Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 132263754
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: 132263754
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 372 characters in sequence are not A, C, G, or T
File 414 of 433
Found at i:127394847 original size:16 final size:17
Alignment explanation
Indices: 127394826--127394857 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
127394816 GACATTCATG
127394826 CATTCATTCA-TGCATC
1 CATTCATTCATTGCATC
127394842 CATTCATTCATTGCAT
1 CATTCATTCATTGCAT
127394858 ATCCCATACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.25, C:0.28, G:0.06, T:0.41
Consensus pattern (17 bp):
CATTCATTCATTGCATC
Found at i:127403072 original size:53 final size:53
Alignment explanation
Indices: 127403012--127403324 Score: 229
Period size: 53 Copynumber: 5.5 Consensus size: 53
127403002 TTTTAAATTG
127403012 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCA
1 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCA
* * * * * **
127403065 ACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGCACGCTGAGGTATTTTTATTTTT--AAATTG
1 ACTCATATTGCGAGAGGTGAGTTAAGCCT--------TTTA---ATTTTTGTTTTTCAAAATCA
127403127 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCA
1 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCA
* * * * * **
127403180 ACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTTATTTTT--AAATTG
1 ACTCATATTGCGAGAGGTGAGTTAAGCCT---------TTTA---ATTTTTGTTTTTCAAAATCA
* *
127403243 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTTATTTTGGTTTTTCAAAATCA
1 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCA
* *
127403296 ACTCATATTGCTAGAGGTGAGTTGAGCCT
1 ACTCATATTGCGAGAGGTGAGTTAAGCCT
127403325 CGGGGCACGC
Statistics
Matches: 201, Mismatches: 32, Indels: 54
0.70 0.11 0.19
Matches are distributed among these distances:
51 21 0.10
53 89 0.44
54 3 0.01
61 2 0.01
62 33 0.16
63 31 0.15
64 11 0.05
65 11 0.05
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.39
Consensus pattern (53 bp):
ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCA
Found at i:127403299 original size:116 final size:116
Alignment explanation
Indices: 127402925--127403345 Score: 774
Period size: 116 Copynumber: 3.6 Consensus size: 116
127402915 GTTGAGGTAT
* * *
127402925 TTTTAATTGTTG-TTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCT
1 TTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCT
*
127402989 GAGGTATTTTTAGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCC
66 GAGGTATTTTTATTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCC
127403040 TTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTC-GGGCACGCT
1 TTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCT
127403104 GAGGTATTTTTATTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCC
66 GAGGTATTTTTATTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCC
127403155 TTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCT
1 TTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCT
127403220 GAGGTATTTTTATTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCC
66 GAGGTATTTTTATTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCC
* *
127403271 TTTTTATTTTGGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCT
1 TTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCT
127403336 GAGGTATTTT
66 GAGGTATTTT
127403346 CAATTTTTGT
Statistics
Matches: 298, Mismatches: 6, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
115 125 0.42
116 173 0.58
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (116 bp):
TTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCT
GAGGTATTTTTATTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCC
Found at i:127403397 original size:72 final size:73
Alignment explanation
Indices: 127403282--127403465 Score: 230
Period size: 72 Copynumber: 2.5 Consensus size: 73
127403272 TTTTATTTTG
* * * * * *
127403282 GTTTTTCAA-AATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTT
1 GTTTGTCAAGAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGATGAGGTAATTT
*
127403346 CAATTTTT
66 CAATTTCT
* ** *
127403354 GTGTT-TTAA-TTTCAACTCATATTGCGAGAGGTGAGTTGTGCCTCAGGACACGATGAGGTAATT
1 GT-TTGTCAAGAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGATGAGGTAATT
127403417 TCAATTTCT
65 TCAATTTCT
*
127403426 GTTTGTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGA
1 GTTTGTCAAGAATCAACTCATATTGCGAGAGGTGAGTTGA
127403466 ACCTTTTAAT
Statistics
Matches: 94, Mismatches: 15, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
71 2 0.02
72 64 0.68
73 28 0.30
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (73 bp):
GTTTGTCAAGAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGATGAGGTAATTT
CAATTTCT
Found at i:127403765 original size:55 final size:56
Alignment explanation
Indices: 127403718--127403825 Score: 157
Period size: 57 Copynumber: 1.9 Consensus size: 56
127403708 ATTTTTGTTG
*
127403718 TTTC-AAAAA-TCAACTCATGTTGCGAGAGGTGAGTTAAGCCTTTTAATTTCTATT
1 TTTCAAAAAATTCAACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTCTATT
* * *
127403772 TTTCAAAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCTTTTTACTTTCT
1 TTTC-AAAAAATTCAACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTCT
127403826 GCGAGAGTTG
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
54 4 0.09
56 5 0.11
57 38 0.81
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.39
Consensus pattern (56 bp):
TTTCAAAAAATTCAACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTCTATT
Found at i:127403831 original size:30 final size:30
Alignment explanation
Indices: 127403795--127403856 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
127403785 CAACTCATAT
*
127403795 TGCGAGAGGTGAGTTGAG-CTTTTTACTTTC
1 TGCGAGAGGTGAGTTGAGTC-TTTTAATTTC
*
127403825 TGCGAGAGTTGAGTTGAGTCTTTTAATTTC
1 TGCGAGAGGTGAGTTGAGTCTTTTAATTTC
127403855 TG
1 TG
127403857 TTTTTCAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.18, C:0.11, G:0.29, T:0.42
Consensus pattern (30 bp):
TGCGAGAGGTGAGTTGAGTCTTTTAATTTC
Found at i:127405145 original size:17 final size:18
Alignment explanation
Indices: 127405123--127405160 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
127405113 GTGGCCGGCT
*
127405123 CCGACGA-CGGGCGGTGA
1 CCGACGATCGGCCGGTGA
127405140 CCGACGATCGGCCGGTGA
1 CCGACGATCGGCCGGTGA
127405158 CCG
1 CCG
127405161 GCCCCCCTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.16, C:0.34, G:0.42, T:0.08
Consensus pattern (18 bp):
CCGACGATCGGCCGGTGA
Found at i:127405546 original size:2 final size:2
Alignment explanation
Indices: 127405539--127405673 Score: 65
Period size: 2 Copynumber: 71.5 Consensus size: 2
127405529 TTCTAATACG
* * *
127405539 TA TA TA TA TA TA TA TA TA TG TA T- TT TA TA TA TA T- TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * *
127405579 TA TA TA TA TT TT TA -A TGC CA T- TA GT- TA TA TA TT TC T- TA TG
1 TA TA TA TA TA TA TA TA T-A TA TA TA -TA TA TA TA TA TA TA TA TA
* * *
127405619 TA TA TA T- TC T- TA AA TA T- TA T- TA TA TA TA CA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
127405657 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
127405674 TTTAAATACC
Statistics
Matches: 102, Mismatches: 19, Indels: 24
0.70 0.13 0.17
Matches are distributed among these distances:
1 10 0.10
2 91 0.89
3 1 0.01
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (2 bp):
TA
Found at i:127405569 original size:15 final size:15
Alignment explanation
Indices: 127405547--127405588 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
127405537 CGTATATATA
127405547 TATATATATATGTAT-
1 TATATATATAT-TATG
*
127405562 TTTATATATATTATG
1 TATATATATATTATG
127405577 TATATATATATT
1 TATATATATATT
127405589 TTTAATGCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 3 0.12
15 21 0.88
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (15 bp):
TATATATATATTATG
Found at i:127408302 original size:19 final size:19
Alignment explanation
Indices: 127408260--127408303 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
127408250 AGTGAAAGTT
*
127408260 TAATGCAAATGTTGCAATG
1 TAATGCAAATGTTGCAACG
*
127408279 TAATGCAAATGTATGGAACG
1 TAATGCAAATGT-TGCAACG
127408299 -AATGC
1 TAATGC
127408304 CAAAGAAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.27
Consensus pattern (19 bp):
TAATGCAAATGTTGCAACG
Found at i:127410930 original size:20 final size:20
Alignment explanation
Indices: 127410877--127410935 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
127410867 AATAAAAAAC
*
127410877 AATACTATATATAAATATATA
1 AATA-TATATATAAAAATATA
*
127410898 AATATATACATAAAAATATA
1 AATATATATATAAAAATATA
* *
127410918 CACTA-ATATATAATAATA
1 -AATATATATATAAAAATA
127410936 ATAGTAATAG
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
20 25 0.78
21 7 0.22
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (20 bp):
AATATATATATAAAAATATA
Found at i:127411157 original size:3 final size:3
Alignment explanation
Indices: 127411144--127411226 Score: 66
Period size: 3 Copynumber: 27.3 Consensus size: 3
127411134 GAGGGCATAT
127411144 ATA AT- ATA ATA ATA AT- ATAA ATA ATA ATA TATA CATGA GA-A ATA
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA -ATA -AT-A -ATA ATA
* * *
127411188 ATA ATA ATA ATA AAA ATA ATA GTA AAA ATA ATA A-A ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
127411227 AAAAAATAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
2 7 0.11
3 49 0.75
4 7 0.11
5 2 0.03
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:127411174 original size:30 final size:28
Alignment explanation
Indices: 127411140--127411226 Score: 79
Period size: 30 Copynumber: 2.9 Consensus size: 28
127411130 TGGAGAGGGC
127411140 ATATATAATATAATAATAATATAAATAATA
1 ATATATAATATAA-AATAATA-AAATAATA
*
127411170 ATATATACATGA-GAAATAATAATAATAATA
1 ATATATA-AT-ATAAAATAATAA-AATAATA
*
127411200 A-AAATAATAGTAAAAATAATAAAATAA
1 ATATATAATA-T-AAAATAATAAAATAA
127411227 AAAAAATAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
27 1 0.02
28 2 0.04
29 10 0.21
30 31 0.65
31 3 0.06
32 1 0.02
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (28 bp):
ATATATAATATAAAATAATAAAATAATA
Found at i:127411188 original size:21 final size:18
Alignment explanation
Indices: 127411149--127411237 Score: 81
Period size: 18 Copynumber: 4.8 Consensus size: 18
127411139 CATATATAAT
*
127411149 ATAATAATAATATAAATA
1 ATAATAATAATAAAAATA
*
127411167 ATAATATATACATGAGAAATA
1 ATAATA-ATA-AT-AAAAATA
127411188 ATAATAATAATAAAAATA
1 ATAATAATAATAAAAATA
* * *
127411206 ATAGTAAAAATAATAA-A
1 ATAATAATAATAAAAATA
* *
127411223 ATAAAAAAAATAAAA
1 ATAATAATAATAAAA
127411238 CAAAGCTCTC
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
17 13 0.22
18 25 0.42
19 5 0.08
20 5 0.08
21 12 0.20
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.26
Consensus pattern (18 bp):
ATAATAATAATAAAAATA
Found at i:127411652 original size:22 final size:25
Alignment explanation
Indices: 127411636--127411720 Score: 94
Period size: 22 Copynumber: 3.6 Consensus size: 25
127411626 AGTGGTTGGG
*
127411636 GTGGTTTAGTGGAGTGGTTTAGTAGG
1 GTGGTTTAGTGGAGTGGTTTAGT-GA
127411662 GTGG-TT-G-GG-GTGGTTTAGTGTA
1 GTGGTTTAGTGGAGTGGTTTAGTG-A
127411684 GTGGTTTAGTGGAGTGG-TT-G-GA
1 GTGGTTTAGTGGAGTGGTTTAGTGA
127411706 GTGGTTTAGTGGAGT
1 GTGGTTTAGTGGAGT
127411721 AAATATATTT
Statistics
Matches: 53, Mismatches: 1, Indels: 14
0.78 0.01 0.21
Matches are distributed among these distances:
21 1 0.02
22 30 0.57
23 5 0.09
24 3 0.06
25 6 0.11
26 8 0.15
ACGTcount: A:0.13, C:0.00, G:0.48, T:0.39
Consensus pattern (25 bp):
GTGGTTTAGTGGAGTGGTTTAGTGA
Found at i:127411654 original size:13 final size:13
Alignment explanation
Indices: 127411636--127411720 Score: 89
Period size: 13 Copynumber: 7.2 Consensus size: 13
127411626 AGTGGTTGGG
127411636 GTGGTTTAGTGGA
1 GTGGTTTAGTGGA
127411649 GTGGTTTAGTAGG-
1 GTGGTTTAGT-GGA
127411662 GTGG-TT-G-GG-
1 GTGGTTTAGTGGA
*
127411671 GTGGTTTAGTGTA
1 GTGGTTTAGTGGA
127411684 GTGGTTTAGTGGA
1 GTGGTTTAGTGGA
127411697 GTGG--T--TGGA
1 GTGGTTTAGTGGA
127411706 GTGGTTTAGTGGA
1 GTGGTTTAGTGGA
127411719 GT
1 GT
127411721 AAATATATTT
Statistics
Matches: 61, Mismatches: 2, Indels: 18
0.75 0.02 0.22
Matches are distributed among these distances:
9 14 0.23
10 2 0.03
11 4 0.07
12 3 0.05
13 36 0.59
14 2 0.03
ACGTcount: A:0.13, C:0.00, G:0.48, T:0.39
Consensus pattern (13 bp):
GTGGTTTAGTGGA
Found at i:127411673 original size:35 final size:35
Alignment explanation
Indices: 127411624--127411720 Score: 160
Period size: 35 Copynumber: 2.8 Consensus size: 35
127411614 GTAGGCAAGC
127411624 GGAGTGGTTGGGGTGGTTTAGTGGAGTGGTTTAGT
1 GGAGTGGTTGGGGTGGTTTAGTGGAGTGGTTTAGT
*
127411659 AGG-GTGGTTGGGGTGGTTTAGTGTAGTGGTTTAGT
1 -GGAGTGGTTGGGGTGGTTTAGTGGAGTGGTTTAGT
*
127411694 GGAGTGGTTGGAGTGGTTTAGTGGAGT
1 GGAGTGGTTGGGGTGGTTTAGTGGAGT
127411721 AAATATATTT
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
34 2 0.04
35 53 0.93
36 2 0.04
ACGTcount: A:0.12, C:0.00, G:0.51, T:0.37
Consensus pattern (35 bp):
GGAGTGGTTGGGGTGGTTTAGTGGAGTGGTTTAGT
Found at i:127417953 original size:27 final size:28
Alignment explanation
Indices: 127417911--127417976 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 28
127417901 ATTTGTAAAG
* *
127417911 TAGGGACAAAATTGTAAAAT-CAAAAAA
1 TAGGGGCAAAACTGTAAAATACAAAAAA
*
127417938 TAGGGGCAAAACTGTAAAATATAAAAAA
1 TAGGGGCAAAACTGTAAAATACAAAAAA
* *
127417966 TTGGGGAAAAA
1 TAGGGGCAAAA
127417977 TAATAAAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
27 18 0.55
28 15 0.45
ACGTcount: A:0.56, C:0.06, G:0.20, T:0.18
Consensus pattern (28 bp):
TAGGGGCAAAACTGTAAAATACAAAAAA
Found at i:127417976 original size:28 final size:27
Alignment explanation
Indices: 127417913--127417976 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
127417903 TTGTAAAGTA
*
127417913 GGGACAAAATTGTAAAATCAAAAAATAG
1 GGGA-AAAACTGTAAAATCAAAAAATAG
* * *
127417941 GGGCAAAACTGTAAAATATAAAAAATTG
1 GGGAAAAACTGTAAAAT-CAAAAAATAG
127417969 GGGAAAAA
1 GGGAAAAA
127417977 TAATAAAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 12 0.40
28 18 0.60
ACGTcount: A:0.56, C:0.06, G:0.20, T:0.17
Consensus pattern (27 bp):
GGGAAAAACTGTAAAATCAAAAAATAG
Found at i:127426795 original size:24 final size:24
Alignment explanation
Indices: 127426768--127426813 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
127426758 AGTCAAATAA
* *
127426768 ATTATGCTAATAAATGCTAAATGT
1 ATTATACTAATAAATACTAAATGT
127426792 ATTATACTAATAAATACTAAAT
1 ATTATACTAATAAATACTAAAT
127426814 CTTCTAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.37
Consensus pattern (24 bp):
ATTATACTAATAAATACTAAATGT
Found at i:127441956 original size:19 final size:19
Alignment explanation
Indices: 127441920--127441956 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
127441910 TAACTAGGCT
* *
127441920 TTAATTAAGTGAATTTAGC
1 TTAATTAAGAGAAATTAGC
127441939 TTAATTAAGAGAAATTAG
1 TTAATTAAGAGAAATTAG
127441957 GAAAAATGGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.16, T:0.38
Consensus pattern (19 bp):
TTAATTAAGAGAAATTAGC
Found at i:127442161 original size:16 final size:18
Alignment explanation
Indices: 127442129--127442162 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
127442119 TTATTACGGT
127442129 TTATATATTAGTTATTAA
1 TTATATATTAGTTATTAA
127442147 TTAT-TATTA-TTATTAA
1 TTATATATTAGTTATTAA
127442163 ATAAATTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 5 0.31
18 4 0.25
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (18 bp):
TTATATATTAGTTATTAA
Found at i:127442524 original size:142 final size:141
Alignment explanation
Indices: 127442268--127442564 Score: 329
Period size: 142 Copynumber: 2.1 Consensus size: 141
127442258 TTTAGAACAA
*
127442268 AAGATATTTATTAATTAAATAATTAAATAATGAGATTTTTGTTTGATAAATAAATTAAATAATGA
1 AAGATATTTATTAATTAAATAATTAAATAATGAGATTTTTGTTTAATAAATAAATTAAATAATGA
* * * * * * * * *
127442333 CAATTGCAATAAATTTATTGGTACAAATGTGAAAATATAAGTGTGTACAATTGTAATATTAGTAT
66 CAAATGCAATAAATTTAGTGGTAC-AATGTGAAAATACAAATGTATACAAATGTAAAATAAATA-
*
127442398 TTGA-TATTAAAT
129 TTAATTATTAAAT
* * * *
127442410 AAGATATTTATTAATTAAATAATTATATTATGAGATTTTT-TTGTAATAAATATATTAAATTATG
1 AAGATATTTATTAATTAAATAATTAAATAATGAGATTTTTGTT-TAATAAATAAATTAAATAATG
*
127442474 ACAAATGTATAGTAAAATTT-GT-G-AC-ATGTGTAATAATACAAATGTATACAAATGTAAAATA
65 ACAAATGCA-A-T-AAATTTAGTGGTACAATGTG-AA-AATACAAATGTATACAAATGTAAAATA
127442535 AATATTAATTATTAAAT
125 AATATTAATTATTAAAT
127442552 -AGATATTTATTAA
1 AAGATATTTATTAA
127442565 CTTATTATAT
Statistics
Matches: 132, Mismatches: 16, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
140 5 0.04
141 20 0.15
142 97 0.73
143 2 0.02
144 2 0.02
145 6 0.05
ACGTcount: A:0.46, C:0.03, G:0.10, T:0.41
Consensus pattern (141 bp):
AAGATATTTATTAATTAAATAATTAAATAATGAGATTTTTGTTTAATAAATAAATTAAATAATGA
CAAATGCAATAAATTTAGTGGTACAATGTGAAAATACAAATGTATACAAATGTAAAATAAATATT
AATTATTAAAT
Found at i:127442571 original size:23 final size:22
Alignment explanation
Indices: 127442537--127442580 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
127442527 GTAAAATAAA
127442537 TATTAATTATTAAATAGATATT
1 TATTAATTATTAAATAGATATT
* *
127442559 TATTAACTTATTATATATATAT
1 TATTAA-TTATTAAATAGATAT
127442581 ATATATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (22 bp):
TATTAATTATTAAATAGATATT
Found at i:127442577 original size:2 final size:2
Alignment explanation
Indices: 127442570--127442599 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
127442560 ATTAACTTAT
127442570 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
127442600 AAACAAAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:127443409 original size:15 final size:15
Alignment explanation
Indices: 127443385--127443435 Score: 77
Period size: 15 Copynumber: 3.5 Consensus size: 15
127443375 CAATGAATTT
127443385 ATTATATTGATTGAA
1 ATTATATTGATTGAA
*
127443400 ATTATTTTGATTGAA
1 ATTATATTGATTGAA
*
127443415 TTTATATTGATTG-A
1 ATTATATTGATTGAA
127443429 ATTATAT
1 ATTATAT
127443436 AATATATATG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
14 7 0.22
15 25 0.78
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
ATTATATTGATTGAA
Found at i:127448327 original size:46 final size:46
Alignment explanation
Indices: 127448275--127448502 Score: 296
Period size: 46 Copynumber: 5.0 Consensus size: 46
127448265 AGTGTGCTCT
*
127448275 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
127448321 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACTATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * *
127448367 GTGATATGAAATGAATAAGAACATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * *
127448413 GTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
127448459 ATGACA-GAAAATGAGTAAGACCATAGTTAAAAGACACTATGGCA
1 CTGATATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCA
127448503 TCATGTCAAA
Statistics
Matches: 165, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
45 1 0.01
46 164 0.99
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:127449585 original size:19 final size:19
Alignment explanation
Indices: 127449547--127449586 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
127449537 ATCATGAATA
* * *
127449547 AAGAAAACAATTGAATCGC
1 AAGAAAAAAATTAAAACGC
127449566 AAGAAAAAAATTAAAACGC
1 AAGAAAAAAATTAAAACGC
127449585 AA
1 AA
127449587 AAACTTTTGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.62, C:0.12, G:0.12, T:0.12
Consensus pattern (19 bp):
AAGAAAAAAATTAAAACGC
Found at i:127452436 original size:23 final size:23
Alignment explanation
Indices: 127452410--127452455 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
127452400 CCTAAACTAA
127452410 CAAAATTGACTAAATAGATCTTT
1 CAAAATTGACTAAATAGATCTTT
127452433 CAAAATTGACTAAATAGATCTTT
1 CAAAATTGACTAAATAGATCTTT
127452456 TGACTGTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.35
Consensus pattern (23 bp):
CAAAATTGACTAAATAGATCTTT
Found at i:127452542 original size:14 final size:14
Alignment explanation
Indices: 127452509--127452535 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
127452499 CAACAAAAAT
127452509 AAAAAAATTCAAAG
1 AAAAAAATTCAAAG
127452523 AAAAAAATTCAAA
1 AAAAAAATTCAAA
127452536 TTCAAAATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.07, G:0.04, T:0.15
Consensus pattern (14 bp):
AAAAAAATTCAAAG
Found at i:127452626 original size:19 final size:18
Alignment explanation
Indices: 127452595--127452652 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 18
127452585 AAAAATCAAA
127452595 ATTAAAATATATAAAAAAT
1 ATTAAAAT-TATAAAAAAT
*
127452614 ATTATTAATTATAAAAAATT
1 ATTA-AAATTATAAAAAA-T
*
127452634 ATTAAAATTATATAAAAT
1 ATTAAAATTATAAAAAAT
127452652 A
1 A
127452653 AAAAATAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 2 0.06
19 24 0.71
20 8 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTAAAATTATAAAAAAT
Found at i:127453657 original size:37 final size:37
Alignment explanation
Indices: 127453607--127453682 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
127453597 AAAAAGAAAA
127453607 CCCATATACCAACTCTTGGCTTGACCCTATTAAAGTT
1 CCCATATACCAACTCTTGGCTTGACCCTATTAAAGTT
*
127453644 CCCATATACCAACTCTTGTCTTGACCCTATTAAAGTT
1 CCCATATACCAACTCTTGGCTTGACCCTATTAAAGTT
127453681 CC
1 CC
127453683 AAAGTCTAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.26, C:0.32, G:0.09, T:0.33
Consensus pattern (37 bp):
CCCATATACCAACTCTTGGCTTGACCCTATTAAAGTT
Found at i:127456089 original size:31 final size:31
Alignment explanation
Indices: 127456054--127456116 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
127456044 CAAAAAAAGG
127456054 ATTCAATGGAGGGTCCAGGTATGTCTTCTTC
1 ATTCAATGGAGGGTCCAGGTATGTCTTCTTC
127456085 ATTCAATGGAGGGTCCAGGTATGTCTTCTTC
1 ATTCAATGGAGGGTCCAGGTATGTCTTCTTC
127456116 A
1 A
127456117 CCGACAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (31 bp):
ATTCAATGGAGGGTCCAGGTATGTCTTCTTC
Found at i:127456628 original size:17 final size:17
Alignment explanation
Indices: 127456608--127456641 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
127456598 AGGTTTAGGT
127456608 TTAAAAATTTTAATTAA
1 TTAAAAATTTTAATTAA
*
127456625 TTAAAATTTTTAATTAA
1 TTAAAAATTTTAATTAA
127456642 AAATCTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAAAAATTTTAATTAA
Found at i:127457399 original size:2 final size:2
Alignment explanation
Indices: 127457392--127457423 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
127457382 TAATTTCATG
127457392 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
127457424 ATCTGATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:127458458 original size:14 final size:14
Alignment explanation
Indices: 127458435--127458465 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
127458425 TGGCTCTTGA
127458435 TTTTTATGTTTTTT
1 TTTTTATGTTTTTT
*
127458449 TTTTTTTGTTTTTT
1 TTTTTATGTTTTTT
127458463 TTT
1 TTT
127458466 GTGTGTGTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.03, C:0.00, G:0.06, T:0.90
Consensus pattern (14 bp):
TTTTTATGTTTTTT
Found at i:127463725 original size:33 final size:33
Alignment explanation
Indices: 127463683--127463750 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 33
127463673 AGGCTATGGA
127463683 CGGAAACAAAGACATTGCAACGGATCAAGTATC
1 CGGAAACAAAGACATTGCAACGGATCAAGTATC
* * * * *
127463716 CGGAAACAAAGATATTTCTATGGATCAAGTCTC
1 CGGAAACAAAGACATTGCAACGGATCAAGTATC
127463749 CG
1 CG
127463751 AAAAAGAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (33 bp):
CGGAAACAAAGACATTGCAACGGATCAAGTATC
Found at i:127464846 original size:20 final size:20
Alignment explanation
Indices: 127464800--127464846 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
127464790 AACGAAACAG
127464800 GGAG-AAGGAAAGAAAGAAA
1 GGAGAAAGGAAAGAAAGAAA
* * * *
127464819 AGAAAAAGGAAAGGAAGGAA
1 GGAGAAAGGAAAGAAAGAAA
127464839 GGAGAAAG
1 GGAGAAAG
127464847 CCACGACCTT
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (20 bp):
GGAGAAAGGAAAGAAAGAAA
Found at i:127469637 original size:15 final size:16
Alignment explanation
Indices: 127469617--127469646 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
127469607 AACAAAAAGA
127469617 AATAGAAA-GAAACAC
1 AATAGAAACGAAACAC
127469632 AATAGAAACGAAACA
1 AATAGAAACGAAACA
127469647 GGGAGAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.67, C:0.13, G:0.13, T:0.07
Consensus pattern (16 bp):
AATAGAAACGAAACAC
Found at i:127469644 original size:20 final size:19
Alignment explanation
Indices: 127469598--127469644 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
127469588 ATATAATAAT
127469598 AAAC-AAAGAAACAAAAAG
1 AAACGAAAGAAACAAAAAG
* *
127469616 AAATAGAAAGAAACACAATAG
1 AAA-CGAAAGAAACA-AAAAG
127469637 AAACGAAA
1 AAACGAAA
127469645 CAGGGAGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 3 0.13
20 13 0.57
21 7 0.30
ACGTcount: A:0.72, C:0.11, G:0.13, T:0.04
Consensus pattern (19 bp):
AAACGAAAGAAACAAAAAG
Found at i:127469659 original size:4 final size:4
Alignment explanation
Indices: 127469650--127469683 Score: 52
Period size: 4 Copynumber: 8.5 Consensus size: 4
127469640 CGAAACAGGG
127469650 AGAA AGAA AGAA AGAAA AGAA A-AA AGAA AGAA AG
1 AGAA AGAA AGAA AG-AA AGAA AGAA AGAA AGAA AG
127469684 GAAGGAGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 3 0.11
4 21 0.75
5 4 0.14
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:127473934 original size:3 final size:3
Alignment explanation
Indices: 127473921--127473971 Score: 50
Period size: 3 Copynumber: 17.3 Consensus size: 3
127473911 AAGAGGTATT
* * * * *
127473921 ATA AT- ATA ATA ATA ATA ATG ATG ATA ATA GTG ATA TTA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
127473968 ATA A
1 ATA A
127473972 AAGTAAAATG
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:127474121 original size:15 final size:15
Alignment explanation
Indices: 127474073--127474165 Score: 81
Period size: 15 Copynumber: 6.2 Consensus size: 15
127474063 GTATATATAT
127474073 GTATAAAATAAATAA
1 GTATAAAATAAATAA
127474088 GTA-AATAAGTGATAA-AA
1 GTATAA-AA-T-A-AATAA
127474105 GTATAAAATAAATAA
1 GTATAAAATAAATAA
127474120 GTATATAAATAATATAA
1 GTATA-AAATAA-ATAA
127474137 --ATAAAAT-AA-AA
1 GTATAAAATAAATAA
*
127474148 GTATAAAATATATAA
1 GTATAAAATAAATAA
127474163 GTA
1 GTA
127474166 AGTGAATAAT
Statistics
Matches: 65, Mismatches: 1, Indels: 24
0.72 0.01 0.27
Matches are distributed among these distances:
11 2 0.03
12 1 0.02
13 8 0.12
14 9 0.14
15 21 0.32
16 8 0.12
17 12 0.18
18 4 0.06
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.28
Consensus pattern (15 bp):
GTATAAAATAAATAA
Found at i:127474149 original size:43 final size:45
Alignment explanation
Indices: 127474099--127474204 Score: 146
Period size: 43 Copynumber: 2.4 Consensus size: 45
127474089 TAAATAAGTG
127474099 ATAAAAGTATAAAATAAATAAGTATA-TAAATAATATA-A-ATAAA
1 ATAAAAGTATAAAATAAATAAGTA-AGTAAATAATATATATATAAA
* * * *
127474142 ATAAAAGTATAAAATATATAAGTAAGTGAATAATATATATTTGAA
1 ATAAAAGTATAAAATAAATAAGTAAGTAAATAATATATATATAAA
127474187 ATAAAAGTATAAAATAAA
1 ATAAAAGTATAAAATAAA
127474205 CGAAGTAAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
42 1 0.02
43 33 0.60
44 1 0.02
45 20 0.36
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (45 bp):
ATAAAAGTATAAAATAAATAAGTAAGTAAATAATATATATATAAA
Found at i:127476552 original size:206 final size:205
Alignment explanation
Indices: 127476174--127476897 Score: 1119
Period size: 206 Copynumber: 3.5 Consensus size: 205
127476164 TGGGAACATC
* ** * *
127476174 TGAAAGTCAAATCTA-CTATGTCTTCGATTTGTTTATTGTAAACACAATGATGCCAAACCATCTT
1 TGAAAGCCAAATC-AGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
* *
127476238 GGATCCGCTTCAGCATAAACATCCGAAGGCGAGATCTGCTATGTGTCTGTTCTCCATCAAAGTGA
65 GGATCTGCTTCAGCATAAACATCCGAAGGCGAGATCTGCTATGTGTCTGCTCTCCATCAAAGTGA
*
127476303 AGATGCCAAACTTCGATTCGTTCTCTGACAATATAGAGATGACAAATCATCTTAGATTTGCTTCA
130 AGATGCCAAACTTCGATTCGTTCTCTGACAATACAGAGATGACAAATCATCTTAGATTTGCTTCA
*
127476368 TCATAATCACG
195 TCGTAATCACG
* * *
127476379 TGAAAGCCAAATCAGCTGTGTCTTTGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTG
1 TGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTG
127476444 GATCTTGCTTCAGCATAAACATCCGAAGGCGAGATCTGCTATGTGTCTGCTCTCCATCAAAGTGA
66 GATC-TGCTTCAGCATAAACATCCGAAGGCGAGATCTGCTATGTGTCTGCTCTCCATCAAAGTGA
127476509 AGATGCCAAACTTCGATTCGTTCTCTGACAATACAGAGATGACAAATCATCTTAGATTTGCTTCA
130 AGATGCCAAACTTCGATTCGTTCTCTGACAATACAGAGATGACAAATCATCTTAGATTTGCTTCA
127476574 TCGTAATCACG
195 TCGTAATCACG
* **
127476585 TGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGAGGCCAATTCATCTTG
1 TGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTG
* * * **
127476650 GATCTTGCTTCAGTATAAACATCTGAAGGTC-AGATCTGCTATGTATCTGCTCTCCATTGAAGTG
66 GATC-TGCTTCAGCATAAACATCCGAAGG-CGAGATCTGCTATGTGTCTGCTCTCCATCAAAGTG
* * * * *
127476714 GAGATGCCAGACTTCGATTTGTTCTCTGACACTACAGAGACGACAAATCATCTTAGATTTGCTTC
129 AAGATGCCAAACTTCGATTCGTTCTCTGACAATACAGAGATGACAAATCATCTTAGATTTGCTTC
*
127476779 ATCGTAAACACG
194 ATCGTAATCACG
* * *
127476791 TGAAAGCCAAATCAGCTATGTCTTCGATCTGCTCCTTGTAAGCACAAGGATACCAAACCATCTTG
1 TGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTG
* *
127476856 GATCTGCTTCAGCATAAACATCTGAAGGCGAGGTCTGCTATG
66 GATCTGCTTCAGCATAAACATCCGAAGGCGAGATCTGCTATG
127476898 CTGCAGCCTA
Statistics
Matches: 480, Mismatches: 35, Indels: 8
0.92 0.07 0.02
Matches are distributed among these distances:
204 2 0.00
205 93 0.19
206 384 0.80
207 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (205 bp):
TGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTG
GATCTGCTTCAGCATAAACATCCGAAGGCGAGATCTGCTATGTGTCTGCTCTCCATCAAAGTGAA
GATGCCAAACTTCGATTCGTTCTCTGACAATACAGAGATGACAAATCATCTTAGATTTGCTTCAT
CGTAATCACG
Found at i:127484938 original size:15 final size:14
Alignment explanation
Indices: 127484896--127484945 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
127484886 ATAACTTTAA
*
127484896 ATGCAAATGATGTG
1 ATGCAAATGATGAG
127484910 ATG-AAATGTTATGAG
1 ATGCAAATG--ATGAG
127484925 ATGCAAATGCATGA-
1 ATGCAAATG-ATGAG
127484939 ATGCAAA
1 ATGCAAA
127484946 AAGAATATCG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 5 0.16
14 10 0.32
15 11 0.35
16 5 0.16
ACGTcount: A:0.42, C:0.08, G:0.24, T:0.26
Consensus pattern (14 bp):
ATGCAAATGATGAG
Found at i:127488793 original size:3 final size:3
Alignment explanation
Indices: 127488780--127488830 Score: 50
Period size: 3 Copynumber: 17.3 Consensus size: 3
127488770 AAGAGGTATT
* * * * *
127488780 ATA AT- ATA ATA ATA ATA ATG ATG ATA ATA GTG ATA TTA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
127488827 ATA A
1 ATA A
127488831 AAGTAAAATG
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:127488980 original size:15 final size:15
Alignment explanation
Indices: 127488932--127489024 Score: 81
Period size: 15 Copynumber: 6.2 Consensus size: 15
127488922 GTATATATAT
127488932 GTATAAAATAAATAA
1 GTATAAAATAAATAA
127488947 GTA-AATAAGTGATAA-AA
1 GTATAA-AA-T-A-AATAA
127488964 GTATAAAATAAATAA
1 GTATAAAATAAATAA
127488979 GTATATAAATAATATAA
1 GTATA-AAATAA-ATAA
127488996 --ATAAAAT-AA-AA
1 GTATAAAATAAATAA
*
127489007 GTATAAAATATATAA
1 GTATAAAATAAATAA
127489022 GTA
1 GTA
127489025 AGTGAATAAT
Statistics
Matches: 65, Mismatches: 1, Indels: 24
0.72 0.01 0.27
Matches are distributed among these distances:
11 2 0.03
12 1 0.02
13 8 0.12
14 9 0.14
15 21 0.32
16 8 0.12
17 12 0.18
18 4 0.06
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.28
Consensus pattern (15 bp):
GTATAAAATAAATAA
Found at i:127489008 original size:43 final size:45
Alignment explanation
Indices: 127488958--127489063 Score: 146
Period size: 43 Copynumber: 2.4 Consensus size: 45
127488948 TAAATAAGTG
127488958 ATAAAAGTATAAAATAAATAAGTATA-TAAATAATATA-A-ATAAA
1 ATAAAAGTATAAAATAAATAAGTA-AGTAAATAATATATATATAAA
* * * *
127489001 ATAAAAGTATAAAATATATAAGTAAGTGAATAATATATATTTGAA
1 ATAAAAGTATAAAATAAATAAGTAAGTAAATAATATATATATAAA
127489046 ATAAAAGTATAAAATAAA
1 ATAAAAGTATAAAATAAA
127489064 CGAAGTAAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
42 1 0.02
43 33 0.60
44 1 0.02
45 20 0.36
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (45 bp):
ATAAAAGTATAAAATAAATAAGTAAGTAAATAATATATATATAAA
Found at i:127492434 original size:16 final size:16
Alignment explanation
Indices: 127492405--127492448 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
127492395 AATAAAACAA
127492405 AGAAACGAAA-AGAAAT
1 AGAAACGAAATAG-AAT
127492421 AGAAA-GAAATAGAAT
1 AGAAACGAAATAGAAT
127492436 AGAAACGAAATAG
1 AGAAACGAAATAG
127492449 GGAGAAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 12 0.46
16 14 0.54
ACGTcount: A:0.66, C:0.05, G:0.20, T:0.09
Consensus pattern (16 bp):
AGAAACGAAATAGAAT
Found at i:127492495 original size:20 final size:20
Alignment explanation
Indices: 127492450--127492495 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
127492440 ACGAAATAGG
127492450 GAGAAA-GAAAGAAAGAAAA
1 GAGAAAGGAAAGAAAGAAAA
* *
127492469 GAAAAAGGAAAGAAAGGAAA
1 GAGAAAGGAAAGAAAGAAAA
*
127492489 GGGAAAG
1 GAGAAAG
127492496 CCATGGTCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (20 bp):
GAGAAAGGAAAGAAAGAAAA
Found at i:127493677 original size:24 final size:24
Alignment explanation
Indices: 127493631--127493677 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
127493621 AAATATACAA
*
127493631 ATGAAATGCATGAATTATGTGTTC
1 ATGAAATGCATAAATTATGTGTTC
*
127493655 ATGAAATGGATAATATTAT-TGTT
1 ATGAAATGCATAA-ATTATGTGTT
127493678 AATTGAGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.36, C:0.04, G:0.19, T:0.40
Consensus pattern (24 bp):
ATGAAATGCATAAATTATGTGTTC
Found at i:127495310 original size:33 final size:32
Alignment explanation
Indices: 127495256--127495344 Score: 99
Period size: 33 Copynumber: 2.7 Consensus size: 32
127495246 GCTTTTTAGG
* *
127495256 TTTAGGGTTAGGGTTATGGTTTTGTCAAAATAA
1 TTTA-GGTTAAGGTTAGGGTTTTGTCAAAATAA
*
127495289 TCTT-GAGTTAAGGTTAGGGTTTTGTTAAAATAA
1 T-TTAG-GTTAAGGTTAGGGTTTTGTCAAAATAA
127495322 TTTAGGTGTAAGGTGTAGGGTTT
1 TTTAGGT-TAAGGT-TAGGGTTT
127495345 AAGAATTTTA
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
32 5 0.10
33 33 0.69
34 10 0.21
ACGTcount: A:0.26, C:0.02, G:0.29, T:0.43
Consensus pattern (32 bp):
TTTAGGTTAAGGTTAGGGTTTTGTCAAAATAA
Found at i:127495399 original size:35 final size:34
Alignment explanation
Indices: 127495360--127495458 Score: 114
Period size: 34 Copynumber: 2.9 Consensus size: 34
127495350 TTTTAAAAAG
*
127495360 TAAATCAGGGTTTAGAGTTTTTTTAAAAAATTAAT
1 TAAATTAGGGTTTAGAG-TTTTTTAAAAAATTAAT
* * *
127495395 TAAATTAGGTTTTAGAG-GTTTTAAATTAATTAAT
1 TAAATTAGGGTTTAGAGTTTTTTAAA-AAATTAAT
*
127495429 TAAATTAGGGTTT--AGTTTTTAAAAAAATTA
1 TAAATTAGGGTTTAGAGTTTTTTAAAAAATTA
127495459 TTTTGTGTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
32 7 0.13
33 13 0.24
34 19 0.35
35 15 0.28
ACGTcount: A:0.40, C:0.01, G:0.14, T:0.44
Consensus pattern (34 bp):
TAAATTAGGGTTTAGAGTTTTTTAAAAAATTAAT
Found at i:127495819 original size:124 final size:123
Alignment explanation
Indices: 127495522--127495916 Score: 504
Period size: 124 Copynumber: 3.2 Consensus size: 123
127495512 GACTTTGTTT
* * * ** * *
127495522 TTTTTCTACTGTAGTTTCAGAAAAATTAATTTTGAGAAGACATTTCTGAAAAGATAATATCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAA-TAATTTTGAGAAGACGGTTCTGAAAA-ATAGTGTCAAAA
* * * * **
127495587 AAGCTTCAAGCAGGATGCACTGTCAGTAAAAATACTAAAAAAAAGCTTTCACGTGGGCGCTC
64 ACGCTTCAAGCAGGATGCACTGTCAGCAAAAATACT--GAAAAAGCTTCCACGTGGATGCTC
* *
127495649 TTTTTCTACAGTAGTTCCTAAAAAATAATTTTGAGAAGATGGTTCTGAATAAATAGTGTCAAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAATAATTTTGAGAAGACGGTTCTGAA-AAATAGTGTCAAAAA
*
127495714 CGCTTCAAGCAGGATGCACTGTCAGCAAAAATACTGAAAAAGCTTCCATGTGGATGCTC
65 CGCTTCAAGCAGGATGCACTGTCAGCAAAAATACTGAAAAAGCTTCCACGTGGATGCTC
* * * *
127495773 TTTTTCTATAGTTGTTCCTGAAAAATAAATTTGAGAAGACGGTTCTGAACAAATGGTGTCAAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAATAATTTTGAGAAGACGGTTCTGAA-AAATAGTGTCAAAAA
* * * *
127495838 CGCTACAAGCAGGATGCACTGTCAGCAAAATTGA-TGAAAAAACTCCCACGTGGATGCTC
65 CGCTTCAAGCAGGATGCACTGTCAGCAAAAAT-ACTGAAAAAGCTTCCACGTGGATGCTC
127495897 TTTTTCTACAGTAGTTCCTG
1 TTTTTCTACAGTAGTTCCTG
127495917 TTTGGCCTTA
Statistics
Matches: 236, Mismatches: 30, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
124 147 0.62
125 1 0.00
126 65 0.28
127 23 0.10
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.29
Consensus pattern (123 bp):
TTTTTCTACAGTAGTTCCTGAAAAATAATTTTGAGAAGACGGTTCTGAAAAATAGTGTCAAAAAC
GCTTCAAGCAGGATGCACTGTCAGCAAAAATACTGAAAAAGCTTCCACGTGGATGCTC
Found at i:127498856 original size:15 final size:15
Alignment explanation
Indices: 127498835--127498872 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
127498825 TTTTTATAAT
*
127498835 TTAAAATTTTC-ATA
1 TTAAAATTTACAATA
127498849 TTACAAATTTACAATA
1 TTA-AAATTTACAATA
127498865 TTAAAATT
1 TTAAAATT
127498873 AAATAATAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 3 0.14
15 12 0.57
16 6 0.29
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAAAATTTACAATA
Found at i:127499676 original size:16 final size:15
Alignment explanation
Indices: 127499655--127499685 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
127499645 ATAATAAGGC
127499655 AAAAAATTAGTCAAAA
1 AAAAAATTAG-CAAAA
127499671 AAAAAATTAGCAAAA
1 AAAAAATTAGCAAAA
127499686 GGAATAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.16
Consensus pattern (15 bp):
AAAAAATTAGCAAAA
Found at i:127500558 original size:2 final size:2
Alignment explanation
Indices: 127500551--127500583 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
127500541 ACCAAAATTA
127500551 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
127500584 AATGCCAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:127503669 original size:2 final size:2
Alignment explanation
Indices: 127503621--127503656 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
127503611 TGGCATATTC
127503621 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
127503657 TATTTTTTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:127506050 original size:21 final size:20
Alignment explanation
Indices: 127506014--127506052 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
127506004 AAAAAAAATC
*
127506014 AAAGTAATTTTCAAATTTTG
1 AAAGTAATTTTAAAATTTTG
127506034 AAAGTAATTTTTAAAATTT
1 AAAGTAA-TTTTAAAATTT
127506053 AAAATATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.46
Consensus pattern (20 bp):
AAAGTAATTTTAAAATTTTG
Found at i:127506077 original size:20 final size:19
Alignment explanation
Indices: 127506046--127506151 Score: 61
Period size: 20 Copynumber: 5.2 Consensus size: 19
127506036 AGTAATTTTT
127506046 AAAATTTAAAATATTTATA
1 AAAATTTAAAATATTTATA
*
127506065 AAAATTCTAAAATTTTTATTTCAA
1 AAAATT-TAAAATATTTA--T--A
* * *
127506089 AAAAGATTATAAATTTTTAAA
1 AAAA-TTTA-AAATATTTATA
* * *
127506110 AAAATCTAAAAAATATATCA
1 AAAATTTAAAATATTTAT-A
127506130 AAAATTTAAAA-ATTTAATA
1 AAAATTTAAAATATTT-ATA
127506149 AAA
1 AAA
127506152 TAAATAATTT
Statistics
Matches: 67, Mismatches: 11, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
19 19 0.28
20 25 0.37
21 5 0.07
22 1 0.01
24 7 0.10
25 10 0.15
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (19 bp):
AAAATTTAAAATATTTATA
Found at i:127511515 original size:22 final size:24
Alignment explanation
Indices: 127511464--127511515 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
127511454 GCAAAGAAAA
*
127511464 AAGAAAGGAAAGTTGGACTTTTCTT
1 AAGAAAAGAAAGTTGGAC-TTTCTT
*
127511489 AAGAAAAGAAAGTTTGA-TTT-TT
1 AAGAAAAGAAAGTTGGACTTTCTT
127511511 AAGAA
1 AAGAA
127511516 CTTGATAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 7 0.28
23 3 0.12
25 15 0.60
ACGTcount: A:0.44, C:0.04, G:0.21, T:0.31
Consensus pattern (24 bp):
AAGAAAAGAAAGTTGGACTTTCTT
Found at i:127514477 original size:9 final size:9
Alignment explanation
Indices: 127514465--127514489 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
127514455 TACACGTGTT
127514465 TATATTATA
1 TATATTATA
127514474 TATATTATA
1 TATATTATA
127514483 TATATTA
1 TATATTA
127514490 AGTAATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TATATTATA
Found at i:127514875 original size:15 final size:18
Alignment explanation
Indices: 127514857--127514903 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
127514847 GTTCTATAAA
127514857 TTTTT-CTTCTTT-TT-C
1 TTTTTACTTCTTTCTTCC
*
127514872 TTTTTCCTTTCTTTCTTCC
1 TTTTTAC-TTCTTTCTTCC
127514891 TTTTTACTTCTTT
1 TTTTTACTTCTTT
127514904 GATTTCTCCT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 5 0.19
16 1 0.04
17 6 0.22
18 8 0.30
19 7 0.26
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTACTTCTTTCTTCC
Found at i:127516307 original size:15 final size:15
Alignment explanation
Indices: 127516283--127516312 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
127516273 ATCTGTCTTG
*
127516283 GATCTGAACTAGAAA
1 GATCTAAACTAGAAA
127516298 GATCTAAACTAGAAA
1 GATCTAAACTAGAAA
127516313 TGTTTCTGTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.13, G:0.17, T:0.20
Consensus pattern (15 bp):
GATCTAAACTAGAAA
Found at i:127518033 original size:49 final size:49
Alignment explanation
Indices: 127517961--127518148 Score: 216
Period size: 49 Copynumber: 3.8 Consensus size: 49
127517951 TGAGGTCACG
* *
127517961 TGTGTAGTACTAAGTGTAGGCTACTACGTGTACCGGATAATTGGTTGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTTGCA
* * * * * *
127518010 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTGTGAT-CA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTG-GTTGCA
* * * *
127518059 CGTGTGTAGTACTAAGTGTAGGCTACTACGTGTACCAAATTATTGGTCGCA
1 --TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTTGCA
* *
127518110 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
127518149 GCTTCGGCTA
Statistics
Matches: 113, Mismatches: 22, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
49 73 0.65
50 3 0.03
51 37 0.33
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.30
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTTGCA
Found at i:127518129 original size:100 final size:100
Alignment explanation
Indices: 127517956--127518143 Score: 340
Period size: 100 Copynumber: 1.9 Consensus size: 100
127517946 TATTGTGAGG
** *
127517956 TCACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTACCGGATAATTGGTTGCATGTGTAGTACT
1 TCACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTACCAAATAATTGGTCGCATGTGTAGTACT
127518021 AAGTGCAGGCTACTATGCGTACCCGAAAACTGTGA
66 AAGTGCAGGCTACTATGCGTACCCGAAAACTGTGA
*
127518056 TCACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTACCAAATTATTGGTCGCATGTGTAGTACT
1 TCACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTACCAAATAATTGGTCGCATGTGTAGTACT
127518121 AAGTGCAGGCTACTATGCGTACC
66 AAGTGCAGGCTACTATGCGTACC
127518144 AGATAGCTTC
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
100 84 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.30
Consensus pattern (100 bp):
TCACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTACCAAATAATTGGTCGCATGTGTAGTACT
AAGTGCAGGCTACTATGCGTACCCGAAAACTGTGA
Found at i:127521715 original size:23 final size:23
Alignment explanation
Indices: 127521671--127521758 Score: 85
Period size: 23 Copynumber: 3.8 Consensus size: 23
127521661 AGCTCCTCCT
* *
127521671 GAGCTGATAAC-AGTAAGTTCTATT
1 GAGCTGA-AACGA-TAAGCTCTATC
127521695 GAGCTGAAACGATAAGCTCTATC
1 GAGCTGAAACGATAAGCTCTATC
127521718 GAGCTGAATA-G-TAAGCTC-ATAC
1 GAGCTGAA-ACGATAAGCTCTAT-C
*
127521740 GAGCTGAAACGGTAAGCTC
1 GAGCTGAAACGATAAGCTC
127521759 CAATGAGTTG
Statistics
Matches: 57, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
21 3 0.05
22 17 0.30
23 28 0.49
24 9 0.16
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (23 bp):
GAGCTGAAACGATAAGCTCTATC
Found at i:127526508 original size:24 final size:22
Alignment explanation
Indices: 127526481--127526527 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
127526471 GAACTTTAAT
*
127526481 ATCTCTTGGTATACTGTTCATATG
1 ATCTCTTCGT-TACT-TTCATATG
*
127526505 ATCTTTTCGTTACTTTCATATG
1 ATCTCTTCGTTACTTTCATATG
127526527 A
1 A
127526528 AAATAGACTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 9 0.43
23 4 0.19
24 8 0.38
ACGTcount: A:0.21, C:0.17, G:0.13, T:0.49
Consensus pattern (22 bp):
ATCTCTTCGTTACTTTCATATG
Found at i:127527500 original size:39 final size:39
Alignment explanation
Indices: 127527416--127527568 Score: 207
Period size: 39 Copynumber: 3.9 Consensus size: 39
127527406 TATGGTAACC
** * *
127527416 CGCACAAAGGCCTTCGGGACTTAACCCGGATATCACAATT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
127527456 TGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAACT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
* * *
127527495 CGCACAATTTCCTTCGGGCTTAGCCCGGGTATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
127527534 TGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
127527569 TCGAACATTC
Statistics
Matches: 99, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
39 84 0.85
40 15 0.15
ACGTcount: A:0.24, C:0.30, G:0.21, T:0.25
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:127527541 original size:78 final size:79
Alignment explanation
Indices: 127527385--127527567 Score: 260
Period size: 78 Copynumber: 2.3 Consensus size: 79
127527375 TCGTTCAAAC
* * **
127527385 GCCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAAGGCCTTCGGGACTTAACCCGGATATC
1 GCCTTCGGG-CTTAGCCCGGATATCATAACCCGCACAAAGGCCTTCGGGACTTAACCCGGATATC
127527450 ACAATTTGCACAATT
65 ACAATTTGCACAATT
* *** * *
127527465 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTTCCTTCGGG-CTTAGCCCGGGTATCA
1 GCCTTCGGGCTTAGCCCGGATATCATAACCCGCACAAAGGCCTTCGGGACTTAACCCGGATATCA
127527529 CAATTTGCACAATT
66 CAATTTGCACAATT
127527543 GCCTTCGGGCTTAGCCCGGATATCA
1 GCCTTCGGGCTTAGCCCGGATATCA
127527568 CTCGAACATT
Statistics
Matches: 93, Mismatches: 10, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
78 53 0.57
79 31 0.33
80 9 0.10
ACGTcount: A:0.23, C:0.30, G:0.22, T:0.25
Consensus pattern (79 bp):
GCCTTCGGGCTTAGCCCGGATATCATAACCCGCACAAAGGCCTTCGGGACTTAACCCGGATATCA
CAATTTGCACAATT
Found at i:127531472 original size:13 final size:13
Alignment explanation
Indices: 127531454--127531484 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
127531444 TTTTCACACG
127531454 GCCGTATCGCACA
1 GCCGTATCGCACA
*
127531467 GCCGTATCGCACG
1 GCCGTATCGCACA
127531480 GCCGT
1 GCCGT
127531485 GGTGCATCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.39, G:0.29, T:0.16
Consensus pattern (13 bp):
GCCGTATCGCACA
Found at i:127536380 original size:23 final size:20
Alignment explanation
Indices: 127536350--127536405 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 20
127536340 ACATACATAT
*
127536350 AAATATATATATAATGGTGTTAG
1 AAATATATATATAA---TATTAG
127536373 AAATATATATAGTAATATTAG
1 AAATATATATA-TAATATTAG
127536394 AAATATATATAT
1 AAATATATATAT
127536406 CTAACAATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
20 1 0.03
21 16 0.52
23 11 0.35
24 3 0.10
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (20 bp):
AAATATATATATAATATTAG
Found at i:127536403 original size:25 final size:24
Alignment explanation
Indices: 127536375--127536426 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
127536365 GGTGTTAGAA
**
127536375 ATATATATAGTAATATTAGAAATAT
1 ATATATATAACAATATTA-AAATAT
*
127536400 ATATATCTAACAATATTAAAATAT
1 ATATATATAACAATATTAAAATAT
127536424 ATA
1 ATA
127536427 CATAACAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 9 0.38
25 15 0.62
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (24 bp):
ATATATATAACAATATTAAAATAT
Found at i:127536461 original size:2 final size:2
Alignment explanation
Indices: 127536454--127536482 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
127536444 GATATTAATA
127536454 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
127536483 GAATAATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:127537300 original size:4 final size:4
Alignment explanation
Indices: 127537291--127537330 Score: 55
Period size: 4 Copynumber: 10.0 Consensus size: 4
127537281 AAGATTTTTC
*
127537291 TTAT TTAT TTAT TTAT TTAT TTAT ATTAT ATAT TT-T TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT -TTAT TTAT TTAT TTAT
127537331 ATTTGCAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 3 0.09
4 25 0.78
5 4 0.12
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
TTAT
Found at i:127537312 original size:16 final size:17
Alignment explanation
Indices: 127537291--127537333 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
127537281 AAGATTTTTC
*
127537291 TTATTTAT-TTATTTAT
1 TTATTTATATTATATAT
127537307 TTATTTATATTATATAT
1 TTATTTATATTATATAT
127537324 TT-TTTATATT
1 TTATTTATATT
127537334 TGCAATATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 16 0.64
17 9 0.36
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TTATTTATATTATATAT
Found at i:127538644 original size:14 final size:14
Alignment explanation
Indices: 127538622--127538669 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
127538612 GAGTTGATTT
*
127538622 TTGACAAACAGAAA
1 TTGAAAAACAGAAA
*
127538636 TTGAAAAACAG-AT
1 TTGAAAAACAGAAA
*
127538649 TTGAAAAATAGAAA
1 TTGAAAAACAGAAA
*
127538663 CTGAAAA
1 TTGAAAA
127538670 TTTCTCAGCA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
13 11 0.39
14 17 0.61
ACGTcount: A:0.58, C:0.08, G:0.15, T:0.19
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:127538743 original size:14 final size:14
Alignment explanation
Indices: 127538724--127538758 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
127538714 GAGTTGATTT
127538724 TTGAAAAAT-GTAAA
1 TTGAAAAATAG-AAA
127538738 TTGAAAAATAGAAA
1 TTGAAAAATAGAAA
127538752 TTGAAAA
1 TTGAAAA
127538759 TACCTCAGCG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 19 0.95
15 1 0.05
ACGTcount: A:0.60, C:0.00, G:0.14, T:0.26
Consensus pattern (14 bp):
TTGAAAAATAGAAA
Found at i:127538801 original size:87 final size:83
Alignment explanation
Indices: 127538649--127538897 Score: 347
Period size: 85 Copynumber: 2.9 Consensus size: 83
127538639 AAAAACAGAT
* **
127538649 TTGAAAAATAGAAACTGAAAATTTCTCAGCATGTGTGCC-GAGGCTCAACTCACCTCTCGCAATA
1 TTGAAAAATAGAAATTGAAAATACCTCAGC--GTGT-CCTGAGGCTCAACTCACCTCTCGCAATA
127538713 TGAGTTGATTTTTGAAAAATGTAAA
63 TGAGTTGATTTTTG-AAAA---AAA
127538738 TTGAAAAATAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAATAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
*
127538803 GTTGATTTTTGAAAAACA
66 GTTGATTTTTGAAAAAAA
* * *
127538821 TTGAAAATAACAGAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATAT
1 TTG-AAA-AATAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATAT
127538886 GAGTTGATTTTT
64 GAGTTGATTTTT
127538898 TTTTGAAACA
Statistics
Matches: 150, Mismatches: 7, Indels: 10
0.90 0.04 0.06
Matches are distributed among these distances:
83 5 0.03
84 3 0.02
85 66 0.44
86 6 0.04
87 43 0.29
89 27 0.18
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (83 bp):
TTGAAAAATAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTTTTGAAAAAAA
Found at i:127538877 original size:85 final size:84
Alignment explanation
Indices: 127538688--127539149 Score: 527
Period size: 85 Copynumber: 5.5 Consensus size: 84
127538678 CATGTGTGCC
* * *
127538688 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA-ATGTAAATTGAAAAATAGAAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAT-TGAA---AATAACAGAAA
*
127538752 TTGAAAATACCTCAGCGTGTCCT
62 TTGAAAATACCTCAGCGTGCCCT
127538775 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATTGAAAATAACAGAAATTG
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAACATTGAAAATAACAGAAATTG
*
127538840 AAATTACCTCAGCGTGCCCT
65 AAAATACCTCAGCGTGCCCT
** * *
127538860 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT-----TTTTGAAACAT---ATAAATTC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACATTGAAA-ATAACAGAAATTG
* * * *
127538917 AAAATACCTCAACATGTCAT
65 AAAATACCTCAGCGTGCCCT
* * *
127538937 GAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTGAAAACA--GATTAATCAACAGAATTT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACATTGA-AAAT-AACAGAAATT
127539000 GAAAATACCTCAGCGTGTCCC-
64 GAAAATACCTCAGCGTG-CCCT
* * * *
127539021 GAGGCTCAACTCACCTCCCGCACTATGAGTTGATTTTTGAAAACTGAATT-AAAACAACAGGAAT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAC---ATTGAAAATAACAGAAAT
*
127539085 TGAAAATACCTCAGTGTGCCCT
63 TGAAAATACCTCAGCGTGCCCT
*
127539107 GAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTGAAAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
127539150 ACAGAAATTA
Statistics
Matches: 319, Mismatches: 36, Indels: 41
0.81 0.09 0.10
Matches are distributed among these distances:
77 58 0.18
79 6 0.02
80 6 0.02
81 1 0.00
84 60 0.19
85 72 0.23
86 64 0.20
87 42 0.13
88 8 0.03
89 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (84 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACATTGAAAATAACAGAAATTGA
AAATACCTCAGCGTGCCCT
Found at i:127538951 original size:162 final size:164
Alignment explanation
Indices: 127538658--127539154 Score: 558
Period size: 162 Copynumber: 2.9 Consensus size: 164
127538648 TTTGAAAAAT
* ** *
127538658 AGAAACTGAAAATTTCTCAGCATGTGTGCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
1 AGAAATTGAAAATACCTCAGC--GTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
* *
127538723 TTTGAAAAATGTAAATTGAAAAATAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCA
64 TTT-----ATGT---TTGAAACATACAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCA
127538788 CCTCTCGCAATATGAGTTGATTTTTGAAAAACATTGA-AAAT-AAC
121 CCTCTCGCAATATGAGTTGATTTTTGAAAAACA--GATAAATCAAC
*
127538832 AGAAATTGAAATTACCTCAGCGTG-CCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
1 AGAAATTGAAAATACCTCAGCGTGTCCC-GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
* * * * * *
127538896 TT-T-TTTGAAACATATAAATTCAAAATACCTCAACATGTCATGAGGCTCAACTCACCTCTCACA
65 TTATGTTTGAAACATACAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCA
*
127538959 ATATGAGTTGATTTTTG-AAAACAGATTAATCAAC
130 ATATGAGTTGATTTTTGAAAAACAGATAAATCAAC
* * *
127538993 AGAATTTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCCCGCACTATGAGTTGATTTT
1 AGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
* * * *
127539058 TGAAAACTGAATTAAAACA-ACAGGAATTGAAAATACCTCAGTGTGCCCTGAGGCTCAACTCACC
66 T----A-TG-TTTGAAACATACA--AATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACC
*
127539122 TCTCGTAATATGAGTTGATTTTTGAAAAACAGA
123 TCTCGCAATATGAGTTGATTTTTGAAAAACAGA
127539155 AATTAAAAGG
Statistics
Matches: 280, Mismatches: 28, Indels: 33
0.82 0.08 0.10
Matches are distributed among these distances:
159 2 0.01
160 3 0.01
161 67 0.24
162 72 0.26
165 1 0.00
166 1 0.00
167 1 0.00
168 2 0.01
169 7 0.03
170 56 0.20
171 10 0.04
172 41 0.15
174 17 0.06
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (164 bp):
AGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
TATGTTTGAAACATACAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAA
TATGAGTTGATTTTTGAAAAACAGATAAATCAAC
Found at i:127539143 original size:247 final size:247
Alignment explanation
Indices: 127538688--127539380 Score: 739
Period size: 246 Copynumber: 2.9 Consensus size: 247
127538678 CATGTGTGCC
* *
127538688 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATGTAAATTGAAAAATAGAAAT
1 GAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTGAAAAATG--AATTGAAAAACAGAAAT
* *
127538753 TGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
64 TGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCCCGCAATATGAGTTGATTTTTGAAAA
* *
127538818 ACATTGAAAATAACAGAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAA
129 ACATTGAAAACAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAA
127538883 TATGAGTTGATTTTTTTTTGAAACATATAAATTCAAAATACCTCAACATGTCAT
194 TATGAGTTGATTTTTTTTTGAAACATATAAATTCAAAATACCTCAACATGTCAT
* *
127538937 GAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTGAAAACA-G-ATT-AATCAACAGAATT
1 GAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTGAAAA-ATGAATTGAA-AAACAGAAAT
*
127538999 TGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCCCGCACTATGAGTTGATTTTTG-AAA
64 TGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCCCGCAATATGAGTTGATTTTTGAAAA
* *
127539063 ACTGAATT-AAAACAACAGGAATTGAAAATACCTCAGTGTGCCCTGAGGCTCAACTCACCTCTCG
129 AC---ATTGAAAACAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCG
*
127539127 TAATATGAGTTGA----TTTTTG----A-A-AAA--CAGAAAT---T--A-A----A-
191 CAATATGAGTTGATTTTTTTTTGAAACATATAAATTCA-AAATACCTCAACATGTCAT
* * * *
127539162 -AGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTGAAAAACATAAATTG-AAAACAGAATT
1 GAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTG-AAAA-ATGAATTGAAAAACAGAAAT
* * * * *
127539225 TGGAAATAACTCGTCA-TGTGACTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT
64 TGAAAAT-AC-C-TCAGCGTGTCCCGAGGCTCAACTCACCTCCCGCAATATGAGTTGA-----TT
* * * * *
127539289 TTTCAAAAAAGAATTTGAAAA-AATAGAATTTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTC
121 TTT-GAAAAA-CA-TTGAAAACAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTC
127539353 ACCTCTCGCAATATGAGTTGATTTTTTT
183 ACCTCTCGCAATATGAGTTGATTTTTTT
127539381 GAAAACAGAA
Statistics
Matches: 387, Mismatches: 30, Indels: 65
0.80 0.06 0.13
Matches are distributed among these distances:
224 36 0.09
225 6 0.02
226 16 0.04
227 6 0.02
228 37 0.10
229 3 0.01
230 1 0.00
231 1 0.00
233 7 0.02
234 60 0.16
235 10 0.03
236 4 0.01
237 3 0.01
238 4 0.01
239 1 0.00
243 6 0.02
245 7 0.02
246 68 0.18
247 64 0.17
248 3 0.01
249 43 0.11
250 1 0.00
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (247 bp):
GAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTGAAAAATGAATTGAAAAACAGAAATTG
AAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCCCGCAATATGAGTTGATTTTTGAAAAAC
ATTGAAAACAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATA
TGAGTTGATTTTTTTTTGAAACATATAAATTCAAAATACCTCAACATGTCAT
Found at i:127539171 original size:54 final size:55
Alignment explanation
Indices: 127539108--127539217 Score: 186
Period size: 54 Copynumber: 2.0 Consensus size: 55
127539098 GTGTGCCCTG
*
127539108 AGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTGAAAAACAGAAATT-AAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAA
* *
127539162 AGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTGAAAAACATAAATTGAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAA
127539217 A
1 A
127539218 CAGAATTTGG
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
54 48 0.92
55 4 0.08
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.30
Consensus pattern (55 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAA
Found at i:127539324 original size:14 final size:14
Alignment explanation
Indices: 127539293--127539324 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
127539283 TTTTTTTTTC
127539293 AAAAAAGAATTTGA
1 AAAAAAGAATTTGA
127539307 AAAAATAGAATTTGA
1 AAAAA-AGAATTTGA
127539322 AAA
1 AAA
127539325 TACCTCAGCG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.66, C:0.00, G:0.12, T:0.22
Consensus pattern (14 bp):
AAAAAAGAATTTGA
Found at i:127539368 original size:234 final size:223
Alignment explanation
Indices: 127538938--127539397 Score: 570
Period size: 234 Copynumber: 2.0 Consensus size: 223
127538928 ACATGTCATG
*
127538938 AGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTGAAAACAGATTAATCAACAGAATTTGAA
1 AGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTGAAAACAAATTAA-CAACAGAATTTGAA
* * * **
127539003 AATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCCCGCACTATGAGTTGATTTTTGAAAACTGA
65 AATACCTCAGCGTGACCCGAGGCTCAACTCACCTCCCGCAATATGAGTTGATTTTTCAAAAAAGA
* * *
127539068 ATTAAAACAACAGGAATTGAAAATACCTCAGTGTGCCCTGAGGCTCAACTCACCTCTCGTAATAT
130 ATTAAAACAACAGGAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATAT
*
127539133 GAGTTGA-TTTTTGAAAAACAGAAATTAAA
195 GAGTTGATTTTTTG-AAAACAGAAATAAAA
* *
127539162 AGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTGAAAAACATAAATTGAA-AACAGAATTT
1 AGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTG-AAAAC--AAATT-AACAACAGAATTT
* * * *
127539226 GGAAATAACTCGTCA-TGTGACTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTT
62 GAAAAT-AC-C-TCAGCGTGACCCGAGGCTCAACTCACCTCCCGCAATATGAGTTGA-----TTT
*
127539290 TTCAAAAAAGAATTTGAAAA-AATA-GAATTTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTC
119 TTCAAAAAAGAA-TT-AAAACAACAGGAA-TTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTC
127539353 ACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATAAAA
181 ACCTCTCGCAATATGAGTTGA-TTTTTTGAAAACAGAAATAAAA
127539397 A
1 A
127539398 CATCAAAATA
Statistics
Matches: 202, Mismatches: 17, Indels: 23
0.83 0.07 0.10
Matches are distributed among these distances:
224 36 0.18
225 5 0.02
226 15 0.07
227 6 0.03
228 39 0.19
229 3 0.01
233 15 0.07
234 58 0.29
235 19 0.09
236 6 0.03
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (223 bp):
AGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTGAAAACAAATTAACAACAGAATTTGAAA
ATACCTCAGCGTGACCCGAGGCTCAACTCACCTCCCGCAATATGAGTTGATTTTTCAAAAAAGAA
TTAAAACAACAGGAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATG
AGTTGATTTTTTGAAAACAGAAATAAAA
Found at i:127557095 original size:18 final size:20
Alignment explanation
Indices: 127557058--127557097 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
127557048 AAGAATAAGC
*
127557058 AAAATATAATGTGAAAATTG
1 AAAATATAACGTGAAAATTG
127557078 AAAAT-TAACGTG-AAATTG
1 AAAATATAACGTGAAAATTG
127557096 AA
1 AA
127557098 TTGTATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 6 0.32
20 5 0.26
ACGTcount: A:0.55, C:0.03, G:0.15, T:0.28
Consensus pattern (20 bp):
AAAATATAACGTGAAAATTG
Found at i:127557775 original size:18 final size:19
Alignment explanation
Indices: 127557752--127557789 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
127557742 GAAATGGCAA
127557752 AGATGAGAAATG-AATATG
1 AGATGAGAAATGAAATATG
127557770 AGATGAGAAATGAAATATG
1 AGATGAGAAATGAAATATG
127557789 A
1 A
127557790 AATAATGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.53, C:0.00, G:0.26, T:0.21
Consensus pattern (19 bp):
AGATGAGAAATGAAATATG
Found at i:127560041 original size:26 final size:26
Alignment explanation
Indices: 127560004--127560139 Score: 227
Period size: 26 Copynumber: 5.2 Consensus size: 26
127559994 TGATACAAAT
* *
127560004 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
127560030 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
* *
127560056 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
127560082 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
*
127560108 TGATAATGGGTTAGGTAAATGTTTCG
1 TGATAATGGGTTAGGTAAATGTTTCA
127560134 TGATAA
1 TGATAA
127560140 GAATATCATG
Statistics
Matches: 103, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 103 1.00
ACGTcount: A:0.32, C:0.05, G:0.26, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:127561799 original size:27 final size:27
Alignment explanation
Indices: 127561758--127561897 Score: 183
Period size: 27 Copynumber: 5.2 Consensus size: 27
127561748 GAGGAAGCGT
*
127561758 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
127561785 TCTGGTGGCTCTGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
127561812 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
127561839 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * * *
127561867 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
127561893 TCTGG
1 TCTGG
127561898 CAGCCATGCT
Statistics
Matches: 102, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
26 5 0.05
27 82 0.80
28 15 0.15
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:127561843 original size:54 final size:55
Alignment explanation
Indices: 127561758--127561897 Score: 203
Period size: 54 Copynumber: 2.6 Consensus size: 55
127561748 GAGGAAGCGT
* * *
127561758 TCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACAAATATCTG-A
1 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTGTA
* *
127561812 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTGTA
* *
127561867 TCTGGTGACTCTGTCACAT-TATCTGTTCTGG
1 TCTGGTGGCTCTGCCACATATATCTGTTCTGG
127561898 CAGCCATGCT
Statistics
Matches: 78, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
54 60 0.77
55 18 0.23
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (55 bp):
TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTGTA
Found at i:127563565 original size:15 final size:15
Alignment explanation
Indices: 127563547--127563575 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
127563537 TCCTTAAATA
127563547 TTTATTAATTAATTT
1 TTTATTAATTAATTT
127563562 TTTATTAATTAATT
1 TTTATTAATTAATT
127563576 AAGATTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTATTAATTAATTT
Found at i:127564157 original size:27 final size:27
Alignment explanation
Indices: 127564127--127564182 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
127564117 ATATAATAGG
*
127564127 ATGTTATAAGATGTTTTTAATTTATAA
1 ATGTTATAAGATGTTTTTAATTGATAA
127564154 ATGTTATAAGATGTTTTTAATTGATAA
1 ATGTTATAAGATGTTTTTAATTGATAA
127564181 AT
1 AT
127564183 TGAGCTAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (27 bp):
ATGTTATAAGATGTTTTTAATTGATAA
Found at i:127566382 original size:285 final size:286
Alignment explanation
Indices: 127565872--127566440 Score: 978
Period size: 285 Copynumber: 2.0 Consensus size: 286
127565862 AAAGAGCTTT
* * *
127565872 TATAAGCTCAATTGAGTCTTGGATTTAATTGTGTATCATATTATGAATGTAGTTAAGGTATGAAC
1 TATAAGCTCAATTAAGTCTCGGATTTAATTGTGTATCATATTATGAATGTAGTTAAAGTATGAAC
*
127565937 ATATGTTTGAATGATGTATTTACAGTATATTTGACGACACTTACTCCGAAAATGGATGTGACATC
66 ATATGTTTGAATGATGTATTTACAGTATATTTGACGACACTTACTCCGAAAATGGATATGACATC
* *
127566002 CTATAGCTCGGACCCGACGATCGGGTTGGGTAAGGGGTATTACAACTTTGACATTATGTCCCCTC
131 CTATAGCTCGAACCCGACGATCGGGTTGGGTAAGGGGTATTACAACTTTGACATCATGTCCCCTC
*
127566067 AACATTCAAATTCCCCCAAGATGTTGTATGACGAGTGCAAAGATCCAAAATTTTGGCAAGGGGTG
196 AACATTCAAATTCCCCCAAGATGTTGTATGACGAGTGCAAAGATCCAAAATTTTGGCAAAGGGTG
127566132 TTGCTGATGAAG-GAGGTATAGAGCC
261 TTGCTGATGAAGTGAGGTATAGAGCC
*
127566157 TATAAGCTCAATTAAGTCTCGGATTTAATTGTGTATCATATTATGAATGTGGTTAAAGTATGAAC
1 TATAAGCTCAATTAAGTCTCGGATTTAATTGTGTATCATATTATGAATGTAGTTAAAGTATGAAC
* * *
127566222 ATATGTTTGAATGATGTATTTACAGTATATTTGACGACAGTTACTTCGAAAATGGATATGGCATC
66 ATATGTTTGAATGATGTATTTACAGTATATTTGACGACACTTACTCCGAAAATGGATATGACATC
* * *
127566287 CTATAGCTCGAACCCGACGATTGGGTTGGGTAAGGGGTATTACAACTTTGACATCATGTCCTCTT
131 CTATAGCTCGAACCCGACGATCGGGTTGGGTAAGGGGTATTACAACTTTGACATCATGTCCCCTC
* * *
127566352 AACGTTCAAATTCCCTCAAGATGTTGTATGACGAGTGCAGAGATCCAAAATTTTGGCAAAGGGTG
196 AACATTCAAATTCCCCCAAGATGTTGTATGACGAGTGCAAAGATCCAAAATTTTGGCAAAGGGTG
127566417 TTGCTGATGAAGTGAGGTATAGAG
261 TTGCTGATGAAGTGAGGTATAGAG
127566441 TATTTTTGAT
Statistics
Matches: 266, Mismatches: 17, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
285 255 0.96
286 11 0.04
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (286 bp):
TATAAGCTCAATTAAGTCTCGGATTTAATTGTGTATCATATTATGAATGTAGTTAAAGTATGAAC
ATATGTTTGAATGATGTATTTACAGTATATTTGACGACACTTACTCCGAAAATGGATATGACATC
CTATAGCTCGAACCCGACGATCGGGTTGGGTAAGGGGTATTACAACTTTGACATCATGTCCCCTC
AACATTCAAATTCCCCCAAGATGTTGTATGACGAGTGCAAAGATCCAAAATTTTGGCAAAGGGTG
TTGCTGATGAAGTGAGGTATAGAGCC
Found at i:127570109 original size:5 final size:5
Alignment explanation
Indices: 127570099--127570136 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
127570089 TTCAAAAATT
*
127570099 AATAA AATAA AATAA AA-AG AATAA AATAA AATAA AATA
1 AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATA
127570137 GGATAGATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 3 0.10
5 27 0.90
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (5 bp):
AATAA
Found at i:127570115 original size:19 final size:19
Alignment explanation
Indices: 127570093--127570135 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
127570083 AGAATCTTCA
*
127570093 AAAATTAATAAAATAAAAT
1 AAAATGAATAAAATAAAAT
*
127570112 AAAAAGAATAAAATAAAAT
1 AAAATGAATAAAATAAAAT
127570131 AAAAT
1 AAAAT
127570136 AGGATAGATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (19 bp):
AAAATGAATAAAATAAAAT
Found at i:127578706 original size:20 final size:20
Alignment explanation
Indices: 127578683--127578720 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
127578673 GTTTATTCGC
*
127578683 GATTTTTAATATTTTGTAAA
1 GATTTTTAAAATTTTGTAAA
127578703 GATTTTTAAAATTTTGTA
1 GATTTTTAAAATTTTGTA
127578721 TTTGGATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.55
Consensus pattern (20 bp):
GATTTTTAAAATTTTGTAAA
Found at i:127580381 original size:28 final size:28
Alignment explanation
Indices: 127580349--127580417 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
127580339 GCGTAGATCA
127580349 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
127580377 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
127580405 CGATA-TACCCCTA
1 CGAAATTACCCCTA
127580418 GGGTTTTAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 8 0.20
28 32 0.80
ACGTcount: A:0.43, C:0.28, G:0.10, T:0.19
Consensus pattern (28 bp):
CGAAATTACCCCTAAAGAGCAAAATTAC
Found at i:127586079 original size:16 final size:15
Alignment explanation
Indices: 127586054--127586089 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
127586044 TTTTCTTAAT
127586054 TTATTAATTATTATA
1 TTATTAATTATTATA
*
127586069 TTATATAATTATTATT
1 TTAT-TAATTATTATA
127586085 TTATT
1 TTATT
127586090 TAAATTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTATTAATTATTATA
Found at i:127586882 original size:38 final size:39
Alignment explanation
Indices: 127586780--127586887 Score: 103
Period size: 38 Copynumber: 2.8 Consensus size: 39
127586770 GACCTCGAGT
**
127586780 CGATGAGACACTGGGTGTCATACTATTACTTCGGATAGATT
1 CGATGAGACACTGGGTGTCA-ACT-TTACTTCGGATAGAGC
* ** * * *
127586821 TGATGAGGTACTGGGT-ACCACTTTACTTCGGCTAG-GC
1 CGATGAGACACTGGGTGTCAACTTTACTTCGGATAGAGC
*
127586858 CGATGAGACACTGGGTGTCAACTTTTCTTC
1 CGATGAGACACTGGGTGTCAACTTTACTTC
127586888 AAACTATTCG
Statistics
Matches: 52, Mismatches: 14, Indels: 5
0.73 0.20 0.07
Matches are distributed among these distances:
37 13 0.25
38 22 0.42
39 3 0.06
40 1 0.02
41 13 0.25
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.31
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAACTTTACTTCGGATAGAGC
Found at i:127587633 original size:42 final size:42
Alignment explanation
Indices: 127587586--127587666 Score: 162
Period size: 42 Copynumber: 1.9 Consensus size: 42
127587576 ATTAAAAATG
127587586 ATAGTAGAATTTTCATTACTTAAGTTGTTAAGTCAATATGTT
1 ATAGTAGAATTTTCATTACTTAAGTTGTTAAGTCAATATGTT
127587628 ATAGTAGAATTTTCATTACTTAAGTTGTTAAGTCAATAT
1 ATAGTAGAATTTTCATTACTTAAGTTGTTAAGTCAATAT
127587667 ATTAAATATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.44
Consensus pattern (42 bp):
ATAGTAGAATTTTCATTACTTAAGTTGTTAAGTCAATATGTT
Found at i:127587805 original size:3 final size:3
Alignment explanation
Indices: 127587797--127587823 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
127587787 AATTTTTATT
127587797 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
127587824 AATGAATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:127589940 original size:26 final size:26
Alignment explanation
Indices: 127589911--127590018 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
127589901 TGGTACAAAT
127589911 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
127589937 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
127589963 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
127589989 CGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
127590015 TGAT
1 TGAT
127590019 GGGAATTTCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.33, C:0.08, G:0.24, T:0.34
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:127590538 original size:26 final size:26
Alignment explanation
Indices: 127590509--127590616 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
127590499 TGGTACAAAT
127590509 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* * *
127590535 TGATAATGGATTAAGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
127590561 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
127590587 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
127590613 TGAT
1 TGAT
127590617 GGAAATTTCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:127590731 original size:598 final size:598
Alignment explanation
Indices: 127589596--127591389 Score: 3437
Period size: 598 Copynumber: 3.0 Consensus size: 598
127589586 TATGTAACGC
*
127589596 CCCAATTTTCGGGAATTCTGTGAATGTTGGCATAGGTTTAATTATGTTAGTGGGCCTCTAGAAAG
1 CCCAATTTTCGGGAATTCTGTGAATGTTGGCATAGGTTTAATTATGTTAGTGGGCCTCTAGAAGG
* *
127589661 CCCAAGCTTAAGATAGAACCCGGCAATTTTAGTTAATATTTGTTTCATAAGAAAAAGGGGGTGAA
66 CCCAAGCTTAAGATAGAACCCGGCAATTTTAGTTAATTTTTGTTCCATAAGAAAAAGGGGGTGAA
127589726 ATTATGAAATAGGACCTATGTGAAAATGTTTGAAAATAT-TATAGGCTAAATTGAAGTGGCCAAA
131 ATTATGAAATAGGACCTATGTGAAAATGTTTGAAAAT-TCTATAGGCTAAATTGAAGTGGCCAAA
127589790 TAAATAGGAGTGCAAAATAGGAGGATTTGCATGACAAACCTCCCATTTTACATGAAGTGGCCATC
195 TAAATAGGAGTGCAAAATAGGAGGATTTGCATGACAAACCTCCCATTTTACATGAAGTGGCCATC
127589855 CATTATGTTGTTGTAGACAATATGAGCACTTGATATCCATAATTCATGGTACAAATTGATAATGG
260 CATTATGTTGTTGTAGACAATATGAGCACTTGATATCCATAATTCATGGTACAAATTGATAATGG
127589920 GTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCATGATAATGGGTTAGGTAAATGT
325 GTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCATGATAATGGGTTAGGTAAATGT
* *
127589985 TCCACGATAATAGGTTAGGTAAATGTTCCATGATGGGAATTTCATGTCTTTTGTATTAAAGAATT
390 TCCATGATAATGGGTTAGGTAAATGTTCCATGATGGGAATTTCATGTCTTTTGTATTAAAGAATT
127590050 AAATGGATGAAATATGAAATTTTTTTAAAAGAAAAAGGGGTGAAAAGAACAAAGTTTTGTCCATC
455 AAATGGATGAAATATGAAATTTTTTTAAAAGAAAAAGGGGTGAAAAGAACAAAGTTTTGTCCATC
127590115 TTTGTTCATCATAACCGAAAGTTAGAGAAGAGAAAGGAGAGGAGAAAGCTCTTGAATGTTCGGTC
520 TTTGTTCATCATAACCGAAAGTTAGAGAAGAGAAAGGAGAGGAGAAAGCTCTTGAATGTTCGGTC
127590180 ACTTGGGGAAGAAA
585 ACTTGGGGAAGAAA
127590194 CCCAATTTTCGGGAATTCTGTGAATGTTGGCATAGGTTTAATTATGTTAGTGGGCCTCTAGAAGG
1 CCCAATTTTCGGGAATTCTGTGAATGTTGGCATAGGTTTAATTATGTTAGTGGGCCTCTAGAAGG
127590259 CCCAAGCTTAAGATAGAACCCGGCAATTTTAGTTAATTTTTGTTCCATAAGAAAAAGGGGGTGAA
66 CCCAAGCTTAAGATAGAACCCGGCAATTTTAGTTAATTTTTGTTCCATAAGAAAAAGGGGGTGAA
127590324 ATTATGAAATAGGACCTATGTGAAAATGTTTGAAAATTCTATAGGCTAAATTGAAGTGGCCAAAT
131 ATTATGAAATAGGACCTATGTGAAAATGTTTGAAAATTCTATAGGCTAAATTGAAGTGGCCAAAT
127590389 AAATAGGAGTGCAAAATAGGAGGATTTGCATGACAAACCTCCCATTTTACATGAAGTGGCCATCC
196 AAATAGGAGTGCAAAATAGGAGGATTTGCATGACAAACCTCCCATTTTACATGAAGTGGCCATCC
127590454 ATTATGTTGTTGTAGACAATATGAGCACTTGATATCCATAATTCATGGTACAAATTGATAATGGG
261 ATTATGTTGTTGTAGACAATATGAGCACTTGATATCCATAATTCATGGTACAAATTGATAATGGG
*
127590519 TTAGGTAAATGTTCCATGATAATGGATTAAGTAAATATTCCATGATAATGGGTTAGGTAAATGTT
326 TTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCATGATAATGGGTTAGGTAAATGTT
* *
127590584 CCATGATAATGGGTTAGGTAAATGTTCCATGATGGAAATTTCATATCTTTTGTATTAAAGAATTA
391 CCATGATAATGGGTTAGGTAAATGTTCCATGATGGGAATTTCATGTCTTTTGTATTAAAGAATTA
127590649 AATGGATGAAATATGAAATTTTTTTAAAAGAAAAAGGGGTGAAAAGAACAAAGTTTTGTCCATCT
456 AATGGATGAAATATGAAATTTTTTTAAAAGAAAAAGGGGTGAAAAGAACAAAGTTTTGTCCATCT
127590714 TTGTTCATCATAACCGAAAGTTAGAGAAGAGAAAGGAGAGGAGAAAGCTCTTGAATGTTCGGTCA
521 TTGTTCATCATAACCGAAAGTTAGAGAAGAGAAAGGAGAGGAGAAAGCTCTTGAATGTTCGGTCA
127590779 CTTGGGGAAGAAA
586 CTTGGGGAAGAAA
127590792 CCCAATTTTCGGGAATTCTGTGAATGTTGGCATAGGTTTAATTATGTTAGTGGGCCTCTAGAAGG
1 CCCAATTTTCGGGAATTCTGTGAATGTTGGCATAGGTTTAATTATGTTAGTGGGCCTCTAGAAGG
*
127590857 CCCAAGCTTAAGATAGAACCCGGTAATTTTAGTTAATTTTTGTTCCATAAGAAAAAGGGGGTGAA
66 CCCAAGCTTAAGATAGAACCCGGCAATTTTAGTTAATTTTTGTTCCATAAGAAAAAGGGGGTGAA
*
127590922 ATTATGAAATAGGACCTATGTGAAAATGTTTGAAAATGCTATAGGCTAAATTGAAGTGGCCAAAT
131 ATTATGAAATAGGACCTATGTGAAAATGTTTGAAAATTCTATAGGCTAAATTGAAGTGGCCAAAT
127590987 AAATAGGAGTGCAAAATAGGAGGATTTGCATGACAAACCTCCCATTTTACATGAAGTGGCCATCC
196 AAATAGGAGTGCAAAATAGGAGGATTTGCATGACAAACCTCCCATTTTACATGAAGTGGCCATCC
*
127591052 ATTATGTTGTTGTAGACAATAAGAGCACTTGATATCCATAATTCATGGTACAAATTGATAATGGG
261 ATTATGTTGTTGTAGACAATATGAGCACTTGATATCCATAATTCATGGTACAAATTGATAATGGG
* *
127591117 TTAGGTAAATGTTCCATTATAATGGATTAGGTAAATATTCCATGATAATGGGTTAGGTAACTGTT
326 TTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCATGATAATGGGTTAGGTAAATGTT
127591182 CCATGATAATGGGTTAGGTAAATGTTCCATGATGGGAATTTCATGTCTTTTGTATTAAAGAATTA
391 CCATGATAATGGGTTAGGTAAATGTTCCATGATGGGAATTTCATGTCTTTTGTATTAAAGAATTA
*
127591247 AATGGATGAAATATGAAATTTTTTTAAAAGAAAAAGGGGTGAAAAGAACAAAATTTTGTCCATCT
456 AATGGATGAAATATGAAATTTTTTTAAAAGAAAAAGGGGTGAAAAGAACAAAGTTTTGTCCATCT
*
127591312 TTGTTCATCATAACCGAAAGTTAGAGAAGAGAAAGGAGAGGAGAAAGCTCTTGAATGTTTGGTCA
521 TTGTTCATCATAACCGAAAGTTAGAGAAGAGAAAGGAGAGGAGAAAGCTCTTGAATGTTCGGTCA
127591377 CTTGGGGAAGAAA
586 CTTGGGGAAGAAA
127591390 ATTGAAGGTA
Statistics
Matches: 1177, Mismatches: 18, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
597 1 0.00
598 1176 1.00
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.31
Consensus pattern (598 bp):
CCCAATTTTCGGGAATTCTGTGAATGTTGGCATAGGTTTAATTATGTTAGTGGGCCTCTAGAAGG
CCCAAGCTTAAGATAGAACCCGGCAATTTTAGTTAATTTTTGTTCCATAAGAAAAAGGGGGTGAA
ATTATGAAATAGGACCTATGTGAAAATGTTTGAAAATTCTATAGGCTAAATTGAAGTGGCCAAAT
AAATAGGAGTGCAAAATAGGAGGATTTGCATGACAAACCTCCCATTTTACATGAAGTGGCCATCC
ATTATGTTGTTGTAGACAATATGAGCACTTGATATCCATAATTCATGGTACAAATTGATAATGGG
TTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCATGATAATGGGTTAGGTAAATGTT
CCATGATAATGGGTTAGGTAAATGTTCCATGATGGGAATTTCATGTCTTTTGTATTAAAGAATTA
AATGGATGAAATATGAAATTTTTTTAAAAGAAAAAGGGGTGAAAAGAACAAAGTTTTGTCCATCT
TTGTTCATCATAACCGAAAGTTAGAGAAGAGAAAGGAGAGGAGAAAGCTCTTGAATGTTCGGTCA
CTTGGGGAAGAAA
Found at i:127591146 original size:26 final size:26
Alignment explanation
Indices: 127591107--127591214 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
127591097 TGGTACAAAT
127591107 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* * *
127591133 TTATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
127591159 TGATAATGGGTTAGGTAACTGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
127591185 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
127591211 TGAT
1 TGAT
127591215 GGGAATTTCA
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 74 1.00
ACGTcount: A:0.31, C:0.08, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:127593140 original size:33 final size:34
Alignment explanation
Indices: 127593063--127593143 Score: 85
Period size: 32 Copynumber: 2.4 Consensus size: 34
127593053 TATAGGCCAT
**
127593063 ACTGTTATCTGAATAAGGGGCTAAGGCCCAGTTT
1 ACTGTTATCTGAATAAGGGGCTAAGGCCCAGTCC
* * **
127593097 ATTGTAATCTGAA-AA-GGGCTCTGGCCCAGTACC
1 ACTGTTATCTGAATAAGGGGCTAAGGCCCAGT-CC
127593130 ACTGTTATCTGAAT
1 ACTGTTATCTGAAT
127593144 GGGCTTAGGC
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
32 13 0.35
33 13 0.35
34 11 0.30
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (34 bp):
ACTGTTATCTGAATAAGGGGCTAAGGCCCAGTCC
Found at i:127597299 original size:16 final size:15
Alignment explanation
Indices: 127597274--127597309 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
127597264 TTTTCTTAAT
127597274 TTATTAATTATTATA
1 TTATTAATTATTATA
*
127597289 TTATATAATTATTATT
1 TTAT-TAATTATTATA
127597305 TTATT
1 TTATT
127597310 TAAATTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTATTAATTATTATA
Found at i:127597470 original size:3 final size:3
Alignment explanation
Indices: 127597462--127597503 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
127597452 AGTAAAAGGA
127597462 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
127597504 GAAATAAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:127597686 original size:16 final size:16
Alignment explanation
Indices: 127597648--127597689 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
127597638 TATAGTGTAT
127597648 TATT-ATTATTAATTTA
1 TATTAATTA-TAATTTA
*
127597664 T-TAAATTATAATTTA
1 TATTAATTATAATTTA
127597679 TATTAATTATA
1 TATTAATTATA
127597690 TTATGAGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATTAATTATAATTTA
Found at i:127598522 original size:17 final size:18
Alignment explanation
Indices: 127598500--127598535 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
127598490 TAAATGAGTT
127598500 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
127598517 AATTAGGGTATAAATTGG
1 AATTAGGATATAAATTGG
127598535 A
1 A
127598536 TAGAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:127599253 original size:38 final size:38
Alignment explanation
Indices: 127599151--127599283 Score: 117
Period size: 38 Copynumber: 3.4 Consensus size: 38
127599141 AACCTCGAGT
* * * *
127599151 CGATGAGATACTAGGTGTCATACTATTACTTCGGATAGGTT
1 CGATGAGACACTGGGTGTCA-ACT-TTACTTCGGCTAGG-C
* * *
127599192 CGATGAGATACTGGGT-ACCACTTTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAACTTTACTTCGGCTAGGC
* * *
127599229 CGATGAGACACTGGGTGTCAACTTTGCTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAACTTTACTTCG-GCTAGGC
*
127599267 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
127599284 CCGAACTGGT
Statistics
Matches: 78, Mismatches: 12, Indels: 7
0.80 0.12 0.07
Matches are distributed among these distances:
37 15 0.19
38 41 0.53
39 6 0.08
40 1 0.01
41 15 0.19
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (38 bp):
CGATGAGACACTGGGTGTCAACTTTACTTCGGCTAGGC
Found at i:127600132 original size:3 final size:3
Alignment explanation
Indices: 127600124--127600159 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
127600114 AATTTTTATT
127600124 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
127600160 AATGAATGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:127606315 original size:23 final size:22
Alignment explanation
Indices: 127606266--127606316 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 22
127606256 GTAAAGATTA
*
127606266 AAATTGTAATTAAGTAAATAAGT
1 AAATTGTAATTAAG-AAAAAAGT
127606289 AAATTGTAATTAA-AATAAAAGT
1 AAATTGTAATTAAGAA-AAAAGT
127606311 CAAATT
1 -AAATT
127606317 AATGTGTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 18 0.72
ACGTcount: A:0.55, C:0.02, G:0.10, T:0.33
Consensus pattern (22 bp):
AAATTGTAATTAAGAAAAAAGT
Found at i:127613222 original size:20 final size:21
Alignment explanation
Indices: 127613184--127613223 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
127613174 CTGTAACTGT
127613184 CACCAATTTCCTCGTGAACCC
1 CACCAATTTCCTCGTGAACCC
*
127613205 CACCATTTTCCTCG-GAACC
1 CACCAATTTCCTCGTGAACC
127613224 ATTCAAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.23, C:0.42, G:0.10, T:0.25
Consensus pattern (21 bp):
CACCAATTTCCTCGTGAACCC
Found at i:127620745 original size:6 final size:6
Alignment explanation
Indices: 127620681--127620794 Score: 147
Period size: 6 Copynumber: 19.0 Consensus size: 6
127620671 ATTATAAATG
* * * * *
127620681 TGTATG TGTACA TGTACA TGTACA TGTACA TGTATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
* * * *
127620729 TGTACA TGTATA TGTATA TGCATA TGAATA TGTATA TGAATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
127620777 TGTATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA
127620795 ATTAAAATAG
Statistics
Matches: 98, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 98 1.00
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.43
Consensus pattern (6 bp):
TGTATA
Found at i:127624635 original size:24 final size:25
Alignment explanation
Indices: 127624596--127624648 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 25
127624586 AATAAAGGTG
127624596 AATAAAAAAAATTTAGAATTTAACA
1 AATAAAAAAAATTTAGAATTTAACA
*
127624621 AATAAAAAAAA-TTAGAATTTAATA
1 AATAAAAAAAATTTAGAATTTAACA
127624645 AATA
1 AATA
127624649 TCTTTTATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 16 0.59
25 11 0.41
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.28
Consensus pattern (25 bp):
AATAAAAAAAATTTAGAATTTAACA
Found at i:127625847 original size:27 final size:25
Alignment explanation
Indices: 127625809--127625860 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 25
127625799 TTAGACGTGC
*
127625809 ATTTTTTTTGTAATTACGTTATTATTT
1 ATTTGTTTTGTAATT-C-TTATTATTT
127625836 ATTTGTTTTGTAATTCTTATTATTT
1 ATTTGTTTTGTAATTCTTATTATTT
127625861 GTCTGAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 9 0.38
26 1 0.04
27 14 0.58
ACGTcount: A:0.21, C:0.04, G:0.08, T:0.67
Consensus pattern (25 bp):
ATTTGTTTTGTAATTCTTATTATTT
Found at i:127632880 original size:43 final size:45
Alignment explanation
Indices: 127632799--127632924 Score: 139
Period size: 43 Copynumber: 2.8 Consensus size: 45
127632789 AGAACAGAAA
*
127632799 TGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGGAT
1 TGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGGAT
* *
127632845 TGAGCCATGTAAG-CCATATT-ATATATGGCATTGGAGACAGGAA
1 TGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGGAT
* ** * * *
127632888 TAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 TGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
127632925 CAGGATATTG
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
43 30 0.45
44 5 0.07
45 8 0.12
46 24 0.36
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (45 bp):
TGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGGAT
Found at i:127640241 original size:43 final size:45
Alignment explanation
Indices: 127640161--127640286 Score: 139
Period size: 43 Copynumber: 2.8 Consensus size: 45
127640151 AGAACAGAAA
*
127640161 TGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGGAT
1 TGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGGAT
* *
127640207 TGAGCCATGTAA-TCCATATT-ATATATGGCATTGGAGACAGGAA
1 TGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGGAT
* ** * * *
127640250 TAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 TGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
127640287 CAGGATATTG
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
43 29 0.43
44 6 0.09
45 9 0.13
46 23 0.34
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (45 bp):
TGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGGAT
Done.