Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167993.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_25, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 17943224
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 94000 characters in sequence are not A, C, G, or T
File 8 of 100
Found at i:1313917 original size:24 final size:24
Alignment explanation
Indices: 1313888--1313936 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1313878 TGCTTTTGGA
1313888 AAATAAGTGCCGAATCTAGGCTTC
1 AAATAAGTGCCGAATCTAGGCTTC
1313912 AAATAAGTGCCGAATCTAGGCTTC
1 AAATAAGTGCCGAATCTAGGCTTC
1313936 A
1 A
1313937 TATCCGCTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.24
Consensus pattern (24 bp):
AAATAAGTGCCGAATCTAGGCTTC
Found at i:1318130 original size:17 final size:18
Alignment explanation
Indices: 1318104--1318139 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1318094 TTATTTGTTT
*
1318104 ATTAATAGAATA-ATAAA
1 ATTAAGAGAATATATAAA
1318121 ATTAAGAGAATATATAAA
1 ATTAAGAGAATATATAAA
1318139 A
1 A
1318140 AAAAAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (18 bp):
ATTAAGAGAATATATAAA
Found at i:1322864 original size:58 final size:58
Alignment explanation
Indices: 1322722--1323140 Score: 296
Period size: 58 Copynumber: 7.0 Consensus size: 58
1322712 GCTTTTATGC
* * * *
1322722 AAGGAAAATTGATACTTTCAACTTTTCCTCAAAA-ATGTTTTTCTTGATAA-TTTTAATTTC
1 AAGGAAAATTGATACTTCCAACTTTTCCTCAAAATA-CTTTTTC--GA-AATTTTTATTTTT
* * * * *
1322782 AAGAAAAATTCATAATTTCAACTTTTTCTCAAAATACTTTTTCGAAATTTTTATTTTT
1 AAGGAAAATTGATACTTCCAACTTTTCCTCAAAATACTTTTTCGAAATTTTTATTTTT
** ** * *
1322840 AAGGAAAATTGGCACTTCCAACTTTTCCTCAAAATGTTTTTTTTTTCTGAAA-TTTTAATTTC
1 AAGGAAAATTGATACTTCCAACTTTTCCTCAAAA----TACTTTTTC-GAAATTTTTATTTTT
* * *
1322902 AAGTAAAATTGATACTTTCAACTTTTCTTCAAAATACTTTTT-GAACATTTTTATTTTT
1 AAGGAAAATTGATACTTCCAACTTTTCCTCAAAATACTTTTTCGAA-ATTTTTATTTTT
* * ** *** * *
1322960 AAGAAAAATTGGTACTTCCAACTTTTCCTCAAAATGTTTTTTTTTTAA-TTTTAATTTC
1 AAGGAAAATTGATACTTCCAACTTTTCCTCAAAAT-ACTTTTTCGAAATTTTTATTTTT
*
1323018 AAGGAAAATTGATACTTTCAAACTTCAACTTTTCC-CAAAATACTTTTT-GAGATTTTTTATTTT
1 AAGGAAAATTGATAC-TT----C--CAACTTTTCCTCAAAATACTTTTTCGA-AATTTTTATTTT
1323081 T
58 T
* * * *
1323082 AAAGAAAATTGATACTTTCAACTTTTCCTTAAAAATA-TTTTTCTTGAAAATTTTATTTT
1 AAGGAAAATTGATACTTCCAACTTTTCC-TCAAAATACTTTTTC--GAAATTTTTATTTT
1323141 ATATTTTTTT
Statistics
Matches: 283, Mismatches: 51, Indels: 50
0.74 0.13 0.13
Matches are distributed among these distances:
56 3 0.01
57 13 0.05
58 108 0.38
59 14 0.05
60 47 0.17
61 3 0.01
62 44 0.16
63 13 0.05
64 28 0.10
65 10 0.04
ACGTcount: A:0.33, C:0.13, G:0.07, T:0.47
Consensus pattern (58 bp):
AAGGAAAATTGATACTTCCAACTTTTCCTCAAAATACTTTTTCGAAATTTTTATTTTT
Found at i:1322921 original size:120 final size:117
Alignment explanation
Indices: 1322722--1323115 Score: 492
Period size: 120 Copynumber: 3.3 Consensus size: 117
1322712 GCTTTTATGC
* *
1322722 AAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATG--TTTTTCTTGATAATTTTAATTTCAAG
1 AAGGAAAATTGATACTTCCAACTTTTCCTC-AAAATGTTTTTTTTTTGA-AATTTTAATTTCAAG
* *
1322785 AAAAATTCATAATTTCAACTTTTTCTCAAAATACTTTTTCGAAATTTTTATTTTT
64 AAAAATTGATACTTTCAACTTTTTCTCAAAATACTTTTT-GAAATTTTTATTTTT
**
1322840 AAGGAAAATTGGCACTTCCAACTTTTCCTCAAAATGTTTTTTTTTTCTGAAATTTTAATTTCAAG
1 AAGGAAAATTGATACTTCCAACTTTTCCTCAAAATG-TTTTTTTTT-TGAAATTTTAATTTCAAG
*
1322905 TAAAATTGATACTTTCAAC-TTTTCTTCAAAATACTTTTTGAACATTTTTATTTTT
64 AAAAATTGATACTTTCAACTTTTTC-TCAAAATACTTTTTGAA-ATTTTTATTTTT
* * *
1322960 AAGAAAAATTGGTACTTCCAACTTTTCCTCAAAATGTTTTTTTTTT--AATTTTAATTTCAAGGA
1 AAGGAAAATTGATACTTCCAACTTTTCCTCAAAATGTTTTTTTTTTGAAATTTTAATTTCAAGAA
* *
1323023 AAATTGATACTTTCAAACTTCAACTTTTCCCAAAATACTTTTTGAGATTTTTTATTTTT
66 AAATTGATACTTTC-AAC-T----TTTTCTCAAAATACTTTTTGA-AATTTTTATTTTT
* * *
1323082 AAAGAAAATTGATACTTTCAACTTTTCCTTAAAA
1 AAGGAAAATTGATACTTCCAACTTTTCCTCAAAA
1323116 ATATTTTTCT
Statistics
Matches: 245, Mismatches: 17, Indels: 24
0.86 0.06 0.08
Matches are distributed among these distances:
116 30 0.12
117 9 0.04
118 28 0.11
119 17 0.07
120 97 0.40
121 3 0.01
122 55 0.22
123 6 0.02
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.46
Consensus pattern (117 bp):
AAGGAAAATTGATACTTCCAACTTTTCCTCAAAATGTTTTTTTTTTGAAATTTTAATTTCAAGAA
AAATTGATACTTTCAACTTTTTCTCAAAATACTTTTTGAAATTTTTATTTTT
Found at i:1323257 original size:16 final size:15
Alignment explanation
Indices: 1323238--1323274 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
1323228 AAAAAATACC
1323238 AAAAAATATATACCAA
1 AAAAAATATATA-CAA
*
1323254 AAAATATATATACAA
1 AAAAAATATATACAA
1323269 AAAAAA
1 AAAAAA
1323275 AATCGAAACG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.73, C:0.08, G:0.00, T:0.19
Consensus pattern (15 bp):
AAAAAATATATACAA
Found at i:1323271 original size:14 final size:14
Alignment explanation
Indices: 1323233--1323263 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1323223 AAATAAAAAA
1323233 ATACCAAAAAATAT
1 ATACCAAAAAATAT
1323247 ATACCAAAAAATAT
1 ATACCAAAAAATAT
1323261 ATA
1 ATA
1323264 TACAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.65, C:0.13, G:0.00, T:0.23
Consensus pattern (14 bp):
ATACCAAAAAATAT
Found at i:1323544 original size:16 final size:16
Alignment explanation
Indices: 1323520--1323552 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1323510 TTGCTTCAGA
1323520 TCTCCCTTCTTCTTTC
1 TCTCCCTTCTTCTTTC
*
1323536 TCTCTCTTCTTCTTTC
1 TCTCCCTTCTTCTTTC
1323552 T
1 T
1323553 TTTCTCTCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (16 bp):
TCTCCCTTCTTCTTTC
Found at i:1324125 original size:29 final size:29
Alignment explanation
Indices: 1324092--1324168 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 29
1324082 CCTATTATCT
* *
1324092 AAAAATAAAATAAATAATAATAAT-AAATC
1 AAAAATAAAA-AAATAATAAAAATAAAATA
* *
1324121 AAAAATAAAAACCAGAATAAAAATAAAATA
1 AAAAATAAAAA-AATAATAAAAATAAAATA
1324151 AAAAATAAAAAAAATAAT
1 AAAAAT-AAAAAAATAAT
1324169 TGGGCCTATC
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
28 1 0.03
29 19 0.49
30 14 0.36
31 5 0.13
ACGTcount: A:0.77, C:0.04, G:0.01, T:0.18
Consensus pattern (29 bp):
AAAAATAAAAAAATAATAAAAATAAAATA
Found at i:1324130 original size:6 final size:6
Alignment explanation
Indices: 1324091--1324161 Score: 51
Period size: 6 Copynumber: 12.0 Consensus size: 6
1324081 TCCTATTATC
* ** *
1324091 TAAAAA T-AAAA T--AAA TAATAA TAATAAA TCAAAAA TAAAAA CCAGAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAA-AAA T-AAAAA TAAAAA TAAAAA
1324138 TAAAAA T-AAAA TAAAAAA TAAAAA
1 TAAAAA TAAAAA T-AAAAA TAAAAA
1324162 AAATAATTGG
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
4 4 0.08
5 10 0.20
6 23 0.45
7 12 0.24
8 2 0.04
ACGTcount: A:0.76, C:0.04, G:0.01, T:0.18
Consensus pattern (6 bp):
TAAAAA
Found at i:1324364 original size:22 final size:22
Alignment explanation
Indices: 1324336--1324450 Score: 115
Period size: 22 Copynumber: 5.2 Consensus size: 22
1324326 ACCATTAATT
1324336 ATTTACTATTAAATTATCATTA
1 ATTTACTATTAAATTATCATTA
* *
1324358 ATTTACTATTAAGTTATCATCA
1 ATTTACTATTAAATTATCATTA
* * * *
1324380 ATTTATTACTAAATTATTAATA
1 ATTTACTATTAAATTATCATTA
* *
1324402 ATTAACTATTAAGTTATCACTT-
1 ATTTACTATTAAATTATCA-TTA
** *
1324424 ATTTTTTATTAAATTATCCTTA
1 ATTTACTATTAAATTATCATTA
1324446 ATTTA
1 ATTTA
1324451 GTACTATGCT
Statistics
Matches: 71, Mismatches: 20, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
21 2 0.03
22 68 0.96
23 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (22 bp):
ATTTACTATTAAATTATCATTA
Found at i:1324384 original size:44 final size:44
Alignment explanation
Indices: 1324336--1324450 Score: 142
Period size: 44 Copynumber: 2.6 Consensus size: 44
1324326 ACCATTAATT
*
1324336 ATTTACTATTAAATTATCATTAATTTACTATTAAGTTATCA-TCA
1 ATTTATTATTAAATTATCATTAATTTACTATTAAGTTATCACT-A
* * * * *
1324380 ATTTATTACTAAATTATTAATAATTAACTATTAAGTTATCACTT
1 ATTTATTATTAAATTATCATTAATTTACTATTAAGTTATCACTA
* *
1324424 ATTTTTTATTAAATTATCCTTAATTTA
1 ATTTATTATTAAATTATCATTAATTTA
1324451 GTACTATGCT
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
44 57 0.98
45 1 0.02
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (44 bp):
ATTTATTATTAAATTATCATTAATTTACTATTAAGTTATCACTA
Found at i:1324419 original size:66 final size:66
Alignment explanation
Indices: 1324329--1324456 Score: 159
Period size: 66 Copynumber: 1.9 Consensus size: 66
1324319 ATTTACTACC
* * * *
1324329 ATTAATTATTTACTATTAAATTATCA-TTAATTTACTATTAAGTTATCATCAATTTATTACTAAA
1 ATTAATAATTAACTATTAAATTATCACTT-ATTTACTATTAAATTATCATCAATTTAGTACTAAA
1324393 TT
65 TT
* ** * *
1324395 ATTAATAATTAACTATTAAGTTATCACTTATTTTTTATTAAATTATCCTTAATTTAGTACTA
1 ATTAATAATTAACTATTAAATTATCACTTATTTACTATTAAATTATCATCAATTTAGTACTA
1324457 TGCTTTAATG
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
66 50 0.96
67 2 0.04
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.50
Consensus pattern (66 bp):
ATTAATAATTAACTATTAAATTATCACTTATTTACTATTAAATTATCATCAATTTAGTACTAAAT
T
Found at i:1324578 original size:22 final size:21
Alignment explanation
Indices: 1324546--1324616 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 21
1324536 CAACTTTGAG
1324546 TACTAAATTATCAATTATTTAC
1 TACTAAATTAT-AATTATTTAC
*
1324568 TACTAATTTATAATTTATTTAC
1 TACTAAATTATAA-TTATTTAC
* * *
1324590 TACTAAGTTATTTATTATTTAT
1 TACTAAATTA-TAATTATTTAC
1324612 TACTA
1 TACTA
1324617 TTAATTAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
21 2 0.05
22 39 0.91
23 2 0.05
ACGTcount: A:0.37, C:0.10, G:0.01, T:0.52
Consensus pattern (21 bp):
TACTAAATTATAATTATTTAC
Found at i:1327041 original size:32 final size:33
Alignment explanation
Indices: 1326977--1327049 Score: 94
Period size: 32 Copynumber: 2.2 Consensus size: 33
1326967 TTAAAAAAAT
* * **
1326977 TAATTTTCTTTTATTTAAAAAAATTATTATACA
1 TAATTTTCTATTATATAAAAAAATTAAAATACA
*
1327010 TAATTTT-TATTATATAAAAATATTAAAATACA
1 TAATTTTCTATTATATAAAAAAATTAAAATACA
1327042 TAATTTTC
1 TAATTTTC
1327050 AAAAATAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
32 27 0.79
33 7 0.21
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.49
Consensus pattern (33 bp):
TAATTTTCTATTATATAAAAAAATTAAAATACA
Found at i:1329135 original size:69 final size:69
Alignment explanation
Indices: 1329024--1329152 Score: 206
Period size: 69 Copynumber: 1.9 Consensus size: 69
1329014 TTCTAAGTCT
* * *
1329024 TGTCCATCCTTTTCTACTAAAACTGCTTTAGCTATACCAATAAGACTCCGTTTGCTTTTGCAATG
1 TGTCCATCCTTTCCTACTAAAACTGCTTTAGCCATACCAATAAGACTCCATTTGCTTTTGCAATG
1329089 ATTA
66 ATTA
*
1329093 TGTCCATCCTTTCCCT-TTAAAACTGCTTTAGCCATACCAATAAGACTCCATTTGCTTTTG
1 TGTCCATCCTTT-CCTACTAAAACTGCTTTAGCCATACCAATAAGACTCCATTTGCTTTTG
1329153 GAAATTACGT
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
69 53 0.96
70 2 0.04
ACGTcount: A:0.25, C:0.26, G:0.11, T:0.39
Consensus pattern (69 bp):
TGTCCATCCTTTCCTACTAAAACTGCTTTAGCCATACCAATAAGACTCCATTTGCTTTTGCAATG
ATTA
Found at i:1330169 original size:51 final size:51
Alignment explanation
Indices: 1330106--1330208 Score: 163
Period size: 51 Copynumber: 2.0 Consensus size: 51
1330096 ACCAACTTTT
* *
1330106 ATTCATATTTCAT-GATGATTTATTGAATGGTCAATAAAACTGTGTAAAATC
1 ATTCATACTTCATAG-TGATATATTGAATGGTCAATAAAACTGTGTAAAATC
*
1330157 ATTCATACTTCATAGTGATATATTGAATGGTCAATAAAGCTGTGTAAAATC
1 ATTCATACTTCATAGTGATATATTGAATGGTCAATAAAACTGTGTAAAATC
1330208 A
1 A
1330209 ACTAGACAAC
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
51 47 0.98
52 1 0.02
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.37
Consensus pattern (51 bp):
ATTCATACTTCATAGTGATATATTGAATGGTCAATAAAACTGTGTAAAATC
Found at i:1336747 original size:21 final size:20
Alignment explanation
Indices: 1336674--1336747 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 20
1336664 TTTTTGGTAA
*
1336674 AATTTTGATAACACTTGATAC
1 AATTTTGGTAACA-TTGATAC
* *
1336695 AATTTTGGTAACATATGACAT
1 AATTTTGGTAACAT-TGATAC
*
1336716 AATTTTAGTAACCATTGATAC
1 AATTTTGGTAA-CATTGATAC
1336737 AATTTTGGTAA
1 AATTTTGGTAA
1336748 TTTTTGATAA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.02
21 40 0.91
22 3 0.07
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (20 bp):
AATTTTGGTAACATTGATAC
Found at i:1336754 original size:21 final size:21
Alignment explanation
Indices: 1336674--1336756 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
1336664 TTTTTGGTAA
* *
1336674 AATTTTGATAACACTTGATAC
1 AATTTTGGTAACATTTGATAC
* * *
1336695 AATTTTGGTAACATATGACAT
1 AATTTTGGTAACATTTGATAC
*
1336716 AATTTTAGTAACCA-TTGATAC
1 AATTTTGGTAA-CATTTGATAC
**
1336737 AATTTTGGTAATTTTTGATA
1 AATTTTGGTAACATTTGATA
1336757 AACTTTTAAT
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
21 46 0.96
22 2 0.04
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.42
Consensus pattern (21 bp):
AATTTTGGTAACATTTGATAC
Found at i:1336764 original size:42 final size:42
Alignment explanation
Indices: 1336653--1336768 Score: 114
Period size: 42 Copynumber: 2.8 Consensus size: 42
1336643 ATATAATTTT
* *
1336653 AATTTTGATAATTTTTGGTAAAATTTT-GATAACACTTGATAC
1 AATTTTGGTAATTTTTGAT-AAATTTTAGATAACACTTGATAC
** * *
1336695 AATTTTGGTAACATATGACATAATTTTAG-TAAC-CATTGATAC
1 AATTTTGGTAATTTTTGATA-AATTTTAGATAACAC-TTGATAC
1336737 AATTTTGGTAATTTTTGATAAACTTTTA-ATAA
1 AATTTTGGTAATTTTTGATAAA-TTTTAGATAA
1336769 TCTCTTCTTG
Statistics
Matches: 59, Mismatches: 10, Indels: 10
0.75 0.13 0.13
Matches are distributed among these distances:
41 4 0.07
42 54 0.92
43 1 0.02
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.44
Consensus pattern (42 bp):
AATTTTGGTAATTTTTGATAAATTTTAGATAACACTTGATAC
Found at i:1337172 original size:22 final size:22
Alignment explanation
Indices: 1337147--1337331 Score: 115
Period size: 22 Copynumber: 8.4 Consensus size: 22
1337137 TGATACACTG
*
1337147 CTAAATTATCAATGATTTATTA
1 CTAAATTATCAATGATTTACTA
* * * * *
1337169 CTAAAATAGCATTGGTTTAGTA
1 CTAAATTATCAATGATTTACTA
* *
1337191 CTAATTTATGAATGATTTACTA
1 CTAAATTATCAATGATTTACTA
* * * *
1337213 CTAAGTTATGATTTATTTACTA
1 CTAAATTATCAATGATTTACTA
* **
1337235 CTAAATTGTTGATGATTTACTA
1 CTAAATTATCAATGATTTACTA
* * *
1337257 TTAAGTTA-CTAATGATTTATTA
1 CTAAATTATC-AATGATTTACTA
1337279 -TAAAATTAT-AATTGATTTACTA
1 CT-AAATTATCAA-TGATTTACTA
* * * *
1337301 TTAATTTATCGATAATTTACTA
1 CTAAATTATCAATGATTTACTA
*
1337323 CAAAATTAT
1 CTAAATTAT
1337332 TAATTATTAA
Statistics
Matches: 122, Mismatches: 35, Indels: 12
0.72 0.21 0.07
Matches are distributed among these distances:
21 3 0.02
22 117 0.96
23 2 0.02
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.45
Consensus pattern (22 bp):
CTAAATTATCAATGATTTACTA
Found at i:1337285 original size:44 final size:43
Alignment explanation
Indices: 1337080--1337480 Score: 125
Period size: 44 Copynumber: 9.0 Consensus size: 43
1337070 ATAATTGACG
* * * * * ** *
1337080 ATTAAGTTATTATTGATTTATTATTATATTATCAGCGATTTACA
1 ATTAAGTTATGAATGATTTACTACTAAATTAT-AATGATTTACT
* * ** * *
1337124 ATTAAGCTATTAATGATACACTGCTAAATTATCAATGATTTATT
1 ATTAAGTTATGAATGATTTACTACTAAATTAT-AATGATTTACT
* ** * * * *
1337168 ACTAAAATA-GCATTGGTTTAGTACTAATTTATGAATGATTTACT
1 ATTAAGTTATG-AATGATTTACTACTAAATTAT-AATGATTTACT
* * * * *
1337212 ACTAAGTTATGATTTATTTACTACTAAATTGTTGATGATTTACT
1 ATTAAGTTATGAATGATTTACTACTAAATT-ATAATGATTTACT
*
1337256 ATTAAGTTACT-AATGATTTATTA-TAAAATTATAATTGATTTACT
1 ATTAAGTTA-TGAATGATTTACTACT-AAATTATAA-TGATTTACT
* * *
1337300 ATTAATTTATCG-ATAATTTACTACAAAATTATTAATTATTAACTAATTTACT
1 ATTAAGTTAT-GAATGATTTACTAC-----TA--AATTA-TAA-TGATTTACT
* ** * *
1337352 ACTAAACTATCACTGATTTA-TAACTAAATTATTAATGATTTACT
1 ATTAAGTTATGAATGATTTACT-ACTAAATTA-TAATGATTTACT
* * * * *
1337396 ACTAAGTTATCAATAATTTAC-ATCTAAGTTATCAA-AATTTACT
1 ATTAAGTTATGAATGATTTACTA-CTAAATTAT-AATGATTTACT
* * * * *
1337439 ATTATGTTAT-TATGCATTTACTATTATATTATCATTGATTTA
1 ATTAAGTTATGAATG-ATTTACTACTAAATTAT-AATGATTTA
1337481 ATACATAGTT
Statistics
Matches: 266, Mismatches: 66, Indels: 50
0.70 0.17 0.13
Matches are distributed among these distances:
42 2 0.01
43 35 0.13
44 181 0.68
45 12 0.05
47 2 0.01
49 1 0.00
50 1 0.00
51 6 0.02
52 26 0.10
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.45
Consensus pattern (43 bp):
ATTAAGTTATGAATGATTTACTACTAAATTATAATGATTTACT
Found at i:1337436 original size:21 final size:22
Alignment explanation
Indices: 1337343--1337448 Score: 92
Period size: 22 Copynumber: 4.9 Consensus size: 22
1337333 AATTATTAAC
** *
1337343 TAATTTACTACTAAACTATCAC
1 TAATTTACTACTAAGTTATCAA
* * *
1337365 TGATTTA-TAACTAAATTATTAA
1 TAATTTACT-ACTAAGTTATCAA
*
1337387 TGATTTACTACTAAGTTATCAA
1 TAATTTACTACTAAGTTATCAA
1337409 TAATTTAC-ATCTAAGTTATCAA
1 TAATTTACTA-CTAAGTTATCAA
* *
1337431 -AATTTACTATTATGTTAT
1 TAATTTACTACTAAGTTAT
1337449 TATGCATTTA
Statistics
Matches: 71, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
21 16 0.23
22 54 0.76
23 1 0.01
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.43
Consensus pattern (22 bp):
TAATTTACTACTAAGTTATCAA
Found at i:1337480 original size:22 final size:22
Alignment explanation
Indices: 1337432--1337473 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1337422 AGTTATCAAA
* *
1337432 ATTTACTATTATGTTATTATGC
1 ATTTACTATTATATTATCATGC
1337454 ATTTACTATTATATTATCAT
1 ATTTACTATTATATTATCAT
1337474 TGATTTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.31, C:0.10, G:0.05, T:0.55
Consensus pattern (22 bp):
ATTTACTATTATATTATCATGC
Found at i:1347355 original size:24 final size:24
Alignment explanation
Indices: 1347328--1347376 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
1347318 TCAACTAGAG
*
1347328 TATGCAGACCTAAAACTTACTTAT
1 TATGCAGACCTAAAACCTACTTAT
1347352 TATGCAGACCTAAAACCTACTTAT
1 TATGCAGACCTAAAACCTACTTAT
1347376 T
1 T
1347377 TAATCAACTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.22, G:0.08, T:0.33
Consensus pattern (24 bp):
TATGCAGACCTAAAACCTACTTAT
Found at i:1351271 original size:19 final size:20
Alignment explanation
Indices: 1351241--1351291 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
1351231 ACGAATGAAA
*
1351241 TTATATATTTTTATTAGTTT
1 TTATACATTTTTATTAGTTT
1351261 TTATA-ATTTTTATTAGTTT
1 TTATACATTTTTATTAGTTT
1351280 TTATACATTTTT
1 TTATACATTTTT
1351292 TAATTTTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 19 0.63
20 11 0.37
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (20 bp):
TTATACATTTTTATTAGTTT
Found at i:1351290 original size:10 final size:9
Alignment explanation
Indices: 1351241--1351304 Score: 58
Period size: 10 Copynumber: 6.7 Consensus size: 9
1351231 ACGAATGAAA
1351241 TTATATATTT
1 TTATA-ATTT
*
1351251 TTATTAGTTT
1 TTA-TAATTT
1351261 TTATAATTT
1 TTATAATTT
*
1351270 TTATTAGTTT
1 TTA-TAATTT
1351280 TTATACATTT
1 TTATA-ATTT
1351290 TT-TAATTTT
1 TTATAA-TTT
1351299 TTATAA
1 TTATAA
1351305 AATAAAAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
8 1 0.02
9 17 0.38
10 25 0.56
11 2 0.04
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.67
Consensus pattern (9 bp):
TTATAATTT
Found at i:1351299 original size:19 final size:19
Alignment explanation
Indices: 1351241--1351304 Score: 76
Period size: 19 Copynumber: 3.3 Consensus size: 19
1351231 ACGAATGAAA
*
1351241 TTATATATTTTTATTAGTTT
1 TTATA-ATTTTTATAAGTTT
*
1351261 TTATAATTTTTATTAGTTT
1 TTATAATTTTTATAAGTTT
*
1351280 TTATACATTTTT-TAATTTT
1 TTATA-ATTTTTATAAGTTT
1351299 TTATAA
1 TTATAA
1351305 AATAAAAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
18 1 0.02
19 29 0.71
20 11 0.27
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.67
Consensus pattern (19 bp):
TTATAATTTTTATAAGTTT
Found at i:1356182 original size:7 final size:7
Alignment explanation
Indices: 1356173--1356227 Score: 55
Period size: 7 Copynumber: 8.1 Consensus size: 7
1356163 CTCAATCATC
*
1356173 TTATATC
1 TTATATA
1356180 TTATAT-
1 TTATATA
1356186 TATATATA
1 T-TATATA
1356194 TATATATA
1 T-TATATA
1356202 TTATATA
1 TTATATA
1356209 TT-TATA
1 TTATATA
1356215 -TATATA
1 TTATATA
1356221 -TATATA
1 TTATATA
1356227 T
1 T
1356228 AAGCCAAAGC
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
5 1 0.02
6 15 0.34
7 19 0.43
8 9 0.20
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (7 bp):
TTATATA
Found at i:1356193 original size:2 final size:2
Alignment explanation
Indices: 1356181--1356228 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
1356171 TCTTATATCT
*
1356181 TA TA T- TA TA TA TA TA TA TA TA T- TA TA TA TT TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1356221 TA TA TA TA
1 TA TA TA TA
1356229 AGCCAAAGCT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:1356219 original size:25 final size:24
Alignment explanation
Indices: 1356181--1356227 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
1356171 TCTTATATCT
1356181 TATATTATATATATATATATATTA
1 TATATTATATATATATATATATTA
1356205 TATATTTATATATATATATATAT
1 TATA-TTATATATATATATATAT
1356228 AAGCCAAAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TATATTATATATATATATATATTA
Found at i:1357668 original size:18 final size:18
Alignment explanation
Indices: 1357645--1357680 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1357635 TTTGAATGAT
1357645 TTTAAAATTATATTTTCA
1 TTTAAAATTATATTTTCA
*
1357663 TTTAAAATTTTATTTTCA
1 TTTAAAATTATATTTTCA
1357681 ACAAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTAAAATTATATTTTCA
Found at i:1365500 original size:13 final size:13
Alignment explanation
Indices: 1365463--1365503 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 13
1365453 AAATTTATTT
1365463 TAATATATTAAAAA
1 TAATATA-TAAAAA
*
1365477 TCATAT-T-AAAA
1 TAATATATAAAAA
1365488 TAATATATAAAAA
1 TAATATATAAAAA
1365501 TAA
1 TAA
1365504 AAAAATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
11 9 0.39
12 2 0.09
13 7 0.30
14 5 0.22
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (13 bp):
TAATATATAAAAA
Found at i:1367600 original size:19 final size:19
Alignment explanation
Indices: 1367576--1367615 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1367566 AATGGAGTGA
1367576 TAAATACATTGCTTATATG
1 TAAATACATTGCTTATATG
1367595 TAAATACATTGCTTATATG
1 TAAATACATTGCTTATATG
1367614 TA
1 TA
1367616 TGTCTGGAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (19 bp):
TAAATACATTGCTTATATG
Found at i:1390282 original size:2 final size:2
Alignment explanation
Indices: 1390275--1390300 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1390265 TAGTAAACTA
1390275 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
1390301 GTAGAACAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1401466 original size:6 final size:6
Alignment explanation
Indices: 1401452--1401482 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
1401442 TCACTTTTTT
1401452 TTTTCAA TTTTAA TTTTAA TTTTAA TTTTAA
1 TTTT-AA TTTTAA TTTTAA TTTTAA TTTTAA
1401483 GTTCTTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.83
7 4 0.17
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (6 bp):
TTTTAA
Found at i:1423036 original size:2 final size:2
Alignment explanation
Indices: 1423029--1423064 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1423019 GCTGTTTAAT
*
1423029 TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1423065 AAGTCTCAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1432434 original size:23 final size:23
Alignment explanation
Indices: 1432389--1432435 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
1432379 TATATCAAAT
* *
1432389 AAAATAAAATATGTATTTTTTAA
1 AAAATAAAATATATATTTATTAA
1432412 AAAATAAAA-ATATATATTATTAA
1 AAAATAAAATATATAT-TTATTAA
1432435 A
1 A
1432436 TGATAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (23 bp):
AAAATAAAATATATATTTATTAA
Found at i:1432528 original size:11 final size:11
Alignment explanation
Indices: 1432512--1432554 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
1432502 GCAAGATATG
1432512 AAAAATATTAA
1 AAAAATATTAA
*
1432523 AAAAATATGTGA
1 AAAAATAT-TAA
*
1432535 AAAAA-ACTAA
1 AAAAATATTAA
1432545 AAAAATATTA
1 AAAAATATTA
1432555 TTTTTCATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
10 7 0.27
11 12 0.46
12 7 0.27
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (11 bp):
AAAAATATTAA
Found at i:1432535 original size:22 final size:22
Alignment explanation
Indices: 1432510--1432552 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1432500 ATGCAAGATA
* *
1432510 TGAAAAATATTAAAAAAATATG
1 TGAAAAAAACTAAAAAAATATG
1432532 TGAAAAAAACTAAAAAAATAT
1 TGAAAAAAACTAAAAAAATAT
1432553 TATTTTTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.23
Consensus pattern (22 bp):
TGAAAAAAACTAAAAAAATATG
Found at i:1434193 original size:22 final size:20
Alignment explanation
Indices: 1434168--1434209 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1434158 ATAAAAAAAT
1434168 TTAATTGAATTATATATTTTTA
1 TTAATT-AA-TATATATTTTTA
*
1434190 TTAATTTATATATATTTTTA
1 TTAATTAATATATATTTTTA
1434210 AAAATTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 12 0.63
21 1 0.05
22 6 0.32
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
TTAATTAATATATATTTTTA
Found at i:1434215 original size:20 final size:19
Alignment explanation
Indices: 1434177--1434220 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
1434167 TTTAATTGAA
**
1434177 TTATATATTTTTATTAATT
1 TTATATATTTTTAAAAATT
1434196 TATATATATTTTTAAAAATT
1 T-TATATATTTTTAAAAATT
1434216 TTATA
1 TTATA
1434221 AAATAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTATATATTTTTAAAAATT
Found at i:1436939 original size:20 final size:20
Alignment explanation
Indices: 1436914--1436954 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1436904 AAAAATATAA
*
1436914 ATAAATTTATAAATTT-TCTT
1 ATAAATTGAT-AATTTATCTT
1436934 ATAAATTGATAATTTATCTT
1 ATAAATTGATAATTTATCTT
1436954 A
1 A
1436955 ATTTTAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.51
Consensus pattern (20 bp):
ATAAATTGATAATTTATCTT
Found at i:1438280 original size:24 final size:20
Alignment explanation
Indices: 1438247--1438301 Score: 58
Period size: 24 Copynumber: 2.6 Consensus size: 20
1438237 AAAAATGGAG
*
1438247 CTTTCCTCCTTTCCTCCTTTCTT
1 CTTTCTTCCTTT-CT-CTTT-TT
1438270 CCTTTCTTCCTTTCTCTTTTT
1 -CTTTCTTCCTTTCTCTTTTT
1438291 CTTT-TTCCTTT
1 CTTTCTTCCTTT
1438302 TTAAAGAGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 7 0.23
20 4 0.13
21 2 0.07
22 4 0.13
23 2 0.07
24 11 0.37
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTCTTCCTTTCTCTTTTT
Found at i:1438284 original size:8 final size:8
Alignment explanation
Indices: 1438247--1438284 Score: 58
Period size: 8 Copynumber: 4.8 Consensus size: 8
1438237 AAAAATGGAG
*
1438247 CTTTCCTC
1 CTTTCTTC
*
1438255 CTTTCCTC
1 CTTTCTTC
1438263 CTTTCTTC
1 CTTTCTTC
1438271 CTTTCTTC
1 CTTTCTTC
1438279 CTTTCT
1 CTTTCT
1438285 CTTTTTCTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (8 bp):
CTTTCTTC
Found at i:1441767 original size:15 final size:16
Alignment explanation
Indices: 1441747--1441781 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1441737 AATGAGAAAA
1441747 AAAAAAAGAAAA-AGG
1 AAAAAAAGAAAAGAGG
*
1441762 AAAAAAATAAAAGAGG
1 AAAAAAAGAAAAGAGG
1441778 AAAA
1 AAAA
1441782 GGAAAGAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (16 bp):
AAAAAAAGAAAAGAGG
Found at i:1441773 original size:22 final size:21
Alignment explanation
Indices: 1441743--1441786 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
1441733 CCCAAATGAG
1441743 AAAAAAAAAAAGAAAAAGGAA
1 AAAAAAAAAAAGAAAAAGGAA
* *
1441764 AAAAATAAAAGAGGAAAAGGAA
1 AAAAA-AAAAAAGAAAAAGGAA
1441786 A
1 A
1441787 GAGTTGAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (21 bp):
AAAAAAAAAAAGAAAAAGGAA
Found at i:1455116 original size:2 final size:2
Alignment explanation
Indices: 1455096--1455142 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
1455086 TTGTATTTGC
* * *
1455096 AT AT AT AC AT AC AT GT 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 AT AT AT
1455138 AT AT A
1 AT AT A
1455143 AACATAGGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1465528 original size:17 final size:17
Alignment explanation
Indices: 1465496--1465533 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1465486 AATTTTATCG
*
1465496 ATTTTATTTGATTTAATA
1 ATTTTATTTAATTTAA-A
1465514 ATTTT-TTTAATTTAAA
1 ATTTTATTTAATTTAAA
1465530 ATTT
1 ATTT
1465534 AAAATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 9 0.47
18 5 0.26
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (17 bp):
ATTTTATTTAATTTAAA
Found at i:1477208 original size:18 final size:18
Alignment explanation
Indices: 1477172--1477210 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1477162 ATTTGCTATT
*
1477172 AATGTTTATACATGATAA
1 AATGTTTAAACATGATAA
* *
1477190 AATGTTTAAATATGTTAA
1 AATGTTTAAACATGATAA
1477208 AAT
1 AAT
1477211 AAATTTTGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.03, G:0.10, T:0.41
Consensus pattern (18 bp):
AATGTTTAAACATGATAA
Found at i:1477333 original size:23 final size:23
Alignment explanation
Indices: 1477275--1477334 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
1477265 TTGAACAATA
1477275 AATAAAAAA-AAATAAAAATGCT
1 AATAAAAAATAAATAAAAATGCT
* * *
1477297 TA-AAAAAATTAATAATAAT-CT
1 AATAAAAAATAAATAAAAATGCT
1477318 AATAAAAAATAGAATAA
1 AATAAAAAATA-AATAA
1477335 GGTAATATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
21 9 0.30
22 16 0.53
23 5 0.17
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.23
Consensus pattern (23 bp):
AATAAAAAATAAATAAAAATGCT
Found at i:1477628 original size:10 final size:10
Alignment explanation
Indices: 1477613--1477672 Score: 69
Period size: 10 Copynumber: 6.6 Consensus size: 10
1477603 TCATTTTTTT
1477613 TAATAATAAA
1 TAATAATAAA
1477623 TAATAATAAA
1 TAATAATAAA
1477633 TAA-AATAAA
1 TAATAATAAA
*
1477642 -AATAA-AGA
1 TAATAATAAA
1477650 T-AT--TAAA
1 TAATAATAAA
1477657 TAATAATAAA
1 TAATAATAAA
1477667 TAATAA
1 TAATAA
1477673 AATCATTAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
7 3 0.07
8 8 0.19
9 8 0.19
10 23 0.55
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (10 bp):
TAATAATAAA
Found at i:1477641 original size:19 final size:19
Alignment explanation
Indices: 1477617--1477669 Score: 60
Period size: 17 Copynumber: 3.0 Consensus size: 19
1477607 TTTTTTTAAT
1477617 AATAAATAATAATAAATAA
1 AATAAATAATAATAAATAA
*
1477636 AATAAA-AATAA-AGAT--
1 AATAAATAATAATAAATAA
*
1477651 ATTAAATAATAATAAATAA
1 AATAAATAATAATAAATAA
1477670 TAAAATCATT
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
15 5 0.19
16 5 0.19
17 6 0.22
18 5 0.19
19 6 0.22
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (19 bp):
AATAAATAATAATAAATAA
Found at i:1477680 original size:26 final size:24
Alignment explanation
Indices: 1477629--1477682 Score: 74
Period size: 26 Copynumber: 2.2 Consensus size: 24
1477619 TAAATAATAA
1477629 TAAATAAAATAAAAATAAAGATAT
1 TAAATAAAATAAAAATAAAGATAT
1477653 TAAATAATAATAAATAATAAA-ATCAT
1 TAAATAA-AATAAA-AATAAAGAT-AT
1477679 TAAA
1 TAAA
1477683 CCCTAAAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
24 7 0.26
25 8 0.30
26 12 0.44
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (24 bp):
TAAATAAAATAAAAATAAAGATAT
Found at i:1477753 original size:22 final size:24
Alignment explanation
Indices: 1477728--1477771 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1477718 AAACACGAAA
1477728 CCTC-AAACC-TTAAAATCCAATT
1 CCTCAAAACCTTTAAAATCCAATT
1477750 CCTCAAAACCTTTAAAATCCAA
1 CCTCAAAACCTTTAAAATCCAA
1477772 AATCCAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 4 0.20
23 5 0.25
24 11 0.55
ACGTcount: A:0.43, C:0.32, G:0.00, T:0.25
Consensus pattern (24 bp):
CCTCAAAACCTTTAAAATCCAATT
Found at i:1477781 original size:24 final size:23
Alignment explanation
Indices: 1477732--1477781 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
1477722 ACGAAACCTC
* *
1477732 AAACCTTAAAATCCAATTCCTCA
1 AAACCTTAAAATCCAAATCCTAA
1477755 AAACCTTTAAAATCCAAAATCC-AA
1 AAACC-TTAAAATCC-AAATCCTAA
1477779 AAA
1 AAA
1477782 TCTCAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 5 0.22
24 13 0.57
25 5 0.22
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.22
Consensus pattern (23 bp):
AAACCTTAAAATCCAAATCCTAA
Found at i:1479841 original size:30 final size:29
Alignment explanation
Indices: 1479805--1479863 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
1479795 AAATAAAGTT
*
1479805 AGGAAAAACAA-AAAAAGATGAAAAAAAAAA
1 AGGAAAAAAAAGAAAAAG-T-AAAAAAAAAA
1479835 AGGAAAAAAAAGTAAAAAGTAAAAAAAAA
1 AGGAAAAAAAAG-AAAAAGTAAAAAAAAA
1479864 GGGATTTGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 19 0.73
31 1 0.04
32 6 0.23
ACGTcount: A:0.80, C:0.02, G:0.14, T:0.05
Consensus pattern (29 bp):
AGGAAAAAAAAGAAAAAGTAAAAAAAAAA
Found at i:1479845 original size:17 final size:17
Alignment explanation
Indices: 1479825--1479863 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1479815 AAAAAAGATG
1479825 AAAAAAAAAAAGGAAAA
1 AAAAAAAAAAAGGAAAA
** *
1479842 AAAAGTAAAAAGTAAAA
1 AAAAAAAAAAAGGAAAA
1479859 AAAAA
1 AAAAA
1479864 GGGATTTGGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.85, C:0.00, G:0.10, T:0.05
Consensus pattern (17 bp):
AAAAAAAAAAAGGAAAA
Found at i:1481263 original size:4 final size:4
Alignment explanation
Indices: 1481247--1481332 Score: 84
Period size: 4 Copynumber: 21.5 Consensus size: 4
1481237 GTGAGTTATG
* ** *
1481247 CATT CACT CATT CATT CATT CATT CATT CATT CATT CATT CATT TGTG
1 CATT CATT CATT CATT CATT CATT CATT CATT CATT CATT CATT CATT
* * * *
1481295 CATT CATT TATT CTTT CATC CATT TATGT -ATT CATT CA
1 CATT CATT CATT CATT CATT CATT CAT-T CATT CATT CA
1481333 ATATAATACA
Statistics
Matches: 65, Mismatches: 15, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
3 1 0.02
4 63 0.97
5 1 0.02
ACGTcount: A:0.23, C:0.23, G:0.03, T:0.50
Consensus pattern (4 bp):
CATT
Found at i:1485311 original size:33 final size:32
Alignment explanation
Indices: 1485167--1485407 Score: 152
Period size: 33 Copynumber: 7.4 Consensus size: 32
1485157 ATTTGGCACC
*
1485167 AATGAAATTTAAGCCCAGTTTATA-TGG-CACT
1 AATGAAATTTAAGCCCAGTTTA-ACTGGCCCCT
* ** *
1485198 AATGAAGTTTTAAGCCCAGTTTAGTTGGCCCTT
1 AATGAA-ATTTAAGCCCAGTTTAACTGGCCCCT
* * * * *
1485231 AATAAAATTTAAGCTCAGTTTATCTAG-CCAT
1 AATGAAATTTAAGCCCAGTTTAACTGGCCCCT
*
1485262 CAATGAAGTTTCAAGCCCAGTTTAACTGGCCCCT
1 -AATGAAATTT-AAGCCCAGTTTAACTGGCCCCT
* * * **
1485296 AAGGAAATCTTAAGCCTAGTTTACCTGGCCATT
1 AATGAAAT-TTAAGCCCAGTTTAACTGGCCCCT
* * * * *
1485329 AA-CAAAGTTTTAAGCCTAGTTTATCTAGCACC-
1 AATGAAA--TTTAAGCCCAGTTTAACTGGCCCCT
* *
1485361 AATGAAGTTTTAAGCCCAGTTTAGCTGG-CCCT
1 AATGAA-ATTTAAGCCCAGTTTAACTGGCCCCT
1485393 CAATGAAATTTAAGC
1 -AATGAAATTTAAGC
1485408 ATAGTTTATT
Statistics
Matches: 161, Mismatches: 36, Indels: 25
0.73 0.16 0.11
Matches are distributed among these distances:
31 11 0.07
32 71 0.44
33 73 0.45
34 6 0.04
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.32
Consensus pattern (32 bp):
AATGAAATTTAAGCCCAGTTTAACTGGCCCCT
Found at i:1485422 original size:32 final size:32
Alignment explanation
Indices: 1485149--1485423 Score: 193
Period size: 32 Copynumber: 8.5 Consensus size: 32
1485139 GGCACGTAAA
* * *
1485149 CCCAGATTATTTGGCAC-CAATGAAATTTAAG
1 CCCAGTTTATCTGGCCCTCAATGAAATTTAAG
* * *
1485180 CCCAGTTTATATGGCACT-AATGAAGTTTTAAG
1 CCCAGTTTATCTGGCCCTCAATGAA-ATTTAAG
* *
1485212 CCCAGTTTAGT-TGGCCCTTAATAAAATTTAAG
1 CCCAGTTTA-TCTGGCCCTCAATGAAATTTAAG
* * * *
1485244 CTCAGTTTATCTAGCCATCAATGAAGTTTCAAG
1 CCCAGTTTATCTGGCCCTCAATGAAATTT-AAG
* *
1485277 CCCAGTTTAACTGGCCC-CTAAGGAAATCTTAAG
1 CCCAGTTTATCTGGCCCTC-AATGAAAT-TTAAG
* * * * *
1485310 CCTAGTTTACCTGGCCATTAA-CAAAGTTTTAAG
1 CCCAGTTTATCTGGCCCTCAATGAAA--TTTAAG
* * * *
1485343 CCTAGTTTATCTAGCAC-CAATGAAGTTTTAAG
1 CCCAGTTTATCTGGCCCTCAATGAA-ATTTAAG
*
1485375 CCCAGTTTAGCTGGCCCTCAATGAAATTTAAG
1 CCCAGTTTATCTGGCCCTCAATGAAATTTAAG
** *
1485407 CATAGTTTATTTGGCCC
1 CCCAGTTTATCTGGCCC
1485424 CAAAAAAGTT
Statistics
Matches: 191, Mismatches: 39, Indels: 27
0.74 0.15 0.11
Matches are distributed among these distances:
31 22 0.12
32 92 0.48
33 74 0.39
34 3 0.02
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (32 bp):
CCCAGTTTATCTGGCCCTCAATGAAATTTAAG
Found at i:1486220 original size:37 final size:37
Alignment explanation
Indices: 1486170--1486577 Score: 136
Period size: 37 Copynumber: 10.9 Consensus size: 37
1486160 TGACCTACGA
*
1486170 TGTTGTCCCGGTCAATTCTTTACTTCTTGACTCGCAG
1 TGTTGTCCTGGTCAATTCTTTACTTCTTGACTCGCAG
* * * * *
1486207 TGTTATCCTGGTC-ATTTTCTTACTTTTTGACTTGCGG
1 TGTTGTCCTGGTCAATTCT-TTACTTCTTGACTCGCAG
* * * * * *
1486244 TGTTGTTCTAGTCGATTATTTACTTCTCGACTCGCAA
1 TGTTGTCCTGGTCAATTCTTTACTTCTTGACTCGCAG
* * * * *
1486281 TATTGT-CTCAGTCATTTTTTTTACTTCTCGACT-GACAG
1 TGTTGTCCT-GGTCA-ATTCTTTACTTCTTGACTCG-CAG
* *
1486319 TGTTGTCCTGG-CTATTTTCTTTACTTCTTAACTCGCAG
1 TGTTGTCCTGGTC-A-ATTCTTTACTTCTTGACTCGCAG
* * * * * *
1486357 TGTTATCCCGAT-TATTTTCTTACTT-TTCGACTCG-TG
1 TGTTGTCCTGGTCAATTCT-TTACTTCTT-GACTCGCAG
*** * * * * **
1486393 ATGTTGTCCCAATCATTTTTTTTACTT-TTCAACTTGTGG
1 -TGTTGTCCTGGTCA-ATTCTTTACTTCTT-GACTCGCAG
* ** * **
1486432 TGTTATCCTGGTCAATTCTTTACTTCTCAACTGGTGG
1 TGTTGTCCTGGTCAATTCTTTACTTCTTGACTCGCAG
* ***
1486469 TGTTGTCCCGGTTGTTTGCTTTACTTCTTGACTCGCAG
1 TGTTGTCCTGGTCAATT-CTTTACTTCTTGACTCGCAG
* * * * *
1486507 TGTTGTCCCGATCATTTTTTTACTT-TTCGACTCAC-G
1 TGTTGTCCTGGTCAATTCTTTACTTCTT-GACTCGCAG
* * * *
1486543 ATGTTGTCCCGATC-ATTCTTTATTTCTCGACTCGC
1 -TGTTGTCCTGGTCAATTCTTTACTTCTTGACTCGC
1486578 GATGTTATCC
Statistics
Matches: 283, Mismatches: 68, Indels: 41
0.72 0.17 0.10
Matches are distributed among these distances:
36 29 0.10
37 137 0.48
38 109 0.39
39 8 0.03
ACGTcount: A:0.14, C:0.23, G:0.16, T:0.46
Consensus pattern (37 bp):
TGTTGTCCTGGTCAATTCTTTACTTCTTGACTCGCAG
Found at i:1486358 original size:38 final size:38
Alignment explanation
Indices: 1486185--1486390 Score: 131
Period size: 38 Copynumber: 5.5 Consensus size: 38
1486175 TCCCGGTCAA
*
1486185 TTCTTTACTTCTTGACTCGCAGTGTTATCCTGG-TCATT
1 TTCTTTACTTCTTGACTCGCAGTGTTGTCCTGGCT-ATT
* * * * * *
1486223 TTC-TTACTTTTTGACTTGCGGTGTTGTTCTAGTCGA--
1 TTCTTTACTTCTTGACTCGCAGTGTTGTCCT-GGCTATT
* * * * * *
1486259 TTATTTACTTCTCGACTCGCAATATTGTCTCAGTC-ATT
1 TTCTTTACTTCTTGACTCGCAGTGTTGTC-CTGGCTATT
* *
1486297 TTTTTTACTTCTCGACT-GACAGTGTTGTCCTGGCTATT
1 TTCTTTACTTCTTGACTCG-CAGTGTTGTCCTGGCTATT
* * * **
1486335 TTCTTTACTTCTTAACTCGCAGTGTTATCCCGATTATT
1 TTCTTTACTTCTTGACTCGCAGTGTTGTCCTGGCTATT
1486373 TTC-TTACTT-TTCGACTCG
1 TTCTTTACTTCTT-GACTCG
1486391 TGATGTTGTC
Statistics
Matches: 129, Mismatches: 29, Indels: 21
0.72 0.16 0.12
Matches are distributed among these distances:
36 5 0.04
37 58 0.45
38 65 0.50
39 1 0.01
ACGTcount: A:0.15, C:0.22, G:0.15, T:0.48
Consensus pattern (38 bp):
TTCTTTACTTCTTGACTCGCAGTGTTGTCCTGGCTATT
Found at i:1486398 original size:75 final size:74
Alignment explanation
Indices: 1486185--1486613 Score: 226
Period size: 75 Copynumber: 5.7 Consensus size: 74
1486175 TCCCGGTCAA
* * * * * * *
1486185 TTCTTTACTTCTTGACTCGCAGTGTTATCCTGGTCATTTTCTTACTTTTTGACTTGCGGTGTTGT
1 TTCTTTACTTCTTAACTCGCAGTGTTATCCCGATCATTTTCTTACTTTTCGACTCGTGATGTTGT
* * ***
1486250 TC-TAGTCGA
66 CCGGA-TATT
* ** * * * * * * **
1486259 TTATTTACTTCTCGACTCGCAATATTGTCTC-AGTCATTTTTTTTACTTCTCGACT-GACAGTGT
1 TTCTTTACTTCTTAACTCGCAGTGTTATCCCGA-TCA-TTTTCTTACTTTTCGACTCGTGA-TGT
*
1486322 TGTCCTGGCTATT
63 TGTCC-GGATATT
*
1486335 TTCTTTACTTCTTAACTCGCAGTGTTATCCCGATTATTTTCTTACTTTTCGACTCGTGATGTTGT
1 TTCTTTACTTCTTAACTCGCAGTGTTATCCCGATCATTTTCTTACTTTTCGACTCGTGATGTTGT
**
1486400 CCCAATCATT
66 CCGGAT-ATT
* * ** * * * * * * *
1486410 TTTTTTACTT-TTCAACTTGTGGTGTTATCCTGGTCA-ATTCTTTACTTCTCAACTGGTGGTGTT
1 TTCTTTACTTCTT-AACTCGCAGTGTTATCCCGATCATTTTC-TTACTTTTCGACTCGTGATGTT
* *
1486473 GTCCCGGTTGTT
64 GT-CCGGATATT
* * * * **
1486485 TGCTTTACTTCTTGACTCGCAGTGTTGTCCCGATCATTTTTTTACTTTTCGACTCACGATGTTGT
1 TTCTTTACTTCTTAACTCGCAGTGTTATCCCGATCATTTTCTTACTTTTCGACTCGTGATGTTGT
*
1486550 CCCGATCA--
66 CCGGAT-ATT
* ** * *
1486558 TTCTTTATTTCTCGACTCGC-GATGTTATCCCTATCATTTTCTTTACTTTTTGACTC
1 TTCTTTACTTCTTAACTCGCAG-TGTTATCCCGATCATTTTC-TTACTTTTCGACTC
1486614 ATGGTGCTAT
Statistics
Matches: 261, Mismatches: 78, Indels: 32
0.70 0.21 0.09
Matches are distributed among these distances:
72 1 0.00
73 33 0.13
74 51 0.20
75 139 0.53
76 36 0.14
77 1 0.00
ACGTcount: A:0.15, C:0.23, G:0.15, T:0.47
Consensus pattern (74 bp):
TTCTTTACTTCTTAACTCGCAGTGTTATCCCGATCATTTTCTTACTTTTCGACTCGTGATGTTGT
CCGGATATT
Found at i:1486435 original size:113 final size:112
Alignment explanation
Indices: 1486262--1486613 Score: 279
Period size: 113 Copynumber: 3.1 Consensus size: 112
1486252 TAGTCGATTA
* * * * * * *
1486262 TTTACTTCTCGACTCGCAATATTGTCTCAGTCATTTTTTTTACTTCTCGACTGACAGTGTTGTCC
1 TTTACTTTTCGACTCG-AATGTTGTCCCAATCATTTTTTTTACTTTTCAACTGACAGTGTTATCC
* * *
1486327 TGG-CTATTTTCTTTACTTCTTAACTCGCAGTGTTATCCCGATTATTTTC
65 TGGTC-A-ATTCTTTACTTCTCAACTCGCAGTGTTATCCCGATTATTTGC
* **
1486376 -TTACTTTTCGACTCGTGATGTTGTCCCAATCATTTTTTTTACTTTTCAACTTG-TGGTGTTATC
1 TTTACTTTTCGACTCG-AATGTTGTCCCAATCATTTTTTTTACTTTTCAAC-TGACAGTGTTATC
* ** * * *
1486439 CTGGTCAATTCTTTACTTCTCAACTGGTGGTGTTGTCCCGGTTGTTTGC
64 CTGGTCAATTCTTTACTTCTCAACTCGCAGTGTTATCCCGATTATTTGC
* * * * *
1486488 TTTACTTCTT-GACTCGCAGTGTTGTCCCGATCA-TTTTTTTACTTTTCGACTCAC-GATGTTGT
1 TTTACTT-TTCGACTCG-AATGTTGTCCCAATCATTTTTTTTACTTTTCAACTGACAG-TGTTAT
* * * * * * *
1486550 CCCGATC-ATTCTTTATTTCTCGACTCGC-GATGTTATCCCTATCATTTTC
63 CCTGGTCAATTCTTTACTTCTCAACTCGCAG-TGTTATCCCGATTATTTGC
*
1486599 TTTACTTTTTGACTC
1 TTTACTTTTCGACTC
1486614 ATGGTGCTAT
Statistics
Matches: 190, Mismatches: 40, Indels: 19
0.76 0.16 0.08
Matches are distributed among these distances:
110 3 0.02
111 44 0.23
112 59 0.31
113 79 0.42
114 5 0.03
ACGTcount: A:0.15, C:0.23, G:0.15, T:0.47
Consensus pattern (112 bp):
TTTACTTTTCGACTCGAATGTTGTCCCAATCATTTTTTTTACTTTTCAACTGACAGTGTTATCCT
GGTCAATTCTTTACTTCTCAACTCGCAGTGTTATCCCGATTATTTGC
Found at i:1486581 original size:36 final size:36
Alignment explanation
Indices: 1486487--1486595 Score: 123
Period size: 36 Copynumber: 3.0 Consensus size: 36
1486477 CGGTTGTTTG
* *
1486487 CTTTACTTCTTGACTCGC-AGTGTTGTCCCGATCATTT
1 CTTTATTTCTCGACTCGCGA-TGTTGTCCCGATCA-TT
* *
1486524 TTTTACTTT-TCGACTCACGATGTTGTCCCGATCATT
1 CTTTA-TTTCTCGACTCGCGATGTTGTCCCGATCATT
* *
1486560 CTTTATTTCTCGACTCGCGATGTTATCCCTATCATT
1 CTTTATTTCTCGACTCGCGATGTTGTCCCGATCATT
1486596 TTCTTTACTT
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
35 3 0.05
36 30 0.49
37 25 0.41
38 3 0.05
ACGTcount: A:0.16, C:0.27, G:0.14, T:0.44
Consensus pattern (36 bp):
CTTTATTTCTCGACTCGCGATGTTGTCCCGATCATT
Found at i:1486662 original size:74 final size:73
Alignment explanation
Indices: 1486493--1486640 Score: 167
Period size: 73 Copynumber: 2.0 Consensus size: 73
1486483 TTTGCTTTAC
* * * *
1486493 TTCTTGACTCGC-AGTGTTGTCCCGATCATTTTTTTACTTTTCGACTCACGATGTTGTCCCGATC
1 TTCTCGACTCGCGA-TGTTATCCCGATCATTTTTTTACTTTTCGACTCACGATGCTATCCCGATC
*
1486557 ATTCTTTAT
65 ATTCTTCAT
* * * *
1486566 TTCTCGACTCGCGATGTTATCCCTATCATTTTCTTTACTTTTTGACTCATGGTGCTATCCC-ATT
1 TTCTCGACTCGCGATGTTATCCCGATCATTTT-TTTACTTTTCGACTCACGATGCTATCCCGA-T
1486630 CATT-TTCAT
64 CATTCTTCAT
1486639 TT
1 TT
1486641 TCCTGACTTG
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
73 34 0.54
74 29 0.46
ACGTcount: A:0.16, C:0.25, G:0.13, T:0.47
Consensus pattern (73 bp):
TTCTCGACTCGCGATGTTATCCCGATCATTTTTTTACTTTTCGACTCACGATGCTATCCCGATCA
TTCTTCAT
Found at i:1486892 original size:106 final size:105
Alignment explanation
Indices: 1486654--1487155 Score: 457
Period size: 106 Copynumber: 4.7 Consensus size: 105
1486644 TGACTTGCGA
* * * * * * * * *
1486654 TTTAATCCCAGTCACTTTTATTTTTCAGACTCGCGGTTCAGTGCCAATCGTCGTTAATTTTTGAC
1 TTTAATCCCAATCACTTTTATTTTT-TGACTTGCGGTTCAATCCCGATCGTCATTAATCTCTGAC
* * * * * * **
1486719 TCGTGGTTTAATCTC-AGTCATTTTTATAATTTCCTGACTTACGG
65 TTGCGGTTTAATCTCGA-TCATTTCTAT--TTT-TTTATTTGTGG
* * * * *
1486763 TTTAATCTCAATTACTTTTATTTTTTGACTTGCGATTCAATCCCGATTGTCATTAATCTCTAACT
1 TTTAATCCCAATCACTTTTATTTTTTGACTTGCGGTTCAATCCCGATCGTCATTAATCTCTGACT
* *
1486828 TACGGTTTAATCCCGATCATTTCTATTTTTTTGATTTGTGG
66 TGCGGTTTAATCTCGATCATTTCTATTTTTTT-ATTTGTGG
* * * *
1486869 TTTAATCCCAATCACTTTTATTTTCTAACTTGCGGTTCAATCTCAATCGTCATTAATCTCTGACT
1 TTTAATCCCAATCACTTTTATTTTTTGACTTGCGGTTCAATCCCGATCGTCATTAATCTCTGACT
* * * * * **
1486934 TGCAGTTTGATCTCGGTTATTTCAATTTTTTTATTTACGG
66 TGCGGTTTAATCTCGATCATTTCTATTTTTTTATTTGTGG
* * * *
1486974 TTTAATCCCAATCACTTTTATTTTTTGACTTGCGGTTCAATCCCGATCATCGTTAATTTTTGACT
1 TTTAATCCCAATCACTTTTATTTTTTGACTTGCGGTTCAATCCCGATCGTCATTAATCTCTGACT
* * * * * * * *
1487039 TGCGATTTAATTTCAATCATTTCTATTTTCCTAACTCGTAG
66 TGCGGTTTAATCTCGATCATTTCTATTTT-TTTATTTGTGG
* * * *
1487080 TTTAAGCCCAATCACTTTTATCTTTTGACTTGCGGTTCAATCTCGATCGTCGTTAATCTCTGACT
1 TTTAATCCCAATCACTTTTATTTTTTGACTTGCGGTTCAATCCCGATCGTCATTAATCTCTGACT
* *
1487145 CGCGATTTAAT
66 TGCGGTTTAAT
1487156 TTCAGTCATT
Statistics
Matches: 318, Mismatches: 72, Indels: 9
0.80 0.18 0.02
Matches are distributed among these distances:
105 85 0.27
106 162 0.51
108 48 0.15
109 23 0.07
ACGTcount: A:0.22, C:0.21, G:0.13, T:0.45
Consensus pattern (105 bp):
TTTAATCCCAATCACTTTTATTTTTTGACTTGCGGTTCAATCCCGATCGTCATTAATCTCTGACT
TGCGGTTTAATCTCGATCATTTCTATTTTTTTATTTGTGG
Found at i:1487010 original size:35 final size:34
Alignment explanation
Indices: 1486622--1487731 Score: 286
Period size: 35 Copynumber: 31.2 Consensus size: 34
1486612 TCATGGTGCT
* * *
1486622 ATCCCATTCATTTTCATTTTCCTGACTTGCGATTTA
1 ATCCCAATCATTTT-ATTTT-TTGACTTGCGGTTTA
* * * *
1486658 ATCCCAGTCACTTTTATTTTTCAGACTCGCGGTTCA
1 ATCCCAATCA-TTTTATTTTT-TGACTTGCGGTTTA
* * * * * * *
1486694 GTGCCAATCGTCGTTAATTTTTGACTCGTGGTTTA
1 ATCCCAATCAT-TTTATTTTTTGACTTGCGGTTTA
* * * *
1486729 ATCTCAGTCATTTTTATAATTTCCTGACTTACGGTTTA
1 ATCCCAATCA-TTTTAT--TTT-TTGACTTGCGGTTTA
* * * *
1486767 ATCTCAATTACTTTTATTTTTTGACTTGCGATTCA
1 ATCCCAATCA-TTTTATTTTTTGACTTGCGGTTTA
* ** * * * * * *
1486802 ATCCCGATTGTCATTAATCTCTAACTTACGGTTTA
1 ATCCCAATCAT-TTTATTTTTTGACTTGCGGTTTA
* * *
1486837 ATCCCGATCATTTCTATTTTTTTGATTTGTGGTTTA
1 ATCCCAATCATTT-TA-TTTTTTGACTTGCGGTTTA
* * *
1486873 ATCCCAATCACTTTTATTTTCTAACTTGCGGTTCA
1 ATCCCAATCA-TTTTATTTTTTGACTTGCGGTTTA
* * * * * * * *
1486908 ATCTCAATCGTCATTAATCTCTGACTTGCAGTTTG
1 ATCCCAATCAT-TTTATTTTTTGACTTGCGGTTTA
* ** * * * * *
1486943 ATCTCGGTTATTTCAATTTTTTTATTTACGGTTTA
1 ATCCCAATCATTT-TATTTTTTGACTTGCGGTTTA
*
1486978 ATCCCAATCACTTTTATTTTTTGACTTGCGGTTCA
1 ATCCCAATCA-TTTTATTTTTTGACTTGCGGTTTA
* * * *
1487013 ATCCCGATCATCGTTAATTTTTGACTTGCGATTTA
1 ATCCCAATCAT-TTTATTTTTTGACTTGCGGTTTA
** * * * **
1487048 ATTTCAATCATTTCTATTTTCCTAACTCGTAGTTTA
1 ATCCCAATCATTT-TATTTT-TTGACTTGCGGTTTA
* * *
1487084 AGCCCAATCACTTTTATCTTTTGACTTGCGGTTCA
1 ATCCCAATCA-TTTTATTTTTTGACTTGCGGTTTA
* * * * * * * * *
1487119 ATCTCGATCGTCGTTAATCTCTGACTCGCGATTTA
1 ATCCCAATCAT-TTTATTTTTTGACTTGCGGTTTA
** * * * *
1487154 ATTTCAGTCA---T-TTTTCTAACTTGCGGTTCA
1 ATCCCAATCATTTTATTTTTTGACTTGCGGTTTA
* ** * * * * *
1487184 ATCCCGATTGTCATTAATCTCTGACTTGTGGTTTA
1 ATCCCAATCAT-TTTATTTTTTGACTTGCGGTTTA
* * * *
1487219 ATCTCGATCATTTTTATTTTTTTGATTTACGGTTTA
1 ATCCCAATCA-TTTTA-TTTTTTGACTTGCGGTTTA
* *
1487255 ATCCCAATCACTTTTATTTTTTTTTAACTTGCGGTTCA
1 ATCCCAATCA-TTTTA---TTTTTTGACTTGCGGTTTA
* * * * * * * *
1487293 ATCCCAGTCATCATTAATCTCTAACTCGTGGTTTA
1 ATCCCAATCAT-TTTATTTTTTGACTTGCGGTTTA
* * * *
1487328 ATCTCAATCATTTCTATTTTCTTGATTTACGGCTTA
1 ATCCCAATCATTT-TATTTT-TTGACTTGCGGTTTA
* * *
1487364 ATCCCAATCACTTTTATTTTATGACTTACGGTTCA
1 ATCCCAATCA-TTTTATTTTTTGACTTGCGGTTTA
* * * * * *
1487399 ATCTCAATCATCGTTAATCTCTGACTTGCGATTTA
1 ATCCCAATCAT-TTTATTTTTTGACTTGCGGTTTA
* *
1487434 ATTCCAATCATTTCTATTTTTTTAACTTGCGGTTTA
1 ATCCCAATCATTT-TA-TTTTTTGACTTGCGGTTTA
* * * * *
1487470 ATCTCAGTCACTTTTATTTTTCTAACTTGCGATTCA
1 ATCCCAATCA-TTTTATTTTT-TGACTTGCGGTTTA
* * * * * * * *
1487506 GTCTCAATCATCATTAATCTTTGACTCGTGATTTA
1 ATCCCAATCAT-TTTATTTTTTGACTTGCGGTTTA
* ** * **
1487541 ATCACTGTCATTTCTATAGTTTCCTT-ACTTACAATTTA
1 ATCCCAATCATTT-TAT--TTT--TTGACTTGCGGTTTA
* * *
1487579 ATCCCAGTCACTTTTATTTTTTTGACTTACGGTTCA
1 ATCCCAATCA-TTTTA-TTTTTTGACTTGCGGTTTA
* * * * ***
1487615 ATCCCAGTCGTCGTTAATTTTTGACTCATGGTTTA
1 ATCCCAATCAT-TTTATTTTTTGACTTGCGGTTTA
** *
1487650 ATCCCAATCATTTCTATAGTATCCTGACTTGCAGTTTA
1 ATCCCAATCATTT-TAT--T-TTTTGACTTGCGGTTTA
** * * *
1487688 ATTTCATTCACTTTTATTTTTCTGACTTGTGGTTCA
1 ATCCCAATCA-TTTTATTTTT-TGACTTGCGGTTTA
*
1487724 GTCCCAAT
1 ATCCCAAT
1487732 TATCGTTAAT
Statistics
Matches: 754, Mismatches: 267, Indels: 106
0.67 0.24 0.09
Matches are distributed among these distances:
30 17 0.02
31 1 0.00
34 13 0.02
35 372 0.49
36 224 0.30
37 26 0.03
38 92 0.12
39 9 0.01
ACGTcount: A:0.22, C:0.21, G:0.12, T:0.46
Consensus pattern (34 bp):
ATCCCAATCATTTTATTTTTTGACTTGCGGTTTA
Found at i:1487060 original size:211 final size:211
Alignment explanation
Indices: 1486757--1487144 Score: 544
Period size: 211 Copynumber: 1.8 Consensus size: 211
1486747 ATTTCCTGAC
* * **
1486757 TTACGGTTTAATCTCAATTACTTTTATTTTTTGACTTGCGATTCAATCCCGATTGTCATTAATCT
1 TTACGGTTTAATCCCAATCACTTTTATTTTTTGACTTGCGATTCAATCCCGATCATCATTAATCT
* * ** * * * * *
1486822 CTAACTTACGGTTTAATCCCGATCATTTCTATTTTTTTGATTTGTGGTTTAATCCCAATCACTTT
66 CTAACTTACGATTTAATCCCAATCATTTCTATTTTCCTAACTCGTAGTTTAAGCCCAATCACTTT
1486887 TAT-TTTCTAACTTGCGGTTCAATCTCAATCGTCATTAATCTCTGACTTGCAGTTTGATCTCGGT
131 TATCTTT-TAACTTGCGGTTCAATCTCAATCGTCATTAATCTCTGACTTGCAGTTTGATCTCGGT
1486951 TATTTCAATTTTTTTAT
195 TATTTCAATTTTTTTAT
* * *
1486968 TTACGGTTTAATCCCAATCACTTTTATTTTTTGACTTGCGGTTCAATCCCGATCATCGTTAATTT
1 TTACGGTTTAATCCCAATCACTTTTATTTTTTGACTTGCGATTCAATCCCGATCATCATTAATCT
* * * **
1487033 TTGACTTGCGATTTAATTTCAATCATTTCTATTTTCCTAACTCGTAGTTTAAGCCCAATCACTTT
66 CTAACTTACGATTTAATCCCAATCATTTCTATTTTCCTAACTCGTAGTTTAAGCCCAATCACTTT
* * *
1487098 TATCTTTTGACTTGCGGTTCAATCTCGATCGTCGTTAATCTCTGACT
131 TATCTTTTAACTTGCGGTTCAATCTCAATCGTCATTAATCTCTGACT
1487145 CGCGATTTAA
Statistics
Matches: 152, Mismatches: 24, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
211 149 0.98
212 3 0.02
ACGTcount: A:0.22, C:0.20, G:0.12, T:0.46
Consensus pattern (211 bp):
TTACGGTTTAATCCCAATCACTTTTATTTTTTGACTTGCGATTCAATCCCGATCATCATTAATCT
CTAACTTACGATTTAATCCCAATCATTTCTATTTTCCTAACTCGTAGTTTAAGCCCAATCACTTT
TATCTTTTAACTTGCGGTTCAATCTCAATCGTCATTAATCTCTGACTTGCAGTTTGATCTCGGTT
ATTTCAATTTTTTTAT
Found at i:1487219 original size:65 final size:65
Alignment explanation
Indices: 1487107--1487233 Score: 175
Period size: 65 Copynumber: 2.0 Consensus size: 65
1487097 TTATCTTTTG
* * *
1487107 ACTTGCGGTTCAATCTCGATCGTCGTTAATCTCTGACTCGCGATTTAATTTC-AGTCATTTTTCT
1 ACTTGCGGTTCAATCCCGATCGTCATTAATCTCTGACTCGCGATTTAATCTCGA-TCATTTTTCT
1487171 A
65 A
* * * *
1487172 ACTTGCGGTTCAATCCCGATTGTCATTAATCTCTGACTTGTGGTTTAATCTCGATCATTTTT
1 ACTTGCGGTTCAATCCCGATCGTCATTAATCTCTGACTCGCGATTTAATCTCGATCATTTTT
1487234 ATTTTTTTGA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
65 53 0.98
66 1 0.02
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.43
Consensus pattern (65 bp):
ACTTGCGGTTCAATCCCGATCGTCATTAATCTCTGACTCGCGATTTAATCTCGATCATTTTTCTA
Found at i:1487290 original size:38 final size:36
Alignment explanation
Indices: 1487207--1487500 Score: 171
Period size: 36 Copynumber: 8.2 Consensus size: 36
1487197 TTAATCTCTG
* * * *
1487207 ACTTGTGGTTTAATCTCGATCATTTTTATTTTTTTG
1 ACTTGCGGTTTAATCCCAATCATTTTTATTTTTTTA
* * *
1487243 ATTTACGGTTTAATCCCAATCACTTTTATTTTTTTTTA
1 ACTTGCGGTTTAATCCCAATCA-TTTT-TATTTTTTTA
* * ** * * *
1487281 ACTTGCGGTTCAATCCCAGTCATCATTA-ATCTCTA
1 ACTTGCGGTTTAATCCCAATCATTTTTATTTTTTTA
* * * * * *
1487316 ACTCGTGGTTTAATCTCAATCATTTCTATTTTCTTG
1 ACTTGCGGTTTAATCCCAATCATTTTTATTTTTTTA
* * * * * *
1487352 ATTTACGGCTTAATCCCAATCACTTTTA-TTTTATG
1 ACTTGCGGTTTAATCCCAATCATTTTTATTTTTTTA
* * * ** * * * *
1487387 ACTTACGGTTCAATCTCAATCATCGTTA-ATCTCTG
1 ACTTGCGGTTTAATCCCAATCATTTTTATTTTTTTA
* * *
1487422 ACTTGCGATTTAATTCCAATCATTTCTATTTTTTTA
1 ACTTGCGGTTTAATCCCAATCATTTTTATTTTTTTA
* * * *
1487458 ACTTGCGGTTTAATCTCAGTCACTTTTATTTTTCTA
1 ACTTGCGGTTTAATCCCAATCATTTTTATTTTTTTA
1487494 ACTTGCG
1 ACTTGCG
1487501 ATTCAGTCTC
Statistics
Matches: 185, Mismatches: 69, Indels: 8
0.71 0.26 0.03
Matches are distributed among these distances:
35 74 0.40
36 79 0.43
37 6 0.03
38 26 0.14
ACGTcount: A:0.22, C:0.20, G:0.10, T:0.48
Consensus pattern (36 bp):
ACTTGCGGTTTAATCCCAATCATTTTTATTTTTTTA
Found at i:1487355 original size:109 final size:107
Alignment explanation
Indices: 1487163--1487813 Score: 579
Period size: 109 Copynumber: 6.0 Consensus size: 107
1487153 AATTTCAGTC
* ** * *
1487163 ATTTTTCTAACTTGCGGTTCAATCCCGATTGTCATTAATCTCTGACTTGTGGTTTAATCTCGATC
1 ATTTTTCTAACTTGCGGTTCAATCCCAATCATCATTAATCTCTGACTCGTGGTTTAATCTCAATC
* * * *
1487228 ATTTTTATTTTTTTGATTTACGGTTTAATCCCAATCACTTTT
66 ATTTCTATTTTCTTGACTTACAGTTTAATCCCAATCACTTTT
* * *
1487270 ATTTTTTTTTAACTTGCGGTTCAATCCCAGTCATCATTAATCTCTAACTCGTGGTTTAATCTCAA
1 A--TTTTTCTAACTTGCGGTTCAATCCCAATCATCATTAATCTCTGACTCGTGGTTTAATCTCAA
* * *
1487335 TCATTTCTATTTTCTTGATTTACGGCTTAATCCCAATCACTTTT
64 TCATTTCTATTTTCTTGACTTACAGTTTAATCCCAATCACTTTT
* * * * * * * *
1487379 A-TTTTATGACTTACGGTTCAATCTCAATCATCGTTAATCTCTGACTTGCGATTTAAT-TCCAAT
1 ATTTTTCTAACTTGCGGTTCAATCCCAATCATCATTAATCTCTGACTCGTGGTTTAATCT-CAAT
* * * * * *
1487442 CATTTCTATTTTTTTAACTTGCGGTTTAATCTCAGTCACTTTT
65 CATTTCTATTTTCTTGACTTACAGTTTAATCCCAATCACTTTT
* * * * * * **
1487485 ATTTTTCTAACTTGCGATTCAGTCTCAATCATCATTAATCTTTGACTCGTGATTTAATCACTGTC
1 ATTTTTCTAACTTGCGGTTCAATCCCAATCATCATTAATCTCTGACTCGTGGTTTAATCTCAATC
* *
1487550 ATTTCTATAGTTTCCTT-ACTTACAATTTAATCCCAGTCACTTTT
66 ATTTCTAT--TTT-CTTGACTTACAGTTTAATCCCAATCACTTTT
* * * * * * * * * *
1487594 ATTTTTTTGACTTACGGTTCAATCCCAGTCGTCGTTAATTTTTGACTCATGGTTTAATCCCAATC
1 ATTTTTCTAACTTGCGGTTCAATCCCAATCATCATTAATCTCTGACTCGTGGTTTAATCTCAATC
* * * ** *
1487659 ATTTCTATAGTATCCTGACTTGCAGTTTAATTTCATTCACTTTT
66 ATTTCTAT--TTTCTTGACTTACAGTTTAATCCCAATCACTTTT
* * * * * * ** *
1487703 ATTTTTCTGACTTGTGGTTCAGTCCCAATTATCGTTAATCTGTGACTCGTATTTTAATCTCAGTC
1 ATTTTTCTAACTTGCGGTTCAATCCCAATCATCATTAATCTCTGACTCGTGGTTTAATCTCAATC
* * * * **
1487768 ATTCCTATGTTCCTGACTTACAGTTTAATCTCAATCGTTTTT
66 ATTTCTATTTTCTTGACTTACAGTTTAATCCCAATCACTTTT
1487810 ATTT
1 ATTT
1487814 AGTTAGCTTC
Statistics
Matches: 446, Mismatches: 89, Indels: 18
0.81 0.16 0.03
Matches are distributed among these distances:
105 1 0.00
106 87 0.20
107 90 0.20
108 2 0.00
109 264 0.59
110 2 0.00
ACGTcount: A:0.22, C:0.20, G:0.11, T:0.46
Consensus pattern (107 bp):
ATTTTTCTAACTTGCGGTTCAATCCCAATCATCATTAATCTCTGACTCGTGGTTTAATCTCAATC
ATTTCTATTTTCTTGACTTACAGTTTAATCCCAATCACTTTT
Found at i:1487946 original size:3 final size:3
Alignment explanation
Indices: 1487938--1487974 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1487928 ATTTTGTTTG
1487938 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1487975 CATTGATTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1489626 original size:22 final size:24
Alignment explanation
Indices: 1489601--1489644 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1489591 AAACACCAAA
1489601 CCTC-AAACC-TTAAAATCCAATT
1 CCTCAAAACCTTTAAAATCCAATT
1489623 CCTCAAAACCTTTAAAATCCAA
1 CCTCAAAACCTTTAAAATCCAA
1489645 AATCCAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 4 0.20
23 5 0.25
24 11 0.55
ACGTcount: A:0.43, C:0.32, G:0.00, T:0.25
Consensus pattern (24 bp):
CCTCAAAACCTTTAAAATCCAATT
Found at i:1489653 original size:23 final size:23
Alignment explanation
Indices: 1489596--1489645 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
1489586 AACCAAAACA
1489596 CCAAA-CCTC-AAACCTTAAAAT
1 CCAAATCCTCAAAACCTTAAAAT
*
1489617 CCAATTCCTCAAAACCTTTAAAAT
1 CCAAATCCTCAAAACC-TTAAAAT
1489641 CCAAA
1 CCAAA
1489646 ATCCAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 4 0.17
22 4 0.17
23 5 0.21
24 11 0.46
ACGTcount: A:0.46, C:0.32, G:0.00, T:0.22
Consensus pattern (23 bp):
CCAAATCCTCAAAACCTTAAAAT
Found at i:1489654 original size:24 final size:23
Alignment explanation
Indices: 1489605--1489664 Score: 59
Period size: 24 Copynumber: 2.6 Consensus size: 23
1489595 ACCAAACCTC
* *
1489605 AAACCTTAAAATCCAATTCCTCA
1 AAACCTTAAAATCCAAATCCTAA
1489628 AAACCTTTAAAATCCAAAATCC-AA
1 AAACC-TTAAAATCC-AAATCCTAA
* *
1489652 AAATCTCAAAATC
1 AAACCTTAAAATC
1489665 TCCAAAGCCA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
23 12 0.39
24 14 0.45
25 5 0.16
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (23 bp):
AAACCTTAAAATCCAAATCCTAA
Found at i:1491229 original size:20 final size:20
Alignment explanation
Indices: 1491206--1491245 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1491196 ATTTATATAA
*
1491206 TTTAAAT-TATTAATATAATT
1 TTTAAATGTA-TAATAAAATT
1491226 TTTAAATGTATAATAAAATT
1 TTTAAATGTATAATAAAATT
1491246 AAAAATAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
TTTAAATGTATAATAAAATT
Found at i:1491426 original size:2 final size:2
Alignment explanation
Indices: 1491419--1491451 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1491409 AAAATTACTC
1491419 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
1491452 AGCTCAGTAT
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:1493080 original size:2 final size:2
Alignment explanation
Indices: 1493073--1493109 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1493063 ATGACCCTCC
1493073 AT AT 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 AT AT A
1493110 ACTTGCAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1493753 original size:109 final size:109
Alignment explanation
Indices: 1493617--1493831 Score: 324
Period size: 109 Copynumber: 2.0 Consensus size: 109
1493607 ATGTAAATTC
* * *
1493617 CAAATGTCTAATAGTAATCGACTTAAATATTTTTATAAATTTTTAAATTAATAAATTAATCATTA
1 CAAATGTCTAATAGTAATCGACATAAATATTCTTATAAAATTTTAAATTAATAAATTAATCATTA
* *
1493682 ACTATATAACTTTCATTAATTTATTTAAGTTTAATTTAAATCAT
66 AATATATAACTTTCATTAATTTATTTAAATTTAATTTAAATCAT
* * *
1493726 CAAAGTGT-TAATAGTAATCGACATAAATGTTCTTATAAAATTTTAAATTAATAAATTTATCTTT
1 CAAA-TGTCTAATAGTAATCGACATAAATATTCTTATAAAATTTTAAATTAATAAATTAATCATT
* *
1493790 AAATATTTAACTTTTATTAATTTATTTAAATTTAATTTAAAT
65 AAATATATAACTTTCATTAATTTATTTAAATTTAATTTAAAT
1493832 AAACTAGATT
Statistics
Matches: 95, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
109 92 0.97
110 3 0.03
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (109 bp):
CAAATGTCTAATAGTAATCGACATAAATATTCTTATAAAATTTTAAATTAATAAATTAATCATTA
AATATATAACTTTCATTAATTTATTTAAATTTAATTTAAATCAT
Found at i:1494208 original size:22 final size:22
Alignment explanation
Indices: 1494182--1494236 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
1494172 AATACTCATA
*
1494182 AATAATTTAATAATAAATTACT
1 AATAATTTAATAATAAATGACT
* * *
1494204 AATAACTTAATAGTAAATGAGT
1 AATAATTTAATAATAAATGACT
*
1494226 GATAATTTAAT
1 AATAATTTAAT
1494237 TGTCAATAGT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.51, C:0.04, G:0.07, T:0.38
Consensus pattern (22 bp):
AATAATTTAATAATAAATGACT
Found at i:1494283 original size:22 final size:21
Alignment explanation
Indices: 1494258--1494355 Score: 79
Period size: 22 Copynumber: 4.5 Consensus size: 21
1494248 GATAATTTTT
1494258 TAATAAATCTATAATAATATAA
1 TAATAAATC-ATAATAATATAA
* *
1494280 TAATAAATGCATAATACTTTAA
1 TAATAAAT-CATAATAATATAA
** *
1494302 TGGTAAATCAATTATAATATAA
1 TAATAAATC-ATAATAATATAA
* * *
1494324 TTATAAATGCATAACAATATAG
1 TAATAAAT-CATAATAATATAA
*
1494346 TACTAAATCA
1 TAATAAATCA
1494356 AGGATAACTT
Statistics
Matches: 59, Mismatches: 14, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
21 3 0.05
22 54 0.92
23 2 0.03
ACGTcount: A:0.52, C:0.08, G:0.05, T:0.35
Consensus pattern (21 bp):
TAATAAATCATAATAATATAA
Found at i:1494406 original size:22 final size:22
Alignment explanation
Indices: 1494381--1494691 Score: 117
Period size: 22 Copynumber: 14.5 Consensus size: 22
1494371 AAAATGAATA
* *
1494381 ATAACTTACTAGTTAATTATTG
1 ATAACTTAATAGTAAATTATTG
* * * * *
1494403 ATAATTTAGTAATAAATCAATG
1 ATAACTTAATAGTAAATTATTG
1494425 ATAACTTAATAGTAAATT-TGTG
1 ATAACTTAATAGTAAATTAT-TG
* *
1494447 ATAATTTAATAGTAAATCAGTT-
1 ATAACTTAATAGTAAATTA-TTG
* **
1494469 TTAGTTTAATAGT-AATTAATT-
1 ATAACTTAATAGTAAATT-ATTG
* * * **
1494490 -T-A--TAGTAGTAGATAATAA
1 ATAACTTAATAGTAAATTATTG
* * *
1494508 ATAACTTAACAATAAATCAATT-
1 ATAACTTAATAGTAAAT-TATTG
* * *
1494530 CTAAATTAATAGTAAATAATTG
1 ATAACTTAATAGTAAATTATTG
* * *
1494552 ATAATTTAATAGTTATTTATTG
1 ATAACTTAATAGTAAATTATTG
* * * *
1494574 AAAACTTAAAAGT-AATCAGT-
1 ATAACTTAATAGTAAATTATTG
* **
1494594 ATAACTTAATAGTAAATCATCA
1 ATAACTTAATAGTAAATTATTG
* * *
1494616 ATAACATAATAGTTAATCATTG
1 ATAACTTAATAGTAAATTATTG
1494638 ATAACTTAATAGTAAATTA-TG
1 ATAACTTAATAGTAAATTATTG
* * * * *
1494659 CATAATTTTATA-TAAAGTAGTA
1 -ATAACTTAATAGTAAATTATTG
1494681 ATAACTTAATA
1 ATAACTTAATA
1494692 ATGATTCATA
Statistics
Matches: 215, Mismatches: 58, Indels: 33
0.70 0.19 0.11
Matches are distributed among these distances:
17 8 0.04
18 2 0.01
19 1 0.00
20 13 0.06
21 35 0.16
22 151 0.70
23 4 0.02
24 1 0.00
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.39
Consensus pattern (22 bp):
ATAACTTAATAGTAAATTATTG
Found at i:1494463 original size:44 final size:44
Alignment explanation
Indices: 1494183--1494465 Score: 132
Period size: 44 Copynumber: 6.4 Consensus size: 44
1494173 ATACTCATAA
* * * *
1494183 ATAATTTAATAATAAATTACTAATAACTTAATAGTAAATGAGTG
1 ATAATTTAATAATAAATCAATAATAACTTAATAGTAAATTATTG
** * * * * ** * *
1494227 ATAATTTAATTGTCAAT-AGTTGATAATTTTTTAATAAATCTA-TA
1 ATAATTTAATAATAAATCA-ATAATAACTTAATAGTAAAT-TATTG
* * *
1494271 ATAATATAATAATAAATGC-ATAAT-ACTTTAATGGTAAATCAATT-
1 ATAATTTAATAATAAAT-CAATAATAAC-TTAATAGTAAAT-TATTG
* * * * * * **
1494315 ATAATATAATTATAAATGC-ATAACAA-TATAGTACTAAATCAAGG
1 ATAATTTAATAATAAAT-CAATAATAACT-TAATAGTAAATTATTG
* * * * * *
1494359 ATAACTTAACAAAAAATGAATAATAACTTACTAGTTAATTATTG
1 ATAATTTAATAATAAATCAATAATAACTTAATAGTAAATTATTG
* *
1494403 ATAATTTAGTAATAAATCAATGATAACTTAATAGTAAATT-TGTG
1 ATAATTTAATAATAAATCAATAATAACTTAATAGTAAATTAT-TG
*
1494447 ATAATTTAATAGTAAATCA
1 ATAATTTAATAATAAATCA
1494466 GTTTTAGTTT
Statistics
Matches: 173, Mismatches: 54, Indels: 24
0.69 0.22 0.10
Matches are distributed among these distances:
43 5 0.03
44 164 0.95
45 4 0.02
ACGTcount: A:0.48, C:0.06, G:0.08, T:0.37
Consensus pattern (44 bp):
ATAATTTAATAATAAATCAATAATAACTTAATAGTAAATTATTG
Found at i:1494752 original size:22 final size:22
Alignment explanation
Indices: 1494711--1494752 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1494701 AGATAATTTA
* *
1494711 GTGATAAATTAGTAATAATTGT
1 GTGATAAATAAGTAAAAATTGT
*
1494733 GTGATAAATAATTAAAAATT
1 GTGATAAATAAGTAAAAATT
1494753 AAGTAGTAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (22 bp):
GTGATAAATAAGTAAAAATTGT
Found at i:1494912 original size:22 final size:22
Alignment explanation
Indices: 1494829--1494914 Score: 73
Period size: 22 Copynumber: 3.9 Consensus size: 22
1494819 AGTCGTAAAT
**
1494829 TGATAATTTAGCAATAAATTAC
1 TGATAATTTAATAATAAATTAC
* * **
1494851 TGGTAATATAATAGCAAATTAC
1 TGATAATTTAATAATAAATTAC
* * ** *
1494873 TAATAACTTAATTGTAAATTAG
1 TGATAATTTAATAATAAATTAC
1494895 TGATAATTTAATAATAAATT
1 TGATAATTTAATAATAAATT
1494915 GATTAATCAT
Statistics
Matches: 47, Mismatches: 17, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (22 bp):
TGATAATTTAATAATAAATTAC
Found at i:1494961 original size:22 final size:22
Alignment explanation
Indices: 1494935--1494997 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 22
1494925 TGATAATTTT
1494935 TTAGTAAATTATTAATAAAGT-AA
1 TTAGTAAATTATT-ATAAA-TAAA
1494958 -TAGTAAATTAGTTATAAATAAA
1 TTAGTAAATTA-TTATAAATAAA
*
1494980 TTAGTAAATCATTGATAA
1 TTAGTAAATTATT-ATAA
1494998 TAATGGTTGG
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
21 1 0.03
22 19 0.54
23 15 0.43
ACGTcount: A:0.51, C:0.02, G:0.10, T:0.38
Consensus pattern (22 bp):
TTAGTAAATTATTATAAATAAA
Found at i:1495394 original size:22 final size:21
Alignment explanation
Indices: 1495362--1495664 Score: 85
Period size: 22 Copynumber: 13.7 Consensus size: 21
1495352 GGTTAATAAA
* *
1495362 AACTTAGTAATTAATAATTGAT
1 AACTTAATAATAAATAA-TGAT
*
1495384 AACTTAATAATAAATCAATAAT
1 AACTTAATAATAAAT-AATGAT
* * *
1495406 AATTTAATAGTAAATTAGTGAT
1 AACTTAATAATAAA-TAATGAT
* **
1495428 AACTTAATAGTAAATCAATTTT
1 AACTTAATAATAAAT-AATGAT
* * *
1495450 AATTTAA-AAGTAATTAGTTGAT
1 AACTTAATAA-TAAATA-ATGAT
* * * * *
1495472 AAATTTAGTAGTAAATTATAAAT
1 -AACTTAATAATAAATAAT-GAT
* *
1495495 AACTTAATAGTAAATCAATGAC
1 AACTTAATAATAAAT-AATGAT
* * * * *
1495517 AATTTAGTAGTTAATCATTAGA-
1 AACTTAATAATAAAT-AAT-GAT
*
1495539 AACTTAAAAATAAATCAAT-AT
1 AACTTAATAATAAAT-AATGAT
* *
1495560 AACTTAA-AAGTCATTAATCATCAAT
1 AACTTAATAA-T-A--AATAAT-GAT
* * *
1495585 AACTTAATAGTTAATCAATAAT
1 AACTTAATAATAAAT-AATGAT
* * *
1495607 AACTTAAGAGTAAATTATGGAT
1 AACTTAATAATAAATAAT-GAT
*
1495629 AATTTAAT-ATAAATCAATGAT
1 AACTTAATAATAAAT-AATGAT
1495650 AACTTAATAATAAAT
1 AACTTAATAATAAAT
1495665 TATGGTTAAT
Statistics
Matches: 208, Mismatches: 51, Indels: 44
0.69 0.17 0.15
Matches are distributed among these distances:
20 3 0.01
21 28 0.13
22 139 0.67
23 23 0.11
24 4 0.02
25 10 0.05
26 1 0.00
ACGTcount: A:0.50, C:0.07, G:0.08, T:0.36
Consensus pattern (21 bp):
AACTTAATAATAAATAATGAT
Found at i:1495414 original size:11 final size:11
Alignment explanation
Indices: 1495382--1495442 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 11
1495372 TTAATAATTG
*
1495382 ATAACTTAATA
1 ATAAATTAATA
*
1495393 ATAAATCAATA
1 ATAAATTAATA
*
1495404 ATAATTTAATA
1 ATAAATTAATA
* * *
1495415 GTAAATTAGTG
1 ATAAATTAATA
*
1495426 ATAACTTAATA
1 ATAAATTAATA
*
1495437 GTAAAT
1 ATAAAT
1495443 CAATTTTAAT
Statistics
Matches: 36, Mismatches: 14, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
11 36 1.00
ACGTcount: A:0.52, C:0.05, G:0.07, T:0.36
Consensus pattern (11 bp):
ATAAATTAATA
Found at i:1495430 original size:44 final size:45
Alignment explanation
Indices: 1495379--1495509 Score: 151
Period size: 44 Copynumber: 2.9 Consensus size: 45
1495369 TAATTAATAA
*
1495379 TTGATAACTTAATAATAAATCAATAATAATTTAATAGTAAATTAG
1 TTGATAACTTAATAGTAAATCAATAATAATTTAATAGTAAATTAG
** *
1495424 -TGATAACTTAATAGTAAATCAATTTTAATTTAAAAGT-AATTAG
1 TTGATAACTTAATAGTAAATCAATAATAATTTAATAGTAAATTAG
* * * *
1495467 TTGATAAATTTAGTAGTAAAT-TATAAATAACTTAATAGTAAAT
1 TTGAT-AACTTAATAGTAAATCAAT-AATAATTTAATAGTAAAT
1495510 CAATGACAAT
Statistics
Matches: 71, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
43 6 0.08
44 39 0.55
45 23 0.32
46 3 0.04
ACGTcount: A:0.49, C:0.04, G:0.08, T:0.39
Consensus pattern (45 bp):
TTGATAACTTAATAGTAAATCAATAATAATTTAATAGTAAATTAG
Found at i:1495543 original size:44 final size:44
Alignment explanation
Indices: 1495473--1495557 Score: 109
Period size: 44 Copynumber: 1.9 Consensus size: 44
1495463 TTAGTTGATA
* * *
1495473 AATTTAGTAGTAAATTATAAATAACTTAATAGTAAATCAATGAC
1 AATTTAGTAGTAAATCATAAATAACTTAAAAATAAATCAATGAC
* *
1495517 AATTTAGTAGTTAATCATTAGA-AACTTAAAAATAAATCAAT
1 AATTTAGTAGTAAATCA-TAAATAACTTAAAAATAAATCAAT
1495558 ATAACTTAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 32 0.91
45 3 0.09
ACGTcount: A:0.51, C:0.07, G:0.08, T:0.34
Consensus pattern (44 bp):
AATTTAGTAGTAAATCATAAATAACTTAAAAATAAATCAATGAC
Found at i:1495652 original size:43 final size:42
Alignment explanation
Indices: 1495548--1495675 Score: 123
Period size: 43 Copynumber: 2.9 Consensus size: 42
1495538 AAACTTAAAA
* ** *
1495548 ATAAATCAATATAACTTAAAAGTCATTAATCATCAATAACTTAAT
1 ATAAATCAATATAACTTAAAAGT-A--AATTATGGATAATTTAAT
* *
1495593 AGTTAATCAATAATAACTTAAGAGTAAATTATGGATAATTTAAT
1 A-TAAATCAAT-ATAACTTAAAAGTAAATTATGGATAATTTAAT
*
1495637 ATAAATCAATGATAACTTAATAA-TAAATTATGGTTAATT
1 ATAAATCAAT-ATAACTTAA-AAGTAAATTATGGATAATT
1495676 CTATAATAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
43 32 0.46
44 16 0.23
45 1 0.01
46 9 0.13
47 12 0.17
ACGTcount: A:0.49, C:0.08, G:0.07, T:0.36
Consensus pattern (42 bp):
ATAAATCAATATAACTTAAAAGTAAATTATGGATAATTTAAT
Found at i:1495779 original size:22 final size:22
Alignment explanation
Indices: 1495754--1495868 Score: 79
Period size: 22 Copynumber: 5.2 Consensus size: 22
1495744 AGTAAATGCA
*
1495754 TAATAACATAATAGTAAATTAT
1 TAATAACTTAATAGTAAATTAT
*
1495776 TAATAATTTAGATA-TAAATTAT
1 TAATAACTTA-ATAGTAAATTAT
* * *
1495798 TGATAACTTAGTAGTAAATCAT
1 TAATAACTTAATAGTAAATTAT
* * * * * *
1495820 TAATGATTTAGTTGTAAATAAC
1 TAATAACTTAATAGTAAATTAT
* * *
1495842 TAGTAATTTAATAGCAAATTAAT
1 TAATAACTTAATAGTAAATT-AT
1495865 TAAT
1 TAAT
1495869 CATTGATAAC
Statistics
Matches: 70, Mismatches: 20, Indels: 5
0.74 0.21 0.05
Matches are distributed among these distances:
21 2 0.03
22 61 0.87
23 7 0.10
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.40
Consensus pattern (22 bp):
TAATAACTTAATAGTAAATTAT
Found at i:1495911 original size:22 final size:22
Alignment explanation
Indices: 1495866--1496093 Score: 124
Period size: 22 Copynumber: 10.2 Consensus size: 22
1495856 CAAATTAATT
* *
1495866 AATCATTGATAACTTT-GTACTA
1 AATCATTGATAA-TTTAATAGTA
*
1495888 AATCATTGATAAATTAATAGTA
1 AATCATTGATAATTTAATAGTA
* *
1495910 AATTAGTT-ATAACTTT-ATAATA
1 AATCA-TTGATAA-TTTAATAGTA
*
1495932 AATCATT-AGCAATTTAATAGTA
1 AATCATTGA-TAATTTAATAGTA
** * *
1495954 AATCATCAACAATTTGATAGTA
1 AATCATTGATAATTTAATAGTA
* * **
1495976 AATCAATCATAATTTAATAACA
1 AATCATTGATAATTTAATAGTA
* * *
1495998 AATCATTCATAAATTAGTAGTA
1 AATCATTGATAATTTAATAGTA
* * *
1496020 AATTAATATTGATAATTTAGTGGTA
1 AA-T--CATTGATAATTTAATAGTA
*
1496045 TATCATTGAT-ATCTTAATAGTA
1 AATCATTGATAAT-TTAATAGTA
** * *
1496067 AATCGCTAATAATATAATAGTA
1 AATCATTGATAATTTAATAGTA
1496089 AATCA
1 AATCA
1496094 ATAATAACTA
Statistics
Matches: 158, Mismatches: 37, Indels: 22
0.73 0.17 0.10
Matches are distributed among these distances:
21 10 0.06
22 123 0.78
23 8 0.05
24 1 0.01
25 16 0.10
ACGTcount: A:0.45, C:0.09, G:0.08, T:0.38
Consensus pattern (22 bp):
AATCATTGATAATTTAATAGTA
Found at i:1496098 original size:22 final size:22
Alignment explanation
Indices: 1496059--1496100 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1496049 ATTGATATCT
**
1496059 TAATAGTAAATCGCTAATAATA
1 TAATAGTAAATCAATAATAATA
1496081 TAATAGTAAATCAATAATAA
1 TAATAGTAAATCAATAATAA
1496101 CTAAATTGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.31
Consensus pattern (22 bp):
TAATAGTAAATCAATAATAATA
Found at i:1496443 original size:22 final size:22
Alignment explanation
Indices: 1496404--1496471 Score: 84
Period size: 22 Copynumber: 3.1 Consensus size: 22
1496394 TATCATAAAT
1496404 TATCAAAAGATTACTAAAATTA
1 TATCAAAAGATTACTAAAATTA
* * * *
1496426 TATCAAGAGGTTATTAAAATTT
1 TATCAAAAGATTACTAAAATTA
*
1496448 TATCAAAA-ATTACCAAAATTA
1 TATCAAAAGATTACTAAAATTA
1496469 TAT
1 TAT
1496472 TCATGGTATC
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
21 12 0.32
22 25 0.68
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.35
Consensus pattern (22 bp):
TATCAAAAGATTACTAAAATTA
Found at i:1496518 original size:20 final size:20
Alignment explanation
Indices: 1496490--1496527 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1496480 TCAAAATTAT
*
1496490 ATCATAAGTCACCAAAATAG
1 ATCAAAAGTCACCAAAATAG
*
1496510 ATCAAAAGTTACCAAAAT
1 ATCAAAAGTCACCAAAAT
1496528 TTTATCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.18, G:0.08, T:0.21
Consensus pattern (20 bp):
ATCAAAAGTCACCAAAATAG
Found at i:1496548 original size:21 final size:21
Alignment explanation
Indices: 1496383--1496541 Score: 112
Period size: 21 Copynumber: 7.6 Consensus size: 21
1496373 TATCAATAAT
*
1496383 TATCAAAAGTATATCATAAA-T-
1 TATCAAAAGT-TACCA-AAATTA
*
1496404 TATCAAAAGATTACTAAAATTA
1 TATCAAAAG-TTACCAAAATTA
* ** *
1496426 TATCAAGAGGTTATTAAAATTT
1 TATCAA-AAGTTACCAAAATTA
*
1496448 TATCAAAAATTACCAAAATTA
1 TATCAAAAGTTACCAAAATTA
* * *
1496469 TATTC--ATGGTATCAAAATTA
1 TA-TCAAAAGTTACCAAAATTA
* *
1496489 TATCATAAGTCACCAAAA-TA
1 TATCAAAAGTTACCAAAATTA
* *
1496509 GATCAAAAGTTACCAAAATTT
1 TATCAAAAGTTACCAAAATTA
1496530 TATCAAAAGTTA
1 TATCAAAAGTTA
1496542 TTAAAATCAA
Statistics
Matches: 107, Mismatches: 23, Indels: 16
0.73 0.16 0.11
Matches are distributed among these distances:
19 2 0.02
20 33 0.31
21 45 0.42
22 25 0.23
23 2 0.02
ACGTcount: A:0.49, C:0.11, G:0.07, T:0.33
Consensus pattern (21 bp):
TATCAAAAGTTACCAAAATTA
Found at i:1496552 original size:16 final size:16
Alignment explanation
Indices: 1496531--1496563 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1496521 CCAAAATTTT
1496531 ATCAAAAGTTAT-TAAA
1 ATCAAAA-TTATATAAA
1496547 ATCAAAATTATATAAA
1 ATCAAAATTATATAAA
1496563 A
1 A
1496564 AATTATCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.30
Consensus pattern (16 bp):
ATCAAAATTATATAAA
Found at i:1504726 original size:54 final size:56
Alignment explanation
Indices: 1504622--1504741 Score: 172
Period size: 54 Copynumber: 2.2 Consensus size: 56
1504612 TGGATGTAAT
*
1504622 TAAAAAAGTAATTGGAAGTCTTGATGAAAAAAAAGACTTTTAATGTTAATTTAATAA
1 TAAAAAAGTAATTGGAAGTCTTGAT-AAAAAAAAGACTTTTAATATTAATTTAATAA
** * *
1504679 TAAAAAAGTCGTTGGAAGTCTTG-T-TAAAAAGGACTTTTAATATTAATTTAATAA
1 TAAAAAAGTAATTGGAAGTCTTGATAAAAAAAAGACTTTTAATATTAATTTAATAA
1504733 TAAAAAAGT
1 TAAAAAAGT
1504742 TAAACTTGTT
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
54 36 0.62
56 1 0.02
57 21 0.36
ACGTcount: A:0.47, C:0.04, G:0.14, T:0.34
Consensus pattern (56 bp):
TAAAAAAGTAATTGGAAGTCTTGATAAAAAAAAGACTTTTAATATTAATTTAATAA
Found at i:1505193 original size:20 final size:21
Alignment explanation
Indices: 1505152--1505201 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
1505142 TTTATTTAAG
1505152 TATATAAAAAAACATATTAAAA
1 TATATAAAAAAACATA-TAAAA
1505174 TATATATAAAAAACA-A-AAAA
1 TATATA-AAAAAACATATAAAA
*
1505194 TAAATAAA
1 TATATAAA
1505202 TTAAAAAACG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 2 0.08
20 9 0.35
22 7 0.27
23 8 0.31
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (21 bp):
TATATAAAAAAACATATAAAA
Found at i:1510556 original size:27 final size:27
Alignment explanation
Indices: 1510521--1510594 Score: 66
Period size: 28 Copynumber: 2.8 Consensus size: 27
1510511 AAAATTGATT
*
1510521 AAATT-TAATTTAAATTAAATTTTAAA
1 AAATTATAATTTAAATTAAATTTAAAA
* *
1510547 AATTTATAATATTATA-TAATATTTAAAA
1 AAATTATAAT-TTAAATTAA-ATTTAAAA
*
1510575 AAATTA-AA-TTAAATTTAATT
1 AAATTATAATTTAAATTAAATT
1510595 CGATCTAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
25 7 0.18
26 6 0.16
27 9 0.24
28 16 0.42
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
AAATTATAATTTAAATTAAATTTAAAA
Found at i:1511761 original size:2 final size:2
Alignment explanation
Indices: 1511754--1511784 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
1511744 TCTTTTTGCA
1511754 AT AT AT AT AT AT AT AT AT AT ACT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
1511785 TGTGTTTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1517290 original size:23 final size:23
Alignment explanation
Indices: 1517264--1517312 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1517254 TTATTTCAAT
*
1517264 AATTTAAAATTACTATCATATAA
1 AATTTAAAATTACTATCAAATAA
* **
1517287 AATTTTAAATTGTTATCAAATAA
1 AATTTAAAATTACTATCAAATAA
1517310 AAT
1 AAT
1517313 AATATAACTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (23 bp):
AATTTAAAATTACTATCAAATAA
Found at i:1518209 original size:13 final size:14
Alignment explanation
Indices: 1518183--1518211 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1518173 TATATTTATA
1518183 TAATTATAATATTT
1 TAATTATAATATTT
1518197 TAATTAT-ATATTT
1 TAATTATAATATTT
1518210 TA
1 TA
1518212 TTCAAATCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TAATTATAATATTT
Found at i:1524881 original size:13 final size:13
Alignment explanation
Indices: 1524863--1524894 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1524853 ATATAATTAA
1524863 AATATACAAAAAT
1 AATATACAAAAAT
*
1524876 AATATACGAAAAT
1 AATATACAAAAAT
1524889 AATATA
1 AATATA
1524895 ATTTAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.66, C:0.06, G:0.03, T:0.25
Consensus pattern (13 bp):
AATATACAAAAAT
Found at i:1527598 original size:20 final size:20
Alignment explanation
Indices: 1527573--1527610 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1527563 TTTTTTGTGG
* *
1527573 CATTGGTCTGTTTGTTTTCT
1 CATTGGCCTATTTGTTTTCT
1527593 CATTGGCCTATTTGTTTT
1 CATTGGCCTATTTGTTTT
1527611 AATTGTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.08, C:0.16, G:0.18, T:0.58
Consensus pattern (20 bp):
CATTGGCCTATTTGTTTTCT
Found at i:1530995 original size:42 final size:42
Alignment explanation
Indices: 1530936--1531022 Score: 165
Period size: 42 Copynumber: 2.1 Consensus size: 42
1530926 TAAAATTCTC
*
1530936 TGTACTTGGATATATACTATAAGAAAAGTCCTAAGGAAACTA
1 TGTACTTGGATATATACTATAAGAAAACTCCTAAGGAAACTA
1530978 TGTACTTGGATATATACTATAAGAAAACTCCTAAGGAAACTA
1 TGTACTTGGATATATACTATAAGAAAACTCCTAAGGAAACTA
1531020 TGT
1 TGT
1531023 TCAGTAATTA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (42 bp):
TGTACTTGGATATATACTATAAGAAAACTCCTAAGGAAACTA
Found at i:1531874 original size:2 final size:2
Alignment explanation
Indices: 1531867--1531905 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1531857 AAAGGTAGTA
*
1531867 CT CT CT CT CT CC CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1531906 AAACGTTCAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (2 bp):
CT
Found at i:1536308 original size:17 final size:17
Alignment explanation
Indices: 1536286--1536318 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1536276 TAGGAATTTA
1536286 AAAAAATAATACAAAAT
1 AAAAAATAATACAAAAT
*
1536303 AAAAAATAATATAAAA
1 AAAAAATAATACAAAA
1536319 AATGATATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (17 bp):
AAAAAATAATACAAAAT
Found at i:1536377 original size:20 final size:22
Alignment explanation
Indices: 1536337--1536379 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
1536327 AATTTAAAAT
*
1536337 TTTAATAAAAATCATAAATATA
1 TTTAATAAAAATCAAAAATATA
1536359 TTTAAT-AAAAT-AAAAATATA
1 TTTAATAAAAATCAAAAATATA
1536379 T
1 T
1536380 AACATAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.45
21 5 0.25
22 6 0.30
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAATAAAAATCAAAAATATA
Found at i:1536379 original size:22 final size:22
Alignment explanation
Indices: 1536337--1536380 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1536327 AATTTAAAAT
* *
1536337 TTTAATAAAAATCATAAATATA
1 TTTAATAAAAATAAAAAATATA
1536359 TTTAAT-AAAATAAAAATATATA
1 TTTAATAAAAATAAAAA-ATATA
1536381 ACATAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (22 bp):
TTTAATAAAAATAAAAAATATA
Found at i:1536535 original size:81 final size:80
Alignment explanation
Indices: 1536443--1536603 Score: 295
Period size: 80 Copynumber: 2.0 Consensus size: 80
1536433 AAAATATAAG
1536443 AATTATTATGTCTAATTAAATCATCCCGAGCTAATGTGAAAAAAAAAAGTGTGTGACAGATTAAT
1 AATTATTATGTCTAATTAAATCATCCCGAGCTAATGTG-AAAAAAAAAGTGTGTGACAGATTAAT
1536508 AAATATTTTAATTGTT
65 AAATATTTTAATTGTT
* *
1536524 AATTATTATGTCTAATTAAATCATCCTGAGCTAATGTGAAAAAAAAAGTGTGTGACAGATTAATG
1 AATTATTATGTCTAATTAAATCATCCCGAGCTAATGTGAAAAAAAAAGTGTGTGACAGATTAATA
1536589 AATATTTTAATTGTT
66 AATATTTTAATTGTT
1536604 TTGTTTATTT
Statistics
Matches: 78, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
80 41 0.53
81 37 0.47
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.37
Consensus pattern (80 bp):
AATTATTATGTCTAATTAAATCATCCCGAGCTAATGTGAAAAAAAAAGTGTGTGACAGATTAATA
AATATTTTAATTGTT
Found at i:1537128 original size:7 final size:7
Alignment explanation
Indices: 1537116--1537150 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
1537106 TCTTTGTTAA
1537116 TATATAT
1 TATATAT
1537123 TATATAT
1 TATATAT
*
1537130 TATATAC
1 TATATAT
1537137 TATATAT
1 TATATAT
*
1537144 AATATAT
1 TATATAT
1537151 AATACTCTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (7 bp):
TATATAT
Found at i:1537202 original size:22 final size:22
Alignment explanation
Indices: 1537177--1537239 Score: 67
Period size: 23 Copynumber: 2.9 Consensus size: 22
1537167 CATTTTTTTT
1537177 GTTCATTTTTTTTATATTTAAA
1 GTTCATTTTTTTTATATTTAAA
1537199 GTTC-TTTTTTTATATATTTTAAA
1 GTTCATTTTTTT-TATA-TTTAAA
* * *
1537222 ATT-ATTTTTATGATATTT
1 GTTCATTTTTTTTATATTT
1537240 TTTTTATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
21 10 0.29
22 11 0.31
23 14 0.40
ACGTcount: A:0.27, C:0.03, G:0.05, T:0.65
Consensus pattern (22 bp):
GTTCATTTTTTTTATATTTAAA
Found at i:1539659 original size:28 final size:28
Alignment explanation
Indices: 1539628--1539689 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
1539618 TATATTTATT
*
1539628 TATTAAAAATAAATGATAAAACTAGACA
1 TATTAAAAATAAATAATAAAACTAGACA
* * *
1539656 TATTAAAAGTAAGTAATAAAATTAGACA
1 TATTAAAAATAAATAATAAAACTAGACA
*
1539684 TGTTAA
1 TATTAA
1539690 TTTTTATTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.56, C:0.05, G:0.10, T:0.29
Consensus pattern (28 bp):
TATTAAAAATAAATAATAAAACTAGACA
Found at i:1540220 original size:14 final size:14
Alignment explanation
Indices: 1540198--1540227 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1540188 GCAATGAACC
1540198 TAAAATTAATTTAA
1 TAAAATTAATTTAA
*
1540212 TAAATTTAATTTAA
1 TAAAATTAATTTAA
1540226 TA
1 TA
1540228 TAATATTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TAAAATTAATTTAA
Found at i:1540608 original size:23 final size:21
Alignment explanation
Indices: 1540581--1540629 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
1540571 TTATTATATG
**
1540581 TTTTTCTTTCTCTCTTTTTTTTT
1 TTTTTCTTT-T-TCTTTTCATTT
*
1540604 TTTTTGTTTTTCTTTTCATTT
1 TTTTTCTTTTTCTTTTCATTT
1540625 TTTTT
1 TTTTT
1540630 ACCATGCAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 14 0.61
22 1 0.04
23 8 0.35
ACGTcount: A:0.02, C:0.12, G:0.02, T:0.84
Consensus pattern (21 bp):
TTTTTCTTTTTCTTTTCATTT
Found at i:1549404 original size:187 final size:189
Alignment explanation
Indices: 1549053--1549475 Score: 572
Period size: 187 Copynumber: 2.3 Consensus size: 189
1549043 TTTTTTTTTT
** * * *
1549053 AAAA-TTTTGAGATTATTAAAGGTATTTTCTAGCAAAAAATACCTTCGATATTTCACTACTCAAA
1 AAAATTTTTGAGATTATTAAAGGTATTTTCTAGTGAAAAATGCATTCAATATTTCACTACTCAAA
* *
1549117 TTTTAAGACGATTAGTGAAAGCGTTTATTCTAAAAAAAAATGCATTCACTAATTCCTTTTAATTT
66 TTTTAAGAAGATTAGTAAAAGCGTTTATTCTAAAAAAAAATGCATTCACTAATTCCTTTTAATTT
* * *
1549182 ATGTACATAATTATTAAAGGTATTTTTTTAGAACAAACGCCTTTAATAATTTT-TTTAAA
131 ATGTACATAATTATTAAAGGCATTTGTTGAGAACAAACGCCTTTAATAATTTTCTTT-AA
* *
1549241 AAAATTTTTGAGATTATTAAAGGTATTTTTTAGTGAAAAACGCATTCAATATTTCACTACTCAAA
1 AAAATTTTTGAGATTATTAAAGGTATTTTCTAGTGAAAAATGCATTCAATATTTCACTACTCAAA
* *
1549306 TTTTAAGATAG-TTAGTAAAAGTGTTTATT-T-TAAAAAAATGTC-TTCACTAATTCCTTTTAAT
66 TTTTAAGA-AGATTAGTAAAAGCGTTTATTCTAAAAAAAAATG-CATTCACTAATTCCTTTTAAT
* * * *
1549367 TTTTGTACATAATTATTGAAGGCATTTGTTGAGAACAAATGCCTTTAATAATTTTCTTTTA
129 TTATGTACATAATTATTAAAGGCATTTGTTGAGAACAAACGCCTTTAATAATTTTCTTTAA
* * *
1549428 AAAATTTTTG-GAATTATTAAATGTGTCTTCTAGTGAAAAATGCATTCA
1 AAAATTTTTGAG-ATTATTAAAGGTATTTTCTAGTGAAAAATGCATTCA
1549476 CTAATTTCTT
Statistics
Matches: 207, Mismatches: 23, Indels: 11
0.86 0.10 0.05
Matches are distributed among these distances:
186 1 0.00
187 119 0.57
188 9 0.04
189 77 0.37
190 1 0.00
ACGTcount: A:0.37, C:0.10, G:0.11, T:0.41
Consensus pattern (189 bp):
AAAATTTTTGAGATTATTAAAGGTATTTTCTAGTGAAAAATGCATTCAATATTTCACTACTCAAA
TTTTAAGAAGATTAGTAAAAGCGTTTATTCTAAAAAAAAATGCATTCACTAATTCCTTTTAATTT
ATGTACATAATTATTAAAGGCATTTGTTGAGAACAAACGCCTTTAATAATTTTCTTTAA
Found at i:1550405 original size:28 final size:28
Alignment explanation
Indices: 1550350--1550414 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
1550340 GTGGTTTGTC
* * *
1550350 GAATGGTATTATGTAATATTGTTTTGCT
1 GAATGGTATTATATAATATTGGTATGCT
*
1550378 GAATGGTATTGTATAATATTGGTATGCT
1 GAATGGTATTATATAATATTGGTATGCT
* *
1550406 AAATCGTAT
1 GAATGGTAT
1550415 GCTGAATGAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.29, C:0.05, G:0.22, T:0.45
Consensus pattern (28 bp):
GAATGGTATTATATAATATTGGTATGCT
Done.