Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 178 of 190
Found at i:51951200 original size:32 final size:31
Alignment explanation
Indices: 51951138--51951200 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
51951128 AAATGTTACG
* * *
51951138 TTTTGGTCACTTATGTTATTGTCTTGTAACA
1 TTTTAGTCACTGATGTTATTGTCATGTAACA
51951169 TTTTAGTCACTGAGTGTTAATTGTCAT-TAACA
1 TTTTAGTCACTGA-TGTT-ATTGTCATGTAACA
51951201 GTGTAACAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 11 0.41
32 9 0.33
33 7 0.26
ACGTcount: A:0.24, C:0.13, G:0.16, T:0.48
Consensus pattern (31 bp):
TTTTAGTCACTGATGTTATTGTCATGTAACA
Found at i:51967185 original size:45 final size:42
Alignment explanation
Indices: 51967115--51967209 Score: 136
Period size: 45 Copynumber: 2.2 Consensus size: 42
51967105 TTAAATTATT
*
51967115 AAAAAATAAATAAAATATAGTTATAAACAATTAAAAATCTTA
1 AAAAAATAAATAAAATATAGCTATAAACAATTAAAAATCTTA
*
51967157 AAAAAATAAAATATAAGATATAGCTATAAAGAATTAAAAATCTTA
1 AAAAAAT-AAATA-AA-ATATAGCTATAAACAATTAAAAATCTTA
51967202 AAAGAAAT
1 AAA-AAAT
51967210 CTTGGTTTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
42 7 0.15
43 5 0.11
44 2 0.04
45 29 0.62
46 4 0.09
ACGTcount: A:0.64, C:0.04, G:0.05, T:0.26
Consensus pattern (42 bp):
AAAAAATAAATAAAATATAGCTATAAACAATTAAAAATCTTA
Found at i:51978878 original size:27 final size:27
Alignment explanation
Indices: 51978848--51978941 Score: 73
Period size: 29 Copynumber: 3.1 Consensus size: 27
51978838 ATTAATAATT
51978848 TTATATACAAAATAATACTAACTAAAA
1 TTATATACAAAATAATACTAACTAAAA
* *
51978875 TTATTAATAACTAACACAATAATAAT-ATTAATAA
1 TTA-T-AT-AC--A-A-AATAATACTAACTAA-AA
51978909 TTTTATATACAAAATAATACTAACTAAAA
1 --TTATATACAAAATAATACTAACTAAAA
51978938 TTAT
1 TTAT
51978942 TAATAACTAA
Statistics
Matches: 52, Mismatches: 4, Indels: 22
0.67 0.05 0.28
Matches are distributed among these distances:
27 7 0.13
28 1 0.02
29 12 0.23
30 7 0.13
31 1 0.02
32 1 0.02
33 7 0.13
34 12 0.23
35 1 0.02
36 3 0.06
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (27 bp):
TTATATACAAAATAATACTAACTAAAA
Found at i:51978887 original size:16 final size:16
Alignment explanation
Indices: 51978866--51978951 Score: 56
Period size: 16 Copynumber: 5.4 Consensus size: 16
51978856 AAAATAATAC
51978866 TAACTAAAATTATTAA
1 TAACTAAAATTATTAA
* *
51978882 TAACTAACACAATAATAA
1 TAACTAA-A-ATTATTAA
*
51978900 T-ATTAATAATT-TT-A
1 TAACTAA-AATTATTAA
* *
51978914 TATAC-AAAA-TAATAC
1 TA-ACTAAAATTATTAA
51978929 TAACTAAAATTATTAA
1 TAACTAAAATTATTAA
51978945 TAACTAA
1 TAACTAA
51978952 CTACAAAAAT
Statistics
Matches: 51, Mismatches: 11, Indels: 16
0.65 0.14 0.21
Matches are distributed among these distances:
13 1 0.02
14 7 0.14
15 9 0.18
16 21 0.41
17 6 0.12
18 7 0.14
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (16 bp):
TAACTAAAATTATTAA
Found at i:51978889 original size:20 final size:20
Alignment explanation
Indices: 51978860--51978954 Score: 58
Period size: 20 Copynumber: 4.7 Consensus size: 20
51978850 ATATACAAAA
51978860 TAAT-ACTAACTAAAATTAT
1 TAATAACTAACTAAAATTAT
*
51978879 TAATAACTAACACAATAATAATAT
1 TAATAACTAAC-TAA-AAT--TAT
*
51978903 TAATAATTTTATA-TACAAA--A-
1 TAATAA--CTA-ACTA-AAATTAT
51978923 TAAT-ACTAACTAAAATTAT
1 TAATAACTAACTAAAATTAT
51978942 TAATAACTAACTA
1 TAATAACTAACTA
51978955 CAAAAATAAT
Statistics
Matches: 58, Mismatches: 4, Indels: 27
0.65 0.04 0.30
Matches are distributed among these distances:
16 4 0.07
17 4 0.07
18 1 0.02
19 9 0.16
20 18 0.31
21 3 0.05
22 3 0.05
24 9 0.16
25 3 0.05
26 3 0.05
27 1 0.02
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.35
Consensus pattern (20 bp):
TAATAACTAACTAAAATTAT
Found at i:51978976 original size:63 final size:63
Alignment explanation
Indices: 51978816--51978970 Score: 283
Period size: 63 Copynumber: 2.4 Consensus size: 63
51978806 CCACTAATCC
51978816 TAATAACTAACACAATAATAATATTAATAATTTTATATACAAAATAATACTAACTAAAATTAT
1 TAATAACTAACACAATAATAATATTAATAATTTTATATACAAAATAATACTAACTAAAATTAT
51978879 TAATAACTAACACAATAATAATATTAATAATTTTATATACAAAATAATACTAACTAAAATTAT
1 TAATAACTAACACAATAATAATATTAATAATTTTATATACAAAATAATACTAACTAAAATTAT
* *
51978942 TAATAACTAACTACAAAAATAATACTAAT
1 TAATAACTAAC-ACAATAATAATATTAAT
51978971 TTTTTACTAA
Statistics
Matches: 89, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
63 74 0.83
64 15 0.17
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (63 bp):
TAATAACTAACACAATAATAATATTAATAATTTTATATACAAAATAATACTAACTAAAATTAT
Found at i:51979010 original size:63 final size:62
Alignment explanation
Indices: 51978816--51978992 Score: 270
Period size: 63 Copynumber: 2.8 Consensus size: 62
51978806 CCACTAATCC
51978816 TAATAACTAACACAATAATAATATTAATAATTTTATATACAAAATAATACTAACTAAAATTAT
1 TAATAACTAACACAATAATAATATTAAT-ATTTTATATACAAAATAATACTAACTAAAATTAT
51978879 TAATAACTAACACAATAATAATATTAATAATTTTATATACAAAATAATACTAACTAAAATTAT
1 TAATAACTAACACAATAATAATATTAAT-ATTTTATATACAAAATAATACTAACTAAAATTAT
* * *
51978942 TAATAACTAACTACAAAAATAATACTAAT-TTTT-TACTA-ACAATAATACTAA
1 TAATAACTAAC-ACAATAATAATATTAATATTTTATA-TACAAAATAATACTAA
51978993 GTAACATCTT
Statistics
Matches: 109, Mismatches: 3, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
61 14 0.13
62 6 0.06
63 74 0.68
64 15 0.14
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (62 bp):
TAATAACTAACACAATAATAATATTAATATTTTATATACAAAATAATACTAACTAAAATTAT
Found at i:51979376 original size:27 final size:27
Alignment explanation
Indices: 51979303--51979380 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 27
51979293 ATAACACGAG
*
51979303 TGGTGCCGCCAACAGAGAAT-CCTTGTT
1 TGGTGCCGCCAACAGAG-TTCCCTTGTT
* *
51979330 TGGTGCCACCAACAGGGTTCCCTTGTT
1 TGGTGCCGCCAACAGAGTTCCCTTGTT
*
51979357 TGGTGCCGCCAACAGTGTTCCCTT
1 TGGTGCCGCCAACAGAGTTCCCTT
51979381 CACCCAGGGA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
26 1 0.02
27 44 0.98
ACGTcount: A:0.17, C:0.29, G:0.26, T:0.28
Consensus pattern (27 bp):
TGGTGCCGCCAACAGAGTTCCCTTGTT
Found at i:51979481 original size:27 final size:29
Alignment explanation
Indices: 51979428--51979498 Score: 103
Period size: 27 Copynumber: 2.5 Consensus size: 29
51979418 CTGTTTTTTT
51979428 TATATATTTTGGTAAATAAAAAAAAAT-TA
1 TATATATTTTGGTAAAT-AAAAAAAATGTA
51979457 TATATATTTTGGTAAAT-AAAAAAATGTA
1 TATATATTTTGGTAAATAAAAAAAATGTA
*
51979485 TA-ACATTTTGGTAA
1 TATATATTTTGGTAA
51979499 TTTTTTAATT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
27 19 0.47
28 4 0.10
29 17 0.43
ACGTcount: A:0.49, C:0.01, G:0.10, T:0.39
Consensus pattern (29 bp):
TATATATTTTGGTAAATAAAAAAAATGTA
Found at i:51981844 original size:23 final size:23
Alignment explanation
Indices: 51981818--51981863 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
51981808 TTATAACTTT
51981818 TTTTTTATTTACCAAAATATATA
1 TTTTTTATTTACCAAAATATATA
51981841 TTTTTTATTTACCAAAATATATA
1 TTTTTTATTTACCAAAATATATA
51981864 AATAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTTTTATTTACCAAAATATATA
Found at i:51981945 original size:27 final size:27
Alignment explanation
Indices: 51981915--51982015 Score: 105
Period size: 27 Copynumber: 3.7 Consensus size: 27
51981905 CCTTGGTCAC
** *
51981915 GCCAATGGGATTGGCGGCACCAAAGGT
1 GCCAATGTCATTGGCGGCACCAATGGT
* *
51981942 GCCAAAGTCATTGGTGGCACCAATGGT
1 GCCAATGTCATTGGCGGCACCAATGGT
**
51981969 GCCAATACCATTGGCGGCACCAATGGT
1 GCCAATGTCATTGGCGGCACCAATGGT
* *
51981996 GCCGTAT-TGATTGGCGGCAC
1 GCC-AATGTCATTGGCGGCAC
51982016 TACTCGTATT
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
27 59 0.97
28 2 0.03
ACGTcount: A:0.24, C:0.25, G:0.32, T:0.20
Consensus pattern (27 bp):
GCCAATGTCATTGGCGGCACCAATGGT
Found at i:51982115 original size:11 final size:11
Alignment explanation
Indices: 51982099--51982138 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
51982089 GTTGTTGCGG
51982099 AAAAGAAGAGA
1 AAAAGAAGAGA
51982110 AAAAG-AGAGA
1 AAAAGAAGAGA
*
51982120 AAAAGAGGAGA
1 AAAAGAAGAGA
51982131 AAAAGAAG
1 AAAAGAAG
51982139 GAATTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 10 0.38
11 16 0.62
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (11 bp):
AAAAGAAGAGA
Found at i:51982200 original size:19 final size:21
Alignment explanation
Indices: 51982162--51982200 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
51982152 AATAATTGAT
*
51982162 TATATTGTTGTTATTATTTTG
1 TATATTGTTGTTAATATTTTG
51982183 TATATT-TTG-TAATATTTT
1 TATATTGTTGTTAATATTTT
51982201 TTGTTTTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (21 bp):
TATATTGTTGTTAATATTTTG
Found at i:51982262 original size:3 final size:3
Alignment explanation
Indices: 51982246--51982280 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
51982236 AAAATAATAG
*
51982246 TAT TAGT TAG TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT T
51982281 GTTGTTGTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:51982285 original size:3 final size:3
Alignment explanation
Indices: 51982279--51982319 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
51982269 ATTATTATTA
*
51982279 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTC TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
51982320 AGTATTAAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.00, C:0.02, G:0.29, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:51987814 original size:24 final size:25
Alignment explanation
Indices: 51987761--51987808 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
51987751 CGTTTTTTTG
51987761 ATATATTTTGGTAAATAAAAAAAAC
1 ATATATTTTGGTAAATAAAAAAAAC
51987786 ATATATTTTGGTAAATAAAAAAA
1 ATATATTTTGGTAAATAAAAAAA
51987809 CTTATAACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.56, C:0.02, G:0.08, T:0.33
Consensus pattern (25 bp):
ATATATTTTGGTAAATAAAAAAAAC
Found at i:51988857 original size:3 final size:3
Alignment explanation
Indices: 51988851--51988897 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
51988841 GTTATCTTTG
*
51988851 TTA TTA -TA TTA TATA TTA CTA TTA TTA TTA -TA TTAA TTA TTA TTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA
51988896 TT
1 TT
51988898 TTAATACATA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
2 4 0.11
3 28 0.74
4 6 0.16
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:51988889 original size:21 final size:19
Alignment explanation
Indices: 51988852--51988897 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
51988842 TTATCTTTGT
51988852 TATTA-TATTATATATTAC
1 TATTATTATTATATATTAC
* *
51988870 TATTATTATTATAT-TAAT
1 TATTATTATTATATATTAC
51988888 TATTATTATT
1 TATTATTATT
51988898 TTAATACATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 17 0.68
19 8 0.32
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
TATTATTATTATATATTAC
Found at i:51988891 original size:15 final size:15
Alignment explanation
Indices: 51988857--51988902 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
51988847 TTTGTTATTA
51988857 TATTA-TATATTACTAT
1 TATTATTATATTA--AT
51988873 TATTATTATATTAAT
1 TATTATTATATTAAT
*
51988888 TATTATTATTTTAAT
1 TATTATTATATTAAT
51988903 ACATATATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 16 0.57
16 5 0.18
17 7 0.25
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTATTATATTAAT
Found at i:51999599 original size:389 final size:390
Alignment explanation
Indices: 51998874--51999654 Score: 1456
Period size: 389 Copynumber: 2.0 Consensus size: 390
51998864 GAAGGTCCAT
51998874 ATGTTGTAAAGAAAGCTTTTTCAGGGGGAGCTTTGATTTTGAGTGAGATGGATGGCAAAGACTTG
1 ATGTTGTAAAGAAAGCTTTTTCAGGGGGAGCTTTGATTTTGAGTGAGATGGATGGCAAAGACTTG
* *
51998939 CCAAACCCTGCAAACTCGGATTCAGTTAAGAAATACTTTTCTTTTAAAAAAAAGGGAAAATGAGA
66 CCAAACCCTGCAAACTCGGATTCAGTTAAGAAATACTTTTCTTTTAAAAAAAAGGAAAAAGGAGA
*
51999004 GGCCAATGTGAAAACCCGTAATGGGCACTTTGAGACCAAAGGGGATTTCAGTTGAAAACCCGAAA
131 GGCCAATGTGAAAACCCGTAAAGGGCACTTTGAGACCAAAGGGGATTTCAGTTGAAAACCCGAAA
51999069 AAAGGCGGCTCAAATGCTGATCAGGTGACGCATTCGGTGATCTTGCAATGATTGAACCAGTAGGA
196 AAAGGCGGCTCAAATGCTGATCAGGTGACGCATTCGGTGATCTTGCAATGATTGAACCAGTAGGA
* *
51999134 AATGGGACGCAACATCTTGGGGCATCGATAGAGTACTGTAGATCTTCTAAGCACATGTCGAATTC
261 AAGGGGACGCAACATCTTGGGGCATCGACAGAGTACTGTAGATCTTCTAAGCACATGTCGAATTC
51999199 AGAGCGGTCTTCAGGAAGTCTGTGCAGAGAAGTTCAAACTGCGATATCTGGGACACCTAGTCTTC
326 AGAGCGGTCTTCAGGAAGTCTGTGCAGAGAAGTTCAAACTGCGATATCTGGGACACCTAGTCTTC
51999264 ATGTTGTAAAGAAAGCTTTTTCAGGGGGAGCTTTGATTTTGAGTGAGATGGATGGCAAAGACTTG
1 ATGTTGTAAAGAAAGCTTTTTCAGGGGGAGCTTTGATTTTGAGTGAGATGGATGGCAAAGACTTG
* *
51999329 CCAAACCCTGTAAACTCGGATTCAGTTAAGAAATATTTTTC-TTTAAAAAAAAGGAAAAAGGAGA
66 CCAAACCCTGCAAACTCGGATTCAGTTAAGAAATACTTTTCTTTTAAAAAAAAGGAAAAAGGAGA
*
51999393 GGCCAATGTGAAAACCCGTAAAGGGCACTTTGAGACCAAAGGGGATTTGAGTTGAAAACCCGAAA
131 GGCCAATGTGAAAACCCGTAAAGGGCACTTTGAGACCAAAGGGGATTTCAGTTGAAAACCCGAAA
*
51999458 AAGGGCGGCTCAAATGCTGATCAGGTGACGCATTCGGTGATCTTGCAATGATTGAACCAGTAGGA
196 AAAGGCGGCTCAAATGCTGATCAGGTGACGCATTCGGTGATCTTGCAATGATTGAACCAGTAGGA
*
51999523 AAGGGGACGCAACATCTTGGGGCATCGACAGAGTAGTGTAGATCTTCTAAGCACATGTCGAATTC
261 AAGGGGACGCAACATCTTGGGGCATCGACAGAGTACTGTAGATCTTCTAAGCACATGTCGAATTC
*
51999588 AGAGTGGTCTTCAGGAAGTCTGTGCAGAGAAGTTCAAACTGCGATATCTGGGACACCTAGTCTTC
326 AGAGCGGTCTTCAGGAAGTCTGTGCAGAGAAGTTCAAACTGCGATATCTGGGACACCTAGTCTTC
51999653 AT
1 AT
51999655 ATTATTTATA
Statistics
Matches: 380, Mismatches: 11, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
389 276 0.73
390 104 0.27
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (390 bp):
ATGTTGTAAAGAAAGCTTTTTCAGGGGGAGCTTTGATTTTGAGTGAGATGGATGGCAAAGACTTG
CCAAACCCTGCAAACTCGGATTCAGTTAAGAAATACTTTTCTTTTAAAAAAAAGGAAAAAGGAGA
GGCCAATGTGAAAACCCGTAAAGGGCACTTTGAGACCAAAGGGGATTTCAGTTGAAAACCCGAAA
AAAGGCGGCTCAAATGCTGATCAGGTGACGCATTCGGTGATCTTGCAATGATTGAACCAGTAGGA
AAGGGGACGCAACATCTTGGGGCATCGACAGAGTACTGTAGATCTTCTAAGCACATGTCGAATTC
AGAGCGGTCTTCAGGAAGTCTGTGCAGAGAAGTTCAAACTGCGATATCTGGGACACCTAGTCTTC
Found at i:52000570 original size:44 final size:44
Alignment explanation
Indices: 52000504--52001127 Score: 375
Period size: 44 Copynumber: 14.6 Consensus size: 44
52000494 ACTTCAGTCT
52000504 TATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCC
* ** *
52000548 TATCTCCCTGAAGTTGCGGTGGAGC-G---GATTAACATCAAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAA-ATC-A-ATCC
** * * * * *
52000591 TATCTTTCTGAGGTTGCA---GAG-AG-CAGATCG-TATCCAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACAGA-AGAAAT-CAATCC
* * *
52000631 TATCTTCCTGAAGTTGCAGTGGAGCAGACAGAAGAAACCAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCC
52000675 TATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCC
** *
52000719 TATCTCCCTGAAGTTGCAGTGGAGC-G---GATTAACATCAAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAA-ATC-A-ATCC
* ** * *
52000762 TATATTTCT-AAGGTTACAG-AGAGCAGACAGAAGAAATCAATCC
1 TATCTCCCTGAA-GTTGCAGTGGAGCAGACAGAAGAAATCAATCC
52000805 TATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCC
* ** *
52000849 TATCTCCCTGAAGTTACAGTGGAGC-G---GATTAACATCCAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAA-AT-CA-ATCC
** * * * * *
52000892 TATCTTTCTGAGGTTGCA---GAG-AG-CAGATCG-TATCCAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACAGA-AGAAAT-CAATCC
*
52000932 TATCTCCCTGAAGTTGCAGTGGAGTAGACAGAAGAAATCAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCC
* * ** *
52000976 TATTTCCCTGAAGTTGCAGCGGAGC-G---GATTAACATCCAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAA-AT-CA-ATCC
** * * * * *
52001019 TATCTTTCTGAGGTTGCA---GAG-AG-CAGATCG-TATCCAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACAGA-AGAAAT-CAATCC
* *
52001059 TATCTCCCTGAAGTTACAGTGGAGCAGACAGAAGAAATTAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCC
* *
52001103 TATCTCCCTAAAGTTACAGTGGAGC
1 TATCTCCCTGAAGTTGCAGTGGAGC
52001128 GGATTAACAT
Statistics
Matches: 450, Mismatches: 80, Indels: 100
0.71 0.13 0.16
Matches are distributed among these distances:
40 82 0.18
41 23 0.05
42 19 0.04
43 95 0.21
44 207 0.46
45 20 0.04
46 4 0.01
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (44 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCC
Found at i:52000786 original size:171 final size:171
Alignment explanation
Indices: 52000501--52000873 Score: 588
Period size: 171 Copynumber: 2.2 Consensus size: 171
52000491 GAAACTTCAG
*
52000501 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTGCG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTGCA
* * * * *
52000566 GTGGAGCGGATTAACATCAAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATC-G-TATCCAGT
66 GTGGAGCGGATTAACATCAAGATCTTATATTTCTAAGGTTACAGAGAGCAGA-CAGAAAT-CAAT
* *
52000629 CTTATCTTCCTGAAGTTGCAGTGGAGCAGACAGAAGAAACCAA
129 CCTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAACCAA
52000672 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTGCA
52000737 GTGGAGCGGATTAACATCAAGATCTTATATTTCTAAGGTTACAGAGAGCAGACAGAAGAAATCAA
66 GTGGAGCGGATTAACATCAAGATCTTATATTTCTAAGGTTACAGAGAGCAGAC---AGAAATCAA
*
52000802 TCCTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAA
128 TCCTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAACCAA
* *
52000846 TCCTATCTCCCTGAAGTTACAGTGGAGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGC
52000874 GGATTAACAT
Statistics
Matches: 186, Mismatches: 11, Indels: 7
0.91 0.05 0.03
Matches are distributed among these distances:
170 1 0.01
171 113 0.61
174 70 0.38
175 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (171 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTGCA
GTGGAGCGGATTAACATCAAGATCTTATATTTCTAAGGTTACAGAGAGCAGACAGAAATCAATCC
TATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAACCAA
Found at i:52000934 original size:40 final size:40
Alignment explanation
Indices: 52000882--52001201 Score: 137
Period size: 40 Copynumber: 7.6 Consensus size: 40
52000872 GCGGATTAAC
* * *
52000882 ATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGT
1 ATCCAG-TCTTATCTTCCTGAAGTTGCAGAGAGCAGATAGT
* *
52000923 ATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACAGA-AGAA
1 ATCCAGTCTTATCTTCCTGAAGTTGCA---GAG-AG-CAGATAG-T
* * * * **
52000968 AT-CAATCCTAT-TTCCCTGAAGTTGCAGCGGAGCGGATTAAC
1 ATCCAGTCTTATCTT-CCTGAAGTTGCAG-AGAGCAGA-TAGT
* * *
52001009 ATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGT
1 ATCCAG-TCTTATCTTCCTGAAGTTGCAGAGAGCAGATAGT
* * *
52001050 ATCCAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACAGA-AGAA
1 ATCCAGTCTTATCTTCCTGAAGTTGCA---GAG-AG-CAGATAG-T
* * * * * * * * **
52001095 AT-TAATCCTATCTCCCTAAAGTTACAGTGGAGCGGATTAAC
1 ATCCAGTCTTATCTTCCTGAAGTTGCAG-AGAGCAGA-TAGT
* * * *
52001136 ATCCAGATCTTATCTTTCTGAGGTTGCAGAAAGCAGATCGT
1 ATCCAG-TCTTATCTTCCTGAAGTTGCAGAGAGCAGATAGT
*
52001177 ATCCAGTCTTATCTCCCTGAAGTTG
1 ATCCAGTCTTATCTTCCTGAAGTTG
52001202 TAGTGGAGCA
Statistics
Matches: 203, Mismatches: 52, Indels: 49
0.67 0.17 0.16
Matches are distributed among these distances:
40 57 0.28
41 30 0.15
42 18 0.09
43 39 0.19
44 47 0.23
45 12 0.06
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.29
Consensus pattern (40 bp):
ATCCAGTCTTATCTTCCTGAAGTTGCAGAGAGCAGATAGT
Found at i:52000952 original size:83 final size:83
Alignment explanation
Indices: 52000849--52001213 Score: 244
Period size: 83 Copynumber: 4.3 Consensus size: 83
52000839 AAATCAATCC
* * * *
52000849 TATCTCCCTGAAGTTACAGTGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGA
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAACATCCAGATCTTATCTTCCTGAAGTTGCAGAGA
*
52000914 GCAGATCGTATCCAGTCT
66 GCAGATAGTATCCAGTCT
** *
52000932 TATCTCCCTGAAGTTGCAGTGGAGTAGACAGAAGAA-AT-CA-ATCCTAT-TTCCCTGAAGTTGC
1 TATCTCCCTGAAGTTGCAGT-G-G-AG-CAGATTAACATCCAGATCTTATCTT-CCTGAAGTTGC
* * **
52000993 AGCGGAGCGGATTAACATCCAGATCT
61 AG-AGAGCAGA-TAGTATCCAG-TCT
** * * *** * *
52001019 TATCTTTCTGAGGTTGCAG-AGAGCAGA-TCGTATCCAG-TCTTATCTCCCTGAAGTTACAGTGG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAACATCCAGATCTTATCTTCCTGAAGTTGCA---G
* * * *
52001081 AGCAGACAGA-AGAAAT-TAATCC
63 AG-AG-CAGATAG-TATCCAGTCT
* * * * * *
52001103 TATCTCCCTAAAGTTACAGTGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAAA
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAACATCCAGATCTTATCTTCCTGAAGTTGCAGAGA
*
52001168 GCAGATCGTATCCAGTCT
66 GCAGATAGTATCCAGTCT
*
52001186 TATCTCCCTGAAGTTGTAGTGGAGCAGA
1 TATCTCCCTGAAGTTGCAGTGGAGCAGA
52001214 CAGAATAAAC
Statistics
Matches: 206, Mismatches: 53, Indels: 46
0.68 0.17 0.15
Matches are distributed among these distances:
82 12 0.06
83 71 0.34
84 38 0.18
85 18 0.09
86 23 0.11
87 44 0.21
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (83 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATTAACATCCAGATCTTATCTTCCTGAAGTTGCAGAGA
GCAGATAGTATCCAGTCT
Found at i:52001291 original size:127 final size:127
Alignment explanation
Indices: 52000672--52001238 Score: 895
Period size: 127 Copynumber: 4.4 Consensus size: 127
52000662 AAGAAACCAA
*
52000672 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTACA
* * * * *
52000737 GTGGAGCGGATTAACATCAAGATCTTATATTTCTAAGGTTACAGAGAGCAGA-CAGAAGAAAT-C
66 GTGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATC----G-TATCC
*
52000800 AA
126 AG
*
52000802 TCCTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTACA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTACA
52000867 GTGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGTATCCAG
66 GTGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGTATCCAG
* * *
52000929 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACAGAAGAAATCAATCCTATTTCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTACA
*
52000994 GCGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGTATCCAG
66 GTGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGTATCCAG
* * *
52001056 TCTTATCTCCCTGAAGTTACAGTGGAGCAGACAGAAGAAATTAATCCTATCTCCCTAAAGTTACA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTACA
*
52001121 GTGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAAAGCAGATCGTATCCAG
66 GTGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGTATCCAG
* * * *
52001183 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGACAGAATAAACCAATCTTATCTCCCT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCT
52001239 AGAGTGGCAG
Statistics
Matches: 408, Mismatches: 27, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
126 2 0.00
127 294 0.72
130 111 0.27
131 1 0.00
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.27
Consensus pattern (127 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTACA
GTGGAGCGGATTAACATCCAGATCTTATCTTTCTGAGGTTGCAGAGAGCAGATCGTATCCAG
Found at i:52002474 original size:3 final size:3
Alignment explanation
Indices: 52002468--52002529 Score: 74
Period size: 3 Copynumber: 20.7 Consensus size: 3
52002458 GTTATCTTTG
*
52002468 TTA TTA -TA TTA TATA TTA CTA TTA TTA TTA -TA TTAA TTA TTA TTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA
*
52002513 TTT TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TT
52002530 TTAATACATA
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
2 4 0.08
3 41 0.80
4 6 0.12
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:52002571 original size:2 final size:2
Alignment explanation
Indices: 52002564--52002594 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
52002554 TGTATCTTAT
*
52002564 TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
52002595 TTTAAATGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:52003839 original size:16 final size:15
Alignment explanation
Indices: 52003818--52003847 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
52003808 AAGAAAAATA
52003818 TATTATTTTAGTATTT
1 TATTATTTTA-TATTT
52003834 TATTATTTTATATT
1 TATTATTTTATATT
52003848 ATTTCAGTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (15 bp):
TATTATTTTATATTT
Found at i:52004441 original size:4 final size:4
Alignment explanation
Indices: 52004425--52004545 Score: 101
Period size: 4 Copynumber: 30.0 Consensus size: 4
52004415 CTCCTTTTTA
*
52004425 TTTC TTTC CTTC TTTC TTTC TTT- TTTC TTCTCC TTTCC TTT- TCTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT-T-C TTT-C TTTC T-TTC
* * *
52004471 -TTC TTTC TTTC TTTC TTTT TTTC TCTTC -TCC TTTCC TTTTC TTTC CTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC T-TTC TTTC TTT-C -TTTC TTTC TTTC
52004520 -TT- TTTC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC
52004546 CCTCTCCTTC
Statistics
Matches: 98, Mismatches: 7, Indels: 24
0.76 0.05 0.19
Matches are distributed among these distances:
3 13 0.13
4 67 0.68
5 12 0.12
6 6 0.06
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTC
Found at i:52004456 original size:44 final size:43
Alignment explanation
Indices: 52004401--52004543 Score: 154
Period size: 44 Copynumber: 3.3 Consensus size: 43
52004391 TTCTTCTTCT
*
52004401 TTTTTTTTTCTCTTCTCCTTTTTATTTCTTTCCTTCTTTCTTTC
1 TTTTTTCTTCTCTTCTCCTTTTT-TTTCTTTCCTTCTTTCTTTC
* *
52004445 TTTTTTCTTCTCCTT-TCC-TTTTCTTC-TTCTTTCTTTCTTTC
1 TTTTTTCTTCT-CTTCTCCTTTTTTTTCTTTCCTTCTTTCTTTC
*
52004486 -TTTTT-TTCTCTTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTC
1 TTTTTTCTTCTCTTCTCCTTT-TTTTTCTTTCCTTC--TTTCTTTC
52004530 TTTCTTTCTT-TCTT
1 TTT-TTTCTTCTCTT
52004544 TCCCTCTCCT
Statistics
Matches: 83, Mismatches: 6, Indels: 18
0.78 0.06 0.17
Matches are distributed among these distances:
38 3 0.04
39 7 0.08
40 7 0.08
41 18 0.22
42 9 0.11
43 4 0.05
44 21 0.25
45 5 0.06
46 7 0.08
47 2 0.02
ACGTcount: A:0.01, C:0.27, G:0.00, T:0.72
Consensus pattern (43 bp):
TTTTTTCTTCTCTTCTCCTTTTTTTTCTTTCCTTCTTTCTTTC
Found at i:52004493 original size:83 final size:79
Alignment explanation
Indices: 52004359--52004546 Score: 233
Period size: 83 Copynumber: 2.3 Consensus size: 79
52004349 AAAAAATACA
52004359 TTTTCTTTTCTTTTTT-TTTCC-TTCCTTCCCTCTTCTTCTTCTTTTTTTTTTCTCTTCTCCTTT
1 TTTTC-TTTCTTTTTTCTTTCCTTTCCTTCCCTCTTCTTCTTCTTTTTTTTTTCTCTTCTCCTTT
*
52004422 -TTATTTCTTTCCTTC
65 CCT-TTTCTTTCCTTC
* *
52004437 -TTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTCTTCTTTCTTTCTTTCTTTTTTTCTCTTCTC
1 TTTTCTTTCTTTTTTCTT-TCCTTTCC-TTCCCTCTTC-TTC-TTCTTT-TTTTTTTCTCTTCTC
52004501 CTTTCCTTTTCTTTCCTTC
61 CTTTCCTTTTCTTTCCTTC
52004520 TTTTTCTTTCTTTCTTTCTTT-CTTTCC
1 -TTTTCTTTCTTT-TTTCTTTCCTTTCC
52004547 CTCTCCTTCT
Statistics
Matches: 96, Mismatches: 3, Indels: 16
0.83 0.03 0.14
Matches are distributed among these distances:
76 10 0.10
77 6 0.06
78 3 0.03
79 4 0.04
80 8 0.08
81 3 0.03
82 6 0.06
83 31 0.32
84 7 0.07
85 12 0.12
86 6 0.06
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.71
Consensus pattern (79 bp):
TTTTCTTTCTTTTTTCTTTCCTTTCCTTCCCTCTTCTTCTTCTTTTTTTTTTCTCTTCTCCTTTC
CTTTTCTTTCCTTC
Found at i:52004512 original size:34 final size:36
Alignment explanation
Indices: 52004365--52004543 Score: 131
Period size: 37 Copynumber: 5.0 Consensus size: 36
52004355 TACATTTTCT
* * *
52004365 TTTCTTTTTTTTTCCT-TCCTTCCCTCTT-CTTCTTC
1 TTTCTTTCTTTTTCTTCTCCTTTCCT-TTCCTTCTTC
** *
52004400 TTT-TTT-TTTTCTCTTCTCCTTTTTATTTCTTTCCTTC
1 TTTCTTTCTTTT-TCTTCTCC-TTTCCTTTCCTT-CTTC
*
52004437 TTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTCTTC
1 TTTCTTTC-TTTTTCTTCTCCTTTCCTTTCCTTCTTC
* *
52004474 TTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCTT-TTC
1 TTTCTTTCTTT-TTCTTCTC-CTT-TCCTTTCCTTCTTC
* *
52004512 TTTCCTTCTTTTTCTT-T-CTTT-CTTTCTTTCTT
1 TTTCTTTCTTTTTCTTCTCCTTTCCTTTCCTTCTT
52004544 TCCCTCTCCT
Statistics
Matches: 117, Mismatches: 15, Indels: 26
0.74 0.09 0.16
Matches are distributed among these distances:
32 7 0.06
33 7 0.06
34 9 0.08
35 8 0.07
36 9 0.08
37 29 0.25
38 27 0.23
39 17 0.15
40 4 0.03
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.71
Consensus pattern (36 bp):
TTTCTTTCTTTTTCTTCTCCTTTCCTTTCCTTCTTC
Found at i:52004630 original size:28 final size:27
Alignment explanation
Indices: 52004585--52004655 Score: 108
Period size: 28 Copynumber: 2.6 Consensus size: 27
52004575 CCCTAATAAA
52004585 CATTGGTGCCGCCAATGG-TATTGGCAC
1 CATTGGTGCCGCCAATGGCT-TTGGCAC
52004612 CATTGGTGCCCGCCAATGGCTTTGGCAC
1 CATTGGTG-CCGCCAATGGCTTTGGCAC
*
52004640 CTTTGGTGCCGCCAAT
1 CATTGGTGCCGCCAAT
52004656 CCCATTGGCG
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
27 16 0.39
28 24 0.59
29 1 0.02
ACGTcount: A:0.15, C:0.30, G:0.28, T:0.27
Consensus pattern (27 bp):
CATTGGTGCCGCCAATGGCTTTGGCAC
Found at i:52004663 original size:27 final size:27
Alignment explanation
Indices: 52004585--52004664 Score: 106
Period size: 28 Copynumber: 2.9 Consensus size: 27
52004575 CCCTAATAAA
*
52004585 CATTGGTGCCGCCAATGGTATTGGCAC
1 CATTGGTGCCGCCAATGGCATTGGCAC
*
52004612 CATTGGTGCCCGCCAATGGCTTTGGCAC
1 CATTGGTG-CCGCCAATGGCATTGGCAC
* **
52004640 CTTTGGTGCCGCCAATCCCATTGGC
1 CATTGGTGCCGCCAATGGCATTGGC
52004665 GTGACCAAGG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 22 0.48
28 24 0.52
ACGTcount: A:0.15, C:0.31, G:0.28, T:0.26
Consensus pattern (27 bp):
CATTGGTGCCGCCAATGGCATTGGCAC
Found at i:52004746 original size:24 final size:24
Alignment explanation
Indices: 52004719--52004765 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
52004709 GTTTTTTTTG
52004719 ATATATTTTGGTAAATAAAAAAAT
1 ATATATTTTGGTAAATAAAAAAAT
*
52004743 ATATTTTTTGGTAAATAAAAAAA
1 ATATATTTTGGTAAATAAAAAAA
52004766 GTTATAACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (24 bp):
ATATATTTTGGTAAATAAAAAAAT
Found at i:52004875 original size:31 final size:30
Alignment explanation
Indices: 52004837--52004899 Score: 99
Period size: 31 Copynumber: 2.1 Consensus size: 30
52004827 CAACTTAACA
52004837 AACAAATGTCTCTAAAATAATAAAAAAAATT
1 AACAAATGTCTCTAAAATAAT-AAAAAAATT
* *
52004868 AACAAATGTCTTTAAAATAATAACAAAATT
1 AACAAATGTCTCTAAAATAATAAAAAAATT
52004898 AA
1 AA
52004900 TAATAAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 10 0.33
31 20 0.67
ACGTcount: A:0.60, C:0.10, G:0.03, T:0.27
Consensus pattern (30 bp):
AACAAATGTCTCTAAAATAATAAAAAAATT
Found at i:52007158 original size:16 final size:17
Alignment explanation
Indices: 52007129--52007163 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
52007119 ATGTAGTTTT
52007129 ATTTTTATTAATTTTAA
1 ATTTTTATTAATTTTAA
*
52007146 ATTTTT-TTCATTTTAA
1 ATTTTTATTAATTTTAA
52007162 AT
1 AT
52007164 ATCCGGACCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (17 bp):
ATTTTTATTAATTTTAA
Found at i:52015412 original size:17 final size:18
Alignment explanation
Indices: 52015368--52015412 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 18
52015358 ATTTATTTTC
52015368 TTATTTATTGTTCTAAATT
1 TTATTTATTGTTCT-AATT
52015387 TTAATTTATTGTTCT-ATT
1 TT-ATTTATTGTTCTAATT
52015405 TTATTTAT
1 TTATTTAT
52015413 CTTAGTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.24
18 5 0.20
19 2 0.08
20 12 0.48
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.67
Consensus pattern (18 bp):
TTATTTATTGTTCTAATT
Found at i:52050601 original size:18 final size:19
Alignment explanation
Indices: 52050562--52050618 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 19
52050552 TTTCATGAAC
* *
52050562 TTTT-TATTTTTAATTTAA
1 TTTTATATTTTTAAATTAT
*
52050580 TTTAAT-TTTTTAAA-TAT
1 TTTTATATTTTTAAATTAT
52050597 TTTTATATTTTTAAATTAT
1 TTTTATATTTTTAAATTAT
52050616 TTT
1 TTT
52050619 AATCTATTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
17 7 0.22
18 18 0.56
19 7 0.22
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTTATATTTTTAAATTAT
Found at i:52050809 original size:17 final size:17
Alignment explanation
Indices: 52050787--52050819 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
52050777 AATATCTAGA
52050787 GGGAAAAAATCATTTTG
1 GGGAAAAAATCATTTTG
52050804 GGGAAAAAATCATTTT
1 GGGAAAAAATCATTTT
52050820 AATATCTAGA
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:0.42, C:0.06, G:0.21, T:0.30
Consensus pattern (17 bp):
GGGAAAAAATCATTTTG
Found at i:52051297 original size:19 final size:19
Alignment explanation
Indices: 52051275--52051320 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
52051265 AAAACACAAA
*
52051275 AAACTTTTGAAGAGAAGCT
1 AAACTTTTGAAGAAAAGCT
52051294 AAACTTTTGAAGAAAAGCT
1 AAACTTTTGAAGAAAAGCT
*
52051313 AAAATTTT
1 AAACTTTT
52051321 CAGCTTCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.46, C:0.09, G:0.15, T:0.30
Consensus pattern (19 bp):
AAACTTTTGAAGAAAAGCT
Found at i:52051402 original size:17 final size:18
Alignment explanation
Indices: 52051376--52051414 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
52051366 AAGTGTTTAG
52051376 AAATGCTTTT-GTCCCAA
1 AAATGCTTTTCGTCCCAA
* *
52051393 AAATGTTTTTCGTCTCAA
1 AAATGCTTTTCGTCCCAA
52051411 AAAT
1 AAAT
52051415 ACTTCTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.38
Consensus pattern (18 bp):
AAATGCTTTTCGTCCCAA
Found at i:52053784 original size:12 final size:13
Alignment explanation
Indices: 52053769--52053807 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
52053759 ATTTTTTATG
*
52053769 TTTTATTTTAATT
1 TTTTATTATAATT
52053782 TTTTATTATAATT
1 TTTTATTATAATT
*
52053795 TTTCACTTATAAT
1 TTTTA-TTATAAT
52053808 AACAACATCC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 16 0.70
14 7 0.30
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTTATTATAATT
Found at i:52056279 original size:40 final size:40
Alignment explanation
Indices: 52056158--52056297 Score: 142
Period size: 40 Copynumber: 3.5 Consensus size: 40
52056148 GACTTTGAGT
* * * *
52056158 CGATGAGACACTGAGTGTCAATTTACTACTTCGGATTAATT
1 CGATGAGACACTGGGTGTCAAATTATTACTTCGGATT-ATC
* * * *
52056199 CGATGAGGCACTGGGTG-CCAA-T-TTACTTCGGTTTAGC
1 CGATGAGACACTGGGTGTCAAATTATTACTTCGGATTATC
* *
52056236 CGATGAGACACTGGGTGTTAAATTATTACTTCGAATTATC
1 CGATGAGACACTGGGTGTCAAATTATTACTTCGGATTATC
* *
52056276 CGATGAGGCACTGGGTGCCAAA
1 CGATGAGACACTGGGTGTCAAA
52056298 CTGGTGTGTT
Statistics
Matches: 79, Mismatches: 17, Indels: 7
0.77 0.17 0.07
Matches are distributed among these distances:
37 17 0.22
38 12 0.15
39 2 0.03
40 33 0.42
41 15 0.19
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (40 bp):
CGATGAGACACTGGGTGTCAAATTATTACTTCGGATTATC
Found at i:52062463 original size:42 final size:42
Alignment explanation
Indices: 52062404--52062486 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
52062394 ACCACCAGCC
*
52062404 CGTGCGCGTGGCCGTGTGTCAAACATGGCTGAGACACACGCT
1 CGTGCGCGTGGCCGTGTGTCAAACACGGCTGAGACACACGCT
* * * * *
52062446 CGTGCGTGTGGTCGTGTGTTACACACGGTTGAGACACACGC
1 CGTGCGCGTGGCCGTGTGTCAAACACGGCTGAGACACACGC
52062487 CCGTATGGAC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.18, C:0.27, G:0.34, T:0.22
Consensus pattern (42 bp):
CGTGCGCGTGGCCGTGTGTCAAACACGGCTGAGACACACGCT
Found at i:52065082 original size:25 final size:26
Alignment explanation
Indices: 52065054--52065102 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
52065044 ACAGGAAGTT
*
52065054 CAAACGAGCC-ATATTAGGAAGCTCA
1 CAAAAGAGCCTATATTAGGAAGCTCA
52065079 CAAAAGAGCCTATATTAGGAAGCT
1 CAAAAGAGCCTATATTAGGAAGCT
52065103 TATAAAGAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.18
Consensus pattern (26 bp):
CAAAAGAGCCTATATTAGGAAGCTCA
Found at i:52066677 original size:99 final size:99
Alignment explanation
Indices: 52066506--52066703 Score: 369
Period size: 99 Copynumber: 2.0 Consensus size: 99
52066496 AGAGATGCTC
52066506 AATATGGTGACTTCTCAAAGTTGAGATGATACTTTAGAATAGTGTAGACTATATATCTTGTCTTG
1 AATATGGTGACTTCTCAAAGTTGAGATGATACTTTAGAATAGTGTAGACTATATATCTTGTCTTG
52066571 TGTCTCCTACTCGATCGATCACTCTTTGTCTTAG
66 TGTCTCCTACTCGATCGATCACTCTTTGTCTTAG
* *
52066605 AATATGGTGACTTCTCTAAGTTGAGATGATACTTTAGAATAGTGTAGGCTATATATCTTGTCTTG
1 AATATGGTGACTTCTCAAAGTTGAGATGATACTTTAGAATAGTGTAGACTATATATCTTGTCTTG
*
52066670 TGTCTCCTACTCGATGGATCACTCTTTGTCTTAG
66 TGTCTCCTACTCGATCGATCACTCTTTGTCTTAG
52066704 TGGTGAAAGC
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
99 96 1.00
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.40
Consensus pattern (99 bp):
AATATGGTGACTTCTCAAAGTTGAGATGATACTTTAGAATAGTGTAGACTATATATCTTGTCTTG
TGTCTCCTACTCGATCGATCACTCTTTGTCTTAG
Found at i:52068314 original size:25 final size:25
Alignment explanation
Indices: 52068230--52068317 Score: 79
Period size: 25 Copynumber: 3.5 Consensus size: 25
52068220 CCGAGAATGT
*
52068230 TCATACGAG-CATGTAAACGAGAAGC
1 TCATACGAGCCATGT-AACGGGAAGC
* * * *
52068255 TCTTTCGAGCCATATAATGGGAAGC
1 TCATACGAGCCATGTAACGGGAAGC
* **
52068280 TTATGTGAGCCATGTAACGGGAAGC
1 TCATACGAGCCATGTAACGGGAAGC
*
52068305 TCATAAGAGCCAT
1 TCATACGAGCCAT
52068318 AATTGGGAAG
Statistics
Matches: 48, Mismatches: 14, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
25 44 0.92
26 4 0.08
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (25 bp):
TCATACGAGCCATGTAACGGGAAGC
Found at i:52068377 original size:25 final size:25
Alignment explanation
Indices: 52068297--52068427 Score: 87
Period size: 25 Copynumber: 5.4 Consensus size: 25
52068287 AGCCATGTAA
**
52068297 CGGGAAGCTCATAAGAGCCAT-AAT
1 CGGGAAGCTCCGAAGAGCCATAAAT
* * *
52068321 TGGGAAG-TTC-AAGCGAGCCA-ATAT
1 CGGGAAGCTCCGAA--GAGCCATAAAT
* *
52068345 CAGGAAGCTCCGGAGAGCCATAAAT
1 CGGGAAGCTCCGAAGAGCCATAAAT
* *
52068370 CGGGAAGCTTCAAAGAG-C-TAATTAT
1 CGGGAAGCTCCGAAGAGCCATAA--AT
*
52068395 CGGGAAGCTCCGAAGAGCCAAAAAT
1 CGGGAAGCTCCGAAGAGCCATAAAT
52068420 -GGGAAGCT
1 CGGGAAGCT
52068428 TGTAGGAACC
Statistics
Matches: 81, Mismatches: 16, Indels: 20
0.69 0.14 0.17
Matches are distributed among these distances:
22 2 0.02
23 4 0.05
24 34 0.42
25 37 0.46
26 2 0.02
27 2 0.02
ACGTcount: A:0.36, C:0.20, G:0.28, T:0.16
Consensus pattern (25 bp):
CGGGAAGCTCCGAAGAGCCATAAAT
Found at i:52068402 original size:50 final size:49
Alignment explanation
Indices: 52068261--52068428 Score: 162
Period size: 50 Copynumber: 3.4 Consensus size: 49
52068251 AAGCTCTTTC
* * * * * **
52068261 GAGCCATATAATGGGAAGCTT-ATGTGAGCCATGTAACGGGAAGCTCATAA
1 GAGCCATA-AATGGGAAGCTTCAAGAGAGCCA-ATATCAGGAAGCTCCGAA
* * *
52068311 GAGCCATAATTGGGAAG-TTCAAGCGAGCCAATATCAGGAAGCTCCGGA
1 GAGCCATAAATGGGAAGCTTCAAGAGAGCCAATATCAGGAAGCTCCGAA
* *
52068359 GAGCCATAAATCGGGAAGCTTCAA-AGAGCTAATTATCGGGAAGCTCCGAA
1 GAGCCATAAAT-GGGAAGCTTCAAGAGAGCCAA-TATCAGGAAGCTCCGAA
*
52068409 GAGCCAAAAATGGGAAGCTT
1 GAGCCATAAATGGGAAGCTT
52068429 GTAGGAACCA
Statistics
Matches: 99, Mismatches: 15, Indels: 9
0.80 0.12 0.07
Matches are distributed among these distances:
48 24 0.24
49 37 0.37
50 38 0.38
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.18
Consensus pattern (49 bp):
GAGCCATAAATGGGAAGCTTCAAGAGAGCCAATATCAGGAAGCTCCGAA
Found at i:52076231 original size:19 final size:18
Alignment explanation
Indices: 52076192--52076231 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
52076182 ATATTACAAG
**
52076192 TTAAAATAAAATAAATTT
1 TTAAAATAAAATAAAACT
52076210 TTAAAATCAAAATAAAACT
1 TTAAAAT-AAAATAAAACT
52076229 TTA
1 TTA
52076232 CCATTATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (18 bp):
TTAAAATAAAATAAAACT
Found at i:52085681 original size:24 final size:24
Alignment explanation
Indices: 52085636--52085687 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
52085626 GATTTCCGCA
*
52085636 GCTGTTGCAATAGCAGCAGCTGCT
1 GCTGTTGCAATAGCAGCAGCTGCG
* *
52085660 GCTGTTGCAA-AGGCTGCGGCTGCG
1 GCTGTTGCAATA-GCAGCAGCTGCG
52085684 GCTG
1 GCTG
52085688 CCAATGTCGC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.15, C:0.25, G:0.37, T:0.23
Consensus pattern (24 bp):
GCTGTTGCAATAGCAGCAGCTGCG
Found at i:52095672 original size:23 final size:25
Alignment explanation
Indices: 52095641--52095687 Score: 62
Period size: 23 Copynumber: 1.9 Consensus size: 25
52095631 ATAATAAGAA
52095641 GAAGAAGAAG-AAGAAA-AATAAAT
1 GAAGAAGAAGAAAGAAAGAATAAAT
*
52095664 GAAGTAGAAGTAAAGAAAGAATAA
1 GAAGAAGAAG-AAAGAAAGAATAA
52095688 GAAAACTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 9 0.45
25 6 0.30
26 5 0.25
ACGTcount: A:0.66, C:0.00, G:0.23, T:0.11
Consensus pattern (25 bp):
GAAGAAGAAGAAAGAAAGAATAAAT
Found at i:52095672 original size:26 final size:26
Alignment explanation
Indices: 52095638--52095687 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
52095628 ATAATAATAA
52095638 GAAGAAGAAGAAGAAGAAA-AATAAAT
1 GAAGAAGAAGAA-AAGAAAGAATAAAT
* *
52095664 GAAGTAGAAGTAAAGAAAGAATAA
1 GAAGAAGAAGAAAAGAAAGAATAA
52095688 GAAAACTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.66, C:0.00, G:0.24, T:0.10
Consensus pattern (26 bp):
GAAGAAGAAGAAAAGAAAGAATAAAT
Found at i:52098562 original size:17 final size:17
Alignment explanation
Indices: 52098537--52098570 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
52098527 CTTAAGATGT
52098537 ATGTATATTTTGATTTA
1 ATGTATATTTTGATTTA
* *
52098554 ATGTTTATTTTTATTTA
1 ATGTATATTTTGATTTA
52098571 TAATCTCTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (17 bp):
ATGTATATTTTGATTTA
Found at i:52098656 original size:2 final size:2
Alignment explanation
Indices: 52098649--52098691 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
52098639 TAACAATAAT
52098649 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
52098691 T
1 T
52098692 CATCTGATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:52105277 original size:18 final size:18
Alignment explanation
Indices: 52105256--52105312 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
52105246 TAAAAGTATA
52105256 AATTTTATAAA-TATTTTG
1 AATTTTA-AAATTATTTTG
*
52105274 AATTTTAAAATTATTTTCA
1 AATTTTAAAATTATTTT-G
52105293 AATTTTGAAAATTATTTTG
1 AATTTT-AAAATTATTTTG
52105312 A
1 A
52105313 TTATTTTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
17 3 0.09
18 13 0.38
19 7 0.21
20 11 0.32
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (18 bp):
AATTTTAAAATTATTTTG
Found at i:52108399 original size:42 final size:40
Alignment explanation
Indices: 52108353--52108443 Score: 121
Period size: 39 Copynumber: 2.2 Consensus size: 40
52108343 TTAAAAGTAT
* *
52108353 TTATATTAAAAAAAAACTACCATAAATATAATAAATGTTTTA
1 TTATATTAAAAAAAAAC-A-AATAAATATAATAAATATTTTA
*
52108395 TTATATT-AAAAAACACAAATAAATATAATAAATATTTTA
1 TTATATTAAAAAAAAACAAATAAATATAATAAATATTTTA
*
52108434 TTGTATTAAA
1 TTATATTAAA
52108444 TATAAATTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
39 26 0.59
40 3 0.07
41 8 0.18
42 7 0.16
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.37
Consensus pattern (40 bp):
TTATATTAAAAAAAAACAAATAAATATAATAAATATTTTA
Found at i:52109651 original size:13 final size:13
Alignment explanation
Indices: 52109626--52109671 Score: 65
Period size: 14 Copynumber: 3.4 Consensus size: 13
52109616 AATGAACGTG
52109626 AATTTTTTAAAAAT
1 AATTTTTT-AAAAT
52109640 AATTTTTTAAAAT
1 AATTTTTTAAAAT
*
52109653 AATTTTTTTAAAAG
1 AA-TTTTTTAAAAT
52109667 AATTT
1 AATTT
52109672 CTGAGCATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 10 0.33
14 20 0.67
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (13 bp):
AATTTTTTAAAAT
Found at i:52118174 original size:13 final size:13
Alignment explanation
Indices: 52118156--52118180 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52118146 ATTTACAAGA
52118156 TTACATAATCAAT
1 TTACATAATCAAT
52118169 TTACATAATCAA
1 TTACATAATCAA
52118181 ATCAAATCAA
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:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (13 bp):
TTACATAATCAAT
Found at i:52118185 original size:5 final size:5
Alignment explanation
Indices: 52118175--52118204 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
52118165 CAATTTACAT
52118175 AATCA AATCA AATCA AATCA AATCA AATCA
1 AATCA AATCA AATCA AATCA AATCA AATCA
52118205 TATAAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.60, C:0.20, G:0.00, T:0.20
Consensus pattern (5 bp):
AATCA
Found at i:52118212 original size:15 final size:15
Alignment explanation
Indices: 52118179--52118212 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
52118169 TTACATAATC
*
52118179 AAATCAAATCAAATC
1 AAATCAAATCAAATA
*
52118194 AAATCAAATCATATA
1 AAATCAAATCAAATA
52118209 AAAT
1 AAAT
52118213 ATGATTCCCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.24
Consensus pattern (15 bp):
AAATCAAATCAAATA
Found at i:52123409 original size:75 final size:75
Alignment explanation
Indices: 52123288--52123495 Score: 317
Period size: 75 Copynumber: 2.8 Consensus size: 75
52123278 CCGTTATTGG
* * * *
52123288 TGGATTCAGCACTTAGCAACCACCAGTGATTTGGGGAATCAGCACTTAACAACCCCTTTCACATT
1 TGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCACATT
* *
52123353 TAAGATACGG
66 TAAAATACGA
* * * *
52123363 TGGGATCAGCACTTAGCAACCACCAATGAGTCGGGGAATAAGCACTTAGCAACCCCCTTCACATT
1 TGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCACATT
52123428 TAAAATACGA
66 TAAAATACGA
*
52123438 TGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAACCAGCACTTAGCAACCCCTT
1 TGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTT
52123496 GGGGGAATCA
Statistics
Matches: 118, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
75 118 1.00
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (75 bp):
TGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCACATT
TAAAATACGA
Found at i:52141530 original size:16 final size:16
Alignment explanation
Indices: 52141511--52141550 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
52141501 TCCCACGTTA
52141511 GGTTTTGGGTTTTTAG
1 GGTTTTGGGTTTTTAG
*
52141527 GGTTTAGGGTTTTTAG
1 GGTTTTGGGTTTTTAG
*
52141543 AGTTTTGG
1 GGTTTTGG
52141551 AGAAAAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.10, C:0.00, G:0.38, T:0.53
Consensus pattern (16 bp):
GGTTTTGGGTTTTTAG
Found at i:52141845 original size:49 final size:49
Alignment explanation
Indices: 52141790--52141936 Score: 267
Period size: 49 Copynumber: 3.0 Consensus size: 49
52141780 CGCTTTTGAG
52141790 CAAATAATATCAAAATATTCAAAATAAACTATTTTGTATTTTATTACAT
1 CAAATAATATCAAAATATTCAAAATAAACTATTTTGTATTTTATTACAT
* *
52141839 CAAATAATATCAAAATATTCAAAATAAACTATTTTATATTTTATTATAT
1 CAAATAATATCAAAATATTCAAAATAAACTATTTTGTATTTTATTACAT
*
52141888 CAAATAATATCAAAATATTCAAATTAAACTATTTTGTATTTTATTACAT
1 CAAATAATATCAAAATATTCAAAATAAACTATTTTGTATTTTATTACAT
52141937 TAATATAAAC
Statistics
Matches: 93, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
49 93 1.00
ACGTcount: A:0.47, C:0.10, G:0.01, T:0.42
Consensus pattern (49 bp):
CAAATAATATCAAAATATTCAAAATAAACTATTTTGTATTTTATTACAT
Found at i:52144281 original size:11 final size:11
Alignment explanation
Indices: 52144253--52144303 Score: 68
Period size: 11 Copynumber: 4.7 Consensus size: 11
52144243 TTAAATATGG
52144253 ATTTGAGAG-A
1 ATTTGAGAGCA
*
52144263 AATTGAGAGCA
1 ATTTGAGAGCA
52144274 ATTTGAGAGCA
1 ATTTGAGAGCA
*
52144285 ATTTGAGAGGA
1 ATTTGAGAGCA
*
52144296 AATTGAGA
1 ATTTGAGA
52144304 AAATAATTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
10 8 0.22
11 28 0.78
ACGTcount: A:0.41, C:0.04, G:0.29, T:0.25
Consensus pattern (11 bp):
ATTTGAGAGCA
Found at i:52150040 original size:6 final size:6
Alignment explanation
Indices: 52150029--52150064 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
52150019 TAAACTTATT
*
52150029 ATATAA ATATAA ATATAA ATATAA AAAGTAA ATATA
1 ATATAA ATATAA ATATAA ATATAA ATA-TAA ATATA
52150065 TTATAAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 22 0.81
7 5 0.19
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (6 bp):
ATATAA
Found at i:52150069 original size:18 final size:18
Alignment explanation
Indices: 52150025--52150071 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 18
52150015 AAATTAAACT
52150025 TATTATATAAATATAAATA
1 TATTATA-AAATATAAATA
*
52150044 TAAATATAAAA-AGTAAATA
1 T-ATTATAAAATA-TAAATA
52150063 TATTATAAA
1 TATTATAAA
52150072 TTATGTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 8 0.33
19 11 0.46
20 5 0.21
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
TATTATAAAATATAAATA
Found at i:52150116 original size:18 final size:19
Alignment explanation
Indices: 52150080--52150117 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
52150070 AATTATGTTA
* *
52150080 TTATATAATGCTTGTAAAT
1 TTATATAATACTTGCAAAT
52150099 TTATA-AATACTTGCAAAT
1 TTATATAATACTTGCAAAT
52150117 T
1 T
52150118 ATTTTAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (19 bp):
TTATATAATACTTGCAAAT
Found at i:52150198 original size:24 final size:24
Alignment explanation
Indices: 52150157--52150204 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
52150147 TGTAATTTAT
52150157 ATTTTATTATTGAATATA-TATAA
1 ATTTTATTATTGAATATATTATAA
* *
52150180 ATTTTAATTATTTATTATATTATAA
1 ATTTT-ATTATTGAATATATTATAA
52150205 TAACATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 5 0.24
24 11 0.52
25 5 0.24
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (24 bp):
ATTTTATTATTGAATATATTATAA
Found at i:52151546 original size:21 final size:21
Alignment explanation
Indices: 52151503--52151564 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
52151493 CGAATACGCC
*
52151503 AACAGAAGCTCG-AA-AGCTG
1 AACAAAAGCTCGTAAGAGCTG
* *
52151522 AACAAAAGCTTGTAAGAGCTT
1 AACAAAAGCTCGTAAGAGCTG
*
52151543 AACAGAAGCTCGTAAGAGCTG
1 AACAAAAGCTCGTAAGAGCTG
52151564 A
1 A
52151565 TCCACCCAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 10 0.29
20 2 0.06
21 23 0.66
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.16
Consensus pattern (21 bp):
AACAAAAGCTCGTAAGAGCTG
Found at i:52161131 original size:9 final size:9
Alignment explanation
Indices: 52161114--52161150 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
52161104 TGAGTTTTCG
52161114 AATTCGAAT
1 AATTCGAAT
*
52161123 AACTCGAAT
1 AATTCGAAT
52161132 AATTCGAAT
1 AATTCGAAT
52161141 AATTCGAAT
1 AATTCGAAT
52161150 A
1 A
52161151 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:52163215 original size:14 final size:15
Alignment explanation
Indices: 52163184--52163219 Score: 56
Period size: 14 Copynumber: 2.4 Consensus size: 15
52163174 TAAATAATTT
52163184 TTTTAAAATTCTTAAA
1 TTTT-AAATTCTTAAA
52163200 TTTTAAATTC-TAAA
1 TTTTAAATTCTTAAA
52163214 TTTTAA
1 TTTTAA
52163220 CCTCAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 10 0.50
15 6 0.30
16 4 0.20
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTTAAATTCTTAAA
Found at i:52171291 original size:5 final size:5
Alignment explanation
Indices: 52171281--52171305 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
52171271 ACCAATGTTG
52171281 GGGTT GGGTT GGGTT GGGTT GGGTT
1 GGGTT GGGTT GGGTT GGGTT GGGTT
52171306 AGATAGATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.60, T:0.40
Consensus pattern (5 bp):
GGGTT
Found at i:52187677 original size:21 final size:21
Alignment explanation
Indices: 52187651--52187703 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
52187641 TGCTGTTTCT
* *
52187651 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAATAACC
** *
52187672 AATCTCACTACTACAATAACT
1 AATCTCACCGCTACAATAACC
52187693 AATCTCACCGC
1 AATCTCACCGC
52187704 CACCGCCGTT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.34, C:0.36, G:0.06, T:0.25
Consensus pattern (21 bp):
AATCTCACCGCTACAATAACC
Found at i:52198646 original size:17 final size:18
Alignment explanation
Indices: 52198609--52198646 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
52198599 TAATTTTCAA
* *
52198609 AAATTTAAAATAATTTTT
1 AAATTCAAAATAATTTAT
52198627 AAATTCAAAAT-ATTTAT
1 AAATTCAAAATAATTTAT
52198644 AAA
1 AAA
52198647 AATTTCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATTCAAAATAATTTAT
Found at i:52198657 original size:27 final size:26
Alignment explanation
Indices: 52198604--52198658 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
52198594 ATAAATAATT
**
52198604 TTCAAAAATTTAAAATAATTTTTAAA
1 TTCAAAAATTTAAAATAATTTCAAAA
52198630 TTCAAAATATTTATAAA-AATTTCAAAA
1 TTCAAAA-ATTTA-AAATAATTTCAAAA
52198657 TT
1 TT
52198659 TATATATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 7 0.28
27 15 0.60
28 3 0.12
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (26 bp):
TTCAAAAATTTAAAATAATTTCAAAA
Found at i:52212770 original size:42 final size:42
Alignment explanation
Indices: 52212704--52212792 Score: 117
Period size: 42 Copynumber: 2.1 Consensus size: 42
52212694 TGCTAAACAG
** *
52212704 AAACCCATAAGGGTTGAACGGAAGCTCGTAAGAGCTGAACGA
1 AAACCCATAAGGGTTGAACGGAAGCTCAAAAAAGCTGAACGA
* *
52212746 AAACCTATAAGGGTT-AAGCTGAAGCTCAAAAAAGCTGAACGA
1 AAACCCATAAGGGTTGAA-CGGAAGCTCAAAAAAGCTGAACGA
52212788 AAACC
1 AAACC
52212793 AATTATGGTT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
41 2 0.05
42 39 0.95
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.15
Consensus pattern (42 bp):
AAACCCATAAGGGTTGAACGGAAGCTCAAAAAAGCTGAACGA
Found at i:52215143 original size:5 final size:5
Alignment explanation
Indices: 52215133--52215157 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
52215123 AAAACTTTTA
52215133 CTCCC CTCCC CTCCC CTCCC CTCCC
1 CTCCC CTCCC CTCCC CTCCC CTCCC
52215158 AACCCCCCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.80, G:0.00, T:0.20
Consensus pattern (5 bp):
CTCCC
Found at i:52215291 original size:30 final size:31
Alignment explanation
Indices: 52215257--52215316 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
52215247 AAACCTTTTA
*
52215257 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
52215287 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
52215317 TCACACCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:52218642 original size:14 final size:16
Alignment explanation
Indices: 52218614--52218645 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
52218604 AAATAATTAT
52218614 ATTATATATACTAAAA
1 ATTATATATACTAAAA
52218630 ATTATAT-TA-TAAAA
1 ATTATATATACTAAAA
52218644 AT
1 AT
52218646 AAATTATGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 2 0.12
16 7 0.44
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (16 bp):
ATTATATATACTAAAA
Found at i:52223918 original size:3 final size:3
Alignment explanation
Indices: 52223910--52223940 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
52223900 CTTACTCCTT
52223910 TTC TTC TTC TTC TTC TTC TTC TTC TT- TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
52223941 TCTCTCAGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:52225593 original size:16 final size:18
Alignment explanation
Indices: 52225557--52225615 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
52225547 TATATTATAA
*
52225557 TAATAGTTATATATGTAT
1 TAATAATTATATATGTAT
52225575 TAATAATTATATAT-T-T
1 TAATAATTATATATGTAT
*
52225591 TAAT-ATTATTTTATGTAT
1 TAATAATTA-TATATGTAT
52225609 TAATAAT
1 TAATAAT
52225616 ATACTAATCT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
15 4 0.11
16 9 0.26
17 2 0.06
18 18 0.51
19 2 0.06
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (18 bp):
TAATAATTATATATGTAT
Found at i:52228890 original size:21 final size:21
Alignment explanation
Indices: 52228866--52228937 Score: 99
Period size: 21 Copynumber: 3.4 Consensus size: 21
52228856 TTAATAACCT
* *
52228866 TGGTCAAAATAGTTGTGGTGA
1 TGGTCAAAATTGTTATGGTGA
* *
52228887 TGGTCCAAATTGTTATGGTGC
1 TGGTCAAAATTGTTATGGTGA
*
52228908 TGGTCAAAATTGTTATGATGA
1 TGGTCAAAATTGTTATGGTGA
52228929 TGGTCAAAA
1 TGGTCAAAA
52228938 GTGAGGTTAT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.29, C:0.08, G:0.28, T:0.35
Consensus pattern (21 bp):
TGGTCAAAATTGTTATGGTGA
Found at i:52239365 original size:22 final size:22
Alignment explanation
Indices: 52239334--52239379 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
52239324 GTAAGGGGGT
*
52239334 GTAAAGGGGATAAATAATTCCA
1 GTAAAAGGGATAAATAATTCCA
52239356 GTAAAAGGGATAAATAATTCCA
1 GTAAAAGGGATAAATAATTCCA
52239378 GT
1 GT
52239380 TTCTCCCCCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.46, C:0.09, G:0.22, T:0.24
Consensus pattern (22 bp):
GTAAAAGGGATAAATAATTCCA
Found at i:52247728 original size:31 final size:30
Alignment explanation
Indices: 52247684--52247797 Score: 92
Period size: 31 Copynumber: 3.8 Consensus size: 30
52247674 AAAAATGTAT
52247684 CAAATTAGAAAAAAGAGTCAAGTTTAGGTAC
1 CAAATTAG-AAAAAGAGTCAAGTTTAGGTAC
** * *
52247715 CAAATTAAGAAAAATTGTCAAATTTGGGTAC
1 CAAATT-AGAAAAAGAGTCAAGTTTAGGTAC
* *
52247746 CAAATTGGACCAAAA-A---AAGTTTAGGTAG
1 CAAATTAGA--AAAAGAGTCAAGTTTAGGTAC
*
52247774 CAAATTAAGAAAAAGTGTCAAGTT
1 CAAATT-AGAAAAAGAGTCAAGTT
52247798 CAAGTACCGA
Statistics
Matches: 64, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
27 4 0.06
28 15 0.23
29 2 0.03
30 2 0.03
31 35 0.55
32 6 0.09
ACGTcount: A:0.47, C:0.10, G:0.18, T:0.25
Consensus pattern (30 bp):
CAAATTAGAAAAAGAGTCAAGTTTAGGTAC
Found at i:52248885 original size:9 final size:9
Alignment explanation
Indices: 52248871--52248978 Score: 127
Period size: 9 Copynumber: 12.4 Consensus size: 9
52248861 GTAGTGATTC
*
52248871 AATTTGGTT
1 AATTCGGTT
*
52248880 AATTTGGTT
1 AATTCGGTT
*
52248889 AATTCGGGT
1 AATTCGGTT
52248898 AATTCGGTT
1 AATTCGGTT
*
52248907 AATTCGGGT
1 AATTCGGTT
52248916 AATTCGGTT
1 AATTCGGTT
*
52248925 AATTCGGGT
1 AATTCGGTT
52248934 AATTCGG--
1 AATTCGGTT
52248941 --TTCGGTT
1 AATTCGGTT
52248948 AATTCAGG-T
1 AATTC-GGTT
52248957 AATTCGGTT
1 AATTCGGTT
52248966 AATTCGGTT
1 AATTCGGTT
52248975 AATT
1 AATT
52248979 TTTAACCAAA
Statistics
Matches: 87, Mismatches: 6, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
5 5 0.06
8 2 0.02
9 78 0.90
10 2 0.02
ACGTcount: A:0.23, C:0.09, G:0.25, T:0.43
Consensus pattern (9 bp):
AATTCGGTT
Found at i:52248958 original size:41 final size:41
Alignment explanation
Indices: 52248900--52248978 Score: 140
Period size: 41 Copynumber: 1.9 Consensus size: 41
52248890 ATTCGGGTAA
*
52248900 TTCGGTTAATTCGGGTAATTCGGTTAATTCGGGTAATTCGG
1 TTCGGTTAATTCAGGTAATTCGGTTAATTCGGGTAATTCGG
*
52248941 TTCGGTTAATTCAGGTAATTCGGTTAATTCGGTTAATT
1 TTCGGTTAATTCAGGTAATTCGGTTAATTCGGGTAATT
52248979 TTTAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.22, C:0.11, G:0.25, T:0.42
Consensus pattern (41 bp):
TTCGGTTAATTCAGGTAATTCGGTTAATTCGGGTAATTCGG
Found at i:52249665 original size:15 final size:15
Alignment explanation
Indices: 52249647--52249677 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
52249637 CTTTTCTTTC
*
52249647 TATTTTTTTTTGTTT
1 TATTTTGTTTTGTTT
52249662 TATTTTGTTTTGTTT
1 TATTTTGTTTTGTTT
52249677 T
1 T
52249678 TCTCCTGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.06, C:0.00, G:0.10, T:0.84
Consensus pattern (15 bp):
TATTTTGTTTTGTTT
Found at i:52250285 original size:20 final size:19
Alignment explanation
Indices: 52250244--52250286 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
52250234 AATCTAGTCC
*
52250244 ATTTTTTTATTGTTTTACT
1 ATTTTTTTATTGTGTTACT
* *
52250263 ATTTTTTTTTTGATGTTATT
1 ATTTTTTTATTG-TGTTACT
52250283 ATTT
1 ATTT
52250287 CTATTATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.16, C:0.02, G:0.07, T:0.74
Consensus pattern (19 bp):
ATTTTTTTATTGTGTTACT
Found at i:52250371 original size:23 final size:23
Alignment explanation
Indices: 52250327--52250379 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
52250317 ATTACTACTG
*
52250327 TATATACATGCGCATAGGTTTTT
1 TATATACATGCACATAGGTTTTT
*
52250350 TATATA-ATGCACATATGTTTTT
1 TATATACATGCACATAGGTTTTT
52250372 TAGTATAC
1 TA-TATAC
52250380 GTTTATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 16 0.62
23 10 0.38
ACGTcount: A:0.30, C:0.11, G:0.13, T:0.45
Consensus pattern (23 bp):
TATATACATGCACATAGGTTTTT
Found at i:52263682 original size:11 final size:11
Alignment explanation
Indices: 52263668--52263706 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
52263658 TTAAAAAATA
52263668 TATAAATTAAT
1 TATAAATTAAT
*
52263679 TATAAAGTATAT
1 TATAAATTA-AT
52263691 TATTAAATTAAT
1 TA-TAAATTAAT
52263703 TATA
1 TATA
52263707 TTATAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 10 0.42
12 8 0.33
13 6 0.25
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (11 bp):
TATAAATTAAT
Found at i:52263718 original size:14 final size:17
Alignment explanation
Indices: 52263686--52263723 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 17
52263676 AATTATAAAG
52263686 TATATTATTAAATTAAT
1 TATATTATTAAATTAAT
52263703 TATATTA-TAAA-T-AT
1 TATATTATTAAATTAAT
52263717 TATATTA
1 TATATTA
52263724 AGAAATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.43
15 1 0.05
16 4 0.19
17 7 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATTATTAAATTAAT
Found at i:52279214 original size:18 final size:18
Alignment explanation
Indices: 52279191--52279240 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
52279181 AATATAAATC
52279191 TTAAATAAATAATAGAAA
1 TTAAATAAATAATAGAAA
52279209 TTAAATAAA-AAT-GAAA
1 TTAAATAAATAATAGAAA
52279225 -TAAA-AAATAAGTAGAA
1 TTAAATAAATAA-TAGAA
52279241 CAAAATTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
14 3 0.10
15 6 0.21
16 5 0.17
17 6 0.21
18 9 0.31
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (18 bp):
TTAAATAAATAATAGAAA
Found at i:52286635 original size:35 final size:36
Alignment explanation
Indices: 52286587--52286655 Score: 122
Period size: 35 Copynumber: 1.9 Consensus size: 36
52286577 ATTTGTTAGA
52286587 TATTGATTATGTTTTAACCTTGTTGGATATTGAATT
1 TATTGATTATGTTTTAACCTTGTTGGATATTGAATT
*
52286623 TATT-ATTATGTTTTAAGCTTGTTGGATATTGAA
1 TATTGATTATGTTTTAACCTTGTTGGATATTGAA
52286656 ATGATTGACA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 28 0.88
36 4 0.12
ACGTcount: A:0.26, C:0.04, G:0.17, T:0.52
Consensus pattern (36 bp):
TATTGATTATGTTTTAACCTTGTTGGATATTGAATT
Found at i:52288022 original size:20 final size:20
Alignment explanation
Indices: 52287997--52288036 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
52287987 AATATTTTCC
*
52287997 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
52288017 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
52288037 TCAGTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:52288045 original size:34 final size:34
Alignment explanation
Indices: 52287985--52288050 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 34
52287975 CAAACACCAG
* *
52287985 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCAGTTTAC-GAAAAGT
52288020 AAAACATTTTCCAG-AAATCAGTTTACGAAAA
1 AAAACATTTTCCAGTAAATCAGTTTACGAAAA
52288051 ATATTTTACT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 5 0.17
34 11 0.38
35 13 0.45
ACGTcount: A:0.47, C:0.14, G:0.09, T:0.30
Consensus pattern (34 bp):
AAAACATTTTCCAGTAAATCAGTTTACGAAAAGT
Found at i:52294158 original size:29 final size:30
Alignment explanation
Indices: 52294125--52294189 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 30
52294115 AAGGAATCTA
*
52294125 TTTGCATACATCATTAAAATTTTA-ATAGT
1 TTTGCATACATCATTAAAATTTTAGATACT
* **
52294154 TTTGCATACATTATTACTATTTTAGATACT
1 TTTGCATACATCATTAAAATTTTAGATACT
52294184 TTTGCA
1 TTTGCA
52294190 GGGAATCTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 21 0.68
30 10 0.32
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.48
Consensus pattern (30 bp):
TTTGCATACATCATTAAAATTTTAGATACT
Found at i:52294292 original size:33 final size:33
Alignment explanation
Indices: 52294234--52294301 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
52294224 ATTCCCTGAA
* *
52294234 TCATTTCAGAAACTTTGCAATGAATCTCACTAT
1 TCATCTCAGAAACTTTGCAAGGAATCTCACTAT
* *
52294267 TCATCTCATAAACTTTGTAAGGAATCTCACTAT
1 TCATCTCAGAAACTTTGCAAGGAATCTCACTAT
52294300 TC
1 TC
52294302 CTTGAATCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.32, C:0.22, G:0.09, T:0.37
Consensus pattern (33 bp):
TCATCTCAGAAACTTTGCAAGGAATCTCACTAT
Found at i:52297606 original size:42 final size:40
Alignment explanation
Indices: 52297540--52297674 Score: 144
Period size: 42 Copynumber: 3.2 Consensus size: 40
52297530 AGGCTGCAAA
* * * * *
52297540 GAAGCACATAAGTGCTAAATGGAAACTCGTAAGGGTTAAACG
1 GAAGCTCATAAGAGCTGAACGGAAAC-C-TAAGGGTTAAACT
52297582 GAAGCTCATAAGAGCTGAACGGAAACCCATAAGGGTTAAACT
1 GAAGCTCATAAGAGCTGAACGGAAA-CC-TAAGGGTTAAACT
* **
52297624 GAAGCTCAAAAGAGCTGAACTAAAACCTGAAGGGTTAAACT
1 GAAGCTCATAAGAGCTGAACGGAAACCT-AAGGGTTAAACT
*
52297665 GAAACTCATA
1 GAAGCTCATA
52297675 TGAGTTAACT
Statistics
Matches: 80, Mismatches: 11, Indels: 5
0.83 0.11 0.05
Matches are distributed among these distances:
40 1 0.01
41 22 0.28
42 56 0.70
43 1 0.01
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.18
Consensus pattern (40 bp):
GAAGCTCATAAGAGCTGAACGGAAACCTAAGGGTTAAACT
Found at i:52297707 original size:21 final size:21
Alignment explanation
Indices: 52297546--52297709 Score: 102
Period size: 21 Copynumber: 7.9 Consensus size: 21
52297536 CAAAGAAGCA
*
52297546 CATAAGTGCTAAA-TGGAAACT
1 CATAAGAGCTAAACT-GAAACT
* * * * *
52297567 CGTAAGGGTTAAACGGAAGCT
1 CATAAGAGCTAAACTGAAACT
* * *
52297588 CATAAGAGCTGAACGGAAACC
1 CATAAGAGCTAAACTGAAACT
* * *
52297609 CATAAGGGTTAAACTGAAGCT
1 CATAAGAGCTAAACTGAAACT
* * *
52297630 CAAAAGAGCTGAACTAAAAC-
1 CATAAGAGCTAAACTGAAACT
* *
52297650 C-TGAAGGGTTAAACTGAAACT
1 CAT-AAGAGCTAAACTGAAACT
* * *
52297671 CATATGAG-TTAACTGAAGCT
1 CATAAGAGCTAAACTGAAACT
52297691 CATAAGAGCTAAACTGAAA
1 CATAAGAGCTAAACTGAAA
52297710 GCAAACACGG
Statistics
Matches: 103, Mismatches: 35, Indels: 10
0.70 0.24 0.07
Matches are distributed among these distances:
20 31 0.30
21 71 0.69
22 1 0.01
ACGTcount: A:0.42, C:0.16, G:0.22, T:0.20
Consensus pattern (21 bp):
CATAAGAGCTAAACTGAAACT
Found at i:52300943 original size:6 final size:6
Alignment explanation
Indices: 52300934--52300997 Score: 58
Period size: 6 Copynumber: 10.2 Consensus size: 6
52300924 TAAGTCTAAG
**
52300934 AAAATA AAAATAA AGAAACTAA AAAATA AAAATA AAAATA AAGCT- AAAATA
1 AAAATA AAAAT-A A-AAA-T-A AAAATA AAAATA AAAATA AAAATA AAAATA
*
52300985 AAAAGA AAAATA A
1 AAAATA AAAATA A
52300998 TAAAAAGAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
5 3 0.06
6 32 0.67
7 3 0.06
8 6 0.12
9 4 0.08
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.14
Consensus pattern (6 bp):
AAAATA
Found at i:52300965 original size:28 final size:27
Alignment explanation
Indices: 52300934--52301008 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 27
52300924 TAAGTCTAAG
* *
52300934 AAAATAAAAATAAAGAAACTAAAAAATA
1 AAAATAAAAATAAAGAAAAT-AAAAAGA
52300962 AAAATAAAAATAAAGCTAAAATAAAAAGA
1 AAAATAAAAATAAAG--AAAATAAAAAGA
*
52300991 AAAATAATAA-AAAGAAAA
1 AAAATAAAAATAAAGAAAA
52301009 CGAAAATCGA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
26 4 0.10
28 19 0.45
29 15 0.36
30 4 0.10
ACGTcount: A:0.79, C:0.03, G:0.05, T:0.13
Consensus pattern (27 bp):
AAAATAAAAATAAAGAAAATAAAAAGA
Found at i:52301021 original size:7 final size:7
Alignment explanation
Indices: 52301005--52301049 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
52300995 TAATAAAAAG
52301005 AAAACGA
1 AAAACGA
*
52301012 AAATCGA
1 AAAACGA
52301019 AAAACGA
1 AAAACGA
52301026 AAAACGA
1 AAAACGA
*
52301033 AAATC-A
1 AAAACGA
*
52301039 AAAAAGA
1 AAAACGA
52301046 AAAA
1 AAAA
52301050 AAAACTCAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
6 4 0.12
7 28 0.88
ACGTcount: A:0.73, C:0.11, G:0.11, T:0.04
Consensus pattern (7 bp):
AAAACGA
Found at i:52301050 original size:21 final size:21
Alignment explanation
Indices: 52300999--52301049 Score: 79
Period size: 20 Copynumber: 2.5 Consensus size: 21
52300989 GAAAAATAAT
52300999 AAAAAG-AAAACGAAAATCGA
1 AAAAAGAAAAACGAAAATCGA
*
52301019 AAAACGAAAAACGAAAATC-A
1 AAAAAGAAAAACGAAAATCGA
52301039 AAAAAGAAAAA
1 AAAAAGAAAAA
52301050 AAAACTCAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.75, C:0.10, G:0.12, T:0.04
Consensus pattern (21 bp):
AAAAAGAAAAACGAAAATCGA
Found at i:52305746 original size:12 final size:12
Alignment explanation
Indices: 52305729--52305753 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
52305719 ATGATCTCTC
52305729 GTGGGATTTCTT
1 GTGGGATTTCTT
52305741 GTGGGATTTCTT
1 GTGGGATTTCTT
52305753 G
1 G
52305754 CAGAGAAGGT
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:0.08, C:0.08, G:0.36, T:0.48
Consensus pattern (12 bp):
GTGGGATTTCTT
Found at i:52305971 original size:287 final size:287
Alignment explanation
Indices: 52305455--52305986 Score: 913
Period size: 287 Copynumber: 1.9 Consensus size: 287
52305445 TGATCTCTCA
52305455 TGGGATTTCTTGCAGAGAAGGTTAAGCCACATGGTCACTACCATTAACAGAAGATTTAAAATCAT
1 TGGGATTTCTTGCAGAGAAGGTTAAGCCACATGGTCACTACCATTAACAGAAGATTTAAAATCAT
* * * * *
52305520 CTTGATCACTATATGTTATAACAGGATCACGAGCTTGTAGAGTAATCGATTCGTCACCTACACGA
66 CTTAATCACTAGATGTTATAACAGAATCACAAGCTTGAAGAGTAATCGATTCGTCACCTACACGA
* *
52305585 AGTATTAACTCACCCGTACCAACATCAATTATGGTTCTAGTAGTTGCTAAAAAGGGCCGCCCTAA
131 AGTATTAACTCACCAGTACCAACATCAATTATGGTTCTAGCAGTTGCTAAAAAGGGCCGCCCTAA
*
52305650 AATTAAAGGTACCTCACTGTCCTCATCCATGTCTAAAACAACAAAGTCAATAGAATCACGAGCTC
196 AATTAAAGGTACCTCACTGTCCTCATCAATGTCTAAAACAACAAAGTCAATAGAATCACGAGCTC
52305715 CTTTATGATCTCTCGTGGGATTTCTTG
261 CTTTATGATCTCTCGTGGGATTTCTTG
*
52305742 TGGGATTTCTTGCAGAGAAGGTTGAGCCACATGGTCACTACCATTAACAGAAGATTTAAAATCAT
1 TGGGATTTCTTGCAGAGAAGGTTAAGCCACATGGTCACTACCATTAACAGAAGATTTAAAATCAT
* *
52305807 CTTAATCACTAGATGTTATAACAGAATCATAAGCTTGAAGAGTAATTGATTCGTCACCTACAC-A
66 CTTAATCACTAGATGTTATAACAGAATCACAAGCTTGAAGAGTAATCGATTCGTCACCTACACGA
* * * *
52305871 AGGTATTAACTCACCAGTACCAACATCAGTTATGGTTCTAGCAGTTGTTAAAAAGGGTCGTCCTA
131 A-GTATTAACTCACCAGTACCAACATCAATTATGGTTCTAGCAGTTGCTAAAAAGGGCCGCCCTA
52305936 AAATTAAAGGTACCTCACTGTCCTCATCAATGTCTAAAACAACAAAGTCAA
195 AAATTAAAGGTACCTCACTGTCCTCATCAATGTCTAAAACAACAAAGTCAA
52305987 CAGGGAATAT
Statistics
Matches: 229, Mismatches: 15, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
286 2 0.01
287 227 0.99
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (287 bp):
TGGGATTTCTTGCAGAGAAGGTTAAGCCACATGGTCACTACCATTAACAGAAGATTTAAAATCAT
CTTAATCACTAGATGTTATAACAGAATCACAAGCTTGAAGAGTAATCGATTCGTCACCTACACGA
AGTATTAACTCACCAGTACCAACATCAATTATGGTTCTAGCAGTTGCTAAAAAGGGCCGCCCTAA
AATTAAAGGTACCTCACTGTCCTCATCAATGTCTAAAACAACAAAGTCAATAGAATCACGAGCTC
CTTTATGATCTCTCGTGGGATTTCTTG
Found at i:52308078 original size:20 final size:20
Alignment explanation
Indices: 52308053--52308090 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
52308043 AAATATAATG
52308053 TAAAAATTA-AACTAAAAAAA
1 TAAAAATTATAA-TAAAAAAA
52308073 TAAAAATTATAATAAAAA
1 TAAAAATTATAATAAAAA
52308091 TAAAAATGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (20 bp):
TAAAAATTATAATAAAAAAA
Found at i:52309719 original size:19 final size:18
Alignment explanation
Indices: 52309695--52309734 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
52309685 TTGTTATAAC
52309695 TTTATAAAATAAACATTTT
1 TTTATAAAATAAAC-TTTT
*
52309714 TTTATAATATAAACTTTT
1 TTTATAAAATAAACTTTT
52309732 TTT
1 TTT
52309735 GGCCATAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (18 bp):
TTTATAAAATAAACTTTT
Found at i:52314568 original size:50 final size:50
Alignment explanation
Indices: 52314514--52314696 Score: 212
Period size: 50 Copynumber: 3.7 Consensus size: 50
52314504 AATATGTGAG
* * **
52314514 CCATGTATGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAACTC
52314564 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAACTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAACTC
* * * * * *
52314614 CCATGTAAGACCATATCTGGGATATGACATTGGCA--GTACA-AAAAACAT-
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGAGAAC-TC
* *
52314662 CTATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCA
52314697 TATTATTATC
Statistics
Matches: 116, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
48 35 0.30
49 3 0.03
50 78 0.67
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.23
Consensus pattern (50 bp):
CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAACTC
Found at i:52319410 original size:5 final size:5
Alignment explanation
Indices: 52319400--52319425 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
52319390 CTCAAAAATT
52319400 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
52319426 CGAATGCTCA
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:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:52319671 original size:46 final size:44
Alignment explanation
Indices: 52319604--52319839 Score: 229
Period size: 46 Copynumber: 5.6 Consensus size: 44
52319594 ATTTGAGTAC
* *
52319604 ATCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGTTACACTT
1 ATCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAG-TACACTT
52319650 ATCTGATCAAGTGACAAAGTGATAA---GTA-C-T-G--CACTT
1 ATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGTACACTT
* *
52319686 ATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTT
1 ATCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAG-TACACTT
*
52319732 ATCTGATCAAGTGAAAAAGTGATAA---GT-GC----TACACTT
1 ATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGTACACTT
*
52319768 ATCTGATCAAGTGACAATGTGATAAGTGGTAGCCTTAGCTACACTT
1 ATCTGATCAAGTGACAAAGTGATAAGTGGTAG-CTTAG-TACACTT
*
52319814 ATCTGATC-AGGGAC-AAGTGATAAGTG
1 ATCTGATCAAGTGACAAAGTGATAAGTG
52319840 ATCATACGTA
Statistics
Matches: 159, Mismatches: 11, Indels: 42
0.75 0.05 0.20
Matches are distributed among these distances:
36 59 0.37
39 5 0.03
40 3 0.02
41 1 0.01
42 4 0.03
43 5 0.03
44 11 0.07
45 5 0.03
46 66 0.42
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (44 bp):
ATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGTACACTT
Found at i:52319686 original size:36 final size:36
Alignment explanation
Indices: 52319645--52319794 Score: 165
Period size: 36 Copynumber: 3.9 Consensus size: 36
52319635 GCTTTAGTTA
52319645 CACTTATCTGATCAAGTGACAAAGTGATAAGTACTG
1 CACTTATCTGATCAAGTGACAAAGTGATAAGTACTG
*
52319681 CACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAG
1 CACTTATCTGATCAAGTGACAAAGTGATAA--G-TA-C--T-G
* * *
52319724 CTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGCTA
1 ---CACTTATCTGATCAAGTGACAAAGTGATAAGTACTG
*
52319763 CACTTATCTGATCAAGTGACAATGTGATAAGT
1 CACTTATCTGATCAAGTGACAAAGTGATAAGT
52319795 GGTAGCCTTA
Statistics
Matches: 97, Mismatches: 7, Indels: 20
0.78 0.06 0.16
Matches are distributed among these distances:
36 59 0.61
38 1 0.01
39 2 0.02
40 2 0.02
42 2 0.02
43 2 0.02
44 1 0.01
46 28 0.29
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (36 bp):
CACTTATCTGATCAAGTGACAAAGTGATAAGTACTG
Found at i:52319741 original size:82 final size:82
Alignment explanation
Indices: 52319604--52319838 Score: 366
Period size: 82 Copynumber: 2.9 Consensus size: 82
52319594 ATTTGAGTAC
* *
52319604 ATCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGTTACACTTATCTGATCAAGTGACAAAG
1 ATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAG
*
52319669 TGATAAGTACTGCACTT
66 TGATAAGTACTACACTT
* *
52319686 ATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAG
1 ATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAG
*
52319751 TGATAAGTGCTACACTT
66 TGATAAGTACTACACTT
* * * *
52319768 ATCTGATCAAGTGACAATGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATC-AGGGAC-AAG
1 ATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAG
52319831 TGATAAGT
66 TGATAAGT
52319839 GATCATACGT
Statistics
Matches: 141, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
80 11 0.08
81 4 0.03
82 126 0.89
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.29
Consensus pattern (82 bp):
ATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAG
TGATAAGTACTACACTT
Found at i:52321524 original size:11 final size:11
Alignment explanation
Indices: 52321508--52321541 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
52321498 TTATATACTA
52321508 AATAAAATAAT
1 AATAAAATAAT
*
52321519 AATAAAATATT
1 AATAAAATAAT
52321530 AATAAAATAAT
1 AATAAAATAAT
52321541 A
1 A
52321542 TTTTCTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:52328714 original size:21 final size:21
Alignment explanation
Indices: 52328675--52328716 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
52328665 TTTACCTAGG
* *
52328675 ATGTGAATTGGATGGAATTGA
1 ATGTGAATTGCATGAAATTGA
*
52328696 ATGTGAATTGCATTAAATTGA
1 ATGTGAATTGCATGAAATTGA
52328717 GTTAAATTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.36
Consensus pattern (21 bp):
ATGTGAATTGCATGAAATTGA
Found at i:52329198 original size:64 final size:64
Alignment explanation
Indices: 52329090--52329216 Score: 155
Period size: 64 Copynumber: 2.0 Consensus size: 64
52329080 CGAGCATCCC
* * * ** * * * * * *
52329090 GATCGGTATTGATCCTGCATGTGTTGCGGATATATCGCAGCTCTTTGTGAGCGTCCTGTTATAT
1 GATCGGTATGGATCCTACATATAATGCGGACATACCGCAACTCTTTATGAACGTCCTGATATAT
52329154 GATCGGTATGGATCCTACATATAATGCGGACATACCGCAACTCTTTATGAACGTCCTGATATA
1 GATCGGTATGGATCCTACATATAATGCGGACATACCGCAACTCTTTATGAACGTCCTGATATA
52329217 GGCTCTTTGT
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
64 52 1.00
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (64 bp):
GATCGGTATGGATCCTACATATAATGCGGACATACCGCAACTCTTTATGAACGTCCTGATATAT
Found at i:52329335 original size:23 final size:24
Alignment explanation
Indices: 52329309--52329355 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
52329299 GAGTTACTTG
*
52329309 TTAAGCTC-AATGAGCTTCCTGTT
1 TTAAACTCTAATGAGCTTCCTGTT
* *
52329332 TTAAACTCTTATGAGTTTCCTGTT
1 TTAAACTCTAATGAGCTTCCTGTT
52329356 ATAGCCTGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.21, C:0.19, G:0.15, T:0.45
Consensus pattern (24 bp):
TTAAACTCTAATGAGCTTCCTGTT
Found at i:52334379 original size:11 final size:11
Alignment explanation
Indices: 52334363--52334388 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
52334353 AAATGGAAGC
52334363 AAAAAAAAGAA
1 AAAAAAAAGAA
52334374 AAAAAAAAGAA
1 AAAAAAAAGAA
52334385 AAAA
1 AAAA
52334389 GAGACCTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:52344273 original size:26 final size:26
Alignment explanation
Indices: 52344243--52344292 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
52344233 CATGTATGTG
*
52344243 AAAATATGTATGAATTATAAAATGGA
1 AAAATATATATGAATTATAAAATGGA
* *
52344269 AAAATGTATATGTATTATAAAATG
1 AAAATATATATGAATTATAAAATG
52344293 TAAATGTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (26 bp):
AAAATATATATGAATTATAAAATGGA
Done.