Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 133 of 325
Found at i:41553414 original size:8 final size:8
Alignment explanation
Indices: 41553384--41553431 Score: 50
Period size: 8 Copynumber: 6.2 Consensus size: 8
41553374 ATTTTATATT
41553384 TAATGATAA
1 TAAT-ATAA
41553393 TAATAT-A
1 TAATATAA
41553400 T--TATAA
1 TAATATAA
41553406 T-ATAGTAA
1 TAATA-TAA
41553414 TAATATAA
1 TAATATAA
41553422 TAATATAA
1 TAATATAA
41553430 TA
1 TA
41553432 TAATATATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
5 3 0.09
6 2 0.06
7 4 0.11
8 19 0.54
9 7 0.20
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (8 bp):
TAATATAA
Found at i:41556579 original size:2 final size:2
Alignment explanation
Indices: 41556572--41556596 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
41556562 CCTAACCTAT
41556572 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
41556597 TTATTTTACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41564737 original size:40 final size:40
Alignment explanation
Indices: 41564675--41564892 Score: 275
Period size: 40 Copynumber: 5.5 Consensus size: 40
41564665 AGACCAAGTA
* * * *
41564675 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
**
41564714 CCTTCGGGACTTAGCCCGGATATAGTAGTTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
41564754 CCTTCGGGACTTAGCCCGGGTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
41564794 CCTTCGAGACTTAGCCCGGA-ATTAGTAACTCGCA-ACAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACA-AATG
* *
41564834 CCTTCGGGACTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
41564874 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
41564893 TTATCATCCG
Statistics
Matches: 160, Mismatches: 14, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
39 15 0.09
40 144 0.90
41 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:41577757 original size:18 final size:18
Alignment explanation
Indices: 41577730--41577764 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
41577720 AAGTCTGTTC
41577730 TGACTCAGGCTCCTATTT
1 TGACTCAGGCTCCTATTT
*
41577748 TGACTTAGGCTCCTATT
1 TGACTCAGGCTCCTATT
41577765 CTGATACAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.26, G:0.17, T:0.40
Consensus pattern (18 bp):
TGACTCAGGCTCCTATTT
Found at i:41581925 original size:44 final size:44
Alignment explanation
Indices: 41581875--41581963 Score: 117
Period size: 44 Copynumber: 2.0 Consensus size: 44
41581865 AAGTAACAGA
*
41581875 AACAGTACGACAC-ACGAAGTGCCTCATCGACACAAAGTCGAAGT
1 AACAGTACGACACTA-GAAGTGCCTCATCAACACAAAGTCGAAGT
** * *
41581919 AACAGTACGACACTATTAGTGCCTCATCAACTCAAGGTCGAAGT
1 AACAGTACGACACTAGAAGTGCCTCATCAACACAAAGTCGAAGT
41581963 A
1 A
41581964 TCCCTGTACA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
44 38 0.97
45 1 0.03
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.18
Consensus pattern (44 bp):
AACAGTACGACACTAGAAGTGCCTCATCAACACAAAGTCGAAGT
Found at i:41582850 original size:5 final size:5
Alignment explanation
Indices: 41582848--41582890 Score: 72
Period size: 5 Copynumber: 9.0 Consensus size: 5
41582838 TGTTTTATAT
41582848 TATTA TATTA TATTA TATTA TATTA TATTA TATTA -A-TA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
41582891 ATTTCTTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 2 0.06
4 2 0.06
5 32 0.89
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TATTA
Found at i:41588952 original size:31 final size:31
Alignment explanation
Indices: 41588883--41588954 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
41588873 AGAGTTGCCA
*
41588883 AAATT-AAAACGATTTAAAACGTAATTGACC
1 AAATTAAAAATGATTTAAAACGTAATTGACC
* * *
41588913 AAAATAAAAATGATTTAAAACATTAA-TGACT
1 AAATTAAAAATGATTTAAAAC-GTAATTGACC
41588944 AAATTAAAAAT
1 AAATTAAAAAT
41588955 TTTTGTAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
30 4 0.11
31 28 0.80
32 3 0.09
ACGTcount: A:0.57, C:0.08, G:0.07, T:0.28
Consensus pattern (31 bp):
AAATTAAAAATGATTTAAAACGTAATTGACC
Found at i:41593566 original size:25 final size:25
Alignment explanation
Indices: 41593518--41593567 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
41593508 CAATTGAAAT
* *
41593518 AAAAATATAAAAAAATATACATTAG
1 AAAAATATAAAAAAATAGAAATTAG
41593543 AAAAATA-AATAAAAATAGAAATTAG
1 AAAAATATAA-AAAAATAGAAATTAG
41593568 TTAAAATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 2 0.09
25 20 0.91
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.22
Consensus pattern (25 bp):
AAAAATATAAAAAAATAGAAATTAG
Found at i:41593985 original size:18 final size:18
Alignment explanation
Indices: 41593962--41594011 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
41593952 TTACAACTTA
41593962 TTAAT-ATTTTTATATTTT
1 TTAATAATTTTTA-ATTTT
41593980 TTAATAATTTTTAATTTT
1 TTAATAATTTTTAATTTT
*
41593998 TCT-ATAAATTTTAA
1 T-TAATAATTTTTAA
41594012 AAGTTATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 21 0.72
19 8 0.28
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (18 bp):
TTAATAATTTTTAATTTT
Found at i:41593987 original size:38 final size:36
Alignment explanation
Indices: 41593891--41593990 Score: 96
Period size: 37 Copynumber: 2.6 Consensus size: 36
41593881 ATATTTTACA
*
41593891 ATTTTTAATTTTATTTAATGATTTTCACAATCTTTTAAT
1 ATTTTTAA-TTT-TTTAATAATTTT-ACAATCTTTTAAT
* *
41593930 -TTGTTAAATTTTTTGATAATCTTTACAA-CTTATTAAT
1 ATT-TTTAATTTTTTAATAAT-TTTACAATCTT-TTAAT
41593967 ATTTTTATATTTTTTAATAATTTT
1 ATTTTTA-ATTTTTTAATAATTTT
41593991 TAATTTTTCT
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
36 3 0.06
37 22 0.43
38 22 0.43
39 4 0.08
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.60
Consensus pattern (36 bp):
ATTTTTAATTTTTTAATAATTTTACAATCTTTTAAT
Found at i:41594009 original size:19 final size:19
Alignment explanation
Indices: 41593962--41593998 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
41593952 TTACAACTTA
41593962 TTAAT-ATTTTTATATTTT
1 TTAATAATTTTTATATTTT
41593980 TTAATAATTTTTA-ATTTT
1 TTAATAATTTTTATATTTT
41593998 T
1 T
41593999 CTATAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TTAATAATTTTTATATTTT
Found at i:41594671 original size:17 final size:17
Alignment explanation
Indices: 41594633--41594672 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
41594623 CTCGAATTCA
41594633 TAATAAATTAAAATCAT
1 TAATAAATTAAAATCAT
* *
41594650 AAATAAATTAAAATTAT
1 TAATAAATTAAAATCAT
41594667 TAATAA
1 TAATAA
41594673 CCCAGCCTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
TAATAAATTAAAATCAT
Found at i:41595201 original size:3 final size:3
Alignment explanation
Indices: 41595151--41595182 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
41595141 TATTGAAAAT
41595151 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
41595183 GAAACATCAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:41598143 original size:26 final size:27
Alignment explanation
Indices: 41598113--41598163 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
41598103 TAATAAATGG
* *
41598113 ATATGAAATGGAA-ATGGAATTGTGAA
1 ATATGAAATGAAATATGAAATTGTGAA
41598139 ATATGAAATGAAATATGAAATTGTG
1 ATATGAAATGAAATATGAAATTGTG
41598164 GAATGAGTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.47, C:0.00, G:0.24, T:0.29
Consensus pattern (27 bp):
ATATGAAATGAAATATGAAATTGTGAA
Found at i:41598152 original size:12 final size:12
Alignment explanation
Indices: 41598135--41598159 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41598125 AATGGAATTG
41598135 TGAAATATGAAA
1 TGAAATATGAAA
41598147 TGAAATATGAAA
1 TGAAATATGAAA
41598159 T
1 T
41598160 TGTGGAATGA
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:0.56, C:0.00, G:0.16, T:0.28
Consensus pattern (12 bp):
TGAAATATGAAA
Found at i:41604931 original size:12 final size:13
Alignment explanation
Indices: 41604895--41604932 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
41604885 AAATATTTGA
41604895 CTTGTTCTTAATT
1 CTTGTTCTTAATT
*
41604908 ATGTGTTCTTAATT
1 CT-TGTTCTTAATT
41604922 CTTG-TCTTAAT
1 CTTGTTCTTAAT
41604933 ATTCCAGGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 7 0.32
13 3 0.14
14 12 0.55
ACGTcount: A:0.18, C:0.13, G:0.11, T:0.58
Consensus pattern (13 bp):
CTTGTTCTTAATT
Found at i:41608423 original size:36 final size:36
Alignment explanation
Indices: 41608354--41608429 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 36
41608344 TGTTATCGGG
**
41608354 TGGACTAGCTCTTATAAGCATCTGGTATGTTTTGGA
1 TGGACTAGCTCTTATAAGCATCTGGTACATTTTGGA
* * * * *
41608390 TGGATTAGCTCTTATGAGCATCTTGTGCATTTTGGT
1 TGGACTAGCTCTTATAAGCATCTGGTACATTTTGGA
41608426 TGGA
1 TGGA
41608430 ATATCGATGT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.20, C:0.13, G:0.26, T:0.41
Consensus pattern (36 bp):
TGGACTAGCTCTTATAAGCATCTGGTACATTTTGGA
Found at i:41610768 original size:46 final size:46
Alignment explanation
Indices: 41610701--41610876 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
41610691 TATTTGGGCA
*
41610701 TCCGAACTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * *
41610747 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---G
* *
41610792 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* *
41610840 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
41610877 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 3 0.03
43 4 0.04
45 3 0.03
46 64 0.58
47 28 0.25
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:41610856 original size:93 final size:93
Alignment explanation
Indices: 41610697--41610868 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
41610687 AGGATATTTG
* *
41610697 GGCATCCGAACTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
41610762 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* * *
41610790 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
41610855 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
41610869 ACTTATGGGC
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:41613209 original size:46 final size:48
Alignment explanation
Indices: 41613104--41613225 Score: 149
Period size: 46 Copynumber: 2.5 Consensus size: 48
41613094 TGTCTTCGAC
** * *
41613104 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATATATCTAAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCC--ATATATATCTAAT
* *
41613154 ATGGGCTTACATGGCTCATTCCTGTCTCCAAAG-C-TATATATCTGAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCATATATATCTAAT
*
41613200 ATGGACTTACATGGCTCATTTCTGTC
1 ATGGACTTACATGGCTCATTCCTGTC
41613226 CTGTCCTGTC
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
46 35 0.55
49 1 0.02
50 28 0.44
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (48 bp):
ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCATATATATCTAAT
Found at i:41616473 original size:29 final size:29
Alignment explanation
Indices: 41616439--41616494 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
41616429 ATAGTATCGT
*
41616439 ATCTTGGGTTTC-TTATTCTGGGTTTCTCA
1 ATCTTGGATTTCTTTATTC-GGGTTTCTCA
*
41616468 ATCTTGGATTTCTTTATTCGGTTTTCT
1 ATCTTGGATTTCTTTATTCGGGTTTCT
41616495 TGTTATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.11, C:0.16, G:0.18, T:0.55
Consensus pattern (29 bp):
ATCTTGGATTTCTTTATTCGGGTTTCTCA
Found at i:41619281 original size:46 final size:46
Alignment explanation
Indices: 41619229--41619404 Score: 184
Period size: 46 Copynumber: 3.8 Consensus size: 46
41619219 TATTTGGGCA
*
41619229 TCCGAACTCGTTGAGTTGAGTCAGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* *
41619275 TCCGAACTCGTTGAGTTGAGTCCGAG-T---TTGTGAGATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GATGCGAAC---G
* *
41619320 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* *
41619368 -CACGAGCTCTTTGAGTTGAGTCCGAGTTCACTTATGG
1 TC-CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
41619405 GTGGGTTACA
Statistics
Matches: 110, Mismatches: 8, Indels: 24
0.77 0.06 0.17
Matches are distributed among these distances:
42 7 0.06
43 4 0.04
45 3 0.03
46 59 0.54
47 25 0.23
48 2 0.02
50 4 0.04
51 6 0.05
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:41619384 original size:93 final size:93
Alignment explanation
Indices: 41619225--41619395 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
41619215 AGGATATTTG
41619225 GGCATCCGAACTCGTTGAGTTGAGTCAGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCAGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
41619290 TTGAGTCCGAGTTTGTGAGATGTAACTA
66 TTGAGTCCGAGTTTGTGAGATGTAACTA
* * * * *
41619318 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG-CACGAGCTCTTTGA
1 GGCATCCGAACTCGTTGAGTTGAGTCAGAGTTCACTTATGGATGCGAACGTC-CGAACTCGTTGA
41619382 GTTGAGTCCGAGTT
65 GTTGAGTCCGAGTT
41619396 CACTTATGGG
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 1 0.01
93 71 0.99
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCAGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
TTGAGTCCGAGTTTGTGAGATGTAACTA
Found at i:41621381 original size:20 final size:20
Alignment explanation
Indices: 41621349--41621386 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
41621339 GCCATTTCAC
*
41621349 AATTATAAGGAATGAAATAA
1 AATTATAAGGAATAAAATAA
41621369 AATTA-AAGAGAATAAAAT
1 AATTATAAG-GAATAAAAT
41621387 TCAGAAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.63, C:0.00, G:0.13, T:0.24
Consensus pattern (20 bp):
AATTATAAGGAATAAAATAA
Found at i:41621646 original size:7 final size:7
Alignment explanation
Indices: 41621634--41621724 Score: 51
Period size: 7 Copynumber: 13.0 Consensus size: 7
41621624 AAAAGAATAT
41621634 AATTGAG
1 AATTGAG
41621641 AATTGAG
1 AATTGAG
*
41621648 GATTGA-
1 AATTGAG
41621654 AGATTGAG
1 A-ATTGAG
*
41621662 GATCT-AG
1 AAT-TGAG
* *
41621669 AAATAAG
1 AATTGAG
* *
41621676 AAATGAA
1 AATTGAG
41621683 AATTGAG
1 AATTGAG
*
41621690 GATTGAG
1 AATTGAG
*
41621697 GATTGAG
1 AATTGAG
*
41621704 TATTGAG
1 AATTGAG
*
41621711 TATTGAG
1 AATTGAG
*
41621718 TATTGAG
1 AATTGAG
41621725 TTGAAAAGAA
Statistics
Matches: 69, Mismatches: 11, Indels: 8
0.78 0.12 0.09
Matches are distributed among these distances:
6 1 0.01
7 67 0.97
8 1 0.01
ACGTcount: A:0.40, C:0.01, G:0.30, T:0.30
Consensus pattern (7 bp):
AATTGAG
Found at i:41621725 original size:7 final size:7
Alignment explanation
Indices: 41621684--41621725 Score: 66
Period size: 7 Copynumber: 6.0 Consensus size: 7
41621674 AGAAATGAAA
*
41621684 ATTGAGG
1 ATTGAGT
*
41621691 ATTGAGG
1 ATTGAGT
41621698 ATTGAGT
1 ATTGAGT
41621705 ATTGAGT
1 ATTGAGT
41621712 ATTGAGT
1 ATTGAGT
41621719 ATTGAGT
1 ATTGAGT
41621726 TGAAAAGAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.29, C:0.00, G:0.33, T:0.38
Consensus pattern (7 bp):
ATTGAGT
Found at i:41630927 original size:18 final size:17
Alignment explanation
Indices: 41630885--41630927 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
41630875 ATGGATTTGG
* *
41630885 GGGAAATTTAGGGATTA
1 GGGAAATGTAGGAATTA
41630902 GGGAAAATGTAGAGAATTA
1 GGG-AAATGTAG-GAATTA
41630921 GGGAAAT
1 GGGAAAT
41630928 CTATTTTGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 3 0.14
18 11 0.50
19 8 0.36
ACGTcount: A:0.42, C:0.00, G:0.35, T:0.23
Consensus pattern (17 bp):
GGGAAATGTAGGAATTA
Found at i:41631433 original size:36 final size:36
Alignment explanation
Indices: 41631393--41631474 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 36
41631383 TCTTAAATCC
* * * *
41631393 TAAACCCTAAACT-CATAACCCATATCCCTTAACCCT
1 TAAACCCTAAA-TACATAACACATAACCCCTAAACCT
* *
41631429 TAAACCATAAATACTTAACACATAACCCCTAAACCT
1 TAAACCCTAAATACATAACACATAACCCCTAAACCT
41631465 TAAACCCTAA
1 TAAACCCTAA
41631475 CACATAATCC
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
35 1 0.03
36 37 0.97
ACGTcount: A:0.43, C:0.34, G:0.00, T:0.23
Consensus pattern (36 bp):
TAAACCCTAAATACATAACACATAACCCCTAAACCT
Found at i:41631474 original size:14 final size:14
Alignment explanation
Indices: 41631351--41631510 Score: 51
Period size: 14 Copynumber: 11.3 Consensus size: 14
41631341 CTAATTAATC
41631351 TAAACCCTAAACCT
1 TAAACCCTAAACCT
* *
41631365 CT-AACCCTTACCCT
1 -TAAACCCTAAACCT
* *
41631379 TAAATCTTAAATCC-
1 TAAACCCTAAA-CCT
41631393 TAAACCCTAAA-CT
1 TAAACCCTAAACCT
* **
41631406 CATAACCCATATCCCT
1 TA-AACCC-TAAACCT
*
41631422 T-AACCCTTAAACCA
1 TAAACCC-TAAACCT
** * *
41631436 TAAATACTTAACACA
1 TAAACCCTAAAC-CT
*
41631451 TAACCCCTAAACCT
1 TAAACCCTAAACCT
*
41631465 TAAACCCT-AACACA
1 TAAACCCTAAAC-CT
* **
41631479 TAATCCCTAAACAA
1 TAAACCCTAAACCT
* *
41631493 TAATCCATAAACCT
1 TAAACCCTAAACCT
41631507 TAAA
1 TAAA
41631511 ATTTAATTCA
Statistics
Matches: 103, Mismatches: 32, Indels: 21
0.66 0.21 0.13
Matches are distributed among these distances:
12 1 0.01
13 5 0.05
14 74 0.72
15 21 0.20
16 2 0.02
ACGTcount: A:0.42, C:0.33, G:0.00, T:0.24
Consensus pattern (14 bp):
TAAACCCTAAACCT
Found at i:41631510 original size:21 final size:21
Alignment explanation
Indices: 41631458--41631532 Score: 55
Period size: 21 Copynumber: 3.6 Consensus size: 21
41631448 ACATAACCCC
**
41631458 TAAACCTTAAACCCTAA-CACA
1 TAAACCTTAAACAATAATC-CA
* *
41631479 TAATCCCTAAACAATAATCCA
1 TAAACCTTAAACAATAATCCA
* *
41631500 TAAACCTTAAA-ATTTAATTCA
1 TAAACCTTAAACA-ATAATCCA
*
41631521 TAAACCATAAAC
1 TAAACCTTAAAC
41631533 CCCTATCCCC
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
20 1 0.02
21 40 0.95
22 1 0.02
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.25
Consensus pattern (21 bp):
TAAACCTTAAACAATAATCCA
Found at i:41631542 original size:7 final size:7
Alignment explanation
Indices: 41631530--41631605 Score: 55
Period size: 7 Copynumber: 10.7 Consensus size: 7
41631520 ATAAACCATA
41631530 AACCCCT
1 AACCCCT
*
41631537 ATCCCCTT
1 AACCCC-T
*
41631545 AACGCCT
1 AACCCCT
41631552 AACCCCT
1 AACCCCT
*
41631559 ATCCCCTT
1 AACCCC-T
* *
41631567 AACACTT
1 AACCCCT
41631574 AACCCCT
1 AACCCCT
*
41631581 AATCCCT
1 AACCCCT
**
41631588 AACCATT
1 AACCCCT
41631595 AACCCC-
1 AACCCCT
41631601 AACCC
1 AACCC
41631606 TTAAACCACC
Statistics
Matches: 51, Mismatches: 16, Indels: 5
0.71 0.22 0.07
Matches are distributed among these distances:
6 5 0.10
7 37 0.73
8 9 0.18
ACGTcount: A:0.29, C:0.49, G:0.01, T:0.21
Consensus pattern (7 bp):
AACCCCT
Found at i:41631587 original size:22 final size:21
Alignment explanation
Indices: 41631530--41631600 Score: 83
Period size: 22 Copynumber: 3.3 Consensus size: 21
41631520 ATAAACCATA
*
41631530 AACCCCTATCCCCTTAACGCCT
1 AACCCCTATCCCCTTAAC-CTT
41631552 AACCCCTATCCCCTTAACACTT
1 AACCCCTATCCCCTTAAC-CTT
41631574 AACCCCTAAT-CCC-TAACCATT
1 AACCCCT-ATCCCCTTAACC-TT
41631595 AACCCC
1 AACCCC
41631601 AACCCTTAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
20 1 0.02
21 12 0.27
22 30 0.67
23 2 0.04
ACGTcount: A:0.28, C:0.48, G:0.01, T:0.23
Consensus pattern (21 bp):
AACCCCTATCCCCTTAACCTT
Found at i:41631600 original size:21 final size:22
Alignment explanation
Indices: 41631530--41631586 Score: 87
Period size: 22 Copynumber: 2.5 Consensus size: 22
41631520 ATAAACCATA
* *
41631530 AACCCCTATCCCCTTAACGCCT
1 AACCCCTATCCCCTTAACACTT
41631552 AACCCCTATCCCCTTAACACTT
1 AACCCCTATCCCCTTAACACTT
41631574 AACCCCTAATCCC
1 AACCCCT-ATCCC
41631587 TAACCATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 27 0.84
23 5 0.16
ACGTcount: A:0.26, C:0.49, G:0.02, T:0.23
Consensus pattern (22 bp):
AACCCCTATCCCCTTAACACTT
Found at i:41632485 original size:15 final size:15
Alignment explanation
Indices: 41632462--41632497 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
41632452 TAAACCACCT
41632462 TTAAA-CCATAATCC
1 TTAAACCCATAATCC
41632476 TTAAACCCATAATCC
1 TTAAACCCATAATCC
*
41632491 ATAAACC
1 TTAAACC
41632498 TTAAGATAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.25
Consensus pattern (15 bp):
TTAAACCCATAATCC
Found at i:41633121 original size:115 final size:115
Alignment explanation
Indices: 41632985--41633278 Score: 428
Period size: 115 Copynumber: 2.5 Consensus size: 115
41632975 CATTAGCGGT
* *
41632985 GTTTTTAAAAAAGCGCTGCTAAAGGTGTACTTATAGCGGCGTTTTTGAAAAGCGCCGCTAAAGCC
1 GTTTTTAAAAAAACGCCGCTAAAGGTGTACTTATAGCGGCGTTTTTGAAAAGCGCCGCTAAAGCC
41633050 ACTAAAAGCTTAATACAAAACGACGTCATTTTGCAAAATTCTTTTACGGC
66 ACTAAAAGCTTAATACAAAACGACGTCATTTTGCAAAATTCTTTTACGGC
* *
41633100 GTTTTTAAAAAAACGCCGCTAAAGGTGTACTTATAGCGGTGTTTTTGAAAAGCGCCACTAAAGCC
1 GTTTTTAAAAAAACGCCGCTAAAGGTGTACTTATAGCGGCGTTTTTGAAAAGCGCCGCTAAAGCC
* *
41633165 ACTAAAAGCTTAATACAAAACGACGTCATTTTGCAAAATTCTTTTGCTGC
66 ACTAAAAGCTTAATACAAAACGACGTCATTTTGCAAAATTCTTTTACGGC
** * * ** * * *
41633215 GTTTTTTGAAAAACGCCACTAAAGATCAAGCAT-TAGCGGCGTTTTTTAAAAAGCGACGCTAAAG
1 GTTTTTAAAAAAACGCCGCTAAAGGTGTA-CTTATAGCGGCG-TTTTTGAAAAGCGCCGCTAAAG
41633279 GTGTACTTAT
Statistics
Matches: 160, Mismatches: 17, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
115 139 0.87
116 21 0.13
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.29
Consensus pattern (115 bp):
GTTTTTAAAAAAACGCCGCTAAAGGTGTACTTATAGCGGCGTTTTTGAAAAGCGCCGCTAAAGCC
ACTAAAAGCTTAATACAAAACGACGTCATTTTGCAAAATTCTTTTACGGC
Found at i:41633144 original size:155 final size:154
Alignment explanation
Indices: 41632711--41633154 Score: 587
Period size: 155 Copynumber: 2.9 Consensus size: 154
41632701 CATTTCTTGT
*
41632711 GGCGTTTTTCAAAAAGCGCCGCTAAAGCCACTAAAAGCTCAATACAAAACGACGTCATTTTGCAA
1 GGCGTTTTT-GAAAAGCGCCGCTAAAGCCACTAAAAGCTCAATACAAAACGACGTCATTTTGCAA
* *
41632776 AATTCTTTTGCGGCGTTTTTTAAAAAGCACCGCTAAAGGTGTACTTATAGCGGTGTTTCTTAAAA
65 AATTCTTTTGCGGCGTTTTTTAAAAAACGCCGCTAAAGGTGTACTTATAGCGGTGTTT-TTAAAA
*
41632841 AAACGCCTCTAATACTCGATCTTTAGC
129 AAGCG-CTCTAATACTCGATCTTTAGC
* ** *
41632868 -GCGTTTTTGAAAAGCGCCGCTAAAGTCACTAAAAGCTCAATACAAAACGACGTTGTTTTGAAAA
1 GGCGTTTTTGAAAAGCGCCGCTAAAGCCACTAAAAGCTCAATACAAAACGACGTCATTTTGCAAA
* * * * * *
41632932 ATTATTTTGCGGCATTTTTTGAAAAACGCCACTAAAGAT-TA-TGCATTAGCGGTGTTTTTAAAA
66 ATTCTTTTGCGGCGTTTTTTAAAAAACGCCGCTAAAGGTGTACT-TA-TAGCGGTGTTTTTAAAA
*
41632995 AAGCGCTGCTAA-AGGT-G-TACTTATAGC
129 AAGCGCT-CTAATA-CTCGAT-CTT-TAGC
*
41633022 GGCGTTTTTGAAAAGCGCCGCTAAAGCCACTAAAAGCTTAATACAAAACGACGTCATTTTGCAAA
1 GGCGTTTTTGAAAAGCGCCGCTAAAGCCACTAAAAGCTCAATACAAAACGACGTCATTTTGCAAA
* * *
41633087 ATTCTTTTACGGCGTTTTTAAAAAAACGCCGCTAAAGGTGTACTTATAGCGGTGTTTTT-GAAAA
66 ATTCTTTTGCGGCGTTTTTTAAAAAACGCCGCTAAAGGTGTACTTATAGCGGTGTTTTTAAAAAA
41633151 GCGC
131 GCGC
41633155 CACTAAAGCC
Statistics
Matches: 249, Mismatches: 29, Indels: 21
0.83 0.10 0.07
Matches are distributed among these distances:
152 1 0.00
153 8 0.03
154 30 0.12
155 198 0.80
156 11 0.04
157 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (154 bp):
GGCGTTTTTGAAAAGCGCCGCTAAAGCCACTAAAAGCTCAATACAAAACGACGTCATTTTGCAAA
ATTCTTTTGCGGCGTTTTTTAAAAAACGCCGCTAAAGGTGTACTTATAGCGGTGTTTTTAAAAAA
GCGCTCTAATACTCGATCTTTAGC
Found at i:41633355 original size:39 final size:41
Alignment explanation
Indices: 41633288--41633370 Score: 100
Period size: 39 Copynumber: 2.1 Consensus size: 41
41633278 GGTGTACTTA
*
41633288 TAGCGGCGTTTCTTAAAAAAGTACCGCTAATACTCGA-TCTT
1 TAGCGGCGTTTCTTAAAAAAGCACCGCTAATACTC-ATTCTT
* * *
41633329 TAGCGGTGTTT-TT-AAAAAGCGCCGCTAATGCTCATTCTT
1 TAGCGGCGTTTCTTAAAAAAGCACCGCTAATACTCATTCTT
41633368 TAG
1 TAG
41633371 TGGCATTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
38 1 0.03
39 24 0.65
40 2 0.05
41 10 0.27
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (41 bp):
TAGCGGCGTTTCTTAAAAAAGCACCGCTAATACTCATTCTT
Found at i:41636891 original size:13 final size:13
Alignment explanation
Indices: 41636867--41636910 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
41636857 GAATGTGAGT
*
41636867 TAAAACAATTATA
1 TAAAAAAATTATA
*
41636880 TAACAAAATTATA
1 TAAAAAAATTATA
*
41636893 -AAAAAAATTACA
1 TAAAAAAATTATA
41636905 TAAAAA
1 TAAAAA
41636911 TTAAATATGG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (13 bp):
TAAAAAAATTATA
Found at i:41638352 original size:28 final size:26
Alignment explanation
Indices: 41638311--41638406 Score: 79
Period size: 28 Copynumber: 3.5 Consensus size: 26
41638301 TTTTATTAAC
41638311 TTTT-TAATTTTTATTA-TTTTAGAAAA
1 TTTTATAATTTTTATTACTTTTAG--AA
*
41638337 TTTTCATAATTTTTATAATATTTTTAGAA
1 TTTT-ATAATTTTTAT--TACTTTTAGAA
*
41638366 TTTTATAAATTTTTAATTACTTTTATAA
1 TTTTAT-AATTTTT-ATTACTTTTAGAA
*
41638394 ATTTATATATTTT
1 TTTTATA-ATTTT
41638407 AAATATTATT
Statistics
Matches: 59, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
26 4 0.07
27 1 0.02
28 31 0.53
29 13 0.22
30 4 0.07
31 6 0.10
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (26 bp):
TTTTATAATTTTTATTACTTTTAGAA
Found at i:41638359 original size:20 final size:18
Alignment explanation
Indices: 41638334--41638378 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
41638324 TTATTTTAGA
*
41638334 AAATTTTCATAATTTTTAT
1 AAATTTTCAGAA-TTTTAT
*
41638353 AATATTTTTAGAATTTTAT
1 AA-ATTTTCAGAATTTTAT
41638372 AAATTTT
1 AAATTTT
41638379 TAATTACTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 10 0.43
20 8 0.35
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (18 bp):
AAATTTTCAGAATTTTAT
Found at i:41638391 original size:20 final size:19
Alignment explanation
Indices: 41638316--41638397 Score: 71
Period size: 20 Copynumber: 4.3 Consensus size: 19
41638306 TTAACTTTTT
*
41638316 AATTTTT-ATTATTTTAGA
1 AATTTTTAATTATTTTATA
* * *
41638334 AAATTTTCATAATTTTTATA
1 AATTTTTAATTA-TTTTATA
41638354 ATATTTTTAGA--ATTTTATA
1 A-ATTTTTA-ATTATTTTATA
41638373 AATTTTTAATTACTTTTATA
1 AATTTTTAATTA-TTTTATA
41638393 AATTT
1 AATTT
41638398 ATATATTTTA
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
17 1 0.02
18 13 0.25
19 12 0.23
20 20 0.38
21 5 0.10
22 1 0.02
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (19 bp):
AATTTTTAATTATTTTATA
Found at i:41638412 original size:9 final size:10
Alignment explanation
Indices: 41638325--41638413 Score: 61
Period size: 9 Copynumber: 9.4 Consensus size: 10
41638315 TAATTTTTAT
*
41638325 TATTTTAGAA
1 TATTTTATAA
*
41638335 AATTTTCATAA
1 TATTTT-ATAA
41638346 T-TTTTATAA
1 TATTTTATAA
41638355 TATTTT-TAGA
1 TATTTTATA-A
41638365 -ATTTTATAA
1 TATTTTATAA
41638374 -ATTTT-TAA
1 TATTTTATAA
41638382 TTACTTTTATAA
1 -TA-TTTTATAA
41638394 -A-TTTAT-A
1 TATTTTATAA
41638401 TATTTTA-AA
1 TATTTTATAA
41638410 TATT
1 TATT
41638414 ATTTTTTTAT
Statistics
Matches: 65, Mismatches: 3, Indels: 23
0.71 0.03 0.25
Matches are distributed among these distances:
7 1 0.02
8 9 0.14
9 27 0.42
10 18 0.28
11 7 0.11
12 3 0.05
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (10 bp):
TATTTTATAA
Found at i:41639375 original size:19 final size:18
Alignment explanation
Indices: 41639310--41639380 Score: 78
Period size: 19 Copynumber: 4.0 Consensus size: 18
41639300 TTTTTAAAAA
41639310 TTATAAAAAA-TAT-ATT
1 TTATAAAAAATTATAATT
41639326 TTA-AAAAAATTTATAAATT
1 TTATAAAAAA-TTAT-AATT
41639345 TT-TAAAAAATTATACATT
1 TTATAAAAAATTATA-ATT
*
41639363 TTATAAAAAATTAAAATT
1 TTATAAAAAATTATAATT
41639381 AAAATTAAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
15 6 0.13
16 3 0.06
17 4 0.09
18 12 0.26
19 22 0.47
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (18 bp):
TTATAAAAAATTATAATT
Found at i:41639844 original size:20 final size:20
Alignment explanation
Indices: 41639819--41639864 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
41639809 AAATTTATTT
*
41639819 ATATTTAGTCATTTTATAAA
1 ATATTTAATCATTTTATAAA
** *
41639839 ATATTTAATTTTTTTATGAA
1 ATATTTAATCATTTTATAAA
41639859 ATATTT
1 ATATTT
41639865 TTTATAATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (20 bp):
ATATTTAATCATTTTATAAA
Found at i:41641524 original size:27 final size:27
Alignment explanation
Indices: 41641466--41641566 Score: 71
Period size: 27 Copynumber: 3.7 Consensus size: 27
41641456 CTGTCCCGGT
* *
41641466 GGACTATCCTATGTTTGCTGACCCAGC
1 GGACTATCCCATGTTTACTGACCCAGC
* *
41641493 AGACTATCCCATGTTTACTG-CCCCGTC
1 GGACTATCCCATGTTTACTGACCCAG-C
** * *
41641520 GGACTA-CCTTGTGTTTACTGTCCCAAC
1 GGACTATCC-CATGTTTACTGACCCAGC
* * *
41641547 AGACTACCCCGTGTTTACTG
1 GGACTATCCCATGTTTACTG
41641567 TTGCAGACTA
Statistics
Matches: 59, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
26 6 0.10
27 48 0.81
28 5 0.08
ACGTcount: A:0.19, C:0.32, G:0.19, T:0.31
Consensus pattern (27 bp):
GGACTATCCCATGTTTACTGACCCAGC
Found at i:41641567 original size:27 final size:27
Alignment explanation
Indices: 41641477--41641567 Score: 83
Period size: 27 Copynumber: 3.4 Consensus size: 27
41641467 GACTATCCTA
* * * * *
41641477 TGTTTGCTGACCCAGCAGACTATCCCA
1 TGTTTACTGTCCCAACAGACTACCCCG
* ** * **
41641504 TGTTTACTGCCCCGTCGGACTACCTTG
1 TGTTTACTGTCCCAACAGACTACCCCG
41641531 TGTTTACTGTCCCAACAGACTACCCCG
1 TGTTTACTGTCCCAACAGACTACCCCG
41641558 TGTTTACTGT
1 TGTTTACTGT
41641568 TGCAGACTAT
Statistics
Matches: 49, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.18, C:0.32, G:0.19, T:0.32
Consensus pattern (27 bp):
TGTTTACTGTCCCAACAGACTACCCCG
Found at i:41644940 original size:34 final size:34
Alignment explanation
Indices: 41644902--41644980 Score: 140
Period size: 34 Copynumber: 2.3 Consensus size: 34
41644892 ACCTTGAGAT
* *
41644902 AATATATATATCATACCAACACATCATGTGTATA
1 AATATATATATCATACCAACACATCATGTGCACA
41644936 AATATATATATCATACCAACACATCATGTGCACA
1 AATATATATATCATACCAACACATCATGTGCACA
41644970 AATATATATAT
1 AATATATATAT
41644981 GTACAAGTAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.46, C:0.18, G:0.05, T:0.32
Consensus pattern (34 bp):
AATATATATATCATACCAACACATCATGTGCACA
Found at i:41645978 original size:43 final size:42
Alignment explanation
Indices: 41645926--41646125 Score: 179
Period size: 43 Copynumber: 4.7 Consensus size: 42
41645916 CGTCCTAGAT
* * * *
41645926 GTGGTCTTACATGTAACCTCATATCAATGCCACTATCCCAGAC
1 GTGGCCTTACATGTAAACACATATCGATGCCAC-ATCCCAGAC
*
41645969 AG-GGCCTTAC-TCGTAAACACATATCGATGCCAACGTCCCAGAC
1 -GTGGCCTTACAT-GTAAACACATATCGATGCC-ACATCCCAGAC
* * * *
41646012 GTGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGAC
1 GTGGCCTTACATGTAAACACATATCGATGCC-ACATCCCAGAC
* * * * *
41646055 GTGGTCTTACACGTAATCACATATCGATTCCAACGTCCCAGAC
1 GTGGCCTTACATGTAAACACATATCGATGCC-ACATCCCAGAC
* * *
41646098 GTGGTCTTACACGTAATCACATATCGAT
1 GTGGCCTTACATGTAAACACATATCGAT
41646126 ATCACATATA
Statistics
Matches: 143, Mismatches: 9, Indels: 9
0.89 0.06 0.06
Matches are distributed among these distances:
42 2 0.01
43 138 0.97
44 3 0.02
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.25
Consensus pattern (42 bp):
GTGGCCTTACATGTAAACACATATCGATGCCACATCCCAGAC
Found at i:41646054 original size:86 final size:86
Alignment explanation
Indices: 41645909--41646125 Score: 303
Period size: 86 Copynumber: 2.5 Consensus size: 86
41645899 ATATCATACA
* * * * * *
41645909 ATGCCAACGTCCTAGATGTGGTCTTACATGTAACCTCATATCAATGCCACTATCCCAGACAG-GG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCGATGCCACTATCCCAGAC-GTGG
*
41645973 CCTTACTCGTAAACACATATCG
65 CCTTACACGTAAACACATATCG
*
41645995 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCGATGCCAAC-GTCCCAGACGTGG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCGATGCC-ACTATCCCAGACGTGG
* *
41646059 TCTTACACGTAATCACATATCG
65 CCTTACACGTAAACACATATCG
*
41646081 ATTCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCGAT
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCGAT
41646126 ATCACATATA
Statistics
Matches: 118, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
85 1 0.01
86 115 0.97
87 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (86 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCGATGCCACTATCCCAGACGTGGC
CTTACACGTAAACACATATCG
Found at i:41650402 original size:38 final size:38
Alignment explanation
Indices: 41650344--41650429 Score: 136
Period size: 38 Copynumber: 2.2 Consensus size: 38
41650334 TATCATTATG
* * *
41650344 TTTCAAATCCGCATATGATTTCTGTCGATCTGAAGCTGC
1 TTTCAAA-CTGCATAAGATTTCTGTCGATCTGAAGCTAC
41650383 TTTCAAACTGCATAAGATTTCTGTCGATCTGAAGCTAC
1 TTTCAAACTGCATAAGATTTCTGTCGATCTGAAGCTAC
41650421 TTTCAAACT
1 TTTCAAACT
41650430 ATCACAAATT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
38 37 0.84
39 7 0.16
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (38 bp):
TTTCAAACTGCATAAGATTTCTGTCGATCTGAAGCTAC
Found at i:41653810 original size:290 final size:290
Alignment explanation
Indices: 41653286--41653869 Score: 1143
Period size: 290 Copynumber: 2.0 Consensus size: 290
41653276 TACGTGAATT
41653286 CTAA-ATCGTGATATTGTAAAACGATACATGAGTGTTAGATGGATCTTTGATATTAAAATTTGTG
1 CTAATATCGTGATATTGTAAAACGATACATGAGTGTTAGATGGATCTTTGATATTAAAATTTGTG
*
41653350 AAATTGTAAGTTTGTGAATATTCGAATATGAAATGATAGTATGGCGTGAAATTGAATTATTCATT
66 AAATTGTAAGTTTATGAATATTCGAATATGAAATGATAGTATGGCGTGAAATTGAATTATTCATT
41653415 GGGAAATGATTAATGTAGATTCGGCCAAGACAAAGTGTATACATGATAGTATATGTGATATGTGA
131 GGGAAATGATTAATGTAGATTCGGCCAAGACAAAGTGTATACATGATAGTATATGTGATATGTGA
41653480 AGTATATTTGGATAATTGTGATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
196 AGTATATTTGGATAATTGTGATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
41653545 GAATGTGAAAGTGTATATATGTGATAACGC
261 GAATGTGAAAGTGTATATATGTGATAACGC
41653575 CTAATATCGTGATATTGTAAAACGATACATGAGTGTTAGATGGATCTTTGATATTAAAATTTGTG
1 CTAATATCGTGATATTGTAAAACGATACATGAGTGTTAGATGGATCTTTGATATTAAAATTTGTG
*
41653640 AAATTGTAAGTTTATGAGTATTCGAATATGAAATGATAGTATGGCGTGAAATTGAATTATTCATT
66 AAATTGTAAGTTTATGAATATTCGAATATGAAATGATAGTATGGCGTGAAATTGAATTATTCATT
41653705 GGGAAATGATTAATGTAGATTCGGCCAAGACAAAGTGTATACATGATAGTATATGTGATATGTGA
131 GGGAAATGATTAATGTAGATTCGGCCAAGACAAAGTGTATACATGATAGTATATGTGATATGTGA
41653770 AGTATATTTGGATAATTGTGATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
196 AGTATATTTGGATAATTGTGATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
41653835 GAATGTGAAAGTGTATATATGTGATAACGC
261 GAATGTGAAAGTGTATATATGTGATAACGC
41653865 CTAAT
1 CTAAT
41653870 GGCCGATGTG
Statistics
Matches: 292, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
289 4 0.01
290 288 0.99
ACGTcount: A:0.35, C:0.07, G:0.23, T:0.35
Consensus pattern (290 bp):
CTAATATCGTGATATTGTAAAACGATACATGAGTGTTAGATGGATCTTTGATATTAAAATTTGTG
AAATTGTAAGTTTATGAATATTCGAATATGAAATGATAGTATGGCGTGAAATTGAATTATTCATT
GGGAAATGATTAATGTAGATTCGGCCAAGACAAAGTGTATACATGATAGTATATGTGATATGTGA
AGTATATTTGGATAATTGTGATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
GAATGTGAAAGTGTATATATGTGATAACGC
Found at i:41653842 original size:47 final size:47
Alignment explanation
Indices: 41653790--41654334 Score: 883
Period size: 47 Copynumber: 11.6 Consensus size: 47
41653780 GATAATTGTG
* *
41653790 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
41653837 ATGTGAAAGTGTATATATGTGATAACGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
41653884 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
41653931 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
41653978 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
41654025 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGTCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
41654072 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
41654119 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
41654168 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
41654215 ATGTGAAAGTGTATATATGTGATGAGACCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * * * * *
41654262 ATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGG
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
41654309 ATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGAAAGTGTATATATGTGATAAG
41654335 TCCCGAAGGG
Statistics
Matches: 462, Mismatches: 34, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
47 417 0.90
49 45 0.10
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (47 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:41659193 original size:12 final size:12
Alignment explanation
Indices: 41659176--41659206 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
41659166 CTACTCAAAG
41659176 CATTCGCGACTA
1 CATTCGCGACTA
41659188 CATTCGCGACTA
1 CATTCGCGACTA
41659200 CATTCGC
1 CATTCGC
41659207 TTTCCCTAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.23, C:0.35, G:0.16, T:0.26
Consensus pattern (12 bp):
CATTCGCGACTA
Found at i:41660004 original size:5 final size:5
Alignment explanation
Indices: 41659994--41660028 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
41659984 TTGATTAAAA
41659994 TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT
41660029 ATAAAAGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:41661173 original size:12 final size:12
Alignment explanation
Indices: 41661153--41661183 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
41661143 GTGTGTCGAA
41661153 TACTGTTACCGT
1 TACTGTTACCGT
*
41661165 TATTGTTACCGT
1 TACTGTTACCGT
41661177 TACTGTT
1 TACTGTT
41661184 TCGGATTTGT
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:0.16, C:0.19, G:0.16, T:0.48
Consensus pattern (12 bp):
TACTGTTACCGT
Found at i:41669732 original size:47 final size:45
Alignment explanation
Indices: 41669573--41669935 Score: 260
Period size: 47 Copynumber: 7.8 Consensus size: 45
41669563 GGGATATATT
41669573 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGC--TCTCATATAA
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTATCTC-TATAA
* * * *
41669619 GCGTGCTGATGCATGTCCCGGACATGTCTTACACTAGCACAACTCT-T-A
1 GC---C-GATGCATGTCCCAGACATGTCTTACACTGGC-TATCTCTATAA
* * *
41669667 GCCAATGCGTGTCCCAGACACGTCTTACACTGGCTATCTCTATCAA
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTATCTCTAT-AA
*
41669713 GACCGATGCATGTCCCAGACATGTCTTACACTGGCACTCATCTCTGT--
1 G-CCGATGCATGTCCCAGACATGTCTTACACTGG--CT-ATCTCTATAA
* *
41669760 GCCGATGTCATGTCCCAGACATGTTCTTACACTGGCTATC-ATAGTATG
1 GCCGATG-CATGTCCCAGACATG-TCTTACACTGGCTATCTCTA-TA-A
* * ** * ** *
41669808 GCTGATGCATGTCCCAGACATGTCTTACACTAGCCCTCGTTTGGAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTATC-TCTATAA
*
41669854 GCCGATGCCATGCCCCAGACATGGTCTTACACTGGC--TCTC-ATAA
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTATCTCTATAA
*
41669898 TGTGGCCGAAGCATGTCCCAGACATGTCTTACACTGGC
1 ----GCCGATGCATGTCCCAGACATGTCTTACACTGGC
41669936 GCACAAATCA
Statistics
Matches: 256, Mismatches: 33, Indels: 56
0.74 0.10 0.16
Matches are distributed among these distances:
43 5 0.02
44 29 0.11
45 6 0.02
46 46 0.18
47 87 0.34
48 51 0.20
49 17 0.07
50 12 0.05
51 3 0.01
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.27
Consensus pattern (45 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGCTATCTCTATAA
Found at i:41669819 original size:94 final size:94
Alignment explanation
Indices: 41669572--41669932 Score: 391
Period size: 94 Copynumber: 3.9 Consensus size: 94
41669562 TGGGATATAT
* * *
41669572 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATAAGCGTGCTGATGCATGTCC
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATATAA-TG-GCCGATGCATGTCC
* *
41669637 CGGACATGTCTTACACTAGCA--CAACTCT-
64 CAGACATGTCTTACACTAGCACTCATCTCTG
* * * * *
41669665 TAGCCAATG-CGTGTCCCAGACA-CGTCTTACACTGGCTATCTCTATCAA-GACCGATGCATGTC
1 T-GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATC-ATAT-AATGGCCGATGCATGTC
*
41669727 CCAGACATGTCTTACACTGGCACTCATCTCTG
63 CCAGACATGTCTTACACTAGCACTCATCTCTG
* * *
41669759 TGCCGATGTCATGTCCCAGACATGTTCTTACACTGGCTATCATAGT-ATGGCTGATGCATGTCCC
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATA-TAATGGCCGATGCATGTCCC
* *
41669823 AGACATGTCTTACACTAGCCCTCGT-T-TGG
65 AGACATGTCTTACACTAGCACTCATCTCT-G
* * * *
41669852 ATGCCGATGCCATGCCCCAGACATGGTCTTACACTGGCTCTCATA-ATGTGGCCGAAGCATGTCC
1 -TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATATA-ATGGCCGATGCATGTCC
41669916 CAGACATGTCTTACACT
64 CAGACATGTCTTACACT
41669933 GGCGCACAAA
Statistics
Matches: 227, Mismatches: 27, Indels: 27
0.81 0.10 0.10
Matches are distributed among these distances:
91 31 0.14
92 18 0.08
93 31 0.14
94 130 0.57
95 17 0.07
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.27
Consensus pattern (94 bp):
TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATATAATGGCCGATGCATGTCCCA
GACATGTCTTACACTAGCACTCATCTCTG
Found at i:41669837 original size:141 final size:137
Alignment explanation
Indices: 41669573--41669935 Score: 378
Period size: 141 Copynumber: 2.6 Consensus size: 137
41669563 GGGATATATT
*
41669573 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATAAGC-GTGCTGATGCATGTCC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCAT-T---CTGTGCCGATGCATGTCC
* * * * *
41669637 CGGACATGTCTTACACTAGCACAACTCTTAGCCAATGCGTGTCCCAGACACGTCTTACACTGGCT
62 CAGACATGTCTTACACTGGCACAACTCATAGCCAATGCATGTCCCAGACACGTCTTACACTAGC-
*
41669702 ATCTC-TAT-CAA
126 -CCTCGTATGCAA
*
41669713 GACCGATG-CATGTCCCAGACAT-GTCTTACACTGGCACTCATCTCTGTGCCGATGTCATGTCCC
1 G-CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCAT-TCTGTGCCGATG-CATGTCCC
* * ** *
41669776 AGACATGTTCTTACACTGGCTATCATAGT-ATGGCTGATGCATGTCCCAGACATGTCTTACACTA
63 AGACATG-TCTTACACTGGC-A-CA-ACTCATAGCCAATGCATGTCCCAGACACGTCTTACACTA
* * *
41669840 GCCCTCGTTTGGAT
124 GCCCTCGTATGCAA
* ** *
41669854 GCCGATGCCATGCCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGAAGCATGTCCCAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATTCTGT-GCCGATGCATGTCCCAG
41669919 ACATGTCTTACACTGGC
65 ACATGTCTTACACTGGC
41669936 GCACAAATCA
Statistics
Matches: 189, Mismatches: 22, Indels: 24
0.80 0.09 0.10
Matches are distributed among these distances:
136 1 0.01
137 8 0.04
138 14 0.07
139 33 0.17
140 36 0.19
141 71 0.38
142 26 0.14
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.27
Consensus pattern (137 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATTCTGTGCCGATGCATGTCCCAGA
CATGTCTTACACTGGCACAACTCATAGCCAATGCATGTCCCAGACACGTCTTACACTAGCCCTCG
TATGCAA
Found at i:41673335 original size:25 final size:25
Alignment explanation
Indices: 41673289--41673339 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
41673279 ATTATGGCTC
*
41673289 CAAACACAACATATACTATATATACT
1 CAAACACAACATATAATATATA-ACT
41673315 CAAAC-CAACATTATAAT-TATAACT
1 CAAACACAACA-TATAATATATAACT
41673339 C
1 C
41673340 CATTACAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 4 0.17
25 9 0.39
26 10 0.43
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (25 bp):
CAAACACAACATATAATATATAACT
Found at i:41689650 original size:29 final size:30
Alignment explanation
Indices: 41689586--41689667 Score: 85
Period size: 31 Copynumber: 2.7 Consensus size: 30
41689576 AATATCAAAA
*
41689586 TTATATATAAATTTTGATTTAATGTGTAATG
1 TTATATATGAATTTTGATTT-ATGTGTAATG
* * * *
41689617 CTATACATGAATTTTGATTT-TGTGTTATT
1 TTATATATGAATTTTGATTTATGTGTAATG
*
41689646 TTATATATGAAAATTTGATTTA
1 TTATATATG-AATTTTGATTTA
41689668 ATTTAATTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
29 14 0.34
30 10 0.24
31 17 0.41
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.52
Consensus pattern (30 bp):
TTATATATGAATTTTGATTTATGTGTAATG
Found at i:41694408 original size:22 final size:23
Alignment explanation
Indices: 41694383--41694428 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
41694373 CAACCAAACC
41694383 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
41694405 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
41694428 A
1 A
41694429 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:41694434 original size:23 final size:23
Alignment explanation
Indices: 41694390--41694434 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
41694380 ACCAATTCAA
*
41694390 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
41694413 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
41694435 CACATACCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:41700787 original size:22 final size:22
Alignment explanation
Indices: 41700759--41700802 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
41700749 AAATAAAAAG
41700759 CCATGTCCATGTTTTTCATTCT
1 CCATGTCCATGTTTTTCATTCT
41700781 CCATGTCCATGTTTTTCATTCT
1 CCATGTCCATGTTTTTCATTCT
41700803 TTCTTGCACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.14, C:0.27, G:0.09, T:0.50
Consensus pattern (22 bp):
CCATGTCCATGTTTTTCATTCT
Found at i:41713320 original size:22 final size:23
Alignment explanation
Indices: 41713295--41713340 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
41713285 CAACCAAACC
41713295 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
41713317 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
41713340 A
1 A
41713341 CGTCATCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:41713346 original size:23 final size:22
Alignment explanation
Indices: 41713302--41713351 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
41713292 ACCAATTCAA
*
41713302 CATATTTTCAAGATAAATTCAT
1 CATATTTTCAAGATAAAGTCAT
*
41713324 GCATATTTAT-AAGATAACGTCAT
1 -CATATTT-TCAAGATAAAGTCAT
41713347 CATAT
1 CATAT
41713352 ACCCAAAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 5 0.21
23 18 0.75
24 1 0.04
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (22 bp):
CATATTTTCAAGATAAAGTCAT
Found at i:41716437 original size:20 final size:20
Alignment explanation
Indices: 41716412--41716455 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
41716402 AACATACATC
*
41716412 CTCTATTTTGTTCTGTTCTG
1 CTCTATTTTATTCTGTTCTG
*
41716432 CTCTATTTTATTTTGTTCTG
1 CTCTATTTTATTCTGTTCTG
41716452 CTCT
1 CTCT
41716456 GTTCAGTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.07, C:0.20, G:0.11, T:0.61
Consensus pattern (20 bp):
CTCTATTTTATTCTGTTCTG
Found at i:41716509 original size:20 final size:20
Alignment explanation
Indices: 41716458--41716509 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
41716448 TCTGCTCTGT
41716458 TCAGTTCAGTTCAACACTGC
1 TCAGTTCAGTTCAACACTGC
* *
41716478 TCTA-TTCTGTTCATTC-CTGC
1 TC-AGTTCAGTTCA-ACACTGC
41716498 TCAGTTCAGTTC
1 TCAGTTCAGTTC
41716510 TGTTATGTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
19 1 0.04
20 23 0.88
21 2 0.08
ACGTcount: A:0.17, C:0.29, G:0.13, T:0.40
Consensus pattern (20 bp):
TCAGTTCAGTTCAACACTGC
Found at i:41719986 original size:49 final size:49
Alignment explanation
Indices: 41719929--41720111 Score: 258
Period size: 49 Copynumber: 3.7 Consensus size: 49
41719919 CTGGTACCTA
*
41719929 TAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCCGATACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCCGGTACACG
* ** * * *
41719978 TAGTAGCCTGCACTTAGTACTACACACGTGATAGAAGTTATCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACATGTGA-CCAA-TTATCCGGTACACG
*
41720029 TAGTAGCCTGCACTTAGTACTACACATGTGACCAATAATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCCGGTACACG
* *
41720078 TAGTAGCCTACACTTAGTACTACACAGGTGACCA
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCA
41720112 CACAATAGAT
Statistics
Matches: 116, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
49 72 0.62
50 4 0.03
51 40 0.34
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCCGGTACACG
Found at i:41720056 original size:100 final size:100
Alignment explanation
Indices: 41719928--41720108 Score: 326
Period size: 100 Copynumber: 1.8 Consensus size: 100
41719918 TCTGGTACCT
* *
41719928 ATAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCCGATACACGTAGTAGCCTGCACTT
1 ATAGTAGCCTGCACTTAGTACTACACATGTGACCAATAATCCGATACACGTAGTAGCCTACACTT
41719993 AGTACTACACACGTGATAGAAGTTATCGGGTACGC
66 AGTACTACACACGTGATAGAAGTTATCGGGTACGC
*
41720028 ATAGTAGCCTGCACTTAGTACTACACATGTGACCAATAATCCGGTACACGTAGTAGCCTACACTT
1 ATAGTAGCCTGCACTTAGTACTACACATGTGACCAATAATCCGATACACGTAGTAGCCTACACTT
*
41720093 AGTACTACACAGGTGA
66 AGTACTACACACGTGA
41720109 CCACACAATA
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
100 77 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.25
Consensus pattern (100 bp):
ATAGTAGCCTGCACTTAGTACTACACATGTGACCAATAATCCGATACACGTAGTAGCCTACACTT
AGTACTACACACGTGATAGAAGTTATCGGGTACGC
Found at i:41722928 original size:22 final size:22
Alignment explanation
Indices: 41722883--41722926 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
41722873 AGATTAAGCT
*
41722883 ATCCCGATCTTAAAAAGATAAA
1 ATCCCGATCTTAAAAAAATAAA
*
41722905 ATCCTGATC-TAAAAAAATAAA
1 ATCCCGATCTTAAAAAAATAAA
41722926 A
1 A
41722927 ATTACTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.55, C:0.16, G:0.07, T:0.23
Consensus pattern (22 bp):
ATCCCGATCTTAAAAAAATAAA
Found at i:41726053 original size:33 final size:34
Alignment explanation
Indices: 41726016--41726079 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
41726006 CTTAAAGTTT
*
41726016 TAGTATGTGAA-CCCCATATTATATAGTATGACG
1 TAGTATGCGAACCCCCATATTATATAGTATGACG
*
41726049 TAGTATGCGAACCCCCATGTTATATAGTATG
1 TAGTATGCGAACCCCCATATTATATAGTATG
41726080 TGATTTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 10 0.36
34 18 0.64
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (34 bp):
TAGTATGCGAACCCCCATATTATATAGTATGACG
Found at i:41726107 original size:15 final size:15
Alignment explanation
Indices: 41726087--41726149 Score: 65
Period size: 15 Copynumber: 4.2 Consensus size: 15
41726077 ATGTGATTTA
41726087 ATATGTGCGAACCCT
1 ATATGTGCGAACCCT
*
41726102 ATATGTGCGAACCTT
1 ATATGTGCGAACCCT
** *
41726117 GCATGTGC-AGATCCT
1 ATATGTGCGA-ACCCT
*
41726132 ATATGTGCGAACCTT
1 ATATGTGCGAACCCT
41726147 ATA
1 ATA
41726150 GATGTGAACT
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
14 1 0.03
15 35 0.95
16 1 0.03
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (15 bp):
ATATGTGCGAACCCT
Found at i:41726124 original size:30 final size:30
Alignment explanation
Indices: 41726089--41726146 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
41726079 GTGATTTAAT
41726089 ATGTGC-GAACCCTATATGTGCGAACCTTGC
1 ATGTGCAG-ACCCTATATGTGCGAACCTTGC
*
41726119 ATGTGCAGATCCTATATGTGCGAACCTT
1 ATGTGCAGACCCTATATGTGCGAACCTT
41726147 ATAGATGTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.29
Consensus pattern (30 bp):
ATGTGCAGACCCTATATGTGCGAACCTTGC
Found at i:41726211 original size:13 final size:14
Alignment explanation
Indices: 41726087--41726211 Score: 60
Period size: 15 Copynumber: 8.5 Consensus size: 14
41726077 ATGTGATTTA
*
41726087 ATATGTGCGAACCCT
1 ATATGTGC-AACCTT
41726102 ATATGTGCGAACCTT
1 ATATGTGC-AACCTT
**
41726117 GCATGTGCAGATCC-T
1 ATATGTGCA-A-CCTT
41726132 ATATGTGCGAACCTT
1 ATATGTGC-AACCTT
*
41726147 ATAGATGTG-AACTCTAG
1 AT--ATGTGCAAC-CT-T
* *
41726164 ATACGT-AAACCTT
1 ATATGTGCAACCTT
*
41726177 AGATGTGCAACC-T
1 ATATGTGCAACCTT
*
41726190 ATATGTGTGAACCTT
1 ATATGTG-CAACCTT
41726205 ATATGTG
1 ATATGTG
41726212 TGAACGCTAC
Statistics
Matches: 85, Mismatches: 13, Indels: 24
0.70 0.11 0.20
Matches are distributed among these distances:
13 11 0.13
14 13 0.15
15 49 0.58
16 5 0.06
17 7 0.08
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (14 bp):
ATATGTGCAACCTT
Found at i:41727841 original size:43 final size:43
Alignment explanation
Indices: 41727793--41727964 Score: 174
Period size: 43 Copynumber: 4.0 Consensus size: 43
41727783 GTTATCGAGA
*
41727793 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
1 TGTGATTACATGTAAGACCATGTCTAGGACATTGGCATTGTAT
* * *
41727836 TGTGATTACGTGTAAGACCATGT-TTGGAACATTGGC-TTCATTAT
1 TGTGATTACATGTAAGACCATGTCTAGG-ACATTGGCATT--GTAT
* * * *
41727880 T-TGATTTCATGTAAGACCCTGTCTAGGACAGTGGCATCG-AT
1 TGTGATTACATGTAAGACCATGTCTAGGACATTGGCATTGTAT
* * *
41727921 ATGTGATAACATGTAAGACCATATCTAGGATA-TGGCATTGTAT
1 -TGTGATTACATGTAAGACCATGTCTAGGACATTGGCATTGTAT
41727964 T
1 T
41727965 AGATATATGT
Statistics
Matches: 105, Mismatches: 16, Indels: 17
0.76 0.12 0.12
Matches are distributed among these distances:
41 2 0.02
42 14 0.13
43 81 0.77
44 8 0.08
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (43 bp):
TGTGATTACATGTAAGACCATGTCTAGGACATTGGCATTGTAT
Found at i:41736996 original size:26 final size:27
Alignment explanation
Indices: 41736932--41737003 Score: 85
Period size: 26 Copynumber: 2.7 Consensus size: 27
41736922 TTAGGGTGAG
*
41736932 AAATTACTATTTTACCCCTAAGTATGA
1 AAATTACTATTATACCCCTAAGTATGA
* *
41736959 AAATTACCATTATACCCCT-AG-GTGCA
1 AAATTACTATTATACCCCTAAGTATG-A
*
41736985 AAATGACTATTATACCCCT
1 AAATTACTATTATACCCCT
41737004 TGGGTTAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
25 2 0.05
26 20 0.51
27 17 0.44
ACGTcount: A:0.36, C:0.24, G:0.08, T:0.32
Consensus pattern (27 bp):
AAATTACTATTATACCCCTAAGTATGA
Found at i:41737138 original size:27 final size:27
Alignment explanation
Indices: 41737108--41737248 Score: 196
Period size: 27 Copynumber: 5.3 Consensus size: 27
41737098 TGGAGGAAGC
*
41737108 GTTCTGGTGGCTATGCCATAAATATCT
1 GTTCTGGTGGCTATGCCACAAATATCT
*
41737135 GTTCTGGGGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTATGCCACAAATATCT
41737162 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTATGCCACAAATATCT
*
41737189 GTTCTGGTGGCTCTGCCAC-AATATCT
1 GTTCTGGTGGCTATGCCACAAATATCT
* * * *
41737215 GTATCTGGTGACTCTGTCAC-ATTATCT
1 GT-TCTGGTGGCTATGCCACAAATATCT
41737242 GTTCTGG
1 GTTCTGG
41737249 CAGCTCTGCT
Statistics
Matches: 106, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
26 14 0.13
27 92 0.87
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.35
Consensus pattern (27 bp):
GTTCTGGTGGCTATGCCACAAATATCT
Found at i:41738600 original size:49 final size:47
Alignment explanation
Indices: 41738463--41738637 Score: 154
Period size: 49 Copynumber: 3.6 Consensus size: 47
41738453 AGATGCCGAC
* * *
41738463 GCCATGTCCCAGACATGGTCTTATACTGGCTAGCAC-ATCAAAGTCGAT
1 GCCATGTCCCAGACA-GGTCTTACACTGGCTATCACTATCGAA-TCGAT
* * * * * *
41738511 GTCATGTCCCACACAGGTCTTACACTGACTTTCAAATATCGAATCCAAT
1 GCCATGTCCCAGACAGGTCTTACACTGGCTATC-ACTATCGAAT-CGAT
* * * * *
41738560 CCCATGTCCCAGACAGGTCTTATACTGGCTCTCATCTATCGATGTTGAT
1 GCCATGTCCCAGACAGGTCTTACACTGGCTATCA-CTATCGA-ATCGAT
*
41738609 GCCATGTCCCAGACATGTCTTACACTGGC
1 GCCATGTCCCAGACAGGTCTTACACTGGC
41738638 ACGCAACAAG
Statistics
Matches: 100, Mismatches: 22, Indels: 9
0.76 0.17 0.07
Matches are distributed among these distances:
47 14 0.14
48 16 0.16
49 69 0.69
50 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (47 bp):
GCCATGTCCCAGACAGGTCTTACACTGGCTATCACTATCGAATCGAT
Found at i:41740467 original size:22 final size:21
Alignment explanation
Indices: 41740441--41740483 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
41740431 TTACTGTTAT
41740441 TGATTGTTTGATACTGAATAAC
1 TGATTG-TTGATACTGAATAAC
* *
41740463 TGATTGTTGTTATTGAATAAC
1 TGATTGTTGATACTGAATAAC
41740484 AATAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.30, C:0.07, G:0.19, T:0.44
Consensus pattern (21 bp):
TGATTGTTGATACTGAATAAC
Found at i:41747647 original size:21 final size:19
Alignment explanation
Indices: 41747618--41747665 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
41747608 ATAAACCGAA
*
41747618 TTTAATATTTAAATTGTTGTT
1 TTTATTATTTAAA-TG-TGTT
*
41747639 TTTATTA-TTATATGTGTT
1 TTTATTATTTAAATGTGTT
41747657 TTTATTATT
1 TTTATTATT
41747666 ATATATGTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 11 0.46
19 3 0.12
20 4 0.17
21 6 0.25
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (19 bp):
TTTATTATTTAAATGTGTT
Found at i:41747666 original size:21 final size:20
Alignment explanation
Indices: 41747632--41747673 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
41747622 ATATTTAAAT
41747632 TGTTGTTTTTATTATTATATG
1 TGTTGTTTTTATTA-TATATG
41747653 TGTT-TTTATTATTATATATG
1 TGTTGTTT-TTATTATATATG
41747673 T
1 T
41747674 ATGGAAAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.21, C:0.00, G:0.12, T:0.67
Consensus pattern (20 bp):
TGTTGTTTTTATTATATATG
Found at i:41747673 original size:20 final size:18
Alignment explanation
Indices: 41747635--41747669 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
41747625 TTTAAATTGT
41747635 TGTTTTTATTATTATATG
1 TGTTTTTATTATTATATG
41747653 TGTTTTTATTATTATAT
1 TGTTTTTATTATTATAT
41747670 ATGTATGGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.69
Consensus pattern (18 bp):
TGTTTTTATTATTATATG
Found at i:41755184 original size:29 final size:30
Alignment explanation
Indices: 41755127--41755289 Score: 106
Period size: 30 Copynumber: 5.4 Consensus size: 30
41755117 AGCCAGAGCT
*
41755127 ATCCCTTTTCATAATTTTGATAGTCGTCACC
1 ATCCCTTTTCAT-ATGTTGATAGTCGTCACC
*
41755158 ATCCCTTTTCAT-TGTTGATGGTCGTCACC
1 ATCCCTTTTCATATGTTGATAGTCGTCACC
* * * *
41755187 ATCCCTTTACATAAT-TTGATAGCCG-AAGCT
1 ATCCCTTTTCAT-ATGTTGATAGTCGTCA-CC
***
41755217 ATCCCTTTTCA-A-GATTAGATAG-CCAAAGCC
1 ATCCCTTTTCATATG-TT-GATAGTCGTCA-CC
* * *
41755247 ATCTCTTTTCATA-GTTCGATGGTCATCACC
1 ATCCCTTTTCATATGTT-GATAGTCGTCACC
41755277 ATCCCTTTTCATA
1 ATCCCTTTTCATA
41755290 ATCGATAGTC
Statistics
Matches: 106, Mismatches: 17, Indels: 19
0.75 0.12 0.13
Matches are distributed among these distances:
28 1 0.01
29 30 0.28
30 58 0.55
31 17 0.16
ACGTcount: A:0.24, C:0.26, G:0.12, T:0.37
Consensus pattern (30 bp):
ATCCCTTTTCATATGTTGATAGTCGTCACC
Found at i:41755308 original size:89 final size:88
Alignment explanation
Indices: 41755093--41755346 Score: 266
Period size: 90 Copynumber: 2.9 Consensus size: 88
41755083 TGATGGTTGG
* * * ***
41755093 CACCA-CCCTTTTCCATAATTCGATAGCC-AGAGCTATCCCTTTTCATAATTTTGATAGTCGTCA
1 CACCATCCC-TTTACATAATTCGATAGCCGA-AGCTATCCCTTTTCGT-A-TTAGATAG-CCAAA
* * *
41755156 -CCATCCCTTTTCATTGTTGATGGTCGT
61 GCCATCACTTTTCATAGTTGATGGTCAT
*
41755183 CACCATCCCTTTACATAATTTGATAGCCGAAGCTATCCCTTTTCAAG-ATTAGATAGCCAAAGCC
1 CACCATCCCTTTACATAATTCGATAGCCGAAGCTATCCCTTTTC--GTATTAGATAGCCAAAGCC
*
41755247 ATCTCTTTTCATAGTTCGATGGTCAT
64 ATCACTTTTCATAGTT-GATGGTCAT
* * * *
41755273 CACCATCCCTTTTCATAA-TCGATAGTCGAAGCTATCCCTTTTCGTATTCGATAGCCAAAGCTAT
1 CACCATCCCTTTACATAATTCGATAGCCGAAGCTATCCCTTTTCGTATTAGATAGCCAAAGCCAT
41755337 CACTTTTCAT
66 CACTTTTCAT
41755347 TTGTTAATGA
Statistics
Matches: 141, Mismatches: 16, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
87 1 0.01
88 28 0.20
89 46 0.33
90 62 0.44
91 4 0.03
ACGTcount: A:0.25, C:0.27, G:0.13, T:0.35
Consensus pattern (88 bp):
CACCATCCCTTTACATAATTCGATAGCCGAAGCTATCCCTTTTCGTATTAGATAGCCAAAGCCAT
CACTTTTCATAGTTGATGGTCAT
Found at i:41755309 original size:29 final size:30
Alignment explanation
Indices: 41755098--41755346 Score: 147
Period size: 29 Copynumber: 8.3 Consensus size: 30
41755088 GTTGGCACCA
* *
41755098 CCCTTTTCCATAATTCGATAG-CCAGAGCTAT
1 CCCTTTT-CATAATTCGATAGTCGA-AGCCAT
* *
41755129 CCCTTTTCATAATTTTGATAGTCGTCA-CCAT
1 CCCTTTTCATAA-TTCGATAGTCG-AAGCCAT
** * *
41755160 CCCTTTTCATTGTT-GATGGTCGTCA-CCAT
1 CCCTTTTCATAATTCGATAGTCG-AAGCCAT
* * * *
41755189 CCCTTTACATAATTTGATAGCCGAAGCTAT
1 CCCTTTTCATAATTCGATAGTCGAAGCCAT
* * *
41755219 CCCTTTTCA-AGATTAGATAGCCAAAGCCAT
1 CCCTTTTCATA-ATTCGATAGTCGAAGCCAT
* * *
41755249 CTCTTTTCATAGTTCGATGGTC-ATCA-CCAT
1 CCCTTTTCATAATTCGATAGTCGA--AGCCAT
*
41755279 CCCTTTTCATAA-TCGATAGTCGAAGCTAT
1 CCCTTTTCATAATTCGATAGTCGAAGCCAT
* * * *
41755308 CCCTTTTCGT-ATTCGATAGCCAAAGCTAT
1 CCCTTTTCATAATTCGATAGTCGAAGCCAT
*
41755337 CACTTTTCAT
1 CCCTTTTCAT
41755347 TTGTTAATGA
Statistics
Matches: 174, Mismatches: 32, Indels: 26
0.75 0.14 0.11
Matches are distributed among these distances:
28 2 0.01
29 71 0.41
30 70 0.40
31 29 0.17
32 2 0.01
ACGTcount: A:0.24, C:0.27, G:0.13, T:0.36
Consensus pattern (30 bp):
CCCTTTTCATAATTCGATAGTCGAAGCCAT
Found at i:41757417 original size:18 final size:18
Alignment explanation
Indices: 41757380--41757417 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
41757370 TGGCATGTGA
*
41757380 AATGGAAATGAGATAGTG
1 AATGGAAATGAAATAGTG
41757398 AATGGAAAATGAAATA-TG
1 AATGG-AAATGAAATAGTG
41757416 AA
1 AA
41757418 ATAGGTTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.53, C:0.00, G:0.26, T:0.21
Consensus pattern (18 bp):
AATGGAAATGAAATAGTG
Found at i:41776654 original size:32 final size:30
Alignment explanation
Indices: 41776577--41776655 Score: 79
Period size: 30 Copynumber: 2.6 Consensus size: 30
41776567 CGTCACCATT
* * * **
41776577 CCTTTACATAGTTTGATAGTCGAAGTTATC
1 CCTTTTCATAGTTCGATAGCCGAAGACATC
41776607 CCTTTTCAT-GATTCGATAGCCGAAGACATCC
1 CCTTTTCATAG-TTCGATAGCCGAAGACAT-C
41776638 ACCTTTTCATAGTTCGAT
1 -CCTTTTCATAGTTCGAT
41776656 GGTCATCACC
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
29 1 0.03
30 22 0.55
31 1 0.03
32 15 0.38
33 1 0.03
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (30 bp):
CCTTTTCATAGTTCGATAGCCGAAGACATC
Found at i:41776686 original size:29 final size:29
Alignment explanation
Indices: 41776639--41776709 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
41776629 AAGACATCCA
* *
41776639 CCTTTTCATAGTTCGATGGTCATCACCATC
1 CCTTTTCATA-ATCTATGGTCATCACCATC
* *
41776669 CTTTTTCATAATCTATGGTCGTCACCATC
1 CCTTTTCATAATCTATGGTCATCACCATC
41776698 CCTTTTCATAAT
1 CCTTTTCATAAT
41776710 TGATAGCTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 27 0.75
30 9 0.25
ACGTcount: A:0.21, C:0.28, G:0.10, T:0.41
Consensus pattern (29 bp):
CCTTTTCATAATCTATGGTCATCACCATC
Found at i:41776688 original size:121 final size:119
Alignment explanation
Indices: 41776486--41776761 Score: 291
Period size: 121 Copynumber: 2.3 Consensus size: 119
41776476 TCGACACCAC
* * * *
41776486 CCCTTTCCATAATTCGATAGCTGAAGCTATCCCTTTTCATAATTTTAATGGTCATCACCATCTCT
1 CCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCATAAGTTCAATGGTCATCACCATCTCT
** * * * *
41776551 TTTCATTGTTGATGGTCGTCACCATTCCTTTACATAGTTTGATAG-TCGAAGTTAT
66 TTTCATAATTGATGGTCGTCACCATCCCTTTACATA-ATTGATAGCT-AAAGCTAT
* *
41776606 CCCTTTTCATGATTCGATAGCCGAAGAC-ATCCACCTTTTCAT-AGTTCGATGGTCATCACCATC
1 CCCTTTTCATAATTCGATAGCCGAAG-CTAT-C-CCTTTTCATAAGTTCAATGGTCATCACCATC
*
41776669 -CTTTTTCATAATCT-ATGGTCGTCACCATCCCTTTTCATAATTGATAGCTAAAGCTAT
63 TC-TTTTCATAAT-TGATGGTCGTCACCATCCCTTTACATAATTGATAGCTAAAGCTAT
* *
41776726 CCCTTTTCGT-ATTCAATAG-C-AA-CTATCCCTTTTCAT
1 CCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCAT
41776762 TCGTCGATGA
Statistics
Matches: 134, Mismatches: 15, Indels: 20
0.79 0.09 0.12
Matches are distributed among these distances:
114 9 0.07
115 2 0.01
116 2 0.01
117 2 0.01
118 1 0.01
119 8 0.06
120 48 0.36
121 52 0.39
122 10 0.07
ACGTcount: A:0.24, C:0.25, G:0.12, T:0.39
Consensus pattern (119 bp):
CCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCATAAGTTCAATGGTCATCACCATCTCT
TTTCATAATTGATGGTCGTCACCATCCCTTTACATAATTGATAGCTAAAGCTAT
Found at i:41776727 original size:29 final size:26
Alignment explanation
Indices: 41776695--41776761 Score: 73
Period size: 29 Copynumber: 2.5 Consensus size: 26
41776685 GGTCGTCACC
*
41776695 ATCCCTTTTCATAATT-GATAGCTAAAGCT
1 ATCCCTTTTCAT-ATTCAATAGC--AA-CT
*
41776724 ATCCCTTTTCGTATTCAATAGCAACT
1 ATCCCTTTTCATATTCAATAGCAACT
41776750 ATCCCTTTTCAT
1 ATCCCTTTTCAT
41776762 TCGTCGATGA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
26 13 0.38
27 2 0.06
28 3 0.09
29 16 0.47
ACGTcount: A:0.27, C:0.25, G:0.07, T:0.40
Consensus pattern (26 bp):
ATCCCTTTTCATATTCAATAGCAACT
Found at i:41778537 original size:17 final size:19
Alignment explanation
Indices: 41778501--41778543 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
41778491 ATATCAAATA
41778501 CTAAAAAATAAAACAAAAC
1 CTAAAAAATAAAACAAAAC
* *
41778520 C-AAAAAA-AAAAGAGAAC
1 CTAAAAAATAAAACAAAAC
41778537 CTAAAAA
1 CTAAAAA
41778544 CAGATTACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 9 0.43
18 11 0.52
19 1 0.05
ACGTcount: A:0.74, C:0.14, G:0.05, T:0.07
Consensus pattern (19 bp):
CTAAAAAATAAAACAAAAC
Found at i:41779283 original size:29 final size:26
Alignment explanation
Indices: 41779243--41779295 Score: 70
Period size: 29 Copynumber: 1.9 Consensus size: 26
41779233 GAATTTGAGT
*
41779243 AATTAGGGCTAAATTGTAAAGATAATA
1 AATTAGGGCTAAAATGTAAA-ATAATA
41779270 AATTGAGGGACTAAAATGTAAAATAA
1 AATT-AGGG-CTAAAATGTAAAATAA
41779296 ATGAAATGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 4 0.17
28 8 0.35
29 11 0.48
ACGTcount: A:0.51, C:0.04, G:0.19, T:0.26
Consensus pattern (26 bp):
AATTAGGGCTAAAATGTAAAATAATA
Found at i:41779866 original size:43 final size:43
Alignment explanation
Indices: 41779805--41779976 Score: 235
Period size: 43 Copynumber: 4.0 Consensus size: 43
41779795 ATAGGATTTC
* * *
41779805 CGATATGTG-TTCTCATGTAAGACCAC-ATCTGGGAC-GTTAGCAT
1 CGATATGTGATT-ACATGTAAGACC-CTGTCTGGGACAG-TGGCAT
41779848 CGATATGTGATTACATGTAAGACCCTGTCTGGGACAGTGGCAT
1 CGATATGTGATTACATGTAAGACCCTGTCTGGGACAGTGGCAT
*
41779891 CGATATGTGATTACATGTAAGACCCTGTCTAGGACAGTGGCAT
1 CGATATGTGATTACATGTAAGACCCTGTCTGGGACAGTGGCAT
*
41779934 CGATATGTGATTACATGTAAGACCAC-GTCTGGGACATTGGCAT
1 CGATATGTGATTACATGTAAGACC-CTGTCTGGGACAGTGGCAT
41779977 TGTATGATAT
Statistics
Matches: 119, Mismatches: 6, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
42 1 0.01
43 114 0.96
44 4 0.03
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (43 bp):
CGATATGTGATTACATGTAAGACCCTGTCTGGGACAGTGGCAT
Found at i:41791509 original size:25 final size:25
Alignment explanation
Indices: 41791470--41791531 Score: 117
Period size: 25 Copynumber: 2.5 Consensus size: 25
41791460 GTAAGGAGGG
41791470 GATAA-GGGAGAAGATTTAGGAGCT
1 GATAAGGGGAGAAGATTTAGGAGCT
41791494 GATAAGGGGAGAAGATTTAGGAGCT
1 GATAAGGGGAGAAGATTTAGGAGCT
41791519 GATAAGGGGAGAA
1 GATAAGGGGAGAA
41791532 AATCAAGAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 5 0.14
25 32 0.86
ACGTcount: A:0.39, C:0.03, G:0.40, T:0.18
Consensus pattern (25 bp):
GATAAGGGGAGAAGATTTAGGAGCT
Found at i:41792801 original size:27 final size:26
Alignment explanation
Indices: 41792763--41792871 Score: 128
Period size: 27 Copynumber: 4.0 Consensus size: 26
41792753 AAGCGTCCTA
*
41792763 GTGGCTATGCCACAATTATCTGATCTG
1 GTGGCTCTGCCAC-ATTATCTGATCTG
*
41792790 GTGGCTCTGCCACATATATCTGTTCTG
1 GTGGCTCTGCCACAT-TATCTGATCTG
41792817 GTGGCTCTGCCACGATTATCTGTATCTG
1 GTGGCTCTGCCAC-ATTATCTG-ATCTG
* * * *
41792845 GTGACTCTGTCACATTTTCTGTTCTG
1 GTGGCTCTGCCACATTATCTGATCTG
41792871 G
1 G
41792872 CAGCCATGCT
Statistics
Matches: 72, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
26 7 0.10
27 48 0.67
28 17 0.24
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.38
Consensus pattern (26 bp):
GTGGCTCTGCCACATTATCTGATCTG
Found at i:41792866 original size:54 final size:54
Alignment explanation
Indices: 41792763--41792871 Score: 157
Period size: 54 Copynumber: 2.0 Consensus size: 54
41792753 AAGCGTCCTA
*
41792763 GTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTTCTG
1 GTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTTCTG
* * * *
41792817 GTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TTTCTGTTCTG
1 GTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATATATCTGTTCTG
41792871 G
1 G
41792872 CAGCCATGCT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
54 31 0.63
55 18 0.37
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.38
Consensus pattern (54 bp):
GTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTTCTG
Found at i:41795534 original size:17 final size:18
Alignment explanation
Indices: 41795514--41795548 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
41795504 AATACTGATG
41795514 AATAAAA-CAAAAATAAA
1 AATAAAACCAAAAATAAA
41795531 AATAAAACCAAAAATAAA
1 AATAAAACCAAAAATAAA
41795549 TTATAGTCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.80, C:0.09, G:0.00, T:0.11
Consensus pattern (18 bp):
AATAAAACCAAAAATAAA
Found at i:41800195 original size:39 final size:39
Alignment explanation
Indices: 41800151--41800229 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
41800141 TTAAATTAAA
41800151 TAAAATAAAAATAAAAGTTATTATCATCATTTTCATGTC
1 TAAAATAAAAATAAAAGTTATTATCATCATTTTCATGTC
41800190 TAAAATAAAAATAAAAGTTATTATCATCATTTTCATGTC
1 TAAAATAAAAATAAAAGTTATTATCATCATTTTCATGTC
41800229 T
1 T
41800230 TCCTCATCGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.39
Consensus pattern (39 bp):
TAAAATAAAAATAAAAGTTATTATCATCATTTTCATGTC
Found at i:41801466 original size:61 final size:62
Alignment explanation
Indices: 41801330--41801586 Score: 281
Period size: 61 Copynumber: 4.2 Consensus size: 62
41801320 AAGTACAAAA
* * * * *
41801330 AGTGAGTCACACGGCATGGGCACACA-G-CCATGTCCCTGGCCATATGGTTTTATACTATGAAT
1 AGTGAGTTACACGGCCT-GGC-CACATGCCCGTGTCCCTGGCCATATGGTTTTATACAATGAAC
* * * *
41801392 AGTGAGTTTCACGGCCTGGCCACATGCCCGTGTCCCTGGTCGTGTGG-TTTATACAATGAAC
1 AGTGAGTTACACGGCCTGGCCACATGCCCGTGTCCCTGGCCATATGGTTTTATACAATGAAC
* ** * *
41801453 AGTGAGTTACACGGCCTGGGCACACT-CTTGTGTCCCTGACCGTATGG-TTTATACAATGAAC
1 AGTGAGTTACACGGCCTGGCCACA-TGCCCGTGTCCCTGGCCATATGGTTTTATACAATGAAC
* * * * *
41801514 AGTGATTTACACGGCCTGGGCACACGCCCGTGTCCCTGGCCATGTGGTTTTATATAATGAAC
1 AGTGAGTTACACGGCCTGGCCACATGCCCGTGTCCCTGGCCATATGGTTTTATACAATGAAC
41801576 AGTGAGTTACA
1 AGTGAGTTACA
41801587 TGGTCGTTCA
Statistics
Matches: 165, Mismatches: 25, Indels: 10
0.82 0.12 0.05
Matches are distributed among these distances:
60 4 0.02
61 107 0.65
62 54 0.33
ACGTcount: A:0.23, C:0.25, G:0.26, T:0.27
Consensus pattern (62 bp):
AGTGAGTTACACGGCCTGGCCACATGCCCGTGTCCCTGGCCATATGGTTTTATACAATGAAC
Found at i:41801550 original size:122 final size:124
Alignment explanation
Indices: 41801360--41801586 Score: 343
Period size: 122 Copynumber: 1.8 Consensus size: 124
41801350 CACACAGCCA
* * * *
41801360 TGTCCCTGGCCATATGGTTTTATACTATGAATAGTGAGTTTCACGGCCTGGCCACATGCCCGTGT
1 TGTCCCTGACCATATGGTTTTATACAATGAACAGTGAGTTTCACGGCCTGGCCACACGCCCGTGT
* *
41801425 CCCTGGTCGTGTGG-TTTATACAATGAACAGTGAGTTACACGGCCTGGGCACACTCTTG
66 CCCTGGCCATGTGGTTTTATACAATGAACAGTGAGTTACACGGCCTGGGCACACTCTTG
* *
41801483 TGTCCCTGACCGTATGG-TTTATACAATGAACAGTGA-TTTACACGGCCTGGGCACACGCCCGTG
1 TGTCCCTGACCATATGGTTTTATACAATGAACAGTGAGTTT-CACGGCCTGGCCACACGCCCGTG
*
41801546 TCCCTGGCCATGTGGTTTTATATAATGAACAGTGAGTTACA
65 TCCCTGGCCATGTGGTTTTATACAATGAACAGTGAGTTACA
41801587 TGGTCGTTCA
Statistics
Matches: 93, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
121 3 0.03
122 51 0.55
123 39 0.42
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.30
Consensus pattern (124 bp):
TGTCCCTGACCATATGGTTTTATACAATGAACAGTGAGTTTCACGGCCTGGCCACACGCCCGTGT
CCCTGGCCATGTGGTTTTATACAATGAACAGTGAGTTACACGGCCTGGGCACACTCTTG
Found at i:41802187 original size:17 final size:16
Alignment explanation
Indices: 41802147--41802220 Score: 62
Period size: 17 Copynumber: 4.6 Consensus size: 16
41802137 ATTAAAAAGG
41802147 AAAAAGGAA-AAAGAA
1 AAAAAGGAAGAAAGAA
*
41802162 AAAAA-GAAGAAATAA
1 AAAAAGGAAGAAAGAA
**
41802177 AATAAAGGAAGAAAGGG
1 AA-AAAGGAAGAAAGAA
* *
41802194 AAAACGAAAGAGAAGAA
1 AAAAAGGAAGA-AAGAA
41802211 AAAAATGGAA
1 AAAAA-GGAA
41802221 AAGAACTAAC
Statistics
Matches: 44, Mismatches: 10, Indels: 7
0.72 0.16 0.11
Matches are distributed among these distances:
14 3 0.07
15 12 0.27
16 10 0.23
17 16 0.36
18 3 0.07
ACGTcount: A:0.72, C:0.01, G:0.23, T:0.04
Consensus pattern (16 bp):
AAAAAGGAAGAAAGAA
Found at i:41807067 original size:18 final size:18
Alignment explanation
Indices: 41807044--41807079 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
41807034 TTTAACAATA
41807044 TTTTTTATCTCAAAAGTG
1 TTTTTTATCTCAAAAGTG
*
41807062 TTTTTTGTCTCAAAAGTG
1 TTTTTTATCTCAAAAGTG
41807080 CTTCTAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.11, G:0.14, T:0.50
Consensus pattern (18 bp):
TTTTTTATCTCAAAAGTG
Found at i:41810971 original size:20 final size:20
Alignment explanation
Indices: 41810927--41810974 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
41810917 GGAAAAATCC
*
41810927 ATATTTTTATACTTTCTAATA
1 ATATTTTTATAATTTCTAA-A
*
41810948 AT-TTTTCATAATTT-TAAA
1 ATATTTTTATAATTTCTAAA
41810966 ATATTTTTA
1 ATATTTTTA
41810975 CAGTTTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 3 0.13
19 8 0.35
20 10 0.43
21 2 0.09
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (20 bp):
ATATTTTTATAATTTCTAAA
Found at i:41814042 original size:10 final size:10
Alignment explanation
Indices: 41814027--41814076 Score: 64
Period size: 10 Copynumber: 5.0 Consensus size: 10
41814017 GATTTTTAGA
41814027 ATTTATTTTT
1 ATTTATTTTT
*
41814037 ATTTATCTTT
1 ATTTATTTTT
*
41814047 ATTTATATTT
1 ATTTATTTTT
* *
41814057 AATTATTTGT
1 ATTTATTTTT
41814067 ATTTATTTTT
1 ATTTATTTTT
41814077 TAGAATTTAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:41815770 original size:15 final size:15
Alignment explanation
Indices: 41815750--41815784 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
41815740 ATAAAATTTT
*
41815750 AAATTAATAATAATA
1 AAATTAAAAATAATA
41815765 AAATTAAAAATAATA
1 AAATTAAAAATAATA
*
41815780 TAATT
1 AAATT
41815785 TTAATTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAATTAAAAATAATA
Found at i:41815775 original size:22 final size:20
Alignment explanation
Indices: 41815740--41815783 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
41815730 TTTATAATTT
* *
41815740 ATAAAATTTTAAATTAATAATA
1 ATAAAA-TTAAAAATAAT-ATA
41815762 ATAAAATTAAAAATAATATA
1 ATAAAATTAAAAATAATATA
41815782 AT
1 AT
41815784 TTTAATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 5 0.25
21 9 0.45
22 6 0.30
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
ATAAAATTAAAAATAATATA
Found at i:41816189 original size:26 final size:25
Alignment explanation
Indices: 41816132--41816185 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 25
41816122 ATCTTTCTAG
41816132 TTATATTATTATAAAAATATAATTTT
1 TTATATTATTATAAAAATAT-ATTTT
*
41816158 TTATATTTTTATATAAAATAT-TTTT
1 TTATATTATTATA-AAAATATATTTT
41816183 TTA
1 TTA
41816186 ATATATAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 7 0.27
26 12 0.46
27 7 0.27
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
TTATATTATTATAAAAATATATTTT
Found at i:41816190 original size:28 final size:27
Alignment explanation
Indices: 41816111--41816191 Score: 69
Period size: 26 Copynumber: 3.0 Consensus size: 27
41816101 TCTATAAAAA
* *
41816111 ATTA-ATAAAATATCTTTCTAGTTATATT
1 ATTATATAAAATATATTTTTA--TATATT
41816139 ATTATA-AAAATATAATTTTT-TATATT
1 ATTATATAAAATAT-ATTTTTATATATT
* *
41816165 TTTATATAAAATATTTTTTTAATATAT
1 ATTATATAAAATATATTTTT-ATATAT
41816192 AAAGTAAATC
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
26 16 0.36
27 7 0.16
28 16 0.36
29 5 0.11
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.54
Consensus pattern (27 bp):
ATTATATAAAATATATTTTTATATATT
Found at i:41819309 original size:3 final size:3
Alignment explanation
Indices: 41819301--41819333 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
41819291 TAGAGTGAAT
41819301 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
41819334 GAAAAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:41821964 original size:26 final size:26
Alignment explanation
Indices: 41821934--41821983 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
41821924 TTAACATTGC
41821934 TTTTGA-AAAGTAATTTTAAAAAGTGA
1 TTTTGAGAAA-TAATTTTAAAAAGTGA
* *
41821960 TTTTGAGAAATACTTTTGAAAAGT
1 TTTTGAGAAATAATTTTAAAAAGT
41821984 TTGATTTAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 18 0.86
27 3 0.14
ACGTcount: A:0.42, C:0.02, G:0.16, T:0.40
Consensus pattern (26 bp):
TTTTGAGAAATAATTTTAAAAAGTGA
Found at i:41822928 original size:22 final size:22
Alignment explanation
Indices: 41822900--41822975 Score: 86
Period size: 22 Copynumber: 3.6 Consensus size: 22
41822890 GATTATTGTT
*
41822900 ATTATTATTAAATTTTAATAAA
1 ATTATTATTAAATTTTAATATA
*
41822922 ATTATTATTAAA-TATAAT-TA
1 ATTATTATTAAATTTTAATATA
* * *
41822942 ATT-TAATCAAATTTTAACATA
1 ATTATTATTAAATTTTAATATA
41822963 ATTATTATTAAAT
1 ATTATTATTAAAT
41822976 ACAATTAAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
19 6 0.14
20 8 0.19
21 10 0.23
22 19 0.44
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (22 bp):
ATTATTATTAAATTTTAATATA
Found at i:41823025 original size:60 final size:61
Alignment explanation
Indices: 41822932--41823065 Score: 161
Period size: 60 Copynumber: 2.2 Consensus size: 61
41822922 ATTATTATTA
41822932 AATATA-ATTAATTTAATCAAATTTTAACATAATTATTATT-AAATA-CAATTAA-ATAAAAT
1 AATATATA-TAATTTAATCAAATTTTAACATAATTATTATTAAAATATCAATTAATA-AAAAT
* *
41822991 AATATATATAATTTAAT-AATATTTTTAATATAATTATTATTAAAATATGAATTAATAAAAAT
1 AATATATATAATTTAATCAA-A-TTTTAACATAATTATTATTAAAATATCAATTAATAAAAAT
*
41823053 CATAATATATAAT
1 AAT-ATATATAAT
41823066 ATTATAAAAA
Statistics
Matches: 65, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
58 2 0.03
59 16 0.25
60 19 0.29
61 5 0.08
62 13 0.20
63 10 0.15
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.43
Consensus pattern (61 bp):
AATATATATAATTTAATCAAATTTTAACATAATTATTATTAAAATATCAATTAATAAAAAT
Found at i:41826178 original size:50 final size:50
Alignment explanation
Indices: 41826124--41826218 Score: 138
Period size: 50 Copynumber: 1.9 Consensus size: 50
41826114 CCGATACTTG
* *
41826124 GCTCTCATGAGCTTC-CAGTTATTTAGCTCTCAAGAGCTTCCCGATTAATA
1 GCTCTCATGAGCTTCTC-GATATTTAGCTCGCAAGAGCTTCCCGATTAATA
* *
41826174 GCTCTCTTGAGCTTCTCGATATTTGGCTCGCAAGAGCTTCCCGAT
1 GCTCTCATGAGCTTCTCGATATTTAGCTCGCAAGAGCTTCCCGAT
41826219 GTTTGGCTCG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
50 39 0.98
51 1 0.03
ACGTcount: A:0.20, C:0.27, G:0.19, T:0.34
Consensus pattern (50 bp):
GCTCTCATGAGCTTCTCGATATTTAGCTCGCAAGAGCTTCCCGATTAATA
Found at i:41826233 original size:75 final size:74
Alignment explanation
Indices: 41826114--41826289 Score: 185
Period size: 75 Copynumber: 2.4 Consensus size: 74
41826104 TATAAGCGTC
* * * * * *
41826114 CCGATACTTGGCTCTCATGAGCTTCCAGTTATTTAGCTCTCAAGAGCTTCCCGATTA-ATAGCTC
1 CCGATATTTGGCTCGCAAGAGCTTCCAGATATTTAGCTCGCAAGAGCTTCCCG-TTATACAGCTC
*
41826178 TC-TTGAGCTT
65 ACATT-AGCTT
* * *
41826188 CTCGATATTTGGCTCGCAAGAGCTTCCCGATGTTTGGCTCGCAAGAGCTTCCCGTTATACAGCTC
1 C-CGATATTTGGCTCGCAAGAGCTTCCAGATATTTAGCTCGCAAGAGCTTCCCGTTATACAGCTC
41826253 ACATTAGCTT
65 ACATTAGCTT
* * *
41826263 CCCATTATATGGCTCGAAAGAGCTTCC
1 CCGA-TATTTGGCTCGCAAGAGCTTCC
41826290 TATTTACATG
Statistics
Matches: 85, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
74 6 0.07
75 77 0.91
76 2 0.02
ACGTcount: A:0.21, C:0.28, G:0.19, T:0.32
Consensus pattern (74 bp):
CCGATATTTGGCTCGCAAGAGCTTCCAGATATTTAGCTCGCAAGAGCTTCCCGTTATACAGCTCA
CATTAGCTT
Found at i:41826236 original size:50 final size:49
Alignment explanation
Indices: 41826112--41826239 Score: 132
Period size: 50 Copynumber: 2.6 Consensus size: 49
41826102 CTTATAAGCG
* * *
41826112 TCCCGATACTTGGCTCTCATGAGCTTCCAGTTATTTAGCTCTCAAGAGCT
1 TCCCGAT-TTTGGCTCTCATGAGCTTCCAGATATTTAGCTCGCAAGAGCT
* * * *
41826162 TCCCGATTAATAGCTCTCTTGAGCTTCTC-GATATTTGGCTCGCAAGAGCT
1 TCCCGATT-TTGGCTCTCATGAGCTTC-CAGATATTTAGCTCGCAAGAGCT
* *
41826212 TCCCGATGTTTGGCTCGCAAGAGCTTCC
1 TCCCGAT-TTTGGCTCTCATGAGCTTCC
41826240 CGTTATACAG
Statistics
Matches: 63, Mismatches: 12, Indels: 7
0.77 0.15 0.09
Matches are distributed among these distances:
49 1 0.02
50 60 0.95
51 2 0.03
ACGTcount: A:0.19, C:0.28, G:0.20, T:0.33
Consensus pattern (49 bp):
TCCCGATTTTGGCTCTCATGAGCTTCCAGATATTTAGCTCGCAAGAGCT
Found at i:41826252 original size:25 final size:25
Alignment explanation
Indices: 41826132--41826289 Score: 111
Period size: 25 Copynumber: 6.3 Consensus size: 25
41826122 TGGCTCTCAT
* * *
41826132 GAGCTTCCAGTTATTTAGCTCTCAA
1 GAGCTTCCCGTTATATAGCTCGCAA
* **
41826157 GAGCTTCCCGATTA-ATAGCTCTCTT
1 GAGCTTCCCG-TTATATAGCTCGCAA
* * * *
41826182 GAGCTTCTCGATATTTGGCTCGCAA
1 GAGCTTCCCGTTATATAGCTCGCAA
* * * *
41826207 GAGCTTCCCGATGTTTGGCTCGCAA
1 GAGCTTCCCGTTATATAGCTCGCAA
* * *
41826232 GAGCTTCCCGTTATACAGCTCACAT
1 GAGCTTCCCGTTATATAGCTCGCAA
* * * *
41826257 TAGCTTCCCATTATATGGCTCGAAA
1 GAGCTTCCCGTTATATAGCTCGCAA
41826282 GAGCTTCC
1 GAGCTTCC
41826290 TATTTACATG
Statistics
Matches: 103, Mismatches: 28, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
24 2 0.02
25 98 0.95
26 3 0.03
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.32
Consensus pattern (25 bp):
GAGCTTCCCGTTATATAGCTCGCAA
Found at i:41829472 original size:33 final size:33
Alignment explanation
Indices: 41829437--41829550 Score: 133
Period size: 33 Copynumber: 3.5 Consensus size: 33
41829427 GGTGTACATT
**
41829437 CCTTTTCAAGTGGTACACACAAAGTATACCTTT
1 CCTTTTCAAGTGGTACACACAAAGTATACCTAA
* *
41829470 CCTTTTCATA-TGGTATACACTAAGTATACCTAA
1 CCTTTTCA-AGTGGTACACACAAAGTATACCTAA
* * *
41829503 CCTTTCCAAGT-GTACACACAAAGTGTACATAA
1 CCTTTTCAAGTGGTACACACAAAGTATACCTAA
*
41829535 CCTTTTCAAGTTGTAC
1 CCTTTTCAAGTGGTAC
41829551 CATTTGGGTA
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
32 28 0.41
33 39 0.57
34 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.33
Consensus pattern (33 bp):
CCTTTTCAAGTGGTACACACAAAGTATACCTAA
Found at i:41832753 original size:14 final size:15
Alignment explanation
Indices: 41832720--41832753 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
41832710 GGAAGAAAGA
*
41832720 GAAAATATTTTTATC
1 GAAAATATTTTTAAC
41832735 GAAAATATTTTTAAC
1 GAAAATATTTTTAAC
41832750 -AAAA
1 GAAAA
41832754 GATAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (15 bp):
GAAAATATTTTTAAC
Found at i:41833619 original size:13 final size:13
Alignment explanation
Indices: 41833601--41833636 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
41833591 GTCAATCAGA
41833601 CAGTCAAATATTC
1 CAGTCAAATATTC
*
41833614 CAGTCAAATATTT
1 CAGTCAAATATTC
41833627 CAGTCAAATA
1 CAGTCAAATA
41833637 GTCAACCAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (13 bp):
CAGTCAAATATTC
Found at i:41834296 original size:14 final size:14
Alignment explanation
Indices: 41834277--41834311 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
41834267 CCAAGAGCTT
*
41834277 TGTATGCAGATGTA
1 TGTATGCAAATGTA
41834291 TGTATGCAAATGTA
1 TGTATGCAAATGTA
*
41834305 TGCATGC
1 TGTATGC
41834312 GGATACCCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.29, C:0.11, G:0.26, T:0.34
Consensus pattern (14 bp):
TGTATGCAAATGTA
Done.