Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 134 of 325
Found at i:40553023 original size:37 final size:37
Alignment explanation
Indices: 40552976--40553055 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
40552966 GGCATGAAGG
* * *
40552976 CCCGAATATAATACCAGCACTAGGCCTACGGGATTTAT
1 CCCG-ATATAATACCAGCACGAAGCCTACGGGATTTAA
*
40553014 CCCGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGATATAATACCAGCACGAAGCCTACGGGATTTAA
40553051 CCCGA
1 CCCGA
40553056 ATACACATCA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
37 34 0.89
38 4 0.11
ACGTcount: A:0.31, C:0.29, G:0.20, T:0.20
Consensus pattern (37 bp):
CCCGATATAATACCAGCACGAAGCCTACGGGATTTAA
Found at i:40560598 original size:28 final size:28
Alignment explanation
Indices: 40560566--40560664 Score: 112
Period size: 28 Copynumber: 3.5 Consensus size: 28
40560556 GCAATAAGCC
*
40560566 CGCACACTTAGTGCTTAATAGTCGAACT
1 CGCACACTTAGTGCTTAATAATCGAACT
*
40560594 CGCACACTTAGTGC-TATATAATCAAACT
1 CGCACACTTAGTGCTTA-ATAATCGAACT
* * *
40560622 TGCACACTTAGTGCTGT-ATAATTTGAACC
1 CGCACACTTAGTGCT-TAATAA-TCGAACT
40560651 CGCACACTTAGTGC
1 CGCACACTTAGTGC
40560665 CAATTTGTGA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
27 2 0.03
28 40 0.67
29 17 0.28
30 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTTAATAATCGAACT
Found at i:40567817 original size:28 final size:28
Alignment explanation
Indices: 40567785--40567883 Score: 112
Period size: 28 Copynumber: 3.5 Consensus size: 28
40567775 GCAATAAGCC
*
40567785 CGCACACTTAGTGCTTAATAGTCGAACT
1 CGCACACTTAGTGCTTAATAATCGAACT
*
40567813 CGCACACTTAGTGC-TATATAATCAAACT
1 CGCACACTTAGTGCTTA-ATAATCGAACT
* * *
40567841 TGCACACTTAGTGCTGT-ATAATTTGAACC
1 CGCACACTTAGTGCT-TAATAA-TCGAACT
40567870 CGCACACTTAGTGC
1 CGCACACTTAGTGC
40567884 CAATTTGTGA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
27 2 0.03
28 40 0.67
29 17 0.28
30 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTTAATAATCGAACT
Found at i:40570624 original size:131 final size:132
Alignment explanation
Indices: 40570464--40570840 Score: 393
Period size: 132 Copynumber: 2.9 Consensus size: 132
40570454 GTGAAAACCT
* ** * ** * * *
40570464 AAAGGAATATTCGATCGTTTTGAACAAACGAGAAATCACAACCCAGCACGATAGGGCATGA-TTC
1 AAAGGGATATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAACACGTTAGGGCACGATTTC
* * ** * * * * * * *
40570528 TCGAATTGTCAAACA-CCGAGTATTGCCTTTGTTTTAGAGGATTTTTAGAAGACCTGAATGGAA-
66 GCGAATTGCCAAACATCAAACT-TTGCCTTCGTTTTAAAGAATTTTTAAAAGACATGAATGAAAG
40570591 TCTC
130 T-TC
*
40570595 AAAGGGATATTTGATTATTTTGAGCAAACGAGAAATTGCAACCCAACACGTTAGGGCACGATTTC
1 AAAGGGATATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAACACGTTAGGGCACGATTTC
* * *
40570660 GCGAATTGCCAAATATCAAACTTTGCCTTCGTTTTAAAGAATTTTTAAAAGGCATGAGTGAAAGT
66 GCGAATTGCCAAACATCAAACTTTGCCTTCGTTTTAAAGAATTTTTAAAAGACATGAATGAAAGT
*
40570725 TT
131 TC
* ** * *
40570727 GAAGGGATATTCGATTATTTTGAGCAAACTCGAAATTGCAACCCAACACGTTAGGGCACTATTCC
1 AAAGGGATATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAACACGTTAGGGCACGATTTC
* * * *
40570792 GCGAATTGCCAAATATCGAA-TCTCGTCTTCGTTTTAAAGAATTTTTAAA
66 GCGAATTGCCAAACATCAAACT-TTGCCTTCGTTTTAAAGAATTTTTAAA
40570841 TGAATACTTG
Statistics
Matches: 208, Mismatches: 34, Indels: 7
0.84 0.14 0.03
Matches are distributed among these distances:
131 52 0.25
132 152 0.73
133 4 0.02
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (132 bp):
AAAGGGATATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAACACGTTAGGGCACGATTTC
GCGAATTGCCAAACATCAAACTTTGCCTTCGTTTTAAAGAATTTTTAAAAGACATGAATGAAAGT
TC
Found at i:40570736 original size:132 final size:132
Alignment explanation
Indices: 40570596--40570840 Score: 402
Period size: 132 Copynumber: 1.9 Consensus size: 132
40570586 TGGAATCTCA
* *
40570596 AAGGGATATTTGATTATTTTGAGCAAACGAGAAATTGCAACCCAACACGTTAGGGCACGATTTCG
1 AAGGGATATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAACACGTTAGGGCACGATTCCG
*
40570661 CGAATTGCCAAATATCAAA-CTTTGCCTTCGTTTTAAAGAATTTTTAAAAGGCATGAGTGAAAGT
66 CGAATTGCCAAATATCAAATC-TCGCCTTCGTTTTAAAGAATTTTTAAAAGGCATGAGTGAAAGT
40570725 TTG
130 TTG
** *
40570728 AAGGGATATTCGATTATTTTGAGCAAACTCGAAATTGCAACCCAACACGTTAGGGCACTATTCCG
1 AAGGGATATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAACACGTTAGGGCACGATTCCG
* *
40570793 CGAATTGCCAAATATCGAATCTCGTCTTCGTTTTAAAGAATTTTTAAA
66 CGAATTGCCAAATATCAAATCTCGCCTTCGTTTTAAAGAATTTTTAAA
40570841 TGAATACTTG
Statistics
Matches: 104, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
132 103 0.99
133 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (132 bp):
AAGGGATATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAACACGTTAGGGCACGATTCCG
CGAATTGCCAAATATCAAATCTCGCCTTCGTTTTAAAGAATTTTTAAAAGGCATGAGTGAAAGTT
TG
Found at i:40574827 original size:17 final size:17
Alignment explanation
Indices: 40574805--40574837 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
40574795 TAACTTTAAT
40574805 ATTAAATTTAATATTAG
1 ATTAAATTTAATATTAG
40574822 ATTAAATTTAATATTA
1 ATTAAATTTAATATTA
40574838 AATCTTTTTA
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:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
ATTAAATTTAATATTAG
Found at i:40583271 original size:2 final size:2
Alignment explanation
Indices: 40583266--40583299 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
40583256 CATAGAATTC
40583266 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40583300 TGTGGAATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40587420 original size:14 final size:14
Alignment explanation
Indices: 40587401--40587430 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
40587391 TCTGTAGTCG
40587401 GACAAATAAATTCA
1 GACAAATAAATTCA
40587415 GACAAATAAATTCA
1 GACAAATAAATTCA
40587429 GA
1 GA
40587431 AGAGTTGCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.57, C:0.13, G:0.10, T:0.20
Consensus pattern (14 bp):
GACAAATAAATTCA
Found at i:40591549 original size:46 final size:46
Alignment explanation
Indices: 40591480--40591707 Score: 303
Period size: 46 Copynumber: 5.0 Consensus size: 46
40591470 TTATCTTTGA
* * * * **
40591480 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTTTGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* *
40591526 CATGTTACCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* * * **
40591572 CACGTTGCCATTGTATCTTTCAACCATGGTCTTATTCATTTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* *
40591618 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* *
40591664 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCAT
40591708 ATCAGAGAGC
Statistics
Matches: 161, Mismatches: 21, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 161 1.00
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.41
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
Found at i:40594486 original size:2 final size:2
Alignment explanation
Indices: 40594479--40594503 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40594469 ATGCATCACT
40594479 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
40594504 TGATAAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40595213 original size:23 final size:23
Alignment explanation
Indices: 40595170--40595215 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
40595160 GAATTAGTTT
* *
40595170 GAATTAAGATTAATTAGGTATAA
1 GAATTAAGATTAATAAAGTATAA
40595193 GAATTAA-ATTGAATAAAGTATAA
1 GAATTAAGATT-AATAAAGTATAA
40595216 AAGCTTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.52, C:0.00, G:0.15, T:0.33
Consensus pattern (23 bp):
GAATTAAGATTAATAAAGTATAA
Found at i:40596292 original size:19 final size:20
Alignment explanation
Indices: 40596264--40596301 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
40596254 GAGTATTAGC
*
40596264 ATTGTGATATTGA-ATTGAT
1 ATTGTAATATTGATATTGAT
40596283 ATTGTAATATTGATATTGA
1 ATTGTAATATTGATATTGA
40596302 ATTAAGTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.47
Consensus pattern (20 bp):
ATTGTAATATTGATATTGAT
Found at i:40598539 original size:46 final size:45
Alignment explanation
Indices: 40598489--40598664 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 45
40598479 TGTTTGGGCA
40598489 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
40598535 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
40598582 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
40598628 -CCTGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
40598665 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 12, Indels: 16
0.80 0.09 0.12
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 3 0.03
46 66 0.60
47 32 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.30
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:40598596 original size:93 final size:93
Alignment explanation
Indices: 40598485--40598656 Score: 292
Period size: 93 Copynumber: 1.8 Consensus size: 93
40598475 AGGATGTTTG
*
40598485 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC-GAACTCGTTGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTGAACTCGTTGA
40598549 GTTGAGTCCGAGTTCGAGAGATGTAACTA
65 GTTGAGTCCGAGTTCGAGAGATGTAACTA
* *
40598578 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCTGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCTGAACTCGTTGAG
*
40598643 TTGAGTCTGAGTTC
66 TTGAGTCCGAGTTC
40598657 ACTTATGGGC
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
92 2 0.03
93 72 0.97
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCTGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:40604960 original size:40 final size:40
Alignment explanation
Indices: 40604897--40604993 Score: 126
Period size: 40 Copynumber: 2.5 Consensus size: 40
40604887 CCATCTCCGT
* *
40604897 CCAACCCAACACACC-A-TGTGGGGATAAAATCAACCCAC
1 CCAACCCTACACACCAAGTATGGGGATAAAATCAACCCAC
* * * *
40604935 CCAGCCCTACACACGAAGTATGGGGATAGAATCAACCCAT
1 CCAACCCTACACACCAAGTATGGGGATAAAATCAACCCAC
40604975 CCAACCCTACACACCAAGT
1 CCAACCCTACACACCAAGT
40604994 GGTACTATAT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
38 12 0.24
39 1 0.02
40 36 0.73
ACGTcount: A:0.37, C:0.36, G:0.14, T:0.12
Consensus pattern (40 bp):
CCAACCCTACACACCAAGTATGGGGATAAAATCAACCCAC
Found at i:40612232 original size:40 final size:40
Alignment explanation
Indices: 40612169--40612261 Score: 109
Period size: 40 Copynumber: 2.4 Consensus size: 40
40612159 ATCTTCGTCG
* * *
40612169 AACCCAACACACC--ATGTGGGGATAAAATCGACCCACCC
1 AACCCTACACACCAAATATGGGGATAAAATCAACCCACCC
* * *
40612207 AGCCCTACACACCAAATATGGGGATAGAATCAACCCATCC
1 AACCCTACACACCAAATATGGGGATAAAATCAACCCACCC
*
40612247 AACCTTACACACCAA
1 AACCCTACACACCAA
40612262 GTGGTACCGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
38 11 0.24
40 34 0.76
ACGTcount: A:0.39, C:0.35, G:0.13, T:0.13
Consensus pattern (40 bp):
AACCCTACACACCAAATATGGGGATAAAATCAACCCACCC
Found at i:40626365 original size:13 final size:13
Alignment explanation
Indices: 40626347--40626371 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40626337 AGGCCGTGTG
40626347 AGGGACACGGGCC
1 AGGGACACGGGCC
40626360 AGGGACACGGGC
1 AGGGACACGGGC
40626372 GTGTGCTCAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.28, G:0.48, T:0.00
Consensus pattern (13 bp):
AGGGACACGGGCC
Found at i:40628926 original size:9 final size:9
Alignment explanation
Indices: 40628912--40628941 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
40628902 AATTTGTGTG
40628912 TTTTTTATT
1 TTTTTTATT
40628921 TTTTTTATT
1 TTTTTTATT
40628930 TTTTTTATT
1 TTTTTTATT
40628939 TTT
1 TTT
40628942 CACAAATTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTTTATT
Found at i:40636546 original size:21 final size:21
Alignment explanation
Indices: 40636508--40636547 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
40636498 TTGATATTTT
*
40636508 TTTATGTTTTTTTTAATTTAA
1 TTTATGTTTTTTTCAATTTAA
40636529 TTTAT-TTTTTTATCAATTT
1 TTTATGTTTTTT-TCAATTT
40636548 TTGCTTGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (21 bp):
TTTATGTTTTTTTCAATTTAA
Found at i:40640848 original size:25 final size:25
Alignment explanation
Indices: 40640814--40640865 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
40640804 ATTAAAGAAC
40640814 ATTGAAATTTATCTTTGCATCAATG
1 ATTGAAATTTATCTTTGCATCAATG
40640839 ATTGAAATTTATCTTTGCATCAATG
1 ATTGAAATTTATCTTTGCATCAATG
40640864 AT
1 AT
40640866 CAAGCCCTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.44
Consensus pattern (25 bp):
ATTGAAATTTATCTTTGCATCAATG
Found at i:40653341 original size:26 final size:26
Alignment explanation
Indices: 40653305--40653360 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
40653295 ATCTCAAAAA
40653305 GAGAAGATATGATCAGAACTTATAAT
1 GAGAAGATATGATCAGAACTTATAAT
40653331 GAGAAGATATGATCAGAACTTATAAT
1 GAGAAGATATGATCAGAACTTATAAT
40653357 GAGA
1 GAGA
40653361 TTATTAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.46, C:0.07, G:0.21, T:0.25
Consensus pattern (26 bp):
GAGAAGATATGATCAGAACTTATAAT
Found at i:40653469 original size:70 final size:72
Alignment explanation
Indices: 40653342--40653483 Score: 252
Period size: 70 Copynumber: 2.0 Consensus size: 72
40653332 AGAAGATATG
40653342 ATCAGAACTTATAATGAGATTATTAAAAATAAAAAACTTTACAAGTAATGTATGAAAAGGAAATT
1 ATCAGAACTTATAATGAGATTATTAAAAATAAAAAACTTTACAAGTAATGTATGAAAAGGAAATT
40653407 TTTTTTT
66 TTTTTTT
* *
40653414 ATCAGAATTTATAATGAGATTATT-AAAA-AAAAAACTTTACAAGTAATGTATGAAAAGGAATTT
1 ATCAGAACTTATAATGAGATTATTAAAAATAAAAAACTTTACAAGTAATGTATGAAAAGGAAATT
40653477 TTTTTTT
66 TTTTTTT
40653484 GACAAAATGA
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
70 41 0.60
71 4 0.06
72 23 0.34
ACGTcount: A:0.46, C:0.05, G:0.11, T:0.37
Consensus pattern (72 bp):
ATCAGAACTTATAATGAGATTATTAAAAATAAAAAACTTTACAAGTAATGTATGAAAAGGAAATT
TTTTTTT
Found at i:40653633 original size:2 final size:2
Alignment explanation
Indices: 40653626--40653660 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
40653616 CACATTGTAT
40653626 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 T
40653661 GAGTAATTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:40661188 original size:40 final size:40
Alignment explanation
Indices: 40661128--40661311 Score: 230
Period size: 40 Copynumber: 4.6 Consensus size: 40
40661118 TATTCGAATG
* *
40661128 ATATCCAGGCTAAG-TCCCGAAGGCTTTTATGCTAGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT
* * *
40661168 ATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAG-TGACT
* * *
40661208 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
*
40661248 ATATCCGGGCTAAG-TCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT
*
40661288 ATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGATCCGAAGGC
40661312 CTTGTGCGAG
Statistics
Matches: 125, Mismatches: 14, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
39 1 0.01
40 121 0.97
41 3 0.02
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
Found at i:40661261 original size:80 final size:80
Alignment explanation
Indices: 40661128--40661311 Score: 255
Period size: 80 Copynumber: 2.3 Consensus size: 80
40661118 TATTCGAATG
* * * *
40661128 ATATCCAGGCTAAGTCCCGAAGGCTTTTATGCTAGTGACTATATCCGGACTAAGAT-CCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATCCGGACTAAG-TCCCGAAGGC
* *
40661192 ATTTGTGCGAGTTG-CT
65 ATTTATGCGAG-TGACC
* *
40661208 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACTATATCCGGGCTAAGTCCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATCCGGACTAAGTCCCGAAGGCA
*
40661273 TTTATGCTAGTGACC
66 TTTATGCGAGTGACC
40661288 ATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
40661312 CTTGTGCGAG
Statistics
Matches: 93, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
79 3 0.03
80 90 0.97
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATCCGGACTAAGTCCCGAAGGCA
TTTATGCGAGTGACC
Found at i:40665808 original size:2 final size:2
Alignment explanation
Indices: 40665749--40665791 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
40665739 AAAACTAAAC
40665749 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40665791 A
1 A
40665792 ACTTAATCCT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:40682702 original size:20 final size:17
Alignment explanation
Indices: 40682663--40682696 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
40682653 AGAGGGAGTA
40682663 AGAGTTTGTTGTACTGG
1 AGAGTTTGTTGTACTGG
40682680 AGAGTTTGTTGTACTGG
1 AGAGTTTGTTGTACTGG
40682697 TCGAGAATGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.06, G:0.35, T:0.41
Consensus pattern (17 bp):
AGAGTTTGTTGTACTGG
Found at i:40695599 original size:47 final size:47
Alignment explanation
Indices: 40695548--40695654 Score: 117
Period size: 47 Copynumber: 2.3 Consensus size: 47
40695538 CTATGGGCCG
* *
40695548 TGGTATAGGTATTTAGAGA-AGAGTTACCTTAATTTGGCTACAGCCCA
1 TGGTATAGGTACTCAGAGATA-AGTTACCTTAATTTGGCTACAGCCCA
* * * * * *
40695595 TGGTACAGGTACTCCGGGATAAGTTACCTTTATTTGGCTACGGGCCA
1 TGGTATAGGTACTCAGAGATAAGTTACCTTAATTTGGCTACAGCCCA
*
40695642 TAGTATAGGTACT
1 TGGTATAGGTACT
40695655 TATCAATTAT
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
47 48 0.98
48 1 0.02
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (47 bp):
TGGTATAGGTACTCAGAGATAAGTTACCTTAATTTGGCTACAGCCCA
Found at i:40704300 original size:21 final size:21
Alignment explanation
Indices: 40704274--40704316 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
40704264 AGAAGAGGGA
40704274 TTCCCAAGTACAATCCTAAAT
1 TTCCCAAGTACAATCCTAAAT
40704295 TTCCCAAGTACAATCCTAAAT
1 TTCCCAAGTACAATCCTAAAT
40704316 T
1 T
40704317 GTGAACCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.28, G:0.05, T:0.30
Consensus pattern (21 bp):
TTCCCAAGTACAATCCTAAAT
Found at i:40712990 original size:28 final size:28
Alignment explanation
Indices: 40712902--40712990 Score: 90
Period size: 28 Copynumber: 3.2 Consensus size: 28
40712892 ACCATATGTA
* * * *
40712902 CCATACTCGATACCTCGCACGCTAAGTG
1 CCATTCTCGATACTTTGCACACTAAGTG
* * *
40712930 CTATTCTGGAT-GTTTCGCACACTAAGTG
1 CCATTCTCGATACTTT-GCACACTAAGTG
*
40712958 TCATTCTCGATACTTTGCACACTAAGTG
1 CCATTCTCGATACTTTGCACACTAAGTG
40712986 CCATT
1 CCATT
40712991 TATATATATA
Statistics
Matches: 47, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
27 1 0.02
28 43 0.91
29 3 0.06
ACGTcount: A:0.24, C:0.28, G:0.17, T:0.31
Consensus pattern (28 bp):
CCATTCTCGATACTTTGCACACTAAGTG
Found at i:40717066 original size:43 final size:44
Alignment explanation
Indices: 40717018--40717126 Score: 141
Period size: 43 Copynumber: 2.5 Consensus size: 44
40717008 TCCTAGATAT
* * *
40717018 GGTCTTACATGTTATCACATAT-CGATGCCACTGTCCCACACAG
1 GGTCTTACATGTAATCACATATACAATGCCAATGTCCCACACAG
* * * *
40717061 GGTCTTACATGAAATCACA-ATACAATGTCAATGTCCCAGACAT
1 GGTCTTACATGTAATCACATATACAATGCCAATGTCCCACACAG
40717104 GGTCTTACATGTAATCACATATA
1 GGTCTTACATGTAATCACATATA
40717127 GAGTCGATGC
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
42 2 0.04
43 51 0.91
44 3 0.05
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (44 bp):
GGTCTTACATGTAATCACATATACAATGCCAATGTCCCACACAG
Found at i:40717201 original size:50 final size:45
Alignment explanation
Indices: 40717091--40717256 Score: 147
Period size: 50 Copynumber: 3.5 Consensus size: 45
40717081 TACAATGTCA
* * *
40717091 ATGTCCCAGACATGGTCTTACA-TGTAATCACATAT-AGAGTCGATGCC
1 ATGTCCCAGATATGGTCTTACACTG--A-CACATATCA-AGCCGAAGCC
* *
40717138 ATGTCCCATATATGGTCTTACACTGACTCTCTTATATCAAGGCCGAAGCC
1 ATGTCCCAGATATGGTCTTACACTGA--CAC--ATATCAA-GCCGAAGCC
* * * *
40717188 ATATCCCAGATATGCTCTTACACTGACACATATCAAGCTGATGCC
1 ATGTCCCAGATATGGTCTTACACTGACACATATCAAGCCGAAGCC
*
40717233 ATGTCCCAGACATGGTCTTACACT
1 ATGTCCCAGATATGGTCTTACACT
40717257 AGTTCACATG
Statistics
Matches: 99, Mismatches: 14, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
45 28 0.28
46 8 0.08
47 23 0.23
48 4 0.04
49 5 0.05
50 31 0.31
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.28
Consensus pattern (45 bp):
ATGTCCCAGATATGGTCTTACACTGACACATATCAAGCCGAAGCC
Found at i:40717240 original size:45 final size:48
Alignment explanation
Indices: 40717131--40717256 Score: 150
Period size: 50 Copynumber: 2.6 Consensus size: 48
40717121 CATATAGAGT
* *
40717131 CGATGCCATGTCCCATATATGGTCTTACACTGACTCTCTTATATCAAGGC
1 CGATGCCATGTCCCAGATATGGTCTTACACTGAC-CAC-TATATCAAGGC
* * *
40717181 CGAAGCCATATCCCAGATATGCTCTTACACTGA-CAC-ATATCAA-GC
1 CGATGCCATGTCCCAGATATGGTCTTACACTGACCACTATATCAAGGC
* *
40717226 TGATGCCATGTCCCAGACATGGTCTTACACT
1 CGATGCCATGTCCCAGATATGGTCTTACACT
40717257 AGTTCACATG
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
45 28 0.42
46 7 0.11
48 2 0.03
50 29 0.44
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.28
Consensus pattern (48 bp):
CGATGCCATGTCCCAGATATGGTCTTACACTGACCACTATATCAAGGC
Found at i:40720054 original size:40 final size:39
Alignment explanation
Indices: 40719994--40720075 Score: 110
Period size: 40 Copynumber: 2.1 Consensus size: 39
40719984 TATATATAGT
*
40719994 CGAAGCTATCTCAAATTGCACACCAAGTGCCACTTTTAAC
1 CGAAGCTATCTCAAACTGCACACCAAGTGCCA-TTTTAAC
* * * *
40720034 CGAAGCTATTTCGAACTGCACACTAAGTGCCATTTTAGC
1 CGAAGCTATCTCAAACTGCACACCAAGTGCCATTTTAAC
40720073 CGA
1 CGA
40720076 TAAGTCATTA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
39 9 0.24
40 28 0.76
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (39 bp):
CGAAGCTATCTCAAACTGCACACCAAGTGCCATTTTAAC
Found at i:40723093 original size:13 final size:13
Alignment explanation
Indices: 40723055--40723120 Score: 60
Period size: 13 Copynumber: 4.8 Consensus size: 13
40723045 GGAGTTTGGA
40723055 GTTTATGGTTTAAG
1 GTTTA-GGTTTAAG
* * *
40723069 ATTCATGGTTTAAT
1 GTTTA-GGTTTAAG
40723083 GTTTAGGTTTAAG
1 GTTTAGGTTTAAG
* *
40723096 GTTTAAGTTTAGG
1 GTTTAGGTTTAAG
40723109 GTTTAGAGTTTA
1 GTTTAG-GTTTA
40723121 TTGGTAAGGT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
13 23 0.55
14 19 0.45
ACGTcount: A:0.24, C:0.02, G:0.26, T:0.48
Consensus pattern (13 bp):
GTTTAGGTTTAAG
Found at i:40723120 original size:20 final size:20
Alignment explanation
Indices: 40723075--40723113 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
40723065 TAAGATTCAT
40723075 GGTTTAATGTTTAGGTTTAA
1 GGTTTAATGTTTAGGTTTAA
40723095 GGTTTAA-GTTTAGGGTTTA
1 GGTTTAATGTTTA-GGTTTA
40723114 GAGTTTATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.49
Consensus pattern (20 bp):
GGTTTAATGTTTAGGTTTAA
Found at i:40723438 original size:26 final size:27
Alignment explanation
Indices: 40723376--40723438 Score: 69
Period size: 25 Copynumber: 2.4 Consensus size: 27
40723366 ATTTAGGAAC
40723376 TAATTATTTAATTTTTGAAAATTTTTAA
1 TAATT-TTTAATTTTTGAAAATTTTTAA
**
40723404 TAA-AATTAA-TTTTGAAAATATTTT-A
1 TAATTTTTAATTTTTGAAAAT-TTTTAA
40723429 TAATTTTTAA
1 TAATTTTTAA
40723439 AATTTTTTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
25 14 0.48
26 12 0.41
28 3 0.10
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (27 bp):
TAATTTTTAATTTTTGAAAATTTTTAA
Found at i:40723446 original size:19 final size:19
Alignment explanation
Indices: 40723410--40723445 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
40723400 TTAATAAAAT
40723410 TAATTTTGAAAATATTTTA
1 TAATTTTGAAAATATTTTA
*
40723429 TAATTTTTAAAAT-TTTT
1 TAATTTTGAAAATATTTT
40723446 TGAGGTTAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (19 bp):
TAATTTTGAAAATATTTTA
Found at i:40725574 original size:17 final size:19
Alignment explanation
Indices: 40725552--40725590 Score: 64
Period size: 17 Copynumber: 2.2 Consensus size: 19
40725542 AACAACAATA
40725552 TTTCTCTCGT-T-TTTTCT
1 TTTCTCTCGTCTATTTTCT
40725569 TTTCTCTCGTCTATTTTCT
1 TTTCTCTCGTCTATTTTCT
40725588 TTT
1 TTT
40725591 AGCATTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 10 0.50
18 1 0.05
19 9 0.45
ACGTcount: A:0.03, C:0.23, G:0.05, T:0.69
Consensus pattern (19 bp):
TTTCTCTCGTCTATTTTCT
Found at i:40727287 original size:46 final size:47
Alignment explanation
Indices: 40727116--40727288 Score: 205
Period size: 46 Copynumber: 3.7 Consensus size: 47
40727106 AACCCGCCCC
* * *
40727116 TAAGTGAACTCGGACTCAACTCAACGAGCTC-GAGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATTCACATCCA
*
40727162 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA-G-C-A-TTCACATCCA
* * *
40727210 TCA-CGATCTCGGACTCAACTCAACGAGTTCGGA-CATTCACATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATTCACATCCA
40727255 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
40727289 TGCTCAACCA
Statistics
Matches: 107, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
44 1 0.01
45 2 0.02
46 58 0.54
47 30 0.28
48 3 0.03
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (47 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATTCACATCCA
Found at i:40729948 original size:27 final size:27
Alignment explanation
Indices: 40729907--40729992 Score: 136
Period size: 27 Copynumber: 3.2 Consensus size: 27
40729897 ATCCTATTAA
* *
40729907 CCTTTGTGGCGTACTATGTATGAATTG
1 CCTTTGTGGCATACTATGTATGGATTG
*
40729934 CCTTTGTGGCATACTTTGTATGGATTG
1 CCTTTGTGGCATACTATGTATGGATTG
*
40729961 CCTTTGTGGCATACTCTGTATGGATTG
1 CCTTTGTGGCATACTATGTATGGATTG
40729988 CCTTT
1 CCTTT
40729993 TTGGTGTATT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 55 1.00
ACGTcount: A:0.15, C:0.17, G:0.24, T:0.43
Consensus pattern (27 bp):
CCTTTGTGGCATACTATGTATGGATTG
Found at i:40730005 original size:27 final size:27
Alignment explanation
Indices: 40729907--40730007 Score: 114
Period size: 27 Copynumber: 3.7 Consensus size: 27
40729897 ATCCTATTAA
* * * *
40729907 CCTTTGTGGCGTACTATGTATGAATTG
1 CCTTTGTGGCATATTCTGTATGGATTG
40729934 CCTTTGTGGCATACTT-TGTATGGATTG
1 CCTTTGTGGCATA-TTCTGTATGGATTG
*
40729961 CCTTTGTGGCATACTCTGTATGGATTG
1 CCTTTGTGGCATATTCTGTATGGATTG
* **
40729988 CCTTTTTGGTGTATTCTGTA
1 CCTTTGTGGCATATTCTGTA
40730008 ATAATAAATT
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
26 1 0.02
27 62 0.97
28 1 0.02
ACGTcount: A:0.15, C:0.16, G:0.25, T:0.45
Consensus pattern (27 bp):
CCTTTGTGGCATATTCTGTATGGATTG
Found at i:40731684 original size:30 final size:28
Alignment explanation
Indices: 40731648--40731748 Score: 107
Period size: 28 Copynumber: 3.5 Consensus size: 28
40731638 GACAAGATTG
40731648 GCACTAAGTGTGCGAGTTTAAAATTGTTCA
1 GCACTAAGTGTGCGAGTTTAAAATT-TT-A
*
40731678 GCACTAAGTGTGCGAGTTT--GATTCTATA
1 GCACTAAGTGTGCGAGTTTAAAATT-T-TA
* * *
40731706 GCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGTTTAAAAT-TTTA
40731735 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
40731749 GATTCACTAT
Statistics
Matches: 61, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
28 22 0.36
29 17 0.28
30 21 0.34
31 1 0.02
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTAAAATTTTA
Found at i:40731760 original size:29 final size:28
Alignment explanation
Indices: 40731677--40731752 Score: 75
Period size: 29 Copynumber: 2.7 Consensus size: 28
40731667 AAAATTGTTC
* *
40731677 AGCACTAAGTGTGCGAGTTTGAT-TCTAT
1 AGCACTAAGTGTGCG-GATTGATATATAT
* *
40731705 AGCACTAAGTGTGC-GAGCTGAAAATATAT
1 AGCACTAAGTGTGCGGA-TTG-ATATATAT
40731734 AGCACTAAGTGTGCGGATT
1 AGCACTAAGTGTGCGGATT
40731753 CACTATATGC
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
26 1 0.03
27 2 0.05
28 15 0.38
29 19 0.49
30 2 0.05
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.29
Consensus pattern (28 bp):
AGCACTAAGTGTGCGGATTGATATATAT
Found at i:40739541 original size:29 final size:30
Alignment explanation
Indices: 40739508--40739607 Score: 118
Period size: 29 Copynumber: 3.5 Consensus size: 30
40739498 GACAAGATTG
* *
40739508 GCACTAAGTGTGCG-GTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
* *
40739537 GCACTAAGTGTGCGAGTTT--GATTCTATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
* *
40739565 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
40739594 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
40739608 GATTCACTAT
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
28 23 0.38
29 33 0.54
30 5 0.08
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGTTTAAAATTATATA
Found at i:40748351 original size:28 final size:29
Alignment explanation
Indices: 40748311--40748383 Score: 85
Period size: 29 Copynumber: 2.6 Consensus size: 29
40748301 CCTCCGAGCT
** * *
40748311 CGCACACCCAGTGCCGTAT-TTTTCAGCT
1 CGCACACTTAGTGCCGTATATTTCCAGCA
* *
40748339 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCGTATATTTCCAGCA
40748368 CGCACACTTAGTGCCG
1 CGCACACTTAGTGCCG
40748384 ATCTCGTCAC
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
28 15 0.42
29 21 0.58
ACGTcount: A:0.22, C:0.33, G:0.18, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCGTATATTTCCAGCA
Found at i:40751883 original size:30 final size:30
Alignment explanation
Indices: 40751847--40752006 Score: 213
Period size: 29 Copynumber: 5.5 Consensus size: 30
40751837 GACAAGATTG
* * * * *
40751847 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
* *
40751877 GCACTAAGTGTGCGAGTTTG---ATTATACA
1 GCACTAAGTGTGCGAG-CTGAAAATTATATA
40751905 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
40751934 GCACTAAGTGTGCGAGCTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
40751964 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
40751993 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
40752007 GATTCACTAT
Statistics
Matches: 120, Mismatches: 5, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
27 2 0.02
28 23 0.19
29 48 0.40
30 45 0.38
31 2 0.02
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGCTGAAAATTATATA
Found at i:40751975 original size:59 final size:57
Alignment explanation
Indices: 40751847--40752006 Score: 214
Period size: 59 Copynumber: 2.8 Consensus size: 57
40751837 GACAAGATTG
* * * * * *
40751847 GCACTAAGTGTGCGGGTTTAAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATACA
1 GCACTAAGTGTGCGAGCTGAAAA-TATATAGCACTAAGTGTGCGAGTCTGATTATACA
*
40751905 GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCGAG-CTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCGAGTCTG---ATTATACA
40751964 GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCG
1 GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCG
40752007 GATTCACTAT
Statistics
Matches: 92, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
56 2 0.02
57 20 0.22
58 20 0.22
59 50 0.54
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (57 bp):
GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCGAGTCTGATTATACA
Found at i:40774332 original size:41 final size:37
Alignment explanation
Indices: 40774256--40774350 Score: 100
Period size: 41 Copynumber: 2.5 Consensus size: 37
40774246 TGGTCCACAC
* * *
40774256 GGGCACAGAGAGTTACATGTGTGACCTTGTGTTACAT
1 GGGCACAGAGAGTTACATGTGTGACCTTATATTACAA
*
40774293 GGTCACAGAGAGTTACATGATTGTGTAACCTTATATTACAA
1 GGGCACAGAGAGTTACATG--TGTG--ACCTTATATTACAA
* *
40774334 GGGCATAGTGAGTTACA
1 GGGCACAGAGAGTTACA
40774351 CGGTGTGCAT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 18 0.38
39 4 0.09
41 25 0.53
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.29
Consensus pattern (37 bp):
GGGCACAGAGAGTTACATGTGTGACCTTATATTACAA
Found at i:40777688 original size:10 final size:10
Alignment explanation
Indices: 40777673--40777697 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
40777663 ATTAATGTAG
40777673 TATTTATGAA
1 TATTTATGAA
40777683 TATTTATGAA
1 TATTTATGAA
40777693 TATTT
1 TATTT
40777698 GTATGAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (10 bp):
TATTTATGAA
Found at i:40781610 original size:21 final size:21
Alignment explanation
Indices: 40781586--40781626 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
40781576 ATATTTTTAG
40781586 AATTTTAATATAATTACTAAT
1 AATTTTAATATAATTACTAAT
** *
40781607 AATTTTTTTATAATTTCTAA
1 AATTTTAATATAATTACTAA
40781627 ACTTTTTAGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (21 bp):
AATTTTAATATAATTACTAAT
Found at i:40801087 original size:2 final size:2
Alignment explanation
Indices: 40801080--40801125 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
40801070 AGTATAGTTG
* * *
40801080 AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT AG AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40801122 AT AT
1 AT AT
40801126 TCGGCCATCA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.43
Consensus pattern (2 bp):
AT
Found at i:40801800 original size:29 final size:29
Alignment explanation
Indices: 40801765--40801838 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
40801755 GTTGTGAGAT
*
40801765 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTGCA
*
40801794 TGGCACTAAGTGTGCGAGTTTAAAGTGCA
1 TGGCACTAAGTGTGCGAGTTGAAAGTGCA
*
40801823 CGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
40801839 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.24, C:0.18, G:0.34, T:0.24
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTGCA
Found at i:40812740 original size:8 final size:8
Alignment explanation
Indices: 40812727--40812775 Score: 57
Period size: 9 Copynumber: 6.0 Consensus size: 8
40812717 GTTAATTTAG
40812727 GTTTAATA
1 GTTTAATA
40812735 GTTTAATTA
1 GTTTAA-TA
40812744 GTTT--TA
1 GTTTAATA
40812750 GGTTTAATA
1 -GTTTAATA
40812759 GTTTAATTA
1 GTTTAA-TA
40812768 GTTTAATA
1 GTTTAATA
40812776 AATATATTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
6 2 0.06
7 4 0.11
8 14 0.39
9 16 0.44
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (8 bp):
GTTTAATA
Found at i:40812747 original size:9 final size:9
Alignment explanation
Indices: 40812727--40812774 Score: 52
Period size: 8 Copynumber: 5.8 Consensus size: 9
40812717 GTTAATTTAG
40812727 GTTTAA-TA
1 GTTTAATTA
40812735 GTTTAATTA
1 GTTTAATTA
40812744 G-TT--TTA
1 GTTTAATTA
40812750 GGTTTAA-TA
1 -GTTTAATTA
40812759 GTTTAATTA
1 GTTTAATTA
40812768 GTTTAAT
1 GTTTAAT
40812775 AAATATATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
6 3 0.09
7 1 0.03
8 16 0.47
9 14 0.41
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (9 bp):
GTTTAATTA
Found at i:40812754 original size:24 final size:24
Alignment explanation
Indices: 40812722--40812771 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
40812712 ATAAGGTTAA
40812722 TTTAGGTTTAATAGTTTAATTAGT
1 TTTAGGTTTAATAGTTTAATTAGT
40812746 TTTAGGTTTAATAGTTTAATTAGT
1 TTTAGGTTTAATAGTTTAATTAGT
40812770 TT
1 TT
40812772 AATAAATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (24 bp):
TTTAGGTTTAATAGTTTAATTAGT
Found at i:40817306 original size:47 final size:49
Alignment explanation
Indices: 40817237--40817453 Score: 236
Period size: 48 Copynumber: 4.6 Consensus size: 49
40817227 AAGGTACCGG
* * *
40817237 TGCCATGTCCCAGACACGGTCTTACACTAGCTCAT-ATCTC-ATGTCGA
1 TGCCATGTCCCAGACAGGGTCTTACACTAGCACATCATCTCGATGCCGA
* *
40817284 TGCCATGTCCCAGACATGGTCTTACACT-G-ACTATCATCTCG-TAGACGA
1 TGCCATGTCCCAGACAGGGTCTTACACTAGCAC-ATCATCTCGAT-GCCGA
* * * *
40817332 TG-CATGTCCCAAACA-TGTCTTACACTAGCAC-CCGTCTCGATGCCGA
1 TGCCATGTCCCAGACAGGGTCTTACACTAGCACATCATCTCGATGCCGA
* * * *
40817378 TTCTATGTCCCAGACAGGGCCTTACACTAGCAC-TCGTCTCGATGCCGA
1 TGCCATGTCCCAGACAGGGTCTTACACTAGCACATCATCTCGATGCCGA
40817426 TGCCATGTCCCAGACAGGGTCTTACACT
1 TGCCATGTCCCAGACAGGGTCTTACACT
40817454 GGTTTCCATA
Statistics
Matches: 144, Mismatches: 17, Indels: 17
0.81 0.10 0.10
Matches are distributed among these distances:
45 1 0.01
46 24 0.17
47 58 0.40
48 61 0.42
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.26
Consensus pattern (49 bp):
TGCCATGTCCCAGACAGGGTCTTACACTAGCACATCATCTCGATGCCGA
Found at i:40817496 original size:142 final size:141
Alignment explanation
Indices: 40817241--40817502 Score: 343
Period size: 142 Copynumber: 1.9 Consensus size: 141
40817231 TACCGGTGCC
* * * *
40817241 ATGTCCCAGACACGGTCTTACACTAGCTCATATCTCATGTCGATGCCATGTCCCAGACATGGTCT
1 ATGTCCCAGACACGGCCTTACACTAGCACATATCTCATGCCGATGCCATGTCCCAGACAGGGTCT
* *
40817306 TACACTGACTATCATCTCGTAGACGATGCATGTCCCAAACATGTCTTACACTAGCACCCGTCTCG
66 TACACTGACTATCATATCGTAGACGATACATGTCCCAAACATGTCTTACACTAGCACCCGTCTCG
40817371 ATGCCGATTCT
131 ATGCCGATTCT
* *
40817382 ATGTCCCAGACAGGGCCTTACACTAGCAC-TCGTCTCGATGCCGATGCCATGTCCCAGACAGGGT
1 ATGTCCCAGACACGGCCTTACACTAGCACAT-ATCTC-ATGCCGATGCCATGTCCCAGACAGGGT
* * * *
40817446 CTTACACTG-GTTTCCATAAT-GT-GGCTGATACATGTCCCAGACATGTCTTACACTAGC
64 CTTACACTGACTAT-CAT-ATCGTAGAC-GATACATGTCCCAAACATGTCTTACACTAGC
40817503 CCACAATAAC
Statistics
Matches: 104, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
140 1 0.01
141 34 0.33
142 68 0.65
143 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.27
Consensus pattern (141 bp):
ATGTCCCAGACACGGCCTTACACTAGCACATATCTCATGCCGATGCCATGTCCCAGACAGGGTCT
TACACTGACTATCATATCGTAGACGATACATGTCCCAAACATGTCTTACACTAGCACCCGTCTCG
ATGCCGATTCT
Found at i:40819437 original size:46 final size:46
Alignment explanation
Indices: 40819387--40819562 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
40819377 TGGTTGAGTA
*
40819387 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
40819433 TCCGAGCTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
40819478 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
40819526 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
40819563 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 63 0.58
47 29 0.27
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:40819545 original size:93 final size:93
Alignment explanation
Indices: 40819386--40819555 Score: 313
Period size: 93 Copynumber: 1.8 Consensus size: 93
40819376 ATGGTTGAGT
* *
40819386 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAGCTCGTTGAGTTG
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGTTG
40819451 AGTCCGAGTTCGTGAAATGTAACTAGGC
66 AGTCCGAGTTCGTGAAATGTAACTAGGC
*
40819479 ATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGTTG
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGTTG
40819544 AGTCCGAGTTCG
66 AGTCCGAGTTCG
40819556 CTTATGGGCG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGTTG
AGTCCGAGTTCGTGAAATGTAACTAGGC
Found at i:40821270 original size:37 final size:37
Alignment explanation
Indices: 40821229--40821301 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
40821219 CCTTCCTAAG
40821229 GTCTATTTTCCCTTTAAGGACCCCCAATTTAGGTTTT
1 GTCTATTTTCCCTTTAAGGACCCCCAATTTAGGTTTT
*
40821266 GTCTATTTTCTCTTTAAGGACCCCCAATTTAGGTTT
1 GTCTATTTTCCCTTTAAGGACCCCCAATTTAGGTTT
40821302 CATGGTAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.19, C:0.23, G:0.14, T:0.44
Consensus pattern (37 bp):
GTCTATTTTCCCTTTAAGGACCCCCAATTTAGGTTTT
Found at i:40821970 original size:43 final size:43
Alignment explanation
Indices: 40821915--40822008 Score: 125
Period size: 43 Copynumber: 2.2 Consensus size: 43
40821905 CACTTATGAG
* *
40821915 CCAGTATAATTGTTTCGACTTGCCTGATGATACATTATGTGTA
1 CCAGTATAATTGTTTCGACTTACCTGATGATACACTATGTGTA
* ** *
40821958 CCAGTATGATTGTTTCGGTTTATCTGATGATACACTATGTGTA
1 CCAGTATAATTGTTTCGACTTACCTGATGATACACTATGTGTA
*
40822001 CTAGTATA
1 CCAGTATA
40822009 TTTACTTTAG
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.40
Consensus pattern (43 bp):
CCAGTATAATTGTTTCGACTTACCTGATGATACACTATGTGTA
Found at i:40822030 original size:43 final size:43
Alignment explanation
Indices: 40821940--40822031 Score: 107
Period size: 43 Copynumber: 2.1 Consensus size: 43
40821930 CGACTTGCCT
* * *
40821940 GATGATACATTATGTGTACCAGTATGATTGTTTCGGTTTATCT
1 GATGATACACTATGTGTACCAGTATGATTGTTTCAGTTTATCA
* *
40821983 GATGATACACTATGTGTACTAGTAT-ATT-TACTTTAGTTTATCA
1 GATGATACACTATGTGTACCAGTATGATTGT--TTCAGTTTATCA
40822026 GATGAT
1 GATGAT
40822032 GTATTATGTG
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
41 1 0.02
42 3 0.07
43 38 0.90
ACGTcount: A:0.27, C:0.11, G:0.18, T:0.43
Consensus pattern (43 bp):
GATGATACACTATGTGTACCAGTATGATTGTTTCAGTTTATCA
Found at i:40822040 original size:43 final size:43
Alignment explanation
Indices: 40821975--40822077 Score: 109
Period size: 43 Copynumber: 2.4 Consensus size: 43
40821965 GATTGTTTCG
* * * *
40821975 GTTTATCTGATGATACACTATGTG-TACTAGTATATTTACTTTA
1 GTTTATCAGATGATGCACTATGTGAT-CTAATATATTTACTTCA
* * * *
40822018 GTTTATCAGATGATGTATTATGTGATCTAATGTATTTACTTCG
1 GTTTATCAGATGATGCACTATGTGATCTAATATATTTACTTCA
*
40822061 GTTTATCCGATGATGCA
1 GTTTATCAGATGATGCA
40822078 TTGTAGTGCC
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
43 48 0.98
44 1 0.02
ACGTcount: A:0.26, C:0.12, G:0.17, T:0.45
Consensus pattern (43 bp):
GTTTATCAGATGATGCACTATGTGATCTAATATATTTACTTCA
Found at i:40822960 original size:36 final size:36
Alignment explanation
Indices: 40822920--40822994 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
40822910 CTCTCTTTTT
40822920 CGGGTGAAAACAAAAATTCTCTCTTTTAATAGAAAC
1 CGGGTGAAAACAAAAATTCTCTCTTTTAATAGAAAC
40822956 CGGGTGAAAACAAAAATTCTCTCTTTTAATAGAAAC
1 CGGGTGAAAACAAAAATTCTCTCTTTTAATAGAAAC
40822992 CGG
1 CGG
40822995 TAGAATTGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.27
Consensus pattern (36 bp):
CGGGTGAAAACAAAAATTCTCTCTTTTAATAGAAAC
Found at i:40830890 original size:12 final size:12
Alignment explanation
Indices: 40830870--40830903 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
40830860 CTGGAGTTTT
40830870 ATATTATTTAGAA
1 ATATTATTTA-AA
40830883 AT-TTATTTAAA
1 ATATTATTTAAA
40830894 ATATTATTTA
1 ATATTATTTA
40830904 TTTATTGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 4 0.20
12 14 0.70
13 2 0.10
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (12 bp):
ATATTATTTAAA
Found at i:40834808 original size:20 final size:20
Alignment explanation
Indices: 40834785--40834827 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
40834775 GGATACTTCT
*
40834785 AATTAA-TTTAATTTTCTAAA
1 AATTAATTTTAAATTT-TAAA
40834805 AATTAATTTTAAATTTTAAA
1 AATTAATTTTAAATTTTAAA
40834825 AAT
1 AAT
40834828 AGAATATGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
AATTAATTTTAAATTTTAAA
Found at i:40834826 original size:21 final size:20
Alignment explanation
Indices: 40834785--40834826 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
40834775 GGATACTTCT
*
40834785 AATTAATTTAATTTTCTAAA
1 AATTAATTTAATTTTCAAAA
40834805 AATTAATTTTAAATTTT-AAAA
1 AATTAA-TTT-AATTTTCAAAA
40834826 A
1 A
40834827 TAGAATATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 7 0.37
22 6 0.32
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
AATTAATTTAATTTTCAAAA
Found at i:40837074 original size:40 final size:41
Alignment explanation
Indices: 40836981--40837074 Score: 127
Period size: 41 Copynumber: 2.3 Consensus size: 41
40836971 TCAAATACAT
* *
40836981 CCTTTTCATTTGTTATCCTTTATGTATAACATCATTTTCAA
1 CCTTTTCATTTGATATCCTTTATGCATAACATCATTTTCAA
* * *
40837022 CCTTTTCATTTGATATCCTTTTTGCAT-ATATCCTTTTCAA
1 CCTTTTCATTTGATATCCTTTATGCATAACATCATTTTCAA
*
40837062 CCTTTTCGTTTGA
1 CCTTTTCATTTGA
40837075 ACTATTACAA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 23 0.49
41 24 0.51
ACGTcount: A:0.20, C:0.21, G:0.06, T:0.52
Consensus pattern (41 bp):
CCTTTTCATTTGATATCCTTTATGCATAACATCATTTTCAA
Found at i:40845958 original size:46 final size:48
Alignment explanation
Indices: 40845836--40845965 Score: 171
Period size: 46 Copynumber: 2.8 Consensus size: 48
40845826 TGTAACCCGC
*
40845836 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCCTAG-T-CAT
* * *
40845886 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG-CAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCCTAGTCAT
40845929 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
40845966 TGCCCAAATA
Statistics
Matches: 71, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
43 3 0.04
44 1 0.01
45 2 0.03
46 32 0.45
47 30 0.42
48 2 0.03
49 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (48 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCCTAGTCAT
Found at i:40845984 original size:46 final size:45
Alignment explanation
Indices: 40845841--40845984 Score: 148
Period size: 46 Copynumber: 3.1 Consensus size: 45
40845831 CCCGCCCATA
* *
40845841 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTC
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA---ACATCCC
* * * * *
40845889 A-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTC-GCATCCATA
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAACATCC--C
*
40845934 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATATCCC
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCC-AACATCCC
40845980 AGTGA
1 AGTGA
40845985 CATGTCACTT
Statistics
Matches: 78, Mismatches: 13, Indels: 12
0.76 0.13 0.12
Matches are distributed among these distances:
43 4 0.05
45 1 0.01
46 37 0.47
47 31 0.40
48 5 0.06
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAACATCCC
Found at i:40848385 original size:29 final size:29
Alignment explanation
Indices: 40848346--40848433 Score: 97
Period size: 29 Copynumber: 3.0 Consensus size: 29
40848336 CAAAGATAAC
*
40848346 AAGAAAACCGAATAAAGAAATCCAAGATA
1 AAGAAACCCGAATAAAGAAATCCAAGATA
*
40848375 GAGAAACCCGAATAAAGAAATCC-AGAATA
1 AAGAAACCCGAATAAAGAAATCCAAG-ATA
* * * *
40848404 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGA-AACCCGAATAAAGAAATCCAAGATA
40848434 CGATACTATG
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
28 2 0.04
29 27 0.55
30 18 0.37
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (29 bp):
AAGAAACCCGAATAAAGAAATCCAAGATA
Found at i:40848404 original size:15 final size:15
Alignment explanation
Indices: 40848346--40848424 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
40848336 CAAAGATAAC
*
40848346 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
40848360 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
40848375 GAGAAA-CCCGAATA
1 AAGAAATCCAGAATA
40848389 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
40848404 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
40848419 AAGAAA
1 AAGAAA
40848425 CCCAAGATAC
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
14 19 0.36
15 34 0.64
ACGTcount: A:0.58, C:0.14, G:0.18, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:40848433 original size:15 final size:15
Alignment explanation
Indices: 40848357--40848433 Score: 77
Period size: 15 Copynumber: 5.2 Consensus size: 15
40848347 AGAAAACCGA
40848357 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* * *
40848372 ATAGAGAAACCCGA-
1 ATAAAGAAATCCAAG
40848386 ATAAAGAAATCC-AG
1 ATAAAGAAATCCAAG
* *
40848400 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
40848416 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
40848431 ATA
1 ATA
40848434 CGATACTATG
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
13 1 0.02
14 10 0.20
15 37 0.76
16 1 0.02
ACGTcount: A:0.56, C:0.16, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:40851458 original size:93 final size:93
Alignment explanation
Indices: 40851346--40851517 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
40851336 GCCCATAAGT
* *
40851346 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40851411 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
40851439 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40851504 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
40851518 AAATATCCCA
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:40851513 original size:46 final size:46
Alignment explanation
Indices: 40851338--40851513 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
40851328 TGTAACCCGC
* * *
40851338 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
40851384 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
40851434 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
40851477 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
40851514 TGCCAAATAT
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 68 0.61
47 32 0.29
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:40857850 original size:53 final size:53
Alignment explanation
Indices: 40857786--40857919 Score: 198
Period size: 53 Copynumber: 2.5 Consensus size: 53
40857776 TCATACCAAA
* * *
40857786 GCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTATCACATTATACCGAT
1 GCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTATCACATTACACAGAT
* *
40857839 GCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTATCACATTGCACAGAT
1 GCCATAGCCCAGCTATGGTCTTATACGGAATCACATTATCACATTACACAGAT
*
40857892 GCCATAGCCCAGCTATGGTCTTAAACGG
1 GCCATAGCCCAGCTATGGTCTTATACGG
40857920 GCACACTTGT
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
52 1 0.01
53 73 0.99
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (53 bp):
GCCATAGCCCAGCTATGGTCTTATACGGAATCACATTATCACATTACACAGAT
Found at i:40859977 original size:2 final size:2
Alignment explanation
Indices: 40859938--40859965 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
40859928 CCAACGCAAA
40859938 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40859966 TGTAAAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40860464 original size:17 final size:17
Alignment explanation
Indices: 40860443--40860485 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
40860433 TAAAAATATT
40860443 AAATATTAAAT-TTAAA
1 AAATATTAAATATTAAA
40860459 ATAATA-TAAATATTAAA
1 A-AATATTAAATATTAAA
*
40860476 AAATGTTAAA
1 AAATATTAAA
40860486 AATAATATAG
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (17 bp):
AAATATTAAATATTAAA
Found at i:40861549 original size:32 final size:32
Alignment explanation
Indices: 40861494--40861554 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
40861484 ACTTTTCCTA
40861494 TCTAGAATTTTTTAAACACTAAATTAGTGGAT
1 TCTAGAATTTTTTAAACACTAAATTAGTGGAT
* *
40861526 TCTATAATTTGTTT-AACATTAAATTAGTG
1 TCTAGAATTT-TTTAAACACTAAATTAGTG
40861555 TAATTATTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
32 23 0.88
33 3 0.12
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.44
Consensus pattern (32 bp):
TCTAGAATTTTTTAAACACTAAATTAGTGGAT
Found at i:40861748 original size:21 final size:21
Alignment explanation
Indices: 40861724--40861768 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
40861714 CTCAATGTGC
*
40861724 TAATCTAAGGATTATGTCAAA
1 TAATCTAAGAATTATGTCAAA
* *
40861745 TAATTTAATAATTATGTCAAA
1 TAATCTAAGAATTATGTCAAA
40861766 TAA
1 TAA
40861769 GCTTAAGTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.38
Consensus pattern (21 bp):
TAATCTAAGAATTATGTCAAA
Found at i:40863096 original size:30 final size:30
Alignment explanation
Indices: 40863060--40863133 Score: 139
Period size: 30 Copynumber: 2.5 Consensus size: 30
40863050 TTAAGTAGGC
*
40863060 CACACGATCGTGTGGTATGGTTGTGTGTGG
1 CACACGACCGTGTGGTATGGTTGTGTGTGG
40863090 CACACGACCGTGTGGTATGGTTGTGTGTGG
1 CACACGACCGTGTGGTATGGTTGTGTGTGG
40863120 CACACGACCGTGTG
1 CACACGACCGTGTG
40863134 ACAACCCATG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.15, C:0.19, G:0.38, T:0.28
Consensus pattern (30 bp):
CACACGACCGTGTGGTATGGTTGTGTGTGG
Found at i:40866259 original size:46 final size:46
Alignment explanation
Indices: 40866204--40866384 Score: 233
Period size: 46 Copynumber: 3.9 Consensus size: 46
40866194 TAGGATGGTT
40866204 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
* * *
40866250 GAGCGTCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAAC
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---C
*
40866296 TAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
1 GA-GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
* ** *
40866343 GAACGCCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
40866385 GCGGGTTACA
Statistics
Matches: 116, Mismatches: 12, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.03
45 2 0.02
46 71 0.61
47 33 0.28
48 2 0.02
50 4 0.03
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
Found at i:40866365 original size:93 final size:93
Alignment explanation
Indices: 40866206--40866376 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
40866196 GGATGGTTGA
* *
40866206 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
40866271 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
40866299 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
40866364 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
40866377 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:40867029 original size:72 final size:72
Alignment explanation
Indices: 40866943--40867086 Score: 288
Period size: 72 Copynumber: 2.0 Consensus size: 72
40866933 TAGCCATTGG
40866943 AATGGCTAATCATGATCATATTTGGTATTATGTATGTCAAATTGCTAGCTAATCCATGGAAACCA
1 AATGGCTAATCATGATCATATTTGGTATTATGTATGTCAAATTGCTAGCTAATCCATGGAAACCA
40867008 TGAAATA
66 TGAAATA
40867015 AATGGCTAATCATGATCATATTTGGTATTATGTATGTCAAATTGCTAGCTAATCCATGGAAACCA
1 AATGGCTAATCATGATCATATTTGGTATTATGTATGTCAAATTGCTAGCTAATCCATGGAAACCA
40867080 TGAAATA
66 TGAAATA
40867087 GGTAAAATTT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (72 bp):
AATGGCTAATCATGATCATATTTGGTATTATGTATGTCAAATTGCTAGCTAATCCATGGAAACCA
TGAAATA
Found at i:40867839 original size:46 final size:45
Alignment explanation
Indices: 40867789--40867916 Score: 143
Period size: 46 Copynumber: 2.8 Consensus size: 45
40867779 ATCAACATCA
*
40867789 AGACGAGTGCTAGTGTAAGACATGTCTGGGACGTGCATCGGCCT-CG
1 AGACGA-TGCTAGTGTAAGACATGTCTGGGACATGCATCGG-CTACG
* * *
40867835 AGACGTAAGCTAGTGTAAGACATGTCTAGGACATGCATTGGCTACG
1 AGACG-ATGCTAGTGTAAGACATGTCTGGGACATGCATCGGCTACG
*
40867881 AGATGATAG-TCAGTGTAAGACCATGTCTGGGACATG
1 AGACGAT-GCT-AGTGTAAGA-CATGTCTGGGACATG
40867917 GCATTGACAT
Statistics
Matches: 70, Mismatches: 7, Indels: 9
0.81 0.08 0.10
Matches are distributed among these distances:
45 4 0.06
46 51 0.73
47 15 0.21
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.23
Consensus pattern (45 bp):
AGACGATGCTAGTGTAAGACATGTCTGGGACATGCATCGGCTACG
Found at i:40867943 original size:47 final size:48
Alignment explanation
Indices: 40867797--40867966 Score: 160
Period size: 47 Copynumber: 3.6 Consensus size: 48
40867787 CAAGACGAGT
* * * *
40867797 GCTAGTGTAAGA-CATGTCTGGGACGT-GCATCGGCCT-CGAGACG-TAA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCAT-TGACTACGAGATGAT-A
* *
40867843 GCTAGTGTAAGA-CATGTCTAGGACAT-GCATTGGCTACGAGATGATA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATTGACTACGAGATGATA
* *
40867889 G-TCAGTGTAAGACCATGTCTGGGACATGGCATTGAC-ATGAGGT-ATGA
1 GCT-AGTGTAAGACCATGTCTGGGACATGGCATTGACTACGAGATGAT-A
*
40867936 GCTAGTGTAAGACCGTGTCTGGGACATGGCA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCA
40867967 CCGGCACCTT
Statistics
Matches: 107, Mismatches: 10, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
45 4 0.04
46 47 0.44
47 48 0.45
48 8 0.07
ACGTcount: A:0.26, C:0.18, G:0.32, T:0.24
Consensus pattern (48 bp):
GCTAGTGTAAGACCATGTCTGGGACATGGCATTGACTACGAGATGATA
Found at i:40871372 original size:29 final size:27
Alignment explanation
Indices: 40871308--40871373 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 27
40871298 ATAAATTATT
*
40871308 AAATTTTAAAACTTTCATGTAACAAAA
1 AAATTTTAAAACATTCATGTAACAAAA
*
40871335 ATCAA-TTTAAAACATTCTATGTTAATAAAA
1 A--AATTTTAAAACATTC-ATG-TAACAAAA
40871365 AAATTTTAA
1 AAATTTTAA
40871374 TTTACTATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
27 1 0.03
28 13 0.41
29 10 0.31
30 8 0.25
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (27 bp):
AAATTTTAAAACATTCATGTAACAAAA
Found at i:40880226 original size:20 final size:22
Alignment explanation
Indices: 40880175--40880227 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
40880165 GTAATATATA
40880175 TAGGGTTCGCATATTTGAATAC
1 TAGGGTTCGCATATTTGAATAC
* *
40880197 -AGGATTCGCATATTT-AA-CC
1 TAGGGTTCGCATATTTGAATAC
40880216 TAGGGTTCGCAT
1 TAGGGTTCGCAT
40880228 GAAACAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 1 0.04
20 12 0.44
21 14 0.52
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (22 bp):
TAGGGTTCGCATATTTGAATAC
Found at i:40881194 original size:23 final size:23
Alignment explanation
Indices: 40881162--40881205 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
40881152 TAACTTTATG
40881162 TTCTTCTTTGTAAGTTCTAAATC
1 TTCTTCTTTGTAAGTTCTAAATC
*
40881185 TTCTTTTTTGTAAGTTCTAAA
1 TTCTTCTTTGTAAGTTCTAAA
40881206 GCAGGTGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.23, C:0.14, G:0.09, T:0.55
Consensus pattern (23 bp):
TTCTTCTTTGTAAGTTCTAAATC
Found at i:40889656 original size:383 final size:367
Alignment explanation
Indices: 40888911--40889666 Score: 1129
Period size: 383 Copynumber: 2.0 Consensus size: 367
40888901 CACCCACCGA
* ** *
40888911 AAAGAAGATAGTTGGTTGCAAGTGGGTATTCAAAAATAAGAAAGGAGGTTTAGGTGACACAAGAT
1 AAAGAAGATAGTTGGTTGCAAGTGGGCATTCAAAAATAAGAAAGGAGGTCCAGGTGACACAAGAC
* * *
40888976 ATAAGGCAAGGTTGGTCGCAAAAGGCTGTAGTCAAGTGGAGGAAGTTGATTTTCATGATGTGTTA
66 ATAAGGCAAGGTTAGTCGCAAAAGGCTATAGTCAAATGGAGGAAGTTGATTTTCATGATGTGTTA
*
40889041 TCTCTTCATCCATTCAACCATTGTTAGCTCTTGTTGCATTAAACAACCTTGAATTAGAGTAGTTA
131 TCTCTTCATCCATTCAACCATTGTTAGCTCTTGTTGCATTAAAAAACCTTGAATTAGAGTAGTTA
* * *
40889106 GATATGAAAATTGTATTCCTTCATGGGGACCTAGAAGGGGATATTTATATGCCGCAACTTGAAGG
196 GATATGAAAATTGCATTCCTTCATGGGGACCTAGAAGGGGATATTTATATGCCACAACCTGAAGG
* * ***
40889171 CTTTAGAATTGAAGGCATGAAAGACAATTTATGCCTTCTACAGAAATCTTTGTATGGCCTGAAGC
261 CTTTAGAATTGAAGGCAAGAAAGACAATGTATGCCTTCTACAGAAATCTTTGTACAACCTGAAGC
40889236 AGTCTCCTCGTCAATGGTATAAGAAGTTTGATTCCTTTATGT
326 AGTCTCCTCGTCAATGGTATAAGAAGTTTGATTCCTTTATGT
*
40889278 AAAGAAGATAGTTGGTTGCAAGTGGGCATTCAAAAAGT-AGGAAGGATTAGGTCCAGGTGACACA
1 AAAGAAGATAGTTGGTTGCAAGTGGGCATTCAAAAA-TAAGAAAGG---AGGTCCAGGTGACACA
*
40889342 AGACATAAGGCAAGGTTAGTCGCAAAGGGCTATAGTCAAATGGAGGAAGTTGATTTTCATGATGT
62 AGACATAAGGCAAGGTTAGTCGCAAAAGGCTATAGTCAAATGGAGGAAGTTGATTTTCATGATGT
**
40889407 GTTATCTCTTATTTTGAAGCATACATCCATTCGGCCATTGTTAGCTCTTGTTGCATTAAAAAACC
127 GTTATCTC------T------T-CATCCATTCAACCATTGTTAGCTCTTGTTGCATTAAAAAACC
* *
40889472 TTGAATTAGAGTAGTTAGATGTGAAAATTGCATTCCTTCATGGTGACCTAG-AGGTGGATATTTA
179 TTGAATTAGAGTAGTTAGATATGAAAATTGCATTCCTTCATGGGGACCTAGAAGG-GGATATTTA
40889536 TATGCCACAACCTGAAGGCTTTAGAATTGAAGGCAAGAAAGACAATGTATGCCTTCTACAGAAAT
243 TATGCCACAACCTGAAGGCTTTAGAATTGAAGGCAAGAAAGACAATGTATGCCTTCTACAGAAAT
40889601 CTTTGTACAACCTGAAGCAGTCTCCTCGTCAATGGTATAAGAAGTTTGATTCCTTTATGT
308 CTTTGTACAACCTGAAGCAGTCTCCTCGTCAATGGTATAAGAAGTTTGATTCCTTTATGT
*
40889661 TAAGAA
1 AAAGAA
40889667 TTGGTTTTGT
Statistics
Matches: 348, Mismatches: 23, Indels: 20
0.89 0.06 0.05
Matches are distributed among these distances:
367 41 0.12
368 1 0.00
370 82 0.24
376 1 0.00
382 4 0.01
383 219 0.63
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.31
Consensus pattern (367 bp):
AAAGAAGATAGTTGGTTGCAAGTGGGCATTCAAAAATAAGAAAGGAGGTCCAGGTGACACAAGAC
ATAAGGCAAGGTTAGTCGCAAAAGGCTATAGTCAAATGGAGGAAGTTGATTTTCATGATGTGTTA
TCTCTTCATCCATTCAACCATTGTTAGCTCTTGTTGCATTAAAAAACCTTGAATTAGAGTAGTTA
GATATGAAAATTGCATTCCTTCATGGGGACCTAGAAGGGGATATTTATATGCCACAACCTGAAGG
CTTTAGAATTGAAGGCAAGAAAGACAATGTATGCCTTCTACAGAAATCTTTGTACAACCTGAAGC
AGTCTCCTCGTCAATGGTATAAGAAGTTTGATTCCTTTATGT
Found at i:40894403 original size:48 final size:47
Alignment explanation
Indices: 40894295--40894470 Score: 194
Period size: 48 Copynumber: 3.7 Consensus size: 47
40894285 GGTATACTGC
* ** *
40894295 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCA-TCCATCAAGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCT-ATTAAATCAAGG
* *
40894342 CGATGCCATGTCCCAAACATGGTCTTACACTAACTATTGAAATCAAGG
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTATT-AAATCAAGG
* * * *
40894390 CGACGCCATGTCCCAGACATGGTCTTACATTAGCTCTTACATATC-TGTG
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTATTA-A-ATCAAG-G
40894439 CCGATGCCATGTCCCAGACATGGTCTTACACT
1 -CGATGCCATGTCCCAGACATGGTCTTACACT
40894471 GACACATCTC
Statistics
Matches: 109, Mismatches: 14, Indels: 9
0.83 0.11 0.07
Matches are distributed among these distances:
46 1 0.01
47 34 0.31
48 41 0.38
49 4 0.04
50 29 0.27
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.27
Consensus pattern (47 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTAGCTATTAAATCAAGG
Found at i:40894534 original size:46 final size:46
Alignment explanation
Indices: 40894293--40894654 Score: 204
Period size: 46 Copynumber: 7.7 Consensus size: 46
40894283 AGGGTATACT
*
40894293 GCCGATGCCATGTCCCAGACATGGTCTTACACTGG--CTCATCCATC-AA
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTCAT-C-TCGAG
* * ** * * ** *
40894340 GTCGATGCCATGTCCCAAACATGGTCTTACACTAACTATTGAAATCAAG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCT-CTCATCTCGAG
* * * * *
40894389 G-CGACGCCATGTCCCAGACATGGTCTTACATTAGCTCTTACATATCTG-T
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTC-T-CATCTC-GAG
* *
40894438 GCCGATGCCATGTCCCAGACATGGTCTTACACT-G-ACACATCTCGTA-
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTCATCTCG-AG
* * *
40894484 GCCGATGCATGTCCCAAACATGTCTTACACTGGCT-TACATTTTGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTCT-CATCTCGAG
* * * * *
40894530 GCCGATGCATGTCCCATACATGTCTTACACTAGCTCTCGTCTCAAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCGAG
* * * *
40894576 GCCGATGCCATATCTCAGACATGATCTTACACTGGCTCTCATAAT-GTG
1 GCCGATG-CATGTCCCAGACATG-TCTTACACTGGCTCTCAT-CTCGAG
* *
40894624 GCTGATGCCTGTCCCAGACATGTCTTACACT
1 GCCGATGCATGTCCCAGACATGTCTTACACT
40894655 AGCACACAAA
Statistics
Matches: 249, Mismatches: 48, Indels: 37
0.75 0.14 0.11
Matches are distributed among these distances:
44 10 0.04
45 16 0.06
46 70 0.28
47 56 0.22
48 57 0.23
49 9 0.04
50 31 0.12
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (46 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCGAG
Found at i:40894631 original size:94 final size:98
Alignment explanation
Indices: 40894292--40894657 Score: 329
Period size: 94 Copynumber: 3.9 Consensus size: 98
40894282 TAGGGTATAC
*
40894292 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCCATCAA-GT---CGATGCCATGT
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATACAT-AATGTGGCCGATGCCATGT
* * * * **
40894353 CCCAAACATGGTCTTACACTAACTATTGAAATCAA
65 CCCAGACATGGTCTTACACTAGCTCTCG-TCTCAA
* * * * * *
40894388 -GGCGACGCCATGTCCCAGACATGGTCTTACATTAGCTCTTACAT-ATCTGTGCCGATGCCATGT
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATACATAATGTG-GCCGATGCCATGT
* * * *
40894451 CCCAGACATGGTCTTACACT-G-ACACATCTC-G
65 CCCAGACATGGTCTTACACTAGCTCTCGTCTCAA
* ** *
40894482 TAGCCGATG-CATGTCCCAAACAT-GTCTTACACTGGCT--TACATTTTGAGGCCGATG-CATGT
1 T-GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATACATAATGTGGCCGATGCCATGT
*
40894542 CCCATACAT-GTCTTACACTAGCTCTCGTCTCAA
65 CCCAGACATGGTCTTACACTAGCTCTCGTCTCAA
* * * *
40894575 TGCCGATGCCATATCTCAGACATGATCTTACACTGGCTC-T-CATAATGTGGCTGATGCC-TGTC
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATACATAATGTGGCCGATGCCATGTC
40894637 CCAGACAT-GTCTTACACTAGC
66 CCAGACATGGTCTTACACTAGC
40894658 ACACAAACAA
Statistics
Matches: 216, Mismatches: 39, Indels: 32
0.75 0.14 0.11
Matches are distributed among these distances:
90 10 0.05
91 14 0.06
92 25 0.12
93 15 0.07
94 62 0.29
95 55 0.25
96 5 0.02
98 30 0.14
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (98 bp):
TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATACATAATGTGGCCGATGCCATGTC
CCAGACATGGTCTTACACTAGCTCTCGTCTCAA
Found at i:40907102 original size:17 final size:18
Alignment explanation
Indices: 40907060--40907108 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
40907050 AGTTGAAAAG
40907060 GAGCATGATTGTCATACTT
1 GAGCATGA-TGTCATACTT
*
40907079 G-GCCATGATG-CATTCTT
1 GAG-CATGATGTCATACTT
40907096 GAGCATGAT-TCAT
1 GAGCATGATGTCAT
40907109 GCTTCTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 16 0.62
18 4 0.15
19 6 0.23
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (18 bp):
GAGCATGATGTCATACTT
Found at i:40907996 original size:40 final size:40
Alignment explanation
Indices: 40907930--40908096 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
40907920 AAATTGAATG
* * *
40907930 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * **
40907969 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
40908009 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
40908049 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
40908089 ATATCCGG
1 ATATCCGG
40908097 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:40915112 original size:17 final size:18
Alignment explanation
Indices: 40915070--40915118 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
40915060 AGTTGAAAAG
40915070 GAGCATGATTGTCATACTT
1 GAGCATGA-TGTCATACTT
*
40915089 G-GCCATGATG-CATTCTT
1 GAG-CATGATGTCATACTT
40915106 GAGCATGAT-TCAT
1 GAGCATGATGTCAT
40915119 GCTTCTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 16 0.62
18 4 0.15
19 6 0.23
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (18 bp):
GAGCATGATGTCATACTT
Found at i:40916007 original size:40 final size:40
Alignment explanation
Indices: 40915941--40916107 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
40915931 AAATTGAATG
* * *
40915941 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * **
40915980 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
40916020 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
40916060 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
40916100 ATATCCGG
1 ATATCCGG
40916108 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:40918067 original size:38 final size:37
Alignment explanation
Indices: 40918016--40918156 Score: 138
Period size: 38 Copynumber: 3.7 Consensus size: 37
40918006 ATGTGTGTAC
*
40918016 GTGTAAGACCATAGCTGGGCTATGGCCTCGTAATTAAA
1 GTGTAAGACCATAGCTGGGCTATGGCATCGTAA-TAAA
* * *
40918054 GTGTAAGACCATAGCTGAGCTATGGCATTGTGATAAA
1 GTGTAAGACCATAGCTGGGCTATGGCATCGTAATAAA
* * * * *
40918091 GTGTAAAGACCATAACTGGGCTCTGGTATTGTGATAAA
1 GTGT-AAGACCATAGCTGGGCTATGGCATCGTAATAAA
* * * *
40918129 ATGTAAAGACCATGGCAGGTCTATGGCA
1 GTGT-AAGACCATAGCTGGGCTATGGCA
40918157 ATATATGTGC
Statistics
Matches: 87, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
37 8 0.09
38 79 0.91
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.26
Consensus pattern (37 bp):
GTGTAAGACCATAGCTGGGCTATGGCATCGTAATAAA
Found at i:40919841 original size:19 final size:18
Alignment explanation
Indices: 40919796--40919844 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
40919786 AAAGTATATC
* *
40919796 TTTTAATTTTAAAAATTA
1 TTTTAATTTTTAAAATAA
*
40919814 TTATGAATTTTTAAAATCAA
1 TT-TTAATTTTTAAAAT-AA
40919834 TTTTAATTTTT
1 TTTTAATTTTT
40919845 TTTGTAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 2 0.08
19 20 0.80
20 3 0.12
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (18 bp):
TTTTAATTTTTAAAATAA
Found at i:40926994 original size:24 final size:24
Alignment explanation
Indices: 40926966--40927018 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
40926956 AAGGCAATTA
* *
40926966 AAGGAAGCTATAAGAGAATGAGGC
1 AAGGAAGCAATAAGAGAATAAGGC
*
40926990 AAGGAAGCAATAAGAGAATAAGGT
1 AAGGAAGCAATAAGAGAATAAGGC
40927014 AAGGA
1 AAGGA
40927019 GAGAGATAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.51, C:0.06, G:0.32, T:0.11
Consensus pattern (24 bp):
AAGGAAGCAATAAGAGAATAAGGC
Found at i:40928157 original size:14 final size:16
Alignment explanation
Indices: 40928127--40928162 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
40928117 AATAAAGAGA
40928127 AATAAAAAGAGTAAAG
1 AATAAAAAGAGTAAAG
40928143 AATAAAAA-A-TAAAG
1 AATAAAAAGAGTAAAG
40928157 AA-AAAA
1 AATAAAA
40928163 TGAGAGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 4 0.20
14 7 0.35
15 1 0.05
16 8 0.40
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (16 bp):
AATAAAAAGAGTAAAG
Found at i:40928872 original size:96 final size:96
Alignment explanation
Indices: 40928758--40928947 Score: 335
Period size: 96 Copynumber: 2.0 Consensus size: 96
40928748 TGATGCATGG
* *
40928758 ACATGTACACATCCACTTCATTTGGACGACAAGACCGTGAAAAATTGGGTCATAAGGATGTTAAT
1 ACATGTACACATCAACTTCATTTGGACGACAAGACCGTGAAAAACTGGGTCATAAGGATGTTAAT
*
40928823 TTGACCCAGTAAAAGATGTGATAAAAGATGT
66 TTGACCCAATAAAAGATGTGATAAAAGATGT
*
40928854 ACATGTACACATCAACTTCATTTGGACGACAAGACCGTGCAAAACTGGGTCATAAGGATGTTAAT
1 ACATGTACACATCAACTTCATTTGGACGACAAGACCGTGAAAAACTGGGTCATAAGGATGTTAAT
*
40928919 TTGACCTAATAAAAGATGTGATAAAAGAT
66 TTGACCCAATAAAAGATGTGATAAAAGAT
40928948 AAACATGTTT
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
96 89 1.00
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (96 bp):
ACATGTACACATCAACTTCATTTGGACGACAAGACCGTGAAAAACTGGGTCATAAGGATGTTAAT
TTGACCCAATAAAAGATGTGATAAAAGATGT
Found at i:40933491 original size:31 final size:31
Alignment explanation
Indices: 40933426--40933507 Score: 83
Period size: 31 Copynumber: 2.6 Consensus size: 31
40933416 TAAAAAAAAA
* ** * *
40933426 AAAAGAATGAAAGAACAAAGGTAAGTTTGTTC
1 AAAAGAAT-AAAAAACAAAGAAAAATTTGCTC
40933458 AAAAGAATAAAAAACAAAGAAAAATTTGCTC
1 AAAAGAATAAAAAACAAAGAAAAATTTGCTC
** *
40933489 AAAAGTCTAAAAAATAAAG
1 AAAAGAATAAAAAACAAAG
40933508 GTTGAGCATG
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
31 34 0.81
32 8 0.19
ACGTcount: A:0.60, C:0.07, G:0.15, T:0.18
Consensus pattern (31 bp):
AAAAGAATAAAAAACAAAGAAAAATTTGCTC
Found at i:40935095 original size:42 final size:37
Alignment explanation
Indices: 40934991--40935066 Score: 118
Period size: 38 Copynumber: 2.1 Consensus size: 37
40934981 CGTACCTAGA
*
40934991 AAAAAATAAAAAAAATAGAATTAAAAGTTTTGATCTG
1 AAAAAATAAAAAAAATAGAAATAAAAGTTTTGATCTG
*
40935028 AAAAAATAAAATAAAACAGAAATAAAAGTTTTGAT-TG
1 AAAAAATAAAA-AAAATAGAAATAAAAGTTTTGATCTG
40935065 AA
1 AA
40935067 TTTCAAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 15 0.42
38 21 0.58
ACGTcount: A:0.62, C:0.03, G:0.11, T:0.25
Consensus pattern (37 bp):
AAAAAATAAAAAAAATAGAAATAAAAGTTTTGATCTG
Found at i:40935816 original size:10 final size:10
Alignment explanation
Indices: 40935789--40935826 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
40935779 TTAAATTCTA
*
40935789 AAAGATAAAT
1 AAAGATAATT
40935799 ACAA-ATAATT
1 A-AAGATAATT
40935809 AAAGATAATT
1 AAAGATAATT
40935819 AAAGATAA
1 AAAGATAA
40935827 ATGAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.66, C:0.03, G:0.08, T:0.24
Consensus pattern (10 bp):
AAAGATAATT
Found at i:40936658 original size:99 final size:99
Alignment explanation
Indices: 40936482--40936671 Score: 274
Period size: 99 Copynumber: 1.9 Consensus size: 99
40936472 TTAATTTATT
**
40936482 ATTTATTTATTTTTGCTTAAGAATATATTGAACCTTTTGACGCGAAGAGAGATGACAACCAAGCA
1 ATTTATTTATTTTTGCTTAAGAATATATCAAACCTTTTGACGCGAAGAGAGATGACAACCAAGCA
*
40936547 CCCCAACTCGGTTACTCAGCCCAACATACTCCTA
66 CCCCAACCCGGTTACTCAGCCCAACATACTCCTA
* * * * *
40936581 ATTTATTATATTTTT-CTTCAGAATATATCAAACCTTTTGACGCGAAGAGATATGATAGCTAAGC
1 ATTTATT-TATTTTTGCTTAAGAATATATCAAACCTTTTGACGCGAAGAGAGATGACAACCAAGC
* *
40936645 ACCTCACCCCGGTTACTCAGCCCAACA
65 ACCCCAACCCGGTTACTCAGCCCAACA
40936672 CATTCTTAAG
Statistics
Matches: 80, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
99 73 0.91
100 7 0.09
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (99 bp):
ATTTATTTATTTTTGCTTAAGAATATATCAAACCTTTTGACGCGAAGAGAGATGACAACCAAGCA
CCCCAACCCGGTTACTCAGCCCAACATACTCCTA
Found at i:40937697 original size:6 final size:6
Alignment explanation
Indices: 40937653--40937720 Score: 77
Period size: 6 Copynumber: 10.8 Consensus size: 6
40937643 ATATCCAAAC
40937653 AAAATA AATTAATA AATAAT- AAAATA AAGTAAT- AAAATA AAAATA AAAATA
1 AAAATA AA--AATA AA-AATA AAAATA AA--AATA AAAATA AAAATA AAAATA
40937704 AAAATA AAAATA AAAAT
1 AAAATA AAAATA AAAAT
40937721 TTGGTTGCCT
Statistics
Matches: 56, Mismatches: 0, Indels: 12
0.82 0.00 0.18
Matches are distributed among these distances:
5 6 0.11
6 35 0.62
7 6 0.11
8 9 0.16
ACGTcount: A:0.76, C:0.00, G:0.01, T:0.22
Consensus pattern (6 bp):
AAAATA
Found at i:40940106 original size:49 final size:50
Alignment explanation
Indices: 40940032--40940258 Score: 237
Period size: 49 Copynumber: 4.6 Consensus size: 50
40940022 TGAGGTCACG
*
40940032 TGTGTAGTACTAAGTGCAGGGTACTACGTGTACCGAATAATT-GGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGAATAATTAGGTCGCA
* * * * * * *
40940081 TGTGTAGTACTAAGTGTAGGCTACTATGCGTACCCG-ATAACTTCGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CCGAATAA-TTAGGTCGCA
* ** * *
40940132 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATC-AGATGGTTAGGTCTCG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGA-ATAATTAGGTCGCA
* * * * *
40940182 TGTGTAGTACTAAGTACAAGCTACTACGTGTACCGGATAACT-GGTCGTA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGAATAATTAGGTCGCA
40940231 TGTGTAGTACTAAGTGCAGGCTACTACG
1 TGTGTAGTACTAAGTGCAGGCTACTACG
40940259 CATACCAATA
Statistics
Matches: 144, Mismatches: 28, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
49 62 0.43
50 47 0.33
51 35 0.24
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.30
Consensus pattern (50 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGAATAATTAGGTCGCA
Found at i:40943083 original size:15 final size:15
Alignment explanation
Indices: 40943054--40943098 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
40943044 AATGTTGTAA
40943054 ATGGTATTTCCTTATC
1 ATGG-ATTTCCTTATC
*
40943070 ATGGATTTCTTTATC
1 ATGGATTTCCTTATC
*
40943085 TTGGATTTCCTTAT
1 ATGGATTTCCTTAT
40943099 TCTGGGCTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 22 0.85
16 4 0.15
ACGTcount: A:0.18, C:0.16, G:0.13, T:0.53
Consensus pattern (15 bp):
ATGGATTTCCTTATC
Found at i:40948818 original size:49 final size:50
Alignment explanation
Indices: 40948736--40948968 Score: 317
Period size: 49 Copynumber: 4.7 Consensus size: 50
40948726 ATCTATTGTG
* *
40948736 AGGTCACGTGTGTAGTACTAAGTGCAGGGTACTACGTGTACCGGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
* * *
40948786 -GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCCGATAACTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA-TT
* * * * * **
40948836 CGATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
*
40948886 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTTCGTGTACCGGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
*
40948936 -GGTCGCATGTGTAGTACTAAGTGCAGGCTACTA
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTA
40948969 TGCGTACCAG
Statistics
Matches: 158, Mismatches: 23, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
49 73 0.46
50 46 0.29
51 39 0.25
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (50 bp):
AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
Found at i:40948933 original size:101 final size:98
Alignment explanation
Indices: 40948739--40948981 Score: 335
Period size: 100 Copynumber: 2.4 Consensus size: 98
40948729 TATTGTGAGG
* * *
40948739 TCACGTGTGTAGTACTAAGTGCAGGGTACTACGTGTACCGGATAATTGGTCGCATGTGTAGTACT
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACATGTGTAGTACT
40948804 AAGTGCAGGCTACTATGTGTACCCGATAACTTCGA
66 AAGTGCAGGCTACTATGTGTACCCGATAA-TT-GA
* **
40948839 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCACATGTGTAGTAC
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT-GGTCACATGTGTAGTAC
* *
40948904 TAAGTGCAGGCTACT-TCGTGTACCGGATAATTGG
65 TAAGTGCAGGCTACTAT-GTGTACCCGATAATTGA
* * * *
40948938 TCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
40948982 GCTTTGGCTA
Statistics
Matches: 127, Mismatches: 14, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
99 39 0.31
100 45 0.35
101 43 0.34
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (98 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACATGTGTAGTACT
AAGTGCAGGCTACTATGTGTACCCGATAATTGA
Found at i:40950891 original size:37 final size:39
Alignment explanation
Indices: 40950850--40950923 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
40950840 TGCGTACCAA
*
40950850 GAAAAAAAT-AAA-AAAACAGTATTAAAAATTTTGATCT
1 GAAAAAAATAAAATAAAACAGAATTAAAAATTTTGATCT
* *
40950887 GAAAAAAATAAAATAAAATAGAATTAAAATTTTTGAT
1 GAAAAAAATAAAATAAAACAGAATTAAAAATTTTGAT
40950924 TGGAATTTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
37 9 0.28
38 3 0.09
39 20 0.62
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.28
Consensus pattern (39 bp):
GAAAAAAATAAAATAAAACAGAATTAAAAATTTTGATCT
Found at i:40963516 original size:40 final size:40
Alignment explanation
Indices: 40963336--40963527 Score: 264
Period size: 40 Copynumber: 4.8 Consensus size: 40
40963326 ATGCTAAGTG
* *
40963336 ACTATATCCGGACTAAGATCTGAAGGCATTTGTGCGAGTT
1 ACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTT
*
40963376 ACTAAATCCGAACTAAGATCCGAAGGCATTTGTGCGAGTT
1 ACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTT
*
40963416 ACTGAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTT
1 ACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTT
**
40963456 ACTAAATCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTT
1 ACTAAATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTT
* *
40963496 ACTATAAT-CGGGCTATG-TCCCGAAGGCATTTG
1 ACTA-AATCCGGACTAAGAT-CCGAAGGCATTTG
40963528 AACGAGTAGC
Statistics
Matches: 140, Mismatches: 10, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
39 1 0.01
40 136 0.97
41 3 0.02
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.27
Consensus pattern (40 bp):
ACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTT
Found at i:40963534 original size:40 final size:40
Alignment explanation
Indices: 40963302--40963527 Score: 255
Period size: 40 Copynumber: 5.7 Consensus size: 40
40963292 TCGAATGATG
* * * * *
40963302 TCCGGGCTGAGTCCCGAAGGC-TTTATGCTAAGTGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* *
40963342 TCCGGACTAAGAT-CTGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
** *
40963382 TCCGAACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTGAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
40963422 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
40963462 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
40963503 T-CGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
40963528 AACGAGTAGC
Statistics
Matches: 166, Mismatches: 16, Indels: 8
0.87 0.08 0.04
Matches are distributed among these distances:
39 1 0.01
40 155 0.93
41 10 0.06
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:40970931 original size:16 final size:16
Alignment explanation
Indices: 40970912--40970950 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
40970902 AATGAATAAG
*
40970912 ACCATGGTTGAAAGAT
1 ACCATGGTTGAAAAAT
40970928 ACCATGGTTGAAAAAT
1 ACCATGGTTGAAAAAT
40970944 ACCATGG
1 ACCATGG
40970951 CAACATGACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (16 bp):
ACCATGGTTGAAAAAT
Found at i:40970937 original size:62 final size:62
Alignment explanation
Indices: 40970866--40970988 Score: 194
Period size: 62 Copynumber: 2.0 Consensus size: 62
40970856 AATGTGTAAG
* * *
40970866 ACCATGGTTGAAAGATACCATGGCAACATGACGGGAAA-TGAATAAGACCATGGTTGAAAGAT
1 ACCATGGTTGAAAAATACCATGGCAACATGAC-AGAAAGTGAATAAGACCATAGTTGAAAGAT
*
40970928 ACCATGGTTGAAAAATACCATGGCAACATGACAGAAAGTGAGTAAGACCATAGTTGAAAGA
1 ACCATGGTTGAAAAATACCATGGCAACATGACAGAAAGTGAATAAGACCATAGTTGAAAGA
40970989 CACTATGGCA
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
61 4 0.07
62 52 0.93
ACGTcount: A:0.42, C:0.15, G:0.24, T:0.19
Consensus pattern (62 bp):
ACCATGGTTGAAAAATACCATGGCAACATGACAGAAAGTGAATAAGACCATAGTTGAAAGAT
Found at i:40971304 original size:16 final size:17
Alignment explanation
Indices: 40971283--40971315 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
40971273 ATGATGGTGC
40971283 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
40971299 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
40971316 TACTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:40972458 original size:20 final size:20
Alignment explanation
Indices: 40972433--40972481 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
40972423 GCGTGTGTCT
*
40972433 CCTCCACATAATCGTGTAGG
1 CCTCCACATAAGCGTGTAGG
**
40972453 CCTCCACATGGGCGTGTAGG
1 CCTCCACATAAGCGTGTAGG
*
40972473 CCTCGACAT
1 CCTCCACAT
40972482 GGCCTAGACA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.20, C:0.33, G:0.24, T:0.22
Consensus pattern (20 bp):
CCTCCACATAAGCGTGTAGG
Found at i:40972482 original size:20 final size:20
Alignment explanation
Indices: 40972445--40972483 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
40972435 TCCACATAAT
40972445 CGTGTAGGCCTCCACATGGG
1 CGTGTAGGCCTCCACATGGG
*
40972465 CGTGTAGGCCTCGACATGG
1 CGTGTAGGCCTCCACATGG
40972484 CCTAGACACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.28, G:0.36, T:0.21
Consensus pattern (20 bp):
CGTGTAGGCCTCCACATGGG
Done.