Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D10
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: 65706892
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869813 characters in sequence are not A, C, G, or T
File 129 of 218
Found at i:39297776 original size:61 final size:61
Alignment explanation
Indices: 39297709--39297899 Score: 230
Period size: 61 Copynumber: 3.2 Consensus size: 61
39297699 ATTTTGTAGT
39297709 ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
1 ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
* * ** * * * * * *
39297770 ATTATATATTTTTATTAAATTATATTTA-ATAATAATTATATTAA-ATT-A-TATTTTA-TAGT
1 ATTATATATTATGATTTTAGTAAATTCATATAAGAA-TAT-TTAATATTAAGAATTTTATTA-A
39297829 ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
1 ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
39297890 ATTATATATT
1 ATTATATATT
39297900 TTTATTAAAT
Statistics
Matches: 102, Mismatches: 20, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
58 6 0.06
59 33 0.32
60 14 0.14
61 43 0.42
62 6 0.06
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.51
Consensus pattern (61 bp):
ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
Found at i:39297783 original size:120 final size:120
Alignment explanation
Indices: 39297659--39297934 Score: 525
Period size: 120 Copynumber: 2.3 Consensus size: 120
39297649 ATATTAAGAA
*
39297659 TTTTATTAAATTATATTTAATAATAATTATGTTAAATTACATTTTGTAGTATTATATATTATGAT
1 TTTTATTAAATTATATTTAATAATAATTATGTTAAATTACATTTTATAGTATTATATATTATGAT
39297724 TTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATAT
66 TTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATAT
* *
39297779 TTTTATTAAATTATATTTAATAATAATTATATTAAATTATATTTTATAGTATTATATATTATGAT
1 TTTTATTAAATTATATTTAATAATAATTATGTTAAATTACATTTTATAGTATTATATATTATGAT
39297844 TTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATAT
66 TTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATAT
39297899 TTTTATTAAATTATATTTAATAATAATTATGTTAAA
1 TTTTATTAAATTATATTTAATAATAATTATGTTAAA
39297935 ATATGATTAA
Statistics
Matches: 152, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 152 1.00
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.51
Consensus pattern (120 bp):
TTTTATTAAATTATATTTAATAATAATTATGTTAAATTACATTTTATAGTATTATATATTATGAT
TTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATAT
Found at i:39297790 original size:56 final size:55
Alignment explanation
Indices: 39297723--39297914 Score: 199
Period size: 56 Copynumber: 3.3 Consensus size: 55
39297713 TATATTATGA
39297723 TTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATAT
1 TTTTAGTAAATT-ATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATAT
* * * * *
39297779 TTTTATTAAATTATATTTAATAATAATT-ATATTAAATTATATTTTA-TAGTATTATATATTAT
1 TTTTAGTAAATTATA--TAAGAATATTTAATATT-AA-GA-ATTTTATTA--AAT-TATA-TAT
39297841 GATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATAT
1 --TTTTAGTAAATT-ATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATAT
*
39297899 TTTTATTAAATTATAT
1 TTTTAGTAAATTATAT
39297915 TTAATAATAA
Statistics
Matches: 111, Mismatches: 11, Indels: 29
0.74 0.07 0.19
Matches are distributed among these distances:
55 7 0.06
56 27 0.24
57 11 0.10
58 6 0.05
59 10 0.09
60 4 0.04
61 10 0.09
62 6 0.05
63 11 0.10
64 16 0.14
65 3 0.03
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (55 bp):
TTTTAGTAAATTATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATAT
Found at i:39297811 original size:26 final size:25
Alignment explanation
Indices: 39297782--39297835 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 25
39297772 TATATATTTT
39297782 TATTAAATTATATTTAATAATAATTA
1 TATTAAATTATATTTAATAAT-ATTA
* *
39297808 TATTAAATTATATTTTATAGTATTA
1 TATTAAATTATATTTAATAATATTA
39297833 TAT
1 TAT
39297836 ATTATGATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 7 0.27
26 19 0.73
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (25 bp):
TATTAAATTATATTTAATAATATTA
Found at i:39297841 original size:222 final size:220
Alignment explanation
Indices: 39297480--39297896 Score: 744
Period size: 222 Copynumber: 1.9 Consensus size: 220
39297470 TATACAATAT
39297480 TTTTATAGCATTATATATTATGATTTTAGTAAATTCATATAAGAATATAATATTAAGAATTTCAT
1 TTTTATAGCATTATATATTATGATTTTAGTAAATTCATATAAGAATATAATATTAAGAATTTCAT
*
39297545 TAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGCATT
66 TAAATTATATATTTTTATTAAATTATATTTAATAATAATTATATTAAATTATATTTTATAGCATT
* * *
39297610 ATATATTATGATTTTAGTAAATTTATATCATAATATTTAATATTAAGAATTTTATTAAATTATAT
131 ATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATAT
39297675 TTAATAATAATTATGTTAAATTACA
196 TTAATAATAATTATGTTAAATTACA
* * *
39297700 TTTTGTAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTT
1 TTTTATAGCATTATATATTATGATTTTAGTAAATTCATATAAGAATA--TAATATTAAGAATTTC
*
39297765 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATATTAAATTATATTTTATAGTA
64 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATATTAAATTATATTTTATAGCA
39297830 TTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTAT
129 TTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTAT
39297895 AT
194 AT
39297897 ATTTTTATTA
Statistics
Matches: 187, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
220 45 0.24
222 142 0.76
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.50
Consensus pattern (220 bp):
TTTTATAGCATTATATATTATGATTTTAGTAAATTCATATAAGAATATAATATTAAGAATTTCAT
TAAATTATATATTTTTATTAAATTATATTTAATAATAATTATATTAAATTATATTTTATAGCATT
ATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATAT
TTAATAATAATTATGTTAAATTACA
Found at i:39301220 original size:23 final size:22
Alignment explanation
Indices: 39301192--39301238 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 22
39301182 AGTGCATGTA
39301192 TTTTT-ATTTTCAAGAATTTAATT
1 TTTTTAATTTT-AA-AATTTAATT
39301215 TTTTTAAATTTTAAAATTTAATT
1 TTTTT-AATTTTAAAATTTAATT
39301238 T
1 T
39301239 CAATTGTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 15 0.68
24 2 0.09
25 5 0.23
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (22 bp):
TTTTTAATTTTAAAATTTAATT
Found at i:39302187 original size:24 final size:24
Alignment explanation
Indices: 39302155--39302206 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
39302145 TGCAGCAATA
39302155 TTTAAAATATTTCCTTATTAAAAT
1 TTTAAAATATTTCCTTATTAAAAT
*
39302179 TTTAAAATATTTCCTTCTTAAAAT
1 TTTAAAATATTTCCTTATTAAAAT
39302203 TTTA
1 TTTA
39302207 TTGGCTATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (24 bp):
TTTAAAATATTTCCTTATTAAAAT
Found at i:39303779 original size:21 final size:21
Alignment explanation
Indices: 39303755--39303800 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
39303745 AAAAAACAAG
*
39303755 AAAATAGCAACAAAACAATAA
1 AAAACAGCAACAAAACAATAA
* *
39303776 AAAACAGCAAGAAAACAGTAA
1 AAAACAGCAACAAAACAATAA
39303797 AAAA
1 AAAA
39303801 AGACATCAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.72, C:0.13, G:0.09, T:0.07
Consensus pattern (21 bp):
AAAACAGCAACAAAACAATAA
Found at i:39305592 original size:5 final size:5
Alignment explanation
Indices: 39305582--39305606 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
39305572 TAGGTAAAGA
39305582 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
39305607 CAAGATCATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:39305594 original size:15 final size:16
Alignment explanation
Indices: 39305576--39305612 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
39305566 TAAAAATAGG
39305576 TAAAGA-AAAATAAAA
1 TAAAGATAAAATAAAA
39305591 TAAA-ATAAAATAAAA
1 TAAAGATAAAATAAAA
*
39305606 TCAAGAT
1 TAAAGAT
39305613 CATGACTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 1 0.05
15 16 0.84
16 2 0.11
ACGTcount: A:0.73, C:0.03, G:0.05, T:0.19
Consensus pattern (16 bp):
TAAAGATAAAATAAAA
Found at i:39308263 original size:9 final size:10
Alignment explanation
Indices: 39308240--39308265 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
39308230 TTCCATAATT
39308240 TTTTTTGAAA
1 TTTTTTGAAA
39308250 TTTTTTGAAA
1 TTTTTTGAAA
39308260 TTTTTT
1 TTTTTT
39308266 ATTTTGTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (10 bp):
TTTTTTGAAA
Found at i:39310265 original size:17 final size:17
Alignment explanation
Indices: 39310229--39310266 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
39310219 TTCTTATTCA
*
39310229 TTTAATTTTTCATTTCT
1 TTTAATTTTTAATTTCT
39310246 TTTAATTTTTGAATTT-T
1 TTTAATTTTT-AATTTCT
39310263 TTTA
1 TTTA
39310267 TCAAATTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTAATTTTTAATTTCT
Found at i:39312305 original size:33 final size:32
Alignment explanation
Indices: 39312216--39312324 Score: 116
Period size: 33 Copynumber: 3.3 Consensus size: 32
39312206 AATTAATGAA
*
39312216 ACATAAAATATTTTAAAAACTTAA-AT-ATAAT
1 ACATAAAATA-TTTAAAAATTTAATATAATAAT
* *
39312247 A-ATAAATGATATCTAAAAAATTTAATATAATGAT
1 ACATAAA--ATAT-TTAAAAATTTAATATAATAAT
*
39312281 ACATGAAATATTTAAATAATTTAATATAATAAT
1 ACATAAAATATTTAAA-AATTTAATATAATAAT
39312314 ACATAAAATAT
1 ACATAAAATAT
39312325 AAATTAATCT
Statistics
Matches: 64, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
30 5 0.08
31 2 0.03
32 17 0.27
33 31 0.48
34 5 0.08
35 4 0.06
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.36
Consensus pattern (32 bp):
ACATAAAATATTTAAAAATTTAATATAATAAT
Found at i:39314410 original size:5 final size:5
Alignment explanation
Indices: 39314394--39314424 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
39314384 TCAAAAAATT
*
39314394 TCGAG TCAAG TCGAG TCGAG TCGAG TCGAG T
1 TCGAG TCGAG TCGAG TCGAG TCGAG TCGAG T
39314425 TAACGAATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.23, C:0.19, G:0.35, T:0.23
Consensus pattern (5 bp):
TCGAG
Found at i:39315810 original size:19 final size:18
Alignment explanation
Indices: 39315777--39315815 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
39315767 GCAAAAATAA
39315777 AAAGAAAGGAAGAAGAAG
1 AAAGAAAGGAAGAAGAAG
*
39315795 AAAGAATAGTAAGAAGAAG
1 AAAGAA-AGGAAGAAGAAG
39315814 AA
1 AA
39315816 GGGAAATGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.67, C:0.00, G:0.28, T:0.05
Consensus pattern (18 bp):
AAAGAAAGGAAGAAGAAG
Found at i:39316308 original size:22 final size:20
Alignment explanation
Indices: 39316258--39316308 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 20
39316248 GATGAAGTGT
*
39316258 AAAAAAAAGAATTAAATATA
1 AAAAAAAAGAAATAAATATA
*
39316278 AAATTAAAAAGAAATAAATAATC
1 AAA--AAAAAGAAATAAAT-ATA
39316301 AAAAAAAA
1 AAAAAAAA
39316309 CCCTCAAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 3 0.12
21 5 0.19
22 13 0.50
23 5 0.19
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.18
Consensus pattern (20 bp):
AAAAAAAAGAAATAAATATA
Found at i:39319901 original size:40 final size:40
Alignment explanation
Indices: 39319842--39320053 Score: 248
Period size: 40 Copynumber: 5.3 Consensus size: 40
39319832 CATTTGAATG
* *
39319842 ATATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * *
39319882 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* * *
39319922 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * * * * *
39319962 TTATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * *
39320002 AAATCCGGGCTAAGACCCGAAGGCATTTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
39320042 ATATCC-GGCTAA
1 ATATCCGGGCTAA
39320054 ATTCCGAAGA
Statistics
Matches: 140, Mismatches: 30, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
39 8 0.06
40 130 0.93
41 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
Found at i:39319982 original size:80 final size:79
Alignment explanation
Indices: 39319846--39320062 Score: 310
Period size: 80 Copynumber: 2.7 Consensus size: 79
39319836 TGAATGATAT
* *
39319846 CCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTTG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCC-GGCTAAGATCCGAAGGCATTTG
* *
39319911 TGCGAGTTGCTATAC
65 TGCGAGTTACTAAAC
*
39319926 CCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGACTAAGATCCGAAGGCATTTG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGG-CTAAGATCCGAAGGCATTTG
*
39319991 TGCGAGTTACTAAAT
65 TGCGAGTTACTAAAC
* * * *
39320006 CCGGGCTAAGACCCGAAGGCATTTGTGCTTGTGGTTATATCCGGCTAA-ATTCCGAAG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGCTAAGA-TCCGAAG
39320063 AAACTTGGGT
Statistics
Matches: 124, Mismatches: 11, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
78 1 0.01
79 13 0.10
80 110 0.89
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (79 bp):
CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGCTAAGATCCGAAGGCATTTGT
GCGAGTTACTAAAC
Found at i:39327971 original size:40 final size:40
Alignment explanation
Indices: 39327912--39328122 Score: 230
Period size: 40 Copynumber: 5.3 Consensus size: 40
39327902 CATTTGAATG
*
39327912 ATATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
* ** *
39327952 TTATCCGGGCTAAGACCCGAAGGC-ATTGTGGGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAG-TGATT
* *
39327991 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
* * * * * * *
39328031 TTATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
* * * *
39328071 AAATCCGGGCTAAGACCCGAAGGCATTTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
39328111 ATATCC-GGCTAA
1 ATATCCGGGCTAA
39328123 ATTCCGAAGA
Statistics
Matches: 138, Mismatches: 30, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
39 38 0.28
40 100 0.72
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
Found at i:39328051 original size:79 final size:79
Alignment explanation
Indices: 39327916--39328131 Score: 292
Period size: 79 Copynumber: 2.7 Consensus size: 79
39327906 TGAATGATAT
* *
39327916 CCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA-TTG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCC-GGCTAAGATCCGAAGGCATTTG
* * *
39327980 TGGGAGTTGCTATAC
65 TGCGAGTTACTAAAC
*
39327995 CCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGACTAAGATCCGAAGGCATTTG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGG-CTAAGATCCGAAGGCATTTG
*
39328060 TGCGAGTTACTAAAT
65 TGCGAGTTACTAAAC
* * * *
39328075 CCGGGCTAAGACCCGAAGGCATTTGTGCTTGTGGTTATATCCGGCTAA-ATTCCGAAG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGCTAAGA-TCCGAAG
39328132 AAACTTGGGT
Statistics
Matches: 122, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
78 3 0.02
79 66 0.54
80 53 0.43
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGCTAAGATCCGAAGGCATTTGT
GCGAGTTACTAAAC
Found at i:39337708 original size:20 final size:21
Alignment explanation
Indices: 39337683--39337724 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
39337673 TTCTGGGATC
39337683 ATTTT-GAAACAAAA-TTGAAA
1 ATTTTGGAAA-AAAACTTGAAA
39337703 ATTTTGGAAAAAAACTTGAAA
1 ATTTTGGAAAAAAACTTGAAA
39337724 A
1 A
39337725 CAAGGGTCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.55, C:0.05, G:0.12, T:0.29
Consensus pattern (21 bp):
ATTTTGGAAAAAAACTTGAAA
Found at i:39339476 original size:41 final size:41
Alignment explanation
Indices: 39339419--39339517 Score: 171
Period size: 41 Copynumber: 2.4 Consensus size: 41
39339409 ATTTCTATCA
*
39339419 TTTTCGACCTTTTCATTTGATATCCTTTCCGGATAACATCC
1 TTTTCAACCTTTTCATTTGATATCCTTTCCGGATAACATCC
*
39339460 TTTTCAACCTTTTCATTTGATATCCTTTTCGGATAACATCC
1 TTTTCAACCTTTTCATTTGATATCCTTTCCGGATAACATCC
*
39339501 TTTTCAACCCTTTCATT
1 TTTTCAACCTTTTCATT
39339518 GATTCAAAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.20, C:0.26, G:0.07, T:0.46
Consensus pattern (41 bp):
TTTTCAACCTTTTCATTTGATATCCTTTCCGGATAACATCC
Found at i:39355517 original size:30 final size:30
Alignment explanation
Indices: 39355481--39355538 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
39355471 TTCGAGCTTT
39355481 GGGGCAAAAGTGTAATTATGTAAAAGTTTA
1 GGGGCAAAAGTGTAATTATGTAAAAGTTTA
* * *
39355511 GGGGCAAAATTGTAATTTTGTCAAAGTT
1 GGGGCAAAAGTGTAATTATGTAAAAGTT
39355539 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.36, C:0.05, G:0.26, T:0.33
Consensus pattern (30 bp):
GGGGCAAAAGTGTAATTATGTAAAAGTTTA
Found at i:39355988 original size:50 final size:50
Alignment explanation
Indices: 39355875--39356173 Score: 293
Period size: 50 Copynumber: 5.9 Consensus size: 50
39355865 ACATTAAGAG
*
39355875 GATGAGA--TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGATA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C---CA-A
* * *
39355928 TTATGAGAGGTCCCATGTGAGACCATGTCTGGGACATGGCGTTGGCACCAA
1 -GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAA
* *
39355979 GATGAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATTGGCACCGA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAA
** * *
39356029 GATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCTA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAA
* ** * * * *
39356079 TATGAGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGTAGTACAA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA--CCAA
** * * *
39356131 GA--A-ACATCCCATGTAAGACTATGTCTGGGACATAGCTTTGGCA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
39356174 TGTTATATTA
Statistics
Matches: 207, Mismatches: 34, Indels: 13
0.81 0.13 0.05
Matches are distributed among these distances:
49 32 0.15
50 128 0.62
51 1 0.00
52 4 0.02
54 6 0.03
55 1 0.00
56 35 0.17
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (50 bp):
GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAA
Found at i:39359215 original size:18 final size:18
Alignment explanation
Indices: 39359192--39359228 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
39359182 TTCAAGGCTA
39359192 AGTAAGCATGAATGCATC
1 AGTAAGCATGAATGCATC
39359210 AGTAAGCATGAATGCATC
1 AGTAAGCATGAATGCATC
39359228 A
1 A
39359229 AGTGAAGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.22
Consensus pattern (18 bp):
AGTAAGCATGAATGCATC
Found at i:39363270 original size:20 final size:21
Alignment explanation
Indices: 39363234--39363281 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
39363224 ATCAACTCAC
*
39363234 TTGAGCTCATTTAAGC-TAGT
1 TTGAGCTCATCTAAGCTTAGT
39363254 TTGAGCTCAATCT-AGCTTAGT
1 TTGAGCTC-ATCTAAGCTTAGT
*
39363275 TTTAGCT
1 TTGAGCT
39363282 AATTTCTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.42
Consensus pattern (21 bp):
TTGAGCTCATCTAAGCTTAGT
Found at i:39368775 original size:20 final size:20
Alignment explanation
Indices: 39368751--39368821 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
39368741 TTTGTACATC
39368751 GGTGCCTCTGTTTGCACTTT
1 GGTGCCTCTGTTTGCACTTT
* * *
39368771 CGTGCCTCT-ATTACACTTT
1 GGTGCCTCTGTTTGCACTTT
* *
39368790 GGTGTCACTGTTTGCACTTT
1 GGTGCCTCTGTTTGCACTTT
*
39368810 GGTGCCTTTGTT
1 GGTGCCTCTGTT
39368822 ACGCATCTAT
Statistics
Matches: 39, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.08, C:0.24, G:0.23, T:0.45
Consensus pattern (20 bp):
GGTGCCTCTGTTTGCACTTT
Found at i:39376041 original size:23 final size:24
Alignment explanation
Indices: 39375997--39376042 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
39375987 TCTTCTTCTT
*
39375997 TTTTTAGTTTTAACTAAACAATTC
1 TTTTTAGTTTAAACTAAACAATTC
39376021 TTTTTA-TTTAAAC-AAATCAATT
1 TTTTTAGTTTAAACTAAA-CAATT
39376043 AACCTTGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 3 0.15
23 11 0.55
24 6 0.30
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (24 bp):
TTTTTAGTTTAAACTAAACAATTC
Found at i:39378078 original size:129 final size:129
Alignment explanation
Indices: 39377928--39378185 Score: 516
Period size: 129 Copynumber: 2.0 Consensus size: 129
39377918 GTCATTGATG
39377928 AATACTTGAGCTTAATAATAGTTGAAGATGAAATATGAAAGATATGTGATAGATTATAATGTTTG
1 AATACTTGAGCTTAATAATAGTTGAAGATGAAATATGAAAGATATGTGATAGATTATAATGTTTG
39377993 TTTTTGAATTTTGATGAATTTGATTATTTTGGGTTAATTTGTAAGGAAATATTAAATTGAGGGA
66 TTTTTGAATTTTGATGAATTTGATTATTTTGGGTTAATTTGTAAGGAAATATTAAATTGAGGGA
39378057 AATACTTGAGCTTAATAATAGTTGAAGATGAAATATGAAAGATATGTGATAGATTATAATGTTTG
1 AATACTTGAGCTTAATAATAGTTGAAGATGAAATATGAAAGATATGTGATAGATTATAATGTTTG
39378122 TTTTTGAATTTTGATGAATTTGATTATTTTGGGTTAATTTGTAAGGAAATATTAAATTGAGGGA
66 TTTTTGAATTTTGATGAATTTGATTATTTTGGGTTAATTTGTAAGGAAATATTAAATTGAGGGA
39378186 TTAAAAGGTG
Statistics
Matches: 129, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
129 129 1.00
ACGTcount: A:0.36, C:0.02, G:0.21, T:0.41
Consensus pattern (129 bp):
AATACTTGAGCTTAATAATAGTTGAAGATGAAATATGAAAGATATGTGATAGATTATAATGTTTG
TTTTTGAATTTTGATGAATTTGATTATTTTGGGTTAATTTGTAAGGAAATATTAAATTGAGGGA
Found at i:39379135 original size:24 final size:25
Alignment explanation
Indices: 39379089--39379136 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
39379079 ATATTATCAT
* *
39379089 TTTTTATTTCAATTAAAATTTAATA
1 TTTTTATTTCAAATAAAACTTAATA
*
39379114 TTTTTATTTTAAAT-AAACTTAAT
1 TTTTTATTTCAAATAAAACTTAAT
39379137 TGTCACCTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (25 bp):
TTTTTATTTCAAATAAAACTTAATA
Found at i:39382619 original size:23 final size:26
Alignment explanation
Indices: 39382589--39382639 Score: 81
Period size: 23 Copynumber: 2.1 Consensus size: 26
39382579 CGGTTATTAT
39382589 TATTTTAAAATAT-A-T-AAAATATA
1 TATTTTAAAATATAATTAAAAATATA
39382612 TATTTTAAAATATAATTAAAAATATA
1 TATTTTAAAATATAATTAAAAATATA
39382638 TA
1 TA
39382640 AAAGCCTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 13 0.52
24 1 0.04
25 1 0.04
26 10 0.40
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
TATTTTAAAATATAATTAAAAATATA
Found at i:39382622 original size:14 final size:13
Alignment explanation
Indices: 39382598--39382639 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
39382588 TTATTTTAAA
*
39382598 ATATATAAAATAT
1 ATATTTAAAATAT
39382611 ATATTTTAAAATAT
1 ATA-TTTAAAATAT
*
39382625 A-ATTAAAAATAT
1 ATATTTAAAATAT
39382637 ATA
1 ATA
39382640 AAAGCCTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 10 0.40
13 5 0.20
14 10 0.40
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
ATATTTAAAATAT
Found at i:39387705 original size:18 final size:19
Alignment explanation
Indices: 39387684--39387720 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
39387674 AAAGAAAGAC
39387684 AGAAAAAGA-AATCAAAAA
1 AGAAAAAGAGAATCAAAAA
*
39387702 AGAAAAAGAGAATGAAAAA
1 AGAAAAAGAGAATCAAAAA
39387721 GAACAAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.76, C:0.03, G:0.16, T:0.05
Consensus pattern (19 bp):
AGAAAAAGAGAATCAAAAA
Found at i:39392388 original size:26 final size:26
Alignment explanation
Indices: 39392352--39392410 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 26
39392342 TATTTTCTTG
39392352 AAATTTTACCAAGGGCAAAATCATCA
1 AAATTTTACCAAGGGCAAAATCATCA
* * *
39392378 AAATTTTACCAGGGGTAAAATCGTCA
1 AAATTTTACCAAGGGCAAAATCATCA
39392404 AAATTTT
1 AAATTTT
39392411 GTTGAGGGGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (26 bp):
AAATTTTACCAAGGGCAAAATCATCA
Found at i:39400219 original size:46 final size:46
Alignment explanation
Indices: 39400148--39400271 Score: 212
Period size: 46 Copynumber: 2.7 Consensus size: 46
39400138 TCTTATAAAA
* *
39400148 ATTCCATCAGTATATATTAACAAAATTATCTTAAAACTCATTTATT
1 ATTCCATTAGTATATATTAATAAAATTATCTTAAAACTCATTTATT
* *
39400194 GTTCCATTAGTATATATTAATAAAATTATCTTAAAATTCATTTATT
1 ATTCCATTAGTATATATTAATAAAATTATCTTAAAACTCATTTATT
39400240 ATTCCATTAGTATATATTAATAAAATTATCTT
1 ATTCCATTAGTATATATTAATAAAATTATCTT
39400272 GGTTTGTATT
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 73 1.00
ACGTcount: A:0.40, C:0.11, G:0.03, T:0.45
Consensus pattern (46 bp):
ATTCCATTAGTATATATTAATAAAATTATCTTAAAACTCATTTATT
Found at i:39400434 original size:24 final size:23
Alignment explanation
Indices: 39400407--39400466 Score: 75
Period size: 24 Copynumber: 2.6 Consensus size: 23
39400397 TTATTAACAT
39400407 TGTTCGTGAACATGTTCAATTATA
1 TGTTCGTGAACATGTTCAATTA-A
* **
39400431 TGTTCATGAACATGTTCGTTTAA
1 TGTTCGTGAACATGTTCAATTAA
*
39400454 TGTTCGTGGACAT
1 TGTTCGTGAACAT
39400467 ATTTGATTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
23 12 0.39
24 19 0.61
ACGTcount: A:0.25, C:0.13, G:0.20, T:0.42
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCAATTAA
Found at i:39405192 original size:46 final size:43
Alignment explanation
Indices: 39405117--39405215 Score: 110
Period size: 46 Copynumber: 2.2 Consensus size: 43
39405107 AATAATAACA
* *
39405117 GATACACGGTGGATTCAGTACACAGCAACCACCATTTGTAATCAAT
1 GATAC-CGGTGGATTCAGCACACAGCAACCACC--TTATAATCAAT
* *
39405163 GATATCCGGTGGGA-TCAGCACATAGCAACCACCTTATAATTAAT
1 GATA-CCGGT-GGATTCAGCACACAGCAACCACCTTATAATCAAT
39405207 GATACCGGT
1 GATACCGGT
39405216 TCACATAGTA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
43 5 0.11
44 13 0.28
46 25 0.53
47 4 0.09
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (43 bp):
GATACCGGTGGATTCAGCACACAGCAACCACCTTATAATCAAT
Found at i:39405323 original size:51 final size:51
Alignment explanation
Indices: 39405215--39405336 Score: 160
Period size: 51 Copynumber: 2.4 Consensus size: 51
39405205 ATGATACCGG
*
39405215 TTCACATAGTAGCC-GTCACATAGTACTACACATGTGACCATCACTATTCGA
1 TTCACATAGTAGCCTG-CACATAGTACTACACACGTGACCATCACTATTCGA
*
39405266 TACACATAGTAGCCTGCACATAGTACTACACACGTGACCATCACT-TTC-A
1 TTCACATAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATTCGA
* *
39405315 CTTTCACATAGTGGCCTACACA
1 --TTCACATAGTAGCCTGCACA
39405337 CAGTCCATGC
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
49 1 0.02
50 3 0.05
51 58 0.92
52 1 0.02
ACGTcount: A:0.31, C:0.30, G:0.13, T:0.26
Consensus pattern (51 bp):
TTCACATAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATTCGA
Found at i:39406457 original size:23 final size:23
Alignment explanation
Indices: 39406430--39406482 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
39406420 AGTGTTATTG
*
39406430 ATCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
39406453 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
39406476 ATCAGTG
1 ATCAGTG
39406483 TGACACTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:39412948 original size:51 final size:51
Alignment explanation
Indices: 39412824--39412959 Score: 195
Period size: 50 Copynumber: 2.7 Consensus size: 51
39412814 AGTGAAAGTG
*
39412824 ATGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGAT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGAT
** * * *
39412875 A-GGTCGTATGTGTAGTACTATGTGTAGGCTACTACGTGTATC-GAATGGT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGAT
39412924 AATGGTCACATGTGTAGTACTATGTGCAGGCTACTA
1 -ATGGTCACATGTGTAGTACTATGTGCAGGCTACTA
39412960 TGTGAACCAA
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
49 6 0.08
50 37 0.50
51 31 0.42
ACGTcount: A:0.24, C:0.15, G:0.29, T:0.32
Consensus pattern (51 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGAT
Found at i:39413021 original size:45 final size:45
Alignment explanation
Indices: 39412970--39413058 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 45
39412960 TGTGAACCAA
* *
39412970 ACATCATTGATTAGTAAAGTAGTTGCTATGTGCTGATTCCACCGG
1 ACATCATTGATTAATAAAGTAGTTGCTATGTGCTGAATCCACCGG
* * *
39413015 ACATCATTGATTAATAAGGTGGTTGCTATGTGTTGAATCCACCG
1 ACATCATTGATTAATAAAGTAGTTGCTATGTGCTGAATCCACCG
39413059 AGTCTCTGTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (45 bp):
ACATCATTGATTAATAAAGTAGTTGCTATGTGCTGAATCCACCGG
Found at i:39417874 original size:50 final size:50
Alignment explanation
Indices: 39417820--39417963 Score: 146
Period size: 49 Copynumber: 2.9 Consensus size: 50
39417810 AGCAAGATCA
* * **
39417820 TGATGTCGTGACTTCAACAAGGGAATATTGCAACTATGGAGACAGTAGCT
1 TGATGTCGTGACTTCAACAAGGGAATGTCGCAACTATGGAGACAACAGCT
* * * ** * *
39417870 TGATGTTGCGACTT-TAGTAGGGAATGTCACGACTATGGAGACAACAGCT
1 TGATGTCGTGACTTCAACAAGGGAATGTCGCAACTATGGAGACAACAGCT
* * * *
39417919 TGATGTCGTAACTTCATCAATGGAATGTCGCAACTATAGAGACAA
1 TGATGTCGTGACTTCAACAAGGGAATGTCGCAACTATGGAGACAA
39417964 TTTTCTCAAG
Statistics
Matches: 71, Mismatches: 22, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
49 37 0.52
50 34 0.48
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (50 bp):
TGATGTCGTGACTTCAACAAGGGAATGTCGCAACTATGGAGACAACAGCT
Found at i:39419753 original size:28 final size:27
Alignment explanation
Indices: 39419707--39419770 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 27
39419697 AATCATATGC
39419707 ATGTTATTTGAGTGATTTTCG-TTTGTTA
1 ATGTTATTTGAGTGATTTT-GATTT-TTA
*
39419735 ATGTTATTTGTGT-AGTTTTGATTTTTA
1 ATGTTATTTGAGTGA-TTTTGATTTTTA
*
39419762 ATTTTATTT
1 ATGTTATTT
39419771 CCCATTTTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 13 0.41
28 19 0.59
ACGTcount: A:0.19, C:0.02, G:0.17, T:0.62
Consensus pattern (27 bp):
ATGTTATTTGAGTGATTTTGATTTTTA
Found at i:39421676 original size:23 final size:24
Alignment explanation
Indices: 39421646--39421690 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
39421636 TTAAAAAATG
39421646 GTTTAATTA-TT-TTGAGATCCTTA
1 GTTTAATTACTTATTGA-ATCCTTA
39421669 GTTTAATTACTTATTGAATCCT
1 GTTTAATTACTTATTGAATCCT
39421691 CAAGTATTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 9 0.45
24 7 0.35
25 4 0.20
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.51
Consensus pattern (24 bp):
GTTTAATTACTTATTGAATCCTTA
Found at i:39423147 original size:19 final size:19
Alignment explanation
Indices: 39423125--39423161 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
39423115 TAAATTATTA
*
39423125 TTTATTTTATAATTAATTT
1 TTTAATTTATAATTAATTT
39423144 TTTAATTTATAATTAATT
1 TTTAATTTATAATTAATT
39423162 ATAATATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTAATTTATAATTAATTT
Found at i:39423170 original size:19 final size:19
Alignment explanation
Indices: 39423130--39423171 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
39423120 TATTATTTAT
**
39423130 TTTATAATTAATTTTTTAA
1 TTTATAATTAATTTAATAA
39423149 TTTATAATTAATTATAAT-A
1 TTTATAATTAATT-TAATAA
39423168 TTTA
1 TTTA
39423172 ATTACATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTATAATTAATTTAATAA
Found at i:39424180 original size:31 final size:31
Alignment explanation
Indices: 39424139--39424197 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
39424129 AAGTTTTTAA
* * *
39424139 ATTTTGAAAAACTCAAAAAATTATAAAAGGT
1 ATTTTCAAAAAATCAAAAAAGTATAAAAGGT
*
39424170 ATTTTCAAAAAATTAAAAAAGTATAAAA
1 ATTTTCAAAAAATCAAAAAAGTATAAAA
39424198 TATATATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.59, C:0.05, G:0.07, T:0.29
Consensus pattern (31 bp):
ATTTTCAAAAAATCAAAAAAGTATAAAAGGT
Found at i:39424188 original size:22 final size:23
Alignment explanation
Indices: 39424151--39424193 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
39424141 TTTGAAAAAC
*
39424151 TCAAAAAATTATAAAAGGTATTT
1 TCAAAAAATTATAAAAAGTATTT
39424174 TCAAAAAATTA-AAAAAGTAT
1 TCAAAAAATTATAAAAAGTAT
39424194 AAAATATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.58, C:0.05, G:0.07, T:0.30
Consensus pattern (23 bp):
TCAAAAAATTATAAAAAGTATTT
Found at i:39434579 original size:19 final size:18
Alignment explanation
Indices: 39434550--39434586 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
39434540 AATTCTTTAA
39434550 TTCTGTAATTTAATATTT
1 TTCTGTAATTTAATATTT
*
39434568 TTCTGATAATTTACTATTT
1 TTCTG-TAATTTAATATTT
39434587 CTCTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.27, C:0.08, G:0.05, T:0.59
Consensus pattern (18 bp):
TTCTGTAATTTAATATTT
Found at i:39436507 original size:19 final size:19
Alignment explanation
Indices: 39436485--39436530 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 19
39436475 AAATGTATTT
39436485 ATATATTA-TTATATACATA
1 ATATATTATTTATATA-ATA
39436504 ATATATTATTTATATAATA
1 ATATATTATTTATATAATA
39436523 ATATATTA
1 ATATATTA
39436531 GAGGAGTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
ATATATTATTTATATAATA
Found at i:39436961 original size:22 final size:21
Alignment explanation
Indices: 39436934--39436997 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 21
39436924 TCGTTTTTAG
39436934 GGGTTTAGGGTATATTAAATTA
1 GGGTTTAGGGT-TATTAAATTA
39436956 GGGTTT-GAGGTT-TT-AATTA
1 GGGTTTAG-GGTTATTAAATTA
*
39436975 GGGTTTAGTGTTTATTAAATTA
1 GGGTTTAG-GGTTATTAAATTA
39436997 G
1 G
39436998 CATTTTAGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
19 11 0.31
20 6 0.17
21 4 0.11
22 15 0.42
ACGTcount: A:0.27, C:0.00, G:0.28, T:0.45
Consensus pattern (21 bp):
GGGTTTAGGGTTATTAAATTA
Found at i:39437011 original size:42 final size:41
Alignment explanation
Indices: 39436934--39437054 Score: 118
Period size: 42 Copynumber: 2.9 Consensus size: 41
39436924 TCGTTTTTAG
* * * *
39436934 GGGTTTAGGGTATATTAAATTAGGGTTTGAGGTTTTAATTA
1 GGGTTTAGTGTTTATTAAATTAGCGTTTTAGGTTTTAATTA
* *
39436975 GGGTTTAGTGTTTATTAAATTAGCATTTTAGTGTTTTATTTA
1 GGGTTTAGTGTTTATTAAATTAGCGTTTTAG-GTTTTAATTA
*** *
39437017 ATTTTTAAGTGTTTATT-AATTAGTGTTTTAGAGTTTTA
1 GGGTTT-AGTGTTTATTAAATTAGCGTTTTAG-GTTTTA
39437055 GGAAAAATAA
Statistics
Matches: 66, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
41 26 0.39
42 30 0.45
43 10 0.15
ACGTcount: A:0.26, C:0.01, G:0.21, T:0.52
Consensus pattern (41 bp):
GGGTTTAGTGTTTATTAAATTAGCGTTTTAGGTTTTAATTA
Found at i:39437031 original size:19 final size:18
Alignment explanation
Indices: 39437000--39437037 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
39436990 TAAATTAGCA
39437000 TTTTAGTGTTTTATTTAAT
1 TTTTAGTGTTTTA-TTAAT
39437019 TTTTAAGTG-TTTATTAAT
1 TTTT-AGTGTTTTATTAAT
39437037 T
1 T
39437038 AGTGTTTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 8 0.44
20 4 0.22
ACGTcount: A:0.24, C:0.00, G:0.11, T:0.66
Consensus pattern (18 bp):
TTTTAGTGTTTTATTAAT
Found at i:39437185 original size:28 final size:28
Alignment explanation
Indices: 39437146--39437209 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 28
39437136 GGGGTTCGAA
* *
39437146 AAAAATGATTTTGACAAGATGGGTTCTG
1 AAAAATAATTTTGACAAGATGAGTTCTG
*
39437174 AAAAATAATTTTGACAAGATGAGTTTTG
1 AAAAATAATTTTGACAAGATGAGTTCTG
39437202 AGAAAATA
1 A-AAAATA
39437210 TCCCAGGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 26 0.81
29 6 0.19
ACGTcount: A:0.44, C:0.05, G:0.20, T:0.31
Consensus pattern (28 bp):
AAAAATAATTTTGACAAGATGAGTTCTG
Found at i:39449561 original size:44 final size:43
Alignment explanation
Indices: 39449450--39449564 Score: 128
Period size: 44 Copynumber: 2.7 Consensus size: 43
39449440 GGCTCATACA
* *
39449450 ATGCCAACGTCCCAGACATGGTCTTACATGTAATCAAACATCT
1 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAACATCC
* *
39449493 ATGCC-ACTGTCTCAGACAG-GGTCTTACATGTAAATCTCAA-ATCC
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACATGT-AATC-AAACATCC
*
39449537 ATGCCAACGTCCCAAACGTGGTCTTACA
1 ATGCCAACGTCCCAGACGTGGTCTTACA
39449565 CGATAACTCA
Statistics
Matches: 60, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
42 2 0.03
43 26 0.43
44 28 0.47
45 4 0.07
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAACATCC
Found at i:39454853 original size:7 final size:7
Alignment explanation
Indices: 39454841--39454868 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
39454831 TGTCTTTTAA
39454841 ATCACAT
1 ATCACAT
39454848 ATCACAT
1 ATCACAT
39454855 ATCACAT
1 ATCACAT
39454862 ATCACAT
1 ATCACAT
39454869 CTCATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.29, G:0.00, T:0.29
Consensus pattern (7 bp):
ATCACAT
Found at i:39459439 original size:17 final size:18
Alignment explanation
Indices: 39459414--39459459 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
39459404 TATAAGAATA
*
39459414 ATTATATTA-AGAATTTT
1 ATTAAATTATAGAATTTT
* *
39459431 ATTAAATTATATATTTTT
1 ATTAAATTATAGAATTTT
39459449 ATTAAATTATA
1 ATTAAATTATA
39459460 TTTAATAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
ATTAAATTATAGAATTTT
Found at i:39459481 original size:27 final size:27
Alignment explanation
Indices: 39459410--39459489 Score: 81
Period size: 28 Copynumber: 2.9 Consensus size: 27
39459400 TTCATATAAG
* * * *
39459410 AATAATTATATTAAGAATTTTATTAAAT
1 AATAATTATTTTTA-AATTATATTTAAT
*
39459438 TATATATT-TTTATTAAATTATATTTAAT
1 AATA-ATTATTT-TTAAATTATATTTAAT
39459466 AATAATTATTTTTAAATTATATTT
1 AATAATTATTTTTAAATTATATTT
39459490 TATAGTATTA
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
27 16 0.37
28 22 0.51
29 5 0.12
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (27 bp):
AATAATTATTTTTAAATTATATTTAAT
Found at i:39459674 original size:120 final size:120
Alignment explanation
Indices: 39459297--39459723 Score: 793
Period size: 120 Copynumber: 3.5 Consensus size: 120
39459287 AGTTTTATCA
39459297 AATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAA
1 AATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAA
*
39459362 TTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATAATT
66 TTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTT
39459417 -ATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTTAA
1 AATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTA-TTTTAA
39459481 ATTATATTTTATAGTATTATATATATTATGATTTTAGTAAATTCATATAAGAATATTT
65 ATTATATTTTATAGTA-T-TATATATTATGATTTTAGTAAATTCATATAAGAATATTT
39459539 AATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAA
1 AATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAA
*
39459604 TTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATGTAAGAATATTT
66 TTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTT
*
39459659 AATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAA
1 AATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAA
39459724 ATATGAATAA
Statistics
Matches: 300, Mismatches: 3, Indels: 8
0.96 0.01 0.03
Matches are distributed among these distances:
119 57 0.19
120 124 0.41
121 2 0.01
122 60 0.20
123 57 0.19
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (120 bp):
AATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAA
TTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTT
Found at i:39459946 original size:16 final size:16
Alignment explanation
Indices: 39459925--39459966 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
39459915 AATTGAATTA
39459925 CTATTAC-GCCTCTATT
1 CTATTACAG-CTCTATT
39459941 CTATTACAGCTCTATT
1 CTATTACAGCTCTATT
*
39459957 CCATTACAGC
1 CTATTACAGC
39459967 GAACCAAACG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 23 0.96
17 1 0.04
ACGTcount: A:0.24, C:0.31, G:0.07, T:0.38
Consensus pattern (16 bp):
CTATTACAGCTCTATT
Found at i:39465814 original size:14 final size:14
Alignment explanation
Indices: 39465791--39465828 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
39465781 GAATGGTAGA
39465791 AAAAATGAAAGGGA-
1 AAAAA-GAAAGGGAG
39465805 AAGAAAGAAAGGGAG
1 AA-AAAGAAAGGGAG
39465820 AAAAAGAAA
1 AAAAAGAAA
39465829 TATAACACCC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 17 0.77
15 5 0.23
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (14 bp):
AAAAAGAAAGGGAG
Found at i:39487186 original size:39 final size:38
Alignment explanation
Indices: 39487093--39487192 Score: 130
Period size: 38 Copynumber: 2.6 Consensus size: 38
39487083 AAAATCCTTG
* * *
39487093 TTATAATTATTGTAATTATAATTTATGATCGAATATTA
1 TTATAATTATTGTAATTATAATTTATCATCAAACATTA
* *
39487131 TTATAATTATTGTAATTGTAATTTTTCACTCAAACATTA
1 TTATAATTATTGTAATTATAATTTATCA-TCAAACATTA
39487170 TTATAATTA-TGATAATTATAATT
1 TTATAATTATTG-TAATTATAATT
39487193 ATTATATTCG
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
38 27 0.50
39 27 0.50
ACGTcount: A:0.39, C:0.05, G:0.06, T:0.50
Consensus pattern (38 bp):
TTATAATTATTGTAATTATAATTTATCATCAAACATTA
Found at i:39491158 original size:29 final size:29
Alignment explanation
Indices: 39491117--39491178 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
39491107 TGGGATTATG
*
39491117 ATGATCTTAAGTCTGAGGATCATATACAT
1 ATGATCTCAAGTCTGAGGATCATATACAT
39491146 ATGATCTCAAGTCTGAGGATCATATACAT
1 ATGATCTCAAGTCTGAGGATCATATACAT
39491175 ATGA
1 ATGA
39491179 AACACTATGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (29 bp):
ATGATCTCAAGTCTGAGGATCATATACAT
Found at i:39496725 original size:66 final size:66
Alignment explanation
Indices: 39496614--39496751 Score: 201
Period size: 66 Copynumber: 2.1 Consensus size: 66
39496604 AAAAGACATA
*
39496614 CCCATTATCCCAACTAACCTAATCATTATTTAACAGACTTTTTAGACTTCAATTTCAATCCAAAT
1 CCCATTATCCCAACTAACCTAATCATTATTTAACAGACTTTTTAGACTGCAATTTCAATCCAAAT
39496679 T
66 T
* * *
39496680 CCCATTATCCCAA-TAAACCTAATCTTTTTTTAACAGA-TTTCTTAGACTGCAATTTGAATCCAA
1 CCCATTATCCCAACT-AACCTAATCATTATTTAACAGACTTT-TTAGACTGCAATTTCAATCCAA
39496743 ATT
64 ATT
39496746 -CCATTA
1 CCCATTA
39496752 GTTGTGCAAC
Statistics
Matches: 66, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
65 10 0.15
66 56 0.85
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.37
Consensus pattern (66 bp):
CCCATTATCCCAACTAACCTAATCATTATTTAACAGACTTTTTAGACTGCAATTTCAATCCAAAT
T
Found at i:39507042 original size:7 final size:7
Alignment explanation
Indices: 39507027--39507060 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
39507017 AAAACATAAA
39507027 TTCATTT
1 TTCATTT
*
39507034 TTTATTT
1 TTCATTT
39507041 TTCATTT
1 TTCATTT
39507048 TTCA-TT
1 TTCATTT
39507054 TTCATTT
1 TTCATTT
39507061 GGGAGAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.74
Consensus pattern (7 bp):
TTCATTT
Found at i:39507138 original size:51 final size:49
Alignment explanation
Indices: 39507040--39507143 Score: 113
Period size: 51 Copynumber: 2.1 Consensus size: 49
39507030 ATTTTTTATT
* * *
39507040 TTTCATTTTTCATTTTCATTTGGGAGAAAATCACATTCATTTTCAAATG
1 TTTCATTTCTCATTTTCATTTGGAAGAAAATCACATTCATTTCCAAATG
* *
39507089 ATTTCATTTCTCTATTTTCATTTTGAAGAAAACCTGA-ATT-ATTTCCAAATG
1 -TTTCATTTCTC-ATTTTCATTTGGAAGAAAA--TCACATTCATTTCCAAATG
39507140 TTTC
1 TTTC
39507144 TTATTGTAAC
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
50 14 0.30
51 27 0.59
52 3 0.07
53 2 0.04
ACGTcount: A:0.29, C:0.15, G:0.09, T:0.47
Consensus pattern (49 bp):
TTTCATTTCTCATTTTCATTTGGAAGAAAATCACATTCATTTCCAAATG
Found at i:39508414 original size:17 final size:17
Alignment explanation
Indices: 39508376--39508416 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
39508366 ATTATCTTTA
39508376 AAATGT-ATGTATGTGT
1 AAATGTGATGTATGTGT
39508392 -AATGTGATGTATGCT-T
1 AAATGTGATGTATG-TGT
39508408 AAATGTGAT
1 AAATGTGAT
39508417 CTTATTTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 5 0.23
16 8 0.36
17 9 0.41
ACGTcount: A:0.32, C:0.02, G:0.24, T:0.41
Consensus pattern (17 bp):
AAATGTGATGTATGTGT
Found at i:39513407 original size:18 final size:18
Alignment explanation
Indices: 39513374--39513408 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39513364 TTCAAAATTT
**
39513374 TGGGCCCACATTCCCGTA
1 TGGGCCCACACACCCGTA
39513392 TGGGCCCACACACCCGT
1 TGGGCCCACACACCCGT
39513409 GTGGCCCATA
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:0.17, C:0.43, G:0.23, T:0.17
Consensus pattern (18 bp):
TGGGCCCACACACCCGTA
Found at i:39517397 original size:4 final size:5
Alignment explanation
Indices: 39517366--39517404 Score: 53
Period size: 5 Copynumber: 7.6 Consensus size: 5
39517356 GATTGAACAG
39517366 AAAACT AAAAT AAAAT AAAAT AAAAT -AAAT AAAAAT AAA
1 AAAA-T AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AAA
39517405 CAAAAGAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
4 4 0.13
5 19 0.61
6 8 0.26
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:39517522 original size:75 final size:75
Alignment explanation
Indices: 39517388--39517584 Score: 261
Period size: 75 Copynumber: 2.6 Consensus size: 75
39517378 AAATAAAATA
* * * **
39517388 AAATAAATAAAAATAAACAAAAGAAAGAAAAGGGATTTGATGGCAAAACATAGGTAATGATGACA
1 AAATAAA-AAAAATAAACAAAACAAAGAAAAGGGAATTGATGGCAAAACAGAGACAATGATGACA
39517453 ATTAAACAATC
65 ATTAAACAATC
* * * *
39517464 AAATAAAGAAAATAAACAAAACAAAGAAAAGGGAAGTAATGGCAAAATAGAGACAATGATGACAA
1 AAATAAAAAAAATAAACAAAACAAAGAAAAGGGAATTGATGGCAAAACAGAGACAATGATGACAA
39517529 TTAAACAATC
66 TTAAACAATC
* * * *
39517539 AAATAAACAAAATAAA-AAAATAAAGACAAGGAAATTGATGGCAAAA
1 AAATAAAAAAAATAAACAAAACAAAGAAAAGGGAATTGATGGCAAAA
39517585 AAATACGATA
Statistics
Matches: 106, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
74 25 0.24
75 74 0.70
76 7 0.07
ACGTcount: A:0.61, C:0.08, G:0.15, T:0.15
Consensus pattern (75 bp):
AAATAAAAAAAATAAACAAAACAAAGAAAAGGGAATTGATGGCAAAACAGAGACAATGATGACAA
TTAAACAATC
Found at i:39524984 original size:27 final size:27
Alignment explanation
Indices: 39524817--39524994 Score: 119
Period size: 27 Copynumber: 6.6 Consensus size: 27
39524807 TAAATTGTAC
*
39524817 AGCACTAAGTGTGCGA-TTCTACTT-TGT
1 AGCACTAAGTGTGCGAGTT-GA-TTATGT
* ** *
39524844 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAGTTGATTATGT
* * ** **
39524870 ATGCACTAAGAGTGCGAATTGACCATAC
1 A-GCACTAAGTGTGCGAGTTGATTATGT
* * *
39524898 GGCACTAAGTGTGCGAGTCTAACTATGT
1 AGCACTAAGTGTGCGAGT-TGATTATGT
* *
39524926 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGAGTTGATTATGT
* * *
39524953 GGCACTAAATGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGATTATGT
*
39524980 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
39524995 GGCTCAATAT
Statistics
Matches: 116, Mismatches: 30, Indels: 10
0.74 0.19 0.06
Matches are distributed among these distances:
26 1 0.01
27 93 0.80
28 22 0.19
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGATTATGT
Found at i:39524985 original size:82 final size:81
Alignment explanation
Indices: 39524814--39524994 Score: 204
Period size: 82 Copynumber: 2.2 Consensus size: 81
39524804 GATTAAATTG
* * * *
39524814 TACAGCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGAGTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
39524879 GAGTGCGAATTGACCA
66 GAGTGCGAATTGACCA
* ** *
39524895 TACGGCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACT
1 TACAGCACTAAGTGTGCGAGTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
39524959 AA-ATGTGCGAGTTGATTA
64 AAGA-GTGCGAATTGACCA
* *
39524977 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
39524995 GGCTCAATAT
Statistics
Matches: 83, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
81 23 0.28
82 60 0.72
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGAGTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GAGTGCGAATTGACCA
Found at i:39532990 original size:27 final size:27
Alignment explanation
Indices: 39532823--39533000 Score: 119
Period size: 27 Copynumber: 6.6 Consensus size: 27
39532813 TAAATTGTAC
*
39532823 AGCACTAAGTGTGCGA-TTCTACTT-TGT
1 AGCACTAAGTGTGCGAGTT-GA-TTATGT
* ** *
39532850 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAGTTGATTATGT
* * ** **
39532876 ATGCACTAAGAGTGCGAATTGACCATAC
1 A-GCACTAAGTGTGCGAGTTGATTATGT
* * *
39532904 GGCACTAAGTGTGCGAGTCTAACTATGT
1 AGCACTAAGTGTGCGAGT-TGATTATGT
* *
39532932 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGAGTTGATTATGT
* * *
39532959 GGCACTAAATGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGATTATGT
*
39532986 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
39533001 GGCTCAATAT
Statistics
Matches: 116, Mismatches: 30, Indels: 10
0.74 0.19 0.06
Matches are distributed among these distances:
26 1 0.01
27 93 0.80
28 22 0.19
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGATTATGT
Found at i:39532991 original size:82 final size:81
Alignment explanation
Indices: 39532820--39533000 Score: 204
Period size: 82 Copynumber: 2.2 Consensus size: 81
39532810 GATTAAATTG
* * * *
39532820 TACAGCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGAGTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
39532885 GAGTGCGAATTGACCA
66 GAGTGCGAATTGACCA
* ** *
39532901 TACGGCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACT
1 TACAGCACTAAGTGTGCGAGTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
39532965 AA-ATGTGCGAGTTGATTA
64 AAGA-GTGCGAATTGACCA
* *
39532983 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
39533001 GGCTCAATAT
Statistics
Matches: 83, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
81 23 0.28
82 60 0.72
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGAGTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GAGTGCGAATTGACCA
Found at i:39540836 original size:6 final size:6
Alignment explanation
Indices: 39540825--39540862 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
39540815 AATTAAATAT
39540825 AATTAC AATTAC AATTAC AATTAC AATTAC AATTAC AA
1 AATTAC AATTAC AATTAC AATTAC AATTAC AATTAC AA
39540863 GATTATACTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.32
Consensus pattern (6 bp):
AATTAC
Found at i:39541141 original size:31 final size:31
Alignment explanation
Indices: 39541106--39541171 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
39541096 TTATAAGTTG
39541106 GTCATTGAACTATTCGAAAA-TTTTCATTCAA
1 GTCATTGAACTATTC-AAAAGTTTTCATTCAA
* * *
39541137 GTCATTGGACTATTCAAAAGTTTTTATTTAA
1 GTCATTGAACTATTCAAAAGTTTTCATTCAA
39541168 GTCA
1 GTCA
39541172 CTATGTTGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (31 bp):
GTCATTGAACTATTCAAAAGTTTTCATTCAA
Found at i:39541761 original size:1 final size:1
Alignment explanation
Indices: 39541755--39541779 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
39541745 CATGAGCCGC
39541755 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
39541780 CCCTTTGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:39542517 original size:21 final size:22
Alignment explanation
Indices: 39542492--39542534 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
39542482 ATTAGATGAT
39542492 TTTAAATT-TCAAAATGTTTTA
1 TTTAAATTATCAAAATGTTTTA
39542513 TTTAAATTATCAAAATGTTTTA
1 TTTAAATTATCAAAATGTTTTA
39542535 AATTTCGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.51
Consensus pattern (22 bp):
TTTAAATTATCAAAATGTTTTA
Found at i:39544265 original size:5 final size:5
Alignment explanation
Indices: 39544255--39544283 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
39544245 GTCTTTTACG
39544255 TTCCC TTCCC TTCCC TTCCC TTCCC TTCC
1 TTCCC TTCCC TTCCC TTCCC TTCCC TTCC
39544284 ATCTTCTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (5 bp):
TTCCC
Found at i:39546869 original size:26 final size:26
Alignment explanation
Indices: 39546814--39546871 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
39546804 TATTAATTGT
**
39546814 TAAAATTGTAAGTTTAAAACTAAGGA
1 TAAAATTGTAAGTTTAAAACTAAAAA
39546840 TAAAATTGTAA-TTATAAAA-TAAAAA
1 TAAAATTGTAAGTT-TAAAACTAAAAA
39546865 CTAAAAT
1 -TAAAAT
39546872 AAATAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 6 0.21
26 22 0.79
ACGTcount: A:0.57, C:0.03, G:0.09, T:0.31
Consensus pattern (26 bp):
TAAAATTGTAAGTTTAAAACTAAAAA
Found at i:39547469 original size:25 final size:24
Alignment explanation
Indices: 39547386--39547623 Score: 111
Period size: 23 Copynumber: 10.1 Consensus size: 24
39547376 AATCTACTCT
** * *
39547386 ATTTGGACAGCCCTCATACATC-A
1 ATTTGGACAGCATTTATACACCAA
*
39547409 ATTTGGACAGCATTTATATACCAA
1 ATTTGGACAGCATTTATACACCAA
* *
39547433 A-CTAGACAGCATTT-TCACACCAAA
1 ATTTGGACAGCATTTAT-ACACC-AA
* *
39547457 ATTTGGACAGCATATATACAAC-A
1 ATTTGGACAGCATTTATACACCAA
* ** *
39547480 ATTTGGGCAGCACATATACAACAA
1 ATTTGGACAGCATTTATACACCAA
* *
39547504 A-TT-GAGCAGTATTTTTACACCAA
1 ATTTGGA-CAGCATTTATACACCAA
* *
39547527 AATTGGACAGC-TTATATACAACAA
1 ATTTGGACAGCATT-TATACACCAA
* * *
39547551 A-TTGGGCAGCATATATATACCAA
1 ATTTGGACAGCATTTATACACCAA
**
39547574 A-TT-GAGCAGCATTTA-AGCATAAA
1 ATTTGGA-CAGCATTTATA-CACCAA
* * * *
39547597 AATTGGACAGCATATATGCAACAA
1 ATTTGGACAGCATTTATACACCAA
39547621 ATT
1 ATT
39547624 GAGCAGTATA
Statistics
Matches: 162, Mismatches: 37, Indels: 31
0.70 0.16 0.13
Matches are distributed among these distances:
22 4 0.02
23 101 0.62
24 38 0.23
25 18 0.11
26 1 0.01
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.26
Consensus pattern (24 bp):
ATTTGGACAGCATTTATACACCAA
Found at i:39547490 original size:23 final size:23
Alignment explanation
Indices: 39547459--39547655 Score: 180
Period size: 23 Copynumber: 8.5 Consensus size: 23
39547449 ACACCAAAAT
* *
39547459 TTGGACAGCATATATACAACAAT
1 TTGGGCAGCATATATACAACAAA
*
39547482 TTGGGCAGCACATATACAACAAA
1 TTGGGCAGCATATATACAACAAA
* * * * *
39547505 TTGAGCAGTATTTTTACACCAAAA
1 TTGGGCAGCATATATACAAC-AAA
* *
39547529 TTGGACAGCTTATATACAACAAA
1 TTGGGCAGCATATATACAACAAA
* *
39547552 TTGGGCAGCATATATATACCAAA
1 TTGGGCAGCATATATACAACAAA
* * *
39547575 TTGAGCAGCATTTA-AGCATAAAAA
1 TTGGGCAGCATATATA-CA-ACAAA
* *
39547599 TTGGACAGCATATATGCAACAAA
1 TTGGGCAGCATATATACAACAAA
* * *
39547622 TTGAGCAGTATATATACAAGAAA
1 TTGGGCAGCATATATACAACAAA
39547645 TTGGGCAGCAT
1 TTGGGCAGCAT
39547656 TTAAGCATCA
Statistics
Matches: 133, Mismatches: 37, Indels: 8
0.75 0.21 0.04
Matches are distributed among these distances:
22 1 0.01
23 100 0.75
24 32 0.24
ACGTcount: A:0.42, C:0.16, G:0.17, T:0.25
Consensus pattern (23 bp):
TTGGGCAGCATATATACAACAAA
Found at i:39547556 original size:70 final size:70
Alignment explanation
Indices: 39547439--39547657 Score: 278
Period size: 70 Copynumber: 3.1 Consensus size: 70
39547429 CCAAACTAGA
* * *
39547439 CAGCATTTTCACACCAAAATTTGGACAGCATATATACAACAATTTGGGCAGCACATATACAACAA
1 CAGCATTTTAACACCAAAA-TTGGACAGCATATATACAACAAATTGGGCAGCATATATACAACAA
39547504 ATTGAG
65 ATTGAG
* * * * *
39547510 CAGTATTTTTACACCAAAATTGGACAGCTTATATACAACAAATTGGGCAGCATATATATACCAAA
1 CAGCATTTTAACACCAAAATTGGACAGCATATATACAACAAATTGGGCAGCATATATACAACAAA
39547575 TTGAG
66 TTGAG
** * * * *
39547580 CAGCA-TTTAAGCATAAAAATTGGACAGCATATATGCAACAAATTGAGCAGTATATATACAAGAA
1 CAGCATTTTAA-CACCAAAATTGGACAGCATATATACAACAAATTGGGCAGCATATATACAACAA
*
39547644 ATTGGG
65 ATTGAG
39547650 CAGCATTT
1 CAGCATTT
39547658 AAGCATCAAA
Statistics
Matches: 127, Mismatches: 19, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
69 4 0.03
70 104 0.82
71 19 0.15
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.26
Consensus pattern (70 bp):
CAGCATTTTAACACCAAAATTGGACAGCATATATACAACAAATTGGGCAGCATATATACAACAAA
TTGAG
Found at i:39547573 original size:47 final size:46
Alignment explanation
Indices: 39547459--39547655 Score: 168
Period size: 47 Copynumber: 4.2 Consensus size: 46
39547449 ACACCAAAAT
* * * * **
39547459 TTGGACAGCATATATACAACAATTTGGGCAGCACATATACAACAAA
1 TTGGGCAGCATATATACACCAAATTGAGCAGCTTATATACAACAAA
* * * *
39547505 TTGAGCAGTATTTTTACACCAAAATTG-GACAGCTTATATACAACAAA
1 TTGGGCAGCATATATACACC-AAATTGAG-CAGCTTATATACAACAAA
* *
39547552 TTGGGCAGCATATATATACCAAATTGAGCAGCATT-TA-AGCATAAAAA
1 TTGGGCAGCATATATACACCAAATTGAGCAGC-TTATATA-CA-ACAAA
* * * *
39547599 TTGGACAGCATATATGCAACAAATTGAGCAG-TATATATACAAGAAA
1 TTGGGCAGCATATATACACCAAATTGAGCAGCT-TATATACAACAAA
39547645 TTGGGCAGCAT
1 TTGGGCAGCAT
39547656 TTAAGCATCA
Statistics
Matches: 121, Mismatches: 21, Indels: 18
0.76 0.13 0.11
Matches are distributed among these distances:
45 2 0.02
46 44 0.36
47 74 0.61
48 1 0.01
ACGTcount: A:0.42, C:0.16, G:0.17, T:0.25
Consensus pattern (46 bp):
TTGGGCAGCATATATACACCAAATTGAGCAGCTTATATACAACAAA
Found at i:39549388 original size:40 final size:39
Alignment explanation
Indices: 39549344--39549455 Score: 127
Period size: 40 Copynumber: 2.8 Consensus size: 39
39549334 ATTATTTATG
* *
39549344 TTTGCACATTGATGCCCCTGTTTGCACATC-GATACCTTTA
1 TTTGCACATTG-TGCCCCTGTTTGCACATCTG-CACCCTTA
* *
39549384 TTTGCACATTTGTGCCCCTGTTTGCATATCTGCACCCTTG
1 TTTGCACA-TTGTGCCCCTGTTTGCACATCTGCACCCTTA
* *
39549424 TTTGCACATCGGTGCCCCTGCTTGCACATCTG
1 TTTGCACAT-TGTGCCCCTGTTTGCACATCTG
39549456 TGTCCCTTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
39 1 0.02
40 57 0.92
41 4 0.06
ACGTcount: A:0.15, C:0.30, G:0.18, T:0.37
Consensus pattern (39 bp):
TTTGCACATTGTGCCCCTGTTTGCACATCTGCACCCTTA
Found at i:39549453 original size:20 final size:19
Alignment explanation
Indices: 39549342--39549508 Score: 93
Period size: 20 Copynumber: 8.3 Consensus size: 19
39549332 CAATTATTTA
*
39549342 TGTTTGCACATTGATGCCCC
1 TGTTTGCACATCG-TGCCCC
* **
39549362 TGTTTGCACATCGATACCTT
1 TGTTTGCACATCG-TGCCCC
* *
39549382 TATTTGCACATTTGTGCCCC
1 TGTTTGCACA-TCGTGCCCC
*
39549402 TGTTTGCATATC-TGCACCC
1 TGTTTGCACATCGTGC-CCC
39549421 TTGTTTGCACATCGGTGCCCC
1 -TGTTTGCACATC-GTGCCCC
* *
39549442 TGCTTGCACATCTGTGTCCCTT
1 TGTTTGCACATC-GTG-CCC-C
* * * *
39549464 TTTTTGCACTTTGGTGCCCT
1 TGTTTGCAC-ATCGTGCCCC
**
39549484 TGACTGCACATCTGTGCCCC
1 TGTTTGCACATC-GTGCCCC
39549504 TGTTT
1 TGTTT
39549509 TACATTAATG
Statistics
Matches: 110, Mismatches: 28, Indels: 18
0.71 0.18 0.12
Matches are distributed among these distances:
18 3 0.03
19 5 0.05
20 77 0.70
21 11 0.10
22 13 0.12
23 1 0.01
ACGTcount: A:0.13, C:0.30, G:0.19, T:0.39
Consensus pattern (19 bp):
TGTTTGCACATCGTGCCCC
Found at i:39549492 original size:42 final size:42
Alignment explanation
Indices: 39549384--39549509 Score: 116
Period size: 42 Copynumber: 3.0 Consensus size: 42
39549374 GATACCTTTA
** * * *
39549384 TTTGCACATTTGTGCCCCTGTTTGCATATC--TGCACCCT-TG
1 TTTGCACATCGGTGCCCCTGCTTGCACATCTGTGC-CCCTGTT
* *
39549424 TTTGCACATCGGTGCCCCTGCTTGCACATCTGTGTCCCTTTT
1 TTTGCACATCGGTGCCCCTGCTTGCACATCTGTGCCCCTGTT
* * *
39549466 TTTGCACTTTGGTGCCCTTGAC-TGCACATCTGTGCCCCTGTT
1 TTTGCACATCGGTGCCCCTG-CTTGCACATCTGTGCCCCTGTT
39549508 TT
1 TT
39549510 ACATTAATGA
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
40 26 0.37
41 4 0.06
42 40 0.56
43 1 0.01
ACGTcount: A:0.10, C:0.31, G:0.19, T:0.40
Consensus pattern (42 bp):
TTTGCACATCGGTGCCCCTGCTTGCACATCTGTGCCCCTGTT
Found at i:39550974 original size:5 final size:5
Alignment explanation
Indices: 39550964--39550990 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
39550954 GTTTATTTAG
39550964 TTTGT TTTGT TTTGT TTTGT TTTGT TT
1 TTTGT TTTGT TTTGT TTTGT TTTGT TT
39550991 GCTTGAGGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (5 bp):
TTTGT
Found at i:39556418 original size:30 final size:30
Alignment explanation
Indices: 39556384--39556452 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
39556374 TGTGCATATA
* *
39556384 GAGCTGAATTAATGCATGAATGTGTTTAAG
1 GAGCTGAATTAAGGCATGAATGTATTTAAG
* * *
39556414 GAGCTGAATTGAGGCATGCATGTATTTAGG
1 GAGCTGAATTAAGGCATGAATGTATTTAAG
39556444 GAGCTGAAT
1 GAGCTGAAT
39556453 GGGGATGCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.30, C:0.09, G:0.30, T:0.30
Consensus pattern (30 bp):
GAGCTGAATTAAGGCATGAATGTATTTAAG
Found at i:39561871 original size:14 final size:13
Alignment explanation
Indices: 39561854--39561885 Score: 55
Period size: 13 Copynumber: 2.4 Consensus size: 13
39561844 TTTTTGTTTC
39561854 TTTTTTTTTCAAA
1 TTTTTTTTTCAAA
39561867 TTTTTTTTTCAAA
1 TTTTTTTTTCAAA
39561880 TATTTT
1 T-TTTT
39561886 ACAAACCTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.78
14 4 0.22
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTTTTTCAAA
Found at i:39565097 original size:20 final size:20
Alignment explanation
Indices: 39565069--39565109 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
39565059 ATAACTTTAT
39565069 AAACACAACCCAATAACCCA
1 AAACACAACCCAATAACCCA
*
39565089 AAACCCAACCCAATAACCCA
1 AAACACAACCCAATAACCCA
39565109 A
1 A
39565110 GGTTGGTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.54, C:0.41, G:0.00, T:0.05
Consensus pattern (20 bp):
AAACACAACCCAATAACCCA
Found at i:39565718 original size:9 final size:9
Alignment explanation
Indices: 39565704--39565732 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
39565694 TTTTTTTTAT
39565704 AATTAAAAA
1 AATTAAAAA
39565713 AATT-AAAA
1 AATTAAAAA
39565721 AATTAAAAA
1 AATTAAAAA
39565730 AAT
1 AAT
39565733 GTGTTATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
AATTAAAAA
Found at i:39568958 original size:28 final size:28
Alignment explanation
Indices: 39568915--39568971 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
39568905 TTTAAAAAGA
39568915 AAGGATATTGAATACTCTACAGCTGATC
1 AAGGATATTGAATACTCTACAGCTGATC
*
39568943 AAGGATATTGAGTACTCTACAGCTGATC
1 AAGGATATTGAATACTCTACAGCTGATC
39568971 A
1 A
39568972 GGTGTTTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (28 bp):
AAGGATATTGAATACTCTACAGCTGATC
Found at i:39572039 original size:43 final size:43
Alignment explanation
Indices: 39571975--39572124 Score: 194
Period size: 43 Copynumber: 3.5 Consensus size: 43
39571965 AGCGGCGTTT
* * *
39571975 TTTTCT-AAAAATGCCGTTAAAGACCAAGACCTTTAGGGGTGC
1 TTTTCTCAAAAACGCCGCTAAAGACCAAGACCTTTAGCGGTGC
*
39572017 TTTTCTCAAAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGC
1 TTTTCTCAAAAACGCCGCTAAAGACCAAGACCTTTAGCGGTGC
* * ** *
39572060 TTTTCTCACAAATGCCGCTAAAGACCACTACCTTTAGTGGTGC
1 TTTTCTCAAAAACGCCGCTAAAGACCAAGACCTTTAGCGGTGC
* *
39572103 TTCTCGCAAAAACGCCGCTAAA
1 TTTTCTCAAAAACGCCGCTAAA
39572125 TATATAACCT
Statistics
Matches: 93, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
42 6 0.06
43 87 0.94
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (43 bp):
TTTTCTCAAAAACGCCGCTAAAGACCAAGACCTTTAGCGGTGC
Found at i:39572082 original size:86 final size:87
Alignment explanation
Indices: 39571961--39572124 Score: 240
Period size: 86 Copynumber: 1.9 Consensus size: 87
39571951 ACGTCGCTAA
* * * * *
39571961 CTTTAGCGGCGTTTTTTTCTAAAAATGCCGTTAAAGACCAAGACCTTTAGGGGTGCTTTTCTCAA
1 CTTTAGCGGCGCTTTTCTCTAAAAATGCCGCTAAAGACCAAGACCTTTAGGGGTGCTTCTCGCAA
39572026 AAACGCCGCTAAAGACCAAGAC
66 AAACGCCGCTAAAGACCAAGAC
* ** *
39572048 CTTTAGCGGCGCTTTTCTC-ACAAATGCCGCTAAAGACCACTACCTTTAGTGGTGCTTCTCGCAA
1 CTTTAGCGGCGCTTTTCTCTAAAAATGCCGCTAAAGACCAAGACCTTTAGGGGTGCTTCTCGCAA
39572112 AAACGCCGCTAAA
66 AAACGCCGCTAAA
39572125 TATATAACCT
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
86 51 0.75
87 17 0.25
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (87 bp):
CTTTAGCGGCGCTTTTCTCTAAAAATGCCGCTAAAGACCAAGACCTTTAGGGGTGCTTCTCGCAA
AAACGCCGCTAAAGACCAAGAC
Found at i:39572871 original size:23 final size:23
Alignment explanation
Indices: 39572821--39572872 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
39572811 GTTAGGTGTC
* *
39572821 AGTATAAAGACATGTCAGATATG
1 AGTATGAAGACATGTCAGAGATG
* * *
39572844 GGTATGAAGGCATGTCTGAGATG
1 AGTATGAAGACATGTCAGAGATG
39572867 AGTATG
1 AGTATG
39572873 TTCAATTTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.08, G:0.31, T:0.27
Consensus pattern (23 bp):
AGTATGAAGACATGTCAGAGATG
Found at i:39574986 original size:31 final size:31
Alignment explanation
Indices: 39574945--39575011 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
39574935 TCATTTCTTG
*
39574945 CAACTGATAAATTAGAAGAGATAGAGAATGA
1 CAACTAATAAATTAGAAGAGATAGAGAATGA
*
39574976 CAACTAATAAATTAGAAGAGATAGAGAATGG
1 CAACTAATAAATTAGAAGAGATAGAGAATGA
39575007 CAACT
1 CAACT
39575012 CAACAGAGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.51, C:0.09, G:0.21, T:0.19
Consensus pattern (31 bp):
CAACTAATAAATTAGAAGAGATAGAGAATGA
Found at i:39576641 original size:26 final size:26
Alignment explanation
Indices: 39576610--39576672 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
39576600 GCTAATTAAT
* *
39576610 CTAAACCCTAACCCGACCCTGAATCC
1 CTAAACCCTAACACGACCATGAATCC
*
39576636 CTAAACCCTAACATGACCATGAATCC
1 CTAAACCCTAACACGACCATGAATCC
*
39576662 CTAACCCCTAA
1 CTAAACCCTAA
39576673 ACATTATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.35, C:0.41, G:0.06, T:0.17
Consensus pattern (26 bp):
CTAAACCCTAACACGACCATGAATCC
Found at i:39577556 original size:41 final size:41
Alignment explanation
Indices: 39577499--39577864 Score: 462
Period size: 41 Copynumber: 8.9 Consensus size: 41
39577489 TTTTATTATT
* * *
39577499 ATTAGCGGCGCTTTTTCAAAAACGTCGTTAAAGGCCCGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGC
* * *
39577540 ATTAGCGGCGCTTTTTCAAAAACACCGCTAAAGGCTCGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGC
* * *
39577581 ATTAGCGACGCTTCTCCAAAAACACCGCTAAAGGCCCGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGC
* *
39577622 ATTAGCGGCGCTTCTTCAAAAAATGCCACTAAAGGCCCGAGC
1 ATTAGCGGCGCTTCTTC-AAAAACGCCGCTAAAGGCCCGAGC
* * *
39577664 AATAGCGGAGCTTCTACAAAAACGCCGCTAAAGGCCCGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGC
* * * *
39577705 ATTAGCGGCGCTTATCCAAAAACGCTGCTAAAGGCTCGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGC
* * * *
39577746 ATTAGCGGTGCTTCTCCAAAAACGCTGCTAAAGGCCCGAGA
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGC
* * * *
39577787 ATTAGTGGTGCTTCTTCAAAAATGCCGCTAAAGACCCGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGC
* * *
39577828 ATTAGCGGCGCTTTTTCAAAAACGTCGTTAAAGGCCC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCC
39577865 CAAAAACTCA
Statistics
Matches: 283, Mismatches: 41, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
41 248 0.88
42 35 0.12
ACGTcount: A:0.30, C:0.27, G:0.23, T:0.20
Consensus pattern (41 bp):
ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGC
Found at i:39577802 original size:165 final size:164
Alignment explanation
Indices: 39577501--39577864 Score: 548
Period size: 165 Copynumber: 2.2 Consensus size: 164
39577491 TTATTATTAT
* *
39577501 TAGCGGCGCTTTTTCAAAAACGTCGTTAAAGGCCCGAGCATTAGCGGCGCTTTTTCAAAAACACC
1 TAGCGGCGCTTTTTCAAAAACGTCGTTAAAGGCCCGAGCATTAGCGGCGCTTATCCAAAAACACC
*
39577566 GCTAAAGGCTCGAGCATTAGCGACGCTTCTCCAAAAACACCGCTAAAGGCCCGAGCATTAGCGGC
66 GCTAAAGGCTCGAGCATTAGCGACGCTTCTCCAAAAACACCGCTAAAGGCCCGAGAATTAGCGGC
*
39577631 GCTTCTTCAAAAAATGCCACTAAAGGCCCGAGCAA
131 GCTTCTTC-AAAAATGCCACTAAAGACCCGAGCAA
* * * * * * *
39577666 TAGCGGAGCTTCTACAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGCTTATCCAAAAACGCT
1 TAGCGGCGCTTTTTCAAAAACGTCGTTAAAGGCCCGAGCATTAGCGGCGCTTATCCAAAAACACC
** * * * *
39577731 GCTAAAGGCTCGAGCATTAGCGGTGCTTCTCCAAAAACGCTGCTAAAGGCCCGAGAATTAGTGGT
66 GCTAAAGGCTCGAGCATTAGCGACGCTTCTCCAAAAACACCGCTAAAGGCCCGAGAATTAGCGGC
* *
39577796 GCTTCTTCAAAAATGCCGCTAAAGACCCGAGCAT
131 GCTTCTTCAAAAATGCCACTAAAGACCCGAGCAA
39577830 TAGCGGCGCTTTTTCAAAAACGTCGTTAAAGGCCC
1 TAGCGGCGCTTTTTCAAAAACGTCGTTAAAGGCCC
39577865 CAAAAACTCA
Statistics
Matches: 175, Mismatches: 24, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
164 53 0.30
165 122 0.70
ACGTcount: A:0.30, C:0.27, G:0.23, T:0.20
Consensus pattern (164 bp):
TAGCGGCGCTTTTTCAAAAACGTCGTTAAAGGCCCGAGCATTAGCGGCGCTTATCCAAAAACACC
GCTAAAGGCTCGAGCATTAGCGACGCTTCTCCAAAAACACCGCTAAAGGCCCGAGAATTAGCGGC
GCTTCTTCAAAAATGCCACTAAAGACCCGAGCAA
Found at i:39577967 original size:39 final size:40
Alignment explanation
Indices: 39577918--39577994 Score: 129
Period size: 39 Copynumber: 1.9 Consensus size: 40
39577908 GTGCTTTTCA
39577918 AAAAACGCTGCTAATGCTT-ATTTTTAGCGGCGTTTTTAT
1 AAAAACGCTGCTAATGCTTGATTTTTAGCGGCGTTTTTAT
* *
39577957 AAAAGCGCTGCTAATGCTTGATTTTTAGTGGCGTTTTT
1 AAAAACGCTGCTAATGCTTGATTTTTAGCGGCGTTTTT
39577995 TGTCCAAACG
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 18 0.51
40 17 0.49
ACGTcount: A:0.23, C:0.14, G:0.21, T:0.42
Consensus pattern (40 bp):
AAAAACGCTGCTAATGCTTGATTTTTAGCGGCGTTTTTAT
Found at i:39580088 original size:24 final size:23
Alignment explanation
Indices: 39580050--39580104 Score: 94
Period size: 24 Copynumber: 2.4 Consensus size: 23
39580040 ACAAAGATAG
39580050 TTTTAA-ATAAACTATATCTTTA
1 TTTTAAGATAAACTATATCTTTA
39580072 TTTTAAGATATAACTATATCTTTA
1 TTTTAAGATA-AACTATATCTTTA
39580096 TTTTAAGAT
1 TTTTAAGAT
39580105 TTTACCTAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 6 0.19
23 3 0.10
24 22 0.71
ACGTcount: A:0.38, C:0.07, G:0.04, T:0.51
Consensus pattern (23 bp):
TTTTAAGATAAACTATATCTTTA
Found at i:39583605 original size:29 final size:29
Alignment explanation
Indices: 39583563--39583619 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
39583553 TGAAAAGTGA
39583563 CATGCCAATAGGGTTTTATGCACGCTTGG
1 CATGCCAATAGGGTTTTATGCACGCTTGG
*
39583592 CATGCCAATAGGGTTTTGTGCACGCTTG
1 CATGCCAATAGGGTTTTATGCACGCTTG
39583620 TATGGGATTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.19, C:0.21, G:0.28, T:0.32
Consensus pattern (29 bp):
CATGCCAATAGGGTTTTATGCACGCTTGG
Found at i:39584650 original size:36 final size:34
Alignment explanation
Indices: 39584577--39584690 Score: 104
Period size: 34 Copynumber: 3.3 Consensus size: 34
39584567 GAATGTATTT
* * * * *
39584577 ATATATATAATTTTTCAAATACATATGCCAAAAGC
1 ATATATAT-ACTTATCAACTACATATGCCGAATGC
*
39584612 ATATATTTATACTTATCAACTACATGTGCCGAATGC
1 ATATA--TATACTTATCAACTACATATGCCGAATGC
* *
39584648 ATATATATACTTAT-AATCCACATATGTCGAATGC
1 ATATATATACTTATCAA-CTACATATGCCGAATGC
*
39584682 ATACATATA
1 ATATATATA
39584691 TATATACAAC
Statistics
Matches: 66, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
33 2 0.03
34 31 0.47
35 5 0.08
36 25 0.38
37 3 0.05
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (34 bp):
ATATATATACTTATCAACTACATATGCCGAATGC
Found at i:39585138 original size:41 final size:41
Alignment explanation
Indices: 39584857--39585127 Score: 409
Period size: 41 Copynumber: 6.6 Consensus size: 41
39584847 TTTAAACAGA
** * *
39584857 TTCACCGATACTTAGCCTGCTAAGCTTATAACCTGATTCAAA
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTC-AG
* *
39584899 TT-ACTGGCACTTAGCCTACTAGGCTTATAACCTGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAG
* * * *
39584939 ATCACCGGCAGTTAGCCAGCTAAGCTTATAACCTGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAG
39584980 TTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAG
* *
39585021 ATCATCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAG
39585062 TTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAG
*
39585103 TTCACCGGCACTTAGCTTGCTAGGC
1 TTCACCGGCACTTAGCCTGCTAGGC
39585128 GCAAAGCCTG
Statistics
Matches: 207, Mismatches: 21, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
40 2 0.01
41 203 0.98
42 2 0.01
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (41 bp):
TTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAG
Found at i:39585545 original size:23 final size:23
Alignment explanation
Indices: 39585517--39585563 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
39585507 ATAACCATAC
*
39585517 ACATTCGAACCTCACATATACAT
1 ACATTCAAACCTCACATATACAT
39585540 ACATTCAAACCTCACATATACAT
1 ACATTCAAACCTCACATATACAT
39585563 A
1 A
39585564 TATAAATTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.30, G:0.02, T:0.26
Consensus pattern (23 bp):
ACATTCAAACCTCACATATACAT
Found at i:39594071 original size:51 final size:51
Alignment explanation
Indices: 39593906--39594100 Score: 200
Period size: 51 Copynumber: 3.8 Consensus size: 51
39593896 GAAGTTGCTA
* * *
39593906 GGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATG-ATA-
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGG-ATGAAAAT
* * * * ***
39593956 GGTCACATGCGTAGTACTATGTGCAAGCTACTATGCGTA-CTGGAT-AGCTT
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATC-GGATGAAAAT
* * *
39594006 CGATCACGTATGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGAAAAT
1 -GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGAAAAT
* *
39594058 GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGAATCGG
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGG
39594101 GTATCATTTA
Statistics
Matches: 116, Mismatches: 23, Indels: 11
0.77 0.15 0.07
Matches are distributed among these distances:
49 3 0.03
50 36 0.31
51 74 0.64
52 3 0.03
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (51 bp):
GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGAAAAT
Found at i:39603884 original size:50 final size:50
Alignment explanation
Indices: 39603766--39603888 Score: 133
Period size: 50 Copynumber: 2.5 Consensus size: 50
39603756 ACATTAGGGG
* * * * *
39603766 GATGAG-AC-CCCATGTAAGACCATGTCTGGGACATGGCGTTGGTATCGA
1 GATGAGAACTCCCATGTAAGACCATGTCTGGAACATGGCATGGGCACCGA
* ***
39603814 GATGAGAAGTCCCCCATAAGACCATGTCTGGAACATGGCATGGGCACCGA
1 GATGAGAACTCCCATGTAAGACCATGTCTGGAACATGGCATGGGCACCGA
* *
39603864 TATGAGAACTCTCATGTAAGACCAT
1 GATGAGAACTCCCATGTAAGACCAT
39603889 ATCTAGGATA
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
48 6 0.10
49 1 0.02
50 51 0.88
ACGTcount: A:0.29, C:0.23, G:0.27, T:0.21
Consensus pattern (50 bp):
GATGAGAACTCCCATGTAAGACCATGTCTGGAACATGGCATGGGCACCGA
Found at i:39611496 original size:56 final size:50
Alignment explanation
Indices: 39611430--39611566 Score: 150
Period size: 56 Copynumber: 2.6 Consensus size: 50
39611420 GGGATGAGAC
* ** *
39611430 CCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTATTGAGGTTATGAGAGGT
1 CCCACGTAAGACCATGTCTGGGACATGGCATTGG---TACCGA-G--ATAAGAGGT
*
39611486 CCCACGTAAGACCATGTCTGGGACATGGCGTTGGTACCGAGATAAGAGGT
1 CCCACGTAAGACCATGTCTGGGACATGGCATTGGTACCGAGATAAGAGGT
* *
39611536 CCCTCGTAAGACCATGTC-GGGATATGGCATT
1 CCCACGTAAGACCATGTCTGGGACATGGCATT
39611567 TGCAGTACAG
Statistics
Matches: 73, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
49 11 0.15
50 25 0.34
52 1 0.01
53 4 0.05
56 32 0.44
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (50 bp):
CCCACGTAAGACCATGTCTGGGACATGGCATTGGTACCGAGATAAGAGGT
Found at i:39614471 original size:42 final size:43
Alignment explanation
Indices: 39614375--39614507 Score: 126
Period size: 43 Copynumber: 3.1 Consensus size: 43
39614365 GGTGGTCTAA
* * * *
39614375 CCATATATTTATGGCAGCTTGACTGTAATTACTGGTGGCTTGT
1 CCATATATTTCTGGCAGCTTAACTGCAATAACTGGTGGCTTGT
* *
39614418 CCAGATCTTTCTGGCAGCTTAACTGCAA-AACTGGTGGCTTGT
1 CCATATATTTCTGGCAGCTTAACTGCAATAACTGGTGGCTTGT
* * * * * * *
39614460 CCATAGATTTCTAGCAG-TATATCTACAATTACTGATGACTTGT
1 CCATATATTTCTGGCAGCT-TAACTGCAATAACTGGTGGCTTGT
39614503 CCATA
1 CCATA
39614508 AATTGGTTTG
Statistics
Matches: 73, Mismatches: 15, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
41 1 0.01
42 33 0.45
43 39 0.53
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (43 bp):
CCATATATTTCTGGCAGCTTAACTGCAATAACTGGTGGCTTGT
Found at i:39616584 original size:21 final size:22
Alignment explanation
Indices: 39616559--39616601 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
39616549 AAAAAAATTG
* *
39616559 AATTATTTAATAT-TATTTTTA
1 AATTAGTTAAAATGTATTTTTA
39616580 AATTAGTTAAAATGTATTTTTA
1 AATTAGTTAAAATGTATTTTTA
39616602 TTTTATAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (22 bp):
AATTAGTTAAAATGTATTTTTA
Found at i:39616657 original size:20 final size:20
Alignment explanation
Indices: 39616632--39616671 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
39616622 ATATAACCAT
39616632 ATAAACACAACCCAATAACC
1 ATAAACACAACCCAATAACC
*
39616652 ATAAACTCAACCCAATAACC
1 ATAAACACAACCCAATAACC
39616672 CAAGGTTGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.53, C:0.35, G:0.00, T:0.12
Consensus pattern (20 bp):
ATAAACACAACCCAATAACC
Found at i:39617472 original size:50 final size:49
Alignment explanation
Indices: 39617411--39617509 Score: 128
Period size: 50 Copynumber: 2.0 Consensus size: 49
39617401 AATAAAGTTT
*
39617411 GTCATGTATTATGTAACTCC-TATATTAATTCAGTTTGCATCTTAAATTAA
1 GTCATGCATTATGTAAC-CCATATATTAATTCAGTTTGCATCTT-AATTAA
* * * *
39617461 GTCATGCATTATGTAACCCATTTGTTTATTTAGTTTGCATCTTAATTAA
1 GTCATGCATTATGTAACCCATATATTAATTCAGTTTGCATCTTAATTAA
39617510 ACTATGCATT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
49 8 0.19
50 35 0.81
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.45
Consensus pattern (49 bp):
GTCATGCATTATGTAACCCATATATTAATTCAGTTTGCATCTTAATTAA
Found at i:39620460 original size:18 final size:18
Alignment explanation
Indices: 39620434--39620482 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
39620424 TTTTAAAAAT
*
39620434 CACAAGAAATAAATCTTA
1 CACAAGAAACAAATCTTA
* *
39620452 CAGAAGAAACAAATCTTG
1 CACAAGAAACAAATCTTA
39620470 CACAAGAAACAAA
1 CACAAGAAACAAA
39620483 CTCCCAAAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.57, C:0.18, G:0.10, T:0.14
Consensus pattern (18 bp):
CACAAGAAACAAATCTTA
Found at i:39624723 original size:13 final size:13
Alignment explanation
Indices: 39624686--39624726 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
39624676 TTTTGCTTTA
39624686 CTGCTTTGCTCTG
1 CTGCTTTGCTCTG
39624699 CT--TTGTGCCTCTG
1 CTGCTT-TG-CTCTG
39624712 CTGCTTTGCTCTG
1 CTGCTTTGCTCTG
39624725 CT
1 CT
39624727 TTGCTTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
11 2 0.08
12 2 0.08
13 16 0.67
14 2 0.08
15 2 0.08
ACGTcount: A:0.00, C:0.32, G:0.22, T:0.46
Consensus pattern (13 bp):
CTGCTTTGCTCTG
Found at i:39636546 original size:2 final size:2
Alignment explanation
Indices: 39636541--39636579 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
39636531 TTTTTTATAA
39636541 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
39636580 TCAGTGTAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:39642954 original size:22 final size:21
Alignment explanation
Indices: 39642916--39642960 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
39642906 TTGATCCTCA
* * *
39642916 CTTTTCTTTCTTTTACATTTT
1 CTTTTCTTTCATGTACAATTT
39642937 CTTTTCTTTTCATGTACAATTT
1 CTTTTC-TTTCATGTACAATTT
39642959 CT
1 CT
39642961 AGTAAGAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.13, C:0.20, G:0.02, T:0.64
Consensus pattern (21 bp):
CTTTTCTTTCATGTACAATTT
Found at i:39662585 original size:13 final size:13
Alignment explanation
Indices: 39662567--39662603 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
39662557 GAAGCATACG
* *
39662567 TAAAACTTATCTT
1 TAAAACATAACTT
39662580 TAAAACATAACTT
1 TAAAACATAACTT
39662593 TAAAACATAAC
1 TAAAACATAAC
39662604 AATTTGCACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.32
Consensus pattern (13 bp):
TAAAACATAACTT
Found at i:39668123 original size:35 final size:35
Alignment explanation
Indices: 39668077--39668147 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
39668067 TATAGTTTCC
39668077 TAAGGAGGTGTTGGGAAAGGAGTTTGCACATTTGG
1 TAAGGAGGTGTTGGGAAAGGAGTTTGCACATTTGG
39668112 TAAGGAGGTGTTGGGAAAGGAGTTTGCACATTTGG
1 TAAGGAGGTGTTGGGAAAGGAGTTTGCACATTTGG
39668147 T
1 T
39668148 GTTCCAAGAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.25, C:0.06, G:0.39, T:0.30
Consensus pattern (35 bp):
TAAGGAGGTGTTGGGAAAGGAGTTTGCACATTTGG
Found at i:39670971 original size:21 final size:22
Alignment explanation
Indices: 39670933--39670981 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
39670923 ATAAATATAT
* *
39670933 TATAA-TTTTTTTTTATAA-AA
1 TATAACTTATTTTTCATAATAA
39670953 TATAACTTATTTTTCATAATAA
1 TATAACTTATTTTTCATAATAA
39670975 -ATAACTT
1 TATAACTT
39670982 TAGAATTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 5 0.20
21 18 0.72
22 2 0.08
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (22 bp):
TATAACTTATTTTTCATAATAA
Done.