Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 130 of 168
Found at i:37901014 original size:181 final size:181
Alignment explanation
Indices: 37900710--37901246 Score: 966
Period size: 181 Copynumber: 3.0 Consensus size: 181
37900700 GACTCACCTA
*
37900710 ATTCTTATCCACTGCAGTTTTAGGCTCCACTATTATTACTCTTGTACATACAAATTACTTATCAT
1 ATTCTTATCCACTGCAGTTCTAGGCTCCACTATTATTACTCTTGTACATACAAATTACTTATCAT
*
37900775 CTCAATTGCTGACAATCTTATGCAAAAACCTTATACTCGTAGTCTTACTGTTCAGATACCATACA
66 CTCAATTGCTGACAATCTCATGCAAAAACCTTATACTCGTAGTCTTACTGTTCAGATACCATACA
*
37900840 TAGATTTACTCATTCAAAACTTAACATGCAAAGCTGGAACACTTATTACTC
131 TAGATTTACTCATTCAAAACTTAACATGCAGAGCTGGAACACTTATTACTC
* *
37900891 ATTCTTATCCACTACAATTCTAGGCTCCACTATTATTACTCTTGTACATACAAATTACTTATCAT
1 ATTCTTATCCACTGCAGTTCTAGGCTCCACTATTATTACTCTTGTACATACAAATTACTTATCAT
*
37900956 CTCAATTGCTGACAATCTCATGCAAAAACTTTATACTCGTAGTCTTACTGTTCAGATACCATACA
66 CTCAATTGCTGACAATCTCATGCAAAAACCTTATACTCGTAGTCTTACTGTTCAGATACCATACA
*
37901021 TAGATTTGCTCATTCAAAACTTAACATGCAGAGCTGGAACACTTATTACTC
131 TAGATTTACTCATTCAAAACTTAACATGCAGAGCTGGAACACTTATTACTC
*
37901072 ATTCTTATCCACTGCAGTTCTAGGCTCCATTATTATTACTCTTGTACATACAAATTACTTATCAT
1 ATTCTTATCCACTGCAGTTCTAGGCTCCACTATTATTACTCTTGTACATACAAATTACTTATCAT
* * *
37901137 CTTAATTGCTGACAATCTCATGCAAAAACCTTATACTCGTAGTCTTATTGTTCAAATACCATACA
66 CTCAATTGCTGACAATCTCATGCAAAAACCTTATACTCGTAGTCTTACTGTTCAGATACCATACA
*
37901202 TAGATTTACTCATTCAAAACTTAACATGCAGAGTTGGAACACTTA
131 TAGATTTACTCATTCAAAACTTAACATGCAGAGCTGGAACACTTA
37901247 CCCTGATATG
Statistics
Matches: 340, Mismatches: 16, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
181 340 1.00
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.35
Consensus pattern (181 bp):
ATTCTTATCCACTGCAGTTCTAGGCTCCACTATTATTACTCTTGTACATACAAATTACTTATCAT
CTCAATTGCTGACAATCTCATGCAAAAACCTTATACTCGTAGTCTTACTGTTCAGATACCATACA
TAGATTTACTCATTCAAAACTTAACATGCAGAGCTGGAACACTTATTACTC
Found at i:37902441 original size:15 final size:15
Alignment explanation
Indices: 37902421--37902450 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
37902411 AGTCTTTCTT
37902421 TCTAATAGTTTAGAA
1 TCTAATAGTTTAGAA
37902436 TCTAATAGTTTAGAA
1 TCTAATAGTTTAGAA
37902451 GGAGCATGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (15 bp):
TCTAATAGTTTAGAA
Found at i:37905777 original size:46 final size:46
Alignment explanation
Indices: 37905703--37905901 Score: 251
Period size: 46 Copynumber: 4.6 Consensus size: 46
37905693 TACGTATGAT
* *
37905703 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
37905747 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* * *
37905793 CACTTATCATTTTGTCTCTTGATTAGATAA--GT-G-T--AG----
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
37905829 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
37905875 CACTTATCACTTTATCTCTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
37905902 AGTACTCAAA
Statistics
Matches: 133, Mismatches: 10, Indels: 22
0.81 0.06 0.13
Matches are distributed among these distances:
36 27 0.20
38 2 0.02
39 1 0.01
40 3 0.02
42 3 0.02
43 1 0.01
44 12 0.09
45 5 0.04
46 79 0.59
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:37905833 original size:36 final size:36
Alignment explanation
Indices: 37905793--37905865 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
37905783 CTAAAGCTAC
* * *
37905793 CACTTATCATTTTGTCTCTTGATTAGATAAGTGTAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
37905829 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
37905865 C
1 C
37905866 TAAAGCTACC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (36 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
Found at i:37905847 original size:82 final size:82
Alignment explanation
Indices: 37905747--37905897 Score: 284
Period size: 82 Copynumber: 1.8 Consensus size: 82
37905737 CTAAGGCTAC
* *
37905747 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCATTTTGTCTCT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCTCT
37905812 TGATTAGATAAGTGTAG
66 TGATTAGATAAGTGTAG
37905829 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCTCT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCTCT
37905894 TGAT
66 TGAT
37905898 CAGAAGTACT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
82 67 1.00
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.38
Consensus pattern (82 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCTCT
TGATTAGATAAGTGTAG
Found at i:37911681 original size:19 final size:19
Alignment explanation
Indices: 37911657--37911696 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
37911647 CCTAGGGTCA
37911657 TCAAGCCTAAGGTTTAGGT
1 TCAAGCCTAAGGTTTAGGT
37911676 TCAAGCCTAAGGTTTAGGT
1 TCAAGCCTAAGGTTTAGGT
37911695 TC
1 TC
37911697 TTCCATTCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (19 bp):
TCAAGCCTAAGGTTTAGGT
Found at i:37918006 original size:32 final size:31
Alignment explanation
Indices: 37917968--37918046 Score: 86
Period size: 32 Copynumber: 2.5 Consensus size: 31
37917958 TTATTTTTAT
**
37917968 TTAAATTTGATTTTTAATTTTTTTAAAAAGAG
1 TTAAATTTGATTTTTAA-TACTTTAAAAAGAG
* *
37918000 TTAAATTTGACTATTAATACTTTAAAAAGAG
1 TTAAATTTGATTTTTAATACTTTAAAAAGAG
* *
37918031 TCAAATTGTTATTTTT
1 TTAAATT-TGATTTTT
37918047 TTAATAAAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
31 18 0.47
32 20 0.53
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (31 bp):
TTAAATTTGATTTTTAATACTTTAAAAAGAG
Found at i:37918150 original size:16 final size:16
Alignment explanation
Indices: 37918131--37918161 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
37918121 CTAATTTTTT
*
37918131 ATTTTTATTTTTTTGC
1 ATTTTTATGTTTTTGC
37918147 ATTTTTATGTTTTTG
1 ATTTTTATGTTTTTG
37918162 AATAATTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.03, G:0.10, T:0.74
Consensus pattern (16 bp):
ATTTTTATGTTTTTGC
Found at i:37918389 original size:23 final size:25
Alignment explanation
Indices: 37918343--37918389 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
37918333 AATGTTAATA
*
37918343 ACTAAATTTAACTAAAAAATTATAG
1 ACTAAATTTAACTAAAAAAGTATAG
37918368 ACTAAA-TTAA-TAAAAAAGTATA
1 ACTAAATTTAACTAAAAAAGTATA
37918390 AACAAAAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 11 0.52
24 4 0.19
25 6 0.29
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.30
Consensus pattern (25 bp):
ACTAAATTTAACTAAAAAAGTATAG
Found at i:37919040 original size:28 final size:27
Alignment explanation
Indices: 37918977--37919042 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 27
37918967 TCATCATGAA
37918977 AAAGTAAAAGGAATCCTTTTTTTATAG
1 AAAGTAAAAGGAATCCTTTTTTTATAG
*
37919004 AAAGTAAAAGGAATCTTTTTTTTATAG
1 AAAGTAAAAGGAATCCTTTTTTTATAG
37919031 AAAGTGAAAAGG
1 AAAGT-AAAAGG
37919043 TTAGTCAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 31 0.84
28 6 0.16
ACGTcount: A:0.44, C:0.05, G:0.18, T:0.33
Consensus pattern (27 bp):
AAAGTAAAAGGAATCCTTTTTTTATAG
Found at i:37920214 original size:20 final size:20
Alignment explanation
Indices: 37920143--37920217 Score: 55
Period size: 20 Copynumber: 3.6 Consensus size: 20
37920133 TTATTTTTTA
*
37920143 TTTTTTTAATTTTAAAATAC
1 TTTTTTAAATTTTAAAATAC
*
37920163 TTTTTTTAAATTTTTTAAAT--
1 -TTTTTTAAA-TTTTAAAATAC
***
37920183 TTTAAAAAAAATTTTAAAATAC
1 TTT--TTTAAATTTTAAAATAC
37920205 TTTTTTAAATTTT
1 TTTTTTAAATTTT
37920218 TTTAATTTTA
Statistics
Matches: 40, Mismatches: 9, Indels: 11
0.67 0.15 0.18
Matches are distributed among these distances:
19 3 0.08
20 15 0.38
21 11 0.28
22 11 0.28
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTTTAAATTTTAAAATAC
Found at i:37920224 original size:29 final size:29
Alignment explanation
Indices: 37920192--37920256 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
37920182 TTTTAAAAAA
**
37920192 AATTTTAAAATACTTTTTTAAAT-TTTTTT
1 AATTTTAAAATA-TTTTAAAAATATTTTTT
37920221 AATTTTAAAATATTTTAAAAATACTTTTTT
1 AATTTTAAAATATTTTAAAAATA-TTTTTT
37920251 AATTTT
1 AATTTT
37920257 TGTTTTAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
28 8 0.25
29 12 0.38
30 12 0.38
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.58
Consensus pattern (29 bp):
AATTTTAAAATATTTTAAAAATATTTTTT
Found at i:37920225 original size:41 final size:41
Alignment explanation
Indices: 37920150--37920281 Score: 169
Period size: 41 Copynumber: 3.1 Consensus size: 41
37920140 TTATTTTTTT
*
37920150 AATTTTAAAATACTTTTTTTAAATTTTTTAAATTTTAAAAAA
1 AATTTTAAAATAC-TTTTTTAAATTTTTTTAATTTTAAAAAA
37920192 AATTTTAAAATACTTTTTTAAATTTTTTTAATTTT--AAAA
1 AATTTTAAAATACTTTTTTAAATTTTTTTAATTTTAAAAAA
* * *
37920231 TATTTTAAAAATACTTTTTTAATTTTTGTTTTAATTTTTAAAATA
1 AATTTT-AAAATACTTTTTTAA-ATTT-TTTTAA-TTTTAAAAAA
37920276 AATTTT
1 AATTTT
37920282 TGGTATTTAT
Statistics
Matches: 79, Mismatches: 5, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
39 9 0.11
40 15 0.19
41 24 0.30
42 19 0.24
43 4 0.05
45 8 0.10
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (41 bp):
AATTTTAAAATACTTTTTTAAATTTTTTTAATTTTAAAAAA
Found at i:37921617 original size:23 final size:24
Alignment explanation
Indices: 37921585--37921635 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
37921575 ATTCTATTTA
37921585 ATTTTTTTAT-ACA-ACTAGTTCT
1 ATTTTTTTATAACAGACTAGTTCT
*
37921607 ATTTTTATTATAATAGACTAGTTCT
1 ATTTTT-TTATAACAGACTAGTTCT
37921632 ATTT
1 ATTT
37921636 AATTAATCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 6 0.24
23 4 0.16
24 2 0.08
25 13 0.52
ACGTcount: A:0.29, C:0.10, G:0.06, T:0.55
Consensus pattern (24 bp):
ATTTTTTTATAACAGACTAGTTCT
Found at i:37928525 original size:48 final size:48
Alignment explanation
Indices: 37928462--37928553 Score: 175
Period size: 48 Copynumber: 1.9 Consensus size: 48
37928452 TAAATAAATG
37928462 CAATATTTCAATAATTATTATTAATGCTTCTATTTTCCAGAAATATTT
1 CAATATTTCAATAATTATTATTAATGCTTCTATTTTCCAGAAATATTT
*
37928510 CAATATTTCAATAATTATTATTAATGCTTCTATTTTCCCGAAAT
1 CAATATTTCAATAATTATTATTAATGCTTCTATTTTCCAGAAAT
37928554 TATGTATTTA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.35, C:0.14, G:0.04, T:0.47
Consensus pattern (48 bp):
CAATATTTCAATAATTATTATTAATGCTTCTATTTTCCAGAAATATTT
Found at i:37928791 original size:50 final size:50
Alignment explanation
Indices: 37928687--37928876 Score: 200
Period size: 50 Copynumber: 3.7 Consensus size: 50
37928677 AAAGAGATCT
* *
37928687 CATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGGTCT
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATGAGAGGTCC
* *
37928743 CATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCC
* * * * * **
37928793 CTTGTAAGACCATGTCTAGGACATGGCATGGGCACCTATATGAGAATTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCC
* * *
37928843 CATGTAAGACCATATCTGGGATATGGTATTGGCA
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCA
37928877 GTACAAGACT
Statistics
Matches: 115, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
50 79 0.69
53 3 0.03
55 1 0.01
56 32 0.28
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.26
Consensus pattern (50 bp):
CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCC
Found at i:37928875 original size:100 final size:104
Alignment explanation
Indices: 37928689--37928876 Score: 231
Period size: 100 Copynumber: 1.8 Consensus size: 104
37928679 AGAGATCTCA
* * * * *
37928689 TGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGGTCTCATGTAAGACC
1 TGTAAGACCATGTCTAGGACATGGCATGGGCATCACT--GATTATGAGAAGTCCCATGTAAGACC
* * *
37928754 ATGTTTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCT
64 ATATCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCT
*
37928795 TGTAAGACCATGTCTAGGACATGGCATGGGCA-C-CT-A-TATGAGAATTCCCATGTAAGACCAT
1 TGTAAGACCATGTCTAGGACATGGCATGGGCATCACTGATTATGAGAAGTCCCATGTAAGACCAT
* *
37928856 ATCTGGGATATGGTATTGGCA
66 ATCTGGGACATGGCATTGGCA
37928877 GTACAAGACT
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
100 38 0.54
101 1 0.01
104 1 0.01
105 1 0.01
106 30 0.42
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.27
Consensus pattern (104 bp):
TGTAAGACCATGTCTAGGACATGGCATGGGCATCACTGATTATGAGAAGTCCCATGTAAGACCAT
ATCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCT
Found at i:37940172 original size:21 final size:22
Alignment explanation
Indices: 37940143--37940183 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
37940133 ATTACATATT
*
37940143 TTTAGTTTT-AATTTTTCAAAA
1 TTTAGTTTTAAAATTTTCAAAA
*
37940164 TTTATTTTTAAAATTTTCAA
1 TTTAGTTTTAAAATTTTCAA
37940184 CCAATCATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (22 bp):
TTTAGTTTTAAAATTTTCAAAA
Found at i:37960705 original size:69 final size:69
Alignment explanation
Indices: 37960608--37960763 Score: 215
Period size: 69 Copynumber: 2.3 Consensus size: 69
37960598 ATTCACAAAT
* * * * *
37960608 ATTTGGACAGTAGTAAAAACATTTGGACAGCAGT-GACTTGTACCAAAAATAGACAGCATTTAAG
1 ATTTGGACAGCATTAATAACATTCGGACAGCA-TAGACTTGTACAAAAAATAGACAGCATTTAAG
*
37960672 TACTA
65 TACCA
* * *
37960677 ATTTGGACAGCATTAATAACATTCGGACAGCATAGATTTGTACAAAAAATGGACTGCATTTAAGT
1 ATTTGGACAGCATTAATAACATTCGGACAGCATAGACTTGTACAAAAAATAGACAGCATTTAAGT
37960742 ACCA
66 ACCA
37960746 ATTTGGACAGCATTAATA
1 ATTTGGACAGCATTAATA
37960764 TGCTAAAAAA
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
68 1 0.01
69 76 0.99
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.28
Consensus pattern (69 bp):
ATTTGGACAGCATTAATAACATTCGGACAGCATAGACTTGTACAAAAAATAGACAGCATTTAAGT
ACCA
Found at i:37960758 original size:23 final size:23
Alignment explanation
Indices: 37960659--37960759 Score: 66
Period size: 23 Copynumber: 4.4 Consensus size: 23
37960649 ACCAAAAATA
*
37960659 GACAGCATTTAAGTACTAATTTG
1 GACAGCATTTAAGTACCAATTTG
* *
37960682 GACAGCA-TTAA-TAAC-ATTCG
1 GACAGCATTTAAGTACCAATTTG
* * **
37960702 GACAGCATAGATT-TGTACAAAAAATG
1 GACAGCAT---TTAAGTAC-CAATTTG
*
37960728 GACTGCATTTAAGTACCAATTTG
1 GACAGCATTTAAGTACCAATTTG
37960751 GACAGCATT
1 GACAGCATT
37960760 AATATGCTAA
Statistics
Matches: 55, Mismatches: 15, Indels: 16
0.64 0.17 0.19
Matches are distributed among these distances:
20 11 0.20
21 2 0.04
22 4 0.07
23 21 0.38
24 8 0.15
26 9 0.16
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (23 bp):
GACAGCATTTAAGTACCAATTTG
Found at i:37960826 original size:34 final size:33
Alignment explanation
Indices: 37960774--37960877 Score: 91
Period size: 38 Copynumber: 2.9 Consensus size: 33
37960764 TGCTAAAAAA
*
37960774 TGGACAGCATTTATACATGTAAAACAACCACATT
1 TGGACAACATTTA-ACATGTAAAACAACCACATT
*
37960808 TGGACAACATTATAACATGTAAAAAAAACAGCCACATT
1 TGGACAACATT-TAACATGT----AAAACAACCACATT
* * * *
37960846 TGGATATCATTGTAATATGCAAAACAACCACA
1 TGGACAACATT-TAACATGTAAAACAACCACA
37960878 CTTTAATACA
Statistics
Matches: 57, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
34 27 0.47
35 2 0.04
38 28 0.49
ACGTcount: A:0.45, C:0.19, G:0.12, T:0.24
Consensus pattern (33 bp):
TGGACAACATTTAACATGTAAAACAACCACATT
Found at i:37961702 original size:43 final size:41
Alignment explanation
Indices: 37961625--37961749 Score: 124
Period size: 43 Copynumber: 3.0 Consensus size: 41
37961615 AAAACACATA
* * * * *
37961625 TATCACATTCAATGCCATATCCCAGATATTGTCTTACATGT
1 TATCACATTCGATGCCATGTCCCAGACATGGTCTTACACGT
*
37961666 TATCACATCTCGATGCCACTGTCCCAGACAGGGTCTTACACGT
1 TATCACAT-TCGATGCCA-TGTCCCAGACATGGTCTTACACGT
* * * *
37961709 AATCTCATATTGATGTCAATGTCCCAGACATGGTCTTACAC
1 TATCACAT-TCGATG-CCATGTCCCAGACATGGTCTTACAC
37961750 AAAATTAAAC
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 8 0.12
42 8 0.12
43 51 0.74
44 2 0.03
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.31
Consensus pattern (41 bp):
TATCACATTCGATGCCATGTCCCAGACATGGTCTTACACGT
Found at i:37965458 original size:13 final size:13
Alignment explanation
Indices: 37965440--37965466 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
37965430 TACTTGGGAA
37965440 ATAAAAAAAAGTT
1 ATAAAAAAAAGTT
37965453 ATAAAAAAAAGTT
1 ATAAAAAAAAGTT
37965466 A
1 A
37965467 CATTGTCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.22
Consensus pattern (13 bp):
ATAAAAAAAAGTT
Found at i:37968787 original size:20 final size:20
Alignment explanation
Indices: 37968762--37968802 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
37968752 TTTTTCATCA
37968762 TGAGGCAGGGAATAAAAACT
1 TGAGGCAGGGAATAAAAACT
37968782 TGAGGCAGGGAATAAAAACT
1 TGAGGCAGGGAATAAAAACT
37968802 T
1 T
37968803 TAAAAAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.10, G:0.29, T:0.17
Consensus pattern (20 bp):
TGAGGCAGGGAATAAAAACT
Found at i:37972835 original size:9 final size:9
Alignment explanation
Indices: 37972806--37972863 Score: 62
Period size: 9 Copynumber: 6.4 Consensus size: 9
37972796 GTAGTGATTC
37972806 AATTCGGTT
1 AATTCGGTT
* *
37972815 AATTTGGGT
1 AATTCGGTT
37972824 AATTCGGTT
1 AATTCGGTT
* *
37972833 AATACAGTT
1 AATTCGGTT
*
37972842 AATTCGGGT
1 AATTCGGTT
*
37972851 AATTCAGTT
1 AATTCGGTT
37972860 AATT
1 AATT
37972864 TTTAACCAAA
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
9 38 1.00
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (9 bp):
AATTCGGTT
Found at i:37976654 original size:163 final size:163
Alignment explanation
Indices: 37976384--37976711 Score: 629
Period size: 163 Copynumber: 2.0 Consensus size: 163
37976374 TGTTTCATAG
* *
37976384 CTAGGTATTCATAGATGATTTTTTTGGTGATGCGAATTACTGTACAATAAGGAAAACAAAGGCTT
1 CTAGGTAGTCATAGATGATTTTTTTGGTGATGCGAATTACTCTACAATAAGGAAAACAAAGGCTT
37976449 GGACTTGACTTGACAAAAGCTACATATTAGGATTCTTTTGCTCGCTATTTGATTTAATCCTATAA
66 GGACTTGACTTGACAAAAGCTACATATTAGGATTCTTTTGCTCGCTATTTGATTTAATCCTATAA
37976514 CCTAATCTAGCCTGGTCAAAAGATATTGCTGAT
131 CCTAATCTAGCCTGGTCAAAAGATATTGCTGAT
*
37976547 CTAGGTAGTCATAGATGATTTTTTTGGTGGTGCGAATTACTCTACAATAAGGAAAACAAAGGCTT
1 CTAGGTAGTCATAGATGATTTTTTTGGTGATGCGAATTACTCTACAATAAGGAAAACAAAGGCTT
37976612 GGACTTGACTTGACAAAAGCTACATATTAGGATTCTTTTGCTCGCTATTTGATTTAATCCTATAA
66 GGACTTGACTTGACAAAAGCTACATATTAGGATTCTTTTGCTCGCTATTTGATTTAATCCTATAA
37976677 CCTAATCTAGCCTGGTCAAAAGATATTGCTGAT
131 CCTAATCTAGCCTGGTCAAAAGATATTGCTGAT
37976710 CT
1 CT
37976712 TGTCAATGGC
Statistics
Matches: 162, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
163 162 1.00
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.35
Consensus pattern (163 bp):
CTAGGTAGTCATAGATGATTTTTTTGGTGATGCGAATTACTCTACAATAAGGAAAACAAAGGCTT
GGACTTGACTTGACAAAAGCTACATATTAGGATTCTTTTGCTCGCTATTTGATTTAATCCTATAA
CCTAATCTAGCCTGGTCAAAAGATATTGCTGAT
Found at i:37982517 original size:6 final size:6
Alignment explanation
Indices: 37982506--37982538 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
37982496 TCTACGGTCT
37982506 GGTTGA GGTTGA GGTTGA GGTTGA GGTTGA GGT
1 GGTTGA GGTTGA GGTTGA GGTTGA GGTTGA GGT
37982539 GAATGTGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.15, C:0.00, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTTGA
Found at i:37982623 original size:36 final size:37
Alignment explanation
Indices: 37982573--37982644 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 37
37982563 ATAAAGTTTC
*
37982573 GGATAACTGAGTATTGAACTTATTAT-TTCTTAGGAT
1 GGATAACTGAGTATTGAACTTAGTATATTCTTAGGAT
* *
37982609 GGATAACTGGGTATTGTACTTAGTATATTCTTAGGA
1 GGATAACTGAGTATTGAACTTAGTATATTCTTAGGA
37982645 GGGCCTGTCG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 23 0.72
37 9 0.28
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.40
Consensus pattern (37 bp):
GGATAACTGAGTATTGAACTTAGTATATTCTTAGGAT
Found at i:37997668 original size:24 final size:24
Alignment explanation
Indices: 37997562--37997693 Score: 171
Period size: 25 Copynumber: 5.5 Consensus size: 24
37997552 ATACGGAACA
* *
37997562 AATA-CAGAGAGCACAAATGTGCT
1 AATATCAGAGAGCACCAACGTGCT
***
37997585 AA-A-CAGAGAGCACTGCCGTGCT
1 AATATCAGAGAGCACCAACGTGCT
37997607 ATATATCAGAGAGCACCAACGTGCT
1 A-ATATCAGAGAGCACCAACGTGCT
37997632 AATAATCAGAGAGCACCAACGTGCT
1 AAT-ATCAGAGAGCACCAACGTGCT
*
37997657 GATATCAGAGAGCACCAACGTGCT
1 AATATCAGAGAGCACCAACGTGCT
37997681 AATATCAGAGAGC
1 AATATCAGAGAGC
37997694 GCGCTAAAGT
Statistics
Matches: 96, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
22 17 0.18
23 3 0.03
24 36 0.38
25 40 0.42
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.17
Consensus pattern (24 bp):
AATATCAGAGAGCACCAACGTGCT
Found at i:37997673 original size:49 final size:50
Alignment explanation
Indices: 37997566--37997693 Score: 167
Period size: 49 Copynumber: 2.7 Consensus size: 50
37997556 GGAACAAATA
* * *** *
37997566 CAGAGAGCACAAATGTGCT-A-AA-CAGAGAGCACTGCCGTGCTATATAT
1 CAGAGAGCACCAACGTGCTAATAATCAGAGAGCACCAACGTGCTAGATAT
37997613 CAGAGAGCACCAACGTGCTAATAATCAGAGAGCACCAACGTGCT-GATAT
1 CAGAGAGCACCAACGTGCTAATAATCAGAGAGCACCAACGTGCTAGATAT
37997662 CAGAGAGCACCAACGTGCTAAT-ATCAGAGAGC
1 CAGAGAGCACCAACGTGCTAATAATCAGAGAGC
37997694 GCGCTAAAGT
Statistics
Matches: 72, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
47 17 0.24
48 11 0.15
49 28 0.39
50 16 0.22
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.16
Consensus pattern (50 bp):
CAGAGAGCACCAACGTGCTAATAATCAGAGAGCACCAACGTGCTAGATAT
Found at i:37998784 original size:40 final size:40
Alignment explanation
Indices: 37998722--37998816 Score: 145
Period size: 40 Copynumber: 2.3 Consensus size: 40
37998712 TTTTTCTTTC
* *
37998722 TTTCTTTCCTTCCTTCCTTCTCTGTTTCGTTTTGCTCTCTG
1 TTTCTTT-CTTTCTCCCTTCTCTGTTTCGTTTTGCTCTCTG
*
37998763 TTTCTTTCTTTCTCCCTTCTCTGTTTTGTTTTGCTCTCTG
1 TTTCTTTCTTTCTCCCTTCTCTGTTTCGTTTTGCTCTCTG
37998803 TTTCTTTTCTTTCT
1 TTTC-TTTCTTTCT
37998817 TTCTTTGTCA
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
40 34 0.68
41 16 0.32
ACGTcount: A:0.00, C:0.28, G:0.08, T:0.63
Consensus pattern (40 bp):
TTTCTTTCTTTCTCCCTTCTCTGTTTCGTTTTGCTCTCTG
Found at i:37998845 original size:8 final size:8
Alignment explanation
Indices: 37998832--37998913 Score: 59
Period size: 8 Copynumber: 10.5 Consensus size: 8
37998822 TGTCATATAT
37998832 ATATAATA
1 ATATAATA
37998840 ATATAAT-
1 ATATAATA
37998847 A-AT-ATA
1 ATATAATA
37998853 ATATAAT-
1 ATATAATA
37998860 ATATTAATA
1 ATA-TAATA
37998869 ATA-ACATA
1 ATATA-ATA
*
37998877 ATATAAAA
1 ATATAATA
* *
37998885 ACATAATC
1 ATATAATA
37998893 AT-TACTATA
1 ATATA--ATA
37998902 ATATAATA
1 ATATAATA
37998910 ATAT
1 ATAT
37998914 TTTTTTAACA
Statistics
Matches: 58, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
5 2 0.03
6 3 0.05
7 9 0.16
8 34 0.59
9 8 0.14
10 2 0.03
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (8 bp):
ATATAATA
Found at i:37998847 original size:5 final size:5
Alignment explanation
Indices: 37998826--37998909 Score: 52
Period size: 5 Copynumber: 16.6 Consensus size: 5
37998816 TTTCTTTGTC
37998826 ATATA TATATA ATA-A TATAATA ATATA ATATA ATAT- AT-TA ATAATA
1 ATATA -ATATA ATATA -AT-ATA ATATA ATATA ATATA ATATA AT-ATA
* * *
37998872 ACATA ATATA A-A-A ACATA ATCATTA CTATA ATATA ATA
1 ATATA ATATA ATATA ATATA AT-A-TA ATATA ATATA ATA
37998910 ATATTTTTTT
Statistics
Matches: 63, Mismatches: 5, Indels: 21
0.71 0.06 0.24
Matches are distributed among these distances:
3 3 0.05
4 7 0.11
5 36 0.57
6 13 0.21
7 4 0.06
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (5 bp):
ATATA
Found at i:37998891 original size:24 final size:24
Alignment explanation
Indices: 37998828--37998910 Score: 71
Period size: 24 Copynumber: 3.4 Consensus size: 24
37998818 TCTTTGTCAT
*
37998828 ATATATATAATAAT-ATAATAATATA
1 ATATA-ATAA-AATAATAATAACATA
* *
37998853 ATATAATATATTAATAATAACATA
1 ATATAATAAAATAATAATAACATA
* *
37998877 ATATAA-AAACATAATCATTACTATA
1 ATATAATAAA-ATAATAATAAC-ATA
37998902 ATATAATAA
1 ATATAATAA
37998911 TATTTTTTTA
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
23 4 0.09
24 27 0.57
25 14 0.30
26 2 0.04
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (24 bp):
ATATAATAAAATAATAATAACATA
Found at i:38000419 original size:2 final size:2
Alignment explanation
Indices: 38000412--38000471 Score: 66
Period size: 2 Copynumber: 29.0 Consensus size: 2
38000402 ACACGCATTT
* ** *
38000412 TA TA TA TA TA TA TA CA TA TA CGC TA TT TA CTA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA
38000456 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
38000472 CATTATTATT
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
2 46 0.96
3 2 0.04
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:38002143 original size:23 final size:23
Alignment explanation
Indices: 38002113--38002181 Score: 79
Period size: 23 Copynumber: 3.1 Consensus size: 23
38002103 TATGAGAGAA
*
38002113 TACCAAAAAAAAACATAAGGAAG
1 TACCAAAAAAAAATATAAGGAAG
* *
38002136 TACC--AAAAAATTATAAGGAAA
1 TACCAAAAAAAAATATAAGGAAG
* *
38002157 TACTAAAAAAAAATATGAGGAAG
1 TACCAAAAAAAAATATAAGGAAG
38002180 TA
1 TA
38002182 TAAAAAATTA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
21 17 0.46
23 20 0.54
ACGTcount: A:0.62, C:0.09, G:0.13, T:0.16
Consensus pattern (23 bp):
TACCAAAAAAAAATATAAGGAAG
Found at i:38002149 original size:44 final size:42
Alignment explanation
Indices: 38002087--38002245 Score: 153
Period size: 44 Copynumber: 3.7 Consensus size: 42
38002077 ACATTGAGGG
* * *
38002087 AGGAAGTACTAACAATTATGAGAGAATACCAAAAAAAAACAT
1 AGGAAGTACAAAAAATTATAAGAGAATACCAAAAAAAAACAT
* *
38002129 AAGGAAGTACCAAAAAATTATAAG-GAAATACTAAAAAAAAATAT
1 -AGGAAGTA-CAAAAAATTATAAGAG-AATACCAAAAAAAAACAT
* * *
38002173 GAGGAAGTATAAAAAATTATGAGAGAACA-C-AAAAAAAACACT
1 -AGGAAGTACAAAAAATTATAAGAGAATACCAAAAAAAAACA-T
* *
38002215 AGAAATTACAAAAAAGTTATAAGAGAATACC
1 AGGAAGTACAAAAAA-TTATAAGAGAATACC
38002246 GAATAATATG
Statistics
Matches: 94, Mismatches: 16, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
41 21 0.22
42 12 0.13
43 25 0.27
44 36 0.38
ACGTcount: A:0.60, C:0.09, G:0.14, T:0.17
Consensus pattern (42 bp):
AGGAAGTACAAAAAATTATAAGAGAATACCAAAAAAAAACAT
Found at i:38002186 original size:21 final size:21
Alignment explanation
Indices: 38002118--38002188 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
38002108 GAGAATACCA
* *
38002118 AAAAAAAACATAAGGAAGTAC
1 AAAAAAAATATAAGGAAGTAT
* * *
38002139 CAAAAAATTATAAGGAAATACT
1 AAAAAAAATATAAGGAAGTA-T
*
38002161 AAAAAAAAATATGAGGAAGTAT
1 -AAAAAAAATATAAGGAAGTAT
38002183 AAAAAA
1 AAAAAA
38002189 TTATGAGAGA
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
21 22 0.56
22 1 0.03
23 16 0.41
ACGTcount: A:0.66, C:0.06, G:0.13, T:0.15
Consensus pattern (21 bp):
AAAAAAAATATAAGGAAGTAT
Found at i:38003020 original size:19 final size:20
Alignment explanation
Indices: 38002977--38003025 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
38002967 ATACACAAAA
* * *
38002977 AATAACAAAAATTATGAGCG
1 AATACCAAAAATTACGAGAG
38002997 AATACCAAAAATTACGAGAG
1 AATACCAAAAATTACGAGAG
38003017 -ATACCAAAA
1 AATACCAAAA
38003026 GAAATGAGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.57, C:0.14, G:0.12, T:0.16
Consensus pattern (20 bp):
AATACCAAAAATTACGAGAG
Found at i:38003087 original size:20 final size:20
Alignment explanation
Indices: 38003064--38003268 Score: 91
Period size: 20 Copynumber: 10.3 Consensus size: 20
38003054 AAAAAGAGAG
38003064 GATGTACCAAAAATTATGAA
1 GATGTACCAAAAATTATGAA
** * *
38003084 GATGTATAAAAAAGTTACGAGG
1 GATGTACCAAAAA-TTATGA-A
*
38003106 GA-ATACCAAAAA-TATGAA
1 GATGTACCAAAAATTATGAA
*
38003124 G--GATACCAAAAATACATG--
1 GATG-TACCAAAAAT-TATGAA
* * * * *
38003142 GATGCACGAAAAAATACGAG
1 GATGTACCAAAAATTATGAA
* *
38003162 GATGCACCAAAAATTATAAA
1 GATGTACCAAAAATTATGAA
*
38003182 GATGTACAAAAAATTATGAGA
1 GATGTACCAAAAATTATGA-A
* * * *
38003203 GA-ATACTAAAAAATATGAG
1 GATGTACCAAAAATTATGAA
* ** **
38003222 GAAGTATAAAAAAAAAATGAA
1 GATGTA-CCAAAAATTATGAA
*
38003243 GATGTACCAAAAATTATAAA
1 GATGTACCAAAAATTATGAA
38003263 GATGTA
1 GATGTA
38003269 TAAATACCAA
Statistics
Matches: 134, Mismatches: 39, Indels: 24
0.68 0.20 0.12
Matches are distributed among these distances:
18 13 0.10
19 13 0.10
20 76 0.57
21 30 0.22
22 2 0.01
ACGTcount: A:0.54, C:0.09, G:0.17, T:0.20
Consensus pattern (20 bp):
GATGTACCAAAAATTATGAA
Found at i:38003231 original size:19 final size:21
Alignment explanation
Indices: 38003189--38003234 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
38003179 AAAGATGTAC
38003189 AAAAAATTATGAGAGAATACT
1 AAAAAATTATGAGAGAATACT
38003210 AAAAAA-TATGAG-GAAGTA-T
1 AAAAAATTATGAGAGAA-TACT
38003229 AAAAAA
1 AAAAAA
38003235 AAAATGAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 10 0.42
20 8 0.33
21 6 0.25
ACGTcount: A:0.63, C:0.02, G:0.15, T:0.20
Consensus pattern (21 bp):
AAAAAATTATGAGAGAATACT
Found at i:38003270 original size:41 final size:42
Alignment explanation
Indices: 38003162--38003272 Score: 111
Period size: 41 Copynumber: 2.7 Consensus size: 42
38003152 AAAATACGAG
* * **
38003162 GATGCACCAAAAATTATAAAGATGTA-CAAAAAATTATGAGA
1 GATGTACCAAAAATTATAAAGATGTATAAAAAAAAAATGAGA
* * * * * *
38003203 GA-ATACTAAAAAATATGAGGAAGTATAAAAAAAAAATGA-A
1 GATGTACCAAAAATTATAAAGATGTATAAAAAAAAAATGAGA
38003243 GATGTACCAAAAATTATAAAGATGTATAAA
1 GATGTACCAAAAATTATAAAGATGTATAAA
38003273 TACCAAAAAA
Statistics
Matches: 52, Mismatches: 16, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
40 19 0.37
41 33 0.63
ACGTcount: A:0.58, C:0.06, G:0.14, T:0.22
Consensus pattern (42 bp):
GATGTACCAAAAATTATAAAGATGTATAAAAAAAAAATGAGA
Found at i:38004661 original size:14 final size:14
Alignment explanation
Indices: 38004639--38004677 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
38004629 TAGTCCATTC
* *
38004639 TTATTATTATTTTA
1 TTATTATTATATCA
*
38004653 TTATCATTATATCA
1 TTATTATTATATCA
38004667 TTATTATTATA
1 TTATTATTATA
38004678 CTGTTTGCTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (14 bp):
TTATTATTATATCA
Found at i:38027586 original size:21 final size:23
Alignment explanation
Indices: 38027544--38027586 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 23
38027534 GATCGAGACC
*
38027544 AACTATAGTGGTATCGCGATACT
1 AACTATAGTGGTATCGCAATACT
*
38027567 AACTAT-G-GGTATTGCAATAC
1 AACTATAGTGGTATCGCAATAC
38027587 CCAACTCCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 11 0.61
22 1 0.06
23 6 0.33
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (23 bp):
AACTATAGTGGTATCGCAATACT
Found at i:38029014 original size:20 final size:22
Alignment explanation
Indices: 38028989--38029030 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
38028979 ACCTTAACTC
38028989 ATATTACA-AA-CCCAAACCCA
1 ATATTACACAAGCCCAAACCCA
*
38029009 ATATTACACAAGCCCAAGCCCA
1 ATATTACACAAGCCCAAACCCA
38029031 CAACCTAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 2 0.11
22 9 0.47
ACGTcount: A:0.45, C:0.36, G:0.05, T:0.14
Consensus pattern (22 bp):
ATATTACACAAGCCCAAACCCA
Found at i:38029225 original size:6 final size:6
Alignment explanation
Indices: 38029209--38029274 Score: 60
Period size: 6 Copynumber: 10.5 Consensus size: 6
38029199 AGAAGAAAGA
* * * * *
38029209 AAAACAC AAAAAC AAAAAT AGAAAT AGAAGC AGAAAAAC AAAAAC AAAAAC
1 AAAA-AC AAAAAC AAAAAC AAAAAC AAAAAC A-AAA-AC AAAAAC AAAAAC
38029260 AAAAAC AAAAAC AAA
1 AAAAAC AAAAAC AAA
38029275 TATTTGTAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
6 40 0.78
7 9 0.18
8 2 0.04
ACGTcount: A:0.77, C:0.14, G:0.06, T:0.03
Consensus pattern (6 bp):
AAAAAC
Found at i:38037249 original size:24 final size:24
Alignment explanation
Indices: 38037193--38037271 Score: 81
Period size: 24 Copynumber: 3.3 Consensus size: 24
38037183 GTCCTCATCT
* *
38037193 TCTTCATCTTCACCTCGACCCTCG
1 TCTTCATCTTCATCTCGACCCTCA
38037217 TAC-TCATCTTCATCTCGACCCTCA
1 T-CTTCATCTTCATCTCGACCCTCA
* * *
38037241 TCTTTATCTTTATCTCCACCC-CTA
1 TCTTCATCTTCATCTCGACCCTC-A
38037265 TCTTCAT
1 TCTTCAT
38037272 TTTTGTCTCC
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
23 2 0.04
24 43 0.93
25 1 0.02
ACGTcount: A:0.16, C:0.41, G:0.04, T:0.39
Consensus pattern (24 bp):
TCTTCATCTTCATCTCGACCCTCA
Found at i:38037280 original size:24 final size:25
Alignment explanation
Indices: 38037220--38037282 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 25
38037210 ACCCTCGTAC
* *
38037220 TCATCTTCATCTCGA-CCCTCATCT
1 TCATCTTTATCTCCACCCCTCATCT
*
38037244 TTATCTTTATCTCCACCCCT-ATCT
1 TCATCTTTATCTCCACCCCTCATCT
* *
38037268 TCATTTTTGTCTCCA
1 TCATCTTTATCTCCA
38037283 TCGTCTTCCT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
24 28 0.88
25 4 0.12
ACGTcount: A:0.16, C:0.37, G:0.03, T:0.44
Consensus pattern (25 bp):
TCATCTTTATCTCCACCCCTCATCT
Found at i:38039328 original size:9 final size:9
Alignment explanation
Indices: 38039314--38039352 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
38039304 TTTCGAAGAA
38039314 AATTGAGAG
1 AATTGAGAG
38039323 AATTGAGAG
1 AATTGAGAG
*
38039332 AGTTTAGAGAG
1 A-ATT-GAGAG
38039343 AATTGAGAG
1 AATTGAGAG
38039352 A
1 A
38039353 GTTAGATTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
9 16 0.62
10 4 0.15
11 6 0.23
ACGTcount: A:0.44, C:0.00, G:0.33, T:0.23
Consensus pattern (9 bp):
AATTGAGAG
Found at i:38039343 original size:20 final size:20
Alignment explanation
Indices: 38039318--38039355 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
38039308 GAAGAAAATT
38039318 GAGAGAATTGAGAGAGTTTA
1 GAGAGAATTGAGAGAGTTTA
38039338 GAGAGAATTGAGAGAGTT
1 GAGAGAATTGAGAGAGTT
38039356 AGATTTGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.37, T:0.24
Consensus pattern (20 bp):
GAGAGAATTGAGAGAGTTTA
Found at i:38041521 original size:108 final size:108
Alignment explanation
Indices: 38041299--38041594 Score: 364
Period size: 108 Copynumber: 2.8 Consensus size: 108
38041289 TAAATAGTTA
* * * * * * *
38041299 TATTCATTTAATATTATTAGTCTT-ATGTTTTTATGTGTCTAAATTTTATTTTGCTCACAATTTA
1 TATTCATTTAGTATTCTTAAT-TTGATGTATTTATGTGTTTAAATTTCATTTTACTCACAATTTA
* ** * *
38041363 ATC--TCTTTTTTCATTTTAATATTGTACATATTTCACGTGTTT
65 ATCTATTTTTTTTCATTTTAATATCATACAAATTTCACGTGTTG
* *
38041405 TATTCATTTAGTATTCTTAATTTGATGTATTTGTGTGTTTAAATTTCATTTTATTCACAATTTAA
1 TATTCATTTAGTATTCTTAATTTGATGTATTTATGTGTTTAAATTTCATTTTACTCACAATTTAA
*
38041470 TCTATTTTTTTTCATTTTAATATCATACAAATTTCATGTGTTG
66 TCTATTTTTTTTCATTTTAATATCATACAAATTTCACGTGTTG
* * * * *
38041513 TATTCATTTAGTATACTTAATCTGATGCATTTATGTGTTTAAATTTCGTTTTACTCACAAGTTAA
1 TATTCATTTAGTATTCTTAATTTGATGTATTTATGTGTTTAAATTTCATTTTACTCACAATTTAA
*
38041578 TCTAATTTTTTTGCATT
66 TCT-ATTTTTTTTCATT
38041595 CTAAGATTGA
Statistics
Matches: 163, Mismatches: 23, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
105 2 0.01
106 55 0.34
108 94 0.58
109 12 0.07
ACGTcount: A:0.26, C:0.11, G:0.08, T:0.55
Consensus pattern (108 bp):
TATTCATTTAGTATTCTTAATTTGATGTATTTATGTGTTTAAATTTCATTTTACTCACAATTTAA
TCTATTTTTTTTCATTTTAATATCATACAAATTTCACGTGTTG
Found at i:38042601 original size:26 final size:25
Alignment explanation
Indices: 38042570--38042620 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
38042560 TATTATTTTT
38042570 AATTTAGTAT-TTAACAATTTTATATA
1 AATTTA-TATATTAA-AATTTTATATA
*
38042596 AATTTATTTATTAAAATTTTATATA
1 AATTTATATATTAAAATTTTATATA
38042621 TAGTCACCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (25 bp):
AATTTATATATTAAAATTTTATATA
Found at i:38045226 original size:18 final size:19
Alignment explanation
Indices: 38045199--38045234 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
38045189 AAAAATTAAT
38045199 TTAAATTTAATATGCACAA
1 TTAAATTTAATATGCACAA
38045218 TTAAA-TTAATATGCACA
1 TTAAATTTAATATGCACA
38045235 TTATTATTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.47, C:0.11, G:0.06, T:0.36
Consensus pattern (19 bp):
TTAAATTTAATATGCACAA
Found at i:38045419 original size:26 final size:25
Alignment explanation
Indices: 38045389--38045438 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
38045379 ACATTGTTTC
* *
38045389 TAAATTTAAAATTTTTAAATCTATT
1 TAAAATTAAAATTTTTAAATATATT
38045414 TAAAATTAAAATTTTTAAATATATT
1 TAAAATTAAAATTTTTAAATATATT
38045439 ACACGTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (25 bp):
TAAAATTAAAATTTTTAAATATATT
Found at i:38047015 original size:8 final size:8
Alignment explanation
Indices: 38047004--38047037 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
38046994 GCCCTTCTGG
38047004 TTTTCTTT
1 TTTTCTTT
38047012 TTTTCTTT
1 TTTTCTTT
38047020 CATTTTCTTT
1 --TTTTCTTT
38047030 TTTTCTTT
1 TTTTCTTT
38047038 GCTTTTCAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 16 0.67
10 8 0.33
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTCTTT
Found at i:38063368 original size:26 final size:26
Alignment explanation
Indices: 38063339--38063395 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
38063329 GGGTCTATTA
38063339 AGTTTAAGTGGGTCT-AAGGACCCTTG
1 AGTTTAAGTGGGT-TGAAGGACCCTTG
* * *
38063365 AGTTTGAGTTGGTTGAAGGACCTTTG
1 AGTTTAAGTGGGTTGAAGGACCCTTG
38063391 AGTTT
1 AGTTT
38063396 GAGTTGGCCG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 1 0.04
26 26 0.96
ACGTcount: A:0.21, C:0.11, G:0.32, T:0.37
Consensus pattern (26 bp):
AGTTTAAGTGGGTTGAAGGACCCTTG
Found at i:38063776 original size:36 final size:36
Alignment explanation
Indices: 38063729--38063801 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
38063719 GGCCAAGATG
38063729 GCCATACCCAATGGGGTGACCATCGAGGGGTCGAGA
1 GCCATACCCAATGGGGTGACCATCGAGGGGTCGAGA
*
38063765 GCCATACCCAATGGGGTGACCATTGAGGGGTCGAGA
1 GCCATACCCAATGGGGTGACCATCGAGGGGTCGAGA
38063801 G
1 G
38063802 GGACTAAGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.25, C:0.23, G:0.37, T:0.15
Consensus pattern (36 bp):
GCCATACCCAATGGGGTGACCATCGAGGGGTCGAGA
Found at i:38071062 original size:2 final size:2
Alignment explanation
Indices: 38071055--38071102 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
38071045 AGGAGGAGGA
38071055 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38071097 AT AT AT
1 AT AT AT
38071103 GTGTGTGTGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38071804 original size:2 final size:2
Alignment explanation
Indices: 38071797--38071841 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
38071787 NNNNNNNNNN
38071797 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
38071839 GT G
1 GT G
38071842 AATATTCACC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.00, G:0.51, T:0.49
Consensus pattern (2 bp):
GT
Found at i:38072624 original size:62 final size:57
Alignment explanation
Indices: 38072553--38072699 Score: 161
Period size: 57 Copynumber: 2.5 Consensus size: 57
38072543 ATTGACGGTA
* *
38072553 AAAAAGATCTAGCCCAGACGGGTGATCCTATCCTGATATAGCCCTCCTAAAGAATATGTGTG
1 AAAAAGATCTAGCCCAGACGGGTGATCC--T--TGATATAGCCCTCCCAAAGAATATATG-G
* * *
38072615 AAAAAGATCTAGCCCGGACAGGTGAT-CTTGATATAGCCCTCCCGAAGAATATATGG
1 AAAAAGATCTAGCCCAGACGGGTGATCCTTGATATAGCCCTCCCAAAGAATATATGG
* * *
38072671 AAAATGGATTTAGCCCAGACGGGTAATCC
1 AAAA-AGATCTAGCCCAGACGGGTGATCC
38072700 AAATTAAGGT
Statistics
Matches: 73, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
56 5 0.07
57 41 0.56
58 1 0.01
59 1 0.01
61 1 0.01
62 24 0.33
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (57 bp):
AAAAAGATCTAGCCCAGACGGGTGATCCTTGATATAGCCCTCCCAAAGAATATATGG
Found at i:38072926 original size:67 final size:67
Alignment explanation
Indices: 38072818--38072952 Score: 216
Period size: 67 Copynumber: 2.0 Consensus size: 67
38072808 TAAGTTTATA
** * * *
38072818 TTACAAGGGATTTAGCCTGGACTGGTAATCCCGTTGTAAGAAATGAGGTTCGCGGGAGTGTGCTC
1 TTACAAGGGATTTAGCCTGGACTGGTAATCCCACTGTAAGAAATAAGGTTCGCGGAAGCGTGCTC
38072883 TC
66 TC
*
38072885 TTACAGGGGATTTAGCCTGGACTGGTAATCCCACTGTAAGAAATAAGGTTCGCGGAAGCGTGCTC
1 TTACAAGGGATTTAGCCTGGACTGGTAATCCCACTGTAAGAAATAAGGTTCGCGGAAGCGTGCTC
38072950 TC
66 TC
38072952 T
1 T
38072953 GAAATGGAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
67 62 1.00
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (67 bp):
TTACAAGGGATTTAGCCTGGACTGGTAATCCCACTGTAAGAAATAAGGTTCGCGGAAGCGTGCTC
TC
Found at i:38080781 original size:2 final size:2
Alignment explanation
Indices: 38080774--38080893 Score: 181
Period size: 2 Copynumber: 61.0 Consensus size: 2
38080764 GGGCTTTTTA
38080774 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
38080816 AT -T AT TT GT CT CT AT -T AT TT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38080856 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38080894 TATTTCTTTG
Statistics
Matches: 110, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
1 2 0.02
2 108 0.98
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.53
Consensus pattern (2 bp):
AT
Found at i:38083279 original size:3 final size:3
Alignment explanation
Indices: 38083271--38083299 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
38083261 CAAACAGACA
38083271 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
38083300 AACGAAACAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:38084545 original size:28 final size:28
Alignment explanation
Indices: 38084493--38084546 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
38084483 TATAAGATAC
*
38084493 AGACAAAAAAATGAAAAACCCAAACCCA
1 AGACAAAAAAATGAAAAACCAAAACCCA
38084521 AGACAAAGTAAAATG-AAAA-CAAAACC
1 AGACAAA--AAAATGAAAAACCAAAACC
38084547 ATTTAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
28 13 0.57
29 4 0.17
30 6 0.26
ACGTcount: A:0.65, C:0.20, G:0.09, T:0.06
Consensus pattern (28 bp):
AGACAAAAAAATGAAAAACCAAAACCCA
Found at i:38092179 original size:121 final size:121
Alignment explanation
Indices: 38091864--38092219 Score: 493
Period size: 121 Copynumber: 2.9 Consensus size: 121
38091854 TACCTAATTG
* *
38091864 AATTTTAATACGACACTATAATAACTTTGTAAATATTAAATAAATAATATTTACTAACTCACTGG
1 AATTTTAATACGACACTCTAATAACGTTGTAAATATTAAATAAATAATATTTACTAACTCACTGG
* *
38091929 TCAGAATTGTGGTCCCAAAACTACTGTTTCTGACACCACTGAAAATGAGTTATTACA
66 TCA-AATTGTGGTCCCAAAATTACTGTTTCCGACACCACTGAAAATGAGTTATTACA
* *
38091986 AATTTTAATACGACACTCTAATAACGTTGCAAATATTAAATAAATAATATTTACTAACTCATTGG
1 AATTTTAATACGACACTCTAATAACGTTGTAAATATTAAATAAATAATATTTACTAACTCACTGG
* * * * *
38092051 TCTAAATTGTGGTCTCAAAATTACGGTTTCCGACTCTACTG-AAATG-GTTTGTTACA
66 TC-AAATTGTGGTCCCAAAATTACTGTTTCCGACACCACTGAAAATGAG-TTATTACA
*
38092107 AATTTTTATACGACACTCTAATAATC-TTGTAAATATTAAATAAATAATATTTACTAACTCACTG
1 AATTTTAATACGACACTCTAATAA-CGTTGTAAATATTAAATAAATAATATTTACTAACTCACTG
* * * * *
38092171 ATCGAAATTGTAGTCCCAAAATAACTGTTTCTGACACCATTGAAAATGA
65 GTC-AAATTGTGGTCCCAAAATTACTGTTTCCGACACCACTGAAAATGA
38092220 CCTGTTACAA
Statistics
Matches: 205, Mismatches: 24, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
120 1 0.00
121 103 0.50
122 100 0.49
123 1 0.00
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (121 bp):
AATTTTAATACGACACTCTAATAACGTTGTAAATATTAAATAAATAATATTTACTAACTCACTGG
TCAAATTGTGGTCCCAAAATTACTGTTTCCGACACCACTGAAAATGAGTTATTACA
Found at i:38092669 original size:40 final size:42
Alignment explanation
Indices: 38092624--38092705 Score: 116
Period size: 40 Copynumber: 2.0 Consensus size: 42
38092614 GATAAAGCAG
38092624 GAAAACG-ATTCCTTGAGGAAGCG-ATT-TGTCCACGTGGACA
1 GAAAACGCA-TCCTTGAGGAAGCGCATTGTGTCCACGTGGACA
* *
38092664 GAAAACGCATCCTTGAGGGAGCGCTTTGTGTCCACGTGGACA
1 GAAAACGCATCCTTGAGGAAGCGCATTGTGTCCACGTGGACA
38092706 AAGTGCTCCC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
40 20 0.54
41 3 0.08
42 14 0.38
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (42 bp):
GAAAACGCATCCTTGAGGAAGCGCATTGTGTCCACGTGGACA
Found at i:38093610 original size:84 final size:83
Alignment explanation
Indices: 38093513--38093758 Score: 278
Period size: 96 Copynumber: 2.8 Consensus size: 83
38093503 AACAACTAGT
* * * *
38093513 TTTATTTTATTTTTCCTTAAAAACTCTAAATATTAAACCCCAATCTAATTTTTTTAAAATTTATA
1 TTTATTTAATTTTTCCTTAAAAAC-CTAAACACTAAACCCTAATCTAATTTTTTTAAAATTTATA
38093578 AAGTAACCCTAAACCCTAA
65 AAGTAACCCTAAACCCTAA
*
38093597 TTTATTTAATTTTTCCCTTAAAACCCTAAACACTAAACCCTAATCTAATTTTTTTAAATTTTATA
1 TTTATTTAATTTTT-CCTTAAAAACCTAAACACTAAACCCTAATCTAATTTTTTTAAA----AT-
38093662 ATTAATTTACTCAAGTAACCCTAAACCCTAA
60 -TT-A--TA---AAGTAACCCTAAACCCTAA
* *
38093693 TTTATTTAATTTTTTCCTTAAAAAGCATAAACACTAAACTCTAATCTAA-TTTTTTAAAATTTAT
1 TTTATTTAA-TTTTTCCTTAAAAA-CCTAAACACTAAACCCTAATCTAATTTTTTTAAAATTTAT
38093757 AA
64 AA
38093759 TTAAGTTAAT
Statistics
Matches: 139, Mismatches: 8, Indels: 30
0.79 0.05 0.17
Matches are distributed among these distances:
84 44 0.32
85 9 0.06
87 2 0.01
88 2 0.01
89 1 0.01
90 4 0.03
91 1 0.01
92 2 0.01
93 2 0.01
96 45 0.32
97 27 0.19
ACGTcount: A:0.39, C:0.17, G:0.01, T:0.42
Consensus pattern (83 bp):
TTTATTTAATTTTTCCTTAAAAACCTAAACACTAAACCCTAATCTAATTTTTTTAAAATTTATAA
AGTAACCCTAAACCCTAA
Found at i:38093618 original size:48 final size:47
Alignment explanation
Indices: 38093558--38093715 Score: 123
Period size: 48 Copynumber: 3.3 Consensus size: 47
38093548 AACCCCAATC
38093558 TAATTTTT--TTAAAATTTATAAAGTAACCCTAAACCCTAATTTATT
1 TAATTTTTCCTTAAAATTTATAAAGTAACCCTAAACCCTAATTTATT
** * * *
38093603 TAATTTTTCCCTTAAAACCCTA-AACACTAAACCCT-AA-TCTAATTTTTT
1 TAATTTTT-CCTTAAAA-TTTATAA-AGT-AACCCTAAACCCTAATTTATT
* * *
38093651 TAAATTTT--ATAATTAATTTACTCAAGTAACCCTAAACCCTAATTTATT
1 TAATTTTTCCTTAA--AATTTA-TAAAGTAACCCTAAACCCTAATTTATT
38093699 TAATTTTTTCCTTAAAA
1 TAA-TTTTTCCTTAAAA
38093716 AGCATAAACA
Statistics
Matches: 83, Mismatches: 15, Indels: 26
0.67 0.12 0.21
Matches are distributed among these distances:
45 11 0.13
46 8 0.10
47 6 0.07
48 37 0.45
49 12 0.14
50 6 0.07
51 3 0.04
ACGTcount: A:0.38, C:0.18, G:0.01, T:0.43
Consensus pattern (47 bp):
TAATTTTTCCTTAAAATTTATAAAGTAACCCTAAACCCTAATTTATT
Found at i:38093686 original size:96 final size:93
Alignment explanation
Indices: 38093570--38093817 Score: 352
Period size: 96 Copynumber: 2.6 Consensus size: 93
38093560 ATTTTTTTAA
38093570 AATTTATAAAGTAACCCTAAACCCTAATTTATTTAATTTTTCCCTTAAAACCCTAAACACTAAAC
1 AATTTATAAAGTAACCCTAAACCCTAATTTATTTAATTTTT-CCTTAAAACCCTAAACACTAAAC
*
38093635 CCTAATCTAATTTTTTTAAATTTTATAATT
65 CCTAATCTAA-TTTTTTAAAATTTATAATT
* * *
38093665 AATTTACTCAAGTAACCCTAAACCCTAATTTATTTAATTTTTTCCTTAAAAAGCATAAACACTAA
1 AATTTA-TAAAGTAACCCTAAACCCTAATTTATTTAA-TTTTTCCTT-AAAACCCTAAACACTAA
*
38093730 ACTCTAATCTAATTTTTTAAAATTTATAATT
63 ACCCTAATCTAATTTTTTAAAATTTATAATT
* * * * *
38093761 AAGTTAATTAAGAAACCCTAAACCCTTATTTATTTAATTTTTCCTTAGAACCCTAAA
1 AA-TTTATAAAGTAACCCTAAACCCTAATTTATTTAATTTTTCCTTAAAACCCTAAA
38093818 ATCTAAAAAC
Statistics
Matches: 137, Mismatches: 12, Indels: 9
0.87 0.08 0.06
Matches are distributed among these distances:
94 8 0.06
95 15 0.11
96 80 0.58
97 34 0.25
ACGTcount: A:0.40, C:0.18, G:0.02, T:0.40
Consensus pattern (93 bp):
AATTTATAAAGTAACCCTAAACCCTAATTTATTTAATTTTTCCTTAAAACCCTAAACACTAAACC
CTAATCTAATTTTTTAAAATTTATAATT
Found at i:38098558 original size:108 final size:108
Alignment explanation
Indices: 38098273--38098592 Score: 504
Period size: 107 Copynumber: 3.0 Consensus size: 108
38098263 AAGGAAAATT
* * * *
38098273 TTTCTAAA-TAAGGCAATATTTTACGTTTAGAAAA-TCGAGAAAATGTGCCCTAATGTGCTGGGT
1 TTTC-AAAGTAAGGCAATGTTTTGCGTTTGGAAAATTCGAGAAAACGTGCCCTAATGTGCTGGGT
38098336 TTCGATTTTTTCGTTCAACCAAATAGCCAAATATCCTTTTAAAA
65 TTCGATTTTTTCGTTCAACCAAATAGCCAAATATCCTTTTAAAA
38098380 TTTCAAAGTAAGGCAATGTTTTGCGTTTGG-AAATTCGAGAAAACGTGCCCTAATGTGCTGGGTT
1 TTTCAAAGTAAGGCAATGTTTTGCGTTTGGAAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTT
38098444 TCGATTTTTTCGTTCAACCAAATAGCCAAATATCCTTTTAAAA
66 TCGATTTTTTCGTTCAACCAAATAGCCAAATATCCTTTTAAAA
* * *
38098487 TTTCAAAGTAAGGCAATGTTTTGCATTTGGAAAATTCGAGAAAACGTGCCCTAATGTGTTAGGTT
1 TTTCAAAGTAAGGCAATGTTTTGCGTTTGGAAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTT
* ** *
38098552 TCGA-TTTCTCGTTTGACCAAATAGCCAAATATCCTCTTAAA
66 TCGATTTTTTCGTTCAACCAAATAGCCAAATATCCTTTTAAA
38098593 TCTCAAACCA
Statistics
Matches: 199, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
106 6 0.03
107 157 0.79
108 36 0.18
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35
Consensus pattern (108 bp):
TTTCAAAGTAAGGCAATGTTTTGCGTTTGGAAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTT
TCGATTTTTTCGTTCAACCAAATAGCCAAATATCCTTTTAAAA
Found at i:38103746 original size:20 final size:20
Alignment explanation
Indices: 38103711--38103748 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
38103701 CAGAAATCTC
**
38103711 TCTTTTCTCTTTTTTCTTTT
1 TCTTTTCTCTACTTTCTTTT
38103731 TCTTTTCTCTACTTTCTT
1 TCTTTTCTCTACTTTCTT
38103749 CTTATCTCAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.74
Consensus pattern (20 bp):
TCTTTTCTCTACTTTCTTTT
Found at i:38107332 original size:43 final size:43
Alignment explanation
Indices: 38107279--38107382 Score: 163
Period size: 46 Copynumber: 2.3 Consensus size: 43
38107269 TCAATATTTA
* *
38107279 GCACTGAGTGTGCGAGTATAGAATAGTTATGGCTATATGATTG
1 GCACTAAGTGTGCGAGTATAGAATAGTTACGGCTATATGATTG
38107322 GCACTAAGTGTTGTGCGAGTATAGAATAGTTACGGCTATATGATTG
1 GCACTAA--G-TGTGCGAGTATAGAATAGTTACGGCTATATGATTG
38107368 GCACTAAGTGTGCGA
1 GCACTAAGTGTGCGA
38107383 AATTAAATAA
Statistics
Matches: 56, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
43 13 0.23
44 1 0.02
45 1 0.02
46 41 0.73
ACGTcount: A:0.28, C:0.12, G:0.30, T:0.31
Consensus pattern (43 bp):
GCACTAAGTGTGCGAGTATAGAATAGTTACGGCTATATGATTG
Found at i:38107342 original size:46 final size:46
Alignment explanation
Indices: 38107287--38107378 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
38107277 TAGCACTGAG
*
38107287 TGTGCGAGTATAGAATAGTTATGGCTATATGATTGGCACTAAGTGT
1 TGTGCGAGTATAGAATAGTTACGGCTATATGATTGGCACTAAGTGT
38107333 TGTGCGAGTATAGAATAGTTACGGCTATATGATTGGCACTAAGTGT
1 TGTGCGAGTATAGAATAGTTACGGCTATATGATTGGCACTAAGTGT
38107379 GCGAAATTAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.28, C:0.10, G:0.28, T:0.34
Consensus pattern (46 bp):
TGTGCGAGTATAGAATAGTTACGGCTATATGATTGGCACTAAGTGT
Found at i:38107415 original size:41 final size:41
Alignment explanation
Indices: 38107368--38107500 Score: 205
Period size: 41 Copynumber: 3.3 Consensus size: 41
38107358 TATATGATTG
* *
38107368 GCACTAAGTGTGCGAAATTAAATAATGATGTTGAATAATGA
1 GCACTAAGTGTGCGAAACTAAATAATGATGTTGAATAACGA
*
38107409 GCACTAAGTGTGCGAAACTAAGTAATGATGTTGAATAACGA
1 GCACTAAGTGTGCGAAACTAAATAATGATGTTGAATAACGA
* * *
38107450 GCACTAAGTGTGCGAAACCAAATAATTATGTT-AATAACGG
1 GCACTAAGTGTGCGAAACTAAATAATGATGTTGAATAACGA
38107490 GCACTAAGTGT
1 GCACTAAGTGT
38107501 AACAGCCCAA
Statistics
Matches: 85, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
40 18 0.21
41 67 0.79
ACGTcount: A:0.39, C:0.12, G:0.23, T:0.26
Consensus pattern (41 bp):
GCACTAAGTGTGCGAAACTAAATAATGATGTTGAATAACGA
Found at i:38107952 original size:8 final size:8
Alignment explanation
Indices: 38107939--38108020 Score: 59
Period size: 8 Copynumber: 10.5 Consensus size: 8
38107929 TGTTAAAAAA
38107939 ATATTATT
1 ATATTATT
38107947 ATATTA-T
1 ATATTATT
*
38107954 AGTAATGATT
1 A-T-ATTATT
* *
38107964 ATGTTTTT
1 ATATTATT
38107972 ATATTATGT
1 ATATTAT-T
38107981 -TATTATT
1 ATATTATT
38107988 A-A-TA-T
1 ATATTATT
38107993 AT-TATATT
1 ATAT-TATT
38108001 ATATTATT
1 ATATTATT
38108009 ATATTATT
1 ATATTATT
38108017 ATAT
1 ATAT
38108021 ATATATGACA
Statistics
Matches: 58, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
5 2 0.03
6 2 0.03
7 6 0.10
8 40 0.69
9 6 0.10
10 2 0.03
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (8 bp):
ATATTATT
Found at i:38107953 original size:5 final size:5
Alignment explanation
Indices: 38107943--38108026 Score: 52
Period size: 5 Copynumber: 16.6 Consensus size: 5
38107933 AAAAAAATAT
* * *
38107943 TATTA TATTA TAGTAA TGATTA TGTT- T-TTA TATTA TGTTA TTATTA
1 TATTA TATTA TA-TTA T-ATTA TATTA TATTA TATTA TATTA -TATTA
38107989 -A-TA TATTA TATTA TATTA T-TATA TTATTA TATATA TAT
1 TATTA TATTA TATTA TATTA TAT-TA -TATTA TAT-TA TAT
38108027 GACAAAGAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 21
0.71 0.06 0.24
Matches are distributed among these distances:
3 4 0.06
4 5 0.08
5 34 0.54
6 18 0.29
7 2 0.03
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (5 bp):
TATTA
Found at i:38107979 original size:13 final size:13
Alignment explanation
Indices: 38107961--38108015 Score: 60
Period size: 13 Copynumber: 4.4 Consensus size: 13
38107951 TATAGTAATG
*
38107961 ATTATGTTTTTAT
1 ATTATGTTATTAT
38107974 ATTATGTTATTAT
1 ATTATGTTATTAT
* *
38107987 -TAAT-ATATTAT
1 ATTATGTTATTAT
*
38107998 ATTATATTATTAT
1 ATTATGTTATTAT
38108011 ATTAT
1 ATTAT
38108016 TATATATATA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
11 6 0.17
12 6 0.17
13 23 0.66
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (13 bp):
ATTATGTTATTAT
Found at i:38108092 original size:40 final size:40
Alignment explanation
Indices: 38108035--38108130 Score: 147
Period size: 40 Copynumber: 2.4 Consensus size: 40
38108025 ATGACAAAGA
38108035 AAGAAAGAAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
1 AAGAAAG-AAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
* *
38108076 GAGAAAGAAAGAAACAGAGAGCAAAACGAAACAGAGAAGG
1 AAGAAAGAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
*
38108116 AAGGAAGGAAAGAAA
1 AA-GAAAGAAAGAAA
38108131 GAAAGAAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 33 0.66
41 17 0.34
ACGTcount: A:0.64, C:0.08, G:0.28, T:0.00
Consensus pattern (40 bp):
AAGAAAGAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
Found at i:38109222 original size:25 final size:24
Alignment explanation
Indices: 38109151--38109282 Score: 153
Period size: 25 Copynumber: 5.5 Consensus size: 24
38109141 ACTTTAGCGC
38109151 GCTCTCTGATATTAGCACGTTGGT
1 GCTCTCTGATATTAGCACGTTGGT
* *
38109175 GCTCTTTGATATCAGCACGTTGGT
1 GCTCTCTGATATTAGCACGTTGGT
*
38109199 ACTCTCTGATTATTAGCACGTTGGT
1 GCTCTCTGA-TATTAGCACGTTGGT
***
38109224 GCTCTCTGATATTTAGCACGGCAGT
1 GCTCTCTGATA-TTAGCACGTTGGT
* *
38109249 GCTCTCTG-T-TTAGCACATTTGT
1 GCTCTCTGATATTAGCACGTTGGT
38109271 GCTCTCTG-TATT
1 GCTCTCTGATATT
38109283 TGTTCCGTAT
Statistics
Matches: 92, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
22 18 0.20
23 2 0.02
24 32 0.35
25 40 0.43
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.39
Consensus pattern (24 bp):
GCTCTCTGATATTAGCACGTTGGT
Found at i:38118437 original size:15 final size:15
Alignment explanation
Indices: 38118417--38118446 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
38118407 ATATTTCATC
38118417 TTTTTATGCTATAAA
1 TTTTTATGCTATAAA
38118432 TTTTTATGCTATAAA
1 TTTTTATGCTATAAA
38118447 AATGATGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (15 bp):
TTTTTATGCTATAAA
Found at i:38121567 original size:73 final size:73
Alignment explanation
Indices: 38121446--38121594 Score: 174
Period size: 73 Copynumber: 2.0 Consensus size: 73
38121436 CCACTTGTCC
* * * * * * ** *
38121446 TTGGACAAGGGGTTCTCTCAAAGGGTGCCTAGTAAGGGGTTGTCTTGGTGGGTTGTGAAGGGTGG
1 TTGGACAAGGGGTACTCTCAAAGAGTGCCCAGTAAGGGATTATCTTGGTGGGTAGCAAAAGGTGG
38121511 CATAACAA
66 CATAACAA
* * *
38121519 TTGGACGAGGGGTACTCTCGAAA-AGTGCCCAGTAAGGGATTATTTTGGTGGGTAGCAAAAGGTT
1 TTGGACAAGGGGTACTCTC-AAAGAGTGCCCAGTAAGGGATTATCTTGGTGGGTAGCAAAAGGTG
38121583 GCATAACAA
65 GCATAACAA
38121592 TTG
1 TTG
38121595 CCTCATTTAG
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
73 60 0.95
74 3 0.05
ACGTcount: A:0.26, C:0.13, G:0.35, T:0.27
Consensus pattern (73 bp):
TTGGACAAGGGGTACTCTCAAAGAGTGCCCAGTAAGGGATTATCTTGGTGGGTAGCAAAAGGTGG
CATAACAA
Found at i:38123885 original size:25 final size:25
Alignment explanation
Indices: 38123857--38123933 Score: 59
Period size: 24 Copynumber: 3.1 Consensus size: 25
38123847 TGAGCTTTCT
38123857 GTTATTAAGCTCGGATAAGCTTCCC
1 GTTATTAAGCTCGGATAAGCTTCCC
* ** * *
38123882 GTTA-CAAGCTCACATGAGCTTCCT
1 GTTATTAAGCTCGGATAAGCTTCCC
** *
38123906 GTTATTTGGCTTGGA-AGAGCTTCCC
1 GTTATTAAGCTCGGATA-AGCTTCCC
38123931 GTT
1 GTT
38123934 TAAATGCTCA
Statistics
Matches: 37, Mismatches: 13, Indels: 4
0.69 0.24 0.07
Matches are distributed among these distances:
24 19 0.51
25 18 0.49
ACGTcount: A:0.21, C:0.23, G:0.22, T:0.34
Consensus pattern (25 bp):
GTTATTAAGCTCGGATAAGCTTCCC
Found at i:38123891 original size:49 final size:49
Alignment explanation
Indices: 38123846--38123949 Score: 124
Period size: 49 Copynumber: 2.1 Consensus size: 49
38123836 TTAAGCTCTT
*
38123846 ATGAGCTTTCTGTTATTAAGCTCGGATA-AGCTTCCCGTTACAAGCTCAC
1 ATGAGCTTCCTGTTATTAAGCTCGGA-AGAGCTTCCCGTTACAAGCTCAC
** *
38123895 ATGAGCTTCCTGTTATTTGGCTTGGAAGAGCTTCCCGTTTA-AATGCTCA-
1 ATGAGCTTCCTGTTATTAAGCTCGGAAGAGCTTCCCG-TTACAA-GCTCAC
38123944 ATGAGC
1 ATGAGC
38123950 ATTCTTGAAC
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
48 1 0.02
49 39 0.81
50 8 0.17
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (49 bp):
ATGAGCTTCCTGTTATTAAGCTCGGAAGAGCTTCCCGTTACAAGCTCAC
Found at i:38124709 original size:22 final size:22
Alignment explanation
Indices: 38124681--38124778 Score: 124
Period size: 22 Copynumber: 4.5 Consensus size: 22
38124671 TTTATTGTTC
*
38124681 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
38124703 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
38124725 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
38124747 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
38124769 AAACATGAGA
1 AAACATGAGA
38124779 AAAATAAAGA
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 67 1.00
ACGTcount: A:0.33, C:0.14, G:0.27, T:0.27
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:38125784 original size:79 final size:78
Alignment explanation
Indices: 38125680--38125861 Score: 262
Period size: 76 Copynumber: 2.3 Consensus size: 78
38125670 TAGCAACCCC
* * *
38125680 TTGGGAGAATCAGCACTTAGCAACCCCCTTTTGCACATTC-AAAAATATGGTGGAATCAGCACTT
1 TTGGG-GAATCAGCACTTAGCAACCCCCTTTT-CACATCCGAAAAA-ACGGTGGAATAAGCACTT
38125744 AGCAACCACCAATGAT
63 AGCAACCACCAATGAT
* *
38125760 TTGGGGAATCAGCACTTAGCAA--CCCTTTTCATATCCGAAGAAACGGTGGAATAAGCACTTAGC
1 TTGGGGAATCAGCACTTAGCAACCCCCTTTTCACATCCGAAAAAACGGTGGAATAAGCACTTAGC
*
38125823 AACCACCGATGAT
66 AACCACCAATGAT
38125836 TTGGGGAATCAGCACTTAGCAACCCC
1 TTGGGGAATCAGCACTTAGCAACCCC
38125862 TTGGGGGAAT
Statistics
Matches: 93, Mismatches: 6, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
76 58 0.62
77 11 0.12
78 2 0.02
79 17 0.18
80 5 0.05
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (78 bp):
TTGGGGAATCAGCACTTAGCAACCCCCTTTTCACATCCGAAAAAACGGTGGAATAAGCACTTAGC
AACCACCAATGAT
Found at i:38126368 original size:21 final size:21
Alignment explanation
Indices: 38126343--38126386 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
38126333 TAGCTTATTT
38126343 AACATTCACATTTAATAAAAA
1 AACATTCACATTTAATAAAAA
38126364 AACATTCACATTTAATAAAAA
1 AACATTCACATTTAATAAAAA
38126385 AA
1 AA
38126387 TCATCGACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.27
Consensus pattern (21 bp):
AACATTCACATTTAATAAAAA
Found at i:38129682 original size:14 final size:14
Alignment explanation
Indices: 38129663--38129689 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
38129653 TAAAAAGAAT
38129663 ACTCGACATTGCCG
1 ACTCGACATTGCCG
38129677 ACTCGACATTGCC
1 ACTCGACATTGCC
38129690 TTCTCTTGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.37, G:0.19, T:0.22
Consensus pattern (14 bp):
ACTCGACATTGCCG
Found at i:38140850 original size:2 final size:2
Alignment explanation
Indices: 38140843--38140916 Score: 86
Period size: 2 Copynumber: 39.5 Consensus size: 2
38140833 GAAATAAATA
*
38140843 AT AT AT AT -T AT AC AT A- AT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
38140882 AT AC AT A- AT AT AT AT AT AT AT AT AC AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
38140917 CAGCCACTAC
Statistics
Matches: 61, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
1 5 0.08
2 56 0.92
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:38140887 original size:30 final size:31
Alignment explanation
Indices: 38140845--38140918 Score: 123
Period size: 30 Copynumber: 2.4 Consensus size: 31
38140835 AATAAATAAT
38140845 ATATATTATACATAATATATATATATATATA-
1 ATATA-TATACATAATATATATATATATATAC
38140876 ATATATATACATAATATATATATATATATAC
1 ATATATATACATAATATATATATATATATAC
38140907 ATAATATATACA
1 AT-ATATATACA
38140919 GCCACTACCC
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
30 25 0.61
31 7 0.17
32 9 0.22
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (31 bp):
ATATATATACATAATATATATATATATATAC
Found at i:38143020 original size:89 final size:89
Alignment explanation
Indices: 38142863--38143121 Score: 446
Period size: 89 Copynumber: 2.9 Consensus size: 89
38142853 TGCACTTTGG
* *
38142863 CCCCCTAAAAATAATAAAAAAATTCATTTAATCCATTAAAAATTATAAAAAAATATAGGCTATTC
1 CCCCCTAAAAATAAT-AAAAATTTGATTTAATCCATTAAAAATTAT--AAAAATATAGGCTATTC
38142928 AAATGGTGAAATTACAATTTAATTTCA
63 AAATGGTGAAATTACAATTTAATTTCA
*
38142955 CCCCCTAAAAATAATAAATATTTGATTTAATCCATTAAAAATTATAAAAATATAGGCTATTCAAA
1 CCCCCTAAAAATAATAAAAATTTGATTTAATCCATTAAAAATTATAAAAATATAGGCTATTCAAA
38143020 TGGTGAAATTACAATTTAATTTCA
66 TGGTGAAATTACAATTTAATTTCA
* *
38143044 CCCCCTAAAAATAATAAAAATTTGATTTAATCCATTGAAAATTATAAAAATATAGGCCATTCAAA
1 CCCCCTAAAAATAATAAAAATTTGATTTAATCCATTAAAAATTATAAAAATATAGGCTATTCAAA
38143109 TGGTGAAATTACA
66 TGGTGAAATTACA
38143122 TTTTTACTAT
Statistics
Matches: 161, Mismatches: 6, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
89 119 0.74
91 27 0.17
92 15 0.09
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.32
Consensus pattern (89 bp):
CCCCCTAAAAATAATAAAAATTTGATTTAATCCATTAAAAATTATAAAAATATAGGCTATTCAAA
TGGTGAAATTACAATTTAATTTCA
Found at i:38144643 original size:21 final size:21
Alignment explanation
Indices: 38144617--38144688 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
38144607 ACAAATGCTA
38144617 AACGGAAACCCATAAGGGTTG
1 AACGGAAACCCATAAGGGTTG
* * * *
38144638 AACGGAAGCTCATAAGAGCTG
1 AACGGAAACCCATAAGGGTTG
* * *
38144659 AACTGAAACCCATTAGGGTTA
1 AACGGAAACCCATAAGGGTTG
*
38144680 AACGAAAAC
1 AACGGAAAC
38144689 TATATGAGTT
Statistics
Matches: 38, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.42, C:0.19, G:0.24, T:0.15
Consensus pattern (21 bp):
AACGGAAACCCATAAGGGTTG
Found at i:38145288 original size:42 final size:42
Alignment explanation
Indices: 38145241--38145422 Score: 165
Period size: 42 Copynumber: 4.3 Consensus size: 42
38145231 TTTTTTTCGA
* *
38145241 AAACGCCGCTATAGATTAAGACGTTTAGTGGCGC-TTTCCCAC
1 AAACGCCGCTATAGA-TAAGACCTTTAGCGGCGCTTTTCCCAC
* * **
38145283 AAACGCCGCTATAGATCAGGACCTTTAGCGGTGC--AACCACAC
1 AAACGCCGCTATAGAT-AAGACCTTTAGCGGCGCTTTTCC-CAC
* * *
38145325 AAAACGCTGCTATAGATAAAGACCTTTAACGGCACTTTTTCCCAC
1 -AAACGCCGCTATAGAT-AAGACCTTTAGCGGCGC-TTTTCCCAC
* **
38145370 AAACGTCGCTATAGA-ACAGACCTTTAGCGGCGCTTTTCATAC
1 AAACGCCGCTATAGATA-AGACCTTTAGCGGCGCTTTTCCCAC
38145412 AAACGCCGCTA
1 AAACGCCGCTA
38145423 AAAACATATC
Statistics
Matches: 112, Mismatches: 21, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
41 3 0.03
42 49 0.44
43 42 0.38
44 13 0.12
45 3 0.03
46 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (42 bp):
AAACGCCGCTATAGATAAGACCTTTAGCGGCGCTTTTCCCAC
Found at i:38145330 original size:85 final size:85
Alignment explanation
Indices: 38145240--38145399 Score: 223
Period size: 85 Copynumber: 1.9 Consensus size: 85
38145230 GTTTTTTTCG
* * ** * *
38145240 AAAACGCCGCTATAGATTAAGACGTTTAGTGGCGC-TTTCCCACAAACGCCGCTATAGATCAGGA
1 AAAACGCCGCTATAGATAAAGACCTTTAACGGCACTTTTCCCACAAACGCCGCTATAGAACA-GA
38145304 CCTTTAGCGGTGCAACCACAC
65 CCTTTAGCGGTGCAACCACAC
* *
38145325 AAAACGCTGCTATAGATAAAGACCTTTAACGGCACTTTTTCCCACAAACGTCGCTATAGAACAGA
1 AAAACGCCGCTATAGATAAAGACCTTTAACGGCAC-TTTTCCCACAAACGCCGCTATAGAACAGA
38145390 CCTTTAGCGG
65 CCTTTAGCGG
38145400 CGCTTTTCAT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
85 29 0.45
86 12 0.18
87 24 0.37
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (85 bp):
AAAACGCCGCTATAGATAAAGACCTTTAACGGCACTTTTCCCACAAACGCCGCTATAGAACAGAC
CTTTAGCGGTGCAACCACAC
Found at i:38150664 original size:21 final size:21
Alignment explanation
Indices: 38150640--38150682 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
38150630 ATAGTTACCT
38150640 ATCCATAACC-CTTAACCCCTA
1 ATCCATAACCTC-TAACCCCTA
*
38150661 ATCCTTAACCTCTAACCCCTA
1 ATCCATAACCTCTAACCCCTA
38150682 A
1 A
38150683 CCCCTCTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.33, C:0.42, G:0.00, T:0.26
Consensus pattern (21 bp):
ATCCATAACCTCTAACCCCTA
Found at i:38150668 original size:14 final size:14
Alignment explanation
Indices: 38150645--38150687 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
38150635 TACCTATCCA
38150645 TAACCCTTAACCCC
1 TAACCCTTAACCCC
* *
38150659 TAATCCTTAACCTC
1 TAACCCTTAACCCC
*
38150673 TAACCCCTAACCCC
1 TAACCCTTAACCCC
38150687 T
1 T
38150688 CTTTTACAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.28, C:0.47, G:0.00, T:0.26
Consensus pattern (14 bp):
TAACCCTTAACCCC
Found at i:38150686 original size:7 final size:7
Alignment explanation
Indices: 38150645--38150687 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
38150635 TACCTATCCA
*
38150645 TAACCCT
1 TAACCCC
38150652 TAACCCC
1 TAACCCC
* *
38150659 TAATCCT
1 TAACCCC
*
38150666 TAACCTC
1 TAACCCC
38150673 TAACCCC
1 TAACCCC
38150680 TAACCCC
1 TAACCCC
38150687 T
1 T
38150688 CTTTTACAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.28, C:0.47, G:0.00, T:0.26
Consensus pattern (7 bp):
TAACCCC
Found at i:38151531 original size:41 final size:41
Alignment explanation
Indices: 38151481--38151672 Score: 192
Period size: 41 Copynumber: 4.7 Consensus size: 41
38151471 ATAAAATGTT
* * * *
38151481 TTAGTGGCGCTTTTTTAAAAAAGCCTCTAAA-AGCCCGAGTA
1 TTAGCGGCGCTTTTTCAAAAAAGCCGCTAAAGA-CCCGAGCA
* * *
38151522 TTAGCGGCGCTTTTTCAAAAATGCCGCTAAAGATCTGAGCA
1 TTAGCGGCGCTTTTTCAAAAAAGCCGCTAAAGACCCGAGCA
* * * * *
38151563 TTAGCGGCGCTTCTCCAAAAACGCCGCTAAAGACCAGGGCA
1 TTAGCGGCGCTTTTTCAAAAAAGCCGCTAAAGACCCGAGCA
* * *
38151604 TTAGCGGCGCTTTTT-AAAAAACGCCGTTAAA-ATCCCGATCT
1 TTAGCGGCGCTTTTTCAAAAAA-GCCGCTAAAGA-CCCGAGCA
*
38151645 TTAGCGGCGCTTTTTCAAAAACGCCGCT
1 TTAGCGGCGCTTTTTCAAAAAAGCCGCT
38151673 TTTTCAGAAA
Statistics
Matches: 124, Mismatches: 23, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
40 6 0.05
41 112 0.90
42 6 0.05
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.26
Consensus pattern (41 bp):
TTAGCGGCGCTTTTTCAAAAAAGCCGCTAAAGACCCGAGCA
Found at i:38151624 original size:82 final size:82
Alignment explanation
Indices: 38151521--38151672 Score: 216
Period size: 82 Copynumber: 1.9 Consensus size: 82
38151511 AAGCCCGAGT
* * *
38151521 ATTAGCGGCGCTTTTTCAAAAATGCCGCTAAAGAT-CTGAGCATTAGCGGCGCTTCTCCAAAAAC
1 ATTAGCGGCGCTTTTTAAAAAACGCCGCTAAA-ATCCCGAGCATTAGCGGCGCTTCTCCAAAAAC
38151585 GCCGCTAAAGACCAGGGC
65 GCCGCTAAAGACCAGGGC
* * * * *
38151603 ATTAGCGGCGCTTTTTAAAAAACGCCGTTAAAATCCCGATCTTTAGCGGCGCTTTTTCAAAAACG
1 ATTAGCGGCGCTTTTTAAAAAACGCCGCTAAAATCCCGAGCATTAGCGGCGCTTCTCCAAAAACG
38151668 CCGCT
66 CCGCT
38151673 TTTTCAGAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
81 2 0.03
82 59 0.97
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.24
Consensus pattern (82 bp):
ATTAGCGGCGCTTTTTAAAAAACGCCGCTAAAATCCCGAGCATTAGCGGCGCTTCTCCAAAAACG
CCGCTAAAGACCAGGGC
Found at i:38151674 original size:17 final size:18
Alignment explanation
Indices: 38151652--38151685 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
38151642 TCTTTAGCGG
38151652 CGCTTTTTCA-AAAACGC
1 CGCTTTTTCAGAAAACGC
38151669 CGCTTTTTCAGAAAACG
1 CGCTTTTTCAGAAAACG
38151686 ATGCCGTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.29
Consensus pattern (18 bp):
CGCTTTTTCAGAAAACGC
Found at i:38152980 original size:184 final size:184
Alignment explanation
Indices: 38152665--38153019 Score: 692
Period size: 184 Copynumber: 1.9 Consensus size: 184
38152655 GAAATCGAGG
*
38152665 TATCGGTACCTCGTTTTCGAAACCACTTAACTTAATAAATTCTTCTAAAACACAATTCACTAATT
1 TATCGATACCTCGTTTTCGAAACCACTTAACTTAATAAATTCTTCTAAAACACAATTCACTAATT
38152730 CAAATGTCTTTCTAAAATCTCATTTGGCTCATAAACACTAAATAATAAAATATACGAGCTCACTT
66 CAAATGTCTTTCTAAAATCTCATTTGGCTCATAAACACTAAATAATAAAATATACGAGCTCACTT
*
38152795 GTCGGATTTGGTGGTCTCGAACCACTATTTCCAACATCACTTGTCAGATTTGAT
131 GTCAGATTTGGTGGTCTCGAACCACTATTTCCAACATCACTTGTCAGATTTGAT
38152849 TATCGATACCTCGTTTTCGAAACCACTTAACTTAATAAATTCTTCTAAAACACAATTCACTAATT
1 TATCGATACCTCGTTTTCGAAACCACTTAACTTAATAAATTCTTCTAAAACACAATTCACTAATT
38152914 CAAATGTCTTTCTAAAATCTCATTTGGCTCATAAACACTAAATAATAAAATATACGAGCTCACTT
66 CAAATGTCTTTCTAAAATCTCATTTGGCTCATAAACACTAAATAATAAAATATACGAGCTCACTT
38152979 GTCAGATTTGGTGGTCTCGAACCACTATTTCCAACATCACT
131 GTCAGATTTGGTGGTCTCGAACCACTATTTCCAACATCACT
38153020 GAAAATCAGG
Statistics
Matches: 169, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
184 169 1.00
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.34
Consensus pattern (184 bp):
TATCGATACCTCGTTTTCGAAACCACTTAACTTAATAAATTCTTCTAAAACACAATTCACTAATT
CAAATGTCTTTCTAAAATCTCATTTGGCTCATAAACACTAAATAATAAAATATACGAGCTCACTT
GTCAGATTTGGTGGTCTCGAACCACTATTTCCAACATCACTTGTCAGATTTGAT
Found at i:38159057 original size:26 final size:27
Alignment explanation
Indices: 38159005--38159058 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
38158995 TCTAACTTGA
* * *
38159005 TTTATGGATCTTTCAAAAGCACTTTAT
1 TTTATGGACCTTTCAAAACCACATTAT
38159032 TTTATGGACCTTTC-AAACCACATTAT
1 TTTATGGACCTTTCAAAACCACATTAT
38159058 T
1 T
38159059 CATGGTCTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 11 0.46
27 13 0.54
ACGTcount: A:0.30, C:0.19, G:0.09, T:0.43
Consensus pattern (27 bp):
TTTATGGACCTTTCAAAACCACATTAT
Found at i:38159219 original size:20 final size:20
Alignment explanation
Indices: 38159194--38159233 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
38159184 CGTAAAATGA
*
38159194 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
38159214 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
38159234 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:38159223 original size:34 final size:35
Alignment explanation
Indices: 38159179--38159245 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
38159169 CAGTAAAATA
*
38159179 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
38159213 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
38159246 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:38159249 original size:14 final size:15
Alignment explanation
Indices: 38159173--38159249 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
38159163 GATTGCCAGT
* *
38159173 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
38159187 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
38159201 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
38159221 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
38159236 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
38159250 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:38160475 original size:11 final size:11
Alignment explanation
Indices: 38160426--38160487 Score: 51
Period size: 10 Copynumber: 6.0 Consensus size: 11
38160416 GTCCAAAATT
38160426 TAATTTTTTTA
1 TAATTTTTTTA
* *
38160437 -ACTTTATTTA
1 TAATTTTTTTA
*
38160447 T-ATATTTTTA
1 TAATTTTTTTA
* *
38160457 GAA-ATTTTTA
1 TAATTTTTTTA
38160467 -AATTTTTTTA
1 TAATTTTTTTA
38160477 TAATTTTTTTA
1 TAATTTTTTTA
38160488 AAAATATAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
9 2 0.05
10 27 0.68
11 11 0.28
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (11 bp):
TAATTTTTTTA
Found at i:38160646 original size:18 final size:18
Alignment explanation
Indices: 38160623--38160662 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
38160613 CACAAATTTG
38160623 TTATTTCAATTATTCGAA
1 TTATTTCAATTATTCGAA
* *
38160641 TTATTTGAGTTATTCGAA
1 TTATTTCAATTATTCGAA
38160659 TTAT
1 TTAT
38160663 AAAATTAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.30, C:0.07, G:0.10, T:0.53
Consensus pattern (18 bp):
TTATTTCAATTATTCGAA
Found at i:38167021 original size:3 final size:3
Alignment explanation
Indices: 38167013--38167040 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
38167003 GGCTTTTTCC
38167013 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
38167041 TTGGCTTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:38167381 original size:21 final size:21
Alignment explanation
Indices: 38167355--38167402 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
38167345 ATTTTTTTTT
**
38167355 AAAAATCATTAAAAATCTTTA-
1 AAAAATCACAAAAAAT-TTTAG
38167376 AAAAATCACAAAAAATTTTAG
1 AAAAATCACAAAAAATTTTAG
38167397 AAAAAT
1 AAAAAT
38167403 TCCAAGAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.62, C:0.08, G:0.02, T:0.27
Consensus pattern (21 bp):
AAAAATCACAAAAAATTTTAG
Found at i:38168477 original size:13 final size:12
Alignment explanation
Indices: 38168461--38168490 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
38168451 AATTTTTCTT
38168461 TTTTTTTTTGGGA
1 TTTTTTTTT-GGA
38168474 TTTTTTTTTGGA
1 TTTTTTTTTGGA
38168486 TTTTT
1 TTTTT
38168491 AACTATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.47
13 9 0.53
ACGTcount: A:0.07, C:0.00, G:0.17, T:0.77
Consensus pattern (12 bp):
TTTTTTTTTGGA
Found at i:38175373 original size:16 final size:16
Alignment explanation
Indices: 38175354--38175389 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
38175344 AATGGGGCTT
*
38175354 TAATGGAATAGAGATG
1 TAATAGAATAGAGATG
*
38175370 TAATAGAATAGAGTTG
1 TAATAGAATAGAGATG
38175386 TAAT
1 TAAT
38175390 CAGTAATTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.25, T:0.31
Consensus pattern (16 bp):
TAATAGAATAGAGATG
Found at i:38175643 original size:56 final size:56
Alignment explanation
Indices: 38175568--38175726 Score: 160
Period size: 56 Copynumber: 2.8 Consensus size: 56
38175558 TTTTAATAAG
* *
38175568 ATTATTATTAAAT-CTAATTTAATAAAAATATTAATAAATAATCATATT-TTAACATA
1 ATTATTATTAAATAC-AATTTAATAAAAATA-TAATAAATAATAACATTCTTAACATA
* * *
38175624 ATTATTATTAAATACAATTTTATAAAAATAATATATAATTTAATAACATTCTTAATATA
1 ATTATTATTAAATACAATTTAATAAAAAT-ATA-ATAA-ATAATAACATTCTTAACATA
* * * *
38175683 ATAATTATTAAAATATAAATTAATAAAAATCATAATATATAATA
1 ATTATTATT-AAATACAATTTAATAAAAAT-ATAATAAATAATA
38175727 TTATAAATTT
Statistics
Matches: 85, Mismatches: 12, Indels: 10
0.79 0.11 0.09
Matches are distributed among these distances:
56 28 0.33
57 6 0.07
58 13 0.15
59 18 0.21
60 20 0.24
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (56 bp):
ATTATTATTAAATACAATTTAATAAAAATATAATAAATAATAACATTCTTAACATA
Found at i:38175700 original size:39 final size:38
Alignment explanation
Indices: 38175651--38175734 Score: 98
Period size: 39 Copynumber: 2.2 Consensus size: 38
38175641 TTTTATAAAA
* * * *
38175651 ATAATATATAATTTAATAACATTCTTAATATAATAATTATT
1 ATAA-ATATAAATTAATAAAAATCATAATAT-ATAA-TATT
38175692 A-AAATATAAATTAATAAAAATCATAATATATAATATT
1 ATAAATATAAATTAATAAAAATCATAATATATAATATT
38175729 ATAAAT
1 ATAAAT
38175735 TTATTTATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
37 5 0.13
38 8 0.21
39 22 0.58
40 2 0.05
41 1 0.03
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (38 bp):
ATAAATATAAATTAATAAAAATCATAATATATAATATT
Found at i:38176973 original size:94 final size:94
Alignment explanation
Indices: 38176812--38177001 Score: 362
Period size: 94 Copynumber: 2.0 Consensus size: 94
38176802 GAGTGATTTT
*
38176812 GTAATGTATTCCAATCGTTCTATTAGTGGGTAACTAAGCTTTCATTCGGAAAGTCTTAGAGGTGG
1 GTAATGTATTCAAATCGTTCTATTAGTGGGTAACTAAGCTTTCATTCGGAAAGTCTTAGAGGTGG
38176877 AGTGATCTAGTTCTAAGTATACGAGTGAG
66 AGTGATCTAGTTCTAAGTATACGAGTGAG
*
38176906 GTAATGTATTCAAATCGTTCTATTAGTGGGTAACTAAGCTTTCATTTGGAAAGTCTTAGAGGTGG
1 GTAATGTATTCAAATCGTTCTATTAGTGGGTAACTAAGCTTTCATTCGGAAAGTCTTAGAGGTGG
38176971 AGTGATCTAGTTCTAAGTATACGAGTGAG
66 AGTGATCTAGTTCTAAGTATACGAGTGAG
38177000 GT
1 GT
38177002 TACAATTTAA
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
94 94 1.00
ACGTcount: A:0.28, C:0.12, G:0.26, T:0.35
Consensus pattern (94 bp):
GTAATGTATTCAAATCGTTCTATTAGTGGGTAACTAAGCTTTCATTCGGAAAGTCTTAGAGGTGG
AGTGATCTAGTTCTAAGTATACGAGTGAG
Found at i:38181141 original size:93 final size:93
Alignment explanation
Indices: 38180982--38181163 Score: 355
Period size: 93 Copynumber: 2.0 Consensus size: 93
38180972 TTAACTCACA
*
38180982 TACAACTTATTATAATTCATCTTTGGTGATCTTATAAAAGCTTTTCTATTTTAAATAATTTGAAA
1 TACAACTTATTATAATTCATCCTTGGTGATCTTATAAAAGCTTTTCTATTTTAAATAATTTGAAA
38181047 TAAATTATGTATATGCAATCATAAACAT
66 TAAATTATGTATATGCAATCATAAACAT
38181075 TACAACTTATTATAATTCATCCTTGGTGATCTTATAAAAGCTTTTCTATTTTAAATAATTTGAAA
1 TACAACTTATTATAATTCATCCTTGGTGATCTTATAAAAGCTTTTCTATTTTAAATAATTTGAAA
38181140 TAAATTATGTATATGCAATCATAA
66 TAAATTATGTATATGCAATCATAA
38181164 TAAATATGAA
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 88 1.00
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (93 bp):
TACAACTTATTATAATTCATCCTTGGTGATCTTATAAAAGCTTTTCTATTTTAAATAATTTGAAA
TAAATTATGTATATGCAATCATAAACAT
Found at i:38197480 original size:19 final size:19
Alignment explanation
Indices: 38197432--38197482 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
38197422 TCAACAAAAA
38197432 TTATAAAAAAGTTCAAAATAT
1 TTAT-AAAAA-TTCAAAATAT
* *
38197453 TTTTCAAAATTCAAAATAT
1 TTATAAAAATTCAAAATAT
38197472 TTATAAAAATT
1 TTATAAAAATT
38197483 ATAAAAATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 19 0.73
20 4 0.15
21 3 0.12
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (19 bp):
TTATAAAAATTCAAAATAT
Found at i:38199872 original size:22 final size:22
Alignment explanation
Indices: 38199847--38199903 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
38199837 TGCACTAATG
38199847 AACAGAGAGCACTAAAGTGCTA
1 AACAGAGAGCACTAAAGTGCTA
* ** *
38199869 AACAAAGAGCACGGATGTGCTA
1 AACAGAGAGCACTAAAGTGCTA
*
38199891 AATAGAGAGCACT
1 AACAGAGAGCACT
38199904 GTCATGCTAG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.14
Consensus pattern (22 bp):
AACAGAGAGCACTAAAGTGCTA
Found at i:38201388 original size:29 final size:29
Alignment explanation
Indices: 38201343--38201401 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
38201333 AACTAGTGGT
*
38201343 ATCATCACTTTCGGTTATCAATCTTTCTA
1 ATCATCACTTTCAGTTATCAATCTTTCTA
38201372 ATCATCACTTTCAGTTATCAATCTTTCTA
1 ATCATCACTTTCAGTTATCAATCTTTCTA
38201401 A
1 A
38201402 GCTCGAATCG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.27, C:0.24, G:0.05, T:0.44
Consensus pattern (29 bp):
ATCATCACTTTCAGTTATCAATCTTTCTA
Found at i:38205061 original size:328 final size:328
Alignment explanation
Indices: 38204464--38205121 Score: 1181
Period size: 328 Copynumber: 2.0 Consensus size: 328
38204454 CTAGCATGAA
38204464 ATCCATAGGACTTGCTCAACACTAATAAAGACTAAGATAAGTAAGCTTATCCCTGATTAGTTACT
1 ATCCATAGGACTTGCTCAACACTAATAAAGACTAAGATAAGTAAGCTTATCCCTGATTAGTTACT
*
38204529 AAGCTTTTTAAGCTCACACATTAGTTGTTTAACACGTGTAGGTTTGGACTTACATAGAAGTCATG
66 AAGCTTTTTAAGCTCACACATTAGTTGTTTAACACGTGTAGGTTTGGACTTACATAGAAGTCATA
**
38204594 ATGTTGGCTTAGGAGCATCACATCATCCATCGAGCTTCTAAGGTTGTAATTCAAGTATTTAAATA
131 ATGTTGGCTTAGGAGCATCACATCATCCATCGAGCTTCTAAGGTTGTAATTCAAACATTTAAATA
*
38204659 CCATTTGTATTGGATTATTGGCATATATACAAAAACTTAGATTACTTGAGCAATTGTAAAGTTAG
196 CCATTTGTATTGGACTATTGGCATATATACAAAAACTTAGATTACTTGAGCAATTGTAAAGTTAG
* *
38204724 ATGATGAACTTGAGCTTCTTTTGTGTTTCTATTAAAAAATATATGTATATTTTGTTTTGGACGTG
261 ATGATGAACTTGAGCCTCTTTTGTGTTTCTATTAAAAAATATATGTATATTTTATTTTGGACGTG
*
38204789 TTC
326 CTC
* *
38204792 ATCCATAGGACTTGCTCAACACTAATAAAGACTAAGATAAGTAAGTTTATCCCTGATTAGTTATT
1 ATCCATAGGACTTGCTCAACACTAATAAAGACTAAGATAAGTAAGCTTATCCCTGATTAGTTACT
*
38204857 GAGCTTTTTAAGCTCACACATTAGTTGTTTAACACGTGTAGGTTTGGACTTACATAGAAGTCATA
66 AAGCTTTTTAAGCTCACACATTAGTTGTTTAACACGTGTAGGTTTGGACTTACATAGAAGTCATA
* * *
38204922 ATGTTGGCTTGGGAGCATCATATCATCCATCGAGCTTCTAAGGTTGTAATTCAAACGTTTAAATA
131 ATGTTGGCTTAGGAGCATCACATCATCCATCGAGCTTCTAAGGTTGTAATTCAAACATTTAAATA
*
38204987 CCATTTGTATTGGACTATTGGCATATATACAAAAACTTAGATTTCTTGAGCAATTGTAAAGTTAG
196 CCATTTGTATTGGACTATTGGCATATATACAAAAACTTAGATTACTTGAGCAATTGTAAAGTTAG
*
38205052 ATGATGAACTTGAGCCTCTTTTGTGTTTCTCTTAAAAAATATATGTATATTTTATTTTGGACGTG
261 ATGATGAACTTGAGCCTCTTTTGTGTTTCTATTAAAAAATATATGTATATTTTATTTTGGACGTG
38205117 CTC
326 CTC
38205120 AT
1 AT
38205122 GCCAAGTTTT
Statistics
Matches: 315, Mismatches: 15, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
328 315 1.00
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (328 bp):
ATCCATAGGACTTGCTCAACACTAATAAAGACTAAGATAAGTAAGCTTATCCCTGATTAGTTACT
AAGCTTTTTAAGCTCACACATTAGTTGTTTAACACGTGTAGGTTTGGACTTACATAGAAGTCATA
ATGTTGGCTTAGGAGCATCACATCATCCATCGAGCTTCTAAGGTTGTAATTCAAACATTTAAATA
CCATTTGTATTGGACTATTGGCATATATACAAAAACTTAGATTACTTGAGCAATTGTAAAGTTAG
ATGATGAACTTGAGCCTCTTTTGTGTTTCTATTAAAAAATATATGTATATTTTATTTTGGACGTG
CTC
Found at i:38216871 original size:5 final size:5
Alignment explanation
Indices: 38216861--38216885 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
38216851 AATGCCCCAT
38216861 CAAAA CAAAA CAAAA CAAAA CAAAA
1 CAAAA CAAAA CAAAA CAAAA CAAAA
38216886 GAAAGCTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.20, G:0.00, T:0.00
Consensus pattern (5 bp):
CAAAA
Found at i:38217931 original size:18 final size:19
Alignment explanation
Indices: 38217892--38217932 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
38217882 AAATTACAAA
* *
38217892 AAAATTTAAAATAATTTTT
1 AAAATTCAAAATAATTTAT
38217911 AAAATTCAAAAT-ATTTAT
1 AAAATTCAAAATAATTTAT
38217929 AAAA
1 AAAA
38217933 ACATCAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAATTCAAAATAATTTAT
Done.