Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 84 of 208
Found at i:29428173 original size:20 final size:20
Alignment explanation
Indices: 29428144--29428197 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
29428134 CGTATATCCT
* *
29428144 AATTTTATTTGATTCTAATC
1 AATTTCATTTAATTCTAATC
*
29428164 AATTTCATTTAATTTTAATC
1 AATTTCATTTAATTCTAATC
29428184 AAATTT-ATTTAATT
1 -AATTTCATTTAATT
29428198 GCTCCTTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 25 0.83
21 5 0.17
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.56
Consensus pattern (20 bp):
AATTTCATTTAATTCTAATC
Found at i:29428627 original size:18 final size:18
Alignment explanation
Indices: 29428600--29428637 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
29428590 TTTAATTTAA
29428600 TTTATATATAAATATTTG
1 TTTATATATAAATATTTG
* *
29428618 TTTATTTATATATATTTG
1 TTTATATATAAATATTTG
29428636 TT
1 TT
29428638 CGCTAATGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (18 bp):
TTTATATATAAATATTTG
Found at i:29436694 original size:5 final size:5
Alignment explanation
Indices: 29436684--29436742 Score: 59
Period size: 5 Copynumber: 11.8 Consensus size: 5
29436674 TATTAACATG
* * *
29436684 AAAAT AAAAT AAAAT AAAAT AAAGT AATAT ATAAT AAAAT AATAA- ATAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA-AAT A-AAAT
29436735 -AAAT AAAA
1 AAAAT AAAA
29436743 ATTGGGTTAC
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
4 4 0.09
5 37 0.84
6 3 0.07
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.24
Consensus pattern (5 bp):
AAAAT
Found at i:29443259 original size:17 final size:17
Alignment explanation
Indices: 29443237--29443270 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
29443227 TAAGTTCACG
*
29443237 CTTTTTGCCTCCAATTT
1 CTTTTTACCTCCAATTT
*
29443254 CTTTTTACCTTCAATTT
1 CTTTTTACCTCCAATTT
29443271 AGTCCCTACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.26, G:0.03, T:0.56
Consensus pattern (17 bp):
CTTTTTACCTCCAATTT
Found at i:29449426 original size:21 final size:21
Alignment explanation
Indices: 29449382--29449426 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
29449372 TTTATTTATC
* *
29449382 TTTTGGGTTTTAAGTTTTAAA
1 TTTTGGGTTTCAAGTTTCAAA
*
29449403 TTTTGGGTTTCAAGTTTCAGA
1 TTTTGGGTTTCAAGTTTCAAA
29449424 TTT
1 TTT
29449427 GATGTTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.04, G:0.20, T:0.56
Consensus pattern (21 bp):
TTTTGGGTTTCAAGTTTCAAA
Found at i:29450159 original size:17 final size:18
Alignment explanation
Indices: 29450133--29450171 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
29450123 ACCATTGTGG
29450133 AAAA-TGTTCTC-AATAT
1 AAAATTGTTCTCTAATAT
*
29450149 AAAATTGTTCTCTCATAT
1 AAAATTGTTCTCTAATAT
29450167 AAAAT
1 AAAAT
29450172 CAAAAGCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 7 0.35
18 9 0.45
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.38
Consensus pattern (18 bp):
AAAATTGTTCTCTAATAT
Found at i:29450348 original size:15 final size:15
Alignment explanation
Indices: 29450328--29450358 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
29450318 AAAACAATAT
29450328 AACTCTTGACCTTTC
1 AACTCTTGACCTTTC
29450343 AACTCTTGACCTTTC
1 AACTCTTGACCTTTC
29450358 A
1 A
29450359 CTTACATGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.32, G:0.06, T:0.39
Consensus pattern (15 bp):
AACTCTTGACCTTTC
Found at i:29453730 original size:15 final size:15
Alignment explanation
Indices: 29453720--29453749 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29453710 TCCCTTCTTG
29453720 ACCACGACCTTTTCC
1 ACCACGACCTTTTCC
*
29453735 ACCACGACCATTTCC
1 ACCACGACCTTTTCC
29453750 TCGATCTCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.47, G:0.07, T:0.23
Consensus pattern (15 bp):
ACCACGACCTTTTCC
Found at i:29454517 original size:17 final size:18
Alignment explanation
Indices: 29454491--29454529 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
29454481 CAAATTGTGG
29454491 AAAA-TGTTCTC-AATAT
1 AAAATTGTTCTCTAATAT
*
29454507 AAAATTGTTCTCTCATAT
1 AAAATTGTTCTCTAATAT
29454525 AAAAT
1 AAAAT
29454530 CAAAAGCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 7 0.35
18 9 0.45
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.38
Consensus pattern (18 bp):
AAAATTGTTCTCTAATAT
Found at i:29454706 original size:15 final size:15
Alignment explanation
Indices: 29454686--29454716 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
29454676 AAAACAATAT
29454686 AACTCTTGACCTTTC
1 AACTCTTGACCTTTC
29454701 AACTCTTGACCTTTC
1 AACTCTTGACCTTTC
29454716 A
1 A
29454717 CTTACATGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.32, G:0.06, T:0.39
Consensus pattern (15 bp):
AACTCTTGACCTTTC
Found at i:29464286 original size:33 final size:33
Alignment explanation
Indices: 29464246--29464314 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
29464236 GAAACACCAT
29464246 CACCACCCACAAATACTGAACCACAT-ATTGAAC
1 CACCACCCACAAATACTGAACCACATGA-TGAAC
29464279 CACCACCCACAAATACTGAACCACATGATGAAC
1 CACCACCCACAAATACTGAACCACATGATGAAC
29464312 CAC
1 CAC
29464315 ATATTGAACC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
33 34 0.97
34 1 0.03
ACGTcount: A:0.42, C:0.38, G:0.07, T:0.13
Consensus pattern (33 bp):
CACCACCCACAAATACTGAACCACATGATGAAC
Found at i:29471304 original size:15 final size:15
Alignment explanation
Indices: 29471284--29471315 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
29471274 ATAAACTAGA
*
29471284 TTCAACATTTAATTT
1 TTCAACACTTAATTT
29471299 TTCAACACTTAATTT
1 TTCAACACTTAATTT
29471314 TT
1 TT
29471316 TAGTTTATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.16, G:0.00, T:0.53
Consensus pattern (15 bp):
TTCAACACTTAATTT
Found at i:29471478 original size:14 final size:14
Alignment explanation
Indices: 29471459--29471497 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
29471449 TTGTTTTACT
*
29471459 GAAAATGGCTTCCG
1 GAAAATGACTTCCG
* *
29471473 GAAAATGATTTCTG
1 GAAAATGACTTCCG
29471487 GAAAATGACTT
1 GAAAATGACTT
29471498 ACTTTTCTGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (14 bp):
GAAAATGACTTCCG
Found at i:29472100 original size:18 final size:18
Alignment explanation
Indices: 29472062--29472097 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
29472052 TTATTATTTT
*
29472062 TAAAATTTACTATTAAAA
1 TAAAATTTAATATTAAAA
29472080 TAAAATTTAAATATTAAA
1 TAAAATTT-AATATTAAA
29472098 TAATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:29476721 original size:27 final size:27
Alignment explanation
Indices: 29476691--29476795 Score: 129
Period size: 27 Copynumber: 3.9 Consensus size: 27
29476681 GACTACTCCA
*
29476691 TGTTCAATGTCCCATCAGACTATCCTG
1 TGTTTAATGTCCCATCAGACTATCCTG
** * *
29476718 TGTTTAACATCCCGTCGGACTATCCTG
1 TGTTTAATGTCCCATCAGACTATCCTG
* **
29476745 TGTTAAATGTCCCATCAGACTATCCCA
1 TGTTTAATGTCCCATCAGACTATCCTG
*
29476772 TGTTTAATGTCCCATCACACTATC
1 TGTTTAATGTCCCATCAGACTATC
29476796 TTCGATGTCA
Statistics
Matches: 64, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 64 1.00
ACGTcount: A:0.24, C:0.30, G:0.13, T:0.33
Consensus pattern (27 bp):
TGTTTAATGTCCCATCAGACTATCCTG
Found at i:29476739 original size:54 final size:54
Alignment explanation
Indices: 29476660--29476778 Score: 150
Period size: 54 Copynumber: 2.2 Consensus size: 54
29476650 TCTTAATATC
* * * *
29476660 CCCACGTTTATCATCCTGGCGGACTACTCC-ATGTTCAATGTCCCATCAGACTAT
1 CCCATGTTTAACATCCCGGCGGACTA-TCCTATGTTAAATGTCCCATCAGACTAT
** * *
29476714 CCTGTGTTTAACATCCCGTCGGACTATCCTGTGTTAAATGTCCCATCAGACTAT
1 CCCATGTTTAACATCCCGGCGGACTATCCTATGTTAAATGTCCCATCAGACTAT
29476768 CCCATGTTTAA
1 CCCATGTTTAA
29476779 TGTCCCATCA
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
53 3 0.06
54 51 0.94
ACGTcount: A:0.23, C:0.30, G:0.15, T:0.32
Consensus pattern (54 bp):
CCCATGTTTAACATCCCGGCGGACTATCCTATGTTAAATGTCCCATCAGACTAT
Found at i:29480754 original size:21 final size:21
Alignment explanation
Indices: 29480730--29480769 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
29480720 ATAAGTTAGG
29480730 TTAAGATAATAAATAAAAGGT
1 TTAAGATAATAAATAAAAGGT
* **
29480751 TTAATATAATCTATAAAAG
1 TTAAGATAATAAATAAAAG
29480770 AGAAAATTGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.55, C:0.03, G:0.10, T:0.33
Consensus pattern (21 bp):
TTAAGATAATAAATAAAAGGT
Found at i:29480843 original size:18 final size:16
Alignment explanation
Indices: 29480820--29480865 Score: 56
Period size: 18 Copynumber: 2.7 Consensus size: 16
29480810 TTAAAATAAC
29480820 ATATATAAAATGATGTAT
1 ATATATAAAAT-ATGT-T
29480838 ATATATAAACATATGTT
1 ATATATAAA-ATATGTT
*
29480855 ATATAAAAAAT
1 ATATATAAAAT
29480866 TAAAATGGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 2 0.08
17 9 0.35
18 13 0.50
19 2 0.08
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (16 bp):
ATATATAAAATATGTT
Found at i:29484247 original size:22 final size:22
Alignment explanation
Indices: 29484217--29484259 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
29484207 ACAGCAGAAC
* *
29484217 AGGTTTTTAGCGGCGTTTTTTT
1 AGGTCTTTAGCGGCGCTTTTTT
29484239 AGGTCTTTAGCGGCGCTTTTT
1 AGGTCTTTAGCGGCGCTTTTT
29484260 AACACCACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.09, C:0.14, G:0.28, T:0.49
Consensus pattern (22 bp):
AGGTCTTTAGCGGCGCTTTTTT
Found at i:29484402 original size:43 final size:42
Alignment explanation
Indices: 29484331--29484684 Score: 439
Period size: 43 Copynumber: 8.4 Consensus size: 42
29484321 ACGTCACTAA
*
29484331 CTTTTGCGGCGCTTACGTAAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTA-G-AAAAAAACGCCGCTAAAGATCATGTT
* * *
29484375 CTTTAGCGACGCTTAGAAAACAAACGCCACTAAAGATCATGCT
1 CTTTAGCGGCGCTTAGAAAA-AAACGCCGCTAAAGATCATGTT
* * *
29484418 CTTTAGCGGCGCTTAGAAAACAAACGCCCCTAAAGATCACGCT
1 CTTTAGCGGCGCTTAGAAAA-AAACGCCGCTAAAGATCATGTT
*
29484461 CTTTAGCGGCGCTTAG--AAAAACGCC-CTTAAAGATCATGCT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGC-TAAAGATCATGTT
*
29484501 CTTTAGCGGCGCTTATAAAAAAA-GCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
*
29484542 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
*
29484584 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
* * ** * *
29484626 CTTTTAGCGGCACTTTGGAAGGAAACGCCTCTAAA-AGTAATGTT
1 C-TTTAGCGGCGC-TTAGAAAAAAACGCCGCTAAAGA-TCATGTT
*
29484670 CTATAGCGGCGCTTA
1 CTTTAGCGGCGCTTA
29484685 TTTCACAAAC
Statistics
Matches: 279, Mismatches: 22, Indels: 20
0.87 0.07 0.06
Matches are distributed among these distances:
39 1 0.00
40 34 0.12
41 38 0.14
42 73 0.26
43 97 0.35
44 36 0.13
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (42 bp):
CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTT
Found at i:29484564 original size:83 final size:84
Alignment explanation
Indices: 29484331--29484685 Score: 441
Period size: 83 Copynumber: 4.2 Consensus size: 84
29484321 ACGTCACTAA
* * *
29484331 CTTTTGCGGCGCTTACGTAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGACGCTTAGAAAAC
1 CTTTAGCGGCGCTTA--TAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAA-
29484396 AAACGCCACTAAAGATCATGCT
63 AAACGCCACTAAAGATCATGCT
* * * *
29484418 CTTTAGCGGCGCTTAGAAAACAAACGCCCCTAAAGATCACGCTCTTTAGCGGCGCTTA-G-AAAA
1 CTTTAGCGGCGCTTATAAAA-AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAA
29484481 ACGCC-CTTAAAGATCATGCT
65 ACGCCAC-TAAAGATCATGCT
29484501 CTTTAGCGGCGCTTATAAAAAAA-GCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAA
1 CTTTAGCGGCGCTTATAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAA
* *
29484565 CGCCGCTAAAGATCATGTT
66 CGCCACTAAAGATCATGCT
** * * *
29484584 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTTCTTTTAGCGGCACTTTGGAAGGA
1 CTTTAGCGGCGCTTATAAAAAAACGCCGCTAAAGATCATGTTC-TTTAGCGGCGCTTAGGAA-AA
* * *
29484649 AACGCCTCTAAA-AGTAATGTT
64 AACGCCACTAAAGA-TCATGCT
*
29484670 CTATAGCGGCGCTTAT
1 CTTTAGCGGCGCTTAT
29484686 TTCACAAACG
Statistics
Matches: 238, Mismatches: 21, Indels: 19
0.86 0.08 0.07
Matches are distributed among these distances:
81 30 0.13
82 5 0.02
83 81 0.34
84 22 0.09
85 21 0.09
86 65 0.27
87 14 0.06
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (84 bp):
CTTTAGCGGCGCTTATAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAA
CGCCACTAAAGATCATGCT
Found at i:29485140 original size:21 final size:21
Alignment explanation
Indices: 29485116--29485184 Score: 102
Period size: 21 Copynumber: 3.3 Consensus size: 21
29485106 GCTTCTATTG
*
29485116 CTGCTTCTCTCGCTGCGGCCT
1 CTGCTTCTCTCGCTGCAGCCT
*
29485137 CTGCTTCTCTCGCTGTAGCCT
1 CTGCTTCTCTCGCTGCAGCCT
* *
29485158 CTGCTTCCCTCGCTGCCGCCT
1 CTGCTTCTCTCGCTGCAGCCT
29485179 CTGCTT
1 CTGCTT
29485185 TAAGTTGCTG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.01, C:0.43, G:0.20, T:0.35
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGCAGCCT
Found at i:29490659 original size:16 final size:16
Alignment explanation
Indices: 29490638--29490698 Score: 68
Period size: 16 Copynumber: 3.7 Consensus size: 16
29490628 GATTTAGGAA
29490638 TAAGTTATGTATTATG
1 TAAGTTATGTATTATG
*
29490654 TAAGTTATGTAAGTTGTG
1 TAAGTTATGT-A-TTATG
*
29490672 TAAGTTGTGTATTATG
1 TAAGTTATGTATTATG
* *
29490688 AAACTTATGTA
1 TAAGTTATGTA
29490699 CGTTATGTCT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
16 22 0.59
17 2 0.05
18 13 0.35
ACGTcount: A:0.31, C:0.02, G:0.21, T:0.46
Consensus pattern (16 bp):
TAAGTTATGTATTATG
Found at i:29490663 original size:9 final size:9
Alignment explanation
Indices: 29490638--29490736 Score: 77
Period size: 9 Copynumber: 11.6 Consensus size: 9
29490628 GATTTAGGAA
29490638 TAAGTTATG
1 TAAGTTATG
29490647 T-A-TTATG
1 TAAGTTATG
29490654 TAAGTTATG
1 TAAGTTATG
*
29490663 TAAGTTGTG
1 TAAGTTATG
*
29490672 TAAGTTGTG
1 TAAGTTATG
29490681 T-A-TTATG
1 TAAGTTATG
* *
29490688 AAACTTATG
1 TAAGTTATG
*
29490697 TACGTTATG
1 TAAGTTATG
*
29490706 T--CTTATG
1 TAAGTTATG
29490713 TAAGTTATG
1 TAAGTTATG
29490722 TATTA-TTATG
1 TA--AGTTATG
29490732 TAAGT
1 TAAGT
29490737 AGGGATGTAG
Statistics
Matches: 73, Mismatches: 8, Indels: 18
0.74 0.08 0.18
Matches are distributed among these distances:
7 16 0.22
8 5 0.07
9 44 0.60
10 7 0.10
11 1 0.01
ACGTcount: A:0.29, C:0.03, G:0.20, T:0.47
Consensus pattern (9 bp):
TAAGTTATG
Found at i:29490675 original size:18 final size:17
Alignment explanation
Indices: 29490649--29490736 Score: 65
Period size: 16 Copynumber: 5.1 Consensus size: 17
29490639 AAGTTATGTA
29490649 TTATGTAAGTTATGTAAG
1 TTATGTAA-TTATGTAAG
* *
29490667 TTGTGTAAGTTGTGT-A-
1 TTATGTAA-TTATGTAAG
* *
29490683 TTATGAAACTTATGTACG
1 TTATGTAA-TTATGTAAG
*
29490701 TTATGT-CTTATGTAAG
1 TTATGTAATTATGTAAG
29490717 TTATGTATTATTATGTAAG
1 TTATGTA--ATTATGTAAG
29490736 T
1 T
29490737 AGGGATGTAG
Statistics
Matches: 54, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
16 25 0.46
17 1 0.02
18 18 0.33
19 10 0.19
ACGTcount: A:0.28, C:0.03, G:0.20, T:0.48
Consensus pattern (17 bp):
TTATGTAATTATGTAAG
Found at i:29490686 original size:25 final size:25
Alignment explanation
Indices: 29490638--29490723 Score: 86
Period size: 25 Copynumber: 3.4 Consensus size: 25
29490628 GATTTAGGAA
29490638 TAAGTTATGT-A-TTATGTAAGTTATG
1 TAAGTTATGTAAGTTATGT-A-TTATG
* *
29490663 TAAGTTGTGTAAGTTGTGTATTATG
1 TAAGTTATGTAAGTTATGTATTATG
* * * *
29490688 AAACTTATGTACGTTATGTCTTATG
1 TAAGTTATGTAAGTTATGTATTATG
29490713 TAAGTTATGTA
1 TAAGTTATGTA
29490724 TTATTATGTA
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
25 42 0.86
26 2 0.04
27 5 0.10
ACGTcount: A:0.29, C:0.03, G:0.21, T:0.47
Consensus pattern (25 bp):
TAAGTTATGTAAGTTATGTATTATG
Found at i:29490818 original size:10 final size:11
Alignment explanation
Indices: 29490803--29490853 Score: 70
Period size: 12 Copynumber: 4.6 Consensus size: 11
29490793 TTTATGGATG
29490803 TTATGTA-TTA
1 TTATGTAGTTA
29490813 TTATGTA-TTA
1 TTATGTAGTTA
29490823 TTATGTAAGTTA
1 TTATGT-AGTTA
29490835 TTATGTAGGTTA
1 TTATGTA-GTTA
29490847 TTATGTA
1 TTATGTA
29490854 AGTCCTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
10 16 0.42
11 2 0.05
12 20 0.53
ACGTcount: A:0.29, C:0.00, G:0.16, T:0.55
Consensus pattern (11 bp):
TTATGTAGTTA
Found at i:29490852 original size:24 final size:24
Alignment explanation
Indices: 29490803--29490871 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
29490793 TTTATGGATG
29490803 TTATGT-A-TTATTATGTA--TTA
1 TTATGTAAGTTATTATGTAGGTTA
29490823 TTATGTAAGTTATTATGTAGGTTA
1 TTATGTAAGTTATTATGTAGGTTA
** *
29490847 TTATGTAAGTCCTTATGTTGGTTA
1 TTATGTAAGTTATTATGTAGGTTA
29490871 T
1 T
29490872 GTAAGTTGTG
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
20 6 0.14
21 1 0.02
22 10 0.24
24 25 0.60
ACGTcount: A:0.26, C:0.03, G:0.17, T:0.54
Consensus pattern (24 bp):
TTATGTAAGTTATTATGTAGGTTA
Found at i:29490864 original size:12 final size:12
Alignment explanation
Indices: 29490810--29490856 Score: 71
Period size: 12 Copynumber: 4.1 Consensus size: 12
29490800 ATGTTATGTA
29490810 TTATTATGT-A-
1 TTATTATGTAAG
29490820 TTATTATGTAAG
1 TTATTATGTAAG
*
29490832 TTATTATGTAGG
1 TTATTATGTAAG
29490844 TTATTATGTAAG
1 TTATTATGTAAG
29490856 T
1 T
29490857 CCTTATGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
10 9 0.27
11 1 0.03
12 23 0.70
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (12 bp):
TTATTATGTAAG
Found at i:29491192 original size:34 final size:36
Alignment explanation
Indices: 29491153--29491245 Score: 100
Period size: 34 Copynumber: 2.6 Consensus size: 36
29491143 AATTTGAACT
**
29491153 TTAAAATAAATTTAATATTTAA-AAAT-ATTCGTGA
1 TTAAAATAAATAAAATATTTAATAAATAATTCGTGA
* **
29491187 TTAAAAAAAATAAAATATTTAATATTTAATTCGTGA
1 TTAAAATAAATAAAATATTTAATAAATAATTCGTGA
* *
29491223 GTAAAATAAAATAAAAAATTTAA
1 TTAAAAT-AAATAAAATATTTAA
29491246 AATATAACTT
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
34 19 0.40
35 2 0.04
36 13 0.27
37 14 0.29
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (36 bp):
TTAAAATAAATAAAATATTTAATAAATAATTCGTGA
Found at i:29492909 original size:45 final size:44
Alignment explanation
Indices: 29492844--29492943 Score: 128
Period size: 45 Copynumber: 2.2 Consensus size: 44
29492834 CTGGAAGGAG
* * *
29492844 GAAGGAGGCGATTTAGGGATTTCGGATTTCAAGAAATTAGGCAA
1 GAAGGAGGCAATTTACGGATTTCGGAATTCAAGAAATTAGGCAA
* * *
29492888 GAAAGGAGGCAATTTTCGGATTTGGGAATTCAAGAAATTGGGCAA
1 G-AAGGAGGCAATTTACGGATTTCGGAATTCAAGAAATTAGGCAA
*
29492933 GAAGGACGCAA
1 GAAGGAGGCAA
29492944 CAATTTCACA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
44 10 0.21
45 38 0.79
ACGTcount: A:0.36, C:0.10, G:0.32, T:0.22
Consensus pattern (44 bp):
GAAGGAGGCAATTTACGGATTTCGGAATTCAAGAAATTAGGCAA
Found at i:29494131 original size:7 final size:7
Alignment explanation
Indices: 29494116--29494174 Score: 64
Period size: 7 Copynumber: 8.3 Consensus size: 7
29494106 TAAATTAAGT
29494116 ACCCTAA
1 ACCCTAA
*
29494123 ACCCCAA
1 ACCCTAA
*
29494130 ACCTTAA
1 ACCCTAA
*
29494137 ACCTTAA
1 ACCCTAA
*
29494144 ACCCCAA
1 ACCCTAA
29494151 ACTCCTAA
1 AC-CCTAA
29494159 ACCCTAA
1 ACCCTAA
*
29494166 ACCCAAA
1 ACCCTAA
29494173 AC
1 AC
29494175 ACCATAATCG
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
7 38 0.86
8 6 0.14
ACGTcount: A:0.44, C:0.42, G:0.00, T:0.14
Consensus pattern (7 bp):
ACCCTAA
Found at i:29494854 original size:115 final size:114
Alignment explanation
Indices: 29494541--29494918 Score: 499
Period size: 115 Copynumber: 3.3 Consensus size: 114
29494531 GCTAACAAAT
* *
29494541 AAGCGCCGCTAATAATATGATTTAGCGGCGATTTCTCGTGAACGCCACTAATTCCAGTATACATC
1 AAGCGCCGCTAATAATATAATTTAGCGGCG-TTTCTCCTGAACGCCACTAATTCCAGTATACATC
* *
29494606 AAGATTTAAACACAGCGTTTCGGTTAATATATATTGCGGCGCTTATAAGA
65 AAGATTTAAACGCAGCGTTTCGGTTAATATATATTGCGGCGCTTCTAAGA
* * * * * * * *
29494656 AAGCGCCGCTAATAGTATACTTTTGCGTCG-TT-TACGGAAAGCGCCACTAATTCAAGTATACGT
1 AAGCGCCGCTAATAATATAATTTAGCGGCGTTTCTCCTG-AA-CGCCACTAATTCCAGTATACAT
* * * **
29494719 CAAGATCTAAACGCAGCGTTTAGGTTAATATATCTTGCGGCGCTTCTATTA
64 CAAGATTTAAACGCAGCGTTTCGGTTAATATATATTGCGGCGCTTCTAAGA
*
29494770 AAGCGCCGCTAATAATATAATTTAGCGGCGATTTCTCCTGAACGCCACTAACTCCAGTATACATC
1 AAGCGCCGCTAATAATATAATTTAGCGGCG-TTTCTCCTGAACGCCACTAATTCCAGTATACATC
*
29494835 AAGATTTAAACGCAGCGTTTCCGTTAATATATATTGCGGCGCTTCTAAGA
65 AAGATTTAAACGCAGCGTTTCGGTTAATATATATTGCGGCGCTTCTAAGA
* * * *
29494885 AAGCGACGCTAATAGTATACTTTTGCGGCGTTTC
1 AAGCGCCGCTAATAATATAATTTAGCGGCGTTTC
29494919 CATAAAGCGC
Statistics
Matches: 222, Mismatches: 36, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
112 2 0.01
113 4 0.02
114 94 0.42
115 115 0.52
116 4 0.02
117 3 0.01
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.30
Consensus pattern (114 bp):
AAGCGCCGCTAATAATATAATTTAGCGGCGTTTCTCCTGAACGCCACTAATTCCAGTATACATCA
AGATTTAAACGCAGCGTTTCGGTTAATATATATTGCGGCGCTTCTAAGA
Found at i:29501278 original size:30 final size:30
Alignment explanation
Indices: 29501233--29501312 Score: 124
Period size: 30 Copynumber: 2.7 Consensus size: 30
29501223 CATATTTATG
29501233 GAAAATCAAAGATATGGGTATCAAATAATA
1 GAAAATCAAAGATATGGGTATCAAATAATA
* * *
29501263 GAAAGTCAAATATATGGGTATCAAATATTA
1 GAAAATCAAAGATATGGGTATCAAATAATA
*
29501293 GAAATTCAAAGATATGGGTA
1 GAAAATCAAAGATATGGGTA
29501313 CCGAGATATT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.49, C:0.06, G:0.19, T:0.26
Consensus pattern (30 bp):
GAAAATCAAAGATATGGGTATCAAATAATA
Found at i:29501286 original size:15 final size:15
Alignment explanation
Indices: 29501237--29501290 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
29501227 TTTATGGAAA
*
29501237 ATCAAAGATATGGGT
1 ATCAAATATATGGGT
* **
29501252 ATCAAATA-ATAGAA
1 ATCAAATATATGGGT
29501266 AGTCAAATATATGGGT
1 A-TCAAATATATGGGT
29501282 ATCAAATAT
1 ATCAAATAT
29501291 TAGAAATTCA
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
14 4 0.13
15 22 0.73
16 4 0.13
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.28
Consensus pattern (15 bp):
ATCAAATATATGGGT
Found at i:29510536 original size:3 final size:3
Alignment explanation
Indices: 29510523--29510553 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
29510513 TCATATCAAA
29510523 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
29510554 GAAAAAACTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:29511566 original size:571 final size:581
Alignment explanation
Indices: 29510464--29511615 Score: 1650
Period size: 571 Copynumber: 2.0 Consensus size: 581
29510454 AAACATTAGG
29510464 AAACCCAAAACGTGAAAGAAAACTCTTATTTTCTTTTTCCCCCTTTTTTTCATATCAAAAATAAA
1 AAACCCAAAACGTGAAAGAAAACTCTTATTTTCTTTTTCCCCCTTTTTTTCATATCAAAAAT-AA
* *
29510529 ATAATAATAATAATAATAATAATAAGAAAAAACTAAAAAATAGAATCCAACGTTTTAAAACCAGA
65 ATAATAATAATAATAATAATAACAAGAAAAAACTAAAAAATAG-ATCCAACCTTTTAAAACCAGA
* *
29510594 ACAAAGCTAAATCAAAATAATTCCCTTAAAGCACACCTGAAGACTCGAACTCCAAACCCCCAAGC
129 ACAAAGCTAAATCAAAATAATTCCCTCAAAGCACACCTGAAGACTCAAACTCCAAACCCCCAAGC
* * *
29510659 TAAACTAGCACACAACCAACCACCAAAGCAGTAGACCCATTCTGACACTTGAATGAAAAAAGATA
194 TAAACTAGAAAACAACCAACCACAAAAGCAGTAGACCCATTCTGACACTTGAATGAAAAAAGATA
* * * * *
29510724 CACAACAGTCCGATTTAGCCACTGCCCCCTTCCTACAACTCACAAAACTTCCAACCTAAGAATCG
259 CACAACAATCCAATTTAGCCACTGCCCCCTTCCCACAACTCACAAAACTTCCAACCCAAGAACCG
* * *
29510789 GGGTGTTACAACTCACCCCTCCTTAAAGAAATTTCGTCCCCAAAATTTCCAACTAACAAATAGCC
324 GGGTGTTACAACTCACCCCTCCTTAAAGAAATTTCATCCCCAAAAATACCAACTAACAAATAGCC
* * *
29510854 GCTCTGAACACAAAAATCACCACTATGCTCCAGATGCACACTTTGATCCCAAAACACTACCGTAC
389 ACTCTGAACACAAAAATCACCACTACGCTCCAGATGCACACTTTGATCCCAAAACACTACCATAC
* *
29510919 TAAACTTTAAAATCCCAGACTCACATTCCAAGAAAGGGGCTTAGACCAAAAACCTCAAACACACA
454 TAAACTTTAAAATCCCAGACTCACATTCCAAGAAAGAGACTTAGACCAAAAACCTCAAACACACA
* * * *
29510984 TCTAGAACACTTAGCCACTGAAGCAGATAGTCAATTATATATATCGCACACACAAACGTTAAA
519 TCCAAAACACTTAGCCACTAAAGCAGATAGTCAATTATATATATCACACACACAAACGTTAAA
* *
29511047 AAACCCAAAACGTGAAAGAAAACTCTTGTTTTCTTTTT-CCCTTTTTTTCTCATATCAAAAAT-A
1 AAACCCAAAACGTGAAAGAAAACTCTTATTTTCTTTTTCCCCCTTTTTT-TCATATCAAAAATAA
* * * *
29511110 A-AA-AAT-AT-A-AAT-A-AGCAA-AACAAA-TAAAAAA-AG-TCTAACCTTTTAAAACTAGAA
65 ATAATAATAATAATAATAATAACAAGAAAAAACTAAAAAATAGATCCAACCTTTTAAAACCAGAA
* * *
29511164 CAAAGCTAAATCAAAATAATTCCCTCAAAGCACACCTGAGGACTCAAAC-CCTGAACCCCCAGGC
130 CAAAGCTAAATCAAAATAATTCCCTCAAAGCACACCTGAAGACTCAAACTCC-AAACCCCCAAGC
* * * * * *
29511228 TAAACTAAGAAAATAACCAACCA-AAAGAGCAGTAGGCCTATTCTGACAGTTGAATGCAAAAATA
194 TAAACT-AGAAAACAACCAACCACAAA-AGCAGTAGACCCATTCTGACACTTGAATGAAAAAAGA
* *
29511292 TACACAACAATCCAATTTAGCTACTGCCCCTTTCCCACAACTCACAAAACTTCCAACCCCAAGAA
257 TACACAACAATCCAATTTAGCCACTGCCCCCTTCCCACAACTCACAAAACTTCCAA-CCCAAGAA
* *
29511357 CCGGGGTGTTACAACTCACCCCTCCTTAAAGAAATTTCATCCCTAAAAATACCAACTAACAGATA
321 CCGGGGTGTTACAACTCACCCCTCCTTAAAGAAATTTCATCCCCAAAAATACCAACTAACAAATA
* * * * * * *
29511422 GCCACTCTGAACACAAAACTCACCATTACGCTCTAGCTGCGCACTTTGATCCCGAAACATTACCA
386 GCCACTCTGAACACAAAAATCACCACTACGCTCCAGATGCACACTTTGATCCCAAAACACTACCA
* * * *
29511487 TACTAAACTTTAAAATCCTAGACTCGCATTCCAAGAATGAGACTTAGACCTAAAACCTCAAACAC
451 TACTAAACTTTAAAATCCCAGACTCACATTCCAAGAAAGAGACTTAGACCAAAAACCTCAAACAC
29511552 ACATCCAAAACACTTAGCCACTAAAGCAGATAGTCAATTATATATATCACACACACAAACGTTA
516 ACATCCAAAACACTTAGCCACTAAAGCAGATAGTCAATTATATATATCACACACACAAACGTTA
29511616 CAATTCTAAA
Statistics
Matches: 510, Mismatches: 54, Indels: 22
0.87 0.09 0.04
Matches are distributed among these distances:
568 2 0.00
569 82 0.16
570 96 0.19
571 242 0.47
572 7 0.01
573 5 0.01
574 3 0.01
575 1 0.00
576 3 0.01
577 1 0.00
578 2 0.00
579 3 0.01
580 2 0.00
581 2 0.00
582 9 0.02
583 50 0.10
ACGTcount: A:0.42, C:0.27, G:0.10, T:0.22
Consensus pattern (581 bp):
AAACCCAAAACGTGAAAGAAAACTCTTATTTTCTTTTTCCCCCTTTTTTTCATATCAAAAATAAA
TAATAATAATAATAATAATAACAAGAAAAAACTAAAAAATAGATCCAACCTTTTAAAACCAGAAC
AAAGCTAAATCAAAATAATTCCCTCAAAGCACACCTGAAGACTCAAACTCCAAACCCCCAAGCTA
AACTAGAAAACAACCAACCACAAAAGCAGTAGACCCATTCTGACACTTGAATGAAAAAAGATACA
CAACAATCCAATTTAGCCACTGCCCCCTTCCCACAACTCACAAAACTTCCAACCCAAGAACCGGG
GTGTTACAACTCACCCCTCCTTAAAGAAATTTCATCCCCAAAAATACCAACTAACAAATAGCCAC
TCTGAACACAAAAATCACCACTACGCTCCAGATGCACACTTTGATCCCAAAACACTACCATACTA
AACTTTAAAATCCCAGACTCACATTCCAAGAAAGAGACTTAGACCAAAAACCTCAAACACACATC
CAAAACACTTAGCCACTAAAGCAGATAGTCAATTATATATATCACACACACAAACGTTAAA
Found at i:29513149 original size:12 final size:12
Alignment explanation
Indices: 29513132--29513158 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
29513122 AAAATAAAAT
29513132 AATAATAAGAAA
1 AATAATAAGAAA
29513144 AATAATAAGAAA
1 AATAATAAGAAA
29513156 AAT
1 AAT
29513159 TTGCAAAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (12 bp):
AATAATAAGAAA
Found at i:29514943 original size:13 final size:13
Alignment explanation
Indices: 29514927--29514984 Score: 66
Period size: 13 Copynumber: 4.5 Consensus size: 13
29514917 GTACTTATTT
*
29514927 AAAGCATTTCTCA
1 AAAGCATTTTTCA
29514940 AAAGCATTTTTCCA
1 AAAGCATTTTT-CA
*
29514954 CAA-CACTTTTT-A
1 AAAGCA-TTTTTCA
29514966 AAAGCATTTTTCA
1 AAAGCATTTTTCA
29514979 AAAGCA
1 AAAGCA
29514985 ATGTTAAACT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
12 8 0.21
13 21 0.55
14 9 0.24
ACGTcount: A:0.40, C:0.21, G:0.07, T:0.33
Consensus pattern (13 bp):
AAAGCATTTTTCA
Found at i:29517686 original size:26 final size:26
Alignment explanation
Indices: 29517648--29517701 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
29517638 TTAAATTTAG
29517648 AAAGCACGATAGTTAG-AACTTTCTGA
1 AAAGCACGATAGTTAGTAA-TTTCTGA
29517674 AAAGCAC-AGTAGTTAGTAATTTCTGA
1 AAAGCACGA-TAGTTAGTAATTTCTGA
29517700 AA
1 AA
29517702 CTATATTGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
25 1 0.04
26 23 0.88
27 2 0.08
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.28
Consensus pattern (26 bp):
AAAGCACGATAGTTAGTAATTTCTGA
Found at i:29523190 original size:18 final size:19
Alignment explanation
Indices: 29523155--29523190 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
29523145 TCAATGGTAA
*
29523155 GTTATGTGTGTTGTTTTGG
1 GTTATGTGTGTTGATTTGG
29523174 GTTATGT-TGTTGATTTG
1 GTTATGTGTGTTGATTTG
29523191 TAGATTTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.08, C:0.00, G:0.33, T:0.58
Consensus pattern (19 bp):
GTTATGTGTGTTGATTTGG
Found at i:29525038 original size:42 final size:42
Alignment explanation
Indices: 29524984--29525073 Score: 173
Period size: 42 Copynumber: 2.2 Consensus size: 42
29524974 AACATGTTTG
29524984 GATC-ATATTGCATGTAATTTCCATACCATACATCCATACAT
1 GATCTATATTGCATGTAATTTCCATACCATACATCCATACAT
29525025 GATCTATATTGCATGTAATTTCCATACCATACATCCATACAT
1 GATCTATATTGCATGTAATTTCCATACCATACATCCATACAT
29525067 GATCTAT
1 GATCTAT
29525074 GTCATTTGGT
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 4 0.08
42 44 0.92
ACGTcount: A:0.33, C:0.23, G:0.08, T:0.36
Consensus pattern (42 bp):
GATCTATATTGCATGTAATTTCCATACCATACATCCATACAT
Found at i:29528189 original size:20 final size:20
Alignment explanation
Indices: 29528164--29528211 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
29528154 TACAATATAT
29528164 ATCAATTTTTTTTTCAAAA-A
1 ATCAATTTTTTTTT-AAAAGA
**
29528184 ATCAATTCATTTTTAAAAGA
1 ATCAATTTTTTTTTAAAAGA
29528204 ATC-ATTTT
1 ATCAATTTT
29528212 CCGACAACCT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (20 bp):
ATCAATTTTTTTTTAAAAGA
Found at i:29529292 original size:28 final size:29
Alignment explanation
Indices: 29529256--29529323 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 29
29529246 TTATCTTTTT
*
29529256 TTTACAATTTTTTAAGAA-TAACCAAATA
1 TTTAGAATTTTTTAAGAATTAACCAAATA
29529284 TTTAGAATTTTTTTAAGAATTAACCAAATA
1 TTTAGAA-TTTTTTAAGAATTAACCAAATA
29529314 TTTAGAATTT
1 TTTAGAATTT
29529324 CATCAAATGA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
28 6 0.16
29 14 0.38
30 17 0.46
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.44
Consensus pattern (29 bp):
TTTAGAATTTTTTAAGAATTAACCAAATA
Found at i:29529303 original size:29 final size:30
Alignment explanation
Indices: 29529263--29529323 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
29529253 TTTTTTACAA
29529263 TTTTTTAAGAA-TAACCAAATATTTAGAAT
1 TTTTTTAAGAATTAACCAAATATTTAGAAT
29529292 TTTTTTAAGAATTAACCAAATATTTAGAAT
1 TTTTTTAAGAATTAACCAAATATTTAGAAT
29529322 TT
1 TT
29529324 CATCAAATGA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.35
30 20 0.65
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.44
Consensus pattern (30 bp):
TTTTTTAAGAATTAACCAAATATTTAGAAT
Found at i:29531781 original size:26 final size:26
Alignment explanation
Indices: 29531752--29531858 Score: 144
Period size: 26 Copynumber: 4.1 Consensus size: 26
29531742 AACACACCAA
* * *
29531752 TATCGCAGCAAAACTGCCAGTAATAG
1 TATCACAGCAAAGCTGCCAGTAACAG
*
29531778 TATCACAACAAAGCTGCCAGTAACAG
1 TATCACAGCAAAGCTGCCAGTAACAG
*
29531804 TATCACAGTAAAGCTGCCAGTAACAG
1 TATCACAGCAAAGCTGCCAGTAACAG
*
29531830 TATCGA-AGCAAAGCTGCTAGTAACAG
1 TATC-ACAGCAAAGCTGCCAGTAACAG
29531856 TAT
1 TAT
29531859 ACTTCCTCCA
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
26 71 0.99
27 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.20
Consensus pattern (26 bp):
TATCACAGCAAAGCTGCCAGTAACAG
Found at i:29534482 original size:65 final size:65
Alignment explanation
Indices: 29534389--29534525 Score: 181
Period size: 65 Copynumber: 2.1 Consensus size: 65
29534379 TCCTCCACTC
* * * * *
29534389 GTGTGATCC-TAT-TTTGTAAATAGCGAGGTATATGGCCTGGACACACGCTCGTGTCCTTGGCCC
1 GTGTGAACCTTATATTTGTAAATAGCGAGGTACACGGCATGGACACACGCCCGTGTCCTTGG-CC
29534452 T
65 T
* *
29534453 -TGTGAACCTTATATTTGTAAATAGTGAGGTACACGGTATGGACACACGCCCGTGTCCTTGGCCT
1 GTGTGAACCTTATATTTGTAAATAGCGAGGTACACGGCATGGACACACGCCCGTGTCCTTGGCCT
29534517 GTGTGAACC
1 GTGTGAACC
29534526 CTACACTAAC
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
63 7 0.11
64 6 0.10
65 50 0.79
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.30
Consensus pattern (65 bp):
GTGTGAACCTTATATTTGTAAATAGCGAGGTACACGGCATGGACACACGCCCGTGTCCTTGGCCT
Found at i:29535167 original size:6 final size:6
Alignment explanation
Indices: 29535157--29535201 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
29535147 GAAGAAGAAT
29535157 AAAAATG AAAAAG -AAAAG AAAAAG AAAAAG --AAAG AAAAATG AAAA
1 AAAAA-G AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA-G AAAA
29535202 GAGGCAAGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
4 4 0.12
5 5 0.15
6 15 0.44
7 10 0.29
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (6 bp):
AAAAAG
Found at i:29535170 original size:16 final size:16
Alignment explanation
Indices: 29535151--29535201 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
29535141 GGAATAGAAG
*
29535151 AAGAATAAAAATGAAA
1 AAGAAAAAAAATGAAA
*
29535167 AAGAAAAGAAAAAGAAA
1 AAGAAAA-AAAATGAAA
29535184 AAGAAAGAAAAATGAAA
1 AAGAAA-AAAAATGAAA
29535201 A
1 A
29535202 GAGGCAAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.20
17 23 0.77
18 1 0.03
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (16 bp):
AAGAAAAAAAATGAAA
Found at i:29535203 original size:16 final size:17
Alignment explanation
Indices: 29535157--29535201 Score: 74
Period size: 17 Copynumber: 2.6 Consensus size: 17
29535147 GAAGAAGAAT
29535157 AAAAATGAAAAAGAAAAG
1 AAAAATGAAAAAG-AAAG
29535175 AAAAA-GAAAAAGAAAG
1 AAAAATGAAAAAGAAAG
29535191 AAAAATGAAAA
1 AAAAATGAAAA
29535202 GAGGCAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.35
17 12 0.46
18 5 0.19
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (17 bp):
AAAAATGAAAAAGAAAG
Found at i:29541986 original size:21 final size:21
Alignment explanation
Indices: 29541962--29542002 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
29541952 TATCTTTCAG
*
29541962 GTTTTAAGTTTTAAATTTTGA
1 GTTTTAAGTTTCAAATTTTGA
**
29541983 GTTTTGGGTTTCAAATTTTG
1 GTTTTAAGTTTCAAATTTTG
29542003 GATTTGATGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.22, C:0.02, G:0.20, T:0.56
Consensus pattern (21 bp):
GTTTTAAGTTTCAAATTTTGA
Found at i:29543777 original size:18 final size:18
Alignment explanation
Indices: 29543756--29543796 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
29543746 AGAAAATATC
* *
29543756 AACTAAAAATCAAATTTA
1 AACTAAAAATAAAATTCA
*
29543774 AACTAAAGATAAAATTCA
1 AACTAAAAATAAAATTCA
29543792 AACTA
1 AACTA
29543797 TTTATAGGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.61, C:0.12, G:0.02, T:0.24
Consensus pattern (18 bp):
AACTAAAAATAAAATTCA
Found at i:29544068 original size:19 final size:19
Alignment explanation
Indices: 29544044--29544080 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
29544034 TCAAAGGTCC
29544044 AATTAACTAAGGTTTAATT
1 AATTAACTAAGGTTTAATT
*
29544063 AATTAATTAAGGTTTAAT
1 AATTAACTAAGGTTTAAT
29544081 CCAAGTATGT
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:0.43, C:0.03, G:0.11, T:0.43
Consensus pattern (19 bp):
AATTAACTAAGGTTTAATT
Found at i:29546197 original size:3 final size:3
Alignment explanation
Indices: 29546176--29546234 Score: 100
Period size: 3 Copynumber: 19.7 Consensus size: 3
29546166 TTTCATACAA
* *
29546176 TAT TAT TAA TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
29546224 TAT TAT TAT TA
1 TAT TAT TAT TA
29546235 CTACTACTAC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:29546550 original size:14 final size:14
Alignment explanation
Indices: 29546514--29546550 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
29546504 TTTCATATTT
*
29546514 TCTACATACATATA
1 TCTACATATATATA
*
29546528 TATACATATATATA
1 TCTACATATATATA
29546542 TCTACATAT
1 TCTACATAT
29546551 TTTAATTCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.43, C:0.16, G:0.00, T:0.41
Consensus pattern (14 bp):
TCTACATATATATA
Found at i:29555995 original size:20 final size:20
Alignment explanation
Indices: 29555960--29556008 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
29555950 TCAAAATGAA
*
29555960 AATGAGAAAAAGAAAT-AAG
1 AATGAAAAAAAGAAATCAAG
*
29555979 AATGAAAAAAGAGAAATCTAG
1 AATGAAAAAA-AGAAATCAAG
29556000 -ATGAAAAAA
1 AATGAAAAAA
29556009 CCATAATGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 9 0.35
20 15 0.58
21 2 0.08
ACGTcount: A:0.67, C:0.02, G:0.18, T:0.12
Consensus pattern (20 bp):
AATGAAAAAAAGAAATCAAG
Found at i:29556947 original size:7 final size:6
Alignment explanation
Indices: 29556911--29556944 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
29556901 GAAAATATGA
29556911 AAAATG AAAATG AAAATG AAAATG AAAATG AAAA
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAA
29556945 ATGGAGAGGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (6 bp):
AAAATG
Found at i:29558394 original size:129 final size:129
Alignment explanation
Indices: 29558162--29558410 Score: 419
Period size: 129 Copynumber: 1.9 Consensus size: 129
29558152 AGTGAATATT
29558162 GCGGATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCGACGAATCTTATCTTCCCCAAGA
1 GCGGATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCGACGAATCTTATCTTCCCCAAGA
* *
29558227 GTAGGGAAACAGATCTATGTGGCGAATCTTATCTTCCCCAAGAGTAGGGAAACAGATCTAAGAG
66 GTAGGGAAACAGATCTAAGCGGCGAATCTTATCTTCCCCAAGAGTAGGGAAACAGATCTAAGAG
* * * * *
29558291 GCGGATCTTATCTTCCCTAGGAGTAGGGAAACAGATCTAAGCGGCGGATCTTATTTTCCCCAGGA
1 GCGGATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCGACGAATCTTATCTTCCCCAAGA
29558356 GTAGGGAAACAGATCTAAGCGGCGAATCTTAT-TCTCCCCAAGAGTAGGGAAACAG
66 GTAGGGAAACAGATCTAAGCGGCGAATCTTATCT-TCCCCAAGAGTAGGGAAACAG
29558411 CTTTAAGCCA
Statistics
Matches: 112, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
128 1 0.01
129 111 0.99
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.22
Consensus pattern (129 bp):
GCGGATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCGACGAATCTTATCTTCCCCAAGA
GTAGGGAAACAGATCTAAGCGGCGAATCTTATCTTCCCCAAGAGTAGGGAAACAGATCTAAGAG
Found at i:29558418 original size:43 final size:43
Alignment explanation
Indices: 29558166--29558410 Score: 375
Period size: 43 Copynumber: 5.7 Consensus size: 43
29558156 AATATTGCGG
* *
29558166 ATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCGACGA
1 ATCTTATCTTCCCCAAGAGTAGGGAAACAGATCTAAGCGGCGA
* *
29558209 ATCTTATCTTCCCCAAGAGTAGGGAAACAGATCTATGTGGCGA
1 ATCTTATCTTCCCCAAGAGTAGGGAAACAGATCTAAGCGGCGA
* *
29558252 ATCTTATCTTCCCCAAGAGTAGGGAAACAGATCTAAGAGGCGG
1 ATCTTATCTTCCCCAAGAGTAGGGAAACAGATCTAAGCGGCGA
* * *
29558295 ATCTTATCTTCCCTAGGAGTAGGGAAACAGATCTAAGCGGCGG
1 ATCTTATCTTCCCCAAGAGTAGGGAAACAGATCTAAGCGGCGA
* *
29558338 ATCTTATTTTCCCCAGGAGTAGGGAAACAGATCTAAGCGGCGA
1 ATCTTATCTTCCCCAAGAGTAGGGAAACAGATCTAAGCGGCGA
29558381 ATCTTAT-TCTCCCCAAGAGTAGGGAAACAG
1 ATCTTATCT-TCCCCAAGAGTAGGGAAACAG
29558411 CTTTAAGCCA
Statistics
Matches: 187, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
42 1 0.01
43 186 0.99
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.23
Consensus pattern (43 bp):
ATCTTATCTTCCCCAAGAGTAGGGAAACAGATCTAAGCGGCGA
Found at i:29558620 original size:44 final size:44
Alignment explanation
Indices: 29558572--29558934 Score: 121
Period size: 44 Copynumber: 8.3 Consensus size: 44
29558562 CCCGAGGTCA
* * *
29558572 CAGTGGGGCAGACTGAAG-AAACAAATCTTATCTCCCTAAGGTTG
1 CAGTGGAGCAGACTGAAGTAAA-AAATCCTATCTCCCTAAAGTTG
* * *
29558616 CAGTGGAGCAGATTGAAGTCAATAATCCTATCTCCCTAAAGTTG
1 CAGTGGAGCAGACTGAAGTAAAAAATCCTATCTCCCTAAAGTTG
* * * * * * * *
29558660 CAATGGAG-AGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTG
1 CAGTGGAGCA-GACTGAAGTAAAAAATCCTATCTCCCTAAAGTTG
* ** * * ** * * *
29558704 CAGTAGAGTGGA-TCACA-T--CAGGTCTTATCTCCCTGAAGTTA
1 CAGTGGAGCAGACTGA-AGTAAAAAATCCTATCTCCCTAAAGTTG
* * ** * * *
29558745 CAGTGGAGCAAACT-AAGTAAGCAGGTCTTATCTCGACTGAAGTTG
1 CAGTGGAGCAGACTGAAGTAA-AAAATCCTATCTC-CCTAAAGTTG
* * ** * * *
29558790 CAGTGGGGCAGA-TCGAAGATGACCAATCTTATCTCCCTGAAGTTA
1 CAGTGGAGCAGACT-GAAG-TAAAAAATCCTATCTCCCTAAAGTTG
* *** * *
29558835 CAGTGGAGCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTTG
1 CAGTGGAGCAGACTGAAGTAAAAAATCCTATCTCCCTAAAGTTG
* * * * * * * * *
29558879 TAGTGGAGCGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTG
1 CAGTGGAGCAGACTGAAGTAAAAAATCCTATCTCCCTAAAGTTG
*
29558923 CAGTAGAGCAGA
1 CAGTGGAGCAGA
29558935 TCACATCAAG
Statistics
Matches: 246, Mismatches: 59, Indels: 28
0.74 0.18 0.08
Matches are distributed among these distances:
40 1 0.00
41 29 0.12
42 1 0.00
43 4 0.02
44 152 0.62
45 43 0.17
46 14 0.06
47 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (44 bp):
CAGTGGAGCAGACTGAAGTAAAAAATCCTATCTCCCTAAAGTTG
Found at i:29564969 original size:20 final size:20
Alignment explanation
Indices: 29564934--29564982 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
29564924 TCAAAATGAA
*
29564934 AATGAGAAAAAGAAAT-AAG
1 AATGAAAAAAAGAAATCAAG
*
29564953 AATGAAAAAAGAGAAATCTAG
1 AATGAAAAAA-AGAAATCAAG
29564974 -ATGAAAAAA
1 AATGAAAAAA
29564983 CCATAATGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 9 0.35
20 15 0.58
21 2 0.08
ACGTcount: A:0.67, C:0.02, G:0.18, T:0.12
Consensus pattern (20 bp):
AATGAAAAAAAGAAATCAAG
Found at i:29565920 original size:7 final size:6
Alignment explanation
Indices: 29565884--29565917 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
29565874 GAAAATATGA
29565884 AAAATG AAAATG AAAATG AAAATG AAAATG AAAA
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAA
29565918 ATGGAGAGGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (6 bp):
AAAATG
Found at i:29567368 original size:129 final size:129
Alignment explanation
Indices: 29567136--29567384 Score: 419
Period size: 129 Copynumber: 1.9 Consensus size: 129
29567126 AGTGAATATT
29567136 GCGGATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCGACGAATCTTATCTTCCCCAAGA
1 GCGGATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCGACGAATCTTATCTTCCCCAAGA
* *
29567201 GTAGGGAAACAGATCTATGTGGCGAATCTTATCTTCCCCAAGAGTAGGGAAACAGATCTAAGAG
66 GTAGGGAAACAGATCTAAGCGGCGAATCTTATCTTCCCCAAGAGTAGGGAAACAGATCTAAGAG
* * * * *
29567265 GCGGATCTTATCTTCCCTAGGAGTAGGGAAACAGATCTAAGCGGCGGATCTTATTTTCCCCAGGA
1 GCGGATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCGACGAATCTTATCTTCCCCAAGA
29567330 GTAGGGAAACAGATCTAAGCGGCGAATCTTAT-TCTCCCCAAGAGTAGGGAAACAG
66 GTAGGGAAACAGATCTAAGCGGCGAATCTTATCT-TCCCCAAGAGTAGGGAAACAG
29567385 CTTTAAGCCA
Statistics
Matches: 112, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
128 1 0.01
129 111 0.99
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.22
Consensus pattern (129 bp):
GCGGATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCGACGAATCTTATCTTCCCCAAGA
GTAGGGAAACAGATCTAAGCGGCGAATCTTATCTTCCCCAAGAGTAGGGAAACAGATCTAAGAG
Found at i:29567392 original size:43 final size:43
Alignment explanation
Indices: 29567140--29567384 Score: 375
Period size: 43 Copynumber: 5.7 Consensus size: 43
29567130 AATATTGCGG
* *
29567140 ATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCGACGA
1 ATCTTATCTTCCCCAAGAGTAGGGAAACAGATCTAAGCGGCGA
* *
29567183 ATCTTATCTTCCCCAAGAGTAGGGAAACAGATCTATGTGGCGA
1 ATCTTATCTTCCCCAAGAGTAGGGAAACAGATCTAAGCGGCGA
* *
29567226 ATCTTATCTTCCCCAAGAGTAGGGAAACAGATCTAAGAGGCGG
1 ATCTTATCTTCCCCAAGAGTAGGGAAACAGATCTAAGCGGCGA
* * *
29567269 ATCTTATCTTCCCTAGGAGTAGGGAAACAGATCTAAGCGGCGG
1 ATCTTATCTTCCCCAAGAGTAGGGAAACAGATCTAAGCGGCGA
* *
29567312 ATCTTATTTTCCCCAGGAGTAGGGAAACAGATCTAAGCGGCGA
1 ATCTTATCTTCCCCAAGAGTAGGGAAACAGATCTAAGCGGCGA
29567355 ATCTTAT-TCTCCCCAAGAGTAGGGAAACAG
1 ATCTTATCT-TCCCCAAGAGTAGGGAAACAG
29567385 CTTTAAGCCA
Statistics
Matches: 187, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
42 1 0.01
43 186 0.99
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.23
Consensus pattern (43 bp):
ATCTTATCTTCCCCAAGAGTAGGGAAACAGATCTAAGCGGCGA
Found at i:29567594 original size:44 final size:44
Alignment explanation
Indices: 29567546--29567908 Score: 121
Period size: 44 Copynumber: 8.3 Consensus size: 44
29567536 CCCGAGGTCA
* * *
29567546 CAGTGGGGCAGACTGAAG-AAACAAATCTTATCTCCCTAAGGTTG
1 CAGTGGAGCAGACTGAAGTAAA-AAATCCTATCTCCCTAAAGTTG
* * *
29567590 CAGTGGAGCAGATTGAAGTCAATAATCCTATCTCCCTAAAGTTG
1 CAGTGGAGCAGACTGAAGTAAAAAATCCTATCTCCCTAAAGTTG
* * * * * * * *
29567634 CAATGGAG-AGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTG
1 CAGTGGAGCA-GACTGAAGTAAAAAATCCTATCTCCCTAAAGTTG
* ** * * ** * * *
29567678 CAGTAGAGTGGA-TCACA-T--CAGGTCTTATCTCCCTGAAGTTA
1 CAGTGGAGCAGACTGA-AGTAAAAAATCCTATCTCCCTAAAGTTG
* * ** * * *
29567719 CAGTGGAGCAAACT-AAGTAAGCAGGTCTTATCTCGACTGAAGTTG
1 CAGTGGAGCAGACTGAAGTAA-AAAATCCTATCTC-CCTAAAGTTG
* * ** * * *
29567764 CAGTGGGGCAGA-TCGAAGATGACCAATCTTATCTCCCTGAAGTTA
1 CAGTGGAGCAGACT-GAAG-TAAAAAATCCTATCTCCCTAAAGTTG
* *** * *
29567809 CAGTGGAGCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTTG
1 CAGTGGAGCAGACTGAAGTAAAAAATCCTATCTCCCTAAAGTTG
* * * * * * * * *
29567853 TAGTGGAGCGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTG
1 CAGTGGAGCAGACTGAAGTAAAAAATCCTATCTCCCTAAAGTTG
*
29567897 CAGTAGAGCAGA
1 CAGTGGAGCAGA
29567909 TCACATCAAG
Statistics
Matches: 246, Mismatches: 59, Indels: 28
0.74 0.18 0.08
Matches are distributed among these distances:
40 1 0.00
41 29 0.12
42 1 0.00
43 4 0.02
44 152 0.62
45 43 0.17
46 14 0.06
47 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (44 bp):
CAGTGGAGCAGACTGAAGTAAAAAATCCTATCTCCCTAAAGTTG
Found at i:29577395 original size:34 final size:35
Alignment explanation
Indices: 29577349--29577420 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 35
29577339 ATAGAAGTAA
**
29577349 ATTATTTTTGTGTTTGACGTTGATACTATCGATCT
1 ATTATTTTTGTGTTTGAAATTGATACTATCGATCT
*
29577384 ATTA-TTTTGTGTTTGAAATTGATGCTATCGATCT
1 ATTATTTTTGTGTTTGAAATTGATACTATCGATCT
29577418 ATT
1 ATT
29577421 GGCGGTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
34 30 0.88
35 4 0.12
ACGTcount: A:0.22, C:0.10, G:0.17, T:0.51
Consensus pattern (35 bp):
ATTATTTTTGTGTTTGAAATTGATACTATCGATCT
Found at i:29601669 original size:43 final size:42
Alignment explanation
Indices: 29601566--29601817 Score: 220
Period size: 43 Copynumber: 5.9 Consensus size: 42
29601556 TTATTTTTAT
* * * ***
29601566 AAACACCGCTAAAGGTCATGTTCTTTAGCGGCGC--TACAAA
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTCCGC
* *
29601606 AAAGCGCCGCTAAAGGTCATGTACTTTAGCGGCGCTTATTCCGC
1 AAA-CGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT-TTCCGC
* **
29601650 AAACGCCGCTAAAGATCATGTTCTTTAGCGACGCTTTTTTTGC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGC-TTTTCCGC
* * *
29601693 AAATGCCGCTAAAGATCATGTTCTTTGGCGGCGCTTTATCCAC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTT-TCCGC
* * * *
29601736 AAATGCCACTAAAGGTCATGTTCTTTTAGCGGCGCTTTTCTGAC
1 AAACGCCGCTAAAGATCATGTTC-TTTAGCGGCGCTTTTCCG-C
* * * ** *
29601780 AAACGTCGTTAAAGACCATGACCTTTAGCGGTGCTTTT
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTT
29601818 TTTAAAAACG
Statistics
Matches: 173, Mismatches: 31, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
40 3 0.02
41 29 0.17
42 3 0.02
43 102 0.59
44 36 0.21
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (42 bp):
AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTCCGC
Found at i:29601809 original size:130 final size:127
Alignment explanation
Indices: 29601571--29601820 Score: 306
Period size: 130 Copynumber: 1.9 Consensus size: 127
29601561 TTTATAAACA
* *
29601571 CCGCTAAAGGTCATGTTCTTTAGCGGCGCTACAAAAAAGCGCCGCTAAAGGTCATGTACTTTAGC
1 CCGCTAAAGATCATGTTCTTTAGCGGCGCTACAAAAAAGCGCCACTAAAGGTCATGTACTTTAGC
* **
29601636 GGCGCTTATTCCGCAAACGCCGCTAAAGATCATGTTCTTTAGCGACGCTTTTTTTGCAAATG
66 GGCGCTTATTCCGCAAACGCCGCTAAAGACCATGACCTTTAGCGACGCTTTTTTTGCAAATG
* * * * *
29601698 CCGCTAAAGATCATGTTCTTTGGCGGCGCTTTATCCACAAA-TGCCACTAAAGGTCATGTTCTTT
1 CCGCTAAAGATCATGTTCTTTAGCGGCGC--TA-CAAAAAAGCGCCACTAAAGGTCATGTAC-TT
* * * **
29601762 TAGCGGCGCTT-TTCTGACAAACGTCGTTAAAGACCATGACCTTTAGCGGTGCTTTTTTT
62 TAGCGGCGCTTATTCCG-CAAACGCCGCTAAAGACCATGACCTTTAGCGACGCTTTTTTT
29601821 AAAAACGCCA
Statistics
Matches: 103, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
127 27 0.26
129 23 0.22
130 53 0.51
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (127 bp):
CCGCTAAAGATCATGTTCTTTAGCGGCGCTACAAAAAAGCGCCACTAAAGGTCATGTACTTTAGC
GGCGCTTATTCCGCAAACGCCGCTAAAGACCATGACCTTTAGCGACGCTTTTTTTGCAAATG
Found at i:29603965 original size:25 final size:24
Alignment explanation
Indices: 29603937--29604009 Score: 67
Period size: 25 Copynumber: 2.9 Consensus size: 24
29603927 TAATGTAATT
29603937 AAGTTATGTAAGCTGTGTATTATTA
1 AAGTTATGTAAG-TGTGTATTATTA
* * * *
29603962 AAGTTAAGT-ATTATGTAAGTTATTT
1 AAGTTATGTAAGTGTGT-A-TTATTA
29603987 AAGTTATGTAAGTGGTGTATTAT
1 AAGTTATGTAAGT-GTGTATTAT
29604010 GTAAGAATAA
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
23 4 0.11
24 2 0.05
25 25 0.68
26 3 0.08
27 3 0.08
ACGTcount: A:0.33, C:0.01, G:0.21, T:0.45
Consensus pattern (24 bp):
AAGTTATGTAAGTGTGTATTATTA
Found at i:29604053 original size:16 final size:16
Alignment explanation
Indices: 29604029--29604191 Score: 56
Period size: 16 Copynumber: 10.0 Consensus size: 16
29604019 AATAAAAAAT
*
29604029 TTATTTAAGTTATGTA
1 TTATGTAAGTTATGTA
29604045 TTATGTAAG---TGTA
1 TTATGTAAGTTATGTA
*
29604058 -TATATAAGTTATGATA
1 TTATGTAAGTTATG-TA
*
29604074 TGAT-TGATAGATT-TG-A
1 TTATGT-A-AG-TTATGTA
29604090 GTTATGTAAGTTATGATA
1 -TTATGTAAGTTATG-TA
* *
29604108 TGATTTATAAGTTATGTA
1 T--TATGTAAGTTATGTA
* *
29604126 TAATGTAAGTTATGAAA
1 TTATGTAAGTTATG-TA
29604143 GTTATGT-A-TTATGTAA
1 -TTATGTAAGTTATGT-A
* *
29604159 TTTATCTAAGTTGTGTA
1 -TTATGTAAGTTATGTA
* *
29604176 TTATGCAAGTCATGTA
1 TTATGTAAGTTATGTA
29604192 GGCTATGTAT
Statistics
Matches: 108, Mismatches: 19, Indels: 40
0.65 0.11 0.24
Matches are distributed among these distances:
12 7 0.06
13 4 0.04
15 4 0.04
16 49 0.45
17 12 0.11
18 19 0.18
19 13 0.12
ACGTcount: A:0.34, C:0.02, G:0.18, T:0.46
Consensus pattern (16 bp):
TTATGTAAGTTATGTA
Found at i:29604101 original size:9 final size:9
Alignment explanation
Indices: 29604089--29604501 Score: 128
Period size: 9 Copynumber: 47.4 Consensus size: 9
29604079 GATAGATTTG
29604089 AGTTATGTA
1 AGTTATGTA
29604098 AGTTATGATA
1 AGTTATG-TA
* *
29604108 TGATT-TATA
1 AG-TTATGTA
29604117 AGTTATGT-
1 AGTTATGTA
*
29604125 A-TAATGTA
1 AGTTATGTA
*
29604133 AGTTATGAA
1 AGTTATGTA
29604142 AGTTATGT-
1 AGTTATGTA
29604150 A-TTATGTA
1 AGTTATGTA
* *
29604158 ATTTATCTA
1 AGTTATGTA
*
29604167 AGTTGTGT-
1 AGTTATGTA
*
29604175 A-TTATGCA
1 AGTTATGTA
*
29604183 AGTCATGTA
1 AGTTATGTA
* *
29604192 GGCTATGT-
1 AGTTATGTA
29604200 A-TTATGTA
1 AGTTATGTA
29604208 AGTTAT-TA
1 AGTTATGTA
*
29604216 TGTTATTATGTA
1 AG---TTATGTA
*
29604228 AGTTATGAA
1 AGTTATGTA
*
29604237 AGTTATATATA
1 AG-T-TATGTA
29604248 AGTTAT-TA
1 AGTTATGTA
**
29604256 A-AAATGT-
1 AGTTATGTA
29604263 A-TTATGTA
1 AGTTATGTA
*
29604271 ATTTATGTA
1 AGTTATGTA
*
29604280 AGTTGTGT-
1 AGTTATGTA
*
29604288 A-TTATGCA
1 AGTTATGTA
*
29604296 AGTCATGTA
1 AGTTATGTA
* *
29604305 GGCTATGT-
1 AGTTATGTA
29604313 A-TTATGTA
1 AGTTATGTA
* *
29604321 AGTTACGAA
1 AGTTATGTA
*
29604330 AGTTTTATATA
1 AG--TTATGTA
*
29604341 AGTGAT-TA
1 AGTTATGTA
**
29604349 A-AAATGT-
1 AGTTATGTA
29604356 A-TTATGTA
1 AGTTATGTA
* *
29604364 ATTTATTTA
1 AGTTATGTA
29604373 AGTTATTATGTA
1 AG---TTATGTA
*
29604385 AGTTATGAA
1 AGTTATGTA
29604394 AGTTATGT-
1 AGTTATGTA
29604402 A-TTATGTA
1 AGTTATGTA
* *
29604410 ATTTATTTA
1 AGTTATGTA
29604419 AGTTATGTA
1 AGTTATGTA
*
29604428 AGTTGTGT-
1 AGTTATGTA
*
29604436 A-TTATGCA
1 AGTTATGTA
*
29604444 AGTCATGTA
1 AGTTATGTA
* *
29604453 GGCTATGT-
1 AGTTATGTA
29604461 A-TTATGTA
1 AGTTATGTA
29604469 AGTTAT-TA
1 AGTTATGTA
*
29604477 TATTATTATGTA
1 -A--GTTATGTA
*
29604489 AGTTATGAA
1 AGTTATGTA
29604498 AGTT
1 AGTT
29604502 GTATATAAGT
Statistics
Matches: 290, Mismatches: 72, Indels: 84
0.65 0.16 0.19
Matches are distributed among these distances:
7 58 0.20
8 32 0.11
9 158 0.54
10 6 0.02
11 23 0.08
12 13 0.04
ACGTcount: A:0.34, C:0.03, G:0.18, T:0.45
Consensus pattern (9 bp):
AGTTATGTA
Found at i:29604149 original size:25 final size:25
Alignment explanation
Indices: 29604115--29604495 Score: 205
Period size: 25 Copynumber: 16.4 Consensus size: 25
29604105 ATATGATTTA
*
29604115 TAAGTTATGTATAATGTAAGTTATG
1 TAAGTTATGTATTATGTAAGTTATG
* * *
29604140 AAAGTTATGTATTATGTAATTTATC
1 TAAGTTATGTATTATGTAAGTTATG
* * *
29604165 TAAGTTGTGTATTATGCAAGTCATG
1 TAAGTTATGTATTATGTAAGTTATG
* *
29604190 TAGGCTATGTATTATGTAAGTTAT-
1 TAAGTTATGTATTATGTAAGTTATG
*
29604214 T-A--TGT-TATTATGTAAGTTATG
1 TAAGTTATGTATTATGTAAGTTATG
*
29604235 AAAGTTA--TA-TA--TAAGTTAT-
1 TAAGTTATGTATTATGTAAGTTATG
** *
29604254 TAA-AAATGTATTATGTAATTTATG
1 TAAGTTATGTATTATGTAAGTTATG
* * *
29604278 TAAGTTGTGTATTATGCAAGTCATG
1 TAAGTTATGTATTATGTAAGTTATG
* * *
29604303 TAGGCTATGTATTATGTAAGTTACG
1 TAAGTTATGTATTATGTAAGTTATG
* *
29604328 AAAGTT-T-TA-TA--TAAGTGAT-
1 TAAGTTATGTATTATGTAAGTTATG
** * *
29604347 TAA-AAATGTATTATGTAATTTATT
1 TAAGTTATGTATTATGTAAGTTATG
29604371 TAAG---T-TATTATGTAAGTTATG
1 TAAGTTATGTATTATGTAAGTTATG
* * *
29604392 AAAGTTATGTATTATGTAATTTATT
1 TAAGTTATGTATTATGTAAGTTATG
*
29604417 TAAGTTATGTAAGTTGTGT-A-TTATG
1 TAAGTTATGT-A-TTATGTAAGTTATG
* * *
29604442 CAAGTCATGTAGGCTATGT-A-TTATG
1 TAAGTTATGTA--TTATGTAAGTTATG
29604467 TAAGTTAT-TA-TAT-T-A-TTATG
1 TAAGTTATGTATTATGTAAGTTATG
29604487 TAAGTTATG
1 TAAGTTATG
29604496 AAAGTTGTAT
Statistics
Matches: 271, Mismatches: 59, Indels: 56
0.70 0.15 0.15
Matches are distributed among these distances:
18 1 0.00
19 5 0.02
20 48 0.18
21 26 0.10
22 6 0.02
23 17 0.06
24 13 0.05
25 148 0.55
26 2 0.01
27 5 0.02
ACGTcount: A:0.34, C:0.03, G:0.18, T:0.45
Consensus pattern (25 bp):
TAAGTTATGTATTATGTAAGTTATG
Found at i:29604217 original size:113 final size:112
Alignment explanation
Indices: 29604091--29604325 Score: 334
Period size: 113 Copynumber: 2.1 Consensus size: 112
29604081 TAGATTTGAG
* * * * * *
29604091 TTATGTAAGTTATGATATGATT-TATAAGTTATG-TA-TA-ATGTAAGTTATGAAAGTTATGTAT
1 TTATGTAAGTTATTATGTTATTATATAAGTTATGAAAGTATATATAAGTTATGAAA--AATGTAT
29604152 TATGTAATTTATCTAAGTTGTGTATTATGCAAGTCATGTAGGCTATGTA
64 TATGTAATTTATCTAAGTTGTGTATTATGCAAGTCATGTAGGCTATGTA
* *
29604201 TTATGTAAGTTATTATGTTATTATGTAAGTTATGAAAGTTATATATAAGTTATTAAAAATGTATT
1 TTATGTAAGTTATTATGTTATTATATAAGTTATGAAAG-TATATATAAGTTATGAAAAATGTATT
*
29604266 ATGTAATTTATGTAAGTTGTGTATTATGCAAGTCATGTAGGCTATGTA
65 ATGTAATTTATCTAAGTTGTGTATTATGCAAGTCATGTAGGCTATGTA
29604314 TTATGTAAGTTA
1 TTATGTAAGTTA
29604326 CGAAAGTTTT
Statistics
Matches: 111, Mismatches: 9, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
110 19 0.17
111 10 0.09
112 1 0.01
113 66 0.59
114 2 0.02
115 13 0.12
ACGTcount: A:0.34, C:0.03, G:0.18, T:0.45
Consensus pattern (112 bp):
TTATGTAAGTTATTATGTTATTATATAAGTTATGAAAGTATATATAAGTTATGAAAAATGTATTA
TGTAATTTATCTAAGTTGTGTATTATGCAAGTCATGTAGGCTATGTA
Found at i:29604224 original size:20 final size:20
Alignment explanation
Indices: 29604195--29604255 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
29604185 TCATGTAGGC
29604195 TATG-TATTATGTAAGTTAT
1 TATGTTATTATGTAAGTTAT
29604214 TATGTTATTATGTAAGTTAT
1 TATGTTATTATGTAAGTTAT
* * *
29604234 GAAAGTTA-TATATAAGTTAT
1 -TATGTTATTATGTAAGTTAT
29604254 TA
1 TA
29604256 AAAATGTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 5 0.14
20 26 0.72
21 5 0.14
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (20 bp):
TATGTTATTATGTAAGTTAT
Found at i:29604379 original size:21 final size:21
Alignment explanation
Indices: 29604355--29604424 Score: 77
Period size: 21 Copynumber: 3.1 Consensus size: 21
29604345 ATTAAAAATG
29604355 TATTATGTAATTTATTTAAGT
1 TATTATGTAATTTATTTAAGT
* **
29604376 TATTATGTAAGTTATGAAAGTTAT
1 TATTATGTAATTTATTTAAG---T
29604400 GTATTATGTAATTTATTTAAGT
1 -TATTATGTAATTTATTTAAGT
29604422 TAT
1 TAT
29604425 GTAAGTTGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
21 20 0.51
22 1 0.03
24 1 0.03
25 17 0.44
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (21 bp):
TATTATGTAATTTATTTAAGT
Found at i:29604565 original size:42 final size:42
Alignment explanation
Indices: 29604518--29604600 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 42
29604508 AAGTTATTAA
*
29604518 AAATA-TACATAAATTTTTAA-TATATATATTAAAAATGTATAT
1 AAATATTA-ATAAATTATTAAGT-TATATATTAAAAATGTATAT
* *
29604560 AAATATTAATAAGTTATTAAGTTATATATTAAAAATTTATA
1 AAATATTAATAAATTATTAAGTTATATATTAAAAATGTATA
29604601 AGTTATGTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
42 33 0.92
43 3 0.08
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.43
Consensus pattern (42 bp):
AAATATTAATAAATTATTAAGTTATATATTAAAAATGTATAT
Found at i:29604590 original size:23 final size:22
Alignment explanation
Indices: 29604562--29604606 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
29604552 ATGTATATAA
*
29604562 ATATTAATAAGTTATTAAGTTAT
1 ATATTAAAAAGTTA-TAAGTTAT
*
29604585 ATATTAAAAATTTATAAGTTAT
1 ATATTAAAAAGTTATAAGTTAT
29604607 GTAAATTATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (22 bp):
ATATTAAAAAGTTATAAGTTAT
Found at i:29604602 original size:30 final size:30
Alignment explanation
Indices: 29604555--29604615 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
29604545 ATTAAAAATG
* *
29604555 TATATAAATATTAATAAGTTAT-TAAGTTA
1 TATATAAAAATTAATAAGTTATGTAAATTA
*
29604584 TATATTAAAAATTTATAAGTTATGTAAATTA
1 TATA-TAAAAATTAATAAGTTATGTAAATTA
29604615 T
1 T
29604616 GCAAGTTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 4 0.15
30 16 0.59
31 7 0.26
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.46
Consensus pattern (30 bp):
TATATAAAAATTAATAAGTTATGTAAATTA
Found at i:29606687 original size:22 final size:22
Alignment explanation
Indices: 29606662--29606711 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
29606652 AGTGCCTAGA
29606662 CTAAAAAAGGTTCAAAGTTGCC
1 CTAAAAAAGGTTCAAAGTTGCC
29606684 CTAAAAAAGGTTCAAAGTTGCC
1 CTAAAAAAGGTTCAAAGTTGCC
29606706 CTAAAA
1 CTAAAA
29606712 TAAACTTACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.44, C:0.18, G:0.16, T:0.22
Consensus pattern (22 bp):
CTAAAAAAGGTTCAAAGTTGCC
Found at i:29607636 original size:102 final size:105
Alignment explanation
Indices: 29607523--29607714 Score: 302
Period size: 105 Copynumber: 1.9 Consensus size: 105
29607513 GCAATTTCAA
29607523 TTTGAACAAAATGACGCCGTTTTGCTATGCACAA-AA-TTT-TTTAT-TTTTTTATAATTTGATT
1 TTTGAACAAAATGACGCCGTTTTGCTATGCA-AATAATTTTATTTATATTTTTTATAATTTGATT
* *
29607584 TATTTTTTGCGGCGTTTTTATGAAAAGCGCTACTATTTGAT
65 TATATTTTGCGGCGTTTTTATAAAAAGCGCTACTATTTGAT
* * *
29607625 TTTGAACAAAATGACGCCGTTTTTCTATGCAAATAATTTTATTTTTATTTTTTATAATTTTATTT
1 TTTGAACAAAATGACGCCGTTTTGCTATGCAAATAATTTTATTTATATTTTTTATAATTTGATTT
29607690 ATATTTTGCGGCGTTTTTATAAAAA
66 ATATTTTGCGGCGTTTTTATAAAAA
29607715 ATGCCGCTAT
Statistics
Matches: 81, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
101 2 0.02
102 32 0.40
103 3 0.04
104 4 0.05
105 40 0.49
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.49
Consensus pattern (105 bp):
TTTGAACAAAATGACGCCGTTTTGCTATGCAAATAATTTTATTTATATTTTTTATAATTTGATTT
ATATTTTGCGGCGTTTTTATAAAAAGCGCTACTATTTGAT
Found at i:29607681 original size:21 final size:21
Alignment explanation
Indices: 29607657--29607696 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
29607647 TTCTATGCAA
*
29607657 ATAATTTTATTTTTATTTTTT
1 ATAATTTTATTTATATTTTTT
29607678 ATAATTTTATTTATATTTT
1 ATAATTTTATTTATATTTT
29607697 GCGGCGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (21 bp):
ATAATTTTATTTATATTTTTT
Found at i:29607725 original size:105 final size:102
Alignment explanation
Indices: 29607505--29607725 Score: 291
Period size: 105 Copynumber: 2.1 Consensus size: 102
29607495 TTAAATTGAT
*
29607505 AAAACGCCGCAATTTCAATTTGAACAAAATGACGCCGTTTTGCTATGCACAAAATTTTTTATTTT
1 AAAACGCCGCTATTTCAATTTGAACAAAATGACGCCGTTTTGCTATGCACAAAATTTTTTATTTT
* *
29607570 TTTATAATTTGATTTATTTTTTGCGGCGTTTTTATGA
66 TTTATAATTTGATTTATATTTTGCGGCGTTTTTATAA
* ** * * * *
29607607 AAAGCGCTACTATTTGATTTTGAACAAAATGACGCCGTTTTTCTATGCA-AATAATTTTATTTTT
1 AAAACGCCGCTATTTCAATTTGAACAAAATGACGCCGTTTTGCTATGCACAA-AA-TTT-TTTAT
*
29607671 ATTTTTTATAATTTTATTTATATTTTGCGGCGTTTTTATAA
63 -TTTTTTATAATTTGATTTATATTTTGCGGCGTTTTTATAA
*
29607712 AAAATGCCGCTATT
1 AAAACGCCGCTATT
29607726 GCTTATCTTT
Statistics
Matches: 100, Mismatches: 15, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
101 2 0.02
102 44 0.44
103 3 0.03
104 4 0.04
105 47 0.47
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.46
Consensus pattern (102 bp):
AAAACGCCGCTATTTCAATTTGAACAAAATGACGCCGTTTTGCTATGCACAAAATTTTTTATTTT
TTTATAATTTGATTTATATTTTGCGGCGTTTTTATAA
Found at i:29607836 original size:137 final size:137
Alignment explanation
Indices: 29607667--29607939 Score: 408
Period size: 137 Copynumber: 2.0 Consensus size: 137
29607657 ATAATTTTAT
* * *
29607667 TTTTATTTTTTATAATTTTATTTATATTTTGCGGCGTTTTTATA-AAAAATGCCGCTA-TTGCTT
1 TTTTATTTTCTATAAATTGATTTATATTTTGCGGCGTTTTTATAGAAAAAT-CCGCTATTTG-TT
* *
29607730 ATCTTTTGCGGCGTTTTTGTGAAAAACGCCGCAAAATATTATTTCATTTTGAACAAAATGACGCC
64 ATCTTTTGCGGCGTTTTTATGAAAAACGCCGCAAAATATTATTTCATTATGAACAAAATGACGCC
29607795 GTTTTGCTA
129 GTTTTGCTA
* *
29607804 TTTTGTTTTCTATAAATTGATTTAT-TTCTTGCGGCGTTTTTATAGAAAACTCCGCTATTTGTTA
1 TTTTATTTTCTATAAATTGATTTATATT-TTGCGGCGTTTTTATAGAAAAATCCGCTATTTGTTA
* * *
29607868 TCTTTTGCGGCGTTTTTATGCAAAACGCTGCAAAATATTATTTCATTATGAACAAAATGACGGCG
65 TCTTTTGCGGCGTTTTTATGAAAAACGCCGCAAAATATTATTTCATTATGAACAAAATGACGCCG
29607933 TTTTGCT
130 TTTTGCT
29607940 CTGCTAATTT
Statistics
Matches: 123, Mismatches: 10, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
136 2 0.02
137 113 0.92
138 8 0.07
ACGTcount: A:0.26, C:0.14, G:0.15, T:0.45
Consensus pattern (137 bp):
TTTTATTTTCTATAAATTGATTTATATTTTGCGGCGTTTTTATAGAAAAATCCGCTATTTGTTAT
CTTTTGCGGCGTTTTTATGAAAAACGCCGCAAAATATTATTTCATTATGAACAAAATGACGCCGT
TTTGCTA
Found at i:29608296 original size:15 final size:15
Alignment explanation
Indices: 29608263--29608304 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
29608253 CCCTAACTCT
**
29608263 TAACCCCT-AACGTC
1 TAACCCCTAAACCCC
*
29608277 TAACCGCTAAACCCC
1 TAACCCCTAAACCCC
29608292 TAACCCCTAAACC
1 TAACCCCTAAACC
29608305 TTAAATCCCA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.33, C:0.45, G:0.05, T:0.17
Consensus pattern (15 bp):
TAACCCCTAAACCCC
Found at i:29608691 original size:296 final size:289
Alignment explanation
Indices: 29608138--29608718 Score: 707
Period size: 296 Copynumber: 2.0 Consensus size: 289
29608128 AATATATTTG
29608138 ATTTATTATTATCTCTTTTACAATTATATAAGAACATATTTAAAATATAAATTAAAAAATAATTA
1 ATTTATTATTATCTCTTTTACAATTATATAAGAACATATTTAAAATATAAATT-AAAAATAATTA
* * *
29608203 ATCTAAACTCAAAAACCTTAACTCGACCCCTGAATCCCTAAACTTTAAATCCCTAACTCTTAACC
65 ATCTAAACCCAAAAACCTTAACTCGACCCCTAAATCCCTAAACTTTAAATCCCTAAATCTTAACC
** * *
29608268 CCTAACGTCTAACCGCTAAACCCCTAACCCCTAAACCTTAAATCCCAACCATTAAACCATAATTC
130 CCTAACCCCTAACCGCTAAACCCCTAACCCCTAAACCTTAAATCCCAACCACTAAACCATAATCC
* *
29608333 CTAAACCCATACTCCCTAAACCTTAAAATATGAACTCCTAAACCGGCCTTAAATCTTAAATAAAT
195 CTAAACCCATACTCCATAAACCTTAAAATACGAACTCCTAAACCGGCCTTAAATCTTAAATAAAT
* *
29608398 CATATACCCTAAACCAAAAGCCCTAAACAA
260 CATAGACCCTAAACCAAAAACCCTAAACAA
29608428 ATTTATTATTATCTCTTTTACAATTATATAAGAACATATTTAAAATATAAATT-AAAA-AATTAA
1 ATTTATTATTATCTCTTTTACAATTATATAAGAACATATTTAAAATATAAATTAAAAATAATTAA
* *
29608491 TCTAAACGCCCAAAATCC-TAACTCGACCCCTAAATCCCT-AACTCTT-AA--CCTCAAATGTTT
66 TCTAAA--CCCAAAAACCTTAACTCGACCCCTAAATCCCTAAACT-TTAAATCCCT-AAAT-CTT
* * * *
29608551 AACCCCTAAACCCCATAACC-CTTTAACCCCTAAACCTTAAATCTCAACCCTTAAA-CCGTAATC
126 AACCCCT-AACCCC-TAACCGC-TAAACCCCT-AACC-----CCT-AAACCTTAAATCC-CAA-C
* * * * *
29608614 C-CTAATCCCTAATCCCTAAACCCATACTCCATATATCTTAAAA-ACGTAACTCCTAAACTGGCC
179 CACTAAACCATAATCCCTAAACCCATACTCCATAAACCTTAAAATACG-AACTCCTAAACCGGCC
*
29608677 TTAAATCTTAAATAATTCATAGACCCTAAACCAAAAACCCTA
243 TTAAATCTTAAATAAATCATAGACCCTAAACCAAAAACCCTA
29608719 TGTTTTTTTT
Statistics
Matches: 250, Mismatches: 23, Indels: 30
0.83 0.08 0.10
Matches are distributed among these distances:
285 3 0.01
286 3 0.01
287 27 0.11
288 31 0.12
289 21 0.08
290 57 0.23
295 6 0.02
296 100 0.40
297 2 0.01
ACGTcount: A:0.41, C:0.28, G:0.03, T:0.28
Consensus pattern (289 bp):
ATTTATTATTATCTCTTTTACAATTATATAAGAACATATTTAAAATATAAATTAAAAATAATTAA
TCTAAACCCAAAAACCTTAACTCGACCCCTAAATCCCTAAACTTTAAATCCCTAAATCTTAACCC
CTAACCCCTAACCGCTAAACCCCTAACCCCTAAACCTTAAATCCCAACCACTAAACCATAATCCC
TAAACCCATACTCCATAAACCTTAAAATACGAACTCCTAAACCGGCCTTAAATCTTAAATAAATC
ATAGACCCTAAACCAAAAACCCTAAACAA
Found at i:29609032 original size:115 final size:114
Alignment explanation
Indices: 29608740--29609400 Score: 857
Period size: 115 Copynumber: 5.8 Consensus size: 114
29608730 CAGCGCTTTA
* * * *
29608740 CTAAAAAACGCCGCTAAATCTCCCGAAAGCTCAGAAAACGACATCGTTGGGCTTAGTTTATTTTG
1 CTAAAAAACGCCACTAAATC-CGCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGTTTATTTTG
* * * * * *
29608805 CGACGCTTCATCAAAAATGCTGCTAAATCCTTGAGCATTAGCCGCGCTTC
65 CGGCGCTTCATCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTC
* *
29608855 CT-AAAAATGCCACTAAATCCGCGAAAGCTCAGAAAACGGCGTTGTTGGGCTTAGTTTATTTTGC
1 CTAAAAAACGCCACTAAATCCGCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGTTTATTTTGC
* ** *
29608919 AGCGCTTCCCCAAAAACGCCGCTAAAGCCCTTAGCATTAGCGGCGCTTTC
66 GGCGCTTCATCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGC-TTC
* * * * * *
29608969 TTAAGAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTAATGTCT-TTTTG
1 CTAAAAAACGCCACTAAATCCGCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTA-GTTTATTTTG
* * * * *
29609033 CGGCGCTTTATCAAAAACACCGTTAAAGCCCTGAGCATTAGCGACACTTC
65 CGGCGCTTCATCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTC
* * *
29609083 CTAAAAAACGCCACTAAATTCGCGAAAGCTCAGAAAACGGTGTCGTTGGCCTTAGTTTATTTTGC
1 CTAAAAAACGCCACTAAATCCGCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGTTTATTTTGC
*
29609148 GGCGCTTCATCAAAAACGCCGCTAAAGCCCTCAGCATTAGCGGCGCTTC
66 GGCGCTTCATCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTC
* * * *
29609197 CTTAAAAAACGCCGCTAAATCCACGAAAGCTCAGAAAACGGCGTCGTTGGACTTATGTCT-TTTT
1 C-TAAAAAACGCCACTAAATCCGCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTA-GTTTATTTT
29609261 GCGGCGCTTTC-TCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTC
64 GCGGCGC-TTCATCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTC
* * *
29609312 CTAAGAAACGCCACTAAATCTGCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTT-TTTTGC
1 CTAAAAAACGCCACTAAATCCGCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGTTTATTTTGC
* *
29609376 GGCGCTTTC-TGAAAAACACCGCTAA
66 GGCGC-TTCATCAAAAACGCCGCTAA
29609401 TACTATTTTT
Statistics
Matches: 475, Mismatches: 64, Indels: 16
0.86 0.12 0.03
Matches are distributed among these distances:
113 111 0.23
114 166 0.35
115 189 0.40
116 9 0.02
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.24
Consensus pattern (114 bp):
CTAAAAAACGCCACTAAATCCGCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGTTTATTTTGC
GGCGCTTCATCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTC
Found at i:29609146 original size:229 final size:228
Alignment explanation
Indices: 29608732--29609400 Score: 952
Period size: 229 Copynumber: 2.9 Consensus size: 228
29608722 TTTTTTTGCA
* *
29608732 GCGCTTTAC-TAAAAAACGCCGCTAAATCTCCCGAAAGCTCAGAAAACGACATCGTTGGGCTTA-
1 GCGCTTT-CTTAAAAAACGCCGCTAAATC-CCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAT
* * * * * * *
29608795 GTTTATTTTGCGACGCTTCATCAAAAATGCTGCTAAATCCTTGAGCATTAGCCGCGCTTCCT-AA
64 GTCT-TTTTGCGGCGCTTTATCAAAAACGCCGCTAAAGCCCTGAGCATTAG-CGCGCTTCCTAAA
* * * *
29608859 AAATGCCACTAAATCCGCGAAAGCTCAGAAAACGGCGTTGTTGGGCTTAGTTTATTTTGCAGCGC
127 AAACGCCACTAAATTCGCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGTTTATTTTGCGGCGC
* *
29608924 TTCCCCAAAAACGCCGCTAAAGCCCTTAGCATTAGCG
192 TTCCTCAAAAACGCCGCTAAAGCCCTCAGCATTAGCG
* *
29608961 GCGCTTTCTTAAGAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTAATGT
1 GCGCTTTCTTAAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTATGT
* * *
29609026 CTTTTTGCGGCGCTTTATCAAAAACACCGTTAAAGCCCTGAGCATTAGCGACACTTCCTAAAAAA
66 CTTTTTGCGGCGCTTTATCAAAAACGCCGCTAAAGCCCTGAGCATTAGCG-CGCTTCCTAAAAAA
* *
29609091 CGCCACTAAATTCGCGAAAGCTCAGAAAACGGTGTCGTTGGCCTTAGTTTATTTTGCGGCGCTTC
130 CGCCACTAAATTCGCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGTTTATTTTGCGGCGCTTC
*
29609156 ATCAAAAACGCCGCTAAAGCCCTCAGCATTAGCG
195 CTCAAAAACGCCGCTAAAGCCCTCAGCATTAGCG
* * *
29609190 GCGCTTCCTTAAAAAACGCCGCTAAATCCACGAAAGCTCAGAAAACGGCGTCGTTGGACTTATGT
1 GCGCTTTCTTAAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTATGT
* *
29609255 CTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCCTAAGAAA
66 CTTTTTGCGGCGCTTTATCAAAAACGCCGCTAAAGCCCTGAGCATTAGC-GCGCTTCCTAAAAAA
*
29609320 CGCCACTAAA-TCTGCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTT-TTTTGCGGCGCTT
130 CGCCACTAAATTC-GCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGTTTATTTTGCGGCGCTT
* * *
29609383 TCTGAAAAACACCGCTAA
194 CCTCAAAAACGCCGCTAA
29609401 TACTATTTTT
Statistics
Matches: 394, Mismatches: 40, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
227 2 0.01
228 106 0.27
229 285 0.72
230 1 0.00
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.24
Consensus pattern (228 bp):
GCGCTTTCTTAAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTATGT
CTTTTTGCGGCGCTTTATCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGCGCTTCCTAAAAAAC
GCCACTAAATTCGCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGTTTATTTTGCGGCGCTTCC
TCAAAAACGCCGCTAAAGCCCTCAGCATTAGCG
Found at i:29625391 original size:44 final size:42
Alignment explanation
Indices: 29625273--29625395 Score: 108
Period size: 44 Copynumber: 3.0 Consensus size: 42
29625263 CTTCAAGTTC
* * *
29625273 TAGCGAAGTAGATCGAAGCTACAAATCTCTTCTCCCTGACAT
1 TAGCGGAGTAGATTGAAGCTACAAATCTCTTCTCCCTGAAAT
* * * * * ***
29625315 T---GGAGCAGATTGAAGCCATAAGTTTAACCTCCCTGAAATT
1 TAGCGGAGTAGATTGAAGCTACAAATCTCTTCTCCCTGAAA-T
29625355 ATAGCGGAGTAGATTGAAGCTACAAATCTCTTCTCCCTGAA
1 -TAGCGGAGTAGATTGAAGCTACAAATCTCTTCTCCCTGAA
29625396 TTTGCAGCGG
Statistics
Matches: 57, Mismatches: 19, Indels: 8
0.68 0.23 0.10
Matches are distributed among these distances:
39 26 0.46
40 1 0.02
41 1 0.02
42 1 0.02
44 28 0.49
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.27
Consensus pattern (42 bp):
TAGCGGAGTAGATTGAAGCTACAAATCTCTTCTCCCTGAAAT
Found at i:29632086 original size:23 final size:23
Alignment explanation
Indices: 29632056--29632100 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
29632046 ACCAAGTTTT
29632056 TTTTTAAG-TTTTGCATCAAGTTC
1 TTTTTAAGCTTTT-CATCAAGTTC
29632079 TTTTTAAGCTTTTCATCAAGTT
1 TTTTTAAGCTTTTCATCAAGTT
29632101 TTCAATCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.22, C:0.13, G:0.11, T:0.53
Consensus pattern (23 bp):
TTTTTAAGCTTTTCATCAAGTTC
Found at i:29634423 original size:21 final size:22
Alignment explanation
Indices: 29634360--29634425 Score: 66
Period size: 21 Copynumber: 3.1 Consensus size: 22
29634350 GACGGGCTAC
* *
29634360 TCACACGACCATGTA-ACTCTT
1 TCACACGGCCGTGTAGACTCTT
* * *
29634381 TCAAACGGGCGTGT-GCCTCTT
1 TCACACGGCCGTGTAGACTCTT
29634402 TCACACGGCCGTGTAGAC-CTT
1 TCACACGGCCGTGTAGACTCTT
29634423 TCA
1 TCA
29634426 TACAGCCTAG
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
21 33 0.94
22 2 0.06
ACGTcount: A:0.21, C:0.32, G:0.20, T:0.27
Consensus pattern (22 bp):
TCACACGGCCGTGTAGACTCTT
Found at i:29636982 original size:72 final size:70
Alignment explanation
Indices: 29636867--29637011 Score: 175
Period size: 72 Copynumber: 2.0 Consensus size: 70
29636857 ATTGCAAATG
** * * * *
29636867 ACAACTATCATCAGTTATCTGACTAGCGCTGGGTACAATAATTTGTCGACTT-GTTCGACTAGTG
1 ACAACTATCATCAGTTATCCAACTAGCACTAGGCACAATAATTTGTCGA-TTGGTGCGACTAGTG
*
29636931 TTAGGC
65 CTAGGC
*
29636937 ACAACTATTTCATCAGTTATCCAACTAGCACTAGGCGCAATAATTTGTCGATTGGTGCGACTAGT
1 ACAACTA--TCATCAGTTATCCAACTAGCACTAGGCACAATAATTTGTCGATTGGTGCGACTAGT
*
29637002 GCTGGGC
64 GCTAGGC
29637009 ACA
1 ACA
29637012 CCAAGAATCT
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
70 7 0.11
71 2 0.03
72 54 0.86
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.30
Consensus pattern (70 bp):
ACAACTATCATCAGTTATCCAACTAGCACTAGGCACAATAATTTGTCGATTGGTGCGACTAGTGC
TAGGC
Found at i:29641202 original size:14 final size:16
Alignment explanation
Indices: 29641177--29641208 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
29641167 AAAATAATTA
29641177 TTTAGTTTTATT-TTT
1 TTTAGTTTTATTATTT
29641192 TTTAG-TTTATTATTT
1 TTTAGTTTTATTATTT
29641207 TT
1 TT
29641209 GGTTGTTGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.16, C:0.00, G:0.06, T:0.78
Consensus pattern (16 bp):
TTTAGTTTTATTATTT
Found at i:29653247 original size:40 final size:38
Alignment explanation
Indices: 29653186--29653263 Score: 86
Period size: 40 Copynumber: 2.0 Consensus size: 38
29653176 AATATTTAAT
29653186 TAATTTTTTAAATTTAAAAAATATTAAAAATATTTTATTA
1 TAATTTTTTAAATTTAAAAAAT-TTAAAAA-ATTTTATTA
* * **
29653226 TAATTTTTTGAACTTT-TAAAATTTTTAAAATTTTATTA
1 TAATTTTTT-AAATTTAAAAAATTTAAAAAATTTTATTA
29653264 AATGATGACG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
38 9 0.27
39 5 0.15
40 14 0.42
41 5 0.15
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (38 bp):
TAATTTTTTAAATTTAAAAAATTTAAAAAATTTTATTA
Found at i:29656409 original size:6 final size:6
Alignment explanation
Indices: 29656398--29656424 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
29656388 ATTATTTTTC
29656398 TTAATT TTAATT TTAATT TTAATT TTA
1 TTAATT TTAATT TTAATT TTAATT TTA
29656425 TTTCCCAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TTAATT
Found at i:29658440 original size:29 final size:29
Alignment explanation
Indices: 29658397--29658457 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
29658387 AAAGTAAGTA
* * *
29658397 TGTGGTATACTGAGTTTCGGTGTCGATCT
1 TGTGGTATACCGAGTTTCAGCGTCGATCT
29658426 TGTGGTATACCGAGTTTCAGCGTCGATCT
1 TGTGGTATACCGAGTTTCAGCGTCGATCT
29658455 TGT
1 TGT
29658458 AAGTACTTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.15, C:0.16, G:0.30, T:0.39
Consensus pattern (29 bp):
TGTGGTATACCGAGTTTCAGCGTCGATCT
Found at i:29674110 original size:30 final size:30
Alignment explanation
Indices: 29674069--29674175 Score: 108
Period size: 30 Copynumber: 3.4 Consensus size: 30
29674059 GATATTCAGA
* *
29674069 AGCTTGAGAAGACCTGATATCTTGTTCAAG
1 AGCTTGGGAAGACCTGATATCTCGTTCAAG
29674099 AGCTTGGGAAGA-CTCGATATCTCGTTCAAG
1 AGCTTGGGAAGACCT-GATATCTCGTTCAAG
* *
29674129 ATCTTGGGATTGAGACGACTTGATATCTCATTCAAG
1 AGCTTGGGA---AGAC--C-TGATATCTCGTTCAAG
29674165 AGCTTGGGAAG
1 AGCTTGGGAAG
29674176 GCTCGATATT
Statistics
Matches: 64, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
29 2 0.03
30 33 0.52
33 5 0.08
36 23 0.36
37 1 0.02
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (30 bp):
AGCTTGGGAAGACCTGATATCTCGTTCAAG
Found at i:29674181 original size:66 final size:66
Alignment explanation
Indices: 29674072--29674251 Score: 220
Period size: 66 Copynumber: 2.7 Consensus size: 66
29674062 ATTCAGAAGC
* * **
29674072 TTGAGAAGACCTGATATCTTGTTCAAGAGCTTGGGAAGACTCGATATCT-CGTTCAAGATCTTGG
1 TTGAGAAGACTTGATATCTTGTTCAAGAGCTTGGGAAGACTCGATAT-TGCGTTCAAGAGCTTAA
29674136 GA
65 GA
* ** * * *
29674138 TTGAGACGACTTGATATCTCATTCAAGAGCTTGGGAAGGCTCGATATTGCGTTTAGGAGCTTAAG
1 TTGAGAAGACTTGATATCTTGTTCAAGAGCTTGGGAAGACTCGATATTGCGTTCAAGAGCTTAAG
29674203 A
66 A
* *
29674204 TTGAAAAGACTTGTTATCTTGTTCAAGAGCTTGGGAAGA-TCCGATATT
1 TTGAGAAGACTTGATATCTTGTTCAAGAGCTTGGGAAGACT-CGATATT
29674252 TATTTTTCTC
Statistics
Matches: 96, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
65 2 0.02
66 94 0.98
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.32
Consensus pattern (66 bp):
TTGAGAAGACTTGATATCTTGTTCAAGAGCTTGGGAAGACTCGATATTGCGTTCAAGAGCTTAAG
A
Found at i:29694399 original size:27 final size:27
Alignment explanation
Indices: 29694369--29694424 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
29694359 TAAAACAAGT
29694369 GAGAAAAAAGAAAAAGAGAATGAAAAG
1 GAGAAAAAAGAAAAAGAGAATGAAAAG
* ** *
29694396 GAGAAAAAAGAGATTGAGAGTGAAAAG
1 GAGAAAAAAGAAAAAGAGAATGAAAAG
29694423 GA
1 GA
29694425 ATGTGAAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.62, C:0.00, G:0.30, T:0.07
Consensus pattern (27 bp):
GAGAAAAAAGAAAAAGAGAATGAAAAG
Found at i:29694438 original size:18 final size:18
Alignment explanation
Indices: 29694417--29694456 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
29694407 GATTGAGAGT
* * *
29694417 GAAAAGGAATGTGAAACA
1 GAAAAGAAAAGTGAAAAA
29694435 GAAAAGAAAAGTGAAAAA
1 GAAAAGAAAAGTGAAAAA
29694453 GAAA
1 GAAA
29694457 TTGAAGAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.65, C:0.03, G:0.25, T:0.07
Consensus pattern (18 bp):
GAAAAGAAAAGTGAAAAA
Found at i:29700485 original size:30 final size:31
Alignment explanation
Indices: 29700427--29700489 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 31
29700417 GGGGGAGTGC
29700427 TGGAGTGATTTTAAGAGGGAAAAAATGGGAT
1 TGGAGTGATTTTAAGAGGGAAAAAATGGGAT
* *
29700458 TGGAGTGATTTTAGGA-GGAAAATATGGGAT
1 TGGAGTGATTTTAAGAGGGAAAAAATGGGAT
29700488 TG
1 TG
29700490 TGGAGTTATC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 15 0.50
31 15 0.50
ACGTcount: A:0.35, C:0.00, G:0.37, T:0.29
Consensus pattern (31 bp):
TGGAGTGATTTTAAGAGGGAAAAAATGGGAT
Found at i:29702452 original size:42 final size:43
Alignment explanation
Indices: 29702384--29702478 Score: 124
Period size: 42 Copynumber: 2.2 Consensus size: 43
29702374 TGTGACATCG
* *
29702384 TGTAAGACCACGTCTGGGAAATTGGCATCA-TATGTT-ATTACA
1 TGTAAGACCACGTCTAGGAAAGTGGCATCATTAT-TTGATTACA
*
29702426 TGTAAGACC-CTGTCTAGGATAGTGGCATCATTATTTGATTACA
1 TGTAAGACCAC-GTCTAGGAAAGTGGCATCATTATTTGATTACA
29702469 TGTAAGACCA
1 TGTAAGACCA
29702479 TGTATGGGAC
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
41 1 0.02
42 27 0.59
43 18 0.39
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.32
Consensus pattern (43 bp):
TGTAAGACCACGTCTAGGAAAGTGGCATCATTATTTGATTACA
Found at i:29702495 original size:43 final size:42
Alignment explanation
Indices: 29702384--29702496 Score: 131
Period size: 43 Copynumber: 2.7 Consensus size: 42
29702374 TGTGACATCG
* *
29702384 TGTAAGACCACGTCTGGGAAATTGGCATCATATGTTATTACA
1 TGTAAGACCATGTCTGGGAAGTTGGCATCATATGTTATTACA
* *
29702426 TGTAAGACCCTGTCTAGGATAG-TGGCATCATTAT-TTGATTACA
1 TGTAAGACCATGTCTGGGA-AGTTGGCATCA-TATGTT-ATTACA
* *
29702469 TGTAAGACCATGTATGGGACGTTGGCAT
1 TGTAAGACCATGTCTGGGAAGTTGGCAT
29702497 TGTACTAGCT
Statistics
Matches: 59, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
42 27 0.46
43 32 0.54
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGAAGTTGGCATCATATGTTATTACA
Found at i:29703305 original size:22 final size:22
Alignment explanation
Indices: 29703280--29703562 Score: 273
Period size: 22 Copynumber: 12.9 Consensus size: 22
29703270 AAGTAAATAT
29703280 TGTTGATTAAATGTTGTCCAAA
1 TGTTGATTAAATGTTGTCCAAA
***
29703302 TGTTGATTAAAT-TCTGTTTGAA
1 TGTTGATTAAATGT-TGTCCAAA
* * * *
29703324 TGTTGATTGAATGGTGTCTAAT
1 TGTTGATTAAATGTTGTCCAAA
* *
29703346 TGTTGATTGAAT-TGTGTCCAAT
1 TGTTGATTAAATGT-TGTCCAAA
* *
29703368 TGTTGATTAAAAGCTGTCCAAA
1 TGTTGATTAAATGTTGTCCAAA
* *
29703390 TGTTGATTAAATGATGTTCAAA
1 TGTTGATTAAATGTTGTCCAAA
* *
29703412 TGTTGATTGAATGTTGTCCAAT
1 TGTTGATTAAATGTTGTCCAAA
* * *
29703434 TGTTGATTGAATGCTGTCCAAT
1 TGTTGATTAAATGTTGTCCAAA
29703456 TGTTGATTAAATGTTGTCCAAA
1 TGTTGATTAAATGTTGTCCAAA
29703478 TGTTGATTAAATGTTGTCCAAA
1 TGTTGATTAAATGTTGTCCAAA
* * * ** *
29703500 TGTTTATTGAATGCTGTATAAT
1 TGTTGATTAAATGTTGTCCAAA
**
29703522 TGTTGATTAAATGTTGTCTGAA
1 TGTTGATTAAATGTTGTCCAAA
* * *
29703544 TGTTGGTTAATTGCTGTCC
1 TGTTGATTAAATGTTGTCC
29703563 GTTTTTGAGC
Statistics
Matches: 216, Mismatches: 41, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
21 1 0.00
22 215 1.00
ACGTcount: A:0.27, C:0.08, G:0.21, T:0.43
Consensus pattern (22 bp):
TGTTGATTAAATGTTGTCCAAA
Found at i:29703364 original size:66 final size:67
Alignment explanation
Indices: 29703280--29703562 Score: 301
Period size: 66 Copynumber: 4.3 Consensus size: 67
29703270 AAGTAAATAT
* * * *
29703280 TGTTGATTAAATGTTGTCCAAATGTTGATTAAATTCTGTTTGAA-TGTTGATTGAATGGTGTCT-
1 TGTTGATTAAATGTTGTCCAAATGTTGATTAAATGCTG-TTCAATTGTTGATTAAATGTTGTCTC
*
29703343 AAT
65 AAA
* * * * * *
29703346 TGTTGATTGAAT-TGTGTCCAATTGTTGATTAAAAGCTGTCCAAATGTTGATTAAATGATGT-TC
1 TGTTGATTAAATGT-TGTCCAAATGTTGATTAAATGCTGTTCAATTGTTGATTAAATGTTGTCTC
29703409 AAA
65 AAA
* * * *
29703412 TGTTGATTGAATGTTGTCCAATTGTTGATTGAATGCTGTCCAATTGTTGATTAAATGTTGTC-CA
1 TGTTGATTAAATGTTGTCCAAATGTTGATTAAATGCTGTTCAATTGTTGATTAAATGTTGTCTCA
29703476 AA
66 AA
* *
29703478 TGTTGATTAAATGTTGTCCAAATGTTTATTGAATGCTGTAT-AATTGTTGATTAAATGTTGTCT-
1 TGTTGATTAAATGTTGTCCAAATGTTGATTAAATGCTGT-TCAATTGTTGATTAAATGTTGTCTC
*
29703541 GAA
65 AAA
* * *
29703544 TGTTGGTTAATTGCTGTCC
1 TGTTGATTAAATGTTGTCC
29703563 GTTTTTGAGC
Statistics
Matches: 189, Mismatches: 21, Indels: 14
0.84 0.09 0.06
Matches are distributed among these distances:
65 5 0.03
66 183 0.97
67 1 0.01
ACGTcount: A:0.27, C:0.08, G:0.21, T:0.43
Consensus pattern (67 bp):
TGTTGATTAAATGTTGTCCAAATGTTGATTAAATGCTGTTCAATTGTTGATTAAATGTTGTCTCA
AA
Found at i:29703548 original size:88 final size:88
Alignment explanation
Indices: 29703278--29703562 Score: 369
Period size: 88 Copynumber: 3.2 Consensus size: 88
29703268 TGAAGTAAAT
* ** *
29703278 ATTGTTGATTAAATGTTGTCCAAATGTTGATTAAAT-TCTGTTTGAATGTTGATTGAATGGTGTC
1 ATTGTTGATTAAATGCTGTCCAAATGTTGATTAAATGT-TGTTCAAATGTTGATTGAATGCTGTC
29703342 TAATTGTTGATTGAAT-TGTGTCCA
65 TAATTGTTGATTGAATGT-TGTCCA
* * * *
29703366 ATTGTTGATTAAAAGCTGTCCAAATGTTGATTAAATGATGTTCAAATGTTGATTGAATGTTGTCC
1 ATTGTTGATTAAATGCTGTCCAAATGTTGATTAAATGTTGTTCAAATGTTGATTGAATGCTGTCT
*
29703431 AATTGTTGATTGAATGCTGTCCA
66 AATTGTTGATTGAATGTTGTCCA
* * * *
29703454 ATTGTTGATTAAATGTTGTCCAAATGTTGATTAAATGTTGTCCAAATGTTTATTGAATGCTGTAT
1 ATTGTTGATTAAATGCTGTCCAAATGTTGATTAAATGTTGTTCAAATGTTGATTGAATGCTGTCT
* *
29703519 AATTGTTGATTAAATGTTGTCTGA
66 AATTGTTGATTGAATGTTGTC-CA
* *
29703543 A-TGTTGGTTAATTGCTGTCC
1 ATTGTTGATTAAATGCTGTCC
29703563 GTTTTTGAGC
Statistics
Matches: 172, Mismatches: 22, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
88 170 0.99
89 2 0.01
ACGTcount: A:0.27, C:0.08, G:0.21, T:0.44
Consensus pattern (88 bp):
ATTGTTGATTAAATGCTGTCCAAATGTTGATTAAATGTTGTTCAAATGTTGATTGAATGCTGTCT
AATTGTTGATTGAATGTTGTCCA
Found at i:29703555 original size:33 final size:33
Alignment explanation
Indices: 29703453--29703556 Score: 97
Period size: 33 Copynumber: 3.2 Consensus size: 33
29703443 AATGCTGTCC
** *
29703453 AATTGTTGATTAAATGTTGTCCAAATGTTGATT
1 AATTGTTGATTAAATGTTGTCTGAATGTTGGTT
* * * *
29703486 AAATGTTG-TCCAAATGTT-TATTGAATGCT-GTAT
1 AATTGTTGAT-TAAATGTTGT-CTGAATGTTGGT-T
29703519 AATTGTTGATTAAATGTTGTCTGAATGTTGGTT
1 AATTGTTGATTAAATGTTGTCTGAATGTTGGTT
29703552 AATTG
1 AATTG
29703557 CTGTCCGTTT
Statistics
Matches: 54, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
32 3 0.06
33 47 0.87
34 4 0.07
ACGTcount: A:0.29, C:0.06, G:0.20, T:0.45
Consensus pattern (33 bp):
AATTGTTGATTAAATGTTGTCTGAATGTTGGTT
Found at i:29711135 original size:38 final size:38
Alignment explanation
Indices: 29711084--29711160 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
29711074 GTGTGGTGGG
* *
29711084 GGAGTGTTGGAGTGATTTTAGGAGGGAAATATAGGATT
1 GGAGTGTTGGAGTGATTTTAGGAGGAAAACATAGGATT
*
29711122 GGAGTGTTGGAGTGATTTTAGGAGGAAAACATGGGATT
1 GGAGTGTTGGAGTGATTTTAGGAGGAAAACATAGGATT
29711160 G
1 G
29711161 TGGAGTTATC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.29, C:0.01, G:0.40, T:0.30
Consensus pattern (38 bp):
GGAGTGTTGGAGTGATTTTAGGAGGAAAACATAGGATT
Found at i:29721497 original size:43 final size:41
Alignment explanation
Indices: 29721449--29721674 Score: 209
Period size: 43 Copynumber: 5.3 Consensus size: 41
29721439 ACGTCGCTAA
29721449 CTTTAGCGGCGCTAAGAAAATAAACGCCGCTAAAGATAATGTT
1 CTTTAGCGGCGCTAAGAAAA-AAACGCCGCTAAA-ATAATGTT
* * * *
29721492 CTTTAGCGGCACTTAGGAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTAAGAAAAAAACGCCGCTAAA-ATAATGTT
** * *
29721534 CTTTAGCGGCGCTTGGGAAGAAAACGCCGCTAAACATCATGTT
1 CTTTAGCGGCGC-TAAGAAAAAAACGCCGCTAAA-ATAATGTT
* * * *
29721577 CTTTCGCGGCGCTTAGGAAGAAAACGTCGCTAAAAGTAATGTT
1 CTTTAGCGGCGC-TAAGAAAAAAACGCCGCTAAAA-TAATGTT
* * ** ** *
29721620 CTATAGCGACGCTTTGTCAAAAACGCCGCTAAAAGTAGTGTT
1 CTTTAGCGGCGCTAAGAAAAAAACGCCGCTAAAA-TAATGTT
29721662 CTTTAGCGGCGCT
1 CTTTAGCGGCGCT
29721675 TATTTCAGAA
Statistics
Matches: 155, Mismatches: 26, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
42 67 0.43
43 88 0.57
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (41 bp):
CTTTAGCGGCGCTAAGAAAAAAACGCCGCTAAAATAATGTT
Found at i:29721567 original size:85 final size:84
Alignment explanation
Indices: 29721470--29721676 Score: 256
Period size: 85 Copynumber: 2.4 Consensus size: 84
29721460 CTAAGAAAAT
* *
29721470 AAACGCCGCTAAAGATAATGTTCTTTAGCGGCACTTAGGAA-AAAACGCCGCT-AAAGATCATGT
1 AAACGCCGCTAAA-ATAATGTTCTTTAGCGGCGCTTAGGAAGAAAACGCCGCTAAAAG-TAATGT
* *
29721533 TCTTTAGCGGCGCTTGGGAAGA
64 TCTATAGCGACGCTTGGGAA-A
* * *
29721555 AAACGCCGCTAAACATCATGTTCTTTCGCGGCGCTTAGGAAGAAAACGTCGCTAAAAGTAATGTT
1 AAACGCCGCTAAA-ATAATGTTCTTTAGCGGCGCTTAGGAAGAAAACGCCGCTAAAAGTAATGTT
* **
29721620 CTATAGCGACGCTTTGTCAA
65 CTATAGCGACGCTTGGGAAA
*
29721640 AAACGCCGCTAAAAGTAGTGTTCTTTAGCGGCGCTTA
1 AAACGCCGCTAAAA-TAATGTTCTTTAGCGGCGCTTA
29721677 TTTCAGAAAC
Statistics
Matches: 105, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
84 1 0.01
85 70 0.67
86 30 0.29
87 4 0.04
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.25
Consensus pattern (84 bp):
AAACGCCGCTAAAATAATGTTCTTTAGCGGCGCTTAGGAAGAAAACGCCGCTAAAAGTAATGTTC
TATAGCGACGCTTGGGAAA
Found at i:29722145 original size:21 final size:21
Alignment explanation
Indices: 29722121--29722184 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
29722111 CTTCTCGCGT
*
29722121 TGCTTCTCTCGCTGCGGCCTC
1 TGCTTCTCTCGCTGCAGCCTC
* **
29722142 TGCTTCTCTCACTATAGCCTC
1 TGCTTCTCTCGCTGCAGCCTC
* *
29722163 TGCTTCCCTCGCTGCCGCCTC
1 TGCTTCTCTCGCTGCAGCCTC
29722184 T
1 T
29722185 ACTTTAAGTT
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.05, C:0.44, G:0.17, T:0.34
Consensus pattern (21 bp):
TGCTTCTCTCGCTGCAGCCTC
Found at i:29727676 original size:9 final size:9
Alignment explanation
Indices: 29727659--29728382 Score: 223
Period size: 9 Copynumber: 80.1 Consensus size: 9
29727649 TAAGTATAAT
*
29727659 TAAGCTATG
1 TAAGTTATG
29727668 TAAGTTATG
1 TAAGTTATG
29727677 T-A-TTATG
1 TAAGTTATG
29727684 TAAGTTAT-
1 TAAGTTATG
*
29727692 TTA-TTATG
1 TAAGTTATG
* *
29727700 AAAATTATG
1 TAAGTTATG
*
29727709 TAAGTTGTG
1 TAAGTTATG
29727718 T-A-TTATG
1 TAAGTTATG
* *
29727725 AAAACTATGCTATG
1 -----TAAGTTATG
29727739 TAAGTTATG
1 TAAGTTATG
* *
29727748 TAAGTCATA
1 TAAGTTATG
29727757 TAAGTTATG
1 TAAGTTATG
29727766 T-A-TTATG
1 TAAGTTATG
29727773 TAAGTTATG
1 TAAGTTATG
29727782 TAAGTTAT-
1 TAAGTTATG
*
29727790 TTA-TTATG
1 TAAGTTATG
* * *
29727798 AAAATTAAG
1 TAAGTTATG
29727807 TAAGTTATG
1 TAAGTTATG
*
29727816 TAATTTATG
1 TAAGTTATG
*
29727825 -AA-TAAT-
1 TAAGTTATG
***
29727831 TAAAAAAATG
1 T-AAGTTATG
29727841 TAAGTTATG
1 TAAGTTATG
29727850 TAAG-T-TG
1 TAAGTTATG
29727857 TAAGTTATG
1 TAAGTTATG
29727866 TAAG-T-TG
1 TAAGTTATG
29727873 TAAGTTATG
1 TAAGTTATG
29727882 TAAGTTATG
1 TAAGTTATG
*
29727891 TATA-ATAT-
1 TA-AGTTATG
29727899 TAA-TTAAT-
1 TAAGTT-ATG
29727907 TAAGTTATG
1 TAAGTTATG
*
29727916 TAATTTATG
1 TAAGTTATG
*
29727925 TATAATATTAATG
1 --TAA-GTT-ATG
29727938 TAAGTTATG
1 TAAGTTATG
*
29727947 TAATTTATG
1 TAAGTTATG
*
29727956 TATAATATTAATG
1 --TAA-GTT-ATG
29727969 TAAGTTATG
1 TAAGTTATG
*
29727978 TAATTTATG
1 TAAGTTATG
*
29727987 TTTAATATTAATG
1 --TAA-GTT-ATG
29728000 TAAGTTATG
1 TAAGTTATG
29728009 TAAG-T-TG
1 TAAGTTATG
29728016 TAAGTTATG
1 TAAGTTATG
29728025 TAAGTTATG
1 TAAGTTATG
*
29728034 TATA-ATAT-
1 TA-AGTTATG
* *
29728042 TAACTAAT-
1 TAAGTTATG
29728050 TAAGTTATG
1 TAAGTTATG
*
29728059 TAATTTATG
1 TAAGTTATG
*
29728068 TATA-ATAT-
1 TA-AGTTATG
29728076 TAA-TTAAT-
1 TAAGTT-ATG
29728084 TAAGTTATG
1 TAAGTTATG
*
29728093 TAATTTATG
1 TAAGTTATG
*
29728102 TATAATATTAATG
1 --TAA-GTT-ATG
29728115 TAAGTTATG
1 TAAGTTATG
*
29728124 TAATTTATG
1 TAAGTTATG
29728133 T-A--TAT-
1 TAAGTTATG
29728138 TAA-TTAAT-
1 TAAGTT-ATG
29728146 TAAGTTATG
1 TAAGTTATG
*
29728155 TAATTTATG
1 TAAGTTATG
*
29728164 TATAATATTAATG
1 --TAA-GTT-ATG
29728177 TAAGTTATG
1 TAAGTTATG
*
29728186 TATAATATTTAT-
1 --T-A-AGTTATG
29728198 TAA-TTAAT-
1 TAAGTT-ATG
29728206 TAAGTTATG
1 TAAGTTATG
*
29728215 TAATTTATG
1 TAAGTTATG
*
29728224 TATAATATTAATG
1 --TAA-GTT-ATG
29728237 TAAGTTATG
1 TAAGTTATG
*
29728246 TAATTTATG
1 TAAGTTATG
*
29728255 TATA-ATAT-
1 TA-AGTTATG
29728263 TAA-TTAAT-
1 TAAGTT-ATG
29728271 TAAGTTATG
1 TAAGTTATG
*
29728280 TAATTTATG
1 TAAGTTATG
*
29728289 TATAATATTAATG
1 --TAA-GTT-ATG
29728302 TAAGTTATG
1 TAAGTTATG
*
29728311 TAATTTATG
1 TAAGTTATG
29728320 T-A--TAT-
1 TAAGTTATG
29728325 TAA-TTAAT-
1 TAAGTT-ATG
29728333 TAAGTTATG
1 TAAGTTATG
*
29728342 TAATTTATG
1 TAAGTTATG
*
29728351 TATAATATTAATG
1 --TAA-GTT-ATG
29728364 TAAGTTATG
1 TAAGTTATG
*
29728373 TAATTTATG
1 TAAGTTATG
29728382 T
1 T
29728383 TTAATATTAA
Statistics
Matches: 556, Mismatches: 70, Indels: 178
0.69 0.09 0.22
Matches are distributed among these distances:
5 2 0.00
6 8 0.01
7 56 0.10
8 82 0.15
9 286 0.51
10 22 0.04
11 49 0.09
12 18 0.03
13 29 0.05
14 4 0.01
ACGTcount: A:0.39, C:0.01, G:0.14, T:0.47
Consensus pattern (9 bp):
TAAGTTATG
Found at i:29727685 original size:16 final size:16
Alignment explanation
Indices: 29727664--29727783 Score: 87
Period size: 16 Copynumber: 7.9 Consensus size: 16
29727654 ATAATTAAGC
29727664 TATGTAAGTTATGTAT
1 TATGTAAGTTATGTAT
*
29727680 TATGTAAGTTATTTAT
1 TATGTAAGTTATGTAT
29727696 TATG-AA---A---AT
1 TATGTAAGTTATGTAT
*
29727705 TATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAT
* ** *
29727721 TATGAAAACTATG--C
1 TATGTAAGTTATGTAT
29727735 TATGTAAGTTATGTAAGT
1 TATGTAAGTTATGT-A-T
* *
29727753 CATATAAGTTATGTAT
1 TATGTAAGTTATGTAT
29727769 TATGTAAGTTATGTA
1 TATGTAAGTTATGTA
29727784 AGTTATTTAT
Statistics
Matches: 78, Mismatches: 15, Indels: 22
0.68 0.13 0.19
Matches are distributed among these distances:
9 6 0.08
10 2 0.03
12 1 0.01
14 10 0.13
15 2 0.03
16 44 0.56
17 1 0.01
18 12 0.15
ACGTcount: A:0.35, C:0.03, G:0.17, T:0.45
Consensus pattern (16 bp):
TATGTAAGTTATGTAT
Found at i:29727706 original size:25 final size:25
Alignment explanation
Indices: 29727678--29727832 Score: 120
Period size: 25 Copynumber: 6.2 Consensus size: 25
29727668 TAAGTTATGT
29727678 ATTATGTAAGTTATTTATTATGAAA
1 ATTATGTAAGTTATTTATTATGAAA
* *
29727703 ATTATGTAAGTTGTGTATTATGAAA
1 ATTATGTAAGTTATTTATTATGAAA
* * *
29727728 ACTATGCTATG-TA---AGTTATGTAA
1 ATTATG-TAAGTTATTTA-TTATGAAA
* * * * *
29727751 GTCATATAAGTTATGTATTATGTAA
1 ATTATGTAAGTTATTTATTATGAAA
*
29727776 GTTATGTAAGTTATTTATTATGAAA
1 ATTATGTAAGTTATTTATTATGAAA
* *
29727801 ATTAAGTAAGTTATGTAATTTATGAATA
1 ATTATGTAAGTTAT-TTA-TTATGAA-A
29727829 ATTA
1 ATTA
29727833 AAAAAATGTA
Statistics
Matches: 103, Mismatches: 18, Indels: 15
0.76 0.13 0.11
Matches are distributed among these distances:
22 4 0.04
23 11 0.11
25 70 0.68
26 6 0.06
27 7 0.07
28 5 0.05
ACGTcount: A:0.38, C:0.02, G:0.15, T:0.45
Consensus pattern (25 bp):
ATTATGTAAGTTATTTATTATGAAA
Found at i:29727810 original size:34 final size:34
Alignment explanation
Indices: 29727736--29728014 Score: 155
Period size: 34 Copynumber: 8.5 Consensus size: 34
29727726 AAACTATGCT
* * **
29727736 ATGTAAGTTATGTAAGTCATATAAGTTAT-GTATT-
1 ATGTAAGTTATGTAAGTTAT-TTA-TTATAAAATTA
29727770 ATGTAAGTTATGTAAGTTATTTATTATGAAAATTA
1 ATGTAAGTTATGTAAGTTATTTATTAT-AAAATTA
* ** * *
29727805 A-GTAAGTTATGTAATTTATGAATAATTAAAA-AA
1 ATGTAAGTTATGTAAGTTATTTATTA-TAAAATTA
* * ** *
29727838 ATGTAAGTTATGTAAGTT-GTAAGTTATGTAAGT-
1 ATGTAAGTTATGTAAGTTATTTA-TTATAAAATTA
* * *
29727871 -TGTAAGTTATGTAAGTTATGTATAATATTAATTA
1 ATGTAAGTTATGTAAGTTATTTATTATA-AAATTA
*
29727905 AT-TAAGTTATGT-A---ATTTATGTATAATATTA
1 ATGTAAGTTATGTAAGTTATTTAT-TATAAAATTA
*
29727935 ATGTAAGTTATGT-A---ATTTATGTATAATATTA
1 ATGTAAGTTATGTAAGTTATTTAT-TATAAAATTA
* * *
29727966 ATGTAAGTTATGTAA-TT-TATGTT-TAATATTA
1 ATGTAAGTTATGTAAGTTATTTATTATAAAATTA
29727997 ATGTAAGTTATGTAAGTT
1 ATGTAAGTTATGTAAGTT
29728015 GTAAGTTATG
Statistics
Matches: 200, Mismatches: 28, Indels: 36
0.76 0.11 0.14
Matches are distributed among these distances:
30 11 0.05
31 67 0.34
32 28 0.14
33 18 0.09
34 73 0.37
35 3 0.01
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.46
Consensus pattern (34 bp):
ATGTAAGTTATGTAAGTTATTTATTATAAAATTA
Found at i:29727860 original size:16 final size:16
Alignment explanation
Indices: 29727839--29727887 Score: 98
Period size: 16 Copynumber: 3.1 Consensus size: 16
29727829 ATTAAAAAAA
29727839 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
29727855 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
29727871 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
29727887 T
1 T
29727888 ATGTATAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.31, C:0.00, G:0.24, T:0.45
Consensus pattern (16 bp):
TGTAAGTTATGTAAGT
Found at i:29727866 original size:25 final size:26
Alignment explanation
Indices: 29727735--29728061 Score: 147
Period size: 25 Copynumber: 12.6 Consensus size: 26
29727725 AAAACTATGC
*
29727735 TATGTAAGTTATGTAAGTCATATAAGT
1 TATGTAAGTTATGTAAGT-ATGTAAGT
29727762 TATGT-A-TTATGTAAGTTATGTAAGT
1 TATGTAAGTTATGTAAG-TATGTAAGT
* * * *
29727787 TAT-TTA-TTATGAAAATTAAGTAAGT
1 TATGTAAGTTATG-TAAGTATGTAAGT
* **
29727812 TATGTAATTTATG-AA-TAAT-TAAAAA
1 TATGTAAGTTATGTAAGT-ATGT-AAGT
*
29727837 AATGTAAGTTATGTAAGT-TGTAAGT
1 TATGTAAGTTATGTAAGTATGTAAGT
29727862 TATGTAAG-T-TGTAAGTTATGTAAGT
1 TATGTAAGTTATGTAAG-TATGTAAGT
* *
29727887 TATGTATA-ATAT-TAATTAAT-TAAGT
1 TATGTA-AGTTATGTAAGT-ATGTAAGT
* *
29727912 TATGTAATTTATGT-A-TA-AT-A-T
1 TATGTAAGTTATGTAAGTATGTAAGT
* *
29727933 TAATGTAAGTTATGTAATTTATGTATAATAT
1 T-ATGTAAGTTATGTAA-GTATG--TAA-GT
* *
29727964 TAATGTAAGTTATGTAATTTATGTTTAATAT
1 T-ATGTAAGTTATGTAA-GTATG--TAA-GT
29727995 TAATGTAAGTTATGTAAGT-TGTAAGT
1 T-ATGTAAGTTATGTAAGTATGTAAGT
* *
29728021 TATGTAAGTTATGTATAATAT-TAACT
1 TATGTAAGTTATGTA-AGTATGTAAGT
*
29728047 AAT-TAAGTTATGTAA
1 TATGTAAGTTATGTAA
29728062 TTTATGTATA
Statistics
Matches: 246, Mismatches: 23, Indels: 65
0.74 0.07 0.19
Matches are distributed among these distances:
21 2 0.01
22 13 0.05
23 9 0.04
24 8 0.03
25 118 0.48
26 27 0.11
27 16 0.07
28 1 0.00
29 3 0.01
30 1 0.00
31 48 0.20
ACGTcount: A:0.39, C:0.01, G:0.15, T:0.45
Consensus pattern (26 bp):
TATGTAAGTTATGTAAGTATGTAAGT
Found at i:29727945 original size:31 final size:31
Alignment explanation
Indices: 29727766--29728402 Score: 690
Period size: 31 Copynumber: 20.5 Consensus size: 31
29727756 ATAAGTTATG
29727766 TATT-ATGTAAGTTATGTAAGTTATTTAT-TATGAA
1 TATTAATGTAAGTTATGT-A---ATTTATGTAT-AA
* *
29727800 AATTAA-GTAAGTTATGTAATTTATGAATAA
1 TATTAATGTAAGTTATGTAATTTATGTATAA
** *
29727830 TTAAAAAAATGTAAGTTATGTAAGTTGTAAGT-T-A
1 -T--ATTAATGTAAGTTATGTAA-TT-TATGTATAA
* *
29727864 T-GTAAGTTGTAAGTTATGTAAGTTATGTATAA
1 TATTAA--TGTAAGTTATGTAATTTATGTATAA
*
29727896 TATTAATTAATTAAGTTATGTAATTTATGTATAA
1 TATTAA-T--GTAAGTTATGTAATTTATGTATAA
29727930 TATTAATGTAAGTTATGTAATTTATGTATAA
1 TATTAATGTAAGTTATGTAATTTATGTATAA
*
29727961 TATTAATGTAAGTTATGTAATTTATGTTTAA
1 TATTAATGTAAGTTATGTAATTTATGTATAA
*
29727992 TATTAATGTAAGTTATGTAA-GT-TG--TAA
1 TATTAATGTAAGTTATGTAATTTATGTATAA
* * *
29728019 -GTT-ATGTAAGTTATGT-A--TA-ATATTA
1 TATTAATGTAAGTTATGTAATTTATGTATAA
*
29728044 -ACTAAT-TAAGTTATGTAATTTATGTATAA
1 TATTAATGTAAGTTATGTAATTTATGTATAA
*
29728073 TATTAATTAATTAAGTTATGTAATTTATGTATAA
1 TATTAA-T--GTAAGTTATGTAATTTATGTATAA
*
29728107 TATTAATGTAAGTTATGTAATTTATGTATAT
1 TATTAATGTAAGTTATGTAATTTATGTATAA
29728138 TAATTAAT-TAAGTTATGTAATTTATGTATAA
1 T-ATTAATGTAAGTTATGTAATTTATGTATAA
* * *
29728169 TATTAATGTAAGTTATGT-ATAATATTTATTA
1 TATTAATGTAAGTTATGTAAT-TTATGTATAA
29728200 -ATTAAT-TAAGTTATGTAATTTATGTATAA
1 TATTAATGTAAGTTATGTAATTTATGTATAA
29728229 TATTAATGTAAGTTATGTAATTTATGTATAA
1 TATTAATGTAAGTTATGTAATTTATGTATAA
*
29728260 TATTAATTAATTAAGTTATGTAATTTATGTATAA
1 TATTAA-T--GTAAGTTATGTAATTTATGTATAA
*
29728294 TATTAATGTAAGTTATGTAATTTATGTATAT
1 TATTAATGTAAGTTATGTAATTTATGTATAA
29728325 TAATTAAT-TAAGTTATGTAATTTATGTATAA
1 T-ATTAATGTAAGTTATGTAATTTATGTATAA
*
29728356 TATTAATGTAAGTTATGTAATTTATGTTTAA
1 TATTAATGTAAGTTATGTAATTTATGTATAA
*
29728387 TATTAATGTAATTTAT
1 TATTAATGTAAGTTAT
29728403 ATATAAATAT
Statistics
Matches: 524, Mismatches: 40, Indels: 81
0.81 0.06 0.13
Matches are distributed among these distances:
23 1 0.00
24 1 0.00
25 26 0.05
26 5 0.01
27 3 0.01
28 2 0.00
29 23 0.04
30 47 0.09
31 253 0.48
32 31 0.06
33 11 0.02
34 114 0.22
35 4 0.01
36 3 0.01
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (31 bp):
TATTAATGTAAGTTATGTAATTTATGTATAA
Found at i:29728000 original size:22 final size:20
Alignment explanation
Indices: 29727911--29728382 Score: 157
Period size: 22 Copynumber: 23.3 Consensus size: 20
29727901 ATTAATTAAG
29727911 TTATGTAATTTATGTATAATA
1 TTATGTAATTTATGT-TAATA
*
29727932 TTAATGTAAGTTATG-TAAT-
1 TT-ATGTAATTTATGTTAATA
*
29727951 TTATGTATAATATTAATG-TAA-G
1 TTATG--TAAT-TT-ATGTTAATA
29727973 TTATGTAATTTATGTTTAATA
1 TTATGTAATTTATG-TTAATA
*
29727994 TTAATGTAAGTTATG-T-A-A
1 TT-ATGTAATTTATGTTAATA
* * *
29728012 GT-TGTAAGTTATG-TAA-G
1 TTATGTAATTTATGTTAATA
* *
29728029 TTATGTATAATATTAACTAATTAA-G
1 TTATG--TAAT-TT-A-T-GTTAATA
29728054 TTATGTAATTTATG-T-ATA
1 TTATGTAATTTATGTTAATA
* * *
29728072 ATAT-TAA-TTA-ATTAA-G
1 TTATGTAATTTATGTTAATA
29728088 TTATGTAATTTATGTATAATA
1 TTATGTAATTTATGT-TAATA
*
29728109 TTAATGTAAGTTATG-TAAT-
1 TT-ATGTAATTTATGTTAATA
*
29728128 TTATGT-ATATTA-ATTAATTAA
1 TTATGTAAT-TTATGTTAA-T-A
29728149 GTTATGTAATTTATGTATAATA
1 -TTATGTAATTTATGT-TAATA
*
29728171 TTAATGTAAGTTATGTATAATA
1 TT-ATGTAATTTATGT-TAATA
* *
29728193 TTTAT-TAA-TTA-ATTAA-G
1 -TTATGTAATTTATGTTAATA
29728210 TTATGTAATTTATGTATAATA
1 TTATGTAATTTATGT-TAATA
*
29728231 TTAATGTAAGTTATG-TAAT-
1 TT-ATGTAATTTATGTTAATA
*
29728250 TTATGTATAATATTA-ATTAATTAA
1 TTATG--TAAT-TTATGTTAA-T-A
29728274 GTTATGTAATTTATGTATAATA
1 -TTATGTAATTTATGT-TAATA
*
29728296 TTAATGTAAGTTATG-TAAT-
1 TT-ATGTAATTTATGTTAATA
*
29728315 TTATGT-ATATTA-ATTAATTAA
1 TTATGTAAT-TTATGTTAA-T-A
29728336 GTTATGTAATTTATGTATAATA
1 -TTATGTAATTTATGT-TAATA
*
29728358 TTAATGTAAGTTATG-TAAT-
1 TT-ATGTAATTTATGTTAATA
29728377 TTATGT
1 TTATGT
29728383 TTAATATTAA
Statistics
Matches: 350, Mismatches: 35, Indels: 135
0.67 0.07 0.26
Matches are distributed among these distances:
16 23 0.07
17 15 0.04
18 50 0.14
19 18 0.05
20 47 0.13
21 28 0.08
22 125 0.36
23 21 0.06
24 9 0.03
25 14 0.04
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (20 bp):
TTATGTAATTTATGTTAATA
Found at i:29728019 original size:16 final size:16
Alignment explanation
Indices: 29727998--29728030 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
29727988 TTAATATTAA
29727998 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
29728014 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
29728030 T
1 T
29728031 ATGTATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.24, T:0.45
Consensus pattern (16 bp):
TGTAAGTTATGTAAGT
Found at i:29730148 original size:24 final size:25
Alignment explanation
Indices: 29730110--29730162 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
29730100 AAATTGAGGG
*
29730110 ATTTTGGGGGGGAAAATCGGGGGCA
1 ATTTTGGGGGAGAAAATCGGGGGCA
* * *
29730135 ATTTT-GGGGAGAAATTTGGGGGGA
1 ATTTTGGGGGAGAAAATCGGGGGCA
29730159 ATTT
1 ATTT
29730163 CGGCTAAGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.25, C:0.04, G:0.43, T:0.28
Consensus pattern (25 bp):
ATTTTGGGGGAGAAAATCGGGGGCA
Done.