Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001111.1 Hibiscus syriacus cultivar Beakdansim tig00002193_pilon, whole genome shotgun sequence
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: 3891333
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 17
Found at i:2548176 original size:3 final size:3
Alignment explanation
Indices: 2548164--2548228 Score: 69
Period size: 3 Copynumber: 21.3 Consensus size: 3
2548154 GTTACCTGGA
* * * *
2548164 AAT AAT -AT AAT AAT AAT AAT AAT AGT ATT AAT AAC AAT AAT AGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2548211 AAT ACAT AATT AAT AAT A
1 AAT A-AT AA-T AAT AAT A
2548229 GACGATTAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
2 2 0.04
3 44 0.85
4 6 0.12
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:2554928 original size:18 final size:18
Alignment explanation
Indices: 2554907--2554945 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
2554897 TCTATATTTC
* * *
2554907 TATATAGTATTATTCAGA
1 TATATAATAATATTAAGA
2554925 TATATAATAATATTAAGA
1 TATATAATAATATTAAGA
2554943 TAT
1 TAT
2554946 TATTAAGAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.44
Consensus pattern (18 bp):
TATATAATAATATTAAGA
Found at i:2554989 original size:11 final size:11
Alignment explanation
Indices: 2554954--2555015 Score: 52
Period size: 11 Copynumber: 5.2 Consensus size: 11
2554944 ATTATTAAGA
2554954 ATAATATTATAT
1 ATAATATTAT-T
**
2554966 ATTTTATTATT
1 ATAATATTATT
*
2554977 ATAATATTCTT
1 ATAATATTATT
2554988 ATAATATATATT
1 ATAATAT-TATT
2555000 ATTTATATATTATT
1 A--TA-ATATTATT
2555014 AT
1 AT
2555016 TATTGAAATA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
11 16 0.40
12 13 0.32
14 7 0.17
15 4 0.10
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (11 bp):
ATAATATTATT
Found at i:2554989 original size:26 final size:26
Alignment explanation
Indices: 2554958--2555019 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 26
2554948 TTAAGAATAA
*
2554958 TATTATATATTTTATTA-TTATAATAT
1 TATTATATATTATATTATTTAT-ATAT
*
2554984 TCTTATA-ATATATATTATTTATATAT
1 TATTATATAT-TATATTATTTATATAT
2555010 TATTAT-TATT
1 TATTATATATT
2555020 GAAATAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
25 3 0.10
26 23 0.77
27 4 0.13
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (26 bp):
TATTATATATTATATTATTTATATAT
Found at i:2555008 original size:29 final size:31
Alignment explanation
Indices: 2554961--2555018 Score: 75
Period size: 29 Copynumber: 1.9 Consensus size: 31
2554951 AGAATAATAT
* *
2554961 TATATATTTTATTATTATAATATTCTTATAA
1 TATATATTATATTATTATAATATTATTATAA
*
2554992 TATATATTAT-TTA-TATATTATTATTAT
1 TATATATTATATTATTATAATATTATTAT
2555019 TGAAATAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 12 0.50
30 3 0.12
31 9 0.38
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (31 bp):
TATATATTATATTATTATAATATTATTATAA
Found at i:2555030 original size:17 final size:17
Alignment explanation
Indices: 2554988--2555030 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
2554978 TAATATTCTT
* *
2554988 ATAATATATATTATTTAT
1 ATAATAT-TATTATTGAA
*
2555006 ATATTATTATTATTGAA
1 ATAATATTATTATTGAA
2555023 ATAATATT
1 ATAATATT
2555031 TAAATTAAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
ATAATATTATTATTGAA
Found at i:2555082 original size:22 final size:22
Alignment explanation
Indices: 2555054--2555097 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
2555044 ATTGAAAGAT
2555054 TTAAAGTATTATTTATAATTTA
1 TTAAAGTATTATTTATAATTTA
2555076 TTAAAGTATTATTTATAATTTA
1 TTAAAGTATTATTTATAATTTA
2555098 ATAATAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (22 bp):
TTAAAGTATTATTTATAATTTA
Found at i:2557465 original size:16 final size:16
Alignment explanation
Indices: 2557444--2557475 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2557434 AAATCTTGGA
*
2557444 TATTATGATTTTTTAT
1 TATTATAATTTTTTAT
2557460 TATTATAATTTTTTAT
1 TATTATAATTTTTTAT
2557476 CTTATTAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (16 bp):
TATTATAATTTTTTAT
Found at i:2558370 original size:16 final size:16
Alignment explanation
Indices: 2558332--2558371 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
2558322 GAATGGTGAT
*
2558332 ACATGGAACCAATGAC
1 ACATGGTACCAATGAC
**
2558348 ATGTGGTACCAATGAC
1 ACATGGTACCAATGAC
2558364 ACATGGTA
1 ACATGGTA
2558372 TCATTCGATT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.38, C:0.20, G:0.23, T:0.20
Consensus pattern (16 bp):
ACATGGTACCAATGAC
Found at i:2561038 original size:3 final size:3
Alignment explanation
Indices: 2561030--2561066 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
2561020 AGGCAACCAA
2561030 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2561067 TATGTCTTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2564525 original size:59 final size:59
Alignment explanation
Indices: 2564433--2564830 Score: 541
Period size: 59 Copynumber: 6.9 Consensus size: 59
2564423 AAATTACCAA
*
2564433 AGGGCACTTTGTGTGCTAAAGTGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* *
2564492 AGGGCACTTTGTGTGCTAAAATGGTAAGAAAATCATACTAAGTGTATGAATTTCCATAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
*
2564551 AGAGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* * * * *
2564610 AGGGCATTTTGTGTGCTAAAATAGTAAGGAAACCATACTAGGTGTATGAATTTTCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* *
2564669 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATTATACTAAGTGTATTAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* *
2564728 AGGGCACTTTGTGTGC-------G--A--AAATCGTACTAGGTGTATGAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* * * * * *
2564776 A-GGCACTTTATGTGCTAAAATGGTAAGAAAATCATATTGATTGTATGAAATTCCA
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCA
2564831 ATTAAAATTA
Statistics
Matches: 298, Mismatches: 30, Indels: 23
0.85 0.09 0.07
Matches are distributed among these distances:
47 13 0.04
48 27 0.09
50 1 0.00
52 1 0.00
54 1 0.00
56 1 0.00
58 21 0.07
59 233 0.78
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.32
Consensus pattern (59 bp):
AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
Found at i:2564775 original size:48 final size:47
Alignment explanation
Indices: 2564704--2564796 Score: 141
Period size: 48 Copynumber: 2.0 Consensus size: 47
2564694 AAGGAAATTA
* *
2564704 TACTAAGTGTATTAATTTCCAGATAGGGCACTTTGTGTGCGAAAATCG
1 TACTAAGTGTATGAATTTCCAGATA-GGCACTTTATGTGCGAAAATCG
* *
2564752 TACTAGGTGTATGAATTTCCAGATAGGCACTTTATGTGCTAAAAT
1 TACTAAGTGTATGAATTTCCAGATAGGCACTTTATGTGCGAAAAT
2564797 GGTAAGAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 18 0.44
48 23 0.56
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34
Consensus pattern (47 bp):
TACTAAGTGTATGAATTTCCAGATAGGCACTTTATGTGCGAAAATCG
Found at i:2568854 original size:23 final size:23
Alignment explanation
Indices: 2568828--2568884 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
2568818 ATAAATGCAC
2568828 CGAAGTGCCACGTAGAATTACAT
1 CGAAGTGCCACGTAGAATTACAT
* * *
2568851 CGAAGTGTCGCGTAGAATTGCAT
1 CGAAGTGCCACGTAGAATTACAT
2568874 CGAAGTGCCAC
1 CGAAGTGCCAC
2568885 ATAAAATATC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.30, C:0.23, G:0.26, T:0.21
Consensus pattern (23 bp):
CGAAGTGCCACGTAGAATTACAT
Found at i:2569402 original size:2 final size:2
Alignment explanation
Indices: 2569395--2569441 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
2569385 ACTCGTAGTC
2569395 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2569437 AT AT A
1 AT AT A
2569442 CATTTTACCT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2570618 original size:64 final size:62
Alignment explanation
Indices: 2570544--2570701 Score: 158
Period size: 64 Copynumber: 2.5 Consensus size: 62
2570534 TAACATGTGC
* *
2570544 ATCGATGCACTACCCATGCATCGATACACAA-AGCACCTTCAATGTTT-TAATCTTAAGGGGGTG
1 ATCGATGCACT-CCCATGCATCGATACACAATAGCA--TTCAATATTTCCAATCTTAA-GGGGTG
2570607 T
62 T
* * * *
2570608 ATCGATGCACTCCCTATGCATCGATGCACTAATTGCATTCAATATTTCCATTTTTAAGGGGTGT
1 ATCGATGCACTCCC-ATGCATCGATACAC-AATAGCATTCAATATTTCCAATCTTAAGGGGTGT
** *
2570672 ATCGATGCACTTCCTGTGCATCCATACACA
1 ATCGATGCAC-TCCCATGCATCGATACACA
2570702 CTGAACAATT
Statistics
Matches: 79, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
63 4 0.05
64 61 0.77
65 11 0.14
66 3 0.04
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (62 bp):
ATCGATGCACTCCCATGCATCGATACACAATAGCATTCAATATTTCCAATCTTAAGGGGTGT
Found at i:2574685 original size:54 final size:53
Alignment explanation
Indices: 2574620--2574757 Score: 170
Period size: 53 Copynumber: 2.6 Consensus size: 53
2574610 CATCTTCAAG
* *
2574620 GGGTATCGATACCATCAAG-AATGTATCGATACCTATAAACATCGAATTTAATTT
1 GGGTACCGATACC--CAAGTAATGTATCGATACCTATAAACATCAAATTTAATTT
* * * *
2574674 GGGTACCGATACCCCAGTAGTGTATTGATACCTGTAAACATCAAATTTAATTT
1 GGGTACCGATACCCAAGTAATGTATCGATACCTATAAACATCAAATTTAATTT
* * *
2574727 GGGTACTGATACCCCAGTAGTGTATCGATAC
1 GGGTACCGATACCCAAGTAATGTATCGATAC
2574758 TCTTCCGAAG
Statistics
Matches: 75, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
52 3 0.04
53 60 0.80
54 12 0.16
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (53 bp):
GGGTACCGATACCCAAGTAATGTATCGATACCTATAAACATCAAATTTAATTT
Found at i:2574706 original size:53 final size:53
Alignment explanation
Indices: 2574641--2574757 Score: 198
Period size: 53 Copynumber: 2.2 Consensus size: 53
2574631 CCATCAAGAA
*
2574641 TGTATCGATACCTATAAACATCGAATTTAATTTGGGTACCGATACCCCAGTAG
1 TGTATCGATACCTATAAACATCAAATTTAATTTGGGTACCGATACCCCAGTAG
* * *
2574694 TGTATTGATACCTGTAAACATCAAATTTAATTTGGGTACTGATACCCCAGTAG
1 TGTATCGATACCTATAAACATCAAATTTAATTTGGGTACCGATACCCCAGTAG
2574747 TGTATCGATAC
1 TGTATCGATAC
2574758 TCTTCCGAAG
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 59 1.00
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (53 bp):
TGTATCGATACCTATAAACATCAAATTTAATTTGGGTACCGATACCCCAGTAG
Found at i:2575269 original size:59 final size:59
Alignment explanation
Indices: 2575167--2575564 Score: 532
Period size: 59 Copynumber: 6.9 Consensus size: 59
2575157 AAATTACCAA
* *
2575167 AGGGCACTTTGTGTGATAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAAAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* * * *
2575226 AGGGAACTTTGTGTGCTAAAATGGTAAGAAAATCATACCAAGTGTATGAATTTCTAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* *
2575285 AGGGCATTTTGTGTGCTAAAATGGTAAGGAAACCATACTAAGTGTATGAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* * *
2575344 AGGGCACTTTGTGTGTTAAAATGGTAAGGAAACCATACTAGGTGTATGAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* *
2575403 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATTATACTAAGTGTATTAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
*
2575462 AGGGCACTTTGTGTGC-------G--A--AAATCATACTAGGTGTATGAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* * * * * *
2575510 A-GGCACTTTATGTGCTAAAATGGTAAGAAAATCATATTGATTGTATGAAATTCCA
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCA
2575565 ATTAAAATTA
Statistics
Matches: 299, Mismatches: 29, Indels: 23
0.85 0.08 0.07
Matches are distributed among these distances:
47 13 0.04
48 28 0.09
50 1 0.00
52 1 0.00
54 1 0.00
56 1 0.00
58 22 0.07
59 232 0.78
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.31
Consensus pattern (59 bp):
AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
Found at i:2575508 original size:48 final size:47
Alignment explanation
Indices: 2575432--2575530 Score: 144
Period size: 48 Copynumber: 2.1 Consensus size: 47
2575422 AATGGTAAGG
* * *
2575432 AAATTATACTAAGTGTATTAATTTCCAGATAGGGCACTTTGTGTGCGA
1 AAATCATACTAAGTGTATGAATTTCCAGATA-GGCACTTTATGTGCGA
* *
2575480 AAATCATACTAGGTGTATGAATTTCCAGATAGGCACTTTATGTGCTA
1 AAATCATACTAAGTGTATGAATTTCCAGATAGGCACTTTATGTGCGA
2575527 AAAT
1 AAAT
2575531 GGTAAGAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
47 18 0.39
48 28 0.61
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.34
Consensus pattern (47 bp):
AAATCATACTAAGTGTATGAATTTCCAGATAGGCACTTTATGTGCGA
Found at i:2576532 original size:44 final size:44
Alignment explanation
Indices: 2576482--2576658 Score: 300
Period size: 44 Copynumber: 4.0 Consensus size: 44
2576472 TGTTACCAAA
* *
2576482 ATAAATGAAAATGCATAACGGTACATTATTGGCAGAAAGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
* *
2576526 ATAAATGAAAATGTATAATGGTGCATTATTGGCAGAAAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
*
2576570 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
*
2576614 ATAAATGAAAATGCATAACAGTGCATTATTGGCAGAAAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
2576658 A
1 A
2576659 CTCATGTTGT
Statistics
Matches: 124, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 124 1.00
ACGTcount: A:0.41, C:0.12, G:0.23, T:0.24
Consensus pattern (44 bp):
ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
Found at i:2581385 original size:21 final size:21
Alignment explanation
Indices: 2581359--2581400 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2581349 ATCTTTAGGG
*
2581359 ATTTGTTTCAAGAGAGACAAA
1 ATTTGTTTCAAGAGAAACAAA
*
2581380 ATTTGTTTCAAGGGAAACAAA
1 ATTTGTTTCAAGAGAAACAAA
2581401 CTCAAAGATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.43, C:0.10, G:0.19, T:0.29
Consensus pattern (21 bp):
ATTTGTTTCAAGAGAAACAAA
Found at i:2581469 original size:64 final size:65
Alignment explanation
Indices: 2581366--2581567 Score: 234
Period size: 64 Copynumber: 3.1 Consensus size: 65
2581356 GGGATTTGTT
*
2581366 TCAAGAGAGACAAAATTTGTTTCAAGGGAAACAAACTCAAAGATGATGTTTCAAGAGAAACT-TT
1 TCAAGAGAGACAAAATTTGTTTCAAGGGAAACAAACTCAAAGATGATGTTTCAAGAGAAACTGTC
* * *
2581430 TTAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGATGATTTTTTTTCCAAGAGAAAC
1 TCAAGAGAGACAAAATTTGTTTCAAGGGAAACAAACTCAAAGATGA---TGTTT-CAAGAGAAAC
2581495 TGTC
62 TGTC
* * *
2581499 TCAAGAGAGACAAAATTT-TTTTAAGAGAAA-AAGACTCAAAGATTTG-TGTTTCAAGGGAAAC-
1 TCAAGAGAGACAAAATTTGTTTCAAGGGAAACAA-ACTCAAAGA--TGATGTTTCAAGAGAAACT
2581560 GATC
63 G-TC
2581564 TCAA
1 TCAA
2581568 AGATGAATTT
Statistics
Matches: 119, Mismatches: 10, Indels: 17
0.82 0.07 0.12
Matches are distributed among these distances:
64 45 0.38
65 15 0.13
66 4 0.03
67 6 0.05
68 29 0.24
69 18 0.15
70 2 0.02
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.27
Consensus pattern (65 bp):
TCAAGAGAGACAAAATTTGTTTCAAGGGAAACAAACTCAAAGATGATGTTTCAAGAGAAACTGTC
Found at i:2581590 original size:82 final size:82
Alignment explanation
Indices: 2581499--2581650 Score: 268
Period size: 82 Copynumber: 1.9 Consensus size: 82
2581489 AGAAACTGTC
* *
2581499 TCAAGAGAGACAAAATTTTTTTAAGAGAAAAAGACTCAAAGATTTGTGTTTCAAGGGAAACGATC
1 TCAAGAGAGACAAAATTTTTTTAAGAGAAAAAGACTCAAAGATTTATGTTTCAAGGGAAACAATC
2581564 TCAAAGATGAATTTTTT
66 TCAAAGATGAATTTTTT
* *
2581581 TCAAGAGAGACAAAATTTTTTTAAGAGAAAAAGACTCAAAGATTTATGTTTTAAGGGAAACAATT
1 TCAAGAGAGACAAAATTTTTTTAAGAGAAAAAGACTCAAAGATTTATGTTTCAAGGGAAACAATC
2581646 TCAAA
66 TCAAA
2581651 TTTTGTATTT
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
82 66 1.00
ACGTcount: A:0.44, C:0.09, G:0.17, T:0.30
Consensus pattern (82 bp):
TCAAGAGAGACAAAATTTTTTTAAGAGAAAAAGACTCAAAGATTTATGTTTCAAGGGAAACAATC
TCAAAGATGAATTTTTT
Found at i:2585058 original size:32 final size:32
Alignment explanation
Indices: 2585022--2585098 Score: 136
Period size: 32 Copynumber: 2.4 Consensus size: 32
2585012 GACATGATAT
2585022 CTACCCAAACATGCTTTTATTAAATAACATTC
1 CTACCCAAACATGCTTTTATTAAATAACATTC
*
2585054 CTACCCGAACATGCTTTTATTAAATAACATTC
1 CTACCCAAACATGCTTTTATTAAATAACATTC
*
2585086 CTACCCAGACATG
1 CTACCCAAACATG
2585099 GTTTCTACCT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.35, C:0.27, G:0.06, T:0.31
Consensus pattern (32 bp):
CTACCCAAACATGCTTTTATTAAATAACATTC
Found at i:2587646 original size:48 final size:48
Alignment explanation
Indices: 2587588--2587698 Score: 186
Period size: 48 Copynumber: 2.3 Consensus size: 48
2587578 AATGCTCTCT
* *
2587588 CCCTCACCGAATGCTCTTTCGGTTCCTCTTTATTTCTTTTCTCTGTCC
1 CCCTCACCGAATGCTCTTTCGGATCCTCTTTATTTCTTTTCTATGTCC
*
2587636 CCCTCACCGAATGCTCTTTCGGATCCTCTTTATTTTTTTTCTATGTCC
1 CCCTCACCGAATGCTCTTTCGGATCCTCTTTATTTCTTTTCTATGTCC
*
2587684 CCCTCACTGAATGCT
1 CCCTCACCGAATGCT
2587699 TTCCTTTTTT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 59 1.00
ACGTcount: A:0.12, C:0.34, G:0.11, T:0.43
Consensus pattern (48 bp):
CCCTCACCGAATGCTCTTTCGGATCCTCTTTATTTCTTTTCTATGTCC
Found at i:2588674 original size:24 final size:25
Alignment explanation
Indices: 2588647--2588693 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
2588637 GTTTAGGTGT
*
2588647 TGGGCTAGGGTTTTGAT-TTGGGCA
1 TGGGCTAGGGTTATGATGTTGGGCA
* *
2588671 TGGGTTTGGGTTATGATGTTGGG
1 TGGGCTAGGGTTATGATGTTGGG
2588694 TATTGGGTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 14 0.74
25 5 0.26
ACGTcount: A:0.11, C:0.04, G:0.45, T:0.40
Consensus pattern (25 bp):
TGGGCTAGGGTTATGATGTTGGGCA
Found at i:2588718 original size:3 final size:3
Alignment explanation
Indices: 2588705--2588817 Score: 113
Period size: 3 Copynumber: 36.3 Consensus size: 3
2588695 ATTGGGTTTG
* * *
2588705 TAA TAAA TAA TAA TAA TAA TAA T-T TTA TAA TAAA TAA TAA TAA TAG
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
* *
2588751 TAA TAA TAA TAA TTTA TAA TAAA TAA TAA TAA TAA TTTA TAA TAAA TAA
1 TAA TAA TAA TAA -TAA TAA T-AA TAA TAA TAA TAA -TAA TAA T-AA TAA
2588800 TAA TAA TAA TAA T-A TAA T
1 TAA TAA TAA TAA TAA TAA T
2588818 GACTGAAAAA
Statistics
Matches: 93, Mismatches: 9, Indels: 16
0.79 0.08 0.14
Matches are distributed among these distances:
2 3 0.03
3 74 0.80
4 16 0.17
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:2588781 original size:23 final size:23
Alignment explanation
Indices: 2588731--2588809 Score: 122
Period size: 23 Copynumber: 3.3 Consensus size: 23
2588721 TAATAATTTT
* *
2588731 ATAATAAATAATAATAATAGTAATA
1 ATAATAATTTATAATAA-A-TAATA
2588756 ATAATAATTTATAATAAATAATA
1 ATAATAATTTATAATAAATAATA
2588779 ATAATAATTTATAATAAATAATA
1 ATAATAATTTATAATAAATAATA
2588802 ATAATAAT
1 ATAATAAT
2588810 AATATAATGA
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
23 36 0.69
24 1 0.02
25 15 0.29
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (23 bp):
ATAATAATTTATAATAAATAATA
Found at i:2600609 original size:13 final size:13
Alignment explanation
Indices: 2600593--2600638 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
2600583 TAAATTGCAC
2600593 TTTTAAAAAACAA
1 TTTTAAAAAACAA
**
2600606 TTTT--AAAACTTC
1 TTTTAAAAAAC-AA
2600618 TTTTAAAAAACAA
1 TTTTAAAAAACAA
2600631 TTTTAAAA
1 TTTTAAAA
2600639 GTTTTTTCTA
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
11 5 0.19
12 4 0.15
13 12 0.46
14 5 0.19
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (13 bp):
TTTTAAAAAACAA
Found at i:2603969 original size:20 final size:20
Alignment explanation
Indices: 2603944--2603986 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2603934 TCTAAAGGCC
2603944 CATTTAGAACCATATAGATG
1 CATTTAGAACCATATAGATG
* * *
2603964 CATTTAGAAGCATTTAGTTG
1 CATTTAGAACCATATAGATG
2603984 CAT
1 CAT
2603987 GTGGTGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (20 bp):
CATTTAGAACCATATAGATG
Found at i:2608560 original size:17 final size:18
Alignment explanation
Indices: 2608528--2608561 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2608518 CTCTCGTTTT
*
2608528 TTTTTTTTTTCTGTTCTG
1 TTTTTTTTGTCTGTTCTG
2608546 TTTTTTTTGTC-GTTCT
1 TTTTTTTTGTCTGTTCT
2608562 CTGCTGTCGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.00, C:0.12, G:0.12, T:0.76
Consensus pattern (18 bp):
TTTTTTTTGTCTGTTCTG
Found at i:2608962 original size:3 final size:3
Alignment explanation
Indices: 2608954--2609065 Score: 143
Period size: 3 Copynumber: 36.7 Consensus size: 3
2608944 TTATTTATTA
*
2608954 AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT AAAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
* * *
2609001 AAT AAT TAT TAT AAT AAT AAT AAT AAT ACT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
** *
2609049 TTT AAT AGT AAT AAT AA
1 AAT AAT AAT AAT AAT AA
2609066 ATTTAAATGA
Statistics
Matches: 95, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
3 89 0.94
4 6 0.06
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:2609322 original size:76 final size:76
Alignment explanation
Indices: 2609191--2609679 Score: 856
Period size: 76 Copynumber: 6.5 Consensus size: 76
2609181 GATGGAAATG
* * *
2609191 TTTGAAAACATCATGCACTGAAGGACTTAGAGATGACCCGAAGGCTTTGAAAACATTAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
2609256 CCCGAAGGCTT
66 CCCGAAGGCTT
*
2609267 TTTGGAAACATCATGTACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
* * *
2609332 CCAGAAAGCAT
66 CCCGAAGGCTT
*
2609343 TTTGGAAACATCATTCACTGAAGGACTTACAGATGACCCGAAGGCTTTG-AAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
2609407 CCCGAAGGCTT
66 CCCGAAGGCTT
*
2609418 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
2609483 CCCGAAAGCTT
66 CCCGAAGGCTT
2609494 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTG-AAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
2609558 CCTGAAGGCTT
66 CCCGAAGGCTT
2609569 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
2609634 CCCGAAGGCTT
66 CCCGAAGGCTT
*
2609645 TTTGGAAACATCATGCATTGAAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
2609680 TGGGAAATAG
Statistics
Matches: 391, Mismatches: 20, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
75 143 0.37
76 248 0.63
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.22
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:2609471 original size:151 final size:151
Alignment explanation
Indices: 2609191--2609679 Score: 870
Period size: 151 Copynumber: 3.2 Consensus size: 151
2609181 GATGGAAATG
* * *
2609191 TTTGAAAACATCATGCACTGAAGGACTTAGAGATGACCCGAAGGCTTTGAAAACATTAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTG-AAACATCAAAAAGCT
*
2609256 CCCGAAGGCTTTTTGGAAACATCATGTACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
65 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
* *
2609321 ATCAAAAAGCTCCAGAAAGCAT
130 ATCAAAAAGCTCCCGAAAGCTT
*
2609343 TTTGGAAACATCATTCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAACATCAAAAAGCTC
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAACATCAAAAAGCTC
*
2609408 CCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACA
66 CCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACA
2609473 TCAAAAAGCTCCCGAAAGCTT
131 TCAAAAAGCTCCCGAAAGCTT
2609494 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAACATCAAAAAGCTC
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAACATCAAAAAGCTC
*
2609559 CTGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACA
66 CCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACA
*
2609624 TCAAAAAGCTCCCGAAGGCTT
131 TCAAAAAGCTCCCGAAAGCTT
*
2609645 TTTGGAAACATCATGCATTGAAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
2609680 TGGGAAATAG
Statistics
Matches: 324, Mismatches: 13, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
151 278 0.86
152 46 0.14
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.22
Consensus pattern (151 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAACATCAAAAAGCTC
CCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACA
TCAAAAAGCTCCCGAAAGCTT
Found at i:2609625 original size:227 final size:227
Alignment explanation
Indices: 2609191--2609679 Score: 863
Period size: 227 Copynumber: 2.2 Consensus size: 227
2609181 GATGGAAATG
* * *
2609191 TTTGAAAACATCATGCACTGAAGGACTTAGAGATGACCCGAAGGCTTTGAAAACATTAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
* *
2609256 CCCGAAGGCTTTTTGGAAACATCATGTACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
66 CCCGAAAGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
*
2609321 ATCAAAAAGCTCCAGAAAGCATTTTGGAAACATCATTCACTGAAGGACTTACAGATGACCCGAAG
131 ATCAAAAAGCTCCAGAAAGCATTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
2609386 GCTTTGAAACATCAAAAAGCTCCCGAAGGCTT
196 GCTTTGAAACATCAAAAAGCTCCCGAAGGCTT
*
2609418 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
2609483 CCCGAAAGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTG-AAAC
66 CCCGAAAGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
* * *
2609547 ATCAAAAAGCTCCTGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
131 ATCAAAAAGCTCCAGAAAGCATTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
2609612 GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
196 GCTTTG-AAACATCAAAAAGCTCCCGAAGGCTT
*
2609645 TTTGGAAACATCATGCATTGAAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
2609680 TGGGAAATAG
Statistics
Matches: 250, Mismatches: 11, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
226 71 0.28
227 179 0.72
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.22
Consensus pattern (227 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAAGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
ATCAAAAAGCTCCAGAAAGCATTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
GCTTTGAAACATCAAAAAGCTCCCGAAGGCTT
Found at i:2610336 original size:13 final size:13
Alignment explanation
Indices: 2610318--2610342 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2610308 AAAACCAACT
2610318 TTTTTTTTTGACA
1 TTTTTTTTTGACA
2610331 TTTTTTTTTGAC
1 TTTTTTTTTGAC
2610343 TTGTGTAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.08, G:0.08, T:0.72
Consensus pattern (13 bp):
TTTTTTTTTGACA
Found at i:2610392 original size:22 final size:22
Alignment explanation
Indices: 2610367--2610421 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
2610357 CATAAAGTTT
*
2610367 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* *
2610389 TCATCTTTAAAAATAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
2610411 TCATCTTTGAA
1 TCATCTTTGAA
2610422 GAGTGTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:2610867 original size:54 final size:52
Alignment explanation
Indices: 2610785--2610903 Score: 132
Period size: 54 Copynumber: 2.3 Consensus size: 52
2610775 AGAATAGCAG
* *** * *
2610785 GTTCGTAAAACATTTGATAGTGCATTCATCCTTTCCTGTGGTTTCTGTTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCAT--TTTCCTGTGGCTTCTGCTCAGAT
**
2610839 GTTCGTAAAACATTTGACAACACATTCATTTTTTTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATTTTCCTGTGGCTTCTGCTCAGAT
*
2610891 GTTC-TCAAACATT
1 GTTCGTAAAACATT
2610904 GAATCTCTTT
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
51 8 0.14
52 23 0.41
54 25 0.45
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (52 bp):
GTTCGTAAAACATTTGACAACACATTCATTTTCCTGTGGCTTCTGCTCAGAT
Found at i:2613314 original size:92 final size:92
Alignment explanation
Indices: 2613190--2613422 Score: 430
Period size: 92 Copynumber: 2.5 Consensus size: 92
2613180 TTTGGAGTTC
* *
2613190 ATACCAAATCAGATCAGATAACTCAAAGAACACTTCCATAAGATGCTATGAGCACATTCATCTTC
1 ATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTC
2613255 CAAATTCAATAACTGGTTATGTGGTTT
66 CAAATTCAATAACTGGTTATGTGGTTT
*
2613282 ATACCAAACCAGATCAGATAACTCAAATAACACTTCCAGAAGATGCTATGAGCACATTCATCTTC
1 ATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTC
*
2613347 CAAATTCAATAACTGGTTCTGTGGTTT
66 CAAATTCAATAACTGGTTATGTGGTTT
2613374 ATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 ATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
2613423 TGAGTCTCCT
Statistics
Matches: 136, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
92 136 1.00
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.27
Consensus pattern (92 bp):
ATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTC
CAAATTCAATAACTGGTTATGTGGTTT
Found at i:2622440 original size:3 final size:3
Alignment explanation
Indices: 2622432--2622525 Score: 134
Period size: 3 Copynumber: 30.7 Consensus size: 3
2622422 TTATTTATTA
*
2622432 AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT AAAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
* **
2622479 AAT AAT AAT AAT ACT AAT AAT AAT AAT AAT TTT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2622526 ATTTAAATGA
Statistics
Matches: 81, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
3 75 0.93
4 6 0.07
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:2627403 original size:21 final size:21
Alignment explanation
Indices: 2627379--2627419 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2627369 ACGTTTTCAC
* *
2627379 CTTTCACTTTTTATCATTTTA
1 CTTTCACTTTCTATAATTTTA
*
2627400 CTTTTACTTTCTATAATTTT
1 CTTTCACTTTCTATAATTTT
2627420 CTTCTCCCTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.17, G:0.00, T:0.63
Consensus pattern (21 bp):
CTTTCACTTTCTATAATTTTA
Found at i:2642201 original size:2 final size:2
Alignment explanation
Indices: 2642194--2642240 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
2642184 AATTCAGATT
2642194 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2642236 T- TA TA
1 TA TA TA
2642241 ATCGCCTTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2642606 original size:21 final size:21
Alignment explanation
Indices: 2642567--2642670 Score: 109
Period size: 21 Copynumber: 4.9 Consensus size: 21
2642557 CACACTGTCT
**
2642567 AGGGGGTACATATTCCCCCTAC
1 AGGGGGTACCGATTCCCCC-AC
*
2642589 AGGGGGTACCGATTCCCCCCC
1 AGGGGGTACCGATTCCCCCAC
*
2642610 AGGGCGTACCGATTCCCCCACC
1 AGGGGGTACCGATTCCCCCA-C
* ** *
2642632 AGGGGGAACAAATTCCCCCCC
1 AGGGGGTACCGATTCCCCCAC
*
2642653 AAGGGGTACCGATTCCCC
1 AGGGGGTACCGATTCCCC
2642671 TTGTCTAACG
Statistics
Matches: 67, Mismatches: 14, Indels: 3
0.80 0.17 0.04
Matches are distributed among these distances:
21 34 0.51
22 33 0.49
ACGTcount: A:0.21, C:0.38, G:0.25, T:0.15
Consensus pattern (21 bp):
AGGGGGTACCGATTCCCCCAC
Found at i:2642647 original size:43 final size:43
Alignment explanation
Indices: 2642569--2642670 Score: 127
Period size: 43 Copynumber: 2.4 Consensus size: 43
2642559 CACTGTCTAG
** * **
2642569 GGGGTACATATTCCCCCTACAGGGGGTACCGATTCCCCCCC-A
1 GGGGTACCGATTCCCCCTACAGGGGGAACAAATTCCCCCCCAA
2642611 GGGCGTACCGATTCCCCC-ACCAGGGGGAACAAATTCCCCCCCAA
1 GGG-GTACCGATTCCCCCTA-CAGGGGGAACAAATTCCCCCCCAA
2642655 GGGGTACCGATTCCCC
1 GGGGTACCGATTCCCC
2642671 TTGTCTAACG
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
42 4 0.08
43 44 0.85
44 4 0.08
ACGTcount: A:0.21, C:0.39, G:0.25, T:0.16
Consensus pattern (43 bp):
GGGGTACCGATTCCCCCTACAGGGGGAACAAATTCCCCCCCAA
Found at i:2643062 original size:34 final size:32
Alignment explanation
Indices: 2643023--2643087 Score: 94
Period size: 34 Copynumber: 2.0 Consensus size: 32
2643013 GTAAAGGGAA
*
2643023 AAGGTTCTAGCTTAGCCCGTGTAAAAGCTAGGGT
1 AAGGTTCTAGCTTAGCCCG-G-AAAAACTAGGGT
*
2643057 AAGGTTCTAGTTTAGCCCGGAAAAACTAGGG
1 AAGGTTCTAGCTTAGCCCGGAAAAACTAGGG
2643088 AGTTTGTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 10 0.34
33 1 0.03
34 18 0.62
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25
Consensus pattern (32 bp):
AAGGTTCTAGCTTAGCCCGGAAAAACTAGGGT
Found at i:2646094 original size:21 final size:22
Alignment explanation
Indices: 2646043--2646151 Score: 148
Period size: 22 Copynumber: 5.0 Consensus size: 22
2646033 ATCAGATTGT
*
2646043 CCAGGGGGTACAGATTCCCCCC
1 CCAGGGGGTACCGATTCCCCCC
*
2646065 TACAGGGGGTACCGATTCCCCCC
1 -CCAGGGGGTACCGATTCCCCCC
*
2646088 CCAGGGGGTACCGATTCCCCCA
1 CCAGGGGGTACCGATTCCCCCC
* *
2646110 CCAGGGGGAACAGATT-CCCCC
1 CCAGGGGGTACCGATTCCCCCC
*
2646131 CCAGGGGATACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
2646152 TGTCTAACGG
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
21 17 0.23
22 38 0.51
23 20 0.27
ACGTcount: A:0.19, C:0.40, G:0.27, T:0.14
Consensus pattern (22 bp):
CCAGGGGGTACCGATTCCCCCC
Found at i:2654475 original size:15 final size:16
Alignment explanation
Indices: 2654457--2654486 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2654447 CAGCGGTTGG
2654457 AAACCCTAG-GGTTTC
1 AAACCCTAGTGGTTTC
2654472 AAACCCTAGTGGTTT
1 AAACCCTAGTGGTTT
2654487 TAGGTTTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (16 bp):
AAACCCTAGTGGTTTC
Found at i:2654588 original size:3 final size:3
Alignment explanation
Indices: 2654580--2654611 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
2654570 ATATATATTA
2654580 AAT AAT AAT AAT AAT AAT AAT AATT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT A
2654612 TTAACGGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:2656647 original size:64 final size:64
Alignment explanation
Indices: 2656568--2656694 Score: 236
Period size: 64 Copynumber: 2.0 Consensus size: 64
2656558 TGATGAAATT
*
2656568 TATCGTGGTGAAAAGTAGATTATTGGTAGGACACACTATCCGTCTCGTCTTCAACCATTTTATC
1 TATCGTGGTGAAAAGTAGATTATTGGTAGGACACACTATCCGCCTCGTCTTCAACCATTTTATC
*
2656632 TATCGTGGTGAAAAGTAGATTATTGGTAGGACACATTATCCGCCTCGTCTTCAACCATTTTAT
1 TATCGTGGTGAAAAGTAGATTATTGGTAGGACACACTATCCGCCTCGTCTTCAACCATTTTAT
2656695 TCATTATGAC
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.35
Consensus pattern (64 bp):
TATCGTGGTGAAAAGTAGATTATTGGTAGGACACACTATCCGCCTCGTCTTCAACCATTTTATC
Found at i:2657889 original size:2 final size:2
Alignment explanation
Indices: 2657882--2657923 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2657872 AACAACTACA
2657882 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2657924 GCATATGATG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2658085 original size:16 final size:16
Alignment explanation
Indices: 2658066--2658100 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2658056 TAAAAGTATA
2658066 TATATAAGTAATTAAG
1 TATATAAGTAATTAAG
* *
2658082 TATATATGTAATTATG
1 TATATAAGTAATTAAG
2658098 TAT
1 TAT
2658101 GATCAATGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (16 bp):
TATATAAGTAATTAAG
Found at i:2658145 original size:19 final size:19
Alignment explanation
Indices: 2658106--2658145 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2658096 TGTATGATCA
*
2658106 ATGATGTATGTACATATGT
1 ATGATGTATGTACATAAGT
*
2658125 ATGATGTATGTAGATAAGT
1 ATGATGTATGTACATAAGT
2658144 AT
1 AT
2658146 ATATATAGTA
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:0.35, C:0.03, G:0.23, T:0.40
Consensus pattern (19 bp):
ATGATGTATGTACATAAGT
Found at i:2658328 original size:18 final size:18
Alignment explanation
Indices: 2658305--2658355 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
2658295 TATATGCATA
2658305 TATGTACATAT-TATGATG
1 TATGTACATATATAT-ATG
*
2658323 TATGTATATATATATATG
1 TATGTACATATATATATG
* *
2658341 TATTTATATATATAT
1 TATGTACATATATAT
2658356 CATAATTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 27 0.90
19 3 0.10
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.51
Consensus pattern (18 bp):
TATGTACATATATATATG
Found at i:2658340 original size:14 final size:14
Alignment explanation
Indices: 2658323--2658353 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2658313 TATTATGATG
2658323 TATGTATATATATA
1 TATGTATATATATA
*
2658337 TATGTATTTATATA
1 TATGTATATATATA
2658351 TAT
1 TAT
2658354 ATCATAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (14 bp):
TATGTATATATATA
Found at i:2658363 original size:18 final size:18
Alignment explanation
Indices: 2658327--2658365 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2658317 ATGATGTATG
*
2658327 TATATATATATATGTATT
1 TATATATATATATGAATT
2658345 TATATATATATCAT-AATT
1 TATATATATAT-ATGAATT
2658363 TAT
1 TAT
2658366 TTTAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (18 bp):
TATATATATATATGAATT
Found at i:2658728 original size:13 final size:13
Alignment explanation
Indices: 2658705--2658748 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
2658695 TAAAATTAAT
*
2658705 TTAATGATTATAA
1 TTAAGGATTATAA
**
2658718 TTAAGTTTTATAA
1 TTAAGGATTATAA
2658731 TATAAGGATTATAA
1 T-TAAGGATTATAA
2658745 TTAA
1 TTAA
2658749 TGTATAAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (13 bp):
TTAAGGATTATAA
Found at i:2661118 original size:32 final size:31
Alignment explanation
Indices: 2661082--2661158 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
2661072 CGGGGCCGTG
*
2661082 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
2661114 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
2661145 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
2661159 GTCACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:2661151 original size:63 final size:62
Alignment explanation
Indices: 2661036--2661158 Score: 149
Period size: 63 Copynumber: 2.0 Consensus size: 62
2661026 ACCTAAGGGA
* * * ** *
2661036 ACATCTTAGGGCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
2661098 ACATCTTAGGGCCGCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
2661159 GTCACATTAG
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
62 14 0.27
63 37 0.73
ACGTcount: A:0.26, C:0.28, G:0.28, T:0.17
Consensus pattern (62 bp):
ACATCTTAGGGCCGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:2666124 original size:63 final size:63
Alignment explanation
Indices: 2666008--2666131 Score: 146
Period size: 63 Copynumber: 2.0 Consensus size: 63
2665998 ACATAAGGGA
* * * * *
2666008 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGTCGTGGGGCCTATCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCAGGGCCGTAGAGCCTACCTAAGAAC
*
2666071 ACATCTTAGGG-CTGCAGAGCCTACCCGAGA-ATGATCTT-AGGGCCGTAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GAT-TTCAGGGCCGTAGAGCCTACCTAAGA
2666132 GTCACATTAG
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
62 4 0.08
63 46 0.88
64 2 0.04
ACGTcount: A:0.27, C:0.25, G:0.27, T:0.21
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCAGGGCCGTAGAGCCTACCTAAGAAC
Found at i:2669004 original size:18 final size:18
Alignment explanation
Indices: 2668977--2669022 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
2668967 CAACGGTCAA
* *
2668977 CGGGTTGGGTCAATGGGT
1 CGGGTCGGGTCAACGGGT
2668995 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
2669013 CGGGTCGGGT
1 CGGGTCGGGT
2669023 TGTGACCGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.09, C:0.17, G:0.52, T:0.22
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:2671068 original size:32 final size:31
Alignment explanation
Indices: 2671030--2671106 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
2671020 CGGGGCTGTG
*
2671030 GGGCCTACCTAAGAACACATCTTAGGGCCGTA
1 GGGCCTACCTAAGAA-ACATCTTAGGGCCGCA
** **
2671062 GGGCCTACCCGAGAATGATCTTAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTTAGGGCCGCA
*
2671093 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
2671107 GTCACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTTAGGGCCGCA
Found at i:2678777 original size:31 final size:31
Alignment explanation
Indices: 2678742--2678824 Score: 94
Period size: 31 Copynumber: 2.7 Consensus size: 31
2678732 ATAGATTTCG
* *
2678742 GGGCCGTGGGGCCTACCTAAGAAACATCTTA
1 GGGCCGTAGGGCCTACCTAAGAAACATCTCA
* ** **
2678773 GGGCCGCAGGGCCTACCCGAGAATGATCTCA
1 GGGCCGTAGGGCCTACCTAAGAAACATCTCA
*
2678804 GGGCCGTAGAGCCTACCTAAG
1 GGGCCGTAGGGCCTACCTAAG
2678825 TGTCACAATA
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.24, C:0.29, G:0.31, T:0.16
Consensus pattern (31 bp):
GGGCCGTAGGGCCTACCTAAGAAACATCTCA
Found at i:2681654 original size:13 final size:13
Alignment explanation
Indices: 2681636--2681666 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
2681626 AACGATCAAC
2681636 GGTCAACGGGTCG
1 GGTCAACGGGTCG
2681649 GGTCAACGGGTCG
1 GGTCAACGGGTCG
2681662 GGTCA
1 GGTCA
2681667 GGTTGTGACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.23, G:0.45, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:2685396 original size:13 final size:13
Alignment explanation
Indices: 2685378--2685405 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2685368 CGGTCAACGA
2685378 TCAACGGGTCGGG
1 TCAACGGGTCGGG
2685391 TCAACGGGTCGGG
1 TCAACGGGTCGGG
2685404 TC
1 TC
2685406 GGGTCAGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.25, G:0.43, T:0.18
Consensus pattern (13 bp):
TCAACGGGTCGGG
Found at i:2694217 original size:13 final size:13
Alignment explanation
Indices: 2694199--2694223 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2694189 AACGGTCAAC
2694199 GGTCAACGGGTCG
1 GGTCAACGGGTCG
2694212 GGTCAACGGGTC
1 GGTCAACGGGTC
2694224 AGGTTGGGTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.24, G:0.44, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:2704178 original size:13 final size:13
Alignment explanation
Indices: 2704160--2704189 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
2704150 GGTCAACACC
2704160 GGTCAACGGGTCG
1 GGTCAACGGGTCG
2704173 GGTCAACGGGTCG
1 GGTCAACGGGTCG
2704186 GGTC
1 GGTC
2704190 GGGTTGTGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:2713956 original size:18 final size:18
Alignment explanation
Indices: 2713933--2713971 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
2713923 ACCGGTCAAC
*
2713933 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCAGGTCG
2713951 GGTCAACGGGTCAGGTCG
1 GGTCAACGGGTCAGGTCG
2713969 GGT
1 GGT
2713972 TGTGACCGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.13, C:0.21, G:0.49, T:0.18
Consensus pattern (18 bp):
GGTCAACGGGTCAGGTCG
Found at i:2718939 original size:13 final size:13
Alignment explanation
Indices: 2718921--2718950 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
2718911 AACGGTCAAC
2718921 GGTCAACGGGTCG
1 GGTCAACGGGTCG
2718934 GGTCAACGGGTCG
1 GGTCAACGGGTCG
2718947 GGTC
1 GGTC
2718951 GGGTCAACTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:2718950 original size:18 final size:18
Alignment explanation
Indices: 2718927--2718972 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
2718917 CAACGGTCAA
2718927 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
*
2718945 CGGGTCGGGTCAACTGGT
1 CGGGTCGGGTCAACGGGT
2718963 CGGGTCGGGT
1 CGGGTCGGGT
2718973 TATGACCGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.09, C:0.22, G:0.50, T:0.20
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:2719938 original size:2 final size:2
Alignment explanation
Indices: 2719931--2719957 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2719921 GACCCGATAG
2719931 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2719958 TAATTTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2721556 original size:30 final size:30
Alignment explanation
Indices: 2721513--2721569 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
2721503 AAAAATTCAA
* *
2721513 GGACTAAATTGAAATTTTAATTAAATTTAG
1 GGACCAAAGTGAAATTTTAATTAAATTTAG
2721543 GGACCAAAGTGAAATTTTAATTAAATT
1 GGACCAAAGTGAAATTTTAATTAAATT
2721570 CATATCTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.44, C:0.05, G:0.14, T:0.37
Consensus pattern (30 bp):
GGACCAAAGTGAAATTTTAATTAAATTTAG
Found at i:2724722 original size:90 final size:89
Alignment explanation
Indices: 2724570--2724746 Score: 275
Period size: 90 Copynumber: 2.0 Consensus size: 89
2724560 CCTAACACAC
*
2724570 CCTTTTATAGCCAAGTTATCCTAATCATATTAGACTTTTATTATTTCAAATTAATTAAATCTATA
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGACTTTTATTATTTCAAATTAATTAAATCTATA
* *
2724635 TTTAATTAATTAGAATTTAATAAT
66 TTTAATTAATTAAAATTAAATAAT
* * *
2724659 CCTTTTTTATCCAAGTTGCCCTAATCATATTAGGGA-TTTTATTATTTCAAATTAATTAAATCTA
1 CCTTTTATAGCCAAGTTACCCTAATCATATTA--GACTTTTATTATTTCAAATTAATTAAATCTA
2724723 TATTTAATTAATTAAAATTAAATA
64 TATTTAATTAATTAAAATTAAATA
2724747 TTTGAGATTA
Statistics
Matches: 80, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
89 28 0.35
90 50 0.62
91 2 0.03
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (89 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATTAGACTTTTATTATTTCAAATTAATTAAATCTATA
TTTAATTAATTAAAATTAAATAAT
Found at i:2724733 original size:20 final size:20
Alignment explanation
Indices: 2724708--2724777 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 20
2724698 TATTATTTCA
2724708 AATTAATTAAATCTATATTT
1 AATTAATTAAATCTATATTT
2724728 AATTAATTAAAAT-TAAATATTT
1 AATTAATT-AAATCT--ATATTT
*
2724750 GAGATT-ATTAAAACATATATTT
1 -A-ATTAATTAAATC-TATATTT
2724772 AATTAA
1 AATTAA
2724778 CTCTAGATAT
Statistics
Matches: 41, Mismatches: 1, Indels: 15
0.72 0.02 0.26
Matches are distributed among these distances:
20 12 0.29
21 6 0.15
22 15 0.37
23 4 0.10
24 4 0.10
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (20 bp):
AATTAATTAAATCTATATTT
Found at i:2724747 original size:22 final size:21
Alignment explanation
Indices: 2724708--2724777 Score: 63
Period size: 20 Copynumber: 3.3 Consensus size: 21
2724698 TATTATTTCA
* *
2724708 AATTAATTAAATC-TATATTT
1 AATTAATTAAAACAAATATTT
*
2724728 AATTAATTAAAATTAAATATTT
1 AATTAATTAAAA-CAAATATTT
*
2724750 GAGATT-ATTAAAACATATATTT
1 -A-ATTAATTAAAACAAATATTT
2724772 AATTAA
1 AATTAA
2724778 CTCTAGATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
20 14 0.35
21 2 0.05
22 13 0.32
23 8 0.20
24 3 0.08
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (21 bp):
AATTAATTAAAACAAATATTT
Found at i:2727665 original size:10 final size:11
Alignment explanation
Indices: 2727632--2727667 Score: 54
Period size: 11 Copynumber: 3.1 Consensus size: 11
2727622 TAAAACACAA
2727632 TTAGTAATTTGTT
1 TTAG-AATTT-TT
2727645 TTAGAATTTTT
1 TTAGAATTTTT
2727656 TTAGAATTTTT
1 TTAGAATTTTT
2727667 T
1 T
2727668 CTACCTCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 14 0.61
12 5 0.22
13 4 0.17
ACGTcount: A:0.25, C:0.00, G:0.11, T:0.64
Consensus pattern (11 bp):
TTAGAATTTTT
Found at i:2727801 original size:14 final size:14
Alignment explanation
Indices: 2727782--2727821 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
2727772 CAACCCGGTC
2727782 TGACTGTTGACCAT
1 TGACTGTTGACCAT
* *
2727796 TGACTGTTGATCTT
1 TGACTGTTGACCAT
2727810 TGACT-TTGACCA
1 TGACTGTTGACCA
2727822 AAAAGTCAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 5 0.23
14 17 0.77
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (14 bp):
TGACTGTTGACCAT
Found at i:2728608 original size:39 final size:39
Alignment explanation
Indices: 2728563--2728638 Score: 109
Period size: 39 Copynumber: 1.9 Consensus size: 39
2728553 ACCTTACTGT
*
2728563 AGGCTCCTCGACTTTGTGCTCAG-GATAAGTCCTTACCAC
1 AGGCTCCTCGACTTTGTGCACAGTG-TAAGTCCTTACCAC
**
2728602 AGGCTCCTTTACTTTGTGCACAGTGTAAGTCCTTACC
1 AGGCTCCTCGACTTTGTGCACAGTGTAAGTCCTTACC
2728639 GCATGTCCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 32 0.97
40 1 0.03
ACGTcount: A:0.20, C:0.29, G:0.20, T:0.32
Consensus pattern (39 bp):
AGGCTCCTCGACTTTGTGCACAGTGTAAGTCCTTACCAC
Found at i:2729809 original size:130 final size:129
Alignment explanation
Indices: 2729597--2729984 Score: 492
Period size: 130 Copynumber: 3.0 Consensus size: 129
2729587 TATTGCATAT
* * *
2729597 TAACTACTAACTTTTATTTTATTGCACTTTAATCATTGTTATTTATTTATTTATTGTTTCTATTA
1 TAACTACTAACTTTTATTTTATTGCATTTTAATCATTATTATTTATTTATTTATTGTTTCTAATA
* * *
2729662 TCCGATTCGACCTTGTGGTGACCTGATCCGAGGTATGATTCGTATTATTATGGTTCAGACTCTAC
66 TTCGATTCGACCTTGTGGTGACCT-ATCCGGGGTATGATTCGTATTATTATGGTTCAGACTCCAC
*
2729727 TAATTACTAACTTTTATTTTATTGCATTTTAATCATTATTATTTATTTATTTATTGTTTCTAATA
1 TAACTACTAACTTTTATTTTATTGCATTTTAATCATTATTATTTATTTATTTATTGTTTCTAATA
* * * * * *
2729792 TTCGATTCGGCCTTGTGGTGATCCAATCCGGGGTATGATCCGCATTATTATGGTTCGGACTCCGC
66 TTCGATTCGACCTTGTGGTGA-CCTATCCGGGGTATGATTCGTATTATTATGGTTCAGACTCCAC
* * * * *
2729857 TAACTACTGAC-TTTATTTTATTGCATTCTAACCATTGTTTATTTATTTATTTATTTTTTATTTC
1 TAACTACTAACTTTTATTTTATTGCATTTTAATCA----TTA-TTATTTATTTATTTATTGTTTC
* * * *
2729921 TAATATTTGATTCGACCTTATGGTGCCCTATCTGGGGTATGA-TCTGTATTATTATGGTTCAGAC
61 TAATATTCGATTCGACCTTGTGGTGACCTATCCGGGGTATGATTC-GTATTATTATGGTTCAGAC
2729985 CCTGCTAACC
Statistics
Matches: 223, Mismatches: 28, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
129 21 0.09
130 123 0.55
131 2 0.01
132 1 0.00
133 34 0.15
134 42 0.19
ACGTcount: A:0.23, C:0.15, G:0.14, T:0.48
Consensus pattern (129 bp):
TAACTACTAACTTTTATTTTATTGCATTTTAATCATTATTATTTATTTATTTATTGTTTCTAATA
TTCGATTCGACCTTGTGGTGACCTATCCGGGGTATGATTCGTATTATTATGGTTCAGACTCCAC
Found at i:2730097 original size:39 final size:39
Alignment explanation
Indices: 2730014--2730094 Score: 101
Period size: 39 Copynumber: 2.1 Consensus size: 39
2730004 ATACTCTATC
* * *
2730014 TTTTA-TTTTATTGTTCATATTAACATACTGACTTTTAT
1 TTTTATTTTTATTGATCATACTAACATACTAACTTTTAT
* *
2730052 TTTTATTTTTATTGATCTTACTAACTTACTAACATTTTAT
1 TTTTATTTTTATTGATCATACTAACATACTAAC-TTTTAT
2730092 TTT
1 TTT
2730095 ATTGCACAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
38 5 0.14
39 22 0.61
40 9 0.25
ACGTcount: A:0.26, C:0.11, G:0.04, T:0.59
Consensus pattern (39 bp):
TTTTATTTTTATTGATCATACTAACATACTAACTTTTAT
Found at i:2730246 original size:19 final size:19
Alignment explanation
Indices: 2730222--2730261 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
2730212 TTGTTGTATT
2730222 TTATTT-CAGTCCTTTTTTA
1 TTATTTCCAG-CCTTTTTTA
*
2730241 TTATTTCCAGCTTTTTTTA
1 TTATTTCCAGCCTTTTTTA
2730260 TT
1 TT
2730262 TGCATTTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 16 0.84
20 3 0.16
ACGTcount: A:0.15, C:0.15, G:0.05, T:0.65
Consensus pattern (19 bp):
TTATTTCCAGCCTTTTTTA
Found at i:2739191 original size:95 final size:95
Alignment explanation
Indices: 2739076--2739265 Score: 326
Period size: 95 Copynumber: 2.0 Consensus size: 95
2739066 ATACCGACAA
* * *
2739076 GGTAGTATCGATACCATGGTAAGGGTATCGATACCAAGCATCATCGAAGCTAAAATTGGTATCGA
1 GGTAGTATCGATACCATGGTAAGGGTATCAATACCAAGCAACATCGAACCTAAAATTGGTATCGA
*
2739141 TACCGGAAGGGGGTATCGGTACCATAGTAT
66 TACCGGAAAGGGGTATCGGTACCATAGTAT
* *
2739171 GGTAGTATCGATTCCATGGTAAGGGTATCAATACCAGGCAACATCGAACCTAAAATTGGTATCGA
1 GGTAGTATCGATACCATGGTAAGGGTATCAATACCAAGCAACATCGAACCTAAAATTGGTATCGA
2739236 TACCGGAAAGGGGTATCGGTACCATAGTAT
66 TACCGGAAAGGGGTATCGGTACCATAGTAT
2739266 AGAAGTATTG
Statistics
Matches: 89, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
95 89 1.00
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.24
Consensus pattern (95 bp):
GGTAGTATCGATACCATGGTAAGGGTATCAATACCAAGCAACATCGAACCTAAAATTGGTATCGA
TACCGGAAAGGGGTATCGGTACCATAGTAT
Found at i:2739273 original size:22 final size:20
Alignment explanation
Indices: 2739248--2739295 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 20
2739238 CCGGAAAGGG
2739248 GTATCGGTACCATAGTATAGAA
1 GTATCGGTACCA-AG-ATAGAA
* *
2739270 GTATTGGTACCAAGATAGTA
1 GTATCGGTACCAAGATAGAA
2739290 GTATCG
1 GTATCG
2739296 ATACTATTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 10 0.43
21 2 0.09
22 11 0.48
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.29
Consensus pattern (20 bp):
GTATCGGTACCAAGATAGAA
Found at i:2739294 original size:95 final size:95
Alignment explanation
Indices: 2739079--2739299 Score: 282
Period size: 95 Copynumber: 2.3 Consensus size: 95
2739069 CCGACAAGGT
* * * * *
2739079 AGTATCGATACCATGGTAAGGGTATCGATACCAAGCATCATCGAAGCTAAAATTGGTATCGATAC
1 AGTATCGATACCAAGATAAGAGTATCGATACCAAGCAACATCGAACCTAAAATTGGTATCGATAC
* * *
2739144 CGGAAGGGGGTATCGGTACCATAGTATGGT
66 CGGAAAGGGGTATCGGTACCATAGTATAGA
* * * * * *
2739174 AGTATCGATTCCATGGTAAGGGTATCAATACCAGGCAACATCGAACCTAAAATTGGTATCGATAC
1 AGTATCGATACCAAGATAAGAGTATCGATACCAAGCAACATCGAACCTAAAATTGGTATCGATAC
2739239 CGGAAAGGGGTATCGGTACCATAGTATAGA
66 CGGAAAGGGGTATCGGTACCATAGTATAGA
* *
2739269 AGTATTGGTACCAAGAT-AGTAGTATCGATAC
1 AGTATCGATACCAAGATAAG-AGTATCGATAC
2739300 TATTGAGCTT
Statistics
Matches: 110, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
94 2 0.02
95 108 0.98
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.24
Consensus pattern (95 bp):
AGTATCGATACCAAGATAAGAGTATCGATACCAAGCAACATCGAACCTAAAATTGGTATCGATAC
CGGAAAGGGGTATCGGTACCATAGTATAGA
Found at i:2739819 original size:79 final size:78
Alignment explanation
Indices: 2739689--2739854 Score: 287
Period size: 79 Copynumber: 2.1 Consensus size: 78
2739679 GAACGAATGA
2739689 ATAAAAGAATAATGCATACGAGGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGG
1 ATAAAAGAATAATGCATACGAGGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGG
2739754 GTGCATTATCAAC
66 GTGCATTATCAAC
* *
2739767 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATG
1 ATAAAAGAATAATGCATACGAG-GCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATG
* *
2739832 GGTGTATTATTAAC
65 GGTGCATTATCAAC
2739846 ATAAAAGAA
1 ATAAAAGAA
2739855 GATTGGTTTC
Statistics
Matches: 83, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
78 20 0.24
79 63 0.76
ACGTcount: A:0.40, C:0.11, G:0.23, T:0.26
Consensus pattern (78 bp):
ATAAAAGAATAATGCATACGAGGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGG
GTGCATTATCAAC
Found at i:2740219 original size:29 final size:29
Alignment explanation
Indices: 2740163--2740219 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
2740153 ACATAAACGG
*
2740163 TTAAACACTGTTGAGTAAAAGATGAAGGA
1 TTAAACACTGTTGAGTAAAAAATGAAGGA
2740192 TTAAACACTGTTGAGTAAAATAAT-AAGG
1 TTAAACACTGTTGAGTAAAA-AATGAAGG
2740220 GACTAGTTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 24 0.92
30 2 0.08
ACGTcount: A:0.46, C:0.07, G:0.21, T:0.26
Consensus pattern (29 bp):
TTAAACACTGTTGAGTAAAAAATGAAGGA
Found at i:2742187 original size:21 final size:21
Alignment explanation
Indices: 2742161--2742233 Score: 69
Period size: 21 Copynumber: 3.4 Consensus size: 21
2742151 ACCGAAGTGG
*
2742161 CACATAATTTTCCAGAATGAC
1 CACATAATTTTCCCGAATGAC
* *
2742182 CACATAGGTTTACACCGAAGTG-C
1 CACATA-ATTTTC-CCGAA-TGAC
2742205 CACAT-ATTTGTCCCGAATGAC
1 CACATAATTT-TCCCGAATGAC
2742226 CACATAAT
1 CACATAAT
2742234 ACCCTCGACT
Statistics
Matches: 41, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
20 2 0.05
21 20 0.49
22 7 0.17
23 10 0.24
24 2 0.05
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.26
Consensus pattern (21 bp):
CACATAATTTTCCCGAATGAC
Found at i:2742851 original size:53 final size:54
Alignment explanation
Indices: 2742779--2742901 Score: 160
Period size: 53 Copynumber: 2.3 Consensus size: 54
2742769 GATACTTCCC
*
2742779 TTCAAGGGTATCA-ATACCTCCTCAAGGTACCGATACCGATATAACATTCAATGT
1 TTCAAGGGTAT-AGATACCTCCTCAAGGTACCGATACCAATATAACATTCAATGT
* * * *
2742833 TTCAA-GGTATAGATACCTCCTTAAGGTACCGATACCAATCTAGCATTCGATGT
1 TTCAAGGGTATAGATACCTCCTCAAGGTACCGATACCAATATAACATTCAATGT
* *
2742886 TTTAAGGGTATCGATA
1 TTCAAGGGTATAGATA
2742902 TCATCCTTCA
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
52 1 0.02
53 45 0.75
54 14 0.23
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (54 bp):
TTCAAGGGTATAGATACCTCCTCAAGGTACCGATACCAATATAACATTCAATGT
Found at i:2742929 original size:20 final size:21
Alignment explanation
Indices: 2742893--2742942 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
2742883 TGTTTTAAGG
*
2742893 GTATCGATA-TCATCCTT-CA
1 GTATCGATACTCACCCTTACA
2742912 TGTATCGATACT-ACCCTTACA
1 -GTATCGATACTCACCCTTACA
2742933 GTATCGATAC
1 GTATCGATAC
2742943 CTCTTCAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 24 0.89
21 3 0.11
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.34
Consensus pattern (21 bp):
GTATCGATACTCACCCTTACA
Found at i:2749562 original size:20 final size:20
Alignment explanation
Indices: 2749537--2749613 Score: 113
Period size: 20 Copynumber: 3.9 Consensus size: 20
2749527 ATATTTTAAG
* *
2749537 GGTATCGATACCATCCTTCA
1 GGTATCGATACTACCCTTCA
2749557 GGTATCGATACTACCCTTACA
1 GGTATCGATACTACCCTT-CA
2749578 -GTATCGATACTACCCTT-A
1 GGTATCGATACTACCCTTCA
2749596 GGTATCGATACTACCCTT
1 GGTATCGATACTACCCTT
2749614 TAATTTTCAA
Statistics
Matches: 53, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
18 1 0.02
19 17 0.32
20 33 0.62
21 2 0.04
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.31
Consensus pattern (20 bp):
GGTATCGATACTACCCTTCA
Found at i:2749604 original size:39 final size:40
Alignment explanation
Indices: 2749538--2749613 Score: 127
Period size: 39 Copynumber: 1.9 Consensus size: 40
2749528 TATTTTAAGG
*
2749538 GTATCGATACCATCCTTCAGGTATCGATACTACCCTTACA
1 GTATCGATACCACCCTTCAGGTATCGATACTACCCTTACA
*
2749578 GTATCGATACTACCCTT-AGGTATCGATACTACCCTT
1 GTATCGATACCACCCTTCAGGTATCGATACTACCCTT
2749614 TAATTTTCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 19 0.56
40 15 0.44
ACGTcount: A:0.26, C:0.29, G:0.13, T:0.32
Consensus pattern (40 bp):
GTATCGATACCACCCTTCAGGTATCGATACTACCCTTACA
Found at i:2753779 original size:54 final size:54
Alignment explanation
Indices: 2753716--2753875 Score: 136
Period size: 54 Copynumber: 3.2 Consensus size: 54
2753706 CGACAAGGTA
2753716 GTATCGATACCATGGTAAGGGTATCGATACCAAGCATCATCGAAGCTAAAATTG
1 GTATCGATACCATGGTAAGGGTATCGATACCAAGCATCATCGAAGCTAAAATTG
* *
2753770 GTATCGATACC--CG-AAGGGGGTATCGGTACCATAG--T-AT-G--G-T---A---
1 GTATCGATACCATGGTAA--GGGTATCGATACCA-AGCATCATCGAAGCTAAAATTG
* * *
2753811 GTATCGATACCATGGTGAGGGTATCGATACCAAGCAACATCGAACCTAAAATTG
1 GTATCGATACCATGGTAAGGGTATCGATACCAAGCATCATCGAAGCTAAAATTG
2753865 GTATCGATACC
1 GTATCGATACC
2753876 GGAAAGGGGT
Statistics
Matches: 80, Mismatches: 7, Indels: 38
0.64 0.06 0.30
Matches are distributed among these distances:
41 13 0.16
42 13 0.16
43 1 0.01
44 4 0.05
45 1 0.01
47 1 0.01
48 2 0.03
50 1 0.01
51 5 0.06
52 2 0.03
53 13 0.16
54 24 0.30
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (54 bp):
GTATCGATACCATGGTAAGGGTATCGATACCAAGCATCATCGAAGCTAAAATTG
Found at i:2753838 original size:95 final size:94
Alignment explanation
Indices: 2753712--2753935 Score: 324
Period size: 95 Copynumber: 2.4 Consensus size: 94
2753702 ATACCGACAA
* *
2753712 GGTAGTATCGATACCATGGTAAGGGTATCGATACCAAGCATCATCGAAGCTAAAATTGGTATCGA
1 GGTAGTATCGATACCATGGT-AGGGTATCGATACCAAGCAACATCGAACCTAAAATTGGTATCGA
*
2753777 TACCCGAAGGGGGTATCGGTACCATAGTAT
65 TACCCGAAAGGGGTATCGGTACCATAGTAT
2753807 GGTAGTATCGATACCATGGTGAGGGTATCGATACCAAGCAACATCGAACCTAAAATTGGTATCGA
1 GGTAGTATCGATACCATGGT-AGGGTATCGATACCAAGCAACATCGAACCTAAAATTGGTATCGA
* *
2753872 TACCGGAAAGGGGTATTGGTACCATAGTAT
65 TACCCGAAAGGGGTATCGGTACCATAGTAT
* * * *
2753902 AGAAGTATC-AGTACCAGGGTAGTAGTATCGATAC
1 GGTAGTATCGA-TACCATGGTAG-GGTATCGATAC
2753936 TATTGAGCTT
Statistics
Matches: 117, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
94 3 0.03
95 114 0.97
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (94 bp):
GGTAGTATCGATACCATGGTAGGGTATCGATACCAAGCAACATCGAACCTAAAATTGGTATCGAT
ACCCGAAAGGGGTATCGGTACCATAGTAT
Found at i:2754390 original size:45 final size:44
Alignment explanation
Indices: 2754339--2754476 Score: 134
Period size: 45 Copynumber: 3.3 Consensus size: 44
2754329 GAATAGTGTG
2754339 TATGGGTGCATTATTGGCATGAAAGGATGACATAGCTGAAATGCA
1 TATGGGTGCATTATTGGCATGAAAGGATG-CATAGCTGAAATGCA
* ** *
2754384 TATGGGTGCATTGTCAGCAT-AAA--A-G-A-A--T--AATGGA
1 TATGGGTGCATTATTGGCATGAAAGGATGCATAGCTGAAATGCA
*
2754418 TATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATACA
1 TATGGGTGCATTATTGGCATGAAAGGATG-CATAGCTGAAATGCA
*
2754463 TATGGGTGTATTAT
1 TATGGGTGCATTAT
2754477 CAACATAAAA
Statistics
Matches: 72, Mismatches: 10, Indels: 22
0.69 0.10 0.21
Matches are distributed among these distances:
34 22 0.31
35 3 0.04
36 1 0.01
37 1 0.01
38 2 0.03
39 1 0.01
40 1 0.01
41 2 0.03
42 1 0.01
43 1 0.01
44 3 0.04
45 34 0.47
ACGTcount: A:0.33, C:0.10, G:0.28, T:0.29
Consensus pattern (44 bp):
TATGGGTGCATTATTGGCATGAAAGGATGCATAGCTGAAATGCA
Found at i:2754454 original size:79 final size:79
Alignment explanation
Indices: 2754323--2754530 Score: 310
Period size: 79 Copynumber: 2.6 Consensus size: 79
2754313 GAATGAATGA
* *
2754323 ATAAAAGAATAGTGTG-TATGGGTGCATTATTGGCATGAAAGGATGACATAGCTGAAATGCATAT
1 ATAAAAGAATAATG-GATATGGGTGCATTATTGGCATGAAAGGATGACATAGCTGAAATACATAT
* *
2754387 GGGTGCATTGTCAGC
65 GGGTGCATTATCAAC
*
2754402 ATAAAAGAATAATGGATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATACATATG
1 ATAAAAGAATAATGGATATGGGTGCATTATTGGCATGAAAGGATGACATAGCTGAAATACATATG
*
2754467 GGTGTATTATCAAC
66 GGTGCATTATCAAC
* * * *
2754481 ATAAAAGAATAATGCATATGAGTGCATTATTGGCATGAAAAGATGTCATA
1 ATAAAAGAATAATGGATATGGGTGCATTATTGGCATGAAAGGATGACATA
2754531 ACTAAAACAA
Statistics
Matches: 118, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
78 1 0.01
79 117 0.99
ACGTcount: A:0.38, C:0.10, G:0.25, T:0.28
Consensus pattern (79 bp):
ATAAAAGAATAATGGATATGGGTGCATTATTGGCATGAAAGGATGACATAGCTGAAATACATATG
GGTGCATTATCAAC
Found at i:2754595 original size:27 final size:27
Alignment explanation
Indices: 2754563--2754655 Score: 101
Period size: 27 Copynumber: 3.7 Consensus size: 27
2754553 ATGTATTAAG
2754563 GCATGAAATGATGCCATAACTAAAAAT
1 GCATGAAATGATGCCATAACTAAAAAT
*
2754590 GCATGAAATGATG-C--AA-T---AAG
1 GCATGAAATGATGCCATAACTAAAAAT
*
2754610 GCATGAAAGGATGCCATAACTAAAAAT
1 GCATGAAATGATGCCATAACTAAAAAT
* *
2754637 GCATGAAATAATGCAATAA
1 GCATGAAATGATGCCATAA
2754656 GGCATGAAAG
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
20 14 0.26
21 1 0.02
23 3 0.06
24 3 0.06
26 1 0.02
27 31 0.58
ACGTcount: A:0.48, C:0.13, G:0.18, T:0.20
Consensus pattern (27 bp):
GCATGAAATGATGCCATAACTAAAAAT
Found at i:2754614 original size:47 final size:47
Alignment explanation
Indices: 2754512--2754681 Score: 232
Period size: 47 Copynumber: 3.6 Consensus size: 47
2754502 GTGCATTATT
* * ** * *
2754512 GGCATGAAAAGATGTCATAACTAAAACAAATAAATGAAATGATGTATTAA
1 GGCATGAAAGGATGCCATAACT--AA-AAATGCATGAAATGATGCAATAA
*
2754562 GGCATGAAATGATGCCATAACTAAAAATGCATGAAATGATGCAATAA
1 GGCATGAAAGGATGCCATAACTAAAAATGCATGAAATGATGCAATAA
*
2754609 GGCATGAAAGGATGCCATAACTAAAAATGCATGAAATAATGCAATAA
1 GGCATGAAAGGATGCCATAACTAAAAATGCATGAAATGATGCAATAA
*
2754656 GGCATGAAAGGATGCCATAAATAAAA
1 GGCATGAAAGGATGCCATAACTAAAA
2754682 TCAACAAGTA
Statistics
Matches: 111, Mismatches: 9, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
47 89 0.80
48 2 0.02
50 20 0.18
ACGTcount: A:0.49, C:0.11, G:0.19, T:0.21
Consensus pattern (47 bp):
GGCATGAAAGGATGCCATAACTAAAAATGCATGAAATGATGCAATAA
Found at i:2754615 original size:20 final size:20
Alignment explanation
Indices: 2754590--2754675 Score: 64
Period size: 20 Copynumber: 4.0 Consensus size: 20
2754580 AACTAAAAAT
*
2754590 GCATGAAATGATGCAATAAG
1 GCATGAAAGGATGCAATAAG
*
2754610 GCATGAAAGGATGCCATAACTAAAAAT
1 GCATGAAAGGATG-C--AA-T---AAG
**
2754637 GCATGAAATAATGCAATAAG
1 GCATGAAAGGATGCAATAAG
*
2754657 GCATGAAAGGATGCCATAA
1 GCATGAAAGGATGCAATAA
2754676 ATAAAATCAA
Statistics
Matches: 51, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
20 30 0.59
21 1 0.02
23 3 0.06
24 3 0.06
26 1 0.02
27 13 0.25
ACGTcount: A:0.47, C:0.13, G:0.22, T:0.19
Consensus pattern (20 bp):
GCATGAAAGGATGCAATAAG
Found at i:2764382 original size:14 final size:16
Alignment explanation
Indices: 2764351--2764387 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
2764341 TATAAACTGA
2764351 TTTATACTAAAGTATT
1 TTTATACTAAAGTATT
*
2764367 TTTAT-CTAAA-TGTT
1 TTTATACTAAAGTATT
2764381 TTTATAC
1 TTTATAC
2764388 ACCGCAAGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 8 0.42
15 6 0.32
16 5 0.26
ACGTcount: A:0.32, C:0.08, G:0.05, T:0.54
Consensus pattern (16 bp):
TTTATACTAAAGTATT
Found at i:2765594 original size:23 final size:23
Alignment explanation
Indices: 2765568--2765612 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2765558 TAGTGGCTAG
*
2765568 TAGTTAGAAATTAGAAAAGTCAA
1 TAGTTAGAAATTAAAAAAGTCAA
*
2765591 TAGTTAGAAGTTAAAAAAGTCA
1 TAGTTAGAAATTAAAAAAGTCA
2765613 GTAGGCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.51, C:0.04, G:0.18, T:0.27
Consensus pattern (23 bp):
TAGTTAGAAATTAAAAAAGTCAA
Found at i:2765777 original size:30 final size:29
Alignment explanation
Indices: 2765741--2765839 Score: 153
Period size: 30 Copynumber: 3.3 Consensus size: 29
2765731 AAATGAAAAG
*
2765741 TATGAAAATTTGAGCATCAGAATCAAGACA
1 TATGAAAATTAGAGCATCAGAATCAA-ACA
*
2765771 TATGAAAATTAGAGCATCAGAATTAAAACA
1 TATGAAAATTAGAGCATCAGAA-TCAAACA
2765801 TATGAAAATTAGAGCATCAGAATCCAAACA
1 TATGAAAATTAGAGCATCAGAAT-CAAACA
2765831 TATGAAAAT
1 TATGAAAAT
2765840 AAGAAAATAA
Statistics
Matches: 64, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
29 1 0.02
30 60 0.94
31 3 0.05
ACGTcount: A:0.51, C:0.12, G:0.14, T:0.23
Consensus pattern (29 bp):
TATGAAAATTAGAGCATCAGAATCAAACA
Found at i:2767698 original size:74 final size:75
Alignment explanation
Indices: 2767330--2767701 Score: 577
Period size: 75 Copynumber: 5.0 Consensus size: 75
2767320 CCAGAGGACT
* *
2767330 TAATCATCAAGAAACCTTTGAAAATAAAACTT-GCTTCTTTAAAAATTCATTTGAAAACATCATA
1 TAATCATCAAGAAACCTTTGAGAATCAAACTTGGCTTCTTTAAAAATTCATTTGAAAACATCATA
**
2767394 TCGGTCAGGG
66 TCGGTTGGGG
* *
2767404 TAATCATCAAGAAACCTTTCAGAATCAAACTTGGCTTCTTTAAAAAGTCATTTGAAAACATCATA
1 TAATCATCAAGAAACCTTTGAGAATCAAACTTGGCTTCTTTAAAAATTCATTTGAAAACATCATA
*
2767469 TCAGTTGGGG
66 TCGGTTGGGG
* *
2767479 TAATCATCAAAAAACCTTTGAAAATCAAACTTGGCTTCTTTAAAAATTCATTTGAAAACATCATA
1 TAATCATCAAGAAACCTTTGAGAATCAAACTTGGCTTCTTTAAAAATTCATTTGAAAACATCATA
**
2767544 TCGGTCAGGG
66 TCGGTTGGGG
* * * *
2767554 AAATCGTCAAGAAACCTTTGAGAATCAAACTCGGCTTCTTTAAAAATTCATTTAAAAACATCATA
1 TAATCATCAAGAAACCTTTGAGAATCAAACTTGGCTTCTTTAAAAATTCATTTGAAAACATCATA
2767619 TCGGTTGGGG
66 TCGGTTGGGG
* *
2767629 TAATCCTCAAGAAACCTTTGAGAATCAAACTTGGCTT-TTTAAAGATTCATTTGAAAACATCATA
1 TAATCATCAAGAAACCTTTGAGAATCAAACTTGGCTTCTTTAAAAATTCATTTGAAAACATCATA
2767693 TCGGTTGGG
66 TCGGTTGGG
2767702 TAACATGCCC
Statistics
Matches: 270, Mismatches: 27, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
74 63 0.23
75 207 0.77
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (75 bp):
TAATCATCAAGAAACCTTTGAGAATCAAACTTGGCTTCTTTAAAAATTCATTTGAAAACATCATA
TCGGTTGGGG
Found at i:2770599 original size:106 final size:106
Alignment explanation
Indices: 2770394--2770599 Score: 272
Period size: 106 Copynumber: 1.9 Consensus size: 106
2770384 GTCTTTTCTC
* * * *
2770394 GGCTAGCTGAATGAATTATCCATAAAGTCAGGGCTTTTAACCAATTGCTTTAGAGGAATATCTCA
1 GGCTAGCTGAAGGAATTATCCATAAAGCCAGGACTTTTAACCAATTACTTTAGAGGAATATCTCA
* * * **
2770459 ATTTTATTGTATATATACATATATATTATTTTCCTTTATTT
66 ACTTTATTATATACATACATATATATTAACTTCCTTTATTT
*
2770500 GGCTAGCTGAAGGAATCTATCCATAAAGCCAGGACTTTTAACCAATTACTTTA-AGGAGTATCTC
1 GGCTAGCTGAAGGAAT-TATCCATAAAGCCAGGACTTTTAACCAATTACTTTAGAGGAATATCTC
* *
2770564 AACTTTGTTATATACATATA-ATCATATTAACTTCCT
65 AACTTTATTATATACATACATAT-ATATTAACTTCCT
2770600 AGGTATACAA
Statistics
Matches: 86, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
105 2 0.02
106 51 0.59
107 33 0.38
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (106 bp):
GGCTAGCTGAAGGAATTATCCATAAAGCCAGGACTTTTAACCAATTACTTTAGAGGAATATCTCA
ACTTTATTATATACATACATATATATTAACTTCCTTTATTT
Found at i:2778448 original size:2 final size:2
Alignment explanation
Indices: 2778436--2778696 Score: 88
Period size: 2 Copynumber: 137.5 Consensus size: 2
2778426 TATAAGAATA
* * *
2778436 AT AT AT GAT AT AT AT GCT AT AT AA AT AT AT AT ACT AT A- AT AC
1 AT AT AT -AT AT AT AT -AT AT AT AT AT AT AT AT A-T AT AT AT AT
* * *
2778478 AT AT A- AC AT A- AT AT AA AT AT -T AT AT -T AT AT A- AT ACC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
*
2778516 A- AT AT AT A- AT A- AT A- AA AT AT AT AT ACT AT A- AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
* * *
2778553 AT AG A- AT AT AT AG A- AT AT AT ACT AT AT AT A- AT AT AT ACT AA
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT
* * *
2778594 AT AT A- AT AC AT ACT AT GT A- AT -T ACT AT AA AT A- AT AT AT A-
1 AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
* *
2778633 AT AT A- AT AT AT A- AT AT ACT AT GT ACT -T AT ACC AT AT A- AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT A-T AT AT AT AT
*
2778672 AT GT AT AT AT AT -T AT AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2778697 CTATCCTAGA
Statistics
Matches: 193, Mismatches: 28, Indels: 76
0.65 0.09 0.26
Matches are distributed among these distances:
1 26 0.13
2 147 0.76
3 20 0.10
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (2 bp):
AT
Found at i:2778520 original size:29 final size:29
Alignment explanation
Indices: 2778459--2778555 Score: 99
Period size: 29 Copynumber: 3.4 Consensus size: 29
2778449 ATGCTATATA
* * * *
2778459 AATATAT-ATACTATAATACATATAACAT
1 AATATATAATAATAAAATATATATACCAT
* * *
2778487 AATATA-AATATTATATTATATAATACCAT
1 AATATATAATAATAAAATATAT-ATACCAT
*
2778516 AATATATAATAATAAAATATATATACTAT
1 AATATATAATAATAAAATATATATACCAT
2778545 AATATATAATA
1 AATATATAATA
2778556 GAATATATAG
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
28 17 0.29
29 29 0.50
30 12 0.21
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (29 bp):
AATATATAATAATAAAATATATATACCAT
Found at i:2778524 original size:7 final size:7
Alignment explanation
Indices: 2778433--2778696 Score: 116
Period size: 7 Copynumber: 36.4 Consensus size: 7
2778423 ATTTATAAGA
2778433 ATAATAT
1 ATAATAT
2778440 ATGATATAT
1 AT-A-ATAT
**
2778449 ATGCTAT
1 ATAATAT
2778456 ATAA-AT
1 ATAATAT
2778462 ATATATACT
1 ATA-ATA-T
*
2778471 ATAATAC
1 ATAATAT
*
2778478 AT-ATAAC
1 ATAAT-AT
2778485 ATAATAT
1 ATAATAT
2778492 A-AATATT
1 ATAATA-T
*
2778499 ATATTAT
1 ATAATAT
*
2778506 ATAATACC
1 ATAATA-T
2778514 ATAATAT
1 ATAATAT
2778521 ATAATA-
1 ATAATAT
*
2778527 ATAAAAT
1 ATAATAT
2778534 ATATATACT
1 ATA-ATA-T
2778543 ATAATAT
1 ATAATAT
*
2778550 ATAATAG
1 ATAATAT
2778557 A-ATATAT
1 ATA-ATAT
*
2778564 AGAATAT
1 ATAATAT
2778571 ATACTATAT
1 ATA--ATAT
2778580 ATAATAT
1 ATAATAT
*
2778587 ATACTAAAT
1 ATA--ATAT
*
2778596 ATAATAC
1 ATAATAT
*
2778603 ATACTAT
1 ATAATAT
*
2778610 GTAAT-T
1 ATAATAT
*
2778616 ACT-ATAA
1 A-TAATAT
2778623 ATAATAT
1 ATAATAT
2778630 AT-A-AT
1 ATAATAT
2778635 ATAATAT
1 ATAATAT
2778642 ATAATAT
1 ATAATAT
*
2778649 ACTATGTACTT
1 A-TA-ATA--T
**
2778660 ATACCAT
1 ATAATAT
2778667 ATAATAT
1 ATAATAT
*
2778674 GT-ATAT
1 ATAATAT
*
2778680 ATATTAT
1 ATAATAT
2778687 ATAATAT
1 ATAATAT
2778694 ATA
1 ATA
2778697 CTATCCTAGA
Statistics
Matches: 194, Mismatches: 34, Indels: 58
0.68 0.12 0.20
Matches are distributed among these distances:
5 4 0.02
6 28 0.14
7 104 0.54
8 24 0.12
9 30 0.15
10 2 0.01
11 2 0.01
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.40
Consensus pattern (7 bp):
ATAATAT
Found at i:2778580 original size:44 final size:44
Alignment explanation
Indices: 2778443--2778647 Score: 116
Period size: 44 Copynumber: 4.5 Consensus size: 44
2778433 ATAATATATG
* * * * * * *
2778443 ATATATATGCTATATAAATATATATACTATAATACA-TATAACATA
1 ATATATATACTATA-ATATATA-ATACAATAATATAGAATAATAAA
* * * * *
2778488 ATATAAATATTATATTATATAATACCATAATATATAATAATAAA
1 ATATATATACTATAATATATAATACAATAATATAGAATAATAAA
* *
2778532 ATATATATACTATAATATATAATAGAAT-ATATAGAATATATACTAT
1 ATATATATACTATAATATATAATACAATAATATAGAATA-ATA--AA
* *
2778578 ATATAATATA-TACTAA-ATATAATAC-ATACTAT-GTAATTACTATAA
1 ATAT-ATATACTA-TAATATATAATACAATAATATAG-AA-TAATA-AA
*
2778623 ATAATATATAATATAATATATAATA
1 AT-ATATATACTATAATATATAATA
2778648 TACTATGTAC
Statistics
Matches: 127, Mismatches: 21, Indels: 23
0.74 0.12 0.13
Matches are distributed among these distances:
43 20 0.16
44 37 0.29
45 26 0.20
46 34 0.27
47 10 0.08
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.39
Consensus pattern (44 bp):
ATATATATACTATAATATATAATACAATAATATAGAATAATAAA
Found at i:2779579 original size:24 final size:24
Alignment explanation
Indices: 2779552--2779598 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2779542 CTCTTTCTAT
*
2779552 CAATCATG-GTTTCTTGATTCTTGC
1 CAATCATGATTTTC-TGATTCTTGC
*
2779576 CAATCCTGATTTTCTGATTCTTG
1 CAATCATGATTTTCTGATTCTTG
2779599 GTTCTTGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.17, C:0.21, G:0.15, T:0.47
Consensus pattern (24 bp):
CAATCATGATTTTCTGATTCTTGC
Found at i:2787053 original size:24 final size:24
Alignment explanation
Indices: 2787004--2787053 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
2786994 GTAGGTTAAG
*
2787004 GAAGCTTGTGCTTTTACCGCAAAT
1 GAAGCTTGTGCTTTTACAGCAAAT
* *
2787028 GAAGCTTGTGCTTTTGCAGCAGAT
1 GAAGCTTGTGCTTTTACAGCAAAT
2787052 GA
1 GA
2787054 GTCTTCTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (24 bp):
GAAGCTTGTGCTTTTACAGCAAAT
Found at i:2787367 original size:21 final size:21
Alignment explanation
Indices: 2787341--2787384 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
2787331 GGTATTGTAA
2787341 TGATGAGATGTGTCCAGTGCT
1 TGATGAGATGTGTCCAGTGCT
* *
2787362 TGATGAGGTGTGTCCAGTTCT
1 TGATGAGATGTGTCCAGTGCT
2787383 TG
1 TG
2787385 TTCCCTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.14, G:0.34, T:0.36
Consensus pattern (21 bp):
TGATGAGATGTGTCCAGTGCT
Found at i:2789716 original size:12 final size:12
Alignment explanation
Indices: 2789699--2789732 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2789689 GTGAGATAGG
2789699 AATAATAATCAA
1 AATAATAATCAA
*
2789711 AATAATAATGAA
1 AATAATAATCAA
*
2789723 AATAAAAATC
1 AATAATAATC
2789733 CCCACCCTAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.68, C:0.06, G:0.03, T:0.24
Consensus pattern (12 bp):
AATAATAATCAA
Found at i:2792101 original size:7 final size:7
Alignment explanation
Indices: 2792091--2792263 Score: 51
Period size: 7 Copynumber: 26.6 Consensus size: 7
2792081 ATATATGATA
2792091 TATATAC
1 TATATAC
2792098 TATA-AC
1 TATATAC
2792104 ATATAATA-
1 -TAT-ATAC
*
2792112 TAATATAA
1 T-ATATAC
*
2792120 TAATATAA
1 T-ATATAC
*
2792128 TATATAT
1 TATATAC
2792135 TATATA-
1 TATATAC
2792141 TA-ATAC
1 TATATAC
2792147 -ATA-A-
1 TATATAC
*
2792151 TATATAA
1 TATATAC
2792158 T-TATAC
1 TATATAC
*
2792164 TATA-AA
1 TATATAC
2792170 TA-ATA-
1 TATATAC
*
2792175 TATAATAT
1 TAT-ATAC
2792183 TATATA-
1 TATATAC
2792189 TAATATAC
1 T-ATATAC
* *
2792197 AATGTAC
1 TATATAC
2792204 T-TATAC
1 TATATAC
*
2792210 CATATA-
1 TATATAC
*
2792216 -ATAT-G
1 TATATAC
*
2792221 TATATGC
1 TATATAC
2792228 TATATA-
1 TATATAC
2792234 TA-ATAC
1 TATATAC
2792240 TA-ATAC
1 TATATAC
*
2792246 TATATAA
1 TATATAC
2792253 TATATAC
1 TATATAC
2792260 TATA
1 TATA
2792264 CTGGACGAAA
Statistics
Matches: 131, Mismatches: 12, Indels: 46
0.69 0.06 0.24
Matches are distributed among these distances:
5 18 0.14
6 34 0.26
7 63 0.48
8 15 0.11
9 1 0.01
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (7 bp):
TATATAC
Found at i:2792112 original size:5 final size:5
Alignment explanation
Indices: 2792036--2792195 Score: 74
Period size: 5 Copynumber: 32.6 Consensus size: 5
2792026 TAAATGGCAC
* * * *
2792036 ATAAT ATAAC ATAAT AT-TT GTAAT AATAAT ATATT A-AAT ATAAT A-ATAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT -ATAAT ATAAT ATAAT ATAAT ATA-AT
* *
2792085 ATGAT AT-AT ATACT ATAACAT ATAAT ATAAT AT-A- ATAAT ATAAT AT-AT
1 ATAAT ATAAT ATAAT AT-A-AT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
* *
2792133 ATTATAT ATAAT ACATAAT AT-AT A-ATT ATACT ATAA- ATAAT AT-AT
1 A-TA-AT ATAAT --ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
*
2792178 AATATT AT-AT ATAAT ATA
1 -ATAAT ATAAT ATAAT ATA
2792196 CAATGTACTT
Statistics
Matches: 118, Mismatches: 16, Indels: 42
0.67 0.09 0.24
Matches are distributed among these distances:
3 2 0.02
4 29 0.25
5 67 0.57
6 9 0.08
7 11 0.09
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (5 bp):
ATAAT
Found at i:2792120 original size:41 final size:41
Alignment explanation
Indices: 2792064--2792188 Score: 116
Period size: 41 Copynumber: 3.0 Consensus size: 41
2792054 TGTAATAATA
*
2792064 ATATATTA-AATATAATAATAT-ATGATATA-TATACTATAAC
1 ATATAATATAATATAATAATATAAT-ATATATTATA-TATAAC
2792104 ATATAATATAATATAATAATATAATATATATTATATATAATAC
1 ATATAATATAATATAATAATATAATATATATTATATAT-A-AC
*
2792147 ATA-ATATATAATTATACTATAA-ATAATATATAATATTATATA
1 ATATA-ATATAA-TATA--ATAATATAATATATATTA-TATATA
2792189 TAATATACAA
Statistics
Matches: 73, Mismatches: 2, Indels: 15
0.81 0.02 0.17
Matches are distributed among these distances:
40 7 0.10
41 21 0.29
42 8 0.11
43 11 0.15
44 4 0.05
45 13 0.18
46 9 0.12
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (41 bp):
ATATAATATAATATAATAATATAATATATATTATATATAAC
Found at i:2792120 original size:70 final size:66
Alignment explanation
Indices: 2792058--2792195 Score: 173
Period size: 65 Copynumber: 2.1 Consensus size: 66
2792048 AATATTTGTA
2792058 ATAATAATATATTAAATATAATA-AT-ATATGAT-ATATATACTATAACATATAATATAATATAA
1 ATAAT-ATATATTAAATATAATACATAATAT-ATAAT-TATACTATAA-ATATAATATAATATAA
2792120 TA-AT
62 TATAT
*
2792124 ATAATATATATTATATATAATACATAATATATAATTATACTATAAATA-ATATATAATAT--TAT
1 ATAATATATATTAAATATAATACATAATATATAATTATACTATAAATATA-ATATAATATAATAT
2792186 AT
65 AT
2792188 ATAATATA
1 ATAATATA
2792196 CAATGTACTT
Statistics
Matches: 66, Mismatches: 1, Indels: 12
0.84 0.01 0.15
Matches are distributed among these distances:
63 2 0.03
64 11 0.17
65 28 0.42
66 19 0.29
67 6 0.09
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (66 bp):
ATAATATATATTAAATATAATACATAATATATAATTATACTATAAATATAATATAATATAATATA
T
Found at i:2792225 original size:48 final size:47
Alignment explanation
Indices: 2792073--2792259 Score: 122
Period size: 48 Copynumber: 4.0 Consensus size: 47
2792063 AATATATTAA
* * **
2792073 ATATAATA--ATATATGA-TATATATACT-ATAACATATAA-TATAAT
1 ATATAATATTATATAT-ATTATATATAATAATAATATATAATTATACC
* *
2792116 ATAATAATATAATATATATTATATATAATACATAATATATAATTATACT
1 AT-ATAATATTATATATATTATATATAATA-ATAATATATAATTATACC
* * *
2792165 ATA-AATAATATATAATATTATATATAAT-ATACA-ATGTACTTATACC
1 ATATAATATTATAT-ATATTATATATAATAATA-ATATATAATTATACC
* * *
2792211 ATATAATATGTATATGCTA-TATATAATACTAATACTATATAATATATAC
1 ATATAATAT-TATAT-ATATTATAT-ATAATAATAATATATAAT-TATAC
2792260 TATACTGGAC
Statistics
Matches: 114, Mismatches: 15, Indels: 23
0.75 0.10 0.15
Matches are distributed among these distances:
43 2 0.02
44 6 0.05
45 1 0.01
46 31 0.27
47 18 0.16
48 36 0.32
49 15 0.13
50 5 0.04
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (47 bp):
ATATAATATTATATATATTATATATAATAATAATATATAATTATACC
Found at i:2792249 original size:16 final size:14
Alignment explanation
Indices: 2792230--2792263 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 14
2792220 GTATATGCTA
2792230 TATATAATACTAATAC
1 TATATAATA-T-ATAC
2792246 TATATAATATATAC
1 TATATAATATATAC
2792260 TATA
1 TATA
2792264 CTGGACGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 1 0.06
16 9 0.50
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (14 bp):
TATATAATATATAC
Found at i:2799744 original size:16 final size:16
Alignment explanation
Indices: 2799723--2799763 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
2799713 TATATAGCGA
2799723 AAATAAATTAT-TTTAT
1 AAAT-AATTATATTTAT
2799739 AAATAATTATATTTAT
1 AAATAATTATATTTAT
*
2799755 AAATCATTA
1 AAATAATTA
2799764 AAAGCAGCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 6 0.26
16 17 0.74
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
AAATAATTATATTTAT
Found at i:2801622 original size:43 final size:43
Alignment explanation
Indices: 2801552--2801668 Score: 180
Period size: 43 Copynumber: 2.7 Consensus size: 43
2801542 CGGCGTTTGT
* *
2801552 AAACGCCGTAATAGGTTTTGACATTTAGCGGCATTTGTGTTAA
1 AAACGCCGCAATAGGTTTTGACATTTAGCGGCATTTGTATTAA
* * *
2801595 AAATGCCGCAATAGGTTTTGACATTTAGCGACGTTTGTATTAA
1 AAACGCCGCAATAGGTTTTGACATTTAGCGGCATTTGTATTAA
*
2801638 AAACACCGCAATAGGTTTTGACATTTAGCGG
1 AAACGCCGCAATAGGTTTTGACATTTAGCGG
2801669 TGTTTTTAGG
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 66 1.00
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.32
Consensus pattern (43 bp):
AAACGCCGCAATAGGTTTTGACATTTAGCGGCATTTGTATTAA
Found at i:2801797 original size:42 final size:43
Alignment explanation
Indices: 2801692--2801801 Score: 152
Period size: 42 Copynumber: 2.6 Consensus size: 43
2801682 AAAACACAGA
*
2801692 TAAAGATCTGGTATATAGCGGCGTTTTAGGATACAAACGCCGC
1 TAAAGATCTGGTATATAGCGGCGTTTTAGGATACAAACGCCAC
*** *
2801735 TGCTGATCTGGTATAT-GCGGCGTTTTAGTATACAAACGCCAC
1 TAAAGATCTGGTATATAGCGGCGTTTTAGGATACAAACGCCAC
*
2801777 TAAAGGT-TGGTATATAGCGGCGTTT
1 TAAAGATCTGGTATATAGCGGCGTTT
2801802 GTAACAAAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
41 8 0.14
42 36 0.63
43 13 0.23
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.30
Consensus pattern (43 bp):
TAAAGATCTGGTATATAGCGGCGTTTTAGGATACAAACGCCAC
Found at i:2802946 original size:39 final size:41
Alignment explanation
Indices: 2802867--2802956 Score: 103
Period size: 39 Copynumber: 2.2 Consensus size: 41
2802857 TTTTAGTTAT
* * * *
2802867 AAACGCCGCTAAATTACCACTTTATTGTGTCGTTTTTTTTAA
1 AAACGCCGCTAAAGTACCAC-TTATTGTGGCATTTGTTTTAA
* *
2802909 AAACGCCGCTAAAGTATCA-TT-TTGTGGCATTTGTTTTAT
1 AAACGCCGCTAAAGTACCACTTATTGTGGCATTTGTTTTAA
2802948 AAACGCCGC
1 AAACGCCGC
2802957 GAAATGCTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
39 23 0.55
40 2 0.05
42 17 0.40
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.38
Consensus pattern (41 bp):
AAACGCCGCTAAAGTACCACTTATTGTGGCATTTGTTTTAA
Done.