Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A03
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: 108673976
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.31
Warning! 5040000 characters in sequence are not A, C, G, or T
File 17 of 333
Found at i:4914594 original size:41 final size:40
Alignment explanation
Indices: 4914547--4914663 Score: 119
Period size: 41 Copynumber: 2.9 Consensus size: 40
4914537 CCTGTATCTC
* * * *
4914547 ACACCGGCACAAGGCCTGCTAGACTCAAAGTCTGATTTTAT
1 ACACCGGCA-AAGGCCTGCTAGGCTCAAAGCCCGATTTAAT
*
4914588 ACACCGGCAATAAGCCTGCTAGGCAT-AAAGCCCGATTTAAT
1 ACACCGGCAA-AGGCCTGCTAGGC-TCAAAGCCCGATTTAAT
* * *
4914629 TCACCAGCAAAAGGCTTGCTAGGCTCAAAGCCCGA
1 ACACCGGC-AAAGGCCTGCTAGGCTCAAAGCCCGA
4914664 ATATCACTAT
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
40 2 0.03
41 58 0.92
42 3 0.05
ACGTcount: A:0.32, C:0.28, G:0.21, T:0.20
Consensus pattern (40 bp):
ACACCGGCAAAGGCCTGCTAGGCTCAAAGCCCGATTTAAT
Found at i:4915123 original size:7 final size:7
Alignment explanation
Indices: 4915111--4915137 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
4915101 CAAAATTCAT
4915111 AAAACAC
1 AAAACAC
4915118 AAAACAC
1 AAAACAC
4915125 AAAACAC
1 AAAACAC
4915132 AAAACA
1 AAAACA
4915138 AACATAATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.74, C:0.26, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAACAC
Found at i:4934018 original size:69 final size:69
Alignment explanation
Indices: 4933907--4934044 Score: 249
Period size: 69 Copynumber: 2.0 Consensus size: 69
4933897 ATCATGCCAT
*
4933907 CCAACTCGCATGTTGCTTTCTACCATATCATTCAAATGAAGTTTTACCATAACGTTCCTCTAGTT
1 CCAACTCGCATGTTGCTTTCTACCACATCATTCAAATGAAGTTTTACCATAACGTTCCTCTAGTT
4933972 TGGA
66 TGGA
* *
4933976 CCAACTCGCATGTTGCTTTCTATCACATCATTCAAATGAAGTTTTACCATAACGTTCCTTTAGTT
1 CCAACTCGCATGTTGCTTTCTACCACATCATTCAAATGAAGTTTTACCATAACGTTCCTCTAGTT
4934041 TGGA
66 TGGA
4934045 ACATTTATTC
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (69 bp):
CCAACTCGCATGTTGCTTTCTACCACATCATTCAAATGAAGTTTTACCATAACGTTCCTCTAGTT
TGGA
Found at i:4934125 original size:22 final size:22
Alignment explanation
Indices: 4934097--4934140 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
4934087 CAATACATAG
4934097 TAATCTACCTATACCTGTATTT
1 TAATCTACCTATACCTGTATTT
4934119 TAATCTACCTATACCTGTATTT
1 TAATCTACCTATACCTGTATTT
4934141 GTATAAATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.23, G:0.05, T:0.45
Consensus pattern (22 bp):
TAATCTACCTATACCTGTATTT
Found at i:4937820 original size:11 final size:11
Alignment explanation
Indices: 4937804--4937829 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
4937794 CATGATCTGC
4937804 CATGAGACTGT
1 CATGAGACTGT
4937815 CATGAGACTGT
1 CATGAGACTGT
4937826 CATG
1 CATG
4937830 CTTTAGTTTC
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:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (11 bp):
CATGAGACTGT
Found at i:4943024 original size:23 final size:23
Alignment explanation
Indices: 4942998--4943043 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
4942988 ACGAAAAATC
4942998 AAATGCTTGACCATCTTACCAAA
1 AAATGCTTGACCATCTTACCAAA
*
4943021 AAATGCTTGATCATCTTACCAAA
1 AAATGCTTGACCATCTTACCAAA
4943044 GAAAATGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.39, C:0.24, G:0.09, T:0.28
Consensus pattern (23 bp):
AAATGCTTGACCATCTTACCAAA
Found at i:4944597 original size:31 final size:31
Alignment explanation
Indices: 4944562--4944628 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
4944552 AAATCCTTAA
*
4944562 AAAGAAAAAAAGTAATTGTGAAGTAGCCTTT
1 AAAGAAAAAAAGTAAATGTGAAGTAGCCTTT
4944593 AAAGAAAAAAAGTAAATGTGAAGTAGCCTTT
1 AAAGAAAAAAAGTAAATGTGAAGTAGCCTTT
4944624 AAAGA
1 AAAGA
4944629 CTTTGGTACT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.52, C:0.06, G:0.19, T:0.22
Consensus pattern (31 bp):
AAAGAAAAAAAGTAAATGTGAAGTAGCCTTT
Found at i:4945576 original size:18 final size:18
Alignment explanation
Indices: 4945553--4945594 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
4945543 GTTTCTTGGT
* * *
4945553 TTATTTTGTTTAGTTTTA
1 TTATTTTGATTACTTTAA
4945571 TTATTTTGATTACTTTAA
1 TTATTTTGATTACTTTAA
4945589 TTATTT
1 TTATTT
4945595 AGGTTATGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.21, C:0.02, G:0.07, T:0.69
Consensus pattern (18 bp):
TTATTTTGATTACTTTAA
Found at i:4948924 original size:19 final size:19
Alignment explanation
Indices: 4948900--4948936 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4948890 AAAACCAAGA
*
4948900 TTTTTACAATATTTATTTT
1 TTTTTAAAATATTTATTTT
*
4948919 TTTTTAAAATTTTTATTT
1 TTTTTAAAATATTTATTT
4948937 AAATTATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTTTAAAATATTTATTTT
Found at i:4951728 original size:11 final size:11
Alignment explanation
Indices: 4951712--4951736 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4951702 AGAAAATTAA
4951712 AATTTTAAAAT
1 AATTTTAAAAT
4951723 AATTTTAAAAT
1 AATTTTAAAAT
4951734 AAT
1 AAT
4951737 AATTTTGCGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
AATTTTAAAAT
Found at i:4954087 original size:19 final size:20
Alignment explanation
Indices: 4954063--4954101 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
4954053 GTCCCATTAT
4954063 TTATTTATTTTT-TGTTTTA
1 TTATTTATTTTTATGTTTTA
4954082 TTATTTATTTTTATGTTTTA
1 TTATTTATTTTTATGTTTTA
4954102 AATGTATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.77
Consensus pattern (20 bp):
TTATTTATTTTTATGTTTTA
Found at i:4954093 original size:20 final size:19
Alignment explanation
Indices: 4954063--4954101 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
4954053 GTCCCATTAT
*
4954063 TTATTTATTTTTTGTTTTA
1 TTATTTATTTTATGTTTTA
4954082 TTATTTATTTTTATGTTTTA
1 TTATTTA-TTTTATGTTTTA
4954102 AATGTATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.77
Consensus pattern (19 bp):
TTATTTATTTTATGTTTTA
Found at i:4954120 original size:25 final size:23
Alignment explanation
Indices: 4954064--4954128 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 23
4954054 TCCCATTATT
*
4954064 TATTTATTTTT-TGTTTT--AT-
1 TATTTATTTTTATATTTTAAATG
*
4954083 TATTTATTTTTATGTTTTAAATG
1 TATTTATTTTTATATTTTAAATG
4954106 TATTTGATTTATTATATTTTAAA
1 TATTT-ATTT-TTATATTTTAAA
4954129 GTTTTTTATT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
19 11 0.28
20 6 0.15
22 2 0.05
23 5 0.13
24 4 0.10
25 11 0.28
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (23 bp):
TATTTATTTTTATATTTTAAATG
Found at i:4960451 original size:12 final size:12
Alignment explanation
Indices: 4960434--4960467 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
4960424 ATATATATTT
*
4960434 AAAAATCATATA
1 AAAAATAATATA
4960446 AAAAATAATATA
1 AAAAATAATATA
*
4960458 AAAATTAATA
1 AAAAATAATA
4960468 CGGGCCAAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (12 bp):
AAAAATAATATA
Found at i:4960659 original size:27 final size:27
Alignment explanation
Indices: 4960624--4960675 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
4960614 CATGAACACC
4960624 TTTAATTGTAACTAATCATTCACATCT
1 TTTAATTGTAACTAATCATTCACATCT
*
4960651 TTTACTTGTAACTAATCATTCACAT
1 TTTAATTGTAACTAATCATTCACAT
4960676 TCTATAGACC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.33, C:0.19, G:0.04, T:0.44
Consensus pattern (27 bp):
TTTAATTGTAACTAATCATTCACATCT
Found at i:4961225 original size:15 final size:15
Alignment explanation
Indices: 4961205--4961233 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4961195 GACGCGAGCA
4961205 AGAAGAAGGCTGCTC
1 AGAAGAAGGCTGCTC
4961220 AGAAGAAGGCTGCT
1 AGAAGAAGGCTGCT
4961234 GCCGCTGCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.17, G:0.34, T:0.14
Consensus pattern (15 bp):
AGAAGAAGGCTGCTC
Found at i:4965219 original size:26 final size:26
Alignment explanation
Indices: 4965190--4965242 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
4965180 GTCCCTTTTA
4965190 AGCTTTTTAAACTTCTTCAAATAGAG
1 AGCTTTTTAAACTTCTTCAAATAGAG
4965216 AGCTTTTTAAACTTCTTCAAATAGAG
1 AGCTTTTTAAACTTCTTCAAATAGAG
4965242 A
1 A
4965243 TGATGAGGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (26 bp):
AGCTTTTTAAACTTCTTCAAATAGAG
Found at i:4971980 original size:13 final size:13
Alignment explanation
Indices: 4971962--4971986 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4971952 ATGGTATTGC
4971962 TTGAATGTTAATA
1 TTGAATGTTAATA
4971975 TTGAATGTTAAT
1 TTGAATGTTAAT
4971987 TACTTATAAA
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:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (13 bp):
TTGAATGTTAATA
Found at i:4972574 original size:85 final size:85
Alignment explanation
Indices: 4972474--4972632 Score: 273
Period size: 85 Copynumber: 1.9 Consensus size: 85
4972464 ATGTGAATAA
* *
4972474 AACCTTTAATCAAAGTTAAACCTAAAAGAGACGTGGTTGAATTATAAACATAACACGACACCGTT
1 AACCTTCAATCAAAGTTAAACATAAAAGAGACGTGGTTGAATTATAAACATAACACGACACCGTT
4972539 TAGTTGGAAGATAGAGAGGC
66 TAGTTGGAAGATAGAGAGGC
* *
4972559 AACCTTCAATCAAAGTTTAACATAAAAGAGACGTGGTTGAATTATAAACATAACACGATACCGTT
1 AACCTTCAATCAAAGTTAAACATAAAAGAGACGTGGTTGAATTATAAACATAACACGACACCGTT
*
4972624 TGGTTGGAA
66 TAGTTGGAA
4972633 TTGAGTCCGT
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
85 69 1.00
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (85 bp):
AACCTTCAATCAAAGTTAAACATAAAAGAGACGTGGTTGAATTATAAACATAACACGACACCGTT
TAGTTGGAAGATAGAGAGGC
Found at i:4973007 original size:15 final size:15
Alignment explanation
Indices: 4972987--4973015 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4972977 GACGCGAGCA
4972987 AGAAGAAGGCTGCTC
1 AGAAGAAGGCTGCTC
4973002 AGAAGAAGGCTGCT
1 AGAAGAAGGCTGCT
4973016 GCCGCTGCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.17, G:0.34, T:0.14
Consensus pattern (15 bp):
AGAAGAAGGCTGCTC
Found at i:4982548 original size:15 final size:14
Alignment explanation
Indices: 4982521--4982547 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4982511 GACAATAGTA
4982521 AAATATTAAAAAAT
1 AAATATTAAAAAAT
4982535 AAATATTAAAAAA
1 AAATATTAAAAAA
4982548 AAAAACATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AAATATTAAAAAAT
Found at i:4987153 original size:19 final size:19
Alignment explanation
Indices: 4987129--4987166 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
4987119 ATAATCCATG
4987129 TTTAAGCTGTAACATTCAA
1 TTTAAGCTGTAACATTCAA
4987148 TTTAAGCTGTAACATTCAA
1 TTTAAGCTGTAACATTCAA
4987167 AACTCAGCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (19 bp):
TTTAAGCTGTAACATTCAA
Found at i:4996978 original size:46 final size:46
Alignment explanation
Indices: 4996931--4997204 Score: 354
Period size: 46 Copynumber: 6.0 Consensus size: 46
4996921 GCTCTCTGAT
** *
4996931 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA-ACTGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA-TGAC
** * * * *
4996977 ATGAAATGTGTAAGACCATGATTAAAAGATACCATGGCAACGTGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
4997023 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** * *
4997069 GGGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAGCGTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
*
4997115 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGACAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * *
4997161 A-GAAAATGAGTAAGACCATGGTTGAAAGACACTATGGCATCATG
1 ATG-AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATG
4997205 TCAAAGATAA
Statistics
Matches: 203, Mismatches: 23, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
45 1 0.00
46 202 1.00
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.21
Consensus pattern (46 bp):
ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:4997084 original size:92 final size:92
Alignment explanation
Indices: 4996927--4997199 Score: 395
Period size: 92 Copynumber: 3.0 Consensus size: 92
4996917 GTGTGCTCTC
** * * *
4996927 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA-ACTGATATGAAATGTGTAAG
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA-TGACAGGAAATGAGTAAG
* *
4996991 ACCATGATTAAAAGATACCATGGCAACG
65 ACCATGGTTGAAAGATACCATGGCAACG
* *
4997019 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACGGGAAATGAATAAGA
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGGAAATGAGTAAGA
*
4997084 CCATGGTTGAAAGATACCATGGCAGCG
66 CCATGGTTGAAAGATACCATGGCAACG
* * *
4997111 TGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGACAACATGACAGAAAATGAGTAAGA
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGGAAATGAGTAAGA
* *
4997176 CCATGGTTGAAAGACACTATGGCA
66 CCATGGTTGAAAGATACCATGGCA
4997200 TCATGTCAAA
Statistics
Matches: 163, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
92 162 0.99
93 1 0.01
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.21
Consensus pattern (92 bp):
TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGGAAATGAGTAAGA
CCATGGTTGAAAGATACCATGGCAACG
Found at i:4997506 original size:16 final size:17
Alignment explanation
Indices: 4997485--4997517 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4997475 ATGATGGAGC
4997485 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
4997501 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
4997518 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:5016820 original size:67 final size:67
Alignment explanation
Indices: 5016736--5016882 Score: 195
Period size: 67 Copynumber: 2.2 Consensus size: 67
5016726 TTAATGTAAG
* * * * *
5016736 ATTAAAATTAATTTTTTAATTTCTTAAATTAAATTTAAAAGTATCTATCTTTTTGTCTTATTAAT
1 ATTAAAATTAACTTTTTAATTTCTTAAATTAAATCTAAAAATATCTATCCTTTTATCTTATTAAT
5016801 TT
66 TT
* * * *
5016803 ATTAAAGTTAACTTTTTAATTTCTTACATTATATCTAAAAATATGTATCCTTTTATCTTATTAAT
1 ATTAAAATTAACTTTTTAATTTCTTAAATTAAATCTAAAAATATCTATCCTTTTATCTTATTAAT
5016868 TT
66 TT
5016870 ATTTATAAATTAA
1 A-TTA-AAATTAA
5016883 AAAAATCTAT
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
67 59 0.87
68 3 0.04
69 6 0.09
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.53
Consensus pattern (67 bp):
ATTAAAATTAACTTTTTAATTTCTTAAATTAAATCTAAAAATATCTATCCTTTTATCTTATTAAT
TT
Found at i:5018321 original size:310 final size:315
Alignment explanation
Indices: 5017712--5018325 Score: 1033
Period size: 310 Copynumber: 2.0 Consensus size: 315
5017702 GTTACGAATC
*
5017712 AGAGAAGCAAACACCAAAAACCTAAACCGAGAACCAAGGTGATTTTTTAATCCCATTTTCGTTTC
1 AGAGAAGCAAACACCAAAAACCTAAACCGAGAACCAAGGTGATTTTTTAATCCCATTTTAGTTTC
5017777 GTTTTTGGGCCTATTTTCTCACATATATATATTAAAACATATAAAAAATATAATAATAATAAAAA
66 GTTTTTGGGCCTATTTTCTCACATATATATATTAAAACATAT--AAAATATAATAATAATAAAAA
* * *
5017842 GAGGGAGATTTACCTTTTCCGGCCACCGTGCACGGTGGCCGGCGCTAGCAACGAACGGCGGTCCG
129 GAGGGAGATTTACCTTTTCCAGCCACCGTGCACGGCGGCCGGCGCCAGCAACGAACGGCGGTCCG
*
5017907 ATGGTTGGACCGGTGACCGGCCCATGGCCGAAAATCTCTTTTCCCTCCCCCTCTCCCTTTACTCT
194 ATGGTCGGACCGGTGACCGGCCCATGGCCGAAAATCTCTTTTCCCTCCCCCTCTCCCTTTACTCT
* *
5017972 CCTTTTTTTCTCTTTTCCTCGTTTCAAATGAATTTTTTTTAAAAAAATTTTGAAATT
259 CATTTTTTTCTCTTTTCCCCGTTTCAAATGAATTTTTTTTAAAAAAATTTTGAAATT
5018029 AGAGAAGCAAACACCAAAAACCTAAACCGAGAACCAAGGTGATTTTTTAATCCCATTTTAGTTTC
1 AGAGAAGCAAACACCAAAAACCTAAACCGAGAACCAAGGTGATTTTTTAATCCCATTTTAGTTTC
5018094 GTTTTTGGGCCTATTTTCTCACATATATATATTAAAACATAT-AAA-A-AATAAT-A-AAAAAGA
66 GTTTTTGGGCCTATTTTCTCACATATATATATTAAAACATATAAAATATAATAATAATAAAAAGA
* * *
5018154 GGGAGATTTACCTTTTCCAGCCACCGTGCACGGCGGCCGGCGCCGGCGACGGACGGCGGTCCGAT
131 GGGAGATTTACCTTTTCCAGCCACCGTGCACGGCGGCCGGCGCCAGCAACGAACGGCGGTCCGAT
* * *
5018219 GGTCGGACCGGTGACCGGCCCATGGCCGGAAATCTCTTTTCCCTCCCCCTCTCCCTTTTCTCTTA
196 GGTCGGACCGGTGACCGGCCCATGGCCGAAAATCTCTTTTCCCTCCCCCTCTCCCTTTACTCTCA
*
5018284 TTTGTTTTTTCTTTTCCCCGTTTCAAATGAA-TTTTTTTAAAA
261 TTT-TTTTCTCTTTTCCCCGTTTCAAATGAATTTTTTTTAAAA
5018326 TTTTTTTTGT
Statistics
Matches: 282, Mismatches: 14, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
310 140 0.50
311 26 0.09
312 6 0.02
313 1 0.00
314 3 0.01
317 106 0.38
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (315 bp):
AGAGAAGCAAACACCAAAAACCTAAACCGAGAACCAAGGTGATTTTTTAATCCCATTTTAGTTTC
GTTTTTGGGCCTATTTTCTCACATATATATATTAAAACATATAAAATATAATAATAATAAAAAGA
GGGAGATTTACCTTTTCCAGCCACCGTGCACGGCGGCCGGCGCCAGCAACGAACGGCGGTCCGAT
GGTCGGACCGGTGACCGGCCCATGGCCGAAAATCTCTTTTCCCTCCCCCTCTCCCTTTACTCTCA
TTTTTTTCTCTTTTCCCCGTTTCAAATGAATTTTTTTTAAAAAAATTTTGAAATT
Found at i:5018774 original size:15 final size:15
Alignment explanation
Indices: 5018754--5018787 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
5018744 ATTAATTTTG
*
5018754 ATATTTTCTATTATT
1 ATATTTACTATTATT
5018769 ATATTTACTATTATT
1 ATATTTACTATTATT
5018784 -TATT
1 ATATT
5018788 GTTATTGGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (15 bp):
ATATTTACTATTATT
Found at i:5019306 original size:26 final size:24
Alignment explanation
Indices: 5019277--5019350 Score: 60
Period size: 26 Copynumber: 2.8 Consensus size: 24
5019267 CTTATGTACA
5019277 TATATTTACATGCATATATTTTCTTT
1 TATATTTA-ATGCATATATTTT-TTT
5019303 TATATATT-ATGCATATACATTTTTTT
1 TATAT-TTAATGCATAT--ATTTTTTT
* *
5019329 AATATTATATATGTATATATTT
1 TATATT-TA-ATGCATATATTT
5019351 ATACTATATT
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
25 9 0.22
26 17 0.43
27 7 0.17
28 7 0.17
ACGTcount: A:0.32, C:0.07, G:0.04, T:0.57
Consensus pattern (24 bp):
TATATTTAATGCATATATTTTTTT
Found at i:5019307 original size:28 final size:26
Alignment explanation
Indices: 5019276--5019350 Score: 66
Period size: 25 Copynumber: 2.8 Consensus size: 26
5019266 TCTTATGTAC
5019276 ATATATTTACATGCATATATTTTCTTTT
1 ATATATTTA-ATGCATATATTTT-TTTT
*
5019304 ATATA-TT-ATGCATATACATTTTTTT
1 ATATATTTAATGCATATA-TTTTTTTT
*
5019329 A-ATATTATATATGTATATATTT
1 ATATATT-TA-ATGCATATATTT
5019351 ATACTATATT
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
24 3 0.08
25 15 0.38
26 4 0.10
27 4 0.10
28 13 0.33
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.56
Consensus pattern (26 bp):
ATATATTTAATGCATATATTTTTTTT
Found at i:5019317 original size:25 final size:24
Alignment explanation
Indices: 5019286--5019336 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
5019276 ATATATTTAC
*
5019286 ATGCATATA-TTTTCTTTTATATATT
1 ATGCATATACATTT-TTTTA-ATATT
5019311 ATGCATATACATTTTTTTAATATT
1 ATGCATATACATTTTTTTAATATT
5019335 AT
1 AT
5019337 ATATGTATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 7 0.29
25 14 0.58
26 3 0.12
ACGTcount: A:0.31, C:0.08, G:0.04, T:0.57
Consensus pattern (24 bp):
ATGCATATACATTTTTTTAATATT
Found at i:5027250 original size:47 final size:48
Alignment explanation
Indices: 5027196--5027292 Score: 142
Period size: 47 Copynumber: 2.0 Consensus size: 48
5027186 AACCTCGATA
* *
5027196 CAATGTCAGCTTGTATGAGCAA-ATTCATAAATGTTAGCTTGTGTGAG
1 CAATGTCAGCTTGTATGAGCAACATTAATAAATGTCAGCTTGTGTGAG
* * *
5027243 CAATGTCAGCTTGTATGAGCAACCTTAATCACTGTCAGCTTGTGTGAG
1 CAATGTCAGCTTGTATGAGCAACATTAATAAATGTCAGCTTGTGTGAG
5027291 CA
1 CA
5027293 CTATAGTTCC
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
47 22 0.50
48 22 0.50
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.32
Consensus pattern (48 bp):
CAATGTCAGCTTGTATGAGCAACATTAATAAATGTCAGCTTGTGTGAG
Found at i:5027253 original size:19 final size:19
Alignment explanation
Indices: 5027225--5027264 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
5027215 CAAATTCATA
* *
5027225 AATGTTAGCTTGTGTGAGC
1 AATGTCAGCTTGTATGAGC
5027244 AATGTCAGCTTGTATGAGC
1 AATGTCAGCTTGTATGAGC
5027263 AA
1 AA
5027265 CCTTAATCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.12, G:0.28, T:0.33
Consensus pattern (19 bp):
AATGTCAGCTTGTATGAGC
Found at i:5035450 original size:15 final size:16
Alignment explanation
Indices: 5035413--5035473 Score: 61
Period size: 16 Copynumber: 3.9 Consensus size: 16
5035403 AAATTTTAAG
* * *
5035413 TTATTTTGAGTTAGGA
1 TTATTTTAAGTTTGAA
5035429 TTATTTTAAGTTTGAA
1 TTATTTTAAGTTTGAA
* *
5035445 -TATTTTAAATTTAAA
1 TTATTTTAAGTTTGAA
*
5035460 TTATTTTGAGTTTG
1 TTATTTTAAGTTTG
5035474 GGATATTCGG
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
15 13 0.36
16 23 0.64
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (16 bp):
TTATTTTAAGTTTGAA
Found at i:5035466 original size:16 final size:16
Alignment explanation
Indices: 5035428--5035466 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
5035418 TTGAGTTAGG
* *
5035428 ATTATTTTAAGTTTGA
1 ATTATTTTAAATTTAA
5035444 A-TATTTTAAATTTAA
1 ATTATTTTAAATTTAA
5035459 ATTATTTT
1 ATTATTTT
5035467 GAGTTTGGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (16 bp):
ATTATTTTAAATTTAA
Found at i:5036317 original size:71 final size:71
Alignment explanation
Indices: 5036201--5036339 Score: 251
Period size: 71 Copynumber: 2.0 Consensus size: 71
5036191 GTTAAGAGGA
* *
5036201 AGCTTCAATTTGGAAGATATCAATTATACCTGTTATCATTTCAAAACCACCAAGCACCCTCTGCC
1 AGCTTCAATTTGGAAGATATCAATTATACCTGTTACCATTTCAAAACCACCAACCACCCTCTGCC
5036266 TGGTCC
66 TGGTCC
*
5036272 AGCTTCAATTTGGAAGATATCAGTTATACCTGTTACCATTTCAAAACCACCAACCACCCTCTGCC
1 AGCTTCAATTTGGAAGATATCAATTATACCTGTTACCATTTCAAAACCACCAACCACCCTCTGCC
5036337 TGG
66 TGG
5036340 CCCTCTCAAC
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 65 1.00
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.29
Consensus pattern (71 bp):
AGCTTCAATTTGGAAGATATCAATTATACCTGTTACCATTTCAAAACCACCAACCACCCTCTGCC
TGGTCC
Found at i:5042801 original size:25 final size:26
Alignment explanation
Indices: 5042741--5042789 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
5042731 ATTTGTTTTA
*
5042741 ATATTTG-TTT-TTATGTTTTTAAAT
1 ATATTTGATTTATTATATTTTTAAAT
5042765 ATATTTGATTTATTATATTTTTAAA
1 ATATTTGATTTATTATATTTTTAAA
5042790 ATTTTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.32
25 3 0.14
26 12 0.55
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (26 bp):
ATATTTGATTTATTATATTTTTAAAT
Found at i:5045760 original size:38 final size:38
Alignment explanation
Indices: 5045709--5045784 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
5045699 ATAATTAGCC
*
5045709 TCCCTAGGAATATGTCTTACCACCCAATGCTCTGTATT
1 TCCCTAGGAATATGTCTTACCACCCAATACTCTGTATT
5045747 TCCCTAGGAATATGTCTTACCACCCAATACTCTGTATT
1 TCCCTAGGAATATGTCTTACCACCCAATACTCTGTATT
5045785 ATGTAGCAAC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.25, C:0.29, G:0.12, T:0.34
Consensus pattern (38 bp):
TCCCTAGGAATATGTCTTACCACCCAATACTCTGTATT
Found at i:5046761 original size:10 final size:10
Alignment explanation
Indices: 5046747--5046791 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
5046737 CAAAATTGAA
5046747 ATTATTTTAT
1 ATTATTTTAT
*
5046757 TTTATTTTAT
1 ATTATTTTAT
*
5046767 AATATTTTAT
1 ATTATTTTAT
5046777 A-TA-TTTA-
1 ATTATTTTAT
5046784 ATTATTTT
1 ATTATTTT
5046792 TAATAAATAC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
7 1 0.03
8 6 0.20
9 5 0.17
10 18 0.60
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
ATTATTTTAT
Found at i:5048778 original size:30 final size:29
Alignment explanation
Indices: 5048742--5048798 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
5048732 TTAATAAAAG
*
5048742 TAAAATTATATTTTAATTTCTTAAAAATGA
1 TAAAATTATAATTTAA-TTCTTAAAAATGA
* *
5048772 TAAAATTTTAATTTAATTCTTTAAAAT
1 TAAAATTATAATTTAATTCTTAAAAAT
5048799 TTATATTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 10 0.42
30 14 0.58
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.49
Consensus pattern (29 bp):
TAAAATTATAATTTAATTCTTAAAAATGA
Found at i:5054107 original size:30 final size:30
Alignment explanation
Indices: 5054073--5054134 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
5054063 CTTTTTCTCA
*
5054073 ACTAGCCACTCCTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
* *
5054103 ACTAGCCACACCTTTTCCACCTCTAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
5054133 AC
1 AC
5054135 CTTTTCCACT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.24, C:0.48, G:0.03, T:0.24
Consensus pattern (30 bp):
ACTAGCCACACCTTTTCCACCACCAACTCC
Found at i:5054139 original size:51 final size:51
Alignment explanation
Indices: 5054083--5054185 Score: 161
Period size: 51 Copynumber: 2.0 Consensus size: 51
5054073 ACTAGCCACT
* *
5054083 CCTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCTCTAACTCCA
1 CCTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAACTCCA
* * *
5054134 CCTTTTCCACTACCAACTCCACTAGCCACTCTTTTTCCACCACCAACTCCA
1 CCTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAACTCCA
5054185 C
1 C
5054186 TAGCCACACC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.23, C:0.49, G:0.02, T:0.26
Consensus pattern (51 bp):
CCTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAACTCCA
Found at i:5054151 original size:21 final size:21
Alignment explanation
Indices: 5054111--5054155 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
5054101 CCACTAGCCA
*
5054111 CACCTTTTCCACCTCTAACTC
1 CACCTTTTCCACCTCCAACTC
5054132 CACCTTTTCCA-CTACCAACTC
1 CACCTTTTCCACCT-CCAACTC
5054153 CAC
1 CAC
5054156 TAGCCACTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.22, C:0.49, G:0.00, T:0.29
Consensus pattern (21 bp):
CACCTTTTCCACCTCCAACTC
Found at i:5054203 original size:30 final size:30
Alignment explanation
Indices: 5054132--5054205 Score: 112
Period size: 30 Copynumber: 2.5 Consensus size: 30
5054122 CCTCTAACTC
*
5054132 CACCTTTTCCACTACCAACTCCACTAGCCA
1 CACCTTTTCCACCACCAACTCCACTAGCCA
* *
5054162 CTCTTTTTCCACCACCAACTCCACTAGCCA
1 CACCTTTTCCACCACCAACTCCACTAGCCA
*
5054192 CACCTTCTCCACCA
1 CACCTTTTCCACCA
5054206 TCACTTGTAC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.24, C:0.49, G:0.03, T:0.24
Consensus pattern (30 bp):
CACCTTTTCCACCACCAACTCCACTAGCCA
Found at i:5054731 original size:23 final size:23
Alignment explanation
Indices: 5054694--5054821 Score: 70
Period size: 23 Copynumber: 5.5 Consensus size: 23
5054684 TCCTTTTTGT
5054694 TATTAT-TATATTTCTTAATATTA
1 TATTATATATA-TTCTTAATATTA
* *
5054717 TATTATATATATTCTT-TTAATA
1 TATTATATATATTCTTAATATTA
**
5054739 TATTAGGTATATT-TTAA-ATTCTA
1 TATTATATATATTCTTAATA-T-TA
* *
5054762 TATTACGTATATA-TATT-ATACTA
1 TATTA--TATATATTCTTAATATTA
* *
5054785 TTTTATGTATATATCTTTAATATTA
1 TATTATATATAT-TC-TTAATATTA
*
5054810 TATTATTTATAT
1 TATTATATATAT
5054822 ATATATATTT
Statistics
Matches: 78, Mismatches: 15, Indels: 22
0.68 0.13 0.19
Matches are distributed among these distances:
21 8 0.10
22 15 0.19
23 25 0.32
24 8 0.10
25 22 0.28
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (23 bp):
TATTATATATATTCTTAATATTA
Found at i:5054797 original size:25 final size:26
Alignment explanation
Indices: 5054769--5054910 Score: 71
Period size: 25 Copynumber: 5.5 Consensus size: 26
5054759 CTATATTACG
*
5054769 TATATATATT-ATACTATTTTATGTA
1 TATATATATTAATACTATATTATGTA
* * *
5054794 TATATCT-TTAATATTATATTATTTATA
1 TATATATATTAATACTATATTA--TGTA
** * *
5054821 TATATATATTTTTAC-ATGTTATCTTA
1 TATATATATTAATACTATATTAT-GTA
* *
5054847 TGTATATATCTTA-ACTATATTATGTA
1 TATATATAT-TAATACTATATTATGTA
* * *
5054873 TGTAT-TTTTAACACTATATTATGTA
1 TATATATATTAATACTATATTATGTA
* *
5054898 CATAT-TTTTAATA
1 TATATATATTAATA
5054911 TTATCACGTA
Statistics
Matches: 90, Mismatches: 19, Indels: 16
0.72 0.15 0.13
Matches are distributed among these distances:
24 4 0.04
25 41 0.46
26 19 0.21
27 22 0.24
28 4 0.04
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.55
Consensus pattern (26 bp):
TATATATATTAATACTATATTATGTA
Found at i:5054821 original size:14 final size:15
Alignment explanation
Indices: 5054773--5054831 Score: 54
Period size: 14 Copynumber: 4.1 Consensus size: 15
5054763 ATTACGTATA
5054773 TATATTATACTAT-TT
1 TATATTATA-TATATT
* *
5054788 TAT-GTATATATCTT
1 TATATTATATATATT
5054802 TAATATTATAT-TATT
1 T-ATATTATATATATT
5054817 TATA-TATATATATT
1 TATATTATATATATT
5054831 T
1 T
5054832 TTACATGTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
13 8 0.22
14 15 0.41
15 9 0.24
16 5 0.14
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (15 bp):
TATATTATATATATT
Found at i:5054829 original size:79 final size:79
Alignment explanation
Indices: 5054746--5054894 Score: 185
Period size: 79 Copynumber: 1.9 Consensus size: 79
5054736 ATATATTAGG
* * *
5054746 TATA-TTTTAAAT-TCTATATTACGTATATATATTATACTATTTTATGTATATATCTTTAATATT
1 TATATTTTTAAATGT-TATATTACGTATATATATTA-ACTATATTATGTATATATCTTTAACACT
5054809 ATATTATTTATATATA
64 ATATTATTTATATATA
* * * * * *
5054825 TATATTTTTACATGTTATCTTATGTATATATCTTAACTATATTATGTATGTATTTTTAACACTAT
1 TATATTTTTAAATGTTATATTACGTATATATATTAACTATATTATGTATATATCTTTAACACTAT
5054890 ATTAT
66 ATTAT
5054895 GTACATATTT
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
79 34 0.58
80 24 0.41
81 1 0.02
ACGTcount: A:0.34, C:0.07, G:0.04, T:0.55
Consensus pattern (79 bp):
TATATTTTTAAATGTTATATTACGTATATATATTAACTATATTATGTATATATCTTTAACACTAT
ATTATTTATATATA
Found at i:5055086 original size:16 final size:15
Alignment explanation
Indices: 5055062--5055109 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
5055052 TAATTATTAT
*
5055062 TATTCTAATATTTTGA
1 TATTTTAATATTTT-A
5055078 TATTTTAATATTTTA
1 TATTTTAATATTTTA
5055093 TATTTTATATATTTTA
1 TATTTTA-ATATTTTA
5055109 T
1 T
5055110 TATTCACATC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (15 bp):
TATTTTAATATTTTA
Found at i:5055097 original size:7 final size:8
Alignment explanation
Indices: 5055062--5055113 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
5055052 TAATTATTAT
*
5055062 TATTCTAA
1 TATTTTAA
*
5055070 TATTTTGA
1 TATTTTAA
5055078 TATTTTAA
1 TATTTTAA
5055086 TATTTT-A
1 TATTTTAA
5055093 TATTTTATA
1 TATTTTA-A
*
5055102 TATTTTAT
1 TATTTTAA
5055110 TATT
1 TATT
5055114 CACATCATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 23 0.61
9 8 0.21
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (8 bp):
TATTTTAA
Found at i:5055914 original size:24 final size:24
Alignment explanation
Indices: 5055868--5055914 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
5055858 TGCATTATGT
** * *
5055868 ATTTTAATTATTATTTTTTAAAAA
1 ATTTTAATTAGAATCTTTCAAAAA
5055892 ATTTTAATTAGAATCTTTCAAAA
1 ATTTTAATTAGAATCTTTCAAAA
5055915 TATTAATTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (24 bp):
ATTTTAATTAGAATCTTTCAAAAA
Found at i:5077138 original size:20 final size:19
Alignment explanation
Indices: 5077099--5077138 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
5077089 AATTAGAGAG
*
5077099 AATTTATTTTCTAAGTATA
1 AATTTATTTTCTAAGAATA
*
5077118 AATTATATTTTCTAGGAATA
1 AATT-TATTTTCTAAGAATA
5077138 A
1 A
5077139 CAATCTTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.47
Consensus pattern (19 bp):
AATTTATTTTCTAAGAATA
Found at i:5077788 original size:21 final size:21
Alignment explanation
Indices: 5077762--5077804 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
5077752 GGTTCGCTGT
*
5077762 ATTGGATTAGAGGTGTATTGG
1 ATTGGATTAGAGGTGTAATGG
5077783 ATTGGATTAGAGGTGTAATGG
1 ATTGGATTAGAGGTGTAATGG
5077804 A
1 A
5077805 ATAGAGGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.37, T:0.35
Consensus pattern (21 bp):
ATTGGATTAGAGGTGTAATGG
Found at i:5077804 original size:16 final size:16
Alignment explanation
Indices: 5077785--5077817 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5077775 TGTATTGGAT
*
5077785 TGGATTAGAGGTGTAA
1 TGGAATAGAGGTGTAA
5077801 TGGAATAGAGGTGTAA
1 TGGAATAGAGGTGTAA
5077817 T
1 T
5077818 AGCAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (16 bp):
TGGAATAGAGGTGTAA
Found at i:5077862 original size:45 final size:44
Alignment explanation
Indices: 5077796--5077890 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
5077786 GGATTAGAGG
* *
5077796 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
5077841 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
5077885 TGTAAT
1 TGTAAT
5077891 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:5078073 original size:18 final size:17
Alignment explanation
Indices: 5078052--5078086 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5078042 TTATTATTTA
*
5078052 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
5078070 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
5078087 GGTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:5078080 original size:28 final size:27
Alignment explanation
Indices: 5078010--5078082 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
5078000 TTTATTATCA
*
5078010 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
5078038 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
5078065 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
5078083 AAATGGTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:5078199 original size:144 final size:147
Alignment explanation
Indices: 5077971--5078242 Score: 469
Period size: 144 Copynumber: 1.9 Consensus size: 147
5077961 ATGATTATTG
5077971 TTATTGTTATTTAAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTA--TATTATCAAAAATAAATAATTTAATCATATTTAA
* *
5078036 ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATGGTTAATAATTAGC
64 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATGCTTAATAATTAGC
5078101 AGAAATTTATTTTGGTAAA
129 AGAAATTTATTTTGGTAAA
*
5078120 TTATT-TTATTTAAATTTTAATAAGATTA-A-TATCAATAATAAATAATTTAATCATATTTAAAC
1 TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
*
5078182 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
66 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATGCTTAATAATTA
5078243 ATATTCTTAT
Statistics
Matches: 119, Mismatches: 4, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
144 90 0.76
145 1 0.01
148 23 0.19
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (147 bp):
TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATGCTTAATAATTAGCAG
AAATTTATTTTGGTAAA
Found at i:5078217 original size:18 final size:17
Alignment explanation
Indices: 5078196--5078230 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5078186 TTATTATTAA
*
5078196 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
5078214 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
5078231 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:5084530 original size:14 final size:15
Alignment explanation
Indices: 5084507--5084539 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
5084497 TTCAAACTTC
*
5084507 AATTATTTAAAT-AT
1 AATTAATTAAATAAT
5084521 AATTAATTAAATAAT
1 AATTAATTAAATAAT
5084536 AATT
1 AATT
5084540 TGAAAACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTAATTAAATAAT
Found at i:5087907 original size:16 final size:16
Alignment explanation
Indices: 5087886--5087917 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
5087876 ATTTTTAAAT
5087886 TTTAAAAAATTAAAAA
1 TTTAAAAAATTAAAAA
5087902 TTTAAAAAATTAAAAA
1 TTTAAAAAATTAAAAA
5087918 AAGTAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
TTTAAAAAATTAAAAA
Found at i:5087909 original size:9 final size:9
Alignment explanation
Indices: 5087886--5087975 Score: 51
Period size: 9 Copynumber: 10.0 Consensus size: 9
5087876 ATTTTTAAAT
5087886 TTTAAAAAA
1 TTTAAAAAA
5087895 -TT-AAAAA
1 TTTAAAAAA
5087902 TTTAAAAAA
1 TTTAAAAAA
*
5087911 TTAAAAAAA
1 TTTAAAAAA
* *
5087920 GTAAAAAAA
1 TTTAAAAAA
* *
5087929 TCTTTAAAAT
1 T-TTAAAAAA
*
5087939 TATTAAAACA
1 T-TTAAAAAA
*
5087949 TATAAAAATA
1 TTTAAAAA-A
**
5087959 TTT-TTAAA
1 TTTAAAAAA
5087967 TTTAAAAAA
1 TTTAAAAAA
5087976 ATAATTAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 10
0.69 0.20 0.12
Matches are distributed among these distances:
7 5 0.08
8 8 0.14
9 31 0.53
10 15 0.25
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.33
Consensus pattern (9 bp):
TTTAAAAAA
Found at i:5087927 original size:8 final size:8
Alignment explanation
Indices: 5087887--5087918 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
5087877 TTTTTAAATT
5087887 TTAAAAAA
1 TTAAAAAA
*
5087895 TTAAAAAT
1 TTAAAAAA
5087903 TTAAAAAA
1 TTAAAAAA
5087911 TTAAAAAA
1 TTAAAAAA
5087919 AGTAAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (8 bp):
TTAAAAAA
Found at i:5090218 original size:17 final size:17
Alignment explanation
Indices: 5090184--5090219 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5090174 GAAAAAATAG
**
5090184 TTTTTTCTTTTTTTAAT
1 TTTTTTCTTTTTAAAAT
5090201 TTTTTTCTTTTTAAAAT
1 TTTTTTCTTTTTAAAAT
5090218 TT
1 TT
5090220 CACACTATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTTCTTTTTAAAAT
Found at i:5093942 original size:16 final size:16
Alignment explanation
Indices: 5093894--5093947 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
5093884 ATTTACTATT
5093894 TATAA-AAGATATTTA
1 TATAATAAGATATTTA
*
5093909 T-TAATTAAG-TAATTA
1 TATAA-TAAGATATTTA
*
5093924 TATTATAAGATATTTA
1 TATAATAAGATATTTA
5093940 TATAATAA
1 TATAATAA
5093948 ATAAATTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
14 3 0.10
15 11 0.35
16 17 0.55
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (16 bp):
TATAATAAGATATTTA
Found at i:5095012 original size:16 final size:15
Alignment explanation
Indices: 5094983--5095032 Score: 55
Period size: 15 Copynumber: 3.0 Consensus size: 15
5094973 TAATATAAAG
5094983 TGAATTGAAATATAT
1 TGAATTGAAATATAT
5094998 TGAATTGAGAATATAT
1 TGAATTGA-AATATAT
5095014 CTGATTAATTGAAATATAT
1 -TG---AATTGAAATATAT
5095033 ACTGATTGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 8 0.27
16 7 0.23
17 2 0.07
19 7 0.23
20 6 0.20
ACGTcount: A:0.44, C:0.02, G:0.14, T:0.40
Consensus pattern (15 bp):
TGAATTGAAATATAT
Found at i:5095025 original size:20 final size:20
Alignment explanation
Indices: 5095000--5095039 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
5094990 AAATATATTG
5095000 AATTGAGAATATAT-CTGATT
1 AATTGA-AATATATACTGATT
5095020 AATTGAAATATATACTGATT
1 AATTGAAATATATACTGATT
5095040 GAAAACTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.40
Consensus pattern (20 bp):
AATTGAAATATATACTGATT
Found at i:5095176 original size:6 final size:6
Alignment explanation
Indices: 5095165--5095191 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5095155 ATGTGCCGAC
5095165 TACTGT TACTGT TACTGT TACTGT TAC
1 TACTGT TACTGT TACTGT TACTGT TAC
5095192 CGATTCGACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.48
Consensus pattern (6 bp):
TACTGT
Found at i:5095385 original size:18 final size:18
Alignment explanation
Indices: 5095365--5095475 Score: 91
Period size: 18 Copynumber: 6.2 Consensus size: 18
5095355 ATAAAGGTAT
*
5095365 TGAATAACTGATTATTAT
1 TGAATAACTGATTATTAC
* * *
5095383 TGAATAATTGACTGTTAC
1 TGAATAACTGATTATTAC
* *
5095401 TAAATAAAC-GACTATTAC
1 TGAAT-AACTGATTATTAC
*
5095419 TGAATAAATGATTATTAC
1 TGAATAACTGATTATTAC
* *
5095437 TAAATAACTGATTAATAC
1 TGAATAACTGATTATTAC
* * *
5095455 TG-ATGACTGACTAATAC
1 TGAATAACTGATTATTAC
5095472 TGAA
1 TGAA
5095476 CAATAAAGAT
Statistics
Matches: 74, Mismatches: 16, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
17 17 0.23
18 55 0.74
19 2 0.03
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.35
Consensus pattern (18 bp):
TGAATAACTGATTATTAC
Found at i:5095407 original size:36 final size:36
Alignment explanation
Indices: 5095367--5095457 Score: 112
Period size: 36 Copynumber: 2.5 Consensus size: 36
5095357 AAAGGTATTG
* * *
5095367 AATAACTGATTATTATTGAATAATTGACTGTTACTA
1 AATAACTGATTATTACTGAATAAATGACTATTACTA
* *
5095403 AATAAAC-GACTATTACTGAATAAATGATTATTACTA
1 AAT-AACTGATTATTACTGAATAAATGACTATTACTA
*
5095439 AATAACTGATTAATACTGA
1 AATAACTGATTATTACTGA
5095458 TGACTGACTA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
35 3 0.07
36 40 0.87
37 3 0.07
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (36 bp):
AATAACTGATTATTACTGAATAAATGACTATTACTA
Found at i:5097359 original size:40 final size:40
Alignment explanation
Indices: 5097304--5097384 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
5097294 ACAGTTAACC
5097304 ATAAGTGCCCTATATGTAGTAAGGCACTAAGTCAAATTAT
1 ATAAGTGCCCTATATGTAGTAAGGCACTAAGTCAAATTAT
5097344 ATAAGTGCCCTATATGTAGTAAGGCACTAAGTCAAATTAT
1 ATAAGTGCCCTATATGTAGTAAGGCACTAAGTCAAATTAT
5097384 A
1 A
5097385 CCAAGTGAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (40 bp):
ATAAGTGCCCTATATGTAGTAAGGCACTAAGTCAAATTAT
Found at i:5112115 original size:17 final size:17
Alignment explanation
Indices: 5112093--5112126 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
5112083 TAAATTTTAG
5112093 AATATATATAA-AAAATA
1 AATATATA-AATAAAATA
5112110 AATATATAAATAAAATA
1 AATATATAAATAAAATA
5112127 TAATTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 14 0.88
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AATATATAAATAAAATA
Found at i:5112659 original size:10 final size:10
Alignment explanation
Indices: 5112646--5112673 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
5112636 AAAAAGAATT
5112646 AATTTTAAAA
1 AATTTTAAAA
5112656 AATTTTAAAA
1 AATTTTAAAA
5112666 AATTTTAA
1 AATTTTAA
5112674 GTCTGAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
AATTTTAAAA
Found at i:5117424 original size:15 final size:17
Alignment explanation
Indices: 5117384--5117424 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 17
5117374 CAATCATTCT
5117384 AGTAAATTAACTCATCA
1 AGTAAATTAACTCATCA
*
5117401 ACT-AATTAA-TC-TCA
1 AGTAAATTAACTCATCA
5117415 AGTAAATTAA
1 AGTAAATTAA
5117425 GTAATTATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
14 5 0.24
15 8 0.38
16 6 0.29
17 2 0.10
ACGTcount: A:0.49, C:0.15, G:0.05, T:0.32
Consensus pattern (17 bp):
AGTAAATTAACTCATCA
Found at i:5122485 original size:18 final size:19
Alignment explanation
Indices: 5122462--5122506 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
5122452 CTTTTATAAA
5122462 TTTATAAAAA-ATATTATT
1 TTTATAAAAACATATTATT
*
5122480 TTTATAAAAACATTTTATT
1 TTTATAAAAACATATTATT
*
5122499 TCTATAAA
1 TTTATAAA
5122507 TTTGTTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 10 0.42
19 14 0.58
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (19 bp):
TTTATAAAAACATATTATT
Found at i:5123821 original size:39 final size:39
Alignment explanation
Indices: 5123744--5123821 Score: 93
Period size: 39 Copynumber: 2.0 Consensus size: 39
5123734 ATATCATGTC
** * *
5123744 ATTAATTACTATGTTTAAAGGAATATCACGTGACACGTT
1 ATTAATTACTATGTGCAAAGGAATACCACATGACACGTT
* * *
5123783 ATTAATTACTATGTGCAAATGAATACCATATGATACGTT
1 ATTAATTACTATGTGCAAAGGAATACCACATGACACGTT
5123822 TTCATTGATA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (39 bp):
ATTAATTACTATGTGCAAAGGAATACCACATGACACGTT
Found at i:5132289 original size:13 final size:13
Alignment explanation
Indices: 5132271--5132295 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5132261 TAAAGGGATA
5132271 AATAAATAAATAC
1 AATAAATAAATAC
5132284 AATAAATAAATA
1 AATAAATAAATA
5132296 TTAAGGAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (13 bp):
AATAAATAAATAC
Found at i:5132528 original size:25 final size:24
Alignment explanation
Indices: 5132499--5132545 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
5132489 AAAGGATAAT
*
5132499 AAATAAATAATAATAATAAATGTGC
1 AAATAAATAAAAATAA-AAATGTGC
5132524 AAATAAATAAAAATAAAAATGT
1 AAATAAATAAAAATAAAAATGT
5132546 AAGCGATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.66, C:0.02, G:0.06, T:0.26
Consensus pattern (24 bp):
AAATAAATAAAAATAAAAATGTGC
Found at i:5140542 original size:15 final size:15
Alignment explanation
Indices: 5140524--5140565 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
5140514 ATAAATTCTA
5140524 AAATTTTAAAATGA-T
1 AAATTTTAAAAT-ATT
*
5140539 AAATTCTAAAATATT
1 AAATTTTAAAATATT
5140554 AATATTTTAAAA
1 AA-ATTTTAAAA
5140566 ATTTATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 1 0.04
15 14 0.61
16 8 0.35
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (15 bp):
AAATTTTAAAATATT
Found at i:5141634 original size:17 final size:17
Alignment explanation
Indices: 5141597--5141637 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
5141587 TCCATTAGAT
*
5141597 TTTTTTAATTTTTATAA
1 TTTTTAAATTTTTATAA
5141614 -TTTTAAATATTTTA-AA
1 TTTTTAAAT-TTTTATAA
5141630 TTTTTAAA
1 TTTTTAAA
5141638 AATTATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTTTAAATTTTTATAA
Found at i:5145570 original size:11 final size:11
Alignment explanation
Indices: 5145556--5145582 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
5145546 AGTTAAAACA
5145556 AAAAAAAAAAG
1 AAAAAAAAAAG
5145567 AAAAAAAAAAG
1 AAAAAAAAAAG
5145578 AAAAA
1 AAAAA
5145583 GAATTTGAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:5145570 original size:12 final size:12
Alignment explanation
Indices: 5145550--5145582 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
5145540 TTTTGTAGTT
*
5145550 AAAACAAAAAAA
1 AAAAGAAAAAAA
5145562 AAAAG-AAAAAA
1 AAAAGAAAAAAA
5145573 AAAAGAAAAA
1 AAAAGAAAAA
5145583 GAATTTGAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 11 0.58
12 8 0.42
ACGTcount: A:0.91, C:0.03, G:0.06, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAAAA
Found at i:5145575 original size:17 final size:17
Alignment explanation
Indices: 5145550--5145585 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5145540 TTTTGTAGTT
*
5145550 AAAACAAAAAAAAAAAG
1 AAAAAAAAAAAAAAAAG
*
5145567 AAAAAAAAAAGAAAAAG
1 AAAAAAAAAAAAAAAAG
5145584 AA
1 AA
5145586 TTTGAGTGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.89, C:0.03, G:0.08, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAAAAAAG
Found at i:5158854 original size:3 final size:3
Alignment explanation
Indices: 5158840--5158892 Score: 52
Period size: 3 Copynumber: 16.7 Consensus size: 3
5158830 AAACATACAC
* * *
5158840 TAA TAT TAA TAA TAA TAA TAA TAAA TAG TAA TAA TAC TACA TTAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TA-A -TAA TAA
5158888 TAA TA
1 TAA TA
5158893 TGTTAATAAC
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
3 35 0.85
4 4 0.10
5 2 0.05
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:5158912 original size:14 final size:14
Alignment explanation
Indices: 5158840--5158923 Score: 64
Period size: 14 Copynumber: 5.9 Consensus size: 14
5158830 AAACATACAC
*
5158840 TAATATTAAT-AA-
1 TAATAATAATAAAT
5158852 TAATAATAATAAAT
1 TAATAATAATAAAT
* *
5158866 AGTAATAATACTACAT
1 --TAATAATAATAAAT
**
5158882 TAATAATAATATGT
1 TAATAATAATAAAT
*
5158896 TAATAACAATAAAT
1 TAATAATAATAAAT
5158910 TAATGAATTAATAA
1 TAAT-AA-TAATAA
5158924 CAAAACAGTA
Statistics
Matches: 56, Mismatches: 10, Indels: 8
0.76 0.14 0.11
Matches are distributed among these distances:
12 9 0.16
13 2 0.04
14 26 0.46
15 2 0.04
16 17 0.30
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.36
Consensus pattern (14 bp):
TAATAATAATAAAT
Found at i:5159219 original size:3 final size:3
Alignment explanation
Indices: 5159213--5159329 Score: 71
Period size: 3 Copynumber: 39.3 Consensus size: 3
5159203 GACAACAAAG
* * * * *
5159213 AAT AAT AGT AGT AAT AAT AAT AAT GAA- AAT AAG AGT AAT ATT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT
* * * * * * *
5159258 AGT ACATT AA- AAT -AC AAT AGT AA- AGT AAT AAG AAT AGT GAT AAT
1 AAT A-A-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5159302 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
5159330 TTGAAATACA
Statistics
Matches: 85, Mismatches: 22, Indels: 14
0.70 0.18 0.12
Matches are distributed among these distances:
2 6 0.07
3 74 0.87
4 3 0.04
5 2 0.02
ACGTcount: A:0.59, C:0.02, G:0.09, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:5163984 original size:46 final size:44
Alignment explanation
Indices: 5163883--5163990 Score: 135
Period size: 44 Copynumber: 2.4 Consensus size: 44
5163873 TGTCTTTGAC
** * * * *
5163883 ATGGACTTACATGAATTATTCCTGTCTCTAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
5163927 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
5163973 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
5163991 TTTCTGTTCT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 32 0.58
46 23 0.42
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:5171242 original size:46 final size:44
Alignment explanation
Indices: 5171138--5171245 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
5171128 TGTCTTTGAC
** * * *
5171138 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
5171182 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
5171228 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
5171246 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:5177062 original size:20 final size:20
Alignment explanation
Indices: 5177037--5177080 Score: 81
Period size: 19 Copynumber: 2.2 Consensus size: 20
5177027 AAGCCCTCCC
5177037 AAAAAAACCTAA-CCCCAAA
1 AAAAAAACCTAACCCCCAAA
5177056 AAAAAAACCTAACCCCCAAA
1 AAAAAAACCTAACCCCCAAA
5177076 AAAAA
1 AAAAA
5177081 CCAAGAAACC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.66, C:0.30, G:0.00, T:0.05
Consensus pattern (20 bp):
AAAAAAACCTAACCCCCAAA
Found at i:5179471 original size:24 final size:24
Alignment explanation
Indices: 5179427--5179473 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
5179417 ATGTTGGTGG
**
5179427 AGGTGAGTTTGTTAGTAGTGGAGA
1 AGGTGAGTTTCCTAGTAGTGGAGA
5179451 AGGTGAGTTTCCTAG-AGGTGGAG
1 AGGTGAGTTTCCTAGTA-GTGGAG
5179474 GTGATCGCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.23, C:0.04, G:0.43, T:0.30
Consensus pattern (24 bp):
AGGTGAGTTTCCTAGTAGTGGAGA
Found at i:5179675 original size:72 final size:72
Alignment explanation
Indices: 5179589--5179842 Score: 363
Period size: 72 Copynumber: 3.5 Consensus size: 72
5179579 TAAAGGTGGT
*
5179589 GGTGAGGGTAATGTTACTAGAGGTGAGTTTCTTGGTTGTGAATGTGACGTTATCGATGGAAATGT
1 GGTGAGGGTAATGTTACTAGAGGTGAGTTTCTTGGTTGTGAATGTGACGTTATCGGTGGAAATGT
5179654 TGTTAGA
66 TGTTAGA
*
5179661 GGTGAGGGTAATGTTACTAGAGGTGAGTTTCTTGGTTGTGAATGTGATGTTATCGGTGGAAATGT
1 GGTGAGGGTAATGTTACTAGAGGTGAGTTTCTTGGTTGTGAATGTGACGTTATCGGTGGAAATGT
5179726 TGTTAGA
66 TGTTAGA
* * *
5179733 GGTGA--GT-TTGTTAGC-AGCAAAAGAAATGAGTTTCTTGGTTGTGAAGGTGACGTTATCGGTG
1 GGTGAGGGTAATGTTA-CTAG----AG--GTGAGTTTCTTGGTTGTGAATGTGACGTTATCGGTG
5179794 GAAATGTTGTTAGA
59 GAAATGTTGTTAGA
*
5179808 GGTGAGGGTGATGTTACTAGAGGTGAGTTTCTTGG
1 GGTGAGGGTAATGTTACTAGAGGTGAGTTTCTTGG
5179843 AGGTGGAAGT
Statistics
Matches: 163, Mismatches: 8, Indels: 22
0.84 0.04 0.11
Matches are distributed among these distances:
69 7 0.04
70 3 0.02
72 87 0.53
73 2 0.01
74 2 0.01
75 52 0.32
77 3 0.02
78 7 0.04
ACGTcount: A:0.23, C:0.06, G:0.36, T:0.35
Consensus pattern (72 bp):
GGTGAGGGTAATGTTACTAGAGGTGAGTTTCTTGGTTGTGAATGTGACGTTATCGGTGGAAATGT
TGTTAGA
Found at i:5179975 original size:6 final size:6
Alignment explanation
Indices: 5179964--5179990 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5179954 GTTGGTCTTT
5179964 TGGAGG TGGAGG TGGAGG TGGAGG TGG
1 TGGAGG TGGAGG TGGAGG TGGAGG TGG
5179991 GGATGAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.67, T:0.19
Consensus pattern (6 bp):
TGGAGG
Found at i:5185895 original size:16 final size:17
Alignment explanation
Indices: 5185863--5185898 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
5185853 ATTAATTTAC
5185863 ATTTATTTAAAAATTAT
1 ATTTATTTAAAAATTAT
*
5185880 ATTTATTT-ATAATTAT
1 ATTTATTTAAAAATTAT
5185896 ATT
1 ATT
5185899 AAATTATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTATTTAAAAATTAT
Found at i:5185895 original size:27 final size:28
Alignment explanation
Indices: 5185846--5185901 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
5185836 TTTTACAAAT
*
5185846 AAATTATATTAATTTACATTTAT-TTAA
1 AAATTATATTAATTTACAATTATATTAA
* *
5185873 AAATTATATTTATTTATAATTATATTAA
1 AAATTATATTAATTTACAATTATATTAA
5185901 A
1 A
5185902 TTATTTAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 20 0.80
28 5 0.20
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (28 bp):
AAATTATATTAATTTACAATTATATTAA
Found at i:5188371 original size:19 final size:20
Alignment explanation
Indices: 5188321--5188371 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
5188311 TAAATTAATT
*
5188321 TTTTTTTTCTTAATTTTTAG
1 TTTTTTTTCTTGATTTTTAG
5188341 TTTTTTTTCTTGATTTTTA-
1 TTTTTTTTCTTGATTTTTAG
5188360 TTTTTTTTCTTG
1 TTTTTTTTCTTG
5188372 TGAAAAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.10, C:0.06, G:0.06, T:0.78
Consensus pattern (20 bp):
TTTTTTTTCTTGATTTTTAG
Found at i:5190513 original size:19 final size:18
Alignment explanation
Indices: 5190476--5190520 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
5190466 TACAAGTTAC
*
5190476 TTAATTTAGCATCAATTT
1 TTAATTTAGCATAAATTT
*
5190494 TTATTTTAGTCATAAATTT
1 TTAATTTAG-CATAAATTT
5190513 TTAATTTA
1 TTAATTTA
5190521 TCAAATTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.56
Consensus pattern (18 bp):
TTAATTTAGCATAAATTT
Found at i:5191796 original size:3 final size:3
Alignment explanation
Indices: 5191783--5191816 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
5191773 TGACGTCCAT
5191783 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5191817 CTCAAAGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:5196650 original size:58 final size:58
Alignment explanation
Indices: 5196580--5196698 Score: 238
Period size: 58 Copynumber: 2.1 Consensus size: 58
5196570 TAAAATTTTT
5196580 AATTTGAAAAATAATTATTAAAAATATCAAAATAGAAAATGTAAAATATAATTATTAA
1 AATTTGAAAAATAATTATTAAAAATATCAAAATAGAAAATGTAAAATATAATTATTAA
5196638 AATTTGAAAAATAATTATTAAAAATATCAAAATAGAAAATGTAAAATATAATTATTAA
1 AATTTGAAAAATAATTATTAAAAATATCAAAATAGAAAATGTAAAATATAATTATTAA
5196696 AAT
1 AAT
5196699 GAATTTAGTT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 61 1.00
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.33
Consensus pattern (58 bp):
AATTTGAAAAATAATTATTAAAAATATCAAAATAGAAAATGTAAAATATAATTATTAA
Found at i:5196669 original size:22 final size:22
Alignment explanation
Indices: 5196622--5196671 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
5196612 TAGAAAATGT
* *
5196622 AAAATATAATTATTAAAATTTG
1 AAAATATAATTATTAAAATATC
5196644 AAAA-ATAATTATTAAAAATATC
1 AAAATATAATTATT-AAAATATC
5196666 AAAATA
1 AAAATA
5196672 GAAAATGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 9 0.38
22 14 0.58
23 1 0.04
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (22 bp):
AAAATATAATTATTAAAATATC
Found at i:5196699 original size:21 final size:20
Alignment explanation
Indices: 5196615--5196699 Score: 70
Period size: 21 Copynumber: 4.3 Consensus size: 20
5196605 ATCAAAATAG
5196615 AAAATGTAAAATATAATTATT
1 AAAATGTAAAA-ATAATTATT
*
5196636 AAAATTTGAAAAATAATTATT
1 AAAATGT-AAAAATAATTATT
* ** *
5196657 AAAA-ATATCAA-AA-TA-G
1 AAAATGTAAAAATAATTATT
5196673 AAAATGTAAAATATAATTATT
1 AAAATGTAAAA-ATAATTATT
5196694 AAAATG
1 AAAATG
5196700 AATTTAGTTA
Statistics
Matches: 49, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
16 4 0.08
17 5 0.10
18 3 0.06
19 5 0.10
20 3 0.06
21 25 0.51
22 4 0.08
ACGTcount: A:0.60, C:0.01, G:0.06, T:0.33
Consensus pattern (20 bp):
AAAATGTAAAAATAATTATT
Found at i:5202344 original size:41 final size:41
Alignment explanation
Indices: 5202235--5202501 Score: 394
Period size: 41 Copynumber: 6.5 Consensus size: 41
5202225 CGTTCTAGAA
*
5202235 AAAACGCCGCT-AAAACCAGAGCATTAGCGGCGCTTTTCCT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTCGT
* * *
5202275 AAAACGCCGCAAAAAAACTAGAGCATTAGCGGCACTTTTCGT
1 AAAACGCCGC-TAAAAACCAGAGCATTAGCGGCGCTTTTCGT
* *
5202317 AAAACGCAGCTAAAAACCAGAGCATTAGCGGCACTTTTCGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTCGT
*
5202358 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTCTCGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTCGT
* * *
5202399 AAAACGTCGCAAAAAACCAGAGCATTAGCGGCGCTTCTCGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTCGT
* *
5202440 AAAACGCCGCTAAAAACCAGAACATTAGCGGCGC-TTTCCT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTCGT
*
5202480 AAAACGTCGCTAAAAACCAGAG
1 AAAACGCCGCTAAAAACCAGAG
5202502 AAAAAAACCA
Statistics
Matches: 206, Mismatches: 19, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
40 34 0.17
41 137 0.67
42 35 0.17
ACGTcount: A:0.36, C:0.27, G:0.20, T:0.18
Consensus pattern (41 bp):
AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTCGT
Found at i:5202508 original size:53 final size:54
Alignment explanation
Indices: 5202451--5202555 Score: 167
Period size: 54 Copynumber: 2.0 Consensus size: 54
5202441 AAACGCCGCT
*
5202451 AAAAACCAGAACATTAGCGGCGC-TTTCCTAAAACGTCGCTAAAAACCAGAGAA
1 AAAAACCAGAACATTAGCGGCGCTTTTCCTAAAACGCCGCTAAAAACCAGAGAA
* * *
5202504 AAAAACCAGAGCATTAGCGGCGCTTTTCGTAAAACGCCGCTAAACACCAGAG
1 AAAAACCAGAACATTAGCGGCGCTTTTCCTAAAACGCCGCTAAAAACCAGAG
5202556 CATCAGCGGC
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
53 22 0.47
54 25 0.53
ACGTcount: A:0.40, C:0.26, G:0.19, T:0.15
Consensus pattern (54 bp):
AAAAACCAGAACATTAGCGGCGCTTTTCCTAAAACGCCGCTAAAAACCAGAGAA
Found at i:5202508 original size:94 final size:95
Alignment explanation
Indices: 5202409--5202590 Score: 303
Period size: 94 Copynumber: 1.9 Consensus size: 95
5202399 AAAACGTCGC
*
5202409 AAAAAACCAGAGCATTAGCGGCGCTTCTCGTAAAACGCCGCTAAAAACCAGAACATTAGCGGCGC
1 AAAAAACCAGAGCATTAGCGGCGCTTCTCGTAAAACGCCGCTAAAAACCAGAACATCAGCGGCGC
*
5202474 -TTTCCTAAAACGTCGCTAAAAACCAGAGA
66 TTTTCCTAAAACGCCGCTAAAAACCAGAGA
* * *
5202503 AAAAAACCAGAGCATTAGCGGCGCTTTTCGTAAAACGCCGCTAAACACCAGAGCATCAGCGGCGC
1 AAAAAACCAGAGCATTAGCGGCGCTTCTCGTAAAACGCCGCTAAAAACCAGAACATCAGCGGCGC
*
5202568 TTTTCGTAAAACGCCGCTAAAAA
66 TTTTCCTAAAACGCCGCTAAAAA
5202591 TCTCATAACC
Statistics
Matches: 81, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
94 61 0.75
95 20 0.25
ACGTcount: A:0.37, C:0.27, G:0.20, T:0.16
Consensus pattern (95 bp):
AAAAAACCAGAGCATTAGCGGCGCTTCTCGTAAAACGCCGCTAAAAACCAGAACATCAGCGGCGC
TTTTCCTAAAACGCCGCTAAAAACCAGAGA
Found at i:5202553 original size:41 final size:41
Alignment explanation
Indices: 5202508--5202588 Score: 153
Period size: 41 Copynumber: 2.0 Consensus size: 41
5202498 AGAGAAAAAA
*
5202508 ACCAGAGCATTAGCGGCGCTTTTCGTAAAACGCCGCTAAAC
1 ACCAGAGCATCAGCGGCGCTTTTCGTAAAACGCCGCTAAAC
5202549 ACCAGAGCATCAGCGGCGCTTTTCGTAAAACGCCGCTAAA
1 ACCAGAGCATCAGCGGCGCTTTTCGTAAAACGCCGCTAAA
5202589 AATCTCATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.19
Consensus pattern (41 bp):
ACCAGAGCATCAGCGGCGCTTTTCGTAAAACGCCGCTAAAC
Found at i:5203738 original size:24 final size:24
Alignment explanation
Indices: 5203688--5203738 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
5203678 TATATGAGAT
* * *
5203688 AAATATATATAAAATATTATTTTA
1 AAATATATATAAAATATCATATGA
5203712 AAATATATAT-AAATATACATATGA
1 AAATATATATAAAATAT-CATATGA
5203736 AAA
1 AAA
5203739 GTGGTTAGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 6 0.26
24 17 0.74
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (24 bp):
AAATATATATAAAATATCATATGA
Found at i:5204720 original size:18 final size:17
Alignment explanation
Indices: 5204699--5204741 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
5204689 ATGATCTTAA
5204699 TGATGATGATGTTGATAC
1 TGATGATGATGTTGAT-C
*
5204717 TGATGTTGATGTTGATC
1 TGATGATGATGTTGATC
5204734 TCGATGAT
1 T-GATGAT
5204742 TATACCCTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.23, C:0.07, G:0.28, T:0.42
Consensus pattern (17 bp):
TGATGATGATGTTGATC
Found at i:5205255 original size:62 final size:62
Alignment explanation
Indices: 5205187--5205366 Score: 321
Period size: 60 Copynumber: 3.0 Consensus size: 62
5205177 CCAAAATTTG
5205187 ATTTCTTTTTTGTCAGTTTTATGTCTGTTGTTTGGATATTTTTGTTCTGAAATGGAAAATTC
1 ATTTCTTTTTTGTCAGTTTTATGTCTGTTGTTTGGATATTTTTGTTCTGAAATGGAAAATTC
*
5205249 ATTTCTTTTTTGTCAGTTTTATGTTTGTTGTTTGG--ATTTTTGTTCTGAAATGGAAAATTC
1 ATTTCTTTTTTGTCAGTTTTATGTCTGTTGTTTGGATATTTTTGTTCTGAAATGGAAAATTC
*
5205309 ATTTCTTTTTTGTCAGTTTTATGTCTGTTGTTTGGAT-TTTTTGTTTTGAAATGGAAAA
1 ATTTCTTTTTTGTCAGTTTTATGTCTGTTGTTTGGATATTTTTGTTCTGAAATGGAAAA
5205367 CTAGTTTGTG
Statistics
Matches: 113, Mismatches: 3, Indels: 5
0.93 0.02 0.04
Matches are distributed among these distances:
60 59 0.52
61 20 0.18
62 34 0.30
ACGTcount: A:0.19, C:0.07, G:0.18, T:0.56
Consensus pattern (62 bp):
ATTTCTTTTTTGTCAGTTTTATGTCTGTTGTTTGGATATTTTTGTTCTGAAATGGAAAATTC
Found at i:5222013 original size:13 final size:13
Alignment explanation
Indices: 5221995--5222031 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
5221985 TATTAATATT
5221995 AAAATATAAAAAA
1 AAAATATAAAAAA
*
5222008 AAAATATATAAAA
1 AAAATATAAAAAA
5222021 AAAATATAAAA
1 AAAATATAAAA
5222032 TTAGCAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (13 bp):
AAAATATAAAAAA
Found at i:5222177 original size:15 final size:15
Alignment explanation
Indices: 5222149--5222188 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
5222139 ATTAATTTAC
*
5222149 ATTTATTTAAAATTAT
1 ATTTA-TTATAATTAT
5222165 ATTTATTATAATTAT
1 ATTTATTATAATTAT
*
5222180 ATTAATTAT
1 ATTTATTAT
5222189 TTAAATATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTTATTATAATTAT
Found at i:5224570 original size:19 final size:19
Alignment explanation
Indices: 5224546--5224594 Score: 66
Period size: 18 Copynumber: 2.6 Consensus size: 19
5224536 ATAAATTAAT
5224546 TTTTTTTTCTT-AATTTTA
1 TTTTTTTTCTTGAATTTTA
*
5224564 GTTTTTTTTCTTGATTTTTA
1 -TTTTTTTTCTTGAATTTTA
5224584 -TTTTTTTCTTG
1 TTTTTTTTCTTG
5224595 TGAAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 11 0.39
19 11 0.39
20 6 0.21
ACGTcount: A:0.10, C:0.06, G:0.06, T:0.78
Consensus pattern (19 bp):
TTTTTTTTCTTGAATTTTA
Found at i:5224570 original size:20 final size:20
Alignment explanation
Indices: 5224544--5224590 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
5224534 TGATAAATTA
5224544 ATTTTTTTTTCTT-AATTTT
1 ATTTTTTTTTCTTGAATTTT
* *
5224563 AGTTTTTTTTCTTGATTTTT
1 ATTTTTTTTTCTTGAATTTT
5224583 ATTTTTTT
1 ATTTTTTT
5224591 CTTGTGAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.13, C:0.04, G:0.04, T:0.79
Consensus pattern (20 bp):
ATTTTTTTTTCTTGAATTTT
Found at i:5226707 original size:19 final size:18
Alignment explanation
Indices: 5226670--5226714 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
5226660 TACAAGTTAC
*
5226670 TTAATTTAGCATCAATTT
1 TTAATTTAGCATAAATTT
*
5226688 TTATTTTAGTCATAAATTT
1 TTAATTTAG-CATAAATTT
5226707 TTAATTTA
1 TTAATTTA
5226715 TCAAATTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.56
Consensus pattern (18 bp):
TTAATTTAGCATAAATTT
Found at i:5227969 original size:3 final size:3
Alignment explanation
Indices: 5227956--5227989 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
5227946 GTGACGTCAT
5227956 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5227990 CTCAAAGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:5232804 original size:58 final size:58
Alignment explanation
Indices: 5232734--5232852 Score: 238
Period size: 58 Copynumber: 2.1 Consensus size: 58
5232724 TTAAAATTTT
5232734 AATTTGAAAAATAATTATTAAAAATATCAAAATAGAAAATGTAAAATATAATTATTAA
1 AATTTGAAAAATAATTATTAAAAATATCAAAATAGAAAATGTAAAATATAATTATTAA
5232792 AATTTGAAAAATAATTATTAAAAATATCAAAATAGAAAATGTAAAATATAATTATTAA
1 AATTTGAAAAATAATTATTAAAAATATCAAAATAGAAAATGTAAAATATAATTATTAA
5232850 AAT
1 AAT
5232853 GAATTTAGTT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 61 1.00
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.33
Consensus pattern (58 bp):
AATTTGAAAAATAATTATTAAAAATATCAAAATAGAAAATGTAAAATATAATTATTAA
Found at i:5232823 original size:22 final size:22
Alignment explanation
Indices: 5232776--5232825 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
5232766 TAGAAAATGT
* *
5232776 AAAATATAATTATTAAAATTTG
1 AAAATATAATTATTAAAATATC
5232798 AAAA-ATAATTATTAAAAATATC
1 AAAATATAATTATT-AAAATATC
5232820 AAAATA
1 AAAATA
5232826 GAAAATGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 9 0.38
22 14 0.58
23 1 0.04
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (22 bp):
AAAATATAATTATTAAAATATC
Found at i:5232853 original size:21 final size:20
Alignment explanation
Indices: 5232769--5232853 Score: 70
Period size: 21 Copynumber: 4.3 Consensus size: 20
5232759 ATCAAAATAG
5232769 AAAATGTAAAATATAATTATT
1 AAAATGTAAAA-ATAATTATT
*
5232790 AAAATTTGAAAAATAATTATT
1 AAAATGT-AAAAATAATTATT
* ** *
5232811 AAAA-ATATCAA-AA-TA-G
1 AAAATGTAAAAATAATTATT
5232827 AAAATGTAAAATATAATTATT
1 AAAATGTAAAA-ATAATTATT
5232848 AAAATG
1 AAAATG
5232854 AATTTAGTTA
Statistics
Matches: 49, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
16 4 0.08
17 5 0.10
18 3 0.06
19 5 0.10
20 3 0.06
21 25 0.51
22 4 0.08
ACGTcount: A:0.60, C:0.01, G:0.06, T:0.33
Consensus pattern (20 bp):
AAAATGTAAAAATAATTATT
Found at i:5238466 original size:41 final size:41
Alignment explanation
Indices: 5238357--5238710 Score: 399
Period size: 41 Copynumber: 8.4 Consensus size: 41
5238347 CGTTCTAGAA
*
5238357 AAAACGCCGCT-AAAACCAGAGCATTAGCGGCGCTTTTCCT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTCGT
* * *
5238397 AAAACGCCGCAAAAAAACTAGAGCATTAGCGGCACTTTTCGT
1 AAAACGCCGC-TAAAAACCAGAGCATTAGCGGCGCTTTTCGT
* *
5238439 AAAACGCAGCTAAAAACCAGAGCATTAGCGGCACTTTTCGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTCGT
*
5238480 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTCTCGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTCGT
* * *
5238521 AAAACGTCGCAAAAAACCAGAGCATTAGCGGCGCTTCTCGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTCGT
* *
5238562 AAAACGCCGCTAAAAACCAGAACATTAGCGGCGC-TTTCCT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTCGT
* * * *
5238602 AAAACGTCGCTAAAAACCAGAGAAAAAAACCA-GAGCATTAGCGGCGCTTTCGT
1 AAAACGCCGCTAAAAACCAGAG--------CATTAGC---GGC-GC-TTTTCGT
* *
5238655 AAAACGCCGCTAAACACCAGAGCATCAGCGGCGCTTTTCGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTCGT
5238696 AAAACGCCGCTAAAA
1 AAAACGCCGCTAAAA
5238711 TCTCATAACC
Statistics
Matches: 269, Mismatches: 28, Indels: 33
0.82 0.08 0.10
Matches are distributed among these distances:
40 34 0.13
41 157 0.58
42 37 0.14
43 2 0.01
45 2 0.01
46 3 0.01
47 3 0.01
48 2 0.01
50 2 0.01
51 2 0.01
53 25 0.09
ACGTcount: A:0.36, C:0.27, G:0.20, T:0.17
Consensus pattern (41 bp):
AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTCGT
Found at i:5238630 original size:53 final size:53
Alignment explanation
Indices: 5238573--5238676 Score: 172
Period size: 53 Copynumber: 2.0 Consensus size: 53
5238563 AAACGCCGCT
*
5238573 AAAAACCAGAACATTAGCGGCGCTTTCCTAAAACGTCGCTAAAAACCAGAGAA
1 AAAAACCAGAACATTAGCGGCGCTTTCCTAAAACGCCGCTAAAAACCAGAGAA
* * *
5238626 AAAAACCAGAGCATTAGCGGCGCTTTCGTAAAACGCCGCTAAACACCAGAG
1 AAAAACCAGAACATTAGCGGCGCTTTCCTAAAACGCCGCTAAAAACCAGAG
5238677 CATCAGCGGC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.40, C:0.26, G:0.19, T:0.14
Consensus pattern (53 bp):
AAAAACCAGAACATTAGCGGCGCTTTCCTAAAACGCCGCTAAAAACCAGAGAA
Found at i:5238630 original size:94 final size:94
Alignment explanation
Indices: 5238531--5238710 Score: 299
Period size: 94 Copynumber: 1.9 Consensus size: 94
5238521 AAAACGTCGC
*
5238531 AAAAAACCAGAGCATTAGCGGCGCTTCTCGTAAAACGCCGCTAAAAACCAGAACATTAGCGGCGC
1 AAAAAACCAGAGCATTAGCGGCGCTT-TCGTAAAACGCCGCTAAAAACCAGAACATCAGCGGCGC
*
5238596 -TTTCCTAAAACGTCGCTAAAAACCAGAGA
65 TTTTCCTAAAACGCCGCTAAAAACCAGAGA
* *
5238625 AAAAAACCAGAGCATTAGCGGCGCTTTCGTAAAACGCCGCTAAACACCAGAGCATCAGCGGCGCT
1 AAAAAACCAGAGCATTAGCGGCGCTTTCGTAAAACGCCGCTAAAAACCAGAACATCAGCGGCGCT
*
5238690 TTTCGTAAAACGCCGCTAAAA
66 TTTCCTAAAACGCCGCTAAAA
5238711 TCTCATAACC
Statistics
Matches: 80, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
93 35 0.44
94 45 0.56
ACGTcount: A:0.37, C:0.27, G:0.20, T:0.16
Consensus pattern (94 bp):
AAAAAACCAGAGCATTAGCGGCGCTTTCGTAAAACGCCGCTAAAAACCAGAACATCAGCGGCGCT
TTTCCTAAAACGCCGCTAAAAACCAGAGA
Found at i:5239865 original size:24 final size:24
Alignment explanation
Indices: 5239815--5239865 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
5239805 TATATGAGAT
* * *
5239815 AAATATATATAAAATATTATTTTA
1 AAATATATATAAAATATCATATGA
5239839 AAATATATAT-AAATATACATATGA
1 AAATATATATAAAATAT-CATATGA
5239863 AAA
1 AAA
5239866 GTGGTTAGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 6 0.26
24 17 0.74
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (24 bp):
AAATATATATAAAATATCATATGA
Done.