Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 7 of 208
Found at i:2565444 original size:18 final size:18
Alignment explanation
Indices: 2565417--2565509 Score: 150
Period size: 18 Copynumber: 5.2 Consensus size: 18
2565407 TACGACCGTT
2565417 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
2565435 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
2565453 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
* *
2565471 TACGGCACTATTCACATA
1 TACGGTACTATTCACGTA
*
2565489 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
2565507 TAC
1 TAC
2565510 AGTAGTTGGG
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:2565464 original size:36 final size:36
Alignment explanation
Indices: 2565417--2565509 Score: 168
Period size: 36 Copynumber: 2.6 Consensus size: 36
2565407 TACGACCGTT
*
2565417 TACGGTACTATTCACGTATACGGCACTATTCACGTA
1 TACGGTACTATTCACGTATACGGCACTATTCACATA
2565453 TACGGTACTATTCACGTATACGGCACTATTCACATA
1 TACGGTACTATTCACGTATACGGCACTATTCACATA
*
2565489 TACGGTACTGTTCACGTATAC
1 TACGGTACTATTCACGTATAC
2565510 AGTAGTTGGG
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 55 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (36 bp):
TACGGTACTATTCACGTATACGGCACTATTCACATA
Found at i:2587601 original size:71 final size:71
Alignment explanation
Indices: 2587511--2587744 Score: 346
Period size: 72 Copynumber: 3.3 Consensus size: 71
2587501 AAAATCATAT
* *
2587511 ATAAACAACTATTGATAAAACTA-ATTTAGTATAAATAAGTAGAACATAAATTCAATATCCAAAG
1 ATAAACAACTATTGATAAAACTAGATTTA-CATAAATAAGTAGAACATAAATTCAATATCCAAAA
2587575 ACCAAAC
65 ACCAAAC
* * *
2587582 ATAAACAACTATTAATAAAACTATAGTATACATAAATAAGTAGAACATAAATTCAATATCCAAAA
1 ATAAACAACTATTGATAAAACTAGA-TTTACATAAATAAGTAGAACATAAATTCAATATCCAAAA
2587647 ACCAAAC
65 ACCAAAC
* *
2587654 ATAAACAACCATTGATAAAACTAGATTACACATAAATAAGTAGAACATAAATTC-ATATCCAAAA
1 ATAAACAACTATTGATAAAACTAGATT-TACATAAATAAGTAGAACATAAATTCAATATCCAAAA
2587718 ACCAAAC
65 ACCAAAC
* *
2587725 ATAAATAACTACTGATAAAA
1 ATAAACAACTATTGATAAAA
2587745 AACTAGTTTA
Statistics
Matches: 148, Mismatches: 12, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
71 57 0.39
72 88 0.59
73 3 0.02
ACGTcount: A:0.56, C:0.15, G:0.06, T:0.24
Consensus pattern (71 bp):
ATAAACAACTATTGATAAAACTAGATTTACATAAATAAGTAGAACATAAATTCAATATCCAAAAA
CCAAAC
Found at i:2617711 original size:41 final size:40
Alignment explanation
Indices: 2617653--2617850 Score: 215
Period size: 41 Copynumber: 4.8 Consensus size: 40
2617643 TTAAACAGAT
* * * *
2617653 TCACCGGCATTTTGCCTGCTAGGCTTAAAGCCTG-ATTCAGTA
1 TCACCGGCA-TTAGCCTGCTAGACTTAAAGTCTGAAAT--GTA
* *
2617695 -CACCGGCACTTAGCCTGCTAGACATATAGTCTGAAATGTA
1 TCACCGGCA-TTAGCCTGCTAGACTTAAAGTCTGAAATGTA
2617735 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAATGTA
1 TCACCGGCATT-AGCCTGCTAGACTTAAAGTCTGAAATGTA
2617776 TCACCGGCATTTAGCCTGCTAGACTTAAAGTCTG-AAT-TA
1 TCACCGGCA-TTAGCCTGCTAGACTTAAAGTCTGAAATGTA
* *
2617815 CTTCACCGGCATTAAGCCTGCTAGACGTAACGTCTG
1 --TCACCGGCATT-AGCCTGCTAGACTTAAAGTCTG
2617851 TATTATATTC
Statistics
Matches: 138, Mismatches: 11, Indels: 15
0.84 0.07 0.09
Matches are distributed among these distances:
39 2 0.01
40 10 0.07
41 122 0.88
42 4 0.03
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (40 bp):
TCACCGGCATTAGCCTGCTAGACTTAAAGTCTGAAATGTA
Found at i:2617790 original size:82 final size:80
Alignment explanation
Indices: 2617653--2617850 Score: 238
Period size: 82 Copynumber: 2.4 Consensus size: 80
2617643 TTAAACAGAT
** * * *
2617653 TCACCGGCATTTTGCCTGCTAGGCTTAAAGCCTGATTCAGTACACCGGCACTTAGCCTGCTAGAC
1 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAT-AGTACACCGGCACTTAGCCTGCTAGAC
*
2617718 ATATAGTCTGAAATGTA-
65 ATAAAGTCTG-AAT-TAC
*
2617735 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAA-ATGTATCACCGGCATTTAGCCTGCTAGA
1 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAATA-GTA-CACCGGCACTTAGCCTGCTAGA
*
2617799 CTTAAAGTCTGAATTAC
64 CATAAAGTCTGAATTAC
* *
2617816 TTCACCGGCATTAAGCCTGCTAGACGTAACGTCTG
1 -TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTG
2617851 TATTATATTC
Statistics
Matches: 102, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
80 3 0.03
81 6 0.06
82 93 0.91
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (80 bp):
TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAATAGTACACCGGCACTTAGCCTGCTAGACA
TAAAGTCTGAATTAC
Found at i:2637561 original size:18 final size:18
Alignment explanation
Indices: 2637538--2637574 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
2637528 TAAATAAATG
2637538 TTAGTTATTTTCTTTATC
1 TTAGTTATTTTCTTTATC
2637556 TTAGTTATTTTCTTTATC
1 TTAGTTATTTTCTTTATC
2637574 T
1 T
2637575 CTAAATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.11, G:0.05, T:0.68
Consensus pattern (18 bp):
TTAGTTATTTTCTTTATC
Found at i:2643441 original size:413 final size:413
Alignment explanation
Indices: 2642674--2643500 Score: 1654
Period size: 413 Copynumber: 2.0 Consensus size: 413
2642664 GACACCTTCC
2642674 CCATTGGGCCATAATCGTTTTCCTAATGTTCATGTGGATTGGCCAGTTGTAACCATATTGTTCAC
1 CCATTGGGCCATAATCGTTTTCCTAATGTTCATGTGGATTGGCCAGTTGTAACCATATTGTTCAC
2642739 ATAACACATGAGAGCTAAAACGAGTGAGAAGTTCCAGAAAATTTAACATAAATCCAAACACTCAT
66 ATAACACATGAGAGCTAAAACGAGTGAGAAGTTCCAGAAAATTTAACATAAATCCAAACACTCAT
2642804 CACTTGAATCTATTTATAAAGCTCTAAAATAAAGAGACATGCTTAAGAATCTAAATAACACAAAC
131 CACTTGAATCTATTTATAAAGCTCTAAAATAAAGAGACATGCTTAAGAATCTAAATAACACAAAC
2642869 CAAGTATTTTTAATGTCACAATTGTAAAACTAGTCAAAACTCTGATGAAACTTGTAGGAGAACAA
196 CAAGTATTTTTAATGTCACAATTGTAAAACTAGTCAAAACTCTGATGAAACTTGTAGGAGAACAA
2642934 AATGCAAGTTTTAAGTAAACAAGAGACAGACAAAAATTATTCCTCGTCGTCATCAATGACCTTGG
261 AATGCAAGTTTTAAGTAAACAAGAGACAGACAAAAATTATTCCTCGTCGTCATCAATGACCTTGG
2642999 TGCCTAAACCCTTCAATCCTTCAGCTGGGATTTCAGCAACCGTTACTAGAGAGTACAGCTCCTCC
326 TGCCTAAACCCTTCAATCCTTCAGCTGGGATTTCAGCAACCGTTACTAGAGAGTACAGCTCCTCC
2643064 TTGGCATCTTCATCATCATTTCT
391 TTGGCATCTTCATCATCATTTCT
2643087 CCATTGGGCCATAATCGTTTTCCTAATGTTCATGTGGATTGGCCAGTTGTAACCATATTGTTCAC
1 CCATTGGGCCATAATCGTTTTCCTAATGTTCATGTGGATTGGCCAGTTGTAACCATATTGTTCAC
2643152 ATAACACATGAGAGCTAAAACGAGTGAGAAGTTCCAGAAAATTTAACATAAATCCAAACACTCAT
66 ATAACACATGAGAGCTAAAACGAGTGAGAAGTTCCAGAAAATTTAACATAAATCCAAACACTCAT
2643217 CACTTGAATCTATTTATAAAGCTCTAAAATAAAGAGACATGCTTAAGAATCTAAATAACACAAAC
131 CACTTGAATCTATTTATAAAGCTCTAAAATAAAGAGACATGCTTAAGAATCTAAATAACACAAAC
2643282 CAAGTATTTTTAATGTCACAATTGTAAAACTAGTCAAAACTCTGATGAAACTTGTAGGAGAACAA
196 CAAGTATTTTTAATGTCACAATTGTAAAACTAGTCAAAACTCTGATGAAACTTGTAGGAGAACAA
2643347 AATGCAAGTTTTAAGTAAACAAGAGACAGACAAAAATTATTCCTCGTCGTCATCAATGACCTTGG
261 AATGCAAGTTTTAAGTAAACAAGAGACAGACAAAAATTATTCCTCGTCGTCATCAATGACCTTGG
2643412 TGCCTAAACCCTTCAATCCTTCAGCTGGGATTTCAGCAACCGTTACTAGAGAGTACAGCTCCTCC
326 TGCCTAAACCCTTCAATCCTTCAGCTGGGATTTCAGCAACCGTTACTAGAGAGTACAGCTCCTCC
2643477 TTGGCATCTTCATCATCATTTCT
391 TTGGCATCTTCATCATCATTTCT
2643500 C
1 C
2643501 TTGCGAGCGA
Statistics
Matches: 414, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
413 414 1.00
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.29
Consensus pattern (413 bp):
CCATTGGGCCATAATCGTTTTCCTAATGTTCATGTGGATTGGCCAGTTGTAACCATATTGTTCAC
ATAACACATGAGAGCTAAAACGAGTGAGAAGTTCCAGAAAATTTAACATAAATCCAAACACTCAT
CACTTGAATCTATTTATAAAGCTCTAAAATAAAGAGACATGCTTAAGAATCTAAATAACACAAAC
CAAGTATTTTTAATGTCACAATTGTAAAACTAGTCAAAACTCTGATGAAACTTGTAGGAGAACAA
AATGCAAGTTTTAAGTAAACAAGAGACAGACAAAAATTATTCCTCGTCGTCATCAATGACCTTGG
TGCCTAAACCCTTCAATCCTTCAGCTGGGATTTCAGCAACCGTTACTAGAGAGTACAGCTCCTCC
TTGGCATCTTCATCATCATTTCT
Found at i:2645274 original size:16 final size:18
Alignment explanation
Indices: 2645245--2645280 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
2645235 CAGAATATAT
2645245 TTATTTTAATAAATATTA
1 TTATTTTAATAAATATTA
2645263 TTATTTT-A-AAATATTA
1 TTATTTTAATAAATATTA
2645279 TT
1 TT
2645281 TTACACCCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
17 1 0.06
18 7 0.39
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTATTTTAATAAATATTA
Found at i:2680150 original size:11 final size:11
Alignment explanation
Indices: 2680134--2680159 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2680124 TTTTACCATA
2680134 AATTATTTTGT
1 AATTATTTTGT
2680145 AATTATTTTGT
1 AATTATTTTGT
2680156 AATT
1 AATT
2680160 TTTCTTTTTT
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:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (11 bp):
AATTATTTTGT
Found at i:2682956 original size:23 final size:23
Alignment explanation
Indices: 2682924--2682967 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2682914 ACTACCATTT
2682924 TCTAAATAAAATAATAATAAATA
1 TCTAAATAAAATAATAATAAATA
* *
2682947 TCTAAGTAAAATATTAATAAA
1 TCTAAATAAAATAATAATAAA
2682968 ATAACATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (23 bp):
TCTAAATAAAATAATAATAAATA
Found at i:2682960 original size:13 final size:11
Alignment explanation
Indices: 2682928--2682970 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
2682918 CCATTTTCTA
*
2682928 AATAAAATAAT
1 AATAAAATATT
2682939 AAT-AAATATCT
1 AATAAAATAT-T
2682950 AAGTAAAATATT
1 AA-TAAAATATT
2682962 AATAAAATA
1 AATAAAATA
2682971 ACATTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 4 0.14
13 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (11 bp):
AATAAAATATT
Found at i:2684073 original size:29 final size:30
Alignment explanation
Indices: 2684016--2684087 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 30
2684006 AAAAATAAAA
* *
2684016 ATTATATATAAATTTTGATTTAATGTGCAAT
1 ATTATATATAAACTTTGATTT-ATATGCAAT
2684047 ATTATATATAAACTTTGATTT-TATGCAAT
1 ATTATATATAAACTTTGATTTATATGCAAT
* *
2684076 TTTATACATAAA
1 ATTATATATAAA
2684088 ATATTAATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 17 0.46
31 20 0.54
ACGTcount: A:0.40, C:0.06, G:0.07, T:0.47
Consensus pattern (30 bp):
ATTATATATAAACTTTGATTTATATGCAAT
Found at i:2684254 original size:29 final size:27
Alignment explanation
Indices: 2684229--2684280 Score: 76
Period size: 23 Copynumber: 2.1 Consensus size: 27
2684219 TAAAAATATG
2684229 TATAAACCACAATTAAAATTTC--A-A
1 TATAAACCACAATTAAAATTTCAAATA
2684253 -ATAAACCACAATTAAAATTTCAAATA
1 TATAAACCACAATTAAAATTTCAAATA
2684279 TA
1 TA
2684281 AAAATTATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
23 21 0.88
25 1 0.04
26 1 0.04
27 1 0.04
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.29
Consensus pattern (27 bp):
TATAAACCACAATTAAAATTTCAAATA
Found at i:2696988 original size:22 final size:24
Alignment explanation
Indices: 2696950--2696999 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
2696940 ATAGATAATG
*
2696950 ATAATCATTATTTTT-AAAATTAA
1 ATAATCAATATTTTTAAAAATTAA
*
2696973 ATAATCAAT-TTTTTAAAAATTAG
1 ATAATCAATATTTTTAAAAATTAA
2696996 ATAA
1 ATAA
2697000 ATATTTAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (24 bp):
ATAATCAATATTTTTAAAAATTAA
Found at i:2697132 original size:17 final size:18
Alignment explanation
Indices: 2697112--2697146 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
2697102 ATCATAAATC
2697112 AATCATAATTA-TCTTTT
1 AATCATAATTACTCTTTT
2697129 AATCATAATTACTCTTTT
1 AATCATAATTACTCTTTT
2697147 GTAACTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.51
Consensus pattern (18 bp):
AATCATAATTACTCTTTT
Found at i:2697245 original size:16 final size:17
Alignment explanation
Indices: 2697213--2697245 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2697203 GGGATGTAGA
*
2697213 CTTTTTTCTTCTTATAG
1 CTTTGTTCTTCTTATAG
2697230 CTTTGTTCTT-TTATAG
1 CTTTGTTCTTCTTATAG
2697246 AACTATATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.12, C:0.15, G:0.09, T:0.64
Consensus pattern (17 bp):
CTTTGTTCTTCTTATAG
Found at i:2703759 original size:30 final size:30
Alignment explanation
Indices: 2703723--2703784 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
2703713 ATCCTGCATG
*
2703723 ATAGAGGTGGCATTTAATGAAATATATCGA
1 ATAGAGGTGGCATTTAATGAAATAAATCGA
*
2703753 ATAGAGGTGGCGTTTAATGAAATAAATCGA
1 ATAGAGGTGGCATTTAATGAAATAAATCGA
2703783 AT
1 AT
2703785 GAAAGAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.40, C:0.06, G:0.24, T:0.29
Consensus pattern (30 bp):
ATAGAGGTGGCATTTAATGAAATAAATCGA
Found at i:2717757 original size:29 final size:29
Alignment explanation
Indices: 2717715--2717773 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
2717705 CCGAGATGTT
2717715 AGAATTTCAAGTTAATTCTTTTGGATACA
1 AGAATTTCAAGTTAATTCTTTTGGATACA
2717744 AGAATTTCAAGTTAATTCTTTTGGATACA
1 AGAATTTCAAGTTAATTCTTTTGGATACA
2717773 A
1 A
2717774 ATCAATACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.41
Consensus pattern (29 bp):
AGAATTTCAAGTTAATTCTTTTGGATACA
Found at i:2722153 original size:10 final size:12
Alignment explanation
Indices: 2722134--2722165 Score: 50
Period size: 10 Copynumber: 2.8 Consensus size: 12
2722124 CCATTCAATT
2722134 TAATTATTTAAA
1 TAATTATTTAAA
2722146 -AA-TATTTAAA
1 TAATTATTTAAA
2722156 TAATTATTTA
1 TAATTATTTA
2722166 TTTTTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
10 8 0.44
11 4 0.22
12 6 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TAATTATTTAAA
Found at i:2738879 original size:3 final size:3
Alignment explanation
Indices: 2738871--2738898 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2738861 TGTTCTCTGT
2738871 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
2738899 TAAAAGAGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:2743722 original size:19 final size:20
Alignment explanation
Indices: 2743689--2743743 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
2743679 TTTTAAATAC
* * *
2743689 AAATTTTTTTAAATTTCTAT
1 AAATTATTTTGAATTTCTAA
*
2743709 AAA-TATTTTGAATTTTTAA
1 AAATTATTTTGAATTTCTAA
2743728 AAATTATTTTGAATTT
1 AAATTATTTTGAATTT
2743744 TTTATAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (20 bp):
AAATTATTTTGAATTTCTAA
Found at i:2743735 original size:20 final size:20
Alignment explanation
Indices: 2743689--2743745 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
2743679 TTTTAAATAC
* * * *
2743689 AAATTTTTTTAAATTTCTAT
1 AAATTATTTTGAATTTTTAA
2743709 AAA-TATTTTGAATTTTTAA
1 AAATTATTTTGAATTTTTAA
2743728 AAATTATTTTGAATTTTT
1 AAATTATTTTGAATTTTT
2743746 TATAATTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.58
Consensus pattern (20 bp):
AAATTATTTTGAATTTTTAA
Found at i:2743752 original size:20 final size:20
Alignment explanation
Indices: 2743706--2743752 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
2743696 TTTAAATTTC
*
2743706 TATAAATATTTTGAATTTTT
1 TATAATTATTTTGAATTTTT
* *
2743726 AAAAATTATTTTGAATTTTT
1 TATAATTATTTTGAATTTTT
2743746 TATAATT
1 TATAATT
2743753 TTTGTTTAGA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.57
Consensus pattern (20 bp):
TATAATTATTTTGAATTTTT
Found at i:2771045 original size:25 final size:25
Alignment explanation
Indices: 2771017--2771065 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
2771007 AATAAAGTTG
2771017 TAATTAAATT-GAATAAATATAATAT
1 TAATTAAATTAG-ATAAATATAATAT
* *
2771042 TAATTTAATTAGATGAATATAATA
1 TAATTAAATTAGATAAATATAATA
2771066 AAATTATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 20 0.95
26 1 0.05
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (25 bp):
TAATTAAATTAGATAAATATAATAT
Found at i:2775111 original size:63 final size:63
Alignment explanation
Indices: 2775033--2775158 Score: 252
Period size: 63 Copynumber: 2.0 Consensus size: 63
2775023 CACTTAAAAA
2775033 GAAAATTATAGTGGAGATTGAAGGAAATTCACCTTGTTGGACAAAGGGTCGTACAATGGTAGC
1 GAAAATTATAGTGGAGATTGAAGGAAATTCACCTTGTTGGACAAAGGGTCGTACAATGGTAGC
2775096 GAAAATTATAGTGGAGATTGAAGGAAATTCACCTTGTTGGACAAAGGGTCGTACAATGGTAGC
1 GAAAATTATAGTGGAGATTGAAGGAAATTCACCTTGTTGGACAAAGGGTCGTACAATGGTAGC
2775159 AGTGAGGTTA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.35, C:0.11, G:0.29, T:0.25
Consensus pattern (63 bp):
GAAAATTATAGTGGAGATTGAAGGAAATTCACCTTGTTGGACAAAGGGTCGTACAATGGTAGC
Found at i:2780544 original size:16 final size:17
Alignment explanation
Indices: 2780507--2780549 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
2780497 ATAATTAAGG
*
2780507 ATATTTTAAAAAGAATA
1 ATATTTTTAAAAGAATA
2780524 A-ATTTTTAAAAGAA-A
1 ATATTTTTAAAAGAATA
2780539 ATATTTATTAA
1 ATATTT-TTAA
2780550 TTCATTTCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 2 0.09
16 16 0.70
17 5 0.22
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (17 bp):
ATATTTTTAAAAGAATA
Found at i:2784381 original size:26 final size:26
Alignment explanation
Indices: 2784350--2784411 Score: 115
Period size: 26 Copynumber: 2.4 Consensus size: 26
2784340 ATAAAAAATA
*
2784350 ATCAAAATCTTATAATTTTTTTATTT
1 ATCAAAATATTATAATTTTTTTATTT
2784376 ATCAAAATATTATAATTTTTTTATTT
1 ATCAAAATATTATAATTTTTTTATTT
2784402 ATCAAAATAT
1 ATCAAAATAT
2784412 ACTAAAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.53
Consensus pattern (26 bp):
ATCAAAATATTATAATTTTTTTATTT
Found at i:2785060 original size:23 final size:23
Alignment explanation
Indices: 2785034--2785105 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 23
2785024 ACTCTATTTT
2785034 AATTTAATAAACTATTCTCATCA
1 AATTTAATAAACTATTCTCATCA
*
2785057 AATTACTTAATAACTCTATT-T--T--
1 AA-T--TTAATAA-ACTATTCTCATCA
2785079 AATTTAATAAACTATTCTCATCA
1 AATTTAATAAACTATTCTCATCA
2785102 AATT
1 AATT
2785106 ACCAAAATAG
Statistics
Matches: 38, Mismatches: 2, Indels: 18
0.66 0.03 0.31
Matches are distributed among these distances:
18 5 0.13
19 8 0.21
21 2 0.05
22 2 0.05
23 6 0.16
24 2 0.05
26 8 0.21
27 5 0.13
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.43
Consensus pattern (23 bp):
AATTTAATAAACTATTCTCATCA
Found at i:2785068 original size:45 final size:45
Alignment explanation
Indices: 2785019--2785107 Score: 178
Period size: 45 Copynumber: 2.0 Consensus size: 45
2785009 TCTAATTAAG
2785019 TAATAACTCTATTTTAATTTAATAAACTATTCTCATCAAATTACT
1 TAATAACTCTATTTTAATTTAATAAACTATTCTCATCAAATTACT
2785064 TAATAACTCTATTTTAATTTAATAAACTATTCTCATCAAATTAC
1 TAATAACTCTATTTTAATTTAATAAACTATTCTCATCAAATTAC
2785108 CAAAATAGAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (45 bp):
TAATAACTCTATTTTAATTTAATAAACTATTCTCATCAAATTACT
Found at i:2785133 original size:15 final size:15
Alignment explanation
Indices: 2785113--2785162 Score: 64
Period size: 15 Copynumber: 3.1 Consensus size: 15
2785103 ATTACCAAAA
2785113 TAGAGTTTATTAAAT
1 TAGAGTTTATTAAAT
2785128 TAGAGTTTATTAAAT
1 TAGAGTTTATTAAAT
*
2785143 GAGAATAGTTTATTAAAT
1 TAG---AGTTTATTAAAT
2785161 TA
1 TA
2785163 AAATAGAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 17 0.57
18 13 0.43
ACGTcount: A:0.42, C:0.00, G:0.14, T:0.44
Consensus pattern (15 bp):
TAGAGTTTATTAAAT
Found at i:2785167 original size:18 final size:18
Alignment explanation
Indices: 2785131--2785168 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2785121 ATTAAATTAG
*
2785131 AGTTTATTAAATGAGAAT
1 AGTTTATTAAATGAAAAT
*
2785149 AGTTTATTAAATTAAAAT
1 AGTTTATTAAATGAAAAT
2785167 AG
1 AG
2785169 AGTTATTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.39
Consensus pattern (18 bp):
AGTTTATTAAATGAAAAT
Found at i:2785455 original size:27 final size:26
Alignment explanation
Indices: 2785403--2785462 Score: 93
Period size: 27 Copynumber: 2.3 Consensus size: 26
2785393 TTTATTTTGT
*
2785403 ATATTTTGGTAAATAAAAAATTTATA
1 ATATTTTGGTAAATAAAAAAGTTATA
*
2785429 TTATTTTGGTAAATAAAAAAAGTTATA
1 ATATTTTGGTAAAT-AAAAAAGTTATA
2785456 ATATTTT
1 ATATTTT
2785463 AGTTATTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 13 0.43
27 17 0.57
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (26 bp):
ATATTTTGGTAAATAAAAAAGTTATA
Found at i:2787912 original size:16 final size:17
Alignment explanation
Indices: 2787880--2787917 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
2787870 AATATTTTTG
**
2787880 TAATAAAATATCCTAAA
1 TAATAAAATATAATAAA
2787897 -AATAAAATATAATAAA
1 TAATAAAATATAATAAA
2787913 TAATA
1 TAATA
2787918 TTTTTACTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (17 bp):
TAATAAAATATAATAAA
Found at i:2789914 original size:15 final size:15
Alignment explanation
Indices: 2789894--2789943 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
2789884 TTCTTCTTCT
2789894 TCATCGTCATCGTCA
1 TCATCGTCATCGTCA
* *
2789909 TCATCGTCATCCTCC
1 TCATCGTCATCGTCA
*
2789924 TCATCTTCATCGTCA
1 TCATCGTCATCGTCA
2789939 TCATC
1 TCATC
2789944 TTCCTCAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.18, C:0.38, G:0.08, T:0.36
Consensus pattern (15 bp):
TCATCGTCATCGTCA
Found at i:2789944 original size:15 final size:15
Alignment explanation
Indices: 2789894--2789973 Score: 72
Period size: 15 Copynumber: 5.3 Consensus size: 15
2789884 TTCTTCTTCT
* *
2789894 TCATCGTCATCGTCA
1 TCATCTTCATCCTCA
* *
2789909 TCATCGTCATCCTCC
1 TCATCTTCATCCTCA
*
2789924 TCATCTTCATCGTCA
1 TCATCTTCATCCTCA
* * *
2789939 TCATCTTCCTCAAT-T
1 TCATCTTCATC-CTCA
2789954 TCATCTTCATCCTCA
1 TCATCTTCATCCTCA
2789969 TCATC
1 TCATC
2789974 CAACTCAAGC
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
14 1 0.02
15 50 0.96
16 1 0.02
ACGTcount: A:0.19, C:0.38, G:0.05, T:0.39
Consensus pattern (15 bp):
TCATCTTCATCCTCA
Found at i:2789956 original size:24 final size:24
Alignment explanation
Indices: 2789900--2789964 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
2789890 TTCTTCATCG
* *
2789900 TCATCGTCATCATCGTCATCCTCC
1 TCATCTTCATCATCATCATCCTCC
* *
2789924 TCATCTTCATCGTCATCATCTTCC
1 TCATCTTCATCATCATCATCCTCC
*
2789948 TCAAT-TTCATCTTCATC
1 TC-ATCTTCATCATCATC
2789965 CTCATCATCC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
24 33 0.94
25 2 0.06
ACGTcount: A:0.18, C:0.37, G:0.05, T:0.40
Consensus pattern (24 bp):
TCATCTTCATCATCATCATCCTCC
Found at i:2789958 original size:30 final size:30
Alignment explanation
Indices: 2789891--2789973 Score: 96
Period size: 30 Copynumber: 2.8 Consensus size: 30
2789881 TTCTTCTTCT
* *
2789891 TCTTCATCGTCATCGTCATCATCGTCATCC
1 TCTTCATCTTCATCGTCATCATCGTCATCA
* * *
2789921 TCCTCATCTTCATCGTCATCATCTTCCTCAA
1 TCTTCATCTTCATCGTCATCATCGTCATC-A
*
2789952 T-TTCATCTTCATCCTCATCATC
1 TCTTCATCTTCATCGTCATCATC
2789974 CAACTCAAGC
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 44 0.98
31 1 0.02
ACGTcount: A:0.18, C:0.37, G:0.05, T:0.40
Consensus pattern (30 bp):
TCTTCATCTTCATCGTCATCATCGTCATCA
Found at i:2789988 original size:30 final size:30
Alignment explanation
Indices: 2789923--2789989 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
2789913 CGTCATCCTC
* *** *
2789923 CTCATCTTCATCGTCATCATCTTCCTCAAT
1 CTCATCTTCATCCTCATCATCCAACTCAAG
*
2789953 TTCATCTTCATCCTCATCATCCAACTCAAG
1 CTCATCTTCATCCTCATCATCCAACTCAAG
2789983 CTCATCT
1 CTCATCT
2789990 CCCTGAATAG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.22, C:0.37, G:0.03, T:0.37
Consensus pattern (30 bp):
CTCATCTTCATCCTCATCATCCAACTCAAG
Found at i:2797527 original size:30 final size:30
Alignment explanation
Indices: 2797486--2797546 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
2797476 GATATACTCT
2797486 TAGATGATGCTGTAGTATCAGAAAAAAAGG
1 TAGATGATGCTGTAGTATCAGAAAAAAAGG
* * *
2797516 TAGATGGTGCTGTGGTATCAGGAAAAAAGG
1 TAGATGATGCTGTAGTATCAGAAAAAAAGG
2797546 T
1 T
2797547 GGAGGAGACG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.38, C:0.07, G:0.31, T:0.25
Consensus pattern (30 bp):
TAGATGATGCTGTAGTATCAGAAAAAAAGG
Found at i:2811764 original size:89 final size:89
Alignment explanation
Indices: 2811609--2811784 Score: 271
Period size: 89 Copynumber: 2.0 Consensus size: 89
2811599 ATTGATGTCA
* * *
2811609 CCGGACATATTAATAACACCTAAATTTATTGTAAAAGAAAATATTATTCATAAAAATAATCTACA
1 CCGGACATATTAATAACACCTAAATTTATTATAAAAGAAAATATTATTCACAAAAATAATCCACA
*
2811674 GTATACTTTATTTTCGTAATTACT
66 GTATACTTCATTTTCGTAATTACT
* * * * *
2811698 CCGGACTTATTAGTGACACCTAAATTTATTATAAAATAAAATATTATTTACAAAAATAATCCACA
1 CCGGACATATTAATAACACCTAAATTTATTATAAAAGAAAATATTATTCACAAAAATAATCCACA
2811763 GTATACTTCATTTTCGTAATTA
66 GTATACTTCATTTTCGTAATTA
2811785 TTCTTTTTAT
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
89 78 1.00
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (89 bp):
CCGGACATATTAATAACACCTAAATTTATTATAAAAGAAAATATTATTCACAAAAATAATCCACA
GTATACTTCATTTTCGTAATTACT
Found at i:2812155 original size:23 final size:23
Alignment explanation
Indices: 2812112--2812156 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
2812102 TGAAACTGTC
*
2812112 ATTTTCAAAAATTAATATTTTTT
1 ATTTTCAAAAATGAATATTTTTT
*
2812135 ATTTT-AAAAATG-ACATTTTTT
1 ATTTTCAAAAATGAATATTTTTT
2812156 A
1 A
2812157 AAATATTAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 9 0.45
22 6 0.30
23 5 0.25
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (23 bp):
ATTTTCAAAAATGAATATTTTTT
Found at i:2820227 original size:20 final size:21
Alignment explanation
Indices: 2820202--2820255 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
2820192 TTTACTCAAA
2820202 CTAATTTTTTATTAAAA-TTT
1 CTAATTTTTTATTAAAATTTT
** *
2820222 CTAATTGATTCTTAAAATTTT
1 CTAATTTTTTATTAAAATTTT
2820243 CT-ATTTTTATATT
1 CTAATTTTT-TATT
2820256 TTCAAAAATT
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.59
Consensus pattern (21 bp):
CTAATTTTTTATTAAAATTTT
Found at i:2820834 original size:30 final size:28
Alignment explanation
Indices: 2820794--2820858 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 28
2820784 GTTAATAAAT
2820794 TATAAAAATTAGATA-AAATTAAAATTTTA
1 TATAAAAATTAGA-ACAAATTAAAA-TTTA
*
2820823 TATATAAAATTATAACAAATTAAAATTTA
1 TATA-AAAATTAGAACAAATTAAAATTTA
2820852 TATAAAA
1 TATAAAA
2820859 CTTATATATT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
28 3 0.09
29 13 0.39
30 17 0.52
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (28 bp):
TATAAAAATTAGAACAAATTAAAATTTA
Found at i:2820873 original size:30 final size:29
Alignment explanation
Indices: 2820809--2820888 Score: 90
Period size: 30 Copynumber: 2.7 Consensus size: 29
2820799 AAATTAGATA
2820809 AAATTAAAATTTTATATATAAAATTATAAC
1 AAATTAAAA-TTTATATATAAAATTATAAC
* *
2820839 AAATTAAAATTTATATA-AAACTTATATATT
1 AAATTAAAATTTATATATAAAATTATA-A-C
* *
2820869 AAATTATAATTTATGTATAA
1 AAATTAAAATTTATATATAA
2820889 TTTTAATATT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
28 8 0.19
29 9 0.21
30 24 0.56
31 2 0.05
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (29 bp):
AAATTAAAATTTATATATAAAATTATAAC
Found at i:2824355 original size:14 final size:15
Alignment explanation
Indices: 2824336--2824365 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2824326 TTTTTCACTT
2824336 TAATAA-TATAAAAA
1 TAATAATTATAAAAA
2824350 TAATAATTATAAAAA
1 TAATAATTATAAAAA
2824365 T
1 T
2824366 GGGCTTAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
TAATAATTATAAAAA
Found at i:2824541 original size:13 final size:13
Alignment explanation
Indices: 2824527--2824570 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
2824517 ACTACATTTG
* *
2824527 AAAAGTGCTTTTG
1 AAAAATGCTTTTA
*
2824540 AAAAATGCTCTTAA
1 AAAAATGCT-TTTA
2824554 AAAAATGCTTTTA
1 AAAAATGCTTTTA
2824567 AAAA
1 AAAA
2824571 GTTTGGTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.48, C:0.09, G:0.11, T:0.32
Consensus pattern (13 bp):
AAAAATGCTTTTA
Found at i:2824557 original size:14 final size:14
Alignment explanation
Indices: 2824540--2824570 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2824530 AGTGCTTTTG
2824540 AAAAATGCTCTTAA
1 AAAAATGCTCTTAA
*
2824554 AAAAATGCTTTTAA
1 AAAAATGCTCTTAA
2824568 AAA
1 AAA
2824571 GTTTGGTTTA
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:0.55, C:0.10, G:0.06, T:0.29
Consensus pattern (14 bp):
AAAAATGCTCTTAA
Found at i:2827975 original size:24 final size:24
Alignment explanation
Indices: 2827904--2828029 Score: 109
Period size: 22 Copynumber: 5.3 Consensus size: 24
2827894 CACTAATGAA
*
2827904 CAGAGAGCACTAAA-GTGCT-ATA-
1 CAGAGAGCAC-AAACGTGCTAAAAT
* *
2827926 CAGAGAGCACAGATGTGCT-AAA-
1 CAGAGAGCACAAACGTGCTAAAAT
**
2827948 CAGAGAGCACTGACGTGCTAAAAT
1 CAGAGAGCACAAACGTGCTAAAAT
* * * *
2827972 CAGAGAGCACCAACATGCTAGTAGT
1 CAGAGAGCACAAACGTGCTA-AAAT
2827997 CAGAGAGCACAAACGTGCTAATAAT
1 CAGAGAGCACAAACGTGCTAA-AAT
2828022 CAGAGAGC
1 CAGAGAGC
2828030 GCGCTAAAGT
Statistics
Matches: 86, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
21 2 0.02
22 34 0.40
23 3 0.03
24 17 0.20
25 30 0.35
ACGTcount: A:0.40, C:0.21, G:0.25, T:0.15
Consensus pattern (24 bp):
CAGAGAGCACAAACGTGCTAAAAT
Found at i:2828005 original size:25 final size:25
Alignment explanation
Indices: 2827948--2828029 Score: 94
Period size: 25 Copynumber: 3.3 Consensus size: 25
2827938 ATGTGCTAAA
** *
2827948 CAGAGAGCACTGACGTGCTAA-AAT
1 CAGAGAGCACAAACATGCTAATAAT
* * *
2827972 CAGAGAGCACCAACATGCTAGTAGT
1 CAGAGAGCACAAACATGCTAATAAT
*
2827997 CAGAGAGCACAAACGTGCTAATAAT
1 CAGAGAGCACAAACATGCTAATAAT
2828022 CAGAGAGC
1 CAGAGAGC
2828030 GCGCTAAAGT
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
24 17 0.35
25 31 0.65
ACGTcount: A:0.39, C:0.22, G:0.24, T:0.15
Consensus pattern (25 bp):
CAGAGAGCACAAACATGCTAATAAT
Found at i:2829112 original size:16 final size:16
Alignment explanation
Indices: 2829091--2829127 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
2829081 GTTTTATGTA
2829091 TATAATAATATAATAT
1 TATAATAATATAATAT
2829107 TATAATAATATAATAT
1 TATAATAATATAATAT
*
2829123 AATAA
1 TATAA
2829128 CTTACTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TATAATAATATAATAT
Found at i:2829127 original size:8 final size:8
Alignment explanation
Indices: 2829090--2829121 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
2829080 TGTTTTATGT
2829090 ATATAATA
1 ATATAATA
2829098 ATATAATA
1 ATATAATA
*
2829106 TTATAATA
1 ATATAATA
2829114 ATATAATA
1 ATATAATA
2829122 TAATAACTTA
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:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
ATATAATA
Found at i:2830750 original size:21 final size:21
Alignment explanation
Indices: 2830726--2830784 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
2830716 AGTGCTAAAT
2830726 AGAAACCCATAAGGGTTGAAC
1 AGAAACCCATAAGGGTTGAAC
* * * * *
2830747 AGAAGCTCGTAAGAGCTGAAC
1 AGAAACCCATAAGGGTTGAAC
*
2830768 AGAAACCTATAAGGGTT
1 AGAAACCCATAAGGGTT
2830785 AAACTGAAGC
Statistics
Matches: 27, Mismatches: 11, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.41, C:0.17, G:0.25, T:0.17
Consensus pattern (21 bp):
AGAAACCCATAAGGGTTGAAC
Found at i:2830750 original size:42 final size:42
Alignment explanation
Indices: 2830703--2830807 Score: 129
Period size: 42 Copynumber: 2.5 Consensus size: 42
2830693 CGAAGGCTGC
* * *
2830703 ACAGAAGCACATAAGTGCTAAATAGAAACCCATAAGGGTTGA
1 ACAGAAGCACATAAGAGCTAAACAGAAACCCATAAGGGTTAA
* * * *
2830745 ACAGAAGCTCGTAAGAGCTGAACAGAAACCTATAAGGGTTAA
1 ACAGAAGCACATAAGAGCTAAACAGAAACCCATAAGGGTTAA
* *
2830787 ACTGAAGCACAAAAGAGCTAA
1 ACAGAAGCACATAAGAGCTAA
2830808 GCTAAAACTT
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (42 bp):
ACAGAAGCACATAAGAGCTAAACAGAAACCCATAAGGGTTAA
Found at i:2834520 original size:12 final size:12
Alignment explanation
Indices: 2834503--2834544 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
2834493 GAACAAAGAG
*
2834503 ATAATGATAGTA
1 ATAATGATAATA
2834515 ATAATGATAATA
1 ATAATGATAATA
2834527 TATAAT-ATAATA
1 -ATAATGATAATA
2834539 ATAATG
1 ATAATG
2834545 TTTTTCTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
11 5 0.19
12 17 0.63
13 5 0.19
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.36
Consensus pattern (12 bp):
ATAATGATAATA
Found at i:2838090 original size:51 final size:51
Alignment explanation
Indices: 2838021--2838118 Score: 160
Period size: 51 Copynumber: 1.9 Consensus size: 51
2838011 TGTGCCGACT
* *
2838021 ACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTATTACTGTC
1 ACTGTTACCGTTACCGATTCGACACTTTGTGTGTCGAATACTATTACTGTC
* *
2838072 ACTGTTACCGTTATCGATTCGACACTTTGTGTGTCGAATACTGTTAC
1 ACTGTTACCGTTACCGATTCGACACTTTGTGTGTCGAATACTATTAC
2838119 CGTTACTGAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.39
Consensus pattern (51 bp):
ACTGTTACCGTTACCGATTCGACACTTTGTGTGTCGAATACTATTACTGTC
Found at i:2839813 original size:34 final size:35
Alignment explanation
Indices: 2839769--2839835 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
2839759 CAGTAAAATA
*
2839769 TTTTCCGTAAAATGATTT-CGGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* *
2839803 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
2839836 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:2859633 original size:336 final size:336
Alignment explanation
Indices: 2859020--2859694 Score: 1341
Period size: 336 Copynumber: 2.0 Consensus size: 336
2859010 TGTTTATATG
2859020 GAACTTCATTGTATAACCAGTTCTTCATGTTCCTACACTTTTGTCTTGTACAAATGTTGGCCAAA
1 GAACTTCATTGTATAACCAGTTCTTCATGTTCCTACACTTTTGTCTTGTACAAATGTTGGCCAAA
2859085 TTGTAGACTCTCAATTTTAAATGTATGGCTGCAAATCTTCTCAAGAACCAGGGACCAAGTATTTG
66 TTGTAGACTCTCAATTTTAAATGTATGGCTGCAAATCTTCTCAAGAACCAGGGACCAAGTATTTG
2859150 GATTCATAACATAGTTTAAGTTCTCTGTCTTGCAAAATAATCAGCACCAATGCTCAAATGAAACA
131 GATTCATAACATAGTTTAAGTTCTCTGTCTTGCAAAATAATCAGCACCAATGCTCAAATGAAACA
2859215 GACCAAATAGAAGGCTTTAGATTTAAAAGTAACATAGGAAAAAGAAAGTTAAAGTTTAAATGCTT
196 GACCAAATAGAAGGCTTTAGATTTAAAAGTAACATAGGAAAAAGAAAGTTAAAGTTTAAATGCTT
2859280 CAGGTGCTAAGCTAGGTTTAGTTATTGAATTTAATTTACAGCATATTTACTACAGCTTTGACTAA
261 CAGGTGCTAAGCTAGGTTTAGTTATTGAATTTAATTTACAGCATATTTACTACAGCTTTGACTAA
2859345 ATTTTTATAAA
326 ATTTTTATAAA
2859356 GAACTTCATTGTATAACCAGTTCTTCATGTTCCTACACTTTTGTCTTGTACAAATGTTGGCCAAA
1 GAACTTCATTGTATAACCAGTTCTTCATGTTCCTACACTTTTGTCTTGTACAAATGTTGGCCAAA
2859421 TTGTAGACTCTCAATTTTAAATGTATGGCTGCAAATCTTCTCAAGAACCAGGGACCAAGTATTTG
66 TTGTAGACTCTCAATTTTAAATGTATGGCTGCAAATCTTCTCAAGAACCAGGGACCAAGTATTTG
2859486 GATTCATAACATAGTTTAAGTTCTCTGTCTTGCAAAATAATCAGCACCAATGCTCAAATGAAACA
131 GATTCATAACATAGTTTAAGTTCTCTGTCTTGCAAAATAATCAGCACCAATGCTCAAATGAAACA
*
2859551 GACCAAATAGAAGGCTTTAGATTTAAAAGTAACATAGGAAAAAGAAAGTTGAAGTTTAAATGCTT
196 GACCAAATAGAAGGCTTTAGATTTAAAAGTAACATAGGAAAAAGAAAGTTAAAGTTTAAATGCTT
2859616 CAGGTGCTAAGCTAGGTTTAGTTATTGAATTTAATTTACAGCATATTTACTACAGCTTTGACTAA
261 CAGGTGCTAAGCTAGGTTTAGTTATTGAATTTAATTTACAGCATATTTACTACAGCTTTGACTAA
2859681 ATTTTTATAAA
326 ATTTTTATAAA
2859692 GAA
1 GAA
2859695 TTTCCCAAAT
Statistics
Matches: 338, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
336 338 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (336 bp):
GAACTTCATTGTATAACCAGTTCTTCATGTTCCTACACTTTTGTCTTGTACAAATGTTGGCCAAA
TTGTAGACTCTCAATTTTAAATGTATGGCTGCAAATCTTCTCAAGAACCAGGGACCAAGTATTTG
GATTCATAACATAGTTTAAGTTCTCTGTCTTGCAAAATAATCAGCACCAATGCTCAAATGAAACA
GACCAAATAGAAGGCTTTAGATTTAAAAGTAACATAGGAAAAAGAAAGTTAAAGTTTAAATGCTT
CAGGTGCTAAGCTAGGTTTAGTTATTGAATTTAATTTACAGCATATTTACTACAGCTTTGACTAA
ATTTTTATAAA
Found at i:2860026 original size:20 final size:22
Alignment explanation
Indices: 2859984--2860027 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
2859974 TTTTATGAAC
*
2859984 TTTATTTTTTTAATGATATATTT
1 TTTATTTTTTT-ATGATAAATTT
2860007 TTTATTTTTTT-T-ATAAATTT
1 TTTATTTTTTTATGATAAATTT
2860027 T
1 T
2860028 AAATTATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 8 0.40
21 1 0.05
23 11 0.55
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (22 bp):
TTTATTTTTTTATGATAAATTT
Found at i:2861489 original size:26 final size:26
Alignment explanation
Indices: 2861428--2861489 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 26
2861418 TGAAATATAA
* *
2861428 TTAAATTATATATTATTTTATTAAAT
1 TTAAATAATATATAATTTTATTAAAT
**
2861454 TATATTTAATA-ATAATTTTATTAAAAT
1 T-TAAATAATATATAATTTTATT-AAAT
2861481 TTAAATAAT
1 TTAAATAAT
2861490 TATTTACCTA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
26 17 0.61
27 11 0.39
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
TTAAATAATATATAATTTTATTAAAT
Found at i:2861494 original size:23 final size:25
Alignment explanation
Indices: 2861439--2861494 Score: 71
Period size: 26 Copynumber: 2.3 Consensus size: 25
2861429 TAAATTATAT
*
2861439 ATTATTTTATTAAATTATATTTAATA
1 ATTATTTTATTAAA-TATATTAAATA
*
2861465 ATAATTTTATTAAA-AT-TTAAATA
1 ATTATTTTATTAAATATATTAAATA
2861488 ATTATTT
1 ATTATTT
2861495 ACCTAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 12 0.44
24 2 0.07
26 13 0.48
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
ATTATTTTATTAAATATATTAAATA
Found at i:2864866 original size:23 final size:23
Alignment explanation
Indices: 2864836--2864908 Score: 94
Period size: 23 Copynumber: 3.2 Consensus size: 23
2864826 TTTCCATGCA
2864836 TGCAAGTGATAGTGGCACTACGG
1 TGCAAGTGATAGTGGCACTACGG
* * *
2864859 TGCAAGTGATAGCGGCAGTACAG
1 TGCAAGTGATAGTGGCACTACGG
* *
2864882 TGCAAGTG-TTGTGGCACTTCGG
1 TGCAAGTGATAGTGGCACTACGG
2864904 TGCAA
1 TGCAA
2864909 AATGACATTT
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
22 14 0.33
23 28 0.67
ACGTcount: A:0.25, C:0.18, G:0.34, T:0.23
Consensus pattern (23 bp):
TGCAAGTGATAGTGGCACTACGG
Found at i:2866417 original size:24 final size:20
Alignment explanation
Indices: 2866368--2866409 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
2866358 GAAATAATAA
*
2866368 ATCTATATAGATCAGTAAGT
1 ATCTATATAGATCAATAAGT
2866388 ATCTATATAGATCAATAAGT
1 ATCTATATAGATCAATAAGT
2866408 AT
1 AT
2866410 AGGACTATCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.36
Consensus pattern (20 bp):
ATCTATATAGATCAATAAGT
Found at i:2868803 original size:50 final size:50
Alignment explanation
Indices: 2868685--2868933 Score: 275
Period size: 50 Copynumber: 4.8 Consensus size: 50
2868675 GATAATAACA
* * * ** * *
2868685 TGCCAAAGCCATGTCCCCGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
2868736 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
2868786 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
2868836 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
2868891 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
2868934 TTACCCAAAT
Statistics
Matches: 169, Mismatches: 22, Indels: 9
0.85 0.11 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 32 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.30, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:2868862 original size:100 final size:104
Alignment explanation
Indices: 2868684--2868933 Score: 348
Period size: 100 Copynumber: 2.4 Consensus size: 104
2868674 TGATAATAAC
* **
2868684 ATGCCAAAGCCATGTCCCCGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
2868749 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
2868786 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
2868849 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
2868891 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
2868934 TTACCCAAAT
Statistics
Matches: 132, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 35 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.20, C:0.30, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:2869049 original size:13 final size:13
Alignment explanation
Indices: 2869028--2869059 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
2869018 GCTTGGATCA
*
2869028 TCATCAAATAAAT
1 TCATAAAATAAAT
2869041 TCATAAAATAAAT
1 TCATAAAATAAAT
2869054 TCATAA
1 TCATAA
2869060 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:2871427 original size:30 final size:30
Alignment explanation
Indices: 2871393--2871457 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
2871383 ACTTATTTTA
*
2871393 TTGTTAATTTTGTTATTATTTTTA-AGACAT
1 TTGTTAATTTTGTTATTA-TTTTAGAAACAT
*
2871423 TTGTTAATTTTTTTATTATTTTAGAAACAT
1 TTGTTAATTTTGTTATTATTTTAGAAACAT
2871453 TTGTT
1 TTGTT
2871458 TGTTAAGTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 5 0.16
30 27 0.84
ACGTcount: A:0.26, C:0.03, G:0.09, T:0.62
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAGAAACAT
Found at i:2874747 original size:5 final size:5
Alignment explanation
Indices: 2874719--2874778 Score: 79
Period size: 5 Copynumber: 12.2 Consensus size: 5
2874709 TTTTTATGTT
* *
2874719 TTATA -TATA TTATT TTAT- TATATA TTATA TTATA TTATA TTATA TTGTA
1 TTATA TTATA TTATA TTATA T-TATA TTATA TTATA TTATA TTATA TTATA
2874768 TTATA TTATA T
1 TTATA TTATA T
2874779 AAATTAAATA
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
4 5 0.10
5 43 0.88
6 1 0.02
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:2891114 original size:2 final size:2
Alignment explanation
Indices: 2891107--2891137 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2891097 TGCTGGAAAA
*
2891107 TC TC TC TC TC TC TC TC TC TC TC TC TA TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2891138 TGTGTTATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.03, C:0.45, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2898223 original size:36 final size:35
Alignment explanation
Indices: 2898171--2898260 Score: 99
Period size: 36 Copynumber: 2.5 Consensus size: 35
2898161 TTTTGGTCCC
* * * *
2898171 ACACATGGGGAAAGGCTTACGTGAGGTCCTGCTCTT
1 ACACATGGGG-GAGGCTTACGGGAGGTCCTACTCCT
* * *
2898207 ATACATGGGAGGAGGCTTATGGGAGGTCGTACTCCT
1 ACACATGGG-GGAGGCTTACGGGAGGTCCTACTCCT
2898243 ACACATGGGGGAGGCTTA
1 ACACATGGGGGAGGCTTA
2898261 TGAGAAGTGA
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
35 9 0.20
36 35 0.78
37 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.34, T:0.23
Consensus pattern (35 bp):
ACACATGGGGGAGGCTTACGGGAGGTCCTACTCCT
Found at i:2898526 original size:50 final size:50
Alignment explanation
Indices: 2898430--2898528 Score: 128
Period size: 50 Copynumber: 2.0 Consensus size: 50
2898420 AGGCCCTGTT
* * * *
2898430 CCCAGACGCATAAAGGGAGGGTTACGAAATATGGTAACGATGATCCTACA
1 CCCAAACGCATAAAGGGAGGCTTACGAAATATGGTAACAATAATCCTACA
* *
2898480 CCCAAACGCATAGAGGGAGGCTTACGAAA-AGTGGTAATAATAATCCTAC
1 CCCAAACGCATAAAGGGAGGCTTACGAAATA-TGGTAACAATAATCCTAC
2898529 TCCTAGATGC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
49 1 0.02
50 41 0.98
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.18
Consensus pattern (50 bp):
CCCAAACGCATAAAGGGAGGCTTACGAAATATGGTAACAATAATCCTACA
Found at i:2899871 original size:18 final size:17
Alignment explanation
Indices: 2899838--2899876 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
2899828 TTTTATAAAT
2899838 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
2899856 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
2899873 TGTG
1 TGTG
2899877 GAAGAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:2900125 original size:23 final size:23
Alignment explanation
Indices: 2900094--2900215 Score: 154
Period size: 23 Copynumber: 5.3 Consensus size: 23
2900084 AGTGTTATTG
2900094 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * * *
2900117 TTCAATGGTAGCTACAGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
2900140 ATCAGTGGTAGCTTCAGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * * *
2900163 TTTAGTGGTAGCTACGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
*
2900186 ATCAGTGGCAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
2900209 ATCAGTG
1 ATCAGTG
2900216 TGGCACTTAT
Statistics
Matches: 82, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 82 1.00
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:2900146 original size:46 final size:46
Alignment explanation
Indices: 2900094--2900208 Score: 176
Period size: 46 Copynumber: 2.5 Consensus size: 46
2900084 AGTGTTATTG
2900094 ATCAGTGGTAGCTTCGGCTACATTTCAATGGTAGCTACAGCTACAT
1 ATCAGTGGTAGCTTCGGCTACATTTCAATGGTAGCTACAGCTACAT
* * * * *
2900140 ATCAGTGGTAGCTTCAGCTACATTTTAGTGGTAGCTACGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACATTTCAATGGTAGCTACAGCTACAT
*
2900186 ATCAGTGGCAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
2900209 ATCAGTGTGG
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 62 1.00
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.30
Consensus pattern (46 bp):
ATCAGTGGTAGCTTCGGCTACATTTCAATGGTAGCTACAGCTACAT
Found at i:2932359 original size:16 final size:16
Alignment explanation
Indices: 2932327--2932358 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
2932317 AATATTTATA
2932327 TATTTATTAAAAATTT
1 TATTTATTAAAAATTT
2932343 TATTTATT-AAAATTT
1 TATTTATTAAAAATTT
2932358 T
1 T
2932359 TTATATAGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTTATTAAAAATTT
Found at i:2935391 original size:18 final size:18
Alignment explanation
Indices: 2935354--2935391 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2935344 ATATCGAGAC
*
2935354 TTAAAATTTTTATTTTAA
1 TTAAAATTTTTATTTAAA
2935372 TTAAAATTTATT-TTTAAA
1 TTAAAATTT-TTATTTAAA
2935390 TT
1 TT
2935392 TGATCATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTAAAATTTTTATTTAAA
Found at i:2935481 original size:20 final size:19
Alignment explanation
Indices: 2935440--2935480 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2935430 ATTCAATCTC
2935440 TTTGAATTTGATTATTGTT
1 TTTGAATTTGATTATTGTT
*
2935459 TTTGCATTTGACTTATT-TT
1 TTTGAATTTGA-TTATTGTT
2935478 TTT
1 TTT
2935481 TTCAAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.17, C:0.05, G:0.12, T:0.66
Consensus pattern (19 bp):
TTTGAATTTGATTATTGTT
Found at i:2937645 original size:18 final size:19
Alignment explanation
Indices: 2937611--2937653 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
2937601 ATTACAAAAA
*
2937611 AAAAATCAAAATAATTTTT
1 AAAAATCAAAATAATTTAT
*
2937630 AAAATTCAAAAT-ATTTAT
1 AAAAATCAAAATAATTTAT
2937648 AAAAAT
1 AAAAAT
2937654 TTTAAACAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAAATCAAAATAATTTAT
Found at i:2941875 original size:9 final size:9
Alignment explanation
Indices: 2941861--2941885 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2941851 AGTCAGATCC
2941861 CACCACCTG
1 CACCACCTG
2941870 CACCACCTG
1 CACCACCTG
2941879 CACCACC
1 CACCACC
2941886 AACAACGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.60, G:0.08, T:0.08
Consensus pattern (9 bp):
CACCACCTG
Found at i:2953827 original size:11 final size:9
Alignment explanation
Indices: 2953794--2953818 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2953784 AAATTTTATT
2953794 TTTTATATG
1 TTTTATATG
2953803 TTTTATATG
1 TTTTATATG
2953812 TTTTATA
1 TTTTATA
2953819 CTAGTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (9 bp):
TTTTATATG
Found at i:2956305 original size:14 final size:14
Alignment explanation
Indices: 2956286--2956315 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2956276 AAGCCTGATA
2956286 TCGTTTTGGACCTT
1 TCGTTTTGGACCTT
2956300 TCGTTTTGGACCTT
1 TCGTTTTGGACCTT
2956314 TC
1 TC
2956316 CTATATGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.07, C:0.23, G:0.20, T:0.50
Consensus pattern (14 bp):
TCGTTTTGGACCTT
Found at i:2956612 original size:51 final size:51
Alignment explanation
Indices: 2956552--2956649 Score: 126
Period size: 51 Copynumber: 1.9 Consensus size: 51
2956542 CATTTAGCCC
* * *
2956552 TCAAATTTTACATATTATATCAAATTAG-TCATAATTTTAAAAAATTAATCT
1 TCAAATTTTACAAATAATATC-AATTAGATCATAATTCTAAAAAATTAATCT
* * *
2956603 TCAAATTTTACAAATAATTTCAATTTGATCCTAATTCTAAAAAATTA
1 TCAAATTTTACAAATAATATCAATTAGATCATAATTCTAAAAAATTA
2956650 TTAATATTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
50 5 0.12
51 35 0.88
ACGTcount: A:0.45, C:0.11, G:0.02, T:0.42
Consensus pattern (51 bp):
TCAAATTTTACAAATAATATCAATTAGATCATAATTCTAAAAAATTAATCT
Found at i:2956914 original size:6 final size:6
Alignment explanation
Indices: 2956905--2956961 Score: 51
Period size: 6 Copynumber: 9.3 Consensus size: 6
2956895 TTTATTTTAT
* * * * * *
2956905 TTAATA TTAATA TAAATA GTAATA TTAATA TAAATT TTAATT TTATTA
1 TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA
2956953 TTATATA TT
1 TTA-ATA TT
2956962 TTTGAAAATG
Statistics
Matches: 40, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
6 36 0.90
7 4 0.10
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (6 bp):
TTAATA
Found at i:2956945 original size:18 final size:18
Alignment explanation
Indices: 2956904--2956945 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
2956894 TTTTATTTTA
2956904 TTTAATATTAATATAAAT
1 TTTAATATTAATATAAAT
**
2956922 AGTAATATTAATATAAAT
1 TTTAATATTAATATAAAT
2956940 TTTAAT
1 TTTAAT
2956946 TTTATTATTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
TTTAATATTAATATAAAT
Found at i:2957769 original size:18 final size:19
Alignment explanation
Indices: 2957746--2957789 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
2957736 TAAATTTTAT
2957746 TAAAAAT-TAGAAA-AAATA
1 TAAAAATCTA-AAAGAAATA
2957764 TAAAAATCGTAAAAGAAATA
1 TAAAAATC-TAAAAGAAATA
2957784 TAAAAA
1 TAAAAA
2957790 ATAGTGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 7 0.30
19 3 0.13
20 13 0.57
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.20
Consensus pattern (19 bp):
TAAAAATCTAAAAGAAATA
Found at i:2957789 original size:59 final size:58
Alignment explanation
Indices: 2957714--2957828 Score: 160
Period size: 59 Copynumber: 2.0 Consensus size: 58
2957704 GTGACATGTG
* * * *
2957714 GTAAAAAATTATAAAAAATATTTAAATTTTATTAAAAATTAGAAAAAATATA-AAAATC
1 GTAAAAAAATATAAAAAATAGTGAAATTTTA-TAAAAATCAGAAAAAATATATAAAATC
*
2957772 GTAAAAGAAATATAAAAAATAGTGAAATTTTATAAAAATCATAAAAAATATATAAAA
1 GTAAAA-AAATATAAAAAATAGTGAAATTTTATAAAAATCAGAAAAAATATATAAAA
2957829 ATGCATCAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
58 24 0.48
59 26 0.52
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (58 bp):
GTAAAAAAATATAAAAAATAGTGAAATTTTATAAAAATCAGAAAAAATATATAAAATC
Found at i:2957825 original size:20 final size:19
Alignment explanation
Indices: 2957756--2957840 Score: 64
Period size: 20 Copynumber: 4.2 Consensus size: 19
2957746 TAAAAATTAG
*
2957756 AAAAAATATAAAAATCGTA
1 AAAAAATATAAAAATCATA
*
2957775 AAAGAAATATAAAAAAT-AGTG
1 AAA-AAATAT-AAAAATCA-TA
***
2957796 AAATTTTATAAAAATCATA
1 AAAAAATATAAAAATCATA
2957815 AAAAATATATAAAAATGCATCA
1 AAAAA-ATATAAAAAT-CAT-A
2957837 AAAA
1 AAAA
2957841 GACTTTTTAA
Statistics
Matches: 50, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
19 13 0.26
20 19 0.38
21 13 0.26
22 5 0.10
ACGTcount: A:0.66, C:0.05, G:0.06, T:0.24
Consensus pattern (19 bp):
AAAAAATATAAAAATCATA
Found at i:2958090 original size:36 final size:36
Alignment explanation
Indices: 2958044--2958117 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
2958034 CTTTACATTA
*
2958044 TTATAATTCTCTTACGACTTTATAAAATATTACAAT
1 TTATAATTCTCTTACGACTTTATAAAATAATACAAT
2958080 TTATAATTCTCTTACGACTTTATAAAATAATACAAT
1 TTATAATTCTCTTACGACTTTATAAAATAATACAAT
2958116 TT
1 TT
2958118 TACATTTTAC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.39, C:0.14, G:0.03, T:0.45
Consensus pattern (36 bp):
TTATAATTCTCTTACGACTTTATAAAATAATACAAT
Found at i:2958094 original size:18 final size:19
Alignment explanation
Indices: 2958044--2958104 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
2958034 CTTTACATTA
2958044 TTATAATTCTCTTACGACT
1 TTATAATTCTCTTACGACT
** * *
2958063 TTATAA-AATATTAC-AAT
1 TTATAATTCTCTTACGACT
2958080 TTATAATTCTCTTACGACT
1 TTATAATTCTCTTACGACT
2958099 TTATAA
1 TTATAA
2958105 AATAATACAA
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
17 8 0.25
18 10 0.31
19 14 0.44
ACGTcount: A:0.36, C:0.15, G:0.03, T:0.46
Consensus pattern (19 bp):
TTATAATTCTCTTACGACT
Found at i:2958219 original size:19 final size:18
Alignment explanation
Indices: 2958172--2958224 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 18
2958162 TTATTTCTAT
*
2958172 TTTTTAAAATAATTTAATA
1 TTTTTATAA-AATTTAATA
2958191 -TTTTATTAAAATTTAATAA
1 TTTTTA-TAAAATTTAAT-A
*
2958210 TTTTTATAAATTTTA
1 TTTTTATAAAATTTA
2958225 TTGGTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 13 0.45
19 11 0.38
20 5 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTTATAAAATTTAATA
Found at i:2958220 original size:18 final size:18
Alignment explanation
Indices: 2958182--2958222 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2958172 TTTTTAAAAT
*
2958182 AATTTAATATTTTATTAA
1 AATTTAATAATTTATTAA
2958200 AATTTAATAATTT-TTATA
1 AATTTAATAATTTATTA-A
2958218 AATTT
1 AATTT
2958223 TATTGGTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AATTTAATAATTTATTAA
Found at i:2961156 original size:26 final size:26
Alignment explanation
Indices: 2961096--2961156 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 26
2961086 AAAGAAAATT
*
2961096 TAAAATATTATTTTATTTTACTTTGAA
1 TAAAATATTATTTTATTTTAC-TTCAA
*
2961123 -AAAGTATTATTTTATTTTTA-TTCAA
1 TAAAATATTATTTTA-TTTTACTTCAA
*
2961148 TAAATTATT
1 TAAAATATT
2961157 CTTATCAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
25 4 0.14
26 20 0.69
27 5 0.17
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (26 bp):
TAAAATATTATTTTATTTTACTTCAA
Found at i:2970223 original size:14 final size:15
Alignment explanation
Indices: 2970206--2970270 Score: 69
Period size: 15 Copynumber: 4.4 Consensus size: 15
2970196 ATAACTTAAA
2970206 TTCAGTACTTAA-TT
1 TTCAGTACTTAATTT
* *
2970220 TTCAATATTTAATTT
1 TTCAGTACTTAATTT
** *
2970235 TTCAACACTTATTTT
1 TTCAGTACTTAATTT
*
2970250 TTCAGCACTTAATTT
1 TTCAGTACTTAATTT
2970265 TTCAGT
1 TTCAGT
2970271 TTATCAAACA
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
14 10 0.24
15 32 0.76
ACGTcount: A:0.28, C:0.15, G:0.05, T:0.52
Consensus pattern (15 bp):
TTCAGTACTTAATTT
Found at i:2970238 original size:15 final size:15
Alignment explanation
Indices: 2970212--2970268 Score: 71
Period size: 15 Copynumber: 3.9 Consensus size: 15
2970202 TAAATTCAGT
*
2970212 ACTTAA-TTTTCAAT
1 ACTTAATTTTTCAAC
*
2970226 ATTTAATTTTTCAAC
1 ACTTAATTTTTCAAC
* *
2970241 ACTTATTTTTTCAGC
1 ACTTAATTTTTCAAC
2970256 ACTTAATTTTTCA
1 ACTTAATTTTTCA
2970269 GTTTATCAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
14 5 0.14
15 31 0.86
ACGTcount: A:0.30, C:0.16, G:0.02, T:0.53
Consensus pattern (15 bp):
ACTTAATTTTTCAAC
Found at i:2986622 original size:5 final size:5
Alignment explanation
Indices: 2986612--2986636 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2986602 GAAAAACAAC
2986612 TATGA TATGA TATGA TATGA TATGA
1 TATGA TATGA TATGA TATGA TATGA
2986637 ATTACTGATA
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:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (5 bp):
TATGA
Found at i:2994549 original size:19 final size:21
Alignment explanation
Indices: 2994525--2994564 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
2994515 TTAAATTGCT
2994525 AAAATAT-AAAAATT-TATGA
1 AAAATATGAAAAATTATATGA
*
2994544 AAAATATGTAAAATTATATGA
1 AAAATATGAAAAATTATATGA
2994565 CGTGTATAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 6 0.33
21 5 0.28
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (21 bp):
AAAATATGAAAAATTATATGA
Found at i:3002701 original size:11 final size:10
Alignment explanation
Indices: 3002664--3002699 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
3002654 CGTTTTTATT
3002664 TTTTAAAATA
1 TTTTAAAATA
3002674 TTTTAAAATA
1 TTTTAAAATA
*
3002684 TTTTATAATA
1 TTTTAAAATA
3002694 TCTTTA
1 T-TTTA
3002700 TAGGCAGGGC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 20 0.83
11 4 0.17
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (10 bp):
TTTTAAAATA
Found at i:3005253 original size:21 final size:21
Alignment explanation
Indices: 3005213--3005261 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
3005203 ATTGTAAGAA
*
3005213 TAAAAATGTTTCCTAAAATTT
1 TAAAAATGTTTCCTAAAATTG
** *
3005234 TAAAAATGTTTGGTATAATTG
1 TAAAAATGTTTCCTAAAATTG
3005255 TAAAAAT
1 TAAAAAT
3005262 AATAATTCCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.41
Consensus pattern (21 bp):
TAAAAATGTTTCCTAAAATTG
Found at i:3009143 original size:14 final size:14
Alignment explanation
Indices: 3009126--3009171 Score: 74
Period size: 14 Copynumber: 3.3 Consensus size: 14
3009116 TAAAAAAATG
3009126 TTATTAAATTATTA
1 TTATTAAATTATTA
* *
3009140 TTATTAAATTAGTG
1 TTATTAAATTATTA
3009154 TTATTAAATTATTA
1 TTATTAAATTATTA
3009168 TTAT
1 TTAT
3009172 ATTTTAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (14 bp):
TTATTAAATTATTA
Found at i:3010084 original size:12 final size:12
Alignment explanation
Indices: 3010067--3010108 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
3010057 ATGTGAGGTA
3010067 AGTATTAATATT
1 AGTATTAATATT
3010079 AGTATTAAT-TT
1 AGTATTAATATT
* *
3010090 ATTATTAGTATT
1 AGTATTAATATT
*
3010102 ATTATTA
1 AGTATTA
3010109 TTATGAGTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 9 0.33
12 18 0.67
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (12 bp):
AGTATTAATATT
Found at i:3032004 original size:148 final size:148
Alignment explanation
Indices: 3031833--3032132 Score: 591
Period size: 148 Copynumber: 2.0 Consensus size: 148
3031823 AAGAAAATGA
3031833 CAATCCATCTTTCAATAAATCGTAATCGATCATCTAAAAACATTACCGATCTAATCAACAAATAC
1 CAATCCATCTTTCAATAAATCGTAATCGATCATCTAAAAACATTACCGATCTAATCAACAAATAC
3031898 AAGTTGAAGAAAATACTGAAATCGACCTTTGGGCTCAAACAAATTATCCTAATTAAACGTCTATC
66 AAGTTGAAGAAAATACTGAAATCGACCTTTGGGCTCAAACAAATTATCCTAATTAAACGTCTATC
3031963 TCAGTTGAAAAACCCATT
131 TCAGTTGAAAAACCCATT
3031981 CAATCCATCTTTCAATAAATCGTAATCGATCATCTAAAAACATTACCGATCTAATCAACAAATAC
1 CAATCCATCTTTCAATAAATCGTAATCGATCATCTAAAAACATTACCGATCTAATCAACAAATAC
*
3032046 AAGTTGAAGAAAATACTGAAATCGACCTTTGGGCTCAAACAAATTATCCTAATTACACGTCTATC
66 AAGTTGAAGAAAATACTGAAATCGACCTTTGGGCTCAAACAAATTATCCTAATTAAACGTCTATC
3032111 TCAGTTGAAAAACCCATT
131 TCAGTTGAAAAACCCATT
3032129 CAAT
1 CAAT
3032133 TACTTCCATT
Statistics
Matches: 151, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
148 151 1.00
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.28
Consensus pattern (148 bp):
CAATCCATCTTTCAATAAATCGTAATCGATCATCTAAAAACATTACCGATCTAATCAACAAATAC
AAGTTGAAGAAAATACTGAAATCGACCTTTGGGCTCAAACAAATTATCCTAATTAAACGTCTATC
TCAGTTGAAAAACCCATT
Found at i:3041717 original size:42 final size:42
Alignment explanation
Indices: 3041650--3041735 Score: 138
Period size: 42 Copynumber: 2.0 Consensus size: 42
3041640 TGCCTGAACC
3041650 ATGAAGGGTGGGTAAAAGCTAAGAAGCTCCCAAAATGGCCAA
1 ATGAAGGGTGGGTAAAAGCTAAGAAGCTCCCAAAATGGCCAA
* *
3041692 ATGAAGGGTGGGTGGAAA-CTTAGAAGCTCCCAAAATGGCCAA
1 ATGAAGGGTGGGT-AAAAGCTAAGAAGCTCCCAAAATGGCCAA
3041734 AT
1 AT
3041736 AAACCAGAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
42 38 0.93
43 3 0.07
ACGTcount: A:0.38, C:0.16, G:0.29, T:0.16
Consensus pattern (42 bp):
ATGAAGGGTGGGTAAAAGCTAAGAAGCTCCCAAAATGGCCAA
Found at i:3071725 original size:6 final size:7
Alignment explanation
Indices: 3071707--3071735 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
3071697 ATATAAAGTT
3071707 CGGGGGG
1 CGGGGGG
3071714 CGGGGGG
1 CGGGGGG
3071721 CGGGGGG
1 CGGGGGG
3071728 CGGGGGG
1 CGGGGGG
3071735 C
1 C
3071736 TTGGTTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.00, C:0.17, G:0.83, T:0.00
Consensus pattern (7 bp):
CGGGGGG
Found at i:3072629 original size:31 final size:31
Alignment explanation
Indices: 3072591--3072651 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
3072581 GTTATATAAC
*
3072591 ATTTCACGTTTGAAATTATAAATATTATGTA
1 ATTTCACGTTTCAAATTATAAATATTATGTA
3072622 ATTTCACGTTTCAAATTATAAATATTATGT
1 ATTTCACGTTTCAAATTATAAATATTATGT
3072652 TCGGATTCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (31 bp):
ATTTCACGTTTCAAATTATAAATATTATGTA
Found at i:3073004 original size:19 final size:18
Alignment explanation
Indices: 3072965--3073013 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
3072955 TTTAAAATTA
3072965 TAATTTATAAATATATTT
1 TAATTTATAAATATATTT
*
3072983 TAATGTTATATATAT-TTAT
1 TAAT-TTATAAATATATT-T
*
3073002 TAATATATAAAT
1 TAATTTATAAAT
3073014 TATAATAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 12 0.46
19 14 0.54
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
TAATTTATAAATATATTT
Found at i:3075144 original size:25 final size:25
Alignment explanation
Indices: 3075104--3075194 Score: 146
Period size: 25 Copynumber: 3.6 Consensus size: 25
3075094 TTATTATGCA
*
3075104 CTAATAAACAGAGAGCACTGACGTG
1 CTAATAATCAGAGAGCACTGACGTG
* *
3075129 CTAGTAATCAGAGAGCACTAACGTG
1 CTAATAATCAGAGAGCACTGACGTG
*
3075154 CTAATAATCAGAGAGCACTGATGTG
1 CTAATAATCAGAGAGCACTGACGTG
3075179 CTAATAATCAGAGAGC
1 CTAATAATCAGAGAGC
3075195 GCACTAAGGT
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 60 1.00
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.20
Consensus pattern (25 bp):
CTAATAATCAGAGAGCACTGACGTG
Found at i:3076437 original size:13 final size:13
Alignment explanation
Indices: 3076419--3076444 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3076409 AACTAATTCT
3076419 ATAAATATTTTTA
1 ATAAATATTTTTA
3076432 ATAAATATTTTTA
1 ATAAATATTTTTA
3076445 CGAGTCCGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATAAATATTTTTA
Found at i:3077183 original size:21 final size:21
Alignment explanation
Indices: 3077159--3077202 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
3077149 AGTAAATTTA
* *
3077159 ATTCATTTTAATACAATTCAC
1 ATTCAATTCAATACAATTCAC
* *
3077180 ATTCAATTCCATCCAATTCAC
1 ATTCAATTCAATACAATTCAC
3077201 AT
1 AT
3077203 CCTAGGAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (21 bp):
ATTCAATTCAATACAATTCAC
Found at i:3077188 original size:11 final size:11
Alignment explanation
Indices: 3077172--3077204 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
3077162 CATTTTAATA
*
3077172 CAATTCACATT
1 CAATTCACATC
3077183 CAATTC-CATC
1 CAATTCACATC
3077193 CAATTCACATC
1 CAATTCACATC
3077204 C
1 C
3077205 TAGGAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.33, C:0.36, G:0.00, T:0.30
Consensus pattern (11 bp):
CAATTCACATC
Found at i:3079500 original size:17 final size:18
Alignment explanation
Indices: 3079478--3079511 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3079468 TAATTGTGAA
3079478 TTAAAT-TATAATTATTT
1 TTAAATGTATAATTATTT
*
3079495 TTAAATGTATAGTTATT
1 TTAAATGTATAATTATT
3079512 ACAATTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (18 bp):
TTAAATGTATAATTATTT
Found at i:3079531 original size:26 final size:27
Alignment explanation
Indices: 3079482--3079537 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
3079472 TGTGAATTAA
* * *
3079482 ATTATAATTATTTTTAAATGTATAGTT
1 ATTACAATTATTTTTAAATCTATAATT
*
3079509 ATTACAATTTTTTTTAAA-CTATAATT
1 ATTACAATTATTTTTAAATCTATAATT
3079535 ATT
1 ATT
3079538 TTAAAAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 9 0.36
27 16 0.64
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.55
Consensus pattern (27 bp):
ATTACAATTATTTTTAAATCTATAATT
Found at i:3080178 original size:22 final size:22
Alignment explanation
Indices: 3080148--3080190 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3080138 TAAAATGCTT
3080148 AAATAATAATT-TAATATAATTA
1 AAATAATAATTATAAT-TAATTA
*
3080170 AAATCATAATTATAATTAATT
1 AAATAATAATTATAATTAATT
3080191 CTTTAAATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
AAATAATAATTATAATTAATTA
Found at i:3086748 original size:35 final size:33
Alignment explanation
Indices: 3086682--3086748 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
3086672 TAACTTTTCC
* *
3086682 ATATATTCTTTAGAATTTTATAATTTTTTAAAA
1 ATATATTCTTTAGAATTTTATAATATCTTAAAA
3086715 ATATATAT-TTTAGAATTTCTATAAATATCTTAAA
1 ATATAT-TCTTTAGAATTT-TAT-AATATCTTAAA
3086749 TTTTACAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 16 0.55
34 4 0.14
35 9 0.31
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.51
Consensus pattern (33 bp):
ATATATTCTTTAGAATTTTATAATATCTTAAAA
Found at i:3105342 original size:29 final size:30
Alignment explanation
Indices: 3105283--3105340 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
3105273 TCCGAGCCTT
*
3105283 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
3105313 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
3105341 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:3105570 original size:13 final size:13
Alignment explanation
Indices: 3105552--3105583 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
3105542 TTTCCAGCAA
3105552 TTATGAATTTATT
1 TTATGAATTTATT
3105565 TTATGAATTTATT
1 TTATGAATTTATT
*
3105578 TGATGA
1 TTATGA
3105584 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:3105791 original size:50 final size:50
Alignment explanation
Indices: 3105678--3105919 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
3105668 ATTTGGGTAA
* * *
3105678 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
3105734 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
3105784 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
3105834 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
3105884 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
3105920 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:3105867 original size:100 final size:103
Alignment explanation
Indices: 3105678--3105927 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
3105668 ATTTGGGTAA
3105678 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
3105743 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
3105784 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
3105846 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
3105884 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
3105928 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:3108049 original size:33 final size:33
Alignment explanation
Indices: 3107967--3108042 Score: 134
Period size: 33 Copynumber: 2.3 Consensus size: 33
3107957 TGGAAAAGCT
*
3107967 AATATTTTCTGGTGTTTGGATGAATCTGTGTAA
1 AATATTTTCTGGTGTTTGAATGAATCTGTGTAA
*
3108000 AATATTTTCTGGTGTTTGAATGAATCTGTGTCA
1 AATATTTTCTGGTGTTTGAATGAATCTGTGTAA
3108033 AATATTTTCT
1 AATATTTTCT
3108043 TTTGTTTTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.25, C:0.08, G:0.20, T:0.47
Consensus pattern (33 bp):
AATATTTTCTGGTGTTTGAATGAATCTGTGTAA
Found at i:3115507 original size:18 final size:17
Alignment explanation
Indices: 3115480--3115513 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3115470 CTCTAACCCC
3115480 TTTTTTTTTTTGTAAAT
1 TTTTTTTTTTTGTAAAT
*
3115497 TTTTTTCTTTTTTTAAA
1 TTTTTT-TTTTTGTAAA
3115514 AAATTCCCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (17 bp):
TTTTTTTTTTTGTAAAT
Found at i:3117601 original size:16 final size:17
Alignment explanation
Indices: 3117580--3117612 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
3117570 ATCCTGTGTC
3117580 TTCTTTTT-TTTTTTTT
1 TTCTTTTTCTTTTTTTT
3117596 TTCTTTTTCTTTTTTTT
1 TTCTTTTTCTTTTTTTT
3117613 CAGCAGGGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (17 bp):
TTCTTTTTCTTTTTTTT
Found at i:3117608 original size:15 final size:15
Alignment explanation
Indices: 3117584--3117613 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3117574 TGTGTCTTCT
*
3117584 TTTTTTTTTTTTTTC
1 TTTTTCTTTTTTTTC
3117599 TTTTTCTTTTTTTTC
1 TTTTTCTTTTTTTTC
3117614 AGCAGGGTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTTTCTTTTTTTTC
Done.