Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 198 of 206
Found at i:59980692 original size:15 final size:15
Alignment explanation
Indices: 59980669--59980714 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
59980659 GTCCGACCCG
*
59980669 AAACCAAAAATAAAT
1 AAACAAAAAATAAAT
59980684 AAACAAAAAAATAAA-
1 AAAC-AAAAAATAAAT
*
59980699 AACCAAAAAATAAAT
1 AAACAAAAAATAAAT
59980714 A
1 A
59980715 GTAAAACCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 10 0.37
15 8 0.30
16 9 0.33
ACGTcount: A:0.78, C:0.11, G:0.00, T:0.11
Consensus pattern (15 bp):
AAACAAAAAATAAAT
Found at i:59982118 original size:12 final size:12
Alignment explanation
Indices: 59982084--59982160 Score: 56
Period size: 12 Copynumber: 6.8 Consensus size: 12
59982074 TTTTTATTCA
59982084 TTTATTATTATT
1 TTTATTATTATT
* **
59982096 GTCGTTATTATT
1 TTTATTATTATT
59982108 TTTA-T-TT-TT
1 TTTATTATTATT
*
59982117 ATTATTATTATT
1 TTTATTATTATT
* *
59982129 TTTCTTGTTA-T
1 TTTATTATTATT
59982140 TTTATTATT-TCT
1 TTTATTATTAT-T
59982152 TTTATTATT
1 TTTATTATT
59982161 TTTGGTACTT
Statistics
Matches: 48, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
9 5 0.10
10 3 0.06
11 11 0.23
12 29 0.60
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.73
Consensus pattern (12 bp):
TTTATTATTATT
Found at i:59982118 original size:15 final size:15
Alignment explanation
Indices: 59982084--59982163 Score: 63
Period size: 15 Copynumber: 5.2 Consensus size: 15
59982074 TTTTTATTCA
* *
59982084 TTTATTATTATTGTC
1 TTTATTATTATTATT
* *
59982099 GTTATTATTTTTATT
1 TTTATTATTATTATT
59982114 TTTATTATTATTATT
1 TTTATTATTATTATT
* *
59982129 TTTCTTGTTATTTTATT
1 TTTATTATTA--TTATT
*
59982146 ATTTCTT-TTATTATT
1 -TTTATTATTATTATT
59982161 TTT
1 TTT
59982164 GGTACTTTCA
Statistics
Matches: 54, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
14 3 0.06
15 37 0.69
17 8 0.15
18 6 0.11
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.74
Consensus pattern (15 bp):
TTTATTATTATTATT
Found at i:59982267 original size:3 final size:3
Alignment explanation
Indices: 59982259--59982330 Score: 119
Period size: 3 Copynumber: 24.3 Consensus size: 3
59982249 TATTATGTTC
59982259 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
59982307 TTA TTA TTA -AA TTA GTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
59982331 AGTATTCTTT
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
2 1 0.02
3 63 0.98
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:59988292 original size:13 final size:13
Alignment explanation
Indices: 59988276--59988300 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59988266 TAATAATATT
59988276 AATTATTAATTAA
1 AATTATTAATTAA
59988289 AATTATTAATTA
1 AATTATTAATTA
59988301 TTCATATATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
AATTATTAATTAA
Found at i:59994564 original size:266 final size:266
Alignment explanation
Indices: 59994083--59994564 Score: 732
Period size: 266 Copynumber: 1.8 Consensus size: 266
59994073 GACATGCTGA
* * *
59994083 ACATACAATCAGTAATACGGATGCAACAAGCATATATTATTCATATATCAAGCATATACAATAAT
1 ACATACAATCAGGAATACAGATGCAACAAGCATATATTATTCACATATCAAGCATATACAATAAT
* * * *
59994148 AATTCGGTCATTCAGATCATGCATTCCAATACTCATATTATCAGGGGTTCAATTGAAAGAAATAA
66 AATTCGGTCATTCAGATCATGCACTCCAATACTAATATTATCAAGGGTTCAATTAAAAGAAATAA
* * * * *
59994213 AACTCTAATAATAGTTTAGGGACTATTTAGAGACTAAACTGAACAAGTTATAAAATTCTGGGAAA
131 AACTCTAAAAATAGTTCAGGGACTATTTAGAGACTAAACTGAACAAATTATAAAAGTCTGGAAAA
* *
59994278 AATTATAAAATCTAAAAAATAGATGCCACACAGCCATGTCACCAAGTCGTTTAACAGACTGTGGC
196 AACTATAAAATATAAAAAATAGATGCCACACAGCCATGTCACCAAGTCGTTTAACAGACTGTGGC
59994343 CATATG
261 CATATG
* * *
59994349 ACATACAATCAGGAATACAGATGCAATATGCATATATTATTCACATATCATGCATATACAATAAT
1 ACATACAATCAGGAATACAGATGCAACAAGCATATATTATTCACATATCAAGCATATACAATAAT
*
59994414 AA-TCTGGTCATTCAGATCATGCACTCCAGTACTAATATTATCAAGGGTTCAATTAAAAGAAATA
66 AATTC-GGTCATTCAGATCATGCACTCCAATACTAATATTATCAAGGGTTCAATTAAAAGAAATA
* * * * *
59994478 AAACTCTAAAAATAGTTCGGGGGCTATTTAGGGAGTAAACTGAATAAATTATAAAAGTCTGGAAA
130 AAACTCTAAAAATAGTTCAGGGACTATTTAGAGACTAAACTGAACAAATTATAAAAGTCTGGAAA
*
59994543 AAACTATAAAATATGAAAAATA
195 AAACTATAAAATATAAAAAATA
59994565 AGGGTCACAC
Statistics
Matches: 191, Mismatches: 24, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
265 2 0.01
266 189 0.99
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (266 bp):
ACATACAATCAGGAATACAGATGCAACAAGCATATATTATTCACATATCAAGCATATACAATAAT
AATTCGGTCATTCAGATCATGCACTCCAATACTAATATTATCAAGGGTTCAATTAAAAGAAATAA
AACTCTAAAAATAGTTCAGGGACTATTTAGAGACTAAACTGAACAAATTATAAAAGTCTGGAAAA
AACTATAAAATATAAAAAATAGATGCCACACAGCCATGTCACCAAGTCGTTTAACAGACTGTGGC
CATATG
Found at i:59999448 original size:231 final size:230
Alignment explanation
Indices: 59999020--59999731 Score: 713
Period size: 231 Copynumber: 3.1 Consensus size: 230
59999010 TAAAACCAAC
* * * * * ** * *
59999020 TAAGGAAACGGCACCGTTTTCCGTAACACCATTTCGATTTTGCGGCGTTTATATATAAG-CGCCA
1 TAAGAAAACGGCGCCGTTTTTCGTAACACAATTTCGATTTTGCAGCGCCTACATATAAGTC-ACA
* * * ** * * * *
59999084 CCAAATATAAGGTCAAACGCAATCGTTTAAA-GCAAACTCCTGTAATCTTTAAAATATATTTACG
65 CTAAATATAAAGTCAAACGCAGTCG--TAAACGCAAAAGCATGAAATCTTTAAAATAAATTAACG
* * * * * * *
59999148 GCGTTTTGGGTGTAACGCCACAAATATC-CTTGAAAACGACGCCGTTTCTGTAACAAAGAAAATA
128 ACGTTTTGGGTGTAACGCCACTAATAACAATGGAAAACGACGCCGTTTCCGTAACAAAGAAAACA
59999212 TACTTGCGGCGTTTTATCTAAAACGCCACTAAATGTAA
193 TACTTGCGGCGTTTTATCTAAAACGCCACTAAATGTAA
* * * *
59999250 TAAGAAAACGGTGCCGTTTTTCGTAACA-AATTTTTC-ATTTTTTCAGC-CCT-CCTGT-AG-CA
1 TAAGAAAACGGCGCCGTTTTTCGTAACACAA--TTTCGA-TTTTGCAGCGCCTACATATAAGTCA
59999309 -AC-AAATCA-AAAG-CAAA--CAGATC-TAAACCAGCCAAAAGCAAT-AAAT-TTATATAATAT
63 CACTAAAT-ATAAAGTCAAACGCAG-TCGTAAA-C-G-CAAAAGC-ATGAAATCTT-TA-AA-A-
59999365 TCCAAATTAAACGACGTTTTGGGTGTAACGCCACTAATAACAATGGAAAACGACGCCGTTTCCGT
118 T--AAATT-AACGACGTTTTGGGTGTAACGCCACTAATAACAATGGAAAACGACGCCGTTTCCGT
59999430 AACAAAGAAAACATACTTGCGGCGTTTTATCTAAAACGCCACTAAATGTAA
180 AACAAAGAAAACATACTTGCGGCGTTTTATCTAAAACGCCACTAAATGTAA
* * ** * *
59999481 TAAGAAAACGGCGCCGTTTTTCGTAACACCATTTCGATTTTGCGGCGTTTATATATAAGTGACAC
1 TAAGAAAACGGCGCCGTTTTTCGTAACACAATTTCGATTTTGCAGCGCCTACATATAAGTCACAC
* * ** * * * ** *
59999546 TAAATATAAGGTCAAACGCAGTCGTTTAACGCAAACTCCTGTAATCTTTAAAATATATTTGCGGC
66 TAAATATAAAGTCAAACGCAGTCG-TAAACGCAAAAGCATGAAATCTTTAAAATAAATTAACGAC
59999611 GTTTTGGGTGTAACGCCACTAATAACAATGGAAAACGACGCCGTTTCCGTAACAAAGAAAACATA
130 GTTTTGGGTGTAACGCCACTAATAACAATGGAAAACGACGCCGTTTCCGTAACAAAGAAAACATA
59999676 CTTGCGGCGTTTTATCTAAAACGCCACTAAATGTAA
195 CTTGCGGCGTTTTATCTAAAACGCCACTAAATGTAA
59999712 TAAGAAAACGGCGCCGTTTT
1 TAAGAAAACGGCGCCGTTTT
59999732 CTTCACAACT
Statistics
Matches: 400, Mismatches: 48, Indels: 67
0.78 0.09 0.13
Matches are distributed among these distances:
220 4 0.01
222 2 0.00
223 5 0.01
224 14 0.04
225 10 0.03
226 4 0.01
227 1 0.00
228 3 0.01
229 7 0.02
230 65 0.16
231 234 0.58
232 7 0.02
233 2 0.00
234 2 0.00
235 4 0.01
236 10 0.03
237 14 0.04
238 5 0.01
239 4 0.01
240 3 0.01
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.28
Consensus pattern (230 bp):
TAAGAAAACGGCGCCGTTTTTCGTAACACAATTTCGATTTTGCAGCGCCTACATATAAGTCACAC
TAAATATAAAGTCAAACGCAGTCGTAAACGCAAAAGCATGAAATCTTTAAAATAAATTAACGACG
TTTTGGGTGTAACGCCACTAATAACAATGGAAAACGACGCCGTTTCCGTAACAAAGAAAACATAC
TTGCGGCGTTTTATCTAAAACGCCACTAAATGTAA
Found at i:60000521 original size:15 final size:16
Alignment explanation
Indices: 60000493--60000523 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
60000483 CCCTAACCCG
60000493 ACCCCTATAACCCTAA
1 ACCCCTATAACCCTAA
60000509 ACCCCTA-AACCCTAA
1 ACCCCTATAACCCTAA
60000524 GTCTTAAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.39, C:0.45, G:0.00, T:0.16
Consensus pattern (16 bp):
ACCCCTATAACCCTAA
Found at i:60000801 original size:18 final size:21
Alignment explanation
Indices: 60000778--60000826 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 21
60000768 ATCAATCGCG
60000778 ATATTAATTTG-GTG-TTT-T
1 ATATTAATTTGTGTGATTTAT
* *
60000796 ATATTACTTTGTTTGATTTAT
1 ATATTAATTTGTGTGATTTAT
60000817 ATATTAATTT
1 ATATTAATTT
60000827 AGTCGAACTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 10 0.40
19 2 0.08
20 3 0.12
21 10 0.40
ACGTcount: A:0.27, C:0.02, G:0.10, T:0.61
Consensus pattern (21 bp):
ATATTAATTTGTGTGATTTAT
Found at i:60001523 original size:114 final size:111
Alignment explanation
Indices: 60001179--60001525 Score: 322
Period size: 113 Copynumber: 3.1 Consensus size: 111
60001169 TCCACAAAAA
* * * * * **
60001179 CGCCGCTAAAGA-ACAAATCATTAGCGGTGCTTTTAACAAAACACCGCTAAAGGCCCAAAAACAA
1 CGCCGCTAAAGACAC-GAGCATTAGCGGCGTTTTTAA-AAAACGCCGCTAAAGGCCCAAAAACTC
* * * ** *
60001243 AGAAAACGGCATCGTTGCCCTTAGGTTTTTTGCGGCACTTCTCAGAAAA
64 AGAAAACGGCGTCGTTGGCCTTAGGTTTTTTGCGGCGCTT-TTTGAAAT
* * * * * **
60001292 CGCCGCTAAAGACAGGAGCATTACCGGCGCTTTTCAAAAAGCGCCGCAAAAGGGACAAAAACTC-
1 CGCCGCTAAAGACACGAGCATTAGCGGCG-TTTTTAAAAAACGCCGCTAAAGGCCCAAAAACTCA
* * *
60001356 GGAAACGACGTCGTTGGCATTAGGTTTTTTGCGGCGCTTTTTAGAAAT
65 GAAAACGGCGTCGTTGGCCTTAGGTTTTTTGCGGCGCTTTTT-GAAAT
* * * *
60001404 TGCCGC-AAAGTCCCCCGAGCATTAGCGGCGTTTTTATAAAAACGCCGCTAATGGCCCAAAAACT
1 CGCCGCTAAAG--ACACGAGCATTAGCGGCGTTTTTA-AAAAACGCCGCTAAAGGCCCAAAAACT
* * *
60001468 CAGTAAACGGCGTCGTTGGCCTTATGTTTTTTGCGGCGCTTTTTGTGAAT
63 CAGAAAACGGCGTCGTTGGCCTTAGGTTTTTTGCGGCGCTTTTTG-AAAT
60001518 CGCCGCTA
1 CGCCGCTA
60001526 TTGCTTATTA
Statistics
Matches: 185, Mismatches: 40, Indels: 16
0.77 0.17 0.07
Matches are distributed among these distances:
111 5 0.03
112 47 0.25
113 80 0.43
114 52 0.28
115 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.24
Consensus pattern (111 bp):
CGCCGCTAAAGACACGAGCATTAGCGGCGTTTTTAAAAAACGCCGCTAAAGGCCCAAAAACTCAG
AAAACGGCGTCGTTGGCCTTAGGTTTTTTGCGGCGCTTTTTGAAAT
Found at i:60003940 original size:19 final size:20
Alignment explanation
Indices: 60003916--60003954 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
60003906 CATTTGTACT
*
60003916 TTGGTTTT-TTTGTTTTCTA
1 TTGGTTTTATTTATTTTCTA
60003935 TTGGTTTTATTTATTTTCTA
1 TTGGTTTTATTTATTTTCTA
60003955 AAATTGGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.10, C:0.05, G:0.13, T:0.72
Consensus pattern (20 bp):
TTGGTTTTATTTATTTTCTA
Found at i:60004862 original size:23 final size:23
Alignment explanation
Indices: 60004815--60004891 Score: 59
Period size: 29 Copynumber: 3.1 Consensus size: 23
60004805 GTGTTATTCC
*
60004815 TGCAAACCCTACATGATTAT-T-TA
1 TGCAAACCCTATAT--TTATATATA
60004838 TGCAAACCCTATATTTATATATA
1 TGCAAACCCTATATTTATATATA
60004861 TGTGCATGCGAACCCTATATTTATATATA
1 --TGCA----AACCCTATATTTATATATA
60004890 TG
1 TG
60004892 TACATGCGAA
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
21 4 0.09
22 1 0.02
23 15 0.33
25 4 0.09
27 2 0.04
29 19 0.42
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (23 bp):
TGCAAACCCTATATTTATATATA
Found at i:60004879 original size:29 final size:29
Alignment explanation
Indices: 60004837--60004906 Score: 122
Period size: 29 Copynumber: 2.4 Consensus size: 29
60004827 ATGATTATTT
* *
60004837 ATGCAAACCCTATATTTATATATATGTGC
1 ATGCGAACCCTATATTTATATATATGTAC
60004866 ATGCGAACCCTATATTTATATATATGTAC
1 ATGCGAACCCTATATTTATATATATGTAC
60004895 ATGCGAACCCTA
1 ATGCGAACCCTA
60004907 GACGAGTAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.34
Consensus pattern (29 bp):
ATGCGAACCCTATATTTATATATATGTAC
Found at i:60007122 original size:28 final size:28
Alignment explanation
Indices: 60007068--60007122 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
60007058 TGTTAGTATA
* *
60007068 TGATAAAATTATATTTTATTCTCTAAAT
1 TGATAAAATTATATTTAATCCTCTAAAT
* *
60007096 TGATAAAATTTTATTTAATCCTTTAAA
1 TGATAAAATTATATTTAATCCTCTAAA
60007123 AAGTTATAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (28 bp):
TGATAAAATTATATTTAATCCTCTAAAT
Found at i:60007644 original size:22 final size:24
Alignment explanation
Indices: 60007608--60007653 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
60007598 ATTTATGCTT
* *
60007608 TTTTTTTTGCATTTT-TAAATTTA
1 TTTTTTTTACATTTTAAAAATTTA
60007631 TTTTTTTTAC-TTTTAAAAATTTA
1 TTTTTTTTACATTTTAAAAATTTA
60007654 ATCCATTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.67
Consensus pattern (24 bp):
TTTTTTTTACATTTTAAAAATTTA
Found at i:60007789 original size:6 final size:6
Alignment explanation
Indices: 60007770--60007810 Score: 66
Period size: 6 Copynumber: 6.8 Consensus size: 6
60007760 AAAATAATAA
60007770 TATATAT TAT-TT TATATT TATATT TATATT TATATT TATAT
1 TATAT-T TATATT TATATT TATATT TATATT TATATT TATAT
60007811 ATTTTAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
5 4 0.12
6 26 0.79
7 3 0.09
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
TATATT
Found at i:60009591 original size:30 final size:33
Alignment explanation
Indices: 60009531--60009596 Score: 93
Period size: 30 Copynumber: 2.1 Consensus size: 33
60009521 ACATGATTTT
*
60009531 TTTAAATAATTATAAAAATATTATAGAAAATTA
1 TTTAAATAACTATAAAAATATTATAGAAAATTA
*
60009564 TTTAAA-AACTATTAAAAT-TTA-AGAAAATTA
1 TTTAAATAACTATAAAAATATTATAGAAAATTA
60009594 TTT
1 TTT
60009597 GATACACTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 12 0.39
31 3 0.10
32 10 0.32
33 6 0.19
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.41
Consensus pattern (33 bp):
TTTAAATAACTATAAAAATATTATAGAAAATTA
Found at i:60012625 original size:47 final size:49
Alignment explanation
Indices: 60012566--60012672 Score: 182
Period size: 49 Copynumber: 2.2 Consensus size: 49
60012556 ACCACTGGTC
60012566 GTGCAGATAAACTGCTGACT-AAAA-ATTGGTGGATGAACCATCCATGG
1 GTGCAGATAAACTGCTGACTAAAAATATTGGTGGATGAACCATCCATGG
*
60012613 GTGCAAATAAACTGCTGACTAAAAATATTGGTGGATGAACCATCCATGG
1 GTGCAGATAAACTGCTGACTAAAAATATTGGTGGATGAACCATCCATGG
*
60012662 GTACAGATAAA
1 GTGCAGATAAA
60012673 AGCTACTTAA
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
47 19 0.35
48 4 0.07
49 32 0.58
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.23
Consensus pattern (49 bp):
GTGCAGATAAACTGCTGACTAAAAATATTGGTGGATGAACCATCCATGG
Found at i:60022023 original size:3 final size:3
Alignment explanation
Indices: 60022017--60022091 Score: 141
Period size: 3 Copynumber: 25.0 Consensus size: 3
60022007 ATAATAATCA
*
60022017 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
60022065 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
60022092 AAAAGGGGGT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:60024058 original size:26 final size:26
Alignment explanation
Indices: 60024004--60024065 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 26
60023994 TAATCCTACT
*
60024004 TTATTATATATTTTATTTATTTCAAA
1 TTATTATATATTTTATTTATATCAAA
*
60024030 TTATTAT-TATTATTATTATATAT-ATA
1 TTATTATATATT-TTATT-TATATCAAA
60024056 TTATT-TATAT
1 TTATTATATAT
60024066 CAAGTTGTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
25 5 0.16
26 22 0.71
27 4 0.13
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (26 bp):
TTATTATATATTTTATTTATATCAAA
Found at i:60036350 original size:44 final size:43
Alignment explanation
Indices: 60036241--60036623 Score: 145
Period size: 44 Copynumber: 8.8 Consensus size: 43
60036231 AAGATGGTGA
* * * ***
60036241 ATCTTATCTCCCTGAGATTACAATGGAGCAGATT-GAAGCCAG
1 ATCTTATCTCTCTGAGATTACAGTGGAGCAGATTAAAATAAAG
* * *
60036283 TAATCCTATTTCCCTGAGATTACAGTGGAGCAGATTAAAATAAATG
1 --ATCTTATCTCTCTGAGATTACAGTGGAGCAGATTAAAATAAA-G
* * *** *
60036329 ATCTTATCTCTCTGA-AGTTACAGTAGAGTAGA-TCGCAT-CAG
1 ATCTTATCTCTCTGAGA-TTACAGTGGAGCAGATTAAAATAAAG
* ** ** *
60036370 GTCTTATCTCTCTGAGATTACAGTGGAATAGACCGAAGAATTACAG
1 ATCTTATCTCTCTGAGATTACAGTGGAGCAGA-TTAA-AA-TAAAG
* * * ***
60036416 ATCTTATCTCCCTGAGATTACAGCGGA-CAGATT-GAAGCCAG
1 ATCTTATCTCTCTGAGATTACAGTGGAGCAGATTAAAATAAAG
* * * *
60036457 TAATCCTATTTCCCTGAGATTACAGTGGAACAGATTAAAATAAAGG
1 --ATCTTATCTCTCTGAGATTACAGTGGAGCAGATTAAAATAAA-G
* * * *** *
60036503 ATCTTATCTCTCT-AAAGTTACAGTAGAGTAGA-TCGCAT-CAG
1 ATCTTATCTCTCTGAGA-TTACAGTGGAGCAGATTAAAATAAAG
* * * ** ** *
60036544 TTCTTATCTCCCTGATATTACAGTGGAATAGACCGAAGAATTACAG
1 ATCTTATCTCTCTGAGATTACAGTGGAGCAGA-TTAA-AA-TAAAG
* *
60036590 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATT
1 ATCTTATCTCTCTGAGATTACAGTGGAGCAGATT
60036624 GAAGCCANNN
Statistics
Matches: 252, Mismatches: 66, Indels: 41
0.70 0.18 0.11
Matches are distributed among these distances:
41 56 0.22
42 7 0.03
43 33 0.13
44 86 0.34
45 11 0.04
46 59 0.23
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.29
Consensus pattern (43 bp):
ATCTTATCTCTCTGAGATTACAGTGGAGCAGATTAAAATAAAG
Found at i:60036424 original size:46 final size:45
Alignment explanation
Indices: 60036371--60036612 Score: 173
Period size: 46 Copynumber: 5.5 Consensus size: 45
60036361 TCGCATCAGG
*
60036371 TCTTATCTCTCTGAGATTACAGTGGAATAGACCGAAGAATTACAGA
1 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAA-TACAGA
* * ** *
60036417 TCTTATCTCCCTGAGATTACAGCGG-ACAGATTGAAG---CCAGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATACAG--A
* * * ** *
60036460 TCCTATTTCCCTGAGATTACAGTGGAACAGA-TTAA-AATAAAGGA
1 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATACA-GA
* * * * * * *
60036504 TCTTATCTCTCT-AAAGTTACAGTAGAGTAGATC---GCAT-CAGT
1 TCTTATCTCCCTGAGA-TTACAGTGGAATAGACCGAAGAATACAGA
*
60036545 TCTTATCTCCCTGATATTACAGTGGAATAGACCGAAGAATTACAGA
1 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAA-TACAGA
60036591 TCTTATCTCCCTGAGATTACAG
1 TCTTATCTCCCTGAGATTACAG
60036613 CGGAGCAGAT
Statistics
Matches: 149, Mismatches: 31, Indels: 32
0.70 0.15 0.15
Matches are distributed among these distances:
41 29 0.19
42 3 0.02
43 30 0.20
44 29 0.19
45 10 0.07
46 48 0.32
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (45 bp):
TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATACAGA
Found at i:60036437 original size:87 final size:88
Alignment explanation
Indices: 60036328--60036612 Score: 307
Period size: 87 Copynumber: 3.3 Consensus size: 88
60036318 TAAAATAAAT
* * *
60036328 GATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGCATCAGGTCTTATCTCTCTGAGATTACA
1 GATCTTATCTCCCTGAGAGTTACAGTAGAGTAGATCGCATCAGATCTTATCTCCCTGAGATTACA
60036392 GTGGAATAGACCGAAGAATTACA
66 GTGGAATAGACCGAAGAATTACA
** * * * * * *
60036415 GATCTTATCTCCCTGAGA-TTACAGCGGA-CAGATTGAAGCCAGTAATCCTATTTCCCTGAGATT
1 GATCTTATCTCCCTGAGAGTTACAGTAGAGTAGATCGCA-TCAG--ATCTTATCTCCCTGAGATT
* ** *
60036478 ACAGTGGAACAGA-TTAA-AA-TAAA
63 ACAGTGGAATAGACCGAAGAATTACA
* * * *
60036501 GGATCTTATCTCTCT-AAAGTTACAGTAGAGTAGATCGCATCAGTTCTTATCTCCCTGATATTAC
1 -GATCTTATCTCCCTGAGAGTTACAGTAGAGTAGATCGCATCAGATCTTATCTCCCTGAGATTAC
60036565 AGTGGAATAGACCGAAGAATTACA
65 AGTGGAATAGACCGAAGAATTACA
60036589 GATCTTATCTCCCTGAGA-TTACAG
1 GATCTTATCTCCCTGAGAGTTACAG
60036613 CGGAGCAGAT
Statistics
Matches: 154, Mismatches: 33, Indels: 22
0.74 0.16 0.11
Matches are distributed among these distances:
85 27 0.18
86 13 0.08
87 73 0.47
88 14 0.09
89 27 0.18
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (88 bp):
GATCTTATCTCCCTGAGAGTTACAGTAGAGTAGATCGCATCAGATCTTATCTCCCTGAGATTACA
GTGGAATAGACCGAAGAATTACA
Found at i:60036532 original size:174 final size:175
Alignment explanation
Indices: 60036241--60036630 Score: 701
Period size: 174 Copynumber: 2.2 Consensus size: 175
60036231 AAGATGGTGA
**
60036241 ATCTTATCTCCCTGAGATTACAATGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTAC
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTAC
* * *
60036306 AGTGGAGCAGATTAAAATAAATGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGG
66 AGTGGAACAGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCATCAGG
*
60036371 TCTTATCTCTCTGAGATTACAGTGGAATAGACCGAAGAATTACAG
131 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTACAG
60036416 ATCTTATCTCCCTGAGATTACAGCGGA-CAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTAC
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTAC
*
60036480 AGTGGAACAGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCATCAGT
66 AGTGGAACAGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCATCAGG
*
60036545 TCTTATCTCCCTGATATTACAGTGGAATAGACCGAAGAATTACAG
131 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTACAG
60036590 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCA
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCA
60036631 NNNNNNNNNN
Statistics
Matches: 206, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
174 168 0.82
175 38 0.18
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.28
Consensus pattern (175 bp):
ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTAC
AGTGGAACAGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCATCAGG
TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTACAG
Found at i:60036571 original size:85 final size:83
Alignment explanation
Indices: 60036293--60036571 Score: 290
Period size: 87 Copynumber: 3.2 Consensus size: 83
60036283 TAATCCTATT
*
60036293 TCCCTGAGATTACAGTGGAGCAGATTAAAATAAATGATCTTATCTCTCTGAAGTTACAGTAGAGT
1 TCCCTGAGATTACAGTGGAACAGATTAAAATAAA-GATCTTATCTCTCT-AAGTTACAGTAGAGT
*
60036358 AGATCGCATCAGGTCTTATC
64 AGATCGCATCAGTTCTTATC
* * ** * * * **
60036378 TCTCTGAGATTACAGTGGAATAGACCGAAGAATTACAGATCTTATCTCCCTGAGATTACAGCGGA
1 TCCCTGAGATTACAGTGGAACAGA-TTAA-AA-TAAAGATCTTATCTCTCTAAG-TTACAGTAGA
* * * * * *
60036443 -CAGATTGAAGCCAGTAATCCTATT
62 GTAGATCGCA-TCAGT--TCTTATC
60036467 TCCCTGAGATTACAGTGGAACAGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGT
1 TCCCTGAGATTACAGTGGAACAGATTAAAATAAA-GATCTTATCTCTCT-AAGTTACAGTAGAGT
60036532 AGATCGCATCAGTTCTTATC
64 AGATCGCATCAGTTCTTATC
*
60036552 TCCCTGATATTACAGTGGAA
1 TCCCTGAGATTACAGTGGAA
60036572 TAGACCGAAG
Statistics
Matches: 151, Mismatches: 33, Indels: 20
0.74 0.16 0.10
Matches are distributed among these distances:
85 45 0.30
86 13 0.09
87 53 0.35
88 13 0.09
89 27 0.18
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (83 bp):
TCCCTGAGATTACAGTGGAACAGATTAAAATAAAGATCTTATCTCTCTAAGTTACAGTAGAGTAG
ATCGCATCAGTTCTTATC
Found at i:60037587 original size:100 final size:100
Alignment explanation
Indices: 60037415--60037875 Score: 771
Period size: 100 Copynumber: 4.6 Consensus size: 100
60037405 NNNNNNNNNN
* *
60037415 AAAGCTACAACAGCGAATCCTACTT-CCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTG
1 AAAGCTACAACAGCGAATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTG
*
60037479 AATCTTGCTTCCCCGACATTGCAGTTAAAAAAATT
66 AATCTTGCTTCCCCGACATTGCAGTTAAAAAGATT
* * *
60037514 AAAGCTACAACAGTGAATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTAAAGCCATATCAGTG
1 AAAGCTACAACAGCGAATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTG
60037579 AATCTTGCTTCCCCGACATTGCAGTTAAAAAGATT
66 AATCTTGCTTCCCCGACATTGCAGTTAAAAAGATT
* *
60037614 AAAGCTACAACAGCGAATCTTACTTCCTAGGCGGTGCAGTGGAACATATTAAAGCCACATCGGTG
1 AAAGCTACAACAGCGAATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTG
*
60037679 AATCTTGCTTCCCCGACATTACAGTTAAAAAGATT
66 AATCTTGCTTCCCCGACATTGCAGTTAAAAAGATT
* *
60037714 AAAGCTACAACAGCGAATCTTACTTCCTAGGTGGTGCAGTGGAACAGATTAAAGCCACATCGGTG
1 AAAGCTACAACAGCGAATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTG
*
60037779 AATTTTGCTTCCCCGACATTGCAGTTAAAAAGATT
66 AATCTTGCTTCCCCGACATTGCAGTTAAAAAGATT
* * * *
60037814 AAAGCTACAACAGCGAATCTTACTTCCCAGGCAGTACCGTGGAATAGATTAAAGCCACATCG
1 AAAGCTACAACAGCGAATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACATCG
60037876 TGGAATAGAT
Statistics
Matches: 339, Mismatches: 22, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
99 23 0.07
100 316 0.93
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (100 bp):
AAAGCTACAACAGCGAATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTG
AATCTTGCTTCCCCGACATTGCAGTTAAAAAGATT
Found at i:60037863 original size:50 final size:50
Alignment explanation
Indices: 60037415--60037868 Score: 363
Period size: 50 Copynumber: 9.1 Consensus size: 50
60037405 NNNNNNNNNN
* * *
60037415 AAAGCTACAACAGCGAATCCTACTT-CCAGGC-GATGCAGTGGAACAGATT
1 AAAGCTACAACAGTGAATCTTACTTCCCAGGCAG-TGCAGTGGAAAAGATT
* * * * * * * ** *
60037464 AAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAAATT
1 AAAGCTACAACAGTGAATCTTACTTCCCAGGCAGTGCAGTGGAAAAGATT
* *
60037514 AAAGCTACAACAGTGAATCTTACTTCCCAGGCGGTGCAGTGGAACAGATT
1 AAAGCTACAACAGTGAATCTTACTTCCCAGGCAGTGCAGTGGAAAAGATT
* * * * * * * **
60037564 AAAGCCATATCAGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATT
1 AAAGCTACAACAGTGAATCTTACTTCCCAGGCAGTGCAGTGGAAAAGATT
* * * * *
60037614 AAAGCTACAACAGCGAATCTTACTTCCTAGGCGGTGCAGTGGAACATATT
1 AAAGCTACAACAGTGAATCTTACTTCCCAGGCAGTGCAGTGGAAAAGATT
* * * * * * * * **
60037664 AAAGCCACATCGGTGAATCTTGCTTCCCCGACATTACAGTTAAAAAGATT
1 AAAGCTACAACAGTGAATCTTACTTCCCAGGCAGTGCAGTGGAAAAGATT
* * ** *
60037714 AAAGCTACAACAGCGAATCTTACTTCCTAGGTGGTGCAGTGGAACAGATT
1 AAAGCTACAACAGTGAATCTTACTTCCCAGGCAGTGCAGTGGAAAAGATT
* * * * * * * * **
60037764 AAAGCCACATCGGTGAATTTTGCTTCCCCGACATTGCAGTTAAAAAGATT
1 AAAGCTACAACAGTGAATCTTACTTCCCAGGCAGTGCAGTGGAAAAGATT
* * * *
60037814 AAAGCTACAACAGCGAATCTTACTTCCCAGGCAGTACCGTGGAATAGATT
1 AAAGCTACAACAGTGAATCTTACTTCCCAGGCAGTGCAGTGGAAAAGATT
60037864 AAAGC
1 AAAGC
60037869 CACATCGTGG
Statistics
Matches: 294, Mismatches: 109, Indels: 3
0.72 0.27 0.01
Matches are distributed among these distances:
49 19 0.06
50 275 0.94
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (50 bp):
AAAGCTACAACAGTGAATCTTACTTCCCAGGCAGTGCAGTGGAAAAGATT
Found at i:60037881 original size:23 final size:23
Alignment explanation
Indices: 60037851--60037894 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
60037841 CAGGCAGTAC
60037851 CGTGGAATAGATTAAAGCCACAT
1 CGTGGAATAGATTAAAGCCACAT
60037874 CGTGGAATAGATTAAAGCCAC
1 CGTGGAATAGATTAAAGCCAC
60037895 GACGGCGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.20
Consensus pattern (23 bp):
CGTGGAATAGATTAAAGCCACAT
Found at i:60039463 original size:26 final size:26
Alignment explanation
Indices: 60039421--60039471 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
60039411 ATTAATAGTA
60039421 TAAATTTATCACATAT-CTTAATTTTT
1 TAAATTTATCACATATCCTT-ATTTTT
**
60039447 TAAATTTATCATGTATCCTTATTTT
1 TAAATTTATCACATATCCTTATTTT
60039472 GAAACTCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 19 0.86
27 3 0.14
ACGTcount: A:0.31, C:0.12, G:0.02, T:0.55
Consensus pattern (26 bp):
TAAATTTATCACATATCCTTATTTTT
Found at i:60039582 original size:26 final size:26
Alignment explanation
Indices: 60039530--60039586 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
60039520 TTTTAGGTTT
*
60039530 TATATTTTTTTAATCCTACTTTATTA
1 TATATTTTTTTAATCCAACTTTATTA
* *
60039556 TATATTTTATTTATTTCAACTTT-TTA
1 TATATTTT-TTTAATCCAACTTTATTA
60039582 T-TATT
1 TATATT
60039587 ATATATATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 4 0.15
26 12 0.44
27 11 0.41
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (26 bp):
TATATTTTTTTAATCCAACTTTATTA
Found at i:60043726 original size:8 final size:8
Alignment explanation
Indices: 60043713--60043752 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
60043703 ACACATTTTA
60043713 ATAAAATT
1 ATAAAATT
60043721 ATAAAATT
1 ATAAAATT
*
60043729 ATAAAATA
1 ATAAAATT
* *
60043737 ATATAATA
1 ATAAAATT
60043745 ATAAAATT
1 ATAAAATT
60043753 GTATTTTGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
ATAAAATT
Found at i:60048305 original size:129 final size:129
Alignment explanation
Indices: 60048075--60048337 Score: 517
Period size: 129 Copynumber: 2.0 Consensus size: 129
60048065 TTACTAATTC
*
60048075 GAAGCATAAAAATTTACTTTGAAAATTAATTTCACTGTTTATAGCAAACTTGTCCAATCGCGTAG
1 GAAGCATAAAAATTTACTTTGAAAATTAATTTCACTGTTTATAGCAAACTTGTCCAATCGCGCAG
60048140 CAGTTAATAAATTGATTATAACTTGAGCTACAGGACTCGAAATTTAATTATGTAAATTTTCCCT
66 CAGTTAATAAATTGATTATAACTTGAGCTACAGGACTCGAAATTTAATTATGTAAATTTTCCCT
60048204 GAAGCATAAAAATTTACTTTGAAAATTAATTTCACTGTTTATAGCAAACTTGTCCAATCGCGCAG
1 GAAGCATAAAAATTTACTTTGAAAATTAATTTCACTGTTTATAGCAAACTTGTCCAATCGCGCAG
60048269 CAGTTAATAAATTGATTATAACTTGAGCTACAGGACTCGAAATTTAATTATGTAAATTTTCCCT
66 CAGTTAATAAATTGATTATAACTTGAGCTACAGGACTCGAAATTTAATTATGTAAATTTTCCCT
60048333 GAAGC
1 GAAGC
60048338 TAGACTCATA
Statistics
Matches: 133, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
129 133 1.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.35
Consensus pattern (129 bp):
GAAGCATAAAAATTTACTTTGAAAATTAATTTCACTGTTTATAGCAAACTTGTCCAATCGCGCAG
CAGTTAATAAATTGATTATAACTTGAGCTACAGGACTCGAAATTTAATTATGTAAATTTTCCCT
Found at i:60049562 original size:50 final size:50
Alignment explanation
Indices: 60049451--60049742 Score: 361
Period size: 50 Copynumber: 5.7 Consensus size: 50
60049441 ACATGTCAAA
** * *
60049451 GCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATTGGTGTCC-AT
1 GCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGGTG-CCAAT
***
60049502 GCCATGTCCCAGACATGGTCTTATGGGGGACCTCTCATCTCGGTGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAT
**
60049552 TTCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAT
* * * *
60049602 GCCATGTCCCACACATGGTCTTACATGAGACCTCTCATCTTGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAT
*
60049652 GCCATGTCCCAGACATGGTTTTACATGGGACCTCTCATGATCTCAAGGATGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC--GG-TGCCAAT
* *
60049708 TCCATGTCCCAGACATGGTTTTACATGGGACCTCT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCT
60049743 TTACCCAAAT
Statistics
Matches: 210, Mismatches: 24, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
49 2 0.01
50 135 0.64
51 27 0.13
53 4 0.02
55 2 0.01
56 40 0.19
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.29
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAT
Found at i:60059589 original size:18 final size:18
Alignment explanation
Indices: 60059555--60059589 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
60059545 TATTGAAAAT
*
60059555 GGAAGTGGAGAGAGAAAG
1 GGAAGTGGAAAGAGAAAG
*
60059573 GGAAGTGGAAAGGGAAA
1 GGAAGTGGAAAGAGAAA
60059590 TACAATGGCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.49, T:0.06
Consensus pattern (18 bp):
GGAAGTGGAAAGAGAAAG
Found at i:60060730 original size:11 final size:10
Alignment explanation
Indices: 60060714--60060748 Score: 52
Period size: 11 Copynumber: 3.3 Consensus size: 10
60060704 ACAAGGAAGG
60060714 AAAAAGAAGAA
1 AAAAAGAA-AA
60060725 AAAAAGAAAA
1 AAAAAGAAAA
60060735 ATAAAAGAAAA
1 A-AAAAGAAAA
60060746 AAA
1 AAA
60060749 TATAAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 5 0.22
11 18 0.78
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:60061099 original size:25 final size:24
Alignment explanation
Indices: 60061071--60061122 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
60061061 CCCAACCGGC
* *
60061071 CAGCCCATTGCTCAGCAGCAGGCCT
1 CAGCCCAGTGCCCAGCAGCAGG-CT
*
60061096 CAGCCTAGTGCCCAGCAGCAGGCT
1 CAGCCCAGTGCCCAGCAGCAGGCT
60061120 CAG
1 CAG
60061123 AAGCACCCAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.21, C:0.38, G:0.27, T:0.13
Consensus pattern (24 bp):
CAGCCCAGTGCCCAGCAGCAGGCT
Found at i:60061195 original size:16 final size:17
Alignment explanation
Indices: 60061174--60061206 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
60061164 AGCCAACTGC
*
60061174 AGAAAA-AAAAGAAAAA
1 AGAAAAGAAAACAAAAA
60061190 AGAAAAGAAAACAAAAA
1 AGAAAAGAAAACAAAAA
60061207 GCTCGAGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (17 bp):
AGAAAAGAAAACAAAAA
Found at i:60064821 original size:3 final size:3
Alignment explanation
Indices: 60064808--60064875 Score: 102
Period size: 3 Copynumber: 22.7 Consensus size: 3
60064798 CATCATCATC
*
60064808 ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
60064856 ATT AATT -TT ATT GTT ATT AT
1 ATT -ATT ATT ATT ATT ATT AT
60064876 CATCAGATTT
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.03
3 54 0.92
4 3 0.05
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:60065773 original size:70 final size:70
Alignment explanation
Indices: 60065660--60065791 Score: 237
Period size: 70 Copynumber: 1.9 Consensus size: 70
60065650 CCTTTCAAAC
*
60065660 TCAAGTTTTAAACGATCTCGGGAATTAAGAGAAGATCGTGTCCTAACTTACTGGGCATGATCATC
1 TCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCATC
60065725 TTTTT
66 TTTTT
* *
60065730 TCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGTTTGTGTCCTAACTTACTGGGCATGATC
1 TCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATC
60065792 CCTTTTCTAT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 59 1.00
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (70 bp):
TCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCATC
TTTTT
Found at i:60068405 original size:88 final size:88
Alignment explanation
Indices: 60068249--60068465 Score: 337
Period size: 88 Copynumber: 2.5 Consensus size: 88
60068239 CCGTTATCTA
* * * * * *
60068249 CAGTCTTAATGTCAGGGAGAGAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCGCTACAACGCTA
1 CAGTCTTAACGCCAGGGAGATAAGATTCGCTGCCTTTAGCTTTAATCTGCTCCGCTACAACGCCA
60068314 GGGAAAAGAAGACTCGCTGTCTT
66 GGGAAAAGAAGACTCGCTGTCTT
*
60068337 CAGTCTTAACGCCAGGGAGATAAGATTCGCTGCCTTTAGCTTTAATCTGCTCCGCTACAATGCCA
1 CAGTCTTAACGCCAGGGAGATAAGATTCGCTGCCTTTAGCTTTAATCTGCTCCGCTACAACGCCA
60068402 GGGAAAAGAAGACTCGCTGTCTT
66 GGGAAAAGAAGACTCGCTGTCTT
* *
60068425 CAGTCTTAACGCCGGGGAGATAAGATTCACTG-CTTTCAGCT
1 CAGTCTTAACGCCAGGGAGATAAGATTCGCTGCCTTT-AGCT
60068466 GCTTTGATCT
Statistics
Matches: 119, Mismatches: 9, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
87 4 0.03
88 115 0.97
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.27
Consensus pattern (88 bp):
CAGTCTTAACGCCAGGGAGATAAGATTCGCTGCCTTTAGCTTTAATCTGCTCCGCTACAACGCCA
GGGAAAAGAAGACTCGCTGTCTT
Found at i:60069704 original size:1 final size:1
Alignment explanation
Indices: 60069689--60069759 Score: 52
Period size: 1 Copynumber: 71.0 Consensus size: 1
60069679 TGGCCTCTCC
* * * * * * * * **
60069689 TTTTTCTTTTCTTTTTTTTCTTTTTTTATTTTTCTTTTCTTTTTTCTTTTTTCTTTTTTTCCTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
60069754 TTTTTT
1 TTTTTT
60069760 GAAATATTCT
Statistics
Matches: 52, Mismatches: 18, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.01, C:0.13, G:0.00, T:0.86
Consensus pattern (1 bp):
T
Found at i:60069708 original size:14 final size:14
Alignment explanation
Indices: 60069689--60069759 Score: 94
Period size: 14 Copynumber: 5.1 Consensus size: 14
60069679 TGGCCTCTCC
60069689 TTTTTCTTTTCTTT
1 TTTTTCTTTTCTTT
60069703 TTTTTCTTTT-TTT
1 TTTTTCTTTTCTTT
60069716 ATTTTTCTTTTCTTT
1 -TTTTTCTTTTCTTT
60069731 TTTCTT-TTTTCTTT
1 TTT-TTCTTTTCTTT
*
60069745 TTTTCCTTTT-TTT
1 TTTTTCTTTTCTTT
60069758 TT
1 TT
60069760 GAAATATTCT
Statistics
Matches: 52, Mismatches: 1, Indels: 9
0.84 0.02 0.15
Matches are distributed among these distances:
13 9 0.17
14 38 0.73
15 5 0.10
ACGTcount: A:0.01, C:0.13, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTTCTTTTCTTT
Found at i:60069726 original size:19 final size:19
Alignment explanation
Indices: 60069689--60069745 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
60069679 TGGCCTCTCC
*
60069689 TTTTTCTTTTCTTTTTTTTCT
1 TTTTTC-TTT-TTTCTTTTCT
60069710 TTTTT-TATTTTTCTTTTCT
1 TTTTTCT-TTTTTCTTTTCT
60069729 TTTTTCTTTTTTCTTTT
1 TTTTTCTTTTTTCTTTT
60069746 TTTCCTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 25 0.76
20 3 0.09
21 5 0.15
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (19 bp):
TTTTTCTTTTTTCTTTTCT
Found at i:60069755 original size:7 final size:7
Alignment explanation
Indices: 60069689--60069747 Score: 72
Period size: 7 Copynumber: 8.7 Consensus size: 7
60069679 TGGCCTCTCC
60069689 TTTTTCT
1 TTTTTCT
60069696 TTTCTT-T
1 TTT-TTCT
60069703 TTTTTCT
1 TTTTTCT
60069710 TTTTT-T
1 TTTTTCT
60069716 ATTTTTC-
1 -TTTTTCT
60069723 -TTTTCT
1 TTTTTCT
60069729 TTTTTCT
1 TTTTTCT
60069736 TTTTTCT
1 TTTTTCT
60069743 TTTTT
1 TTTTT
60069748 TCCTTTTTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
5 5 0.11
6 3 0.07
7 36 0.78
8 2 0.04
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTCT
Found at i:60071453 original size:9 final size:9
Alignment explanation
Indices: 60071439--60071532 Score: 102
Period size: 9 Copynumber: 10.4 Consensus size: 9
60071429 TTTGGTTAAA
*
60071439 AATTAACAG
1 AATTAACCG
60071448 AATTAACCG
1 AATTAACCG
60071457 AATT-ACCTG
1 AATTAACC-G
60071466 AATTAACCG
1 AATTAACCG
*
60071475 AATT-ACTTG
1 AATTAAC-CG
60071484 AATTAACCG
1 AATTAACCG
*
60071493 AATTACCCG
1 AATTAACCG
* *
60071502 AGTTACCCG
1 AATTAACCG
60071511 AATTAACCG
1 AATTAACCG
*
60071520 AATTAACCT
1 AATTAACCG
60071529 AATT
1 AATT
60071533 GAATCATACA
Statistics
Matches: 73, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
8 5 0.07
9 63 0.86
10 5 0.07
ACGTcount: A:0.40, C:0.21, G:0.11, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:60071487 original size:36 final size:36
Alignment explanation
Indices: 60071439--60071532 Score: 118
Period size: 36 Copynumber: 2.6 Consensus size: 36
60071429 TTTGGTTAAA
* *
60071439 AATTAACAGAATTAACCGAATTACCTGAATTAACCG
1 AATTAACCGAATTAACCGAATTACCCGAATTAACCG
* * *
60071475 AATT-ACTTGAATTAACCGAATTACCCGAGTTACCCG
1 AATTAAC-CGAATTAACCGAATTACCCGAATTAACCG
*
60071511 AATTAACCGAATTAACCTAATT
1 AATTAACCGAATTAACCGAATT
60071533 GAATCATACA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
35 2 0.04
36 46 0.92
37 2 0.04
ACGTcount: A:0.40, C:0.21, G:0.11, T:0.28
Consensus pattern (36 bp):
AATTAACCGAATTAACCGAATTACCCGAATTAACCG
Found at i:60075062 original size:25 final size:25
Alignment explanation
Indices: 60075033--60075093 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
60075023 TATAAATTAT
*
60075033 AAAAATATATATATGT-ACATATAAG
1 AAAAATATATATATGTGA-ATAAAAG
*
60075058 AAAAATATATCTATGTGAATAAAAG
1 AAAAATATATATATGTGAATAAAAG
*
60075083 AAATATATATA
1 AAAAATATATA
60075094 AATATATATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 30 0.97
26 1 0.03
ACGTcount: A:0.57, C:0.03, G:0.08, T:0.31
Consensus pattern (25 bp):
AAAAATATATATATGTGAATAAAAG
Found at i:60075079 original size:23 final size:24
Alignment explanation
Indices: 60075033--60075117 Score: 77
Period size: 23 Copynumber: 3.6 Consensus size: 24
60075023 TATAAATTAT
60075033 AAAAATATATATATGTACATATAA
1 AAAAATATATATATGTACATATAA
*
60075057 GAAAAATATATCTATGTGA-ATA-AA
1 -AAAAATATATATATGT-ACATATAA
* ** *
60075081 AGAAATATATATAAATATATAT-A
1 AAAAATATATATATGTACATATAA
*
60075104 AAAAATATACATAT
1 AAAAATATATATAT
60075118 TTTAAAATGT
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
22 1 0.02
23 27 0.55
24 2 0.04
25 18 0.37
26 1 0.02
ACGTcount: A:0.59, C:0.04, G:0.06, T:0.32
Consensus pattern (24 bp):
AAAAATATATATATGTACATATAA
Found at i:60076886 original size:27 final size:27
Alignment explanation
Indices: 60076818--60076880 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 27
60076808 AAAAAAAATA
**
60076818 ACCAAAATATTAT-AGCTTTTTTATTT
1 ACCAAAATATTATAAATTTTTTTATTT
60076844 ACCAAAATATTATAAATTTTTTTATTT
1 ACCAAAATATTATAAATTTTTTTATTT
60076871 ACCAAAATAT
1 ACCAAAATAT
60076881 ACTAAAAAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
26 13 0.38
27 21 0.62
ACGTcount: A:0.41, C:0.11, G:0.02, T:0.46
Consensus pattern (27 bp):
ACCAAAATATTATAAATTTTTTTATTT
Found at i:60077057 original size:42 final size:41
Alignment explanation
Indices: 60077009--60077213 Score: 256
Period size: 42 Copynumber: 5.0 Consensus size: 41
60076999 AGGAGAGGGC
60077009 AAGAAAGAAAGAAAGAAAGGAA-AAGAAAGAAAAGGAAAGGAG
1 AAGAAAGAAAGAAAGAAA--AAGAAGAAAGAAAAGGAAAGGAG
*
60077051 AGGAAAGAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAG
1 AAGAAAGAAAGAAAGAAAAAGAA-GAAAGAAAAGGAAAGGAG
*
60077093 AAGAAA-AAAGAAAGAAAAAGAGGAAAGAAAAGGAAAGGAG
1 AAGAAAGAAAGAAAGAAAAAGAAGAAAGAAAAGGAAAGGAG
* * *
60077133 AAGAAAAAAAGAAAGAAAACGAAGGAAAGAAAAGGAAATGAG
1 AAGAAAGAAAGAAAGAAAAAGAA-GAAAGAAAAGGAAAGGAG
* * * *
60077175 AAGAGAGAAA-AAAAAAGAAAGAAG-AAGAAGAGGGAAGGA
1 AAGAAAGAAAGAAAGAA-AAAGAAGAAAGAAAAGGAAAGGA
60077214 AGGAAAAAAA
Statistics
Matches: 145, Mismatches: 13, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
40 38 0.26
41 37 0.26
42 70 0.48
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.00
Consensus pattern (41 bp):
AAGAAAGAAAGAAAGAAAAAGAAGAAAGAAAAGGAAAGGAG
Found at i:60077144 original size:82 final size:82
Alignment explanation
Indices: 60077009--60077224 Score: 280
Period size: 82 Copynumber: 2.6 Consensus size: 82
60076999 AGGAGAGGGC
*
60077009 AAGAAAGAAAGAAAGAAAGGAA-AAGAAAGAAAAGGAAAGGAGAGGAAAGAAAGAAAGAAAAAGA
1 AAGAAA-AAAGAAAGAAA--AAGAAGAAAGAAAAGGAAAGGAGAGGAAAAAAAGAAAGAAAAAGA
60077073 AGGAAAGAAAAGGAAAGGAG
63 AGGAAAGAAAAGGAAAGGAG
* * *
60077093 AAGAAAAAAGAAAGAAAAAGAGGAAAGAAAAGGAAAGGAGAAGAAAAAAAGAAAGAAAACGAAGG
1 AAGAAAAAAGAAAGAAAAAGAAGAAAGAAAAGGAAAGGAGAGGAAAAAAAGAAAGAAAAAGAAGG
*
60077158 AAAGAAAAGGAAATGAG
66 AAAGAAAAGGAAAGGAG
* *
60077175 AAGAGAGAAAA-AAA-AAGAAAGAAG-AAGAAGAGGGAAGGA-AGGAAAAAAAG
1 AAGA-A-AAAAGAAAGAA-AAAGAAGAAAGAAAAGGAAAGGAGAGGAAAAAAAG
60077225 GTAATTTTTA
Statistics
Matches: 119, Mismatches: 9, Indels: 11
0.86 0.06 0.08
Matches are distributed among these distances:
81 12 0.10
82 76 0.64
83 21 0.18
84 10 0.08
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (82 bp):
AAGAAAAAAGAAAGAAAAAGAAGAAAGAAAAGGAAAGGAGAGGAAAAAAAGAAAGAAAAAGAAGG
AAAGAAAAGGAAAGGAG
Found at i:60077200 original size:24 final size:24
Alignment explanation
Indices: 60077130--60077202 Score: 71
Period size: 24 Copynumber: 3.0 Consensus size: 24
60077120 AAAAGGAAAG
60077130 GAGAAGAAAAAAAGAAAGAA-AACGA
1 GAGAA-AAAAAAAGAAAGAAGAA-GA
* *
60077155 -AGGAAAGAAAAGGAAATG-AGAAGA
1 GA-GAAAAAAAAAGAAA-GAAGAAGA
60077179 GAGAAAAAAAAAGAAAGAAGAAGA
1 GAGAAAAAAAAAGAAAGAAGAAGA
60077203 AGAGGGAAGG
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
23 1 0.03
24 31 0.79
25 7 0.18
ACGTcount: A:0.70, C:0.01, G:0.27, T:0.01
Consensus pattern (24 bp):
GAGAAAAAAAAAGAAAGAAGAAGA
Found at i:60077202 original size:10 final size:10
Alignment explanation
Indices: 60077009--60077203 Score: 85
Period size: 10 Copynumber: 19.5 Consensus size: 10
60076999 AGGAGAGGGC
60077009 AAGAAAGAAAG
1 AAGAAAG-AAG
60077020 AAAGAAAGGAA-
1 -AAGAAA-GAAG
60077031 AAGAAAGAA-
1 AAGAAAGAAG
*
60077040 AAGGAAAGGAG
1 AA-GAAAGAAG
*
60077051 AGGAAAGAAAG
1 AAGAAAG-AAG
60077062 AAAGAAA-AAG
1 -AAGAAAGAAG
60077072 AAGGAAAGAA-
1 AA-GAAAGAAG
*
60077082 AAGGAAAGGAG
1 AA-GAAAGAAG
*
60077093 AAGAAAAAAG
1 AAGAAAGAAG
60077103 AAAGAAA-AAG
1 -AAGAAAGAAG
*
60077113 AGGAAAGAA-
1 AAGAAAGAAG
*
60077122 AAGGAAAGGAG
1 AA-GAAAGAAG
60077133 AAGAAA-AA-
1 AAGAAAGAAG
60077141 AAGAAAGAA-
1 AAGAAAGAAG
*
60077150 AACGAAGGAAAG
1 AA-GAAAG-AAG
*
60077162 AA-AAGGAA-
1 AAGAAAGAAG
*
60077170 ATGAGAAGAGAG
1 AAGA-AAGA-AG
60077182 AA-AAA-AA-
1 AAGAAAGAAG
60077189 AAGAAAGAAG
1 AAGAAAGAAG
60077199 AAGAA
1 AAGAA
60077204 GAGGGAAGGA
Statistics
Matches: 145, Mismatches: 15, Indels: 48
0.70 0.07 0.23
Matches are distributed among these distances:
7 2 0.01
8 11 0.08
9 24 0.17
10 72 0.50
11 19 0.13
12 16 0.11
13 1 0.01
ACGTcount: A:0.70, C:0.01, G:0.29, T:0.01
Consensus pattern (10 bp):
AAGAAAGAAG
Found at i:60080730 original size:11 final size:11
Alignment explanation
Indices: 60080714--60080740 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
60080704 TTTATAACTT
60080714 AATTTGGATAC
1 AATTTGGATAC
60080725 AATTTGGATAC
1 AATTTGGATAC
60080736 AATTT
1 AATTT
60080741 AAGCATAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (11 bp):
AATTTGGATAC
Found at i:60083028 original size:18 final size:18
Alignment explanation
Indices: 60083005--60083042 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
60082995 ATCCCAATGA
*
60083005 TCGCCATCACCTTCTTCT
1 TCGCCAGCACCTTCTTCT
60083023 TCGCCAGCACCTTCTTCT
1 TCGCCAGCACCTTCTTCT
60083041 TC
1 TC
60083043 ACCACCAACC
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:0.11, C:0.45, G:0.08, T:0.37
Consensus pattern (18 bp):
TCGCCAGCACCTTCTTCT
Found at i:60083910 original size:6 final size:6
Alignment explanation
Indices: 60083899--60084033 Score: 92
Period size: 6 Copynumber: 22.5 Consensus size: 6
60083889 ATCTTAATAC
* * * *
60083899 TAACAA TAACAA CT-ACAA CAACAA CAACAA CAACAA CAACAA TAACAA
1 TAACAA TAACAA -TAACAA TAACAA TAACAA TAACAA TAACAA TAACAA
* * * * * * * *
60083947 CAACAA CAACAA CAACAA CAACAA TAATAA TAATAA TAATAA TAATAA
1 TAACAA TAACAA TAACAA TAACAA TAACAA TAACAA TAACAA TAACAA
* * * * * *
60083995 TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA TAA
1 TAACAA TAACAA TAACAA TAACAA TAACAA TAACAA TAA
60084034 TACTAACTAA
Statistics
Matches: 122, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
6 121 0.99
7 1 0.01
ACGTcount: A:0.66, C:0.16, G:0.00, T:0.19
Consensus pattern (6 bp):
TAACAA
Found at i:60083921 original size:3 final size:3
Alignment explanation
Indices: 60083900--60083970 Score: 115
Period size: 3 Copynumber: 23.7 Consensus size: 3
60083890 TCTTAATACT
* * *
60083900 AAC AAT AAC AAC TAC AAC AAC AAC AAC AAC AAC AAC AAC AAT AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
60083948 AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AA
60083971 TAATAATAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.66, C:0.30, G:0.00, T:0.04
Consensus pattern (3 bp):
AAC
Found at i:60083975 original size:3 final size:3
Alignment explanation
Indices: 60083969--60084035 Score: 134
Period size: 3 Copynumber: 22.3 Consensus size: 3
60083959 CAACAACAAC
60083969 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
60084017 AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT A
60084036 CTAACTAAAA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:60084311 original size:27 final size:27
Alignment explanation
Indices: 60084273--60084377 Score: 147
Period size: 27 Copynumber: 3.9 Consensus size: 27
60084263 AACACGAGTA
* *
60084273 GTGCCGCCAATCAGTATGGCACCATTG
1 GTGCCGCCAATCACTTTGGCACCATTG
* * **
60084300 GTGCCGCCAATCTCCTTGGCACCAACG
1 GTGCCGCCAATCACTTTGGCACCATTG
*
60084327 GTGCCGCCAATCACTTTGGCACCTTTG
1 GTGCCGCCAATCACTTTGGCACCATTG
60084354 GTGCCGCCAATCACTTTGGCACCA
1 GTGCCGCCAATCACTTTGGCACCA
60084378 CCAGGGTGTT
Statistics
Matches: 66, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 66 1.00
ACGTcount: A:0.19, C:0.35, G:0.23, T:0.23
Consensus pattern (27 bp):
GTGCCGCCAATCACTTTGGCACCATTG
Found at i:60084355 original size:54 final size:54
Alignment explanation
Indices: 60084273--60084377 Score: 165
Period size: 54 Copynumber: 1.9 Consensus size: 54
60084263 AACACGAGTA
* *
60084273 GTGCCGCCAATCAGTATGGCACCATTGGTGCCGCCAATCTCCTTGGCACCAACG
1 GTGCCGCCAATCACTATGGCACCATTGGTGCCGCCAATCACCTTGGCACCAACG
* * *
60084327 GTGCCGCCAATCACTTTGGCACCTTTGGTGCCGCCAATCACTTTGGCACCA
1 GTGCCGCCAATCACTATGGCACCATTGGTGCCGCCAATCACCTTGGCACCA
60084378 CCAGGGTGTT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.19, C:0.35, G:0.23, T:0.23
Consensus pattern (54 bp):
GTGCCGCCAATCACTATGGCACCATTGGTGCCGCCAATCACCTTGGCACCAACG
Found at i:60084463 original size:27 final size:27
Alignment explanation
Indices: 60084433--60084496 Score: 128
Period size: 27 Copynumber: 2.4 Consensus size: 27
60084423 TTTTTTTGGT
60084433 ATATTTTGGTAAATAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAGTTATA
60084460 ATATTTTGGTAAATAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAGTTATA
60084487 ATATTTTGGT
1 ATATTTTGGT
60084497 TATTTTTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (27 bp):
ATATTTTGGTAAATAAAAAAAGTTATA
Found at i:60086776 original size:26 final size:29
Alignment explanation
Indices: 60086733--60086788 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 29
60086723 CATAAAACCC
60086733 AATTACAACCCAAACCC-AAGACCCAACA
1 AATTACAACCCAAACCCAAAGACCCAACA
* *
60086761 AATTA-AA-CCAAGCCCAAATACCCAACA
1 AATTACAACCCAAACCCAAAGACCCAACA
60086788 A
1 A
60086789 GCCCAAAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 7 0.28
27 13 0.52
28 5 0.20
ACGTcount: A:0.52, C:0.36, G:0.04, T:0.09
Consensus pattern (29 bp):
AATTACAACCCAAACCCAAAGACCCAACA
Found at i:60088031 original size:20 final size:20
Alignment explanation
Indices: 60087976--60088032 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
60087966 CTATTACAAC
* *
60087976 TATT-TATATATACATACCT
1 TATTATATATATATATATCT
* *
60087995 TATTATATATCTTTATATCT
1 TATTATATATATATATATCT
*
60088015 TATTATGTATATATATAT
1 TATTATATATATATATAT
60088033 ATCTATCTCT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 4 0.13
20 26 0.87
ACGTcount: A:0.35, C:0.09, G:0.02, T:0.54
Consensus pattern (20 bp):
TATTATATATATATATATCT
Found at i:60088307 original size:35 final size:37
Alignment explanation
Indices: 60088239--60088308 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
60088229 ATTTTAAATA
* *
60088239 TATATATACATATATTCTTCTTATTTTTATTTTTACG
1 TATATACACATATATTCTTCTTATTGTTATTTTTACG
60088276 TATATACACATATATATCTT-TTA-TGTT-TTTTTA
1 TATATACACATATAT-TCTTCTTATTGTTATTTTTA
60088309 GTTTTATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 6 0.20
36 3 0.10
37 17 0.57
38 4 0.13
ACGTcount: A:0.29, C:0.10, G:0.03, T:0.59
Consensus pattern (37 bp):
TATATACACATATATTCTTCTTATTGTTATTTTTACG
Found at i:60088315 original size:16 final size:15
Alignment explanation
Indices: 60088294--60088327 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
60088284 CATATATATC
*
60088294 TTTTATGTTTTTTTAG
1 TTTTATATTTTTTT-G
60088310 TTTTATATTTTTTTG
1 TTTTATATTTTTTTG
60088325 TTT
1 TTT
60088328 ATTTCTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.79
Consensus pattern (15 bp):
TTTTATATTTTTTTG
Found at i:60088936 original size:109 final size:109
Alignment explanation
Indices: 60088740--60089046 Score: 449
Period size: 109 Copynumber: 2.8 Consensus size: 109
60088730 TTAAATAATA
* *
60088740 AAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTCTCGATTTTTC
1 AAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTC
*
60088805 TCGTTCAACCAAATAGCCAAATATCCTTTCAAAAATTCCAAAAT
66 TCGTTCAACCAAATAGCCAAATATCCTTCCAAAAATTCCAAAAT
* * * *
60088849 AAGGCAATGTTTTGCATTTGGGAATTCGAGAAAACATGCCCTAATATGCTGGGTTTCGATTTTTC
1 AAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTC
* * * *
60088914 TTGTTCAACCAAATGGCTAAATATCCTTCCAAAAATTTCAAAAT
66 TCGTTCAACCAAATAGCCAAATATCCTTCCAAAAATTCCAAAAT
* * *
60088958 AAGACAATGTTTTGCGTTTGGAAATTCGAG-GAACGTGCCCTAATGTGTTGGGTTTCGA--TTTC
1 AAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTC
* *
60089020 TCGTTTAACCAAATTGCCAAATATCCT
66 TCGTTCAACCAAATAGCCAAATATCCT
60089047 CTTGAATTTT
Statistics
Matches: 176, Mismatches: 22, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
106 27 0.15
108 24 0.14
109 125 0.71
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (109 bp):
AAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTC
TCGTTCAACCAAATAGCCAAATATCCTTCCAAAAATTCCAAAAT
Found at i:60090455 original size:11 final size:11
Alignment explanation
Indices: 60090436--60090479 Score: 65
Period size: 11 Copynumber: 4.2 Consensus size: 11
60090426 AACACCGAAC
*
60090436 TTTTTGGGTAA
1 TTTTCGGGTAA
60090447 TTTTCGGGTAA
1 TTTTCGGGTAA
60090458 --TTCGGGTAA
1 TTTTCGGGTAA
60090467 TTTTCGGGTAA
1 TTTTCGGGTAA
60090478 TT
1 TT
60090480 CGGTTAATTC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 9 0.30
11 21 0.70
ACGTcount: A:0.18, C:0.07, G:0.27, T:0.48
Consensus pattern (11 bp):
TTTTCGGGTAA
Found at i:60090463 original size:9 final size:9
Alignment explanation
Indices: 60090449--60090523 Score: 98
Period size: 9 Copynumber: 8.2 Consensus size: 9
60090439 TTGGGTAATT
60090449 TTCGGGTAA
1 TTCGGGTAA
60090458 TTCGGGTAA
1 TTCGGGTAA
60090467 TTTTCGGGTAA
1 --TTCGGGTAA
*
60090478 TTCGGTTAA
1 TTCGGGTAA
*
60090487 TTCGGTTAA
1 TTCGGGTAA
*
60090496 TTCGGTTAA
1 TTCGGGTAA
60090505 -TCGGGTAA
1 TTCGGGTAA
60090513 TTCGGGTAA
1 TTCGGGTAA
60090522 TT
1 TT
60090524 TTTAACCAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
8 7 0.11
9 45 0.74
11 9 0.15
ACGTcount: A:0.21, C:0.11, G:0.28, T:0.40
Consensus pattern (9 bp):
TTCGGGTAA
Found at i:60090466 original size:20 final size:20
Alignment explanation
Indices: 60090441--60090525 Score: 108
Period size: 20 Copynumber: 4.5 Consensus size: 20
60090431 CGAACTTTTT
60090441 GGGTAATTTTCGGGTAATTC
1 GGGTAATTTTCGGGTAATTC
60090461 GGGTAATTTTCGGGTAATTC
1 GGGTAATTTTCGGGTAATTC
* *
60090481 GGTTAA--TTCGGTTAATTC
1 GGGTAATTTTCGGGTAATTC
*
60090499 GGTTAA---TCGGGTAATTC
1 GGGTAATTTTCGGGTAATTC
60090516 GGGTAATTTT
1 GGGTAATTTT
60090526 TAACCAAAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
17 15 0.26
18 17 0.29
20 26 0.45
ACGTcount: A:0.21, C:0.09, G:0.28, T:0.41
Consensus pattern (20 bp):
GGGTAATTTTCGGGTAATTC
Found at i:60090702 original size:12 final size:12
Alignment explanation
Indices: 60090685--60090709 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
60090675 AGCAATTTCG
60090685 GGTCGGTTAACC
1 GGTCGGTTAACC
60090697 GGTCGGTTAACC
1 GGTCGGTTAACC
60090709 G
1 G
60090710 AATGAACACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:60105180 original size:3 final size:3
Alignment explanation
Indices: 60105174--60105245 Score: 90
Period size: 3 Copynumber: 24.0 Consensus size: 3
60105164 ACTAATTAGG
* *
60105174 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA GTA TTA GTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
60105222 TTA ATA TTA CTG TTA TTA TCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
60105246 CATTTCCATT
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.33, C:0.03, G:0.04, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:60105575 original size:4 final size:4
Alignment explanation
Indices: 60105561--60105590 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
60105551 TTTTTATAAT
60105561 TTTA TTTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA -TTTA TTTA TTTA TTTA TTTA TTTA T
60105591 GCTTTCATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:60111052 original size:14 final size:14
Alignment explanation
Indices: 60111033--60111070 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
60111023 AGTTTTAGTT
60111033 TATAAAGATAAT-AA
1 TATAAA-ATAATAAA
*
60111047 TATAAAAAAATAAA
1 TATAAAATAATAAA
60111061 TATAAAATAA
1 TATAAAATAA
60111071 AGTAAGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 4 0.19
14 17 0.81
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (14 bp):
TATAAAATAATAAA
Found at i:60117535 original size:16 final size:16
Alignment explanation
Indices: 60117514--60117544 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
60117504 CGTTTATGAG
60117514 TTAGGGATTTCAGAAC
1 TTAGGGATTTCAGAAC
*
60117530 TTAGGGATTTTAGAA
1 TTAGGGATTTCAGAA
60117545 TAGGGAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.35
Consensus pattern (16 bp):
TTAGGGATTTCAGAAC
Found at i:60119653 original size:41 final size:41
Alignment explanation
Indices: 60119607--60119703 Score: 124
Period size: 41 Copynumber: 2.4 Consensus size: 41
60119597 GTTCTTACAC
*
60119607 AAACGCCGCTATAGACC-CAAGATTTACCGGCGCTTCTCCAG
1 AAACGCCGCTATAGACCGCAA-ATTTACCGGCGATTCTCCAG
* * * *
60119648 GAACGCCGCTATAGACCGGAAATTTAGCGGCGATTCTCCAT
1 AAACGCCGCTATAGACCGCAAATTTACCGGCGATTCTCCAG
*
60119689 AAACGCCGCTTTAGA
1 AAACGCCGCTATAGA
60119704 GCGGAGCATC
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 46 0.96
42 2 0.04
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (41 bp):
AAACGCCGCTATAGACCGCAAATTTACCGGCGATTCTCCAG
Found at i:60120011 original size:114 final size:112
Alignment explanation
Indices: 60119812--60120159 Score: 500
Period size: 113 Copynumber: 3.1 Consensus size: 112
60119802 CGCTTAACGC
* * * *
60119812 AAAACGCCGCTGTAGAACGGATTATTAGCGGCGTTTGGGAAAATACCGCCACTAGTGTTCCAAAA
1 AAAACGCCGCTGTAGAACGGAGTATTAGCGGCGCTTGGGAAAA-ACCGCCACTAATGTTCCCAAA
* * *
60119877 TATACGAAAACGGCGTCGTTCTGTGTTACTGTATTTGCGACGCATTTTGT
65 TATATGAAAACGGCGTCGTTCTGTGTTACTCTA-TTGCGGCGC-TTTTGT
* * *
60119927 AAAACGCCGCTGAAGAATGGAGTATTAGCGGCGCTTGGGCAAAACCGCCACTAATGTTCCCAAAT
1 AAAACGCCGCTGTAGAACGGAGTATTAGCGGCGCTTGGGAAAAACCGCCACTAATGTTCCCAAAT
* * *
60119992 ATATGAAAACGGCGTCGTTCTGTATTACTCCATTGCGGCGCTTTGTAT
66 ATATGAAAACGGCGTCGTTCTGTGTTACTCTATTGCGGCGCTTT-TGT
*
60120040 AAAACGCCGCTGTAGAACGGAGTTTTAGCGGCGCTT-GGAAATAACCGCCACTAATGTTCCCAAA
1 AAAACGCCGCTGTAGAACGGAGTATTAGCGGCGCTTGGGAAA-AACCGCCACTAATGTTCCCAAA
*
60120104 TATATGAAAACGGCGTCGTTCTGTGTGACTCTATTGCGGCGCTTTTTGT
65 TATATGAAAACGGCGTCGTTCTGTGTTACTCTATTGCGGCGC-TTTTGT
60120153 AAAACGC
1 AAAACGC
60120160 TGTTAATGCT
Statistics
Matches: 209, Mismatches: 21, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
112 7 0.03
113 113 0.54
114 51 0.24
115 38 0.18
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (112 bp):
AAAACGCCGCTGTAGAACGGAGTATTAGCGGCGCTTGGGAAAAACCGCCACTAATGTTCCCAAAT
ATATGAAAACGGCGTCGTTCTGTGTTACTCTATTGCGGCGCTTTTGT
Found at i:60120283 original size:41 final size:40
Alignment explanation
Indices: 60120197--60120286 Score: 101
Period size: 40 Copynumber: 2.2 Consensus size: 40
60120187 TTTTATGTAG
* *
60120197 CGCCGCTAATGCTCGATATTTTGCGGCGTTTTTCGTAAAA
1 CGCCGCTAATGCTCGATATCTAGCGGCGTTTTTCGTAAAA
* * * *
60120237 TGCCGCTAATGCTCGAT-TACTAGTGGCGTTTTTTGTCCAAA
1 CGCCGCTAATGCTCGATAT-CTAGCGGCGTTTTTCGT-AAAA
60120278 CGCCGCTAA
1 CGCCGCTAA
60120287 AAGTGCCGCT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
39 1 0.02
40 29 0.71
41 11 0.27
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.33
Consensus pattern (40 bp):
CGCCGCTAATGCTCGATATCTAGCGGCGTTTTTCGTAAAA
Found at i:60122846 original size:27 final size:28
Alignment explanation
Indices: 60122815--60122868 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
60122805 AATTTTTGTA
*
60122815 ATTTTTATAATTAAAT-TTAAATAAAAT
1 ATTTTAATAATTAAATATTAAATAAAAT
* *
60122842 ATTTTAATCATTAAATATTAATTAAAA
1 ATTTTAATAATTAAATATTAAATAAAA
60122869 ATATAAGCCC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 14 0.61
28 9 0.39
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (28 bp):
ATTTTAATAATTAAATATTAAATAAAAT
Found at i:60131507 original size:2 final size:2
Alignment explanation
Indices: 60131500--60131536 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
60131490 TTTCTAAATT
60131500 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
60131537 TAAACAGATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:60134443 original size:9 final size:9
Alignment explanation
Indices: 60134426--60134455 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
60134416 TTTTTTCTCC
60134426 AAAACCCTA
1 AAAACCCTA
*
60134435 AAAATCCTA
1 AAAACCCTA
60134444 AAAACCCTA
1 AAAACCCTA
60134453 AAA
1 AAA
60134456 TCCTAAACCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.60, C:0.27, G:0.00, T:0.13
Consensus pattern (9 bp):
AAAACCCTA
Found at i:60134465 original size:15 final size:16
Alignment explanation
Indices: 60134426--60134480 Score: 76
Period size: 15 Copynumber: 3.4 Consensus size: 16
60134416 TTTTTTCTCC
60134426 AAAACCCTAAAAATCCT
1 AAAACCCT-AAAATCCT
60134443 AAAAACCCTAAAATCCT
1 -AAAACCCTAAAATCCT
*
60134460 -AAACCCTAAAATCCA
1 AAAACCCTAAAATCCT
60134475 AAAACC
1 AAAACC
60134481 TACAAGTGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
15 14 0.40
16 5 0.14
17 8 0.23
18 8 0.23
ACGTcount: A:0.55, C:0.31, G:0.00, T:0.15
Consensus pattern (16 bp):
AAAACCCTAAAATCCT
Found at i:60140187 original size:11 final size:11
Alignment explanation
Indices: 60140171--60140199 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
60140161 TATAGAAGAA
60140171 TGTAAAATTTC
1 TGTAAAATTTC
60140182 TGTAAAATTTC
1 TGTAAAATTTC
60140193 TGTAAAA
1 TGTAAAA
60140200 ATCAAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.41
Consensus pattern (11 bp):
TGTAAAATTTC
Found at i:60143192 original size:28 final size:28
Alignment explanation
Indices: 60143140--60143193 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
60143130 CCTAATCCTC
* *
60143140 AAGTTAAGTGTATTACTCGACCAAAAAA
1 AAGTTAAGTATATTACTCGAACAAAAAA
60143168 AAGTTAAGTATATTACAT-GAACAAAA
1 AAGTTAAGTATATTAC-TCGAACAAAA
60143194 GCCATTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 22 0.96
29 1 0.04
ACGTcount: A:0.50, C:0.11, G:0.13, T:0.26
Consensus pattern (28 bp):
AAGTTAAGTATATTACTCGAACAAAAAA
Found at i:60143569 original size:5 final size:5
Alignment explanation
Indices: 60143561--60143586 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
60143551 GAGATGGAAT
60143561 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
60143587 ATATTTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:60143586 original size:26 final size:26
Alignment explanation
Indices: 60143535--60143586 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
60143525 TGAAGTTTTC
* * *
60143535 TCGAATCGAGTCGAGTGAGATGGAAT
1 TCGAATCGAATCGAATGAGATCGAAT
60143561 TCGAATCGAATCGAATCGA-ATCGAAT
1 TCGAATCGAATCGAAT-GAGATCGAAT
60143587 ATATTTGTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (26 bp):
TCGAATCGAATCGAATGAGATCGAAT
Found at i:60144426 original size:30 final size:30
Alignment explanation
Indices: 60144392--60144448 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
60144382 AGAAAGGAGG
60144392 GGAGTAAAAGTTTTGGGGGGAAAGTGGGAA
1 GGAGTAAAAGTTTTGGGGGGAAAGTGGGAA
*
60144422 GGAGTAAAAGTTTTGGGGGGGAAGTGG
1 GGAGTAAAAGTTTTGGGGGGAAAGTGG
60144449 ACAGGTTTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.30, C:0.00, G:0.49, T:0.21
Consensus pattern (30 bp):
GGAGTAAAAGTTTTGGGGGGAAAGTGGGAA
Found at i:60147636 original size:42 final size:40
Alignment explanation
Indices: 60147568--60147693 Score: 129
Period size: 42 Copynumber: 3.2 Consensus size: 40
60147558 TGGCCCGACC
60147568 CAAAT-TATATATT-AA-ATATATATTTTTTATTTTTAAT
1 CAAATATATATATTAAATATATATATTTTTTATTTTTAAT
* * *
60147605 CAAATATACTTTTTTTAAATATATATATTTTTTGGACTTTTAAT
1 CAAATATA--TATATTAAATATATATATTTTTT--ATTTTTAAT
*
60147649 CTGAAT-TATATATTAAATATATATA--TTTTATTTTTAAT
1 C-AAATATATATATTAAATATATATATTTTTTATTTTTAAT
60147687 CAAATAT
1 CAAATAT
60147694 GGTTCGGGCC
Statistics
Matches: 72, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
37 8 0.11
38 12 0.17
40 8 0.11
41 2 0.03
42 28 0.39
44 11 0.15
45 3 0.04
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (40 bp):
CAAATATATATATTAAATATATATATTTTTTATTTTTAAT
Found at i:60162107 original size:29 final size:30
Alignment explanation
Indices: 60162074--60162153 Score: 85
Period size: 29 Copynumber: 2.7 Consensus size: 30
60162064 AACCTAAGAT
60162074 ATAAAAT-TTTAATATTTATATTTAATACA
1 ATAAAATATTTAATATTTATATTTAATACA
* * *
60162103 ATAAAATATTT-AT-TTGTGTTTTTAATATA
1 ATAAAATATTTAATATT-TATATTTAATACA
60162132 ATAAAATATTTATTATATTTAT
1 ATAAAATATTTA--ATATTTAT
60162154 GATAGTGCTT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
28 2 0.05
29 30 0.73
30 3 0.07
32 4 0.10
33 2 0.05
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.53
Consensus pattern (30 bp):
ATAAAATATTTAATATTTATATTTAATACA
Found at i:60163317 original size:62 final size:62
Alignment explanation
Indices: 60163220--60163341 Score: 217
Period size: 62 Copynumber: 2.0 Consensus size: 62
60163210 AAAAAGATAA
* *
60163220 CCACTAAGAATGAAACAATTGGTGAATTGAACTAAATCTATAACTTTAGGCATAATACATAG
1 CCACTAAGAATGAAACAATTGGTGAACTGAACTAAATCTACAACTTTAGGCATAATACATAG
*
60163282 CCACTAAGAATGAACCAATTGGTGAACTGAACTAAATCTACAACTTTAGGCATAATACAT
1 CCACTAAGAATGAAACAATTGGTGAACTGAACTAAATCTACAACTTTAGGCATAATACAT
60163342 GACTAATGAC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 57 1.00
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (62 bp):
CCACTAAGAATGAAACAATTGGTGAACTGAACTAAATCTACAACTTTAGGCATAATACATAG
Found at i:60163724 original size:20 final size:20
Alignment explanation
Indices: 60163701--60163743 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
60163691 TCATGGTTTT
*
60163701 AAAAATT-TTAAAAAATATTA
1 AAAAATTCTGAAAAAATA-TA
60163721 AAAAATTCTGAAAAAATATA
1 AAAAATTCTGAAAAAATATA
60163741 AAA
1 AAA
60163744 TATAGATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (20 bp):
AAAAATTCTGAAAAAATATA
Found at i:60167813 original size:2 final size:2
Alignment explanation
Indices: 60167806--60167850 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
60167796 AGCTGTAAAA
60167806 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
60167848 AG A
1 AG A
60167851 AAATCACATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:60169446 original size:31 final size:31
Alignment explanation
Indices: 60169408--60169467 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
60169398 ATTTGGCCAG
* *
60169408 TGAACTATTCGAAAG-TTTTCGTTTAAGTCAC
1 TGAACTATTCAAAAGCTTTT-ATTTAAGTCAC
60169439 TGAACTATTCAAAAGCTTTTATTTAAGTC
1 TGAACTATTCAAAAGCTTTTATTTAAGTC
60169468 GTCGTGCTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (31 bp):
TGAACTATTCAAAAGCTTTTATTTAAGTCAC
Found at i:60178696 original size:20 final size:20
Alignment explanation
Indices: 60178659--60178704 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
60178649 AATGGGCATG
* *
60178659 AATTATTATTTAAATAATGA
1 AATTATTATCTAAATAATCA
**
60178679 AATTATTATCTACTTAATCA
1 AATTATTATCTAAATAATCA
60178699 AATTAT
1 AATTAT
60178705 AAAAATATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.46
Consensus pattern (20 bp):
AATTATTATCTAAATAATCA
Found at i:60180474 original size:29 final size:30
Alignment explanation
Indices: 60180428--60180484 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
60180418 GCAATGTTAT
60180428 ACATGAACTTTGATTTTG-TGCAATTTTGA
1 ACATGAACTTTGATTTTGATGCAATTTTGA
*
60180457 ACATGATACTTTGA-TTTGATTCAATTTT
1 ACATGA-ACTTTGATTTTGATGCAATTTT
60180485 TTTTAGCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.47
Consensus pattern (30 bp):
ACATGAACTTTGATTTTGATGCAATTTTGA
Found at i:60180836 original size:55 final size:55
Alignment explanation
Indices: 60180765--60180879 Score: 203
Period size: 55 Copynumber: 2.1 Consensus size: 55
60180755 CACAAAATCT
60180765 TTCAAATGAAAATAAAAGCAAAGCAAAAAAAACCACTTCATGAAAACATCAACAA
1 TTCAAATGAAAATAAAAGCAAAGCAAAAAAAACCACTTCATGAAAACATCAACAA
* * *
60180820 TTCAAATGAAAATAAAAGCAAAGCAAAAAAAACCACTTTATGGAATCATCAACAA
1 TTCAAATGAAAATAAAAGCAAAGCAAAAAAAACCACTTCATGAAAACATCAACAA
60180875 TTCAA
1 TTCAA
60180880 CTTGGAATAG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.57, C:0.17, G:0.08, T:0.17
Consensus pattern (55 bp):
TTCAAATGAAAATAAAAGCAAAGCAAAAAAAACCACTTCATGAAAACATCAACAA
Found at i:60184448 original size:12 final size:12
Alignment explanation
Indices: 60184430--60184459 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
60184420 TATCGCAAAG
60184430 AAAATAGAAATA
1 AAAATAGAAATA
*
60184442 GAAATAGAAATA
1 AAAATAGAAATA
60184454 AAAATA
1 AAAATA
60184460 AAGAACACAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (12 bp):
AAAATAGAAATA
Found at i:60184976 original size:31 final size:33
Alignment explanation
Indices: 60184941--60185002 Score: 83
Period size: 31 Copynumber: 1.9 Consensus size: 33
60184931 ATGTGTAGAA
*
60184941 TTGAATCAAAAT-TAAAGTTT-TATGTATATTT
1 TTGAATCAAAATCAAAAGTTTATATGTATATTT
*
60184972 TTGAATTAAAATCAAAAGTTTAATATGTATA
1 TTGAATCAAAATCAAAAGTTT-ATATGTATA
60185003 ATTGCACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 11 0.42
32 7 0.27
34 8 0.31
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.44
Consensus pattern (33 bp):
TTGAATCAAAATCAAAAGTTTATATGTATATTT
Found at i:60185154 original size:53 final size:54
Alignment explanation
Indices: 60185097--60185208 Score: 208
Period size: 54 Copynumber: 2.1 Consensus size: 54
60185087 CACAGAATCT
*
60185097 TTCAAATGAAAATAAAAGCAAAGC-AAAAAACTACTTTATGGAAACATCAACAA
1 TTCAAATGAAAATAAAAGCAAAGCAAAAAAACCACTTTATGGAAACATCAACAA
60185150 TTCAAATGAAAATAAAAGCAAAGCAAAAAAACCACTTTATGGAAACATCAACAA
1 TTCAAATGAAAATAAAAGCAAAGCAAAAAAACCACTTTATGGAAACATCAACAA
60185204 TTCAA
1 TTCAA
60185209 CTTGGAATAG
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
53 24 0.42
54 33 0.58
ACGTcount: A:0.56, C:0.16, G:0.09, T:0.19
Consensus pattern (54 bp):
TTCAAATGAAAATAAAAGCAAAGCAAAAAAACCACTTTATGGAAACATCAACAA
Found at i:60186360 original size:31 final size:30
Alignment explanation
Indices: 60186320--60186379 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
60186310 TTTAAATATG
60186320 TACATTGAATCA-AAATCAAAGCTTCATGTA
1 TACATTGAATCACAAATCAAA-CTTCATGTA
* *
60186350 TACATATGAATTACAATTCAAACTTCATGT
1 TACAT-TGAATCACAAATCAAACTTCATGT
60186380 GTATAATTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 5 0.19
31 14 0.54
32 7 0.27
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.33
Consensus pattern (30 bp):
TACATTGAATCACAAATCAAACTTCATGTA
Found at i:60191725 original size:15 final size:15
Alignment explanation
Indices: 60191701--60191732 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
60191691 TATGCATGCA
*
60191701 AAATATAAAAGACAT
1 AAATACAAAAGACAT
60191716 AAATACAAAAGACAT
1 AAATACAAAAGACAT
60191731 AA
1 AA
60191733 TAGTGAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATACAAAAGACAT
Found at i:60195059 original size:13 final size:13
Alignment explanation
Indices: 60195024--60195061 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
60195014 TTTTTATGTA
60195024 AAATCTAAAAAAT
1 AAATCTAAAAAAT
*
60195037 GAAT-TAAAAAATT
1 AAATCTAAAAAA-T
60195050 AAATCTAAAAAA
1 AAATCTAAAAAA
60195062 ATATAGATAG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
12 7 0.33
13 7 0.33
14 7 0.33
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (13 bp):
AAATCTAAAAAAT
Found at i:60200534 original size:18 final size:18
Alignment explanation
Indices: 60200511--60200554 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 18
60200501 CTATTCACCT
60200511 AACCCAATTATCC-AACCC
1 AACCCAATTA-CCTAACCC
60200529 AACCCAATTACCTAACCC
1 AACCCAATTACCTAACCC
60200547 AACCCAAT
1 AACCCAAT
60200555 CATAAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 2 0.08
18 23 0.92
ACGTcount: A:0.41, C:0.43, G:0.00, T:0.16
Consensus pattern (18 bp):
AACCCAATTACCTAACCC
Found at i:60200722 original size:18 final size:18
Alignment explanation
Indices: 60200671--60200724 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
60200661 ATTATATAGT
*
60200671 GATTCAATTCGGTTAATTC
1 GATT-AATTCGGGTAATTC
** **
60200690 GGGTAATTCATGTAATTC
1 GATTAATTCGGGTAATTC
60200708 GATTAATTCGGGTAATT
1 GATTAATTCGGGTAATT
60200725 TTTAACCAAA
Statistics
Matches: 26, Mismatches: 9, Indels: 1
0.72 0.25 0.03
Matches are distributed among these distances:
18 24 0.92
19 2 0.08
ACGTcount: A:0.28, C:0.11, G:0.20, T:0.41
Consensus pattern (18 bp):
GATTAATTCGGGTAATTC
Found at i:60207043 original size:16 final size:17
Alignment explanation
Indices: 60207006--60207060 Score: 69
Period size: 17 Copynumber: 3.3 Consensus size: 17
60206996 TACGAATTTT
60207006 TTTTTAAAACACGACAA
1 TTTTTAAAACACGACAA
* *
60207023 TTTTTGAAACACGATAA
1 TTTTTAAAACACGACAA
60207040 TTTTTCAAAACAC-A-AA
1 TTTTT-AAAACACGACAA
60207056 TTTTT
1 TTTTT
60207061 TTTAAAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
16 7 0.21
17 21 0.62
18 6 0.18
ACGTcount: A:0.42, C:0.15, G:0.05, T:0.38
Consensus pattern (17 bp):
TTTTTAAAACACGACAA
Found at i:60207044 original size:36 final size:34
Alignment explanation
Indices: 60206977--60207060 Score: 82
Period size: 36 Copynumber: 2.4 Consensus size: 34
60206967 GAAATTTTCG
* * * *
60206977 AACACGAAAATTTTAGAAATACGAATTTTTTTTTAA
1 AACACG-AAATTTTTGAAACACGAA-TATTTTTCAA
60207013 AACACGACAATTTTTGAAACACG-ATAATTTTTCAA
1 AACACGA-AATTTTTGAAACACGAAT-ATTTTTCAA
60207048 AACAC-AAATTTTT
1 AACACGAAATTTTT
60207061 TTTAAAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
33 7 0.17
34 2 0.05
35 14 0.33
36 19 0.45
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.36
Consensus pattern (34 bp):
AACACGAAATTTTTGAAACACGAATATTTTTCAA
Found at i:60207060 original size:53 final size:51
Alignment explanation
Indices: 60206953--60207069 Score: 130
Period size: 53 Copynumber: 2.3 Consensus size: 51
60206943 TTTTTTTTTG
* * *
60206953 TTTTTTAAAAAAACGAAATTTTCGAACACGAAAATTTTAGAAATACGAATT
1 TTTTTTTAAAAAACGAAATTTTCGAACACGAAAATTTTAGAAACACGAAAT
* * *
60207004 TTTTTTTAAAACACGACAATTTTTGAAACACGATAATTTTTCA-AAACAC-AAAT
1 TTTTTTTAAAAAACGA-AATTTTCG-AACACGA-AAATTTT-AGAAACACGAAAT
60207057 TTTTTTTAAAAAA
1 TTTTTTTAAAAAA
60207070 AAAACATGAC
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
51 14 0.25
52 7 0.13
53 22 0.40
54 11 0.20
55 1 0.02
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.37
Consensus pattern (51 bp):
TTTTTTTAAAAAACGAAATTTTCGAACACGAAAATTTTAGAAACACGAAAT
Found at i:60207173 original size:18 final size:18
Alignment explanation
Indices: 60207102--60207324 Score: 178
Period size: 17 Copynumber: 12.7 Consensus size: 18
60207092 ACTAGAGTCA
* *
60207102 TTGAAAACATGGAAATTT
1 TTGAAAACACGAAAATTT
* *
60207120 GTGAAAA-ACGAAATTTT
1 TTGAAAACACGAAAATTT
* *
60207137 TTG-AAGCAC-AGAATTTT
1 TTGAAAACACGA-AAATTT
60207154 TTAGAAAACACGAAAA-TT
1 TT-GAAAACACGAAAATTT
***
60207172 TTGAAAACACGTGGATTT
1 TTGAAAACACGAAAATTT
**
60207190 TTG-AAACACGAATTTTTT
1 TTGAAAACACGAA-AATTT
*
60207208 TTGAAAATACGAAAATTT
1 TTGAAAACACGAAAATTT
60207226 TTGAAAACAC-ATAAATTT
1 TTGAAAACACGA-AAATTT
* **
60207244 TT-AAAACTCGGGAATTT
1 TTGAAAACACGAAAATTT
60207261 TTG-AAACACTG-AAATTT
1 TTGAAAACAC-GAAAATTT
*
60207278 TTGAAAACACGAGAATTT
1 TTGAAAACACGAAAATTT
*
60207296 TTTAAAACACGAAAATTT
1 TTGAAAACACGAAAATTT
60207314 TTG-AAACACGA
1 TTGAAAACACGA
60207325 GAAAAAATTT
Statistics
Matches: 163, Mismatches: 28, Indels: 29
0.74 0.13 0.13
Matches are distributed among these distances:
16 3 0.02
17 72 0.44
18 72 0.44
19 15 0.09
20 1 0.01
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.32
Consensus pattern (18 bp):
TTGAAAACACGAAAATTT
Found at i:60207179 original size:17 final size:17
Alignment explanation
Indices: 60207102--60207324 Score: 170
Period size: 18 Copynumber: 12.7 Consensus size: 17
60207092 ACTAGAGTCA
*
60207102 TTGAAAACATGGAAATTT
1 TTGAAAACA-CGAAATTT
*
60207120 GTGAAAA-ACGAAATTTT
1 TTGAAAACACGAAA-TTT
* *
60207137 TTG-AAGCACAGAATTTT
1 TTGAAAACAC-GAAATTT
*
60207154 TTAGAAAACACGAAAATT
1 TT-GAAAACACGAAATTT
**
60207172 TTGAAAACACGTGGATTT
1 TTGAAAACACG-AAATTT
*
60207190 TTG-AAACACGAATTTTTT
1 TTGAAAACACGAA--ATTT
*
60207208 TTGAAAATACGAAAATTT
1 TTGAAAACACG-AAATTT
*
60207226 TTGAAAACACATAAATTT
1 TTGAAAACAC-GAAATTT
* *
60207244 TT-AAAACTCGGGAATTT
1 TTGAAAACAC-GAAATTT
60207261 TTG-AAACACTGAAATTT
1 TTGAAAACAC-GAAATTT
60207278 TTGAAAACACGAGAATTT
1 TTGAAAACACGA-AATTT
*
60207296 TTTAAAACACGAAAATTT
1 TTGAAAACACG-AAATTT
60207314 TTG-AAACACGA
1 TTGAAAACACGA
60207325 GAAAAAATTT
Statistics
Matches: 163, Mismatches: 27, Indels: 32
0.73 0.12 0.14
Matches are distributed among these distances:
16 7 0.04
17 65 0.40
18 77 0.47
19 12 0.07
20 2 0.01
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.32
Consensus pattern (17 bp):
TTGAAAACACGAAATTT
Found at i:60207191 original size:53 final size:54
Alignment explanation
Indices: 60207134--60207324 Score: 157
Period size: 53 Copynumber: 3.6 Consensus size: 54
60207124 AAAACGAAAT
*
60207134 TTTTTGAAGCACAGAA-TTTTTTAGAAAACACGAAAA-TTTTGAAAACACGTGGA
1 TTTTTGAAACAC-GAATTTTTTTAGAAAACACGAAAATTTTTGAAAACACGTGGA
* * * **
60207187 TTTTTGAAACACGAATTTTTTTTGAAAATACGAAAATTTTTGAAAACACATAAA
1 TTTTTGAAACACGAATTTTTTTAGAAAACACGAAAATTTTTGAAAACACGTGGA
* * * *
60207241 TTTTTAAAACTCGGGAA--TTTTT-G-AAACACTG-AAATTTTTGAAAACACGAGAA
1 TTTTTGAAACAC--GAATTTTTTTAGAAAACAC-GAAAATTTTTGAAAACACGTGGA
* **
60207293 TTTTTTAAAACACGAAAATTTTT-G-AAACACGA
1 -TTTTTGAAACACGAATTTTTTTAGAAAACACGA
60207325 GAAAAAATTT
Statistics
Matches: 116, Mismatches: 13, Indels: 18
0.79 0.09 0.12
Matches are distributed among these distances:
51 3 0.03
52 27 0.23
53 54 0.47
54 29 0.25
56 3 0.03
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (54 bp):
TTTTTGAAACACGAATTTTTTTAGAAAACACGAAAATTTTTGAAAACACGTGGA
Found at i:60207662 original size:6 final size:6
Alignment explanation
Indices: 60207642--60207691 Score: 52
Period size: 6 Copynumber: 8.7 Consensus size: 6
60207632 AAAAGTATTC
* *
60207642 AAAA-T AAAA-T AAAATT AAAATT -GAATT AAATTT AAAATTT AAAATT
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAA-TT AAAATT
60207688 AAAA
1 AAAA
60207692 ATATAAATAC
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
5 13 0.34
6 19 0.50
7 6 0.16
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (6 bp):
AAAATT
Found at i:60207740 original size:26 final size:25
Alignment explanation
Indices: 60207696--60207752 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
60207686 TTAAAAATAT
* *
60207696 AAATACAAAAATATAAAAATGCACA
1 AAATACAAAAATATAAAAATGAAAA
* *
60207721 AAATACTAATAATATTAAAATGAAAA
1 AAATAC-AAAAATATAAAAATGAAAA
60207747 AAATAC
1 AAATAC
60207753 GAGCATTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
25 6 0.22
26 21 0.78
ACGTcount: A:0.67, C:0.09, G:0.04, T:0.21
Consensus pattern (25 bp):
AAATACAAAAATATAAAAATGAAAA
Found at i:60207870 original size:17 final size:17
Alignment explanation
Indices: 60207850--60207891 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
60207840 TTTTTTTCCC
*
60207850 TTTTTTCTTTTCTCTCT
1 TTTTTTCTTCTCTCTCT
* *
60207867 TTTTTTCTTCTCTTTTT
1 TTTTTTCTTCTCTCTCT
60207884 TTTTTTCT
1 TTTTTTCT
60207892 GGCCTGCTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTTTCTTCTCTCTCT
Found at i:60207881 original size:29 final size:28
Alignment explanation
Indices: 60207837--60207891 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
60207827 CAAATTGAAC
60207837 CTTTTTTTTTCCCTTTTTTCTTTTCTCT
1 CTTTTTTTTTCCCTTTTTTCTTTTCTCT
* *
60207865 CTTTTTTTCTTCTCTTTTTTTTTTTCT
1 CTTTTTTT-TTCCCTTTTTTCTTTTCT
60207892 GGCCTGCTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 8 0.33
29 16 0.67
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (28 bp):
CTTTTTTTTTCCCTTTTTTCTTTTCTCT
Found at i:60208116 original size:7 final size:7
Alignment explanation
Indices: 60208104--60208158 Score: 74
Period size: 7 Copynumber: 7.6 Consensus size: 7
60208094 TATTTATTTA
60208104 TTTTTCT
1 TTTTTCT
60208111 TTTTTCT
1 TTTTTCT
60208118 TTTTTCT
1 TTTTTCT
*
60208125 TTCTTCTT
1 TTTTTC-T
60208133 TTTCTTCT
1 TTT-TTCT
60208141 TTTTTCT
1 TTTTTCT
*
60208148 TTCTTCT
1 TTTTTCT
60208155 TTTT
1 TTTT
60208159 CTTCTTCCCC
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
7 32 0.76
8 7 0.17
9 3 0.07
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTTCT
Found at i:60208136 original size:9 final size:9
Alignment explanation
Indices: 60208124--60208164 Score: 54
Period size: 9 Copynumber: 5.0 Consensus size: 9
60208114 TTCTTTTTTC
60208124 TTTCTTCTT
1 TTTCTTCTT
60208133 TTTCTTC-T
1 TTTCTTCTT
60208141 TTT-TTC--
1 TTTCTTCTT
60208147 TTTCTTCTT
1 TTTCTTCTT
60208156 TTTCTTCTT
1 TTTCTTCTT
60208165 CCCCGTTCAG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
6 3 0.10
7 6 0.21
8 4 0.14
9 16 0.55
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTCTTCTT
Found at i:60208144 original size:23 final size:23
Alignment explanation
Indices: 60208110--60208164 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
60208100 TTTATTTTTC
60208110 TTTT-TTCTTTTTTCTTTCTTCT
1 TTTTCTTCTTTTTTCTTTCTTCT
60208132 TTTTCTTCTTTTTTCTTTCTTCT
1 TTTTCTTCTTTTTTCTTTCTTCT
60208155 TTTTCTTCTT
1 TTTTCTTCTT
60208165 CCCCGTTCAG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 4 0.12
23 28 0.88
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTTCTTCTTTTTTCTTTCTTCT
Found at i:60208161 original size:20 final size:21
Alignment explanation
Indices: 60208090--60208158 Score: 86
Period size: 23 Copynumber: 3.2 Consensus size: 21
60208080 CCCGACTGAA
* *
60208090 TTTTTATTTATTTATTT-TTCT
1 TTTTTCTTT-TTTCTTTCTTCT
60208111 TTTTTCTTTTTTCTTTCTTCTT
1 TTTTTCTTTTTTCTTTCTTC-T
60208133 TTTCTTCTTTTTTCTTTCTTCT
1 TTT-TTCTTTTTTCTTTCTTCT
60208155 TTTT
1 TTTT
60208159 CTTCTTCCCC
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
20 6 0.14
21 12 0.28
22 8 0.19
23 17 0.40
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.81
Consensus pattern (21 bp):
TTTTTCTTTTTTCTTTCTTCT
Found at i:60208279 original size:17 final size:17
Alignment explanation
Indices: 60208247--60208323 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 17
60208237 ACGCTCCTCC
60208247 CTTTTCTTTCTCTTCTTTT
1 CTTTT-TTT-TCTTCTTTT
60208266 CTTTTTTTTCTTC--TT
1 CTTTTTTTTCTTCTTTT
*
60208281 -TGTTTTTTCTTGCTTGTT
1 CTTTTTTTTCTT-CTT-TT
*
60208299 GTTGTTTTTTCTT-TCTTT
1 CTT-TTTTTTCTTCT-TTT
60208317 CTTTTTT
1 CTTTTTT
60208324 ATTTTTGCTT
Statistics
Matches: 48, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
14 10 0.21
15 3 0.06
17 9 0.19
18 10 0.21
19 7 0.15
20 9 0.19
ACGTcount: A:0.00, C:0.17, G:0.06, T:0.77
Consensus pattern (17 bp):
CTTTTTTTTCTTCTTTT
Found at i:60208328 original size:20 final size:19
Alignment explanation
Indices: 60208248--60208320 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 19
60208238 CGCTCCTCCC
60208248 TTTTCTTTCTCTTCTTT-TCT
1 TTTTCTTTCT-TTCTTTGT-T
60208268 TTTT-TTTC-TTCTTTGTT
1 TTTTCTTTCTTTCTTTGTT
*
60208285 TTTTCTTGCTTGT-TGTTGTT
1 TTTTCTTTCTT-TCT-TTGTT
60208305 TTTTCTTTCTTTCTTT
1 TTTTCTTTCTTTCTTT
60208321 TTTATTTTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
17 11 0.24
18 4 0.09
19 9 0.20
20 21 0.47
ACGTcount: A:0.00, C:0.16, G:0.07, T:0.77
Consensus pattern (19 bp):
TTTTCTTTCTTTCTTTGTT
Found at i:60208680 original size:30 final size:30
Alignment explanation
Indices: 60208646--60208794 Score: 169
Period size: 30 Copynumber: 5.0 Consensus size: 30
60208636 GGGCCGAAAC
* * *
60208646 GTAATTTTGAGAAAGTTAAAGGGTTCAAAT
1 GTAATTTTAAGAAAGTTTAAGGGTTAAAAT
* *
60208676 GTAATTTCAAGAAAGTTTAAGGGTCAAAAT
1 GTAATTTTAAGAAAGTTTAAGGGTTAAAAT
* * *
60208706 GTAA-TTT-AGAAAAGTTTAGGGGTTGAACT
1 GTAATTTTAAG-AAAGTTTAAGGGTTAAAAT
*
60208735 GTAATTTTAAGAAAGTTTAGGGGTTAAAAT
1 GTAATTTTAAGAAAGTTTAAGGGTTAAAAT
*
60208765 GCAATTTT-AGAAAAGTTTAAGGGTTAAAAT
1 GTAATTTTAAG-AAAGTTTAAGGGTTAAAAT
60208795 ACAAAAAAAT
Statistics
Matches: 101, Mismatches: 14, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
28 2 0.02
29 23 0.23
30 74 0.73
31 2 0.02
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.34
Consensus pattern (30 bp):
GTAATTTTAAGAAAGTTTAAGGGTTAAAAT
Done.