Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 61 of 230
Found at i:16764493 original size:71 final size:71
Alignment explanation
Indices: 16764373--16764514 Score: 239
Period size: 71 Copynumber: 2.0 Consensus size: 71
16764363 GAAAAATGAT
* * *
16764373 TAATTTGTGGTGTATTCAAACACCATATAAACTTATTTATTTACGTCTAGTGAATTTGTATTCGG
1 TAATTTGTGGTGTATTCAAACACCAAATAAACTTATTTATTTACATCTAGTGAATTTGTATTCGA
16764438 CTAGTA
66 CTAGTA
* *
16764444 TAATTTGTGGTGTATTCAAACACTAAATAAATTTATTTATTTACATCTAGTGAATTTGTATTCGA
1 TAATTTGTGGTGTATTCAAACACCAAATAAACTTATTTATTTACATCTAGTGAATTTGTATTCGA
16764509 CTAGTA
66 CTAGTA
16764515 CAAATTATTT
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
71 66 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (71 bp):
TAATTTGTGGTGTATTCAAACACCAAATAAACTTATTTATTTACATCTAGTGAATTTGTATTCGA
CTAGTA
Found at i:16765407 original size:7 final size:7
Alignment explanation
Indices: 16765395--16765440 Score: 56
Period size: 7 Copynumber: 6.1 Consensus size: 7
16765385 ATCTTCTCCA
16765395 ACCTTTC
1 ACCTTTC
16765402 ACCTTTC
1 ACCTTTC
*
16765409 ATCTTCCTC
1 ACCTT--TC
16765418 AACCTTTC
1 -ACCTTTC
16765426 ACCTTTC
1 ACCTTTC
16765433 ACCTTTC
1 ACCTTTC
16765440 A
1 A
16765441 TCTTCCTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
7 26 0.76
8 2 0.06
9 2 0.06
10 4 0.12
ACGTcount: A:0.17, C:0.41, G:0.00, T:0.41
Consensus pattern (7 bp):
ACCTTTC
Found at i:16765407 original size:24 final size:24
Alignment explanation
Indices: 16765378--16765433 Score: 96
Period size: 24 Copynumber: 2.3 Consensus size: 24
16765368 TGGATGTTCA
16765378 ACCTTTCATCTT-CTCCAACCTTTC
1 ACCTTTCATCTTCCT-CAACCTTTC
16765402 ACCTTTCATCTTCCTCAACCTTTC
1 ACCTTTCATCTTCCTCAACCTTTC
16765426 ACCTTTCA
1 ACCTTTCA
16765434 CCTTTCATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 29 0.94
25 2 0.06
ACGTcount: A:0.18, C:0.41, G:0.00, T:0.41
Consensus pattern (24 bp):
ACCTTTCATCTTCCTCAACCTTTC
Found at i:16765424 original size:17 final size:16
Alignment explanation
Indices: 16765400--16765447 Score: 64
Period size: 14 Copynumber: 3.1 Consensus size: 16
16765390 CTCCAACCTT
16765400 TCACCTTTCATCTTCC
1 TCACCTTTCATCTTCC
*
16765416 TCAACCTTTCACCTT--
1 TC-ACCTTTCATCTTCC
16765431 TCACCTTTCATCTTCC
1 TCACCTTTCATCTTCC
16765447 T
1 T
16765448 TAACTCTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
14 11 0.41
15 2 0.07
16 3 0.11
17 11 0.41
ACGTcount: A:0.15, C:0.42, G:0.00, T:0.44
Consensus pattern (16 bp):
TCACCTTTCATCTTCC
Found at i:16765433 original size:31 final size:31
Alignment explanation
Indices: 16765395--16765464 Score: 115
Period size: 31 Copynumber: 2.3 Consensus size: 31
16765385 ATCTTCTCCA
16765395 ACCTTTCACCTTTCATCTTCCTCAAC-CTTTC
1 ACCTTTCACCTTTCATCTTCCTCAACTC-TTC
*
16765426 ACCTTTCACCTTTCATCTTCCTTAACTCTTC
1 ACCTTTCACCTTTCATCTTCCTCAACTCTTC
16765457 ACCTTTCA
1 ACCTTTCA
16765465 TCTTATTGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
31 36 0.97
32 1 0.03
ACGTcount: A:0.17, C:0.40, G:0.00, T:0.43
Consensus pattern (31 bp):
ACCTTTCACCTTTCATCTTCCTCAACTCTTC
Found at i:16766657 original size:6 final size:6
Alignment explanation
Indices: 16766646--16766727 Score: 164
Period size: 6 Copynumber: 13.7 Consensus size: 6
16766636 GTTAATGAAC
16766646 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
16766694 TATTTA TATTTA TATTTA TATTTA TATTTA TATT
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATT
16766728 GTAGCAATAG
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 76 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATTTA
Found at i:16767995 original size:16 final size:16
Alignment explanation
Indices: 16767974--16768025 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
16767964 TTTGGTTCGC
16767974 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
16767990 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
16768006 TGTATTGGAATAGAGG
1 TGTATTGGATTAGAGG
16768022 TGTA
1 TGTA
16768026 ATAGCAAATC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.27, C:0.00, G:0.37, T:0.37
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:16772838 original size:43 final size:44
Alignment explanation
Indices: 16772725--16772882 Score: 144
Period size: 43 Copynumber: 3.6 Consensus size: 44
16772715 TTCCGATATG
* * * * * *
16772725 TGATTTCGTGTAAGACCATATCTGGGACGTTGGCATTGATTTGA
1 TGATTTCGTGTAAGACCATGTCTGGGACATCGGCATCGATATAA
16772769 -GATTTACGTGTAAGACCATGTCTGGGACATCGGCATCG-TATAA
1 TGATTT-CGTGTAAGACCATGTCTGGGACATCGGCATCGATATAA
* * * * *
16772812 TGATTTCGTGTAAGACCCTGTTTGGGATAGT-GGCATCAATAT-T
1 TGATTTCGTGTAAGACCATGTCTGGGACA-TCGGCATCGATATAA
* * *
16772855 TGATTACATGTAAGACCACGTCTGGGAC
1 TGATTTCGTGTAAGACCATGTCTGGGAC
16772883 GTTGGCATTG
Statistics
Matches: 93, Mismatches: 17, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
43 56 0.60
44 37 0.40
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.32
Consensus pattern (44 bp):
TGATTTCGTGTAAGACCATGTCTGGGACATCGGCATCGATATAA
Found at i:16780059 original size:42 final size:41
Alignment explanation
Indices: 16779947--16780061 Score: 115
Period size: 44 Copynumber: 2.7 Consensus size: 41
16779937 TTCCGATATG
** * *
16779947 TGATTTCGTGTAAGACCAC-GTCTGGGACATTGGCATTGATT
1 TGATTTCGTGTAAGACC-CTGTCTGGGACATCAGCATCGATA
* *
16779988 TGAGATTTACGTGTAAGACCATGCCTGGGACATCAGCATCGTATA
1 T--GATTT-CGTGTAAGACCCTGTCTGGGACATCAGCATCG-ATA
*
16780033 TGATTTCGTGTAAGACCCTGTTTGGGACA
1 TGATTTCGTGTAAGACCCTGTCTGGGACA
16780062 GTGGAGTCGA
Statistics
Matches: 60, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
41 1 0.02
42 20 0.33
43 10 0.17
44 26 0.43
45 3 0.05
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.31
Consensus pattern (41 bp):
TGATTTCGTGTAAGACCCTGTCTGGGACATCAGCATCGATA
Found at i:16781674 original size:11 final size:11
Alignment explanation
Indices: 16781658--16781688 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
16781648 AGTTGTAAAG
16781658 TTTTATTTTTT
1 TTTTATTTTTT
16781669 TTTTATTTTTT
1 TTTTATTTTTT
16781680 TATTTATTT
1 T-TTTATTT
16781689 ATTTACTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.63
12 7 0.37
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (11 bp):
TTTTATTTTTT
Found at i:16784034 original size:12 final size:12
Alignment explanation
Indices: 16784017--16784049 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
16784007 TGAGGAAAAA
16784017 GAAAAAGAGAAT
1 GAAAAAGAGAAT
16784029 GAAAAAGAGAAT
1 GAAAAAGAGAAT
16784041 GAAAAAGAG
1 GAAAAAGAG
16784050 CAAAAAGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.27, T:0.06
Consensus pattern (12 bp):
GAAAAAGAGAAT
Found at i:16784089 original size:18 final size:18
Alignment explanation
Indices: 16784068--16784106 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
16784058 GATTGAGAGT
* *
16784068 GAAAAGGAATGTGAAACA
1 GAAAAGAAATGTGAAAAA
*
16784086 GAAAAGAAATTTGAAAAA
1 GAAAAGAAATGTGAAAAA
16784104 GAA
1 GAA
16784107 GTTGAAGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.23, T:0.13
Consensus pattern (18 bp):
GAAAAGAAATGTGAAAAA
Found at i:16789523 original size:78 final size:78
Alignment explanation
Indices: 16789372--16789796 Score: 550
Period size: 78 Copynumber: 5.5 Consensus size: 78
16789362 ATATATGTAT
*
16789372 TTCTTGAATTTAGTTAAAAGTATGTATGTTATATTTATATATATAAAGTTC--AGATATA--TAT
1 TTCTTGAATTTAGTTAAAAGTATGTATGTTATATTTATATATATAAAGTTCGGATATATATGTAT
16789433 ATACATGAATAAA
66 ATACATGAATAAA
** *
16789446 TTCTTGAATTTAGTTAAAAGTATGTATGTTATATTTATATATATAAAGTTCATATATATACGTAT
1 TTCTTGAATTTAGTTAAAAGTATGTATGTTATATTTATATATATAAAGTTCGGATATATATGTAT
16789511 ATACATGAATAAA
66 ATACATGAATAAA
*
16789524 TTCTTGAATTTAGCTAAAAGTATGTATGTTATATTTATATATATAAAGTTCGGATATATATGTAT
1 TTCTTGAATTTAGTTAAAAGTATGTATGTTATATTTATATATATAAAGTTCGGATATATATGTAT
16789589 ATACATGAATAAA
66 ATACATGAATAAA
*
16789602 TTCTTGAATTTAGTTAAAAGTACGTATGTTATATTTATATATATAAAGTTCGGATATATATGTAT
1 TTCTTGAATTTAGTTAAAAGTATGTATGTTATATTTATATATATAAAGTTCGGATATATATGTAT
*
16789667 ATACATGAATAAG
66 ATACATGAATAAA
* * * * * * **
16789680 TT-TTGAATTTAGTT-AATGT-TGAATGTTATA--TATGTTTACAAGAGGTTCGAATAGGTATGT
1 TTCTTGAATTTAGTTAAAAGTATGTATGTTATATTTATATATATAA-A-GTTCGGATATATATGT
16789740 ATAT--ATGAGTATAAA
64 ATATACATGA--ATAAA
* * * *
16789755 TTCTTGGATTT-GATTAAAAGTATGGATGTTACATATATATAT
1 TTCTTGAATTTAG-TTAAAAGTATGTATGTTATATTTATATAT
16789797 GTATAATATA
Statistics
Matches: 313, Mismatches: 24, Indels: 22
0.87 0.07 0.06
Matches are distributed among these distances:
73 12 0.04
74 52 0.17
75 33 0.11
76 19 0.06
77 16 0.05
78 176 0.56
80 5 0.02
ACGTcount: A:0.39, C:0.04, G:0.14, T:0.43
Consensus pattern (78 bp):
TTCTTGAATTTAGTTAAAAGTATGTATGTTATATTTATATATATAAAGTTCGGATATATATGTAT
ATACATGAATAAA
Found at i:16789932 original size:76 final size:75
Alignment explanation
Indices: 16789836--16790047 Score: 192
Period size: 78 Copynumber: 2.8 Consensus size: 75
16789826 AATAAGCATG
* * * *
16789836 TATATATATGTATAATTACTTATATTGAGTATAAGTATGAAATTATATATGTATATGTTAAATTC
1 TATATACAAGTATAAGTACTTGTATTGA-TATAAGTATGAAATTATATATGTATATGTTAAATTC
*
16789901 AAAAATGTATG
65 AAAAATGTATA
* * * *
16789912 TGTATACAAGTATAAGTACTTGT-TTCGAATGTAAGTATAAAATTATATATGTATATATGTTAGA
1 TATATACAAGTATAAGTACTTGTATT-G-ATATAAGTATGAAATTATATATG--TATATGTTAAA
* *
16789976 TTCGAATATGTATA
62 TTCAAAAATGTATA
* * ** * ** *
16789990 TATGTACATGTATAAGTTTTTGTATTGAAATGGGGTATGAAATTATATAGGTATATGT
1 TATATACAAGTATAAGTACTTGTATTGATAT-AAGTATGAAATTATATATGTATATGT
16790048 GAGATTCGAA
Statistics
Matches: 108, Mismatches: 22, Indels: 12
0.76 0.15 0.08
Matches are distributed among these distances:
75 2 0.02
76 46 0.43
77 3 0.03
78 55 0.51
79 2 0.02
ACGTcount: A:0.38, C:0.03, G:0.16, T:0.42
Consensus pattern (75 bp):
TATATACAAGTATAAGTACTTGTATTGATATAAGTATGAAATTATATATGTATATGTTAAATTCA
AAAATGTATA
Found at i:16790033 original size:78 final size:76
Alignment explanation
Indices: 16789867--16790058 Score: 208
Period size: 78 Copynumber: 2.5 Consensus size: 76
16789857 ATATTGAGTA
* * * * *
16789867 TAAGTATGAAATTATATATGTATATGTTAAATTCAAAAATGTATGTGTATACAAGTATAAGTACT
1 TAAGTATGAAATTATATATGTATATGTTAGATTCGAATATGTATATATATACAAGTATAAGTACT
16789932 TGTTTCGAATG
66 TGTTTCGAATG
* * * *
16789943 TAAGTATAAAATTATATATGTATATATGTTAGATTCGAATATGTATATATGTACATGTATAAGTT
1 TAAGTATGAAATTATATATG--TATATGTTAGATTCGAATATGTATATATATACAAGTATAAGTA
*
16790008 TTTGTATT-GAAATG
64 CTTGT-TTCG-AATG
** * *
16790022 -GGGTATGAAATTATATAGGTATATGTGAGATTCGAAT
1 TAAGTATGAAATTATATATGTATATGTTAGATTCGAAT
16790059 GTTAAATGTA
Statistics
Matches: 97, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
76 36 0.37
78 55 0.57
79 6 0.06
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.41
Consensus pattern (76 bp):
TAAGTATGAAATTATATATGTATATGTTAGATTCGAATATGTATATATATACAAGTATAAGTACT
TGTTTCGAATG
Found at i:16790494 original size:41 final size:41
Alignment explanation
Indices: 16790392--16790754 Score: 440
Period size: 41 Copynumber: 8.8 Consensus size: 41
16790382 CGTTTCAGAC
* ** * * *
16790392 TATAAGTCTAGCAGGCTAAAAGCTGGTGAACTAAATCAGGT
1 TATAAGCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGT
* * * * *
16790433 TTTAAAACCTAGCAAGCTAAGTGCCGGTGACCTGAACCAGGT
1 TAT-AAGCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGT
* *
16790475 TATAAGCCTAGTAGGCTAAGTGCCGGTGATCTGAATCAGGC
1 TATAAGCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGT
* ** * * *
16790516 TATAAGCCTAGCAAGCTAAGTGCTAGTGATCTAAACCGGGT
1 TATAAGCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGT
*
16790557 TATAAGCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGC
1 TATAAGCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGT
* *
16790598 TATAAGCCTAGCAGGCTCAGTGCCGGTGATCTGAATCAGGC
1 TATAAGCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGT
*
16790639 TATAAGCCTAGCAGGCTAAGGGCCGGTGATCTGAATCAGGT
1 TATAAGCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGT
* *
16790680 TATAAGCCTAGCAGGCAAAGTGCTGGTGATCTGAATCAGGCT
1 TATAAGCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGG-T
* * *
16790722 T-TAAGCCTAACAGGTTAAGTACCGGTGAATCTG
1 TATAAGCCTAGCAGGCTAAGTGCCGGTG-ATCTG
16790755 TTTAAATTAA
Statistics
Matches: 275, Mismatches: 44, Indels: 5
0.85 0.14 0.02
Matches are distributed among these distances:
41 237 0.86
42 38 0.14
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.23
Consensus pattern (41 bp):
TATAAGCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGT
Found at i:16790603 original size:123 final size:123
Alignment explanation
Indices: 16790386--16790754 Score: 486
Period size: 123 Copynumber: 3.0 Consensus size: 123
16790376 ATGAAACGTT
* * * * * * *
16790386 TCAGACTATAAGTCTAGCAGGCTAAAAGCTGGTGAACTAAATCAGGTTTTAAAACCTAGCAAGCT
1 TCAGGCTATAAGCCTAGCAGGCTAAGAGCTGGTGATCTAAATCAGGTTAT-AAGCCTAGCAGGCT
* * * *
16790451 AAGTGCCGGTGACCTGAACCAGGTTATAAGCCTAGTAGGCTAAGTGCCGGTGATCTGAA
65 AAGTGCCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGATCTGAA
* * * * *
16790510 TCAGGCTATAAGCCTAGCAAGCTAAGTGCTAGTGATCTAAACCGGGTTATAAGCCTAGCAGGCTA
1 TCAGGCTATAAGCCTAGCAGGCTAAGAGCTGGTGATCTAAATCAGGTTATAAGCCTAGCAGGCTA
*
16790575 AGTGCCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTCAGTGCCGGTGATCTGAA
66 AGTGCCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGATCTGAA
* * * *
16790633 TCAGGCTATAAGCCTAGCAGGCTAAGGGCCGGTGATCTGAATCAGGTTATAAGCCTAGCAGGCAA
1 TCAGGCTATAAGCCTAGCAGGCTAAGAGCTGGTGATCTAAATCAGGTTATAAGCCTAGCAGGCTA
* * * * *
16790698 AGTGCTGGTGATCTGAATCAGGCTTTAAGCCTAACAGGTTAAGTACCGGTGAATCTG
66 AGTGCCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTG-ATCTG
16790755 TTTAAATTAA
Statistics
Matches: 213, Mismatches: 31, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
123 168 0.79
124 45 0.21
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.23
Consensus pattern (123 bp):
TCAGGCTATAAGCCTAGCAGGCTAAGAGCTGGTGATCTAAATCAGGTTATAAGCCTAGCAGGCTA
AGTGCCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGATCTGAA
Found at i:16790992 original size:34 final size:35
Alignment explanation
Indices: 16790923--16790996 Score: 89
Period size: 34 Copynumber: 2.1 Consensus size: 35
16790913 GTTGGATATA
* * *
16790923 TATATATGTATGCATTCGGTATATGTGGATTATAAG
1 TATATATG-ATGCATTCGGCACATGTGAATTATAAG
16790959 TATATATG-TGCATTCGGCACATGT-AATTGATAAG
1 TATATATGATGCATTCGGCACATGTGAATT-ATAAG
16790993 TATA
1 TATA
16790997 AATATATGCT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
33 3 0.09
34 23 0.68
36 8 0.24
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.39
Consensus pattern (35 bp):
TATATATGATGCATTCGGCACATGTGAATTATAAG
Found at i:16793998 original size:24 final size:24
Alignment explanation
Indices: 16793952--16794025 Score: 71
Period size: 24 Copynumber: 3.1 Consensus size: 24
16793942 ATTGCACAAC
*
16793952 TTAAGGAAGATGGAAA-GTTAAAGG
1 TTAAGGAAGAT-GAAAGGTGAAAGG
* *
16793976 TTAAAGAAGATGAAAGGTGAAAGA
1 TTAAGGAAGATGAAAGGTGAAAGG
* *
16794000 TCAAGGGAA-ATGAAAGATGAAAGG
1 TTAA-GGAAGATGAAAGGTGAAAGG
16794024 TT
1 TT
16794026 GAACATCCAT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
23 4 0.10
24 33 0.82
25 3 0.08
ACGTcount: A:0.49, C:0.01, G:0.31, T:0.19
Consensus pattern (24 bp):
TTAAGGAAGATGAAAGGTGAAAGG
Found at i:16794666 original size:14 final size:16
Alignment explanation
Indices: 16794647--16794686 Score: 66
Period size: 14 Copynumber: 2.6 Consensus size: 16
16794637 AAGATTTAAA
16794647 TATTGAATTTT-TA-G
1 TATTGAATTTTATAGG
16794661 TATTGAATTTTATAGG
1 TATTGAATTTTATAGG
16794677 TATTGAATTT
1 TATTGAATTT
16794687 ATATTAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 11 0.46
15 2 0.08
16 11 0.46
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (16 bp):
TATTGAATTTTATAGG
Found at i:16795638 original size:5 final size:5
Alignment explanation
Indices: 16795628--16795663 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
16795618 TTAAAGTGAT
16795628 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A
16795664 AATCTATTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:16797774 original size:16 final size:18
Alignment explanation
Indices: 16797748--16797780 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
16797738 TTCAATTAAC
16797748 TAAATTAATTTT-TCAAT
1 TAAATTAATTTTCTCAAT
16797765 TAAA-TAATTTTCTCAA
1 TAAATTAATTTTCTCAA
16797781 CTCAATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (18 bp):
TAAATTAATTTTCTCAAT
Found at i:16801747 original size:18 final size:18
Alignment explanation
Indices: 16801715--16801760 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
16801705 AATCTCACAA
*
16801715 TTAAATAATTTAATT-TT
1 TTAAAAAATTTAATTATT
16801732 TTAAAAAATATTAATTATT
1 TTAAAAAAT-TTAATTATT
*
16801751 ATAAAAAATT
1 TTAAAAAATT
16801761 ATCAATAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 8 0.32
18 7 0.28
19 10 0.40
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TTAAAAAATTTAATTATT
Found at i:16813430 original size:9 final size:10
Alignment explanation
Indices: 16813413--16813441 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
16813403 ATGTATGTAT
16813413 TTATTTATTA
1 TTATTTATTA
16813423 TT-TTTATTA
1 TTATTTATTA
16813432 TTATTTATTA
1 TTATTTATTA
16813442 ACATTATTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TTATTTATTA
Found at i:16822850 original size:9 final size:9
Alignment explanation
Indices: 16822836--16822864 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
16822826 TAAACAATTC
16822836 AATAATATA
1 AATAATATA
16822845 AATAATATA
1 AATAATATA
16822854 AATAATATA
1 AATAATATA
16822863 AA
1 AA
16822865 ATGTGAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
AATAATATA
Found at i:16823246 original size:20 final size:20
Alignment explanation
Indices: 16823206--16823246 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
16823196 AAATACTTTA
* *
16823206 AAAATATTTTTTTTATTTTT
1 AAAATATATTTTTTATGTTT
*
16823226 AAAATATATTTTTTGTGTTT
1 AAAATATATTTTTTATGTTT
16823246 A
1 A
16823247 TTAAAAATCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (20 bp):
AAAATATATTTTTTATGTTT
Found at i:16828136 original size:15 final size:15
Alignment explanation
Indices: 16828116--16828146 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
16828106 ATTTACGTAC
16828116 ATAATCAAAAAAATG
1 ATAATCAAAAAAATG
*
16828131 ATAATCAAGAAAATG
1 ATAATCAAAAAAATG
16828146 A
1 A
16828147 GTCATTTTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.06, G:0.10, T:0.19
Consensus pattern (15 bp):
ATAATCAAAAAAATG
Found at i:16828381 original size:31 final size:31
Alignment explanation
Indices: 16828344--16828414 Score: 124
Period size: 31 Copynumber: 2.3 Consensus size: 31
16828334 CTAAATTAAA
16828344 TGTCATGTGATACTTTAACTCAATTAAAAAG
1 TGTCATGTGATACTTTAACTCAATTAAAAAG
*
16828375 TGTCATGTGATACTTTAACTTAATTAAAAAG
1 TGTCATGTGATACTTTAACTCAATTAAAAAG
*
16828406 TATCATGTG
1 TGTCATGTG
16828415 GCATCTATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.38
Consensus pattern (31 bp):
TGTCATGTGATACTTTAACTCAATTAAAAAG
Found at i:16828682 original size:19 final size:20
Alignment explanation
Indices: 16828636--16828682 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
16828626 TATCAATTAA
* *
16828636 ACTATTTTTTAAATTTTTTT
1 ACTATTTTTTAAATCTATTT
*
16828656 A-TAATTTTT-AATCTATTT
1 ACTATTTTTTAAATCTATTT
16828674 ACTATTTTT
1 ACTATTTTT
16828683 ATTACATATG
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
18 8 0.36
19 13 0.59
20 1 0.05
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (20 bp):
ACTATTTTTTAAATCTATTT
Found at i:16839779 original size:12 final size:12
Alignment explanation
Indices: 16839762--16839786 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16839752 GGTGTTCATT
16839762 CGGTTAACCGAC
1 CGGTTAACCGAC
16839774 CGGTTAACCGAC
1 CGGTTAACCGAC
16839786 C
1 C
16839787 CGAAATTACT
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:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:16839961 original size:9 final size:9
Alignment explanation
Indices: 16839947--16839998 Score: 86
Period size: 9 Copynumber: 5.8 Consensus size: 9
16839937 TTTGGTTAAA
16839947 AATTACCCG
1 AATTACCCG
16839956 AATTACCCG
1 AATTACCCG
16839965 AATTACCCG
1 AATTACCCG
*
16839974 AATTAACCG
1 AATTACCCG
*
16839983 AATTAACCG
1 AATTACCCG
16839992 AATTACC
1 AATTACC
16839999 GAAAAATACC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 41 1.00
ACGTcount: A:0.38, C:0.29, G:0.10, T:0.23
Consensus pattern (9 bp):
AATTACCCG
Found at i:16841304 original size:14 final size:15
Alignment explanation
Indices: 16841282--16841312 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
16841272 TTATCACGTA
16841282 TATTTTTTTAAATAT
1 TATTTTTTTAAATAT
16841297 TATTTTTTTAAATAT
1 TATTTTTTTAAATAT
16841312 T
1 T
16841313 TTACTGTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TATTTTTTTAAATAT
Found at i:16843198 original size:12 final size:12
Alignment explanation
Indices: 16843181--16843205 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16843171 AATAATACAT
16843181 TAATATGTATTA
1 TAATATGTATTA
16843193 TAATATGTATTA
1 TAATATGTATTA
16843205 T
1 T
16843206 TAGGGGAAAA
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:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (12 bp):
TAATATGTATTA
Found at i:16843745 original size:13 final size:13
Alignment explanation
Indices: 16843729--16843769 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
16843719 AATAAATTAT
16843729 TTAAAGTAAAAAC
1 TTAAAGTAAAAAC
16843742 TTAAA--AAAAA-
1 TTAAAGTAAAAAC
16843752 TTAAAGTAAAAAC
1 TTAAAGTAAAAAC
16843765 TTAAA
1 TTAAA
16843770 AAAAATTATG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 5 0.20
11 5 0.20
12 5 0.20
13 10 0.40
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (13 bp):
TTAAAGTAAAAAC
Found at i:16843756 original size:23 final size:23
Alignment explanation
Indices: 16843729--16843777 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
16843719 AATAAATTAT
16843729 TTAAAGTAAAAACTTAAAAAAAA
1 TTAAAGTAAAAACTTAAAAAAAA
16843752 TTAAAGTAAAAACTTAAAAAAAA
1 TTAAAGTAAAAACTTAAAAAAAA
16843775 TTA
1 TTA
16843778 TGTATGATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.24
Consensus pattern (23 bp):
TTAAAGTAAAAACTTAAAAAAAA
Found at i:16862326 original size:9 final size:9
Alignment explanation
Indices: 16862312--16862396 Score: 107
Period size: 9 Copynumber: 9.4 Consensus size: 9
16862302 TTTGGTTAAA
16862312 AATTAACCG
1 AATTAACCG
16862321 AATTAACCG
1 AATTAACCG
*
16862330 AATTAATCG
1 AATTAACCG
*
16862339 AATTAACCA
1 AATTAACCG
*
16862348 AATTACCCG
1 AATTAACCG
16862357 AATTAACCG
1 AATTAACCG
* * *
16862366 AATCACCCA
1 AATTAACCG
16862375 AATTAACCG
1 AATTAACCG
*
16862384 AATTAACTG
1 AATTAACCG
16862393 AATT
1 AATT
16862397 GAATCACTAC
Statistics
Matches: 63, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 63 1.00
ACGTcount: A:0.45, C:0.22, G:0.08, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:16862539 original size:18 final size:18
Alignment explanation
Indices: 16862499--16862542 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
16862489 AATTTTTATG
**
16862499 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGAATA
16862517 ATTGGGTTGGGTTGAATA
1 ATTGGGTTGGGTTGAATA
*
16862535 CTTGGGTT
1 ATTGGGTT
16862543 TGGATTGGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.02, G:0.43, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAATA
Found at i:16863764 original size:24 final size:24
Alignment explanation
Indices: 16863719--16863771 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
16863709 GTAGTAATTG
* *
16863719 GAAAAGAAAGGAGGAAATGAAAAA
1 GAAAAGAAAGGAAGAAAGGAAAAA
16863743 GAAAAG-AAGGAAGAACAGGAAAAA
1 GAAAAGAAAGGAAGAA-AGGAAAAA
*
16863767 CAAAA
1 GAAAA
16863772 AAAAATAAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 8 0.32
24 17 0.68
ACGTcount: A:0.68, C:0.04, G:0.26, T:0.02
Consensus pattern (24 bp):
GAAAAGAAAGGAAGAAAGGAAAAA
Found at i:16863787 original size:30 final size:30
Alignment explanation
Indices: 16863738--16863794 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
16863728 GGAGGAAATG
16863738 AAAAAGAAAAGAAGGAAGAACAGGAAAAAC
1 AAAAAGAAAAGAAGGAAGAACAGGAAAAAC
* *
16863768 AAAAA-AAAATAAGGAAAGAAGAGGAAA
1 AAAAAGAAAAGAAGG-AAGAACAGGAAA
16863795 CATTAATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.72, C:0.04, G:0.23, T:0.02
Consensus pattern (30 bp):
AAAAAGAAAAGAAGGAAGAACAGGAAAAAC
Found at i:16864161 original size:7 final size:7
Alignment explanation
Indices: 16864145--16864181 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
16864135 AGAATTTGAA
16864145 TTTTTA-
1 TTTTTAT
16864151 TTTTTAT
1 TTTTTAT
16864158 TTTTTAT
1 TTTTTAT
16864165 TTTTTAT
1 TTTTTAT
16864172 TTTTTAT
1 TTTTTAT
16864179 TTT
1 TTT
16864182 GTTAATTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 6 0.20
7 24 0.80
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTAT
Found at i:16864229 original size:45 final size:46
Alignment explanation
Indices: 16864170--16864265 Score: 124
Period size: 45 Copynumber: 2.1 Consensus size: 46
16864160 TTTATTTTTT
* *
16864170 ATTTTTTATTTTGTTAATT-TGTTGCATGTAAATTGTCAAACTATTG
1 ATTTTTTATTTTGTTAATTCT-TTGCATATAAATTATCAAACTATTG
* **
16864216 ATTTTTT-TTTTGTTAATTCTTTGCATATAAGTTATTGAACTATTG
1 ATTTTTTATTTTGTTAATTCTTTGCATATAAATTATCAAACTATTG
16864261 ATTTT
1 ATTTT
16864266 AGGTCAATGC
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
45 36 0.82
46 8 0.18
ACGTcount: A:0.25, C:0.06, G:0.11, T:0.57
Consensus pattern (46 bp):
ATTTTTTATTTTGTTAATTCTTTGCATATAAATTATCAAACTATTG
Found at i:16872079 original size:3 final size:3
Alignment explanation
Indices: 16872071--16872095 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
16872061 CAAACTTTAG
16872071 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
16872096 TTGTTTGCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:16877292 original size:11 final size:11
Alignment explanation
Indices: 16877276--16877311 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
16877266 TATAGTGGGA
16877276 TTTTATTTTAT
1 TTTTATTTTAT
*
16877287 TTTTATTTGAT
1 TTTTATTTTAT
*
16877298 TTTTATTTTGT
1 TTTTATTTTAT
16877309 TTT
1 TTT
16877312 CAAAAATTCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.06, T:0.81
Consensus pattern (11 bp):
TTTTATTTTAT
Found at i:16888755 original size:39 final size:39
Alignment explanation
Indices: 16888712--16888877 Score: 224
Period size: 39 Copynumber: 4.3 Consensus size: 39
16888702 TGAAAGTGCT
* *
16888712 ATCAGGAGTACCGAAGTACAACAGGGGCACGTAAGTTCG
1 ATCAGGGGTACCGAAGTACAACAGGGGCACGTAAGTACG
* *
16888751 ATCAGGGGTACCGAAGTACAATAGCGGCACGTAAGTACG
1 ATCAGGGGTACCGAAGTACAACAGGGGCACGTAAGTACG
* * *
16888790 ATCAAGGGTACCGAAGTACAATAGGGGCAGGTAAGTACG
1 ATCAGGGGTACCGAAGTACAACAGGGGCACGTAAGTACG
* * * * *
16888829 ATCAGGGGTGCCAAAATACAACAAGGGCACGTAAGTGCG
1 ATCAGGGGTACCGAAGTACAACAGGGGCACGTAAGTACG
16888868 ATCAGGGGTA
1 ATCAGGGGTA
16888878 TAATTATATA
Statistics
Matches: 111, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 111 1.00
ACGTcount: A:0.34, C:0.19, G:0.32, T:0.15
Consensus pattern (39 bp):
ATCAGGGGTACCGAAGTACAACAGGGGCACGTAAGTACG
Found at i:16888758 original size:20 final size:20
Alignment explanation
Indices: 16888733--16888836 Score: 90
Period size: 20 Copynumber: 5.3 Consensus size: 20
16888723 CGAAGTACAA
*
16888733 CAGGGGCACGTAAGTTCGAT
1 CAGGGGCACGTAAGTACGAT
* *
16888753 CAGGGGTACCG-AAGTACAAT
1 CAGGGGCA-CGTAAGTACGAT
*
16888773 -AGCGGCACGTAAGTACGAT
1 CAGGGGCACGTAAGTACGAT
* * *
16888792 CAAGGGTACCG-AAGTACAAT
1 CAGGGGCA-CGTAAGTACGAT
*
16888812 -AGGGGCAGGTAAGTACGAT
1 CAGGGGCACGTAAGTACGAT
16888831 CAGGGG
1 CAGGGG
16888837 TGCCAAAATA
Statistics
Matches: 64, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
18 3 0.05
19 26 0.41
20 31 0.48
21 4 0.06
ACGTcount: A:0.32, C:0.18, G:0.35, T:0.15
Consensus pattern (20 bp):
CAGGGGCACGTAAGTACGAT
Found at i:16891758 original size:34 final size:34
Alignment explanation
Indices: 16891666--16891765 Score: 101
Period size: 34 Copynumber: 2.9 Consensus size: 34
16891656 ACCACATGAT
* * * * *
16891666 AAGCATATTATTTACCACCGTATCGAACTGTTAT
1 AAGCATATTAATTGCCACCGTATTGATCTGTTAA
** * * *
16891700 AAGCATATTGGTTGCTACCATATTGTTCTGTTAA
1 AAGCATATTAATTGCCACCGTATTGATCTGTTAA
*
16891734 AAGCATATTAAATGCCACCGTATTGATCTGTT
1 AAGCATATTAATTGCCACCGTATTGATCTGTT
16891766 TTGAACATGC
Statistics
Matches: 51, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
34 51 1.00
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (34 bp):
AAGCATATTAATTGCCACCGTATTGATCTGTTAA
Found at i:16895446 original size:2 final size:2
Alignment explanation
Indices: 16895439--16895469 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
16895429 AGAAAGAAAA
16895439 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
16895470 AGGAAAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:16896839 original size:18 final size:18
Alignment explanation
Indices: 16896818--16896871 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
16896808 TTTTTAGATT
16896818 TTTTTGAAATTTTTATAA
1 TTTTTGAAATTTTTATAA
* ** *
16896836 TTTTTAAAAAATATATAA
1 TTTTTGAAATTTTTATAA
* *
16896854 ATTTTGGAATTTTTATAA
1 TTTTTGAAATTTTTATAA
16896872 ATATTTTTAA
Statistics
Matches: 26, Mismatches: 10, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.54
Consensus pattern (18 bp):
TTTTTGAAATTTTTATAA
Found at i:16896885 original size:18 final size:19
Alignment explanation
Indices: 16896864--16896903 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
16896854 ATTTTGGAAT
*
16896864 TTTTATAAA-TATTTTTAA
1 TTTTAAAAATTATTTTTAA
16896882 TTTTAAAAATTATTTTTAA
1 TTTTAAAAATTATTTTTAA
16896901 TTT
1 TTT
16896904 CTGAAAACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTAAAAATTATTTTTAA
Found at i:16896910 original size:20 final size:19
Alignment explanation
Indices: 16896864--16896916 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
16896854 ATTTTGGAAT
*
16896864 TTTTATAAA-TATTTTTAA
1 TTTTAAAAACTATTTTTAA
*
16896882 TTTTAAAAATTATTTTTAA
1 TTTTAAAAACTATTTTTAA
*
16896901 TTTCTGAAAACTATTT
1 TTT-TAAAAACTATTT
16896917 GGATTTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
18 8 0.27
19 12 0.40
20 10 0.33
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.57
Consensus pattern (19 bp):
TTTTAAAAACTATTTTTAA
Found at i:16899498 original size:20 final size:19
Alignment explanation
Indices: 16899473--16899513 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
16899463 GTAGAAATTA
*
16899473 TTATTCCCAGAAAATAGAAT
1 TTATTCCAAGAAAATA-AAT
*
16899493 TTATTCTAAGAAAATAAAT
1 TTATTCCAAGAAAATAAAT
16899512 TT
1 TT
16899514 TCACTACTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.37
Consensus pattern (19 bp):
TTATTCCAAGAAAATAAAT
Found at i:16909097 original size:3 final size:3
Alignment explanation
Indices: 16909091--16909142 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
16909081 ATCTTTTGAC
*
16909091 TCT TCT TCT TCC TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
16909139 TCT T
1 TCT T
16909143 TTGTATACTC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:16911557 original size:22 final size:20
Alignment explanation
Indices: 16911532--16911579 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 20
16911522 TTTTCAAAAA
16911532 TTATAATTTTTTAAAAATAATT
1 TTATAATTTTTTAAAAAT--TT
* *
16911554 TTATATTTTTTTTAAAATTT
1 TTATAATTTTTTAAAAATTT
16911574 TTATAA
1 TTATAA
16911580 AGTACGTCCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 7 0.30
22 16 0.70
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTATAATTTTTTAAAAATTT
Found at i:16911831 original size:69 final size:69
Alignment explanation
Indices: 16911736--16911868 Score: 257
Period size: 69 Copynumber: 1.9 Consensus size: 69
16911726 TCCTCATGCC
*
16911736 AAAAAAATAGCAAACTCAAAGTTGTGTATGTAATTTGCCAGCGGGTTGATTACATCTAGACTTAG
1 AAAAAAATAGCAAACTCAAAGTTGTGTATGTAATTTGCCAGCAGGTTGATTACATCTAGACTTAG
16911801 ATCA
66 ATCA
16911805 AAAAAAATAGCAAACTCAAAGTTGTGTATGTAATTTGCCAGCAGGTTGATTACATCTAGACTTA
1 AAAAAAATAGCAAACTCAAAGTTGTGTATGTAATTTGCCAGCAGGTTGATTACATCTAGACTTA
16911869 TCAAAGATTA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
69 63 1.00
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.29
Consensus pattern (69 bp):
AAAAAAATAGCAAACTCAAAGTTGTGTATGTAATTTGCCAGCAGGTTGATTACATCTAGACTTAG
ATCA
Found at i:16917210 original size:20 final size:20
Alignment explanation
Indices: 16917172--16917210 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
16917162 TGGAGCAGGA
*
16917172 ATATCAATACCATAGGAAAT
1 ATATCAATACCATAAGAAAT
* *
16917192 ATATCGATACCTTAAGAAA
1 ATATCAATACCATAAGAAA
16917211 AGTTTCGATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.49, C:0.15, G:0.10, T:0.26
Consensus pattern (20 bp):
ATATCAATACCATAAGAAAT
Found at i:16918590 original size:33 final size:33
Alignment explanation
Indices: 16918542--16918608 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
16918532 TGAATAGGTT
*
16918542 GCTCCCCCTTAATAAAAGTCATTTCCAATTTAA
1 GCTCCCCCTTAATAAAAATCATTTCCAATTTAA
**
16918575 GCTCCCCC-TAGATAAAAATCATTTTGAATTTAA
1 GCTCCCCCTTA-ATAAAAATCATTTCCAATTTAA
16918608 G
1 G
16918609 GCATAAAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 2 0.07
33 28 0.93
ACGTcount: A:0.34, C:0.24, G:0.09, T:0.33
Consensus pattern (33 bp):
GCTCCCCCTTAATAAAAATCATTTCCAATTTAA
Found at i:16928298 original size:26 final size:26
Alignment explanation
Indices: 16928262--16928327 Score: 105
Period size: 26 Copynumber: 2.5 Consensus size: 26
16928252 TCCAACCCAT
* * *
16928262 AGCTCATGTGAGTAGGCCTATTTCAC
1 AGCTCGTGTGAGCAGGCCCATTTCAC
16928288 AGCTCGTGTGAGCAGGCCCATTTCAC
1 AGCTCGTGTGAGCAGGCCCATTTCAC
16928314 AGCTCGTGTGAGCA
1 AGCTCGTGTGAGCA
16928328 ACGATGTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.21, C:0.26, G:0.27, T:0.26
Consensus pattern (26 bp):
AGCTCGTGTGAGCAGGCCCATTTCAC
Found at i:16931208 original size:27 final size:28
Alignment explanation
Indices: 16931177--16931235 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 28
16931167 AATAAATATA
16931177 TTTATTTTTAAAATA-TTTTTTTATTTT
1 TTTATTTTTAAAATACTTTTTTTATTTT
16931204 TTTATTTTTAAAATACTTTTTTTATTTT
1 TTTATTTTTAAAATACTTTTTTTATTTT
16931232 TTTA
1 TTTA
16931236 AAATTTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 15 0.48
28 16 0.52
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (28 bp):
TTTATTTTTAAAATACTTTTTTTATTTT
Found at i:16931243 original size:20 final size:19
Alignment explanation
Indices: 16931198--16931245 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 19
16931188 AATATTTTTT
16931198 TATTTTTTTATTTTTAAAA
1 TATTTTTTTATTTTTAAAA
16931217 TACTTTTTTTATTTTTTTAAAA
1 TA-TTTTTTTA--TTTTTAAAA
16931239 T-TTTTTT
1 TATTTTTT
16931246 GGTGTTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 2 0.08
20 14 0.54
22 10 0.38
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (19 bp):
TATTTTTTTATTTTTAAAA
Found at i:16937633 original size:33 final size:34
Alignment explanation
Indices: 16937585--16937657 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 34
16937575 CCCAACCTTA
*
16937585 TTTG-TTTTCAGATTTGGGAAC-AAAACAGTCAT
1 TTTGTTTTTCAGATTTGAGAACTAAAACAGTCAT
* *
16937617 TTTGTTTTTCATATTTGAGAACTAAAACAGTGAT
1 TTTGTTTTTCAGATTTGAGAACTAAAACAGTCAT
16937651 TATTGTT
1 T-TTGTT
16937658 GGTTTCTCCC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
32 4 0.11
33 15 0.43
34 11 0.31
35 5 0.14
ACGTcount: A:0.30, C:0.10, G:0.16, T:0.44
Consensus pattern (34 bp):
TTTGTTTTTCAGATTTGAGAACTAAAACAGTCAT
Found at i:16938403 original size:11 final size:11
Alignment explanation
Indices: 16938387--16938452 Score: 61
Period size: 11 Copynumber: 6.4 Consensus size: 11
16938377 TTTTTCTTAA
16938387 TTTTAAAATAC
1 TTTTAAAATAC
16938398 TTTTAAAATAC
1 TTTTAAAATAC
**
16938409 TTTT--TTTA-
1 TTTTAAAATAC
*
16938417 TTTTTAAA-A-
1 TTTTAAAATAC
16938426 TTTTAAAATAC
1 TTTTAAAATAC
16938437 TTTTTAAAATAC
1 -TTTTAAAATAC
16938449 TTTT
1 TTTT
16938453 TTTTATTTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
8 4 0.09
9 10 0.22
10 1 0.02
11 19 0.42
12 11 0.24
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:16938443 original size:12 final size:12
Alignment explanation
Indices: 16938426--16938453 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
16938416 ATTTTTAAAA
16938426 TTTTAAAATACT
1 TTTTAAAATACT
16938438 TTTTAAAATACT
1 TTTTAAAATACT
16938450 TTTT
1 TTTT
16938454 TTTATTTTTT
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:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (12 bp):
TTTTAAAATACT
Found at i:16938481 original size:40 final size:39
Alignment explanation
Indices: 16938378--16938481 Score: 156
Period size: 40 Copynumber: 2.6 Consensus size: 39
16938368 GCATCATGAT
16938378 TTTTCTTAATTTTAAAATAC-TTTTAAAATACTTTTTTTA
1 TTTT-TTAATTTTAAAATACTTTTTAAAATACTTTTTTTA
*
16938417 TTTTTAAAATTTTAAAATACTTTTTAAAATACTTTTTTTTA
1 TTTTT-TAATTTTAAAATACTTTTTAAAATAC-TTTTTTTA
*
16938458 TTTTTTATTTTTAAAATACTTTTT
1 TTTTTTAATTTTAAAATACTTTTT
16938482 TTATTTTTTT
Statistics
Matches: 59, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
38 1 0.02
39 17 0.29
40 28 0.47
41 13 0.22
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.62
Consensus pattern (39 bp):
TTTTTTAATTTTAAAATACTTTTTAAAATACTTTTTTTA
Found at i:16938484 original size:27 final size:29
Alignment explanation
Indices: 16938437--16938503 Score: 120
Period size: 28 Copynumber: 2.4 Consensus size: 29
16938427 TTTAAAATAC
16938437 TTTTTAAAATACTTTTTTTTA-TTTTTTA
1 TTTTTAAAATACTTTTTTTTATTTTTTTA
16938465 TTTTTAAAATAC-TTTTTTTATTTTTTTA
1 TTTTTAAAATACTTTTTTTTATTTTTTTA
16938493 TTTTTAAAATA
1 TTTTTAAAATA
16938504 AATTTTTGGT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
27 8 0.21
28 30 0.79
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (29 bp):
TTTTTAAAATACTTTTTTTTATTTTTTTA
Found at i:16951888 original size:125 final size:125
Alignment explanation
Indices: 16951688--16952039 Score: 614
Period size: 125 Copynumber: 2.8 Consensus size: 125
16951678 TAATTTCGAG
* * * *
16951688 TTGACGTTTCTAATCAAATAGTATAAAATCGCTTCTAGCAGTATGCTATTTGAGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTA
16951753 AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATGGAAGAAATAATTTTTTT
66 AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATGGAAGAAATAATTTTTTT
16951813 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTA
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTA
* * *
16951878 AAATCACGCCCTCGTGGACGCGCTTTTGCTATAGTCGGTCATGGAAGAAATAATTTTTTT
66 AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATGGAAGAAATAATTTTTTT
* *
16951938 TTGACATTTCTGAGCAAATAGTATAAAATCGCTTCTAACAGGATGCTATTTGAGAAGAATTTGTA
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTA
*
16952003 AAATTGCGCCCTCGTGGACGCGCTTTTGCTACAGTAG
66 AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAG
16952040 CATGTCTGGC
Statistics
Matches: 214, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
125 214 1.00
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.33
Consensus pattern (125 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTA
AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATGGAAGAAATAATTTTTTT
Found at i:16955253 original size:116 final size:116
Alignment explanation
Indices: 16955049--16955407 Score: 648
Period size: 116 Copynumber: 3.1 Consensus size: 116
16955039 ATTTTGTGAT
16955049 ATTATTAATTGATAAATTGTATTAATGGTTAGTAAAAATTATCAAATTATATAAAATTATTAATT
1 ATTATTAATTGATAAATTGTATTAATGGTTAGTAAAAATTATCAAATTATATAAAATTATTAATT
*
16955114 GTTAGTACGAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAA
66 GTTAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAA
16955165 ATTATTAATTGATAAATTGTATTAATGGTTAGTAAAAATTATCAAATTATATAAAATTATTAATT
1 ATTATTAATTGATAAATTGTATTAATGGTTAGTAAAAATTATCAAATTATATAAAATTATTAATT
16955230 GTTAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAA
66 GTTAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAA
*
16955281 ATTATTAATTGATAAATTGTATTAATGATTAGT-AAAATTATCAAATTATATAAAATTATTAATT
1 ATTATTAATTGATAAATTGTATTAATGGTTAGTAAAAATTATCAAATTATATAAAATTATTAATT
** *
16955345 GTTAGTACCAGAAAAAAAACATTTTTCCAAATCTAACATTATGTGAAAGTAAA
66 GTTAGTACCAG--TCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAA
16955398 ATTATTAATT
1 ATTATTAATT
16955408 TAGTTTAGGG
Statistics
Matches: 236, Mismatches: 5, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
115 42 0.18
116 147 0.62
117 47 0.20
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (116 bp):
ATTATTAATTGATAAATTGTATTAATGGTTAGTAAAAATTATCAAATTATATAAAATTATTAATT
GTTAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAA
Found at i:16955344 original size:17 final size:17
Alignment explanation
Indices: 16955277--16955344 Score: 57
Period size: 17 Copynumber: 3.8 Consensus size: 17
16955267 TATGTGAATG
*
16955277 TAAAATTATTAATT-GA
1 TAAAATTATTAATTATA
* *
16955293 TAAATTGTATTAATGATTA
1 TAAAAT-TATTAATTA-TA
*
16955312 GTAAAATTATCAAATTATA
1 -TAAAATTAT-TAATTATA
16955331 TAAAATTATTAATT
1 TAAAATTATTAATT
16955345 GTTAGTACCA
Statistics
Matches: 40, Mismatches: 7, Indels: 9
0.71 0.12 0.16
Matches are distributed among these distances:
16 5 0.12
17 11 0.28
18 9 0.22
19 6 0.15
20 9 0.22
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.44
Consensus pattern (17 bp):
TAAAATTATTAATTATA
Found at i:16955433 original size:23 final size:22
Alignment explanation
Indices: 16955401--16955964 Score: 522
Period size: 23 Copynumber: 25.1 Consensus size: 22
16955391 AAGTAAAATT
*
16955401 ATTAATTTAGTTTAGGGTTTTTA
1 ATTAA-TTAGGTTAGGGTTTTTA
16955424 ATTAAATTAGGTTAGGGTTTTTA
1 ATT-AATTAGGTTAGGGTTTTTA
* *
16955447 AGT--TTAGGGTTTACGGTTTTTA
1 ATTAATTA-GG-TTAGGGTTTTTA
**
16955469 ATTAAATTAGGTTAGAATTTTTA
1 ATT-AATTAGGTTAGGGTTTTTA
16955492 ATTTAATTAGGTTAGGGTTTTTA
1 A-TTAATTAGGTTAGGGTTTTTA
16955515 AGTTAATTAGGTTAGGGTTTTTA
1 A-TTAATTAGGTTAGGGTTTTTA
*
16955538 AGTTAA-GAGGGTTAGGGTTTTTA
1 A-TTAATTA-GGTTAGGGTTTTTA
* *
16955561 AGT--TTAGGGTTTAAGGTTTTTA
1 ATTAATTA-GG-TTAGGGTTTTTA
16955583 ATTAAATTAGGTTAGGGGTTTTTA
1 ATT-AATTAGGTTA-GGGTTTTTA
*
16955607 AGTT--TAAGGTTTAGGGTTTTTA
1 A-TTAATTAGG-TTAGGGTTTTTA
16955629 ATTAAATTAGGTTAGGGTTTTTA
1 ATT-AATTAGGTTAGGGTTTTTA
16955652 ATTTAATTAGGTTAGGGTTTTTA
1 A-TTAATTAGGTTAGGGTTTTTA
16955675 AGTTAATTAGGTTAGGGTTTTTA
1 A-TTAATTAGGTTAGGGTTTTTA
**
16955698 AGTTAA-GGGGTTAGGGTTTTTA
1 A-TTAATTAGGTTAGGGTTTTTA
* *
16955720 AGT--TTAGGGTTTAGGGTTCTTA
1 ATTAATTA-GG-TTAGGGTTTTTA
16955742 ATTTAATTAGGTTAGGGTTTTTA
1 A-TTAATTAGGTTAGGGTTTTTA
*
16955765 ATTTAATTAGGTTATGGTTTTTA
1 A-TTAATTAGGTTAGGGTTTTTA
*
16955788 AGT--TTAGGGTTTAGGGTTTTTA
1 ATTAATTA-GG-TTAGGGTTTTTA
16955810 ATTAAATTAGGTTAGGGTTTTTA
1 ATT-AATTAGGTTAGGGTTTTTA
16955833 ATCTAATTAGGTTAGGGTTTTTA
1 AT-TAATTAGGTTAGGGTTTTTA
*
16955856 AGT--TTAGG--A---TTTTTA
1 ATTAATTAGGTTAGGGTTTTTA
*
16955871 ATTAAATTAAGTTAGGGTTTTTA
1 ATT-AATTAGGTTAGGGTTTTTA
* *
16955894 AGT--TTAGGGTTTAGGATTTTTA
1 ATTAATTA-GG-TTAGGGTTTTTA
16955916 ATTAAGTTAGGTTAGGGTTTTTA
1 ATTAA-TTAGGTTAGGGTTTTTA
16955939 ATTTAATTAGGTTAGGGTTTTTA
1 A-TTAATTAGGTTAGGGTTTTTA
16955962 ATT
1 ATT
16955965 TAAGGGTATT
Statistics
Matches: 456, Mismatches: 39, Indels: 93
0.78 0.07 0.16
Matches are distributed among these distances:
15 8 0.02
18 5 0.01
20 15 0.03
21 14 0.03
22 99 0.22
23 264 0.58
24 34 0.07
25 17 0.04
ACGTcount: A:0.26, C:0.01, G:0.24, T:0.49
Consensus pattern (22 bp):
ATTAATTAGGTTAGGGTTTTTA
Found at i:16955510 original size:68 final size:68
Alignment explanation
Indices: 16955402--16955967 Score: 513
Period size: 68 Copynumber: 8.4 Consensus size: 68
16955392 AGTAAAATTA
* * * *
16955402 TTAATTTAGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTAGGGTTTACGGTTTT
1 TTAAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTTAGGG-TTAGGGTTTT
16955467 TAA-
65 TAAG
**
16955470 TTAAATTAGGTTAGAATTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAATTA-GGTTAGGGTT
1 TTAAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAG-T--TTAGGGTTAGGGTT
16955534 TTTAAG
63 TTTAAG
* * * *
16955540 TTAAGA--GGGTTAGGGTTTTTAAGTTT-A--GGGTTTAAGGTTTTTAATTAAATTA-GGTTAGG
1 TTAA-ATTAGGTTAGGGTTTTTAA-TTTAATTAGG-TTAGGGTTTTTAAGT---TTAGGGTTA-G
16955599 GGTTTTTAAG
59 GGTTTTTAAG
* * *
16955609 TT---TAAGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAA-TTTAATTAGGTTAGGGT
1 TTAAATTAGG-TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTT-A--GGGTTAGGGT
16955670 TTTTAAG
62 TTTTAAG
* ** *
16955677 TT-AATTAGGTTAGGGTTTTTAAGTTAA-GGGGTTAGGGTTTTTAAGTTTAGGGTTTAGGGTTCT
1 TTAAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTTAGGG-TTAGGGTTTT
16955740 TAA-
65 TAAG
* *
16955743 TTTAATTAGGTTAGGGTTTTTAATTTAATTAGGTTATGGTTTTTAAGTTTAGGGTTTAGGGTTTT
1 TTAAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTTAGGG-TTAGGGTTTT
16955808 TAA-
65 TAAG
*
16955811 TTAAATTAGGTTAGGGTTTTTAATCTAATTAGGTTAGGGTTTTTAAGTTTA-GG--A---TTTTT
1 TTAAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTTAGGGTTAGGGTTTTT
16955870 AA-
66 AAG
* * * *
16955872 TTAAATTAAGTTAGGGTTTTTAAGTTT-A--GGGTTTAGGATTTTTAA-TTAAGTTAGGTTAGGG
1 TTAAATTAGGTTAGGGTTTTTAA-TTTAATTAGG-TTAGGGTTTTTAAGTTTAG---GGTTAGGG
16955933 TTTTTAA-
61 TTTTTAAG
*
16955940 TTTAATTAGGTTAGGGTTTTTAATTTAA
1 TTAAATTAGGTTAGGGTTTTTAATTTAA
16955968 GGGTATTAAA
Statistics
Matches: 423, Mismatches: 38, Indels: 74
0.79 0.07 0.14
Matches are distributed among these distances:
59 5 0.01
60 12 0.03
61 30 0.07
62 2 0.00
63 2 0.00
64 1 0.00
65 3 0.01
66 5 0.01
67 48 0.11
68 220 0.52
69 76 0.18
70 15 0.04
71 4 0.01
ACGTcount: A:0.26, C:0.01, G:0.24, T:0.49
Consensus pattern (68 bp):
TTAAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTTAGGGTTAGGGTTTTT
AAG
Found at i:16955512 original size:91 final size:89
Alignment explanation
Indices: 16955402--16955964 Score: 588
Period size: 91 Copynumber: 6.3 Consensus size: 89
16955392 AGTAAAATTA
* *
16955402 TTAATTTAGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTAGGGTTTACGGTTTT
1 TTAA-TTAGGTTAGGGTTTTTAATT-AATTAGGTTAGGGTTTTTAAGTTTAGGGTTTAGGGTTTT
**
16955467 TAATTAAATTAGGTTAGAATTTTTAAT
64 TAATT-AATTAGGTTAGGGTTTTTAAT
* *
16955494 TTAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTAAGAGGGTTAGGGTTTT
1 TTAATTAGGTTAGGGTTTTTAA-TTAATTAGGTTAGGGTTTTTAAGTTTAG-GGTTTAGGGTTTT
* *
16955559 TAAGT--TTAGGGTTTAAGGTTTTTAAT
64 TAATTAATTA-GG-TTAGGGTTTTTAAT
* * *
16955585 TAAATTAGGTTAGGGGTTTTTAAGTT--TAAGGTTTAGGGTTTTTAATTAAATTA-GG-TTAGGG
1 TTAATTAGGTTA-GGGTTTTTAA-TTAATTAGG-TTAGGGTTTTTAAGT---TTAGGGTTTAGGG
*
16955646 TTTTTAATTTAATTAGGTTAGGGTTTTTAAG
60 TTTTTAA-TTAATTAGGTTAGGGTTTTTAAT
** *
16955677 TTAATTAGGTTAGGGTTTTTAAGTTAA-GGGGTTAGGGTTTTTAAGTTTAGGGTTTAGGGTTCTT
1 TTAATTAGGTTAGGGTTTTTAA-TTAATTAGGTTAGGGTTTTTAAGTTTAGGGTTTAGGGTTTTT
16955741 AATTTAATTAGGTTAGGGTTTTTAAT
65 AA-TTAATTAGGTTAGGGTTTTTAAT
* * *
16955767 TTAATTAGGTTATGGTTTTTAAGT--TTAGGGTTTAGGGTTTTTAATTAAATTA-GG-TTAGGGT
1 TTAATTAGGTTAGGGTTTTTAATTAATTA-GG-TTAGGGTTTTTAAGT---TTAGGGTTTAGGGT
16955828 TTTTAATCTAATTAGGTTAGGGTTTTTAA-
61 TTTTAAT-TAATTAGGTTAGGGTTTTTAAT
* * *
16955857 GT--TTAGG--A---TTTTTAATTAAATTAAGTTAGGGTTTTTAAGTTTAGGGTTTAGGATTTTT
1 TTAATTAGGTTAGGGTTTTTAATT-AATTAGGTTAGGGTTTTTAAGTTTAGGGTTTAGGGTTTTT
16955915 AATTAAGTTAGGTTAGGGTTTTTAAT
65 AATTAA-TTAGGTTAGGGTTTTTAAT
16955941 TTAATTAGGTTAGGGTTTTTAATT
1 TTAATTAGGTTAGGGTTTTTAATT
16955965 TAAGGGTATT
Statistics
Matches: 401, Mismatches: 33, Indels: 75
0.79 0.06 0.15
Matches are distributed among these distances:
81 3 0.01
82 5 0.01
83 39 0.10
84 15 0.04
85 1 0.00
86 9 0.02
88 9 0.02
89 8 0.02
90 78 0.19
91 160 0.40
92 64 0.16
93 5 0.01
94 5 0.01
ACGTcount: A:0.26, C:0.01, G:0.24, T:0.49
Consensus pattern (89 bp):
TTAATTAGGTTAGGGTTTTTAATTAATTAGGTTAGGGTTTTTAAGTTTAGGGTTTAGGGTTTTTA
ATTAATTAGGTTAGGGTTTTTAAT
Found at i:16955863 original size:38 final size:38
Alignment explanation
Indices: 16955821--16955905 Score: 136
Period size: 38 Copynumber: 2.2 Consensus size: 38
16955811 TTAAATTAGG
*
16955821 TTAGGGTTTTTAATCT-AATTAGGTTAGGGTTTTTAAGT
1 TTAGGGTTTTTAAT-TAAATTAAGTTAGGGTTTTTAAGT
*
16955859 TTAGGATTTTTAATTAAATTAAGTTAGGGTTTTTAAGT
1 TTAGGGTTTTTAATTAAATTAAGTTAGGGTTTTTAAGT
16955897 TTAGGGTTT
1 TTAGGGTTT
16955906 AGGATTTTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
37 1 0.02
38 42 0.98
ACGTcount: A:0.26, C:0.01, G:0.22, T:0.51
Consensus pattern (38 bp):
TTAGGGTTTTTAATTAAATTAAGTTAGGGTTTTTAAGT
Found at i:16955896 original size:14 final size:15
Alignment explanation
Indices: 16955877--16955905 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16955867 TTTAATTAAA
16955877 TTAAG-TTAGGGTTT
1 TTAAGTTTAGGGTTT
16955891 TTAAGTTTAGGGTTT
1 TTAAGTTTAGGGTTT
16955906 AGGATTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.21, C:0.00, G:0.28, T:0.52
Consensus pattern (15 bp):
TTAAGTTTAGGGTTT
Found at i:16956060 original size:20 final size:22
Alignment explanation
Indices: 16956013--16956060 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 22
16956003 CAAAAATTTC
16956013 TATTTTATTACATCAAATAAACTTA
1 TATTTTATTACATCAAAT-AA--TA
16956038 TATTTTATTACATCAAATAATA
1 TATTTTATTACATCAAATAATA
16956060 T
1 T
16956061 CAAAATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 3 0.13
24 2 0.09
25 18 0.78
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (22 bp):
TATTTTATTACATCAAATAATA
Found at i:16956513 original size:18 final size:18
Alignment explanation
Indices: 16956490--16956525 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
16956480 TAGAAAATGG
*
16956490 TACATATAAGGGTTAGGA
1 TACATATAAGGGCTAGGA
16956508 TACATATAAGGGCTAGGA
1 TACATATAAGGGCTAGGA
16956526 AACGCACCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.08, G:0.28, T:0.25
Consensus pattern (18 bp):
TACATATAAGGGCTAGGA
Found at i:16957186 original size:7 final size:7
Alignment explanation
Indices: 16957176--16957201 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
16957166 TTATATACAT
16957176 AATACTA
1 AATACTA
16957183 AATACTA
1 AATACTA
16957190 AATACTA
1 AATACTA
16957197 AATAC
1 AATAC
16957202 CAATCGACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:16957408 original size:20 final size:21
Alignment explanation
Indices: 16957366--16957408 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
16957356 ATACTTTTAT
*
16957366 TTTTAAAAATCTACATAATAA
1 TTTTAAAAATCTACATAAAAA
16957387 TTTT-AAAATCTA-ATATAAAA
1 TTTTAAAAATCTACATA-AAAA
16957407 TT
1 TT
16957409 CACCTCATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 3 0.15
20 13 0.65
21 4 0.20
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (21 bp):
TTTTAAAAATCTACATAAAAA
Found at i:16958326 original size:12 final size:12
Alignment explanation
Indices: 16958302--16958344 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 12
16958292 ATTTTTACGG
16958302 TTTAAAAAA-AT
1 TTTAAAAAATAT
16958313 TTTAAAAAATAT
1 TTTAAAAAATAT
* *
16958325 TTTTAAAATTA-
1 TTTAAAAAATAT
16958336 TTTAAAAAA
1 TTTAAAAAA
16958345 AGGGAGTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TTTAAAAAATAT
Found at i:16958367 original size:11 final size:11
Alignment explanation
Indices: 16958351--16958392 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
16958341 AAAAAGGGAG
16958351 TTAAGAGAAAC
1 TTAAGAGAAAC
*
16958362 TTAAGAGGAAC
1 TTAAGAGAAAC
*
16958373 TTAAGAGTAAC
1 TTAAGAGAAAC
16958384 TTAAGAGAA
1 TTAAGAGAA
16958393 TTTTTGAAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.50, C:0.07, G:0.21, T:0.21
Consensus pattern (11 bp):
TTAAGAGAAAC
Found at i:16967185 original size:23 final size:22
Alignment explanation
Indices: 16967116--16967201 Score: 95
Period size: 23 Copynumber: 3.9 Consensus size: 22
16967106 CCTGATCAAT
16967116 ATACGACACAT-AAGTGCCTGA
1 ATACGACACATAAAGTGCCTGA
** * **
16967137 A-ACGACACACGAGGTGTTTGGA
1 ATACGACACATAAAGTGCCT-GA
16967159 ATACGACACATAAAGTGCCTGA
1 ATACGACACATAAAGTGCCTGA
16967181 TATACGACACATAAAGTGCCT
1 -ATACGACACATAAAGTGCCT
16967202 AATCAGCAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
20 8 0.15
21 6 0.12
22 5 0.10
23 33 0.63
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.20
Consensus pattern (22 bp):
ATACGACACATAAAGTGCCTGA
Found at i:16968166 original size:13 final size:13
Alignment explanation
Indices: 16968125--16968166 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
16968115 CTACGAAAAT
*
16968125 AATAATAATTTAC
1 AATATTAATTTAC
*
16968138 AGTATTAA-TTAC
1 AATATTAATTTAC
*
16968150 AATATTAATTTAT
1 AATATTAATTTAC
16968163 AATA
1 AATA
16968167 ATAGAATTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (13 bp):
AATATTAATTTAC
Found at i:16968598 original size:5 final size:6
Alignment explanation
Indices: 16968583--16968607 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
16968573 CAAACCTTAG
16968583 TTTTTC TTTTTC TTTTTC TTTTTC T
1 TTTTTC TTTTTC TTTTTC TTTTTC T
16968608 CCTTTCTCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTC
Found at i:16970709 original size:15 final size:14
Alignment explanation
Indices: 16970665--16970699 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
16970655 GTTGCTTTTG
* *
16970665 AAAATTGTTATAAA
1 AAAAGTGTTGTAAA
16970679 AAAAGTGTTGTAAA
1 AAAAGTGTTGTAAA
16970693 AAAAGTG
1 AAAAGTG
16970700 CTTTTGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (14 bp):
AAAAGTGTTGTAAA
Found at i:16982614 original size:18 final size:16
Alignment explanation
Indices: 16982587--16982622 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 16
16982577 ATTAAAATAA
16982587 TATTTAATAATAGTTAT
1 TATTTAATAATAG-TAT
16982604 TATTATAATAATAGTAT
1 TATT-TAATAATAGTAT
16982621 TA
1 TA
16982623 ATGTGATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (16 bp):
TATTTAATAATAGTAT
Found at i:16983822 original size:22 final size:20
Alignment explanation
Indices: 16983790--16983834 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 20
16983780 GATGATATTT
*
16983790 TTAATTATTTTTATTTTTAA
1 TTAATTATTTTTACTTTTAA
16983810 TTAATGTACTTTTTACTTTTAA
1 TTAAT-TA-TTTTTACTTTTAA
16983832 TTA
1 TTA
16983835 TTTTTATAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.23
21 2 0.09
22 15 0.68
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.64
Consensus pattern (20 bp):
TTAATTATTTTTACTTTTAA
Found at i:16988458 original size:16 final size:17
Alignment explanation
Indices: 16988430--16988461 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
16988420 GACATTATTT
16988430 ATTAAATTAATTTTCTA
1 ATTAAATTAATTTTCTA
16988447 ATTAAA-TAATTTTCT
1 ATTAAATTAATTTTCT
16988462 CAACTCAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTAAATTAATTTTCTA
Found at i:16991589 original size:13 final size:14
Alignment explanation
Indices: 16991573--16991602 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
16991563 AAAAAAGAAC
16991573 AAAAAA-TAATAAA
1 AAAAAATTAATAAA
16991586 AAAAAATTAATAAA
1 AAAAAATTAATAAA
16991600 AAA
1 AAA
16991603 TAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (14 bp):
AAAAAATTAATAAA
Found at i:16993301 original size:174 final size:174
Alignment explanation
Indices: 16992965--16993520 Score: 747
Period size: 174 Copynumber: 3.2 Consensus size: 174
16992955 ATCTACTCCT
* * * * *
16992965 CTGCAACTTCAGG-GAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATC
1 CTGCAACTTCAGGAGA-ATAAGACTTGCTGCGATCTACTCTCTGCAACTTCAAAGAGATAAAATC
** * * * * * *
16993029 CAAAATTTGTGGTTCCAATCCGCTCCATTGCAACTTCAAGG-AGATAGGATTATTGGTTTTAATC
65 C-AAGGTT-T--TT--AATCCACTTCACTGCAACTTC-AGGAAGATAGGATTATCGGCTTTAACC
* *
16993093 TGCTCCACTGCAACTTCATGGAGATAAGATTTGCCATCTTCAATCTGCCTCA
123 TGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCA
*
16993145 CTGCAACTTCAGGAGAATAAGACTTGCTGCGATCTACTCTTTGCAACTTCAAAGAGATAAAATCC
1 CTGCAACTTCAGGAGAATAAGACTTGCTGCGATCTACTCTCTGCAACTTCAAAGAGATAAAATCC
* * *
16993210 AAGGTTTTTAATCTATTTCACTGCAACTTCAGGAAGATAGGATTATCGACTTTAACCTGCTCCAC
66 AAGGTTTTTAATCCACTTCACTGCAACTTCAGGAAGATAGGATTATCGGCTTTAACCTGCTCCAC
* *
16993275 TGCAACTTCGGGGAGATAAGATTTGCCATCTTCAGTCTGACTCA
131 TGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCA
* * * * * *
16993319 CTGCAACTTTAGGAGAATAAGACTTGCTGCGATCTGCTCTCTGTAACTTCAGAGAGATAAGATTC
1 CTGCAACTTCAGGAGAATAAGACTTGCTGCGATCTACTCTCTGCAACTTCAAAGAGATAAAATCC
* *
16993384 AAGGTTTTTAATCCACTTCACTGCAACTTCAGGAAGATAGGGTTATCGGCTTTAACCTACTCCAC
66 AAGGTTTTTAATCCACTTCACTGCAACTTCAGGAAGATAGGATTATCGGCTTTAACCTGCTCCAC
*
16993449 TGCAACTTCAGGGAGATAAGATTTGTCATCTTCAGTCTGCCTCA
131 TGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCA
*
16993493 CTGCAACTTCAGGAAAATAAGACTTGCT
1 CTGCAACTTCAGGAGAATAAGACTTGCT
16993521 TGCTTAGTCT
Statistics
Matches: 336, Mismatches: 38, Indels: 10
0.88 0.10 0.03
Matches are distributed among these distances:
173 3 0.01
174 268 0.80
176 2 0.01
178 1 0.00
179 4 0.01
180 56 0.17
181 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (174 bp):
CTGCAACTTCAGGAGAATAAGACTTGCTGCGATCTACTCTCTGCAACTTCAAAGAGATAAAATCC
AAGGTTTTTAATCCACTTCACTGCAACTTCAGGAAGATAGGATTATCGGCTTTAACCTGCTCCAC
TGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCA
Found at i:16993320 original size:89 final size:88
Alignment explanation
Indices: 16993057--16993558 Score: 309
Period size: 89 Copynumber: 5.7 Consensus size: 88
16993047 TCCGCTCCAT
* * * *
16993057 TGCAACTTCAAGG-AGATAGGATTATTGGTTTTAATCTGCTCCACTGCAACTTCATGGAGATAAG
1 TGCAACTTC-AGGAAGATAGGATTA-TCGCTTTAACCTGCTCCACTGCAACTTCAGGGAGATAAG
* *
16993121 ATTTGCCATCTTCAATCTGCCTCAC
64 ATTTGCCATCTTCAGTCTGACTCAC
* * *** * * ** **
16993146 TGCAACTTCAGG-AGAATAAGACT-T-GCTGCGATCTACT-CTTTGCAACTTCAAAGAGATAA-A
1 TGCAACTTCAGGAAG-ATAGGATTATCGCTTTAACCTGCTCCACTGCAACTTCAGGGAGATAAGA
* * * * *
16993206 -AT-CCAAGGTTTTTAATCT-ATTTCAC
65 TTTGCC-A--TCTTCAGTCTGA-CTCAC
*
16993231 TGCAACTTCAGGAAGATAGGATTATCGACTTTAACCTGCTCCACTGCAACTTCGGGGAGATAAGA
1 TGCAACTTCAGGAAGATAGGATTATCG-CTTTAACCTGCTCCACTGCAACTTCAGGGAGATAAGA
16993296 TTTGCCATCTTCAGTCTGACTCAC
65 TTTGCCATCTTCAGTCTGACTCAC
* * * *** * * * *
16993320 TGCAACTTTAGG-AGAATAAGACT-T-GCTGCGATCTGCT-CTCTGTAACTTCAGAGAGATAAGA
1 TGCAACTTCAGGAAG-ATAGGATTATCGCTTTAACCTGCTCCACTGCAACTTCAGGGAGATAAGA
* * * * *
16993381 -TT-CAAGGTTTTTAATC-CACTTCAC
65 TTTGCCA--TCTTCAGTCTGAC-TCAC
* *
16993405 TGCAACTTCAGGAAGATAGGGTTATCGGCTTTAACCTACTCCACTGCAACTTCAGGGAGATAAGA
1 TGCAACTTCAGGAAGATAGGATTATC-GCTTTAACCTGCTCCACTGCAACTTCAGGGAGATAAGA
* *
16993470 TTTGTCATCTTCAGTCTGCCTCAC
65 TTTGCCATCTTCAGTCTGACTCAC
* * * * ** *
16993494 TGCAACTTCAGGAAAATAAGACTTGCTTGC-TTAGTCTGCTCCACTGCAACTTCAGGGAGACAAG
1 TGCAACTTCAGGAAGATAGGA-TT-ATCGCTTTAACCTGCTCCACTGCAACTTCAGGGAGATAAG
16993558 A
64 A
16993559 CTAGATGCGA
Statistics
Matches: 308, Mismatches: 77, Indels: 56
0.70 0.17 0.13
Matches are distributed among these distances:
82 2 0.01
83 4 0.01
84 5 0.02
85 94 0.31
86 22 0.07
87 3 0.01
88 23 0.07
89 140 0.45
90 9 0.03
91 4 0.01
92 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.30
Consensus pattern (88 bp):
TGCAACTTCAGGAAGATAGGATTATCGCTTTAACCTGCTCCACTGCAACTTCAGGGAGATAAGAT
TTGCCATCTTCAGTCTGACTCAC
Found at i:16993498 original size:45 final size:44
Alignment explanation
Indices: 16993443--16993639 Score: 167
Period size: 44 Copynumber: 4.5 Consensus size: 44
16993433 CTTTAACCTA
*
16993443 CTCCACTGCAACTTCAGGGAGATAAGATTTGTCAT-CTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTG-CATGCTT-AGTCTG
* * *
16993488 C-CTCACTGCAACTTCAGGAAAATAAGACTTGCTTGCTTAGTCTG
1 CTC-CACTGCAACTTCAGGGAGATAAGACTTGCATGCTTAGTCTG
* * *
16993532 CTCCACTGCAACTTCAGGGAGACAAGACTAG-ATGC-GA-TCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCATGCTTAGTCTG
* * * * **
16993573 CT-CTCTGCAACTTCAGAGAGATAAGATCTGTG-AT-TTTAATCCA
1 CTCCACTGCAACTTCAGGGAGATAAGA-CT-TGCATGCTTAGTCTG
*
16993616 CTCCACTGCAACTTCAGGAAGATA
1 CTCCACTGCAACTTCAGGGAGATA
16993640 GGATTATCGG
Statistics
Matches: 123, Mismatches: 21, Indels: 17
0.76 0.13 0.11
Matches are distributed among these distances:
40 21 0.17
41 8 0.07
42 5 0.04
43 7 0.06
44 52 0.42
45 30 0.24
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.27
Consensus pattern (44 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTTGCATGCTTAGTCTG
Found at i:16993559 original size:44 final size:45
Alignment explanation
Indices: 16993266--16993560 Score: 152
Period size: 45 Copynumber: 6.7 Consensus size: 45
16993256 CGACTTTAAC
* * *
16993266 CTGCTCCACTGCAACTTCGGGGAGATAAGATTTGCCATCTTCAGT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTCATCTTCAGT
* *
16993311 CTGACT-CACTGCAACTTTA-GGAGAATAAGACTTG----CTGC-GAT
1 CTG-CTCCACTGCAACTTCAGGGAG-ATAAGACTTGTCATCTTCAG-T
* * * * * *
16993352 CTGCT-CTCTGTAACTTCAGAGAGATAAGA--T-TCAAGGTTTTTAAT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTC-A--TCTTCAGT
** * * ** * ** * **
16993396 CCACTTCACTGCAACTTCAGGAAGAT-AGGGTTATCGGCTTTAAC
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTCATCTTCAGT
* *
16993440 CTACTCCACTGCAACTTCAGGGAGATAAGATTTGTCATCTTCAGT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTCATCTTCAGT
* * *
16993485 CTGC-CTCACTGCAACTTCAGGAAAATAAGACTTG-CTTGCTT-AGT
1 CTGCTC-CACTGCAACTTCAGGGAGATAAGACTTGTCAT-CTTCAGT
*
16993529 CTGCTCCACTGCAACTTCAGGGAGACAAGACT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACT
16993561 AGATGCGATC
Statistics
Matches: 188, Mismatches: 42, Indels: 41
0.69 0.15 0.15
Matches are distributed among these distances:
38 1 0.01
40 19 0.10
41 10 0.05
44 72 0.38
45 81 0.43
46 3 0.02
47 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (45 bp):
CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTCATCTTCAGT
Found at i:17005995 original size:12 final size:12
Alignment explanation
Indices: 17005980--17006012 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
17005970 TATAAAAAAG
17005980 AATAAAAATAA-T
1 AATAAAAA-AATT
17005992 AATAAAAAAATT
1 AATAAAAAAATT
17006004 AATAAAAAA
1 AATAAAAAA
17006013 TAAAGAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 2 0.10
12 18 0.90
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (12 bp):
AATAAAAAAATT
Found at i:17006014 original size:22 final size:22
Alignment explanation
Indices: 17005963--17006015 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
17005953 AATAAATACG
17005963 AAAAATATATAAAAAAGAATAAA
1 AAAAATA-ATAAAAAAGAATAAA
* *
17005986 AATAATAATAAAAAA-ATTAATA
1 AAAAATAATAAAAAAGAATAA-A
17006008 AAAAATAA
1 AAAAATAA
17006016 AGAAAAGGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 4 0.15
22 16 0.62
23 6 0.23
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (22 bp):
AAAAATAATAAAAAAGAATAAA
Found at i:17008117 original size:18 final size:16
Alignment explanation
Indices: 17008094--17008127 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
17008084 ACTGAAATTT
17008094 TTTAAAATGTAGATAAAA
1 TTTAAAA-GTA-ATAAAA
17008112 TTTAAAAGTAATAAAA
1 TTTAAAAGTAATAAAA
17008128 AATTTTAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 3 0.19
18 7 0.44
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.32
Consensus pattern (16 bp):
TTTAAAAGTAATAAAA
Found at i:17010612 original size:24 final size:23
Alignment explanation
Indices: 17010585--17010640 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
17010575 AAATATTATC
* *
17010585 AAATATAATAGTAATAACGATAAT
1 AAATATAATA-TAAAAACAATAAT
*
17010609 AAATAGTAATATAAAAATAATAAT
1 AAATA-TAATATAAAAACAATAAT
17010633 AAAT-TAAT
1 AAATATAAT
17010641 TAATAGCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 4 0.14
24 19 0.68
25 5 0.18
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.30
Consensus pattern (23 bp):
AAATATAATATAAAAACAATAAT
Found at i:17013918 original size:25 final size:26
Alignment explanation
Indices: 17013888--17013948 Score: 90
Period size: 24 Copynumber: 2.4 Consensus size: 26
17013878 CTGTTGTTGA
*
17013888 AGTTTTCAATTGAAATTGGTTTCTGT
1 AGTTTTCAATTGAAAATGGTTTCTGT
*
17013914 ATTTTTC--TTGAAAATGGTTTCTGT
1 AGTTTTCAATTGAAAATGGTTTCTGT
17013938 AGTTTTCAATT
1 AGTTTTCAATT
17013949 TGTGAGTGCT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 22 0.73
26 8 0.27
ACGTcount: A:0.23, C:0.08, G:0.16, T:0.52
Consensus pattern (26 bp):
AGTTTTCAATTGAAAATGGTTTCTGT
Found at i:17014986 original size:24 final size:24
Alignment explanation
Indices: 17014954--17015002 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
17014944 TTATAATTTG
*
17014954 AACCTAAATCACATTTGAGGTGAT
1 AACCCAAATCACATTTGAGGTGAT
17014978 AACCCAAATCACATTTGAGGTGAT
1 AACCCAAATCACATTTGAGGTGAT
17015002 A
1 A
17015003 GATACTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (24 bp):
AACCCAAATCACATTTGAGGTGAT
Found at i:17015637 original size:45 final size:44
Alignment explanation
Indices: 17015548--17015640 Score: 134
Period size: 45 Copynumber: 2.1 Consensus size: 44
17015538 ATTACAACAT
*
17015548 CATTCCATTCAACCAAACACAAGAATACTATTACGCCTCTATTC
1 CATTCCATTCAACCAAACACAAGAATACTATTACGCATCTATTC
* *
17015592 CATTCCATTCAACCAAACA-ATTGGATTACTATTACGCATCTATTC
1 CATTCCATTCAACCAAACACA--AGAATACTATTACGCATCTATTC
17015637 CATT
1 CATT
17015641 ACAGCTCTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 19 0.43
45 24 0.55
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.31
Consensus pattern (44 bp):
CATTCCATTCAACCAAACACAAGAATACTATTACGCATCTATTC
Found at i:17015649 original size:16 final size:16
Alignment explanation
Indices: 17015630--17015672 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
17015620 CTATTACGCA
*
17015630 TCTATTCCATTACAGC
1 TCTATTCCATTACACC
17015646 TCTATTCCATTACACC
1 TCTATTCCATTACACC
17015662 TCTATTCCATT
1 TCTATTCCATT
17015673 TCATTCAACC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.23, C:0.33, G:0.02, T:0.42
Consensus pattern (16 bp):
TCTATTCCATTACACC
Found at i:17015736 original size:16 final size:16
Alignment explanation
Indices: 17015715--17015752 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
17015705 TTTGGTTCGC
17015715 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
17015731 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
*
17015747 CGTAAT
1 TGTAAT
17015753 AGTAATTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.37, C:0.03, G:0.34, T:0.26
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:17015798 original size:45 final size:43
Alignment explanation
Indices: 17015734--17015826 Score: 143
Period size: 45 Copynumber: 2.1 Consensus size: 43
17015724 ATAGAGGTGT
17015734 AATGGAATAGAGGCGTAATAGTAATTCAATTG-TTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGT-ATTC--TTGATTTGGTTGAATGG
17015779 AATGGAATAGAGGCGTAATAGTATTCTTGTATTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGTATTCTTG-ATTTGGTTGAATGG
17015823 AATG
1 AATG
17015827 ATGTTGTAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
42 3 0.07
44 21 0.46
45 22 0.48
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.34
Consensus pattern (43 bp):
AATGGAATAGAGGCGTAATAGTATTCTTGATTTGGTTGAATGG
Found at i:17016119 original size:102 final size:102
Alignment explanation
Indices: 17016003--17016222 Score: 386
Period size: 102 Copynumber: 2.2 Consensus size: 102
17015993 TAATAAAAAT
* *
17016003 ATATAATTTGATAAAATTCTTAATATGAAATATTCTTATATGAATTTACTAAAATCAAAATATAT
1 ATATAATTTAATAAAATTCTTAATATGAAATATTCTTATATGAATTTAATAAAATCAAAATATAT
* *
17016068 AATAGTATAAAATATAATTTAAAATAATTATTATTAA
66 AATACTATAAAATATAATCTAAAATAATTATTATTAA
* *
17016105 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTAATAAAATCATAATATAT
1 ATATAATTTAATAAAATTCTTAATATGAAATATTCTTATATGAATTTAATAAAATCAAAATATAT
17016170 AATACTATAAAATATAATCTAAAATAATTATTATTAA
66 AATACTATAAAATATAATCTAAAATAATTATTATTAA
17016207 ATATAATTTAATAAAA
1 ATATAATTTAATAAAA
17016223 ATATATAATT
Statistics
Matches: 112, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
102 112 1.00
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.41
Consensus pattern (102 bp):
ATATAATTTAATAAAATTCTTAATATGAAATATTCTTATATGAATTTAATAAAATCAAAATATAT
AATACTATAAAATATAATCTAAAATAATTATTATTAA
Found at i:17016226 original size:59 final size:59
Alignment explanation
Indices: 17016163--17016351 Score: 217
Period size: 59 Copynumber: 3.2 Consensus size: 59
17016153 ATAAAATCAT
17016163 AATATATAATACTATAAAATATAATCTAAAATAATTATTATTAAATATAATTTAATAAA
1 AATATATAATACTATAAAATATAATCTAAAATAATTATTATTAAATATAATTTAATAAA
* * * * * * *
17016222 AATATATAAT-TTAATAAAAT-T-CT-TAATATTAAATATTCTTAAAT-GAATTTACTAAAATCA
1 AATATATAATACT-ATAAAATATAATCTAA-AATAATTATTATTAAATATAATTTA--ATAA--A
17016282 TAATATATAATACTATAAAATATAATCTAAAATAATTATTATTAAATATAATTTAATAAA
1 -AATATATAATACTATAAAATATAATCTAAAATAATTATTATTAAATATAATTTAATAAA
17016342 AATATATAAT
1 AATATATAAT
17016352 TTAATAAAAT
Statistics
Matches: 104, Mismatches: 14, Indels: 24
0.73 0.10 0.17
Matches are distributed among these distances:
56 9 0.09
57 15 0.14
58 5 0.05
59 27 0.26
60 2 0.02
61 17 0.16
62 5 0.05
63 15 0.14
64 9 0.09
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (59 bp):
AATATATAATACTATAAAATATAATCTAAAATAATTATTATTAAATATAATTTAATAAA
Found at i:17016229 original size:120 final size:120
Alignment explanation
Indices: 17016105--17016425 Score: 592
Period size: 120 Copynumber: 2.7 Consensus size: 120
17016095 TTATTATTAA
*
17016105 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTAATAAAATCATAATATAT
1 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATAT
17016170 AATACTATAAAATATAATCTAAAATAATTATTATTAAATATAATTTAATAAAAAT
66 AATACTATAAAATATAATCTAAAATAATTATTATTAAATATAATTTAATAAAAAT
*
17016225 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTAAATGAATTTACTAAAATCATAATATAT
1 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATAT
17016290 AATACTATAAAATATAATCTAAAATAATTATTATTAAATATAATTTAATAAAAAT
66 AATACTATAAAATATAATCTAAAATAATTATTATTAAATATAATTTAATAAAAAT
* *
17016345 ATATAATTTAATAAAATTCTTAATA-TAATTATTCTTATATGAATTTACTAAAATAATAATATAT
1 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATAT
17016409 AATACTATAAAA-ATAAT
66 AATACTATAAAATATAAT
17016426 ATATAATCTA
Statistics
Matches: 196, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
118 5 0.03
119 48 0.24
120 143 0.73
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.41
Consensus pattern (120 bp):
ATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATAT
AATACTATAAAATATAATCTAAAATAATTATTATTAAATATAATTTAATAAAAAT
Found at i:17016415 original size:21 final size:21
Alignment explanation
Indices: 17016390--17016432 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
17016380 TATATGAATT
17016390 TACTA-AAATAATAATATATAA
1 TACTATAAA-AATAATATATAA
17016411 TACTATAAAAATAATATATAA
1 TACTATAAAAATAATATATAA
17016432 T
1 T
17016433 CTACTTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (21 bp):
TACTATAAAAATAATATATAA
Found at i:17016437 original size:23 final size:22
Alignment explanation
Indices: 17016380--17016437 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 22
17016370 TAATTATTCT
17016380 TATATGAATTTACTAAAATAATAA
1 TATAT-AA-TTACTAAAATAATAA
17016404 TATATAA-TACTATAAA-AATAA
1 TATATAATTACTA-AAATAATAA
17016425 TATATAATCTACT
1 TATATAAT-TACT
17016438 TTATAATGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
21 17 0.55
22 3 0.10
23 6 0.19
24 5 0.16
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.38
Consensus pattern (22 bp):
TATATAATTACTAAAATAATAA
Found at i:17019649 original size:29 final size:29
Alignment explanation
Indices: 17019607--17019666 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
17019597 AAAAATTACC
17019607 TGAAATATCTATGTCTCCTCTGCAATCAA
1 TGAAATATCTATGTCTCCTCTGCAATCAA
17019636 TGAAATATCTATGTCTCCTCTGCAATCAA
1 TGAAATATCTATGTCTCCTCTGCAATCAA
17019665 TG
1 TG
17019667 GAAAAAAAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (29 bp):
TGAAATATCTATGTCTCCTCTGCAATCAA
Found at i:17019845 original size:14 final size:14
Alignment explanation
Indices: 17019828--17019857 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
17019818 ATTAAGCAGC
17019828 CAATTTTAAGAATA
1 CAATTTTAAGAATA
17019842 CAATTTTAAGAATA
1 CAATTTTAAGAATA
17019856 CA
1 CA
17019858 CTTGTAATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.50, C:0.10, G:0.07, T:0.33
Consensus pattern (14 bp):
CAATTTTAAGAATA
Found at i:17023691 original size:25 final size:25
Alignment explanation
Indices: 17023644--17023694 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
17023634 TTTAATCGAA
**
17023644 TTTTGATTTTGATTTTGGGTTTTTT
1 TTTTGATTTTGATTTTAAGTTTTTT
*
17023669 TTTTGTTTTTGATTTTAA-TTTTTT
1 TTTTGATTTTGATTTTAAGTTTTTT
17023693 TT
1 TT
17023695 GTCAAAGGCG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 8 0.35
25 15 0.65
ACGTcount: A:0.10, C:0.00, G:0.14, T:0.76
Consensus pattern (25 bp):
TTTTGATTTTGATTTTAAGTTTTTT
Found at i:17040669 original size:16 final size:16
Alignment explanation
Indices: 17040648--17040680 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
17040638 TTCGCTATAT
17040648 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
17040664 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
17040680 T
1 T
17040681 AGCAAATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.06, G:0.36, T:0.21
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:17040934 original size:18 final size:17
Alignment explanation
Indices: 17040913--17041067 Score: 56
Period size: 18 Copynumber: 9.0 Consensus size: 17
17040903 TTATTATTAA
*
17040913 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
17040931 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
* ***
17040948 -TCTTAATATTAAATATTCTT
1 AT-ATAAT-TT-AATA-AAAT
17040968 ATATGAATTTAATAAAAT
1 ATAT-AATTTAATAAAAT
* * *
17040986 -CATAATAT-ATAATACT
1 ATATAATTTAATAA-AAT
* *
17041002 ATAAAATATAATCTAAAAT
1 ATATAATTTAA--TAAAAT
* *
17041021 A-ATTA-TT-ATTAAAT
1 ATATAATTTAATAAAAT
17041035 A--TAATTTAATAAAAAT
1 ATATAATTTAAT-AAAAT
17041051 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
17041068 TCTTAATATT
Statistics
Matches: 100, Mismatches: 21, Indels: 33
0.65 0.14 0.21
Matches are distributed among these distances:
13 2 0.02
14 8 0.08
15 6 0.06
16 13 0.13
17 24 0.24
18 25 0.25
19 11 0.11
20 7 0.07
21 4 0.04
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.43
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:17041036 original size:120 final size:120
Alignment explanation
Indices: 17040899--17041264 Score: 669
Period size: 120 Copynumber: 3.0 Consensus size: 120
17040889 ATATTTTAAC
17040899 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATATTAAATAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATATTAAATAT
*
17040964 TCTTATATGAATTTAATAAAATCATAATATATAATACTATAAAATATAATCTAAA
66 TCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATCTAAA
* *
17041019 ATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATATTAAATAT
* * *
17041084 TCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTGAA
66 TCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATCTAAA
*
17041139 ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATATTAAATAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATATTAAATAT
17041204 TCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATCTAAA
66 TCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATCTAAA
17041259 ATAATT
1 ATAATT
17041265 GATTTTGTGG
Statistics
Matches: 234, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
120 234 1.00
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (120 bp):
ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATATTAAATAT
TCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATCTAAA
Found at i:17041174 original size:18 final size:17
Alignment explanation
Indices: 17041151--17041187 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
17041141 AATTATTATT
17041151 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
17041167 AAATATATGATTTAATA
1 AAATATATGATTTAATA
17041184 AAAT
1 AAAT
17041188 TCTTAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:17043015 original size:13 final size:13
Alignment explanation
Indices: 17042999--17043028 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
17042989 TAGACCAAGC
17042999 TTTTCAAAAGCAT
1 TTTTCAAAAGCAT
*
17043012 TTTTCATAAGCAT
1 TTTTCAAAAGCAT
17043025 TTTT
1 TTTT
17043029 TTGCAGCACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.13, G:0.07, T:0.50
Consensus pattern (13 bp):
TTTTCAAAAGCAT
Found at i:17045504 original size:107 final size:107
Alignment explanation
Indices: 17045295--17045590 Score: 308
Period size: 107 Copynumber: 2.8 Consensus size: 107
17045285 ATATTTTGCT
* * * * *
17045295 CTGATGATATACACCATCACGATGGCTGACATCCTACATATGTCT-CGGATTCTCGACAGCTTGT
1 CTGATGAAATAGATCATTACGATGGCTGAGATCCTACATATGT-TGCGGATTCTCGACAGCTTGT
* ** *
17045359 ATGAGCAGCATCGTGAACTGGTGAATAGAATGGCTACTCTATT
65 GTGAGCAGCATCGTGAACTGGTGAATAGAATGAATACTCTATA
* * * * * *
17045402 CTGATGACATAGATCGTTCCGATGGCTGAGATCCTACACATGTTGCAGATTCTCAACAGCTTGTG
1 CTGATGAAATAGATCATTACGATGGCTGAGATCCTACATATGTTGCGGATTCTCGACAGCTTGTG
* * *
17045467 TGAGCAGCATCGTGAATTGGTGAA-ATGAATTAATACTCTGTA
66 TGAGCAGCATCGTGAACTGGTGAATA-GAATGAATACTCTATA
* ** * * * ** *
17045509 CTGATGAAATGGATCATTATAATGACTGAGATCCTGCATACGTTGCGGATTCTCGTTAGCTTTTG
1 CTGATGAAATAGATCATTACGATGGCTGAGATCCTACATATGTTGCGGATTCTCGACAGCTTGTG
*
17045574 TGAGCAGCTTCGTGAAC
66 TGAGCAGCATCGTGAAC
17045591 CGGTCAAGAC
Statistics
Matches: 153, Mismatches: 34, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
106 2 0.01
107 151 0.99
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (107 bp):
CTGATGAAATAGATCATTACGATGGCTGAGATCCTACATATGTTGCGGATTCTCGACAGCTTGTG
TGAGCAGCATCGTGAACTGGTGAATAGAATGAATACTCTATA
Found at i:17058146 original size:9 final size:9
Alignment explanation
Indices: 17058130--17058169 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
17058120 GTTAAACAAC
17058130 TCGAGTTAA
1 TCGAGTTAA
*
17058139 TTGAGTTAA
1 TCGAGTTAA
17058148 TCGAGTTAA
1 TCGAGTTAA
*
17058157 TCGAGTTAT
1 TCGAGTTAA
17058166 TCGA
1 TCGA
17058170 ATCAACTCGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.30, C:0.10, G:0.23, T:0.38
Consensus pattern (9 bp):
TCGAGTTAA
Found at i:17058240 original size:9 final size:9
Alignment explanation
Indices: 17058223--17058259 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
17058213 TGAGTTTTCG
17058223 AATTCGAAT
1 AATTCGAAT
*
17058232 AACTCGAAT
1 AATTCGAAT
17058241 AATTCGAAT
1 AATTCGAAT
17058250 AATTCGAAT
1 AATTCGAAT
17058259 A
1 A
17058260 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:17058505 original size:27 final size:27
Alignment explanation
Indices: 17058472--17058523 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
17058462 AAACTTTTTA
*
17058472 TTTTTCCCCAAAATTTTTACTCCCTAC
1 TTTTTCCCCAAAACTTTTACTCCCTAC
* *
17058499 TTTTTCCCTAAAACTTTTATTCCCT
1 TTTTTCCCCAAAACTTTTACTCCCT
17058524 TCTCACTCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.21, C:0.31, G:0.00, T:0.48
Consensus pattern (27 bp):
TTTTTCCCCAAAACTTTTACTCCCTAC
Found at i:17059294 original size:5 final size:5
Alignment explanation
Indices: 17059284--17059316 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
17059274 AAAATTTTTT
*
17059284 GATTC GATTC GATTC GATTA GATTC GATTC GAT
1 GATTC GATTC GATTC GATTC GATTC GATTC GAT
17059317 CGAATGCTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.39
Consensus pattern (5 bp):
GATTC
Found at i:17060479 original size:17 final size:17
Alignment explanation
Indices: 17060457--17060490 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
17060447 GTGACCATGG
17060457 GTCGTTCGTCTTTGTGA
1 GTCGTTCGTCTTTGTGA
17060474 GTCGTTCGTCTTTGTGA
1 GTCGTTCGTCTTTGTGA
17060491 TGAATGACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.06, C:0.18, G:0.29, T:0.47
Consensus pattern (17 bp):
GTCGTTCGTCTTTGTGA
Found at i:17061086 original size:16 final size:18
Alignment explanation
Indices: 17061060--17061092 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
17061050 TAAAATTAGG
17061060 TTGAGAAAA-TTATTTAA
1 TTGAGAAAATTTATTTAA
17061077 TTGA-AAAATTTATTTA
1 TTGAGAAAATTTATTTA
17061093 TTTAAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (18 bp):
TTGAGAAAATTTATTTAA
Done.