Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold121
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1096690
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.30
Warning! 96926 characters in sequence are not A, C, G, or T
File 4 of 3
Found at i:810522 original size:38 final size:39
Alignment explanation
Indices: 810480--810576 Score: 101
Period size: 40 Copynumber: 2.5 Consensus size: 39
810470 CTGTCAGTGT
* *
810480 AACTGCTTTAAGTTTCTATGCTA-AAGAAG-TGCTAATGA
1 AACTGCTTTAAGTTTCTATGCTATAA-AAGATGCCAATAA
* * *
810518 AACTGCTATAAGTTTGTTTTGCTATAAAAGATGCCAATAA
1 AACTGCTTTAAGTTT-CTATGCTATAAAAGATGCCAATAA
810558 AACTGCTGTT-AGTTTCTAT
1 AACTGCT-TTAAGTTTCTAT
810577 TTAGAGTCAC
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
38 14 0.30
39 11 0.23
40 21 0.45
41 1 0.02
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.37
Consensus pattern (39 bp):
AACTGCTTTAAGTTTCTATGCTATAAAAGATGCCAATAA
Found at i:815906 original size:8 final size:8
Alignment explanation
Indices: 815893--815932 Score: 53
Period size: 8 Copynumber: 4.8 Consensus size: 8
815883 CGATAAAGTA
815893 AGAGAGAC
1 AGAGAGAC
815901 AGAGAGAC
1 AGAGAGAC
*
815909 AGACAGACAC
1 AG--AGAGAC
815919 AGAGAGAC
1 AGAGAGAC
815927 AGAGAG
1 AGAGAG
815933 CATGCATGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 21 0.75
10 7 0.25
ACGTcount: A:0.50, C:0.15, G:0.35, T:0.00
Consensus pattern (8 bp):
AGAGAGAC
Found at i:825331 original size:24 final size:24
Alignment explanation
Indices: 825302--825380 Score: 124
Period size: 24 Copynumber: 3.3 Consensus size: 24
825292 ACTTCACCCA
* *
825302 CTTCCACTA-AGTCCTTGCCCCCTT
1 CTTCCAC-AGAGTCCCTGTCCCCTT
825326 CTTCCACAGAGTCCCTGTCCCCTT
1 CTTCCACAGAGTCCCTGTCCCCTT
825350 CTTCCACAGAGTCCCTGTCCCCTT
1 CTTCCACAGAGTCCCTGTCCCCTT
825374 CTTCCAC
1 CTTCCAC
825381 CCCCTCCCCC
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
23 1 0.02
24 51 0.98
ACGTcount: A:0.13, C:0.47, G:0.10, T:0.30
Consensus pattern (24 bp):
CTTCCACAGAGTCCCTGTCCCCTT
Found at i:826456 original size:101 final size:101
Alignment explanation
Indices: 826310--826559 Score: 383
Period size: 101 Copynumber: 2.5 Consensus size: 101
826300 ACAAAATGTA
* *
826310 AATCATTTCTGGAAAACATGGCGATTGCTTTACTTCATATTTCATATGGTATCTAAACTTCAAGA
1 AATCATTTCTGGAAGACATAGCGATTGCTTTACTTCATATTTCATATGGTATCTAAACTTCAAGA
* *
826375 CTCAACAATTGCACTATTCATAGCTATAGTACTACC
66 CACAACAATTGCACTATTCATAGCTAAAGTACTACC
* * * * * *
826411 ATTCATTTCTGGAAGACACAACGATTGTTTTACTTTAAATTTCATATGGTATCTAAACTTCAAGA
1 AATCATTTCTGGAAGACATAGCGATTGCTTTACTTCATATTTCATATGGTATCTAAACTTCAAGA
* * *
826476 CAGAGCAATTGCACTATTTATAGCTAAAGTACTACC
66 CACAACAATTGCACTATTCATAGCTAAAGTACTACC
826512 AATCATTTCTGGAAGACATAGCGATTGCTTTACTTCATATTTCATATG
1 AATCATTTCTGGAAGACATAGCGATTGCTTTACTTCATATTTCATATG
826560 ATTTAAAGAC
Statistics
Matches: 130, Mismatches: 19, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
101 130 1.00
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.36
Consensus pattern (101 bp):
AATCATTTCTGGAAGACATAGCGATTGCTTTACTTCATATTTCATATGGTATCTAAACTTCAAGA
CACAACAATTGCACTATTCATAGCTAAAGTACTACC
Found at i:833813 original size:4 final size:4
Alignment explanation
Indices: 833799--833845 Score: 69
Period size: 4 Copynumber: 11.8 Consensus size: 4
833789 TCAATAAATG
*
833799 TTGT CTTGT TTGT TTGT TTGT TT-T TTGT TTGT TTGT TTGT TTTT TTG
1 TTGT -TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTG
833846 GGTTTTTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
3 3 0.08
4 32 0.82
5 4 0.10
ACGTcount: A:0.00, C:0.02, G:0.21, T:0.77
Consensus pattern (4 bp):
TTGT
Found at i:833827 original size:15 final size:15
Alignment explanation
Indices: 833807--833836 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
833797 TGTTGTCTTG
833807 TTTGTTTGTTTGTTT
1 TTTGTTTGTTTGTTT
833822 TTTGTTTGTTTGTTT
1 TTTGTTTGTTTGTTT
833837 GTTTTTTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (15 bp):
TTTGTTTGTTTGTTT
Found at i:833828 original size:19 final size:19
Alignment explanation
Indices: 833804--833843 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
833794 AAATGTTGTC
833804 TTGTTTGTTTGTTTGTTTT
1 TTGTTTGTTTGTTTGTTTT
833823 TTGTTTGTTTGTTTGTTTT
1 TTGTTTGTTTGTTTGTTTT
833842 TT
1 TT
833844 TGGGTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (19 bp):
TTGTTTGTTTGTTTGTTTT
Found at i:847566 original size:23 final size:21
Alignment explanation
Indices: 847530--847571 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
847520 GTTCTTGTAA
*
847530 AAAAGATTCTAATACATTTAT
1 AAAAGATTCTAATAAATTTAT
847551 AAAAGATTTCTGAATAAATTT
1 AAAAGA-TTCT-AATAAATTT
847572 CCTAAGTACC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 4 0.22
23 8 0.44
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (21 bp):
AAAAGATTCTAATAAATTTAT
Found at i:852509 original size:31 final size:31
Alignment explanation
Indices: 852473--852534 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
852463 ACCCTTTCCT
*
852473 GAGTGAGAATGGATTAATTAATCTTTTGTTG
1 GAGTGAGAATGGATTAATTAATCGTTTGTTG
*
852504 GAGTGAGAATGGATTAATTGATCGTTTGTTG
1 GAGTGAGAATGGATTAATTAATCGTTTGTTG
852535 ATCGATTTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.27, C:0.03, G:0.29, T:0.40
Consensus pattern (31 bp):
GAGTGAGAATGGATTAATTAATCGTTTGTTG
Found at i:856029 original size:17 final size:16
Alignment explanation
Indices: 855986--856031 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
855976 ATCTTCGCAA
855986 AATTTACAGATATAAT
1 AATTTACAGATATAAT
*
856002 AAATT-CAGATATAAT
1 AATTTACAGATATAAT
*
856017 GATTTTACAGATATA
1 -AATTTACAGATATA
856032 GTGAACTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
15 10 0.40
16 7 0.28
17 8 0.32
ACGTcount: A:0.48, C:0.07, G:0.09, T:0.37
Consensus pattern (16 bp):
AATTTACAGATATAAT
Found at i:873722 original size:15 final size:15
Alignment explanation
Indices: 873702--873737 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
873692 AGTGAAGACA
873702 GCTCCTCCTCAACCT
1 GCTCCTCCTCAACCT
*
873717 GCTCCTCCTCAGCCT
1 GCTCCTCCTCAACCT
873732 GCTCCT
1 GCTCCT
873738 ATAGGGTATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.08, C:0.53, G:0.11, T:0.28
Consensus pattern (15 bp):
GCTCCTCCTCAACCT
Found at i:880334 original size:13 final size:13
Alignment explanation
Indices: 880294--880347 Score: 54
Period size: 13 Copynumber: 3.9 Consensus size: 13
880284 CCTTGTTATG
*
880294 TGTATGTGGAAATC
1 TGTATGTGG-AGTC
*
880308 TGTATGTGTGGAGTT
1 TGTA--TGTGGAGTC
*
880323 TGTATTTGGAGTC
1 TGTATGTGGAGTC
880336 TGTATGTGGAGT
1 TGTATGTGGAGT
880348 GTGGAGTCTC
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
13 18 0.55
14 4 0.12
15 6 0.18
16 5 0.15
ACGTcount: A:0.19, C:0.04, G:0.35, T:0.43
Consensus pattern (13 bp):
TGTATGTGGAGTC
Found at i:886496 original size:16 final size:16
Alignment explanation
Indices: 886475--886506 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
886465 TCACCGAGAC
886475 GAGGCATCAACTTTAT
1 GAGGCATCAACTTTAT
*
886491 GAGGCATCACCTTTAT
1 GAGGCATCAACTTTAT
886507 AACCACCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (16 bp):
GAGGCATCAACTTTAT
Found at i:886990 original size:22 final size:23
Alignment explanation
Indices: 886947--886990 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
886937 GTATTGTATG
886947 ATATTGTATCATATTTGATACACA
1 ATATTGTATCATA-TTGATACACA
886971 ATATTGTATCATA-TGATACA
1 ATATTGTATCATATTGATACA
886991 ATATAATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
24 13 0.65
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (23 bp):
ATATTGTATCATATTGATACACA
Found at i:887036 original size:15 final size:15
Alignment explanation
Indices: 886977--887089 Score: 65
Period size: 15 Copynumber: 7.5 Consensus size: 15
886967 CACAATATTG
886977 TATCATATGATACAA
1 TATCATATGATACAA
* *
886992 TATAATTTGATA-AA
1 TATCATATGATACAA
* *
887006 -A-CAT-TGTTTC-A
1 TATCATATGATACAA
887017 TATCATATGATACAA
1 TATCATATGATACAA
*
887032 TATCATCTGATACAGTACGA
1 TATCATATGATAC---A--A
* *
887052 TATTATATAATACAA
1 TATCATATGATACAA
* *
887067 TATCATTTTATACAA
1 TATCATATGATACAA
887082 TATCATAT
1 TATCATAT
887090 TATATGATAT
Statistics
Matches: 73, Mismatches: 15, Indels: 20
0.68 0.14 0.19
Matches are distributed among these distances:
11 4 0.05
12 3 0.04
13 4 0.05
14 6 0.08
15 43 0.59
17 1 0.01
18 1 0.01
20 11 0.15
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.39
Consensus pattern (15 bp):
TATCATATGATACAA
Found at i:887072 original size:35 final size:35
Alignment explanation
Indices: 887014--887094 Score: 101
Period size: 35 Copynumber: 2.3 Consensus size: 35
887004 AAACATTGTT
* * *
887014 TCATATCATATGATACAATATCATCTGATACAGTA
1 TCATATTATATAATACAATATCATCTGATACAATA
* *
887049 -CGATATTATATAATACAATATCATTTTATACAATA
1 TC-ATATTATATAATACAATATCATCTGATACAATA
887084 TCATATTATAT
1 TCATATTATAT
887095 GATATCTTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
34 1 0.03
35 37 0.95
36 1 0.03
ACGTcount: A:0.42, C:0.14, G:0.05, T:0.40
Consensus pattern (35 bp):
TCATATTATATAATACAATATCATCTGATACAATA
Found at i:887092 original size:15 final size:15
Alignment explanation
Indices: 887051--887309 Score: 80
Period size: 15 Copynumber: 17.3 Consensus size: 15
887041 ATACAGTACG
* *
887051 ATATTATATAATACA
1 ATATCATATTATACA
*
887066 ATATCATTTTATACA
1 ATATCATATTATACA
**
887081 ATATCATATTATATG
1 ATATCATATTATACA
887096 ATATC---TTAT--A
1 ATATCATATTATACA
*
887106 ATATCATATAATACA
1 ATATCATATTATACA
*
887121 ATTTCATGTATTTTATAACA
1 ATATCA--TA--TTAT-ACA
*
887141 ATAT-ATTATATAAACCA
1 ATATCA-TAT-TATA-CA
*
887158 ATATCAAATTATACA
1 ATATCATATTATACA
** * *
887173 ATATTGTATCATACG
1 ATATCATATTATACA
887188 ATATGCTATAATTAT--A
1 ATAT-C-AT-ATTATACA
887204 ATATACA-A-TAT-C-
1 ATAT-CATATTATACA
* *
887216 GTATCATATGATACA
1 ATATCATATTATACA
*
887231 ATATCATA-TATTGCA
1 ATATCATATTA-TACA
* * *
887246 ATATAATATGAAACA
1 ATATCATATTATACA
* *
887261 ATATCAT-TCGATAAA
1 ATATCATAT-TATACA
887276 ATAAT-ATATTATACA
1 AT-ATCATATTATACA
*
887291 ATATCATATTCTACA
1 ATATCATATTATACA
887306 ATAT
1 ATAT
887310 TGTATAATAA
Statistics
Matches: 177, Mismatches: 40, Indels: 54
0.65 0.15 0.20
Matches are distributed among these distances:
10 5 0.03
11 2 0.01
12 11 0.06
13 6 0.03
14 5 0.03
15 104 0.59
16 14 0.08
17 13 0.07
18 7 0.04
19 4 0.02
20 6 0.03
ACGTcount: A:0.46, C:0.11, G:0.04, T:0.39
Consensus pattern (15 bp):
ATATCATATTATACA
Found at i:887443 original size:20 final size:20
Alignment explanation
Indices: 887405--887453 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
887395 GATATTACAT
*
887405 TGTATCATATAAAACAATAG
1 TGTATCATATAAAACAATAC
* * *
887425 TGTATCATATCATAGAATAC
1 TGTATCATATAAAACAATAC
*
887445 TATATCATA
1 TGTATCATA
887454 GGAATCATGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.45, C:0.12, G:0.08, T:0.35
Consensus pattern (20 bp):
TGTATCATATAAAACAATAC
Found at i:887820 original size:19 final size:19
Alignment explanation
Indices: 887792--887828 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
887782 GAGGGCACCT
*
887792 GCTCTAAAAACTTTAACCA
1 GCTCTAAAAACCTTAACCA
*
887811 GCTCTTAAAACCTTAACC
1 GCTCTAAAAACCTTAACC
887829 TCATCCAGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.30, G:0.05, T:0.27
Consensus pattern (19 bp):
GCTCTAAAAACCTTAACCA
Found at i:888273 original size:19 final size:19
Alignment explanation
Indices: 888245--888281 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
888235 GAGGGCACCT
*
888245 GCTCTAAAAACTTTAACCA
1 GCTCTAAAAACCTTAACCA
*
888264 GCTCTTAAAACCTTAACC
1 GCTCTAAAAACCTTAACC
888282 TCATCCAGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.30, G:0.05, T:0.27
Consensus pattern (19 bp):
GCTCTAAAAACCTTAACCA
Found at i:888536 original size:176 final size:177
Alignment explanation
Indices: 888101--888854 Score: 1070
Period size: 177 Copynumber: 4.3 Consensus size: 177
888091 AAAAAAACTA
888101 AACCTCATCCAGCATCCGAAACCTATGGCTCAGATTCAGCATTCAAGCCTGTCAGGTGCATCAGT
1 AACCTCATCCAGCATCCGAAACCTATGGCTCAGATTCAGCATTCAAGCCTGTCAGGTGCATCAGT
* * * *
888166 ATCATAAGACACACCATCCATGTAAGTTTGGTAAAGTTAGGACCAGTAATAACTAAGATATGATC
66 ATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTTAGGACCAGTAGTAACTAAGAAATGATC
* * *
888231 ATCAGAGGGCACCTGC-TCTAAAAACTTTAACCAGCTCTTAAAACCTT
131 ATCAAAGGGCACCTGCAAC-AAAAACTTTAACCAGCTCTAAAAACCTT
888278 AACCTCATCCAGCATCCGAAACCTATGGCTCAGATTCAGCATTCAAGCCTGTCAGGTGCATCAGT
1 AACCTCATCCAGCATCCGAAACCTATGGCTCAGATTCAGCATTCAAGCCTGTCAGGTGCATCAGT
* * * * * *
888343 ATCATAAAACGCACCATCTATGCAAGTTTGGTGAAGTTGGGACCAGTAGTAACTTAGAAATG-GC
66 ATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTTAGGACCAGTAGTAACTAAGAAATGATC
* *
888407 TATCAAAGGGCACCTGCAACAAAAACTTTAACCTGCTCGAAAAACC-T
131 -ATCAAAGGGCACCTGCAACAAAAACTTTAACCAGCTCTAAAAACCTT
* * **
888454 AACTTCATCTAGCATCCGAAACCT-TCGGCTCAGATTCAGCATTCAAGCCTGTCAGGTGCAAAAG
1 AACCTCATCCAGCATCCGAAACCTAT-GGCTCAGATTCAGCATTCAAGCCTGTCAGGTGCATCAG
* * * *
888518 TATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTAAGGACCAGTAGTAAGTAAGATATAAT
65 TATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTTAGGACCAGTAGTAACTAAGAAATGAT
* **
888583 CATCAGAGGGCACCTGCTCCAAAAACTTTAACCAGCTCTAAAAACCTT
130 CATCAAAGGGCACCTGCAACAAAAACTTTAACCAGCTCTAAAAACCTT
*
888631 AACCTCATCCAGCATCCGAAACCTATGGCTCAGATTCAGCATTCAAGCCTGTTAGGTGCATCAGT
1 AACCTCATCCAGCATCCGAAACCTATGGCTCAGATTCAGCATTCAAGCCTGTCAGGTGCATCAGT
* * * *
888696 ATCATAAGACACACCATCTATGCAAGTTTGGTGAAGTTTGGACCAGTAGTAACTTAGAAATG-GC
66 ATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTTAGGACCAGTAGTAACTAAGAAATGATC
* * *
888760 TATCAAAGGGCACCTGCAACAAAAACTTTAACCTGCTCCAAACACCTT
131 -ATCAAAGGGCACCTGCAACAAAAACTTTAACCAGCTCTAAAAACCTT
* * * * *
888808 AACCTCCTCCAGCATCTGAAA-TTCATGGCCCAGATTCAGCATCCAAG
1 AACCTCATCCAGCATCCGAAACCT-ATGGCTCAGATTCAGCATTCAAG
888855 TCTCTCAAGT
Statistics
Matches: 511, Mismatches: 58, Indels: 16
0.87 0.10 0.03
Matches are distributed among these distances:
175 1 0.00
176 156 0.31
177 352 0.69
178 2 0.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (177 bp):
AACCTCATCCAGCATCCGAAACCTATGGCTCAGATTCAGCATTCAAGCCTGTCAGGTGCATCAGT
ATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTTAGGACCAGTAGTAACTAAGAAATGATC
ATCAAAGGGCACCTGCAACAAAAACTTTAACCAGCTCTAAAAACCTT
Found at i:888625 original size:19 final size:19
Alignment explanation
Indices: 888598--888634 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
888588 GAGGGCACCT
*
888598 GCTCCAAAAACTTTAACCA
1 GCTCCAAAAACCTTAACCA
*
888617 GCTCTAAAAACCTTAACC
1 GCTCCAAAAACCTTAACC
888635 TCATCCAGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.32, G:0.05, T:0.22
Consensus pattern (19 bp):
GCTCCAAAAACCTTAACCA
Found at i:888757 original size:353 final size:354
Alignment explanation
Indices: 888082--888854 Score: 1257
Period size: 353 Copynumber: 2.2 Consensus size: 354
888072 TAAACATGTG
* * *
888082 ACCTGTTCCAAAAAAACTAAACCTCATCCAGCATCCGAAACCTAT-GGCTCAGATTCAGCATTCA
1 ACCTGCTCC-AAAAACCTTAACCTCATCCAGCATCCGAAACCT-TCGGCTCAGATTCAGCATTCA
** * *
888146 AGCCTGTCAGGTGCATCAGTATCATAAGACACACCATCCATGTAAGTTTGGTAAAGTTAGGACCA
64 AGCCTGTCAGGTGCAAAAGTATCATAAGACACACCATCCATGCAAGTTTGGTAAAGTAAGGACCA
* * *
888211 GTAATAACTAAGATATGATCATCAGAGGGCACCTGCTCTAAAAACTTTAACCAGCTCTTAAAACC
129 GTAATAACTAAGATATAATCATCAGAGGGCACCTGCTCCAAAAACTTTAACCAGCTCTAAAAACC
888276 TTAACCTCATCCAGCATCCGAAACCTATGGCTCAGATTCAGCATTCAAGCCTGTCAGGTGCATCA
194 TTAACCTCATCCAGCATCCGAAACCTATGGCTCAGATTCAGCATTCAAGCCTGTCAGGTGCATCA
*
888341 GTATCATAAAACGCACCATCTATGCAAGTTTGGTGAAGTTGGGACCAGTAGTAACTTAGAAATGG
259 GTATCATAAAACACACCATCTATGCAAGTTTGGTGAAGTTGGGACCAGTAGTAACTTAGAAATGG
888406 CTATCAAAGGGCACCTGCAACAAAAACTTTA
324 CTATCAAAGGGCACCTGCAACAAAAACTTTA
* * *
888437 ACCTGCTCGAAAAACC-TAACTTCATCTAGCATCCGAAACCTTCGGCTCAGATTCAGCATTCAAG
1 ACCTGCTCCAAAAACCTTAACCTCATCCAGCATCCGAAACCTTCGGCTCAGATTCAGCATTCAAG
*
888501 CCTGTCAGGTGCAAAAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTAAGGACCAGT
66 CCTGTCAGGTGCAAAAGTATCATAAGACACACCATCCATGCAAGTTTGGTAAAGTAAGGACCAGT
* *
888566 AGTAAGTAAGATATAATCATCAGAGGGCACCTGCTCCAAAAACTTTAACCAGCTCTAAAAACCTT
131 AATAACTAAGATATAATCATCAGAGGGCACCTGCTCCAAAAACTTTAACCAGCTCTAAAAACCTT
*
888631 AACCTCATCCAGCATCCGAAACCTATGGCTCAGATTCAGCATTCAAGCCTGTTAGGTGCATCAGT
196 AACCTCATCCAGCATCCGAAACCTATGGCTCAGATTCAGCATTCAAGCCTGTCAGGTGCATCAGT
* *
888696 ATCATAAGACACACCATCTATGCAAGTTTGGTGAAGTTTGGACCAGTAGTAACTTAGAAATGGCT
261 ATCATAAAACACACCATCTATGCAAGTTTGGTGAAGTTGGGACCAGTAGTAACTTAGAAATGGCT
888761 ATCAAAGGGCACCTGCAACAAAAACTTTA
326 ATCAAAGGGCACCTGCAACAAAAACTTTA
* * * * *
888790 ACCTGCTCCAAACACCTTAACCTCCTCCAGCATCTGAAA--TTCATGGCCCAGATTCAGCATCCA
1 ACCTGCTCCAAAAACCTTAACCTCATCCAGCATCCGAAACCTTC--GGCTCAGATTCAGCATTCA
888853 AG
64 AG
888855 TCTCTCAAGT
Statistics
Matches: 386, Mismatches: 28, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
352 4 0.01
353 332 0.86
354 43 0.11
355 7 0.02
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (354 bp):
ACCTGCTCCAAAAACCTTAACCTCATCCAGCATCCGAAACCTTCGGCTCAGATTCAGCATTCAAG
CCTGTCAGGTGCAAAAGTATCATAAGACACACCATCCATGCAAGTTTGGTAAAGTAAGGACCAGT
AATAACTAAGATATAATCATCAGAGGGCACCTGCTCCAAAAACTTTAACCAGCTCTAAAAACCTT
AACCTCATCCAGCATCCGAAACCTATGGCTCAGATTCAGCATTCAAGCCTGTCAGGTGCATCAGT
ATCATAAAACACACCATCTATGCAAGTTTGGTGAAGTTGGGACCAGTAGTAACTTAGAAATGGCT
ATCAAAGGGCACCTGCAACAAAAACTTTA
Found at i:888801 original size:19 final size:19
Alignment explanation
Indices: 888779--888818 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
888769 GCACCTGCAA
* *
888779 CAAAAACTTTAACCTGCTC
1 CAAAAACCTTAACCTCCTC
*
888798 CAAACACCTTAACCTCCTC
1 CAAAAACCTTAACCTCCTC
888817 CA
1 CA
888819 GCATCTGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.35, C:0.40, G:0.03, T:0.23
Consensus pattern (19 bp):
CAAAAACCTTAACCTCCTC
Found at i:888977 original size:6 final size:6
Alignment explanation
Indices: 888966--888991 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
888956 ACCAGGTCCG
888966 GACGCC GACGCC GACGCC GACGCC GA
1 GACGCC GACGCC GACGCC GACGCC GA
888992 GGGTATAGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.46, G:0.35, T:0.00
Consensus pattern (6 bp):
GACGCC
Found at i:893838 original size:2 final size:2
Alignment explanation
Indices: 893831--893872 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
893821 AAACTTGCAT
893831 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
893873 ATGTTAATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:894514 original size:55 final size:55
Alignment explanation
Indices: 894430--894703 Score: 295
Period size: 58 Copynumber: 4.9 Consensus size: 55
894420 ACACTGTGCA
* *
894430 ATGAAAATATCCATTCAGGGTGATTTTATGATTAATCCAGTAATTGTTTTATATT
1 ATGAAAATATCCATTCAGGATGATTTTATGATTAATCCAGTAATTATTTTATATT
* *
894485 ATGAAAATATCCATTCAGGGTGATTTTATGATTAATCCAGTAATTATTTTATATA
1 ATGAAAATATCCATTCAGGATGATTTTATGATTAATCCAGTAATTATTTTATATT
* * * * *
894540 AAGAAAATATCCAATTGATCGGATGATTTTTTGATTAATCCAGTAATTATTTTACATC
1 ATGAAAATATCC-ATTCA--GGATGATTTTATGATTAATCCAGTAATTATTTTATATT
* * * *
894598 AAGAAAATATCCAATTGATCA-GATGATTTTTTTATTAATCCAGTAATTATTTTAT-GT
1 ATGAAAATATCC-A-T--TCAGGATGATTTTATGATTAATCCAGTAATTATTTTATATT
* ** *
894655 ATAAAAATATCCAACCAGGATGATTTTATGA-TAATCAAGTACA-TATTTT
1 ATGAAAATATCCATTCAGGATGATTTTATGATTAATCCAGTA-ATTATTTT
894704 CCTATCGAGT
Statistics
Matches: 191, Mismatches: 20, Indels: 18
0.83 0.09 0.08
Matches are distributed among these distances:
53 17 0.09
54 12 0.06
55 64 0.34
56 5 0.03
57 10 0.05
58 80 0.42
59 1 0.01
61 2 0.01
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (55 bp):
ATGAAAATATCCATTCAGGATGATTTTATGATTAATCCAGTAATTATTTTATATT
Found at i:894575 original size:113 final size:114
Alignment explanation
Indices: 894450--894668 Score: 300
Period size: 113 Copynumber: 1.9 Consensus size: 114
894440 CCATTCAGGG
* * * * *
894450 TGATTTTATGATTAATCCAGTAATTGTTTTATATTATGAAAATATCC-A-T-TCAGGGTGATTTT
1 TGATTTTATGATTAATCCAGTAATTATTTTACATCAAGAAAATATCCAATTATCA-GATGATTTT
894512 ATGATTAATCCAGTAATTATTTTATATAAAGAAAATATCCAATTGATCGGA
65 ATGATTAATCCAGTAATTATTTTATATAAA-AAAATATCCAATTGATCGGA
*
894563 TGATTTTTTGATTAATCCAGTAATTATTTTACATCAAGAAAATATCCAATTGATCAGATGATTTT
1 TGATTTTATGATTAATCCAGTAATTATTTTACATCAAGAAAATATCCAATT-ATCAGATGATTTT
* * * *
894628 TTTATTAATCCAGTAATTATTTTATGTATAAAAATATCCAA
65 ATGATTAATCCAGTAATTATTTTATATAAAAAAATATCCAA
894669 CCAGGATGAT
Statistics
Matches: 92, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
113 42 0.46
114 1 0.01
115 12 0.13
116 34 0.37
117 3 0.03
ACGTcount: A:0.37, C:0.10, G:0.11, T:0.42
Consensus pattern (114 bp):
TGATTTTATGATTAATCCAGTAATTATTTTACATCAAGAAAATATCCAATTATCAGATGATTTTA
TGATTAATCCAGTAATTATTTTATATAAAAAAATATCCAATTGATCGGA
Found at i:897155 original size:14 final size:14
Alignment explanation
Indices: 897136--897162 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
897126 ACACACTGCT
897136 TTCAACAACAATTG
1 TTCAACAACAATTG
897150 TTCAACAACAATT
1 TTCAACAACAATT
897163 TGAAAATAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.22, G:0.04, T:0.30
Consensus pattern (14 bp):
TTCAACAACAATTG
Found at i:912016 original size:38 final size:38
Alignment explanation
Indices: 911974--912050 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
911964 TGATTAAAAC
* * **
911974 CAAGATTTTTAATGCTATTTTTAACAATTTTTTGACCT
1 CAAGATTTTAAATGCTATTTTTAAAAAAATTTTGACCT
912012 CAAGATTTTAAATGCTATTTTTAAAAAAATTTTGACCT
1 CAAGATTTTAAATGCTATTTTTAAAAAAATTTTGACCT
912050 C
1 C
912051 GAGCCTACGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (38 bp):
CAAGATTTTAAATGCTATTTTTAAAAAAATTTTGACCT
Found at i:915380 original size:161 final size:159
Alignment explanation
Indices: 915095--915436 Score: 551
Period size: 161 Copynumber: 2.1 Consensus size: 159
915085 GAAACATCCA
** * * *
915095 CAAAGAAAATGAATGTAAACTGCAAATAACTGGAATTTTTCTACGTCCAAGGGCCATAACTGTTG
1 CAAAGAAAATGAGCGGAAACTGAAAATAACTGGAATTTTTCTACGTCCAAGGGCCATAACTGTCG
* *
915160 AAAATTTCTCGATCGTACCCAATATCGAACTTTACCTAGATATTATCATGATAAACCTGTATACC
66 AAAATTGCTCGATCGTACCCAATATCGAACTTGACCTAGATATTATCATGATAAACCTGTATACC
*
915225 AAATTTCATTCCATTACGTTCATCCTCTG
131 AAATTTCATTCCAATACGTTCATCCTCTG
915254 CAAAGAAAATGAGCGGAAACTGAAAATAACTGGAATTTTTCTACGTCCAAGGGCCATAACTCTGT
1 CAAAGAAAATGAGCGGAAACTGAAAATAACTGGAATTTTTCTACGTCCAAGGGCCATAA--CTGT
*
915319 CGAAAATTGCTCGATCGTACCCAATATCGAAGTTGACCTAGATATTATCATGATAAACCTGTATA
64 CGAAAATTGCTCGATCGTACCCAATATCGAACTTGACCTAGATATTATCATGATAAACCTGTATA
* *
915384 CCAAATTTCATTTCAATATGTTCATCCTCTG
129 CCAAATTTCATTCCAATACGTTCATCCTCTG
915415 CAAAGAAAATG-GACGGAAACTG
1 CAAAGAAAATGAG-CGGAAACTG
915437 TTGGTGGACC
Statistics
Matches: 169, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
159 55 0.33
160 1 0.01
161 113 0.67
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (159 bp):
CAAAGAAAATGAGCGGAAACTGAAAATAACTGGAATTTTTCTACGTCCAAGGGCCATAACTGTCG
AAAATTGCTCGATCGTACCCAATATCGAACTTGACCTAGATATTATCATGATAAACCTGTATACC
AAATTTCATTCCAATACGTTCATCCTCTG
Found at i:918361 original size:19 final size:19
Alignment explanation
Indices: 918322--918361 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
918312 GCACCTGCAA
* **
918322 CAAAAACTTTAACCTTGTC
1 CAAAAACCTTAACCTCCTC
918341 CAAAAACCTTAACCTCCTC
1 CAAAAACCTTAACCTCCTC
918360 CA
1 CA
918362 GCATCCGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.35, G:0.03, T:0.25
Consensus pattern (19 bp):
CAAAAACCTTAACCTCCTC
Found at i:918613 original size:177 final size:175
Alignment explanation
Indices: 918303--918628 Score: 424
Period size: 177 Copynumber: 1.8 Consensus size: 175
918293 NNNNNNNNNN
*
918303 TATCAAAGGGCACCTGCAACAAAAACTTTAACCTTGTCCAAAAACCTTAACCTCCTCCAGCATCC
1 TATCAAAGGGCACCTGCAACAAAAACTTTAACCTGGTCCAAAAACCTTAACCTCCTCCAGCATCC
* * ** * *
918368 GAAACCTATAGCTCAGATTCAGCACTTAAGCCTGTCTGGTGCATCAGTATCATAAGACACACCAT
66 GAAA-CTATAGCTAAGATTCAGCACTCAAGCCTGTCAAGTCCATAAGTATCA-AAGACACACCAT
918433 CCATGCAAGTTTGGTGAAGTACGGACCTGCAGTAACTTAGATATTGC
129 CCATGCAAGTTTGGTGAAGTACGGACCTGCAGTAACTTAGATATTGC
* *
918480 TATCAAAGGGCACCTGCAACAAAAACTTTAACCTGGTCCAACAACCTTAACCTCCTCCAGCATCT
1 TATCAAAGGGCACCTGCAACAAAAACTTTAACCTGGTCCAAAAACCTTAACCTCCTCCAGCATCC
* * * * ** *
918545 GAAA-TTTAGGACTAAGATTCAGCA-TCCAAGTCTTTCAAGTCCATAAGTAGGTC-CAGATGCAT
66 GAAACTATA-G-CTAAGATTCAGCACT-CAAGCCTGTCAAGTCCATAAGTA--TCAAAGACACAC
918607 CATCCATGCAAGTTTGGTGAAG
126 CATCCATGCAAGTTTGGTGAAG
918629 ATAGGACAAG
Statistics
Matches: 128, Mismatches: 16, Indels: 10
0.83 0.10 0.06
Matches are distributed among these distances:
175 3 0.02
176 2 0.02
177 121 0.95
179 2 0.02
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.25
Consensus pattern (175 bp):
TATCAAAGGGCACCTGCAACAAAAACTTTAACCTGGTCCAAAAACCTTAACCTCCTCCAGCATCC
GAAACTATAGCTAAGATTCAGCACTCAAGCCTGTCAAGTCCATAAGTATCAAAGACACACCATCC
ATGCAAGTTTGGTGAAGTACGGACCTGCAGTAACTTAGATATTGC
Found at i:926079 original size:40 final size:40
Alignment explanation
Indices: 926026--926110 Score: 116
Period size: 40 Copynumber: 2.1 Consensus size: 40
926016 GGATGTTTAA
*
926026 TAGTTTATAATTATGGTGTATATATATAAATGTTTCATGT
1 TAGTTTATAATTATGGTATATATATATAAATGTTTCATGT
* * * *
926066 TAGTTTATGATTATGGTATGTATATCTGAATGTTTCATGT
1 TAGTTTATAATTATGGTATATATATATAAATGTTTCATGT
*
926106 AAGTT
1 TAGTT
926111 GACTTTTGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.29, C:0.04, G:0.18, T:0.49
Consensus pattern (40 bp):
TAGTTTATAATTATGGTATATATATATAAATGTTTCATGT
Found at i:933621 original size:1 final size:1
Alignment explanation
Indices: 933615--933645 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
933605 AGATTTGTGA
933615 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
933646 TCGTNNNNNN
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:935282 original size:1 final size:1
Alignment explanation
Indices: 935276--935300 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
935266 TTACAGCATG
935276 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
935301 ACAACAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:936971 original size:163 final size:164
Alignment explanation
Indices: 936785--937150 Score: 610
Period size: 166 Copynumber: 2.2 Consensus size: 164
936775 CGTTGAAATT
* *
936785 ATCAAGTTTTACATAGTAATATATAGAGAAAATCTTTAAAAA-ACTTCTCAAAAACTATTAGGGC
1 ATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATACTTCTCAAAAACTATTAGGCC
* *
936849 AGAAAAGCTCAAATTAAATTGGAAGCATACTCAGGTAGTGTAGATTCAAATTTGTTCAAATCATA
66 AGAAAAGCTCAAATTAAAATGGAAGCATACTCAGGTAGTGTAAATTCAAATTTGTTCAAATCATA
936914 GTCCCTGGGGGTAG-GATGGGGCCACAATGGGGGG
131 GTCCCTGGGGGTAGAGA-GGGGCCACAATGGGGGG
* *
936948 ATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTATTTGG
1 ATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAA--TACTTCTCAAAAACTATTAGG
* *
937013 CCAGAAAAGCTCAAATTAAAATGGAAGCATCCTCAGGTAGTGTAAATTCAAGTTTGTTCAAATCA
64 CCAGAAAAGCTCAAATTAAAATGGAAGCATACTCAGGTAGTGTAAATTCAAATTTGTTCAAATCA
937078 TAGTCCCTGGGGGTAGAGAGGGGCCACAATGGGGGG
129 TAGTCCCTGGGGGTAGAGAGGGGCCACAATGGGGGG
*
937114 ATCAAGTTTTACATAGGAATATATAGAAAAAATCTTT
1 ATCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
937151 TTAAAGACTA
Statistics
Matches: 190, Mismatches: 9, Indels: 5
0.93 0.04 0.02
Matches are distributed among these distances:
163 41 0.22
166 147 0.77
167 2 0.01
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.28
Consensus pattern (164 bp):
ATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATACTTCTCAAAAACTATTAGGCC
AGAAAAGCTCAAATTAAAATGGAAGCATACTCAGGTAGTGTAAATTCAAATTTGTTCAAATCATA
GTCCCTGGGGGTAGAGAGGGGCCACAATGGGGGG
Found at i:938136 original size:1 final size:1
Alignment explanation
Indices: 938130--938161 Score: 55
Period size: 1 Copynumber: 32.0 Consensus size: 1
938120 CGTGAGGCAT
*
938130 CCCCCCCCCCCCCCCCCCCCCCCCCCTCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
938162 ATCCGATGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.97, G:0.00, T:0.03
Consensus pattern (1 bp):
C
Found at i:938442 original size:2 final size:2
Alignment explanation
Indices: 938437--938471 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
938427 TTCAGCAGTT
938437 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
938472 GCGAATGTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:946026 original size:20 final size:20
Alignment explanation
Indices: 946003--946046 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
945993 TGTTTTCAAT
*
946003 TTTTGTAATTTGTTTTTTT-G
1 TTTTGT-ATTTATTTTTTTGG
*
946023 TTTTGTTTTTATTTTTTTGG
1 TTTTGTATTTATTTTTTTGG
946043 TTTT
1 TTTT
946047 TTTTGTTGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.07, C:0.00, G:0.14, T:0.80
Consensus pattern (20 bp):
TTTTGTATTTATTTTTTTGG
Found at i:946047 original size:15 final size:13
Alignment explanation
Indices: 946011--946049 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
946001 ATTTTTGTAA
946011 TTTGTTTTTTTGT
1 TTTGTTTTTTTGT
*
946024 TTTGTTTTTATTTT
1 TTTGTTTTT-TTGT
946038 TTTGGTTTTTTT
1 TTT-GTTTTTTT
946050 TGTTGCTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 9 0.39
14 8 0.35
15 6 0.26
ACGTcount: A:0.03, C:0.00, G:0.13, T:0.85
Consensus pattern (13 bp):
TTTGTTTTTTTGT
Found at i:948193 original size:15 final size:15
Alignment explanation
Indices: 948175--948205 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
948165 CGATGACAAT
*
948175 GAAGATGATGATGAA
1 GAAGATGACGATGAA
948190 GAAGATGACGATGAA
1 GAAGATGACGATGAA
948205 G
1 G
948206 GCTTTATGCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.03, G:0.35, T:0.16
Consensus pattern (15 bp):
GAAGATGACGATGAA
Found at i:956701 original size:17 final size:17
Alignment explanation
Indices: 956679--956713 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
956669 GTAACTCTTG
956679 ATAGCTGGACAATTATC
1 ATAGCTGGACAATTATC
956696 ATAGCTGGACAATTATC
1 ATAGCTGGACAATTATC
956713 A
1 A
956714 GTATCGCTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (17 bp):
ATAGCTGGACAATTATC
Found at i:961910 original size:179 final size:180
Alignment explanation
Indices: 961609--962333 Score: 1233
Period size: 179 Copynumber: 4.0 Consensus size: 180
961599 GTGAAATGGA
961609 GTACCCTATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTTCATAAA
1 GTACCCTATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTTCATAAA
961674 TTATCAGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAG
66 TTATCAGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAG
* * * *
961739 AACAACTTCTTATCTTGAAAACTGTAGGAGGAGTTATCCGTACAGTGAGG
131 AACAACTTCCTATCTTGAAAACTGGAGGAGGAGTTATCCATACAATGAGG
*
961789 GTACCCTATATGCAATATTTTTCC-AAAAATGACTAAGTTCAAAAGCTGGTATTTTTTTCATAAA
1 GTACCCTATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTTCATAAA
* *
961853 TTATCGGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTTCAATTGATCTGCAAAAG
66 TTATCAGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAG
* *
961918 AACAACTTCTTATCTTGAAAACTGGGGGAGGAGTTATCCATACAATGAGG
131 AACAACTTCCTATCTTGAAAACTGGAGGAGGAGTTATCCATACAATGAGG
* * *
961968 GTACCCCATATGCAATATTTTGCCAAAAAA-GACTAAGTTCAAAATCTAGT-TTTTTTTCGATAA
1 GTACCCTATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTTC-ATAA
* *
962031 ATTATCAGAAATCAAAATCCTCGCAATATGCACACCTCTGATATATGTAGAATTGATCTGCAAAA
65 ATTATCAGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAA
* *
962096 GAACAACTTCCTATCTTGAAAACTGTA-GATGGAGTTATCCGTACAATGAGG
130 GAACAACTTCCTATCTTGAAAACTGGAGGA-GGAGTTATCCATACAATGAGG
*
962147 GTACCCTATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTTCATATA
1 GTACCCTATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTTCATAAA
*
962212 TTATCGGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAG
66 TTATCAGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAG
*
962277 AACAACTTCCTATCTTGAAAACTGGGGGAGGAGTTATCCATACAATGAGG
131 AACAACTTCCTATCTTGAAAACTGGAGGAGGAGTTATCCATACAATGAGG
962327 GTACCCT
1 GTACCCT
962334 TTTGGCAGCC
Statistics
Matches: 510, Mismatches: 29, Indels: 12
0.93 0.05 0.02
Matches are distributed among these distances:
178 10 0.02
179 327 0.64
180 163 0.32
181 10 0.02
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.30
Consensus pattern (180 bp):
GTACCCTATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTTCATAAA
TTATCAGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAG
AACAACTTCCTATCTTGAAAACTGGAGGAGGAGTTATCCATACAATGAGG
Found at i:962275 original size:359 final size:359
Alignment explanation
Indices: 961609--962332 Score: 1301
Period size: 359 Copynumber: 2.0 Consensus size: 359
961599 GTGAAATGGA
* *
961609 GTACCCTATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTTCATAAA
1 GTACCCCATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTAGTATTTTTTTCATAAA
961674 TTATCAGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAG
66 TTATCAGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAG
* *
961739 AACAACTTCTTATCTTGAAAACTGTAGGAGGAGTTATCCGTACAGTGAGGGTACCCTATATGCAA
131 AACAACTTCCTATCTTGAAAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCCTATATGCAA
*
961804 TATTTTTCCAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTTCATAAATTATCGGAAATCAAAA
196 TATTTTGCCAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTTCATAAATTATCGGAAATCAAAA
* *
961869 TCCTAGCAATATGCACACCTCTGATATATGTTCAATTGATCTGCAAAAGAACAACTTCTTATCTT
261 TCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAACTTCCTATCTT
961934 GAAAACTGGGGGAGGAGTTATCCATACAATGAGG
326 GAAAACTGGGGGAGGAGTTATCCATACAATGAGG
*
961968 GTACCCCATATGCAATATTTTGCCAAAAAA-GACTAAGTTCAAAATCTAGT-TTTTTTTCGATAA
1 GTACCCCATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTAGTATTTTTTTC-ATAA
* *
962031 ATTATCAGAAATCAAAATCCTCGCAATATGCACACCTCTGATATATGTAGAATTGATCTGCAAAA
65 ATTATCAGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAA
962096 GAACAACTTCCTATCTTGAAAACTGTA-GATGGAGTTATCCGTACAATGAGGGTACCCTATATGC
130 GAACAACTTCCTATCTTGAAAACTGTAGGA-GGAGTTATCCGTACAATGAGGGTACCCTATATGC
*
962160 AATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTTCATATATTATCGGAAATCA
194 AATATTTTGCC-AAAAATGACTAAGTTCAAAAGCTGGTATTTTTTTCATAAATTATCGGAAATCA
962225 AAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAACTTCCTAT
258 AAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAACTTCCTAT
962290 CTTGAAAACTGGGGGAGGAGTTATCCATACAATGAGG
323 CTTGAAAACTGGGGGAGGAGTTATCCATACAATGAGG
962327 GTACCC
1 GTACCC
962333 TTTTGGCAGC
Statistics
Matches: 351, Mismatches: 11, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
357 10 0.03
358 154 0.44
359 187 0.53
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.30
Consensus pattern (359 bp):
GTACCCCATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTAGTATTTTTTTCATAAA
TTATCAGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAG
AACAACTTCCTATCTTGAAAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCCTATATGCAA
TATTTTGCCAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTTCATAAATTATCGGAAATCAAAA
TCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAACTTCCTATCTT
GAAAACTGGGGGAGGAGTTATCCATACAATGAGG
Found at i:965891 original size:2 final size:2
Alignment explanation
Indices: 965886--965938 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
965876 TCATTGCATT
965886 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
965928 TC TC TC TC TC T
1 TC TC TC TC TC T
965939 GAATTGTAGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:966001 original size:2 final size:2
Alignment explanation
Indices: 965994--966033 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
965984 TTGCATTTTA
965994 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
966034 GTGAATTGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:974399 original size:2 final size:2
Alignment explanation
Indices: 974392--974447 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
974382 AGGGACAACA
974392 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
974434 TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC
974448 AGAGAATACT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:976562 original size:1 final size:1
Alignment explanation
Indices: 976517--976547 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
976507 GAAACAGGCA
976517 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
976548 TTTCTCCTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:982968 original size:2 final size:2
Alignment explanation
Indices: 982963--983011 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
982953 AAATTGAAAA
*
982963 CT CT CT CT CT CT CT CT CT CT CT CT CT AT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
983005 CT CT CT C
1 CT CT CT C
983012 CTATCATATA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.02, C:0.49, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:985437 original size:2 final size:2
Alignment explanation
Indices: 985430--985490 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
985420 TATGCAAGAT
*
985430 GA GA GA GA GA GA GA GA GA GA AA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
985472 GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA G
985491 GCTCTGGACA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:990840 original size:15 final size:15
Alignment explanation
Indices: 990831--991014 Score: 262
Period size: 15 Copynumber: 12.3 Consensus size: 15
990821 GGGTTCCGGT
*
990831 GTTGTAGGTTCTGGA
1 GTTGTAGGTTCAGGA
990846 GTTGTAGGTTCAGGA
1 GTTGTAGGTTCAGGA
*
990861 GTTGTAGGTTCAGGG
1 GTTGTAGGTTCAGGA
*
990876 GTTGTAGGTTCAGGT
1 GTTGTAGGTTCAGGA
*
990891 GTTGTAGGTTCTGGA
1 GTTGTAGGTTCAGGA
*
990906 GTTGTAGGTTCTGGA
1 GTTGTAGGTTCAGGA
990921 GTTGTAGGTTCAGGA
1 GTTGTAGGTTCAGGA
* *
990936 GTTGTAGGTTCTGGT
1 GTTGTAGGTTCAGGA
*
990951 GTTGTAGGCTCAGGA
1 GTTGTAGGTTCAGGA
*
990966 GTTGTAGGTTCTGGA
1 GTTGTAGGTTCAGGA
990981 GTTGTAGGTTCTAGG-
1 GTTGTAGGTTC-AGGA
*
990996 GTTGTAGGTTCAGGT
1 GTTGTAGGTTCAGGA
991011 GTTG
1 GTTG
991015 AACTTTCAGT
Statistics
Matches: 153, Mismatches: 14, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
14 3 0.02
15 148 0.97
16 2 0.01
ACGTcount: A:0.14, C:0.07, G:0.41, T:0.38
Consensus pattern (15 bp):
GTTGTAGGTTCAGGA
Found at i:990856 original size:45 final size:44
Alignment explanation
Indices: 990807--991014 Score: 254
Period size: 45 Copynumber: 4.6 Consensus size: 44
990797 TTCTGGAATT
* * * * *
990807 GGTTCAGGTTCTGTGGGTTCCGGTGTTGTAGGTTCTGGAGTTGTA
1 GGTTCAGGGT-TGTAGGTTCAGGAGTTGTAGGTTCAGGAGTTGTA
* *
990852 GGTTCAGGAGTTGTAGGTTCAGGGGTTGTAGGTTCAGGTGTTGTA
1 GGTTCAGG-GTTGTAGGTTCAGGAGTTGTAGGTTCAGGAGTTGTA
* *
990897 GGTTCTGGAGTTGTAGGTTCTGGAGTTGTAGGTTCAGGAGTTGTA
1 GGTTCAGG-GTTGTAGGTTCAGGAGTTGTAGGTTCAGGAGTTGTA
* * *
990942 GGTTCTGGTGTTGTAGGCTCAGGAGTTGTAGGTTCTGGAGTTGTA
1 GGTTCAGG-GTTGTAGGTTCAGGAGTTGTAGGTTCAGGAGTTGTA
*
990987 GGTTCTAGGGTTGTAGGTTCAGGTGTTG
1 GGTTC-AGGGTTGTAGGTTCAGGAGTTG
991015 AACTTTCAGT
Statistics
Matches: 144, Mismatches: 17, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
45 141 0.98
46 3 0.02
ACGTcount: A:0.13, C:0.08, G:0.41, T:0.38
Consensus pattern (44 bp):
GGTTCAGGGTTGTAGGTTCAGGAGTTGTAGGTTCAGGAGTTGTA
Found at i:995187 original size:20 final size:20
Alignment explanation
Indices: 995162--995203 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
995152 GATTCCTGAG
995162 GCGTGTTCAGCAAAGCGACT
1 GCGTGTTCAGCAAAGCGACT
995182 GCGTGTTCAGCAAAGCGACT
1 GCGTGTTCAGCAAAGCGACT
995202 GC
1 GC
995204 TCGCGAGCGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.26, G:0.31, T:0.19
Consensus pattern (20 bp):
GCGTGTTCAGCAAAGCGACT
Found at i:1006158 original size:37 final size:39
Alignment explanation
Indices: 1006088--1006162 Score: 111
Period size: 37 Copynumber: 1.9 Consensus size: 39
1006078 ATGCTTCTTA
1006088 TTGATTATTAATAAAAAATAATAAATCAGATATCTGAACG
1 TTGATTATTAAT-AAAAATAATAAATCAGATATCTGAACG
1006128 TTGATTATTAAT-AAAA-AATAAATCTA-ATATCTGAA
1 TTGATTATTAATAAAAATAATAAATC-AGATATCTGAA
1006163 TAACGGTGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
37 17 0.50
38 5 0.15
40 12 0.35
ACGTcount: A:0.51, C:0.07, G:0.08, T:0.35
Consensus pattern (39 bp):
TTGATTATTAATAAAAATAATAAATCAGATATCTGAACG
Found at i:1012705 original size:141 final size:141
Alignment explanation
Indices: 1012451--1012731 Score: 562
Period size: 141 Copynumber: 2.0 Consensus size: 141
1012441 TATCAAAATT
1012451 GTTAAAAAAGCCAGAAAACGTCAGATATTTCGGACTAGTCAACAATGCATATCTCTGCTAATGTA
1 GTTAAAAAAGCCAGAAAACGTCAGATATTTCGGACTAGTCAACAATGCATATCTCTGCTAATGTA
1012516 TACAAATTGTCGAATAACCTTTTCTGGGGAACACTTTTTACTGATTCGCTCCTGCCAGAAAAAAT
66 TACAAATTGTCGAATAACCTTTTCTGGGGAACACTTTTTACTGATTCGCTCCTGCCAGAAAAAAT
1012581 AGGCCTATCCC
131 AGGCCTATCCC
1012592 GTTAAAAAAGCCAGAAAACGTCAGATATTTCGGACTAGTCAACAATGCATATCTCTGCTAATGTA
1 GTTAAAAAAGCCAGAAAACGTCAGATATTTCGGACTAGTCAACAATGCATATCTCTGCTAATGTA
1012657 TACAAATTGTCGAATAACCTTTTCTGGGGAACACTTTTTACTGATTCGCTCCTGCCAGAAAAAAT
66 TACAAATTGTCGAATAACCTTTTCTGGGGAACACTTTTTACTGATTCGCTCCTGCCAGAAAAAAT
1012722 AGGCCTATCC
131 AGGCCTATCC
1012732 TTCGGGATTA
Statistics
Matches: 140, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
141 140 1.00
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.28
Consensus pattern (141 bp):
GTTAAAAAAGCCAGAAAACGTCAGATATTTCGGACTAGTCAACAATGCATATCTCTGCTAATGTA
TACAAATTGTCGAATAACCTTTTCTGGGGAACACTTTTTACTGATTCGCTCCTGCCAGAAAAAAT
AGGCCTATCCC
Found at i:1018656 original size:180 final size:180
Alignment explanation
Indices: 1018331--1018692 Score: 541
Period size: 180 Copynumber: 2.0 Consensus size: 180
1018321 TACCATACAG
* * * * *
1018331 GGTACCTCTATTGGATGGACAACTCCTCCTTCACTTTTCAAGATAGGAAGTTGTCCTTTTGCAGA
1 GGTACCCCTATTGGACGGACAAATCCTCCTTCACTTTTCAAGATAGGAAGTTGTCCTTATACAGA
* **
1018396 TCAATTGTACATATATTAGAGGTGTGCATAGTGCTAGGATTTTGATTTTTGATAATTTTTTAAGA
66 TCAATTGTACATATATTAGAGGTGTGCATAGTGCTAGGATTTCGATTACTGATAATTTTTTAAGA
1018461 AAATAGCAGCTTTTGAACTTAGTCATTTTTT-GACAAAATATTGCAAATA
131 AAATAGCAGCTTTTGAACTTAGTCATTTTTTGGACAAAATATTGCAAATA
* *
1018510 GGTACCCCTATTTGGACGGATAAATCCTCCTTCACTTTTCAAGATAGGAAGTTGTTCTTATACAG
1 GGTACCCCTA-TTGGACGGACAAATCCTCCTTCACTTTTCAAGATAGGAAGTTGTCCTTATACAG
* **
1018575 ATCAGTTGTACATATATTAGAGGTGTGCATTTTGCTAGGATTTCGATTACTGAT-ATTTTTTAAA
65 ATCAATTGTACATATATTAGAGGTGTGCATAGTGCTAGGATTTCGATTACTGATAATTTTTT-AA
* *
1018639 GAAAATA-CAAGCTTTTGAACTTAGTCATTTTTTGGGCAAAATATTGCATATA
129 GAAAATAGC-AGCTTTTGAACTTAGTCATTTTTTGGACAAAATATTGCAAATA
1018691 GG
1 GG
1018693 GTACTCCATT
Statistics
Matches: 164, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
179 17 0.10
180 129 0.79
181 18 0.11
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (180 bp):
GGTACCCCTATTGGACGGACAAATCCTCCTTCACTTTTCAAGATAGGAAGTTGTCCTTATACAGA
TCAATTGTACATATATTAGAGGTGTGCATAGTGCTAGGATTTCGATTACTGATAATTTTTTAAGA
AAATAGCAGCTTTTGAACTTAGTCATTTTTTGGACAAAATATTGCAAATA
Found at i:1020998 original size:12 final size:11
Alignment explanation
Indices: 1020972--1021021 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
1020962 CCCTATTTGC
1020972 AAAAAA-AAA-
1 AAAAAAGAAAT
1020981 AAAAAATGAAAT
1 AAAAAA-GAAAT
*
1020993 AAAAAAAAAAAT
1 -AAAAAAGAAAT
*
1021005 AAATAAGAAAT
1 AAAAAAGAAAT
1021016 AAAAAA
1 AAAAAA
1021022 CAGATTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
9 6 0.18
11 17 0.52
12 4 0.12
13 6 0.18
ACGTcount: A:0.86, C:0.00, G:0.04, T:0.10
Consensus pattern (11 bp):
AAAAAAGAAAT
Found at i:1020998 original size:16 final size:16
Alignment explanation
Indices: 1020976--1021021 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 16
1020966 ATTTGCAAAA
1020976 AAAAAAAAAAATGAAAT
1 AAAAAAAAAAAT-AAAT
1020993 AAAAAAAAAAATAAAT
1 AAAAAAAAAAATAAAT
1021009 AAGAAATAAAAAA
1 AA-AAA-AAAAAA
1021022 CAGATTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.22
17 15 0.56
18 6 0.22
ACGTcount: A:0.85, C:0.00, G:0.04, T:0.11
Consensus pattern (16 bp):
AAAAAAAAAAATAAAT
Found at i:1021002 original size:23 final size:23
Alignment explanation
Indices: 1020972--1021021 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
1020962 CCCTATTTGC
*
1020972 AAAAAAAAAA-AAAAATGAAATA
1 AAAAAAAAAATAAAAAAGAAATA
*
1020994 AAAAAAAAAATAAATAAGAAATA
1 AAAAAAAAAATAAAAAAGAAATA
1021017 AAAAA
1 AAAAA
1021022 CAGATTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 10 0.40
23 15 0.60
ACGTcount: A:0.86, C:0.00, G:0.04, T:0.10
Consensus pattern (23 bp):
AAAAAAAAAATAAAAAAGAAATA
Found at i:1024684 original size:1 final size:1
Alignment explanation
Indices: 1024673--1024702 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
1024663 ACTTTCTAAA
*
1024673 CCCCACCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1024703 AACCCACTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.03, C:0.97, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:1034188 original size:169 final size:169
Alignment explanation
Indices: 1033909--1034241 Score: 612
Period size: 169 Copynumber: 2.0 Consensus size: 169
1033899 AAGTAGTGTT
1033909 ATTTTGTCCATTTCTATAGAGATTGTGAGAGAAAAAGCTTATGATTTGTATTCAAATACTGGATA
1 ATTTTGTCCATTTCTATAGAGATTGTGAGAGAAAAAGCTTATGATTTGTATTCAAATACTGGATA
*
1033974 TTAACTTTTAAAGGTAAAGTTTACAAGAAATATACACACTGTAGTATGTACAGATAGACATTTTT
66 TTAACTTTAAAAGGTAAAGTTTACAAGAAATATACACACTGTAGTATGTACAGATAGACATTTTT
*
1034039 GTATTGCATTTCATAATTTCATAATAAGAAACATTACAG
131 GTACTGCATTTCATAATTTCATAATAAGAAACATTACAG
* * *
1034078 ATTTTGTCCATTTCTATAGAGATTGTGAGAGAAATAGCTTATGATTTGTGTTCATATACTGGATA
1 ATTTTGTCCATTTCTATAGAGATTGTGAGAGAAAAAGCTTATGATTTGTATTCAAATACTGGATA
1034143 TTAACTTTAAAAGGTAAAGTTTACAAGAAATATACACACTGTAGTATGTACAGATAGACATTTTT
66 TTAACTTTAAAAGGTAAAGTTTACAAGAAATATACACACTGTAGTATGTACAGATAGACATTTTT
*
1034208 GTACTGCATTTCATAATTTCATACTAAGAAACAT
131 GTACTGCATTTCATAATTTCATAATAAGAAACAT
1034242 AACACATAAA
Statistics
Matches: 158, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
169 158 1.00
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (169 bp):
ATTTTGTCCATTTCTATAGAGATTGTGAGAGAAAAAGCTTATGATTTGTATTCAAATACTGGATA
TTAACTTTAAAAGGTAAAGTTTACAAGAAATATACACACTGTAGTATGTACAGATAGACATTTTT
GTACTGCATTTCATAATTTCATAATAAGAAACATTACAG
Found at i:1036454 original size:14 final size:14
Alignment explanation
Indices: 1036435--1036476 Score: 84
Period size: 14 Copynumber: 3.0 Consensus size: 14
1036425 TAGTATAGAA
1036435 GTTTGTATCTATAT
1 GTTTGTATCTATAT
1036449 GTTTGTATCTATAT
1 GTTTGTATCTATAT
1036463 GTTTGTATCTATAT
1 GTTTGTATCTATAT
1036477 CAGTTGATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.21, C:0.07, G:0.14, T:0.57
Consensus pattern (14 bp):
GTTTGTATCTATAT
Found at i:1046861 original size:2 final size:2
Alignment explanation
Indices: 1046852--1046885 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1046842 TGTTTTTGCA
1046852 CT CT -T CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1046886 CTTTAAACTG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1048578 original size:21 final size:21
Alignment explanation
Indices: 1048554--1048594 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1048544 TAATAACACA
*
1048554 CATACGTACATAAACATCACG
1 CATACGTAAATAAACATCACG
1048575 CATACGTAAATAAACATCAC
1 CATACGTAAATAAACATCAC
1048595 ACGTACATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.46, C:0.27, G:0.07, T:0.20
Consensus pattern (21 bp):
CATACGTAAATAAACATCACG
Found at i:1052218 original size:2 final size:2
Alignment explanation
Indices: 1052213--1052252 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1052203 GTATACGCAA
1052213 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1052253 ATATTATTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1055362 original size:164 final size:162
Alignment explanation
Indices: 1054972--1055676 Score: 728
Period size: 164 Copynumber: 4.3 Consensus size: 162
1054962 CCCCCCCCAA
** * ***
1054972 TGTGGCCCCAACCTACCCCC-GGGATTATGATTTGAAAAAAAAAGAATCTACACTATCTGAGGAT
1 TGTGGCCCC-ACCTACCCCCGGGGACCATGATTTGAACAAATTTGAATCTACACTATCTGAGGAT
* * * * * *
1055036 GCTTCCACTCAAATTTGAGCTTTTCT-ACCTAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTT
65 GTTTCCACACAAGTTTAAGCTTTTCTGGCCGAATAGTTTTT-AG-AGAAGATTTTTAAAGATTTT
* ** *
1055100 CTCTTTATATTCCTTTGTAAAAATTCACCCCCTCCCCCTAT
128 CTCTATATATTCCAATGTAAAAATT-----CGT-CCCCTAT
* * * *
1055141 TGT-GCCCCACCTTACCCCCAGGGACCATAATTTAAACAAATATGAATCTACACTATCTGAGGAT
1 TGTGGCCCCACC-TACCCCCGGGGACCATGATTTGAACAAATTTGAATCTACACTATCTGAGGAT
*
1055205 GTTTCCACACAAGTTTAAGCTTTTCTGGCCGAATAGTTTTTCG-GAAGATTTTTAAAGATTTTTC
65 GTTTCCACACAAGTTTAAGCTTTTCTGGCCGAATAGTTTTTAGAGAAGATTTTTAAAGA-TTTTC
*
1055269 TCTATATATTCCAATGTAAAAATTCGTCCCCAAAT
129 TCTATATATTCCAATGTAAAAATTCGTCCCC-TAT
* * *
1055304 TCTGGCCCCGCTCTACCCCTGGGGACCATGATTTGAACAAATTTGAATCTACACTATCTGAGGAT
1 TGTGGCCCCAC-CTACCCCCGGGGACCATGATTTGAACAAATTTGAATCTACACTATCTGAGGAT
* *
1055369 GTTTCCACACAAGTTTATGCTTTTCTGGCCGAATA-TTTATAAGAAGAAGATTTTTAAAAGATTT
65 GTTTCCACACAAGTTTAAGCTTTTCTGGCCGAATAGTTT-TTAG-AGAAGATTTTT-AAAGATTT
* *
1055433 TCTCTATATATTCCAATGTAAAAATTTGACTCCCCTGT
127 TCTCTATATATTCCAATGTAAAAATTCG--TCCCCTAT
* * * * *
1055471 TTTGGCCCCAACCTA-CCCCGGGGACCATGATTTGAACAAACTTGAATCTACACAACCTGAGAAT
1 TGTGGCCCC-ACCTACCCCCGGGGACCATGATTTGAACAAATTTGAATCTACACTATCTGAGGAT
* * ** *
1055535 GCTTT-AATACAAGTTTAATTTTTTTTTGG-CGTAATAGTTTTTA-AGAAGATTTTTAAAGATTT
65 G-TTTCCACACAAGTTTAA-GCTTTTCTGGCCG-AATAGTTTTTAGAGAAGATTTTTAAAGATTT
* * * * *
1055597 TCTCTATATATTCCTATGT-AAAAGTCAATCCCCCAG
127 TCTCTATATATTCCAATGTAAAAATTC-GTCCCCTAT
1055633 TGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAATTT
1 TGTGGCCCCA-CCTACCCCCGGGGACCATGATTTGAACAAATTT
1055677 AATATCTGAC
Statistics
Matches: 460, Mismatches: 55, Indels: 48
0.82 0.10 0.09
Matches are distributed among these distances:
161 1 0.00
162 21 0.05
163 41 0.09
164 115 0.25
165 12 0.03
166 97 0.21
167 51 0.11
168 47 0.10
169 63 0.14
170 12 0.03
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (162 bp):
TGTGGCCCCACCTACCCCCGGGGACCATGATTTGAACAAATTTGAATCTACACTATCTGAGGATG
TTTCCACACAAGTTTAAGCTTTTCTGGCCGAATAGTTTTTAGAGAAGATTTTTAAAGATTTTCTC
TATATATTCCAATGTAAAAATTCGTCCCCTAT
Found at i:1055618 original size:330 final size:329
Alignment explanation
Indices: 1054974--1055676 Score: 809
Period size: 330 Copynumber: 2.1 Consensus size: 329
1054964 CCCCCCAATG
* ** * ***
1054974 TGGCCCCAACCTACCCCC-GGGATTATGATTTGAAAAAAAAAGAATCTACACTATCTGAGGATGC
1 TGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAATTTGAATCTACACTATCTGAGGATGC
* * * *
1055038 TTCCACTCAAATTTGAGCTTTTCTACCTAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTC
66 TTCCACACAAATTTGAGCTTTTCTACCGAATAGTTTATAAGAAGAAGATTTTTAAAGATTTTCTC
* **
1055103 TTTATATTCCTTTGTAAAAATTCACCCCCTCCCCCTATTGTGCCCCACCTTACCCCCAGGGACCA
131 TATATATTCCAATGTAAAAATTCACCCCCT---CCTATTGTGCCCCACCTTACCCCCAGGGACCA
* * * *
1055168 TAATTTAAACAAATATGAATCTACACTATCTGAGGATGTTTCCACACAAGTTTAAGCTTTTCTGG
193 TAATTTAAACAAATATGAATCTACACAACCTGAGAATGTTTCAACACAAGTTTAAGCTTTTCTGG
** * *
1055233 CCGAATAGTTTTTCGGAAGATTTTTAAAGATTTTTCTCTATATATTCCAATGTAAAAATTC-GTC
258 CCGAATAGTTTTTAAGAAGATTTTTAAAGATTTTTCTCTATATATTCCAATGT-AAAAGTCAATC
*
1055297 CCCAAATTC
322 CCC-AAGTC
* * * *
1055306 TGGCCCCGCTCTACCCCTGGGGACCATGATTTGAACAAATTTGAATCTACACTATCTGAGGATGT
1 TGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAATTTGAATCTACACTATCTGAGGATGC
* *
1055371 TTCCACACAAGTTT-ATGCTTTTCTGGCCGAATA-TTTATAAGAAGAAGATTTTTAAAAGATTTT
66 TTCCACACAAATTTGA-GCTTTTCT-ACCGAATAGTTTATAAGAAGAAGATTTTT-AAAGATTTT
* * * *
1055434 CTCTATATATTCCAATGTAAAAATTTGACTCCCCT-GTTTTG-GCCCCAACC-TA-CCCCGGGGA
128 CTCTATATATTCCAATGTAAAAA-TTCAC-CCCCTCCTATTGTGCCCC-ACCTTACCCCCAGGGA
* * * **
1055495 CCATGATTTGAACAAACT-TGAATCTACACAACCTGAGAATGCTTT-AATACAAGTTTAATTTTT
190 CCATAATTTAAACAAA-TATGAATCTACACAACCTGAGAATG-TTTCAACACAAGTTTAA-GCTT
* *
1055558 TTTTGG-CGTAATAGTTTTTAAGAAGATTTTTAAAGA-TTTTCTCTATATATTCCTATGTAAAAG
252 TTCTGGCCG-AATAGTTTTTAAGAAGATTTTTAAAGATTTTTCTCTATATATTCCAATGTAAAAG
* *
1055621 TCAATCCCCCAGTG
316 TCAATCCCCAAGTC
1055635 TGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAATTT
1 TGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAATTT
1055677 AATATCTGAC
Statistics
Matches: 314, Mismatches: 45, Indels: 27
0.81 0.12 0.07
Matches are distributed among these distances:
329 47 0.15
330 81 0.26
331 43 0.14
332 22 0.07
333 77 0.25
334 35 0.11
335 4 0.01
336 5 0.02
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (329 bp):
TGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAATTTGAATCTACACTATCTGAGGATGC
TTCCACACAAATTTGAGCTTTTCTACCGAATAGTTTATAAGAAGAAGATTTTTAAAGATTTTCTC
TATATATTCCAATGTAAAAATTCACCCCCTCCTATTGTGCCCCACCTTACCCCCAGGGACCATAA
TTTAAACAAATATGAATCTACACAACCTGAGAATGTTTCAACACAAGTTTAAGCTTTTCTGGCCG
AATAGTTTTTAAGAAGATTTTTAAAGATTTTTCTCTATATATTCCAATGTAAAAGTCAATCCCCA
AGTC
Found at i:1064831 original size:2 final size:2
Alignment explanation
Indices: 1064824--1064871 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1064814 TAAACACATC
1064824 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1064866 AG AG AG
1 AG AG AG
1064872 CAAGAGTATC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1088573 original size:61 final size:61
Alignment explanation
Indices: 1088497--1088620 Score: 230
Period size: 61 Copynumber: 2.0 Consensus size: 61
1088487 ATCGGGCACG
1088497 GTCTCCAAATAAAATGTAAGCGATAAACTAAAATAATATTCATTGAATTTTTACATTTTTT
1 GTCTCCAAATAAAATGTAAGCGATAAACTAAAATAATATTCATTGAATTTTTACATTTTTT
* *
1088558 GTCTCCAAGTAAAATGTAAGCGATAAACTAAAATAATATTCGTTGAATTTTTACATTTTTT
1 GTCTCCAAATAAAATGTAAGCGATAAACTAAAATAATATTCATTGAATTTTTACATTTTTT
1088619 GT
1 GT
1088621 ATTCATCCGC
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.40
Consensus pattern (61 bp):
GTCTCCAAATAAAATGTAAGCGATAAACTAAAATAATATTCATTGAATTTTTACATTTTTT
Found at i:1088815 original size:1 final size:1
Alignment explanation
Indices: 1088809--1088837 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
1088799 CCTCTCCCGA
1088809 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1088838 GGGAGAGGGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1090029 original size:2 final size:2
Alignment explanation
Indices: 1090024--1090091 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
1090014 ACTGAAAAAA
1090024 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1090066 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
1090092 ATTTGCTTTT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1096565 original size:24 final size:24
Alignment explanation
Indices: 1096535--1096594 Score: 111
Period size: 24 Copynumber: 2.5 Consensus size: 24
1096525 AATTCTACAG
1096535 GGTAAGATAATCATTAATCTTCCA
1 GGTAAGATAATCATTAATCTTCCA
1096559 GGTAAGATAATCATTAATCTTCCA
1 GGTAAGATAATCATTAATCTTCCA
*
1096583 GGTAAGACAATC
1 GGTAAGATAATC
1096595 TAATAACATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (24 bp):
GGTAAGATAATCATTAATCTTCCA
Done.