Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A01
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: 115637255
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5450143 characters in sequence are not A, C, G, or T
File 9 of 349
Found at i:2681981 original size:21 final size:22
Alignment explanation
Indices: 2681941--2681981 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2681931 TATAATGTGT
* *
2681941 TTTTTTTTTTTTTTACAAACAA
1 TTTTTTTTTGTTCTACAAACAA
2681963 TTTTTTTTTGTTCTA-AAAC
1 TTTTTTTTTGTTCTACAAAC
2681982 CCTAATGACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.24, C:0.10, G:0.02, T:0.63
Consensus pattern (22 bp):
TTTTTTTTTGTTCTACAAACAA
Found at i:2685795 original size:21 final size:23
Alignment explanation
Indices: 2685747--2685793 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
2685737 AATTATTATA
**
2685747 ATTT-ATATATAATAAATTTTTT
1 ATTTAATATATAATAAATTAATT
2685769 ATTTAATATATAA-AAATTAATT
1 ATTTAATATATAATAAATTAATT
2685791 ATT
1 ATT
2685794 AAAGTTATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
ATTTAATATATAATAAATTAATT
Found at i:2695907 original size:2 final size:2
Alignment explanation
Indices: 2695900--2695928 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2695890 AACTAAAAGA
2695900 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2695929 ATTCCCATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2704182 original size:13 final size:13
Alignment explanation
Indices: 2704164--2704190 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2704154 GGACAACTAT
2704164 AAACATCGAAACG
1 AAACATCGAAACG
2704177 AAACATCGAAACG
1 AAACATCGAAACG
2704190 A
1 A
2704191 TTAACTTTTA
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:0.56, C:0.22, G:0.15, T:0.07
Consensus pattern (13 bp):
AAACATCGAAACG
Found at i:2707186 original size:18 final size:18
Alignment explanation
Indices: 2707159--2707193 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2707149 AATAATATAC
*
2707159 TTTTTATTTTATAATTTA
1 TTTTTATTTTAAAATTTA
*
2707177 TTTTTTTTTTAAAATTT
1 TTTTTATTTTAAAATTT
2707194 CGTTGATTAA
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:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTATTTTAAAATTTA
Found at i:2717508 original size:16 final size:15
Alignment explanation
Indices: 2717489--2717518 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2717479 CTCTACAAAT
2717489 TATAAAAAATATAAAC
1 TATAAAAAAT-TAAAC
2717505 TATAAAAAATTAAA
1 TATAAAAAATTAAA
2717519 ATTTCAATCG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (15 bp):
TATAAAAAATTAAAC
Found at i:2720617 original size:12 final size:12
Alignment explanation
Indices: 2720602--2720629 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
2720592 ACTTAAGATG
2720602 TATCGAATTTCT
1 TATCGAATTTCT
2720614 TATCGAATTTCT
1 TATCGAATTTCT
2720626 TATC
1 TATC
2720630 ACTCGATCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.18, G:0.07, T:0.50
Consensus pattern (12 bp):
TATCGAATTTCT
Found at i:2739448 original size:19 final size:19
Alignment explanation
Indices: 2739424--2739461 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2739414 TTGAGATTGC
*
2739424 CAACCTATTTGCTTGAAAT
1 CAACCTATTTGCCTGAAAT
2739443 CAACCTATTTGCCTGAAAT
1 CAACCTATTTGCCTGAAAT
2739462 TATTCATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.34
Consensus pattern (19 bp):
CAACCTATTTGCCTGAAAT
Found at i:2758292 original size:3 final size:3
Alignment explanation
Indices: 2758284--2758782 Score: 150
Period size: 3 Copynumber: 162.3 Consensus size: 3
2758274 AATAAGGTGG
* * * *
2758284 TAA TAA TAA TAC TAA TAA TAA TAA TGA TAA TAG TAA TAA TAA TAA TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
** * * * * * * *
2758332 TAA TGG TAA TAGCA TAA TAG TTA TAA GAAA CAA TAC TAG TAG TAA TAA
1 TAA TAA TAA TA--A TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA
* * * *
2758380 TAA TAA T-A TAAA TAA CAA T-A TAT TAA TGAGA -AA TAA CAA TAA TAG
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA T-A-A TAA TAA TAA TAA TAA
* * * * * * *
2758425 TAA TAA TAG TAA CAA TAA TAT TGA TAA TGGA TAT TAA TAA TAA AAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
* * * * * * * * *
2758471 GGAG TAA TAA TAT TAG TAG TAAA TAA AAA TAG TGA TAA CAA TAA TGAA
1 -TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA T-AA
* * * * **
2758519 -AA TAG TAA TAA TAA TAA TAA TAA TAA TAG TAAA TAG TAA GGAA TGG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA -TAA TAA
* * * * * *
2758565 TGA TAA TAA TGA TAA TAAA CAA TAG TAAA TAA TAA TAA TGA TAG TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
* * *** * * * * *
2758612 CAA AAA CGG CAA TGA TAA TAT TAA TAT TGA TAA TAAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
* * ** *
2758658 TAA T-A TAA -ACA TTGA TAA TAA TAGA AAA TAA TAA TGT TAA AACA TAA
1 TAA TAA TAA TA-A -TAA TAA TAA TA-A TAA TAA TAA TAA TAA TA-A TAA
* ** * *
2758705 TAA CAA TGG TGAA -AA TAA TAA TAA TAT TAA TAA TAA TAA T-A TAC
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* **
2758749 TAA TGA GGA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
2758783 GATGATGATG
Statistics
Matches: 348, Mismatches: 120, Indels: 56
0.66 0.23 0.11
Matches are distributed among these distances:
2 14 0.04
3 302 0.87
4 28 0.08
5 4 0.01
ACGTcount: A:0.57, C:0.03, G:0.10, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:2758662 original size:31 final size:31
Alignment explanation
Indices: 2758626--2758697 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
2758616 AACGGCAATG
* *
2758626 ATAATATTAATATTGATAATAAATA-ATAATA
1 ATAATATTAACATTGATAAT-AATAGAAAATA
*
2758657 ATAATATAAACATTGATAATAATAGAAAATA
1 ATAATATTAACATTGATAATAATAGAAAATA
*
2758688 ATAATGTTAA
1 ATAATATTAA
2758698 AACATAATAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 4 0.11
31 31 0.89
ACGTcount: A:0.58, C:0.01, G:0.06, T:0.35
Consensus pattern (31 bp):
ATAATATTAACATTGATAATAATAGAAAATA
Found at i:2758688 original size:34 final size:33
Alignment explanation
Indices: 2758641--2758745 Score: 92
Period size: 34 Copynumber: 3.2 Consensus size: 33
2758631 ATTAATATTG
*
2758641 ATAATA-AATAATAATAATAATATAAACATTGATA
1 ATAATAGAA-AATAATAATAATATAAACA-TAATA
**
2758675 ATAATAGAAAATAATAATGTTA-AAACATAATA
1 ATAATAGAAAATAATAATAATATAAACATAATA
* * *
2758707 ACAATGGTGAAAATAATAATAATAT-TA-ATAATA
1 ATAAT--AGAAAATAATAATAATATAAACATAATA
2758740 ATAATA
1 ATAATA
2758746 TACTAATGAG
Statistics
Matches: 57, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
32 8 0.14
33 15 0.26
34 32 0.56
35 2 0.04
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.30
Consensus pattern (33 bp):
ATAATAGAAAATAATAATAATATAAACATAATA
Found at i:2758787 original size:3 final size:3
Alignment explanation
Indices: 2758781--2758808 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2758771 AATAATAATA
2758781 ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG A
2758809 AAATATGAAT
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:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:2773763 original size:28 final size:28
Alignment explanation
Indices: 2773710--2773795 Score: 109
Period size: 28 Copynumber: 3.0 Consensus size: 28
2773700 AACTTTGTGC
*
2773710 TATTCTGCTGTGTTTTGGATGGATTATAT
1 TATTCTGATGTGTTTTGGA-GGATTATAT
*
2773739 TATTCTGATGTGTTTGGGAGGATTATAT
1 TATTCTGATGTGTTTTGGAGGATTATAT
* * * *
2773767 GATACTGGTGTGTTTTGAAGGATTATAT
1 TATTCTGATGTGTTTTGGAGGATTATAT
2773795 T
1 T
2773796 GGTGTGTTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
28 32 0.65
29 17 0.35
ACGTcount: A:0.21, C:0.05, G:0.27, T:0.48
Consensus pattern (28 bp):
TATTCTGATGTGTTTTGGAGGATTATAT
Found at i:2774027 original size:23 final size:21
Alignment explanation
Indices: 2773997--2774080 Score: 98
Period size: 21 Copynumber: 4.0 Consensus size: 21
2773987 GCTATACTGA
* *
2773997 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTCATGTGTCG--TT
*
2774020 TCAGGCACCTCGTGTGTCGTT
1 TCAGGCACCTCATGTGTCGTT
*
2774041 TCAGGCACCTCGTGTGTCGTT
1 TCAGGCACCTCATGTGTCGTT
*
2774062 TCAGGCA-CTTATGTGTCGT
1 TCAGGCACCTCATGTGTCGT
2774081 ATACTGATCA
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
20 10 0.18
21 30 0.54
23 16 0.29
ACGTcount: A:0.13, C:0.24, G:0.26, T:0.37
Consensus pattern (21 bp):
TCAGGCACCTCATGTGTCGTT
Found at i:2774042 original size:21 final size:21
Alignment explanation
Indices: 2774009--2774069 Score: 104
Period size: 21 Copynumber: 2.8 Consensus size: 21
2773999 AGGCACTTTA
2774009 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCG--TTTCAGGCACCTCG
2774032 TGTGTCGTTTCAGGCACCTCG
1 TGTGTCGTTTCAGGCACCTCG
2774053 TGTGTCGTTTCAGGCAC
1 TGTGTCGTTTCAGGCAC
2774070 TTATGTGTCG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
21 31 0.82
23 7 0.18
ACGTcount: A:0.11, C:0.26, G:0.28, T:0.34
Consensus pattern (21 bp):
TGTGTCGTTTCAGGCACCTCG
Found at i:2775319 original size:46 final size:48
Alignment explanation
Indices: 2775161--2775347 Score: 163
Period size: 46 Copynumber: 3.9 Consensus size: 48
2775151 TGGTTGGACC
2775161 ATGGCATCA-A-TGTGATATGTGA-TCTGTGTAAGACCATAGCTGGGCT
1 ATGGCATCAGAGTGTGATATGTGATTC-GTGTAAGACCATAGCTGGGCT
* * * * *
2775207 ATGGCATCAGAGATATGTGATTACGTGCTTCCGTATAAGACCATATCTGGGAT
1 ATGGCATCAGAG---TGTGA-TATGTGATT-CGTGTAAGACCATAGCTGGGCT
*
2775260 ATGGCATC--AGTGTGATATGTGATTCGTGTAAGACCATGGCTGGGCT
1 ATGGCATCAGAGTGTGATATGTGATTCGTGTAAGACCATAGCTGGGCT
* * *
2775306 ATGGC-TACGGTGTGTGATATGTGACTAT-GTGCAAGACCATAG
1 ATGGCAT-CAGAGTGTGATATGTGA-T-TCGTGTAAGACCATAG
2775348 TTTTACTATG
Statistics
Matches: 114, Mismatches: 14, Indels: 23
0.75 0.09 0.15
Matches are distributed among these distances:
45 1 0.01
46 33 0.29
47 8 0.07
48 18 0.16
49 13 0.11
50 1 0.01
51 7 0.06
52 5 0.04
53 27 0.24
54 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.30
Consensus pattern (48 bp):
ATGGCATCAGAGTGTGATATGTGATTCGTGTAAGACCATAGCTGGGCT
Found at i:2779929 original size:16 final size:17
Alignment explanation
Indices: 2779891--2779931 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
2779881 TCCAAACTTG
*
2779891 AAAATAATTTAAAACTC
1 AAAATGATTTAAAACTC
*
2779908 AAAATGATTTAAAA-TT
1 AAAATGATTTAAAACTC
2779924 AAAATGAT
1 AAAATGAT
2779932 CCAAACCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.32
Consensus pattern (17 bp):
AAAATGATTTAAAACTC
Found at i:2787256 original size:51 final size:51
Alignment explanation
Indices: 2787185--2787298 Score: 183
Period size: 51 Copynumber: 2.2 Consensus size: 51
2787175 CTGATCACAT
* *
2787185 TTATCACTTGTCACTGATCAGATAATTGTAGTTAAAACTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
*
2787236 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
* *
2787287 TTGTCGCTTGTC
1 TTATCACTTGTC
2787299 GCTTGTCACT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 58 1.00
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (51 bp):
TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
Found at i:2787321 original size:14 final size:14
Alignment explanation
Indices: 2787277--2787327 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
2787267 CTAAAGCTAC
2787277 CACTTATCACTTGT
1 CACTTATCACTTGT
* * *
2787291 CGCTTGTCGCTTGT
1 CACTTATCACTTGT
*
2787305 CACTTATCACTTAT
1 CACTTATCACTTGT
*
2787319 CACTGATCA
1 CACTTATCA
2787328 GATAAGTGTA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.20, C:0.29, G:0.12, T:0.39
Consensus pattern (14 bp):
CACTTATCACTTGT
Found at i:2793707 original size:17 final size:17
Alignment explanation
Indices: 2793685--2793718 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2793675 ATCCACTAAT
*
2793685 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
2793702 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
2793719 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:2798346 original size:17 final size:17
Alignment explanation
Indices: 2798324--2798357 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2798314 ATCCACTAAT
*
2798324 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
2798341 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
2798358 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:2798845 original size:24 final size:25
Alignment explanation
Indices: 2798818--2798874 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
2798808 TAACTACATA
2798818 ATATATATAAA-TTTAAAATATA-TG
1 ATATATATAAACTTTAAAATA-ACTG
*
2798842 ATATGTA-AAACTTTAAAATAACTG
1 ATATATATAAACTTTAAAATAACTG
*
2798866 GTATATATA
1 ATATATATA
2798875 TATATATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
23 4 0.15
24 22 0.81
25 1 0.04
ACGTcount: A:0.51, C:0.04, G:0.07, T:0.39
Consensus pattern (25 bp):
ATATATATAAACTTTAAAATAACTG
Found at i:2809688 original size:18 final size:18
Alignment explanation
Indices: 2809651--2809689 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
2809641 CAATCCCAAC
* *
2809651 TACTGTATATGTGAACAG
1 TACTGTATACGTAAACAG
*
2809669 TACTGTATACGTAAATAG
1 TACTGTATACGTAAACAG
2809687 TAC
1 TAC
2809690 CATATATATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (18 bp):
TACTGTATACGTAAACAG
Found at i:2810722 original size:14 final size:14
Alignment explanation
Indices: 2810703--2810731 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2810693 AATATAGAAG
2810703 TATGATTCTAAGTT
1 TATGATTCTAAGTT
2810717 TATGATTCTAAGTT
1 TATGATTCTAAGTT
2810731 T
1 T
2810732 TCCTTAAGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.07, G:0.14, T:0.52
Consensus pattern (14 bp):
TATGATTCTAAGTT
Found at i:2814575 original size:35 final size:35
Alignment explanation
Indices: 2814536--2814607 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
2814526 GTCTCAACAC
2814536 TATATTCTCTATCCGCAAAACTAAACTCAAAATCT
1 TATATTCTCTATCCGCAAAACTAAACTCAAAATCT
2814571 TATATTCTCTATCCGCAAAACTAAACTCAAAATCT
1 TATATTCTCTATCCGCAAAACTAAACTCAAAATCT
2814606 TA
1 TA
2814608 GTTAAGGAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.40, C:0.25, G:0.03, T:0.32
Consensus pattern (35 bp):
TATATTCTCTATCCGCAAAACTAAACTCAAAATCT
Found at i:2816579 original size:29 final size:29
Alignment explanation
Indices: 2816546--2816601 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
2816536 CTTCAATTGG
2816546 TGGGAACGTATATTTCCTTGAATTGTTGA
1 TGGGAACGTATATTTCCTTGAATTGTTGA
*
2816575 TGGGAATGTATATTTCCTTGAATTGTT
1 TGGGAACGTATATTTCCTTGAATTGTT
2816602 CTCGAATAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.23, C:0.09, G:0.23, T:0.45
Consensus pattern (29 bp):
TGGGAACGTATATTTCCTTGAATTGTTGA
Found at i:2819715 original size:61 final size:61
Alignment explanation
Indices: 2819620--2819741 Score: 235
Period size: 61 Copynumber: 2.0 Consensus size: 61
2819610 AAAGTTCAAT
*
2819620 CGGTGTTAAACTCGAGCAGCTTCCACTATTCAATTTCGAACAACTTGCCACCGCGACCAAC
1 CGGTGTTAAACCCGAGCAGCTTCCACTATTCAATTTCGAACAACTTGCCACCGCGACCAAC
2819681 CGGTGTTAAACCCGAGCAGCTTCCACTATTCAATTTCGAACAACTTGCCACCGCGACCAAC
1 CGGTGTTAAACCCGAGCAGCTTCCACTATTCAATTTCGAACAACTTGCCACCGCGACCAAC
2819742 AACTTCCATC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.28, C:0.34, G:0.16, T:0.22
Consensus pattern (61 bp):
CGGTGTTAAACCCGAGCAGCTTCCACTATTCAATTTCGAACAACTTGCCACCGCGACCAAC
Found at i:2820737 original size:20 final size:20
Alignment explanation
Indices: 2820714--2820751 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2820704 GCTGTCTACA
*
2820714 TTTTTTTTTTGAATTTTCAC
1 TTTTTTATTTGAATTTTCAC
2820734 TTTTTTATTTGAATTTTC
1 TTTTTTATTTGAATTTTC
2820752 TCTCTCTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.08, G:0.05, T:0.71
Consensus pattern (20 bp):
TTTTTTATTTGAATTTTCAC
Found at i:2824102 original size:16 final size:17
Alignment explanation
Indices: 2824073--2824108 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
2824063 TTAAATTGAT
*
2824073 TTTTTTAATCTTTAAAA
1 TTTTTGAATCTTTAAAA
2824090 TTTTTGAAT-TTTAAAA
1 TTTTTGAATCTTTAAAA
2824106 TTT
1 TTT
2824109 AATCCTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (17 bp):
TTTTTGAATCTTTAAAA
Found at i:2831642 original size:125 final size:125
Alignment explanation
Indices: 2831418--2831668 Score: 493
Period size: 125 Copynumber: 2.0 Consensus size: 125
2831408 CATATAAAAA
2831418 TTGAATTTTCTCAAATATTAACTCGTTCTTAAACTTCATTCGTTAATAATAGTAACACAATTTCA
1 TTGAATTTTCTCAAATATTAACTCGTTCTTAAACTTCATTCGTTAATAATAGTAACACAATTTCA
*
2831483 ACTATTTATCAATTTCAATCAAATATCATGGACTTCAATTTTCTTCACTACATCAACGTT
66 ACTATTTATCAATTTCAATCAAATATCATAGACTTCAATTTTCTTCACTACATCAACGTT
2831543 TTGAATTTTCTCAAATATTAACTCGTTCTTAAACTTCATTCGTTAATAATAGTAACACAATTTCA
1 TTGAATTTTCTCAAATATTAACTCGTTCTTAAACTTCATTCGTTAATAATAGTAACACAATTTCA
2831608 ACTATTTATCAATTTCAATCAAATATCATAGACTTCAATTTTCTTCACTACATCAACGTT
66 ACTATTTATCAATTTCAATCAAATATCATAGACTTCAATTTTCTTCACTACATCAACGTT
2831668 T
1 T
2831669 AGTTCATGCC
Statistics
Matches: 125, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
125 125 1.00
ACGTcount: A:0.35, C:0.19, G:0.05, T:0.41
Consensus pattern (125 bp):
TTGAATTTTCTCAAATATTAACTCGTTCTTAAACTTCATTCGTTAATAATAGTAACACAATTTCA
ACTATTTATCAATTTCAATCAAATATCATAGACTTCAATTTTCTTCACTACATCAACGTT
Found at i:2832587 original size:22 final size:24
Alignment explanation
Indices: 2832545--2832588 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
2832535 TAAATAAGTT
2832545 TACTTACTTTTCTAACTTAATTCA
1 TACTTACTTTTCTAACTTAATTCA
2832569 TACTT-CTTTTCT-ACTTAATT
1 TACTTACTTTTCTAACTTAATT
2832589 TCTTGCCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.40
23 7 0.35
24 5 0.25
ACGTcount: A:0.25, C:0.20, G:0.00, T:0.55
Consensus pattern (24 bp):
TACTTACTTTTCTAACTTAATTCA
Found at i:2833315 original size:19 final size:18
Alignment explanation
Indices: 2833288--2833323 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2833278 TTTATTCATT
*
2833288 AATTTAATAATATAATATC
1 AATTAAATAATA-AATATC
2833307 AATTAAATAATAAATAT
1 AATTAAATAATAAATAT
2833324 AATAAGTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
AATTAAATAATAAATATC
Found at i:2839213 original size:22 final size:23
Alignment explanation
Indices: 2839188--2839236 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
2839178 ATTTTCTTAT
* *
2839188 TATTTTC-CTCCTATTTTGCTAC
1 TATTTTCACTACTATGTTGCTAC
*
2839210 TA-TTTCACTATTATGTTGCTAC
1 TATTTTCACTACTATGTTGCTAC
2839232 TATTT
1 TATTT
2839237 GTTGTTGTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 4 0.18
22 16 0.73
23 2 0.09
ACGTcount: A:0.18, C:0.20, G:0.06, T:0.55
Consensus pattern (23 bp):
TATTTTCACTACTATGTTGCTAC
Found at i:2839636 original size:44 final size:44
Alignment explanation
Indices: 2839573--2839661 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
2839563 GCACCTCTAC
2839573 TACCAACATATATTTACTCAAACTTATCCAAACTTGAATTAATA
1 TACCAACATATATTTACTCAAACTTATCCAAACTTGAATTAATA
2839617 TACCAACATATATTTACTCAAACTTATCCAAACTTGAATTAATA
1 TACCAACATATATTTACTCAAACTTATCCAAACTTGAATTAATA
2839661 T
1 T
2839662 CTCTTTAACA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.43, C:0.20, G:0.02, T:0.35
Consensus pattern (44 bp):
TACCAACATATATTTACTCAAACTTATCCAAACTTGAATTAATA
Found at i:2843814 original size:21 final size:20
Alignment explanation
Indices: 2843790--2843828 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2843780 GCTGTCTATA
*
2843790 TTTTTTTTTCTGAATTTTCAC
1 TTTTTTCTT-TGAATTTTCAC
2843811 TTTTTTCTTTGAATTTTC
1 TTTTTTCTTTGAATTTTC
2843829 TCTCTCTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.13, C:0.13, G:0.05, T:0.69
Consensus pattern (20 bp):
TTTTTTCTTTGAATTTTCAC
Found at i:2845972 original size:16 final size:17
Alignment explanation
Indices: 2845947--2845989 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
2845937 AATATAATCT
2845947 AAACTC-AAAATGATGC
1 AAACTCAAAAATGATGC
* *
2845963 AAACTTAAAAATGATTC
1 AAACTCAAAAATGATGC
*
2845980 AAAATCAAAA
1 AAACTCAAAA
2845990 TATTCAAGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.58, C:0.14, G:0.07, T:0.21
Consensus pattern (17 bp):
AAACTCAAAAATGATGC
Found at i:2849528 original size:21 final size:21
Alignment explanation
Indices: 2849479--2849537 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
2849469 ATAATAAATT
*
2849479 AAAT-ATATTTAAAA-ACATAA
1 AAATAATA-TTAAAACAAATAA
*
2849499 AAACAAATATTAAAACAAATAA
1 AAA-TAATATTAAAACAAATAA
*
2849521 AAATAATACTAAAACAA
1 AAATAATATTAAAACAA
2849538 TTCTTAAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 3 0.09
21 18 0.56
22 11 0.34
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.22
Consensus pattern (21 bp):
AAATAATATTAAAACAAATAA
Found at i:2849620 original size:16 final size:17
Alignment explanation
Indices: 2849581--2849635 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
2849571 AAAAAATGGT
2849581 TATATTAAAAATTTAAAA
1 TATATTAAAAA-TTAAAA
*
2849599 T-GATTAAAAA-TAAAA
1 TATATTAAAAATTAAAA
* *
2849614 TATATTAATATATTAATA
1 TATATTAA-AAATTAAAA
2849632 TATA
1 TATA
2849636 ATTCGGGCCG
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
15 6 0.20
16 5 0.17
17 10 0.33
18 9 0.30
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (17 bp):
TATATTAAAAATTAAAA
Found at i:2850236 original size:17 final size:17
Alignment explanation
Indices: 2850188--2850239 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 17
2850178 TTGGTAGAGG
2850188 GGAA-AGAAAATTAGAA
1 GGAATAGAAAATTAGAA
*
2850204 -GAATAAAAAATT-GAA
1 GGAATAGAAAATTAGAA
**
2850219 GGGGTAGAAAATTAGAA
1 GGAATAGAAAATTAGAA
2850236 GGAA
1 GGAA
2850240 AGATGTGTAG
Statistics
Matches: 27, Mismatches: 6, Indels: 5
0.71 0.16 0.13
Matches are distributed among these distances:
15 6 0.22
16 16 0.59
17 5 0.19
ACGTcount: A:0.58, C:0.00, G:0.27, T:0.15
Consensus pattern (17 bp):
GGAATAGAAAATTAGAA
Found at i:2860741 original size:40 final size:40
Alignment explanation
Indices: 2860697--2860783 Score: 138
Period size: 40 Copynumber: 2.2 Consensus size: 40
2860687 GTTTTAATGG
* *
2860697 AAAACGCCGCTAAAGGACGAGCATTAGCGGCGCTTTTTGA
1 AAAACGCCGCTAAAGAACGAGCATTAGCGGCGCTTTTTAA
* *
2860737 AAAACACCGCTAAAGAACGAGTATTAGCGGCGCTTTTTAA
1 AAAACGCCGCTAAAGAACGAGCATTAGCGGCGCTTTTTAA
2860777 AAAACGC
1 AAAACGC
2860784 TACTATAGGT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.20
Consensus pattern (40 bp):
AAAACGCCGCTAAAGAACGAGCATTAGCGGCGCTTTTTAA
Found at i:2861391 original size:22 final size:22
Alignment explanation
Indices: 2861366--2861410 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2861356 GAGTTACTAT
* *
2861366 TTTAAGGTTTATGCTTTATGGG
1 TTTAAGGATTATGCTTTAAGGG
* *
2861388 TTTAGGGATTATGGTTTAAGGG
1 TTTAAGGATTATGCTTTAAGGG
2861410 T
1 T
2861411 GGTTTAAGGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.20, C:0.02, G:0.31, T:0.47
Consensus pattern (22 bp):
TTTAAGGATTATGCTTTAAGGG
Found at i:2861499 original size:22 final size:21
Alignment explanation
Indices: 2861461--2861517 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
2861451 CATGGTTCAG
* *
2861461 GGTTTATGTTTTA-TGATTTAA
1 GGTTTAAGGTTTAGTGA-TTAA
*
2861482 GGTTTAAGGTTTAGTGATTAG
1 GGTTTAAGGTTTAGTGATTAA
*
2861503 GAGTTTAGGGTTTAG
1 G-GTTTAAGGTTTAG
2861518 ATTAATTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 15 0.50
22 15 0.50
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (21 bp):
GGTTTAAGGTTTAGTGATTAA
Found at i:2861514 original size:29 final size:28
Alignment explanation
Indices: 2861425--2861516 Score: 78
Period size: 29 Copynumber: 3.2 Consensus size: 28
2861415 TAAGGGTTGC
* * *
2861425 GGTTTAAGGTTTAGGTGTTAGGGGTTCAT
1 GGTTTAAGGTTTA-GTGTTAGGAGTTTAA
* * * *
2861454 GGTTCAGGGTTTATGTTTTATGA-TTTAA
1 GGTTTAAGGTTTA-GTGTTAGGAGTTTAA
*
2861482 GGTTTAAGGTTTAGTGATTAGGAGTTTAG
1 GGTTTAAGGTTTAGTG-TTAGGAGTTTAA
2861511 GGTTTA
1 GGTTTA
2861517 GATTAATTAA
Statistics
Matches: 48, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
27 2 0.04
28 19 0.40
29 27 0.56
ACGTcount: A:0.21, C:0.02, G:0.33, T:0.45
Consensus pattern (28 bp):
GGTTTAAGGTTTAGTGTTAGGAGTTTAA
Found at i:2861655 original size:20 final size:21
Alignment explanation
Indices: 2861630--2861668 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
2861620 AGGGTTTATA
2861630 GTTTAAAGTG-ATGAGTTAGG
1 GTTTAAAGTGTATGAGTTAGG
2861650 GTTTAAAGTGTATGAGTTA
1 GTTTAAAGTGTATGAGTTA
2861669 CTATTTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.31, C:0.00, G:0.31, T:0.38
Consensus pattern (21 bp):
GTTTAAAGTGTATGAGTTAGG
Found at i:2861698 original size:22 final size:21
Alignment explanation
Indices: 2861673--2861722 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
2861663 GAGTTACTAT
*
2861673 TTTAAGGTTTATGAATTATGGG
1 TTTAAGGATTATGAATTAT-GG
* **
2861695 TTTAGGGATTATGGTTTATGG
1 TTTAAGGATTATGAATTATGG
2861716 TTTAAGG
1 TTTAAGG
2861723 GTTGGGGTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.24, C:0.00, G:0.30, T:0.46
Consensus pattern (21 bp):
TTTAAGGATTATGAATTATGG
Found at i:2861755 original size:21 final size:21
Alignment explanation
Indices: 2861721--2861763 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
2861711 TATGGTTTAA
2861721 GGGTTGGGGTTTAA-AGCTTAG
1 GGGTTGGGGTTTAAGAG-TTAG
2861742 GGGTTAGGGG-TTAAGAGTTAG
1 GGGTT-GGGGTTTAAGAGTTAG
2861763 G
1 G
2861764 TTTTAGAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.21, C:0.02, G:0.47, T:0.30
Consensus pattern (21 bp):
GGGTTGGGGTTTAAGAGTTAG
Found at i:2861791 original size:301 final size:299
Alignment explanation
Indices: 2861228--2861794 Score: 797
Period size: 301 Copynumber: 1.9 Consensus size: 299
2861218 TGACTGATTG
*
2861228 TTTTTAAATTTATATGTTAAATATTTTCTTATATAATTGTAAAAGAGATAGTATTAATTTTAAAA
1 TTTTTAAATTTATATGATAAATATTTTCTTATATAATTGTAAAAGAGATAGTATTAATTTTAAAA
* * * *
2861293 TATTGAACTAATTATCATTATAGTTTAGGGTTTACAATATATGGTTAAGGGTTTAATGTTTATGA
66 TATTAAACTAATTATCATTATAGTTTAGGGTTTACAAAATATGGTTAAGGGTTTAAAGTGTATGA
**
2861358 GTTACTATTTTAAGGTTTATGCTTTATGGGTTTAGGGATTATGGTTTAAGGGTGGTTTAAGGGTT
131 GTTACTATTTTAAGGTTTATGAATTATGGGTTTAGGGATTATGGTTTAA--GTGGTTTAAGGGTT
* * * * ** *
2861423 GCGGTTTAAGGTTTAGGTGTTAGGGGTTCATGGTTCAGGGTTTATGTTTTATGATTTAAGGTTTA
194 GCGGTTTAAAGCTTAGGGGTTAGGGGTTCAAGGTTCAGGGTTTATGGATTATGATTTAAGATTTA
2861488 AGGTTTAGTGATTAGGAGTTTAGGGTTTAGATTAATTAATA
259 AGGTTTAGTGATTAGGAGTTTAGGGTTTAGATTAATTAATA
*
2861529 TTTTTTAATTTATATGATAAATATTTTCTTATATAATTGTAAAAGAGATAGTATTAATTTTAAAA
1 TTTTTAAATTTATATGATAAATATTTTCTTATATAATTGTAAAAGAGATAGTATTAATTTTAAAA
* *
2861594 TATTAAATTAATTATCATTATAGTTTAGGGTTTATAGTTTAAAGTGATGAGTT-AGGGTTTAAAG
66 TATTAAACTAATTATCATTATAGTTTAGGGTTTACA----AAA-T-ATG-GTTAAGGGTTTAAAG
2861658 TGTATGAGTTACTATTTTAAGGTTTATGAATTATGGGTTTAGGGATTATGGTTT-A-TGGTTTAA
124 TGTATGAGTTACTATTTTAAGGTTTATGAATTATGGGTTTAGGGATTATGGTTTAAGTGGTTTAA
* *
2861721 GGGTTGGGGTTTAAAGCTTAGGGGTTAGGGGTT-AAGAGTT-AGGTTTTA-GAGATTATG-TTTA
189 GGGTTGCGGTTTAAAGCTTAGGGGTTAGGGGTTCAAG-GTTCAGGGTTTATG-GATTATGATTTA
**
2861782 TTATTTAAGGTTT
252 AGATTTAAGGTTT
2861795 TGGGGGTAGG
Statistics
Matches: 236, Mismatches: 21, Indels: 18
0.86 0.08 0.07
Matches are distributed among these distances:
301 111 0.47
302 14 0.06
303 40 0.17
305 2 0.01
306 2 0.01
307 64 0.27
308 3 0.01
ACGTcount: A:0.30, C:0.02, G:0.23, T:0.46
Consensus pattern (299 bp):
TTTTTAAATTTATATGATAAATATTTTCTTATATAATTGTAAAAGAGATAGTATTAATTTTAAAA
TATTAAACTAATTATCATTATAGTTTAGGGTTTACAAAATATGGTTAAGGGTTTAAAGTGTATGA
GTTACTATTTTAAGGTTTATGAATTATGGGTTTAGGGATTATGGTTTAAGTGGTTTAAGGGTTGC
GGTTTAAAGCTTAGGGGTTAGGGGTTCAAGGTTCAGGGTTTATGGATTATGATTTAAGATTTAAG
GTTTAGTGATTAGGAGTTTAGGGTTTAGATTAATTAATA
Found at i:2861976 original size:58 final size:59
Alignment explanation
Indices: 2861882--2862010 Score: 192
Period size: 58 Copynumber: 2.2 Consensus size: 59
2861872 TTATTCATTT
* *
2861882 CCCCTTTCTCCCCAGTTTATTTCCCCCATTTTCCCTAATTCGAATCCCTAAAATAATCA
1 CCCCTTTCTCCCCAGTTTATTTCCCCCATTTCCCCTAATCCGAATCCCTAAAATAATCA
*
2861941 CCCC-TTCTCTCCAGTTTATTT-CCCCACTTTCCCCTAATCCGAATCCCTAAAATAATCA
1 CCCCTTTCTCCCCAGTTTATTTCCCCCA-TTTCCCCTAATCCGAATCCCTAAAATAATCA
*
2861999 CCCATTT-TCCCC
1 CCCCTTTCTCCCC
2862011 CAATTTAAAC
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
57 5 0.08
58 52 0.83
59 6 0.10
ACGTcount: A:0.22, C:0.40, G:0.03, T:0.34
Consensus pattern (59 bp):
CCCCTTTCTCCCCAGTTTATTTCCCCCATTTCCCCTAATCCGAATCCCTAAAATAATCA
Found at i:2862310 original size:8 final size:8
Alignment explanation
Indices: 2862292--2862356 Score: 73
Period size: 7 Copynumber: 8.2 Consensus size: 8
2862282 AAATCTTCAA
2862292 AAAAAATTT
1 AAAAAA-TT
2862301 AAAAAATT
1 AAAAAATT
2862309 -AAAAATT
1 AAAAAATT
2862316 -AAAAATT
1 AAAAAATT
2862323 -AAAAATT
1 AAAAAATT
2862330 AAAAAACTT
1 AAAAAA-TT
*
2862339 AAAAACTT
1 AAAAAATT
*
2862347 AAAAATTT
1 AAAAAATT
2862355 AA
1 AA
2862357 TATTTAATAT
Statistics
Matches: 52, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
7 21 0.40
8 18 0.35
9 13 0.25
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (8 bp):
AAAAAATT
Found at i:2862312 original size:7 final size:7
Alignment explanation
Indices: 2862302--2862353 Score: 77
Period size: 7 Copynumber: 7.0 Consensus size: 7
2862292 AAAAAATTTA
2862302 AAAAATT
1 AAAAATT
2862309 AAAAATT
1 AAAAATT
2862316 AAAAATT
1 AAAAATT
2862323 AAAAATT
1 AAAAATT
2862330 AAAAAACTT
1 -AAAAA-TT
2862339 AAAAACTT
1 AAAAA-TT
2862347 AAAAATT
1 AAAAATT
2862354 TAATATTTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
7 23 0.53
8 18 0.42
9 2 0.05
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (7 bp):
AAAAATT
Found at i:2862314 original size:16 final size:15
Alignment explanation
Indices: 2862293--2862356 Score: 85
Period size: 16 Copynumber: 4.1 Consensus size: 15
2862283 AATCTTCAAA
2862293 AAAAATTTAAAAAATT
1 AAAAA-TTAAAAAATT
2862309 AAAAATT-AAAAATT
1 AAAAATTAAAAAATT
2862323 AAAAATTAAAAAACTT
1 AAAAATTAAAAAA-TT
*
2862339 AAAAACTTAAAAATTT
1 AAAAA-TTAAAAAATT
2862355 AA
1 AA
2862357 TATTTAATAT
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
14 14 0.32
15 7 0.16
16 16 0.36
17 7 0.16
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (15 bp):
AAAAATTAAAAAATT
Found at i:2865823 original size:6 final size:6
Alignment explanation
Indices: 2865783--2865836 Score: 56
Period size: 6 Copynumber: 8.7 Consensus size: 6
2865773 ATTTAATCTA
* *
2865783 ATTTTT ATTATTT A-TTTT AGTTTTG ATTCTAT ATTTTT ATTTTT ATTTTT
1 ATTTTT ATT-TTT ATTTTT A-TTTTT ATT-TTT ATTTTT ATTTTT ATTTTT
2865833 ATTT
1 ATTT
2865837 GATAATGAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 4 0.10
6 24 0.60
7 12 0.30
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.74
Consensus pattern (6 bp):
ATTTTT
Found at i:2869088 original size:14 final size:14
Alignment explanation
Indices: 2869069--2869098 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2869059 TATTTTCAAG
2869069 ATAGATTAACGCAT
1 ATAGATTAACGCAT
*
2869083 ATAGATTCACGCAT
1 ATAGATTAACGCAT
2869097 AT
1 AT
2869099 TTATAAGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (14 bp):
ATAGATTAACGCAT
Found at i:2871774 original size:25 final size:27
Alignment explanation
Indices: 2871746--2871797 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
2871736 AATCAGTAAA
*
2871746 ATTTTTCTATCA-AT-ATTTTCATACG
1 ATTTTCCTATCATATAATTTTCATACG
2871771 ATTTTCCTATCATATCAATTTTCATAC
1 ATTTTCCTATCATAT-AATTTTCATAC
2871798 AAAAATATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 11 0.48
26 2 0.09
28 10 0.43
ACGTcount: A:0.29, C:0.19, G:0.02, T:0.50
Consensus pattern (27 bp):
ATTTTCCTATCATATAATTTTCATACG
Found at i:2877412 original size:29 final size:30
Alignment explanation
Indices: 2877336--2877413 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 30
2877326 TTTAACGGAA
* *
2877336 GAGTGACTAAAATATTAAATTTTGATAACGT
1 GAGTGACTAAAATA-GAAATTTTGATAACCT
* * *
2877367 TAGTAACTAAAATAGAAATTTTTA-AACCT
1 GAGTGACTAAAATAGAAATTTTGATAACCT
*
2877396 GAGTGACTAAAACAGAAA
1 GAGTGACTAAAATAGAAA
2877414 CACACTAATA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 19 0.49
30 8 0.21
31 12 0.31
ACGTcount: A:0.47, C:0.09, G:0.14, T:0.29
Consensus pattern (30 bp):
GAGTGACTAAAATAGAAATTTTGATAACCT
Found at i:2878774 original size:21 final size:21
Alignment explanation
Indices: 2878748--2878803 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
2878738 AACAGCGGTG
*
2878748 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
* *
2878769 GCGGTGAGATTGGATATTGTA
1 GCGGTGAGATTAGATACTGTA
2878790 GCGGTGAGATTAGA
1 GCGGTGAGATTAGA
2878804 AACAGCGGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.25, C:0.07, G:0.38, T:0.30
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:2879043 original size:18 final size:18
Alignment explanation
Indices: 2879020--2879102 Score: 70
Period size: 18 Copynumber: 4.8 Consensus size: 18
2879010 TATTTTAATG
2879020 AATTATATAATCAATTTA
1 AATTATATAATCAATTTA
* *
2879038 AATTAT-TTATTAGA--TA
1 AATTATATAATCA-ATTTA
*
2879054 AA--ATGATAAT-AATTTTT
1 AATTAT-ATAATCAA-TTTA
2879071 AATTATATAATCAATTTA
1 AATTATATAATCAATTTA
2879089 AATTATATAATCAA
1 AATTATATAATCAA
2879103 CAGGCCAGGG
Statistics
Matches: 51, Mismatches: 5, Indels: 18
0.69 0.07 0.24
Matches are distributed among these distances:
14 3 0.06
15 1 0.02
16 7 0.14
17 7 0.14
18 29 0.57
19 4 0.08
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (18 bp):
AATTATATAATCAATTTA
Found at i:2881211 original size:18 final size:17
Alignment explanation
Indices: 2881188--2881230 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
2881178 ATCGTGTTTG
2881188 ATTTTTATTTCTAAATTT
1 ATTTTTATTT-TAAATTT
*
2881206 ATTTTTGATTTTAGATTT
1 ATTTTT-ATTTTAAATTT
*
2881224 ATCTTTA
1 ATTTTTA
2881231 ACATATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 1 0.05
18 17 0.77
19 4 0.18
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.65
Consensus pattern (17 bp):
ATTTTTATTTTAAATTT
Found at i:2886248 original size:47 final size:49
Alignment explanation
Indices: 2886171--2886266 Score: 142
Period size: 47 Copynumber: 2.0 Consensus size: 49
2886161 TATTTATTTT
* * *
2886171 TGTTAAAAGGTGGCAACAAACAGCATATGT-A-TTATCCGGATGAAATA
1 TGTTAAAAGGTGGCAACAAACAGCACATGTAAGTTACCCGGACGAAATA
*
2886218 TGTTAAAAGGTGGCAACAAATAGCACATGTAAGTTACCCGGACGAAATA
1 TGTTAAAAGGTGGCAACAAACAGCACATGTAAGTTACCCGGACGAAATA
2886267 CAGCAACATG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
47 28 0.65
48 1 0.02
49 14 0.33
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.23
Consensus pattern (49 bp):
TGTTAAAAGGTGGCAACAAACAGCACATGTAAGTTACCCGGACGAAATA
Found at i:2895445 original size:46 final size:46
Alignment explanation
Indices: 2895393--2895706 Score: 405
Period size: 46 Copynumber: 6.8 Consensus size: 46
2895383 AGTGTGCTCT
* ** **
2895393 CTGATATGGAATGTGTAAGACCATGGTTGAAAGATACCATTACAAC
1 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
**
2895439 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
* ** *
2895485 GTGATATGAAATGTGTAAGACCATGGTTGAAAGATACAATGGCAAC
1 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
*
2895531 GTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
2895577 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
* ***
2895623 ATGACGGGAAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATG-AAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
2895670 ATGACA-GAAAACGAGTAAAACCATAGTTGAAAGATAC
1 CTGATATG-AAATGAATAAGACCATGGTTGAAAGATAC
2895707 TATGACATCA
Statistics
Matches: 249, Mismatches: 18, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
46 206 0.83
47 43 0.17
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:2898930 original size:49 final size:49
Alignment explanation
Indices: 2898858--2898955 Score: 153
Period size: 49 Copynumber: 2.0 Consensus size: 49
2898848 CAAGGAGGAG
* *
2898858 TGTTAAAAGGTGGCAACAAACAGCATATGTACGTTA-TCCGGATGAAATA
1 TGTTAAAAGGTGGCAACAAACAGCACATGTAAGTTACT-CGGATGAAATA
*
2898907 TGTTAAATGGTGGCAACAAACAGCACATGTAAGTTACTCGGATGAAATA
1 TGTTAAAAGGTGGCAACAAACAGCACATGTAAGTTACTCGGATGAAATA
2898956 CAGCAACATG
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
49 44 0.98
50 1 0.02
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.24
Consensus pattern (49 bp):
TGTTAAAAGGTGGCAACAAACAGCACATGTAAGTTACTCGGATGAAATA
Found at i:2900739 original size:22 final size:22
Alignment explanation
Indices: 2900696--2900760 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 22
2900686 TAAATCTTAA
2900696 AAAAAATTATGTTTTATA--TTTT
1 AAAAAA-TAT-TTTTATATTTTTT
* *
2900718 AAATAATTTTTTTATATTTTTT
1 AAAAAATATTTTTATATTTTTT
*
2900740 AAAAAATATTATTATTATTTT
1 AAAAAATATTTTTA-TATTTT
2900761 CACAGCAGTC
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
20 7 0.20
21 2 0.06
22 20 0.57
23 6 0.17
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
AAAAAATATTTTTATATTTTTT
Found at i:2902884 original size:20 final size:20
Alignment explanation
Indices: 2902859--2902908 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
2902849 TGGCTTAAAA
2902859 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
2902879 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
2902896 GTGGTAGTGGATT
1 TTGGTAGTGGATT
2902909 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:2907523 original size:20 final size:20
Alignment explanation
Indices: 2907498--2907547 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
2907488 TGGCTTAAAA
2907498 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
2907518 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
2907535 GTGGTAGTGGATT
1 TTGGTAGTGGATT
2907548 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:2908086 original size:11 final size:12
Alignment explanation
Indices: 2908065--2908094 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
2908055 TTAGATTATA
2908065 AAAATATATTTT
1 AAAATATATTTT
2908077 AAAA-ATATTTT
1 AAAATATATTTT
2908088 AAAATAT
1 AAAATAT
2908095 CAATAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
AAAATATATTTT
Found at i:2908147 original size:15 final size:15
Alignment explanation
Indices: 2908127--2908157 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2908117 TAAAATATGT
2908127 TAATATCGATACATA
1 TAATATCGATACATA
*
2908142 TAATATCTATACATA
1 TAATATCGATACATA
2908157 T
1 T
2908158 CAGTATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.13, G:0.03, T:0.39
Consensus pattern (15 bp):
TAATATCGATACATA
Found at i:2908745 original size:23 final size:23
Alignment explanation
Indices: 2908719--2908764 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
2908709 TGGTTAGTAA
2908719 CTTATTTTAATCCTGTTTTATTT
1 CTTATTTTAATCCTGTTTTATTT
2908742 CTTATTTTAATCCTGTTTTATTT
1 CTTATTTTAATCCTGTTTTATTT
2908765 TCTTGTGACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.17, C:0.13, G:0.04, T:0.65
Consensus pattern (23 bp):
CTTATTTTAATCCTGTTTTATTT
Found at i:2913098 original size:13 final size:13
Alignment explanation
Indices: 2913080--2913104 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2913070 TAAATCTTAA
2913080 AAAATATAAAATT
1 AAAATATAAAATT
2913093 AAAATATAAAAT
1 AAAATATAAAAT
2913105 ATTATTTTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAATATAAAATT
Found at i:2914767 original size:13 final size:15
Alignment explanation
Indices: 2914749--2914782 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
2914739 CCTAGGAATA
2914749 TAGAGG-AA-TGGAG
1 TAGAGGTAATTGGAG
2914762 TAGAGGTAATTGGAG
1 TAGAGGTAATTGGAG
2914777 TAGAGG
1 TAGAGG
2914783 GTGTTTTAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.32
14 2 0.11
15 11 0.58
ACGTcount: A:0.35, C:0.00, G:0.44, T:0.21
Consensus pattern (15 bp):
TAGAGGTAATTGGAG
Found at i:2917288 original size:21 final size:21
Alignment explanation
Indices: 2917262--2917302 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2917252 ATCTGCTCAA
* *
2917262 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
2917283 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
2917303 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:2930354 original size:9 final size:9
Alignment explanation
Indices: 2930340--2930373 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
2930330 TTGGTAAAGC
2930340 ATTTCTTGT
1 ATTTCTTGT
2930349 ATTTCTTGT
1 ATTTCTTGT
2930358 ATTTCTTGT
1 ATTTCTTGT
*
2930367 ATATCTT
1 ATTTCTT
2930374 AAGAAACCAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.15, C:0.12, G:0.09, T:0.65
Consensus pattern (9 bp):
ATTTCTTGT
Found at i:2932255 original size:21 final size:21
Alignment explanation
Indices: 2932231--2932284 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
2932221 TCCTACAGCC
2932231 ACTGTTTTTCCTGTTTTGGAA
1 ACTGTTTTTCCTGTTTTGGAA
2932252 ACTGTTTTTCCTGTTTTGGAA
1 ACTGTTTTTCCTGTTTTGGAA
*
2932273 CCTGTTTTTCCT
1 ACTGTTTTTCCT
2932285 ATCTCCACTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.11, C:0.19, G:0.17, T:0.54
Consensus pattern (21 bp):
ACTGTTTTTCCTGTTTTGGAA
Found at i:2943227 original size:11 final size:11
Alignment explanation
Indices: 2943193--2943227 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
2943183 TAAATGTCTC
2943193 TAAAATAATAA
1 TAAAATAATAA
*
2943204 CAAAATTAATAA
1 TAAAA-TAATAA
2943216 TAAAATAATAA
1 TAAAATAATAA
2943227 T
1 T
2943228 TATACAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (11 bp):
TAAAATAATAA
Found at i:2943275 original size:23 final size:22
Alignment explanation
Indices: 2943246--2943288 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
2943236 ATCCAAACAT
2943246 TAATAATAAAATAATTAGCAATA
1 TAATAATAAAATAA-TAGCAATA
* *
2943269 TAATAATGAAATGATAGCAA
1 TAATAATAAAATAATAGCAA
2943289 CAAGAGCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.58, C:0.05, G:0.09, T:0.28
Consensus pattern (22 bp):
TAATAATAAAATAATAGCAATA
Found at i:2943349 original size:40 final size:40
Alignment explanation
Indices: 2943304--2943384 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
2943294 GCAAAAAAGA
*
2943304 AAGTTTAGGTTATTCGAGCTAGGCCCGAACCAAAAAATCT
1 AAGTTTAGGTTATTCGAGCCAGGCCCGAACCAAAAAATCT
2943344 AAGTTTAGGTTATTCGAGCCAGGCCCGAACCAAAAAATCT
1 AAGTTTAGGTTATTCGAGCCAGGCCCGAACCAAAAAATCT
2943384 A
1 A
2943385 CTCGGGACCT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (40 bp):
AAGTTTAGGTTATTCGAGCCAGGCCCGAACCAAAAAATCT
Found at i:2945240 original size:21 final size:22
Alignment explanation
Indices: 2945210--2945255 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 22
2945200 ATGTATATAT
2945210 ATCATATATATCATATATTTTC
1 ATCATATATATCATATATTTTC
2945232 ATCTATATATATCATATATTTTC
1 ATC-ATATATATCATATATTTTC
2945255 A
1 A
2945256 CACACATACA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 3 0.13
23 20 0.87
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (22 bp):
ATCATATATATCATATATTTTC
Found at i:2946935 original size:17 final size:18
Alignment explanation
Indices: 2946897--2946932 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2946887 TATATATATG
2946897 TATTGAAAATTTTGATTT
1 TATTGAAAATTTTGATTT
* *
2946915 TATTGAAATTTTTTATTT
1 TATTGAAAATTTTGATTT
2946933 ATTTTTAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (18 bp):
TATTGAAAATTTTGATTT
Found at i:2951715 original size:27 final size:27
Alignment explanation
Indices: 2951682--2951736 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
2951672 TAGTGGGAGT
2951682 AAGTTTTATATTTGGCTTTATATGTTA
1 AAGTTTTATATTTGGCTTTATATGTTA
*
2951709 AAGTTTTATATTTGGTTTTATATGTTA
1 AAGTTTTATATTTGGCTTTATATGTTA
2951736 A
1 A
2951737 TGACATACTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.27, C:0.02, G:0.15, T:0.56
Consensus pattern (27 bp):
AAGTTTTATATTTGGCTTTATATGTTA
Found at i:2951728 original size:12 final size:12
Alignment explanation
Indices: 2951684--2951731 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
2951674 GTGGGAGTAA
2951684 GTTTTATATTTG
1 GTTTTATATTTG
* *
2951696 GCTTTATATGTTAAA
1 GTTTTATAT-TT--G
2951711 GTTTTATATTTG
1 GTTTTATATTTG
2951723 GTTTTATAT
1 GTTTTATAT
2951732 GTTAATGACA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
12 17 0.59
13 2 0.07
14 2 0.07
15 8 0.28
ACGTcount: A:0.23, C:0.02, G:0.15, T:0.60
Consensus pattern (12 bp):
GTTTTATATTTG
Found at i:2962737 original size:24 final size:24
Alignment explanation
Indices: 2962703--2962757 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
2962693 ATATGTATAC
*
2962703 ATGAGTTGATGAAAGTTATGAATT
1 ATGAGTCGATGAAAGTTATGAATT
2962727 ATGAGTCGATGAAAGTTATGAATT
1 ATGAGTCGATGAAAGTTATGAATT
2962751 ATGAGTC
1 ATGAGTC
2962758 CTGATGGAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.35
Consensus pattern (24 bp):
ATGAGTCGATGAAAGTTATGAATT
Found at i:2963198 original size:81 final size:83
Alignment explanation
Indices: 2963063--2963219 Score: 219
Period size: 81 Copynumber: 1.9 Consensus size: 83
2963053 TAAAGACATT
* *
2963063 TTAAGTTAAGACTTACCAGTATTGTCAGTTTAGATTTCTGCAGAGGCATTATGTTGTT-T-TATG
1 TTAAGTTAAGACTTACCAGTATTGTCAGTTTAAAGTTCTGCAGAGGCATTATGTTGTTCTGTATG
* *
2963126 TATTGTATATGAGCTATG
66 GATTGCATATGAGCTATG
* * * * *
2963144 TTAAGTTCAGATTTACCAGTATTGTCAGTTTAAAGTTCTGCGGAGTCCTTATGTTGTTCTGTATG
1 TTAAGTTAAGACTTACCAGTATTGTCAGTTTAAAGTTCTGCAGAGGCATTATGTTGTTCTGTATG
2963209 GATTGCATATG
66 GATTGCATATG
2963220 TTCAATATTA
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
81 51 0.78
82 1 0.02
83 13 0.20
ACGTcount: A:0.24, C:0.11, G:0.22, T:0.43
Consensus pattern (83 bp):
TTAAGTTAAGACTTACCAGTATTGTCAGTTTAAAGTTCTGCAGAGGCATTATGTTGTTCTGTATG
GATTGCATATGAGCTATG
Found at i:2964034 original size:3 final size:3
Alignment explanation
Indices: 2964026--2964057 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2964016 CTTTGCTTTT
2964026 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
2964058 TATTATTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:2965212 original size:24 final size:24
Alignment explanation
Indices: 2965183--2965233 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
2965173 CTCCATTCAA
*
2965183 TCGTAGACGTAGCCCTTCTCCAAT
1 TCGTAGACGGAGCCCTTCTCCAAT
* *
2965207 TCGTAGGCGGAGCCGTTCTCCAAT
1 TCGTAGACGGAGCCCTTCTCCAAT
2965231 TCG
1 TCG
2965234 CAGGCCTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.18, C:0.31, G:0.24, T:0.27
Consensus pattern (24 bp):
TCGTAGACGGAGCCCTTCTCCAAT
Found at i:2965238 original size:24 final size:24
Alignment explanation
Indices: 2965193--2965238 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
2965183 TCGTAGACGT
*
2965193 AGCCCTTCTCCAATTCGTAGGCGG
1 AGCCCTTCTCCAATTCGCAGGCGG
*
2965217 AGCCGTTCTCCAATTCGCAGGC
1 AGCCCTTCTCCAATTCGCAGGC
2965239 CTCTTCGTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.17, C:0.35, G:0.24, T:0.24
Consensus pattern (24 bp):
AGCCCTTCTCCAATTCGCAGGCGG
Found at i:2966981 original size:15 final size:16
Alignment explanation
Indices: 2966951--2966989 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
2966941 TAGTAAAAAT
2966951 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
*
2966968 ATAATTTA-TATTTTT
1 ATAATTTATTATTTTA
2966983 ATAATTT
1 ATAATTT
2966990 TCAAAATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Found at i:2972910 original size:29 final size:26
Alignment explanation
Indices: 2972853--2972911 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
2972843 TTGAAAAAAT
* *
2972853 ATATTTGATAATTTTAATTATCTCAA
1 ATATTTAATAATTTTAATTATATCAA
2972879 ATATTTAATAATTTTAGCAATTATATCAA
1 ATATTTAATAATTTT---AATTATATCAA
2972908 ATAT
1 ATAT
2972912 ATTTGCAGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 14 0.50
29 14 0.50
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.47
Consensus pattern (26 bp):
ATATTTAATAATTTTAATTATATCAA
Found at i:2978282 original size:22 final size:23
Alignment explanation
Indices: 2978250--2978306 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
2978240 AAAGGGGGGG
*
2978250 ATCGATGGTATTTTGAGGA-AGA
1 ATCGATTGTATTTTGAGGAGAGA
*
2978272 ATCGATTGTATTTTGGGGAGAGA
1 ATCGATTGTATTTTGAGGAGAGA
**
2978295 AGAGATTGTATT
1 ATCGATTGTATT
2978307 AGAGGGGGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 17 0.57
23 13 0.43
ACGTcount: A:0.30, C:0.04, G:0.32, T:0.35
Consensus pattern (23 bp):
ATCGATTGTATTTTGAGGAGAGA
Found at i:2978301 original size:23 final size:22
Alignment explanation
Indices: 2978257--2978306 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
2978247 GGGATCGATG
**
2978257 GTATTTTGAGGAAGAATCGATT
1 GTATTTTGAGGAAGAAGAGATT
*
2978279 GTATTTTGGGGAGAGAAGAGATT
1 GTATTTTGAGGA-AGAAGAGATT
2978302 GTATT
1 GTATT
2978307 AGAGGGGGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.30, C:0.02, G:0.32, T:0.36
Consensus pattern (22 bp):
GTATTTTGAGGAAGAAGAGATT
Found at i:2979022 original size:39 final size:40
Alignment explanation
Indices: 2978910--2979064 Score: 233
Period size: 39 Copynumber: 3.9 Consensus size: 40
2978900 ATAAAGTATG
* *
2978910 GTTTTAATTAATAATAAAAACAAAATAGTATGGGAGAATG
1 GTTTTAATTAATAATAAAAACAAAATAGTATGGGGGAATA
*
2978950 GTTTTAATTAATAATAAAAAACAAAATATTATGGGGGAATA
1 GTTTTAATTAATAAT-AAAAACAAAATAGTATGGGGGAATA
*
2978991 GTTTTAATTAATAAT-AAAACAAAATAGTATGGGGGAGTA
1 GTTTTAATTAATAATAAAAACAAAATAGTATGGGGGAATA
* *
2979030 GTTTTAATTAATAAT-AAAACAAAGTAGCATGGGGG
1 GTTTTAATTAATAATAAAAACAAAATAGTATGGGGG
2979065 GAGTGAAATC
Statistics
Matches: 107, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
39 55 0.51
40 15 0.14
41 37 0.35
ACGTcount: A:0.48, C:0.03, G:0.19, T:0.30
Consensus pattern (40 bp):
GTTTTAATTAATAATAAAAACAAAATAGTATGGGGGAATA
Found at i:2980880 original size:13 final size:13
Alignment explanation
Indices: 2980862--2980886 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2980852 GAGTTTTGAG
2980862 TTCTTCGATCTGC
1 TTCTTCGATCTGC
2980875 TTCTTCGATCTG
1 TTCTTCGATCTG
2980887 TTCCCTGTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.28, G:0.16, T:0.48
Consensus pattern (13 bp):
TTCTTCGATCTGC
Found at i:2980933 original size:44 final size:44
Alignment explanation
Indices: 2980869--2981131 Score: 284
Period size: 44 Copynumber: 6.0 Consensus size: 44
2980859 GAGTTCTTCG
* *
2980869 ATCTGCT-TCTTCGA-TCTGTTCCCTGTAAACACAGGGATGCCAA
1 ATCTGCTATCTTCAACT-TGTTCCCTATAAACACAGGGATGCCAA
*
2980912 ATCTGCTGTCTTCAACTTGTTCCCTATAAACACAGGGATGCCAA
1 ATCTGCTATCTTCAACTTGTTCCCTATAAACACAGGGATGCCAA
2980956 ATCTGCTATCTTCAACTTGTTCCCTATAAACACAGGGATGCC--
1 ATCTGCTATCTTCAACTTGTTCCCTATAAACACAGGGATGCCAA
** * * * * * * *
2980998 ATGCTGAAATCTTCGA-TCTGCTTCACTGTAAGCACAGGAATGTCAG
1 AT-CTGCTATCTTCAACT-TG-TTCCCTATAAACACAGGGATGCCAA
* * *
2981044 ATCTGCTATCTTCGATTTGTTCCCTATAAGCACAGGGATGCCAA
1 ATCTGCTATCTTCAACTTGTTCCCTATAAACACAGGGATGCCAA
* * *
2981088 ATCTGCTGTTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCA
1 ATCTGCT-ATCTTCAACTTGTTCCCTATAAACACAGGGATGCCA
2981132 TGCTGAAATC
Statistics
Matches: 189, Mismatches: 22, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
42 3 0.02
43 19 0.10
44 118 0.62
45 46 0.24
46 3 0.02
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (44 bp):
ATCTGCTATCTTCAACTTGTTCCCTATAAACACAGGGATGCCAA
Found at i:2981180 original size:132 final size:130
Alignment explanation
Indices: 2980876--2981187 Score: 437
Period size: 132 Copynumber: 2.4 Consensus size: 130
2980866 TCGATCTGCT
* * * *
2980876 TCTTCGATCTG-TTCCCTGTAAACACAGGGATGCCAAATCTGCTGTCTTCAACTTGTTCCCTATA
1 TCTTCGATCTGCTTCACTGT-AACACA-GGAAGGCAAATCTGCTATCTTCAACTTGTTCCCTATA
2980940 AACACAGGGATGCCAAATCTGCTATCTTCAACTTGTTCCCTATAAACACAGGGATGCCATGCTGA
64 AACACAGGGATGCCAAATCTGCTATCTTCAACTTGTTCCCTATAAACACAGGGATGCCATGCTGA
2981005 AA
129 AA
* * * *
2981007 TCTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCGATTTGTTCCCTATA
1 TCTTCGATCTGCTTCACTGTAA-CACAGGAA-GGCAAATCTGCTATCTTCAACTTGTTCCCTATA
* * * *
2981072 AGCACAGGGATGCCAAATCTGCTGTTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTG
64 AACACAGGGATGCCAAATCTGCT-ATCTTCAACTTGTTCCCTATAAACACAGGGATGCCATGCTG
2981137 AAA
128 AAA
* *
2981140 TCTTCGATCTGCTTCACTGTAACTCAGGAAGGCGATATCTGCTATCTT
1 TCTTCGATCTGCTTCACTGTAACACAGGAAGGC-AAATCTGCTATCTT
2981188 TGATCTGCCC
Statistics
Matches: 162, Mismatches: 14, Indels: 9
0.88 0.08 0.05
Matches are distributed among these distances:
131 18 0.11
132 81 0.50
133 63 0.39
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (130 bp):
TCTTCGATCTGCTTCACTGTAACACAGGAAGGCAAATCTGCTATCTTCAACTTGTTCCCTATAAA
CACAGGGATGCCAAATCTGCTATCTTCAACTTGTTCCCTATAAACACAGGGATGCCATGCTGAAA
Found at i:2981220 original size:133 final size:132
Alignment explanation
Indices: 2980876--2981224 Score: 393
Period size: 132 Copynumber: 2.6 Consensus size: 132
2980866 TCGATCTGCT
* * * * * * * **
2980876 TCTTCGATCTG-TTCCCTGTAAACACAGGGATGCCAAATCTGCTGTCTTC-AACTTGTTCCCTAT
1 TCTTCGATCTGCTTCACTGTAAGCACAGGAATGGCAGATCTGCTATCTTCGATC-TGCCCCCTAT
* * *
2980939 AAACACAGGGATGCCAAATCTGCTATCTTCAACTTGTTCCCTATAAACACAGGGATGCCATGCTG
65 AAGCACAGAGACGCCAAATCTGCTATCTTCAACTTGTTCCCTATAAACACAGGGATGCCATGCTG
2981004 AAA
130 AAA
* * **
2981007 TCTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCGATTTGTTCCCTATA
1 TCTTCGATCTGCTTCACTGTAAGCACAGGAATGGCAGATCTGCTATCTTCGATCTGCCCCCTATA
* * * * *
2981072 AGCACAGGGATGCCAAATCTGCTGTTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTG
66 AGCACAGAGACGCCAAATCTGCT-ATCTTCAACTTGTTCCCTATAAACACAGGGATGCCATGCTG
2981137 AAA
130 AAA
* * *
2981140 TCTTCGATCTGCTTCACTGTAA-CTCAGGAA-GGCGATATCTGCTATCTTTGATCTGCCCCCTAT
1 TCTTCGATCTGCTTCACTGTAAGCACAGGAATGGC-AGATCTGCTATCTTCGATCTGCCCCCTAT
*
2981203 CTA-CTACAGAGACGCCAAATCT
65 -AAGC-ACAGAGACGCCAAATCT
2981225 ATTTCTTCGA
Statistics
Matches: 190, Mismatches: 22, Indels: 10
0.86 0.10 0.05
Matches are distributed among these distances:
131 13 0.07
132 97 0.51
133 80 0.42
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (132 bp):
TCTTCGATCTGCTTCACTGTAAGCACAGGAATGGCAGATCTGCTATCTTCGATCTGCCCCCTATA
AGCACAGAGACGCCAAATCTGCTATCTTCAACTTGTTCCCTATAAACACAGGGATGCCATGCTGA
AA
Found at i:2981581 original size:205 final size:205
Alignment explanation
Indices: 2981229--2981810 Score: 1015
Period size: 205 Copynumber: 2.8 Consensus size: 205
2981219 AAATCTATTT
* *
2981229 CTTCGATTTGTTCCCTGACGATACAGAGACGACAAATCATCTTAGATTTGCTTTCTCGTAATCAC
1 CTTCGATTCGTTCTCTGACGATACAGAGACGACAAATCATCTTAGATTTGCTTTCTCGTAATCAC
*
2981294 GTGAAAGCCAAATCAGCTATGTCTTTGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTT
*
2981359 GGATCTGCTTCAGTGAAATCATCTGAAGGCGAGATCTGCTATGTGTTTGCTCTCCATCAAAACGA
131 GGATCTGCTTCAGTGAAATCATCTGAAGGCGAGATCTGCTATGTGTCTGCTCTCCATCAAAACGA
2981424 AGATGCCAAA
196 AGATGCCAAA
2981434 CTTCGATTCGTTCTCTGACGATACAGAGACGACAAATCATCTTAGATTTGCTTTCTCGTAATCAC
1 CTTCGATTCGTTCTCTGACGATACAGAGACGACAAATCATCTTAGATTTGCTTTCTCGTAATCAC
*
2981499 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATATT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTT
* **
2981564 GGATCTGCTTCAGTGAAATCATTTGAAGGCGAGATCTGCTATGTGTCTGCTCTCCATCAAAGTGA
131 GGATCTGCTTCAGTGAAATCATCTGAAGGCGAGATCTGCTATGTGTCTGCTCTCCATCAAAACGA
2981629 AGATGCCAAA
196 AGATGCCAAA
2981639 CTTCGATTCGTTCTCTGACGATACAGAGACGACAAATCATCTTAGATTTGCTTTCTCGTAATCAC
1 CTTCGATTCGTTCTCTGACGATACAGAGACGACAAATCATCTTAGATTTGCTTTCTCGTAATCAC
* * *
2981704 GTGAAAGCTAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAACACAAGGATGCCAAACCATCTC
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTT
* * *
2981769 GGATCTGTTTCAGT-ATAA-CATCTGAAGGCCAGATCTGTTATG
131 GGATCTGCTTCAGTGA-AATCATCTGAAGGCGAGATCTGCTATG
2981811 CTGCGGCCTA
Statistics
Matches: 360, Mismatches: 16, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
204 22 0.06
205 338 0.94
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.31
Consensus pattern (205 bp):
CTTCGATTCGTTCTCTGACGATACAGAGACGACAAATCATCTTAGATTTGCTTTCTCGTAATCAC
GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTT
GGATCTGCTTCAGTGAAATCATCTGAAGGCGAGATCTGCTATGTGTCTGCTCTCCATCAAAACGA
AGATGCCAAA
Found at i:2989789 original size:14 final size:14
Alignment explanation
Indices: 2989772--2989798 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2989762 CAGATTTTCT
2989772 TTTCTACCTCTCTC
1 TTTCTACCTCTCTC
2989786 TTTCTACCTCTCT
1 TTTCTACCTCTCT
2989799 GGAAAGTAAA
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:0.07, C:0.41, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTCTACCTCTCTC
Found at i:2989884 original size:15 final size:14
Alignment explanation
Indices: 2989842--2989891 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
2989832 ATAACTTTGA
*
2989842 ATGCAAATGATGTG
1 ATGCAAATGATGAG
2989856 ATG-AAATGTTATGAG
1 ATGCAAATG--ATGAG
2989871 ATGCAAATGCATGA-
1 ATGCAAATG-ATGAG
2989885 ATGCAAA
1 ATGCAAA
2989892 AAGAATATCG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 5 0.16
14 10 0.32
15 11 0.35
16 5 0.16
ACGTcount: A:0.42, C:0.08, G:0.24, T:0.26
Consensus pattern (14 bp):
ATGCAAATGATGAG
Found at i:2994324 original size:38 final size:39
Alignment explanation
Indices: 2994270--2994422 Score: 236
Period size: 40 Copynumber: 3.9 Consensus size: 39
2994260 GATTCCACTC
* * *
2994270 CCCCCATGCTACTTTGTTTTATTATTAATTAAAACTACT
1 CCCCCATACTATTTTGTTTTATTATTAATTAAAACTATT
2994309 -CCCCATACTATTTTGTTTTATTATTAATTAAAACTATT
1 CCCCCATACTATTTTGTTTTATTATTAATTAAAACTATT
* *
2994347 CCCCCATACTATTTTATTTTTATTATTAATTAAAACCATT
1 CCCCCATACTATTTT-GTTTTATTATTAATTAAAACTATT
2994387 CCCCCATACTATTTTGTTTTTATTATTAATTAAAAC
1 CCCCCATACTATTTTG-TTTTATTATTAATTAAAAC
2994423 CATACTTTAT
Statistics
Matches: 105, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
38 35 0.33
39 14 0.13
40 56 0.53
ACGTcount: A:0.31, C:0.20, G:0.03, T:0.47
Consensus pattern (39 bp):
CCCCCATACTATTTTGTTTTATTATTAATTAAAACTATT
Found at i:2995078 original size:22 final size:23
Alignment explanation
Indices: 2995030--2995086 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
2995020 AACCCCCTCT
**
2995030 AATACAATCTCTTCTCTCCCCAA
1 AATACAATCGATTCTCTCCCCAA
*
2995053 AATACAATCGATTCT-TCCTCAA
1 AATACAATCGATTCTCTCCCCAA
*
2995075 AATACCATCGAT
1 AATACAATCGAT
2995087 CCCCCCTCCC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 17 0.57
23 13 0.43
ACGTcount: A:0.35, C:0.32, G:0.04, T:0.30
Consensus pattern (23 bp):
AATACAATCGATTCTCTCCCCAA
Found at i:2995094 original size:22 final size:22
Alignment explanation
Indices: 2995050--2995094 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2995040 CTTCTCTCCC
* **
2995050 CAAAATACAATCGATTCTTCCT
1 CAAAATACAATCGATCCCCCCT
*
2995072 CAAAATACCATCGATCCCCCCT
1 CAAAATACAATCGATCCCCCCT
2995094 C
1 C
2995095 CCCTACAATC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.38, G:0.04, T:0.24
Consensus pattern (22 bp):
CAAAATACAATCGATCCCCCCT
Found at i:2999618 original size:16 final size:17
Alignment explanation
Indices: 2999599--2999631 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2999589 ATTTTAGAGC
2999599 ATATAAATTTGA-AACT
1 ATATAAATTTGATAACT
*
2999615 ATATATATTTGATAACT
1 ATATAAATTTGATAACT
2999632 TTTTCAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.42
Consensus pattern (17 bp):
ATATAAATTTGATAACT
Found at i:2999749 original size:21 final size:19
Alignment explanation
Indices: 2999721--2999770 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 19
2999711 TATTTTAGAA
2999721 AATTTTTAAATTTCTTTAT
1 AATTTTTAAATTTCTTTAT
* *
2999740 ATATTATTTAGATTTTTTTAT
1 A-ATT-TTTAAATTTCTTTAT
2999761 AATTTTTAAA
1 AATTTTTAAA
2999771 AAATATAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 6 0.23
20 6 0.23
21 14 0.54
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (19 bp):
AATTTTTAAATTTCTTTAT
Found at i:3007749 original size:24 final size:24
Alignment explanation
Indices: 3007722--3007771 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
3007712 AACCCAATTG
*
3007722 ATTGGATTTTTAATTTAATTTT-TT
1 ATTGGATTTTTAA-ATAATTTTATT
**
3007746 ATTGTTTTTTTAAATAATTTTATT
1 ATTGGATTTTTAAATAATTTTATT
3007770 AT
1 AT
3007772 AGGTTTGGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (24 bp):
ATTGGATTTTTAAATAATTTTATT
Found at i:3008218 original size:3 final size:3
Alignment explanation
Indices: 3008210--3008243 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
3008200 TTTCTCTCTC
3008210 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
3008244 ATTTTTCTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:3011731 original size:23 final size:25
Alignment explanation
Indices: 3011704--3011752 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
3011694 AAAAGTTTTA
3011704 ATTTAAGAAA-AT-TTGATAATTAT
1 ATTTAAGAAATATATTGATAATTAT
**
3011727 ATTTATTAAATATATTGATAATTAT
1 ATTTAAGAAATATATTGATAATTAT
3011752 A
1 A
3011753 AAAACCTTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 8 0.36
24 2 0.09
25 12 0.55
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (25 bp):
ATTTAAGAAATATATTGATAATTAT
Found at i:3016646 original size:14 final size:14
Alignment explanation
Indices: 3016627--3016657 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
3016617 AAATATATTT
3016627 AATTTCCTCATTCA
1 AATTTCCTCATTCA
3016641 AATTTCCTCATTCA
1 AATTTCCTCATTCA
3016655 AAT
1 AAT
3016658 GGATTCATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.00, T:0.42
Consensus pattern (14 bp):
AATTTCCTCATTCA
Found at i:3016905 original size:17 final size:17
Alignment explanation
Indices: 3016883--3016917 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
3016873 GTCATTCCAC
3016883 TATAGTATTATGACTGT
1 TATAGTATTATGACTGT
*
3016900 TATAGTATTATGATTGT
1 TATAGTATTATGACTGT
3016917 T
1 T
3016918 CATGACTGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.03, G:0.17, T:0.51
Consensus pattern (17 bp):
TATAGTATTATGACTGT
Found at i:3018247 original size:3 final size:3
Alignment explanation
Indices: 3018239--3018267 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3018229 ATATCTGGCA
3018239 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3018268 ACAAAAAAGC
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3022205 original size:9 final size:10
Alignment explanation
Indices: 3022181--3022208 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
3022171 TTTCTGCTGT
3022181 TAAAAATTAA
1 TAAAAATTAA
3022191 TAAAAATTAA
1 TAAAAATTAA
3022201 TAAAAATT
1 TAAAAATT
3022209 TTAACGGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
TAAAAATTAA
Found at i:3024323 original size:54 final size:54
Alignment explanation
Indices: 3024259--3024366 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
3024249 GTTATTATTC
3024259 ATTGTATGTTATTTTCACTACATGCATCATTTTAATCAATGGTAATTAAGTTTA
1 ATTGTATGTTATTTTCACTACATGCATCATTTTAATCAATGGTAATTAAGTTTA
3024313 ATTGTATGTTATTTTCACTACATGCATCATTTTAATCAATGGTAATTAAGTTTA
1 ATTGTATGTTATTTTCACTACATGCATCATTTTAATCAATGGTAATTAAGTTTA
3024367 GGATTAAATA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.46
Consensus pattern (54 bp):
ATTGTATGTTATTTTCACTACATGCATCATTTTAATCAATGGTAATTAAGTTTA
Found at i:3034295 original size:17 final size:17
Alignment explanation
Indices: 3034236--3034286 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
3034226 ACGAAACAGT
*
3034236 ATAAATGATATACA-AA
1 ATAAATAATATACACAA
3034252 AT-AATATATATACACAA
1 ATAAATA-ATATACACAA
3034269 ATAAATAATATACACAA
1 ATAAATAATATACACAA
3034286 A
1 A
3034287 ATACAAATAG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
15 3 0.10
16 9 0.29
17 15 0.48
18 4 0.13
ACGTcount: A:0.63, C:0.10, G:0.02, T:0.25
Consensus pattern (17 bp):
ATAAATAATATACACAA
Found at i:3034915 original size:17 final size:17
Alignment explanation
Indices: 3034893--3034926 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3034883 GTGGCAAGTA
3034893 GGGTGATGGAGTTAGTG
1 GGGTGATGGAGTTAGTG
3034910 GGGTGATGGAGTTAGTG
1 GGGTGATGGAGTTAGTG
3034927 ATCGGTTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.00, G:0.53, T:0.29
Consensus pattern (17 bp):
GGGTGATGGAGTTAGTG
Found at i:3037563 original size:18 final size:18
Alignment explanation
Indices: 3037512--3037564 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
3037502 CAGTTGCTCT
* *
3037512 ATAACAGTCAGTTATACA
1 ATAACAGTCAATTATTCA
*
3037530 ATAACAGTCATTTATTCA
1 ATAACAGTCAATTATTCA
*
3037548 GTAACAGTCAATTATTC
1 ATAACAGTCAATTATTC
3037565 TGTAGCAAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (18 bp):
ATAACAGTCAATTATTCA
Found at i:3043878 original size:3 final size:3
Alignment explanation
Indices: 3043824--3043861 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
3043814 TGTATTTCAA
* *
3043824 TAT TAT TAC TAT TAT CAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3043862 GTGTATATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:3043904 original size:147 final size:147
Alignment explanation
Indices: 3043696--3044149 Score: 687
Period size: 147 Copynumber: 3.1 Consensus size: 147
3043686 TTTCGTTTCT
*
3043696 TTATTAATTATTATTATTATTAGTGTATACTTTTTA-T-TATA--TACGTATATGTATATATATT
1 TTATT-ATTATTATTATTATTAGTGTATA-TTTTTATTATATATGTATGTATATGTATATATATT
**
3043757 TACGTATAGTATTATTTTTTATTACTTTATTTTAATATTTTTATTATATTTGCTTTTTGTATTTC
64 TATATATAGTATTATTTTTTATTACTTTATTTTAATATTTTTATTATATTTGCTTTTTGTATTTC
3043822 AATATTATTACTATTATCA
129 AATATTATTACTATTATCA
*
3043841 TTATTATTATTATTATTATTAGTGTATATTTTTATTATATATGTATGTATATGTATATATATTTG
1 TTATTATTATTATTATTATTAGTGTATATTTTTATTATATATGTATGTATATGTATATATATTTA
3043906 TATATAGTATTATTTTTTATTACTTTATTTTAATATTTTTATTATATTTGCTTTTTGTATTTCAA
66 TATATAGTATTATTTTTTATTACTTTATTTTAATATTTTTATTATATTTGCTTTTTGTATTTCAA
3043971 TATTATTACTATTATC-
131 TATTATTACTATTATCA
3043987 --ATTATTATTA--A-TATTAGTGTATATTTTTATTATATATGTATGTATATGTATATATATTTA
1 TTATTATTATTATTATTATTAGTGTATATTTTTATTATATATGTATGTATATGTATATATATTTA
* *
3044047 TATATAGTATTATTCTTTTATTACTTTATTCTAATATTATTATTATATTTGC-TTTTGTATTTCA
66 TATATAGTATTATT-TTTTATTACTTTATTTTAATATTTTTATTATATTTGCTTTTTGTATTTCA
* * * *
3044111 TTATTATTGCTAGTATTA
130 ATATTATTACTATTATCA
* * *
3044129 TTATCATTATCATCATTATTA
1 TTATTATTATTATTATTATTA
3044150 ACATATACAT
Statistics
Matches: 285, Mismatches: 13, Indels: 20
0.90 0.04 0.06
Matches are distributed among these distances:
141 87 0.31
142 36 0.13
143 6 0.02
144 42 0.15
145 9 0.03
146 1 0.00
147 104 0.36
ACGTcount: A:0.30, C:0.05, G:0.06, T:0.59
Consensus pattern (147 bp):
TTATTATTATTATTATTATTAGTGTATATTTTTATTATATATGTATGTATATGTATATATATTTA
TATATAGTATTATTTTTTATTACTTTATTTTAATATTTTTATTATATTTGCTTTTTGTATTTCAA
TATTATTACTATTATCA
Found at i:3044030 original size:23 final size:22
Alignment explanation
Indices: 3043991--3044033 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
3043981 ATTATCATTA
3043991 TTATTAATATTAGTGTATATTT
1 TTATTAATATTAGTGTATATTT
3044013 TTATTATATATGTA-TGTATAT
1 TTATTA-ATAT-TAGTGTATAT
3044034 GTATATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.32
23 11 0.58
24 2 0.11
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (22 bp):
TTATTAATATTAGTGTATATTT
Found at i:3044034 original size:10 final size:10
Alignment explanation
Indices: 3044017--3044056 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
3044007 ATATTTTTAT
3044017 TATATATGTA
1 TATATATGTA
*
3044027 TGTATATGTA
1 TATATATGTA
*
3044037 TATATATTTA
1 TATATATGTA
3044047 TATATA-GTA
1 TATATATGTA
3044056 T
1 T
3044057 TATTCTTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
9 3 0.12
10 23 0.88
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.53
Consensus pattern (10 bp):
TATATATGTA
Found at i:3044060 original size:16 final size:16
Alignment explanation
Indices: 3044006--3044052 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
3043996 AATATTAGTG
*
3044006 TATATTTTTAT-TATA
1 TATATATTTATATATA
* * *
3044021 TATGTATGTATATGTA
1 TATATATTTATATATA
3044037 TATATATTTATATATA
1 TATATATTTATATATA
3044053 GTATTATTCT
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
15 8 0.33
16 16 0.67
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.57
Consensus pattern (16 bp):
TATATATTTATATATA
Found at i:3046721 original size:18 final size:20
Alignment explanation
Indices: 3046679--3046715 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3046669 ATATTTTATG
*
3046679 ATTA-TTTAATTAGATATAT
1 ATTATTTTAATGAGATATAT
3046698 ATTATTTTAATGAGATAT
1 ATTATTTTAATGAGATAT
3046716 TTTATTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (20 bp):
ATTATTTTAATGAGATATAT
Found at i:3048925 original size:46 final size:46
Alignment explanation
Indices: 3048873--3049148 Score: 410
Period size: 46 Copynumber: 6.0 Consensus size: 46
3048863 AGTGTGCTCT
3048873 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
3048919 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
3048965 CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
3049011 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* ** *** *
3049057 ATGA-CGGAAAATAAATAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * **
3049103 GTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
3049149 ATGACAAAAA
Statistics
Matches: 212, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
45 1 0.00
46 210 0.99
47 1 0.00
ACGTcount: A:0.38, C:0.16, G:0.25, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:3049154 original size:46 final size:46
Alignment explanation
Indices: 3048873--3049183 Score: 399
Period size: 46 Copynumber: 6.7 Consensus size: 46
3048863 AGTGTGCTCT
*
3048873 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGACATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
3048919 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGACATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * *
3048965 CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGACATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
3049011 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGACATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * *** *
3049057 ATGAC-GGAAAATAAATAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGACATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* **
3049103 GTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGACATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* ** * * *
3049149 ATGACAAAAAAATGAGTAAGACAATAGTTGAAAGA
1 CTGAC-ATGAAATGTGTAAGACCATGGTTGAAAGA
3049184 CACTGTGGCA
Statistics
Matches: 241, Mismatches: 21, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
45 1 0.00
46 215 0.89
47 25 0.10
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.21
Consensus pattern (46 bp):
CTGACATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Done.