Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008497.1 Hibiscus syriacus cultivar Beakdansim tig00111342_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: 1504768
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 5 of 6
Found at i:950558 original size:25 final size:25
Alignment explanation
Indices: 950524--950574 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
950514 ACACTGATTC
*
950524 GAGGTGTGACCATGCCCTTTGAGCG
1 GAGGCGTGACCATGCCCTTTGAGCG
950549 GAGGCGTGACCATGCCCTTTGAGCG
1 GAGGCGTGACCATGCCCTTTGAGCG
950574 G
1 G
950575 TGTCGTCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.16, C:0.25, G:0.37, T:0.22
Consensus pattern (25 bp):
GAGGCGTGACCATGCCCTTTGAGCG
Found at i:954463 original size:23 final size:23
Alignment explanation
Indices: 954414--954464 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
954404 GTGTTATATT
**
954414 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
954437 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
954460 ATATT
1 ATATT
954465 ATTAGATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:954495 original size:10 final size:9
Alignment explanation
Indices: 954453--954524 Score: 58
Period size: 10 Copynumber: 7.6 Consensus size: 9
954443 TAAATATCTT
954453 TATTAA-AA
1 TATTAATAA
*
954461 TATTATTAGA
1 TATTAATA-A
954471 TTATTAGATTAA
1 -TATTA-A-TAA
954483 TATTAAATAA
1 TATT-AATAA
*
954493 TATTATTAA
1 TATTAATAA
954502 TTATTAATAA
1 -TATTAATAA
954512 T-TTAATAA
1 TATTAATAA
954520 TATTA
1 TATTA
954525 TTTCTATGAA
Statistics
Matches: 52, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
8 13 0.25
9 9 0.17
10 16 0.31
11 10 0.19
12 2 0.04
13 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (9 bp):
TATTAATAA
Found at i:954497 original size:24 final size:27
Alignment explanation
Indices: 954470--954526 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
954460 ATATTATTAG
954470 ATTATT-A-GATTAAT-ATTAAATAAT
1 ATTATTAATGATTAATAATTAAATAAT
* *
954494 ATTATTAATTATTAATAATTTAATAAT
1 ATTATTAATGATTAATAATTAAATAAT
954521 ATTATT
1 ATTATT
954527 TCTATGAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 6 0.21
25 1 0.04
26 6 0.21
27 15 0.54
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (27 bp):
ATTATTAATGATTAATAATTAAATAAT
Found at i:954592 original size:29 final size:29
Alignment explanation
Indices: 954567--954664 Score: 89
Period size: 29 Copynumber: 3.4 Consensus size: 29
954557 ATTAATAATT
954567 TATTATATATTATTAAAATAAAAATATAA
1 TATTATATATTATTAAAATAAAAATATAA
* * * *
954596 TATTTTATATTATTATAAT-ATAAT-TGAT
1 TATTATATATTATTAAAATAAAAATAT-AA
*
954624 TATT-T-TATTA-TAATATTAAAAATATAA
1 TATTATATATTATTAA-AATAAAAATATAA
954651 TATTATATTATTAT
1 TATTATA-TATTAT
954665 AATATTATAT
Statistics
Matches: 53, Mismatches: 8, Indels: 14
0.71 0.11 0.19
Matches are distributed among these distances:
25 2 0.04
26 7 0.13
27 11 0.21
28 11 0.21
29 17 0.32
30 5 0.09
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (29 bp):
TATTATATATTATTAAAATAAAAATATAA
Found at i:954611 original size:8 final size:8
Alignment explanation
Indices: 954595--954675 Score: 55
Period size: 8 Copynumber: 10.6 Consensus size: 8
954585 TAAAAATATA
954595 ATATT-TT
1 ATATTATT
954602 ATATTATT
1 ATATTATT
*
954610 ATAATA-T
1 ATATTATT
954617 A-ATTGATT
1 ATATT-ATT
*
954625 ATTTTATT
1 ATATTATT
*
954633 ATAATATT
1 ATATTATT
* *
954641 A-A-AAAT
1 ATATTATT
*
954647 ATAATATT
1 ATATTATT
954655 ATATTATT
1 ATATTATT
*
954663 ATAATATT
1 ATATTATT
954671 ATATT
1 ATATT
954676 TTAAATATTT
Statistics
Matches: 56, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
6 5 0.09
7 10 0.18
8 39 0.70
9 2 0.04
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (8 bp):
ATATTATT
Found at i:954691 original size:25 final size:24
Alignment explanation
Indices: 954655--954701 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
954645 ATATAATATT
*
954655 ATATTATTATAATATTATATTTTAA
1 ATATTATTATAAT-TAATATTTTAA
954680 ATATT-TTAATAATTAATATTTT
1 ATATTATT-ATAATTAATATTTT
954702 GATTGAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
ATATTATTATAATTAATATTTTAA
Found at i:954692 original size:55 final size:53
Alignment explanation
Indices: 954585--954692 Score: 130
Period size: 55 Copynumber: 2.0 Consensus size: 53
954575 ATTATTAAAA
* *
954585 TAAAAATATAATATTTTATATTATTATAATATAATTGATTATTTTATTATAATAT
1 TAAAAATATAATA-TTTATATTATTATAATATAATTAAATATTTTA-TATAATAT
954640 TAAAAATATAATA-TTATATTATTATAATATTATATTTTAAATATTTTA-ATAAT
1 TAAAAATATAATATTTATATTATTATAATA-TA-A--TTAAATATTTTATATAAT
954693 TAATATTTTG
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
53 16 0.34
54 2 0.04
55 19 0.40
57 10 0.21
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (53 bp):
TAAAAATATAATATTTATATTATTATAATATAATTAAATATTTTATATAATAT
Found at i:955108 original size:22 final size:20
Alignment explanation
Indices: 955069--955108 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
955059 TATATTTTAG
955069 ATTTATTTTAAAAATTATTA
1 ATTTATTTTAAAAATTATTA
955089 ATTTATTGTTAATAAATTAT
1 ATTTATT-TTAA-AAATTAT
955109 ATAGTCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 4 0.22
22 7 0.39
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
ATTTATTTTAAAAATTATTA
Found at i:955989 original size:25 final size:24
Alignment explanation
Indices: 955934--955991 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
955924 ATGTATTGTA
* **
955934 TATAGTTATAAAAAACCATTTTTT
1 TATAATTATAAAAAACCATTTAAT
*
955958 TATTAATTATAAAAGACCATTTAAAT
1 TA-TAATTATAAAAAACCATTT-AAT
955984 TATAATTA
1 TATAATTA
955992 AATAATATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
24 2 0.07
25 23 0.82
26 3 0.11
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (24 bp):
TATAATTATAAAAAACCATTTAAT
Found at i:956003 original size:16 final size:17
Alignment explanation
Indices: 955982--956028 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
955972 GACCATTTAA
955982 ATTATAATTAAAT-AAT
1 ATTATAATTAAATAAAT
*
955998 ATTATAA-TATTATAAAT
1 ATTATAATTA-AATAAAT
956015 ATTTATAATTAAAT
1 A-TTATAATTAAAT
956029 TTAAACAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 2 0.08
16 9 0.36
17 4 0.16
18 8 0.32
19 2 0.08
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTATAATTAAATAAAT
Found at i:956320 original size:74 final size:74
Alignment explanation
Indices: 956194--956334 Score: 219
Period size: 74 Copynumber: 1.9 Consensus size: 74
956184 ACATCATTCG
* ** * *
956194 ATTGGAGGGTTAAATTTATTTTAATTTATTAAAAGTATGACTAAATTGAGAGAATATGTAAATAT
1 ATTGGAGGATTAAATTTATTTTAATTTATTAAAAGTAAAACTAAATTAAGAGAATACGTAAATAT
956259 CAGTGACCA
66 CAGTGACCA
* *
956268 ATTGTAGGATTAAATTTATTTTAATTTATTAAAAGTAAAACTCAATTAAGAGAATACGTAAATAT
1 ATTGGAGGATTAAATTTATTTTAATTTATTAAAAGTAAAACTAAATTAAGAGAATACGTAAATAT
956333 CA
66 CA
956335 AAAATTAAAT
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
74 60 1.00
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (74 bp):
ATTGGAGGATTAAATTTATTTTAATTTATTAAAAGTAAAACTAAATTAAGAGAATACGTAAATAT
CAGTGACCA
Found at i:957247 original size:21 final size:21
Alignment explanation
Indices: 957227--957298 Score: 54
Period size: 21 Copynumber: 3.4 Consensus size: 21
957217 TTCACGATAT
*
957227 TGATGTGACGATCCACAATAT
1 TGATGTGACGATCCACAATAC
* * * ** *
957248 TAATATAATAATTCACAATAC
1 TGATGTGACGATCCACAATAC
* *
957269 TGATGTGATGATCCACGATAC
1 TGATGTGACGATCCACAATAC
*
957290 TGACGTGAC
1 TGATGTGAC
957299 AGTTCATATG
Statistics
Matches: 36, Mismatches: 15, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (21 bp):
TGATGTGACGATCCACAATAC
Found at i:961912 original size:21 final size:21
Alignment explanation
Indices: 961873--961912 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
961863 AGCAAATGCA
* * *
961873 TAATTTTATTTTTATTTAAAG
1 TAATTATATTTATAATTAAAG
961894 TAATTATATTTATAATTAA
1 TAATTATATTTATAATTAA
961913 CATTTTATTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (21 bp):
TAATTATATTTATAATTAAAG
Found at i:962664 original size:22 final size:22
Alignment explanation
Indices: 962632--962683 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
962622 TGAATAGAAT
*
962632 CATTCAACGCTGAATGTTGAAC
1 CATTCAACGCTGAATGCTGAAC
* *
962654 CGTTCAGCGCTGAATGCTGAAC
1 CATTCAACGCTGAATGCTGAAC
962676 CATTCAAC
1 CATTCAAC
962684 ATTCAGACTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (22 bp):
CATTCAACGCTGAATGCTGAAC
Found at i:969350 original size:21 final size:21
Alignment explanation
Indices: 969324--969378 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
969314 CAGAGTGTGG
* *
969324 CGGCGGGCGGCGAACTGCAGA
1 CGGCGGACGGCGAACGGCAGA
* * *
969345 CGGCGGATGTCGGACGGCAGA
1 CGGCGGACGGCGAACGGCAGA
*
969366 CGGCGGCCGGCGA
1 CGGCGGACGGCGA
969379 TGATAAACGA
Statistics
Matches: 25, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.16, C:0.29, G:0.49, T:0.05
Consensus pattern (21 bp):
CGGCGGACGGCGAACGGCAGA
Found at i:970138 original size:29 final size:29
Alignment explanation
Indices: 970096--970154 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
970086 ATTTTCACCT
970096 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
970125 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
970154 A
1 A
970155 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:974384 original size:29 final size:29
Alignment explanation
Indices: 974350--974408 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
974340 CCTAAATTAA
974350 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
974379 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
974408 T
1 T
974409 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:979066 original size:29 final size:29
Alignment explanation
Indices: 979032--979090 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
979022 CCTAAATTAA
979032 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
979061 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
979090 T
1 T
979091 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:979796 original size:29 final size:29
Alignment explanation
Indices: 979754--979812 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
979744 ATTTTCACCT
979754 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
979783 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
979812 A
1 A
979813 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:980769 original size:2 final size:2
Alignment explanation
Indices: 980762--980796 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
980752 AAACACAGTT
980762 TA TA TA TA 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 TA TA TA TA T
980797 GCAAGGTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:985752 original size:6 final size:6
Alignment explanation
Indices: 985720--985751 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
985710 TCGGTGCATG
985720 TTTT-T TTTTCT TTTTCT TTTTCT TTTT-T TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT
985752 TATCTCGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 9 0.35
6 17 0.65
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (6 bp):
TTTTCT
Found at i:985752 original size:12 final size:12
Alignment explanation
Indices: 985720--985752 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
985710 TCGGTGCATG
985720 TTTTTTTTTCTT
1 TTTTTTTTTCTT
*
985732 TTTCTTTTTCTT
1 TTTTTTTTTCTT
985744 TTTTTTTTT
1 TTTTTTTTT
985753 ATCTCGTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (12 bp):
TTTTTTTTTCTT
Found at i:986809 original size:12 final size:12
Alignment explanation
Indices: 986792--986828 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
986782 AATCAGACAG
986792 TGATGAAGATGA
1 TGATGAAGATGA
986804 TGATGAAGATGA
1 TGATGAAGATGA
*
986816 TAATGAAGATGA
1 TGATGAAGATGA
986828 T
1 T
986829 TTAATGGATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (12 bp):
TGATGAAGATGA
Found at i:987655 original size:27 final size:27
Alignment explanation
Indices: 987636--987696 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 27
987626 TTTATAGTTG
987636 TAAATTTAGCTGATAAATTTCAAATTA
1 TAAATTTAGCTGATAAATTTCAAATTA
* *
987663 TATATTTAGCTGATAAATGTCAAATTA
1 TAAATTTAGCTGATAAATTTCAAATTA
*
987690 TATATTT
1 TAAATTT
987697 TTTAATTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.44
Consensus pattern (27 bp):
TAAATTTAGCTGATAAATTTCAAATTA
Found at i:988671 original size:7 final size:7
Alignment explanation
Indices: 988659--988709 Score: 57
Period size: 7 Copynumber: 7.3 Consensus size: 7
988649 TGATTTTGTG
988659 AACCTTA
1 AACCTTA
988666 AACCTTA
1 AACCTTA
*
988673 AACCCTA
1 AACCTTA
*
988680 AACCCTA
1 AACCTTA
*
988687 AACTTTA
1 AACCTTA
*
988694 AACCCTA
1 AACCTTA
*
988701 AATCTTA
1 AACCTTA
988708 AA
1 AA
988710 AATATTTTGG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.25
Consensus pattern (7 bp):
AACCTTA
Found at i:988681 original size:14 final size:14
Alignment explanation
Indices: 988659--988709 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
988649 TGATTTTGTG
*
988659 AACCTTAAACCTTA
1 AACCTTAAACCCTA
*
988673 AACCCTAAACCCTA
1 AACCTTAAACCCTA
*
988687 AACTTTAAACCCTA
1 AACCTTAAACCCTA
*
988701 AATCTTAAA
1 AACCTTAAA
988710 AATATTTTGG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.25
Consensus pattern (14 bp):
AACCTTAAACCCTA
Found at i:988709 original size:21 final size:21
Alignment explanation
Indices: 988659--988709 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
988649 TGATTTTGTG
988659 AACCTTAAACCTTAAACCCTA
1 AACCTTAAACCTTAAACCCTA
* *
988680 AACCCTAAACTTTAAACCCTA
1 AACCTTAAACCTTAAACCCTA
*
988701 AATCTTAAA
1 AACCTTAAA
988710 AATATTTTGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.25
Consensus pattern (21 bp):
AACCTTAAACCTTAAACCCTA
Found at i:989023 original size:14 final size:14
Alignment explanation
Indices: 989001--989044 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
988991 TTATTGTTGA
* *
989001 AAACTCTAAATGCT
1 AAACACTAAATCCT
* *
989015 AAACCCTAAACCCT
1 AAACACTAAATCCT
989029 AAACACTAAATCCT
1 AAACACTAAATCCT
989043 AA
1 AA
989045 CCATTCTCCC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.48, C:0.30, G:0.02, T:0.20
Consensus pattern (14 bp):
AAACACTAAATCCT
Found at i:989435 original size:294 final size:284
Alignment explanation
Indices: 988728--989439 Score: 1057
Period size: 285 Copynumber: 2.5 Consensus size: 284
988718 GGTTATTGCT
* *
988728 AAAAACCCTAAACCTTAAACACTAAACCCTAACCATTCTCCCTCCAATCAATTTCTTCTTATAAA
1 AAAAA-CCTAAACCCTAAACACTAAA-TCTAACCATTCTCCCTCCAATCAATTTCTTCTTATAAA
988793 AAACAAATATGTAACCACCATCATGGTAGATATCACCATCCTCTACCCCCTTCATTGCCCTCAAC
64 AAACAAATATGTAACCACCATCATGGTAGATATCACCATCCTCTACCCCCTTCATTGCCCTCAAC
* * * *
988858 ATATCATGAATTTATAAAGATTTTCAGCAATAATCAAAATTTTAGGGTTTAAGGTTCCAAAATCA
129 ATATCATGAACTTATAAAGATTTTCAACAATAACCAAAATTTTAGGGTTTAAGCTTCCAAAATCA
988923 ATATACAACAAATAATATAAGGAACTATGATTTGTAAACCTTAAACCCTAAACCCTAAAATATTT
194 ATATACAACAAATAATATAAGGAACTATGATTTGTAAACCTTAAACCCTAAACCCTAAAATATTT
* * **
988988 TGGTTATTGTTGAAAACTCTAAATGC
259 TGGTTATTATTGAAAACCCTAAAACC
* *
989014 TAAACCCTAAACCCTAAACACTAAATCCTAACCATTCTCCCTCCAATCAATTTCTTCTTATAAAA
1 AAAAACCTAAACCCTAAACACTAAAT-CTAACCATTCTCCCTCCAATCAATTTCTTCTTATAAAA
*
989079 ACCAAATATGTAACCACCATCATGGTAGATATCACCATCCTCTACCCCCTTCATTGCCCTCAACA
65 AACAAATATGTAACCACCATCATGGTAGATATCACCATCCTCTACCCCCTTCATTGCCCTCAACA
*
989144 TATCATGAACTTATAAAGGTTTTCAACAATAACCAAAATATTTTAGGGTTTAAGCTTCCAAAATC
130 TATCATGAACTTATAAAGATTTTCAACAATAACC-AAA-ATTTTAGGGTTTAAGCTTCCAAAATC
* * * *
989209 AATATACAAC-AATAATATCAGTAACTATTGATTTTGCAAACCCTAAATCTTAAACCTTAAACCC
193 AATATACAACAAATAATATAAGGAACTA-TGA-TTTG-------TAAACCTTAAACCCTAAACCC
* *
989273 TAAAATTTTTTGGTTGTTATTGAAAACCCTAAAACC
249 TAAAATATTTTGGTTATTATTGAAAACCCTAAAACC
* *
989309 AAAAATCTAAACCCTAAACACTAAATCTAAACATTCTCCCTCCAATCAATTTCTTCTTATAAAAA
1 AAAAACCTAAACCCTAAACACTAAATCTAACCATTCTCCCTCCAATCAATTTCTTCTTATAAAAA
* * * *
989374 ATAAATATGTAACCACCATCATGGTAGATACCACCATCCTCTACCCCTTTCATTACCCTCAACAT
66 ACAAATATGTAACCACCATCATGGTAGATATCACCATCCTCTACCCCCTTCATTGCCCTCAACAT
989439 A
131 A
989440 CCATTGCCAT
Statistics
Matches: 385, Mismatches: 29, Indels: 16
0.90 0.07 0.04
Matches are distributed among these distances:
285 151 0.39
286 21 0.05
287 38 0.10
288 4 0.01
294 99 0.26
295 72 0.19
ACGTcount: A:0.39, C:0.25, G:0.06, T:0.30
Consensus pattern (284 bp):
AAAAACCTAAACCCTAAACACTAAATCTAACCATTCTCCCTCCAATCAATTTCTTCTTATAAAAA
ACAAATATGTAACCACCATCATGGTAGATATCACCATCCTCTACCCCCTTCATTGCCCTCAACAT
ATCATGAACTTATAAAGATTTTCAACAATAACCAAAATTTTAGGGTTTAAGCTTCCAAAATCAAT
ATACAACAAATAATATAAGGAACTATGATTTGTAAACCTTAAACCCTAAACCCTAAAATATTTTG
GTTATTATTGAAAACCCTAAAACC
Found at i:989643 original size:22 final size:21
Alignment explanation
Indices: 989621--989661 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
989611 CTATTTTTTA
989621 AATCA-TTAGATAATAAAAATT
1 AATCATTTA-ATAATAAAAATT
989642 AATCATTTAATAATAAAAAT
1 AATCATTTAATAATAAAAAT
989662 AATATTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (21 bp):
AATCATTTAATAATAAAAATT
Found at i:989645 original size:21 final size:19
Alignment explanation
Indices: 989621--989673 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 19
989611 CTATTTTTTA
989621 AATCATTAGATAATAAAAATT
1 AATCATTA-ATAATAAAAA-T
989642 AATCATTTAATAATAAAAAT
1 AATCA-TTAATAATAAAAAT
989662 AAT-ATTATATAA
1 AATCATTA-ATAA
989674 AACAAATCTG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
18 3 0.10
19 5 0.17
20 4 0.13
21 15 0.50
22 3 0.10
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (19 bp):
AATCATTAATAATAAAAAT
Found at i:990284 original size:30 final size:30
Alignment explanation
Indices: 990238--990314 Score: 111
Period size: 30 Copynumber: 2.6 Consensus size: 30
990228 TATTTGAAAA
*
990238 GTTA-AAAATCGGTCACTAATGTTATCCTTT
1 GTTACAAAAT-GGTCACTAACGTTATCCTTT
*
990268 GTTACAAAATGGTCACTAACGTTATCGTTT
1 GTTACAAAATGGTCACTAACGTTATCCTTT
*
990298 GTTACAAAATGATCACT
1 GTTACAAAATGGTCACT
990315 CATCGTTAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
30 38 0.88
31 5 0.12
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.36
Consensus pattern (30 bp):
GTTACAAAATGGTCACTAACGTTATCCTTT
Found at i:991725 original size:18 final size:18
Alignment explanation
Indices: 991702--991736 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
991692 ATTAAAAATA
991702 ATTAAA-TTAGGTATAAAG
1 ATTAAATTTAGG-ATAAAG
991720 ATTAAATTTAGGATAAA
1 ATTAAATTTAGGATAAA
991737 TTACGCGCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.51, C:0.00, G:0.14, T:0.34
Consensus pattern (18 bp):
ATTAAATTTAGGATAAAG
Found at i:995478 original size:17 final size:19
Alignment explanation
Indices: 995444--995482 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
995434 ATTTAGGTTG
*
995444 ATATATTTGATATATTAAA
1 ATATAATTGATATATTAAA
995463 ATATAATTGA-AT-TTAAA
1 ATATAATTGATATATTAAA
995480 ATA
1 ATA
995483 ATATATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 2 0.11
19 9 0.47
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (19 bp):
ATATAATTGATATATTAAA
Found at i:998167 original size:30 final size:30
Alignment explanation
Indices: 998131--998191 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
998121 CCACACGACC
998131 CACGACCATCCATATCAGCTCTAGCACCAT
1 CACGACCATCCATATCAGCTCTAGCACCAT
998161 CACGACCATCCATATCAGCTCTAGCACCAT
1 CACGACCATCCATATCAGCTCTAGCACCAT
998191 C
1 C
998192 GGTATTGACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.30, C:0.41, G:0.10, T:0.20
Consensus pattern (30 bp):
CACGACCATCCATATCAGCTCTAGCACCAT
Found at i:1003720 original size:6 final size:6
Alignment explanation
Indices: 1003709--1003755 Score: 94
Period size: 6 Copynumber: 7.8 Consensus size: 6
1003699 TCTAAAGTTG
1003709 ATGAAC ATGAAC ATGAAC ATGAAC ATGAAC ATGAAC ATGAAC ATGAA
1 ATGAAC ATGAAC ATGAAC ATGAAC ATGAAC ATGAAC ATGAAC ATGAA
1003756 GAACATCAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.51, C:0.15, G:0.17, T:0.17
Consensus pattern (6 bp):
ATGAAC
Found at i:1005097 original size:667 final size:664
Alignment explanation
Indices: 1003810--1005110 Score: 1680
Period size: 667 Copynumber: 2.0 Consensus size: 664
1003800 TCACCATTTC
* *
1003810 CATCTTCCTCAATGATGTTTTTTCTTGAATGTCCTCAACACTTTGTTGCCTGCTCGTTGAATCAT
1 CATCTTCCTCAATGATATTTTTTCTTGAATGTCCTCAACACTTTGTTGCCTGCTCGTTGAACCAT
* * *
1003875 CCCGACAAGCCATTTTGGTTTCCTGATTGTCATCATTATATATCCTGCTGAAAATCCCAACACTG
66 CCCAACAAGCCATTTTGGCTTCCTGATTGTCATCATTATATATCCTGCTGAAAATCCCAACACCG
* * * *
1003940 CTCCACATCCATAGCCCATAATTATAGATTTCCATTCCAATCTGAATGTAGAATCAGCTTCTTGT
131 CTCCACATCCATAACCCATAATCATAGATTTCCAATCCAATCCGAATGTAGAATCAGCTTCTTGT
* * *
1004005 TCGTCAAAAGTTGTTGCTGGTGGTGGTTCACTGCGGCCGCAACTTTTCGAAACTGGAAACCCACA
196 TCATCAAAAGTAGTTGCTGGTGGTGGTTCACTGCGGCCACAACTTTTCGAAACTGGAAACCCACA
** * *
1004070 CAAGCCTGGATTGCCAACGTAGGAATCATTCATGAAGGTATTGAATTGTTTTCCCTGAGGAATGA
261 CAAGCCAAGATTGCCAACGTAGGAATCATTCATAAAGGTATTGAATTGTTTCCCCTGAGGAATGA
* * * *
1004135 GCCCAACAAGCTGGTTCTCTGACAGGTTTAACACCGCAAGAAAGTTCAAGTCAGTCAACTGTGAA
326 GCCCAACAAGCTGGTTCTCCGACAGGTTTAACACCGAAAGAAAATTCAAGTCAGTCAACTGCGAA
** * * *
1004200 GGAATTTTCCCAACTAGCACGTTGTAGGAGAGATCTAATGACTCAAGTGTTGCCAAATTCCCTAA
391 GGAATTCCCCCAACAAGCACGTTGTAGGAGAGATCTAAAGACTCAAGTGCTGCCAAATTCCCTAA
** * * * *
1004265 TGCTGAAGGAATTTGGCCGGTTAAGTGGTTATGAGAAAAGTTGAGCACGTTGAGAGACACAAGGT
456 TGAGGAAGGAATGTGACCGGTGAAGTGGTTATGAGAAAAATTGAGCACGTTGAGAGACACAAGGT
* * * * * *
1004330 TTCCAACTGTTTCTGGAATTGTTCCTTCGAATCGGTTGCTCGACATGTCGATGGTTGCAAAAATA
521 TTCCAACTGTTTCCGAAATCGTTCCCTCGAATCGGTTGCTCGACATATCAATGGTTGCAAAAATA
* *
1004395 GTGAGGATTCTCTTGAGTTCGACCTCCACACCTTTCATTGCGATAACCAGAATACAACCAGGCAC
586 GTGAGGATTCTCTTCAGCTCGACCTCCACACCTTTCATTGCGATAACCAGAATACAACCAGGCAC
1004460 CGATGAGCAATCAT
651 CGATGAGCAATCAT
* *
1004474 CATCTTCCTCAATGATATTTTTTCTTGAATGTCCTTAGA-ACTTTGTTGCCTGCTCTTTGAACCA
1 CATCTTCCTCAATGATATTTTTTCTTGAATGTCCTCA-ACACTTTGTTGCCTGCTCGTTGAACCA
**
1004538 TTTCAACAAGCCATTTTGGCTTCCTGATTGTCATCATTATATATCCTGCTGAAAATCCCAACACC
65 TCCCAACAAGCCATTTTGGCTTCCTGATTGTCATCATTATATATCCTGCTGAAAATCCCAACACC
* * * *
1004603 GCTCCACATCCATAACTCATTATCA-CGATTTTCCAATCCAATCCG-A-GCTCGGAATCAGCTTC
130 GCTCCACATCCATAACCCATAATCATAGA-TTTCCAATCCAATCCGAATG-T-AGAATCAGCTTC
** *
1004665 TTGTTCATCAAAAGTAGTTGCTGCCGGTGGTGGTTCACTTTGGCCACAAC-TTTCTGAAACTGGG
192 TTGTTCATCAAAAGTAGTTGCT---GGTGGTGGTTCACTGCGGCCACAACTTTTC-GAAACTGGA
* * * * * * *
1004729 AACCCGCATAATCCAATATTGCCGATGTAGGAATCATTC-TCAAAGGTGTTGAATTGTTTCCCCT
253 AACCCACACAAGCCAAGATTGCCAACGTAGGAATCATTCAT-AAAGGTATTGAATTGTTTCCCCT
* * * ***** *
1004793 TAGGAATTG-GTCCGACAAGCTGGTTCTCCGACAGGTTTAGTGTGGAAAGAAAATTCAAGTCGGT
317 GAGGAA-TGAGCCCAACAAGCTGGTTCTCCGACAGGTTTAACACCGAAAGAAAATTCAAGTCAGT
** ** ** * *
1004857 CAACTGCGAAGGAATTCCCCCGGCAAGCTTGTTGTCTGAGAGATCTAAAGATTCAAGTGCTGTCA
381 CAACTGCGAAGGAATTCCCCCAACAAGCACGTTGTAGGAGAGATCTAAAGACTCAAGTGCTGCCA
** * * *
1004922 TTTTCCCTAATGAGGAAGGGATGTGACCGGTGAGGTGGTTATGAGAAAAATTGAGCACTTTGAGA
446 AATTCCCTAATGAGGAAGGAATGTGACCGGTGAAGTGGTTATGAGAAAAATTGAGCACGTTGAGA
* * *
1004987 GATATAAGGTTTCCAACTGTTTCCGAAATCGTTCCCTCGAATCGGTTGCTTGACATATCAATGGT
511 GACACAAGGTTTCCAACTGTTTCCGAAATCGTTCCCTCGAATCGGTTGCTCGACATATCAATGGT
** * * *
1005052 TGCAAAAATAGTGAGGATTCTCTTCAGCTCGATGTCGATACCTTTCATTGTGATAACCA
576 TGCAAAAATAGTGAGGATTCTCTTCAGCTCGACCTCCACACCTTTCATTGCGATAACCA
1005111 CAGAATCTTC
Statistics
Matches: 540, Mismatches: 87, Indels: 17
0.84 0.14 0.03
Matches are distributed among these distances:
662 1 0.00
663 4 0.01
664 184 0.34
665 1 0.00
666 5 0.01
667 343 0.64
668 2 0.00
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (664 bp):
CATCTTCCTCAATGATATTTTTTCTTGAATGTCCTCAACACTTTGTTGCCTGCTCGTTGAACCAT
CCCAACAAGCCATTTTGGCTTCCTGATTGTCATCATTATATATCCTGCTGAAAATCCCAACACCG
CTCCACATCCATAACCCATAATCATAGATTTCCAATCCAATCCGAATGTAGAATCAGCTTCTTGT
TCATCAAAAGTAGTTGCTGGTGGTGGTTCACTGCGGCCACAACTTTTCGAAACTGGAAACCCACA
CAAGCCAAGATTGCCAACGTAGGAATCATTCATAAAGGTATTGAATTGTTTCCCCTGAGGAATGA
GCCCAACAAGCTGGTTCTCCGACAGGTTTAACACCGAAAGAAAATTCAAGTCAGTCAACTGCGAA
GGAATTCCCCCAACAAGCACGTTGTAGGAGAGATCTAAAGACTCAAGTGCTGCCAAATTCCCTAA
TGAGGAAGGAATGTGACCGGTGAAGTGGTTATGAGAAAAATTGAGCACGTTGAGAGACACAAGGT
TTCCAACTGTTTCCGAAATCGTTCCCTCGAATCGGTTGCTCGACATATCAATGGTTGCAAAAATA
GTGAGGATTCTCTTCAGCTCGACCTCCACACCTTTCATTGCGATAACCAGAATACAACCAGGCAC
CGATGAGCAATCAT
Found at i:1008900 original size:6 final size:6
Alignment explanation
Indices: 1008889--1008921 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
1008879 ACTCTAAAGT
1008889 ACATGA ACATGA ACATGA ACATGA ACATGA ACA
1 ACATGA ACATGA ACATGA ACATGA ACATGA ACA
1008922 ACATCAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.52, C:0.18, G:0.15, T:0.15
Consensus pattern (6 bp):
ACATGA
Found at i:1015293 original size:26 final size:27
Alignment explanation
Indices: 1015264--1015321 Score: 84
Period size: 26 Copynumber: 2.2 Consensus size: 27
1015254 AGAATATCAC
* *
1015264 CAAGCTC-AGAAATGAATGGATATCCT
1 CAAGCTCTAGAAATAAATAGATATCCT
1015290 CAAGC-CTAGAAATAAATAGATATCCT
1 CAAGCTCTAGAAATAAATAGATATCCT
1015316 CAAGCT
1 CAAGCT
1015322 TTAAAATGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 1 0.04
26 27 0.96
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.22
Consensus pattern (27 bp):
CAAGCTCTAGAAATAAATAGATATCCT
Found at i:1018356 original size:24 final size:24
Alignment explanation
Indices: 1018304--1018357 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
1018294 ATGATGATGC
*
1018304 AGGGCTTGGGTTGTAAGAAGCACA
1 AGGGCTTGGGTTGTAAGAAGAACA
*
1018328 AGGGCTT-GGTTGGTAAGACGAACA
1 AGGGCTTGGGTT-GTAAGAAGAACA
*
1018352 GGGGCT
1 AGGGCT
1018358 CAACGTTGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 4 0.15
24 22 0.85
ACGTcount: A:0.26, C:0.13, G:0.41, T:0.20
Consensus pattern (24 bp):
AGGGCTTGGGTTGTAAGAAGAACA
Found at i:1022252 original size:15 final size:16
Alignment explanation
Indices: 1022229--1022266 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1022219 ACCCGACCCT
*
1022229 ATACAATCGGG-TTGG
1 ATACCATCGGGTTTGG
1022244 ATACCATCGGGTTTGG
1 ATACCATCGGGTTTGG
*
1022260 ATCCCAT
1 ATACCAT
1022267 GCCATTTCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (16 bp):
ATACCATCGGGTTTGG
Found at i:1023216 original size:22 final size:22
Alignment explanation
Indices: 1023188--1023235 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
1023178 TTTGAAATAA
1023188 TAATAATGATAATAATAAGGGT
1 TAATAATGATAATAATAAGGGT
*
1023210 TAATAATGATACTAATAAGGGT
1 TAATAATGATAATAATAAGGGT
1023232 TAAT
1 TAAT
1023236 TGACTTATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.48, C:0.02, G:0.17, T:0.33
Consensus pattern (22 bp):
TAATAATGATAATAATAAGGGT
Found at i:1023729 original size:2 final size:2
Alignment explanation
Indices: 1023722--1023753 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1023712 GTGTTTGCAG
1023722 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1023754 AGTTTACAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1030569 original size:13 final size:13
Alignment explanation
Indices: 1030553--1030636 Score: 57
Period size: 13 Copynumber: 6.2 Consensus size: 13
1030543 ATGTATAAAT
1030553 TAAATTAATATAA
1 TAAATTAATATAA
*
1030566 TAAATAAATATAA
1 TAAATTAATATAA
*
1030579 TAAAAATAATAATTAA
1 T-AAATTAAT-A-TAA
*
1030595 TAATATTAAT-TAT
1 TAA-ATTAATATAA
1030608 TAAATATAATAATAA
1 TAAAT-TAAT-ATAA
*
1030623 TTAA--AATATAA
1 TAAATTAATATAA
1030634 TAA
1 TAA
1030637 TATATAAATA
Statistics
Matches: 56, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
11 6 0.11
12 5 0.09
13 22 0.39
14 6 0.11
15 8 0.14
16 9 0.16
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
TAAATTAATATAA
Found at i:1030595 original size:16 final size:16
Alignment explanation
Indices: 1030576--1030656 Score: 55
Period size: 16 Copynumber: 5.2 Consensus size: 16
1030566 TAAATAAATA
1030576 TAATAAAAATAATAAT
1 TAATAAAAATAATAAT
*
1030592 TAAT---AATATTAAT
1 TAATAAAAATAATAAT
* *
1030605 TATTAAATATAATAA-
1 TAATAAAAATAATAAT
1030620 TAATTAAAATATAATAA-
1 TAA-TAAAA-ATAATAAT
* *
1030637 TATATAAATATAGTAAT
1 TA-ATAAAAATAATAAT
1030654 TAA
1 TAA
1030657 AATAGATATT
Statistics
Matches: 50, Mismatches: 8, Indels: 14
0.69 0.11 0.19
Matches are distributed among these distances:
13 11 0.22
15 2 0.04
16 21 0.42
17 15 0.30
18 1 0.02
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (16 bp):
TAATAAAAATAATAAT
Found at i:1030656 original size:46 final size:42
Alignment explanation
Indices: 1030581--1030688 Score: 71
Period size: 46 Copynumber: 2.5 Consensus size: 42
1030571 AAATATAATA
*
1030581 AAAATAATAATTAATAATATTAATTATTAAATATAATAATAATTA
1 AAAATAATAATTAATAATATTAATAATTAAATA-AAT-ATAA-TA
* * **
1030626 AAATATAATAA-TATATAA-ATATAGTAATTAAAATAGATATTCTA
1 AAA-ATAATAATTA-ATAATAT-TAATAATT-AAATAAATATAATA
1030670 TAAAA-AATAATT-ATAATAT
1 -AAAATAATAATTAATAATAT
1030689 ATTTTGTAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
42 4 0.08
43 7 0.14
44 4 0.08
45 12 0.24
46 19 0.37
47 5 0.10
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (42 bp):
AAAATAATAATTAATAATATTAATAATTAAATAAATATAATA
Found at i:1031078 original size:4 final size:4
Alignment explanation
Indices: 1031069--1031098 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
1031059 ATATTTTTTC
1031069 TATT TATT TATT TATT TAGTT TATT TATT T
1 TATT TATT TATT TATT TA-TT TATT TATT T
1031099 TGGTATTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:1037417 original size:32 final size:33
Alignment explanation
Indices: 1037363--1037441 Score: 90
Period size: 32 Copynumber: 2.5 Consensus size: 33
1037353 GAGTAGACTC
* * *
1037363 TAATAATAAATATTATAAAAAAACT-AAGCCTA
1 TAATAATAAATATTAGAAAAAAAATAAACCCTA
**
1037395 TAATAATAAATATTAGGGAAAAAATAAACCCTA
1 TAATAATAAATATTAGAAAAAAAATAAACCCTA
*
1037428 -AATAATAAGTATTA
1 TAATAATAAATATTA
1037442 AACATAATTG
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
32 34 0.85
33 6 0.15
ACGTcount: A:0.58, C:0.08, G:0.06, T:0.28
Consensus pattern (33 bp):
TAATAATAAATATTAGAAAAAAAATAAACCCTA
Found at i:1046686 original size:29 final size:29
Alignment explanation
Indices: 1046651--1046732 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
1046641 AAACTAAATT
*
1046651 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
1046680 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
1046709 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
1046733 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:1051447 original size:29 final size:29
Alignment explanation
Indices: 1051412--1051493 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
1051402 AAACTAAATT
*
1051412 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
1051441 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
1051470 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
1051494 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:1067200 original size:9 final size:9
Alignment explanation
Indices: 1067156--1067199 Score: 79
Period size: 9 Copynumber: 4.9 Consensus size: 9
1067146 GTTCGGTAAG
1067156 TTCAATAGA
1 TTCAATAGA
1067165 TTCAATAGA
1 TTCAATAGA
1067174 TTCAATAGA
1 TTCAATAGA
*
1067183 TTCAATAGC
1 TTCAATAGA
1067192 TTCAATAG
1 TTCAATAG
1067200 CCCATGATAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (9 bp):
TTCAATAGA
Found at i:1092330 original size:15 final size:15
Alignment explanation
Indices: 1092310--1092344 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1092300 ATTTTTATTT
1092310 TCATTTAATAAACGA
1 TCATTTAATAAACGA
1092325 TCATTTAATAAACGA
1 TCATTTAATAAACGA
*
1092340 ACATT
1 TCATT
1092345 CTGTTCATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.34
Consensus pattern (15 bp):
TCATTTAATAAACGA
Found at i:1096537 original size:21 final size:21
Alignment explanation
Indices: 1096512--1096556 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
1096502 TTTTATGTTT
*
1096512 GTTGCTTATGTATAACTTATG
1 GTTGCTTATGTATAACTTAAG
1096533 GTTGCTTATGTATAACTTAAG
1 GTTGCTTATGTATAACTTAAG
1096554 GTT
1 GTT
1096557 ACTGTTAGGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.24, C:0.09, G:0.20, T:0.47
Consensus pattern (21 bp):
GTTGCTTATGTATAACTTAAG
Found at i:1106393 original size:66 final size:66
Alignment explanation
Indices: 1106312--1106438 Score: 191
Period size: 66 Copynumber: 1.9 Consensus size: 66
1106302 TGGTCCCTTT
* * *
1106312 TCTTCTTCTGCTTGGTGGGTGCAGCTTCTCTCCCACGTTCCTCGGTAACAGTCGACTCGTTGGTG
1 TCTTCTTCGGCTTGGTGGGTGCAGCTTCTCTCCCACGTCCCTCGGTAACAGTCGAATCGTTGGTG
1106377 C
66 C
* * * *
1106378 TCTTCTTCGGGTTGGTGGGTGCAGTTTCTTTCCCACGTCCCTCGGTAGCAGTCGAATCGTT
1 TCTTCTTCGGCTTGGTGGGTGCAGCTTCTCTCCCACGTCCCTCGGTAACAGTCGAATCGTT
1106439 CGAGTTCCCG
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
66 54 1.00
ACGTcount: A:0.09, C:0.28, G:0.27, T:0.35
Consensus pattern (66 bp):
TCTTCTTCGGCTTGGTGGGTGCAGCTTCTCTCCCACGTCCCTCGGTAACAGTCGAATCGTTGGTG
C
Found at i:1108719 original size:29 final size:32
Alignment explanation
Indices: 1108651--1108716 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 32
1108641 TATTCAAAGT
* *
1108651 TTGGCCACCAACCAAGATGAAATTTTCAATAAG
1 TTGGCCACCAACCAAGATGAAATTTTC-ACAAC
1108684 TTGGCCACCAACCAAGATGAAA-TTTC-CAAC
1 TTGGCCACCAACCAAGATGAAATTTTCACAAC
1108714 TTG
1 TTG
1108717 CCAACTTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 5 0.16
32 4 0.13
33 22 0.71
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.24
Consensus pattern (32 bp):
TTGGCCACCAACCAAGATGAAATTTTCACAAC
Found at i:1113419 original size:24 final size:24
Alignment explanation
Indices: 1113392--1113438 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
1113382 TTGTATACTT
1113392 TACCCATATTATAATAATCTTTTA
1 TACCCATATTATAATAATCTTTTA
*
1113416 TACCCATATTATAATTATCTTTT
1 TACCCATATTATAATAATCTTTT
1113439 TATATATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.49
Consensus pattern (24 bp):
TACCCATATTATAATAATCTTTTA
Found at i:1114347 original size:2 final size:2
Alignment explanation
Indices: 1114340--1114379 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
1114330 TTGATTGTCG
* *
1114340 TA TA TA TA TA TA TA TA TT TA TA CA 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
1114380 GAGAGAGAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1124099 original size:2 final size:2
Alignment explanation
Indices: 1124092--1124142 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
1124082 TTCCTTAATG
1124092 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
1124134 AT AT A- AT AT
1 AT AT AT AT AT
1124143 TTTGACTAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1141433 original size:2 final size:2
Alignment explanation
Indices: 1141426--1141456 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1141416 TCATCTAATA
1141426 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1141457 AATAACTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1144483 original size:2 final size:2
Alignment explanation
Indices: 1144476--1144510 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1144466 TATGTACCAA
1144476 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1144511 CTAGTACTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1146096 original size:12 final size:12
Alignment explanation
Indices: 1146079--1146103 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1146069 TCGGTAAAAA
1146079 AAATAATATTTT
1 AAATAATATTTT
1146091 AAATAATATTTT
1 AAATAATATTTT
1146103 A
1 A
1146104 TTGGATATAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AAATAATATTTT
Found at i:1152869 original size:472 final size:472
Alignment explanation
Indices: 1151985--1153401 Score: 2699
Period size: 472 Copynumber: 3.0 Consensus size: 472
1151975 TGCAATAGAC
*
1151985 TGTTTGCATCAATGGAAACCAATGCATGTGATGACAGCCCCAAAATTGTCAAAGTCGATACATTG
1 TGTTTGCATCAATGGAAACCAATGCATGAGATGACAGCCCCAAAATTGTCAAAGTCGATACATTG
1152050 AAGACAAGATCAAGGTCACGTAGGTTCAACTTCAATGCATTATCAGAATGTGGGGATGAATTGCC
66 AAGACAAGATCAAGGTCACGTAGGTTCAACTTCAATGCATTATCAGAATGTGGGGATGAATTGCC
1152115 ATACCAGACAGTATCATCGCCCCTTCCGTGTCCTGTTCGATCATCCACACCCAATCAAAAAAATG
131 ATACCAGACAGTATCATCGCCCCTTCCGTGTCCTGTTCGATCATCCACACCCAATCAAAAAAATG
1152180 TTCATGATTTCGAATGGTGTTTCGCTGACAAGGAATGTAAGTTTTCTACTGCTCAGACCACTCCT
196 TTCATGATTTCGAATGGTGTTTCGCTGACAAGGAATGTAAGTTTTCTACTGCTCAGACCACTCCT
1152245 CGTTTCGGGCAGTAATGCCTTGAAATTTGACTAAGAAACTCTCCCATGTAAAGATTAGTGAATAT
261 CGTTTCGGGCAGTAATGCCTTGAAATTTGACTAAGAAACTCTCCCATGTAAAGATTAGTGAATAT
1152310 TGGCTTGATGCCTCGGCAAACCACAGAGATTATGGGGGCATAGGTACCCGATTCCTTGTTTTGAC
326 TGGCTTGATGCCTCGGCAAACCACAGAGATTATGGGGGCATAGGTACCCGATTCCTTGTTTTGAC
1152375 CTGCTTAATAAGCAAGTAAACAAGAAAATGTTATACCCGAGAACTTGGAAGTTGTTCATGTAGCC
391 CTGCTTAATAAGCAAGTAAACAAGAAAATGTTATACCCGAGAACTTGGAAGTTGTTCATGTAGCC
1152440 TTTTGCATACATACTTT
456 TTTTGCATACATACTTT
1152457 TGTTTGCATCAATGGAAACCAATGCATGAGATGACAGCCCCAAAATTGTCAAAGTCGATACATTG
1 TGTTTGCATCAATGGAAACCAATGCATGAGATGACAGCCCCAAAATTGTCAAAGTCGATACATTG
*
1152522 AAGACAAGATCAAGGTCACGTAGGTTCAACCTCAATGCATTATCAGAATGTGGGGATGAATTGCC
66 AAGACAAGATCAAGGTCACGTAGGTTCAACTTCAATGCATTATCAGAATGTGGGGATGAATTGCC
* * *
1152587 ATACCAGACAATATCATCGCCCCTTCCGTGTCCTGTTCGATCATCCACACTCGATCAAAAAAATG
131 ATACCAGACAGTATCATCGCCCCTTCCGTGTCCTGTTCGATCATCCACACCCAATCAAAAAAATG
*
1152652 TTCATGATTTCGAATGGTGTTTTGCTGACAAGGAATGTAAGTTTTCTACTGCTCAGACCACTCCT
196 TTCATGATTTCGAATGGTGTTTCGCTGACAAGGAATGTAAGTTTTCTACTGCTCAGACCACTCCT
1152717 CGTTTCGGGCAGTAATGCCTTGAAATTTGACTAAGAAACTCTCCCATGTAAAGATTAGTGAATAT
261 CGTTTCGGGCAGTAATGCCTTGAAATTTGACTAAGAAACTCTCCCATGTAAAGATTAGTGAATAT
1152782 TGGCTTGATGCCTCGGCAAACCACAGAGATTATGGGGGCATAGGTACCCGATTCCTTGTTTTGAC
326 TGGCTTGATGCCTCGGCAAACCACAGAGATTATGGGGGCATAGGTACCCGATTCCTTGTTTTGAC
1152847 CTGCTTAATAAGCAAGTAAACAAGAAAATGTTATACCCGAGAACTTGGAAGTTGTTCATGTAGCC
391 CTGCTTAATAAGCAAGTAAACAAGAAAATGTTATACCCGAGAACTTGGAAGTTGTTCATGTAGCC
1152912 TTTTGCATACATACTTT
456 TTTTGCATACATACTTT
1152929 TGTTTGCATCAATGGAAACCAATGCATGAGATGACAGCCCCAAAATTGTCAAAGTCGATACATTG
1 TGTTTGCATCAATGGAAACCAATGCATGAGATGACAGCCCCAAAATTGTCAAAGTCGATACATTG
1152994 AAGACAAGATCAAGGTCACGTAGGTTCAACTTCAATGCATTATCAGAATGTGGGGATGAATTGCC
66 AAGACAAGATCAAGGTCACGTAGGTTCAACTTCAATGCATTATCAGAATGTGGGGATGAATTGCC
1153059 ATACCAGACAGTATCATCGCCCCTTCCGTGTCCTGTTCGATCATCCACACCCAATCAAAAAAATG
131 ATACCAGACAGTATCATCGCCCCTTCCGTGTCCTGTTCGATCATCCACACCCAATCAAAAAAATG
1153124 TTCATGATTTCGAATGGTGTTTCGCTGACAAGGAATGTAAGTTTTCTACTGCTCAGACCACTCCT
196 TTCATGATTTCGAATGGTGTTTCGCTGACAAGGAATGTAAGTTTTCTACTGCTCAGACCACTCCT
*
1153189 CGTTTCGGGCAGTAATGCCTTGAAATTTGACTAAGAAACTCTCCCATGTAAAGATTAGTGGATAT
261 CGTTTCGGGCAGTAATGCCTTGAAATTTGACTAAGAAACTCTCCCATGTAAAGATTAGTGAATAT
* * ** * *
1153254 TGGATTGATGCCTCGGTAAACCACAGAGATTATGGGGGCATAGGTGGCTGATTCCTTGTTTTGGC
326 TGGCTTGATGCCTCGGCAAACCACAGAGATTATGGGGGCATAGGTACCCGATTCCTTGTTTTGAC
*
1153319 CGTGCTTAATAAGCAAGTAAACAAGAAAATGTTATACCCGAGATCTTGGAAGTTGTTCATGTAGC
391 C-TGCTTAATAAGCAAGTAAACAAGAAAATGTTATACCCGAGAACTTGGAAGTTGTTCATGTAGC
1153384 CTTTTGCATACATACTTT
455 CTTTTGCATACATACTTT
1153402 GGATCATCAA
Statistics
Matches: 925, Mismatches: 19, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
472 845 0.91
473 80 0.09
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (472 bp):
TGTTTGCATCAATGGAAACCAATGCATGAGATGACAGCCCCAAAATTGTCAAAGTCGATACATTG
AAGACAAGATCAAGGTCACGTAGGTTCAACTTCAATGCATTATCAGAATGTGGGGATGAATTGCC
ATACCAGACAGTATCATCGCCCCTTCCGTGTCCTGTTCGATCATCCACACCCAATCAAAAAAATG
TTCATGATTTCGAATGGTGTTTCGCTGACAAGGAATGTAAGTTTTCTACTGCTCAGACCACTCCT
CGTTTCGGGCAGTAATGCCTTGAAATTTGACTAAGAAACTCTCCCATGTAAAGATTAGTGAATAT
TGGCTTGATGCCTCGGCAAACCACAGAGATTATGGGGGCATAGGTACCCGATTCCTTGTTTTGAC
CTGCTTAATAAGCAAGTAAACAAGAAAATGTTATACCCGAGAACTTGGAAGTTGTTCATGTAGCC
TTTTGCATACATACTTT
Found at i:1160419 original size:2 final size:2
Alignment explanation
Indices: 1160412--1160438 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1160402 GTCCCGATGC
1160412 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
1160439 TTTTAATATC
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:1166851 original size:15 final size:16
Alignment explanation
Indices: 1166830--1166863 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1166820 TCTCGGGGGG
1166830 ACAAAAAGTCGGGGAA
1 ACAAAAAGTCGGGGAA
1166846 ACAAAAAGTCGGGGAA
1 ACAAAAAGTCGGGGAA
1166862 AC
1 AC
1166864 GGCTGTCGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.50, C:0.15, G:0.29, T:0.06
Consensus pattern (16 bp):
ACAAAAAGTCGGGGAA
Found at i:1167103 original size:21 final size:20
Alignment explanation
Indices: 1167030--1167104 Score: 53
Period size: 21 Copynumber: 3.6 Consensus size: 20
1167020 CAGTTTCCAG
* **
1167030 ATTCGCAACGCGATTATGACT
1 ATTCGCAATGCGATT-TTCCT
*
1167051 A-TCGCAATGCGATTTTCCA
1 ATTCGCAATGCGATTTTCCT
***
1167070 ATTTCGTGTTGCGATTTTCCCT
1 A-TTCGCAATGCGATTTT-CCT
1167092 ATTCGCAATGCGA
1 ATTCGCAATGCGA
1167105 ATAAGTAAAT
Statistics
Matches: 40, Mismatches: 11, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
19 3 0.08
20 12 0.30
21 22 0.55
22 3 0.08
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.35
Consensus pattern (20 bp):
ATTCGCAATGCGATTTTCCT
Found at i:1167136 original size:20 final size:20
Alignment explanation
Indices: 1167113--1167247 Score: 121
Period size: 20 Copynumber: 6.7 Consensus size: 20
1167103 GAATAAGTAA
* *
1167113 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATAATGACT
*
1167133 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATAATGAC--T
*
1167154 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATAATGACT
* *
1167174 TTCGCAACGCGATAATAACT
1 ATCGCAACGCGATAATGACT
* **
1167194 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATAATGACT
*
1167214 ATCGCAACGAGATAAT-ACAT
1 ATCGCAACGCGATAATGAC-T
*
1167234 AATCGCAATGCGAT
1 -ATCGCAACGCGAT
1167248 TTTCAAAGTT
Statistics
Matches: 93, Mismatches: 17, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
19 4 0.04
20 61 0.66
21 26 0.28
22 2 0.02
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATAATGACT
Found at i:1167156 original size:41 final size:41
Alignment explanation
Indices: 1167111--1167247 Score: 186
Period size: 41 Copynumber: 3.4 Consensus size: 41
1167101 GCGAATAAGT
*
1167111 AAATCGCAATGCGATACTGACTATCGCAACGCGATAATACA
1 AAATCGCAACGCGATACTGACTATCGCAACGCGATAATACA
*
1167152 AAATCGCAACGCGATACTGACTTTCGCAACGCGATAATA-A
1 AAATCGCAACGCGATACTGACTATCGCAACGCGATAATACA
*** * *
1167192 CTTTCGCAACGCGATTCTGACTATCGCAACGAGATAATACA
1 AAATCGCAACGCGATACTGACTATCGCAACGCGATAATACA
* *
1167233 TAATCGCAATGCGAT
1 AAATCGCAACGCGAT
1167248 TTTCAAAGTT
Statistics
Matches: 83, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
40 34 0.41
41 49 0.59
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.22
Consensus pattern (41 bp):
AAATCGCAACGCGATACTGACTATCGCAACGCGATAATACA
Found at i:1167400 original size:12 final size:12
Alignment explanation
Indices: 1167381--1167414 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1167371 CTCTCCGACG
1167381 ACATCCGTTCCT
1 ACATCCGTTCCT
*
1167393 ATATCCGTTCCT
1 ACATCCGTTCCT
1167405 ACATCC-TTCC
1 ACATCCGTTCC
1167415 CCATTCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:1167996 original size:24 final size:24
Alignment explanation
Indices: 1167969--1168022 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1167959 GTATTCGAAA
*
1167969 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
1167993 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
1168017 TTTGAT
1 TTTGAT
1168023 GATGTTTCAG
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:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:1170396 original size:20 final size:20
Alignment explanation
Indices: 1170371--1170439 Score: 129
Period size: 20 Copynumber: 3.5 Consensus size: 20
1170361 CAACGGGGAA
1170371 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
1170391 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
*
1170411 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGAAAATGGCT
1170431 ATCGCAACG
1 ATCGCAACG
1170440 AGAGAATCGC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.33, C:0.26, G:0.26, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:1170481 original size:20 final size:20
Alignment explanation
Indices: 1170444--1170496 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
1170434 GCAACGAGAG
1170444 AATCGCAATGCG-AAATGAA
1 AATCGCAATGCGAAAATGAA
1170463 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCGAAAATGAA
*
1170483 AATCACAATGCGAA
1 AATCGCAATGCGAA
1170497 TTTAGTTTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 12 0.38
20 20 0.62
ACGTcount: A:0.49, C:0.17, G:0.19, T:0.15
Consensus pattern (20 bp):
AATCGCAATGCGAAAATGAA
Found at i:1170601 original size:20 final size:20
Alignment explanation
Indices: 1170576--1170614 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1170566 CGATTCTCTC
1170576 GTTGCGATAGTCAGTTTTGT
1 GTTGCGATAGTCAGTTTTGT
*
1170596 GTTGCGATAGTCTGTTTTG
1 GTTGCGATAGTCAGTTTTG
1170615 CCTTCAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.10, G:0.31, T:0.46
Consensus pattern (20 bp):
GTTGCGATAGTCAGTTTTGT
Found at i:1170603 original size:34 final size:34
Alignment explanation
Indices: 1170520--1170585 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
1170510 TTGCGATTTT
*
1170520 CATTT-CGCATTGCGATTCTCTCGTTGCGATAGC
1 CATTTCCGCGTTGCGATTCTCTCGTTGCGATAGC
1170553 CATTTCCGCGTTGCGATTCTCTCGTTGCGATAG
1 CATTTCCGCGTTGCGATTCTCTCGTTGCGATAG
1170586 TCAGTTTTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 5 0.16
34 26 0.84
ACGTcount: A:0.14, C:0.27, G:0.23, T:0.36
Consensus pattern (34 bp):
CATTTCCGCGTTGCGATTCTCTCGTTGCGATAGC
Found at i:1170729 original size:14 final size:14
Alignment explanation
Indices: 1170710--1170746 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1170700 CATCAATTAA
1170710 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1170724 ACAAATCATCTTTT
1 ACAAATCAACATTT
1170738 ACAAATCAA
1 ACAAATCAA
1170747 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1172201 original size:41 final size:41
Alignment explanation
Indices: 1172156--1172247 Score: 132
Period size: 41 Copynumber: 2.2 Consensus size: 41
1172146 CCTCTTCAAC
*
1172156 GATGACAGTGGCCTCTTGAACGGTGGGAGGGG-CTCTTGAGG
1 GATGACAG-GGCCTCTTGAACGATGGGAGGGGACTCTTGAGG
* *
1172197 GATGATAAGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGA-CAGGGCCTCTTGAACGATGGGAGGGGACTCTTGAGG
1172239 GATGACAGG
1 GATGACAGG
1172248 TGAGTCGGGC
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
41 29 0.64
42 16 0.36
ACGTcount: A:0.22, C:0.15, G:0.41, T:0.22
Consensus pattern (41 bp):
GATGACAGGGCCTCTTGAACGATGGGAGGGGACTCTTGAGG
Found at i:1172633 original size:20 final size:20
Alignment explanation
Indices: 1172610--1172683 Score: 78
Period size: 20 Copynumber: 3.7 Consensus size: 20
1172600 GAAACTTAAA
1172610 ATCGCAACGCAAAAATGACT
1 ATCGCAACGCAAAAATGACT
** *
1172630 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGCAAAAATGACT
* **
1172650 ATCGCAATGC-AAAATGAAA
1 ATCGCAACGCAAAAATGACT
1172669 ATCGCAACGACAAAA
1 ATCGCAACG-CAAAA
1172684 TCGCAACGCA
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
19 13 0.30
20 27 0.63
21 3 0.07
ACGTcount: A:0.45, C:0.23, G:0.19, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCAAAAATGACT
Found at i:1172683 original size:14 final size:13
Alignment explanation
Indices: 1172666--1172696 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
1172656 ATGCAAAATG
1172666 AAAATCGCAACGAC
1 AAAATCGCAACG-C
1172680 AAAATCGCAACGC
1 AAAATCGCAACGC
1172693 AAAA
1 AAAA
1172697 CACAAATCGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.55, C:0.26, G:0.13, T:0.06
Consensus pattern (13 bp):
AAAATCGCAACGC
Found at i:1172736 original size:20 final size:19
Alignment explanation
Indices: 1172706--1172756 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
1172696 ACACAAATCG
*
1172706 CATTGCAATTTTCATTTTCA
1 CATTGCGATTTTCA-TTTCA
* *
1172726 CGTTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCA
1172745 CATTGCGATTTT
1 CATTGCGATTTT
1172757 GTCGTTGCGA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.18, C:0.20, G:0.14, T:0.49
Consensus pattern (19 bp):
CATTGCGATTTTCATTTCA
Found at i:1172805 original size:20 final size:19
Alignment explanation
Indices: 1172771--1172826 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
1172761 TTGCGATTTT
*
1172771 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1172790 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
1172810 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
1172827 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1173211 original size:21 final size:21
Alignment explanation
Indices: 1173187--1173233 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1173177 ATCGTCTTTG
* *
1173187 CGTAAAGTATCGACCTCCTCA
1 CGTAAAGCATCGACCTCATCA
* *
1173208 CGTAAGGCATTGACCTCATCA
1 CGTAAAGCATCGACCTCATCA
1173229 CGTAA
1 CGTAA
1173234 CTCCCTAACT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (21 bp):
CGTAAAGCATCGACCTCATCA
Found at i:1173418 original size:18 final size:18
Alignment explanation
Indices: 1173395--1173442 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
1173385 CGGGTCGATC
1173395 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
1173413 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
1173431 AGGTGATGGCTC
1 AGGTGATGGCTC
1173443 CCGAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:1174791 original size:20 final size:20
Alignment explanation
Indices: 1174768--1174823 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
1174758 TTTGAAACTT
1174768 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
1174788 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** *
1174808 ACTATCGCAACGCGAA
1 AAAATCGCAACACGAA
1174824 TTTGACTATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.50, C:0.23, G:0.16, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:1174829 original size:20 final size:20
Alignment explanation
Indices: 1174771--1174839 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 20
1174761 GAAACTTAAA
* **
1174771 ATCGCAACACGAAAATGAAA
1 ATCGCAACGCGAAAATGACT
*
1174791 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
1174811 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
1174831 ATCGCAACG
1 ATCGCAACG
1174840 AGAGAATCGC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.42, C:0.25, G:0.17, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1175531 original size:21 final size:21
Alignment explanation
Indices: 1175460--1175529 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 21
1175450 GAAAATCACA
1175460 TTGCGATTATGTATTATCGCG
1 TTGCGATTATGTATTATCGCG
* *
1175481 TTGCGA--AAGTCAGTATCGCG
1 TTGCGATTATGT-ATTATCGCG
*
1175501 TTGCGATTTTGTATTATCGCG
1 TTGCGATTATGTATTATCGCG
1175522 TTGCGATT
1 TTGCGATT
1175530 TTCCAAATTC
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
19 3 0.07
20 14 0.34
21 22 0.54
22 2 0.05
ACGTcount: A:0.19, C:0.16, G:0.26, T:0.40
Consensus pattern (21 bp):
TTGCGATTATGTATTATCGCG
Found at i:1175610 original size:21 final size:22
Alignment explanation
Indices: 1175558--1175610 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
1175548 ATTTACTTAT
1175558 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
* **
1175579 TCACAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
1175600 TCGCATTGCGA
1 TCGCATTGCGA
1175611 TAGTCATAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:1177269 original size:21 final size:21
Alignment explanation
Indices: 1177243--1177282 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1177233 GACTGTCACA
*
1177243 TCAACATCATAAATCATCATG
1 TCAACACCATAAATCATCATG
*
1177264 TCAACACCATAAATTATCA
1 TCAACACCATAAATCATCA
1177283 CGTTAGTACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.25, G:0.03, T:0.28
Consensus pattern (21 bp):
TCAACACCATAAATCATCATG
Found at i:1178904 original size:18 final size:20
Alignment explanation
Indices: 1178871--1178909 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1178861 AAAAAATTTA
*
1178871 ATTTACTCATTATTTT-TTC
1 ATTTACTCACTATTTTGTTC
1178890 ATTTACTC-CTATTTTGTTC
1 ATTTACTCACTATTTTGTTC
1178909 A
1 A
1178910 CTTGATTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.21, C:0.18, G:0.03, T:0.59
Consensus pattern (20 bp):
ATTTACTCACTATTTTGTTC
Found at i:1182794 original size:3 final size:3
Alignment explanation
Indices: 1182782--1182840 Score: 104
Period size: 3 Copynumber: 20.3 Consensus size: 3
1182772 CACCCCCAAT
1182782 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1182828 ATA ATA ATA ATA A
1 ATA ATA ATA ATA A
1182841 AGTGAAGAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 4 0.07
3 50 0.93
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1183135 original size:17 final size:17
Alignment explanation
Indices: 1183113--1183145 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1183103 GAATGTTCAA
*
1183113 CTCAAAGAAGGTGAATG
1 CTCAAAGAAGATGAATG
1183130 CTCAAAGAAGATGAAT
1 CTCAAAGAAGATGAAT
1183146 AACCAAACAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.12, G:0.24, T:0.18
Consensus pattern (17 bp):
CTCAAAGAAGATGAATG
Found at i:1183462 original size:29 final size:29
Alignment explanation
Indices: 1183376--1183480 Score: 104
Period size: 29 Copynumber: 3.6 Consensus size: 29
1183366 TTTTTCATTC
* * * *
1183376 AAGTATCTAAAG-AATTTTTGATCAAAAC
1 AAGTACCTAAAGTATTTTTTGATAAAAAT
* * *
1183404 AAATATCTAAATTTATCTTTTTGATAAAAAT
1 AAGTACCTAAA-GTAT-TTTTTGATAAAAAT
* *
1183435 AGGTACCTAAAGTATTTTTTGATCAAAAT
1 AAGTACCTAAAGTATTTTTTGATAAAAAT
1183464 AAGTACCTAAAGTATTT
1 AAGTACCTAAAGTATTT
1183481 AAATTTTTTT
Statistics
Matches: 63, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
28 10 0.16
29 29 0.46
30 4 0.06
31 20 0.32
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.38
Consensus pattern (29 bp):
AAGTACCTAAAGTATTTTTTGATAAAAAT
Found at i:1183505 original size:31 final size:31
Alignment explanation
Indices: 1183463--1183542 Score: 133
Period size: 31 Copynumber: 2.6 Consensus size: 31
1183453 TTGATCAAAA
* *
1183463 TAAGTACCTAAAGTATTTAAATTTTTTTATC
1 TAAGTATCTAAAGTATTCAAATTTTTTTATC
*
1183494 TAAGTATCTAAAGTATTCAATTTTTTTTATC
1 TAAGTATCTAAAGTATTCAAATTTTTTTATC
1183525 TAAGTATCTAAAGTATTC
1 TAAGTATCTAAAGTATTC
1183543 TTTAATTAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.35, C:0.10, G:0.07, T:0.47
Consensus pattern (31 bp):
TAAGTATCTAAAGTATTCAAATTTTTTTATC
Found at i:1191978 original size:12 final size:13
Alignment explanation
Indices: 1191961--1191993 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
1191951 AATTATTTTT
1191961 TAAAATAAA-AAA
1 TAAAATAAAGAAA
1191973 TAAAATAAAGAAA
1 TAAAATAAAGAAA
1191986 T-AAATAAA
1 TAAAATAAA
1191994 TAATTGTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (13 bp):
TAAAATAAAGAAA
Found at i:1199162 original size:18 final size:18
Alignment explanation
Indices: 1199139--1199180 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
1199129 CAGTAATCCT
1199139 ATTCC-CTGATAATCTTAC
1 ATTCCACTGATAATC-TAC
*
1199157 ATTCCCACTGGTAATCTAC
1 ATT-CCACTGATAATCTAC
1199176 ATTCC
1 ATTCC
1199181 GTGAATCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 5 0.24
19 8 0.38
20 8 0.38
ACGTcount: A:0.26, C:0.31, G:0.07, T:0.36
Consensus pattern (18 bp):
ATTCCACTGATAATCTAC
Found at i:1201120 original size:22 final size:21
Alignment explanation
Indices: 1201089--1201134 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
1201079 TCATGTGACC
*
1201089 ATTTAATTATTGTCAGATTTT
1 ATTTAATTATTGTCAGATTGT
*
1201110 ATTTATATTATTGTTAGATTGT
1 ATTTA-ATTATTGTCAGATTGT
1201132 ATT
1 ATT
1201135 CTGAGTATCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.28, C:0.02, G:0.11, T:0.59
Consensus pattern (21 bp):
ATTTAATTATTGTCAGATTGT
Found at i:1206938 original size:171 final size:174
Alignment explanation
Indices: 1206610--1206957 Score: 571
Period size: 171 Copynumber: 2.0 Consensus size: 174
1206600 GTTATTTGTG
* *
1206610 AGTGATATTAATGGGGTATATGCCACTTTCCCATTTGCAGCTTTTATTCAAACTTTTGAACCTTT
1 AGTGATATTAATGGAGTATATGCCACTTTCACATTTGCAGCTTTTATTCAAACTTTTGAACCTTT
1206675 CTCTCTCCATGCTCTACTCTTTCTCTGCTTCATTGCTTCAAACAAATTTTTTAAGACATTTTCCT
66 CTCTCTCCATGCTCTA-TC-TTCTCTGCTTCA-TGCTTCAAACAAATTTTTTAAGACATTTTCCT
1206740 TTCTCCATTGATTTGCATTTCAGTACTAAAAGCTTCCTCAGCTCTCT
128 TTCTCCATTGATTTGCATTTCAGTACTAAAAGCTTCCTCAGCTCTCT
1206787 AGTGATATTAATGGAGTATATGCCACTTTCACATTTGCAGCTTTTATTCAAACTTTTGAACCCTT
1 AGTGATATTAATGGAGTATATGCCACTTTCACATTTGCAGCTTTTATTCAAACTTTTGAA-CCTT
* *
1206852 CTTTCTCTCCATGCTCT-TC-TCT-TTC-TC-TGCTTCAAACAAATTTTTTAAGACATTTTCCTT
65 -TCTCTCTCCATGCTCTATCTTCTCTGCTTCATGCTTCAAACAAATTTTTTAAGACATTTTCCTT
*
1206912 TCTCCATTGATTTGCATTTCAGTACTAAAAGCTTCCTCAGGTCTCT
129 TCTCCATTGATTTGCATTTCAGTACTAAAAGCTTCCTCAGCTCTCT
1206958 CATGGCTTAA
Statistics
Matches: 164, Mismatches: 5, Indels: 10
0.92 0.03 0.06
Matches are distributed among these distances:
171 78 0.48
173 2 0.01
174 2 0.01
175 3 0.02
177 60 0.37
178 4 0.02
179 15 0.09
ACGTcount: A:0.22, C:0.24, G:0.11, T:0.43
Consensus pattern (174 bp):
AGTGATATTAATGGAGTATATGCCACTTTCACATTTGCAGCTTTTATTCAAACTTTTGAACCTTT
CTCTCTCCATGCTCTATCTTCTCTGCTTCATGCTTCAAACAAATTTTTTAAGACATTTTCCTTTC
TCCATTGATTTGCATTTCAGTACTAAAAGCTTCCTCAGCTCTCT
Found at i:1207524 original size:18 final size:18
Alignment explanation
Indices: 1207501--1207537 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1207491 CCTGGCCTCC
1207501 CTTTGATCATACATACAT
1 CTTTGATCATACATACAT
1207519 CTTTGATCATACATACAT
1 CTTTGATCATACATACAT
1207537 C
1 C
1207538 ACCTTGAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.38
Consensus pattern (18 bp):
CTTTGATCATACATACAT
Found at i:1207981 original size:12 final size:12
Alignment explanation
Indices: 1207966--1208001 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
1207956 GAATGTTGTG
*
1207966 CTTGTTCTTGTT
1 CTTGTTCATGTT
1207978 CTTGTTCATGTT
1 CTTGTTCATGTT
*
1207990 CATGTTCATGTT
1 CTTGTTCATGTT
1208002 TGTTAGTAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.08, C:0.17, G:0.17, T:0.58
Consensus pattern (12 bp):
CTTGTTCATGTT
Found at i:1211101 original size:23 final size:23
Alignment explanation
Indices: 1211075--1211119 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1211065 GATGAAGTAT
*
1211075 ATTTTTAT-TATATTGATATATTA
1 ATTTTTATGTAAATTG-TATATTA
1211098 ATTTTTATGTAAATTGTATATT
1 ATTTTTATGTAAATTGTATATT
1211120 TAGTACTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (23 bp):
ATTTTTATGTAAATTGTATATTA
Found at i:1212923 original size:10 final size:10
Alignment explanation
Indices: 1212910--1212979 Score: 52
Period size: 10 Copynumber: 6.7 Consensus size: 10
1212900 AAAATAAACG
*
1212910 AACGAACGTA
1 AACGAACATA
1212920 AACGAACATA
1 AACGAACATA
*
1212930 AACAAACACAATA
1 AAC-GA-AC-ATA
*
1212943 AATGCAA-ATA
1 AACG-AACATA
* *
1212953 AATGAACATC
1 AACGAACATA
1212963 AACGAACATA
1 AACGAACATA
1212973 AACGAAC
1 AACGAAC
1212980 TTGCATCGGA
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
9 2 0.04
10 36 0.75
11 1 0.02
12 3 0.06
13 6 0.12
ACGTcount: A:0.59, C:0.20, G:0.10, T:0.11
Consensus pattern (10 bp):
AACGAACATA
Found at i:1213260 original size:24 final size:24
Alignment explanation
Indices: 1213233--1213289 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
1213223 AACATGCACG
1213233 AACATAAACATACATAAACGAACA
1 AACATAAACATACATAAACGAACA
1213257 AACATAAACATACATAAACGAACA
1 AACATAAACATACATAAACGAACA
1213281 AACATAAAC
1 AACATAAAC
1213290 GGAAATAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.63, C:0.21, G:0.04, T:0.12
Consensus pattern (24 bp):
AACATAAACATACATAAACGAACA
Found at i:1213261 original size:14 final size:14
Alignment explanation
Indices: 1213239--1213290 Score: 58
Period size: 14 Copynumber: 4.0 Consensus size: 14
1213229 CACGAACATA
*
1213239 AACATACATAAACG
1 AACAAACATAAACG
1213253 AACAAACAT--A--
1 AACAAACATAAACG
*
1213263 AACATACATAAACG
1 AACAAACATAAACG
1213277 AACAAACATAAACG
1 AACAAACATAAACG
1213291 GAAATAAATG
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
10 8 0.26
12 2 0.06
14 21 0.68
ACGTcount: A:0.62, C:0.21, G:0.06, T:0.12
Consensus pattern (14 bp):
AACAAACATAAACG
Found at i:1213297 original size:24 final size:24
Alignment explanation
Indices: 1213233--1213308 Score: 89
Period size: 24 Copynumber: 3.2 Consensus size: 24
1213223 AACATGCACG
* *
1213233 AACATAAACATACATAAACGAACA
1 AACATAAACAGAAATAAACGAACA
* *
1213257 AACATAAACATACATAAACGAACA
1 AACATAAACAGAAATAAACGAACA
* * *
1213281 AACATAAACGGAAATAAATGAACG
1 AACATAAACAGAAATAAACGAACA
1213305 AACA
1 AACA
1213309 CAAATGAACA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.62, C:0.18, G:0.08, T:0.12
Consensus pattern (24 bp):
AACATAAACAGAAATAAACGAACA
Found at i:1213722 original size:13 final size:13
Alignment explanation
Indices: 1213704--1213729 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1213694 CAAATTACAA
1213704 GCTTATAAAATTC
1 GCTTATAAAATTC
1213717 GCTTATAAAATTC
1 GCTTATAAAATTC
1213730 TCGCTAGGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (13 bp):
GCTTATAAAATTC
Found at i:1216484 original size:20 final size:20
Alignment explanation
Indices: 1216461--1216518 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
1216451 GTGTTAAGGA
*
1216461 AAACAAAAGTATATATATAT
1 AAACAAACGTATATATATAT
1216481 AAACAAACGTATATATATAT
1 AAACAAACGTATATATATAT
1216501 AAACAAACGTATATATAT
1 AAACAAACGTATATATAT
1216519 GGATCAAGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.57, C:0.09, G:0.05, T:0.29
Consensus pattern (20 bp):
AAACAAACGTATATATATAT
Found at i:1217492 original size:7 final size:8
Alignment explanation
Indices: 1217468--1217501 Score: 59
Period size: 8 Copynumber: 4.1 Consensus size: 8
1217458 GATGACAAAC
1217468 TTTATTTCT
1 TTTATTT-T
1217477 TTTATTTT
1 TTTATTTT
1217485 TTTATTTT
1 TTTATTTT
1217493 TTTATTTT
1 TTTATTTT
1217501 T
1 T
1217502 GTTTAGATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.72
9 7 0.28
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (8 bp):
TTTATTTT
Found at i:1217712 original size:12 final size:12
Alignment explanation
Indices: 1217695--1217719 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1217685 AGTATGCTCA
1217695 GGTGATACATGT
1 GGTGATACATGT
1217707 GGTGATACATGT
1 GGTGATACATGT
1217719 G
1 G
1217720 ATTCTTGAAA
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:0.24, C:0.08, G:0.36, T:0.32
Consensus pattern (12 bp):
GGTGATACATGT
Found at i:1230191 original size:12 final size:12
Alignment explanation
Indices: 1230176--1230213 Score: 55
Period size: 10 Copynumber: 3.4 Consensus size: 12
1230166 ATATATAAGC
1230176 ATATATATTATA
1 ATATATATTATA
1230188 ATATATA-TAT-
1 ATATATATTATA
1230198 ATATAT-TTATA
1 ATATATATTATA
1230209 ATATA
1 ATATA
1230214 AATATAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.38
11 8 0.33
12 7 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
ATATATATTATA
Found at i:1230209 original size:21 final size:20
Alignment explanation
Indices: 1230176--1230219 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
1230166 ATATATAAGC
*
1230176 ATATATATTATAATATATAT
1 ATATATATTATAATATAAAT
1230196 ATATATATTTATAATATAAAT
1 ATATATA-TTATAATATAAAT
1230217 ATA
1 ATA
1230220 AACTTAAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
ATATATATTATAATATAAAT
Found at i:1230789 original size:21 final size:20
Alignment explanation
Indices: 1230749--1230823 Score: 55
Period size: 20 Copynumber: 3.7 Consensus size: 20
1230739 CAACGCGAAC
*
1230749 TCCAATTTCGCAAC-ACAATT
1 TCCAAATTCGCAACTA-AATT
1230769 TCCAAATTCGCAACTTAAATT
1 TCCAAATTCGCAAC-TAAATT
*** * *
1230790 T-CTTTTTCGCAACGTGATTT
1 TCCAAATTCGCAAC-TAAATT
1230810 TCCAAATTCGCAAC
1 TCCAAATTCGCAAC
1230824 ACAGAAGTCA
Statistics
Matches: 42, Mismatches: 10, Indels: 5
0.74 0.18 0.09
Matches are distributed among these distances:
20 27 0.64
21 14 0.33
22 1 0.02
ACGTcount: A:0.31, C:0.27, G:0.08, T:0.35
Consensus pattern (20 bp):
TCCAAATTCGCAACTAAATT
Found at i:1231065 original size:22 final size:22
Alignment explanation
Indices: 1231001--1231070 Score: 113
Period size: 22 Copynumber: 3.2 Consensus size: 22
1230991 CTCTCTACGA
* *
1231001 CGACATCCCTCCCCATCTCCAG
1 CGACATCCGTCCCCATCTCCGG
1231023 CGACATCCGTCCCCATCTCCGG
1 CGACATCCGTCCCCATCTCCGG
*
1231045 CGACATCCGTCCCCATCTCCGA
1 CGACATCCGTCCCCATCTCCGG
1231067 CGAC
1 CGAC
1231071 CCCCATCTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.17, C:0.51, G:0.14, T:0.17
Consensus pattern (22 bp):
CGACATCCGTCCCCATCTCCGG
Found at i:1231198 original size:24 final size:24
Alignment explanation
Indices: 1231157--1231210 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1231147 CTGAAACATC
* *
1231157 ATCAAAATCTGAGTATTGACCAAG
1 ATCAAAATCCGAGAATTGACCAAG
*
1231181 ATCAAAGTCCGAGAATTGACCAAG
1 ATCAAAATCCGAGAATTGACCAAG
1231205 ATCAAA
1 ATCAAA
1231211 TTTCGAATAC
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:0.44, C:0.19, G:0.17, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGAATTGACCAAG
Found at i:1231982 original size:14 final size:16
Alignment explanation
Indices: 1231947--1231983 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1231937 GAAATCATTG
1231947 AAAATTATATAGAAAT
1 AAAATTATATAGAAAT
*
1231963 AAAATTATGTA-AAA-
1 AAAATTATATAGAAAT
1231977 AAAATTA
1 AAAATTA
1231984 GAGATGGGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 3 0.15
16 10 0.50
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (16 bp):
AAAATTATATAGAAAT
Found at i:1232223 original size:20 final size:20
Alignment explanation
Indices: 1232148--1232329 Score: 111
Period size: 20 Copynumber: 9.1 Consensus size: 20
1232138 GCTGTTGTAA
*
1232148 AATTA-AAATTCGTGTTGCG
1 AATTAGAAAATCGTGTTGCG
* * *
1232167 AATTCGAAAATCGAGTTGTG
1 AATTAGAAAATCGTGTTGCG
* *
1232187 AA-AACAAAATTCGTGTTGCG
1 AATTAGAAAA-TCGTGTTGCG
*
1232207 AATTAGAAAATCTTGTTGCG
1 AATTAGAAAATCGTGTTGCG
* * *
1232227 AA-AAGGAAACTTGTGTTGCG
1 AATTA-GAAAATCGTGTTGCG
** * *
1232247 AAAAAGAAATTCGCGTTGCG
1 AATTAGAAAATCGTGTTGCG
* *
1232267 AATTCAG-AAATCGAGTTGAG
1 AATT-AGAAAATCGTGTTGCG
* *
1232287 AATTTGAAATTCCGTGTTGCG
1 AATTAGAAAAT-CGTGTTGCG
* * *
1232308 AATTTGGAAATCGCGTTGCG
1 AATTAGAAAATCGTGTTGCG
1232328 AA
1 AA
1232330 AAAGAAACTG
Statistics
Matches: 124, Mismatches: 31, Indels: 15
0.73 0.18 0.09
Matches are distributed among these distances:
19 10 0.08
20 89 0.72
21 25 0.20
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (20 bp):
AATTAGAAAATCGTGTTGCG
Found at i:1232230 original size:40 final size:41
Alignment explanation
Indices: 1232152--1232268 Score: 130
Period size: 40 Copynumber: 2.9 Consensus size: 41
1232142 TTGTAAAATT
* *
1232152 AAAATTCGTGTTGCGAATTCGAAAATCGAGTTGTGAAAA-C
1 AAAATTCGTGTTGCGAATTAGAAAATCGAGTTGCGAAAAGC
** *
1232192 AAAATTCGTGTTGCGAATTAGAAAATCTTGTTGCGAAAAGG
1 AAAATTCGTGTTGCGAATTAGAAAATCGAGTTGCGAAAAGC
* ** * *
1232233 AAACTT-GTGTTGCGAAAAAGAAATTCGCGTTGCGAA
1 AAAATTCGTGTTGCGAATTAGAAAATCGAGTTGCGAA
1232269 TTCAGAAATC
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
40 60 0.92
41 5 0.08
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (41 bp):
AAAATTCGTGTTGCGAATTAGAAAATCGAGTTGCGAAAAGC
Found at i:1232373 original size:20 final size:20
Alignment explanation
Indices: 1232193--1232374 Score: 65
Period size: 20 Copynumber: 9.1 Consensus size: 20
1232183 TGTGAAAACA
*
1232193 AAATTCGTGTTGCG-AATTAGA
1 AAATT-GTGTTGCGAAATT-GG
*
1232214 AAATCT-TGTTGCGAAA-AGG
1 AAAT-TGTGTTGCGAAATTGG
**
1232233 AAACTTGTGTTGCGAAA-AAG
1 AAA-TTGTGTTGCGAAATTGG
* *
1232253 AAATTCGCGTTGCG-AATTCAG
1 AAATT-GTGTTGCGAAATT-GG
* * * *
1232274 AAATCGAGTTGAG-AATTTG
1 AAATTGTGTTGCGAAATTGG
*
1232293 AAATTCCGTGTTGCGAATTTGG
1 AAATT--GTGTTGCGAAATTGG
* * **
1232315 AAATCGCGTTGCGAAA-AAG
1 AAATTGTGTTGCGAAATTGG
* * *
1232334 AAACTGAT-TTGTGAATTTGG
1 AAATTG-TGTTGCGAAATTGG
1232354 AAATTGTGTTGCGAAATTGG
1 AAATTGTGTTGCGAAATTGG
1232374 A
1 A
1232375 GTTCGCGTTG
Statistics
Matches: 119, Mismatches: 29, Indels: 27
0.68 0.17 0.15
Matches are distributed among these distances:
19 26 0.22
20 66 0.55
21 18 0.15
22 9 0.08
ACGTcount: A:0.34, C:0.10, G:0.26, T:0.30
Consensus pattern (20 bp):
AAATTGTGTTGCGAAATTGG
Found at i:1232381 original size:59 final size:60
Alignment explanation
Indices: 1232231--1232389 Score: 171
Period size: 61 Copynumber: 2.6 Consensus size: 60
1232221 GTTGCGAAAA
** * **
1232231 GGAAACTTGTGTTGCGAAAAAGAAATTCGCGTTGCGAATTCAGAAATCGAGTTGAGAATTT
1 GGAAA-TTGTGTTGCGAAATTGGAATTCGCGTTGCGAATAAAGAAATCGAGTTGAGAATTT
* * * *
1232292 -GAAATTCCGTGTTGCGAATTTGGAAATCGCGTTGCGAA-AAAGAAA-CTGATTTGTGAATTT
1 GGAAATT--GTGTTGCGAAATTGGAATTCGCGTTGCGAATAAAGAAATC-GAGTTGAGAATTT
*
1232352 GGAAATTGTGTTGCGAAATTGGAGTTCGCGTTGCGAAT
1 GGAAATTGTGTTGCGAAATTGGAATTCGCGTTGCGAAT
1232390 TTGTTGGTTA
Statistics
Matches: 81, Mismatches: 12, Indels: 11
0.78 0.12 0.11
Matches are distributed among these distances:
59 30 0.37
60 20 0.25
61 31 0.38
ACGTcount: A:0.31, C:0.11, G:0.28, T:0.30
Consensus pattern (60 bp):
GGAAATTGTGTTGCGAAATTGGAATTCGCGTTGCGAATAAAGAAATCGAGTTGAGAATTT
Found at i:1233258 original size:15 final size:15
Alignment explanation
Indices: 1233238--1233274 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
1233228 TTGCTCTGAT
1233238 ATCACTTATCACATG
1 ATCACTTATCACATG
1233253 ATCACTTATCACATG
1 ATCACTTATCACATG
1233268 ATCACTT
1 ATCACTT
1233275 TTCTTTTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.35
Consensus pattern (15 bp):
ATCACTTATCACATG
Found at i:1234013 original size:18 final size:18
Alignment explanation
Indices: 1233990--1234026 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1233980 GGGGAACGAA
*
1233990 GGGTCCGAGTCGGGATCC
1 GGGTCCGAGTCGGAATCC
1234008 GGGTCCGAGTCGGAATCC
1 GGGTCCGAGTCGGAATCC
1234026 G
1 G
1234027 AATCCGAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.14, C:0.27, G:0.43, T:0.16
Consensus pattern (18 bp):
GGGTCCGAGTCGGAATCC
Found at i:1234032 original size:18 final size:18
Alignment explanation
Indices: 1233993--1234033 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1233983 GAACGAAGGG
* **
1233993 TCCGAGTCGGGATCCGGG
1 TCCGAGTCGGAATCCGAA
1234011 TCCGAGTCGGAATCCGAA
1 TCCGAGTCGGAATCCGAA
1234029 TCCGA
1 TCCGA
1234034 ATCCGACACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.20, C:0.29, G:0.34, T:0.17
Consensus pattern (18 bp):
TCCGAGTCGGAATCCGAA
Done.