Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr4
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: 31929104
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1434590 characters in sequence are not A, C, G, or T
File 37 of 82
Found at i:13606566 original size:19 final size:21
Alignment explanation
Indices: 13606542--13606584 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
13606532 CTATAAATAA
13606542 CTTG-AATTTCCAGCAGCT-T
1 CTTGAAATTTCCAGCAGCTGT
13606561 CTTGAAATTTCCAGCAGCTGT
1 CTTGAAATTTCCAGCAGCTGT
13606582 CTT
1 CTT
13606585 CTTCTTCCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 4 0.18
20 14 0.64
21 4 0.18
ACGTcount: A:0.21, C:0.26, G:0.16, T:0.37
Consensus pattern (21 bp):
CTTGAAATTTCCAGCAGCTGT
Found at i:13607494 original size:37 final size:40
Alignment explanation
Indices: 13607453--13607554 Score: 138
Period size: 37 Copynumber: 2.6 Consensus size: 40
13607443 ATAGTGCCCG
*
13607453 TGTGCACGATGTGGGGGGATGTACACGAT-G-GACTGAT-
1 TGTGCACGATGTGGGGGGATGTACACGATGGTGACGGATA
* * * *
13607490 TGTGCACGATGTGGGGGGGTGCACACGATGGTGTCGGCTA
1 TGTGCACGATGTGGGGGGATGTACACGATGGTGACGGATA
13607530 TGTGCACGATGTGGGGGGATGTACA
1 TGTGCACGATGTGGGGGGATGTACA
13607555 TGAGCTGGGT
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
37 27 0.49
38 1 0.02
39 4 0.07
40 23 0.42
ACGTcount: A:0.19, C:0.15, G:0.43, T:0.24
Consensus pattern (40 bp):
TGTGCACGATGTGGGGGGATGTACACGATGGTGACGGATA
Found at i:13613713 original size:40 final size:40
Alignment explanation
Indices: 13613669--13613760 Score: 132
Period size: 40 Copynumber: 2.3 Consensus size: 40
13613659 AGATTTATTT
* * *
13613669 TCGCTACAGCGAAATTTCCTTGCTGTAG-AGAGATTGAATC
1 TCGCTGCAGCGAAATTTCCTTACTATAGCA-AGATTGAATC
*
13613709 TCGCTGCAGAGAAATTTCCTTACTATAGCAAGATTGAATC
1 TCGCTGCAGCGAAATTTCCTTACTATAGCAAGATTGAATC
13613749 TCGCTGCAGCGA
1 TCGCTGCAGCGA
13613761 GAAATAGGGC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 45 0.98
41 1 0.02
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (40 bp):
TCGCTGCAGCGAAATTTCCTTACTATAGCAAGATTGAATC
Found at i:13614107 original size:49 final size:49
Alignment explanation
Indices: 13614035--13614203 Score: 241
Period size: 49 Copynumber: 3.4 Consensus size: 49
13614025 CATTCATCGT
* *
13614035 CATAGCCGGGTCATCATCATCATCGGCTTATGCACACTCCCTACTCACA
1 CATAGCCGGGTCATCATCATCATCGGCTTATGCGCACTCCCTACTCGCA
*
13614084 CATAGCCGGGTCATCATCATCATCGACTTATGCGCACTCCCTACTCGCA
1 CATAGCCGGGTCATCATCATCATCGGCTTATGCGCACTCCCTACTCGCA
* * * **
13614133 CATAGCCGGGTCATCATCATTATCAGTTTATGCGCACTCTTTACTCGCA
1 CATAGCCGGGTCATCATCATCATCGGCTTATGCGCACTCCCTACTCGCA
*
13614182 CATAGCTGGGTCAAT-ATCATCA
1 CATAGCCGGGTC-ATCATCATCA
13614204 CACAACATTA
Statistics
Matches: 108, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
49 106 0.98
50 2 0.02
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.27
Consensus pattern (49 bp):
CATAGCCGGGTCATCATCATCATCGGCTTATGCGCACTCCCTACTCGCA
Found at i:13616325 original size:17 final size:17
Alignment explanation
Indices: 13616295--13616327 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
13616285 TTCTTGATAA
13616295 AATAAAACTCCTTATTG
1 AATAAAACTCCTTATTG
13616312 AATAATAACT-CTTATT
1 AATAA-AACTCCTTATT
13616328 TTATTATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.39
Consensus pattern (17 bp):
AATAAAACTCCTTATTG
Found at i:13616520 original size:30 final size:29
Alignment explanation
Indices: 13616469--13616637 Score: 182
Period size: 30 Copynumber: 5.7 Consensus size: 29
13616459 TTAAGACAAC
*
13616469 TCTTGTCTTTAATTAAGACAAAAATATTTT
1 TCTTGTC-TAAATTAAGACAAAAATATTTT
*
13616499 ATCTTGTCTAAATTGAGAC--AAATATGTTT
1 -TCTTGTCTAAATTAAGACAAAAATAT-TTT
* * *
13616528 TCTTGTGTAGATTAAGATAGAAAATATTTT
1 TCTTGTCTAAATTAAGACA-AAAATATTTT
*
13616558 TCTTGTCTTAAATTAAGACAAACATATTTT
1 TCTTGTC-TAAATTAAGACAAAAATATTTT
* * *
13616588 TTTTGTCTAAATTAAAAC-CAAATATGTTT
1 TCTTGTCTAAATTAAGACAAAAATAT-TTT
13616617 TCTTGTCTAAATTAAGACAAA
1 TCTTGTCTAAATTAAGACAAA
13616638 CATGTTAAAA
Statistics
Matches: 114, Mismatches: 17, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
28 25 0.22
29 32 0.28
30 34 0.30
31 23 0.20
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (29 bp):
TCTTGTCTAAATTAAGACAAAAATATTTT
Found at i:13616531 original size:28 final size:27
Alignment explanation
Indices: 13616469--13616637 Score: 158
Period size: 29 Copynumber: 5.8 Consensus size: 27
13616459 TTAAGACAAC
*
13616469 TCTTGTCTTTAATTAAGACAAAAATATTTT
1 TCTTGTC-TAAATTAAGAC--AAATATTTT
*
13616499 ATCTTGTCTAAATTGAGACAAATATGTTT
1 -TCTTGTCTAAATTAAGACAAATAT-TTT
* * *
13616528 TCTTGTGTAGATTAAGATAGAAAATATTTT
1 TCTTGTCTAAATTAAG--A-CAAATATTTT
13616558 TCTTGTCTTAAATTAAGACAAACATATTTT
1 TCTTGTC-TAAATTAAGAC-AA-ATATTTT
* *
13616588 TTTTGTCTAAATTAAAACCAAATATGTTT
1 TCTTGTCTAAATTAAGA-CAAATAT-TTT
13616617 TCTTGTCTAAATTAAGACAAA
1 TCTTGTCTAAATTAAGACAAA
13616638 CATGTTAAAA
Statistics
Matches: 116, Mismatches: 13, Indels: 21
0.77 0.09 0.14
Matches are distributed among these distances:
28 27 0.23
29 35 0.30
30 33 0.28
31 21 0.18
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (27 bp):
TCTTGTCTAAATTAAGACAAATATTTT
Found at i:13616620 original size:89 final size:89
Alignment explanation
Indices: 13616469--13616633 Score: 251
Period size: 89 Copynumber: 1.9 Consensus size: 89
13616459 TTAAGACAAC
* * *
13616469 TCTTGTCTTTAATTAAGACAAAAATATTTTATCTTGTCTAAATTGAGACAAATATGTTTTCTTGT
1 TCTTGTCTTAAATTAAGACAAAAATATTTTATCTTGTCTAAATTAAAACAAATATGTTTTCTTGT
* *
13616534 GTAGATTAAGATAGAAAATATTTT
66 CTAAATTAAGATAGAAAATATTTT
* *
13616558 TCTTGTCTTAAATTAAGACAAACATATTTT-TTTTGTCTAAATTAAAACCAAATATGTTTTCTTG
1 TCTTGTCTTAAATTAAGACAAAAATATTTTATCTTGTCTAAATTAAAA-CAAATATGTTTTCTTG
13616622 TCTAAATTAAGA
65 TCTAAATTAAGA
13616634 CAAACATGTT
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
88 14 0.21
89 54 0.79
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (89 bp):
TCTTGTCTTAAATTAAGACAAAAATATTTTATCTTGTCTAAATTAAAACAAATATGTTTTCTTGT
CTAAATTAAGATAGAAAATATTTT
Found at i:13616635 original size:58 final size:60
Alignment explanation
Indices: 13616469--13616640 Score: 194
Period size: 58 Copynumber: 2.9 Consensus size: 60
13616459 TTAAGACAAC
* * *
13616469 TCTTGTCTTTAATTAAGACA-AAAATATTTTATCTTGTCTAAATTGAGAC-AA-ATATGTTT
1 TCTTGTC-TAAATTAAGATACAAAATATTTT-TCTTGTCTAAATTAAGACAAACATATGTTT
* * *
13616528 TCTTGTGTAGATTAAGATAGAAAATATTTTTCTTGTCTTAAATTAAGACAAACATAT-TTT
1 TCTTGTCTAAATTAAGATACAAAATATTTTTCTTGTC-TAAATTAAGACAAACATATGTTT
* *
13616588 TTTTGTCTAAATTAA-A-ACCAAATATGTTTTCTTGTCTAAATTAAGACAAACAT
1 TCTTGTCTAAATTAAGATACAAAATAT-TTTTCTTGTCTAAATTAAGACAAACAT
13616641 GTTAAAACTG
Statistics
Matches: 98, Mismatches: 10, Indels: 11
0.82 0.08 0.09
Matches are distributed among these distances:
58 40 0.41
59 37 0.38
60 17 0.17
61 4 0.04
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.42
Consensus pattern (60 bp):
TCTTGTCTAAATTAAGATACAAAATATTTTTCTTGTCTAAATTAAGACAAACATATGTTT
Found at i:13639745 original size:20 final size:20
Alignment explanation
Indices: 13639719--13639764 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
13639709 AATCTTACCT
* *
13639719 TTTTTCACTTGTTTCCTTGAA
1 TTTTACACTT-TTCCCTTGAA
13639740 TTTTCACACTTTTCCCTTGAA
1 TTTT-ACACTTTTCCCTTGAA
13639761 TTTT
1 TTTT
13639765 TCCACCTAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.15, C:0.22, G:0.07, T:0.57
Consensus pattern (20 bp):
TTTTACACTTTTCCCTTGAA
Found at i:13639766 original size:22 final size:22
Alignment explanation
Indices: 13639724--13639764 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
13639714 TACCTTTTTT
*
13639724 CACTTGTTTCCTTGAATTTTCA
1 CACTTGTTCCCTTGAATTTTCA
13639746 CACTT-TTCCCTTGAATTTT
1 CACTTGTTCCCTTGAATTTT
13639765 TCCACCTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.17, C:0.24, G:0.07, T:0.51
Consensus pattern (22 bp):
CACTTGTTCCCTTGAATTTTCA
Found at i:13642674 original size:63 final size:63
Alignment explanation
Indices: 13642567--13642721 Score: 170
Period size: 63 Copynumber: 2.5 Consensus size: 63
13642557 TATCGGCATG
* ** * * * *
13642567 TGCACTGCCCACTCCACACATGCATAGTTGTAAGTGTAACAACATTGTCATTCGAGCAG-TATA
1 TGCACTGCCCACTCCGCACATGCACGGTTGTAAGTGTAACAACATCGTCA-TCCAACAGACATA
* * * * *
13642630 TGCACTGGCCACTCCGCATATGCACGGTTGT-AGTTGTCATAACATCGTCATCCAACCGACATA
1 TGCACTGCCCACTCCGCACATGCACGGTTGTAAG-TGTAACAACATCGTCATCCAACAGACATA
13642693 TGCACTGCCCACTCCGCACATGCACGGTT
1 TGCACTGCCCACTCCGCACATGCACGGTT
13642722 ACATTAATTA
Statistics
Matches: 76, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
62 7 0.09
63 69 0.91
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.25
Consensus pattern (63 bp):
TGCACTGCCCACTCCGCACATGCACGGTTGTAAGTGTAACAACATCGTCATCCAACAGACATA
Found at i:13644353 original size:4 final size:4
Alignment explanation
Indices: 13644333--13644394 Score: 56
Period size: 4 Copynumber: 15.5 Consensus size: 4
13644323 TACTTTATCA
* * *
13644333 TTTC -TTC TTTC TCTC TTTC TTTT TTTCC TTTCC TTTC -TCC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTT-C TTT-C TTTC TTTC TTTC TTTC
*
13644381 TTTC TTCC TTTC TT
1 TTTC TTTC TTTC TT
13644395 CCTTAGCTTC
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
3 5 0.11
4 34 0.72
5 8 0.17
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (4 bp):
TTTC
Found at i:13644395 original size:8 final size:8
Alignment explanation
Indices: 13644362--13644398 Score: 58
Period size: 8 Copynumber: 4.8 Consensus size: 8
13644352 TTTTTTTCCT
13644362 TTCCTTTC
1 TTCCTTTC
13644370 -TCCTTTC
1 TTCCTTTC
*
13644377 TTTCTTTC
1 TTCCTTTC
13644385 TTCCTTTC
1 TTCCTTTC
13644393 TTCCTT
1 TTCCTT
13644399 AGCTTCTTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
7 7 0.27
8 19 0.73
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (8 bp):
TTCCTTTC
Found at i:13645695 original size:21 final size:21
Alignment explanation
Indices: 13645661--13645700 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
13645651 TTTTAAACAT
*
13645661 ATTTCCATCTCAATCATGCCG
1 ATTTCCATCACAATCATGCCG
*
13645682 ATTTCGATCACAATCATGC
1 ATTTCCATCACAATCATGC
13645701 TTACTTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.30, G:0.10, T:0.33
Consensus pattern (21 bp):
ATTTCCATCACAATCATGCCG
Found at i:13647146 original size:20 final size:20
Alignment explanation
Indices: 13647089--13647151 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
13647079 TATATACCCA
*
13647089 TCATCATCATC-TCACCAAC
1 TCATCATCATCATCACCAGC
*
13647108 CCATCATCATCATCACCAGC
1 TCATCATCATCATCACCAGC
13647128 TCATCATCATCATCACCAGC
1 TCATCATCATCATCACCAGC
13647148 TCAT
1 TCAT
13647152 GCGCACTCCC
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 10 0.25
20 30 0.75
ACGTcount: A:0.30, C:0.41, G:0.03, T:0.25
Consensus pattern (20 bp):
TCATCATCATCATCACCAGC
Found at i:13647201 original size:43 final size:43
Alignment explanation
Indices: 13647150--13647294 Score: 184
Period size: 43 Copynumber: 3.4 Consensus size: 43
13647140 TCACCAGCTC
* ** *
13647150 ATGCGCACTCCCTACTCACATATGGCTGGGTCATCATCGGGTT
1 ATGCGCACTCCCTACTCGCATATAACCGGGTCATCATCGGGTT
* * * *
13647193 ATGTGCACTCCCTACTCGCACATAACCGGGTCATCACCGAGTT
1 ATGCGCACTCCCTACTCGCATATAACCGGGTCATCATCGGGTT
* *
13647236 ATGCGCACTCCCTACTCGC-TCATAACCGGGTCATCCTCGGCTT
1 ATGCGCACTCCCTACTCGCAT-ATAACCGGGTCATCATCGGGTT
13647279 ATGCGCACTCCCTACT
1 ATGCGCACTCCCTACT
13647295 TGCACATAGC
Statistics
Matches: 87, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
43 87 1.00
ACGTcount: A:0.19, C:0.36, G:0.19, T:0.26
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCATATAACCGGGTCATCATCGGGTT
Found at i:13647240 original size:86 final size:86
Alignment explanation
Indices: 13647137--13647311 Score: 219
Period size: 86 Copynumber: 2.0 Consensus size: 86
13647127 CTCATCATCA
** * * *
13647137 TCATCACCAGCTCATGCGCACTCCCTACTCACAT-ATGGCTGGGTCATCATCGGGTTATGTGCAC
1 TCATCACCAGCTCATGCGCACTCCCTACTCAC-TCATAACCGGGTCATCATCGGCTTATGCGCAC
*
13647201 TCCCTACTCGCACATAACCGGG
65 TCCCTACTCGCACATAACCGAG
* * *
13647223 TCATCACCGAG-TTATGCGCACTCCCTACTCGCTCATAACCGGGTCATCCTCGGCTTATGCGCAC
1 TCATCACC-AGCTCATGCGCACTCCCTACTCACTCATAACCGGGTCATCATCGGCTTATGCGCAC
* *
13647287 TCCCTACTTGCACATAGCCGAG
65 TCCCTACTCGCACATAACCGAG
13647309 TCA
1 TCA
13647312 ACATAATTAC
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
85 1 0.01
86 73 0.96
87 2 0.03
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.25
Consensus pattern (86 bp):
TCATCACCAGCTCATGCGCACTCCCTACTCACTCATAACCGGGTCATCATCGGCTTATGCGCACT
CCCTACTCGCACATAACCGAG
Found at i:13654977 original size:8 final size:8
Alignment explanation
Indices: 13654912--13654980 Score: 54
Period size: 8 Copynumber: 8.6 Consensus size: 8
13654902 CTCTACTTTA
13654912 TCCTTTCT
1 TCCTTTCT
*
13654920 T-CTTT-A
1 TCCTTTCT
13654926 TCTCTTTCT
1 TC-CTTTCT
*
13654935 TTCTTTCCTT
1 TCCTTT-C-T
13654945 TCCTTTC-
1 TCCTTTCT
*
13654952 TCCTCTCT
1 TCCTTTCT
*
13654960 TTCTTTCT
1 TCCTTTCT
13654968 TCCTTTCT
1 TCCTTTCT
13654976 TCCTT
1 TCCTT
13654981 AATTTCTTAA
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
6 1 0.02
7 10 0.21
8 27 0.57
9 3 0.06
10 6 0.13
ACGTcount: A:0.01, C:0.35, G:0.00, T:0.64
Consensus pattern (8 bp):
TCCTTTCT
Found at i:13657382 original size:35 final size:37
Alignment explanation
Indices: 13657329--13657402 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 37
13657319 AATCATCCTA
13657329 TGCACTCCCACACCGCACAAGGCA-ATAACATC-ATG
1 TGCACTCCCACACCGCACAAGGCATATAACATCAATG
* ** * *
13657364 TGCACTCCTACATTGCACATGGCATATATCATCAATG
1 TGCACTCCCACACCGCACAAGGCATATAACATCAATG
13657401 TG
1 TG
13657403 TGTACTCACA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
35 20 0.62
36 7 0.22
37 5 0.16
ACGTcount: A:0.31, C:0.31, G:0.15, T:0.23
Consensus pattern (37 bp):
TGCACTCCCACACCGCACAAGGCATATAACATCAATG
Found at i:13657455 original size:73 final size:73
Alignment explanation
Indices: 13657362--13657506 Score: 200
Period size: 73 Copynumber: 2.0 Consensus size: 73
13657352 AATAACATCA
* ** * *
13657362 TGTGCACTCCTACATTGCACATGGCATATATCATCAATGTGTGTACTCACACAGCACACCACTAT
1 TGTGCACTCCCACACCGCACATGGCACATATCATCAATGTGTGCACTCACACAGCACACCACTAT
13657427 CACCGTCG
66 CACCGTCG
* * * *
13657435 TGTGCACTCCCACACCGCACATGGTACATATCATTAGTGTGTGCACTCACACAGCACACCATTAT
1 TGTGCACTCCCACACCGCACATGGCACATATCATCAATGTGTGCACTCACACAGCACACCACTAT
*
13657500 CATCGTC
66 CACCGTC
13657507 AAGTGCATTT
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
73 62 1.00
ACGTcount: A:0.27, C:0.32, G:0.15, T:0.26
Consensus pattern (73 bp):
TGTGCACTCCCACACCGCACATGGCACATATCATCAATGTGTGCACTCACACAGCACACCACTAT
CACCGTCG
Found at i:13657513 original size:73 final size:73
Alignment explanation
Indices: 13657363--13657528 Score: 197
Period size: 73 Copynumber: 2.3 Consensus size: 73
13657353 ATAACATCAT
* ** * *
13657363 GTGCACTCCTACATTGCACATGGCATATATCATCAATGTGTGTACTCACACAGCACACCACTATC
1 GTGCACTCCCACACCGCACATGGCACATATCATCAATGTGTGCACTCACACAGCACACCACTATC
**
13657428 ACCGTCGT
66 ACCGTCAA
* * * *
13657436 GTGCACTCCCACACCGCACATGGTACATATCATTAGTGTGTGCACTCACACAGCACACCATTATC
1 GTGCACTCCCACACCGCACATGGCACATATCATCAATGTGTGCACTCACACAGCACACCACTATC
*
13657501 ATCGTCAA
66 ACCGTCAA
* * *
13657509 GTGCATTTCCACACCACACA
1 GTGCACTCCCACACCGCACA
13657529 CGCACGATCA
Statistics
Matches: 78, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
73 78 1.00
ACGTcount: A:0.28, C:0.33, G:0.14, T:0.24
Consensus pattern (73 bp):
GTGCACTCCCACACCGCACATGGCACATATCATCAATGTGTGCACTCACACAGCACACCACTATC
ACCGTCAA
Found at i:13664741 original size:18 final size:18
Alignment explanation
Indices: 13664718--13664772 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
13664708 TATAAGCTAC
13664718 TTTAAAACATAATCTAAA
1 TTTAAAACATAATCTAAA
13664736 TTTAAAAC-T-A-C----
1 TTTAAAACATAATCTAAA
13664747 TTTAAAACATAATCTAAA
1 TTTAAAACATAATCTAAA
13664765 TTTAAAAC
1 TTTAAAAC
13664773 TTACTTACTC
Statistics
Matches: 30, Mismatches: 0, Indels: 14
0.68 0.00 0.32
Matches are distributed among these distances:
11 8 0.27
12 1 0.03
13 1 0.03
14 1 0.03
15 1 0.03
16 1 0.03
17 1 0.03
18 16 0.53
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.35
Consensus pattern (18 bp):
TTTAAAACATAATCTAAA
Found at i:13664746 original size:29 final size:29
Alignment explanation
Indices: 13664714--13664778 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
13664704 CCGTTATAAG
13664714 CTACTTTAAAACATAATCTAAATTTAAAA
1 CTACTTTAAAACATAATCTAAATTTAAAA
13664743 CTACTTTAAAACATAATCTAAATTTAAAA
1 CTACTTTAAAACATAATCTAAATTTAAAA
13664772 CTTACTT
1 C-TACTT
13664779 ACTCTTTTCC
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 30 0.86
30 5 0.14
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (29 bp):
CTACTTTAAAACATAATCTAAATTTAAAA
Found at i:13668193 original size:43 final size:43
Alignment explanation
Indices: 13668145--13668306 Score: 182
Period size: 43 Copynumber: 3.8 Consensus size: 43
13668135 TCAGCAACTC
**** * *
13668145 ATGCGCACTCCCTACTCGCACATGGTTGGGTCATCACCCGATT
1 ATGCGCACTCCCTACTCGCACATAACCGAGTCATCACCAGATT
*
13668188 ATGCGCACTCCCTACTCGCACATAACCGAGTCATCACCAGGTT
1 ATGCGCACTCCCTACTCGCACATAACCGAGTCATCACCAGATT
* * * *
13668231 ATGCGCACTCCCTATTCGCACATAACCGGGTCATC-CTCGGCTT
1 ATGCGCACTCCCTACTCGCACATAACCGAGTCATCAC-CAGATT
* * *
13668274 ATGCACACTCCTTACTCGCACATAGCCGAGTCA
1 ATGCGCACTCCCTACTCGCACATAACCGAGTCA
13668307 ACATAATTAC
Statistics
Matches: 102, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
42 1 0.01
43 101 0.99
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.23
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAACCGAGTCATCACCAGATT
Found at i:13668277 original size:86 final size:86
Alignment explanation
Indices: 13668145--13668306 Score: 218
Period size: 86 Copynumber: 1.9 Consensus size: 86
13668135 TCAGCAACTC
**** *
13668145 ATGCGCACTCCCTACTCGCACATGGTTGGGTCATCACCCGATTATGCGCACTCCCTACTCGCACA
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCACCCGATTATGCACACTCCCTACTCGCACA
13668210 TAACCGAGTCATCACCAGGTT
66 TAACCGAGTCATCACCAGGTT
* * * *
13668231 ATGCGCACTCCCTATTCGCACATAACCGGGTCATC-CTCGGCTTATGCACACTCCTTACTCGCAC
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCAC-CCGATTATGCACACTCCCTACTCGCAC
*
13668295 ATAGCCGAGTCA
65 ATAACCGAGTCA
13668307 ACATAATTAC
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
85 1 0.02
86 64 0.98
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.23
Consensus pattern (86 bp):
ATGCGCACTCCCTACTCGCACATAACCGGGTCATCACCCGATTATGCACACTCCCTACTCGCACA
TAACCGAGTCATCACCAGGTT
Found at i:13675941 original size:3 final size:3
Alignment explanation
Indices: 13675933--13675997 Score: 62
Period size: 3 Copynumber: 22.3 Consensus size: 3
13675923 TACAACCATA
* * * * *
13675933 ATC ATC ATC ATC ATC ATC ATC GTC ACC AAC -CC ATC ATC ATC ATC ACC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
*
13675980 AGC -TC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC A
13675998 CCAACTCATG
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
2 2 0.04
3 49 0.96
ACGTcount: A:0.32, C:0.38, G:0.03, T:0.26
Consensus pattern (3 bp):
ATC
Found at i:13676005 original size:20 final size:20
Alignment explanation
Indices: 13675943--13676006 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
13675933 ATCATCATCA
*
13675943 TCATCATCATCGTCACCAAC
1 TCATCATCATCATCACCAAC
* *
13675963 CCATCATCATCATCACCAGC
1 TCATCATCATCATCACCAAC
13675983 TCATCATCATCATCACCAAC
1 TCATCATCATCATCACCAAC
13676003 TCAT
1 TCAT
13676007 GCGCACTCCC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.31, C:0.41, G:0.03, T:0.25
Consensus pattern (20 bp):
TCATCATCATCATCACCAAC
Found at i:13678804 original size:21 final size:21
Alignment explanation
Indices: 13678780--13678840 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
13678770 TTTGAATGAT
*
13678780 GGTGTCATTCTTTGTCATGTA
1 GGTGTCAGTCTTTGTCATGTA
*
13678801 GGTGTCAGTCTTTGTCATGAA
1 GGTGTCAGTCTTTGTCATGTA
** *
13678822 GGCATTAGTCTTTGTCATG
1 GGTGTCAGTCTTTGTCATG
13678841 ATTTGCATGA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.16, C:0.15, G:0.26, T:0.43
Consensus pattern (21 bp):
GGTGTCAGTCTTTGTCATGTA
Found at i:13683861 original size:43 final size:43
Alignment explanation
Indices: 13683800--13683914 Score: 140
Period size: 43 Copynumber: 2.7 Consensus size: 43
13683790 GTAATTATAT
* *
13683800 TGACTCGGCTATGTGCGAGTAGGGAGTGCACATAAGCCGAAGA
1 TGACTCGACTATGTGCGAGTAGGGAGTGCACATAACCCGAAGA
* * * *
13683843 TGACTCGATTATGTGCGAGTAGGGAGTACGCATAACCCGATGA
1 TGACTCGACTATGTGCGAGTAGGGAGTGCACATAACCCGAAGA
* * * *
13683886 TGACCCAACCATGTGCAAGTAGGGAGTGC
1 TGACTCGACTATGTGCGAGTAGGGAGTGC
13683915 GCATGAGCTG
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.28, C:0.20, G:0.32, T:0.20
Consensus pattern (43 bp):
TGACTCGACTATGTGCGAGTAGGGAGTGCACATAACCCGAAGA
Found at i:13684382 original size:60 final size:60
Alignment explanation
Indices: 13684284--13684431 Score: 217
Period size: 60 Copynumber: 2.5 Consensus size: 60
13684274 CACTGTAGCT
*
13684284 TCTCGCTGCAGTGAGAAACTTTCTGTTTCTGGATTACAATTTCGCTGCAGCGAGATTGAA
1 TCTCACTGCAGTGAGAAACTTTCTGTTTCTGGATTACAATTTCGCTGCAGCGAGATTGAA
* * *
13684344 TTTCACTGCAGCGAGAAACGTTCTGTTTCTAGG-TTACAATTTCGCTGCAGCGAGATTGAA
1 TCTCACTGCAGTGAGAAACTTTCTGTTTCT-GGATTACAATTTCGCTGCAGCGAGATTGAA
* * *
13684404 TCTCGCTACAGTGAAAAACTTTCTGTTT
1 TCTCACTGCAGTGAGAAACTTTCTGTTT
13684432 TGGTCTCCTA
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
60 75 0.97
61 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (60 bp):
TCTCACTGCAGTGAGAAACTTTCTGTTTCTGGATTACAATTTCGCTGCAGCGAGATTGAA
Found at i:13694408 original size:26 final size:25
Alignment explanation
Indices: 13694367--13694425 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 25
13694357 AAAAACTGAT
* *
13694367 AAATAATAACTAAATTAAGATATATAA
1 AAATAA-AATTAAATTAACATA-ATAA
*
13694394 ACATAAAATTAAATTAACATAATAA
1 AAATAAAATTAAATTAACATAATAA
13694419 AAATAAA
1 AAATAAA
13694426 CTAAATAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 10 0.36
26 13 0.46
27 5 0.18
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (25 bp):
AAATAAAATTAAATTAACATAATAA
Found at i:13694420 original size:19 final size:18
Alignment explanation
Indices: 13694396--13694450 Score: 55
Period size: 19 Copynumber: 3.2 Consensus size: 18
13694386 ATATATAAAC
*
13694396 ATAAAATTAAATTAACATA
1 ATAAAATTAAACTAA-ATA
*
13694415 ATAAAAATAAACTAAATA
1 ATAAAATTAAACTAAATA
13694433 A-AAAA-T-AACTAAA-A
1 ATAAAATTAAACTAAATA
13694447 ATAA
1 ATAA
13694451 CGAAATTCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 2 0.06
15 9 0.27
16 1 0.03
17 4 0.12
18 4 0.12
19 13 0.39
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (18 bp):
ATAAAATTAAACTAAATA
Found at i:13708727 original size:10 final size:11
Alignment explanation
Indices: 13708700--13708734 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
13708690 TATGGATGGC
*
13708700 CAAAGCAAGAA
1 CAAAGGAAGAA
13708711 CAAAGGAAGAA
1 CAAAGGAAGAA
13708722 -AAAGGAAGAA
1 CAAAGGAAGAA
13708732 CAA
1 CAA
13708735 GAACCCTAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 10 0.45
11 12 0.55
ACGTcount: A:0.66, C:0.11, G:0.23, T:0.00
Consensus pattern (11 bp):
CAAAGGAAGAA
Found at i:13711477 original size:23 final size:23
Alignment explanation
Indices: 13711329--13711479 Score: 155
Period size: 23 Copynumber: 6.7 Consensus size: 23
13711319 ATTTTTGAGA
* *
13711329 ATTGCGTGACTAGTT-TTTAGGC
1 ATTGCGTGACTAGTTAGTAAGGC
* * * *
13711351 ATTGCGTGACTA-ATATTTAGGT
1 ATTGCGTGACTAGTTAGTAAGGC
* * *
13711373 ATTACGTGACTAATT-GATATGGC
1 ATTGCGTGACTAGTTAG-TAAGGC
13711396 ATTGCGTGACTAGTTAGTAAGGC
1 ATTGCGTGACTAGTTAGTAAGGC
* *
13711419 ATTGCGTGATTGGTTAGTAAGGC
1 ATTGCGTGACTAGTTAGTAAGGC
*
13711442 ATTGCATGACTAGTTAGTAAGGC
1 ATTGCGTGACTAGTTAGTAAGGC
*
13711465 ATTGTGTGACTAGTT
1 ATTGCGTGACTAGTT
13711480 TTTAGGCATC
Statistics
Matches: 107, Mismatches: 18, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
21 1 0.01
22 29 0.27
23 76 0.71
24 1 0.01
ACGTcount: A:0.25, C:0.11, G:0.27, T:0.36
Consensus pattern (23 bp):
ATTGCGTGACTAGTTAGTAAGGC
Found at i:13711608 original size:22 final size:22
Alignment explanation
Indices: 13711576--13711644 Score: 84
Period size: 22 Copynumber: 3.1 Consensus size: 22
13711566 GCAATGATTA
* *
13711576 AGTCACGCAATGCCTAAAAACT
1 AGTCACACAATGTCTAAAAACT
* *
13711598 AGTCTCACAATATCTAAAAACT
1 AGTCACACAATGTCTAAAAACT
* *
13711620 AGTGACATAATGTCTAAAAACT
1 AGTCACACAATGTCTAAAAACT
13711642 AGT
1 AGT
13711645 AATGCAATAC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.43, C:0.20, G:0.12, T:0.25
Consensus pattern (22 bp):
AGTCACACAATGTCTAAAAACT
Found at i:13712040 original size:22 final size:23
Alignment explanation
Indices: 13712010--13712056 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
13712000 ATATAGAGTT
13712010 ATTTGAGCTTAATT-TTAATAGTA
1 ATTTGAGCTTAATTCTT-ATAGTA
*
13712033 ATTT-AGCTTAGTTCTTATAGTA
1 ATTTGAGCTTAATTCTTATAGTA
13712055 AT
1 AT
13712057 GCATAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.49
Consensus pattern (23 bp):
ATTTGAGCTTAATTCTTATAGTA
Found at i:13714248 original size:118 final size:118
Alignment explanation
Indices: 13714040--13714276 Score: 357
Period size: 118 Copynumber: 2.0 Consensus size: 118
13714030 CATTTAAATG
* * * *
13714040 CAACATCTCCCACTCATTCACATTGGTATCAACTTATACCATTCTCAATTTAATTCATTCTCCAT
1 CAACATCTCCCACCCATACACATTGGCATCAACTTATACCATTCTCAATTTAACTCATTCTCCAT
* * * *
13714105 TCATTGTCATATAGGGAAAATGGAATTTACGACCAAAGAGAAAATAATGGTAC
66 CCATTGTCATACAGGGAAAATGGAATGTACAACCAAAGAGAAAATAATGGTAC
* *
13714158 CAACATCTCTCACCCGTACACATTGGCATCAACTTATACCATTCTCAATTTAACTCATTCTCCAT
1 CAACATCTCCCACCCATACACATTGGCATCAACTTATACCATTCTCAATTTAACTCATTCTCCAT
* **
13714223 CCATTGTCATACAGGGAAAATGGAATGTGCAACCAGCGAGAAAATAATGGTAC
66 CCATTGTCATACAGGGAAAATGGAATGTACAACCAAAGAGAAAATAATGGTAC
13714276 C
1 C
13714277 CGTGAGCAGT
Statistics
Matches: 106, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
118 106 1.00
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (118 bp):
CAACATCTCCCACCCATACACATTGGCATCAACTTATACCATTCTCAATTTAACTCATTCTCCAT
CCATTGTCATACAGGGAAAATGGAATGTACAACCAAAGAGAAAATAATGGTAC
Found at i:13720560 original size:20 final size:20
Alignment explanation
Indices: 13720535--13720580 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
13720525 ATTTGGCCCC
*
13720535 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGCATA
*
13720555 ATTTGACTTATTGGAGCATG
1 ATTTGACTTATTGGAGCATA
13720575 ATTTGA
1 ATTTGA
13720581 GGTTTAGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.28, C:0.07, G:0.22, T:0.43
Consensus pattern (20 bp):
ATTTGACTTATTGGAGCATA
Found at i:13723916 original size:254 final size:253
Alignment explanation
Indices: 13723467--13723972 Score: 699
Period size: 254 Copynumber: 2.0 Consensus size: 253
13723457 CTGGTAATTT
* * * * * *
13723467 AAATTAAATAAAATCATGATCAAAACACGCTTTTAAAATATACACAAATTAATAGGATGAAAGCA
1 AAATTAAATAAAATCATAATCAAAACACGCTGTCAAAATATACAAAAATTAAAAAGATGAAAGCA
* * * * * * *
13723532 AGCTAAAACTTGCTCTGATACTATTGTTGGGAGGGGGGTTTACTTTTTTAGATAAATATTCCACT
66 AGCCAAAACTTGCTCTGACACCACTGTTGGGAGGGGGGCTTACCTTCTTAGATAAATATTCCACT
* * * * * *
13723597 TCCTTTCTGATCGAAGAAACTTGCTTTACGAATCTTCCTTCATGTACATAATAATTTCTTCACTC
131 TCCTTTCTAATCGAAGAAACTTACCTTACAAATCTTCCTTCATGCACACAATAATTTCTTCACTC
* *
13723662 TCATTGTTATGGAGTGGCTACTAGAGTCCTCCACAAGGAATTACACGTTCCAAAACCCA
196 TCATTGTTATGAAGTGGCGACTAGAGTCCTCCACAA-GAATTACACGTTCCAAAACCCA
*
13723721 AAATTAAATAAAATCATAATCAAAACACTCTGTCAAAATATACAAAAATTAAAAAGATGAAAGCA
1 AAATTAAATAAAATCATAATCAAAACACGCTGTCAAAATATACAAAAATTAAAAAGATGAAAGCA
* * * *
13723786 AGCCAAAACTTGCTTTGACACCACTGTTGGTAGGTGGGCTTACCTTCTTAGATAAATATTTCAC-
66 AGCCAAAACTTGCTCTGACACCACTGTTGGGAGGGGGGCTTACCTTCTTAGATAAATATTCCACT
* * **
13723850 TCCTTTTCTAATCGAATAAGCTTACCTTACAAATCTTCCTTTGTGCACACAATAATTTCTTCACT
131 TCC-TTTCTAATCGAAGAAACTTACCTTACAAATCTTCCTTCATGCACACAATAATTTCTTCACT
* *
13723915 CTCATTGTTATGAAGTGTCGACTAGAGTCCTCCATAAGAATTACACGTTCCAAAACCC
195 CTCATTGTTATGAAGTGGCGACTAGAGTCCTCCACAAGAATTACACGTTCCAAAACCC
13723973 TTTGGTCTTT
Statistics
Matches: 219, Mismatches: 32, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
253 24 0.11
254 195 0.89
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.31
Consensus pattern (253 bp):
AAATTAAATAAAATCATAATCAAAACACGCTGTCAAAATATACAAAAATTAAAAAGATGAAAGCA
AGCCAAAACTTGCTCTGACACCACTGTTGGGAGGGGGGCTTACCTTCTTAGATAAATATTCCACT
TCCTTTCTAATCGAAGAAACTTACCTTACAAATCTTCCTTCATGCACACAATAATTTCTTCACTC
TCATTGTTATGAAGTGGCGACTAGAGTCCTCCACAAGAATTACACGTTCCAAAACCCA
Found at i:13724168 original size:21 final size:21
Alignment explanation
Indices: 13724143--13724259 Score: 87
Period size: 21 Copynumber: 5.5 Consensus size: 21
13724133 AGGATATCAT
*
13724143 ATTTAAATTTAAGCAAATTAA
1 ATTTAAATTTAAACAAATTAA
* ** **
13724164 ATTTAAATGT-AATTAATCTTT
1 ATTTAAATTTAAACAAAT-TAA
*
13724185 ATTTAAATTTAAAAAAATTAA
1 ATTTAAATTTAAACAAATTAA
* * *
13724206 ATTTAAATATAATGGATAGA-T-A
1 ATTTAAATTTAA---ACAAATTAA
13724228 ATTTAAATTTAAACAAATTAA
1 ATTTAAATTTAAACAAATTAA
13724249 ATTTAAATTTA
1 ATTTAAATTTA
13724260 TATTCTATCT
Statistics
Matches: 72, Mismatches: 17, Indels: 14
0.70 0.17 0.14
Matches are distributed among these distances:
19 3 0.04
20 5 0.07
21 43 0.60
22 17 0.24
23 1 0.01
24 3 0.04
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.42
Consensus pattern (21 bp):
ATTTAAATTTAAACAAATTAA
Found at i:13724188 original size:42 final size:43
Alignment explanation
Indices: 13724142--13724256 Score: 151
Period size: 42 Copynumber: 2.7 Consensus size: 43
13724132 TAGGATATCA
* * * *
13724142 TATTTAAATTTAAGCAAATTAAATTTAAATGTAATTAAT-CTT
1 TATTTAAATTTAAACAAATTAAATTTAAATATAATGAATACAT
* * *
13724184 TATTTAAATTTAAAAAAATTAAATTTAAATATAATGGATAGAT
1 TATTTAAATTTAAACAAATTAAATTTAAATATAATGAATACAT
*
13724227 AATTTAAATTTAAACAAATTAAATTTAAAT
1 TATTTAAATTTAAACAAATTAAATTTAAAT
13724257 TTATATTCTA
Statistics
Matches: 63, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
42 34 0.54
43 29 0.46
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.42
Consensus pattern (43 bp):
TATTTAAATTTAAACAAATTAAATTTAAATATAATGAATACAT
Found at i:13729879 original size:3 final size:3
Alignment explanation
Indices: 13729871--13729914 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
13729861 CATGACAACC
13729871 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
13729915 GTCTTAAGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:13749166 original size:43 final size:43
Alignment explanation
Indices: 13749103--13749210 Score: 144
Period size: 43 Copynumber: 2.5 Consensus size: 43
13749093 TATTGACTCG
** **
13749103 GCTATGTGCGAGTAGGGAGTGCGCATAAGTCGAGGATGACCTG
1 GCTATGTGCGAGTAGGGAGTGCGCATAACCCGAGGATGACCCC
* *
13749146 GTTATGTGCGAGTAGGGAGTGCGCATAACCCGATGATGACCCC
1 GCTATGTGCGAGTAGGGAGTGCGCATAACCCGAGGATGACCCC
* *
13749189 GCCATGTGCGAGTGGGGAGTGC
1 GCTATGTGCGAGTAGGGAGTGC
13749211 ACATGAGCTG
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.21, C:0.19, G:0.39, T:0.20
Consensus pattern (43 bp):
GCTATGTGCGAGTAGGGAGTGCGCATAACCCGAGGATGACCCC
Found at i:13749662 original size:60 final size:60
Alignment explanation
Indices: 13749569--13749754 Score: 259
Period size: 60 Copynumber: 3.1 Consensus size: 60
13749559 TAGCTTCTCA
13749569 CTGCAGCGAAATACATTCTCGCTACAGCGAGAAACTTTCTGTTTCTGGGTTGTAATTTCG
1 CTGCAGCGAAATACATTCTCGCTACAGCGAGAAACTTTCTGTTTCTGGGTTGTAATTTCG
* * * * * * ** *
13749629 CTGCAGCGAGATTGA-ATT-TTGCTGCAGCGAGAAACATTATATTTCTGGGTTACAATTTTG
1 CTGCAGCGA-AAT-ACATTCTCGCTACAGCGAGAAACTTTCTGTTTCTGGGTTGTAATTTCG
13749689 CTGCAGCGAAATACATTCTCGCTACAGCGAGAAACTTTCTGTTTCTGGGTTGTAATTTCG
1 CTGCAGCGAAATACATTCTCGCTACAGCGAGAAACTTTCTGTTTCTGGGTTGTAATTTCG
13749749 CTGCAG
1 CTGCAG
13749755 AAAAACTTTC
Statistics
Matches: 104, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
58 1 0.01
59 5 0.05
60 92 0.88
61 5 0.05
62 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (60 bp):
CTGCAGCGAAATACATTCTCGCTACAGCGAGAAACTTTCTGTTTCTGGGTTGTAATTTCG
Found at i:13758128 original size:19 final size:19
Alignment explanation
Indices: 13758082--13758130 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
13758072 CCTAGTACAC
*
13758082 CTTTTCTTCCACATTTGAA
1 CTTTTCTTTCACATTTGAA
*
13758101 CTTTTCTTTCACCTTTGAA
1 CTTTTCTTTCACATTTGAA
13758120 CTTTTCTTTCA
1 CTTTTCTTTCA
13758131 TCAATACTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.16, C:0.27, G:0.04, T:0.53
Consensus pattern (19 bp):
CTTTTCTTTCACATTTGAA
Found at i:13763228 original size:10 final size:10
Alignment explanation
Indices: 13763202--13763240 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
13763192 GGAAAACATT
13763202 AATAAATAATA
1 AATAAA-AATA
13763213 AATAAAAATA
1 AATAAAAATA
*
13763223 AGTAAAAATA
1 AATAAAAATA
13763233 AATAAAAA
1 AATAAAAA
13763241 AAGGTCAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 20 0.77
11 6 0.23
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.21
Consensus pattern (10 bp):
AATAAAAATA
Found at i:13767270 original size:12 final size:12
Alignment explanation
Indices: 13767253--13767277 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13767243 AAATCCTTAC
13767253 TACTTACCTCTT
1 TACTTACCTCTT
13767265 TACTTACCTCTT
1 TACTTACCTCTT
13767277 T
1 T
13767278 TCCATTGCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.32, G:0.00, T:0.52
Consensus pattern (12 bp):
TACTTACCTCTT
Found at i:13778882 original size:30 final size:32
Alignment explanation
Indices: 13778846--13778908 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
13778836 ATTCAATGTA
13778846 TTACCTTTT-TA-TGGTTAAAGCATAACCACT
1 TTACCTTTTCTATTGGTTAAAGCATAACCACT
* *
13778876 TTACCTTTTCTATTGGTTAAGGTATAACCACT
1 TTACCTTTTCTATTGGTTAAAGCATAACCACT
13778908 T
1 T
13778909 AAGCAAGTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 9 0.31
31 2 0.07
32 18 0.62
ACGTcount: A:0.27, C:0.19, G:0.11, T:0.43
Consensus pattern (32 bp):
TTACCTTTTCTATTGGTTAAAGCATAACCACT
Found at i:13780159 original size:13 final size:13
Alignment explanation
Indices: 13780141--13780165 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13780131 TTATGGTTAC
13780141 TGAATATATTGAA
1 TGAATATATTGAA
13780154 TGAATATATTGA
1 TGAATATATTGA
13780166 CTAAAATGTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (13 bp):
TGAATATATTGAA
Found at i:13784197 original size:20 final size:19
Alignment explanation
Indices: 13784172--13784209 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
13784162 ACAGTCTCCA
13784172 ATTACTAAATTTCTAAAATC
1 ATTACTAAATTTC-AAAATC
*
13784192 ATTACTCAATTTCAAAAT
1 ATTACTAAATTTCAAAAT
13784210 GATTTATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (19 bp):
ATTACTAAATTTCAAAATC
Found at i:13799325 original size:26 final size:26
Alignment explanation
Indices: 13799287--13799338 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
13799277 NNNNNNNNNN
13799287 ATGGGATGATGTGCATGATGATGATG
1 ATGGGATGATGTGCATGATGATGATG
* *
13799313 ATGGGATGGTGTGCATGTTGATGATG
1 ATGGGATGATGTGCATGATGATGATG
13799339 GGTATATGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.23, C:0.04, G:0.40, T:0.33
Consensus pattern (26 bp):
ATGGGATGATGTGCATGATGATGATG
Found at i:13803909 original size:68 final size:68
Alignment explanation
Indices: 13803795--13804059 Score: 316
Period size: 68 Copynumber: 3.9 Consensus size: 68
13803785 CACATACATG
* * *
13803795 CTTACTCATCTCATAAGGTATATGGAAAATACATCATATACATAATCTCATGGCATTCATCATGC
1 CTTAATCATCTCATATGGTATATGGAATATACATCATATACATAATCTCATGGCATTCATCATGC
* *
13803860 TTT
66 ATA
* * *
13803863 CTCAATCATCTCATGTAGTATATGGAATATACATCATATACATAATCTCATGGCATTCATCATGC
1 CTTAATCATCTCATATGGTATATGGAATATACATCATATACATAATCTCATGGCATTCATCATGC
13803928 ATA
66 ATA
* * * * * ** * * * *
13803931 CTTAATCATCTCATATGGTATATGAAATTTACATTATATACACAATTTTGTAGTAATCATCTTGC
1 CTTAATCATCTCATATGGTATATGGAATATACATCATATACATAATCTCATGGCATTCATCATGC
13803996 ATA
66 ATA
* * * *
13803999 CTTAATCATCTCATATGGTATAT-GACTTTACATCATATACATAATCTTATGGCATTTATCA
1 CTTAATCATCTCATATGGTATATGGAATATACATCATATACATAATCTCATGGCATTCATCA
13804060 CACCAAACAT
Statistics
Matches: 164, Mismatches: 33, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
67 27 0.16
68 137 0.84
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.38
Consensus pattern (68 bp):
CTTAATCATCTCATATGGTATATGGAATATACATCATATACATAATCTCATGGCATTCATCATGC
ATA
Found at i:13805246 original size:16 final size:15
Alignment explanation
Indices: 13805220--13805249 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
13805210 TAAAAATATC
13805220 CAAAAAATCAAAATT
1 CAAAAAATCAAAATT
13805235 CAAAAGAATCAAAAT
1 CAAAA-AATCAAAAT
13805250 CTTAAGTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.67, C:0.13, G:0.03, T:0.17
Consensus pattern (15 bp):
CAAAAAATCAAAATT
Found at i:13805879 original size:20 final size:20
Alignment explanation
Indices: 13805843--13805880 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
13805833 GTAGTTTAGT
*
13805843 TTAGGTTAAATTAAGTTAAG
1 TTAGGTTAAAATAAGTTAAG
13805863 TTAGGTTATAAAT-AGTTA
1 TTAGGTTA-AAATAAGTTA
13805881 GCTTAAGGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.42
Consensus pattern (20 bp):
TTAGGTTAAAATAAGTTAAG
Found at i:13814614 original size:43 final size:43
Alignment explanation
Indices: 13814555--13814690 Score: 209
Period size: 43 Copynumber: 3.2 Consensus size: 43
13814545 TTGTGTGATA
* *
13814555 ATGATGACCCAGCTATGTGAGGTGTGGGAGTGCACAAGAGCTG
1 ATGATGACCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTG
** *
13814598 ATGATGACTTAGCTATGTGCGGTGTGGGAGTGCAGATGAGCTG
1 ATGATGACCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTG
* *
13814641 ATGATGACCCAGCTATGTGCGGTGTGGGAGTGCACGTGAGTTG
1 ATGATGACCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTG
13814684 ATGATGA
1 ATGATGA
13814691 TGATATTGCA
Statistics
Matches: 83, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 83 1.00
ACGTcount: A:0.23, C:0.14, G:0.38, T:0.25
Consensus pattern (43 bp):
ATGATGACCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTG
Found at i:13817697 original size:30 final size:30
Alignment explanation
Indices: 13817662--13817720 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
13817652 GGTATTCTCT
*
13817662 TAGTTTGTAATATGAATGCTCGGGTATTGA
1 TAGTTTGTAATATGAATGCTCGAGTATTGA
*
13817692 TAGTTTGTAGTATGAATGCTCGAGTATTG
1 TAGTTTGTAATATGAATGCTCGAGTATTG
13817721 TTTGATCTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.25, C:0.07, G:0.27, T:0.41
Consensus pattern (30 bp):
TAGTTTGTAATATGAATGCTCGAGTATTGA
Found at i:13831701 original size:43 final size:43
Alignment explanation
Indices: 13831644--13831762 Score: 177
Period size: 43 Copynumber: 2.8 Consensus size: 43
13831634 GTAATTATAT
* *
13831644 TGACTCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCCGAG-GA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCG-GTGA
*
13831687 TGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
* *
13831730 TGACCCAGCCATGTGCGAGTAGGGAGTGCGCAT
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCAT
13831763 GAGCTGGTGA
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
42 1 0.01
43 68 0.99
ACGTcount: A:0.22, C:0.21, G:0.38, T:0.19
Consensus pattern (43 bp):
TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
Found at i:13831772 original size:43 final size:43
Alignment explanation
Indices: 13831654--13831775 Score: 174
Period size: 43 Copynumber: 2.8 Consensus size: 43
13831644 TGACTCGGCT
* **
13831654 ATGTGCGAGTAGGGAGTGCGCATAAGCCGAG-GATGACCCGGTT
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCG-GTGATGACCCAGCC
*
13831697 ATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCCAGCC
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAGCC
* *
13831740 ATGTGCGAGTAGGGAGTGCGCATGAGCTGGTGATGA
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGA
13831776 TGATGATGGG
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
42 1 0.01
43 70 0.99
ACGTcount: A:0.23, C:0.19, G:0.39, T:0.19
Consensus pattern (43 bp):
ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAGCC
Found at i:13841026 original size:19 final size:19
Alignment explanation
Indices: 13841002--13841104 Score: 66
Period size: 19 Copynumber: 5.3 Consensus size: 19
13840992 ATAGTGCCTG
13841002 TGTACACGATGTGGGGGGA
1 TGTACACGATGTGGGGGGA
* *** *
13841021 TGTACATGATG-GCACTGAA
1 TGTACACGATGTG-GGGGGA
*
13841040 TGTACATGATGTGGGGGGA
1 TGTACACGATGTGGGGGGA
* **
13841059 TGCACACGATG-GCGTCGGCTA
1 TGTACACGATGTG-G--GGGGA
*
13841080 TGTGCACGATGTGGGGGGA
1 TGTACACGATGTGGGGGGA
13841099 TGTACA
1 TGTACA
13841105 TGAGCCGGGT
Statistics
Matches: 60, Mismatches: 18, Indels: 12
0.67 0.20 0.13
Matches are distributed among these distances:
18 2 0.03
19 43 0.72
20 1 0.02
21 13 0.22
22 1 0.02
ACGTcount: A:0.22, C:0.15, G:0.40, T:0.23
Consensus pattern (19 bp):
TGTACACGATGTGGGGGGA
Found at i:13841045 original size:38 final size:40
Alignment explanation
Indices: 13841002--13841107 Score: 135
Period size: 38 Copynumber: 2.7 Consensus size: 40
13840992 ATAGTGCCTG
*
13841002 TGTACACGATGTGGGGGGATGTACATGATGGC-ACTG-AA
1 TGTACACGATGTGGGGGGATGTACATGATGGCGACGGCAA
* * * * *
13841040 TGTACATGATGTGGGGGGATGCACACGATGGCGTCGGCTA
1 TGTACACGATGTGGGGGGATGTACATGATGGCGACGGCAA
*
13841080 TGTGCACGATGTGGGGGGATGTACATGA
1 TGTACACGATGTGGGGGGATGTACATGA
13841108 GCCGGGTGTG
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
38 29 0.52
39 2 0.04
40 25 0.45
ACGTcount: A:0.23, C:0.14, G:0.40, T:0.24
Consensus pattern (40 bp):
TGTACACGATGTGGGGGGATGTACATGATGGCGACGGCAA
Found at i:13842500 original size:22 final size:20
Alignment explanation
Indices: 13842459--13842499 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
13842449 TTAAAGCAAA
* *
13842459 GCTTCTCTTTTTTTTCTTTT
1 GCTTCTCTTTGTATTCTTTT
13842479 GCTTCTCTCTTGTATTCTTTT
1 GCTTCTCT-TTGTATTCTTTT
13842500 TCCTTTTCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.02, C:0.22, G:0.07, T:0.68
Consensus pattern (20 bp):
GCTTCTCTTTGTATTCTTTT
Found at i:13850280 original size:43 final size:42
Alignment explanation
Indices: 13850153--13850286 Score: 205
Period size: 42 Copynumber: 3.2 Consensus size: 42
13850143 TTATGTGATA
* *
13850153 ATGATGACCTAGCTATGTTCGTGTGGGAGTGCACATGAGCTG
1 ATGATGACCTAACTATGTGCGTGTGGGAGTGCACATGAGCTG
* *
13850195 ATGATGACCTAACTATGTGTGTGTGGGAGTGTACATGAGCTG
1 ATGATGACCTAACTATGTGCGTGTGGGAGTGCACATGAGCTG
* *
13850237 ATGATGACCCAACTATGTGCGAGTAGGGAGTGCACATGAGCTG
1 ATGATGACCTAACTATGTGCGTGT-GGGAGTGCACATGAGCTG
13850280 ATGATGA
1 ATGATGA
13850287 TGGGATGCTA
Statistics
Matches: 83, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
42 59 0.71
43 24 0.29
ACGTcount: A:0.25, C:0.15, G:0.33, T:0.27
Consensus pattern (42 bp):
ATGATGACCTAACTATGTGCGTGTGGGAGTGCACATGAGCTG
Found at i:13850316 original size:2 final size:2
Alignment explanation
Indices: 13850309--13850345 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
13850299 CATGATGATG
*
13850309 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13850346 GTGTTATAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:13868805 original size:46 final size:46
Alignment explanation
Indices: 13868738--13868830 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
13868728 GAGTAAGCGA
*
13868738 GAGAAAGGATAGTTTTCAGGTGATGTAGATAGATAACCAACCGAGG
1 GAGAAAGGACAGTTTTCAGGTGATGTAGATAGATAACCAACCGAGG
13868784 GAGAAAGGACAGTTTTCAGGTGATGTAGATAGATAACCAACCGAGG
1 GAGAAAGGACAGTTTTCAGGTGATGTAGATAGATAACCAACCGAGG
13868830 G
1 G
13868831 TATTACTATT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.37, C:0.12, G:0.31, T:0.20
Consensus pattern (46 bp):
GAGAAAGGACAGTTTTCAGGTGATGTAGATAGATAACCAACCGAGG
Found at i:13875040 original size:2 final size:2
Alignment explanation
Indices: 13875033--13875058 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13875023 TCGTTGTTAT
13875033 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
13875059 CATGCATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13877474 original size:19 final size:20
Alignment explanation
Indices: 13877450--13877487 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
13877440 CTATAAATAC
13877450 CTTGAA-TTTCCAGCAGCTT
1 CTTGAATTTTCCAGCAGCTT
*
13877469 CTTGAATTTTTCAGCAGCT
1 CTTGAATTTTCCAGCAGCT
13877488 GGTCTTCTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.21, C:0.24, G:0.16, T:0.39
Consensus pattern (20 bp):
CTTGAATTTTCCAGCAGCTT
Found at i:13878535 original size:43 final size:43
Alignment explanation
Indices: 13878361--13878522 Score: 245
Period size: 43 Copynumber: 3.8 Consensus size: 43
13878351 GTAATTATAT
* *
13878361 TGACTCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCCGAGGA
1 TGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAAGCCGAGGA
13878404 TGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAAGCCGAGGA
1 TGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAAGCCGAGGA
*
13878447 TGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAACCCG-GTGA
1 TGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAAGCCGAG-GA
** **
13878490 TGACCTAGCCATGTGCGAGTAGGGAGTGCGCAT
1 TGACCCGGTTATGTGCGAGTAGGGAGTGCGCAT
13878523 GAGCTGGTGA
Statistics
Matches: 111, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
42 1 0.01
43 110 0.99
ACGTcount: A:0.22, C:0.20, G:0.38, T:0.20
Consensus pattern (43 bp):
TGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAAGCCGAGGA
Found at i:13882358 original size:19 final size:19
Alignment explanation
Indices: 13882334--13882371 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
13882324 AAGTGAAAAA
13882334 TTATTTATAAAATAATATT
1 TTATTTATAAAATAATATT
*
13882353 TTATTTATAGAATAATATT
1 TTATTTATAAAATAATATT
13882372 AAAATATTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (19 bp):
TTATTTATAAAATAATATT
Found at i:13882379 original size:22 final size:22
Alignment explanation
Indices: 13882330--13882379 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 22
13882320 AGACAAGTGA
13882330 AAAATTATTTATAAAATAATATT
1 AAAA-TATTTATAAAATAATATT
* *
13882353 ---TTATTTATAGAATAATATT
1 AAAATATTTATAAAATAATATT
13882372 AAAATATT
1 AAAATATT
13882380 ACTATTTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 7
0.68 0.10 0.23
Matches are distributed among these distances:
19 17 0.81
22 4 0.19
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
AAAATATTTATAAAATAATATT
Found at i:13883900 original size:35 final size:35
Alignment explanation
Indices: 13883861--13883968 Score: 162
Period size: 35 Copynumber: 3.1 Consensus size: 35
13883851 GGAGTGCGTG
*
13883861 TGATGATATTGAAATGTTCGTGTAGGGAGTGCACA
1 TGATGATATTGAAATGTGCGTGTAGGGAGTGCACA
13883896 TGATGATATTGAAATGTGCGTGTAGGGAGTGCACA
1 TGATGATATTGAAATGTGCGTGTAGGGAGTGCACA
*** * *
13883931 TGATGATATTGCCTTATGAGTGTAGGGAGTGCACA
1 TGATGATATTGAAATGTGCGTGTAGGGAGTGCACA
13883966 TGA
1 TGA
13883969 GTTGAGTAAG
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 67 1.00
ACGTcount: A:0.28, C:0.09, G:0.32, T:0.31
Consensus pattern (35 bp):
TGATGATATTGAAATGTGCGTGTAGGGAGTGCACA
Found at i:13891889 original size:15 final size:14
Alignment explanation
Indices: 13891869--13891898 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
13891859 CTTTATTTCC
13891869 TTCTTCTTCTTTCTT
1 TTCTTCTTC-TTCTT
13891884 TTCTTCTTCTTCTT
1 TTCTTCTTCTTCTT
13891898 T
1 T
13891899 GGCTAGCCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (14 bp):
TTCTTCTTCTTCTT
Found at i:13893028 original size:43 final size:42
Alignment explanation
Indices: 13892966--13893097 Score: 140
Period size: 43 Copynumber: 3.0 Consensus size: 42
13892956 ACAATGCAAT
*
13892966 ATCATCATCATGTGCACTCCCTACTCGCACATAGCCGAGTCATC
1 ATCATC-TCATGTGCACTCCC-ACACGCACATAGCCGAGTCATC
** * *
13893010 ATCATCTCATGTATACTCCCACACTACACATAG-CTAGGTCATC
1 ATCATCTCATGTGCACTCCCACAC-GCACATAGCCGA-GTCATC
* * *
13893053 ATCAACTCATGTGCACTCCCACACCGCACATAGCTGGGTCATC
1 ATCATCTCATGTGCACTCCCACA-CGCACATAGCCGAGTCATC
13893096 AT
1 AT
13893098 TATCACACAA
Statistics
Matches: 72, Mismatches: 12, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
42 5 0.07
43 60 0.83
44 7 0.10
ACGTcount: A:0.27, C:0.35, G:0.13, T:0.25
Consensus pattern (42 bp):
ATCATCTCATGTGCACTCCCACACGCACATAGCCGAGTCATC
Found at i:13909738 original size:60 final size:60
Alignment explanation
Indices: 13909558--13909799 Score: 330
Period size: 60 Copynumber: 4.1 Consensus size: 60
13909548 TGACATCATC
* * ** * ** *
13909558 ACCTACTCGTCGGAACTGCCCATGCCACC--ATATGAATTAGGGCTTCAGGTCCCCTTTT
1 ACCTACTCGTGGGAACTACCCACACCACCATATATAAATCGGGGCTTCAGGTCCCCCTTT
* * * * *
13909616 ACCTACTCGTGGGAACTACTCACGCCACC--ATATGAATCGAGGCTTCAGGTCCCTCTTT
1 ACCTACTCGTGGGAACTACCCACACCACCATATATAAATCGGGGCTTCAGGTCCCCCTTT
*
13909674 ACCTACTCGTGGGAATTACCCACACCACCATATATAAATCGGGGCTTCAGGTCCCCCTTT
1 ACCTACTCGTGGGAACTACCCACACCACCATATATAAATCGGGGCTTCAGGTCCCCCTTT
13909734 ACCTACTCGTGGGAACTACCCACACCACCATATATAAATCGGGGCTTCAGGTCCCCCTTT
1 ACCTACTCGTGGGAACTACCCACACCACCATATATAAATCGGGGCTTCAGGTCCCCCTTT
13909794 ACCTAC
1 ACCTAC
13909800 CCAGAATATC
Statistics
Matches: 166, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
58 75 0.45
60 91 0.55
ACGTcount: A:0.24, C:0.34, G:0.17, T:0.25
Consensus pattern (60 bp):
ACCTACTCGTGGGAACTACCCACACCACCATATATAAATCGGGGCTTCAGGTCCCCCTTT
Found at i:13910855 original size:11 final size:11
Alignment explanation
Indices: 13910839--13910869 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
13910829 TTTTTCTCTT
13910839 TCTTTCTTCTC
1 TCTTTCTTCTC
13910850 TCTTTCTTCTC
1 TCTTTCTTCTC
13910861 -CTTTCTTCT
1 TCTTTCTTCT
13910870 TTTATTTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (11 bp):
TCTTTCTTCTC
Found at i:13911026 original size:34 final size:35
Alignment explanation
Indices: 13910971--13911051 Score: 82
Period size: 34 Copynumber: 2.4 Consensus size: 35
13910961 TCAGCTTTTT
* * *
13910971 TTCTTCTCTCTNCTTTCCC-TT-TTCTCTTTCTTTC
1 TTCTTCTCTTTTCTTTCCCTTTCTTCT-TTTATTTC
13911005 TTCTTCTCTTTTC-TTCTCCTTTCTTCTTTTATTTC
1 TTCTTCTCTTTTCTTTC-CCTTTCTTCTTTTATTTC
13911040 -TCTT-TCTTTTCT
1 TTCTTCTCTTTTCT
13911052 CCTCGGCTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
33 10 0.25
34 17 0.43
35 9 0.22
36 4 0.10
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.67
Consensus pattern (35 bp):
TTCTTCTCTTTTCTTTCCCTTTCTTCTTTTATTTC
Found at i:13911032 original size:162 final size:161
Alignment explanation
Indices: 13910821--13911145 Score: 609
Period size: 162 Copynumber: 2.0 Consensus size: 161
13910811 TGGTCGGCGG
13910821 CTTTCCCCTTTTTCTCTTTCTTTCTTCTCTCTTTCTTCTCCTTTCTTCTTTTATTTCTCTTTCTT
1 CTTTCCCCTTTTTCTCTTTCTTTCTTCTCTCTTTCTTCTCCTTTCTTCTTTTATTTCTCTTTCTT
13910886 TTCTCCTCGGCTTAGCAGATTTTCTTTCGCTCTCTACCAGCCGGCGATACCAGCTCTCTCTTCTT
66 TTCTCCTCGGCTTAGCAGATTTTCTTTCGCTCTCTACCAGCCGGCGATACCAGCTCTCTCTTCTT
13910951 TCTATTTCTTTCAGCTTTTTTTCTTCTCTCT
131 TCTATTTCTTTCAGCTTTTTTTCTTCTCTCT
13910982 NCTTT-CCC-TTTTCTCTTTCTTTCTTCTTCTCTTTTCTTCTCCTTTCTTCTTTTATTTCTCTTT
1 -CTTTCCCCTTTTTCTCTTTCTTTCTTC-TCTC-TTTCTTCTCCTTTCTTCTTTTATTTCTCTTT
13911045 CTTTTCTCCTCGGCTTAGCAGATTTTCTTTCGCTCTCTACCAGCCGGCGATACCAGCTCTCTCTT
63 CTTTTCTCCTCGGCTTAGCAGATTTTCTTTCGCTCTCTACCAGCCGGCGATACCAGCTCTCTCTT
13911110 CTTTCTATTTCTTTCAGCTTTTTTTCTTCTCTCT
128 CTTTCTATTTCTTTCAGCTTTTTTTCTTCTCTCT
13911144 CT
1 CT
13911146 CTTTCTCTTT
Statistics
Matches: 161, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
160 18 0.11
161 9 0.06
162 134 0.83
ACGTcount: A:0.07, C:0.32, G:0.07, T:0.54
Consensus pattern (161 bp):
CTTTCCCCTTTTTCTCTTTCTTTCTTCTCTCTTTCTTCTCCTTTCTTCTTTTATTTCTCTTTCTT
TTCTCCTCGGCTTAGCAGATTTTCTTTCGCTCTCTACCAGCCGGCGATACCAGCTCTCTCTTCTT
TCTATTTCTTTCAGCTTTTTTTCTTCTCTCT
Found at i:13911034 original size:18 final size:18
Alignment explanation
Indices: 13911005--13911047 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
13910995 TCTTTCTTTC
13911005 TTCTTCTCTTT-TCTTCTCCT
1 TTCTTCT-TTTAT-TTCT-CT
13911025 TTCTTCTTTTATTTCTCT
1 TTCTTCTTTTATTTCTCT
13911043 TTCTT
1 TTCTT
13911048 TTCTCCTCGG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 7 0.32
19 7 0.32
20 8 0.36
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (18 bp):
TTCTTCTTTTATTTCTCT
Found at i:13911051 original size:23 final size:22
Alignment explanation
Indices: 13910991--13911048 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 22
13910981 TNCTTTCCCT
*
13910991 TTTCTCTTTCTTTCTTCTTCTC
1 TTTCTCTTTCTTTCTTCTTCTA
*
13911013 TTT-TCTTCTCCTTTCTTCTTTTA
1 TTTCTCTT-T-CTTTCTTCTTCTA
13911036 TTTCTCTTTCTTT
1 TTTCTCTTTCTTT
13911049 TCTCCTCGGC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
21 4 0.13
22 8 0.26
23 15 0.48
24 4 0.13
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTCTCTTTCTTTCTTCTTCTA
Found at i:13911137 original size:25 final size:24
Alignment explanation
Indices: 13911108--13911163 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
13911098 CAGCTCTCTC
*
13911108 TTCTTTCTATTTCTTTCAGCTTTTT
1 TTCTTTCTATCTCTTTC-GCTTTTT
* *
13911133 TTCTTCTCTCTCTCTTTCTCTTTTT
1 TTCTT-TCTATCTCTTTCGCTTTTT
13911158 TT-TTTC
1 TTCTTTC
13911164 CTTCTTTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 2 0.07
24 2 0.07
25 13 0.48
26 10 0.37
ACGTcount: A:0.04, C:0.25, G:0.02, T:0.70
Consensus pattern (24 bp):
TTCTTTCTATCTCTTTCGCTTTTT
Found at i:13911835 original size:43 final size:43
Alignment explanation
Indices: 13911721--13911845 Score: 162
Period size: 43 Copynumber: 2.9 Consensus size: 43
13911711 ATTACAATCA
* * * * *
13911721 TCATGTGCACTCCTTAC-TCGCACATAGCCAAGTCATCATTAGC
1 TCATGTGCACT-CTCACACCGCACATAGCTAGGTCATCATCAGC
* *
13911764 TCATGTGCACTCCCACACTGCACATAGCTAGGTCATCATCAGC
1 TCATGTGCACTCTCACACCGCACATAGCTAGGTCATCATCAGC
*
13911807 TCATGTGCACTCTCACACCGCACATAGCTGGGTCATCAT
1 TCATGTGCACTCTCACACCGCACATAGCTAGGTCATCAT
13911846 TATCACACAA
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
42 3 0.04
43 68 0.96
ACGTcount: A:0.25, C:0.34, G:0.16, T:0.26
Consensus pattern (43 bp):
TCATGTGCACTCTCACACCGCACATAGCTAGGTCATCATCAGC
Found at i:13915057 original size:35 final size:35
Alignment explanation
Indices: 13915018--13915134 Score: 153
Period size: 35 Copynumber: 3.3 Consensus size: 35
13915008 ATGTGGGTGA
**
13915018 GAGTGCATGTGATGATATTGAAATGTGCGTGTAGG
1 GAGTGCACATGATGATATTGAAATGTGCGTGTAGG
13915053 GAGTGCACATGATGATATTGAAATGTGCGTGTAGG
1 GAGTGCACATGATGATATTGAAATGTGCGTGTAGG
* *** * *
13915088 AAGTGCACATGATGATATTGCCTTGTGTGTCTAGG
1 GAGTGCACATGATGATATTGAAATGTGCGTGTAGG
*
13915123 AAGTGCACATGA
1 GAGTGCACATGA
13915135 GCTGAGTAAG
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 74 1.00
ACGTcount: A:0.27, C:0.10, G:0.32, T:0.30
Consensus pattern (35 bp):
GAGTGCACATGATGATATTGAAATGTGCGTGTAGG
Found at i:13915173 original size:2 final size:2
Alignment explanation
Indices: 13915166--13915207 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
13915156 GTACTTGTAC
13915166 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13915208 NNNNNNNNNN
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):
AT
Found at i:13915319 original size:2 final size:2
Alignment explanation
Indices: 13915312--13915357 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
13915302 NNNNNNNNNN
13915312 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13915354 AT AT
1 AT AT
13915358 GCTATAGACA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13919152 original size:25 final size:24
Alignment explanation
Indices: 13919109--13919163 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
13919099 ATGACATTAA
13919109 AAATT-AAATAACGTTAG-AAGCAC
1 AAATTAAAATAACGTTAGAAAG-AC
13919132 AAATTAAATATAAC-TTGAGAAAGAC
1 AAATTAAA-ATAACGTT-AGAAAGAC
13919157 AAATTAA
1 AAATTAA
13919164 TTAAAAATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
23 5 0.18
24 4 0.14
25 16 0.57
26 3 0.11
ACGTcount: A:0.56, C:0.09, G:0.11, T:0.24
Consensus pattern (24 bp):
AAATTAAAATAACGTTAGAAAGAC
Found at i:13920357 original size:60 final size:60
Alignment explanation
Indices: 13920236--13920366 Score: 136
Period size: 60 Copynumber: 2.2 Consensus size: 60
13920226 CCCATGCCAT
* * * * **
13920236 CAAATATAAATCAAAGCTTTAGGTCCCCCTTTACCTACTAGTGCGAACTCTCTACGCCAC
1 CAAATATAAATCAAAGCTTCAGGTCCCCCTTTACATACTAGTGCGAACTCCCCACAACAC
** * * * *
13920296 CAAATATAAATCGTAGCTTCAGGTCCCCTTTTACATAGTCGTGGGAACTCCCCACAACAC
1 CAAATATAAATCAAAGCTTCAGGTCCCCCTTTACATACTAGTGCGAACTCCCCACAACAC
* *
13920356 CATATCTAAAT
1 CAAATATAAAT
13920367 TGGGGCTTCA
Statistics
Matches: 57, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.31, C:0.30, G:0.12, T:0.27
Consensus pattern (60 bp):
CAAATATAAATCAAAGCTTCAGGTCCCCCTTTACATACTAGTGCGAACTCCCCACAACAC
Found at i:13922910 original size:22 final size:22
Alignment explanation
Indices: 13922882--13922952 Score: 97
Period size: 22 Copynumber: 3.2 Consensus size: 22
13922872 GGTGAATGAA
13922882 GCATTGCATGACTAGGTTGTAG
1 GCATTGCATGACTAGGTTGTAG
* *
13922904 GCATTGCATGACTAGTTTTTAG
1 GCATTGCATGACTAGGTTGTAG
* * *
13922926 TCATTACATGACAAGGTTGTAG
1 GCATTGCATGACTAGGTTGTAG
13922948 GCATT
1 GCATT
13922953 ACGTGAATAA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.35
Consensus pattern (22 bp):
GCATTGCATGACTAGGTTGTAG
Found at i:13924927 original size:29 final size:28
Alignment explanation
Indices: 13924880--13925022 Score: 146
Period size: 29 Copynumber: 5.0 Consensus size: 28
13924870 TGGCAACTTT
13924880 AACATGTTTGTCTTAATTTAGACAAGAA
1 AACATGTTTGTCTTAATTTAGACAAGAA
13924908 AACATGTTTGGTCTTAATTTAGACAA-ACA
1 AACATGTTT-GTCTTAATTTAGACAAGA-A
**
13924937 AATTTGTTTGTCTT-ATTTAAGACAAGAAA
1 AACATGTTTGTCTTAATTT-AGACAAG-AA
* * *
13924966 AATATTTTTTGTCTTAATCTAGACAAGAA
1 AACA-TGTTTGTCTTAATTTAGACAAGAA
* * *
13924995 TACATATTTGTCTCAAATTTAGACAAGA
1 AACATGTTTGTCT-TAATTTAGACAAGA
13925023 TAAAATATTT
Statistics
Matches: 97, Mismatches: 10, Indels: 15
0.80 0.08 0.12
Matches are distributed among these distances:
27 4 0.04
28 29 0.30
29 44 0.45
30 17 0.18
31 3 0.03
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (28 bp):
AACATGTTTGTCTTAATTTAGACAAGAA
Found at i:13926491 original size:37 final size:37
Alignment explanation
Indices: 13926449--13926541 Score: 143
Period size: 37 Copynumber: 2.5 Consensus size: 37
13926439 TTGCTTATGT
*
13926449 GCGATGTGGGGGTTGCACATAATGGCATTAGTTGTGC
1 GCGATGTGGGGGTTGCACACAATGGCATTAGTTGTGC
* *
13926486 GCGATGTGAGGGTTGCACACAATGGTATTAGTTGTGC
1 GCGATGTGGGGGTTGCACACAATGGCATTAGTTGTGC
*
13926523 GCGATGT-GGGGCTGCACAC
1 GCGATGTGGGGGTTGCACAC
13926542 GATGACTCCA
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
36 10 0.20
37 41 0.80
ACGTcount: A:0.19, C:0.16, G:0.38, T:0.27
Consensus pattern (37 bp):
GCGATGTGGGGGTTGCACACAATGGCATTAGTTGTGC
Found at i:13926626 original size:2 final size:2
Alignment explanation
Indices: 13926613--13926646 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
13926603 TATTCATGTT
*
13926613 TA TA TA TG 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
13926647 CTTATGCAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13932171 original size:15 final size:15
Alignment explanation
Indices: 13932151--13932181 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
13932141 GAGAATGAAT
*
13932151 TACACTAACAGATTG
1 TACACTAAAAGATTG
13932166 TACACTAAAAGATTG
1 TACACTAAAAGATTG
13932181 T
1 T
13932182 CGAAGAACCC
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:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (15 bp):
TACACTAAAAGATTG
Found at i:13934349 original size:41 final size:41
Alignment explanation
Indices: 13934304--13934386 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
13934294 GCCTTGAACT
13934304 AGTTCAAATAGAAATTCTAAGAGGAATTTGAAAATTTTGAA
1 AGTTCAAATAGAAATTCTAAGAGGAATTTGAAAATTTTGAA
13934345 AGTTCAAATAGAAATTCTAAGAGGAATTTGAAAATTTTGAA
1 AGTTCAAATAGAAATTCTAAGAGGAATTTGAAAATTTTGAA
13934386 A
1 A
13934387 TCCACAGAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.47, C:0.05, G:0.17, T:0.31
Consensus pattern (41 bp):
AGTTCAAATAGAAATTCTAAGAGGAATTTGAAAATTTTGAA
Found at i:13936177 original size:19 final size:19
Alignment explanation
Indices: 13936153--13936251 Score: 74
Period size: 19 Copynumber: 5.1 Consensus size: 19
13936143 TGCCCGTGTG
13936153 CACGATGTGGGGGGATGTA
1 CACGATGTGGGGGGATGTA
**** *
13936172 CACGATG-GCACTGATTGTG
1 CACGATGTGGGGGGA-TGTA
*
13936191 CACGATGTGGGGGGATGCA
1 CACGATGTGGGGGGATGTA
* ** *
13936210 CACGATGGTGCCGGCTATGTG
1 CACGAT-GTG-GGGGGATGTA
13936231 CACGATGTGGGGGGATGTA
1 CACGATGTGGGGGGATGTA
13936250 CA
1 CA
13936252 TGAGCCGGGT
Statistics
Matches: 56, Mismatches: 20, Indels: 8
0.67 0.24 0.10
Matches are distributed among these distances:
18 3 0.05
19 33 0.59
20 9 0.16
21 11 0.20
ACGTcount: A:0.20, C:0.17, G:0.41, T:0.21
Consensus pattern (19 bp):
CACGATGTGGGGGGATGTA
Found at i:13936191 original size:38 final size:40
Alignment explanation
Indices: 13936149--13936251 Score: 149
Period size: 38 Copynumber: 2.6 Consensus size: 40
13936139 ATAGTGCCCG
*
13936149 TGTGCACGATGTGGGGGGATGTACACGAT-G-GCACTGAT-
1 TGTGCACGATGTGGGGGGATGTACACGATGGTGC-CGGATA
* *
13936187 TGTGCACGATGTGGGGGGATGCACACGATGGTGCCGGCTA
1 TGTGCACGATGTGGGGGGATGTACACGATGGTGCCGGATA
13936227 TGTGCACGATGTGGGGGGATGTACA
1 TGTGCACGATGTGGGGGGATGTACA
13936252 TGAGCCGGGT
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
38 28 0.48
39 4 0.07
40 26 0.45
ACGTcount: A:0.19, C:0.17, G:0.42, T:0.22
Consensus pattern (40 bp):
TGTGCACGATGTGGGGGGATGTACACGATGGTGCCGGATA
Found at i:13938386 original size:53 final size:52
Alignment explanation
Indices: 13938328--13938429 Score: 159
Period size: 53 Copynumber: 1.9 Consensus size: 52
13938318 CAAAGTAGTT
* *
13938328 TGCATGTGATAAATTTATTTTATGTTATTTGATAAATGCTATGCAATGCAGTA
1 TGCATGTGATAAATTTATTTTATGTGATTTAATAAATGCTATGC-ATGCAGTA
* *
13938381 TGCATGTGATAGATTTATTTTATGTGATTTAATAAATGTTATGCATGCA
1 TGCATGTGATAAATTTATTTTATGTGATTTAATAAATGCTATGCATGCA
13938430 AAGATGAGAC
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
52 5 0.11
53 40 0.89
ACGTcount: A:0.31, C:0.07, G:0.18, T:0.44
Consensus pattern (52 bp):
TGCATGTGATAAATTTATTTTATGTGATTTAATAAATGCTATGCATGCAGTA
Found at i:13941190 original size:29 final size:29
Alignment explanation
Indices: 13941142--13941357 Score: 200
Period size: 29 Copynumber: 7.7 Consensus size: 29
13941132 TGGCAGCTTT
* *
13941142 AACATGTTTTGTTTTGATTTAGACAAGAA
1 AACATGTTTTGTCTTAATTTAGACAAGAA
*
13941171 AACATGTTTTGTCTTAATTTAG---ATAA
1 AACATGTTTTGTCTTAATTTAGACAAGAA
* * *
13941197 TA-A----TTGTCTTAATTTAGATATGAA
1 AACATGTTTTGTCTTAATTTAGACAAGAA
* *
13941221 AGCATATTTTGTCTTAATTTAGACAAGAA
1 AACATGTTTTGTCTTAATTTAGACAAGAA
* *
13941250 AATATG-TTTGTCTTAATTTAAGAGAAGAAA
1 AACATGTTTTGTCTTAATTT-AGACAAG-AA
* *
13941280 AATATGTTTTGTCTTAATCTAGACAAGAA
1 AACATGTTTTGTCTTAATTTAGACAAGAA
* * *
13941309 AACAT-ATTTGTCTCAATTTAGACAAGAT
1 AACATGTTTTGTCTTAATTTAGACAAGAA
*
13941337 AACATGTTTTATCTTAATTTA
1 AACATGTTTTGTCTTAATTTA
13941358 AAACAATCTT
Statistics
Matches: 151, Mismatches: 24, Indels: 24
0.76 0.12 0.12
Matches are distributed among these distances:
21 14 0.09
24 2 0.01
25 2 0.01
26 4 0.03
28 37 0.25
29 66 0.44
30 14 0.09
31 12 0.08
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.41
Consensus pattern (29 bp):
AACATGTTTTGTCTTAATTTAGACAAGAA
Found at i:13941303 original size:59 final size:57
Alignment explanation
Indices: 13941200--13941354 Score: 175
Period size: 59 Copynumber: 2.7 Consensus size: 57
13941190 TAGATAATAA
* * * * * * * *
13941200 TTGTCTTAATTTAGATATGAAAGCATATTTTGTCTTAATTTAGACAAGAAAATATGT
1 TTGTCTCAATTTAGACAAGAAAACATGTTTTGTCTTAATCTAGACAAGAAAACATAT
* * *
13941257 TTGTCTTAATTTAAGAGAAGAAAAATATGTTTTGTCTTAATCTAGACAAGAAAACATAT
1 TTGTCTCAATTT-AGACAAG-AAAACATGTTTTGTCTTAATCTAGACAAGAAAACATAT
* *
13941316 TTGTCTCAATTTAGACAAGATAACATGTTTTATCTTAAT
1 TTGTCTCAATTTAGACAAGAAAACATGTTTTGTCTTAAT
13941355 TTAAAACAAT
Statistics
Matches: 83, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
57 29 0.35
58 11 0.13
59 43 0.52
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (57 bp):
TTGTCTCAATTTAGACAAGAAAACATGTTTTGTCTTAATCTAGACAAGAAAACATAT
Found at i:13954485 original size:40 final size:37
Alignment explanation
Indices: 13954441--13954547 Score: 135
Period size: 40 Copynumber: 2.8 Consensus size: 37
13954431 TCACACCCGG
13954441 CTCATGTACATCCCCCCACATCGTGCACAT-AGCTGGCACC
1 CTCATGTACATCCCCCCACATCGTGCACATCAG-T-G--CC
*
13954481 CTCATGTGCATCCCCCCACATCGTGCACAATCAGTGCC
1 CTCATGTACATCCCCCCACATCGTGCAC-ATCAGTGCC
* *
13954519 ATCGTGTACATCCCCCCACATCGTGCACA
1 CTCATGTACATCCCCCCACATCGTGCACA
13954548 CGGGCACTAT
Statistics
Matches: 61, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
37 1 0.02
38 27 0.44
40 28 0.46
41 3 0.05
42 2 0.03
ACGTcount: A:0.22, C:0.42, G:0.15, T:0.21
Consensus pattern (37 bp):
CTCATGTACATCCCCCCACATCGTGCACATCAGTGCC
Found at i:13954540 original size:38 final size:40
Alignment explanation
Indices: 13954442--13954547 Score: 139
Period size: 38 Copynumber: 2.7 Consensus size: 40
13954432 CACACCCGGC
*
13954442 TCATGTACATCCCCCCACATCGTGCAC-ATAGCTGGCACCC
1 TCATGTACATCCCCCCACATCGTGCACAATAGCTGG-ACCA
*
13954482 TCATGTGCATCCCCCCACATCGTGCACAATCAG-T-G-CCA
1 TCATGTACATCCCCCCACATCGTGCACAAT-AGCTGGACCA
*
13954520 TCGTGTACATCCCCCCACATCGTGCACA
1 TCATGTACATCCCCCCACATCGTGCACA
13954548 CGGGCACTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
38 28 0.47
40 27 0.45
41 3 0.05
42 2 0.03
ACGTcount: A:0.23, C:0.42, G:0.15, T:0.21
Consensus pattern (40 bp):
TCATGTACATCCCCCCACATCGTGCACAATAGCTGGACCA
Found at i:13954669 original size:15 final size:19
Alignment explanation
Indices: 13954632--13954673 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
13954622 ACGGTTACAG
13954632 TCATTATACACAATATCAT
1 TCATTATACACAATATCAT
13954651 TCATTATACACAATATCAT
1 TCATTATACACAATATCAT
13954670 TCAT
1 TCAT
13954674 CATGCACAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.40, C:0.21, G:0.00, T:0.38
Consensus pattern (19 bp):
TCATTATACACAATATCAT
Found at i:13954681 original size:19 final size:19
Alignment explanation
Indices: 13954632--13954682 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
13954622 ACGGTTACAG
*
13954632 TCATTATACACAATATCAT
1 TCATCATACACAATATCAT
*
13954651 TCATTATACACAATATCAT
1 TCATCATACACAATATCAT
*
13954670 TCATCATGCACAA
1 TCATCATACACAA
13954683 CACACACATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.41, C:0.24, G:0.02, T:0.33
Consensus pattern (19 bp):
TCATCATACACAATATCAT
Found at i:13956400 original size:37 final size:37
Alignment explanation
Indices: 13956278--13956401 Score: 99
Period size: 37 Copynumber: 3.2 Consensus size: 37
13956268 GTACGAGATG
* * *
13956278 TGGGGGGAGCACATGACGGCATTAGTTGTGCGTGATG
1 TGGGGGGAGCACATGATGGCATTAGTTGTGCGCGATA
* *
13956315 TGGGGGTGCA-CACAATGATGATG-ATATATGGCATGTGTGCGATA
1 TGGGGG-G-AGCAC-ATGATG--GCAT-TA--G-TTGTGCGCGATA
*
13956359 TGGGGGGAGCACATGATGGCATTAGTTGTGCGCGATT
1 TGGGGGGAGCACATGATGGCATTAGTTGTGCGCGATA
13956396 TGGGGG
1 TGGGGG
13956402 TGCACACAAT
Statistics
Matches: 68, Mismatches: 8, Indels: 22
0.69 0.08 0.22
Matches are distributed among these distances:
37 21 0.31
38 5 0.07
39 6 0.09
40 5 0.07
41 5 0.07
42 7 0.10
43 5 0.07
44 14 0.21
ACGTcount: A:0.21, C:0.12, G:0.41, T:0.26
Consensus pattern (37 bp):
TGGGGGGAGCACATGATGGCATTAGTTGTGCGCGATA
Found at i:13958442 original size:22 final size:23
Alignment explanation
Indices: 13958417--13958493 Score: 68
Period size: 23 Copynumber: 3.4 Consensus size: 23
13958407 GCAGTCACAT
*
13958417 AATGCC-TAAAAATCAGACATGC
1 AATGCCTTAAAAATCAGACACGC
* *
13958439 AATGCCTTATAAATCAGTCACGC
1 AATGCCTTAAAAATCAGACACGC
* * * *
13958462 AATGCCCTATAAACCAGCCACGC
1 AATGCCTTAAAAATCAGACACGC
*
13958485 ATTG-CTTAA
1 AATGCCTTAA
13958494 GTCACACAAT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
22 9 0.20
23 36 0.80
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.22
Consensus pattern (23 bp):
AATGCCTTAAAAATCAGACACGC
Found at i:13958455 original size:23 final size:22
Alignment explanation
Indices: 13958417--13958485 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 22
13958407 GCAGTCACAT
* *
13958417 AATGCCTAAAAATCAGACATGC
1 AATGCCTATAAATCAGACACGC
*
13958439 AATGCCTTATAAATCAGTCACGC
1 AATGCC-TATAAATCAGACACGC
* *
13958462 AATGCCCTATAAACCAGCCACGC
1 AATG-CCTATAAATCAGACACGC
13958485 A
1 A
13958486 TTGCTTAAGT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
22 6 0.15
23 32 0.80
24 2 0.05
ACGTcount: A:0.39, C:0.29, G:0.13, T:0.19
Consensus pattern (22 bp):
AATGCCTATAAATCAGACACGC
Found at i:13958466 original size:45 final size:44
Alignment explanation
Indices: 13958372--13958620 Score: 163
Period size: 45 Copynumber: 5.7 Consensus size: 44
13958362 CCAGTTAATT
* * * * * *
13958372 AATGACTAAAAACTAGTCATGCAATTCCCTATGAAGCAGTCACAT
1 AATGCCTAAAAACCAGTCATGCAATGCCTTAT-AAACAGTCACAC
* * *
13958417 AATGCCTAAAAATCAGACATGCAATGCCTTATAAATCAGTCACGC
1 AATGCCTAAAAACCAGTCATGCAATGCCTTATAAA-CAGTCACAC
* * * *
13958462 AATGCCCTATAAACCAGCCACGCATTG-C-T-T--A-AGTCACAC
1 AATG-CCTAAAAACCAGTCATGCAATGCCTTATAAACAGTCACAC
** * *
13958501 AATGCCTAAATGCCAGTCATGCAATGCCTTACAAACCAGTCACGC
1 AATGCCTAAAAACCAGTCATGCAATGCCTTATAAA-CAGTCACAC
* * ***
13958546 AATGACTAAAAACCAGTCATGCAATGAC-TA-AAACCAAAAACAC
1 AATGCCTAAAAACCAGTCATGCAATGCCTTATAAA-CAGTCACAC
* * * *
13958589 AACGCCTAAAAGCCAATCACGCAATGCCTTAT
1 AATGCCTAAAAACCAGTCATGCAATGCCTTAT
13958621 CAACCAATCG
Statistics
Matches: 156, Mismatches: 37, Indels: 22
0.73 0.17 0.10
Matches are distributed among these distances:
38 16 0.10
39 12 0.08
40 1 0.01
41 1 0.01
43 33 0.21
44 7 0.04
45 69 0.44
46 17 0.11
ACGTcount: A:0.40, C:0.27, G:0.13, T:0.20
Consensus pattern (44 bp):
AATGCCTAAAAACCAGTCATGCAATGCCTTATAAACAGTCACAC
Found at i:13958617 original size:22 final size:21
Alignment explanation
Indices: 13958408--13958617 Score: 106
Period size: 22 Copynumber: 9.8 Consensus size: 21
13958398 CCCTATGAAG
** *
13958408 CAGTCACATAATGCCTAAAAAT
1 CAGTCACGCAATGCCT-AAAAC
* * *
13958430 CAGACATGCAATGCCTTATAAAT
1 CAGTCACGCAATGCC-TA-AAAC
13958453 CAGTCACGCAATGCCCTATAAAC
1 CAGTCACGCAATG-CCTA-AAAC
* * *
13958476 CAGCCACGCATTG-CT--TA-
1 CAGTCACGCAATGCCTAAAAC
* *
13958493 -AGTCACACAATGCCTAAATGC
1 CAGTCACGCAATGCCTAAA-AC
*
13958514 CAGTCATGCAATGCCTTACAAAC
1 CAGTCACGCAATGCC-TA-AAAC
*
13958537 CAGTCACGCAATGACTAAAAAC
1 CAGTCACGCAATGCCT-AAAAC
* *
13958559 CAGTCATGCAATGACTAAAAC
1 CAGTCACGCAATGCCTAAAAC
*** * *
13958580 CAAAAACACAACGCCTAAAAGC
1 CAGTCACGCAATGCCTAAAA-C
*
13958602 CAATCACGCAATGCCT
1 CAGTCACGCAATGCCT
13958618 TATCAACCAA
Statistics
Matches: 143, Mismatches: 32, Indels: 26
0.71 0.16 0.13
Matches are distributed among these distances:
16 9 0.06
17 2 0.01
18 1 0.01
21 20 0.14
22 57 0.40
23 50 0.35
24 4 0.03
ACGTcount: A:0.40, C:0.29, G:0.13, T:0.19
Consensus pattern (21 bp):
CAGTCACGCAATGCCTAAAAC
Found at i:13958716 original size:81 final size:80
Alignment explanation
Indices: 13958560--13958785 Score: 258
Period size: 81 Copynumber: 2.8 Consensus size: 80
13958550 ACTAAAAACC
* ** * * * *
13958560 AGTCATGCAATGACTAAAACCAAAAACAC-AACGCCTAAAAGCCAATCACGCAATGCCTTATCAA
1 AGTCATGCAATGCCTAAAACCCTAAAC-CTAAAGCCTAAAA-CTAGTCACGC-ATGCCCTATCAA
13958624 CCAATCGTGCAAACCCTA
63 CCAATCGTGCAAACCCTA
*
13958642 AGTCATGCAATGCCTAAAACACCTAAACCTAAAGCCTAAAACTAGTCATGCATGCCCTATCAACC
1 AGTCATGCAATGCCTAAAAC-CCTAAACCTAAAGCCTAAAACTAGTCACGCATGCCCTATCAACC
*
13958707 AAT-GATGCAAACCTTA
65 AATCG-TGCAAACCCTA
* * * * *
13958723 AGTCAAGTAATGCTTAAAACCCCTAAACCTAATGCCTACAACTAGTCACGCATGCCCTATCAA
1 AGTCATGCAATGCCTAAAA-CCCTAAACCTAAAGCCTAAAACTAGTCACGCATGCCCTATCAA
13958786 TGTTCGATCC
Statistics
Matches: 125, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
80 1 0.01
81 81 0.65
82 28 0.22
83 15 0.12
ACGTcount: A:0.40, C:0.30, G:0.11, T:0.19
Consensus pattern (80 bp):
AGTCATGCAATGCCTAAAACCCTAAACCTAAAGCCTAAAACTAGTCACGCATGCCCTATCAACCA
ATCGTGCAAACCCTA
Found at i:13958968 original size:15 final size:15
Alignment explanation
Indices: 13958948--13958978 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
13958938 ACTTACCCTG
13958948 GTGAGGAATGCACTA
1 GTGAGGAATGCACTA
*
13958963 GTGAGGAATGCTCTA
1 GTGAGGAATGCACTA
13958978 G
1 G
13958979 AGATGAATGG
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:0.29, C:0.13, G:0.35, T:0.23
Consensus pattern (15 bp):
GTGAGGAATGCACTA
Found at i:13960051 original size:23 final size:23
Alignment explanation
Indices: 13960025--13960077 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
13960015 TTTGGTAACT
*
13960025 TGATGGTGCGTATTGACCATGGA
1 TGATGGTGCATATTGACCATGGA
* *
13960048 TGATGGTGTATATTGACGATGGA
1 TGATGGTGCATATTGACCATGGA
13960071 TGATGGT
1 TGATGGT
13960078 CCGAAGATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.23, C:0.08, G:0.36, T:0.34
Consensus pattern (23 bp):
TGATGGTGCATATTGACCATGGA
Found at i:13962088 original size:2 final size:2
Alignment explanation
Indices: 13962081--13962105 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13962071 ACATAGTATT
13962081 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
13962106 CAACATTATA
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:13962221 original size:2 final size:2
Alignment explanation
Indices: 13962214--13962238 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13962204 GCANTAGTAT
13962214 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
13962239 CAACATTATA
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:13962240 original size:133 final size:133
Alignment explanation
Indices: 13962072--13962339 Score: 520
Period size: 133 Copynumber: 2.0 Consensus size: 133
13962062 CCATTTATGA
13962072 CATAGTATTTATATATATATATATATATATATATCAACATTATACAAAAACATATGGATTCATCC
1 CATAGTATTTATATATATATATATATATATATATCAACATTATACAAAAACATATGGATTCATCC
13962137 TTTTGCACATTTCACTTTTCACAACATCAAACATTTTATCAATGGCTTGTTCCCAGGAAATTTTA
66 TTTTGCACATTTCACTTTTCACAACATCAAACATTTTATCAATGGCTTGTTCCCAGGAAATTTTA
13962202 AAG
131 AAG
13962205 CANTAGTA-TTATATATATATATATATATATATATCAACATTATACAAAAACATATGGATTCATC
1 CA-TAGTATTTATATATATATATATATATATATATCAACATTATACAAAAACATATGGATTCATC
13962269 CTTTTGCACATTTCACTTTTCACAACATCAAACATTTTATCAATGGCTTGTTCCCAGGAAATTTT
65 CTTTTGCACATTTCACTTTTCACAACATCAAACATTTTATCAATGGCTTGTTCCCAGGAAATTTT
13962334 AAAG
130 AAAG
13962338 CA
1 CA
13962340 AAAATTGATG
Statistics
Matches: 134, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
133 129 0.96
134 5 0.04
ACGTcount: A:0.38, C:0.17, G:0.07, T:0.38
Consensus pattern (133 bp):
CATAGTATTTATATATATATATATATATATATATCAACATTATACAAAAACATATGGATTCATCC
TTTTGCACATTTCACTTTTCACAACATCAAACATTTTATCAATGGCTTGTTCCCAGGAAATTTTA
AAG
Found at i:13965487 original size:27 final size:27
Alignment explanation
Indices: 13965457--13965514 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
13965447 TTGGAGTAAA
*
13965457 AGGGTAAAATGGTAATTTTGCCACC-CC
1 AGGGCAAAATGGTAATTTT-CCACCACC
*
13965484 AGGGGCAAAATTGTAATTTTCCACCACC
1 A-GGGCAAAATGGTAATTTTCCACCACC
13965512 AGG
1 AGG
13965515 ACATTTTTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 8 0.30
28 19 0.70
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.24
Consensus pattern (27 bp):
AGGGCAAAATGGTAATTTTCCACCACC
Found at i:13966645 original size:13 final size:13
Alignment explanation
Indices: 13966627--13966651 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13966617 AGAGAAATTG
13966627 TGATTTTATAAAA
1 TGATTTTATAAAA
13966640 TGATTTTATAAA
1 TGATTTTATAAA
13966652 TTTTCTGGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:13968065 original size:15 final size:15
Alignment explanation
Indices: 13968045--13968088 Score: 72
Period size: 15 Copynumber: 2.9 Consensus size: 15
13968035 GATCAGATAT
13968045 TTTGATTTTAAAG-C
1 TTTGATTTTAAAGTC
13968059 ATTTGATTTTAAAGTC
1 -TTTGATTTTAAAGTC
13968075 TTTGATTTTAAAGT
1 TTTGATTTTAAAGT
13968089 TGTTTTAAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 27 0.96
16 1 0.04
ACGTcount: A:0.30, C:0.05, G:0.14, T:0.52
Consensus pattern (15 bp):
TTTGATTTTAAAGTC
Found at i:13972252 original size:20 final size:20
Alignment explanation
Indices: 13972207--13972244 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
13972197 TTTTGGCCCC
13972207 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
13972227 ATTTGACTTATTGGAGTA
1 ATTTGACTTATTGGAGTA
13972245 AGATTTGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.45
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:13979746 original size:54 final size:54
Alignment explanation
Indices: 13979668--13979887 Score: 332
Period size: 54 Copynumber: 4.1 Consensus size: 54
13979658 TCATTATGTG
* *
13979668 CATCTCACCCAGCTCATGTTCATCCCACCACATCGTGCACATAGCCGGACATCT
1 CATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACATCC
* *
13979722 CATCTCACCCAGCTCATGTGCATCCCAACACATCGTGCACATAGCTGGACATCC
1 CATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACATCC
* * * *
13979776 CATCTCACCCAACTCTTGTGCATCCCACCACGTCTTGCACATAGCCGGACATCC
1 CATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACATCC
* * * *
13979830 CATCTCGCTCAGCTCATGTGCATCCCACCACATCATGCACATAGCCAGACATCC
1 CATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACATCC
13979884 CATC
1 CATC
13979888 CATCTTCCTC
Statistics
Matches: 149, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 149 1.00
ACGTcount: A:0.25, C:0.41, G:0.13, T:0.21
Consensus pattern (54 bp):
CATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACATCC
Found at i:13981336 original size:47 final size:47
Alignment explanation
Indices: 13981261--13981354 Score: 156
Period size: 47 Copynumber: 2.0 Consensus size: 47
13981251 CAACAACCCA
13981261 CTATGCACCTTTCTTCACCAATTGAAATTA-TTTTTTTATCCTACTC
1 CTATGCACCTTTCTTCACCAATTGAAATTATTTTTTTTATCCTACTC
13981307 CNTATGCACCTTTCTTCACCAA-TGAAAATTATTTTTTTTATCCTACTC
1 C-TATGCACCTTTCTTCACCAATTG-AAATTATTTTTTTTATCCTACTC
13981355 TTATAACGAC
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
46 3 0.07
47 26 0.58
48 16 0.36
ACGTcount: A:0.24, C:0.26, G:0.04, T:0.45
Consensus pattern (47 bp):
CTATGCACCTTTCTTCACCAATTGAAATTATTTTTTTTATCCTACTC
Found at i:13992519 original size:32 final size:32
Alignment explanation
Indices: 13992483--13992631 Score: 149
Period size: 35 Copynumber: 4.5 Consensus size: 32
13992473 TTTACCGAGA
*
13992483 TCAACTAAAACCCAAAGTGGTTTTTCAAAGGC
1 TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
* **
13992515 TCAACCATAACCTTTCACAA-TGGTTTTTCACGGGC
1 TCAACCAAAACC---CA-AAGTGGTTTTTCAAAGGC
13992550 TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
1 TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
* * *
13992582 TCAACCATAACCTACAACAATGGTTTTTCACAA-GA
1 TCAACCAAAACC--CAA-AGTGGTTTTTCA-AAGGC
13992617 TCAACCAAAACCCAA
1 TCAACCAAAACCCAA
13992632 TAACTAACTT
Statistics
Matches: 97, Mismatches: 11, Indels: 17
0.78 0.09 0.14
Matches are distributed among these distances:
31 2 0.02
32 36 0.37
33 3 0.03
34 3 0.03
35 49 0.51
36 4 0.04
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.24
Consensus pattern (32 bp):
TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
Found at i:13992564 original size:67 final size:67
Alignment explanation
Indices: 13992456--13992631 Score: 266
Period size: 67 Copynumber: 2.6 Consensus size: 67
13992446 GTTTAGCCAA
* *
13992456 AACCTTTCACAATTGTTTTT-ACCGAGATCAACTAAAACCCAAAGTGGTTTTTCAAAGGCTCAAC
1 AACCTTTCACAATGGTTTTTCA-CGAGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAAC
13992520 CAT
65 CAT
* *
13992523 AACCTTTCACAATGGTTTTTCACGGGCTCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
1 AACCTTTCACAATGGTTTTTCACGAGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
13992588 AT
66 AT
* *
13992590 AACC-TACAACAATGGTTTTTCACAAGATCAACCAAAACCCAA
1 AACCTTTC-ACAATGGTTTTTCACGAGATCAACCAAAACCCAA
13992632 TAACTAACTT
Statistics
Matches: 99, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
66 2 0.02
67 96 0.97
68 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.12, T:0.26
Consensus pattern (67 bp):
AACCTTTCACAATGGTTTTTCACGAGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
AT
Done.