Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 135 of 210
Found at i:41121322 original size:94 final size:91
Alignment explanation
Indices: 41121178--41121370 Score: 266
Period size: 94 Copynumber: 2.1 Consensus size: 91
41121168 TTTGTAGTCA
41121178 TTTTAAAG-GAAAGTTTAAATTTTTAAAAAAAATTGATTTTTTTCAACTATTTCAAAATAAAAGC
1 TTTTAAAGAGAAAGTTTAAATTTTTAAAAAAAATTGATTTTTTTCAACTATTTCAAAATAAAA-C
* *
41121242 TTTGATCT-TTAAGAAAAATAGT-GTTT
65 TTTGAT-TGTTAAGAAAAATAATAATTT
* *
41121268 TTTTAAAGAGAAAGTTTAGATTTTTAAAATAAAATTTTGATTTTTTTCAACTATTTCGAAATAAA
1 TTTTAAAGAGAAAGTTTAAATTTTTAAAA-AAAA--TTGATTTTTTTCAACTATTTCAAAATAAA
* *
41121333 ATTTTGATTGTTAAGAAAAGTAATAATTT
63 ACTTTGATTGTTAAGAAAAATAATAATTT
41121362 TTTTAAAGA
1 TTTTAAAGA
41121371 AAACTTTGAT
Statistics
Matches: 91, Mismatches: 6, Indels: 8
0.87 0.06 0.08
Matches are distributed among these distances:
90 8 0.09
91 19 0.21
92 5 0.05
93 18 0.20
94 41 0.45
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.44
Consensus pattern (91 bp):
TTTTAAAGAGAAAGTTTAAATTTTTAAAAAAAATTGATTTTTTTCAACTATTTCAAAATAAAACT
TTGATTGTTAAGAAAAATAATAATTT
Found at i:41121362 original size:145 final size:145
Alignment explanation
Indices: 41121027--41121365 Score: 357
Period size: 145 Copynumber: 2.3 Consensus size: 145
41121017 AAAAATTTAG
* * * *
41121027 TCATTTTAAAGGAAAGTTTAAAATT-TTAAAAAAAAATTTTGATTTTTTTTAACTATTTCAAAAT
1 TCATTTGAAAGGAAAATTT-AAATTGTT-AAAAAAAA--TTAATTTTTTTCAACTATTTCAAAAT
* *
41121091 AAAAGCTTTGATCATTAATAAAAATAATGTTTTTTTAAAAAGAGAGTTTAGATTTTAAAAAATAA
62 AAAAGCTTTGATCATTAAGAAAAATAATGTTTTTTTAAAAAGAAAGTTTAGATTTTAAAAAATAA
** *
41121156 AAATCTATCTTTTTTGTAG
127 AAATCTATCTTTTTTCAAC
* * * *
41121175 TCATTTTAAAGGAAAGTTTAAATTTTTAAAAAAAATTGATTTTTTTCAACTATTTCAAAATAAAA
1 TCATTTGAAAGGAAAATTTAAATTGTTAAAAAAAATTAATTTTTTTCAACTATTTCAAAATAAAA
* * * * *
41121240 GCTTTGATCTTTAAGAAAAATAGTGTTTTTTTAAAGAGAAAGTTTAGATTTT-TAAAATAAAATT
66 GCTTTGATCATTAAGAAAAATAATGTTTTTTTAAAAAGAAAGTTTAGATTTTAAAAAATAAAAAT
*
41121304 TTGAT-TTTTTTCAAC
131 CT-ATCTTTTTTCAAC
* **
41121319 T-ATTTCGAAA-TAAAATTTTGATTGTTAAGAAAAGTAA-TAATTTTTTT
1 TCATTT-GAAAGGAAAATTTAAATTGTTAA-AAAA--AATTAATTTTTTT
41121366 AAAGAAAACT
Statistics
Matches: 166, Mismatches: 19, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
143 17 0.10
144 26 0.16
145 87 0.52
146 2 0.01
147 13 0.08
148 21 0.13
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (145 bp):
TCATTTGAAAGGAAAATTTAAATTGTTAAAAAAAATTAATTTTTTTCAACTATTTCAAAATAAAA
GCTTTGATCATTAAGAAAAATAATGTTTTTTTAAAAAGAAAGTTTAGATTTTAAAAAATAAAAAT
CTATCTTTTTTCAAC
Found at i:41122644 original size:3 final size:3
Alignment explanation
Indices: 41122636--41122667 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
41122626 TCTTTTAAAA
41122636 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
41122668 AAGATCAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:41123685 original size:27 final size:27
Alignment explanation
Indices: 41123655--41123712 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
41123645 TCCATGATGG
* * *
41123655 TAAACACGGGTTAGTCTACCGAGACAA
1 TAAACACAGGATAGTCCACCGAGACAA
**
41123682 TAAACACAGGATAGTCCATTGAGACAA
1 TAAACACAGGATAGTCCACCGAGACAA
41123709 TAAA
1 TAAA
41123713 AATAGGGTAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.19
Consensus pattern (27 bp):
TAAACACAGGATAGTCCACCGAGACAA
Found at i:41128660 original size:23 final size:23
Alignment explanation
Indices: 41128628--41128685 Score: 107
Period size: 23 Copynumber: 2.5 Consensus size: 23
41128618 TGACTATTAA
*
41128628 GCCTTAGTGGTGTATTTTGTGTT
1 GCCTTTGTGGTGTATTTTGTGTT
41128651 GCCTTTGTGGTGTATTTTGTGTT
1 GCCTTTGTGGTGTATTTTGTGTT
41128674 GCCTTTGTGGTG
1 GCCTTTGTGGTG
41128686 AATTCTAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.05, C:0.10, G:0.33, T:0.52
Consensus pattern (23 bp):
GCCTTTGTGGTGTATTTTGTGTT
Found at i:41130500 original size:98 final size:98
Alignment explanation
Indices: 41130386--41130580 Score: 329
Period size: 98 Copynumber: 2.0 Consensus size: 98
41130376 TTTGCTCAAA
*
41130386 TACTTTAGTTTTAATCATTTGTTTTCTTTTCT-TCTTATTTTTAGTTTGTCTATTTTTGTTTTTG
1 TACTTTAGTTTTAATCATGTGTTTTCTTTT-TGTCTTATTTTTAGTTTGTCTATTTTTGTTTTTG
* * *
41130450 TTTTTTGTTTACTTGAGGACAAGCAACGACTTAG
65 TTTTTCGTTTACTTAAGGACAAACAACGACTTAG
41130484 TACTTTAGTTTTAATCATGTGTTTTCTTTTTGTCTTATTTTTAGTTTGTCTATTTTTGTTTTTGT
1 TACTTTAGTTTTAATCATGTGTTTTCTTTTTGTCTTATTTTTAGTTTGTCTATTTTTGTTTTTGT
*
41130549 TTTTCGTTTACTTAAGGACAAACAATGACTTA
66 TTTTCGTTTACTTAAGGACAAACAACGACTTA
41130581 AGTGTGGGGG
Statistics
Matches: 91, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
97 1 0.01
98 90 0.99
ACGTcount: A:0.18, C:0.11, G:0.13, T:0.58
Consensus pattern (98 bp):
TACTTTAGTTTTAATCATGTGTTTTCTTTTTGTCTTATTTTTAGTTTGTCTATTTTTGTTTTTGT
TTTTCGTTTACTTAAGGACAAACAACGACTTAG
Found at i:41130539 original size:15 final size:15
Alignment explanation
Indices: 41130512--41130544 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
41130502 GTGTTTTCTT
41130512 TTTGTCTTATTTTTAG
1 TTTGTCTTATTTTT-G
41130528 TTTGTC-TATTTTTG
1 TTTGTCTTATTTTTG
41130542 TTT
1 TTT
41130545 TTGTTTTTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 7 0.41
16 6 0.35
ACGTcount: A:0.09, C:0.06, G:0.12, T:0.73
Consensus pattern (15 bp):
TTTGTCTTATTTTTG
Found at i:41130680 original size:24 final size:24
Alignment explanation
Indices: 41130650--41130698 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
41130640 TTAATGAGAT
41130650 TGTTTTTCTAGTTATTTTAATATC
1 TGTTTTTCTAGTTATTTTAATATC
41130674 TGTTTTTCTAGTTATTTTAATATC
1 TGTTTTTCTAGTTATTTTAATATC
41130698 T
1 T
41130699 TTTATTACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.08, G:0.08, T:0.63
Consensus pattern (24 bp):
TGTTTTTCTAGTTATTTTAATATC
Found at i:41132676 original size:15 final size:16
Alignment explanation
Indices: 41132651--41132681 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
41132641 GCAAAACGAA
41132651 AAAGAAAAGGAGAAAG
1 AAAGAAAAGGAGAAAG
41132667 AAAG-AAAGGAGAAAG
1 AAAGAAAAGGAGAAAG
41132682 CAAACCTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (16 bp):
AAAGAAAAGGAGAAAG
Found at i:41135256 original size:20 final size:20
Alignment explanation
Indices: 41135223--41135261 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
41135213 TTTTAAAGTT
*
41135223 AATAATAATTTTAAAATTTA
1 AATAATAATCTTAAAATTTA
* *
41135243 AATAATACTCTTAATATTT
1 AATAATAATCTTAAAATTT
41135262 TACAAAAATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (20 bp):
AATAATAATCTTAAAATTTA
Found at i:41135293 original size:24 final size:23
Alignment explanation
Indices: 41135255--41135301 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
41135245 TAATACTCTT
*
41135255 AATATTTTACAAAAATATTATATA
1 AATATTTTACAAAAA-AATATATA
**
41135279 AATATTTTAGTAAAAAATATATA
1 AATATTTTACAAAAAAATATATA
41135302 CTACAATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
AATATTTTACAAAAAAATATATA
Found at i:41137921 original size:31 final size:31
Alignment explanation
Indices: 41137886--41137959 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
41137876 AAAGATTAAC
* * * *
41137886 TACCAAATTA-AAAATAATTGTTAAGTTTAGG
1 TACCAAATTAGAAAA-AAGTGTCAAGTTCAAG
*
41137917 TACCAAATTAGGAAAAAGTGTCAAGTTCAAG
1 TACCAAATTAGAAAAAAGTGTCAAGTTCAAG
41137948 TACCAAATTAGA
1 TACCAAATTAGA
41137960 CCAAAAAATG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
31 33 0.92
32 3 0.08
ACGTcount: A:0.46, C:0.11, G:0.15, T:0.28
Consensus pattern (31 bp):
TACCAAATTAGAAAAAAGTGTCAAGTTCAAG
Found at i:41144181 original size:26 final size:26
Alignment explanation
Indices: 41144152--41144261 Score: 166
Period size: 26 Copynumber: 4.2 Consensus size: 26
41144142 GTGTTGATCG
41144152 AAATACCCTCGATGGGTAAATTACCA
1 AAATACCCTCGATGGGTAAATTACCA
* *
41144178 AAATACCCTCGATGGGTAAATTATCG
1 AAATACCCTCGATGGGTAAATTACCA
* *
41144204 AAATACCCTTGATGGGTAAATTATCA
1 AAATACCCTCGATGGGTAAATTACCA
* *
41144230 AAATGCCCTCGATGGGTAAATTACCG
1 AAATACCCTCGATGGGTAAATTACCA
41144256 AAATAC
1 AAATAC
41144262 TCCCGTAGGG
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.25
Consensus pattern (26 bp):
AAATACCCTCGATGGGTAAATTACCA
Found at i:41144205 original size:52 final size:52
Alignment explanation
Indices: 41144148--41144261 Score: 192
Period size: 52 Copynumber: 2.2 Consensus size: 52
41144138 CATGGTGTTG
41144148 ATCGAAATACCCTCGATGGGTAAATTACCAAAATACCCTCGATGGGTAAATT
1 ATCGAAATACCCTCGATGGGTAAATTACCAAAATACCCTCGATGGGTAAATT
* * *
41144200 ATCGAAATACCCTTGATGGGTAAATTATCAAAATGCCCTCGATGGGTAAATT
1 ATCGAAATACCCTCGATGGGTAAATTACCAAAATACCCTCGATGGGTAAATT
*
41144252 ACCGAAATAC
1 ATCGAAATAC
41144262 TCCCGTAGGG
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 58 1.00
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (52 bp):
ATCGAAATACCCTCGATGGGTAAATTACCAAAATACCCTCGATGGGTAAATT
Found at i:41149464 original size:18 final size:18
Alignment explanation
Indices: 41149432--41149482 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
41149422 AAATTTTATT
*
41149432 TATTTTTCTTGGGAATCTA
1 TATTTTCCTT-GGAATCTA
41149451 TATTTTCCTTGGAATCTA
1 TATTTTCCTTGGAATCTA
*
41149469 -ACTTTCCCTTGGAA
1 TA-TTTTCCTTGGAA
41149483 GTTATTTTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 1 0.03
18 19 0.66
19 9 0.31
ACGTcount: A:0.22, C:0.18, G:0.14, T:0.47
Consensus pattern (18 bp):
TATTTTCCTTGGAATCTA
Found at i:41153588 original size:40 final size:41
Alignment explanation
Indices: 41153533--41153610 Score: 131
Period size: 40 Copynumber: 1.9 Consensus size: 41
41153523 GCCATTTTTC
*
41153533 AGCAAAAGCGCTTCCAGTAGGAAGCTCTTTT-CTCCAAGTT
1 AGCAAAAGCGCTTCCACTAGGAAGCTCTTTTCCTCCAAGTT
*
41153573 AGCAAAATCGCTTCCACTAGGAAGCTCTTTTCCTCCAA
1 AGCAAAAGCGCTTCCACTAGGAAGCTCTTTTCCTCCAA
41153611 CTGTCACCTG
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 29 0.83
41 6 0.17
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (41 bp):
AGCAAAAGCGCTTCCACTAGGAAGCTCTTTTCCTCCAAGTT
Found at i:41156047 original size:19 final size:20
Alignment explanation
Indices: 41156015--41156052 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
41156005 GTTTAGTTAT
* *
41156015 TTTTTTTATCTTTTTATTAA
1 TTTTTTAATCTTTTAATTAA
41156035 TTTTTTAAT-TTTTAATTA
1 TTTTTTAATCTTTTAATTA
41156053 TTCATTTCTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTTTAATCTTTTAATTAA
Found at i:41168756 original size:22 final size:23
Alignment explanation
Indices: 41168731--41168783 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
41168721 AAGGAACTTG
*
41168731 AATTGATATATAA-TAACTA-GAA
1 AATT-ATATAGAATTAACTATGAA
*
41168753 AATTATTTAGAATTAACTATGAA
1 AATTATATAGAATTAACTATGAA
41168776 AATT-TATA
1 AATTATATA
41168784 AATATTAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 6 0.23
22 13 0.50
23 7 0.27
ACGTcount: A:0.51, C:0.04, G:0.08, T:0.38
Consensus pattern (23 bp):
AATTATATAGAATTAACTATGAA
Found at i:41171053 original size:10 final size:11
Alignment explanation
Indices: 41171025--41171057 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
41171015 TTATATTACT
*
41171025 TAAAATAGAAA
1 TAAAATAAAAA
41171036 TAAAATAAAAA
1 TAAAATAAAAA
41171047 T-AAATAAAAA
1 TAAAATAAAAA
41171057 T
1 T
41171058 TATTTATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (11 bp):
TAAAATAAAAA
Found at i:41173515 original size:14 final size:14
Alignment explanation
Indices: 41173496--41173526 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
41173486 ACAAATATCC
*
41173496 CAGATAAGATTACA
1 CAGATAAGAGTACA
41173510 CAGATAAGAGTACA
1 CAGATAAGAGTACA
41173524 CAG
1 CAG
41173527 TCAATGTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.16, G:0.19, T:0.16
Consensus pattern (14 bp):
CAGATAAGAGTACA
Found at i:41178035 original size:21 final size:21
Alignment explanation
Indices: 41178009--41178057 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
41177999 TCTACATGGT
41178009 CGTGTGAAAGAGACACATTGCC
1 CGTGTGAAAGAGACACA-TGCC
**
41178031 C-TGTGGTAGAGACACATGCC
1 CGTGTGAAAGAGACACATGCC
41178051 CGTGTGA
1 CGTGTGA
41178058 GTAGCCTATG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 5 0.22
21 17 0.74
22 1 0.04
ACGTcount: A:0.27, C:0.22, G:0.31, T:0.20
Consensus pattern (21 bp):
CGTGTGAAAGAGACACATGCC
Found at i:41180278 original size:19 final size:18
Alignment explanation
Indices: 41180254--41180292 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
41180244 ATTCCGTGTT
*
41180254 TGAATAGAAATAAAATAAA
1 TGAATAGAAA-AAAAGAAA
*
41180273 TGAATAGGAAAAAAGAAA
1 TGAATAGAAAAAAAGAAA
41180291 TG
1 TG
41180293 GGAAACATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.64, C:0.00, G:0.18, T:0.18
Consensus pattern (18 bp):
TGAATAGAAAAAAAGAAA
Found at i:41187831 original size:14 final size:15
Alignment explanation
Indices: 41187809--41187844 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
41187799 ACAAATGAGT
41187809 TATAT-GAAATTG-C
1 TATATGGAAATTGAC
41187822 TATATGGAAATTGAC
1 TATATGGAAATTGAC
41187837 T-TATGGAA
1 TATATGGAA
41187845 GGGACGTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 5 0.24
14 14 0.67
15 2 0.10
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.36
Consensus pattern (15 bp):
TATATGGAAATTGAC
Found at i:41189791 original size:31 final size:31
Alignment explanation
Indices: 41189756--41189815 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
41189746 GATTCCAAGT
*
41189756 TCTAAGAAATAGCTAGAAAGATGAGGTGGGC
1 TCTAAGAAATAGCTAGAAAGATAAGGTGGGC
*
41189787 TCTAAGAAATAGCTAGAAAGCTAAGGTGG
1 TCTAAGAAATAGCTAGAAAGATAAGGTGG
41189816 AATCTTTGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.10, G:0.30, T:0.20
Consensus pattern (31 bp):
TCTAAGAAATAGCTAGAAAGATAAGGTGGGC
Found at i:41194298 original size:27 final size:27
Alignment explanation
Indices: 41194258--41194509 Score: 203
Period size: 27 Copynumber: 9.4 Consensus size: 27
41194248 GATTCATGGG
* * *
41194258 AAAATGACTGAAATACCCTCAAAAGGT
1 AAAATGACTAAAATACCCTCGAAGGGT
41194285 AAAATGACTAAAATACCC-CTGAAGGGT
1 AAAATGACTAAAATACCCTC-GAAGGGT
* *
41194312 AAAATGACTGAAATACCC-CTGAAGGGG
1 AAAATGACTAAAATACCCTC-GAAGGGT
* * *
41194339 AAAATTACCAAAATACCC-CAAAGGGT
1 AAAATGACTAAAATACCCTCGAAGGGT
** *
41194365 GGAATGA-TCGAAATA-CCTCCGAAGGGT
1 AAAATGACT-AAAATACCCT-CGAAGGGT
* *
41194392 AAAATGACCAAAATACCCTTGAAGGGT
1 AAAATGACTAAAATACCCTCGAAGGGT
* * *
41194419 AAAATGACTAAGATACCCCCGGAGGGT
1 AAAATGACTAAAATACCCTCGAAGGGT
* * *
41194446 AAAAT-AATCGAAATACTCTCGAAGGGT
1 AAAATGACT-AAAATACCCTCGAAGGGT
* * *
41194473 AAAATGACTGAAATACCCT-TATAGGAT
1 AAAATGACTAAAATACCCTCGA-AGGGT
41194500 AAAATGACTA
1 AAAATGACTA
41194510 TGATACCCCT
Statistics
Matches: 179, Mismatches: 37, Indels: 18
0.76 0.16 0.08
Matches are distributed among these distances:
25 2 0.01
26 18 0.10
27 154 0.86
28 5 0.03
ACGTcount: A:0.44, C:0.18, G:0.19, T:0.19
Consensus pattern (27 bp):
AAAATGACTAAAATACCCTCGAAGGGT
Found at i:41194322 original size:54 final size:54
Alignment explanation
Indices: 41194258--41194519 Score: 234
Period size: 54 Copynumber: 4.9 Consensus size: 54
41194248 GATTCATGGG
* *
41194258 AAAATGACTGAAATACCCTCAAAAGGTAAAATGACTAAAATACCCCTGAAGGGT
1 AAAATGACTGAAATACCCTCGAAGGGTAAAATGACTAAAATACCCCTGAAGGGT
* * * *
41194312 AAAATGACTGAAATACCC-CTGAAGGGGAAAATTACCAAAATACCCC-AAAGGGT
1 AAAATGACTGAAATACCCTC-GAAGGGTAAAATGACTAAAATACCCCTGAAGGGT
** * *
41194365 GGAATGA-TCGAAATA-CCTCCGAAGGGTAAAATGACCAAAATACCCTTGAAGGGT
1 AAAATGACT-GAAATACCCT-CGAAGGGTAAAATGACTAAAATACCCCTGAAGGGT
* * * * *
41194419 AAAATGACT-AAGATACCCCCGGAGGGTAAAAT-AATCGAAATA-CTCTCGAAGGGT
1 AAAATGACTGAA-ATACCCTCGAAGGGTAAAATGACT-AAAATACCCCT-GAAGGGT
* * **
41194473 AAAATGACTGAAATACCCT-TATAGGATAAAATGACTATGATACCCCT
1 AAAATGACTGAAATACCCTCGA-AGGGTAAAATGACTAAAATACCCCT
41194520 AGGAGATGAA
Statistics
Matches: 164, Mismatches: 30, Indels: 27
0.74 0.14 0.12
Matches are distributed among these distances:
52 3 0.02
53 46 0.28
54 105 0.64
55 10 0.06
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.19
Consensus pattern (54 bp):
AAAATGACTGAAATACCCTCGAAGGGTAAAATGACTAAAATACCCCTGAAGGGT
Found at i:41194389 original size:80 final size:81
Alignment explanation
Indices: 41194255--41194490 Score: 255
Period size: 80 Copynumber: 2.9 Consensus size: 81
41194245 TGCGATTCAT
** * * * *
41194255 GGGAAAATGACTGAAATACCCTCAAAAGGTAAAATGA-CTAAAATACC-CCTGAAGGGTAAAATG
1 GGGAAAATGACCAAAATACCCCCAAAGGGTAAAATAATC-GAAATACCTCC-GAAGGGTAAAATG
41194318 ACTGAAATACCCCTGAAG
64 ACTGAAATACCCCTGAAG
* ** *
41194336 GGGAAAATTACCAAAATA-CCCCAAAGGGTGGAATGATCGAAATACCTCCGAAGGGTAAAATGAC
1 GGGAAAATGACCAAAATACCCCCAAAGGGTAAAATAATCGAAATACCTCCGAAGGGTAAAATGAC
** *
41194400 CAAAATACCCTTGAAG
66 TGAAATACCCCTGAAG
* * * **
41194416 GGTAAAATGACTAAGATACCCCCGGAGGGTAAAATAATCGAAATA-CTCTCGAAGGGTAAAATGA
1 GGGAAAATGACCAAAATACCCCCAAAGGGTAAAATAATCGAAATACCTC-CGAAGGGTAAAATGA
41194480 CTGAAATACCC
65 CTGAAATACCC
41194491 TTATAGGATA
Statistics
Matches: 129, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
80 66 0.51
81 63 0.49
ACGTcount: A:0.43, C:0.19, G:0.21, T:0.17
Consensus pattern (81 bp):
GGGAAAATGACCAAAATACCCCCAAAGGGTAAAATAATCGAAATACCTCCGAAGGGTAAAATGAC
TGAAATACCCCTGAAG
Found at i:41194479 original size:81 final size:81
Alignment explanation
Indices: 41194258--41194518 Score: 273
Period size: 81 Copynumber: 3.2 Consensus size: 81
41194248 GATTCATGGG
* * * *
41194258 AAAATGACTGAA-ATACCCTCAAAAGGTAAAATGA-CTAAAATACC-CCTGAAGGGTAAAATGAC
1 AAAATGACT-AAGATACCCCCAAAGGGTAAAATAATC-GAAATACCTCC-GAAGGGTAAAATGAC
* *
41194320 TGAAATACCCCTGAAGGGG
63 TGAAATACCCTTGAAGGGT
* * * ** * **
41194339 AAAATTACCAAAATA-CCCCAAAGGGTGGAATGATCGAAATACCTCCGAAGGGTAAAATGACCAA
1 AAAATGACTAAGATACCCCCAAAGGGTAAAATAATCGAAATACCTCCGAAGGGTAAAATGACTGA
41194403 AATACCCTTGAAGGGT
66 AATACCCTTGAAGGGT
**
41194419 AAAATGACTAAGATACCCCCGGAGGGTAAAATAATCGAAATA-CTCTCGAAGGGTAAAATGACTG
1 AAAATGACTAAGATACCCCCAAAGGGTAAAATAATCGAAATACCTC-CGAAGGGTAAAATGACTG
*
41194483 AAATACCCTT-ATAGGAT
65 AAATACCCTTGA-AGGGT
*
41194500 AAAATGACTATGATACCCC
1 AAAATGACTAAGATACCCC
41194519 TAGGAGATGA
Statistics
Matches: 151, Mismatches: 23, Indels: 12
0.81 0.12 0.06
Matches are distributed among these distances:
80 69 0.46
81 82 0.54
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.19
Consensus pattern (81 bp):
AAAATGACTAAGATACCCCCAAAGGGTAAAATAATCGAAATACCTCCGAAGGGTAAAATGACTGA
AATACCCTTGAAGGGT
Found at i:41194915 original size:28 final size:28
Alignment explanation
Indices: 41194860--41194915 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
41194850 CACTATACTG
*
41194860 GTTACTGTATTGGGCTAAGGCCGGCACT
1 GTTACTGTATTGGGCTAAGGCCGACACT
*
41194888 GTTACTGTTTTGGGCTAAGGTCC-ACACT
1 GTTACTGTATTGGGCTAAGG-CCGACACT
41194916 ATACTGTGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 23 0.92
29 2 0.08
ACGTcount: A:0.18, C:0.21, G:0.29, T:0.32
Consensus pattern (28 bp):
GTTACTGTATTGGGCTAAGGCCGACACT
Found at i:41198964 original size:18 final size:19
Alignment explanation
Indices: 41198943--41198990 Score: 53
Period size: 21 Copynumber: 2.5 Consensus size: 19
41198933 TGCTCATCTC
41198943 AGCTTGTT-TGATGATGGT
1 AGCTTGTTGTGATGATGGT
* *
41198961 AGCTTATTGGCTGATGATTGT
1 AGCTTGTT-G-TGATGATGGT
41198982 AGCTTGTTG
1 AGCTTGTTG
41198991 GCTGAGCTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 7 0.29
20 1 0.04
21 16 0.67
ACGTcount: A:0.17, C:0.08, G:0.31, T:0.44
Consensus pattern (19 bp):
AGCTTGTTGTGATGATGGT
Found at i:41198977 original size:21 final size:21
Alignment explanation
Indices: 41198951--41198995 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
41198941 TCAGCTTGTT
41198951 TGATGATGGTAGCTTATTGGC
1 TGATGATGGTAGCTTATTGGC
* *
41198972 TGATGATTGTAGCTTGTTGGC
1 TGATGATGGTAGCTTATTGGC
41198993 TGA
1 TGA
41198996 GCTACAAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.18, C:0.09, G:0.33, T:0.40
Consensus pattern (21 bp):
TGATGATGGTAGCTTATTGGC
Found at i:41201753 original size:27 final size:27
Alignment explanation
Indices: 41201714--41201881 Score: 164
Period size: 27 Copynumber: 6.3 Consensus size: 27
41201704 AATTCGTAGG
* * *
41201714 AAAATAACCGAAATACCCTCGAAGGAT
1 AAAATGACTGAAATACCCTCGAAGGGT
* *
41201741 AAAATGACTGAAATACCTTAGAAGGGT
1 AAAATGACTGAAATACCCTCGAAGGGT
* *
41201768 AAAATGACTAAAATACCCCCGAAAGGG-
1 AAAATGACTGAAATACCCTCG-AAGGGT
* *
41201795 -AAATAACGGAAATACCC-CTGAAGGGT
1 AAAATGACTGAAATACCCTC-GAAGGGT
** *
41201821 AAAATGACCAAAATACCCCCGAAGGGT
1 AAAATGACTGAAATACCCTCGAAGGGT
*
41201848 AAAATGGCTGAAATACCCTC-ATAGGGT
1 AAAATGACTGAAATACCCTCGA-AGGGT
41201875 AAAATGA
1 AAAATGA
41201882 TTGTGATACC
Statistics
Matches: 115, Mismatches: 20, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
25 6 0.05
26 16 0.14
27 87 0.76
28 6 0.05
ACGTcount: A:0.45, C:0.19, G:0.20, T:0.16
Consensus pattern (27 bp):
AAAATGACTGAAATACCCTCGAAGGGT
Found at i:41201848 original size:80 final size:80
Alignment explanation
Indices: 41201715--41201865 Score: 205
Period size: 80 Copynumber: 1.9 Consensus size: 80
41201705 ATTCGTAGGA
** **
41201715 AAATAACCGAAATACCCTCGAAGGATAAAATGACTGAAATACCTTAGAAGGGTAAAATGACTAAA
1 AAATAACCGAAATACCCTCGAAGGATAAAATGACCAAAATACCCCAGAAGGGTAAAATGACTAAA
41201780 ATACCCCCGAAAGGG
66 ATACCCCCGAAAGGG
* * * * *
41201795 AAATAACGGAAATACCC-CTGAAGGGTAAAATGACCAAAATACCCCCGAAGGGTAAAATGGCTGA
1 AAATAACCGAAATACCCTC-GAAGGATAAAATGACCAAAATACCCCAGAAGGGTAAAATGACTAA
41201859 AATACCC
65 AATACCC
41201866 TCATAGGGTA
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
79 1 0.02
80 60 0.98
ACGTcount: A:0.45, C:0.21, G:0.19, T:0.15
Consensus pattern (80 bp):
AAATAACCGAAATACCCTCGAAGGATAAAATGACCAAAATACCCCAGAAGGGTAAAATGACTAAA
ATACCCCCGAAAGGG
Found at i:41202275 original size:28 final size:28
Alignment explanation
Indices: 41202235--41202292 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
41202225 CACTGTACTA
* * *
41202235 GTTACTGTATTGGGCTAAGGCCCGCATT
1 GTTACTATATTGGGCTAAAGCCCACATT
*
41202263 GTTACTATTTTGGGCTAAAGCCCACATT
1 GTTACTATATTGGGCTAAAGCCCACATT
41202291 GT
1 GT
41202293 ACTGTGACTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (28 bp):
GTTACTATATTGGGCTAAAGCCCACATT
Found at i:41218144 original size:25 final size:25
Alignment explanation
Indices: 41218106--41218157 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
41218096 TCTGAGTAGG
*
41218106 GTCACACACCCGTGTGCCAGGCCGT
1 GTCACACACCCGTGTGCCAGGCAGT
* *
41218131 GTCACACGCGCGTGTGCCAGGCAGT
1 GTCACACACCCGTGTGCCAGGCAGT
41218156 GT
1 GT
41218158 GCTACCTAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.15, C:0.35, G:0.33, T:0.17
Consensus pattern (25 bp):
GTCACACACCCGTGTGCCAGGCAGT
Found at i:41219242 original size:35 final size:35
Alignment explanation
Indices: 41219174--41219314 Score: 140
Period size: 35 Copynumber: 4.0 Consensus size: 35
41219164 AGTACATCGA
* *
41219174 CAATCCAACCAAAATACACCAAATGCTCATAAGAGC
1 CAATCCATCCAAAACACACC-AATGCTCATAAGAGC
* *
41219210 CAATCCATCCAAAACACACCAATGCTCGTAAGAGT
1 CAATCCATCCAAAACACACCAATGCTCATAAGAGC
* * * * *
41219245 TAATCCCTCCAAAACACACCGATGCTCATAACAGT
1 CAATCCATCCAAAACACACCAATGCTCATAAGAGC
* * * *
41219280 TAATCCCTCCTAAACATACCAATGCTCGA-AAGAGC
1 CAATCCATCCAAAACACACCAATGCTC-ATAAGAGC
41219315 TAGTCCAACT
Statistics
Matches: 90, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
35 71 0.79
36 19 0.21
ACGTcount: A:0.40, C:0.32, G:0.10, T:0.18
Consensus pattern (35 bp):
CAATCCATCCAAAACACACCAATGCTCATAAGAGC
Found at i:41219330 original size:70 final size:70
Alignment explanation
Indices: 41219175--41219334 Score: 176
Period size: 70 Copynumber: 2.3 Consensus size: 70
41219165 GTACATCGAC
* * * *
41219175 AATCCAACCAAAATACACCAAATGCTCATAAGAGCCAATCCATCCAAAACACACCAATGCTCGTA
1 AATCCAACCAAAACACACC-GATGCTCATAACAGCCAATCCATCCAAAACACACCAATGCTCGAA
*
41219240 AGAGTT
65 AGAGCT
** ** * * *
41219246 AATCCCTCCAAAACACACCGATGCTCATAACAGTTAATCCCTCCTAAACATACCAATGCTCGAAA
1 AATCCAACCAAAACACACCGATGCTCATAACAGCCAATCCATCCAAAACACACCAATGCTCGAAA
41219311 GAGCT
66 GAGCT
* **
41219316 AGTCCAACTGAAACACACC
1 AATCCAACCAAAACACACC
41219335 AAAACAAAGA
Statistics
Matches: 72, Mismatches: 17, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
70 56 0.78
71 16 0.22
ACGTcount: A:0.41, C:0.32, G:0.10, T:0.17
Consensus pattern (70 bp):
AATCCAACCAAAACACACCGATGCTCATAACAGCCAATCCATCCAAAACACACCAATGCTCGAAA
GAGCT
Found at i:41238001 original size:12 final size:13
Alignment explanation
Indices: 41237972--41238005 Score: 52
Period size: 12 Copynumber: 2.6 Consensus size: 13
41237962 ATTTGGGTTA
41237972 GGGTTTGGTAATTT
1 GGGTTT-GTAATTT
41237986 GGGTTTGTAA-TT
1 GGGTTTGTAATTT
41237998 GGGTTTGT
1 GGGTTTGT
41238006 TGTATTGGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 10 0.50
13 4 0.20
14 6 0.30
ACGTcount: A:0.12, C:0.00, G:0.38, T:0.50
Consensus pattern (13 bp):
GGGTTTGTAATTT
Found at i:41238894 original size:44 final size:44
Alignment explanation
Indices: 41238845--41239052 Score: 155
Period size: 44 Copynumber: 4.5 Consensus size: 44
41238835 GTCTACTCTG
41238845 CTGCAACTTCAGGGAGATAAGGCTAGTGGCTTCAATCTGCTCCA
1 CTGCAACTTCAGGGAGATAAGGCTAGTGGCTTCAATCTGCTCCA
* * * * *
41238889 CTGCAACTTCAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAATCAGTTCCA
1 CTGCAACTTCAGGGAGATAAG----G-C-T-A---GTGGCTTCAATCTGCTCCA
** * ** * * *
41238943 CTGCAACGCCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCA
1 CTGCAACTTCAGGGAGATAAGGCTAG-TGGCTTCAATCTGCTCCA
* * *
41238988 CCGCAACTTCAGGGAGATAAGGCTGGTGGCTTCACTCTGCTCCA
1 CTGCAACTTCAGGGAGATAAGGCTAGTGGCTTCAATCTGCTCCA
* *
41239032 CTGCAAGTTCAGGAAGATAAG
1 CTGCAACTTCAGGGAGATAAG
41239053 ATCCGCCATA
Statistics
Matches: 123, Mismatches: 30, Indels: 22
0.70 0.17 0.13
Matches are distributed among these distances:
44 55 0.45
45 31 0.25
48 2 0.02
49 1 0.01
50 1 0.01
51 1 0.01
54 32 0.26
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (44 bp):
CTGCAACTTCAGGGAGATAAGGCTAGTGGCTTCAATCTGCTCCA
Found at i:41238897 original size:143 final size:143
Alignment explanation
Indices: 41238731--41239115 Score: 538
Period size: 143 Copynumber: 2.7 Consensus size: 143
41238721 GATTTGGTAA
* * * * * ** *
41238731 CTTCAACCTACTCCACTGTAACTTCAGGGAGATAAGGTTTGCCATAATTTGTAACTTTAATTTGT
1 CTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAATTTGT
** * * ** *
41238796 TCCGTTGCAACGCCAGAGAAATAAGATTTGTTGTCTTCAGTCTACTCTGCTGCAACTTCAGGGAG
66 TCCACTGCAACGCCAGAGAAATAAGATTCGCTGTCTTCAGTCTACTCCACCGCAACTTCAGGGAG
41238861 ATAAGGCTAGTGG
131 ATAAGGCTAGTGG
**
41238874 CTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAATCAGT
1 CTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAATTTGT
* *
41238939 TCCACTGCAACGCCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCACCGCAACTTCAGGGAG
66 TCCACTGCAACGCCAGAGAAATAAGATTCGCTGTCTTCAGTCTACTCCACCGCAACTTCAGGGAG
*
41239004 ATAAGGCTGGTGG
131 ATAAGGCTAGTGG
* *
41239017 CTTCACTCTGCTCCACTGCAAGTTCAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAATTTGT
1 CTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAATTTGT
* *
41239082 TCCACTGCAATGCCA-AGGAAATAAGATTCTCTGT
66 TCCACTGCAACGCCAGA-GAAATAAGATTCGCTGT
41239116 AATGACTTCA
Statistics
Matches: 214, Mismatches: 27, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
143 214 1.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (143 bp):
CTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAATTTGT
TCCACTGCAACGCCAGAGAAATAAGATTCGCTGTCTTCAGTCTACTCCACCGCAACTTCAGGGAG
ATAAGGCTAGTGG
Found at i:41240784 original size:1 final size:1
Alignment explanation
Indices: 41240774--41240866 Score: 51
Period size: 1 Copynumber: 93.0 Consensus size: 1
41240764 CCGGTAGAGG
* * * * * * * * * *
41240774 TTTTTATTTTTTTGTTTTTTTGTTCTTTGTTTTGTTTTTTGTTCTTTGTTTTTTTTTTGTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * *
41240839 TTGTATTTTTTTGTTATTTTTTGTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
41240867 CTTTCCTCTA
Statistics
Matches: 62, Mismatches: 30, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
1 62 1.00
ACGTcount: A:0.03, C:0.02, G:0.11, T:0.84
Consensus pattern (1 bp):
T
Found at i:41240847 original size:19 final size:19
Alignment explanation
Indices: 41240781--41240866 Score: 99
Period size: 19 Copynumber: 4.6 Consensus size: 19
41240771 AGGTTTTTAT
41240781 TTTTTTG-TTTTTTTGTTC
1 TTTTTTGTTTTTTTTGTTC
*
41240799 TTTGTTT-TGTTTTTTGTTC
1 TTT-TTTGTTTTTTTTGTTC
*
41240818 TTTGTT-TTTTTTTTGTT-
1 TTTTTTGTTTTTTTTGTTC
*
41240835 TTTTTTGTATTTTTTTGTTA
1 TTTTTTGT-TTTTTTTGTTC
41240855 TTTTTTGTTTTT
1 TTTTTTGTTTTT
41240867 CTTTCCTCTA
Statistics
Matches: 59, Mismatches: 4, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
17 5 0.08
18 16 0.27
19 30 0.51
20 8 0.14
ACGTcount: A:0.02, C:0.02, G:0.12, T:0.84
Consensus pattern (19 bp):
TTTTTTGTTTTTTTTGTTC
Found at i:41240860 original size:34 final size:35
Alignment explanation
Indices: 41240774--41240870 Score: 85
Period size: 37 Copynumber: 2.7 Consensus size: 35
41240764 CCGGTAGAGG
41240774 TTTTTATTTTTTTGTTTTTTTGTTCTTTGTTTTGTTT
1 TTTTTA-TTTTTT-TTTTTTTGTTCTTTGTTTTGTTT
*
41240811 TTTGTTCTTTGTTTTTTTTTTG-T-TTT-TTTTGTATT
1 TTT-TTATTT-TTTTTTTTTTGTTCTTTGTTTTGT-TT
* * *
41240846 TTTTTGTTATTTTTTGTTT-TTCTTT
1 TTTTTATTTTTTTTTTTTTGTTCTTT
41240871 CCTCTACTAC
Statistics
Matches: 51, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
33 10 0.20
34 13 0.25
35 8 0.16
36 1 0.02
37 14 0.27
38 5 0.10
ACGTcount: A:0.03, C:0.03, G:0.10, T:0.84
Consensus pattern (35 bp):
TTTTTATTTTTTTTTTTTTGTTCTTTGTTTTGTTT
Found at i:41248964 original size:12 final size:14
Alignment explanation
Indices: 41248935--41248966 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
41248925 GTTTGGGATA
41248935 GGGTTTGGTAATTT
1 GGGTTTGGTAATTT
41248949 GGGTTT-GTAA-TT
1 GGGTTTGGTAATTT
41248961 GGGTTT
1 GGGTTT
41248967 TTGTATTGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.44
13 4 0.22
14 6 0.33
ACGTcount: A:0.12, C:0.00, G:0.38, T:0.50
Consensus pattern (14 bp):
GGGTTTGGTAATTT
Found at i:41252237 original size:13 final size:14
Alignment explanation
Indices: 41252219--41252247 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
41252209 AAAAATGAAC
41252219 AAAATGA-ATAGGA
1 AAAATGACATAGGA
41252232 AAAATGACATAGGA
1 AAAATGACATAGGA
41252246 AA
1 AA
41252248 TATTCAGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.62, C:0.03, G:0.21, T:0.14
Consensus pattern (14 bp):
AAAATGACATAGGA
Found at i:41252485 original size:26 final size:26
Alignment explanation
Indices: 41252449--41252498 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
41252439 GAACATGTTG
*
41252449 ATCGTTAAAATTTTATAAGGGGTACA
1 ATCGTTAAAATTTAATAAGGGGTACA
*
41252475 ATCGTTAAAATTTAATTAGGGGTA
1 ATCGTTAAAATTTAATAAGGGGTA
41252499 AAATAGGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.38, C:0.06, G:0.20, T:0.36
Consensus pattern (26 bp):
ATCGTTAAAATTTAATAAGGGGTACA
Found at i:41253337 original size:27 final size:27
Alignment explanation
Indices: 41253307--41253367 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
41253297 GGCATCCTTT
*
41253307 GATAGTCTGA-TGGGAAAATAATCACAG
1 GATAGTCT-ATTGGGAAAATAAACACAG
* * *
41253334 GATAGTCTATTGGGACACTAAACATAG
1 GATAGTCTATTGGGAAAATAAACACAG
41253361 GATAGTC
1 GATAGTC
41253368 CACCGGGATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 1 0.03
27 28 0.97
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.25
Consensus pattern (27 bp):
GATAGTCTATTGGGAAAATAAACACAG
Found at i:41257401 original size:13 final size:14
Alignment explanation
Indices: 41257383--41257424 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
41257373 GCTAGGGAGG
41257383 TTTTGACAATAA-A
1 TTTTGACAATAATA
*
41257396 TTTTGAAAATAATA
1 TTTTGACAATAATA
*
41257410 TTTTCACAATTAATA
1 TTTTGACAA-TAATA
41257425 AGATAAGTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 11 0.46
14 8 0.33
15 5 0.21
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (14 bp):
TTTTGACAATAATA
Found at i:41264210 original size:12 final size:12
Alignment explanation
Indices: 41264193--41264218 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
41264183 AGGATATGCA
41264193 ATCTTAGATATG
1 ATCTTAGATATG
41264205 ATCTTAGATATG
1 ATCTTAGATATG
41264217 AT
1 AT
41264219 ATATGCAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (12 bp):
ATCTTAGATATG
Found at i:41264241 original size:19 final size:20
Alignment explanation
Indices: 41264205--41264253 Score: 82
Period size: 19 Copynumber: 2.5 Consensus size: 20
41264195 CTTAGATATG
41264205 ATCTTAGATATGATATATGCA
1 ATCTTAGATATGA-ATATGCA
41264226 ATCTTAGATATG-ATATGCA
1 ATCTTAGATATGAATATGCA
41264245 ATCTTAGAT
1 ATCTTAGAT
41264254 GATATGATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 16 0.57
21 12 0.43
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.39
Consensus pattern (20 bp):
ATCTTAGATATGAATATGCA
Found at i:41264257 original size:17 final size:18
Alignment explanation
Indices: 41264205--41264259 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 18
41264195 CTTAGATATG
41264205 ATCTTAGATATGATATATGCA
1 ATCTTAGA-ATG--ATATGCA
41264226 ATCTTAGATATGATATGCA
1 ATCTTAGA-ATGATATGCA
41264245 ATCTTAG-ATGATATG
1 ATCTTAGAATGATATG
41264260 ATTTTGTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.24
19 14 0.41
21 12 0.35
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.38
Consensus pattern (18 bp):
ATCTTAGAATGATATGCA
Found at i:41264555 original size:3 final size:3
Alignment explanation
Indices: 41264549--41264640 Score: 55
Period size: 3 Copynumber: 30.0 Consensus size: 3
41264539 ATTTTTTTAT
* * * *
41264549 TTA TTA TTTA TTA TTTA TTA TTTA TTT TTA TTA -AA TT- TGA TT- TTC
1 TTA TTA -TTA TTA -TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
41264594 TTG TTA TTAA GTTA TTA TTA TTG TTA TTA TTA TCA TTA TTA TTA TTA
1 TTA TTA TT-A -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
41264641 CTATATATAC
Statistics
Matches: 69, Mismatches: 12, Indels: 16
0.71 0.12 0.16
Matches are distributed among these distances:
2 4 0.06
3 52 0.75
4 11 0.16
5 2 0.03
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:41264557 original size:7 final size:7
Alignment explanation
Indices: 41264545--41264581 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
41264535 TTTAATTTTT
41264545 TTATTTA
1 TTATTTA
41264552 TTATTTA
1 TTATTTA
41264559 TTATTTA
1 TTATTTA
41264566 TTATTTA
1 TTATTTA
41264573 TT-TTTA
1 TTATTTA
41264579 TTA
1 TTA
41264582 AATTTGATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTATTTA
Found at i:41264798 original size:17 final size:17
Alignment explanation
Indices: 41264765--41264866 Score: 75
Period size: 17 Copynumber: 5.9 Consensus size: 17
41264755 CATAACTTTT
*
41264765 ATATACATATATATATAC
1 ATATACAT-TTTATATAC
*
41264783 ATTTACATTTTATATAC
1 ATATACATTTTATATAC
* *
41264800 ATATACATTTTTTATTTC
1 ATATACATTTTATA-TAC
*
41264818 ATA-AC-TTTTATATGC
1 ATATACATTTTATATAC
* *
41264833 ATATATATATATATATATAT
1 ATATACAT-T-T-TATATAC
41264853 ATATAC-TTTTATAT
1 ATATACATTTTATAT
41264867 TTTTTTTGAT
Statistics
Matches: 67, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
15 5 0.07
16 12 0.18
17 24 0.36
18 14 0.21
19 2 0.03
20 10 0.15
ACGTcount: A:0.39, C:0.09, G:0.01, T:0.51
Consensus pattern (17 bp):
ATATACATTTTATATAC
Found at i:41264840 original size:2 final size:2
Alignment explanation
Indices: 41264833--41264857 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
41264823 TTTTATATGC
41264833 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
41264858 CTTTTATATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41264928 original size:24 final size:25
Alignment explanation
Indices: 41264896--41264946 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
41264886 TATAAGTATG
41264896 TTTTCTTATAT-TAT-TCTTCATAAAA
1 TTTTCTTATATATATAT-TTC-TAAAA
41264921 TTTT-TTATATATATATTTCTAAAA
1 TTTTCTTATATATATATTTCTAAAA
41264945 TT
1 TT
41264947 AATTAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
24 13 0.54
25 10 0.42
26 1 0.04
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (25 bp):
TTTTCTTATATATATATTTCTAAAA
Found at i:41269920 original size:44 final size:44
Alignment explanation
Indices: 41269807--41270199 Score: 287
Period size: 44 Copynumber: 8.9 Consensus size: 44
41269797 GCAGGTCCTA
* * * * *
41269807 TCTTCCTATATTGGTACGAAGTGGATCGAAG-ATGCAGATCTTG
1 TCTTCATATATTGGCATGAAGTAGATCGAAGAAAGCAGATCTTG
** *** * *
41269850 TCTTCCCATATTGGTGGCGGAGTAGATCGTAGAAAGCAGATCTTG
1 TCTTCATATATTGG-CATGAAGTAGATCGAAGAAAGCAGATCTTG
* * *
41269895 CCTTCATATATTGGCATGAAGTAGATCGAAGATAGCAGATCCTG
1 TCTTCATATATTGGCATGAAGTAGATCGAAGAAAGCAGATCTTG
* * * * *
41269939 TCTTCCTATATTGGTAGCGAAGTGGATCGAAG-ATGCAGATCTTG
1 TCTTCATATATTGGCA-TGAAGTAGATCGAAGAAAGCAGATCTTG
**
41269983 TCTTCCCATACTGGTGGC--GAAGTAGATCGAAGAAAGCAGATCTTG
1 TCTT--CATA-TATTGGCATGAAGTAGATCGAAGAAAGCAGATCTTG
* * * * ** *
41270028 TCTTCATGTATTGGTATGAAGTAGATCAAAGATAGCAGGCCCTG
1 TCTTCATATATTGGCATGAAGTAGATCGAAGAAAGCAGATCTTG
* * * * * *
41270072 TCTTCCTATATTGGTAGGAAGTGGATCGAAG-ATGTAGATCTTG
1 TCTTCATATATTGGCATGAAGTAGATCGAAGAAAGCAGATCTTG
**
41270115 TCTTCCCATACTGGTGGC--GAAGTAGATCGAAGAAAGCAGATCTTG
1 TCTT--CATA-TATTGGCATGAAGTAGATCGAAGAAAGCAGATCTTG
* * * * *
41270160 TCTTCATGTATTGGCGTGAAGTAGAACAAAGATAGCAGAT
1 TCTTCATATATTGGCATGAAGTAGATCGAAGAAAGCAGAT
41270200 ATTGCCTTTC
Statistics
Matches: 271, Mismatches: 64, Indels: 29
0.74 0.18 0.08
Matches are distributed among these distances:
42 9 0.03
43 29 0.11
44 155 0.57
45 67 0.25
46 7 0.03
47 4 0.01
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (44 bp):
TCTTCATATATTGGCATGAAGTAGATCGAAGAAAGCAGATCTTG
Found at i:41270159 original size:132 final size:132
Alignment explanation
Indices: 41269791--41270197 Score: 679
Period size: 132 Copynumber: 3.1 Consensus size: 132
41269781 CAGATCAGTG
* *
41269791 AAGATAGCAGGTCCTATCTTCCTATATTGGTACGAAGTGGATCGAAGATGCAGATCTTGTCTTCC
1 AAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCC
* * * * *
41269856 CATATTGGTGGCGGAGTAGATCGTAGAAAGCAGATCTTGCCTTCATATATTGGCATGAAGTAGAT
66 CATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGAT
*
41269921 CG
131 CA
*
41269923 AAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTTC
1 AAGATAGCAGGTCCTGTCTTCCTATATTGGTAG-GAAGTGGATCGAAGATGCAGATCTTGTCTTC
*
41269988 CCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGTATGAAGTAGA
65 CCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGA
41270053 TCA
130 TCA
* *
41270056 AAGATAGCAGGCCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGTAGATCTTGTCTTCC
1 AAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCC
* *
41270121 CATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGAA
66 CATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGAT
41270186 CA
131 CA
41270188 AAGATAGCAG
1 AAGATAGCAG
41270198 ATATTGCCTT
Statistics
Matches: 258, Mismatches: 16, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
132 135 0.52
133 123 0.48
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.29
Consensus pattern (132 bp):
AAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCC
CATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGAT
CA
Found at i:41270292 original size:44 final size:44
Alignment explanation
Indices: 41270244--41270475 Score: 139
Period size: 44 Copynumber: 5.3 Consensus size: 44
41270234 AGACACCAGC
*
41270244 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGCTAAAAATAGCAGAT
1 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGATAAAAATAGCAGAT
* ***** ** * * * * *
41270288 CTTGCCTTCCTGCACCAACAGCAAAGCA-GATCGAAGACACCAG-C
1 CTTGCCTCCCTG-GGTTGCAGCGGAGCAGGAT-AAAAATAGCAGAT
*
41270332 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGCTAAAAATAGCAGAT
1 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGATAAAAATAGCAGAT
* **** * * * * * *
41270376 CTTGCCTTCCTGCACCGACAGCGAAGTA-GATCGAAGACACCAGA-
1 CTTGCCTCCCTGGGTTG-CAGCGGAGCAGGAT-AAAAATAGCAGAT
* *
41270420 CTTGCCTCACTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGATAAAAATAGCAGAT
*
41270464 CTTGCCTTCCTG
1 CTTGCCTCCCTG
41270476 CACCGACAGC
Statistics
Matches: 125, Mismatches: 55, Indels: 16
0.64 0.28 0.08
Matches are distributed among these distances:
43 31 0.25
44 63 0.50
45 31 0.25
ACGTcount: A:0.26, C:0.28, G:0.25, T:0.20
Consensus pattern (44 bp):
CTTGCCTCCCTGGGTTGCAGCGGAGCAGGATAAAAATAGCAGAT
Found at i:41270541 original size:88 final size:88
Alignment explanation
Indices: 41270191--41270508 Score: 537
Period size: 88 Copynumber: 3.6 Consensus size: 88
41270181 TAGAACAAAG
* * *
41270191 ATAGCAGATATTGCCTTTCTACACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
41270256 GGTTGCAGCGGAGCAGGCTAAAA
66 GGTTGCAGCGGAGCAGGCTAAAA
* *
41270279 ATAGCAGATCTTGCCTTCCTGCACCAACAGCAAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
41270344 GGTTGCAGCGGAGCAGGCTAAAA
66 GGTTGCAGCGGAGCAGGCTAAAA
* * *
41270367 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGTAGATCGAAGACACCAGACTTGCCTCACTG
1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
*
41270432 GGTTGCAGCGGAGCAGGTTAAAA
66 GGTTGCAGCGGAGCAGGCTAAAA
* *
41270455 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGATGACCCCAGCC
1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCC
41270509 CTATCTCCCT
Statistics
Matches: 215, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
88 215 1.00
ACGTcount: A:0.28, C:0.30, G:0.25, T:0.18
Consensus pattern (88 bp):
ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
GGTTGCAGCGGAGCAGGCTAAAA
Found at i:41270715 original size:44 final size:44
Alignment explanation
Indices: 41270508--41270717 Score: 289
Period size: 44 Copynumber: 4.8 Consensus size: 44
41270498 TGACCCCAGC
*
41270508 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
* *
41270552 CCTATCTCCCTAGTCAGCAGTGGAATAGGTTGAAGATTGAGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
* ** ** * *
41270596 TCTATCTCCCTGGGAAGCAGTGGAATATATTGAAAATTGT-AGGT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGA-AT
41270640 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
*
41270684 CCTATCTCCCTGAG-CAGCAGTGGAGTAGGTTGAA
1 CCTATCTCCCTG-GTCAGCAGTGGAATAGGTTGAA
41270718 AATAGCAAAT
Statistics
Matches: 143, Mismatches: 20, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
43 1 0.01
44 140 0.98
45 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (44 bp):
CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
Found at i:41271838 original size:7 final size:7
Alignment explanation
Indices: 41271826--41271862 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
41271816 TAGTCCTTTT
41271826 TTATTTA
1 TTATTTA
41271833 TTATTTA
1 TTATTTA
41271840 TTATTTA
1 TTATTTA
41271847 TTATTTA
1 TTATTTA
41271854 TTA-TTA
1 TTATTTA
41271860 TTA
1 TTA
41271863 AATTTTATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 6 0.20
7 24 0.80
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
TTATTTA
Found at i:41271843 original size:3 final size:3
Alignment explanation
Indices: 41271830--41271927 Score: 76
Period size: 3 Copynumber: 32.0 Consensus size: 3
41271820 CCTTTTTTAT
* *
41271830 TTA TTA TTTA TTA TTTA TTA TTTA TTA TTA TTA -AA TT- TTA TT- TTC
1 TTA TTA -TTA TTA -TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * **
41271875 TTG TTA TTAA GTTA TTA TTA TTG TTA TTA ACA TTA TTA TTA TTA TTA
1 TTA TTA TT-A -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
41271922 TTA TTA
1 TTA TTA
41271928 CTATATATAC
Statistics
Matches: 77, Mismatches: 10, Indels: 16
0.75 0.10 0.16
Matches are distributed among these distances:
2 5 0.06
3 59 0.77
4 11 0.14
5 2 0.03
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:41271883 original size:21 final size:22
Alignment explanation
Indices: 41271843--41271927 Score: 86
Period size: 24 Copynumber: 3.9 Consensus size: 22
41271833 TTATTTATTA
*
41271843 TTTATTATTTATTATTATTAAAT
1 TTTATTA-TTATTGTTATTAAAT
*
41271866 TTTATT-TTCTTGTTATT-AA-
1 TTTATTATTATTGTTATTAAAT
*
41271885 GTTATTATTATTGTTATTAACAT
1 TTTATTATTATTGTTATTAA-AT
*
41271908 TATTATTATTATTATTATTA
1 T-TTATTATTATTGTTATTA
41271928 CTATATATAC
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
19 5 0.10
20 12 0.24
21 10 0.20
22 1 0.02
23 6 0.12
24 17 0.33
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.64
Consensus pattern (22 bp):
TTTATTATTATTGTTATTAAAT
Found at i:41272289 original size:30 final size:29
Alignment explanation
Indices: 41272235--41272328 Score: 81
Period size: 28 Copynumber: 3.3 Consensus size: 29
41272225 AATTAATTAA
* *
41272235 TTTTA-ATATATGTA-AT-TATTATTATT
1 TTTTATATATATATATATATATAATTATT
*
41272261 TGTTTATATATATATATATATGTAATTATCT
1 T-TTTATATATATATATATATATAATTAT-T
* * *
41272292 TTTT-TATA-ATCTATGTATATAATTTTT
1 TTTTATATATATATATATATATAATTATT
41272319 TTTTATATAT
1 TTTTATATAT
41272329 GTACATGTAT
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
26 1 0.02
27 9 0.17
28 26 0.48
29 6 0.11
30 10 0.19
31 2 0.04
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (29 bp):
TTTTATATATATATATATATATAATTATT
Found at i:41272299 original size:23 final size:23
Alignment explanation
Indices: 41272273--41272331 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
41272263 TTTATATATA
*
41272273 TATATATATGTA-ATTATCTTTTT
1 TATATATATGTATATAAT-TTTTT
*
41272296 TATAATCTATGTATATAATTTTTT
1 TAT-ATATATGTATATAATTTTTT
*
41272320 TTTATATATGTA
1 TATATATATGTA
41272332 CATGTATATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
23 11 0.37
24 15 0.50
25 4 0.13
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.59
Consensus pattern (23 bp):
TATATATATGTATATAATTTTTT
Found at i:41272499 original size:12 final size:11
Alignment explanation
Indices: 41272474--41272516 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 11
41272464 CATGTTATTG
41272474 ATTTATTT-TT
1 ATTTATTTGTT
41272484 ATTTATTTAGTT
1 ATTTATTT-GTT
41272496 ATTTATTTGTTT
1 ATTTATTTG-TT
41272508 ATATTATTT
1 AT-TTATTT
41272517 CTATGCCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 8 0.28
11 1 0.03
12 14 0.48
13 6 0.21
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (11 bp):
ATTTATTTGTT
Found at i:41272503 original size:26 final size:25
Alignment explanation
Indices: 41272467--41272516 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
41272457 TGCTTTGCAT
*
41272467 GTTATTGATTTATTTTTATTTATTTA
1 GTTATTGATTTATTTATA-TTATTTA
* *
41272493 GTTATTTATTTGTTTATATTATTT
1 GTTATTGATTTATTTATATTATTT
41272517 CTATGCCATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.70
Consensus pattern (25 bp):
GTTATTGATTTATTTATATTATTTA
Found at i:41285062 original size:1 final size:1
Alignment explanation
Indices: 41285056--41285085 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
41285046 ACATATCACC
*
41285056 TTTTTTTTTTTTTTTTTTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
41285086 GCCTTTTATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:41285359 original size:20 final size:20
Alignment explanation
Indices: 41285334--41285371 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
41285324 TCACCTATCA
* *
41285334 AAATTAAATTATAATTTTTT
1 AAATTAAAATAAAATTTTTT
41285354 AAATTAAAATAAAATTTT
1 AAATTAAAATAAAATTTT
41285372 ATTATTGTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATTAAAATAAAATTTTTT
Found at i:41289968 original size:21 final size:24
Alignment explanation
Indices: 41289943--41290002 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 24
41289933 AACTTACATG
41289943 GTTATTAATAATAAA-AT-AATTT
1 GTTATTAATAATAAATATCAATTT
41289965 -TTATTAATAATAAATATCAATTT
1 GTTATTAATAATAAATATCAATTT
41289988 GTTAAATTAATAATA
1 GTT--ATTAATAATA
41290003 TTTTATATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
21 14 0.42
22 2 0.06
23 5 0.15
24 2 0.06
26 10 0.30
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (24 bp):
GTTATTAATAATAAATATCAATTT
Found at i:41291517 original size:3 final size:3
Alignment explanation
Indices: 41291502--41291667 Score: 65
Period size: 3 Copynumber: 56.0 Consensus size: 3
41291492 GATAGCAGTG
* * * *
41291502 ATA ATA TTA ATA ATA A-A AGTA ATA CTA ATA ATA ATA TTA GTA ATA
1 ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
41291547 ACA AAA ATA ATA GTA ATA A-A AGTA ATA A-A GATA ATA ATA CT- ATA
1 ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA -ATA ATA ATA ATA ATA
* * * ** * * * * *
41291591 GTA ATG ATG ACG TTA ATA ATA ATA ATA TTA AAA ATA AAA ATA ACA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
41291638 ACTA CTA ATA ATA AAA ATA ATG ATA A-A ATA
1 A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA
41291668 GCAAAGATAT
Statistics
Matches: 118, Mismatches: 35, Indels: 20
0.68 0.20 0.12
Matches are distributed among these distances:
2 10 0.08
3 102 0.86
4 6 0.05
ACGTcount: A:0.61, C:0.04, G:0.06, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:41293214 original size:100 final size:100
Alignment explanation
Indices: 41293051--41293315 Score: 334
Period size: 100 Copynumber: 2.6 Consensus size: 100
41293041 CTTGACTGTG
* * * * * *
41293051 ATGTCGGGGAAGCAAGATTCGCCGTTGTGTCTTCAATCTATTCCACTGCACCGCCTGGAAAGTAA
1 ATGTCAGGGAAGCAAGATTCGCCGTTGTGGCTTTAATCTGTTCCACTGCACTGCCTGGGAAGTAA
* * *
41293116 GATTCACCATTGTGGCTTTATTCTTTATAACTGTA
66 GATTCACCATTGTAGCTTTAATCTTTATAACTGCA
* * * * *
41293151 ATGTCATGGATGCAAGATTCGTCGTTGTGGCTTTAATCTGTTCCACTACACTGCTTGGGAAGTAA
1 ATGTCAGGGAAGCAAGATTCGCCGTTGTGGCTTTAATCTGTTCCACTGCACTGCCTGGGAAGTAA
* * *
41293216 GATTCGCCGTTGTAGCTTTAATCTTTTTAACTGCA
66 GATTCACCATTGTAGCTTTAATCTTTATAACTGCA
* * *
41293251 ATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCA-TCGCCTGGGAAGTA
1 ATGTCAGGGAAGCAAGATTCGCCGTTGTGGCTTTAATCTGTTCCACTGCACT-GCCTGGGAAGTA
41293315 A
65 A
41293316 AACTGGTATT
Statistics
Matches: 139, Mismatches: 25, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
99 1 0.01
100 138 0.99
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (100 bp):
ATGTCAGGGAAGCAAGATTCGCCGTTGTGGCTTTAATCTGTTCCACTGCACTGCCTGGGAAGTAA
GATTCACCATTGTAGCTTTAATCTTTATAACTGCA
Found at i:41293218 original size:50 final size:49
Alignment explanation
Indices: 41293057--41293315 Score: 182
Period size: 50 Copynumber: 5.2 Consensus size: 49
41293047 TGTGATGTCG
* * * * * *
41293057 GGGAAGCAAGATTCGCCGTTGTGTCTTCAATCTATTCCACTGCACCGCCT
1 GGGAAGTAAGATTCGCCGTTGTGGCTTTAATCTGTTCCACTGCA-TGCTT
* * * * ** * *
41293107 GGAAAGTAAGATTCACCATTGTGGCTTTATTCT-TTATAACTGTAATGTCAT
1 GGGAAGTAAGATTCGCCGTTGTGGCTTTAATCTGTT-CCACTG-CATG-CTT
* * * *
41293158 -GGATGCAAGATTCGTCGTTGTGGCTTTAATCTGTTCCACTACACTGCTT
1 GGGAAGTAAGATTCGCCGTTGTGGCTTTAATCTGTTCCACTGCA-TGCTT
* * ** *
41293207 GGGAAGTAAGATTCGCCGTTGTAGCTTTAATCTTTTTAACTGCAATG-TCG
1 GGGAAGTAAGATTCGCCGTTGTGGCTTTAATCTGTTCCACTGC-ATGCT-T
* * * *
41293257 GGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCATCGCCT
1 GGGAAGTAAGATTCGCCGTTGTGGCTTTAATCTGTTCCACTGCAT-GCTT
41293307 GGGAAGTAA
1 GGGAAGTAA
41293316 AACTGGTATT
Statistics
Matches: 156, Mismatches: 43, Indels: 20
0.71 0.20 0.09
Matches are distributed among these distances:
49 8 0.05
50 142 0.91
51 6 0.04
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.33
Consensus pattern (49 bp):
GGGAAGTAAGATTCGCCGTTGTGGCTTTAATCTGTTCCACTGCATGCTT
Found at i:41300541 original size:3 final size:3
Alignment explanation
Indices: 41300526--41300688 Score: 57
Period size: 3 Copynumber: 55.0 Consensus size: 3
41300516 GATAGCAGTG
* * * * *
41300526 ATA ATA TTA ATA ATA A-A AGTA ATA CTA ACA ATA ATA TTA GTA ATA
1 ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
41300571 AGA AAA ATA ATA GTA ATA ATA GTA ATA A-A GATA ATA ATA CT- ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA
* * * ** * * * * *
41300615 GTA ATG ATG ACG TTA ATA ATA ATA TTA AAA ATA AAA ATA ACA A-A ACTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA
* * *
41300663 CTA ATA ATA AAA ATA ATG ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
41300689 GCAAAGATAT
Statistics
Matches: 113, Mismatches: 39, Indels: 16
0.67 0.23 0.10
Matches are distributed among these distances:
2 8 0.07
3 101 0.89
4 4 0.04
ACGTcount: A:0.60, C:0.04, G:0.07, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:41302178 original size:100 final size:100
Alignment explanation
Indices: 41302038--41302328 Score: 375
Period size: 100 Copynumber: 2.9 Consensus size: 100
41302028 GATTCGTAAC
* ** * * * *
41302038 TTGTAACTTTAATCTACTTGACTGTGATGTCGGGGAAGCAAGATTCGCCGTTGTGTCTTCAATCT
1 TTGTAGCTTTAATCTTTTTAACTGTAATGTCGGGGAAGCAAGATTCGCCGTTGTGGCTTTAATCT
*
41302103 GTTCCACTGTACCACCTGGGAAGTAAGATTCACCA
66 GTTCCACTGCACCACCTGGGAAGTAAGATTCACCA
* * *
41302138 TTGTGGCTTTATTCTTTTTAACTGTAATGTCAGGGAAGCAAGATTCGCCGTTGTGGCTTTAATCT
1 TTGTAGCTTTAATCTTTTTAACTGTAATGTCGGGGAAGCAAGATTCGCCGTTGTGGCTTTAATCT
* ** * * *
41302203 GTTACACTGCACTGCTTGGGAAGTAAGATTCGCCG
66 GTTCCACTGCACCACCTGGGAAGTAAGATTCACCA
* * *
41302238 TTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCT
1 TTGTAGCTTTAATCTTTTTAACTGTAATGTCGGGGAAGCAAGATTCGCCGTTGTGGCTTTAATCT
* * *
41302303 GTTCCACTGCATCGCCTGGAAAGTAA
66 GTTCCACTGCACCACCTGGGAAGTAA
41302329 AACTAGTATT
Statistics
Matches: 163, Mismatches: 28, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
100 163 1.00
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (100 bp):
TTGTAGCTTTAATCTTTTTAACTGTAATGTCGGGGAAGCAAGATTCGCCGTTGTGGCTTTAATCT
GTTCCACTGCACCACCTGGGAAGTAAGATTCACCA
Found at i:41302312 original size:50 final size:50
Alignment explanation
Indices: 41302064--41302313 Score: 241
Period size: 50 Copynumber: 5.0 Consensus size: 50
41302054 CTTGACTGTG
* * *
41302064 ATGTCGGGGAAGCAAGATTCGCCGTTGTGTCTTCAATCTGTTCCACTGTA
1 ATGTCGGGGAAGCAAGATTCGCCGTTGTGGCTTTAATCTGTTCCACTGCA
**** * * * * * * ** *
41302114 CCACCTGGGAAGTAAGATTCACCATTGTGGCTTTATTCTTTTTAACTGTA
1 ATGTCGGGGAAGCAAGATTCGCCGTTGTGGCTTTAATCTGTTCCACTGCA
* *
41302164 ATGTCAGGGAAGCAAGATTCGCCGTTGTGGCTTTAATCTGTTACACTGCA
1 ATGTCGGGGAAGCAAGATTCGCCGTTGTGGCTTTAATCTGTTCCACTGCA
* * * * * **
41302214 CTG-CTTGGGAAGTAAGATTCGCCGTTGTAGCTTTAATCTTTTTAACTGCA
1 ATGTC-GGGGAAGCAAGATTCGCCGTTGTGGCTTTAATCTGTTCCACTGCA
* *
41302264 ATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCA
1 ATGTCGGGGAAGCAAGATTCGCCGTTGTGGCTTTAATCTGTTCCACTGCA
41302314 TCGCCTGGAA
Statistics
Matches: 155, Mismatches: 43, Indels: 4
0.77 0.21 0.02
Matches are distributed among these distances:
49 1 0.01
50 153 0.99
51 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (50 bp):
ATGTCGGGGAAGCAAGATTCGCCGTTGTGGCTTTAATCTGTTCCACTGCA
Found at i:41302879 original size:14 final size:14
Alignment explanation
Indices: 41302860--41302895 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
41302850 ACCTCTTCCT
41302860 ATTGCTTGGTGATC
1 ATTGCTTGGTGATC
41302874 ATTGCTTGGTGATC
1 ATTGCTTGGTGATC
41302888 ATTGCTTG
1 ATTGCTTG
41302896 CTTGTTTATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.28, T:0.44
Consensus pattern (14 bp):
ATTGCTTGGTGATC
Found at i:41306184 original size:19 final size:19
Alignment explanation
Indices: 41306160--41306200 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
41306150 TTTTAAATTT
*
41306160 AAAAAATTA-AAAATTATTA
1 AAAAAAGTATAAAATTA-TA
41306179 AAAAAAGTATAAAATTATA
1 AAAAAAGTATAAAATTATA
41306198 AAA
1 AAA
41306201 TTTTTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (19 bp):
AAAAAAGTATAAAATTATA
Found at i:41319137 original size:20 final size:19
Alignment explanation
Indices: 41319112--41319160 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
41319102 TTCAAGGGTC
41319112 ATTTTGAAACAAAATAGAAA
1 ATTTTGAAA-AAAATAGAAA
* *
41319132 ATTTTGGAAAAAATTGAAA
1 ATTTTGAAAAAAATAGAAA
41319151 ATTTTGAAAA
1 ATTTTGAAAA
41319161 CAAGGGTCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 18 0.69
20 8 0.31
ACGTcount: A:0.55, C:0.02, G:0.12, T:0.31
Consensus pattern (19 bp):
ATTTTGAAAAAAATAGAAA
Found at i:41320963 original size:12 final size:10
Alignment explanation
Indices: 41320933--41320975 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
41320923 AATATGAACA
*
41320933 TAATGAATTT
1 TAATTAATTT
41320943 TAATTAATTT
1 TAATTAATTT
41320953 TATAGTTAATTT
1 TA-A-TTAATTT
*
41320965 TGATTAATTT
1 TAATTAATTT
41320975 T
1 T
41320976 GACTATTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 19 0.66
11 2 0.07
12 8 0.28
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (10 bp):
TAATTAATTT
Found at i:41332336 original size:48 final size:47
Alignment explanation
Indices: 41332261--41332416 Score: 161
Period size: 47 Copynumber: 3.3 Consensus size: 47
41332251 ATCCACAATT
* * * * *
41332261 ATTTGGACAACATTGATTTG-TACAAAAATGAACAGCATTTAAGCACC
1 ATTTGGACAACATTAATATGCTA-AAAAATGGACAGCATTTAAACAAC
* * * * *
41332308 AATTTGGACAGCATTAATATGCTAAAAAACGGACAACATTCAACCAAC
1 -ATTTGGACAACATTAATATGCTAAAAAATGGACAGCATTTAAACAAC
* * *
41332356 ATTCGAACAACATTAGTATGCTAAAAAATGGACAGCATTTAAACAAC
1 ATTTGGACAACATTAATATGCTAAAAAATGGACAGCATTTAAACAAC
*
41332403 ATTTGGACCACATT
1 ATTTGGACAACATT
41332417 TAATCAACAT
Statistics
Matches: 87, Mismatches: 20, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
47 50 0.57
48 35 0.40
49 2 0.02
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.25
Consensus pattern (47 bp):
ATTTGGACAACATTAATATGCTAAAAAATGGACAGCATTTAAACAAC
Found at i:41332409 original size:22 final size:22
Alignment explanation
Indices: 41332384--41332622 Score: 111
Period size: 22 Copynumber: 10.5 Consensus size: 22
41332374 TGCTAAAAAA
41332384 TGGACAGCATTTAAACAACATT
1 TGGACAGCATTTAAACAACATT
*
41332406 TGGACCA-CATTTAATCAACATT
1 TGGA-CAGCATTTAAACAACATT
* ** * **
41332428 TGGACATCATTAGTATGCTAAAAAA
1 TGGACAGCATT--TAAAC-AACATT
*
41332453 TGGACAGTATTTAAACAACATT
1 TGGACAGCATTTAAACAACATT
** * *
41332475 CAGACAACATTTAACCAACATT
1 TGGACAGCATTTAAACAACATT
* ** * **
41332497 TGGACAACATTAGTATGCTAAAAAA
1 TGGACAGCATT--TAAAC-AACATT
* * **
41332522 TGGAAAACATTTAAACAACAGC
1 TGGACAGCATTTAAACAACATT
* * *
41332544 CGGACAACATTTAACCAACATT
1 TGGACAGCATTTAAACAACATT
** * **
41332566 TGGACAGCATTAGTATGCTAAAAAA
1 TGGACAGCATT--TAAAC-AACATT
41332591 TGGACAGCATTTAAACAACATT
1 TGGACAGCATTTAAACAACATT
41332613 TGGACAGCAT
1 TGGACAGCAT
41332623 CTTGTCATAA
Statistics
Matches: 158, Mismatches: 48, Indels: 22
0.69 0.21 0.10
Matches are distributed among these distances:
21 2 0.01
22 97 0.61
23 11 0.07
24 9 0.06
25 39 0.25
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.26
Consensus pattern (22 bp):
TGGACAGCATTTAAACAACATT
Found at i:41332426 original size:69 final size:69
Alignment explanation
Indices: 41332337--41332618 Score: 429
Period size: 69 Copynumber: 4.1 Consensus size: 69
41332327 TGCTAAAAAA
* * *
41332337 CGGACAACATTCAACCAACATTCGAACAACATTAGTATGCTAAAAAATGGACAGCATTTAAACAA
1 CGGACAACATTTAACCAACATTTGGACAACATTAGTATGCTAAAAAATGGACAGCATTTAAACAA
41332402 CATT
66 CATT
* * * * *
41332406 TGGACCACATTTAATCAACATTTGGACATCATTAGTATGCTAAAAAATGGACAGTATTTAAACAA
1 CGGACAACATTTAACCAACATTTGGACAACATTAGTATGCTAAAAAATGGACAGCATTTAAACAA
41332471 CATT
66 CATT
* * *
41332475 CAGACAACATTTAACCAACATTTGGACAACATTAGTATGCTAAAAAATGGAAAACATTTAAACAA
1 CGGACAACATTTAACCAACATTTGGACAACATTAGTATGCTAAAAAATGGACAGCATTTAAACAA
**
41332540 CAGC
66 CATT
*
41332544 CGGACAACATTTAACCAACATTTGGACAGCATTAGTATGCTAAAAAATGGACAGCATTTAAACAA
1 CGGACAACATTTAACCAACATTTGGACAACATTAGTATGCTAAAAAATGGACAGCATTTAAACAA
41332609 CATT
66 CATT
*
41332613 TGGACA
1 CGGACA
41332619 GCATCTTGTC
Statistics
Matches: 188, Mismatches: 25, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
69 188 1.00
ACGTcount: A:0.44, C:0.19, G:0.13, T:0.24
Consensus pattern (69 bp):
CGGACAACATTTAACCAACATTTGGACAACATTAGTATGCTAAAAAATGGACAGCATTTAAACAA
CATT
Found at i:41332483 original size:11 final size:11
Alignment explanation
Indices: 41332461--41332507 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
41332451 AATGGACAGT
*
41332461 ATTTAAACAAC
1 ATTTAGACAAC
*
41332472 ATTCAGACAAC
1 ATTTAGACAAC
41332483 ATTTA-ACCAAC
1 ATTTAGA-CAAC
*
41332494 ATTTGGACAAC
1 ATTTAGACAAC
41332505 ATT
1 ATT
41332508 AGTATGCTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
10 1 0.03
11 28 0.93
12 1 0.03
ACGTcount: A:0.45, C:0.21, G:0.06, T:0.28
Consensus pattern (11 bp):
ATTTAGACAAC
Found at i:41335695 original size:28 final size:27
Alignment explanation
Indices: 41335631--41335696 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
41335621 GAAAATGGAG
* *
41335631 GCCTTTGTGGCAATCTCTATATAGGAA
1 GCCTTTGTGGCAATCTCTATAAAAGAA
* *
41335658 GCCTTTGTGGCTATCTCTGTAAAAGAA
1 GCCTTTGTGGCAATCTCTATAAAAGAA
*
41335685 TGCCTTCGTGGC
1 -GCCTTTGTGGC
41335697 GTAATCTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
27 23 0.70
28 10 0.30
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.33
Consensus pattern (27 bp):
GCCTTTGTGGCAATCTCTATAAAAGAA
Found at i:41340553 original size:27 final size:27
Alignment explanation
Indices: 41340511--41340570 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
41340501 AAACCGCTAG
* *
41340511 AAATATATATACGTGG-CTAAGCCACC
1 AAATAGATATACGTGGTCTAAACCACC
*
41340537 ATAATAGATATATGTGGTTCTAAACCACC
1 A-AATAGATATACGTGG-TCTAAACCACC
41340566 AAATA
1 AAATA
41340571 AGGCAAATGA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
26 1 0.04
27 13 0.46
28 4 0.14
29 10 0.36
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (27 bp):
AAATAGATATACGTGGTCTAAACCACC
Found at i:41341596 original size:5 final size:5
Alignment explanation
Indices: 41341586--41341610 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
41341576 TCTTTTTCTA
41341586 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
41341611 TATAAGCCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:41344350 original size:24 final size:25
Alignment explanation
Indices: 41344298--41344356 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
41344288 TGGCTCTCAC
* * *
41344298 GAGCTTCCCGTTATATGGTTCTTGC
1 GAGCTTCCCGTTATATAGCTCTTGA
*
41344323 GAGCTTCCCGTTA-ATAGCTCTTTA
1 GAGCTTCCCGTTATATAGCTCTTGA
*
41344347 GAGCATCCCG
1 GAGCTTCCCG
41344357 ATTGGTTGTG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 16 0.55
25 13 0.45
ACGTcount: A:0.17, C:0.27, G:0.22, T:0.34
Consensus pattern (25 bp):
GAGCTTCCCGTTATATAGCTCTTGA
Found at i:41355955 original size:29 final size:29
Alignment explanation
Indices: 41355901--41355959 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 29
41355891 AGCCCATATA
*
41355901 TTTCACAATTTCTCACATTTGACCCACAAT
1 TTTCACAATTTCTCACATTTAACCCA-AAT
41355931 TTTCAC-ATTTCTCA-ATTTAACCCCAAAT
1 TTTCACAATTTCTCACATTTAA-CCCAAAT
41355959 T
1 T
41355960 GACATTTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 9 0.33
29 12 0.44
30 6 0.22
ACGTcount: A:0.31, C:0.29, G:0.02, T:0.39
Consensus pattern (29 bp):
TTTCACAATTTCTCACATTTAACCCAAAT
Found at i:41370356 original size:14 final size:13
Alignment explanation
Indices: 41370332--41370386 Score: 65
Period size: 14 Copynumber: 4.1 Consensus size: 13
41370322 TTGTTACCGC
*
41370332 TATTATGTTATAT
1 TATTATTTTATAT
*
41370345 CATTAGTTTTATAT
1 TATTA-TTTTATAT
41370359 TATTATTGTTATAT
1 TATTATT-TTATAT
*
41370373 TTTTATTTTATAT
1 TATTATTTTATAT
41370386 T
1 T
41370387 TACTTATTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
13 13 0.36
14 23 0.64
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.65
Consensus pattern (13 bp):
TATTATTTTATAT
Found at i:41370362 original size:27 final size:27
Alignment explanation
Indices: 41370332--41370386 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
41370322 TTGTTACCGC
41370332 TATTA-TGTTATATCATTAGTTTTATAT
1 TATTATTGTTATATCATTA-TTTTATAT
**
41370359 TATTATTGTTATATTTTTATTTTATAT
1 TATTATTGTTATATCATTATTTTATAT
41370386 T
1 T
41370387 TACTTATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 14 0.56
28 11 0.44
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.65
Consensus pattern (27 bp):
TATTATTGTTATATCATTATTTTATAT
Found at i:41375211 original size:23 final size:24
Alignment explanation
Indices: 41375202--41375267 Score: 64
Period size: 23 Copynumber: 2.8 Consensus size: 24
41375192 GAAAAAAATC
41375202 AAAATCAAAATCAAAATAAAGAAA
1 AAAATCAAAATCAAAATAAAGAAA
** *
41375226 AAAA-CAAAAAGAAAA-AGAGAAA
1 AAAATCAAAATCAAAATAAAGAAA
** *
41375248 TCAATCAAAGTCAAAATAAA
1 AAAATCAAAATCAAAATAAA
41375268 AATATGAAAA
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
22 8 0.26
23 17 0.55
24 6 0.19
ACGTcount: A:0.73, C:0.09, G:0.08, T:0.11
Consensus pattern (24 bp):
AAAATCAAAATCAAAATAAAGAAA
Found at i:41375227 original size:52 final size:50
Alignment explanation
Indices: 41375171--41375292 Score: 145
Period size: 52 Copynumber: 2.3 Consensus size: 50
41375161 TCGATTCGAA
*
41375171 AAAAAAAGGAAAAGAAAAAGAGAAAAAAATCAAAATCAAAATCAAAATAAAG
1 AAAAAAA-GAAAAGAAAAAGAGAAAAAAATCAAAATCAAAATAAAAAT-AAG
* ** * *
41375223 AAAAAAACAAAAAGAAAAAGAGAAATCAATCAAAGTCAAAATAAAAATATG
1 AAAAAAA-GAAAAGAAAAAGAGAAAAAAATCAAAATCAAAATAAAAATAAG
41375274 AAAAGCAAAGAAAAGAAAA
1 AAAA--AAAGAAAAGAAAA
41375293 GAAGAGGCCA
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
51 6 0.10
52 51 0.85
53 3 0.05
ACGTcount: A:0.74, C:0.07, G:0.11, T:0.08
Consensus pattern (50 bp):
AAAAAAAGAAAAGAAAAAGAGAAAAAAATCAAAATCAAAATAAAAATAAG
Found at i:41375691 original size:7 final size:6
Alignment explanation
Indices: 41375655--41375682 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
41375645 AAAAGGATGA
41375655 AAAATG AAAATG AAAATG AAAATG AAAA
1 AAAATG AAAATG AAAATG AAAATG AAAA
41375683 AAATGAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (6 bp):
AAAATG
Found at i:41375697 original size:15 final size:15
Alignment explanation
Indices: 41375654--41375691 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 15
41375644 AAAAAGGATG
41375654 AAAAATGAAAATG--
1 AAAAATGAAAATGAA
41375667 -AAAATGAAAATGAA
1 AAAAATGAAAATGAA
41375681 AAAAATGAAAA
1 AAAAATGAAAA
41375692 GTAAAATGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 12 0.55
15 10 0.45
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (15 bp):
AAAAATGAAAATGAA
Found at i:41377072 original size:86 final size:86
Alignment explanation
Indices: 41376927--41378133 Score: 1641
Period size: 86 Copynumber: 14.0 Consensus size: 86
41376917 TAGTGAAGAT
* * * * * *
41376927 AGCAGATCTTGCCTTCCTACATTAACAGTGAAGCAGATTGAAAACAAAACCTTACCTCCATCGGT
1 AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGT
* *
41376992 GGCAATGGAGCTGGTTAAAAA
66 TGCAGTGGAGCTGGTTAAAAA
*
41377013 AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATTGAAAACAAAGCCTTGCCTCCATCGGT
1 AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGT
*
41377078 TGCAGTGGAGCTGGTTAAAGA
66 TGCAGTGGAGCTGGTTAAAAA
* * *
41377099 AGCAGATATTGTCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGTCTTGCCTCCATCGGT
1 AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGT
*
41377164 TGCAGTGGAGCTGGTTAAAGA
66 TGCAGTGGAGCTGGTTAAAAA
* * *
41377185 AGCAGATCTTGCCTTCCTGCGTTAACAGTGAAGCAGATCGAAAACAAAGCCTTACCTCTATCGGT
1 AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGT
*
41377250 TGCAGTGGAGCTGGTTAAAGA
66 TGCAGTGGAGCTGGTTAAAAA
** * *
41377271 AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAATCTTGTCTCCATCAGT
1 AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGT
* * *
41377336 GGCAATGGAGCTGGTTAAAGA
66 TGCAGTGGAGCTGGTTAAAAA
* *
41377357 AGCAGCTCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGAT
1 AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGT
* * *
41377422 TACAGTGGAACTGGATAAAAA
66 TGCAGTGGAGCTGGTTAAAAA
* *
41377443 AGCAGATCTTACCTTCCTGCGTTAACAACGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGT
1 AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGT
*
41377508 TGCAGTGGAGCTGGTTAAAGA
66 TGCAGTGGAGCTGGTTAAAAA
*
41377529 AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAATAAAGCCTTGCCTCCATCGGT
1 AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGT
* *
41377594 TGCAATGGAGCTGGTTAAAGA
66 TGCAGTGGAGCTGGTTAAAAA
*
41377615 AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATTGGT
1 AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGT
41377680 TGCAGTGGAGCTGGTTAAAAA
66 TGCAGTGGAGCTGGTTAAAAA
* * *
41377701 AGCAGATCTTGCCTTCCTGCCTTAACAGCGAAGCAGATCGAAAACAAAACCTTACCTCTC-TCGG
1 AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTC-CATCGG
* * *
41377765 TTGTAGTGGAGCGGGTTGAAGACA
65 TTGCAGTGGAGCTGGTT-AA-AAA
* * * **
41377789 A-CAGATCTTGTCTTCCTGCCTTGACAGCGAAGCAGATCGAAGATACAAA-CCTTTTCTCTC-TC
1 AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAA-A-ACAAAGCCTTGCCTC-CATC
* ** *
41377851 GGTTGTAGCAGAGCTGGTTAAAGAT
63 GGTTGCAGTGGAGCTGGTTAAA-AA
* * * *
41377876 AGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGA-CAAAAAAAAAGCATTGCCTCCATCGGT
1 AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGT
* * *
41377940 TGCAGGGGAGCTGGTTTAAGAT
66 TGCAGTGGAGCTGG-TTAAAAA
* *
41377962 AGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATTGAAAACAAAGCCTTGCCTCCATCGGT
1 AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGT
* * * *
41378027 TGCAATAGAGCTGGTTGAAGAT
66 TGCAGTGGAGCTGGTT-AAAAA
* * * * * *
41378049 AGCAGCTCTTGCCTTCCTGCATTAACAGCGATGCAGATCAAAAACAAAGTCTTGCCTCCATCGAT
1 AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGT
* *
41378114 TACAGTGGAGCGGGTTAAAA
66 TGCAGTGGAGCTGGTTAAAA
41378134 TAAAAGATCT
Statistics
Matches: 1008, Mismatches: 101, Indels: 24
0.89 0.09 0.02
Matches are distributed among these distances:
85 5 0.00
86 774 0.77
87 161 0.16
88 63 0.06
89 5 0.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (86 bp):
AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGT
TGCAGTGGAGCTGGTTAAAAA
Found at i:41377583 original size:43 final size:42
Alignment explanation
Indices: 41377364--41377753 Score: 132
Period size: 43 Copynumber: 9.1 Consensus size: 42
41377354 AGAAGCAGCT
41377364 CTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGC
1 CTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAA-AAAGC
* * *
41377407 CTTGCC-TCCAT-CGATT-ACAGTGGAA-CTGGAT--AAAAAAGCAGAT
1 CTTGCCTTCC-TGCG-TTAACAG-CGAAGC-AGATCGAAAAAA--AG-C
* *
41377450 CTTACCTTCCTGCGTTAACAACGAAGCAGATCGAAAACAAAGC
1 CTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAA-AAAGC
* * * * * * * *
41377493 CTTGCC-TCCAT-CGGTT-GCAGTGGAGCTGGT-TAAAGAAGCAGAT
1 CTTGCCTTCC-TGC-GTTAACAGCGAAGCAGATCGAAA-AA-AAG-C
41377536 CTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAATAAAGC
1 CTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAA-AAAGC
* ** * * * * * *
41377579 CTTGCC-TCCAT-CGGTT-GCAATGGAGCTGGT-TAAAGAAGCAGAT
1 CTTGCCTTCC-TGC-GTTAACAGCGAAGCAGATCGAAA-AA-AAG-C
41377622 CTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGC
1 CTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAA-AAAGC
* * * * * * *
41377665 CTTGCC-TCCATTG-GTT-GCAGTGGAGCTGGT-TAAAAAAGCAGAT
1 CTTGCCTTCC--TGCGTTAACAGCGAAGCAGATCGAAAAAA--AG-C
* *
41377708 CTTGCCTTCCTGCCTTAACAGCGAAGCAGATCGAAAACAAAAC
1 CTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAA-AAAGC
41377751 CTT
1 CTT
41377754 ACCTCTCTCG
Statistics
Matches: 243, Mismatches: 60, Indels: 88
0.62 0.15 0.23
Matches are distributed among these distances:
40 4 0.02
41 16 0.07
42 58 0.24
43 88 0.36
44 57 0.23
45 16 0.07
46 4 0.02
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (42 bp):
CTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAAAAAGC
Found at i:41378370 original size:129 final size:129
Alignment explanation
Indices: 41378178--41378419 Score: 378
Period size: 129 Copynumber: 1.9 Consensus size: 129
41378168 TAGATCACAT
41378178 CAGATTGAAGCCAAAAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTT
1 CAGATTGAAGCCAAAAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTT
* * * * *
41378243 ATTTTTCTGAAGTTACAGTAGAGTAGATCGTATCAGGTCTTATCTCCCTGAGATTACAGCAGAG
66 ATCTCTCTAAAGTTACACTAGAGTAGATCGTATCAGGTCTTACCTCCCTGAGATTACAGCAGAG
* ** *
41378307 CAGATTGAAGCTAGTAATCCTATCTCCTTGAGATTACAGTGGAGCGGATTAAAAT-AAGTGATCT
1 CAGATTGAAGCCAAAAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAG-GATCT
*
41378371 TATCTCTCTAAAGTTACACTAGAGTATATCGTATCAGGTCTTACCTCCC
65 TATCTCTCTAAAGTTACACTAGAGTAGATCGTATCAGGTCTTACCTCCC
41378420 AGGCGGTCCA
Statistics
Matches: 102, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
128 3 0.03
129 99 0.97
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Consensus pattern (129 bp):
CAGATTGAAGCCAAAAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTT
ATCTCTCTAAAGTTACACTAGAGTAGATCGTATCAGGTCTTACCTCCCTGAGATTACAGCAGAG
Found at i:41378375 original size:44 final size:43
Alignment explanation
Indices: 41378198--41378376 Score: 123
Period size: 44 Copynumber: 4.1 Consensus size: 43
41378188 CCAAAAATCC
* *
41378198 TATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCT
1 TATCTCCCTGAGATTACAGTAGAGCAGATTAAAAT-AAGGATCT
* ** * *** *
41378242 TATTTTTCTGA-AGTTACAGTAGAGTAGA-TCGTATCAGG-TCT
1 TATCTCCCTGAGA-TTACAGTAGAGCAGATTAAAATAAGGATCT
* ** * *
41378283 TATCTCCCTGAGATTACAGCAGAGCAGATTGAAGCT-AGTAATCC
1 TATCTCCCTGAGATTACAGTAGAGCAGATT-AAAATAAG-GATCT
* * *
41378327 TATCTCCTTGAGATTACAGTGGAGCGGATTAAAATAAGTGATCT
1 TATCTCCCTGAGATTACAGTAGAGCAGATTAAAATAAG-GATCT
41378371 TATCTC
1 TATCTC
41378377 TCTAAAGTTA
Statistics
Matches: 99, Mismatches: 29, Indels: 14
0.70 0.20 0.10
Matches are distributed among these distances:
41 24 0.24
42 7 0.07
43 8 0.08
44 60 0.61
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (43 bp):
TATCTCCCTGAGATTACAGTAGAGCAGATTAAAATAAGGATCT
Found at i:41378647 original size:44 final size:44
Alignment explanation
Indices: 41378541--41378626 Score: 118
Period size: 44 Copynumber: 2.0 Consensus size: 44
41378531 GATTAAAACC
*
41378541 ACAAACCTTATCTCTCTGAAGTTGCAGTAGAGTAGGTTGAAGTA
1 ACAAACCTTATCTCCCTGAAGTTGCAGTAGAGTAGGTTGAAGTA
* * * * *
41378585 ACAAACCTTACCCCCCTGAAGTTGCATTGGGGTAGGTTGAAG
1 ACAAACCTTATCTCCCTGAAGTTGCAGTAGAGTAGGTTGAAG
41378627 ATACAGGTCT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (44 bp):
ACAAACCTTATCTCCCTGAAGTTGCAGTAGAGTAGGTTGAAGTA
Found at i:41380177 original size:2 final size:2
Alignment explanation
Indices: 41380172--41380198 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
41380162 TGTCTCTTAT
41380172 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 T
41380199 CTTTATAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41381771 original size:9 final size:9
Alignment explanation
Indices: 41381757--41381787 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
41381747 GTTAAACGAA
41381757 TCGAGTTAT
1 TCGAGTTAT
*
41381766 TCGAGTTAA
1 TCGAGTTAT
41381775 TCGAGTTAT
1 TCGAGTTAT
41381784 TCGA
1 TCGA
41381788 ATCAACTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:41381857 original size:9 final size:9
Alignment explanation
Indices: 41381840--41381876 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
41381830 TGAGTTTTCG
41381840 AATTCGAAT
1 AATTCGAAT
*
41381849 AACTCGAAT
1 AATTCGAAT
41381858 AATTCGAAT
1 AATTCGAAT
41381867 AATTCGAAT
1 AATTCGAAT
41381876 A
1 A
41381877 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:41381983 original size:29 final size:29
Alignment explanation
Indices: 41381928--41381983 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
41381918 CCTTTTTACT
* *
41381928 TTTCCCTCAAAACTTTTACTCCTTCCCAC
1 TTTCCCCCAAAACTTTTACTCCCTCCCAC
41381957 TTTCCCCCAAAACTTTTA-TCCCCTCCC
1 TTTCCCCCAAAACTTTTACT-CCCTCCC
41381984 CTCCCAACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 1 0.04
29 23 0.96
ACGTcount: A:0.20, C:0.45, G:0.00, T:0.36
Consensus pattern (29 bp):
TTTCCCCCAAAACTTTTACTCCCTCCCAC
Found at i:41382510 original size:5 final size:5
Alignment explanation
Indices: 41382500--41382525 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
41382490 GAACAAATAT
41382500 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
41382526 ATTCTATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Found at i:41382625 original size:5 final size:5
Alignment explanation
Indices: 41382615--41382645 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
41382605 CTCGAAAATT
*
41382615 TTCGA TTCGA TTCGA TTAGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA T
41382646 CGAATGCTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:41384690 original size:2 final size:2
Alignment explanation
Indices: 41384683--41384723 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
41384673 CCGACTTTTA
41384683 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
41384724 ATGTGTGTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:41389836 original size:30 final size:31
Alignment explanation
Indices: 41389780--41389837 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
41389770 ATTATTGAAC
*
41389780 TATTCAAAAGTTTTCATTTAAGTCATTAAAT
1 TATTCAAAAGTTTTCATTTAAATCATTAAAT
*
41389811 TATTCAAAA-TTTTTATTTAAATCATTA
1 TATTCAAAAGTTTTCATTTAAATCATTA
41389838 GGCTGCTAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 16 0.64
31 9 0.36
ACGTcount: A:0.40, C:0.09, G:0.03, T:0.48
Consensus pattern (31 bp):
TATTCAAAAGTTTTCATTTAAATCATTAAAT
Found at i:41390495 original size:13 final size:14
Alignment explanation
Indices: 41390463--41390495 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
41390453 ATAAATTAAA
*
41390463 AAAATTAAATGTTG
1 AAAATTAAATATTG
41390477 AAAATTAAATATT-
1 AAAATTAAATATTG
41390490 AAAATT
1 AAAATT
41390496 TTCAGTATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (14 bp):
AAAATTAAATATTG
Found at i:41390837 original size:30 final size:31
Alignment explanation
Indices: 41390768--41390841 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
41390758 TGATTGAATA
*
41390768 ACAATCAAAGTTTCATGTATATATTTGAACC
1 ACAATCAAAGTTTCATGTATATAATTGAACC
* * *
41390799 ACAATCAAAGTTTTATGTGTATAATTGTACC
1 ACAATCAAAGTTTCATGTATATAATTGAACC
41390830 A-AATCAAAGTTT
1 ACAATCAAAGTTT
41390842 ATATATCAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 11 0.28
31 28 0.72
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (31 bp):
ACAATCAAAGTTTCATGTATATAATTGAACC
Found at i:41396515 original size:15 final size:15
Alignment explanation
Indices: 41396495--41396526 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
41396485 CATTTCACTA
*
41396495 TTATGTCTTTTATAT
1 TTATGTATTTTATAT
41396510 TTATGTATTTTATAT
1 TTATGTATTTTATAT
41396525 TT
1 TT
41396527 TGCATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.03, G:0.06, T:0.69
Consensus pattern (15 bp):
TTATGTATTTTATAT
Found at i:41398212 original size:26 final size:26
Alignment explanation
Indices: 41398142--41398214 Score: 78
Period size: 26 Copynumber: 2.7 Consensus size: 26
41398132 TTTTAGTAGT
41398142 TTAATATTAAATTTAATTTAATACTTATC
1 TTAATATTAAATTTAA---AATACTTATC
*
41398171 TTAATAGT-AATATTAAAATGA-TTATC
1 TTAATATTAAAT-TTAAAAT-ACTTATC
41398197 TTAATATTAAATTTAAAA
1 TTAATATTAAATTTAAAA
41398215 CATTCTATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
26 21 0.54
27 4 0.10
28 3 0.08
29 11 0.28
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.47
Consensus pattern (26 bp):
TTAATATTAAATTTAAAATACTTATC
Found at i:41400448 original size:26 final size:26
Alignment explanation
Indices: 41400412--41400484 Score: 85
Period size: 26 Copynumber: 2.8 Consensus size: 26
41400402 TATTTTCTTG
*
41400412 AAATTTTACCAGGGGTAAAATCG-TTA
1 AAATTTTACCAGGGGTAAAAT-GATCA
*
41400438 AAATTTTACCAAGGGTAAAATGATCA
1 AAATTTTACCAGGGGTAAAATGATCA
***
41400464 AAATTTTGTTAGGGGTAAAAT
1 AAATTTTACCAGGGGTAAAAT
41400485 AGGGATGAGA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
25 1 0.03
26 39 0.98
ACGTcount: A:0.41, C:0.08, G:0.19, T:0.32
Consensus pattern (26 bp):
AAATTTTACCAGGGGTAAAATGATCA
Found at i:41417324 original size:3 final size:3
Alignment explanation
Indices: 41417316--41417360 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
41417306 GTTTTCTTCC
41417316 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
41417361 GTTGTTTTAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:41427659 original size:17 final size:17
Alignment explanation
Indices: 41427637--41427671 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
41427627 AAATGGATCA
41427637 TGGTTTATCTTTAGTTC
1 TGGTTTATCTTTAGTTC
41427654 TGGTTTATCTTTAGTTC
1 TGGTTTATCTTTAGTTC
41427671 T
1 T
41427672 CAATTTGGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.17, T:0.60
Consensus pattern (17 bp):
TGGTTTATCTTTAGTTC
Found at i:41428446 original size:43 final size:43
Alignment explanation
Indices: 41428378--41428476 Score: 146
Period size: 43 Copynumber: 2.3 Consensus size: 43
41428368 TAGCTCTCTC
*
41428378 TTATAACTACCATTAGTGTGCCTTAATTGGACATTTAGCGTGG
1 TTATAACTACCATTAGTGTGCCTTAATTGGACATTTAACGTGG
* * *
41428421 TTATGATTACCATTAGTGTTG-CTTAATTGGACATTTAACGTTG
1 TTATAACTACCATTAGTG-TGCCTTAATTGGACATTTAACGTGG
41428464 TTATAACTACCAT
1 TTATAACTACCAT
41428477 CAAACTTTCC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
43 47 0.96
44 2 0.04
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.40
Consensus pattern (43 bp):
TTATAACTACCATTAGTGTGCCTTAATTGGACATTTAACGTGG
Found at i:41429080 original size:47 final size:47
Alignment explanation
Indices: 41429029--41429172 Score: 129
Period size: 47 Copynumber: 3.1 Consensus size: 47
41429019 ATTATTAAGA
*
41429029 ATTTTATGAAATTATATATCATTATTAAATTATATTTAATATAAATT
1 ATTTTATGAAATTATATATAATTATTAAATTATATTTAATATAAATT
* ** * * **
41429076 A-TTT-T-AAATTATACA-AATTCATATAAAAAAT-TTTATTATCAAGA
1 ATTTTATGAAATTATATATAATT-AT-TAAATTATATTTAATATAAATT
* *
41429120 ATTTTATGAAATTATATATTATTATTAATTTATATTTAATA-ATAATT
1 ATTTTATGAAATTATATATAATTATTAAATTATATTTAATATA-AATT
41429167 ATTTTA
1 ATTTTA
41429173 AATTATACAA
Statistics
Matches: 72, Mismatches: 17, Indels: 16
0.69 0.16 0.15
Matches are distributed among these distances:
43 3 0.04
44 21 0.29
45 10 0.14
46 9 0.12
47 26 0.36
48 3 0.04
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (47 bp):
ATTTTATGAAATTATATATAATTATTAAATTATATTTAATATAAATT
Found at i:41429137 original size:91 final size:91
Alignment explanation
Indices: 41428999--41429204 Score: 319
Period size: 91 Copynumber: 2.3 Consensus size: 91
41428989 TGGTTTTAGT
* *
41428999 AAATTCATAT-AAGAATATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATA
1 AAATTCATATAAAAAAT-TTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
41429063 TTTAAT-ATAAATTATTTTAAATTATAC
65 TTTAATAAT-AATTATTTTAAATTATAC
* *
41429090 AAATTCATATAAAAAATTTTATTATCAAGAATTTTATGAAATTATATATTATTATTAATTTATAT
1 AAATTCATATAAAAAATTTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATAT
41429155 TTAATAATAATTATTTTAAATTATAC
66 TTAATAATAATTATTTTAAATTATAC
*
41429181 AAATTCATAATACAAAA-TTTATTA
1 AAATTCAT-ATAAAAAATTTTATTA
41429205 GTAATAATTA
Statistics
Matches: 107, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
91 93 0.87
92 14 0.13
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (91 bp):
AAATTCATATAAAAAATTTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATAT
TTAATAATAATTATTTTAAATTATAC
Found at i:41429212 original size:47 final size:45
Alignment explanation
Indices: 41429072--41429217 Score: 122
Period size: 47 Copynumber: 3.2 Consensus size: 45
41429062 ATTTAATATA
*
41429072 AATTATTTTAAATTATACAAATTCATATAAAAAATTTTATTATCAAG
1 AATTATTTTAAATTATACAAATTCATATAAAAAA-TTTATTAT-AAT
* * ** *
41429119 AATT-TTATGAAATTAT--ATATT-AT-TATTAATTTATATTTAATAAT
1 AATTATT-TTAAATTATACAAATTCATATAAAAAATT-TA-TT-ATAAT
*
41429163 AATTATTTTAAATTATACAAATTCATAATACAAAATTTATTAGTAAT
1 AATTATTTTAAATTATACAAATTCAT-ATAAAAAATTTATTA-TAAT
41429210 AATTATTT
1 AATTATTT
41429218 NNNNNNNNNN
Statistics
Matches: 77, Mismatches: 11, Indels: 22
0.70 0.10 0.20
Matches are distributed among these distances:
42 2 0.03
43 6 0.08
44 18 0.23
45 8 0.10
46 7 0.09
47 28 0.36
48 2 0.03
49 6 0.08
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (45 bp):
AATTATTTTAAATTATACAAATTCATATAAAAAATTTATTATAAT
Done.