Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008702.1 Hibiscus syriacus cultivar Beakdansim tig00111741_pilon, whole genome shotgun sequence
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: 3201804
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 14
Found at i:2610544 original size:43 final size:43
Alignment explanation
Indices: 2610451--2610699 Score: 394
Period size: 43 Copynumber: 5.8 Consensus size: 43
2610441 ACCATTACAG
2610451 CAGGTCCCTTCTGCTGTGTGCAAGGGTAAGCCTTACAGTTT-CC
1 CAGGTCCCTT-TGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
* *
2610494 TAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCT
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
* *
2610537 CATGTCCCTTTGCTGTGTGCAAGGGTAAACCTTACAGTTT-CC
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
*
2610579 CAGGCCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
2610622 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
* * *
2610665 CAGGTCCCTTTACTATGTGCAAGGATAAGACCTTA
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAG-CCTTA
2610700 TCATTTTTGC
Statistics
Matches: 190, Mismatches: 13, Indels: 5
0.91 0.06 0.02
Matches are distributed among these distances:
42 68 0.36
43 117 0.62
44 5 0.03
ACGTcount: A:0.18, C:0.27, G:0.24, T:0.31
Consensus pattern (43 bp):
CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
Found at i:2610605 original size:85 final size:85
Alignment explanation
Indices: 2610451--2610699 Score: 399
Period size: 85 Copynumber: 2.9 Consensus size: 85
2610441 ACCATTACAG
*
2610451 CAGGTCCCTTCTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCTAGGTCCCTTTGCTGTGTGCAA
1 CAGGTCCCTT-TGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTCCCTTTGCTGTGTGCAA
*
2610516 GGGTAAGCCTTACAGTTTCCT
65 GGGTAAGCCTTACAGTTTCCC
* * *
2610537 CATGTCCCTTTGCTGTGTGCAAGGGTAAACCTTACAGTTTCCCAGGCCCCTTTGCTGTGTGCAAG
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTCCCTTTGCTGTGTGCAAG
2610602 GGTAAGCCTTACAGTTTCCC
66 GGTAAGCCTTACAGTTTCCC
* *
2610622 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTCCCTTTACTATGTGCAA
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTT-CCCAGGTCCCTTTGCTGTGTGCAA
*
2610687 GGATAAGACCTTA
65 GGGTAAG-CCTTA
2610700 TCATTTTTGC
Statistics
Matches: 150, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
85 109 0.73
86 36 0.24
87 5 0.03
ACGTcount: A:0.18, C:0.27, G:0.24, T:0.31
Consensus pattern (85 bp):
CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTCCCTTTGCTGTGTGCAAG
GGTAAGCCTTACAGTTTCCC
Found at i:2612672 original size:18 final size:18
Alignment explanation
Indices: 2612651--2612695 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
2612641 CCTGACCCAT
*
2612651 CCCGTTTACCAGACCCGA
1 CCCGTTGACCAGACCCGA
*
2612669 CCCGTTGACCCGACCCGA
1 CCCGTTGACCAGACCCGA
*
2612687 CTCGTTGAC
1 CCCGTTGAC
2612696 TGTTAACCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.18, C:0.44, G:0.20, T:0.18
Consensus pattern (18 bp):
CCCGTTGACCAGACCCGA
Found at i:2613567 original size:17 final size:19
Alignment explanation
Indices: 2613540--2613585 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 19
2613530 GGTTTTTTTA
* *
2613540 AAGACATATTGATTTG-AT
1 AAGAAATATTGATGTGCAT
2613558 AA-AAATATTGATGTGCAT
1 AAGAAATATTGATGTGCAT
2613576 AAGAAATATT
1 AAGAAATATT
2613586 AGTTTTACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 11 0.46
18 6 0.25
19 7 0.29
ACGTcount: A:0.46, C:0.04, G:0.15, T:0.35
Consensus pattern (19 bp):
AAGAAATATTGATGTGCAT
Found at i:2615658 original size:43 final size:43
Alignment explanation
Indices: 2615539--2615830 Score: 349
Period size: 43 Copynumber: 6.8 Consensus size: 43
2615529 CCGTTACAGT
* *
2615539 AGGTCCCTTTTGCTGTGTACAAGGGTAAGCCTTACAGTTT-CCT
1 AGGTCCC-TTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
** * *
2615582 AGGTCATTTTGTTTTGTGCAAGGGTAAGCCTTACAGTTTCCCC
1 AGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
* * * * *
2615625 ATGTACTTTTACTGCGTGCAAGGGTAAGCCTTACAGTTT-CCC
1 AGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
* *
2615667 AGGTCCCTTTACTGTGTACAAGGGTAAGCCTTACAGTTTCCCC
1 AGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
* * *
2615710 AAGTCCCTTTGCTGTGTGTAAGGATAAGCCTTACAGTTTCCCC
1 AGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
*
2615753 AGGTCCCTTTGCTGTGTGCAAGGATAAGCCTTACAGTTT-CCC
1 AGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
* * *
2615795 AGG-CTCTTTTGCTATGTGCAAGGATAAGACCTTACA
1 AGGTC-CCTTTGCTGTGTGCAAGGGTAAG-CCTTACA
2615831 TTTTTTTATA
Statistics
Matches: 218, Mismatches: 27, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
41 1 0.00
42 93 0.43
43 124 0.57
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.33
Consensus pattern (43 bp):
AGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
Found at i:2615820 original size:85 final size:85
Alignment explanation
Indices: 2615545--2615830 Score: 360
Period size: 85 Copynumber: 3.4 Consensus size: 85
2615535 CAGTAGGTCC
* * * ** * *
2615545 CTTTTGCTGTGTACAAGGGTAAGCCTTACAGTTTCCTAGGTCATTTTGTTTTGTGCAAGGGTAAG
1 CTTTTGCTGTGTGCAAGGATAAGCCTTACAGTTTCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAG
*
2615610 CCTTACAGTTTCCCCATGTA
66 CCTTACAGTTTCCCCAAGTA
* * * * *
2615630 CTTTTACTGCGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTCCCTTTACTGTGTACAAGGGTAAG
1 CTTTTGCTGTGTGCAAGGATAAGCCTTACAGTTTCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAG
*
2615695 CCTTACAGTTTCCCCAAGTC
66 CCTTACAGTTTCCCCAAGTA
* * *
2615715 CCTTTGCTGTGTGTAAGGATAAGCCTTACAGTTTCCCCAGGTCCCTTTGCTGTGTGCAAGGATAA
1 CTTTTGCTGTGTGCAAGGATAAGCCTTACAGTTT-CCCAGGTCCCTTTGCTGTGTGCAAGGGTAA
*
2615780 GCCTTACAGTTT-CCCAGGCT-
65 GCCTTACAGTTTCCCCAAG-TA
*
2615800 CTTTTGCTATGTGCAAGGATAAGACCTTACA
1 CTTTTGCTGTGTGCAAGGATAAG-CCTTACA
2615831 TTTTTTTATA
Statistics
Matches: 174, Mismatches: 24, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
85 127 0.73
86 47 0.27
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.33
Consensus pattern (85 bp):
CTTTTGCTGTGTGCAAGGATAAGCCTTACAGTTTCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAG
CCTTACAGTTTCCCCAAGTA
Found at i:2623434 original size:18 final size:18
Alignment explanation
Indices: 2623413--2623452 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
2623403 GTCATTCAAC
2623413 GGTCAACGGGTTGGATCG
1 GGTCAACGGGTTGGATCG
*
2623431 GGTCAACGGGTTGGGTCG
1 GGTCAACGGGTTGGATCG
2623449 GGTC
1 GGTC
2623453 GGGTCAAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.12, C:0.17, G:0.47, T:0.23
Consensus pattern (18 bp):
GGTCAACGGGTTGGATCG
Found at i:2623475 original size:23 final size:23
Alignment explanation
Indices: 2623428--2623475 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
2623418 ACGGGTTGGA
* * *
2623428 TCGGGTCAACGGGTTGGGTCGGG
1 TCGGGTCAAAGGGTTGGATCAGG
*
2623451 TCGGGTCAAATGGTTGGATCAGG
1 TCGGGTCAAAGGGTTGGATCAGG
2623474 TC
1 TC
2623476 AACAGGTCGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.15, C:0.17, G:0.44, T:0.25
Consensus pattern (23 bp):
TCGGGTCAAAGGGTTGGATCAGG
Found at i:2623497 original size:41 final size:41
Alignment explanation
Indices: 2623421--2623498 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
2623411 ACGGTCAACG
* * * * *
2623421 GGTTGGATCGGGTCAACGGGTTGGGTCGGGTCGGGTCAAAT
1 GGTTGGATCAGGTCAACAGGTCGGGTCGAGCCGGGTCAAAT
*
2623462 GGTTGGATCAGGTCAACAGGTCGGGTCTAGCCGGGTC
1 GGTTGGATCAGGTCAACAGGTCGGGTCGAGCCGGGTC
2623499 GGGTCGGGTC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.15, C:0.18, G:0.44, T:0.23
Consensus pattern (41 bp):
GGTTGGATCAGGTCAACAGGTCGGGTCGAGCCGGGTCAAAT
Found at i:2625503 original size:3 final size:3
Alignment explanation
Indices: 2625490--2625532 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
2625480 TCTCTCGGTC
2625490 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2625533 TACAACATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:2625766 original size:22 final size:22
Alignment explanation
Indices: 2625741--2625784 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2625731 TGATTGTGGA
*
2625741 TGCTCCAATCATCATACCCTGC
1 TGCTCCAATCACCATACCCTGC
*
2625763 TGCTCCAGTCACCATACCCTGC
1 TGCTCCAATCACCATACCCTGC
2625785 CTGTTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.43, G:0.11, T:0.25
Consensus pattern (22 bp):
TGCTCCAATCACCATACCCTGC
Found at i:2640298 original size:37 final size:37
Alignment explanation
Indices: 2640255--2640384 Score: 149
Period size: 37 Copynumber: 3.6 Consensus size: 37
2640245 CAAAGTGCCC
*
2640255 TCTCGCTAGAGACAATTTTTCTTAAAAACAAATTTTG
1 TCTCGCTTGAGACAATTTTTCTTAAAAACAAATTTTG
* * * *
2640292 TCTCGCTTGAGA-TAGTTTTCTCTATAAATAAATTTTG
1 TCTCGCTTGAGACAATTTTTCT-TAAAAACAAATTTTG
* * **
2640329 TCTCGCTTGAGACAATTTCTCTT-AAAACAAATCTCA
1 TCTCGCTTGAGACAATTTTTCTTAAAAACAAATTTTG
2640365 TCTCGCTTGAGAC-ATTTTTC
1 TCTCGCTTGAGACAATTTTTC
2640385 CTTTGATATG
Statistics
Matches: 77, Mismatches: 14, Indels: 6
0.79 0.14 0.06
Matches are distributed among these distances:
35 6 0.08
36 28 0.36
37 37 0.48
38 6 0.08
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (37 bp):
TCTCGCTTGAGACAATTTTTCTTAAAAACAAATTTTG
Found at i:2640973 original size:19 final size:20
Alignment explanation
Indices: 2640948--2640995 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
2640938 AAAGATTTAA
* *
2640948 AAAATAAAATAGATAATAAT
1 AAAATAAAAGAGAAAATAAT
*
2640968 -AAATAAAAGGGAAAATAAT
1 AAAATAAAAGAGAAAATAAT
2640987 AAAATAAAA
1 AAAATAAAA
2640996 ATAATAGTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.19
Consensus pattern (20 bp):
AAAATAAAAGAGAAAATAAT
Found at i:2641695 original size:12 final size:12
Alignment explanation
Indices: 2641678--2641705 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
2641668 AAATACCTAA
2641678 AAATAATATTCT
1 AAATAATATTCT
2641690 AAATAATATTCT
1 AAATAATATTCT
2641702 AAAT
1 AAAT
2641706 CCTAATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (12 bp):
AAATAATATTCT
Found at i:2641843 original size:76 final size:74
Alignment explanation
Indices: 2641631--2641855 Score: 237
Period size: 76 Copynumber: 3.1 Consensus size: 74
2641621 TAAAACATCT
* * *
2641631 TAAATCTTAATTAAAATGCTTAAAACTATTTAAACTAAAATAC---CTAAAA-ATAATATTCT-A
1 TAAATCTTAATTAAAATACTAAAAACTATTTAAACTAAAATACAAAATAAAATATAATATT-TAA
*
2641691 AATAATATTC
65 AATAATATCC
* * * * * * *
2641701 TAAATCCTAATTAAAATACTGAAACCTATTAAAACTAAAATACCTAAAACAAAGATAAAATA-TA
1 TAAATCTTAATTAAAATACTAAAAACTATTTAAACTAAAATA-C-AAAATAAA-ATATAATATTT
2641765 AAAATAATATCC
63 AAAATAATATCC
* *
2641777 TAAAACTTAATTAAAATACTAAAAACTATTTAAACTAAAATACAAAGATAAAATATAATGTTTAA
1 TAAATCTTAATTAAAATACTAAAAACTATTTAAACTAAAATACAAA-ATAAAATATAATATTTAA
*
2641842 AATATTATCC
65 AATAATATCC
2641852 TAAA
1 TAAA
2641856 CTTGAGTTTA
Statistics
Matches: 125, Mismatches: 20, Indels: 15
0.78 0.12 0.09
Matches are distributed among these distances:
70 37 0.30
71 1 0.01
74 9 0.07
75 24 0.19
76 49 0.39
77 5 0.04
ACGTcount: A:0.56, C:0.12, G:0.02, T:0.31
Consensus pattern (74 bp):
TAAATCTTAATTAAAATACTAAAAACTATTTAAACTAAAATACAAAATAAAATATAATATTTAAA
ATAATATCC
Found at i:2642298 original size:13 final size:13
Alignment explanation
Indices: 2642280--2642304 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2642270 TTCAAACCTT
2642280 TCGTCGTGAATCG
1 TCGTCGTGAATCG
2642293 TCGTCGTGAATC
1 TCGTCGTGAATC
2642305 TTTAATTTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.24, G:0.28, T:0.32
Consensus pattern (13 bp):
TCGTCGTGAATCG
Found at i:2645370 original size:24 final size:24
Alignment explanation
Indices: 2645316--2645410 Score: 91
Period size: 24 Copynumber: 4.0 Consensus size: 24
2645306 ATTTCCAACT
* * * * *
2645316 TGAATTTTGTTATGATATATTACC
1 TGAATTCTGTTATGATTTCTGATC
* *
2645340 TGAATTCTGTTCTGATTTCTGATT
1 TGAATTCTGTTATGATTTCTGATC
* * *
2645364 TGGATTCTGTTATGATATCTTATC
1 TGAATTCTGTTATGATTTCTGATC
*
2645388 TGAATTCTGTTTTGATTTCTGAT
1 TGAATTCTGTTATGATTTCTGAT
2645411 ATCTCTGTTT
Statistics
Matches: 55, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.21, C:0.11, G:0.16, T:0.53
Consensus pattern (24 bp):
TGAATTCTGTTATGATTTCTGATC
Found at i:2657429 original size:19 final size:19
Alignment explanation
Indices: 2657407--2657443 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2657397 ATTTAATAAA
* *
2657407 ATAAAATAGATAATAATAT
1 ATAAAAGAGAAAATAATAT
2657426 ATAAAAGAGAAAATAATA
1 ATAAAAGAGAAAATAATA
2657444 AAATAATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (19 bp):
ATAAAAGAGAAAATAATAT
Found at i:2657530 original size:12 final size:12
Alignment explanation
Indices: 2657515--2657548 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2657505 ATAAAAATTA
2657515 AATTAAAGAAAT
1 AATTAAAGAAAT
*
2657527 AATTAAATAAAT
1 AATTAAAGAAAT
2657539 AATCTAAAGA
1 AAT-TAAAGA
2657549 GATAGGGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.65, C:0.03, G:0.06, T:0.26
Consensus pattern (12 bp):
AATTAAAGAAAT
Found at i:2657532 original size:17 final size:18
Alignment explanation
Indices: 2657496--2657537 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
2657486 GTTGTTTTTA
2657496 AAATAAAAGATAAAAATT
1 AAATAAAAGATAAAAATT
* *
2657514 AAATTAAAGA-AATAATT
1 AAATAAAAGATAAAAATT
2657531 AAATAAA
1 AAATAAA
2657538 TAATCTAAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (18 bp):
AAATAAAAGATAAAAATT
Found at i:2657737 original size:12 final size:12
Alignment explanation
Indices: 2657720--2657747 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
2657710 AAATACCTTA
2657720 AAATAATATTCT
1 AAATAATATTCT
2657732 AAATAATATTCT
1 AAATAATATTCT
2657744 AAAT
1 AAAT
2657748 CCTAATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (12 bp):
AAATAATATTCT
Found at i:2657786 original size:70 final size:73
Alignment explanation
Indices: 2657673--2657861 Score: 215
Period size: 76 Copynumber: 2.6 Consensus size: 73
2657663 CAATACATCT
* * * **
2657673 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCT-TAAA-ATAATAT-TCTAA
1 TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTACAAAGATAAAATATAAAA
*
2657734 ATAATATTC
65 ATAATATCC
*
2657743 TAAATCCTAATTAAAATACTAAAACCTATTTAAACAAAAATACCTAAAACAAAGATAAAATATAA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCT---ACAAAGATAAAATATAA
2657808 AAATAATATCC
63 AAATAATATCC
* * * *
2657819 TAAAACTTAATTAAAATTCTAAAACCTATTTAAATTAAAATAC
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATAC
2657862 AAAGAAAAAA
Statistics
Matches: 100, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
69 5 0.05
70 37 0.37
74 3 0.03
75 6 0.06
76 49 0.49
ACGTcount: A:0.55, C:0.14, G:0.01, T:0.31
Consensus pattern (73 bp):
TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTACAAAGATAAAATATAAAAA
TAATATCC
Found at i:2657885 original size:76 final size:75
Alignment explanation
Indices: 2657732--2657897 Score: 190
Period size: 76 Copynumber: 2.2 Consensus size: 75
2657722 ATAATATTCT
* * * *
2657732 AAATAATATTCTAAATCCTAATTAAAATACTAAAACCTATTTAAACAAAAATACCTAAAACAAAG
1 AAATAATATCCTAAAACCTAATTAAAATACTAAAACCTATTTAAACAAAAATACCAAAAAAAAAG
2657797 ATAAAATATAA
66 ATAAAATAT-A
* * **
2657808 AAATAATATCCTAAAACTTAATTAAAATTCTAAAACCTATTTAAATTAAAATA-CAAAGAAAAAA
1 AAATAATATCCTAAAACCTAATTAAAATACTAAAACCTATTTAAACAAAAATACCAAA-AAAAAA
* ** *
2657872 TATAATGTTTA
65 GATAAAATATA
*
2657883 AAATATTATCCTAAA
1 AAATAATATCCTAAA
2657898 CTTGAGTTTA
Statistics
Matches: 76, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
75 18 0.24
76 58 0.76
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (75 bp):
AAATAATATCCTAAAACCTAATTAAAATACTAAAACCTATTTAAACAAAAATACCAAAAAAAAAG
ATAAAATATA
Found at i:2658124 original size:6 final size:6
Alignment explanation
Indices: 2658115--2658181 Score: 80
Period size: 6 Copynumber: 11.2 Consensus size: 6
2658105 TATATATACA
* * * * *
2658115 TATCAT TATCAT TATCAC TATCAT TATTAA CATCAT TATCAT TATCAA
1 TATCAT TATCAT TATCAT TATCAT TATCAT TATCAT TATCAT TATCAT
*
2658163 CATCAT TATCAT TATCAT T
1 TATCAT TATCAT TATCAT T
2658182 CATTGTTCAT
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.36, C:0.19, G:0.00, T:0.45
Consensus pattern (6 bp):
TATCAT
Found at i:2658367 original size:24 final size:24
Alignment explanation
Indices: 2658292--2658355 Score: 119
Period size: 24 Copynumber: 2.7 Consensus size: 24
2658282 CAGCTCGTAT
*
2658292 AAATTGAACCGAAGTGCAGAGTAG
1 AAATTGCACCGAAGTGCAGAGTAG
2658316 AAATTGCACCGAAGTGCAGAGTAG
1 AAATTGCACCGAAGTGCAGAGTAG
2658340 AAATTGCACCGAAGTG
1 AAATTGCACCGAAGTG
2658356 TCACATAGAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.39, C:0.16, G:0.28, T:0.17
Consensus pattern (24 bp):
AAATTGCACCGAAGTGCAGAGTAG
Found at i:2658409 original size:46 final size:46
Alignment explanation
Indices: 2658357--2658449 Score: 127
Period size: 46 Copynumber: 2.0 Consensus size: 46
2658347 ACCGAAGTGT
*
2658357 CACATAGAAATATACC-AAAGTACCACATAGTATTATC-CTGAAGGAC
1 CACATAGAAATATACCAAAAG-ACCACATAGAATTATCTC-GAAGGAC
* *
2658403 CACATAGAAATGTCCCAAAAGACCACATAGAATTATCTCGAAGGAC
1 CACATAGAAATATACCAAAAGACCACATAGAATTATCTCGAAGGAC
2658449 C
1 C
2658450 CCGTAGAACC
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
46 37 0.88
47 5 0.12
ACGTcount: A:0.43, C:0.24, G:0.14, T:0.19
Consensus pattern (46 bp):
CACATAGAAATATACCAAAAGACCACATAGAATTATCTCGAAGGAC
Found at i:2658449 original size:23 final size:22
Alignment explanation
Indices: 2658357--2658449 Score: 78
Period size: 23 Copynumber: 4.0 Consensus size: 22
2658347 ACCGAAGTGT
* * *
2658357 CACATAGAAATATACCAAAGTAC
1 CACATAGAATTAT-CCGAAGGAC
*
2658380 CACATAGTATTATCCTGAAGGAC
1 CACATAGAATTATCC-GAAGGAC
* * * *
2658403 CACATAGAAATGTCCCAAAAGAC
1 CACATAGAATTAT-CCGAAGGAC
2658426 CACATAGAATTATCTCGAAGGAC
1 CACATAGAATTATC-CGAAGGAC
2658449 C
1 C
2658450 CCGTAGAACC
Statistics
Matches: 54, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
22 3 0.06
23 49 0.91
24 2 0.04
ACGTcount: A:0.43, C:0.24, G:0.14, T:0.19
Consensus pattern (22 bp):
CACATAGAATTATCCGAAGGAC
Found at i:2658668 original size:45 final size:45
Alignment explanation
Indices: 2658619--2658729 Score: 143
Period size: 45 Copynumber: 2.5 Consensus size: 45
2658609 ACATTATTCA
* ** *
2658619 ATATCATATAGCTTATATCATATATTCATATGTTTACGTAGTTCG
1 ATATCATATAGCTTATATCATATATTCACATGTACACATAGTTCG
* *
2658664 ATATCATATAGTTTATATCACATATTCACATGTACACATAGTTCG
1 ATATCATATAGCTTATATCATATATTCACATGTACACATAGTTCG
*
2658709 GTATC-TCATAGCTTATATCAT
1 ATATCAT-ATAGCTTATATCAT
2658730 TTTCTCAAAT
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
44 1 0.02
45 55 0.98
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.41
Consensus pattern (45 bp):
ATATCATATAGCTTATATCATATATTCACATGTACACATAGTTCG
Found at i:2659189 original size:20 final size:20
Alignment explanation
Indices: 2659164--2659212 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
2659154 TTCTGATTAG
2659164 TATCGATATCCCAGGTACAA
1 TATCGATATCCCAGGTACAA
* *
2659184 TATCGATATCCTAGGTACAG
1 TATCGATATCCCAGGTACAA
*
2659204 TATCTATAT
1 TATCGATAT
2659213 TCCTTAATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (20 bp):
TATCGATATCCCAGGTACAA
Found at i:2659299 original size:19 final size:20
Alignment explanation
Indices: 2659275--2659314 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2659265 GGAATATGTT
2659275 CTTAAA-AATGGTAATGATA
1 CTTAAACAATGGTAATGATA
* *
2659294 CTTAAACATTGGTATTGATA
1 CTTAAACAATGGTAATGATA
2659314 C
1 C
2659315 CCCTAGTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (20 bp):
CTTAAACAATGGTAATGATA
Found at i:2667101 original size:21 final size:19
Alignment explanation
Indices: 2667073--2667118 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
2667063 TTATTGATTC
2667073 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
2667093 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
2667112 ACTTAGT
1 A-TTAGT
2667119 AGGATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Found at i:2683757 original size:24 final size:24
Alignment explanation
Indices: 2683727--2683845 Score: 168
Period size: 24 Copynumber: 5.0 Consensus size: 24
2683717 AAACATATTT
* *
2683727 CATGTCAAGTATCATATCAAAATC
1 CATGTCAAGTATCAGATCAGAATC
*
2683751 CAGGTCAAGTATCAGATCAGAATC
1 CATGTCAAGTATCAGATCAGAATC
* *
2683775 CAAGTCAAGTATCAAATCAGAATC
1 CATGTCAAGTATCAGATCAGAATC
*
2683799 CATGTC-AGATATCATATCAGAATC
1 CATGTCAAG-TATCAGATCAGAATC
2683823 CATGTCAAGTATCAGATCAGAAT
1 CATGTCAAGTATCAGATCAGAAT
2683846 TAAAATCGAA
Statistics
Matches: 85, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
23 2 0.02
24 81 0.95
25 2 0.02
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.25
Consensus pattern (24 bp):
CATGTCAAGTATCAGATCAGAATC
Found at i:2685473 original size:17 final size:19
Alignment explanation
Indices: 2685435--2685475 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
2685425 AAGTGAAACT
2685435 AATATTTCTTATACGCATC
1 AATATTTCTTATACGCATC
*
2685454 AATATTT-TTAT-CGGATC
1 AATATTTCTTATACGCATC
2685471 AATAT
1 AATAT
2685476 GTCTGTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.48
18 4 0.19
19 7 0.33
ACGTcount: A:0.34, C:0.15, G:0.07, T:0.44
Consensus pattern (19 bp):
AATATTTCTTATACGCATC
Found at i:2686465 original size:82 final size:82
Alignment explanation
Indices: 2686313--2686601 Score: 357
Period size: 82 Copynumber: 3.5 Consensus size: 82
2686303 TTTGTTCAAT
* * *
2686313 ATCTGTGCCTCTTTTTTTC-GGTAGACAAATCTATGTTGGAAGACGTGTCTGCTCCACCATTTAT
1 ATCTGTGCCTC--TTTTTCGGGTAGACAAATCAATGTTCGAATACGTGTCTGCTCCACCATTTAT
2686377 TCAGGGGAAATTAGACTTG
64 TCAGGGGAAATTAGACTTG
* * * * * * * *
2686396 ATTTGTTCCTCTTTTTCGGGTAGACAAATCGATGTTGGAATACGTATTTGCTCTACCATTTATTT
1 ATCTGTGCCTCTTTTTCGGGTAGACAAATCAATGTTCGAATACGTGTCTGCTCCACCATTTATTC
*
2686461 AGGGGAAATCAGACTTG
66 AGGGGAAATTAGACTTG
* * * * *
2686478 ATCTATGCCTCTTTTTTGGGTTGACAAATCAATGTTCGAAGT-CGTGTCTGCTCCACAATTAATT
1 ATCTGTGCCTCTTTTTCGGGTAGACAAATCAATGTTCGAA-TACGTGTCTGCTCCACCATTTATT
2686542 CAGGGGAAATTAGACTTG
65 CAGGGGAAATTAGACTTG
* * *
2686560 ATCCGTGCCTTTTTTTCGAGTAGACAAATCAATGTTCGAATA
1 ATCTGTGCCTCTTTTTCGGGTAGACAAATCAATGTTCGAATA
2686602 GAAGTCTGCT
Statistics
Matches: 174, Mismatches: 29, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
81 7 0.04
82 157 0.90
83 10 0.06
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (82 bp):
ATCTGTGCCTCTTTTTCGGGTAGACAAATCAATGTTCGAATACGTGTCTGCTCCACCATTTATTC
AGGGGAAATTAGACTTG
Found at i:2687979 original size:10 final size:10
Alignment explanation
Indices: 2687948--2687979 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
2687938 CTTTTATTTA
2687948 TTTTTTCTTT
1 TTTTTTCTTT
2687958 CTTTTTTCTTT
1 -TTTTTTCTTT
2687969 TTTTTTCTTT
1 TTTTTTCTTT
2687979 T
1 T
2687980 CTAATTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.52
11 10 0.48
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:2693607 original size:23 final size:23
Alignment explanation
Indices: 2693577--2693625 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
2693567 CTTAATCATT
*
2693577 TGACACCATACCCAATACATGGG
1 TGACACCATACCCAATACATGAG
2693600 TGACACCATACCCAATACATGAG
1 TGACACCATACCCAATACATGAG
2693623 TGA
1 TGA
2693626 TTCCACTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.37, C:0.29, G:0.16, T:0.18
Consensus pattern (23 bp):
TGACACCATACCCAATACATGAG
Found at i:2695283 original size:20 final size:20
Alignment explanation
Indices: 2695246--2695285 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2695236 TAAAATGCGG
** *
2695246 TGCAAAAAATTTAGATGCAT
1 TGCAAAAAATAAAAATGCAT
2695266 TGCAAAAAATAAAAATGCAT
1 TGCAAAAAATAAAAATGCAT
2695286 ATGAAAAATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.10, G:0.12, T:0.25
Consensus pattern (20 bp):
TGCAAAAAATAAAAATGCAT
Found at i:2701401 original size:20 final size:21
Alignment explanation
Indices: 2701376--2701415 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
2701366 ACCCGTTAAC
*
2701376 CATTGATCG-TCGTTGACCGT
1 CATTGATCGACCGTTGACCGT
2701396 CATTGATCGACCGTTGACCG
1 CATTGATCGACCGTTGACCG
2701416 ACCATTGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.17, C:0.28, G:0.25, T:0.30
Consensus pattern (21 bp):
CATTGATCGACCGTTGACCGT
Found at i:2705656 original size:10 final size:10
Alignment explanation
Indices: 2705641--2705699 Score: 64
Period size: 10 Copynumber: 5.8 Consensus size: 10
2705631 GACCGTTGAT
*
2705641 CGTTGACCGC
1 CGTTGACTGC
*
2705651 CGTTGACTAC
1 CGTTGACTGC
**
2705661 CGTTGACCAC
1 CGTTGACTGC
2705671 CGTTGACTGC
1 CGTTGACTGC
*
2705681 CATTGACTGAC
1 CGTTGACTG-C
2705692 CGTTGACT
1 CGTTGACT
2705700 TTTTTCGGGT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
10 33 0.80
11 8 0.20
ACGTcount: A:0.17, C:0.32, G:0.24, T:0.27
Consensus pattern (10 bp):
CGTTGACTGC
Found at i:2705666 original size:20 final size:20
Alignment explanation
Indices: 2705641--2705699 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
2705631 GACCGTTGAT
2705641 CGTTGACCGCCGTTGACTAC
1 CGTTGACCGCCGTTGACTAC
* *
2705661 CGTTGACCACCGTTGACTGC
1 CGTTGACCGCCGTTGACTAC
* *
2705681 CATTGACTGACCGTTGACT
1 CGTTGACCG-CCGTTGACT
2705700 TTTTTCGGGT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
20 24 0.73
21 9 0.27
ACGTcount: A:0.17, C:0.32, G:0.24, T:0.27
Consensus pattern (20 bp):
CGTTGACCGCCGTTGACTAC
Found at i:2705677 original size:30 final size:31
Alignment explanation
Indices: 2705641--2705698 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
2705631 GACCGTTGAT
*
2705641 CGTTGACCGCCGTTGACT-ACCGTTGACCAC
1 CGTTGACCGCCATTGACTGACCGTTGACCAC
*
2705671 CGTTGACTGCCATTGACTGACCGTTGAC
1 CGTTGACCGCCATTGACTGACCGTTGAC
2705699 TTTTTTCGGG
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:0.17, C:0.33, G:0.24, T:0.26
Consensus pattern (31 bp):
CGTTGACCGCCATTGACTGACCGTTGACCAC
Found at i:2708634 original size:30 final size:30
Alignment explanation
Indices: 2708620--2708693 Score: 130
Period size: 30 Copynumber: 2.5 Consensus size: 30
2708610 AATTTCAGAC
* *
2708620 TGAATTTCATTTTCAATTTTAATTTGAGTT
1 TGAATTTCAATTTCAATTTTAATTTAAGTT
2708650 TGAATTTCAATTTCAATTTTAATTTAAGTT
1 TGAATTTCAATTTCAATTTTAATTTAAGTT
2708680 TGAATTTCAATTTC
1 TGAATTTCAATTTC
2708694 GCCTTCACTA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.30, C:0.08, G:0.08, T:0.54
Consensus pattern (30 bp):
TGAATTTCAATTTCAATTTTAATTTAAGTT
Found at i:2708693 original size:6 final size:6
Alignment explanation
Indices: 2708600--2708693 Score: 66
Period size: 6 Copynumber: 15.7 Consensus size: 6
2708590 TTTATACATT
* * * * * * *
2708600 TTTCAT TTTCAA TTTCAGA -CTGAA TTTCAT TTTCAA TTTTAA TTTGAG
1 TTTCAA TTTCAA TTTCA-A TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA
* * *
2708648 TTTGAA TTTCAA TTTCAA TTTTAA TTT-AA GTTTGAA TTTCAA TTTC
1 TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA -TTTCAA TTTCAA TTTC
2708694 GCCTTCACTA
Statistics
Matches: 70, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
5 3 0.04
6 64 0.91
7 3 0.04
ACGTcount: A:0.29, C:0.11, G:0.07, T:0.53
Consensus pattern (6 bp):
TTTCAA
Found at i:2709842 original size:4 final size:4
Alignment explanation
Indices: 2709833--2709858 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2709823 GAGATTTTAT
2709833 ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC AT
2709859 CTTTGTATCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:2710098 original size:26 final size:25
Alignment explanation
Indices: 2710050--2710106 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
2710040 TATTTTTTAT
**
2710050 AAAAAATATTTAACTTACTTAAAAC
1 AAAAAATATTTAACTTAAATAAAAC
*
2710075 AAAACATATCTTAACTTAAAT-AAAC
1 AAAAAATAT-TTAACTTAAATAAAAC
2710100 AACAAAA
1 AA-AAAA
2710107 GAGAGGTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 14 0.54
26 12 0.46
ACGTcount: A:0.60, C:0.14, G:0.00, T:0.26
Consensus pattern (25 bp):
AAAAAATATTTAACTTAAATAAAAC
Found at i:2710584 original size:59 final size:58
Alignment explanation
Indices: 2710511--2710851 Score: 502
Period size: 59 Copynumber: 5.8 Consensus size: 58
2710501 AAGTAATATT
* *
2710511 ATTTTCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTTATACACCTAGTATG
1 ATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGG-AATTTATACACTTAGTATG
* *
2710570 ATTTCCTTACCATTTTAGCACCCAAAGTGCCCTATTTGGAATTTAATACACTTAGTATG
1 ATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAATTT-ATACACTTAGTATG
* * * *
2710629 TTTTCCTTACCATTTTAGCACCCAAAGTGCCCTATCTGGAATTTCATACACGTAGTATT
1 ATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAATTT-ATACACTTAGTATG
* * *
2710688 ATTTCCTTACTATTTTAGCACACAAAGTGCCCTATTTGGAATATCATACACTTAGTATG
1 ATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAT-TTATACACTTAGTATG
* *
2710747 ACTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTAGTATG
1 ATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGG-AATTTATACACTTAGTATG
*
2710806 ATTTCCTTGCCATTTTAGCACACAAAGTGCCCTATCTGGAAATTTA
1 ATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGG-AATTTA
2710852 CCATACATTT
Statistics
Matches: 257, Mismatches: 22, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
58 5 0.02
59 248 0.96
60 4 0.02
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (58 bp):
ATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAATTTATACACTTAGTATG
Found at i:2710803 original size:177 final size:178
Alignment explanation
Indices: 2710487--2710846 Score: 562
Period size: 177 Copynumber: 2.0 Consensus size: 178
2710477 TAAATTCAAT
*
2710487 TGGAATTTCATACAAAGTAATATTATTTTCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAA
1 TGGAATTTCATACAAAGTAATATTATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAA
* * * * *
2710552 ATTTATACACCTAGTATGATTTCCTTACCATTTTAGCACCCAAAGTGCCCTATTTGGAATTTAAT
66 ATTCATACACCTAGTATGACTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTAAT
* *
2710617 ACACTTAGTATGTTTTCCTTACCATTTTAGCACCCAAAGTGCCCTATC
131 ACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
* * * *
2710665 TGGAATTTCATAC-ACGTAGTATTATTTCCTTACTATTTTAGCACACAAAGTGCCCTATTTGG-A
1 TGGAATTTCATACAAAGTAATATTATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAA
* *
2710728 ATATCATACACTTAGTATGACTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCA
66 AT-TCATACACCTAGTATGACTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTAA
*
2710793 TACACTTAGTATGATTTCCTTGCCATTTTAGCACACAAAGTGCCCTATC
130 TACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
2710842 TGGAA
1 TGGAA
2710847 ATTTACCATA
Statistics
Matches: 166, Mismatches: 15, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
176 3 0.02
177 150 0.90
178 13 0.08
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.36
Consensus pattern (178 bp):
TGGAATTTCATACAAAGTAATATTATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAA
ATTCATACACCTAGTATGACTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTAAT
ACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
Found at i:2711313 original size:53 final size:53
Alignment explanation
Indices: 2711250--2711367 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 53
2711240 CCTTTAGAAG
*
2711250 GGTATCGATACACTACTGGGGTATCGGTACCCAAATTAAATTCGATGTTTACA
1 GGTATCGATACACTACTGGGGTATCGGTACCCAAATAAAATTCGATGTTTACA
*
2711303 GGTATCGATACACTACTGGGGTATCGGTACCCAAATAAAATTTGATGTTTACA
1 GGTATCGATACACTACTGGGGTATCGGTACCCAAATAAAATTCGATGTTTACA
*
2711356 GGTATCAATACA
1 GGTATCGATACA
2711368 TGCCTGATGG
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 62 1.00
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (53 bp):
GGTATCGATACACTACTGGGGTATCGGTACCCAAATAAAATTCGATGTTTACA
Found at i:2716938 original size:26 final size:24
Alignment explanation
Indices: 2716889--2716938 Score: 57
Period size: 26 Copynumber: 2.0 Consensus size: 24
2716879 GTTTTTTTTT
*
2716889 ATAAAAATATTTAACTAACTTAAA
1 ATAAAAATATTTAACTAACATAAA
2716913 ATAAAACATATCTTAACTTAA-ATAAA
1 ATAAAA-ATAT-TTAAC-TAACATAAA
2716939 CAACAAAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
24 6 0.27
25 4 0.18
26 9 0.41
27 3 0.14
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.32
Consensus pattern (24 bp):
ATAAAAATATTTAACTAACATAAA
Found at i:2717411 original size:59 final size:59
Alignment explanation
Indices: 2717319--2717739 Score: 610
Period size: 59 Copynumber: 7.1 Consensus size: 59
2717309 TAAATTTAAT
* * * * * * *
2717319 TGGAATTTCATACAGTCAATATGATTTTCTTACCATTTTAGCACATAAAGTGCCCTATA
1 TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
* * * * * *
2717378 TGGAAATTCGTACACCTATTATGATTTCTTTACCATTTTAGCACCCAAAGTGCCATATC
1 TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
* * *
2717437 TGGAATTTCATACACTTAGTATGATTTCCTTACCATTTTAGCACCCAAAGTGCTCTATC
1 TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
* * *
2717496 TAGAATTTCATACACTTAGTATGATTTCTTTACCATTTTAGCACACAAAGTGCCCTATC
1 TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
**
2717555 TGG-AATATCATACACTTAGTATGACATCCTTACCATTTTAGCACACAAAGTGCCCTATC
1 TGGAAAT-TCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
* *
2717614 TGGAAATTCATACATTTAGTATGATTTCCTTACAATTTTAGCACACAAAGTGCCCTATC
1 TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
*
2717673 TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATA
1 TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
2717732 TGGAAATT
1 TGGAAATT
2717740 TAACATACAT
Statistics
Matches: 325, Mismatches: 35, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
58 2 0.01
59 320 0.98
60 3 0.01
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (59 bp):
TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
Found at i:2718223 original size:53 final size:53
Alignment explanation
Indices: 2718141--2718257 Score: 180
Period size: 53 Copynumber: 2.2 Consensus size: 53
2718131 CTTCAGAAGG
* * *
2718141 GTATCGATACACTACTGGGGTATCGGTACCCAAAATAAATTCGTTGTTTACAA
1 GTATCGATACACTACTGGCGTATCAGTACCCAAAATAAATTCGATGTTTACAA
* * *
2718194 GTATCGATACACTATTGGCGTATCAGTACCCAAATTAAATTCGATGTTTACAG
1 GTATCGATACACTACTGGCGTATCAGTACCCAAAATAAATTCGATGTTTACAA
2718247 GTATCGATACA
1 GTATCGATACA
2718258 TGCCTGATGG
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 58 1.00
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (53 bp):
GTATCGATACACTACTGGCGTATCAGTACCCAAAATAAATTCGATGTTTACAA
Found at i:2720061 original size:21 final size:21
Alignment explanation
Indices: 2719995--2720051 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
2719985 TTTACATAAA
*
2719995 GTATTGATACTTTTTGTATAT
1 GTATCGATACTTTTTGTATAT
*
2720016 GTATCGATACGTTTTGTATAT
1 GTATCGATACTTTTTGTATAT
2720037 GTATCGATACTTTTT
1 GTATCGATACTTTTT
2720052 TGTCCAGTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.23, C:0.09, G:0.16, T:0.53
Consensus pattern (21 bp):
GTATCGATACTTTTTGTATAT
Found at i:2729702 original size:21 final size:21
Alignment explanation
Indices: 2729678--2729724 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
2729668 GCAATTAGGG
2729678 ATTCTCATGAGTGATTACCTT
1 ATTCTCATGAGTGATTACCTT
*
2729699 ATTCTGATGAGTGATTACCTT
1 ATTCTCATGAGTGATTACCTT
2729720 ATTCT
1 ATTCT
2729725 TTACCACTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.23, C:0.17, G:0.15, T:0.45
Consensus pattern (21 bp):
ATTCTCATGAGTGATTACCTT
Found at i:2732394 original size:12 final size:12
Alignment explanation
Indices: 2732377--2732401 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2732367 TTGTTGTATG
2732377 TTTTGATACAGT
1 TTTTGATACAGT
2732389 TTTTGATACAGT
1 TTTTGATACAGT
2732401 T
1 T
2732402 AAACATACTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.52
Consensus pattern (12 bp):
TTTTGATACAGT
Found at i:2733965 original size:2 final size:2
Alignment explanation
Indices: 2733958--2734029 Score: 135
Period size: 2 Copynumber: 35.5 Consensus size: 2
2733948 CGTAAGAACG
2733958 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2734000 TA TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
2734030 GTTTGTCTTG
Statistics
Matches: 69, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 67 0.97
3 2 0.03
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2743988 original size:20 final size:20
Alignment explanation
Indices: 2743951--2743988 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2743941 GAGCCTCTCC
*
2743951 TTGAACCAAAAATTAAATAT
1 TTGAACCAAAAATCAAATAT
2743971 TTGAAGCCAAAAA-CAAAT
1 TTGAA-CCAAAAATCAAAT
2743989 TTTCAAATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.55, C:0.13, G:0.08, T:0.24
Consensus pattern (20 bp):
TTGAACCAAAAATCAAATAT
Found at i:2755764 original size:3 final size:3
Alignment explanation
Indices: 2755756--2755823 Score: 118
Period size: 3 Copynumber: 22.7 Consensus size: 3
2755746 ACATAGGAAC
* *
2755756 TAT TAT TAT TAT TAT TAT TGT TAT TAT TAT TAT TAT TAT AAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2755804 TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
2755824 CTACTTTAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:2759959 original size:27 final size:27
Alignment explanation
Indices: 2759913--2759980 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
2759903 TAAATGAAAG
* *
2759913 GACTAAAATACTCTTGAACTATAAAAT
1 GACTAAAATACCCTTAAACTATAAAAT
*
2759940 GACTAAAATACCCTTAAACTCTAAAAT
1 GACTAAAATACCCTTAAACTATAAAAT
* *
2759967 AACCAAAATACCCT
1 GACTAAAATACCCT
2759981 GAGCTCTGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.49, C:0.22, G:0.04, T:0.25
Consensus pattern (27 bp):
GACTAAAATACCCTTAAACTATAAAAT
Found at i:2760765 original size:39 final size:38
Alignment explanation
Indices: 2760707--2760828 Score: 154
Period size: 39 Copynumber: 3.1 Consensus size: 38
2760697 ATGCTACGAC
* * *
2760707 TAGGGTAAGTCATTGCCGCAGACTCATTTTCTTTGTGCA
1 TAGGGTAAGTCCTTACCGCA-ACTCATTTGCTTTGTGCA
*
2760746 TAGGGTAAGTCCTTACCGCATACTCCTTTGCTTTGTGCA
1 TAGGGTAAGTCCTTACCGCA-ACTCATTTGCTTTGTGCA
* * *
2760785 TAGGGTAAGTTCTTACCGTAAGCTCATTTGCTTCGTGCA
1 TAGGGTAAGTCCTTACCGCAA-CTCATTTGCTTTGTGCA
2760824 TAGGG
1 TAGGG
2760829 GAAAACATTA
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
38 1 0.01
39 72 0.99
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.35
Consensus pattern (38 bp):
TAGGGTAAGTCCTTACCGCAACTCATTTGCTTTGTGCA
Found at i:2760840 original size:39 final size:38
Alignment explanation
Indices: 2760729--2760907 Score: 119
Period size: 39 Copynumber: 4.6 Consensus size: 38
2760719 TTGCCGCAGA
* * ** * * *
2760729 CTCATTTTCTTTGTGCATAGGGTAAGTCCTTACCGCATA
1 CTCATTTGC-TTGTGCATAGGGGAAAACATTACCGTATG
* * ** *
2760768 CTCCTTTGCTTTGTGCATAGGGTAAGTTC-TTACCGTAAG
1 CTCATTTGC-TTGTGCATAGGGGAA-AACATTACCGTATG
*
2760807 CTCATTTGCTTCGTGCATAGGGGAAAACATTACCGCATG
1 CTCATTTGCTT-GTGCATAGGGGAAAACATTACCGTATG
* * *
2760846 CCCATTTTG-TATAGTGCATAGGGGAAAACTTTATCGTATG
1 CTCA-TTTGCT-T-GTGCATAGGGGAAAACATTACCGTATG
*
2760886 CTCCTTTGCCTTGTGCATAGGG
1 CTCATTTG-CTTGTGCATAGGG
2760908 AAATTTGTCT
Statistics
Matches: 114, Mismatches: 19, Indels: 14
0.78 0.13 0.10
Matches are distributed among these distances:
38 3 0.03
39 76 0.67
40 34 0.30
41 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.35
Consensus pattern (38 bp):
CTCATTTGCTTGTGCATAGGGGAAAACATTACCGTATG
Found at i:2761250 original size:28 final size:27
Alignment explanation
Indices: 2761211--2761263 Score: 88
Period size: 28 Copynumber: 1.9 Consensus size: 27
2761201 TTTAAATTTT
*
2761211 AAAAAATTGAAAAACTGAATAAATACTA
1 AAAAAATTGAAAAACT-AAAAAATACTA
2761239 AAAAAATTGAAAAACTAAAAAATAC
1 AAAAAATTGAAAAACTAAAAAATAC
2761264 CAACGATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.68, C:0.08, G:0.06, T:0.19
Consensus pattern (27 bp):
AAAAAATTGAAAAACTAAAAAATACTA
Found at i:2767837 original size:32 final size:31
Alignment explanation
Indices: 2767796--2767883 Score: 108
Period size: 32 Copynumber: 2.8 Consensus size: 31
2767786 GTAACACTTG
* *
2767796 GGTAGGCTCTAGAGCCCCAATGTATTTCCTT
1 GGTAGGCTCTAGAGCCCCAAGGTATTCCCTT
2767827 CGGTAGGCTCTA-AGGCCCCAAGGTATTCCCTT
1 -GGTAGGCTCTAGA-GCCCCAAGGTATTCCCTT
2767859 GCGTAGGCTCTCAG-GCCCCAAGGTA
1 G-GTAGGCTCT-AGAGCCCCAAGGTA
2767884 CACTATTGGG
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
31 2 0.04
32 47 0.94
33 1 0.02
ACGTcount: A:0.19, C:0.30, G:0.26, T:0.25
Consensus pattern (31 bp):
GGTAGGCTCTAGAGCCCCAAGGTATTCCCTT
Found at i:2767897 original size:32 final size:32
Alignment explanation
Indices: 2767793--2767911 Score: 107
Period size: 32 Copynumber: 3.7 Consensus size: 32
2767783 AAGGTAACAC
* **
2767793 TTGGGTAGGCTCT-AGAGCCCCAATGTATTTCC-
1 TTGGGTAGGCTCTCAG-GCCCCAAGGTA-CACCA
* * ** *
2767825 TTCGGTAGGCTCTAAGGCCCCAAGGTATTCCC
1 TTGGGTAGGCTCTCAGGCCCCAAGGTACACCA
* *
2767857 TTGCGTAGGCTCTCAGGCCCCAAGGTACACTA
1 TTGGGTAGGCTCTCAGGCCCCAAGGTACACCA
*
2767889 TTGGGTAGGCTCTCGGGCCCCAA
1 TTGGGTAGGCTCTCAGGCCCCAA
2767912 AATAATCCCT
Statistics
Matches: 74, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
31 4 0.05
32 68 0.92
33 2 0.03
ACGTcount: A:0.18, C:0.29, G:0.27, T:0.25
Consensus pattern (32 bp):
TTGGGTAGGCTCTCAGGCCCCAAGGTACACCA
Found at i:2786035 original size:19 final size:22
Alignment explanation
Indices: 2785991--2786048 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
2785981 GTTTCAGTTT
*
2785991 TTTCGTTTTGGTTCGAATAATGG
1 TTTC-TTTTTGTTCGAATAATGG
2786014 TTT-TTTTTGTTCGAAT-AT-G
1 TTTCTTTTTGTTCGAATAATGG
2786033 TTTCTTTTT-TTCGAAT
1 TTTCTTTTTGTTCGAAT
2786049 GGGTTTTTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 11 0.33
20 7 0.21
21 12 0.36
23 3 0.09
ACGTcount: A:0.16, C:0.09, G:0.17, T:0.59
Consensus pattern (22 bp):
TTTCTTTTTGTTCGAATAATGG
Found at i:2786054 original size:19 final size:19
Alignment explanation
Indices: 2785996--2786056 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 19
2785986 AGTTTTTTCG
*
2785996 TTTTGGTTCGAATAATGGTTT
1 TTTTTGTTCGAAT-A-GGTTT
*
2786017 TTTTTGTTCGAATATGTTT
1 TTTTTGTTCGAATAGGTTT
*
2786036 CTTTTT-TTCGAATGGGTTT
1 -TTTTTGTTCGAATAGGTTT
2786055 TT
1 TT
2786057 GAATGCTTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
18 2 0.06
19 15 0.43
20 6 0.17
21 12 0.34
ACGTcount: A:0.15, C:0.07, G:0.20, T:0.59
Consensus pattern (19 bp):
TTTTTGTTCGAATAGGTTT
Found at i:2786563 original size:24 final size:24
Alignment explanation
Indices: 2786536--2786619 Score: 100
Period size: 24 Copynumber: 3.5 Consensus size: 24
2786526 TTATAAAGCC
2786536 TGAAAACACA-AAT-AGAAATAAGAA
1 TGAAAACA-AGAATGAG-AATAAGAA
*
2786560 TGAAAATAAGAATGAGAATAAGAA
1 TGAAAACAAGAATGAGAATAAGAA
* *
2786584 TGAGAATAAGAATGAGAATAAGAA
1 TGAAAACAAGAATGAGAATAAGAA
*
2786608 TGAGAACAAGAA
1 TGAAAACAAGAA
2786620 CAAGAACAAG
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
23 1 0.02
24 52 0.95
25 2 0.04
ACGTcount: A:0.62, C:0.04, G:0.20, T:0.14
Consensus pattern (24 bp):
TGAAAACAAGAATGAGAATAAGAA
Found at i:2786568 original size:12 final size:12
Alignment explanation
Indices: 2786552--2786619 Score: 118
Period size: 12 Copynumber: 5.7 Consensus size: 12
2786542 CACAAATAGA
*
2786552 AATAAGAATGAA
1 AATAAGAATGAG
2786564 AATAAGAATGAG
1 AATAAGAATGAG
2786576 AATAAGAATGAG
1 AATAAGAATGAG
2786588 AATAAGAATGAG
1 AATAAGAATGAG
2786600 AATAAGAATGAG
1 AATAAGAATGAG
*
2786612 AACAAGAA
1 AATAAGAA
2786620 CAAGAACAAG
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 54 1.00
ACGTcount: A:0.62, C:0.01, G:0.22, T:0.15
Consensus pattern (12 bp):
AATAAGAATGAG
Found at i:2786589 original size:6 final size:6
Alignment explanation
Indices: 2786556--2786613 Score: 71
Period size: 6 Copynumber: 9.7 Consensus size: 6
2786546 AATAGAAATA
* * * * *
2786556 AGAATG AAAATA AGAATG AGAATA AGAATG AGAATA AGAATG AGAATA
1 AGAATG AGAATG AGAATG AGAATG AGAATG AGAATG AGAATG AGAATG
2786604 AGAATG AGAA
1 AGAATG AGAA
2786614 CAAGAACAAG
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.60, C:0.00, G:0.24, T:0.16
Consensus pattern (6 bp):
AGAATG
Found at i:2786619 original size:6 final size:6
Alignment explanation
Indices: 2786610--2786967 Score: 716
Period size: 6 Copynumber: 59.7 Consensus size: 6
2786600 AATAAGAATG
2786610 AGAACA AGAACA AGAACA AGAACA AGAACA AGAACA AGAACA AGAACA
1 AGAACA AGAACA AGAACA AGAACA AGAACA AGAACA AGAACA AGAACA
2786658 AGAACA AGAACA AGAACA AGAACA AGAACA AGAACA AGAACA AGAACA
1 AGAACA AGAACA AGAACA AGAACA AGAACA AGAACA AGAACA AGAACA
2786706 AGAACA AGAACA AGAACA AGAACA AGAACA AGAACA AGAACA AGAACA
1 AGAACA AGAACA AGAACA AGAACA AGAACA AGAACA AGAACA AGAACA
2786754 AGAACA AGAACA AGAACA AGAACA AGAACA AGAACA AGAACA AGAACA
1 AGAACA AGAACA AGAACA AGAACA AGAACA AGAACA AGAACA AGAACA
2786802 AGAACA AGAACA AGAACA AGAACA AGAACA AGAACA AGAACA AGAACA
1 AGAACA AGAACA AGAACA AGAACA AGAACA AGAACA AGAACA AGAACA
2786850 AGAACA AGAACA AGAACA AGAACA AGAACA AGAACA AGAACA AGAACA
1 AGAACA AGAACA AGAACA AGAACA AGAACA AGAACA AGAACA AGAACA
2786898 AGAACA AGAACA AGAACA AGAACA AGAACA AGAACA AGAACA AGAACA
1 AGAACA AGAACA AGAACA AGAACA AGAACA AGAACA AGAACA AGAACA
2786946 AGAACA AGAACA AGAACA AGAA
1 AGAACA AGAACA AGAACA AGAA
2786968 AGACTTACTA
Statistics
Matches: 352, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 352 1.00
ACGTcount: A:0.67, C:0.16, G:0.17, T:0.00
Consensus pattern (6 bp):
AGAACA
Found at i:2787383 original size:234 final size:233
Alignment explanation
Indices: 2786964--2788023 Score: 1188
Period size: 234 Copynumber: 4.5 Consensus size: 233
2786954 AACAAGAACA
* * ** * * *
2786964 AGAAAGACTTACTAATGGCCCGAAGGACATT-CCAACTTTGGAAATAGTTTACTAGGTAAGAAAC
1 AGAAAGACTTACTGATGGCCCGAATGAC-TTATAAATTTTGAAAATAGTTTACTAGGTAAGAAAT
* * *
2787028 CATTTTTTACTTTTCAAAAATTTCAATTTTTAGATTTAAATGAGAAACCTTTCTCATTTTTCGAG
65 C-TTTCTTACTTTTCAAAAATTTCAATTTTCATATTTAAATGAGAAACCTTTCTCATTTTTCGAG
* * ** * *
2787093 AAACATATGAAAACATCCTGCTCGAAGGTCTCGTGGATGGCCAGAAGGACTTATCATCTTTCTCT
129 AAACATGTGAAAACATCCTGCCCGAAGGTCTTATGGATGGCCTGAAGGACTTATCATCTTTCTCG
* **
2787158 AAAGACTTACACATGATTCAAAGGATTTAAGCATCATTCTT
194 AAAGACTTACAGATGACCCAAAGGATTTAAGCATCATTC-T
* *
2787199 AG-AAGACTTAGTGATGGCCCGAACGACTTATAAATTTTGAAAATAGTTTACTAGGTAAGAAATC
1 AGAAAGACTTACTGATGGCCCGAATGACTTATAAATTTTGAAAATAGTTTACTAGGTAAGAAATC
* * *
2787263 TTTCTTACTTTTCAAAAAAATTCAATTTTCAGATTTAAATGAGAAACCTTTCTCATTTTTTGAGA
66 TTTCTTACTTTTC-AAAAATTTCAATTTTCATATTTAAATGAGAAACCTTTCTCATTTTTCGAGA
* * * ** *
2787328 GACATGTGAAAACATCGTGCCCGAAGGTCTTACGGATGGCCTGAAGGGTTTATCATCTTACTCGA
130 AACATGTGAAAACATCCTGCCCGAAGGTCTTATGGATGGCCTGAAGGACTTATCATCTTTCTCGA
* * ** * *
2787393 AAGGCTTACAGATGAACTGAAGAATTTAAGCATCATGCT
195 AAGACTTACAGATGACCCAAAGGATTTAAGCATCATTCT
* * *
2787432 TGAAAGACTTACTGATAGCCCAAATGACTTACT-AATTTT-AGAAATAGTTTACTAGGTAAGAAA
1 AGAAAGACTTACTGATGGCCCGAATGACTTA-TAAATTTTGA-AAATAGTTTACTAGGTAAGAAA
* * * *
2787495 GT-TTCCTTACTTTTCAAAAGTTTTAATTTTCATATTTAAATGAGAAACCTTTCTCATTTTTTGA
64 -TCTTTCTTACTTTTCAAAAATTTCAATTTTCATATTTAAATGAGAAACCTTTCTCATTTTTCGA
* * ** *
2787559 GAAACATGTGAAAATATCCTTCTTGAAGGTCTTATGGATGGCCCT-AAGGGCTTATCATCTTTCT
128 GAAACATGTGAAAACATCCTGCCCGAAGGTCTTATGGATGG-CCTGAAGGACTTATCATCTTTCT
* * **
2787623 CGAAAGGCTTACAGATGACCCAAAGGATTTAATCATCATGAT
192 CGAAAGACTTACAGATGACCCAAAGGATTTAAGCATCATTCT
* * * * * *
2787665 CGAGAGACTTACTGATGGCCCGAATAACTTTTCAATTTTTGGAAATAGTTTACTAGGTAAGAAAT
1 AGAAAGACTTACTGATGGCCCGAATGACTTAT-AAATTTTGAAAATAGTTTACTAGGTAAGAAAT
* * *
2787730 CTTTCTTTCTTTTTCAAAATTTTC-ATATTTCATATTTAAATGAGAAACATTTCTCATTTTTCGA
65 CTTTCTTAC-TTTTCAAAAATTTCAAT-TTTCATATTTAAATGAGAAACCTTTCTCATTTTTCGA
* * * *
2787794 GAGACATGTGAAAATATTCTGCCCGAAGGTCTTATGGATGGCTTGAAGGACTTATCATCTTGT-T
128 GAAACATGTGAAAACATCCTGCCCGAAGGTCTTATGGATGGCCTGAAGGACTTATCATCTT-TCT
* * * * *
2787858 CGAAAGACTTACAGATGACCCGAATGACTTAAGCATCGTACT
192 CGAAAGACTTACAGATGACCCAAAGGATTTAAGCATCATTCT
* * * * *
2787900 CGAAAGACTTATTGATGGCCCGAAGGAC-TA-AAATTTTTTGAAAATAATTTACTATGTAAGAAA
1 AGAAAGACTTACTGATGGCCCGAATGACTTATAAA--TTTTGAAAATAGTTTACTAGGTAAGAAA
* * * * *
2787963 CCTTTCTTACTTTTCAAAAAATTT-ATTTTTTATTTTTAAATGAGAAACATTTCTCATTTTT
64 TCTTTCTTACTTTTC-AAAAATTTCAATTTTCATATTTAAATGAGAAACCTTTCTCATTTTT
2788024 ATAAAACGAC
Statistics
Matches: 705, Mismatches: 101, Indels: 40
0.83 0.12 0.05
Matches are distributed among these distances:
232 3 0.00
233 212 0.30
234 328 0.47
235 161 0.23
236 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (233 bp):
AGAAAGACTTACTGATGGCCCGAATGACTTATAAATTTTGAAAATAGTTTACTAGGTAAGAAATC
TTTCTTACTTTTCAAAAATTTCAATTTTCATATTTAAATGAGAAACCTTTCTCATTTTTCGAGAA
ACATGTGAAAACATCCTGCCCGAAGGTCTTATGGATGGCCTGAAGGACTTATCATCTTTCTCGAA
AGACTTACAGATGACCCAAAGGATTTAAGCATCATTCT
Found at i:2787851 original size:468 final size:466
Alignment explanation
Indices: 2787004--2788023 Score: 1318
Period size: 468 Copynumber: 2.2 Consensus size: 466
2786994 TCCAACTTTG
* * *
2787004 GAAATAGTTTACTAGGTAAGAAACCATTTTTTACTTTTCAAAAATTTCAATTTTTAGATTTAAAT
1 GAAATAGTTTACTAGGTAAGAAA-CATTTCTTACTTTTCAAAAATTTTAATTTTTATATTTAAAT
*
2787069 GAGAAACCTTTCTCATTTTTCGAGAAACATATGAAAACATCCTGCTCGAAGGTCTCGTGGATGGC
65 GAGAAACCTTTCTCATTTTTCGAGAAACATATGAAAACATCCTGCTCGAAGGTCTCATGGATGGC
* ** *
2787134 CAGAAGGACTTATCATCTTTCTCTAAAGACTTACACATGATTCAAAGGATTTAAGCATCATTCTT
130 CAGAAGGACTTATCATCTTTCTCGAAAGACTTACACATGACCCAAAGGATTTAAGCATCATTCTG
* *
2787199 AGAAGACTTAGTGATGGCCCGAACGACTTATAAATTTTGAAAATAGTTTACTAGGTAAGAAATCT
195 AGAAGACTTACTGATGGCCCGAACAACTTATAAATTTTGAAAATAGTTTACTAGGTAAGAAATCT
* *
2787264 TTCTTACTTTTCAAAAAAATTCAATTTTCAGATTTAAATGAGAAACCTTTCTCATTTTTTGAGAG
260 TTCTTACTTTTCAAAAAAATTCAATTTTCAGATTTAAATGAGAAACATTTCTCATTTTTCGAGAG
**
2787329 ACATGTGAAAACATCGTGCCCGAAGGTCTTACGGATGGCCTGAAGGGTTTATCATCTTACTCGAA
325 ACATGTGAAAACATCGTGCCCGAAGGTCTTACGGATGGCCTGAAGGACTTATCATCTTACTCGAA
* * * * * *
2787394 AGGCTTACAGATGAACTGAA-GAATTTAAGCATCATGCTTGAAAGACTTACTGATAGCCCAAATG
390 AGACTTACAGATGAACCGAATG-ACTTAAGCATCATACTCGAAAGACTTACTGATAGCCCAAAGG
*
2787458 ACTTACTAA-TTTTA
454 AC-TA-AAATTTTTA
* * *
2787472 GAAATAGTTTACTAGGTAAGAAA-GTTTCCTTACTTTTCAAAAGTTTTAATTTTCATATTTAAAT
1 GAAATAGTTTACTAGGTAAGAAACATTT-CTTACTTTTCAAAAATTTTAATTTTTATATTTAAAT
* * * * * *
2787536 GAGAAACCTTTCTCATTTTTTGAGAAACATGTGAAAATATCCTTCTTGAAGGTCTTATGGATGGC
65 GAGAAACCTTTCTCATTTTTCGAGAAACATATGAAAACATCCTGCTCGAAGGTCTCATGGATGGC
** * * * *
2787601 CCTAAGGGCTTATCATCTTTCTCGAAAGGCTTACAGATGACCCAAAGGATTTAATCATCATGATC
130 CAGAAGGACTTATCATCTTTCTCGAAAGACTTACACATGACCCAAAGGATTTAAGCATCAT--TC
* * * *
2787666 -GAG-AGACTTACTGATGGCCCGAATAACTTTTCAATTTTTGGAAATAGTTTACTAGGTAAGAAA
193 TGAGAAGACTTACTGATGGCCCGAACAACTTAT-AAATTTTGAAAATAGTTTACTAGGTAAGAAA
* ** *
2787729 TCTTTCTTTCTTTTTC-AAAATTTTC-ATATTTCATATTTAAATGAGAAACATTTCTCATTTTTC
257 TCTTTCTTAC-TTTTCAAAAAAATTCAAT-TTTCAGATTTAAATGAGAAACATTTCTCATTTTTC
* * * *
2787792 GAGAGACATGTGAAAATATTC-TGCCCGAAGGTCTTATGGATGGCTTGAAGGACTTATCATCTTG
320 GAGAGACATGTGAAAACA-TCGTGCCCGAAGGTCTTACGGATGGCCTGAAGGACTTATCATCTTA
* * * * *
2787856 TTCGAAAGACTTACAGATGACCCGAATGACTTAAGCATCGTACTCGAAAGACTTATTGATGGCCC
384 CTCGAAAGACTTACAGATGAACCGAATGACTTAAGCATCATACTCGAAAGACTTACTGATAGCCC
* *
2787921 GAAGGACTAAAATTTTTT
449 AAAGGACTAAAATTTTTA
* * * * * *
2787939 GAAAATAATTTACTATGTAAGAAACCTTTCTTACTTTTCAAAAAATTTATTTTTTATTTTTAAAT
1 G-AAATAGTTTACTAGGTAAGAAACATTTCTTACTTTTCAAAAATTTTAATTTTTATATTTAAAT
*
2788004 GAGAAACATTTCTCATTTTT
65 GAGAAACCTTTCTCATTTTT
2788024 ATAAAACGAC
Statistics
Matches: 477, Mismatches: 64, Indels: 22
0.85 0.11 0.04
Matches are distributed among these distances:
466 5 0.01
467 174 0.36
468 285 0.60
469 13 0.03
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (466 bp):
GAAATAGTTTACTAGGTAAGAAACATTTCTTACTTTTCAAAAATTTTAATTTTTATATTTAAATG
AGAAACCTTTCTCATTTTTCGAGAAACATATGAAAACATCCTGCTCGAAGGTCTCATGGATGGCC
AGAAGGACTTATCATCTTTCTCGAAAGACTTACACATGACCCAAAGGATTTAAGCATCATTCTGA
GAAGACTTACTGATGGCCCGAACAACTTATAAATTTTGAAAATAGTTTACTAGGTAAGAAATCTT
TCTTACTTTTCAAAAAAATTCAATTTTCAGATTTAAATGAGAAACATTTCTCATTTTTCGAGAGA
CATGTGAAAACATCGTGCCCGAAGGTCTTACGGATGGCCTGAAGGACTTATCATCTTACTCGAAA
GACTTACAGATGAACCGAATGACTTAAGCATCATACTCGAAAGACTTACTGATAGCCCAAAGGAC
TAAAATTTTTA
Found at i:2787908 original size:22 final size:20
Alignment explanation
Indices: 2787857--2787910 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
2787847 ATCATCTTGT
2787857 TCGAAAGACTTACAGATGAC
1 TCGAAAGACTTACAGATGAC
* *
2787877 CCGAATGACTTA-AGCATCGTAC
1 TCGAAAGACTTACAG-AT-G-AC
2787899 TCGAAAGACTTA
1 TCGAAAGACTTA
2787911 TTGATGGCCC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
19 2 0.07
20 12 0.44
21 1 0.04
22 12 0.44
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (20 bp):
TCGAAAGACTTACAGATGAC
Found at i:2795458 original size:3 final size:3
Alignment explanation
Indices: 2795450--2795522 Score: 87
Period size: 3 Copynumber: 24.7 Consensus size: 3
2795440 CATAAACAGA
*
2795450 AAT AAT AAT AAT AAT AA- AAT -AT AAT AAT AAT AAT AAT CAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
2795496 AAT AAAT AAC ATT AGT AAT AAT AAT AA
1 AAT -AAT AAT AAT AAT AAT AAT AAT AA
2795523 AACTAGAACA
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
2 4 0.07
3 53 0.88
4 3 0.05
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2795466 original size:22 final size:22
Alignment explanation
Indices: 2795441--2795500 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
2795431 GCCCAAAAAC
2795441 ATAAACAGA-AATAATAATAATA
1 ATAAA-AGATAATAATAATAATA
*
2795463 ATAAAATATAATAATAATAATA
1 ATAAAAGATAATAATAATAATA
* *
2795485 ATCATA-ATAATAATAA
1 ATAAAAGATAATAATAA
2795501 ATAACATTAG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 12 0.35
22 22 0.65
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (22 bp):
ATAAAAGATAATAATAATAATA
Found at i:2795503 original size:22 final size:21
Alignment explanation
Indices: 2795450--2795522 Score: 87
Period size: 22 Copynumber: 3.5 Consensus size: 21
2795440 CATAAACAGA
2795450 AATAATAATAATAATAA-AAT
1 AATAATAATAATAATAATAAT
*
2795470 -ATAATAATAATAATAATCAT
1 AATAATAATAATAATAATAAT
* * *
2795490 AATAATAATAAATAACATTAGT
1 AATAATAAT-AATAATAATAAT
2795512 AATAATAATAA
1 AATAATAATAA
2795523 AACTAGAACA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
19 16 0.36
20 2 0.04
21 10 0.22
22 17 0.38
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (21 bp):
AATAATAATAATAATAATAAT
Found at i:2795515 original size:37 final size:37
Alignment explanation
Indices: 2795451--2795522 Score: 110
Period size: 37 Copynumber: 1.9 Consensus size: 37
2795441 ATAAACAGAA
2795451 ATAATAATAATAATAAAATATAATAATAATAATAATC
1 ATAATAATAATAATAAAATATAATAATAATAATAATC
* *
2795488 ATAATAATAATAAATAACAT-TAGTAATAATAATAA
1 ATAATAATAAT-AATAAAATATAATAATAATAATAA
2795523 AACTAGAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
37 25 0.78
38 7 0.22
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (37 bp):
ATAATAATAATAATAAAATATAATAATAATAATAATC
Found at i:2795523 original size:22 final size:19
Alignment explanation
Indices: 2795451--2795522 Score: 92
Period size: 19 Copynumber: 3.7 Consensus size: 19
2795441 ATAAACAGAA
*
2795451 ATAATAATAATAATAAAAT
1 ATAATAATAATAATAAATT
*
2795470 ATAATAATAATAAT-AATC
1 ATAATAATAATAATAAATT
2795488 ATAATAATAATAAATAACATT
1 ATAATAATAAT-AATAA-ATT
2795509 AGTAATAATAATAA
1 A-TAATAATAATAA
2795523 AACTAGAACA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
18 13 0.28
19 17 0.37
20 1 0.02
21 5 0.11
22 10 0.22
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (19 bp):
ATAATAATAATAATAAATT
Found at i:2801852 original size:24 final size:24
Alignment explanation
Indices: 2801824--2801870 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2801814 ACAAAAACAT
2801824 AGAAAAAGAACAAACATCCATTAA
1 AGAAAAAGAACAAACATCCATTAA
***
2801848 AGAAAAAGCTTAAACATCCATTA
1 AGAAAAAGAACAAACATCCATTA
2801871 TTAACTCCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.57, C:0.17, G:0.09, T:0.17
Consensus pattern (24 bp):
AGAAAAAGAACAAACATCCATTAA
Found at i:2802568 original size:10 final size:11
Alignment explanation
Indices: 2802543--2802601 Score: 63
Period size: 10 Copynumber: 5.7 Consensus size: 11
2802533 ACCGTAATAG
2802543 TGAACCTAAAA
1 TGAACCTAAAA
*
2802554 TGAACCT-ATA
1 TGAACCTAAAA
2802564 TGAACCTAAAA
1 TGAACCTAAAA
**
2802575 TG-ACC-ATTA
1 TGAACCTAAAA
2802584 TGAACCTAAAA
1 TGAACCTAAAA
2802595 T-AACCTA
1 TGAACCTA
2802602 TATGAACTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
9 4 0.10
10 21 0.54
11 14 0.36
ACGTcount: A:0.47, C:0.20, G:0.08, T:0.24
Consensus pattern (11 bp):
TGAACCTAAAA
Found at i:2802569 original size:21 final size:21
Alignment explanation
Indices: 2802543--2802608 Score: 102
Period size: 20 Copynumber: 3.2 Consensus size: 21
2802533 ACCGTAATAG
2802543 TGAACCTAAAATGAACCTATA
1 TGAACCTAAAATGAACCTATA
2802564 TGAACCTAAAATG-ACC-ATTA
1 TGAACCTAAAATGAACCTA-TA
2802584 TGAACCTAAAAT-AACCTATA
1 TGAACCTAAAATGAACCTATA
2802604 TGAAC
1 TGAAC
2802609 TTTTAAACAA
Statistics
Matches: 42, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
19 1 0.02
20 27 0.64
21 14 0.33
ACGTcount: A:0.47, C:0.20, G:0.09, T:0.24
Consensus pattern (21 bp):
TGAACCTAAAATGAACCTATA
Found at i:2806899 original size:15 final size:15
Alignment explanation
Indices: 2806879--2806944 Score: 132
Period size: 15 Copynumber: 4.4 Consensus size: 15
2806869 TATAAAGACT
2806879 AAAATATAATGAAGA
1 AAAATATAATGAAGA
2806894 AAAATATAATGAAGA
1 AAAATATAATGAAGA
2806909 AAAATATAATGAAGA
1 AAAATATAATGAAGA
2806924 AAAATATAATGAAGA
1 AAAATATAATGAAGA
2806939 AAAATA
1 AAAATA
2806945 GAAGAAAATT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 51 1.00
ACGTcount: A:0.68, C:0.00, G:0.12, T:0.20
Consensus pattern (15 bp):
AAAATATAATGAAGA
Found at i:2807678 original size:2 final size:2
Alignment explanation
Indices: 2807671--2807697 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2807661 TTTTTAAAAC
2807671 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 A
2807698 CCCTCATCCG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2807937 original size:24 final size:24
Alignment explanation
Indices: 2807910--2808021 Score: 163
Period size: 24 Copynumber: 4.7 Consensus size: 24
2807900 CATAAATCAA
* * *
2807910 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAT
*
2807934 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
2807958 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
2807982 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
*
2808006 GTCAAGTATCATATCA
1 GTCAAGTATCAGATCA
2808022 TAATTCAAAT
Statistics
Matches: 81, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
23 2 0.02
24 77 0.95
25 2 0.02
ACGTcount: A:0.39, C:0.21, G:0.15, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:2812566 original size:24 final size:24
Alignment explanation
Indices: 2812539--2812614 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 24
2812529 TATATAAAAA
2812539 ATCAAAACATAAATC-AGGTCAAGT
1 ATCAAAACA-AAATCTAGGTCAAGT
* * *
2812563 ATCATATCAAAATCTCGGTCAAGT
1 ATCAAAACAAAATCTAGGTCAAGT
* * * * *
2812587 ATCAGATCAGAATCCAAGTCAAGT
1 ATCAAAACAAAATCTAGGTCAAGT
2812611 ATCA
1 ATCA
2812615 TATCAGAATC
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
23 5 0.12
24 38 0.88
ACGTcount: A:0.43, C:0.20, G:0.13, T:0.24
Consensus pattern (24 bp):
ATCAAAACAAAATCTAGGTCAAGT
Found at i:2812619 original size:24 final size:24
Alignment explanation
Indices: 2812556--2812657 Score: 127
Period size: 24 Copynumber: 4.2 Consensus size: 24
2812546 CATAAATCAG
* *
2812556 GTCAAGTATCATATCAAAATCTC-G
1 GTCAAGTATCATATCAGAATC-CAA
*
2812580 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCATATCAGAATCCAA
* *
2812604 GTCAAGTATCATATCAGAATCTAT
1 GTCAAGTATCATATCAGAATCCAA
2812628 GTC-AGATATCATATCAGAATCCAA
1 GTCAAG-TATCATATCAGAATCCAA
2812652 GTCAAG
1 GTCAAG
2812658 AATTCATGTG
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
23 3 0.04
24 62 0.93
25 2 0.03
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.26
Consensus pattern (24 bp):
GTCAAGTATCATATCAGAATCCAA
Found at i:2812625 original size:48 final size:48
Alignment explanation
Indices: 2812556--2812657 Score: 152
Period size: 48 Copynumber: 2.1 Consensus size: 48
2812546 CATAAATCAG
*
2812556 GTCAAGTATCATATCAAAATCTCGGTCA-AGTATCAGATCAGAATCCAA
1 GTCAAGTATCATATCAAAATCTAGGTCAGA-TATCAGATCAGAATCCAA
* * *
2812604 GTCAAGTATCATATCAGAATCTATGTCAGATATCATATCAGAATCCAA
1 GTCAAGTATCATATCAAAATCTAGGTCAGATATCAGATCAGAATCCAA
2812652 GTCAAG
1 GTCAAG
2812658 AATTCATGTG
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
48 48 0.98
49 1 0.02
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.26
Consensus pattern (48 bp):
GTCAAGTATCATATCAAAATCTAGGTCAGATATCAGATCAGAATCCAA
Found at i:2814326 original size:24 final size:24
Alignment explanation
Indices: 2814294--2814374 Score: 135
Period size: 24 Copynumber: 3.4 Consensus size: 24
2814284 AACTCGATCT
*
2814294 GATCAGAATCCAAGTCAAGTATCA
1 GATCAGAATCCATGTCAAGTATCA
*
2814318 GATCAGAATCCATGTCAAATATCA
1 GATCAGAATCCATGTCAAGTATCA
*
2814342 TATCAGAATCCATGTCAAGTATCA
1 GATCAGAATCCATGTCAAGTATCA
2814366 GATCAGAAT
1 GATCAGAAT
2814375 TCAAATAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.25
Consensus pattern (24 bp):
GATCAGAATCCATGTCAAGTATCA
Found at i:2816799 original size:24 final size:24
Alignment explanation
Indices: 2816772--2816847 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
2816762 TATATCAAAA
2816772 ATCAAAACATAAATC-AGGTCAAGT
1 ATCAAAACA-AAATCTAGGTCAAGT
* *
2816796 ATCATATCAAAATCTAGGTCAAGT
1 ATCAAAACAAAATCTAGGTCAAGT
* * * * *
2816820 ATCAGATCAGAATCCAAGTCAAGT
1 ATCAAAACAAAATCTAGGTCAAGT
2816844 ATCA
1 ATCA
2816848 GATCAGAATC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 5 0.11
24 40 0.89
ACGTcount: A:0.45, C:0.18, G:0.13, T:0.24
Consensus pattern (24 bp):
ATCAAAACAAAATCTAGGTCAAGT
Found at i:2816848 original size:24 final size:24
Alignment explanation
Indices: 2816789--2816904 Score: 162
Period size: 24 Copynumber: 4.8 Consensus size: 24
2816779 CATAAATCAG
* * *
2816789 GTCAAGTATCATATCAAAATCTAG
1 GTCAAGTATCATATCAGAATCCAT
* *
2816813 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCATATCAGAATCCAT
*
2816837 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCATATCAGAATCCAT
2816861 GTC-AGATATCATATCAGAATCCAT
1 GTCAAG-TATCATATCAGAATCCAT
2816885 GTCAAGTATCATATCAGAAT
1 GTCAAGTATCATATCAGAAT
2816905 TCAAATCGAA
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
23 2 0.02
24 80 0.95
25 2 0.02
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.27
Consensus pattern (24 bp):
GTCAAGTATCATATCAGAATCCAT
Found at i:2819333 original size:24 final size:24
Alignment explanation
Indices: 2819306--2819381 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
2819296 TATATCAAAA
2819306 ATCAAAACATAAATC-AGGTCAAGT
1 ATCAAAACA-AAATCTAGGTCAAGT
* *
2819330 ATCATATCAAAATCTAGGTCAAGT
1 ATCAAAACAAAATCTAGGTCAAGT
* * * * *
2819354 ATCAGATCAGAATCCAAGTCAAGT
1 ATCAAAACAAAATCTAGGTCAAGT
2819378 ATCA
1 ATCA
2819382 GATCAGAATC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 5 0.11
24 40 0.89
ACGTcount: A:0.45, C:0.18, G:0.13, T:0.24
Consensus pattern (24 bp):
ATCAAAACAAAATCTAGGTCAAGT
Found at i:2819382 original size:24 final size:24
Alignment explanation
Indices: 2819323--2819438 Score: 169
Period size: 24 Copynumber: 4.8 Consensus size: 24
2819313 CATAAATCAG
* * * *
2819323 GTCAAGTATCATATCAAAATCTAG
1 GTCAAGTATCAGATCAGAATCCAT
*
2819347 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
2819371 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
* *
2819395 GTCAAATATCATATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
2819419 GTCAAGTATCAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
2819439 TCAAATCGAA
Statistics
Matches: 83, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 83 1.00
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.26
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:2819454 original size:72 final size:72
Alignment explanation
Indices: 2819323--2819456 Score: 189
Period size: 72 Copynumber: 1.9 Consensus size: 72
2819313 CATAAATCAG
* * * *
2819323 GTCAAGTATCATATCAAAATCTAGGTCAAGTATCAGATCAGAATCCAAGTCAAGTATCAGATCAG
1 GTCAAATATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAATCAAGAATCAGATCAG
2819388 AATCCAT
66 AATCCAT
* * *
2819395 GTCAAATATCATATCAGAATCCATGTCAAGTATCAGATCAGAATTCAAATCGAA-AATCAGAT
1 GTCAAATATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAATC-AAGAATCAGAT
2819457 AAAATATTCA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
72 52 0.96
73 2 0.04
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (72 bp):
GTCAAATATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAATCAAGAATCAGATCAG
AATCCAT
Found at i:2821866 original size:24 final size:24
Alignment explanation
Indices: 2821839--2821914 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
2821829 TATATCAAAA
2821839 ATCAAAACATAAATC-AGGTCAAGT
1 ATCAAAACA-AAATCTAGGTCAAGT
* *
2821863 ATCATATCAAAATCTAGGTCAAGT
1 ATCAAAACAAAATCTAGGTCAAGT
* * * * *
2821887 ATCAGATCAGAATCCAAGTCAAGT
1 ATCAAAACAAAATCTAGGTCAAGT
2821911 ATCA
1 ATCA
2821915 GATCAGAATC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 5 0.11
24 40 0.89
ACGTcount: A:0.45, C:0.18, G:0.13, T:0.24
Consensus pattern (24 bp):
ATCAAAACAAAATCTAGGTCAAGT
Found at i:2821915 original size:24 final size:24
Alignment explanation
Indices: 2821856--2821968 Score: 156
Period size: 24 Copynumber: 4.7 Consensus size: 24
2821846 CATAAATCAG
* * * *
2821856 GTCAAGTATCATATCAAAATCTAG
1 GTCAAGTATCAGATCAGAATCCAT
*
2821880 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
2821904 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
*
2821928 GTC-AGATATCATATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
2821952 GTCAAGTATCAGATCAG
1 GTCAAGTATCAGATCAG
2821969 GATTCAAATT
Statistics
Matches: 80, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
23 2 0.03
24 76 0.95
25 2 0.03
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.26
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:2824395 original size:24 final size:23
Alignment explanation
Indices: 2824368--2824496 Score: 98
Period size: 24 Copynumber: 5.4 Consensus size: 23
2824358 TATATCAAAA
*
2824368 ATCAAAACATAAATCAGGTCAAGT
1 ATCAAATCA-AAATCAGGTCAAGT
*
2824392 ATCATATCAAAATCTAGGTCAAGT
1 ATCAAATCAAAATC-AGGTCAAGT
* * *
2824416 ATCAGATCAGAATCCAAGTCAAGT
1 ATCAAATCAAAAT-CAGGTCAAGT
* *
2824440 ATCAAATCAGAATCCATGT-AAGAT
1 ATCAAATCAAAAT-CAGGTCAAG-T
* * *
2824464 ATCATATCAGAATCCATGTCAAGT
1 ATCAAATCAAAAT-CAGGTCAAGT
*
2824488 ATCAGATCA
1 ATCAAATCA
2824497 TAATTCAAAT
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
23 8 0.09
24 80 0.87
25 4 0.04
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.25
Consensus pattern (23 bp):
ATCAAATCAAAATCAGGTCAAGT
Found at i:2824467 original size:48 final size:48
Alignment explanation
Indices: 2824385--2824496 Score: 145
Period size: 48 Copynumber: 2.3 Consensus size: 48
2824375 CATAAATCAG
* *
2824385 GTCAAGTATCATATCAAAATCTAGGTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAAATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAA
* * * *
2824433 GTCAAGTATCAAATCAGAATCCATGT-AAGATATCATATCAGAATCCAT
1 GTCAAGTATCAAATCAAAATCCAGGTCAAG-TATCAGATCAGAATCCAA
*
2824481 GTCAAGTATCAGATCA
1 GTCAAGTATCAAATCA
2824497 TAATTCAAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
47 3 0.05
48 53 0.95
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.26
Consensus pattern (48 bp):
GTCAAGTATCAAATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAA
Found at i:2826923 original size:24 final size:24
Alignment explanation
Indices: 2826896--2827019 Score: 92
Period size: 24 Copynumber: 5.2 Consensus size: 24
2826886 TATATCAAAA
2826896 ATCAAAACATAAAT-CAGGTCAAGT
1 ATCAAAACA-AAATCCAGGTCAAGT
* *
2826920 ATCATATCAAAATCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* *
2826944 ATCAGATA-AAAATCCAAGTCAAGT
1 ATCA-AAACAAAATCCAGGTCAAGT
* * * *
2826968 ATCAGATCAGAATCCATGTC-AGAT
1 ATCAAAACAAAATCCAGGTCAAG-T
* * * *
2826992 ATCATATCAGAATCCATGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
2827016 ATCA
1 ATCA
2827020 TATCATAATT
Statistics
Matches: 83, Mismatches: 12, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
23 6 0.07
24 75 0.90
25 2 0.02
ACGTcount: A:0.44, C:0.19, G:0.13, T:0.24
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGGTCAAGT
Found at i:2827020 original size:24 final size:24
Alignment explanation
Indices: 2826913--2827024 Score: 145
Period size: 24 Copynumber: 4.7 Consensus size: 24
2826903 CATAAATCAG
*
2826913 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCATATCAAAATCCAT
* * *
2826937 GTCAAGTATCAGATAAAAATCCAA
1 GTCAAGTATCATATCAAAATCCAT
* *
2826961 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCATATCAAAATCCAT
*
2826985 GTC-AGATATCATATCAGAATCCAT
1 GTCAAG-TATCATATCAAAATCCAT
2827009 GTCAAGTATCATATCA
1 GTCAAGTATCATATCA
2827025 TAATTCAAAT
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
23 2 0.03
24 75 0.95
25 2 0.03
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.26
Consensus pattern (24 bp):
GTCAAGTATCATATCAAAATCCAT
Found at i:2830479 original size:6 final size:6
Alignment explanation
Indices: 2830468--2830496 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
2830458 TTTCATATCA
2830468 TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
2830497 AGTTTTACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTC
Found at i:2830502 original size:18 final size:18
Alignment explanation
Indices: 2830468--2830502 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2830458 TTTCATATCA
**
2830468 TTTTTCTTTTTCTTTTTC
1 TTTTTCTTTTTAGTTTTC
2830486 TTTTTCTTTTTAGTTTT
1 TTTTTCTTTTTAGTTTT
2830503 ACTTGTTATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.03, C:0.11, G:0.03, T:0.83
Consensus pattern (18 bp):
TTTTTCTTTTTAGTTTTC
Found at i:2835529 original size:16 final size:15
Alignment explanation
Indices: 2835508--2835545 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
2835498 ACAGGAGGGA
2835508 AATTTTTAACATTTTT-
1 AATTTTT-A-ATTTTTG
2835524 AATTTTTAATTTTTG
1 AATTTTTAATTTTTG
2835539 AATTTTT
1 AATTTTT
2835546 TATGTTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.29
15 8 0.38
16 7 0.33
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (15 bp):
AATTTTTAATTTTTG
Found at i:2835560 original size:7 final size:7
Alignment explanation
Indices: 2835508--2835559 Score: 52
Period size: 7 Copynumber: 7.0 Consensus size: 7
2835498 ACAGGAGGGA
2835508 AATTTTT
1 AATTTTT
2835515 AACATTTTT
1 -A-ATTTTT
2835524 AATTTTT
1 AATTTTT
2835531 AATTTTT
1 AATTTTT
2835538 GAATTTTT
1 -AATTTTT
*
2835546 TATGTTTT
1 AAT-TTTT
2835554 -ATTTTT
1 AATTTTT
2835560 TTCATATAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
6 4 0.10
7 17 0.43
8 13 0.32
9 6 0.15
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (7 bp):
AATTTTT
Found at i:2843307 original size:90 final size:91
Alignment explanation
Indices: 2843146--2843325 Score: 256
Period size: 90 Copynumber: 2.0 Consensus size: 91
2843136 CCTAACACAC
* * *
2843146 CCTTTTATAGCCAAGTTACCCTAGTCATATTAGGGTTTTTTTATTATTATTTCAAATTAATTAAA
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGG---TATTATTATTATTTCAAATTAATTAAA
* *
2843211 TTTATATTTAATTAATTAGAATTTAATAAT
63 TCTATATTTAATTAATT-GAAATTAATAAT
*
2843241 CCTTTTATATCCAAGTTACCCTAATCATATCAGGG-ATT-TTATTATTTCAAATTAATTAAATCT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGTATTATTATTATTTCAAATTAATTAAATCT
2843304 ATATTTAATTAATTGAAATTAA
66 ATATTTAATTAATTGAAATTAA
2843326 ATATTCAAGA
Statistics
Matches: 79, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
89 7 0.09
90 38 0.48
91 2 0.03
95 32 0.41
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.46
Consensus pattern (91 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGTATTATTATTATTTCAAATTAATTAAATCT
ATATTTAATTAATTGAAATTAATAAT
Found at i:2845656 original size:795 final size:795
Alignment explanation
Indices: 2844126--2845718 Score: 3042
Period size: 795 Copynumber: 2.0 Consensus size: 795
2844116 GCGTATTATT
2844126 ATTGTCCATGCCCATAATAATACTTGACTATGGATCTTTTAATAATAACAATTATGTCATTATAT
1 ATTGTCCATGCCCATAATAATACTTGACTATGGATCTTTTAATAATAACAATTATGTCATTATAT
2844191 GGACTTTATTATCTTCCAGTTTATGTTATACACATATATATAACTGAAAATAATAGCGGCAATGC
66 GGACTTTATTATCTTCCAGTTTATGTTATACACATATATATAACTGAAAATAATAGCGGCAATGC
2844256 CTTTATTCAATAAAATCGGTAAATAAAAGTATTATTATTACAATAATCATATGATTGGTCTTTGG
131 CTTTATTCAATAAAATCGGTAAATAAAAGTATTATTATTACAATAATCATATGATTGGTCTTTGG
2844321 GCATACTTTAACAATTTCCCACTAGCACTAAGACCAATCACTCACATATCTAATACCGAGTGACT
196 GCATACTTTAACAATTTCCCACTAGCACTAAGACCAATCACTCACATATCTAATACCGAGTGACT
2844386 CAGTGTGACGATCATGCCTCTGTTGTGTAAGAGGCTTCGTCAAGGGATCAGCAATGTTGTCATCC
261 CAGTGTGACGATCATGCCTCTGTTGTGTAAGAGGCTTCGTCAAGGGATCAGCAATGTTGTCATCC
*
2844451 GTGTATACTATACATATTTCCACATCTCCTCGATTAATGATCTCTCAAATGAGATGAAAGCGCCT
326 GTGTATACTATACATATTTCCACATCTCCTCGATCAATGATCTCTCAAATGAGATGAAAGCGCCT
* *
2844516 AAGAATATGTTTGGATCGTTGATGAGATCTGGGTTTCTTTGCTTGTGCAATGGCTCCATTATTGT
391 AAGAATATGTTTGGATCGTTGATGAGATATGGGTTCCTTTGCTTGTGCAATGGCTCCATTATTGT
*
2844581 CATAACGGAGTTCTACAGCATCTGATATGCTGGGAACAACCCCTTATTCCATTATAAATTTCTTG
456 CATAACGGAGTTCTACAGCATCTGATATGCTAGGAACAACCCCTTATTCCATTATAAATTTCTTG
2844646 ATCCAAACAGCCTCTTTTGCTGCTTCACTAGCTGCAATGTATTCAGCCTCTGTTGTAGAATCAGC
521 ATCCAAACAGCCTCTTTTGCTGCTTCACTAGCTGCAATGTATTCAGCCTCTGTTGTAGAATCAGC
* * *
2844711 TACTGTGTCTTGCTTTGAACTTTTCCAGCTCACAACACCTCCATTAAGACAAAACACAAAACCCG
586 TACTGTGTCTTACTTCGAACTTTTCCAGCTCACAACACCTCCATTAACACAAAACACAAAACCCG
*
2844776 ATTGCGATCGTGAGTCATCCTTGTCAGTTTGGAAGCTGGCATCAGTATAACCTTTTATACAAAGC
651 ATTGCGATCGTGAGTCATCCTTGTCAGTTTGGAAGATGGCATCAGTATAACCTTTTATACAAAGC
2844841 TCTTTCTCTCCTCCATAGACAAGAAATTTATCCTTAGTTCTTCTTAAGTACTTAAGGATATTTTT
716 TCTTTCTCTCCTCCATAGACAAGAAATTTATCCTTAGTTCTTCTTAAGTACTTAAGGATATTTTT
*
2844906 AACCGCTACCCAATG
781 AACCGCAACCCAATG
2844921 ATTGTCCATGCCCATAATAATACTTGACTATGGATCTTTTAATAATAACAATTATGTCATTATAT
1 ATTGTCCATGCCCATAATAATACTTGACTATGGATCTTTTAATAATAACAATTATGTCATTATAT
2844986 GGACTTTATTATCTTCCAGTTTATGTTATACACATATATATAACTGAAAATAATAGCGGCAATGC
66 GGACTTTATTATCTTCCAGTTTATGTTATACACATATATATAACTGAAAATAATAGCGGCAATGC
2845051 CTTTATTCAATAAAATCGGTAAATAAAAGTATTATTATTACAATAATCATATGATTGGTCTTTGG
131 CTTTATTCAATAAAATCGGTAAATAAAAGTATTATTATTACAATAATCATATGATTGGTCTTTGG
2845116 GCATACTTTAACAATTTCCCACTAGCACTAAGACCAATCACTCACATATCTAATACCGAGTGACT
196 GCATACTTTAACAATTTCCCACTAGCACTAAGACCAATCACTCACATATCTAATACCGAGTGACT
2845181 CAGTGTGACGATCATGCCTCTGTTGTGTAAGAGGCTTCGTCAAGGGATCAGCAATGTTGTCATCC
261 CAGTGTGACGATCATGCCTCTGTTGTGTAAGAGGCTTCGTCAAGGGATCAGCAATGTTGTCATCC
* *
2845246 GTGTGTACTATACATATTTCCACATCTCCTCGATCAATGATCTCTCGAATGAGATGAAAGCGCCT
326 GTGTATACTATACATATTTCCACATCTCCTCGATCAATGATCTCTCAAATGAGATGAAAGCGCCT
2845311 AAGAATATGTTTGGATCGTTGATGAGATATGGGTTCCTTTGCTTGTGCAATGGCTCCATTATTGT
391 AAGAATATGTTTGGATCGTTGATGAGATATGGGTTCCTTTGCTTGTGCAATGGCTCCATTATTGT
*
2845376 CATAACGGAGTTCTACAGTATCTGATATGCTAGGAACAACCCCTTATTCCATTATAAATTTCTTG
456 CATAACGGAGTTCTACAGCATCTGATATGCTAGGAACAACCCCTTATTCCATTATAAATTTCTTG
*
2845441 ATCCAAACAGCCTCTTTTGCTGCTTCACTAGCTGCAATGTATTCAGCCTCTGTTGTAGGATCAGC
521 ATCCAAACAGCCTCTTTTGCTGCTTCACTAGCTGCAATGTATTCAGCCTCTGTTGTAGAATCAGC
*
2845506 TACTGTGTCTTACTTCGAACTTTTCCAGCTCACAGCACCTCCATTAACACAAAACACAAAACCCG
586 TACTGTGTCTTACTTCGAACTTTTCCAGCTCACAACACCTCCATTAACACAAAACACAAAACCCG
2845571 ATTGCGATCGTGAGTCATCCTTGTCAGTTTGGAAGATGGCATCAGTATAACCTTTTATACAAAGC
651 ATTGCGATCGTGAGTCATCCTTGTCAGTTTGGAAGATGGCATCAGTATAACCTTTTATACAAAGC
*
2845636 TCTTTCTCTCCTCCATAGACAAGAAATTTATCCTTAGTTGTTCTTAAGTACTTAAGGATATTTTT
716 TCTTTCTCTCCTCCATAGACAAGAAATTTATCCTTAGTTCTTCTTAAGTACTTAAGGATATTTTT
*
2845701 AACCGCAACCTAATG
781 AACCGCAACCCAATG
2845716 ATT
1 ATT
2845719 TTCACCAGGG
Statistics
Matches: 782, Mismatches: 16, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
795 782 1.00
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.34
Consensus pattern (795 bp):
ATTGTCCATGCCCATAATAATACTTGACTATGGATCTTTTAATAATAACAATTATGTCATTATAT
GGACTTTATTATCTTCCAGTTTATGTTATACACATATATATAACTGAAAATAATAGCGGCAATGC
CTTTATTCAATAAAATCGGTAAATAAAAGTATTATTATTACAATAATCATATGATTGGTCTTTGG
GCATACTTTAACAATTTCCCACTAGCACTAAGACCAATCACTCACATATCTAATACCGAGTGACT
CAGTGTGACGATCATGCCTCTGTTGTGTAAGAGGCTTCGTCAAGGGATCAGCAATGTTGTCATCC
GTGTATACTATACATATTTCCACATCTCCTCGATCAATGATCTCTCAAATGAGATGAAAGCGCCT
AAGAATATGTTTGGATCGTTGATGAGATATGGGTTCCTTTGCTTGTGCAATGGCTCCATTATTGT
CATAACGGAGTTCTACAGCATCTGATATGCTAGGAACAACCCCTTATTCCATTATAAATTTCTTG
ATCCAAACAGCCTCTTTTGCTGCTTCACTAGCTGCAATGTATTCAGCCTCTGTTGTAGAATCAGC
TACTGTGTCTTACTTCGAACTTTTCCAGCTCACAACACCTCCATTAACACAAAACACAAAACCCG
ATTGCGATCGTGAGTCATCCTTGTCAGTTTGGAAGATGGCATCAGTATAACCTTTTATACAAAGC
TCTTTCTCTCCTCCATAGACAAGAAATTTATCCTTAGTTCTTCTTAAGTACTTAAGGATATTTTT
AACCGCAACCCAATG
Found at i:2851643 original size:24 final size:24
Alignment explanation
Indices: 2851610--2851666 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
2851600 CATCTCTATG
*
2851610 TCAATGACAACTCGTTGTCATCAA
1 TCAATAACAACTCGTTGTCATCAA
2851634 TCAATAACAACTCGTTGTCATCAA
1 TCAATAACAACTCGTTGTCATCAA
2851658 TCAATAACA
1 TCAATAACA
2851667 TGTTAGTCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.39, C:0.25, G:0.09, T:0.28
Consensus pattern (24 bp):
TCAATAACAACTCGTTGTCATCAA
Found at i:2872037 original size:24 final size:24
Alignment explanation
Indices: 2872005--2872050 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
2871995 TCTTCCAGAT
*
2872005 GATGTATAAAACATCTATGTACAC
1 GATGTATAAAACATATATGTACAC
*
2872029 GATGTATAAAATATATATGTAC
1 GATGTATAAAACATATATGTAC
2872051 CATATCATGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (24 bp):
GATGTATAAAACATATATGTACAC
Found at i:2873136 original size:30 final size:30
Alignment explanation
Indices: 2873102--2873160 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
2873092 TTTGCTCCCT
* *
2873102 AAACTTTTCAAAATTTATACTTTGGTCACC
1 AAACTTTACAAAATTTATAATTTGGTCACC
*
2873132 AAACTTTACCAAATTTATAATTTGGTCAC
1 AAACTTTACAAAATTTATAATTTGGTCAC
2873161 TAAATAAATC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.36, C:0.19, G:0.07, T:0.39
Consensus pattern (30 bp):
AAACTTTACAAAATTTATAATTTGGTCACC
Found at i:2878171 original size:38 final size:36
Alignment explanation
Indices: 2878120--2878469 Score: 295
Period size: 37 Copynumber: 9.4 Consensus size: 36
2878110 TATATACCTA
* * *
2878120 TATATATTATATAG-TTTGCAAACGGTTTTTGAAATAC
1 TATATAATATATAGTTTTGAAAAC-ATTTTTGAAA-AC
*
2878157 GTATATAATATATAGTTTTTAAAACATTTTTGAAAAC
1 -TATATAATATATAGTTTTGAAAACATTTTTGAAAAC
* *
2878194 TATATAATATATA-TTTTTAAAACATTTTAGAAAA-
1 TATATAATATATAGTTTTGAAAACATTTTTGAAAAC
* *
2878228 TATATATGCTATATAGTTTTTAAAATCA-TTTTGAAAAC
1 TATATA--ATATATAGTTTTGAAAA-CATTTTTGAAAAC
* *
2878266 TTATATAAAATATAGTTTTGAAAACATTTTTGAAAATT
1 -TATATAATATATAGTTTTGAAAACATTTTTGAAAA-C
2878304 TATATAATATATAGTTTTGAAAACA-TTTTGAAAAC
1 TATATAATATATAGTTTTGAAAACATTTTTGAAAAC
* * *
2878339 ATTTATATATTACATAGTTTTTGAAAAACA-TTTTGGAAA-
1 ---TATATAATATATAG-TTTTG-AAAACATTTTTGAAAAC
* *
2878378 TATATATATAATATAGTTTTTAAAACAATTTTGAAAA-
1 TATATA-AT-ATATAGTTTTGAAAACATTTTTGAAAAC
* *
2878415 TATATATATTATATAGTTTTTTAAAACGTTTTTGGAAAA-
1 TATATA-A-TATATAG-TTTTGAAAACATTTTT-GAAAAC
2878454 TACATATAATATATAG
1 T--ATATAATATATAG
2878470 CCTTTAAAAA
Statistics
Matches: 268, Mismatches: 22, Indels: 43
0.80 0.07 0.13
Matches are distributed among these distances:
34 6 0.02
35 20 0.07
36 42 0.16
37 93 0.35
38 56 0.21
39 31 0.12
40 15 0.06
41 5 0.02
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44
Consensus pattern (36 bp):
TATATAATATATAGTTTTGAAAACATTTTTGAAAAC
Found at i:2878264 original size:37 final size:36
Alignment explanation
Indices: 2878158--2878478 Score: 344
Period size: 37 Copynumber: 8.6 Consensus size: 36
2878148 TTGAAATACG
*
2878158 TATATAATATATAGTTTTTAAAACATTTTTGAAAA-C
1 TATATAATATATAGTTTTTAAAACA-TTTTGAAAATA
2878194 TATATAATATATA-TTTTTAAAACATTTTAGAAAATA
1 TATATAATATATAGTTTTTAAAACATTTT-GAAAATA
**
2878230 TATATGCTATATAGTTTTTAAAATCATTTTGAAAACT-
1 TATATAATATATAGTTTTTAAAA-CATTTTGAAAA-TA
* * *
2878267 TATATAAAATATAGTTTTGAAAACATTTTTGAAAATT
1 TATATAATATATAGTTTTTAAAACA-TTTTGAAAATA
* *
2878304 TATATAATATATAGTTTTGAAAACATTTTGAAAACATT
1 TATATAATATATAGTTTTTAAAACATTTTG-AAA-ATA
* * *
2878342 TATATATTACATAGTTTTTGAAAAACATTTTGGAAATA
1 TATATAATATATAGTTTTT--AAAACATTTTGAAAATA
2878380 TATAT-ATAATATAGTTTTTAAAACAATTTTGAAAATA
1 TATATAAT-ATATAGTTTTTAAAAC-ATTTTGAAAATA
* *
2878417 TATATATTATATAGTTTTTTAAAACGTTTTTGGAAAATA
1 TATATAATATATAG-TTTTTAAAAC-ATTTT-GAAAATA
* **
2878456 CATATAATATATAGCCTTTAAAA
1 TATATAATATATAGTTTTTAAAA
2878479 AATATTTTAG
Statistics
Matches: 246, Mismatches: 23, Indels: 30
0.82 0.08 0.10
Matches are distributed among these distances:
34 4 0.02
35 16 0.07
36 37 0.15
37 92 0.37
38 65 0.26
39 21 0.09
40 11 0.04
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (36 bp):
TATATAATATATAGTTTTTAAAACATTTTGAAAATA
Found at i:2878334 original size:11 final size:11
Alignment explanation
Indices: 2878318--2878342 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2878308 TAATATATAG
2878318 TTTTGAAAACA
1 TTTTGAAAACA
2878329 TTTTGAAAACA
1 TTTTGAAAACA
2878340 TTT
1 TTT
2878343 ATATATTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:2879624 original size:5 final size:5
Alignment explanation
Indices: 2879616--2879734 Score: 74
Period size: 5 Copynumber: 24.0 Consensus size: 5
2879606 AATTTAATCT
2879616 TTTTA TTTT- TTTTA TTTT- TTTTA TTTTCA -TTT- TTTTA TTTTCA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT-A TTTTA TTTTA TTTT-A TTTTA
*** * *
2879664 TTTTTA TTTTA CTTGTTA -TTT- TTTTA -TTTA TACGA TATTA TATT-
1 -TTTTA TTTTA -TT-TTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
2879708 TTTTA TTTTTA TATTTA TTTTA TTTTA
1 TTTTA -TTTTA T-TTTA TTTTA TTTTA
2879735 ATCCTTTAAT
Statistics
Matches: 93, Mismatches: 6, Indels: 30
0.72 0.05 0.23
Matches are distributed among these distances:
4 23 0.25
5 44 0.47
6 23 0.25
7 3 0.03
ACGTcount: A:0.19, C:0.03, G:0.02, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:2879633 original size:6 final size:6
Alignment explanation
Indices: 2879615--2879733 Score: 52
Period size: 6 Copynumber: 19.7 Consensus size: 6
2879605 TAATTTAATC
* * *
2879615 TTTTTA TTTTT- TTTATTT TTTTTA TTTTCATT TTTTTA TTTTCA -TTTTA
1 TTTTTA TTTTTA TTT-TTA TTTTTA TTTT--TA TTTTTA TTTTTA TTTTTA
* *** *
2879664 TTTTTA -TTTTA CTTGTTA TTTTT- TTATTTA -TACGA TATTATA TTTTTTA
1 TTTTTA TTTTTA -TTTTTA TTTTTA TT-TTTA TTTTTA T-TTTTA -TTTTTA
*
2879713 TTTTTA TATTTA -TTTTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTT
2879734 AATCCTTTAA
Statistics
Matches: 84, Mismatches: 16, Indels: 26
0.67 0.13 0.21
Matches are distributed among these distances:
5 19 0.23
6 46 0.55
7 13 0.15
8 6 0.07
ACGTcount: A:0.18, C:0.03, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTTTA
Found at i:2879808 original size:2 final size:2
Alignment explanation
Indices: 2879796--2879836 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
2879786 CTACTTTGTT
*
2879796 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2879837 ACTATTATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2879847 original size:3 final size:3
Alignment explanation
Indices: 2879839--2879871 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
2879829 ATATTATAAC
2879839 TAT TAT TAT TAT TAT TAT TATT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TA
2879872 ACGTATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2879940 original size:5 final size:5
Alignment explanation
Indices: 2879930--2879963 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
2879920 TATATATATT
2879930 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
2879964 CTATTTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:2879983 original size:25 final size:24
Alignment explanation
Indices: 2879926--2880021 Score: 77
Period size: 25 Copynumber: 3.8 Consensus size: 24
2879916 TCATTATATA
* * *
2879926 TATTTTTTATTTTATTTTATTTTAT
1 TATTTTTTATTTTCTATT-TTTAAT
2879951 T-TTATTTTATTTTCTATTTTTAAT
1 TATT-TTTTATTTTCTATTTTTAAT
* *
2879975 GTATTTTTTCTTTTCTAGTTTTTAGT
1 -TATTTTTTATTTTCTA-TTTTTAAT
* *
2880001 TATTTATTTATTGTATATTTT
1 TATTT-TTTATTTTCTATTTT
2880022 ATTTTGTTCC
Statistics
Matches: 58, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
24 7 0.12
25 34 0.59
26 17 0.29
ACGTcount: A:0.19, C:0.03, G:0.04, T:0.74
Consensus pattern (24 bp):
TATTTTTTATTTTCTATTTTTAAT
Found at i:2880117 original size:66 final size:70
Alignment explanation
Indices: 2880005--2880145 Score: 193
Period size: 68 Copynumber: 2.1 Consensus size: 70
2879995 TTTAGTTATT
* *
2880005 TATTTATTGTATATTTTATTTTGTTCCCTTATTTCTTCTTTCTTTATATTT-TT-TTATTATATT
1 TATTTATTCTATATTTTATTTTGTTCCCTTACTTCTTCTTTCTTTATATTTATTATTATTATATT
2880068 TATCC
66 TATCC
* * *
2880073 TATTTA-TCTATATTTTAGTTTT-TT-CCTTGCTTCTTTTTTCTTTATATTTATTATTATTATTT
1 TATTTATTCTATATTTTA-TTTTGTTCCCTTACTTCTTCTTTCTTTATATTTATTATTATTATAT
2880135 TTATCC
65 TTATCC
2880141 TATTT
1 TATTT
2880146 GTCTTCATTT
Statistics
Matches: 65, Mismatches: 5, Indels: 6
0.86 0.07 0.08
Matches are distributed among these distances:
66 22 0.34
67 14 0.22
68 29 0.45
ACGTcount: A:0.18, C:0.11, G:0.03, T:0.68
Consensus pattern (70 bp):
TATTTATTCTATATTTTATTTTGTTCCCTTACTTCTTCTTTCTTTATATTTATTATTATTATATT
TATCC
Found at i:2885416 original size:84 final size:84
Alignment explanation
Indices: 2885286--2887186 Score: 1535
Period size: 84 Copynumber: 23.0 Consensus size: 84
2885276 TCAAGGCACA
* * * *
2885286 AAGGGTTATCTGCCAACAAAAGACCTTCGAATTCGACTATGCTCAGCTCCAAGGCGCAACATTTA
1 AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTA
* * * *
2885351 CAGCATAGCTCAAGGATAA
66 CAGCATAACTTAAGGCTAG
** * *
2885370 AAGGACTATCTGCCAACAAAAGACCTTCGAGTTCGACTATGCTCAGCTCCAAGGCATATCATTTA
1 AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTA
* * *
2885435 TAGCATAACTTAAGTCGAG
66 CAGCATAACTTAAGGCTAG
* * * * * *
2885454 AAGGGTTATCTACCAAC-CAAGGCCTTCGAGTTTGACTACGCTCAGCTCTAAGGCACATCATTTC
1 AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTA
* * *
2885518 CAGCATAGCTTAAGTCGAG
66 CAGCATAACTTAAGGCTAG
* * * * *
2885537 AAGGGTTATCTG-C--C-AAAGACCCTCGAGTTTGATTACACTCAGCTTCAAGGGCACATCATTT
1 AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTT
*
2885598 ACAGCATAACTCAAGGCTAG
65 ACAGCATAACTTAAGGCTAG
* ** * * * * *
2885618 AAGGGTTATATGTTACCAAAAGTCCTTCGAGTTCGACTACGTTCAGCTCCAAGGCATATCATTTG
1 AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTA
* * *
2885683 TAGCATAACTTAAGCCGAG
66 CAGCATAACTTAAGGCTAG
* * * * * * * *
2885702 AATGGTTATATGCCAACCAAACACCTTCGGGTTTGACTACTCTCAGCTCCAAGGCACATCATTTG
1 AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTA
* * *
2885767 CAGCATAGCTTAAGTCGAG
66 CAGCATAACTTAAGGCTAG
* * * * * * * * *
2885786 AA-GGTCTATCT----ACCAAAGACCCTCAAGTTTGATTACACTCAGCTTCGAGGATACATCATT
1 AAGGGT-TATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG-CACATCATT
*
2885846 TACAGCATAACTCAAGGCTAG
64 TACAGCATAACTTAAGGCTAG
** * * * * * * *
2885867 AAGGGTTATCTATCACCAAAAGACCTTCGAGTTCGACTACACTTAGCTCCAGGGCATATAATTTG
1 AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTA
* *
2885932 CAGTATAACTTAA-GTTGAG
66 CAGCATAACTTAAGGCT-AG
* * * * *
2885951 AAGGGTTATCTGCCAACCAAATACCTTCGATTTCGACTACGCTCAACTCCAAGGCATATCATTTA
1 AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTA
* * * *
2886016 TAGCATAGCTTAAGTCGAG
66 CAGCATAACTTAAGGCTAG
* * * * * * * *
2886035 AAGAGCTATCTG-C--C-AAAGA-CTCTCGAGTTTGATTACACTCAGCTTCGAGGGTACATCATT
1 AAGGGTTATCTGCCAACAAAAGACCT-TCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATT
*
2886095 TACAACATAA-TTCAAGGCTAG
64 TACAGCATAACTT-AAGGCTAG
* * * * * *
2886116 AAGGGTTATCTCCCACCAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGACATATTATTTA
1 AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTA
* * * *
2886181 CAGCACAACTTAAGTCGAT
66 CAGCATAACTTAAGGCTAG
* * *
2886200 AAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTTAGCTCCAAGGCACATCATTTG
1 AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTA
* * *
2886265 CAGCATAGCTTAAGTCGAG
66 CAGCATAACTTAAGGCTAG
* * * * * * * *
2886284 AAGGGCTATCT----ACCAAAGACCCTCAAGTTCGATTACACTCAGCTTCGAGGGCACATCATTT
1 AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTT
*
2886345 ACAGCATAACTCAAGGCTAG
65 ACAGCATAACTTAAGGCTAG
* * *
2886365 AAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCC-AGGACATATCATTT
1 AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG-CACATCATTT
* * * * *
2886429 GCGGTATAACTTAAGTCGAG
65 ACAGCATAACTTAAGGCTAG
* * *
2886449 AAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTATGCTCAGCTCCAAGGCACATCATTTC
1 AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTA
* *
2886514 CAGCAT-AGTTGAA-GTTGAG
66 CAGCATAACTT-AAGGCT-AG
* * * * * * * * *
2886533 AA-GGCTATCTG-C--C-AAAGACCCTCGAGTTCGATTACACTCAACTTCGAGGGTACATTATTT
1 AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTT
* *
2886593 ATAGCATAACTCAAGGCTAG
65 ACAGCATAACTTAAGGCTAG
** * * * * *
2886613 AAGGGTTATCTATCACCAAAAGACCTTTGAGTTTGACTACGCTCAGCTCCAATGCATATCATTTA
1 AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTA
* * *
2886678 CAACATAACTTAAGTCGAG
66 CAGCATAACTTAAGGCTAG
* * * * * * *
2886697 ATGGGTTATCTTCCAACCAAAGACCTTCGAGTTTGACTACACTCAACTCCAAGGCACATCATTTG
1 AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTA
* * *
2886762 CAGCATAGCTTAAGTCGAG
66 CAGCATAACTTAAGGCTAG
* * * * * * * * *
2886781 AAGGGCTGTCT-TC--C-AAAGACCCTCAAGTTCGATTACACTCAGCTTCGAGGGCACATCATTT
1 AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTT
* * *
2886842 ACAGTATAAATCAAGGCTAG
65 ACAGCATAACTTAAGGCTAG
* * * ** * * * *
2886862 AAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCAACTACGCTCAATTCTAGGGAATATCATTTA
1 AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTA
* *
2886927 CAGCATAACTTAAGTCGAG
66 CAGCATAACTTAAGGCTAG
* *
2886946 AAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTATGCTCAGCTCCAAGGCACATCATTTA
1 AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTA
* * *
2887011 CAGCATATCTTAAGTCGAG
66 CAGCATAACTTAAGGCTAG
* * * * * *
2887030 AAGGGATATCTG-C--C-AAAGACC--CAAGTTCGATTACAC-CAGCTTCAAGGGCATATCATTT
1 AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTT
* *
2887088 ACAGCATAACTCAAGGCTAA
65 ACAGCATAACTTAAGGCTAG
* * * * ** * *
2887108 AAGGGTTATTTGTC-ACCAAAGACCTTCAAGTTTTACTACGCTTAGCTCCAAGGCACATCATTTG
1 AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTA
* *
2887172 TAGCATAGCTTAAGG
66 CAGCATAACTTAAGG
2887187 GCTATCTGTC
Statistics
Matches: 1440, Mismatches: 325, Indels: 105
0.77 0.17 0.06
Matches are distributed among these distances:
77 8 0.01
78 47 0.03
79 27 0.02
80 165 0.11
81 201 0.14
82 9 0.01
83 123 0.09
84 704 0.49
85 154 0.11
86 2 0.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (84 bp):
AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTA
CAGCATAACTTAAGGCTAG
Found at i:2885823 original size:249 final size:249
Alignment explanation
Indices: 2885345--2887185 Score: 2584
Period size: 249 Copynumber: 7.4 Consensus size: 249
2885335 CAAGGCGCAA
* * * ** * * *
2885345 CATTTACAGCATAGCTCAAGGATAAAAGGACTATCTGCCAACAAAAGACCTTCGAGTTCGACTAT
1 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTAC
* *
2885410 GCTCAGCTCCAAGGCATATCATTTATAGCATAACTTAAGTCGAGAAGGGTTATCTACCAACC-AA
66 GCTCAGCTCCAAGGCATATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAA
* * *
2885474 GGCCTTCGAGTTTGACTACGCTCAGCTCTAAGGCACATCATTTCCAGCATAGCTTAAGTCGAGAA
131 GACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAA
* * * *
2885539 GGGTTATCTGCCAAAGACCCTCGAGTTTGATTACACTCAGCTTCAAGGGCACAT
196 GGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCGAGGGCACAT
* * *
2885593 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATATGTTACCAAAAGTCCTTCGAGTTCGACTAC
1 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTAC
* ** * * *
2885658 GTTCAGCTCCAAGGCATATCATTTGTAGCATAACTTAAGCCGAGAATGGTTATATGCCAACCAAA
66 GCTCAGCTCCAAGGCATATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAA
* * *
2885723 CACCTTCGGGTTTGACTACTCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAA
131 GACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAA
* * * **
2885788 GGTCTATCTACCAAAGACCCTCAAGTTTGATTACACTCAGCTTCGAGGATACAT
196 GGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCGAGGGCACAT
*
2885842 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTATCACCAAAAGACCTTCGAGTTCGACTAC
1 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTAC
* * * * * * *
2885907 ACTTAGCTCCAGGGCATATAATTTGCAGTATAACTTAAGTTGAGAAGGGTTATCTGCCAACCAAA
66 GCTCAGCTCCAAGGCATATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAA
* * * **
2885972 TACCTTCGA-TTTCGACTACGCTCAACTCCAAGGCATATCATTTATAGCATAGCTTAAGTCGAGA
131 GACCTTCGAGTTT-GACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGA
* * * * *
2886036 AGAGCTATCTGCCAAAGACTCTCGAGTTTGATTACACTCAGCTTCGAGGGTACAT
195 AGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCGAGGGCACAT
* * ** *
2886091 CATTTACAACATAATTCAAGGCTAGAAGGGTTATCTCCCACCAAAAGACCTTTGAGTTCGACTAC
1 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTAC
* * * *
2886156 GCTCAGCTCCAAGACATATTATTTACAGCACAACTTAAGTCGATAAGGGTTATCTGCCAACCAAA
66 GCTCAGCTCCAAGGCATATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAA
* *
2886221 GACCTTCGAGTTCGACTACGCTTAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAA
131 GACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAA
*
2886286 GGGCTATCTACCAAAGACCCTCAAGTTCGATTACACTCAGCTTCGAGGGCACAT
196 GGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCGAGGGCACAT
2886340 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTAC
1 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTAC
* * *
2886405 GCTCAGCTCC-AGGACATATCATTTGCGGTATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAA
66 GCTCAGCTCCAAGG-CATATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAA
* * * *
2886469 AGACCTTCGAGTTCGACTATGCTCAGCTCCAAGGCACATCATTTCCAGCATAG-TTGAAGTTGAG
130 AGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTT-AAGTCGAG
* * *
2886533 AA-GGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAACTTCGAGGGTACAT
194 AAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCGAGGGCACAT
* * * * *
2886588 TATTTATAGCATAACTCAAGGCTAGAAGGGTTATCTATCACCAAAAGACCTTTGAGTTTGACTAC
1 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTAC
* * * *
2886653 GCTCAGCTCCAATGCATATCATTTACAACATAACTTAAGTCGAGATGGGTTATCTTCCAACCAAA
66 GCTCAGCTCCAAGGCATATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAA
* *
2886718 GACCTTCGAGTTTGACTACACTCAACTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAA
131 GACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAA
* *
2886783 GGGCTGTCTTCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCGAGGGCACAT
196 GGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCGAGGGCACAT
* * *
2886837 CATTTACAGTATAAATCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCAACTAC
1 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTAC
** * * *
2886902 GCTCAATTCTAGGGAATATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAA
66 GCTCAGCTCCAAGGCATATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAA
* * * *
2886967 GACCTTCGAGTTCGACTATGCTCAGCTCCAAGGCACATCATTTACAGCATATCTTAAGTCGAGAA
131 GACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAA
* * *
2887032 GGGATATCTGCCAAAGA-CC-CAAGTTCGATTACAC-CAGCTTCAAGGGCATAT
196 GGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCGAGGGCACAT
* * * **
2887083 CATTTACAGCATAACTCAAGGCTAAAAGGGTTATTTGTCACC-AAAGACCTTCAAGTTTTACTAC
1 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTAC
* * ** *
2887147 GCTTAGCTCCAAGGCACATCATTTGTAGCATAGCTTAAG
66 GCTCAGCTCCAAGGCATATCATTTACAGCATAACTTAAG
2887186 GGCTATCTGT
Statistics
Matches: 1411, Mismatches: 174, Indels: 19
0.88 0.11 0.01
Matches are distributed among these distances:
245 48 0.03
246 53 0.04
247 15 0.01
248 339 0.24
249 954 0.68
250 2 0.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (249 bp):
CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTAC
GCTCAGCTCCAAGGCATATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAA
GACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAA
GGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCGAGGGCACAT
Found at i:2887795 original size:2 final size:2
Alignment explanation
Indices: 2887790--2887926 Score: 195
Period size: 2 Copynumber: 69.0 Consensus size: 2
2887780 GTCCACACAT
*
2887790 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
2887832 TA TA CA TA TG TG TA TA TA TA TA TA TA TA TA TA TA TA CA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
2887874 TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA CA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2887916 TA TA T- TA TA TA
1 TA TA TA TA TA TA
2887927 GTTTGCAAAC
Statistics
Matches: 122, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
1 1 0.01
2 121 0.99
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Done.