Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007994.1 Hibiscus syriacus cultivar Beakdansim tig00110444_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: 788627
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 3 of 4
Found at i:515519 original size:15 final size:16
Alignment explanation
Indices: 515487--515532 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
515477 CCAACGTTTT
* *
515487 TGTTCGTTTATATTCG
1 TGTTCATTTATGTTCG
515503 TGTTCATTTA-GTTCG
1 TGTTCATTTATGTTCG
*
515518 TGTTCGTTTATGTTC
1 TGTTCATTTATGTTC
515533 ATTTATTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.11, C:0.13, G:0.20, T:0.57
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:518344 original size:13 final size:13
Alignment explanation
Indices: 518326--518363 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
518316 TTACAACCCG
* *
518326 ACCCGACTCGTTT
1 ACCCGACCCGTTC
518339 ACCCGACCCGTTC
1 ACCCGACCCGTTC
518352 ACCCGACCCGTT
1 ACCCGACCCGTT
518364 GACCGTTGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.16, C:0.47, G:0.16, T:0.21
Consensus pattern (13 bp):
ACCCGACCCGTTC
Found at i:529621 original size:15 final size:16
Alignment explanation
Indices: 529601--529631 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
529591 GACTTTGACC
529601 GAAAAGTCA-ATTTTA
1 GAAAAGTCATATTTTA
529616 GAAAAGTCATATTTTA
1 GAAAAGTCATATTTTA
529632 TGTTTTTCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.35
Consensus pattern (16 bp):
GAAAAGTCATATTTTA
Found at i:532463 original size:44 final size:43
Alignment explanation
Indices: 532373--532732 Score: 517
Period size: 44 Copynumber: 8.3 Consensus size: 43
532363 GTTCCTTTAC
* *
532373 TGTGTGCAAGAGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGT
1 TGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTCCCTTTGT
* *
532416 TGTGTGCAAGGGTAAGCTTTATAGTTTCCCCCAGGTCCCTTTGT
1 TGTGTGCAAGGGTAAGCCTTACAGTTT-CCCCAGGTCCCTTTGT
*
532460 TGTGTGCAAGGGTAAGCCTTACAGTTTTCCTCAGGTCCCTTTTGT
1 TGTGTGCAAGGGTAAGCCTTACAG-TTTCCCCAGGTCCC-TTTGT
*
532505 TGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTCCCTTTGC
1 TGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTCCCTTTGT
*
532548 TGTGTGCAAGGGTAAGCCTTACAGTTTCCCTCAGGTCCCTTTGC
1 TGTGTGCAAGGGTAAGCCTTACAGTTTCCC-CAGGTCCCTTTGT
* ** *
532592 TATGTGCAAGGGTAAGCCTTACAGTTTCCCCCATTTCCCTTTGC
1 TGTGTGCAAGGGTAAGCCTTACAGTTT-CCCCAGGTCCCTTTGT
*
532636 TGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTT-T
1 TGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTCCCTTTGT
*
532678 CTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGG-CTCTTTTGT
1 -TGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTC-CCTTTGT
*
532722 TATGTGCAAGG
1 TGTGTGCAAGG
532733 ATAACACCTT
Statistics
Matches: 289, Mismatches: 20, Indels: 16
0.89 0.06 0.05
Matches are distributed among these distances:
43 117 0.40
44 137 0.47
45 35 0.12
ACGTcount: A:0.17, C:0.25, G:0.24, T:0.34
Consensus pattern (43 bp):
TGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTCCCTTTGT
Found at i:537837 original size:16 final size:16
Alignment explanation
Indices: 537794--537840 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
537784 CCAACGTTTT
*
537794 TGTTCGTTTATATTCG
1 TGTTCGTTTATGTTCG
*
537810 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
537826 TGTTCGTTTATGTTC
1 TGTTCGTTTATGTTC
537841 ATTTATTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.11, C:0.13, G:0.19, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:537933 original size:16 final size:16
Alignment explanation
Indices: 537912--537944 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
537902 AAAAAAAATT
*
537912 TGTTCGTTTATGTTCG
1 TGTTCGTTTAAGTTCG
537928 TGTTCGTTTAAGTTCG
1 TGTTCGTTTAAGTTCG
537944 T
1 T
537945 TTATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.09, C:0.12, G:0.24, T:0.55
Consensus pattern (16 bp):
TGTTCGTTTAAGTTCG
Found at i:540682 original size:13 final size:13
Alignment explanation
Indices: 540654--540690 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
540644 TTACAACCCG
*
540654 ACCCGA-CCGTTT
1 ACCCGACCCGTTC
540666 ACCCGACCCGTTC
1 ACCCGACCCGTTC
540679 ACCCGACCCGTT
1 ACCCGACCCGTT
540691 GACCGTTGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 6 0.26
13 17 0.74
ACGTcount: A:0.16, C:0.49, G:0.16, T:0.19
Consensus pattern (13 bp):
ACCCGACCCGTTC
Found at i:543242 original size:48 final size:48
Alignment explanation
Indices: 543190--543281 Score: 121
Period size: 48 Copynumber: 1.9 Consensus size: 48
543180 TCCAACTTGA
* * *
543190 ATTCTGTTCTGATACATGACCTGAATTCTGTTCTGATTTTTGATCTGG
1 ATTCTGTTATGATACATGACCTAAATTCTGTTCTGATTTATGATCTGG
* ** *
543238 ATTCTGTTATGATATATGTTCTAAATTCTGTTTTGATTTATGAT
1 ATTCTGTTATGATACATGACCTAAATTCTGTTCTGATTTATGAT
543282 ATCTTCGTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 37 1.00
ACGTcount: A:0.22, C:0.12, G:0.16, T:0.50
Consensus pattern (48 bp):
ATTCTGTTATGATACATGACCTAAATTCTGTTCTGATTTATGATCTGG
Found at i:554787 original size:44 final size:44
Alignment explanation
Indices: 554715--555088 Score: 529
Period size: 44 Copynumber: 8.5 Consensus size: 44
554705 CCATTACAGT
* * *
554715 AGGTTCCTTTGCTGTGTGCAAGAGTAAGCCTTACAATTTCCCCC
1 AGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCC
* * * *
554759 AGGTCCCTTTGTTGTGTGCAAGGCTAAGCTTTACAGTTTCCCTC
1 AGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCC
* *
554803 ATGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCC
1 AGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCC
*
554847 AGGTCCCTTTTGCTGTGTGCAAAGGTAAGCCTTACAGTTTCCCCC
1 AGGTCCC-TTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCC
* *
554892 AGGTCCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCTC
1 AGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCC
*
554936 AGGTCCCTTTGCTATGTGCAAGGGTAAGCCTTACAGTTTCCCCC
1 AGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCC
* * *
554980 ATGTCCCTTTGTTGTGTACAAGGGTAAGCCTTACAGTTT-CCCC
1 AGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCC
* *
555023 AGGTTCCTTTTCTGTGTGCAAGGGTAAGCCTTACAGTTT-CCCC
1 AGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCC
* *
555066 AGG-CTCTTTTGCTATGTGCAAGG
1 AGGTC-CCTTTGCTGTGTGCAAGG
555089 ATAACACCTT
Statistics
Matches: 293, Mismatches: 35, Indels: 5
0.88 0.11 0.02
Matches are distributed among these distances:
43 60 0.20
44 190 0.65
45 43 0.15
ACGTcount: A:0.17, C:0.26, G:0.23, T:0.33
Consensus pattern (44 bp):
AGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCC
Found at i:554960 original size:133 final size:132
Alignment explanation
Indices: 554715--555088 Score: 560
Period size: 133 Copynumber: 2.8 Consensus size: 132
554705 CCATTACAGT
* *
554715 AGGTTCCTTTGCTGTGTGC-AAGAGTAAGCCTTACAATTTCCCCCAGGTCCCTTTGTTGTGTGCA
1 AGGTCCCTTTGCTGTGTGCAAAG-GTAAGCCTTACAGTTTCCCCCAGGTCCCTTTGTTGTGTGCA
* * * * *
554779 AGGCTAAGCTTTACAGTTTCCCTCATGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCC
65 AGGGTAAGCCTTACAGTTTCCCTCAGGTCCCTTTGCTATGTGCAAGGGTAAGCCTTACAGTTTCC
554844 CCC
130 CCC
554847 AGGTCCCTTTTGCTGTGTGCAAAGGTAAGCCTTACAGTTTCCCCCAGGTCCCTTTGTTGTGTGCA
1 AGGTCCC-TTTGCTGTGTGCAAAGGTAAGCCTTACAGTTTCCCCCAGGTCCCTTTGTTGTGTGCA
554912 AGGGTAAGCCTTACAGTTTCCCTCAGGTCCCTTTGCTATGTGCAAGGGTAAGCCTTACAGTTTCC
65 AGGGTAAGCCTTACAGTTTCCCTCAGGTCCCTTTGCTATGTGCAAGGGTAAGCCTTACAGTTTCC
554977 CCC
130 CCC
* * * * *
554980 ATGTCCCTTTGTTGTGTACAAGGGTAAGCCTTACAGTTT-CCCCAGGTTCCTTT-TCTGTGTGCA
1 AGGTCCCTTTGCTGTGTGCAAAGGTAAGCCTTACAGTTTCCCCCAGGTCCCTTTGT-TGTGTGCA
*
555043 AGGGTAAGCCTTACAGTTTCCC-CAGG-CTCTTTTGCTATGTGCAAGG
65 AGGGTAAGCCTTACAGTTTCCCTCAGGTC-CCTTTGCTATGTGCAAGG
555089 ATAACACCTT
Statistics
Matches: 225, Mismatches: 13, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
129 1 0.00
130 22 0.10
131 43 0.19
132 35 0.16
133 121 0.54
134 3 0.01
ACGTcount: A:0.17, C:0.26, G:0.23, T:0.33
Consensus pattern (132 bp):
AGGTCCCTTTGCTGTGTGCAAAGGTAAGCCTTACAGTTTCCCCCAGGTCCCTTTGTTGTGTGCAA
GGGTAAGCCTTACAGTTTCCCTCAGGTCCCTTTGCTATGTGCAAGGGTAAGCCTTACAGTTTCCC
CC
Found at i:558297 original size:18 final size:18
Alignment explanation
Indices: 558274--558325 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
558264 ACCGGTTACA
*
558274 ACCCGACCAGACCCGTTG
1 ACCCGACCCGACCCGTTG
558292 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
558310 ACCCTACCCGACCCGT
1 ACCCGACCCGACCCGT
558326 CGACTGGCGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.19, C:0.50, G:0.19, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:559657 original size:18 final size:18
Alignment explanation
Indices: 559631--559665 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
559621 TCGAAAGGAC
*
559631 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
559649 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
559666 CCGAAAGAAA
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:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:560837 original size:24 final size:24
Alignment explanation
Indices: 560810--560892 Score: 123
Period size: 24 Copynumber: 3.5 Consensus size: 24
560800 ATTATATATC
*
560810 TGACCTGGATTCTGATCGAATACT
1 TGACCTGGATTTTGATCGAATACT
*
560834 TGACCTGGATTTTGATTGAATACT
1 TGACCTGGATTTTGATCGAATACT
560858 TGACCTGGATTTTGATCTG-ATACT
1 TGACCTGGATTTTGATC-GAATACT
*
560882 TGAACTGGATT
1 TGACCTGGATT
560893 ATGTTATGAT
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
24 53 0.98
25 1 0.02
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.39
Consensus pattern (24 bp):
TGACCTGGATTTTGATCGAATACT
Found at i:561973 original size:303 final size:303
Alignment explanation
Indices: 561377--561977 Score: 902
Period size: 303 Copynumber: 2.0 Consensus size: 303
561367 ACTATTTTAT
* * *
561377 TCAATATTTCAGGTTAAAAGAATTGTACCAATGCAACTATCGACATCAGTAAAGGAATTCTTCCG
1 TCAACATTGCAGGTTAAAAGAATTATACCAATGCAACTATCGACATCAGTAAAGGAATTCTTCCG
*
561442 GCGTTGTTTCCAGAGAATGATACATGTGATTAGGGGGCATGTAATTGAATTTTGTTTTATGTACG
66 GCGTTGTTTCCAGAGAATGATACATGTGATTAGGGGGCATGTAATTGAATTTTGTTTTATATACG
* *
561507 AGCCTGAAAATCTGTTTTATTTATACATACTGATAAATCATTTTATAAGTTTACATGTTCTGATA
131 AGCCTGAAAATATGTTTTATTTATACATACTGATAAATCATTTTATAAGTTTACATGTTCTAATA
* *
561572 AAAAGTTTTAAATTTTCCGCTATTTTTACGGTGGGTCGCTCCGGTGACCCTAATGTGACTTCCCA
196 AAAAGTTTTAAATTTTCCGCTATTTTTACAGTGGGTCGCTCCGGTGACCCTAATGTGACCTCCCA
*
561637 GATCGGATCAGGTTACCTGCATCGGTCAGGGGGTTACAATTAC
261 GATCGGATCAGGTTACCCGCATCGGTCAGGGGGTTACAATTAC
* * * * * *
561680 TCAACATTGCAGGTTAAAATAATTATACCAGTGCAGCTATCGACTTCAGTAAGGGAGTTCTTCCG
1 TCAACATTGCAGGTTAAAAGAATTATACCAATGCAACTATCGACATCAGTAAAGGAATTCTTCCG
* * * * *
561745 GCGTTGTTTGCAGAGTATGGTACATGTGATTGGGGGGCATGTAATTGTATTTTGTTTTATATACG
66 GCGTTGTTTCCAGAGAATGATACATGTGATTAGGGGGCATGTAATTGAATTTTGTTTTATATACG
* * * * *
561810 AGTCTGAAAATATGTTTTATTTCTTCGTACTGATAAATCATTTTATAA-TTTACATGTTTTAAT-
131 AGCCTGAAAATATGTTTTATTTATACATACTGATAAATCATTTTATAAGTTTACATGTTCTAATA
*
561873 AAAAGTTTTAAATTTTCCGCTATTTTTACAGTGGGTTGCTCCGGTGACCCTAATGTGACACT-CC
196 AAAAGTTTTAAATTTTCCGCTATTTTTACAGTGGGTCGCTCCGGTGACCCTAATGTGAC-CTCCC
* *
561937 AGATCGGATCGGGTTACCCGCATCGATGTGAGGGGGTTACA
260 AGATCGGATCAGGTTACCCGCATCG--GTCAGGGGGTTACA
561978 GATTTCCACA
Statistics
Matches: 267, Mismatches: 28, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
301 82 0.31
302 14 0.05
303 171 0.64
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (303 bp):
TCAACATTGCAGGTTAAAAGAATTATACCAATGCAACTATCGACATCAGTAAAGGAATTCTTCCG
GCGTTGTTTCCAGAGAATGATACATGTGATTAGGGGGCATGTAATTGAATTTTGTTTTATATACG
AGCCTGAAAATATGTTTTATTTATACATACTGATAAATCATTTTATAAGTTTACATGTTCTAATA
AAAAGTTTTAAATTTTCCGCTATTTTTACAGTGGGTCGCTCCGGTGACCCTAATGTGACCTCCCA
GATCGGATCAGGTTACCCGCATCGGTCAGGGGGTTACAATTAC
Found at i:564816 original size:17 final size:18
Alignment explanation
Indices: 564783--564834 Score: 61
Period size: 17 Copynumber: 2.8 Consensus size: 18
564773 TCAAAGTTCT
564783 GGTCAACGGTTGTCAACGCC
1 GGTCAACGG--GTCAACGCC
*
564803 GGTCAAC-GGTCAACGCT
1 GGTCAACGGGTCAACGCC
*
564820 GGTGAACGGGTCAAC
1 GGTCAACGGGTCAAC
564835 AATTTTACAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 14 0.48
18 7 0.24
19 1 0.03
20 7 0.24
ACGTcount: A:0.23, C:0.27, G:0.33, T:0.17
Consensus pattern (18 bp):
GGTCAACGGGTCAACGCC
Found at i:564827 original size:27 final size:25
Alignment explanation
Indices: 564783--564834 Score: 59
Period size: 27 Copynumber: 2.0 Consensus size: 25
564773 TCAAAGTTCT
* *
564783 GGTCAACGGTTGTCAACGCCGGTCAAC
1 GGTCAACGCTGGTCAACG--GGTCAAC
*
564810 GGTCAACGCTGGTGAACGGGTCAAC
1 GGTCAACGCTGGTCAACGGGTCAAC
564835 AATTTTACAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 7 0.32
27 15 0.68
ACGTcount: A:0.23, C:0.27, G:0.33, T:0.17
Consensus pattern (25 bp):
GGTCAACGCTGGTCAACGGGTCAAC
Found at i:570349 original size:109 final size:109
Alignment explanation
Indices: 570158--570363 Score: 333
Period size: 109 Copynumber: 1.9 Consensus size: 109
570148 TGATTTTGTA
* * * *
570158 TGATAGATTCTATGTGCCGTTTTTGACTAATATAAATGGCTCAGCTAAGAAAAACATTTGGAACC
1 TGATAGATTCTATGTGCCGGTTTTGACTAATATAAATGGCCCAGCCAAGAAAAACATTAGGAACC
* *
570223 CTGTTCTGTTCCCCAAAGCAAAGACTATAGAAATGAATATATTT
66 CTATTCTGTTACCCAAAGCAAAGACTATAGAAATGAATATATTT
570267 TGATAGATTCTATGTGCCGGTTTTGACTAATATAAATGGCCCAGCCAAGAAAAACATTAGGAA-C
1 TGATAGATTCTATGTGCCGGTTTTGACTAATATAAATGGCCCAGCCAAGAAAAACATTAGGAACC
*
570331 CTCATTCTGTTACCCAAAGCATAGACTATAGAA
66 CT-ATTCTGTTACCCAAAGCAAAGACTATAGAA
570364 TCTATTCTTA
Statistics
Matches: 89, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
108 3 0.03
109 86 0.97
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (109 bp):
TGATAGATTCTATGTGCCGGTTTTGACTAATATAAATGGCCCAGCCAAGAAAAACATTAGGAACC
CTATTCTGTTACCCAAAGCAAAGACTATAGAAATGAATATATTT
Found at i:579060 original size:109 final size:109
Alignment explanation
Indices: 578869--579074 Score: 331
Period size: 109 Copynumber: 1.9 Consensus size: 109
578859 TGATTTTGTA
* * * ** *
578869 TGATAGATTCTATGTGCCGTTTTTTATTAATATAAATGGCTTAGCTAAGAAAAACATTTGGAACC
1 TGATAGATTCTATGTGCCGGTTTTGACTAATATAAATGGCCCAGCTAAGAAAAACATTAGGAACC
*
578934 CCGTTCTGTTCCCCAAAGCAAAGACTATAGAAATGAATATATTT
66 CCATTCTGTTCCCCAAAGCAAAGACTATAGAAATGAATATATTT
578978 TGATAGATTCTATGTGCCGGTTTTGACTAATATAAATGGCCCAGCTAAGAAAAACATTAGGAACC
1 TGATAGATTCTATGTGCCGGTTTTGACTAATATAAATGGCCCAGCTAAGAAAAACATTAGGAACC
* *
579043 TCATTCTGTTCCCCAAAGCATAGACTATAGAA
66 CCATTCTGTTCCCCAAAGCAAAGACTATAGAA
579075 TCTATTCTTA
Statistics
Matches: 88, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
109 88 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (109 bp):
TGATAGATTCTATGTGCCGGTTTTGACTAATATAAATGGCCCAGCTAAGAAAAACATTAGGAACC
CCATTCTGTTCCCCAAAGCAAAGACTATAGAAATGAATATATTT
Found at i:594477 original size:37 final size:37
Alignment explanation
Indices: 594389--594545 Score: 208
Period size: 37 Copynumber: 4.3 Consensus size: 37
594379 ATCAGACTCG
* *
594389 AGATTGATTTGCTTCACTACTCTTCCTTAAAGGC-TA
1 AGATTGATTTGCTTCACTACTCTTCCGTGAAGGCTTA
*
594425 AGATTGATTTTCTTCACTACTCTTCCGTGAAGGCTTA
1 AGATTGATTTGCTTCACTACTCTTCCGTGAAGGCTTA
* * *
594462 AGATTGACTTGCTTCACTACTCTTTCGTGAAGGATTA
1 AGATTGATTTGCTTCACTACTCTTCCGTGAAGGCTTA
* * * *
594499 AGAATGATTTGTTTCACTACTTTTTCGTGAAGGCTTA
1 AGATTGATTTGCTTCACTACTCTTCCGTGAAGGCTTA
*
594536 ATATTGATTT
1 AGATTGATTT
594546 TTTGAAGGTC
Statistics
Matches: 106, Mismatches: 14, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
36 31 0.29
37 75 0.71
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.41
Consensus pattern (37 bp):
AGATTGATTTGCTTCACTACTCTTCCGTGAAGGCTTA
Found at i:595579 original size:16 final size:16
Alignment explanation
Indices: 595558--595592 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
595548 ACAAGTATTG
595558 AATCTCATGTGCATTC
1 AATCTCATGTGCATTC
595574 AATCTCATGTGCATTC
1 AATCTCATGTGCATTC
595590 AAT
1 AAT
595593 TTCTCTCCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (16 bp):
AATCTCATGTGCATTC
Found at i:610730 original size:15 final size:15
Alignment explanation
Indices: 610710--610739 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
610700 AGAGAAACAA
610710 CCGAGTTTTAATGCT
1 CCGAGTTTTAATGCT
610725 CCGAGTTTTAATGCT
1 CCGAGTTTTAATGCT
610740 TCTCTATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (15 bp):
CCGAGTTTTAATGCT
Found at i:612750 original size:40 final size:41
Alignment explanation
Indices: 612673--612750 Score: 131
Period size: 40 Copynumber: 1.9 Consensus size: 41
612663 AAATTAAAAA
*
612673 TAAATACAATAACCTTTAATTTAAAAGTTTTTCTAATCTCC
1 TAAATACAATAACCTTTAATTTAAAAGTTTTTATAATCTCC
*
612714 TAAATACAATAACC-TTCATTTAAAAGTTTTTATAATC
1 TAAATACAATAACCTTTAATTTAAAAGTTTTTATAATC
612751 CGATAGAACG
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 21 0.60
41 14 0.40
ACGTcount: A:0.41, C:0.15, G:0.03, T:0.41
Consensus pattern (41 bp):
TAAATACAATAACCTTTAATTTAAAAGTTTTTATAATCTCC
Found at i:618786 original size:37 final size:35
Alignment explanation
Indices: 618736--618812 Score: 109
Period size: 37 Copynumber: 2.1 Consensus size: 35
618726 GGTCAAATCG
* *
618736 TTGAGTTTGACTGAGTCAACCCGTTGACCGTTGATCT
1 TTGACTTTGACTGAGTCAACCCATTGA-CGTTGA-CT
*
618773 TTGACTTTGACTGAGTCAACCCATTGACTTTGACT
1 TTGACTTTGACTGAGTCAACCCATTGACGTTGACT
618808 TTGAC
1 TTGAC
618813 CAAAAAGTCA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 7 0.19
36 5 0.14
37 25 0.68
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (35 bp):
TTGACTTTGACTGAGTCAACCCATTGACGTTGACT
Found at i:622106 original size:62 final size:62
Alignment explanation
Indices: 622037--622161 Score: 205
Period size: 62 Copynumber: 2.0 Consensus size: 62
622027 TAAATAACTC
* * *
622037 TATTACATTTAAGTACATTATTAAAGCGTGATGAGTCATTAAGCTTACCTGAGAAGTTGTTT
1 TATTACATTTAAATACATTATTAAAGCATGATGAGTCATTAAGCATACCTGAGAAGTTGTTT
* *
622099 TATTACATTTAAATACGTTATTAAAGCATGATGAGTCATTAAGCATGCCTGAGAAGTTGTTT
1 TATTACATTTAAATACATTATTAAAGCATGATGAGTCATTAAGCATACCTGAGAAGTTGTTT
622161 T
1 T
622162 CTCCAACGGT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 58 1.00
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (62 bp):
TATTACATTTAAATACATTATTAAAGCATGATGAGTCATTAAGCATACCTGAGAAGTTGTTT
Found at i:623261 original size:19 final size:19
Alignment explanation
Indices: 623217--623264 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
623207 CAATTTGAAT
*
623217 TATTTTTCATTTTTAATCCA
1 TATTTTT-ATTTTTAATACA
* *
623237 -AATTTTATTTTTAATATA
1 TATTTTTATTTTTAATACA
623255 TATTTTTATT
1 TATTTTTATT
623265 ATTTTTAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 10 0.43
19 13 0.57
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (19 bp):
TATTTTTATTTTTAATACA
Found at i:623655 original size:2 final size:2
Alignment explanation
Indices: 623648--623679 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
623638 CAAATAACTC
623648 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
623680 ATATATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:623684 original size:2 final size:2
Alignment explanation
Indices: 623679--623731 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
623669 TCTCTCTCTC
623679 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
623721 TA TA TA TA TA T
1 TA TA TA TA TA T
623732 TTGACATGAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:627135 original size:178 final size:177
Alignment explanation
Indices: 626617--627167 Score: 845
Period size: 177 Copynumber: 3.1 Consensus size: 177
626607 GCTTGAAAGA
*
626617 CTTATAGATGACCCGAAGGA-TT-TAAGCATCAAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGT
1 CTTATGGATGACCCGAAGGACTTATAA--ATCAAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGT
* * * *
626680 CAAGGAACCCCTTAAAAGACTTAGCTTCCTTTAACAACTCTTTTAAAATAATTAATAAACCCCTA
64 CAAGGAACCCCTTAAAAGGCTTAGCTTCCTTTAACAACTCTTTTGAGATAATTAAGAAACCCCTA
*
626745 AAAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCACTAAAGGT
129 AAAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGAAGGT
* * * * *
626794 CTTATGGATGGCCCGAAGGACTTACAAACCAAGAAACCCTCGAAGGCTTAGTTTCTTTGTTGTCA
1 CTTATGGATGACCCGAAGGACTTATAAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCA
**
626859 AATAACCCCTTAAAAGGCTTAGCTTCCTTTAACAACTCTTTTGAGATAATTAAGAAACCCCTAAA
66 AGGAACCCCTTAAAAGGCTTAGCTTCCTTTAACAACTCTTTTGAGATAATTAAGAAACCCCTAAA
* *
626924 AGGCTTAGTTTCTAAAATATCATTTGAAAACATCCTACACTGAAGGT
131 AGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGAAGGT
*
626971 CTTATGGATGGCCCGAAGGACTTATAAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCA
1 CTTATGGATGACCCGAAGGACTTATAAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCA
* *** * **
627036 AGGAACCTCTTTGTTAGGCTTAGCTTCCTTTAACAACTCTTTTGAGATAATTAGGAAACCCCCGA
66 AGGAACC-CCTTAAAAGGCTTAGCTTCCTTTAACAACTCTTTTGAGATAATTAAGAAACCCCTAA
627101 AAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGAAGGT
130 AAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGAAGGT
*
627149 CTTATGGATGACCCTAAGG
1 CTTATGGATGACCCGAAGG
627168 CTTTAACATC
Statistics
Matches: 339, Mismatches: 32, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
177 222 0.65
178 115 0.34
179 2 0.01
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (177 bp):
CTTATGGATGACCCGAAGGACTTATAAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCA
AGGAACCCCTTAAAAGGCTTAGCTTCCTTTAACAACTCTTTTGAGATAATTAAGAAACCCCTAAA
AGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGAAGGT
Found at i:627201 original size:41 final size:42
Alignment explanation
Indices: 627155--627256 Score: 152
Period size: 42 Copynumber: 2.5 Consensus size: 42
627145 AGGTCTTATG
* * * *
627155 GATGACCCTAAGGCTTTAA-CATCTTGCTCGAAAGGCTTACA
1 GATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACA
*
627196 GATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACG
1 GATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACA
627238 GATGACCCGAAGGATTTAA
1 GATGACCCGAAGGATTTAA
627257 AAATTTGGGA
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
41 17 0.31
42 38 0.69
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.24
Consensus pattern (42 bp):
GATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACA
Found at i:628294 original size:54 final size:54
Alignment explanation
Indices: 628195--628303 Score: 157
Period size: 54 Copynumber: 2.0 Consensus size: 54
628185 TAATCATTGG
* *
628195 TTCGTAAAACATTTGACAACACATTCATTCTTTCCTATGGTTTCTGTCC-AGATT
1 TTCGTAAAACATTTGACAACACATTCATCCTTTCCTATGGCTTCTG-CCTAGATT
* * *
628249 TTCGTAAAGCATTTGACAACACATTCATCCTTTCTTGTGGCTTCTGCCTAGATT
1 TTCGTAAAACATTTGACAACACATTCATCCTTTCCTATGGCTTCTGCCTAGATT
628303 T
1 T
628304 CTTATCAGTT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
53 2 0.04
54 47 0.96
ACGTcount: A:0.24, C:0.23, G:0.13, T:0.40
Consensus pattern (54 bp):
TTCGTAAAACATTTGACAACACATTCATCCTTTCCTATGGCTTCTGCCTAGATT
Found at i:630256 original size:5 final size:5
Alignment explanation
Indices: 630246--630325 Score: 83
Period size: 5 Copynumber: 16.0 Consensus size: 5
630236 CTTGATTCAA
* * * *
630246 TTTCT TTTCT TTTCT TTTCT TTTACA TCTCT TTT-T TTCCT TTCCT TTTCTT
1 TTTCT TTTCT TTTCT TTTCT TTT-CT TTTCT TTTCT TTTCT TTTCT TTTC-T
*
630297 TTTTT TTTCT TTTCT TTTCT TTT-T TTTCT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT
630326 AATAGATGAC
Statistics
Matches: 63, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
4 7 0.11
5 49 0.78
6 7 0.11
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTCT
Found at i:630302 original size:21 final size:21
Alignment explanation
Indices: 630276--630323 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
630266 TTTACATCTC
630276 TTTTTTTCCTTTCCTTTTCTT
1 TTTTTTTCCTTTCCTTTTCTT
* *
630297 TTTTTTTTCTTTTCTTTTCTT
1 TTTTTTTCCTTTCCTTTTCTT
630318 TTTTTT
1 TTTTTT
630324 CTAATAGATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (21 bp):
TTTTTTTCCTTTCCTTTTCTT
Found at i:630897 original size:7 final size:7
Alignment explanation
Indices: 630885--630914 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
630875 AAATCAATCC
630885 TTCTTTT
1 TTCTTTT
630892 TTCTTTTT
1 TTC-TTTT
630900 TTCTTTT
1 TTCTTTT
630907 TTCTTTT
1 TTCTTTT
630914 T
1 T
630915 CTTCTTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (7 bp):
TTCTTTT
Found at i:630901 original size:8 final size:8
Alignment explanation
Indices: 630888--630923 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
630878 TCAATCCTTC
630888 TTTTTTCT
1 TTTTTTCT
630896 TTTTTTC-
1 TTTTTTCT
630903 TTTTTTCT
1 TTTTTTCT
630911 TTTTCTTCT
1 TTTT-TTCT
630920 TTTT
1 TTTT
630924 ACTTCGAGCC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 7 0.27
8 11 0.42
9 8 0.31
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (8 bp):
TTTTTTCT
Found at i:630905 original size:15 final size:16
Alignment explanation
Indices: 630884--630923 Score: 73
Period size: 15 Copynumber: 2.6 Consensus size: 16
630874 TAAATCAATC
630884 CTTCTTTTTTCTTTTT
1 CTTCTTTTTTCTTTTT
630900 -TTCTTTTTTCTTTTT
1 CTTCTTTTTTCTTTTT
630915 CTTCTTTTT
1 CTTCTTTTT
630924 ACTTCGAGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.82
Consensus pattern (16 bp):
CTTCTTTTTTCTTTTT
Found at i:633496 original size:27 final size:28
Alignment explanation
Indices: 633458--633514 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 28
633448 CATCATGCAG
*
633458 AATGCGAAGATGCAAATACATATG-AAA
1 AATGCAAAGATGCAAATACATATGCAAA
*
633485 AATGCAAAGATGCAAATGCATATGCAAA
1 AATGCAAAGATGCAAATACATATGCAAA
633513 AA
1 AA
633515 ATGTTGATCC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.81
28 5 0.19
ACGTcount: A:0.53, C:0.12, G:0.18, T:0.18
Consensus pattern (28 bp):
AATGCAAAGATGCAAATACATATGCAAA
Found at i:636907 original size:3 final size:3
Alignment explanation
Indices: 636899--636925 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
636889 GCCTGCCAAT
636899 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
636926 TATTTCAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:640910 original size:2 final size:2
Alignment explanation
Indices: 640903--640927 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
640893 GCAACAATCT
640903 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
640928 TAACATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:642046 original size:110 final size:110
Alignment explanation
Indices: 641853--642051 Score: 294
Period size: 110 Copynumber: 1.8 Consensus size: 110
641843 AATGTGATAT
* ***
641853 TATACCTTTTTAAGGTGTTATTAGAAAGGTCAATATGCTAAAGAGAAATAAGATTCTTAATATTT
1 TATACCTTTTTAAGGTGTTATTAGAAAGGTCAATATGCTAAAGAGAAATAAGATTCTCAATAAGA
641918 GATGAAATTTCACCTGAAACATATAATAAATTCGTCAAAATTTAA
66 GATGAAATTTCACCTGAAACATATAATAAATTCGTCAAAATTTAA
* * *
641963 TATACCTTTTTAAGGTGTTATTAGAAAGGTCAATATGCTTAAGAGAAGTAAGGTT-TCCAATAAG
1 TATACCTTTTTAAGGTGTTATTAGAAAGGTCAATATGCTAAAGAGAAATAAGATTCT-CAATAAG
*
642027 AGATTG-GATTTCACCTGAAACATAT
65 AGA-TGAAATTTCACCTGAAACATAT
642052 GATTAGATTC
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
109 1 0.01
110 76 0.96
111 2 0.03
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.35
Consensus pattern (110 bp):
TATACCTTTTTAAGGTGTTATTAGAAAGGTCAATATGCTAAAGAGAAATAAGATTCTCAATAAGA
GATGAAATTTCACCTGAAACATATAATAAATTCGTCAAAATTTAA
Found at i:642899 original size:287 final size:288
Alignment explanation
Indices: 642404--642922 Score: 882
Period size: 287 Copynumber: 1.8 Consensus size: 288
642394 AAGAAATACG
* *
642404 AATGAGGAAATGTTTACCTTTGAGGTTATTGTAACCAAGATACAAAGATTGGAGCATAGTCAAGT
1 AATGAGGAAATGTTTACCTTTGAAGTTATTGTAACCAAGATACAAAGATTGGAGCATAGTCAAAT
* *
642469 TTCCGATTTCTATAGGTATACTTCCTTCAATAGAGTTGTTCCATAAAGATAAAAACATCAACTCT
66 TTCCGATTTCTATAGGGATACTTCCTTCAATAGAGTTGTTCCACAAAGATAAAAACATCAACTCT
*
642534 TTGCACTTGAACAAACTATTAGGAATGCTACCAGAAATTTGATTCCCAGCTAAGCTTAATACTTG
131 TTGCACTTGAACAAACTATTAGGAATGCTACCAGAAATTTGATTCCCAGCTAAACTTAATACTTG
642599 CAATTTAGACATGTTATCAAATATTCCCGAC-CTAGAGATTGTTAATTATAAAACAACTTTTATC
196 CAATTTAGACATGTTATCAAATATTCCCGACTCTAGAGATTGTTAATTATAAAACAACTTTTATC
642663 TAATGAAAATAAAAGAGAACGGAATGCA
261 TAATGAAAATAAAAGAGAACGGAATGCA
* *
642691 AATGAGG-AATTTTCTACCTTTGAAGTTGTTGTAACCAAGATACAAAGATTGGAGCATAGTCAAA
1 AATGAGGAAATGTT-TACCTTTGAAGTTATTGTAACCAAGATACAAAGATTGGAGCATAGTCAAA
** * * *
642755 TTTCCGATTTCTATAGGGATACTTCCTTTTATAGAGTTGTTCCACAATGATAAATACCTCAACTC
65 TTTCCGATTTCTATAGGGATACTTCCTTCAATAGAGTTGTTCCACAAAGATAAAAACATCAACTC
*
642820 TTTGCACTTGAATAAACTATTAGGAATGCTACCAGAAATTTGATTCCCAG-TCAAACTTAATACT
130 TTTGCACTTGAACAAACTATTAGGAATGCTACCAGAAATTTGATTCCCAGCT-AAACTTAATACT
642884 TGCAATTTAGACATGTTATCAAATATTCCCGACTCTAGA
194 TGCAATTTAGACATGTTATCAAATATTCCCGACTCTAGA
642923 TGGCCTGTAG
Statistics
Matches: 216, Mismatches: 13, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
286 6 0.03
287 205 0.95
288 5 0.02
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (288 bp):
AATGAGGAAATGTTTACCTTTGAAGTTATTGTAACCAAGATACAAAGATTGGAGCATAGTCAAAT
TTCCGATTTCTATAGGGATACTTCCTTCAATAGAGTTGTTCCACAAAGATAAAAACATCAACTCT
TTGCACTTGAACAAACTATTAGGAATGCTACCAGAAATTTGATTCCCAGCTAAACTTAATACTTG
CAATTTAGACATGTTATCAAATATTCCCGACTCTAGAGATTGTTAATTATAAAACAACTTTTATC
TAATGAAAATAAAAGAGAACGGAATGCA
Found at i:647086 original size:29 final size:29
Alignment explanation
Indices: 647053--647362 Score: 387
Period size: 29 Copynumber: 10.7 Consensus size: 29
647043 CCCGACCCAT
* *
647053 TGATATTTTGGGAATTATTTTTAAAACGG
1 TGATATTTTGGTAATTATTTTTAAAAAGG
647082 TGATATTTTAGG-AATTATTTTTAAAATA-G
1 TGATATTTT-GGTAATTATTTTTAAAA-AGG
*
647111 TGATATTTTCGG-AATTATTTTTAAAACGG
1 TGATATTTT-GGTAATTATTTTTAAAAAGG
* *
647140 TGATATTTTTGGGAATTATTTTTAAAACGG
1 TGATA-TTTTGGTAATTATTTTTAAAAAGG
*
647170 TGATATTTTGAG-AATTATTTTTAAAACGG
1 TGATATTTTG-GTAATTATTTTTAAAAAGG
* *
647199 TGATATTTTGGTAATTATTTTGAAAAAAG
1 TGATATTTTGGTAATTATTTTTAAAAAGG
** *
647228 TGATATTTTGGTAATTATTTCGAAAAAAG
1 TGATATTTTGGTAATTATTTTTAAAAAGG
*
647257 TGATATTTTGGTAATTATTTCTAAAAA-G
1 TGATATTTTGGTAATTATTTTTAAAAAGG
* *
647285 TGATATTTTGATAATTATTTTGAAAAAGG
1 TGATATTTTGGTAATTATTTTTAAAAAGG
* * *
647314 TGGTATTTTGATAATTATTTTGAAAAAGG
1 TGATATTTTGGTAATTATTTTTAAAAAGG
647343 TGATATTTTGGTAATTATTT
1 TGATATTTTGGTAATTATTT
647363 AAAAAGTTCT
Statistics
Matches: 259, Mismatches: 14, Indels: 16
0.90 0.05 0.06
Matches are distributed among these distances:
28 26 0.10
29 204 0.79
30 29 0.11
ACGTcount: A:0.34, C:0.02, G:0.17, T:0.46
Consensus pattern (29 bp):
TGATATTTTGGTAATTATTTTTAAAAAGG
Found at i:647152 original size:88 final size:85
Alignment explanation
Indices: 647053--647369 Score: 390
Period size: 88 Copynumber: 3.7 Consensus size: 85
647043 CCCGACCCAT
* *
647053 TGATATTTTGGGAATTATTTTTAAAACGGTGATATTTTAGG-AATTATTTTTAAAATAGTGATAT
1 TGATATTTTGGGAATTATTTTGAAAAAGGTGATATTTT-GGTAATTATTTTTAAAA-AGTGATAT
* *
647117 TTTCGGAATTATTTTTAAAACGG
64 TTT-GGAATTATTTTGAAAAAGG
* * *
647140 TGATATTTTTGGGAATTATTTTTAAAACGGTGATATTTTGAG-AATTATTTTTAAAACGGTGATA
1 TGATA-TTTTGGGAATTATTTTGAAAAAGGTGATATTTTG-GTAATTATTTTTAAAA-AGTGATA
*
647204 TTTTGGTAATTATTTTGAAAAAAG
63 TTTTGG-AATTATTTTGAAAAAGG
* * * *
647228 TGATATTTTGGTAATTATTTCGAAAAAAGTGATATTTTGGTAATTATTTCTAAAAAGTGATATTT
1 TGATATTTTGGGAATTATTTTGAAAAAGGTGATATTTTGGTAATTATTTTTAAAAAGTGATATTT
*
647293 TGATAATTATTTTGAAAAAGG
66 TG-GAATTATTTTGAAAAAGG
* **
647314 TGGTATTTTGATAATTATTTTGAAAAAGGTGATATTTTGGTAATTA--TTTAAAAAGT
1 TGATATTTTGGGAATTATTTTGAAAAAGGTGATATTTTGGTAATTATTTTTAAAAAGT
647370 TCTATTTTCG
Statistics
Matches: 206, Mismatches: 19, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
84 9 0.04
86 70 0.34
87 50 0.24
88 77 0.37
ACGTcount: A:0.35, C:0.02, G:0.17, T:0.45
Consensus pattern (85 bp):
TGATATTTTGGGAATTATTTTGAAAAAGGTGATATTTTGGTAATTATTTTTAAAAAGTGATATTT
TGGAATTATTTTGAAAAAGG
Found at i:647322 original size:17 final size:16
Alignment explanation
Indices: 647300--647352 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 16
647290 TTTTGATAAT
647300 TATTTTGAAAAAGGTGG
1 TATTTTGAAAAAGGT-G
*
647317 TATTTTG-ATAA--T-
1 TATTTTGAAAAAGGTG
647329 TATTTTGAAAAAGGTG
1 TATTTTGAAAAAGGTG
647345 ATATTTTG
1 -TATTTTG
647353 GTAATTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
12 7 0.24
13 3 0.10
14 1 0.03
15 1 0.03
16 3 0.10
17 14 0.48
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (16 bp):
TATTTTGAAAAAGGTG
Found at i:654877 original size:28 final size:29
Alignment explanation
Indices: 654722--654943 Score: 259
Period size: 29 Copynumber: 7.7 Consensus size: 29
654712 GTCCGACCCA
* **
654722 GTGATATTTTGGGAATTATTTTTAAAATA
1 GTGATATTTTGGTAATTATTTTTAAAACG
** * *
654751 ACGATATTTTGGGAATTATTTTTAAAACA
1 GTGATATTTTGGTAATTATTTTTAAAACG
* *
654780 ATGATATTTTGGGAATTATTTTTAAAACG
1 GTGATATTTTGGTAATTATTTTTAAAACG
* *
654809 GTGATATTTTGGGAATTATTTTTAAAATG
1 GTGATATTTTGGTAATTATTTTTAAAACG
**
654838 GTGATATTTTGGTAATTATTTCGAAAA-G
1 GTGATATTTTGGTAATTATTTTTAAAACG
* **
654866 GTGATATTTTGGTAATTA-TTTCAAAAAA
1 GTGATATTTTGGTAATTATTTTTAAAACG
* *
654894 GTGATATTTTGGTAATTATTTTGAAAAAG
1 GTGATATTTTGGTAATTATTTTTAAAACG
*
654923 GTGATATTTTTGTAATTATTT
1 GTGATATTTTGGTAATTATTT
654944 AAAAAAGTGT
Statistics
Matches: 175, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
27 6 0.03
28 37 0.21
29 132 0.75
ACGTcount: A:0.34, C:0.02, G:0.18, T:0.46
Consensus pattern (29 bp):
GTGATATTTTGGTAATTATTTTTAAAACG
Found at i:657808 original size:29 final size:28
Alignment explanation
Indices: 657738--657864 Score: 105
Period size: 29 Copynumber: 4.4 Consensus size: 28
657728 TCAAAATTTT
*
657738 ATTACAATAAAGGAATAAA-TCTTTTATAA
1 ATTACAATGAAGGAA-AAACT-TTTTATAA
* * *
657767 ATTGCATTAAAGGATAAAACTTTTTATAA
1 ATTACAATGAAGGA-AAAACTTTTTATAA
* * *
657796 ATTATAATGAAGGACAGAACCTTTTATAA
1 ATTACAATGAAGGA-AAAACTTTTTATAA
* *
657825 ATTACAAT-ATAAGACAAACTTTTTTATAA
1 ATTACAATGA-AGGAAAAAC-TTTTTATAA
657854 ATTACAATGAA
1 ATTACAATGAA
657865 CGTCAAAACT
Statistics
Matches: 79, Mismatches: 14, Indels: 10
0.77 0.14 0.10
Matches are distributed among these distances:
28 4 0.05
29 72 0.91
30 3 0.04
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.35
Consensus pattern (28 bp):
ATTACAATGAAGGAAAAACTTTTTATAA
Found at i:662264 original size:70 final size:72
Alignment explanation
Indices: 662178--662347 Score: 200
Period size: 75 Copynumber: 2.3 Consensus size: 72
662168 AATTAAACTC
** * * * *
662178 AAGTTTTAGGATAATATTTTTTATCTT-TGTTTTA-GGTATTTTAGTTTAAATATGTTTTAGTAT
1 AAGTTTTAGGATAATATTTTAAATATTATATTTTATGGTATTTTAGTTTAAATAGGTTTTAGTAA
662241 TTTAATT
66 TTTAATT
* *
662248 AAGTTTTAGGATAATATTTTAAATATTATATTTTATCTTTGTATTTTATTTTAAATAGGTTTTAG
1 AAGTTTTAGGATAATATTTTAAATATTATATTTTA---TGGTATTTTAGTTTAAATAGGTTTTAG
662313 TAATTTAATT
63 TAATTTAATT
* * *
662323 AGGATTTAGGATATTATTTTAAATA
1 AAGTTTTAGGATAATATTTTAAATA
662348 GCATTTTATT
Statistics
Matches: 84, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
70 24 0.29
71 6 0.07
75 54 0.64
ACGTcount: A:0.32, C:0.01, G:0.12, T:0.55
Consensus pattern (72 bp):
AAGTTTTAGGATAATATTTTAAATATTATATTTTATGGTATTTTAGTTTAAATAGGTTTTAGTAA
TTTAATT
Found at i:663193 original size:17 final size:19
Alignment explanation
Indices: 663153--663193 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
663143 ATTATTTTCC
*
663153 CTTTTATTTATTATTATAT
1 CTTTTATTTATTATTAAAT
*
663172 ATTTTA-TT-TTATTAAAT
1 CTTTTATTTATTATTAAAT
663189 CTTTT
1 CTTTT
663194 CAACTTTACC
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
17 12 0.63
18 2 0.11
19 5 0.26
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (19 bp):
CTTTTATTTATTATTAAAT
Found at i:673116 original size:10 final size:10
Alignment explanation
Indices: 673103--673141 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
673093 TTTCGTTCTA
*
673103 TTTTATTTCC
1 TTTTATTTCG
*
673113 TTTTATTTTTG
1 TTTTA-TTTCG
673124 TTTTATTTCG
1 TTTTATTTCG
673134 TTTTATTT
1 TTTTATTT
673142 TTAGCAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 17 0.68
11 8 0.32
ACGTcount: A:0.10, C:0.08, G:0.05, T:0.77
Consensus pattern (10 bp):
TTTTATTTCG
Found at i:673129 original size:21 final size:21
Alignment explanation
Indices: 673103--673143 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
673093 TTTCGTTCTA
673103 TTTTATTTCCTTTTATTTTTG
1 TTTTATTTCCTTTTATTTTTG
*
673124 TTTTATTTCGTTTTATTTTT
1 TTTTATTTCCTTTTATTTTT
673144 AGCAAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.10, C:0.07, G:0.05, T:0.78
Consensus pattern (21 bp):
TTTTATTTCCTTTTATTTTTG
Found at i:673157 original size:5 final size:5
Alignment explanation
Indices: 673149--673190 Score: 68
Period size: 5 Copynumber: 8.6 Consensus size: 5
673139 TTTTTAGCAA
*
673149 ATTTT ATTTT ATTCT A-TTT ATTTT ATTTT ATTTT ATTTT ATT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATT
673191 GAGCAGATTC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
4 3 0.09
5 31 0.91
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.76
Consensus pattern (5 bp):
ATTTT
Found at i:673170 original size:14 final size:15
Alignment explanation
Indices: 673149--673190 Score: 68
Period size: 14 Copynumber: 2.9 Consensus size: 15
673139 TTTTTAGCAA
673149 ATTTTATTTTATTCT
1 ATTTTATTTTATTCT
*
673164 A-TTTATTTTATTTT
1 ATTTTATTTTATTCT
673178 ATTTTATTTTATT
1 ATTTTATTTTATT
673191 GAGCAGATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.76
Consensus pattern (15 bp):
ATTTTATTTTATTCT
Found at i:673173 original size:19 final size:19
Alignment explanation
Indices: 673149--673186 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
673139 TTTTTAGCAA
673149 ATTTTATTTTATTCTATTT
1 ATTTTATTTTATTCTATTT
*
673168 ATTTTATTTTATTTTATTT
1 ATTTTATTTTATTCTATTT
673187 TATTGAGCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (19 bp):
ATTTTATTTTATTCTATTT
Found at i:673227 original size:15 final size:15
Alignment explanation
Indices: 673209--673238 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
673199 TCGAACAATG
*
673209 CAGTGCAGAAAAAAA
1 CAGTACAGAAAAAAA
673224 CAGTACAGAAAAAAA
1 CAGTACAGAAAAAAA
673239 ACAGATTTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.13, G:0.17, T:0.07
Consensus pattern (15 bp):
CAGTACAGAAAAAAA
Found at i:673267 original size:31 final size:31
Alignment explanation
Indices: 673222--673360 Score: 101
Period size: 29 Copynumber: 4.5 Consensus size: 31
673212 TGCAGAAAAA
* *
673222 AACAGTACAGAAAAAAAACAGATTTGGTTTG
1 AACAGTGCAGAAAAAAAACAGATTTGGTTCG
*
673253 AACTA-TGCAG--AAAAAACTGATTTGGTTCG
1 AAC-AGTGCAGAAAAAAAACAGATTTGGTTCG
* *
673282 AACAGTGCAGAAAAATACACAGCA---GATTCG
1 AACAGTGCAGAAAAA-AAACAG-ATTTGGTTCG
* *
673312 AACAATGCAATGCAGAAAAAAACAGATTTGGTTCA
1 AACAGTGC-A-G-A-AAAAAAACAGATTTGGTTCG
*
673347 AACTGTGCAGAAAA
1 AACAGTGCAGAAAA
673361 GTTCGAACAG
Statistics
Matches: 83, Mismatches: 12, Indels: 26
0.69 0.10 0.21
Matches are distributed among these distances:
28 1 0.01
29 25 0.30
30 12 0.14
31 14 0.17
32 8 0.10
33 8 0.10
34 5 0.06
35 10 0.12
ACGTcount: A:0.46, C:0.14, G:0.19, T:0.20
Consensus pattern (31 bp):
AACAGTGCAGAAAAAAAACAGATTTGGTTCG
Found at i:675914 original size:59 final size:58
Alignment explanation
Indices: 675791--676012 Score: 209
Period size: 59 Copynumber: 3.8 Consensus size: 58
675781 ATGACACTAT
* * * * * * *
675791 ATGTGCTAAAATGATAAGAAAAGCATACTGAGTGTATGGATTTCCATAT-GGAGAACTGA
1 ATGTGCTAAAATGATAAGGAAATCATATTGAATGTATGGATTTCCAAATAGG-GCA-TTA
* * *
675850 GTGTGCTAAAATGATAAGGAAATCATATTGAATATATGGATTTCCAGATAGGGCATTA
1 ATGTGCTAAAATGATAAGGAAATCATATTGAATGTATGGATTTCCAAATAGGGCATTA
* * ** **
675908 TATGTGCTAAAATGGTAAGGGAATCATACTT-AATGTATGGATTTCCAAATAAAGCCCTA
1 -ATGTGCTAAAATGATAAGGAAATCATA-TTGAATGTATGGATTTCCAAATAGGGCATTA
* *
675967 AGGGTGCT-AAATGATAAGGAAATCATATGGAATGTATGGA-TTCCAA
1 A-TGTGCTAAAATGATAAGGAAATCATATTGAATGTATGGATTTCCAA
676013 TAATGACTGA
Statistics
Matches: 136, Mismatches: 22, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
57 7 0.05
58 30 0.22
59 95 0.70
60 4 0.03
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.29
Consensus pattern (58 bp):
ATGTGCTAAAATGATAAGGAAATCATATTGAATGTATGGATTTCCAAATAGGGCATTA
Found at i:678191 original size:24 final size:24
Alignment explanation
Indices: 678086--678192 Score: 65
Period size: 24 Copynumber: 4.3 Consensus size: 24
678076 TAGGTTTTAG
* *
678086 TATTTTAATTAGGATTTAGGATAT
1 TATTTTAATTAGGATTTAAGTTAT
* * *
678110 TATTTTAAATAGTATTTTA-TT-T
1 TATTTTAATTAGGATTTAAGTTAT
** * *
678132 TATATTTGTTTTAGGTATTTTAGTTTAAA
1 TAT-TTT-AATTAGG-ATTTAAG-TT-AT
678161 TAGTTTTAATTAGGATTTAAGTTAT
1 TA-TTTTAATTAGGATTTAAGTTAT
678186 TATTTTA
1 TATTTTA
678193 GGAATTATTT
Statistics
Matches: 61, Mismatches: 14, Indels: 16
0.67 0.15 0.18
Matches are distributed among these distances:
22 4 0.07
23 4 0.07
24 23 0.38
25 9 0.15
26 2 0.03
27 8 0.13
28 5 0.08
29 5 0.08
30 1 0.02
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.57
Consensus pattern (24 bp):
TATTTTAATTAGGATTTAAGTTAT
Found at i:678891 original size:15 final size:16
Alignment explanation
Indices: 678871--678919 Score: 61
Period size: 15 Copynumber: 3.2 Consensus size: 16
678861 ATTTTACTAC
678871 TATTATTTAT-TATTT
1 TATTATTTATCTATTT
678886 TATTATTT-TCCT-TTT
1 TATTATTTAT-CTATTT
678901 TATTA-TTATCTATTT
1 TATTATTTATCTATTT
678916 TATT
1 TATT
678920 TTATTAAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
14 5 0.17
15 24 0.80
16 1 0.03
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.71
Consensus pattern (16 bp):
TATTATTTATCTATTT
Found at i:686920 original size:165 final size:161
Alignment explanation
Indices: 686648--686973 Score: 600
Period size: 165 Copynumber: 2.0 Consensus size: 161
686638 CAGCTTACAA
686648 TGCAGACTCATAAAATTTGTTGTAGAATTGTTGGCAAAGAGCTGTTACAACCGTGTTCCATATCG
1 TGCAGACTCATAAAATTTGTTGTAGAATTGTTGGCAAAGAGCTGTTACAACCGTGTTCCATATCG
686713 CAGGAGTCGATTCAGCACCAACAAACTGAGGAAGAAGATGACAAACTGATGGTGGAAAGAATACA
66 CAGGAGTCGATTCAGCACCAACAAACTGAGGAAGAAGATGAC-AACTGATGGTGGAAAGAATACA
686778 CGATGCAAGCACACTGTCTTGCGCCACAAAATCCT
130 C---GCAAGCACACTGTCTTGCGCCACAAAATCCT
686813 TGCAGACTCATAAAATTTGTTGTAGAATCTGTTGGCAAAGAGCTGTTAC-ACCGTGTTCCATATC
1 TGCAGACTCATAAAATTTGTTGTAGAAT-TGTTGGCAAAGAGCTGTTACAACCGTGTTCCATATC
686877 GCAGGAGTCGATTCAGCACCAACAAACTGAGGAAGAAGATGACAACTGATGGTGGAAAGAATACA
65 GCAGGAGTCGATTCAGCACCAACAAACTGAGGAAGAAGATGACAACTGATGGTGGAAAGAATACA
686942 CGCAAGCACACTGTCTTGCGCCACAAAATCCT
130 CGCAAGCACACTGTCTTGCGCCACAAAATCCT
686974 CAAAAGCATC
Statistics
Matches: 160, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
161 31 0.19
164 23 0.14
165 86 0.54
166 20 0.12
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.22
Consensus pattern (161 bp):
TGCAGACTCATAAAATTTGTTGTAGAATTGTTGGCAAAGAGCTGTTACAACCGTGTTCCATATCG
CAGGAGTCGATTCAGCACCAACAAACTGAGGAAGAAGATGACAACTGATGGTGGAAAGAATACAC
GCAAGCACACTGTCTTGCGCCACAAAATCCT
Found at i:694565 original size:22 final size:25
Alignment explanation
Indices: 694522--694576 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 25
694512 CATTTTAAAA
* *
694522 AATAT-TAATTATTAACATTAA-T-
1 AATATATAATAATTAACAATAATTC
694544 AATATATAATAATT-ACAATAATTC
1 AATATATAATAATTAACAATAATTC
694568 AATATATAA
1 AATATATAA
694577 GCTATTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 11 0.39
23 8 0.29
24 9 0.32
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (25 bp):
AATATATAATAATTAACAATAATTC
Found at i:694622 original size:16 final size:18
Alignment explanation
Indices: 694579--694625 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 18
694569 ATATATAAGC
694579 TATTATA-TATTTAATAAA
1 TATTATATTA-TTAATAAA
*
694597 TATTAAATTATTAAT-AA
1 TATTATATTATTAATAAA
694614 -ATTATATTATTA
1 TATTATATTATTA
694626 TAACAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 11 0.42
17 2 0.08
18 11 0.42
19 2 0.08
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TATTATATTATTAATAAA
Found at i:695995 original size:30 final size:29
Alignment explanation
Indices: 695954--696013 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
695944 AAAAATCCAC
* *
695954 ATAAAAATAATATAAACTTAGAATTTTATA
1 ATAAAAATAATATAAACATA-AAATTTATA
*
695984 ATAATAATAATATAAACATAAAATTTATA
1 ATAAAAATAATATAAACATAAAATTTATA
696013 A
1 A
696014 ATCTAAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 9 0.33
30 18 0.67
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (29 bp):
ATAAAAATAATATAAACATAAAATTTATA
Found at i:696060 original size:13 final size:14
Alignment explanation
Indices: 696044--696079 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
696034 AAATAAAATT
696044 TAAAATACAAA-AA
1 TAAAATACAAATAA
696057 TAAAATA-AAATAA
1 TAAAATACAAATAA
696070 TAAAATACAA
1 TAAAATACAA
696080 CTAAATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 3 0.14
13 16 0.76
14 2 0.10
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (14 bp):
TAAAATACAAATAA
Found at i:696076 original size:18 final size:19
Alignment explanation
Indices: 696031--696068 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
696021 TTATATAATC
696031 CAAAAATAAAATTTAAAATA
1 CAAAAATAAAA-TTAAAATA
696051 CAAAAATAAAA-TAAAATA
1 CAAAAATAAAATTAAAATA
696069 ATAAAATACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
20 11 0.61
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (19 bp):
CAAAAATAAAATTAAAATA
Found at i:698796 original size:13 final size:13
Alignment explanation
Indices: 698780--698806 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
698770 TGTAGTGATC
698780 TTTTTGAGTGGTG
1 TTTTTGAGTGGTG
698793 TTTTTGAGTGGTG
1 TTTTTGAGTGGTG
698806 T
1 T
698807 AGTGGGTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.00, G:0.37, T:0.56
Consensus pattern (13 bp):
TTTTTGAGTGGTG
Found at i:699309 original size:19 final size:20
Alignment explanation
Indices: 699285--699375 Score: 71
Period size: 20 Copynumber: 4.6 Consensus size: 20
699275 ATAACCAACG
* *
699285 AATTCGCAACGTG-ATTTCA
1 AATTCGTAACATGAATTTCA
*
699304 AATTCGTAACACGAATTTCA
1 AATTCGTAACATGAATTTCA
* * *
699324 ATTTTGTAACAT-AGTTTTCA
1 AATTCGTAACATGA-ATTTCA
*
699344 AATTCGTAACGTGAATTT-A
1 AATTCGTAACATGAATTTCA
*
699363 GAATTCGCAACAT
1 -AATTCGTAACAT
699376 AAAATTTGGA
Statistics
Matches: 55, Mismatches: 13, Indels: 7
0.73 0.17 0.09
Matches are distributed among these distances:
19 12 0.22
20 42 0.76
21 1 0.02
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (20 bp):
AATTCGTAACATGAATTTCA
Found at i:699375 original size:40 final size:41
Alignment explanation
Indices: 699284--699376 Score: 102
Period size: 40 Copynumber: 2.3 Consensus size: 41
699274 AATAACCAAC
*
699284 GAATTCGCAACGT-GATTTCAAATTCGTAACACGAATTTCA
1 GAATTCGCAACATAGATTTCAAATTCGTAACACGAATTTCA
* * * * **
699324 -ATTTTGTAACATAGTTTTCAAATTCGTAACGTGAATTT-A
1 GAATTCGCAACATAGATTTCAAATTCGTAACACGAATTTCA
699363 GAATTCGCAACATA
1 GAATTCGCAACATA
699377 AAATTTGGAA
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
39 9 0.22
40 32 0.78
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.34
Consensus pattern (41 bp):
GAATTCGCAACATAGATTTCAAATTCGTAACACGAATTTCA
Found at i:699387 original size:21 final size:21
Alignment explanation
Indices: 699357--699415 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
699347 TCGTAACGTG
* * *
699357 AATTTAGAATTCGCAACATAA
1 AATTTGGAATTTGCAACACAA
699378 AATTTGGAATTTGCAACACAA
1 AATTTGGAATTTGCAACACAA
*
699399 AATTTGAAATTTGCAAC
1 AATTTGGAATTTGCAAC
699416 GCGAATTTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.31
Consensus pattern (21 bp):
AATTTGGAATTTGCAACACAA
Found at i:699443 original size:21 final size:20
Alignment explanation
Indices: 699377--699444 Score: 73
Period size: 21 Copynumber: 3.3 Consensus size: 20
699367 TCGCAACATA
* *
699377 AAATTTGGAATTTGCAACAC
1 AAATTTGAAATTTGCAACGC
699397 AAAATTTGAAATTTGCAACGC
1 -AAATTTGAAATTTGCAACGC
* * *
699418 GAATTTGAATTTTCGTAACGC
1 AAATTTGAAATTT-GCAACGC
699439 AAATTT
1 AAATTT
699445 CTTTTTAATC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
20 11 0.28
21 29 0.73
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (20 bp):
AAATTTGAAATTTGCAACGC
Found at i:699675 original size:15 final size:16
Alignment explanation
Indices: 699651--699680 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
699641 TTTGACTCTA
699651 TTTTATTTTAACTTTT
1 TTTTATTTTAACTTTT
699667 TTTTA-TTTAACTTT
1 TTTTATTTTAACTTT
699681 ATTTCATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTATTTTAACTTTT
Found at i:700267 original size:21 final size:21
Alignment explanation
Indices: 700230--700283 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
700220 GATTAAAAAG
* *
700230 AAATTCGC-TTGCGAAAATTC
1 AAATTTGCGTTGCAAAAATTC
*
700250 AAATTTGCGTTGCAAAAATTT
1 AAATTTGCGTTGCAAAAATTC
*
700271 AAATTTGTGTTGC
1 AAATTTGCGTTGC
700284 GAATTTCAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 7 0.24
21 22 0.76
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (21 bp):
AAATTTGCGTTGCAAAAATTC
Found at i:700292 original size:41 final size:41
Alignment explanation
Indices: 700230--700330 Score: 107
Period size: 41 Copynumber: 2.5 Consensus size: 41
700220 GATTAAAAAG
* *
700230 AAATTCGC-TTGCGAAAATTCAAATT-TGCGTTGCAAAAATTT
1 AAATTTGCGTTGCG-AATTTCAAATTCTGCGTTG-AAAAATTT
* * ** *
700271 AAATTTGTGTTGCGAATTTCAAATTCTGTGTTGTGAATTTT
1 AAATTTGCGTTGCGAATTTCAAATTCTGCGTTGAAAAATTT
700312 AAATTTGCGTTGCGAATTT
1 AAATTTGCGTTGCGAATTT
700331 GGAAACTGTG
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
41 39 0.78
42 11 0.22
ACGTcount: A:0.30, C:0.11, G:0.18, T:0.42
Consensus pattern (41 bp):
AAATTTGCGTTGCGAATTTCAAATTCTGCGTTGAAAAATTT
Found at i:700328 original size:20 final size:20
Alignment explanation
Indices: 700250--700330 Score: 90
Period size: 21 Copynumber: 4.0 Consensus size: 20
700240 GCGAAAATTC
* *
700250 AAATTTGCGTTGCAAAAATTT
1 AAATTTGCGTTGC-GAATTTT
* *
700271 AAATTTGTGTTGCGAATTTC
1 AAATTTGCGTTGCGAATTTT
* *
700291 AAATTCTGTGTTGTGAATTTT
1 AAATT-TGCGTTGCGAATTTT
700312 AAATTTGCGTTGCGAATTT
1 AAATTTGCGTTGCGAATTT
700331 GGAAACTGTG
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
20 21 0.41
21 30 0.59
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.44
Consensus pattern (20 bp):
AAATTTGCGTTGCGAATTTT
Found at i:700343 original size:20 final size:20
Alignment explanation
Indices: 700266--700368 Score: 95
Period size: 20 Copynumber: 5.2 Consensus size: 20
700256 GCGTTGCAAA
*
700266 AATTT-AAATTTGTGTTGCG
1 AATTTGAAATCTGTGTTGCG
* *
700285 AATTTCAAATTCTGTGTTGTG
1 AATTTGAAA-TCTGTGTTGCG
* * *
700306 AATTTTAAATTTGCGTTGCG
1 AATTTGAAATCTGTGTTGCG
700326 AATTTGGAAA-CTGTGTTGCG
1 AATTT-GAAATCTGTGTTGCG
* *
700346 AAATTGAAATC-GCGTTGCG
1 AATTTGAAATCTGTGTTGCG
700365 AATT
1 AATT
700369 CGTTGGTTAT
Statistics
Matches: 68, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
19 19 0.28
20 29 0.43
21 20 0.29
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.41
Consensus pattern (20 bp):
AATTTGAAATCTGTGTTGCG
Found at i:700362 original size:19 final size:20
Alignment explanation
Indices: 700317--700366 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
700307 ATTTTAAATT
*
700317 TGCGTTGCGAATTTGGAAAC
1 TGCGTTGCGAAATTGGAAAC
*
700337 TGTGTTGCGAAATT-GAAA-
1 TGCGTTGCGAAATTGGAAAC
700355 TCGCGTTGCGAA
1 T-GCGTTGCGAA
700367 TTCGTTGGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 1 0.04
19 13 0.50
20 12 0.46
ACGTcount: A:0.26, C:0.14, G:0.30, T:0.30
Consensus pattern (20 bp):
TGCGTTGCGAAATTGGAAAC
Found at i:702567 original size:16 final size:17
Alignment explanation
Indices: 702535--702567 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
702525 TCCATTCTGT
*
702535 CTTATTATTTAATTCCA
1 CTTATCATTTAATTCCA
702552 CTTATCATTT-ATTCCA
1 CTTATCATTTAATTCCA
702568 GACATTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.21, G:0.00, T:0.52
Consensus pattern (17 bp):
CTTATCATTTAATTCCA
Found at i:703457 original size:17 final size:17
Alignment explanation
Indices: 703435--703470 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
703425 ACTGATCGAC
703435 CATAAAAATTCCATTCA
1 CATAAAAATTCCATTCA
703452 CATAAAAATTCCATTCA
1 CATAAAAATTCCATTCA
703469 CA
1 CA
703471 CGCCTTTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.28
Consensus pattern (17 bp):
CATAAAAATTCCATTCA
Found at i:711282 original size:16 final size:16
Alignment explanation
Indices: 711261--711294 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
711251 TGGTTGGAAA
* *
711261 AATTGTTTTATTAGAC
1 AATTGTTCTATTAAAC
711277 AATTGTTCTATTAAAC
1 AATTGTTCTATTAAAC
711293 AA
1 AA
711295 ATAGAGGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (16 bp):
AATTGTTCTATTAAAC
Found at i:714258 original size:784 final size:784
Alignment explanation
Indices: 712752--714324 Score: 3146
Period size: 784 Copynumber: 2.0 Consensus size: 784
712742 TGCATTGAGG
712752 AATTATTGGAAGTTGAATTAAGGATCGAGGACTTTCAAATGAAAATTAATGATCGATCAATATGG
1 AATTATTGGAAGTTGAATTAAGGATCGAGGACTTTCAAATGAAAATTAATGATCGATCAATATGG
712817 CACGAAAATCGAGGTAATACTTTACTACCTCTTTATGCTTTATGAAACATGTTGATATTACTTGT
66 CACGAAAATCGAGGTAATACTTTACTACCTCTTTATGCTTTATGAAACATGTTGATATTACTTGT
712882 GAAAGCTTCAAATAGTTTTAATTTTTGAATTCAAACACATTTTTTACCTGAGAAATTGTTATCAA
131 GAAAGCTTCAAATAGTTTTAATTTTTGAATTCAAACACATTTTTTACCTGAGAAATTGTTATCAA
712947 AAAGATCTATGTATACAAGAGAAGTCAGAGTTCCAATAACCGATGAAATTTCACCTGAAACATGT
196 AAAGATCTATGTATACAAGAGAAGTCAGAGTTCCAATAACCGATGAAATTTCACCTGAAACATGT
713012 AATTAAATTCGTCAAAAGTTATCTATAATTTTCTAACTCTTTGTTGAGCACTATAGGGATCTATT
261 AATTAAATTCGTCAAAAGTTATCTATAATTTTCTAACTCTTTGTTGAGCACTATAGGGATCTATT
713077 TTCCATTTCTTTTCTTTTATTCTTAAATGTGAACTTATATTGTCAAGCAAAAAGAAAAATTGTAC
326 TTCCATTTCTTTTCTTTTATTCTTAAATGTGAACTTATATTGTCAAGCAAAAAGAAAAATTGTAC
713142 AAGAAAAGACAAAATACGTATAATATTATACCTTTTAAATTGTTACCAGAAAGGTCAATCTTCTT
391 AAGAAAAGACAAAATACGTATAATATTATACCTTTTAAATTGTTACCAGAAAGGTCAATCTTCTT
713207 AAGAGAAATAATGTTTCCAATAACATATGGAATTTCACCTGAAATATAAAATCAAATATGTCAAA
456 AAGAGAAATAATGTTTCCAATAACATATGGAATTTCACCTGAAATATAAAATCAAATATGTCAAA
713272 AATACGGTAGAAATTTATTAATATTTTTTTCTAGCAAATCCTTAATTTCTTTGTTCAGCACTAGA
521 AATACGGTAGAAATTTATTAATATTTTTTTCTAGCAAATCCTTAATTTCTTTGTTCAGCACTAGA
713337 GAATCTGTTTCTTTTCTTTCTTTTTCTAAACATGAAAATACTATTCAATTTTTTTACCATTTATG
586 GAATCTGTTTCTTTTCTTTCTTTTTCTAAACATGAAAATACTATTCAATTTTTTTACCATTTATG
713402 AAAGCTCCAAATAGTAACTCAATTTTATAAATTTAGTGGCAAATAAAAGTTCATCCATCCAAGGT
651 AAAGCTCCAAATAGTAACTCAATTTTATAAATTTAGTGGCAAATAAAAGTTCATCCATCCAAGGT
713467 TTGAGATATAATATTGACAACGATTATCATACTTCAATATCTAAACAATTGTTCATAAAAAATTA
716 TTGAGATATAATATTGACAACGATTATCATACTTCAATATCTAAACAATTGTTCATAAAAAATTA
713532 AAAA
781 AAAA
713536 AATTATTGGAAGTTGAATTAAGGATCGAGGACTTTCAAATGAAAATTAATGATCGATCAATATGG
1 AATTATTGGAAGTTGAATTAAGGATCGAGGACTTTCAAATGAAAATTAATGATCGATCAATATGG
713601 CACGAAAATCGAGGTAATACTTTACTACCTCTTTATGCTTTATGAAACATGTTGATATTACTTGT
66 CACGAAAATCGAGGTAATACTTTACTACCTCTTTATGCTTTATGAAACATGTTGATATTACTTGT
713666 GAAAGCTTCAAATAGTTTTAATTTTTGAATTCAAACACATTTTTTACCTGAGAAATTGTTATCAA
131 GAAAGCTTCAAATAGTTTTAATTTTTGAATTCAAACACATTTTTTACCTGAGAAATTGTTATCAA
713731 AAAGATCTATGTATACAAGAGAAGTCAGAGTTCCAATAACCGATGAAATTTCACCTGAAACATGT
196 AAAGATCTATGTATACAAGAGAAGTCAGAGTTCCAATAACCGATGAAATTTCACCTGAAACATGT
713796 AATTAAATTCGTCAAAAGTTATCTATAATTTTCTAACTCTTTGTTGAGCACTATAGGGATCTATT
261 AATTAAATTCGTCAAAAGTTATCTATAATTTTCTAACTCTTTGTTGAGCACTATAGGGATCTATT
713861 TTCCATTTCTTTTCTTTTATTCTTAAATGTGAACTTATATTGTCAAGCAAAAAGAAAAATTGTAC
326 TTCCATTTCTTTTCTTTTATTCTTAAATGTGAACTTATATTGTCAAGCAAAAAGAAAAATTGTAC
713926 AAGAAAAGACAAAATACGTATAATATTATACCTTTTAAATTGTTACCAGAAAGGTCAATCTTCTT
391 AAGAAAAGACAAAATACGTATAATATTATACCTTTTAAATTGTTACCAGAAAGGTCAATCTTCTT
713991 AAGAGAAATAATGTTTCCAATAACATATGGAATTTCACCTGAAATATAAAATCAAATATGTCAAA
456 AAGAGAAATAATGTTTCCAATAACATATGGAATTTCACCTGAAATATAAAATCAAATATGTCAAA
714056 AATACGGTAGAAATTTATTAATATTTTTTTCTAGCAAATCCTTAATTTCTTTGTTCAGCACTAGA
521 AATACGGTAGAAATTTATTAATATTTTTTTCTAGCAAATCCTTAATTTCTTTGTTCAGCACTAGA
714121 GAATCTGTTTCTTTTCTTTCTTTTTCTAAACATGAAAATACTATTCAATTTTTTTACCATTTATG
586 GAATCTGTTTCTTTTCTTTCTTTTTCTAAACATGAAAATACTATTCAATTTTTTTACCATTTATG
714186 AAAGCTCCAAATAGTAACTCAATTTTATAAATTTAGTGGCAAATAAAAGTTCATCCATCCAAGGT
651 AAAGCTCCAAATAGTAACTCAATTTTATAAATTTAGTGGCAAATAAAAGTTCATCCATCCAAGGT
714251 TTGAGATATAATATTGACAACGATTATCATACTTCAATATCTAAACAATTGTTCATAAAAAATTA
716 TTGAGATATAATATTGACAACGATTATCATACTTCAATATCTAAACAATTGTTCATAAAAAATTA
714316 AAAA
781 AAAA
714320 AATTA
1 AATTA
714325 AACGAGTCAT
Statistics
Matches: 789, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
784 789 1.00
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (784 bp):
AATTATTGGAAGTTGAATTAAGGATCGAGGACTTTCAAATGAAAATTAATGATCGATCAATATGG
CACGAAAATCGAGGTAATACTTTACTACCTCTTTATGCTTTATGAAACATGTTGATATTACTTGT
GAAAGCTTCAAATAGTTTTAATTTTTGAATTCAAACACATTTTTTACCTGAGAAATTGTTATCAA
AAAGATCTATGTATACAAGAGAAGTCAGAGTTCCAATAACCGATGAAATTTCACCTGAAACATGT
AATTAAATTCGTCAAAAGTTATCTATAATTTTCTAACTCTTTGTTGAGCACTATAGGGATCTATT
TTCCATTTCTTTTCTTTTATTCTTAAATGTGAACTTATATTGTCAAGCAAAAAGAAAAATTGTAC
AAGAAAAGACAAAATACGTATAATATTATACCTTTTAAATTGTTACCAGAAAGGTCAATCTTCTT
AAGAGAAATAATGTTTCCAATAACATATGGAATTTCACCTGAAATATAAAATCAAATATGTCAAA
AATACGGTAGAAATTTATTAATATTTTTTTCTAGCAAATCCTTAATTTCTTTGTTCAGCACTAGA
GAATCTGTTTCTTTTCTTTCTTTTTCTAAACATGAAAATACTATTCAATTTTTTTACCATTTATG
AAAGCTCCAAATAGTAACTCAATTTTATAAATTTAGTGGCAAATAAAAGTTCATCCATCCAAGGT
TTGAGATATAATATTGACAACGATTATCATACTTCAATATCTAAACAATTGTTCATAAAAAATTA
AAAA
Found at i:715901 original size:14 final size:14
Alignment explanation
Indices: 715882--715908 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
715872 AACAGAATTC
715882 ATATCATATATCAG
1 ATATCATATATCAG
715896 ATATCATATATCA
1 ATATCATATATCA
715909 AAACATAATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.15, G:0.04, T:0.37
Consensus pattern (14 bp):
ATATCATATATCAG
Found at i:715932 original size:24 final size:25
Alignment explanation
Indices: 715905--715964 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
715895 GATATCATAT
* *
715905 ATCAAAACATAATCCAG-ATCAGAA
1 ATCAGAACATAATCCAGAATCAAAA
* *
715929 ATCAGAACATAGTTCAGAATCAAAA
1 ATCAGAACATAATCCAGAATCAAAA
715954 ATCAGAACATA
1 ATCAGAACATA
715965 TTTCAAATCG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
24 14 0.45
25 17 0.55
ACGTcount: A:0.53, C:0.18, G:0.10, T:0.18
Consensus pattern (25 bp):
ATCAGAACATAATCCAGAATCAAAA
Found at i:715933 original size:38 final size:38
Alignment explanation
Indices: 715856--715934 Score: 95
Period size: 38 Copynumber: 2.1 Consensus size: 38
715846 CAATAAACGG
* * * *
715856 AGATATCAAAAATCAAAACAGAATTCATATCATATATC
1 AGATATCAAAAATCAAAACAGAATCCAGATCAGAAATC
* * *
715894 AGATATCATATATCAAAACATAATCCAGATCAGAAATC
1 AGATATCAAAAATCAAAACAGAATCCAGATCAGAAATC
715932 AGA
1 AGA
715935 ACATAGTTCA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.52, C:0.16, G:0.08, T:0.24
Consensus pattern (38 bp):
AGATATCAAAAATCAAAACAGAATCCAGATCAGAAATC
Found at i:715979 original size:24 final size:25
Alignment explanation
Indices: 715905--715983 Score: 90
Period size: 24 Copynumber: 3.2 Consensus size: 25
715895 GATATCATAT
* * *
715905 ATCAAAACATAATCCAG-ATCAGAA
1 ATCAGAACATAGTTCAGAATCAGAA
*
715929 ATCAGAACATAGTTCAGAATCAAAA
1 ATCAGAACATAGTTCAGAATCAGAA
* *
715954 ATCAGAACATATTTCA-AATCGGAA
1 ATCAGAACATAGTTCAGAATCAGAA
715978 ATCAGA
1 ATCAGA
715984 TAAAATATTC
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
24 26 0.55
25 21 0.45
ACGTcount: A:0.51, C:0.18, G:0.11, T:0.20
Consensus pattern (25 bp):
ATCAGAACATAGTTCAGAATCAGAA
Found at i:716885 original size:15 final size:15
Alignment explanation
Indices: 716865--716894 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
716855 AAGTACTTTG
716865 TCATTCAGGGTCAAC
1 TCATTCAGGGTCAAC
716880 TCATTCAGGGTCAAC
1 TCATTCAGGGTCAAC
716895 CCAGACTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (15 bp):
TCATTCAGGGTCAAC
Found at i:717998 original size:14 final size:15
Alignment explanation
Indices: 717979--718010 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
717969 GTCAACTTTG
717979 GTCAACGGTCAAC-A
1 GTCAACGGTCAACGA
717993 GTCAACGGTCAACGA
1 GTCAACGGTCAACGA
718008 GTC
1 GTC
718011 GGGTCAACGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.31, C:0.28, G:0.25, T:0.16
Consensus pattern (15 bp):
GTCAACGGTCAACGA
Found at i:718050 original size:18 final size:18
Alignment explanation
Indices: 718008--718085 Score: 86
Period size: 18 Copynumber: 4.4 Consensus size: 18
717998 CGGTCAACGA
718008 GTCGGGTCAACGGGTC-G
1 GTCGGGTCAACGGGTCGG
** *
718025 GTTTGGTCAATGGGTCGG
1 GTCGGGTCAACGGGTCGG
* *
718043 GTTGGGTCAACTGGTCGG
1 GTCGGGTCAACGGGTCGG
* *
718061 GTCGTGTAAACGGGTCGG
1 GTCGGGTCAACGGGTCGG
718079 GTCGGGT
1 GTCGGGT
718086 TGTGACCGGT
Statistics
Matches: 49, Mismatches: 11, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
17 13 0.27
18 36 0.73
ACGTcount: A:0.12, C:0.17, G:0.46, T:0.26
Consensus pattern (18 bp):
GTCGGGTCAACGGGTCGG
Found at i:720142 original size:2 final size:2
Alignment explanation
Indices: 720135--720161 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
720125 TAATAACAAT
720135 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
720162 TAGTGTGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:720498 original size:2 final size:2
Alignment explanation
Indices: 720491--720520 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
720481 CTTTGCAAAT
720491 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
720521 AAAGCTTATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:724455 original size:3 final size:3
Alignment explanation
Indices: 724449--724496 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
724439 TTTACTCATG
* *
724449 TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA TAA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
724497 AAAAAATAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:724472 original size:15 final size:15
Alignment explanation
Indices: 724449--724496 Score: 87
Period size: 15 Copynumber: 3.2 Consensus size: 15
724439 TTTACTCATG
*
724449 TTATTATTATTATTA
1 TTATAATTATTATTA
724464 TTATAATTATTATTA
1 TTATAATTATTATTA
724479 TTATAATTATTATTA
1 TTATAATTATTATTA
724494 TTA
1 TTA
724497 AAAAAATAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTATAATTATTATTA
Found at i:729990 original size:15 final size:15
Alignment explanation
Indices: 729970--730001 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
729960 ATCAATACCT
729970 TTTTGCATACATACA
1 TTTTGCATACATACA
*
729985 TTTTGCATACATTCA
1 TTTTGCATACATACA
730000 TT
1 TT
730002 ATTCATTTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATACA
Found at i:737333 original size:6 final size:6
Alignment explanation
Indices: 737322--737370 Score: 57
Period size: 6 Copynumber: 8.3 Consensus size: 6
737312 ATGCTTGAAG
* *
737322 AGAAAA AGAAAA AGAAAA AGAAAA A-AAAA GAGAAAG AGAGAA A-AAAA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA -AGAAAA AGAAAA AGAAAA
737369 AG
1 AG
737371 GGTCAATGTG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
5 8 0.22
6 25 0.69
7 3 0.08
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:738657 original size:83 final size:83
Alignment explanation
Indices: 738518--738814 Score: 558
Period size: 83 Copynumber: 3.6 Consensus size: 83
738508 ATGCAAGGTA
* *
738518 CTCATAGCATCTTATGGAAGTGTTCTTTGATTTATCTGATCTGGTTTGGTAAAACCAATCATTGA
1 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGA
738583 ATTTGAAAGATGAATGTG
66 ATTTGAAAGATGAATGTG
*
738601 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTTGGTAAAACCAATCATTGA
1 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGA
738666 ATTTGAAAGATGAATGTG
66 ATTTGAAAGATGAATGTG
738684 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGA
1 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGA
738749 ATTTGAAAGATGAATGTG
66 ATTTGAAAGATGAATGTG
*
738767 ATCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
1 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
738815 ATATGAAACC
Statistics
Matches: 209, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 209 1.00
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (83 bp):
CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGA
ATTTGAAAGATGAATGTG
Found at i:739851 original size:113 final size:113
Alignment explanation
Indices: 739649--740646 Score: 1784
Period size: 113 Copynumber: 8.8 Consensus size: 113
739639 TAGCAAAGAT
*
739649 TCAAATCCATCACTTAATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGA
*
739714 AGAAGGAAGAAGAAATTCACAATGAGAAGAATTTGTTTAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
739762 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGA
739827 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
*
739875 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTTGAGTTCATAATGAGAAGAATTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGA
739940 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
739988 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGA
*
740053 AGAAGGAAGAAGAAATTCATAATGAAAAGAATTTGTTTAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
740101 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGA
*
740166 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTCGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
740214 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGA
740279 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
740327 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGA
* *
740392 AGAATGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTCGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
740440 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGA
* * **
740505 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTAT
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
* * * **** *
740553 TCAAATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATAAGAAGAACTT-ATCTG
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAA-TTCATCTG
* *
740617 AAG-AGGAAGAAGAAGTTCACAATGAGAAGA
65 AAGAAGGAAGAAGAAATTCATAATGAGAAGA
740647 GCATGTTCAA
Statistics
Matches: 859, Mismatches: 25, Indels: 3
0.97 0.03 0.00
Matches are distributed among these distances:
112 26 0.03
113 831 0.97
114 2 0.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.30
Consensus pattern (113 bp):
TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGA
AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
Found at i:739854 original size:24 final size:23
Alignment explanation
Indices: 739811--739855 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
739801 GTTCATAATG
*
739811 AGAAGAATTCATCTGAAGAAGGA
1 AGAAGAATTCATATGAAGAAGGA
739834 AGAAGAAATTCATAATG-AGAAG
1 AGAAG-AATTCAT-ATGAAGAAG
739856 AATTTGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.26
24 12 0.63
25 2 0.11
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.18
Consensus pattern (23 bp):
AGAAGAATTCATATGAAGAAGGA
Found at i:739967 original size:24 final size:23
Alignment explanation
Indices: 739924--739968 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
739914 GTTCATAATG
*
739924 AGAAGAATTCATCTGAAGAAGGA
1 AGAAGAATTCATATGAAGAAGGA
739947 AGAAGAAATTCATAATG-AGAAG
1 AGAAG-AATTCAT-ATGAAGAAG
739969 AATTTGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.26
24 12 0.63
25 2 0.11
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.18
Consensus pattern (23 bp):
AGAAGAATTCATATGAAGAAGGA
Found at i:740193 original size:24 final size:23
Alignment explanation
Indices: 740150--740194 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
740140 GTTCATAATG
*
740150 AGAAGAATTCATCTGAAGAAGGA
1 AGAAGAATTCATATGAAGAAGGA
740173 AGAAGAAATTCATAATG-AGAAG
1 AGAAG-AATTCAT-ATGAAGAAG
740195 AATTTGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.26
24 12 0.63
25 2 0.11
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.18
Consensus pattern (23 bp):
AGAAGAATTCATATGAAGAAGGA
Found at i:740306 original size:24 final size:23
Alignment explanation
Indices: 740263--740307 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
740253 GTTCATAATG
*
740263 AGAAGAATTCATCTGAAGAAGGA
1 AGAAGAATTCATATGAAGAAGGA
740286 AGAAGAAATTCATAATG-AGAAG
1 AGAAG-AATTCAT-ATGAAGAAG
740308 AATTTGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.26
24 12 0.63
25 2 0.11
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.18
Consensus pattern (23 bp):
AGAAGAATTCATATGAAGAAGGA
Found at i:740532 original size:24 final size:23
Alignment explanation
Indices: 740489--740533 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
740479 GTTCATAATG
*
740489 AGAAGAATTCATCTGAAGAAGGA
1 AGAAGAATTCATATGAAGAAGGA
740512 AGAAGAAGTTCATAATG-AGAAG
1 AGAAGAA-TTCAT-ATGAAGAAG
740534 AACTTGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 7 0.37
24 10 0.53
25 2 0.11
ACGTcount: A:0.49, C:0.07, G:0.27, T:0.18
Consensus pattern (23 bp):
AGAAGAATTCATATGAAGAAGGA
Found at i:740813 original size:118 final size:113
Alignment explanation
Indices: 739687--740869 Score: 467
Period size: 113 Copynumber: 10.3 Consensus size: 113
739677 TTCCAGTTCG
* * * * * ** *
739687 AGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAAGAAATTCACAATGAGAAGAATTTGTTT
1 AGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
** * * * * ****
739752 AACCTTTTGCTCAAATCCATCAC--TTGAT-GGATCAGCTTTTCCAGTTCG
66 AACCTTTTAAT-AAAT-TATCACAAATGATAGG-TCAACCTTTCCAGAGAA
* * * * ** *
739800 AGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTT
1 AGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
** * * * * ****
739865 AACCTTTTGCTCAAATCCATCAC--TTGAT-GGATCAGCTTTTCCAGTTTG
66 AACCTTTTAAT-AAAT-TATCACAAATGATAGG-TCAACCTTTCCAGAGAA
* * * * ** *
739913 AGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTT
1 AGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
** * * * * ****
739978 AACCTTTTGCTCAAATCCATCAC--TTGAT-GGATCAGCTTTTCCAGTTCG
66 AACCTTTTAAT-AAAT-TATCACAAATGATAGG-TCAACCTTTCCAGAGAA
* * * * * ** *
740026 AGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAAGAAATTCATAATGAAAAGAATTTGTTT
1 AGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
** * * * * ****
740091 AACCTTTTGCTCAAATCCATCAC--TTGAT-GGATCAGCTTTTCCAGTTCG
66 AACCTTTTAAT-AAAT-TATCACAAATGATAGG-TCAACCTTTCCAGAGAA
* * * * ** *
740139 AGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTT
1 AGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
*** * * * * ****
740204 AACCTTTCGCTCAAATCCATCAC--TTGAT-GGATCAGCTTTTCCAGTTCG
66 AACCTTTTAAT-AAAT-TATCACAAATGATAGG-TCAACCTTTCCAGAGAA
* * * * ** *
740252 AGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTT
1 AGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
** * * * * ****
740317 AACCTTTTGCTCAAATCCATCAC--TTGAT-GGATCAGCTTTTCCAGTTCG
66 AACCTTTTAAT-AAAT-TATCACAAATGATAGG-TCAACCTTTCCAGAGAA
* * * **
740365 AGTTCATAATGAGAAGAATTCATCTGAAGAATG-AAGAAGAAATTCATAATGAGAAGAATTTGTT
1 AGTTCATAATGAGAAGAACTCATCTGAA-AAAGAAAGAAGAAGTTCATAATGAGAAGAGCTTGTT
* *** * * * * ****
740429 TAACCTTTCGCTCAAATCCATCAC--TTGAT-GGATCAGCTTTTCCAGTTCG
65 CAACCTTTTAAT-AAAT-TATCACAAATGATAGG-TCAACCTTTCCAGAGAA
* * * * *
740478 AGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTT
1 AGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
* * *
740543 AACCTTTTATTCAAATTCATCAC--TTGAT-GGATCAACATTTCCAGAGAA
66 AACCTTTTAAT-AAATT-ATCACAAATGATAGG-TCAACCTTTCCAGAGAA
* * * * * *
740591 AGTTCATAATAAGAAGAACTTATCTG-AAGAGGAAGAAGAAGTTCACAATGAGAAGAGCATGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
* * **
740655 AACCTTTTACATAATTTTATCACATATATGTTACCATCAACCTTTCCAGAGAA
66 AACCTTTTA-ATAA-ATTATCACA-A-ATGATA-GGTCAACCTTTCCAGAGAA
*
740708 AGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAGAAGAAGTTCATAATGAGAAGAGCTTATTC
1 AGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
* * * * **
740773 AACCTTTGGAATGACTCTATCACAAAAGGAAATAGGTCAACATCATCCCCA-ACGGAA
66 AACCTTT-TAATAAAT-TATCAC-AAATG--ATAGGTCAAC--C-TTTCCAGA--GAA
*
740830 AGTTCATAATGAGAAGAACTTATCTGAAGAAAGAGAAGAA
1 AGTTCATAATGAGAAGAACTCATCTGAA-AAAGA-AAGAA
740870 TTTATTCAAC
Statistics
Matches: 989, Mismatches: 57, Indels: 37
0.91 0.05 0.03
Matches are distributed among these distances:
112 50 0.05
113 786 0.79
114 2 0.00
116 3 0.00
117 43 0.04
118 55 0.06
119 4 0.00
120 2 0.00
121 4 0.00
122 30 0.03
123 5 0.01
124 5 0.01
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (113 bp):
AGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
AACCTTTTAATAAATTATCACAAATGATAGGTCAACCTTTCCAGAGAA
Found at i:741018 original size:3 final size:3
Alignment explanation
Indices: 741012--741050 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
741002 TTTACTCATG
*
741012 TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
741051 AAAAAATAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:744721 original size:2 final size:2
Alignment explanation
Indices: 744714--744776 Score: 55
Period size: 2 Copynumber: 32.5 Consensus size: 2
744704 ACTTTCATAA
744714 AT AT AT AT AT AT AT A- AGT CAT A- AT AT A- AT AT A- AT ACT A-
1 AT AT AT AT AT AT AT AT A-T -AT AT AT AT AT AT AT AT AT A-T AT
*
744752 AT AT AT AT AT AA AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
744777 CAAACACACG
Statistics
Matches: 51, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
1 5 0.10
2 42 0.82
3 3 0.06
4 1 0.02
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (2 bp):
AT
Found at i:747589 original size:29 final size:29
Alignment explanation
Indices: 747547--747620 Score: 139
Period size: 29 Copynumber: 2.6 Consensus size: 29
747537 TTAGTAAAAT
747547 GAAGACTCTTGACGTGGACTTGGGTATGC
1 GAAGACTCTTGACGTGGACTTGGGTATGC
*
747576 GAAGACTATTGACGTGGACTTGGGTATGC
1 GAAGACTCTTGACGTGGACTTGGGTATGC
747605 GAAGACTCTTGACGTG
1 GAAGACTCTTGACGTG
747621 TTTTTCCCCT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.23, C:0.16, G:0.34, T:0.27
Consensus pattern (29 bp):
GAAGACTCTTGACGTGGACTTGGGTATGC
Found at i:747691 original size:17 final size:17
Alignment explanation
Indices: 747669--747723 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
747659 AATTTCGATT
747669 ATTTGATTATAAAATCA
1 ATTTGATTATAAAATCA
**
747686 ATTTGAATT-T-CGATC-
1 ATTTG-ATTATAAAATCA
*
747701 GTTTGATTATAAAATCA
1 ATTTGATTATAAAATCA
747718 ATTTGA
1 ATTTGA
747724 ATTTCGATTG
Statistics
Matches: 28, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
14 3 0.11
15 5 0.18
16 6 0.21
17 11 0.39
18 3 0.11
ACGTcount: A:0.38, C:0.07, G:0.11, T:0.44
Consensus pattern (17 bp):
ATTTGATTATAAAATCA
Found at i:747692 original size:32 final size:32
Alignment explanation
Indices: 747651--747737 Score: 156
Period size: 32 Copynumber: 2.7 Consensus size: 32
747641 TTCAGTTAAG
*
747651 TCAATTTGAATTTCGATTATTTGATTATAAAA
1 TCAATTTGAATTTCGATTGTTTGATTATAAAA
*
747683 TCAATTTGAATTTCGATCGTTTGATTATAAAA
1 TCAATTTGAATTTCGATTGTTTGATTATAAAA
747715 TCAATTTGAATTTCGATTGTTTG
1 TCAATTTGAATTTCGATTGTTTG
747738 TTCAGTACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.32, C:0.08, G:0.13, T:0.47
Consensus pattern (32 bp):
TCAATTTGAATTTCGATTGTTTGATTATAAAA
Found at i:749076 original size:21 final size:21
Alignment explanation
Indices: 749052--749094 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
749042 TAAACAACCG
*
749052 AAAACATGCCATAGAGACAGA
1 AAAACATGCCATAAAGACAGA
* *
749073 AAAACGTGCCATAAAGATAGA
1 AAAACATGCCATAAAGACAGA
749094 A
1 A
749095 GAATACGTGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.53, C:0.16, G:0.19, T:0.12
Consensus pattern (21 bp):
AAAACATGCCATAAAGACAGA
Found at i:749212 original size:17 final size:17
Alignment explanation
Indices: 749190--749222 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
749180 AATTATTAAG
*
749190 AATAAAAAAATAAGTTT
1 AATAAAAAAACAAGTTT
749207 AATAAAAAAACAAGTT
1 AATAAAAAAACAAGTT
749223 AGATTATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.24
Consensus pattern (17 bp):
AATAAAAAAACAAGTTT
Found at i:753007 original size:21 final size:20
Alignment explanation
Indices: 752981--753050 Score: 68
Period size: 21 Copynumber: 3.4 Consensus size: 20
752971 CTGTCATCCC
752981 TCAAGAGTCCCCTCCAATCGT
1 TCAAGAGTCCCCTCC-ATCGT
* * **
753002 TCAAGAGGCCCCTATCATCCC
1 TCAAGAGTCCCCT-CCATCGT
*
753023 TCAAGAGTCCCCTCCCACCGT
1 TCAAGAGTCCCCT-CCATCGT
753044 TCAAGAG
1 TCAAGAG
753051 GCCACTGTCA
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
21 37 0.97
22 1 0.03
ACGTcount: A:0.24, C:0.40, G:0.16, T:0.20
Consensus pattern (20 bp):
TCAAGAGTCCCCTCCATCGT
Found at i:753065 original size:21 final size:21
Alignment explanation
Indices: 752997--753077 Score: 72
Period size: 21 Copynumber: 3.9 Consensus size: 21
752987 GTCCCCTCCA
752997 ATCGTTCAAGAGGCCCCTATC
1 ATCGTTCAAGAGGCCCCTATC
** * **
753018 ATCCCTCAAGAGTCCCCTCCC
1 ATCGTTCAAGAGGCCCCTATC
* * *
753039 ACCGTTCAAGAGGCCACTGTC
1 ATCGTTCAAGAGGCCCCTATC
* *
753060 ATCGTTGAAGAGGTCCCT
1 ATCGTTCAAGAGGCCCCT
753078 CCCACCATTC
Statistics
Matches: 44, Mismatches: 16, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.22, C:0.36, G:0.20, T:0.22
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCCCTATC
Found at i:753083 original size:42 final size:42
Alignment explanation
Indices: 752974--753062 Score: 142
Period size: 42 Copynumber: 2.1 Consensus size: 42
752964 GACTCACCTG
* * *
752974 TCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
753016 TCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
753058 TCATC
1 TCATC
753063 GTTGAAGAGG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.22, C:0.42, G:0.15, T:0.21
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:754487 original size:14 final size:14
Alignment explanation
Indices: 754468--754503 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
754458 ATTGTTTAAT
754468 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
754482 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
754496 TGATTTGT
1 TGATTTGT
754504 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:754649 original size:14 final size:14
Alignment explanation
Indices: 754630--754690 Score: 59
Period size: 14 Copynumber: 4.0 Consensus size: 14
754620 GAAACTGACT
*
754630 ATCGCAACGAGAGA
1 ATCGCAACGAGAAA
754644 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
754663 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
*
754677 ATCGCAACGCGAAA
1 ATCGCAACGAGAAA
754691 CACAAATCGC
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
14 24 0.60
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.25
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.10
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:754667 original size:19 final size:18
Alignment explanation
Indices: 754643--754709 Score: 70
Period size: 19 Copynumber: 3.8 Consensus size: 18
754633 GCAACGAGAG
754643 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAA-GAA
754662 AATCGCAA--CG--AGAA
1 AATCGCAATGCGAAAGAA
* *
754676 AATCGCAACGCGAAACACA
1 AATCGCAATGCGAAAGA-A
754695 AATCGCAATGCGAAA
1 AATCGCAATGCGAAA
754710 CTAAATTCGC
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
14 11 0.27
15 1 0.02
16 2 0.05
17 2 0.05
18 2 0.05
19 23 0.56
ACGTcount: A:0.48, C:0.22, G:0.19, T:0.10
Consensus pattern (18 bp):
AATCGCAATGCGAAAGAA
Found at i:754698 original size:33 final size:33
Alignment explanation
Indices: 754630--754702 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 33
754620 GAAACTGACT
* * *
754630 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAAAATCGCAACGCGAAATCAAA
754663 ATCGCAACGAGAAAATCGCAACGCGAAA-CACAA
1 ATCGCAACGAGAAAATCGCAACGCGAAATCA-AA
754696 ATCGCAA
1 ATCGCAA
754703 TGCGAAACTA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
32 1 0.03
33 35 0.97
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.10
Consensus pattern (33 bp):
ATCGCAACGAGAAAATCGCAACGCGAAATCAAA
Found at i:754740 original size:20 final size:19
Alignment explanation
Indices: 754715--754767 Score: 88
Period size: 20 Copynumber: 2.7 Consensus size: 19
754705 CGAAACTAAA
754715 TTCGCATTGCGATTTTCATT
1 TTCGCATTGCGATTTTCA-T
*
754735 TTCGCATTACGATTTTCAT
1 TTCGCATTGCGATTTTCAT
754754 TTCGCATTGCGATT
1 TTCGCATTGCGATT
754768 CTCTCGTTGC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.17, C:0.21, G:0.15, T:0.47
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:754797 original size:20 final size:20
Alignment explanation
Indices: 754772--754880 Score: 134
Period size: 20 Copynumber: 5.5 Consensus size: 20
754762 GCGATTCTCT
*
754772 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAATTTCG
*
754792 CGTTGCGATAG-CCATTTCCG
1 CGTTGCGATAGTCAATTT-CG
*
754812 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAATTTCG
754832 CGTTGCGATAGTC-ATTTCCG
1 CGTTGCGATAGTCAATTT-CG
*
754852 TGTTGCGATAGTC-ATATTCG
1 CGTTGCGATAGTCAAT-TTCG
754872 CGTTGCGAT
1 CGTTGCGAT
754881 TTCCCCGTTG
Statistics
Matches: 78, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
19 7 0.09
20 65 0.83
21 6 0.08
ACGTcount: A:0.17, C:0.22, G:0.26, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTTCG
Found at i:754832 original size:40 final size:40
Alignment explanation
Indices: 754772--754880 Score: 182
Period size: 40 Copynumber: 2.7 Consensus size: 40
754762 GCGATTCTCT
*
754772 CGTTGCGATAGTCAAATTCGCGTTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATATTCGCGTTGCGATAGCCATTTCCG
* *
754812 CGTTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATATTCGCGTTGCGATAGCCATTTCCG
*
754852 TGTTGCGATAGTCATATTCGCGTTGCGAT
1 CGTTGCGATAGTCATATTCGCGTTGCGAT
754881 TTCCCCGTTG
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 64 1.00
ACGTcount: A:0.17, C:0.22, G:0.26, T:0.35
Consensus pattern (40 bp):
CGTTGCGATAGTCATATTCGCGTTGCGATAGCCATTTCCG
Found at i:756761 original size:29 final size:30
Alignment explanation
Indices: 756699--756769 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
756689 ACCATATACC
* *
756699 ATTAAACTTTTAACATTATATCATTTATACT
1 ATTAAAC-TTTAACATTATATCAATTATAAT
*
756730 ATTAAACTTTAA-ATTTTATCAATTATAAT
1 ATTAAACTTTAACATTATATCAATTATAAT
756759 ATT-AACTTTAA
1 ATTAAACTTTAA
756770 TTTCCACTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 8 0.22
29 17 0.46
30 5 0.14
31 7 0.19
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (30 bp):
ATTAAACTTTAACATTATATCAATTATAAT
Found at i:757134 original size:12 final size:12
Alignment explanation
Indices: 757117--757141 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
757107 TAATCAGTCA
757117 TCTTTCTTCTCC
1 TCTTTCTTCTCC
757129 TCTTTCTTCTCC
1 TCTTTCTTCTCC
757141 T
1 T
757142 ACGATTATTT
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:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (12 bp):
TCTTTCTTCTCC
Found at i:757779 original size:29 final size:28
Alignment explanation
Indices: 757721--757779 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 28
757711 TTGAAGCAAA
* *
757721 AAAATCAAAATTCAGTGTTATAATTGAT
1 AAAATCAAAATTCAGTGGTATAAGTGAT
*
757749 AAAATTAAAAGTTCAGTGGTATATAGT-AT
1 AAAATCAAAA-TTCAGTGGTATA-AGTGAT
757778 AA
1 AA
757780 TTTACCCTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 9 0.35
29 15 0.58
30 2 0.08
ACGTcount: A:0.47, C:0.05, G:0.14, T:0.34
Consensus pattern (28 bp):
AAAATCAAAATTCAGTGGTATAAGTGAT
Found at i:757998 original size:21 final size:21
Alignment explanation
Indices: 757958--758005 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
757948 ATCATCAAAT
757958 TTTTATTGAAATGTTATAAAA
1 TTTTATTGAAATGTTATAAAA
757979 TATTTATT-AAAT-TTATTAAAA
1 T-TTTATTGAAATGTTA-TAAAA
758000 TTTTAT
1 TTTTAT
758006 ATTTATTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 8 0.32
21 11 0.44
22 6 0.24
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (21 bp):
TTTTATTGAAATGTTATAAAA
Done.