Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr8
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: 70076365
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3341059 characters in sequence are not A, C, G, or T
File 156 of 210
Found at i:52189880 original size:133 final size:133
Alignment explanation
Indices: 52189716--52189988 Score: 458
Period size: 133 Copynumber: 2.1 Consensus size: 133
52189706 TCCCCTTGAG
*
52189716 GTTGCAGTGGGGTAGATCGAAGATGGAAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGA
1 GTTGCAGTGGGGCAGATCGAAGATGGAAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGA
52189781 AGCCGATAATCCTATCTCCCTAAAATTGTAGTGGAGC-GAATTAAAGTAATAAATCTTATCTCTC
66 AGCCGATAATCCTATCTCCCTAAAATTGTAGTGGAGCAG-ATTAAAGTAATAAATCTTATCTCTC
52189845 TGAA
130 TGAA
* *
52189849 GTTGCAGTGGGGCAGATCGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGA
1 GTTGCAGTGGGGCAGATCGAAGATGGAAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGA
* * * * *
52189914 AGTCGATAATCCTATCTCCCTGAAGTTGTAGTGGCGCAGATTAAAGTAATAGATCTTATCTCTCT
66 AGCCGATAATCCTATCTCCCTAAAATTGTAGTGGAGCAGATTAAAGTAATAAATCTTATCTCTCT
52189979 GAA
131 GAA
52189982 GTTGCAG
1 GTTGCAG
52189989 CAGAGTGGAT
Statistics
Matches: 131, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
133 130 0.99
134 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.29
Consensus pattern (133 bp):
GTTGCAGTGGGGCAGATCGAAGATGGAAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGA
AGCCGATAATCCTATCTCCCTAAAATTGTAGTGGAGCAGATTAAAGTAATAAATCTTATCTCTCT
GAA
Found at i:52189930 original size:89 final size:87
Alignment explanation
Indices: 52189425--52189954 Score: 355
Period size: 89 Copynumber: 6.1 Consensus size: 87
52189415 AGAGTAAGGA
** * * * * * *
52189425 AGCAGATTTAAGCCGCAAATCCTATCTCCCTGAAGATGTAGTGGAGCGGATTAAAGTAATAGATC
1 AGCAGATCGAAGCCGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTGATA-ATC
** *
52189490 TTATCTATCTGAAGTTGCAGTAG
65 TTATCTCCCTGAAGTTGCAGTGG
* ** * * * ** *
52189513 AGTAGATC---GCATCAGATCTTATCTCCCTGAGGTTGCAGTAGAGCAGACCGAAG-AAGTAGAT
1 AGCAGATCGAAGCCGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTGA-TA-AT
** *
52189574 CTTATCTCCCT-AAGCAGTAGTGG
64 CTTATCTCCCTGAAGTTGCAGTGG
* * * * * * *
52189597 AGCAGATTGAAGCCG-ATAATCCTATTTCCCTAAAGTTGTAGTGGAGCAGATTAAAGTAATAGAT
1 AGCAGATCGAAGCCGCA-AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTGATA-AT
* * *
52189661 CTTATCTCTCTAAAGTTGCAGTAG
64 CTTATCTCCCTGAAGTTGCAGTGG
* * * * * * * *
52189685 AGTAGATCGTA---GCAAGTCTTATC-CCCTTGAGGTTGCAGTGGGGTAGATCGAAGATGGAAAA
1 AGCAGATCGAAGCCGCAAATCTTATCTCCC-TGAAGTTGCAGTGGAGCAGATTGAAG-T-GATAA
*
52189746 TCTTATCTCCCTGAAGTTACAGTGG
63 TCTTATCTCCCTGAAGTTGCAGTGG
* * * * * * *
52189771 AGCAGATTGAAGCCG-ATAATCCTATCTCCCTAAAATTGTAGTGGAGC-GAATTAAAGTAATAAA
1 AGCAGATCGAAGCCGCA-AATCTTATCTCCCTGAAGTTGCAGTGGAGCAG-ATTGAAGTGAT-AA
*
52189834 TCTTATCTCTCTGAAGTTGCAGTGG
63 TCTTATCTCCCTGAAGTTGCAGTGG
* **
52189859 GGCAGATCGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTCGATAAT
1 AGCAGATCGAAG-CCGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGT-GATAAT
* *
52189924 CCTATCTCCCTGAAGTTGTAGTGG
64 CTTATCTCCCTGAAGTTGCAGTGG
*
52189948 CGCAGAT
1 AGCAGAT
52189955 TAAAGTAATA
Statistics
Matches: 331, Mismatches: 89, Indels: 43
0.71 0.19 0.09
Matches are distributed among these distances:
84 19 0.06
85 73 0.22
86 33 0.10
87 49 0.15
88 62 0.19
89 88 0.27
90 7 0.02
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (87 bp):
AGCAGATCGAAGCCGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTGATAATCT
TATCTCCCTGAAGTTGCAGTGG
Found at i:52191608 original size:4 final size:4
Alignment explanation
Indices: 52191594--52191623 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
52191584 AATTAATCCT
52191594 TTTA TTTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA -TTTA TTTA TTTA TTTA TTTA TTTA T
52191624 GTTTGCAGCC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:52197002 original size:27 final size:27
Alignment explanation
Indices: 52196964--52197020 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
52196954 GAGTGGAGAA
52196964 AAGAGCCCAACGAGGATAACTTAACTC
1 AAGAGCCCAACGAGGATAACTTAACTC
52196991 AAGAGCCCAACGAGGATAACTTAACTC
1 AAGAGCCCAACGAGGATAACTTAACTC
52197018 AAG
1 AAG
52197021 TGAAAGGGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.42, C:0.25, G:0.19, T:0.14
Consensus pattern (27 bp):
AAGAGCCCAACGAGGATAACTTAACTC
Found at i:52198971 original size:13 final size:13
Alignment explanation
Indices: 52198953--52198977 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52198943 TCTTATACAC
52198953 AATACACTTGAAG
1 AATACACTTGAAG
52198966 AATACACTTGAA
1 AATACACTTGAA
52198978 ATCAGATTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.16, G:0.12, T:0.24
Consensus pattern (13 bp):
AATACACTTGAAG
Found at i:52208164 original size:110 final size:110
Alignment explanation
Indices: 52208033--52208265 Score: 434
Period size: 110 Copynumber: 2.1 Consensus size: 110
52208023 ATTTTGCAAA
52208033 TCTTAATTTTTT--TATTATATCATAAATTAATTTTTGATCTCTAGGACGGAATATTTTTACAAC
1 TCTT-ATTTTTTAATATTATATCATAAATTAATTTTTGATCTCTAGGACGGAATATTTTTACAAC
52208096 TTATATTTTTTTTTGTAAATTTAAAATTATTTTTAAAAATTTATTC
65 TTATATTTTTTTTTGTAAATTTAAAATTATTTTTAAAAATTTATTC
52208142 TCTTATTTTTTAATATTATATCATAAATTAATTTTTGATCTCTAGGACGGAATATTTTTACAACT
1 TCTTATTTTTTAATATTATATCATAAATTAATTTTTGATCTCTAGGACGGAATATTTTTACAACT
52208207 TATATTTTTTTTTGTAAATTTAAAATTATTTTTAAAAATTTATTC
66 TATATTTTTTTTTGTAAATTTAAAATTATTTTTAAAAATTTATTC
52208252 TCTTTATTTTTTAA
1 TC-TTATTTTTTAA
52208266 ATTTAGAGAA
Statistics
Matches: 121, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
108 7 0.06
109 4 0.03
110 99 0.82
111 11 0.09
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (110 bp):
TCTTATTTTTTAATATTATATCATAAATTAATTTTTGATCTCTAGGACGGAATATTTTTACAACT
TATATTTTTTTTTGTAAATTTAAAATTATTTTTAAAAATTTATTC
Found at i:52213900 original size:21 final size:21
Alignment explanation
Indices: 52213876--52213920 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
52213866 TTCGGGTGGA
*
52213876 TCAGCTCTTATGATCTTCTGT
1 TCAGCTCTTATGAGCTTCTGT
52213897 TCAGCTCTTATGAGCTTCTGT
1 TCAGCTCTTATGAGCTTCTGT
52213918 TCA
1 TCA
52213921 CGTGTTTCGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.16, C:0.24, G:0.16, T:0.44
Consensus pattern (21 bp):
TCAGCTCTTATGAGCTTCTGT
Found at i:52218559 original size:56 final size:56
Alignment explanation
Indices: 52218492--52218690 Score: 248
Period size: 56 Copynumber: 3.7 Consensus size: 56
52218482 GGGAATGAAA
52218492 TCCCATGTAAGACCATATCTGAGACATGACATTGGCATTATTGAGGTTATGAGAGG
1 TCCCATGTAAGACCATATCTGAGACATGACATTGGCATTATTGAGGTTATGAGAGG
* * * * * * **
52218548 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGC---ACTGA---TACGAGAAC
1 TCCCATGTAAGACCATATCTGAGACATGACATTGGCATTATTGAGGTTATGAGAGG
52218598 TCCCATGTAAGACCATATCTGAGACATGACATTGGCATTATTGAGGTTATGAGAGG
1 TCCCATGTAAGACCATATCTGAGACATGACATTGGCATTATTGAGGTTATGAGAGG
* * * *
52218654 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
1 TCCCATGTAAGACCATATCTGAGACATGACATTGGCA
52218691 CTGATACGAG
Statistics
Matches: 117, Mismatches: 20, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
50 38 0.32
53 8 0.07
56 71 0.61
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.26
Consensus pattern (56 bp):
TCCCATGTAAGACCATATCTGAGACATGACATTGGCATTATTGAGGTTATGAGAGG
Found at i:52218607 original size:50 final size:50
Alignment explanation
Indices: 52218548--52218787 Score: 250
Period size: 50 Copynumber: 4.7 Consensus size: 50
52218538 TTATGAGAGG
*
52218548 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGATACGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGATACGAGAAC
* * * * * **
52218598 TCCCATGTAAGACCATATCTGAGACATGACATTGGCATTATTGAGGTTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGC---ACTGA---TACGAGAAC
*
52218654 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGATACGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGATACGAGAAC
* * * * * *
52218704 TCCCATGTAAGACCATATCTGGGATATAGCATTGGCAGT-ACAGGA-AAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGATACGAGAAC
* *
52218752 ATCCCATGTAAGACCATGTCTGAGACATGGCTTTGG
1 -TCCCATGTAAGACCATGTCTGGGACATGGCATTGG
52218788 AATGTTATTA
Statistics
Matches: 155, Mismatches: 28, Indels: 15
0.78 0.14 0.08
Matches are distributed among these distances:
48 3 0.02
49 34 0.22
50 72 0.46
53 8 0.05
56 38 0.25
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGATACGAGAAC
Found at i:52218740 original size:106 final size:106
Alignment explanation
Indices: 52218492--52218724 Score: 466
Period size: 106 Copynumber: 2.2 Consensus size: 106
52218482 GGGAATGAAA
52218492 TCCCATGTAAGACCATATCTGAGACATGACATTGGCATTATTGAGGTTATGAGAGGTCCCATGTA
1 TCCCATGTAAGACCATATCTGAGACATGACATTGGCATTATTGAGGTTATGAGAGGTCCCATGTA
52218557 AGACCATGTCTGGGACATGGCGTTGGCACTGATACGAGAAC
66 AGACCATGTCTGGGACATGGCGTTGGCACTGATACGAGAAC
52218598 TCCCATGTAAGACCATATCTGAGACATGACATTGGCATTATTGAGGTTATGAGAGGTCCCATGTA
1 TCCCATGTAAGACCATATCTGAGACATGACATTGGCATTATTGAGGTTATGAGAGGTCCCATGTA
52218663 AGACCATGTCTGGGACATGGCGTTGGCACTGATACGAGAAC
66 AGACCATGTCTGGGACATGGCGTTGGCACTGATACGAGAAC
52218704 TCCCATGTAAGACCATATCTG
1 TCCCATGTAAGACCATATCTG
52218725 GGATATAGCA
Statistics
Matches: 127, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
106 127 1.00
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (106 bp):
TCCCATGTAAGACCATATCTGAGACATGACATTGGCATTATTGAGGTTATGAGAGGTCCCATGTA
AGACCATGTCTGGGACATGGCGTTGGCACTGATACGAGAAC
Found at i:52219015 original size:20 final size:20
Alignment explanation
Indices: 52218990--52219039 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
52218980 ATGAGTTATT
52218990 TAAGTAAGCAAGTAAGTAAA
1 TAAGTAAGCAAGTAAGTAAA
52219010 TAAGTAAG-AGAGTAAGTAAA
1 TAAGTAAGCA-AGTAAGTAAA
*
52219030 GAAG-AAGCAA
1 TAAGTAAGCAA
52219040 AGACTATGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 5 0.19
20 22 0.81
ACGTcount: A:0.56, C:0.04, G:0.24, T:0.16
Consensus pattern (20 bp):
TAAGTAAGCAAGTAAGTAAA
Found at i:52221158 original size:54 final size:54
Alignment explanation
Indices: 52220959--52221169 Score: 255
Period size: 54 Copynumber: 3.9 Consensus size: 54
52220949 AGACGGGTAT
* *
52220959 AGACACGGGCT-GGACACGGCCGTGTGTCTTTAGTTCAAATGTTACATGGGCAG
1 AGACACGGGCTGGGACACGGCCGTGTGTCTCTAGTTCGAATGTTACATGGGCAG
** * * *
52221012 AGACACGGGCTGGGACACAACCGTGTGTCTCTAGTTAGAATGTTACACGGTCAG
1 AGACACGGGCTGGGACACGGCCGTGTGTCTCTAGTTCGAATGTTACATGGGCAG
** *
52221066 AGACACGACCTGGGACACGGCCATGTGTCTCTAGTTCGAATGTTACATGGGCA-
1 AGACACGGGCTGGGACACGGCCGTGTGTCTCTAGTTCGAATGTTACATGGGCAG
* * * * * *
52221119 AGGACACGGGCTAGGACATGGCCGTGTGTCCCTATTTCGATTGTTGCATGG
1 A-GACACGGGCTGGGACACGGCCGTGTGTCTCTAGTTCGAATGTTACATGG
52221170 CTTGAGACAC
Statistics
Matches: 132, Mismatches: 24, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
53 12 0.09
54 120 0.91
ACGTcount: A:0.23, C:0.22, G:0.31, T:0.24
Consensus pattern (54 bp):
AGACACGGGCTGGGACACGGCCGTGTGTCTCTAGTTCGAATGTTACATGGGCAG
Found at i:52221877 original size:20 final size:20
Alignment explanation
Indices: 52221852--52221895 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
52221842 TTTTTCGTCA
52221852 AATTGAGAATAAAATTATGG
1 AATTGAGAATAAAATTATGG
52221872 AATTGAGAATAAAATTATGG
1 AATTGAGAATAAAATTATGG
52221892 AATT
1 AATT
52221896 ATCCAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.18, T:0.32
Consensus pattern (20 bp):
AATTGAGAATAAAATTATGG
Found at i:52223670 original size:22 final size:21
Alignment explanation
Indices: 52223629--52223679 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
52223619 AATAAGTAAC
*
52223629 ATTTTCTTTATTATCTATTTT
1 ATTTTCTTGATTATCTATTTT
52223650 ATTTTGCTTGATTA-CTAATTTT
1 ATTTT-CTTGATTATCT-ATTTT
*
52223672 TTTTTCTT
1 ATTTTCTT
52223680 TTGAAATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 10 0.38
22 16 0.62
ACGTcount: A:0.18, C:0.10, G:0.04, T:0.69
Consensus pattern (21 bp):
ATTTTCTTGATTATCTATTTT
Found at i:52240342 original size:5 final size:5
Alignment explanation
Indices: 52240325--52240362 Score: 69
Period size: 5 Copynumber: 7.8 Consensus size: 5
52240315 CATCGGCTTT
52240325 TGATA TG-TA TGATA TGATA TGATA TGATA TGATA TGAT
1 TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGAT
52240363 CTGTGCTGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.37, C:0.00, G:0.21, T:0.42
Consensus pattern (5 bp):
TGATA
Found at i:52241822 original size:26 final size:25
Alignment explanation
Indices: 52241784--52241855 Score: 92
Period size: 26 Copynumber: 2.8 Consensus size: 25
52241774 CCCGATATAT
* *
52241784 GGCTCTTCGGAGCTTCCTGATTAAA
1 GGCTCTTTGGAGCTTCCTAATTAAA
*
52241809 GGCT-TTATGTGAGCTTCCTAATTAAT
1 GGCTCTT-TG-GAGCTTCCTAATTAAA
52241835 GGCTCTTTGGAGCTTCCTAAT
1 GGCTCTTTGGAGCTTCCTAAT
52241856 ATGGCTCGCT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
24 2 0.05
25 17 0.41
26 20 0.49
27 2 0.05
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.38
Consensus pattern (25 bp):
GGCTCTTTGGAGCTTCCTAATTAAA
Found at i:52242032 original size:25 final size:25
Alignment explanation
Indices: 52241923--52242034 Score: 79
Period size: 25 Copynumber: 4.6 Consensus size: 25
52241913 TTCAGAGATA
*
52241923 CCCGTTAT-TGGCTCGCATGAGCTT
1 CCCGTTATATGGCTCACATGAGCTT
* *
52241947 CCTGAT-TATGGCTC-CTATGAGCTT
1 CCCGTTATATGGCTCAC-ATGAGCTT
*** * *
52241971 CCCGTTATACATCCCGA-ATAAGCTT
1 CCCGTTATATGGCTC-ACATGAGCTT
* **
52241996 CCTGTTGCATGGCTCACATGAGCTT
1 CCCGTTATATGGCTCACATGAGCTT
52242021 CCCGTTATATGGCT
1 CCCGTTATATGGCT
52242035 TGAGAAAGGG
Statistics
Matches: 62, Mismatches: 20, Indels: 11
0.67 0.22 0.12
Matches are distributed among these distances:
23 2 0.03
24 23 0.37
25 37 0.60
ACGTcount: A:0.18, C:0.29, G:0.21, T:0.33
Consensus pattern (25 bp):
CCCGTTATATGGCTCACATGAGCTT
Found at i:52247506 original size:25 final size:24
Alignment explanation
Indices: 52247478--52247545 Score: 66
Period size: 26 Copynumber: 2.7 Consensus size: 24
52247468 CTCGATATAC
52247478 GGCTCTTCGGAGCTTCTCGATTAAA
1 GGCTCTTCGGAGCTTC-CGATTAAA
** *
52247503 GGCTCTTTATGAGCTTCCTGATTAAT
1 GGCTC-TTCGGAGCTTCC-GATTAAA
52247529 GGCTC-TCTGGAGCTTCC
1 GGCTCTTC-GGAGCTTCC
52247546 CGATAAGGCT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
24 1 0.03
25 14 0.40
26 20 0.57
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (24 bp):
GGCTCTTCGGAGCTTCCGATTAAA
Found at i:52247614 original size:25 final size:25
Alignment explanation
Indices: 52247478--52247654 Score: 102
Period size: 25 Copynumber: 7.2 Consensus size: 25
52247468 CTCGATATAC
* * *
52247478 GGCTCTTCGGAGCTTCTCGATTAAA
1 GGCTCTTCAGAGCTTCCCGATTAAT
* *
52247503 GGCTCTTTATGAGCTTCCTGATTAAT
1 GGCTCTTCA-GAGCTTCCCGATTAAT
*
52247529 GGCTC-TCTGGAGCTTCCCGA-TAA-
1 GGCTCTTC-AGAGCTTCCCGATTAAT
* *
52247552 GGCTCGCTT--GAACTTCCCTA-TATAT
1 GGCT--CTTCAGAGCTTCCCGATTA-AT
* * *
52247577 GACTATTCGGAGCTTCCCGATTAAT
1 GGCTCTTCAGAGCTTCCCGATTAAT
* **
52247602 GGCTCTTCAGAGCTACCCG-TTCTT
1 GGCTCTTCAGAGCTTCCCGATTAAT
*
52247626 GGCTC-TCATGAGCTTCCTGATT-AT
1 GGCTCTTCA-GAGCTTCCCGATTAAT
52247650 GGCTC
1 GGCTC
52247655 CTATGAGCCT
Statistics
Matches: 117, Mismatches: 23, Indels: 25
0.71 0.14 0.15
Matches are distributed among these distances:
23 20 0.17
24 26 0.22
25 50 0.43
26 21 0.18
ACGTcount: A:0.18, C:0.27, G:0.21, T:0.34
Consensus pattern (25 bp):
GGCTCTTCAGAGCTTCCCGATTAAT
Found at i:52247729 original size:25 final size:24
Alignment explanation
Indices: 52247627--52247729 Score: 66
Period size: 25 Copynumber: 4.2 Consensus size: 24
52247617 CCCGTTCTTG
* * *
52247627 GCTCTCATGAGCTTCCTGAT-TATG
1 GCTC-CATGAGCTTCCCGTTATATA
* *
52247651 GCTCCTATGAGCCTCCCGTTATACA
1 GCTCC-ATGAGCTTCCCGTTATATA
* ** *
52247676 GC-CCGGATAAGCTTCCCGTTGCATG
1 GCTCC--ATGAGCTTCCCGTTATATA
52247701 GCTCACATGAGCTTCCCGTTATATA
1 GCTC-CATGAGCTTCCCGTTATATA
52247726 GCTC
1 GCTC
52247730 GAGAGAGGGC
Statistics
Matches: 58, Mismatches: 16, Indels: 9
0.70 0.19 0.11
Matches are distributed among these distances:
23 1 0.02
24 17 0.29
25 38 0.66
26 1 0.02
27 1 0.02
ACGTcount: A:0.18, C:0.31, G:0.20, T:0.30
Consensus pattern (24 bp):
GCTCCATGAGCTTCCCGTTATATA
Found at i:52253036 original size:16 final size:16
Alignment explanation
Indices: 52253015--52253046 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
52253005 CAGATACACC
*
52253015 AGCCTCTTCGTGTCGT
1 AGCCTCTACGTGTCGT
52253031 AGCCTCTACGTGTCGT
1 AGCCTCTACGTGTCGT
52253047 CTAACATCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.09, C:0.31, G:0.25, T:0.34
Consensus pattern (16 bp):
AGCCTCTACGTGTCGT
Found at i:52255619 original size:23 final size:23
Alignment explanation
Indices: 52255593--52255691 Score: 128
Period size: 23 Copynumber: 4.3 Consensus size: 23
52255583 ATAAGCGTCA
*
52255593 CACTGATATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
52255616 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
52255639 CACTG-TAATGTAGCCGTAGCTAC
1 CACTGAT-ATGTAGCCGAAGCTAC
** * *
52255662 CGTTGAAATGTAACCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
52255685 CACTGAT
1 CACTGAT
52255692 CAATAACACT
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
22 1 0.02
23 63 0.98
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.23
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:52257078 original size:12 final size:12
Alignment explanation
Indices: 52257063--52257110 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
52257053 AAATCTAGTA
*
52257063 TTATATATTTAT
1 TTATGTATTTAT
* *
52257075 TTATTTATTCAT
1 TTATGTATTTAT
* *
52257087 TCACGTATTTAT
1 TTATGTATTTAT
52257099 TTATGTATTTAT
1 TTATGTATTTAT
52257111 CTATCGGTTT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.27, C:0.06, G:0.04, T:0.62
Consensus pattern (12 bp):
TTATGTATTTAT
Found at i:52257247 original size:27 final size:26
Alignment explanation
Indices: 52257206--52257257 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
52257196 TATATTACTC
*
52257206 TTTTTTGTTATTTTTTATTT-TTATTT
1 TTTTTTGTTA-CTTTTATTTGTTATTT
52257232 TTTTCTTGTTACTTTTATTTGTTATT
1 TTTT-TTGTTACTTTTATTTGTTATT
52257258 ATTATTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.12, C:0.04, G:0.06, T:0.79
Consensus pattern (26 bp):
TTTTTTGTTACTTTTATTTGTTATTT
Found at i:52261414 original size:13 final size:13
Alignment explanation
Indices: 52261365--52261415 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
52261355 CTCTTTTATA
52261365 GTTATTTTTATTT
1 GTTATTTTTATTT
*
52261378 -TTATTTTTTTCTT
1 GTTATTTTTAT-TT
*
52261391 GTTACTTTTATTT
1 GTTATTTTTATTT
*
52261404 GTTATTATTATT
1 GTTATTTTTATT
52261416 GTTTTATACT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
12 9 0.29
13 14 0.45
14 8 0.26
ACGTcount: A:0.16, C:0.04, G:0.06, T:0.75
Consensus pattern (13 bp):
GTTATTTTTATTT
Found at i:52266621 original size:80 final size:80
Alignment explanation
Indices: 52266488--52266647 Score: 320
Period size: 80 Copynumber: 2.0 Consensus size: 80
52266478 TAATTTACTA
52266488 ACAAAATAATTTACCCATAAATTTATTCCAATTTAAGAAAAATTGTCCTGAGGTGGACCCGTAAG
1 ACAAAATAATTTACCCATAAATTTATTCCAATTTAAGAAAAATTGTCCTGAGGTGGACCCGTAAG
52266553 GACTGGATCAGGCAT
66 GACTGGATCAGGCAT
52266568 ACAAAATAATTTACCCATAAATTTATTCCAATTTAAGAAAAATTGTCCTGAGGTGGACCCGTAAG
1 ACAAAATAATTTACCCATAAATTTATTCCAATTTAAGAAAAATTGTCCTGAGGTGGACCCGTAAG
52266633 GACTGGATCAGGCAT
66 GACTGGATCAGGCAT
52266648 GTAACTTTGG
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 80 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (80 bp):
ACAAAATAATTTACCCATAAATTTATTCCAATTTAAGAAAAATTGTCCTGAGGTGGACCCGTAAG
GACTGGATCAGGCAT
Found at i:52270254 original size:68 final size:68
Alignment explanation
Indices: 52270174--52270309 Score: 272
Period size: 68 Copynumber: 2.0 Consensus size: 68
52270164 AAATACCATG
52270174 GGCAGAATTGCCAACAAGACACACTTGAAAGTTTATAAATGCAATACGGCTCGAGAAGTTAAAAG
1 GGCAGAATTGCCAACAAGACACACTTGAAAGTTTATAAATGCAATACGGCTCGAGAAGTTAAAAG
52270239 ATT
66 ATT
52270242 GGCAGAATTGCCAACAAGACACACTTGAAAGTTTATAAATGCAATACGGCTCGAGAAGTTAAAAG
1 GGCAGAATTGCCAACAAGACACACTTGAAAGTTTATAAATGCAATACGGCTCGAGAAGTTAAAAG
52270307 ATT
66 ATT
52270310 ACTTGAAACC
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (68 bp):
GGCAGAATTGCCAACAAGACACACTTGAAAGTTTATAAATGCAATACGGCTCGAGAAGTTAAAAG
ATT
Found at i:52272972 original size:189 final size:189
Alignment explanation
Indices: 52272652--52273031 Score: 760
Period size: 189 Copynumber: 2.0 Consensus size: 189
52272642 CCTGTTTTTC
52272652 CTTTACGTCTTCCCCCTGCTACAATTTATTAACTCAGAATATTTTACTCAATGTTTGTTAGTGTT
1 CTTTACGTCTTCCCCCTGCTACAATTTATTAACTCAGAATATTTTACTCAATGTTTGTTAGTGTT
52272717 AGTTTAGCAATATTTTTGAAAAGTATTGTGAAAAGGTGTTTTTGAGAAATATTTTTAAAAAGTTT
66 AGTTTAGCAATATTTTTGAAAAGTATTGTGAAAAGGTGTTTTTGAGAAATATTTTTAAAAAGTTT
52272782 GGTTTAAAATTTAAGTATTTAATATTACTGTTAAAAATTACTTTTAAAAAATAAAATAT
131 GGTTTAAAATTTAAGTATTTAATATTACTGTTAAAAATTACTTTTAAAAAATAAAATAT
52272841 CTTTACGTCTTCCCCCTGCTACAATTTATTAACTCAGAATATTTTACTCAATGTTTGTTAGTGTT
1 CTTTACGTCTTCCCCCTGCTACAATTTATTAACTCAGAATATTTTACTCAATGTTTGTTAGTGTT
52272906 AGTTTAGCAATATTTTTGAAAAGTATTGTGAAAAGGTGTTTTTGAGAAATATTTTTAAAAAGTTT
66 AGTTTAGCAATATTTTTGAAAAGTATTGTGAAAAGGTGTTTTTGAGAAATATTTTTAAAAAGTTT
52272971 GGTTTAAAATTTAAGTATTTAATATTACTGTTAAAAATTACTTTTAAAAAATAAAATAT
131 GGTTTAAAATTTAAGTATTTAATATTACTGTTAAAAATTACTTTTAAAAAATAAAATAT
52273030 CT
1 CT
52273032 ATTTTAGACA
Statistics
Matches: 191, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
189 191 1.00
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.43
Consensus pattern (189 bp):
CTTTACGTCTTCCCCCTGCTACAATTTATTAACTCAGAATATTTTACTCAATGTTTGTTAGTGTT
AGTTTAGCAATATTTTTGAAAAGTATTGTGAAAAGGTGTTTTTGAGAAATATTTTTAAAAAGTTT
GGTTTAAAATTTAAGTATTTAATATTACTGTTAAAAATTACTTTTAAAAAATAAAATAT
Found at i:52286045 original size:12 final size:13
Alignment explanation
Indices: 52286028--52286057 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
52286018 CTCATACATG
52286028 AATAAATAAA-GC
1 AATAAATAAATGC
52286040 AATAAATAAATGC
1 AATAAATAAATGC
52286053 AATAA
1 AATAA
52286058 TTATAGCTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.67, C:0.07, G:0.07, T:0.20
Consensus pattern (13 bp):
AATAAATAAATGC
Found at i:52287980 original size:29 final size:29
Alignment explanation
Indices: 52287946--52288054 Score: 143
Period size: 29 Copynumber: 3.8 Consensus size: 29
52287936 TAGGTCACTA
52287946 AACTTTAATTTATT-TCGTTTTGGTCTTTG
1 AACTTTAATTTATTAT-GTTTTGGTCTTTG
* *
52287975 AACTTTAATTTATT-TCGTTTTGATCATTG
1 AACTTTAATTTATTAT-GTTTTGGTCTTTG
*
52288004 GACTTTAATTTATTATGTTTTGGT-TATTG
1 AACTTTAATTTATTATGTTTTGGTCT-TTG
52288033 AACTTTAATTTATTATGTTTTG
1 AACTTTAATTTATTATGTTTTG
52288055 ATCACTAATG
Statistics
Matches: 72, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
29 71 0.99
30 1 0.01
ACGTcount: A:0.22, C:0.07, G:0.13, T:0.58
Consensus pattern (29 bp):
AACTTTAATTTATTATGTTTTGGTCTTTG
Found at i:52288037 original size:58 final size:58
Alignment explanation
Indices: 52287947--52288058 Score: 176
Period size: 58 Copynumber: 1.9 Consensus size: 58
52287937 AGGTCACTAA
52287947 ACTTTAATTTATTTCGTTTTGGTCTTTGAACTTTAATTTATT-TCGTTTTGATCATTGG
1 ACTTTAATTTATTTCGTTTTGGTCTTTGAACTTTAATTTATTAT-GTTTTGATCATTGG
52288005 ACTTTAATTTATTAT-GTTTTGGT-TATTGAACTTTAATTTATTATGTTTTGATCA
1 ACTTTAATTTATT-TCGTTTTGGTCT-TTGAACTTTAATTTATTATGTTTTGATCA
52288059 CTAATGTTAT
Statistics
Matches: 51, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
57 1 0.02
58 48 0.94
59 2 0.04
ACGTcount: A:0.22, C:0.08, G:0.12, T:0.57
Consensus pattern (58 bp):
ACTTTAATTTATTTCGTTTTGGTCTTTGAACTTTAATTTATTATGTTTTGATCATTGG
Found at i:52288429 original size:3 final size:3
Alignment explanation
Indices: 52288421--52288454 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
52288411 CCCTAGATGG
52288421 GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA G
1 GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA G
52288455 AAGAAGAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (3 bp):
GTA
Found at i:52288459 original size:3 final size:3
Alignment explanation
Indices: 52288453--52288487 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
52288443 TAGTAGTAGT
52288453 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
52288488 GCACTACACC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:52288589 original size:41 final size:39
Alignment explanation
Indices: 52288538--52288643 Score: 117
Period size: 41 Copynumber: 2.7 Consensus size: 39
52288528 AAATGCCACA
52288538 AAAAATCGAGCATTAGCGGCGCTTTACGCAAAACGCCGCC
1 AAAAA-CGAGCATTAGCGGCGCTTTACGCAAAACGCCGCC
* * *
52288578 AAAGATACGAGCATTAGCGGCGCTATT-TGTAAAACGCCGCT
1 AAA-A-ACGAGCATTAGCGGCGCT-TTACGCAAAACGCCGCC
* *
52288619 AAAAACAAGCATTAGCAGCG-TTTAC
1 AAAAACGAGCATTAGCGGCGCTTTAC
52288644 AAATAAGCAC
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
37 2 0.04
38 1 0.02
39 14 0.25
40 4 0.07
41 32 0.57
42 3 0.05
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.19
Consensus pattern (39 bp):
AAAAACGAGCATTAGCGGCGCTTTACGCAAAACGCCGCC
Found at i:52288768 original size:41 final size:42
Alignment explanation
Indices: 52288723--52288931 Score: 140
Period size: 41 Copynumber: 5.2 Consensus size: 42
52288713 TTTCAAAACA
* * *
52288723 CGCCGCTAATGCTCCTATCTTTAGCGGCGTTTTTG-AATAAT
1 CGCCGCTAATGCTCCAATCTTTAGCGGCGTTTTTGTAAGAAG
* * *
52288764 CGCCGCTAATGCT-CAGGTCTTTAGCGGCG-CTTTGTAAGAGG
1 CGCCGCTAATGCTCCA-ATCTTTAGCGGCGTTTTTGTAAGAAG
52288805 CGCCGCTAATGCT-CAAGTCTTTAGCGGCGTTTTT-TACA-AAG
1 CGCCGCTAATGCTCCAA-TCTTTAGCGGCGTTTTTGTA-AGAAG
* ** * *
52288846 TGCCGCTAA-----CGGTCTTTAGCGGCG--TTTCTCAGAAAG
1 CGCCGCTAATGCTCCAATCTTTAGCGGCGTTTTTGTAAG-AAG
* ** * *
52288882 CGCTGCTAATGCTCCGGTCTTTAGCGGCGTTTCT-TAAAAAG
1 CGCCGCTAATGCTCCAATCTTTAGCGGCGTTTTTGTAAGAAG
52288923 CGCCGCTAA
1 CGCCGCTAA
52288932 ATACCTGAGC
Statistics
Matches: 134, Mismatches: 19, Indels: 30
0.73 0.10 0.16
Matches are distributed among these distances:
34 4 0.03
35 1 0.01
36 22 0.16
37 1 0.01
40 5 0.04
41 93 0.69
42 6 0.04
43 2 0.01
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.30
Consensus pattern (42 bp):
CGCCGCTAATGCTCCAATCTTTAGCGGCGTTTTTGTAAGAAG
Found at i:52288902 original size:77 final size:78
Alignment explanation
Indices: 52288702--52288931 Score: 231
Period size: 77 Copynumber: 2.9 Consensus size: 78
52288692 TTTTGGGCCC
* *
52288702 TTAGCGGCGCTTTTCA-AAACACGCCGCTAATGCTCCTA-TCTTTAGCGGCGTTTTTGAATAA-T
1 TTAGCGGCGCTTTTCAGAAA-GCGCCGCTAATGCTCC-AGTCTTTAGCGGCGTTTTTTAA-AAGT
52288764 CGCCGCTAATGCTCAGGTCT
63 -GCCGCTAA---TCAGGTCT
* * *
52288784 TTAGCGGCGCTTTGTAAG-AGGCGCCGCTAATGCTCAAGTCTTTAGCGGCGTTTTTTACAAAGTG
1 TTAGCGGCGCTTT-TCAGAAAGCGCCGCTAATGCTCCAGTCTTTAGCGGCGTTTTTTA-AAAGTG
52288848 CCGCTAA-C-GGTCT
64 CCGCTAATCAGGTCT
* * * *
52288861 TTAGCGGCG-TTTCTCAGAAAGCGCTGCTAATGCTCCGGTCTTTAGCGGCGTTTCTTAAAAAGCG
1 TTAGCGGCGCTTT-TCAGAAAGCGCCGCTAATGCTCCAGTCTTTAGCGGCGTTT-TTTAAAAGTG
52288925 CCGCTAA
64 CCGCTAA
52288932 ATACCTGAGC
Statistics
Matches: 128, Mismatches: 13, Indels: 19
0.80 0.08 0.12
Matches are distributed among these distances:
76 6 0.05
77 57 0.45
78 4 0.03
81 1 0.01
82 55 0.43
83 5 0.04
ACGTcount: A:0.20, C:0.25, G:0.24, T:0.30
Consensus pattern (78 bp):
TTAGCGGCGCTTTTCAGAAAGCGCCGCTAATGCTCCAGTCTTTAGCGGCGTTTTTTAAAAGTGCC
GCTAATCAGGTCT
Found at i:52288947 original size:41 final size:41
Alignment explanation
Indices: 52288861--52288995 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
52288851 CTAACGGTCT
* * * * * * *
52288861 TTAGCGGCGTTTCTCAGAAAGCGCTGCTAATGCTCCGG-TCT
1 TTAGCGGCGTTTCTTAGAAAACGCAGCTAAAG-ACCGGAGCA
* * *
52288902 TTAGCGGCGTTTCTTA-AAAAGCGCCGCTAAATACCTGAGCA
1 TTAGCGGCGTTTCTTAGAAAA-CGCAGCTAAAGACCGGAGCA
**
52288943 TTAGCGGCGCATCTTAGAAAACGCAGCTAAAGACCGGAGCA
1 TTAGCGGCGTTTCTTAGAAAACGCAGCTAAAGACCGGAGCA
52288984 TTAGCGGCGTTT
1 TTAGCGGCGTTT
52288996 TGTAGCTAGG
Statistics
Matches: 75, Mismatches: 16, Indels: 6
0.77 0.16 0.06
Matches are distributed among these distances:
40 6 0.08
41 65 0.87
42 4 0.05
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.24
Consensus pattern (41 bp):
TTAGCGGCGTTTCTTAGAAAACGCAGCTAAAGACCGGAGCA
Found at i:52293060 original size:15 final size:14
Alignment explanation
Indices: 52293040--52293073 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
52293030 CACCAATTTG
*
52293040 TTTTCATTTGTACT
1 TTTTCATTTATACT
52293054 ATTTTCATTTATACT
1 -TTTTCATTTATACT
52293069 TTTTC
1 TTTTC
52293074 CTTTTATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.18, C:0.15, G:0.03, T:0.65
Consensus pattern (14 bp):
TTTTCATTTATACT
Found at i:52306742 original size:66 final size:66
Alignment explanation
Indices: 52306636--52306769 Score: 155
Period size: 66 Copynumber: 2.0 Consensus size: 66
52306626 NNNNNNNNNN
* * * * *
52306636 GGTTCAAAAAAGATATGAAGAACTCTAGCTACAACTTAAAGGAGATGTAGCAGTGAGAGAAGCTG
1 GGTTCAAAAAAGATATGAAGAACTCCAGCTACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCAG
52306701 A
66 A
* * * *
52306702 GGTTCAACGAAAG-TATGAAGAACTCCAG-TAGTAGCTTAAAGCAGATGCGGCAGCGAGAGAAGC
1 GGTTCAA-AAAAGATATGAAGAACTCCAGCTA-CAACTTAAAGCAGATGCAGCAGCGAGAGAAGC
52306765 AGA
64 AGA
52306768 GG
1 GG
52306770 CTGCAGTGAG
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
65 2 0.04
66 51 0.89
67 4 0.07
ACGTcount: A:0.40, C:0.14, G:0.29, T:0.17
Consensus pattern (66 bp):
GGTTCAAAAAAGATATGAAGAACTCCAGCTACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCAG
A
Found at i:52306766 original size:21 final size:21
Alignment explanation
Indices: 52306740--52306787 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
52306730 TAGTAGCTTA
*
52306740 AAGCAGATGCGGCAGCGAGAG
1 AAGCAGAGGCGGCAGCGAGAG
* * *
52306761 AAGCAGAGGCTGCAGTGAGGG
1 AAGCAGAGGCGGCAGCGAGAG
52306782 AAGCAG
1 AAGCAG
52306788 CGTAGCGTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.17, G:0.44, T:0.06
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCGAGAG
Found at i:52306973 original size:10 final size:10
Alignment explanation
Indices: 52306960--52306991 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
52306950 AATTTCATTT
52306960 TATTTATTGA
1 TATTTATTGA
52306970 TATTTATTGA
1 TATTTATTGA
52306980 TATTTATT-A
1 TATTTATTGA
52306989 TAT
1 TAT
52306992 ATTACAGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.62
Consensus pattern (10 bp):
TATTTATTGA
Found at i:52307179 original size:43 final size:43
Alignment explanation
Indices: 52307113--52307367 Score: 191
Period size: 43 Copynumber: 5.9 Consensus size: 43
52307103 GCATTTTTAA
* * * *
52307113 AAAAACGCCACTAAAGGTAATGGTCTTTAGCGGCGTTTGTGGT
1 AAAAGCGCCGCTAAAGTTCATGGTCTTTAGCGGCGTTTGTGGT
* *
52307156 AAAAGCGCCGCTAAAGTTCATGGTCTTCAGCGGCGTTT-TGGAG
1 AAAAGCGCCGCTAAAGTTCATGGTCTTTAGCGGCGTTTGTGG-T
* * * *
52307199 AAAAACGCCGCTAAAGATT-AGGGTCTTTAGCGGCGTTT-TATGC
1 AAAAGCGCCGCTAAAG-TTCATGGTCTTTAGCGGCGTTTGT-GGT
* * * *
52307242 AGAAGCGCCGCTAAAGATCAGGGTATTTAGCGGCGTTTGTAAGG-
1 AAAAGCGCCGCTAAAGTTCATGGTCTTTAGCGGCGTTTGT--GGT
* * * * *
52307286 -GAAGCGCTGCTAAAGGTCATTGTCTTTTGCGGCGTTTGTTTGGT
1 AAAAGCGCCGCTAAAGTTCATGGTCTTTAGCGGCGTTTG--TGGT
* ** *
52307330 --AAGCGCCGCTAAAGTCCATGACCTTCAGCGGCGTTTGT
1 AAAAGCGCCGCTAAAGTTCATGGTCTTTAGCGGCGTTTGT
52307368 TTTGTAAGTG
Statistics
Matches: 173, Mismatches: 30, Indels: 20
0.78 0.13 0.09
Matches are distributed among these distances:
41 1 0.01
42 4 0.02
43 161 0.93
44 4 0.02
45 3 0.02
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.28
Consensus pattern (43 bp):
AAAAGCGCCGCTAAAGTTCATGGTCTTTAGCGGCGTTTGTGGT
Found at i:52307360 original size:86 final size:85
Alignment explanation
Indices: 52307113--52307367 Score: 241
Period size: 86 Copynumber: 3.0 Consensus size: 85
52307103 GCATTTTTAA
*
52307113 AAAAACGCCACTAAAGGTAATGGTCTTTAGCGGCGTTTG-TGGTAAAAGCGCCGCTAAAGTTCAT
1 AAAAACGCCGCTAAAGGTAATGGTCTTTAGCGGCGTTTGTTGGT--AAGCGCCGCTAAAG-TCAT
*
52307177 GGTCTTCAGCGGCGTTT-TGGAG
63 GGTCTTCAGCGGCGTTTGTGAAG
* * *
52307199 AAAAACGCCGCTAAAGATTAGGGTCTTTAGCGGCGTTT-TATGCAG-AAGCGCCGCTAAAGATCA
1 AAAAACGCCGCTAAAGGTAATGGTCTTTAGCGGCGTTTGT-TG--GTAAGCGCCGCTAAAG-TCA
* * *
52307262 GGGTATTTAGCGGCGTTTGT-AAG
62 TGGTCTTCAGCGGCGTTTGTGAAG
** * * * * *
52307285 GGAAGCGCTGCTAAAGGTCATTGTCTTTTGCGGCGTTTGTTTGGTAAGCGCCGCTAAAGTCCATG
1 AAAAACGCCGCTAAAGGTAATGGTCTTTAGCGGCGTTTG-TTGGTAAGCGCCGCTAAAGT-CATG
**
52307350 ACCTTCAGCGGCGTTTGT
64 GTCTTCAGCGGCGTTTGT
52307368 TTTGTAAGTG
Statistics
Matches: 137, Mismatches: 23, Indels: 18
0.77 0.13 0.10
Matches are distributed among these distances:
85 2 0.01
86 128 0.93
87 5 0.04
88 1 0.01
89 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.28
Consensus pattern (85 bp):
AAAAACGCCGCTAAAGGTAATGGTCTTTAGCGGCGTTTGTTGGTAAGCGCCGCTAAAGTCATGGT
CTTCAGCGGCGTTTGTGAAG
Found at i:52307368 original size:43 final size:43
Alignment explanation
Indices: 52307314--52307408 Score: 138
Period size: 43 Copynumber: 2.2 Consensus size: 43
52307304 ATTGTCTTTT
* *
52307314 GCGGCGTTTGTTTGGTAAGCGCCGCTAAAGTCCATGA-CCTTCA
1 GCGGCGTTTGTTTGGTAAGCGCCACTAAAGACCATGACCCTT-A
* *
52307357 GCGGCGTTTGTTTTGTAAGTGCCACTAAAGACCATGACCCTTA
1 GCGGCGTTTGTTTGGTAAGCGCCACTAAAGACCATGACCCTTA
52307400 GCGGCGTTT
1 GCGGCGTTT
52307409 TTAGAAATAA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
43 43 0.91
44 4 0.09
ACGTcount: A:0.19, C:0.24, G:0.27, T:0.29
Consensus pattern (43 bp):
GCGGCGTTTGTTTGGTAAGCGCCACTAAAGACCATGACCCTTA
Found at i:52307496 original size:22 final size:22
Alignment explanation
Indices: 52307469--52307510 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
52307459 TTGCGGCGCT
* *
52307469 AAAAGCGTCGCTAAAGGCCTAA
1 AAAAGCGCCGCTAAAAGCCTAA
52307491 AAAAGCGCCGCTAAAAGCCT
1 AAAAGCGCCGCTAAAAGCCT
52307511 GTTTTGGTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.26, G:0.21, T:0.12
Consensus pattern (22 bp):
AAAAGCGCCGCTAAAAGCCTAA
Found at i:52307536 original size:3 final size:3
Alignment explanation
Indices: 52307528--52307581 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
52307518 TGTAGTGAGG
52307528 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
52307576 AGA AGA
1 AGA AGA
52307582 TAAGCCAATT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:52307612 original size:19 final size:19
Alignment explanation
Indices: 52307588--52307625 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
52307578 AAGATAAGCC
*
52307588 AATTTCCTGATATGAAAGG
1 AATTTCCTAATATGAAAGG
52307607 AATTTCCTAATATGAAAGG
1 AATTTCCTAATATGAAAGG
52307626 CCATTCTATT
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:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (19 bp):
AATTTCCTAATATGAAAGG
Found at i:52308407 original size:20 final size:19
Alignment explanation
Indices: 52308381--52308431 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 19
52308371 TTGGAGCAGG
*
52308381 AATATCGATACCTTAGGAA
1 AATATCGATACCTTAAGAA
52308400 ATATATCGATACCTTAAGAA
1 A-ATATCGATACCTTAAGAA
52308420 AAGTATCGATAC
1 AA-TATCGATAC
52308432 TGGATCGATA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 2 0.07
20 27 0.93
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.27
Consensus pattern (19 bp):
AATATCGATACCTTAAGAA
Found at i:52309394 original size:24 final size:25
Alignment explanation
Indices: 52309362--52309408 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
52309352 CTACTTCTTC
52309362 TATTCCTTC-TCATTCTCCTCTTCCT
1 TATTCCTTCTTC-TTCTCCTCTTCCT
*
52309387 TATT-CTTCTTCTTCTTCTCTTC
1 TATTCCTTCTTCTTCTCCTCTTC
52309409 TTCTACTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.06, C:0.36, G:0.00, T:0.57
Consensus pattern (25 bp):
TATTCCTTCTTCTTCTCCTCTTCCT
Found at i:52312916 original size:16 final size:17
Alignment explanation
Indices: 52312879--52312918 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
52312869 TTCCAAAAAT
*
52312879 TATTAAAAATGATAGAA
1 TATTAAAAATGATACAA
52312896 -A-TAAAAAT-ATACAA
1 TATTAAAAATGATACAA
52312910 TATTAAAAA
1 TATTAAAAA
52312919 ATGCTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 5
0.77 0.04 0.19
Matches are distributed among these distances:
14 5 0.25
15 8 0.40
16 7 0.35
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.28
Consensus pattern (17 bp):
TATTAAAAATGATACAA
Found at i:52327065 original size:6 final size:6
Alignment explanation
Indices: 52327054--52327112 Score: 73
Period size: 6 Copynumber: 9.7 Consensus size: 6
52327044 AGGTTTCTTA
* * * *
52327054 AAATGG AAATGG AAATGG AAATGG AAATAG AAATAG AAATAG AAATAG
1 AAATAG AAATAG AAATAG AAATAG AAATAG AAATAG AAATAG AAATAG
52327102 AAATTAG AAAT
1 AAA-TAG AAAT
52327113 GATACATTTA
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
6 45 0.88
7 6 0.12
ACGTcount: A:0.59, C:0.00, G:0.22, T:0.19
Consensus pattern (6 bp):
AAATAG
Found at i:52327077 original size:18 final size:18
Alignment explanation
Indices: 52327054--52327113 Score: 84
Period size: 18 Copynumber: 3.3 Consensus size: 18
52327044 AGGTTTCTTA
* *
52327054 AAATGGAAATGGAAATGG
1 AAATGGAAATAGAAATAG
52327072 AAATGGAAATAGAAATAG
1 AAATGGAAATAGAAATAG
*
52327090 AAATAGAAATAGAAATTAG
1 AAATGGAAATAGAAA-TAG
52327109 AAATG
1 AAATG
52327114 ATACATTTAC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
18 30 0.81
19 7 0.19
ACGTcount: A:0.58, C:0.00, G:0.23, T:0.18
Consensus pattern (18 bp):
AAATGGAAATAGAAATAG
Found at i:52334609 original size:6 final size:6
Alignment explanation
Indices: 52334598--52334633 Score: 63
Period size: 6 Copynumber: 5.8 Consensus size: 6
52334588 AGGTTTCTCA
52334598 AAATGG AAATGG AAATGG AAATGG AAATGAG AAATG
1 AAATGG AAATGG AAATGG AAATGG AAATG-G AAATG
52334634 ATATATTTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.53, C:0.00, G:0.31, T:0.17
Consensus pattern (6 bp):
AAATGG
Found at i:52340041 original size:2 final size:2
Alignment explanation
Indices: 52340034--52340063 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
52340024 TACATTAGTA
52340034 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
52340064 TTACTAGTAG
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:52340760 original size:41 final size:41
Alignment explanation
Indices: 52340701--52340782 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
52340691 AAAATTCATT
52340701 TTCGGTGGTGCCAAAAATAATGGTTTCGGGACCATGATTTC
1 TTCGGTGGTGCCAAAAATAATGGTTTCGGGACCATGATTTC
* * *
52340742 TTCGGTGGTGTCAGAAATAATGGTTTTGGGACCATGATTTC
1 TTCGGTGGTGCCAAAAATAATGGTTTCGGGACCATGATTTC
52340783 GATAAGTGAG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.34
Consensus pattern (41 bp):
TTCGGTGGTGCCAAAAATAATGGTTTCGGGACCATGATTTC
Found at i:52350871 original size:18 final size:18
Alignment explanation
Indices: 52350848--52350887 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
52350838 AATAAGATTG
52350848 CATCTTCATCAAAACCAA
1 CATCTTCATCAAAACCAA
*
52350866 CATCTTCATCAAAACCAG
1 CATCTTCATCAAAACCAA
52350884 CATC
1 CATC
52350888 ACGCTTCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.40, C:0.35, G:0.03, T:0.23
Consensus pattern (18 bp):
CATCTTCATCAAAACCAA
Found at i:52355884 original size:20 final size:20
Alignment explanation
Indices: 52355861--52355903 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
52355851 CATGTAACTG
*
52355861 CAATAAGGGGTATTGAAGTA
1 CAATAAGGGGTATCGAAGTA
*
52355881 CAATCAGGGGTATCGAAGTA
1 CAATAAGGGGTATCGAAGTA
52355901 CAA
1 CAA
52355904 ATAGGAGCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.40, C:0.12, G:0.28, T:0.21
Consensus pattern (20 bp):
CAATAAGGGGTATCGAAGTA
Found at i:52358878 original size:39 final size:39
Alignment explanation
Indices: 52358838--52358975 Score: 215
Period size: 39 Copynumber: 3.5 Consensus size: 39
52358828 ATGCACTTTT
* *
52358838 AAGCATATATCACATTACAT-ATATAATCACATAACATTT
1 AAGCATATATCACAATAC-TCATATAATCACATAACATTC
52358877 AAGCATATATCACAATACTCATATAATCACATAACATTC
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
* *
52358916 AAGCATATATCACAATACTCATGTAATCATATAACATTC
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
*
52358955 AAGCATCTATCACAATACTCA
1 AAGCATATATCACAATACTCA
52358976 AAAACATGTT
Statistics
Matches: 93, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
38 1 0.01
39 92 0.99
ACGTcount: A:0.45, C:0.22, G:0.04, T:0.30
Consensus pattern (39 bp):
AAGCATATATCACAATACTCATATAATCACATAACATTC
Found at i:52395327 original size:15 final size:16
Alignment explanation
Indices: 52395298--52395353 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
52395288 CATCTCATAA
52395298 TCATTT-ATCATATTTT
1 TCATTTCAT-ATATTTT
52395314 TCATTTCA-ATATTTT
1 TCATTTCATATATTTT
*
52395329 CTCATCTCATATTCATTTT
1 -TCATTTCATA-T-ATTTT
52395348 TCATTT
1 TCATTT
52395354 TTTCCATTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
15 7 0.21
16 13 0.39
17 2 0.06
18 6 0.18
19 5 0.15
ACGTcount: A:0.23, C:0.18, G:0.00, T:0.59
Consensus pattern (16 bp):
TCATTTCATATATTTT
Found at i:52395335 original size:43 final size:43
Alignment explanation
Indices: 52395285--52395368 Score: 134
Period size: 43 Copynumber: 2.0 Consensus size: 43
52395275 ATATCTCATA
52395285 TCTCATCTCATAATCATTTATCATATTTTT-CATTTCAATATTT
1 TCTCATCTCATAATCATTTATCAT-TTTTTCCATTTCAATATTT
* *
52395328 TCTCATCTCATATTCATTTTTCATTTTTTCCATTTCAATAT
1 TCTCATCTCATAATCATTTATCATTTTTTCCATTTCAATAT
52395369 AAATCACATA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
42 5 0.13
43 33 0.87
ACGTcount: A:0.25, C:0.20, G:0.00, T:0.55
Consensus pattern (43 bp):
TCTCATCTCATAATCATTTATCATTTTTTCCATTTCAATATTT
Found at i:52404525 original size:51 final size:50
Alignment explanation
Indices: 52404399--52404578 Score: 166
Period size: 50 Copynumber: 3.6 Consensus size: 50
52404389 TGATGGTCAA
* ** ** *
52404399 GTGTGTAGTACTATGTGTAGGCTACTACGTGTCCCAG-AA-TGAAAGGTCGC
1 GTGTGTAGTACTATGTGTAGGCTACTACGCGAACCAGAAAGTTCAA--TCAC
* * * * *
52404449 ATGTGTAGTACTATGTGTAGGCTACTATGCGTACCAGATAGCTTCGATCAC
1 GTGTGTAGTACTATGTGTAGGCTACTACGCGAACCAGAAAG-TTCAATCAC
* ** *
52404500 GTGTGTAGTACTATGTGTAGGCTACTACGTGAACTGGAAAGTTTAATCAC
1 GTGTGTAGTACTATGTGTAGGCTACTACGCGAACCAGAAAGTTCAATCAC
* *
52404550 GTGTGTATTACTATGTGAAGGCTACTACG
1 GTGTGTAGTACTATGTGTAGGCTACTACG
52404579 TGTATCGAAT
Statistics
Matches: 107, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
50 67 0.63
51 38 0.36
53 2 0.02
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.31
Consensus pattern (50 bp):
GTGTGTAGTACTATGTGTAGGCTACTACGCGAACCAGAAAGTTCAATCAC
Found at i:52407299 original size:30 final size:30
Alignment explanation
Indices: 52407263--52407335 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 30
52407253 TTGACATATT
* *
52407263 CCTTTTCGTAATTCGATAACCGAAGTTATC
1 CCTTTTCATAATTCGATAACCGAAGCTATC
* * *
52407293 CCTTTTCATAGTTCGATAGCTGAAGCTATC
1 CCTTTTCATAATTCGATAACCGAAGCTATC
52407323 CCTTTTCATAATT
1 CCTTTTCATAATT
52407336 TGATGGTCTT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.25, C:0.23, G:0.12, T:0.40
Consensus pattern (30 bp):
CCTTTTCATAATTCGATAACCGAAGCTATC
Found at i:52407357 original size:30 final size:30
Alignment explanation
Indices: 52407323--52407399 Score: 104
Period size: 30 Copynumber: 2.6 Consensus size: 30
52407313 TGAAGCTATC
*
52407323 CCTTTTCATAATTTGATGGTCTTCACCATT
1 CCTTTTCATAATTTGATGGTCATCACCATT
*
52407353 CC-TTTC-TATTTTTCGATGGTCATCACCATT
1 CCTTTTCATA-ATTT-GATGGTCATCACCATT
52407383 CCTTTTCATAATTTGAT
1 CCTTTTCATAATTTGAT
52407400 AGCCAAAGCC
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
28 2 0.05
29 7 0.17
30 22 0.55
31 7 0.17
32 2 0.05
ACGTcount: A:0.19, C:0.23, G:0.09, T:0.48
Consensus pattern (30 bp):
CCTTTTCATAATTTGATGGTCATCACCATT
Found at i:52407419 original size:30 final size:30
Alignment explanation
Indices: 52407378--52407490 Score: 106
Period size: 30 Copynumber: 3.8 Consensus size: 30
52407368 ATGGTCATCA
*
52407378 CCATTCCTTTTCATAATTTGATAGCCAAAG
1 CCATCCCTTTTCATAATTTGATAGCCAAAG
* ** *
52407408 CCATCCCTTTTCA-GATATCAATAGCCGAAG
1 CCATCCCTTTTCATAAT-TTGATAGCCAAAG
* ** *
52407438 CCATCCCTTTTCATAAGTTGATAATCATCA-
1 CCATCCCTTTTCATAATTTGATAGCCA-AAG
52407468 CCATCCCTTTTCATAA-TTGATAG
1 CCATCCCTTTTCATAATTTGATAG
52407491 TTGAAGCTAT
Statistics
Matches: 66, Mismatches: 14, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
29 8 0.12
30 56 0.85
31 2 0.03
ACGTcount: A:0.29, C:0.27, G:0.10, T:0.35
Consensus pattern (30 bp):
CCATCCCTTTTCATAATTTGATAGCCAAAG
Found at i:52407477 original size:120 final size:120
Alignment explanation
Indices: 52407260--52407477 Score: 285
Period size: 120 Copynumber: 1.8 Consensus size: 120
52407250 TGGTTGACAT
* * ** * * * *
52407260 ATTCCTTTTCGTAATTCGATAACCGAAGTTATCCCTTTTCATAGTTCGATAGCTGAAGCTATCCC
1 ATTCCTTTTCATAATTCGATAACCAAAGCCATCCCTTTTCAGAGTTCAATAGCCGAAGCCATCCC
* ** * *
52407325 TTTTCATAATTTGATGGTCTTCACCATTCCTTTCTATTTTTCGATGGTCATCACC
66 TTTTCATAAGTTGATAATCATCACCATCCCTTTCTATTTTTCGATGGTCATCACC
* *
52407380 ATTCCTTTTCATAATTTGATAGCCAAAGCCATCCCTTTTCAGA-TATCAATAGCCGAAGCCATCC
1 ATTCCTTTTCATAATTCGATAACCAAAGCCATCCCTTTTCAGAGT-TCAATAGCCGAAGCCATCC
52407444 CTTTTCATAAGTTGATAATCATCACCATCCCTTT
65 CTTTTCATAAGTTGATAATCATCACCATCCCTTT
52407478 TCATAATTGA
Statistics
Matches: 82, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
119 1 0.01
120 81 0.99
ACGTcount: A:0.25, C:0.26, G:0.11, T:0.39
Consensus pattern (120 bp):
ATTCCTTTTCATAATTCGATAACCAAAGCCATCCCTTTTCAGAGTTCAATAGCCGAAGCCATCCC
TTTTCATAAGTTGATAATCATCACCATCCCTTTCTATTTTTCGATGGTCATCACC
Found at i:52414309 original size:41 final size:43
Alignment explanation
Indices: 52414212--52414317 Score: 146
Period size: 41 Copynumber: 2.5 Consensus size: 43
52414202 TTCCCTGAGG
* *
52414212 GGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTGTGAAAGT
1 GGTTGCTAAGTGCTGATTCCACCGTATCCTTGAATATGAAAGT
* *
52414255 GGTTGCTATGTGCTGATTCC-CCGTATCAC-TGAATAT-AAGGT
1 GGTTGCTAAGTGCTGATTCCACCGTATC-CTTGAATATGAAAGT
52414296 GGTTGCTAAGTGCTGATTCCAC
1 GGTTGCTAAGTGCTGATTCCAC
52414318 AGAGTAACAG
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
41 23 0.41
42 13 0.23
43 20 0.36
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (43 bp):
GGTTGCTAAGTGCTGATTCCACCGTATCCTTGAATATGAAAGT
Found at i:52418827 original size:27 final size:27
Alignment explanation
Indices: 52418769--52418827 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
52418759 AATATTGTTA
*
52418769 AAATTCTTCTAAAAAAACACTCAAGAG
1 AAATTCTTCTAAAAAAACACTCAAAAG
*
52418796 AAATTCTT-TAAAAGAAA-ACTTAAAAG
1 AAATTCTTCTAAAA-AAACACTCAAAAG
52418822 AGAATT
1 A-AATT
52418828 TTATCAACTC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 13 0.46
27 15 0.54
ACGTcount: A:0.54, C:0.12, G:0.08, T:0.25
Consensus pattern (27 bp):
AAATTCTTCTAAAAAAACACTCAAAAG
Found at i:52420597 original size:21 final size:21
Alignment explanation
Indices: 52420537--52420604 Score: 57
Period size: 21 Copynumber: 3.1 Consensus size: 21
52420527 TATTTTTTAT
* *
52420537 ATTTTTTATTTATATGCTTTTAA
1 ATTTTTTATTTAAAT--TTTAAA
* *
52420560 ATTATTTT-TTCTGAATTTTGAA
1 ATT-TTTTATT-TAAATTTTAAA
52420582 ATTTTTTATTTAAATTTTAAA
1 ATTTTTTATTTAAATTTTAAA
52420603 AT
1 AT
52420605 ATATATATAC
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
21 15 0.41
22 10 0.27
23 5 0.14
24 7 0.19
ACGTcount: A:0.31, C:0.03, G:0.04, T:0.62
Consensus pattern (21 bp):
ATTTTTTATTTAAATTTTAAA
Found at i:52421700 original size:24 final size:24
Alignment explanation
Indices: 52421660--52421716 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
52421650 TTTTAAAATA
** * *
52421660 TTTTT-AAAATACTTTTTTATTTT
1 TTTTTAAAAATAAATTTTTAGTGT
52421683 TTTTTAAAAATAAATTTTTAGTGT
1 TTTTTAAAAATAAATTTTTAGTGT
*
52421707 TTATTAAAAA
1 TTTTTAAAAA
52421717 AATGGGCCGG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 5 0.18
24 23 0.82
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.58
Consensus pattern (24 bp):
TTTTTAAAAATAAATTTTTAGTGT
Found at i:52423711 original size:231 final size:231
Alignment explanation
Indices: 52423308--52423770 Score: 926
Period size: 231 Copynumber: 2.0 Consensus size: 231
52423298 TTATTTATTT
52423308 ATTTTTTTTTAAAAATAAATTTTTAGTGTTTATTAAAAAAATGGGCCGGACTCGGGCTTAAGAAT
1 ATTTTTTTTTAAAAATAAATTTTTAGTGTTTATTAAAAAAATGGGCCGGACTCGGGCTTAAGAAT
52423373 TTTTTCTCAGGCCGGGCCTAGACAAAATTTCAGGCCCATATTTTGGGCTGGGCCAAGCTTGAACC
66 TTTTTCTCAGGCCGGGCCTAGACAAAATTTCAGGCCCATATTTTGGGCTGGGCCAAGCTTGAACC
52423438 TAGGACGCGGGCCAAAATTTTTTCTAGACCTGGCTCGTACCCGGCCCAGCCCGGCCCATGAACAC
131 TAGGACGCGGGCCAAAATTTTTTCTAGACCTGGCTCGTACCCGGCCCAGCCCGGCCCATGAACAC
52423503 CTCTAGATGTGACACGTCATTTATTTTGTTAGGTGA
196 CTCTAGATGTGACACGTCATTTATTTTGTTAGGTGA
52423539 ATTTTTTTTTAAAAATAAATTTTTAGTGTTTATTAAAAAAATGGGCCGGACTCGGGCTTAAGAAT
1 ATTTTTTTTTAAAAATAAATTTTTAGTGTTTATTAAAAAAATGGGCCGGACTCGGGCTTAAGAAT
52423604 TTTTTCTCAGGCCGGGCCTAGACAAAATTTCAGGCCCATATTTTGGGCTGGGCCAAGCTTGAACC
66 TTTTTCTCAGGCCGGGCCTAGACAAAATTTCAGGCCCATATTTTGGGCTGGGCCAAGCTTGAACC
52423669 TAGGACGCGGGCCAAAATTTTTTCTAGACCTGGCTCGTACCCGGCCCAGCCCGGCCCATGAACAC
131 TAGGACGCGGGCCAAAATTTTTTCTAGACCTGGCTCGTACCCGGCCCAGCCCGGCCCATGAACAC
52423734 CTCTAGATGTGACACGTCATTTATTTTGTTAGGTGA
196 CTCTAGATGTGACACGTCATTTATTTTGTTAGGTGA
52423770 A
1 A
52423771 AAAGGCCAAT
Statistics
Matches: 232, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
231 232 1.00
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.31
Consensus pattern (231 bp):
ATTTTTTTTTAAAAATAAATTTTTAGTGTTTATTAAAAAAATGGGCCGGACTCGGGCTTAAGAAT
TTTTTCTCAGGCCGGGCCTAGACAAAATTTCAGGCCCATATTTTGGGCTGGGCCAAGCTTGAACC
TAGGACGCGGGCCAAAATTTTTTCTAGACCTGGCTCGTACCCGGCCCAGCCCGGCCCATGAACAC
CTCTAGATGTGACACGTCATTTATTTTGTTAGGTGA
Found at i:52425684 original size:31 final size:33
Alignment explanation
Indices: 52425613--52425691 Score: 92
Period size: 36 Copynumber: 2.4 Consensus size: 33
52425603 ATATATGAAT
*
52425613 TATAAATAAGTTATAAAATATGTATGGGTATAGGTA
1 TATATATAA-TTATAAAATATGTAT-GGTATA-GTA
52425649 TATATATATATTATAAAA-ATGTAT-GTAT-GTA
1 TATATATA-ATTATAAAATATGTATGGTATAGTA
52425680 TATATATAATTA
1 TATATATAATTA
52425692 AATCCAAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
30 4 0.10
31 11 0.27
33 4 0.10
35 6 0.15
36 15 0.37
37 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.13, T:0.42
Consensus pattern (33 bp):
TATATATAATTATAAAATATGTATGGTATAGTA
Found at i:52427981 original size:219 final size:219
Alignment explanation
Indices: 52427546--52428525 Score: 1532
Period size: 219 Copynumber: 4.5 Consensus size: 219
52427536 CACTGCAACT
* * *
52427546 TCAGGG-GATAAGCCTGGTGCTTTCAATCTGCTTCACTGCCAGTACAAGAAGACAAGATCTACAA
1 TCAGGGAGATAAGGCTGGTGCTTTCGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTACAA
* * * * **
52427610 TCATCGACCTACTCCACTGCTACTTAGGGAGATAAGG-CTAATGGCTTAAATCTACTTCCCTACT
66 TCTTCGACCTACTCCGCTGCTGCTCAGGGAGAT-AGGACTGGTGGCTTAAATCTACTT-CCTACT
* * ** * *
52427674 ACCTTGGGAAGATAAGATTCGTCGTCTTTAATCTGCTCCACTATTGCCTAGGGAGATAAGATCTA
129 ATCTTGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTA
52427739 CAATCTTCAACCTACTCCACTGCTCC
194 CAATCTTCAACCTACTCCACTGCTCC
52427765 TCAGGGAGATAAGGCTGGTGCTTTCGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTACAA
1 TCAGGGAGATAAGGCTGGTGCTTTCGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTACAA
* *
52427830 TCTTCGACCTACTTCGCTGCTGCTCAGGGAGATAGGACTGGTGGCTTAAATCTATTTCCTACTAT
66 TCTTCGACCTACTCCGCTGCTGCTCAGGGAGATAGGACTGGTGGCTTAAATCTACTTCCTACTAT
* *
52427895 CTTGGGAAGATAAGATTCGTCGTCTTCGATCTGCTCCAGTACTGCTTAGGGAGATAAGATCTACA
131 CTTGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACA
52427960 ATCTTCAACCTACTCCACTGCTCC
196 ATCTTCAACCTACTCCACTGCTCC
* *
52427984 TCAGGGAGATAAGGCTGGTGCTTTCGATCTGCTTCACTGCCAGTAAAGAAAGACAAGATCTACAA
1 TCAGGGAGATAAGGCTGGTGCTTTCGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTACAA
* * *
52428049 TCTTCGACCTACTCCACTGTTGCTCAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCTACTAT
66 TCTTCGACCTACTCCGCTGCTGCTCAGGGAGATAGGACTGGTGGCTTAAATCTACTTCCTACTAT
* *
52428114 CTTGGGAAGATAAGATTCGCCATCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTACA
131 CTTGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACA
*
52428179 ATCTTCAACCTACTCCACTGCTGC
196 ATCTTCAACCTACTCCACTGCTCC
* * * *
52428203 TGAGAGAGATAAGGCTGGTGCTTTCGATCTGCTTCACTGCCAATACAGGAAGACAAGATCTATAA
1 TCAGGGAGATAAGGCTGGTGCTTTCGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTACAA
* * *
52428268 TCTTCAACCTACTCCGCTGCTGCTCAGGGACATAGGACTGGTGGCTTAAATCTGCTTCCTACTAT
66 TCTTCGACCTACTCCGCTGCTGCTCAGGGAGATAGGACTGGTGGCTTAAATCTACTTCCTACTAT
* *
52428333 TTTGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTTCTTAGGGAGATAAGATCTACA
131 CTTGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACA
*
52428398 ATCTTCAACCTACTCCACTGCTGC
196 ATCTTCAACCTACTCCACTGCTCC
* * * *
52428422 TCAGGGAGATAAGGCTGGTGCTGTCAATCTACTTCACTACCAGTACAGGAAGACAAGATCTACAA
1 TCAGGGAGATAAGGCTGGTGCTTTCGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTACAA
* * *
52428487 TCTTTGACCTACTCCGTTGCTGCTCAGAGAGATAGGACT
66 TCTTCGACCTACTCCGCTGCTGCTCAGGGAGATAGGACT
52428526 TGATATGATG
Statistics
Matches: 703, Mismatches: 56, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
219 603 0.86
220 100 0.14
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (219 bp):
TCAGGGAGATAAGGCTGGTGCTTTCGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTACAA
TCTTCGACCTACTCCGCTGCTGCTCAGGGAGATAGGACTGGTGGCTTAAATCTACTTCCTACTAT
CTTGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACA
ATCTTCAACCTACTCCACTGCTCC
Found at i:52428905 original size:24 final size:24
Alignment explanation
Indices: 52428853--52428908 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
52428843 GATTACCCCT
52428853 ACTGTAATCTTCAAAATTCAATCC
1 ACTGTAATCTTCAAAATTCAATCC
* **
52428877 GCTGTAATCTTCAAGGTT-AAGTCC
1 ACTGTAATCTTCAAAATTCAA-TCC
52428901 ACTGTAAT
1 ACTGTAAT
52428909 TTTGGGACAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 2 0.07
24 25 0.93
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.34
Consensus pattern (24 bp):
ACTGTAATCTTCAAAATTCAATCC
Found at i:52429878 original size:22 final size:22
Alignment explanation
Indices: 52429852--52429894 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
52429842 TGGCCTCTCC
52429852 TTTTTCTTTTCTTTTCTTTTTA
1 TTTTTCTTTTCTTTTCTTTTTA
*
52429874 TTTTTCTTTTCTTTTTTTTTT
1 TTTTTCTTTTCTTTTCTTTTT
52429895 TGAACATTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (22 bp):
TTTTTCTTTTCTTTTCTTTTTA
Found at i:52429880 original size:12 final size:11
Alignment explanation
Indices: 52429851--52429894 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
52429841 TTGGCCTCTC
*
52429851 CTTTTTCTTTT
1 CTTTTTTTTTT
*
52429862 CTTTTCTTTTT
1 CTTTTTTTTTT
* *
52429873 ATTTTTCTTTT
1 CTTTTTTTTTT
52429884 CTTTTTTTTTT
1 CTTTTTTTTTT
52429895 TGAACATTCT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (11 bp):
CTTTTTTTTTT
Found at i:52429895 original size:17 final size:17
Alignment explanation
Indices: 52429852--52429895 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
52429842 TGGCCTCTCC
*
52429852 TTTTTCTTTTCTTTTCT
1 TTTTTTTTTTCTTTTCT
*
52429869 TTTTATTTTTCTTTTCT
1 TTTTTTTTTTCTTTTCT
52429886 TTTTTTTTTT
1 TTTTTTTTTT
52429896 GAACATTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.02, C:0.11, G:0.00, T:0.86
Consensus pattern (17 bp):
TTTTTTTTTTCTTTTCT
Found at i:52432170 original size:12 final size:12
Alignment explanation
Indices: 52432139--52432172 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
52432129 TTTTTCTAGT
52432139 TGTTCTTGCATC
1 TGTTCTTGCATC
**
52432151 TGGGCTTGCATC
1 TGTTCTTGCATC
52432163 TGTTCTTGCA
1 TGTTCTTGCA
52432173 ATTGCTCTAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.09, C:0.24, G:0.24, T:0.44
Consensus pattern (12 bp):
TGTTCTTGCATC
Found at i:52434863 original size:415 final size:415
Alignment explanation
Indices: 52434093--52434926 Score: 1668
Period size: 415 Copynumber: 2.0 Consensus size: 415
52434083 CCAAAATTGG
52434093 TTCCTAGTTGGTTAATTAGTGTCTTGGTGTCGAAAATTAAAAAATCAAAAAGAATTTAAAAAAAT
1 TTCCTAGTTGGTTAATTAGTGTCTTGGTGTCGAAAATTAAAAAATCAAAAAGAATTTAAAAAAAT
52434158 ACGATCCCTCTTTATATTGTGTTATTTCAAAATTACTCGAATAAATCAAAATGGAAAATGCCTCC
66 ACGATCCCTCTTTATATTGTGTTATTTCAAAATTACTCGAATAAATCAAAATGGAAAATGCCTCC
52434223 TTATCTCAAAGTAACAAGATGTCACATCCAGTAACTTAGGACACGATACCTCGTATTTTTTAGAG
131 TTATCTCAAAGTAACAAGATGTCACATCCAGTAACTTAGGACACGATACCTCGTATTTTTTAGAG
52434288 TAAGCTTTCCTTTTATTTTTTATTTAAACCTCATTTATTTCAATTTTAAAAGGATATTCGGTTAT
196 TAAGCTTTCCTTTTATTTTTTATTTAAACCTCATTTATTTCAATTTTAAAAGGATATTCGGTTAT
52434353 TTAGATTCAACGCGAGAAAAATCGAAACCCAGTAAGTTAGGGCACGACTTCTCGAATTTCTAAAT
261 TTAGATTCAACGCGAGAAAAATCGAAACCCAGTAAGTTAGGGCACGACTTCTCGAATTTCTAAAT
52434418 ACAAAATATTGCCTTTATTATTTTTAGAAAAATCTTCATCTCGAGGAAACAATGTGTCATATCCA
326 ACAAAATATTGCCTTTATTATTTTTAGAAAAATCTTCATCTCGAGGAAACAATGTGTCATATCCA
52434483 ATGCGTTAGGACACGACGTATTGAA
391 ATGCGTTAGGACACGACGTATTGAA
52434508 TTCCTAGTTGGTTAATTAGTGTCTTGGTGTCGAAAATTAAAAAATCAAAAAGAATTTAAAAAAAT
1 TTCCTAGTTGGTTAATTAGTGTCTTGGTGTCGAAAATTAAAAAATCAAAAAGAATTTAAAAAAAT
52434573 ACGATCCCTCTTTATATTGTGTTATTTCAAAATTACTCGAATAAATCAAAATGGAAAATGCCTCC
66 ACGATCCCTCTTTATATTGTGTTATTTCAAAATTACTCGAATAAATCAAAATGGAAAATGCCTCC
52434638 TTATCTCAAAGTAACAAGATGTCACATCCAGTAACTTAGGACACGATACCTCGTATTTTTTAGAG
131 TTATCTCAAAGTAACAAGATGTCACATCCAGTAACTTAGGACACGATACCTCGTATTTTTTAGAG
52434703 TAAGCTTTCCTTTTATTTTTTATTTAAACCTCATTTATTTCAATTTTAAAAGGATATTCGGTTAT
196 TAAGCTTTCCTTTTATTTTTTATTTAAACCTCATTTATTTCAATTTTAAAAGGATATTCGGTTAT
52434768 TTAGATTCAACGCGAGAAAAATCGAAACCCAGTAAGTTAGGGCACGACTTCTCGAATTTCTAAAT
261 TTAGATTCAACGCGAGAAAAATCGAAACCCAGTAAGTTAGGGCACGACTTCTCGAATTTCTAAAT
52434833 ACAAAATATTGCCTTTATTATTTTTAGAAAAATCTTCATCTCGAGGAAACAATGTGTCATATCCA
326 ACAAAATATTGCCTTTATTATTTTTAGAAAAATCTTCATCTCGAGGAAACAATGTGTCATATCCA
52434898 ATGCGTTAGGACACGACGTATTGAA
391 ATGCGTTAGGACACGACGTATTGAA
52434923 TTCC
1 TTCC
52434927 CGGTAATGAG
Statistics
Matches: 419, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
415 419 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (415 bp):
TTCCTAGTTGGTTAATTAGTGTCTTGGTGTCGAAAATTAAAAAATCAAAAAGAATTTAAAAAAAT
ACGATCCCTCTTTATATTGTGTTATTTCAAAATTACTCGAATAAATCAAAATGGAAAATGCCTCC
TTATCTCAAAGTAACAAGATGTCACATCCAGTAACTTAGGACACGATACCTCGTATTTTTTAGAG
TAAGCTTTCCTTTTATTTTTTATTTAAACCTCATTTATTTCAATTTTAAAAGGATATTCGGTTAT
TTAGATTCAACGCGAGAAAAATCGAAACCCAGTAAGTTAGGGCACGACTTCTCGAATTTCTAAAT
ACAAAATATTGCCTTTATTATTTTTAGAAAAATCTTCATCTCGAGGAAACAATGTGTCATATCCA
ATGCGTTAGGACACGACGTATTGAA
Found at i:52435298 original size:9 final size:9
Alignment explanation
Indices: 52435284--52435338 Score: 53
Period size: 9 Copynumber: 6.2 Consensus size: 9
52435274 CAAATAAGAC
52435284 AATAATAAA
1 AATAATAAA
*
52435293 AATAATGAA
1 AATAATAAA
52435302 AATAA-ATAA
1 AATAATA-AA
*
52435311 AATTATAAA
1 AATAATAAA
52435320 AATAA-AAA
1 AATAATAAA
52435328 TAA-AATAAA
1 -AATAATAAA
52435337 AA
1 AA
52435339 AGGGGACTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
8 7 0.18
9 30 0.79
10 1 0.03
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (9 bp):
AATAATAAA
Found at i:52435305 original size:18 final size:18
Alignment explanation
Indices: 52435264--52435339 Score: 59
Period size: 18 Copynumber: 4.2 Consensus size: 18
52435254 ACACATAAAG
*
52435264 AAATAAATATCAAATAAGA
1 AAATAAATA-AAAATAAGA
*
52435283 CAAT-AATAAAAATAATGA
1 AAATAAATAAAAATAA-GA
*
52435301 AAATAAATAAAATTATA-A
1 AAATAAATAAAAATA-AGA
*
52435319 AAATAAAAATAAAATAA-A
1 AAATAAATA-AAAATAAGA
52435337 AAA
1 AAA
52435340 GGGGACTATT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
17 6 0.13
18 23 0.49
19 17 0.36
20 1 0.02
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (18 bp):
AAATAAATAAAAATAAGA
Found at i:52435791 original size:19 final size:20
Alignment explanation
Indices: 52435769--52435810 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
52435759 GGCGAAGGCT
*
52435769 CCGGCCATCGGCCGCC-GCG
1 CCGGCCACCGGCCGCCGGCG
*
52435788 CCGGCCACCGGTCGCCGGCG
1 CCGGCCACCGGCCGCCGGCG
52435808 CCG
1 CCG
52435811 CCTTGGGGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.05, C:0.52, G:0.38, T:0.05
Consensus pattern (20 bp):
CCGGCCACCGGCCGCCGGCG
Found at i:52440478 original size:19 final size:19
Alignment explanation
Indices: 52440454--52440491 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
52440444 TGGGCCACGT
52440454 TGGGCTGAAATGGGC-CGTG
1 TGGGCT-AAATGGGCTCGTG
*
52440473 TGGGCTCAATGGGCTCGTG
1 TGGGCTAAATGGGCTCGTG
52440492 GGCCCTACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.13, C:0.18, G:0.45, T:0.24
Consensus pattern (19 bp):
TGGGCTAAATGGGCTCGTG
Found at i:52440935 original size:27 final size:27
Alignment explanation
Indices: 52440725--52440924 Score: 240
Period size: 27 Copynumber: 7.4 Consensus size: 27
52440715 ACCCTAAAAT
* *
52440725 GGGTAAAATAATCGAAATACCCCCATA
1 GGGTAAAATGACCGAAATACCCCCATA
* * *
52440752 AGATAAAATGACCAAAATACCCCCATA
1 GGGTAAAATGACCGAAATACCCCCATA
* **
52440779 GGATAAAATGACCGAAATACCCTTATA
1 GGGTAAAATGACCGAAATACCCCCATA
* *
52440806 GGGTAAAATGACTGAAATATCCCCATA
1 GGGTAAAATGACCGAAATACCCCCATA
** *
52440833 GGGTAAAATGATAGGAATACCCCCATA
1 GGGTAAAATGACCGAAATACCCCCATA
* * * *
52440860 AGGTAGAATGAGCGAAATA-CCCCATG
1 GGGTAAAATGACCGAAATACCCCCATA
52440886 GGGTAAAATGACCGAAATACCCCCATA
1 GGGTAAAATGACCGAAATACCCCCATA
52440913 GGGTAAAATGAC
1 GGGTAAAATGAC
52440925 TGTTATACCC
Statistics
Matches: 144, Mismatches: 28, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
26 22 0.15
27 122 0.85
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.18
Consensus pattern (27 bp):
GGGTAAAATGACCGAAATACCCCCATA
Found at i:52446736 original size:19 final size:19
Alignment explanation
Indices: 52446720--52446769 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
52446710 TCAACTCTTC
52446720 CAACTCTCTCAAACTCTCT
1 CAACTCTCTCAAACTCTCT
* *
52446739 CAACTCTGTCAAACCCTCT
1 CAACTCTCTCAAACTCTCT
*
52446758 CAAGTCTCTCAA
1 CAACTCTCTCAA
52446770 CTTTCTCGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.28, C:0.40, G:0.04, T:0.28
Consensus pattern (19 bp):
CAACTCTCTCAAACTCTCT
Found at i:52446742 original size:28 final size:28
Alignment explanation
Indices: 52446710--52446771 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
52446700 CATCCTTCTT
* *
52446710 TCAACTCT-TCCAACTCTCTCAAACTCTC
1 TCAACTCTGTCAAACCCTCTC-AACTCTC
*
52446738 TCAACTCTGTCAAACCCTCTCAAGTCTC
1 TCAACTCTGTCAAACCCTCTCAACTCTC
52446766 TCAACT
1 TCAACT
52446772 TTCTCGTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 20 0.67
29 10 0.33
ACGTcount: A:0.26, C:0.40, G:0.03, T:0.31
Consensus pattern (28 bp):
TCAACTCTGTCAAACCCTCTCAACTCTC
Found at i:52446750 original size:9 final size:9
Alignment explanation
Indices: 52446710--52446776 Score: 64
Period size: 9 Copynumber: 7.2 Consensus size: 9
52446700 CATCCTTCTT
52446710 TCAACTCT-
1 TCAACTCTC
52446718 TCCAACTCTC
1 T-CAACTCTC
52446728 TCAAACTCTC
1 TC-AACTCTC
*
52446738 TCAACTCTG
1 TCAACTCTC
*
52446747 TCAAACCCTC
1 TC-AACTCTC
*
52446757 TCAAGTCTC
1 TCAACTCTC
*
52446766 TCAACTTTC
1 TCAACTCTC
52446775 TC
1 TC
52446777 GTTTTAAATT
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
8 1 0.02
9 30 0.62
10 17 0.35
ACGTcount: A:0.24, C:0.40, G:0.03, T:0.33
Consensus pattern (9 bp):
TCAACTCTC
Found at i:52459541 original size:218 final size:219
Alignment explanation
Indices: 52459283--52459720 Score: 869
Period size: 218 Copynumber: 2.0 Consensus size: 219
52459273 TGTAATAGTT
52459283 AAAATATTCATGAGTCTTTATACTCTTTACGAATTTAGAATTTAGTCTTTTCACTTTTAGATTTA
1 AAAATATTCATGAGTCTTTATACTCTTTACGAATTTAGAATTTAGTCTTTTCACTTTTAGATTTA
52459348 GCAATTCAGAGCTAACTATTAATACTCTTAAAATTATTTTGATAAATACAGGTTTAGTACAACAT
66 GCAATTCAGAGCTAACTATTAATACTCTTAAAATTATTTTGATAAATACAGGTTTAGTACAACAT
52459413 CATTTAACAAAAAAAAATAACAGTGTTAACAAATAGACCTAAATTTAAATTTAAAAAATAACTAA
131 CATTTAACAAAAAAAAATAACAGTGTTAACAAATAGACCTAAATTTAAATTTAAAAAATAACTAA
52459478 AATTTTGAAAATAAAAATATATAA
196 AATTTTGAAAATAAAAATATATAA
52459502 AAAATATTCAT-AGTCTTTATACTCTTTACGAATTTAGAATTTAGTCTTTTCACTTTTAGATTTA
1 AAAATATTCATGAGTCTTTATACTCTTTACGAATTTAGAATTTAGTCTTTTCACTTTTAGATTTA
52459566 GCAATTCAGAGCTAACTATTAATACTCTTAAAATTATTTTGATAAATACAGGTTTAGTACAACAT
66 GCAATTCAGAGCTAACTATTAATACTCTTAAAATTATTTTGATAAATACAGGTTTAGTACAACAT
52459631 CATTTAACAAAAAAAAATAACAGTGTTAACAAATAGACCTAAATTTAAATTTAAAAAATAACTAA
131 CATTTAACAAAAAAAAATAACAGTGTTAACAAATAGACCTAAATTTAAATTTAAAAAATAACTAA
52459696 AATTTTGAAAATAAAAATATATAA
196 AATTTTGAAAATAAAAATATATAA
52459720 A
1 A
52459721 CTAAAGGCTA
Statistics
Matches: 219, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
218 208 0.95
219 11 0.05
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (219 bp):
AAAATATTCATGAGTCTTTATACTCTTTACGAATTTAGAATTTAGTCTTTTCACTTTTAGATTTA
GCAATTCAGAGCTAACTATTAATACTCTTAAAATTATTTTGATAAATACAGGTTTAGTACAACAT
CATTTAACAAAAAAAAATAACAGTGTTAACAAATAGACCTAAATTTAAATTTAAAAAATAACTAA
AATTTTGAAAATAAAAATATATAA
Found at i:52460837 original size:6 final size:6
Alignment explanation
Indices: 52460826--52460856 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
52460816 TTACTTCAAA
52460826 TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT T
1 TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT T
52460857 GGCATTCGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (6 bp):
TTTTGT
Found at i:52460973 original size:15 final size:15
Alignment explanation
Indices: 52460953--52461056 Score: 61
Period size: 15 Copynumber: 6.6 Consensus size: 15
52460943 TACCAAAGTA
*
52460953 TGTTATGTATATTAC
1 TGTTATGTATATTAT
* *
52460968 TGTTATGTATGTTGT
1 TGTTATGTATATTAT
*
52460983 TATTATTGT-TATGTATGT
1 TGTTA-TGTATAT-TA--T
52461001 ATGTTATGTATATTAT
1 -TGTTATGTATATTAT
*
52461017 TGTTATGTAT-GT-T
1 TGTTATGTATATTAT
*
52461030 TGTTACGTGGTATATTGT
1 TGTTA--T-GTATATTAT
52461048 TGTTATGTA
1 TGTTATGTA
52461057 CGTAACAGTT
Statistics
Matches: 69, Mismatches: 9, Indels: 22
0.69 0.09 0.22
Matches are distributed among these distances:
13 6 0.09
14 1 0.01
15 32 0.46
16 10 0.14
17 1 0.01
18 12 0.17
19 7 0.10
ACGTcount: A:0.21, C:0.02, G:0.20, T:0.57
Consensus pattern (15 bp):
TGTTATGTATATTAT
Found at i:52460980 original size:9 final size:9
Alignment explanation
Indices: 52460950--52461029 Score: 62
Period size: 9 Copynumber: 8.8 Consensus size: 9
52460940 CTTTACCAAA
52460950 GTATGTTAT
1 GTATGTTAT
*
52460959 GTATATTACT
1 GTATGTTA-T
52460969 GTTATG-TAT
1 G-TATGTTAT
52460978 GT-TGTTAT
1 GTATGTTAT
52460986 -TATTGTTAT
1 GTA-TGTTAT
52460995 GTATG-TAT
1 GTATGTTAT
52461003 GTTATGTATAT
1 G-TATGT-TAT
52461014 -TATTGTTAT
1 GTA-TGTTAT
52461023 GTATGTT
1 GTATGTT
52461030 TGTTACGTGG
Statistics
Matches: 58, Mismatches: 2, Indels: 22
0.71 0.02 0.27
Matches are distributed among these distances:
7 3 0.05
8 8 0.14
9 30 0.52
10 11 0.19
11 6 0.10
ACGTcount: A:0.23, C:0.01, G:0.19, T:0.57
Consensus pattern (9 bp):
GTATGTTAT
Found at i:52460992 original size:21 final size:22
Alignment explanation
Indices: 52460950--52461029 Score: 83
Period size: 21 Copynumber: 3.5 Consensus size: 22
52460940 CTTTACCAAA
52460950 GTATGTTATGTATATTACTGTTAT
1 GTATG-TATGT-TATTACTGTTAT
*
52460974 GTATGT-TGTTATTATTGTTAT
1 GTATGTATGTTATTACTGTTAT
*
52460995 GTATGTATGTTATGTA-TATTATT
1 GTATGTATGTTAT-TACTGTTA-T
52461018 GTTATGTATGTT
1 G-TATGTATGTT
52461030 TGTTACGTGG
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
21 17 0.34
22 13 0.26
23 5 0.10
24 15 0.30
ACGTcount: A:0.23, C:0.01, G:0.19, T:0.57
Consensus pattern (22 bp):
GTATGTATGTTATTACTGTTAT
Found at i:52461043 original size:31 final size:28
Alignment explanation
Indices: 52460950--52461056 Score: 111
Period size: 28 Copynumber: 4.0 Consensus size: 28
52460940 CTTTACCAAA
*
52460950 GTATGTTATGTATATTACTG---T-TAT
1 GTATGTTATGTATATTATTGTTATGTAT
52460974 GTATG-T-TGT-TATTATTGTTATGTAT
1 GTATGTTATGTATATTATTGTTATGTAT
52460999 GTATGTTATGTATATTATTGTTATGTAT
1 GTATGTTATGTATATTATTGTTATGTAT
* *
52461027 GTTTGTTACGTGGTATATTGTTGTTATGTA
1 GTATGTTA--T-GTATATTATTGTTATGTA
52461057 CGTAACAGTT
Statistics
Matches: 70, Mismatches: 3, Indels: 13
0.81 0.03 0.15
Matches are distributed among these distances:
21 7 0.10
22 3 0.04
23 1 0.01
24 6 0.09
25 8 0.11
26 1 0.01
27 3 0.04
28 23 0.33
30 1 0.01
31 17 0.24
ACGTcount: A:0.21, C:0.02, G:0.21, T:0.56
Consensus pattern (28 bp):
GTATGTTATGTATATTATTGTTATGTAT
Found at i:52461101 original size:33 final size:31
Alignment explanation
Indices: 52460975--52461102 Score: 120
Period size: 33 Copynumber: 4.1 Consensus size: 31
52460965 TACTGTTATG
* *
52460975 TATGTTGT-TATTATTGTTATGTATGTATGT
1 TATGTGGTATATTATTGTTATGTATGTCTGT
*
52461005 TA--T-GTATATTATTGTTATGTATGTTTGT
1 TATGTGGTATATTATTGTTATGTATGTCTGT
* * * *
52461033 TACGTGGTATATTGTTGTTATGTACGTAACAGT
1 TATGTGGTATATTATTGTTATGTATGT--CTGT
*
52461066 TATGTGGTATATTACTGTTATGAATATGTCTGT
1 TATGTGGTATATTATTGTTATG--TATGTCTGT
52461099 TATG
1 TATG
52461103 CTTGTATGTT
Statistics
Matches: 80, Mismatches: 10, Indels: 13
0.78 0.10 0.13
Matches are distributed among these distances:
27 2 0.03
28 24 0.30
30 3 0.04
31 19 0.24
33 28 0.35
35 4 0.05
ACGTcount: A:0.23, C:0.04, G:0.21, T:0.52
Consensus pattern (31 bp):
TATGTGGTATATTATTGTTATGTATGTCTGT
Found at i:52461203 original size:79 final size:79
Alignment explanation
Indices: 52461050--52461204 Score: 206
Period size: 79 Copynumber: 2.0 Consensus size: 79
52461040 TATATTGTTG
* * * *
52461050 TTATGTACGTAACAGTTATGTGGTATATTACTGTTATGAATATGTCTGTTATGCTTGTATGTTCT
1 TTATGTACGTAACAGTTATGTGGTATATTACTATTATAAACATGTCTGTTATGCTTGTATATTCT
*
52461115 GTAGTATTTTACTA
66 GTAGCATTTTACTA
* * *
52461129 TTATGTATGTGACTGTTATGTGGTATATTACTATTATAAACATGTCTGTTATG-TATGTATATTA
1 TTATGTACGTAACAGTTATGTGGTATATTACTATTATAAACATGTCTGTTATGCT-TGTATATT-
52461193 C-GTAGCATTTTA
64 CTGTAGCATTTTA
52461205 ATGTTTATGA
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
78 1 0.02
79 64 0.97
80 1 0.02
ACGTcount: A:0.26, C:0.08, G:0.18, T:0.48
Consensus pattern (79 bp):
TTATGTACGTAACAGTTATGTGGTATATTACTATTATAAACATGTCTGTTATGCTTGTATATTCT
GTAGCATTTTACTA
Found at i:52461229 original size:9 final size:9
Alignment explanation
Indices: 52461215--52461261 Score: 62
Period size: 9 Copynumber: 5.4 Consensus size: 9
52461205 ATGTTTATGA
*
52461215 ATGTATATT
1 ATGTATGTT
52461224 ATGTATGTT
1 ATGTATGTT
*
52461233 ATGT-T-TA
1 ATGTATGTT
52461240 ATGTATGTT
1 ATGTATGTT
52461249 ATGTATGTT
1 ATGTATGTT
52461258 ATGT
1 ATGT
52461262 TTAAAGAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
7 5 0.15
8 2 0.06
9 26 0.79
ACGTcount: A:0.26, C:0.00, G:0.19, T:0.55
Consensus pattern (9 bp):
ATGTATGTT
Found at i:52461245 original size:25 final size:25
Alignment explanation
Indices: 52461214--52461265 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
52461204 AATGTTTATG
52461214 AATGTATATTATGTATGTTATGTTT
1 AATGTATATTATGTATGTTATGTTT
*
52461239 AATGTATGTTATGTATGTTATGTTT
1 AATGTATATTATGTATGTTATGTTT
52461264 AA
1 AA
52461266 AGAATGTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.29, C:0.00, G:0.17, T:0.54
Consensus pattern (25 bp):
AATGTATATTATGTATGTTATGTTT
Found at i:52461272 original size:25 final size:25
Alignment explanation
Indices: 52461222--52461277 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
52461212 TGAATGTATA
* *
52461222 TTATGTATGTTATGTTTAATGTATG
1 TTATGTATGTTATGTTTAAAGAATG
52461247 TTATGTATGTTATGTTTAAAGAATG
1 TTATGTATGTTATGTTTAAAGAATG
52461272 TTATGT
1 TTATGT
52461278 TTAGCACTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.27, C:0.00, G:0.20, T:0.54
Consensus pattern (25 bp):
TTATGTATGTTATGTTTAAAGAATG
Found at i:52466776 original size:30 final size:31
Alignment explanation
Indices: 52466742--52466801 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
52466732 AAACCTTTTA
*
52466742 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
52466772 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
52466802 TCNNNNNNNN
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:52470248 original size:25 final size:25
Alignment explanation
Indices: 52470220--52470274 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
52470210 ATGCTCCTTT
*
52470220 GAGCTGAATAACGGTAAGCTCATGC
1 GAGCTGAATAACGGTAAGCTCATAC
* *
52470245 GAGCTGAGTATCGGTAAGCTCATAC
1 GAGCTGAATAACGGTAAGCTCATAC
52470270 GAGCT
1 GAGCT
52470275 AAAATCAGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (25 bp):
GAGCTGAATAACGGTAAGCTCATAC
Found at i:52471826 original size:30 final size:31
Alignment explanation
Indices: 52471786--52471849 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 31
52471776 TAATAAATAA
52471786 AATTATCCAACCCAACCCAATGACCCAACCC
1 AATTATCCAACCCAACCCAATGACCCAACCC
* * *
52471817 AATTA-CCAACCTAACCTAATTACCCAACCC
1 AATTATCCAACCCAACCCAATGACCCAACCC
52471847 AAT
1 AAT
52471850 AAAACTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 25 0.83
31 5 0.17
ACGTcount: A:0.41, C:0.41, G:0.02, T:0.17
Consensus pattern (31 bp):
AATTATCCAACCCAACCCAATGACCCAACCC
Found at i:52471827 original size:12 final size:13
Alignment explanation
Indices: 52471795--52471819 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52471785 AAATTATCCA
52471795 ACCCAACCCAATG
1 ACCCAACCCAATG
52471808 ACCCAACCCAAT
1 ACCCAACCCAAT
52471820 TACCAACCTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.48, G:0.04, T:0.08
Consensus pattern (13 bp):
ACCCAACCCAATG
Found at i:52471837 original size:17 final size:18
Alignment explanation
Indices: 52471812--52471845 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
52471802 CCAATGACCC
52471812 AACCCAATTA-CCAACCT
1 AACCCAATTACCCAACCT
*
52471829 AACCTAATTACCCAACC
1 AACCCAATTACCCAACC
52471846 CAATAAAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.41, C:0.41, G:0.00, T:0.18
Consensus pattern (18 bp):
AACCCAATTACCCAACCT
Found at i:52471886 original size:38 final size:39
Alignment explanation
Indices: 52471834--52471907 Score: 132
Period size: 38 Copynumber: 1.9 Consensus size: 39
52471824 AACCTAACCT
*
52471834 AATTACCCAACCCAATAAAACTAAAACTAAAGTCTACCC
1 AATTACCCAACCCAATAAAAATAAAACTAAAGTCTACCC
52471873 AATTA-CCAACCCAATAAAAATAAAACTAAAGTCTA
1 AATTACCCAACCCAATAAAAATAAAACTAAAGTCTA
52471908 ACTCTTAAGT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
38 29 0.85
39 5 0.15
ACGTcount: A:0.53, C:0.26, G:0.03, T:0.19
Consensus pattern (39 bp):
AATTACCCAACCCAATAAAAATAAAACTAAAGTCTACCC
Found at i:52472066 original size:37 final size:37
Alignment explanation
Indices: 52472039--52472113 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 37
52472029 TGTTAATTTC
* *
52472039 AAGAATTATGTAATGTTTTTAATTATGTAGTAATTCA
1 AAGAATTATGTAATATTTTTAAATATGTAGTAATTCA
* *
52472076 AAGACTTATGTAATATTTTTAAATATGTAGTGATTCA
1 AAGAATTATGTAATATTTTTAAATATGTAGTAATTCA
52472113 A
1 A
52472114 TTCGGGTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.39, C:0.04, G:0.13, T:0.44
Consensus pattern (37 bp):
AAGAATTATGTAATATTTTTAAATATGTAGTAATTCA
Found at i:52476030 original size:44 final size:44
Alignment explanation
Indices: 52475927--52476079 Score: 155
Period size: 44 Copynumber: 3.4 Consensus size: 44
52475917 CAATCATATT
* **
52475927 TAATGTCATAGTATCTTTTCAACTATGGTCTTGTTCATTTTTCGGTA
1 TAATGCCATAGTATCTTTT-AACTATGGTCTTACTCA--TTTCGGTA
* * * * * *
52475974 TAGTGTCGTAGTATCTTTTAACTAAGGTCTTACCCATTTCGGTT
1 TAATGCCATAGTATCTTTTAACTATGGTCTTACTCATTTCGGTA
* * *
52476018 TAATGCCATAGTATCTTTCAACTATGGTCTTTCTCATTTCAGTA
1 TAATGCCATAGTATCTTTTAACTATGGTCTTACTCATTTCGGTA
52476062 TAATGCCAT-GATATCTTT
1 TAATGCCATAG-TATCTTT
52476080 CAACCATTGT
Statistics
Matches: 89, Mismatches: 16, Indels: 5
0.81 0.15 0.05
Matches are distributed among these distances:
43 1 0.01
44 58 0.65
46 13 0.15
47 17 0.19
ACGTcount: A:0.23, C:0.18, G:0.14, T:0.45
Consensus pattern (44 bp):
TAATGCCATAGTATCTTTTAACTATGGTCTTACTCATTTCGGTA
Found at i:52478643 original size:21 final size:21
Alignment explanation
Indices: 52478587--52478643 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
52478577 ATAAACAAGC
*
52478587 CAAGTCTCAAGACTTATAGGT
1 CAAGTTTCAAGACTTATAGGT
* *
52478608 TAAGTATT-AAAACTTATAGGT
1 CAAGT-TTCAAGACTTATAGGT
52478629 CAAGTTTCAAGACTT
1 CAAGTTTCAAGACTT
52478644 GACATTCAAG
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 2 0.07
21 26 0.90
22 1 0.03
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (21 bp):
CAAGTTTCAAGACTTATAGGT
Found at i:52479315 original size:24 final size:24
Alignment explanation
Indices: 52479245--52479314 Score: 63
Period size: 24 Copynumber: 2.9 Consensus size: 24
52479235 AAAAAATGAA
* *
52479245 TTTTTATATAATTTTTAAACTTTTA-
1 TTTTTAAAT-ATTTTTATA-TTTTAT
* *
52479270 -TTTTCAATATTTTTTTATTTTAT
1 TTTTTAAATATTTTTATATTTTAT
52479293 TTTTTAAATATTTTATATATTT
1 TTTTTAAATATTTT-TATATTT
52479315 AAAAAATTGT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
22 5 0.14
23 7 0.19
24 18 0.50
25 6 0.17
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.69
Consensus pattern (24 bp):
TTTTTAAATATTTTTATATTTTAT
Found at i:52491267 original size:12 final size:12
Alignment explanation
Indices: 52491250--52491275 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
52491240 CCACTAAATT
52491250 AAAGAATTAAAG
1 AAAGAATTAAAG
52491262 AAAGAATTAAAG
1 AAAGAATTAAAG
52491274 AA
1 AA
52491276 TCAAAACTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (12 bp):
AAAGAATTAAAG
Found at i:52492564 original size:13 final size:14
Alignment explanation
Indices: 52492541--52492569 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
52492531 AAAATATTAA
52492541 ATTATTTATATATT
1 ATTATTTATATATT
52492555 ATTA-TTATATATT
1 ATTATTTATATATT
52492568 AT
1 AT
52492570 AATTCTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
ATTATTTATATATT
Found at i:52495799 original size:19 final size:18
Alignment explanation
Indices: 52495749--52495801 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
52495739 TTTTGTAGAA
52495749 TTTTCATAATTTCTATAAT
1 TTTTCATAATTT-TATAAT
*
52495768 TTCTCAT--TTTTATAAT
1 TTTTCATAATTTTATAAT
52495784 TTTTCTATAATTTTATAA
1 TTTTC-ATAATTTTATAA
52495802 CTATTTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
16 10 0.34
17 5 0.17
19 14 0.48
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTCATAATTTTATAAT
Found at i:52495929 original size:21 final size:20
Alignment explanation
Indices: 52495860--52495931 Score: 58
Period size: 21 Copynumber: 3.5 Consensus size: 20
52495850 ATAATATTTC
*
52495860 AATAATTTTTAGTAACTCTTT
1 AATAATTTTTTGTAA-TCTTT
* *
52495881 AATATTTTTTTTATAAAT-TTT
1 AATA-ATTTTTTGT-AATCTTT
52495902 -ATAAATTATTTTGTAATCTTT
1 AAT-AATT-TTTTGTAATCTTT
52495923 AATAATTTT
1 AATAATTTT
52495932 ATAATATTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 13
0.69 0.09 0.22
Matches are distributed among these distances:
20 9 0.22
21 20 0.50
22 9 0.22
23 2 0.05
ACGTcount: A:0.35, C:0.04, G:0.03, T:0.58
Consensus pattern (20 bp):
AATAATTTTTTGTAATCTTT
Found at i:52496352 original size:6 final size:6
Alignment explanation
Indices: 52496341--52496368 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
52496331 TATTGTAGTT
52496341 ATTAAA ATTAAA ATTAAA ATTAAA ATTA
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTA
52496369 GGACATGTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
ATTAAA
Found at i:52508716 original size:7 final size:7
Alignment explanation
Indices: 52508704--52508730 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
52508694 AATACATACT
52508704 ATATTAA
1 ATATTAA
52508711 ATATTAA
1 ATATTAA
52508718 ATATTAA
1 ATATTAA
52508725 ATATTA
1 ATATTA
52508731 TTGTTTACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
ATATTAA
Found at i:52509022 original size:20 final size:20
Alignment explanation
Indices: 52508997--52509035 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
52508987 GCAAATTTCG
52508997 GGTAAAATTGAATTAATTCA
1 GGTAAAATTGAATTAATTCA
52509017 GGTAAAATTGAATTAATTC
1 GGTAAAATTGAATTAATTC
52509036 GGTTACAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.36
Consensus pattern (20 bp):
GGTAAAATTGAATTAATTCA
Found at i:52513025 original size:49 final size:50
Alignment explanation
Indices: 52512917--52513091 Score: 144
Period size: 49 Copynumber: 3.5 Consensus size: 50
52512907 GGTAAAGAGA
* * * **
52512917 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTAAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGAACTAAGATGAGAAC
* * *
52512967 TCCCCTGTAAGACCATGTTTGGGA-ATGGCATGGGAACCT-ATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGAA-CTAAGATGAGAAC
* * * * * *
52513016 TCCCATGTAAGACCATATCTGGGATATGACATTGGCAGTACA-A-GA-AAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGAACTA-AGATGAGAAC
* *
52513064 ATCCCATGTAAGACTATGTCTAGGACAT
1 -TCCCATGTAAGACCATGTCTGGGACAT
52513092 AGCTTTGGCA
Statistics
Matches: 101, Mismatches: 19, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
48 3 0.03
49 63 0.62
50 34 0.34
51 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.24
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATGGGAACTAAGATGAGAAC
Found at i:52513330 original size:16 final size:17
Alignment explanation
Indices: 52513279--52513336 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 17
52513269 GCAATGAAGG
* *
52513279 AGTAAGTTAAGCAAGCA
1 AGTAAGTAAAGCAAGAA
*
52513296 AGTAAGTAAACGAGTAAGAA
1 AGTAAGT-AA--AGCAAGAA
52513316 AGTAAGTAAAG-AAGAA
1 AGTAAGTAAAGCAAGAA
52513332 AGTAA
1 AGTAA
52513337 AGATCTTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
16 10 0.29
17 9 0.26
18 1 0.03
19 2 0.06
20 13 0.37
ACGTcount: A:0.55, C:0.05, G:0.24, T:0.16
Consensus pattern (17 bp):
AGTAAGTAAAGCAAGAA
Found at i:52526272 original size:34 final size:34
Alignment explanation
Indices: 52526220--52526291 Score: 117
Period size: 34 Copynumber: 2.1 Consensus size: 34
52526210 ATGTTCCAGA
* *
52526220 CATGGTCTTACATGGGATCTCATCCCCCTAATGT
1 CATGCTCTTACATAGGATCTCATCCCCCTAATGT
*
52526254 CATGCTCTTACATAGGATCTCATCGCCCTAATGT
1 CATGCTCTTACATAGGATCTCATCCCCCTAATGT
52526288 CATG
1 CATG
52526292 ACATTTGTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.22, C:0.29, G:0.17, T:0.32
Consensus pattern (34 bp):
CATGCTCTTACATAGGATCTCATCCCCCTAATGT
Found at i:52533746 original size:18 final size:18
Alignment explanation
Indices: 52533723--52533757 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
52533713 ATTTACTTCC
*
52533723 CATTCATTCATCCCTCAT
1 CATTCAATCATCCCTCAT
*
52533741 CATTCAATGATCCCTCA
1 CATTCAATCATCCCTCA
52533758 CTTCACATCT
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:0.26, C:0.37, G:0.03, T:0.34
Consensus pattern (18 bp):
CATTCAATCATCCCTCAT
Found at i:52534637 original size:16 final size:17
Alignment explanation
Indices: 52534616--52534648 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
52534606 ATTCATACAC
52534616 TTAGGTTAA-TTTGCAT
1 TTAGGTTAATTTTGCAT
52534632 TTAGGTTAATTTTGCAT
1 TTAGGTTAATTTTGCAT
52534649 CTAGTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.24, C:0.06, G:0.18, T:0.52
Consensus pattern (17 bp):
TTAGGTTAATTTTGCAT
Found at i:52534655 original size:16 final size:16
Alignment explanation
Indices: 52534617--52534652 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
52534607 TTCATACACT
*
52534617 TAGGTTAATTTGCATT
1 TAGGTTAATTTGCATC
52534633 TAGGTTAATTTTGCATC
1 TAGGTTAA-TTTGCATC
52534650 TAG
1 TAG
52534653 TTATTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.25, C:0.08, G:0.19, T:0.47
Consensus pattern (16 bp):
TAGGTTAATTTGCATC
Done.