Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr11
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: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 12 of 205
Found at i:3669983 original size:22 final size:22
Alignment explanation
Indices: 3669898--3669983 Score: 93
Period size: 22 Copynumber: 3.7 Consensus size: 22
3669888 TTTAGTATCA
*
3669898 TTTTTAT-TTATTTTAATATTTG
1 TTTTTATGTT-TTTAAATATTTG
*
3669920 TTTTTATGTTTTTAAATATATTTAA
1 TTTTTATGTTTTT-AA-ATATTT-G
*
3669945 TTTATTATATTTTTAAATATTTG
1 TTT-TTATGTTTTTAAATATTTG
3669968 TTTTTATGTTTTTAAA
1 TTTTTATGTTTTTAAA
3669984 ACTCATATTA
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
22 22 0.41
23 6 0.11
24 12 0.22
25 5 0.09
26 9 0.17
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (22 bp):
TTTTTATGTTTTTAAATATTTG
Found at i:3673337 original size:29 final size:30
Alignment explanation
Indices: 3673290--3673357 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
3673280 TGGCCCAAGA
* *
3673290 GTAAATACTCAAAATTTGAAGGATTAA-AGT
1 GTAAATA-TCAAAAGTTGAAGGACTAATAGT
*
3673320 GTAAATATGAAAAGTTGAAGGACTAATAGT
1 GTAAATATCAAAAGTTGAAGGACTAATAGT
*
3673350 GCAAATAT
1 GTAAATAT
3673358 TTTAAGGGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (30 bp):
GTAAATATCAAAAGTTGAAGGACTAATAGT
Found at i:3675055 original size:850 final size:850
Alignment explanation
Indices: 3673415--3675117 Score: 3361
Period size: 850 Copynumber: 2.0 Consensus size: 850
3673405 ACCAAATTGA
*
3673415 ATAGGTGAAGAATTATGAGGGACTAAATTACAATTTTACCAAATTAAGTGATGACTCAAGAATGG
1 ATAGGTGAAGAATTATGAGGGACTAAATTACAATTTTACCAAATTAAGTAATGACTCAAGAATGG
3673480 AATTTTAAAAGATCACTAAAGGCAAAATGGTCAATTGGAAGAGAGAGAAATCTAGAGACAATGAT
66 AATTTTAAAAGATCACTAAAGGCAAAATGGTCAATTGGAAGAGAGAGAAATCTAGAGACAATGAT
3673545 GATGTTGGAGATATTTTAGATAAATTAAATAAATAAATATTAGTTTATTAATACTTTAAATTGAT
131 GATGTTGGAGATATTTTAGATAAATTAAATAAATAAATATTAGTTTATTAATACTTTAAATTGAT
3673610 TTTTAAATGATATTTTATTATTTTATTATTATTTTATTTAGTATATATAAGGAAAGAAAGATGAA
196 TTTTAAATGATATTTTATTATTTTATTATTATTTTATTTAGTATATATAAGGAAAGAAAGATGAA
3673675 GAATCATCATCTTTTCTTTCCGATGCAAACTAACGTGAGAGAGGAAGAAGAAAAGAAGTTTTCTT
261 GAATCATCATCTTTTCTTTCCGATGCAAACTAACGTGAGAGAGGAAGAAGAAAAGAAGTTTTCTT
3673740 TCTTTACAATCTAGTCCTTCCACCAAAAATTCATTATTTTCACCTAAAAATTGAAAGAATTTCCA
326 TCTTTACAATCTAGTCCTTCCACCAAAAATTCATTATTTTCACCTAAAAATTGAAAGAATTTCCA
3673805 TAGCCATCAAGAGAGAAAGATAGCAAGGAGATGATGGGGAGCAAGAATATCAAGTTGGATTCAAG
391 TAGCCATCAAGAGAGAAAGATAGCAAGGAGATGATGGGGAGCAAGAATATCAAGTTGGATTCAAG
3673870 AAATAGAAGCTGGAGGAGAGAGAAAAATCAAGTTGAAGATTGAAGTCAATAAGAAAAGGTAAGAA
456 AAATAGAAGCTGGAGGAGAGAGAAAAATCAAGTTGAAGATTGAAGTCAATAAGAAAAGGTAAGAA
3673935 CATCAAGATTTCAATATATTTTTAAGTTTAATATTATTGAAAAAGCCTGGAATTGATGTTTATTT
521 CATCAAGATTTCAATATATTTTTAAGTTTAATATTATTGAAAAAGCCTGGAATTGATGTTTATTT
3674000 AGAGTTTTCTTATATATTGTCTTATATTCTTGTCATGTTAGTGAAGAGAAAATAAGGGTGTTATA
586 AGAGTTTTCTTATATATTGTCTTATATTCTTGTCATGTTAGTGAAGAGAAAATAAGGGTGTTATA
3674065 AACATGGTAAATAATACTTTGCACTAAAACAGTTTTGAACAGCAGCAATAGTCTAAATTTGAAAA
651 AACATGGTAAATAATACTTTGCACTAAAACAGTTTTGAACAGCAGCAATAGTCTAAATTTGAAAA
3674130 ATCACCAAAAATTGTGGGAATCGAATTAGAGGTTAAATAAAATATGAAATTAAATCTTATTGAGT
716 ATCACCAAAAATTGTGGGAATCGAATTAGAGGTTAAATAAAATATGAAATTAAATCTTATTGAGT
3674195 CTAGTTTCTTATAAAAGAAATGTTGTAAGAAATGAAATTGTAAATTGTGAGATATAGTAAATTTG
781 CTAGTTTCTTATAAAAGAAATGTTGTAAGAAATGAAATTGTAAATTGTGAGATATAGTAAATTTG
3674260 GTGAG
846 GTGAG
* *
3674265 ATAGGTGAAGAATTATGAGGGACTAAATTGCAATTTTACCAAATTAAGTAATGACTCGAGAATGG
1 ATAGGTGAAGAATTATGAGGGACTAAATTACAATTTTACCAAATTAAGTAATGACTCAAGAATGG
*
3674330 AATTTTAAAAGATCACTAAAGGCAAAATGGTCAATTGTAAGAGAGAGAAATCTAGAGACAATGAT
66 AATTTTAAAAGATCACTAAAGGCAAAATGGTCAATTGGAAGAGAGAGAAATCTAGAGACAATGAT
3674395 GATGTTGGAGATATTTTAGATAAATTAAATAAATAAATATTAGTTTATTAATACTTTAAATTGAT
131 GATGTTGGAGATATTTTAGATAAATTAAATAAATAAATATTAGTTTATTAATACTTTAAATTGAT
3674460 TTTTAAATGATATTTTATTATTTTATTATTATTTTATTTAGTATATATAAGGAAAGAAAGATGAA
196 TTTTAAATGATATTTTATTATTTTATTATTATTTTATTTAGTATATATAAGGAAAGAAAGATGAA
3674525 GAATCATCATCTTTTCTTTCCGATGCAAACTAACGTGAGAGAGGAAGAAGAAAAGAAGTTTTCTT
261 GAATCATCATCTTTTCTTTCCGATGCAAACTAACGTGAGAGAGGAAGAAGAAAAGAAGTTTTCTT
*
3674590 TCTTTACAATCTAGTCCTTCCACCAAAAATTCATTATTTTCACCTAAAAATTGAAAGAATTTCCG
326 TCTTTACAATCTAGTCCTTCCACCAAAAATTCATTATTTTCACCTAAAAATTGAAAGAATTTCCA
3674655 TAGCCATCAAGAGAGAAAGATAGCAAGGAGATGATGGGGAGCAAGAATATCAAGTTGGATTCAAG
391 TAGCCATCAAGAGAGAAAGATAGCAAGGAGATGATGGGGAGCAAGAATATCAAGTTGGATTCAAG
3674720 AAATAGAAGCTGGAGGAGAGAGAAAAATCAAGTTGAAGATTGAAGTCAATAAGAAAAGGTAAGAA
456 AAATAGAAGCTGGAGGAGAGAGAAAAATCAAGTTGAAGATTGAAGTCAATAAGAAAAGGTAAGAA
3674785 CATCAAGATTTCAATATATTTTTAAGTTTAATATTATTGAAAAAGCCTGGAATTGATGTTTATTT
521 CATCAAGATTTCAATATATTTTTAAGTTTAATATTATTGAAAAAGCCTGGAATTGATGTTTATTT
3674850 AGAGTTTTCTTATATATTGTCTTATATTCTTGTCATGTTAGTGAAGAGAAAATAAGGGTGTTATA
586 AGAGTTTTCTTATATATTGTCTTATATTCTTGTCATGTTAGTGAAGAGAAAATAAGGGTGTTATA
3674915 AACATGGTAAATAATACTTTGCACTAAAACAGTTTTGAACAGCAGCAATAGTCTAAATTTGAAAA
651 AACATGGTAAATAATACTTTGCACTAAAACAGTTTTGAACAGCAGCAATAGTCTAAATTTGAAAA
3674980 ATCACCAAAAATTGTGGGAATCGAATTAGAGGTTAAATAAAATATGAAATTAAATCTTATTGAGT
716 ATCACCAAAAATTGTGGGAATCGAATTAGAGGTTAAATAAAATATGAAATTAAATCTTATTGAGT
3675045 CTAGTTTCTTATAAAAGAAATGTTGTAAGAAATGAAATTGTAAATTGTGAGATATAGTAAATTTG
781 CTAGTTTCTTATAAAAGAAATGTTGTAAGAAATGAAATTGTAAATTGTGAGATATAGTAAATTTG
3675110 GTGAG
846 GTGAG
3675115 ATA
1 ATA
3675118 AGGTCAGAAT
Statistics
Matches: 848, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
850 848 1.00
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.32
Consensus pattern (850 bp):
ATAGGTGAAGAATTATGAGGGACTAAATTACAATTTTACCAAATTAAGTAATGACTCAAGAATGG
AATTTTAAAAGATCACTAAAGGCAAAATGGTCAATTGGAAGAGAGAGAAATCTAGAGACAATGAT
GATGTTGGAGATATTTTAGATAAATTAAATAAATAAATATTAGTTTATTAATACTTTAAATTGAT
TTTTAAATGATATTTTATTATTTTATTATTATTTTATTTAGTATATATAAGGAAAGAAAGATGAA
GAATCATCATCTTTTCTTTCCGATGCAAACTAACGTGAGAGAGGAAGAAGAAAAGAAGTTTTCTT
TCTTTACAATCTAGTCCTTCCACCAAAAATTCATTATTTTCACCTAAAAATTGAAAGAATTTCCA
TAGCCATCAAGAGAGAAAGATAGCAAGGAGATGATGGGGAGCAAGAATATCAAGTTGGATTCAAG
AAATAGAAGCTGGAGGAGAGAGAAAAATCAAGTTGAAGATTGAAGTCAATAAGAAAAGGTAAGAA
CATCAAGATTTCAATATATTTTTAAGTTTAATATTATTGAAAAAGCCTGGAATTGATGTTTATTT
AGAGTTTTCTTATATATTGTCTTATATTCTTGTCATGTTAGTGAAGAGAAAATAAGGGTGTTATA
AACATGGTAAATAATACTTTGCACTAAAACAGTTTTGAACAGCAGCAATAGTCTAAATTTGAAAA
ATCACCAAAAATTGTGGGAATCGAATTAGAGGTTAAATAAAATATGAAATTAAATCTTATTGAGT
CTAGTTTCTTATAAAAGAAATGTTGTAAGAAATGAAATTGTAAATTGTGAGATATAGTAAATTTG
GTGAG
Found at i:3678867 original size:9 final size:9
Alignment explanation
Indices: 3678850--3678887 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
3678840 TATTTTGTCA
3678850 TTATTATTT
1 TTATTATTT
*
3678859 TTATCATTT
1 TTATTATTT
3678868 TTATTATTT
1 TTATTATTT
3678877 ATT-TTATTT
1 -TTATTATTT
3678886 TT
1 TT
3678888 CTTTGATTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
8 2 0.08
9 22 0.85
10 2 0.08
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (9 bp):
TTATTATTT
Found at i:3680702 original size:15 final size:17
Alignment explanation
Indices: 3680682--3680719 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
3680672 GTATAAAACG
3680682 TTTTTTAAAGAAC-C-T
1 TTTTTTAAAGAACTCAT
*
3680697 TTTTTTATAGAACTCAT
1 TTTTTTAAAGAACTCAT
3680714 TTTTTT
1 TTTTTT
3680720 GCCATGTCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 12 0.60
16 1 0.05
17 7 0.35
ACGTcount: A:0.26, C:0.11, G:0.05, T:0.58
Consensus pattern (17 bp):
TTTTTTAAAGAACTCAT
Found at i:3681324 original size:21 final size:23
Alignment explanation
Indices: 3681284--3681328 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
3681274 GTTTTCCAAT
3681284 ATATTACTAAATTAATTTTAAAA
1 ATATTACTAAATTAATTTTAAAA
*
3681307 ATATTA-TAATTTAA-TTTAAAA
1 ATATTACTAAATTAATTTTAAAA
3681328 A
1 A
3681329 GTTGTGTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.38
22 7 0.33
23 6 0.29
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
ATATTACTAAATTAATTTTAAAA
Found at i:3681654 original size:3 final size:3
Alignment explanation
Indices: 3681646--3681685 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
3681636 TTAGAATTAT
3681646 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3681686 GATGAAGAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3682429 original size:15 final size:15
Alignment explanation
Indices: 3682405--3682444 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 15
3682395 AAATAAAAAT
3682405 AAAATTACATT-ATA
1 AAAATTACATTAATA
3682419 AAAATTTACATTAATAA
1 AAAA-TTACATTAAT-A
3682436 AAAATTACA
1 AAAATTACA
3682445 AAACACTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 4 0.17
15 7 0.30
16 7 0.30
17 5 0.22
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAATTACATTAATA
Found at i:3682931 original size:17 final size:19
Alignment explanation
Indices: 3682901--3682937 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
3682891 TTAGTAGTTA
3682901 TATTATAAACAAATAATTT
1 TATTATAAACAAATAATTT
*
3682920 TATTA-AAA-AAATTATTT
1 TATTATAAACAAATAATTT
3682937 T
1 T
3682938 CTCCTTGTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 9 0.53
18 3 0.18
19 5 0.29
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (19 bp):
TATTATAAACAAATAATTT
Found at i:3684494 original size:28 final size:28
Alignment explanation
Indices: 3684462--3684524 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 28
3684452 TCCCATATTA
3684462 ATGGGGTATAGGAAAAGTTTCATAACTT
1 ATGGGGTATAGGAAAAGTTTCATAACTT
* *
3684490 ATGGGGTATAGGAAGAGTTTTATAACTT
1 ATGGGGTATAGGAAAAGTTTCATAACTT
3684518 ATGGGGT
1 ATGGGGT
3684525 TGATAATGAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.32, C:0.05, G:0.30, T:0.33
Consensus pattern (28 bp):
ATGGGGTATAGGAAAAGTTTCATAACTT
Found at i:3689160 original size:28 final size:28
Alignment explanation
Indices: 3689129--3689191 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
3689119 TCCCATATTA
3689129 ATGGGGTATAGGAAAAGTCTCATAACTT
1 ATGGGGTATAGGAAAAGTCTCATAACTT
** * *
3689157 ATGGGGTATAGGAAGGGTTTTATAACTT
1 ATGGGGTATAGGAAAAGTCTCATAACTT
3689185 ATGGGGT
1 ATGGGGT
3689192 TGATAATGAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.30, C:0.06, G:0.32, T:0.32
Consensus pattern (28 bp):
ATGGGGTATAGGAAAAGTCTCATAACTT
Found at i:3689402 original size:13 final size:13
Alignment explanation
Indices: 3689377--3689409 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
3689367 CTATTTTTCG
3689377 AGAAAATAAAAAT
1 AGAAAATAAAAAT
3689390 A-AAAATGAAAAAT
1 AGAAAAT-AAAAAT
3689403 AGAAAAT
1 AGAAAAT
3689410 TTAAAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 5 0.28
13 8 0.44
14 5 0.28
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (13 bp):
AGAAAATAAAAAT
Found at i:3691065 original size:20 final size:20
Alignment explanation
Indices: 3691021--3691059 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3691011 ATATATCAAC
*
3691021 GTTATAAAAACTATTTAAAA
1 GTTATAAAAACTATTAAAAA
3691041 GTTATAAAAACT-TTAAAAA
1 GTTATAAAAACTATTAAAAA
3691060 TTTTATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.33
Consensus pattern (20 bp):
GTTATAAAAACTATTAAAAA
Found at i:3697062 original size:3 final size:3
Alignment explanation
Indices: 3697054--3697084 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
3697044 AAAAACTGAA
*
3697054 TTC TTC TTC TTC TTC TTC TTC TTA TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
3697085 GACAGGCGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:3704833 original size:130 final size:130
Alignment explanation
Indices: 3704600--3704858 Score: 500
Period size: 130 Copynumber: 2.0 Consensus size: 130
3704590 ATAGGCCCAA
3704600 AGCGCGTCATTGAGCCGAAGACTCCAATCCTTACGGTTGGGTCGAACCGTTTTTTCCAAAATTGA
1 AGCGCGTCATTGAGCCGAAGACTCCAATCCTTACGGTTGGGTCGAACCGTTTTTTCCAAAATTGA
3704665 CTTGATCTCCCTATTTGAAACCTCTGCTAGGCCGTTCGTTTGGGGATGATAGGCTGTTGCTATAT
66 CTTGATCTCCCTATTTGAAACCTCTGCTAGGCCGTTCGTTTGGGGATGATAGGCTGTTGCTATAT
3704730 AGCGCGTCATTGAGCCGAAGACTCCAATCCTTACGGTTGGGTCGAACCGTTTTTTCCAAAATTGA
1 AGCGCGTCATTGAGCCGAAGACTCCAATCCTTACGGTTGGGTCGAACCGTTTTTTCCAAAATTGA
* *
3704795 CTTGATCTCCCTGTTTGAAACCTCTGCTAGGCCGTTCGTTTGGGGATGGTAGGCTGTTGCTATA
66 CTTGATCTCCCTATTTGAAACCTCTGCTAGGCCGTTCGTTTGGGGATGATAGGCTGTTGCTATA
3704859 CGATGATGAA
Statistics
Matches: 127, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
130 127 1.00
ACGTcount: A:0.20, C:0.23, G:0.25, T:0.32
Consensus pattern (130 bp):
AGCGCGTCATTGAGCCGAAGACTCCAATCCTTACGGTTGGGTCGAACCGTTTTTTCCAAAATTGA
CTTGATCTCCCTATTTGAAACCTCTGCTAGGCCGTTCGTTTGGGGATGATAGGCTGTTGCTATAT
Found at i:3717707 original size:18 final size:18
Alignment explanation
Indices: 3717666--3717701 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3717656 CCTAAATTTG
3717666 AATAATCCTAATAATTAT
1 AATAATCCTAATAATTAT
3717684 AATAATCCTAATAATTAT
1 AATAATCCTAATAATTAT
3717702 CTTAATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (18 bp):
AATAATCCTAATAATTAT
Found at i:3723330 original size:30 final size:30
Alignment explanation
Indices: 3723296--3723352 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
3723286 TAAAATTTGT
3723296 AAAT-GTTGGTGCAATAAAATTAATTTTCTA
1 AAATGGTT-GTGCAATAAAATTAATTTTCTA
*
3723326 AAATGGTTGTGCAATAAAATTATTTTT
1 AAATGGTTGTGCAATAAAATTAATTTT
3723353 TAGTAATGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 22 0.88
31 3 0.12
ACGTcount: A:0.39, C:0.05, G:0.14, T:0.42
Consensus pattern (30 bp):
AAATGGTTGTGCAATAAAATTAATTTTCTA
Found at i:3723731 original size:21 final size:20
Alignment explanation
Indices: 3723706--3723758 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
3723696 CAAAATTAGT
3723706 AGAAGGAA-AAAGAGAGAAAGA
1 AGAAGGAAGAAAG-GA-AAAGA
3723727 AGAAGGGAAGAAAGGAAAAGA
1 AGAA-GGAAGAAAGGAAAAGA
3723748 AGAA-GAAGAAA
1 AGAAGGAAGAAA
3723759 AATAAGGTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
19 7 0.23
21 13 0.43
22 6 0.20
23 4 0.13
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (20 bp):
AGAAGGAAGAAAGGAAAAGA
Found at i:3727097 original size:33 final size:33
Alignment explanation
Indices: 3727060--3727227 Score: 174
Period size: 33 Copynumber: 5.1 Consensus size: 33
3727050 AGAATGTCGA
* *
3727060 TGGATACGAGCCAGAAGGAACGGAGTACGGTGG
1 TGGATACGAGCTAGAAGGAGCGGAGTACGGTGG
* *
3727093 TGGATACGAGCTAGAAAGAGCGGAGTACAGTGG
1 TGGATACGAGCTAGAAGGAGCGGAGTACGGTGG
* ** *
3727126 TGGATATGAGCTAGAATAAGCGGAGTATGGTGG
1 TGGATACGAGCTAGAAGGAGCGGAGTACGGTGG
* * ** **
3727159 TGGATACGAGTTGGAAGGAGTAGAGTATTGTGG
1 TGGATACGAGCTAGAAGGAGCGGAGTACGGTGG
** * *
3727192 TGGATACGAGCCGGAATGAGCGGAGTACGATGG
1 TGGATACGAGCTAGAAGGAGCGGAGTACGGTGG
3727225 TGG
1 TGG
3727228 GCTGAAGATA
Statistics
Matches: 110, Mismatches: 25, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 110 1.00
ACGTcount: A:0.29, C:0.10, G:0.42, T:0.19
Consensus pattern (33 bp):
TGGATACGAGCTAGAAGGAGCGGAGTACGGTGG
Found at i:3729786 original size:26 final size:28
Alignment explanation
Indices: 3729757--3729818 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 28
3729747 TATAATCTTA
3729757 AATTACTAAA-A-AAATAATTT-TAAAAT
1 AATTACTAAACACAAA-AATTTATAAAAT
*
3729783 AATTAC-AAACACAAAAATTTATCAAAT
1 AATTACTAAACACAAAAATTTATAAAAT
3729810 AATT-CTAAA
1 AATTACTAAA
3729819 TTACTAACAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
25 3 0.10
26 13 0.42
27 15 0.48
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.31
Consensus pattern (28 bp):
AATTACTAAACACAAAAATTTATAAAAT
Found at i:3729875 original size:3 final size:3
Alignment explanation
Indices: 3729869--3729906 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
3729859 TAACCTTTTT
*
3729869 TTC TTC TTA TTC TTC TTTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC T
3729907 CTTTTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:3735499 original size:811 final size:811
Alignment explanation
Indices: 3733937--3735558 Score: 3190
Period size: 811 Copynumber: 2.0 Consensus size: 811
3733927 TTAAAACCTC
*
3733937 TGGTAGGGTGTTGAAATCTTTCACCGCTTTATCTCTAGAAGCAACCGACATTGTTCCATCAAGTC
1 TGGTAGGGTGTTGAAATCTTTCACCGCTTTATCTCTAGAAGCAACCGACATAGTTCCATCAAGTC
3734002 TTCTATATTGGATGGAAGAACTTTTAAGACAGGCTTCAAATAAATCCAACATCCTCGTCCACTGG
66 TTCTATATTGGATGGAAGAACTTTTAAGACAGGCTTCAAATAAATCCAACATCCTCGTCCACTGG
*
3734067 GAAAATACTATGGCTTTCTCTCCAAGTACATTAGAAGAACCATTCAAACTTTCACCTGTAACCGA
131 GAAAAAACTATGGCTTTCTCTCCAAGTACATTAGAAGAACCATTCAAACTTTCACCTGTAACCGA
3734132 AATTTTTTCATCATGAAAACCATTTGGTGAGTCCCCAGATTGGAGGCCAGATGAACCTTCTGGAC
196 AATTTTTTCATCATGAAAACCATTTGGTGAGTCCCCAGATTGGAGGCCAGATGAACCTTCTGGAC
3734197 AGCCACTAATCTTTAATCTATCATCTTGAGGTTTAGCTAGTGACTTCAGGACATCAAGGGCAGCC
261 AGCCACTAATCTTTAATCTATCATCTTGAGGTTTAGCTAGTGACTTCAGGACATCAAGGGCAGCC
3734262 TTGATTTTGGAAGAACCATACAAACTATCCTCTGAATAAGGCCCAATTACCTCAGCAACTTTAGA
326 TTGATTTTGGAAGAACCATACAAACTATCCTCTGAATAAGGCCCAATTACCTCAGCAACTTTAGA
3734327 ACCAGAACTATTGAGGGAACTTTCCCGACTAGGCAGCTCAGTGAGGGAACTGTTTAAAGTGGCAT
391 ACCAGAACTATTGAGGGAACTTTCCCGACTAGGCAGCTCAGTGAGGGAACTGTTTAAAGTGGCAT
3734392 TTGAAAACACAGATGATGCACCAAGTCTAACTTTGCAATTTGCAGTGGGACACTGGTAGTCATCA
456 TTGAAAACACAGATGATGCACCAAGTCTAACTTTGCAATTTGCAGTGGGACACTGGTAGTCATCA
3734457 CCAGTGAGATGTTCAGAGATGCATTGGTTGCAGAAAACATGACCACATACAGCAACAACAGCATC
521 CCAGTGAGATGTTCAGAGATGCATTGGTTGCAGAAAACATGACCACATACAGCAACAACAGCATC
3734522 TTCTGGTGGATCCTACAGAAACCACAAAAATTGCAAAGATACTAAAGGAATAACTACAAAGAAAT
586 TTCTGGTGGATCCTACAGAAACCACAAAAATTGCAAAGATACTAAAGGAATAACTACAAAGAAAT
*
3734587 TTTTTTCCAAATGAGACAATTGACCATCACCATTATGAACATATATAGATAAGACTGTAATTGCA
651 TTTTTTCCAAATGAGACAATTGACCATCACCATTATGAACATATATAGATAAGACAGTAATTGCA
3734652 TTATCAAAGAGCAAGCAAAGTTCTTGGGAATATTCGACCATATAGAGATTGAGGGAAATGAATCT
716 TTATCAAAGAGCAAGCAAAGTTCTTGGGAATATTCGACCATATAGAGATTGAGGGAAATGAATCT
3734717 CACAGGGGAAAAAATTTGTCAAAGCTGTTCA
781 CACAGGGGAAAAAATTTGTCAAAGCTGTTCA
3734748 TGGTAGGGTGTTGAAATCTTTCACCGCTTTATCTCTAGAAGCAACCGACATAGTTCCATCAAGTC
1 TGGTAGGGTGTTGAAATCTTTCACCGCTTTATCTCTAGAAGCAACCGACATAGTTCCATCAAGTC
3734813 TTCTATATTGGATGGAAGAACTTTTAAGACAGGCTTCAAATAAATCCAACATCCTCGTCCACTGG
66 TTCTATATTGGATGGAAGAACTTTTAAGACAGGCTTCAAATAAATCCAACATCCTCGTCCACTGG
3734878 GAAAAAACTATGGCTTTCTCTCCAAGTACATTAGAAGAACCATTCAAACTTTCACCTGTAACCGA
131 GAAAAAACTATGGCTTTCTCTCCAAGTACATTAGAAGAACCATTCAAACTTTCACCTGTAACCGA
* *
3734943 AATTTTTTCTTCATGATAACCATTTGGTGAGTCCCCAGATTGGAGGCCAGATGAACCTTCTGGAC
196 AATTTTTTCATCATGAAAACCATTTGGTGAGTCCCCAGATTGGAGGCCAGATGAACCTTCTGGAC
3735008 AGCCACTAATCTTTAATCTATCATCTTGAGGTTTAGCTAGTGACTTCAGGACATCAAGGGCAGCC
261 AGCCACTAATCTTTAATCTATCATCTTGAGGTTTAGCTAGTGACTTCAGGACATCAAGGGCAGCC
3735073 TTGATTTTGGAAGAACCATACAAACTATCCTCTGAATAAGGCCCAATTACCTCAGCAACTTTAGA
326 TTGATTTTGGAAGAACCATACAAACTATCCTCTGAATAAGGCCCAATTACCTCAGCAACTTTAGA
3735138 ACCAGAACTATTGAGGGAACTTTCCCGACTAGGCAGCTCAGTGAGGGAACTGTTTAAAGTGGCAT
391 ACCAGAACTATTGAGGGAACTTTCCCGACTAGGCAGCTCAGTGAGGGAACTGTTTAAAGTGGCAT
3735203 TTGAAAACACAGATGATGCACCAAGTCTAACTTTGCAATTTGCAGTGGGACACTGGTAGTCATCA
456 TTGAAAACACAGATGATGCACCAAGTCTAACTTTGCAATTTGCAGTGGGACACTGGTAGTCATCA
3735268 CCAGTGAGATGTTCAGAGATGCATTGGTTGCAGAAAACATGACCACATACAGCAACAACAGCATC
521 CCAGTGAGATGTTCAGAGATGCATTGGTTGCAGAAAACATGACCACATACAGCAACAACAGCATC
3735333 TTCTGGTGGATCCTACAGAAACCACAAAAATTGCAAAGATACTAAAGGAATAACTACAAAGAAAT
586 TTCTGGTGGATCCTACAGAAACCACAAAAATTGCAAAGATACTAAAGGAATAACTACAAAGAAAT
3735398 TTTTTTCCAAATGAGACAATTGACCATCACCATTATGAACATATATAGATAAGACAGTAATTGCA
651 TTTTTTCCAAATGAGACAATTGACCATCACCATTATGAACATATATAGATAAGACAGTAATTGCA
3735463 TTATCAAAGAGCAAGCAAAGTTCTTGGGAATATTCGACCATATAGAGATTGAGGGAAATGAATCT
716 TTATCAAAGAGCAAGCAAAGTTCTTGGGAATATTCGACCATATAGAGATTGAGGGAAATGAATCT
*
3735528 CACAGTGGAAAAAATTTGTCAAAGCTGTTCA
781 CACAGGGGAAAAAATTTGTCAAAGCTGTTCA
3735559 GTTTTAACCG
Statistics
Matches: 805, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
811 805 1.00
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (811 bp):
TGGTAGGGTGTTGAAATCTTTCACCGCTTTATCTCTAGAAGCAACCGACATAGTTCCATCAAGTC
TTCTATATTGGATGGAAGAACTTTTAAGACAGGCTTCAAATAAATCCAACATCCTCGTCCACTGG
GAAAAAACTATGGCTTTCTCTCCAAGTACATTAGAAGAACCATTCAAACTTTCACCTGTAACCGA
AATTTTTTCATCATGAAAACCATTTGGTGAGTCCCCAGATTGGAGGCCAGATGAACCTTCTGGAC
AGCCACTAATCTTTAATCTATCATCTTGAGGTTTAGCTAGTGACTTCAGGACATCAAGGGCAGCC
TTGATTTTGGAAGAACCATACAAACTATCCTCTGAATAAGGCCCAATTACCTCAGCAACTTTAGA
ACCAGAACTATTGAGGGAACTTTCCCGACTAGGCAGCTCAGTGAGGGAACTGTTTAAAGTGGCAT
TTGAAAACACAGATGATGCACCAAGTCTAACTTTGCAATTTGCAGTGGGACACTGGTAGTCATCA
CCAGTGAGATGTTCAGAGATGCATTGGTTGCAGAAAACATGACCACATACAGCAACAACAGCATC
TTCTGGTGGATCCTACAGAAACCACAAAAATTGCAAAGATACTAAAGGAATAACTACAAAGAAAT
TTTTTTCCAAATGAGACAATTGACCATCACCATTATGAACATATATAGATAAGACAGTAATTGCA
TTATCAAAGAGCAAGCAAAGTTCTTGGGAATATTCGACCATATAGAGATTGAGGGAAATGAATCT
CACAGGGGAAAAAATTTGTCAAAGCTGTTCA
Found at i:3745039 original size:31 final size:32
Alignment explanation
Indices: 3744988--3745048 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
3744978 ATTCAAATCT
* * *
3744988 TTTTCAAAATGTTGATTGTCAACTTTAACTTG
1 TTTTCAAAAAGTTGAATGTCAAATTTAACTTG
3745020 TTTT-AAAAAGTTGAATGTCAAATTTAACT
1 TTTTCAAAAAGTTGAATGTCAAATTTAACT
3745049 AAAAAATGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.34, C:0.10, G:0.11, T:0.44
Consensus pattern (32 bp):
TTTTCAAAAAGTTGAATGTCAAATTTAACTTG
Found at i:3749615 original size:22 final size:22
Alignment explanation
Indices: 3749590--3749637 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
3749580 TTTGCTGATA
*
3749590 TTTTATACAT-TTTTTTGAAAAC
1 TTTTAGACATATTTTTTG-AAAC
*
3749612 TTTTAGATATATTTTTTGAAAC
1 TTTTAGACATATTTTTTGAAAC
3749634 TTTT
1 TTTT
3749638 TTTAAATGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.58
Consensus pattern (22 bp):
TTTTAGACATATTTTTTGAAAC
Found at i:3750639 original size:19 final size:20
Alignment explanation
Indices: 3750587--3750641 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
3750577 TTTTTAATAG
* *
3750587 TTTTTATAACTTTTGATATT
1 TTTTTATAATTTTTTATATT
**
3750607 TTTAAATAATTTTTTAT-TT
1 TTTTTATAATTTTTTATATT
3750626 TTTTTATAATTTTTTA
1 TTTTTATAATTTTTTA
3750642 AAAACTATTT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (20 bp):
TTTTTATAATTTTTTATATT
Found at i:3750641 original size:10 final size:10
Alignment explanation
Indices: 3750587--3750641 Score: 51
Period size: 10 Copynumber: 5.6 Consensus size: 10
3750577 TTTTTAATAG
*
3750587 TTTTTATAAC
1 TTTTTATAAT
*
3750597 TTTTGAT-AT
1 TTTTTATAAT
*
3750606 TTTTAAATAAT
1 TTTT-TATAAT
*
3750617 TTTTTAT-TT
1 TTTTTATAAT
3750626 TTTTTATAAT
1 TTTTTATAAT
3750636 TTTTTA
1 TTTTTA
3750642 AAAACTATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
9 13 0.36
10 17 0.47
11 6 0.17
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:3752603 original size:8 final size:8
Alignment explanation
Indices: 3752590--3752614 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
3752580 CTCCTTAAAG
3752590 AATTTTAA
1 AATTTTAA
3752598 AATTTTAA
1 AATTTTAA
3752606 AATTTTAA
1 AATTTTAA
3752614 A
1 A
3752615 TTAGTGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
AATTTTAA
Found at i:3752694 original size:25 final size:25
Alignment explanation
Indices: 3752664--3752712 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
3752654 ATAAAATTCT
* * *
3752664 GATTTAATCTTTTAAAAATTATAAA
1 GATTTAAGCTATTAAAAATCATAAA
*
3752689 GATTTAGGCTATTAAAAATCATAA
1 GATTTAAGCTATTAAAAATCATAA
3752713 TTTCAATTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.39
Consensus pattern (25 bp):
GATTTAAGCTATTAAAAATCATAAA
Found at i:3755820 original size:31 final size:31
Alignment explanation
Indices: 3755761--3755840 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 31
3755751 ACACACATAT
*
3755761 ATATACTAAATAAAATAATAAAATAATAATAA
1 ATAT-CTAATTAAAATAATAAAATAATAATAA
* *
3755793 ATATCTTATTAAAAT-ATTAAATAAATAATAA
1 ATATCTAATTAAAATAATAAAAT-AATAATAA
*
3755824 TTATCTAATT-AAATAAT
1 ATATCTAATTAAAATAAT
3755841 TATAAAGTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
30 10 0.24
31 27 0.66
32 4 0.10
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (31 bp):
ATATCTAATTAAAATAATAAAATAATAATAA
Found at i:3755826 original size:23 final size:23
Alignment explanation
Indices: 3755767--3755826 Score: 56
Period size: 23 Copynumber: 2.7 Consensus size: 23
3755757 ATATATATAC
3755767 TAAAT-AA-AATAA-TAAAATAA
1 TAAATAAATAATAATTAAAATAA
* * *
3755787 T-AATAAATATCTTATTAAAATAT
1 TAAATAAATA-ATAATTAAAATAA
3755810 TAAATAAATAATAATTA
1 TAAATAAATAATAATTA
3755827 TCTAATTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
19 3 0.10
20 3 0.10
21 1 0.03
22 2 0.07
23 13 0.43
24 8 0.27
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (23 bp):
TAAATAAATAATAATTAAAATAA
Found at i:3768459 original size:16 final size:15
Alignment explanation
Indices: 3768420--3768468 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
3768410 TCAGTTTGAT
*
3768420 TTATTTTTAAATTTA
1 TTATTTTTATATTTA
*
3768435 TAATATTTTATATTATA
1 TTAT-TTTTATATT-TA
3768452 TTATTTTTATATATTA
1 TTATTTTTATAT-TTA
3768468 T
1 T
3768469 ATAATCTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 3 0.11
16 19 0.68
17 6 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTATTTTTATATTTA
Found at i:3768978 original size:30 final size:30
Alignment explanation
Indices: 3768937--3768995 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
3768927 TGGAATTTTT
* * *
3768937 TCTTAACAATAATTTTAAAAAATTAAAAAA
1 TCTTAAAAATAAATATAAAAAATTAAAAAA
*
3768967 TCTTAAAAATAAATATAAAATATTAAAAA
1 TCTTAAAAATAAATATAAAAAATTAAAAA
3768996 TTATGTTAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (30 bp):
TCTTAAAAATAAATATAAAAAATTAAAAAA
Found at i:3769091 original size:18 final size:20
Alignment explanation
Indices: 3769060--3769097 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
3769050 TTTTTAATAA
*
3769060 TTTATATTTATTTTTAAATT
1 TTTATATTTATTTTAAAATT
3769080 TTTA-ATTT-TTTTAAAATT
1 TTTATATTTATTTTAAAATT
3769098 GTTGTTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
19 4 0.24
20 4 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTATATTTATTTTAAAATT
Found at i:3779391 original size:20 final size:21
Alignment explanation
Indices: 3779366--3779404 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
3779356 AATTTTATAA
*
3779366 TTAATTGAT-TGAGTATTAAC
1 TTAATTGATATGAATATTAAC
3779386 TTAATTGATATGAATATTA
1 TTAATTGATATGAATATTA
3779405 TTGTCAACAC
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:0.38, C:0.03, G:0.13, T:0.46
Consensus pattern (21 bp):
TTAATTGATATGAATATTAAC
Found at i:3794668 original size:23 final size:23
Alignment explanation
Indices: 3794642--3794686 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
3794632 TATATACTAA
*
3794642 ATATATATATTTTATTTTTAATC
1 ATATATACATTTTATTTTTAATC
*
3794665 ATATTTACATTTTATTTTTAAT
1 ATATATACATTTTATTTTTAAT
3794687 TTTAATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (23 bp):
ATATATACATTTTATTTTTAATC
Found at i:3795948 original size:15 final size:15
Alignment explanation
Indices: 3795910--3795951 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
3795900 TATCGTACGT
3795910 ATTGAATTTTAATCA
1 ATTGAATTTTAATCA
* *
3795925 ATT-ATATTTTTATTA
1 ATTGA-ATTTTAATCA
3795940 ATTGAATTTTAA
1 ATTGAATTTTAA
3795952 GGAGAATTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
14 1 0.05
15 20 0.91
16 1 0.05
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (15 bp):
ATTGAATTTTAATCA
Found at i:3798145 original size:85 final size:85
Alignment explanation
Indices: 3798041--3798213 Score: 337
Period size: 85 Copynumber: 2.0 Consensus size: 85
3798031 AATTTTTCCA
*
3798041 ATTAAATATGGATCAAAAGCTTAATTTTTATTGGAATTTAAAATAAATAATATGGATATTAAAAG
1 ATTAAAAATGGATCAAAAGCTTAATTTTTATTGGAATTTAAAATAAATAATATGGATATTAAAAG
3798106 AAAGAATATAATACCGACTG
66 AAAGAATATAATACCGACTG
3798126 ATTAAAAATGGATCAAAAGCTTAATTTTTATTGGAATTTAAAATAAATAATATGGATATTAAAAG
1 ATTAAAAATGGATCAAAAGCTTAATTTTTATTGGAATTTAAAATAAATAATATGGATATTAAAAG
3798191 AAAGAATATAATACCGACTG
66 AAAGAATATAATACCGACTG
3798211 ATT
1 ATT
3798214 CTACTTTCCC
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 87 1.00
ACGTcount: A:0.49, C:0.06, G:0.13, T:0.33
Consensus pattern (85 bp):
ATTAAAAATGGATCAAAAGCTTAATTTTTATTGGAATTTAAAATAAATAATATGGATATTAAAAG
AAAGAATATAATACCGACTG
Found at i:3803303 original size:54 final size:55
Alignment explanation
Indices: 3803197--3803303 Score: 189
Period size: 54 Copynumber: 2.0 Consensus size: 55
3803187 TATATAATCA
*
3803197 TACATGGTTTAGCAACTAGATATTAAACGATATAGCAAGTACTTATACTGTATGG
1 TACATGGTTAAGCAACTAGATATTAAACGATATAGCAAGTACTTATACTGTATGG
*
3803252 TACATGGTTAAGCAACTAGATATT-AATGATATAGCAAGTACTTATACTGTAT
1 TACATGGTTAAGCAACTAGATATTAAACGATATAGCAAGTACTTATACTGTAT
3803304 ATTCCCCTCT
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
54 27 0.54
55 23 0.46
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (55 bp):
TACATGGTTAAGCAACTAGATATTAAACGATATAGCAAGTACTTATACTGTATGG
Found at i:3808380 original size:21 final size:21
Alignment explanation
Indices: 3808356--3808395 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
3808346 ACTATTTATT
3808356 TATAT-TATTTTTAAATATACA
1 TATATATA-TTTTAAATATACA
3808377 TATATATATTTTAAATATA
1 TATATATATTTTAAATATA
3808396 TTATTTCTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (21 bp):
TATATATATTTTAAATATACA
Found at i:3808387 original size:31 final size:32
Alignment explanation
Indices: 3808326--3808387 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 32
3808316 GTATATAAAT
** *
3808326 TATTATTTTTAAAATATTTTACTATTTATTTA
1 TATTATTTTTAAAATATCATACTATATATTTA
3808358 TATTATTTTT-AAATATACATA-TATATATTT
1 TATTATTTTTAAAATAT-CATACTATATATTT
3808388 TAAATATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
31 14 0.54
32 12 0.46
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (32 bp):
TATTATTTTTAAAATATCATACTATATATTTA
Found at i:3809849 original size:19 final size:19
Alignment explanation
Indices: 3809827--3809864 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
3809817 TATTTTTGAA
3809827 AAATAATTTACTTTTCTAG
1 AAATAATTTACTTTTCTAG
*
3809846 AAATGATTTACTTTTCTAG
1 AAATAATTTACTTTTCTAG
3809865 TGTTTGAATG
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:0.34, C:0.11, G:0.08, T:0.47
Consensus pattern (19 bp):
AAATAATTTACTTTTCTAG
Found at i:3813243 original size:57 final size:57
Alignment explanation
Indices: 3813176--3813291 Score: 189
Period size: 58 Copynumber: 2.0 Consensus size: 57
3813166 AATATTTAAG
*
3813176 AAGTTGAAGAACGGAAG-AGAAGAAAAAGACTTACCTGGATGAAGAAGGAGATGGAAA
1 AAGTTGAAGAACAGAAGAAGAAGAAAAAGACTTACCTGGATGAAGAAGGAGAT-GAAA
* *
3813233 AAGTTGAAGAACAGAAGAAGAAGAAGAAGACTTACCTGGATGAAGAAGGGGATGAAA
1 AAGTTGAAGAACAGAAGAAGAAGAAAAAGACTTACCTGGATGAAGAAGGAGATGAAA
3813290 AA
1 AA
3813292 TGTCTTACTG
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
57 22 0.40
58 33 0.60
ACGTcount: A:0.50, C:0.07, G:0.31, T:0.12
Consensus pattern (57 bp):
AAGTTGAAGAACAGAAGAAGAAGAAAAAGACTTACCTGGATGAAGAAGGAGATGAAA
Found at i:3817708 original size:27 final size:28
Alignment explanation
Indices: 3817661--3817718 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
3817651 ATAATAATAT
*
3817661 AATATAATATAATATACTTAAT-TATTA
1 AATATAATATAATATACTTAATCAATTA
**
3817688 AATA-AATATATATATTTTTAATCAATTA
1 AATATAATATA-ATATACTTAATCAATTA
3817716 AAT
1 AAT
3817719 CTTTGATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 6 0.23
27 13 0.50
28 7 0.27
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (28 bp):
AATATAATATAATATACTTAATCAATTA
Found at i:3828929 original size:7 final size:7
Alignment explanation
Indices: 3828917--3828957 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
3828907 ATCAAAATAA
3828917 TTAAAAT
1 TTAAAAT
3828924 TTAAAAT
1 TTAAAAT
3828931 TTAAAAT
1 TTAAAAT
3828938 TTAAAA-
1 TTAAAAT
*
3828944 TAAATAAT
1 TTAA-AAT
3828952 TTAAAA
1 TTAAAA
3828958 GTAGTTAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 3 0.10
7 24 0.80
8 3 0.10
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (7 bp):
TTAAAAT
Found at i:3836424 original size:14 final size:14
Alignment explanation
Indices: 3836407--3836435 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3836397 ATATCAAACA
3836407 TAAAATATATTTAT
1 TAAAATATATTTAT
3836421 TAAAATATATTTAT
1 TAAAATATATTTAT
3836435 T
1 T
3836436 TATGCGCAAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TAAAATATATTTAT
Found at i:3841510 original size:54 final size:54
Alignment explanation
Indices: 3841452--3841560 Score: 218
Period size: 54 Copynumber: 2.0 Consensus size: 54
3841442 AGAAAATGAA
3841452 ATTGCATTCTCTTTTTAGATTTGTAAATCCATTTCTTCATATTGAAAATGATTC
1 ATTGCATTCTCTTTTTAGATTTGTAAATCCATTTCTTCATATTGAAAATGATTC
3841506 ATTGCATTCTCTTTTTAGATTTGTAAATCCATTTCTTCATATTGAAAATGATTC
1 ATTGCATTCTCTTTTTAGATTTGTAAATCCATTTCTTCATATTGAAAATGATTC
3841560 A
1 A
3841561 ATCATTTTAG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.28, C:0.15, G:0.09, T:0.48
Consensus pattern (54 bp):
ATTGCATTCTCTTTTTAGATTTGTAAATCCATTTCTTCATATTGAAAATGATTC
Found at i:3843747 original size:40 final size:40
Alignment explanation
Indices: 3843692--3843771 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
3843682 TAAAACGTTT
3843692 TGAATACAAGTTGGATCGACATTTTTGTCCCCTTCTCCGA
1 TGAATACAAGTTGGATCGACATTTTTGTCCCCTTCTCCGA
3843732 TGAATACAAGTTGGATCGACATTTTTGTCCCCTTCTCCGA
1 TGAATACAAGTTGGATCGACATTTTTGTCCCCTTCTCCGA
3843772 CACATGTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (40 bp):
TGAATACAAGTTGGATCGACATTTTTGTCCCCTTCTCCGA
Found at i:3857618 original size:22 final size:22
Alignment explanation
Indices: 3857593--3857634 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3857583 TAGTCATATG
3857593 ATAAATTATTAATATAATAAAT
1 ATAAATTATTAATATAATAAAT
* * *
3857615 ATAATTTATTATTTTAATAA
1 ATAAATTATTAATATAATAA
3857635 GTTATTTAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAAATTATTAATATAATAAAT
Found at i:3857674 original size:13 final size:14
Alignment explanation
Indices: 3857656--3857697 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
3857646 TTTCAATTCT
3857656 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
3857669 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
3857684 ATTTTAAATAATAT
1 ATTTT-AATAATAT
3857698 TATTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:3857682 original size:16 final size:16
Alignment explanation
Indices: 3857660--3857696 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
3857650 AATTCTATTT
3857660 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
3857677 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
3857692 TAATA
1 TAATA
3857697 TTATTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:3858149 original size:14 final size:14
Alignment explanation
Indices: 3858121--3858164 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
3858111 TAAAAATGAC
*
3858121 TTTTATGAAAT-AT
1 TTTTAAGAAATCAT
3858134 TTTTAAGAAATCAT
1 TTTTAAGAAATCAT
**
3858148 TTTCCAGAAATCAT
1 TTTTAAGAAATCAT
3858162 TTT
1 TTT
3858165 CCAAAAGTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 10 0.37
14 17 0.63
ACGTcount: A:0.36, C:0.09, G:0.07, T:0.48
Consensus pattern (14 bp):
TTTTAAGAAATCAT
Found at i:3858165 original size:14 final size:14
Alignment explanation
Indices: 3858139--3858179 Score: 66
Period size: 14 Copynumber: 2.9 Consensus size: 14
3858129 AATATTTTTA
3858139 AGAAATCATTTTCC
1 AGAAATCATTTTCC
3858153 AGAAATCATTTTCC
1 AGAAATCATTTTCC
3858167 A-AAAGTCATTTTC
1 AGAAA-TCATTTTC
3858180 AGTGAAACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 3 0.12
14 23 0.88
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.37
Consensus pattern (14 bp):
AGAAATCATTTTCC
Found at i:3873848 original size:5 final size:5
Alignment explanation
Indices: 3873838--3873875 Score: 60
Period size: 5 Copynumber: 7.6 Consensus size: 5
3873828 ATGTGTGTTC
3873838 TTTAT TTTAT TTT-T TTTATT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTA-T TTTAT TTTAT TTTAT TTT
3873876 CAAAAATTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 4 0.13
5 22 0.71
6 5 0.16
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (5 bp):
TTTAT
Found at i:3892733 original size:12 final size:12
Alignment explanation
Indices: 3892718--3892748 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
3892708 TTCTCTTTTA
3892718 TTTTTCTTTCCC
1 TTTTTCTTTCCC
*
3892730 TTTTTCTTTCTC
1 TTTTTCTTTCCC
3892742 TTTTTCT
1 TTTTTCT
3892749 CCCCTGCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTCTTTCCC
Found at i:3892849 original size:16 final size:16
Alignment explanation
Indices: 3892828--3892858 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3892818 TTTATTATTT
3892828 TATTAACATAATATAA
1 TATTAACATAATATAA
*
3892844 TATTAATATAATATA
1 TATTAACATAATATA
3892859 TTAAAATATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
TATTAACATAATATAA
Found at i:3897834 original size:26 final size:26
Alignment explanation
Indices: 3897803--3897858 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
3897793 AATTTTTTTG
*
3897803 AAGTTAGACTTATAATTCACAATAAC
1 AAGTTAGACTTACAATTCACAATAAC
* * *
3897829 AAGTTATATTTACAGTTCACAATAAC
1 AAGTTAGACTTACAATTCACAATAAC
3897855 AAGT
1 AAGT
3897859 AATACCATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (26 bp):
AAGTTAGACTTACAATTCACAATAAC
Found at i:3907588 original size:29 final size:29
Alignment explanation
Indices: 3907546--3907603 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
3907536 ACTAAGCCAG
*
3907546 ACAAAACAG-CCCCCCTCATGATTAATACC
1 ACAAAACAGACCCCCC-AATGATTAATACC
3907575 ACAAAACAGACCCCCCAATGATTAATACC
1 ACAAAACAGACCCCCCAATGATTAATACC
3907604 TATGTGAAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 21 0.78
30 6 0.22
ACGTcount: A:0.41, C:0.36, G:0.07, T:0.16
Consensus pattern (29 bp):
ACAAAACAGACCCCCCAATGATTAATACC
Found at i:3912996 original size:90 final size:90
Alignment explanation
Indices: 3912843--3913018 Score: 352
Period size: 90 Copynumber: 2.0 Consensus size: 90
3912833 GTTTTCAATA
3912843 GGGTGTGCATAATTCGGGTAAAACCGAAAAAATTCGGTTAACCGACCGAATTCGGTTAATCGGTC
1 GGGTGTGCATAATTCGGGTAAAACCGAAAAAATTCGGTTAACCGACCGAATTCGGTTAATCGGTC
3912908 GGTTAACCGAATTTTTTCGGTGTAG
66 GGTTAACCGAATTTTTTCGGTGTAG
3912933 GGGTGTGCATAATTCGGGTAAAACCGAAAAAATTCGGTTAACCGACCGAATTCGGTTAATCGGTC
1 GGGTGTGCATAATTCGGGTAAAACCGAAAAAATTCGGTTAACCGACCGAATTCGGTTAATCGGTC
3912998 GGTTAACCGAATTTTTTCGGT
66 GGTTAACCGAATTTTTTCGGT
3913019 CGGGGATCGG
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 86 1.00
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (90 bp):
GGGTGTGCATAATTCGGGTAAAACCGAAAAAATTCGGTTAACCGACCGAATTCGGTTAATCGGTC
GGTTAACCGAATTTTTTCGGTGTAG
Found at i:3913337 original size:9 final size:9
Alignment explanation
Indices: 3913321--3913363 Score: 77
Period size: 9 Copynumber: 4.8 Consensus size: 9
3913311 GGTATTTTTC
3913321 GGTAATTCG
1 GGTAATTCG
*
3913330 GTTAATTCG
1 GGTAATTCG
3913339 GGTAATTCG
1 GGTAATTCG
3913348 GGTAATTCG
1 GGTAATTCG
3913357 GGTAATT
1 GGTAATT
3913364 TTTAACCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.23, C:0.09, G:0.30, T:0.37
Consensus pattern (9 bp):
GGTAATTCG
Found at i:3913541 original size:12 final size:12
Alignment explanation
Indices: 3913524--3913548 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3913514 AGTAATTTCG
3913524 GGTCGGTTAACC
1 GGTCGGTTAACC
3913536 GGTCGGTTAACC
1 GGTCGGTTAACC
3913548 G
1 G
3913549 AATGAACACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:3918060 original size:30 final size:28
Alignment explanation
Indices: 3917992--3918062 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 28
3917982 TTTTCACAAA
* *
3917992 TTTAAAATTTAATCATTGTATTTTTATT
1 TTTAAAATTTAGTCATTGTATTTTTAAT
* *
3918020 TTTAAGAATTTAGTCCTTTTACTTTTTAGAT
1 TTTAA-AATTTAGTCATTGTA-TTTTTA-AT
3918051 TTTAAAATTTAG
1 TTTAAAATTTAG
3918063 GTTCAGTTGT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 5 0.14
29 12 0.33
30 13 0.36
31 6 0.17
ACGTcount: A:0.31, C:0.06, G:0.07, T:0.56
Consensus pattern (28 bp):
TTTAAAATTTAGTCATTGTATTTTTAAT
Found at i:3919618 original size:23 final size:23
Alignment explanation
Indices: 3919588--3919631 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
3919578 TACCTTCTGA
*
3919588 TCTCACTTTATCTTGATATTCGG
1 TCTCACTTTATATTGATATTCGG
3919611 TCTCACTTTATATTGATATTC
1 TCTCACTTTATATTGATATTC
3919632 TCTTAAGGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.09, T:0.50
Consensus pattern (23 bp):
TCTCACTTTATATTGATATTCGG
Found at i:3921636 original size:5 final size:5
Alignment explanation
Indices: 3921626--3921656 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
3921616 AATAATTAAG
3921626 TATAT TATAT TATAT TATAT TATTAT TATAT
1 TATAT TATAT TATAT TATAT TA-TAT TATAT
3921657 ATAAAAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:3921726 original size:31 final size:30
Alignment explanation
Indices: 3921691--3921751 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
3921681 GATACAGAAT
*
3921691 GAAAGCAAACGAAAC-AGAGAAGAACAGGGGA
1 GAAAG-AAACGAAACAAGA-AAGAAAAGGGGA
* *
3921722 GAAAGAAAGGAAAGAAGAAAGAAAAGGGGA
1 GAAAGAAACGAAACAAGAAAGAAAAGGGGA
3921752 AATAGGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.59, C:0.07, G:0.34, T:0.00
Consensus pattern (30 bp):
GAAAGAAACGAAACAAGAAAGAAAAGGGGA
Found at i:3923327 original size:39 final size:39
Alignment explanation
Indices: 3923220--3923354 Score: 123
Period size: 39 Copynumber: 3.4 Consensus size: 39
3923210 GACCTCGAGT
* * *
3923220 CGATGAGACACTGGGTGTC-ACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCAAC--TATTACTTCGGCTAG-TC
** ** *
3923261 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
*
3923299 CGATGAGACACTGGGTGTCAACTATTACTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAACTATTACTTCG-GCTAGTC
*
3923338 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
3923355 CCATATTGGT
Statistics
Matches: 76, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
38 19 0.25
39 36 0.47
40 4 0.05
41 15 0.20
42 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
Found at i:3937111 original size:88 final size:87
Alignment explanation
Indices: 3936961--3937692 Score: 1137
Period size: 88 Copynumber: 8.3 Consensus size: 87
3936951 GGATAGATTG
* * * * * *
3936961 AGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAGGTCAGATCCT
1 AGATCGAAGAAAGTAGATCTTGTCTTCAT-CATTAGCATGAAGTAGATCGAAGATG-CAGATCTT
* * * *
3937026 ATCCTCCTATATTGGTAG-GAAGT
64 GTCTTCCCATATTGGTGGCGAAGT
* * * * * ** **
3937049 GGATCGAAG-ATGCAGATCTTGTTTTCCCAT-ATTGGTGGTGAAGTAGATCGAAGAAAACAGATC
1 AGATCGAAGAAAGTAGATCTTGTCTT--CATCATTAG-CATGAAGTAGATCGAAG-ATGCAGATC
3937112 TTGTCTTCCCATATTGGTGGCGAAGT
62 TTGTCTTCCCATATTGGTGGCGAAGT
3937138 AGATCGAAGAAAGTAGATCTTGTCTTCATGCATTAGCATGAAGTAGATCGAAGATGCAGATCTTG
1 AGATCGAAGAAAGTAGATCTTGTCTTCAT-CATTAGCATGAAGTAGATCGAAGATGCAGATCTTG
3937203 TCTTCCCATATTGGTGGCGAAGT
65 TCTTCCCATATTGGTGGCGAAGT
3937226 AGATCGAAGAAAGTAGATCTTGTCTTCATGCATTAGCATGAAGTAGATCGAAGATGCAGATCTTG
1 AGATCGAAGAAAGTAGATCTTGTCTTCAT-CATTAGCATGAAGTAGATCGAAGATGCAGATCTTG
3937291 TCTTCCCATATTGGTGGCGAAGT
65 TCTTCCCATATTGGTGGCGAAGT
3937314 AGATCGAAGAAAGTAGATCTTGTCTTCATGCATTAGCATGAAGTAGATCGAAGATGCAGATCTTG
1 AGATCGAAGAAAGTAGATCTTGTCTTCAT-CATTAGCATGAAGTAGATCGAAGATGCAGATCTTG
3937379 TCTTCCCATATTGGTGGCGAAGT
65 TCTTCCCATATTGGTGGCGAAGT
3937402 AGATCGAAGAAAGTAGATCTTGTCTTCATGCATTAGCATGAAGTAGATCGAAGATGCAGATCTTG
1 AGATCGAAGAAAGTAGATCTTGTCTTCAT-CATTAGCATGAAGTAGATCGAAGATGCAGATCTTG
3937467 TCTTCCCATATTGGTGGCGAAGT
65 TCTTCCCATATTGGTGGCGAAGT
3937490 AGATCGAAGAAAGTAGATCTTGTCTTCATGCATTAGCATGAAGTAGATCGAAGATGCAGATCTTG
1 AGATCGAAGAAAGTAGATCTTGTCTTCAT-CATTAGCATGAAGTAGATCGAAGATGCAGATCTTG
3937555 TCTTCCCATATTGGTGGCGAAGT
65 TCTTCCCATATTGGTGGCGAAGT
3937578 AGATCGAAGAAAGTAGATCTTGTCTTCATGCATTAGCATGAAGTAGATCGAAGATGCAGATCTTG
1 AGATCGAAGAAAGTAGATCTTGTCTTCAT-CATTAGCATGAAGTAGATCGAAGATGCAGATCTTG
*
3937643 TCTTCCCATATTGGTGGTGAAGT
65 TCTTCCCATATTGGTGGCGAAGT
**
3937666 AGATCGAAGAAAACAGATCTTGTCTTC
1 AGATCGAAGAAAGTAGATCTTGTCTTC
3937693 CCATATTGGT
Statistics
Matches: 613, Mismatches: 23, Indels: 16
0.94 0.04 0.02
Matches are distributed among these distances:
87 19 0.03
88 545 0.89
89 32 0.05
90 17 0.03
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (87 bp):
AGATCGAAGAAAGTAGATCTTGTCTTCATCATTAGCATGAAGTAGATCGAAGATGCAGATCTTGT
CTTCCCATATTGGTGGCGAAGT
Found at i:3937803 original size:88 final size:90
Alignment explanation
Indices: 3936998--3937817 Score: 495
Period size: 88 Copynumber: 9.3 Consensus size: 90
3936988 ATGTATTGGC
* * * * * *
3936998 GTGAAGTAGATCGAAGA-GGTCAGATCCTATCCTCCTATATTGGTAG-GAAGTGGATCGAAG-AT
1 GTGAAGTAGATCGAAGATAG-CAGATCCTATCTTCCCATATTGGTAGTGAAGTAGACCGAAGAAA
* * * *
3937060 GCAGATCTTGTTTTCCCATATTGGTG
65 ACAGATCTTGTCTTCCCACACTGGTG
* * * * * * * *
3937086 GTGAAGTAGATCGAAGAAAACAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAG
1 GTGAAGTAGATCGAAGATAGCAGATCCTATCTTCCCATATTGGTAGTGAAGTAGACCGAAGAAAA
* *** * * *
3937151 TAGATCTTGTCTTCATGCATTAG-C
66 CAGATCTTGTCTTCCCACACTGGTG
* * * * * * *
3937175 ATGAAGTAGATCGAAGAT-GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAG
1 GTGAAGTAGATCGAAGATAGCAGATCCTATCTTCCCATATTGGTAGTGAAGTAGACCGAAGAAAA
* *** * * *
3937239 TAGATCTTGTCTTCATGCATTAG-C
66 CAGATCTTGTCTTCCCACACTGGTG
* * * * * * *
3937263 ATGAAGTAGATCGAAGAT-GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAG
1 GTGAAGTAGATCGAAGATAGCAGATCCTATCTTCCCATATTGGTAGTGAAGTAGACCGAAGAAAA
* *** * * *
3937327 TAGATCTTGTCTTCATGCATTAG-C
66 CAGATCTTGTCTTCCCACACTGGTG
* * * * * * *
3937351 ATGAAGTAGATCGAAGAT-GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAG
1 GTGAAGTAGATCGAAGATAGCAGATCCTATCTTCCCATATTGGTAGTGAAGTAGACCGAAGAAAA
* *** * * *
3937415 TAGATCTTGTCTTCATGCATTAG-C
66 CAGATCTTGTCTTCCCACACTGGTG
* * * * * * *
3937439 ATGAAGTAGATCGAAGAT-GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAG
1 GTGAAGTAGATCGAAGATAGCAGATCCTATCTTCCCATATTGGTAGTGAAGTAGACCGAAGAAAA
* *** * * *
3937503 TAGATCTTGTCTTCATGCATTAG-C
66 CAGATCTTGTCTTCCCACACTGGTG
* * * * * * *
3937527 ATGAAGTAGATCGAAGAT-GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAG
1 GTGAAGTAGATCGAAGATAGCAGATCCTATCTTCCCATATTGGTAGTGAAGTAGACCGAAGAAAA
* *** * * *
3937591 TAGATCTTGTCTTCATGCATTAG-C
66 CAGATCTTGTCTTCCCACACTGGTG
* * * * *
3937615 ATGAAGTAGATCGAAGAT-GCAGATCTTGTCTTCCCATATTGGTGGTGAAGTAGATCGAAGAAAA
1 GTGAAGTAGATCGAAGATAGCAGATCCTATCTTCCCATATTGGTAGTGAAGTAGACCGAAGAAAA
* *
3937679 CAGATCTTGTCTTCCCATATTGGTG
66 CAGATCTTGTCTTCCCACACTGGTG
* * * * * **
3937704 GTAAAGTAGATCGAAGATATCAGATCCTATCTTCCTATATTGGTAG-GAAGTGGACCGACG-ATG
1 GTGAAGTAGATCGAAGATAGCAGATCCTATCTTCCCATATTGGTAGTGAAGTAGACCGAAGAAAA
* *
3937767 CAGATTTTGTTTTCCCACACTGGTG
66 CAGATCTTGTCTTCCCACACTGGTG
* *
3937792 GTGAAGAAGATCGAAGAAAGCAGATC
1 GTGAAGTAGATCGAAGATAGCAGATC
3937818 GACGATGGCG
Statistics
Matches: 678, Mismatches: 49, Indels: 10
0.92 0.07 0.01
Matches are distributed among these distances:
88 582 0.86
89 56 0.08
90 40 0.06
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (90 bp):
GTGAAGTAGATCGAAGATAGCAGATCCTATCTTCCCATATTGGTAGTGAAGTAGACCGAAGAAAA
CAGATCTTGTCTTCCCACACTGGTG
Found at i:3938410 original size:23 final size:23
Alignment explanation
Indices: 3938380--3938459 Score: 119
Period size: 23 Copynumber: 3.5 Consensus size: 23
3938370 AAACCCAACT
3938380 AACCTAGCCCAATACCCTAAACC
1 AACCTAGCCCAATACCCTAAACC
3938403 AACCTAGCCCAATACCCTAAACC
1 AACCTAGCCCAATACCCTAAACC
*
3938426 AACCTAGCCCAAT--CCTAAAAC
1 AACCTAGCCCAATACCCTAAACC
*
3938447 TACCTGAGCCCAA
1 AACCT-AGCCCAA
3938460 ATTTTAAAAC
Statistics
Matches: 54, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
21 11 0.20
22 7 0.13
23 36 0.67
ACGTcount: A:0.39, C:0.41, G:0.06, T:0.14
Consensus pattern (23 bp):
AACCTAGCCCAATACCCTAAACC
Found at i:3941581 original size:17 final size:17
Alignment explanation
Indices: 3941556--3941589 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3941546 ATATGGAAAC
*
3941556 TAATCTTAGAAGATTTG
1 TAATATTAGAAGATTTG
3941573 TAATATTAGAAGATTTG
1 TAATATTAGAAGATTTG
3941590 ATTTCGTAAT
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:0.38, C:0.03, G:0.18, T:0.41
Consensus pattern (17 bp):
TAATATTAGAAGATTTG
Found at i:3941599 original size:23 final size:22
Alignment explanation
Indices: 3941567--3941610 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
3941557 AATCTTAGAA
3941567 GATTTGTAATATTAGAAGATTT
1 GATTTGTAATATTAGAAGATTT
* *
3941589 GATTTCGTAATGTTAGAGGATT
1 GATTT-GTAATATTAGAAGATT
3941611 GTGTAAATCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.32, C:0.02, G:0.23, T:0.43
Consensus pattern (22 bp):
GATTTGTAATATTAGAAGATTT
Found at i:3942998 original size:46 final size:46
Alignment explanation
Indices: 3942928--3943066 Score: 154
Period size: 46 Copynumber: 3.0 Consensus size: 46
3942918 TATTGCCCAC
* * * *
3942928 AGGTTCCGAGGTCTAGCATTTGTTGCGAACTTGAGAATACAAGAAT
1 AGGTTCCGAGCTCCAGCATATGTTGCGGACTTGAGAATACAAGAAT
* * * **
3942974 AGGTTCCGAGCTCCAGTA-AGTGTTGCGGACTCGAGAATACAGGTTT
1 AGGTTCCGAGCTCCAGCATA-TGTTGCGGACTTGAGAATACAAGAAT
* * *
3943020 AGGTTCTGAGCTCCTGCATATGTTGCGGACTTGAGAATATAAGAAT
1 AGGTTCCGAGCTCCAGCATATGTTGCGGACTTGAGAATACAAGAAT
3943066 A
1 A
3943067 TTAAGCCCAA
Statistics
Matches: 74, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
46 73 0.99
47 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (46 bp):
AGGTTCCGAGCTCCAGCATATGTTGCGGACTTGAGAATACAAGAAT
Found at i:3946046 original size:246 final size:246
Alignment explanation
Indices: 3945612--3946106 Score: 981
Period size: 246 Copynumber: 2.0 Consensus size: 246
3945602 AAAATCTAAC
3945612 ATGGGCTTTTTATATTGGTCTAATAACAAATTTAGCACTCGAATGTTTACATATTCTATAAATTT
1 ATGGGCTTTTTATATTGGTCTAATAACAAATTTAGCACTCGAATGTTTACATATTCTATAAATTT
3945677 GATCCTAAATATAAAAAGATAAACAAATTTAGCCTTCAATGTTTACAAAATTTGTCATTTTAGTT
66 GATCCTAAATATAAAAAGATAAACAAATTTAGCCTTCAATGTTTACAAAATTTGTCATTTTAGTT
3945742 TAAATTCTAAAAAAATCAATAAATTTAGCTTTCAATATTTACAAAATGACAAATTTTGCTTCTTA
131 TAAATTCTAAAAAAATCAATAAATTTAGCTTTCAATATTTACAAAATGACAAATTTTGCTTCTTA
3945807 ATAATTTTAGTTATGTTATACCCCGAGTAGTGACCCTCAACATACCTGTAG
196 ATAATTTTAGTTATGTTATACCCCGAGTAGTGACCCTCAACATACCTGTAG
3945858 ATGGGCTTTTTATATTGGTCTAATAACAAATTTAGCACTCGAATGTTTACATATTCTATAAATTT
1 ATGGGCTTTTTATATTGGTCTAATAACAAATTTAGCACTCGAATGTTTACATATTCTATAAATTT
*
3945923 GATCCTAAATATAAAATGATAAACAAATTTAGCCTTCAATGTTTACAAAATTTGTCATTTTAGTT
66 GATCCTAAATATAAAAAGATAAACAAATTTAGCCTTCAATGTTTACAAAATTTGTCATTTTAGTT
3945988 TAAATTCTAAAAAAATCAATAAATTTAGCTTTCAATATTTACAAAATGACAAATTTTGCTTCTTA
131 TAAATTCTAAAAAAATCAATAAATTTAGCTTTCAATATTTACAAAATGACAAATTTTGCTTCTTA
3946053 ATAATTTTAGTTATGTTATACCCCGAGTAGTGACCCTCAACATACCTGTAG
196 ATAATTTTAGTTATGTTATACCCCGAGTAGTGACCCTCAACATACCTGTAG
3946104 ATG
1 ATG
3946107 AGTTTGACAC
Statistics
Matches: 248, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
246 248 1.00
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.38
Consensus pattern (246 bp):
ATGGGCTTTTTATATTGGTCTAATAACAAATTTAGCACTCGAATGTTTACATATTCTATAAATTT
GATCCTAAATATAAAAAGATAAACAAATTTAGCCTTCAATGTTTACAAAATTTGTCATTTTAGTT
TAAATTCTAAAAAAATCAATAAATTTAGCTTTCAATATTTACAAAATGACAAATTTTGCTTCTTA
ATAATTTTAGTTATGTTATACCCCGAGTAGTGACCCTCAACATACCTGTAG
Found at i:3946164 original size:20 final size:20
Alignment explanation
Indices: 3946136--3946175 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
3946126 CCATAGACCC
*
3946136 AGAGTTAGTCCGTGAACCTT
1 AGAGCTAGTCCGTGAACCTT
**
3946156 AGAGCTAGTTTGTGAACCTT
1 AGAGCTAGTCCGTGAACCTT
3946176 CAGAACAAGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (20 bp):
AGAGCTAGTCCGTGAACCTT
Found at i:3952854 original size:22 final size:22
Alignment explanation
Indices: 3952805--3952848 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3952795 TTTGGGATAT
* *
3952805 AAGGGTTAGGAGTTAGGGGTTA
1 AAGGTTTAGGAGTTAAGGGTTA
*
3952827 AAGGTTTAGGATTTAAGGGTTA
1 AAGGTTTAGGAGTTAAGGGTTA
3952849 GGGGTTAAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.39, T:0.32
Consensus pattern (22 bp):
AAGGTTTAGGAGTTAAGGGTTA
Found at i:3952856 original size:14 final size:14
Alignment explanation
Indices: 3952807--3952859 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
3952797 TGGGATATAA
3952807 GGGTT-AGGAGTTAG
1 GGGTTAAGG-GTTAG
*
3952821 GGGTTAAAGGTTTAG
1 GGGTT-AAGGGTTAG
**
3952836 GATTTAAGGGTTAG
1 GGGTTAAGGGTTAG
3952850 GGGTTAAGGG
1 GGGTTAAGGG
3952860 ATTAATGATT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
14 21 0.68
15 7 0.23
16 3 0.10
ACGTcount: A:0.25, C:0.00, G:0.45, T:0.30
Consensus pattern (14 bp):
GGGTTAAGGGTTAG
Found at i:3952874 original size:29 final size:28
Alignment explanation
Indices: 3952810--3952876 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 28
3952800 GATATAAGGG
*
3952810 TTAGGAGTTAGGGGTTAAAGGTTTAGGAT
1 TTAGG-GTTAGGGGTTAAAGGTTAAGGAT
* *
3952839 TTAAGGGTTAGGGGTTAAGGGATTAATGAT
1 TT-AGGGTTAGGGGTTAAAGG-TTAAGGAT
3952869 TTAGGGTT
1 TTAGGGTT
3952877 TAGGAATTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 22 0.67
30 11 0.33
ACGTcount: A:0.27, C:0.00, G:0.37, T:0.36
Consensus pattern (28 bp):
TTAGGGTTAGGGGTTAAAGGTTAAGGAT
Found at i:3953744 original size:270 final size:270
Alignment explanation
Indices: 3953205--3953887 Score: 843
Period size: 270 Copynumber: 2.5 Consensus size: 270
3953195 TAGTTAAACT
* ** * * * *
3953205 TTTAGTGGCGTTTTTTTTGAAATCGCCGCAAATATTGGATGCATTAGTGGCGTTTTTACAAG-AA
1 TTTAGTGGC-ATTTTTAGGAAAACGCCGAAAAT-TTGGAAGCAATAGTGGCGTTTTTAC-AGTAA
* * ** * * *
3953269 ACGCCGCAAAAGTGTCTTAAAATTTTGAGTAAACGATGCCGTTTCTCTCCACGATTTTTAACTTA
63 ACGCCGCAAAAGGGTATTAAAATAATGAGTAAACGGTGCCGTTTCTGTACACGATTTTTAACTTA
* * * ** *
3953334 TAAAAAGTTTAGAATTATTTACTTAAAACGTCACCGTTTGGCTTAAAGTACGTTAAGTATTAGTG
128 GAAAAATTTTAGAATTATTTACTTAAAACATCACCGTTTGGCTTAAAGTAAATTAAGTATTAATG
* * * **
3953399 GCGTTTTAACATAAAACGCCAGAAACAATGCAATTTGAGAGTAACAAAACGGCGCCGTTTCTGTT
193 ACGTTTTAACATAAAACACCAGAAACAATGCAATTTGAGACTAACAAAACGGCGCCGTTTCCCTT
*
3953464 TACGACTTTAAATA
258 TACAACTTT-AATA
* * * * *
3953478 TTT-GTGGCGTTTTT-GGCAAAACGCCGGAACTTTGGAAGCAATAGCGGCGTTTGTACAGTAAAC
1 TTTAGTGGCATTTTTAGG-AAAACGCCGAAAATTTGGAAGCAATAGTGGCGTTTTTACAGTAAAC
** **
3953541 GCCGCAAAAGGGTATTAAAATAATGTCTAAACGGCACCGTTTCTGTACACGATTTTTAACTTA-A
65 GCCGCAAAAGGGTATTAAAATAATGAGTAAACGGTGCCGTTTCTGTACACGATTTTTAACTTAGA
* *
3953605 AGAAATTTTAGAATTATTTATTTAAAACATCACCGTTTGGGTTAAAGTAAATTAAGTATTAATGA
130 A-AAATTTTAGAATTATTTACTTAAAACATCACCGTTTGGCTTAAAGTAAATTAAGTATTAATGA
* * *
3953670 CGTTTTTACATAAAACACTAGAAATAATGCAATTTGAGACTAACAAAACGGCGCCGTTTCCCTTT
194 CGTTTTAACATAAAACACCAGAAACAATGCAATTTGAGACTAACAAAACGGCGCCGTTTCCCTTT
3953735 ACAACTTTAATA
259 ACAACTTTAATA
* * * *
3953747 TTTAGTGGCATTTTTAGGAAAACGCCGAAAATGTGGAATCAATAGTGGCGTTTTTATAGTAAATG
1 TTTAGTGGCATTTTTAGGAAAACGCCGAAAATTTGGAAGCAATAGTGGCGTTTTTACAGTAAACG
* * * **
3953812 CCGCAAAAGGGTATTAGAGTAATGGGTAAACGGTGCCGTTTCTGTGTACGATTTTTAACTTAGAA
66 CCGCAAAAGGGTATTAAAATAATGAGTAAACGGTGCCGTTTCTGTACACGATTTTTAACTTAGAA
3953877 AAATTTTAGAA
131 AAATTTTAGAA
3953888 ATCAAGTATT
Statistics
Matches: 351, Mismatches: 53, Indels: 15
0.84 0.13 0.04
Matches are distributed among these distances:
269 11 0.03
270 312 0.89
271 20 0.06
272 5 0.01
273 3 0.01
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (270 bp):
TTTAGTGGCATTTTTAGGAAAACGCCGAAAATTTGGAAGCAATAGTGGCGTTTTTACAGTAAACG
CCGCAAAAGGGTATTAAAATAATGAGTAAACGGTGCCGTTTCTGTACACGATTTTTAACTTAGAA
AAATTTTAGAATTATTTACTTAAAACATCACCGTTTGGCTTAAAGTAAATTAAGTATTAATGACG
TTTTAACATAAAACACCAGAAACAATGCAATTTGAGACTAACAAAACGGCGCCGTTTCCCTTTAC
AACTTTAATA
Found at i:3954068 original size:233 final size:233
Alignment explanation
Indices: 3953653--3954120 Score: 654
Period size: 233 Copynumber: 2.0 Consensus size: 233
3953643 GGGTTAAAGT
* * * *
3953653 AAATTAAGTATTAATGACGTTTTTACATAAAACACTAGAAATAATGCAATTTGAGACTAACAAAA
1 AAATCAAGTATTAATGACGTTTTTACATAAAACACCAGAAAAAATGCAATTAGAGACTAACAAAA
*
3953718 CGGCGCCGTTTCCCTTTACAACTTTAATATTTAGTGGCATTTTTAGGAAAACGCCGAAAATGTGG
66 CGGCGCCGTTTCCCTTTACAACTTTAATATATAGTGGCATTTTTAGGAAAACGCCGAAAATGTGG
* ** * * * * ** **
3953783 AATCAATAGTGGCGTTTTTATAGTAAATGCCGCAAAAGGGTATTAGAGTAATGGGTAAACGGTGC
131 AAGCAATAACGGCGTTTGTATAGAAAATGCAGCAAAAGGGTATTAAAGTAATGCCTAAACGACGC
* **
3953848 CGTTTCTGTGTACGATTTTTAACTTAGAAAAATTTTAG
196 CGTTTCCGTAAACGATTTTTAACTTAGAAAAATTTTAG
* * * *
3953886 AAATCAAGTATTAGTGGCGTTTTTACGTAAAACGCCAGAAAAAATGCAATTAGAGACTAACAAAA
1 AAATCAAGTATTAATGACGTTTTTACATAAAACACCAGAAAAAATGCAATTAGAGACTAACAAAA
* *
3953951 CGGCGTCG-TTCCTCTTTACAACTTTAATATATAGTGGCGTTTTTAGGAAAACGCC-AGAAATGT
66 CGGCGCCGTTTCC-CTTTACAACTTTAATATATAGTGGCATTTTTAGGAAAACGCCGA-AAATGT
*
3954014 GTAAGCAATAACGGCGTTTGTACT-GAAAATGCAGCAAAAGGGTATTAAAGTAATGCCTAAACGA
129 GGAAGCAATAACGGCGTTTGTA-TAGAAAATGCAGCAAAAGGGTATTAAAGTAATGCCTAAACGA
3954078 CGCCGTTTCCGTAAACGATTTTTAACTTAGAAAAATTTTAG
193 CGCCGTTTCCGTAAACGATTTTTAACTTAGAAAAATTTTAG
3954119 AA
1 AA
3954121 TTATTTATTT
Statistics
Matches: 206, Mismatches: 26, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
232 5 0.02
233 200 0.97
234 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (233 bp):
AAATCAAGTATTAATGACGTTTTTACATAAAACACCAGAAAAAATGCAATTAGAGACTAACAAAA
CGGCGCCGTTTCCCTTTACAACTTTAATATATAGTGGCATTTTTAGGAAAACGCCGAAAATGTGG
AAGCAATAACGGCGTTTGTATAGAAAATGCAGCAAAAGGGTATTAAAGTAATGCCTAAACGACGC
CGTTTCCGTAAACGATTTTTAACTTAGAAAAATTTTAG
Found at i:3954355 original size:503 final size:502
Alignment explanation
Indices: 3953388--3954376 Score: 1256
Period size: 503 Copynumber: 2.0 Consensus size: 502
3953378 AAAGTACGTT
* * *
3953388 AAGTATTAGTGGCGTTTTAACATAAAACGCCAGAAACAATGCAATTTGAGAGTAACAAAACGGCG
1 AAGTATTAGTGGCGTTTTAACATAAAACGCCAGAAAAAATGCAATTAGAGACTAACAAAACGGCG
* * * * * * *
3953453 CCGTTTCTGTTTACGACTTTAAATATTTGTGGCGTTTTTGGCAAAACGCCGGAACTTTGGAAGCA
66 CCGTTCCTCTTTACAACTTTAAATATTAGTGGCGTTTTTGGCAAAACGCCAGAAATGTGGAAGCA
* * * * *
3953518 ATAGCGGCGTTTGTACAGTAAACGCCGCAAAAGGGTATTAAAATAATGTCTAAACGGCACCGTTT
131 ATAACGGCGTTTGTACAGAAAACGCAGCAAAAGGGTATTAAAATAATGCCTAAACGACACCGTTT
* * **
3953583 CTGTACACGATTTTTAACTTAAAGAAATTTTAGAATTATTTATTTAAAACATCACCGTTTGGGTT
196 CCGTAAACGATTTTTAACTTAAAGAAATTTTAGAATTATTTATTTAAAACATCACCGTTTGACTT
* * * *
3953648 AAAGTAAATTAAGTATTAATGACGTTTTTACATAAAACACTAGAAATAATGCAATTTGAGACTAA
261 AAAGTAAATTAAGTATTAATGACGTTTTTACATAAAACACCACAAAAAATGCAATTTCAGACTAA
*
3953713 CAAAACGGCGCCGTTTCCCTTTACAACTTTAATATTTAGTGGCATTTTTAGGAAAACGCCGAAAA
326 CAAAACAGCGCCGTTTCCCTTTACAACTTTAATATTTAGTGGCATTTTTAGGAAAACGCCGAAAA
* * * *
3953778 TGTGGAATCAATAGTGGCGTTTTTATAGTAAATGCCGCAAAAGGGTATTAGAGTAATGGGTAAAC
391 TGTGGAATCAATAGTGGCGTTTTTAGAG-AAATACCGCAAAAGGGTATTAGAATAATGGCTAAAC
** ** *
3953843 GGTGCCGTTTCTGTGTACGATTTTTAACTTAGAAAAATTTTAGAAATC
455 GACGCCGTTTCTCCGGACGATTTTTAACTTAGAAAAATTTTAGAAATC
* *
3953891 AAGTATTAGTGGCGTTTTTACGTAAAACGCCAGAAAAAATGCAATTAGAGACTAACAAAACGGCG
1 AAGTATTAGTGGCGTTTTAACATAAAACGCCAGAAAAAATGCAATTAGAGACTAACAAAACGGCG
* *
3953956 TCGTTCCTCTTTACAACTTT-AATATATAGTGGCGTTTTTAGG-AAAACGCCAGAAATGTGTAAG
66 CCGTTCCTCTTTACAACTTTAAATAT-TAGTGGCGTTTTT-GGCAAAACGCCAGAAATGTGGAAG
* * * *
3954019 CAATAACGGCGTTTGTACTGAAAATGCAGCAAAAGGGTATTAAAGTAATGCCTAAACGACGCCGT
129 CAATAACGGCGTTTGTACAGAAAACGCAGCAAAAGGGTATTAAAATAATGCCTAAACGACACCGT
*
3954084 TTCCGTAAACGATTTTTAACTTAGAA-AAATTTTAGAATTATTTATTTAAAACGTCACCGTTTGA
194 TTCCGTAAACGATTTTTAACTTA-AAGAAATTTTAGAATTATTTATTTAAAACATCACCGTTTGA
* * * * * *
3954148 CTTAAAGTAAATTAAGTGTTAGTGGCGTTTTTACATTAAACGCCACAAAAAATGTAATTTCAGAC
258 CTTAAAGTAAATTAAGTATTAATGACGTTTTTACATAAAACACCACAAAAAATGCAATTTCAGAC
** * * * **
3954213 TAACAGAAA-AGCGCCGTTTCTGTTTACAAGTTTAATCTATT-GTGGCGTTTTGTCTGAAAACGC
323 TAACA-AAACAGCGCCGTTTCCCTTTACAACTTTAATAT-TTAGTGGCATTTT-TAGGAAAACGC
* * * * **
3954276 CGGAAATGTGGAAT-AAGTA-TGGCGTTTGTTCGAG-AATCACCGCAAATGTGTATTAGAATTTT
385 CGAAAATGTGGAATCAA-TAGTGGCGTTT-TTAGAGAAAT-ACCGCAAAAGGGTATTAGAATAAT
* * *
3954338 TGCTGAACGACGCCGTTTCTCCGGACGTTTTTTAACTTA
447 GGCTAAACGACGCCGTTTCTCCGGACGATTTTTAACTTA
3954377 TCATTTACTC
Statistics
Matches: 413, Mismatches: 64, Indels: 18
0.83 0.13 0.04
Matches are distributed among these distances:
502 8 0.02
503 368 0.89
504 37 0.09
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (502 bp):
AAGTATTAGTGGCGTTTTAACATAAAACGCCAGAAAAAATGCAATTAGAGACTAACAAAACGGCG
CCGTTCCTCTTTACAACTTTAAATATTAGTGGCGTTTTTGGCAAAACGCCAGAAATGTGGAAGCA
ATAACGGCGTTTGTACAGAAAACGCAGCAAAAGGGTATTAAAATAATGCCTAAACGACACCGTTT
CCGTAAACGATTTTTAACTTAAAGAAATTTTAGAATTATTTATTTAAAACATCACCGTTTGACTT
AAAGTAAATTAAGTATTAATGACGTTTTTACATAAAACACCACAAAAAATGCAATTTCAGACTAA
CAAAACAGCGCCGTTTCCCTTTACAACTTTAATATTTAGTGGCATTTTTAGGAAAACGCCGAAAA
TGTGGAATCAATAGTGGCGTTTTTAGAGAAATACCGCAAAAGGGTATTAGAATAATGGCTAAACG
ACGCCGTTTCTCCGGACGATTTTTAACTTAGAAAAATTTTAGAAATC
Found at i:3954926 original size:60 final size:60
Alignment explanation
Indices: 3954855--3954978 Score: 214
Period size: 60 Copynumber: 2.1 Consensus size: 60
3954845 GTGAATTTTG
* * *
3954855 TGAATTTTGGTTACAGTGTGTGAGGGATTTAGGTATAATTTGTTTATTTAGCAGTTGCCC
1 TGAATTTTGGTTACAATGTATGAGGGATTTAGGTATAAATTGTTTATTTAGCAGTTGCCC
3954915 TGAATTTTGGTTACAATGTATGAGGGATTTAGGTATAAATTGTTTATTTAGCAGTTGCCC
1 TGAATTTTGGTTACAATGTATGAGGGATTTAGGTATAAATTGTTTATTTAGCAGTTGCCC
3954975 -GAAT
1 TGAAT
3954979 GAATTTTGTG
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
59 4 0.07
60 57 0.93
ACGTcount: A:0.25, C:0.08, G:0.25, T:0.42
Consensus pattern (60 bp):
TGAATTTTGGTTACAATGTATGAGGGATTTAGGTATAAATTGTTTATTTAGCAGTTGCCC
Found at i:3955043 original size:13 final size:13
Alignment explanation
Indices: 3955019--3955059 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
3955009 ATTTTGTGAG
*
3955019 ATTTTCTAAATGA
1 ATTTTCTTAATGA
3955032 ATTTT-TTGAATGA
1 ATTTTCTT-AATGA
3955045 ATTTTCTTAATGA
1 ATTTTCTTAATGA
3955058 AT
1 AT
3955060 ATAGTAAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 1 0.04
13 22 0.88
14 2 0.08
ACGTcount: A:0.34, C:0.05, G:0.10, T:0.51
Consensus pattern (13 bp):
ATTTTCTTAATGA
Found at i:3955409 original size:23 final size:23
Alignment explanation
Indices: 3955357--3955409 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
3955347 TCTTCATTTT
* *
3955357 TTTGCT-TGCATTTCTTTGCTTA
1 TTTGCTCTACATTTCTTCGCTTA
3955379 TCTT-CTCTACATTTCTTCGCTTA
1 T-TTGCTCTACATTTCTTCGCTTA
3955402 TTTGCTCT
1 TTTGCTCT
3955410 TTGTTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 5 0.19
23 21 0.81
ACGTcount: A:0.09, C:0.25, G:0.09, T:0.57
Consensus pattern (23 bp):
TTTGCTCTACATTTCTTCGCTTA
Found at i:3956598 original size:50 final size:47
Alignment explanation
Indices: 3956479--3956598 Score: 122
Period size: 51 Copynumber: 2.4 Consensus size: 47
3956469 CAATATTTAT
3956479 TATAT-TTTTTAATATA-TTTTTAAAATTTAATTTAACTTATTACTAA
1 TATATATTTTTAATATATTTTTTAAAATTTAATTTAACTTATTAC-AA
*
3956525 TATATATTGTTAATATATAATTTTTTAAAATTTATATCTT-ACATTACTTA-AA
1 TATATATT-TTTA-ATAT-ATTTTTTAAAATTTA-AT-TTAAC-TTA-TTACAA
3956577 TATATATTTTTAAGTATATTTT
1 TATATATTTTTAA-TATATTTT
3956599 ACATTACTTA
Statistics
Matches: 62, Mismatches: 2, Indels: 16
0.77 0.03 0.20
Matches are distributed among these distances:
46 5 0.08
47 2 0.03
48 3 0.05
49 4 0.06
50 7 0.11
51 19 0.31
52 14 0.23
53 5 0.08
54 3 0.05
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (47 bp):
TATATATTTTTAATATATTTTTTAAAATTTAATTTAACTTATTACAA
Found at i:3956649 original size:13 final size:13
Alignment explanation
Indices: 3956633--3956718 Score: 57
Period size: 13 Copynumber: 6.5 Consensus size: 13
3956623 TTACTAAAAT
* *
3956633 TTACTTTAATATA
1 TTACTTAAATAAA
3956646 TTACTTAAATAAA
1 TTACTTAAATAAA
*
3956659 TTACTTAAATACA
1 TTACTTAAATAAA
* *
3956672 TCACTTACTAA-AAT
1 TTACTTA--AATAAA
** **
3956686 TTGGTTAAATTTA
1 TTACTTAAATAAA
*
3956699 TTACTTAAATACA
1 TTACTTAAATAAA
3956712 TTACTTA
1 TTACTTA
3956719 CTAAAATTTA
Statistics
Matches: 54, Mismatches: 16, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
12 2 0.04
13 45 0.83
14 5 0.09
15 2 0.04
ACGTcount: A:0.42, C:0.12, G:0.02, T:0.44
Consensus pattern (13 bp):
TTACTTAAATAAA
Found at i:3956751 original size:9 final size:9
Alignment explanation
Indices: 3956737--3957085 Score: 179
Period size: 9 Copynumber: 40.4 Consensus size: 9
3956727 TAAGTATATA
*
3956737 TTACATTAC
1 TTACATAAC
3956746 TTACATAAC
1 TTACATAAC
3956755 TTACATAA-
1 TTACATAAC
3956763 -TACATAAC
1 TTACATAAC
*
3956771 TCT-GATAAC
1 T-TACATAAC
*
3956780 TAACAT-A-
1 TTACATAAC
*
3956787 -TACACAAC
1 TTACATAAC
3956795 TTACATAA-
1 TTACATAAC
* *
3956803 -GACATTAC
1 TTACATAAC
3956811 TTACATAAC
1 TTACATAAC
*
3956820 TTACATTA-
1 TTACATAAC
3956828 -TACATAAC
1 TTACATAAC
*
3956836 TTACATAAT
1 TTACATAAC
*** *
3956845 TTTTTTAATAT
1 TTACAT-A-AC
3956856 TATACATAAC
1 T-TACATAAC
* *
3956866 ATACATTA-
1 TTACATAAC
3956874 -TACATAAC
1 TTACATAAC
3956882 TTACATAAC
1 TTACATAAC
3956891 -T-CATAAC
1 TTACATAAC
3956898 TTACATAAC
1 TTACATAAC
*
3956907 TTA-ATTAC
1 TTACATAAC
**
3956915 ATTATGCA-CCC
1 -TTA--CATAAC
3956926 TTTACATAAC
1 -TTACATAAC
3956936 TTACATAAC
1 TTACATAAC
* *
3956945 TTACACAGC
1 TTACATAAC
*
3956954 TTACAT-TC
1 TTACATAAC
*
3956962 -TACACAAC
1 TTACATAAC
3956970 TTACATAAC
1 TTACATAAC
* *
3956979 ATACATTAC
1 TTACATAAC
**
3956988 TTTGATAAC
1 TTACATAAC
3956997 TTACATAAC
1 TTACATAAC
3957006 TTACATAA-
1 TTACATAAC
*
3957014 -TACACAAC
1 TTACATAAC
*
3957022 TTACATAGC
1 TTACATAAC
*
3957031 TTACTTAA-
1 TTACATAAC
3957039 -TACATAAC
1 TTACATAAC
3957047 TTACATAAC
1 TTACATAAC
3957056 TT--ATACAC
1 TTACATA-AC
*
3957064 GTACATAAC
1 TTACATAAC
*
3957073 TTACATAAT
1 TTACATAAC
3957082 TTAC
1 TTAC
3957086 TTAATACATA
Statistics
Matches: 254, Mismatches: 54, Indels: 64
0.68 0.15 0.17
Matches are distributed among these distances:
6 3 0.01
7 50 0.20
8 12 0.05
9 171 0.67
10 7 0.03
11 8 0.03
12 3 0.01
ACGTcount: A:0.42, C:0.21, G:0.02, T:0.35
Consensus pattern (9 bp):
TTACATAAC
Found at i:3956767 original size:25 final size:24
Alignment explanation
Indices: 3956738--3956802 Score: 69
Period size: 25 Copynumber: 2.7 Consensus size: 24
3956728 AAGTATATAT
* *
3956738 TACATTACTTACATAACTTACATAA
1 TACATAACTTACATAACTAACAT-A
*
3956763 TACATAACTCT-GATAACTAACATA
1 TACATAACT-TACATAACTAACATA
*
3956787 TACACAACTTACATAA
1 TACATAACTTACATAA
3956803 GACATTACTT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
23 1 0.03
24 13 0.39
25 18 0.55
26 1 0.03
ACGTcount: A:0.46, C:0.22, G:0.02, T:0.31
Consensus pattern (24 bp):
TACATAACTTACATAACTAACATA
Found at i:3956820 original size:25 final size:25
Alignment explanation
Indices: 3956787--3956843 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
3956777 AACTAACATA
* *
3956787 TACACAACTTACATAAGACATTACT
1 TACATAACTTACATAAGACATAACT
* *
3956812 TACATAACTTACATTATACATAACT
1 TACATAACTTACATAAGACATAACT
3956837 TACATAA
1 TACATAA
3956844 TTTTTTTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.46, C:0.21, G:0.02, T:0.32
Consensus pattern (25 bp):
TACATAACTTACATAAGACATAACT
Found at i:3956831 original size:16 final size:16
Alignment explanation
Indices: 3956812--3956919 Score: 77
Period size: 16 Copynumber: 7.1 Consensus size: 16
3956802 AGACATTACT
3956812 TACATAACTTACATTA
1 TACATAACTTACATTA
3956828 TACATAACTTACA-TA
1 TACATAACTTACATTA
* *** *
3956843 -A-TTTTTTTAATATTA
1 TACATAACTT-ACATTA
*
3956858 TACATAACATACATTA
1 TACATAACTTACATTA
*
3956874 TACATAACTTACATAA
1 TACATAACTTACATTA
3956890 CT-CATAACTTACA-TA
1 -TACATAACTTACATTA
*
3956905 -ACTTAA-TTACATTA
1 TACATAACTTACATTA
3956919 T
1 T
3956920 GCACCCTTTA
Statistics
Matches: 69, Mismatches: 15, Indels: 17
0.68 0.15 0.17
Matches are distributed among these distances:
13 8 0.12
14 9 0.13
15 5 0.07
16 44 0.64
17 3 0.04
ACGTcount: A:0.44, C:0.17, G:0.00, T:0.40
Consensus pattern (16 bp):
TACATAACTTACATTA
Found at i:3956965 original size:25 final size:26
Alignment explanation
Indices: 3956937--3957096 Score: 141
Period size: 25 Copynumber: 6.3 Consensus size: 26
3956927 TTACATAACT
* * *
3956937 TACATAACTTACACAGCTTACATT-C
1 TACATAACTTACATAACTTACATTAA
* * *
3956962 TACACAACTTACATAACATACATTACT
1 TACATAACTTACATAACTTACATTA-A
**
3956989 TTGATAACTTACATAACTTACA-TAA
1 TACATAACTTACATAACTTACATTAA
* *
3957014 TACACAACTTACATAGCTTAC-TTAA
1 TACATAACTTACATAACTTACATTAA
* * *
3957039 TACATAACTTACATAACTTATA-CACG
1 TACATAACTTACATAACTTACATTA-A
*
3957065 TACATAACTTACATAATTTAC-TTAA
1 TACATAACTTACATAACTTACATTAA
3957090 TACATAA
1 TACATAA
3957097 ATATATATCA
Statistics
Matches: 106, Mismatches: 23, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
25 66 0.62
26 22 0.21
27 18 0.17
ACGTcount: A:0.42, C:0.22, G:0.03, T:0.33
Consensus pattern (26 bp):
TACATAACTTACATAACTTACATTAA
Found at i:3957034 original size:34 final size:33
Alignment explanation
Indices: 3956927--3957081 Score: 109
Period size: 34 Copynumber: 4.5 Consensus size: 33
3956917 TATGCACCCT
* *
3956927 TTACATAACTTACATAACTTACACAGCTTACATTC
1 TTACATAACTTACATAA--TACACAACTTACATAC
* ** **
3956962 -TACACAACTTACATAACATACATTACTTTGATAAC
1 TTACATAACTTACAT-A-ATACACAACTTACAT-AC
3956997 TTACATAACTTACATAATACACAACTTACATAGC
1 TTACATAACTTACATAATACACAACTTACATA-C
* * * *
3957031 TTACTTAA--TACATAACTTACATAACTTATACAC
1 TTACATAACTTACATAA--TACACAACTTACATAC
*
3957064 GTACATAACTTACATAAT
1 TTACATAACTTACATAAT
3957082 TTACTTAATA
Statistics
Matches: 93, Mismatches: 18, Indels: 20
0.71 0.14 0.15
Matches are distributed among these distances:
32 7 0.08
33 9 0.10
34 53 0.57
35 10 0.11
36 14 0.15
ACGTcount: A:0.42, C:0.23, G:0.03, T:0.33
Consensus pattern (33 bp):
TTACATAACTTACATAATACACAACTTACATAC
Found at i:3963043 original size:114 final size:113
Alignment explanation
Indices: 3962909--3963971 Score: 1606
Period size: 114 Copynumber: 9.3 Consensus size: 113
3962899 TGCAAGCGCT
*
3962909 GCAAAATATCTTAACCAAAACGCAGCGTTAGGTCTTGAGGTATATTAGAATTAGTGGCGCTTATG
1 GCAAAATATCTTAA-CAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTATG
* * * *
3962974 CAAAAATGCCGCTAAAGCACAGTATTAGGGGCACATTGTAAAAAATGCC
65 CAAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTATAAAAAATGCC
* *
3963023 GCAAAATATCTTAACAAAAACGCAACATTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTATG
1 GCAAAATATCTTAAC-AAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTATG
* * * *
3963088 CAAAAATGCCGCTAAAGCACAGTATTAGGGGCACATTGTAAAAAATGCC
65 CAAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTATAAAAAATGCC
* *
3963137 GCAAAATATCTTAACAAAAACGCAACATTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTATG
1 GCAAAATATCTTAAC-AAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTATG
* **
3963202 CAAAAACGCCGCTAAAGCACAGTATTAGCGGCGTATTATAAAAAGCGCC
65 CAAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTATAAAAAATGCC
3963251 GCAAAATATCTTAATCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTATG
1 GCAAAATATCTTAA-CAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTATG
* **
3963316 CAAAAACGCCGCTAAAGCACAGTATTAGCGGCGTATTATAAAAAGCGCC
65 CAAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTATAAAAAATGCC
3963365 GCAAAATATCTTAATCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTATG
1 GCAAAATATCTTAA-CAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTATG
* **
3963430 CAAAAACGCCGCTAAAGCACAGTATTAGCGGCGTATTATAAAAAGCGCC
65 CAAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTATAAAAAATGCC
3963479 GCAAAATATCTTAATCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTATG
1 GCAAAATATCTTAA-CAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTATG
* **
3963544 CAAAAACGCCGCTAAAGCACAGTATTAGCGGCGTATTATAAAAAGCGCC
65 CAAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTATAAAAAATGCC
3963593 GCAAAATATCTTAATCAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTATG
1 GCAAAATATCTTAA-CAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTATG
* * * *
3963658 GAAAAACACCGCTAAAGCACAGTATTAGCAGCGCATTATACAAAATGCC
65 CAAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTATAAAAAATGCC
* * *
3963707 GTAAAATATCTTAACCAAAACACAGTGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTATG
1 GCAAAATATCTTAA-CAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTATG
* * * *
3963772 GAAAAACACCGCTAAAGCACAGTATTAGCAGCGCATTATACAAAATGCC
65 CAAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTATAAAAAATGCC
* * *
3963821 GTAAAATATCTTAACCAAAACACAGTGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTATG
1 GCAAAATATCTTAA-CAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTATG
* * * * *
3963886 -AAAAACGCCGCTAAATCACAGTATTAGCGGCGCTTTGTGAAAAATGTC
65 CAAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTATAAAAAATGCC
** *
3963934 GCAAAATATCTTAACCAAAACAAAGTGTTTGGTCTTGA
1 GCAAAATATCTTAA-CAAAACGCAGCGTTTGGTCTTGA
3963972 TTTATAGAGC
Statistics
Matches: 914, Mismatches: 33, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
113 77 0.08
114 836 0.91
115 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.26
Consensus pattern (113 bp):
GCAAAATATCTTAACAAAACGCAGCGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTATGC
AAAAACGCCGCTAAAGCACAGTATTAGCGGCGCATTATAAAAAATGCC
Found at i:3964494 original size:7 final size:7
Alignment explanation
Indices: 3964479--3964548 Score: 63
Period size: 7 Copynumber: 10.0 Consensus size: 7
3964469 TATGATGTAT
3964479 GTTTA-G
1 GTTTAGG
3964485 GTTTAGG
1 GTTTAGG
*
3964492 GTTTAAG
1 GTTTAGG
*
3964499 GTTTGAGA
1 GTTT-AGG
3964507 GTTT-GAG
1 GTTTAG-G
*
3964514 GTTTAAG
1 GTTTAGG
*
3964521 GTTTGGG
1 GTTTAGG
3964528 GTTTAGG
1 GTTTAGG
*
3964535 GTTTGGG
1 GTTTAGG
3964542 GTTTAGG
1 GTTTAGG
3964549 CTGCTTTAGT
Statistics
Matches: 50, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
6 6 0.12
7 39 0.78
8 5 0.10
ACGTcount: A:0.16, C:0.00, G:0.41, T:0.43
Consensus pattern (7 bp):
GTTTAGG
Found at i:3964502 original size:14 final size:14
Alignment explanation
Indices: 3964479--3964548 Score: 79
Period size: 14 Copynumber: 5.0 Consensus size: 14
3964469 TATGATGTAT
3964479 GTTT-AGGTTTAGG
1 GTTTGAGGTTTAGG
* *
3964492 GTTTAAGGTTTGAGA
1 GTTTGAGGTTT-AGG
*
3964507 GTTTGAGGTTTAAG
1 GTTTGAGGTTTAGG
*
3964521 GTTTGGGGTTTAGG
1 GTTTGAGGTTTAGG
*
3964535 GTTTGGGGTTTAGG
1 GTTTGAGGTTTAGG
3964549 CTGCTTTAGT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
13 4 0.08
14 33 0.67
15 12 0.24
ACGTcount: A:0.16, C:0.00, G:0.41, T:0.43
Consensus pattern (14 bp):
GTTTGAGGTTTAGG
Found at i:3964510 original size:22 final size:21
Alignment explanation
Indices: 3964485--3964538 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 21
3964475 GTATGTTTAG
3964485 GTTTAGGGTTTAAGGTTTGAGA
1 GTTTAGGGTTTAAGGTTTG-GA
*
3964507 GTTT-GAGGTTTAAGGTTTGGG
1 GTTTAG-GGTTTAAGGTTTGGA
3964528 GTTTAGGGTTT
1 GTTTAGGGTTT
3964539 GGGGTTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 11 0.38
22 18 0.62
ACGTcount: A:0.17, C:0.00, G:0.39, T:0.44
Consensus pattern (21 bp):
GTTTAGGGTTTAAGGTTTGGA
Found at i:3964990 original size:44 final size:45
Alignment explanation
Indices: 3964939--3965038 Score: 125
Period size: 44 Copynumber: 2.3 Consensus size: 45
3964929 ATGACCATAG
*
3964939 CGGCGTTTGTTGAAAAAAACGCCGCT-AAAGAACATTA-CTTGTAA
1 CGGCGTTTGTTGAAAAAAACGCCGCTAAAAGAACATGAGCTT-TAA
* ** *
3964983 CGGCGTTTG-TGGAAAAGGCGCCGCTAAAAGAACATGAGCTTTAG
1 CGGCGTTTGTTGAAAAAAACGCCGCTAAAAGAACATGAGCTTTAA
3965027 CGGCGTTTGTTG
1 CGGCGTTTGTTG
3965039 GTATGCGTCG
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
43 13 0.27
44 30 0.62
45 5 0.10
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.25
Consensus pattern (45 bp):
CGGCGTTTGTTGAAAAAAACGCCGCTAAAAGAACATGAGCTTTAA
Found at i:3965214 original size:84 final size:85
Alignment explanation
Indices: 3965063--3965245 Score: 235
Period size: 84 Copynumber: 2.2 Consensus size: 85
3965053 AGGTAATGTT
* * * *
3965063 CTTTAGCGGCGTTTGTCATAGAATCGCCGCTAAAGAACATTACCTTTAGCGGCATTTCTGAGAAA
1 CTTTAGCGGCGTTTGTCATAGAAGCGCCACTAAAGAACATGACCTTTAGCGACATTTCTGAGAAA
*
3965128 GCGCTGCTAAAGAACATGAC
66 GCGCTACTAAAGAACATGAC
** * * * **
3965148 CTTTAGCGGCGTTT-TTTTTGAAGCGCCACTAAAGAACATGACCTTTAGCGACGTTTATTTTG-A
1 CTTTAGCGGCGTTTGTCATAGAAGCGCCACTAAAGAACATGACCTTTAGCGACATTT-CTGAGAA
3965211 AGCGCTACTAAAGAACATGAC
65 AGCGCTACTAAAGAACATGAC
3965232 CTTTAGCGGCGTTT
1 CTTTAGCGGCGTTT
3965246 ATTTCTGTAA
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
84 69 0.81
85 16 0.19
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (85 bp):
CTTTAGCGGCGTTTGTCATAGAAGCGCCACTAAAGAACATGACCTTTAGCGACATTTCTGAGAAA
GCGCTACTAAAGAACATGAC
Found at i:3965245 original size:42 final size:42
Alignment explanation
Indices: 3965092--3965249 Score: 219
Period size: 42 Copynumber: 3.8 Consensus size: 42
3965082 AGAATCGCCG
* * * ** *
3965092 CTAAAGAACATTACCTTTAGCGGCATTT-CTGAGAAAGCGCTG
1 CTAAAGAACATGACCTTTAGCGGCGTTTATTTTG-AAGCGCTA
* *
3965134 CTAAAGAACATGACCTTTAGCGGCGTTTTTTTTGAAGCGCCA
1 CTAAAGAACATGACCTTTAGCGGCGTTTATTTTGAAGCGCTA
*
3965176 CTAAAGAACATGACCTTTAGCGACGTTTATTTTGAAGCGCTA
1 CTAAAGAACATGACCTTTAGCGGCGTTTATTTTGAAGCGCTA
3965218 CTAAAGAACATGACCTTTAGCGGCGTTTATTT
1 CTAAAGAACATGACCTTTAGCGGCGTTTATTT
3965250 CTGTAAACGC
Statistics
Matches: 104, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
42 102 0.98
43 2 0.02
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.30
Consensus pattern (42 bp):
CTAAAGAACATGACCTTTAGCGGCGTTTATTTTGAAGCGCTA
Found at i:3968618 original size:3 final size:3
Alignment explanation
Indices: 3968612--3968657 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
3968602 AAGAAGAGCT
3968612 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3968658 GTAACAACTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3975945 original size:29 final size:29
Alignment explanation
Indices: 3975888--3975945 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
3975878 GTGCTGGTGA
* *
3975888 TTACAGTTTTCAAGTATTATGTACCAGTG
1 TTACAGTTTTCAAGCATTATGTACAAGTG
* * *
3975917 TTACAGTTTTCAGGCATTCTGTGCAAGTG
1 TTACAGTTTTCAAGCATTATGTACAAGTG
3975946 ATATATTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.40
Consensus pattern (29 bp):
TTACAGTTTTCAAGCATTATGTACAAGTG
Found at i:3977041 original size:24 final size:25
Alignment explanation
Indices: 3977001--3977055 Score: 62
Period size: 24 Copynumber: 2.2 Consensus size: 25
3976991 GTTAGATGAT
*
3977001 TAAAATAATTAAGAATT-AATTAAA
1 TAAAATAATTAAAAATTAAATTAAA
3977025 TAAAAT-ATTAAAAAATTAGAATTAAA
1 TAAAATAATT-AAAAATTA-AATTAAA
3977051 -AAAAT
1 TAAAAT
3977056 TAGGTTAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 3 0.11
24 12 0.44
25 5 0.19
26 7 0.26
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (25 bp):
TAAAATAATTAAAAATTAAATTAAA
Found at i:3977050 original size:14 final size:14
Alignment explanation
Indices: 3976999--3977076 Score: 50
Period size: 15 Copynumber: 5.3 Consensus size: 14
3976989 GGGTTAGATG
3976999 ATTAAAATAATTAAGA
1 ATTAAAA-AATT-AGA
* * *
3977015 ATTAATTAAATAAAA
1 ATTAA-AAAATTAGA
3977030 TATTAAAAAATTAGA
1 -ATTAAAAAATTAGA
3977045 ATTAAAAAAATTAG-
1 ATT-AAAAAATTAGA
* * *
3977059 GTTAAGAAATTAAA
1 ATTAAAAAATTAGA
3977073 ATTA
1 ATTA
3977077 GGTGTCTGGG
Statistics
Matches: 48, Mismatches: 10, Indels: 10
0.71 0.15 0.15
Matches are distributed among these distances:
13 8 0.17
14 8 0.17
15 18 0.38
16 13 0.27
17 1 0.02
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (14 bp):
ATTAAAAAATTAGA
Found at i:3978543 original size:23 final size:23
Alignment explanation
Indices: 3978510--3978627 Score: 134
Period size: 23 Copynumber: 5.1 Consensus size: 23
3978500 TATGTTGAAA
3978510 GGTA-TATTGGTTGTGTTTGGAG
1 GGTATTATTGGTTGTGTTTGGAG
* *
3978532 GGTATTCTTGGTTGTGTTCGGAG
1 GGTATTATTGGTTGTGTTTGGAG
* *
3978555 GTTATATATATGGTTGTGTTCGGAG
1 GGTAT-TAT-TGGTTGTGTTTGGAG
3978580 GGTGATTA-TGGTTGTGTTTGGAG
1 GGT-ATTATTGGTTGTGTTTGGAG
* *
3978603 GGTA-GATTGGTTGTGTTTGGTG
1 GGTATTATTGGTTGTGTTTGGAG
3978625 GGT
1 GGT
3978628 GATAGCTTTA
Statistics
Matches: 83, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
21 1 0.01
22 22 0.27
23 37 0.45
24 2 0.02
25 19 0.23
26 2 0.02
ACGTcount: A:0.13, C:0.03, G:0.41, T:0.44
Consensus pattern (23 bp):
GGTATTATTGGTTGTGTTTGGAG
Found at i:3978580 original size:48 final size:47
Alignment explanation
Indices: 3978512--3978630 Score: 136
Period size: 48 Copynumber: 2.6 Consensus size: 47
3978502 TGTTGAAAGG
* *
3978512 TATATTGGTTGTGTTTGGAGGGT-ATTCTTGGTTGTGTTCGGAGGTTA
1 TATATTGGTTGTGTTCGGAGGGTGATT-ATGGTTGTGTTCGGAGGTTA
* *
3978559 TATATATGGTTGTGTTCGGAGGGTGATTATGGTTGTGTTTGGAGG--G
1 TATAT-TGGTTGTGTTCGGAGGGTGATTATGGTTGTGTTCGGAGGTTA
* * *
3978605 TAGATTGGTTGTGTTTGGTGGGTGAT
1 TATATTGGTTGTGTTCGGAGGGTGAT
3978631 AGCTTTATGC
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
45 19 0.30
46 4 0.06
47 5 0.08
48 32 0.51
49 3 0.05
ACGTcount: A:0.13, C:0.03, G:0.39, T:0.45
Consensus pattern (47 bp):
TATATTGGTTGTGTTCGGAGGGTGATTATGGTTGTGTTCGGAGGTTA
Found at i:3986958 original size:25 final size:25
Alignment explanation
Indices: 3986883--3986975 Score: 100
Period size: 25 Copynumber: 3.8 Consensus size: 25
3986873 TCATTAAGGA
*
3986883 TTACCTATTCTCAGCTCGTATGAGC
1 TTACCGATTCTCAGCTCGTATGAGC
* * *
3986908 TTACCGATT-GCAACTCGTAAGAGC
1 TTACCGATTCTCAGCTCGTATGAGC
* *
3986932 TTATCGATTCTCAGCTCATATGAGC
1 TTACCGATTCTCAGCTCGTATGAGC
*
3986957 TTACC-ATTTTACAGCTCGT
1 TTACCGATTCT-CAGCTCGT
3986976 GAGAGCATAC
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
24 24 0.44
25 30 0.56
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (25 bp):
TTACCGATTCTCAGCTCGTATGAGC
Found at i:3991222 original size:12 final size:12
Alignment explanation
Indices: 3991201--3991231 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
3991191 CCACACGCCC
3991201 GTGTGCCAAACT
1 GTGTGCCAAACT
*
3991213 GTGTGTCAAACT
1 GTGTGCCAAACT
3991225 GTGTGCC
1 GTGTGCC
3991232 CTTTCGAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.19, C:0.23, G:0.29, T:0.29
Consensus pattern (12 bp):
GTGTGCCAAACT
Found at i:3992275 original size:37 final size:39
Alignment explanation
Indices: 3992184--3992281 Score: 110
Period size: 40 Copynumber: 2.5 Consensus size: 39
3992174 AACACACCAG
* **
3992184 TTTGGCACCCAGTGCCTCATCGGATAATTCGAAATAGTAA
1 TTTGGCACCCAGTGTCTCATCGGATAAACCG-AATAGTAA
* * * *
3992224 ATTGACACCAAGTGTCTCATCGGTTAAACCG-A-AGTAA
1 TTTGGCACCCAGTGTCTCATCGGATAAACCGAATAGTAA
3992261 TTTGGCACCCAGTGTCTCATC
1 TTTGGCACCCAGTGTCTCATC
3992282 AACTCGAAGT
Statistics
Matches: 48, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
37 23 0.48
38 1 0.02
40 24 0.50
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (39 bp):
TTTGGCACCCAGTGTCTCATCGGATAAACCGAATAGTAA
Found at i:3993142 original size:4 final size:4
Alignment explanation
Indices: 3993133--3993208 Score: 70
Period size: 4 Copynumber: 19.0 Consensus size: 4
3993123 TGTGTTTCTC
*
3993133 CTTT CTTT CTTT CTTT CTTT CCCTT -TTT C-TT -TTT CTTT CTTT C-TT
1 CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CTTT CTTT
*
3993178 CTTT CTGTTT CGTTT CTAT CTTT CTTT CTTT
1 CTTT C--TTT C-TTT CTTT CTTT CTTT CTTT
3993209 ATTTTTTATT
Statistics
Matches: 61, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
3 9 0.15
4 40 0.66
5 8 0.13
6 4 0.07
ACGTcount: A:0.01, C:0.25, G:0.03, T:0.71
Consensus pattern (4 bp):
CTTT
Found at i:3993158 original size:22 final size:23
Alignment explanation
Indices: 3993127--3993181 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 23
3993117 TAGCCTTGTG
3993127 TTTCTCCTTTCTT-TCTTTCTTTC
1 TTTCTCCTTT-TTCTCTTTCTTTC
*
3993150 TTTC-CCTTTTTCTTTTTCTTTC
1 TTTCTCCTTTTTCTCTTTCTTTC
*
3993172 TTTCTTCTTT
1 TTTCTCCTTT
3993182 CTGTTTCGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 2 0.07
22 18 0.64
23 8 0.29
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (23 bp):
TTTCTCCTTTTTCTCTTTCTTTC
Found at i:3993193 original size:26 final size:29
Alignment explanation
Indices: 3993125--3993208 Score: 93
Period size: 27 Copynumber: 2.9 Consensus size: 29
3993115 CCTAGCCTTG
*
3993125 TGTTTCTCCTTTCTTTCTTTCTTTCTTTCCC
1 TGTTTCT-GTTTCTTTCTTTCTTTCTTT-CC
* *
3993156 TTTTTCTTTTTCTTTCTTTC-TTCTTT-C
1 TGTTTCTGTTTCTTTCTTTCTTTCTTTCC
*
3993183 TGTTTC-GTTTCTATCTTTCTTTCTTT
1 TGTTTCTGTTTCTTTCTTTCTTTCTTT
3993209 ATTTTTTATT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
26 11 0.23
27 12 0.26
29 6 0.13
30 12 0.26
31 6 0.13
ACGTcount: A:0.01, C:0.25, G:0.04, T:0.70
Consensus pattern (29 bp):
TGTTTCTGTTTCTTTCTTTCTTTCTTTCC
Found at i:3993202 original size:34 final size:34
Alignment explanation
Indices: 3993133--3993208 Score: 91
Period size: 34 Copynumber: 2.2 Consensus size: 34
3993123 TGTGTTTCTC
* * *
3993133 CTTTCTTTCTTTCTTTCTTTCCCTTTTTCTTTTT
1 CTTTCTTTCTTTCTTTCTTTCCCTTTCTATCTTT
* *
3993167 CTTTCTTTC-TTCTTTCTGTTTCGTTTCTATCTTT
1 CTTTCTTTCTTTCTTTCT-TTCCCTTTCTATCTTT
3993201 CTTTCTTT
1 CTTTCTTT
3993209 ATTTTTTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
33 8 0.22
34 28 0.78
ACGTcount: A:0.01, C:0.25, G:0.03, T:0.71
Consensus pattern (34 bp):
CTTTCTTTCTTTCTTTCTTTCCCTTTCTATCTTT
Found at i:3995236 original size:21 final size:21
Alignment explanation
Indices: 3995211--3995264 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 21
3995201 ATGAACATAC
* *
3995211 ATATATTTATATCTTTTTTGT
1 ATATATTTATATCATTTTTCT
*
3995232 ATATATCTTAAAATCATTTTTCT
1 ATATAT-TT-ATATCATTTTTCT
3995255 ATAT-TTTATA
1 ATATATTTATA
3995265 AGTTGTATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
20 2 0.07
21 8 0.30
22 3 0.11
23 14 0.52
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.59
Consensus pattern (21 bp):
ATATATTTATATCATTTTTCT
Found at i:4001921 original size:34 final size:34
Alignment explanation
Indices: 4001878--4001945 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
4001868 ACAATTCCAG
* *
4001878 GGAAAGAGAGCTTGGTAAATGCTTCAGGAGAGGA
1 GGAAAGAGAGCTTGGTAAACGCTTCAAGAGAGGA
4001912 GGAAAGAGAGCTTGGTAAACGCTTCAAGAGAGGA
1 GGAAAGAGAGCTTGGTAAACGCTTCAAGAGAGGA
4001946 CGAAGGATTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.37, C:0.10, G:0.37, T:0.16
Consensus pattern (34 bp):
GGAAAGAGAGCTTGGTAAACGCTTCAAGAGAGGA
Found at i:4006593 original size:45 final size:46
Alignment explanation
Indices: 4006542--4006641 Score: 152
Period size: 45 Copynumber: 2.2 Consensus size: 46
4006532 ACAAAAATAT
4006542 CAAGAAAATT-GTAGGGAAAATGACTGAAACCTACAAAGACTGGCA
1 CAAGAAAATTAGTAGGGAAAATGACTGAAACCTACAAAGACTGGCA
* *
4006587 CAAG-AAATTNGTAGGGAAAATGACTGAAACCTACAAAGATTGGCA
1 CAAGAAAATTAGTAGGGAAAATGACTGAAACCTACAAAGACTGGCA
*
4006632 CGA-AAAATTA
1 CAAGAAAATTA
4006642 CCTTTTGCCC
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
44 5 0.10
45 45 0.90
ACGTcount: A:0.47, C:0.14, G:0.21, T:0.17
Consensus pattern (46 bp):
CAAGAAAATTAGTAGGGAAAATGACTGAAACCTACAAAGACTGGCA
Found at i:4008434 original size:45 final size:45
Alignment explanation
Indices: 4008367--4008460 Score: 116
Period size: 45 Copynumber: 2.1 Consensus size: 45
4008357 CAGATTAATG
* * * *
4008367 AAGACATCAGATCTTACTTTCCTGTATTGACTGCGAAGTAGATCA
1 AAGACAACAGATCTTACCTTCCTGCATTGACAGCGAAGTAGATCA
* * * *
4008412 AAGACAACAGATCTTGCCTTCCTGCCTTGACAGTGAAGTAGATCG
1 AAGACAACAGATCTTACCTTCCTGCATTGACAGCGAAGTAGATCA
4008457 AAGA
1 AAGA
4008461 TACAAGCTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (45 bp):
AAGACAACAGATCTTACCTTCCTGCATTGACAGCGAAGTAGATCA
Found at i:4008586 original size:87 final size:88
Alignment explanation
Indices: 4008422--4008586 Score: 217
Period size: 87 Copynumber: 1.9 Consensus size: 88
4008412 AAGACAACAG
* ** * * * *
4008422 ATCTTGCCTTCCTGCCTTGACAGTGAAGTAGATCGAAGATACAAGCTTTGTCTCCATCGGTTGCG
1 ATCTTGCCTTCCTGCCTTAACAACGAAGCAGATCGAAGATACAAGCCTTGCCTCCATCGGTTGCA
*
4008487 GTGGAGCTGATTGAAGATAGCAT
66 GTGGAGCAGATTGAAGATAGCAT
* *
4008510 ATCTTGCCTTCCTGCGTTAACAACGAAGCAGATCGAA-A-ACAAAGCCTTGCCTCCATTGGTTGC
1 ATCTTGCCTTCCTGCCTTAACAACGAAGCAGATCGAAGATAC-AAGCCTTGCCTCCATCGGTTGC
4008573 AGTGGAGCAGATTG
65 AGTGGAGCAGATTG
4008587 TGTCAGATCT
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
86 2 0.03
87 32 0.48
88 32 0.48
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.27
Consensus pattern (88 bp):
ATCTTGCCTTCCTGCCTTAACAACGAAGCAGATCGAAGATACAAGCCTTGCCTCCATCGGTTGCA
GTGGAGCAGATTGAAGATAGCAT
Found at i:4008647 original size:44 final size:42
Alignment explanation
Indices: 4008572--4009343 Score: 323
Period size: 44 Copynumber: 18.1 Consensus size: 42
4008562 CCATTGGTTG
*
4008572 CAGTGGAGCAGATTG-TGTCAG-ATCTTATCTCCCTGAGATTA
1 CAGTGGAGCAGATTGAAG-CAGAATCTTATCTCCCTGAGATTA
*
4008613 CAGCGGAGCAGATTGAAGCTAGTAATCTTATCTCCCTGAGATTA
1 CAGTGGAGCAGATTGAAGC-AG-AATCTTATCTCCCTGAGATTA
* ** * * * *
4008657 CGGTGGAGTGGATTAAAATGAAGGATCTTATCTCTCTGA-AGTTA
1 CAGTGGAGCAGATT-GAA-GCAGAATCTTATCTCCCTGAGA-TTA
* * * * * * *
4008701 CAGTAGAGTAGATCGCACCAG-GTCTTATTTCCCTGAGATTA
1 CAGTGGAGCAGATTGAAGCAGAATCTTATCTCCCTGAGATTA
* * *
4008742 CAGTGGAACAGACTGAAGAATTTCAG-ATCTTATCTCCCTGATATTA
1 CAGTGGAGCAGATTGAAG-----CAGAATCTTATCTCCCTGAGATTA
* * *
4008788 CAGCGGAGCAGATTGAAGCTAGTAATCATATCTCCTTGAGATTA
1 CAGTGGAGCAGATTGAAGC-AG-AATCTTATCTCCCTGAGATTA
* * * * *
4008832 CAGTGGAACGGATT-AA-AAG-ATCTTATCTCTCT-AAAGTTA
1 CAGTGGAGCAGATTGAAGCAGAATCTTATCTCCCTGAGA-TTA
* ** * * * * *
4008871 CAGTAGAGTGGATCGCACCAG-GTCTTATTTCCCTGAGATTA
1 CAGTGGAGCAGATTGAAGCAGAATCTTATCTCCCTGAGATTA
* ** * *
4008912 TAGTGGAATAGACTGAAGAATTTCAG-ATCTTATCTCCCTAAGATTA
1 CAGTGGAGCAGATTGAAG-----CAGAATCTTATCTCCCTGAGATTA
* * * *
4008958 CAGCGCAGCAGATTGAAGCTAGTAATCCTATCTCCTTGAGATTA
1 CAGTGGAGCAGATTGAAGC-AG-AATCTTATCTCCCTGAGATTA
* * *
4009002 CAGTGGAGCGGATT-AA--AGGATCTTATCTCTCTGA-AGTTA
1 CAGTGGAGCAGATTGAAGCAGAATCTTATCTCCCTGAGA-TTA
* ** * * * *
4009041 CAGTAGAGTGGATCGTATCAG-GTCTTATCTCCCTGAGATTA
1 CAGTGGAGCAGATTGAAGCAGAATCTTATCTCCCTGAGATTA
**
4009082 CAGTGGAGCAGACCGAAGAATTACAG-ATCTTATCTCCCTGAGATTA
1 CAGTGGAGCAGATTGAAG-----CAGAATCTTATCTCCCTGAGATTA
* * *
4009128 CAGCGGAGCAGA-TCAGAGACAGTAATCCTATCTCCCTGAGATTA
1 CAGTGGAGCAGATTGA-AG-CAG-AATCTTATCTCCCTGAGATTA
** * ** * *
4009172 CAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTGA-AGTTA
1 CAGTGGAGCAGATT-GAA-GCAGAATCTTATCTCCCTGAGA-TTA
* * * * * *
4009216 CAGTAGAGAAGATCGTATCAG-GTCTTATCTCCCTGAGATTA
1 CAGTGGAGCAGATTGAAGCAGAATCTTATCTCCCTGAGATTA
* ** * * *
4009257 CAGCGGAGCAGATCAAAGACAGTAATCCTGTCTCCTTGAGATTA
1 CAGTGGAGCAGATTGAAG-CAG-AATCTTATCTCCCTGAGATTA
* * *
4009301 CAGTGGAGCGGATT-AA--AGGATCTTATCTCTCTGA-AGTTA
1 CAGTGGAGCAGATTGAAGCAGAATCTTATCTCCCTGAGA-TTA
4009340 CAGT
1 CAGT
4009344 AGAGTGAATC
Statistics
Matches: 545, Mismatches: 136, Indels: 102
0.70 0.17 0.13
Matches are distributed among these distances:
38 4 0.01
39 67 0.12
40 6 0.01
41 126 0.23
42 25 0.05
43 10 0.02
44 194 0.36
45 9 0.02
46 104 0.19
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (42 bp):
CAGTGGAGCAGATTGAAGCAGAATCTTATCTCCCTGAGATTA
Found at i:4008890 original size:170 final size:172
Alignment explanation
Indices: 4008589--4009268 Score: 985
Period size: 170 Copynumber: 3.9 Consensus size: 172
4008579 GCAGATTGTG
*
4008589 TCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCTTATCTCCCTGAGA
1 TCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
* *
4008654 TTACGGTGGAGTGGATTAAAATGAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAC
66 TTACAGTGGAGCGGATT-AAA--AAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAC
*
4008719 CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACTGAAGAATT
128 CAGGTCTTATCTCCCTGAGATTACAGTGGAACAGACTGAAGAATT
* * *
4008764 TCAGATCTTATCTCCCTGATATTACAGCGGAGCAGATTGAAGCTAGTAATCATATCTCCTTGAGA
1 TCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
* * *
4008829 TTACAGTGGAACGGATT-AAAA-GATCTTATCTCTCTAAAGTTACAGTAGAGTGGATCGCACCAG
66 TTACAGTGGAGCGGATTAAAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCACCAG
* * *
4008892 GTCTTATTTCCCTGAGATTATAGTGGAATAGACTGAAGAATT
131 GTCTTATCTCCCTGAGATTACAGTGGAACAGACTGAAGAATT
* * *
4008934 TCAGATCTTATCTCCCTAAGATTACAGCGCAGCAGATTGAAGCTAGTAATCCTATCTCCTTGAGA
1 TCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
* * *
4008999 TTACAGTGGAGCGGATT--AAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTGGATCGTATCAG
66 TTACAGTGGAGCGGATTAAAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCACCAG
* *
4009062 GTCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATT
131 GTCTTATCTCCCTGAGATTACAGTGGAACAGACTGAAGAATT
* *
4009104 ACAGATCTTATCTCCCTGAGATTACAGCGGAGCAGA-TCAGAGAC-AGTAATCCTATCTCCCTGA
1 TCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGA-AG-CTAGTAATCCTATCTCCCTGA
* * *
4009167 GATTACAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCGT
64 GATTACAGTGGAGCGGATT--AA-AAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGC
* * *
4009232 ATCAGGTCTTATCTCCCTGAGATTACAGCGGAGCAGA
126 ACCAGGTCTTATCTCCCTGAGATTACAGTGGAACAGA
4009269 TCAAAGACAG
Statistics
Matches: 465, Mismatches: 32, Indels: 16
0.91 0.06 0.03
Matches are distributed among these distances:
169 5 0.01
170 304 0.65
171 3 0.01
173 2 0.00
175 151 0.32
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (172 bp):
TCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
TTACAGTGGAGCGGATTAAAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCACCAG
GTCTTATCTCCCTGAGATTACAGTGGAACAGACTGAAGAATT
Found at i:4009258 original size:129 final size:124
Alignment explanation
Indices: 4009109--4009416 Score: 402
Period size: 124 Copynumber: 2.4 Consensus size: 124
4009099 GAATTACAGA
*
4009109 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAGAGACAGTAATCCTATCTCCCTGAGATTACA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACAGTAATCCTATCTCCCTGAGATTACA
*
4009174 GTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGA-AGATCGTATCAGG
66 GTGGAGCGGA-T----TAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAGA-ATCGTATCAGG
* *
4009238 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACAGTAATCCTGTCTCCTTGAGATTACA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACAGTAATCCTATCTCCCTGAGATTACA
*
4009303 GTGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTGAATCGTATCAGG
66 GTGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAGAATCGTATCAGG
* * * * * * * * ** * *
4009362 TTTTACCTTCCTGTGGTTACAGTGGAGTACATTGAAGTCAGTAATTCTATCTCCC
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACAGTAATCCTATCTCCC
4009417 CGACGTTGCG
Statistics
Matches: 159, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
124 86 0.54
125 1 0.01
128 1 0.01
129 71 0.45
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (124 bp):
TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACAGTAATCCTATCTCCCTGAGATTACA
GTGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAGAATCGTATCAGG
Found at i:4011414 original size:21 final size:21
Alignment explanation
Indices: 4011389--4011442 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 21
4011379 ATGAACATAC
* *
4011389 ATATATTTATATCTTTTTTGT
1 ATATATTTATATCATTTTTCT
*
4011410 ATATATCTTAAAATCATTTTTCT
1 ATATAT-TT-ATATCATTTTTCT
4011433 ATAT-TTTATA
1 ATATATTTATA
4011443 AGTTGTATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
20 2 0.07
21 8 0.30
22 3 0.11
23 14 0.52
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.59
Consensus pattern (21 bp):
ATATATTTATATCATTTTTCT
Found at i:4011606 original size:11 final size:11
Alignment explanation
Indices: 4011587--4011625 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
4011577 TTTTTCCTTT
4011587 TTTTA-ATATA
1 TTTTATATATA
*
4011597 CTTTATATATA
1 TTTTATATATA
*
4011608 TTTTTTATATA
1 TTTTATATATA
4011619 TTTTATA
1 TTTTATA
4011626 ATTTATGCAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
10 4 0.17
11 20 0.83
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (11 bp):
TTTTATATATA
Done.