Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 138 of 313
Found at i:44473342 original size:87 final size:87
Alignment explanation
Indices: 44473196--44473458 Score: 427
Period size: 87 Copynumber: 3.0 Consensus size: 87
44473186 ACTTGTAATC
* * * *
44473196 TTCGATCTGTTTCACTGTTGACGCAGGAGGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
1 TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
**
44473261 CTAATGGAGGCAAGGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
* *
44473283 TTCGATCTGCTTCGCTGTTAATGCAGGAAGGAAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
1 TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
*
44473348 CCGATAGAGGCAAGGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
*
44473370 TTCGATCTGCTTCGCTGTTAACGTAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
1 TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
*
44473435 CCGATGGAGGCAAGGCTTTATT
66 CCGATGGAGGCAAGGCTTTGTT
44473457 TT
1 TT
44473459 TTATTTTCAC
Statistics
Matches: 162, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 162 1.00
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (87 bp):
TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
CCGATGGAGGCAAGGCTTTGTT
Found at i:44474709 original size:13 final size:13
Alignment explanation
Indices: 44474691--44474724 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
44474681 TACTTTTTCG
*
44474691 TCATTTTTTATTT
1 TCATTTTTTAATT
44474704 TCA-TTTTTAATT
1 TCATTTTTTAATT
44474716 TCATTTTTT
1 TCATTTTTT
44474725 TTGAAATCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.74
Consensus pattern (13 bp):
TCATTTTTTAATT
Found at i:44475083 original size:30 final size:28
Alignment explanation
Indices: 44475043--44475110 Score: 91
Period size: 30 Copynumber: 2.4 Consensus size: 28
44475033 CTTTTTCATA
*
44475043 TTTTTATTTTGACTTTGATTGATTTCTCTT
1 TTTTTCTTTTGACTTTGATT-ATTTCTC-T
* *
44475073 TTTTTCTTTTGACTTTGATTTTTTTTCT
1 TTTTTCTTTTGACTTTGATTATTTCTCT
44475101 TTTTTCTTTT
1 TTTTTCTTTT
44475111 TTCTTTTCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
28 11 0.31
29 5 0.14
30 19 0.54
ACGTcount: A:0.09, C:0.10, G:0.07, T:0.74
Consensus pattern (28 bp):
TTTTTCTTTTGACTTTGATTATTTCTCT
Found at i:44475103 original size:7 final size:7
Alignment explanation
Indices: 44475093--44475117 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
44475083 GACTTTGATT
44475093 TTTTTTC
1 TTTTTTC
44475100 TTTTTTC
1 TTTTTTC
44475107 TTTTTTC
1 TTTTTTC
44475114 TTTT
1 TTTT
44475118 CAAATCTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:44476282 original size:9 final size:9
Alignment explanation
Indices: 44476268--44476304 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
44476258 TATAGTTTGA
44476268 TATTCGAAT
1 TATTCGAAT
44476277 TATTCGAAT
1 TATTCGAAT
*
44476286 TATTCGAGT
1 TATTCGAAT
44476295 TATTCGAAT
1 TATTCGAAT
44476304 T
1 T
44476305 TGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:44476376 original size:9 final size:9
Alignment explanation
Indices: 44476359--44476389 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
44476349 TTGAGTTGAT
44476359 TCGAATAAC
1 TCGAATAAC
*
44476368 TCGATTAAC
1 TCGAATAAC
44476377 TCGAATAAC
1 TCGAATAAC
44476386 TCGA
1 TCGA
44476390 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:44476732 original size:87 final size:87
Alignment explanation
Indices: 44476586--44476848 Score: 427
Period size: 87 Copynumber: 3.0 Consensus size: 87
44476576 ACTTGTAATC
* * * *
44476586 TTCGATCTGTTTCACTGTTGACGCAGGAGGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
1 TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
**
44476651 CTAATGGAGGCAAGGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
* *
44476673 TTCGATCTGCTTCGCTGTTAATGCAGGAAGGAAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
1 TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
*
44476738 CCGATAGAGGCAAGGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
*
44476760 TTCGATCTGCTTCGCTGTTAACGTAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
1 TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
*
44476825 CCGATGGAGGCAAGGCTTTATT
66 CCGATGGAGGCAAGGCTTTGTT
44476847 TT
1 TT
44476849 TTATTTTCAC
Statistics
Matches: 162, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 162 1.00
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (87 bp):
TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
CCGATGGAGGCAAGGCTTTGTT
Found at i:44478099 original size:13 final size:13
Alignment explanation
Indices: 44478081--44478114 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
44478071 TACTTTTTCG
*
44478081 TCATTTTTTATTT
1 TCATTTTTTAATT
44478094 TCA-TTTTTAATT
1 TCATTTTTTAATT
44478106 TCATTTTTT
1 TCATTTTTT
44478115 TTGAAATCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.74
Consensus pattern (13 bp):
TCATTTTTTAATT
Found at i:44478473 original size:30 final size:28
Alignment explanation
Indices: 44478433--44478500 Score: 91
Period size: 30 Copynumber: 2.4 Consensus size: 28
44478423 CTTTTTCATA
*
44478433 TTTTTATTTTGACTTTGATTGATTTCTCTT
1 TTTTTCTTTTGACTTTGATT-ATTTCTC-T
* *
44478463 TTTTTCTTTTGACTTTGATTTTTTTTCT
1 TTTTTCTTTTGACTTTGATTATTTCTCT
44478491 TTTTTCTTTT
1 TTTTTCTTTT
44478501 TTCTTTTCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
28 11 0.31
29 5 0.14
30 19 0.54
ACGTcount: A:0.09, C:0.10, G:0.07, T:0.74
Consensus pattern (28 bp):
TTTTTCTTTTGACTTTGATTATTTCTCT
Found at i:44478493 original size:7 final size:7
Alignment explanation
Indices: 44478483--44478507 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
44478473 GACTTTGATT
44478483 TTTTTTC
1 TTTTTTC
44478490 TTTTTTC
1 TTTTTTC
44478497 TTTTTTC
1 TTTTTTC
44478504 TTTT
1 TTTT
44478508 CAAATCTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:44481021 original size:20 final size:21
Alignment explanation
Indices: 44480979--44481022 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
44480969 TCTTTTTGCA
44480979 TTTGCTCCAGTTTCTCTAATC
1 TTTGCTCCAGTTTCTCTAATC
* * *
44481000 TTTGGTCCA-TTTCTTTAGTC
1 TTTGCTCCAGTTTCTCTAATC
44481020 TTT
1 TTT
44481023 CGACAAGTAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.11, C:0.23, G:0.11, T:0.55
Consensus pattern (21 bp):
TTTGCTCCAGTTTCTCTAATC
Found at i:44495426 original size:3 final size:3
Alignment explanation
Indices: 44495418--44495515 Score: 74
Period size: 3 Copynumber: 30.7 Consensus size: 3
44495408 TAAATGGGTA
*
44495418 AAT AAT AAT GAT AAT AAT AAGGT AAGT AAT AAT AAT AAAT GCAAT AAT
1 AAT AAT AAT AAT AAT AAT AA--T AA-T AAT AAT AAT -AAT --AAT AAT
* * *
44495466 AAT AAT AAT AAT AA- AACT ACTT AGT -TT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AA-T A-AT AAT AAT AAT AAT AAT AAT AAT AAT
44495511 AAT AA
1 AAT AA
44495516 CGAGACTAAA
Statistics
Matches: 80, Mismatches: 7, Indels: 16
0.78 0.07 0.16
Matches are distributed among these distances:
2 3 0.04
3 61 0.76
4 10 0.12
5 6 0.08
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:44504756 original size:30 final size:31
Alignment explanation
Indices: 44504720--44504782 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
44504710 CTTGTTATTG
44504720 GACTTAAA-AAAAACTTTTGAATAGTTCAAT
1 GACTTAAATAAAAACTTTTGAATAGTTCAAT
*
44504750 GACTTAAATGAAAACTTTTGAATAGTTCAAT
1 GACTTAAATAAAAACTTTTGAATAGTTCAAT
44504781 GA
1 GA
44504783 TCATTTTGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 8 0.26
31 23 0.74
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (31 bp):
GACTTAAATAAAAACTTTTGAATAGTTCAAT
Found at i:44507803 original size:17 final size:17
Alignment explanation
Indices: 44507781--44507817 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
44507771 ACACCAAACA
44507781 TAACTTAAACATGTCAT
1 TAACTTAAACATGTCAT
44507798 TAACTTAAACATGTCAT
1 TAACTTAAACATGTCAT
44507815 TAA
1 TAA
44507818 GGTCATGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.35
Consensus pattern (17 bp):
TAACTTAAACATGTCAT
Found at i:44512984 original size:18 final size:18
Alignment explanation
Indices: 44512961--44513017 Score: 96
Period size: 18 Copynumber: 3.2 Consensus size: 18
44512951 CCCAACTACT
* *
44512961 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTGCC
44512979 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTGCC
44512997 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTGCC
44513015 GTA
1 GTA
44513018 AACGGTCGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (18 bp):
GTATACGTGAATAGTGCC
Found at i:44514530 original size:22 final size:20
Alignment explanation
Indices: 44514501--44514544 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
44514491 TGTTGTTCAC
44514501 AAGATTGAAAAAAATAATAGA
1 AAGATTGAAAAAAA-AATAGA
*
44514522 AAGAGTTGAAAATAAAATAGA
1 AAGA-TTGAAAAAAAAATAGA
44514543 AA
1 AA
44514545 AATCGGTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.18
Consensus pattern (20 bp):
AAGATTGAAAAAAAAATAGA
Found at i:44515624 original size:2 final size:2
Alignment explanation
Indices: 44515617--44515643 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
44515607 TAGAATGGGA
44515617 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
44515644 ACATTGGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:44521237 original size:5 final size:5
Alignment explanation
Indices: 44521229--44521257 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
44521219 GTATTTTATT
44521229 AAATA AAATA AAATA AAATA AAATA AAAT
1 AAATA AAATA AAATA AAATA AAATA AAAT
44521258 TTTAAGTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AAATA
Found at i:44523677 original size:21 final size:21
Alignment explanation
Indices: 44523588--44523731 Score: 112
Period size: 21 Copynumber: 6.9 Consensus size: 21
44523578 TTCCGTGTTT
*
44523588 GCTTTCAGTTTAGCTCTTATGA
1 GCTTT-AGTTTAACTCTTATGA
*
44523610 GCTTTAG-TTAACTCATATGA
1 GCTTTAGTTTAACTCTTATGA
* * * *
44523630 GTTTTAGTTTAACCCTAATGG
1 GCTTTAGTTTAACTCTTATGA
* * *
44523651 GTTTTAGTTTAGCTCTTCTGA
1 GCTTTAGTTTAACTCTTATGA
*
44523672 GCTTTAGATTAACTCTTATG-
1 GCTTTAGTTTAACTCTTATGA
* * *
44523692 GGTTTCCGTTTAGCTCTTATGA
1 GCTTT-AGTTTAACTCTTATGA
** *
44523714 GCTTCCGTTTAACCCTTA
1 GCTTTAGTTTAACTCTTA
44523732 CGGGTTTCCA
Statistics
Matches: 95, Mismatches: 24, Indels: 7
0.75 0.19 0.06
Matches are distributed among these distances:
20 21 0.22
21 66 0.69
22 8 0.08
ACGTcount: A:0.20, C:0.18, G:0.17, T:0.44
Consensus pattern (21 bp):
GCTTTAGTTTAACTCTTATGA
Found at i:44523684 original size:42 final size:42
Alignment explanation
Indices: 44523625--44523753 Score: 125
Period size: 42 Copynumber: 3.1 Consensus size: 42
44523615 AGTTAACTCA
* * *
44523625 TATGAGTTTTAGTTTAACCCTAATGGGTTTTAGTTTAGCTCT
1 TATGAGCTTTAGATTAACCCTAATGGGTTTCAGTTTAGCTCT
* * * *
44523667 TCTGAGCTTTAGATTAACTCTTATGGGTTTCCGTTTAGCTCT
1 TATGAGCTTTAGATTAACCCTAATGGGTTTCAGTTTAGCTCT
** * * * *
44523709 TATGAGCTTCCGTTTAACCCTTACGGGTTTCCA-TTTAGCACT
1 TATGAGCTTTAGATTAACCCTAATGGGTTT-CAGTTTAGCTCT
44523751 TAT
1 TAT
44523754 ATGCTTTTTT
Statistics
Matches: 71, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
42 70 0.99
43 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.18, T:0.44
Consensus pattern (42 bp):
TATGAGCTTTAGATTAACCCTAATGGGTTTCAGTTTAGCTCT
Found at i:44523740 original size:21 final size:21
Alignment explanation
Indices: 44523680--44523745 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
44523670 GAGCTTTAGA
44523680 TTAACTCTTATGGGTTTCCGT
1 TTAACTCTTATGGGTTTCCGT
* * *
44523701 TTAGCTCTTATGAGCTTCCGT
1 TTAACTCTTATGGGTTTCCGT
* * *
44523722 TTAACCCTTACGGGTTTCCAT
1 TTAACTCTTATGGGTTTCCGT
44523743 TTA
1 TTA
44523746 GCACTTATAT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.44
Consensus pattern (21 bp):
TTAACTCTTATGGGTTTCCGT
Found at i:44523752 original size:21 final size:21
Alignment explanation
Indices: 44523686--44523753 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
44523676 TAGATTAACT
*
44523686 CTTATGGGTTTCCGTTTAGCT
1 CTTATGGGTTTCCGTTTAGCA
* * * *
44523707 CTTATGAGCTTCCGTTTAACC
1 CTTATGGGTTTCCGTTTAGCA
* *
44523728 CTTACGGGTTTCCATTTAGCA
1 CTTATGGGTTTCCGTTTAGCA
44523749 CTTAT
1 CTTAT
44523754 ATGCTTTTTT
Statistics
Matches: 36, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.16, C:0.24, G:0.18, T:0.43
Consensus pattern (21 bp):
CTTATGGGTTTCCGTTTAGCA
Found at i:44531480 original size:174 final size:174
Alignment explanation
Indices: 44531190--44531537 Score: 696
Period size: 174 Copynumber: 2.0 Consensus size: 174
44531180 AAGTAATAGA
44531190 AATAATAGAAATTGATAGGCTATAAAAGGAAAAACACTATCTTTGTATTTTTTGGGAACAGAAAA
1 AATAATAGAAATTGATAGGCTATAAAAGGAAAAACACTATCTTTGTATTTTTTGGGAACAGAAAA
44531255 GTGAATGAAAAGCAAAAAAAAAATCAAAAAGAGGTTGATTCTAGTATTCTTTTTCTTCTGTTCGT
66 GTGAATGAAAAGCAAAAAAAAAATCAAAAAGAGGTTGATTCTAGTATTCTTTTTCTTCTGTTCGT
44531320 GTGCATTGTTTTTTGTTTTTTTTTTTATTTTCTTTGTTATTTGT
131 GTGCATTGTTTTTTGTTTTTTTTTTTATTTTCTTTGTTATTTGT
44531364 AATAATAGAAATTGATAGGCTATAAAAGGAAAAACACTATCTTTGTATTTTTTGGGAACAGAAAA
1 AATAATAGAAATTGATAGGCTATAAAAGGAAAAACACTATCTTTGTATTTTTTGGGAACAGAAAA
44531429 GTGAATGAAAAGCAAAAAAAAAATCAAAAAGAGGTTGATTCTAGTATTCTTTTTCTTCTGTTCGT
66 GTGAATGAAAAGCAAAAAAAAAATCAAAAAGAGGTTGATTCTAGTATTCTTTTTCTTCTGTTCGT
44531494 GTGCATTGTTTTTTGTTTTTTTTTTTATTTTCTTTGTTATTTGT
131 GTGCATTGTTTTTTGTTTTTTTTTTTATTTTCTTTGTTATTTGT
44531538 TTTTTTACTC
Statistics
Matches: 174, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
174 174 1.00
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.43
Consensus pattern (174 bp):
AATAATAGAAATTGATAGGCTATAAAAGGAAAAACACTATCTTTGTATTTTTTGGGAACAGAAAA
GTGAATGAAAAGCAAAAAAAAAATCAAAAAGAGGTTGATTCTAGTATTCTTTTTCTTCTGTTCGT
GTGCATTGTTTTTTGTTTTTTTTTTTATTTTCTTTGTTATTTGT
Found at i:44532248 original size:29 final size:29
Alignment explanation
Indices: 44532215--44532278 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
44532205 TAGTCCCTTT
* *
44532215 TATTTTAT-TTTTCTTTCAATTTCGCCCTA
1 TATTTTATGTTTTATTTCAATTTAGCCC-A
*
44532244 TATTTT-TGTTTTATTTCGATTTAGCCCA
1 TATTTTATGTTTTATTTCAATTTAGCCCA
44532272 TATTTTA
1 TATTTTA
44532279 GCAATTTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 8 0.27
29 22 0.73
ACGTcount: A:0.19, C:0.16, G:0.06, T:0.59
Consensus pattern (29 bp):
TATTTTATGTTTTATTTCAATTTAGCCCA
Found at i:44532298 original size:3 final size:3
Alignment explanation
Indices: 44532290--44532367 Score: 95
Period size: 3 Copynumber: 26.3 Consensus size: 3
44532280 CAATTTTATG
* * *
44532290 TTA TTA TTA TTA TTA TTA TTA TTA TTA ATA TTA TTA TTA GT- TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
** *
44532337 TTA TTA TTA TGG TTA TTA TTA TTA CTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
44532368 CGTTAGTATT
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
2 1 0.02
3 61 0.98
ACGTcount: A:0.32, C:0.03, G:0.04, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:44536308 original size:17 final size:18
Alignment explanation
Indices: 44536286--44536320 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
44536276 TATATTTTGA
*
44536286 CATAAA-ACAGAACATAT
1 CATAAAGACACAACATAT
44536303 CATAAAGACACAACATAT
1 CATAAAGACACAACATAT
44536321 AGGCTCTAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.57, C:0.20, G:0.06, T:0.17
Consensus pattern (18 bp):
CATAAAGACACAACATAT
Found at i:44542202 original size:12 final size:12
Alignment explanation
Indices: 44542185--44542209 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44542175 GCTTTCACTT
44542185 CCACTTCCGCTA
1 CCACTTCCGCTA
44542197 CCACTTCCGCTA
1 CCACTTCCGCTA
44542209 C
1 C
44542210 TTTCACTACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.52, G:0.08, T:0.24
Consensus pattern (12 bp):
CCACTTCCGCTA
Found at i:44542211 original size:27 final size:27
Alignment explanation
Indices: 44542181--44542251 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
44542171 CACTGCTTTC
*
44542181 ACTTCCACTTCCGCTACCACTTCCGCT
1 ACTTCCACTTCCGCTACCACTTCCACT
* * *
44542208 ACTTTCACTACCGCTACCGCTTCCACT
1 ACTTCCACTTCCGCTACCACTTCCACT
*
44542235 AC-TCTCACTTCCACTAC
1 ACTTC-CACTTCCGCTAC
44542252 TACTACTCGA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
26 1 0.03
27 35 0.97
ACGTcount: A:0.18, C:0.46, G:0.06, T:0.30
Consensus pattern (27 bp):
ACTTCCACTTCCGCTACCACTTCCACT
Found at i:44553337 original size:5 final size:5
Alignment explanation
Indices: 44553327--44553358 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
44553317 GCCTAAGATG
44553327 TGAAT TGAAT TGAAT TGAAT TGAAT ATGAAT T
1 TGAAT TGAAT TGAAT TGAAT TGAAT -TGAAT T
44553359 ATATTAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (5 bp):
TGAAT
Found at i:44553879 original size:26 final size:25
Alignment explanation
Indices: 44553835--44553902 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 25
44553825 ATACACCACA
* * *
44553835 GCTCTTATAAGCATCCCGA-TATATG
1 GCTCTTATGAGCTTCCCGATTA-AAG
44553860 GCTCTTCATGAGCTTCCCGATTAAAG
1 GCTCTT-ATGAGCTTCCCGATTAAAG
44553886 GCTCTTTATGAGCTTCC
1 GCTC-TTATGAGCTTCC
44553903 TAATTAATGG
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
25 6 0.16
26 27 0.73
27 4 0.11
ACGTcount: A:0.22, C:0.26, G:0.18, T:0.34
Consensus pattern (25 bp):
GCTCTTATGAGCTTCCCGATTAAAG
Found at i:44553908 original size:26 final size:26
Alignment explanation
Indices: 44553859--44553915 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
44553849 CCCGATATAT
*
44553859 GGCTCTTCATGAGCTTCCCGATTAAA
1 GGCTCTTCATGAGCTTCCCAATTAAA
* * *
44553885 GGCTCTTTATGAGCTTCCTAATTAAT
1 GGCTCTTCATGAGCTTCCCAATTAAA
44553911 GGCTC
1 GGCTC
44553916 CCCGAACCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (26 bp):
GGCTCTTCATGAGCTTCCCAATTAAA
Found at i:44557641 original size:31 final size:31
Alignment explanation
Indices: 44557557--44557658 Score: 84
Period size: 31 Copynumber: 3.4 Consensus size: 31
44557547 TTTTACAAAA
* * *
44557557 TACCTAAATTACCCTTATTATGTTTTAATA-
1 TACCTAAAATACCCCTATTATTTTTTAATAC
* * * **
44557587 T--TTAAACTATCCCTATTGGTTTTTAATAC
1 TACCTAAAATACCCCTATTATTTTTTAATAC
*
44557616 TACCTAAAATACCCCTATTATTTTTTAACAC
1 TACCTAAAATACCCCTATTATTTTTTAATAC
* *
44557647 CACTTAAAATAC
1 TACCTAAAATAC
44557659 ACTTCTTAAT
Statistics
Matches: 54, Mismatches: 15, Indels: 5
0.73 0.20 0.07
Matches are distributed among these distances:
28 20 0.37
29 1 0.02
30 1 0.02
31 32 0.59
ACGTcount: A:0.34, C:0.21, G:0.03, T:0.42
Consensus pattern (31 bp):
TACCTAAAATACCCCTATTATTTTTTAATAC
Found at i:44560884 original size:226 final size:226
Alignment explanation
Indices: 44560490--44560941 Score: 759
Period size: 226 Copynumber: 2.0 Consensus size: 226
44560480 GTTCATATCC
44560490 GGGTTTAATCCAAATTGATTTGCCAAAATAGATTATTCTCCTTAGGGTTTATTACTTCATATTTA
1 GGGTTTAATCCAAATTGATTTGCCAAAATAGATTATTCTCCTTAGGGTTTATTACTTCATATTTA
*
44560555 GGCTTAATACAAGTTGTTTTATTAGTGCATGTAGTTCCTTGGTTCTACCACTTAAGTTTGTAACC
66 GGCTTAATACAAGTTGTTTTATTAGTGCATGTAGTTCCTTGGTTCTACCACTAAAGTTTGTAACC
* *
44560620 TTATTGTTTGCTTCAATAAAATTTAATAGCTTTTGTATGTATGTATGTGTCCATGCT-TGCT-TT
131 TTATTGTTTGCTTCAATAAAATTTAATAGCTTTTGTATGTATGTATGTATCCATG-TATG-TATC
* *
44560683 GGAAGGAGTGTTGCATTAAAGGCTTGCAAGTCT
194 AGAAGGAGTGTTACATTAAAGGCTTGCAAGTCT
*
44560716 GGGTTTAATCCAAATTGATTTGCCAAAATAGATTATTCTCCTTGGGGTTTATTACTTCATATTTA
1 GGGTTTAATCCAAATTGATTTGCCAAAATAGATTATTCTCCTTAGGGTTTATTACTTCATATTTA
44560781 GGCTTAAT-CAAAGTTGTTTTATTAGTGCATGTAGTTCCTTGGTTCT-CTCACTAAAGTTTGTAA
66 GGCTTAATAC-AAGTTGTTTTATTAGTGCATGTAGTTCCTTGGTTCTAC-CACTAAAGTTTGTAA
* **
44560844 CCTTTTTGTTTGCTTCAATAAAATTTAATAGCTTTTGTATGTATGTATGTATGTATGTATGTATC
129 CCTTATTGTTTGCTTCAATAAAATTTAATAGCTTTTGTATGTATGTATGTATCCATGTATGTATC
44560909 AGAAGGAGTGTTACATTAAAGGCTTGCAAGTCT
194 AGAAGGAGTGTTACATTAAAGGCTTGCAAGTCT
44560942 TGAAAGCCCA
Statistics
Matches: 213, Mismatches: 9, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
225 4 0.02
226 209 0.98
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.43
Consensus pattern (226 bp):
GGGTTTAATCCAAATTGATTTGCCAAAATAGATTATTCTCCTTAGGGTTTATTACTTCATATTTA
GGCTTAATACAAGTTGTTTTATTAGTGCATGTAGTTCCTTGGTTCTACCACTAAAGTTTGTAACC
TTATTGTTTGCTTCAATAAAATTTAATAGCTTTTGTATGTATGTATGTATCCATGTATGTATCAG
AAGGAGTGTTACATTAAAGGCTTGCAAGTCT
Found at i:44560888 original size:4 final size:4
Alignment explanation
Indices: 44560879--44560907 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
44560869 TAATAGCTTT
44560879 TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
44560908 CAGAAGGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TGTA
Found at i:44561137 original size:22 final size:22
Alignment explanation
Indices: 44561109--44561156 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
44561099 TTAAAGCGAC
44561109 CAAGGCTCTCTAGCTCTTCTTT
1 CAAGGCTCTCTAGCTCTTCTTT
44561131 CAAGGCTCTCTAGCTCTTCTTT
1 CAAGGCTCTCTAGCTCTTCTTT
44561153 CAAG
1 CAAG
44561157 TTCAGTTAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.17, C:0.31, G:0.15, T:0.38
Consensus pattern (22 bp):
CAAGGCTCTCTAGCTCTTCTTT
Found at i:44573061 original size:15 final size:17
Alignment explanation
Indices: 44573033--44573072 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
44573023 TTTGATTAGT
*
44573033 TTTAA-TTTATCATTTA
1 TTTAATTTTATCATTGA
44573049 -TTAATTTTA-CATTGA
1 TTTAATTTTATCATTGA
44573064 TTTAATTTT
1 TTTAATTTT
44573073 GTGTTATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (17 bp):
TTTAATTTTATCATTGA
Found at i:44586059 original size:18 final size:18
Alignment explanation
Indices: 44586038--44586072 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
44586028 GCAAAAAACG
*
44586038 ATAAAAAAATAAAAATAA
1 ATAAAAAAAGAAAAATAA
*
44586056 ATAAAAATAGAAAAATA
1 ATAAAAAAAGAAAAATA
44586073 TTAAATATTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (18 bp):
ATAAAAAAAGAAAAATAA
Found at i:44586107 original size:20 final size:21
Alignment explanation
Indices: 44586066--44586113 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
44586056 ATAAAAATAG
*
44586066 AAAAATATTAAATATTGATAA
1 AAAAATATTAAATATCGATAA
44586087 AAAAATATTTAAA-ATCG-TAA
1 AAAAATA-TTAAATATCGATAA
44586107 AAAAATA
1 AAAAATA
44586114 CAAAATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 10 0.40
21 10 0.40
22 5 0.20
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (21 bp):
AAAAATATTAAATATCGATAA
Found at i:44586404 original size:10 final size:10
Alignment explanation
Indices: 44586391--44586437 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
44586381 TTTTGATGCA
44586391 TTTTATAATT
1 TTTTATAATT
*
44586401 TTTTATGATT
1 TTTTATAATT
**
44586411 TTTTATAAAA
1 TTTTATAATT
*
44586421 TTTTACAA-T
1 TTTTATAATT
44586430 TTTTATAA
1 TTTTATAA
44586438 AAAATTATAA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
9 7 0.23
10 23 0.77
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (10 bp):
TTTTATAATT
Found at i:44586413 original size:19 final size:20
Alignment explanation
Indices: 44586408--44586496 Score: 80
Period size: 19 Copynumber: 4.5 Consensus size: 20
44586398 ATTTTTTATG
44586408 ATTTTTTATAAAATTTTACA
1 ATTTTTTATAAAATTTTACA
** *
44586428 A-TTTTTATAAAAAATTATA
1 ATTTTTTATAAAATTTTACA
44586447 A-TTTTTATAAAA-TTT-CA
1 ATTTTTTATAAAATTTTACA
44586464 ATATTTTTATTAAAATTTAATA-A
1 AT-TTTTTA-TAAAATTT--TACA
44586487 ATTTTTTATA
1 ATTTTTTATA
44586497 TTTTTTATTG
Statistics
Matches: 57, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
17 2 0.04
18 2 0.04
19 33 0.58
20 6 0.11
21 4 0.07
22 6 0.11
23 4 0.07
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
ATTTTTTATAAAATTTTACA
Found at i:44586424 original size:20 final size:19
Alignment explanation
Indices: 44586391--44586496 Score: 79
Period size: 19 Copynumber: 5.4 Consensus size: 19
44586381 TTTTGATGCA
**
44586391 TTTTATAATTTTTTATGATT
1 TTTTATAAAATTTTAT-ATT
* *
44586411 TTTTATAAAATTTTACAAT
1 TTTTATAAAATTTTATATT
** *
44586430 TTTTATAAAAAATTATAAT
1 TTTTATAAAATTTTATATT
*
44586449 TTTTATAAAATTTCA-ATAT
1 TTTTATAAAATTTTATAT-T
*
44586468 TTTTATTAAAATTTAATAAATT
1 TTTTA-TAAAATTT--TATATT
44586490 TTTTATA
1 TTTTATA
44586497 TTTTTTATTG
Statistics
Matches: 69, Mismatches: 12, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
18 1 0.01
19 36 0.52
20 21 0.30
21 2 0.03
22 7 0.10
23 2 0.03
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.57
Consensus pattern (19 bp):
TTTTATAAAATTTTATATT
Found at i:44586452 original size:38 final size:40
Alignment explanation
Indices: 44586410--44586492 Score: 109
Period size: 38 Copynumber: 2.1 Consensus size: 40
44586400 TTTTTATGAT
*
44586410 TTTTTATAAAATTTTACA-ATTTTTATAAAAAATT-AT-AA
1 TTTTTATAAAATTTCA-ATATTTTTATAAAAAATTAATAAA
* *
44586448 TTTTTATAAAATTTCAATATTTTTATTAAAATTTAATAAA
1 TTTTTATAAAATTTCAATATTTTTATAAAAAATTAATAAA
44586488 TTTTT
1 TTTTT
44586493 TATATTTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
37 1 0.03
38 29 0.74
39 2 0.05
40 7 0.18
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (40 bp):
TTTTTATAAAATTTCAATATTTTTATAAAAAATTAATAAA
Found at i:44591580 original size:21 final size:21
Alignment explanation
Indices: 44591554--44591599 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
44591544 CGAGGATCCA
44591554 AGCCGACAAAGCTTATTCTAG
1 AGCCGACAAAGCTTATTCTAG
*
44591575 AGCCGACAAAGCTTATTTTAG
1 AGCCGACAAAGCTTATTCTAG
44591596 AGCC
1 AGCC
44591600 TCCAACATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (21 bp):
AGCCGACAAAGCTTATTCTAG
Found at i:44593382 original size:19 final size:18
Alignment explanation
Indices: 44593346--44593398 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
44593336 TGCCTCTTTT
*
44593346 TGCATTAATTCCATTCATCA
1 TGCATTAATTTCA-TCAT-A
44593366 -GCATTACATTTCATCATA
1 TGCATTA-ATTTCATCATA
44593384 TGCATTAAATTTCAT
1 TGCATT-AATTTCAT
44593399 AAAAAGACCC
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 1 0.03
19 22 0.76
20 6 0.21
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.42
Consensus pattern (18 bp):
TGCATTAATTTCATCATA
Found at i:44595527 original size:101 final size:101
Alignment explanation
Indices: 44595346--44595591 Score: 393
Period size: 101 Copynumber: 2.4 Consensus size: 101
44595336 AAAGGATGAA
*
44595346 TTGATGGATAAGACCATAACTGGGTTATGGCACTATGAACGTAAGACCATGGTTGAACCATGGCA
1 TTGAT-GATAAGACCATAACTGGGTTATGGCACTATGAACGTAAGACCATGGTTGAACCATGACA
44595411 GTGTTTATATGTAAGACCATAGCTGGGCCATGAAATT
65 GTGTTTATATGTAAGACCATAGCTGGGCCATGAAATT
* * *
44595448 TTGATGATAAAACCATAACTGGGTTATAGCACTATGAACGTAAGACCATGGTTGGACCATGACAG
1 TTGATGATAAGACCATAACTGGGTTATGGCACTATGAACGTAAGACCATGGTTGAACCATGACAG
* *
44595513 TGTTTATATGTAAGACCATAGCTGGGCTATGACATT
66 TGTTTATATGTAAGACCATAGCTGGGCCATGAAATT
* * * *
44595549 CTGATGATAAGACCATAACTAGGTTATGGCACTACGAATGTAA
1 TTGATGATAAGACCATAACTGGGTTATGGCACTATGAACGTAA
44595592 AGGATAAATT
Statistics
Matches: 132, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
101 127 0.96
102 5 0.04
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.28
Consensus pattern (101 bp):
TTGATGATAAGACCATAACTGGGTTATGGCACTATGAACGTAAGACCATGGTTGAACCATGACAG
TGTTTATATGTAAGACCATAGCTGGGCCATGAAATT
Found at i:44595565 original size:33 final size:32
Alignment explanation
Indices: 44595419--44595565 Score: 98
Period size: 33 Copynumber: 4.4 Consensus size: 32
44595409 CAGTGTTTAT
*
44595419 ATGTAAGACCATAGCTGGGCCATGAAATTTTG
1 ATGTAAGACCATAGCTGGGCCATGACATTTTG
* * ** * *
44595451 ATGATAAAACCATAACTGGGTTAT-AGCACTATG
1 ATG-TAAGACCATAGCTGGGCCATGA-CATTTTG
* * * * *
44595484 AACGTAAGACCATGGTTGGACCATGACAGTGTTTAT
1 -ATGTAAGACCATAGCTGGGCCATGACA-T-TTT-G
* *
44595520 ATGTAAGACCATAGCTGGGCTATGACATTCTG
1 ATGTAAGACCATAGCTGGGCCATGACATTTTG
44595552 ATGATAAGACCATA
1 ATG-TAAGACCATA
44595566 ACTAGGTTAT
Statistics
Matches: 82, Mismatches: 25, Indels: 15
0.67 0.20 0.12
Matches are distributed among these distances:
32 7 0.09
33 47 0.57
34 4 0.05
35 24 0.29
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.27
Consensus pattern (32 bp):
ATGTAAGACCATAGCTGGGCCATGACATTTTG
Found at i:44598372 original size:24 final size:23
Alignment explanation
Indices: 44598346--44598430 Score: 82
Period size: 24 Copynumber: 3.6 Consensus size: 23
44598336 TGGCTATCCG
44598346 GAGCTTCCCGTTAATGGCTCTTT
1 GAGCTTCCCGTTAATGGCTCTTT
* * * **
44598369 GGAGCTACCTGTTATTGGCTCGCAT
1 -GAGCTTCCCGTTAATGGCTC-TTT
44598394 GAGCTTCCCGATT-ATGGCTCTTAT
1 GAGCTTCCCG-TTAATGGCTCTT-T
44598418 GAGCTTCCCGTTA
1 GAGCTTCCCGTTA
44598431 TATAGCCCGA
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
23 2 0.04
24 42 0.89
25 3 0.06
ACGTcount: A:0.15, C:0.26, G:0.24, T:0.35
Consensus pattern (23 bp):
GAGCTTCCCGTTAATGGCTCTTT
Found at i:44598374 original size:72 final size:72
Alignment explanation
Indices: 44598284--44598430 Score: 170
Period size: 72 Copynumber: 2.0 Consensus size: 72
44598274 AGCTTCCTAA
* * *
44598284 TTAATGGCTCTCCAGAGCTTCCTGATA-TGGCTCGCTTGAACTCCCCGATATATGGCTATCCGGA
1 TTAATGGCTCTCCAGAGCTACCTGATATTGGCTCGCATGAACTCCCCGAT-TATGGCTATCAGGA
44598348 GCTTCCCG
65 GCTTCCCG
*** * * * * * *
44598356 TTAATGGCTCTTTGGAGCTACCTGTTATTGGCTCGCATGAGCTTCCCGATTATGGCTCTTATGAG
1 TTAATGGCTCTCCAGAGCTACCTGATATTGGCTCGCATGAACTCCCCGATTATGGCTATCAGGAG
44598421 CTTCCCG
66 CTTCCCG
44598428 TTA
1 TTA
44598431 TATAGCCCGA
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
72 43 0.69
73 19 0.31
ACGTcount: A:0.17, C:0.27, G:0.22, T:0.33
Consensus pattern (72 bp):
TTAATGGCTCTCCAGAGCTACCTGATATTGGCTCGCATGAACTCCCCGATTATGGCTATCAGGAG
CTTCCCG
Found at i:44598889 original size:12 final size:12
Alignment explanation
Indices: 44598874--44598907 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
44598864 CAACAAGAGA
44598874 ATGATATGTATC
1 ATGATATGTATC
44598886 ATGATATGTATC
1 ATGATATGTATC
44598898 ATGATATGTA
1 ATGATATGTA
44598908 AATATGTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.35, C:0.06, G:0.18, T:0.41
Consensus pattern (12 bp):
ATGATATGTATC
Found at i:44599558 original size:167 final size:167
Alignment explanation
Indices: 44599282--44599615 Score: 668
Period size: 167 Copynumber: 2.0 Consensus size: 167
44599272 TGACTTGTGT
44599282 GTCATGCATATGGAATAAGTGTGGAAAGTAAAGAAATGCAAATGAAAATAAATAATTTTAGAAGA
1 GTCATGCATATGGAATAAGTGTGGAAAGTAAAGAAATGCAAATGAAAATAAATAATTTTAGAAGA
44599347 GTTAAAGTTATATAAAATCCTACTAAGCTTGGGATAATATGTATAAGTGATACTGTGGATTTATT
66 GTTAAAGTTATATAAAATCCTACTAAGCTTGGGATAATATGTATAAGTGATACTGTGGATTTATT
44599412 CATCTTGTCAATTGATGAATGTAACTTCATGAGTATA
131 CATCTTGTCAATTGATGAATGTAACTTCATGAGTATA
44599449 GTCATGCATATGGAATAAGTGTGGAAAGTAAAGAAATGCAAATGAAAATAAATAATTTTAGAAGA
1 GTCATGCATATGGAATAAGTGTGGAAAGTAAAGAAATGCAAATGAAAATAAATAATTTTAGAAGA
44599514 GTTAAAGTTATATAAAATCCTACTAAGCTTGGGATAATATGTATAAGTGATACTGTGGATTTATT
66 GTTAAAGTTATATAAAATCCTACTAAGCTTGGGATAATATGTATAAGTGATACTGTGGATTTATT
44599579 CATCTTGTCAATTGATGAATGTAACTTCATGAGTATA
131 CATCTTGTCAATTGATGAATGTAACTTCATGAGTATA
44599616 TGTGGTATCA
Statistics
Matches: 167, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
167 167 1.00
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.33
Consensus pattern (167 bp):
GTCATGCATATGGAATAAGTGTGGAAAGTAAAGAAATGCAAATGAAAATAAATAATTTTAGAAGA
GTTAAAGTTATATAAAATCCTACTAAGCTTGGGATAATATGTATAAGTGATACTGTGGATTTATT
CATCTTGTCAATTGATGAATGTAACTTCATGAGTATA
Found at i:44603068 original size:20 final size:20
Alignment explanation
Indices: 44603040--44603079 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
44603030 GTCACTGTAT
*
44603040 GCCAGCCAAGGACTGTGACA
1 GCCAACCAAGGACTGTGACA
44603060 GCCAACCAAGGACTGTGACA
1 GCCAACCAAGGACTGTGACA
44603080 ACCAGCCACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.30, G:0.28, T:0.10
Consensus pattern (20 bp):
GCCAACCAAGGACTGTGACA
Found at i:44604131 original size:34 final size:35
Alignment explanation
Indices: 44604076--44604142 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
44604066 CAAACACTAG
*
44604076 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
44604111 AAAACATTTTCCCG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
44604143 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:44610447 original size:44 final size:44
Alignment explanation
Indices: 44610374--44610534 Score: 182
Period size: 44 Copynumber: 3.6 Consensus size: 44
44610364 ACTGTGGTGA
* * *
44610374 ATCTTATCTCCCTGAAGCTGCAGTAGAGCAAATTAAAACTACAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACTACAG
* * * *
44610418 ATCTTATCTCCCTAAAGTTACAATGGAGCAGATTGAAGA-TA-ATG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAACTACA-G
* * *
44610462 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACAA
1 -ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACTACAG
*
44610507 ATCTTATCTCCCTGAAGTTGTAGTGGAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAG
44610535 ATTGGAGTTA
Statistics
Matches: 97, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
43 1 0.01
44 60 0.62
45 35 0.36
46 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (44 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACTACAG
Found at i:44610534 original size:89 final size:89
Alignment explanation
Indices: 44610373--44610722 Score: 280
Period size: 89 Copynumber: 3.9 Consensus size: 89
44610363 CACTGTGGTG
* * * * * * *
44610373 AATCTTATCTCCCTGAAGCTGCAGTAGAGCAAATTAAAACTACAGATCTTATCTCCCTAAAGTTA
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTATCTCCCTAAAGTTG
*
44610438 CAATGGAGCAGATTGAAGATAATG
66 CAATGGAGCAGATTGAAGATAATA
* * *
44610462 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACAAATCTTATCTCCCTGAAGTTG
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTATCTCCCTAAAGTTG
* * * *
44610527 TAGT-G-G-AGATTGGAG-TTATA
66 CAATGGAGCAGATTGAAGATAATA
* * * * * * *
44610547 AATATTATCTCCCTAAATTTGCAGTGGAGTAGATTGAAGTTACAAATCTTAT-TTCCTAAAGCTG
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTATCTCCCTAAAGTTG
* * *
44610611 CAGTGGAACAGATT-ACAGCTACAAGTTACA
66 CAATGGAGCAGATTGA-AG--ATAA--T--A
* * * * ** *
44610641 AATCTTATCTCCCTAAAGTTGCAATGGAGCAGATTGAAGTTACAAGTCTTATCTCATTGAAGTTG
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTATCTCCCTAAAGTTG
* * *
44610706 TAATGAAGTAGATTGAA
66 CAATGGAGCAGATTGAA
44610723 ACTAAATCCT
Statistics
Matches: 205, Mismatches: 43, Indels: 20
0.76 0.16 0.07
Matches are distributed among these distances:
84 12 0.06
85 49 0.24
86 8 0.04
87 8 0.04
88 1 0.00
89 59 0.29
90 1 0.00
92 1 0.00
94 48 0.23
95 17 0.08
96 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (89 bp):
AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTATCTCCCTAAAGTTG
CAATGGAGCAGATTGAAGATAATA
Found at i:44610704 original size:44 final size:44
Alignment explanation
Indices: 44610413--44610722 Score: 182
Period size: 44 Copynumber: 7.0 Consensus size: 44
44610403 AAATTAAAAC
* * * * *
44610413 TACAGATCTTATCTCCCTAAAGTTACAATGGAGCAGATTGAAGA
1 TACAAATCTTATCTCACTAAAGTTGCAATGAAGCAGATTGAAGT
* * * * * *
44610457 TA-ATGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGC
1 TACA--AATCTTATCTCACTAAAGTTGCAATGAAGCAGATTGAAGT
* * * * * *
44610502 CACAAATCTTATCTCCCTGAAGTTGTAGTG--G-AGATTGGAGT
1 TACAAATCTTATCTCACTAAAGTTGCAATGAAGCAGATTGAAGT
* * * * * * *
44610543 TATAAATATTATCTCCCTAAATTTGCAGTGGAGTAGATTGAAGT
1 TACAAATCTTATCTCACTAAAGTTGCAATGAAGCAGATTGAAGT
* * *
44610587 TACAAATCTTATTTC-CTAAAGCTGCAGTGGAA-CAGATTACAGCTACAAGT
1 TACAAATCTTATCTCACTAAAGTTGCAAT-GAAGCAGATT---G----AAGT
* *
44610637 TACAAATCTTATCTCCCTAAAGTTGCAATGGAGCAGATTGAAGT
1 TACAAATCTTATCTCACTAAAGTTGCAATGAAGCAGATTGAAGT
* * * * *
44610681 TACAAGTCTTATCTCATTGAAGTTGTAATGAAGTAGATTGAA
1 TACAAATCTTATCTCACTAAAGTTGCAATGAAGCAGATTGAA
44610723 ACTAAATCCT
Statistics
Matches: 214, Mismatches: 36, Indels: 32
0.76 0.13 0.11
Matches are distributed among these distances:
41 31 0.14
42 1 0.00
43 18 0.08
44 89 0.42
45 35 0.16
46 2 0.01
48 1 0.00
50 20 0.09
51 17 0.08
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (44 bp):
TACAAATCTTATCTCACTAAAGTTGCAATGAAGCAGATTGAAGT
Found at i:44612487 original size:22 final size:22
Alignment explanation
Indices: 44612454--44612497 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
44612444 ATTTTATCCC
*
44612454 TTTTACTATTATTGTCATTATT
1 TTTTACTATTATTCTCATTATT
*
44612476 TTTTA-TATTTATTCTTATTATT
1 TTTTACTA-TTATTCTCATTATT
44612498 CTTATTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.23, C:0.07, G:0.02, T:0.68
Consensus pattern (22 bp):
TTTTACTATTATTCTCATTATT
Found at i:44624415 original size:20 final size:20
Alignment explanation
Indices: 44624382--44624420 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
44624372 CTAGATGTAA
* *
44624382 AGTCTGAAATATTTCACCGC
1 AGTCTAAAACATTTCACCGC
44624402 AGTCTAAAACATTTCACCG
1 AGTCTAAAACATTTCACCG
44624421 ACATCAAGCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.26, G:0.13, T:0.28
Consensus pattern (20 bp):
AGTCTAAAACATTTCACCGC
Found at i:44627118 original size:17 final size:17
Alignment explanation
Indices: 44627098--44627132 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
44627088 AAAAATTAAA
44627098 AATATATTAAAAATTTT
1 AATATATTAAAAATTTT
* *
44627115 AATATTTTTAAAATTTT
1 AATATATTAAAAATTTT
44627132 A
1 A
44627133 TAAATCAGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
AATATATTAAAAATTTT
Found at i:44632385 original size:40 final size:41
Alignment explanation
Indices: 44632308--44632392 Score: 104
Period size: 40 Copynumber: 2.1 Consensus size: 41
44632298 ATAAAGCAGG
* *
44632308 AAAACGCTTCCTTAAGGAAGCGCTTTGTCCACGTGGACA-A
1 AAAACGCTTCCTCAAGGAAGCGCTTTGTCCACATGGACAGA
*
44632348 AAAACGCTTCCTCAA-GAACGCGCTTTG-CACATATGGACAGA
1 AAAACGCTTCCTCAAGGAA-GCGCTTTGTC-CACATGGACAGA
44632389 AAAA
1 AAAA
44632393 TTAGGGTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
39 4 0.10
40 30 0.77
41 5 0.13
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (41 bp):
AAAACGCTTCCTCAAGGAAGCGCTTTGTCCACATGGACAGA
Found at i:44633370 original size:97 final size:97
Alignment explanation
Indices: 44633159--44633446 Score: 440
Period size: 97 Copynumber: 3.0 Consensus size: 97
44633149 AACAACTAGT
* *
44633159 TTTATTTGATTTTTCCTTAAAAACCCTAAATACTAAACCCCAATCTAATTTTTTTTAAAA-TTAT
1 TTTATTTGATTTTTCCTTAAAAACCCTAAACACTAAACCCTAATCTAATTTTTTTTAAAATTTAT
*
44633223 AATTAATTTACTCAAGTAACTCTAAACCCTAA
66 AATTAATTTACTCAAGTAACCCTAAACCCTAA
* *
44633255 TTTATTTGATGTTACCTTAAAAACCCTAAACACTAAACCCTAATCTAATTTTTTTTAAAATTTAT
1 TTTATTTGATTTTTCCTTAAAAACCCTAAACACTAAACCCTAATCTAATTTTTTTTAAAATTTAT
44633320 AATTAATTTACTCAAGTAACCCTAAACCCTAA
66 AATTAATTTACTCAAGTAACCCTAAACCCTAA
* *
44633352 TTTATTT-ATTTTTTCCTTAAAAACCATAAACACTAAACTCTAATCTAA--TTTTTTAAAATTTA
1 TTTATTTGA-TTTTTCCTTAAAAACCCTAAACACTAAACCCTAATCTAATTTTTTTTAAAATTTA
* * * *
44633414 TAATTAATTTAATTAAGAAATCCTAAACCCTAA
65 TAATTAATTTACTCAAGTAACCCTAAACCCTAA
44633447 ACCCTTATTT
Statistics
Matches: 177, Mismatches: 13, Indels: 5
0.91 0.07 0.03
Matches are distributed among these distances:
95 43 0.24
96 57 0.32
97 77 0.44
ACGTcount: A:0.40, C:0.18, G:0.02, T:0.40
Consensus pattern (97 bp):
TTTATTTGATTTTTCCTTAAAAACCCTAAACACTAAACCCTAATCTAATTTTTTTTAAAATTTAT
AATTAATTTACTCAAGTAACCCTAAACCCTAA
Found at i:44633604 original size:40 final size:39
Alignment explanation
Indices: 44633544--44633663 Score: 123
Period size: 40 Copynumber: 2.9 Consensus size: 39
44633534 TCAAGGAAGG
*
44633544 TCCACGTGGACACAAAGCGCTTCCTCAAGGAAGCGTTTTCTA
1 TCCACGTGG--ACAAAGCGCTTCCT-GAGGAAGCGTTTTCTA
* * * * *
44633586 TTCACGTGGACAAAGCGCTTCGATGGGGAAGCGTTTTTTG
1 TCCACGTGGACAAAGCGCTTC-CTGAGGAAGCGTTTTCTA
* *
44633626 TCCACGTGGACAAAGTGTTTCCTTGAGGAAGCGTTTTC
1 TCCACGTGGACAAAGCGCTTCC-TGAGGAAGCGTTTTC
44633664 CTGCTTTATC
Statistics
Matches: 64, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
40 55 0.86
41 1 0.02
42 8 0.12
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.28
Consensus pattern (39 bp):
TCCACGTGGACAAAGCGCTTCCTGAGGAAGCGTTTTCTA
Found at i:44633980 original size:18 final size:18
Alignment explanation
Indices: 44633957--44633993 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
44633947 TTGTTATCCA
* *
44633957 AATATAAATGTTATATAT
1 AATATAAATATCATATAT
44633975 AATATAAATATCATATAT
1 AATATAAATATCATATAT
44633993 A
1 A
44633994 TAATTTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (18 bp):
AATATAAATATCATATAT
Found at i:44634503 original size:29 final size:29
Alignment explanation
Indices: 44634440--44634503 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
44634430 TGAATAGTTA
*
44634440 GGTAACCATTTTGTATCTTTTCATAGCTG
1 GGTAACCATTTTGTATCTTTTCATAACTG
* * *
44634469 GTTAACTATTTTGTATCTTTTCATAATTG
1 GGTAACCATTTTGTATCTTTTCATAACTG
44634498 GGTAAC
1 GGTAAC
44634504 AAAAGAAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.23, C:0.14, G:0.16, T:0.47
Consensus pattern (29 bp):
GGTAACCATTTTGTATCTTTTCATAACTG
Found at i:44635462 original size:5 final size:5
Alignment explanation
Indices: 44635452--44635477 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
44635442 AAAAGAGTAC
44635452 GTATG GTATG GTATG GTATG GTATG G
1 GTATG GTATG GTATG GTATG GTATG G
44635478 GGCATGGCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.42, T:0.38
Consensus pattern (5 bp):
GTATG
Found at i:44642059 original size:15 final size:15
Alignment explanation
Indices: 44642039--44642068 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
44642029 AAATAATGAA
*
44642039 ATAAACAAAAGAAAT
1 ATAAACAAAAAAAAT
44642054 ATAAACAAAAAAAAT
1 ATAAACAAAAAAAAT
44642069 TATTAAGAAA
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:0.77, C:0.07, G:0.03, T:0.13
Consensus pattern (15 bp):
ATAAACAAAAAAAAT
Found at i:44642672 original size:2 final size:2
Alignment explanation
Indices: 44642665--44642691 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
44642655 ATCCTTCCCC
44642665 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
44642692 CTACTTTGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:44644990 original size:17 final size:18
Alignment explanation
Indices: 44644958--44644992 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
44644948 GAAAACTTCA
44644958 AATAATTATGTGATAAAT
1 AATAATTATGTGATAAAT
*
44644976 AATAA-TATGTTATAAAT
1 AATAATTATGTGATAAAT
44644993 TAAAGTACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (18 bp):
AATAATTATGTGATAAAT
Found at i:44645129 original size:17 final size:17
Alignment explanation
Indices: 44645109--44645164 Score: 62
Period size: 17 Copynumber: 3.3 Consensus size: 17
44645099 TTTATTTCTT
*
44645109 ATATATATTATTAATTA
1 ATATATATTATAAATTA
44645126 ATATAT-TATATGAAATTA
1 ATATATAT-TAT-AAATTA
*
44645144 A-ATATATTATAAAATA
1 ATATATATTATAAATTA
44645160 ATATA
1 ATATA
44645165 AATTTTAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
16 7 0.21
17 19 0.58
18 7 0.21
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (17 bp):
ATATATATTATAAATTA
Found at i:44645131 original size:15 final size:15
Alignment explanation
Indices: 44645111--44645182 Score: 58
Period size: 15 Copynumber: 4.5 Consensus size: 15
44645101 TATTTCTTAT
44645111 ATATATTATTAATTA
1 ATATATTATTAATTA
44645126 ATATATTATATGAAATTAA
1 ATATATTAT-T--AATT-A
* *
44645145 ATATATTATAAAATA
1 ATATATTATTAATTA
44645160 ATATAAATT-TTAA-TA
1 ATAT--ATTATTAATTA
44645175 ATATATTA
1 ATATATTA
44645183 AATTATGTAT
Statistics
Matches: 47, Mismatches: 3, Indels: 15
0.72 0.05 0.23
Matches are distributed among these distances:
13 3 0.06
15 20 0.43
16 7 0.15
17 3 0.06
18 4 0.09
19 10 0.21
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (15 bp):
ATATATTATTAATTA
Found at i:44646975 original size:17 final size:18
Alignment explanation
Indices: 44646943--44646977 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
44646933 GAAAACTTCA
44646943 AATAATTATGTGATAAAT
1 AATAATTATGTGATAAAT
*
44646961 AATAA-TATGTTATAAAT
1 AATAATTATGTGATAAAT
44646978 TAAAGTACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (18 bp):
AATAATTATGTGATAAAT
Found at i:44648686 original size:44 final size:44
Alignment explanation
Indices: 44648638--44648757 Score: 129
Period size: 44 Copynumber: 2.7 Consensus size: 44
44648628 TCGACTTCAA
* * *
44648638 TCTGCTCCACTGCAACCTCAGGGAGATAATATTTGCTTATT-T-GG
1 TCTGCTCCACTGCAACCTCAGGGAGATAAGACTTG-TT-TTCTCAG
* ** *
44648682 TCTGCCCCACTGTGACTTCAGAGG-GATAAGACTTGTTTTCTCAG
1 TCTGCTCCACTGCAACCTCAG-GGAGATAAGACTTGTTTTCTCAG
44648726 TCTGCTCCACTGCAACCTCAGGGAGATAAGAC
1 TCTGCTCCACTGCAACCTCAGGGAGATAAGAC
44648758 CTGATGCGAT
Statistics
Matches: 61, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
42 2 0.03
43 5 0.08
44 52 0.85
45 2 0.03
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (44 bp):
TCTGCTCCACTGCAACCTCAGGGAGATAAGACTTGTTTTCTCAG
Found at i:44648917 original size:217 final size:215
Alignment explanation
Indices: 44648536--44649314 Score: 1122
Period size: 217 Copynumber: 3.6 Consensus size: 215
44648526 TCTAGTCAGC
* ** * * * * *
44648536 AAGACTTGATGCGATCTGCTCTACTGCAACTTCAGAGACATAAGATCTATTCCTTTAACCCGCTT
1 AAGACCTGATGCGATCCACTCTACTGCAACTTCGGAGAGATAAGATCTATTACTTTAATCCGCTC
* * *
44648601 CACTACAACTTCAGGGAGATAGGATTATCGACTTCAATCTGCTCCACTGCAACCTCAGGGAGATA
66 CACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTACTCCACTACAACCTCAGGGAGATA
* * * * *
44648666 ATATTTGCTTATTTGGTCTGCCCCACTGTGACTTCAGAGGGATAAGACTTGTTTTCTCAGTCTGC
131 AGATTTACTTCTTCGGTCTGCCCCACTGTGACTTCAGGGGGATAAGACTTGTTTTCTCAGTCTGC
44648731 TCCACTGCAACCTCAGGGAGAT
196 TCCACT-CAA-CTCAGGGAGAT
** *
44648753 AAGACCTGATGCGATCCACTCTACTGCAACTTCGGAGAGATAAGATCTATTACTTTAATTTGATC
1 AAGACCTGATGCGATCCACTCTACTGCAACTTCGGAGAGATAAGATCTATTACTTTAATCCGCTC
* *
44648818 CACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTACTCTACTGCAACCTCAGGGAGATA
66 CACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTACTCCACTACAACCTCAGGGAGATA
*
44648883 AGATTTACTTCTTCGGTCTGCCCCACTGTGACTTCAGGGGGATAAAACTTGTTTTCTCAGTCTGC
131 AGATTTACTTCTTCGGTCTGCCCCACTGTGACTTCAGGGGGATAAGACTTGTTTTCTCAGTCTGC
44648948 T---C-C-A--CAGGGAGAT
196 TCCACTCAACTCAGGGAGAT
* *
44648961 AAGACCTGATGCAATCCACTCTACTGCAACTTCGAAGAGATAAGATCTATTACTTTAATCCGCTC
1 AAGACCTGATGCGATCCACTCTACTGCAACTTCGGAGAGATAAGATCTATTACTTTAATCCGCTC
* *
44649026 CACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTGCTCCACTACATCCTCAGGGAGATA
66 CACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTACTCCACTACAACCTCAGGGAGATA
* * * * *
44649091 AGATTTGCCATCTTCGATCTGCCTCACTGTGACTTCAGGGGGATAAGACTTGTTTTCTTAGTCTG
131 AGATTT-ACTTCTTCGGTCTGCCCCACTGTGACTTCAGGGGGATAAGACTTGTTTTCTCAGTCTG
**
44649156 CTCCACTACAAACTCAAAGAGAT
195 CTCCACT-C-AACTCAGGGAGAT
* *
44649179 AAGACATGATACGATCCACTCTACTGCAACTTCGGAGAGATAAGATCTATTACTTTAATCCGCTC
1 AAGACCTGATGCGATCCACTCTACTGCAACTTCGGAGAGATAAGATCTATTACTTTAATCCGCTC
* * *
44649244 CATTACAACTTTAGGGAGATAGGATTATCGGCTTCAATCTACTCCACTACATCCTCAGGGAGATA
66 CACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTACTCCACTACAACCTCAGGGAGATA
44649309 AGATTT
131 AGATTT
44649315 GTGATCTTCG
Statistics
Matches: 508, Mismatches: 44, Indels: 19
0.89 0.08 0.03
Matches are distributed among these distances:
208 136 0.27
209 54 0.11
211 1 0.00
212 2 0.00
214 2 0.00
216 1 0.00
217 176 0.35
218 136 0.27
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (215 bp):
AAGACCTGATGCGATCCACTCTACTGCAACTTCGGAGAGATAAGATCTATTACTTTAATCCGCTC
CACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTACTCCACTACAACCTCAGGGAGATA
AGATTTACTTCTTCGGTCTGCCCCACTGTGACTTCAGGGGGATAAGACTTGTTTTCTCAGTCTGC
TCCACTCAACTCAGGGAGAT
Found at i:44649045 original size:44 final size:44
Alignment explanation
Indices: 44648997--44649358 Score: 165
Period size: 44 Copynumber: 8.3 Consensus size: 44
44648987 CAACTTCGAA
* * *
44648997 GAGATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCAGG
1 GAGATAAGATCTATGACTTCAATCTGCTCCACTACAACTTCAGG
* * * *
44649041 GAGATAGGAT-TATCGGCTTCAATCTGCTCCACTACATCCTCAGG
1 GAGATAAGATCTAT-GACTTCAATCTGCTCCACTACAACTTCAGG
* ***
44649085 GAGATAAGAT-T-TGCCATCTTCGATCTGC-CTCACTGTGACTTCAGG
1 GAGATAAGATCTATG--A-CTTCAATCTGCTC-CACTACAACTTCAGG
* ** * **
44649130 GGGATAAGA-CT-TGTTTTCTTAGTCTGCTCCACTACAAAC-TCAAA
1 GAGATAAGATCTATGACTTC--AATCTGCTCCACTAC-AACTTCAGG
* * ** * *
44649174 GAGATAAGA-C-ATGA-TACGATCCACTCTACTGCAACTTC-GG
1 GAGATAAGATCTATGACTTCAATCTGCTCCACTACAACTTCAGG
* * * * *
44649214 AGAGATAAGATCTATTACTTTAATCCGCTCCATTACAACTTTAGG
1 -GAGATAAGATCTATGACTTCAATCTGCTCCACTACAACTTCAGG
* * * * *
44649259 GAGATAGGAT-TATCGGCTTCAATCTACTCCACTACATCCTCAGG
1 GAGATAAGATCTAT-GACTTCAATCTGCTCCACTACAACTTCAGG
* * * * * **
44649303 GAGATAAGATTTGTGATCTTCGATCTGCTTCGCTACTGCTT-AGG
1 GAGATAAGATCTATGA-CTTCAATCTGCTCCACTACAACTTCAGG
*
44649347 GAGACAAGATCT
1 GAGATAAGATCT
44649359 GTAATTTCTA
Statistics
Matches: 231, Mismatches: 67, Indels: 40
0.68 0.20 0.12
Matches are distributed among these distances:
40 3 0.01
41 20 0.09
42 5 0.02
43 12 0.05
44 136 0.59
45 55 0.24
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (44 bp):
GAGATAAGATCTATGACTTCAATCTGCTCCACTACAACTTCAGG
Found at i:44649467 original size:128 final size:128
Alignment explanation
Indices: 44649304--44650174 Score: 1323
Period size: 128 Copynumber: 6.8 Consensus size: 128
44649294 ATCCTCAGGG
* * *
44649304 AGATAAGATTTG-TGATCTTCGATCTGCTTCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCT
1 AGATAAGATTTGCCGCT-TTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCT
* * * * * *
44649368 AACCTACTCCACTGCCGACCAAGGAGATAGGACTTGTGGCTTAAATCTGCTTCTTTACACTTGA
65 AACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGA
* * *
44649432 AGATAAGCTTCGTCG-TCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCC
1 AGATAAGATTTGCCGCT-TTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTT-C
* * *
44649496 CAACTTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATTTGCTTCCTTACTCTTGA
64 TAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGA
* * *
44649561 AGATAATATTTGCCGCTTTCGATCTGCTCTGCTACTGCTTAGGGAGACAAAATCTGTAATTTCTA
1 AGATAAGATTTGCCGCTTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCTA
* * *
44649626 ACCTATTTCACTGCTGACCAGGGATATAGGACCTGTGGCTTAAATCTGCTTCCGTACTCTTGA
66 ACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGA
* * * * *
44649689 AGATAAGATTTGTCGCTTTCGATCTGCTCTGCTACTGCTTAAGGAGACAAGATCTATAATTTCCA
1 AGATAAGATTTGCCGCTTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCTA
* *
44649754 ACCTATTCCACTACTGACCAGGGATATAGGACTTGTGGCTTAAATCTTCTTCCTTACTCTTGA
66 ACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGA
* *
44649817 AGATAAGATTTGCCGCTTTCGATCTGCTCCGCTACTGTTTAGGGAGACAAGATCTGTAATTTCCA
1 AGATAAGATTTGCCGCTTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCTA
44649882 ACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGA
66 ACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGA
* * *
44649945 AGATAAGATTTGCCGCTTTTGATCTGCTCCGCTACTACTTAAGGAGACAAGATCTGTAATTTCTA
1 AGATAAGATTTGCCGCTTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCTA
* * *
44650010 ACCTATTTCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTACTTCCTTACTATTGA
66 ACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGA
* ** * *
44650073 AAATAAGATTTTTCGCTTTCGATCTGCTCCGCTACTACTTAGGGAGACAAGATCTGTAATATCTA
1 AGATAAGATTTGCCGCTTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCTA
*
44650138 AACTATTCCACTGCTGACCAGGGATATAGGACTTGTG
66 ACCTATTCCACTGCTGACCAGGGATATAGGACTTGTG
44650175 ATTTCACCGA
Statistics
Matches: 681, Mismatches: 59, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
128 568 0.83
129 112 0.16
130 1 0.00
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.33
Consensus pattern (128 bp):
AGATAAGATTTGCCGCTTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCTA
ACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGA
Found at i:44651442 original size:16 final size:17
Alignment explanation
Indices: 44651414--44651446 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
44651404 TTAGCCTCTC
44651414 CATTTTTACTTTTTCAT
1 CATTTTTACTTTTTCAT
44651431 CATTTTTA-TTTTTCAT
1 CATTTTTACTTTTTCAT
44651447 TTTCATTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.18, C:0.15, G:0.00, T:0.67
Consensus pattern (17 bp):
CATTTTTACTTTTTCAT
Found at i:44654152 original size:14 final size:14
Alignment explanation
Indices: 44654133--44654160 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
44654123 TAGAAGGGGG
44654133 CCACCACATATGCA
1 CCACCACATATGCA
44654147 CCACCACATATGCA
1 CCACCACATATGCA
44654161 TTAAATAGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.43, G:0.07, T:0.14
Consensus pattern (14 bp):
CCACCACATATGCA
Found at i:44660682 original size:9 final size:9
Alignment explanation
Indices: 44660663--44660699 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
44660653 TGAGTTTTCG
44660663 AATTCGAAT
1 AATTCGAAT
44660672 AACTT-GAAT
1 AA-TTCGAAT
44660681 AATTCGAAT
1 AATTCGAAT
44660690 AATTCGAAT
1 AATTCGAAT
44660699 A
1 A
44660700 TCAAACTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 2 0.08
9 22 0.85
10 2 0.08
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:44660948 original size:30 final size:31
Alignment explanation
Indices: 44660914--44660973 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
44660904 AAACCTTTTA
*
44660914 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
44660944 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
44660974 TCTCACCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:44672518 original size:19 final size:19
Alignment explanation
Indices: 44672466--44672518 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
44672456 CAAATAATTT
*
44672466 AAAATTTATAAAAATATTC
1 AAAAATTATAAAAATATTC
* *
44672485 AAAAA-TAAAATAAAAATTC
1 AAAAATTATAA-AAATATTC
44672504 AAAAAATTATAAAAA
1 -AAAAATTATAAAAA
44672519 CTTGATAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
18 4 0.15
19 11 0.41
20 8 0.30
21 4 0.15
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (19 bp):
AAAAATTATAAAAATATTC
Found at i:44680703 original size:39 final size:40
Alignment explanation
Indices: 44680642--44680803 Score: 222
Period size: 40 Copynumber: 4.1 Consensus size: 40
44680632 TATTATACTC
*
44680642 TCTGTCTAGTGTG-TTCGGTTGGACTAGCTCTTATGAGCA
1 TCTGTCTAGTGTGTTTCAGTTGGACTAGCTCTTATGAGCA
* *
44680681 TCTATCTAGTATG-TTC-GATTGGACTAGCTCTTATGAGCA
1 TCTGTCTAGTGTGTTTCAG-TTGGACTAGCTCTTATGAGCA
* * *
44680720 TCTGTTTGGTGTGTTTCAGTTGGACTAGCTCTTATAAGCA
1 TCTGTCTAGTGTGTTTCAGTTGGACTAGCTCTTATGAGCA
* *
44680760 TCTGTCTAGTGCGTTTCAGTTGGACTAGCTATTATGAGCA
1 TCTGTCTAGTGTGTTTCAGTTGGACTAGCTCTTATGAGCA
44680800 TCTG
1 TCTG
44680804 GTCTGTTTTC
Statistics
Matches: 108, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
38 1 0.01
39 44 0.41
40 62 0.57
41 1 0.01
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.40
Consensus pattern (40 bp):
TCTGTCTAGTGTGTTTCAGTTGGACTAGCTCTTATGAGCA
Found at i:44682876 original size:18 final size:19
Alignment explanation
Indices: 44682846--44682887 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
44682836 CACCAGTAAA
44682846 CAGTAATCAGTAAC-GATAG
1 CAGTAATCAGTAACAG-TAG
44682865 CAGTAA-CAGTAACAGTAG
1 CAGTAATCAGTAACAGTAG
44682883 CAGTA
1 CAGTA
44682888 TTCAACACAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.43, C:0.17, G:0.21, T:0.19
Consensus pattern (19 bp):
CAGTAATCAGTAACAGTAG
Found at i:44682918 original size:45 final size:44
Alignment explanation
Indices: 44682865--44683016 Score: 187
Period size: 45 Copynumber: 3.4 Consensus size: 44
44682855 GTAACGATAG
* * *
44682865 CAGTAACAGTAACAGTAGCAGTATTCAACACACAAAATACTGAAT
1 CAGTAACAGTAACAGTAACAGTATTCGACACACAAAGT-CTGAAT
* * *
44682910 CTGTAACAGTAACGGTAACAGTATTCGACACACAAAGTGCCGAAT
1 CAGTAACAGTAACAGTAACAGTATTCGACACACAAAGT-CTGAAT
* * * *
44682955 CGGTAACAGTAACAGTAATAGTATTTGACACACAAAGTGTCGAAT
1 CAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTCT-GAAT
44683000 CAGTAACAGTAACAGTA
1 CAGTAACAGTAACAGTA
44683017 GTTGGCACAT
Statistics
Matches: 92, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
45 92 1.00
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Consensus pattern (44 bp):
CAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTCTGAAT
Found at i:44683273 original size:40 final size:39
Alignment explanation
Indices: 44683218--44683305 Score: 113
Period size: 39 Copynumber: 2.2 Consensus size: 39
44683208 AATTTATTAC
* * *
44683218 TTCAGTAATTTCACAATTCAATGCATTATACATAACAATA
1 TTCAGTATTTTCACAATTCAAT-CAGTATACAAAACAATA
* *
44683258 TTCAGTATTTTCACAATTCACTCAGTATTCAAAACAATA
1 TTCAGTATTTTCACAATTCAATCAGTATACAAAACAATA
*
44683297 TCCAGTATT
1 TTCAGTATT
44683306 CCCTAATTCA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
39 22 0.52
40 20 0.48
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.36
Consensus pattern (39 bp):
TTCAGTATTTTCACAATTCAATCAGTATACAAAACAATA
Found at i:44690944 original size:18 final size:18
Alignment explanation
Indices: 44690901--44690944 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
44690891 ACCCAATCCA
* *
44690901 AACCCAAGTATTCAACCC
1 AACCCAATTATCCAACCC
44690919 AACCCAATTATCCAACCC
1 AACCCAATTATCCAACCC
44690937 AACCCAAT
1 AACCCAAT
44690945 CATAAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.41, C:0.41, G:0.02, T:0.16
Consensus pattern (18 bp):
AACCCAATTATCCAACCC
Found at i:44691067 original size:9 final size:9
Alignment explanation
Indices: 44691055--44691105 Score: 75
Period size: 9 Copynumber: 5.7 Consensus size: 9
44691045 TCAATTCAGT
44691055 TAATTCGGG
1 TAATTCGGG
* *
44691064 TAATCCGGT
1 TAATTCGGG
*
44691073 TAATTCGGT
1 TAATTCGGG
44691082 TAATTCGGG
1 TAATTCGGG
44691091 TAATTCGGG
1 TAATTCGGG
44691100 TAATTC
1 TAATTC
44691106 TTAACCAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 38 1.00
ACGTcount: A:0.24, C:0.14, G:0.25, T:0.37
Consensus pattern (9 bp):
TAATTCGGG
Found at i:44691083 original size:27 final size:27
Alignment explanation
Indices: 44691047--44691105 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
44691037 GTAGTGATTC
*
44691047 AATTCAGTTAATTCGGGTAATCCGGTT
1 AATTCAGTTAATTCGGGTAATCCGGGT
* *
44691074 AATTCGGTTAATTCGGGTAATTCGGGT
1 AATTCAGTTAATTCGGGTAATCCGGGT
44691101 AATTC
1 AATTC
44691106 TTAACCAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.37
Consensus pattern (27 bp):
AATTCAGTTAATTCGGGTAATCCGGGT
Found at i:44706379 original size:13 final size:13
Alignment explanation
Indices: 44706361--44706386 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
44706351 GGGTACTGTT
44706361 GATCTTTTAAGCA
1 GATCTTTTAAGCA
44706374 GATCTTTTAAGCA
1 GATCTTTTAAGCA
44706387 CATGTCAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
GATCTTTTAAGCA
Found at i:44707454 original size:45 final size:45
Alignment explanation
Indices: 44707369--44707984 Score: 426
Period size: 45 Copynumber: 13.9 Consensus size: 45
44707359 AATAGATCGG
* * * * * *
44707369 TGAAGATAACAAATCCTATCTCCATGAAGTTGCAGTGGAGTGGAT
1 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTGCAGCGGAGTAGAT
* * * *
44707414 TAAAAATAGCAAGTCTTATCTCCCTGAGGTTACAGCGGAGTAGAT
1 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTGCAGCGGAGTAGAT
* * * ** *
44707459 TGAAGATAGCAAATCCTATCTCCTTGAAGTTGCAGTTGAGTGGAT
1 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTGCAGCGGAGTAGAT
* * * * * * *
44707504 TGAAAATAACAAGTTTTATCTCTCTGAAGTTGCAGCGGAGCAAAC
1 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTGCAGCGGAGTAGAT
* * * * * *
44707549 TGAAGATAACAAGTCTTATCTCTCTGAGGTTGCTGCGGAATAGAC
1 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTGCAGCGGAGTAGAT
* * * *
44707594 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGAT
1 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTGCAGCGGAGTAGAT
* * * *
44707639 TGAAGATAACAAGTCTTATCTCCTTGAAGTTGCAGCGGAGCAGAC
1 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTGCAGCGGAGTAGAT
* * * **
44707684 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGAT
1 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTGCAGCGGAGTAGAT
* * * * * **
44707729 TAAAGATAGTAAGTCTTATCTCTCTAAAGTTGCAGTGGAACAGAT
1 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTGCAGCGGAGTAGAT
* ** * * * **
44707774 TGAAGAAAATAA-TCCTATCTCTCTGAAGTTGCAGTGGAGCGGAT
1 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTGCAGCGGAGTAGAT
* * * *
44707818 T-AAGACT-G-TAGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-
1 TGAAGA-TAGCAAG-TCTTATCTCCCTGAAGTTGCAGCGGAGTAGAT
* * * * * *
44707860 T-CACAT--CTAGTCTTATCTCCCTGAAGTTGCAGAGGAGCAGAC
1 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTGCAGCGGAGTAGAT
* * * * * * *
44707902 TGAATAAACCAA-TCTGATTTCCCTGAAGTTGCAGTGGAGCAGAT
1 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTGCAGCGGAGTAGAT
* ** * *
44707946 TGAAGAAAATAATTC-TATCTCCCTGAAGTTGCAGTGGAG
1 TGAAGATAGCAAGTCTTATCTCCCTGAAGTTGCAGCGGAG
44707985 CGAATTAAAA
Statistics
Matches: 458, Mismatches: 103, Indels: 21
0.79 0.18 0.04
Matches are distributed among these distances:
40 21 0.05
41 11 0.02
42 5 0.01
43 12 0.03
44 109 0.24
45 300 0.66
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (45 bp):
TGAAGATAGCAAGTCTTATCTCCCTGAAGTTGCAGCGGAGTAGAT
Found at i:44707735 original size:135 final size:134
Alignment explanation
Indices: 44707369--44707993 Score: 491
Period size: 135 Copynumber: 4.7 Consensus size: 134
44707359 AATAGATCGG
* * ** * * * *
44707369 TGAAGATAACAAATCCTATCTCCATGAAGTTGCAGTGGAGTGGATTAAAAATAGCAAGTCTTATC
1 TGAAGATAAC-AATCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATC
* * * * * *
44707434 TCCCTGAGGTTACAGCGGAGTAGATTGAAGATAGCAAATCCTATCTCCTTGAAGTTGCAGTTGAG
65 TCCCTGAAGTTGCAGCGGAGCAGATTAAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAG
**
44707499 TGGAT
130 CAGAT
* * * * * *
44707504 TGAAAATAACAAGTTTTATCT-CTCTGAAGTTGCAGCGGAGCAAACTGAAGATAACAAGTCTTAT
1 TGAAGATAACAA-TCTTATCTCCT-TGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTAT
* * * ** * *
44707568 CTCTCTGAGGTTGCTGCGGAATAGACTGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGA
64 CTCCCTGAAGTTGCAGCGGAGCAGATTAAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGA
**
44707633 GTGGAT
129 GCAGAT
* *
44707639 TGAAGATAACAAGTCTTATCTCCTTGAAGTTGCAGCGGAGCAGACTGAAGATAGCAAATCCTATC
1 TGAAGATAACAA-TCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATC
* * * * * * * *
44707704 TCCCTGAAGTTGCAGTGGAGCGGATTAAAGATAGTAAGTCTTATCTCTCTAAAGTTGCAGTGGAA
65 TCCCTGAAGTTGCAGCGGAGCAGATTAAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAG
44707769 CAGAT
130 CAGAT
* * * * * * *
44707774 TGAAGAAAATAATCCTATCT-CTCTGAAGTTGCAGTGGAGCGGA-TTAAGACT-GTAGATCTTAT
1 TGAAGATAACAATCTTATCTCCT-TGAAGTTGCAGTGGAGCAGACTGAAGA-TAGCAAATCTTAT
* * * * * * * *
44707836 CTCTCTGAAGTTGCAG-AGAGCAGA-T-CACAT--CTAGTCTTATCTCCCTGAAGTTGCAGAGGA
64 CTCCCTGAAGTTGCAGCGGAGCAGATTAAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGA
*
44707896 GCAGAC
129 GCAGAT
* * * * * * ** *
44707902 TGAATA-AACCAATCTGATTTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAAATAATTC-TATC
1 TGAAGATAA-CAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATC
*
44707965 TCCCTGAAGTTGCAGTGGAGC-GAATTAAA
65 TCCCTGAAGTTGCAGCGGAGCAG-ATTAAA
44707994 ATCAGATCTT
Statistics
Matches: 399, Mismatches: 78, Indels: 30
0.79 0.15 0.06
Matches are distributed among these distances:
127 2 0.01
128 79 0.20
129 15 0.04
130 4 0.01
131 2 0.01
132 6 0.02
133 30 0.08
134 29 0.07
135 230 0.58
136 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (134 bp):
TGAAGATAACAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATCT
CCCTGAAGTTGCAGCGGAGCAGATTAAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGC
AGAT
Found at i:44707778 original size:90 final size:89
Alignment explanation
Indices: 44707369--44707986 Score: 479
Period size: 90 Copynumber: 7.0 Consensus size: 89
44707359 AATAGATCGG
* * * ** * * * *
44707369 TGAAGATAACAAATCCTATCTC-CATGAAGTTGCAGTGGAGTGGATTAAAAATAGCAAGTCTTAT
1 TGAAGATAGCAAGTCTTATCTCTC-TGAAGTTGCAGTGGAGCAGATTGAAGATA-CAAATCCTAT
* * * **
44707433 CTCCCTGAGGTTACAGCGGAGTAGAT
64 CTCCCTGAAGTTGCAGTGGAGCGGAT
* * * ** * * **
44707459 TGAAGATAGCAAATCCTATCTC-CTTGAAGTTGCAGTTGAGTGGATTGAAAATAACAAGTTTTAT
1 TGAAGATAGCAAGTCTTATCTCTC-TGAAGTTGCAGTGGAGCAGATTGAAGAT-ACAAATCCTAT
* * ** *
44707523 CTCTCTGAAGTTGCAGCGGAGCAAAC
64 CTCCCTGAAGTTGCAGTGGAGCGGAT
* * * * ** *
44707549 TGAAGATAACAAGTCTTATCTCTCTGAGGTTGCTGCGGAATAGACTGAAGATAGCAAATCCTATC
1 TGAAGATAGCAAGTCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAGATA-CAAATCCTATC
*
44707614 TCCCTGAAGTTGCAGTGGAGTGGAT
65 TCCCTGAAGTTGCAGTGGAGCGGAT
* * *
44707639 TGAAGATAACAAGTCTTATCTC-CTTGAAGTTGCAGCGGAGCAGACTGAAGATAGCAAATCCTAT
1 TGAAGATAGCAAGTCTTATCTCTC-TGAAGTTGCAGTGGAGCAGATTGAAGATA-CAAATCCTAT
44707703 CTCCCTGAAGTTGCAGTGGAGCGGAT
64 CTCCCTGAAGTTGCAGTGGAGCGGAT
* * * * *
44707729 TAAAGATAGTAAGTCTTATCTCTCTAAAGTTGCAGTGGAACAGATTGAAGA-AAATAATCCTATC
1 TGAAGATAGCAAGTCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAGATACA-AATCCTATC
*
44707793 TCTCTGAAGTTGCAGTGGAGCGGAT
65 TCCCTGAAGTTGCAGTGGAGCGGAT
* * * * * * *
44707818 T-AAGACT-G-TAGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-T-CACAT-CTAGTCTTAT
1 TGAAGA-TAGCAAG-TCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAGATACAAATCCTAT
* * *
44707876 CTCCCTGAAGTTGCAGAGGAGCAGAC
64 CTCCCTGAAGTTGCAGTGGAGCGGAT
* * * * * * * *
44707902 TGAATAAACCAA-TCTGATTTCCCTGAAGTTGCAGTGGAGCAGATTGAAGA-AAATAATTCTATC
1 TGAAGATAGCAAGTCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAGATACA-AATCCTATC
44707965 TCCCTGAAGTTGCAGTGGAGCG
65 TCCCTGAAGTTGCAGTGGAGCG
44707987 AATTAAAATC
Statistics
Matches: 435, Mismatches: 76, Indels: 36
0.80 0.14 0.07
Matches are distributed among these distances:
84 48 0.11
85 12 0.03
86 3 0.01
87 10 0.02
88 53 0.12
89 38 0.09
90 268 0.62
91 3 0.01
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (89 bp):
TGAAGATAGCAAGTCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAGATACAAATCCTATCT
CCCTGAAGTTGCAGTGGAGCGGAT
Found at i:44707965 original size:128 final size:131
Alignment explanation
Indices: 44707610--44707993 Score: 354
Period size: 128 Copynumber: 2.9 Consensus size: 131
44707600 TAGCAAATCC
** * *
44707610 TATCTCCCTGAAGTTGCAGTGGAGTGGATTGAAGATAACAAGTCTTATCTCCTTGAAGTTGCAGC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGA-AACAA-TC-TATCTCCCTGAAGTTGCAGT
* * * * * * *
44707675 GGAGCAGACTGAAGATAGCA-AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAGATAGT
63 GGAGCAGATTGAAGA-A-AATAATTCTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAACATACT
44707739 AAGTCT
126 AAGTCT
* * * * *
44707745 TATCTCTCTAAAGTTGCAGTGGAACAGATTGAAGAAAATAATCCTATCTCTCTGAAGTTGCAGTG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-AAACAAT-CTATCTCCCTGAAGTTGCAGTG
* *** * *
44707810 GAGCGGATT-AAGACTGTAGA-TCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-T-CACAT-CT-
64 GAGCAGATTGAAGAAAATA-ATTC-TATCTCCCTGAAGTTGCAGTAGAGCAGATTAAACATACTA
44707868 AGTCT
127 AGTCT
* * * *
44707873 TATCTCCCTGAAGTTGCAGAGGAGCAGACTGAATAAACCAATCTGATTTCCCTGAAGTTGCAGTG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAA-CAATCT-ATCTCCCTGAAGTTGCAGTG
*
44707938 GAGCAGATTGAAGAAAATAATTCTATCTCCCTGAAGTTGCAGTGGAGC-GAATTAAA
64 GAGCAGATTGAAGAAAATAATTCTATCTCCCTGAAGTTGCAGTAGAGCAG-ATTAAA
44707994 ATCAGATCTT
Statistics
Matches: 199, Mismatches: 37, Indels: 30
0.75 0.14 0.11
Matches are distributed among these distances:
127 5 0.03
128 82 0.41
129 14 0.07
130 4 0.02
131 2 0.01
132 8 0.04
133 23 0.12
134 26 0.13
135 34 0.17
136 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (131 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAACAATCTATCTCCCTGAAGTTGCAGTGGA
GCAGATTGAAGAAAATAATTCTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAACATACTAAGTC
T
Found at i:44710444 original size:19 final size:20
Alignment explanation
Indices: 44710420--44710457 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
44710410 TTTGTGTCAT
44710420 ATTTCTCAT-TGTTCTTCTC
1 ATTTCTCATGTGTTCTTCTC
*
44710439 ATTTCTCATGTGTTTTTCT
1 ATTTCTCATGTGTTCTTCT
44710458 TTCTTCTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.11, C:0.21, G:0.08, T:0.61
Consensus pattern (20 bp):
ATTTCTCATGTGTTCTTCTC
Found at i:44711405 original size:21 final size:22
Alignment explanation
Indices: 44711378--44711444 Score: 73
Period size: 22 Copynumber: 3.1 Consensus size: 22
44711368 ATATCTAAAT
44711378 AATAATAACAAAATAGTA-CAA
1 AATAATAACAAAATAGTATCAA
* * *
44711399 TATAATAGCAAAATAGCATCAA
1 AATAATAACAAAATAGTATCAA
* * *
44711421 AAGAACAACAAAATAGTAGCAA
1 AATAATAACAAAATAGTATCAA
44711443 AA
1 AA
44711445 AAAATTAGCT
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
21 15 0.42
22 21 0.58
ACGTcount: A:0.63, C:0.12, G:0.09, T:0.16
Consensus pattern (22 bp):
AATAATAACAAAATAGTATCAA
Found at i:44720320 original size:16 final size:16
Alignment explanation
Indices: 44720298--44720366 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
44720288 TTTGGTTCGC
44720298 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
44720314 CGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
44720330 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
44720347 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
44720363 TGTA
1 TGTA
44720367 ATAGCTAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
16 34 0.68
17 16 0.32
ACGTcount: A:0.25, C:0.01, G:0.38, T:0.36
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:44720344 original size:33 final size:32
Alignment explanation
Indices: 44720298--44720366 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
44720288 TTTGGTTCGC
44720298 TGTATTGGATTAGAGGCGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGCGTATTGGATTAGAGG
*
44720330 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATT-GGATTAGAGGCGTATTGGATTAGAGG
44720363 TGTA
1 TGTA
44720367 ATAGCTAATC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 6 0.17
33 29 0.83
ACGTcount: A:0.25, C:0.01, G:0.38, T:0.36
Consensus pattern (32 bp):
TGTATTGGATTAGAGGCGTATTGGATTAGAGG
Found at i:44720431 original size:44 final size:45
Alignment explanation
Indices: 44720347--44720437 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
44720337 GGATTAGAGG
* * *
44720347 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
44720392 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
44720436 TG
1 TG
44720438 GAATAGAAGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:44720623 original size:17 final size:17
Alignment explanation
Indices: 44720602--44720635 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
44720592 TTATTATTAA
44720602 ATAT-ATTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
44720619 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
44720636 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:44720762 original size:17 final size:18
Alignment explanation
Indices: 44720721--44720755 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
44720711 TTATTATTAA
44720721 ATATAATTTAATTAAAAT
1 ATATAATTTAATTAAAAT
44720739 ATATAATTTAA-TAAAAT
1 ATATAATTTAATTAAAAT
44720756 TCTTAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATATAATTTAATTAAAAT
Found at i:44720797 original size:120 final size:120
Alignment explanation
Indices: 44720585--44721689 Score: 1953
Period size: 120 Copynumber: 9.2 Consensus size: 120
44720575 ATCATATTTA
44720585 AACATAATTATTATTAAATAT-ATTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATAATTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
44720649 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
44720704 AACATAATTATTATTAAATATAATTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATAATTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
44720769 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
** * * *
44720824 AACATAATTATTATGCAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATAATTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
44720889 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
** * * *
44720944 AACATAATTATTATGCAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATAATTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
44721009 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
*
44721064 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATAATTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
44721129 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
44721184 AACATAATTATTATTAAATATAATTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATAATTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
44721249 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
44721304 AACATAATTATTATTAAATATAATTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATAATTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
44721369 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
* * *
44721424 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATAATTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
44721489 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
* *
44721544 AACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAGTAAAATTCTTAAT-ATTAA
1 AACATAATTATTATTAAATATAATTTAATTAAAATATATAATTTAATAAAATTCTTAATAATT-A
* * * * * *
44721608 ATATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATAAAATATAATTT
65 ATATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
44721664 AACATAATTATTATTAAATATAATTT
1 AACATAATTATTATTAAATATAATTT
44721690 NNNNNNNNNN
Statistics
Matches: 957, Mismatches: 27, Indels: 3
0.97 0.03 0.00
Matches are distributed among these distances:
119 24 0.03
120 933 0.97
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (120 bp):
AACATAATTATTATTAAATATAATTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:44721102 original size:18 final size:17
Alignment explanation
Indices: 44721081--44721115 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
44721071 TTATTATTAA
*
44721081 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
44721099 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
44721116 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:44721242 original size:17 final size:18
Alignment explanation
Indices: 44721201--44721235 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
44721191 TTATTATTAA
44721201 ATATAATTTAATTAAAAT
1 ATATAATTTAATTAAAAT
44721219 ATATAATTTAA-TAAAAT
1 ATATAATTTAATTAAAAT
44721236 TCTTAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATATAATTTAATTAAAAT
Found at i:44721362 original size:17 final size:18
Alignment explanation
Indices: 44721321--44721355 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
44721311 TTATTATTAA
44721321 ATATAATTTAATTAAAAT
1 ATATAATTTAATTAAAAT
44721339 ATATAATTTAA-TAAAAT
1 ATATAATTTAATTAAAAT
44721356 TCTTAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATATAATTTAATTAAAAT
Found at i:44734234 original size:29 final size:28
Alignment explanation
Indices: 44734203--44734256 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
44734193 AAAGCCCTTT
44734203 TTTTTAA-ATTTACCGAAATGGGCCACA
1 TTTTTAATATTTACCGAAATGGGCCACA
*
44734230 TTTTTAATTATTTACCGGAATGGGCCA
1 TTTTTAA-TATTTACCGAAATGGGCCA
44734257 TTTTCCGCGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 7 0.29
29 17 0.71
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.37
Consensus pattern (28 bp):
TTTTTAATATTTACCGAAATGGGCCACA
Found at i:44734707 original size:125 final size:125
Alignment explanation
Indices: 44734479--44734748 Score: 429
Period size: 125 Copynumber: 2.2 Consensus size: 125
44734469 TTATTTCGAG
** *
44734479 TTGACGTTTCTG-GTCAAATAGTATAAAATCGCTTCTACCAGGATGCTATCAGGGAAGAAATTGT
1 TTGACGTTTCTGAG-CAAATAGTATAAAATCGCTGATACCAGGATGCTATCAGAGAAGAAATTGT
*
44734543 GAAATCGTGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATT-TTTT
65 GAAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTATTTT
*
44734603 TTGACGTTTTCTGAGCAATTAGTATAAAATCGCTGATACCAGGATGCTAT-ATGAGAAGAAATTG
1 TTGACG-TTTCTGAGCAAATAGTATAAAATCGCTGATACCAGGATGCTATCA-GAGAAGAAATTG
* *
44734667 TGAAATCGCGCCCTCGTGGACGCGATTTCGTTACAGTTGGTCATGTAGGAAATAATTATTTT
64 TGAAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTATTTT
44734729 TTGACGTTTCTGAGCAAATA
1 TTGACGTTTCTGAGCAAATA
44734749 ATGTCAAATT
Statistics
Matches: 134, Mismatches: 8, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
124 7 0.05
125 116 0.87
126 11 0.08
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.33
Consensus pattern (125 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTGATACCAGGATGCTATCAGAGAAGAAATTGTG
AAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTATTTT
Found at i:44740948 original size:90 final size:89
Alignment explanation
Indices: 44740795--44740973 Score: 313
Period size: 90 Copynumber: 2.0 Consensus size: 89
44740785 ACCTTGAAAC
*
44740795 GGAACATGCGTACTACAACGGCCGATTGCTACGTGGATGCCAAGTGTTCAAACGCCTATTTTGGA
1 GGAACATGCGTACTACAACGACCGATTGCTACGTGGATGCCAAGTGTTCAAACGCCTATTTTGGA
* * *
44740860 CCTTTAAGCAATGTCGAGACGCAT
66 CCTTTAAACAATGCCAAGACGCAT
44740884 NGGAACATGCGTACTACAACGACCGATTGCTACGTGGATGCCAAGTGTTCAAACGCCTATTTTGG
1 -GGAACATGCGTACTACAACGACCGATTGCTACGTGGATGCCAAGTGTTCAAACGCCTATTTTGG
44740949 ACCTTTAAACAATGCCAAGACGCAT
65 ACCTTTAAACAATGCCAAGACGCAT
44740974 TTTCATACTG
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
90 85 1.00
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.24
Consensus pattern (89 bp):
GGAACATGCGTACTACAACGACCGATTGCTACGTGGATGCCAAGTGTTCAAACGCCTATTTTGGA
CCTTTAAACAATGCCAAGACGCAT
Found at i:44742465 original size:23 final size:24
Alignment explanation
Indices: 44742439--44743481 Score: 233
Period size: 28 Copynumber: 38.4 Consensus size: 24
44742429 TTTTGTTAAT
44742439 GGTTAGGGTTTTTAATTAAAATAGGTTA
1 GGTTAGGGTTTTTAATT-AAA-A--TTA
*
44742467 GGGTTAGGGTTTTTAATTAAAA-TG
1 -GGTTAGGGTTTTTAATTAAAATTA
44742491 GGTTAGGGTTTTTAATTAAATTAAATTA
1 GGTTAGGGTTTTTAATT--A--AAATTA
44742519 GGTTAGGGTTTTTAATTAAAATGGGTTAA
1 GGTTAGGGTTTTTAATTAAAA----TT-A
44742548 GGTTAGGGTTTTTAATTAAATTAAATTA
1 GGTTAGGGTTTTTAATT--A--AAATTA
44742576 GGTTAGGGTTTTTAATT-AAATTA
1 GGTTAGGGTTTTTAATTAAAATTA
* *
44742599 GTTTAGCGTTTTTAATTAAAATGGGTTA
1 GGTTAGGGTTTTTAATTAAAA----TTA
*
44742627 GGGTTAGGGTTTTAAATT-AAATTA
1 -GGTTAGGGTTTTTAATTAAAATTA
* * ***
44742651 GGTTAGGGTTTAGTATTTAGGGTTTA
1 GGTTAGGGTTT-TTAATTA-AAATTA
* *
44742677 GGGTAAATTAGGGTTAAGGTTTAGGGTTTTTAAATTA
1 -GG----TTAGGGTT----TTTA----ATTAAAATTA
** *
44742714 AATTAAATTAGGGTTAGGGTTTTTAATTAAAA-TG
1 -----GGTTA-GG-----GTTTTTAATTAAAATTA
44742748 GGTTAGGGTTTTTAATTAAATTAAATTA
1 GGTTAGGGTTTTTAATT--A--AAATTA
44742776 GGTTAGGGTTTTTAATTAAATTAAATTA
1 GGTTAGGGTTTTTAATT--A--AAATTA
44742804 GGTTAGGGTTTTTAATTAAAATGGGTTA
1 GGTTAGGGTTTTTAATTAAAA----TTA
*
44742832 GATTTAGGGTTTTTAATTAAATTAAATTA
1 G-GTTAGGGTTTTTAATT--A--AAATTA
*
44742861 GGTTAGAGTTTTTAATT-AAATTA
1 GGTTAGGGTTTTTAATTAAAATTA
*
44742884 GTTTAGGGTTTTTAATTAAAATGGATTA
1 GGTTAGGGTTTTTAATT-AAA---ATTA
44742912 GGGTTAGGGTTTTTAATT-AAATTA
1 -GGTTAGGGTTTTTAATTAAAATTA
**
44742936 GGTTAGGGTTTAGGGTTTAGGACAAATTAAGGTTA
1 GGTTAGGG-TT----TTTA--ATTAA--AA--TTA
*
44742971 GAGTTTAGGGTTCTTAAAATT-AAATTA
1 G-G-TTAGGGTT-TTTA-ATTAAAATTA
**
44742998 AATTAGGGTTAGGGTTTTTAATTAAAATGGGTTA
1 GGTTA------GGGTTTTTAATTAAAA----TTA
44743032 GGGTTAGGGTTTTTAATTAAATTAAATTA
1 -GGTTAGGGTTTTTAATT--A--AAATTA
44743061 GGTTAGGGTTTTTAATT-AAATTA
1 GGTTAGGGTTTTTAATTAAAATTA
*
44743084 GTTTAGGGTTTTTAATTAAAATGGGTTA
1 GGTTAGGGTTTTTAATTAAAA----TTA
* *
44743112 GGGTTAAGGTTGTTAATT-AAATTA
1 -GGTTAGGGTTTTTAATTAAAATTA
* **
44743136 GGTTAGGGTTTAGGGTTTAGGACAAATTA
1 GGTTAGGGTTT----TTAATTA-AAATTA
*
44743165 GGGTTAGGGTTCTTAAATTAAAATTA
1 -GGTTAGGGTT-TTTAATTAAAATTA
44743191 GAGTTAGGGTTTTTAATTAAAATT-
1 G-GTTAGGGTTTTTAATTAAAATTA
**** ***
44743215 GGTTAGGG-TTAGGGTTAGGGTT-
1 GGTTAGGGTTTTTAATTAAAATTA
* * *
44743237 -TTTA----ATTAAATT-AAATTA
1 GGTTAGGGTTTTTAATTAAAATTA
44743255 GGTTAGGGTCTTAAATTAAATT-AAATTA
1 GGTTAGGGT-TT---TT-AATTAAAATTA
*
44743283 GGGTTAGGGATTTTAATTAAAA-TA
1 -GGTTAGGGTTTTTAATTAAAATTA
**
44743307 GGTTAGGGTTTAGGGTTTAGGGT-AAATTA
1 GGTTAGGG-TT----TTTA-ATTAAAATTA
44743336 GGGTTAGGGTTTTTAATTAAAATGGGTTA
1 -GGTTAGGGTTTTTAATTAAAA----TTA
44743365 GGGTTAGGGTTTTTAATTAAATTAAATTA
1 -GGTTAGGGTTTTTAATT--A--AAATTA
*
44743394 AGTTAGGG-TTTTAATTAAATTAAATTA
1 GGTTAGGGTTTTTAATT--A--AAATTA
44743421 GGTTAGGGTTTTTAATTAAATTAAATTA
1 GGTTAGGGTTTTTAATT--A--AAATTA
*
44743449 GGTTAGGGTTTTCAATTAAAATT-
1 GGTTAGGGTTTTTAATTAAAATTA
44743472 GGTTAGGGTT
1 GGTTAGGGTT
44743482 AGGGTTAGGG
Statistics
Matches: 785, Mismatches: 87, Indels: 290
0.68 0.07 0.25
Matches are distributed among these distances:
17 2 0.00
18 3 0.00
19 3 0.00
21 3 0.00
22 7 0.01
23 144 0.18
24 43 0.05
25 32 0.04
26 21 0.03
27 47 0.06
28 205 0.26
29 166 0.21
30 25 0.03
31 20 0.03
32 1 0.00
33 17 0.02
34 6 0.01
35 13 0.02
36 3 0.00
37 12 0.02
38 5 0.01
39 4 0.01
43 3 0.00
ACGTcount: A:0.32, C:0.01, G:0.24, T:0.43
Consensus pattern (24 bp):
GGTTAGGGTTTTTAATTAAAATTA
Found at i:44743047 original size:200 final size:195
Alignment explanation
Indices: 44742439--44743487 Score: 322
Period size: 200 Copynumber: 5.5 Consensus size: 195
44742429 TTTTGTTAAT
* ** * *
44742439 GGTTAGGGTTTTTAATTAAAATAGGTTAGGGTTAGGGTTTTTAATTAAAAT-GGGTTAGGGTTTT
1 GGTTAGGGTTTTTAATTAAATTAAATTA-GGTTAGGGTTTTTAATTAAATTAGGTTTAGGGTTTT
* * * * *** *
44742503 TAATTAAATTAAATTA-GGTTAGGGTTTTTAATTAAAATGGGTTAAGG-TTAGGGTTTTTAATTA
65 TAATTAAAATAAATTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTAGGA-CA
* * *
44742566 AATTAAATTAGGTTAGGG-TTT---TT-AATTAAATTAGTTTAGCGTTTTTAATTAAAATGGGTT
129 AATTAAGTTAGGTTAGGGTTTTAAATTAAATTAAATTAGGTTAGGGTTTTTAATTAAAATGGGTT
44742626 AG
194 AG
* *
44742628 GGTTAGGG---TT--TTAAATTAAATTAGGTTAGGG--TTT-AGT-ATTTAGGGTTTAGGG---T
1 GGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTA-GGTTTAGGGTTTT
* *** * * ** **
44742681 AAATTAGGGT---TAAGGTTTAGGGTTTTTAAATTAAATTAAATTAGGG-TTAGGGTTT----TT
65 TAATTAAAATAAATTAGGGTTAGGGTTTTT-AATTAAATTAGGTTAGGGTTTAGGGTTTAGGACA
** * * * ***
44742738 AATTAAAATGGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTAAATT
129 AATTAAGTTAGGTTAGGGTTTTAAATTAAATTAAATTAGGTTAGGGTTTTTAATTAAAATGGGTT
44742803 A-
194 AG
* *** * *
44742804 GGTTAGGGTTTTTAATTAAAATGGGTTAGATTTAGGGTTTTTAATTAAATTAAATTAGG-TTAGA
1 GGTTAGGGTTTTTAATTAAATTAAATTAG-GTTAGGG--TTT--TT-AATTAAATTAGGTTTAGG
* * *
44742868 GTTTTTAA-T----TAAATTA-GTTTAGGGTTTTTAATTAAAAT-GGATTAGGG-TTAGGGTTTT
60 GTTTTTAATTAAAATAAATTAGGGTTAGGGTTTTTAATTAAATTAGG-TTAGGGTTTAGGGTTTA
** * * * * * *
44742925 TAATTAAATTAGGTTAGGGTTTAGGG-TTTAGGA-CAAATTAAGGTTAGAGTTTAGGGTTCTTAA
124 GGA-CAAATTAAGTTA-GG-TTAGGGTTTTA-AATTAAATTAA-ATTAG-G-TTAGGGTT-TT-T
* ***
44742988 AATTAAATTAAATTAG
180 AATTAAAATGGGTTAG
* ***
44743004 GGTTAGGGTTTTTAATTAAAATGGGTTAGGGTTAGGGTTTTTAATTAAATTAAATTAGG-TTAGG
1 GGTTAGGGTTTTTAATTAAATTAAATTA-GGTTAGGG--TTT--TT-AATTAAATTAGGTTTAGG
* * * *
44743068 GTTTTTAA-T----TAAATTA-GTTTAGGGTTTTTAATTAAAATGGGTTAGGG-TTAAGG-TT--
60 GTTTTTAATTAAAATAAATTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTAG
** * ** * * *
44743123 G-TTAATTAAATTAGGTTAGGG-TTTAGGGTTTAGGA-CAAATTAGGGTTAGGGTTCTTAAATTA
125 GACAAATTAAGTTAGGTTAGGGTTTTA--AATTA-AATTAAATTA-GGTTAGGGTT-TTTAATTA
44743185 AAA----TTAG
185 AAATGGGTTAG
* **
44743192 AGTTAGGGTTTTTAATTAAAATTGGTTAGGGTTAGGGTTAGGGTTTTTAATTAAATTAAATTAGG
1 GGTTAGGGTTTTTAATT-AAA----TTA-AATTA-GGTTAGGG--TTT--TT-AATTAAATTAGG
* * * * *
44743257 -TTAGGGTCTTAAATTAAATTAAATTAGGGTTAGGGATTTTAATTAAAATAGGTTAGGGTTTAGG
54 TTTAGGGTTTTTAATTAAAATAAATTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGG
** * * ***
44743321 GTTTAGGGTAAATT-AG---GGTTAGGGTTTTTAATTAAAATGGGTTAGGGTTAGGGTTTTTAAT
119 GTTTAGGACAAATTAAGTTAGGTTAGGGTTTTAAATTAAATTAAATTA-GGTTAGGGTTTTTAAT
* ***
44743382 TAAATTAAATTA-
183 TAAAATGGGTTAG
*
44743394 AGTTAGGG-TTTTAATTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTAAATTAGG-TTAGGG
1 GGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGG--TTT--TT-AATTAAATTAGGTTTAGGG
* ***
44743457 TTTTCAATTAAAATTGGTTAGGGTTAGGGTT
61 TTTTTAATTAAAATAAATTAGGGTTAGGGTT
44743488 AGGGTTTTTA
Statistics
Matches: 693, Mismatches: 93, Indels: 143
0.75 0.10 0.15
Matches are distributed among these distances:
172 17 0.02
173 3 0.00
175 2 0.00
176 22 0.03
177 54 0.08
178 7 0.01
179 4 0.01
180 2 0.00
181 21 0.03
182 6 0.01
183 8 0.01
184 10 0.01
186 3 0.00
187 1 0.00
188 45 0.06
189 29 0.04
190 6 0.01
191 5 0.01
192 11 0.02
193 29 0.04
194 127 0.18
195 28 0.04
196 5 0.01
197 8 0.01
198 2 0.00
199 34 0.05
200 157 0.23
201 24 0.03
202 13 0.02
203 3 0.00
204 2 0.00
205 5 0.01
ACGTcount: A:0.32, C:0.01, G:0.24, T:0.43
Consensus pattern (195 bp):
GGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTTAGGGTTTTT
AATTAAAATAAATTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTAGGACAAA
TTAAGTTAGGTTAGGGTTTTAAATTAAATTAAATTAGGTTAGGGTTTTTAATTAAAATGGGTTAG
Found at i:44743196 original size:26 final size:24
Alignment explanation
Indices: 44743159--44743224 Score: 89
Period size: 26 Copynumber: 2.7 Consensus size: 24
44743149 GGTTTAGGAC
44743159 AAATTAGGGTTAGGGTTCTTAAATTA
1 AAATTA-GGTTAGGGTT-TTAAATTA
*
44743185 AAATTAGAGTTAGGGTTTTTAATTA
1 AAATTAG-GTTAGGGTTTTAAATTA
44743210 AAATT-GGTTAGGGTT
1 AAATTAGGTTAGGGTT
44743225 AGGGTTAGGG
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
23 9 0.24
24 1 0.03
25 13 0.34
26 15 0.39
ACGTcount: A:0.33, C:0.02, G:0.24, T:0.41
Consensus pattern (24 bp):
AAATTAGGTTAGGGTTTTAAATTA
Found at i:44743522 original size:63 final size:63
Alignment explanation
Indices: 44743329--44743544 Score: 264
Period size: 63 Copynumber: 3.6 Consensus size: 63
44743319 GGGTTTAGGG
*
44743329 TAAATTAGGGTTAGGGTTTTTAATTAAA--A---T-GGGTTAGGGTTAGGGTTTTTAATTAAAT
1 TAAATTA-GGTTAGGGTTTTCAATTAAATTAGGTTAGGGTTAGGGTTAGGGTTTTTAATTAAAT
* *
44743387 TAAATTAAGTTAGGGTTTT-AATTAAATTA----A--ATTA-GGTTAGGGTTTTTAATTAAAT
1 TAAATTAGGTTAGGGTTTTCAATTAAATTAGGTTAGGGTTAGGGTTAGGGTTTTTAATTAAAT
44743442 TAAATTAGGTTAGGGTTTTCAATTAAAATT-GGTTAGGGTTAGGGTTAGGGTTTTTAATTAAAT
1 TAAATTAGGTTAGGGTTTTCAATT-AAATTAGGTTAGGGTTAGGGTTAGGGTTTTTAATTAAAT
* *
44743505 TAAATTAGGTTAGGGTTTTTAATTAAATTAGTTTAGGGTT
1 TAAATTAGGTTAGGGTTTTCAATTAAATTAGGTTAGGGTT
44743545 TTTAATACAA
Statistics
Matches: 139, Mismatches: 6, Indels: 21
0.84 0.04 0.13
Matches are distributed among these distances:
55 39 0.28
56 14 0.10
57 16 0.12
58 8 0.06
60 1 0.01
62 8 0.06
63 53 0.38
ACGTcount: A:0.32, C:0.00, G:0.23, T:0.44
Consensus pattern (63 bp):
TAAATTAGGTTAGGGTTTTCAATTAAATTAGGTTAGGGTTAGGGTTAGGGTTTTTAATTAAAT
Found at i:44743528 original size:23 final size:23
Alignment explanation
Indices: 44743502--44743568 Score: 91
Period size: 23 Copynumber: 2.9 Consensus size: 23
44743492 TTTTTAATTA
44743502 AATTAAATTAGGTTAGGGTTTTT
1 AATTAAATTAGGTTAGGGTTTTT
*
44743525 AATTAAATTAGTTTAGGGTTTTT
1 AATTAAATTAGGTTAGGGTTTTT
* *
44743548 AA-TACAAATGGGTTAGGGTTT
1 AATTA-AATTAGGTTAGGGTTT
44743569 AGGGTTTAGG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
22 2 0.05
23 37 0.95
ACGTcount: A:0.31, C:0.01, G:0.22, T:0.45
Consensus pattern (23 bp):
AATTAAATTAGGTTAGGGTTTTT
Found at i:44744366 original size:7 final size:7
Alignment explanation
Indices: 44744356--44744380 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
44744346 TTATATACAT
44744356 AATACTA
1 AATACTA
44744363 AATACTA
1 AATACTA
44744370 AATACTA
1 AATACTA
44744377 AATA
1 AATA
44744381 TCAATCCACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:44745327 original size:14 final size:15
Alignment explanation
Indices: 44745310--44745343 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
44745300 AATAATTATC
44745310 TAAAAATA-CATAAA
1 TAAAAATATCATAAA
*
44745324 TAAAAATATCTTAAA
1 TAAAAATATCATAAA
44745339 TAAAA
1 TAAAA
44745344 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAAAATATCATAAA
Found at i:44745504 original size:29 final size:28
Alignment explanation
Indices: 44745441--44745497 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 28
44745431 TTGAAAATTT
44745441 TAAAAATTTTAAAATTATTTTTAAAAAA
1 TAAAAATTTTAAAATTATTTTTAAAAAA
44745469 TAAAAATATTTAAAATT-TTCTTTAAAAAA
1 TAAAAAT-TTTAAAATTATT-TTTAAAAAA
44745498 ATGAAATTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 9 0.33
29 18 0.67
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (28 bp):
TAAAAATTTTAAAATTATTTTTAAAAAA
Found at i:44745558 original size:22 final size:21
Alignment explanation
Indices: 44745533--44745583 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
44745523 TAATATGGAT
*
44745533 TTGAGAGATTTTTTGAAGGAAA
1 TTGAGAGA-TTTTGGAAGGAAA
*
44745555 TTGAGAGGATTTTGGAAGGAAT
1 TTGAGA-GATTTTGGAAGGAAA
44745577 TTGAGAG
1 TTGAGAG
44745584 TTTAAGAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 1 0.04
22 23 0.88
23 2 0.08
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (21 bp):
TTGAGAGATTTTGGAAGGAAA
Found at i:44755387 original size:22 final size:22
Alignment explanation
Indices: 44755332--44755393 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
44755322 GCTGTATTAA
*
44755332 CTGTTCAACACTTTGGTGCTCT
1 CTGTTCAACACTTTGGTGATCT
* *
44755354 TTGATT-AGCACTTAT-GTGATCT
1 CTG-TTCAACACTT-TGGTGATCT
44755376 CTGTTCAACACTTTGGTG
1 CTGTTCAACACTTTGGTG
44755394 CTCTTTGATT
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
21 3 0.10
22 25 0.81
23 3 0.10
ACGTcount: A:0.18, C:0.21, G:0.19, T:0.42
Consensus pattern (22 bp):
CTGTTCAACACTTTGGTGATCT
Found at i:44755438 original size:22 final size:22
Alignment explanation
Indices: 44755340--44755469 Score: 115
Period size: 22 Copynumber: 6.0 Consensus size: 22
44755330 AACTGTTCAA
*
44755340 CACTTTGGTGCTCTTTGATTAG
1 CACTTTGGTGCTCTCTGATTAG
* *
44755362 CACTTAT-GTGATCTCTG-TTCAA
1 CACTT-TGGTGCTCTCTGATT-AG
*
44755384 CACTTTGGTGCTCTTTGATTAG
1 CACTTTGGTGCTCTCTGATTAG
* * *
44755406 TAAATTT-GTGCTCTCTGTTTAG
1 -CACTTTGGTGCTCTCTGATTAG
*
44755428 CACTTCGGTGCTCTCTGATTAG
1 CACTTTGGTGCTCTCTGATTAG
**
44755450 CACTTTTATGCTCTCT-ATTA
1 CACTTTGGTGCTCTCTGATTA
44755470 TGGTGCTTTC
Statistics
Matches: 85, Mismatches: 17, Indels: 13
0.74 0.15 0.11
Matches are distributed among these distances:
21 10 0.12
22 68 0.80
23 7 0.08
ACGTcount: A:0.17, C:0.21, G:0.18, T:0.45
Consensus pattern (22 bp):
CACTTTGGTGCTCTCTGATTAG
Found at i:44755462 original size:44 final size:44
Alignment explanation
Indices: 44755332--44755465 Score: 178
Period size: 44 Copynumber: 3.0 Consensus size: 44
44755322 GCTGTATTAA
* *
44755332 CTGTTCAACACTTTGGTGCTCTTTGATTAGCACTTATGTGATCT
1 CTGTTCAACACTTTGGTGCTCTTTGATTAGCACTTTTGTGCTCT
* **
44755376 CTGTTCAACACTTTGGTGCTCTTTGATTAGTAAATTTGTGCTCT
1 CTGTTCAACACTTTGGTGCTCTTTGATTAGCACTTTTGTGCTCT
* * * * *
44755420 CTGTTTAGCACTTCGGTGCTCTCTGATTAGCACTTTTATGCTCT
1 CTGTTCAACACTTTGGTGCTCTTTGATTAGCACTTTTGTGCTCT
44755464 CT
1 CT
44755466 ATTATGGTGC
Statistics
Matches: 77, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 77 1.00
ACGTcount: A:0.16, C:0.22, G:0.18, T:0.44
Consensus pattern (44 bp):
CTGTTCAACACTTTGGTGCTCTTTGATTAGCACTTTTGTGCTCT
Found at i:44762664 original size:62 final size:61
Alignment explanation
Indices: 44762563--44762681 Score: 211
Period size: 62 Copynumber: 1.9 Consensus size: 61
44762553 TTCCTTCTTC
*
44762563 TAATTCGAATACCCGAGAATCTCGGACACTATGTGCCAACATGTGGTCAAAACCACTAGAA
1 TAATTCGAATACCCGAGAATCTCGCACACTATGTGCCAACATGTGGTCAAAACCACTAGAA
*
44762624 TAATATCGAATACCCGAGAATCTTGCACACTATGTGCCAACATGTGGTCAAAACCACT
1 TAAT-TCGAATACCCGAGAATCTCGCACACTATGTGCCAACATGTGGTCAAAACCACT
44762682 GCTATCTCAT
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
61 4 0.07
62 51 0.93
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (61 bp):
TAATTCGAATACCCGAGAATCTCGCACACTATGTGCCAACATGTGGTCAAAACCACTAGAA
Found at i:44766398 original size:15 final size:15
Alignment explanation
Indices: 44766379--44766586 Score: 121
Period size: 15 Copynumber: 13.9 Consensus size: 15
44766369 TTTAGTACAA
44766379 CAGCATTTGGTACCG
1 CAGCATTTGGTACCG
* *
44766394 TAGCATTTGGTACAG
1 CAGCATTTGGTACCG
* * *
44766409 CAACACTTGCTACCG
1 CAGCATTTGGTACCG
* * **
44766424 CAACGTTTGGTACAA
1 CAGCATTTGGTACCG
* * *
44766439 CAACATTTGGTATCA
1 CAGCATTTGGTACCG
*
44766454 CAGCATTTGGTACAG
1 CAGCATTTGGTACCG
* * *
44766469 TAGTATTTGCTACCG
1 CAGCATTTGGTACCG
* * * * *
44766484 TAACGTTTTGTACAG
1 CAGCATTTGGTACCG
* * * **
44766499 AAACATTTGGAATAG
1 CAGCATTTGGTACCG
44766514 CAGCATTTGGTACCG
1 CAGCATTTGGTACCG
*
44766529 CAGCAATTGGTACAC-
1 CAGCATTTGGTAC-CG
*
44766544 CTGCATTTGGTACCG
1 CAGCATTTGGTACCG
* *
44766559 CAGCATTTGGTGCTG
1 CAGCATTTGGTACCG
*
44766574 TAGCATTTGGTAC
1 CAGCATTTGGTAC
44766587 AATGGAAGAG
Statistics
Matches: 144, Mismatches: 47, Indels: 4
0.74 0.24 0.02
Matches are distributed among these distances:
14 1 0.01
15 142 0.99
16 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (15 bp):
CAGCATTTGGTACCG
Found at i:44766440 original size:60 final size:60
Alignment explanation
Indices: 44766373--44766537 Score: 179
Period size: 60 Copynumber: 2.8 Consensus size: 60
44766363 TCCGCATTTA
* * * *
44766373 GTACAACAGCATTTGGTACCGTAGCATTTGGTACAGCAACACTTGCTACCGCAACGTTTG
1 GTACAACAACATTTGGTACCGCAGCATTTGGTACAGCAGCAATTGCTACCGCAACGTTTG
* * * * * * *
44766433 GTACAACAACATTTGGTATCACAGCATTTGGTACAGTAGTATTTGCTACCGTAACGTTTT
1 GTACAACAACATTTGGTACCGCAGCATTTGGTACAGCAGCAATTGCTACCGCAACGTTTG
* ** *
44766493 GTACAGA-AACATTTGGAATAGCAGCATTTGGTACCGCAGCAATTG
1 GTACA-ACAACATTTGGTACCGCAGCATTTGGTACAGCAGCAATTG
44766538 GTACACCTGC
Statistics
Matches: 87, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
60 86 0.99
61 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (60 bp):
GTACAACAACATTTGGTACCGCAGCATTTGGTACAGCAGCAATTGCTACCGCAACGTTTG
Done.