Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold153
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: 3137677
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 499 characters in sequence are not A, C, G, or T
File 1 of 24
Found at i:1936 original size:42 final size:42
Alignment explanation
Indices: 1883--2687 Score: 806
Period size: 42 Copynumber: 18.8 Consensus size: 42
1873 TTTTGTTTTC
1883 CCTT-AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTT
1 CCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTT
*
1924 CCTTCAGCCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTT
1 CCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTT
* *
1966 CCCTT-AGTCTACCTGTTGGCTTTGACCCTGGAGACTTTGGAGACTTTCCTAT
1 -CCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGAC--T------TTT-CT-T
* * **
2018 CCCTTCAGTCTGCCTGTCAGCTTTGACTCTGGAGACTGCCTCATT
1 -CCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACT-TTTC-TT
** *
2063 --TAAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCATC
1 CCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC-TT
*
2104 CCTT-AGTCTGCCTGTCGGCTTTGACCCTAGAGA-TTTTCCTT
1 CCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTT-CTT
* * * **
2145 CCCTT-AGTCTGCTTGTCGGCTTTGTCCCTGAAGACTTTTCAA
1 -CCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTT
* * *
2187 CCCTCAATCTACCTGTCGGCTTTGACCCTGGAGACTTTTCTTT
1 CCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC-TT
* * * * * *
2230 CCCTAAGTCTGCCTATCGGCTTCGTCCCTAGAGAC-TTTCTTT
1 CCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC-TT
* *
2272 CCCTCAGTCTACCTGTCGGCTTTGACCCTGGAGACTTTTCTTT
1 CCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC-TT
* * *
2315 CCCTAAGTCTGCCTGTCGGCTTTGGCCCTGGAGACTTTTCTT
1 CCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTT
*
2357 CCCTT-AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTT
1 -CCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTT
* *
2399 CCCTT-AGTCGGCCTGTCGGCTTTGACCCTGGAGACTTTCCTT
1 -CCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTT
2441 CCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTT
1 CCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTT
* * *
2483 CCTTCAATCTGCCTATCGGCTTTGACCCTGGAGACTTTCCTAT
1 CCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCT-T
* * **
2526 CCCTTCAGTCTGCCTGTCAGCTTTGACTCTGGAGAC-TGCCTT
1 -CCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTT
** * * *
2568 ATTTAAAGTCTGTCTGTCGGCTTTGACCCTGGAGACTTTTCATC
1 CCTT-CAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC-TT
* * *
2612 CCTT-AGTCTACCTGTCGGTTTTGACCTTGGAGACTTTTCTTT
1 CCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC-TT
* * * * *
2654 CCCTAAGTCTGCCCGTTGGCTTTGACCCGGGAGA
1 CCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGA
2688 GTATTTTCTT
Statistics
Matches: 645, Mismatches: 89, Indels: 58
0.81 0.11 0.07
Matches are distributed among these distances:
41 22 0.03
42 432 0.67
43 114 0.18
44 35 0.05
45 2 0.00
46 2 0.00
50 3 0.00
51 3 0.00
52 6 0.01
53 26 0.04
ACGTcount: A:0.13, C:0.30, G:0.21, T:0.36
Consensus pattern (42 bp):
CCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTT
Found at i:2034 original size:53 final size:51
Alignment explanation
Indices: 1952--2054 Score: 143
Period size: 53 Copynumber: 2.0 Consensus size: 51
1942 GCTTTGACCC
* **
1952 TGGAGACTTTTCTTCCCTTAGTCTACCTGTTGGCTTTGACCCTGGAGACTT
1 TGGAGACTTTCCTTCCCTTAGTCTACCTGTCAGCTTTGACCCTGGAGACTT
* *
2003 TGGAGACTTTCCTATCCCTTCAGTCTGCCTGTCAGCTTTGACTCTGGAGACT
1 TGGAGACTTTCCT-TCCCTT-AGTCTACCTGTCAGCTTTGACCCTGGAGACT
2055 GCCTCATTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
51 12 0.27
52 6 0.13
53 27 0.60
ACGTcount: A:0.15, C:0.27, G:0.21, T:0.37
Consensus pattern (51 bp):
TGGAGACTTTCCTTCCCTTAGTCTACCTGTCAGCTTTGACCCTGGAGACTT
Found at i:2385 original size:254 final size:253
Alignment explanation
Indices: 1880--2687 Score: 1075
Period size: 254 Copynumber: 3.1 Consensus size: 253
1870 CTTTTTTGTT
*
1880 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTTCCTTCAGCCTGCCTGTCGGCT
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTTCCTTCAGTCTGCCTGTCGGCT
* * * *
1945 TTGACCCTGGAGACTTTTCTTCCCTTAGTCTACCTGTTGGCTTTGACCCTGGAGACTTTGGAGAC
66 TTGACCCTGGAGACTTTTCTTCCCTAAGTCTGCCTATCGGCTTTGACCCT----A-----GAGAC
*
2010 TTTCCTATCCCTTCAGTCTGCCTGTCAGCTTTGACTCTGGAGACTGCCTCATTTAAAGTCTGCCT
122 TTTCCTATCCCTTCAGTCTGCCTGTCAGCTTTGACTCTGGAGACTGCTTC-TTTAAAGTCTGCCT
*
2075 GTCGGCTTTGACCCTGGAGACTTTTCATCCCTTAGTCTGCCTGTCGGCTTTGACCCTAGAGATTT
186 GTCGGCTTTGACCCTGGAGACTTTTCATCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGATTT
2140 TCC
251 TCC
* * * ** * * *
2143 TTCCCTTAGTCTGCTTGTCGGCTTTGTCCCTGAAGACTTTTCAACCCTCAATCTACCTGTCGGCT
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTTCCTTCAGTCTGCCTGTCGGCT
* * *
2208 TTGACCCTGGAGACTTTTCTTTCCCTAAGTCTGCCTATCGGCTTCGTCCCTAGAGACTTT-CTTT
66 TTGACCCTGGAGACTTTTC-TTCCCTAAGTCTGCCTATCGGCTTTGACCCTAGAGACTTTCCTAT
* * * * *
2272 CCC-TCAGTCTACCTGTCGGCTTTGACCCTGGAGACT-TTTCTTTCCCTAAGTCTGCCTGTCGGC
130 CCCTTCAGTCTGCCTGTCAGCTTTGACTCTGGAGACTGCTTCTTT---AAAGTCTGCCTGTCGGC
* * *
2335 TTTGGCCCTGGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCC
192 TTTGACCCTGGAGACTTTTCATCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGATTTTCC
* *
2397 TTCCCTTAGTCGGCCTGTCGGCTTTGACCCTGGAGACTTTCCTTCCTTCAGTCTGCCTGTCGGCT
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTTCCTTCAGTCTGCCTGTCGGCT
* *
2462 TTGACCCTGGAGACTTTTCTTCCTTCAA-TCTGCCTATCGGCTTTGACCCTGGAGACTTTCCTAT
66 TTGACCCTGGAGACTTTTCTTCCCT-AAGTCTGCCTATCGGCTTTGACCCTAGAGACTTTCCTAT
* *
2526 CCCTTCAGTCTGCCTGTCAGCTTTGACTCTGGAGACTGCCTTATTTAAAGTCTGTCTGTCGGCTT
130 CCCTTCAGTCTGCCTGTCAGCTTTGACTCTGGAGACTG-CTTCTTTAAAGTCTGCCTGTCGGCTT
* * * *
2591 TGACCCTGGAGACTTTTCATCCCTTAGTCTACCTGTCGGTTTTGACCTTGGAGACTTTTCT
194 TGACCCTGGAGACTTTTCATCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGA-TTTTCC
* * * *
2652 TTCCCTAAGTCTGCCCGTTGGCTTTGACCCGGGAGA
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGA
2688 GTATTTTCTT
Statistics
Matches: 475, Mismatches: 60, Indels: 28
0.84 0.11 0.05
Matches are distributed among these distances:
251 3 0.01
252 2 0.00
253 63 0.13
254 228 0.48
255 73 0.15
257 5 0.01
260 1 0.00
263 75 0.16
264 25 0.05
ACGTcount: A:0.13, C:0.30, G:0.21, T:0.36
Consensus pattern (253 bp):
TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTTCCTTCAGTCTGCCTGTCGGCT
TTGACCCTGGAGACTTTTCTTCCCTAAGTCTGCCTATCGGCTTTGACCCTAGAGACTTTCCTATC
CCTTCAGTCTGCCTGTCAGCTTTGACTCTGGAGACTGCTTCTTTAAAGTCTGCCTGTCGGCTTTG
ACCCTGGAGACTTTTCATCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGATTTTCC
Found at i:3175 original size:43 final size:43
Alignment explanation
Indices: 3124--3247 Score: 187
Period size: 43 Copynumber: 2.9 Consensus size: 43
3114 CATTGCATGC
* *
3124 ATTTTCATTTCATGTTTTTCATGTAACATTTCATGCATGCATA
1 ATTTTCATTTCATGCTTTTCACGTAACATTTCATGCATGCATA
3167 ATTTTCATTTCATGCTTTTCACGTAACATTTCATGCATGCATA
1 ATTTTCATTTCATGCTTTTCACGTAACATTTCATGCATGCATA
* **
3210 ATTTTCATTTCATGCATTTCA-AAAACATTTCATTGCAT
1 ATTTTCATTTCATGCTTTTCACGTAACATTTCA-TGCAT
3248 TGCACTTCAT
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
42 9 0.12
43 66 0.88
ACGTcount: A:0.27, C:0.19, G:0.08, T:0.46
Consensus pattern (43 bp):
ATTTTCATTTCATGCTTTTCACGTAACATTTCATGCATGCATA
Found at i:3178 original size:22 final size:22
Alignment explanation
Indices: 3150--3226 Score: 81
Period size: 22 Copynumber: 3.5 Consensus size: 22
3140 TTTCATGTAA
3150 CATTTCATGCATGCATAATTTT
1 CATTTCATGCATGCATAATTTT
* *
3172 CATTTCATGCTTTTCACGTAA----
1 CATTTCATGC-ATGCA--TAATTTT
3193 CATTTCATGCATGCATAATTTT
1 CATTTCATGCATGCATAATTTT
3215 CATTTCATGCAT
1 CATTTCATGCAT
3227 TTCAAAAACA
Statistics
Matches: 44, Mismatches: 4, Indels: 14
0.71 0.06 0.23
Matches are distributed among these distances:
18 3 0.07
20 3 0.07
21 10 0.23
22 22 0.50
23 3 0.07
25 3 0.07
ACGTcount: A:0.26, C:0.21, G:0.09, T:0.44
Consensus pattern (22 bp):
CATTTCATGCATGCATAATTTT
Found at i:3248 original size:5 final size:5
Alignment explanation
Indices: 3235--3358 Score: 140
Period size: 5 Copynumber: 24.8 Consensus size: 5
3225 ATTTCAAAAA
* * * * * *
3235 CATTT CATTG CATTG CACTT CATTT CATTT CATTG CATTT CATTG CATTG
1 CATTT CATTT CATTT CATTT CATTT CATTT CATTT CATTT CATTT CATTT
* * *
3285 CATTT CATTT CATTT CATTT CATTT CATTT CATTG CATTG CATTT CATTA
1 CATTT CATTT CATTT CATTT CATTT CATTT CATTT CATTT CATTT CATTT
* * *
3335 CATTG CATTG CATTT CATTA CATT
1 CATTT CATTT CATTT CATTT CATT
3359 GCTTTCATGC
Statistics
Matches: 105, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 105 1.00
ACGTcount: A:0.22, C:0.21, G:0.07, T:0.50
Consensus pattern (5 bp):
CATTT
Found at i:3258 original size:20 final size:20
Alignment explanation
Indices: 3235--3360 Score: 163
Period size: 20 Copynumber: 6.5 Consensus size: 20
3225 ATTTCAAAAA
*
3235 CATTTCATTGCATTGCACTT
1 CATTTCATTGCATTGCATTT
*
3255 CATTTCA-T---TT-CATTG
1 CATTTCATTGCATTGCATTT
3270 CATTTCATTGCATTGCATTT
1 CATTTCATTGCATTGCATTT
* *
3290 CATTTCATTTCATTTCATTT
1 CATTTCATTGCATTGCATTT
3310 CATTTCATTGCATTGCATTT
1 CATTTCATTGCATTGCATTT
*
3330 CATTACATTGCATTGCATTT
1 CATTTCATTGCATTGCATTT
*
3350 CATTACATTGC
1 CATTTCATTGC
3361 TTTCATGCAT
Statistics
Matches: 93, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
15 10 0.11
16 3 0.03
19 3 0.03
20 77 0.83
ACGTcount: A:0.21, C:0.21, G:0.08, T:0.49
Consensus pattern (20 bp):
CATTTCATTGCATTGCATTT
Found at i:8620 original size:111 final size:115
Alignment explanation
Indices: 8410--8624 Score: 307
Period size: 113 Copynumber: 1.9 Consensus size: 115
8400 ACAAAAAACT
* *
8410 AATCATTATATAGTAAAATTGAAAACTAAAAAAATATTATTTAATTAATTTATTAATTTTAAGTT
1 AATCATTATATAATAAAATTGAAAACTAAAAAAATATTATTTAATTAATATATTAATTTTAAGTT
8475 TAGAAGAAAGATATAAAATATAATTTTATAAATTAGTTATGAAATAAAAA
66 TAGAAGAAAGATATAAAATATAATTTTATAAATTAGTTATGAAATAAAAA
* * *
8525 AATCATTATTTAATAGAATTGAAAACT-AAAAATTATT-TTTAATTAATATATT-ATTTATAAGT
1 AATCATTATATAATAAAATTGAAAACTAAAAAAATATTATTTAATTAATATATTAATTT-TAAGT
* *
8587 TATA-AATAAGGAT-T-AAATATAATTTTATAAATTAGTTA
65 T-TAGAAGAAAGATATAAAATATAATTTTATAAATTAGTTA
8625 AATTATTGTT
Statistics
Matches: 91, Mismatches: 7, Indels: 8
0.86 0.07 0.08
Matches are distributed among these distances:
111 24 0.26
112 5 0.05
113 27 0.30
114 11 0.12
115 24 0.26
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.41
Consensus pattern (115 bp):
AATCATTATATAATAAAATTGAAAACTAAAAAAATATTATTTAATTAATATATTAATTTTAAGTT
TAGAAGAAAGATATAAAATATAATTTTATAAATTAGTTATGAAATAAAAA
Found at i:9174 original size:48 final size:48
Alignment explanation
Indices: 9027--9176 Score: 187
Period size: 48 Copynumber: 3.1 Consensus size: 48
9017 TTTGCTCAAC
* * *
9027 AAATTAATTTGCTGCATGTATAGGAGAAAGGTG-ATGAATACATTTAAT
1 AAATTAATTTGGTTCATGTATAGGAGAGAGG-GAATGAATACATTTAAT
* * *
9075 AAAGTAATTTGGTTCATGTATAGGAGAGA-AGAGATGAATATATTTAAT
1 AAATTAATTTGGTTCATGTATAGGAGAGAGGGA-ATGAATACATTTAAT
* * *
9123 AAATTAATTTGGTTCATGTATGGGAGAGAGGGAATGTATACATATAAT
1 AAATTAATTTGGTTCATGTATAGGAGAGAGGGAATGAATACATTTAAT
9171 AAATTA
1 AAATTA
9177 TTTTAATAAA
Statistics
Matches: 87, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
46 1 0.01
48 84 0.97
49 2 0.02
ACGTcount: A:0.41, C:0.04, G:0.22, T:0.33
Consensus pattern (48 bp):
AAATTAATTTGGTTCATGTATAGGAGAGAGGGAATGAATACATTTAAT
Found at i:9986 original size:3 final size:3
Alignment explanation
Indices: 9978--10004 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
9968 AAATAAAGAA
9978 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
10005 GATCCCACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:20459 original size:13 final size:13
Alignment explanation
Indices: 20441--20471 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
20431 ACAATTCATC
20441 ATGTATTGATACA
1 ATGTATTGATACA
20454 ATGTATTGATACA
1 ATGTATTGATACA
20467 ATGTA
1 ATGTA
20472 CCATGTATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.16, T:0.39
Consensus pattern (13 bp):
ATGTATTGATACA
Found at i:20486 original size:33 final size:33
Alignment explanation
Indices: 20419--20487 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
20409 CCATTAGAAG
* **
20419 CAATGTATCGATACAATTCATCATGTATTGATA
1 CAATGTATCGATACAATTCACCATGTATCAATA
*
20452 CAATGTATTGATACAATGT-ACCATGTATCAATA
1 CAATGTATCGATACAAT-TCACCATGTATCAATA
20485 CAA
1 CAA
20488 ACAGTGGTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 30 0.97
34 1 0.03
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (33 bp):
CAATGTATCGATACAATTCACCATGTATCAATA
Found at i:20564 original size:19 final size:19
Alignment explanation
Indices: 20517--20572 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
20507 TTGCCAGTTT
**
20517 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
*
20537 CATGCATCGATACAATGAA
1 CATGTATCGATACAATGAA
20556 CATGTATCGATACAATG
1 CATGTATCGATACAATG
20573 TATCAATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:34257 original size:1 final size:1
Alignment explanation
Indices: 34247--34387 Score: 111
Period size: 1 Copynumber: 141.0 Consensus size: 1
34237 TGGCAATTGG
* * * ** * * * *
34247 AAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAGAAAAAAAAAACAAAACAAAAAAAAAAAAGA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * ** * * * * *
34312 AAAAAACAAAACAAAAAAAAGGAAAAAGAAAGAAAAAAAACAAAACAAAAAAAAGAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
34377 CAAAAAAAAAA
1 AAAAAAAAAAA
34388 GTGAAGATTT
Statistics
Matches: 106, Mismatches: 34, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 106 1.00
ACGTcount: A:0.87, C:0.06, G:0.07, T:0.00
Consensus pattern (1 bp):
A
Found at i:34277 original size:29 final size:29
Alignment explanation
Indices: 34245--34385 Score: 181
Period size: 29 Copynumber: 5.0 Consensus size: 29
34235 CATGGCAATT
34245 GGAAAAAGAAAAAAACAAAACAAAAAAAA
1 GGAAAAAGAAAAAAACAAAACAAAAAAAA
34274 GGAAAAAGAAAAAAAAAACAAAAC-AAAAAAA
1 GGAAAAAG---AAAAAAACAAAACAAAAAAAA
34305 --AAAAAGAAAAAAACAAAACAAAAAAAA
1 GGAAAAAGAAAAAAACAAAACAAAAAAAA
*
34332 GGAAAAAGAAAGAAAA-AAAACAAAACAAA
1 GGAAAAAGAAA-AAAACAAAACAAAAAAAA
34361 --AAAAAG-AAAAAA-AAAACAAAAAAAA
1 GGAAAAAGAAAAAAACAAAACAAAAAAAA
34386 AAGTGAAGAT
Statistics
Matches: 103, Mismatches: 2, Indels: 18
0.84 0.02 0.15
Matches are distributed among these distances:
25 16 0.16
26 15 0.15
27 13 0.13
29 35 0.34
30 4 0.04
31 7 0.07
32 13 0.13
ACGTcount: A:0.85, C:0.06, G:0.09, T:0.00
Consensus pattern (29 bp):
GGAAAAAGAAAAAAACAAAACAAAAAAAA
Found at i:34313 original size:58 final size:60
Alignment explanation
Indices: 34247--34387 Score: 245
Period size: 58 Copynumber: 2.4 Consensus size: 60
34237 TGGCAATTGG
34247 AAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAG-AA-AAAAAAAACAAAACAAAAAAA
1 AAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAGAAAGAAAAAAAACAAAACAAAAAAA
34305 AAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAGAAAGAAAAAAAACAAAACAAAAAAA
1 AAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAGAAAGAAAAAAAACAAAACAAAAAAA
*
34365 AGAAA-AAAAAAACAAAA-AAAAAA
1 AAAAAGAAAAAAACAAAACAAAAAA
34388 GTGAAGATTT
Statistics
Matches: 80, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
58 41 0.51
59 14 0.17
60 25 0.31
ACGTcount: A:0.87, C:0.06, G:0.07, T:0.00
Consensus pattern (60 bp):
AAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAGAAAGAAAAAAAACAAAACAAAAAAA
Found at i:34366 original size:34 final size:34
Alignment explanation
Indices: 34249--34385 Score: 170
Period size: 34 Copynumber: 4.4 Consensus size: 34
34239 GCAATTGGAA
34249 AAAG-AAAAAAACAAAACAAAAAAAAGGAAAAAG
1 AAAGAAAAAAAACAAAACAAAAAAAAGGAAAAAG
34282 -AA-AAAAAAAACAAAAC----AAAA--AAAAA-
1 AAAGAAAAAAAACAAAACAAAAAAAAGGAAAAAG
34307 AAAG-AAAAAAACAAAACAAAAAAAAGGAAAAAG
1 AAAGAAAAAAAACAAAACAAAAAAAAGGAAAAAG
* *
34340 AAAGAAAAAAAACAAAACAAAAAAAAGAAAAAAA
1 AAAGAAAAAAAACAAAACAAAAAAAAGGAAAAAG
*
34374 AAACAAAAAAAA
1 AAAGAAAAAAAA
34386 AAGTGAAGAT
Statistics
Matches: 90, Mismatches: 3, Indels: 21
0.79 0.03 0.18
Matches are distributed among these distances:
26 20 0.22
28 4 0.04
30 4 0.04
32 20 0.22
33 4 0.04
34 38 0.42
ACGTcount: A:0.86, C:0.07, G:0.07, T:0.00
Consensus pattern (34 bp):
AAAGAAAAAAAACAAAACAAAAAAAAGGAAAAAG
Found at i:45858 original size:1 final size:1
Alignment explanation
Indices: 45852--45938 Score: 66
Period size: 1 Copynumber: 87.0 Consensus size: 1
45842 CGTCCTCCAC
* * * * ** * * *
45852 AAAAAAAAAAAAACAAAACAAAACAAAACAAAAAAAAAGCAAAAACAAAAAAAAACAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
45917 AACACAAAAAAAAAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAA
45939 GGGTCCGGAT
Statistics
Matches: 63, Mismatches: 23, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 63 1.00
ACGTcount: A:0.86, C:0.11, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:45924 original size:41 final size:41
Alignment explanation
Indices: 45852--45938 Score: 124
Period size: 41 Copynumber: 2.1 Consensus size: 41
45842 CGTCCTCCAC
*
45852 AAAAAAAAAAAAACAAAACAAAACAAAACAAAAAAAAAGCA
1 AAAAAAAAAAAAACAAAACAAAACAAAACAAAAAAAAAACA
*
45893 AAAACAAAAAAAAACAAAGA-AAAA-AACACAAAAAAAAAACA
1 AAAA-AAAAAAAAACAAA-ACAAAACAAAACAAAAAAAAAACA
45934 AAAAA
1 AAAAA
45939 GGGTCCGGAT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
40 1 0.02
41 23 0.55
42 17 0.40
43 1 0.02
ACGTcount: A:0.86, C:0.11, G:0.02, T:0.00
Consensus pattern (41 bp):
AAAAAAAAAAAAACAAAACAAAACAAAACAAAAAAAAAACA
Found at i:45937 original size:10 final size:10
Alignment explanation
Indices: 45850--45938 Score: 92
Period size: 10 Copynumber: 8.8 Consensus size: 10
45840 GGCGTCCTCC
45850 ACAAAAAAAA
1 ACAAAAAAAA
*
45860 A-AAAACAAA
1 ACAAAAAAAA
*
45869 ACAAAACAAA
1 ACAAAAAAAA
45879 ACAAAAAAAA
1 ACAAAAAAAA
45889 AGCAAAAACAAA
1 A-CAAAAA-AAA
*
45901 A-AAAAACAA
1 ACAAAAAAAA
* *
45910 AGAAAAAAAC
1 ACAAAAAAAA
45920 ACAAAAAAAAA
1 AC-AAAAAAAA
45931 ACAAAAAA
1 ACAAAAAA
45939 GGGTCCGGAT
Statistics
Matches: 67, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
9 11 0.16
10 37 0.55
11 15 0.22
12 4 0.06
ACGTcount: A:0.85, C:0.12, G:0.02, T:0.00
Consensus pattern (10 bp):
ACAAAAAAAA
Found at i:45937 original size:22 final size:20
Alignment explanation
Indices: 45852--45938 Score: 93
Period size: 21 Copynumber: 4.2 Consensus size: 20
45842 CGTCCTCCAC
*
45852 AAAAAAAAAAAAACAAAACA
1 AAAAAAAAAAAAAAAAAACA
* *
45872 AAACAAAACAAAAAAAAAGCA
1 AAA-AAAAAAAAAAAAAAACA
* * *
45893 AAAACAAAAAAAAACAAAGA
1 AAAAAAAAAAAAAAAAAACA
*
45913 AAAAAACACAAAAAAAAAACA
1 AAAAAA-AAAAAAAAAAAACA
45934 AAAAA
1 AAAAA
45939 GGGTCCGGAT
Statistics
Matches: 53, Mismatches: 12, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 20 0.38
21 33 0.62
ACGTcount: A:0.86, C:0.11, G:0.02, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAAAAAAAAAACA
Found at i:47433 original size:30 final size:29
Alignment explanation
Indices: 47378--47756 Score: 296
Period size: 30 Copynumber: 12.9 Consensus size: 29
47368 TCACCCTTCA
* **
47378 AAAGTCCACAAGTCAGTGGCATTTTTTTC
1 AAAGCCCACAAGTCAGTGGCACCTTTTTC
**
47407 AAAGCCCACAAGTCAGTGGCATTTTTTTC
1 AAAGCCCACAAGTCAGTGGCACCTTTTTC
47436 GAAAGCCCACAAGTCAGTGGCAACC---TTC
1 -AAAGCCCACAAGTCAGTGGC-ACCTTTTTC
*
47464 AAAGCCCACAAATCAGTGGCACCCTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-CCTTTTTC
* * * *
47494 GAAGCCCACAAGTCGGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCACCTTTTTC
* * *
47523 AAAGTCCACAACTCCGTGGCACTCTTTTTC
1 AAAGCCCACAAGTCAGTGGCAC-CTTTTTC
* * * *
47553 TTTTGTAAGCTCACAACTCTA-TAGCA-CTCTTTTC
1 -----AAAGCCCACAAGTC-AGTGGCACCT-TTTTC
* *
47587 --AGCCCACAAGTTAGTGGCACCCTTTTC
1 AAAGCCCACAAGTCAGTGGCACCTTTTTC
*
47614 AAAAGCCCACAAGTCAGTGGCAACC--TTTA
1 -AAAGCCCACAAGTCAGTGGC-ACCTTTTTC
47643 AAAGCCCACAAGTCAGTGGCAACC---TTC
1 AAAGCCCACAAGTCAGTGGC-ACCTTTTTC
* *
47670 AAAGCCCACAAATCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-CCTTTTTC
* *
47700 GAAGCCCACAAATCAGTGGCACCCTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-CCTTTTTC
* *
47730 GAAGCCCACAAGTCGGTGGCACCTTTT
1 AAAGCCCACAAGTCAGTGGCACCTTTT
47757 CCATCTTTAA
Statistics
Matches: 292, Mismatches: 34, Indels: 48
0.78 0.09 0.13
Matches are distributed among these distances:
26 3 0.01
27 62 0.21
28 28 0.10
29 60 0.21
30 113 0.39
31 4 0.01
33 2 0.01
34 5 0.02
35 15 0.05
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.25
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCACCTTTTTC
Found at i:47480 original size:57 final size:58
Alignment explanation
Indices: 47404--47754 Score: 283
Period size: 57 Copynumber: 6.0 Consensus size: 58
47394 TGGCATTTTT
**
47404 TTCAAAGCCCACAAGTCAGTGGCA-TTTTTTTCGAAAGCCCACAAGTCAGTGGCAACC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTTTCGAAAGCCCACAAGTCAGTGGCAACC
* * * *
47461 TTCAAAGCCCACAAATCAGTGGCACCCTTTTTCG-AAGCCCACAAGTCGGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTTTCGAAAGCCCACAAGTCAGTGGCAAC-C
* * * * * * * *
47519 TTCCAAAGTCCACAACTCCGTGGCACTCTTTTTCTTTTGTAAGCTCACAACTCTA-TAGC-ACTC
1 TT-CAAAGCCCACAAGTCAGTGGCACCCTTTTTC----GAAAGCCCACAAGTC-AGTGGCAAC-C
*** * *
47582 TTTTCAGCCCACAAGTTAGTGGCACCC-TTTTCAAAAGCCCACAAGTCAGTGGCAACC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTTTCGAAAGCCCACAAGTCAGTGGCAACC
* * * *
47639 TTTAAAAGCCCACAAGTCAGTGGCAACC---TTC-AAAGCCCACAAATCAGTGGCACCC
1 -TTCAAAGCCCACAAGTCAGTGGCACCCTTTTTCGAAAGCCCACAAGTCAGTGGCAACC
* * *
47694 TTTTCCGAAGCCCACAAATCAGTGGCACCCTTTTTCG-AAGCCCACAAGTCGGTGGC-ACC
1 --TT-CAAAGCCCACAAGTCAGTGGCACCCTTTTTCGAAAGCCCACAAGTCAGTGGCAACC
47753 TT
1 TT
47755 TTCCATCTTT
Statistics
Matches: 233, Mismatches: 43, Indels: 36
0.75 0.14 0.12
Matches are distributed among these distances:
55 22 0.09
56 7 0.03
57 81 0.35
58 33 0.14
59 29 0.12
60 20 0.09
61 5 0.02
62 17 0.07
63 5 0.02
64 14 0.06
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.24
Consensus pattern (58 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCTTTTTCGAAAGCCCACAAGTCAGTGGCAACC
Found at i:47707 original size:85 final size:85
Alignment explanation
Indices: 47377--47754 Score: 235
Period size: 85 Copynumber: 4.3 Consensus size: 85
47367 ATCACCCTTC
* ** * *** *
47377 AAAAGTCCACAAGTCAGTGGCATTTTTTTCAAAGCCCACAAGTCAGTGGCATTTTTTTCGAAAGC
1 AAAAGCCCACAAGTCAGTGGCA---CCTTCAAAGCCCACAAATCAGTGGCACCCTTTTCAAAAGC
*
47442 CCACAAGTCAGTGGCAACC--TT
63 CCACAAATCAGTGGCAACCTTTT
* * * * * * *
47463 CAAAGCCCACAAATCAGTGGCACCCTTTTTCGAAGCCCACAAGTCGGTGGCA-TCTTTTCCAAAG
1 AAAAGCCCACAAGTCAGTGGCA-CC---TTCAAAGCCCACAAATCAGTGGCACCCTTTTCAAAAG
* * * *
47527 TCCACAACTCCGTGGCACTCTTTTTCTTTT
62 CCCACAAATCAGTGGCA-AC-----CTTTT
** * * * *** * *
47557 GTAAGCTCACAACTCTA-TAGCACTCTTTTCAGCCCACAAGTTAGTGGCACCCTTTTCAAAAGCC
1 AAAAGCCCACAAGTC-AGTGGCAC-CTTCAAAGCCCACAAATCAGTGGCACCCTTTTCAAAAGCC
*
47621 CACAAGTCAGTGGCAACC-TTT
64 CACAAATCAGTGGCAACCTTTT
**
47642 AAAAGCCCACAAGTCAGTGGCAACCTTCAAAGCCCACAAATCAGTGGCACCCTTTTCCGAAGCCC
1 AAAAGCCCACAAGTCAGTGGC-ACCTTCAAAGCCCACAAATCAGTGGCACCCTTTTCAAAAGCCC
*
47707 ACAAATCAGTGGCACCCTTTTT
65 ACAAATCAGTGGCAACC-TTTT
** *
47729 CGAAGCCCACAAGTCGGTGGCACCTT
1 AAAAGCCCACAAGTCAGTGGCACCTT
47755 TTCCATCTTT
Statistics
Matches: 227, Mismatches: 47, Indels: 36
0.73 0.15 0.12
Matches are distributed among these distances:
84 1 0.00
85 66 0.29
86 51 0.22
87 44 0.19
91 20 0.09
92 25 0.11
93 1 0.00
94 18 0.08
95 1 0.00
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (85 bp):
AAAAGCCCACAAGTCAGTGGCACCTTCAAAGCCCACAAATCAGTGGCACCCTTTTCAAAAGCCCA
CAAATCAGTGGCAACCTTTT
Found at i:47829 original size:43 final size:43
Alignment explanation
Indices: 47761--47850 Score: 144
Period size: 43 Copynumber: 2.1 Consensus size: 43
47751 CCTTTTCCAT
*
47761 CTTTAAGTCCAATGTAGCCGACCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCCGACCTTGAATCAGCACATTGGCAC
* * *
47804 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATATAGCCGACCTTGAATCAGCACATTGGCAC
47847 CTTT
1 CTTT
47851 TCCATCTTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.30
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCCGACCTTGAATCAGCACATTGGCAC
Found at i:47882 original size:52 final size:53
Alignment explanation
Indices: 47804--47957 Score: 184
Period size: 52 Copynumber: 2.9 Consensus size: 53
47794 ACATTGGCAC
*
47804 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAG
* * * *
47856 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAG
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC-TTTTCTCAG
* * * * * *
47911 CTTTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCATCTTT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTT
47958 ATCACTTTTC
Statistics
Matches: 84, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
52 38 0.45
53 5 0.06
54 6 0.07
55 35 0.42
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (53 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAG
Found at i:48806 original size:13 final size:13
Alignment explanation
Indices: 48788--48812 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48778 CATAAAGTGT
48788 TGTATCGATACAA
1 TGTATCGATACAA
48801 TGTATCGATACA
1 TGTATCGATACA
48813 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:48810 original size:33 final size:33
Alignment explanation
Indices: 48768--48834 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
48758 TTCAACGATT
48768 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
48801 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
48834 T
1 T
48835 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:48893 original size:13 final size:13
Alignment explanation
Indices: 48875--48899 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48865 ATCACTTAAA
48875 TGTATCGATACAT
1 TGTATCGATACAT
48888 TGTATCGATACA
1 TGTATCGATACA
48900 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:49035 original size:52 final size:52
Alignment explanation
Indices: 48888--49036 Score: 228
Period size: 52 Copynumber: 2.9 Consensus size: 52
48878 ATCGATACAT
** *
48888 TGTATCGATACACTGA-TCTTTGTATCGATACATGCAGGCAAATGTGCCCAGA
1 TGTATCGATACACT-ATTCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
* **
48940 TGTATCGATACATTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
48992 TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTT
49037 TCATATTTCG
Statistics
Matches: 87, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
51 1 0.01
52 86 0.99
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:52420 original size:130 final size:130
Alignment explanation
Indices: 52187--52436 Score: 428
Period size: 130 Copynumber: 1.9 Consensus size: 130
52177 ATCAGACCTG
*
52187 TTTAGGTGGTTAAAAAAGTTTAGTTGGACCGAAAGCTATCTAGTCTAGAGCTTTATAGAAAACTA
1 TTTAGGTGGTTAAAAAAGTTTAGTTGAACCGAAAGCTATCTAGTCTAGAGCTTTATAGAAAACTA
* * * *
52252 AAATTTATTTTACCCAACGTAAAATTGTTCAACTAGTAAAAACCAAGAAAATAAACCACCAAAAA
66 AAATTTAGTTTAACCAACATAAAATTATTCAACTAGTAAAAACCAAGAAAATAAACCACCAAAAA
**
52317 TTTAGGTGGTTAAACCAGTTTAGTTGAACCGAAAGCTATCTAGTCTAGAGCTTTATAGAAAACTA
1 TTTAGGTGGTTAAAAAAGTTTAGTTGAACCGAAAGCTATCTAGTCTAGAGCTTTATAGAAAACTA
*
52382 AAATTTAGTTTAACCAGCATAAAATTATTCAACTAGTAAAAACCAAGAAAATAAA
66 AAATTTAGTTTAACCAACATAAAATTATTCAACTAGTAAAAACCAAGAAAATAAA
52437 TCGTTTTATT
Statistics
Matches: 112, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 112 1.00
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (130 bp):
TTTAGGTGGTTAAAAAAGTTTAGTTGAACCGAAAGCTATCTAGTCTAGAGCTTTATAGAAAACTA
AAATTTAGTTTAACCAACATAAAATTATTCAACTAGTAAAAACCAAGAAAATAAACCACCAAAAA
Found at i:53007 original size:15 final size:16
Alignment explanation
Indices: 52976--53008 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
52966 AAGGACAAGA
*
52976 CAAATATTCGATCATT
1 CAAAGATTCGATCATT
52992 CAAAGATTCG-TCATT
1 CAAAGATTCGATCATT
53007 CA
1 CA
53009 TTTTGCAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.33
Consensus pattern (16 bp):
CAAAGATTCGATCATT
Found at i:57349 original size:27 final size:28
Alignment explanation
Indices: 57305--57360 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
57295 ATTACACCTT
*
57305 AATCTTTCTTAATATAACCTTTTAATTA
1 AATCTTTCTAAATATAACCTTTTAATTA
* *
57333 AATC-TTCTAAATTTAACCTTTTATTTA
1 AATCTTTCTAAATATAACCTTTTAATTA
57360 A
1 A
57361 TTAAATCTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 21 0.84
28 4 0.16
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (28 bp):
AATCTTTCTAAATATAACCTTTTAATTA
Found at i:61944 original size:19 final size:19
Alignment explanation
Indices: 61910--61960 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
61900 AGTTTTGAAA
*
61910 TTTTCATTTATTTTCATAAG
1 TTTTCATTT-TTTTCAAAAG
*
61930 TTTTCATTTTTTTCAAAAT
1 TTTTCATTTTTTTCAAAAG
61949 TTTTCTATTTTT
1 TTTTC-ATTTTT
61961 GAAATATGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.22, C:0.10, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTTCATTTTTTTCAAAAG
Found at i:64041 original size:142 final size:142
Alignment explanation
Indices: 63696--64087 Score: 493
Period size: 143 Copynumber: 2.7 Consensus size: 142
63686 AAAATTAATC
* * * * * *
63696 ATTTTTATATATTTCTATTATTCCTATGG-TTTTCTGTAGAAGTATAAAAATCTTCAAAACATTT
1 ATTTTTAAAGATTTCTAATATTCTTATGGTTTTTC-GTAGAGGTATAAAAATCTTCAAAACTTTT
* *
63760 CATATCTTTTCGGTTCTCCATTAAGGTATGAAATGATTTTTTTAAAAAAATAAAAAATTAAATGA
65 CATATCTTTTCGGTTCTCCATTAAGGTATGAAATGAATTTTTT-AAAAAATAAAAAATTAAATAA
63825 AAATTATTACCATA
129 AAATTATTACCATA
* * *
63839 ATTTTTCAAGATTTCTAATATTCTTATGGTTTTTCGTAG-GAATATAGAAATCTTCAAAACTTTT
1 ATTTTTAAAGATTTCTAATATTCTTATGGTTTTTCGTAGAG-GTATAAAAATCTTCAAAACTTTT
* * *
63903 CATATCTTTTCGGTTCTCCATTAAGGTACGAAATGAATTTTTT-AGAAATTAAAAATTAAATAAA
65 CATATCTTTTCGGTTCTCCATTAAGGTATGAAATGAATTTTTTAAAAAATAAAAAATTAAATAAA
* *
63967 AATTATTATCTTCA
130 AATTATTACCAT-A
* * * * * * *
63981 TTTTTTAAAGATTTCTAATATTTTTATTGTTTTTCGTAGAGGTATATAAACCTTCGAAACTTTTT
1 ATTTTTAAAGATTTCTAATATTCTTATGGTTTTTCGTAGAGGTATAAAAATCTTCAAAACTTTTC
* *
64046 ATATCTTTTTGGTTCTCTATTAAGGTATGAAATGAGATTTTT
66 ATATCTTTTCGGTTCTCCATTAAGGTATGAAATGA-ATTTTT
64088 GAAATCTATA
Statistics
Matches: 216, Mismatches: 28, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
141 28 0.13
142 87 0.40
143 96 0.44
144 5 0.02
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.45
Consensus pattern (142 bp):
ATTTTTAAAGATTTCTAATATTCTTATGGTTTTTCGTAGAGGTATAAAAATCTTCAAAACTTTTC
ATATCTTTTCGGTTCTCCATTAAGGTATGAAATGAATTTTTTAAAAAATAAAAAATTAAATAAAA
ATTATTACCATA
Found at i:64428 original size:156 final size:153
Alignment explanation
Indices: 64267--64645 Score: 424
Period size: 153 Copynumber: 2.4 Consensus size: 153
64257 CAAGTCCTAA
* ** *
64267 GTTGTCACCGAGTTTGCTTTTATGCTGAAGGTGGGTATTTAGGATAGGTTCATCCCGTCTATAAT
1 GTTGTCACCG-GTCTGCTTTTATGCCAAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAAT
* * * * *
64332 CTTTTTTAGGTCTTCTAA-GGATACCGGGTACTTCTATA-TTGAAGGTAACCT-TTAGGGATATT
65 CTTTTTTAAGTCTTCTAAGGGA-ACCGGGCACTTCTA-AGTTGAAGGT-ACCTCATAAGGACATT
*
64394 TATGTAATTTTTTCAAAACTGAGTCTCAG
127 TATGTAATTTTTT--AAACTAAGTCTCAG
* * * *
64423 GTTGTCACTGGGTCTGTTTTTATGCCAAAAGTAGGTATTTAGGATAGGTTCATCCCATCTATAAT
1 GTTGTCAC-CGGTCTGCTTTTATGCCAAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAAT
* ** * *
64488 C-TTTTTAAGTCTTTTAAGGGAATTGGGCACTTCTAAGTTGAAGGTATCTCATAAGGACATTTTT
65 CTTTTTTAAGTCTTCTAAGGGAACCGGGCACTTCTAAGTTGAAGGTACCTCATAAGGACATTTAT
*
64552 GTAATTTTTTAAACTAAGTCTGAG
130 GTAATTTTTTAAACTAAGTCTCAG
** * * *
64576 GTCATCACCGGATCCGCGTTTATGCCAAAGGTGGATATTTAGGATAGGTTCATCCCATCTATAAT
1 GTTGTCACCGG-TCTGCTTTTATGCCAAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAA-
64641 TCTTT
64 TCTTT
64646 CCAAGCCCTC
Statistics
Matches: 187, Mismatches: 29, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
152 2 0.01
153 64 0.34
154 6 0.03
155 55 0.29
156 59 0.32
157 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.39
Consensus pattern (153 bp):
GTTGTCACCGGTCTGCTTTTATGCCAAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAATC
TTTTTTAAGTCTTCTAAGGGAACCGGGCACTTCTAAGTTGAAGGTACCTCATAAGGACATTTATG
TAATTTTTTAAACTAAGTCTCAG
Found at i:67867 original size:12 final size:12
Alignment explanation
Indices: 67850--67876 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
67840 TACTTTGAAA
67850 AAATTTAATTTT
1 AAATTTAATTTT
67862 AAATTTAATTTT
1 AAATTTAATTTT
67874 AAA
1 AAA
67877 AAAAATGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
AAATTTAATTTT
Found at i:69853 original size:15 final size:15
Alignment explanation
Indices: 69833--69869 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
69823 CTTATTTATG
69833 TATTTATTTAAAAAT
1 TATTTATTTAAAAAT
69848 TATTTATTTAAAAAT
1 TATTTATTTAAAAAT
69863 TATTTAT
1 TATTTAT
69870 GAACATTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TATTTATTTAAAAAT
Found at i:69949 original size:14 final size:14
Alignment explanation
Indices: 69899--69949 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
69889 TATTTATTTA
*
69899 TATATGCAATTAAGT
1 TATATGTAATTAA-T
*
69914 ATATATGAAATT-AT
1 -TATATGTAATTAAT
*
69928 TTTATGTAATTAAT
1 TATATGTAATTAAT
69942 TATATGTA
1 TATATGTA
69950 GATAAATATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
13 9 0.30
14 10 0.33
15 1 0.03
16 10 0.33
ACGTcount: A:0.41, C:0.02, G:0.10, T:0.47
Consensus pattern (14 bp):
TATATGTAATTAAT
Found at i:72264 original size:623 final size:616
Alignment explanation
Indices: 71041--72297 Score: 1853
Period size: 623 Copynumber: 2.0 Consensus size: 616
71031 TTTATCTATT
* * *
71041 AATTAGTTAAGATTCAATATGATTTTATATTTGATAGATATAAAAGTTAAATTTTAAATTCACAA
1 AATTAGTTAAGATTCAATATGATATTATATTTGACAAATATAAAAGTTAAATTTTAAATTCACAA
* * *
71106 ATATTTATAGTTATTTCAAAATTCACACATATGACAAATCTATGAATTAAAAACAAAACCATGAA
66 ATATTTATAGCTACTTCAAAATTCACACATATAACAAATCTATGAATTAAAAACAAAACCATGAA
* * *
71171 TATTATGTTACATATTTTTTATTACATAATTTATATTATTTTTAAAATCTAAATATATTTTTTGA
131 TATTATGTTACATATTTTTTATTACATAATTTATATTATTTTTAAAATCTAAATACATCTTTTAA
*
71236 AATTTAAAAAATTACTTTTAATTAACTTAGATAAGAACAATCGATTTTTTATAAATTTGACAAAT
196 AATTTAAAAAATTACTTTTAATTAACTTAGATAACAACAATCGATTTTTTATAAATTTGACAAAT
*
71301 CAATTTAAATTTTTTAAGTTAATTACAAAAACAACATGATCAAAAACCAATTTGAATCCAAGATC
261 CAATATAAATTTTTTAAGTTAATTACAAAAACAACATGATCAAAAACCAATTTGAATCCAAG---
*
71366 AAGTCATCAGGTCGATCATTAAGCCAATTTGAGTTTAATAACTATGATGATGATAGAATAATTAT
323 AAGTCATCAGGTCGATCATGAAGCCAATTTGAGTTTAATAACTATGATGATGATAGAATAATTAT
* *
71431 TATACAAGTATATGGTGTTTATGAGCTCAACTATCTTTCCAAATCCGAAGGTTCATTTAATATTT
388 TATACAAGTATATGGTGTTTATGAACTCAACTATCTATCCAAATCCGAAGGTTCATTTAATATTT
** *
71496 GGGATAATATAGATAAAAATATTAAAAGCGAAAAATGAGCACGGCCTTGCCATTAAAAATGAGTT
453 AAGATAATATAGATAAAAATATTAAAAGCGAAAAATGAGCACGGCCTTGCCATTAAAAATGAGTC
* * *
71561 GCGAATTGGCTACAACATTTAAGGTTAGGTCTTGGTTTGACTCTTTTTTAATTATATAATATGTT
518 GCGAATTGGCTACAACATTTAAAGTTAGCTCTTGATTTGACTCTTTTTTAATTATATAATATGTT
71626 AATTTTATATTTATATATTATAAAATTTTTAATATAAA
583 AA---TATATTTATAT-TTATAAAATTTTTAATATAAA
71664 AATTAGTTAAGATTCAATATGATATTATATTTGACAAATATAAAAGTTAAATTTTAAATTCACAA
1 AATTAGTTAAGATTCAATATGATATTATATTTGACAAATATAAAAGTTAAATTTTAAATTCACAA
* *
71729 GTATTTATAGCTACTTCAAAATTCACACATATAACAAATCTATG-ATATAGAAACAAAACCATGA
66 ATATTTATAGCTACTTCAAAATTCACACATATAACAAATCTATGAAT-TAAAAACAAAACCATGA
* * *
71793 ATATTATGTTACATATTTTTTATTACATAATTTATATTATTTTTAAAATTTAGATCCATCTTTTA
130 ATATTATGTTACATATTTTTTATTACATAATTTATATTATTTTTAAAATCTAAATACATCTTTTA
71858 AAATTTAAAAAATTACTTTTAATTAACTTAGATAATAACAAATTCAACAAATTATCGATTTTTTA
195 AAATTTAAAAAATTACTTTTAATTAACTTAG---AT----AA--CAAC--A--ATCGATTTTTTA
* *
71923 TAAATTTGATAAATCAATATGAATTTTTTAAGTTAATTACAAAAACAACATGATCAAAAACCAAT
247 TAAATTTGACAAATCAATATAAATTTTTTAAGTTAATTACAAAAACAACATGATCAAAAACCAAT
* * *
71988 TTGGATCCAAG-A-TCATCGGGTCGATCATGAAGCCAATTTGAGTTTAATAATTATGATGATGAT
312 TTGAATCCAAGAAGTCATCAGGTCGATCATGAAGCCAATTTGAGTTTAATAACTATGATGATGAT
*
72051 AGAATAATTATTATACAAGTATATGGTGTTTATGAACTCAACTATCTATCCAAATCTGAAGGTTC
377 AGAATAATTATTATACAAGTATATGGTGTTTATGAACTCAACTATCTATCCAAATCCGAAGGTTC
* * *
72116 ATTTAATATTTAAGATAATATAGATAAAAATATTAAAAGC-AAAATTGAGCATGGCTTTGCCATT
442 ATTTAATATTTAAGATAATATAGATAAAAATATTAAAAGCGAAAAATGAGCACGGCCTTGCCATT
* * *
72180 TACAATGAGTCGCGAATTGGCT-CTAACATTTAAAGTTAGCTCTTGATCTT-A-TTTTTTTTAAT
507 AAAAATGAGTCGCGAATTGGCTAC-AACATTTAAAGTTAGCTCTTGAT-TTGACTCTTTTTTAAT
* *
72242 TGTATAATATGTTAATTTTATATTTATATATTATAAAAAAATTTTAATATAAA
570 TATATAATATGTTAA---TATATTTATAT-TTAT--AAAATTTTTAATATAAA
72295 AAT
1 AAT
72298 AAATGTATAA
Statistics
Matches: 577, Mismatches: 39, Indels: 28
0.90 0.06 0.04
Matches are distributed among these distances:
622 2 0.00
623 208 0.36
626 2 0.00
629 44 0.08
630 63 0.11
631 169 0.29
632 4 0.01
634 1 0.00
636 84 0.15
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (616 bp):
AATTAGTTAAGATTCAATATGATATTATATTTGACAAATATAAAAGTTAAATTTTAAATTCACAA
ATATTTATAGCTACTTCAAAATTCACACATATAACAAATCTATGAATTAAAAACAAAACCATGAA
TATTATGTTACATATTTTTTATTACATAATTTATATTATTTTTAAAATCTAAATACATCTTTTAA
AATTTAAAAAATTACTTTTAATTAACTTAGATAACAACAATCGATTTTTTATAAATTTGACAAAT
CAATATAAATTTTTTAAGTTAATTACAAAAACAACATGATCAAAAACCAATTTGAATCCAAGAAG
TCATCAGGTCGATCATGAAGCCAATTTGAGTTTAATAACTATGATGATGATAGAATAATTATTAT
ACAAGTATATGGTGTTTATGAACTCAACTATCTATCCAAATCCGAAGGTTCATTTAATATTTAAG
ATAATATAGATAAAAATATTAAAAGCGAAAAATGAGCACGGCCTTGCCATTAAAAATGAGTCGCG
AATTGGCTACAACATTTAAAGTTAGCTCTTGATTTGACTCTTTTTTAATTATATAATATGTTAAT
ATATTTATATTTATAAAATTTTTAATATAAA
Found at i:73596 original size:13 final size:13
Alignment explanation
Indices: 73578--73603 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
73568 TACAGCAAGT
73578 ATGTATCGATACA
1 ATGTATCGATACA
73591 ATGTATCGATACA
1 ATGTATCGATACA
73604 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:75489 original size:13 final size:13
Alignment explanation
Indices: 75471--75495 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
75461 CATAAAATGT
75471 TGTATCGATACAA
1 TGTATCGATACAA
75484 TGTATCGATACA
1 TGTATCGATACA
75496 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:75493 original size:33 final size:33
Alignment explanation
Indices: 75451--75517 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
75441 TTCAACGATT
75451 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
75484 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
75517 T
1 T
75518 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:75576 original size:13 final size:13
Alignment explanation
Indices: 75558--75582 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
75548 ATCACTTAAA
75558 TGTATCGATACAT
1 TGTATCGATACAT
75571 TGTATCGATACA
1 TGTATCGATACA
75583 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:75635 original size:52 final size:52
Alignment explanation
Indices: 75591--75719 Score: 249
Period size: 52 Copynumber: 2.5 Consensus size: 52
75581 CACTGATCTT
*
75591 TGTATCGATACATGCAAGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
75643 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
75695 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
75720 TCATATTTCG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 76 1.00
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:79860 original size:10 final size:10
Alignment explanation
Indices: 79845--79871 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
79835 TGCTAACTAA
79845 GTTTTTGTTT
1 GTTTTTGTTT
79855 GTTTTTGTTT
1 GTTTTTGTTT
79865 GTTTTTG
1 GTTTTTG
79872 CTTGATACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (10 bp):
GTTTTTGTTT
Found at i:89583 original size:20 final size:19
Alignment explanation
Indices: 89558--89632 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 19
89548 GGCGTCCTCC
**
89558 AAAAAAAA-AAACGAACGA
1 AAAAAAAACAAAAAAACGA
89576 AAAAAAAACGAAAAAAACGA
1 AAAAAAAAC-AAAAAAACGA
* **
89596 AAAAACAACGAAAAAAAAAA
1 AAAAAAAAC-AAAAAAACGA
89616 AAACAAAAACAAAAAAA
1 AAA-AAAAACAAAAAAA
89633 GGGGGTCCGG
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
18 8 0.17
20 35 0.73
21 5 0.10
ACGTcount: A:0.83, C:0.11, G:0.07, T:0.00
Consensus pattern (19 bp):
AAAAAAAACAAAAAAACGA
Found at i:89585 original size:11 final size:11
Alignment explanation
Indices: 89571--89632 Score: 71
Period size: 11 Copynumber: 6.0 Consensus size: 11
89561 AAAAAAAACG
89571 AACGAAAAAAA
1 AACGAAAAAAA
89582 AACG--AAAAA
1 AACGAAAAAAA
*
89591 AACGAAAAAAC
1 AACGAAAAAAA
89602 AACGAAAAAAA
1 AACGAAAAAAA
89613 AA--AAAACAAA
1 AACGAAAA-AAA
89623 AAC-AAAAAAA
1 AACGAAAAAAA
89633 GGGGGTCCGG
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
9 13 0.29
10 8 0.18
11 24 0.53
ACGTcount: A:0.82, C:0.11, G:0.06, T:0.00
Consensus pattern (11 bp):
AACGAAAAAAA
Found at i:89591 original size:9 final size:9
Alignment explanation
Indices: 89577--89612 Score: 54
Period size: 9 Copynumber: 3.8 Consensus size: 9
89567 AACGAACGAA
89577 AAAAAAACG
1 AAAAAAACG
89586 AAAAAAACG
1 AAAAAAACG
89595 AAAAAACAACG
1 -AAAAA-AACG
89606 AAAAAAA
1 AAAAAAA
89613 AAAAAACAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 11 0.44
10 10 0.40
11 4 0.16
ACGTcount: A:0.81, C:0.11, G:0.08, T:0.00
Consensus pattern (9 bp):
AAAAAAACG
Found at i:89606 original size:31 final size:33
Alignment explanation
Indices: 89558--89632 Score: 102
Period size: 31 Copynumber: 2.4 Consensus size: 33
89548 GGCGTCCTCC
**
89558 AAAA-AAAAAAACGAACGAAAAAAAAACGAA-A
1 AAAACAAAAAAACGAACGAAAAAAAAAAAAACA
*
89589 AAAACGAAAAAAC-AACGAAAAAAAAAAAAACA
1 AAAACAAAAAAACGAACGAAAAAAAAAAAAACA
89621 AAAACAAAAAAA
1 AAAACAAAAAAA
89633 GGGGGTCCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 19 0.50
32 19 0.50
ACGTcount: A:0.83, C:0.11, G:0.07, T:0.00
Consensus pattern (33 bp):
AAAACAAAAAAACGAACGAAAAAAAAAAAAACA
Found at i:91404 original size:58 final size:59
Alignment explanation
Indices: 91067--91545 Score: 336
Period size: 58 Copynumber: 8.1 Consensus size: 59
91057 TTCATCACCC
* *** ***
91067 TTCAAAAGTCCACAAGTCAGTGGCATATTTTTC-AAAGCCCACAAGTCAGTGGCATTTTTT
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCA--ACCT
* * *
91127 TTCAAAAGCCCACAAGTCAGTGGCAACC--TTC-AAAGCCCACAAATCAGTGGCACCCTT
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCAACC-T
** * * * * * *
91184 TTCCGAAGCCCACAAGTCGGTGGCA-TCTTTTCCAAAGTCCACAACTCCGTGGC-ACTCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCAAC-C--T
** * * * ** *** * *
91244 TTCTTTTGTAAGCTCACAACTCTA-TAGCACTTTTTTTCTTTTTCAGCCCACAAGTTAGTGGCAC
1 TTC----AAAAGCCCACAAGTC-AGTGGCAC-CCTTTTC---AAAAGCCCACAAGTCAGTGGCAA
91308 CCTT
57 CC-T
***
91312 TTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCCACAAGTCAGTGGCAACCT
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCAACCT
* * **
91371 TT-AAAAGCCCATAAGTTAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCATATTT
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCA-ACCT
*
91430 TTCAAAAGCCCACAAGTCAGTGGCAACC-TTT-AAAAGCCCACAAGTCAGTGGCAACC-
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCAACCT
* ** *
91486 TTC-AAAGCCCACAAATCAGTGGCACCCTTTTCCGAAGCCCACAAGTCGGTGGC-ACCT
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCAACCT
91543 TTC
1 TTC
91546 CATCTTTAAG
Statistics
Matches: 336, Mismatches: 60, Indels: 49
0.76 0.13 0.11
Matches are distributed among these distances:
55 22 0.07
56 10 0.03
57 45 0.13
58 96 0.29
59 28 0.08
60 71 0.21
63 7 0.02
64 30 0.09
66 6 0.02
68 5 0.01
69 15 0.04
70 1 0.00
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (59 bp):
TTCAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCAACCT
Found at i:91437 original size:88 final size:88
Alignment explanation
Indices: 91288--91544 Score: 396
Period size: 88 Copynumber: 3.0 Consensus size: 88
91278 TTTCTTTTTC
91288 AGCCCACAAGTTAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCC
1 AGCCCACAAGTTAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCC
91353 ACAAGTCAGTGGCAACCTTTAAA
66 ACAAGTCAGTGGCAACCTTTAAA
*
91376 AGCCCATAAGTTAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCC
1 AGCCCACAAGTTAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCC
91441 ACAAGTCAGTGGCAACCTTTAAA
66 ACAAGTCAGTGGCAACCTTTAAA
* * * *** **
91464 AGCCCACAAGTCAGTGGCAACC--TTC-AAAGCCCACAAATCAGTGGCACCCTTTTCCGAAGCCC
1 AGCCCACAAGTTAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCC
*
91526 ACAAGTCGGTGGC-ACCTTT
66 ACAAGTCAGTGGCAACCTTT
91545 CCATCTTTAA
Statistics
Matches: 158, Mismatches: 11, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
84 6 0.04
85 43 0.27
86 3 0.02
88 106 0.67
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (88 bp):
AGCCCACAAGTTAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCC
ACAAGTCAGTGGCAACCTTTAAA
Found at i:91540 original size:30 final size:30
Alignment explanation
Indices: 91067--91541 Score: 364
Period size: 30 Copynumber: 15.9 Consensus size: 30
91057 TTCATCACCC
* ***
91067 TTCAAAAGTCCACAAGTCAGTGGCATATTT
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTT
***
91097 TTC-AAAGCCCACAAGTCAGTGGCATTTTTT
1 TTCAAAAGCCCACAAGTCAGTGGCA-CCCTT
*
91127 TTCAAAAGCCCACAAGTCAGTGGCAACC--
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTT
*
91155 TTC-AAAGCCCACAAATCAGTGGCACCCTT
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTT
** * *
91184 TTCCGAAGCCCACAAGTCGGTGGCA-TCTT
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTT
* * * * *
91213 TTCCAAAGTCCACAACTCCGTGGCACTCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCAC-CCTT
** * * * **
91244 TTCTTTTGTAAGCTCACAACTCTA-TAGCACTTTTT
1 TTC----AAAAGCCCACAAGTC-AGTGGCAC-CCTT
*** *
91279 TTCTTTTTCAGCCCACAAGTTAGTGGCACCCTT
1 TTC---AAAAGCCCACAAGTCAGTGGCACCCTT
***
91312 TTCAAAAGCCCACAAGTCAGTGGCATATTT
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTT
*
91342 TTCAAAAGCCCACAAGTCAGTGGCAACC-T
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTT
* *
91371 TT-AAAAGCCCATAAGTTAGTGGCACCCTT
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTT
***
91400 TTCAAAAGCCCACAAGTCAGTGGCATATTT
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTT
*
91430 TTCAAAAGCCCACAAGTCAGTGGCAACC-T
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTT
*
91459 TT-AAAAGCCCACAAGTCAGTGGCAACC--
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTT
*
91486 TTC-AAAGCCCACAAATCAGTGGCACCCTT
1 TTCAAAAGCCCACAAGTCAGTGGCACCCTT
** *
91515 TTCCGAAGCCCACAAGTCGGTGGCACC
1 TTCAAAAGCCCACAAGTCAGTGGCACC
91542 TTTCCATCTT
Statistics
Matches: 368, Mismatches: 58, Indels: 38
0.79 0.12 0.08
Matches are distributed among these distances:
27 46 0.12
28 50 0.14
29 59 0.16
30 140 0.38
31 26 0.07
33 6 0.02
34 18 0.05
35 23 0.06
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (30 bp):
TTCAAAAGCCCACAAGTCAGTGGCACCCTT
Found at i:91610 original size:43 final size:43
Alignment explanation
Indices: 91549--91638 Score: 153
Period size: 43 Copynumber: 2.1 Consensus size: 43
91539 ACCTTTCCAT
*
91549 CTTTAAGTCCAATGTAGCTGACCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCTGACCTTGAATCAGCACATTGGCAC
* *
91592 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATATAGCTGACCTTGAATCAGCACATTGGCAC
91635 CTTT
1 CTTT
91639 TCCATCTTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCTGACCTTGAATCAGCACATTGGCAC
Found at i:91670 original size:52 final size:53
Alignment explanation
Indices: 91592--91713 Score: 156
Period size: 52 Copynumber: 2.3 Consensus size: 53
91582 ACATTGGCAC
* *
91592 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CCTTTTCCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTCCAT
* * * *
91644 CTTTAAGTTCAATGTAGCTGGTCTTGAATCAGCACATTGACATCCTTTTTCTCAA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCC-TTTTC-CAT
*
91699 CTTTAAGCCCAATAT
1 CTTTAAGTCCAATAT
91714 CATTGGCCGT
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
52 37 0.64
53 2 0.03
54 5 0.09
55 14 0.24
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (53 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTCCAT
Found at i:92017 original size:11 final size:11
Alignment explanation
Indices: 92001--92030 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
91991 TGACCATATT
92001 CTTCCAAATCC
1 CTTCCAAATCC
92012 CTTCCAAATCC
1 CTTCCAAATCC
92023 CTTCCAAA
1 CTTCCAAA
92031 CGTTACATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.30, C:0.43, G:0.00, T:0.27
Consensus pattern (11 bp):
CTTCCAAATCC
Found at i:92605 original size:13 final size:13
Alignment explanation
Indices: 92587--92611 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
92577 CATAAAATGT
92587 TGTATCGATACAA
1 TGTATCGATACAA
92600 TGTATCGATACA
1 TGTATCGATACA
92612 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:92609 original size:33 final size:33
Alignment explanation
Indices: 92567--92633 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
92557 TTCAACGATT
92567 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
92600 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
92633 T
1 T
92634 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:92692 original size:13 final size:13
Alignment explanation
Indices: 92674--92698 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
92664 ATCACTTAAA
92674 TGTATCGATACAT
1 TGTATCGATACAT
92687 TGTATCGATACA
1 TGTATCGATACA
92699 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:92763 original size:52 final size:52
Alignment explanation
Indices: 92707--92887 Score: 335
Period size: 52 Copynumber: 3.5 Consensus size: 52
92697 CACTGATCTT
*
92707 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
92759 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
**
92811 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
92863 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
92888 TCATATTTCG
Statistics
Matches: 126, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 126 1.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:96590 original size:21 final size:21
Alignment explanation
Indices: 96557--96601 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
96547 TTGCAAGTTG
*
96557 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
96579 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
96599 AAA
1 AAA
96602 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:98425 original size:15 final size:15
Alignment explanation
Indices: 98405--98435 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
98395 TAAAAATGTC
*
98405 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
98420 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
98435 C
1 C
98436 CAAACGAAAT
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:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:100467 original size:20 final size:20
Alignment explanation
Indices: 100441--100518 Score: 75
Period size: 20 Copynumber: 3.6 Consensus size: 20
100431 AATGTCCAAA
100441 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATGTTTCT
* *
100461 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACA--T-G--TTTCT
*
100486 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATGTTTCT
*
100506 TTGTATCGATACA
1 ATGTATCGATACA
100519 CTGTATCGAT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
20 28 0.60
22 1 0.02
23 2 0.04
25 16 0.34
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATGTTTCT
Found at i:100525 original size:13 final size:13
Alignment explanation
Indices: 100507--100531 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
100497 CATTTTTCTT
100507 TGTATCGATACAC
1 TGTATCGATACAC
100520 TGTATCGATACA
1 TGTATCGATACA
100532 GGGTGATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:103020 original size:13 final size:13
Alignment explanation
Indices: 103002--103027 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
102992 TACAGCAAGT
103002 ATGTATCGATACA
1 ATGTATCGATACA
103015 ATGTATCGATACA
1 ATGTATCGATACA
103028 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:104838 original size:17 final size:16
Alignment explanation
Indices: 104818--104872 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 16
104808 GATCATGAGC
104818 AAAAAAGACAAAAAGGG
1 AAAAAAGA-AAAAAGGG
*
104835 AAAAAAAGAAAAAGAGAG
1 -AAAAAAGAAAAA-AGGG
*
104853 AAAAAAGAAAAAAAGG
1 AAAAAAGAAAAAAGGG
104869 AAAA
1 AAAA
104873 GAAAGTTCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 6 0.18
17 16 0.48
18 11 0.33
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (16 bp):
AAAAAAGAAAAAAGGG
Found at i:104841 original size:18 final size:17
Alignment explanation
Indices: 104818--104877 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 17
104808 GATCATGAGC
104818 AAAAAAGACAAAAAGGGA
1 AAAAAAGA-AAAAAGGGA
*
104836 AAAAAAG-AAAAAGAGA
1 AAAAAAGAAAAAAGGGA
*
104852 GAAAAAAGAAAAAAAGGA
1 -AAAAAAGAAAAAAGGGA
104870 AAAGAAAG
1 AAA-AAAG
104878 TTCTTTCAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
16 8 0.22
17 10 0.28
18 18 0.50
ACGTcount: A:0.77, C:0.02, G:0.22, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAAAAAGGGA
Found at i:106117 original size:249 final size:249
Alignment explanation
Indices: 105679--106179 Score: 1002
Period size: 249 Copynumber: 2.0 Consensus size: 249
105669 GCTCTTGAAA
105679 AATATAAAACTCTTTGATCTTTGAAAACTTTGATTGCTAGATGTTTCTTGCTTGGTTATTCTTGT
1 AATATAAAACTCTTTGATCTTTGAAAACTTTGATTGCTAGATGTTTCTTGCTTGGTTATTCTTGT
105744 GTTTTGCTGCTGGAAGCTCTTATTTATAGGCTTCAATGTTGTTGTAGCCGTTGGAGATTGATTGG
66 GTTTTGCTGCTGGAAGCTCTTATTTATAGGCTTCAATGTTGTTGTAGCCGTTGGAGATTGATTGG
105809 TGGAGTTTATAGCCGTTGTTGACTTGTTGAAGCTTATTTTAATGCAATCCCGTGTAAATGTATCG
131 TGGAGTTTATAGCCGTTGTTGACTTGTTGAAGCTTATTTTAATGCAATCCCGTGTAAATGTATCG
105874 ATATAATTTAGGATGTATCGATACATGCATTTGAAAATATAGCCGTTACAAGTC
196 ATATAATTTAGGATGTATCGATACATGCATTTGAAAATATAGCCGTTACAAGTC
105928 AATATAAAACTCTTTGATCTTTGAAAACTTTGATTGCTAGATGTTTCTTGCTTGGTTATTCTTGT
1 AATATAAAACTCTTTGATCTTTGAAAACTTTGATTGCTAGATGTTTCTTGCTTGGTTATTCTTGT
105993 GTTTTGCTGCTGGAAGCTCTTATTTATAGGCTTCAATGTTGTTGTAGCCGTTGGAGATTGATTGG
66 GTTTTGCTGCTGGAAGCTCTTATTTATAGGCTTCAATGTTGTTGTAGCCGTTGGAGATTGATTGG
106058 TGGAGTTTATAGCCGTTGTTGACTTGTTGAAGCTTATTTTAATGCAATCCCGTGTAAATGTATCG
131 TGGAGTTTATAGCCGTTGTTGACTTGTTGAAGCTTATTTTAATGCAATCCCGTGTAAATGTATCG
106123 ATATAATTTAGGATGTATCGATACATGCATTTGAAAATATAGCCGTTACAAGTC
196 ATATAATTTAGGATGTATCGATACATGCATTTGAAAATATAGCCGTTACAAGTC
106177 AAT
1 AAT
106180 GTATCGATAC
Statistics
Matches: 252, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
249 252 1.00
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.41
Consensus pattern (249 bp):
AATATAAAACTCTTTGATCTTTGAAAACTTTGATTGCTAGATGTTTCTTGCTTGGTTATTCTTGT
GTTTTGCTGCTGGAAGCTCTTATTTATAGGCTTCAATGTTGTTGTAGCCGTTGGAGATTGATTGG
TGGAGTTTATAGCCGTTGTTGACTTGTTGAAGCTTATTTTAATGCAATCCCGTGTAAATGTATCG
ATATAATTTAGGATGTATCGATACATGCATTTGAAAATATAGCCGTTACAAGTC
Found at i:106216 original size:13 final size:13
Alignment explanation
Indices: 106198--106223 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
106188 ACATTTTGGG
106198 ATGTATCGATACA
1 ATGTATCGATACA
106211 ATGTATCGATACA
1 ATGTATCGATACA
106224 TATTGTGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:106218 original size:33 final size:32
Alignment explanation
Indices: 106176--106243 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
106166 CGTTACAAGT
*
106176 CAATGTATCGATACATTTTGGGATGTATCGATA
1 CAATGTATCGATACATATTGGG-TGTATCGATA
*
106209 CAATGTATCGATACATATTGTGTGTATCGATA
1 CAATGTATCGATACATATTGGGTGTATCGATA
106241 CAA
1 CAA
106244 ATTTGGCTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATATTGGGTGTATCGATA
Found at i:106323 original size:20 final size:21
Alignment explanation
Indices: 106276--106327 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
106266 CCCAATGACC
**
106276 TGTATCGATACATTCTTTTCA
1 TGTATCGATACATTCTGGTCA
*
106297 AGTATCGATACATT-TGGTCA
1 TGTATCGATACATTCTGGTCA
106317 TGTATCGATAC
1 TGTATCGATAC
106328 TGTGCAATCT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATTCTGGTCA
Found at i:108758 original size:13 final size:13
Alignment explanation
Indices: 108740--108777 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
108730 ATAAACCCCT
*
108740 TGTATCGATACAC
1 TGTATCGATACAA
108753 TGTATCGATACAA
1 TGTATCGATACAA
*
108766 TCTATCGATACA
1 TGTATCGATACA
108778 GAGAATGCTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:114965 original size:19 final size:20
Alignment explanation
Indices: 114920--114971 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
114910 TTACAAGCCA
*
114920 ATGTATCGATACATTTTGGG
1 ATGTATCGATACATATTGGG
* *
114940 ATGTATCAATACATATTGTG
1 ATGTATCGATACATATTGGG
114960 -TGTATCGATACA
1 ATGTATCGATACA
114972 AATTTGGCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATATTGGG
Found at i:115052 original size:20 final size:21
Alignment explanation
Indices: 115005--115057 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
114995 CCCAATGACC
**
115005 TGTATCGATACATTCTTTTCA
1 TGTATCGATACATTCTGGTCA
*
115026 AGTATCGATACATT-TGGTCA
1 TGTATCGATACATTCTGGTCA
115046 TGTATCGATACA
1 TGTATCGATACA
115058 ATATATTGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATTCTGGTCA
Found at i:115776 original size:59 final size:59
Alignment explanation
Indices: 115680--115828 Score: 149
Period size: 59 Copynumber: 2.5 Consensus size: 59
115670 CTATAGATTC
* * * ** *
115680 TAGGATCATTTAGGTTATTTTCTATAATC-CGGAGACTATTT-AGTAATTTTTATACATTT
1 TAGGATCAATTAAGTTATTTTCCATAATCTATG-GACTATTTGA-TAATTTTCATACATTT
* * * **
115739 TAGGGTCAATTAGGTTGTTTTCCATAATCTATGGACTATTTGATAATTTTCATGTATTT
1 TAGGATCAATTAAGTTATTTTCCATAATCTATGGACTATTTGATAATTTTCATACATTT
* *
115798 TAGGATCATTTAAGTTATTTTTCATAATCTA
1 TAGGATCAATTAAGTTATTTTCCATAATCTA
115829 GAAAAAATTT
Statistics
Matches: 74, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
59 72 0.97
60 2 0.03
ACGTcount: A:0.28, C:0.10, G:0.14, T:0.48
Consensus pattern (59 bp):
TAGGATCAATTAAGTTATTTTCCATAATCTATGGACTATTTGATAATTTTCATACATTT
Found at i:115928 original size:49 final size:49
Alignment explanation
Indices: 115870--115976 Score: 128
Period size: 49 Copynumber: 2.2 Consensus size: 49
115860 AGCCCTTTGA
* * *
115870 GTTAGTTTTGTACCCATC-ATCAGAATCTATC-AAAATTAAATCTTTTAAG
1 GTTAGTTTTGTA-CCATCTATC-GAAACTAACTAAAATCAAATCTTTTAAG
** *
115919 GTTAGTTTTGTACTTTCTGTCGAAACTAACTAAAATCAAATCTTTTAAG
1 GTTAGTTTTGTACCATCTATCGAAACTAACTAAAATCAAATCTTTTAAG
115968 GTTAGTTTT
1 GTTAGTTTT
115977 ATACTTTTTG
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
48 10 0.20
49 40 0.80
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (49 bp):
GTTAGTTTTGTACCATCTATCGAAACTAACTAAAATCAAATCTTTTAAG
Found at i:117836 original size:16 final size:15
Alignment explanation
Indices: 117810--117840 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
117800 TAAAAAAAGA
117810 ATTTTTTATTATTTT
1 ATTTTTTATTATTTT
117825 ATTTTGTTATTATTTT
1 ATTTT-TTATTATTTT
117841 TATGGAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.77
Consensus pattern (15 bp):
ATTTTTTATTATTTT
Found at i:119005 original size:16 final size:16
Alignment explanation
Indices: 118984--119017 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
118974 TTTTTTGAAT
*
118984 ATTTTTTATTTCTTTA
1 ATTTTTAATTTCTTTA
*
119000 ATTTTTAATTTTTTTA
1 ATTTTTAATTTCTTTA
119016 AT
1 AT
119018 ATATATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (16 bp):
ATTTTTAATTTCTTTA
Found at i:119711 original size:131 final size:128
Alignment explanation
Indices: 119546--120229 Score: 685
Period size: 131 Copynumber: 5.3 Consensus size: 128
119536 GCAAACTTAG
* * * * *
119546 GGAAAGAAAAGCCTCTAAGGTCAAAGCCGACAGGCAGAATGAGGAAATAAAAGTCTCCA-AGATC
1 GGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGG-AATAAAAGTCTCCAGGGATC
* * * *
119610 AAAGCCGACAGGCAGACTAAGGGATA-AAAAGTCTCCAAGGACGAAGCCGACAAGCAGACTAAGG
65 AAAGCCGACAGGTAGACTAAGGGA-AGGAAAGTCTCCAGGGACGAAGCCGACAGGCAGACTAA--
119674 GAA
127 G-A
**
119677 GGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGGTTGAAAAGTCTCCAGGGA-C
1 GGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGAAT-AAAAGTCTCCAGGGATC
* *
119741 AAAGCCGACAGGTAGACTAAGGGAAGGAAAGTCTTCAGGGACGAAGCTGACAGGCAGACTAACGA
65 AAAGCCGACAGGTAGACTAAGGGAAGGAAAGTCTCCAGGGACGAAGCCGACAGGCAGACTAA-G-
119806 AA
128 -A
* * ** *
119808 GGAAAGAAAAGTCTACAAGGTCAAAGCCGACAGGCAGACTGAGGGTTGAAAAGTCTCTAGGGAT-
1 GGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGAAT-AAAAGTCTCCAGGGATC
* * * * *
119872 GAAGCCTATAGGTAGACTAAGGGAAGGAAAGTCTCCAGGGATGAAGCCGACAGGTAGACTAAG-
65 AAAGCCGACAGGTAGACTAAGGGAAGGAAAGTCTCCAGGGACGAAGCCGACAGGCAGACTAAGA
* * * * **
119935 GG-TAGAAAAGTCTCCAGGGTCAAAGCCGACAAGTAGACTAAGGGAAGGAAAGTCTCCAGGGA-C
1 GGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGA-GGAATAAAAGTCTCCAGGGATC
*
119998 AAAGCCGACAGGTAGACTAAGGGAAGGAAAGAAAAGTCTCCAGGG-CAAAGCCGACAGGCAGACT
65 AAAGCCGACAGGTAGACTAAGGGAA-G---G-AAAGTCTCCAGGGACGAAGCCGACAGGCAGACT
120062 --GA
125 AAGA
*** * * * * * * * *
120064 GGGTTGAAAAGTCTCCAGGGACGAAGCCGATAGGCAGAATAAGGGTAGAAAAGTGTCC-GAGG-T
1 GGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGA-GGAATAAAAGTCTCCAG-GGAT
* *
120127 CAAAGCCGACAGGTAGACTAAGGGAAGGAAAGTCTCCAGGGACGAAGCCGACAGGTAGAATAAG-
64 CAAAGCCGACAGGTAGACTAAGGGAAGGAAAGTCTCCAGGGACGAAGCCGACAGGCAGACTAAGA
* ** *
120191 GG-TAGAAAAGTCTCTGGGGTCAAAGCCGACAGGTAGACT
1 GGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACT
120230 AAGGGAAAAC
Statistics
Matches: 472, Mismatches: 62, Indels: 43
0.82 0.11 0.07
Matches are distributed among these distances:
125 13 0.03
126 114 0.24
127 7 0.01
128 2 0.00
129 4 0.01
130 94 0.20
131 236 0.50
132 2 0.00
ACGTcount: A:0.38, C:0.18, G:0.32, T:0.12
Consensus pattern (128 bp):
GGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAGGAATAAAAGTCTCCAGGGATCA
AAGCCGACAGGTAGACTAAGGGAAGGAAAGTCTCCAGGGACGAAGCCGACAGGCAGACTAAGA
Found at i:120224 original size:42 final size:42
Alignment explanation
Indices: 119544--120236 Score: 622
Period size: 42 Copynumber: 16.1 Consensus size: 42
119534 GGGCAAACTT
* * * * * *
119544 AGGGAAAGAAAAGCCTCTAAGGTCAAAGCCGACAGGCAGAATG
1 AGGG-AAGAAAAGTCTCCAGGGTCAAAGCCGACAGGTAGACTA
* * * * *
119587 AGGAAATAAAAGTCTCCAAGATCAAAGCCGACAGGCAGACTA
1 AGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGTAGACTA
* * * * *
119629 AGGGATA-AAAAGTCTCCAAGGACGAAGCCGACAAGCAGACTA
1 AGGGA-AGAAAAGTCTCCAGGGTCAAAGCCGACAGGTAGACTA
* *
119671 AGGGAAGGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTG
1 A--G--GG-AAGAAAAGTCTCCAGGGTCAAAGCCGACAGGTAGACTA
** *
119718 AGGGTTGAAAAGTCTCCAGGGACAAAGCCGACAGGTAGACTA
1 AGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGTAGACTA
* * * * * *
119760 AGGGAAGGAAAGTCTTCAGGGACGAAGCTGACAGGCAGACTA
1 AGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGTAGACTA
* * * *
119802 ACGAAAGGAAAGAAAAGTCTACAAGGTCAAAGCCGACAGGCAGACTG
1 A-G---GG-AAGAAAAGTCTCCAGGGTCAAAGCCGACAGGTAGACTA
** * * * *
119849 AGGGTTGAAAAGTCTCTAGGGAT-GAAGCCTATAGGTAGACTA
1 AGGGAAGAAAAGTCTCCAGGG-TCAAAGCCGACAGGTAGACTA
* *
119891 AGGGAAGGAAAGTCTCCAGGGAT-GAAGCCGACAGGTAGACTA
1 AGGGAAGAAAAGTCTCCAGGG-TCAAAGCCGACAGGTAGACTA
* *
119933 AGGGTAGAAAAGTCTCCAGGGTCAAAGCCGACAAGTAGACTA
1 AGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGTAGACTA
* *
119975 AGGGAAGGAAAGTCTCCAGGGACAAAGCCGACAGGTAGACTA
1 AGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGTAGACTA
* *
120017 AGGGAAGGAAAGAAAAGTCTCCAGGG-CAAAGCCGACAGGCAGACTG
1 A--G--GG-AAGAAAAGTCTCCAGGGTCAAAGCCGACAGGTAGACTA
** * * * * *
120063 AGGGTTGAAAAGTCTCCAGGGACGAAGCCGATAGGCAGAATA
1 AGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGTAGACTA
* *
120105 AGGGTAGAAAAGTGTCC-GAGGTCAAAGCCGACAGGTAGACTA
1 AGGGAAGAAAAGTCTCCAG-GGTCAAAGCCGACAGGTAGACTA
* * * *
120147 AGGGAAGGAAAGTCTCCAGGGACGAAGCCGACAGGTAGAATA
1 AGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGTAGACTA
* **
120189 AGGGTAGAAAAGTCTCTGGGGTCAAAGCCGACAGGTAGACTA
1 AGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGTAGACTA
120231 AGGGAA
1 AGGGAA
120237 AACAAAAAAG
Statistics
Matches: 538, Mismatches: 90, Indels: 45
0.80 0.13 0.07
Matches are distributed among these distances:
41 17 0.03
42 399 0.74
43 11 0.02
44 3 0.01
45 1 0.00
46 27 0.05
47 80 0.15
ACGTcount: A:0.38, C:0.18, G:0.32, T:0.12
Consensus pattern (42 bp):
AGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGTAGACTA
Found at i:129760 original size:34 final size:35
Alignment explanation
Indices: 129722--129788 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
129712 CCTTACAACA
129722 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
129756 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
129789 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:130285 original size:13 final size:13
Alignment explanation
Indices: 130267--130292 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
130257 CTATTTATGA
130267 TGTATCGATACAC
1 TGTATCGATACAC
130280 TGTATCGATACAC
1 TGTATCGATACAC
130293 ACAAATATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:130437 original size:22 final size:22
Alignment explanation
Indices: 130382--130437 Score: 105
Period size: 21 Copynumber: 2.6 Consensus size: 22
130372 ACAGTGACCT
130382 ATGAACAGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
130404 ATGAA-AGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
130425 ATGAACAGTGATG
1 ATGAACAGTGATG
130438 AATAGTGATG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.64
22 12 0.36
ACGTcount: A:0.38, C:0.11, G:0.25, T:0.27
Consensus pattern (22 bp):
ATGAACAGTGATGTATCGATAC
Found at i:130444 original size:10 final size:10
Alignment explanation
Indices: 130425--130455 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
130415 GTATCGATAC
130425 ATGAACAGTG
1 ATGAACAGTG
*
130435 ATGAATAGTG
1 ATGAACAGTG
130445 ATGAACAGTG
1 ATGAACAGTG
130455 A
1 A
130456 AAATGAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:130595 original size:20 final size:20
Alignment explanation
Indices: 130550--130603 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
130540 TACATATTTG
*
130550 TGTGTATCGATACTATGCAA
1 TGTGTATCGATACTATGAAA
* *
130570 TTTGTATCGATAC-ATTTAAA
1 TGTGTATCGATACTA-TGAAA
130590 TGTGTATCGATACT
1 TGTGTATCGATACT
130604 TTTCAGGGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.41
Consensus pattern (20 bp):
TGTGTATCGATACTATGAAA
Found at i:130668 original size:21 final size:21
Alignment explanation
Indices: 130642--130682 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
130632 GTCAACCTTG
130642 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
130663 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
130683 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:135372 original size:16 final size:16
Alignment explanation
Indices: 135351--135384 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
135341 TTTTTTGAAT
*
135351 ATTTTTTATTTCTTTA
1 ATTTTTAATTTCTTTA
*
135367 ATTTTTAATTTTTTTA
1 ATTTTTAATTTCTTTA
135383 AT
1 AT
135385 ATATATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (16 bp):
ATTTTTAATTTCTTTA
Found at i:137542 original size:21 final size:22
Alignment explanation
Indices: 137509--137556 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
137499 AAATAATAAG
* * *
137509 AATTATTTTTAAAATTATTTTT
1 AATTATTTATAAAATTAATTCT
*
137531 AATTA-TTATAAATTTAATTCT
1 AATTATTTATAAAATTAATTCT
137552 AATTA
1 AATTA
137557 AATTATCTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
AATTATTTATAAAATTAATTCT
Found at i:137917 original size:26 final size:26
Alignment explanation
Indices: 137888--137951 Score: 60
Period size: 26 Copynumber: 2.5 Consensus size: 26
137878 AAAATAAAAT
*
137888 AAAATATTTTTAATTTAAAAAATCAA
1 AAAATATTTTTAATCTAAAAAATCAA
** *
137914 AAAA-ATTGTAAAATCTAAAAATTCAA
1 AAAATATT-TTTAATCTAAAAAATCAA
*
137940 AATAT-TTTTTAA
1 AAAATATTTTTAA
137952 AAAATCCTTA
Statistics
Matches: 29, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
25 6 0.21
26 23 0.79
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.38
Consensus pattern (26 bp):
AAAATATTTTTAATCTAAAAAATCAA
Found at i:138639 original size:16 final size:16
Alignment explanation
Indices: 138593--138637 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
138583 TTCTTTTTAT
**
138593 TTTTTAATTTTTCGAAA
1 TTTTT-ATTTTTTAAAA
138610 TTTTTATTTTTTAAAA
1 TTTTTATTTTTTAAAA
138626 TTTCTTATTTTT
1 TTT-TTATTTTT
138638 AATTTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 12 0.48
17 13 0.52
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.69
Consensus pattern (16 bp):
TTTTTATTTTTTAAAA
Found at i:138646 original size:18 final size:18
Alignment explanation
Indices: 138625--138667 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
138615 ATTTTTTAAA
* *
138625 ATTTCTTATTTTTAATTT
1 ATTTCTTATTTTGAATCT
*
138643 ATTTTTTATTTTGAATCT
1 ATTTCTTATTTTGAATCT
138661 ATTTCTT
1 ATTTCTT
138668 TTAAGAATAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.21, C:0.07, G:0.02, T:0.70
Consensus pattern (18 bp):
ATTTCTTATTTTGAATCT
Found at i:138647 original size:44 final size:44
Alignment explanation
Indices: 138563--138649 Score: 104
Period size: 44 Copynumber: 2.0 Consensus size: 44
138553 ATATTTCAAA
* *
138563 AAATCTTTATGTTTTAAATTTTCTTTTTATTTTTTAATTTTTCG
1 AAATCTTTATGTTTTAAAATTTCTTTTTATTATTTAATTTTTCG
* * *
138607 AAATTTTTATTTTTTAAAATTTCTTATTT-TTAATTTATTTTTT
1 AAATCTTTATGTTTTAAAATTTCTT-TTTATT-ATTTAATTTTT
138650 ATTTTGAATC
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
44 24 0.67
45 12 0.33
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68
Consensus pattern (44 bp):
AAATCTTTATGTTTTAAAATTTCTTTTTATTATTTAATTTTTCG
Found at i:139974 original size:3 final size:3
Alignment explanation
Indices: 139966--139995 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
139956 TTGATTTCAC
139966 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
139996 GAGAAATTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:141907 original size:30 final size:30
Alignment explanation
Indices: 141866--141947 Score: 105
Period size: 30 Copynumber: 2.8 Consensus size: 30
141856 TGTTCCACGT
*
141866 CCTCCACCTCCAAAGCCTCCTCTATCACCG
1 CCTCTACCTCCAAAGCCTCCTCTATCACCG
* * *
141896 GCTCTACCTCCACAGCCTCCTCCATCACCG
1 CCTCTACCTCCAAAGCCTCCTCTATCACCG
141926 CCTCTA-CTGCCAAA-CCTCCTCT
1 CCTCTACCT-CCAAAGCCTCCTCT
141948 GTCAGATCTC
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 9 0.20
30 35 0.80
ACGTcount: A:0.18, C:0.52, G:0.07, T:0.22
Consensus pattern (30 bp):
CCTCTACCTCCAAAGCCTCCTCTATCACCG
Found at i:142814 original size:229 final size:228
Alignment explanation
Indices: 142233--142920 Score: 911
Period size: 228 Copynumber: 3.0 Consensus size: 228
142223 AATCCTCGCC
* * ** * * * *
142233 TGCACTACTAGAACCCTG-GTTCCAACAGCCATTTTTGCCCCAAGCAGAGTCTTGGCCAGAATCA
1 TGCACTACTAGAA-CCAGAGATCCAACAGCCCCTTTTGCTCCGACCAGAGTCTTGGCCAGCATCA
* *
142297 ACAGTTCCAGTACCCCAACTGCTTTTCTTACCCCAGTTTGAATCGTCATTTGCATCTGCAGATCC
65 ACAGTTCCAGCACCCCAACTGCTTTTCTTACCCCAGTTTGAATCCTCATTTGCATCTGCAGATCC
* * * * * * * * *
142362 CGAGGTCTATTCACTTTTC-TTCCCGCAACTAGAATCTTTGGTTACATCACCAGATGCAAAATCC
130 TGAGTTCCAGTCACTTTTCTTTCCC-CAGCTAGAATCTTTGGTTGCATCACCAGATCCAAAGTCA
* *
142426 GAATCATTTTTCTTAGCCCAACCAGGATCTTGGTT
194 GAATCATTTTTCTTAGCCCAACCAGAATCCTGGTT
* * *
142461 TGCACTACTAGAACCAGAGTTCCAACTGCCCCTTTTTCTCCGACCAGAGTCTTGGCCAGCATCAA
1 TGCACTACTAGAACCAGAGATCCAACAGCCCCTTTTGCTCCGACCAGAGTCTTGGCCAGCATCAA
* *
142526 TAGTAT-CAGCACCCCAACTGCTTTTCTTACCCCAGTTTGAATCCTCATTTGCATCTGCAGAGCC
66 CAGT-TCCAGCACCCCAACTGCTTTTCTTACCCCAGTTTGAATCCTCATTTGCATCTGCAGATCC
* * *
142590 TGATTTCCAGTCACTTTTCTTTCCCCAGCTAGAATATTTGGTTGCAGT-ACCAGATCCAAAGTCT
130 TGAGTTCCAGTCACTTTTCTTTCCCCAGCTAGAATCTTTGGTTGCA-TCACCAGATCCAAAGTCA
*
142654 GAATCATTTTTCTTAGCCAAACCAGAATCCTGGTT
194 GAATCATTTTTCTTAGCCCAACCAGAATCCTGGTT
* * * ** *
142689 TGCATTAC-CGCAACCAGAGATCCTAACAGTCCCTTTTGCTCCGACCAGCA-TCTTGGCTGGCTT
1 TGCACTACTAG-AACCAGAGATCC-AACAGCCCCTTTTGCTCCGACCAG-AGTCTTGGCCAGCAT
* *
142752 CAACAGTTCCAGCACCCCAACTGCTTTTCCTACCCCAGTTTGAGTCCTCATTTGCATCTGCAGAT
63 CAACAGTTCCAGCACCCCAACTGCTTTTCTTACCCCAGTTTGAATCCTCATTTGCATCTGCAGAT
* *
142817 CCTGAGTTCCAGTCATTTTTCTTTCCCCAGCTAGAATCTTTGGTTGCATCACCAGATTCAAAGTC
128 CCTGAGTTCCAGTCACTTTTCTTTCCCCAGCTAGAATCTTTGGTTGCATCACCAGATCCAAAGTC
142882 AGAATCATTTTTCTTAGCCCAACCAGAATCCTGGTT
193 AGAATCATTTTTCTTAGCCCAACCAGAATCCTGGTT
142918 TGC
1 TGC
142921 GTTCCCACAA
Statistics
Matches: 405, Mismatches: 46, Indels: 17
0.87 0.10 0.04
Matches are distributed among these distances:
227 4 0.01
228 207 0.51
229 193 0.48
230 1 0.00
ACGTcount: A:0.24, C:0.30, G:0.16, T:0.31
Consensus pattern (228 bp):
TGCACTACTAGAACCAGAGATCCAACAGCCCCTTTTGCTCCGACCAGAGTCTTGGCCAGCATCAA
CAGTTCCAGCACCCCAACTGCTTTTCTTACCCCAGTTTGAATCCTCATTTGCATCTGCAGATCCT
GAGTTCCAGTCACTTTTCTTTCCCCAGCTAGAATCTTTGGTTGCATCACCAGATCCAAAGTCAGA
ATCATTTTTCTTAGCCCAACCAGAATCCTGGTT
Found at i:153884 original size:20 final size:20
Alignment explanation
Indices: 153859--153929 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
153849 AGACATAATG
153859 TATCGATACATT-AAAGAATA
1 TATCGATACATTCAAA-AATA
* *
153879 TATCGATACATTCATACATA
1 TATCGATACATTCAAAAATA
* * * *
153899 CATCGATATATTGAAAAATG
1 TATCGATACATTCAAAAATA
153919 TATCGATACAT
1 TATCGATACAT
153930 CTGGGTAAAA
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 38 0.95
21 2 0.05
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (20 bp):
TATCGATACATTCAAAAATA
Found at i:154601 original size:28 final size:29
Alignment explanation
Indices: 154489--155238 Score: 779
Period size: 28 Copynumber: 25.3 Consensus size: 29
154479 TTTTTAAAAA
* *
154489 AAAAGGGTGCCACTAACTTATGTGGGCCTTG
1 AAAAGGGTGCCACTGAC-T-TGTGGGCTTTG
* **
154520 AAAAGAGTTGCCACCAACTCGTGTGGGCTTTG
1 AAAAG-GGTGCCACTGACT--TGTGGGCTTTG
* * * * *
154552 AAAAGAGTTACCGCTGGCTTGTGAGCTTT-
1 AAAAG-GGTGCCACTGACTTGTGGGCTTTG
154581 AAAAGGGTGCCACTGACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
* *
154610 GAAA-GGTGCCACTGACTTGCGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
*
154638 GAAA-GGTGCCACTGACTTACGTGGGCTTTG
1 AAAAGGGTGCCACTGACTT--GTGGGCTTTG
*
154668 AAAGGGGTGCCACTGACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
154697 -AAAGGGTGCCACTGACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
* ** *
154725 AAAAGAGTTGCCACCAACTCGTGTGGACTTTG
1 AAAAG-GGTGCCACTGACT--TGTGGGCTTTG
*
154757 AAAAGAGTGCCACTGACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
*
154786 AAAAGAGTGCCACTGACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
154815 -AAAGGGTGCCACTGACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
*
154843 -AAAGGGTGCCACTGTCTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
** * *
154871 AAAAGAATACCACAGACTTGTGGGCTTT-
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
*
154899 AAAAGGGTGTCACTGACTTGCGTGGGCTTTG
1 AAAAGGGTGCCACTGACTT--GTGGGCTTTG
* *
154930 AAAGGGGTGCCACTGACTTGTGGG-TTTT
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
*
154958 AAAAGGGTGCCACTAACTTGCGTGGGCTTT-
1 AAAAGGGTGCCACTGACTT--GTGGGCTTTG
*
154988 AAAAGGAGTGCCACTAACTTGTGGGCTTTG
1 AAAAGG-GTGCCACTGACTTGTGGGCTTTG
* *
155018 -AAAGGGTACCACTAACTTGTGTGGGCTTTG
1 AAAAGGGTGCCACTGAC-T-TGTGGGCTTTG
* *
155048 AAAGGGGTGCCACTGACTTGTGGGCATTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
155077 -AAAGGGTGCCACTGACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
*
155105 AAAAAGGGGTGCCACCGACTCGTGTGGGCTTTG
1 -AAAA-GGGTGCCACTGACT--TGTGGGCTTTG
* *
155138 AAAAGAGTGCCACTGATCCACTGACTTGTGAGTTTTG
1 AAAAG-G-G----TG--CCACTGACTTGTGGGCTTTG
*
155175 AAAGGGGTGCCACTGACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
* *
155204 -AAAGAGTGCCACTGACTTGTGAGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
155232 -AAAGGGT
1 AAAAGGGT
155239 TTGAACGTTC
Statistics
Matches: 619, Mismatches: 65, Indels: 73
0.82 0.09 0.10
Matches are distributed among these distances:
28 241 0.39
29 131 0.21
30 65 0.11
31 91 0.15
32 54 0.09
33 12 0.02
35 1 0.00
36 1 0.00
37 15 0.02
39 8 0.01
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.27
Consensus pattern (29 bp):
AAAAGGGTGCCACTGACTTGTGGGCTTTG
Found at i:154693 original size:59 final size:56
Alignment explanation
Indices: 154490--155238 Score: 746
Period size: 59 Copynumber: 12.6 Consensus size: 56
154480 TTTTAAAAAA
* * * **
154490 AAAGGGTGCCACTAACTTATGTGGGCCTTGAAAAGAGTTGCCACCAACTCGTGTGGGCTTTG
1 AAAGGGTGCCACTGAC-T-TGTGGGCTTTG-AAAG-GGTGCCACTGACT--TGTGGGCTTTG
* * * * * *
154552 AAAAGAGTTACCGCTGGCTTGTGAGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGG
1 -AAAG-GGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTT-G
*
154611 AAA-GGTGCCACTGACTTGCGGGCTTTGGAAA-GGTGCCACTGACTTACGTGGGCTTTG
1 AAAGGGTGCCACTGACTTGTGGGCTTT-GAAAGGGTGCCACTGACTT--GTGGGCTTTG
154668 AAAGGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG
1 AAA-GGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG
* ** * *
154725 AAAAGAGTTGCCACCAACTCGTGTGGACTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
1 -AAAG-GGTGCCACTGACT--TGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTG
*
154786 AAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG
1 -AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG
* ** * * *
154843 AAAGGGTGCCACTGTCTTGTGGGCTTTGAAAAGAATACCACAGACTTGTGGGCTTTA
1 AAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTG
* * *
154900 AAAGGGTGTCACTGACTTGCGTGGGCTTTGAAAGGGGTGCCACTGACTTGTGGGTTTTA
1 AAAGGGTGCCACTGACTT--GTGGGCTTTGAAA-GGGTGCCACTGACTTGTGGGCTTTG
* * *
154959 AAAGGGTGCCACTAACTTGCGTGGGCTTTAAAAGGAGTGCCACTAACTTGTGGGCTTTG
1 AAAGGGTGCCACTGACTT--GTGGGCTTTGAAAGG-GTGCCACTGACTTGTGGGCTTTG
* * *
155018 AAAGGGTACCACTAACTTGTGTGGGCTTTGAAAGGGGTGCCACTGACTTGTGGGCATTG
1 AAAGGGTGCCACTGAC-T-TGTGGGCTTTGAAA-GGGTGCCACTGACTTGTGGGCTTTG
*
155077 AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAAGGGGTGCCACCGACTCGTGTGGGCTTTG
1 AAAGGGTGCCACTGACTTGTGGGCTTTG--AAA-GGGTGCCACTGACT--TGTGGGCTTTG
* *
155138 AAAAGAGTGCCACTGATCCACTGACTTGTGAGTTTTGAAAGGGGTGCCACTGACTTGTGGGCTTT
1 -AAAG-G-G----TG--CCACTGACTTGTGGGCTTTGAAA-GGGTGCCACTGACTTGTGGGCTTT
155203 G
56 G
* *
155204 AAAGAGTGCCACTGACTTGTGAGCTTTGAAAGGGT
1 AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGT
155239 TTGAACGTTC
Statistics
Matches: 589, Mismatches: 63, Indels: 75
0.81 0.09 0.10
Matches are distributed among these distances:
56 61 0.10
57 117 0.20
58 55 0.09
59 198 0.34
60 32 0.05
61 47 0.08
62 12 0.02
63 7 0.01
64 8 0.01
65 4 0.01
66 11 0.02
68 19 0.03
70 18 0.03
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.27
Consensus pattern (56 bp):
AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG
Found at i:156500 original size:15 final size:14
Alignment explanation
Indices: 156482--156512 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
156472 TTCTAGTTTC
156482 TTTTTTTGTTTTGTT
1 TTTTTTTGTTTT-TT
156497 TTTTTTTGTTTTTT
1 TTTTTTTGTTTTTT
156511 TT
1 TT
156513 GGGTGTAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (14 bp):
TTTTTTTGTTTTTT
Found at i:170361 original size:20 final size:20
Alignment explanation
Indices: 170336--170406 Score: 90
Period size: 20 Copynumber: 3.5 Consensus size: 20
170326 AGACATAATG
*
170336 TATCGATACATTGAAGAATA
1 TATCGATACATTGAAAAATA
*
170356 TATCGATACATT-AATACATA
1 TATCGATACATTGAA-AAATA
* *
170376 TATCGATATATTGAAAAATG
1 TATCGATACATTGAAAAATA
170396 TATCGATACAT
1 TATCGATACAT
170407 CTGGGTAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
19 2 0.05
20 39 0.91
21 2 0.05
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34
Consensus pattern (20 bp):
TATCGATACATTGAAAAATA
Found at i:173464 original size:168 final size:166
Alignment explanation
Indices: 173270--173785 Score: 471
Period size: 166 Copynumber: 3.1 Consensus size: 166
173260 TTAAAACATC
* * * * * ** *
173270 AAAATTCCTCAAATATTATCATTTAATTCCA-ATCATATCAGTTTTCAGAAATTTCCTTTATTTT
1 AAAATTCATCAAATATTATTATTTAATTCCATATCAAATCAATTTTCA-AAAATTAATTCATTTT
* * * * * * * *
173334 -TGGAGTTATTG-ATTTTCTTTC-AGAATTCCTCTTATTTTC-AAATTACAGGGTTTTTTTTCTC
65 AT-AAATTATTGAATTTT-TTCCTAAAATT-CTCTTATTTTCGAAA-AACAGAG-TTTTCTACTC
173395 CGTAAATTTCTTTCAAGAGGATTTTTCTTGCTTTTTAATTTTT
125 CGTAAATTT-TTTCAAGAGGATTTTTCTTGCTTTTTAATTTTT
* *
173438 AAAATTTATCAAATATTATTATTTAATT-CATATTAAATCAATTTTCAAAAATTAATTCATTTTC
1 AAAATTCATCAAATATTATTATTTAATTCCATATCAAATCAATTTTCAAAAATTAATTCATTTT-
* *
173502 ATAAATTTTTGAATTTTTTCCTAAAATTCTCTTGTTTTCGAAAAACAGAGTTTTCTACTCCGTAA
65 ATAAATTATTGAATTTTTTCCTAAAATTCTCTTATTTTCGAAAAACAGAGTTTTCTACTCCGTAA
* *
173567 ATTTTTTCGAGAGGATTTTTCTTGGTTTTTAATTTTT
130 ATTTTTTCAAGAGGATTTTTCTTGCTTTTTAATTTTT
* * * * * *
173604 AAAATTCATAAAATACTGTTATTTAATT-CATATTAAATCAATTTTAAAAAATTAATTTATTTTC
1 AAAATTCATCAAATATTATTATTTAATTCCATATCAAATCAATTTTCAAAAATTAATTCATTTT-
* * * * * *
173668 ATGAGTT-TTGAA-TTTTTCTTTAAAA-TCTCCCTATTTTCGAAAAACTGAGTTTTCTA-TCTCA
65 ATAAATTATTGAATTTTTTC-CTAAAATTCT-CTTATTTTCGAAAAACAGAGTTTTCTACTC-CG
* * * * * *
173729 TAAATATTTTCAAAAAGATTTTTCTCGGTTTTAAATTTTT
127 TAAATTTTTTCAAGAGGATTTTTCTTGCTTTTTAATTTTT
173769 AAAATTCAT-ATAATATT
1 AAAATTCATCA-AATATT
173786 GTTACAAAAC
Statistics
Matches: 296, Mismatches: 42, Indels: 23
0.82 0.12 0.06
Matches are distributed among these distances:
164 12 0.04
165 83 0.28
166 94 0.32
167 31 0.10
168 62 0.21
169 14 0.05
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.49
Consensus pattern (166 bp):
AAAATTCATCAAATATTATTATTTAATTCCATATCAAATCAATTTTCAAAAATTAATTCATTTTA
TAAATTATTGAATTTTTTCCTAAAATTCTCTTATTTTCGAAAAACAGAGTTTTCTACTCCGTAAA
TTTTTTCAAGAGGATTTTTCTTGCTTTTTAATTTTT
Found at i:173598 original size:166 final size:165
Alignment explanation
Indices: 173392--173783 Score: 529
Period size: 166 Copynumber: 2.4 Consensus size: 165
173382 GGTTTTTTTT
* * * *
173392 CTCCGTAAATTTCTTTCAAGAGGATTTTTCTTGCTTTTTAATTTTTAAAATTTATCAAATATTAT
1 CTCCGTAAATTT-TTTCAAGAGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATAAAATACTAT
* *
173457 TATTTAATTCATATTAAATCAATTTTCAAAAATTAATTCATTTTCATAAATTTTTGAATTTTT-T
65 TATTTAATTCATATTAAATCAATTTTAAAAAATTAATTCATTTTCAT-AAGTTTTGAATTTTTCT
* *
173521 CCTAAAAT-TCTCTTGTTTTCGAAAAACAGAGTTTTCTA
129 -CTAAAATCTC-CCTATTTTCGAAAAACAGAGTTTTCTA
* *
173559 CTCCGTAAATTTTTTCGAGAGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATAAAATACTGTT
1 CTCCGTAAATTTTTTCAAGAGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATAAAATACTATT
* * *
173624 ATTTAATTCATATTAAATCAATTTTAAAAAATTAATTTATTTTCATGAGTTTTGAATTTTTCTTT
66 ATTTAATTCATATTAAATCAATTTTAAAAAATTAATTCATTTTCATAAGTTTTGAATTTTTCTCT
*
173689 AAAATCTCCCTATTTTCGAAAAACTGAGTTTTCTA
131 AAAATCTCCCTATTTTCGAAAAACAGAGTTTTCTA
* * * * * * *
173724 -TCTCATAAATATTTTCAAAAAGATTTTTCTCGGTTTTAAATTTTTAAAATTCATATAATA
1 CTC-CGTAAATTTTTTCAAGAGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATAAAATA
173784 TTGTTACAAA
Statistics
Matches: 200, Mismatches: 22, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
164 2 0.01
165 92 0.46
166 94 0.47
167 12 0.06
ACGTcount: A:0.33, C:0.11, G:0.07, T:0.48
Consensus pattern (165 bp):
CTCCGTAAATTTTTTCAAGAGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATAAAATACTATT
ATTTAATTCATATTAAATCAATTTTAAAAAATTAATTCATTTTCATAAGTTTTGAATTTTTCTCT
AAAATCTCCCTATTTTCGAAAAACAGAGTTTTCTA
Found at i:173775 original size:165 final size:166
Alignment explanation
Indices: 173405--173830 Score: 540
Period size: 165 Copynumber: 2.6 Consensus size: 166
173395 CGTAAATTTC
* * * *
173405 TTTCAAGAGGATTTTTCTTGCTTTTTAATTTTTAAAATTTATCAAATATTATTATTTAATTCATA
1 TTTCAAGAGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATAAAATATTGTTATTTAATTCATA
* * * *
173470 TTAAATCAATTTTCAAAAATTAATTCATTTTCATAAATTTTTGAATTTTTTCCTAAAATTCTCTT
66 TTAAATCAATTTTAAAAAATTAATTTATTTTCATAAAGTTTTGAATTTTTTCCTAAAATTCTCCT
* * *
173535 GTTTTCGAAAAACAGAGTTTTCTACTCCGTAAATTT
131 ATTTTCGAAAAACAGAGTTTTCTACTCCATAAATAT
* *
173571 TTTCGAGAGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATAAAATACTGTTATTTAATTCATA
1 TTTCAAGAGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATAAAATATTGTTATTTAATTCATA
* *
173636 TTAAATCAATTTTAAAAAATTAATTTATTTTCAT-GAGTTTTGAA-TTTTTCTTTAAAA-TCTCC
66 TTAAATCAATTTTAAAAAATTAATTTATTTTCATAAAGTTTTGAATTTTTTC-CTAAAATTCT-C
*
173698 CTATTTTCGAAAAACTGAGTTTTCTA-TCTCATAAATAT
129 CTATTTTCGAAAAACAGAGTTTTCTACTC-CATAAATAT
* * * * * ***
173736 TTTCAAAAAGATTTTTCTCGGTTTTAAATTTTTAAAATTCATATAATATTGTTACAAAACTTC--
1 TTTCAAGAGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATAAAATATTGTTATTTAA-TTCAT
*
173799 ATTAAATCAGTTTTAAAAAATTCAATTTATTT
65 ATTAAATCAATTTTAAAAAATT-AATTTATTT
173831 CTTATTTTTT
Statistics
Matches: 228, Mismatches: 27, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
164 32 0.14
165 102 0.45
166 94 0.41
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.48
Consensus pattern (166 bp):
TTTCAAGAGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATAAAATATTGTTATTTAATTCATA
TTAAATCAATTTTAAAAAATTAATTTATTTTCATAAAGTTTTGAATTTTTTCCTAAAATTCTCCT
ATTTTCGAAAAACAGAGTTTTCTACTCCATAAATAT
Found at i:174848 original size:21 final size:21
Alignment explanation
Indices: 174809--174849 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
174799 ACATCATGGG
* *
174809 AGAGATATTTTATGAATTTTT
1 AGAGACATTTTAAGAATTTTT
*
174830 AGAGACATTTTAAGCATTTT
1 AGAGACATTTTAAGAATTTT
174850 AACATTTTAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.46
Consensus pattern (21 bp):
AGAGACATTTTAAGAATTTTT
Found at i:176047 original size:155 final size:157
Alignment explanation
Indices: 175660--176048 Score: 387
Period size: 155 Copynumber: 2.5 Consensus size: 157
175650 TCGAAGGTAC
* * * *
175660 TCTTAGGTTGTCA-TCGAGTTCGCTTTTTTATTGAAGTTGGGCATTTAAGATAGGTTCATCCGAT
1 TCTTAGGTTGTCACT-GAGTTCGCTTTTTTACTGAAGGTAGGCATTTAAGATAGGTTCATCCCAT
* * ** *
175724 CTATAATCTTTTT--AGTATCCACTAGGGTTATCAGATATTTTTATGTCGAAGGTATCCCTTAAG
65 CTATAATCTTTTTAAAGTATCCACTAGGGGTATCAGATACTTTTACATCGAAGATATCCCTTAAG
* * *
175787 GGCATTTTTGTAACTTCTTAGAGCCAAG
130 GGCATTTTCGTAACTTCTTAAAACCAAG
* * * * * **
175815 TCCTAGGTTGTCACCGAG-TCTGGTTTTTTACTGAAGGTAGGTATTTAGGATAGGTTCATCTTAT
1 TCTTAGGTTGTCACTGAGTTC-GCTTTTTTACTGAAGGTAGGCATTTAAGATAGGTTCATCCCAT
* * ** * * * *
175879 TTATAATCATTTTAAAGT-T-CTTTAGGGGTATTAGGTACTTTTACATCGAAGATATTCCTTATG
65 CTATAATCTTTTTAAAGTATCCACTAGGGGTATCAGATACTTTTACATCGAAGATATCCCTTAAG
* * **
175942 GGCATTTTCGTAATTTTTTAAAACTGAG
130 GGCATTTTCGTAACTTCTTAAAACCAAG
* * *
175970 TCTTAGGTTGTCACTGGGTTCGCTTTTTTGCCGAAGGTAGGCATTTTAAGATAGGTTCA-CCCAT
1 TCTTAGGTTGTCACTGAGTTCGCTTTTTTACTGAAGGTAGGCA-TTTAAGATAGGTTCATCCCAT
*
176034 CTATCATCTTTTTAA
65 CTATAATCTTTTTAA
176049 GTCTTTTAGG
Statistics
Matches: 185, Mismatches: 43, Indels: 12
0.77 0.18 0.05
Matches are distributed among these distances:
154 2 0.01
155 163 0.88
156 17 0.09
157 3 0.02
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (157 bp):
TCTTAGGTTGTCACTGAGTTCGCTTTTTTACTGAAGGTAGGCATTTAAGATAGGTTCATCCCATC
TATAATCTTTTTAAAGTATCCACTAGGGGTATCAGATACTTTTACATCGAAGATATCCCTTAAGG
GCATTTTCGTAACTTCTTAAAACCAAG
Found at i:179501 original size:14 final size:14
Alignment explanation
Indices: 179482--179561 Score: 92
Period size: 14 Copynumber: 5.6 Consensus size: 14
179472 TTCTCTAAAT
*
179482 AAGAAAAATAAAAA
1 AAGAAAAAGAAAAA
*
179496 AAGAAAAACCAAAAA
1 AAGAAAAA-GAAAAA
*
179511 AA-AAAAAGAAAGA
1 AAGAAAAAGAAAAA
179524 AAGAAAAAGAAAAA
1 AAGAAAAAGAAAAA
179538 AAGAAAAA-AAATGAA
1 AAGAAAAAGAAA--AA
179553 AAGAAAAAG
1 AAGAAAAAG
179562 TGTAGATAGT
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
13 9 0.16
14 31 0.54
15 17 0.30
ACGTcount: A:0.82, C:0.03, G:0.12, T:0.03
Consensus pattern (14 bp):
AAGAAAAAGAAAAA
Found at i:179502 original size:8 final size:8
Alignment explanation
Indices: 179485--179560 Score: 59
Period size: 8 Copynumber: 9.4 Consensus size: 8
179475 TCTAAATAAG
*
179485 AAAAATAA
1 AAAAAGAA
179493 AAAAAGAA
1 AAAAAGAA
179501 AAACCAA-AA
1 AAA--AAGAA
179510 AAAAA-AA
1 AAAAAGAA
*
179517 AGAAAGAAA
1 AAAAAG-AA
179526 GAAAAAGAA
1 -AAAAAGAA
179535 AAAAAGAA
1 AAAAAGAA
*
179543 AAAAA-AT
1 AAAAAGAA
*
179550 GAAAAGAA
1 AAAAAGAA
179558 AAA
1 AAA
179561 GTGTAGATAG
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
7 13 0.24
8 26 0.47
9 9 0.16
10 7 0.13
ACGTcount: A:0.84, C:0.03, G:0.11, T:0.03
Consensus pattern (8 bp):
AAAAAGAA
Found at i:180140 original size:20 final size:19
Alignment explanation
Indices: 180130--180183 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
180120 ACATTATGCT
180130 TTGTATCGATACATGTTCA
1 TTGTATCGATACATGTTCA
**
180149 TTGTATCGATACATGCACAA
1 TTGTATCGATACATGTTC-A
*
180169 TTGCATCGATACATG
1 TTGTATCGATACATG
180184 AAATTGGTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.35
Consensus pattern (19 bp):
TTGTATCGATACATGTTCA
Found at i:180154 original size:19 final size:20
Alignment explanation
Indices: 180130--180298 Score: 81
Period size: 20 Copynumber: 8.7 Consensus size: 20
180120 ACATTATGCT
**
180130 TTGTATCGATACATGTTC-A
1 TTGTATCGATACATGCACAA
180149 TTGTATCGATACATGCACAA
1 TTGTATCGATACATGCACAA
*
180169 TTGCATCGATACATG-A-AA
1 TTGTATCGATACATGCACAA
* * * * **
180187 TTGGTAGTAGCTATCCTACTACTGT
1 TT-GTA-TCGATA-CATGC-AC-AA
180212 TTGTATCGATACATGGCAC-A
1 TTGTATCGATACAT-GCACAA
180232 TTGTATCG----AT--AC-A
1 TTGTATCGATACATGCACAA
* *
180245 TTGTATCGATACATGAAAAA
1 TTGTATCGATACATGCACAA
* * *
180265 TTATATCGATACATGAAAAA
1 TTGTATCGATACATGCACAA
180285 TTGTATCGATACAT
1 TTGTATCGATACAT
180299 TGTCCCAAAC
Statistics
Matches: 116, Mismatches: 18, Indels: 31
0.70 0.11 0.19
Matches are distributed among these distances:
13 11 0.09
16 2 0.02
17 2 0.02
18 4 0.03
19 20 0.17
20 60 0.52
21 2 0.02
22 4 0.03
23 6 0.05
24 3 0.03
25 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (20 bp):
TTGTATCGATACATGCACAA
Found at i:180247 original size:13 final size:13
Alignment explanation
Indices: 180229--180258 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
180219 GATACATGGC
180229 ACATTGTATCGAT
1 ACATTGTATCGAT
180242 ACATTGTATCGAT
1 ACATTGTATCGAT
180255 ACAT
1 ACAT
180259 GAAAAATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:180254 original size:33 final size:33
Alignment explanation
Indices: 180212--180278 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
180202 CTACTACTGT
** * *
180212 TTGTATCGATACATGGCACATTGTATCGATACA
1 TTGTATCGATACATGAAAAATTATATCGATACA
180245 TTGTATCGATACATGAAAAATTATATCGATACA
1 TTGTATCGATACATGAAAAATTATATCGATACA
180278 T
1 T
180279 GAAAAATTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (33 bp):
TTGTATCGATACATGAAAAATTATATCGATACA
Found at i:180273 original size:20 final size:20
Alignment explanation
Indices: 180248--180298 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
180238 CGATACATTG
180248 TATCGATACATGAAAAATTA
1 TATCGATACATGAAAAATTA
*
180268 TATCGATACATGAAAAATTG
1 TATCGATACATGAAAAATTA
180288 TATCGATACAT
1 TATCGATACAT
180299 TGTCCCAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (20 bp):
TATCGATACATGAAAAATTA
Found at i:181916 original size:15 final size:15
Alignment explanation
Indices: 181896--181930 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
181886 AACCATCAAA
181896 GATGATGAAGATAAT
1 GATGATGAAGATAAT
*
181911 GATGATGATGATAAT
1 GATGATGAAGATAAT
181926 GATGA
1 GATGA
181931 AGTTGACTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (15 bp):
GATGATGAAGATAAT
Found at i:188118 original size:89 final size:89
Alignment explanation
Indices: 187926--188112 Score: 209
Period size: 89 Copynumber: 2.1 Consensus size: 89
187916 GCACATTCTT
* * ** * ** *
187926 AATCATATCCCCTTTATTTAACCACTAGATGATATTGATGCATCACAAAGTTTGATTTCCTTGGG
1 AATCATATCTCCTTCATCCAACGACTAGATGATATTGATGCATCACAAAGTCCGATTTCATTGGG
*
187991 GCAAAGTATAGCCCACATATTCCC
66 GCAAAGGATAGCCCACATATTCCC
*
188015 AATCATATCTCCTTCATCCAACGACTAGAT-AGTATTGATGCATCACAAAG-CCGATTTTATTGG
1 AATCATATCTCCTTCATCCAACGACTAGATGA-TATTGATGCATCACAAAGTCCGATTTCATTGG
*
188078 GGC-AAGGATATCCCGACCATTCATTCCC
65 GGCAAAGGATAGCCC-A-CA-T-ATTCCC
188106 AATCATA
1 AATCATA
188113 CCCTTCTCTT
Statistics
Matches: 82, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
87 9 0.11
88 14 0.17
89 45 0.55
90 1 0.01
91 13 0.16
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (89 bp):
AATCATATCTCCTTCATCCAACGACTAGATGATATTGATGCATCACAAAGTCCGATTTCATTGGG
GCAAAGGATAGCCCACATATTCCC
Found at i:188353 original size:35 final size:35
Alignment explanation
Indices: 188309--188384 Score: 118
Period size: 35 Copynumber: 2.2 Consensus size: 35
188299 AACTCCTCTA
* *
188309 TCAAA-TTTTCCCATCATCGTTTGACTATATCTGG
1 TCAAACTTTTCCCACCACCGTTTGACTATATCTGG
*
188343 TCAAACTTTTCCCACCACCGTTTGACTGTATCTGG
1 TCAAACTTTTCCCACCACCGTTTGACTATATCTGG
188378 TCAAACT
1 TCAAACT
188385 CTTTTCATCC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
34 5 0.13
35 33 0.87
ACGTcount: A:0.24, C:0.28, G:0.12, T:0.37
Consensus pattern (35 bp):
TCAAACTTTTCCCACCACCGTTTGACTATATCTGG
Found at i:188511 original size:48 final size:48
Alignment explanation
Indices: 188440--188648 Score: 217
Period size: 48 Copynumber: 4.4 Consensus size: 48
188430 CCTCGTTTGA
188440 AGGGCCTGGTCAAACTCAAATCTTCCCTCGTTTGACTATATTGGTGTT
1 AGGGCCTGGTCAAACTCAAATCTTCCCTCGTTTGACTATATTGGTGTT
** * *
188488 AGGGCCTGGTCAAACTCAAATCTTCTATCGTTTGACTTTATTAGTGTT
1 AGGGCCTGGTCAAACTCAAATCTTCCCTCGTTTGACTATATTGGTGTT
* * *** * * *
188536 AGAGCCTAGTCAAACTCTTTTCATCCCTCGTTTGCCTGTATTGGTGTT
1 AGGGCCTGGTCAAACTCAAATCTTCCCTCGTTTGACTATATTGGTGTT
* * * * *
188584 AGGCCCTGGTCAAACTC---TTTTCACCTTTCATTTAACTATATTGGTGTC
1 AGGGCCTGGTCAAACTCAAATCTTC-CC--TCGTTTGACTATATTGGTGTT
188632 AGGGCCTGGTCAAACTC
1 AGGGCCTGGTCAAACTC
188649 TTCTCTTTCC
Statistics
Matches: 132, Mismatches: 26, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
45 3 0.02
46 2 0.02
48 127 0.96
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (48 bp):
AGGGCCTGGTCAAACTCAAATCTTCCCTCGTTTGACTATATTGGTGTT
Found at i:188644 original size:96 final size:96
Alignment explanation
Indices: 188440--188650 Score: 242
Period size: 96 Copynumber: 2.2 Consensus size: 96
188430 CCTCGTTTGA
** * *
188440 AGGGCCTGGTCAAACTCAAATCTTCCCTCGTTTGACTATATTGGTGTTAGGGCCTGGTCAAACTC
1 AGGGCCTGGTCAAACTCTTATCATCCCTCGTTTGACTATATTGGTGTTAGGCCCTGGTCAAACTC
** * * * *
188505 AAATCTTCTATCGTTTGACTTTATTAGTGTT
66 AAATCACCTATCATTTAACTATATTAGTGTC
* * * * *
188536 AGAGCCTAGTCAAACTCTTTTCATCCCTCGTTTGCCTGTATTGGTGTTAGGCCCTGGTCAAACTC
1 AGGGCCTGGTCAAACTCTTATCATCCCTCGTTTGACTATATTGGTGTTAGGCCCTGGTCAAACTC
*** * *
188601 TTTTCACCTTTCATTTAACTATATTGGTGTC
66 AAATCACCTATCATTTAACTATATTAGTGTC
188632 AGGGCCTGGTCAAACTCTT
1 AGGGCCTGGTCAAACTCTT
188651 CTCTTTCCTG
Statistics
Matches: 93, Mismatches: 22, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
96 93 1.00
ACGTcount: A:0.20, C:0.23, G:0.19, T:0.37
Consensus pattern (96 bp):
AGGGCCTGGTCAAACTCTTATCATCCCTCGTTTGACTATATTGGTGTTAGGCCCTGGTCAAACTC
AAATCACCTATCATTTAACTATATTAGTGTC
Found at i:188758 original size:87 final size:89
Alignment explanation
Indices: 188653--188820 Score: 241
Period size: 88 Copynumber: 1.9 Consensus size: 89
188643 AAACTCTTCT
* * * * * * *
188653 CTTTCCTGTCTGATGTATGGTTACTACCCTGGTC-AGTTTTTTTTATTTCGATTTGAGGTATGGT
1 CTTTCCTGTCTAACGTATGGTTACCACCCTGGTCAAATTTTTTTCATTCCGATTTGACGTATGGT
**
188717 TACCACTCTGGTCAAATCCACCTC
66 TACCACTAGGGTCAAATCCACCTC
188741 CTTT-CTGTCTAACGTATGGTTACCACCCTGGTCAAATTTTTTTCATTCCGATTTGACGTATGGT
1 CTTTCCTGTCTAACGTATGGTTACCACCCTGGTCAAATTTTTTTCATTCCGATTTGACGTATGGT
188805 TACCACTAGGGTCAAA
66 TACCACTAGGGTCAAA
188821 CGATTTGCAT
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
87 26 0.37
88 44 0.63
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.40
Consensus pattern (89 bp):
CTTTCCTGTCTAACGTATGGTTACCACCCTGGTCAAATTTTTTTCATTCCGATTTGACGTATGGT
TACCACTAGGGTCAAATCCACCTC
Found at i:188800 original size:44 final size:44
Alignment explanation
Indices: 188667--188810 Score: 130
Period size: 44 Copynumber: 3.3 Consensus size: 44
188657 CCTGTCTGAT
* * * * *
188667 GTATGGTTACTACCCTGGTC-AGTTTTTTTTATTTCGATTTGAG
1 GTATGGTTACCACCCTGGTCAAATTTTTTTCATTCCGATTTGAC
* **** * * * * *
188710 GTATGGTTACCACTCTGGTCAAATCCACCTCCTTTCTG-TCTAAC
1 GTATGGTTACCACCCTGGTCAAAT-TTTTTTCATTCCGATTTGAC
188754 GTATGGTTACCACCCTGGTCAAATTTTTTTCATTCCGATTTGAC
1 GTATGGTTACCACCCTGGTCAAATTTTTTTCATTCCGATTTGAC
188798 GTATGGTTACCAC
1 GTATGGTTACCAC
188811 TAGGGTCAAA
Statistics
Matches: 73, Mismatches: 25, Indels: 5
0.71 0.24 0.05
Matches are distributed among these distances:
43 24 0.33
44 45 0.62
45 4 0.05
ACGTcount: A:0.19, C:0.23, G:0.17, T:0.40
Consensus pattern (44 bp):
GTATGGTTACCACCCTGGTCAAATTTTTTTCATTCCGATTTGAC
Found at i:189756 original size:20 final size:22
Alignment explanation
Indices: 189728--189770 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
189718 TAAGGTGTCG
189728 AATTGTGAATTTT-ATAA-ATT
1 AATTGTGAATTTTCATAATATT
*
189748 AATTTTGAATTTTCATAATATT
1 AATTGTGAATTTTCATAATATT
189770 A
1 A
189771 CGAGTACTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 12 0.60
21 4 0.20
22 4 0.20
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (22 bp):
AATTGTGAATTTTCATAATATT
Done.