Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 129 of 202
Found at i:39983760 original size:30 final size:30
Alignment explanation
Indices: 39983724--39983798 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 30
39983714 GGTTGATACC
* * *
39983724 TCCCTTTTCGTAATTCCATAATCGAAGTTA
1 TCCCTTTTCATAATTCCATAACCGAAGCTA
* * *
39983754 TCCCTTTTCATAGTTCGATAGCCGAAGCTA
1 TCCCTTTTCATAATTCCATAACCGAAGCTA
39983784 TCCCTTTTCATAATT
1 TCCCTTTTCATAATT
39983799 TGATGGTCGT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.24, C:0.25, G:0.11, T:0.40
Consensus pattern (30 bp):
TCCCTTTTCATAATTCCATAACCGAAGCTA
Found at i:39983817 original size:30 final size:30
Alignment explanation
Indices: 39983783--39983862 Score: 106
Period size: 30 Copynumber: 2.7 Consensus size: 30
39983773 AGCCGAAGCT
*
39983783 ATCCCTTTTCATAATTTGATGGTCGTCACC
1 ATCCCTTTTCATAATTTGATGGCCGTCACC
* ** * *
39983813 ATCCCTCTTCATTGTTCGACGGCCGTCACC
1 ATCCCTTTTCATAATTTGATGGCCGTCACC
39983843 ATCCCTTTTCATAATTTGAT
1 ATCCCTTTTCATAATTTGAT
39983863 AGCCAAAGCT
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.19, C:0.30, G:0.12, T:0.39
Consensus pattern (30 bp):
ATCCCTTTTCATAATTTGATGGCCGTCACC
Found at i:39983817 original size:60 final size:60
Alignment explanation
Indices: 39983753--39983953 Score: 185
Period size: 60 Copynumber: 3.4 Consensus size: 60
39983743 AATCGAAGTT
* *
39983753 ATCCCTTTTCATAGTTCGATAGCCGAAGCTATCCCTTTTCATAATTTGATGGTCGTCACC
1 ATCCCTTTTCATAGATCGATAGCCGAAGCCATCCCTTTTCATAATTTGATGGTCGTCACC
* * * ** * * *** *
39983813 ATCCCTCTTCATTGTTCGACGGCCGTCA-CCATCCCTTTTCATAATTTGATAG-CCAAAGCT
1 ATCCCTTTTCATAGATCGATAGCCG-AAGCCATCCCTTTTCATAATTTGATGGTCGTCA-CC
** ** *
39983873 ATCCCTTTTCATAGATC-AGTAGCCGAAGCCATCTTTTTTCATAGCTCGATGGTCGTCACC
1 ATCCCTTTTCATAGATCGA-TAGCCGAAGCCATCCCTTTTCATAATTTGATGGTCGTCACC
39983933 ATCCCTTTTCATA-ATCGATAG
1 ATCCCTTTTCATAGATCGATAG
39983954 ACGTATCCTT
Statistics
Matches: 108, Mismatches: 27, Indels: 13
0.73 0.18 0.09
Matches are distributed among these distances:
59 10 0.09
60 95 0.88
61 3 0.03
ACGTcount: A:0.22, C:0.28, G:0.14, T:0.35
Consensus pattern (60 bp):
ATCCCTTTTCATAGATCGATAGCCGAAGCCATCCCTTTTCATAATTTGATGGTCGTCACC
Found at i:39983896 original size:30 final size:31
Alignment explanation
Indices: 39983841--39983916 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 31
39983831 ACGGCCGTCA
**
39983841 CCATCCCTTTTCATA-ATTTGATAGCCAAAG
1 CCATCCCTTTTCATAGATCAGATAGCCAAAG
* *
39983871 CTATCCCTTTTCATAGATCAG-TAGCCGAAG
1 CCATCCCTTTTCATAGATCAGATAGCCAAAG
**
39983901 CCATCTTTTTTCATAG
1 CCATCCCTTTTCATAG
39983917 CTCGATGGTC
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
30 35 0.92
31 3 0.08
ACGTcount: A:0.26, C:0.26, G:0.12, T:0.36
Consensus pattern (31 bp):
CCATCCCTTTTCATAGATCAGATAGCCAAAG
Found at i:39983905 original size:90 final size:90
Alignment explanation
Indices: 39983753--39983953 Score: 228
Period size: 90 Copynumber: 2.2 Consensus size: 90
39983743 AATCGAAGTT
* * ** * * *
39983753 ATCCCTTTTCATAGTTCGATAGCCGAAGCTATCCCTTTTCATAATTTGATGGTCGTCACCATCCC
1 ATCCCTTTTCATAATTCGATAGCCAAAGCTATCCCTTTTCATAATCAGATAGCCGTAACCATCCC
* *
39983818 TCTTCATTGTTCGACGGCCGTCACC
66 TCTTCATAGCTCGACGGCCGTCACC
*
39983843 ATCCCTTTTCATAATTTGATAGCCAAAGCTATCCCTTTTCATAGATCAG-TAGCCG-AAGCCATC
1 ATCCCTTTTCATAATTCGATAGCCAAAGCTATCCCTTTTCATA-ATCAGATAGCCGTAA-CCATC
** * * *
39983906 TTTTTTCATAGCTCGATGGTCGTCACC
64 CCTCTTCATAGCTCGACGGCCGTCACC
39983933 ATCCCTTTTCATAA-TCGATAG
1 ATCCCTTTTCATAATTCGATAG
39983954 ACGTATCCTT
Statistics
Matches: 93, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
89 7 0.08
90 83 0.89
91 3 0.03
ACGTcount: A:0.22, C:0.28, G:0.14, T:0.35
Consensus pattern (90 bp):
ATCCCTTTTCATAATTCGATAGCCAAAGCTATCCCTTTTCATAATCAGATAGCCGTAACCATCCC
TCTTCATAGCTCGACGGCCGTCACC
Found at i:39991431 original size:30 final size:31
Alignment explanation
Indices: 39991397--39991473 Score: 106
Period size: 30 Copynumber: 2.5 Consensus size: 31
39991387 ACCCGAAGCT
**
39991397 ATCCCTTTTCATACTTTC-ATGGTTGTCACC
1 ATCCCTTTTCATACTTTCGATGGTCATCACC
39991427 ATCCCTTTTCAT--TGTTCGATGGTCATCACC
1 ATCCCTTTTCATACT-TTCGATGGTCATCACC
39991457 ATCCCTTTTCATACTTT
1 ATCCCTTTTCATACTTT
39991474 GATAGTCGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
28 1 0.02
29 3 0.07
30 34 0.83
31 2 0.05
32 1 0.02
ACGTcount: A:0.17, C:0.30, G:0.09, T:0.44
Consensus pattern (31 bp):
ATCCCTTTTCATACTTTCGATGGTCATCACC
Found at i:39991491 original size:30 final size:30
Alignment explanation
Indices: 39991455--39991528 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 30
39991445 ATGGTCATCA
** * *
39991455 CCATCCCTTTTCATACTTTGATAGTCGAAG
1 CCATCCCTTTTCATAAATCGATAGCCGAAG
*
39991485 CTATCCCTTTTCATAAATCGATAGCCGAAG
1 CCATCCCTTTTCATAAATCGATAGCCGAAG
39991515 CCAT-CCTTTTCATA
1 CCATCCCTTTTCATA
39991529 GCTAGATGGT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
29 10 0.26
30 28 0.74
ACGTcount: A:0.26, C:0.28, G:0.11, T:0.35
Consensus pattern (30 bp):
CCATCCCTTTTCATAAATCGATAGCCGAAG
Found at i:40006806 original size:25 final size:25
Alignment explanation
Indices: 40006769--40006819 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
40006759 AAGGAAGAGG
* *
40006769 GTGACTGGCTCGGGTGGCAAAAATT
1 GTGAATGGCTCGGGTAGCAAAAATT
*
40006794 GTGAATGGGTCGGGTAGCAAAAATT
1 GTGAATGGCTCGGGTAGCAAAAATT
40006819 G
1 G
40006820 ACTTAAATTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.27, C:0.12, G:0.37, T:0.24
Consensus pattern (25 bp):
GTGAATGGCTCGGGTAGCAAAAATT
Found at i:40009416 original size:32 final size:29
Alignment explanation
Indices: 40009364--40009429 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 29
40009354 TATCATCTTA
*
40009364 AATATATATATCAAACTTATAATATAACAT
1 AATATATATATCAAACTTATAACATAA-AT
40009394 AATATATATTAT-AAACAATTATAACATAAAT
1 AATATATA-TATCAAAC--TTATAACATAAAT
40009425 -ATATA
1 AATATA
40009430 AGGAGATGGG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
30 17 0.53
31 5 0.16
32 10 0.31
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (29 bp):
AATATATATATCAAACTTATAACATAAAT
Found at i:40018567 original size:17 final size:18
Alignment explanation
Indices: 40018545--40018579 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
40018535 ATTTGGGTCA
40018545 TGTGGGC-CACACGGGCG
1 TGTGGGCGCACACGGGCG
40018562 TGTGGGCGCACACGGGCG
1 TGTGGGCGCACACGGGCG
40018580 AACATCATGG
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:0.11, C:0.29, G:0.49, T:0.11
Consensus pattern (18 bp):
TGTGGGCGCACACGGGCG
Found at i:40022545 original size:11 final size:11
Alignment explanation
Indices: 40022529--40022568 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
40022519 GGCCCAAGAG
*
40022529 AGAAAAAGTAA
1 AGAAAAAGAAA
*
40022540 AGAAAAAGGAA
1 AGAAAAAGAAA
40022551 AGAAAAAGAAA
1 AGAAAAAGAAA
*
40022562 ATAAAAA
1 AGAAAAA
40022569 CAAAGGCCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (11 bp):
AGAAAAAGAAA
Found at i:40023052 original size:42 final size:42
Alignment explanation
Indices: 40022962--40023265 Score: 369
Period size: 42 Copynumber: 7.3 Consensus size: 42
40022952 CTTCATATAC
* ** ** *
40022962 AATGCAATGAAAAGTAAATAAACCT-CACAGTTGGGCCTCTA
1 AATGCAATGAAAGGTAAATGGACCTCCACACCTAGGCCTCTA
*
40023003 AATGCAATGAAAGGTAAATGGACCTCCACACCTGGGCCTCTA
1 AATGCAATGAAAGGTAAATGGACCTCCACACCTAGGCCTCTA
* * *
40023045 AATGCAATGAAACGTAAAAGGACCTCCACACTTAGGCCTCTA
1 AATGCAATGAAAGGTAAATGGACCTCCACACCTAGGCCTCTA
* * *
40023087 AATGTAATTAAAGGTAAATAGACCTCCACACCTAGGCCTCTA
1 AATGCAATGAAAGGTAAATGGACCTCCACACCTAGGCCTCTA
* *
40023129 AATGCAATGAAACGTAAATGGGCCTCCACACCT-GAGCCTCTA
1 AATGCAATGAAAGGTAAATGGACCTCCACACCTAG-GCCTCTA
* *
40023171 AATGCAATGAAAGATAAATGGACCTCCACACCTAGGCCTATA
1 AATGCAATGAAAGGTAAATGGACCTCCACACCTAGGCCTCTA
* * * * * * *
40023213 AACGTAATGAAAAGTACATGGACCTCCACAGCTTGGCCTATA
1 AATGCAATGAAAGGTAAATGGACCTCCACACCTAGGCCTCTA
40023255 AATGCAATGAA
1 AATGCAATGAA
40023266 TTATTTCCTT
Statistics
Matches: 227, Mismatches: 33, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
41 23 0.10
42 203 0.89
43 1 0.00
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (42 bp):
AATGCAATGAAAGGTAAATGGACCTCCACACCTAGGCCTCTA
Found at i:40023146 original size:126 final size:126
Alignment explanation
Indices: 40022967--40023265 Score: 413
Period size: 126 Copynumber: 2.4 Consensus size: 126
40022957 TATACAATGC
* ** * *
40022967 AATGAAAAGTAAATAAACCT-CACAGTTGGGCCTCTAAATGCAATGAAAGGTAAATGGACCTCCA
1 AATGAAAAGTAAATAGACCTCCACACCTAGGCCTCTAAATGCAATGAAACGTAAATGGACCTCCA
* * * *
40023031 CACCTGGGCCTCTAAATGCAATGAAACG-TAAAAGGACCTCCACACTTAGGCCTCTAAATGT
66 CACCTGAGCCTCTAAATGCAATGAAA-GATAAAAGGACCTCCACACCTAGGCCTATAAACGT
* * *
40023092 AATTAAAGGTAAATAGACCTCCACACCTAGGCCTCTAAATGCAATGAAACGTAAATGGGCCTCCA
1 AATGAAAAGTAAATAGACCTCCACACCTAGGCCTCTAAATGCAATGAAACGTAAATGGACCTCCA
*
40023157 CACCTGAGCCTCTAAATGCAATGAAAGATAAATGGACCTCCACACCTAGGCCTATAAACGT
66 CACCTGAGCCTCTAAATGCAATGAAAGATAAAAGGACCTCCACACCTAGGCCTATAAACGT
* * * * *
40023218 AATGAAAAGTACATGGACCTCCACAGCTTGGCCTATAAATGCAATGAA
1 AATGAAAAGTAAATAGACCTCCACACCTAGGCCTCTAAATGCAATGAA
40023266 TTATTTCCTT
Statistics
Matches: 152, Mismatches: 20, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
125 18 0.12
126 134 0.88
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (126 bp):
AATGAAAAGTAAATAGACCTCCACACCTAGGCCTCTAAATGCAATGAAACGTAAATGGACCTCCA
CACCTGAGCCTCTAAATGCAATGAAAGATAAAAGGACCTCCACACCTAGGCCTATAAACGT
Found at i:40023684 original size:11 final size:11
Alignment explanation
Indices: 40023668--40023738 Score: 62
Period size: 11 Copynumber: 6.6 Consensus size: 11
40023658 TGCTCTCTCC
40023668 CTTTTTTTCTT
1 CTTTTTTTCTT
*
40023679 CTTTTTTTGTTT
1 CTTTTTTT-CTT
40023691 CTTTTTTGT-TT
1 CTTTTTT-TCTT
*
40023702 -TGTTGTTT-TT
1 CT-TTTTTTCTT
40023712 C-TTTTTTCTT
1 CTTTTTTTCTT
40023722 CTTTTTTTCTT
1 CTTTTTTTCTT
40023733 -TTTTTT
1 CTTTTTT
40023739 ATTTAGGGAA
Statistics
Matches: 51, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
9 5 0.10
10 13 0.25
11 23 0.45
12 9 0.18
13 1 0.02
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.83
Consensus pattern (11 bp):
CTTTTTTTCTT
Found at i:40024994 original size:51 final size:51
Alignment explanation
Indices: 40024930--40025031 Score: 161
Period size: 51 Copynumber: 2.0 Consensus size: 51
40024920 AGCATTTTCA
*
40024930 GCACAAGGTAATTCTTTGTTCGATTCTGAGAAGGTTGAAAGG-AGGATGCCG
1 GCACAAGGCAATTCTTTGTTCGATTCTGAGAAGGTTGAAAGGAAGG-TGCCG
* *
40024981 GCACAAGGCAATTCTTTGTTCGGTTCTGATAAGGTTGAAAGGAAGGTGCCG
1 GCACAAGGCAATTCTTTGTTCGATTCTGAGAAGGTTGAAAGGAAGGTGCCG
40025032 AATGTTCTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 44 0.94
52 3 0.06
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.27
Consensus pattern (51 bp):
GCACAAGGCAATTCTTTGTTCGATTCTGAGAAGGTTGAAAGGAAGGTGCCG
Found at i:40039676 original size:4 final size:4
Alignment explanation
Indices: 40039660--40039702 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
40039650 ACAAATTAGC
* * * *
40039660 GAAT GAGT GAAT GAAT GGAT GAAT GAAT GATT GAAT GATT GAA
1 GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAA
40039703 ATTTAGGCAC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.42, C:0.00, G:0.30, T:0.28
Consensus pattern (4 bp):
GAAT
Found at i:40044053 original size:19 final size:21
Alignment explanation
Indices: 40044002--40044053 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 21
40043992 ACCTGAAAAT
*
40044002 AAATCAAAG-TTTTCTTTAAA
1 AAATCAATGTTTTTCTTTAAA
* *
40044022 AAATCACTATTTTTC-TT-AA
1 AAATCAATGTTTTTCTTTAAA
40044041 AAATCAATGTTTT
1 AAATCAATGTTTT
40044054 ATTTCGAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 13 0.50
20 8 0.31
21 5 0.19
ACGTcount: A:0.40, C:0.12, G:0.04, T:0.44
Consensus pattern (21 bp):
AAATCAATGTTTTTCTTTAAA
Found at i:40044397 original size:3 final size:3
Alignment explanation
Indices: 40044389--40044414 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
40044379 ACTAGAATGC
40044389 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
40044415 TTACCTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:40044488 original size:2 final size:2
Alignment explanation
Indices: 40044481--40044506 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40044471 ATTTCATTTC
40044481 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
40044507 GTTTTAATCT
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):
AT
Found at i:40044565 original size:16 final size:15
Alignment explanation
Indices: 40044521--40044567 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
40044511 TAATCTTTTT
40044521 TATTTAATAAAA-AA
1 TATTTAATAAAATAA
*
40044535 GA-TTAATAATAATAA
1 TATTTAATAA-AATAA
40044550 TATTTAATAAAGATAA
1 TATTTAATAAA-ATAA
40044566 TA
1 TA
40044568 ATACTATTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
13 7 0.26
14 3 0.11
15 4 0.15
16 13 0.48
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (15 bp):
TATTTAATAAAATAA
Found at i:40052311 original size:58 final size:59
Alignment explanation
Indices: 40052217--40052343 Score: 159
Period size: 58 Copynumber: 2.2 Consensus size: 59
40052207 ATTACTTTAA
* *
40052217 TATTAAATTAATATAATACTTATCAAGATAAATATTAGATTAAATTTAATATTAAATAT
1 TATTAAATTAATAAAATACTTATCAAGATAAATATTAAATTAAATTTAATATTAAATAT
* * * * * *
40052276 TATTATATTAATAAAATAC-TATTAAGATGAGTATTAAATTTAATTTAATATTAAA-AC
1 TATTAAATTAATAAAATACTTATCAAGATAAATATTAAATTAAATTTAATATTAAATAT
*
40052333 TATTAAGTTAA
1 TATTAAATTAA
40052344 CATTATTTTT
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
57 10 0.17
58 31 0.53
59 17 0.29
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.43
Consensus pattern (59 bp):
TATTAAATTAATAAAATACTTATCAAGATAAATATTAAATTAAATTTAATATTAAATAT
Found at i:40055840 original size:46 final size:46
Alignment explanation
Indices: 40055771--40055863 Score: 141
Period size: 46 Copynumber: 2.0 Consensus size: 46
40055761 GACGACAACA
* * *
40055771 ATTAGAGTTTTAGTTTTATTTATTTTCTTTATTGTATCAGATTTTT
1 ATTAGAGTTTTAGTTTTACTTATTTTCTCTATTATATCAGATTTTT
* *
40055817 ATTAGAGTTTTAGTTTTACTTATTTTCTCTATTATATTAGGTTTTT
1 ATTAGAGTTTTAGTTTTACTTATTTTCTCTATTATATCAGATTTTT
40055863 A
1 A
40055864 ATTCCTTTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.23, C:0.05, G:0.11, T:0.61
Consensus pattern (46 bp):
ATTAGAGTTTTAGTTTTACTTATTTTCTCTATTATATCAGATTTTT
Found at i:40057376 original size:46 final size:46
Alignment explanation
Indices: 40057285--40057379 Score: 129
Period size: 46 Copynumber: 2.1 Consensus size: 46
40057275 GGAGACGATA
* * *
40057285 ATTAGAGTTTTAGTTTTATATATTTTCTTTATTATATCATATTTTT
1 ATTAGAGTTTTAGTTTTATATATTTCCTCTATTATATCAGATTTTT
* *
40057331 ATTAGAGTTTTAGTTTTACT-TATTTCCTCTATTATATTAGGTTTTT
1 ATTAGAGTTTTAGTTTTA-TATATTTCCTCTATTATATCAGATTTTT
40057377 ATT
1 ATT
40057380 TCTTTTATAA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
46 42 0.98
47 1 0.02
ACGTcount: A:0.24, C:0.06, G:0.08, T:0.61
Consensus pattern (46 bp):
ATTAGAGTTTTAGTTTTATATATTTCCTCTATTATATCAGATTTTT
Found at i:40058112 original size:10 final size:9
Alignment explanation
Indices: 40058094--40058136 Score: 50
Period size: 10 Copynumber: 4.4 Consensus size: 9
40058084 AAAACTACTG
*
40058094 TTTTTCTTT
1 TTTTTATTT
40058103 TTTTTACTTT
1 TTTTTA-TTT
40058113 TTTTTATTT
1 TTTTTATTT
40058122 TCTTGTTATTT
1 T-TT-TTATTT
40058133 TTTT
1 TTTT
40058137 CACTATTTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
9 10 0.33
10 13 0.43
11 7 0.23
ACGTcount: A:0.07, C:0.07, G:0.02, T:0.84
Consensus pattern (9 bp):
TTTTTATTT
Found at i:40066842 original size:16 final size:16
Alignment explanation
Indices: 40066799--40066848 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
40066789 AAGTTTTTTT
40066799 TAAATATAATATA--A
1 TAAATATAATATATTA
*
40066813 TAAATCTGAA-ATATTA
1 TAAATAT-AATATATTA
40066829 TAAATATAATATATTTA
1 TAAATATAATATA-TTA
40066846 TAA
1 TAA
40066849 TGTTATGGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
14 9 0.31
15 4 0.14
16 10 0.34
17 6 0.21
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (16 bp):
TAAATATAATATATTA
Found at i:40067209 original size:24 final size:24
Alignment explanation
Indices: 40067158--40067210 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
40067148 TTCAGTATTT
* *
40067158 ATTAGTATAATATATTTAGCATTT
1 ATTAGCATAATATATTTAGCATTG
40067182 ATTAGCATAATATATTT-GACATTG
1 ATTAGCATAATATATTTAG-CATTG
40067206 ATTAG
1 ATTAG
40067211 AATTATGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 25 0.96
ACGTcount: A:0.38, C:0.06, G:0.11, T:0.45
Consensus pattern (24 bp):
ATTAGCATAATATATTTAGCATTG
Found at i:40071047 original size:19 final size:19
Alignment explanation
Indices: 40071023--40071076 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
40071013 AATCTTCAAG
40071023 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
40071042 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
40071061 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
40071077 AGATATGGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:40071052 original size:36 final size:36
Alignment explanation
Indices: 40071012--40071083 Score: 94
Period size: 38 Copynumber: 2.0 Consensus size: 36
40071002 TATGGAAACA
40071012 TAATCTT-CA-AGGATATGCAATCTTAGATATGATATG
1 TAATCTTACATAGGATATGCAATCTTAGA-A-GATATG
* *
40071048 TAATCTTAGATATGATATGCAATCTTAGAAGATATG
1 TAATCTTACATAGGATATGCAATCTTAGAAGATATG
40071084 GTTTTGTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 13 0.41
37 2 0.06
38 17 0.53
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.36
Consensus pattern (36 bp):
TAATCTTACATAGGATATGCAATCTTAGAAGATATG
Found at i:40080400 original size:20 final size:20
Alignment explanation
Indices: 40080375--40080443 Score: 61
Period size: 20 Copynumber: 3.3 Consensus size: 20
40080365 CTTTTTTTGT
40080375 TTATTTTATTTATTATTATA
1 TTATTTTATTTATTATTATA
*
40080395 TTATTTT-TATTATTATGTTAGA
1 TTATTTTAT-TTATTA--TTATA
*
40080417 TTTATTTTA-TTGTTATTATTA
1 -TTATTTTATTTATTATTA-TA
40080438 TTATTT
1 TTATTT
40080444 CCATTTTTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
19 1 0.03
20 22 0.55
21 1 0.03
22 9 0.22
23 7 0.17
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (20 bp):
TTATTTTATTTATTATTATA
Found at i:40080403 original size:17 final size:17
Alignment explanation
Indices: 40080383--40080442 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
40080373 GTTTATTTTA
*
40080383 TTTATTATTATATTATT
1 TTTATTATTATGTTATT
**
40080400 TTTATTATTATGTTAGA
1 TTTATTATTATGTTATT
40080417 TTTATT-TTATTGTTATT
1 TTTATTATTA-TGTTATT
*
40080434 ATTATTATT
1 TTTATTATT
40080443 TCCATTTTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
16 3 0.09
17 30 0.86
18 2 0.06
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (17 bp):
TTTATTATTATGTTATT
Found at i:40084605 original size:23 final size:23
Alignment explanation
Indices: 40084579--40084625 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 23
40084569 TAATACATCA
40084579 AGAGGGCATGG-AGGTATAAGACC
1 AGAGGGCA-GGAAGGTATAAGACC
40084602 AGAGGGCAGGAAGGTATAAGACC
1 AGAGGGCAGGAAGGTATAAGACC
40084625 A
1 A
40084626 TGTGGGAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 2 0.09
23 21 0.91
ACGTcount: A:0.38, C:0.13, G:0.38, T:0.11
Consensus pattern (23 bp):
AGAGGGCAGGAAGGTATAAGACC
Found at i:40088098 original size:8 final size:8
Alignment explanation
Indices: 40088085--40088119 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
40088075 CTCCTTTTTA
40088085 TTAAATAT
1 TTAAATAT
40088093 TTAAATAT
1 TTAAATAT
*
40088101 CTAATATAT
1 TTAA-ATAT
40088110 TTAAATAT
1 TTAAATAT
40088118 TT
1 TT
40088120 GGCTAATTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 17 0.71
9 7 0.29
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (8 bp):
TTAAATAT
Found at i:40089445 original size:114 final size:114
Alignment explanation
Indices: 40089277--40090089 Score: 1181
Period size: 114 Copynumber: 7.1 Consensus size: 114
40089267 AAAATAAGCA
* * * * * **
40089277 TTAGCGGCGTTTTCGA-AAATGCGCCGC-AAAATACCTAAGCCCAATGATGCCGTTTTCCAAGCT
1 TTAGCGGCGTTTTTGATAAA-GCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
*
40089340 TTCGGGGATTTAGCGGCTTTTTTAA-TAAAGCGCCGCTAATGCTCAGGGCT
65 TTCGGGGATTTAGCGGCGTTTTTAAGT-AAGCGCCGCTAATGCTCAGGGCT
* *
40089390 TTAGCAGCGTTTTTGATAAAGCGCCACAAAAAAACCTAAGCCCAATGACGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGATAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* * *
40089455 TCGAGGATTTAGTGGCGTTTTTAAGTAAGTGCCGCTAATGCTCAGGGCT
66 TCGGGGATTTAGCGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGGCT
*
40089504 TTAGCGGCGTTTTTGTTAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGATAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* ** * *
40089569 TCGGGGATTTAGCGGTGTTTTTAAGTTCGCGCCGCTGATGCTCAAGGCT
66 TCGGGGATTTAGCGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGGCT
* *
40089618 TTAGCGGCGTTTTTGATAAAGCGCCATAAAAAAACCTAAGCCCAACGACACCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGATAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
*
40089683 TCGGGGATTTAGCGGCGTTTTTAAGTAAGTGCCGCTAATGCTCAGGGCT
66 TCGGGGATTTAGCGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGGCT
*
40089732 TTAGCGGCGTTTTTGATAAAGCGCCATAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGATAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
40089797 TCGGGGATTT-GCCGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGGCT
66 TCGGGGATTTAG-CGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGGCT
* * * * * **
40089846 CTAGCAGTGTTTTTGATAAAGCGCCACAGAAAAACCTAAGCCCAAAGATTCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGATAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
*
40089911 TCGGGGATTTAGCGGCGTTTTTAAGTACGCGCCGCTAATGCTCAGGGCT
66 TCGGGGATTTAGCGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGGCT
* *
40089960 TTAGCGGCGTTTTTGGA-AAAGCGCCGC-AAAAAACCTAAGCCCAACGACGCCGTTTTCTTAGCT
1 TTAGCGGCGTTTTT-GATAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
** * *
40090023 TTCGGGGATTTAGTAGCATTTTTTAA-TAAAGCGCCGCTAATGCTCAGTGCT
65 TTCGGGGATTTAGCGGC-GTTTTTAAGT-AAGCGCCGCTAATGCTCAGGGCT
*
40090074 TTAGTGGCGTTTTTGA
1 TTAGCGGCGTTTTTGA
40090090 GGATGCGCCG
Statistics
Matches: 635, Mismatches: 57, Indels: 16
0.90 0.08 0.02
Matches are distributed among these distances:
113 70 0.11
114 561 0.88
115 4 0.01
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.29
Consensus pattern (114 bp):
TTAGCGGCGTTTTTGATAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
TCGGGGATTTAGCGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGGCT
Found at i:40090691 original size:15 final size:14
Alignment explanation
Indices: 40090671--40090714 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
40090661 AAGTTTTATA
40090671 GATTATGGAATTAAG
1 GATTATGG-ATTAAG
*
40090686 GATTATGGATTAGG
1 GATTATGGATTAAG
* *
40090700 GATTCTGGTTTAAG
1 GATTATGGATTAAG
40090714 G
1 G
40090715 GTTAATATGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
14 17 0.68
15 8 0.32
ACGTcount: A:0.30, C:0.02, G:0.32, T:0.36
Consensus pattern (14 bp):
GATTATGGATTAAG
Found at i:40090868 original size:7 final size:7
Alignment explanation
Indices: 40090858--40090897 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
40090848 ATATATTAAA
*
40090858 TAAGGTT
1 TAAGGGT
40090865 TAAGGGT
1 TAAGGGT
*
40090872 TAGGGGT
1 TAAGGGT
*
40090879 TAGGGGT
1 TAAGGGT
40090886 TAAGGGT
1 TAAGGGT
40090893 TAAGG
1 TAAGG
40090898 ATTCAAGATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.25, C:0.00, G:0.45, T:0.30
Consensus pattern (7 bp):
TAAGGGT
Found at i:40091024 original size:82 final size:85
Alignment explanation
Indices: 40090915--40091134 Score: 329
Period size: 83 Copynumber: 2.6 Consensus size: 85
40090905 ATTGGGTTAT
*
40090915 GGTTTAGGGTTTAGTTTAATTAGTGTTTTTAATTTATATATTAAATAAAGTTTAGGGGTTAGGGG
1 GGTTTAGGGTTTAGATTAATTAGTGTTTTTAATTTATATATTAAATAAAGTTTAGGGGTTAGGGG
40090980 TTAGGGATTTGAGGTC-G-A
66 TTAGGGATTTGAGGTCAGTA
40090998 -GTTTAGGGTTTAGATTAATTAGTGTTTGTTAATTTATATATTAAATAAAGTTTAGGGGTTAGGG
1 GGTTTAGGGTTTAGATTAATTAGTGTTT-TTAATTTATATATTAAATAAAGTTTAGGGGTTAGGG
*
40091062 GTTAGGGATTTGGGGTCAGGTTA
65 GTTAGGGATTTGAGGTCA-G-TA
* * *
40091085 GGGTTTAAGATTTAGATTAATTAGTACTTTTTAATTTATATATTAAATAA
1 -GGTTTAGGGTTTAGATTAATTAGT-GTTTTTAATTTATATATTAAATAA
40091135 GTTCTTTATA
Statistics
Matches: 124, Mismatches: 5, Indels: 10
0.89 0.04 0.07
Matches are distributed among these distances:
82 26 0.21
83 52 0.42
85 1 0.01
87 1 0.01
89 41 0.33
90 3 0.02
ACGTcount: A:0.29, C:0.01, G:0.25, T:0.44
Consensus pattern (85 bp):
GGTTTAGGGTTTAGATTAATTAGTGTTTTTAATTTATATATTAAATAAAGTTTAGGGGTTAGGGG
TTAGGGATTTGAGGTCAGTA
Found at i:40091614 original size:84 final size:83
Alignment explanation
Indices: 40091542--40091720 Score: 218
Period size: 84 Copynumber: 2.1 Consensus size: 83
40091532 AAATTTTTTT
* **
40091542 GTGGCATTTTTAATAAAAACGCCGCAAG-GATTTATTAAAATTTGCCAGAGT-GGCGCCGTTTCT
1 GTGGCATTTTTAAGAAAAACGCCGCAAGAG-TGAATTAAAATTTGCCA-A-TAGGCGCCGTTTCT
40091605 CTACTGGAATAAAATCTTATA
63 CTACTGGAATAAAATCTTATA
* * * * **
40091626 GTGGCGTTTTTTAGGAAAACGCTGCAAGAGTGAATTAATGTTTGCCAATACGGCGCCGTTTCTCT
1 GTGGCATTTTTAAGAAAAACGCCGCAAGAGTGAATTAAAATTTGCCAATA-GGCGCCGTTTCTCT
40091691 ACTGGAATAAAATCTTATA
65 ACTGGAATAAAATCTTATA
*
40091710 GTGGCGTTTTT
1 GTGGCATTTTT
40091721 TAAGTCGCAA
Statistics
Matches: 83, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
82 1 0.01
83 1 0.01
84 80 0.96
85 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (83 bp):
GTGGCATTTTTAAGAAAAACGCCGCAAGAGTGAATTAAAATTTGCCAATAGGCGCCGTTTCTCTA
CTGGAATAAAATCTTATA
Found at i:40093308 original size:25 final size:25
Alignment explanation
Indices: 40093251--40093400 Score: 104
Period size: 25 Copynumber: 6.2 Consensus size: 25
40093241 ATTATATATA
*
40093251 AACTTGCATAACTTACATAATA-AC
1 AACTTACATAACTTACATAATACAC
40093275 -A--TA-ATAACTTACATAATACAC
1 AACTTACATAACTTACATAATACAC
40093296 AACTTACATAACTTA-ATAACTTACA-
1 AACTTACATAACTTACATAA--TACAC
* * **
40093321 TA-GTACATAACTTTGATAACTA-AC
1 AACTTACATAACTTACATAA-TACAC
* * *
40093345 -ATTATACACAACTTACATAATACAT
1 AACT-TACATAACTTACATAATACAC
**
40093370 TTCTTACATAACTTACATAATACAC
1 AACTTACATAACTTACATAATACAC
40093395 AACTTA
1 AACTTA
40093401 ATTAATATTA
Statistics
Matches: 97, Mismatches: 16, Indels: 25
0.70 0.12 0.18
Matches are distributed among these distances:
20 15 0.15
21 3 0.03
22 1 0.01
23 3 0.03
24 20 0.21
25 50 0.52
26 5 0.05
ACGTcount: A:0.46, C:0.20, G:0.02, T:0.32
Consensus pattern (25 bp):
AACTTACATAACTTACATAATACAC
Found at i:40093316 original size:8 final size:9
Alignment explanation
Indices: 40093251--40093549 Score: 149
Period size: 9 Copynumber: 34.8 Consensus size: 9
40093241 ATTATATATA
*
40093251 AACTTGCAT
1 AACTTACAT
40093260 AACTTACAT
1 AACTTACAT
*
40093269 AA-TAACATAAT
1 AACTTAC---AT
40093280 AACTTACAT
1 AACTTACAT
*
40093289 AA--TACAC
1 AACTTACAT
40093296 AACTTACAT
1 AACTTACAT
40093305 AACTTA-AT
1 AACTTACAT
40093313 AACTTACAT
1 AACTTACAT
*
40093322 -A-GTACAT
1 AACTTACAT
**
40093329 AACTTTGAT
1 AACTTACAT
*
40093338 AACTAACAT
1 AACTTACAT
* *
40093347 TA--TACAC
1 AACTTACAT
40093354 AACTTACAT
1 AACTTACAT
40093363 AA--TACAT
1 AACTTACAT
**
40093370 TTCTTACAT
1 AACTTACAT
40093379 AACTTACAT
1 AACTTACAT
*
40093388 AA--TACAC
1 AACTTACAT
40093395 AACTTA-ATT
1 AACTTACA-T
*
40093404 AATATTATACAT
1 -A-ACT-TACAT
*
40093416 AACATACAT
1 AACTTACAT
*
40093425 AA-TACACAT
1 AACT-TACAT
40093434 AACTTACAT
1 AACTTACAT
*
40093443 -A-GTACAT
1 AACTTACAT
*
40093450 AACTAACAT
1 AACTTACAT
*
40093459 AA--TACAC
1 AACTTACAT
*
40093466 AACTTACGT
1 AACTTACAT
*
40093475 AACTTAAAT
1 AACTTACAT
40093484 AACTTACAT
1 AACTTACAT
*
40093493 AGCTTACAT
1 AACTTACAT
40093502 AA--TACAT
1 AACTTACAT
40093509 AACTTACAT
1 AACTTACAT
*
40093518 GACTT-CTAT
1 AACTTAC-AT
40093527 AA--TACAT
1 AACTTACAT
40093534 AACTTACAT
1 AACTTACAT
*
40093543 AATTTAC
1 AACTTAC
40093550 CTAATACATA
Statistics
Matches: 214, Mismatches: 44, Indels: 64
0.66 0.14 0.20
Matches are distributed among these distances:
7 48 0.22
8 18 0.08
9 131 0.61
10 3 0.01
11 7 0.03
12 6 0.03
13 1 0.00
ACGTcount: A:0.46, C:0.19, G:0.02, T:0.32
Consensus pattern (9 bp):
AACTTACAT
Found at i:40093360 original size:41 final size:41
Alignment explanation
Indices: 40093313--40093517 Score: 148
Period size: 41 Copynumber: 5.2 Consensus size: 41
40093303 ATAACTTAAT
* ** *
40093313 AACTTACATAGTACATAACTTTGATAACTAACATTATACAC
1 AACTTACATAATACATAACTTACATAACTAACATAATACAC
** *
40093354 AACTTACATAATACATTTCTTACATAACTTACATAATACAC
1 AACTTACATAATACATAACTTACATAACTAACATAATACAC
*
40093395 AACTTA-AT--TA-AT-ATTATACATAAC-ATACATAATACAC
1 AACTTACATAATACATAACT-TACATAACTA-ACATAATACAC
* *
40093432 -A-TAAC-T--TACAT-A-GTACATAACTAACATAATACAC
1 AACTTACATAATACATAACTTACATAACTAACATAATACAC
* * * * *
40093466 AACTTACGTAACTTAAATAACTTACATAGCTTACATAATACAT
1 AACTTACATAA--TACATAACTTACATAACTAACATAATACAC
40093509 AACTTACAT
1 AACTTACAT
40093518 GACTTCTATA
Statistics
Matches: 131, Mismatches: 19, Indels: 26
0.74 0.11 0.15
Matches are distributed among these distances:
34 19 0.15
35 7 0.05
36 8 0.06
37 22 0.17
38 2 0.02
40 2 0.02
41 44 0.34
42 1 0.01
43 26 0.20
ACGTcount: A:0.46, C:0.20, G:0.02, T:0.32
Consensus pattern (41 bp):
AACTTACATAATACATAACTTACATAACTAACATAATACAC
Found at i:40093515 original size:25 final size:25
Alignment explanation
Indices: 40093411--40093560 Score: 121
Period size: 25 Copynumber: 5.9 Consensus size: 25
40093401 ATTAATATTA
*
40093411 TACATAACATACATAATACACATAACT
1 TACATAACTTACATAAT--ACATAACT
*
40093438 TACAT-A-GTACATAACTAACATAA--
1 TACATAACTTACATAA-T-ACATAACT
* * *
40093461 TACACAACTTACGTAACTTAAATAACT
1 TACATAACTTACATAA--TACATAACT
*
40093488 TACATAGCTTACATAATACATAACT
1 TACATAACTTACATAATACATAACT
*
40093513 TACATGACTT-CTATAATACATAACT
1 TACATAACTTAC-ATAATACATAACT
* *
40093538 TACATAATTTACCTAATACATAA
1 TACATAACTTACATAATACATAA
40093561 ATATATATCA
Statistics
Matches: 99, Mismatches: 16, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
23 4 0.04
24 2 0.02
25 71 0.72
26 4 0.04
27 18 0.18
ACGTcount: A:0.47, C:0.20, G:0.03, T:0.31
Consensus pattern (25 bp):
TACATAACTTACATAATACATAACT
Found at i:40093542 original size:34 final size:34
Alignment explanation
Indices: 40093270--40093589 Score: 191
Period size: 34 Copynumber: 9.4 Consensus size: 34
40093260 AACTTACATA
* *
40093270 ATAACATA-ATAACTTACATAATACACAACTTAC
1 ATAACTTACATAACTTACATAATACATAACTTAC
* **
40093303 ATAACTTA-ATAACTTACATAGTACATAACTTTG
1 ATAACTTACATAACTTACATAATACATAACTTAC
* * *
40093336 ATAACTAACATTA--TACACAACTTACATAA--TAC
1 ATAACTTACATAACTTACATAA--TACATAACTTAC
** *
40093368 ATTTCTTACATAACTTACATAATACACAACTTA-
1 ATAACTTACATAACTTACATAATACATAACTTAC
* *
40093401 ATTAATATTATACATAACATACATAATACACATAACTTAC
1 A-T-A-ACT-TACATAACTTACATAAT--ACATAACTTAC
* * *
40093441 AT-A-GTACATAACTAACATAATACACAACTTAC
1 ATAACTTACATAACTTACATAATACATAACTTAC
* * *
40093473 GTAACTTAAATAACTTACATAGCTTACATAA--TAC
1 ATAACTTACATAACTTACATA--ATACATAACTTAC
*
40093507 ATAACTTACATGACTT-CTATAATACATAACTTAC
1 ATAACTTACATAACTTAC-ATAATACATAACTTAC
* * * * * *
40093541 ATAATTTACCTAA--TACATAAATATATATCATATG
1 ATAACTTACATAACTTACAT-AATACATAACTTA-C
40093575 ATAACTTACATAACT
1 ATAACTTACATAACT
40093590 CATTTATAGT
Statistics
Matches: 216, Mismatches: 45, Indels: 49
0.70 0.15 0.16
Matches are distributed among these distances:
32 42 0.19
33 49 0.23
34 90 0.42
36 8 0.04
37 16 0.07
39 10 0.05
40 1 0.00
ACGTcount: A:0.47, C:0.19, G:0.02, T:0.33
Consensus pattern (34 bp):
ATAACTTACATAACTTACATAATACATAACTTAC
Found at i:40093544 original size:16 final size:16
Alignment explanation
Indices: 40093257--40093545 Score: 128
Period size: 16 Copynumber: 17.9 Consensus size: 16
40093247 TATAAACTTG
40093257 CATAACTTACATAATAA
1 CATAACTTACATAAT-A
40093274 CATAATAACTTACATAATA
1 C---ATAACTTACATAATA
*
40093293 CACAACTTACATAACTTA
1 CATAACTTACATAA--TA
*
40093311 -ATAACTTACATAGTA
1 CATAACTTACATAATA
40093326 CATAAC-T---T--T-
1 CATAACTTACATAATA
* * *
40093335 GATAACTAACATTATA
1 CATAACTTACATAATA
*
40093351 CACAACTTACATAATA
1 CATAACTTACATAATA
40093367 CAT---TT-C-T--TA
1 CATAACTTACATAATA
40093376 CATAACTTACATAATA
1 CATAACTTACATAATA
* *
40093392 CACAACTTAATTAATATTATA
1 CATAACTT-A--CATA--ATA
*
40093413 CATAACATACATAATACA
1 CATAACTTACATAAT--A
*
40093431 CATAACTTACATAGTA
1 CATAACTTACATAATA
*
40093447 CATAACTAACATAATA
1 CATAACTTACATAATA
* *
40093463 CACAACTTACGTAACTTA
1 CATAACTTACATAA--TA
* *
40093481 AATAACTTACATAGCTTA
1 CATAACTTACATA--ATA
40093499 CATAA--TACATAACTTA
1 CATAACTTACATAA--TA
*
40093515 CATGACTT-CTATAATA
1 CATAACTTAC-ATAATA
40093531 CATAACTTACATAAT
1 CATAACTTACATAAT
40093546 TTACCTAATA
Statistics
Matches: 205, Mismatches: 30, Indels: 75
0.66 0.10 0.24
Matches are distributed among these distances:
9 10 0.05
10 1 0.00
11 1 0.00
12 4 0.02
13 4 0.02
14 1 0.00
15 4 0.02
16 94 0.46
17 15 0.07
18 42 0.20
19 5 0.02
20 15 0.07
21 9 0.04
ACGTcount: A:0.47, C:0.19, G:0.02, T:0.32
Consensus pattern (16 bp):
CATAACTTACATAATA
Found at i:40093772 original size:25 final size:26
Alignment explanation
Indices: 40093742--40093805 Score: 103
Period size: 25 Copynumber: 2.5 Consensus size: 26
40093732 CATAATAACT
40093742 TACATAACTTAATAACTCATA-TATA
1 TACATAACTTAATAACTCATATTATA
* *
40093767 TGCATAACTTAATAACTCATATTATT
1 TACATAACTTAATAACTCATATTATA
40093793 TACATAACTTAAT
1 TACATAACTTAAT
40093806 CATTGTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
25 20 0.57
26 15 0.43
ACGTcount: A:0.44, C:0.16, G:0.02, T:0.39
Consensus pattern (26 bp):
TACATAACTTAATAACTCATATTATA
Found at i:40095453 original size:43 final size:43
Alignment explanation
Indices: 40095368--40095665 Score: 314
Period size: 43 Copynumber: 6.9 Consensus size: 43
40095358 GCGTTTTTAG
** * **
40095368 GAAAAGCGCCGCTAAAGGTCATCAGACAATAGCGGCGTTTGTGA
1 GAAAAGCGCCGCTAAAGAACATGA-ACTTTAGCGGCGTTTGTGA
**
40095412 GGGAAGCGCCGCTAAAGAACATGAACTTTAGCGGCGTTTGTGA
1 GAAAAGCGCCGCTAAAGAACATGAACTTTAGCGGCGTTTGTGA
*** *
40095455 GAAAAGCGCATTTAAAGAACATG-ACATTTAGCGGGGTTTGTGA
1 GAAAAGCGCCGCTAAAGAACATGAAC-TTTAGCGGCGTTTGTGA
* * *
40095498 -AAGAGGCGCCGCTAAAGAACATGACCTTTAGCGGCGCTTGTGA
1 GAA-AAGCGCCGCTAAAGAACATGAACTTTAGCGGCGTTTGTGA
* * *
40095541 GAGAGGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTGTGA
1 GAAAAGCGCCGCTAAAGAACATGAACTTTAGCGGCGTTTGTGA
* * * *
40095584 GAAATGCGCCGCTAAGGAACATG-ACTATTAGCAGCGTTTGTGG
1 GAAAAGCGCCGCTAAAGAACATGAACT-TTAGCGGCGTTTGTGA
* * **
40095627 GAAAAGCACCGCTAAAAAACATGTTCTTTAGCGGCGTTT
1 GAAAAGCGCCGCTAAAGAACATGAACTTTAGCGGCGTTT
40095666 ATTTCTATAA
Statistics
Matches: 214, Mismatches: 34, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
42 6 0.03
43 185 0.86
44 23 0.11
ACGTcount: A:0.30, C:0.19, G:0.29, T:0.22
Consensus pattern (43 bp):
GAAAAGCGCCGCTAAAGAACATGAACTTTAGCGGCGTTTGTGA
Found at i:40095639 original size:129 final size:129
Alignment explanation
Indices: 40095397--40095662 Score: 349
Period size: 129 Copynumber: 2.1 Consensus size: 129
40095387 CATCAGACAA
* *
40095397 TAGCGGCGTTTGTGAGGGAAGCGCCGCTAAAGAACATGAACTTTAGCGGCGTTTGTGAGAAAAGC
1 TAGCGGCGCTTGTGAGAGAAGCGCCGCTAAAGAACATGAACTTTAGCGGCGTTTGTGAGAAAAGC
** * * * *
40095462 GCATTTAAAGAACATGACATTTAGCGGGGTTTGTGAAAGAGGCGCCGCTAAAGAACATGACCTT
66 GCAGCTAAAGAACATGACATTTAGCAGCGTTTGTGAAAGAGGCACCGCTAAAAAACATGACCTT
* * *
40095526 TAGCGGCGCTTGTGAGAGAGGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTGTGAGAAATGC
1 TAGCGGCGCTTGTGAGAGAAGCGCCGCTAAAGAACATGAACTTTAGCGGCGTTTGTGAGAAAAGC
* * **
40095591 GCCGCTAAGGAACATGAC-TATTAGCAGCGTTTGTGGGAAA-A-GCACCGCTAAAAAACATGTTC
66 GCAGCTAAAGAACATGACAT-TTAGCAGCGTTTGT--GAAAGAGGCACCGCTAAAAAACATGACC
40095653 TT
128 TT
40095655 TAGCGGCG
1 TAGCGGCG
40095663 TTTATTTCTA
Statistics
Matches: 119, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
128 1 0.01
129 113 0.95
130 1 0.01
131 4 0.03
ACGTcount: A:0.29, C:0.19, G:0.30, T:0.22
Consensus pattern (129 bp):
TAGCGGCGCTTGTGAGAGAAGCGCCGCTAAAGAACATGAACTTTAGCGGCGTTTGTGAGAAAAGC
GCAGCTAAAGAACATGACATTTAGCAGCGTTTGTGAAAGAGGCACCGCTAAAAAACATGACCTT
Found at i:40098689 original size:26 final size:26
Alignment explanation
Indices: 40098660--40098709 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
40098650 TGAGAATAGC
40098660 TTTTAAAAAATACTGTGAAAAAATAA
1 TTTTAAAAAATACTGTGAAAAAATAA
* * *
40098686 TTTTGAAAAATACTTTTAAAAAAT
1 TTTTAAAAAATACTGTGAAAAAAT
40098710 TTAGTTTAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.36
Consensus pattern (26 bp):
TTTTAAAAAATACTGTGAAAAAATAA
Found at i:40098694 original size:13 final size:13
Alignment explanation
Indices: 40098660--40098709 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
40098650 TGAGAATAGC
*
40098660 TTTTAAAAAATAC
1 TTTTAAAAAATAA
* *
40098673 TGTGAAAAAATAA
1 TTTTAAAAAATAA
* *
40098686 TTTTGAAAAATAC
1 TTTTAAAAAATAA
40098699 TTTTAAAAAAT
1 TTTTAAAAAAT
40098710 TTAGTTTAAG
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.36
Consensus pattern (13 bp):
TTTTAAAAAATAA
Found at i:40101498 original size:16 final size:16
Alignment explanation
Indices: 40101466--40101496 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
40101456 GTTCTTTTAA
40101466 CTTTCTTTCTTTTTTT
1 CTTTCTTTCTTTTTTT
40101482 CTTT-TTTCTTTTTTT
1 CTTTCTTTCTTTTTTT
40101497 TCCATTCTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
CTTTCTTTCTTTTTTT
Found at i:40101773 original size:24 final size:25
Alignment explanation
Indices: 40101746--40101795 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
40101736 ATAGGAAAGT
40101746 TTAAACAACATAAAA-GAAAAAAAA
1 TTAAACAACATAAAACGAAAAAAAA
** *
40101770 TTAAATTACTTAAAACGAAAAAAAA
1 TTAAACAACATAAAACGAAAAAAAA
40101795 T
1 T
40101796 ATGGGGATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.68, C:0.08, G:0.04, T:0.20
Consensus pattern (25 bp):
TTAAACAACATAAAACGAAAAAAAA
Found at i:40103100 original size:8 final size:9
Alignment explanation
Indices: 40103077--40103103 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
40103067 ACAATATGAA
40103077 ATAAAAATT
1 ATAAAAATT
40103086 ATAAAAATT
1 ATAAAAATT
40103095 ATAAAAATT
1 ATAAAAATT
40103104 TTTAGAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
ATAAAAATT
Found at i:40105810 original size:17 final size:18
Alignment explanation
Indices: 40105784--40105817 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
40105774 CTAATGAACA
*
40105784 AATAATCAAT-CAATACC
1 AATAAGCAATACAATACC
40105801 AATAAGCAATACAATAC
1 AATAAGCAATACAATAC
40105818 ACATGAGGGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.56, C:0.21, G:0.03, T:0.21
Consensus pattern (18 bp):
AATAAGCAATACAATACC
Found at i:40106274 original size:3 final size:3
Alignment explanation
Indices: 40106266--40106312 Score: 51
Period size: 3 Copynumber: 15.3 Consensus size: 3
40106256 ATAATCAAAT
* *
40106266 ATA ATA AT- ATCA ATA ATA ATA AGA GTA ATA ATTA ATA ATA ATA ATA
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA
40106312 A
1 A
40106313 ATTAATTAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
2 2 0.05
3 30 0.81
4 5 0.14
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:40106332 original size:21 final size:21
Alignment explanation
Indices: 40106294--40106333 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
40106284 ATAAGAGTAA
* *
40106294 TAATTAATAATAATAATAAAT
1 TAATTAATAACAAAAATAAAT
*
40106315 TAATTAATAGCAAAAATAA
1 TAATTAATAACAAAAATAA
40106334 CAAACAGGAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (21 bp):
TAATTAATAACAAAAATAAAT
Found at i:40107863 original size:45 final size:42
Alignment explanation
Indices: 40107790--40107908 Score: 134
Period size: 41 Copynumber: 2.8 Consensus size: 42
40107780 TCTGTAACCC
* *
40107790 GTCTTCAATCTGCTCCACTGTAATTTCAGGGAAGTGAGATCTGCT
1 GTCTTCAATCTGCTCCACTGCAACTTCAGGG-AG-GAGA-CTGCT
* *
40107835 GTCTTCAGTCTGCTCCATTGCAACTTCAGGG-GGAGACTGCT
1 GTCTTCAATCTGCTCCACTGCAACTTCAGGGAGGAGACTGCT
* *
40107876 GTTTTTAAT-TCGCTCCACTGCAACTTCAGGGAG
1 GTCTTCAATCT-GCTCCACTGCAACTTCAGGGAG
40107909 ATAGAATTGT
Statistics
Matches: 64, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
40 1 0.02
41 30 0.47
42 5 0.08
43 1 0.02
45 27 0.42
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.32
Consensus pattern (42 bp):
GTCTTCAATCTGCTCCACTGCAACTTCAGGGAGGAGACTGCT
Found at i:40107987 original size:41 final size:43
Alignment explanation
Indices: 40107887--40107988 Score: 122
Period size: 44 Copynumber: 2.4 Consensus size: 43
40107877 TTTTTAATTC
*
40107887 GCTCCACTGCAACTTCAGGGAGATAGAATTGTAGGATGTAATAT
1 GCTCCACTGCAACTTCAGGGAGATAGAATTGTAGCATG-AATAT
*
40107931 GCTCCACTGCAACTTCAGGGAGATA-AGATT-T-GCCATG-ATTT
1 GCTCCACTGCAACTTCAGGGAGATAGA-ATTGTAG-CATGAATAT
*
40107972 GCTCTACTGCAACTTCA
1 GCTCCACTGCAACTTCA
40107989 TAGACATAAG
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
41 19 0.36
42 1 0.02
43 5 0.09
44 28 0.53
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (43 bp):
GCTCCACTGCAACTTCAGGGAGATAGAATTGTAGCATGAATAT
Found at i:40108180 original size:223 final size:222
Alignment explanation
Indices: 40107706--40108362 Score: 755
Period size: 223 Copynumber: 3.0 Consensus size: 222
40107696 ACTTGATTTC
* * *
40107706 AATTTGTCCCGCTGCAACTTCAGGGAGATAAGATTCACTATGATCTGCTCTACTGCAACTTCAGA
1 AATTTGTTCCGCTGCAACTTCAGGGAGATAAGATTCGCCATGATCTGCTCTACTGCAACTTCAGA
* *** * * ** * *
40107771 GAGATAAGATCTGTAACCCGT-CTTCAATCTGCTCCACTGTAATTTCAGGGAAGTGAGA-TCTGC
66 GAGATAAGATCTGTGATTTGTACTTTAATCTGTTCCACTACAATTTCAGGGAAATAAGATTC-GC
* * * * * * * * * *
40107834 TGTCTTCAGTCTGCTCCATTGCAACTTCAGGGGGAGACTGCTGT--TTTTAATTCGCTCCACTGC
130 TATCTTTAGTCTGCTCCACTGCAACTTCAGGGAGATAATACT-TCACTTCAATCCGCTCCACTGC
* *
40107897 AACTTCAGGGAGATAGAATTGTAGGATGT
194 AACTTCAGGGAGATAGGATTATAGGATGT
* * * * * *
40107926 AATATGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATGATTTGCTCTACTGCAACTTCATA
1 AATTTGTTCCGCTGCAACTTCAGGGAGATAAGATTCGCCATGATCTGCTCTACTGCAACTTCAGA
* * * *
40107991 GACATAAGATCTGTGATTTGTAACTTTAATTTATTCCACTACAACTTCAGGGAAATAAGATTCGC
66 GAGATAAGATCTGTGATTTGT-ACTTTAATCTGTTCCACTACAATTTCAGGGAAATAAGATTCGC
* * *
40108056 TATCTTTAATCTGCTCCACTGCAACTTCAGGAAGATAATACTTCACTTCAATCCGCTCCATTGCA
130 TATCTTTAGTCTGCTCCACTGCAACTTCAGGGAGATAATACTTCACTTCAATCCGCTCCACTGCA
* * *
40108121 ACTTCAGGGAGATAGGATTATTGGCTTT
195 ACTTCAGGGAGATAGGATTATAGGATGT
* * * * *
40108149 AATTTGTTCCGGTGCAAATTCAGGGAGATAAGATTCGCCATGATCTGCTCTATTGCAATTTTAGA
1 AATTTGTTCCGCTGCAACTTCAGGGAGATAAGATTCGCCATGATCTGCTCTACTGCAACTTCAGA
* * * *
40108214 GAGATAAGATCTGTGATTTATAGCTTTAATCTGTTTCACTACAATTTTAGGGAAATAAGATTCGT
66 GAGATAAGATCTGTGATTTGTA-CTTTAATCTGTTCCACTACAATTTCAGGGAAATAAGATTCGC
* * * *
40108279 TATCTTTAGTCTACTCCACTACAACTTCAGGGAGATAAAACTTCACTTCAATCCACTCCACTGCA
130 TATCTTTAGTCTGCTCCACTGCAACTTCAGGGAGATAATACTTCACTTCAATCCGCTCCACTGCA
*
40108344 ACTTCAGGGAGATAAGATT
195 ACTTCAGGGAGATAGGATT
40108363 CGCAATGATC
Statistics
Matches: 363, Mismatches: 68, Indels: 9
0.82 0.15 0.02
Matches are distributed among these distances:
220 72 0.20
221 1 0.00
222 64 0.18
223 226 0.62
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (222 bp):
AATTTGTTCCGCTGCAACTTCAGGGAGATAAGATTCGCCATGATCTGCTCTACTGCAACTTCAGA
GAGATAAGATCTGTGATTTGTACTTTAATCTGTTCCACTACAATTTCAGGGAAATAAGATTCGCT
ATCTTTAGTCTGCTCCACTGCAACTTCAGGGAGATAATACTTCACTTCAATCCGCTCCACTGCAA
CTTCAGGGAGATAGGATTATAGGATGT
Found at i:40108362 original size:179 final size:179
Alignment explanation
Indices: 40108161--40108541 Score: 602
Period size: 179 Copynumber: 2.1 Consensus size: 179
40108151 TTTGTTCCGG
* * * * *
40108161 TGCAAATTCAGGGAGATAAGATTCGCCATGATCTGCTCTATTGCAATTTTAGAGAGATAAGATCT
1 TGCAACTTCAGGGAGATAAGATTCGCAATGATCTGCTCTATTGCAACTTCAGAGAGATAAGATAT
* * * * * *
40108226 GTGATTTATAGCTTTAATCTGTTTCACTACAATTTTAGGGAAATAAGATTCGTTATCTTTAGTCT
66 GTGATTTATAGCTTTAATCTATTCCACTACAATTTCAAGGAAATAAGATTCGCTATCTTCAGTCT
40108291 ACTCCACTACAACTTCAGGGAGATAAAACTTCACTTCAATC-CACTCCAC
131 ACTCCACTACAACTTCAGGGAGATAAAACTTCACTTCAATCTCA-TCCAC
40108340 TGCAACTTCAGGGAGATAAGATTCGCAATGATCTGCTCTATTGCAACTTCAGAGAGATAAGATAT
1 TGCAACTTCAGGGAGATAAGATTCGCAATGATCTGCTCTATTGCAACTTCAGAGAGATAAGATAT
*
40108405 GTGATTTATAGCTTTAATCTATTCCACTGCAATTTCAAGGAAATAAGATTCGCTATCTTCAGTCT
66 GTGATTTATAGCTTTAATCTATTCCACTACAATTTCAAGGAAATAAGATTCGCTATCTTCAGTCT
* * *
40108470 ACTCCACTGCAACTTCAGGGAGATAAGACTTCACTTCAATCTGATCCAC
131 ACTCCACTACAACTTCAGGGAGATAAAACTTCACTTCAATCTCATCCAC
*
40108519 TGCAACTTCAGGGAGATAGGATT
1 TGCAACTTCAGGGAGATAAGATT
40108542 ATTGGCTTTA
Statistics
Matches: 185, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
179 184 0.99
180 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (179 bp):
TGCAACTTCAGGGAGATAAGATTCGCAATGATCTGCTCTATTGCAACTTCAGAGAGATAAGATAT
GTGATTTATAGCTTTAATCTATTCCACTACAATTTCAAGGAAATAAGATTCGCTATCTTCAGTCT
ACTCCACTACAACTTCAGGGAGATAAAACTTCACTTCAATCTCATCCAC
Found at i:40108411 original size:402 final size:402
Alignment explanation
Indices: 40107932--40108764 Score: 1265
Period size: 402 Copynumber: 2.1 Consensus size: 402
40107922 ATGTAATATG
* * * *
40107932 CTCCACTGCAACTTCAGGGAGATAAGATTTGCCATGATTTGCTCTACTGCAACTTCATAGACATA
1 CTCCACTGCAACTTCAGGGAGATAAGATTCGCAATGATCTGCTCTACTGCAACTTCAGAGACATA
* * * *
40107997 AGATCTGTGATTTGTAACTTTAATTTATTCCACTACAACTTCAGGGAAATAAGATTCGCTATCTT
66 AGATATGTGATTTATAACTTTAATCTATTCCACTACAACTTCAAGGAAATAAGATTCGCTATCTT
* * * * *
40108062 TAATCTGCTCCACTGCAACTTCAGGAAGATAATACTTCACTTCAATCCGCTCCATTGCAACTTCA
131 CAATCTACTCCACTGCAACTTCAGGAAGATAAGACTTCACTTCAATCCGATCCACTGCAACTTCA
* * **
40108127 GGGAGATAGGATTATTGGCTTTAATTTGTTCCGGTGCAAATTCAGGGAGATAAGATTCGCCATGA
196 GGGAGATAGGATTATTGGCTTTAATCTGCTCCACTGCAAATTCAGGGAGATAAGATTCGCCATGA
* * *
40108192 TCTGCTCTATTGCAATTTTAGAGAGATAAGATCTGTGATTTATAGCTTTAATCTGTT-TCACTAC
261 TCTGCTCTACTACAACTTTAGAGAGATAAGATCTGTGATTTATAGCTTTAATCTGTTCT-ACTAC
* ** *
40108256 AATTTTAGGGAAATAAGATTC-GTTATCTTTAGTCTACTCCACTACAACTTCAGGGAGATAAAAC
325 AATTTCAAAGAAATAAGATTCAG-TATCTTCAGTCTACTCCACTACAACTTCAGGGAGATAAAAC
40108320 TTCACTTCAATCCA
389 TTCACTTCAATCCA
* *
40108334 CTCCACTGCAACTTCAGGGAGATAAGATTCGCAATGATCTGCTCTATTGCAACTTCAGAGAGATA
1 CTCCACTGCAACTTCAGGGAGATAAGATTCGCAATGATCTGCTCTACTGCAACTTCAGAGACATA
* * *
40108399 AGATATGTGATTTATAGCTTTAATCTATTCCACTGCAATTTCAAGGAAATAAGATTCGCTATCTT
66 AGATATGTGATTTATAACTTTAATCTATTCCACTACAACTTCAAGGAAATAAGATTCGCTATCTT
* * *
40108464 CAGTCTACTCCACTGCAACTTCAGGGAGATAAGACTTCACTTCAATCTGATCCACTGCAACTTCA
131 CAATCTACTCCACTGCAACTTCAGGAAGATAAGACTTCACTTCAATCCGATCCACTGCAACTTCA
* *
40108529 GGGAGATAGGATTATTGGCTTTAATCTGCTCCACTGTAACTTCAGGGAGATAAGATTCGCCATGA
196 GGGAGATAGGATTATTGGCTTTAATCTGCTCCACTGCAAATTCAGGGAGATAAGATTCGCCATGA
* *
40108594 TTTGCTCTACTACAACTTTAGAGAGATAAGATCTGTGATTTATAGCTTTAATCTGTTCTACTGCA
261 TCTGCTCTACTACAACTTTAGAGAGATAAGATCTGTGATTTATAGCTTTAATCTGTTCTACTACA
* * *
40108659 ATTTCAAAGAAATAAGATTCAGTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTT
326 ATTTCAAAGAAATAAGATTCAGTATCTTCAGTCTACTCCACTACAACTTCAGGGAGATAAAACTT
40108724 CACTTCAATCCA
391 CACTTCAATCCA
* *
40108736 CTCTACTGCAACTTCAGGGAGATAGGATT
1 CTCCACTGCAACTTCAGGGAGATAAGATT
40108765 ATTGGCTTTA
Statistics
Matches: 388, Mismatches: 41, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
402 386 0.99
403 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (402 bp):
CTCCACTGCAACTTCAGGGAGATAAGATTCGCAATGATCTGCTCTACTGCAACTTCAGAGACATA
AGATATGTGATTTATAACTTTAATCTATTCCACTACAACTTCAAGGAAATAAGATTCGCTATCTT
CAATCTACTCCACTGCAACTTCAGGAAGATAAGACTTCACTTCAATCCGATCCACTGCAACTTCA
GGGAGATAGGATTATTGGCTTTAATCTGCTCCACTGCAAATTCAGGGAGATAAGATTCGCCATGA
TCTGCTCTACTACAACTTTAGAGAGATAAGATCTGTGATTTATAGCTTTAATCTGTTCTACTACA
ATTTCAAAGAAATAAGATTCAGTATCTTCAGTCTACTCCACTACAACTTCAGGGAGATAAAACTT
CACTTCAATCCA
Found at i:40108563 original size:223 final size:222
Alignment explanation
Indices: 40108334--40109037 Score: 1045
Period size: 223 Copynumber: 3.2 Consensus size: 222
40108324 CTTCAATCCA
* * *
40108334 CTCCACTGCAACTTCAGGGAGATAAGATTCGCAATGATCTGCTCTATTGCAACTTCAGAGAGATA
1 CTCCACTACAACTTCAGGGAGATAAGATTCGCCATGATCTGCTCTAATGCAACTTCAGAGAGATA
40108399 AGATATGTGATTTATAGCTTTAATCTATTCCACTGCAATTTCAAGGAAATAAGATTCGCTATCTT
66 AGATATGTGATTTATAGCTTTAATCTATTCCACTGCAATTTCAAGGAAATAAGATTCGCTATCTT
40108464 CAGTCTACTCCACTGCAACTTCAGGGAGATAAGACTTCACTTCAATCTGATCCACTGCAACTTCA
131 CAGTCTACTCCACTGCAACTTCAGGGAGATAAGACTTCACTTCAATC-GATCCACTGCAACTTCA
40108529 GGGAGATAGGATTATTGGCTTTAATCTG
195 GGGAGATAGGATTATTGGCTTTAATCTG
** * * * *
40108557 CTCCACTGTAACTTCAGGGAGATAAGATTCGCCATGATTTGCTCTACTACAACTTTAGAGAGATA
1 CTCCACTACAACTTCAGGGAGATAAGATTCGCCATGATCTGCTCTAATGCAACTTCAGAGAGATA
* * * *
40108622 AGATCTGTGATTTATAGCTTTAATCTGTTCTACTGCAATTTCAAAGAAATAAGATTCAG-TATCT
66 AGATATGTGATTTATAGCTTTAATCTATTCCACTGCAATTTCAAGGAAATAAGATTC-GCTATCT
* * *
40108686 TCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTCACTTCAATCCACTCTACTGCAACTTC
130 TCAGTCTACTCCACTGCAACTTCAGGGAGATAAGACTTCACTTCAATCGA-TCCACTGCAACTTC
40108751 AGGGAGATAGGATTATTGGCTTTAATCTG
194 AGGGAGATAGGATTATTGGCTTTAATCTG
* * *
40108780 CTCCACTACAACTTTAGGGAGATAAGATTCACCATGATCTGTTCTAATGCAACTTCAGAGAGATA
1 CTCCACTACAACTTCAGGGAGATAAGATTCGCCATGATCTGCTCTAATGCAACTTCAGAGAGATA
* * * *
40108845 AGATTTGTGATTTATAGCTTTAATCTATTTCATTGCAACTTC-AGGAAAATAAGATTCGCTATCT
66 AGATATGTGATTTATAGCTTTAATCTATTCCACTGCAATTTCAAGG-AAATAAGATTCGCTATCT
* * * * * * **
40108909 TTAGTCTACTCCATTGCAACTTTAGGGAGATAATACTTCACTTCAATCCGCTTCACTAAAACTTC
130 TCAGTCTACTCCACTGCAACTTCAGGGAGATAAGACTTCACTTCAAT-CGATCCACTGCAACTTC
*
40108974 AGGGAGAT-GGAATTATTGGCTTTAATTTG
194 AGGGAGATAGG-ATTATTGGCTTTAATCTG
40109003 CTCCACTACAACTTCAGGGAGATAAGATTCGCCAT
1 CTCCACTACAACTTCAGGGAGATAAGATTCGCCAT
40109038 CTTCTTCAAT
Statistics
Matches: 432, Mismatches: 43, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
222 6 0.01
223 424 0.98
224 2 0.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.32
Consensus pattern (222 bp):
CTCCACTACAACTTCAGGGAGATAAGATTCGCCATGATCTGCTCTAATGCAACTTCAGAGAGATA
AGATATGTGATTTATAGCTTTAATCTATTCCACTGCAATTTCAAGGAAATAAGATTCGCTATCTT
CAGTCTACTCCACTGCAACTTCAGGGAGATAAGACTTCACTTCAATCGATCCACTGCAACTTCAG
GGAGATAGGATTATTGGCTTTAATCTG
Found at i:40108570 original size:44 final size:44
Alignment explanation
Indices: 40108025--40108808 Score: 273
Period size: 42 Copynumber: 17.6 Consensus size: 44
40108015 TTTAATTTAT
* * ** *
40108025 TCCACTACAACTTCAGGGAAATAAGATT-CGCTATCTTTAATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTATTC-A-CTTCAATCTGC
* *
40108070 TCCACTGCAACTTCAGGAAGAT-A-A-TACTTCACTTCAATCCGC
1 TCCACTGCAACTTCAGGGAGATAAGATTA-TTCACTTCAATCTGC
* * ** * * *
40108112 TCCATTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATTTGT
1 TCCACTGCAACTTCAGGGAGATAAGATTATTCACTTCAATCTGC
** * ** * *
40108156 TCCGGTGCAAATTCAGGGAGATAAGATT-CGC-CAT-GATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTATTCACTTCAATCTGC
* * * * * * * *
40108197 TCTATTGCAATTTTAGAGAGATAAGATCTGTGATTTATAGCTTTAATCTGT
1 TCCACTGCAACTTCAGGGAGATAAGA--T-T-A-TT-CA-CTTCAATCTGC
* * * * * * * * *
40108248 TTCACTACAATTTTAGGGAAATAAGATTCGTT-ATCTTTAGTCTAC
1 TCCACTGCAACTTCAGGGAGATAAGATT-ATTCA-CTTCAATCTGC
* **
40108293 TCCACTACAACTTCAGGGAGATAA-A--ACTTCACTTCAATCCAC
1 TCCACTGCAACTTCAGGGAGATAAGATTA-TTCACTTCAATCTGC
** * *
40108335 TCCACTGCAACTTCAGGGAGATAAGATT-CGCA-AT-GATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTATTCACTTCAATCTGC
* * * * * **
40108376 TCTATTGCAACTTCAGAGAGATAAGATATGTGATTTATAGCTTTAATCTAT
1 TCCACTGCAACTTCAGGGAGATAAG--AT-T-A-TT-CA-CTTCAATCTGC
* * * ** * *
40108427 TCCACTGCAATTTCAAGGAAATAAGATT-CGCTATCTTCAGTCTAC
1 TCCACTGCAACTTCAGGGAGATAAGATTATTC-A-CTTCAATCTGC
* *
40108472 TCCACTGCAACTTCAGGGAGATAAGA--CTTCACTTCAATCTGA
1 TCCACTGCAACTTCAGGGAGATAAGATTATTCACTTCAATCTGC
* ** *
40108514 TCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTATTCACTTCAATCTGC
* ** * * *
40108558 TCCACTGTAACTTCAGGGAGATAAGATT-CGC-CAT-GATTTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTATTCACTTCAATCTGC
* * * * * * *
40108599 TCTACTACAACTTTAGAGAGATAAGATCTGTGATTTATAGCTTTAATCTGT
1 TCCACTGCAACTTCAGGGAGATAAGA--T-T-A-TT-CA-CTTCAATCTGC
* * ** * * *
40108650 TCTACTGCAATTTCAAAGAAATAAGATTCAGT-ATCTTCAGTCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATT-ATTCA-CTTCAATCTGC
* **
40108695 TCCACTGCAACTTCAGGGAGATAAGA--CTTCACTTCAATCCAC
1 TCCACTGCAACTTCAGGGAGATAAGATTATTCACTTCAATCTGC
* * ** *
40108737 TCTACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTATTCACTTCAATCTGC
* *
40108781 TCCACTACAACTTTAGGGAGATAAGATT
1 TCCACTGCAACTTCAGGGAGATAAGATT
40108809 CACCATGATC
Statistics
Matches: 536, Mismatches: 156, Indels: 95
0.68 0.20 0.12
Matches are distributed among these distances:
41 76 0.14
42 134 0.25
43 12 0.02
44 112 0.21
45 112 0.21
47 3 0.01
48 5 0.01
49 4 0.01
50 5 0.01
51 73 0.14
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (44 bp):
TCCACTGCAACTTCAGGGAGATAAGATTATTCACTTCAATCTGC
Found at i:40108856 original size:625 final size:621
Alignment explanation
Indices: 40107717--40108981 Score: 1692
Period size: 625 Copynumber: 2.0 Consensus size: 621
40107707 ATTTGTCCCG
* *
40107717 CTGCAACTTCAGGGAGATAAGATTCACTATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATC
1 CTGCAACTTCAGGGAGATAAGATTCACAATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATA
* * * * * * * *
40107782 TGTAACCCGTCTTCAATCTGCTCCACTGTAATTTCAGGGAAGTGAGATCTGCTGTCTTCAGTCTG
66 TGTAACCCATCTTCAATCTACTCCACTGCAATTTCAAGGAAATAAGATCTGCTATCTTCAGTCTA
* * *** * *
40107847 CTCCATTGCAACTTCAGGGGGAGACTGCTGTTTTTAATTCGCTCCACTGCAACTTCAGGGAGATA
131 CTCCACTGCAACTTCAGGGGAAGACT-CTCACTTCAATTCGATCCACTGCAACTTCAGGGAGATA
* *
40107912 GAATTGTAGGATGTAATATGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATGATTTGCTCT
195 GAATTATAGGATGTAATATGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATGATTTGCTCT
* * * * **
40107977 ACTGCAACTTCATAGACATAAGATCTGTGATTTGTAACTTTAATTTATTCCACTACAACTTCAGG
260 ACTACAACTTCAGAGACATAAGATCTGTGATTTATAACTTTAATCTATTCCACTACAACTTCAAA
* *
40108042 GAAATAAGATTCGCTATCTTTAATCTGCTCCACTGCAACTTCAGGAAGATAATACTTCACTTCAA
325 GAAATAAGATTCGCTATCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGACTTCACTTCAA
* * * * ** *
40108107 TCCGCTCCATTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATTTGTTCCGGTGCAAATTCAG
390 TCCACTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCCACTACAAATTCAG
* * * *
40108172 GGAGATAAGATTCGCCATGATCTGCTCTATTGCAATTTTAGAGAGATAAGATCTGTGATTTATAG
455 GGAGATAAGATTCACCATGATCTGCTCTAATGCAACTTCAGAGAGATAAGATCTGTGATTTATAG
* * * * *
40108237 CTTTAATCTGTTTCACTACAATTTTAGGGAAATAAGATTCGTTATCTTTAGTCTACTCCACTACA
520 CTTTAATCTATTTCACTACAACTTCAGGAAAATAAGATTCGCTATCTTTAGTCTACTCCACTACA
40108302 ACTTCAGGGAGATAAAACTTCACTTCAATCCACTCCA
585 ACTTCAGGGAGATAAAACTTCACTTCAATCCACTCCA
* *
40108339 CTGCAACTTCAGGGAGATAAGATTCGCAATGATCTGCTCTATTGCAACTTCAGAGAGATAAGATA
1 CTGCAACTTCAGGGAGATAAGATTCACAATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATA
* *** * *
40108404 TGTGATTTATAGCTTTAATCTATTCCACTGCAATTTCAAGGAAATAAGAT-TCGCTATCTTCAGT
66 TGTAACCCAT--CTTCAATCTACTCCACTGCAATTTCAAGGAAATAAGATCT-GCTATCTTCAGT
40108468 CTACTCCACTGCAACTTCAGGGAGATAAGACT-TCACTTCAA-TCTGATCCACTGCAACTTCAGG
128 CTACTCCACTGCAACTTCAGGG-G--AAGACTCTCACTTCAATTC-GATCCACTGCAACTTCAGG
* * * * * *
40108531 GAGATAGGATTATTGGCTTTAATCTGCTCCACTGTAACTTCAGGGAGATAAGATTCGCCATGATT
189 GAGATAGAATTATAGGATGTAATATGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATGATT
* * * * * * *
40108596 TGCTCTACTACAACTTTAGAGAGATAAGATCTGTGATTTATAGCTTTAATCTGTTCTACTGCAAT
254 TGCTCTACTACAACTTCAGAGACATAAGATCTGTGATTTATAACTTTAATCTATTCCACTACAAC
* *
40108661 TTCAAAGAAATAAGATTCAG-TATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTC
319 TTCAAAGAAATAAGATTC-GCTATCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGACTTC
*
40108725 ACTTCAATCCACTCTACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCCACTACA
383 ACTTCAATCCACTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCCACTACA
* * * *
40108790 ACTTTAGGGAGATAAGATTCACCATGATCTGTTCTAATGCAACTTCAGAGAGATAAGATTTGTGA
448 AATTCAGGGAGATAAGATTCACCATGATCTGCTCTAATGCAACTTCAGAGAGATAAGATCTGTGA
* *
40108855 TTTATAGCTTTAATCTATTTCATTGCAACTTCAGGAAAATAAGATTCGCTATCTTTAGTCTACTC
513 TTTATAGCTTTAATCTATTTCACTACAACTTCAGGAAAATAAGATTCGCTATCTTTAGTCTACTC
* * * * * *
40108920 CATTGCAACTTTAGGGAGATAATACTTCACTTCAATCCGCTTCA
578 CACTACAACTTCAGGGAGATAAAACTTCACTTCAATCCACTCCA
**
40108964 CTAAAACTTCAGGGAGAT
1 CTGCAACTTCAGGGAGAT
40108982 GGAATTATTG
Statistics
Matches: 554, Mismatches: 81, Indels: 13
0.85 0.12 0.02
Matches are distributed among these distances:
622 66 0.12
623 1 0.00
624 64 0.12
625 417 0.75
626 1 0.00
627 5 0.01
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (621 bp):
CTGCAACTTCAGGGAGATAAGATTCACAATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATA
TGTAACCCATCTTCAATCTACTCCACTGCAATTTCAAGGAAATAAGATCTGCTATCTTCAGTCTA
CTCCACTGCAACTTCAGGGGAAGACTCTCACTTCAATTCGATCCACTGCAACTTCAGGGAGATAG
AATTATAGGATGTAATATGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATGATTTGCTCTA
CTACAACTTCAGAGACATAAGATCTGTGATTTATAACTTTAATCTATTCCACTACAACTTCAAAG
AAATAAGATTCGCTATCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGACTTCACTTCAAT
CCACTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCCACTACAAATTCAGG
GAGATAAGATTCACCATGATCTGCTCTAATGCAACTTCAGAGAGATAAGATCTGTGATTTATAGC
TTTAATCTATTTCACTACAACTTCAGGAAAATAAGATTCGCTATCTTTAGTCTACTCCACTACAA
CTTCAGGGAGATAAAACTTCACTTCAATCCACTCCA
Found at i:40108974 original size:402 final size:396
Alignment explanation
Indices: 40107932--40108981 Score: 965
Period size: 402 Copynumber: 2.6 Consensus size: 396
40107922 ATGTAATATG
* * * * * * * *
40107932 CTCCACTGCAACTTCAGGGAGATAAGATTTGCCATGATTTGCTCTACTGCAACTTCATAGACATA
1 CTCCACTGCAACTTCAGGGAGATAAGATTCGCAATAATCTGCTCCACTACAACTTCAGAGAGATA
* * *** * * * * *
40107997 AGATCTGTGATTTGTAACTTTAATTTATTCCACTACAACTTCAGGGAAATAAGATTCGCTATCTT
66 AGA-ATGTCATCCAT-A--GT-ATCTATTCCAATGCAACTTCAAGGAAATAAGATTCGCTATCTT
* * * * * * *
40108062 TAATCTGCTCCACTGCAACTTCAGGAAGATAATACTTCACTTCAATCCGCTCCATTGCAACTTCA
126 CAATCTACTCCACTGCAACTTCAGGAAAATAAGACTTCACTTCAATCTGATCCACTGCAACTTCA
** * ** * ** *
40108127 GGGAGATAGGATTATTGGCTTTAATTTGTTCCGGTGCAAA-TTCAGGGAGATAAGATTCGCCATG
191 GGGAGATA-GATTATTCACTTCAATCCGCTCCACT-AAAACTTCAGGGAGATAAGATTCGCCATG
* * *
40108191 ATCTGCTCTATTGCAATTTTAGAGAGATAAGATCTGTGATTTATAGCTTTAATCTGTTTCACTAC
254 ATCTGCTCTACTACAACTTTAGAGAGATAAGATCTGTGATTTATAGCTTTAATCTGTTTCACTAC
* ** *
40108256 AATTTTAGGGAAATAAGATTCGTTATCTTTAGTCTACTCCACTACAACTTCAGGGAGATAAAACT
319 AATTTCAAAGAAATAAGATTCGTTATCTTCAGTCTACTCCACTACAACTTCAGGGAGATAAAACT
40108321 TCACTTCAATCCA
384 TCACTTCAATCCA
* * * *
40108334 CTCCACTGCAACTTCAGGGAGATAAGATTCGCAATGATCTGCTCTATTGCAACTTCAGAGAGATA
1 CTCCACTGCAACTTCAGGGAGATAAGATTCGCAATAATCTGCTCCACTACAACTTCAGAGAGATA
* ** * *
40108399 AGATATGTGATTTATAGCTTTAATCTATTCCACTGCAATTTCAAGGAAATAAGATTCGCTATCTT
66 AGA-ATGTCATCCATAG---T-ATCTATTCCAATGCAACTTCAAGGAAATAAGATTCGCTATCTT
* * *
40108464 CAGTCTACTCCACTGCAACTTCAGGGAGATAAGACTTCACTTCAATCTGATCCACTGCAACTTCA
126 CAATCTACTCCACTGCAACTTCAGGAAAATAAGACTTCACTTCAATCTGATCCACTGCAACTTCA
** * * **
40108529 GGGAGATAGGATTATTGGCTTTAATCTGCTCCACTGTAACTTCAGGGAGATAAGATTCGCCATGA
191 GGGAGATA-GATTATTCACTTCAATCCGCTCCACTAAAACTTCAGGGAGATAAGATTCGCCATGA
* *
40108594 TTTGCTCTACTACAACTTTAGAGAGATAAGATCTGTGATTTATAGCTTTAATCTG-TTCTACTGC
255 TCTGCTCTACTACAACTTTAGAGAGATAAGATCTGTGATTTATAGCTTTAATCTGTTTC-ACTAC
* * *
40108658 AATTTCAAAGAAATAAGATTCAG-TATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGAC
319 AATTTCAAAGAAATAAGATTC-GTTATCTTCAGTCTACTCCACTACAACTTCAGGGAGATAAAAC
40108722 TTCACTTCAATCCA
383 TTCACTTCAATCCA
* * * ** * *
40108736 CTCTACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCCACTACAACTTTAGGGAG
1 CTCCACTGCAACTTCAGGGAGATA--A-GATTCGCAATAATCTGCTCCACTACAACTTCAGAGAG
* * * * *
40108801 ATAAG-AT-TCA-CCAT-G-ATCTGTTCTAATGCAACTTC-AGAGAGATAAGATTTGTGATTTAT
63 ATAAGAATGTCATCCATAGTATCTATTCCAATGCAACTTCAAG-GAAATAAGA-TT-CG--CTAT
* * * * * * *
40108860 AGCTTTAATCTATTTCATTGCAACTTCAGGAAAATAAGA-TTCGCTATCTTTAGTCT-ACTCCAT
123 --CTTCAATCTACTCCACTGCAACTTCAGGAAAATAAGACTT--C-A-CTTCAATCTGA-TCCAC
* *
40108923 TGCAACTTTAGGGAGATA-A-TACTTCACTTCAATCCGCTTCACTAAAACTTCAGGGAGAT
181 TGCAACTTCAGGGAGATAGATTA-TTCACTTCAATCCGCTCCACTAAAACTTCAGGGAGAT
40108982 GGAATTATTG
Statistics
Matches: 548, Mismatches: 78, Indels: 44
0.82 0.12 0.07
Matches are distributed among these distances:
394 2 0.00
395 24 0.04
396 2 0.00
397 1 0.00
399 3 0.01
400 3 0.01
401 40 0.07
402 407 0.74
403 5 0.01
404 29 0.05
405 32 0.06
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (396 bp):
CTCCACTGCAACTTCAGGGAGATAAGATTCGCAATAATCTGCTCCACTACAACTTCAGAGAGATA
AGAATGTCATCCATAGTATCTATTCCAATGCAACTTCAAGGAAATAAGATTCGCTATCTTCAATC
TACTCCACTGCAACTTCAGGAAAATAAGACTTCACTTCAATCTGATCCACTGCAACTTCAGGGAG
ATAGATTATTCACTTCAATCCGCTCCACTAAAACTTCAGGGAGATAAGATTCGCCATGATCTGCT
CTACTACAACTTTAGAGAGATAAGATCTGTGATTTATAGCTTTAATCTGTTTCACTACAATTTCA
AAGAAATAAGATTCGTTATCTTCAGTCTACTCCACTACAACTTCAGGGAGATAAAACTTCACTTC
AATCCA
Found at i:40110318 original size:49 final size:45
Alignment explanation
Indices: 40110259--40110385 Score: 164
Period size: 45 Copynumber: 2.7 Consensus size: 45
40110249 CCCCTTTCGT
* *
40110259 CTCAAGGCGCCCTTTGCGGGTTTTCACCTTGGCCTCTTTTTTTTTAGGA
1 CTCAAAGCGCCCTTTGCGGGTTTTCACCTTGG----TTTCTTTTTAGGA
* *
40110308 CTCAAAGCGCCCTTTGTGAGTTTTCACCTTGGTTTCTTTTTAGGA
1 CTCAAAGCGCCCTTTGCGGGTTTTCACCTTGGTTTCTTTTTAGGA
* *
40110353 CTTAAAGCACCCTTTGCGGGTTTTCACCTTGGT
1 CTCAAAGCGCCCTTTGCGGGTTTTCACCTTGGT
40110386 CCCTTCTCCT
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
45 41 0.59
49 29 0.41
ACGTcount: A:0.13, C:0.25, G:0.21, T:0.40
Consensus pattern (45 bp):
CTCAAAGCGCCCTTTGCGGGTTTTCACCTTGGTTTCTTTTTAGGA
Found at i:40111362 original size:11 final size:11
Alignment explanation
Indices: 40111346--40111389 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
40111336 GGCCTCTCCT
40111346 TTTTCTTTTCC
1 TTTTCTTTTCC
*
40111357 TTTTCTTTT-T
1 TTTTCTTTTCC
*
40111367 TTTCTCTTTTTC
1 TTT-TCTTTTCC
40111379 TTTTCTTTTCC
1 TTTTCTTTTCC
40111390 ATCATTTTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
10 3 0.11
11 22 0.79
12 3 0.11
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTCTTTTCC
Found at i:40111364 original size:5 final size:5
Alignment explanation
Indices: 40111346--40111388 Score: 50
Period size: 5 Copynumber: 8.0 Consensus size: 5
40111336 GGCCTCTCCT
*
40111346 TTTTC TTTTCC TTTTC TTTTT TTTCTC TTTTTC TTTTC TTTTC
1 TTTTC TTTT-C TTTTC TTTTC TTT-TC -TTTTC TTTTC TTTTC
40111389 CATCATTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
5 22 0.67
6 8 0.24
7 3 0.09
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTC
Found at i:40111381 original size:22 final size:21
Alignment explanation
Indices: 40111345--40111387 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
40111335 TGGCCTCTCC
40111345 TTTTTCTTTTCCTTTTCTTTT
1 TTTTTCTTTTCCTTTTCTTTT
*
40111366 TTTTCTCTTTTTCTTTTCTTTT
1 TTTT-TCTTTTCCTTTTCTTTT
40111388 CCATCATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (21 bp):
TTTTTCTTTTCCTTTTCTTTT
Found at i:40111397 original size:28 final size:25
Alignment explanation
Indices: 40111346--40111414 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 25
40111336 GGCCTCTCCT
*
40111346 TTTTCTTTTCCTTTTCTTTT--T--
1 TTTTCTTTTTCTTTTCTTTTCATCA
40111367 TTTCTCTTTTTCTTTTCTTTTCCATCA
1 TTT-TCTTTTTCTTTTCTTTT-CATCA
*
40111394 TTTTCATTTTCATTTTCTTTT
1 TTTTCTTTTTC-TTTTCTTTT
40111415 TAAAATATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
21 3 0.08
22 16 0.41
25 1 0.03
26 7 0.18
27 12 0.31
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.74
Consensus pattern (25 bp):
TTTTCTTTTTCTTTTCTTTTCATCA
Found at i:40111415 original size:6 final size:6
Alignment explanation
Indices: 40111344--40111415 Score: 51
Period size: 6 Copynumber: 12.0 Consensus size: 6
40111334 TTGGCCTCTC
* *
40111344 CTTTTT C-TTTT CCTTTT CTTTTT -TTTCT CTTTTT C-TTTT CTTTTCCAT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTT---T
* * *
40111392 CATTTT CATTTT CATTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT
40111416 AAAATATATA
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
5 14 0.25
6 36 0.65
9 5 0.09
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.74
Consensus pattern (6 bp):
CTTTTT
Found at i:40114339 original size:19 final size:18
Alignment explanation
Indices: 40114297--40114339 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
40114287 TCTTTTGGTG
* *
40114297 GAATTTAATGCATATGAT
1 GAATGTAATGCAAATGAT
40114315 GTAATGTAATGCAAATGCAT
1 G-AATGTAATGCAAATG-AT
40114335 GAATG
1 GAATG
40114340 CAAAAAGAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 17 0.81
20 3 0.14
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.33
Consensus pattern (18 bp):
GAATGTAATGCAAATGAT
Found at i:40115695 original size:12 final size:12
Alignment explanation
Indices: 40115678--40115702 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40115668 GATAAATCTT
40115678 TAAATATTTGTA
1 TAAATATTTGTA
40115690 TAAATATTTGTA
1 TAAATATTTGTA
40115702 T
1 T
40115703 CCCGTAAGTT
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:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (12 bp):
TAAATATTTGTA
Found at i:40116263 original size:17 final size:18
Alignment explanation
Indices: 40116237--40116270 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
40116227 CTAATGAATA
*
40116237 AATAATCAAT-CAATACC
1 AATAAGCAATACAATACC
40116254 AATAAGCAATACAATAC
1 AATAAGCAATACAATAC
40116271 ACATGAGGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.56, C:0.21, G:0.03, T:0.21
Consensus pattern (18 bp):
AATAAGCAATACAATACC
Found at i:40116736 original size:3 final size:3
Alignment explanation
Indices: 40116728--40116777 Score: 57
Period size: 3 Copynumber: 16.3 Consensus size: 3
40116718 ATAACCAAAT
* *
40116728 ATA ATA ATA AT- ATCA ATA ATA ATA AGA GTA ATA ATTA ATA ATA ATA
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA
40116774 ATA A
1 ATA A
40116778 ATTAATTAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 2 0.05
3 33 0.82
4 5 0.12
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:40116770 original size:25 final size:25
Alignment explanation
Indices: 40116742--40116792 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
40116732 TAATAATATC
40116742 AATAATAATAAGAGTAA-TAATTAAT
1 AATAATAATAA-AGTAATTAATTAAT
*
40116767 AATAATAATAAATTAATTAATTAAT
1 AATAATAATAAAGTAATTAATTAAT
40116792 A
1 A
40116793 GCAAAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (25 bp):
AATAATAATAAAGTAATTAATTAAT
Found at i:40116800 original size:21 final size:21
Alignment explanation
Indices: 40116759--40116800 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
40116749 ATAAGAGTAA
*
40116759 TAATTAATAATAATAATAAAT
1 TAATTAATAATAACAATAAAT
*
40116780 TAATTAATTAATAGCAA-AAAT
1 TAATTAA-TAATAACAATAAAT
40116801 AACAAACAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (21 bp):
TAATTAATAATAACAATAAAT
Found at i:40120856 original size:33 final size:33
Alignment explanation
Indices: 40120788--40120861 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 33
40120778 TTCTTGATTG
*
40120788 CTTTCTTCACTCGTTTCTTTTGAAAACTCTTTTT
1 CTTT-TTCACTCGTTTCTTTTGAAAACTCTATTT
* *
40120822 CTTTTTCATTCGATTTCTTTT-CAAACTCTATTT
1 CTTTTTCACTCG-TTTCTTTTGAAAACTCTATTT
40120855 CTTTTTC
1 CTTTTTC
40120862 TTTTCTTTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
33 24 0.67
34 12 0.33
ACGTcount: A:0.15, C:0.23, G:0.04, T:0.58
Consensus pattern (33 bp):
CTTTTTCACTCGTTTCTTTTGAAAACTCTATTT
Found at i:40120867 original size:28 final size:27
Alignment explanation
Indices: 40120835--40120921 Score: 68
Period size: 27 Copynumber: 3.1 Consensus size: 27
40120825 TTTCATTCGA
40120835 TTTCTTTTCAAACTCTATTTCTTTTTCT
1 TTTCTTTTCAAACTCT-TTTCTTTTTCT
** *
40120863 TTTC-TTTCAATTTCTTTTTCATTTTCAT
1 TTTCTTTTCAAACTC-TTTTCTTTTTC-T
*** *
40120891 TTTCTCGCCTACACTCTTTTCTTTTTCT
1 TTTCTTTTC-AAACTCTTTTCTTTTTCT
40120919 TTT
1 TTT
40120922 GCCTCACTTG
Statistics
Matches: 45, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
27 17 0.38
28 14 0.31
29 11 0.24
30 3 0.07
ACGTcount: A:0.11, C:0.23, G:0.01, T:0.64
Consensus pattern (27 bp):
TTTCTTTTCAAACTCTTTTCTTTTTCT
Found at i:40128072 original size:15 final size:16
Alignment explanation
Indices: 40128046--40128075 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
40128036 ACGTGATGAA
40128046 AAATTGAAAAAAAATT
1 AAATTGAAAAAAAATT
40128062 AAATT-AAAAAAAAT
1 AAATTGAAAAAAAAT
40128076 AGGAAAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (16 bp):
AAATTGAAAAAAAATT
Found at i:40130610 original size:23 final size:23
Alignment explanation
Indices: 40130580--40130626 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
40130570 ATAAGCGGAC
40130580 TAAAATTTGTTGTTACTCTTTAT
1 TAAAATTTGTTGTTACTCTTTAT
40130603 TAAAATTTGTTGTTACTCTTTAT
1 TAAAATTTGTTGTTACTCTTTAT
40130626 T
1 T
40130627 TGAAATACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.09, G:0.09, T:0.57
Consensus pattern (23 bp):
TAAAATTTGTTGTTACTCTTTAT
Found at i:40139588 original size:27 final size:27
Alignment explanation
Indices: 40139556--40139645 Score: 112
Period size: 27 Copynumber: 3.3 Consensus size: 27
40139546 AGGGGTATAA
40139556 CAGTCATTTTACCCTTCGAGGGTATTT
1 CAGTCATTTTACCCTTCGAGGGTATTT
* *
40139583 CGGTCATTTTACCCCTCGAGGGTATTT
1 CAGTCATTTTACCCTTCGAGGGTATTT
**
40139610 CTA-TCATTTTA-CCTTTTAGGGGTATTT
1 C-AGTCATTTTACCCTTCGA-GGGTATTT
40139637 CAGTCATTT
1 CAGTCATTT
40139646 AACAACCTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
26 5 0.09
27 49 0.91
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.43
Consensus pattern (27 bp):
CAGTCATTTTACCCTTCGAGGGTATTT
Found at i:40146235 original size:41 final size:40
Alignment explanation
Indices: 40146190--40146288 Score: 126
Period size: 41 Copynumber: 2.4 Consensus size: 40
40146180 TCAGAACACT
** *
40146190 GGCATTAAGTCTGCTAGACATAAAGTCTGAAATATTTCGCC
1 GGCATTAAG-CTGCTAGACATAAAGTCCAAAATATTTCACC
*
40146231 GGCATTAAGCTTGCTAGACGTAAAGTCCAAAATATTTCACC
1 GGCATTAAGC-TGCTAGACATAAAGTCCAAAATATTTCACC
*
40146272 GCCATTAAGCCTGCTAG
1 GGCATTAAG-CTGCTAG
40146289 GCACAGAGCC
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
40 1 0.02
41 49 0.96
42 1 0.02
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.27
Consensus pattern (40 bp):
GGCATTAAGCTGCTAGACATAAAGTCCAAAATATTTCACC
Found at i:40146686 original size:67 final size:63
Alignment explanation
Indices: 40146500--40146689 Score: 145
Period size: 67 Copynumber: 2.9 Consensus size: 63
40146490 CATGTATAAT
* * * *
40146500 TATATAT-AA-TTACTAACATTAAGTTCAGCTCAAAGAAACTTGTAGCT-TACATTCGAACCTCT
1 TATATATAAATTTA-TAACATGAAGTTCAACTCAAAG-AA-TTGTA-TTATACATTCGAACCACT
40146562 TA
62 TA
* * * * * * **
40146564 TATATATATATTTGATAACATTGCA-TTAAATTCAAAGACATTGCATCATTTATTCGAACCACAT
1 TATATATAAATTT-ATAACA-TGAAGTTCAACTCAAAGA-ATTGTATTATACATTCGAACCAC-T
40146628 ATA
62 -TA
40146631 TATATATACAATTTATAACATGAAGTTCAACTCAAAGAATTTGTATTATACATTCGAAC
1 TATATATA-AATTTATAACATGAAGTTCAACTCAAAGAA-TTGTATTATACATTCGAAC
40146690 ATAATGTTCA
Statistics
Matches: 95, Mismatches: 20, Indels: 19
0.71 0.15 0.14
Matches are distributed among these distances:
64 7 0.07
65 17 0.18
66 22 0.23
67 45 0.47
68 4 0.04
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (63 bp):
TATATATAAATTTATAACATGAAGTTCAACTCAAAGAATTGTATTATACATTCGAACCACTTA
Found at i:40146699 original size:40 final size:40
Alignment explanation
Indices: 40146647--40146734 Score: 160
Period size: 40 Copynumber: 2.2 Consensus size: 40
40146637 TACAATTTAT
40146647 AACATGAA-GTTCAACTCAAAGAATTTGTATTATACATTCG
1 AACAT-AATGTTCAACTCAAAGAATTTGTATTATACATTCG
40146687 AACATAATGTTCAACTCAAAGAATTTGTATTATACATTCG
1 AACATAATGTTCAACTCAAAGAATTTGTATTATACATTCG
40146727 AACATAAT
1 AACATAAT
40146735 CATATATTTA
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
39 2 0.04
40 45 0.96
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (40 bp):
AACATAATGTTCAACTCAAAGAATTTGTATTATACATTCG
Found at i:40147664 original size:31 final size:31
Alignment explanation
Indices: 40147616--40147689 Score: 130
Period size: 31 Copynumber: 2.4 Consensus size: 31
40147606 GCTTGTTTTT
*
40147616 TTGTTTTAATTATAACATATATTATCATATTA
1 TTGTTTT-ACTATAACATATATTATCATATTA
40147648 TTGTTTTACTATAACATATATTATCATATTA
1 TTGTTTTACTATAACATATATTATCATATTA
40147679 TTGTTTTACTA
1 TTGTTTTACTA
40147690 AATTAACCTT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
31 34 0.83
32 7 0.17
ACGTcount: A:0.34, C:0.08, G:0.04, T:0.54
Consensus pattern (31 bp):
TTGTTTTACTATAACATATATTATCATATTA
Found at i:40154244 original size:2 final size:2
Alignment explanation
Indices: 40154237--40154262 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40154227 AACATACATG
40154237 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
40154263 CAATCACCAT
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:40154694 original size:41 final size:41
Alignment explanation
Indices: 40154649--40154751 Score: 170
Period size: 41 Copynumber: 2.5 Consensus size: 41
40154639 TGATTCAGAA
*
40154649 CACCGACATTAAGCCTGCTAGACATAAAGTCTGAAATATTT
1 CACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATATTT
*
40154690 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAAATATTT
1 CACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATATTT
* *
40154731 AACTGGCATTAAGCCTGCTAG
1 CACCGGCATTAAGCCTGCTAG
40154752 GCAGAGAGCC
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 58 1.00
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.26
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATATTT
Found at i:40155145 original size:63 final size:63
Alignment explanation
Indices: 40154963--40155148 Score: 171
Period size: 63 Copynumber: 2.9 Consensus size: 63
40154953 CATGTATAAT
* * * * *
40154963 TATATATAATTACTAACATTAAGTTCAGCTCAAAGAAACTTGTATCT-TACATTTGAACCTCTTA
1 TATATACAATTA-TAACATTAAGTTCAACTCAAAG-AA-TTGTAT-TATACATTCGAACCACATA
40155027 TA
62 TA
* * * * * **
40155029 TATATATATTTCATAACATTACA-TTCAATTCAAAGACATTGCATCATTTATTCGAACCACATAT
1 TATATACAATT-ATAACATTA-AGTTCAACTCAAAGA-ATTGTATTATACATTCGAACCACATAT
40155093 A
63 A
40155094 TATATACAATT-TAACATTAAGTTCAACTCAAAGAATTTGTATTATACATTCGAAC
1 TATATACAATTATAACATTAAGTTCAACTCAAAGAA-TTGTATTATACATTCGAAC
40155149 ATCATCACAT
Statistics
Matches: 97, Mismatches: 17, Indels: 15
0.75 0.13 0.12
Matches are distributed among these distances:
62 2 0.02
63 35 0.36
65 29 0.30
66 29 0.30
67 2 0.02
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.37
Consensus pattern (63 bp):
TATATACAATTATAACATTAAGTTCAACTCAAAGAATTGTATTATACATTCGAACCACATATA
Found at i:40162198 original size:27 final size:27
Alignment explanation
Indices: 40162167--40162230 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 27
40162157 TTCTCTCAAT
*
40162167 GTTCGTCATATACACTATTTCTTT-AGA
1 GTTCGTCATATACACCA-TTCTTTCAGA
* **
40162194 GTTCGCCATATGTACCATTCTTTCAGA
1 GTTCGTCATATACACCATTCTTTCAGA
*
40162221 GTTCATCATA
1 GTTCGTCATA
40162231 CCATTTAGTC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
26 6 0.20
27 24 0.80
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.41
Consensus pattern (27 bp):
GTTCGTCATATACACCATTCTTTCAGA
Found at i:40162454 original size:26 final size:26
Alignment explanation
Indices: 40162419--40162480 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 26
40162409 TTTCATTAAT
*
40162419 TGCCACAAAGCCTTACATTTTAGATA
1 TGCCACAAAGCCTTACATTTCAGATA
* *
40162445 TGCCACAAAGGCTTTCATTTCAGATA
1 TGCCACAAAGCCTTACATTTCAGATA
**
40162471 CACCACAAAG
1 TGCCACAAAG
40162481 GGTTTTGTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.35, C:0.26, G:0.13, T:0.26
Consensus pattern (26 bp):
TGCCACAAAGCCTTACATTTCAGATA
Found at i:40162543 original size:53 final size:53
Alignment explanation
Indices: 40162397--40162629 Score: 195
Period size: 53 Copynumber: 4.4 Consensus size: 53
40162387 TAGATCACCG
* * *
40162397 CAAAGGCTTCCATTTCATTAAT-TGCCACAAAGCCTTAC-ATTT--TAGATATGCCA
1 CAAAGGCTTCCATTTCA--AATACGCCACAAAGGCTT-CTGTTTCATAGAT-TGCCA
* * * * * * *
40162450 CAAAGGCTTTCATTTCAGATACACCACAAAGGGTTTTGTTTCAAATATTGCCA
1 CAAAGGCTTCCATTTCAAATACGCCACAAAGGCTTCTGTTTCATAGATTGCCA
* ** **
40162503 CAAAGACTTCCATTTCAAATACGCCATGAAGGCTTCTGTTTCATAGATTTTCA
1 CAAAGGCTTCCATTTCAAATACGCCACAAAGGCTTCTGTTTCATAGATTGCCA
* * ** * * *
40162556 TAAAGGCTTCCATTTTAAATTTGCCACAAATGCTTCCGTTTCATAGATTGCTA
1 CAAAGGCTTCCATTTCAAATACGCCACAAAGGCTTCTGTTTCATAGATTGCCA
*
40162609 CAAAGGCTTCCATTTCTAATA
1 CAAAGGCTTCCATTTCAAATA
40162630 AACTACAAAG
Statistics
Matches: 138, Mismatches: 38, Indels: 8
0.75 0.21 0.04
Matches are distributed among these distances:
51 2 0.01
52 13 0.09
53 120 0.87
54 3 0.02
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.34
Consensus pattern (53 bp):
CAAAGGCTTCCATTTCAAATACGCCACAAAGGCTTCTGTTTCATAGATTGCCA
Found at i:40162590 original size:26 final size:26
Alignment explanation
Indices: 40162557--40162623 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 26
40162547 AGATTTTCAT
40162557 AAAGGCTTCCATTT-TAAATTTGCCAC
1 AAAGGCTTCCATTTATAAA-TTGCCAC
* * * *
40162583 AAATGCTTCCGTTTCATAGATTGCTAC
1 AAAGGCTTCCATTT-ATAAATTGCCAC
40162610 AAAGGCTTCCATTT
1 AAAGGCTTCCATTT
40162624 CTAATAAACT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
26 12 0.36
27 18 0.55
28 3 0.09
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.36
Consensus pattern (26 bp):
AAAGGCTTCCATTTATAAATTGCCAC
Found at i:40164550 original size:33 final size:34
Alignment explanation
Indices: 40164487--40164562 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 34
40164477 ACTCTATATA
* * *
40164487 TGGTGTGATGGTTGGTTTAGCTCTTATGAGCAT-
1 TGGTGTGATGGATGGATTAGCTCTGATGAGCATC
*
40164520 TGGTGTGATGGATGGATTGGCT-TGAGTGAGCATC
1 TGGTGTGATGGATGGATTAGCTCTGA-TGAGCATC
*
40164554 TAGTGTGAT
1 TGGTGTGAT
40164563 TGGTTGGACT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
32 2 0.06
33 26 0.72
34 8 0.22
ACGTcount: A:0.17, C:0.08, G:0.37, T:0.38
Consensus pattern (34 bp):
TGGTGTGATGGATGGATTAGCTCTGATGAGCATC
Found at i:40168240 original size:27 final size:27
Alignment explanation
Indices: 40168207--40168261 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
40168197 TTCTCAAAGA
*
40168207 TAGATCTCAGATCTAGGCATTATCAAT
1 TAGATCTCAAATCTAGGCATTATCAAT
* *
40168234 TAGATCTCAAATCTGGGTATTATCAAT
1 TAGATCTCAAATCTAGGCATTATCAAT
40168261 T
1 T
40168262 GAAAGTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (27 bp):
TAGATCTCAAATCTAGGCATTATCAAT
Found at i:40171804 original size:33 final size:33
Alignment explanation
Indices: 40171767--40171850 Score: 114
Period size: 33 Copynumber: 2.5 Consensus size: 33
40171757 CTATTTGATA
* * *
40171767 TGATGGTTGGTTTAGCTCTTGTGAGCATTGGTC
1 TGATGGTTGGATTAGCTCTTATGAGCATTAGTC
*
40171800 TGATGGTTGGATTAGCTCTTATGAGCATTAGTG
1 TGATGGTTGGATTAGCTCTTATGAGCATTAGTC
* *
40171833 TGATGGATGGATTGGCTC
1 TGATGGTTGGATTAGCTC
40171851 AAGTGAGCAT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.17, C:0.11, G:0.33, T:0.39
Consensus pattern (33 bp):
TGATGGTTGGATTAGCTCTTATGAGCATTAGTC
Found at i:40171858 original size:33 final size:34
Alignment explanation
Indices: 40171767--40171868 Score: 102
Period size: 33 Copynumber: 3.1 Consensus size: 34
40171757 CTATTTGATA
* * * * *
40171767 TGATGGTTGGTTTAGCTCT-TGTGAGCATTGGTC
1 TGATGGATGGATTAGCTCTAAGTGAGCATTAGTG
* *
40171800 TGATGGTTGGATTAGCTCTTA-TGAGCATTAGTG
1 TGATGGATGGATTAGCTCTAAGTGAGCATTAGTG
*
40171833 TGATGGATGGATTGGCTC-AAGTGAGCATCTAGTG
1 TGATGGATGGATTAGCTCTAAGTGAGCAT-TAGTG
40171867 TG
1 TG
40171869 TTTGGTTGGA
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
32 1 0.02
33 51 0.86
34 7 0.12
ACGTcount: A:0.19, C:0.11, G:0.33, T:0.37
Consensus pattern (34 bp):
TGATGGATGGATTAGCTCTAAGTGAGCATTAGTG
Found at i:40185532 original size:42 final size:43
Alignment explanation
Indices: 40185388--40185540 Score: 202
Period size: 43 Copynumber: 3.6 Consensus size: 43
40185378 CAATGACAAC
* *
40185388 GTCCCAGAC-GTGGTCTTACATGTAATCAAATAACGATGCCACT
1 GTCCCAGACAG-GGTCTTACACGTAATTAAATAACGATGCCACT
*
40185431 GTCCCAGACAGGGTCTTACACGTAATTAAATAACGATGCTACT
1 GTCCCAGACAGGGTCTTACACGTAATTAAATAACGATGCCACT
* * * *
40185474 GTCCTAGACAGGGTCTTACACGTAATTATAT-ACGACGCCAAT
1 GTCCCAGACAGGGTCTTACACGTAATTAAATAACGATGCCACT
**
40185516 GTCCCAGACTTGGTCTTACACGTAA
1 GTCCCAGACAGGGTCTTACACGTAA
40185541 ATCTCAAATC
Statistics
Matches: 98, Mismatches: 11, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
42 30 0.31
43 67 0.68
44 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (43 bp):
GTCCCAGACAGGGTCTTACACGTAATTAAATAACGATGCCACT
Found at i:40187651 original size:7 final size:7
Alignment explanation
Indices: 40187639--40187677 Score: 78
Period size: 7 Copynumber: 5.6 Consensus size: 7
40187629 AGAACATTAC
40187639 TAAAAAT
1 TAAAAAT
40187646 TAAAAAT
1 TAAAAAT
40187653 TAAAAAT
1 TAAAAAT
40187660 TAAAAAT
1 TAAAAAT
40187667 TAAAAAT
1 TAAAAAT
40187674 TAAA
1 TAAA
40187678 CCACGTTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
TAAAAAT
Found at i:40191267 original size:6 final size:6
Alignment explanation
Indices: 40191258--40191288 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
40191248 CCAAAAAAAA
40191258 AAATTT AAATTT AAATTT AAAATTT AAATTT
1 AAATTT AAATTT AAATTT -AAATTT AAATTT
40191289 TTTATTTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AAATTT
Found at i:40191282 original size:13 final size:12
Alignment explanation
Indices: 40191258--40191288 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
40191248 CCAAAAAAAA
40191258 AAATTTAAATTT
1 AAATTTAAATTT
40191270 AAATTTAAAATTT
1 AAATTT-AAATTT
40191283 AAATTT
1 AAATTT
40191289 TTTATTTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AAATTTAAATTT
Found at i:40198297 original size:42 final size:43
Alignment explanation
Indices: 40198251--40198331 Score: 128
Period size: 43 Copynumber: 1.9 Consensus size: 43
40198241 TATTCTAGAA
* * *
40198251 AAAAAAGAATTTAAAAA-AGGAGAAGATAATCTTGGGTTGTTG
1 AAAAAAGAATTTAAAAAGAGGAAAAGATAAACATGGGTTGTTG
40198293 AAAAAAGAATTTAAAAAGAGGAAAAGATAAACATGGGTT
1 AAAAAAGAATTTAAAAAGAGGAAAAGATAAACATGGGTT
40198332 ATTGGATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
42 17 0.49
43 18 0.51
ACGTcount: A:0.53, C:0.02, G:0.22, T:0.22
Consensus pattern (43 bp):
AAAAAAGAATTTAAAAAGAGGAAAAGATAAACATGGGTTGTTG
Found at i:40202162 original size:12 final size:12
Alignment explanation
Indices: 40202143--40202175 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
40202133 TTCACTTCAT
*
40202143 AATTTTTTATTC
1 AATTTTTTTTTC
40202155 -ATTTTTTTTTC
1 AATTTTTTTTTC
40202166 AATTTTTTTT
1 AATTTTTTTT
40202176 AGAACAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (12 bp):
AATTTTTTTTTC
Found at i:40203144 original size:6 final size:6
Alignment explanation
Indices: 40203129--40203211 Score: 50
Period size: 6 Copynumber: 14.5 Consensus size: 6
40203119 TATAATTCTG
* * ** * *
40203129 AAAAAT -AAAAT -AAAA- ACAAAT AACAAT AAAAAT AAATGT ACAACT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
* *
40203174 AAAAAT AAAAAG AAAAAT --AAAT AAAACAT AAAACT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA-AT AAAAAT AAA
40203212 TAGACTCAGT
Statistics
Matches: 58, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
4 4 0.07
5 12 0.21
6 36 0.62
7 6 0.10
ACGTcount: A:0.75, C:0.07, G:0.02, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:40203158 original size:16 final size:15
Alignment explanation
Indices: 40203131--40203165 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
40203121 TAATTCTGAA
40203131 AAATAAAATAAAAAC
1 AAATAAAATAAAAAC
*
40203146 AAATAACAATAAAAAT
1 AAATAA-AATAAAAAC
40203162 AAAT
1 AAAT
40203166 GTACAACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.17
Consensus pattern (15 bp):
AAATAAAATAAAAAC
Found at i:40203180 original size:24 final size:22
Alignment explanation
Indices: 40203129--40203211 Score: 78
Period size: 24 Copynumber: 3.7 Consensus size: 22
40203119 TATAATTCTG
40203129 AAAAAT-AAAATAAAAACAAAT
1 AAAAATAAAAATAAAAACAAAT
* * *
40203150 AACAATAAAAATAAATGTACAACT
1 AAAAATAAAAATAAA--AACAAAT
* *
40203174 AAAAATAAAAAGAAAAATAAAT
1 AAAAATAAAAATAAAAACAAAT
*
40203196 AAAACATAAAACTAAA
1 AAAA-ATAAAAATAAA
40203212 TAGACTCAGT
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
21 5 0.10
22 16 0.33
23 9 0.19
24 18 0.38
ACGTcount: A:0.75, C:0.07, G:0.02, T:0.16
Consensus pattern (22 bp):
AAAAATAAAAATAAAAACAAAT
Found at i:40203197 original size:16 final size:17
Alignment explanation
Indices: 40203176--40203213 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
40203166 GTACAACTAA
40203176 AAATAAAA-AGAAAAAT
1 AAATAAAACAGAAAAAT
* *
40203192 AAATAAAACATAAAACT
1 AAATAAAACAGAAAAAT
40203209 AAATA
1 AAATA
40203214 GACTCAGTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.76, C:0.05, G:0.03, T:0.16
Consensus pattern (17 bp):
AAATAAAACAGAAAAAT
Found at i:40211198 original size:72 final size:72
Alignment explanation
Indices: 40211115--40211258 Score: 252
Period size: 72 Copynumber: 2.0 Consensus size: 72
40211105 AAGGAAATTT
* *
40211115 AATATATAATTGTTTAAAAAGTTCAAGAAATTTACCAAATTGTTCATCCATGTGGTCTTTCTTCA
1 AATATATAATTGTTTAAAAAGTTCAAGAAATTTACCAAATTGTTCATCCATGCGATCTTTCTTCA
40211180 ACTTTGC
66 ACTTTGC
* *
40211187 AATATGTAATTGTTTAAAAAGTTCAAGAAATTTACCAAATTGTTCGTCCATGCGATCTTTCTTCA
1 AATATATAATTGTTTAAAAAGTTCAAGAAATTTACCAAATTGTTCATCCATGCGATCTTTCTTCA
40211252 ACTTTGC
66 ACTTTGC
40211259 CGGATATGAA
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 68 1.00
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.40
Consensus pattern (72 bp):
AATATATAATTGTTTAAAAAGTTCAAGAAATTTACCAAATTGTTCATCCATGCGATCTTTCTTCA
ACTTTGC
Found at i:40217480 original size:23 final size:24
Alignment explanation
Indices: 40217453--40217499 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
40217443 TAGACATAAA
40217453 TTTGAAA-AA-AAATATTTTTGAGG
1 TTTGAAAGAAGAAA-ATTTTTGAGG
40217476 TTTGAAAGAAGTAAAATTTTTGAG
1 TTTGAAAGAAG-AAAATTTTTGAG
40217500 AGAAAAGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 7 0.33
24 2 0.10
25 9 0.43
26 3 0.14
ACGTcount: A:0.43, C:0.00, G:0.19, T:0.38
Consensus pattern (24 bp):
TTTGAAAGAAGAAAATTTTTGAGG
Found at i:40217509 original size:20 final size:20
Alignment explanation
Indices: 40217484--40217532 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
40217474 GGTTTGAAAG
*
40217484 AAGTAAAA-TTTTTGAGAGAA
1 AAGTAAAAGTTTTAGAG-GAA
*
40217504 AAGTAAACGTTTTAGAGGAA
1 AAGTAAAAGTTTTAGAGGAA
40217524 AAGTAAAAG
1 AAGTAAAAG
40217533 AAAAAAGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 18 0.72
21 7 0.28
ACGTcount: A:0.51, C:0.02, G:0.22, T:0.24
Consensus pattern (20 bp):
AAGTAAAAGTTTTAGAGGAA
Found at i:40221170 original size:2 final size:2
Alignment explanation
Indices: 40221163--40221188 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40221153 ATACTATTAA
40221163 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
40221189 TTGATAGATT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:40226932 original size:15 final size:15
Alignment explanation
Indices: 40226908--40226940 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
40226898 AACTTAATCT
40226908 ATATAAGTTATAATA
1 ATATAAGTTATAATA
*
40226923 ATATATGTTATAATA
1 ATATAAGTTATAATA
40226938 ATA
1 ATA
40226941 AAATTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (15 bp):
ATATAAGTTATAATA
Found at i:40227756 original size:43 final size:43
Alignment explanation
Indices: 40227702--40227787 Score: 136
Period size: 43 Copynumber: 2.0 Consensus size: 43
40227692 TATGTGATTG
*
40227702 ATATTGAAATGGAAAATATGAGAAATGAATATGTGATGAGAAA
1 ATATTGAAATGGAAAATATGAGAAATGAATATGAGATGAGAAA
* * *
40227745 ATATTGGAATGGCAAATATGAGAAATGATTATGAGATGAGAAA
1 ATATTGAAATGGAAAATATGAGAAATGAATATGAGATGAGAAA
40227788 TGAGATATGA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.49, C:0.01, G:0.24, T:0.26
Consensus pattern (43 bp):
ATATTGAAATGGAAAATATGAGAAATGAATATGAGATGAGAAA
Found at i:40229890 original size:20 final size:20
Alignment explanation
Indices: 40229865--40229903 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
40229855 TGGAACAGGA
*
40229865 ATATCGATACCTTAGGAAAT
1 ATATCGATACCTTAAGAAAT
40229885 ATATCGATACCTTAAGAAA
1 ATATCGATACCTTAAGAAA
40229904 AATTATTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (20 bp):
ATATCGATACCTTAAGAAAT
Found at i:40231873 original size:23 final size:23
Alignment explanation
Indices: 40231847--40231901 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
40231837 GACTAAGCGC
40231847 GCAAGTGATAATGGCACTATAGT
1 GCAAGTGATAATGGCACTATAGT
* * *
40231870 GCAAGTGTTAGTGGCACTTTAGT
1 GCAAGTGATAATGGCACTATAGT
40231893 GCAAAGTGA
1 GC-AAGTGA
40231902 CATCCACATG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 22 0.81
24 5 0.19
ACGTcount: A:0.31, C:0.13, G:0.29, T:0.27
Consensus pattern (23 bp):
GCAAGTGATAATGGCACTATAGT
Found at i:40234926 original size:16 final size:16
Alignment explanation
Indices: 40234890--40234922 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
40234880 GTCAGATCCC
40234890 TATTTATTCAATTTTA
1 TATTTATTCAATTTTA
40234906 TATTTATT--ATTTTA
1 TATTTATTCAATTTTA
40234920 TAT
1 TAT
40234923 ATTTGAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
16 8 0.47
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (16 bp):
TATTTATTCAATTTTA
Found at i:40237689 original size:126 final size:126
Alignment explanation
Indices: 40237535--40237828 Score: 473
Period size: 126 Copynumber: 2.3 Consensus size: 126
40237525 AGTGTTAATT
* * *
40237535 TAAAA-AAGCTTCCACGTGGACGCTCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTTGAGAAG
1 TAAAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGAAG
* * * *
40237599 ACATTTTTGAGCAAATAGTGTCAAAAACACTTTAAGCAGGATGCTTTGTCAGCAAAAATAT
66 ACATTTCTGAGCAAATAGTGTCAAAAACACTTTAAGCAGGATGCTTTGACAACAAAAATAC
* *
40237660 TGAAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAG
1 TAAAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGAAG
* *
40237725 ACGTTTCTGAGCAAATAGTGTCAAAAACACTTTAAGCAGGATGCTTTGACAACAAAAGTAC
66 ACATTTCTGAGCAAATAGTGTCAAAAACACTTTAAGCAGGATGCTTTGACAACAAAAATAC
*
40237786 TAAAAGAAGCTCCCACGTGGACGTGCTTTTGCTACAGTAGCTC
1 TAAAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTC
40237829 ATGTTTGGCC
Statistics
Matches: 155, Mismatches: 13, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
125 4 0.03
126 151 0.97
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (126 bp):
TAAAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGAAG
ACATTTCTGAGCAAATAGTGTCAAAAACACTTTAAGCAGGATGCTTTGACAACAAAAATAC
Found at i:40241218 original size:21 final size:21
Alignment explanation
Indices: 40241194--40241240 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
40241184 TTGTCCAGCT
* *
40241194 TCCGGCGGGGGTTGTGGTTGC
1 TCCGGCGGGGATTGTGGTTCC
*
40241215 TCCGGCGGGGATTTTGGTTCC
1 TCCGGCGGGGATTGTGGTTCC
40241236 TCCGG
1 TCCGG
40241241 TAGGGGATCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.02, C:0.23, G:0.45, T:0.30
Consensus pattern (21 bp):
TCCGGCGGGGATTGTGGTTCC
Found at i:40241520 original size:18 final size:18
Alignment explanation
Indices: 40241494--40241536 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
40241484 GGTTAGAAAA
* * *
40241494 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
40241512 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
40241530 AGGATAC
1 AGGATAC
40241537 GCGCCTGACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:40243393 original size:11 final size:11
Alignment explanation
Indices: 40243379--40243415 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
40243369 AGCTTTTTTA
40243379 AGAGGAATTTG
1 AGAGGAATTTG
40243390 AGAGGAATTTG
1 AGAGGAATTTG
*
40243401 AAAGGAATTTG
1 AGAGGAATTTG
40243412 AGAG
1 AGAG
40243416 AATATTGGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.35, T:0.24
Consensus pattern (11 bp):
AGAGGAATTTG
Found at i:40243406 original size:22 final size:24
Alignment explanation
Indices: 40243381--40243437 Score: 77
Period size: 22 Copynumber: 2.5 Consensus size: 24
40243371 CTTTTTTAAG
40243381 AGGAATTTGAGAGGAAT-TT-GAA
1 AGGAATTTGAGAGGAATATTGGAA
40243403 AGGAATTTGAGA-GAATATTGGAA
1 AGGAATTTGAGAGGAATATTGGAA
*
40243426 A-GAAATTGAGAG
1 AGGAATTTGAGAG
40243438 AAAGGATTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
21 4 0.13
22 23 0.74
23 4 0.13
ACGTcount: A:0.44, C:0.00, G:0.32, T:0.25
Consensus pattern (24 bp):
AGGAATTTGAGAGGAATATTGGAA
Found at i:40244661 original size:12 final size:12
Alignment explanation
Indices: 40244631--40244663 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
40244621 TATATATTTT
40244631 AAAATT-ATATA
1 AAAATTAATATA
40244642 AAAA-TAATATA
1 AAAATTAATATA
40244653 AAAATTAATAT
1 AAAATTAATAT
40244664 GGGCGGGCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Done.