Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
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: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 131 of 141
Found at i:39235978 original size:10 final size:9
Alignment explanation
Indices: 39235948--39235984 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
39235938 CTAGTTAGTG
39235948 TTTAACTTGT
1 TTTAA-TTGT
*
39235958 TTTAATTTT
1 TTTAATTGT
39235967 TTTAATTGT
1 TTTAATTGT
39235976 TTTAATTGT
1 TTTAATTGT
39235985 GGGTAAACCC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 20 0.80
10 5 0.20
ACGTcount: A:0.22, C:0.03, G:0.08, T:0.68
Consensus pattern (9 bp):
TTTAATTGT
Found at i:39236033 original size:18 final size:18
Alignment explanation
Indices: 39236006--39236051 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
39235996 AAAAATTTTC
39236006 TAAA-TATTTTTTAAATT
1 TAAATTATTTTTTAAATT
* *
39236023 TTAATTATTTTTTAAGTT
1 TAAATTATTTTTTAAATT
39236041 TAAATTCATTT
1 TAAATT-ATTT
39236052 GCTGACGTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 3 0.12
18 17 0.71
19 4 0.17
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (18 bp):
TAAATTATTTTTTAAATT
Found at i:39242378 original size:5 final size:5
Alignment explanation
Indices: 39242368--39242397 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
39242358 TGTTTCAAGC
39242368 TTTAT TTTAT TTTAT TTTAT TTTACT TTTA
1 TTTAT TTTAT TTTAT TTTAT TTTA-T TTTA
39242398 ATTCATCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTAT
Found at i:39242553 original size:20 final size:19
Alignment explanation
Indices: 39242528--39242566 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
39242518 CTCCTTTAAT
39242528 TATATAAATAAATTAATAAA
1 TATATAAATAAA-TAATAAA
*
39242548 TATATAAATATATAATAAA
1 TATATAAATAAATAATAAA
39242567 AAAATTTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
TATATAAATAAATAATAAA
Found at i:39261867 original size:54 final size:54
Alignment explanation
Indices: 39261795--39261931 Score: 238
Period size: 54 Copynumber: 2.5 Consensus size: 54
39261785 ATTGTCGTTG
* * *
39261795 CAGGGGATTTAGCCTGGACTAGTAATCCTGACAATACTCTATGAATTTATATTA
1 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCCATGAATTTATATTA
*
39261849 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCCATGAGTTTATATTA
1 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCCATGAATTTATATTA
39261903 CAGGGGATTTAGCCTGGACTGGTAATCCC
1 CAGGGGATTTAGCCTGGACTGGTAATCCC
39261932 ATTGTAAGGA
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 79 1.00
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.30
Consensus pattern (54 bp):
CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCCATGAATTTATATTA
Found at i:39263621 original size:98 final size:97
Alignment explanation
Indices: 39263516--39263702 Score: 268
Period size: 98 Copynumber: 1.9 Consensus size: 97
39263506 ATAAAATACA
* *
39263516 TTTAACATAATGATAAATATAAAA-AAATATTTTTATTATATAATTATATAATTATTAATTTATT
1 TTTAACATAATGATAAATATAAAATAAATA-TTTTATTATATAATTACAT-ATAATTAATTTATT
* *
39263580 TATATAAATAGAGGAGTTATTAATTAGAAATATT
64 TATATAAATAAAAGAGTTATTAATTAGAAATATT
* * * *
39263614 TTTAACATAATGATATATTTAAAATAGATATTTTATTATATAATTACATATAATTATTTTATTTA
1 TTTAACATAATGATAAATATAAAATAAATATTTTATTATATAATTACATATAATTAATTTATTTA
*
39263679 TATAAATAAAAGATTTATTAATTA
66 TATAAATAAAAGAGTTATTAATTA
39263703 AAAAGATGAA
Statistics
Matches: 79, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
97 35 0.44
98 40 0.51
99 4 0.05
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (97 bp):
TTTAACATAATGATAAATATAAAATAAATATTTTATTATATAATTACATATAATTAATTTATTTA
TATAAATAAAAGAGTTATTAATTAGAAATATT
Found at i:39263655 original size:25 final size:27
Alignment explanation
Indices: 39263626--39263683 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 27
39263616 TAACATAATG
*
39263626 ATATATTTA-AAATAGA-TATTTTA-TT
1 ATATAATTACAAATA-ATTATTTTATTT
*
39263651 ATATAATTACATATAATTATTTTATTT
1 ATATAATTACAAATAATTATTTTATTT
39263678 ATATAA
1 ATATAA
39263684 ATAAAAGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 9 0.32
26 11 0.39
27 8 0.29
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (27 bp):
ATATAATTACAAATAATTATTTTATTT
Found at i:39268434 original size:51 final size:49
Alignment explanation
Indices: 39268313--39268551 Score: 201
Period size: 51 Copynumber: 4.8 Consensus size: 49
39268303 TATCATTCGA
** * *
39268313 TACACGTAGTAGCCTTAACATAGTACTACACATGTGATCAAACTTTTCGG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGATCAAA-TTTCCGG
** * * * * *
39268363 TTTATGTAGTAGTCTGCACATAGTACTACACACGTAATCATTAATATCCGA
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGATCA--AATTTCCGG
*
39268414 TACACGTAGTAGCCTGCACATAGTACTACACACGTGATCGAAGCTTTCCGG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGATC-AA-ATTTCCGG
* *** * * ***
39268465 TGCGTATAGTAGCCTGCACATAGTACTACACATGCGA-CCTTTCATTCCGG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGATCAAAT--TTCCGG
* *
39268515 TACACGTAGTAGCCTACACATAGTACTACACATGTGA
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGA
39268552 CCATCACTTT
Statistics
Matches: 149, Mismatches: 34, Indels: 12
0.76 0.17 0.06
Matches are distributed among these distances:
48 1 0.01
50 71 0.48
51 74 0.50
52 3 0.02
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (49 bp):
TACACGTAGTAGCCTGCACATAGTACTACACACGTGATCAAATTTCCGG
Found at i:39268451 original size:101 final size:101
Alignment explanation
Indices: 39268310--39268551 Score: 308
Period size: 101 Copynumber: 2.4 Consensus size: 101
39268300 TATTATCATT
* ** *
39268310 CGATACACGTAGTAGCCTTA-ACATAGTACTACACATGTGATC-AAACTTTTCGGTTTATGTAGT
1 CGATACACGTAGTAGCC-TACACATAGTACTACACATGTGATCGAAACTTTCCGGTGCATATAGT
* * *
39268373 AGTCTGCACATAGTACTACACACGTAATCATTAATATC
65 AGCCTGCACATAGTACTACACACGCAACCATTAAT-TC
* * * *
39268411 CGATACACGTAGTAGCCTGCACATAGTACTACACACGTGATCGAAGCTTTCCGGTGCGTATAGTA
1 CGATACACGTAGTAGCCTACACATAGTACTACACATGTGATCGAAACTTTCCGGTGCATATAGTA
* * * *
39268476 GCCTGCACATAGTACTACACATGCGACCTTTCATTC
66 GCCTGCACATAGTACTACACACGCAACCATTAATTC
*
39268512 CGGTACACGTAGTAGCCTACACATAGTACTACACATGTGA
1 CGATACACGTAGTAGCCTACACATAGTACTACACATGTGA
39268552 CCATCACTTT
Statistics
Matches: 121, Mismatches: 18, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
100 1 0.01
101 77 0.64
102 43 0.36
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (101 bp):
CGATACACGTAGTAGCCTACACATAGTACTACACATGTGATCGAAACTTTCCGGTGCATATAGTA
GCCTGCACATAGTACTACACACGCAACCATTAATTC
Found at i:39268535 original size:50 final size:50
Alignment explanation
Indices: 39268304--39268554 Score: 216
Period size: 50 Copynumber: 5.0 Consensus size: 50
39268294 TTTAACTATT
* ** *
39268304 ATCATT-CGATACACGTAGTAGCCTTAACATAGTACTACACATGTGATCA
1 ATCATTCCGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCA
* * * ** * * * * *
39268353 AACTTTTCGGTTTATGTAGTAGTCTGCACATAGTACTACACACGTAATCA
1 ATCATTCCGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCA
* * * * *
39268403 TTAATATCCGATACACGTAGTAGCCTGCACATAGTACTACACACGTGATCGA
1 ATCAT-TCCGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGA-CCA
* * * *** * *
39268455 AGCTTTCCGGTGCGTATAGTAGCCTGCACATAGTACTACACATGCGACCT
1 ATCATTCCGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCA
* *
39268505 TTCATTCCGGTACACGTAGTAGCCTACACATAGTACTACACATGTGACCA
1 ATCATTCCGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCA
39268555 TCACTTTCAC
Statistics
Matches: 152, Mismatches: 47, Indels: 5
0.75 0.23 0.02
Matches are distributed among these distances:
49 4 0.03
50 76 0.50
51 70 0.46
52 2 0.01
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (50 bp):
ATCATTCCGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCA
Found at i:39271064 original size:26 final size:26
Alignment explanation
Indices: 39271034--39271088 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
39271024 TTGCTTCTTG
*
39271034 GTTGTTAATCAG-TTATTTTGTGATTT
1 GTTGTTAA-CAGATTATTTCGTGATTT
*
39271060 GTTGTTAACCGATTATTTCGTGATTT
1 GTTGTTAACAGATTATTTCGTGATTT
39271086 GTT
1 GTT
39271089 CTTTGTTGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 2 0.08
26 24 0.92
ACGTcount: A:0.18, C:0.07, G:0.20, T:0.55
Consensus pattern (26 bp):
GTTGTTAACAGATTATTTCGTGATTT
Found at i:39273022 original size:95 final size:93
Alignment explanation
Indices: 39272922--39273115 Score: 207
Period size: 93 Copynumber: 2.1 Consensus size: 93
39272912 TTTTGTTATA
* * * *
39272922 TATATACACATGCATATATATTTATAGTATACGTA-CATT-ATTTTTAT-AATTTATATATACAC
1 TATATACACAT-C-TATATATATATA-TATACATATCATTAATTTTCATAAATATATATATACAC
*
39272984 GCGTACTTATATATATTT-TTATATTTTATAATT
63 GCGTA--TATATAT-TTTATTATATCTTATAATT
* * ** * *
39273017 TATATACATATCTATATATATCTATATACATATTTTTAATTTTCATAAATATATATATACATGCT
1 TATATACACATCTATATATATATATATACATATCATTAATTTTCATAAATATATATATACACGCG
39273082 TATATATATTTTATTATATCTTATAATT
66 TATATATATTTTATTATATCTTATAATT
39273110 TATATA
1 TATATA
39273116 TATGTGTATA
Statistics
Matches: 84, Mismatches: 11, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
92 10 0.12
93 39 0.46
94 8 0.10
95 27 0.32
ACGTcount: A:0.38, C:0.09, G:0.03, T:0.51
Consensus pattern (93 bp):
TATATACACATCTATATATATATATATACATATCATTAATTTTCATAAATATATATATACACGCG
TATATATATTTTATTATATCTTATAATT
Found at i:39273611 original size:72 final size:72
Alignment explanation
Indices: 39273494--39273636 Score: 232
Period size: 72 Copynumber: 2.0 Consensus size: 72
39273484 TCTTTTCAAA
* * * **
39273494 CTCAAGTTTTAAAGGATCTCGGGAATTAAGAAGAGATTGTGTCCTAACTTACTGGGTATGATCCA
1 CTCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGACTGTGTCCTAACTTACTGGACATGATCCA
39273559 TTTTTTT
66 TTTTTTT
*
39273566 CTCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGACTGTGTCCTAACTTACTGGACATGATCCC
1 CTCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGACTGTGTCCTAACTTACTGGACATGATCCA
39273631 TTTTTT
66 TTTTTT
39273637 AAATCCGAGA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 65 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (72 bp):
CTCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGACTGTGTCCTAACTTACTGGACATGATCCA
TTTTTTT
Found at i:39276053 original size:38 final size:38
Alignment explanation
Indices: 39276002--39276282 Score: 562
Period size: 38 Copynumber: 7.4 Consensus size: 38
39275992 TTTCGGTAAA
39276002 ACATGGTGTGTAGGGATGGGTGGGTTGATTTAATCCCC
1 ACATGGTGTGTAGGGATGGGTGGGTTGATTTAATCCCC
39276040 ACATGGTGTGTAGGGATGGGTGGGTTGATTTAATCCCC
1 ACATGGTGTGTAGGGATGGGTGGGTTGATTTAATCCCC
39276078 ACATGGTGTGTAGGGATGGGTGGGTTGATTTAATCCCC
1 ACATGGTGTGTAGGGATGGGTGGGTTGATTTAATCCCC
39276116 ACATGGTGTGTAGGGATGGGTGGGTTGATTTAATCCCC
1 ACATGGTGTGTAGGGATGGGTGGGTTGATTTAATCCCC
39276154 ACATGGTGTGTAGGGATGGGTGGGTTGATTTAATCCCC
1 ACATGGTGTGTAGGGATGGGTGGGTTGATTTAATCCCC
39276192 ACATGGTGTGTAGGGATGGGTGGGTTGATTTAATCCCC
1 ACATGGTGTGTAGGGATGGGTGGGTTGATTTAATCCCC
39276230 ACATGGTGTGTAGGGATGGGTGGGTTGATTTAATCCCC
1 ACATGGTGTGTAGGGATGGGTGGGTTGATTTAATCCCC
39276268 ACATGGTGTGTAGGG
1 ACATGGTGTGTAGGG
39276283 GTGGACGAAG
Statistics
Matches: 243, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 243 1.00
ACGTcount: A:0.19, C:0.13, G:0.37, T:0.31
Consensus pattern (38 bp):
ACATGGTGTGTAGGGATGGGTGGGTTGATTTAATCCCC
Found at i:39277527 original size:31 final size:32
Alignment explanation
Indices: 39277466--39277528 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 32
39277456 AATTGAATGG
39277466 AGAGAAAATAAAATAATTGAAAACACTGAAATT
1 AGAGAAAATAAAATAATT-AAAACACTGAAATT
* * *
39277499 AGAGAAAATAAGATAGTT-AAACATTGAAAT
1 AGAGAAAATAAAATAATTAAAACACTGAAAT
39277529 GAAAATTACA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 11 0.41
33 16 0.59
ACGTcount: A:0.59, C:0.05, G:0.14, T:0.22
Consensus pattern (32 bp):
AGAGAAAATAAAATAATTAAAACACTGAAATT
Found at i:39279203 original size:31 final size:32
Alignment explanation
Indices: 39279142--39279204 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 32
39279132 AATTGAATGG
39279142 AGAGAAAATAAAATAATTGAAAACACTGAAATT
1 AGAGAAAATAAAATAATT-AAAACACTGAAATT
* * *
39279175 AGAGAAAATAAGATAGTT-AAACATTGAAAT
1 AGAGAAAATAAAATAATTAAAACACTGAAAT
39279205 GAAAATTACA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 11 0.41
33 16 0.59
ACGTcount: A:0.59, C:0.05, G:0.14, T:0.22
Consensus pattern (32 bp):
AGAGAAAATAAAATAATTAAAACACTGAAATT
Found at i:39280575 original size:17 final size:16
Alignment explanation
Indices: 39280553--39280586 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
39280543 TCCAATTACC
39280553 TATTAATTATCATATAT
1 TATTAATTAT-ATATAT
*
39280570 TATTAATTCTATATAT
1 TATTAATTATATATAT
39280586 T
1 T
39280587 TTCCTTGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (16 bp):
TATTAATTATATATAT
Found at i:39281238 original size:19 final size:18
Alignment explanation
Indices: 39281214--39281270 Score: 55
Period size: 20 Copynumber: 3.1 Consensus size: 18
39281204 AAATTTTGAT
*
39281214 AAAATTGTAAAAGTTTATA
1 AAAATTATAAAAGTTTA-A
*
39281233 AAAATTTATAAAATTTTAA
1 AAAA-TTATAAAAGTTTAA
39281252 AAAATTA-AAATA-TTTAA
1 AAAATTATAAA-AGTTTAA
39281269 AA
1 AA
39281271 TGTTTAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
17 10 0.29
18 4 0.12
19 9 0.26
20 11 0.32
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (18 bp):
AAAATTATAAAAGTTTAA
Found at i:39281280 original size:9 final size:9
Alignment explanation
Indices: 39281241--39281281 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
39281231 TAAAAATTTA
39281241 TAAAAT-TT
1 TAAAATATT
*
39281249 TAAAA-AAT
1 TAAAATATT
39281257 TAAAATATT
1 TAAAATATT
*
39281266 TAAAATGTT
1 TAAAATATT
39281275 TAAAATA
1 TAAAATA
39281282 ATAATTTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
8 11 0.41
9 16 0.59
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (9 bp):
TAAAATATT
Found at i:39285011 original size:13 final size:13
Alignment explanation
Indices: 39284993--39285017 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39284983 AGCATTAGAT
39284993 AAAAAAGAGAAGA
1 AAAAAAGAGAAGA
39285006 AAAAAAGAGAAG
1 AAAAAAGAGAAG
39285018 CTCCACTTGT
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:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AAAAAAGAGAAGA
Found at i:39288633 original size:14 final size:14
Alignment explanation
Indices: 39288614--39288667 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
39288604 CTCTTGTACC
39288614 TCTTTTTCTTTTTT
1 TCTTTTTCTTTTTT
*
39288628 TCTTTTTC--ATTT
1 TCTTTTTCTTTTTT
*
39288640 TC-CTTTCTTTTCTT
1 TCTTTTTCTTTT-TT
39288654 TCCTTTTTCTTTTT
1 T-CTTTTTCTTTTT
39288668 CCTTACCCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
11 4 0.13
12 5 0.16
13 1 0.03
14 11 0.35
15 2 0.06
16 8 0.26
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (14 bp):
TCTTTTTCTTTTTT
Found at i:39288659 original size:27 final size:25
Alignment explanation
Indices: 39288618--39288671 Score: 81
Period size: 27 Copynumber: 2.1 Consensus size: 25
39288608 TGTACCTCTT
39288618 TTTCTTTTTTTCTTTTTCATTTTCC
1 TTTCTTTTTTTCTTTTTCATTTTCC
*
39288643 TTTCTTTTCTTTCCTTTTTCTTTTTCC
1 TTTCTTTT-TTT-CTTTTTCATTTTCC
39288670 TT
1 TT
39288672 ACCCATTCCC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 8 0.31
26 3 0.12
27 15 0.58
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (25 bp):
TTTCTTTTTTTCTTTTTCATTTTCC
Found at i:39288770 original size:27 final size:27
Alignment explanation
Indices: 39288732--39288788 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
39288722 AAAATATCAT
*
39288732 TGTCGTTCGTTGTCATTCACCATTCAC
1 TGTCATTCGTTGTCATTCACCATTCAC
*
39288759 TGTCATTCGTTGTCGTTCACCATTCAC
1 TGTCATTCGTTGTCATTCACCATTCAC
39288786 TGT
1 TGT
39288789 GTTTAGCAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.14, C:0.28, G:0.16, T:0.42
Consensus pattern (27 bp):
TGTCATTCGTTGTCATTCACCATTCAC
Found at i:39289709 original size:17 final size:18
Alignment explanation
Indices: 39289687--39289721 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
39289677 AACAATTAAA
39289687 TAAATT-GGAAATAAAAT
1 TAAATTGGGAAATAAAAT
39289704 TAAATTGGGAAATAAAAT
1 TAAATTGGGAAATAAAAT
39289722 CAGATTTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.57, C:0.00, G:0.14, T:0.29
Consensus pattern (18 bp):
TAAATTGGGAAATAAAAT
Found at i:39298417 original size:43 final size:43
Alignment explanation
Indices: 39298369--39298480 Score: 170
Period size: 43 Copynumber: 2.6 Consensus size: 43
39298359 TTCCAATATT
39298369 GATTTGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGCATC
1 GATTTGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGCATC
* *
39298412 GATTTGATATTTCGTGTAAGACCATAGCTGGGCTATTGGCGTC
1 GATTTGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGCATC
** *
39298455 GATACGAGATTTCCATGTAAGACCAT
1 GATTTGAGATTT-CGTGTAAGACCAT
39298481 GTCTGGGACA
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
43 50 0.81
44 12 0.19
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (43 bp):
GATTTGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGCATC
Found at i:39300953 original size:16 final size:17
Alignment explanation
Indices: 39300921--39300953 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
39300911 TATAGAATGG
*
39300921 ATTTTGCAATTAAACAA
1 ATTTTGCAATGAAACAA
39300938 ATTTTGCAA-GAAACAA
1 ATTTTGCAATGAAACAA
39300954 GGAAATGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.30
Consensus pattern (17 bp):
ATTTTGCAATGAAACAA
Found at i:39301937 original size:4 final size:4
Alignment explanation
Indices: 39301928--39301952 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
39301918 AACTTGAGCC
39301928 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
39301953 GTACAAGCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:39303858 original size:13 final size:14
Alignment explanation
Indices: 39303840--39303868 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
39303830 TTCCTTCCCC
39303840 TTTTCT-TTTTTTT
1 TTTTCTCTTTTTTT
39303853 TTTTCTCTTTTTTT
1 TTTTCTCTTTTTTT
39303867 TT
1 TT
39303869 GGGCTTGTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (14 bp):
TTTTCTCTTTTTTT
Found at i:39306053 original size:11 final size:12
Alignment explanation
Indices: 39306010--39306056 Score: 60
Period size: 13 Copynumber: 3.8 Consensus size: 12
39306000 TGTTTTGTTA
39306010 CAAAATAAAATAT
1 CAAAATAAAA-AT
39306023 CAACAATAAAAAT
1 CAA-AATAAAAAT
39306036 ACAAAATAAAAAT
1 -CAAAATAAAAAT
39306049 C-AAATAAA
1 CAAAATAAA
39306057 CATAAATTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
11 7 0.22
12 1 0.03
13 14 0.44
14 10 0.31
ACGTcount: A:0.72, C:0.11, G:0.00, T:0.17
Consensus pattern (12 bp):
CAAAATAAAAAT
Found at i:39307654 original size:25 final size:26
Alignment explanation
Indices: 39307610--39307658 Score: 91
Period size: 25 Copynumber: 1.9 Consensus size: 26
39307600 TCTCATCTCA
39307610 ATTTTACCCTTGATAAAATTTTGATG
1 ATTTTACCCTTGATAAAATTTTGATG
39307636 ATTTTACCC-TGATAAAATTTTGA
1 ATTTTACCCTTGATAAAATTTTGA
39307659 GAAAATTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (26 bp):
ATTTTACCCTTGATAAAATTTTGATG
Found at i:39311322 original size:13 final size:13
Alignment explanation
Indices: 39311306--39311342 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
39311296 AAAAAAAACC
39311306 AAGAAAGATGAAG
1 AAGAAAGATGAAG
39311319 AAG--AG-TGAAG
1 AAGAAAGATGAAG
39311329 AAGAAAGATGAAG
1 AAGAAAGATGAAG
39311342 A
1 A
39311343 CAAAGATACG
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
10 8 0.38
11 2 0.10
12 2 0.10
13 9 0.43
ACGTcount: A:0.59, C:0.00, G:0.32, T:0.08
Consensus pattern (13 bp):
AAGAAAGATGAAG
Found at i:39311371 original size:39 final size:39
Alignment explanation
Indices: 39311325--39311412 Score: 108
Period size: 39 Copynumber: 2.3 Consensus size: 39
39311315 GAAGAAGAGT
* *
39311325 GAAGAAGAAAGAT-GAAGACAAAGATA-CGTAAAAGAAAAA
1 GAAGAAGAAAAATGGAAGA-AAAGA-AGCGAAAAAGAAAAA
*
39311364 GAAGAAGAAAAATGGAAGAAAAGAAGGGAAAAAGAAAAA
1 GAAGAAGAAAAATGGAAGAAAAGAAGCGAAAAAGAAAAA
*
39311403 GAAAAAGAAA
1 GAAGAAGAAA
39311413 TACAATAGGA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
38 1 0.02
39 37 0.86
40 5 0.12
ACGTcount: A:0.68, C:0.02, G:0.25, T:0.05
Consensus pattern (39 bp):
GAAGAAGAAAAATGGAAGAAAAGAAGCGAAAAAGAAAAA
Found at i:39317081 original size:49 final size:49
Alignment explanation
Indices: 39317024--39317171 Score: 278
Period size: 49 Copynumber: 3.0 Consensus size: 49
39317014 AGTTCAAAGG
39317024 ATCATACATTTACAAAACATCGCCAATCAACTGCTAGATTCATTTACTA
1 ATCATACATTTACAAAACATCGCCAATCAACTGCTAGATTCATTTACTA
*
39317073 ATCATACATTTACAAAACATCGCCAATCAACTACTAGATTCATTTACTA
1 ATCATACATTTACAAAACATCGCCAATCAACTGCTAGATTCATTTACTA
*
39317122 ATCATACATTTACAAAACATCGCCAATCAAATGCTAGATTCATTTACTA
1 ATCATACATTTACAAAACATCGCCAATCAACTGCTAGATTCATTTACTA
39317171 A
1 A
39317172 CCTAAAGAGA
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
49 96 1.00
ACGTcount: A:0.41, C:0.24, G:0.05, T:0.30
Consensus pattern (49 bp):
ATCATACATTTACAAAACATCGCCAATCAACTGCTAGATTCATTTACTA
Found at i:39326435 original size:18 final size:18
Alignment explanation
Indices: 39326401--39326435 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39326391 ATTTCAGAAA
* *
39326401 TATGGGCCTACATGCCCG
1 TATGGGCCCACACGCCCG
39326419 TATGGGCCCACACGCCC
1 TATGGGCCCACACGCCC
39326436 AACTTGGCCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.40, G:0.26, T:0.17
Consensus pattern (18 bp):
TATGGGCCCACACGCCCG
Found at i:39341999 original size:151 final size:152
Alignment explanation
Indices: 39341679--39341984 Score: 596
Period size: 152 Copynumber: 2.0 Consensus size: 152
39341669 GATTTGGGTA
39341679 AAAAAATTAAGAATTAAAGTGAAAAAACGGTAGAAACTAAAATAATGCATCAAAAATTGTTAAAT
1 AAAAAATTAAGAATTAAAGTGAAAAAACGGTAGAAACTAAAATAATGCATCAAAAATTGTTAAAT
39341744 TGTGCTTGTTTACCTCCTTGTCATAAGTTCTATTTTTTTTTTCAAAATTGAAATTTTAAACTTCA
66 TGTGCTTGTTTACCTCCTTGTCATAAGTTCTATTTTTTTTTTCAAAATTGAAATTTTAAACTTCA
*
39341809 AAGCATCAACCTCAATTAAATG
131 AAACATCAACCTCAATTAAATG
39341831 AAAAAATTAAGAATTAAAGTGAAAAAACGGTAGAAACTAAAATAATGCATCAAAAATTGTTAAAT
1 AAAAAATTAAGAATTAAAGTGAAAAAACGGTAGAAACTAAAATAATGCATCAAAAATTGTTAAAT
39341896 TGTGCTTGTTTACCTCCTTGTCATAAGTTCTA-TTTTTTTTTCAAAATTGAAATTTTAAACTTCA
66 TGTGCTTGTTTACCTCCTTGTCATAAGTTCTATTTTTTTTTTCAAAATTGAAATTTTAAACTTCA
39341960 AAACATCAACCTCAATTAAATG
131 AAACATCAACCTCAATTAAATG
39341982 AAA
1 AAA
39341985 GTGAATTATT
Statistics
Matches: 153, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
151 56 0.37
152 97 0.63
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.34
Consensus pattern (152 bp):
AAAAAATTAAGAATTAAAGTGAAAAAACGGTAGAAACTAAAATAATGCATCAAAAATTGTTAAAT
TGTGCTTGTTTACCTCCTTGTCATAAGTTCTATTTTTTTTTTCAAAATTGAAATTTTAAACTTCA
AAACATCAACCTCAATTAAATG
Found at i:39348718 original size:25 final size:25
Alignment explanation
Indices: 39348679--39348726 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
39348669 TTGTAGAGAG
*
39348679 AAAATTCTCTGAAGAAATTATTTCAA
1 AAAATTCTCTAAAGAAATT-TTTCAA
*
39348705 AAAATT-TCTAAAGATATTTTTC
1 AAAATTCTCTAAAGAAATTTTTC
39348727 TTATTTACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.20
25 10 0.50
26 6 0.30
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (25 bp):
AAAATTCTCTAAAGAAATTTTTCAA
Found at i:39350559 original size:36 final size:35
Alignment explanation
Indices: 39350492--39350560 Score: 86
Period size: 35 Copynumber: 1.9 Consensus size: 35
39350482 AATATAATCT
* * *
39350492 CTGTCATATGGTATGAAAACATATCTACATATTTA
1 CTGTCACATGGCATGAAAACATACCTACATATTTA
39350527 CTGTCACATGGCATGAATAACATACCCT-CATATT
1 CTGTCACATGGCATGAA-AACATA-CCTACATATT
39350561 CACTTTCATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
35 15 0.52
36 12 0.41
37 2 0.07
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (35 bp):
CTGTCACATGGCATGAAAACATACCTACATATTTA
Found at i:39353830 original size:481 final size:481
Alignment explanation
Indices: 39352928--39353879 Score: 1859
Period size: 481 Copynumber: 2.0 Consensus size: 481
39352918 TCTCATTGGA
*
39352928 CTACTGTCAAGCAAATCCTTTGCTATTTGATAGGCATTATTGATTATGGACTGGTATTCTCTTCC
1 CTACTGTCAAGCAAATCCTTTGCTATTTGATAGGAATTATTGATTATGGACTGGTATTCTCTTCC
39352993 AATACAGTGATGAACCTGACTACGTACTCTGATGTTGACTGGAAAAGTGATGCTGATGATCGAAA
66 AATACAGTGATGAACCTGACTACGTACTCTGATGTTGACTGGAAAAGTGATGCTGATGATCGAAA
*
39353058 GTCCACATTTGGCCATTGTGTTTTTCTAGGAACTAGTATTGTCTCATGAAACTCCAAGAAACAAA
131 GTCCACATTTGGCCATTATGTTTTTCTAGGAACTAGTATTGTCTCATGAAACTCCAAGAAACAAA
39353123 GGTTTATTTCTCGCTCAGCTATTGAAACAGAGTACAGAAGCCTCGTTGATACAACATTTGATATC
196 GGTTTATTTCTCGCTCAGCTATTGAAACAGAGTACAGAAGCCTCGTTGATACAACATTTGATATC
39353188 ATCTAGTTACAGTCCCTGTTATCAGACTTTCACTTCAATTTGGCTAAACCACTCAAGATCTAGTG
261 ATCTAGTTACAGTCCCTGTTATCAGACTTTCACTTCAATTTGGCTAAACCACTCAAGATCTAGTG
39353253 TGACAACTCACGCACAGTTGTTATGGCTGCTAATCATGTTCTTTATTCAAAAATCAAGCATGTGG
326 TGACAACTCACGCACAGTTGTTATGGCTGCTAATCATGTTCTTTATTCAAAAATCAAGCATGTGG
39353318 ATTTAGATCTTGATTTTGTTCGTGAAAAGGTGTTCAACAATCAATTACAAGCCGTATATGTTCCT
391 ATTTAGATCTTGATTTTGTTCGTGAAAAGGTGTTCAACAATCAATTACAAGCCGTATATGTTCCT
39353383 TCCAAGCACCAAGTTATGAACTAGTG
456 TCCAAGCACCAAGTTATGAACTAGTG
*
39353409 CTACTGTCAAGCAAATCCTTTGCTATTTGATGGGAATTATTGATTATGGACTGGTATTCTCTTCC
1 CTACTGTCAAGCAAATCCTTTGCTATTTGATAGGAATTATTGATTATGGACTGGTATTCTCTTCC
*
39353474 AATACAGTGATGAACCTGACTACGTACTCTGATGTTGACTGGAGAAGTGATGCTGATGATCGAAA
66 AATACAGTGATGAACCTGACTACGTACTCTGATGTTGACTGGAAAAGTGATGCTGATGATCGAAA
*
39353539 GTCCACATTTGGCCATTATGTTTTTTTAGGAACTAGTATTGTCTCATGAAACTCCAAGAAACAAA
131 GTCCACATTTGGCCATTATGTTTTTCTAGGAACTAGTATTGTCTCATGAAACTCCAAGAAACAAA
39353604 GGTTTATTTCTCGCTCAGCTATTGAAACAGAGTACAGAAGCCTCGTTGATACAACATTTGATATC
196 GGTTTATTTCTCGCTCAGCTATTGAAACAGAGTACAGAAGCCTCGTTGATACAACATTTGATATC
39353669 ATCTAGTTACAGTCCCTGTTATCAGACTTTCACTTCAATTTGGCTAAACCACTCAAGATCTAGTG
261 ATCTAGTTACAGTCCCTGTTATCAGACTTTCACTTCAATTTGGCTAAACCACTCAAGATCTAGTG
39353734 TGACAACTCACGCACAGTTGTTATGGCTGCTAATCATGTTCTTTATTCAAAAATCAAGCATGTGG
326 TGACAACTCACGCACAGTTGTTATGGCTGCTAATCATGTTCTTTATTCAAAAATCAAGCATGTGG
39353799 ATTTAGATCTTGATTTTGTTCGTGAAAAGGTGTTCAACAATCAATTACAAGCCGTATATGTTCCT
391 ATTTAGATCTTGATTTTGTTCGTGAAAAGGTGTTCAACAATCAATTACAAGCCGTATATGTTCCT
39353864 TCCAAGCACCAAGTTA
456 TCCAAGCACCAAGTTA
39353880 CAGATATTTT
Statistics
Matches: 466, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
481 466 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.33
Consensus pattern (481 bp):
CTACTGTCAAGCAAATCCTTTGCTATTTGATAGGAATTATTGATTATGGACTGGTATTCTCTTCC
AATACAGTGATGAACCTGACTACGTACTCTGATGTTGACTGGAAAAGTGATGCTGATGATCGAAA
GTCCACATTTGGCCATTATGTTTTTCTAGGAACTAGTATTGTCTCATGAAACTCCAAGAAACAAA
GGTTTATTTCTCGCTCAGCTATTGAAACAGAGTACAGAAGCCTCGTTGATACAACATTTGATATC
ATCTAGTTACAGTCCCTGTTATCAGACTTTCACTTCAATTTGGCTAAACCACTCAAGATCTAGTG
TGACAACTCACGCACAGTTGTTATGGCTGCTAATCATGTTCTTTATTCAAAAATCAAGCATGTGG
ATTTAGATCTTGATTTTGTTCGTGAAAAGGTGTTCAACAATCAATTACAAGCCGTATATGTTCCT
TCCAAGCACCAAGTTATGAACTAGTG
Found at i:39366127 original size:5 final size:5
Alignment explanation
Indices: 39366117--39366157 Score: 82
Period size: 5 Copynumber: 8.2 Consensus size: 5
39366107 AAATTTAATA
39366117 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT T
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT T
39366158 TACTTAATGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:39367478 original size:16 final size:16
Alignment explanation
Indices: 39367459--39367498 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
39367449 TAATATATGT
39367459 TTATATTTGTAATTTC
1 TTATATTTGTAATTTC
39367475 TTATATTTGTAATTTC
1 TTATATTTGTAATTTC
39367491 TTATATTT
1 TTATATTT
39367499 AAATATTCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.25, C:0.05, G:0.05, T:0.65
Consensus pattern (16 bp):
TTATATTTGTAATTTC
Found at i:39372044 original size:68 final size:69
Alignment explanation
Indices: 39371930--39372059 Score: 181
Period size: 68 Copynumber: 1.9 Consensus size: 69
39371920 CACTCCAATA
* * * **
39371930 TGTGGACGAAGTCACCAATATTCGTAGACAAGCTGCCATGTAGGTTGTGGACAAA-CCACCATGT
1 TGTGAACGAAGCCACCAATATTCGCAGACAAGCTGCCATGTAGGTTGCAGACAAAGCCACCATGT
39371994 AGGT
66 AGGT
* * *
39371998 TGTGAACGAAGCCACCAATATTTGCAGACAAGTTGCCATGTTGGTTGCAGACAAAGCCACCA
1 TGTGAACGAAGCCACCAATATTCGCAGACAAGCTGCCATGTAGGTTGCAGACAAAGCCACCA
39372060 ATTCTTCCTC
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
68 47 0.89
69 6 0.11
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.22
Consensus pattern (69 bp):
TGTGAACGAAGCCACCAATATTCGCAGACAAGCTGCCATGTAGGTTGCAGACAAAGCCACCATGT
AGGT
Found at i:39389623 original size:12 final size:12
Alignment explanation
Indices: 39389606--39389630 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39389596 GATCATGCTC
39389606 AAATAAGTTGAT
1 AAATAAGTTGAT
39389618 AAATAAGTTGAT
1 AAATAAGTTGAT
39389630 A
1 A
39389631 TGAGATATCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (12 bp):
AAATAAGTTGAT
Found at i:39394376 original size:32 final size:31
Alignment explanation
Indices: 39394340--39394419 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 31
39394330 CTAGCTGCTT
*
39394340 TGTTCACACTCAATGGACCATCCAACTCTTGA
1 TGTTCACACTCAA-GGACCATCCAACTCCTGA
* * *
39394372 TGTTCACA-TCCAAGGGACCGTCTAAGTCCTGA
1 TGTTCACACT-CAA-GGACCATCCAACTCCTGA
39394404 TGTTCACAC-CAAGGAC
1 TGTTCACACTCAAGGAC
39394420 TTTTCAGACG
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
30 4 0.10
31 4 0.10
32 33 0.80
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (31 bp):
TGTTCACACTCAAGGACCATCCAACTCCTGA
Found at i:39395731 original size:51 final size:51
Alignment explanation
Indices: 39395654--39395926 Score: 415
Period size: 51 Copynumber: 5.4 Consensus size: 51
39395644 CGGATCACGT
* *
39395654 TTATCACGTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
* * * *
39395705 TTATCACTTGTCACTTGTCACCGATCAAATAAGTGTAGGT-AAGCTACCAC
1 TTATCACTTGTCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
*
39395755 TTATCACTTGTCACTTATCACTGATCAGATAAGTGCAGCTAAAGCTACCAC
1 TTATCACTTGTCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
* * *
39395806 TTGTAACTTGTCACTTATCACTGATCAGATAAGTGCAGCTAAAGCTACCAC
1 TTATCACTTGTCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
* *
39395857 TTACCACTTGTCACTTATCACTGATCAGATAAGAGTAGCTAAA-CTACCAC
1 TTATCACTTGTCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
*
39395907 TTATCACTTGTCACTGATCA
1 TTATCACTTGTCACTTATCA
39395927 AAAGTACTCA
Statistics
Matches: 203, Mismatches: 18, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
50 70 0.34
51 133 0.66
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.30
Consensus pattern (51 bp):
TTATCACTTGTCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
Found at i:39395777 original size:101 final size:102
Alignment explanation
Indices: 39395654--39395926 Score: 415
Period size: 101 Copynumber: 2.7 Consensus size: 102
39395644 CGGATCACGT
* *
39395654 TTATCACGTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCAC
1 TTATCACTTGTCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCAC
* * *
39395719 TTGTCACCGATCAAATAAGTGTAGGT-AAGCTACCAC
66 TTATCACCGATCAAATAAGTGCAGCTAAAGCTACCAC
* * *
39395755 TTATCACTTGTCACTTATCACTGATCAGATAAGTGCAGCTAAAGCTACCACTTGTAACTTGTCAC
1 TTATCACTTGTCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCAC
* *
39395820 TTATCACTGATCAGATAAGTGCAGCTAAAGCTACCAC
66 TTATCACCGATCAAATAAGTGCAGCTAAAGCTACCAC
* *
39395857 TTACCACTTGTCACTTATCACTGATCAGATAAGAGTAGCTAAA-CTACCACTTATCACTTGTCAC
1 TTATCACTTGTCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCAC
*
39395921 TGATCA
66 TTATCA
39395927 AAAGTACTCA
Statistics
Matches: 155, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
101 105 0.68
102 50 0.32
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.30
Consensus pattern (102 bp):
TTATCACTTGTCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCAC
TTATCACCGATCAAATAAGTGCAGCTAAAGCTACCAC
Found at i:39396022 original size:17 final size:17
Alignment explanation
Indices: 39396000--39396032 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
39395990 TATTCTCAAT
39396000 TCATCA-ACAAATATATC
1 TCATCATAC-AATATATC
39396017 TCATCATACAATATAT
1 TCATCATACAATATAT
39396033 AATTCATGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
TCATCATACAATATATC
Found at i:39398583 original size:14 final size:16
Alignment explanation
Indices: 39398564--39398601 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
39398554 AGTTGAAGTT
*
39398564 TAAAAAAAT-TTTGA-
1 TAAAAAAATATTCGAG
39398578 TAAAAAAATATTCGAG
1 TAAAAAAATATTCGAG
39398594 TAAAAAAA
1 TAAAAAAA
39398602 ACAAACAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.43
15 4 0.19
16 8 0.38
ACGTcount: A:0.63, C:0.03, G:0.08, T:0.26
Consensus pattern (16 bp):
TAAAAAAATATTCGAG
Found at i:39406118 original size:85 final size:85
Alignment explanation
Indices: 39405989--39406167 Score: 349
Period size: 85 Copynumber: 2.1 Consensus size: 85
39405979 TTTTTTATTG
*
39405989 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCATTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
39406054 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
39406074 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
39406139 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
39406159 CCCATGCTC
1 CCCATGCTC
39406168 ATGGCCGGCC
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 93 1.00
ACGTcount: A:0.26, C:0.27, G:0.08, T:0.39
Consensus pattern (85 bp):
CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
TAGCCATAACATCTTGTCCA
Found at i:39407703 original size:32 final size:31
Alignment explanation
Indices: 39407656--39407733 Score: 111
Period size: 32 Copynumber: 2.5 Consensus size: 31
39407646 CCAGCTGATT
* *
39407656 TGTTCACACCTAAGGGACCGTCTAACTCTTGA
1 TGTTCACACC-AAGGGACCGTCGAACTCCTGA
*
39407688 TGTTCACATCCAAGGGACCGTCGAAGTCCTGA
1 TGTTCACA-CCAAGGGACCGTCGAACTCCTGA
39407720 TGTTCACACCAAGG
1 TGTTCACACCAAGG
39407734 ACTTTTTTAG
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
31 6 0.14
32 34 0.81
33 2 0.05
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (31 bp):
TGTTCACACCAAGGGACCGTCGAACTCCTGA
Found at i:39410218 original size:99 final size:99
Alignment explanation
Indices: 39410047--39410244 Score: 351
Period size: 99 Copynumber: 2.0 Consensus size: 99
39410037 TTGGAGAACC
*
39410047 ATCTAGAAAATGGATTTAGTGTAATTGTGTGTAATTACACAGTGATGCCATGTTTGGATAACCAC
1 ATCTAGAAAATGGATTTAGTGTAATTGTGTGTAATTACACAGAGATGCCATGTTTGGATAACCAC
**
39410112 TATAATTAAGGGTCCCACTGAATTAGGTGTTATT
66 TATAATTAAGGGTCCCACCAAATTAGGTGTTATT
* *
39410146 ATCTAGTAATTGGATTTAGTGTAATTGTGTGTAATTACACAGAGATGCCATGTTTGGATAACCAC
1 ATCTAGAAAATGGATTTAGTGTAATTGTGTGTAATTACACAGAGATGCCATGTTTGGATAACCAC
39410211 TATAATTAAGGGTCCCACCAAATTAGGTGTTATT
66 TATAATTAAGGGTCCCACCAAATTAGGTGTTATT
39410245 GGAGCACCCC
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
99 94 1.00
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (99 bp):
ATCTAGAAAATGGATTTAGTGTAATTGTGTGTAATTACACAGAGATGCCATGTTTGGATAACCAC
TATAATTAAGGGTCCCACCAAATTAGGTGTTATT
Found at i:39420631 original size:24 final size:24
Alignment explanation
Indices: 39420597--39420658 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
39420587 TCACAAAATT
*
39420597 CACTATCACTATCATCATAATTTA
1 CACTATTACTATCATCATAATTTA
* * *
39420621 CATTATTACTATCATCATAGTTTG
1 CACTATTACTATCATCATAATTTA
39420645 CACTATTACTATCA
1 CACTATTACTATCA
39420659 ACTTCTTCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.34, C:0.23, G:0.03, T:0.40
Consensus pattern (24 bp):
CACTATTACTATCATCATAATTTA
Found at i:39430729 original size:5 final size:5
Alignment explanation
Indices: 39430719--39430744 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
39430709 AACAATATAA
39430719 ACCCC ACCCC ACCCC ACCCC ACCCC A
1 ACCCC ACCCC ACCCC ACCCC ACCCC A
39430745 ATGCAATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.77, G:0.00, T:0.00
Consensus pattern (5 bp):
ACCCC
Found at i:39439988 original size:17 final size:18
Alignment explanation
Indices: 39439968--39440003 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
39439958 CACACTCATT
39439968 TTCTCAATGTTTTT-TTC
1 TTCTCAATGTTTTTCTTC
*
39439985 TTCTCCATGTTTTTCTTC
1 TTCTCAATGTTTTTCTTC
39440003 T
1 T
39440004 ACTGCTGCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.08, C:0.22, G:0.06, T:0.64
Consensus pattern (18 bp):
TTCTCAATGTTTTTCTTC
Found at i:39444573 original size:24 final size:25
Alignment explanation
Indices: 39444546--39444592 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
39444536 ACTGGTCATA
39444546 GAGAGAATTGAGGAG-GAATATTTG
1 GAGAGAATTGAGGAGAGAATATTTG
* *
39444570 GAGAGATTTGGGGAGAGAATATT
1 GAGAGAATTGAGGAGAGAATATT
39444593 GGGATTTTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.36, C:0.00, G:0.38, T:0.26
Consensus pattern (25 bp):
GAGAGAATTGAGGAGAGAATATTTG
Found at i:39445298 original size:27 final size:27
Alignment explanation
Indices: 39445262--39445618 Score: 390
Period size: 27 Copynumber: 13.2 Consensus size: 27
39445252 AGAGGTCCAT
* *
39445262 AAATGACCAAAATACCCCAATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * * *
39445289 AAATAACCAAAATACCCCTATAGAGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
39445316 AATTGACTGAAATACCCCCGTAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
39445343 GAATGACCGAAATACTCCTATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
**
39445370 AAATGATTGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
39445397 AAATGACTGAAATACCCCTATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
39445424 GAATGATCGAAATACCCCCATAGGATA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
39445451 GAATGACCGAAATACCCCAATAAGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
39445478 AATTGATCGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
39445505 AAATGACCGAAATAACCCTATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * * *
39445532 AAATGATCAAAATACCCCTATATGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* ** * *
39445559 GAATGACTAAAATACCCTCATAAGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
*
39445586 AAATGATCGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
39445613 AAATGA
1 AAATGA
39445619 TTGTTATACC
Statistics
Matches: 273, Mismatches: 57, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 273 1.00
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (27 bp):
AAATGACCGAAATACCCCCATAGGGTA
Found at i:39445453 original size:108 final size:105
Alignment explanation
Indices: 39445262--39445618 Score: 464
Period size: 108 Copynumber: 3.3 Consensus size: 105
39445252 AGAGGTCCAT
* * * * * *
39445262 AAATGACCAAAATACCCCAATAGGGTAAAATAACCAAAATACCCCTATAGAGTAAATTGA-CTGA
1 AAATGATCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCTATAGGGTAAA-TGATC-GA
* *
39445326 AATACCCCCGTAGGGTAGAATGACCGAAATACTCCTATAGGGTA
64 AATACCCCCATA-GGTAGAATGACCGAAATAC-CCTATAAGGTA
* *
39445370 AAATGATTGAAATACCCCCATAGGGTAAAATGACTGAAATACCCCTATAGGGTAGAATGATCGAA
1 AAATGATCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCTATAGGGTA-AATGATCGAA
*
39445435 ATACCCCCATAGGATAGAATGACCGAAATACCCCAATAAGGTA
65 ATACCCCCATAGG-TAGAATGACCGAAATA-CCCTATAAGGTA
* * *
39445478 AATTGATCGAAATACCCCCATAGGGTAAAATGACCGAAATAACCCTATAGGGTAAAATGATCAAA
1 AAATGATCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCTATAGGGT-AAATGATCGAA
* **
39445543 ATACCCCTATATGGTAGAATGACTAAAATACCCTCATAAGGTA
65 ATACCCCCATA-GGTAGAATGACCGAAATACCCT-ATAAGGTA
39445586 AAATGATCGAAATACCCCCATAGGGTAAAATGA
1 AAATGATCGAAATACCCCCATAGGGTAAAATGA
39445619 TTGTTATACC
Statistics
Matches: 221, Mismatches: 21, Indels: 14
0.86 0.08 0.05
Matches are distributed among these distances:
107 5 0.02
108 209 0.95
109 7 0.03
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (105 bp):
AAATGATCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCTATAGGGTAAATGATCGAAA
TACCCCCATAGGTAGAATGACCGAAATACCCTATAAGGTA
Found at i:39456245 original size:14 final size:14
Alignment explanation
Indices: 39456226--39456253 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
39456216 GCATGTAATT
39456226 TTGAAAATGACTTC
1 TTGAAAATGACTTC
39456240 TTGAAAATGACTTC
1 TTGAAAATGACTTC
39456254 GGCAGACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (14 bp):
TTGAAAATGACTTC
Found at i:39457242 original size:22 final size:22
Alignment explanation
Indices: 39457217--39457258 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
39457207 TTCACTTAAA
*
39457217 TTATTATTATATTAAATTTTAG
1 TTATTATTATAATAAATTTTAG
*
39457239 TTATTTTTATAATAAATTTT
1 TTATTATTATAATAAATTTT
39457259 CACAATTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
TTATTATTATAATAAATTTTAG
Found at i:39469804 original size:18 final size:18
Alignment explanation
Indices: 39469775--39469818 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
39469765 CTATTTCTTT
39469775 TCTTTCTTCAATCTTTT-TC
1 TCTTT-TTCAAT-TTTTGTC
*
39469794 TCTTTTTCAATTTTTGTT
1 TCTTTTTCAATTTTTGTC
39469812 TCTTTTT
1 TCTTTTT
39469819 TTCTTCTCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 4 0.17
18 14 0.61
19 5 0.22
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.70
Consensus pattern (18 bp):
TCTTTTTCAATTTTTGTC
Found at i:39469823 original size:26 final size:27
Alignment explanation
Indices: 39469786--39469841 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
39469776 CTTTCTTCAA
*
39469786 TCTTTTTCTCTT-TTTCAATTTTTGTT
1 TCTTTTTCTCTTCTCTCAATTTTTGTT
* *
39469812 TCTTTTTTTCTTCTCTCAATTTTTTTT
1 TCTTTTTCTCTTCTCTCAATTTTTGTT
39469839 TCT
1 TCT
39469842 CGCTTCCTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 11 0.42
27 15 0.58
ACGTcount: A:0.07, C:0.18, G:0.02, T:0.73
Consensus pattern (27 bp):
TCTTTTTCTCTTCTCTCAATTTTTGTT
Found at i:39472006 original size:9 final size:9
Alignment explanation
Indices: 39471992--39472025 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
39471982 TGATTTAAGC
39471992 AACTAAATT
1 AACTAAATT
39472001 AACTAAGATT
1 AACTAA-ATT
*
39472011 AACTTAATT
1 AACTAAATT
39472020 AACTAA
1 AACTAA
39472026 GATGAGTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.53, C:0.12, G:0.03, T:0.32
Consensus pattern (9 bp):
AACTAAATT
Found at i:39472019 original size:19 final size:19
Alignment explanation
Indices: 39471992--39472028 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
39471982 TGATTTAAGC
39471992 AACTAAATTAACTAAGATT
1 AACTAAATTAACTAAGATT
*
39472011 AACTTAATTAACTAAGAT
1 AACTAAATTAACTAAGAT
39472029 GAGTAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (19 bp):
AACTAAATTAACTAAGATT
Found at i:39472049 original size:54 final size:54
Alignment explanation
Indices: 39471984--39472107 Score: 194
Period size: 54 Copynumber: 2.3 Consensus size: 54
39471974 TAAACTAATG
* * * *
39471984 ATTTAAGCAACTAAATTAACTAAGATTAACTTAATTAACTAAGATGAGTAATTT
1 ATTTCAGCAACTAAATTAACTAAGATGAACTCAATTAACTAAAATGAGTAATTT
*
39472038 ATTTCAGCAACTTAATTAACTAAGATGAACTCAATTAACTAAAATGAGTAATTT
1 ATTTCAGCAACTAAATTAACTAAGATGAACTCAATTAACTAAAATGAGTAATTT
*
39472092 ATTCCAGCAACTAAAT
1 ATTTCAGCAACTAAAT
39472108 ACTTATTCCA
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 63 1.00
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (54 bp):
ATTTCAGCAACTAAATTAACTAAGATGAACTCAATTAACTAAAATGAGTAATTT
Found at i:39472073 original size:19 final size:19
Alignment explanation
Indices: 39472046--39472084 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
39472036 TTATTTCAGC
* *
39472046 AACTTAATTAACTAAGATG
1 AACTCAATTAACTAAAATG
39472065 AACTCAATTAACTAAAATG
1 AACTCAATTAACTAAAATG
39472084 A
1 A
39472085 GTAATTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.51, C:0.13, G:0.08, T:0.28
Consensus pattern (19 bp):
AACTCAATTAACTAAAATG
Found at i:39472212 original size:20 final size:21
Alignment explanation
Indices: 39472183--39472222 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
39472173 AGCTTGAAGA
* *
39472183 AGCTAGAATTGAGC-TCATTG
1 AGCTAAAATTAAGCTTCATTG
39472203 AGCTAAAATTAAGCTTCATT
1 AGCTAAAATTAAGCTTCATT
39472223 TTTCACTTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (21 bp):
AGCTAAAATTAAGCTTCATTG
Found at i:39474934 original size:28 final size:28
Alignment explanation
Indices: 39474893--39474997 Score: 131
Period size: 28 Copynumber: 3.8 Consensus size: 28
39474883 GTCTCATTAA
* *
39474893 ACTTACCCCGTGTTT-CTTATCTGGACAG
1 ACTTACCCCATGTTTAC-TATCTAGACAG
* *
39474921 ACTTACCCCATGTTTACTATCTCGACGG
1 ACTTACCCCATGTTTACTATCTAGACAG
* *
39474949 ACTTACCCTATGTTTACTATCTAGACAA
1 ACTTACCCCATGTTTACTATCTAGACAG
*
39474977 ACTTACCTCATGTTTACTATC
1 ACTTACCCCATGTTTACTATC
39474998 CCAGTGGACT
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
28 66 0.99
29 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.11, T:0.36
Consensus pattern (28 bp):
ACTTACCCCATGTTTACTATCTAGACAG
Found at i:39475008 original size:28 final size:29
Alignment explanation
Indices: 39474920--39475028 Score: 109
Period size: 28 Copynumber: 3.9 Consensus size: 29
39474910 TATCTGGACA
* *
39474920 GACTTACCCCATGTTTACTATCTC-GACG
1 GACTTACCTCATGTTTACTATCCCAGACG
* *
39474948 GACTTACC-CTATGTTTACTAT-CTAGACA
1 GACTTACCTC-ATGTTTACTATCCCAGACG
* *
39474976 AACTTACCTCATGTTTACTATCCCAG-TG
1 GACTTACCTCATGTTTACTATCCCAGACG
* *
39475004 GACTTACCTCGTGTTTACTGTCCCA
1 GACTTACCTCATGTTTACTATCCCA
39475029 ACAGACTATC
Statistics
Matches: 67, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
27 1 0.01
28 62 0.93
29 4 0.06
ACGTcount: A:0.23, C:0.29, G:0.13, T:0.35
Consensus pattern (29 bp):
GACTTACCTCATGTTTACTATCCCAGACG
Found at i:39475019 original size:56 final size:55
Alignment explanation
Indices: 39474893--39475022 Score: 147
Period size: 56 Copynumber: 2.3 Consensus size: 55
39474883 GTCTCATTAA
* * *
39474893 ACTTACCCCGTGTTT-CTTATCTGGACAGACTTACCCCATGTTTACTATCTCGACGG
1 ACTTA-CCCGTGTTTAC-TATCTAGACAAACTTACCCCATGTTTACTATCCCGACGG
* * *
39474949 ACTTACCCTATGTTTACTATCTAGACAAACTTACCTCATGTTTACTATCCC-AGTGG
1 ACTTACCC-GTGTTTACTATCTAGACAAACTTACCCCATGTTTACTATCCCGA-CGG
39475005 ACTTACCTCGTGTTTACT
1 ACTTACC-CGTGTTTACT
39475023 GTCCCAACAG
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
55 4 0.06
56 57 0.90
57 2 0.03
ACGTcount: A:0.22, C:0.28, G:0.13, T:0.36
Consensus pattern (55 bp):
ACTTACCCGTGTTTACTATCTAGACAAACTTACCCCATGTTTACTATCCCGACGG
Found at i:39483492 original size:25 final size:25
Alignment explanation
Indices: 39483459--39483513 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
39483449 TATTGAATGC
*
39483459 ATGA-TTGACTATCGAGCTAAGCTT
1 ATGACTTGACTATCAAGCTAAGCTT
*
39483483 ATGACTTGACTTTCAAGCTAAGCTT
1 ATGACTTGACTATCAAGCTAAGCTT
39483508 ATGACT
1 ATGACT
39483514 GTCGTATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
24 4 0.14
25 24 0.86
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (25 bp):
ATGACTTGACTATCAAGCTAAGCTT
Found at i:39487371 original size:23 final size:23
Alignment explanation
Indices: 39487344--39487391 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
39487334 AAGGTGGATA
* *
39487344 ACCAAATCTTCCACACAGACATC
1 ACCAAATATGCCACACAGACATC
* *
39487367 ACCAAATATGCCACATAGGCATC
1 ACCAAATATGCCACACAGACATC
39487390 AC
1 AC
39487392 AGGATTCGTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.35, G:0.08, T:0.17
Consensus pattern (23 bp):
ACCAAATATGCCACACAGACATC
Found at i:39496580 original size:17 final size:18
Alignment explanation
Indices: 39496552--39496601 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 18
39496542 CATCCGATAA
*
39496552 CATTTGCTATTTCAATAG
1 CATTTGCCATTTCAATAG
*
39496570 CA-TTGCCATTTCAATAT
1 CATTTGCCATTTCAATAG
*
39496587 CATTTGTCATTTCAA
1 CATTTGCCATTTCAA
39496602 AGTAATTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 15 0.54
18 13 0.46
ACGTcount: A:0.28, C:0.20, G:0.08, T:0.44
Consensus pattern (18 bp):
CATTTGCCATTTCAATAG
Found at i:39503392 original size:17 final size:17
Alignment explanation
Indices: 39503358--39503393 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
39503348 TGGTAATTCA
* *
39503358 AAAAATAATAGTATAAT
1 AAAAATAATAGAAAAAT
39503375 AAAAATAATAGAAAAAT
1 AAAAATAATAGAAAAAT
39503392 AA
1 AA
39503394 GAAAACAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (17 bp):
AAAAATAATAGAAAAAT
Found at i:39504898 original size:16 final size:16
Alignment explanation
Indices: 39504877--39504910 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
39504867 CTAGTTGACG
39504877 AAATTTTAAATTATTT
1 AAATTTTAAATTATTT
39504893 AAATTTTAAATTATTT
1 AAATTTTAAATTATTT
39504909 AA
1 AA
39504911 GTGAGCATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AAATTTTAAATTATTT
Found at i:39506323 original size:4 final size:4
Alignment explanation
Indices: 39506314--39506347 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
39506304 AAGTTTTATT
39506314 TTTA TTTA TTTA TTTA TTTA TTTTA TTTA GTTTA
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA -TTTA
39506348 AATTTTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:39506355 original size:22 final size:22
Alignment explanation
Indices: 39506297--39506356 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
39506287 AAGTGGCCCA
*
39506297 AGTTGTAAAGTTTTATTTTTATTT
1 AGTT-TAAATTTTTA-TTTTATTT
*
39506321 A-TTT-ATTTATTTATTTTATTT
1 AGTTTAAATT-TTTATTTTATTT
39506342 AGTTTAAATTTTTAT
1 AGTTTAAATTTTTAT
39506357 ATTCAGTCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 11 0.37
22 13 0.43
23 5 0.17
24 1 0.03
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (22 bp):
AGTTTAAATTTTTATTTTATTT
Found at i:39510180 original size:54 final size:54
Alignment explanation
Indices: 39510093--39510202 Score: 177
Period size: 54 Copynumber: 2.0 Consensus size: 54
39510083 GAGAGGATCA
*
39510093 AGGTAACCAAAATTAAAGCTTGGATTTGTTTGGTTAATCACTTAG-TTGTGGTTG
1 AGGTAACCAAAATTAAAGCTTGGATTTGCTTGGTTAATCACTT-GCTTGTGGTTG
* *
39510147 AGGTAATCGAAATTAAAGCTTGGATTTGCTTGGTTAATCACTTGCTTGTGGTTG
1 AGGTAACCAAAATTAAAGCTTGGATTTGCTTGGTTAATCACTTGCTTGTGGTTG
39510201 AG
1 AG
39510203 TTAGTTGTGT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
53 1 0.02
54 51 0.98
ACGTcount: A:0.26, C:0.10, G:0.25, T:0.38
Consensus pattern (54 bp):
AGGTAACCAAAATTAAAGCTTGGATTTGCTTGGTTAATCACTTGCTTGTGGTTG
Found at i:39516854 original size:22 final size:22
Alignment explanation
Indices: 39516826--39516873 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
39516816 GAAGCTCACA
39516826 CAAAGTGTGCTAAACACATGGT
1 CAAAGTGTGCTAAACACATGGT
*
39516848 CAAAGTGTGTTAAACACATGGT
1 CAAAGTGTGCTAAACACATGGT
39516870 CAAA
1 CAAA
39516874 ACCATTCCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.23
Consensus pattern (22 bp):
CAAAGTGTGCTAAACACATGGT
Found at i:39525257 original size:3 final size:3
Alignment explanation
Indices: 39525249--39525335 Score: 158
Period size: 3 Copynumber: 29.0 Consensus size: 3
39525239 CAGACCTTGA
39525249 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
39525297 ATT ATT ATT ATT ATT ATT ATT -TT GATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT
39525336 TTGAGTTCTA
Statistics
Matches: 82, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.02
3 78 0.95
4 2 0.02
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:39533026 original size:16 final size:16
Alignment explanation
Indices: 39532989--39533028 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
39532979 TTAATAAAAT
* *
39532989 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
39533005 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
39533021 TAAAATTA
1 TAAAATTA
39533029 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:39533098 original size:66 final size:59
Alignment explanation
Indices: 39533031--39533150 Score: 197
Period size: 59 Copynumber: 2.1 Consensus size: 59
39533021 TAAAATTATC
* * *
39533031 AAATTAT-TAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTA
1 AAATTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
*
39533089 AATTTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
1 AAATTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
39533148 AAA
1 AAA
39533151 CAAACTTGAT
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
58 6 0.11
59 50 0.89
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (59 bp):
AAATTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
Found at i:39533263 original size:23 final size:24
Alignment explanation
Indices: 39533216--39533261 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
39533206 AAATAAACTT
39533216 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
39533240 AAAATAAAAAA-TATATATATTT
1 AAAATAAAAAACTAT-TATATTT
39533262 AATATTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:39533864 original size:11 final size:11
Alignment explanation
Indices: 39533848--39533873 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
39533838 TGTACTTTCC
39533848 TAAAATAAATT
1 TAAAATAAATT
39533859 TAAAATAAATT
1 TAAAATAAATT
39533870 TAAA
1 TAAA
39533874 TTTAAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
TAAAATAAATT
Found at i:39534016 original size:21 final size:21
Alignment explanation
Indices: 39533985--39534037 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
39533975 TAAAAGAGAA
39533985 AAAAATA-CAAACAATATCAG
1 AAAAATATCAAACAATATCAG
39534005 AAAAATATCAAACAATATCAG
1 AAAAATATCAAACAATATCAG
39534026 AAAAATATCAAA
1 AAAAATATCAAA
39534038 AAAAAATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 7 0.22
21 25 0.78
ACGTcount: A:0.66, C:0.13, G:0.04, T:0.17
Consensus pattern (21 bp):
AAAAATATCAAACAATATCAG
Found at i:39534039 original size:10 final size:10
Alignment explanation
Indices: 39533984--39534040 Score: 71
Period size: 11 Copynumber: 5.6 Consensus size: 10
39533974 ATAAAAGAGA
39533984 AAAAAATA-C
1 AAAAAATATC
*
39533993 AAACAATATC
1 AAAAAATATC
39534003 AGAAAAATATC
1 A-AAAAATATC
*
39534014 AAACAATATC
1 AAAAAATATC
39534024 AGAAAAATATC
1 A-AAAAATATC
39534035 AAAAAA
1 AAAAAA
39534041 AAATTTAACA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
9 7 0.17
10 16 0.39
11 18 0.44
ACGTcount: A:0.68, C:0.12, G:0.04, T:0.16
Consensus pattern (10 bp):
AAAAAATATC
Found at i:39534146 original size:10 final size:10
Alignment explanation
Indices: 39534131--39534192 Score: 58
Period size: 9 Copynumber: 6.4 Consensus size: 10
39534121 ACATAAAGTT
39534131 AAAAAAATA-
1 AAAAAAATAC
39534140 AAAAAAATAC
1 AAAAAAATAC
*
39534150 AAAAGAATATC
1 AAAAAAATA-C
39534161 AAAAAAAT-C
1 AAAAAAATAC
* *
39534170 AGAAAAATAT
1 AAAAAAATAC
*
39534180 TAAAAAATA-
1 AAAAAAATAC
39534189 AAAA
1 AAAA
39534193 TCAGGAAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
9 20 0.47
10 15 0.35
11 8 0.19
ACGTcount: A:0.77, C:0.05, G:0.03, T:0.15
Consensus pattern (10 bp):
AAAAAAATAC
Found at i:39534363 original size:23 final size:22
Alignment explanation
Indices: 39534337--39534382 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
39534327 TACAAATATC
39534337 TTAACTCTCTT-TTACTATTTTTT
1 TTAA-TCTCTTCTTAC-ATTTTTT
*
39534360 TTAATTTCTTCTTACATTTTTT
1 TTAATCTCTTCTTACATTTTTT
39534382 T
1 T
39534383 CATATTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.17, C:0.15, G:0.00, T:0.67
Consensus pattern (22 bp):
TTAATCTCTTCTTACATTTTTT
Found at i:39534389 original size:23 final size:22
Alignment explanation
Indices: 39534344--39534389 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
39534334 ATCTTAACTC
*
39534344 TCTTTTACTATTTTTTTTAATT
1 TCTTTTACTATTTTTTTCAATT
39534366 TCTTCTTAC-ATTTTTTTCATATT
1 TCTT-TTACTATTTTTTTCA-ATT
39534389 T
1 T
39534390 TCTCTTTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (22 bp):
TCTTTTACTATTTTTTTCAATT
Found at i:39539029 original size:15 final size:15
Alignment explanation
Indices: 39538993--39539036 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
39538983 GAAGTTAATT
**
39538993 TATAATTTTTTGCAA
1 TATAATTTTTTTAAA
39539008 TATTAATTTTTTTAAA
1 TA-TAATTTTTTTAAA
39539024 TATAATTCTTTTT
1 TATAATT-TTTTT
39539037 TACATTTAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 7 0.28
16 18 0.72
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (15 bp):
TATAATTTTTTTAAA
Found at i:39541239 original size:30 final size:30
Alignment explanation
Indices: 39541203--39541260 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
39541193 CACGAGCTGG
* *
39541203 CACATGGGGGTGTGTCCAACCCGTGTGGCT
1 CACATGGGCGTGTGTCCAACCCATGTGGCT
*
39541233 CACATGGGCGTGTGTCCAGCCCATGTGG
1 CACATGGGCGTGTGTCCAACCCATGTGG
39541261 AAATGCCCAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.14, C:0.28, G:0.36, T:0.22
Consensus pattern (30 bp):
CACATGGGCGTGTGTCCAACCCATGTGGCT
Found at i:39541622 original size:3 final size:3
Alignment explanation
Indices: 39541614--39541638 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
39541604 GTAAGTATAT
39541614 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
39541639 GGGTAAAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:39541877 original size:3 final size:3
Alignment explanation
Indices: 39541869--39541933 Score: 98
Period size: 3 Copynumber: 22.3 Consensus size: 3
39541859 ACTGGGCAGT
*
39541869 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG- AGA AAA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
*
39541916 AGA AAA AGA AGA A-A AGA A
1 AGA AGA AGA AGA AGA AGA A
39541934 ATGAAGATGT
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
2 4 0.07
3 52 0.93
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:39546402 original size:75 final size:75
Alignment explanation
Indices: 39546274--39546423 Score: 273
Period size: 75 Copynumber: 2.0 Consensus size: 75
39546264 ACTGAGAGTA
*
39546274 AATTTTTGTGAATAGTAGGTACATGTAACATATTTGCTAGGTGAAAAATTTTACAGGAAGTAAAA
1 AATTTTTGTGAATAGTAGGTACATGTAACATATTTGCTAGGTGAAAAAGTTTACAGGAAGTAAAA
*
39546339 ATGGCCATAT
66 ATGGCAATAT
*
39546349 AATTTTTGTGAATAGTAGGTACATGTAACATATTTGCTAGGTGAAAAAGTTTACGGGAAGTAAAA
1 AATTTTTGTGAATAGTAGGTACATGTAACATATTTGCTAGGTGAAAAAGTTTACAGGAAGTAAAA
39546414 ATGGCAATAT
66 ATGGCAATAT
39546424 GGCATAAACG
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
75 72 1.00
ACGTcount: A:0.39, C:0.07, G:0.21, T:0.33
Consensus pattern (75 bp):
AATTTTTGTGAATAGTAGGTACATGTAACATATTTGCTAGGTGAAAAAGTTTACAGGAAGTAAAA
ATGGCAATAT
Found at i:39549455 original size:28 final size:28
Alignment explanation
Indices: 39549413--39549468 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
39549403 GGAAAACTTC
*
39549413 ATGTTTTCTTTTATAATATATATTTCTT
1 ATGTTTTCTTCTATAATATATATTTCTT
*
39549441 ATGTTTTCTTCTATAATATATTTTTCTT
1 ATGTTTTCTTCTATAATATATATTTCTT
39549469 TGTCTGTACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.23, C:0.09, G:0.04, T:0.64
Consensus pattern (28 bp):
ATGTTTTCTTCTATAATATATATTTCTT
Found at i:39550791 original size:46 final size:46
Alignment explanation
Indices: 39550729--39551098 Score: 245
Period size: 46 Copynumber: 8.1 Consensus size: 46
39550719 TTATTGCTGT
* * * * * *
39550729 AATTGAGGTGTATAAATATTATTAATAG-AGATGTTAAAGTGTTGGA
1 AATTGAAGTGTTTAAATGTTGTTAATTGAAG-TGTTAAAGTGTTGCA
*
39550775 AATTGAAGTGTTTAAATGTTGTAAATTGAAGTGTTAAAGTGTTGCA
1 AATTGAAGTGTTTAAATGTTGTTAATTGAAGTGTTAAAGTGTTGCA
* *
39550821 AATTGATGTATTTAAATGTTGTGT-ATTGAAGTGTTAAAGTGTTGCA
1 AATTGAAGTGTTTAAATGTTGT-TAATTGAAGTGTTAAAGTGTTGCA
* * **
39550867 AATTGAAGTGTTTAAATGTTGTAAATTGAAGTGTTTTAAGTACTGCA
1 AATTGAAGTGTTTAAATGTTGTTAATTGAAGTG-TTAAAGTGTTGCA
* ** * * * * *
39550914 AATTGAATTGTTTAGTTGCTAG-AAATTG-AGATGTT-TA-TCGCTG-T
1 AATTGAAGTGTTTAAATG-TTGTTAATTGAAG-TGTTAAAGT-GTTGCA
* * * * *
39550958 AATTGAGGTGTATAAATGTTCTTAATTG-GGATGTTAAAGTGTTGTA
1 AATTGAAGTGTTTAAATGTTGTTAATTGAAG-TGTTAAAGTGTTGCA
* * * * * * **
39551004 AGTTGAGGTGTTTAAATGTTGTAAATTGAAGTGTTTAATTGCTATA
1 AATTGAAGTGTTTAAATGTTGTTAATTGAAGTGTTAAAGTGTTGCA
* * * * * *
39551050 AATTGATGTGCTGAAATGATGTAAATTGAAGTGTTTAAA-TGCTGCA
1 AATTGAAGTGTTTAAATGTTGTTAATTGAAGTG-TTAAAGTGTTGCA
39551096 AAT
1 AAT
39551099 AATATATAAT
Statistics
Matches: 259, Mismatches: 52, Indels: 26
0.77 0.15 0.08
Matches are distributed among these distances:
43 1 0.00
44 25 0.10
45 8 0.03
46 183 0.71
47 40 0.15
48 2 0.01
ACGTcount: A:0.33, C:0.03, G:0.24, T:0.40
Consensus pattern (46 bp):
AATTGAAGTGTTTAAATGTTGTTAATTGAAGTGTTAAAGTGTTGCA
Found at i:39551098 original size:23 final size:23
Alignment explanation
Indices: 39550762--39551090 Score: 246
Period size: 23 Copynumber: 14.3 Consensus size: 23
39550752 AATAGAGATG
*
39550762 TTAAAGTGTTGGAAATTGAAGTGT
1 TTAAA-TGTTGTAAATTGAAGTGT
39550786 TTAAATGTTGTAAATTGAAGTG-
1 TTAAATGTTGTAAATTGAAGTGT
* * *
39550808 TTAAAGTGTTGCAAATTGATGTAT
1 TTAAA-TGTTGTAAATTGAAGTGT
**
39550832 TTAAATGTTGTGTATTGAAGTG-
1 TTAAATGTTGTAAATTGAAGTGT
*
39550854 TTAAAGTGTTGCAAATTGAAGTGT
1 TTAAA-TGTTGTAAATTGAAGTGT
39550878 TTAAATGTTGTAAATTGAAGTGT
1 TTAAATGTTGTAAATTGAAGTGT
* * *
39550901 TTTAA-GTACTGCAAATTGAATTGT
1 TTAAATGT--TGTAAATTGAAGTGT
** *
39550925 TTAGTTGCTAG-AAATTG-AGATGT
1 TTAAATG-TTGTAAATTGAAG-TGT
* *
39550948 TT--ATCGCTGT-AATTGAGGTGT
1 TTAAAT-GTTGTAAATTGAAGTGT
* * * *
39550969 ATAAATGTTCTTAATTG-GGATG-
1 TTAAATGTTGTAAATTGAAG-TGT
* *
39550991 TTAAAGTGTTGTAAGTTGAGGTGT
1 TTAAA-TGTTGTAAATTGAAGTGT
39551015 TTAAATGTTGTAAATTGAAGTGT
1 TTAAATGTTGTAAATTGAAGTGT
* * * * *
39551038 TTAATTGCTATAAATTGATGTGC
1 TTAAATGTTGTAAATTGAAGTGT
* *
39551061 TGAAATGATGTAAATTGAAGTGT
1 TTAAATGTTGTAAATTGAAGTGT
39551084 TTAAATG
1 TTAAATG
39551091 CTGCAAATAA
Statistics
Matches: 240, Mismatches: 46, Indels: 39
0.74 0.14 0.12
Matches are distributed among these distances:
21 11 0.05
22 24 0.10
23 165 0.69
24 38 0.16
25 1 0.00
26 1 0.00
ACGTcount: A:0.32, C:0.03, G:0.24, T:0.41
Consensus pattern (23 bp):
TTAAATGTTGTAAATTGAAGTGT
Found at i:39554070 original size:289 final size:289
Alignment explanation
Indices: 39553551--39554128 Score: 1156
Period size: 289 Copynumber: 2.0 Consensus size: 289
39553541 GTGTTATAAT
39553551 TTTATAAAGTGTTGACCTTTTGATTCATAATATTGAACTTAATTTTAATTTGTATTTTTTTCTTA
1 TTTATAAAGTGTTGACCTTTTGATTCATAATATTGAACTTAATTTTAATTTGTATTTTTTTCTTA
39553616 ATATAGTTATGTCAGGTTTTTCACAATCAAGTGTTTCTTCCCAAAATTCTCGAGGAACCAAAAGA
66 ATATAGTTATGTCAGGTTTTTCACAATCAAGTGTTTCTTCCCAAAATTCTCGAGGAACCAAAAGA
39553681 AAATGGGTTCCAGAAGAAGATGCTGCATTGGTTGCCTGTATGGTCGACTTGCACAATGTTGGAAC
131 AAATGGGTTCCAGAAGAAGATGCTGCATTGGTTGCCTGTATGGTCGACTTGCACAATGTTGGAAC
39553746 CTTTAATGTTGATACGGGATTCAAAGCCGATTATTTAAATGAATTAGAAAAAATGTTAGAAAAAG
196 CTTTAATGTTGATACGGGATTCAAAGCCGATTATTTAAATGAATTAGAAAAAATGTTAGAAAAAG
39553811 TTTTACCCAATGCCATGTTGAAGGCTAAA
261 TTTTACCCAATGCCATGTTGAAGGCTAAA
39553840 TTTATAAAGTGTTGACCTTTTGATTCATAATATTGAACTTAATTTTAATTTGTATTTTTTTCTTA
1 TTTATAAAGTGTTGACCTTTTGATTCATAATATTGAACTTAATTTTAATTTGTATTTTTTTCTTA
39553905 ATATAGTTATGTCAGGTTTTTCACAATCAAGTGTTTCTTCCCAAAATTCTCGAGGAACCAAAAGA
66 ATATAGTTATGTCAGGTTTTTCACAATCAAGTGTTTCTTCCCAAAATTCTCGAGGAACCAAAAGA
39553970 AAATGGGTTCCAGAAGAAGATGCTGCATTGGTTGCCTGTATGGTCGACTTGCACAATGTTGGAAC
131 AAATGGGTTCCAGAAGAAGATGCTGCATTGGTTGCCTGTATGGTCGACTTGCACAATGTTGGAAC
39554035 CTTTAATGTTGATACGGGATTCAAAGCCGATTATTTAAATGAATTAGAAAAAATGTTAGAAAAAG
196 CTTTAATGTTGATACGGGATTCAAAGCCGATTATTTAAATGAATTAGAAAAAATGTTAGAAAAAG
39554100 TTTTACCCAATGCCATGTTGAAGGCTAAA
261 TTTTACCCAATGCCATGTTGAAGGCTAAA
39554129 CCTAATCTTG
Statistics
Matches: 289, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
289 289 1.00
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (289 bp):
TTTATAAAGTGTTGACCTTTTGATTCATAATATTGAACTTAATTTTAATTTGTATTTTTTTCTTA
ATATAGTTATGTCAGGTTTTTCACAATCAAGTGTTTCTTCCCAAAATTCTCGAGGAACCAAAAGA
AAATGGGTTCCAGAAGAAGATGCTGCATTGGTTGCCTGTATGGTCGACTTGCACAATGTTGGAAC
CTTTAATGTTGATACGGGATTCAAAGCCGATTATTTAAATGAATTAGAAAAAATGTTAGAAAAAG
TTTTACCCAATGCCATGTTGAAGGCTAAA
Found at i:39555972 original size:58 final size:57
Alignment explanation
Indices: 39555838--39555974 Score: 179
Period size: 58 Copynumber: 2.4 Consensus size: 57
39555828 TTAATTCATA
**
39555838 TAATAATAATTATATTAAGAA-ATTTATTAAATTATATATTATTTTATTAAATTATATT
1 TAATAATAATTATATTAA-AATA-TGGTTAAATTATATATTATTTTATTAAATTATATT
* * *
39555896 TAATAATAATTATGTTAAAATATGGTTAAATTATTTATTATTTTTATTAAATTATTTT
1 TAATAATAATTATATTAAAATATGGTTAAATTATATATTA-TTTTATTAAATTATATT
39555954 TAATAATAATCT-TATTAAAAT
1 TAATAATAAT-TATATTAAAAT
39555975 TTAATAACAA
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
57 17 0.24
58 52 0.74
59 1 0.01
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.52
Consensus pattern (57 bp):
TAATAATAATTATATTAAAATATGGTTAAATTATATATTATTTTATTAAATTATATT
Found at i:39575822 original size:42 final size:42
Alignment explanation
Indices: 39575767--39576017 Score: 321
Period size: 42 Copynumber: 6.0 Consensus size: 42
39575757 CGCTTACAGA
*
39575767 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTATG
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGG
* * *
39575809 AAAAAATGCCGCTACAGATCATGTTATTTAGCGGCGCTTAGG
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGG
*
39575851 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTGGG
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGG
*
39575893 AAAAAACGCCGCTAAAGATCTTGTTCTTTAGCGGCGCTTAGG
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGG
* * *
39575935 AAGAAAATGCCGCTAAA-AGTAATGTTCTATAGCGGCGCTT-GG
1 AA-AAAACGCCGCTAAAGA-TCATGTTCTTTAGCGGCGCTTAGG
* * *
39575977 TCAAAAATGCTGCTAACAG-T-AGTGTTCTTTAGCGGCGCTTA
1 -AAAAAACGCCGCTAA-AGATCA-TGTTCTTTAGCGGCGCTTA
39576018 TTTCACAAAC
Statistics
Matches: 185, Mismatches: 17, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
41 1 0.01
42 151 0.82
43 33 0.18
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (42 bp):
AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGG
Found at i:39581237 original size:9 final size:9
Alignment explanation
Indices: 39581225--39581358 Score: 72
Period size: 9 Copynumber: 15.9 Consensus size: 9
39581215 GTATGTATTA
*
39581225 TTATGTAAC
1 TTATGTAAG
* *
39581234 TTATTTAAT
1 TTATGTAAG
*
39581243 TTATGTAGG
1 TTATGTAAG
*
39581252 GTATGTAAG
1 TTATGTAAG
39581261 TTATGTAAG
1 TTATGTAAG
*
39581270 TTGTGT-A-
1 TTATGTAAG
*
39581277 TTATTTACA-
1 TTATGTA-AG
*
39581286 -CATGTAAG
1 TTATGTAAG
*
39581294 TTGTGT-A-
1 TTATGTAAG
39581301 TTATGTAAG
1 TTATGTAAG
*
39581310 TTATGCAAG
1 TTATGTAAG
39581319 TTATGT-A-
1 TTATGTAAG
* *
39581326 TTAAGTAGG
1 TTATGTAAG
39581335 TTATGTAAG
1 TTATGTAAG
*
39581344 TTACGT-A-
1 TTATGTAAG
39581351 TTATGTAA
1 TTATGTAA
39581359 ATTAATATAT
Statistics
Matches: 92, Mismatches: 24, Indels: 19
0.68 0.18 0.14
Matches are distributed among these distances:
7 20 0.22
8 10 0.11
9 62 0.67
ACGTcount: A:0.31, C:0.04, G:0.20, T:0.46
Consensus pattern (9 bp):
TTATGTAAG
Found at i:39581264 original size:18 final size:17
Alignment explanation
Indices: 39581206--39581267 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 17
39581196 NNNNNNNNNN
39581206 TTATGTAGGGTATGTATTA
1 TTATGTAGGGTATGTA--A
*** *
39581225 TTATGTAACTTATTTAA
1 TTATGTAGGGTATGTAA
39581242 TTTATGTAGGGTATGTAA
1 -TTATGTAGGGTATGTAA
39581260 GTTATGTA
1 -TTATGTA
39581268 AGTTGTGTAT
Statistics
Matches: 33, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
17 1 0.03
18 20 0.61
19 12 0.36
ACGTcount: A:0.29, C:0.02, G:0.21, T:0.48
Consensus pattern (17 bp):
TTATGTAGGGTATGTAA
Found at i:39581337 original size:25 final size:25
Alignment explanation
Indices: 39581291--39581358 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 25
39581281 TTACACATGT
* *
39581291 AAGTTGTGTATTATGTAAGTTATGC
1 AAGTTATGTATTAAGTAAGTTATGC
* *
39581316 AAGTTATGTATTAAGTAGGTTATGT
1 AAGTTATGTATTAAGTAAGTTATGC
* *
39581341 AAGTTACGTATTATGTAA
1 AAGTTATGTATTAAGTAA
39581359 ATTAATATAT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.32, C:0.03, G:0.22, T:0.43
Consensus pattern (25 bp):
AAGTTATGTATTAAGTAAGTTATGC
Found at i:39581354 original size:16 final size:17
Alignment explanation
Indices: 39581243--39581358 Score: 64
Period size: 16 Copynumber: 6.9 Consensus size: 17
39581233 CTTATTTAAT
*
39581243 TTATGTAGGGTATGTAAG
1 TTATGTA-GTTATGTAAG
*
39581261 TTATGTAAGTTGTGT-A-
1 TTATGT-AGTTATGTAAG
* ***
39581277 TTATTTACACATGTAAG
1 TTATGTAGTTATGTAAG
*
39581294 TTGTGTA-TTATGTAAG
1 TTATGTAGTTATGTAAG
*
39581310 TTATGCAAGTTATGT-A-
1 TTATG-TAGTTATGTAAG
*
39581326 TTAAGTAGGTTATGTAAG
1 TTATGTA-GTTATGTAAG
*
39581344 TTACGTA-TTATGTAA
1 TTATGTAGTTATGTAA
39581359 ATTAATATAT
Statistics
Matches: 74, Mismatches: 16, Indels: 18
0.69 0.15 0.17
Matches are distributed among these distances:
15 5 0.07
16 36 0.49
17 9 0.12
18 23 0.31
19 1 0.01
ACGTcount: A:0.30, C:0.03, G:0.22, T:0.44
Consensus pattern (17 bp):
TTATGTAGTTATGTAAG
Found at i:39586120 original size:41 final size:40
Alignment explanation
Indices: 39586010--39586230 Score: 144
Period size: 41 Copynumber: 5.4 Consensus size: 40
39586000 TAGATTTTAT
* * * *
39586010 TATTAGCGGCGCTTTTTGGAAAAGCGCCGCTAAAAGA-ACGAA
1 TATTAGCGGCGC-TTTT-AAAAAACGCCGCTAAATGACAC-AG
* * * * *
39586052 CAATAGTGGCGTTTTTAAACAAGCGCCGCTAAATGACACAG
1 TATTAGCGGCGCTTTTAAA-AAACGCCGCTAAATGACACAG
* *
39586093 TATTACCGGCGCTTTTCCAAAAACGCCGCT-AATGAC-CAG
1 TATTAGCGGCGCTTTT-AAAAAACGCCGCTAAATGACACAG
* * * *
39586132 ATCATTAGTGGCGCTTATTAAAAAACGCCGCTAAAGGCCAGAG
1 -T-ATTAGCGGCGCTT-TTAAAAAACGCCGCTAAATGACACAG
* * * *
39586175 CATTAGCGGCGCTTATAAGAAAACGCCGCTAAA-GGCTAGAG
1 TATTAGCGGCGCTTTTAA-AAAACGCCGCTAAATGAC-ACAG
*
39586216 CATTAGCGGCGCTTT
1 TATTAGCGGCGCTTT
39586231 ACGAAAACAT
Statistics
Matches: 144, Mismatches: 25, Indels: 21
0.76 0.13 0.11
Matches are distributed among these distances:
39 3 0.02
40 14 0.10
41 107 0.74
42 18 0.12
43 2 0.01
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.22
Consensus pattern (40 bp):
TATTAGCGGCGCTTTTAAAAAACGCCGCTAAATGACACAG
Found at i:39586161 original size:82 final size:83
Alignment explanation
Indices: 39586028--39586229 Score: 196
Period size: 82 Copynumber: 2.4 Consensus size: 83
39586018 GCGCTTTTTG
* * * * * *
39586028 GAAAAGCGCCGCTAAAAGAAC-GAACAATAGTGGCG-TTTTTAAACAAGCGCCGCTAAATGACAC
1 GAAAA-CGCCGCT-AAAGACCAGAGCATTAGTGGCGCTTATTAAACAAACGCCGCTAAAGGACAC
* * *
39586091 AGTATTACCGGCGCTTTTCCA
64 AGCATTACCGGCGCTTAT-AA
* * * *
39586112 -AAAACGCCGCTAATGACCAGATCATTAGTGGCGCTTATTAAA-AAACGCCGCTAAAGGCCAGAG
1 GAAAACGCCGCTAAAGACCAGAGCATTAGTGGCGCTTATTAAACAAACGCCGCTAAAGGACACAG
*
39586175 CATTAGCGGCGCTTATAA
66 CATTACCGGCGCTTATAA
* * *
39586193 GAAAACGCCGCTAAAGGCTAGAGCATTAGCGGCGCTT
1 GAAAACGCCGCTAAAGACCAGAGCATTAGTGGCGCTT
39586230 TACGAAAACA
Statistics
Matches: 97, Mismatches: 18, Indels: 8
0.79 0.15 0.07
Matches are distributed among these distances:
81 6 0.06
82 80 0.82
83 11 0.11
ACGTcount: A:0.34, C:0.24, G:0.23, T:0.19
Consensus pattern (83 bp):
GAAAACGCCGCTAAAGACCAGAGCATTAGTGGCGCTTATTAAACAAACGCCGCTAAAGGACACAG
CATTACCGGCGCTTATAA
Found at i:39586745 original size:40 final size:40
Alignment explanation
Indices: 39586690--39586784 Score: 120
Period size: 40 Copynumber: 2.4 Consensus size: 40
39586680 GCTTTTCCAA
39586690 AAAACGCCGCTAAAGGCCAGAACATTAGCAGCGCTTATAAG
1 AAAACGCCGCTAAAGGCCAGAACATTAGCAGCGCTT-TAAG
* * * *
39586731 AAAA-GCCGCTAAAGGCTAGAGCATTAGCGGCGCTTTACG
1 AAAACGCCGCTAAAGGCCAGAACATTAGCAGCGCTTTAAG
*
39586770 AAAATCGCCACTAAA
1 AAAA-CGCCGCTAAA
39586785 AGTACTGAGA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
39 7 0.15
40 28 0.60
41 12 0.26
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (40 bp):
AAAACGCCGCTAAAGGCCAGAACATTAGCAGCGCTTTAAG
Found at i:39592595 original size:17 final size:17
Alignment explanation
Indices: 39592564--39592616 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 17
39592554 GGACCCATAT
39592564 GCCCATGTGGGCCCACAC
1 GCCCATGT-GGCCCACAC
*
39592582 GCCCGTGTGGCCCACAC
1 GCCCATGTGGCCCACAC
*
39592599 GCCCATTTGGCCCACAC
1 GCCCATGTGGCCCACAC
39592616 G
1 G
39592617 ACCTGGCCCA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
17 25 0.78
18 7 0.22
ACGTcount: A:0.15, C:0.45, G:0.26, T:0.13
Consensus pattern (17 bp):
GCCCATGTGGCCCACAC
Found at i:39596349 original size:39 final size:39
Alignment explanation
Indices: 39596274--39596349 Score: 89
Period size: 39 Copynumber: 1.9 Consensus size: 39
39596264 CATATTGCAT
* * *
39596274 ATATAATCACCTAACATACAAGCATTTATCACAATACCC
1 ATATAATCACATAACATACAAACATATATCACAATACCC
** * *
39596313 ATATAATCACATAACATTTAAACATATGTCAGAATAC
1 ATATAATCACATAACATACAAACATATATCACAATAC
39596350 TCGAAAACAT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
39 30 1.00
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.28
Consensus pattern (39 bp):
ATATAATCACATAACATACAAACATATATCACAATACCC
Found at i:39596518 original size:66 final size:67
Alignment explanation
Indices: 39596405--39596556 Score: 207
Period size: 66 Copynumber: 2.3 Consensus size: 67
39596395 ATAAACACAT
* * * * * * *
39596405 ATCACAATACACATATGTTCATAATTTAGGATAATTTGCATAACAACCACATACTTATTTGGGCA
1 ATCACATTACACATATATACAT-ATTTAAGATAATTTGCATAACAACCACATACTCATTTAGACA
39596470 TAC
65 TAC
*
39596473 ATCACATTACACATATATACAT-TTTAAGATAATTTGCATAGCAACCACATACTCATTTAGACAT
1 ATCACATTACACATATATACATATTTAAGATAATTTGCATAACAACCACATACTCATTTAGACAT
*
39596537 TC
66 AC
39596539 ATCACATTACACATATAT
1 ATCACATTACACATATAT
39596557 CACAATACAC
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
66 56 0.75
68 19 0.25
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.33
Consensus pattern (67 bp):
ATCACATTACACATATATACATATTTAAGATAATTTGCATAACAACCACATACTCATTTAGACAT
AC
Found at i:39604055 original size:85 final size:86
Alignment explanation
Indices: 39603909--39604123 Score: 263
Period size: 85 Copynumber: 2.5 Consensus size: 86
39603899 AGTGTATTGT
* * * *
39603909 GGTAAACTGCTGTACAAACAGGTTGTAGTTTAAACTGCCAGATCAAAAATAGTACATAGCAAAGC
1 GGTAAACTGCTGTACAAATAAGTTGTAG-TTAAACTGCCAGATCAAAAATAATACACAGCAAAGC
*
39603974 TGACGTACATGT-G-AAAGTAC
65 TGACGTACAAGTGGTAAAGTAC
* *
39603994 GGTAAACTGCTGTACAAATAAGTTGTAGTTAAACTGCCAGATCAGATAATAATACGCAGCAAAGC
1 GGTAAACTGCTGTACAAATAAGTTGTAGTTAAACTGCCAGATCA-AAAATAATACACAGCAAAGC
* *
39604059 TGATGTACAAGTGGTATAGTAC
65 TGACGTACAAGTGGTAAAGTAC
** ** **
39604081 GGTAAACCACTGTACTGATAAGTTACAGTTAAACTGCCAGATC
1 GGTAAACTGCTGTACAAATAAGTTGTAGTTAAACTGCCAGATC
39604124 TGATCAGAAT
Statistics
Matches: 112, Mismatches: 15, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
84 16 0.14
85 52 0.46
86 1 0.01
87 43 0.38
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.25
Consensus pattern (86 bp):
GGTAAACTGCTGTACAAATAAGTTGTAGTTAAACTGCCAGATCAAAAATAATACACAGCAAAGCT
GACGTACAAGTGGTAAAGTAC
Found at i:39605349 original size:6 final size:6
Alignment explanation
Indices: 39605338--39605373 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
39605328 AGAATGAGCC
39605338 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
39605374 GATTAAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:39605893 original size:23 final size:23
Alignment explanation
Indices: 39605867--39605914 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
39605857 CATATAAACA
*
39605867 AACATGTTCATGAATGTTAAATG
1 AACATGTTCATGAATGCTAAATG
*
39605890 AACATGTTCGTGAATGCTAAATG
1 AACATGTTCATGAATGCTAAATG
39605913 AA
1 AA
39605915 TCGAGCCCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (23 bp):
AACATGTTCATGAATGCTAAATG
Found at i:39609268 original size:50 final size:51
Alignment explanation
Indices: 39609173--39609268 Score: 124
Period size: 50 Copynumber: 1.9 Consensus size: 51
39609163 AAAGGAAAGG
*
39609173 AATGGTAAGTGTTCAAAATGAACTATGTCATGTATTTATGAAAATGATTGA
1 AATGGTAAGTGTTCAAAATGAACTATGTCATATATTTATGAAAATGATTGA
* * * *
39609224 AATGGTAAGT-TTCCAAATGAAAGTATGT-TTATATTTATGGAAATG
1 AATGGTAAGTGTTCAAAATG-AACTATGTCATATATTTATGAAAATG
39609269 TGAATGACTC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
50 22 0.56
51 17 0.44
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.36
Consensus pattern (51 bp):
AATGGTAAGTGTTCAAAATGAACTATGTCATATATTTATGAAAATGATTGA
Found at i:39627261 original size:27 final size:27
Alignment explanation
Indices: 39627218--39627411 Score: 151
Period size: 27 Copynumber: 7.2 Consensus size: 27
39627208 AAAAGGTTGT
* *
39627218 TAAAATGATCG-ATTACCCCCGAAGGG
1 TAAAATTATCGAAATACCCCCGAAGGG
* * *
39627244 TAAAGTTA-CTGATATACCTCCGAAGGG
1 TAAAATTATC-GAAATACCCCCGAAGGG
* * *
39627271 TAAAATTATCGAAATACCCCCAAATGA
1 TAAAATTATCGAAATACCCCCGAAGGG
* * * * *
39627298 TAAAATTACCAAAATACTCTCGAAGGA
1 TAAAATTATCGAAATACCCCCGAAGGG
* * *
39627325 TAAAATTATCAAAATA-TCCCAAAGGG
1 TAAAATTATCGAAATACCCCCGAAGGG
* ***
39627351 TAAAATTACCGAAATACCCTTAAAGGG
1 TAAAATTATCGAAATACCCCCGAAGGG
* *
39627378 TAAAAATTACCGAAATACCCTCGAAGGG
1 T-AAAATTATCGAAATACCCCCGAAGGG
39627406 TAAAAT
1 TAAAAT
39627412 GACTGTTATG
Statistics
Matches: 135, Mismatches: 28, Indels: 9
0.78 0.16 0.05
Matches are distributed among these distances:
25 1 0.01
26 28 0.21
27 80 0.59
28 26 0.19
ACGTcount: A:0.44, C:0.19, G:0.15, T:0.22
Consensus pattern (27 bp):
TAAAATTATCGAAATACCCCCGAAGGG
Found at i:39627390 original size:28 final size:27
Alignment explanation
Indices: 39627239--39627411 Score: 161
Period size: 27 Copynumber: 6.4 Consensus size: 27
39627229 ATTACCCCCG
* * * *
39627239 AAGGGTAAAGTTACTGATATA-CCTCCG
1 AAGGGTAAAATTACCGAAATACCCT-CA
* *
39627266 AAGGGTAAAATTATCGAAATACCCCCA
1 AAGGGTAAAATTACCGAAATACCCTCA
* * * * *
39627293 AATGATAAAATTACCAAAATACTCTCG
1 AAGGGTAAAATTACCGAAATACCCTCA
* * * *
39627320 AAGGATAAAATTATCAAAATATCC-CA
1 AAGGGTAAAATTACCGAAATACCCTCA
*
39627346 AAGGGTAAAATTACCGAAATACCCTTA
1 AAGGGTAAAATTACCGAAATACCCTCA
*
39627373 AAGGGTAAAAATTACCGAAATACCCTCG
1 AAGGGT-AAAATTACCGAAATACCCTCA
39627401 AAGGGTAAAAT
1 AAGGGTAAAAT
39627412 GACTGTTATG
Statistics
Matches: 118, Mismatches: 25, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
26 21 0.18
27 70 0.59
28 27 0.23
ACGTcount: A:0.45, C:0.18, G:0.15, T:0.22
Consensus pattern (27 bp):
AAGGGTAAAATTACCGAAATACCCTCA
Found at i:39628104 original size:17 final size:17
Alignment explanation
Indices: 39628082--39628122 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
39628072 CGTTAGACGG
39628082 TTCGGAGCTGCGTGGGA
1 TTCGGAGCTGCGTGGGA
39628099 TTCGGAGCTGCGTGGGA
1 TTCGGAGCTGCGTGGGA
*
39628116 CTCGGAG
1 TTCGGAG
39628123 AGGGCCACAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.12, C:0.20, G:0.46, T:0.22
Consensus pattern (17 bp):
TTCGGAGCTGCGTGGGA
Found at i:39632518 original size:19 final size:20
Alignment explanation
Indices: 39632470--39632519 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
39632460 AGCTAAACAC
39632470 AACTAAAATCAATAATAAAATA
1 AACTAAAA--AATAATAAAATA
*
39632492 AA-TGAAAAATAATAAAA-A
1 AACTAAAAAATAATAAAATA
39632510 AACTAAAAAA
1 AACTAAAAAA
39632520 GTGCAAAGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 3 0.12
19 16 0.64
21 4 0.16
22 2 0.08
ACGTcount: A:0.74, C:0.06, G:0.02, T:0.18
Consensus pattern (20 bp):
AACTAAAAAATAATAAAATA
Found at i:39637647 original size:27 final size:27
Alignment explanation
Indices: 39637591--39637648 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
39637581 AGAGCATATG
* *
39637591 TGGGTCAAAACCCACTACAAAATTATT
1 TGGGTCAAAACCCACTACAAAATCAAT
*
39637618 TGGGTCACAACCCA-TAACAAAATCAAT
1 TGGGTCAAAACCCACT-ACAAAATCAAT
39637645 TGGG
1 TGGG
39637649 CCTAGCCCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 1 0.04
27 26 0.96
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (27 bp):
TGGGTCAAAACCCACTACAAAATCAAT
Found at i:39638267 original size:27 final size:27
Alignment explanation
Indices: 39638237--39638324 Score: 83
Period size: 27 Copynumber: 3.3 Consensus size: 27
39638227 GGGATTTCGA
39638237 TAATTTTTCAAACTGAGGGTATTTTAG
1 TAATTTTTCAAACTGAGGGTATTTTAG
*
39638264 TAATTTTGT-AAACT-AGGGGTACTTTAG
1 TAATTTT-TCAAACTGA-GGGTATTTTAG
* * * *
39638291 TAATTTTAC-AAGTCGAGGGTATTTCAA
1 TAATTTTTCAAACT-GAGGGTATTTTAG
39638318 TAATTTT
1 TAATTTT
39638325 AGAAATCAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
26 4 0.08
27 44 0.88
28 2 0.04
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.43
Consensus pattern (27 bp):
TAATTTTTCAAACTGAGGGTATTTTAG
Found at i:39639992 original size:3 final size:3
Alignment explanation
Indices: 39639984--39640021 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
39639974 GTTAAAATCT
* *
39639984 TTA TTA TTA TTG TTG TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
39640022 TCAATTTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:39642912 original size:27 final size:27
Alignment explanation
Indices: 39642882--39642960 Score: 99
Period size: 27 Copynumber: 2.9 Consensus size: 27
39642872 GCTGACCGAT
*
39642882 TTACCCCCACAAGGTAACATGACTGAA
1 TTACCCCCACAAGGTAAAATGACTGAA
*
39642909 TTACCCCCAC-AGGATAAAATGAAC-AAA
1 TTACCCCCACAAGG-TAAAATG-ACTGAA
*
39642936 TTACCCCCACAGGGTAAAATGACTG
1 TTACCCCCACAAGGTAAAATGACTG
39642961 TTATACCCCT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
26 5 0.11
27 35 0.80
28 4 0.09
ACGTcount: A:0.39, C:0.28, G:0.15, T:0.18
Consensus pattern (27 bp):
TTACCCCCACAAGGTAAAATGACTGAA
Done.