Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D07
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: 56457815
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1765025 characters in sequence are not A, C, G, or T
File 140 of 189
Found at i:42564832 original size:44 final size:45
Alignment explanation
Indices: 42564760--42564883 Score: 137
Period size: 44 Copynumber: 2.8 Consensus size: 45
42564750 TGAAGCCGAT
* * * **
42564760 AATCCTATCTCCCTGAAATTGTAATGGAGCGGATTA-AAGTAATG
1 AATCCTATCTCCCTGAAGTTGCAATGGAGCGGATTAGAAGAAACC
* * * *
42564804 GAT-CTCATCTCCCTGAAGTTGCAGTGGAGCAGA-CAGAAGAAACC
1 AATCCT-ATCTCCCTGAAGTTGCAATGGAGCGGATTAGAAGAAACC
42564848 AATCCTATCTCCCTGAAGTTGCAATGGAGCGGATTA
1 AATCCTATCTCCCTGAAGTTGCAATGGAGCGGATTA
42564884 CAACTACAGA
Statistics
Matches: 63, Mismatches: 13, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
43 3 0.05
44 57 0.90
45 3 0.05
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (45 bp):
AATCCTATCTCCCTGAAGTTGCAATGGAGCGGATTAGAAGAAACC
Found at i:42564896 original size:88 final size:86
Alignment explanation
Indices: 42564760--42565006 Score: 234
Period size: 88 Copynumber: 2.8 Consensus size: 86
42564750 TGAAGCCGAT
* * *
42564760 AATCCTATCTCCCTGAAATTGTAATGGAGCGGATTA-AAGTA-ATGGATCTCATCTCCCTGAAGT
1 AATCCTATCTCCCTGAAGTTGCAATGGAGCGGATTACAACTACA--GATCTCATCTCCCTGAAGT
* *
42564823 TGCAGTGGAGCAGACAGA-AGAAACC
64 TGTAGT-GA-AAG-CAGATAGAAACC
* * *
42564848 AATCCTATCTCCCTGAAGTTGCAATGGAGCGGATTACAACTACAGATCTTATCTCTCTAAAGTTG
1 AATCCTATCTCCCTGAAGTTGCAATGGAGCGGATTACAACTACAGATCTCATCTCCCTGAAGTTG
* * *
42564913 TAGT-AAAGCAGATCGCATCC
66 TAGTGAAAGCAGATAGAAACC
* ** * * *
42564933 AGT-CTCATCTCCCTGAAGTTGCTGTGGAGCTGATTACAACCACAGACCTCACATCTCCCTGAAG
1 AATCCT-ATCTCCCTGAAGTTGCAATGGAGCGGATTACAACTACAGA--TCTCATCTCCCTGAAG
42564997 TTGTAGTGAA
63 TTGTAGTGAA
42565007 GCGGATCAAA
Statistics
Matches: 132, Mismatches: 20, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
84 6 0.05
85 44 0.33
86 1 0.01
87 19 0.14
88 57 0.43
89 4 0.03
90 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.26
Consensus pattern (86 bp):
AATCCTATCTCCCTGAAGTTGCAATGGAGCGGATTACAACTACAGATCTCATCTCCCTGAAGTTG
TAGTGAAAGCAGATAGAAACC
Found at i:42564901 original size:44 final size:44
Alignment explanation
Indices: 42564804--42565004 Score: 135
Period size: 44 Copynumber: 4.6 Consensus size: 44
42564794 TAAAGTAATG
* * **
42564804 GATCTCATCTCCCTGAAGTTGCAGTGGAGCAGA-CAGAAGAAACCA
1 GATCTCATCTCCCTGAAGTTGCAGTGGAGCAGATTACAA-CTA-CA
* *
42564849 -ATC-CTATCTCCCTGAAGTTGCAATGGAGCGGATTACAACTACA
1 GATCTC-ATCTCCCTGAAGTTGCAGTGGAGCAGATTACAACTACA
* * * * ** ** *
42564892 GATCTTATCTCTCTAAAGTTGTAGTAAAGCAGATCGC-A-TCCA
1 GATCTCATCTCCCTGAAGTTGCAGTGGAGCAGATTACAACTACA
* * *
42564934 G-TCTCATCTCCCTGAAGTTGCTGTGGAGCTGATTACAACCACA
1 GATCTCATCTCCCTGAAGTTGCAGTGGAGCAGATTACAACTACA
* *
42564977 GACCTCACATCTCCCTGAAGTTGTAGTG
1 GA--TCTCATCTCCCTGAAGTTGCAGTG
42565005 AAGCGGATCA
Statistics
Matches: 115, Mismatches: 32, Indels: 17
0.70 0.20 0.10
Matches are distributed among these distances:
41 25 0.22
42 5 0.04
43 7 0.06
44 54 0.47
45 3 0.03
46 21 0.18
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.26
Consensus pattern (44 bp):
GATCTCATCTCCCTGAAGTTGCAGTGGAGCAGATTACAACTACA
Found at i:42566333 original size:3 final size:3
Alignment explanation
Indices: 42566325--42566381 Score: 98
Period size: 3 Copynumber: 19.3 Consensus size: 3
42566315 TAATATTTCC
*
42566325 ATT ATT ATT ATT ATT ATT ATT -TT ATT ATT ATT ATT ATT ATT ATC ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
42566372 ATT ATT ATT A
1 ATT ATT ATT A
42566382 GCTTTTTTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 49 0.96
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:42567189 original size:3 final size:3
Alignment explanation
Indices: 42567164--42567205 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
42567154 TTACCCCTTT
* *
42567164 TTA TTA TTG TTA TTT TTA TTTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TT
42567206 TATTTTTCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:42567192 original size:22 final size:22
Alignment explanation
Indices: 42567164--42567209 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
42567154 TTACCCCTTT
* *
42567164 TTATTATTGTTATTTTTATTTA
1 TTATTATTATTATTATTATTTA
42567186 TTATTATTATTATTATTATTTA
1 TTATTATTATTATTATTATTTA
42567208 TT
1 TT
42567210 TTTCTTGCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (22 bp):
TTATTATTATTATTATTATTTA
Found at i:42567209 original size:19 final size:19
Alignment explanation
Indices: 42567163--42567202 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
42567153 TTTACCCCTT
* *
42567163 TTTATTATTGTTATTTTTA
1 TTTATTATTATTATTATTA
42567182 TTTATTATTATTATTATTA
1 TTTATTATTATTATTATTA
42567201 TT
1 TT
42567203 ATTTATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (19 bp):
TTTATTATTATTATTATTA
Found at i:42568670 original size:7 final size:6
Alignment explanation
Indices: 42568650--42568725 Score: 75
Period size: 6 Copynumber: 12.5 Consensus size: 6
42568640 GTTTTATTTG
* * *
42568650 TTTTAT TTTTAT TTTTAAT TTTCT-T TTTTAT GTTTAT GTTTAT TTCTAT
1 TTTTAT TTTTAT TTTT-AT TTT-TAT TTTTAT TTTTAT TTTTAT TTTTAT
*
42568699 TTTTAGT TGTT-T TTTTAT TTTTAT TTT
1 TTTTA-T TTTTAT TTTTAT TTTTAT TTT
42568726 ATTGTACTTC
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
5 5 0.08
6 44 0.75
7 9 0.15
8 1 0.02
ACGTcount: A:0.14, C:0.03, G:0.05, T:0.78
Consensus pattern (6 bp):
TTTTAT
Found at i:42569245 original size:187 final size:187
Alignment explanation
Indices: 42568925--42569292 Score: 601
Period size: 187 Copynumber: 2.0 Consensus size: 187
42568915 GGTAGTTTCA
* *
42568925 GTTTCCTCCCTCTCATATGATATTATGTTTATACTGTGATTATATTTGTTTGCACATTGAGGACA
1 GTTTCCTCCCTCTCATATGATATTATGTTTATACTATGATTATATTTGTTTGCACATTAAGGACA
* * **
42568990 ATGTAGATCTTAAGTGTGGGGAGGTTATTTATATATTTACTAGAAAATCTTTGAACTATGTCTTG
66 ATGTACATCTTAAGTGTGGGGAGGTTATTTATATAATTACTAGAAAATCCCTGAACTATGTCTTG
*
42569055 TATTTAAGTAATTTTCTCATACTTCAATTAGAATTAATTTTTGACGATTTGAAATGT
131 TATTTAAGTAATTTTCTCATACTTCAATTAGAATGAATTTTTGACGATTTGAAATGT
* * * *
42569112 GTTTTCTCCCTCTCATATGATATTCTGTTTATATTATGATTATATTTGTTTGTACATTAAGGACA
1 GTTTCCTCCCTCTCATATGATATTATGTTTATACTATGATTATATTTGTTTGCACATTAAGGACA
* *
42569177 ATGTACATCTTAAGTGTGGGGAGGTTATTTATATAATTATTAGAAAATCCCTGAATTATGTCTTG
66 ATGTACATCTTAAGTGTGGGGAGGTTATTTATATAATTACTAGAAAATCCCTGAACTATGTCTTG
* *
42569242 TATTTAATTAATTTTCTCATACTTCTATTAGAATGAATTTTTGACGATTTG
131 TATTTAAGTAATTTTCTCATACTTCAATTAGAATGAATTTTTGACGATTTG
42569293 GAATTTTTGT
Statistics
Matches: 166, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
187 166 1.00
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.45
Consensus pattern (187 bp):
GTTTCCTCCCTCTCATATGATATTATGTTTATACTATGATTATATTTGTTTGCACATTAAGGACA
ATGTACATCTTAAGTGTGGGGAGGTTATTTATATAATTACTAGAAAATCCCTGAACTATGTCTTG
TATTTAAGTAATTTTCTCATACTTCAATTAGAATGAATTTTTGACGATTTGAAATGT
Found at i:42578889 original size:21 final size:22
Alignment explanation
Indices: 42578852--42578915 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 22
42578842 AAATATAAAA
*
42578852 AATATATATAATAAAATAG-ATGT
1 AATATATA-AAT-AAATAGAATAT
*
42578875 AATATATAAATAAATTGAATAT
1 AATATATAAATAAATAGAATAT
*
42578897 AATAT-TAAATATATA-AATA
1 AATATATAAATAAATAGAATA
42578916 AATTAAACCA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 4 0.11
21 13 0.36
22 11 0.31
23 8 0.22
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (22 bp):
AATATATAAATAAATAGAATAT
Found at i:42578920 original size:17 final size:17
Alignment explanation
Indices: 42578875--42578922 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 17
42578865 AAATAGATGT
42578875 AATATATAAATAAATT-
1 AATATATAAATAAATTA
*
42578891 GA-ATAT-AAT--ATTA
1 AATATATAAATAAATTA
42578904 AATATATAAATAAATTA
1 AATATATAAATAAATTA
42578921 AA
1 AA
42578923 CCAAAAGAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 9
0.69 0.06 0.25
Matches are distributed among these distances:
12 3 0.12
13 1 0.04
14 7 0.28
15 7 0.28
16 1 0.04
17 6 0.24
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (17 bp):
AATATATAAATAAATTA
Found at i:42580822 original size:25 final size:25
Alignment explanation
Indices: 42580767--42580859 Score: 96
Period size: 25 Copynumber: 3.7 Consensus size: 25
42580757 TACAGATTTT
* * *
42580767 AGCTCCTATGAGCTTACCGATACTC
1 AGCTCGTATGAGCTTACCGTTATTC
*
42580792 AGCTCGTATAAGCTTACCGTTATTC
1 AGCTCGTATGAGCTTACCGTTATTC
* * *
42580817 AGCTCGGAGGAGCTTACCATTATTC
1 AGCTCGTATGAGCTTACCGTTATTC
* * *
42580842 AACTCGGAGGAGCTTACC
1 AGCTCGTATGAGCTTACC
42580860 ATTTACTGCT
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 59 1.00
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (25 bp):
AGCTCGTATGAGCTTACCGTTATTC
Found at i:42580860 original size:25 final size:25
Alignment explanation
Indices: 42580802--42580862 Score: 104
Period size: 25 Copynumber: 2.4 Consensus size: 25
42580792 AGCTCGTATA
* *
42580802 AGCTTACCGTTATTCAGCTCGGAGG
1 AGCTTACCATTATTCAACTCGGAGG
42580827 AGCTTACCATTATTCAACTCGGAGG
1 AGCTTACCATTATTCAACTCGGAGG
42580852 AGCTTACCATT
1 AGCTTACCATT
42580863 TACTGCTTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.30
Consensus pattern (25 bp):
AGCTTACCATTATTCAACTCGGAGG
Found at i:42583484 original size:8 final size:8
Alignment explanation
Indices: 42583473--42583545 Score: 50
Period size: 9 Copynumber: 9.5 Consensus size: 8
42583463 CTTTTCTTTC
42583473 TTTTTCATT
1 TTTTTCA-T
42583482 TTTTTCAGT
1 TTTTTCA-T
42583491 TTTTTCAGT
1 TTTTTCA-T
*
42583500 TTTTTTA-
1 TTTTTCAT
42583507 TTTTT-AT
1 TTTTTCAT
*
42583514 TTTAT--T
1 TTTTTCAT
42583520 TTTTTC-T
1 TTTTTCAT
42583527 TTTTTCAT
1 TTTTTCAT
*
42583535 TTGTTC-T
1 TTTTTCAT
42583542 TTTT
1 TTTT
42583546 CTCTCATTTG
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
6 6 0.11
7 20 0.36
8 6 0.11
9 23 0.42
ACGTcount: A:0.10, C:0.08, G:0.04, T:0.78
Consensus pattern (8 bp):
TTTTTCAT
Found at i:42583485 original size:9 final size:9
Alignment explanation
Indices: 42583473--42583536 Score: 62
Period size: 9 Copynumber: 7.1 Consensus size: 9
42583463 CTTTTCTTTC
42583473 TTTTTCATT
1 TTTTTCATT
*
42583482 TTTTTCAGT
1 TTTTTCATT
42583491 TTTTTCAGTT
1 TTTTTCA-TT
42583501 TTTTT-ATTT
1 TTTTTCA-TT
*
42583510 TTATTTTATT
1 TT-TTTCATT
42583520 TTTTTC--T
1 TTTTTCATT
42583527 TTTTTCATT
1 TTTTTCATT
42583536 T
1 T
42583537 GTTCTTTTTC
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
7 7 0.15
9 25 0.54
10 13 0.28
11 1 0.02
ACGTcount: A:0.11, C:0.08, G:0.03, T:0.78
Consensus pattern (9 bp):
TTTTTCATT
Found at i:42586372 original size:17 final size:18
Alignment explanation
Indices: 42586343--42586377 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
42586333 ATACTCAAAT
*
42586343 TTTTTTTACTTCATATAC
1 TTTTTTTACTTCAAATAC
42586361 TTTTTTTA-TTCAAATAC
1 TTTTTTTACTTCAAATAC
42586378 AATTGAACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.26, C:0.14, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTTTTACTTCAAATAC
Found at i:42587662 original size:21 final size:21
Alignment explanation
Indices: 42587623--42587662 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
42587613 AAAACTTTAT
42587623 CTAGACAAATTAAATAACATG
1 CTAGACAAATTAAATAACATG
42587644 CTAGAACAAATTAAA-AACA
1 CTAG-ACAAATTAAATAACA
42587663 GTTAATTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.57, C:0.15, G:0.07, T:0.20
Consensus pattern (21 bp):
CTAGACAAATTAAATAACATG
Found at i:42588215 original size:32 final size:32
Alignment explanation
Indices: 42588143--42588303 Score: 198
Period size: 32 Copynumber: 5.1 Consensus size: 32
42588133 AAAAACAAAA
* * * *
42588143 TAACGGTAACATGATTGGCAC-ATGCCATCAA
1 TAACGGTAATATGATCGGCACAAAGCCATCAG
*
42588174 TAACGGTAATATGATCGACACAAAGCCATCAG
1 TAACGGTAATATGATCGGCACAAAGCCATCAG
* * *
42588206 TAACTGTAATATGATCGGTACATAGCCATCAG
1 TAACGGTAATATGATCGGCACAAAGCCATCAG
* *
42588238 TAACGGTAATACGATTGGCACAAAGCCATCAG
1 TAACGGTAATATGATCGGCACAAAGCCATCAG
** *
42588270 TAATAGTAATATGATCGGTACAAAGCCATCAG
1 TAACGGTAATATGATCGGCACAAAGCCATCAG
42588302 TA
1 TA
42588304 GCATCGCAGC
Statistics
Matches: 110, Mismatches: 19, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
31 18 0.16
32 92 0.84
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (32 bp):
TAACGGTAATATGATCGGCACAAAGCCATCAG
Found at i:42588267 original size:64 final size:64
Alignment explanation
Indices: 42588143--42588303 Score: 218
Period size: 64 Copynumber: 2.5 Consensus size: 64
42588133 AAAAACAAAA
* * * * * *
42588143 TAACGGTAACATGATTGGCACAT-GCCATCAATAACGGTAATATGATCGACACAAAGCCATCAG
1 TAACTGTAATATGATCGGTACATAGCCATCAGTAACGGTAATACGATCGACACAAAGCCATCAG
* *
42588206 TAACTGTAATATGATCGGTACATAGCCATCAGTAACGGTAATACGATTGGCACAAAGCCATCAG
1 TAACTGTAATATGATCGGTACATAGCCATCAGTAACGGTAATACGATCGACACAAAGCCATCAG
*
42588270 TAA-TAGTAATATGATCGGTACAAAGCCATCAGTA
1 TAACT-GTAATATGATCGGTACATAGCCATCAGTA
42588304 GCATCGCAGC
Statistics
Matches: 87, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
63 20 0.23
64 67 0.77
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (64 bp):
TAACTGTAATATGATCGGTACATAGCCATCAGTAACGGTAATACGATCGACACAAAGCCATCAG
Found at i:42588514 original size:24 final size:24
Alignment explanation
Indices: 42588478--42588531 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
42588468 GCTCAGAATT
42588478 AGTCATACAAATCACAAACAAATC
1 AGTCATACAAATCACAAACAAATC
* * *
42588502 AGTCATACCAATCATAGACAAATC
1 AGTCATACAAATCACAAACAAATC
42588526 AGTCAT
1 AGTCAT
42588532 TTACATGTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.48, C:0.24, G:0.07, T:0.20
Consensus pattern (24 bp):
AGTCATACAAATCACAAACAAATC
Found at i:42588619 original size:27 final size:27
Alignment explanation
Indices: 42588577--42588829 Score: 183
Period size: 27 Copynumber: 9.4 Consensus size: 27
42588567 GGACAAAATA
* * *
42588577 GTCA-TTTACCCTACAGGGGCATTACG
1 GTCATTTTACCTTACAGGGGTATTTCG
*
42588603 GTCATTTTACCTTACAGGGGTATTACG
1 GTCATTTTACCTTACAGGGGTATTTCG
* *
42588630 ATCATTTTACCTTACAGGGGCATTAT-G
1 GTCATTTTACCTTACAGGGGTATT-TCG
* * * ** *
42588657 ATCATTTTACCCTATAGGGGTATCACA
1 GTCATTTTACCTTACAGGGGTATTTCG
*
42588684 GTCATTTTACCCTTTA-A-AGGTATTTCG
1 GTCATTTTA-CC-TTACAGGGGTATTTCG
** *
42588711 ACCATTTTACCATT-CAGGGGTATTTCA
1 GTCATTTTACC-TTACAGGGGTATTTCG
* *** * **
42588738 GTCTTTTTACCTTTTGGGGGCATTTTA
1 GTCATTTTACCTTACAGGGGTATTTCG
*
42588765 GTCATTTTACCTTATAGGGGTATTTCG
1 GTCATTTTACCTTACAGGGGTATTTCG
* * *
42588792 GTCATTTTACCCTATAGGGGTATTTTG
1 GTCATTTTACCTTACAGGGGTATTTCG
*
42588819 GTCATTCTACC
1 GTCATTTTACC
42588830 CTATCAAGGT
Statistics
Matches: 181, Mismatches: 38, Indels: 15
0.77 0.16 0.06
Matches are distributed among these distances:
26 11 0.06
27 165 0.91
28 3 0.02
29 2 0.01
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.40
Consensus pattern (27 bp):
GTCATTTTACCTTACAGGGGTATTTCG
Found at i:42588646 original size:54 final size:54
Alignment explanation
Indices: 42588576--42588829 Score: 203
Period size: 54 Copynumber: 4.7 Consensus size: 54
42588566 GGGACAAAAT
* **
42588576 AGTCA-TTTACCCTACAGGGGCATTACGGTCATTTTACCTTACAGGGGTATTAC
1 AGTCATTTTACCTTACAGGGGCATTTTGGTCATTTTACCTTACAGGGGTATTAC
* * * * *
42588629 -GATCATTTTACCTTACAGGGGCATTATGATCATTTTACCCTATAGGGGTATCAC
1 AG-TCATTTTACCTTACAGGGGCATTTTGGTCATTTTACCTTACAGGGGTATTAC
* * * ** *
42588683 AGTCATTTTACCCTTTA-A-AGGTATTTCGACCATTTTACCATT-CAGGGGTATTTC
1 AGTCATTTTA-CC-TTACAGGGGCATTTTGGTCATTTTACC-TTACAGGGGTATTAC
* *** * * *
42588737 AGTCTTTTTACCTTTTGGGGGCATTTTAGTCATTTTACCTTATAGGGGTATTTC
1 AGTCATTTTACCTTACAGGGGCATTTTGGTCATTTTACCTTACAGGGGTATTAC
* * * * *
42588791 GGTCATTTTACCCTATAGGGGTATTTTGGTCATTCTACC
1 AGTCATTTTACCTTACAGGGGCATTTTGGTCATTTTACC
42588830 CTATCAAGGT
Statistics
Matches: 159, Mismatches: 33, Indels: 17
0.76 0.16 0.08
Matches are distributed among these distances:
52 3 0.02
53 7 0.04
54 141 0.89
55 5 0.03
56 3 0.02
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (54 bp):
AGTCATTTTACCTTACAGGGGCATTTTGGTCATTTTACCTTACAGGGGTATTAC
Found at i:42588676 original size:81 final size:79
Alignment explanation
Indices: 42588581--42588833 Score: 240
Period size: 81 Copynumber: 3.1 Consensus size: 79
42588571 AAAATAGTCA
* * *
42588581 TTTACCCTACAGGGGCATTACGGTCATTTTACCTTACAGGGGTATTACGATCATTTTACCTTACA
1 TTTACCCTATAGGGGCATTACAGTCATTTTACCTTA-AGGGGTATTTCGATCATTTTACCTTACA
*
42588646 GGGGCATTATGATCAT
65 GGGGTATT-TGATCAT
* * * *
42588662 TTTACCCTATAGGGGTATCACAGTCATTTTACCCTTTAA-AGGTATTTCGACCATTTTACCATT-
1 TTTACCCTATAGGGGCATTACAGTCATTTTA-CC-TTAAGGGGTATTTCGATCATTTTACC-TTA
* *
42588725 CAGGGGTATTTCAGTCTT
63 CAGGGGTATTTGA-TCAT
* * * ** * * *
42588743 TTTACCTTTTGGGGGCATTTTAGTCATTTTACCTTATAGGGGTATTTCGGTCATTTTACCCTATA
1 TTTACCCTATAGGGGCATTACAGTCATTTTACCTTA-AGGGGTATTTCGATCATTTTACCTTACA
*
42588808 GGGGTATTTTGGTCAT
65 GGGGTA-TTTGATCAT
*
42588824 TCTACCCTAT
1 TTTACCCTAT
42588834 CAAGGTATTT
Statistics
Matches: 136, Mismatches: 28, Indels: 16
0.76 0.16 0.09
Matches are distributed among these distances:
79 3 0.02
80 6 0.04
81 116 0.85
82 8 0.06
83 3 0.02
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.40
Consensus pattern (79 bp):
TTTACCCTATAGGGGCATTACAGTCATTTTACCTTAAGGGGTATTTCGATCATTTTACCTTACAG
GGGTATTTGATCAT
Found at i:42588840 original size:27 final size:27
Alignment explanation
Indices: 42588765--42588845 Score: 92
Period size: 27 Copynumber: 3.0 Consensus size: 27
42588755 GGGCATTTTA
* * *
42588765 GTCATTTTACCTTATAGGGGTATTTCG
1 GTCATTCTACCCTATAGAGGTATTTCG
* * *
42588792 GTCATTTTACCCTATAGGGGTATTTTG
1 GTCATTCTACCCTATAGAGGTATTTCG
42588819 GTCATTCTACCCTATCA-AGGTATTTCG
1 GTCATTCTACCCTAT-AGAGGTATTTCG
42588846 ATCCAGATAT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 47 0.98
28 1 0.02
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.42
Consensus pattern (27 bp):
GTCATTCTACCCTATAGAGGTATTTCG
Found at i:42592613 original size:27 final size:27
Alignment explanation
Indices: 42592554--42592625 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
42592544 TCCAAACTAA
42592554 TATAAAATGACTGTTATGCCTCCACGT
1 TATAAAATGACTGTTATGCCTCCACGT
** * *
42592581 GGTAAAATGGCTGTTATGCC-CCTATGT
1 TATAAAATGACTGTTATGCCTCC-ACGT
42592608 TATAAAATGACTG-TATGC
1 TATAAAATGACTGTTATGC
42592626 TTTATGTTAT
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
26 7 0.19
27 30 0.81
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.33
Consensus pattern (27 bp):
TATAAAATGACTGTTATGCCTCCACGT
Found at i:42599210 original size:27 final size:27
Alignment explanation
Indices: 42599151--42599212 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
42599141 CCCAAACTGA
*
42599151 TATAAAGTGACTATTATGCCCCCACGT
1 TATAAAATGACTATTATGCCCCCACGT
** * *
42599178 GGTAAAATGACTATTATGCCCCTATGT
1 TATAAAATGACTATTATGCCCCCACGT
42599205 TATAAAAT
1 TATAAAAT
42599213 AATTGTATGC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (27 bp):
TATAAAATGACTATTATGCCCCCACGT
Found at i:42600606 original size:25 final size:25
Alignment explanation
Indices: 42600564--42600628 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 25
42600554 GCAACGGATT
*
42600564 CATGTTAGGGG-TGTGACAACACGAG
1 CATGTGAGGGGTTG-GACAACACGAG
*
42600589 CATGTGAGGGGTTGG---ACACGGG
1 CATGTGAGGGGTTGGACAACACGAG
42600611 CATGTGAGGGGTTGGACA
1 CATGTGAGGGGTTGGACA
42600629 CAGGCATGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
22 21 0.62
25 11 0.32
26 2 0.06
ACGTcount: A:0.23, C:0.14, G:0.43, T:0.20
Consensus pattern (25 bp):
CATGTGAGGGGTTGGACAACACGAG
Found at i:42600613 original size:22 final size:22
Alignment explanation
Indices: 42600582--42600638 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
42600572 GGGTGTGACA
*
42600582 ACACGAGCATGTGAGGGGTTGG
1 ACACGGGCATGTGAGGGGTTGG
42600604 ACACGGGCATGTGAGGGGTTGG
1 ACACGGGCATGTGAGGGGTTGG
*
42600626 ACACAGGCATGTG
1 ACACGGGCATGTG
42600639 GAAACTGGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.23, C:0.16, G:0.44, T:0.18
Consensus pattern (22 bp):
ACACGGGCATGTGAGGGGTTGG
Found at i:42604820 original size:21 final size:21
Alignment explanation
Indices: 42604794--42604850 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
42604784 AGCTAAGAAC
42604794 TGATAGGTAAATTTTCTTGCA
1 TGATAGGTAAATTTTCTTGCA
*
42604815 TGATAGGTAAATCTTCTTGCA
1 TGATAGGTAAATTTTCTTGCA
42604836 TGATAGGTAAATTTT
1 TGATAGGTAAATTTT
42604851 AACCATTTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.42
Consensus pattern (21 bp):
TGATAGGTAAATTTTCTTGCA
Found at i:42605153 original size:8 final size:8
Alignment explanation
Indices: 42605140--42605164 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
42605130 AAATGTTGAT
42605140 AATTTTGG
1 AATTTTGG
42605148 AATTTTGG
1 AATTTTGG
42605156 AATTTTGG
1 AATTTTGG
42605164 A
1 A
42605165 TTTAGGAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (8 bp):
AATTTTGG
Found at i:42605172 original size:15 final size:16
Alignment explanation
Indices: 42605140--42605172 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
42605130 AAATGTTGAT
*
42605140 AATTTTGGAATTTTGG
1 AATTTTGGAATTTAGG
42605156 AATTTTGG-ATTTAGG
1 AATTTTGGAATTTAGG
42605171 AA
1 AA
42605173 CTAAATTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.30, C:0.00, G:0.24, T:0.45
Consensus pattern (16 bp):
AATTTTGGAATTTAGG
Found at i:42615476 original size:357 final size:358
Alignment explanation
Indices: 42614813--42615528 Score: 1263
Period size: 357 Copynumber: 2.0 Consensus size: 358
42614803 TTGCAATCAC
* * *
42614813 TGACACTGGAAAGTGTAGTGACAGTTTGAGCCAAGAAGCATTACAACAGAAGTTGAGTGAGGATT
1 TGACACTGGAAAGTGCAGTGACAGTTTGAGCCAACAAGCATTACAACAGAAGTTGAGTGAGGAAT
42614878 AGAGGAACTTAGTCCACTTGTTCTTAATAGTGCCGTATTGCCATCATCGAAAGGTGAGGTTAGTA
66 AGAGGAACTTAGTCCACTTGTTCTTAATAGTGCCGTATTGCCATCATCGAAAGGTGAGGTTAGTA
*
42614943 TGCATGTTTAAGTCTCAGATTAAATAGAGGAGTGATGCTGGGTAAGATATACATTGAACTTTATT
131 TGCATGTTTAAGTCTCAGATTAAACAGAGGAGTGATGCTGGGTAAGATATACATTGAACTTTATT
* *
42615008 GCTTCGACAATCACCTATCCTTTTTATACCTTGTGAGCACTTTGTATTTTACTGAAGATTCATGT
196 GCTTCGACAATCACCTATCCTTTTTATACCTTGTGAGCACATAGTATTTTACTGAAGATTCATGT
* * * *
42615073 TGGGGATCTCATTTTGTCATTATCATATTTTATTTTATTTTTTTCAAGTTATTGCATTGACAACT
261 TGGGGATCCCAGTTTATCATTATCATATTTTATTTTATTGTTTTCAAGTTATTGCATTGACAACT
42615138 ATTCTCACAATTTATCTTGTTTCCATCTAGTTG
326 ATTCTCACAATTTATCTTGTTTCCATCTAGTTG
*
42615171 TGACACTGGAAATTGCAGTGACAGTTTGAGCCAACAAGCATTACAACAGAAGTTGAGTGAGGAAT
1 TGACACTGGAAAGTGCAGTGACAGTTTGAGCCAACAAGCATTACAACAGAAGTTGAGTGAGGAAT
* * * * *
42615236 AGAGGAATTTA-TCCACTTGTTTTTAATAGTGTCGTATTTCCATCATCGGAAGGTGAGGTTAGTA
66 AGAGGAACTTAGTCCACTTGTTCTTAATAGTGCCGTATTGCCATCATCGAAAGGTGAGGTTAGTA
42615300 TGCATGTTTAAGTCTCAGATTAAACAGAGGAGTGATGCTGGGTAAGATATACATTGAACTTTATT
131 TGCATGTTTAAGTCTCAGATTAAACAGAGGAGTGATGCTGGGTAAGATATACATTGAACTTTATT
* *
42615365 GCTTCGACGATCACCTATCCTTTTTATACCTTGTGAGCACATAGTATTTTACTGAAGATTTATGT
196 GCTTCGACAATCACCTATCCTTTTTATACCTTGTGAGCACATAGTATTTTACTGAAGATTCATGT
42615430 TGGGGATCCCAGTTTATCATTATCATATTTTATTTTATTGTTTTCAAGTTATTGCATTGACAACT
261 TGGGGATCCCAGTTTATCATTATCATATTTTATTTTATTGTTTTCAAGTTATTGCATTGACAACT
42615495 ATTCTCACAATTTATCTTGTTTCCATCTAGTTG
326 ATTCTCACAATTTATCTTGTTTCCATCTAGTTG
42615528 T
1 T
42615529 TGCACCGACA
Statistics
Matches: 340, Mismatches: 18, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
357 269 0.79
358 71 0.21
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (358 bp):
TGACACTGGAAAGTGCAGTGACAGTTTGAGCCAACAAGCATTACAACAGAAGTTGAGTGAGGAAT
AGAGGAACTTAGTCCACTTGTTCTTAATAGTGCCGTATTGCCATCATCGAAAGGTGAGGTTAGTA
TGCATGTTTAAGTCTCAGATTAAACAGAGGAGTGATGCTGGGTAAGATATACATTGAACTTTATT
GCTTCGACAATCACCTATCCTTTTTATACCTTGTGAGCACATAGTATTTTACTGAAGATTCATGT
TGGGGATCCCAGTTTATCATTATCATATTTTATTTTATTGTTTTCAAGTTATTGCATTGACAACT
ATTCTCACAATTTATCTTGTTTCCATCTAGTTG
Found at i:42620511 original size:22 final size:22
Alignment explanation
Indices: 42620470--42620512 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
42620460 CATCCATTTG
*
42620470 AAGGAGGCACACACTCGTGTGA
1 AAGGAGGCACAAACTCGTGTGA
42620492 AAGGAGGCACAAAGCT-GTGTG
1 AAGGAGGCACAAA-CTCGTGTG
42620513 GCTAAGGCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.33, C:0.19, G:0.35, T:0.14
Consensus pattern (22 bp):
AAGGAGGCACAAACTCGTGTGA
Found at i:42623470 original size:64 final size:64
Alignment explanation
Indices: 42623396--42623524 Score: 258
Period size: 64 Copynumber: 2.0 Consensus size: 64
42623386 TGATATATTT
42623396 ATATGTTAGAAACACACAGGAACAAAACTTAGTGGAAAGTTAGAGGATCCCATGATCACTCTCG
1 ATATGTTAGAAACACACAGGAACAAAACTTAGTGGAAAGTTAGAGGATCCCATGATCACTCTCG
42623460 ATATGTTAGAAACACACAGGAACAAAACTTAGTGGAAAGTTAGAGGATCCCATGATCACTCTCG
1 ATATGTTAGAAACACACAGGAACAAAACTTAGTGGAAAGTTAGAGGATCCCATGATCACTCTCG
42623524 A
1 A
42623525 ATTTGAGAAG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.22
Consensus pattern (64 bp):
ATATGTTAGAAACACACAGGAACAAAACTTAGTGGAAAGTTAGAGGATCCCATGATCACTCTCG
Found at i:42624628 original size:22 final size:22
Alignment explanation
Indices: 42624603--42624648 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
42624593 GGCAGCGAAA
* * *
42624603 TGCGAAGCAGTAGGCACCGTAG
1 TGCGAAGCAATAAGCACCATAG
*
42624625 TGCGAATCAATAAGCACCATAG
1 TGCGAAGCAATAAGCACCATAG
42624647 TG
1 TG
42624649 AAAACCCCGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.22, G:0.28, T:0.17
Consensus pattern (22 bp):
TGCGAAGCAATAAGCACCATAG
Found at i:42636154 original size:5 final size:5
Alignment explanation
Indices: 42636140--42636186 Score: 60
Period size: 5 Copynumber: 9.4 Consensus size: 5
42636130 AGTTGACTCG
* *
42636140 TTTT- TTTTA TTTTA TGTTA CTTTA TTTTA TTTTA TTTTA TCTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T-TTTA TT
42636187 GGGTTGTTGC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
4 4 0.11
5 28 0.76
6 5 0.14
ACGTcount: A:0.17, C:0.04, G:0.02, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:42649876 original size:25 final size:25
Alignment explanation
Indices: 42649848--42649896 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
42649838 AAATTTACCA
42649848 AGGGTAAAATCATCAAAATTTTACT
1 AGGGTAAAATCATCAAAATTTTACT
*
42649873 AGGGTAAAATCGTCAAAATTTTAC
1 AGGGTAAAATCATCAAAATTTTAC
42649897 AGTGGGTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (25 bp):
AGGGTAAAATCATCAAAATTTTACT
Found at i:42656352 original size:13 final size:13
Alignment explanation
Indices: 42656336--42656365 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
42656326 TTAATATAAC
*
42656336 ATATATAACTTAT
1 ATATATAAATTAT
42656349 ATATATAAATTAT
1 ATATATAAATTAT
42656362 ATAT
1 ATAT
42656366 CTCTTGACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (13 bp):
ATATATAAATTAT
Found at i:42667034 original size:12 final size:13
Alignment explanation
Indices: 42667010--42667038 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
42667000 GGGCTATAAC
42667010 TATTGCATTTATT
1 TATTGCATTTATT
42667023 TATTGC-TTTATT
1 TATTGCATTTATT
42667035 TATT
1 TATT
42667039 CATGTATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (13 bp):
TATTGCATTTATT
Found at i:42671656 original size:50 final size:50
Alignment explanation
Indices: 42671589--42671720 Score: 149
Period size: 50 Copynumber: 2.6 Consensus size: 50
42671579 TTTTGAGGTT
* * *
42671589 ATGAGAGCTCTCACGTAATACCATGTCTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGCTCTCACGTAAGACCATGTCTGGGACATGGCATGGGCACCGAG
* * * *
42671639 ATGAGAGGTCCTC-CGTAAGACCCTGTCTGGGACATGGCATGGGCACTGAT
1 ATGAGAGCT-CTCACGTAAGACCATGTCTGGGACATGGCATGGGCACCGAG
* * * *
42671689 ATGAGAACTCCCATGTAAGACCATATCTGGGA
1 ATGAGAGCTCTCACGTAAGACCATGTCTGGGA
42671721 TATGACATTG
Statistics
Matches: 67, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
49 2 0.03
50 62 0.93
51 3 0.04
ACGTcount: A:0.26, C:0.23, G:0.29, T:0.22
Consensus pattern (50 bp):
ATGAGAGCTCTCACGTAAGACCATGTCTGGGACATGGCATGGGCACCGAG
Found at i:42671986 original size:20 final size:19
Alignment explanation
Indices: 42671961--42672008 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
42671951 TGAGTTATTT
42671961 AAGTAAGTATGTAACTAAAG
1 AAGTAAGTAT-TAACTAAAG
* *
42671981 AAGTAAGAGATTAAGTAAAG
1 AAGTAAG-TATTAACTAAAG
42672001 AAG-AAGTA
1 AAGTAAGTA
42672009 AAGATCATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 1 0.04
19 3 0.12
20 18 0.75
21 2 0.08
ACGTcount: A:0.54, C:0.02, G:0.23, T:0.21
Consensus pattern (19 bp):
AAGTAAGTATTAACTAAAG
Found at i:42679198 original size:56 final size:50
Alignment explanation
Indices: 42679125--42679308 Score: 145
Period size: 50 Copynumber: 3.6 Consensus size: 50
42679115 GAGACCCTAT
* *
42679125 GTAAGACCAT-TTCTGGGACATGGCATTGACATTATTGAGGTTATGAGAGGTCTCAC
1 GTAAGACCATGTT-TGGGACATGGCATTGAC---ATCGA-G--ATGAGAGGTCCCAC
* * *
42679181 GTAAGACCATGTTTGGGACATGCCATTGGCATCGAGATGAGAGGTCCCCC
1 GTAAGACCATGTTTGGGACATGGCATTGACATCGAGATGAGAGGTCCCAC
* * * * * ** *
42679231 GTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTCCCAT
1 GTAAGACCATGTTTGGGACATGGCATTGACATCGAGATGAGAGGTCCCAC
* * * *
42679281 GTAAGACCATATCTGGGATATGGAATTG
1 GTAAGACCATGTTTGGGACATGGCATTG
42679309 GCAGTACAGG
Statistics
Matches: 109, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
50 77 0.71
52 1 0.01
53 4 0.04
56 25 0.23
57 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (50 bp):
GTAAGACCATGTTTGGGACATGGCATTGACATCGAGATGAGAGGTCCCAC
Found at i:42679225 original size:50 final size:50
Alignment explanation
Indices: 42679167--42679298 Score: 165
Period size: 50 Copynumber: 2.6 Consensus size: 50
42679157 TATTGAGGTT
* * * *
42679167 ATGAGAGGTCTCACGTAAGACCATGTTTGGGACATGCCATTGGCATCGAG
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGCCATGGGCACCGAG
* * *
42679217 ATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGAT
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGCCATGGGCACCGAG
** * *
42679267 ATGAGAACTCCCATGTAAGACCATATCTGGGA
1 ATGAGAGGTCCCACGTAAGACCATGTCTGGGA
42679299 TATGGAATTG
Statistics
Matches: 70, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 70 1.00
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.21
Consensus pattern (50 bp):
ATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGCCATGGGCACCGAG
Found at i:42679359 original size:49 final size:49
Alignment explanation
Indices: 42679181--42679360 Score: 166
Period size: 50 Copynumber: 3.6 Consensus size: 49
42679171 GAGGTCTCAC
* * * * ** **
42679181 GTAAGACCATGTTTGGGACATGCCATTGGCATCGAGATGAGAGGTCCCCC
1 GTAAGACCATGTCTGGGACATGGCATTGGCA-CGACAGGAGAACTCCCAT
* * *
42679231 GTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTCCCAT
1 GTAAGACCATGTCTGGGACATGGCATTGGCA-CGACAGGAGAACTCCCAT
* * *
42679281 GTAAGACCATATCTGGGATATGGAATTGGCA-GTACAGGA-AACATCCCAT
1 GTAAGACCATGTCTGGGACATGGCATTGGCACG-ACAGGAGAAC-TCCCAT
* *
42679330 GTAAGACCATGTCTGGTACATGGCTTTGGCA
1 GTAAGACCATGTCTGGGACATGGCATTGGCA
42679361 TGTTATTATC
Statistics
Matches: 108, Mismatches: 20, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
48 4 0.04
49 36 0.33
50 68 0.63
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.23
Consensus pattern (49 bp):
GTAAGACCATGTCTGGGACATGGCATTGGCACGACAGGAGAACTCCCAT
Found at i:42679587 original size:20 final size:20
Alignment explanation
Indices: 42679562--42679604 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
42679552 TGAGTTATTT
42679562 AAGTAAG-CATGTAAGTAAAG
1 AAGTAAGACAT-TAAGTAAAG
*
42679582 AAGTAAGAGATTAAGTAAAG
1 AAGTAAGACATTAAGTAAAG
42679602 AAG
1 AAG
42679605 AAGTAAAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.53, C:0.02, G:0.26, T:0.19
Consensus pattern (20 bp):
AAGTAAGACATTAAGTAAAG
Found at i:42680411 original size:30 final size:30
Alignment explanation
Indices: 42680370--42680433 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
42680360 TTGTTTACTT
42680370 ACTTGCGTATTTAAATAACTCATGATTATA
1 ACTTGCGTATTTAAATAACTCATGATTATA
*
42680400 ACTTGCTTATTTAAATAACTCATGATTATA
1 ACTTGCGTATTTAAATAACTCATGATTATA
42680430 ACTT
1 ACTT
42680434 CTCCTCCCTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.42
Consensus pattern (30 bp):
ACTTGCGTATTTAAATAACTCATGATTATA
Found at i:42680737 original size:50 final size:50
Alignment explanation
Indices: 42680662--42680854 Score: 199
Period size: 50 Copynumber: 3.7 Consensus size: 50
42680652 TTTCCTGTAC
* * **
42680662 TGCCAATGCCATATCCTAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATATCGG
* * ** *
42680712 TGCCCATGCCATGTCCAAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATATCGG
* * **
42680762 TGCCAACGCCATGTCCTAGACATGGTGTTACATGGGACCTCTCATAACCTCAATAA
1 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
42680818 TGCCAATGCCATGT-CTCAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCT-AGACATGGTCTTACATGGGA
42680855 TCTCATCCCC
Statistics
Matches: 116, Mismatches: 20, Indels: 8
0.81 0.14 0.06
Matches are distributed among these distances:
50 80 0.69
53 2 0.02
55 2 0.02
56 32 0.28
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:42683387 original size:23 final size:22
Alignment explanation
Indices: 42683355--42683401 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
42683345 ACTTAGGAAA
*
42683355 TTCTTATTTTTATTTTTTGTTTT
1 TTCTTA-TTTTATTTTTAGTTTT
* *
42683378 TTCTTCTTTTCTTTTTAGTTTT
1 TTCTTATTTTATTTTTAGTTTT
42683400 TT
1 TT
42683402 AATTATTAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.06, C:0.09, G:0.04, T:0.81
Consensus pattern (22 bp):
TTCTTATTTTATTTTTAGTTTT
Found at i:42685391 original size:18 final size:17
Alignment explanation
Indices: 42685347--42685394 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
42685337 GGTTTATTGA
*
42685347 TTTAGTTCATTTGTTTAT
1 TTTAGTT-ATTTATTTAT
**
42685365 TTTTCTTATTTATATTAT
1 TTTAGTTATTTAT-TTAT
42685383 TTTAGTTATTTA
1 TTTAGTTATTTA
42685395 GTTTTCTTTC
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
17 5 0.21
18 19 0.79
ACGTcount: A:0.21, C:0.04, G:0.06, T:0.69
Consensus pattern (17 bp):
TTTAGTTATTTATTTAT
Found at i:42685451 original size:3 final size:3
Alignment explanation
Indices: 42685443--42685514 Score: 144
Period size: 3 Copynumber: 24.0 Consensus size: 3
42685433 ATAGGGATTA
42685443 ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT
1 ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT
42685491 ACT ACT ACT ACT ACT ACT ACT ACT
1 ACT ACT ACT ACT ACT ACT ACT ACT
42685515 TAGACTTATT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ACT
Found at i:42686864 original size:45 final size:45
Alignment explanation
Indices: 42686815--42687033 Score: 296
Period size: 45 Copynumber: 4.9 Consensus size: 45
42686805 ATACCAGAAA
*
42686815 CGAGTAAGACCATGACTGAAAGACGTTATGGCATCACTATTCTAT
1 CGAGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTAT
* * *
42686860 CGAGTAAGACCATGACTAAAAGACGTTATGGAATCACAATTCTAT
1 CGAGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTAT
* * *
42686905 CAAGTAAGAACATGACTGAAAGACGTTATGGCATCACGATCCTAT
1 CGAGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTAT
* *
42686950 CGAGTATGACCATGACTGAATGACGTTATGGCATCACGATTCTAT
1 CGAGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTAT
* * ***
42686995 CGGGTAAGACCAT-AGCTAAAAGACACAATGGCATCACGA
1 CGAGTAAGACCATGA-CTGAAAGACGTTATGGCATCACGA
42687034 ATCAAAGGAA
Statistics
Matches: 152, Mismatches: 21, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
44 1 0.01
45 151 0.99
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (45 bp):
CGAGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTAT
Found at i:42687070 original size:135 final size:135
Alignment explanation
Indices: 42686815--42687072 Score: 315
Period size: 135 Copynumber: 1.9 Consensus size: 135
42686805 ATACCAGAAA
*
42686815 CGAGTAAGACCATGACTGAAAGACGTTATGGCATCACTATTCTATCGAGTAAGACCATGACTAAA
1 CGAGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTATCGAGTAAGACCATGACTAAA
*** * * **
42686880 AGACGTTATGGAATCACAATTCTATCAAGTAAGAACATGACTGAAAGACGTTATGGCATCACGAT
66 AGACACAATGGAATCACAATTCAAGCAAGTAAGAACATGACTGAAAGACACTATGGCATCACGAT
42686945 CCTAT
131 CCTAT
* * *
42686950 CGAGTATGACCATGACTGAATGACGTTATGGCATCACGATTCTATCGGGTAAGACCAT-AGCTAA
1 CGAGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTATCGAGTAAGACCATGA-CTAA
* * * ** *
42687014 AAGACACAATGGCATCACGAA-TCAAAGGAA-TAAGACCATGGGTGAAATACACTATGGCA
65 AAGACACAATGGAATCAC-AATTC-AAGCAAGTAAGAACATGACTGAAAGACACTATGGCA
42687073 ACTCGACAGA
Statistics
Matches: 103, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
134 1 0.01
135 97 0.94
136 5 0.05
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.22
Consensus pattern (135 bp):
CGAGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTATCGAGTAAGACCATGACTAAA
AGACACAATGGAATCACAATTCAAGCAAGTAAGAACATGACTGAAAGACACTATGGCATCACGAT
CCTAT
Found at i:42687071 original size:45 final size:47
Alignment explanation
Indices: 42686999--42687118 Score: 122
Period size: 47 Copynumber: 2.6 Consensus size: 47
42686989 TTCTATCGGG
* *
42686999 TAAGACCATAGCTAAAAGACACAATGGC-A-TC-AC-GAATCAAAGGAA
1 TAAGACCATGGCTGAAAGACACAATGGCAACTCGACAGAA--AAAGGAA
* * * *
42687044 TAAGACCATGGGTGAAATACACTATGGCAACTCGACAGAAAAATGAA
1 TAAGACCATGGCTGAAAGACACAATGGCAACTCGACAGAAAAAGGAA
* *
42687091 TAAGACCATGGTTGAAAGACACCATGGC
1 TAAGACCATGGCTGAAAGACACAATGGC
42687119 GCACTCCGAC
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
45 23 0.37
46 1 0.02
47 33 0.53
48 2 0.03
49 3 0.05
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.16
Consensus pattern (47 bp):
TAAGACCATGGCTGAAAGACACAATGGCAACTCGACAGAAAAAGGAA
Found at i:42694043 original size:49 final size:47
Alignment explanation
Indices: 42693983--42694394 Score: 619
Period size: 47 Copynumber: 8.6 Consensus size: 47
42693973 GATAATTGTG
* *
42693983 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
42694030 ATGTGAAAGTGTATATACATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATAT--ATGTGATAAGGCCTAATGGCCGATGTGATGA
*
42694079 ATGTGAAAGTGTATATATATGTGATAAGGTCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
42694128 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
42694175 ATGTGAAAGTGTATATATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG------TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
42694228 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
42694275 ATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * * * *
42694322 ATGTGAAAGTGTATATATGTGA-CAGAGCCGAGTGGCCAACGTGATGG
1 ATGTGAAAGTGTATATATGTGATAAG-GCCTAATGGCCGATGTGATGA
42694369 ATGTGAAAGTGTATATATGTGATAAG
1 ATGTGAAAGTGTATATATGTGATAAG
42694395 TCCCGAAGGG
Statistics
Matches: 339, Mismatches: 14, Indels: 23
0.90 0.04 0.06
Matches are distributed among these distances:
46 2 0.01
47 200 0.59
48 2 0.01
49 83 0.24
51 5 0.01
53 47 0.14
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (47 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:42694141 original size:147 final size:142
Alignment explanation
Indices: 42693983--42694394 Score: 630
Period size: 147 Copynumber: 2.9 Consensus size: 142
42693973 GATAATTGTG
* *
42693983 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAC
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA-
*
42694048 ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGTCTAA
65 ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAA
*
42694113 TGGCCGATGTGATGA
128 TAGCCGATGTGATGA
42694128 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG----TAT
42694193 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
62 ATA-ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
42694258 AATAGCCGATGTGATGA
126 AATAGCCGATGTGATGA
*
42694275 ATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT-A
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAA
* * * * * *
42694339 TGTGA-CAGAGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATATATGTGATAAG
66 TGTGATAAG-GCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
42694395 TCCCGAAGGG
Statistics
Matches: 250, Mismatches: 12, Indels: 14
0.91 0.04 0.05
Matches are distributed among these distances:
140 2 0.01
141 48 0.19
143 5 0.02
145 56 0.22
147 91 0.36
149 48 0.19
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (142 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAA
TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAG
CCGATGTGATGA
Found at i:42707608 original size:31 final size:31
Alignment explanation
Indices: 42707549--42707644 Score: 183
Period size: 31 Copynumber: 3.1 Consensus size: 31
42707539 GGCAAATTAC
42707549 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
42707581 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
42707612 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
42707643 AA
1 AA
42707645 ATTATCTAAG
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
31 44 0.69
32 20 0.31
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.31
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:42709804 original size:9 final size:9
Alignment explanation
Indices: 42709781--42709890 Score: 66
Period size: 9 Copynumber: 11.4 Consensus size: 9
42709771 AGGCAACTTT
42709781 TTTTTTTGC
1 TTTTTTTGC
42709790 TCTTTTTTGC
1 T-TTTTTTGC
42709800 --TTTTTGC
1 TTTTTTTGC
42709807 TTTTTTTTTGCGC
1 --TTTTTTT--GC
*
42709820 TTTTTACT-C
1 TTTTT-TTGC
42709829 TTTTTTTTACGC
1 -TTTTTTT--GC
42709841 -TTTTTTGC
1 TTTTTTTGC
*
42709849 TTTTTTTGT
1 TTTTTTTGC
42709858 TTTTTTTGC
1 TTTTTTTGC
*
42709867 TATTTTTGC
1 TTTTTTTGC
42709876 TGTTTTTTTGC
1 --TTTTTTTGC
42709887 TTTT
1 TTTT
42709891 ATTTAAAAAA
Statistics
Matches: 80, Mismatches: 6, Indels: 30
0.69 0.05 0.26
Matches are distributed among these distances:
7 7 0.09
8 2 0.03
9 30 0.38
10 19 0.24
11 18 0.22
12 2 0.03
13 2 0.03
ACGTcount: A:0.03, C:0.13, G:0.11, T:0.74
Consensus pattern (9 bp):
TTTTTTTGC
Found at i:42709804 original size:21 final size:20
Alignment explanation
Indices: 42709798--42709855 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 20
42709788 GCTCTTTTTT
*
42709798 GCTTTTTGCTTTTTTTTTGC
1 GCTTTTTGCTTTTTTTTTAC
*
42709818 GCTTTTTACTCTTTTTTTTAC
1 GCTTTTTGCT-TTTTTTTTAC
42709839 GCTTTTTTGCTTTTTTT
1 GC-TTTTTGCTTTTTTT
42709856 GTTTTTTTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 9 0.27
21 17 0.52
22 7 0.21
ACGTcount: A:0.03, C:0.16, G:0.10, T:0.71
Consensus pattern (20 bp):
GCTTTTTGCTTTTTTTTTAC
Found at i:42709832 original size:28 final size:28
Alignment explanation
Indices: 42709779--42709832 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
42709769 GTAGGCAACT
* *
42709779 TTTTTTTTTGCTCTTTTTTGCTTTTTGC
1 TTTTTTTTTGCGCTTTTTTACTTTTTGC
42709807 TTTTTTTTTGCGC-TTTTTACTCTTTT
1 TTTTTTTTTGCGCTTTTTTACT-TTTT
42709833 TTTTACGCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.02, C:0.15, G:0.09, T:0.74
Consensus pattern (28 bp):
TTTTTTTTTGCGCTTTTTTACTTTTTGC
Found at i:42709851 original size:49 final size:49
Alignment explanation
Indices: 42709780--42709884 Score: 131
Period size: 49 Copynumber: 2.1 Consensus size: 49
42709770 TAGGCAACTT
* * *
42709780 TTTTTTTTGCTCTTTTTTGCTTTTTGCT-TTTTTTTTGCGCTTTTTACTC
1 TTTTTTTTACGCTTTTTTGCTTTTT-CTGTTTTTTTTGCGATTTTTACTC
* * * *
42709829 TTTTTTTTACGCTTTTTTGCTTTTTTTGTTTTTTTTGCTATTTTTGCTG
1 TTTTTTTTACGCTTTTTTGCTTTTTCTGTTTTTTTTGCGATTTTTACTC
42709878 TTTTTTT
1 TTTTTTT
42709885 GCTTTTATTT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
48 1 0.02
49 47 0.98
ACGTcount: A:0.03, C:0.12, G:0.10, T:0.74
Consensus pattern (49 bp):
TTTTTTTTACGCTTTTTTGCTTTTTCTGTTTTTTTTGCGATTTTTACTC
Found at i:42710127 original size:16 final size:15
Alignment explanation
Indices: 42710104--42710135 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
42710094 AAAATTAGTT
42710104 AAATAATAAATAAAA
1 AAATAATAAATAAAA
42710119 AAATAAATAAATAAAA
1 AAAT-AATAAATAAAA
42710135 A
1 A
42710136 GGATAGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (15 bp):
AAATAATAAATAAAA
Found at i:42710531 original size:31 final size:31
Alignment explanation
Indices: 42710438--42710533 Score: 165
Period size: 31 Copynumber: 3.1 Consensus size: 31
42710428 GGAAAATTAC
*
42710438 AAGAGTAATTGAATCCTAATAAAACTCTTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
42710469 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
*
42710501 AAGAGTAATTGAATCATAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
42710532 AA
1 AA
42710534 ATTATCTAAG
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
31 33 0.53
32 29 0.47
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.31
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:42711700 original size:20 final size:19
Alignment explanation
Indices: 42711675--42711737 Score: 53
Period size: 18 Copynumber: 3.4 Consensus size: 19
42711665 TAAATATCTT
42711675 TAATATTATTAATAATTTGA
1 TAATATTATTAATAATTT-A
*
42711695 TAATA-T-TTAAT-ATATAA
1 TAATATTATTAATAAT-TTA
* *
42711712 TGATATTATTTATAATTTA
1 TAATATTATTAATAATTTA
42711731 T-ATATTA
1 TAATATTA
42711738 ATTTTTATCA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
17 7 0.20
18 13 0.37
19 8 0.23
20 7 0.20
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52
Consensus pattern (19 bp):
TAATATTATTAATAATTTA
Found at i:42713323 original size:10 final size:10
Alignment explanation
Indices: 42713310--42713339 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
42713300 AGTTTTATAG
42713310 TTAATTTTGA
1 TTAATTTTGA
42713320 TTAATTTTGA
1 TTAATTTTGA
42713330 TTAATTTTGA
1 TTAATTTTGA
42713340 CTATTTTCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.10, T:0.60
Consensus pattern (10 bp):
TTAATTTTGA
Found at i:42721674 original size:226 final size:226
Alignment explanation
Indices: 42721280--42721960 Score: 1326
Period size: 226 Copynumber: 3.0 Consensus size: 226
42721270 TAAAATAGGG
42721280 TCATACGACCATGTGGCTAGGCCATGTAAAGCAAGGTTACATGGTCATGTTGCCAAGTCCTATAA
1 TCATACGACCATGTGGCTAGGCCATGTAAAGCAAGGTTACATGGTCATGTTGCCAAGTCCTATAA
42721345 CAAACTGTGGTCGTGTGGACTTAAATGTAAAATCCTACAAACATTCGCACGGCCATATCGCCAAG
66 CAAACTGTGGTCGTGTGGACTTAAATGTAAAATCCTACAAACATTCGCACGGCCATATCGCCAAG
42721410 CCATGTGAGAGACTGTAATCAAGTTTAACCCAAACCACTATTATAATACAGAGCACATGGACATG
131 CCATGTGAGAGACTGTAATCAAGTTTAACCCAAACCACTATTATAATACAGAGCACATGGACATG
42721475 TCACTTGCCTGTGTGTGAGAAAATATGCCTT
196 TCACTTGCCTGTGTGTGAGAAAATATGCCTT
*
42721506 TCATACGACCATGTGGCTAGGCCATGTAAAGCAAGGTTACATGGTCATGGTGCCAAGTCCTATAA
1 TCATACGACCATGTGGCTAGGCCATGTAAAGCAAGGTTACATGGTCATGTTGCCAAGTCCTATAA
*
42721571 CAAACTGTGGTCGTGTGGACTTAAATGTAAAATCCTACAAACATTCGCACGGCTATATCGCCAAG
66 CAAACTGTGGTCGTGTGGACTTAAATGTAAAATCCTACAAACATTCGCACGGCCATATCGCCAAG
*
42721636 CCATGTGAGAGACTGTAATCAAGTTTAACCCAAACCACTATTATAATACAGAGCATATGGACATG
131 CCATGTGAGAGACTGTAATCAAGTTTAACCCAAACCACTATTATAATACAGAGCACATGGACATG
42721701 TCACTTGCCTGTGTGTGAGAAAATATGCCTT
196 TCACTTGCCTGTGTGTGAGAAAATATGCCTT
*
42721732 TCATACGACTATGTGGCTAGGCCATGTAAAGCAAGGTTACATGGTCATGTTGCCAAGTCCTATAA
1 TCATACGACCATGTGGCTAGGCCATGTAAAGCAAGGTTACATGGTCATGTTGCCAAGTCCTATAA
42721797 CAAACTGTGGTCGTGTGGACTTAAATGTAAAATCCTACAAACATTCGCACGGCCATATCGCCAAG
66 CAAACTGTGGTCGTGTGGACTTAAATGTAAAATCCTACAAACATTCGCACGGCCATATCGCCAAG
42721862 CCATGTGAGAGACTGTAATCAAGTTTAACCCAAACCACTATTATAATACAGAGCACATGGACATG
131 CCATGTGAGAGACTGTAATCAAGTTTAACCCAAACCACTATTATAATACAGAGCACATGGACATG
42721927 TCACTTGCCTGTGTGTGAGAAAATATGCCTT
196 TCACTTGCCTGTGTGTGAGAAAATATGCCTT
42721958 TCA
1 TCA
42721961 AATCAAGTCA
Statistics
Matches: 448, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
226 448 1.00
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (226 bp):
TCATACGACCATGTGGCTAGGCCATGTAAAGCAAGGTTACATGGTCATGTTGCCAAGTCCTATAA
CAAACTGTGGTCGTGTGGACTTAAATGTAAAATCCTACAAACATTCGCACGGCCATATCGCCAAG
CCATGTGAGAGACTGTAATCAAGTTTAACCCAAACCACTATTATAATACAGAGCACATGGACATG
TCACTTGCCTGTGTGTGAGAAAATATGCCTT
Found at i:42730847 original size:7 final size:6
Alignment explanation
Indices: 42730808--42730877 Score: 76
Period size: 6 Copynumber: 12.0 Consensus size: 6
42730798 GACCCCTTCT
* *
42730808 ATTAAA A-T-AA A-TAAA ACTAAT ATTAAA ATTAAA GATTAAA GATTAAA
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA -ATTAAA -ATTAAA
42730855 A-TAAA ATTAAA ATTAAA ATTAAA
1 ATTAAA ATTAAA ATTAAA ATTAAA
42730878 GACAAAGATA
Statistics
Matches: 57, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
4 4 0.07
5 9 0.16
6 31 0.54
7 13 0.23
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (6 bp):
ATTAAA
Found at i:42730892 original size:6 final size:7
Alignment explanation
Indices: 42730829--42730896 Score: 71
Period size: 6 Copynumber: 10.9 Consensus size: 7
42730819 TAAAACTAAT
42730829 ATTAAA-
1 ATTAAAG
42730835 ATTAAAG
1 ATTAAAG
42730842 ATTAAAG
1 ATTAAAG
42730849 ATTAAA-
1 ATTAAAG
42730855 A-TAAA-
1 ATTAAAG
42730860 ATTAAA-
1 ATTAAAG
42730866 ATTAAA-
1 ATTAAAG
42730872 ATTAAAG
1 ATTAAAG
*
42730879 A-CAAAG
1 ATTAAAG
42730885 A-TAAAG
1 ATTAAAG
42730891 ATTAAA
1 ATTAAA
42730897 ATGAGAAATA
Statistics
Matches: 56, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
5 5 0.09
6 33 0.59
7 18 0.32
ACGTcount: A:0.65, C:0.01, G:0.07, T:0.26
Consensus pattern (7 bp):
ATTAAAG
Found at i:42730898 original size:37 final size:37
Alignment explanation
Indices: 42730816--42730886 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
42730806 CTATTAAAAT
* * *
42730816 AAATAAAACTAATATTAAAATTAAAGATTAAAGATTA
1 AAATAAAATTAAAATTAAAATTAAAGATCAAAGATTA
42730853 AAATAAAATTAAAATTAAAATTAAAGA-CAAAGAT
1 AAATAAAATTAAAATTAAAATTAAAGATCAAAGAT
42730887 AAAGATTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
36 6 0.19
37 25 0.81
ACGTcount: A:0.65, C:0.03, G:0.06, T:0.27
Consensus pattern (37 bp):
AAATAAAATTAAAATTAAAATTAAAGATCAAAGATTA
Found at i:42735127 original size:20 final size:21
Alignment explanation
Indices: 42735102--42735142 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
42735092 TTGGACTAAA
* *
42735102 TCAGAAACTCA-GAGAATTTT
1 TCAGAAAATCATGAAAATTTT
42735122 TCAGAAAATCATGAAAATTTT
1 TCAGAAAATCATGAAAATTTT
42735143 CAACACTGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (21 bp):
TCAGAAAATCATGAAAATTTT
Found at i:42740169 original size:339 final size:341
Alignment explanation
Indices: 42739511--42740171 Score: 863
Period size: 339 Copynumber: 1.9 Consensus size: 341
42739501 GGATGATTAG
* *
42739511 GTAACATTTAACGTCTTTAAGTCTATGTAGTTTCTTGACACAATAGATGATTGCTCTGTAGTGTC
1 GTAACATTTAACGTCTTTAAGTCTATGGAGTTTCCTGACACAATAGATGATTGCTCTGTAGTGTC
* * * *
42739576 CAATTTAGAGGATTTAATAGTGGAGAAGGAACTAAACTATGTTGAGGGCCCACTGGAAAGAATTT
66 CAATTTAGAGGAATTAATAATGGAAAAGGAACTAAACTATGTTGAGGACCCACTGGAAAGAATTT
** * * *
42739641 TGACATTGGATCCTCCAAATGATGAAGAGGAGGATGAATACTTAGCTTTGCTAGAAGCTAATCAA
131 TGACATCAGACCCTCCAAATGATGAAGAGGAGGACGAATACTTAGCTTTGCTAGAAGATAATCAA
** * * *
42739706 AGGGGATTTAATCCACAATCCTGTTTTGAATCTTTGGAGTTAGAAAAGAGGGACTATTCTCAACC
196 AGCAGATTTAATCCACAATCCCGTTTTGAATCTCTGGAGTTAGAAAAGAGGGACTATCCTCAACC
* * * * *
42739771 AAAAGCATCGATCAAAGAGCCACCTAAATTAGAACTCAAGGTATTACCTTCTCATTTAAAATGCG
261 AAAAGCATCAATCAAAGAGCAACATAAATTAGAACTCAAAGTATTACCCTCTCATTTAAAATGCG
42739836 TATTCAGGACGACCAA
326 TATTCAGGACGACCAA
* * * * *
42739852 GTAACATTTAATGTTTTTAAGTCT-TGCGA-TTTCCTGACACAATTGATTATTGTTCTGTAGTGT
1 GTAACATTTAACGTCTTTAAGTCTATG-GAGTTTCCTGACACAATAGATGATTGCTCTGTAGTGT
* * *
42739915 CTAATTTAGAGGAATTAATAATGGAAAAGGAACTCAACTATGTTGAGGACCCA-TTGAACA-AAT
65 CCAATTTAGAGGAATTAATAATGGAAAAGGAACTAAACTATGTTGAGGACCCACTGGAA-AGAAT
*
42739978 TTTGACATCAGACCCTCCGAATGATGAAGAGGAGGACGAATACTTAGCTTTGCTAGAAGATAATC
129 TTTGACATCAGACCCTCCAAATGATGAAGAGGAGGACGAATACTTAGCTTTGCTAGAAGATAATC
* * *
42740043 AAAGCAGATTTAATCTACAATCCCGTTTTGAATCTCTGGAGTTA-AAGAATAGGGATTATGCCT-
194 AAAGCAGATTTAATCCACAATCCCGTTTTGAATCTCTGGAGTTAGAA-AAGAGGGACTAT-CCTC
* * * *
42740106 AACCAAAAG-AGTCAATCGAGGAGCAACATAAATTAGAATTGAAAGTACTT-CCCTCAT-ATTTA
257 AACCAAAAGCA-TCAATCAAAGAGCAACATAAATTAGAACTCAAAGTA-TTACCCTC-TCATTTA
42740168 AAAT
319 AAAT
42740172 ATGTTTATTT
Statistics
Matches: 276, Mismatches: 37, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
338 3 0.01
339 165 0.60
340 85 0.31
341 23 0.08
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.30
Consensus pattern (341 bp):
GTAACATTTAACGTCTTTAAGTCTATGGAGTTTCCTGACACAATAGATGATTGCTCTGTAGTGTC
CAATTTAGAGGAATTAATAATGGAAAAGGAACTAAACTATGTTGAGGACCCACTGGAAAGAATTT
TGACATCAGACCCTCCAAATGATGAAGAGGAGGACGAATACTTAGCTTTGCTAGAAGATAATCAA
AGCAGATTTAATCCACAATCCCGTTTTGAATCTCTGGAGTTAGAAAAGAGGGACTATCCTCAACC
AAAAGCATCAATCAAAGAGCAACATAAATTAGAACTCAAAGTATTACCCTCTCATTTAAAATGCG
TATTCAGGACGACCAA
Found at i:42743430 original size:24 final size:22
Alignment explanation
Indices: 42743385--42743428 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
42743375 TGATAATCAT
42743385 TAATATATAATTATATCTATTA
1 TAATATATAATTATATCTATTA
42743407 TAATATATATATTA-AT-TATTA
1 TAATATATA-ATTATATCTATTA
42743428 T
1 T
42743429 TAACTTTGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 6 0.29
22 11 0.52
23 4 0.19
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
TAATATATAATTATATCTATTA
Found at i:42743948 original size:8 final size:8
Alignment explanation
Indices: 42743935--42743972 Score: 51
Period size: 8 Copynumber: 4.6 Consensus size: 8
42743925 AATTTTAATT
42743935 TTATTTAA
1 TTATTTAA
42743943 TTATTTAA
1 TTATTTAA
42743951 TT-TTTAAA
1 TTATTT-AA
42743959 GTTATTTAA
1 -TTATTTAA
42743968 TTATT
1 TTATT
42743973 AATGTTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
7 3 0.11
8 17 0.63
9 4 0.15
10 3 0.11
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (8 bp):
TTATTTAA
Found at i:42743991 original size:24 final size:25
Alignment explanation
Indices: 42743939--42743991 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
42743929 TTAATTTTAT
*
42743939 TTAATTATTTAATTTTTAAAGTTAT
1 TTAATTATTTAATTTTTAAAGTTAA
*
42743964 TTAATTA-TTAATGTTTTATA-TTAA
1 TTAATTATTTAAT-TTTTAAAGTTAA
42743988 TTAA
1 TTAA
42743992 ATTTTTGTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 12 0.48
25 13 0.52
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (25 bp):
TTAATTATTTAATTTTTAAAGTTAA
Found at i:42743994 original size:25 final size:25
Alignment explanation
Indices: 42743935--42743994 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
42743925 AATTTTAATT
*
42743935 TTATTTAATTATTTAATTTTTAAAG
1 TTATTAAATTATTTAATTTTTAAAG
* *
42743960 TTATTTAATTA-TTAATGTTTTATA-
1 TTATTAAATTATTTAAT-TTTTAAAG
42743984 TTAATTAAATT
1 TT-ATTAAATT
42743995 TTTGTGAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 7 0.23
25 24 0.77
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (25 bp):
TTATTAAATTATTTAATTTTTAAAG
Found at i:42744874 original size:3 final size:3
Alignment explanation
Indices: 42744866--42744890 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
42744856 GAGGATCCTA
42744866 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
42744891 TCCCACAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:42750720 original size:51 final size:52
Alignment explanation
Indices: 42750607--42750731 Score: 175
Period size: 51 Copynumber: 2.4 Consensus size: 52
42750597 TGACTCAAAT
*
42750607 GTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTCACAAGT
1 GTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTCACAAGG
* * *
42750659 GTAGTGCTATGTGAAGGCCACTTTGTGAAG-AAGGTAGCTTTGG-CTACAAGG
1 GTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTC-ACAAGG
42750710 GTGGTACTATGTGCAA-GCCACT
1 GTGGTACTATGTG-AAGGCCACT
42750732 GGGTATCTGT
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
50 1 0.02
51 34 0.52
52 30 0.46
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.28
Consensus pattern (52 bp):
GTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTCACAAGG
Found at i:42753244 original size:30 final size:30
Alignment explanation
Indices: 42753210--42753285 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 30
42753200 TGGTTGACCC
* * * *
42753210 ATCCCTTTTCGTAATTCGATAACTAAAGTT
1 ATCCCTTTTCATAATTCGACAACCAAAGCT
*
42753240 ATCCCTTTTCATAGTTCGACAACCAAAGCT
1 ATCCCTTTTCATAATTCGACAACCAAAGCT
42753270 ATCCCTTTTCATAATT
1 ATCCCTTTTCATAATT
42753286 TGATGGTGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.29, C:0.25, G:0.08, T:0.38
Consensus pattern (30 bp):
ATCCCTTTTCATAATTCGACAACCAAAGCT
Found at i:42753397 original size:60 final size:61
Alignment explanation
Indices: 42753210--42753439 Score: 166
Period size: 60 Copynumber: 3.8 Consensus size: 61
42753200 TGGTTGACCC
* * * * * * *
42753210 ATCCCTTTTCGTAATTCGATAACT-AAAGTTATCCCTTTTCATAGTTCGACAACCAAAGCT
1 ATCCCTTTTCATAATTCGATAGCTCGAAGCTATCCCTTTTCATAGTTCGATAGCCGAAGCT
* * * * * * * ** * *
42753270 ATCCCTTTTCATAATTTGAT-GGTGGTCACCT-TCCCTTTTCATTGTTCGATGGTTGTCA-CC
1 ATCCCTTTTCATAATTCGATAGCTCG-AAGCTATCCCTTTTCATAGTTCGATAGCCG-AAGCT
* * * *
42753330 ATGCCTTTTTATAATTTGATAGCT-GAAGCTATCCCTTTCCATAGTTCGATAGCCGAAGCT
1 ATCCCTTTTCATAATTCGATAGCTCGAAGCTATCCCTTTTCATAGTTCGATAGCCGAAGCT
* * * *
42753390 ATCCCTTTTCATAGTTCAATAG-TCGGAGCCATCCCTTTTCATAGTTCGAT
1 ATCCCTTTTCATAATTCGATAGCTCGAAGCTATCCCTTTTCATAGTTCGAT
42753440 GGTCGTCACC
Statistics
Matches: 126, Mismatches: 37, Indels: 14
0.71 0.21 0.08
Matches are distributed among these distances:
59 6 0.05
60 115 0.91
61 5 0.04
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.38
Consensus pattern (61 bp):
ATCCCTTTTCATAATTCGATAGCTCGAAGCTATCCCTTTTCATAGTTCGATAGCCGAAGCT
Found at i:42753426 original size:120 final size:119
Alignment explanation
Indices: 42753198--42753459 Score: 312
Period size: 120 Copynumber: 2.2 Consensus size: 119
42753188 GTAATAATAT
* * * *
42753198 GATGGTTGAC-CCATCCCTTTTCGTAATTCGATAACTAAAGTTATCCCTTTTCATAGTTCGACAA
1 GATGGTTGTCACCATCCCTTTTCATAATTCGATAACTAAAGCTATCCCTTTCCATAGTTCGACAA
** * * *
42753262 CCAAAGCTATCCCTTTTCATAATTTGATGGTGGTCACCTTCCCTTTTCATTGTTC
66 CCAAAGCTATCCCTTTTCATAATTCAATAGTGG-CACCATCCCTTTTCATAGTTC
* * * * * * *
42753317 GATGGTTGTCACCATGCCTTTTTATAATTTGATAGCTGAAGCTATCCCTTTCCATAGTTCGATAG
1 GATGGTTGTCACCATCCCTTTTCATAATTCGATAACTAAAGCTATCCCTTTCCATAGTTCGACAA
* *
42753382 CCGAAGCTATCCCTTTTCATAGTTCAATAGTCGG-AGCCATCCCTTTTCATAGTTC
66 CCAAAGCTATCCCTTTTCATAATTCAATAGT-GGCA-CCATCCCTTTTCATAGTTC
*
42753437 GATGGTCGTCACCATCCCTTTTC
1 GATGGTTGTCACCATCCCTTTTC
42753460 TTTGTTGATG
Statistics
Matches: 119, Mismatches: 21, Indels: 5
0.82 0.14 0.03
Matches are distributed among these distances:
119 10 0.08
120 107 0.90
121 2 0.02
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (119 bp):
GATGGTTGTCACCATCCCTTTTCATAATTCGATAACTAAAGCTATCCCTTTCCATAGTTCGACAA
CCAAAGCTATCCCTTTTCATAATTCAATAGTGGCACCATCCCTTTTCATAGTTC
Found at i:42753477 original size:29 final size:30
Alignment explanation
Indices: 42753270--42753491 Score: 157
Period size: 30 Copynumber: 7.4 Consensus size: 30
42753260 AACCAAAGCT
* * *
42753270 ATCCCTTTTCATAATTTGATGGTGGTCACC
1 ATCCCTTTTCATAGTTCGATGGTCGTCACC
* * *
42753300 TTCCCTTTTCATTGTTCGATGGTTGTCACC
1 ATCCCTTTTCATAGTTCGATGGTCGTCACC
* * * * * * *
42753330 ATGCCTTTTTATAATTTGATAG-C-TGAAGCT
1 ATCCCTTTTCATAGTTCGATGGTCGT-CA-CC
* * * * *
42753360 ATCCCTTTCCATAGTTCGATAGCCG-AAGCT
1 ATCCCTTTTCATAGTTCGATGGTCGTCA-CC
* * *
42753390 ATCCCTTTTCATAGTTCAATAGTCG-GAGCC
1 ATCCCTTTTCATAGTTCGATGGTCGTCA-CC
42753420 ATCCCTTTTCATAGTTCGATGGTCGTCACC
1 ATCCCTTTTCATAGTTCGATGGTCGTCACC
* *
42753450 ATCCCTTTTCTTTGTT-GATGGTCGTCACC
1 ATCCCTTTTCATAGTTCGATGGTCGTCACC
*
42753479 ATCCCTTTGCATA
1 ATCCCTTTTCATA
42753492 ATCTATAGCC
Statistics
Matches: 154, Mismatches: 33, Indels: 11
0.78 0.17 0.06
Matches are distributed among these distances:
28 1 0.01
29 24 0.16
30 127 0.82
31 2 0.01
ACGTcount: A:0.19, C:0.26, G:0.16, T:0.39
Consensus pattern (30 bp):
ATCCCTTTTCATAGTTCGATGGTCGTCACC
Found at i:42759409 original size:7 final size:6
Alignment explanation
Indices: 42759372--42759486 Score: 52
Period size: 6 Copynumber: 18.0 Consensus size: 6
42759362 ATCAAAAAAG
* * ** *
42759372 AAGAAA AAGAAA AGGCAA GTGAAA AAGAAA AAGAAA AAAAAGA GAATGAAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAA-A -AA-GAAA
* ** * * *
42759423 ATGAGAAA AAGAAA AAG-AG AAGTGA GAGAAA ACGAAA ACGAAA AAGAGAA
1 A--AGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGA-AA
42759473 AATTGAAA AAGAAA
1 AA--GAAA AAGAAA
42759487 TTGAGATTGA
Statistics
Matches: 82, Mismatches: 18, Indels: 18
0.69 0.15 0.15
Matches are distributed among these distances:
5 4 0.05
6 55 0.67
7 6 0.07
8 12 0.15
9 5 0.06
ACGTcount: A:0.70, C:0.03, G:0.23, T:0.05
Consensus pattern (6 bp):
AAGAAA
Found at i:42759411 original size:27 final size:26
Alignment explanation
Indices: 42759366--42759486 Score: 70
Period size: 27 Copynumber: 4.3 Consensus size: 26
42759356 AATAAAATCA
*
42759366 AAAAAGAAGAAA-AAGAAAAG-GCAAGTG
1 AAAAAGAA-AAAGAAAAAAAGAG-AA-TG
42759393 AAAAAGAAAAAGAAAAAAAAGAGAATG
1 AAAAAGAAAAAG-AAAAAAAGAGAATG
42759420 AAAATGAGAAAAAG--AAAAAGAGAAGTGAG
1 AAAA--AGAAAAAGAAAAAAAGAGAA-T--G
* * *
42759449 AGAAAACGAAAACGAAAAAGAGAAAATTG
1 A-AAAA-GAAAAAGAAAAAAAGAGAA-TG
42759478 AAAAAGAAA
1 AAAAAGAAA
42759487 TTGAGATTGA
Statistics
Matches: 77, Mismatches: 5, Indels: 24
0.73 0.05 0.23
Matches are distributed among these distances:
26 13 0.17
27 19 0.25
28 14 0.18
29 19 0.25
30 3 0.04
31 9 0.12
ACGTcount: A:0.70, C:0.02, G:0.22, T:0.05
Consensus pattern (26 bp):
AAAAAGAAAAAGAAAAAAAGAGAATG
Found at i:42759492 original size:21 final size:20
Alignment explanation
Indices: 42759392--42759492 Score: 76
Period size: 21 Copynumber: 4.8 Consensus size: 20
42759382 AAAGGCAAGT
* *
42759392 GAAAAAGAAAAAGAAAAAAAA
1 GAAAAAGAAAATG-AGAAAAA
* *
42759413 GAGAATGAAAATGAGAAAAA
1 GAAAAAGAAAATGAGAAAAA
*
42759433 GAAAAAGAGAAGTGAGAGAAAA
1 GAAAAAGA-AAATGAGA-AAAA
* * *
42759455 CGAAAACGAAAAAGAGAAAATT
1 -GAAAAAGAAAATGAGAAAA-A
*
42759477 GAAAAAGAAATTGAGA
1 GAAAAAGAAAATGAGA
42759493 TTGAGAAAGG
Statistics
Matches: 62, Mismatches: 14, Indels: 8
0.74 0.17 0.10
Matches are distributed among these distances:
20 12 0.19
21 33 0.53
22 10 0.16
23 7 0.11
ACGTcount: A:0.68, C:0.02, G:0.23, T:0.07
Consensus pattern (20 bp):
GAAAAAGAAAATGAGAAAAA
Found at i:42763541 original size:40 final size:40
Alignment explanation
Indices: 42763482--42763732 Score: 285
Period size: 40 Copynumber: 6.3 Consensus size: 40
42763472 CATTTGAATG
*
42763482 ATATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
* * * *
42763522 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAG-TGATT
* * *
42763562 ATACCCGAGTTAAGACCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
* * * *
42763602 TTATCCGAGTTAAAACCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
* * * *
42763642 TTATCCAGGCTAAGA-CCGAAGGCATTTGTGCGAGTTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAG-TGATT
* * *
42763681 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
42763721 ATATCC-GGCTAA
1 ATATCCGGGCTAA
42763733 ATTCCGAAGA
Statistics
Matches: 180, Mismatches: 26, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
39 41 0.23
40 137 0.76
41 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
Found at i:42763726 original size:119 final size:120
Alignment explanation
Indices: 42763497--42763727 Score: 374
Period size: 119 Copynumber: 1.9 Consensus size: 120
42763487 CGGGCTAAGT
* *
42763497 CCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 CCCGAAGGCAATTGTGCTAGTGATTTTATCCAGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
* *
42763562 ATACCCGAGTTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGAGTTAAAA
66 ATACCCGAGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATATCCGAGTTAAAA
42763617 CCCGAAGGCAATTGTGCTAGTGATTTTATCCAGGCTAAGA-CCGAAGGCATTTGTGCGAGTTGAT
1 CCCGAAGGCAATTGTGCTAGTGATTTTATCCAGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
* * * * *
42763681 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTTGTGGTTATATCCG
66 ATACCCGAGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATATCCG
42763728 GCTAAATTCC
Statistics
Matches: 102, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
119 63 0.62
120 39 0.38
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (120 bp):
CCCGAAGGCAATTGTGCTAGTGATTTTATCCAGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
ATACCCGAGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATATCCGAGTTAAAA
Found at i:42779732 original size:60 final size:60
Alignment explanation
Indices: 42779668--42779842 Score: 242
Period size: 60 Copynumber: 2.9 Consensus size: 60
42779658 GTAAAATCAC
* * * * *
42779668 GATGGTTGTCACTATCCCTTATCATAGTTTGATAGCCGAAGCTATCCCTTTTCATAATTT
1 GATGGTCGTCACCATCCCTTTTCATAATTTGATAGCTGAAGCTATCCCTTTTCATAATTT
* * *
42779728 GATGGTCGTCACCAACCCTTTTCATAATTTGATAGTTGAAGTTATCCCTTTTCATAATTT
1 GATGGTCGTCACCATCCCTTTTCATAATTTGATAGCTGAAGCTATCCCTTTTCATAATTT
* * **
42779788 GATGGTCGTCACCATTCATTTTCATAATCCGATAGCTGAAGCTATCCCTTTTCAT
1 GATGGTCGTCACCATCCCTTTTCATAATTTGATAGCTGAAGCTATCCCTTTTCAT
42779843 TGGTCGATGA
Statistics
Matches: 100, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 100 1.00
ACGTcount: A:0.24, C:0.22, G:0.14, T:0.39
Consensus pattern (60 bp):
GATGGTCGTCACCATCCCTTTTCATAATTTGATAGCTGAAGCTATCCCTTTTCATAATTT
Found at i:42779747 original size:30 final size:30
Alignment explanation
Indices: 42779711--42779815 Score: 122
Period size: 30 Copynumber: 3.5 Consensus size: 30
42779701 AGCCGAAGCT
42779711 ATCCCTTTTCATAATTTGATGGTCGTCACC
1 ATCCCTTTTCATAATTTGATGGTCGTCACC
* * * * **
42779741 AACCCTTTTCATAATTTGATAGTTG-AAGTT
1 ATCCCTTTTCATAATTTGATGGTCGTCA-CC
42779771 ATCCCTTTTCATAATTTGATGGTCGTCACC
1 ATCCCTTTTCATAATTTGATGGTCGTCACC
* *
42779801 ATTCATTTTCATAAT
1 ATCCCTTTTCATAAT
42779816 CCGATAGCTG
Statistics
Matches: 59, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
29 1 0.02
30 57 0.97
31 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.11, T:0.43
Consensus pattern (30 bp):
ATCCCTTTTCATAATTTGATGGTCGTCACC
Found at i:42789868 original size:19 final size:20
Alignment explanation
Indices: 42789826--42789868 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
42789816 TCATGCTTTC
*
42789826 TATTCACATTTTCATATTCA
1 TATTCACATTTTCAAATTCA
42789846 -ATTCACATTTTCAAATT-A
1 TATTCACATTTTCAAATTCA
42789864 TATTC
1 TATTC
42789869 CACTTAGTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 20 0.95
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.49
Consensus pattern (20 bp):
TATTCACATTTTCAAATTCA
Found at i:42790107 original size:51 final size:50
Alignment explanation
Indices: 42789991--42790186 Score: 187
Period size: 51 Copynumber: 3.9 Consensus size: 50
42789981 TCAATGGTAC
* * * *
42789991 CCGGTTCACATAGTAGCCTACACATAGTACTACACATGTGACCATTTTTAT
1 CCGGTACACATAGTAGCCTACACATAGTACTACACACGTGACCA-ATCTAT
* * * * * *
42790042 CTGATACACGTAGTAGCCTGCACATAGTACTACACACGTGATCGAAGCTAT
1 CCGGTACACATAGTAGCCTACACATAGTACTACACACGTGA-CCAATCTAT
* * * * * * * *
42790093 CCGGTACGCATAGTACCCTACACATAGAATTACACATGCGGCCCATC-ATT
1 CCGGTACACATAGTAGCCTACACATAGTACTACACACGTGACCAATCTA-T
*
42790143 CCGGTACACATAGTAGCCTGCACATAGTACTACACACGTGACCA
1 CCGGTACACATAGTAGCCTACACATAGTACTACACACGTGACCA
42790187 TCACTTCTGT
Statistics
Matches: 110, Mismatches: 33, Indels: 5
0.74 0.22 0.03
Matches are distributed among these distances:
49 1 0.01
50 39 0.35
51 68 0.62
52 2 0.02
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.24
Consensus pattern (50 bp):
CCGGTACACATAGTAGCCTACACATAGTACTACACACGTGACCAATCTAT
Found at i:42796353 original size:27 final size:27
Alignment explanation
Indices: 42796322--42796529 Score: 267
Period size: 27 Copynumber: 7.7 Consensus size: 27
42796312 ATAATGGGCC
* * *
42796322 TAAAATTATCGAAATACCCTTAATGGC
1 TAAAATTACCGAAATACCCTCAATGGG
* *
42796349 TAAAATTATCGAAATACCCTCAAAGGG
1 TAAAATTACCGAAATACCCTCAATGGG
42796376 TAAAATTACCGAAATACCCTCAATGGG
1 TAAAATTACCGAAATACCCTCAATGGG
**
42796403 TAAAATTATGGAAATACCCTCAATGGG
1 TAAAATTACCGAAATACCCTCAATGGG
*
42796430 TAAAATTACCAAAATACCCTCAATGGG
1 TAAAATTACCGAAATACCCTCAATGGG
42796457 TAAAATTACCGAAATACTCC-CGAA-GGG
1 TAAAATTACCGAAATAC-CCTC-AATGGG
* * * *
42796484 TAAAATGACTGAAATACCCTCGATAGG
1 TAAAATTACCGAAATACCCTCAATGGG
*
42796511 TGAAATTACCGAAATACCC
1 TAAAATTACCGAAATACCC
42796530 CTAAAAGGTA
Statistics
Matches: 159, Mismatches: 18, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
26 3 0.02
27 152 0.96
28 4 0.03
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.23
Consensus pattern (27 bp):
TAAAATTACCGAAATACCCTCAATGGG
Found at i:42796749 original size:26 final size:26
Alignment explanation
Indices: 42796720--42796769 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
42796710 TTGCCACATA
*
42796720 TACTGTTACTTGCAGCCTTGCTGCGT
1 TACTGTTACTAGCAGCCTTGCTGCGT
*
42796746 TACTGTTACTAGCAGCTTTGCTGC
1 TACTGTTACTAGCAGCCTTGCTGC
42796770 ATCATTATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.14, C:0.26, G:0.22, T:0.38
Consensus pattern (26 bp):
TACTGTTACTAGCAGCCTTGCTGCGT
Found at i:42804021 original size:16 final size:15
Alignment explanation
Indices: 42803994--42804027 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
42803984 ATAATTAGTA
*
42803994 TATAATTATATTTAT
1 TATAATTATATTAAT
42804009 TATAATATATATTAAT
1 TATAAT-TATATTAAT
42804025 TAT
1 TAT
42804028 TATGAACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATAATTATATTAAT
Found at i:42807419 original size:45 final size:45
Alignment explanation
Indices: 42807352--42807439 Score: 158
Period size: 45 Copynumber: 2.0 Consensus size: 45
42807342 CTATTTTTGT
*
42807352 TATCATAAGAATAGTTGGGACTAATTTGAATGACATGTATACTGC
1 TATCATAAGAATAGTTGAGACTAATTTGAATGACATGTATACTGC
*
42807397 TATCATAAGAATAGTTGAGACTAATTTGAATGATATGTATACT
1 TATCATAAGAATAGTTGAGACTAATTTGAATGACATGTATACT
42807440 TAAGTAGCAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (45 bp):
TATCATAAGAATAGTTGAGACTAATTTGAATGACATGTATACTGC
Found at i:42809561 original size:12 final size:12
Alignment explanation
Indices: 42809544--42809570 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
42809534 TATAGTATCA
42809544 AGTTCTAATATG
1 AGTTCTAATATG
42809556 AGTTCTAATATG
1 AGTTCTAATATG
42809568 AGT
1 AGT
42809571 CTTAAATCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.19, T:0.41
Consensus pattern (12 bp):
AGTTCTAATATG
Found at i:42810754 original size:13 final size:13
Alignment explanation
Indices: 42810718--42810756 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
42810708 TTTAGTTTTG
*
42810718 TAATTTGAAAGCT
1 TAATTTGAAAACT
42810731 TAAGTTTTGAAAACT
1 TAA--TTTGAAAACT
42810746 TAATTTGAAAA
1 TAATTTGAAAA
42810757 TTTGAAAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 11 0.48
15 12 0.52
ACGTcount: A:0.44, C:0.05, G:0.13, T:0.38
Consensus pattern (13 bp):
TAATTTGAAAACT
Found at i:42811049 original size:34 final size:34
Alignment explanation
Indices: 42811011--42811175 Score: 177
Period size: 34 Copynumber: 4.8 Consensus size: 34
42811001 TCACTTTTCT
* *
42811011 TTTCTTGTAGGGAATCTCTCTTGTTCACACATCA
1 TTTCTTGCAGGGAATCTCTCCTGTTCACACATCA
** ** *
42811045 TTTCTTATAGGGAATCTCTCCTGTTCACGTATTA
1 TTTCTTGCAGGGAATCTCTCCTGTTCACACATCA
* *
42811079 TTTTGTTGCAGGGAATCTCTCCTATTCACACATCA
1 -TTTCTTGCAGGGAATCTCTCCTGTTCACACATCA
* *
42811114 TTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
1 TTTCTTGCAGGGAATCTCTCCTGTTCACACATCA
* * * *
42811148 TGTTGTTACAGGGAATCTATCCAGTTCA
1 T-TTCTTGCAGGGAATCTCTCCTGTTCA
42811176 TGTATCATTT
Statistics
Matches: 109, Mismatches: 20, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
34 60 0.55
35 49 0.45
ACGTcount: A:0.21, C:0.23, G:0.16, T:0.39
Consensus pattern (34 bp):
TTTCTTGCAGGGAATCTCTCCTGTTCACACATCA
Found at i:42811130 original size:69 final size:69
Alignment explanation
Indices: 42811010--42811165 Score: 231
Period size: 69 Copynumber: 2.3 Consensus size: 69
42811000 TTCACTTTTC
* * * * * *
42811010 TTTTCTTGTAGGGAATCTCTCTTGTTCACACATCATTTCTTATAGGGAATCTCTCCTGTTCACGT
1 TTTTGTTGCAGGGAATCTCTCCTATTCACACATCATTTCTTACAGGGAATCTCTCCTGTTCACGC
42811075 ATTA
66 ATTA
*
42811079 TTTTGTTGCAGGGAATCTCTCCTATTCACACATCATTTCTTGCAGGGAATCTCTCCTGTTCACGC
1 TTTTGTTGCAGGGAATCTCTCCTATTCACACATCATTTCTTACAGGGAATCTCTCCTGTTCACGC
42811144 ATTA
66 ATTA
* *
42811148 TGTTGTTACAGGGAATCT
1 TTTTGTTGCAGGGAATCT
42811166 ATCCAGTTCA
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 78 1.00
ACGTcount: A:0.21, C:0.22, G:0.17, T:0.40
Consensus pattern (69 bp):
TTTTGTTGCAGGGAATCTCTCCTATTCACACATCATTTCTTACAGGGAATCTCTCCTGTTCACGC
ATTA
Found at i:42814641 original size:108 final size:106
Alignment explanation
Indices: 42814476--42814690 Score: 396
Period size: 108 Copynumber: 2.0 Consensus size: 106
42814466 ATTTTCTTCA
42814476 GGTTCAGGTTCAGGTTCAGTTTCTGATGAACTTTTTCTGAGGTTTCGTGTTTTAAGGACTTATTT
1 GGTTCAGGTTCAGGTTCAGTTTCTGATGAACTTTTTCTGAGGTTTCGTGTTTTAAGGAC-TATTT
42814541 GTTCTTTCATTTCTTGGTTGTTCTATTTAAGCTGAGAAAGTTCT
65 GTTCTTTCATTTCTT-GTTGTTCTATTTAAGC-GAGAAAGTTCT
42814585 GGTTCAGGTTCAGGTTCAGTTTCTGATG-ACTTTTTCTGAGGTTTCGTGTTTTAAGGACTATTTG
1 GGTTCAGGTTCAGGTTCAGTTTCTGATGAACTTTTTCTGAGGTTTCGTGTTTTAAGGACTATTTG
42814649 TTCTTTCATTTCTTGTTGTTCTATTTAAGCGAGAAAGTTCT
66 TTCTTTCATTTCTTGTTGTTCTATTTAAGCGAGAAAGTTCT
42814690 G
1 G
42814691 ATTTAATCTG
Statistics
Matches: 106, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
105 12 0.11
106 16 0.15
107 20 0.19
108 30 0.28
109 28 0.26
ACGTcount: A:0.17, C:0.13, G:0.22, T:0.47
Consensus pattern (106 bp):
GGTTCAGGTTCAGGTTCAGTTTCTGATGAACTTTTTCTGAGGTTTCGTGTTTTAAGGACTATTTG
TTCTTTCATTTCTTGTTGTTCTATTTAAGCGAGAAAGTTCT
Found at i:42818174 original size:29 final size:29
Alignment explanation
Indices: 42818136--42818477 Score: 302
Period size: 29 Copynumber: 11.8 Consensus size: 29
42818126 ATCGATTAAA
* *
42818136 GAAAATGGATAGTTTCGACCATCGACTAT
1 GAAAAGGGATGGTTTCGACCATCGACTAT
** * *
42818165 GAAAAGGGATGGTAACGACCATCAACAAT
1 GAAAAGGGATGGTTTCGACCATCGACTAT
* *
42818194 GAAAAGGGATGGTGAT-GACCATCAACTAT
1 GAAAAGGGATGGT-TTCGACCATCGACTAT
** ** *
42818223 GAAAAGGGATGGTGACGACCATAAAATAT
1 GAAAAGGGATGGTTTCGACCATCGACTAT
* * *
42818252 GAAAAGGGATAGTTTCGACTATCAACTAT
1 GAAAAGGGATGGTTTCGACCATCGACTAT
* * *
42818281 GAAAAGGGATGGTGAT-GATCATCGAATAT
1 GAAAAGGGATGGT-TTCGACCATCGACTAT
* * *
42818310 GAAAAGGGAT-GTTTTGACTATTGACTAT
1 GAAAAGGGATGGTTTCGACCATCGACTAT
* * *
42818338 GAAAAGGGATGGTGAT-GACCATCAAATAT
1 GAAAAGGGATGGT-TTCGACCATCGACTAT
*
42818367 GAAAAGGGA-GAGTTTCGACTATCGACTAT
1 GAAAAGGGATG-GTTTCGACCATCGACTAT
* * *
42818396 GAAAAGGGATGGTGAT-GACCATTGATTAT
1 GAAAAGGGATGGT-TTCGACCATCGACTAT
* *
42818425 GAAAAGGGATGGTTCCGACCATCGAATAT
1 GAAAAGGGATGGTTTCGACCATCGACTAT
42818454 GAAAAGGGATGGTTAT-GACCATCG
1 GAAAAGGGATGGTT-TCGACCATCG
42818478 TTTAGCACAC
Statistics
Matches: 254, Mismatches: 47, Indels: 24
0.78 0.14 0.07
Matches are distributed among these distances:
27 1 0.00
28 23 0.09
29 225 0.89
30 5 0.02
ACGTcount: A:0.37, C:0.12, G:0.27, T:0.23
Consensus pattern (29 bp):
GAAAAGGGATGGTTTCGACCATCGACTAT
Found at i:42818226 original size:58 final size:56
Alignment explanation
Indices: 42818136--42818476 Score: 353
Period size: 58 Copynumber: 5.9 Consensus size: 56
42818126 ATCGATTAAA
* * * * *
42818136 GAAAATGGATAGTTTCGACCATCGACTATGAAAAGGGATGGTAACGACCATCAACAAT
1 GAAAAGGGATGGTTT-GACCATCAACTATGAAAAGGGATGGTGATGACCATCAA-AAT
* * *
42818194 GAAAAGGGATGGTGATGACCATCAACTATGAAAAGGGATGGTGACGACCATAAAATAT
1 GAAAAGGGATGGT-TTGACCATCAACTATGAAAAGGGATGGTGATGACCATCAAA-AT
* * * *
42818252 GAAAAGGGATAGTTTCGACTATCAACTATGAAAAGGGATGGTGATGATCATCGAATAT
1 GAAAAGGGATGGTTT-GACCATCAACTATGAAAAGGGATGGTGATGACCATC-AAAAT
* * **
42818310 GAAAAGGGATGTTTTGACTATTGACTATGAAAAGGGATGGTGATGACCATCAAATAT
1 GAAAAGGGATGGTTTGACCATCAACTATGAAAAGGGATGGTGATGACCATCAAA-AT
* * * **
42818367 GAAAAGGGA-GAGTTTCGACTATCGACTATGAAAAGGGATGGTGATGACCATTGATTAT
1 GAAAAGGGATG-GTTT-GACCATCAACTATGAAAAGGGATGGTGATGACCA-TCAAAAT
* *
42818425 GAAAAGGGATGGTTCCGACCATCGAA-TATGAAAAGGGATGGTTATGACCATC
1 GAAAAGGGATGGTT-TGACCATC-AACTATGAAAAGGGATGGTGATGACCATC
42818477 GTTTAGCACA
Statistics
Matches: 243, Mismatches: 29, Indels: 23
0.82 0.10 0.08
Matches are distributed among these distances:
56 3 0.01
57 50 0.21
58 183 0.75
59 7 0.03
ACGTcount: A:0.38, C:0.12, G:0.27, T:0.23
Consensus pattern (56 bp):
GAAAAGGGATGGTTTGACCATCAACTATGAAAAGGGATGGTGATGACCATCAAAAT
Found at i:42818283 original size:87 final size:87
Alignment explanation
Indices: 42818152--42818476 Score: 358
Period size: 87 Copynumber: 3.7 Consensus size: 87
42818142 GGATAGTTTC
* * * *
42818152 GACCATCGACTATGAAAAGGGATGGTAACGACCATCAACAATGAAAAGGGATGGTGATGACCATC
1 GACCATTGAATATGAAAAGGGATGGTATCGACCATCAACTATGAAAAGGGATGGTGATGACCATC
*
42818217 AACTATGAAAAGGGATGGTGAC
66 AACTATGAAAAGGGATGGTGAT
** * * * *
42818239 GACCATAAAATATGAAAAGGGATAGTTTCGACTATCAACTATGAAAAGGGATGGTGATGATCATC
1 GACCATTGAATATGAAAAGGGATGGTATCGACCATCAACTATGAAAAGGGATGGTGATGACCATC
**
42818304 GAA-TATGAAAAGGGAT-GTTTT
66 -AACTATGAAAAGGGATGGTGAT
* * * * *
42818325 GACTATTGACTATGAAAAGGGATGGTGAT-GACCATCAAATATGAAAAGGGA-GAGT-TTCGACT
1 GACCATTGAATATGAAAAGGGATGGT-ATCGACCATCAACTATGAAAAGGGATG-GTGAT-GACC
*
42818387 ATCGACTATGAAAAGGGATGGTGAT
63 ATCAACTATGAAAAGGGATGGTGAT
* *
42818412 GACCATTGATTATGAAAAGGGATGGT-TCCGACCATCGAA-TATGAAAAGGGATGGTTATGACCA
1 GACCATTGAATATGAAAAGGGATGGTAT-CGACCATC-AACTATGAAAAGGGATGGTGATGACCA
42818475 TC
64 TC
42818477 GTTTAGCACA
Statistics
Matches: 197, Mismatches: 30, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
85 4 0.02
86 63 0.32
87 124 0.63
88 6 0.03
ACGTcount: A:0.38, C:0.13, G:0.27, T:0.23
Consensus pattern (87 bp):
GACCATTGAATATGAAAAGGGATGGTATCGACCATCAACTATGAAAAGGGATGGTGATGACCATC
AACTATGAAAAGGGATGGTGAT
Found at i:42818616 original size:20 final size:20
Alignment explanation
Indices: 42818591--42818629 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
42818581 TTATGAAAGG
42818591 AACGATTTAAGTGATGTTAA
1 AACGATTTAAGTGATGTTAA
42818611 AACGATTTAAGTGATGTTA
1 AACGATTTAAGTGATGTTA
42818630 TGTTTATGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.21, T:0.36
Consensus pattern (20 bp):
AACGATTTAAGTGATGTTAA
Found at i:42819841 original size:99 final size:99
Alignment explanation
Indices: 42819665--42819868 Score: 309
Period size: 99 Copynumber: 2.1 Consensus size: 99
42819655 GCTCGATTGG
* *
42819665 GTTGAAAGCTAGTCAGAGATCTATCACACTATCCATAGATTTTATCGATAGATTTTTATGCTTTG
1 GTTGAAAGCTAATCAGAGATCCATCACACTATCCATAGATTTTATCGATAGATTTTTATGCTTTG
*
42819730 GTCACAGTTATAATGACATGTATAGGTGTTTTAT
66 GTCACAGTTATAATAACATGTATAGGTGTTTTAT
* * * *
42819764 GTTGGAAGCTAATCAGAGATCCATCACACTATCCATCGATTTTATCGGTATATTTTTATGCTTTG
1 GTTGAAAGCTAATCAGAGATCCATCACACTATCCATAGATTTTATCGATAGATTTTTATGCTTTG
* * *
42819829 GTCGCGGTTATAATAACATGTGTAGGTGTTTTAT
66 GTCACAGTTATAATAACATGTATAGGTGTTTTAT
42819863 GCTTGA
1 G-TTGA
42819869 TGATATGGTC
Statistics
Matches: 93, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
99 90 0.97
100 3 0.03
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (99 bp):
GTTGAAAGCTAATCAGAGATCCATCACACTATCCATAGATTTTATCGATAGATTTTTATGCTTTG
GTCACAGTTATAATAACATGTATAGGTGTTTTAT
Found at i:42822122 original size:29 final size:30
Alignment explanation
Indices: 42822032--42822209 Score: 141
Period size: 30 Copynumber: 6.0 Consensus size: 30
42822022 CACGATTGTT
*
42822032 GTCACCATCCCTTTTCATAGTTCAATAGTC
1 GTCACCATCCCTTTTCATAGTTCGATAGTC
* * * *
42822062 G-AAGCTATCCCTTATCATAATTCGATAGTC
1 GTCA-CCATCCCTTTTCATAGTTCGATAGTC
* *
42822092 GTCACCATCCCTTTTCATTGTT-TATAGTC
1 GTCACCATCCCTTTTCATAGTTCGATAGTC
* * *
42822121 GTCACCATCCTTTTTCATTGTT-GATGGTC
1 GTCACCATCCCTTTTCATAGTTCGATAGTC
* * *
42822150 GTCACCATCCGC-TTTCACAATTCGATAGCC
1 GTCACCATCC-CTTTTCATAGTTCGATAGTC
* * * *
42822180 G-AAGCTATCCCTTTTCGTATTTCGATAGTC
1 GTCA-CCATCCCTTTTCATAGTTCGATAGTC
42822210 AAAGCTATCC
Statistics
Matches: 116, Mismatches: 26, Indels: 12
0.75 0.17 0.08
Matches are distributed among these distances:
29 52 0.45
30 63 0.54
31 1 0.01
ACGTcount: A:0.21, C:0.28, G:0.13, T:0.38
Consensus pattern (30 bp):
GTCACCATCCCTTTTCATAGTTCGATAGTC
Found at i:42822215 original size:30 final size:30
Alignment explanation
Indices: 42822170--42822227 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
42822160 GCTTTCACAA
*
42822170 TTCGATAGCCGAAGCTATCCCTTTTCGTAT
1 TTCGATAGCCAAAGCTATCCCTTTTCGTAT
*
42822200 TTCGATAGTCAAAGCTATCCCTTTTCGT
1 TTCGATAGCCAAAGCTATCCCTTTTCGT
42822228 TGGTCGACGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.21, C:0.26, G:0.16, T:0.38
Consensus pattern (30 bp):
TTCGATAGCCAAAGCTATCCCTTTTCGTAT
Found at i:42824708 original size:138 final size:137
Alignment explanation
Indices: 42824455--42824725 Score: 418
Period size: 138 Copynumber: 2.0 Consensus size: 137
42824445 CCATCAAGCC
* * * *
42824455 ACTTGATGATCTCTTTCTTAACAAAATTCTTCATGATTGGATTCAACCTTCTTTTTTGTTCAATA
1 ACTTAATGATCTCTTTCTTAACAAAATTCTTCATGATTAGATTCAACCTCCTTTGTTGTTCAATA
* * * *
42824520 GAATTTCTATGGCAGTCTTCCAGTAAAATTTTATGCATATAGAAAGTAGGGTTGATTCCCTTGAT
66 GAATTTCTATGGAAATCCTCCAGTAAAATTTTATGCATACAGAAAGTAGGG-TGATTCCCTTGAT
42824585 GTCGGAAA
130 GTCGGAAA
*
42824593 ACTTAATGATCTCTTTCTTAAC-AACTTCTTTCATGATTAGATTCAACCTCCTTTGTTGTTCAAT
1 ACTTAATGATCTCTTTCTTAACAAAATTC-TTCATGATTAGATTCAACCTCCTTTGTTGTTCAAT
* *
42824657 AGAATTTCTATGGAAATCCTCCAGTAAAATTTTATGGATACAGATAGTAGGGTGATTCCCTTGAT
65 AGAATTTCTATGGAAATCCTCCAGTAAAATTTTATGCATACAGAAAGTAGGGTGATTCCCTTGAT
42824722 GTCG
130 GTCG
42824726 ACAATTTTCC
Statistics
Matches: 121, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
137 22 0.18
138 99 0.82
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.39
Consensus pattern (137 bp):
ACTTAATGATCTCTTTCTTAACAAAATTCTTCATGATTAGATTCAACCTCCTTTGTTGTTCAATA
GAATTTCTATGGAAATCCTCCAGTAAAATTTTATGCATACAGAAAGTAGGGTGATTCCCTTGATG
TCGGAAA
Found at i:42836222 original size:18 final size:18
Alignment explanation
Indices: 42836199--42836233 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
42836189 CAAGAATAGT
42836199 AAGCATAAAAATAGTTTC
1 AAGCATAAAAATAGTTTC
*
42836217 AAGCATGAAAATAGTTT
1 AAGCATAAAAATAGTTT
42836234 GGCACATCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.29
Consensus pattern (18 bp):
AAGCATAAAAATAGTTTC
Found at i:42838403 original size:60 final size:60
Alignment explanation
Indices: 42838304--42838430 Score: 166
Period size: 60 Copynumber: 2.1 Consensus size: 60
42838294 AAGGAGGAAG
* * * **
42838304 TACTGGCAGTTTATCTGCATCATTGGTGGCTTGAACACATTGCTGGCAGCTTGTCTGCAC
1 TACTGGTAGTTTATCTGCATCATTCGTAGCTTGAACACATAACTGGCAGCTTGTCTGCAC
* * *
42838364 TACTGGTAGTTTATCTGCATTATTCGTAGCTT-AACCACATAACTGGCATCTTGTCTGCAT
1 TACTGGTAGTTTATCTGCATCATTCGTAGCTTGAA-CACATAACTGGCAGCTTGTCTGCAC
42838424 TACTGGT
1 TACTGGT
42838431 GGCTTGTCCA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
59 2 0.03
60 56 0.97
ACGTcount: A:0.20, C:0.22, G:0.21, T:0.36
Consensus pattern (60 bp):
TACTGGTAGTTTATCTGCATCATTCGTAGCTTGAACACATAACTGGCAGCTTGTCTGCAC
Found at i:42850530 original size:63 final size:63
Alignment explanation
Indices: 42850441--42850598 Score: 217
Period size: 63 Copynumber: 2.5 Consensus size: 63
42850431 TGTCTCTGTG
* * * *
42850441 GATGCCATGGAGTCTTTCATCAATGGTCTTACAATGATCCGCCACCCTAGCGTACTATCATAT
1 GATGCCATGGAGTCTTTCATCCATGGTCTTACAATAATCCACCACCCTAGCGTACTATCATAC
* * * * * * *
42850504 GATGTCATGCAGTCTTTCATCCATGGTCTTACAATAATCCACTATCTTGGCGTGCTATCATAC
1 GATGCCATGGAGTCTTTCATCCATGGTCTTACAATAATCCACCACCCTAGCGTACTATCATAC
42850567 GATGCCATGGAGTCTTTCATCCATGGTCTTAC
1 GATGCCATGGAGTCTTTCATCCATGGTCTTAC
42850599 TCATTATACC
Statistics
Matches: 82, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
63 82 1.00
ACGTcount: A:0.23, C:0.26, G:0.18, T:0.33
Consensus pattern (63 bp):
GATGCCATGGAGTCTTTCATCCATGGTCTTACAATAATCCACCACCCTAGCGTACTATCATAC
Found at i:42853299 original size:27 final size:27
Alignment explanation
Indices: 42853184--42853288 Score: 160
Period size: 27 Copynumber: 3.9 Consensus size: 27
42853174 CGGATGATTG
*
42853184 AAATACCCCCGAAGGGTAAAATGACCA
1 AAATACCCTCGAAGGGTAAAATGACCA
* *
42853211 AAATACCCT-AAAGGGTAAAATAACCA
1 AAATACCCTCGAAGGGTAAAATGACCA
42853237 AAATACCCTCGAAGGGTAAAATGACCA
1 AAATACCCTCGAAGGGTAAAATGACCA
42853264 AAATACCCTCGTAA-GGTAAAATGAC
1 AAATACCCTCG-AAGGGTAAAATGAC
42853289 TGATATACCC
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
26 24 0.34
27 45 0.63
28 2 0.03
ACGTcount: A:0.47, C:0.22, G:0.16, T:0.15
Consensus pattern (27 bp):
AAATACCCTCGAAGGGTAAAATGACCA
Found at i:42859951 original size:12 final size:12
Alignment explanation
Indices: 42859934--42859958 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42859924 CCTTATACAC
42859934 ATTACACATTGA
1 ATTACACATTGA
42859946 ATTACACATTGA
1 ATTACACATTGA
42859958 A
1 A
42859959 ATCAGATTTT
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:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (12 bp):
ATTACACATTGA
Found at i:42861979 original size:18 final size:18
Alignment explanation
Indices: 42861958--42861996 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
42861948 AAAGGTAGAC
42861958 AGAAAAAGA-AATCGAAAA
1 AGAAAAAGAGAAT-GAAAA
42861976 AGAAAAAGAGAATGAAAA
1 AGAAAAAGAGAATGAAAA
42861994 AGA
1 AGA
42861997 GCAAAAAGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.72, C:0.03, G:0.21, T:0.05
Consensus pattern (18 bp):
AGAAAAAGAGAATGAAAA
Found at i:42863804 original size:33 final size:34
Alignment explanation
Indices: 42863767--42863838 Score: 110
Period size: 33 Copynumber: 2.1 Consensus size: 34
42863757 GAGTTAGTTT
*
42863767 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAG-A
1 ATTAAATTTAGTTCAACTCAAATAAGTGTTAGTA
* *
42863800 ATTAATTTTAGTTCAACTTAAATAAGTGTTAGTA
1 ATTAAATTTAGTTCAACTCAAATAAGTGTTAGTA
42863834 ATTAA
1 ATTAA
42863839 TTTGTTTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
33 29 0.83
34 6 0.17
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.40
Consensus pattern (34 bp):
ATTAAATTTAGTTCAACTCAAATAAGTGTTAGTA
Found at i:42864944 original size:12 final size:12
Alignment explanation
Indices: 42864927--42864951 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42864917 CCTTATACAC
42864927 ATTACACATTGA
1 ATTACACATTGA
42864939 ATTACACATTGA
1 ATTACACATTGA
42864951 A
1 A
42864952 ATCAGATTTT
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:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (12 bp):
ATTACACATTGA
Found at i:42866945 original size:27 final size:27
Alignment explanation
Indices: 42866906--42867080 Score: 228
Period size: 27 Copynumber: 6.5 Consensus size: 27
42866896 TCGTGGGCGG
*
42866906 ATGACTGAGATA-CCCTCGAAGGGTAAA
1 ATGACTGAAATACCCCT-GAAGGGTAAA
* *
42866933 ATGACCGAAATACCCTTGAAGGGTAAA
1 ATGACTGAAATACCCCTGAAGGGTAAA
* * *
42866960 ATAACTAAAATACCCCTAAAGGGTAAA
1 ATGACTGAAATACCCCTGAAGGGTAAA
*
42866987 ATGACTGAAATACCCCTAAAGGGTAAA
1 ATGACTGAAATACCCCTGAAGGGTAAA
42867014 ATGACTGAAATACCCCTGAAGGGTAAA
1 ATGACTGAAATACCCCTGAAGGGTAAA
* *
42867041 ATGA-TCGAAATACCCCCGTAGGGTAAA
1 ATGACT-GAAATACCCCTGAAGGGTAAA
*
42867068 ATGACTGATATAC
1 ATGACTGAAATAC
42867081 ACCTAAGAGT
Statistics
Matches: 131, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
26 1 0.01
27 126 0.96
28 4 0.03
ACGTcount: A:0.42, C:0.19, G:0.20, T:0.19
Consensus pattern (27 bp):
ATGACTGAAATACCCCTGAAGGGTAAA
Found at i:42868463 original size:12 final size:12
Alignment explanation
Indices: 42868446--42868471 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42868436 TTTTATTTTC
42868446 TTTTCAATTCTT
1 TTTTCAATTCTT
42868458 TTTTCAATTCTT
1 TTTTCAATTCTT
42868470 TT
1 TT
42868472 CCAAAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTCAATTCTT
Found at i:42869458 original size:27 final size:27
Alignment explanation
Indices: 42869427--42869679 Score: 253
Period size: 27 Copynumber: 9.4 Consensus size: 27
42869417 CTAATAGATG
*
42869427 AAAATGACTGAAATACCCCTATAGGGT
1 AAAATGACTGAAATACCCCCATAGGGT
42869454 AAAATGACTGAAATACCCCCATAGGGT
1 AAAATGACTGAAATACCCCCATAGGGT
* * *
42869481 AAAATAACTTAAATACCCTCATAGGGT
1 AAAATGACTGAAATACCCCCATAGGGT
* ** *
42869508 AAAATGACTGAAATGCCCAAATAGGAT
1 AAAATGACTGAAATACCCCCATAGGGT
* *
42869535 AAAATAACTGAAATACCCTCATAGGGT
1 AAAATGACTGAAATACCCCCATAGGGT
* *
42869562 AACATGATTGAAATACCCCCATAGGGT
1 AAAATGACTGAAATACCCCCATAGGGT
* * * *
42869589 AACATGA-TCGAAATAACCCCATAAGAT
1 AAAATGACT-GAAATACCCCCATAGGGT
* *
42869616 AAAATGA-TCAAAATACCCCCATAGTGT
1 AAAATGACT-GAAATACCCCCATAGGGT
* **
42869643 AAAATAACTGTTATA-CCCC-TAGGAGAT
1 AAAATGACTGAAATACCCCCATAGG-G-T
42869670 AAAATGACTG
1 AAAATGACTG
42869680 TTATGGCCTT
Statistics
Matches: 188, Mismatches: 34, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
25 3 0.02
26 6 0.03
27 178 0.95
28 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.22
Consensus pattern (27 bp):
AAAATGACTGAAATACCCCCATAGGGT
Found at i:42870089 original size:28 final size:29
Alignment explanation
Indices: 42870039--42870184 Score: 176
Period size: 28 Copynumber: 5.2 Consensus size: 29
42870029 TTATTGCACT
*
42870039 ACACTG-TTATTGTATTGGGCTAAGGCCC
1 ACACTGATTACTGTATTGGGCTAAGGCCC
* * *
42870067 ACATTGATT-CTGTATTGGACTAAGCCCC
1 ACACTGATTACTGTATTGGGCTAAGGCCC
* * *
42870095 ACGCTG-TTACTGTATTAGACTAAGGCCC
1 ACACTGATTACTGTATTGGGCTAAGGCCC
*
42870123 ACACTGATT-CTGTATTGGGCTAAGGCCT
1 ACACTGATTACTGTATTGGGCTAAGGCCC
*
42870151 ACACT-ATTACTGTATTGGGCTAAGGACC
1 ACACTGATTACTGTATTGGGCTAAGGCCC
42870179 ACACTG
1 ACACTG
42870185 TACTGTCACT
Statistics
Matches: 99, Mismatches: 14, Indels: 9
0.81 0.11 0.07
Matches are distributed among these distances:
27 5 0.05
28 90 0.91
29 4 0.04
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (29 bp):
ACACTGATTACTGTATTGGGCTAAGGCCC
Found at i:42870131 original size:56 final size:56
Alignment explanation
Indices: 42870039--42870184 Score: 202
Period size: 56 Copynumber: 2.6 Consensus size: 56
42870029 TTATTGCACT
* *
42870039 ACACTGTTATTGTATTGGGCTAAGGCCCACATTGATTCTGTATTGGACTAAGCCCC
1 ACACTGTTACTGTATTGGGCTAAGGCCCACACTGATTCTGTATTGGACTAAGCCCC
* * * * * *
42870095 ACGCTGTTACTGTATTAGACTAAGGCCCACACTGATTCTGTATTGGGCTAAGGCCT
1 ACACTGTTACTGTATTGGGCTAAGGCCCACACTGATTCTGTATTGGACTAAGCCCC
* *
42870151 ACACTATTACTGTATTGGGCTAAGGACCACACTG
1 ACACTGTTACTGTATTGGGCTAAGGCCCACACTG
42870185 TACTGTCACT
Statistics
Matches: 77, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
56 77 1.00
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (56 bp):
ACACTGTTACTGTATTGGGCTAAGGCCCACACTGATTCTGTATTGGACTAAGCCCC
Found at i:42877213 original size:16 final size:16
Alignment explanation
Indices: 42877192--42877248 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
42877182 TCCTATAGTG
42877192 TCACAATTTATAGTTT
1 TCACAATTTATAGTTT
*
42877208 TCACAATTCTATTG-TT
1 TCACAATT-TATAGTTT
*
42877224 TCA-AAGTCTATAGTTT
1 TCACAA-TTTATAGTTT
42877240 TCAC-ATTTA
1 TCACAATTTA
42877249 AACAACACTT
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
15 9 0.27
16 20 0.61
17 4 0.12
ACGTcount: A:0.30, C:0.16, G:0.07, T:0.47
Consensus pattern (16 bp):
TCACAATTTATAGTTT
Done.