Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: 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: 104050246
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4660000 characters in sequence are not A, C, G, or T
File 12 of 316
Found at i:3639081 original size:20 final size:20
Alignment explanation
Indices: 3639060--3639098 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
3639050 TTTTAATATA
3639060 AAAATTAAA-AAAT-AATTT
1 AAAATTAAATAAATAAATTT
*
3639078 TAAATTAAATAAATAAATTT
1 AAAATTAAATAAATAAATTT
3639098 A
1 A
3639099 TTCAATTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 2
0.81 0.10 0.10
Matches are distributed among these distances:
18 8 0.47
19 4 0.24
20 5 0.29
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAATTAAATAAATAAATTT
Found at i:3639084 original size:18 final size:19
Alignment explanation
Indices: 3639061--3639098 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
3639051 TTTAATATAA
*
3639061 AAATTAAA-AAATAATTTT
1 AAATTAAATAAATAAATTT
3639079 AAATTAAATAAATAAATTT
1 AAATTAAATAAATAAATTT
3639098 A
1 A
3639099 TTCAATTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AAATTAAATAAATAAATTT
Found at i:3642978 original size:11 final size:11
Alignment explanation
Indices: 3642942--3642979 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
3642932 CAAACACCTA
3642942 AAAATTAATTTT
1 AAAA-TAATTTT
*
3642954 AAAAT-ATTTC
1 AAAATAATTTT
3642964 AAAATAATTTT
1 AAAATAATTTT
3642975 AAAAT
1 AAAAT
3642980 CCTATAATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 9 0.39
11 10 0.43
12 4 0.17
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (11 bp):
AAAATAATTTT
Found at i:3644052 original size:12 final size:12
Alignment explanation
Indices: 3644035--3644060 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3644025 TCACAAGATA
3644035 TCATGCTTGAAT
1 TCATGCTTGAAT
3644047 TCATGCTTGAAT
1 TCATGCTTGAAT
3644059 TC
1 TC
3644061 GGTTTGATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.42
Consensus pattern (12 bp):
TCATGCTTGAAT
Found at i:3645343 original size:13 final size:13
Alignment explanation
Indices: 3645321--3645383 Score: 65
Period size: 13 Copynumber: 4.8 Consensus size: 13
3645311 TTTGGCAATA
*
3645321 CTTTTGAAAAGTG
1 CTTTTAAAAAGTG
3645334 CTTTTAAAAAGTG
1 CTTTTAAAAAGTG
* *
3645347 -TTGTGAAAAAGTA
1 CTT-TTAAAAAGTG
*
3645360 CTTTTGAAAAGTG
1 CTTTTAAAAAGTG
3645373 CTTTTGAAAAA
1 CTTTT-AAAAA
3645384 TTTAATTTAA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
12 2 0.05
13 32 0.80
14 6 0.15
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.37
Consensus pattern (13 bp):
CTTTTAAAAAGTG
Found at i:3645363 original size:26 final size:27
Alignment explanation
Indices: 3645327--3645383 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 27
3645317 AATACTTTTG
*
3645327 AAAAGTGCTTTTAAAAAGTG-TTGTGA
1 AAAAGTACTTTTAAAAAGTGCTTGTGA
* *
3645353 AAAAGTACTTTTGAAAAGTGCTTTTGA
1 AAAAGTACTTTTAAAAAGTGCTTGTGA
3645380 AAAA
1 AAAA
3645384 TTTAATTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 18 0.67
27 9 0.33
ACGTcount: A:0.42, C:0.05, G:0.19, T:0.33
Consensus pattern (27 bp):
AAAAGTACTTTTAAAAAGTGCTTGTGA
Found at i:3648048 original size:69 final size:69
Alignment explanation
Indices: 3647937--3648081 Score: 281
Period size: 69 Copynumber: 2.1 Consensus size: 69
3647927 CATTATACCA
3647937 ATAAAATATATGGTTACTTTGTTAAGAACAGATAAAAGAACTGTTCTTAGCATTCAATCATAAAT
1 ATAAAATATATGGTTACTTTGTTAAGAACAGATAAAAGAACTGTTCTTAGCATTCAATCATAAAT
3648002 GCTG
66 GCTG
3648006 ATAAAATATATGGTTACTTTGTTAAGAACAGATAAAAGAACTGTTCTTAGCATTCAATCATAAAT
1 ATAAAATATATGGTTACTTTGTTAAGAACAGATAAAAGAACTGTTCTTAGCATTCAATCATAAAT
3648071 GCTG
66 GCTG
3648075 ATCAAAA
1 AT-AAAA
3648082 GAGAAACACT
Statistics
Matches: 75, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
69 71 0.95
70 4 0.05
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (69 bp):
ATAAAATATATGGTTACTTTGTTAAGAACAGATAAAAGAACTGTTCTTAGCATTCAATCATAAAT
GCTG
Found at i:3656744 original size:3 final size:3
Alignment explanation
Indices: 3656736--3656789 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
3656726 TCATCAGTCA
3656736 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3656784 TAT TAT
1 TAT TAT
3656790 AGTGCAACAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3659855 original size:22 final size:22
Alignment explanation
Indices: 3659810--3659856 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
3659800 AATTATTATA
**
3659810 ATTTATATATAATAAATTTTTT
1 ATTTATATATAATAAATTAATT
3659832 ATTTAATATATAA-AAATTAATT
1 ATTT-ATATATAATAAATTAATT
3659854 ATT
1 ATT
3659857 GAAGTTATAA
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 (22 bp):
ATTTATATATAATAAATTAATT
Found at i:3668781 original size:16 final size:15
Alignment explanation
Indices: 3668735--3668782 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
3668725 TAACTTAATT
*
3668735 TAATTACATTTTATAA
1 TAATTACATATTAT-A
*
3668751 TAATTA-ATATAATA
1 TAATTACATATTATA
3668765 TAATTATCATATTATA
1 TAATTA-CATATTATA
3668781 TA
1 TA
3668783 CCTCACTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 7 0.26
15 5 0.19
16 15 0.56
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (15 bp):
TAATTACATATTATA
Found at i:3669967 original size:2 final size:2
Alignment explanation
Indices: 3669960--3669984 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3669950 AACTAAAAGA
3669960 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 A
3669985 AAATTCCCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3678283 original size:13 final size:13
Alignment explanation
Indices: 3678265--3678291 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3678255 GGACAACTAT
3678265 AAACATCGAAACG
1 AAACATCGAAACG
3678278 AAACATCGAAACG
1 AAACATCGAAACG
3678291 A
1 A
3678292 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:3691225 original size:16 final size:15
Alignment explanation
Indices: 3691206--3691235 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
3691196 CTCTACAAAT
3691206 TATAAAAAATATAAAC
1 TATAAAAAAT-TAAAC
3691222 TATAAAAAATTAAA
1 TATAAAAAATTAAA
3691236 ATTTCATTCG
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:3694329 original size:12 final size:12
Alignment explanation
Indices: 3694314--3694341 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
3694304 ACTTAAGATG
3694314 TATCGAATTTCT
1 TATCGAATTTCT
3694326 TATCGAATTTCT
1 TATCGAATTTCT
3694338 TATC
1 TATC
3694342 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:3717842 original size:19 final size:19
Alignment explanation
Indices: 3717818--3717855 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
3717808 TTGAGATTGC
*
3717818 CAACCTATTTGCTTGAAAT
1 CAACCTATTTGCCTGAAAT
3717837 CAACCTATTTGCCTGAAAT
1 CAACCTATTTGCCTGAAAT
3717856 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:3718945 original size:11 final size:12
Alignment explanation
Indices: 3718922--3718946 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3718912 CATCATTTTT
3718922 AAATCGAAAAAA
1 AAATCGAAAAAA
3718934 AAATCGAAAAAA
1 AAATCGAAAAAA
3718946 A
1 A
3718947 TGGTTTCGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.08, G:0.08, T:0.08
Consensus pattern (12 bp):
AAATCGAAAAAA
Found at i:3734743 original size:5 final size:5
Alignment explanation
Indices: 3734727--3734775 Score: 50
Period size: 5 Copynumber: 9.8 Consensus size: 5
3734717 CTAATCTAAC
3734727 ATAAA ATCAAA ATAAA ATAAA AT-AA ATAATA A-ATAA A-AAA ATAAA
1 ATAAA AT-AAA ATAAA ATAAA ATAAA ATAA-A ATA-AA ATAAA ATAAA
3734772 ATAA
1 ATAA
3734776 GATTTTTTCT
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
4 7 0.18
5 24 0.62
6 8 0.21
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:3736602 original size:3 final size:3
Alignment explanation
Indices: 3736594--3737125 Score: 216
Period size: 3 Copynumber: 173.3 Consensus size: 3
3736584 AATAAGGTGG
* * * * *
3736594 TAA TAA TAA TAC TAA TAA TAA TAA TGA TAA TAG TAT TAA TAA TAA TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
** * * * * * *
3736642 TAA TGG TAA TAGCA TAA TAG TTA TAA GAAA TAA TAC TAG TAG TAA TAA
1 TAA TAA TAA TA--A TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA
* * *
3736690 TAA TAA TAA T-A TAAA TAA CAA T-A TAT TAA TGAGA -AA TAA CAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA T-A-A TAA TAA TAA TAA
* * * * * *
3736735 TAA TAA TAA TAG TAA CAA TAA TAT TGA TAA TGGA TAT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
* * * * * * * * * *
3736781 AAA GGAG TAA TAA TAT TAG TAG TAAA TAA AAA TAG TGA TAA CAA TAA
1 TAA -TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
* * *
3736828 TGAA -AA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAG TAAA TAG TAA
1 T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA
* ** * * * * *
3736874 GGAA TGG TGA TAA TAA TGA TAA TAAA CAA TAG TAAA TAA TAA TAA TGA
1 -TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA T-AA TAA TAA TAA TAA
* * * *** * * * * *
3736922 TAG TAA CAA AAA CGG CAA TGA TAA TAT TAA TAT TGA TAA TAAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA
* * ** *
3736968 TAA TAA T-A TAA -ACA TTGA TAA TAA TAGA AAA TAA TAA TGT TAA AACA
1 TAA TAA TAA TAA TA-A -TAA TAA TAA TA-A TAA TAA TAA TAA TAA TA-A
* ** * *
3737015 TAA TAA CAA TGG TGAA -AA TAA TAA TAA TAT TAA AAA TAA TAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * **
3737060 T-A TAC TAA TGA GGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3737107 TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA T
3737126 GATGATGATG
Statistics
Matches: 381, Mismatches: 120, Indels: 56
0.68 0.22 0.10
Matches are distributed among these distances:
2 14 0.04
3 335 0.88
4 28 0.07
5 4 0.01
ACGTcount: A:0.58, C:0.03, G:0.09, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:3737130 original size:3 final size:3
Alignment explanation
Indices: 3737124--3737157 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
3737114 AATAATAATA
3737124 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
3737158 AAATATGAAT
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:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:3753474 original size:16 final size:17
Alignment explanation
Indices: 3753436--3753476 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
3753426 TCCAAACTTG
*
3753436 AAAATAATTTAAAACTC
1 AAAATGATTTAAAACTC
*
3753453 AAAATGATTTAAAA-TT
1 AAAATGATTTAAAACTC
3753469 AAAATGAT
1 AAAATGAT
3753477 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:3760802 original size:51 final size:51
Alignment explanation
Indices: 3760730--3760843 Score: 183
Period size: 51 Copynumber: 2.2 Consensus size: 51
3760720 CTAATCACAT
*
3760730 TTATCACTTGTCACTGATCAGATAATTGTAGCTAAAACTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
* *
3760781 TTATCACTTGTCACTGGTCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
* *
3760832 TTGTCGCTTGTC
1 TTATCACTTGTC
3760844 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:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (51 bp):
TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
Found at i:3780192 original size:18 final size:18
Alignment explanation
Indices: 3780155--3780193 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
3780145 CAATCCCAAC
*
3780155 TACTGTATACGTGAACAG
1 TACTGTATACGTAAACAG
*
3780173 TACTGTATACGTAAATAG
1 TACTGTATACGTAAACAG
3780191 TAC
1 TAC
3780194 CATATATATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (18 bp):
TACTGTATACGTAAACAG
Found at i:3780884 original size:19 final size:19
Alignment explanation
Indices: 3780847--3780884 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
3780837 AATAAACTTC
*
3780847 TAATTTTTTTTAAAGTTTT
1 TAATTTTTTTTAAACTTTT
3780866 TAATGTTTTTTT-AACTTTT
1 TAAT-TTTTTTTAAACTTTT
3780885 AAAAATCAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.24, C:0.03, G:0.05, T:0.68
Consensus pattern (19 bp):
TAATTTTTTTTAAACTTTT
Found at i:3785063 original size:35 final size:35
Alignment explanation
Indices: 3785024--3785095 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
3785014 GTCTCAACAC
3785024 TATATTCTCTATCCGCAAAACTAAACTCAAAATCT
1 TATATTCTCTATCCGCAAAACTAAACTCAAAATCT
3785059 TATATTCTCTATCCGCAAAACTAAACTCAAAATCT
1 TATATTCTCTATCCGCAAAACTAAACTCAAAATCT
3785094 TA
1 TA
3785096 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:3786027 original size:16 final size:16
Alignment explanation
Indices: 3786006--3786040 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3785996 TAAATTGATT
3786006 TTTTTA-ATTCTTAAAA
1 TTTTTAGATT-TTAAAA
3786022 TTTTTAGATTTTAAAA
1 TTTTTAGATTTTAAAA
3786038 TTT
1 TTT
3786041 AATCCTAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.83
17 3 0.17
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (16 bp):
TTTTTAGATTTTAAAA
Found at i:3787065 original size:29 final size:29
Alignment explanation
Indices: 3787028--3787087 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
3787018 AATTCTTCAA
3787028 TTGGTGGGAACGTATATTTCCTTGAATTG
1 TTGGTGGGAACGTATATTTCCTTGAATTG
3787057 TTGGTGGGAACGTATATTTCCTTGAATTG
1 TTGGTGGGAACGTATATTTCCTTGAATTG
3787086 TT
1 TT
3787088 CTCGAATAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.20, C:0.10, G:0.27, T:0.43
Consensus pattern (29 bp):
TTGGTGGGAACGTATATTTCCTTGAATTG
Found at i:3788033 original size:3 final size:3
Alignment explanation
Indices: 3788025--3788052 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3788015 TATAGATCTT
3788025 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3788053 ACTAAGGAAA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3790209 original size:61 final size:61
Alignment explanation
Indices: 3790114--3790235 Score: 235
Period size: 61 Copynumber: 2.0 Consensus size: 61
3790104 AAAGTTCAAT
*
3790114 CGGTGTTAAACTCGAGCAGCTTCCACTATTCAATTTCGAACAACTTGCCACCGCGACCAAC
1 CGGTGTTAAACCCGAGCAGCTTCCACTATTCAATTTCGAACAACTTGCCACCGCGACCAAC
3790175 CGGTGTTAAACCCGAGCAGCTTCCACTATTCAATTTCGAACAACTTGCCACCGCGACCAAC
1 CGGTGTTAAACCCGAGCAGCTTCCACTATTCAATTTCGAACAACTTGCCACCGCGACCAAC
3790236 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:3794599 original size:16 final size:16
Alignment explanation
Indices: 3794576--3794612 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
3794566 CTTTAAATTG
*
3794576 ATTTTTTAATCTTTAAA
1 ATTTTTAAAT-TTTAAA
3794593 ATTTTTAAATTTTAAA
1 ATTTTTAAATTTTAAA
3794609 ATTT
1 ATTT
3794613 AATCCTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTTTTAAATTTTAAA
Found at i:3802056 original size:18 final size:18
Alignment explanation
Indices: 3802033--3802125 Score: 141
Period size: 18 Copynumber: 5.2 Consensus size: 18
3802023 CTCAACTATT
*
3802033 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
3802051 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
* *
3802069 GTATACGTGAACAGTACT
1 GTATACGTGAATAGTACC
*
3802087 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
3802105 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
3802123 GTA
1 GTA
3802126 AACGGTCGTA
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 66 1.00
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:3802080 original size:36 final size:36
Alignment explanation
Indices: 3802033--3802125 Score: 168
Period size: 36 Copynumber: 2.6 Consensus size: 36
3802023 CTCAACTATT
3802033 GTATACGTGAACAGTACCGTATACGTGAATAGTGCC
1 GTATACGTGAACAGTACCGTATACGTGAATAGTGCC
*
3802069 GTATACGTGAACAGTACTGTATACGTGAATAGTGCC
1 GTATACGTGAACAGTACCGTATACGTGAATAGTGCC
*
3802105 GTATACGTGAATAGTACCGTA
1 GTATACGTGAACAGTACCGTA
3802126 AACGGTCGTA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (36 bp):
GTATACGTGAACAGTACCGTATACGTGAATAGTGCC
Found at i:3807375 original size:125 final size:125
Alignment explanation
Indices: 3807153--3807403 Score: 502
Period size: 125 Copynumber: 2.0 Consensus size: 125
3807143 CATATAAAAA
3807153 TTGAATTTTCTCAAATATTAACTCGTTCTTAAACTTCATTCGTTAATAATAGTAACACAATTTCA
1 TTGAATTTTCTCAAATATTAACTCGTTCTTAAACTTCATTCGTTAATAATAGTAACACAATTTCA
3807218 ACTATTTATCAATTTCAATCAAATATCATAGACTTCAATTTTCTTCACTACATCAACGTT
66 ACTATTTATCAATTTCAATCAAATATCATAGACTTCAATTTTCTTCACTACATCAACGTT
3807278 TTGAATTTTCTCAAATATTAACTCGTTCTTAAACTTCATTCGTTAATAATAGTAACACAATTTCA
1 TTGAATTTTCTCAAATATTAACTCGTTCTTAAACTTCATTCGTTAATAATAGTAACACAATTTCA
3807343 ACTATTTATCAATTTCAATCAAATATCATAGACTTCAATTTTCTTCACTACATCAACGTT
66 ACTATTTATCAATTTCAATCAAATATCATAGACTTCAATTTTCTTCACTACATCAACGTT
3807403 T
1 T
3807404 AGTTCATGCC
Statistics
Matches: 126, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
125 126 1.00
ACGTcount: A:0.35, C:0.19, G:0.05, T:0.41
Consensus pattern (125 bp):
TTGAATTTTCTCAAATATTAACTCGTTCTTAAACTTCATTCGTTAATAATAGTAACACAATTTCA
ACTATTTATCAATTTCAATCAAATATCATAGACTTCAATTTTCTTCACTACATCAACGTT
Found at i:3808322 original size:22 final size:24
Alignment explanation
Indices: 3808280--3808323 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
3808270 TAAATAAGTT
3808280 TACTTACTTTTCTAACTTAATTCA
1 TACTTACTTTTCTAACTTAATTCA
3808304 TACTT-CTTTTCT-ACTTAATT
1 TACTTACTTTTCTAACTTAATT
3808324 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:3809050 original size:19 final size:18
Alignment explanation
Indices: 3809023--3809058 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
3809013 TTTATTCATT
*
3809023 AATTTAATAATATAATATC
1 AATTAAATAATA-AATATC
3809042 AATTAAATAATAAATAT
1 AATTAAATAATAAATAT
3809059 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:3812066 original size:13 final size:14
Alignment explanation
Indices: 3812036--3812071 Score: 65
Period size: 13 Copynumber: 2.6 Consensus size: 14
3812026 ATGGATTCTT
3812036 AAATATTTATTAAA
1 AAATATTTATTAAA
3812050 AAATATTTATT-AA
1 AAATATTTATTAAA
3812063 AAATATTTA
1 AAATATTTA
3812072 CGAAGTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AAATATTTATTAAA
Found at i:3812677 original size:13 final size:13
Alignment explanation
Indices: 3812659--3812684 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3812649 GCAGGGGAGA
3812659 AAAAGAAAGAAAG
1 AAAAGAAAGAAAG
3812672 AAAAGAAAGAAAG
1 AAAAGAAAGAAAG
3812685 GGAGAAAAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (13 bp):
AAAAGAAAGAAAG
Found at i:3814967 original size:22 final size:23
Alignment explanation
Indices: 3814942--3814990 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
3814932 ATTTTCTTAT
* *
3814942 TATTTTC-CTCCTATTTTGCTAC
1 TATTTTCACTACTATGTTGCTAC
*
3814964 TA-TTTCACTATTATGTTGCTAC
1 TATTTTCACTACTATGTTGCTAC
3814986 TATTT
1 TATTT
3814991 GTTGTTATTG
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:3815390 original size:44 final size:44
Alignment explanation
Indices: 3815327--3815415 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
3815317 GCACCTCTAC
3815327 TACCAACATATATTTACTCAAACTTATCCAAACTTGAATTAATA
1 TACCAACATATATTTACTCAAACTTATCCAAACTTGAATTAATA
*
3815371 TACCAACATATGTTTACTCAAACTTATCCAAACTTGAATTAATA
1 TACCAACATATATTTACTCAAACTTATCCAAACTTGAATTAATA
3815415 T
1 T
3815416 CTCTTTAACA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.42, C:0.20, G:0.03, T:0.35
Consensus pattern (44 bp):
TACCAACATATATTTACTCAAACTTATCCAAACTTGAATTAATA
Found at i:3819087 original size:29 final size:29
Alignment explanation
Indices: 3819054--3819112 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
3819044 TTCAAACTCC
3819054 TAAGTGTTCATATTTAACTCCAATTAAAT
1 TAAGTGTTCATATTTAACTCCAATTAAAT
3819083 TAAGTGTTCATATTTAACTCCAATTAAAT
1 TAAGTGTTCATATTTAACTCCAATTAAAT
3819112 T
1 T
3819113 TAAAGTCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.42
Consensus pattern (29 bp):
TAAGTGTTCATATTTAACTCCAATTAAAT
Found at i:3821747 original size:16 final size:17
Alignment explanation
Indices: 3821722--3821764 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
3821712 AATATAATCT
3821722 AAACTC-AAAATGATGC
1 AAACTCAAAAATGATGC
* *
3821738 AAACTTAAAAATGATTC
1 AAACTCAAAAATGATGC
*
3821755 AAAATCAAAA
1 AAACTCAAAA
3821765 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:3824865 original size:22 final size:21
Alignment explanation
Indices: 3824824--3824882 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
3824814 ATAATAAATT
*
3824824 AAAT-ATATTTAAAA-ACATAA
1 AAATAATA-TTAAAACAAATAA
3824844 AAATCAATATTAAAACAAATAA
1 AAAT-AATATTAAAACAAATAA
*
3824866 AAATAATACTAAAACAA
1 AAATAATATTAAAACAA
3824883 TTCTTAAAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 4 0.12
21 18 0.53
22 12 0.35
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (21 bp):
AAATAATATTAAAACAAATAA
Found at i:3824965 original size:16 final size:17
Alignment explanation
Indices: 3824926--3824966 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
3824916 AAAAAATGGT
3824926 TATATTAAAAATTTAAAA
1 TATATTAAAAA-TTAAAA
*
3824944 T-GATTAAAAA-TAAAA
1 TATATTAAAAATTAAAA
3824959 TATATTAA
1 TATATTAA
3824967 TATATAATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
15 6 0.30
16 5 0.25
17 8 0.40
18 1 0.05
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (17 bp):
TATATTAAAAATTAAAA
Found at i:3825563 original size:17 final size:17
Alignment explanation
Indices: 3825515--3825566 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 17
3825505 TTGGTAGAGG
3825515 GGAA-AGAAAATTAGAA
1 GGAATAGAAAATTAGAA
*
3825531 -GAATAAAAAATT-GAA
1 GGAATAGAAAATTAGAA
**
3825546 GGGGTAGAAAATTAGAA
1 GGAATAGAAAATTAGAA
3825563 GGAA
1 GGAA
3825567 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:3836080 original size:40 final size:40
Alignment explanation
Indices: 3836036--3836171 Score: 157
Period size: 40 Copynumber: 3.4 Consensus size: 40
3836026 GTTTTAATGG
*
3836036 AAAACGCCGCTAAAGGACGAGCATTAGCGGCGCTTTTTGA
1 AAAACGCCGCTAAAGGACGAGCATTAGCGGCGCTTTTTAA
* *
3836076 AAAACGCCGCTAAAGAACGAGTATTAGCGGCGCTTTTTAA
1 AAAACGCCGCTAAAGGACGAGCATTAGCGGCGCTTTTTAA
* * * * * *
3836116 AAAACGCTGCTATAGGTTC-ATCTTTAGTGGCGCTTTTTAAA
1 AAAACGCCGCTAAAGG-ACGAGCATTAGCGGCGCTTTTT-AA
*
3836157 AAAACGCCGCAAAAG
1 AAAACGCCGCTAAAG
3836172 ATTTAACACA
Statistics
Matches: 80, Mismatches: 14, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
40 65 0.81
41 15 0.19
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.24
Consensus pattern (40 bp):
AAAACGCCGCTAAAGGACGAGCATTAGCGGCGCTTTTTAA
Found at i:3836270 original size:76 final size:74
Alignment explanation
Indices: 3836137--3836323 Score: 191
Period size: 76 Copynumber: 2.5 Consensus size: 74
3836127 ATAGGTTCAT
* * *
3836137 CTTTAGTGGCGCTTTTTAAAAAAACGCCGCAAAAGATTTAACACAACGTCGTCGTTTTGTATTGA
1 CTTTAGCGGCGCTTTTT--AAAAACGCCGCAAAAGATTTAACAAAACGCCGTCGTTTTGTATTGA
3836202 GCATTTAGTAGG
64 GCATTTAGT-GG
** *
3836214 -TTTAGCGGCGCTTTTTAAAAACGCCGCAAAA-ATTTTTTTGCAAAACGCCGTTGTTTTGTATTG
1 CTTTAGCGGCGCTTTTTAAAAACGCCGCAAAAGA---TTTAACAAAACGCCGTCGTTTTGTATTG
*
3836277 AGCTTTTAGTGG
63 AGCATTTAGTGG
* * * *
3836289 CTTTCA-CGGCACTTTTTGAAAATGCCGCTAAAGAT
1 CTTT-AGCGGCGCTTTTTAAAAACGCCGCAAAAGAT
3836324 CGAGTATTAG
Statistics
Matches: 93, Mismatches: 11, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
73 1 0.01
74 16 0.17
75 2 0.02
76 72 0.77
77 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (74 bp):
CTTTAGCGGCGCTTTTTAAAAACGCCGCAAAAGATTTAACAAAACGCCGTCGTTTTGTATTGAGC
ATTTAGTGG
Found at i:3836803 original size:22 final size:22
Alignment explanation
Indices: 3836778--3836822 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
3836768 GAGTTACTAT
* *
3836778 TTTAAGGTTTATGCTTTATGGG
1 TTTAAGGATTATGCTTTAAGGG
* *
3836800 TTTAGGGATTATGGTTTAAGGG
1 TTTAAGGATTATGCTTTAAGGG
3836822 T
1 T
3836823 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:3836914 original size:21 final size:23
Alignment explanation
Indices: 3836882--3836929 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
3836872 GGGTTTATGT
3836882 TTTA-TGATTTAGG-GCTTAAGG
1 TTTAGTGATTTAGGAGCTTAAGG
* *
3836903 TTTAGTGA-TTAGGAGTTTAGGG
1 TTTAGTGATTTAGGAGCTTAAGG
3836925 TTTAG
1 TTTAG
3836930 ATTAATTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.23, C:0.02, G:0.31, T:0.44
Consensus pattern (23 bp):
TTTAGTGATTTAGGAGCTTAAGG
Found at i:3837067 original size:21 final size:21
Alignment explanation
Indices: 3837041--3837081 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
3837031 TAGGGTTTAT
3837041 GGTTTAAAGTGTATGAGTTAG
1 GGTTTAAAGTGTATGAGTTAG
3837062 GGTTTAAAGTGTATGAGTTA
1 GGTTTAAAGTGTATGAGTTA
3837082 CTATTTTAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.32, T:0.39
Consensus pattern (21 bp):
GGTTTAAAGTGTATGAGTTAG
Found at i:3837398 original size:59 final size:59
Alignment explanation
Indices: 3837295--3837415 Score: 174
Period size: 59 Copynumber: 2.1 Consensus size: 59
3837285 TTATTCATTT
* * * *
3837295 CCCCTTTCTCCCTAGTTTATTTCCCCCATTTTCCTTAATTCGAATCCCTAAAATAATCA
1 CCCCCTTCTCCCTAGTTTATTTCCCCCATTTCCCCTAATCCGAATCCCTAAAATAATCA
3837354 CCCCCTTCTCTCC-AGTTTATTT-CCCCACTTTCCCCTAATCCGAATCCCTAAAATAATCA
1 CCCCCTTCTC-CCTAGTTTATTTCCCCCA-TTTCCCCTAATCCGAATCCCTAAAATAATCA
3837413 CCC
1 CCC
3837416 ATTTTCCCCC
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
58 5 0.09
59 49 0.88
60 2 0.04
ACGTcount: A:0.23, C:0.39, G:0.03, T:0.35
Consensus pattern (59 bp):
CCCCCTTCTCCCTAGTTTATTTCCCCCATTTCCCCTAATCCGAATCCCTAAAATAATCA
Found at i:3837726 original size:7 final size:7
Alignment explanation
Indices: 3837714--3837767 Score: 81
Period size: 7 Copynumber: 7.3 Consensus size: 7
3837704 AAAAAAAATT
3837714 TTAAAAA
1 TTAAAAA
3837721 TTAAAAA
1 TTAAAAA
3837728 TTAAAAA
1 TTAAAAA
3837735 TTAAAAA
1 TTAAAAA
3837742 TTAAAAAA
1 TT-AAAAA
3837750 CTTAAAAA
1 -TTAAAAA
3837758 CTTAAAAA
1 -TTAAAAA
3837766 TT
1 TT
3837768 TAATATTTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
7 25 0.56
8 18 0.40
9 2 0.04
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.30
Consensus pattern (7 bp):
TTAAAAA
Found at i:3837727 original size:8 final size:8
Alignment explanation
Indices: 3837706--3837770 Score: 64
Period size: 7 Copynumber: 8.2 Consensus size: 8
3837696 AAATCTTCAA
3837706 AAAAAATTT
1 AAAAAA-TT
*
3837715 TAAAAATT
1 AAAAAATT
3837723 -AAAAATT
1 AAAAAATT
3837730 -AAAAATT
1 AAAAAATT
3837737 -AAAAATT
1 AAAAAATT
3837744 AAAAAACTT
1 AAAAAA-TT
*
3837753 AAAAACTT
1 AAAAAATT
*
3837761 AAAAATTT
1 AAAAAATT
3837769 AA
1 AA
3837771 TATTTAATAT
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
7 21 0.41
8 18 0.35
9 12 0.24
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (8 bp):
AAAAAATT
Found at i:3838030 original size:41 final size:40
Alignment explanation
Indices: 3837935--3838034 Score: 119
Period size: 41 Copynumber: 2.5 Consensus size: 40
3837925 GTTTTTGGAG
3837935 AAAACGCCGAAAAAATTAAACTATAATGACGTTTTTACTA
1 AAAACGCCGAAAAAATTAAACTATAATGACGTTTTTACTA
** * * * *
3837975 AAAATACCTTAAAAAATTGAGCTATAATGACGTTTTTATTA
1 AAAACGCC-GAAAAAATTAAACTATAATGACGTTTTTACTA
*
3838016 AAAACGTCGCAAAAAATTA
1 AAAACGCCG-AAAAAATTA
3838035 TTATTTAAAA
Statistics
Matches: 47, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
40 6 0.13
41 41 0.87
ACGTcount: A:0.48, C:0.13, G:0.10, T:0.29
Consensus pattern (40 bp):
AAAACGCCGAAAAAATTAAACTATAATGACGTTTTTACTA
Found at i:3841963 original size:6 final size:6
Alignment explanation
Indices: 3841923--3841976 Score: 56
Period size: 6 Copynumber: 8.7 Consensus size: 6
3841913 ATTTAATCTA
* *
3841923 ATTTTT ATTATTT A-TTTT AGTTTTG ATTCTAT ATTTTT ATTTTT ATTTTT
1 ATTTTT ATT-TTT ATTTTT A-TTTTT ATT-TTT ATTTTT ATTTTT ATTTTT
3841973 ATTT
1 ATTT
3841977 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:3845233 original size:14 final size:14
Alignment explanation
Indices: 3845214--3845243 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3845204 TATTTTCAAG
3845214 ATAGATTAATGCAT
1 ATAGATTAATGCAT
*
3845228 ATAGATTCATGCAT
1 ATAGATTAATGCAT
3845242 AT
1 AT
3845244 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:0.10, G:0.13, T:0.37
Consensus pattern (14 bp):
ATAGATTAATGCAT
Found at i:3847874 original size:25 final size:27
Alignment explanation
Indices: 3847846--3847897 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
3847836 AATCAGTAAA
*
3847846 ATTTTTCTATCA-AT-ATTTTCATACG
1 ATTTTCCTATCATATAATTTTCATACG
3847871 ATTTTCCTATCATATCAATTTTCATAC
1 ATTTTCCTATCATAT-AATTTTCATAC
3847898 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:3848654 original size:18 final size:18
Alignment explanation
Indices: 3848607--3848655 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
3848597 TTCATGGCTA
*
3848607 TGGTCAAAATTATAATGC
1 TGGTCAAAATTGTAATGC
3848625 TGGTCAAAATTGTAATGC
1 TGGTCAAAATTGTAATGC
3848643 TGGTCAAAATTGT
1 TGGTCAAAATTGT
3848656 TCTCTGCCCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (18 bp):
TGGTCAAAATTGTAATGC
Found at i:3853523 original size:29 final size:30
Alignment explanation
Indices: 3853452--3853529 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 30
3853442 TTTAACGGAA
* * *
3853452 GAGTGACTAAAATATTAAATTTTGATAACGT
1 GAGTGACTAAAACA-GAAATTTTGATAACCT
* * * *
3853483 TAGTAACTAAAAGAGAAATTTTTA-AACCT
1 GAGTGACTAAAACAGAAATTTTGATAACCT
3853512 GAGTGACTAAAACAGAAA
1 GAGTGACTAAAACAGAAA
3853530 CACACTAATA
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
29 19 0.50
30 8 0.21
31 11 0.29
ACGTcount: A:0.47, C:0.09, G:0.15, T:0.28
Consensus pattern (30 bp):
GAGTGACTAAAACAGAAATTTTGATAACCT
Found at i:3854893 original size:21 final size:21
Alignment explanation
Indices: 3854867--3854921 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
3854857 ACAGCGGTGA
*
3854867 CGGTGAGATTAGTTACTGTAG
1 CGGTGAGATTAGATACTGTAG
*
3854888 CGGTGAGATTGGATACTGTAG
1 CGGTGAGATTAGATACTGTAG
3854909 CGGTGAGATTAGA
1 CGGTGAGATTAGA
3854922 AACAGCGGTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.25, C:0.09, G:0.36, T:0.29
Consensus pattern (21 bp):
CGGTGAGATTAGATACTGTAG
Found at i:3855161 original size:18 final size:18
Alignment explanation
Indices: 3855138--3855220 Score: 70
Period size: 18 Copynumber: 4.8 Consensus size: 18
3855128 TATTTTAATG
3855138 AATTATATAATCAATTTA
1 AATTATATAATCAATTTA
* *
3855156 AATTAT-TTATTAGA--TA
1 AATTATATAATCA-ATTTA
*
3855172 AA--ATGATAAT-AATTTTT
1 AATTAT-ATAATCAA-TTTA
3855189 AATTATATAATCAATTTA
1 AATTATATAATCAATTTA
3855207 AATTATATAATCAA
1 AATTATATAATCAA
3855221 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:3857331 original size:18 final size:17
Alignment explanation
Indices: 3857308--3857350 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
3857298 ATCGTGTTTG
3857308 ATTTTTATTTCTAAATTT
1 ATTTTTATTT-TAAATTT
*
3857326 ATTTTTGATTTTAGATTT
1 ATTTTT-ATTTTAAATTT
*
3857344 ATCTTTA
1 ATTTTTA
3857351 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:3862385 original size:49 final size:49
Alignment explanation
Indices: 3862289--3862386 Score: 135
Period size: 49 Copynumber: 2.0 Consensus size: 49
3862279 TATTTATTTT
* * *
3862289 TGTTAAAAGGTGGCAACAAACAGCATATGTACATTATCCGAATGAAATA
1 TGTTAAAAGGTGGCAACAAACAGCACATGTACATTACCCGAACGAAATA
* *
3862338 TGTTAAAAGGTGGCAACAAATAGCACATGTA-AGTTACCCGGACGAAATA
1 TGTTAAAAGGTGGCAACAAACAGCACATGTACA-TTACCCGAACGAAATA
3862387 CAGCAACATG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
48 1 0.02
49 42 0.98
ACGTcount: A:0.42, C:0.15, G:0.20, T:0.22
Consensus pattern (49 bp):
TGTTAAAAGGTGGCAACAAACAGCACATGTACATTACCCGAACGAAATA
Found at i:3867767 original size:5 final size:5
Alignment explanation
Indices: 3867757--3867785 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
3867747 CAATTTGTGA
3867757 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
3867786 GAACACACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:3871629 original size:46 final size:46
Alignment explanation
Indices: 3871578--3871844 Score: 365
Period size: 46 Copynumber: 5.8 Consensus size: 46
3871568 GTGTGCTCTC
* * *
3871578 TGATATGGAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
* *
3871624 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACG
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
* * *
3871670 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACAATGGCAACG
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
*
3871716 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
*** *
3871762 TGACGGGAAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
1 TGATATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
* * *
3871809 TGATA-GAAAACGAGTAAAACCATAGTTGAAAGATAC
1 TGATATG-AAATGAGTAAGACCATGGTTGAAAGATAC
3871845 TATGACATCA
Statistics
Matches: 204, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
46 162 0.79
47 42 0.21
ACGTcount: A:0.41, C:0.13, G:0.24, T:0.22
Consensus pattern (46 bp):
TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
Found at i:3875067 original size:49 final size:49
Alignment explanation
Indices: 3874995--3875092 Score: 153
Period size: 49 Copynumber: 2.0 Consensus size: 49
3874985 CAAGGAGGAG
* *
3874995 TGTTAAAAGGTGGCAACAAACAGCATATGTACGTTA-TCTGGATGAAATA
1 TGTTAAAAGGTGGCAACAAACAGCACATGTAAGTTACTC-GGATGAAATA
*
3875044 TGTTAAATGGTGGCAACAAACAGCACATGTAAGTTACTCGGATGAAATA
1 TGTTAAAAGGTGGCAACAAACAGCACATGTAAGTTACTCGGATGAAATA
3875093 CAGCAACATG
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
49 43 0.96
50 2 0.04
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.26
Consensus pattern (49 bp):
TGTTAAAAGGTGGCAACAAACAGCACATGTAAGTTACTCGGATGAAATA
Found at i:3876880 original size:21 final size:22
Alignment explanation
Indices: 3876835--3876899 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 22
3876825 TAAATCTTAA
*
3876835 AAAAAATTATGTTTT-TATATTTT
1 AAAAAA-TAT-TTTTATATTTTTT
*
3876858 AAATAAT-TTTTTATATTTTTT
1 AAAAAATATTTTTATATTTTTT
*
3876879 AAAAAATATTATTATTATTTT
1 AAAAAATATTTTTA-TATTTT
3876900 CACAGCAGTC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
20 4 0.11
21 14 0.40
22 6 0.17
23 11 0.31
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
AAAAAATATTTTTATATTTTTT
Found at i:3879129 original size:11 final size:12
Alignment explanation
Indices: 3879108--3879137 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
3879098 TTAGATTATA
3879108 AAAATATATTTT
1 AAAATATATTTT
3879120 AAAA-ATATTTT
1 AAAATATATTTT
3879131 AAAATAT
1 AAAATAT
3879138 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:3879190 original size:15 final size:15
Alignment explanation
Indices: 3879170--3879200 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3879160 TAAAATATGT
3879170 TAATATCGATACATA
1 TAATATCGATACATA
*
3879185 TAATATCTATACATA
1 TAATATCGATACATA
3879200 T
1 T
3879201 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:3879788 original size:23 final size:23
Alignment explanation
Indices: 3879762--3879807 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
3879752 TGGTTAGTAA
3879762 CTTATTTTAATCCTGTTTTATTT
1 CTTATTTTAATCCTGTTTTATTT
3879785 CTTATTTTAATCCTGTTTTATTT
1 CTTATTTTAATCCTGTTTTATTT
3879808 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:3884115 original size:37 final size:36
Alignment explanation
Indices: 3884041--3884117 Score: 88
Period size: 37 Copynumber: 2.1 Consensus size: 36
3884031 TGAATTGATG
*
3884041 AAATTGTAGAATAAGAAAATTTATTTTTGAGGAATT
1 AAATTGTAGAATAAGAAAATTTATTTTAGAGGAATT
3884077 AAATTGTAGAATGATA-AAAATTTAGATTTTAGA-G-ATT
1 AAATTGTAGAAT-A-AGAAAATTT--ATTTTAGAGGAATT
3884114 AAAT
1 AAAT
3884118 CTTAAAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
36 12 0.33
37 15 0.42
38 2 0.06
39 7 0.19
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.38
Consensus pattern (36 bp):
AAATTGTAGAATAAGAAAATTTATTTTAGAGGAATT
Found at i:3884142 original size:13 final size:13
Alignment explanation
Indices: 3884124--3884148 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3884114 AAATCTTAAA
3884124 AAAATATAAAATT
1 AAAATATAAAATT
3884137 AAAATATAAAAT
1 AAAATATAAAAT
3884149 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:3891791 original size:65 final size:65
Alignment explanation
Indices: 3891687--3891817 Score: 262
Period size: 65 Copynumber: 2.0 Consensus size: 65
3891677 AACGATAAGT
3891687 CTACTATGTTTAATGCTGTTTCAATGCTTAATAGTGAGATTTCAAATTTTAACACACAAAAATGA
1 CTACTATGTTTAATGCTGTTTCAATGCTTAATAGTGAGATTTCAAATTTTAACACACAAAAATGA
3891752 CTACTATGTTTAATGCTGTTTCAATGCTTAATAGTGAGATTTCAAATTTTAACACACAAAAATGA
1 CTACTATGTTTAATGCTGTTTCAATGCTTAATAGTGAGATTTCAAATTTTAACACACAAAAATGA
3891817 C
1 C
3891818 GTGCTTTCAC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.37
Consensus pattern (65 bp):
CTACTATGTTTAATGCTGTTTCAATGCTTAATAGTGAGATTTCAAATTTTAACACACAAAAATGA
Found at i:3891858 original size:31 final size:31
Alignment explanation
Indices: 3891823--3891888 Score: 132
Period size: 31 Copynumber: 2.1 Consensus size: 31
3891813 ATGACGTGCT
3891823 TTCACTCAAACACCATTAATCACCCATAATG
1 TTCACTCAAACACCATTAATCACCCATAATG
3891854 TTCACTCAAACACCATTAATCACCCATAATG
1 TTCACTCAAACACCATTAATCACCCATAATG
3891885 TTCA
1 TTCA
3891889 AAATAGGGCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.38, C:0.32, G:0.03, T:0.27
Consensus pattern (31 bp):
TTCACTCAAACACCATTAATCACCCATAATG
Found at i:3896092 original size:9 final size:9
Alignment explanation
Indices: 3896078--3896111 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
3896068 TTGGTAAAGC
3896078 ATTTCTTGT
1 ATTTCTTGT
3896087 ATTTCTTGT
1 ATTTCTTGT
3896096 ATTTCTTGT
1 ATTTCTTGT
*
3896105 ATATCTT
1 ATTTCTT
3896112 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:3903182 original size:18 final size:18
Alignment explanation
Indices: 3903159--3903195 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
3903149 GGATGTCAAT
3903159 TTAATTTGGATTTAATTA
1 TTAATTTGGATTTAATTA
3903177 TTAATTTGGATTTAATTA
1 TTAATTTGGATTTAATTA
3903195 T
1 T
3903196 CCCTTTTGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (18 bp):
TTAATTTGGATTTAATTA
Found at i:3908844 original size:11 final size:11
Alignment explanation
Indices: 3908810--3908844 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
3908800 TAAATGTCTC
3908810 TAAAATAATAA
1 TAAAATAATAA
*
3908821 CAAAATTAATAA
1 TAAAA-TAATAA
3908833 TAAAATAATAA
1 TAAAATAATAA
3908844 T
1 T
3908845 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:3908966 original size:40 final size:40
Alignment explanation
Indices: 3908921--3909001 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
3908911 GCAAAAAAGA
*
3908921 AAGTTTAGGTTATTCGAGCTAGGCCCGAACCAAAAAATCT
1 AAGTTTAGGTTATTCGAGCCAGGCCCGAACCAAAAAATCT
3908961 AAGTTTAGGTTATTCGAGCCAGGCCCGAACCAAAAAATCT
1 AAGTTTAGGTTATTCGAGCCAGGCCCGAACCAAAAAATCT
3909001 A
1 A
3909002 CTCAGGACCT
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:3911505 original size:31 final size:32
Alignment explanation
Indices: 3911448--3911507 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
3911438 ATATGTATGA
*
3911448 TTGAACTAAAAATTAAAGTTTCATGTATACAT
1 TTGAACTAAAAATCAAAGTTTCATGTATACAT
* *
3911480 TTGAACT-ACAATCAAAGTTTTATGTATA
1 TTGAACTAAAAATCAAAGTTTCATGTATA
3911508 TAATTGCACC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 18 0.72
32 7 0.28
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (32 bp):
TTGAACTAAAAATCAAAGTTTCATGTATACAT
Found at i:3912521 original size:17 final size:18
Alignment explanation
Indices: 3912483--3912518 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3912473 TATATATATG
3912483 TATTGAAAATTTTGATTT
1 TATTGAAAATTTTGATTT
* *
3912501 TATTGAAATTTTTTATTT
1 TATTGAAAATTTTGATTT
3912519 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:3917291 original size:12 final size:12
Alignment explanation
Indices: 3917274--3917321 Score: 60
Period size: 12 Copynumber: 3.8 Consensus size: 12
3917264 GTGGGAGTAA
3917274 GTTTTATATTTG
1 GTTTTATATTTG
*
3917286 GTTTTATATGTTAAA
1 GTTTTATAT-TT--G
3917301 GTTTTATATTTG
1 GTTTTATATTTG
3917313 GTTTTATAT
1 GTTTTATAT
3917322 GTTAATGACA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
12 18 0.58
13 2 0.06
14 2 0.06
15 9 0.29
ACGTcount: A:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (12 bp):
GTTTTATATTTG
Found at i:3917302 original size:27 final size:27
Alignment explanation
Indices: 3917272--3917326 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
3917262 TAGTGGGAGT
3917272 AAGTTTTATATTTGGTTTTATATGTTA
1 AAGTTTTATATTTGGTTTTATATGTTA
3917299 AAGTTTTATATTTGGTTTTATATGTTA
1 AAGTTTTATATTTGGTTTTATATGTTA
3917326 A
1 A
3917327 TGACATACTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (27 bp):
AAGTTTTATATTTGGTTTTATATGTTA
Found at i:3917306 original size:15 final size:15
Alignment explanation
Indices: 3917286--3917326 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 15
3917276 TTTATATTTG
3917286 GTTTTATATGTTAAA
1 GTTTTATATGTTAAA
*
3917301 GTTTTATAT-TT--G
1 GTTTTATATGTTAAA
3917313 GTTTTATATGTTAA
1 GTTTTATATGTTAA
3917327 TGACATACTG
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
12 9 0.41
13 2 0.09
14 2 0.09
15 9 0.41
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.59
Consensus pattern (15 bp):
GTTTTATATGTTAAA
Found at i:3926240 original size:25 final size:26
Alignment explanation
Indices: 3926212--3926264 Score: 81
Period size: 25 Copynumber: 2.0 Consensus size: 26
3926202 AAAAAATTAA
*
3926212 AAATTAGAAAAAAA-ATAAAACAAAC
1 AAATTAGAAAAAAACATAAAAAAAAC
3926237 AAATTAGAAAAAAATCATAAAAAAAAC
1 AAATTAGAAAAAAA-CATAAAAAAAAC
3926264 A
1 A
3926265 CTAAGTATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 14 0.56
27 11 0.44
ACGTcount: A:0.75, C:0.08, G:0.04, T:0.13
Consensus pattern (26 bp):
AAATTAGAAAAAAACATAAAAAAAAC
Found at i:3928400 original size:24 final size:24
Alignment explanation
Indices: 3928366--3928420 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
3928356 ATATGTATAC
*
3928366 ATGAGTTGATGAAAGTTATGAATT
1 ATGAGTCGATGAAAGTTATGAATT
3928390 ATGAGTCGATGAAAGTTATGAATT
1 ATGAGTCGATGAAAGTTATGAATT
3928414 ATGAGTC
1 ATGAGTC
3928421 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:3928861 original size:81 final size:83
Alignment explanation
Indices: 3928726--3928882 Score: 219
Period size: 81 Copynumber: 1.9 Consensus size: 83
3928716 TAAAGACATT
* *
3928726 TTAAGTTAAGACTTACCAGTATTGTCAGTTTAGATTTCTGCAGAGGCATTATGTTGTT-T-TATG
1 TTAAGTTAAGACTTACCAGTATTGTCAGTTTAAAGTTCTGCAGAGGCATTATGTTGTTCTGTATG
* *
3928789 TATTGTATATGAGCTATG
66 GATTGCATATGAGCTATG
* * * * *
3928807 TTAAGTTCAGATTTACCAGTATTGTCAGTTTAAAGTTCTGCGGAGTCCTTATGTTGTTCTGTATG
1 TTAAGTTAAGACTTACCAGTATTGTCAGTTTAAAGTTCTGCAGAGGCATTATGTTGTTCTGTATG
3928872 GATTGCATATG
66 GATTGCATATG
3928883 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:3929697 original size:3 final size:3
Alignment explanation
Indices: 3929689--3929720 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3929679 CTTTGCTTTT
3929689 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
3929721 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:3930875 original size:24 final size:24
Alignment explanation
Indices: 3930846--3930896 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
3930836 CTCCATTCAA
*
3930846 TCGTAGACGTAGCCCTTCTCCAAT
1 TCGTAGACGGAGCCCTTCTCCAAT
* *
3930870 TCGTAGGCGGAGCCGTTCTCCAAT
1 TCGTAGACGGAGCCCTTCTCCAAT
3930894 TCG
1 TCG
3930897 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:3930901 original size:24 final size:24
Alignment explanation
Indices: 3930856--3930901 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
3930846 TCGTAGACGT
*
3930856 AGCCCTTCTCCAATTCGTAGGCGG
1 AGCCCTTCTCCAATTCGCAGGCGG
*
3930880 AGCCGTTCTCCAATTCGCAGGC
1 AGCCCTTCTCCAATTCGCAGGC
3930902 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:3932651 original size:15 final size:16
Alignment explanation
Indices: 3932621--3932659 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
3932611 TAGTAAAAAT
3932621 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
*
3932638 ATAATTTA-TATTTTT
1 ATAATTTATTATTTTA
3932653 ATAATTT
1 ATAATTT
3932660 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:3938590 original size:29 final size:26
Alignment explanation
Indices: 3938533--3938591 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
3938523 TTGAAAAAAT
* *
3938533 ATATTTGATAATTTTAATTATCTCAA
1 ATATTTAATAATTTTAATTATATCAA
3938559 ATATTTAATAATTTTAGCAATTATATCAA
1 ATATTTAATAATTTT---AATTATATCAA
3938588 ATAT
1 ATAT
3938592 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:3944719 original size:79 final size:79
Alignment explanation
Indices: 3944606--3944760 Score: 258
Period size: 79 Copynumber: 2.0 Consensus size: 79
3944596 ATAAAGTATG
*
3944606 GTTTTAATTAATAATAAAAACAAAATAGTATGGGGGAATGGTTTTAATTAATAATAAAAACAAAA
1 GTTTTAATTAATAATAAAAACAAAATAGTATGGGGGAATAGTTTTAATTAATAAT-AAAACAAAA
*
3944671 TAGTATGGGGGAATA
65 TAGCATGGGGGAATA
* *
3944686 GTTTTAATTAATAAT-AAAACAAAATAGTATGGGGGAGTAGTTTTAATTAATAATAAAACAAAGT
1 GTTTTAATTAATAATAAAAACAAAATAGTATGGGGGAATAGTTTTAATTAATAATAAAACAAAAT
3944750 AGCATGGGGGA
66 AGCATGGGGGA
3944761 GTGAAATCAA
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
78 19 0.27
79 37 0.52
80 15 0.21
ACGTcount: A:0.47, C:0.03, G:0.20, T:0.30
Consensus pattern (79 bp):
GTTTTAATTAATAATAAAAACAAAATAGTATGGGGGAATAGTTTTAATTAATAATAAAACAAAAT
AGCATGGGGGAATA
Found at i:3944762 original size:39 final size:40
Alignment explanation
Indices: 3944606--3944760 Score: 260
Period size: 39 Copynumber: 3.9 Consensus size: 40
3944596 ATAAAGTATG
*
3944606 GTTTTAATTAATAATAAAAACAAAATAGTATGGGGGAATG
1 GTTTTAATTAATAATAAAAACAAAATAGTATGGGGGAATA
3944646 GTTTTAATTAATAATAAAAACAAAATAGTATGGGGGAATA
1 GTTTTAATTAATAATAAAAACAAAATAGTATGGGGGAATA
*
3944686 GTTTTAATTAATAAT-AAAACAAAATAGTATGGGGGAGTA
1 GTTTTAATTAATAATAAAAACAAAATAGTATGGGGGAATA
* *
3944725 GTTTTAATTAATAAT-AAAACAAAGTAGCATGGGGGA
1 GTTTTAATTAATAATAAAAACAAAATAGTATGGGGGA
3944761 GTGAAATCAA
Statistics
Matches: 111, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
39 57 0.51
40 54 0.49
ACGTcount: A:0.47, C:0.03, G:0.20, T:0.30
Consensus pattern (40 bp):
GTTTTAATTAATAATAAAAACAAAATAGTATGGGGGAATA
Found at i:3946576 original size:13 final size:13
Alignment explanation
Indices: 3946558--3946582 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3946548 GAGTTTTGAG
3946558 TTCTTCGATCTGC
1 TTCTTCGATCTGC
3946571 TTCTTCGATCTG
1 TTCTTCGATCTG
3946583 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:3946629 original size:44 final size:44
Alignment explanation
Indices: 3946565--3946827 Score: 277
Period size: 44 Copynumber: 6.0 Consensus size: 44
3946555 GAGTTCTTCG
* *
3946565 ATCTGCT-TCTTCGATCTGTTCCCTGTAAACACAGGGATGCCAA
1 ATCTGCTATCTTCAATCTGTTCCCTATAAACACAGGGATGCCAA
*
3946608 ATCTGCTGTCTTCAA-CTTGTTCCCTATAAACACAGGGATGCCAA
1 ATCTGCTATCTTCAATC-TGTTCCCTATAAACACAGGGATGCCAA
3946652 ATCTGCTATCTTCAA-CTTGTTCCCTATAAACACAGGGATGCC--
1 ATCTGCTATCTTCAATC-TGTTCCCTATAAACACAGGGATGCCAA
** * * * * * * *
3946694 ATGCTGAAATCTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAG
1 AT-CTGCTATCTTCAATCTG-TTCCCTATAAACACAGGGATGCCAA
* *
3946740 ATCTGCTATCTTCGATCTGTTCCCTATAAGCACAGGGATGCCAA
1 ATCTGCTATCTTCAATCTGTTCCCTATAAACACAGGGATGCCAA
* * *
3946784 ATCTGCTGTTTTTCAA-CTTGTTCCCTATAAGCACAGGGATGCCA
1 ATCTGCT-ATCTTCAATC-TGTTCCCTATAAACACAGGGATGCCA
3946828 TGCTGAAATC
Statistics
Matches: 190, Mismatches: 21, Indels: 16
0.84 0.09 0.07
Matches are distributed among these distances:
42 2 0.01
43 20 0.11
44 120 0.63
45 46 0.24
46 2 0.01
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.30
Consensus pattern (44 bp):
ATCTGCTATCTTCAATCTGTTCCCTATAAACACAGGGATGCCAA
Found at i:3946876 original size:132 final size:130
Alignment explanation
Indices: 3946572--3946890 Score: 435
Period size: 132 Copynumber: 2.4 Consensus size: 130
3946562 TCGATCTGCT
* * * * *
3946572 TCTTCGATCTG-TTCCCTGTAAACACAGGGATGCCAAATCTGCTGTCTTC-AACTTGTTCCCTAT
1 TCTTCGATCTGCTTCACTGT-AACACA-GGAAGGCAAATCTGCTATCTTCGATC-TGTTCCCTAT
3946635 AAACACAGGGATGCCAAATCTGCTATCTTCAACTTGTTCCCTATAAACACAGGGATGCCATGCTG
63 AAACACAGGGATGCCAAATCTGCTATCTTCAACTTGTTCCCTATAAACACAGGGATGCCATGCTG
3946700 AAA
128 AAA
* *
3946703 TCTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCGATCTGTTCCCTATA
1 TCTTCGATCTGCTTCACTGTAA-CACAGGAA-GGCAAATCTGCTATCTTCGATCTGTTCCCTATA
* * * *
3946768 AGCACAGGGATGCCAAATCTGCTGTTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTG
64 AACACAGGGATGCCAAATCTGCT-ATCTTCAACTTGTTCCCTATAAACACAGGGATGCCATGCTG
3946833 AAA
128 AAA
* * *
3946836 TCTTCGATCTGCTTCACTGTAACTCAGGAAGGCGATATCTGCTATCTTTGATCTG
1 TCTTCGATCTGCTTCACTGTAACACAGGAAGGC-AAATCTGCTATCTTCGATCTG
3946891 CCCCCTATCT
Statistics
Matches: 168, Mismatches: 14, Indels: 11
0.87 0.07 0.06
Matches are distributed among these distances:
131 18 0.11
132 85 0.51
133 65 0.39
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (130 bp):
TCTTCGATCTGCTTCACTGTAACACAGGAAGGCAAATCTGCTATCTTCGATCTGTTCCCTATAAA
CACAGGGATGCCAAATCTGCTATCTTCAACTTGTTCCCTATAAACACAGGGATGCCATGCTGAAA
Found at i:3947277 original size:205 final size:205
Alignment explanation
Indices: 3946925--3947506 Score: 1033
Period size: 205 Copynumber: 2.8 Consensus size: 205
3946915 AAATCTATTT
* *
3946925 CTTCGATTTGTTCCCTGACGATACAGAGACGACAAATCATCTTAGATTTACTTTCTCGTAATCAC
1 CTTCGATTCGTTCTCTGACGATACAGAGACGACAAATCATCTTAGATTTACTTTCTCGTAATCAC
*
3946990 GTGAAAGCCAAATCAGCTATGTCTTTGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTT
*
3947055 GGATCTGCTTCAGTGAAATCATCTGAAGGCGAGATCTGCTATGTGTTTGCTCTCCATCAAAACGA
131 GGATCTGCTTCAGTGAAATCATCTGAAGGCGAGATCTGCTATGTGTCTGCTCTCCATCAAAACGA
3947120 AGATGCCAAA
196 AGATGCCAAA
3947130 CTTCGATTCGTTCTCTGACGATACAGAGACGACAAATCATCTTAGATTTACTTTCTCGTAATCAC
1 CTTCGATTCGTTCTCTGACGATACAGAGACGACAAATCATCTTAGATTTACTTTCTCGTAATCAC
*
3947195 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATATT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTT
**
3947260 GGATCTGCTTCAGTGAAATCATCTGAAGGCGAGATCTGCTATGTGTCTGCTCTCCATCAAAGTGA
131 GGATCTGCTTCAGTGAAATCATCTGAAGGCGAGATCTGCTATGTGTCTGCTCTCCATCAAAACGA
3947325 AGATGCCAAA
196 AGATGCCAAA
*
3947335 CTTCGATTCGTTCTCTGACGATACAGAGACGACAAATCATCTTAGATTTGCTTTCTCGTAATCAC
1 CTTCGATTCGTTCTCTGACGATACAGAGACGACAAATCATCTTAGATTTACTTTCTCGTAATCAC
* *
3947400 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAACACAAGGATGCCAAACCATCTC
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTT
* *
3947465 GGATCTGCTTCAGT-ATAA-CATCTGAAGGCCAGATCTGTTATG
131 GGATCTGCTTCAGTGA-AATCATCTGAAGGCGAGATCTGCTATG
3947507 CTGCGGCCTA
Statistics
Matches: 363, Mismatches: 13, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
204 23 0.06
205 340 0.94
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (205 bp):
CTTCGATTCGTTCTCTGACGATACAGAGACGACAAATCATCTTAGATTTACTTTCTCGTAATCAC
GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTT
GGATCTGCTTCAGTGAAATCATCTGAAGGCGAGATCTGCTATGTGTCTGCTCTCCATCAAAACGA
AGATGCCAAA
Found at i:3963095 original size:38 final size:38
Alignment explanation
Indices: 3962955--3963100 Score: 160
Period size: 37 Copynumber: 3.9 Consensus size: 38
3962945 TAAAGTATGG
* *
3962955 TTAATTAATAA-AAA-AAACATA--AT-GGGGAATGGTT
1 TTAATTAATAATAAACAAA-ATAGTATGGGGGAGTAGTT
*
3962989 TTAATTAATAATAAAAAACAAAATAGTATGGGGGAATAGTT
1 TTAATTAATAAT---AAACAAAATAGTATGGGGGAGTAGTT
*
3963030 TTAATT-ATAATAAACAAAATAGTATGGGAGAGTAGTT
1 TTAATTAATAATAAACAAAATAGTATGGGGGAGTAGTT
* *
3963067 TTAATTAATAATAAACAAAGTAGCATGGGGGAGT
1 TTAATTAATAATAAACAAAATAGTATGGGGGAGT
3963101 GAAATCAACT
Statistics
Matches: 97, Mismatches: 6, Indels: 14
0.83 0.05 0.12
Matches are distributed among these distances:
34 11 0.11
37 30 0.31
38 30 0.31
39 3 0.03
40 7 0.07
41 16 0.16
ACGTcount: A:0.48, C:0.03, G:0.19, T:0.29
Consensus pattern (38 bp):
TTAATTAATAATAAACAAAATAGTATGGGGGAGTAGTT
Found at i:3965393 original size:195 final size:192
Alignment explanation
Indices: 3965038--3965528 Score: 775
Period size: 195 Copynumber: 2.5 Consensus size: 192
3965028 AACATCACAC
3965038 TGAAAG-CAAATC-GCTATGTCTT-GATTTGTTCCTTGTAA-ACAAAGGATGCCAAACCATCTTG
1 TGAAAGCCAAATCAGCTATGTCTTCGATTTGTT-CTTGTAACAC-AAGGATGCCAAACCATCTTG
3965099 GATCTGCTTCAGTAAAACATCTGAAGGCAGATCTGCTATGTTTGCTCTCCATCAAAGTAGATGCA
64 GATCTGCTTCAGT-AAACATCTGAAGGCAGATCTGCTATGTTTGCTCTCCATCAAAGTAGATGCA
3965164 AACTTCGATTCGTTCTCTGACATACAGAGACGACAAATCATCTTAGATTT-CTTCTCGTAA-ACG
128 AACTTCGATTCGTTCTCTGACATACAGAGACGACAAATCATCTTAGATTTGCTTCTCGTAATACG
3965227 TGAAAGCCAAATCAGCTATGTCTTCGA-TTGTTCTTGTAACACAAGGATGCCAAACCAT-TTGGA
1 TGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCTTGTAACACAAGGATGCCAAACCATCTTGGA
3965290 TCTGCTTCAGTAAATCATCTGAAGGCGAGATCTGCTATGTGTCTGCTCTCCATCAAAGTGAAGAT
66 TCTGCTTCAGTAAA-CATCTGAAGGC-AGATCTGCTATGT-T-TGCTCTCCATCAAAGT--AGAT
3965355 GCCAAACTTCGATTCGTTCTCTGACATACAGAGACGACAAATCATCTTAGATTTGCTTCTCGTAA
125 G-CAAACTTCGATTCGTTCTCTGACATACAGAGACGACAAATCATCTTAGATTTGCTTCTCGTAA
3965420 TACG
189 TACG
*
3965424 TGAAAGCC-AATCAGCTATGTCTTCGATTTGCTCCTTGTAAACACAAGGATGCCAAACCATCTTG
1 TGAAAGCCAAATCAGCTATGTCTTCGATTTG-TTCTTGT-AACACAAGGATGCCAAACCATCTTG
*
3965488 GATCTGCTTCAGTATAACATCTGAAGGCCAGATCTGTTATG
64 GATCTGCTTCAGTA-AACATCTGAAGG-CAGATCTGCTATG
3965529 CTGCGGCCTA
Statistics
Matches: 281, Mismatches: 2, Indels: 27
0.91 0.01 0.09
Matches are distributed among these distances:
188 3 0.01
189 33 0.12
190 42 0.15
191 18 0.06
192 18 0.06
194 5 0.02
195 52 0.19
196 28 0.10
197 14 0.05
198 6 0.02
199 21 0.07
200 38 0.14
201 3 0.01
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.30
Consensus pattern (192 bp):
TGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCTTGTAACACAAGGATGCCAAACCATCTTGGA
TCTGCTTCAGTAAACATCTGAAGGCAGATCTGCTATGTTTGCTCTCCATCAAAGTAGATGCAAAC
TTCGATTCGTTCTCTGACATACAGAGACGACAAATCATCTTAGATTTGCTTCTCGTAATACG
Found at i:3973352 original size:13 final size:15
Alignment explanation
Indices: 3973322--3973352 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3973312 TTCCAGATTT
3973322 TCTTTTCTACCTCTC
1 TCTTTTCTACCTCTC
3973337 TCTTTTCTACCTCTC
1 TCTTTTCTACCTCTC
3973352 T
1 T
3973353 GGAAAGTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.39, G:0.00, T:0.55
Consensus pattern (15 bp):
TCTTTTCTACCTCTC
Found at i:3977942 original size:40 final size:39
Alignment explanation
Indices: 3977792--3977948 Score: 251
Period size: 39 Copynumber: 4.0 Consensus size: 39
3977782 TTGATTCCAC
* * * *
3977792 TCCCCCATGCTACTTTGTTTTATTATTAATTAAAACTAC
1 TCCCCCATACTATTTTGTTTTATTATTAATTAAAACCAT
*
3977831 TCCCCCATACTATTTTGTTTTATTATTAATTAAAACTAT
1 TCCCCCATACTATTTTGTTTTATTATTAATTAAAACCAT
*
3977870 TCCCCCATACTATTTTATTTTATTATTAATTAAAACCAT
1 TCCCCCATACTATTTTGTTTTATTATTAATTAAAACCAT
3977909 TCCCCCATACTATTTTGTTTTTATTATTAATTAAAACCAT
1 TCCCCCATACTATTTTG-TTTTATTATTAATTAAAACCAT
3977949 ACTTTATTTT
Statistics
Matches: 111, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
39 89 0.80
40 22 0.20
ACGTcount: A:0.31, C:0.20, G:0.03, T:0.46
Consensus pattern (39 bp):
TCCCCCATACTATTTTGTTTTATTATTAATTAAAACCAT
Found at i:3978587 original size:23 final size:22
Alignment explanation
Indices: 3978550--3978606 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
3978540 AACCCCCTCT
**
3978550 AATACAATCTCTTCTCTCCCCAA
1 AATACAATCGATTCT-TCCCCAA
*
3978573 AATACAATCGATTCTTCCTCAA
1 AATACAATCGATTCTTCCCCAA
* *
3978595 AACACCATCGAT
1 AATACAATCGAT
3978607 CCCCCCTCCC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 16 0.55
23 13 0.45
ACGTcount: A:0.35, C:0.33, G:0.04, T:0.28
Consensus pattern (22 bp):
AATACAATCGATTCTTCCCCAA
Found at i:3983114 original size:16 final size:17
Alignment explanation
Indices: 3983095--3983127 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
3983085 ATTTTAGAGC
3983095 ATATAAATTTGA-AACT
1 ATATAAATTTGATAACT
*
3983111 ATATATATTTGATAACT
1 ATATAAATTTGATAACT
3983128 TTTTCAAAGC
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:3983245 original size:21 final size:19
Alignment explanation
Indices: 3983217--3983266 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 19
3983207 TATTTTAGAA
3983217 AATTTTTAAATTTCTTTAT
1 AATTTTTAAATTTCTTTAT
* *
3983236 ATATTCTTTAGATTTTTTTAT
1 A-ATT-TTTAAATTTCTTTAT
3983257 AATTTTTAAA
1 AATTTTTAAA
3983267 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:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (19 bp):
AATTTTTAAATTTCTTTAT
Found at i:3991171 original size:24 final size:24
Alignment explanation
Indices: 3991144--3991193 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
3991134 AACCCAATTG
*
3991144 ATTGGATTTTTAATTTAATTTT-TT
1 ATTGGATTTTTAA-ATAATTTTATT
**
3991168 ATTGTTTTTTTAAATAATTTTATT
1 ATTGGATTTTTAAATAATTTTATT
3991192 AT
1 AT
3991194 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:4000083 original size:14 final size:14
Alignment explanation
Indices: 4000064--4000094 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
4000054 AAATATATTT
4000064 AATTTCCTCATTCA
1 AATTTCCTCATTCA
4000078 AATTTCCTCATTCA
1 AATTTCCTCATTCA
4000092 AAT
1 AAT
4000095 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:4001661 original size:3 final size:3
Alignment explanation
Indices: 4001653--4001684 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
4001643 ATATCTGGCA
4001653 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
4001685 ACAAAAAAGC
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:4007727 original size:54 final size:54
Alignment explanation
Indices: 4007663--4007770 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
4007653 GTTATTATTC
4007663 ATTGTATGTTATTTTCACTACATGCATCATTTTAATCAATGGTAATTAAGTTTA
1 ATTGTATGTTATTTTCACTACATGCATCATTTTAATCAATGGTAATTAAGTTTA
4007717 ATTGTATGTTATTTTCACTACATGCATCATTTTAATCAATGGTAATTAAGTTTA
1 ATTGTATGTTATTTTCACTACATGCATCATTTTAATCAATGGTAATTAAGTTTA
4007771 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:4010239 original size:14 final size:14
Alignment explanation
Indices: 4010220--4010246 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4010210 ACCCGAATTC
4010220 AAATAAAATAAATA
1 AAATAAAATAAATA
4010234 AAATAAAATAAAT
1 AAATAAAATAAAT
4010247 TATTTAAATT
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:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
AAATAAAATAAATA
Found at i:4017477 original size:2 final size:2
Alignment explanation
Indices: 4017472--4017500 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4017462 AATTATATAT
4017472 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
4017501 TTTAAAAGGA
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4017728 original size:17 final size:17
Alignment explanation
Indices: 4017669--4017719 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
4017659 ACGAAACAGT
*
4017669 ATAAATGATATACA-AA
1 ATAAATAATATACACAA
4017685 AT-AATATATATACACAA
1 ATAAATA-ATATACACAA
4017702 ATAAATAATATACACAA
1 ATAAATAATATACACAA
4017719 A
1 A
4017720 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:4017756 original size:17 final size:18
Alignment explanation
Indices: 4017676--4017763 Score: 71
Period size: 16 Copynumber: 5.2 Consensus size: 18
4017666 AGTATAAATG
4017676 ATATACAAAAT-AAT-AT
1 ATATACAAAATAAATAAT
4017692 ATATACACAAATAAATAAT
1 ATATACA-AAATAAATAAT
* *
4017711 ATACACAAAATACA-AAT
1 ATATACAAAATAAATAAT
** * *
4017728 AGCT-TAATATAAATAAT
1 ATATACAAAATAAATAAT
4017745 ATATA-AAAAT-AATAAT
1 ATATACAAAATAAATAAT
4017761 ATA
1 ATA
4017764 ATATTTAAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
16 22 0.39
17 17 0.30
18 9 0.16
19 8 0.14
ACGTcount: A:0.62, C:0.08, G:0.01, T:0.28
Consensus pattern (18 bp):
ATATACAAAATAAATAAT
Found at i:4017766 original size:21 final size:20
Alignment explanation
Indices: 4017736--4017774 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
4017726 ATAGCTTAAT
4017736 ATAAATAATATATAAAAATA
1 ATAAATAATATATAAAAATA
*
4017756 ATAATATAATATTTAAAAA
1 ATAA-ATAATATATAAAAA
4017775 ATGTTCATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAAATAATATATAAAAATA
Found at i:4018316 original size:13 final size:13
Alignment explanation
Indices: 4018298--4018323 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4018288 GGTAATAGGG
4018298 TTAGTGGGGTGAT
1 TTAGTGGGGTGAT
4018311 TTAGTGGGGTGAT
1 TTAGTGGGGTGAT
4018324 GGAATTAGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.46, T:0.38
Consensus pattern (13 bp):
TTAGTGGGGTGAT
Found at i:4020999 original size:18 final size:18
Alignment explanation
Indices: 4020948--4021000 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
4020938 CAGTTGCTCT
* *
4020948 ATAACAGTCAGTTATACA
1 ATAACAGTCAATTATTCA
*
4020966 ATAACAGTCATTTATTCA
1 ATAACAGTCAATTATTCA
*
4020984 GTAACAGTCAATTATTC
1 ATAACAGTCAATTATTC
4021001 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:4022205 original size:15 final size:15
Alignment explanation
Indices: 4022181--4022216 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
4022171 CAATTTTTCC
*
4022181 CTTT-TTCCTTCTTT
1 CTTTCTTCCTTCCTT
4022195 CTTTCTTCCTTCCTT
1 CTTTCTTCCTTCCTT
4022210 CTTTCTT
1 CTTTCTT
4022217 TCCCCCTGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 4 0.20
15 16 0.80
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (15 bp):
CTTTCTTCCTTCCTT
Found at i:4027330 original size:23 final size:23
Alignment explanation
Indices: 4027286--4027474 Score: 81
Period size: 23 Copynumber: 8.1 Consensus size: 23
4027276 CTATTATCAT
*
4027286 TATTATTATTA-ATAT-TAGTGTA
1 TATTTTTATTATATATGTA-TGTA
4027308 TATTTTTATTATATATGTATGTA
1 TATTTTTATTATATATGTATGTA
* * * *
4027331 TATGTATA-TATATTTGTATATA
1 TATTTTTATTATATATGTATGTA
* * *
4027353 GTATTATTTTTTAT-TACTTTATTTTAA
1 -TATT-TTTATTATATA-TGTA-TGT-A
* * * *
4027380 TATTTTTATTATATTTGCTTTTTG
1 TATTTTTATTATATATG-TATGTA
* *
4027404 TATTTCAATATTAT-TA-CTAT-TA
1 TATTT--TTATTATATATGTATGTA
*
4027426 TCATTATTATTA-ATAT-TAGTGTA
1 T-ATTTTTATTATATATGTA-TGTA
4027449 TATTTTTATTATATATGTATGTA
1 TATTTTTATTATATATGTATGTA
4027472 TAT
1 TAT
4027475 GTATATATAT
Statistics
Matches: 124, Mismatches: 24, Indels: 37
0.67 0.13 0.20
Matches are distributed among these distances:
21 9 0.07
22 34 0.27
23 36 0.29
24 12 0.10
25 18 0.15
26 14 0.11
27 1 0.01
ACGTcount: A:0.31, C:0.03, G:0.07, T:0.60
Consensus pattern (23 bp):
TATTTTTATTATATATGTATGTA
Found at i:4027342 original size:144 final size:144
Alignment explanation
Indices: 4027147--4027580 Score: 693
Period size: 144 Copynumber: 3.0 Consensus size: 144
4027137 CTTTATTTAT
* * **
4027147 TTATTATTATTATTAGTGTATACTTTTTA-T-TATA--TACGTATATGTATATATATTTACGTAT
1 TTATTATTAATATTAGTGTATA-TTTTTATTATATATGTATGTATATGTATATATATTTATATAT
4027208 AGTATTATTTTTTATTACTTTATTTTAATATTTTTATTATATTTGCTTTTTGTATTTCAATATTA
65 AGTATTATTTTTTATTACTTTATTTTAATATTTTTATTATATTTGCTTTTTGTATTTCAATATTA
4027273 TTACTATTATCATTA
130 TTACTATTATCATTA
*
4027288 TTATTATTAATATTAGTGTATATTTTTATTATATATGTATGTATATGTATATATATTTGTATATA
1 TTATTATTAATATTAGTGTATATTTTTATTATATATGTATGTATATGTATATATATTTATATATA
4027353 GTATTATTTTTTATTACTTTATTTTAATATTTTTATTATATTTGCTTTTTGTATTTCAATATTAT
66 GTATTATTTTTTATTACTTTATTTTAATATTTTTATTATATTTGCTTTTTGTATTTCAATATTAT
4027418 TACTATTATC---A
131 TACTATTATCATTA
4027429 TTATTATTAATATTAGTGTATATTTTTATTATATATGTATGTATATGTATATATATTTATATATA
1 TTATTATTAATATTAGTGTATATTTTTATTATATATGTATGTATATGTATATATATTTATATATA
* * *
4027494 GTATTATTCTTTTATTACTTTATTCTAATATTATTATTATATTTGCTTTTTGTATTTCATTATTA
66 GTATTATT-TTTTATTACTTTATTTTAATATTTTTATTATATTTGCTTTTTGTATTTCAATATTA
* * *
4027559 TTGCTAGTATTATTA
130 TTACTATTATCATTA
*
4027574 TCATTAT
1 TTATTAT
4027581 CATCATTATT
Statistics
Matches: 272, Mismatches: 13, Indels: 12
0.92 0.04 0.04
Matches are distributed among these distances:
140 6 0.02
141 95 0.35
142 65 0.24
144 99 0.36
145 7 0.03
ACGTcount: A:0.29, C:0.05, G:0.06, T:0.60
Consensus pattern (144 bp):
TTATTATTAATATTAGTGTATATTTTTATTATATATGTATGTATATGTATATATATTTATATATA
GTATTATTTTTTATTACTTTATTTTAATATTTTTATTATATTTGCTTTTTGTATTTCAATATTAT
TACTATTATCATTA
Found at i:4027475 original size:10 final size:10
Alignment explanation
Indices: 4027458--4027497 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
4027448 ATATTTTTAT
4027458 TATATATGTA
1 TATATATGTA
*
4027468 TGTATATGTA
1 TATATATGTA
*
4027478 TATATATTTA
1 TATATATGTA
4027488 TATATA-GTA
1 TATATATGTA
4027497 T
1 T
4027498 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:4027501 original size:16 final size:16
Alignment explanation
Indices: 4027447--4027493 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
4027437 AATATTAGTG
*
4027447 TATATTTTTAT-TATA
1 TATATATTTATATATA
* * *
4027462 TATGTATGTATATGTA
1 TATATATTTATATATA
4027478 TATATATTTATATATA
1 TATATATTTATATATA
4027494 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:4030164 original size:18 final size:20
Alignment explanation
Indices: 4030122--4030158 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4030112 ATATTTTATG
*
4030122 ATTA-TTTAATTAGATATAT
1 ATTATTTTAATGAGATATAT
4030141 ATTATTTTAATGAGATAT
1 ATTATTTTAATGAGATAT
4030159 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:4032369 original size:46 final size:46
Alignment explanation
Indices: 4032317--4032627 Score: 424
Period size: 46 Copynumber: 6.7 Consensus size: 46
4032307 AGTGTGCTCT
4032317 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
4032363 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
4032409 CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
4032455 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *** *** *
4032501 ATGACGGGAAATAAATAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * **
4032547 GTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * ** * *
4032593 ATGACAAAAAAATGAGTAAGACCATAGTTGAAAGA
1 CTGA-TATGAAATGTGTAAGACCATGGTTGAAAGA
4032628 CACTGTGGCA
Statistics
Matches: 241, Mismatches: 23, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
46 216 0.90
47 25 0.10
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Done.