Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 98 of 335
Found at i:31292384 original size:16 final size:15
Alignment explanation
Indices: 31292339--31292380 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
31292329 CGGCCGGAAC
*
31292339 CCCTCTCTCCTTTCT
1 CCCTCTCTCTTTTCT
31292354 CCCTCTCTCTTTTCT
1 CCCTCTCTCTTTTCT
31292369 CCCT-TCTCTTTT
1 CCCTCTCTCTTTT
31292381 TTCTTTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 8 0.31
15 18 0.69
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (15 bp):
CCCTCTCTCTTTTCT
Found at i:31293004 original size:21 final size:22
Alignment explanation
Indices: 31292980--31293060 Score: 64
Period size: 21 Copynumber: 3.8 Consensus size: 22
31292970 TATACTTTAA
*
31292980 ATATTATATTTT-ATATGTATC
1 ATATTATATTTTAATATGTATT
*
31293001 ATATT-T-TTTTAATGTTGTA-T
1 ATATTATATTTTAAT-ATGTATT
*
31293021 -TATTATATTTTAATATTATATT
1 ATATTATATTTTAATA-TGTATT
*
31293043 ATATATATATTTTCATAT
1 ATAT-TATATTTTAATAT
31293061 TATATTATTT
Statistics
Matches: 47, Mismatches: 5, Indels: 14
0.71 0.08 0.21
Matches are distributed among these distances:
19 8 0.17
20 4 0.09
21 19 0.40
22 1 0.02
23 4 0.09
24 11 0.23
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (22 bp):
ATATTATATTTTAATATGTATT
Found at i:31293039 original size:13 final size:12
Alignment explanation
Indices: 31292980--31293105 Score: 64
Period size: 13 Copynumber: 9.8 Consensus size: 12
31292970 TATACTTTAA
31292980 ATATTATATTTT
1 ATATTATATTTT
31292992 ATATGTATCATATTT
1 ATAT-TAT-AT-TTT
*
31293007 -TTTTA-ATGTTGT
1 ATATTATAT-TT-T
31293019 ATTATTATATTTT
1 A-TATTATATTTT
*
31293032 AATATTATATTAT
1 -ATATTATATTTT
31293045 ATA-TATATTTT
1 ATATTATATTTT
31293056 CATATTATATTATT
1 -ATATTATATT-TT
*
31293070 -TACATATATTTTCT
1 ATA-TTATA-TTT-T
31293084 ATATATATATTTT
1 ATAT-TATATTTT
*
31293097 TTA-TATATT
1 ATATTATATT
31293106 ATCATGTATA
Statistics
Matches: 90, Mismatches: 8, Indels: 33
0.69 0.06 0.25
Matches are distributed among these distances:
11 17 0.19
12 13 0.14
13 30 0.33
14 19 0.21
15 11 0.12
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.61
Consensus pattern (12 bp):
ATATTATATTTT
Found at i:31293093 original size:15 final size:15
Alignment explanation
Indices: 31293042--31293104 Score: 71
Period size: 15 Copynumber: 4.5 Consensus size: 15
31293032 AATATTATAT
31293042 TATATATATATTTTC
1 TATATATATATTTTC
*
31293057 -ATAT-TATATTAT-
1 TATATATATATTTTC
*
31293069 T-TACATATATTTTC
1 TATATATATATTTTC
*
31293083 TATATATATATTTTT
1 TATATATATATTTTC
31293098 TATATAT
1 TATATAT
31293105 TATCATGTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
12 2 0.05
13 14 0.36
14 5 0.13
15 18 0.46
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (15 bp):
TATATATATATTTTC
Found at i:31293121 original size:90 final size:96
Alignment explanation
Indices: 31292939--31293145 Score: 220
Period size: 97 Copynumber: 2.2 Consensus size: 96
31292929 TACTTGGGTC
*
31292939 TTATATTATATATATATTTTTATATGTCATATATACTTTAAATATTATATTTTATATGTATCATA
1 TTATATTATATATATATTTTCATATGTCATATATACTTTAAATATTATATTTTATA-GTATCATA
* * *
31293004 TTTTTTTAATGTTGTATTATTATATTTTAATA
65 TTTTTTTAATATTATATTATTACATTTTAATA
*
31293036 TTATATTATATATATATTTTCATAT-T-ATAT-TA-TTTACATA-TAT-TTTCTATA-TAT-ATA
1 TTATATTATATATATATTTTCATATGTCATATATACTTTAAATATTATATTT-TATAGTATCATA
*
31293093 -TTTTTTATATATTATCATGTA-TACATTTTGATA
65 TTTTTTTA-ATATTAT-AT-TATTACATTTTAATA
31293126 TTACTAGTTATATAT-TATTT
1 TTA-TA-TTATATATATATTT
31293146 ATATATTTCC
Statistics
Matches: 98, Mismatches: 6, Indels: 18
0.80 0.05 0.15
Matches are distributed among these distances:
88 7 0.07
89 8 0.08
90 18 0.18
91 12 0.12
92 15 0.15
93 7 0.07
94 2 0.02
95 4 0.04
96 1 0.01
97 24 0.24
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.58
Consensus pattern (96 bp):
TTATATTATATATATATTTTCATATGTCATATATACTTTAAATATTATATTTTATAGTATCATAT
TTTTTTAATATTATATTATTACATTTTAATA
Found at i:31293171 original size:19 final size:22
Alignment explanation
Indices: 31293141--31293190 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 22
31293131 AGTTATATAT
31293141 TATTTATATATT-TCC-ATGTA
1 TATTTATATATTGTCCTATGTA
31293161 TATTT-TATATTGTCCTATGTACA
1 TATTTATATATTGTCCTATGT--A
31293184 TATTTAT
1 TATTTAT
31293191 GTGGTGTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 6 0.24
20 8 0.32
21 4 0.16
23 6 0.24
24 1 0.04
ACGTcount: A:0.28, C:0.10, G:0.06, T:0.56
Consensus pattern (22 bp):
TATTTATATATTGTCCTATGTA
Found at i:31293389 original size:29 final size:30
Alignment explanation
Indices: 31293345--31293407 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 30
31293335 TTATCTTATG
*
31293345 TATATATTCTTAAATACTAT-TATATGTATA
1 TATATATTCTTAAATACCATAT-TATGTATA
*
31293375 TATATATT-TTTAATACCATATTATGTATA
1 TATATATTCTTAAATACCATATTATGTATA
31293404 TATA
1 TATA
31293408 GTAGTGTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 21 0.70
30 9 0.30
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.51
Consensus pattern (30 bp):
TATATATTCTTAAATACCATATTATGTATA
Found at i:31305798 original size:75 final size:72
Alignment explanation
Indices: 31305707--31306232 Score: 414
Period size: 74 Copynumber: 7.0 Consensus size: 72
31305697 GATGTTTCAT
31305707 TTCTGTTTTCAAAAAAATCAACTCATAATTGCGAGAGGTGAGTTGAGCCTCGAGGCACGCTGAGG
1 TTCT-TTTTCAAAAAAATCAACTCAT-ATTGCGAGAGGTGAGTTGAGCCTC-AGGCACGCTGAGG
31305772 TATTTTCAAA
63 TATTTTCAAA
* ** * *
31305782 TTCTACTTTCAAAAAAATCAACTCATATCACGAGAGGTGAGTTGAGCCT-TGGCTTACG-TGTTG
1 TTCT-TTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGC--ACGCTG-AG
* *
31305845 AGTCACTTTCAAT
62 -GT-ATTTTCAAA
* * *
31305858 TTCTGTTTT------TATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTAAGGT
1 TTCT-TTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGGCACGCTGAGGT
31305917 ATTTTC-AA
64 ATTTTCAAA
* * *
31305925 TTGCTGTTTGTC--AAAAATCAACTCATAATTGTGAGAGGTGAGTTGAGCCTCAGGGTACACTGA
1 TT-CT-TTT-TCAAAAAAATCAACTCAT-ATTGCGAGAGGTGAGTTGAGCCTCA-GGCACGCTGA
* *
31305988 GGTAGTTTCAAT
61 GGTATTTTCAAA
* *
31306000 TTCTGCTTTCTAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGG
1 TTCT-TTTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-CACGCTGAGG
**
31306065 TATTTTCGATT
63 TATTTTC-AAA
*
31306076 TTCGTTTTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
1 TTC-TTTTTC-A---A--------AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AG
31306141 GCACGCTGAGGTATTTTC-AA
52 GCACGCTGAGGTATTTTCAAA
*
31306161 TTACTATTTGTC--AAAAATCAACTCATAATTGCGAGAGGTGAGTTGAGCCTCAGGGTACGCTGA
1 TT-CT-TTT-TCAAAAAAATCAACTCAT-ATTGCGAGAGGTGAGTTGAGCCTCA-GGCACGCTGA
31306224 GGTATTTTC
61 GGTATTTTC
31306233 GATTTCCGTT
Statistics
Matches: 370, Mismatches: 41, Indels: 81
0.75 0.08 0.16
Matches are distributed among these distances:
67 3 0.01
68 11 0.03
69 3 0.01
70 35 0.09
71 1 0.00
72 6 0.02
73 28 0.08
74 112 0.30
75 66 0.18
76 38 0.10
77 1 0.00
79 1 0.00
85 3 0.01
86 4 0.01
87 56 0.15
88 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (72 bp):
TTCTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGCACGCTGAGGTAT
TTTCAAA
Found at i:31306228 original size:161 final size:160
Alignment explanation
Indices: 31305918--31306469 Score: 624
Period size: 161 Copynumber: 3.3 Consensus size: 160
31305908 CGCTAAGGTA
** * * * *
31305918 TTTTCAATTGCTGTTTGTCAAAAATCAACTCATAATTGTGAGAGGTGAGTTGAGCCTCAGGGTAC
1 TTTTCAATTTATGTTTTTCAAAAATCAACTCAT-ATTGCGAGAGGTGAGTTGAGCCTCGGGGCAC
* * * * *
31305983 ACTGAGGTAGTTTCAATTTCTGCTTTCTAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGC
65 GCTGAGGTATTTTCAATTACT-ATTTCT-CAAAAATCAACTCATATTACGAGAGGTGAGTTGAGC
**
31306048 CTCAGGACACGCTGAGGTATTTTCGATTTTCGT
128 CTCAGGGTACGCTGAGGTATTTTCGATTTTCGT
31306081 TTTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACG
1 TTTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACG
* *
31306146 CTGAGGTATTTTCAATTACTATTTGTCAAAAATCAACTCATAATTGCGAGAGGTGAGTTGAGCCT
66 CTGAGGTATTTTCAATTACTATTTCTCAAAAATCAACTCAT-ATTACGAGAGGTGAGTTGAGCCT
*
31306211 CAGGGTACGCTGAGGTATTTTCGATTTCCGT
130 CAGGGTACGCTGAGGTATTTTCGATTTTCGT
*
31306242 TTTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACG
1 TTTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACG
* * *
31306307 CTGAGTTATTCTCAATTAATGTTTTTCAATTTATACTTTTCAAAAATCAACTCATATTACGAGAG
66 CTGAGGTATTTTCAATT-A-------C----TAT--TTCTCAAAAATCAACTCATATTACGAGAG
* ***
31306372 GTGAGTTGAGCCTCA-GGTCACATGCCGAGGTATTTTC-AAAATCTGT
117 GTGAGTTGAGCCTCAGGGT-AC--GCTGAGGTATTTTCGATTTTC-GT
* * * * *
31306418 TTTGCAAATTCTG-TTTTCAAAAATCAACTCATATTGCAAGAAGTGAGTTGAG
1 TTTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
31306470 TCTTTGCTCA
Statistics
Matches: 339, Mismatches: 31, Indels: 26
0.86 0.08 0.07
Matches are distributed among these distances:
160 14 0.04
161 133 0.39
162 47 0.14
163 30 0.09
169 1 0.00
173 6 0.02
174 26 0.08
175 57 0.17
176 25 0.07
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (160 bp):
TTTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACG
CTGAGGTATTTTCAATTACTATTTCTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTC
AGGGTACGCTGAGGTATTTTCGATTTTCGT
Found at i:31306308 original size:87 final size:88
Alignment explanation
Indices: 31306154--31306469 Score: 379
Period size: 87 Copynumber: 3.6 Consensus size: 88
31306144 CGCTGAGGTA
* *
31306154 TTTTCAA-TTACTATTTGTCAAAAATCAACTCATAATTGCGAGAGGTGAGTTGAGCCTCAGGG-T
1 TTTTCAATTTA-TATTTTTCAAAAATCAACTCAT-ATTGCGAGAGGTGAGTTGAGCCTCAGGGAC
* *
31306217 ACGCTGAGGTATTTTCGATTTCCGT
64 ACGCTGAGGTATTTTCAATTTCTGT
*
31306242 TTTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGGACAC
1 TTTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGACAC
* * **
31306306 GCTGAGTTATTCTCAATTAATGT
66 GCTGAGGTATTTTCAATTTCTGT
* * *
31306329 TTTTCAATTTATACTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGTCACA
1 TTTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-GACA
* * **
31306394 TGCCGAGGTATTTTCAAAATCTGT
65 CGCTGAGGTATTTTCAATTTCTGT
* * * * * *
31306418 TTTGCAAATTCT-GTTTTCAAAAATCAACTCATATTGCAAGAAGTGAGTTGAG
1 TTTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
31306470 TCTTTGCTCA
Statistics
Matches: 196, Mismatches: 28, Indels: 8
0.84 0.12 0.03
Matches are distributed among these distances:
86 3 0.02
87 97 0.49
88 65 0.33
89 31 0.16
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.35
Consensus pattern (88 bp):
TTTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGACAC
GCTGAGGTATTTTCAATTTCTGT
Found at i:31306430 original size:14 final size:13
Alignment explanation
Indices: 31306404--31306439 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
31306394 TGCCGAGGTA
31306404 TTTTCAAAATCTG
1 TTTTCAAAATCTG
*
31306417 TTTTGCAAATTCTG
1 TTTT-CAAAATCTG
31306431 TTTTCAAAA
1 TTTTCAAAA
31306440 ATCAACTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (13 bp):
TTTTCAAAATCTG
Found at i:31306445 original size:175 final size:175
Alignment explanation
Indices: 31306154--31306469 Score: 453
Period size: 175 Copynumber: 1.8 Consensus size: 175
31306144 CGCTGAGGTA
*
31306154 TTTTCAATTACTATTTGTCAAAAATCAACTCATAATTGCGAGAGGTGAGTTGAGCCTCAGGGTAC
1 TTTTCAATTACTATTTGTCAAAAATCAACTCATAATTACGAGAGGTGAGTTGAGCCTCAGGGTAC
* * ** * * *
31306219 GCTGAGGTATTTTCGATTTCCGTTTTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGA
66 GCCGAGGTATTTTCAAAATCCGTTTTGCAAATTATGTTTTTCAAAAATCAACTCATATTGCAAGA
*
31306284 GGTGAGTTGAGCCTCGGGACACGCTGAGTTATTCTCAATTAATGT
131 AGTGAGTTGAGCCTCGGGACACGCTGAGTTATTCTCAATTAATGT
31306329 TTTTCAATTTA-TACTTT-TCAAAAATCAACTCAT-ATTACGAGAGGTGAGTTGAGCCTCA-GGT
1 TTTTCAA-TTACTA-TTTGTCAAAAATCAACTCATAATTACGAGAGGTGAGTTGAGCCTCAGGGT
* *
31306390 CACATGCCGAGGTATTTTCAAAATCTGTTTTGCAAATTCTG-TTTTCAAAAATCAACTCATATTG
64 -AC--GCCGAGGTATTTTCAAAATCCGTTTTGCAAATTATGTTTTTCAAAAATCAACTCATATTG
31306454 CAAGAAGTGAGTTGAG
126 CAAGAAGTGAGTTGAG
31306470 TCTTTGCTCA
Statistics
Matches: 125, Mismatches: 11, Indels: 10
0.86 0.08 0.07
Matches are distributed among these distances:
173 3 0.02
174 26 0.21
175 62 0.50
176 34 0.27
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.35
Consensus pattern (175 bp):
TTTTCAATTACTATTTGTCAAAAATCAACTCATAATTACGAGAGGTGAGTTGAGCCTCAGGGTAC
GCCGAGGTATTTTCAAAATCCGTTTTGCAAATTATGTTTTTCAAAAATCAACTCATATTGCAAGA
AGTGAGTTGAGCCTCGGGACACGCTGAGTTATTCTCAATTAATGT
Found at i:31307682 original size:9 final size:8
Alignment explanation
Indices: 31307669--31307693 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
31307659 ATACAATATT
31307669 TAAAAAAA
1 TAAAAAAA
31307677 TAAAAAAA
1 TAAAAAAA
31307685 TAAAAAAA
1 TAAAAAAA
31307693 T
1 T
31307694 CTAAAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (8 bp):
TAAAAAAA
Found at i:31308382 original size:32 final size:32
Alignment explanation
Indices: 31308346--31308415 Score: 74
Period size: 32 Copynumber: 2.2 Consensus size: 32
31308336 ACTTGGGTAT
*
31308346 TATATTA-TATATATA-TATATATTTATATGTCA
1 TATATTACTATAAATATTATAT-TTTATATGT-A
*
31308378 TATA-TACTTTAAATATTATATTTTATATGTA
1 TATATTACTATAAATATTATATTTTATATGTA
31308409 TCATATT
1 T-ATATT
31308416 TTTTTAATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
31 4 0.12
32 22 0.69
33 6 0.19
ACGTcount: A:0.39, C:0.04, G:0.03, T:0.54
Consensus pattern (32 bp):
TATATTACTATAAATATTATATTTTATATGTA
Found at i:31308404 original size:23 final size:22
Alignment explanation
Indices: 31308343--31308405 Score: 63
Period size: 25 Copynumber: 2.7 Consensus size: 22
31308333 TATACTTGGG
*
31308343 TATTATATTATATATATATATA
1 TATTATATTATATATATATAAA
*
31308365 TATTTATATGTCATATATACTTTAAA
1 TA-TTATAT-T-ATATATA-TATAAA
*
31308391 TATTATATTTTATAT
1 TATTATATTATATAT
31308406 GTATCATATT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
22 2 0.06
23 11 0.32
24 2 0.06
25 13 0.38
26 6 0.18
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.56
Consensus pattern (22 bp):
TATTATATTATATATATATAAA
Found at i:31308414 original size:21 final size:21
Alignment explanation
Indices: 31308391--31308463 Score: 66
Period size: 21 Copynumber: 3.5 Consensus size: 21
31308381 ATACTTTAAA
31308391 TATTATATTTTATATGTATCA-
1 TATTATATTTTATATGTAT-AT
*
31308412 TATT-T-TTTTA-ATGTTGTAT
1 TATTATATTTTATATG-TATAT
31308431 TATTATATTTTAATAT-TATAT
1 TATTATATTTT-ATATGTATAT
31308452 TATATATATTTT
1 TAT-TATATTTT
31308464 TTCATATTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 13
0.74 0.03 0.22
Matches are distributed among these distances:
18 4 0.09
19 11 0.26
20 2 0.05
21 15 0.35
22 9 0.21
23 2 0.05
ACGTcount: A:0.32, C:0.01, G:0.04, T:0.63
Consensus pattern (21 bp):
TATTATATTTTATATGTATAT
Found at i:31308439 original size:24 final size:25
Alignment explanation
Indices: 31308411--31308478 Score: 74
Period size: 24 Copynumber: 2.9 Consensus size: 25
31308401 TATATGTATC
* *
31308411 ATATTTTTTTAATGTTGTATTAT-T
1 ATATTTTTTTAATATTATATTATAT
31308435 ATA---TTTTAATATTATATTATAT
1 ATATTTTTTTAATATTATATTATAT
*
31308457 ATA-TTTTTTCATATTATATTAT
1 ATATTTTTTTAATATTATATTAT
31308479 GTACATATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
21 15 0.39
22 4 0.11
24 19 0.50
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.63
Consensus pattern (25 bp):
ATATTTTTTTAATATTATATTATAT
Found at i:31308498 original size:28 final size:24
Alignment explanation
Indices: 31308400--31308498 Score: 71
Period size: 24 Copynumber: 4.0 Consensus size: 24
31308390 ATATTATATT
* *
31308400 TTATATGTATCATAT-TTTTTTAATG
1 TTATAT-TAT-ATATATTTTCTAATA
*
31308425 TTGTATTAT-TATA-TTT-TAATA
1 TTATATTATATATATTTTCTAATA
* *
31308446 TTATATTATATATATTTTTTCATA
1 TTATATTATATATATTTTCTAATA
31308470 TTATATTATGTACATATATTTTCTAATA
1 TTATATTA--T--ATATATTTTCTAATA
31308498 T
1 T
31308499 ATTTTTTTTA
Statistics
Matches: 60, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
21 12 0.20
22 10 0.17
23 3 0.05
24 15 0.25
25 5 0.08
26 1 0.02
28 14 0.23
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (24 bp):
TTATATTATATATATTTTCTAATA
Found at i:31308582 original size:21 final size:24
Alignment explanation
Indices: 31308545--31308601 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 24
31308535 TTACTAGTTA
31308545 TATATTATTTATATATT-TCC-ATG
1 TATA-TATTTATATATTGTCCTATG
31308568 TATATATTT-TATATTGTCCTATG
1 TATATATTTATATATTGTCCTATG
*
31308591 TACATATTTAT
1 TATATATTTAT
31308602 GTGGTGTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 6 0.20
22 8 0.27
23 15 0.50
24 1 0.03
ACGTcount: A:0.30, C:0.09, G:0.05, T:0.56
Consensus pattern (24 bp):
TATATATTTATATATTGTCCTATG
Found at i:31308801 original size:28 final size:28
Alignment explanation
Indices: 31308758--31308819 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
31308748 TTATCTTATG
31308758 TATATATTCTTAAATA-C-TATTATATGTA
1 TATATATTCTTAAATATCATA-T-TATGTA
* *
31308786 TATATATTTTTTAATATCATATTATGTA
1 TATATATTCTTAAATATCATATTATGTA
31308814 TATATA
1 TATATA
31308820 GTAGTGTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 26 0.87
29 2 0.07
30 2 0.07
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (28 bp):
TATATATTCTTAAATATCATATTATGTA
Found at i:31312257 original size:2 final size:2
Alignment explanation
Indices: 31312250--31312278 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
31312240 AACCAGAACA
31312250 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
31312279 ATCTAAAAAA
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:31315382 original size:21 final size:20
Alignment explanation
Indices: 31315341--31315382 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
31315331 TTAATTATAT
*
31315341 AATAATAAATAATTTAATTA
1 AATAATAAATAATATAATTA
*
31315361 AATAATAAAATAATATATTTA
1 AATAAT-AAATAATATAATTA
31315382 A
1 A
31315383 CTTAATGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AATAATAAATAATATAATTA
Found at i:31320863 original size:24 final size:24
Alignment explanation
Indices: 31320810--31320865 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
31320800 TTTGTTCGTA
*
31320810 AACATATTCAATTATATGTTCATG
1 AACATGTTCAATTATATGTTCATG
*
31320834 AACATGTTCAATTATATGTTCATT
1 AACATGTTCAATTATATGTTCATG
31320858 AACATGTT
1 AACATGTT
31320866 TGAAACACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.43
Consensus pattern (24 bp):
AACATGTTCAATTATATGTTCATG
Found at i:31320887 original size:34 final size:34
Alignment explanation
Indices: 31320849--31320931 Score: 89
Period size: 34 Copynumber: 2.4 Consensus size: 34
31320839 GTTCAATTAT
*
31320849 ATGTTCATTAACATGTTTGAA-ACACATTC-CTTTA
1 ATGTTCATGAACATGTTT-AAGACACATTCGC-TTA
* *
31320883 ATGTTCGTGAACATGTTTAAGACACGTTCGCTTA
1 ATGTTCATGAACATGTTTAAGACACATTCGCTTA
**
31320917 ATGTTTGTGAACATG
1 ATGTTCATGAACATG
31320932 GTCAATTAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
33 2 0.05
34 40 0.93
35 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.39
Consensus pattern (34 bp):
ATGTTCATGAACATGTTTAAGACACATTCGCTTA
Found at i:31321143 original size:2 final size:2
Alignment explanation
Indices: 31321136--31321164 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
31321126 GTGGTATTTG
31321136 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
31321165 AATACATTAA
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:31321357 original size:31 final size:31
Alignment explanation
Indices: 31321322--31321384 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
31321312 AGTATTTTTC
*
31321322 TTCTAATTTTCTTTTTTTCAAATTTTAACAT
1 TTCTAATTTTCTTTTTTTCAAATTTCAACAT
*
31321353 TTCTAATTTTGTTTTTTTCAAATTTCAACAT
1 TTCTAATTTTCTTTTTTTCAAATTTCAACAT
31321384 T
1 T
31321385 GTACTAACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.13, G:0.02, T:0.60
Consensus pattern (31 bp):
TTCTAATTTTCTTTTTTTCAAATTTCAACAT
Found at i:31325396 original size:6 final size:6
Alignment explanation
Indices: 31325385--31325409 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
31325375 ACAACCGATG
31325385 CCGGTT CCGGTT CCGGTT CCGGTT C
1 CCGGTT CCGGTT CCGGTT CCGGTT C
31325410 TGGTGCTGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.36, G:0.32, T:0.32
Consensus pattern (6 bp):
CCGGTT
Found at i:31325990 original size:17 final size:17
Alignment explanation
Indices: 31325952--31325990 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
31325942 TGAAACTTTA
*
31325952 AAATTATATATATTTTT
1 AAATTATATATATATTT
*
31325969 TAATTATATATATATTT
1 AAATTATATATATATTT
31325986 AAATT
1 AAATT
31325991 TTAAGTGATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AAATTATATATATATTT
Found at i:31329254 original size:21 final size:20
Alignment explanation
Indices: 31329229--31329267 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
31329219 TTTTTAAAAT
*
31329229 TTTAAAGAAACTGATTATATA
1 TTTAAAGAAAATG-TTATATA
31329250 TTTAAAGAAAATGTTATA
1 TTTAAAGAAAATGTTATA
31329268 AATAATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.49, C:0.03, G:0.10, T:0.38
Consensus pattern (20 bp):
TTTAAAGAAAATGTTATATA
Found at i:31329588 original size:6 final size:6
Alignment explanation
Indices: 31329577--31329603 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
31329567 AAATTTACTT
31329577 TTTCTA TTTCTA TTTCTA TTTCTA TTT
1 TTTCTA TTTCTA TTTCTA TTTCTA TTT
31329604 TCACTCACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTCTA
Found at i:31334972 original size:31 final size:31
Alignment explanation
Indices: 31334936--31334996 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
31334926 TCTTTAGGTT
31334936 GATGGATGAATTTTATTCACTCATTTACTTG
1 GATGGATGAATTTTATTCACTCATTTACTTG
31334967 GATGGATGAATTTTATTCACTCATTTACTT
1 GATGGATGAATTTTATTCACTCATTTACTT
31334997 AGGAATGTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.46
Consensus pattern (31 bp):
GATGGATGAATTTTATTCACTCATTTACTTG
Found at i:31335798 original size:17 final size:17
Alignment explanation
Indices: 31335778--31335810 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
31335768 AACATATTGT
31335778 ATTTATTTT-ATAATTTG
1 ATTT-TTTTCATAATTTG
31335795 ATTTTTTTCATAATTT
1 ATTTTTTTCATAATTT
31335811 TCTCATTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.67
Consensus pattern (17 bp):
ATTTTTTTCATAATTTG
Found at i:31335911 original size:3 final size:3
Alignment explanation
Indices: 31335903--31335941 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
31335893 TTTTTCAGAC
31335903 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
31335942 GTTTTAAGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:31336651 original size:20 final size:19
Alignment explanation
Indices: 31336626--31336679 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
31336616 ATTTGTGTGC
31336626 TTATTATATTTATAATATAA
1 TTATTATATTT-TAATATAA
* *
31336646 TTATTAATATTTTTATTTAA
1 TTATT-ATATTTTAATATAA
*
31336666 TTATTATATATTAA
1 TTATTATATTTTAA
31336680 AAATAATATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 7 0.24
20 16 0.55
21 6 0.21
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTATTATATTTTAATATAA
Found at i:31339842 original size:17 final size:18
Alignment explanation
Indices: 31339820--31339853 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
31339810 AGTATATTTT
*
31339820 AAAATTTTTAT-TTTATG
1 AAAATTATTATGTTTATG
31339837 AAAATTATTATGTTTAT
1 AAAATTATTATGTTTAT
31339854 TGTGATAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (18 bp):
AAAATTATTATGTTTATG
Found at i:31345258 original size:12 final size:12
Alignment explanation
Indices: 31345241--31345266 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
31345231 AAAAAGATTG
31345241 TATATATATGTA
1 TATATATATGTA
31345253 TATATATATGTA
1 TATATATATGTA
31345265 TA
1 TA
31345267 GGGTGTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
TATATATATGTA
Found at i:31345393 original size:2 final size:2
Alignment explanation
Indices: 31345386--31345417 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
31345376 TAGCATTAAA
31345386 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
31345418 GAAAAGATAT
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):
AT
Found at i:31345606 original size:17 final size:16
Alignment explanation
Indices: 31345575--31345612 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
31345565 ATGCTGATAA
31345575 TAATAATAATAAAATG
1 TAATAATAATAAAATG
31345591 CTAATAAGTAAT-AAATG
1 -TAATAA-TAATAAAATG
31345608 TAATA
1 TAATA
31345613 TAACACTAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 5 0.25
17 11 0.55
18 4 0.20
ACGTcount: A:0.58, C:0.03, G:0.08, T:0.32
Consensus pattern (16 bp):
TAATAATAATAAAATG
Found at i:31346035 original size:18 final size:18
Alignment explanation
Indices: 31345998--31346037 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
31345988 AGGTAACGAA
* *
31345998 AATAATACTGACACTGAC
1 AATAATACTGACAATAAC
*
31346016 AATAATACTGATAATAAC
1 AATAATACTGACAATAAC
31346034 AATA
1 AATA
31346038 TATTAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.53, C:0.15, G:0.07, T:0.25
Consensus pattern (18 bp):
AATAATACTGACAATAAC
Found at i:31346070 original size:26 final size:26
Alignment explanation
Indices: 31346016--31346089 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 26
31346006 TGACACTGAC
*
31346016 AATAATACTGATAATAACAATATATT
1 AATAATACTGATAATAACAATATAAT
*
31346042 AATAATACTGAT-ATATTC-ATCATAAT
1 AATAATACTGATAATA-ACAAT-ATAAT
* * *
31346068 AATAATAATAATAATAATAATA
1 AATAATACTGATAATAACAATA
31346090 ATAGTAGAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
25 5 0.13
26 28 0.74
27 5 0.13
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.35
Consensus pattern (26 bp):
AATAATACTGATAATAACAATATAAT
Found at i:31346142 original size:3 final size:3
Alignment explanation
Indices: 31346063--31346122 Score: 61
Period size: 3 Copynumber: 20.0 Consensus size: 3
31346053 TATATTCATC
* * *
31346063 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA GA-A ATA ACA ATC
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA
31346108 AT- ATA AGTA ATA ATA
1 ATA ATA A-TA ATA ATA
31346123 GTACGCATAG
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
2 3 0.06
3 42 0.88
4 3 0.06
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:31349563 original size:17 final size:19
Alignment explanation
Indices: 31349518--31349563 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 19
31349508 AGTAGAATTA
31349518 ATTTTA-TATTATTTTGTG
1 ATTTTATTATTATTTTGTG
31349536 ATTTT-TT-TTATTTT-T-
1 ATTTTATTATTATTTTGTG
31349551 ATTTTATTATTAT
1 ATTTTATTATTAT
31349564 CGGATCAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
15 5 0.20
16 3 0.12
17 11 0.44
18 6 0.24
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (19 bp):
ATTTTATTATTATTTTGTG
Found at i:31353061 original size:25 final size:26
Alignment explanation
Indices: 31353033--31353102 Score: 106
Period size: 26 Copynumber: 2.7 Consensus size: 26
31353023 TCAGCATTGT
31353033 CCACGACCCTCAA-GTATTGGACTGC
1 CCACGACCCTCAAGGTATTGGACTGC
*
31353058 CCACGACCTTCAAGGTATTGGACTGC
1 CCACGACCCTCAAGGTATTGGACTGC
* *
31353084 CCACGATCCTCTAGGTATT
1 CCACGACCCTCAAGGTATT
31353103 AGGGCTAACA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
25 12 0.30
26 28 0.70
ACGTcount: A:0.23, C:0.33, G:0.20, T:0.24
Consensus pattern (26 bp):
CCACGACCCTCAAGGTATTGGACTGC
Found at i:31357399 original size:31 final size:32
Alignment explanation
Indices: 31357364--31357424 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
31357354 TTCATACTTT
31357364 ATATTTCA-TAACACTGGGCCGAAGCCTTTTC
1 ATATTTCATTAACACTGGGCCGAAGCCTTTTC
** *
31357395 ATATTTCATTATTACTGGGCCGATGCCTTT
1 ATATTTCATTAACACTGGGCCGAAGCCTTT
31357425 ACTGTAAACG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 8 0.31
32 18 0.69
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (32 bp):
ATATTTCATTAACACTGGGCCGAAGCCTTTTC
Found at i:31357738 original size:24 final size:24
Alignment explanation
Indices: 31357618--31357737 Score: 188
Period size: 24 Copynumber: 5.0 Consensus size: 24
31357608 GCTTTATCAT
*
31357618 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
*
31357643 ATAACTGGGGCAAAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
31357667 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
31357691 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
31357715 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
31357738 GTACTTCCTC
Statistics
Matches: 90, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
24 78 0.87
25 12 0.13
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:31357818 original size:11 final size:11
Alignment explanation
Indices: 31357787--31357842 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
31357777 TTATAAATAC
31357787 ATCATGTGCAT
1 ATCATGTGCAT
*
31357798 ATCA--TACAT
1 ATCATGTGCAT
31357807 ATCATGTGCAT
1 ATCATGTGCAT
*
31357818 ATCA--TACAT
1 ATCATGTGCAT
*
31357827 GTCATGTGCAT
1 ATCATGTGCAT
31357838 ATCAT
1 ATCAT
31357843 ACATGCCATG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:31357847 original size:20 final size:20
Alignment explanation
Indices: 31357788--31357853 Score: 114
Period size: 20 Copynumber: 3.3 Consensus size: 20
31357778 TATAAATACA
*
31357788 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATG
31357808 TCATGTGCATATCATACATG
1 TCATGTGCATATCATACATG
31357828 TCATGTGCATATCATACATG
1 TCATGTGCATATCATACATG
*
31357848 CCATGT
1 TCATGT
31357854 TTATCAAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (20 bp):
TCATGTGCATATCATACATG
Found at i:31357922 original size:25 final size:25
Alignment explanation
Indices: 31357890--31357939 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
31357880 ATACCTAAAC
* * *
31357890 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
31357915 CCTAGGGGCAAAACGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
31357940 TGTTATAAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:31361845 original size:20 final size:20
Alignment explanation
Indices: 31361798--31361836 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
31361788 ATACCTTCTA
31361798 AATTTTTATAATATTTTTTC
1 AATTTTTATAATATTTTTTC
31361818 AATTTTTAT-ATATTATTTT
1 AATTTTTATAATATT-TTTT
31361837 GATTTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (20 bp):
AATTTTTATAATATTTTTTC
Found at i:31362255 original size:23 final size:25
Alignment explanation
Indices: 31362196--31362256 Score: 65
Period size: 23 Copynumber: 2.6 Consensus size: 25
31362186 ATATATATAA
* **
31362196 AAAAGTTTAAAAATATTATTTTCAT
1 AAAATTTTAAAAATATTATAATCAT
*
31362221 AAAATTCT-AAAATA-TATAATCAT
1 AAAATTTTAAAAATATTATAATCAT
31362244 -AAATTTTAAAAAT
1 AAAATTTTAAAAAT
31362257 TCAAAATAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
22 6 0.20
23 12 0.40
24 6 0.20
25 6 0.20
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (25 bp):
AAAATTTTAAAAATATTATAATCAT
Found at i:31362283 original size:21 final size:19
Alignment explanation
Indices: 31362259--31362300 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
31362249 TTAAAAATTC
31362259 AAAATAATA-TATAAAAACT
1 AAAA-AATATTATAAAAACT
* *
31362278 AAAAAATGTTATAAAAATT
1 AAAAAATATTATAAAAACT
31362297 AAAA
1 AAAA
31362301 GGTATCTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.26
Consensus pattern (19 bp):
AAAAAATATTATAAAAACT
Found at i:31367100 original size:46 final size:46
Alignment explanation
Indices: 31367047--31367171 Score: 216
Period size: 46 Copynumber: 2.7 Consensus size: 46
31367037 GAGTAAGCAC
* *
31367047 CATTGAGATAGCTTC-GACTATGTATTGGCACTTTGTGTGGGAGATT
1 CATTGAGATAGCTTCAG-CTATGTATTGGCACTTCGTGTGCGAGATT
31367093 CATTGAGATAGCTTCAGCTATGTATTGGCACTTCGTGTGCGAGATT
1 CATTGAGATAGCTTCAGCTATGTATTGGCACTTCGTGTGCGAGATT
31367139 CATTGAGATAGCTTCAGCTATGTATTGGCACTT
1 CATTGAGATAGCTTCAGCTATGTATTGGCACTT
31367172 AGGGTGCAAG
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
46 75 0.99
47 1 0.01
ACGTcount: A:0.22, C:0.16, G:0.26, T:0.36
Consensus pattern (46 bp):
CATTGAGATAGCTTCAGCTATGTATTGGCACTTCGTGTGCGAGATT
Found at i:31369561 original size:25 final size:25
Alignment explanation
Indices: 31369533--31369606 Score: 85
Period size: 25 Copynumber: 3.0 Consensus size: 25
31369523 GAAGCTTCTC
*
31369533 TGAGCTGAATAATAGGAAGCTCATG
1 TGAGCTAAATAATAGGAAGCTCATG
* * * *
31369558 TGAGTTAAATTATGGGAAGCTTATG
1 TGAGCTAAATAATAGGAAGCTCATG
* *
31369583 AGAGCTAAATATTAGGAAGCTCAT
1 TGAGCTAAATAATAGGAAGCTCAT
31369607 AAGAGCTGTG
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.36, C:0.09, G:0.26, T:0.28
Consensus pattern (25 bp):
TGAGCTAAATAATAGGAAGCTCATG
Found at i:31372964 original size:41 final size:40
Alignment explanation
Indices: 31372871--31372951 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 40
31372861 ATATGTGAAA
* *
31372871 AAGGACTAAATTGTAATGTTTAAATTATTATTTTTGTACAT
1 AAGGAC-AAATTGTAATGTTTAAATTATTAATTTTGTAAAT
31372912 AAGGACTAAATTGTAATGTTTAAATTATTAATTTTG-AAAT
1 AAGGAC-AAATTGTAATGTTTAAATTATTAATTTTGTAAAT
31372952 TGATGTGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
40 3 0.08
41 35 0.92
ACGTcount: A:0.40, C:0.04, G:0.12, T:0.44
Consensus pattern (40 bp):
AAGGACAAATTGTAATGTTTAAATTATTAATTTTGTAAAT
Found at i:31384084 original size:15 final size:15
Alignment explanation
Indices: 31384064--31384115 Score: 79
Period size: 15 Copynumber: 3.5 Consensus size: 15
31384054 CGATGAATTT
31384064 ATTGAATTTATATTG
1 ATTGAATTTATATTG
* *
31384079 ATTGAAATTATTTTG
1 ATTGAATTTATATTG
31384094 ATTGAA-TTATATTG
1 ATTGAATTTATATTG
31384108 ATTGAATT
1 ATTGAATT
31384116 ATAATATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
14 13 0.39
15 20 0.61
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:31384103 original size:14 final size:14
Alignment explanation
Indices: 31384064--31384118 Score: 83
Period size: 14 Copynumber: 3.8 Consensus size: 14
31384054 CGATGAATTT
31384064 ATTGAATTTATATTG
1 ATTGAA-TTATATTG
*
31384079 ATTGAAATTATTTTG
1 ATTG-AATTATATTG
31384094 ATTGAATTATATTG
1 ATTGAATTATATTG
31384108 ATTGAATTATA
1 ATTGAATTATA
31384119 ATATATATGA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
14 20 0.54
15 15 0.41
16 2 0.05
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (14 bp):
ATTGAATTATATTG
Found at i:31384516 original size:23 final size:23
Alignment explanation
Indices: 31384486--31384572 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
31384476 GCTTTATCGA
* *
31384486 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTCATGTGTCGTATT
*
31384509 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACCTCATGTGTCGTATT
*
31384530 TCAGGCACCTCGTGTGTCGT-TT
1 TCAGGCACCTCATGTGTCGTATT
* *
31384552 T-AGGCACTTTATGTGTCGTAT
1 TCAGGCACCTCATGTGTCGTAT
31384573 ACTGATCAGG
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
21 35 0.64
22 2 0.04
23 18 0.33
ACGTcount: A:0.15, C:0.22, G:0.25, T:0.38
Consensus pattern (23 bp):
TCAGGCACCTCATGTGTCGTATT
Found at i:31386379 original size:2 final size:2
Alignment explanation
Indices: 31386372--31386403 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
31386362 TTATGAAATA
31386372 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
31386404 CAGTCAGAGA
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):
AT
Found at i:31390087 original size:15 final size:15
Alignment explanation
Indices: 31390067--31390123 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
31390057 CGATGAATTT
*
31390067 ATTGAATTTATATTG
1 ATTGAAATTATATTG
*
31390082 ATTGAAATTATTTTG
1 ATTGAAATTATATTG
31390097 ATTGAAATTATATTG
1 ATTGAAATTATATTG
31390112 ATTG-AATTATAT
1 ATTGAAATTATAT
31390124 AATATATATG
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
14 8 0.21
15 31 0.79
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (15 bp):
ATTGAAATTATATTG
Found at i:31390526 original size:23 final size:23
Alignment explanation
Indices: 31390496--31390582 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
31390486 GCTTTACTGA
* *
31390496 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTCATGTGTCGTATT
*
31390519 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACCTCATGTGTCGTATT
*
31390540 TCAGGCACCTCGTGTGTCGT-TT
1 TCAGGCACCTCATGTGTCGTATT
* *
31390562 T-AGGCACTTTATGTGTCGTAT
1 TCAGGCACCTCATGTGTCGTAT
31390583 ACTGATCAGG
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
21 35 0.64
22 2 0.04
23 18 0.33
ACGTcount: A:0.15, C:0.22, G:0.25, T:0.38
Consensus pattern (23 bp):
TCAGGCACCTCATGTGTCGTATT
Found at i:31399229 original size:20 final size:20
Alignment explanation
Indices: 31399206--31399243 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
31399196 GTGGGGGTCA
31399206 ACACACCCATGTGGAAGGGC
1 ACACACCCATGTGGAAGGGC
* *
31399226 ACACGCCCGTGTGGAAGG
1 ACACACCCATGTGGAAGG
31399244 AAGCATACGA
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:0.26, C:0.29, G:0.34, T:0.11
Consensus pattern (20 bp):
ACACACCCATGTGGAAGGGC
Found at i:31399260 original size:22 final size:20
Alignment explanation
Indices: 31399215--31399261 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
31399205 AACACACCCA
*
31399215 TGTGGAAGGGCACACGCCCG
1 TGTGGAAGGGCACACGACCG
*
31399235 TGTGGAAGGAAGCATACGACCG
1 TGTGGAAGG--GCACACGACCG
31399257 TGTGG
1 TGTGG
31399262 CTAAGGTACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 9 0.39
22 14 0.61
ACGTcount: A:0.23, C:0.21, G:0.40, T:0.15
Consensus pattern (20 bp):
TGTGGAAGGGCACACGACCG
Found at i:31399991 original size:16 final size:18
Alignment explanation
Indices: 31399970--31400003 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
31399960 GAGAACATAC
31399970 AAACAAAA-AA-AAAAAA
1 AAACAAAAGAAGAAAAAA
31399986 AAACAAAAGAAGAAAAAA
1 AAACAAAAGAAGAAAAAA
31400004 TTAAAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 2 0.12
18 6 0.38
ACGTcount: A:0.88, C:0.06, G:0.06, T:0.00
Consensus pattern (18 bp):
AAACAAAAGAAGAAAAAA
Found at i:31404658 original size:24 final size:24
Alignment explanation
Indices: 31404624--31404677 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
31404614 ACTGACCTGG
*
31404624 AATATTATTTATCATTCACCAA-A
1 AATATTATTTATCATCCACCAACA
*
31404647 AAGTATTGTTTATCATCCACCAACA
1 AA-TATTATTTATCATCCACCAACA
31404672 AATATT
1 AATATT
31404678 TAATATGCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 2 0.07
24 22 0.81
25 3 0.11
ACGTcount: A:0.41, C:0.19, G:0.04, T:0.37
Consensus pattern (24 bp):
AATATTATTTATCATCCACCAACA
Found at i:31406428 original size:12 final size:12
Alignment explanation
Indices: 31406411--31406435 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31406401 TCCATATTGG
31406411 TTGTTTTTTTTT
1 TTGTTTTTTTTT
31406423 TTGTTTTTTTTT
1 TTGTTTTTTTTT
31406435 T
1 T
31406436 CATTTGATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (12 bp):
TTGTTTTTTTTT
Found at i:31415419 original size:40 final size:40
Alignment explanation
Indices: 31415257--31415437 Score: 165
Period size: 40 Copynumber: 4.6 Consensus size: 40
31415247 CGAATGATGT
* * * *
31415257 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTCGTGC-AAGTTACTAAAC
* * * * *
31415297 CCGGACTAGGAT-CCGAAGGCATTCGTGCGAGTTAATAAAT
1 CCGGGCTAAG-TCCCGAAGGCATTCGTGCAAGTTACTAAAC
*
31415337 CCGGGCTAA-TCCCGAAGGC-TTTGTGCAAGTTACTAAAC
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTAAAC
* **
31415375 CCGGGTTAAGTCCCGAAGGCATTCGTGCAAGTCGCTATAA-
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTA-AAC
**
31415415 CCGGGCTTCGTCCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATT
31415438 TGAGCGAGTC
Statistics
Matches: 115, Mismatches: 20, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
38 24 0.21
39 18 0.16
40 64 0.56
41 9 0.08
ACGTcount: A:0.24, C:0.25, G:0.27, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTAAAC
Found at i:31415421 original size:78 final size:79
Alignment explanation
Indices: 31415256--31415407 Score: 200
Period size: 78 Copynumber: 1.9 Consensus size: 79
31415246 TCGAATGATG
* * *
31415256 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATATCCGGACTAGGATCCGAAGGCATTC
1 TCCGGGCTAA-TCCCGAAGGCTTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATTC
* *
31415321 GTGCGAGTTAATAAA
65 GTGCAAGTCAATAAA
* **
31415336 TCCGGGCTAATCCCGAAGGCTTTGTGC-AAGTTACTAAACCCGGGTTAAG-TCCCGAAGGCATTC
1 TCCGGGCTAATCCCGAAGGCTTTGTGCTAAGTGACTAAACCCGGACTAAGAT-CCGAAGGCATTC
31415399 GTGCAAGTC
65 GTGCAAGTC
31415408 GCTATAACCG
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
77 1 0.02
78 35 0.56
79 17 0.27
80 10 0.16
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (79 bp):
TCCGGGCTAATCCCGAAGGCTTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATTCG
TGCAAGTCAATAAA
Found at i:31424247 original size:24 final size:24
Alignment explanation
Indices: 31424203--31424249 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
31424193 TATAGTATTA
*
31424203 GAAATATATACATGGGATAATATG
1 GAAATATATACATGAGATAATATG
*
31424227 GAAATATGTACAT-AGAGTAATAT
1 GAAATATATACATGAGA-TAATAT
31424250 ATACAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.47, C:0.04, G:0.19, T:0.30
Consensus pattern (24 bp):
GAAATATATACATGAGATAATATG
Found at i:31425303 original size:54 final size:54
Alignment explanation
Indices: 31425239--31425418 Score: 154
Period size: 54 Copynumber: 3.2 Consensus size: 54
31425229 ACCTATTTTC
*
31425239 TCAACTTATCACACTTGAATTTAATAATAGTCTCAACTTACATAATTTCCTTTA
1 TCAACATATCACACTTGAATTTAATAATAGTCTCAACTTACATAATTTCCTTTA
* ** * *
31425293 TCAACATATCAAAGAT-AATTATATATGTACAT-GTCAC-A-TTCAACATTAATATACCTATTTT
1 TCAACATATCACACTTGAATT-TA-A--TA-ATAGTCTCAACTT--ACA-TAAT-TTCC---TTT
*
31425354 C
54 A
31425355 TCAAC-TATCACACTTGAATTTAATAATAGTCTCAACTTACATAATTTCCTTTA
1 TCAACATATCACACTTGAATTTAATAATAGTCTCAACTTACATAATTTCCTTTA
31425408 TCAACATATCA
1 TCAACATATCA
31425419 AAGATAATTA
Statistics
Matches: 96, Mismatches: 13, Indels: 34
0.67 0.09 0.24
Matches are distributed among these distances:
53 12 0.12
54 19 0.20
55 3 0.03
56 4 0.04
57 15 0.16
58 15 0.16
59 4 0.04
60 3 0.03
61 9 0.09
62 12 0.12
ACGTcount: A:0.38, C:0.20, G:0.04, T:0.38
Consensus pattern (54 bp):
TCAACATATCACACTTGAATTTAATAATAGTCTCAACTTACATAATTTCCTTTA
Found at i:31425396 original size:115 final size:116
Alignment explanation
Indices: 31425214--31425445 Score: 457
Period size: 115 Copynumber: 2.0 Consensus size: 116
31425204 TTTCATATAA
31425214 ATTCAACATTAATATACCTATTTTCTCAACTTATCACACTTGAATTTAATAATAGTCTCAACTTA
1 ATTCAACATTAATATACCTATTTTCTCAACTTATCACACTTGAATTTAATAATAGTCTCAACTTA
31425279 CATAATTTCCTTTATCAACATATCAAAGATAATTATATATGTACATGTCAC
66 CATAATTTCCTTTATCAACATATCAAAGATAATTATATATGTACATGTCAC
31425330 ATTCAACATTAATATACCTATTTTCTCAAC-TATCACACTTGAATTTAATAATAGTCTCAACTTA
1 ATTCAACATTAATATACCTATTTTCTCAACTTATCACACTTGAATTTAATAATAGTCTCAACTTA
31425394 CATAATTTCCTTTATCAACATATCAAAGATAATTATATATGTACATGTCAC
66 CATAATTTCCTTTATCAACATATCAAAGATAATTATATATGTACATGTCAC
31425445 A
1 A
31425446 AAATATATTA
Statistics
Matches: 116, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
115 86 0.74
116 30 0.26
ACGTcount: A:0.38, C:0.19, G:0.04, T:0.38
Consensus pattern (116 bp):
ATTCAACATTAATATACCTATTTTCTCAACTTATCACACTTGAATTTAATAATAGTCTCAACTTA
CATAATTTCCTTTATCAACATATCAAAGATAATTATATATGTACATGTCAC
Found at i:31425928 original size:93 final size:92
Alignment explanation
Indices: 31425800--31426285 Score: 676
Period size: 93 Copynumber: 5.3 Consensus size: 92
31425790 TGATGTCATA
* * * * *
31425800 GTATCTTTCAACTATGGTTTTACTCGTTTTC-TGTCATGTTGCCATGGTATCTTTCAACCATGGT
1 GTATCTTTCAACCATGGTCTTACAC-ATTTCATGTCACGTTGCCATGGTATCTTTCAACCATGGT
*** *
31425864 CTTATTCATTTTCCCGTCATGTTGCCATG
65 CTTATTCA-TTTCATATCAGGTTGCCATG
* *
31425893 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCAGGTTGCCATGGTATCTTTCAACCATGGTC
1 GTATCTTTCAACCATGGTCTTACACATTTCATGTCACGTTGCCATGGTATCTTTCAACCATGGTC
*** *
31425958 TTATTCATTTTCCCGTCATGTTGCCATG
66 TTATTCA-TTTCATATCAGGTTGCCATG
* *
31425986 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCACGTTG-CATGGTATCTTTCAACCACGGTC
1 GTATCTTTCAACCATGGTCTTACACATTTCATGTCACGTTGCCATGGTATCTTTCAACCATGGTC
*
31426050 TTATTCATTTCATATCACGTTGCCATG
66 TTATTCATTTCATATCAGGTTGCCATG
* *
31426077 GTAT-TTTCAACCACGGTCTTACACATTTCATATCA-GTTGCCATGGTATCTTTCAACCATGGTC
1 GTATCTTTCAACCATGGTCTTACACATTTCATGTCACGTTGCCATGGTATCTTTCAACCATGGTC
**
31426140 TTACACATTTCATATCAGGTTGCCATG
66 TTATTCATTTCATATCAGGTTGCCATG
* *
31426167 GTATCTTTCAACCATGGTC-TACACATTCCATATCACGTTGCCATGGTATCTTTCAACCATGGTC
1 GTATCTTTCAACCATGGTCTTACACATTTCATGTCACGTTGCCATGGTATCTTTCAACCATGGTC
**
31426231 TTACACATTTCATATCAGGTTGCCATG
66 TTATTCATTTCATATCAGGTTGCCATG
31426258 GTATCTTTCAACCATGGTCTTACACATT
1 GTATCTTTCAACCATGGTCTTACACATT
31426286 CCATATCAGA
Statistics
Matches: 369, Mismatches: 19, Indels: 11
0.92 0.05 0.03
Matches are distributed among these distances:
89 4 0.01
90 93 0.25
91 107 0.29
92 41 0.11
93 124 0.34
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.40
Consensus pattern (92 bp):
GTATCTTTCAACCATGGTCTTACACATTTCATGTCACGTTGCCATGGTATCTTTCAACCATGGTC
TTATTCATTTCATATCAGGTTGCCATG
Found at i:31426033 original size:45 final size:46
Alignment explanation
Indices: 31425800--31426293 Score: 656
Period size: 46 Copynumber: 10.8 Consensus size: 46
31425790 TGATGTCATA
* * * * *
31425800 GTATCTTTCAACTATGGTTTTACTCGTTTTC-TGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTC-ATTTCATATCACGTTGCCATG
* *** *
31425846 GTATCTTTCAACCATGGTCTTATTCATTTTCCCGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCA-TTTCATATCACGTTGCCATG
* *
31425893 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCACGTTGCCATG
* *** *
31425939 GTATCTTTCAACCATGGTCTTATTCATTTTCCCGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCA-TTTCATATCACGTTGCCATG
*
31425986 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCACGTTG-CATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCACGTTGCCATG
* *
31426031 GTATCTTTCAACCACGGTCTTATTCATTTCATATCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCACGTTGCCATG
* *
31426077 GTAT-TTTCAACCACGGTCTTACACATTTCATATCA-GTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCACGTTGCCATG
* *
31426121 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCACGTTGCCATG
* *
31426167 GTATCTTTCAACCATGGTC-TACACATTCCATATCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCACGTTGCCATG
* *
31426212 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCACGTTGCCATG
* *
31426258 GTATCTTTCAACCATGGTCTTACACATTCCATATCA
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCA
31426294 GAGAGCACAC
Statistics
Matches: 413, Mismatches: 28, Indels: 14
0.91 0.06 0.03
Matches are distributed among these distances:
44 13 0.03
45 144 0.35
46 175 0.42
47 81 0.20
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.39
Consensus pattern (46 bp):
GTATCTTTCAACCATGGTCTTACTCATTTCATATCACGTTGCCATG
Found at i:31429774 original size:23 final size:23
Alignment explanation
Indices: 31429744--31429789 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
31429734 CCCCTCTTTG
*
31429744 CTCATTGTCGTGTAACGGGAATA
1 CTCATTGTCGTGTAACGAGAATA
31429767 CTCATTGTCGTGTAACGAGAATA
1 CTCATTGTCGTGTAACGAGAATA
31429790 GAGCAAAGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.30
Consensus pattern (23 bp):
CTCATTGTCGTGTAACGAGAATA
Found at i:31430481 original size:73 final size:75
Alignment explanation
Indices: 31430345--31430500 Score: 246
Period size: 73 Copynumber: 2.1 Consensus size: 75
31430335 AAAAACAGAG
*
31430345 TTTG-AAAGACAGAATTTGAAAATACCTCAGCATGTGACCCGAGGCTCAACTCACCTCTCGCAAT
1 TTTGAAAAGACAGAAATTGAAAATACCTCAGCA-GTGACCCGAGGCTCAACTCACCTCTCGCAAT
31430409 ACGAGTTGATT
65 ACGAGTTGATT
* *
31430420 TTTGAAAAG-CAGAAATTGAAATTACCTCAGC-GTGCCCCGAGGCTCAACTCACCTCTCGCAATA
1 TTTGAAAAGACAGAAATTGAAAATACCTCAGCAGTGACCCGAGGCTCAACTCACCTCTCGCAATA
*
31430483 TGAGTTGATT
66 CGAGTTGATT
31430493 TTTGAAAA
1 TTTGAAAA
31430501 ATATAGATTG
Statistics
Matches: 76, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
73 48 0.63
75 24 0.32
76 4 0.05
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (75 bp):
TTTGAAAAGACAGAAATTGAAAATACCTCAGCAGTGACCCGAGGCTCAACTCACCTCTCGCAATA
CGAGTTGATT
Found at i:31430635 original size:83 final size:84
Alignment explanation
Indices: 31430421--31430835 Score: 514
Period size: 83 Copynumber: 4.8 Consensus size: 84
31430411 GAGTTGATTT
* * *
31430421 TTGAAAAGCAGAAATTGAAATTACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGA
*
31430486 GTTGATTTTTGAAAAATATAGA
66 GTTGA-TTTT-AAAAATAGA-A
* * *
31430508 TTGGAAAAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTTAACTCACCTCTCGCAATAT
1 TT-G-AAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATAT
31430573 GAGTTGA-TTTAAAAATAGACA
64 GAGTTGATTTTAAAAATAGA-A
* * *
31430594 TT-AAGAACAGAGATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGA
31430658 GTTGATTTTTTAAAACAT-GAA
66 GTTGA--TTTTAAAA-ATAGAA
* * * *
31430679 TTAAAAAACAGAAATTGGAAATACCTCAGCATGTGAGCC-GAGGCTCAACTCACTTCTCGCAATA
1 TTGAAAAACAGAAATTGAAAATACCTCAGC--GTG-CCCTGAGGCTCAACTCACCTCTCGCAATA
* *
31430743 TGAGTTGATTTTTGAAAACAGAA
63 TGAGTTGA-TTTTAAAAATAGAA
** *
31430766 TTGAAAAACAGAAATTGAAGTTACCTCAGCGTGCCCTGAGGCTCAACTCACTTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGA
31430831 GTTGA
66 GTTGA
31430836 CTTCTTTTTT
Statistics
Matches: 292, Mismatches: 24, Indels: 26
0.85 0.07 0.08
Matches are distributed among these distances:
83 63 0.22
84 2 0.01
85 39 0.13
86 45 0.15
87 44 0.15
88 36 0.12
89 63 0.22
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (84 bp):
TTGAAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTTTAAAAATAGAA
Found at i:31430638 original size:172 final size:171
Alignment explanation
Indices: 31430421--31430835 Score: 570
Period size: 173 Copynumber: 2.4 Consensus size: 171
31430411 GAGTTGATTT
* *
31430421 TTGAAAAGCAGAAATTGAAATTACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGA
* * *
31430486 GTTGATTTTTGAAAAATAT-AGATTGGAAAAAACAGAAATTGAAAATACCTCAGC-GTG-TCTTG
66 GTTGATTTTT-AAAAACATGA-ATT--AAAAAACAGAAATTGAAAATACCTCAGCAGTGAGC-CG
* *
31430548 AGGCTTAACTCACCTCTCGCAATATGAGTTGA-TTTAAAAATAGACA
126 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAAAAACAGA-A
* * * *
31430594 TT-AAGAACAGAGATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGA
* *
31430658 GTTGATTTTTTAAAACATGAATTAAAAAACAGAAATTGGAAATACCTCAGCATGTGAGCCGAGGC
66 GTTGATTTTTAAAAACATGAATTAAAAAACAGAAATTGAAAATACCTCAGCA-GTGAGCCGAGGC
* *
31430723 TCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAACAGAA
130 TCAACTCACCTCTCGCAATATGAGTTGA-TTTTAAAAACAGAA
* *
31430766 TTGAAAAACAGAAATTGAAGTTACCTCAGCGTGCCCTGAGGCTCAACTCACTTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGA
31430831 GTTGA
66 GTTGA
31430836 CTTCTTTTTT
Statistics
Matches: 214, Mismatches: 21, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
169 27 0.13
171 43 0.20
172 71 0.33
173 73 0.34
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (171 bp):
TTGAAAAACAGAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTTTTAAAAACATGAATTAAAAAACAGAAATTGAAAATACCTCAGCAGTGAGCCGAGGCT
CAACTCACCTCTCGCAATATGAGTTGATTTTAAAAACAGAA
Found at i:31430826 original size:173 final size:172
Alignment explanation
Indices: 31430421--31430835 Score: 572
Period size: 172 Copynumber: 2.4 Consensus size: 172
31430411 GAGTTGATTT
* *
31430421 TTGAAAAGCAGAAATTGAAATTACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGA
* * *
31430486 GTTGATTTTTGAAAAATATAGATTGGAAAAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGG
66 GTTGATTTTTGAAAAATAGAGATT-GAAAAAACAGAAATTGAAAATACCTCAGCGTGGCTCGAGG
* *
31430551 CTTAACTCACCTCTCGCAATATGAGTTGATTTAAAAATAGACA
130 CTCAACTCACCTCTCGCAATATGAGTTGATTTAAAAACAGACA
* * * *
31430594 TT-AAGAACAGAGATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGA
* *
31430658 GTTGATTTTTTAAAACAT-GA-ATT-AAAAAACAGAAATTGGAAATACCTCAGCATGTGAGC-CG
66 GTTGATTTTTGAAAA-ATAGAGATTGAAAAAACAGAAATTGAAAATACCTCAGC--GTG-GCTCG
* *
31430719 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAACAGA-A
127 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTAAAAACAGACA
* *
31430766 TTGAAAAACAGAAATTGAAGTTACCTCAGCGTGCCCTGAGGCTCAACTCACTTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGA
31430831 GTTGA
66 GTTGA
31430836 CTTCTTTTTT
Statistics
Matches: 214, Mismatches: 21, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
169 27 0.13
171 37 0.17
172 75 0.35
173 75 0.35
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (172 bp):
TTGAAAAACAGAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTTTTGAAAAATAGAGATTGAAAAAACAGAAATTGAAAATACCTCAGCGTGGCTCGAGGC
TCAACTCACCTCTCGCAATATGAGTTGATTTAAAAACAGACA
Found at i:31444323 original size:21 final size:21
Alignment explanation
Indices: 31444299--31444380 Score: 58
Period size: 21 Copynumber: 3.7 Consensus size: 21
31444289 AATATATACA
31444299 AAAATATAACTAATAATATTT
1 AAAATATAACTAATAATATTT
*** *
31444320 AAAATAATAA-TAGGGATATTA
1 AAAAT-ATAACTAATAATATTT
* *
31444341 AAAATACTTAGTATATAATATTT
1 AAAATA-TAACTA-ATAATATTT
31444364 AAAATATATACATAATA
1 AAAATATA-AC-TAATA
31444381 CAAAAACATA
Statistics
Matches: 44, Mismatches: 11, Indels: 10
0.68 0.17 0.15
Matches are distributed among these distances:
20 1 0.02
21 19 0.43
22 7 0.16
23 15 0.34
24 2 0.05
ACGTcount: A:0.56, C:0.04, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAATATAACTAATAATATTT
Found at i:31444386 original size:42 final size:39
Alignment explanation
Indices: 31444288--31444386 Score: 92
Period size: 44 Copynumber: 2.4 Consensus size: 39
31444278 GTACATAGAG
*
31444288 TAATATATACAAAAATATAACTAATAATATTTAAAATAA
1 TAATAGATACAAAAATATAACTAATAATATTTAAAATAA
* * *
31444327 TAATAGGGATATTAAAAATACTTAGTATATAATATTTAAAATATA
1 TAATA--GATA-CAAAAATA-TAACTA-ATAATATTTAAAATA-A
31444372 TACATA-ATACAAAAA
1 TA-ATAGATACAAAAA
31444387 CATATATAAC
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
39 5 0.10
41 3 0.06
42 12 0.25
43 7 0.15
44 15 0.31
45 3 0.06
46 3 0.06
ACGTcount: A:0.58, C:0.05, G:0.04, T:0.33
Consensus pattern (39 bp):
TAATAGATACAAAAATATAACTAATAATATTTAAAATAA
Found at i:31446766 original size:24 final size:22
Alignment explanation
Indices: 31446727--31446777 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 22
31446717 CAACCAAGCG
* *
31446727 GAAAAAGAAAAGAGAAGCAAAA
1 GAAAAAGAAAAAAGAAGAAAAA
31446749 GAAAAGAGCAAAAAAGAAGAAAAA
1 GAAAA-AG-AAAAAAGAAGAAAAA
31446773 GAAAA
1 GAAAA
31446778 CAAATGTAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 5 0.20
23 2 0.08
24 18 0.72
ACGTcount: A:0.75, C:0.04, G:0.22, T:0.00
Consensus pattern (22 bp):
GAAAAAGAAAAAAGAAGAAAAA
Found at i:31453486 original size:3 final size:3
Alignment explanation
Indices: 31453478--31453530 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
31453468 TCCAATTGCA
31453478 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
31453526 AAT AA
1 AAT AA
31453531 AACATTCTAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:31468688 original size:5 final size:5
Alignment explanation
Indices: 31468680--31468704 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
31468670 CATGTAAGTA
31468680 ACTAT ACTAT ACTAT ACTAT ACTAT
1 ACTAT ACTAT ACTAT ACTAT ACTAT
31468705 CCCATATCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (5 bp):
ACTAT
Found at i:31475136 original size:15 final size:15
Alignment explanation
Indices: 31475116--31475145 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
31475106 CCATTATTAG
31475116 CTTTCTCTCTCTCTC
1 CTTTCTCTCTCTCTC
31475131 CTTTCTCTCTCTCTC
1 CTTTCTCTCTCTCTC
31475146 TCTGCGGACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (15 bp):
CTTTCTCTCTCTCTC
Found at i:31475488 original size:16 final size:18
Alignment explanation
Indices: 31475469--31475502 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
31475459 TTTTAATTAT
31475469 TATTAATT-T-TCTTCAA
1 TATTAATTATCTCTTCAA
31475485 TATTAATTATCTCTTCAA
1 TATTAATTATCTCTTCAA
31475503 ATCTTTCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 1 0.06
18 7 0.44
ACGTcount: A:0.32, C:0.15, G:0.00, T:0.53
Consensus pattern (18 bp):
TATTAATTATCTCTTCAA
Found at i:31476922 original size:18 final size:18
Alignment explanation
Indices: 31476901--31476937 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
31476891 ATATACATAT
*
31476901 ATATATAAAATTTAGAAA
1 ATATATAAAATCTAGAAA
*
31476919 ATATATATAATCTAGAAA
1 ATATATAAAATCTAGAAA
31476937 A
1 A
31476938 ATAACAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.32
Consensus pattern (18 bp):
ATATATAAAATCTAGAAA
Found at i:31477616 original size:31 final size:31
Alignment explanation
Indices: 31477559--31477617 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
31477549 AAGTTTAAAA
* * *
31477559 ATATTTTTTATAAAATTCTAAAAATATAATT
1 ATATATTTTATAAAAGTCAAAAAATATAATT
31477590 ATATATTTTA-AAAAGTCAAAATAATATA
1 ATATATTTTATAAAAGTCAAAA-AATATA
31477618 TAAAAATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 9 0.38
31 15 0.62
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (31 bp):
ATATATTTTATAAAAGTCAAAAAATATAATT
Found at i:31477727 original size:15 final size:15
Alignment explanation
Indices: 31477707--31477737 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
31477697 CCTTTTTAGA
31477707 ATTTTAGAATTATAT
1 ATTTTAGAATTATAT
*
31477722 ATTTTAGAATTTTAT
1 ATTTTAGAATTATAT
31477737 A
1 A
31477738 AAAAAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (15 bp):
ATTTTAGAATTATAT
Found at i:31477892 original size:10 final size:10
Alignment explanation
Indices: 31477877--31477924 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
31477867 TATAATTTAA
31477877 ATATTTTTCT
1 ATATTTTTCT
*
31477887 ATATTTTATGT
1 ATATTTT-TCT
*
31477898 ATTTTTTTCT
1 ATATTTTTCT
*
31477908 A-ATTTTTAT
1 ATATTTTTCT
31477917 ATATTTTT
1 ATATTTTT
31477925 TTCATCTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
9 7 0.23
10 16 0.52
11 8 0.26
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.71
Consensus pattern (10 bp):
ATATTTTTCT
Found at i:31477906 original size:21 final size:21
Alignment explanation
Indices: 31477880--31477942 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
31477870 AATTTAAATA
*
31477880 TTTTTCTATATTTTATGTATT
1 TTTTTCTATATTTTATATATT
31477901 TTTTTCTA-ATTTTTATATATT
1 TTTTTCTATA-TTTTATATATT
*
31477922 TTTTTC-ATCTTTTATAT-TT
1 TTTTTCTATATTTTATATATT
31477941 TT
1 TT
31477943 AATGTGTATA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
19 4 0.11
20 10 0.26
21 24 0.63
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.73
Consensus pattern (21 bp):
TTTTTCTATATTTTATATATT
Found at i:31481869 original size:20 final size:20
Alignment explanation
Indices: 31481844--31481883 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
31481834 ATTTTATACT
31481844 AAACCCCAAACATTAAATTC
1 AAACCCCAAACATTAAATTC
* * *
31481864 AAACCCTAATCTTTAAATTC
1 AAACCCCAAACATTAAATTC
31481884 CAAGCACCAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.28, G:0.00, T:0.28
Consensus pattern (20 bp):
AAACCCCAAACATTAAATTC
Found at i:31487996 original size:16 final size:16
Alignment explanation
Indices: 31487958--31487996 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
31487948 ATCTCCAAAA
*
31487958 AAAAACTAGCCTCTCC
1 AAAAACTAGCCTCTAC
*
31487974 AAAAACTAGCCTTTAC
1 AAAAACTAGCCTCTAC
*
31487990 AATAACT
1 AAAAACT
31487997 CTTCTCCTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.44, C:0.28, G:0.05, T:0.23
Consensus pattern (16 bp):
AAAAACTAGCCTCTAC
Found at i:31488198 original size:30 final size:30
Alignment explanation
Indices: 31488162--31488250 Score: 151
Period size: 30 Copynumber: 3.0 Consensus size: 30
31488152 AGTGGTGGTG
*
31488162 GAGCAAGTGTGGCTAGTGGAGTAGGTAGTA
1 GAGCAAGTGTGGCTAGTGGAGTTGGTAGTA
* *
31488192 GAGCAAGTGTGGCTAGTGGAGTTGGTGGTG
1 GAGCAAGTGTGGCTAGTGGAGTTGGTAGTA
31488222 GAGCAAGTGTGGCTAGTGGAGTTGGTAGT
1 GAGCAAGTGTGGCTAGTGGAGTTGGTAGT
31488251 GGCAAAGGCT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 55 1.00
ACGTcount: A:0.21, C:0.07, G:0.46, T:0.26
Consensus pattern (30 bp):
GAGCAAGTGTGGCTAGTGGAGTTGGTAGTA
Found at i:31489705 original size:74 final size:73
Alignment explanation
Indices: 31489511--31490266 Score: 606
Period size: 74 Copynumber: 9.9 Consensus size: 73
31489501 GAAATAAAAG
* **
31489511 AACAGAAATGGAAAATACCTCAGCGTATGACCCGAGGCTCAACTCACCTCTTACAATATGAGTTT
1 AACAGAAATTGAAAATACCTCAGCG--TG-CCCGAGGCTCAACTCACCTCTCGCAATATGAG-TT
* *
31489576 GTTTTTTTAAAAACA
62 GATTTTTT---GACA
* * * * *
31489591 AACAGAAATTGAAAATACCTCAGTGTGCCTTGATGCTCAACTCACCTCTCACAATATGAGTTGGT
1 AACAGAAATTGAAAATACCTCAGCGTGCC-CGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
31489656 TTTTTGACA
65 TTTTTGACA
*
31489665 AACAGAAATTGAAAATACCTCAGTGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
1 AACAGAAATTGAAAATACCTCAGCGTGCCC-GAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
***
31489730 TTTGACAAACAA
65 TTT--TTGAC-A
* * *
31489742 AGACAGAAATTGAAAATACCTCAGCACGTGAGCCGAGGCTTAACTCACCTCTTGCAATATGAGTT
1 A-ACAGAAATTGAAAATACCTCAG--CGTG-CCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
*
31489807 TATTTTTTTGAC-
62 GA-TTTTTTGACA
* * * * * * *
31489819 AATAGAAATTGCAATTACCTCAGCATGTCTCGAGGCTCAACTCACATCTTGCAATATGAGTTTTT
1 AACAGAAATTGAAAATACCTCAGCGTG-CCCGAGGCTCAACTCACCTCTCGCAATATGAG---TT
** *
31489884 TTTTTTTTGATAAA
62 GATTTTTTG--ACA
* * * * * * *
31489898 AATAGAATTTGAAAATATCTCAGCGTGTCCTGAGGCTCAACTCACTTATCGCAACATGAGTTGA-
1 AACAGAAATTGAAAATACCTCAGCGTG-CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
31489962 TTTTTGACA
65 TTTTTGACA
* *
31489971 AACAGCAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCCCGCAATATGAGTTGAT
1 AACAGAAATTGAAAATACCTCAGCGTG-CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
***
31490036 TTAAAAAACAGACATAAA
65 TT-----TTTGAC----A
* * * * * *
31490054 AACAGAAATTGAAAGTGA-CTCAACACGTGAGCCAATGCTCAACTCACCTCTCGCAATATGCGTT
1 AACAGAAATTGAAAAT-ACCTC-A-GCGTG-CCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
*
31490118 AATTTTTTGA-A
62 GATTTTTTGACA
** * * * * *
31490129 AGTAGAATTTGAAAATACCTCGGCGTGCCC-CGGCTCAACTCACCTCCCGCAACATGAGTTGA-T
1 AACAGAAATTGAAAATACCTCAGCGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
31490192 TTTTGACA
66 TTTTGACA
* * *
31490200 AACAGCAATTGAAAATACCTCAGCGTGCCCCGAGGCTTAACTCACCTCCCGCAATATGAGTTGAT
1 AACAGAAATTGAAAATACCTCAGCGTG-CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
31490265 TT
65 TT
31490267 AAAAACAGAC
Statistics
Matches: 548, Mismatches: 94, Indels: 74
0.77 0.13 0.10
Matches are distributed among these distances:
70 7 0.01
71 49 0.09
72 5 0.01
73 89 0.16
74 102 0.19
75 22 0.04
76 30 0.05
77 17 0.03
78 52 0.09
79 54 0.10
80 58 0.11
81 6 0.01
83 18 0.03
84 2 0.00
85 37 0.07
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.28
Consensus pattern (73 bp):
AACAGAAATTGAAAATACCTCAGCGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
TTTTGACA
Found at i:31489966 original size:79 final size:77
Alignment explanation
Indices: 31489044--31490266 Score: 595
Period size: 75 Copynumber: 15.9 Consensus size: 77
31489034 AACACAGAAA
* * * * * *
31489044 TTGAAGAACAAAAATGGAAAACACCTCAGCGT--CTTGAGGTTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGA
*
31489107 GCTGA--TTTTT
66 GTTGATTTTTTT
* * * * * * * * *
31489117 TTGAAAGACAGAAATTGAAAATACCTTAACTTGTCTTGAGGCTCAACTCACTTCTTGCAGTATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGA
*
31489182 GTTGA--ATTTT
66 GTTGATTTTTTT
* * * * * * * *
31489192 TTGAAAGACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACTTCTTGTAGTATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGA
*
31489257 GTTGA----ATT
66 GTTGATTTTTTT
* * *
31489265 TTG--AAACAGAAA-TAAAAATTATCTCAGCGTGTCCC-AAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAACAGAAATTGAAAA-TACCTCAGCGTG-CCCTGAGGCTCAACTCACCTCTCGCAATAT
31489326 GAGTTGA-TTTTTT
64 GAGTTGATTTTTTT
* * *
31489339 TTGAAAGACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGA
31489404 GTTGA--TTTTT
66 GTTGATTTTTTT
*** * * ** *
31489414 TTGAAAGGTAAAAATTGAAAATACCTCAACGTGTCAGTCAAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTG-CCCT-GAGGCTCAACTCACCTCTCGCAATAT
*
31489479 GAGCTGATTTTTTT
64 GAGTTGATTTTTTT
* * ** * * * * *
31489493 GAACCGTAGAAATAAAAGAACA--G-AAATGGAAAAT-A-CCT-CAGC-GTATGACCCGAGGCTC
1 ------TTGAAA-AACAGAA-ATTGAAAAT---ACCTCAGCGTGC-CCTG-A-GGCTC-A-ACTC
* * ** * * *
31489551 AACTCAC-CTCT-TACAATATGAGTTTGTTTTT
50 ACCTCTCGCAATAT-GAGT-TGA-TTTT--TTT
* * * * *
31489582 TTAAAAACAAACAGAAATTGAAAATACCTCAGTGTGCCTTGATGCTCAACTCACCTCTCACAATA
1 TT--GAA-AAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATA
*
31489647 TGAGTTG---GTTTT
63 TGAGTTGATTTTTTT
* *
31489659 TTGACAAACAGAAATTGAAAATACCTCAGTGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGA
**
31489724 GTTGA-TTTTGA
66 GTTGATTTTTTT
*** * * *
31489735 CAAACAAAGACAGAAATTGAAAATACCTCAGCACGTGAGCC-GAGGCTTAACTCACCTCTTGCAA
1 TTGA-AAA-ACAGAAATTGAAAATACCTCAG--CGTG-CCCTGAGGCTCAACTCACCTCTCGCAA
*
31489799 TATGAGTT--TATTTTT
61 TATGAGTTGATTTTTTT
* * * * * * * *
31489814 TTG-ACAATAGAAATTGCAATTACCTCAGCATG-TCTCGAGGCTCAACTCACATCTTGCAATATG
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGCCCT-GAGGCTCAACTCACCTCTCGCAATATG
**
31489877 AGTTTTTTTTTTT
65 AGTTGATTTTTTT
* * * * * * *
31489890 TTGATAAAAATAGAATTTGAAAATATCTCAGCGTGTCCTGAGGCTCAACTCACTTATCGCAACAT
1 TTG--AAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATAT
31489955 GAGTTGA----TTT
64 GAGTTGATTTTTTT
* * * *
31489965 TTGACAAACAGCAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCCCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGA
****
31490030 GTTGATTTAAAAAA
66 GTTGATTT--TTTT
** * * * * *
31490044 CAGACATAAAAACAGAAATTGAAAGTGA-CTCAACACGTGAGCC-AATGCTCAACTCACCTCTCG
1 TTG----AAAAACAGAAATTGAAAAT-ACCTC-A-GCGTG-CCCTGAGGCTCAACTCACCTCTCG
* *
31490107 CAATATGCGTT-A--ATTTT
58 CAATATGAGTTGATTTTTTT
** * * * * *
31490124 TTG-AAAGTAGAATTTGAAAATACCTCGGCGTGCCC--CGGCTCAACTCACCTCCCGCAACATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGA
31490186 GTTGA----TTT
66 GTTGATTTTTTT
* * * * *
31490194 TTGACAAACAGCAATTGAAAATACCTCAGCGTGCCCCGAGGCTTAACTCACCTCCCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGA
31490259 GTTGATTT
66 GTTGATTT
31490267 AAAAACAGAC
Statistics
Matches: 878, Mismatches: 186, Indels: 169
0.71 0.15 0.14
Matches are distributed among these distances:
70 11 0.01
71 97 0.11
72 5 0.01
73 118 0.13
74 99 0.11
75 161 0.18
76 83 0.09
77 44 0.05
78 22 0.03
79 59 0.07
80 35 0.04
81 2 0.00
83 32 0.04
84 19 0.02
85 55 0.06
86 21 0.02
87 12 0.01
89 3 0.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.29
Consensus pattern (77 bp):
TTGAAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTTTTTT
Found at i:31490007 original size:152 final size:150
Alignment explanation
Indices: 31489511--31490266 Score: 595
Period size: 152 Copynumber: 5.0 Consensus size: 150
31489501 GAAATAAAAG
* * **
31489511 AACAGAAATGGAAAATACCTCAGCGTATGACCCGAGGCTCAACTCACCTCTTACAATATGAG-TT
1 AACAGAAATTGAAAATACCTCAGCG--TGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTT
* * *
31489575 TGTTTTTTTAAAAACAAACAGAAATTGAAAATACCTCAGTGTGCCTTGATGCTCAACTCACCTCT
64 TTTTTTTTTAAAAA-AAACAGAAATTGAAAATACCTCAGCGTGCC-TGAGGCTCAACTCACCTCT
* *
31489640 CACAATATGAGTTGGTTTTTTGACA
127 CGCAATATGAGTT-GATTTTTGACA
* * **
31489665 AACAGAAATTGAAAATACCTCAGTGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAG-TTGA
1 AACAGAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTTTT
*** * *
31489729 TTTTGACAAACAAAGACAGAAATTGAAAATACCTCAGCACGTGAGCC-GAGGCTTAACTCACCTC
66 TTTTTTTAAA-AAAAACAGAAATTGAAAATACCTCAG--CGT--GCCTGAGGCTCAACTCACCTC
* *
31489793 TTGCAATATGAGTTTATTTTTTTGAC-
126 TCGCAATATGAGTTGA--TTTTTGACA
* * * * * * * *
31489819 AATAGAAATTGCAATTACCTCAGCATGTCTCGAGGCTCAACTCACATCTTGCAATATGAGTTTTT
1 AACAGAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAG-TTTT
* * * * * * *
31489884 TTTTTTTTGATAAAAATAGAATTTGAAAATATCTCAGCGTGTCCTGAGGCTCAACTCACTTATCG
65 TTTTTTTTAAAAAAAACAGAAATTGAAAATACCTCAGCGTG-CCTGAGGCTCAACTCACCTCTCG
*
31489949 CAACATGAGTTGATTTTTGACA
129 CAATATGAGTTGATTTTTGACA
* *
31489971 AACAGCAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCCCGCAATATGAGTTGAT
1 AACAGAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTT--T
******* * * * *
31490036 TTAAAAAACAGACATAAAAACAGAAATTGAAAGTGA-CTCAACACGTGAGCC-AATGCTCAACTC
64 TTTTTTTTTA-A-A-AAAAACAGAAATTGAAAAT-ACCTC-A-GCGT--GCCTGAGGCTCAACTC
* *
31490099 ACCTCTCGCAATATGCGTTAATTTTTTGA-A
121 ACCTCTCGCAATATGAGTTGA-TTTTTGACA
** * * * *
31490129 AGTAGAATTTGAAAATACCTCGGCGTGCCCC--GGCTCAACTCACCTCCCGCAACATGAG---TT
1 AACAGAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTTTT
** * * * * * *
31490189 GATTTTT--GACAAACAGCAATTGAAAATACCTCAGCGTGCCCCGAGGCTTAACTCACCTCCCGC
66 TTTTTTTAAAAAAAACAGAAATTGAAAATACCTCAGCGTG-CCTGAGGCTCAACTCACCTCTCGC
31490252 AATATGAGTTGATTT
130 AATATGAGTTGATTT
31490267 AAAAACAGAC
Statistics
Matches: 477, Mismatches: 99, Indels: 63
0.75 0.15 0.10
Matches are distributed among these distances:
142 1 0.00
143 5 0.01
144 30 0.06
145 2 0.00
146 19 0.04
151 14 0.03
152 115 0.24
153 35 0.07
154 103 0.22
155 30 0.06
156 55 0.12
157 2 0.00
158 56 0.12
159 9 0.02
160 1 0.00
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.28
Consensus pattern (150 bp):
AACAGAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTTTT
TTTTTTTAAAAAAAACAGAAATTGAAAATACCTCAGCGTGCCTGAGGCTCAACTCACCTCTCGCA
ATATGAGTTGATTTTTGACA
Found at i:31490193 original size:229 final size:231
Alignment explanation
Indices: 31489625--31490358 Score: 793
Period size: 228 Copynumber: 3.2 Consensus size: 231
31489615 GTGCCTTGAT
* * ** * *
31489625 GCTCAACTCACCTCTCACAATATGAGTTG-GTTTTTTGACAAACAGAAATTGAAAATACCTCAGT
1 GCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTGA-AAGTAGAATTTGAAAATACCTCAGC
* * *
31489689 GTGCCCTGAGGCTCAACTCACCT-CTCGCAATATGAGTTGA-TTTTGACAAACAAAGACAGAAAT
65 GTGTCCTCAGGCTCAACTCACCTAC-CGCAACATGAGTTGATTTTTGACAAAC--AG-C---AAT
** * ** * **
31489752 TGAAAATACCTCAGCACGTGAGCCGAGGCTTAACTCACCTCTTGCAATATGAGTTTATTT---TT
123 TGAAAATACCTCAG--CGTGCCCCGAGGCTCAACTCACCTCCCGCAATATGAGTTGATTTAAAAA
** * * * * * *
31489814 TTGAC-----AATAGAAATTGCAA-TTACCTCAGCA--TG-TCTCGAG
186 CAGACATAAAAACAGAAATTGAAAGTGA-CTCAACACGTGAGC-CAAG
* * *** * *
31489853 GCTCAACTCACATCTTGCAATATGAGTTTTTTTTTTTTTGATAAAAATAGAATTTGAAAATATCT
1 GCTCAACTCACCTCTCGCAATATGAG--TTGAATTTTTTG---AAAGTAGAATTTGAAAATACCT
* * *
31489918 CAGCGTGTCCTGAGGCTCAACTCACTTATCGCAACATGAGTTGATTTTTGACAAACAGCAATTGA
61 CAGCGTGTCCTCAGGCTCAACTCACCTACCGCAACATGAGTTGATTTTTGACAAACAGCAATTGA
31489983 AAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCCCGCAATATGAGTTGATTTAAAAAACAGA
126 AAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCCCGCAATATGAGTTGATTT-AAAAACAGA
*
31490048 CATAAAAACAGAAATTGAAAGTGACTCAACACGTGAGCCAAT
190 CATAAAAACAGAAATTGAAAGTGACTCAACACGTGAGCCAAG
* *
31490090 GCTCAACTCACCTCTCGCAATATGCGTT-AATTTTTTGAAAGTAGAATTTGAAAATACCTCGGCG
1 GCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTGAAAGTAGAATTTGAAAATACCTCAGCG
* *
31490154 TG-CC-CCGGCTCAACTCACCTCCCGCAACATGAGTTGATTTTTGACAAACAGCAATTGAAAATA
66 TGTCCTCAGGCTCAACTCACCTACCGCAACATGAGTTGATTTTTGACAAACAGCAATTGAAAATA
*
31490217 CCTCAGCGTGCCCCGAGGCTTAACTCACCTCCCGCAATATGAGTTGATTTAAAAACAGACATAAA
131 CCTCAGCGTGCCCCGAGGCTCAACTCACCTCCCGCAATATGAGTTGATTTAAAAACAGACATAAA
31490282 AACAGAAATTGAAAGTGACTCAACACGTGAGCCAAG
196 AACAGAAATTGAAAGTGACTCAACACGTGAGCCAAG
* *
31490318 GCTCAACTCACCTCTCGTAATATGAGTTGATTTTTTTGAAA
1 GCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTGAAA
31490359 ACAGAAATGA
Statistics
Matches: 436, Mismatches: 48, Indels: 43
0.83 0.09 0.08
Matches are distributed among these distances:
226 38 0.09
228 116 0.27
229 114 0.26
230 7 0.02
231 34 0.08
232 2 0.00
233 56 0.13
234 19 0.04
235 20 0.05
236 2 0.00
237 27 0.06
238 1 0.00
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (231 bp):
GCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTGAAAGTAGAATTTGAAAATACCTCAGCG
TGTCCTCAGGCTCAACTCACCTACCGCAACATGAGTTGATTTTTGACAAACAGCAATTGAAAATA
CCTCAGCGTGCCCCGAGGCTCAACTCACCTCCCGCAATATGAGTTGATTTAAAAACAGACATAAA
AACAGAAATTGAAAGTGACTCAACACGTGAGCCAAG
Found at i:31490212 original size:71 final size:71
Alignment explanation
Indices: 31490090--31490266 Score: 232
Period size: 71 Copynumber: 2.5 Consensus size: 71
31490080 GTGAGCCAAT
* * * ** *
31490090 GCTCAACTCACCTCTCGCAATATGCGTTAATTTTTTGAAAGTAGAATTTGAAAATACCTCGGCGT
1 GCTCAACTCACCTCCCGCAATATGAGTTGA-TTTTTGAAAACAGAATTTGAAAATACCTCAGCGT
31490155 GCCCC-G
65 GCCCCAG
*
31490161 GCTCAACTCACCTCCCGCAACATGAGTTGATTTTTGACAAACAGCAA-TTGAAAATACCTCAGCG
1 GCTCAACTCACCTCCCGCAATATGAGTTGATTTTTGA-AAACAG-AATTTGAAAATACCTCAGCG
31490225 TGCCCCGAG
64 TGCCCC-AG
*
31490234 GCTTAACTCACCTCCCGCAATATGAGTTGATTT
1 GCTCAACTCACCTCCCGCAATATGAGTTGATTT
31490267 AAAAACAGAC
Statistics
Matches: 93, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
70 7 0.08
71 52 0.56
72 2 0.02
73 32 0.34
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.27
Consensus pattern (71 bp):
GCTCAACTCACCTCCCGCAATATGAGTTGATTTTTGAAAACAGAATTTGAAAATACCTCAGCGTG
CCCCAG
Found at i:31505883 original size:73 final size:74
Alignment explanation
Indices: 31505759--31506425 Score: 416
Period size: 73 Copynumber: 8.7 Consensus size: 74
31505749 TCTATTTTTT
***
31505759 AAATCAACTCATATTGCGGGAGGTGAGTTGAGCCTTTCGGCACGCTGAGGTATTTAC-AATTGTT
1 AAATCAACTCATATTGCGGGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTACAAATTGTT
31505823 GTTTGTCAA
66 GTTTGTCAA
* * ** * * *
31505832 AAATCAACTCATGTTACGGGAGGTGAGTTGAGCCTCGGGGCACGCCAAGGTATTTTCAAATTCTA
1 AAATCAACTCATATTGCGGGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTACAAATTGTT
* ***
31505897 CTTTCAAAA
66 GTTTGTCAA
* * * ** *
31505906 AAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTTGGCCCACG-TGTTGAGTCACTTT-CAATT
1 AAATCAACTCATATTGCGGGAGGTGAGTTGAGCCTCGGGGCACGCTG-AG-GT-A-TTTACAA--
* ***
31505969 TCTATTTTTATGTTTGTTTTTT
60 ---A-TTGT-TGTTTG--TCAA
* * *
31505991 AAATCAACTCATATTCCGGGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTC-AATTGCT
1 AAATCAACTCATATTGCGGGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTACAAATTGTT
31506055 GTTTGTCAA
66 GTTTGTCAA
* * * * * * * *
31506064 AAATCAACTCATGTTGCGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGATATTTTCAAATTCTA
1 AAATCAACTCATATTGCGGGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTACAAATTGT-
* * *
31506129 TTTTTATAAA
65 TGTTTGTCAA
** ** * * * *
31506139 AAAAAAACTCATATTGCAAGAGGTGAGTTGAGCCTC-GGACATGCTGAGGTAATTGC-AATT-TC
1 AAATCAACTCATATTGCGGGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTACAAATTGT-
*
31506201 T-ATTGTCAAA
65 TGTTTGTC-AA
* ** ** * *
31506211 AAATCAACTAATATTGCAAGAGGTGAGTTGAGCCTCGGCTCACGTGCTGAGGTATTTTCAATTTC
1 AAATCAACTCATATTGCGGGAGGTGAGTTGAGCCTCGGGGCAC--GCTGAGGTATTTACAA-AT-
31506276 TGTCTCTGTTTGTC-A
62 TG--T-TGTTTGTCAA
* * * * * *
31506291 CAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGTACGCTGAGGTATTTTCAATTTCTG
1 AAATCAACTCATATTGCGGGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTACAA-AT-TG
* *
31506356 TTTGTTTTTAAA
64 -TTGTTTGTCAA
* ** *
31506368 AAAACAAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGTCATACGCTGAGGTATTT
1 AAATC-AACTCATATTGCGGGAGGTGAGTTGAGCCTCGGGGC--ACGCTGAGGTATTT
31506426 TCCATTTCTG
Statistics
Matches: 466, Mismatches: 95, Indels: 59
0.75 0.15 0.10
Matches are distributed among these distances:
71 3 0.01
72 37 0.08
73 107 0.23
74 68 0.15
75 58 0.12
76 13 0.03
77 10 0.02
78 55 0.12
80 51 0.11
81 4 0.01
82 12 0.03
83 5 0.01
84 2 0.00
85 39 0.08
86 2 0.00
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (74 bp):
AAATCAACTCATATTGCGGGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTACAAATTGTT
GTTTGTCAA
Found at i:31506072 original size:232 final size:232
Alignment explanation
Indices: 31505660--31506173 Score: 794
Period size: 232 Copynumber: 2.2 Consensus size: 232
31505650 GATGTTTCAT
* *
31505660 TTCTATTTTCAAAAAAATCAACTCATATTGCGGGAGGTGAGTTGAGCCTTGGCTCACGTGTTGAG
1 TTCTATTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCCCACGTGTTGAG
*
31505725 TCACTTTAAATTTCTATTTTTATGTCTATTTTTTAAATCAACTCATATTGCGGGAGGTGAGTTGA
66 TCACTTTAAATTTCTATTTTTATGTCTATTTTTTAAATCAACTCATATTCCGGGAGGTGAGTTGA
** * * *
31505790 GCCTTTCGGCACGCTGAGGTATTTACAATTGTTGTTTGTCAAAAATCAACTCATGTTACGGGAGG
131 GCCTCGCGGCACGCTGAGGTATTTACAATTGCTGTTTGTCAAAAATCAACTCATGTTACGAGAAG
* * *
31505855 TGAGTTGAGCCTCGGGGCACGCCAAGGTATTTTCAAA
196 TGAGTTGAGCCTCAGGACACGCCAAGATATTTTCAAA
* *
31505892 TTCTACTTTCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTTGGCCCACGTGTTGAG
1 TTCTATTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCCCACGTGTTGAG
* * *
31505957 TCACTTTCAATTTCTATTTTTATGTTTGTTTTTTAAATCAACTCATATTCCGGGAGGTGAGTTGA
66 TCACTTTAAATTTCTATTTTTATGTCTATTTTTTAAATCAACTCATATTCCGGGAGGTGAGTTGA
* * *
31506022 GCCTCGGGGCACGCTGAGGTATTTTCAATTGCTGTTTGTCAAAAATCAACTCATGTTGCGAGAAG
131 GCCTCGCGGCACGCTGAGGTATTTACAATTGCTGTTTGTCAAAAATCAACTCATGTTACGAGAAG
**
31506087 TGAGTTGAGCCTCAGGACACGCTGAGATATTTTCAAA
196 TGAGTTGAGCCTCAGGACACGCCAAGATATTTTCAAA
* ** *
31506124 TTCTATTTTTATAAAAAAAAAACTCATATTGCAAGAGGTGAGTTGAGCCT
1 TTCTATTTTCA-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
31506174 CGGACATGCT
Statistics
Matches: 254, Mismatches: 27, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
232 220 0.87
233 34 0.13
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (232 bp):
TTCTATTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCCCACGTGTTGAG
TCACTTTAAATTTCTATTTTTATGTCTATTTTTTAAATCAACTCATATTCCGGGAGGTGAGTTGA
GCCTCGCGGCACGCTGAGGTATTTACAATTGCTGTTTGTCAAAAATCAACTCATGTTACGAGAAG
TGAGTTGAGCCTCAGGACACGCCAAGATATTTTCAAA
Found at i:31506402 original size:158 final size:151
Alignment explanation
Indices: 31505763--31506894 Score: 735
Period size: 148 Copynumber: 7.4 Consensus size: 151
31505753 TTTTTTAAAT
* *
31505763 CAACTCATATTGCGGGAGGTGAGTTGAGCCTTTCGG-CACGCTGAGGTATTTACAA--T-TG--T
1 CAACTCATATTGCGAGAGGTGAGTTGAGCC--TCGGACACGCTGAGGTATTTTCAATTTCTGTCT
* * * * **
31505822 TGTTTGTCAAAAATCAACTCATGTTACGGGAGGTGAGTTGAGCCTCGGGGCACGCCAAGGTATTT
64 TGTTTGTC-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTT
* **
31505887 TCAAATTC--TACTTTCAAAAAAA
128 TCAATTTCTGTTGTTTCAAAAAAA
* * * * *
31505909 TCAGCTCATATTGCGAGAGGTGAGTTGAGCCTTGGCCCACG-TGTTGAGTCACTTTCAATTTCTA
1 -CAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG-ACACGCTG-AG-GT-ATTTTCAATTTC--
* * ** * * *
31505973 TTTTTATGTTTGTTTTTTAAATCAACTCATATTCCGGGAGGTGAGTTGAGCCTCGGGGCACGCTG
59 TGTCT-TGTTTG---TCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTG
* * *
31506038 AGGTATTTTCAATTGCTGTT-TGTC-AAAAAT
120 AGGTATTTTCAATTTCTGTTGTTTCAAAAAAA
* * * * *
31506068 CAACTCATGTTGCGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGATATTTTCAAATTCTAT-TT
1 CAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGACACGCTGAGGTATTTTCAATTTCTGTCTT
** ** * * * * *
31506132 -TTAT-AAAAAAAAAACTCATATTGCAAGAGGTGAGTTGAGCCTC-GGACATGCTGAGGTAATTG
65 GTT-TGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTT
* *
31506194 CAATTTCTATTG--TCAAAAAAT
129 CAATTTCTGTTGTTTCAAAAAAA
* * *
31506215 CAACTAATATTGCAAGAGGTGAGTTGAGCCTCGGCTCACGTGCTGAGGTATTTTCAATTTCTGTC
1 CAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG-ACAC--GCTGAGGTATTTTCAATTTCTGTC
* *
31506280 TCTGTTTGTCACAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGTACGCTGAGGTATT
63 T-TGTTTGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATT
*
31506345 TTCAATTTCTGTTTGTTTTTAAAAAAA
127 TTCAATTTCTG-TTG-TTTCAAAAAAA
* * *
31506372 CAAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGTCATACGCTGAGGTATTTTCCATTTCTGT
1 C-AACTCATATTGCGAGAGGTGAGTTGAGCCTC-GG--ACACGCTGAGGTATTTTCAATTTCTG-
* * * * *
31506437 TCTTTAATTTCTACGGTTCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTTGACTGA
61 TC-TT--GTT-T---G-TC---AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC-TCA-GGG
* **
31506502 CACGTTGAGGTATTTTCAATTTCTG-CCTTTCAAAAAAA
113 CACGCTGAGGTATTTTCAATTTCTGTTGTTTCAAAAAAA
*
31506540 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTCT
1 -CAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGACACGCTGAGGTATTTTCAATTTCTGTCT
***** * *
31506605 T-TCAAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-TGGGACACGCTGAGATA
64 TGT---TTGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGG-CACGCTGAGGT-
* **
31506668 ATTTT-TATTTC---TGTTTC-AAAATT
124 ATTTTCAATTTCTGTTGTTTCAAAAAAA
* * * * * *
31506691 CAACTCATA--ACAAAAAGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGTC--
1 CAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGACACGCTGAGGTATTTTCAATTTCTGTCTT
*** * * * * * * **
31506752 -TTTCAAAAAATTCAACTCATACTGCAAGAAGTGAGTTAAGCCTCAAGACACTTTGAGGTATTTT
65 GTTTGTCAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTT
*
31506816 CAATTTCTG-TCTTTCAAAAAAA
129 CAATTTCTGTTGTTTCAAAAAAA
* * * * * * *
31506838 TCAGCTCATATTGCGAGAGGTGAGTGGAACCTC-AAGACGCTGAGGTGTTTTCCATTT
1 -CAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACGCTGAGGTATTTTCAATTT
31506895 TTGTTCTTCA
Statistics
Matches: 782, Mismatches: 136, Indels: 133
0.74 0.13 0.13
Matches are distributed among these distances:
143 11 0.01
144 41 0.05
145 4 0.01
146 12 0.02
147 98 0.13
148 105 0.13
149 26 0.03
150 25 0.03
151 9 0.01
152 41 0.05
153 24 0.03
154 20 0.03
155 6 0.01
156 45 0.06
157 15 0.02
158 84 0.11
159 71 0.09
160 8 0.01
161 4 0.01
162 1 0.00
164 2 0.00
165 3 0.00
166 25 0.03
168 42 0.05
169 34 0.04
170 2 0.00
171 24 0.03
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.33
Consensus pattern (151 bp):
CAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACGCTGAGGTATTTTCAATTTCTGTCTTG
TTTGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCA
ATTTCTGTTGTTTCAAAAAAA
Found at i:31506404 original size:305 final size:296
Alignment explanation
Indices: 31505763--31506862 Score: 849
Period size: 305 Copynumber: 3.6 Consensus size: 296
31505753 TTTTTTAAAT
* * * *
31505763 CAACTCATATTGCGGGAGGTGAGTTGAGCCTTTCGG-CACGCTGAGGTATTTACAATTGTTGTTT
1 CAACTCATATTGCGAGAGGTGAGTTGAGCC--TCGGACACGCTGAGGTATTTTCAATTCTTTTTT
* * ** * * * * ** *
31505827 GTCAAAAATCAACTCATGTTACGGGAGGTGAGTTGAGCCTCGGGGCACGCCAAGGTATTTTCAAA
64 ATAAAAAAAAAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGACACGCTGAGGTATTTTCAAT
* * * *
31505892 TTCTACTTTCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTTGGCCCACGTGTTGA-
128 TTCTA-TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCACACGTGCTGAG
* * * * * *
31505956 GTCACTTTCAATTTCTATTTTTATGTTTGTTTTTTAAATCAACTCATATTCCGGGAGGTGAGTTG
192 GT-AATTTCAATTTC--TGTCTATGTTTG----TAAAATCAACTCATATTGCGAGAGGTGAGTTG
* * *
31506021 AGCCTCGGGGCACGCTGAGGTATTTTCAATTGCTGTTTGTCAAAAAT
250 AGCCTCAGGGCACGCTGAGGTATTTTCAATTGCTGTTTGTAAAAAAA
* * *
31506068 CAACTCATGTTGCGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGATATTTTCAAATTCTATTTT
1 CAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGACACGCTGAGGTATTTTC-AATTCT-TTTT
* * * *
31506133 TATAAAAAAAAAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGACATGCTGAGGTAATTGCAAT
63 TATAAAAAAAAAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACGCTGAGGTATTTTCAAT
* * *
31506198 TTCTATTGTC-AAAAAATCAACTAATATTGCAAGAGGTGAGTTGAGCCTCGGCTCACGTGCTGAG
128 TTCTATT-TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCACACGTGCTGAG
* * *
31506262 GTATTTTCAATTTCTGTCTCTGTTTGTCACAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
192 GTAATTTCAATTTCTGTCTATGTTTGT-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
* *
31506327 AGGGTACGCTGAGGTATTTTCAATTTCTGTTTGTTTTTAAAAAAA
256 AGGGCACGCTGAGGTATTTTCAATTGCTGTTTG----TAAAAAAA
* * *
31506372 CAAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGTCATACGCTGAGGTATTTTCCATTTCTGT
1 C-AACTCATATTGCGAGAGGTGAGTTGAGCCTC-GG--ACACGCTGAGGTATTTT-CAATTCT-T
* *
31506437 TCTTTAATTTCTACGGTTCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTTGACTGA
60 T-TTT-A----TA------AAAAAAA--AACTCATATTGCGAGAGGTGAGTTGAGCC-T--CGGA
* *
31506502 CACGTTGAGGTATTTTCAATTTCTGCCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTG
108 CACGCTGAGGTATTTTCAATTTCT--ATTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTG
* ******
31506567 AGCCTCAGG-ACAC--GCTGAGGTAATTTCAATTTCTGTCTTTCAAAAAAAAAAATCAACTCATA
171 AGCCTC-GGCACACGTGCTGAGGTAATTTCAATTTCTGTCTAT--GTTTGTAAAATCAACTCATA
* * * * * *
31506629 TTGCGAGAGGTGAGTTGAGCCT-TGGGACACGCTGAGATAATTTT-TATTTCTG-TT-TCAAAAT
233 TTGCGAGAGGTGAGTTGAGCCTCAGGG-CACGCTGAGGT-ATTTTCAATTGCTGTTTGTAAAAAA
*
31506690 T
296 A
* * * * * *
31506691 CAACTCATA--ACAAAAAGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGTCTT
1 CAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGACACGCTGAGGTATTTTCAA-TTCT-T-TT
* *** * * * * * **
31506754 TCA-AAAAATTCAACTCATACTGCAAGAAGTGAGTTAAGCCTCAAGACACTTTGAGGTATTTTCA
62 TTATAAAAAAAAAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGACACGCTGAGGTATTTTCA
* *
31506818 ATTTCTGTCTTTCAAAAAAATCAGCTCATATTGCGAGAGGTGAGT
126 ATTTC--TATTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGT
31506863 GGAACCTCAA
Statistics
Matches: 654, Mismatches: 96, Indels: 97
0.77 0.11 0.11
Matches are distributed among these distances:
297 1 0.00
298 60 0.09
299 2 0.00
300 88 0.13
302 4 0.01
303 11 0.02
304 9 0.01
305 132 0.20
306 30 0.05
307 59 0.09
308 5 0.01
309 1 0.00
313 5 0.01
314 23 0.04
315 1 0.00
316 19 0.03
318 8 0.01
319 13 0.02
321 27 0.04
322 1 0.00
324 53 0.08
325 53 0.08
326 47 0.07
327 2 0.00
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (296 bp):
CAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACGCTGAGGTATTTTCAATTCTTTTTTAT
AAAAAAAAAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACGCTGAGGTATTTTCAATTTC
TATTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCACACGTGCTGAGGTAA
TTTCAATTTCTGTCTATGTTTGTAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGC
ACGCTGAGGTATTTTCAATTGCTGTTTGTAAAAAAA
Found at i:31506648 original size:79 final size:75
Alignment explanation
Indices: 31506453--31506894 Score: 488
Period size: 75 Copynumber: 5.9 Consensus size: 75
31506443 ATTTCTACGG
* * * *
31506453 TTCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTTGACTGACACGTTGAGGTATTTT
1 TTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC-TCA-AGACACGCTGAGGTATTTT
*
31506518 CAATTTCTGCCT
64 CAATTTCTGTCT
* *
31506530 TTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCA
1 TTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCA
31506595 ATTTCTGTCT
66 ATTTCTGTCT
*** *
31506605 TTCAAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGACACGCTGAGATAAT
1 TTC----AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGT-AT
*
31506670 TTT-TATTTCTG--T
61 TTTCAATTTCTGTCT
* * * * * *
31506682 TTC--AAAATTCAACTCATA--ACAAAAAGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCA
1 TTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCA
31506743 ATTTCTGTCT
66 ATTTCTGTCT
* * * * * **
31506753 TTCAAAAAATTCAACTCATACTGCAAGAAGTGAGTTAAGCCTCAAGACACTTTGAGGTATTTTCA
1 TTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCA
31506818 ATTTCTGTCT
66 ATTTCTGTCT
* * * * *
31506828 TTCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTGGAACCTCAAG--ACGCTGAGGTGTTTTCC
1 TTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCA
31506891 ATTT
66 ATTT
31506895 TTGTTCTTCA
Statistics
Matches: 315, Mismatches: 38, Indels: 28
0.83 0.10 0.07
Matches are distributed among these distances:
68 5 0.02
69 34 0.11
71 18 0.06
73 32 0.10
75 117 0.37
76 2 0.01
77 44 0.14
79 59 0.19
80 4 0.01
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (75 bp):
TTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCA
ATTTCTGTCT
Found at i:31508717 original size:25 final size:23
Alignment explanation
Indices: 31508665--31508719 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
31508655 TATAAATAGT
31508665 AATAGTGTTAGAAATATACTATA
1 AATAGTGTTAGAAATATACTATA
* *
31508688 TATAGTGTTTGAAGTATATAC-ATAA
1 AATAGTGTTAGAA--ATATACTAT-A
31508713 AATAGTG
1 AATAGTG
31508720 AAACTATAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 11 0.42
24 2 0.08
25 13 0.50
ACGTcount: A:0.44, C:0.04, G:0.16, T:0.36
Consensus pattern (23 bp):
AATAGTGTTAGAAATATACTATA
Found at i:31508801 original size:22 final size:22
Alignment explanation
Indices: 31508775--31508849 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 22
31508765 TATAAAATAG
*
31508775 ATATAAAAAAAATATGTACATA
1 ATATAAAAAAAATATATACATA
* *
31508797 ATATAGTGTAAAAAATACATACATA
1 ATATA---AAAAAAATATATACATA
**
31508822 ATATAATTAAAATATATACATA
1 ATATAAAAAAAATATATACATA
*
31508844 AGATAA
1 ATATAA
31508850 CATGTAGAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
22 23 0.55
25 19 0.45
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.29
Consensus pattern (22 bp):
ATATAAAAAAAATATATACATA
Found at i:31508819 original size:25 final size:25
Alignment explanation
Indices: 31508781--31508989 Score: 117
Period size: 25 Copynumber: 8.4 Consensus size: 25
31508771 ATAGATATAA
* *
31508781 AAAAAATATGTACATAATATAGTGT
1 AAAAAATATATACATAATATAGTAT
*
31508806 AAAAAATACATACATAATATA--AT
1 AAAAAATATATACATAATATAGTAT
* * *
31508829 -TAAAATATATACATAAGATAACATGTAG
1 AAAAAATATATACAT-A-AT-ATA-GTAT
* *
31508857 AAAAAAAATATAAATAATATAGTAT
1 AAAAAATATATACATAATATAGTAT
* * *
31508882 TAAAGATATATACATAAAATAGTAT
1 AAAAAATATATACATAATATAGTAT
* * * *
31508907 AATATATATATACGTAATATAGAAT
1 AAAAAATATATACATAATATAGTAT
** * *
31508932 -TTAGA-ATATACCTAATATA-T-T
1 AAAAAATATATACATAATATAGTAT
* *
31508953 AAAAGAATATATATATAATATAATATT
1 AAAA-AATATATACATAATATAGTA-T
*
31508980 AAGAAATATA
1 AAAAAATATA
31508990 ATAATAACAA
Statistics
Matches: 138, Mismatches: 33, Indels: 25
0.70 0.17 0.13
Matches are distributed among these distances:
21 1 0.01
22 13 0.09
23 16 0.12
24 17 0.12
25 64 0.46
26 8 0.06
27 6 0.04
28 2 0.01
29 11 0.08
ACGTcount: A:0.57, C:0.04, G:0.07, T:0.32
Consensus pattern (25 bp):
AAAAAATATATACATAATATAGTAT
Found at i:31508895 original size:76 final size:81
Alignment explanation
Indices: 31508745--31508916 Score: 192
Period size: 76 Copynumber: 2.2 Consensus size: 81
31508735 ATGTTAAGAT
* * * * *
31508745 ATATATAATATATACATATGTATAAAATAGATATAAAAAAAATATGTACATAATATAGTGTAAAA
1 ATATAAAATATATACATAAGTATAAAATAGATAGAAAAAAAATA-GTAAATAATATAGTATAAAA
*
31508810 AATACATACATAATATA
65 AATACATACATAAAATA
* * *
31508827 AT-TAAAATATATACATAAG-ATAACAT-G-TAGAAAAAAAATA-TAAATAATATAGTATTAAAG
1 ATATAAAATATATACATAAGTATAAAATAGATAGAAAAAAAATAGTAAATAATATAGTATAAAAA
*
31508887 ATATATACATAAAATA
66 ATACATACATAAAATA
* *
31508903 GTATAATATATATA
1 ATATAAAATATATA
31508917 TACGTAATAT
Statistics
Matches: 77, Mismatches: 12, Indels: 7
0.80 0.12 0.07
Matches are distributed among these distances:
76 31 0.40
77 10 0.13
78 12 0.16
79 1 0.01
80 6 0.08
81 15 0.19
82 2 0.03
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.31
Consensus pattern (81 bp):
ATATAAAATATATACATAAGTATAAAATAGATAGAAAAAAAATAGTAAATAATATAGTATAAAAA
ATACATACATAAAATA
Found at i:31508971 original size:24 final size:23
Alignment explanation
Indices: 31508944--31508995 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
31508934 AGAATATACC
*
31508944 TAATATATTA-AAAGAATATATATA
1 TAATATAATATAAAGAA-ATATA-A
*
31508968 TAATATAATATTAAGAAATATAA
1 TAATATAATATAAAGAAATATAA
31508991 TAATA
1 TAATA
31508996 ACAAAAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 6 0.24
24 14 0.56
25 5 0.20
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (23 bp):
TAATATAATATAAAGAAATATAA
Found at i:31509315 original size:16 final size:16
Alignment explanation
Indices: 31509277--31509315 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
31509267 ATCTCCAAAA
*
31509277 AAAAACTAGCCTCTCC
1 AAAAACTAGCCTCTAC
*
31509293 AAAAACTAGCCTTTAC
1 AAAAACTAGCCTCTAC
*
31509309 AATAACT
1 AAAAACT
31509316 CTTCTCCTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.44, C:0.28, G:0.05, T:0.23
Consensus pattern (16 bp):
AAAAACTAGCCTCTAC
Found at i:31509500 original size:18 final size:18
Alignment explanation
Indices: 31509477--31509560 Score: 57
Period size: 18 Copynumber: 5.3 Consensus size: 18
31509467 ACAAGTGGTG
31509477 GTGGAGCAAGTGTGGCTA
1 GTGGAGCAAGTGTGGCTA
*
31509495 GT-G-G--AGT-AGG-TA
1 GTGGAGCAAGTGTGGCTA
*
31509507 GTAGAGCAAGTGTGGCTA
1 GTGGAGCAAGTGTGGCTA
*
31509525 GT--AG--AGT-TGG-TG
1 GTGGAGCAAGTGTGGCTA
31509537 GTGGAGCAAGTGTGGCTA
1 GTGGAGCAAGTGTGGCTA
31509555 GTGGAG
1 GTGGAG
31509561 TTGGTGATGG
Statistics
Matches: 50, Mismatches: 4, Indels: 24
0.64 0.05 0.31
Matches are distributed among these distances:
12 7 0.14
13 6 0.12
14 9 0.18
16 9 0.18
17 6 0.12
18 13 0.26
ACGTcount: A:0.23, C:0.07, G:0.46, T:0.24
Consensus pattern (18 bp):
GTGGAGCAAGTGTGGCTA
Found at i:31509562 original size:30 final size:30
Alignment explanation
Indices: 31509472--31509566 Score: 154
Period size: 30 Copynumber: 3.2 Consensus size: 30
31509462 TAGGTACAAG
31509472 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
* * * *
31509502 AGGTAGTAGAGCAAGTGTGGCTAGTAGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
31509532 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
31509562 TGGTG
1 TGGTG
31509567 ATGGCAAAGG
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 57 1.00
ACGTcount: A:0.20, C:0.06, G:0.47, T:0.26
Consensus pattern (30 bp):
TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
Found at i:31510200 original size:30 final size:30
Alignment explanation
Indices: 31510164--31510225 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
31510154 GATTGCATTT
31510164 GATCGATTATACTAAATCTCTTTGATCAAG
1 GATCGATTATACTAAATCTCTTTGATCAAG
*
31510194 GATCGATTATACTAAATCTCTTTGATTAAG
1 GATCGATTATACTAAATCTCTTTGATCAAG
31510224 GA
1 GA
31510226 ATTGAGCACT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.37
Consensus pattern (30 bp):
GATCGATTATACTAAATCTCTTTGATCAAG
Found at i:31512708 original size:19 final size:19
Alignment explanation
Indices: 31512684--31512720 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
31512674 TAGTCCACAC
31512684 GAAAGACGCATTCTTACAT
1 GAAAGACGCATTCTTACAT
31512703 GAAAGACGCATTCTTACA
1 GAAAGACGCATTCTTACA
31512721 GAACATCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (19 bp):
GAAAGACGCATTCTTACAT
Found at i:31517180 original size:21 final size:21
Alignment explanation
Indices: 31517154--31517194 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
31517144 AGACAAGCGA
* *
31517154 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
31517175 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
31517195 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:31524919 original size:12 final size:12
Alignment explanation
Indices: 31524902--31524932 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
31524892 AGTACTACCT
*
31524902 CGGCCTCGACGA
1 CGGCCTCGACCA
31524914 CGGCCTCGACCA
1 CGGCCTCGACCA
31524926 CGGCCTC
1 CGGCCTC
31524933 TTCCCCGAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.13, C:0.48, G:0.29, T:0.10
Consensus pattern (12 bp):
CGGCCTCGACCA
Found at i:31526477 original size:9 final size:9
Alignment explanation
Indices: 31526465--31526497 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
31526455 GAATTATTCG
31526465 AATCGAGTT
1 AATCGAGTT
31526474 AATCGAGTT
1 AATCGAGTT
*
31526483 AATCGAATT
1 AATCGAGTT
31526492 AATCGA
1 AATCGA
31526498 ATCAACTCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.30
Consensus pattern (9 bp):
AATCGAGTT
Found at i:31526498 original size:9 final size:9
Alignment explanation
Indices: 31526465--31526510 Score: 56
Period size: 9 Copynumber: 5.0 Consensus size: 9
31526455 GAATTATTCG
*
31526465 AATCGAGTT
1 AATCGAATT
*
31526474 AATCGAGTT
1 AATCGAATT
31526483 AATCGAATT
1 AATCGAATT
*
31526492 AATCGAATC
1 AATCGAATT
31526501 AACTCGAATT
1 AA-TCGAATT
31526511 TTTTTTTCGA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
9 27 0.82
10 6 0.18
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.30
Consensus pattern (9 bp):
AATCGAATT
Found at i:31526896 original size:22 final size:23
Alignment explanation
Indices: 31526869--31526914 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
31526859 TTATTCAAAC
31526869 CCCTTA-CCCCATTTCAACGAAA
1 CCCTTACCCCCATTTCAACGAAA
*
31526891 CCCTTACCCCCCATTTCTACGAAA
1 CCCTTA-CCCCCATTTCAACGAAA
31526915 GACGAAACCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 6 0.29
24 15 0.71
ACGTcount: A:0.28, C:0.43, G:0.04, T:0.24
Consensus pattern (23 bp):
CCCTTACCCCCATTTCAACGAAA
Found at i:31532503 original size:32 final size:32
Alignment explanation
Indices: 31532466--31532562 Score: 176
Period size: 32 Copynumber: 3.0 Consensus size: 32
31532456 AATGCTTATC
31532466 ATGCCCATCATCCATTAACTATTAAAATGCTA
1 ATGCCCATCATCCATTAACTATTAAAATGCTA
*
31532498 ATGCCCATCATTCATTAACTATTAAAATGCTA
1 ATGCCCATCATCCATTAACTATTAAAATGCTA
*
31532530 ATGCACATCATCCATTAACTATTAAAATGCTA
1 ATGCCCATCATCCATTAACTATTAAAATGCTA
31532562 A
1 A
31532563 AATGCATACA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 62 1.00
ACGTcount: A:0.39, C:0.23, G:0.06, T:0.32
Consensus pattern (32 bp):
ATGCCCATCATCCATTAACTATTAAAATGCTA
Found at i:31532582 original size:32 final size:30
Alignment explanation
Indices: 31532479--31532583 Score: 113
Period size: 32 Copynumber: 3.3 Consensus size: 30
31532469 CCCATCATCC
31532479 ATTAACTATTAAAATGCTAATGCCCAT-CATT
1 ATTAACTATTAAAATGCTAATG--CATACATT
* *
31532510 CATTAACTATTAAAATGCTAATGCACATCATCC
1 -ATTAACTATTAAAATGCTAATGCATA-CAT-T
31532543 ATTAACTATTAAAATGCTAAAATGCATACATT
1 ATTAACTATTAAAATGCT--AATGCATACATT
*
31532575 ATCAACTAT
1 ATTAACTAT
31532584 CCATCACCTT
Statistics
Matches: 63, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
30 2 0.03
32 51 0.81
33 3 0.05
34 7 0.11
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.33
Consensus pattern (30 bp):
ATTAACTATTAAAATGCTAATGCATACATT
Found at i:31534481 original size:27 final size:25
Alignment explanation
Indices: 31534451--31534513 Score: 67
Period size: 24 Copynumber: 2.4 Consensus size: 25
31534441 TCAAATCTTC
*
31534451 AAGGTGGAGATTGTTGAAAAGTCAAA
1 AAGGTGGAG-GTGTTGAAAAGTCAAA
31534477 TAAGGT--AGGTGTTGAAAAGTCAAA
1 -AAGGTGGAGGTGTTGAAAAGTCAAA
31534501 AATGGTGGGAGGT
1 AA-GGT-GGAGGT
31534514 ACAATTGGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
23 2 0.06
24 18 0.58
25 2 0.06
27 9 0.29
ACGTcount: A:0.38, C:0.03, G:0.35, T:0.24
Consensus pattern (25 bp):
AAGGTGGAGGTGTTGAAAAGTCAAA
Done.