 122
1363559 AAATATTCAC
* * *
1363569 AATATTAACTCAAAAATCAAGGCTTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCAG
1 AATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCAA
* * *
1363634 TTTTTGGGATGTGACAATAAGGATTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
66 TTTTTAGGATGTGACAATAGGGGTTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
1363691 AATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCAA
1 AATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCAA
1363756 TTTTTAGGATGTGACAATAGGGGTTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
66 TTTTTAGGATGTGACAATAGGGGTTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
* * * ***
1363813 AATATTAACTCAAAAATTAGGGCGTGACCGCTCTTGGATCCACTAACCCAATCCTTCTAACTTGA
1 AATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCAA
* * * *
1363878 TTTTTCA-GATGTGATAATAGGAGTTTTAATTAGAAATAAAGTTGAATTAATCAAC
66 TTTTT-AGGATGTGACAATAGGGGTTTTAATTAGAAAGAAAGTTCAATTAATCAAC
1363933 TTAGAGTCAG
Statistics
Matches: 225, Mismatches: 16, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
122 224 1.00
123 1 0.00
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (122 bp):
AATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCAA
TTTTTAGGATGTGACAATAGGGGTTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
Found at i:1366546 original size:71 final size:71
Alignment explanation
Indices: 1366448--1366588 Score: 230
Period size: 71 Copynumber: 2.0 Consensus size: 71
1366438 AGAGTATTGG
*
1366448 TAGAAGTGAAAGGAATGTTGAACTTTTGCTACTGACTTGACTTGTTTCAATAGAAGTCCTCAAGG
1 TAGAAGTGAAAGGAATGCTGAACTTTTGCTACTGACTTGACTTGTTTCAATAGAAGTCCTCAAGG
1366513 TATCGA
66 TATCGA
* **
1366519 TAGAAGTGCAA-GAGATGCTGAACTTTTGCTACTGACTTGACTTGTTTCTGTAGAAGTCCTCAAG
1 TAGAAGTGAAAGGA-ATGCTGAACTTTTGCTACTGACTTGACTTGTTTCAATAGAAGTCCTCAAG
1366583 GTATCG
65 GTATCG
1366589 GTAACACTTT
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
70 2 0.03
71 63 0.97
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (71 bp):
TAGAAGTGAAAGGAATGCTGAACTTTTGCTACTGACTTGACTTGTTTCAATAGAAGTCCTCAAGG
TATCGA
Found at i:1368744 original size:105 final size:107
Alignment explanation
Indices: 1368619--1368816 Score: 283
Period size: 108 Copynumber: 1.9 Consensus size: 107
1368609 TGAAATTCAA
*
1368619 AAGGATATTTGACTATTTGGTTAAACGAG-AAATCGAAACACAACACATTAGGGAACG-TTCCTC
1 AAGGATATTCGACTATTTGGTTAAACGAGAAAATCGAAACACAACACATTAGGGAACGTTTCCTC
* *
1368682 GAATTTCCAAACGTAAAACATTGCCTTATTTGAAATTTTTGG
66 GAATTTCCAAACGCAAAACATTACCTTATTTGAAATTTTTGG
* * * * * *
1368724 AAGGATATTCGGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCT
1 AAGGATATTCGACTATTTGGTTAAACGAG-AAAATCGAAACACAACACATTAGGGAACGTTTCCT
*
1368789 CGAATTTCCAAACGCAAAATATTACCTT
65 CGAATTTCCAAACGCAAAACATTACCTT
1368817 TATTATTTTT
Statistics
Matches: 80, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
105 26 0.32
107 25 0.31
108 29 0.36
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (107 bp):
AAGGATATTCGACTATTTGGTTAAACGAGAAAATCGAAACACAACACATTAGGGAACGTTTCCTC
GAATTTCCAAACGCAAAACATTACCTTATTTGAAATTTTTGG
Found at i:1369461 original size:358 final size:358
Alignment explanation
Indices: 1368804--1369518 Score: 1369
Period size: 358 Copynumber: 2.0 Consensus size: 358
1368794 TTCCAAACGC
1368804 AAAATATTACCTTTATTATTTTTTAGAAAAATTCTCATATCGAGTAAACAATGTGTCATATCCAA
1 AAAATATTACCTTTATTATTTTTTAGAAAAATTCTCATATCGAGTAAACAATGTGTCATATCCAA
*
1368869 TGTGTTAGGACACAACGTATTGAATTCCCGATAATGAGCTTTTTTATACATTTTTTTAAAGAGTA
66 TGTGTTAGGACACAACGTATTAAATTCCCGATAATGAGCTTTTTTATACATTTTTTTAAAGAGTA
* *
1368934 ATCTCGATTATTTAGATTCAACGAAGAAAGTCAGAACCTAATACGTTAGGGCTCGATTCTCTCGA
131 ATCTCGATTATTTAAATTCAACGAAGAAAGTCAGAACCCAATACGTTAGGGCTCGATTCTCTCGA
*
1368999 ATATCTAAAATACTGAATATTACTTATTTTTAAAATTTTTTGTTTTTTGATAAATCCGAGTAAAA
196 ATATCTAAAATACCGAATATTACTTATTTTTAAAATTTTTTGTTTTTTGATAAATCCGAGTAAAA
*
1369064 ATGGAAGCAAAATAATGTTAATGATGGCAATGTAAATGAGATAATTCAAACACAACTAAAATGAG
261 ATGGAAGCAAAATAATGTTAATGATGACAATGTAAATGAGATAATTCAAACACAACTAAAATGAG
1369129 CAACAAATAAAATACATAATAAACAAATCAAAT
326 CAACAAATAAAATACATAATAAACAAATCAAAT
1369162 AAAATATTACCTTTATTATTTTTTAGAAAAATTCTCATATCGAGTAAACAATGTGTCATATCCAA
1 AAAATATTACCTTTATTATTTTTTAGAAAAATTCTCATATCGAGTAAACAATGTGTCATATCCAA
1369227 TGTGTTAGGACACAACGTATTAAATTCCCGATAATGAGCTTTTTTATACATTTTTTTAAAGAGTA
66 TGTGTTAGGACACAACGTATTAAATTCCCGATAATGAGCTTTTTTATACATTTTTTTAAAGAGTA
1369292 ATCTCGATTATTTAAATTCAACGAAGAAAGTCAGAACCCAATACGTTAGGGCTCGATTCTCTCGA
131 ATCTCGATTATTTAAATTCAACGAAGAAAGTCAGAACCCAATACGTTAGGGCTCGATTCTCTCGA
1369357 ATATCTAAAATACCGAATATTACTTATTTTTTAAAA-TTTTTGTTTTTTGATAAATCCGAGTAAA
196 ATATCTAAAATACCGAATATTACTTA-TTTTTAAAATTTTTTGTTTTTTGATAAATCCGAGTAAA
1369421 AATGGAAGCAAAATAATGTTAATGATGACAATGTAAATGAGATAATTCAAACACAACTAAAATGA
260 AATGGAAGCAAAATAATGTTAATGATGACAATGTAAATGAGATAATTCAAACACAACTAAAATGA
1369486 GCAACAAATAAAATACATAATAAACAAATCAAA
325 GCAACAAATAAAATACATAATAAACAAATCAAA
1369519 GATACATGAA
Statistics
Matches: 351, Mismatches: 5, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
358 342 0.97
359 9 0.03
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.33
Consensus pattern (358 bp):
AAAATATTACCTTTATTATTTTTTAGAAAAATTCTCATATCGAGTAAACAATGTGTCATATCCAA
TGTGTTAGGACACAACGTATTAAATTCCCGATAATGAGCTTTTTTATACATTTTTTTAAAGAGTA
ATCTCGATTATTTAAATTCAACGAAGAAAGTCAGAACCCAATACGTTAGGGCTCGATTCTCTCGA
ATATCTAAAATACCGAATATTACTTATTTTTAAAATTTTTTGTTTTTTGATAAATCCGAGTAAAA
ATGGAAGCAAAATAATGTTAATGATGACAATGTAAATGAGATAATTCAAACACAACTAAAATGAG
CAACAAATAAAATACATAATAAACAAATCAAAT
Found at i:1370720 original size:13 final size:13
Alignment explanation
Indices: 1370702--1370726 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1370692 AAGAAAGGGT
1370702 ATAAAACAAAATG
1 ATAAAACAAAATG
1370715 ATAAAACAAAAT
1 ATAAAACAAAAT
1370727 AAAATGAAAA
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:0.72, C:0.08, G:0.04, T:0.16
Consensus pattern (13 bp):
ATAAAACAAAATG
Found at i:1371734 original size:44 final size:44
Alignment explanation
Indices: 1371686--1371774 Score: 117
Period size: 44 Copynumber: 2.0 Consensus size: 44
1371676 CCACTGTAAC
* * *
1371686 CTTAGGGAGGTAAAATTCG-ACATCTTCGATCTACTCCACTACTG
1 CTTAGGGAGATAAAATCCGTA-ATCTTCAATCTACTCCACTACTG
* *
1371730 CTTAGGGAGATAAGATCCGTAATCTTCAATCTATTCCACTACTG
1 CTTAGGGAGATAAAATCCGTAATCTTCAATCTACTCCACTACTG
1371774 C
1 C
1371775 CCAAGGAGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
44 38 0.97
45 1 0.03
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (44 bp):
CTTAGGGAGATAAAATCCGTAATCTTCAATCTACTCCACTACTG
Found at i:1372179 original size:174 final size:174
Alignment explanation
Indices: 1371867--1372180 Score: 389
Period size: 174 Copynumber: 1.8 Consensus size: 174
1371857 CTGTAATCTT
* * * * *
1371867 AGGGAGATAAGACCTGATGCGATCTATTTTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTA
1 AGGGAGATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTGATCTTA
* * * * * * * *
1371932 ATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTGCCTTCTGTCTGTTCCGCTGTAATCTCA
66 ATCCACTCCACTGCAACCTCAGGAAGATAGGATTACTGCCTTCTGTCTGCTCCACTGCAACCTCA
1371997 AAGAGATAAGGCTGAAGTTCTTCGGTCCACTCCACTGTACCCTC
131 AAGAGATAAGGCTGAAGTTCTTCGGTCCACTCCACTGTACCCTC
* * *
1372041 AGGGAGATAAGGCTTGATACGATCTACTCTACTGTAACTTCAGAGAGATAAGAT-CTGTGGTCTT
1 AGGGAGATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCT-TGATCTT
* * ** **
1372105 AGTCCACTCCAGTGCAACCTCAAGGAAG-TAGGATTGGTTTCTTCTGTCTGCTCCACTGCAACCT
65 AATCCACTCCACTGCAACCTC-AGGAAGATAGGATTACTGCCTTCTGTCTGCTCCACTGCAACCT
*
1372169 CAAGGAGATAAG
129 CAAAGAGATAAG
1372181 ACTGGATACA
Statistics
Matches: 115, Mismatches: 23, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
173 2 0.02
174 108 0.94
175 5 0.04
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (174 bp):
AGGGAGATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTGATCTTA
ATCCACTCCACTGCAACCTCAGGAAGATAGGATTACTGCCTTCTGTCTGCTCCACTGCAACCTCA
AAGAGATAAGGCTGAAGTTCTTCGGTCCACTCCACTGTACCCTC
Found at i:1372286 original size:129 final size:129
Alignment explanation
Indices: 1372026--1372354 Score: 347
Period size: 129 Copynumber: 2.5 Consensus size: 129
1372016 CTTCGGTCCA
* * * * *
1372026 CTCCACTGTACCCTCAGGGAGATAAGGCTTGATACGATCTACTCTACTGTAACTTCAGAGAGATA
1 CTCCACTGTAACCTCAGGGAGATAAGACTGGATACAATCTGCTCTACTGTAACTTCAGAGAGATA
* ** ** **
1372091 AGATCTGTGGTCTTAGTCCACTCCAGTGCAACCTCAAGGAAGTAGGATTGGTTTCTTCTGTCTG
66 AGATCTGTGGTCTTAGTCCACTCCACTGCAACCTCAAGGAAGTAGGATTACTAGCTTCAATCTG
* * *
1372155 CTCCACTGCAACCTCAAGGAGATAAGACTGGATACAATCTGCTCTACTGCAACTTCAGAGAGATA
1 CTCCACTGTAACCTCAGGGAGATAAGACTGGATACAATCTGCTCTACTGTAACTTCAGAGAGATA
* * * * *
1372220 AGATCTGTGGT-TTTGATCCGCTCCACTGCAACTTC-AGGGAGATAGGATTACTAGCTTCAATTT
66 AGATCTGTGGTCTTAG-TCCACTCCACTGCAACCTCAAGGAAG-TAGGATTACTAGCTTCAATCT
1372283 G
129 G
* * * * * * * *
1372284 CTCCGCTGTAATCTCAGGGAAATAAGATCCCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAG
1 CTCCACTGTAACCTCAGGGAGATAAGA---CTGGATACAATCTGCTCTACTGTAACTTCAGAGAG
1372349 ATAAGA
63 ATAAGA
1372355 CCTGATGCGA
Statistics
Matches: 164, Mismatches: 31, Indels: 7
0.81 0.15 0.03
Matches are distributed among these distances:
128 8 0.05
129 121 0.74
132 35 0.21
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (129 bp):
CTCCACTGTAACCTCAGGGAGATAAGACTGGATACAATCTGCTCTACTGTAACTTCAGAGAGATA
AGATCTGTGGTCTTAGTCCACTCCACTGCAACCTCAAGGAAGTAGGATTACTAGCTTCAATCTG
Found at i:1372287 original size:44 final size:44
Alignment explanation
Indices: 1372151--1373499 Score: 504
Period size: 44 Copynumber: 30.8 Consensus size: 44
1372141 GTTTCTTCTG
* * * * * *
1372151 TCTGCTCCACTGCAACCTCAAGGAGATAAG---ACTGGATACAA
1 TCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTAGCTTCAA
* * * ** * * **
1372192 TCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTGA
1 TCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTAGCTTCAA
* * * *
1372236 TCCGCTCCACTGCAACTTCAGGGAGATAGGATTACTAGCTTCAA
1 TCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTAGCTTCAA
* * * * *
1372280 TTTGCTCCGCTGTAA-TCTCAGGGAAATAAGATCCCTGGCTTCAA
1 TCTGCTCCACTGTAACT-TCAGGGAGATAAGATCACTAGCTTCAA
* * * *
1372324 TCTGCTCCACTGTAACCTCAGGGAGATAAGA-C-CT-GATGCGA
1 TCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTAGCTTCAA
* ** * * * *
1372365 TCTACTCTGCTGTAACTTCAGAGAGATAAGATC-CTTGATTTTAA
1 TCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTAG-CTTCAA
** * * * *
1372409 TCCACTCCACTATAA-TCTCAGGGAGATAGGATTACTATCTTCAA
1 TCTGCTCCACTGTAACT-TCAGGGAGATAAGATCACTAGCTTCAA
* * * *
1372453 TCTGCTCCGCTGTAA-TCTCACGGAGATAAGATCTCTGGCTTCAA
1 TCTGCTCCACTGTAACT-TCAGGGAGATAAGATCACTAGCTTCAA
* * * **
1372497 TCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGA-AATTCTTCGG
1 TCTGCTCCACTGTAACTTCAGGGAGATAAGATC--ACTA-GCTTCAA
* * * * * *
1372543 TCTACTCCACTGTAACATT-AGGGAGATAAGGTTTGA-AATTCTTCAG
1 TCTGCTCCACTGTAAC-TTCAGGGAGATAA-G-ATCACTA-GCTTCAA
* * * * *
1372589 TCTACTCCACTGTAACCTCAGGGAGATAAGA-C-CT-GATGCGA
1 TCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTAGCTTCAA
* ** * * * *
1372630 TCTACTCTGCTGTAACTTCAGAGAGATAAGATC-CTTGATTTTAA
1 TCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTAG-CTTCAA
** * * * * * *
1372674 TCCACTCCACTATAA-TCTCAGGGAGGTAGGATGACTATCTTGAA
1 TCTGCTCCACTGTAACT-TCAGGGAGATAAGATCACTAGCTTCAA
* * * *
1372718 TCTGCTCCGCTGTAA-TCTCACGGAGATAAGATCTCTGGCTTCAA
1 TCTGCTCCACTGTAACT-TCAGGGAGATAAGATCACTAGCTTCAA
* * * **
1372762 TCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGA-AATTCTTCGG
1 TCTGCTCCACTGTAACTTCAGGGAGATAAGATC--ACTA-GCTTCAA
* * * * * *
1372808 TCTACTCCACTGTAACATT-AGGGAGATAAGGTTTGA-AATTCTTCAG
1 TCTGCTCCACTGTAAC-TTCAGGGAGATAA-G-ATCACTA-GCTTCAA
* * * * *
1372854 TCTACTCCACTGTAACCTCAGGGAGATAAGA-C-CT-GATGCGA
1 TCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTAGCTTCAA
* ** * ** * *
1372895 TCTACTCTGCTGTAACTTCAGAGAGATAAGATCTGT-GATTTTAA
1 TCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTAG-CTTCAA
* * *
1372939 T-TCGCTCCACTGTAA-TCTCAGGGAGATAGGATTACTATCTTCAA
1 TCT-GCTCCACTGTAACT-TCAGGGAGATAAGATCACTAGCTTCAA
* * *
1372983 TCTGCTCCGCTGTAA-TCTCAGGGAGATAAGATCTCTGGCTTCAA
1 TCTGCTCCACTGTAACT-TCAGGGAGATAAGATCACTAGCTTCAA
* * * **
1373027 TCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGA-AATTCTTCGG
1 TCTGCTCCACTGTAACTTCAGGGAGATAAGATC--ACTA-GCTTCAA
* * * * * *
1373073 TCTACTCCACTGTAACATT-AGGGAGATAAGGTTTGA-AATTCTTCAG
1 TCTGCTCCACTGTAAC-TTCAGGGAGATAA-G-ATCACTA-GCTTCAA
* * * * *
1373119 TCTACTCCACTGTAACCTCAGGGAGATAAGA-C-CT-GATGCGA
1 TCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTAGCTTCAA
* ** * ** * *
1373160 TCTACTCTGCTGTAACTTCAGAGAGATAAGATCTGT-GATTTTAA
1 TCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTAG-CTTCAA
* * *
1373204 T-TCGCTCCACTGTAATCTT-AGGGAGATAGGATTACTATCTTCAA
1 TCT-GCTCCACTGTAA-CTTCAGGGAGATAAGATCACTAGCTTCAA
* * *
1373248 TCTGCTCCGCTGTAA-TCTCAGGGAGATAAGATCTCTGGCTTCAA
1 TCTGCTCCACTGTAACT-TCAGGGAGATAAGATCACTAGCTTCAA
* * * * **
1373292 TCTGCTCCACTGTAACCTCAGAGAGATAAGATCTGA-AATTCTTCGG
1 TCTGCTCCACTGTAACTTCAGGGAGATAAGATC--ACTA-GCTTCAA
* * * * * *
1373338 TCTACTCCACTGTAACCTCAGGGAGATAA-AAC-CT-GATGCGA
1 TCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTAGCTTCAA
* ** * * * *
1373379 TCTACTCTGCTGTAACTTCAGAGAGATAAGATC-CTTGATTTTAA
1 TCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTAG-CTTCAA
* * * * * *
1373423 TCCGCTCCACTGTAA-TCTCAAGGAGATAGGATTATTATCTTCAA
1 TCTGCTCCACTGTAACT-TCAGGGAGATAAGATCACTAGCTTCAA
*
1373467 TCTGCTCCGCTGTAA-TCTCAGGGAGATAAGATC
1 TCTGCTCCACTGTAACT-TCAGGGAGATAAGATC
1373500 TCTAATATTC
Statistics
Matches: 977, Mismatches: 263, Indels: 133
0.71 0.19 0.10
Matches are distributed among these distances:
41 171 0.18
42 15 0.02
43 16 0.02
44 522 0.53
45 18 0.02
46 226 0.23
47 6 0.01
48 3 0.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30
Consensus pattern (44 bp):
TCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTAGCTTCAA
Found at i:1372384 original size:173 final size:172
Alignment explanation
Indices: 1372151--1373062 Score: 787
Period size: 173 Copynumber: 5.2 Consensus size: 172
1372141 GTTTCTTCTG
* * * * * * *
1372151 TCTGCTCCACTGCAACCTCAAGGAGATAAGACTGGATACAATCTGCTCTACTGCAACTTCAGAGA
1 TCTGCTCCACTGTAACCTCAGGGAGATAAGACT-GATGCGATCTACTCTGCTGTAACTTCAGAGA
* * * *
1372216 GATAAGATCTGTGGTTTTGATCCGCTCCACTGCAACTTCAGGGAGATAGGATTACTAGCTTCAAT
65 GATAAGATCTGTGATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTACTATCTTCAAT
* *
1372281 TTGCTCCGCTGTAATCTCAGGGAAATAAGATCCCTGGCTTCAA
130 CTGCTCCGCTGTAATCTCAGGGAGATAAGATCCCTGGCTTCAA
1372324 TCTGCTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAGA
1 TCTGCTCCACTGTAACCTCAGGGAGATAAGA-CTGATGCGATCTACTCTGCTGTAACTTCAGAGA
* *
1372389 GATAAGATCCT-TGATTTTAATCCACTCCACTATAA-TCTCAGGGAGATAGGATTACTATCTTCA
65 GATAAGAT-CTGTGATTTTAATCCGCTCCACTGTAACT-TCAGGGAGATAGGATTACTATCTTCA
* *
1372452 ATCTGCTCCGCTGTAATCTCACGGAGATAAGATCTCTGGCTTCAA
128 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCCCTGGCTTCAA
* * **
1372497 TCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACATT
1 TCTGCTCCACTGTAACCTCAGGGAGATAAGA-CTG--A---TGCGATCTACTCTGCTGTAAC-TT
* * * ** * ** * * *
1372562 -AGGGAGATAAGGTTTGAAATTCTTCAGTCTACTCCACTGTAACCTCAGGGAGATAAGA--CCTG
59 CAGAGAGATAAGATCTGTGATT-TT-AATCCGCTCCACTGTAACTTCAGGGAGATAGGATTACT-
* * * * * * ** *
1372624 A--TGCGATCTACTCTGCTGTAA-CTTCAGAGAGATAAGATCCTTGATTTTAA
121 ATCTTCAATCTGCTCCGCTGTAATC-TCAGGGAGATAAGATCCCTGGCTTCAA
** * * * * *
1372674 TCCACTCCACTATAATCTCAGGGAGGTAGGATGACT-AT-CTTGAATCTGCTCCGCTGTAA-TCT
1 TCTGCTCCACTGTAACCTCAGGGAGATA--A-GACTGATGC--G-ATCTACTCTGCTGTAACT-T
* ** * * * * *
1372736 CACG-GAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGA-A
59 CA-GAGAGATAAGATCTGTGATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGAT-T-ACT
** * * * * * * *
1372799 ATTCTTCGGTCTACTCCACTGTAA-CATTAGGGAGATAAGGT--TTGAAATTCTTCAG
121 A-TCTTCAATCTGCTCCGCTGTAATC-TCAGGGAGATAAGATCCCTG----GCTTCAA
*
1372854 TCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAGA
1 TCTGCTCCACTGTAACCTCAGGGAGATAAGA-CTGATGCGATCTACTCTGCTGTAACTTCAGAGA
*
1372919 GATAAGATCTGTGATTTTAATTCGCTCCACTGTAA-TCTCAGGGAGATAGGATTACTATCTTCAA
65 GATAAGATCTGTGATTTTAATCCGCTCCACTGTAACT-TCAGGGAGATAGGATTACTATCTTCAA
*
1372983 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAA
129 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCCCTGGCTTCAA
1373027 TCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGA
1 TCTGCTCCACTGTAACCTCAGGGAGATAAGA-CTGA
1373063 AATTCTTCGG
Statistics
Matches: 592, Mismatches: 102, Indels: 90
0.76 0.13 0.11
Matches are distributed among these distances:
172 2 0.00
173 254 0.43
174 7 0.01
175 59 0.10
176 10 0.02
177 126 0.21
178 67 0.11
179 10 0.02
180 57 0.10
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (172 bp):
TCTGCTCCACTGTAACCTCAGGGAGATAAGACTGATGCGATCTACTCTGCTGTAACTTCAGAGAG
ATAAGATCTGTGATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTACTATCTTCAATC
TGCTCCGCTGTAATCTCAGGGAGATAAGATCCCTGGCTTCAA
Found at i:1372566 original size:46 final size:44
Alignment explanation
Indices: 1372318--1373500 Score: 609
Period size: 44 Copynumber: 26.9 Consensus size: 44
1372308 AGATCCCTGG
* *
1372318 CTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGACCTG-A--
1 CTTCAATCTACTCCACTGTAA-CTCAGGGAGATAAGATCTGAATT
* * ** *
1372360 -TGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTG-ATT
1 CTTCAATCTACTCCACTGTAAC-TCAGGGAGATAAGAT-C-TGAATT
* * * *
1372405 -TT-AATCCACTCCACTATAATCTCAGGGAGATAGGAT-T-ACTAT
1 CTTCAATCTACTCCACTGTAA-CTCAGGGAGATAAGATCTGAAT-T
* * * * *
1372447 CTTCAATCTGCTCCGCTGTAATCTCACGGAGATAAGATCT--CTGG
1 CTTCAATCTACTCCACTGTAA-CTCAGGGAGATAAGATCTGAAT-T
*
1372491 CTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATT
1 CTTCAATCTACTCCACTGTAA-CTCAGGGAGATAAGATCTG-AATT
** * * *
1372537 CTTCGGTCTACTCCACTGTAACATTAGGGAGATAAGGTTTGAAATT
1 CTTCAATCTACTCCACTGTAAC-TCAGGGAGATAAGATCTG-AATT
* *
1372583 CTTCAGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTG-A--
1 CTTCAATCTACTCCACTGTAA-CTCAGGGAGATAAGATCTGAATT
* * ** *
1372625 -TGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTG-ATT
1 CTTCAATCTACTCCACTGTAAC-TCAGGGAGATAAGAT-C-TGAATT
* * * * *
1372670 -TT-AATCCACTCCACTATAATCTCAGGGAGGTAGGA--TGACTAT
1 CTTCAATCTACTCCACTGTAA-CTCAGGGAGATAAGATCTGAAT-T
* * * * * *
1372712 CTTGAATCTGCTCCGCTGTAATCTCACGGAGATAAGATCT--CTGG
1 CTTCAATCTACTCCACTGTAA-CTCAGGGAGATAAGATCTGAAT-T
*
1372756 CTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATT
1 CTTCAATCTACTCCACTGTAA-CTCAGGGAGATAAGATCTG-AATT
** * * *
1372802 CTTCGGTCTACTCCACTGTAACATTAGGGAGATAAGGTTTGAAATT
1 CTTCAATCTACTCCACTGTAAC-TCAGGGAGATAAGATCTG-AATT
* *
1372848 CTTCAGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTG-A--
1 CTTCAATCTACTCCACTGTAA-CTCAGGGAGATAAGATCTGAATT
* * ** * *
1372890 -TGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCTGTGATT
1 CTTCAATCTACTCCACTGTAAC-TCAGGGAGATAAGATCTG-AATT
* * *
1372935 -TT-AAT-TCGCTCCACTGTAATCTCAGGGAGATAGGAT-T-ACTAT
1 CTTCAATCT-ACTCCACTGTAA-CTCAGGGAGATAAGATCTGAAT-T
* * * *
1372977 CTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT--CTGG
1 CTTCAATCTACTCCACTGTAA-CTCAGGGAGATAAGATCTGAAT-T
*
1373021 CTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATT
1 CTTCAATCTACTCCACTGTAA-CTCAGGGAGATAAGATCTG-AATT
** * * *
1373067 CTTCGGTCTACTCCACTGTAACATTAGGGAGATAAGGTTTGAAATT
1 CTTCAATCTACTCCACTGTAAC-TCAGGGAGATAAGATCTG-AATT
* *
1373113 CTTCAGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTG-A--
1 CTTCAATCTACTCCACTGTAA-CTCAGGGAGATAAGATCTGAATT
* * ** * *
1373155 -TGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCTGTGATT
1 CTTCAATCTACTCCACTGTAAC-TCAGGGAGATAAGATCTG-AATT
* * * *
1373200 -TT-AAT-TCGCTCCACTGTAATCTTAGGGAGATAGGAT-T-ACTAT
1 CTTCAATCT-ACTCCACTGTAA-CTCAGGGAGATAAGATCTGAAT-T
* * * *
1373242 CTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT--CTGG
1 CTTCAATCTACTCCACTGTAA-CTCAGGGAGATAAGATCTGAAT-T
* *
1373286 CTTCAATCTGCTCCACTGTAACCTCAGAGAGATAAGATCTGAAATT
1 CTTCAATCTACTCCACTGTAA-CTCAGGGAGATAAGATCTG-AATT
** * *
1373332 CTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAAACCTG-A--
1 CTTCAATCTACTCCACTGTAA-CTCAGGGAGATAAGATCTGAATT
* * ** *
1373374 -TGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTG-ATT
1 CTTCAATCTACTCCACTGTAAC-TCAGGGAGATAAGAT-C-TGAATT
** * * *
1373419 -TT-AATCCGCTCCACTGTAATCTCAAGGAGATAGGAT-T-ATTAT
1 CTTCAATCTACTCCACTGTAA-CTCAGGGAGATAAGATCTGAAT-T
* *
1373461 CTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT
1 CTTCAATCTACTCCACTGTAA-CTCAGGGAGATAAGATCT
1373501 CTAATATTCA
Statistics
Matches: 893, Mismatches: 172, Indels: 149
0.74 0.14 0.12
Matches are distributed among these distances:
40 7 0.01
41 153 0.17
42 8 0.01
43 25 0.03
44 422 0.47
45 19 0.02
46 252 0.28
47 7 0.01
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30
Consensus pattern (44 bp):
CTTCAATCTACTCCACTGTAACTCAGGGAGATAAGATCTGAATT
Found at i:1372634 original size:265 final size:265
Alignment explanation
Indices: 1372318--1373366 Score: 1913
Period size: 265 Copynumber: 4.0 Consensus size: 265
1372308 AGATCCCTGG
* *
1372318 CTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTT
1 CTTCAGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTT
1372383 CAGAGAGATAAGATCCT-TGATTTTAATCCACTCCACTATAATCTCAGGGAGATAGGATTACTAT
66 CAGAGAGATAAGAT-CTGTGATTTTAATCCACTCCACTATAATCTCAGGGAGATAGGATTACTAT
1372447 CTTCAATCTGCTCCGCTGTAATCTCACGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAA
130 CTTCAATCTGCTCCGCTGTAATCTCACGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAA
1372512 CCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACATTAGGGAGATAAGGTTT
195 CCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACATTAGGGAGATAAGGTTT
1372577 GAAATT
260 GAAATT
1372583 CTTCAGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTT
1 CTTCAGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTT
* *
1372648 CAGAGAGATAAGATCCT-TGATTTTAATCCACTCCACTATAATCTCAGGGAGGTAGGATGACTAT
66 CAGAGAGATAAGAT-CTGTGATTTTAATCCACTCCACTATAATCTCAGGGAGATAGGATTACTAT
*
1372712 CTTGAATCTGCTCCGCTGTAATCTCACGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAA
130 CTTCAATCTGCTCCGCTGTAATCTCACGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAA
1372777 CCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACATTAGGGAGATAAGGTTT
195 CCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACATTAGGGAGATAAGGTTT
1372842 GAAATT
260 GAAATT
1372848 CTTCAGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTT
1 CTTCAGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTT
* * *
1372913 CAGAGAGATAAGATCTGTGATTTTAATTCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATC
66 CAGAGAGATAAGATCTGTGATTTTAATCCACTCCACTATAATCTCAGGGAGATAGGATTACTATC
*
1372978 TTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAAC
131 TTCAATCTGCTCCGCTGTAATCTCACGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAAC
1373043 CTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACATTAGGGAGATAAGGTTTG
196 CTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACATTAGGGAGATAAGGTTTG
1373108 AAATT
261 AAATT
1373113 CTTCAGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTT
1 CTTCAGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTT
* * * *
1373178 CAGAGAGATAAGATCTGTGATTTTAATTCGCTCCACTGTAATCTTAGGGAGATAGGATTACTATC
66 CAGAGAGATAAGATCTGTGATTTTAATCCACTCCACTATAATCTCAGGGAGATAGGATTACTATC
*
1373243 TTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAAC
131 TTCAATCTGCTCCGCTGTAATCTCACGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAAC
* * *
1373308 CTCAGAGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAA
196 CTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACATTAGGGAGATAA
1373367 AACCTGATGC
Statistics
Matches: 767, Mismatches: 16, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
264 2 0.00
265 765 1.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30
Consensus pattern (265 bp):
CTTCAGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTT
CAGAGAGATAAGATCTGTGATTTTAATCCACTCCACTATAATCTCAGGGAGATAGGATTACTATC
TTCAATCTGCTCCGCTGTAATCTCACGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAAC
CTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACATTAGGGAGATAAGGTTTG
AAATT
Found at i:1373374 original size:219 final size:218
Alignment explanation
Indices: 1372981--1373502 Score: 769
Period size: 219 Copynumber: 2.4 Consensus size: 218
1372971 TACTATCTTC
* * * ** * *
1372981 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT-CTGGCTTCAATCTGCTCCACTGTAACCT
1 AATCCGCTCCACTGTAATCTCAGGGAGATAGGAT-TACTATCTTCAATCTGCTCCGCTGTAATCT
* * ** * * * *
1373045 CAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACATTAGGGAGATAAGGTTTGAA
65 CAGGGAGATAAGATCT---CTGCTTCAATCTACTCCACTGTAACATCAGAGAGATAAGATCTGAA
*
1373110 ATTCTTCAGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAA
127 ATTCTTCAGTCTACTCCACTGTAACCTCAGGGAGATAAAACCTGATGCGATCTACTCTGCTGTAA
1373175 CTTCAGAGAGATAAGAT-CTGTGATTTT
192 CTTCAGAGAGATAAGATCCT-TGATTTT
* *
1373202 AATTCGCTCCACTGTAATCTTAGGGAGATAGGATTACTATCTTCAATCTGCTCCGCTGTAATCTC
1 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAATCTGCTCCGCTGTAATCTC
* *
1373267 AGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGAGAGATAAGATCTGAAATT
66 AGGGAGATAAGATCTCT-GCTTCAATCTACTCCACTGTAACATCAGAGAGATAAGATCTGAAATT
*
1373332 CTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAAACCTGATGCGATCTACTCTGCTGTAACTT
130 CTTCAGTCTACTCCACTGTAACCTCAGGGAGATAAAACCTGATGCGATCTACTCTGCTGTAACTT
1373397 CAGAGAGATAAGATCCTTGATTTT
195 CAGAGAGATAAGATCCTTGATTTT
* *
1373421 AATCCGCTCCACTGTAATCTCAAGGAGATAGGATTATTATCTTCAATCTGCTCCGCTGTAATCTC
1 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAATCTGCTCCGCTGTAATCTC
1373486 AGGGAGATAAGATCTCT
66 AGGGAGATAAGATCTCT
1373503 AATATTCACT
Statistics
Matches: 273, Mismatches: 25, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
218 1 0.00
219 200 0.73
220 3 0.01
221 69 0.25
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (218 bp):
AATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAATCTGCTCCGCTGTAATCTC
AGGGAGATAAGATCTCTGCTTCAATCTACTCCACTGTAACATCAGAGAGATAAGATCTGAAATTC
TTCAGTCTACTCCACTGTAACCTCAGGGAGATAAAACCTGATGCGATCTACTCTGCTGTAACTTC
AGAGAGATAAGATCCTTGATTTT
Found at i:1374758 original size:20 final size:20
Alignment explanation
Indices: 1374733--1374789 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
1374723 GCCTCTCCAT
1374733 TTTTCATTTTTCATTTTTCA
1 TTTTCATTTTTCATTTTTCA
1374753 TTTTCATTTTTCATTTTTCA
1 TTTTCATTTTTCATTTTTCA
*
1374773 TTCTCATTTTTC-TTTTT
1 TTTTCATTTTTCATTTTT
1374790 TTTTGACTCA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
19 5 0.14
20 31 0.86
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTCATTTTTCATTTTTCA
Found at i:1374779 original size:13 final size:14
Alignment explanation
Indices: 1374730--1374789 Score: 90
Period size: 13 Copynumber: 4.5 Consensus size: 14
1374720 TTAGCCTCTC
1374730 CATTTTTCATTTTT
1 CATTTTTCATTTTT
1374744 CATTTTTCA-TTTT
1 CATTTTTCATTTTT
1374757 CATTTTTCATTTTT
1 CATTTTTCATTTTT
*
1374771 CA-TTCTCATTTTT
1 CATTTTTCATTTTT
1374784 C-TTTTT
1 CATTTTT
1374790 TTTTGACTCA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
13 27 0.64
14 15 0.36
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (14 bp):
CATTTTTCATTTTT
Found at i:1374784 original size:27 final size:27
Alignment explanation
Indices: 1374730--1374782 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
1374720 TTAGCCTCTC
*
1374730 CATTTTTCATTTTTCATTTTTCATTTT
1 CATTTTTCATTTTTCATTTCTCATTTT
1374757 CATTTTTCATTTTTCA-TTCTCATTTT
1 CATTTTTCATTTTTCATTTCTCATTTT
1374783 TCTTTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 9 0.36
27 16 0.64
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.68
Consensus pattern (27 bp):
CATTTTTCATTTTTCATTTCTCATTTT
Found at i:1374790 original size:7 final size:7
Alignment explanation
Indices: 1374730--1374789 Score: 90
Period size: 7 Copynumber: 9.0 Consensus size: 7
1374720 TTAGCCTCTC
1374730 CATTTTT
1 CATTTTT
1374737 CATTTTT
1 CATTTTT
1374744 CATTTTT
1 CATTTTT
1374751 CA-TTTT
1 CATTTTT
1374757 CATTTTT
1 CATTTTT
1374764 CATTTTT
1 CATTTTT
*
1374771 CA-TTCT
1 CATTTTT
1374777 CATTTTT
1 CATTTTT
1374784 C-TTTTT
1 CATTTTT
1374790 TTTTGACTCA
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
6 16 0.33
7 33 0.67
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (7 bp):
CATTTTT
Found at i:1375793 original size:50 final size:50
Alignment explanation
Indices: 1375699--1375796 Score: 119
Period size: 50 Copynumber: 2.0 Consensus size: 50
1375689 AGATTTCTCT
1375699 TTTTTTATTCTTCTTTCTTTTTCTCGTTTTCATTTTGATCTTGATTTTGA
1 TTTTTTATTCTTCTTTCTTTTTCTCGTTTTCATTTTGATCTTGATTTTGA
* * * * *
1375749 TTTTTTCTTCTT-TCTTCTTTTTGT-TTTTTTATTTTGATTTTTGATTTT
1 TTTTTTATTCTTCT-TTCTTTTTCTCGTTTTCATTTTGA-TCTTGATTTT
1375797 TTTCATTTTC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
49 12 0.29
50 29 0.71
ACGTcount: A:0.08, C:0.11, G:0.07, T:0.73
Consensus pattern (50 bp):
TTTTTTATTCTTCTTTCTTTTTCTCGTTTTCATTTTGATCTTGATTTTGA
Found at i:1378255 original size:5 final size:5
Alignment explanation
Indices: 1378237--1378277 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
1378227 CTTTCCTAAG
*
1378237 ATGCAA ATGCA ATGTA ATGCA AT-C- ATGCA ATGCA ATGCA AT
1 ATGC-A ATGCA ATGCA ATGCA ATGCA ATGCA ATGCA ATGCA AT
1378278 CATAATCAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
3 2 0.06
4 2 0.06
5 23 0.74
6 4 0.13
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.24
Consensus pattern (5 bp):
ATGCA
Found at i:1378266 original size:18 final size:18
Alignment explanation
Indices: 1378243--1378280 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
1378233 TAAGATGCAA
*
1378243 ATGCAATGTAATGCAATC
1 ATGCAATGCAATGCAATC
1378261 ATGCAATGCAATGCAATC
1 ATGCAATGCAATGCAATC
1378279 AT
1 AT
1378281 AATCAAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.26
Consensus pattern (18 bp):
ATGCAATGCAATGCAATC
Found at i:1379320 original size:105 final size:107
Alignment explanation
Indices: 1379195--1379392 Score: 283
Period size: 108 Copynumber: 1.9 Consensus size: 107
1379185 TGAAATTCAA
*
1379195 AAGGATATTTGACTATTTGGTTAAACGAG-AAATCGAAACACAACACATTAGGGAACG-TTCCTC
1 AAGGATATTCGACTATTTGGTTAAACGAGAAAATCGAAACACAACACATTAGGGAACGTTTCCTC
* *
1379258 GAATTTCCAAACGTAAAACATTGCCTTATTTGAAATTTTTGG
66 GAATTTCCAAACGCAAAACATTACCTTATTTGAAATTTTTGG
* * * * * *
1379300 AAGGATATTCGGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCT
1 AAGGATATTCGACTATTTGGTTAAACGAG-AAAATCGAAACACAACACATTAGGGAACGTTTCCT
*
1379365 CGAATTTCCAAACGCAAAATATTACCTT
65 CGAATTTCCAAACGCAAAACATTACCTT
1379393 TATTATTTTT
Statistics
Matches: 80, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
105 26 0.32
107 25 0.31
108 29 0.36
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (107 bp):
AAGGATATTCGACTATTTGGTTAAACGAGAAAATCGAAACACAACACATTAGGGAACGTTTCCTC
GAATTTCCAAACGCAAAACATTACCTTATTTGAAATTTTTGG
Found at i:1380924 original size:13 final size:13
Alignment explanation
Indices: 1380906--1380930 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1380896 AAGAAAGGTT
1380906 ATAAAACAAAATG
1 ATAAAACAAAATG
1380919 ATAAAACAAAAT
1 ATAAAACAAAAT
1380931 AAAATGAAAA
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:0.72, C:0.08, G:0.04, T:0.16
Consensus pattern (13 bp):
ATAAAACAAAATG
Found at i:1382766 original size:25 final size:25
Alignment explanation
Indices: 1382737--1382784 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
1382727 TTTGCTATTC
*
1382737 ATATACACGCATATTTTTATATACA
1 ATATACACGCATATTTTAATATACA
***
1382762 ATATATGTGCATATTTTAATATA
1 ATATACACGCATATTTTAATATA
1382785 TACTTTTAAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.44
Consensus pattern (25 bp):
ATATACACGCATATTTTAATATACA
Found at i:1382908 original size:33 final size:29
Alignment explanation
Indices: 1382871--1382941 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 29
1382861 TTTATACTAT
1382871 ATATATACTTACACACCTTTTTTATTTTTGTAA
1 ATATATACTTACACA---TTTTTA-TTTTGTAA
* *
1382904 ATATATACATATACATTTTTATTTTGTAA
1 ATATATACTTACACATTTTTATTTTGTAA
1382933 ATATATACT
1 ATATATACT
1382942 GGTACATGCT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 16 0.46
30 6 0.17
33 13 0.37
ACGTcount: A:0.35, C:0.11, G:0.03, T:0.51
Consensus pattern (29 bp):
ATATATACTTACACATTTTTATTTTGTAA
Found at i:1386378 original size:19 final size:17
Alignment explanation
Indices: 1386324--1386381 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 17
1386314 TATTAATTTT
*
1386324 AAATAAATAAATTTTGAA
1 AAATTAATAAATTTT-AA
1386342 AAATTAAGTAATATTTTAA
1 AAATTAA-TAA-ATTTTAA
1386361 AGAATTAGATAAATTTTAA
1 A-AATTA-ATAAATTTTAA
1386380 AA
1 AA
1386382 TTTTTATATA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
18 7 0.20
19 14 0.40
20 13 0.37
21 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (17 bp):
AAATTAATAAATTTTAA
Found at i:1386683 original size:10 final size:10
Alignment explanation
Indices: 1386636--1386695 Score: 50
Period size: 10 Copynumber: 5.8 Consensus size: 10
1386626 AAAATAAAAG
1386636 TTTAAAATCTT
1 TTTAAAATC-T
* *
1386647 TTTTAAAT-A
1 TTTAAAATCT
**
1386656 TTTAAAAAAT
1 TTTAAAATCT
1386666 TTTAAAATCT
1 TTTAAAATCT
1386676 TTTAAAATTCAT
1 TTTAAAA-TC-T
1386688 TTTAAAAT
1 TTTAAAAT
1386696 TTTAAATCAC
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
9 6 0.15
10 15 0.38
11 10 0.26
12 8 0.21
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (10 bp):
TTTAAAATCT
Found at i:1386692 original size:12 final size:12
Alignment explanation
Indices: 1386664--1386696 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1386654 TATTTAAAAA
1386664 ATTTTAAAA-TC
1 ATTTTAAAATTC
1386675 -TTTTAAAATTC
1 ATTTTAAAATTC
1386686 ATTTTAAAATT
1 ATTTTAAAATT
1386697 TTAAATCACG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 8 0.40
11 2 0.10
12 10 0.50
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (12 bp):
ATTTTAAAATTC
Found at i:1386695 original size:30 final size:30
Alignment explanation
Indices: 1386629--1386701 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 30
1386619 TATTATAAAA
* *
1386629 ATAAAAGTTTAAAATCTTTTTTAAATATTT
1 ATAAAATTTTAAAATCTTTTTAAAATATTT
*
1386659 AAAAAATTTTAAAATC-TTTTAAAATTCATTT
1 ATAAAATTTTAAAATCTTTTTAAAA-T-ATTT
1386690 -TAAAATTTTAAA
1 ATAAAATTTTAAA
1386702 TCACGAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 7 0.19
30 26 0.70
31 4 0.11
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (30 bp):
ATAAAATTTTAAAATCTTTTTAAAATATTT
Found at i:1386698 original size:20 final size:19
Alignment explanation
Indices: 1386630--1386701 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 19
1386620 ATTATAAAAA
* *
1386630 TAAAAGTTTAAAATCTTTT
1 TAAAATTTTAAAATCATTT
* *
1386649 TTAAATATTTAAAA-AATTT
1 TAAAAT-TTTAAAATCATTT
1386668 TAAAATCTTTTAAAATTCATTT
1 TAAAA--TTTTAAAA-TCATTT
1386690 TAAAATTTTAAA
1 TAAAATTTTAAA
1386702 TCACGAAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
19 11 0.26
20 21 0.50
21 1 0.02
22 9 0.21
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (19 bp):
TAAAATTTTAAAATCATTT
Found at i:1387645 original size:29 final size:30
Alignment explanation
Indices: 1387612--1387680 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 30
1387602 CTCTAACCCG
1387612 ACCCTTAACCCCTAAATCC-T-AAACCCTAA
1 ACCCTTAACCCCTAAA-CCTTAAAACCCTAA
1387641 ACCCTTAA-CCCTAAACCTTAAAACCCTAA
1 ACCCTTAACCCCTAAACCTTAAAACCCTAA
*
1387670 ACCCATAACCC
1 ACCCTTAACCC
1387681 TCAGCCTCTA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
27 2 0.06
28 8 0.22
29 24 0.67
30 2 0.06
ACGTcount: A:0.39, C:0.42, G:0.00, T:0.19
Consensus pattern (30 bp):
ACCCTTAACCCCTAAACCTTAAAACCCTAA
Found at i:1387667 original size:15 final size:14
Alignment explanation
Indices: 1387614--1387672 Score: 68
Period size: 14 Copynumber: 4.1 Consensus size: 14
1387604 CTAACCCGAC
*
1387614 CCTTAACCCCTAAA
1 CCTTAAACCCTAAA
1387628 TCC-TAAACCCTAAA
1 -CCTTAAACCCTAAA
1387642 CCCTT-AACCCTAAA
1 -CCTTAAACCCTAAA
1387656 CCTTAAAACCCTAAA
1 CCTT-AAACCCTAAA
1387671 CC
1 CC
1387673 CATAACCCTC
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
13 4 0.10
14 21 0.54
15 14 0.36
ACGTcount: A:0.39, C:0.41, G:0.00, T:0.20
Consensus pattern (14 bp):
CCTTAAACCCTAAA
Found at i:1387670 original size:8 final size:7
Alignment explanation
Indices: 1387621--1387673 Score: 70
Period size: 7 Copynumber: 7.4 Consensus size: 7
1387611 GACCCTTAAC
1387621 CCCTAAA
1 CCCTAAA
*
1387628 TCCTAAA
1 CCCTAAA
1387635 CCCTAAA
1 CCCTAAA
*
1387642 CCCTTAA
1 CCCTAAA
1387649 CCCTAAA
1 CCCTAAA
*
1387656 CCTTAAAA
1 CCCT-AAA
1387664 CCCTAAA
1 CCCTAAA
1387671 CCC
1 CCC
1387674 ATAACCCTCA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
7 33 0.85
8 6 0.15
ACGTcount: A:0.40, C:0.42, G:0.00, T:0.19
Consensus pattern (7 bp):
CCCTAAA
Found at i:1387681 original size:14 final size:14
Alignment explanation
Indices: 1387633--1387681 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
1387623 CTAAATCCTA
*
1387633 AACCCTAAACCCTT
1 AACCCTAAACCCAT
* *
1387647 AACCCTAAACCTTAA
1 AACCCTAAACC-CAT
1387662 AACCCTAAACCCAT
1 AACCCTAAACCCAT
1387676 AACCCT
1 AACCCT
1387682 CAGCCTCTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
14 18 0.62
15 11 0.38
ACGTcount: A:0.41, C:0.41, G:0.00, T:0.18
Consensus pattern (14 bp):
AACCCTAAACCCAT
Found at i:1387696 original size:29 final size:29
Alignment explanation
Indices: 1387612--1387701 Score: 85
Period size: 29 Copynumber: 3.1 Consensus size: 29
1387602 CTCTAACCCG
* *
1387612 ACCCTTAACCCCTAAATC-CTAAACCCTAA
1 ACCCATAA-CCCTAAACCTCTAAACCCTAA
*
1387641 ACCCTTAACCCTAAACCT-TAAAACCCTAA
1 ACCCATAACCCTAAACCTCT-AAACCCTAA
* * * *
1387670 ACCCATAACCCTCAGCCTCTAACCCCTGA
1 ACCCATAACCCTAAACCTCTAAACCCTAA
1387699 ACC
1 ACC
1387702 TTATTTAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
28 9 0.17
29 42 0.81
30 1 0.02
ACGTcount: A:0.36, C:0.43, G:0.02, T:0.19
Consensus pattern (29 bp):
ACCCATAACCCTAAACCTCTAAACCCTAA
Found at i:1410378 original size:25 final size:25
Alignment explanation
Indices: 1410350--1410495 Score: 120
Period size: 25 Copynumber: 5.9 Consensus size: 25
1410340 CGTTATTTAT
* **
1410350 CTCTTATGAGCATCCTGTTATATGG
1 CTCTTATGAGCTTCCCATTATATGG
* * * *
1410375 CTCTCACGAGCTTCCCAATATTTGG
1 CTCTTATGAGCTTCCCATTATATGG
*
1410400 CTCTCATGAGCTTCCCAATTA-ATGG
1 CTCTTATGAGCTTCCC-ATTATATGG
*
1410425 CTCTCT-TGAGCTTCCCGTT-TATGG
1 CTCT-TATGAGCTTCCCATTATATGG
*
1410449 CTCTTATGAGCTTCCCGATAAT-TGG
1 CTCTTATGAGCTTCCC-ATTATATGG
* * *
1410474 CTCGTAAGATCTTCCCATTATA
1 CTCTTATGAGCTTCCCATTATA
1410496 CAGCTCGCAT
Statistics
Matches: 96, Mismatches: 18, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
23 1 0.01
24 24 0.25
25 67 0.70
26 4 0.04
ACGTcount: A:0.20, C:0.27, G:0.17, T:0.36
Consensus pattern (25 bp):
CTCTTATGAGCTTCCCATTATATGG
Found at i:1410501 original size:25 final size:25
Alignment explanation
Indices: 1410481--1410568 Score: 97
Period size: 25 Copynumber: 3.5 Consensus size: 25
1410471 TGGCTCGTAA
*
1410481 GATCTTCCCATTATACAGCTCGCAT
1 GATCTTCCCGTTATACAGCTCGCAT
* *
1410506 GAGT-TTCTCGTTATACAGCTCACAT
1 GA-TCTTCCCGTTATACAGCTCGCAT
* *
1410531 GAGCTTCCCGTTATACAGCTCACAT
1 GATCTTCCCGTTATACAGCTCGCAT
* *
1410556 AAGCTTCCCGTTA
1 GATCTTCCCGTTA
1410569 CATGACTCAG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
25 54 0.98
26 1 0.02
ACGTcount: A:0.24, C:0.30, G:0.15, T:0.32
Consensus pattern (25 bp):
GATCTTCCCGTTATACAGCTCGCAT
Found at i:1410577 original size:25 final size:25
Alignment explanation
Indices: 1410519--1410602 Score: 86
Period size: 25 Copynumber: 3.4 Consensus size: 25
1410509 TTTCTCGTTA
* *
1410519 TACA-GCTCACATGAGCTTCCCGTT
1 TACATGCTCACATAAGCTTCCCGAT
1410543 ATACA-GCTCACATAAGCTTCCCG-T
1 -TACATGCTCACATAAGCTTCCCGAT
*
1410567 TACATGACTCAGA-AGAGCTTCCCGAT
1 TACATG-CTCACATA-AGCTTCCCGAT
1410593 TACATGCTCA
1 TACATGCTCA
1410603 TATGGACATA
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
23 4 0.08
24 3 0.06
25 39 0.74
26 7 0.13
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.26
Consensus pattern (25 bp):
TACATGCTCACATAAGCTTCCCGAT
Found at i:1410585 original size:50 final size:50
Alignment explanation
Indices: 1410479--1410590 Score: 120
Period size: 50 Copynumber: 2.2 Consensus size: 50
1410469 ATTGGCTCGT
* * * * * *
1410479 AAGATCTTCCCATTATACAGCTCGCATGAGTTTCTCGTTATACAGCTCAC
1 AAGAGCTTCCCGTTATACAGCTCACATAAGCTTCCCGTTATACAGCTCAC
* *
1410529 ATGAGCTTCCCGTTATACAGCTCACATAAGCTTCCCG-T-TACATGACTCAG
1 AAGAGCTTCCCGTTATACAGCTCACATAAGCTTCCCGTTATACA-G-CTCAC
1410579 AAGAGCTTCCCG
1 AAGAGCTTCCCG
1410591 ATTACATGCT
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
48 4 0.08
49 2 0.04
50 45 0.88
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (50 bp):
AAGAGCTTCCCGTTATACAGCTCACATAAGCTTCCCGTTATACAGCTCAC
Found at i:1415443 original size:35 final size:35
Alignment explanation
Indices: 1415403--1415477 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
1415393 CTCTAACAAT
**
1415403 CATTTCCATGATGCTGCTACGTAGAGCCAGTACAC
1 CATTTCCATGATGCCACTACGTAGAGCCAGTACAC
* *
1415438 CATTTCCATGATGCCACTCCGTAGAGCCAGTAGAC
1 CATTTCCATGATGCCACTACGTAGAGCCAGTACAC
1415473 CATTT
1 CATTT
1415478 TCGACCAAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (35 bp):
CATTTCCATGATGCCACTACGTAGAGCCAGTACAC
Found at i:1419116 original size:87 final size:86
Alignment explanation
Indices: 1418993--1419300 Score: 293
Period size: 87 Copynumber: 3.6 Consensus size: 86
1418983 TCTAAAAGTG
* ** * * * *
1418993 AATAAAATATGTTTTGGGATTTATTCTA-GCCATTCAATAGATTTTATTCCAATTTGATTTTATT
1 AATAAAATCTGTTTCAGGATTTATTC-ACGCCGTTCAAAAGATTTTATTCCATTTTAATTTTATT
1419057 TCCAAAACGAGAATTTAAATTAA
65 TCCAAAACGAGAATTTAAATT-A
* * * * *
1419080 AATAAAATCTATTTCAGGATTTATTCACGCCGTTCAACATATTTTATT-CTTTTTTATTTTATTT
1 AATAAAATCTGTTTCAGGATTTATTCACGCCGTTCAAAAGATTTTATTCCATTTTAATTTTATTT
*
1419144 CCAAAACGAGAAATTAAAATTA
66 CCAAAACGAG-AATTTAAATTA
* * * *
1419166 AATAAAATCTGTTTCAGGATTTATTCCCGCCGATT-AACAAGATTCTATTCGATTTTAATTTTGT
1 AATAAAATCTGTTTCAGGATTTATTCACGCCG-TTCAA-AAGATTTTATTCCATTTTAATTTTAT
* **
1419230 TT-CTAAATTAGAA-TTAAATTA
64 TTCCAAAACGAGAATTTAAATTA
* * * * * *
1419251 AATAAAATCTGTTACGGGATTTATTCTCGTCATTTAACAAGATTTTATTC
1 AATAAAATCTGTTTCAGGATTTATTCACGCCGTTCAA-AAGATTTTATTC
1419301 AATATCAATT
Statistics
Matches: 185, Mismatches: 30, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
84 2 0.01
85 48 0.26
86 59 0.32
87 64 0.35
88 12 0.06
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.43
Consensus pattern (86 bp):
AATAAAATCTGTTTCAGGATTTATTCACGCCGTTCAAAAGATTTTATTCCATTTTAATTTTATTT
CCAAAACGAGAATTTAAATTA
Found at i:1419174 original size:86 final size:84
Alignment explanation
Indices: 1418993--1419301 Score: 300
Period size: 86 Copynumber: 3.6 Consensus size: 84
1418983 TCTAAAAGTG
* ** * * * *
1418993 AATAAAATATGTTTTGGGATTTATTCTA-GCCATTCAATAGATTTTATTCCAATTTGATTTTATT
1 AATAAAATCTGTTTCAGGATTTATTC-ACGCCGTTCAACAGATTTTATT-CATTTTAATTTTATT
1419057 TCCAAAACGAGAATTTAAATTAA
64 TCCAAAACGAGAA-TTAAATT-A
* * * *
1419080 AATAAAATCTATTTCAGGATTTATTCACGCCGTTCAACATATTTTATTCTTTTTTATTTTATTTC
1 AATAAAATCTGTTTCAGGATTTATTCACGCCGTTCAACAGATTTTATTCATTTTAATTTTATTTC
1419145 CAAAACGAGAAATTAAAATTA
66 CAAAACGAG-AATT-AAATTA
* * *
1419166 AATAAAATCTGTTTCAGGATTTATTCCCGCCGATT-AACAAGATTCTATTCGATTTTAATTTTGT
1 AATAAAATCTGTTTCAGGATTTATTCACGCCG-TTCAAC-AGATTTTATTC-ATTTTAATTTTAT
* **
1419230 TT-CTAAATTAGAATTAAATTA
63 TTCCAAAACGAGAATTAAATTA
* * * * * *
1419251 AATAAAATCTGTTACGGGATTTATTCTCGTCATTTAACAAGATTTTATTCA
1 AATAAAATCTGTTTCAGGATTTATTCACGCCGTTCAAC-AGATTTTATTCA
1419302 ATATCAATTT
Statistics
Matches: 189, Mismatches: 26, Indels: 17
0.81 0.11 0.07
Matches are distributed among these distances:
84 3 0.02
85 47 0.25
86 64 0.34
87 63 0.33
88 12 0.06
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (84 bp):
AATAAAATCTGTTTCAGGATTTATTCACGCCGTTCAACAGATTTTATTCATTTTAATTTTATTTC
CAAAACGAGAATTAAATTA
Found at i:1419311 original size:85 final size:85
Alignment explanation
Indices: 1419155--1419316 Score: 220
Period size: 85 Copynumber: 1.9 Consensus size: 85
1419145 CAAAACGAGA
* * *
1419155 AATTAAAATTAAATAAAATCTGTTTCAGGATTTATTCCCGCCGATTAACAAGATTCTATTCGATT
1 AATTAAAATTAAATAAAATCTGTTACAGGATTTATTCCCGCCGATTAACAAGATTCTATTCAATA
*
1419220 TTAATTTTGTTTCTAAATTAG
66 TCAA-TTTGTTTCTAAATTAG
* * * *
1419241 AATT-AAATTAAATAAAATCTGTTACGGGATTTATTCTCGTC-ATTTAACAAGATTTTATTCAAT
1 AATTAAAATTAAATAAAATCTGTTACAGGATTTATTCCCGCCGA-TTAACAAGATTCTATTCAAT
1419304 ATCAATTTGTTTC
65 ATCAATTTGTTTC
1419317 CAAACGAAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
84 9 0.13
85 54 0.81
86 4 0.06
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (85 bp):
AATTAAAATTAAATAAAATCTGTTACAGGATTTATTCCCGCCGATTAACAAGATTCTATTCAATA
TCAATTTGTTTCTAAATTAG
Found at i:1426195 original size:41 final size:43
Alignment explanation
Indices: 1426094--1426207 Score: 142
Period size: 41 Copynumber: 2.7 Consensus size: 43
1426084 ATATCGAACA
* * * **
1426094 ATGCCAATGTCCCAGACGTGGTCTTACATGCTATCTCATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACGCAATCAAATATCG
* *
1426137 ATGCCACTGTCCCAGACAAGGTCTTACACG-AATCAAATA-CG
1 ATGCCAATGTCCCAGACATGGTCTTACACGCAATCAAATATCG
*
1426178 ATGCCAATGTCCTAGACATGGTCTTACACG
1 ATGCCAATGTCCCAGACATGGTCTTACACG
1426208 TAAACACAAG
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
41 29 0.48
42 6 0.10
43 26 0.43
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.25
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGCAATCAAATATCG
Found at i:1444473 original size:27 final size:27
Alignment explanation
Indices: 1444440--1444589 Score: 151
Period size: 27 Copynumber: 5.6 Consensus size: 27
1444430 AGACCCTAAA
*
1444440 ATAAGGTAAAATGACCAAAATACCCCT
1 ATAAGGTAAAATGACCGAAATACCCCT
* *
1444467 AGAAGGTAAAATGACTGAAATACCCCT
1 ATAAGGTAAAATGACCGAAATACCCCT
* * * *
1444494 ATAGGGTAAAATAACCGAAATACCACA
1 ATAAGGTAAAATGACCGAAATACCCCT
* * * *
1444521 ATAGGGTAAAATAATCGAAATACCCCC
1 ATAAGGTAAAATGACCGAAATACCCCT
*
1444548 AT-AGGATAAAATGACCAAAATA-CCCT
1 ATAAGG-TAAAATGACCGAAATACCCCT
*
1444574 CATATGGTAAAATGAC
1 -ATAAGGTAAAATGAC
1444590 TGTTATACCC
Statistics
Matches: 102, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
26 5 0.05
27 95 0.93
28 2 0.02
ACGTcount: A:0.47, C:0.19, G:0.15, T:0.19
Consensus pattern (27 bp):
ATAAGGTAAAATGACCGAAATACCCCT
Found at i:1444529 original size:54 final size:53
Alignment explanation
Indices: 1444444--1444602 Score: 167
Period size: 54 Copynumber: 2.9 Consensus size: 53
1444434 CCTAAAATAA
* *
1444444 GGTAAAATGACCAAAATACCCCTAGAAGGTAAAATGACTGAAATACCCCTATAG
1 GGTAAAATGACCAAAATA-CCCAATAAGGTAAAATGACTGAAATACCCCTATAG
* * * * *
1444498 GGTAAAATAACCGAAATACCACAATAGGGTAAAAT-AATCGAAATACCCCCATAG
1 GGTAAAATGACCAAAATACC-CAATAAGGTAAAATGACT-GAAATACCCCTATAG
* * * **
1444552 GATAAAATGACCAAAATACCCTCATATGGTAAAATGACTGTTATACCCCTA
1 GGTAAAATGACCAAAATACCC-AATAAGGTAAAATGACTGAAATACCCCTA
1444603 GTATATGAAA
Statistics
Matches: 85, Mismatches: 16, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
53 5 0.06
54 78 0.92
55 2 0.02
ACGTcount: A:0.45, C:0.21, G:0.14, T:0.20
Consensus pattern (53 bp):
GGTAAAATGACCAAAATACCCAATAAGGTAAAATGACTGAAATACCCCTATAG
Found at i:1447705 original size:39 final size:39
Alignment explanation
Indices: 1447651--1448090 Score: 637
Period size: 39 Copynumber: 11.2 Consensus size: 39
1447641 AAATCTTATA
1447651 CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGCATT
1 CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGCATT
*
1447690 CAGTATAATCAGTGGATAATGTTCGTTTGAGCAAGCATT
1 CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGCATT
* * *
1447729 CAGCATAATCAGTGGGTAATGCTCGTTTAAGCAAGCATT
1 CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGCATT
* * *
1447768 CAGCATAATCAGTGGGTAATGCTCGTTTAAGCAAGCATT
1 CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGCATT
** *
1447807 CAACATAATCAGTGGATATTGCTCGTTTGAGCAAGCATT
1 CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGCATT
* **
1447846 CAGCATAATCAGTGGATAATGCTTATTTGAGCAAGCATT
1 CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGCATT
* * *
1447885 CAGTATAATTAATGGATAATGCTAGTTTGAGCAAGCATT
1 CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGCATT
* *
1447924 CAGCATAATCAGTGGATAATGCTCATTTTGAGCAAGCATT
1 CAGTATAATCAGTGGATAATGCTC-GTTTGAGCAAGCATT
* *
1447964 CAATATAATCAGTGGATAATGCTCGTTTGAGCAAACATT
1 CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGCATT
*
1448003 CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAACATT
1 CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGCATT
* * * *
1448042 CAATATAATCAGTGGATATTGCTCGTTTGAACAAATCATT
1 CAGTATAATCAGTGGATAATGCTCGTTTGAGC-AAGCATT
1448082 CAGTATAAT
1 CAGTATAAT
1448091 TAGTATTCTA
Statistics
Matches: 366, Mismatches: 33, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
39 316 0.86
40 50 0.14
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.31
Consensus pattern (39 bp):
CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGCATT
Found at i:1455632 original size:63 final size:63
Alignment explanation
Indices: 1455555--1455697 Score: 180
Period size: 63 Copynumber: 2.3 Consensus size: 63
1455545 TGGTAATCCA
* * * *
1455555 TGTAACTCACTGTTTTTGAATTGGAGGCACACGAGCTAGGGGCATGGGCATGTGTCTAAGCT-G
1 TGTAACTCACTGTTTTAGAATTAGAGGCACACGAGCTAGGGACATGGACATGTGTC-AAGCTCG
* * * * *
1455618 TGTAACTCACTGTTTTAGATTTAGAGTCACACGGGCTAGGGACATGGACATGTGTCCAGGTCG
1 TGTAACTCACTGTTTTAGAATTAGAGGCACACGAGCTAGGGACATGGACATGTGTCAAGCTCG
*
1455681 TGTAACTCACTATTTTA
1 TGTAACTCACTGTTTTA
1455698 AGCCACATGG
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
62 3 0.04
63 66 0.96
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (63 bp):
TGTAACTCACTGTTTTAGAATTAGAGGCACACGAGCTAGGGACATGGACATGTGTCAAGCTCG
Found at i:1456541 original size:22 final size:22
Alignment explanation
Indices: 1456516--1456569 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
1456506 ATAGATATCT
1456516 TATTGTTTGTTTAATTTCAAAC
1 TATTGTTTGTTTAATTTCAAAC
* ** *
1456538 TATTGTATGTTTTGTTTCAGAC
1 TATTGTTTGTTTAATTTCAAAC
*
1456560 TATGGTTTGT
1 TATTGTTTGT
1456570 AAACTCGAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.20, C:0.07, G:0.17, T:0.56
Consensus pattern (22 bp):
TATTGTTTGTTTAATTTCAAAC
Found at i:1459891 original size:22 final size:21
Alignment explanation
Indices: 1459844--1459893 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
1459834 TTCCTAAAAT
* *
1459844 ATTATTTATTTAATCAATTAT
1 ATTATTTATTTAATCAACTAA
* *
1459865 TTTATTTAGTTTAATTAACTAA
1 ATTATTTA-TTTAATCAACTAA
1459887 ATTATTT
1 ATTATTT
1459894 TTTCAATTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (21 bp):
ATTATTTATTTAATCAACTAA
Found at i:1459906 original size:17 final size:17
Alignment explanation
Indices: 1459884--1459916 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1459874 TTTAATTAAC
1459884 TAAATTATTTTTTCAAT
1 TAAATTATTTTTTCAAT
1459901 TAAATTATTTTTTCAA
1 TAAATTATTTTTTCAA
1459917 CCCAATTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (17 bp):
TAAATTATTTTTTCAAT
Found at i:1459923 original size:17 final size:17
Alignment explanation
Indices: 1459885--1459923 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1459875 TTAATTAACT
**
1459885 AAATTATTTTTTCAATT
1 AAATTATTTTTTCAACC
1459902 AAATTATTTTTTCAACC
1 AAATTATTTTTTCAACC
*
1459919 CAATT
1 AAATT
1459924 CTAATTCTGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.13, G:0.00, T:0.51
Consensus pattern (17 bp):
AAATTATTTTTTCAACC
Found at i:1469084 original size:16 final size:16
Alignment explanation
Indices: 1469065--1469103 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
1469055 TTTTTAAGAA
1469065 TTTAATTAGTTT-ATTT
1 TTTAATT-GTTTAATTT
*
1469081 TTTAATTTTTTAATTT
1 TTTAATTGTTTAATTT
1469097 TTTAATT
1 TTTAATT
1469104 TAAATTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 3 0.14
16 18 0.86
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (16 bp):
TTTAATTGTTTAATTT
Found at i:1469089 original size:7 final size:8
Alignment explanation
Indices: 1469077--1469104 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
1469067 TAATTAGTTT
1469077 ATTTTTTA
1 ATTTTTTA
1469085 ATTTTTTA
1 ATTTTTTA
1469093 ATTTTTTA
1 ATTTTTTA
1469101 ATTT
1 ATTT
1469105 AAATTTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (8 bp):
ATTTTTTA
Found at i:1469307 original size:31 final size:34
Alignment explanation
Indices: 1469272--1469341 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 34
1469262 ACTAAACAAT
*
1469272 TTGATTTT-CTTTTA-AAAAC-ACATTCAAAGAA
1 TTGATTTTGCTTTAAGAAAACAACATTCAAAGAA
1469303 TTGATTTTGCTTTAAGAAAACAGACATTCAAAGAA
1 TTGATTTTGCTTTAAGAAAACA-ACATTCAAAGAA
1469338 TTGA
1 TTGA
1469342 CAAATTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
31 8 0.24
32 5 0.15
33 5 0.15
35 16 0.47
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.36
Consensus pattern (34 bp):
TTGATTTTGCTTTAAGAAAACAACATTCAAAGAA
Found at i:1469876 original size:26 final size:26
Alignment explanation
Indices: 1469825--1469878 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
1469815 ACATTCAATA
*
1469825 TAATCCATTATTCTTGTTAAATAATG
1 TAATCCATTATTCTTGTTAAAGAATG
* *
1469851 TAATTCATTATTCTTGTTAAGGAATG
1 TAATCCATTATTCTTGTTAAAGAATG
1469877 TA
1 TA
1469879 CTAGTATTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.33, C:0.09, G:0.11, T:0.46
Consensus pattern (26 bp):
TAATCCATTATTCTTGTTAAAGAATG
Found at i:1472400 original size:20 final size:20
Alignment explanation
Indices: 1472375--1472414 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1472365 TGTGGTTAAC
*
1472375 TTTGATGACGATACAGAAGT
1 TTTGATGAAGATACAGAAGT
1472395 TTTGATGAAGATACAGAAGT
1 TTTGATGAAGATACAGAAGT
1472415 GTTGGAGCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.07, G:0.25, T:0.30
Consensus pattern (20 bp):
TTTGATGAAGATACAGAAGT
Found at i:1477267 original size:21 final size:22
Alignment explanation
Indices: 1477243--1477285 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1477233 AGGTTTTTCA
1477243 AGAA-TTTTTTTCATAAATTTT
1 AGAATTTTTTTTCATAAATTTT
*
1477264 AGAATTTTTTTTTATAAATTTT
1 AGAATTTTTTTTCATAAATTTT
1477286 TTTGGCCTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (22 bp):
AGAATTTTTTTTCATAAATTTT
Found at i:1477691 original size:26 final size:25
Alignment explanation
Indices: 1477642--1477691 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
1477632 TTGGTCGCTT
* *
1477642 TATTAAAATTTTCATCTATTTTTAC
1 TATTAAAATTTTCATCCATGTTTAC
1477667 TATTAAAAATTTTCATCCATGTTTA
1 TATT-AAAATTTTCATCCATGTTTA
1477692 ATTATCTAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.34, C:0.12, G:0.02, T:0.52
Consensus pattern (25 bp):
TATTAAAATTTTCATCCATGTTTAC
Found at i:1481835 original size:23 final size:23
Alignment explanation
Indices: 1481805--1481848 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
1481795 GTTAATTCAC
*
1481805 ATGTTAGTTATTTTTTTTTCTAT
1 ATGTTAGTTAATTTTTTTTCTAT
1481828 ATGTTAGTTAATTTTTTTTCT
1 ATGTTAGTTAATTTTTTTTCT
1481849 TTCTTTCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.18, C:0.05, G:0.09, T:0.68
Consensus pattern (23 bp):
ATGTTAGTTAATTTTTTTTCTAT
Found at i:1485549 original size:18 final size:20
Alignment explanation
Indices: 1485511--1485550 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
1485501 AATTTTACTA
1485511 TTGATATAATATTAAAAATT
1 TTGATATAATATTAAAAATT
*
1485531 TTGA-ATAAT-TTAAACATT
1 TTGATATAATATTAAAAATT
1485549 TT
1 TT
1485551 AGTAGATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 5 0.26
20 4 0.21
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (20 bp):
TTGATATAATATTAAAAATT
Found at i:1487152 original size:18 final size:18
Alignment explanation
Indices: 1487131--1487166 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1487121 AACTGATAAT
1487131 ACATATATAAATTCATTC
1 ACATATATAAATTCATTC
* *
1487149 ACATATTTATATTCATTC
1 ACATATATAAATTCATTC
1487167 CGAACACATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.17, G:0.00, T:0.44
Consensus pattern (18 bp):
ACATATATAAATTCATTC
Found at i:1487324 original size:28 final size:28
Alignment explanation
Indices: 1487253--1487351 Score: 128
Period size: 28 Copynumber: 3.6 Consensus size: 28
1487243 ACACGTGACC
* * * *
1487253 AATTTGCTCACACAACCTCTAATATTCG
1 AATTTGCTCACACAAGCTGTGATATTTG
*
1487281 AATTTGCTCACACAAGTTGTGATATTTG
1 AATTTGCTCACACAAGCTGTGATATTTG
1487309 AATTTGCTCACACAAGCTGTGATATTTG
1 AATTTGCTCACACAAGCTGTGATATTTG
**
1487337 -GGTTGCTCACACAAG
1 AATTTGCTCACACAAG
1487352 TGTAGGTTAG
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
27 13 0.21
28 50 0.79
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.33
Consensus pattern (28 bp):
AATTTGCTCACACAAGCTGTGATATTTG
Found at i:1488931 original size:8 final size:8
Alignment explanation
Indices: 1488918--1488962 Score: 63
Period size: 8 Copynumber: 5.5 Consensus size: 8
1488908 AATGAAACAG
1488918 AGAAGGAA
1 AGAAGGAA
1488926 AGAAGGAA
1 AGAAGGAA
1488934 AGAAGGAA
1 AGAAGGAA
*
1488942 AGAAAGAAA
1 AG-AAGGAA
*
1488951 AGAAAGAA
1 AGAAGGAA
1488959 AGAA
1 AGAA
1488963 AAGGGAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
8 26 0.79
9 7 0.21
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (8 bp):
AGAAGGAA
Found at i:1488939 original size:16 final size:16
Alignment explanation
Indices: 1488918--1488962 Score: 63
Period size: 17 Copynumber: 2.8 Consensus size: 16
1488908 AATGAAACAG
*
1488918 AGAAGGAAAGAAGGAA
1 AGAAGGAAAGAAGAAA
1488934 AGAAGGAAAGAAAGAAA
1 AGAAGGAAAG-AAGAAA
*
1488951 AGAAAGAAAGAA
1 AGAAGGAAAGAA
1488963 AAGGGAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 12 0.46
17 14 0.54
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (16 bp):
AGAAGGAAAGAAGAAA
Found at i:1488948 original size:4 final size:4
Alignment explanation
Indices: 1488918--1488963 Score: 56
Period size: 4 Copynumber: 11.2 Consensus size: 4
1488908 AATGAAACAG
* * *
1488918 AGAA GGAA AGAA GGAA AGAA GGAA AGAA AGAAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AG-AA AGAA AGAA AGAA A
1488964 AGGGAAAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
4 31 0.89
5 4 0.11
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:1488957 original size:13 final size:13
Alignment explanation
Indices: 1488924--1488965 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
1488914 ACAGAGAAGG
*
1488924 AAAGAAGGAAAG-
1 AAAGAAAGAAAGA
*
1488936 AAGGAAAGAAAGA
1 AAAGAAAGAAAGA
1488949 AAAGAAAGAAAGA
1 AAAGAAAGAAAGA
1488962 AAAG
1 AAAG
1488966 GGAAAATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAAAGA
Found at i:1490107 original size:23 final size:23
Alignment explanation
Indices: 1490080--1490145 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
1490070 TCTACCGATT
*
1490080 AGGCACTTTATGTGTCGTGTATC
1 AGGCACTTTATGTGTCGTATATC
*
1490103 AGGCACTTTATGTGTCGTATTTC
1 AGGCACTTTATGTGTCGTATATC
* **
1490126 AGGCACCTCGTGTGTCGTAT
1 AGGCACTTTATGTGTCGTAT
1490146 CAGACACCTC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.38
Consensus pattern (23 bp):
AGGCACTTTATGTGTCGTATATC
Found at i:1490161 original size:23 final size:22
Alignment explanation
Indices: 1490113--1490164 Score: 79
Period size: 21 Copynumber: 2.4 Consensus size: 22
1490103 AGGCACTTTA
*
1490113 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTA-TTCAGACACCTCG
1490136 TGTGTCGTA-TCAGACACCTCG
1 TGTGTCGTATTCAGACACCTCG
1490157 TGTGTCGT
1 TGTGTCGT
1490165 TTTATGCACT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 19 0.68
23 9 0.32
ACGTcount: A:0.13, C:0.25, G:0.27, T:0.35
Consensus pattern (22 bp):
TGTGTCGTATTCAGACACCTCG
Found at i:1491192 original size:19 final size:19
Alignment explanation
Indices: 1491168--1491208 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1491158 TTAACATAAA
*
1491168 TAACTAATCATAATTAACT
1 TAACTAAACATAATTAACT
* *
1491187 TAACTAAACCTTATTAACT
1 TAACTAAACATAATTAACT
1491206 TAA
1 TAA
1491209 TATAATGATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.37
Consensus pattern (19 bp):
TAACTAAACATAATTAACT
Found at i:1500008 original size:25 final size:25
Alignment explanation
Indices: 1499954--1500014 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
1499944 GGCTCTTAAT
* **
1499954 GAGCTTCCT-A-ATATGGCTCACTT
1 GAGCTTCCTGATATATGGCTAACCG
*
1499977 GAACTTCCTGATATATGGCTAACCG
1 GAGCTTCCTGATATATGGCTAACCG
1500002 GAGCTTCCTGATA
1 GAGCTTCCTGATA
1500015 ATAGCTCTTC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 8 0.26
24 1 0.03
25 22 0.71
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.31
Consensus pattern (25 bp):
GAGCTTCCTGATATATGGCTAACCG
Found at i:1504145 original size:39 final size:39
Alignment explanation
Indices: 1504116--1504309 Score: 244
Period size: 39 Copynumber: 5.0 Consensus size: 39
1504106 ATCCTATTAC
*
1504116 ACATATAATCACCTAACATTCAAGCATATATCACAATAT
1 ACATATAATCACATAACATTCAAGCATATATCACAATAT
* * * * **
1504155 ATATTTAATCTCATAACATTTAAGCATATATCACAACCT
1 ACATATAATCACATAACATTCAAGCATATATCACAATAT
* *
1504194 TCATATAATCACATAATATTCAAGCATATATCACAATAT
1 ACATATAATCACATAACATTCAAGCATATATCACAATAT
* * *
1504233 ACATATAATCTCATAAAATTTAAGCATATATCACAATAT
1 ACATATAATCACATAACATTCAAGCATATATCACAATAT
** * *
1504272 ACATATAATCTTATAACATTTAAACATATATCACAATA
1 ACATATAATCACATAACATTCAAGCATATATCACAATA
1504310 ATAAAAAACA
Statistics
Matches: 133, Mismatches: 22, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 133 1.00
ACGTcount: A:0.46, C:0.19, G:0.02, T:0.33
Consensus pattern (39 bp):
ACATATAATCACATAACATTCAAGCATATATCACAATAT
Found at i:1504199 original size:78 final size:78
Alignment explanation
Indices: 1504116--1504309 Score: 280
Period size: 78 Copynumber: 2.5 Consensus size: 78
1504106 ATCCTATTAC
* * * *
1504116 ACATATAATCACCTAACATTCAAGCATATATCACAATATATATTTAATCTCATAACATTTAAGCA
1 ACATATAATCACATAACATTCAAGCATATATCACAATATACATATAATCTCATAAAATTTAAGCA
*
1504181 TATATCACAACCT
66 TATATCACAACAT
* *
1504194 TCATATAATCACATAATATTCAAGCATATATCACAATATACATATAATCTCATAAAATTTAAGCA
1 ACATATAATCACATAACATTCAAGCATATATCACAATATACATATAATCTCATAAAATTTAAGCA
*
1504259 TATATCACAATAT
66 TATATCACAACAT
** * *
1504272 ACATATAATCTTATAACATTTAAACATATATCACAATA
1 ACATATAATCACATAACATTCAAGCATATATCACAATA
1504310 ATAAAAAACA
Statistics
Matches: 102, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
78 102 1.00
ACGTcount: A:0.46, C:0.19, G:0.02, T:0.33
Consensus pattern (78 bp):
ACATATAATCACATAACATTCAAGCATATATCACAATATACATATAATCTCATAAAATTTAAGCA
TATATCACAACAT
Found at i:1506720 original size:244 final size:242
Alignment explanation
Indices: 1506123--1506761 Score: 926
Period size: 244 Copynumber: 2.6 Consensus size: 242
1506113 ACATTTTAAA
* * * *
1506123 AAAAACCAT-AAAAA-ATTACTAATATAACATGTCGCAAAATTTCGAACGCACTAAGGCTAAAAT
1 AAAAACCATAAAAAACATTACCAATATAACATGTCGCAAAA-TTCTAACACTCTAAGGCTAAAAT
* * * *
1506186 TCTTAAAATA-CCCTAAAATTCCTAGGCCTTATTTTAGGGTGTTACATACACATTCAAGATTGTC
65 TCCTAAAATACCCCTAAAACTCCTAGGCCCTATTTTGGGGTGTTACATACACATTCAAGATTGTC
* * *
1506250 TCTTATTAAATATTTTCCCAAGAAACACTCTAAGGTTAAAATTCATAAAATATCCCTAAAACCAT
130 TCTTATTAAATATTTTCCCAAGAAACAATCTAAGGCTAAAATTCATAAAATACCCCTAAAACCAT
* *
1506315 AAAAAACCATAAATATTTTCCCTAAAACAATCTAAGGCTTAAATTCCT
195 AAAAAACCATAAATATTTTCCCTAAAACAATCGAAGGCTAAAATTCCT
* * * * *
1506363 AAAAAGCATAAAAAACATTATCGATATATCATATCGCAAAATTCTGAACACTCTAAGGCTAAAAT
1 AAAAACCATAAAAAACATTACCAATATAACATGTCGCAAAATTCT-AACACTCTAAGGCTAAAAT
** *
1506428 TCCTAAAATACCTTTAAAACTCCTAGGCCCTATTTTGGGGTCTTACATACACATTCAAGATTGTC
65 TCCTAAAATACCCCTAAAACTCCTAGGCCCTATTTTGGGGTGTTACATACACATTCAAGATTGTC
* *
1506493 TCTTATT-AATATTTTCCCAAGAAACAATCTAAGGCTAAAATTCCTAAAGTACCCCTAAAACCAT
130 TCTTATTAAATATTTTCCCAAGAAACAATCTAAGGCTAAAATTCATAAAATACCCCTAAAACCAT
* *
1506557 GAAAAAACCATAAATATTTTCCCTAAAACACTCGAAGGCTAAAATTTCT
195 -AAAAAACCATAAATATTTTCCCTAAAACAATCGAAGGCTAAAATTCCT
* * *
1506606 AAAAACCATAAAAAAACATTACCAATATACCATGTCACAAAATTCCTAATACTCTAAGGCTAAAA
1 AAAAACCAT-AAAAAACATTACCAATATAACATGTCGCAAAATT-CTAACACTCTAAGGCTAAAA
* *
1506671 TTCCTAAAATACCCCTAAAACTCTTAGGCCCTATTTTGGGGTGTTACATACACATTCAAAATTGT
64 TTCCTAAAATACCCCTAAAACTCCTAGGCCCTATTTTGGGGTGTTACATACACATTCAAGATTGT
*
1506736 CTCTTATTAAATATTTTTCCAAGAAA
129 CTCTTATTAAATATTTTCCCAAGAAA
1506762 TGATATTTAA
Statistics
Matches: 353, Mismatches: 38, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
240 8 0.02
241 8 0.02
242 98 0.28
243 107 0.30
244 114 0.32
245 18 0.05
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.30
Consensus pattern (242 bp):
AAAAACCATAAAAAACATTACCAATATAACATGTCGCAAAATTCTAACACTCTAAGGCTAAAATT
CCTAAAATACCCCTAAAACTCCTAGGCCCTATTTTGGGGTGTTACATACACATTCAAGATTGTCT
CTTATTAAATATTTTCCCAAGAAACAATCTAAGGCTAAAATTCATAAAATACCCCTAAAACCATA
AAAAACCATAAATATTTTCCCTAAAACAATCGAAGGCTAAAATTCCT
Found at i:1507707 original size:21 final size:21
Alignment explanation
Indices: 1507681--1507720 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1507671 CTAAAAGACG
1507681 CATAATATGACATGTTTATGC
1 CATAATATGACATGTTTATGC
* *
1507702 CATAATTTGACTTGTTTAT
1 CATAATATGACATGTTTAT
1507721 TTGTTGTTCC
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:0.30, C:0.12, G:0.12, T:0.45
Consensus pattern (21 bp):
CATAATATGACATGTTTATGC
Found at i:1508256 original size:13 final size:13
Alignment explanation
Indices: 1508238--1508263 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1508228 AGTAGATGAG
1508238 GTTTTATTTTTAT
1 GTTTTATTTTTAT
1508251 GTTTTATTTTTAT
1 GTTTTATTTTTAT
1508264 TTCGTGTGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (13 bp):
GTTTTATTTTTAT
Found at i:1519706 original size:22 final size:22
Alignment explanation
Indices: 1519664--1519706 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1519654 TTTTGTTTCC
* *
1519664 AAAATTTAAATTTTAGCAAAAA
1 AAAATTAAAATTTAAGCAAAAA
*
1519686 AAAATTAAAATTTAAGTAAAA
1 AAAATTAAAATTTAAGCAAAA
1519707 TAAGGAAACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (22 bp):
AAAATTAAAATTTAAGCAAAAA
Found at i:1531218 original size:6 final size:6
Alignment explanation
Indices: 1531183--1531273 Score: 64
Period size: 6 Copynumber: 14.8 Consensus size: 6
1531173 TCTTTAACAT
*
1531183 TTTTTC TTTTATC TTCTTT- TGTTCTTC TTTTTC -TTTTC TTCTTTC TTTCGTC
1 TTTTTC TTTT-TC TT-TTTC T-TT-TTC TTTTTC TTTTTC TT-TTTC TTT-TTC
** *
1531235 TTTCAC -CTTTC -TTTTC TTTTTC TTTTTC TTTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
1531274 GCTTGCTTCC
Statistics
Matches: 69, Mismatches: 7, Indels: 18
0.73 0.07 0.19
Matches are distributed among these distances:
5 11 0.16
6 34 0.49
7 21 0.30
8 3 0.04
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.75
Consensus pattern (6 bp):
TTTTTC
Found at i:1531230 original size:18 final size:18
Alignment explanation
Indices: 1531196--1531272 Score: 72
Period size: 18 Copynumber: 4.4 Consensus size: 18
1531186 TTCTTTTATC
*
1531196 TTCTTTTGTTC-TTCTTT
1 TTCTTTTCTTCTTTCTTT
1531213 TTCTTTTCTTCTTTCTTT
1 TTCTTTTCTTCTTTCTTT
* **
1531231 CGTC-TTTCACCTTTC-TT
1 -TTCTTTTCTTCTTTCTTT
1531248 TTCTTTTTCTT-TTTCTTT
1 TTC-TTTTCTTCTTTCTTT
1531266 TTCTTTT
1 TTCTTTT
1531273 TGCTTGCTTC
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
16 2 0.04
17 20 0.42
18 24 0.50
19 2 0.04
ACGTcount: A:0.01, C:0.22, G:0.03, T:0.74
Consensus pattern (18 bp):
TTCTTTTCTTCTTTCTTT
Done.