Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 15 of 438
Found at i:4142023 original size:21 final size:20
Alignment explanation
Indices: 4141999--4142043 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
4141989 TAATTTTTAA
4141999 AATTTTAAAATATTAAAAAGT
1 AATTTTAAAATATTAAAAA-T
* * *
4142020 AATTTTTATATTTTAAAAAT
1 AATTTTAAAATATTAAAAAT
4142040 AATT
1 AATT
4142044 AAATATTGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
AATTTTAAAATATTAAAAAT
Found at i:4142025 original size:30 final size:31
Alignment explanation
Indices: 4141989--4142046 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
4141979 TTTATTAAAT
4141989 TAATTTTTAAAATTTT-AAAAT-ATTAAAAAG
1 TAATTTTT-AAATTTTAAAAATAATTAAAAAG
*
4142019 TAATTTTTATATTTTAAAAATAATTAAA
1 TAATTTTTAAATTTTAAAAATAATTAAA
4142047 TATTGACATG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 6 0.24
30 13 0.52
31 6 0.24
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (31 bp):
TAATTTTTAAATTTTAAAAATAATTAAAAAG
Found at i:4144438 original size:12 final size:12
Alignment explanation
Indices: 4144418--4144448 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
4144408 GGAAAACAGG
4144418 AAAGAAGATGAA
1 AAAGAAGATGAA
*
4144430 AAAGGAGATGAA
1 AAAGAAGATGAA
4144442 AAAGAAG
1 AAAGAAG
4144449 CGAAAAGATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.29, T:0.06
Consensus pattern (12 bp):
AAAGAAGATGAA
Found at i:4150216 original size:18 final size:17
Alignment explanation
Indices: 4150187--4150221 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
4150177 TGAATCGGTT
*
4150187 TTTTAAATATTTTTTAA
1 TTTTAAATATTTATTAA
4150204 TTTTAAATAATTTATTAA
1 TTTTAAAT-ATTTATTAA
4150222 ATTGAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTTAAATATTTATTAA
Found at i:4152624 original size:22 final size:22
Alignment explanation
Indices: 4152599--4152642 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
4152589 ATGTTTTTGG
4152599 AAGATAGTTTCTCTTCAGAGGA
1 AAGATAGTTTCTCTTCAGAGGA
4152621 AAGATAGTTTCTCTTCAGAGGA
1 AAGATAGTTTCTCTTCAGAGGA
4152643 CCATTTACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (22 bp):
AAGATAGTTTCTCTTCAGAGGA
Found at i:4165150 original size:21 final size:21
Alignment explanation
Indices: 4165109--4165150 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
4165099 TTTTATTTGG
4165109 ACTAAATTTATTTTAATTACT
1 ACTAAATTTATTTTAATTACT
4165130 ACTAAATTTATTTTAATTACT
1 ACTAAATTTATTTTAATTACT
4165151 TTTTTATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (21 bp):
ACTAAATTTATTTTAATTACT
Found at i:4165267 original size:24 final size:23
Alignment explanation
Indices: 4165234--4165319 Score: 72
Period size: 24 Copynumber: 3.7 Consensus size: 23
4165224 ATAATTGTTG
*
4165234 TATATAATATATAATATATAATTT
1 TATAT-ATATATAATATAGAATTT
* *
4165258 TATATTATATATTATAAAGAATTT
1 TATA-TATATATAATATAGAATTT
4165282 TCA-A-ATA-A-AATATAGAATTT
1 T-ATATATATATAATATAGAATTT
*
4165302 TATATCATTTATAATATA
1 TATAT-ATATATAATATA
4165320 TATAATGGAA
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
19 1 0.02
20 12 0.24
21 1 0.02
22 5 0.10
23 1 0.02
24 27 0.55
25 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
TATATATATATAATATAGAATTT
Found at i:4166206 original size:39 final size:40
Alignment explanation
Indices: 4166138--4166216 Score: 92
Period size: 39 Copynumber: 2.0 Consensus size: 40
4166128 CTATTAAAAA
*
4166138 TTAAAAAAAAATTATATTTATATATTTTT-ATAGTTAAAT
1 TTAAAAAAAAATTATATTTATATATTTTTAATAGTGAAAT
* *
4166177 TTAAATAAAAA-TATTTTTAT-TATTGTTTTAATAGTGAAAT
1 TTAAAAAAAAATTATATTTATATA-T-TTTTAATAGTGAAAT
4166217 GGGTCATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
37 2 0.06
38 9 0.26
39 14 0.41
40 9 0.26
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (40 bp):
TTAAAAAAAAATTATATTTATATATTTTTAATAGTGAAAT
Found at i:4166966 original size:2 final size:2
Alignment explanation
Indices: 4166959--4166992 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4166949 TAATCAACTA
4166959 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4166993 GATCCATCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4182655 original size:29 final size:29
Alignment explanation
Indices: 4182614--4182675 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
4182604 AGGCAAAAAT
4182614 TGATGATAGATCGATGTCCTCTATCCAAA
1 TGATGATAGATCGATGTCCTCTATCCAAA
4182643 TGATGATAGATCGATGTCCTCTATCCAAA
1 TGATGATAGATCGATGTCCTCTATCCAAA
4182672 TGAT
1 TGAT
4182676 TCTTCAGCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (29 bp):
TGATGATAGATCGATGTCCTCTATCCAAA
Found at i:4185172 original size:17 final size:17
Alignment explanation
Indices: 4185144--4185184 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
4185134 TGTCTTTCTT
*
4185144 TTTATTTCTTTTA-TTA
1 TTTATTTATTTTACTTA
4185160 TTTCATTTATTTTACTTA
1 TTT-ATTTATTTTACTTA
4185178 TTTATTT
1 TTTATTT
4185185 TATCACTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 3 0.14
17 13 0.59
18 6 0.27
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTATTTATTTTACTTA
Found at i:4187429 original size:19 final size:20
Alignment explanation
Indices: 4187391--4187429 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
4187381 ATATATAAAT
*
4187391 ATTCAATATCATATAGCATA
1 ATTCAATATCACATAGCATA
*
4187411 ATTC-ATATCACATATCATA
1 ATTCAATATCACATAGCATA
4187430 TATTAATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.44, C:0.18, G:0.03, T:0.36
Consensus pattern (20 bp):
ATTCAATATCACATAGCATA
Found at i:4196393 original size:18 final size:18
Alignment explanation
Indices: 4196370--4196404 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
4196360 GTAAAGGATC
4196370 AGGATCAGCATCAGCCAA
1 AGGATCAGCATCAGCCAA
4196388 AGGATCAGCATCAGCCA
1 AGGATCAGCATCAGCCA
4196405 CAGCTAAGCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.37, C:0.29, G:0.23, T:0.11
Consensus pattern (18 bp):
AGGATCAGCATCAGCCAA
Found at i:4197968 original size:9 final size:9
Alignment explanation
Indices: 4197905--4198011 Score: 64
Period size: 10 Copynumber: 11.8 Consensus size: 9
4197895 AATAACTTTT
4197905 AAAA-TTAA
1 AAAATTTAA
4197913 AAATATTTATA
1 AAA-ATTTA-A
*
4197924 AAAATTT-C
1 AAAATTTAA
4197932 AAAATTT--
1 AAAATTTAA
* *
4197939 ATATTTTAA
1 AAAATTTAA
4197948 GAAAATTATAA
1 -AAAATT-TAA
4197959 AAAATTT-A
1 AAAATTTAA
4197967 AAAATTCTAA
1 AAAATT-TAA
4197977 AAAATATATAA
1 AAAAT-T-TAA
*
4197988 AAAAGTT-A
1 AAAATTTAA
*
4197996 AAATTTTAA
1 AAAATTTAA
4198005 AAAATTT
1 AAAATTT
4198012 CTAAAATAAT
Statistics
Matches: 78, Mismatches: 10, Indels: 21
0.72 0.09 0.19
Matches are distributed among these distances:
7 5 0.06
8 23 0.29
9 11 0.14
10 24 0.31
11 15 0.19
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (9 bp):
AAAATTTAA
Found at i:4198016 original size:28 final size:29
Alignment explanation
Indices: 4197941--4198017 Score: 95
Period size: 28 Copynumber: 2.7 Consensus size: 29
4197931 CAAAATTTAT
*
4197941 ATTTTAAGAAAA-TTATAAAAAATTTAAAA
1 ATTTTAA-AAAATTTATAAAAAAGTTAAAA
* *
4197970 ATTCTAAAAAATATATAAAAAAGTT-AAA
1 ATTTTAAAAAATTTATAAAAAAGTTAAAA
*
4197998 ATTTTAAAAAATTTCTAAAA
1 ATTTTAAAAAATTTATAAAA
4198018 TAATAATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
28 24 0.59
29 17 0.41
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.34
Consensus pattern (29 bp):
ATTTTAAAAAATTTATAAAAAAGTTAAAA
Found at i:4201359 original size:49 final size:49
Alignment explanation
Indices: 4201230--4201449 Score: 349
Period size: 49 Copynumber: 4.6 Consensus size: 49
4201220 CCCTTCGGGA
* *
4201230 CTTATCACAT-T-TATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
4201277 CCTATCAC--ATATATACACCTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
4201324 CTTATCACATTTATATACACTTTCACATTCTTCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
4201373 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
4201422 CTTATCACATATATATACACTTTCACAT
1 CTTATCACATATATATACACTTTCACAT
4201450 ATATACACAC
Statistics
Matches: 157, Mismatches: 12, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
46 1 0.01
47 47 0.30
49 109 0.69
ACGTcount: A:0.29, C:0.30, G:0.07, T:0.34
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:4201449 original size:18 final size:18
Alignment explanation
Indices: 4201426--4201467 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
4201416 TTAGGCCTTA
*
4201426 TCACATATATATACACTT
1 TCACATATATACACACTT
4201444 TCACATATATACACACTT
1 TCACATATATACACACTT
4201462 TCACAT
1 TCACAT
4201468 TCATCACATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.38, C:0.26, G:0.00, T:0.36
Consensus pattern (18 bp):
TCACATATATACACACTT
Found at i:4201449 original size:67 final size:66
Alignment explanation
Indices: 4201377--4201515 Score: 260
Period size: 67 Copynumber: 2.1 Consensus size: 66
4201367 TTAGGCCTTA
*
4201377 TCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
1 TCACATATATACACACTTTCACATTCATCACATCAGCCATTA-GCCTTATCACATATATATACAC
4201442 TT
65 TT
4201444 TCACATATATACACACTTTCACATTCATCACATCAGCCATTAGCCTTATCACATATATATACACT
1 TCACATATATACACACTTTCACATTCATCACATCAGCCATTAGCCTTATCACATATATATACACT
4201509 T
66 T
4201510 TCACAT
1 TCACAT
4201516 TCATCACGTC
Statistics
Matches: 71, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
66 30 0.42
67 41 0.58
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.33
Consensus pattern (66 bp):
TCACATATATACACACTTTCACATTCATCACATCAGCCATTAGCCTTATCACATATATATACACT
T
Found at i:4201531 original size:115 final size:117
Alignment explanation
Indices: 4201328--4201566 Score: 401
Period size: 115 Copynumber: 2.1 Consensus size: 117
4201318 TTAGGCCTTA
* * * *
4201328 TCACATTTATATACACTTTCACATTCTTCACATCGGCCATTAGGCCTTATCACATATATACACAC
1 TCACATATATACACACTTTCACATTCATCACATCAGCCATTAGGCCTTATCACATATATACACAC
4201393 TTTCACATTCATCACATCGGCCATTAGGCCTTAT-CACATATATATACACTT
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATACACATATATATACACTT
*
4201444 TCACATATATACACACTTTCACATTCATCACATCAGCCATTA-GCCTTATCACATATATATACAC
1 TCACATATATACACACTTTCACATTCATCACATCAGCCATTAGGCCTTATCACATATATACACAC
*
4201508 TTTCACATTCATCACGTCGGCCATTAGGCCTTATCACACATATATATACACTT
66 TTTCACATTCATCACATCGGCCATTAGGCCTTAT-ACACATATATATACACTT
4201561 TCACAT
1 TCACAT
4201567 TCATCACATC
Statistics
Matches: 115, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
115 54 0.47
116 38 0.33
117 23 0.20
ACGTcount: A:0.31, C:0.29, G:0.06, T:0.33
Consensus pattern (117 bp):
TCACATATATACACACTTTCACATTCATCACATCAGCCATTAGGCCTTATCACATATATACACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATACACATATATATACACTT
Found at i:4201602 original size:164 final size:162
Alignment explanation
Indices: 4201281--4201605 Score: 544
Period size: 166 Copynumber: 2.0 Consensus size: 162
4201271 TTCGGCCCTA
* *
4201281 TCACATATATACACCTTCACATTCATCACATCGGCCATTAGGCCTTATCACATTTATATACACTT
1 TCACATATATACACCTTCACATTCATCACATCAGCCATTAGGCCTTATCACATATATATACACTT
*
4201346 TCACATTCTTCACATCGGCCATTAGGCCTTATCACATATATACACACTTTCACATTCATCACATC
66 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACACTTTCACATTCATCACATC
4201411 GGCCATTAGGCCTTATCACATATATATACACTT
131 GGCCATTAGGCCTTATCACA-ATATATACACTT
4201444 TCACATATATACACACTTTCACATTCATCACATCAGCCATTA-GCCTTATCACATATATATACAC
1 TCACATATATACAC-C-TTCACATTCATCACATCAGCCATTAGGCCTTATCACATATATATACAC
* *
4201508 TTTCACATTCATCACGTCGGCCATTAGGCCTTATCACACATATATATACACTTTCACATTCATCA
64 TTTCACATTCATCACATCGGCCATTAGGCCTTAT--CACATATATACACACTTTCACATTCATCA
4201573 CATCGGCCATTAGGCCTTATCACATATATATAC
127 CATCGGCCATTAGGCCTTATCACA-ATATATAC
4201606 CTCATACAAA
Statistics
Matches: 153, Mismatches: 5, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
163 14 0.09
164 54 0.35
165 24 0.16
166 61 0.40
ACGTcount: A:0.31, C:0.29, G:0.07, T:0.33
Consensus pattern (162 bp):
TCACATATATACACCTTCACATTCATCACATCAGCCATTAGGCCTTATCACATATATATACACTT
TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACACTTTCACATTCATCACATC
GGCCATTAGGCCTTATCACAATATATACACTT
Found at i:4201621 original size:51 final size:49
Alignment explanation
Indices: 4201444--4201605 Score: 272
Period size: 51 Copynumber: 3.3 Consensus size: 49
4201434 ATATACACTT
* *
4201444 TCACATATATACACACTTTCACATTCATCACATCAGCCATTA-GCCTTA
1 TCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
*
4201492 TCACATATATATACACTTTCACATTCATCACGTCGGCCATTAGGCCTTA
1 TCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
4201541 TCACACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 T--CACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
4201592 TCACATATATATAC
1 TCACATATATATAC
4201606 CTCATACAAA
Statistics
Matches: 107, Mismatches: 4, Indels: 5
0.92 0.03 0.04
Matches are distributed among these distances:
48 39 0.36
49 20 0.19
51 48 0.45
ACGTcount: A:0.32, C:0.29, G:0.07, T:0.32
Consensus pattern (49 bp):
TCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
Found at i:4204021 original size:15 final size:14
Alignment explanation
Indices: 4204003--4204032 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
4203993 CAAATCAAAC
4204003 AAAAAATAACAAAAT
1 AAAAAATAA-AAAAT
4204018 AAAAAATAAAAAAT
1 AAAAAATAAAAAAT
4204032 A
1 A
4204033 TTAGTGAGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.13
Consensus pattern (14 bp):
AAAAAATAAAAAAT
Found at i:4204028 original size:6 final size:7
Alignment explanation
Indices: 4204003--4204032 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
4203993 CAAATCAAAC
4204003 AAAAAAT
1 AAAAAAT
4204010 AACAAAAT
1 AA-AAAAT
4204018 AAAAAAT
1 AAAAAAT
4204025 AAAAAAT
1 AAAAAAT
4204032 A
1 A
4204033 TTAGTGAGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.13
Consensus pattern (7 bp):
AAAAAAT
Found at i:4212578 original size:47 final size:47
Alignment explanation
Indices: 4212514--4212624 Score: 145
Period size: 47 Copynumber: 2.4 Consensus size: 47
4212504 GACATTGAGT
*
4212514 CGATG-AGACACTATGTGT-CGACTACTATTAAAGTTCCGGATTTGTTC
1 CGATGAAG-CACTATGTGTACGA-TAATATTAAAGTTCCGGATTTGTTC
* * * *
4212561 CGATGAAGTACTTTGTGTACTATAATGTTAAAGTTCCGGATTTGTTC
1 CGATGAAGCACTATGTGTACGATAATATTAAAGTTCCGGATTTGTTC
4212608 CGATGAAGCACTATGTG
1 CGATGAAGCACTATGTG
4212625 CTTATCCCGG
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
47 51 0.93
48 4 0.07
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (47 bp):
CGATGAAGCACTATGTGTACGATAATATTAAAGTTCCGGATTTGTTC
Found at i:4217157 original size:35 final size:35
Alignment explanation
Indices: 4217117--4217186 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
4217107 AACCTAATAG
*
4217117 TTAAATTTATCAGTATATTTGTATTTTTCATGCAT
1 TTAAATTTATCAATATATTTGTATTTTTCATGCAT
4217152 TTAAATTTATCAATATATTTGTATTTTTCATGCAT
1 TTAAATTTATCAATATATTTGTATTTTTCATGCAT
4217187 GTAACTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.30, C:0.09, G:0.07, T:0.54
Consensus pattern (35 bp):
TTAAATTTATCAATATATTTGTATTTTTCATGCAT
Found at i:4217177 original size:18 final size:18
Alignment explanation
Indices: 4217121--4217177 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
4217111 TAATAGTTAA
*
4217121 ATTTATCAGTATATTTGT
1 ATTTATCAATATATTTGT
* ** **
4217139 ATTTTTC-ATGCATTTAA
1 ATTTATCAATATATTTGT
4217156 ATTTATCAATATATTTGT
1 ATTTATCAATATATTTGT
4217174 ATTT
1 ATTT
4217178 TTCATGCATG
Statistics
Matches: 27, Mismatches: 11, Indels: 2
0.68 0.28 0.05
Matches are distributed among these distances:
17 11 0.41
18 16 0.59
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.56
Consensus pattern (18 bp):
ATTTATCAATATATTTGT
Found at i:4219516 original size:2 final size:2
Alignment explanation
Indices: 4219509--4219540 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4219499 TGAGTAAAGC
4219509 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4219541 GCACTATTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4220800 original size:20 final size:20
Alignment explanation
Indices: 4220763--4220800 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4220753 TGTGGATTCC
**
4220763 ACACGCCCGTGTGGCTTGGG
1 ACACGCCCGTGTCCCTTGGG
4220783 ACACGCCCGTGTCCCTTG
1 ACACGCCCGTGTCCCTTG
4220801 TCCGTGGAGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.37, G:0.32, T:0.21
Consensus pattern (20 bp):
ACACGCCCGTGTCCCTTGGG
Found at i:4223101 original size:15 final size:16
Alignment explanation
Indices: 4223081--4223258 Score: 106
Period size: 15 Copynumber: 11.2 Consensus size: 16
4223071 TAATAACAGC
4223081 AATAATATATAA-AAT
1 AATAATATATAATAAT
*
4223096 AATAATATGGTAA-AAT
1 AATAATAT-ATAATAAT
* * *
4223112 AATGATAATGTATTAAT
1 AATAAT-ATATAATAAT
*
4223129 AAGAATGATAATAATAA-
1 AATAAT-AT-ATAATAAT
* *
4223146 AATAAGATTATAATAGT
1 AATAATA-TATAATAAT
* *
4223163 AGTATTATATAA-AA-
1 AATAATATATAATAAT
* *
4223177 AATAGACATGA-AAGAAAT
1 AATA-ATAT-ATAA-TAAT
*
4223195 AGTAATA-ATAATAAT
1 AATAATATATAATAAT
4223210 AATAATA-ATAATAAT
1 AATAATATATAATAAT
4223225 AATAATA-ATAATAAT
1 AATAATATATAATAAT
4223240 AATAATATA-AATAAT
1 AATAATATATAATAAT
4223255 AATA
1 AATA
4223259 TTGAGATACA
Statistics
Matches: 128, Mismatches: 22, Indels: 26
0.73 0.12 0.15
Matches are distributed among these distances:
14 3 0.02
15 63 0.49
16 30 0.23
17 24 0.19
18 8 0.06
ACGTcount: A:0.61, C:0.01, G:0.07, T:0.31
Consensus pattern (16 bp):
AATAATATATAATAAT
Found at i:4223205 original size:3 final size:3
Alignment explanation
Indices: 4223192--4223258 Score: 109
Period size: 3 Copynumber: 22.3 Consensus size: 3
4223182 ACATGAAAGA
*
4223192 AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4223240 AAT AAT -AT AAAT AAT AAT A
1 AAT AAT AAT -AAT AAT AAT A
4223259 TTGAGATACA
Statistics
Matches: 60, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
2 2 0.03
3 56 0.93
4 2 0.03
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:4227260 original size:25 final size:25
Alignment explanation
Indices: 4227223--4227289 Score: 64
Period size: 25 Copynumber: 2.7 Consensus size: 25
4227213 TTATTTTGGG
* * * *
4227223 ATGTTTCTTTATATTATATTATTTAT
1 ATGTTT-TATATAGTATATCATTTAA
*
4227249 ATGTTTTATATAGTATCTCATTTAA
1 ATGTTTTATATAGTATATCATTTAA
*
4227274 ATGTTTTTTAT-GTATA
1 ATGTTTTATATAGTATA
4227290 ATGGTACGTA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
24 4 0.12
25 24 0.71
26 6 0.18
ACGTcount: A:0.28, C:0.04, G:0.07, T:0.60
Consensus pattern (25 bp):
ATGTTTTATATAGTATATCATTTAA
Found at i:4228253 original size:130 final size:130
Alignment explanation
Indices: 4228020--4228277 Score: 367
Period size: 130 Copynumber: 2.0 Consensus size: 130
4228010 ATTCATAAAA
* * *
4228020 AAAAATTCTTAAAAACAAAGGCGATATTCGATGTTTGGCAATTCGGGGAATCGTGCCCTATCGTA
1 AAAAATTCTTAAAAACAAAGGCAATATTCGATGTTTGGCAATTCGGGGAATCGTACCCAATCGTA
* * * *
4228085 CTGGGTTGCAATTTCTCGTTTGTTCAAAATGATCGAATATTCCC-TTGGAATTTCACACATGTTT
66 CTGGGTTGCAATTTCTCATTTGGTCAAAATAATCGAATA-TCCCTTTAGAATTTCACACATGTTT
4228149 T
130 T
* * * * *
4228150 AAAAATTCTTTAAAACAAAGGTAATGTTTGATGTTTGGCAATTCGGGGAATCGTACCCAATCGTG
1 AAAAATTCTTAAAAACAAAGGCAATATTCGATGTTTGGCAATTCGGGGAATCGTACCCAATCGTA
*
4228215 CTGGGTTGCAATTTC-CTATTTGGTCAAAATAATCGAATATCCCTTTAGAATTTCACCCATGTT
66 CTGGGTTGCAATTTCTC-ATTTGGTCAAAATAATCGAATATCCCTTTAGAATTTCACACATGTT
4228278 CTCTAAATTC
Statistics
Matches: 113, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
129 5 0.04
130 108 0.96
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.34
Consensus pattern (130 bp):
AAAAATTCTTAAAAACAAAGGCAATATTCGATGTTTGGCAATTCGGGGAATCGTACCCAATCGTA
CTGGGTTGCAATTTCTCATTTGGTCAAAATAATCGAATATCCCTTTAGAATTTCACACATGTTTT
Found at i:4231304 original size:30 final size:30
Alignment explanation
Indices: 4231268--4231327 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
4231258 TTCTCGAGCC
4231268 TAGGGGCAAAA-GTGTAATTATGCAAAAGTT
1 TAGGGGCAAAATG-GTAATTATGCAAAAGTT
* *
4231298 TAGGGGCAAAATGGTAATTTTGCCAAAGTT
1 TAGGGGCAAAATGGTAATTATGCAAAAGTT
4231328 CGTATTAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.37, C:0.08, G:0.27, T:0.28
Consensus pattern (30 bp):
TAGGGGCAAAATGGTAATTATGCAAAAGTT
Found at i:4241789 original size:46 final size:47
Alignment explanation
Indices: 4241738--4241859 Score: 210
Period size: 46 Copynumber: 2.6 Consensus size: 47
4241728 ATCCATAAGT
4241738 GAACTCGAACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC
1 GAACTCGAACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC
4241785 -AACTCGAACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC
1 GAACTCGAACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC
* * *
4241831 GAACTTGGACTCAACTCAACGAGTACGGA
1 GAACTCGAACTCAACTCAACGAGTTCGGA
4241860 CATTTCACAT
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
46 46 0.65
47 25 0.35
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (47 bp):
GAACTCGAACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:4242348 original size:5 final size:5
Alignment explanation
Indices: 4242338--4242378 Score: 75
Period size: 5 Copynumber: 8.4 Consensus size: 5
4242328 TTATGTTTTA
4242338 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT A-TAT AT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
4242379 AAACTAAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 4 0.11
5 31 0.89
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTAT
Found at i:4242414 original size:20 final size:20
Alignment explanation
Indices: 4242386--4242424 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4242376 TATAAACTAA
* *
4242386 AGAAGCAAATGAAAGGAAAT
1 AGAAACAAATGAAACGAAAT
4242406 AGAAACAAATGAAACGAAA
1 AGAAACAAATGAAACGAAA
4242425 CAGAGAGCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.64, C:0.08, G:0.21, T:0.08
Consensus pattern (20 bp):
AGAAACAAATGAAACGAAAT
Found at i:4243666 original size:15 final size:15
Alignment explanation
Indices: 4243646--4243702 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
4243636 CGATGAATTT
4243646 ATTGAATTTATATTG
1 ATTGAATTTATATTG
* *
4243661 ATTGAAATTATTTTG
1 ATTGAATTTATATTG
4243676 ATTGAATTTATATTG
1 ATTGAATTTATATTG
4243691 ATTGAA-TTATAT
1 ATTGAATTTATAT
4243703 AATATATATG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
14 6 0.16
15 32 0.84
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:4244121 original size:21 final size:21
Alignment explanation
Indices: 4244086--4244167 Score: 128
Period size: 21 Copynumber: 3.8 Consensus size: 21
4244076 AGGCACTTTA
4244086 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTA--TCAGGCACCTCG
4244109 TGTGTCGTATCAGGCACCTCG
1 TGTGTCGTATCAGGCACCTCG
4244130 TGTGTCGTATCAGGCACCTCG
1 TGTGTCGTATCAGGCACCTCG
* *
4244151 TGTGTCGTTTTAGGCAC
1 TGTGTCGTATCAGGCAC
4244168 TTTATGTATC
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
21 48 0.84
23 9 0.16
ACGTcount: A:0.13, C:0.26, G:0.28, T:0.33
Consensus pattern (21 bp):
TGTGTCGTATCAGGCACCTCG
Found at i:4244180 original size:42 final size:42
Alignment explanation
Indices: 4244073--4244181 Score: 146
Period size: 42 Copynumber: 2.5 Consensus size: 42
4244063 GGCTTTATCG
4244073 ATCAGGCACTTTATGTGTCGTATTTCAGGCACCTCGTGTGTCGT
1 ATCAGGCACTTTATGTGTCGTA--TCAGGCACCTCGTGTGTCGT
* **
4244117 ATCAGGCACCTCGTGTGTCGTATCAGGCACCTCGTGTGTCGT
1 ATCAGGCACTTTATGTGTCGTATCAGGCACCTCGTGTGTCGT
* * *
4244159 TTTAGGCACTTTATGTATCGTAT
1 ATCAGGCACTTTATGTGTCGTAT
4244182 ACTGATCAGG
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
42 37 0.66
44 19 0.34
ACGTcount: A:0.17, C:0.23, G:0.25, T:0.36
Consensus pattern (42 bp):
ATCAGGCACTTTATGTGTCGTATCAGGCACCTCGTGTGTCGT
Found at i:4248621 original size:60 final size:60
Alignment explanation
Indices: 4248551--4248672 Score: 217
Period size: 60 Copynumber: 2.0 Consensus size: 60
4248541 TTTACGTTGT
*
4248551 TATTGTAATATTTTAGTCATTGAATTATTAATTGTCATTAATGATGTAACAATAAATTTA
1 TATTGTAATATTTTAGTCATTGAATTATTAATTGTCATTAATGATGTAACAATAAAATTA
* *
4248611 TATTGTAATATTTTAGTCGTTTAATTATTAATTGTCATTAATGATGTAACAATAAAATTA
1 TATTGTAATATTTTAGTCATTGAATTATTAATTGTCATTAATGATGTAACAATAAAATTA
4248671 TA
1 TA
4248673 AAAATTTGAG
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.39, C:0.05, G:0.10, T:0.47
Consensus pattern (60 bp):
TATTGTAATATTTTAGTCATTGAATTATTAATTGTCATTAATGATGTAACAATAAAATTA
Found at i:4253997 original size:68 final size:68
Alignment explanation
Indices: 4253848--4254005 Score: 153
Period size: 68 Copynumber: 2.3 Consensus size: 68
4253838 CTAGCCGATT
* * * *
4253848 TATCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACTCATGCGACCTAGCTACA
1 TATCTCGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACA
*
4253913 TTTA
65 TATA
* * *
4253917 TCTCTCACGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTA
1 TATCT--CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTA
4253979 CTATATA
63 C-ATATA
4253986 GTATCTCGTAGC-CTTCTTGT
1 -TATCTCGTAGCTC-TCTTGT
4254006 ACACATGATG
Statistics
Matches: 74, Mismatches: 9, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
67 1 0.01
68 34 0.46
69 9 0.12
70 5 0.07
71 25 0.34
ACGTcount: A:0.21, C:0.27, G:0.16, T:0.36
Consensus pattern (68 bp):
TATCTCGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACAT
ATA
Found at i:4271475 original size:30 final size:30
Alignment explanation
Indices: 4271439--4271495 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
4271429 CTTGAAAACC
*
4271439 TTGAGCTCTCTCTTAAGCTCATTGATCATT
1 TTGAGCTCTCCCTTAAGCTCATTGATCATT
*
4271469 TTGAGCTCTCCCTTAAGCTTATTGATC
1 TTGAGCTCTCCCTTAAGCTCATTGATC
4271496 TCCTCCTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.19, C:0.25, G:0.14, T:0.42
Consensus pattern (30 bp):
TTGAGCTCTCCCTTAAGCTCATTGATCATT
Found at i:4273922 original size:49 final size:51
Alignment explanation
Indices: 4273850--4273977 Score: 215
Period size: 49 Copynumber: 2.5 Consensus size: 51
4273840 ACTAGTGACT
4273850 CAAGTGTGGTACTATGTGAAGGCCACTTTGAGAAG-AGATAGC-TTGGTCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGAGAAGAAGATAGCGTTGGTCA
*
4273899 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCGTTGGTCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGAGAAG-AAGATAGCGTTGGTCA
*
4273951 CAAGTGTGGTACTATGTGCAGGCCACT
1 CAAGTGTGGTACTATGTGAAGGCCACT
4273978 AGGTATCCGT
Statistics
Matches: 74, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
49 34 0.46
51 7 0.09
52 33 0.45
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.27
Consensus pattern (51 bp):
CAAGTGTGGTACTATGTGAAGGCCACTTTGAGAAGAAGATAGCGTTGGTCA
Found at i:4276322 original size:3 final size:3
Alignment explanation
Indices: 4276314--4276347 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
4276304 AAAGTTCAAG
4276314 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
4276348 GAGATAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:4277793 original size:143 final size:143
Alignment explanation
Indices: 4277553--4277848 Score: 407
Period size: 143 Copynumber: 2.1 Consensus size: 143
4277543 CGACTATCGT
*
4277553 TGGGCGCAAAATCGTTGGTTTATCCAACTAGAGCTGGGCTCACTAAATTATTTGTCAGTTTATCC
1 TGGGCGCAAAATCGTTAGTTTATCCAACTAGAGCTGGGCTCACTAAATTATTTGTCAGTTTATCC
* * * * *
4277618 GACTAGCGCTAGGCGCAACTTTCGTCAATTTATCTAACTAGTGGTAGACACACATTCGTCT-GTT
66 GACCAACGCTAGGCGCAACCTCCGTCAATTTATCTAACTAGTGCTAGACACACATTCGT-TGGTT
4277682 TATCCGACTAGTAC
130 TATCCGACTAGTAC
* *
4277696 TGGGTGCAAATATTGTTAGTTTATCCAACTAGAGCTGGGCTCACT-AATTATTTGTCAGTTTATC
1 TGGGCGCAAA-ATCGTTAGTTTATCCAACTAGAGCTGGGCTCACTAAATTATTTGTCAGTTTATC
* * * * * * *
4277760 TGACCAACGCTGGGCGCAACCTCCGTCAGTTTATCTGACTAGTGCTGGGCACACATTTGTTGGTT
65 CGACCAACGCTAGGCGCAACCTCCGTCAATTTATCTAACTAGTGCTAGACACACATTCGTTGGTT
**
4277825 TATCCGACTAGCGC
130 TATCCGACTAGTAC
4277839 TGGGCGCAAA
1 TGGGCGCAAA
4277849 CTCTTTCGCG
Statistics
Matches: 133, Mismatches: 18, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
142 1 0.01
143 100 0.75
144 32 0.24
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (143 bp):
TGGGCGCAAAATCGTTAGTTTATCCAACTAGAGCTGGGCTCACTAAATTATTTGTCAGTTTATCC
GACCAACGCTAGGCGCAACCTCCGTCAATTTATCTAACTAGTGCTAGACACACATTCGTTGGTTT
ATCCGACTAGTAC
Found at i:4277847 original size:69 final size:69
Alignment explanation
Indices: 4277610--4277847 Score: 194
Period size: 69 Copynumber: 3.4 Consensus size: 69
4277600 TTATTTGTCA
* * * * * * *
4277610 GTTTATCCGACTAGCGCTAGGCGCAACTTTCGTCAATTTATCTAACTAGTGGTAGACACACATTC
1 GTTTATCCGACTAGCGCTGGGCGCAACATTCGTCAGTTTATCTAACTAGTGCTGGGCACACATTT
4277675 GTCT-
66 GT-TG
** * * * * * *
4277679 GTTTATCCGACTAGTACTGGGTGCAA-ATATTGTTAGTTTATCCAACTAGAGCTGGGCTCACTAA
1 GTTTATCCGACTAGCGCTGGGCGCAACAT-TCGTCAGTTTATCTAACTAGTGCTGGGCACAC--A
4277743 TTAT-TTG
63 TT-TGTTG
* * * * * *
4277750 TCAGTTTATCTGACCAACGCTGGGCGCAACCTCCGTCAGTTTATCTGACTAGTGCTGGGCACACA
1 ---GTTTATCCGACTAGCGCTGGGCGCAACATTCGTCAGTTTATCTAACTAGTGCTGGGCACACA
4277815 TTTGTTG
63 TTTGTTG
4277822 GTTTATCCGACTAGCGCTGGGCGCAA
1 GTTTATCCGACTAGCGCTGGGCGCAA
4277848 ACTCTTTCGC
Statistics
Matches: 127, Mismatches: 32, Indels: 20
0.71 0.18 0.11
Matches are distributed among these distances:
68 1 0.01
69 68 0.54
70 1 0.01
71 5 0.04
72 6 0.05
74 45 0.35
75 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.32
Consensus pattern (69 bp):
GTTTATCCGACTAGCGCTGGGCGCAACATTCGTCAGTTTATCTAACTAGTGCTGGGCACACATTT
GTTG
Found at i:4285335 original size:17 final size:17
Alignment explanation
Indices: 4285315--4285349 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
4285305 CAAAATTAAA
4285315 TTTTTATAA-ATGCTTAT
1 TTTTTA-AATATGCTTAT
4285332 TTTTTAAATATGCTTAT
1 TTTTTAAATATGCTTAT
4285349 T
1 T
4285350 ATATTATGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 15 0.88
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.60
Consensus pattern (17 bp):
TTTTTAAATATGCTTAT
Found at i:4299875 original size:2 final size:2
Alignment explanation
Indices: 4299868--4299895 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4299858 GTCCAGATTC
4299868 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4299896 GACATAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4305120 original size:13 final size:14
Alignment explanation
Indices: 4305095--4305125 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
4305085 AGAATTTTTG
4305095 GTTTGAGATTTAAA
1 GTTTGAGATTTAAA
4305109 GTTTGA-ATTTAAA
1 GTTTGAGATTTAAA
4305122 GTTT
1 GTTT
4305126 AAAGTTCAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.48
Consensus pattern (14 bp):
GTTTGAGATTTAAA
Found at i:4305168 original size:14 final size:14
Alignment explanation
Indices: 4305149--4305175 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4305139 AAAGTTAAGA
4305149 TTTAAGATTTAGAT
1 TTTAAGATTTAGAT
4305163 TTTAAGATTTAGA
1 TTTAAGATTTAGA
4305176 ATTAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (14 bp):
TTTAAGATTTAGAT
Found at i:4305406 original size:27 final size:27
Alignment explanation
Indices: 4305376--4305437 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
4305366 AATTTATAAA
4305376 ATTTTAA-ATTAATAATAATAAAATTAT
1 ATTTTAATATTAA-AATAATAAAATTAT
* *
4305403 ATTTTAATTTTAAAATAATAAAATTTT
1 ATTTTAATATTAAAATAATAAAATTAT
*
4305430 AATTTAAT
1 ATTTTAAT
4305438 TTTTTAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 27 0.87
28 4 0.13
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
ATTTTAATATTAAAATAATAAAATTAT
Found at i:4305438 original size:27 final size:28
Alignment explanation
Indices: 4305384--4305471 Score: 90
Period size: 27 Copynumber: 3.1 Consensus size: 28
4305374 AAATTTTAAA
*
4305384 TTAATAATAATAAAATTATATTTTAATT
1 TTAATAATAATAAAATTATAATTTAATT
*
4305412 TTAA-AATAATAAAATTTTAATTTAATTTT
1 TTAATAATAATAAAATTATAATTTAA--TT
* * *
4305441 TTAAAAATTATAAAAATATAGA-TTAATT
1 TTAATAATAATAAAATTATA-ATTTAATT
4305469 TTA
1 TTA
4305472 CTTAAAAATA
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
27 19 0.37
28 9 0.18
29 6 0.12
30 16 0.31
31 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (28 bp):
TTAATAATAATAAAATTATAATTTAATT
Found at i:4305448 original size:30 final size:30
Alignment explanation
Indices: 4305384--4305482 Score: 98
Period size: 30 Copynumber: 3.3 Consensus size: 30
4305374 AAATTTTAAA
* *
4305384 TTAATAATAATAAAATTATATTTTAA--TT
1 TTAAAAATAATAAAATTATAATTTAATTTT
*
4305412 TT-AAAATAATAAAATTTTAATTTAATTTT
1 TTAAAAATAATAAAATTATAATTTAATTTT
* *
4305441 TTAAAAATTATAAAAATATAGA-TTAATTTT
1 TTAAAAATAATAAAATTATA-ATTTAATTTT
4305471 ACTTAAAAATAA
1 --TTAAAAATAA
4305483 ATTTCCGCCG
Statistics
Matches: 58, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
27 20 0.34
28 2 0.03
29 4 0.07
30 22 0.38
31 1 0.02
32 9 0.16
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (30 bp):
TTAAAAATAATAAAATTATAATTTAATTTT
Found at i:4312992 original size:17 final size:18
Alignment explanation
Indices: 4312970--4313005 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
4312960 GTTTTTGAAT
*
4312970 GGAGGAGATTAAT-AAAA
1 GGAGGAAATTAATCAAAA
4312987 GGAGGAAATTAATCAAAA
1 GGAGGAAATTAATCAAAA
4313005 G
1 G
4313006 CAGTAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.53, C:0.03, G:0.28, T:0.17
Consensus pattern (18 bp):
GGAGGAAATTAATCAAAA
Found at i:4317642 original size:2 final size:2
Alignment explanation
Indices: 4317637--4317672 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4317627 ACAAATGATA
4317637 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4317673 TTGTGAAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4321918 original size:160 final size:159
Alignment explanation
Indices: 4321605--4321952 Score: 525
Period size: 160 Copynumber: 2.2 Consensus size: 159
4321595 CTCAACTTGG
* * * * *
4321605 TGCCAATTGATTTTAAGTTTGATGCTTAACATCGAACTTAACGTCCAAGTTGTATTCTGTTGTTA
1 TGCCAATTAACTTTAAGTTGGATGCTTAACATCGAACTTAACGCCCAAGTTGTATTCTATTGTTA
* *
4321670 TTGTCTATTTTCTGACCAATAACCCTTTCGAGTTTGTTACATCATAACCTCTTTTGTCTTCGTGA
66 TTGTCTATTTTCTGACCAATAACCCTTTCGAGTTTGTAAAATCATAACCTCTTTTGTCTTCGTGA
* * **
4321735 GTATTAATTCGATTTTGTATTATTTGTGA
131 GTATCAATTCGATTTTGTATTATTCGCAA
* * * *
4321764 TGCCAATTAACTTTAAGTTGGATGCTTAACATCGTATTTAACGCCCAAGTTTTGTTCTATTGTTA
1 TGCCAATTAACTTTAAGTTGGATGCTTAACATCGAACTTAACGCCCAAGTTGTATTCTATTGTTA
**
4321829 TTGTCTATTTTCTGACCCAATAACCCTTTCGAGTTTGTAAAATTGTAACCTCTTTTGTCTTCGTG
66 TTGTCTATTTTCTGA-CCAATAACCCTTTCGAGTTTGTAAAATCATAACCTCTTTTGTCTTCGTG
4321894 AGTATCAATTCGATTTTGTATTATTCGCAA
130 AGTATCAATTCGATTTTGTATTATTCGCAA
*
4321924 TGCCAATTAACTTTAAGTTGGGTGCTTAA
1 TGCCAATTAACTTTAAGTTGGATGCTTAA
4321953 AATTCCCATA
Statistics
Matches: 170, Mismatches: 18, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
159 71 0.42
160 99 0.58
ACGTcount: A:0.24, C:0.17, G:0.15, T:0.44
Consensus pattern (159 bp):
TGCCAATTAACTTTAAGTTGGATGCTTAACATCGAACTTAACGCCCAAGTTGTATTCTATTGTTA
TTGTCTATTTTCTGACCAATAACCCTTTCGAGTTTGTAAAATCATAACCTCTTTTGTCTTCGTGA
GTATCAATTCGATTTTGTATTATTCGCAA
Found at i:4332154 original size:34 final size:34
Alignment explanation
Indices: 4332094--4332161 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 34
4332084 CACTGGTATA
4332094 AGTATTATTCGAGTGACAACAATTAAACTAAAATG
1 AGTATTATTCGAGTGA-AACAATTAAACTAAAATG
*
4332129 AGTATTATTTCGAGTG-TACAATTAAACTAAAAT
1 AGTATTA-TTCGAGTGAAACAATTAAACTAAAAT
4332162 TAAAATTCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
34 16 0.52
35 7 0.23
36 8 0.26
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.32
Consensus pattern (34 bp):
AGTATTATTCGAGTGAAACAATTAAACTAAAATG
Found at i:4350541 original size:2 final size:2
Alignment explanation
Indices: 4350534--4350569 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4350524 CTTTGGCTCA
4350534 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4350570 CGGTGGAGTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4357928 original size:18 final size:18
Alignment explanation
Indices: 4357871--4357928 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 18
4357861 TTTTCAAACT
4357871 TCAATTATAATTTCATAA
1 TCAATTATAATTTCATAA
* * * *
4357889 TGAATAATGA-TTCAAAA
1 TCAATTATAATTTCATAA
* *
4357906 ACAATTATAATTTCATAT
1 TCAATTATAATTTCATAA
4357924 TCAAT
1 TCAAT
4357929 GGATTCATAA
Statistics
Matches: 28, Mismatches: 11, Indels: 2
0.68 0.27 0.05
Matches are distributed among these distances:
17 12 0.43
18 16 0.57
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (18 bp):
TCAATTATAATTTCATAA
Found at i:4366107 original size:2 final size:2
Alignment explanation
Indices: 4366056--4366087 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4366046 TGATGAAGGA
4366056 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4366088 GTGTTCTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4369606 original size:30 final size:31
Alignment explanation
Indices: 4369545--4369618 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 31
4369535 TTGAGATAAA
* * *
4369545 AAGCCTTAAAAGGATTAAAGAGGATTTTAGTT
1 AAGCCTTAAAA-GACTAAAAAGGATTCTAGTT
*
4369577 GAGCCTTAAAA-ACTAAAAAGGATTCTAGTT
1 AAGCCTTAAAAGACTAAAAAGGATTCTAGTT
4369607 AAGCCATTAAAA
1 AAGCC-TTAAAA
4369619 CTAGGAGAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
30 20 0.56
31 6 0.17
32 10 0.28
ACGTcount: A:0.45, C:0.11, G:0.18, T:0.27
Consensus pattern (31 bp):
AAGCCTTAAAAGACTAAAAAGGATTCTAGTT
Found at i:4372045 original size:116 final size:119
Alignment explanation
Indices: 4371887--4372206 Score: 443
Period size: 116 Copynumber: 2.7 Consensus size: 119
4371877 GTTTTTAAAG
*
4371887 CTAAGCTGCATTAGTTGAAATCAACCCGGAAAAACTTTTCTTTTACATGTTTCTATTCTAGTGAT
1 CTAAGCTGCATTAGTTGAAATCAACCCAGAAAAACTTTTCTTTTACATGTTTCTATTCTAGTGAT
4371952 ATATTGCTTGAGCACCATTCACTTATTCGTATCAGCCACGGTCG-A-A-TG-ACA
66 ATATTGCTTGAGCACCATTCACTTATTCGTATCAGCCACGGTCGAATATTGTA-A
* *
4372003 CTAAGCTGCATTAGTTGAAATCAACCCTGAAGAACTTTTCTTTTACATGTTTCTATTCTAGTGAT
1 CTAAGCTGCATTAGTTGAAATCAACCCAGAAAAACTTTTCTTTTACATGTTTCTATTCTAGTGAT
** * * * *
4372068 ATATTGCTTGAGCACCATTTTCTTATTTGTATCATCCATGGTTGAATATTGTTTTTAA
66 ATATTGCTTGAGCACCATTCACTTATTCGTATCAGCCACGGTCGAATATTG----TAA
**
4372126 CGATAAGCTGCATTAGTTGAAATCAACCCAGAAAAAAATTTCTTTTACATGTTTCTATTCTAGTG
1 C--TAAGCTGCATTAGTTGAAATCAACCCAGAAAAACTTTTCTTTTACATGTTTCTATTCTAGTG
4372191 -TATATTGCTTGAGCAC
64 ATATATTGCTTGAGCAC
4372207 TATCTTATTC
Statistics
Matches: 182, Mismatches: 12, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
116 101 0.55
117 1 0.01
118 1 0.01
119 2 0.01
123 2 0.01
124 17 0.09
125 58 0.32
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.38
Consensus pattern (119 bp):
CTAAGCTGCATTAGTTGAAATCAACCCAGAAAAACTTTTCTTTTACATGTTTCTATTCTAGTGAT
ATATTGCTTGAGCACCATTCACTTATTCGTATCAGCCACGGTCGAATATTGTAA
Found at i:4372423 original size:127 final size:127
Alignment explanation
Indices: 4372254--4372954 Score: 575
Period size: 127 Copynumber: 5.6 Consensus size: 127
4372244 TCAACCCGAA
* *
4372254 AAAAACTTTTCTTTTACATGTTTCTATTCTA-CTGATATATTGCTTGACCACCATTAACTTATTC
1 AAAAACTTTTCTTTTACATGTTTCTATTCTAGC-GATAGATTGCTTGACCACCATTATCTTATTC
* * * *
4372318 GTGTCATCCATGATCAAATCGTGTTTTTTTATAGCTAAGCTGCGTTAGTTGAAATCTATCTGG
65 GTATCATCCATGATCAAATCATGTTTTTTTATAGCTAAGCTGCATTAGTTGAAATCTACCTGG
* * *
4372381 AAAAACTTTTCTTTTTCATGTTTGTATTCTAGCGATAGATTGCTTGA-GAGCCATTATCTTATTC
1 AAAAACTTTTCTTTTACATGTTTCTATTCTAGCGATAGATTGCTTGACCA-CCATTATCTTATTC
* ** * * * * *
4372445 GTATCATCCATGGTTGAGTCATG--TTTTTAAAGCTAAGCTGCATTAATTGCAATCAACCT-G
65 GTATCATCCATGATCAAATCATGTTTTTTTATAGCTAAGCTGCATTAGTTGAAATCTACCTGG
* * * * * * *
4372505 ACAAAACTTTTCTTTTATATGTTTCTATTCTAGTGATATATTGCTTGAACACCGTTTTCTTTTTT
1 A-AAAACTTTTCTTTTACATGTTTCTATTCTAGCGATAGATTGCTTGACCACCATTATC-TTATT
* ** * *
4372570 CGTATCATCCATAATTGAATCATGTTTTTCTATAGCTAAGCTGCATTAGTTGAAAT-TGACCCGG
64 CGTATCATCCATGATCAAATCATGTTTTTTTATAGCTAAGCTGCATTAGTTGAAATCT-ACCTGG
* *
4372634 AAACACTTTTCTTTTACATGTTTCTATTCTAGTGAT-GTATTGCTTGACCA-CATTATCTTATTC
1 AAAAACTTTTCTTTTACATGTTTCTATTCTAGCGATAG-ATTGCTTGACCACCATTATCTTATTC
* * * * * **
4372697 GTGTCATCTATGGTCAAATCATGTTTTTTATATAGCTAAGCTGCATTGGTTTAAAT-TGACCCAG
65 GTATCATCCATGATCAAATCATGTTTTTT-TATAGCTAAGCTGCATTAGTTGAAATCT-ACCTGG
* * * * *
4372761 AAATACTTTTCTTTTTACATG-TTCT-TAT-T---GATATATTGCTTGAGCACCAGTCA-ATTAT
1 AAAAACTTTTC-TTTTACATGTTTCTAT-TCTAGCGATAGATTGCTTGACCACCA-TTATCTTAT
* * * * * * *
4372819 TCATATCATCCATGGT-AGGATCATG---TTCTAAAGCTAAGCTGCATTAGTTGAAATCGATCTG
63 TCGTATCATCCATGATCA-AATCATGTTTTTTTATAGCTAAGCTGCATTAGTTGAAATCTACCTG
4372880 G
127 G
* * * * * * * * *
4372881 TAAAGCTTATCTTTTACATGTTCCGATTCCT-GTGAT--ATTGCTCGAGCACCAGTATCTTATTC
1 AAAAACTTTTCTTTTACATGTTTCTATT-CTAGCGATAGATTGCTTGACCACCATTATCTTATTC
* *
4372943 ATGTCATCCATG
65 GTATCATCCATG
4372955 GTTGAATAAG
Statistics
Matches: 469, Mismatches: 80, Indels: 55
0.78 0.13 0.09
Matches are distributed among these distances:
119 9 0.02
120 36 0.08
121 4 0.01
122 32 0.07
123 15 0.03
124 30 0.06
125 79 0.17
126 56 0.12
127 123 0.26
128 83 0.18
129 2 0.00
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.42
Consensus pattern (127 bp):
AAAAACTTTTCTTTTACATGTTTCTATTCTAGCGATAGATTGCTTGACCACCATTATCTTATTCG
TATCATCCATGATCAAATCATGTTTTTTTATAGCTAAGCTGCATTAGTTGAAATCTACCTGG
Found at i:4372425 original size:349 final size:338
Alignment explanation
Indices: 4371907--4372552 Score: 852
Period size: 349 Copynumber: 1.9 Consensus size: 338
4371897 TTAGTTGAAA
* * * *
4371907 TCAACCCGGAAAAACTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGCACCATTC
1 TCAACCCGAAAAAACTTTTCTTTTACATGTTTCTATTCTACTGATATATTGCTTGACCACCATTA
* * *
4371972 ACTTATTCGTATCAGCCACGGTCGAATGACACTAAGCTGCATTAGTTGAAATCAACCCTGAAGAA
66 ACTTATTCGTATCAGCCACGATCAAATGACACTAAGCTGCATTAGTTGAAATCAACCCTGAAAAA
* * * *
4372037 CTTTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGCA-CCATTTTCTTATTTGTATC
131 CTTTTCTTTTACATGTTTCTATTCTAGCGATAGATTGCTTGAG-AGCCATTATCTTATTCGTATC
* *
4372101 ATCCATGGTTGAAT-ATTGTTTTTAACGATAAGCTGCATTAGTTGAAATCAACCCAGA-AAAAAA
195 ATCCATGGTTGAATCA-TGTTTTTAAAGATAAGCTGCATTAATTGAAATCAA-CCAGACAAAAAA
4372164 TTTCTTTTACATGTTTCTATTCTAGTG-TATATTGCTTGAGCACTATCTTATTCATATCATCCAT
258 TTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGCACTATCTTATTCATATCATCCAT
4372228 GGTTGAGTCTAATTTT
323 GGTTGAGTCTAATTTT
4372244 TCAACCCGAAAAAAACTTTTCTTTTACATGTTTCTATTCTACTGATATATTGCTTGACCACCATT
1 TCAACCCG-AAAAAACTTTTCTTTTACATGTTTCTATTCTACTGATATATTGCTTGACCACCATT
* * * * *
4372309 AACTTATTCGTGTCATCCATGATCAAATCGTGTTTTTTTATAGCTAAGCTGCGTTAGTTGAAATC
65 AACTTATTCGTATCAGCCACGATCAAA---TG-------ACA-CTAAGCTGCATTAGTTGAAATC
* * * *
4372374 TA-TCTGGAAAAACTTTTCTTTTTCATGTTTGTATTCTAGCGATAGATTGCTTGAGAGCCATTAT
119 AACCCT-GAAAAACTTTTCTTTTACATGTTTCTATTCTAGCGATAGATTGCTTGAGAGCCATTAT
* * *
4372438 CTTATTCGTATCATCCATGGTTGAGTCATGTTTTTAAAGCTAAGCTGCATTAATTGCAATCAACC
183 CTTATTCGTATCATCCATGGTTGAATCATGTTTTTAAAGATAAGCTGCATTAATTGAAATCAACC
* ** *
4372503 TGACAAAACTTTTCTTTTATATGTTTCTATTCTAGTGATATATTGCTTGA
248 AGACAAAAAATTTCTTTTACATGTTTCTATTCTAGTGATATATTGCTTGA
4372553 ACACCGTTTT
Statistics
Matches: 263, Mismatches: 29, Indels: 21
0.84 0.09 0.07
Matches are distributed among these distances:
337 8 0.03
338 74 0.28
341 2 0.01
348 9 0.03
349 157 0.60
350 13 0.05
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (338 bp):
TCAACCCGAAAAAACTTTTCTTTTACATGTTTCTATTCTACTGATATATTGCTTGACCACCATTA
ACTTATTCGTATCAGCCACGATCAAATGACACTAAGCTGCATTAGTTGAAATCAACCCTGAAAAA
CTTTTCTTTTACATGTTTCTATTCTAGCGATAGATTGCTTGAGAGCCATTATCTTATTCGTATCA
TCCATGGTTGAATCATGTTTTTAAAGATAAGCTGCATTAATTGAAATCAACCAGACAAAAAATTT
CTTTTACATGTTTCTATTCTAGTGATATATTGCTTGAGCACTATCTTATTCATATCATCCATGGT
TGAGTCTAATTTT
Found at i:4377496 original size:48 final size:48
Alignment explanation
Indices: 4377426--4377521 Score: 165
Period size: 48 Copynumber: 2.0 Consensus size: 48
4377416 GCGGGAGGAA
4377426 GGTGGTGGCCAAGCCGTTGATGCTGCCGCATAAAATCAACATTCATCT
1 GGTGGTGGCCAAGCCGTTGATGCTGCCGCATAAAATCAACATTCATCT
* * *
4377474 GGTGGTGGCCAAGTCGTTGATGCTGCTGCATAAAATCAGCATTCATCT
1 GGTGGTGGCCAAGCCGTTGATGCTGCCGCATAAAATCAACATTCATCT
4377522 CTGGTATCGT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (48 bp):
GGTGGTGGCCAAGCCGTTGATGCTGCCGCATAAAATCAACATTCATCT
Found at i:4384181 original size:2 final size:2
Alignment explanation
Indices: 4384174--4384200 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4384164 TTGGTAAATA
4384174 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
4384201 AGGTGCAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4393306 original size:44 final size:44
Alignment explanation
Indices: 4393253--4393481 Score: 222
Period size: 44 Copynumber: 5.3 Consensus size: 44
4393243 ACCTGTTACC
4393253 CTACTGCTTAGGGGTTTAAGGTTCTTCGTCTTCGATCTGCTCCA
1 CTACTGCTTAGGGGTTTAAGGTTCTTCGTCTTCGATCTGCTCCA
* * * ** * * *
4393297 CTACTGCTTAGGGAG-ATAA-GATCTGC-AATTCAACCTGTTACC-
1 CTACTGCTTAGGG-GTTTAAGGTTCTTCGTCTTCGATCTGCT-CCA
4393339 CTACTGCTTAGGGGTTTAAGGTTCTTCGTCTTCGATCTGCTCCA
1 CTACTGCTTAGGGGTTTAAGGTTCTTCGTCTTCGATCTGCTCCA
* * * ** * * *
4393383 CTACTGCTTAGGGAG-ATAA-GATCTGCAAC-TCAACCTGTTACC-
1 CTACTGCTTAGGG-GTTTAAGGTTCTTCGTCTTCGATCTGCT-CCA
4393425 CTACTGCTTAGGGGTTTAAGGTTCTTCGTCTTCGATCTGCTCCA
1 CTACTGCTTAGGGGTTTAAGGTTCTTCGTCTTCGATCTGCTCCA
4393469 CTACTGCTTAGGG
1 CTACTGCTTAGGG
4393482 ATATAAGATC
Statistics
Matches: 141, Mismatches: 32, Indels: 24
0.72 0.16 0.12
Matches are distributed among these distances:
41 2 0.01
42 47 0.33
43 30 0.21
44 60 0.43
45 2 0.01
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (44 bp):
CTACTGCTTAGGGGTTTAAGGTTCTTCGTCTTCGATCTGCTCCA
Found at i:4393348 original size:86 final size:86
Alignment explanation
Indices: 4393135--4393580 Score: 567
Period size: 86 Copynumber: 5.2 Consensus size: 86
4393125 GCAACTCCAT
* * * * * * * *
4393135 GGAGATAAGATCTGTGATTTTCAGCCTATTACCCTACTACTTAGGGGATTAAGGCTT-GTCATCT
1 GGAGATAAGATCTG-CA-ATTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGG-TTCTTCGTCT
* *
4393199 TTGATCTGTTTCC-CTACTGCTTAG
63 TCGATCTG-CTCCACTACTGCTTAG
** * *
4393223 GG-TTTTAGATCTGTAATTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTTCTTCGTCTTCG
1 GGAGATAAGATCTGCAATTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTTCTTCGTCTTCG
4393287 ATCTGCTCCACTACTGCTTAG
66 ATCTGCTCCACTACTGCTTAG
4393308 GGAGATAAGATCTGCAATTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTTCTTCGTCTTCG
1 GGAGATAAGATCTGCAATTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTTCTTCGTCTTCG
4393373 ATCTGCTCCACTACTGCTTAG
66 ATCTGCTCCACTACTGCTTAG
*
4393394 GGAGATAAGATCTGCAACTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTTCTTCGTCTTCG
1 GGAGATAAGATCTGCAATTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTTCTTCGTCTTCG
4393459 ATCTGCTCCACTACTGCTTAG
66 ATCTGCTCCACTACTGCTTAG
* * * * * * * *
4393480 GGATATAAGATCTGGAATTTAGCCTGTTACCCTACTGCTTAGGAGTTTATGGTCTCGTCATCTTC
1 GGAGATAAGATCTGCAATTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGT-TCTTCGTCTTC
* *
4393545 AATCTGTTTCC-CTACTGCTTAG
65 GATCTG-CTCCACTACTGCTTAG
* *
4393567 GGGGTTAAGATCTG
1 GGAGATAAGATCTG
4393581 TAAATTTTCA
Statistics
Matches: 321, Mismatches: 32, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
84 5 0.02
85 56 0.17
86 211 0.66
87 44 0.14
88 5 0.02
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (86 bp):
GGAGATAAGATCTGCAATTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTTCTTCGTCTTCG
ATCTGCTCCACTACTGCTTAG
Found at i:4393351 original size:42 final size:41
Alignment explanation
Indices: 4393204--4393580 Score: 211
Period size: 42 Copynumber: 8.8 Consensus size: 41
4393194 CATCTTTGAT
* * * *
4393204 CTGTTTCCCTACTGCTTAGGGTTTTAGATCTGTAATTCAAC
1 CTGTTACCCTACTGCTTAGGGGTTAAGATCTGCAATTCAAC
* * ** * *
4393245 CTGTTACCCTACTGCTTAGGGGTTTAAGGTTCTTCGTCTTCGAT
1 CTGTTACCCTACTGCTTAGGGG-TTAA-GATCTGC-AATTCAAC
* *
4393289 CTGCT-CCACTACTGCTTAGGGAGATAAGATCTGCAATTCAAC
1 CTGTTACC-CTACTGCTTAGGG-GTTAAGATCTGCAATTCAAC
* * ** * *
4393331 CTGTTACCCTACTGCTTAGGGGTTTAAGGTTCTTCGTCTTCGAT
1 CTGTTACCCTACTGCTTAGGGG-TTAA-GATCTGC-AATTCAAC
* * *
4393375 CTGCT-CCACTACTGCTTAGGGAGATAAGATCTGCAACTCAAC
1 CTGTTACC-CTACTGCTTAGGG-GTTAAGATCTGCAATTCAAC
* * ** * *
4393417 CTGTTACCCTACTGCTTAGGGGTTTAAGGTTCTTCGTCTTCGAT
1 CTGTTACCCTACTGCTTAGGGG-TTAA-GATCTGC-AATTCAAC
* * * * *
4393461 CTGCT-CCACTACTGCTTAGGGATATAAGATCTGGAATTTAGC
1 CTGTTACC-CTACTGCTTAGGGGT-TAAGATCTGCAATTCAAC
* * * * *
4393503 CTGTTACCCTACTGCTTAGGAGTTTATGGTCTCGTCATCTTCAAT
1 CTGTTACCCTACTGCTTAGG-GGTTAAGATCT-G-CA-ATTCAAC
*
4393548 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTG
1 CTGTTACCCTACTGCTTA-GGGGTTAAGATCTG
4393581 TAAATTTTCA
Statistics
Matches: 245, Mismatches: 68, Indels: 43
0.69 0.19 0.12
Matches are distributed among these distances:
41 22 0.09
42 74 0.30
43 44 0.18
44 73 0.30
45 30 0.12
46 2 0.01
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.36
Consensus pattern (41 bp):
CTGTTACCCTACTGCTTAGGGGTTAAGATCTGCAATTCAAC
Found at i:4393435 original size:172 final size:171
Alignment explanation
Indices: 4393135--4393580 Score: 635
Period size: 172 Copynumber: 2.6 Consensus size: 171
4393125 GCAACTCCAT
* * * *
4393135 GGAGATAAGATCTGTGATTTTCAGCCTATTACCCTACTACTTAGGGGATTAAGGCTT-GTCATCT
1 GGAGATAAGATCTG-GA-ATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGG-TTCGTCATCT
* * * * *
4393199 TTGATCTGTTTCCCTACTGCTTAGGGTTTTAGATCTGTAATTCAACCTGTTACCCTACTGCTTAG
63 TCGATCTGTTTCCCTACTGCTTAGGGGTTAAGATCTGCAACTCAACCTGTTACCCTACTGCTTAG
4393264 GGGTTTAAGGTTCTTCGTCTTCGATCTGCTCCACTACTGCTTAG
128 GGGTTTAAGGTTCTTCGTCTTCGATCTGCTCCACTACTGCTTAG
* * * *
4393308 GGAGATAAGATCTGCAATTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTTCTTCGTCTTCG
1 GGAGATAAGATCTGGAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGTTCGTCATCTTCG
* *
4393373 ATCTG-CTCCACTACTGCTTAGGGAGATAAGATCTGCAACTCAACCTGTTACCCTACTGCTTAGG
66 ATCTGTTTCC-CTACTGCTTAGGG-GTTAAGATCTGCAACTCAACCTGTTACCCTACTGCTTAGG
4393437 GGTTTAAGGTTCTTCGTCTTCGATCTGCTCCACTACTGCTTAG
129 GGTTTAAGGTTCTTCGTCTTCGATCTGCTCCACTACTGCTTAG
* * * *
4393480 GGATATAAGATCTGGAATTTAGCCTGTTACCCTACTGCTTAGGAGTTTATGGTCTCGTCATCTTC
1 GGAGATAAGATCTGGAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGT-TCGTCATCTTC
*
4393545 AATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTG
65 GATCTGTTTCCCTACTGCTTA-GGGGTTAAGATCTG
4393581 TAAATTTTCA
Statistics
Matches: 241, Mismatches: 26, Indels: 12
0.86 0.09 0.04
Matches are distributed among these distances:
170 5 0.02
171 56 0.23
172 126 0.52
173 48 0.20
174 6 0.02
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (171 bp):
GGAGATAAGATCTGGAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGTTCGTCATCTTCG
ATCTGTTTCCCTACTGCTTAGGGGTTAAGATCTGCAACTCAACCTGTTACCCTACTGCTTAGGGG
TTTAAGGTTCTTCGTCTTCGATCTGCTCCACTACTGCTTAG
Found at i:4412856 original size:22 final size:23
Alignment explanation
Indices: 4412828--4412872 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
4412818 CACTGGTAAT
4412828 GTATTTTT-TTTTTATAAACTGC
1 GTATTTTTGTTTTTATAAACTGC
4412850 GTATTTTTGTTTTTATAAACTGC
1 GTATTTTTGTTTTTATAAACTGC
4412873 TTTAAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.22, C:0.09, G:0.11, T:0.58
Consensus pattern (23 bp):
GTATTTTTGTTTTTATAAACTGC
Found at i:4413238 original size:23 final size:22
Alignment explanation
Indices: 4413212--4413258 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
4413202 TTTCTGAATT
4413212 ATATTTA-TATGTTAAGTTTTTAA
1 ATATTTATTA-GTTAA-TTTTTAA
*
4413235 ATATTTATTAGTTTATTTTTAA
1 ATATTTATTAGTTAATTTTTAA
4413257 AT
1 AT
4413259 TTTCAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 9 0.41
23 11 0.50
24 2 0.09
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (22 bp):
ATATTTATTAGTTAATTTTTAA
Found at i:4413541 original size:28 final size:27
Alignment explanation
Indices: 4413493--4413550 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
4413483 TTTTAAATAT
*
4413493 TTTTAAATTTATATTTATATTACTTTA
1 TTTTAAATTAATATTTATATTACTTTA
**
4413520 TTTTAATATTAATAATTT-TATTTTTTTA
1 TTTTAA-ATTAAT-ATTTATATTACTTTA
4413548 TTT
1 TTT
4413551 ATTGAAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 6 0.23
28 16 0.62
29 4 0.15
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (27 bp):
TTTTAAATTAATATTTATATTACTTTA
Found at i:4414701 original size:30 final size:30
Alignment explanation
Indices: 4414657--4414715 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
4414647 ACTTAACAAG
4414657 CAAATACCTCTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
* *
4414687 CAAATGCCTTTAAAATAATAACAAAATTA
1 CAAATACCTCTAAAATAATAACAAAATTA
4414716 TTAATAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.58, C:0.15, G:0.02, T:0.25
Consensus pattern (30 bp):
CAAATACCTCTAAAATAATAACAAAATTAA
Found at i:4417098 original size:61 final size:61
Alignment explanation
Indices: 4417026--4417144 Score: 139
Period size: 61 Copynumber: 2.0 Consensus size: 61
4417016 ATCTAAACAG
* * * * * * * *
4417026 TCAACAAATTTAACCCTTAATATTTACAAAATTTTTCATTTTAGTTCTAATTCTAAAAAAT
1 TCAACAAATTTAACCCTCAAAATCTACAAAAATTGTCAATTTAGTTCAAACTCTAAAAAAT
* * *
4417087 TCAATAAATTTATCTCTCAAAATCTACAAAAATTGTCAATTTAGTTCAAACTCTAAAA
1 TCAACAAATTTAACCCTCAAAATCTACAAAAATTGTCAATTTAGTTCAAACTCTAAAA
4417145 GTTTTAAAAA
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.43, C:0.16, G:0.03, T:0.39
Consensus pattern (61 bp):
TCAACAAATTTAACCCTCAAAATCTACAAAAATTGTCAATTTAGTTCAAACTCTAAAAAAT
Found at i:4433727 original size:3 final size:3
Alignment explanation
Indices: 4433719--4433759 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
4433709 TGGGTTGGTT
4433719 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
4433760 TAATTGAAGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:4435185 original size:6 final size:6
Alignment explanation
Indices: 4435174--4435198 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
4435164 TTTTGAATAC
4435174 AAATTA AAATTA AAATTA AAATTA A
1 AAATTA AAATTA AAATTA AAATTA A
4435199 TAAACTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATTA
Found at i:4440248 original size:29 final size:29
Alignment explanation
Indices: 4440207--4440263 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
4440197 TTTATTTTCT
* *
4440207 TCTCTAAAAATATATCGTATTTTTTAAAA
1 TCTCTAAAAATATATCATATTTATTAAAA
4440236 TCTC-AAATAATATATCATATTTATTAAA
1 TCTCTAAA-AATATATCATATTTATTAAA
4440264 TTTCGATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 22 0.88
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.44
Consensus pattern (29 bp):
TCTCTAAAAATATATCATATTTATTAAAA
Found at i:4442769 original size:12 final size:14
Alignment explanation
Indices: 4442740--4442771 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
4442730 GGTTCAATGA
4442740 GAGGAGTTTTGCTT
1 GAGGAGTTTTGCTT
4442754 GAGGAG-TTTG-TT
1 GAGGAGTTTTGCTT
4442766 GAGGAG
1 GAGGAG
4442772 CCTTCGCGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.44
13 4 0.22
14 6 0.33
ACGTcount: A:0.19, C:0.03, G:0.44, T:0.34
Consensus pattern (14 bp):
GAGGAGTTTTGCTT
Found at i:4450186 original size:40 final size:40
Alignment explanation
Indices: 4450119--4450211 Score: 118
Period size: 40 Copynumber: 2.4 Consensus size: 40
4450109 ACCATTGGTC
*
4450119 AACCGTTG-TTTTTGCTAATTTATTGCATATAAAATGTTT
1 AACCGTTGATTTTTGCTAATTTATTGCATATAAAATGTTG
* * *
4450158 AACCATTGATTTTTGTTAATTTCA-TGCATATAAATTGTTG
1 AACCGTTGATTTTTGCTAATTT-ATTGCATATAAAATGTTG
*
4450198 AACTGTTGATTTTT
1 AACCGTTGATTTTT
4450212 TAAGTCAATA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
39 7 0.15
40 38 0.83
41 1 0.02
ACGTcount: A:0.28, C:0.10, G:0.13, T:0.49
Consensus pattern (40 bp):
AACCGTTGATTTTTGCTAATTTATTGCATATAAAATGTTG
Found at i:4453389 original size:30 final size:29
Alignment explanation
Indices: 4453353--4453409 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
4453343 CACGGCCAGG
* *
4453353 CACACGGGCATGTGTCTAGGCTATGTGAGC
1 CACACGGGCATGTGGC-AGGCCATGTGAGC
4453383 CACACGGGCATGTGGCAGGCCATGTGA
1 CACACGGGCATGTGGCAGGCCATGTGA
4453410 TCGGCCATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.21, C:0.25, G:0.35, T:0.19
Consensus pattern (29 bp):
CACACGGGCATGTGGCAGGCCATGTGAGC
Found at i:4458296 original size:29 final size:30
Alignment explanation
Indices: 4458259--4458317 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
4458249 TATGGTTTAA
* *
4458259 TGTGCAATTATATACATG-AATTTTGATTT
1 TGTGAAATTATATAAATGAAATTTTGATTT
*
4458288 TGTGAAATTCTATAAATGAAATTTTGATTT
1 TGTGAAATTATATAAATGAAATTTTGATTT
4458318 GATCAAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.47
Consensus pattern (30 bp):
TGTGAAATTATATAAATGAAATTTTGATTT
Found at i:4458326 original size:30 final size:29
Alignment explanation
Indices: 4458264--4458333 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 29
4458254 TTTAATGTGC
* * *
4458264 AATTATATACATGAATTTTGATTTTGTGA
1 AATTCTATAAATGAATTTTGATTTTGTCA
4458293 AATTCTATAAATGAAATTTTGA-TTTGATCA
1 AATTCTATAAATG-AATTTTGATTTTG-TCA
4458323 AATTCTTATAA
1 AATTC-TATAA
4458334 TTTTATTAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 15 0.43
30 15 0.43
31 5 0.14
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.46
Consensus pattern (29 bp):
AATTCTATAAATGAATTTTGATTTTGTCA
Found at i:4461785 original size:16 final size:16
Alignment explanation
Indices: 4461761--4461793 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
4461751 TTTTATATAT
*
4461761 TAAATTATTATATTAA
1 TAAAATATTATATTAA
4461777 TAAAATATTATATTAA
1 TAAAATATTATATTAA
4461793 T
1 T
4461794 TAGATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TAAAATATTATATTAA
Found at i:4461833 original size:13 final size:13
Alignment explanation
Indices: 4461815--4461842 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
4461805 TATATCATAA
4461815 ATTATATTATATT
1 ATTATATTATATT
4461828 ATTATATTATATT
1 ATTATATTATATT
4461841 AT
1 AT
4461843 AAAATAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
ATTATATTATATT
Found at i:4463082 original size:23 final size:23
Alignment explanation
Indices: 4463056--4463145 Score: 153
Period size: 23 Copynumber: 3.9 Consensus size: 23
4463046 CTTAGTGTTG
4463056 TTCTGGTGTGTTTGGGTGGATTA
1 TTCTGGTGTGTTTGGGTGGATTA
*
4463079 TTCTGGTGTGTTTGGGTGGATCA
1 TTCTGGTGTGTTTGGGTGGATTA
*
4463102 TTCTGGTGTGTTTGGTTGGATTA
1 TTCTGGTGTGTTTGGGTGGATTA
*
4463125 TTCTGGTGTGTTTGGTTGGAT
1 TTCTGGTGTGTTTGGGTGGAT
4463146 CCATGTATCC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 64 1.00
ACGTcount: A:0.08, C:0.06, G:0.38, T:0.49
Consensus pattern (23 bp):
TTCTGGTGTGTTTGGGTGGATTA
Found at i:4474364 original size:15 final size:16
Alignment explanation
Indices: 4474344--4474376 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
4474334 ATATAATTTT
4474344 TTATTTT-ATTTTTAA
1 TTATTTTAATTTTTAA
4474359 TTATTTTAAATTTTTAA
1 TTATTTT-AATTTTTAA
4474376 T
1 T
4474377 ATAACTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTTTAATTTTTAA
Found at i:4474456 original size:12 final size:12
Alignment explanation
Indices: 4474441--4474469 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
4474431 GTATTATTTT
4474441 TATTTATTTTAA
1 TATTTATTTTAA
4474453 TATTTATTTTAA
1 TATTTATTTTAA
4474465 TATTT
1 TATTT
4474470 TTAAATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TATTTATTTTAA
Found at i:4474456 original size:21 final size:20
Alignment explanation
Indices: 4474433--4474512 Score: 56
Period size: 21 Copynumber: 3.7 Consensus size: 20
4474423 TTGTTTTAGT
4474433 ATTATTTTTATTTATTTTAA
1 ATTATTTTTATTTATTTTAA
* *
4474453 TATTTATTTTAATAT-TTTTAA
1 -A-TTATTTTTATTTATTTTAA
4474474 ATATATTTGATTTATTATATTTTTAA
1 AT-TA-TT--TTTATT-TA-TTTTAA
4474500 ATT-TTTTTATTTA
1 ATTATTTTTATTTA
4474513 ATAAAATAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 17
0.69 0.06 0.25
Matches are distributed among these distances:
19 1 0.02
20 5 0.11
21 15 0.32
22 10 0.21
23 6 0.13
24 1 0.02
25 1 0.02
26 8 0.17
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (20 bp):
ATTATTTTTATTTATTTTAA
Found at i:4474493 original size:26 final size:24
Alignment explanation
Indices: 4474452--4474515 Score: 76
Period size: 26 Copynumber: 2.6 Consensus size: 24
4474442 ATTTATTTTA
4474452 ATATTTATTTTAATATTTTTAAAT
1 ATATTTATTTTAATATTTTTAAAT
*
4474476 ATATTTGATTTATTATATTTTTAAAT
1 ATATTT-ATTT-TAATATTTTTAAAT
* *
4474502 TTTTTTA-TTTAATA
1 ATATTTATTTTAATA
4474516 AAATAAGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
23 4 0.12
24 8 0.24
25 5 0.15
26 17 0.50
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (24 bp):
ATATTTATTTTAATATTTTTAAAT
Found at i:4481070 original size:17 final size:16
Alignment explanation
Indices: 4481038--4481068 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4481028 TTATTTCATA
4481038 AATATTTCTAAAAAAT
1 AATATTTCTAAAAAAT
*
4481054 AATATTTTTAAAAAA
1 AATATTTCTAAAAAA
4481069 ATTTAAATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (16 bp):
AATATTTCTAAAAAAT
Found at i:4483388 original size:5 final size:5
Alignment explanation
Indices: 4483378--4483412 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
4483368 TTCTCATACA
4483378 CATCC CATCC CATCC CATCC CATCC CATCC CATCC
1 CATCC CATCC CATCC CATCC CATCC CATCC CATCC
4483413 ACAGCTAACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.20, C:0.60, G:0.00, T:0.20
Consensus pattern (5 bp):
CATCC
Found at i:4485639 original size:19 final size:20
Alignment explanation
Indices: 4485606--4485647 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
4485596 TTAAAATTTT
4485606 TTTTATTATAATATTTATAA
1 TTTTATTATAATATTTATAA
* *
4485626 TTTT-TTATATTATTTTTAA
1 TTTTATTATAATATTTATAA
4485645 TTT
1 TTT
4485648 AATTTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTTATTATAATATTTATAA
Found at i:4488467 original size:2 final size:2
Alignment explanation
Indices: 4488460--4488492 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4488450 TTAATAAACA
4488460 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4488493 AAAGCAGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4496326 original size:22 final size:22
Alignment explanation
Indices: 4496298--4496349 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
4496288 TGTAATAAAT
4496298 TATTTAAAATATTTTAT-ATTAA
1 TATTTAAAAT-TTTTATAATTAA
4496320 TATTTAATAATTTTTATAATTAA
1 TATTTAA-AATTTTTATAATTAA
4496343 T-TTTAAA
1 TATTTAAA
4496350 TAAAAATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
21 1 0.04
22 18 0.64
23 9 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TATTTAAAATTTTTATAATTAA
Found at i:4496950 original size:2 final size:2
Alignment explanation
Indices: 4496943--4496978 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
4496933 AGGCACTTAG
4496943 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4496979 AAATATGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4497317 original size:12 final size:11
Alignment explanation
Indices: 4497285--4497338 Score: 56
Period size: 12 Copynumber: 4.8 Consensus size: 11
4497275 TTAATTTGTG
4497285 TATTATTTTAA
1 TATTATTTTAA
*
4497296 GAATTATTTTAA
1 -TATTATTTTAA
*
4497308 TATTATTTTTA
1 TATTATTTTAA
*
4497319 T-TTGTTTTAA
1 TATTATTTTAA
4497329 TATTTATTTT
1 TA-TTATTTT
4497339 TATGTTTTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 8 0.24
11 10 0.29
12 16 0.47
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.67
Consensus pattern (11 bp):
TATTATTTTAA
Found at i:4497328 original size:21 final size:20
Alignment explanation
Indices: 4497302--4497349 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 20
4497292 TTAAGAATTA
*
4497302 TTTTAATATTATTTTTATTT
1 TTTTAATATTATTTTTATGT
4497322 GTTTTAATATTTATTTTTATGT
1 -TTTTAATA-TTATTTTTATGT
4497344 TTTTAA
1 TTTTAA
4497350 ATATATTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (20 bp):
TTTTAATATTATTTTTATGT
Found at i:4497338 original size:22 final size:21
Alignment explanation
Indices: 4497302--4497383 Score: 71
Period size: 22 Copynumber: 3.8 Consensus size: 21
4497292 TTAAGAATTA
*
4497302 TTTTAATA-TTATTTTTATTT
1 TTTTAATATTTATTTTTATGT
4497322 GTTTTAATATTTATTTTTATGT
1 -TTTTAATATTTATTTTTATGT
*
4497344 TTTTAAATATATTTGATTTATTATAT
1 TTTT--A-ATATTT-ATTT-TTATGT
4497370 TTTTAA-ATTT-TTTT
1 TTTTAATATTTATTTT
4497384 ATTTAATGAA
Statistics
Matches: 53, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
19 1 0.02
20 3 0.06
21 12 0.23
22 15 0.28
23 2 0.04
24 7 0.13
25 4 0.08
26 9 0.17
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.70
Consensus pattern (21 bp):
TTTTAATATTTATTTTTATGT
Found at i:4497374 original size:26 final size:24
Alignment explanation
Indices: 4497328--4497387 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
4497318 ATTTGTTTTA
*
4497328 ATATTTATTTTTATGTTTTTAAAT
1 ATATTTATTTTTATATTTTTAAAT
4497352 ATATTTGATTTATTATATTTTTAAAT
1 ATATTT-ATTT-TTATATTTTTAAAT
* *
4497378 TTTTTTATTT
1 ATATTTATTT
4497388 AATGAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.19
25 8 0.26
26 17 0.55
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.68
Consensus pattern (24 bp):
ATATTTATTTTTATATTTTTAAAT
Found at i:4500648 original size:2 final size:2
Alignment explanation
Indices: 4500641--4500666 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4500631 ATGTATTTGG
4500641 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
4500667 ATAATTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4507185 original size:23 final size:24
Alignment explanation
Indices: 4507130--4507186 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 24
4507120 ATTTTTAAGT
* *
4507130 AAAAATATTTAAAATTATGATTAA
1 AAAAATATTTTAAATTATAATTAA
**
4507154 GTAAA-ATTTTAAATTA-AATTAA
1 AAAAATATTTTAAATTATAATTAA
4507176 AAAAATATTTT
1 AAAAATATTTT
4507187 TATTGAACAT
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
22 8 0.31
23 15 0.58
24 3 0.12
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (24 bp):
AAAAATATTTTAAATTATAATTAA
Found at i:4510972 original size:19 final size:19
Alignment explanation
Indices: 4510948--4510995 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
4510938 AGGTTGTCAA
4510948 ACATTTGT-AAGGCATGATT
1 ACATTTGTGAAGG-ATGATT
**
4510967 ACATTTGTGATTGATGATT
1 ACATTTGTGAAGGATGATT
4510986 ACATTTGTGA
1 ACATTTGTGA
4510996 TTGATATTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 24 0.92
20 2 0.08
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.42
Consensus pattern (19 bp):
ACATTTGTGAAGGATGATT
Found at i:4510996 original size:19 final size:19
Alignment explanation
Indices: 4510961--4511000 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
4510951 TTTGTAAGGC
4510961 ATGATTACATTTGTGATTG
1 ATGATTACATTTGTGATTG
4510980 ATGATTACATTTGTGATTG
1 ATGATTACATTTGTGATTG
4510999 AT
1 AT
4511001 ATTGGTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.28, C:0.05, G:0.20, T:0.47
Consensus pattern (19 bp):
ATGATTACATTTGTGATTG
Found at i:4514870 original size:3 final size:3
Alignment explanation
Indices: 4514862--4514919 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
4514852 TCTGGAACCT
4514862 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
4514910 ATA ATA ATA A
1 ATA ATA ATA A
4514920 GGAAAACCCA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:4516784 original size:4 final size:4
Alignment explanation
Indices: 4516775--4516823 Score: 98
Period size: 4 Copynumber: 12.2 Consensus size: 4
4516765 TTATTAGCCA
4516775 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
4516823 T
1 T
4516824 GTGTTTAATG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:4520001 original size:16 final size:16
Alignment explanation
Indices: 4519977--4520025 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
4519967 TAAATAGTCT
*
4519977 TTATATTTAATTTTGA
1 TTATTTTTAATTTTGA
4519993 TTATTTTTAATATTGTGA
1 TTATTTTTAAT-TT-TGA
*
4520011 TT-TTTCTAATTTTGA
1 TTATTTTTAATTTTGA
4520026 AATTTAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
15 3 0.10
16 12 0.41
17 9 0.31
18 5 0.17
ACGTcount: A:0.27, C:0.02, G:0.08, T:0.63
Consensus pattern (16 bp):
TTATTTTTAATTTTGA
Found at i:4522102 original size:176 final size:176
Alignment explanation
Indices: 4521612--4522141 Score: 774
Period size: 177 Copynumber: 3.0 Consensus size: 176
4521602 GCATTGTATT
* *
4521612 ATACGAGCCTTAACCCCCTTAGTAGTAGGGTAACAGGCTAAAAATTGCAGATCTTATCTCCATGT
1 ATACGAGCCTTAA-CCCCTAAGTAGTAGGGTAACAGGCTGAAAATTGCAGATCTTATCTCCATGT
* * * * * *
4521677 GTCGGCTATGGAGCAGATAAAAAATGGCAATTCTTATCTCCATTTATCGGCTATGGAGCAGATTT
65 ATCGGCTATGGAGCAGATCAGAAATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTT
** *
4521742 AAGCCACCGGCCTTATCTCTCTGAAATAGTAAGAGAGCAAGTTGAAG
130 AAGCCACCGGCCTTATCTCTCTGAGGTAGCAAGAGAGCAAGTTGAAG
* *
4521789 ATACGAGCCTTAACCCTCTAAGCAGTAGGGTAACAGGATGAAAATTGCAGATCTTATCTCCATGT
1 ATACGAGCCTTAACCC-CTAAGTAGTAGGGTAACAGGCTGAAAATTGCAGATCTTATCTCCATGT
* *
4521854 ATCGGTTATGGAACAGATC-GAAAATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATT
65 ATCGGCTATGGAGCAGATCAG-AAATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATT
*
4521918 TAAGCCACCGGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAG
129 TAAGCCACCGGCCTTATCTCTCTGAGGTAGCAAGAGAGCAAGTTGAAG
* * *
4521966 ATACAAGCCTTAACCCCTAAGTAGTAGGGTAACGGGCTGAAAATTACAGATCTTATCTCCATGTA
1 ATACGAGCCTTAACCCCTAAGTAGTAGGGTAACAGGCTGAAAATTGCAGATCTTATCTCCATGTA
* * * *
4522031 CCAGCTATGGAGCAGATCAGAAATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGTAGATTTT
66 TCGGCTATGGAGCAGATCAGAAATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTA
* * * **
4522096 AGCCACCAGCCCTATCTCTCTAAGGTAGCAAGAGAGTGAGTTGAAG
131 AGCCACCGGCCTTATCTCTCTGAGGTAGCAAGAGAGCAAGTTGAAG
4522142 TTACAAACTT
Statistics
Matches: 317, Mismatches: 33, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
176 145 0.46
177 172 0.54
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (176 bp):
ATACGAGCCTTAACCCCTAAGTAGTAGGGTAACAGGCTGAAAATTGCAGATCTTATCTCCATGTA
TCGGCTATGGAGCAGATCAGAAATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTA
AGCCACCGGCCTTATCTCTCTGAGGTAGCAAGAGAGCAAGTTGAAG
Found at i:4524024 original size:53 final size:53
Alignment explanation
Indices: 4523883--4524033 Score: 205
Period size: 53 Copynumber: 2.8 Consensus size: 53
4523873 ATAAGTGCGC
* ** *
4523883 CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCAATATGATAATGTGACT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
*
4523936 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGATT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
* *
4523989 CCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGATATGTGA
1 CCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A-ATGTGA
4524034 ACCGTGTAAG
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
52 1 0.01
53 80 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (53 bp):
CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
Found at i:4528199 original size:8 final size:8
Alignment explanation
Indices: 4528183--4528216 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
4528173 TCATAATTTT
4528183 ATATAAAA
1 ATATAAAA
4528191 ATATTAAAA
1 ATA-TAAAA
4528200 AT-TAAAA
1 ATATAAAA
4528207 ATATAAAA
1 ATATAAAA
4528215 AT
1 AT
4528217 CAAACAATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 7 0.29
8 10 0.42
9 7 0.29
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (8 bp):
ATATAAAA
Found at i:4528225 original size:16 final size:16
Alignment explanation
Indices: 4528187--4528225 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
4528177 AATTTTATAT
*
4528187 AAAAATATTAAAAATT
1 AAAAATATTAAAAATC
4528203 AAAAATA-TAAAAATC
1 AAAAATATTAAAAATC
4528218 AAACAATA
1 AAA-AATA
4528226 CAAATTTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAAATATTAAAAATC
Found at i:4529651 original size:13 final size:13
Alignment explanation
Indices: 4529607--4529654 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
4529597 AATAAATAAA
4529607 AAATATTAAATTGTT
1 AAATATTAAA-T-TT
*
4529622 AAATATTAAATTA
1 AAATATTAAATTT
**
4529635 AAATATTAGTTTT
1 AAATATTAAATTT
4529648 AAATATT
1 AAATATT
4529655 TAAAAATAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
13 18 0.62
14 1 0.03
15 10 0.34
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (13 bp):
AAATATTAAATTT
Found at i:4530779 original size:14 final size:13
Alignment explanation
Indices: 4530760--4530797 Score: 67
Period size: 13 Copynumber: 2.8 Consensus size: 13
4530750 CTAGAAGCAA
4530760 AGAAAAAAAGAAAG
1 AGAAAAAAA-AAAG
4530774 AGAAAAAAAAAAG
1 AGAAAAAAAAAAG
4530787 AGAAAAAAAAA
1 AGAAAAAAAAA
4530798 GTAAAGGAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 15 0.62
14 9 0.38
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AGAAAAAAAAAAG
Found at i:4530781 original size:13 final size:12
Alignment explanation
Indices: 4530758--4530798 Score: 57
Period size: 12 Copynumber: 3.3 Consensus size: 12
4530748 TGCTAGAAGC
4530758 AAAGA-AAAAAA
1 AAAGAGAAAAAA
4530769 GAAAGAGAAAAAAA
1 -AAAGAG-AAAAAA
4530783 AAAGAGAAAAAA
1 AAAGAGAAAAAA
4530795 AAAG
1 AAAG
4530799 TAAAGGAGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 15 0.56
13 6 0.22
14 6 0.22
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (12 bp):
AAAGAGAAAAAA
Found at i:4531049 original size:33 final size:33
Alignment explanation
Indices: 4531003--4531068 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
4530993 CAGAACATGA
* * *
4531003 AGAACCTCGAACTCAAACCCAAACCTTGAACCC
1 AGAACCCCAAACTCAAACCCAAACCTAGAACCC
*
4531036 AGAACCCCAAACTCAAACTCAAACCTAGAACCC
1 AGAACCCCAAACTCAAACCCAAACCTAGAACCC
4531069 TAAAGTTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.42, C:0.39, G:0.08, T:0.11
Consensus pattern (33 bp):
AGAACCCCAAACTCAAACCCAAACCTAGAACCC
Found at i:4534238 original size:13 final size:12
Alignment explanation
Indices: 4534188--4534236 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 12
4534178 CAACATAAAT
4534188 CAAATAGAAAAAA
1 CAAA-AGAAAAAA
4534201 CAAAAGAAAAACA
1 CAAAAGAAAAA-A
4534214 CAAAAGAAAACAA
1 CAAAAGAAAA-AA
*
4534227 CAAACGAAAA
1 CAAAAGAAAA
4534237 CAGAAACCAG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
12 7 0.21
13 25 0.76
14 1 0.03
ACGTcount: A:0.76, C:0.14, G:0.08, T:0.02
Consensus pattern (12 bp):
CAAAAGAAAAAA
Found at i:4534352 original size:15 final size:16
Alignment explanation
Indices: 4534327--4534356 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4534317 GTAAAATGTA
4534327 AAAAAAGATATAAAAC
1 AAAAAAGATATAAAAC
4534343 AAAAAA-ATATAAAA
1 AAAAAAGATATAAAA
4534357 TTTTTACCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.80, C:0.03, G:0.03, T:0.13
Consensus pattern (16 bp):
AAAAAAGATATAAAAC
Found at i:4540876 original size:73 final size:72
Alignment explanation
Indices: 4540676--4540906 Score: 327
Period size: 73 Copynumber: 3.2 Consensus size: 72
4540666 TTGATGTTTT
* * * **
4540676 ATTTTTGTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGT
1 ATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGT
4540741 ATTTTCA
66 ATTTTCA
* *
4540748 ATTTCTATCTTTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACACTGA
1 ATTTCTGT-TTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGA
* *
4540813 AGTAATTTCA
63 GGTATTTTCA
*
4540823 ATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTCAGGACACACTGAGG
1 ATTTCTGTTT-TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGG
4540888 TATTTTCA
65 TATTTTCA
*
4540896 AATTCTGTTTT
1 ATTTCTGTTTT
4540907 TCAATTTCTA
Statistics
Matches: 140, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
72 7 0.05
73 69 0.49
74 2 0.01
75 62 0.44
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (72 bp):
ATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGT
ATTTTCA
Found at i:4540967 original size:89 final size:89
Alignment explanation
Indices: 4540836--4540999 Score: 274
Period size: 89 Copynumber: 1.8 Consensus size: 89
4540826 TCTGTTTGTC
* *
4540836 AAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTCAGGACACACTGAGGTATTTTCAAATTC
1 AAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTCAGGACACACTGAGATAATTTCAAATTC
*
4540901 TGTTTTTCAATTTCTATCTTTCAA
66 TGTTTGTCAATTTCTATCTTTCAA
* * *
4540925 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGATAATTTCAACTTC
1 AAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTCAGGACACACTGAGATAATTTCAAATTC
4540990 TGTTTGTCAA
66 TGTTTGTCAA
4541000 AAATCAACTC
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
89 69 1.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (89 bp):
AAAAATCAACTCATATTGCGAGAGGTAAGTTGAGCCTCAGGACACACTGAGATAATTTCAAATTC
TGTTTGTCAATTTCTATCTTTCAA
Found at i:4541009 original size:162 final size:162
Alignment explanation
Indices: 4540742--4541325 Score: 698
Period size: 162 Copynumber: 3.6 Consensus size: 162
4540732 CGTTGAGGTA
4540742 TTTTCAATTTCTATCTTTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACA
1 TTTTCAATTTCTATCTTTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACA
* *
4540807 CACTGA-AGTAATTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTAAGTTGAGC
66 CGCTGAGA-TAATTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
4540871 CTCAGGACACACTGAGGTATTTTCAAATTCTGT
130 CTCAGGACACACTGAGGTATTTTCAAATTCTGT
*
4540904 TTTTCAATTTCTATCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
1 TTTTCAATTTCTATCTTTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACA
*
4540969 CGCTGAGATAATTTCAACTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
66 CGCTGAGATAATTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
* *
4541034 TCAGGGCACACTGAGGTATTTTC-AATTTTCGT
131 TCAGGACACACTGAGGTATTTTCAAATTCT-GT
* * ** *
4541066 TTTCCAA-CT-TATGCTTTTCAAAAAAAATTGACTCATATTGCGAGAAGTGAGTTGAGCCTCGGG
1 TTTTCAATTTCTAT-C-TTTC-AAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGG
* * * * * * * *
4541129 TCGCACGCTGAGGT-ATTGTTAGTTTATATTTTTCAAAAAAATCAACTCATTTTGCGAGAGGTGA
63 --ACACGCTGAGATAATT-TCAATTTCTGTTTGTC--AAAAATCAACTCATATTGCGAGAGGTGA
*
4541193 GTTGAGCCTCA-GAGCACACTGAGGTATTTTCAATTTCT-T
123 GTTGAGCCTCAGGA-CACACTGAGGTATTTTCAAATTCTGT
* * * * * * * * *
4541232 CTTTTTAATTTTTGTTTTTCAAGAAAATCAACCCATATTGCGAGAGGTGAGTTGAGCCT-TGGCT
1 -TTTTCAATTTCTATCTTTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGG-A
* *
4541296 CACGTGCTGAGCTATTTTCAATTTCTGTTT
64 CAC--GCTGAGATAATTTCAATTTCTGTTT
4541326 TTAATGTCTG
Statistics
Matches: 362, Mismatches: 42, Indels: 32
0.83 0.10 0.07
Matches are distributed among these distances:
160 3 0.01
161 7 0.02
162 158 0.44
163 40 0.11
164 7 0.02
165 22 0.06
166 52 0.14
167 66 0.18
168 5 0.01
169 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.35
Consensus pattern (162 bp):
TTTTCAATTTCTATCTTTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACA
CGCTGAGATAATTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
TCAGGACACACTGAGGTATTTTCAAATTCTGT
Done.