Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001129.1 Hibiscus syriacus cultivar Beakdansim tig00002237_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: 21326069
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 89
Found at i:2782101 original size:133 final size:133
Alignment explanation
Indices: 2781859--2782157 Score: 417
Period size: 133 Copynumber: 2.2 Consensus size: 133
2781849 TAGTTCAACA
* *
2781859 GAAAC-GATCTCAAAGATTTTGTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCGTTTTA
1 GAAACAGAT-TCAAAGATTTTGTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCGTTTCA
* * * * *
2781923 AGCGAAACGATCTTAAAGATTTTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTC
65 AGCGAAACGATATTAAAGATTTTTATTTCAAGAGAAACTGCCTCAAGAGAAACAAAATTTGTTTC
2781988 AAGG
130 AAGG
* * * * * *
2781992 GAAACAGATTCAAAGA-TTGGTGTTTTAAGGGAAACTGTCTCAAGGGAGACAAACTTTGTTTCAA
1 GAAACAGATTCAAAGATTTTGTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCGTTTCAA
2782056 TG-GAAAC-ATATTCAAAGATTTTGTATTTCAAGAGAAACTGCCTCAAGAGAAACAAAATTTGTT
66 -GCGAAACGATATT-AAAGATTTT-TATTTCAAGAGAAACTGCCTCAAGAGAAACAAAATTTGTT
2782119 TCAAGG
128 TCAAGG
2782125 GAAACAGATTCAAAGATTTTGTGTTTCAAGGGA
1 GAAACAGATTCAAAGATTTTGTGTTTCAAGGGA
2782158 GACAAACTTA
Statistics
Matches: 146, Mismatches: 15, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
131 4 0.03
132 54 0.37
133 71 0.49
134 17 0.12
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (133 bp):
GAAACAGATTCAAAGATTTTGTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCGTTTCAA
GCGAAACGATATTAAAGATTTTTATTTCAAGAGAAACTGCCTCAAGAGAAACAAAATTTGTTTCA
AGG
Found at i:2782121 original size:67 final size:67
Alignment explanation
Indices: 2781859--2782154 Score: 402
Period size: 66 Copynumber: 4.4 Consensus size: 67
2781849 TAGTTCAACA
* * *
2781859 GAAAC-GATCTCAAAGATTTTGTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCGTTTTA
1 GAAACAGAT-TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCA
*
2781923 AGC
65 AGG
* *
2781926 GAAAC-GATCTTAAAGATTTT-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCA
1 GAAACAGAT-TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCA
2781989 AGG
65 AGG
* * * * *
2781992 GAAACAGATTCAAAGA-TTGGTGTTTTAAGGGAAACTGTCTCAAGGGAGACAAACTTTGTTTCAA
1 GAAACAGATTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAA
*
2782056 TG
66 GG
* * * *
2782058 GAAACATATTCAAAGATTTTGTATTTCAAGAGAAACTGCCTCAAGAGAAACAAAATTTGTTTCAA
1 GAAACAGATTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAA
2782123 GG
66 GG
2782125 GAAACAGATTCAAAGATTTTGTGTTTCAAG
1 GAAACAGATTCAAAGATTTTGTGTTTCAAG
2782155 GGAGACAAAC
Statistics
Matches: 202, Mismatches: 24, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
65 2 0.01
66 109 0.54
67 91 0.45
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (67 bp):
GAAACAGATTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAA
GG
Found at i:2782319 original size:72 final size:74
Alignment explanation
Indices: 2782177--2782320 Score: 170
Period size: 72 Copynumber: 2.0 Consensus size: 74
2782167 ATTTTGAGTA
* * * * *
2782177 AAAATTGTCTCAAGTGAGACAAAATTTATTTTTTGGAGAAAACAATCACAAGTGAGATTAATTTT
1 AAAATTGTCTCAAGCGAGACAAAATTTACTTCTTAGAGAAAACAATCACAAGTGAGATCAATTTT
2782242 ATTTTAATT
66 ATTTTAATT
* *
2782251 AAAATTGTCT-ACAGCGAGACAAAATTT-CTTCTTAG-GAAAACTATCTCATA-TGAGATCAATT
1 AAAATTGTCTCA-AGCGAGACAAAATTTACTTCTTAGAGAAAACAATCACA-AGTGAGATCAATT
*
2782312 TTGTTTTAA
64 TTATTTTAA
2782321 ATATTTCAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
72 29 0.48
73 7 0.12
74 24 0.40
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (74 bp):
AAAATTGTCTCAAGCGAGACAAAATTTACTTCTTAGAGAAAACAATCACAAGTGAGATCAATTTT
ATTTTAATT
Found at i:2783857 original size:2 final size:2
Alignment explanation
Indices: 2783845--2783918 Score: 132
Period size: 2 Copynumber: 37.5 Consensus size: 2
2783835 AGCTTTATTT
*
2783845 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A 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
2783886 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 T
2783919 GTGTATACGG
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
1 1 0.01
2 68 0.99
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2784649 original size:18 final size:18
Alignment explanation
Indices: 2784626--2784664 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
2784616 ATCGGAAACC
2784626 TTATCTTATTATAATATT
1 TTATCTTATTATAATATT
2784644 TTATCTTATTATAATATT
1 TTATCTTATTATAATATT
2784662 TTA
1 TTA
2784665 ATGAATGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATCTTATTATAATATT
Found at i:2787264 original size:51 final size:51
Alignment explanation
Indices: 2787209--2787320 Score: 138
Period size: 51 Copynumber: 2.2 Consensus size: 51
2787199 ATAAAATAAC
** *
2787209 AGTGACTAAAATGCAAGAAAATAAAA-ATTAGTAGTTAAATAAGAAA-TAAAT
1 AGTGACTAAAATGCAA-AAAATAAAATAACAGTAGCTAAATAAGAAACT-AAT
* * *
2787260 AGTGACAAAAATGCAAAAATTAAAATAACAGTAGCTAAATCAGAAACTAAT
1 AGTGACTAAAATGCAAAAAATAAAATAACAGTAGCTAAATAAGAAACTAAT
2787311 AGTGACTAAA
1 AGTGACTAAA
2787321 TTAAAATAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
50 8 0.15
51 43 0.83
52 1 0.02
ACGTcount: A:0.57, C:0.08, G:0.13, T:0.21
Consensus pattern (51 bp):
AGTGACTAAAATGCAAAAAATAAAATAACAGTAGCTAAATAAGAAACTAAT
Found at i:2789268 original size:21 final size:21
Alignment explanation
Indices: 2789244--2789297 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
2789234 TATGAGAAAC
*
2789244 AGTATCAATAGTAGATGAACT
1 AGTATCAATACTAGATGAACT
** *
2789265 AGTATTGATACTAGATGAATT
1 AGTATCAATACTAGATGAACT
* *
2789286 GGTATCGATACT
1 AGTATCAATACT
2789298 GTTCATATTC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.37, C:0.09, G:0.20, T:0.33
Consensus pattern (21 bp):
AGTATCAATACTAGATGAACT
Found at i:2789441 original size:20 final size:20
Alignment explanation
Indices: 2789418--2789463 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
2789408 CTGAAAACTC
2789418 GGTATCAATATCG-TATGCTT
1 GGTATCAATATCGATATG-TT
*
2789438 GGTATCGATATCGATATGTT
1 GGTATCAATATCGATATGTT
2789458 GGTATC
1 GGTATC
2789464 CATACCCGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.24, C:0.13, G:0.24, T:0.39
Consensus pattern (20 bp):
GGTATCAATATCGATATGTT
Found at i:2789473 original size:21 final size:21
Alignment explanation
Indices: 2789418--2789474 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 21
2789408 CTGAAAACTC
* *
2789418 GGTATCAATATCG-TATGCTT
1 GGTATCCATACCGATATGCTT
* *
2789438 GGTATCGATATCGATATG-TT
1 GGTATCCATACCGATATGCTT
2789458 GGTATCCATACCCGATA
1 GGTATCCATA-CCGATA
2789475 AACTGGTATC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 23 0.72
21 9 0.28
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (21 bp):
GGTATCCATACCGATATGCTT
Found at i:2789550 original size:21 final size:21
Alignment explanation
Indices: 2789512--2789551 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2789502 ATCTATATCG
* *
2789512 GATGAGTTGATATTCATACTA
1 GATGAATTGATATCCATACTA
*
2789533 GATGAATTGGTATCCATAC
1 GATGAATTGATATCCATAC
2789552 CGTAGATTGA
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:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (21 bp):
GATGAATTGATATCCATACTA
Found at i:2794174 original size:20 final size:20
Alignment explanation
Indices: 2794123--2794174 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
2794113 CGTGTATTCG
*
2794123 GTATGGAGACCAATTTTCCA
1 GTATGGAGACCAATCTTCCA
* *
2794143 GTATAGAAACCAATCCTT-CA
1 GTATGGAGACCAAT-CTTCCA
2794163 GTATGGAGACCA
1 GTATGGAGACCA
2794175 GTTTTTTAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 24 0.92
21 2 0.08
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (20 bp):
GTATGGAGACCAATCTTCCA
Found at i:2803518 original size:21 final size:19
Alignment explanation
Indices: 2803484--2803524 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
2803474 TGCATCAAGG
*
2803484 TCTTTTTTGAGGCCATGAAA
1 TCTTTTTCGAGGCCAT-AAA
2803504 TCTTTTGTCGAGGCCATAAA
1 TCTTTT-TCGAGGCCATAAA
2803524 T
1 T
2803525 TCCTGTAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (19 bp):
TCTTTTTCGAGGCCATAAA
Found at i:2803566 original size:12 final size:12
Alignment explanation
Indices: 2803549--2803584 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
2803539 CTCAAAGGAG
2803549 TTAGTATTAGAA
1 TTAGTATTAGAA
2803561 TTAGTATTAGAA
1 TTAGTATTAGAA
2803573 TTAGTATTAGAA
1 TTAGTATTAGAA
2803585 GAAGAAGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.17, T:0.42
Consensus pattern (12 bp):
TTAGTATTAGAA
Found at i:2825258 original size:29 final size:29
Alignment explanation
Indices: 2825217--2825274 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
2825207 ATTTTTATTG
2825217 TTATAATTATATTATT-ATAATATATAATA
1 TTATAATTATATT-TTAATAATATATAATA
* *
2825246 TTATACTTTTATTTTAATAATATATAATA
1 TTATAATTATATTTTAATAATATATAATA
2825275 AATTGTTAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 2 0.08
29 24 0.92
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (29 bp):
TTATAATTATATTTTAATAATATATAATA
Found at i:2825405 original size:29 final size:27
Alignment explanation
Indices: 2825361--2825419 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 27
2825351 ATCCTTAAAA
* **
2825361 TATAATTTAATATTTTTATTCTAATAT
1 TATAATTTAATATTTTAATAATAATAT
2825388 TATAATTTTGAATATTTTAATAATAATAT
1 TATAA-TTT-AATATTTTAATAATAATAT
2825417 TAT
1 TAT
2825420 TTTTTTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 5 0.19
28 3 0.11
29 19 0.70
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (27 bp):
TATAATTTAATATTTTAATAATAATAT
Found at i:2825479 original size:13 final size:13
Alignment explanation
Indices: 2825461--2825485 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2825451 TTTATTTCCA
2825461 AACCGGTTAAAAT
1 AACCGGTTAAAAT
2825474 AACCGGTTAAAA
1 AACCGGTTAAAA
2825486 AAAATCCGAT
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:0.48, C:0.16, G:0.16, T:0.20
Consensus pattern (13 bp):
AACCGGTTAAAAT
Found at i:2825569 original size:28 final size:29
Alignment explanation
Indices: 2825521--2825576 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
2825511 GGTTTTCCCC
*
2825521 AAATCCGATTTCGGATATTTTT-TGCACA
1 AAATCCGATTTCGAATATTTTTGTGCACA
*
2825549 AAATCGGATATTCGAAT-TTTTTGTGCAC
1 AAATCCGAT-TTCGAATATTTTTGTGCAC
2825577 CTCTACCCCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (29 bp):
AAATCCGATTTCGAATATTTTTGTGCACA
Found at i:2827422 original size:22 final size:21
Alignment explanation
Indices: 2827379--2827449 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 21
2827369 TAACTACAAC
* *
2827379 AATAATATTTTCTTTTCTAAA
1 AATAAAATATTCTTTTCTAAA
*
2827400 AATAAGATATTCTTTCTCTAAA
1 AATAAAATATTCTTT-TCTAAA
*
2827422 AATAAAATATTATTTTCCTAATA
1 AATAAAATATTCTTTT-CTAA-A
2827445 AATAA
1 AATAA
2827450 CATAACATTA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
21 14 0.33
22 23 0.53
23 6 0.14
ACGTcount: A:0.45, C:0.10, G:0.01, T:0.44
Consensus pattern (21 bp):
AATAAAATATTCTTTTCTAAA
Found at i:2827836 original size:20 final size:21
Alignment explanation
Indices: 2827811--2827903 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
2827801 TTTTCCCAAT
*
2827811 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
2827831 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
2827852 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
2827872 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
2827893 TCGCAATGCGA
1 TCGCAATGCGA
2827904 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:2827868 original size:41 final size:41
Alignment explanation
Indices: 2827811--2827903 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
2827801 TTTTCCCAAT
2827811 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
2827852 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
2827893 TCGCAATGCGA
1 TCGCAATGCGA
2827904 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:2827916 original size:41 final size:41
Alignment explanation
Indices: 2827830--2827964 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
2827820 GAATAAGTAA
* *
2827830 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
2827871 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
2827912 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
2827953 TTCGCAACGCGA
1 ATCGCAACGCGA
2827965 TACTGACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:2827917 original size:20 final size:20
Alignment explanation
Indices: 2827892--2828006 Score: 115
Period size: 20 Copynumber: 5.7 Consensus size: 20
2827882 AATTGGGAAA
*
2827892 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
2827912 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
2827933 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
2827953 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
2827973 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
2827993 TTCGCAACGCGATA
1 ATCGCAACGCGATA
2828007 ATACATAATC
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:2827965 original size:41 final size:41
Alignment explanation
Indices: 2827889--2828026 Score: 154
Period size: 41 Copynumber: 3.4 Consensus size: 41
2827879 GCGAATTGGG
* * *
2827889 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* * *
2827930 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATACTGAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAAT-AC
** *
2827972 --TTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* *
2828011 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
2828027 TTTCAAAGCG
Statistics
Matches: 79, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
39 2 0.03
40 31 0.39
41 44 0.56
42 2 0.03
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:2828222 original size:22 final size:22
Alignment explanation
Indices: 2828194--2828237 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2828184 CACTCTCTCA
2828194 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
2828216 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
2828238 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:2828544 original size:20 final size:20
Alignment explanation
Indices: 2828500--2828559 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
2828490 GCGATTATCT
**
2828500 CGTTGCGATAGTCAAATTCA
1 CGTTGCGATAGTCATTTTCA
*
2828520 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCA
* **
2828540 TGTTGCGATTTTCATTTTCA
1 CGTTGCGATAGTCATTTTCA
2828560 GAAACTATTC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCA
Found at i:2829899 original size:18 final size:18
Alignment explanation
Indices: 2829878--2829922 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
2829868 TCCACTTCGG
*
2829878 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
2829896 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
2829914 GAGCCATCA
1 GAGCCATCA
2829923 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:2830458 original size:19 final size:20
Alignment explanation
Indices: 2830404--2830470 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
2830394 TAGTTTACTT
* *
2830404 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
2830424 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
2830444 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
2830463 TCGCAACG
1 TCGCAACG
2830471 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:2830478 original size:14 final size:14
Alignment explanation
Indices: 2830459--2830514 Score: 67
Period size: 14 Copynumber: 3.7 Consensus size: 14
2830449 ATGCGAAATG
2830459 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
2830473 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
2830489 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
2830505 AAAATCGCAA
1 AAAATCGCAA
2830515 TGCAAAATGA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
14 19 0.53
16 8 0.22
18 9 0.25
ACGTcount: A:0.50, C:0.23, G:0.16, T:0.11
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:2830501 original size:32 final size:33
Alignment explanation
Indices: 2830443--2830533 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
2830433 GGAAATGGCT
2830443 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
2830476 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
2830508 ATCGCAATGCAAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
2830534 TGTGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.48, C:0.21, G:0.18, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:2830569 original size:14 final size:14
Alignment explanation
Indices: 2830550--2830607 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
2830540 TTGTGTTTCG
2830550 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
2830564 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
2830580 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
2830596 CGTTGCGATTTT
1 CGTTGCGATTTT
2830608 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:2830581 original size:32 final size:33
Alignment explanation
Indices: 2830545--2830623 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
2830535 GTGATTTGTG
2830545 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
2830577 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
2830610 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
2830624 AGCCATTTTC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:2830622 original size:19 final size:19
Alignment explanation
Indices: 2830564--2830681 Score: 95
Period size: 20 Copynumber: 6.4 Consensus size: 19
2830554 GCGATTTTGT
2830564 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
2830582 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
2830596 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
2830615 CATTGCGATAGCCATTTTCG
1 CGTTGCGATTTTCA-TTTCG
**
2830635 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
2830654 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
2830674 TGTTGCGA
1 CGTTGCGA
2830682 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 11 0.14
19 26 0.32
20 29 0.36
ACGTcount: A:0.14, C:0.19, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:2830673 original size:39 final size:37
Alignment explanation
Indices: 2830545--2830681 Score: 105
Period size: 39 Copynumber: 3.9 Consensus size: 37
2830535 GTGATTTGTG
2830545 TTTCGCGTTGCGATTTT-G--T--CGTTGCGATTTCA
1 TTTCGCGTTGCGATTTTAGTTTCGCGTTGCGATTTCA
2830577 TTTCGCGTTGCGATTTT-G--T--CGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTAGTTTCGCGTTGCGA-TTTCA
* *** * *
2830610 TTTCGCATTGCGATAGCCATTTTCGCGTTGCGATAGTCA
1 TTTCGCGTTGCGAT-TTTAGTTTCGCGTTGCGAT-TTCA
*
2830649 TTTCGCGTTGCGATTTTAAGTTTCGTGTTGCGA
1 TTTCGCGTTGCGATTTT-AGTTTCGCGTTGCGA
2830682 AAGTAAACTA
Statistics
Matches: 84, Mismatches: 12, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
32 27 0.32
33 18 0.21
37 1 0.01
38 1 0.01
39 37 0.44
ACGTcount: A:0.12, C:0.19, G:0.25, T:0.44
Consensus pattern (37 bp):
TTTCGCGTTGCGATTTTAGTTTCGCGTTGCGATTTCA
Found at i:2832551 original size:14 final size:14
Alignment explanation
Indices: 2832532--2832567 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2832522 ATTGTTTAAT
2832532 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
2832546 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
2832560 TGATTTGT
1 TGATTTGT
2832568 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2832706 original size:19 final size:19
Alignment explanation
Indices: 2832684--2832770 Score: 139
Period size: 19 Copynumber: 4.8 Consensus size: 19
2832674 ATCGCAACGA
2832684 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
2832703 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
2832722 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
2832741 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
2832755 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
2832771 TTTTCATTTC
Statistics
Matches: 65, Mismatches: 0, Indels: 8
0.89 0.00 0.11
Matches are distributed among these distances:
14 11 0.17
15 1 0.02
16 2 0.03
17 2 0.03
19 49 0.75
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:2832726 original size:38 final size:33
Alignment explanation
Indices: 2832655--2832770 Score: 151
Period size: 33 Copynumber: 3.4 Consensus size: 33
2832645 AAAATAGACT
* ***
2832655 ATCGCAACGCGAAATGGCTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
2832688 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAA
2832726 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
2832759 ATCGCAATGCGA
1 ATCGCAATGCGA
2832771 TTTTCATTTC
Statistics
Matches: 74, Mismatches: 4, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
33 38 0.51
34 1 0.01
35 2 0.03
36 2 0.03
37 1 0.01
38 30 0.41
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:2832814 original size:20 final size:20
Alignment explanation
Indices: 2832789--2832826 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2832779 TCGCATTGCA
*
2832789 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
2832809 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
2832827 TCAAATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:2833890 original size:24 final size:24
Alignment explanation
Indices: 2833863--2833916 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2833853 GTATTTGAAA
* *
2833863 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
2833887 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
2833911 TTTGAT
1 TTTGAT
2833917 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:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:2834108 original size:12 final size:12
Alignment explanation
Indices: 2834091--2834115 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2834081 ATATAATCCT
2834091 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2834103 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2834115 G
1 G
2834116 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:2836423 original size:19 final size:19
Alignment explanation
Indices: 2836401--2836531 Score: 94
Period size: 19 Copynumber: 7.7 Consensus size: 19
2836391 GGAAATTACT
2836401 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2836420 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
2836434 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
2836453 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
2836467 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
2836486 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
2836500 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2836519 ATCGCAACGCGAA
1 ATCGCAATGCGAA
2836532 TTTAATTTCG
Statistics
Matches: 84, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
14 27 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 39 0.46
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2836443 original size:33 final size:33
Alignment explanation
Indices: 2836401--2836527 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
2836391 GGAAATTACT
2836401 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
2836434 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
2836466 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
2836500 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
2836528 CGAATTTAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 83 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:2836508 original size:66 final size:66
Alignment explanation
Indices: 2836402--2836534 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
2836392 GAAATTACTA
*
2836402 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
2836467 T
66 T
*
2836468 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
2836533 T
66 T
2836534 T
1 T
2836535 AATTTCGCGT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:2836549 original size:19 final size:19
Alignment explanation
Indices: 2836527--2836568 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2836517 AAATCGCAAC
2836527 GCGAATTTAATTTCGCGTT
1 GCGAATTTAATTTCGCGTT
* * *
2836546 GCGATTTTCATTTCGTGTT
1 GCGAATTTAATTTCGCGTT
2836565 GCGA
1 GCGA
2836569 TTCTCTCGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.17, C:0.17, G:0.24, T:0.43
Consensus pattern (19 bp):
GCGAATTTAATTTCGCGTT
Found at i:2836601 original size:19 final size:19
Alignment explanation
Indices: 2836536--2836602 Score: 72
Period size: 19 Copynumber: 3.8 Consensus size: 19
2836526 CGCGAATTTA
2836536 ATTTCGCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
*
2836555 ATTTCGTGTTGCGA--TTC
1 ATTTCGCGTTGCGATTTTC
*
2836572 ---TCTCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
*
2836588 ATTTCGCATTGCGAT
1 ATTTCGCGTTGCGAT
2836603 AGTACTTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
14 9 0.24
16 3 0.08
17 3 0.08
19 23 0.61
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.46
Consensus pattern (19 bp):
ATTTCGCGTTGCGATTTTC
Found at i:2836727 original size:14 final size:14
Alignment explanation
Indices: 2836708--2836741 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
2836698 CATCAATTAA
2836708 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2836722 ACAAATCACCTTTT
1 ACAAATCAACTTTT
2836736 ACAAAT
1 ACAAAT
2836742 AAATTAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2838162 original size:21 final size:21
Alignment explanation
Indices: 2838096--2838162 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2838086 GTGAATCGGG
*
2838096 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
2838116 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
2838138 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
2838159 CTCT
1 CTCT
2838163 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:2838181 original size:42 final size:41
Alignment explanation
Indices: 2838096--2838218 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
2838086 GTGAATCGGG
* * * *
2838096 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
2838138 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
2838180 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
2838219 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:2840265 original size:20 final size:20
Alignment explanation
Indices: 2840228--2840278 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
2840218 TGAAATGAAA
*
2840228 AATCGCAACGAGATAATGAG
1 AATCGCAACGAGATAATGAC
*
2840248 AATCGCAACGCGGA-AATGAC
1 AATCGCAACG-AGATAATGAC
*
2840268 TATCGCAACGA
1 AATCGCAACGA
2840279 TAGAATCGCA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 24 0.92
21 2 0.08
ACGTcount: A:0.41, C:0.22, G:0.24, T:0.14
Consensus pattern (20 bp):
AATCGCAACGAGATAATGAC
Found at i:2840288 original size:14 final size:14
Alignment explanation
Indices: 2840269--2840305 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2840259 GGAAATGACT
*
2840269 ATCGCAACGATAGA
1 ATCGCAACGAGAGA
2840283 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
2840297 ATCGCAACG
1 ATCGCAACG
2840306 CGAAATGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.41, C:0.24, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:2840333 original size:47 final size:48
Alignment explanation
Indices: 2840245--2840338 Score: 138
Period size: 47 Copynumber: 2.0 Consensus size: 48
2840235 ACGAGATAAT
* *
2840245 GAGAATCGCAACGCGGAAATGACTATCGCAACGATAGAATCGCAACGA
1 GAGAATCGCAACGCGGAAATGACTATCGCAACGAGACAATCGCAACGA
*
2840293 GAGAATCGCAACGC-GAAATGACTATCGCGATC-AGACAATCGCAACG
1 GAGAATCGCAACGCGGAAATGACTATCGC-AACGAGACAATCGCAACG
2840339 CGAAATGAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
47 26 0.62
48 16 0.38
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.13
Consensus pattern (48 bp):
GAGAATCGCAACGCGGAAATGACTATCGCAACGAGACAATCGCAACGA
Found at i:2840351 original size:19 final size:19
Alignment explanation
Indices: 2840329--2840418 Score: 162
Period size: 19 Copynumber: 4.7 Consensus size: 19
2840319 GCGATCAGAC
2840329 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
2840348 AATCGCAACCGCGAAATGAA
1 AATCGCAA-CGCGAAATGAA
2840368 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
2840387 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
2840406 AATCGCAATGCGA
1 AATCGCAACGCGA
2840419 TTTTTGTTTC
Statistics
Matches: 69, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
19 50 0.72
20 19 0.28
ACGTcount: A:0.46, C:0.22, G:0.21, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:2840372 original size:39 final size:38
Alignment explanation
Indices: 2840329--2840418 Score: 162
Period size: 39 Copynumber: 2.3 Consensus size: 38
2840319 GCGATCAGAC
2840329 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCGCAA-CGCGAAATGAA
2840368 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAA
*
2840406 AATCGCAATGCGA
1 AATCGCAACGCGA
2840419 TTTTTGTTTC
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
38 23 0.46
39 27 0.54
ACGTcount: A:0.46, C:0.22, G:0.21, T:0.11
Consensus pattern (38 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAA
Found at i:2840450 original size:19 final size:19
Alignment explanation
Indices: 2840414--2840458 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
2840404 AAAATCGCAA
*
2840414 TGCGATTTTTGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
2840433 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
2840452 TGCGATT
1 TGCGATT
2840459 CTCTCGTTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.07, C:0.16, G:0.24, T:0.53
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:2841040 original size:20 final size:20
Alignment explanation
Indices: 2841012--2841064 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
2841002 GCGCTATGTA
2841012 AATCACGTTGCGAAAGTCAG
1 AATCACGTTGCGAAAGTCAG
*
2841032 AATCGCGTTGCGAAAGTCAG
1 AATCACGTTGCGAAAGTCAG
* *
2841052 TATCTCGTTGCGA
1 AATCACGTTGCGA
2841065 TTTTGTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (20 bp):
AATCACGTTGCGAAAGTCAG
Found at i:2841098 original size:20 final size:20
Alignment explanation
Indices: 2841073--2841126 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
2841063 GATTTTGTAT
2841073 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
2841093 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
2841113 TATCGCATTGCGAT
1 TATCGCATTGCGAT
2841127 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:2841145 original size:61 final size:61
Alignment explanation
Indices: 2841017--2841147 Score: 147
Period size: 61 Copynumber: 2.1 Consensus size: 61
2841007 ATGTAAATCA
* * * * * ** *
2841017 CGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATTATCG
1 CGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAATATCG
* * *
2841078 CATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT-TCG
1 CGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAATATCG
2841139 CGTTGCGAT
1 CGTTGCGAT
2841148 TTACTTATTC
Statistics
Matches: 57, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
61 55 0.96
62 2 0.04
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
CGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAATATCG
Found at i:2841237 original size:21 final size:21
Alignment explanation
Indices: 2841197--2841237 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2841187 ACTATATACC
**
2841197 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
2841218 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
2841238 GCGAATTTGC
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:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:2845383 original size:40 final size:40
Alignment explanation
Indices: 2845338--2845414 Score: 136
Period size: 40 Copynumber: 1.9 Consensus size: 40
2845328 ACGTTAAATC
2845338 AAATTATGTTACTAAGTTATGCAATATGCATAAATTGATA
1 AAATTATGTTACTAAGTTATGCAATATGCATAAATTGATA
* *
2845378 AAATTATGTTACTAATTTATGCAATATGCATGAATTG
1 AAATTATGTTACTAAGTTATGCAATATGCATAAATTG
2845415 TATTTTTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (40 bp):
AAATTATGTTACTAAGTTATGCAATATGCATAAATTGATA
Found at i:2848343 original size:2 final size:2
Alignment explanation
Indices: 2848336--2848386 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
2848326 TTTAAAATGT
2848336 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
2848378 TA TA TA TA T
1 TA TA TA TA T
2848387 GAATTAAGAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2849104 original size:2 final size:2
Alignment explanation
Indices: 2849097--2849127 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2849087 TTATTTTTAA
2849097 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
2849128 ACTCTAAAAT
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:2849349 original size:39 final size:38
Alignment explanation
Indices: 2849283--2849374 Score: 103
Period size: 39 Copynumber: 2.4 Consensus size: 38
2849273 TTTAAAAAAT
* * * * *
2849283 AATTTAGAACGTTAATTTGTAATAATTTAATAAATTAAG
1 AATTTAGAACGTT-ATATATAAAAATTTAAGAAATCAAG
2849322 AATTTAGAACGTTATGATATAAAAATTTAAGAAATCAAG
1 AATTTAGAACGTTAT-ATATAAAAATTTAAGAAATCAAG
* *
2849361 ATTTTAGAATGTTA
1 AATTTAGAACGTTA
2849375 GAATGAAATA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
38 2 0.04
39 43 0.96
ACGTcount: A:0.47, C:0.03, G:0.12, T:0.38
Consensus pattern (38 bp):
AATTTAGAACGTTATATATAAAAATTTAAGAAATCAAG
Found at i:2849388 original size:39 final size:40
Alignment explanation
Indices: 2849303--2849388 Score: 106
Period size: 39 Copynumber: 2.2 Consensus size: 40
2849293 GTTAATTTGT
* *
2849303 AATAATTTAATAAATTAAGAATTTAGAACGTTATGATATA
1 AATAATTTAAGAAATCAAGAATTTAGAACGTTATGATATA
* *
2849343 AA-AATTTAAGAAATCAAGATTTTAGAATGTTA-GA-ATGA
1 AATAATTTAAGAAATCAAGAATTTAGAACGTTATGATAT-A
2849381 AATAATTT
1 AATAATTT
2849389 GAGGATTATG
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
37 2 0.05
38 5 0.12
39 31 0.77
40 2 0.05
ACGTcount: A:0.50, C:0.02, G:0.12, T:0.36
Consensus pattern (40 bp):
AATAATTTAAGAAATCAAGAATTTAGAACGTTATGATATA
Found at i:2849852 original size:31 final size:31
Alignment explanation
Indices: 2849789--2849855 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
2849779 GATAAACACG
*
2849789 TCTTAATTAAATAAAAACGAAAGTGACTATA
1 TCTTAATTAAATAAAAACGAAAGTAACTATA
2849820 TCTTAATTAAATAAAAAC-AAAGATAA-TCATA
1 TCTTAATTAAATAAAAACGAAAG-TAACT-ATA
2849851 TCTTA
1 TCTTA
2849856 TATTTTCTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
30 5 0.15
31 28 0.85
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.31
Consensus pattern (31 bp):
TCTTAATTAAATAAAAACGAAAGTAACTATA
Found at i:2851574 original size:4 final size:4
Alignment explanation
Indices: 2851565--2851655 Score: 67
Period size: 4 Copynumber: 21.8 Consensus size: 4
2851555 GGAGGTAATT
* * *
2851565 TTTA TTTA TTTA TTTA CTTTGA ATTA TTTA TTTA TTT- TCGTA TTCA TTTA
1 TTTA TTTA TTTA TTTA -TTT-A TTTA TTTA TTTA TTTA T-TTA TTTA TTTA
* * * *
2851615 TTTCAA ATAA ATTA TTTA CTTA TTTA TTTA TTTA TTTA TTT
1 TTT--A TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
2851656 GAAGGAGTAT
Statistics
Matches: 69, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
3 1 0.01
4 59 0.86
5 6 0.09
6 3 0.04
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.65
Consensus pattern (4 bp):
TTTA
Found at i:2851593 original size:18 final size:19
Alignment explanation
Indices: 2851570--2851617 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
2851560 TAATTTTTAT
2851570 TTATTTATTTACTTT-GAA
1 TTATTTATTTACTTTCGAA
* *
2851588 TTATTTATTTATTTTCGTA
1 TTATTTATTTACTTTCGAA
2851607 TTCATTTATTT
1 TT-ATTTATTT
2851618 CAAATAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 14 0.54
19 4 0.15
20 8 0.31
ACGTcount: A:0.23, C:0.06, G:0.04, T:0.67
Consensus pattern (19 bp):
TTATTTATTTACTTTCGAA
Found at i:2853778 original size:23 final size:23
Alignment explanation
Indices: 2853751--2853816 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 23
2853741 TTTTATATGG
2853751 CACTTTGGTGCATTTCTACGTGA
1 CACTTTGGTGCATTTCTACGTGA
* * * * *
2853774 CACTTCGATACAATTCTACGTGG
1 CACTTTGGTGCATTTCTACGTGA
*
2853797 CACTTCT-GTGCATTTATACG
1 CACTT-TGGTGCATTTCTACG
2853817 AGCTGTGGTG
Statistics
Matches: 32, Mismatches: 10, Indels: 2
0.73 0.23 0.05
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.36
Consensus pattern (23 bp):
CACTTTGGTGCATTTCTACGTGA
Found at i:2853893 original size:3 final size:3
Alignment explanation
Indices: 2853885--2853964 Score: 81
Period size: 3 Copynumber: 25.7 Consensus size: 3
2853875 GATATTATGA
* * *
2853885 TAT TAT TAT TAT TAC TAT TAT TAC TAT TAT TAT ATAT AAT ATAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT -TAT TAT
*
2853932 ATAT TGAT TAT TAT AAT TAT TAT T-T TAT TAT TA
1 -TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TA
2853965 CAAATGGAGG
Statistics
Matches: 64, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
2 2 0.03
3 51 0.80
4 11 0.17
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:2853950 original size:9 final size:8
Alignment explanation
Indices: 2853876--2853962 Score: 70
Period size: 9 Copynumber: 10.2 Consensus size: 8
2853866 GACCGAGTTG
*
2853876 ATATTATG
1 ATATTATT
2853884 ATATTA-T
1 ATATTATT
2853891 -TATTATT
1 ATATTATT
2853898 ACTATTATT
1 A-TATTATT
2853907 ACTATTATT
1 A-TATTATT
*
2853916 ATATATAAT
1 ATAT-TATT
2853925 ATATTATAT
1 ATATTAT-T
2853934 ATTGATTATT
1 A-T-ATTATT
2853944 ATAATTATT
1 AT-ATTATT
*
2853953 ATTTTATT
1 ATATTATT
2853961 AT
1 AT
2853963 TACAAATGGA
Statistics
Matches: 67, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
6 5 0.07
7 1 0.01
8 18 0.27
9 35 0.52
10 3 0.04
11 5 0.07
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (8 bp):
ATATTATT
Found at i:2855268 original size:22 final size:24
Alignment explanation
Indices: 2855243--2855297 Score: 60
Period size: 27 Copynumber: 2.2 Consensus size: 24
2855233 TATTATTATT
2855243 ATATTT-AGT-ACCTAAAAATATA
1 ATATTTAAGTAACCTAAAAATATA
*
2855265 ATATTTGACAAGTAACCTAAAAATTTA
1 ATATTT---AAGTAACCTAAAAATATA
2855292 ATATTT
1 ATATTT
2855298 TATATTTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 6 0.22
26 3 0.11
27 18 0.67
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.38
Consensus pattern (24 bp):
ATATTTAAGTAACCTAAAAATATA
Found at i:2858236 original size:21 final size:22
Alignment explanation
Indices: 2858212--2858253 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
2858202 CATACATTTT
2858212 TCATTTACACATTTT-GCATTC
1 TCATTTACACATTTTAGCATTC
**
2858233 TCATTTTTACATTTTAGCATT
1 TCATTTACACATTTTAGCATT
2858254 TGCATCATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.24, C:0.19, G:0.05, T:0.52
Consensus pattern (22 bp):
TCATTTACACATTTTAGCATTC
Found at i:2861931 original size:3 final size:3
Alignment explanation
Indices: 2861923--2861999 Score: 84
Period size: 3 Copynumber: 24.7 Consensus size: 3
2861913 GATATTATGA
* *
2861923 TAT TAT TAT TAT TAC TAT TAT TAT TAT TAT ATAT AAT ATAT TAT ATATT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT -TAT TAT -TA-T
*
2861972 TAT TAT TAT AAT TAT TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2862000 CAAGTGGAGG
Statistics
Matches: 63, Mismatches: 6, Indels: 10
0.80 0.08 0.13
Matches are distributed among these distances:
2 2 0.03
3 51 0.81
4 9 0.14
5 1 0.02
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:2870052 original size:15 final size:16
Alignment explanation
Indices: 2870023--2870055 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2870013 ACAACATCTT
2870023 CATGAGGTATCGATAC
1 CATGAGGTATCGATAC
*
2870039 CATG-GGTATTGATAC
1 CATGAGGTATCGATAC
2870054 CA
1 CA
2870056 GAAAGGCAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.27
Consensus pattern (16 bp):
CATGAGGTATCGATAC
Found at i:2870815 original size:23 final size:23
Alignment explanation
Indices: 2870788--2870856 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
2870778 ACATTTTATA
2870788 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTTCGGTGCATTTCTACG
* * *
2870811 TGGCACTTTGGTGCAATTCTATG
1 TGGCACTTCGGTGCATTTCTACG
*
2870834 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCATTTCTACG
2870857 AGTTGTGGTG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.16, C:0.22, G:0.26, T:0.36
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:2873057 original size:28 final size:27
Alignment explanation
Indices: 2873021--2873079 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 27
2873011 AAATTTACAC
2873021 TTTTTTAGTTAATCAAACTACATTTTCT
1 TTTTTTAGTTAATCAAACTACA-TTTCT
*
2873049 TTTTTTAGTTAATCAAACTCCATTTCT
1 TTTTTTAGTTAATCAAACTACATTTCT
2873076 TTTT
1 TTTT
2873080 AAAAAAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 9 0.30
28 21 0.70
ACGTcount: A:0.25, C:0.15, G:0.03, T:0.56
Consensus pattern (27 bp):
TTTTTTAGTTAATCAAACTACATTTCT
Found at i:2878356 original size:19 final size:21
Alignment explanation
Indices: 2878332--2878379 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
2878322 CAAGAGCATT
2878332 TATTTTCA-TT-AAAATCATG
1 TATTTTCATTTAAAAATCATG
2878351 TATTTTCATTTAAAAATCATG
1 TATTTTCATTTAAAAATCATG
2878372 TATTTTCA
1 TATTTTCA
2878380 AAGGGATTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 8 0.30
20 2 0.07
21 17 0.63
ACGTcount: A:0.35, C:0.10, G:0.04, T:0.50
Consensus pattern (21 bp):
TATTTTCATTTAAAAATCATG
Found at i:2879486 original size:19 final size:19
Alignment explanation
Indices: 2879453--2879502 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
2879443 AAAAATTATC
*
2879453 AAATCTTTTTGAGTTGATT-A
1 AAATGTTTTT-AGTT-ATTAA
*
2879473 AAATGTTTTTAGTTTTTAA
1 AAATGTTTTTAGTTATTAA
2879492 AAATGTTTTTA
1 AAATGTTTTTA
2879503 AAGCTTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 2 0.07
19 16 0.59
20 9 0.33
ACGTcount: A:0.32, C:0.02, G:0.12, T:0.54
Consensus pattern (19 bp):
AAATGTTTTTAGTTATTAA
Found at i:2879512 original size:21 final size:19
Alignment explanation
Indices: 2879472--2879514 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
2879462 TGAGTTGATT
*
2879472 AAAATGTTTTTAGTTTTTA
1 AAAATGTTTTTAGCTTTTA
2879491 AAAATGTTTTTAAAGCTTTTA
1 AAAATGTTTTT--AGCTTTTA
2879512 AAA
1 AAA
2879515 CATAAAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.52
21 10 0.48
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (19 bp):
AAAATGTTTTTAGCTTTTA
Found at i:2884193 original size:12 final size:13
Alignment explanation
Indices: 2884172--2884205 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
2884162 TAAGATTTTC
2884172 TTTGAAAATC-AT
1 TTTGAAAATCAAT
*
2884184 TTTTAAAATCAAT
1 TTTGAAAATCAAT
2884197 TTTGAAAAT
1 TTTGAAAAT
2884206 TACTCCCCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (13 bp):
TTTGAAAATCAAT
Found at i:2888404 original size:12 final size:12
Alignment explanation
Indices: 2888387--2888435 Score: 80
Period size: 12 Copynumber: 4.1 Consensus size: 12
2888377 ATGATGGTTC
2888387 TCCAACGTCATG
1 TCCAACGTCATG
2888399 TCCAACGTCATG
1 TCCAACGTCATG
* *
2888411 TCTAAGGTCATG
1 TCCAACGTCATG
2888423 TCCAACGTCATG
1 TCCAACGTCATG
2888435 T
1 T
2888436 GCATTTACAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (12 bp):
TCCAACGTCATG
Found at i:2900163 original size:21 final size:21
Alignment explanation
Indices: 2900122--2900164 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
2900112 TTATGGGTTG
*
2900122 TGTGCATCGATGCATATTCAA
1 TGTGCATCGATGCATACTCAA
*
2900143 TGTGTATCGATGCACT-CTCAA
1 TGTGCATCGATGCA-TACTCAA
2900164 T
1 T
2900165 TAAAGGAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.35
Consensus pattern (21 bp):
TGTGCATCGATGCATACTCAA
Found at i:2909729 original size:2 final size:2
Alignment explanation
Indices: 2909724--2909768 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
2909714 CCCTCTCTCT
2909724 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
2909766 TA T
1 TA T
2909769 TCAATTAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2911571 original size:18 final size:18
Alignment explanation
Indices: 2911548--2911708 Score: 193
Period size: 18 Copynumber: 8.9 Consensus size: 18
2911538 ACTGAATATT
2911548 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
* *
2911566 TGTCCCGTAGGACCACTT
1 TGTCCCGAAGGACCACTA
2911584 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
* *
2911602 TGTTCC-ATAGGACCACTT
1 TGTCCCGA-AGGACCACTA
2911620 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
* *
2911638 TGTTCC-ATAGGACCACTT
1 TGTCCCGA-AGGACCACTA
*
2911656 TGTCCCGAAGGACCAGTA
1 TGTCCCGAAGGACCACTA
* *
2911674 TGTTCC-ATAGGACCACTT
1 TGTCCCGA-AGGACCACTA
2911692 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
2911709 CCTTAAGAAC
Statistics
Matches: 120, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
17 3 0.03
18 114 0.95
19 3 0.03
ACGTcount: A:0.24, C:0.31, G:0.21, T:0.24
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:2911587 original size:36 final size:36
Alignment explanation
Indices: 2911546--2911708 Score: 299
Period size: 36 Copynumber: 4.5 Consensus size: 36
2911536 GCACTGAATA
* *
2911546 TTTGTCCCGAAGGACCACTATGTCCCGTAGGACCAC
1 TTTGTCCCGAAGGACCACTATGTTCCATAGGACCAC
2911582 TTTGTCCCGAAGGACCACTATGTTCCATAGGACCAC
1 TTTGTCCCGAAGGACCACTATGTTCCATAGGACCAC
2911618 TTTGTCCCGAAGGACCACTATGTTCCATAGGACCAC
1 TTTGTCCCGAAGGACCACTATGTTCCATAGGACCAC
*
2911654 TTTGTCCCGAAGGACCAGTATGTTCCATAGGACCAC
1 TTTGTCCCGAAGGACCACTATGTTCCATAGGACCAC
2911690 TTTGTCCCGAAGGACCACT
1 TTTGTCCCGAAGGACCACT
2911709 CCTTAAGAAC
Statistics
Matches: 123, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 123 1.00
ACGTcount: A:0.24, C:0.31, G:0.21, T:0.25
Consensus pattern (36 bp):
TTTGTCCCGAAGGACCACTATGTTCCATAGGACCAC
Found at i:2918285 original size:2 final size:2
Alignment explanation
Indices: 2918278--2918334 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
2918268 TATAACAATA
2918278 AT AT AT AT AT AT AT AT AT -T 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
2918319 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
2918335 GCATGTACAT
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 53 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2920717 original size:19 final size:17
Alignment explanation
Indices: 2920682--2920715 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2920672 TTTTTTATCG
2920682 GTTTTTGAAAATATATA
1 GTTTTTGAAAATATATA
2920699 GTTTTTGAAAATATATA
1 GTTTTTGAAAATATATA
2920716 TAATATAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (17 bp):
GTTTTTGAAAATATATA
Found at i:2920786 original size:39 final size:40
Alignment explanation
Indices: 2920701--2920952 Score: 334
Period size: 39 Copynumber: 6.6 Consensus size: 40
2920691 AATATATAGT
*
2920701 TTTTGAAAATATATATA-ATATA-A-AGTTTTTGAAAACA
1 TTTTAAAAATATATATATATATATATAGTTTTTGAAAACA
*
2920738 TTTT--GAATATATATATATATA-ATAGTTTTTGAAAACA
1 TTTTAAAAATATATATATATATATATAGTTTTTGAAAACA
2920775 TTTTAAAAATATATATATA-ATATATAGTTTTTGAAAACA
1 TTTTAAAAATATATATATATATATATAGTTTTTGAAAACA
*
2920814 TTTTAAAAATATATATATA-ATATATAGTTTTTGAAAACG
1 TTTTAAAAATATATATATATATATATAGTTTTTGAAAACA
* *
2920853 TTTTGAAAATATATATATA-ATATATAGTTTTTAAAAACA
1 TTTTAAAAATATATATATATATATATAGTTTTTGAAAACA
*
2920892 TTTTGAAAAT-T-TATATA-ATATATAG-TTTTGAAAACA
1 TTTTAAAAATATATATATATATATATAGTTTTTGAAAACA
2920928 TTTTTAAAAA-ATATATATGATATAT
1 -TTTTAAAAATATATATAT-ATATAT
2920953 TTTTGAAAAT
Statistics
Matches: 197, Mismatches: 8, Indels: 17
0.89 0.04 0.08
Matches are distributed among these distances:
35 10 0.05
36 16 0.08
37 45 0.23
38 9 0.05
39 113 0.57
40 4 0.02
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (40 bp):
TTTTAAAAATATATATATATATATATAGTTTTTGAAAACA
Found at i:2920841 original size:78 final size:78
Alignment explanation
Indices: 2920709--2920952 Score: 374
Period size: 76 Copynumber: 3.2 Consensus size: 78
2920699 GTTTTTGAAA
* *
2920709 ATATATATAATATAAAGTTTTTGAAAACATTTTGAATATATATATAT-ATA-ATAGTTTTTGAAA
1 ATATATATAATATATAGTTTTTGAAAACATTTTGAAAATATATATATAATATATAGTTTTTGAAA
2920772 ACATTTTAAAAAT
66 ACATTTTAAAAAT
*
2920785 ATATATATAATATATAGTTTTTGAAAACATTTTAAAAATATATATATAATATATAGTTTTTGAAA
1 ATATATATAATATATAGTTTTTGAAAACATTTTGAAAATATATATATAATATATAGTTTTTGAAA
* *
2920850 ACGTTTTGAAAAT
66 ACATTTTAAAAAT
*
2920863 ATATATATAATATATAGTTTTTAAAAACATTTTGAAAAT-T-TATATAATATATAG-TTTTGAAA
1 ATATATATAATATATAGTTTTTGAAAACATTTTGAAAATATATATATAATATATAGTTTTTGAAA
2920925 ACATTTTTAAAAA-
66 ACA-TTTTAAAAAT
*
2920938 ATATATATGATATAT
1 ATATATATAATATAT
2920953 TTTTGAAAAT
Statistics
Matches: 155, Mismatches: 10, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
75 24 0.15
76 66 0.43
77 4 0.03
78 61 0.39
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (78 bp):
ATATATATAATATATAGTTTTTGAAAACATTTTGAAAATATATATATAATATATAGTTTTTGAAA
ACATTTTAAAAAT
Found at i:2922351 original size:20 final size:21
Alignment explanation
Indices: 2922326--2922373 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
2922316 TTATTATCCC
2922326 TTTTTACTAATTTT-TTTTAT
1 TTTTTACTAATTTTATTTTAT
*
2922346 TTTTTACTTATTTTATTTTAT
1 TTTTTACTAATTTTATTTTAT
2922367 TTATTTA
1 TT-TTTA
2922374 TTTTAAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 13 0.52
21 8 0.32
22 4 0.16
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTTTACTAATTTTATTTTAT
Found at i:2922359 original size:18 final size:18
Alignment explanation
Indices: 2922340--2922378 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
2922330 TACTAATTTT
2922340 TTTTA-TTT-TTTACTTA
1 TTTTATTTTATTTACTTA
*
2922356 TTTTATTTTATTTATTTA
1 TTTTATTTTATTTACTTA
2922374 TTTTA
1 TTTTA
2922379 AATTACTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 3 0.15
18 12 0.60
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTATTTTATTTACTTA
Found at i:2924685 original size:24 final size:24
Alignment explanation
Indices: 2924658--2924703 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
2924648 AGGACTACAA
2924658 AAGGACTCATCTACTACAAAAGCG
1 AAGGACTCATCTACTACAAAAGCG
* * * *
2924682 AAGGCCTCGTCTGCTATAAAAG
1 AAGGACTCATCTACTACAAAAG
2924704 TACAGACTTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.20
Consensus pattern (24 bp):
AAGGACTCATCTACTACAAAAGCG
Found at i:2928338 original size:85 final size:85
Alignment explanation
Indices: 2928195--2928604 Score: 658
Period size: 85 Copynumber: 4.8 Consensus size: 85
2928185 TCCTAGCCTA
* * *
2928195 TTACAGTATAGATCAAGGTGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTC
1 TTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTC
2928260 AGCTCAAGGGCATATCAAAT
66 AGCTCAAGGGCATATCAAAT
* *
2928280 TTACAGCATAGCTCAAGGCGAGAAGGGCTATCTATCAACAAAAACCTTCGATTTCGATTACATTC
1 TTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTC
2928345 AGCTCAAGGGCATATCAAAT
66 AGCTCAAGGGCATATCAAAT
* *
2928365 TTACAGCATAGCTCAAGGCAAGAAGGGTTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTC
1 TTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTC
* *
2928430 AGCTGAAGGGCATATTAAAT
66 AGCTCAAGGGCATATCAAAT
* * * * *
2928450 TTACAGCATAGCTCAAGGCAAGAAGGGTTATCTGTCAACAAAAACCTTCGCGTTTGATTATATTC
1 TTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTC
*
2928515 AACTCAAGGGCATATCAAAT
66 AGCTCAAGGGCATATCAAAT
* **
2928535 TTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCGACAAAAACCTTCGAGTTCGATCCCATTC
1 TTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTC
2928600 AGCTC
66 AGCTC
2928605 GATGACAGCG
Statistics
Matches: 299, Mismatches: 26, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
85 299 1.00
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.25
Consensus pattern (85 bp):
TTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTC
AGCTCAAGGGCATATCAAAT
Found at i:2929277 original size:39 final size:38
Alignment explanation
Indices: 2929226--2929516 Score: 181
Period size: 39 Copynumber: 8.2 Consensus size: 38
2929216 GTTTTCGAAA
2929226 AAAAAATATATA-ATATATAGTTTTTGAAAACATTTTG
1 AAAAAATATATATATATATAGTTTTTGAAAACATTTTG
*
2929263 AAAAAATATATATAATAGATAGTTTTTG-AAA-A---T-
1 AAAAAATATATAT-ATATATAGTTTTTGAAAACATTTTG
* *
2929296 -----ATATATA-ATATATAGTTTTTGAAAAAAATTTG
1 AAAAAATATATATATATATAGTTTTTGAAAACATTTTG
* *
2929328 AAAATATATATACGATATATAGTTTTTGAAAACATTTTG
1 AAAAAATATATA-TATATATAGTTTTTGAAAACATTTTG
* *
2929367 AAAATATATATACGATATATAGTTTTTGAAAAC----T-
1 AAAAAATATATA-TATATATAGTTTTTGAAAACATTTTG
*
2929401 ------TATATA-ATATATAG-TTTTGAAAACATTTTT
1 AAAAAATATATATATATATAGTTTTTGAAAACATTTTG
* *
2929431 AAAAAATATATATATGATATA-TAGTTTT-AAAATATTTTT
1 AAAAAATATATATAT-ATATAGT--TTTTGAAAACATTTTG
* * * *
2929470 TAAAAACATATAT-TATATAGTTTTGGAAAATATTTTTG
1 AAAAAATATATATATATATAGTTTTTGAAAACA-TTTTG
*
2929508 AAAATATAT
1 AAAAAATAT
2929517 TATTATTATT
Statistics
Matches: 208, Mismatches: 12, Indels: 67
0.72 0.04 0.23
Matches are distributed among these distances:
25 10 0.05
26 21 0.10
27 3 0.01
28 14 0.07
29 1 0.00
31 1 0.00
34 1 0.00
35 1 0.00
36 9 0.04
37 33 0.16
38 20 0.10
39 90 0.43
40 4 0.02
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.42
Consensus pattern (38 bp):
AAAAAATATATATATATATAGTTTTTGAAAACATTTTG
Found at i:2929289 original size:28 final size:28
Alignment explanation
Indices: 2929258--2929322 Score: 107
Period size: 26 Copynumber: 2.4 Consensus size: 28
2929248 TTTGAAAACA
2929258 TTTTGAAAAAATATATATAATAGATAGT
1 TTTTGAAAAAATATATATAATAGATAGT
*
2929286 TTTTG--AAAATATATATAATATATAGT
1 TTTTGAAAAAATATATATAATAGATAGT
2929312 TTTTGAAAAAA
1 TTTTGAAAAAA
2929323 ATTTGAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
26 25 0.74
28 9 0.26
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (28 bp):
TTTTGAAAAAATATATATAATAGATAGT
Found at i:2929315 original size:65 final size:65
Alignment explanation
Indices: 2929226--2929359 Score: 205
Period size: 65 Copynumber: 2.1 Consensus size: 65
2929216 GTTTTCGAAA
* * *
2929226 AAAAAATATATAATATATAGTTTTTGAAAACATTTTGAAAAAATATATATAATAGATAGTTTTTG
1 AAAAAATATATAATATATAGTTTTTGAAAAAAATTTGAAAAAATATATACAATAGATAGTTTTTG
* * * *
2929291 AAAATATATATAATATATAGTTTTTGAAAAAAATTTGAAAATATATATACGATATATAGTTTTTG
1 AAAAAATATATAATATATAGTTTTTGAAAAAAATTTGAAAAAATATATACAATAGATAGTTTTTG
2929356 AAAA
1 AAAA
2929360 CATTTTGAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
65 62 1.00
ACGTcount: A:0.50, C:0.01, G:0.09, T:0.40
Consensus pattern (65 bp):
AAAAAATATATAATATATAGTTTTTGAAAAAAATTTGAAAAAATATATACAATAGATAGTTTTTG
Found at i:2929334 original size:26 final size:26
Alignment explanation
Indices: 2929265--2929335 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 26
2929255 ACATTTTGAA
* * *
2929265 AAAATATATATAATAGATAGTTTTTG
1 AAAATAAATATAAAATATAGTTTTTG
* *
2929291 AAAATATATATAATATATAGTTTTTG
1 AAAATAAATATAAAATATAGTTTTTG
*
2929317 AAAA-AAATTTGAAAATATA
1 AAAATAAATAT-AAAATATA
2929336 TATACGATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
25 4 0.10
26 36 0.90
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.39
Consensus pattern (26 bp):
AAAATAAATATAAAATATAGTTTTTG
Found at i:2929411 original size:26 final size:27
Alignment explanation
Indices: 2929362--2929424 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 27
2929352 TTTGAAAACA
2929362 TTTTGAAAA-TATATATACGATATATAG
1 TTTTGAAAACTATATATAC-ATATATAG
2929389 TTTTTGAAAACT-TATATA-ATATATAG
1 -TTTTGAAAACTATATATACATATATAG
2929415 TTTTGAAAAC
1 TTTTGAAAAC
2929425 ATTTTTAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
25 10 0.29
26 8 0.24
28 15 0.44
29 1 0.03
ACGTcount: A:0.43, C:0.05, G:0.10, T:0.43
Consensus pattern (27 bp):
TTTTGAAAACTATATATACATATATAG
Found at i:2929430 original size:37 final size:37
Alignment explanation
Indices: 2929389--2929511 Score: 135
Period size: 40 Copynumber: 3.3 Consensus size: 37
2929379 CGATATATAG
* *
2929389 TTTTTGAAAACTTATATAATATATAGTTTTGAAAACA
1 TTTTTAAAAACTTATATAATATATAGTTTTGAAAATA
*
2929426 TTTTTAAAAAATATATATATGATATATAGTTTT-AAAATA
1 TTTTTAAAAACT-TATATA--ATATATAGTTTTGAAAATA
*
2929465 TTTTTTAAAAAC--ATATATTATATAGTTTTGGAAAATA
1 -TTTTTAAAAACTTATATAATATATAGTTTT-GAAAATA
*
2929502 TTTTTGAAAA
1 TTTTTAAAAA
2929512 TATATTATTA
Statistics
Matches: 74, Mismatches: 6, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
35 11 0.15
36 9 0.12
37 21 0.28
38 6 0.08
39 5 0.07
40 22 0.30
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.46
Consensus pattern (37 bp):
TTTTTAAAAACTTATATAATATATAGTTTTGAAAATA
Found at i:2929521 original size:37 final size:37
Alignment explanation
Indices: 2929389--2929522 Score: 150
Period size: 37 Copynumber: 3.6 Consensus size: 37
2929379 CGATATATAG
* *
2929389 TTTTTGAAAACT-TATATAATATATAGTTTTGAAAACA
1 TTTTTGAAAA-TATATATATTATATAGTTTTGAAAATA
*
2929426 TTTTTAAAAAATATATATATGATATATAGTTTT-AAAATA
1 TTTTT-GAAAATATATATAT--TATATAGTTTTGAAAATA
* *
2929465 TTTTTTAAAA-ACATATATTATATAGTTTTGGAAAATA
1 TTTTTGAAAATATATATATTATATAGTTTT-GAAAATA
2929502 TTTTTGAAAATATAT-TATTAT
1 TTTTTGAAAATATATATATTAT
2929523 TATTATTATT
Statistics
Matches: 83, Mismatches: 7, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
35 11 0.13
37 34 0.41
38 17 0.20
39 10 0.12
40 11 0.13
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (37 bp):
TTTTTGAAAATATATATATTATATAGTTTTGAAAATA
Found at i:2929564 original size:16 final size:17
Alignment explanation
Indices: 2929514--2929583 Score: 63
Period size: 16 Copynumber: 3.9 Consensus size: 17
2929504 TTTGAAAATA
*
2929514 TATTATTATTATTATTATTA
1 TATT-TTATTA-TATT-TTT
2929534 TATCTTTATTTATATTTTT
1 TAT-TTTA-TTATATTTTT
*
2929553 TA-TTTATTATATGTTT
1 TATTTTATTATATTTTT
2929569 TATTTTATTA-ATTTT
1 TATTTTATTATATTTT
2929584 ATTTCATTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
16 15 0.34
17 11 0.25
19 4 0.09
20 10 0.23
21 4 0.09
ACGTcount: A:0.27, C:0.01, G:0.01, T:0.70
Consensus pattern (17 bp):
TATTTTATTATATTTTT
Found at i:2929564 original size:28 final size:29
Alignment explanation
Indices: 2929516--2929587 Score: 87
Period size: 28 Copynumber: 2.5 Consensus size: 29
2929506 TGAAAATATA
2929516 TTATTATTATTA-TTATTATAT-CTTTATT
1 TTATTATT-TTATTTATTATATGCTTTATT
*
2929544 TATATT-TTTTATTTATTATATGTTTTATT
1 T-TATTATTTTATTTATTATATGCTTTATT
2929573 TTATTAATTTTATTT
1 TTATT-ATTTTATTT
2929588 CATTTTCGGT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
27 3 0.08
28 16 0.42
29 11 0.29
30 8 0.21
ACGTcount: A:0.26, C:0.01, G:0.01, T:0.71
Consensus pattern (29 bp):
TTATTATTTTATTTATTATATGCTTTATT
Found at i:2929575 original size:17 final size:17
Alignment explanation
Indices: 2929511--2929578 Score: 59
Period size: 17 Copynumber: 3.9 Consensus size: 17
2929501 ATTTTTGAAA
*
2929511 ATATATTATTATTATTAT
1 ATATTTTATT-TTATTAT
*
2929529 -TATTATATCTTTATT-T
1 ATATTTTAT-TTTATTAT
*
2929545 ATATTTTTTATTTATTAT
1 ATATTTTAT-TTTATTAT
*
2929563 ATGTTTTATTTTATTA
1 ATATTTTATTTTATTA
2929579 ATTTTATTTC
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
16 1 0.03
17 30 0.75
18 9 0.22
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.68
Consensus pattern (17 bp):
ATATTTTATTTTATTAT
Found at i:2929583 original size:14 final size:15
Alignment explanation
Indices: 2929517--2929587 Score: 60
Period size: 14 Copynumber: 4.7 Consensus size: 15
2929507 GAAAATATAT
2929517 TATTATTATTATTATTA
1 TATT-TTATT-TTATTA
2929534 TATCTTTA-TTTA-TA
1 TAT-TTTATTTTATTA
*
2929548 TTTTTTA-TTTATTA
1 TATTTTATTTTATTA
2929562 TATGTTTTATTTTATTA
1 TA--TTTTATTTTATTA
2929579 -ATTTTATTT
1 TATTTTATTT
2929588 CATTTTCGGT
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
13 8 0.17
14 15 0.32
15 3 0.06
16 7 0.15
17 13 0.28
18 1 0.02
ACGTcount: A:0.27, C:0.01, G:0.01, T:0.70
Consensus pattern (15 bp):
TATTTTATTTTATTA
Found at i:2938231 original size:17 final size:17
Alignment explanation
Indices: 2938195--2938227 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2938185 ATTATATTAA
*
2938195 ATTTAAAATTTTCAAAT
1 ATTTAAAAATTTCAAAT
2938212 ATTTAAAAATTT-AAAT
1 ATTTAAAAATTTCAAAT
2938228 TATTAACATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
ATTTAAAAATTTCAAAT
Found at i:2938238 original size:25 final size:26
Alignment explanation
Indices: 2938193--2938246 Score: 69
Period size: 25 Copynumber: 2.1 Consensus size: 26
2938183 AAATTATATT
2938193 AAATTTAAAATTTTCAAATAT-TTAA
1 AAATTTAAAATTTTCAAATATATTAA
2938218 AAATTT-AAATTATT-AACATATATTAA
1 AAATTTAAAATT-TTCAA-ATATATTAA
2938244 AAA
1 AAA
2938247 CTAAATATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
24 7 0.27
25 12 0.46
26 7 0.27
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.41
Consensus pattern (26 bp):
AAATTTAAAATTTTCAAATATATTAA
Found at i:2939589 original size:21 final size:20
Alignment explanation
Indices: 2939559--2939613 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
2939549 CGCTGCTGGA
2939559 AACC-GGTTTGACCGGTTTTC
1 AACCGGGTTTGACCGG-TTTC
2939579 AACCGGGTTTGACCGGTTTC
1 AACCGGGTTTGACCGGTTTC
* *
2939599 GACCGGTTTTGACCG
1 AACCGGGTTTGACCG
2939614 ATTCGAATCG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 21 0.66
21 11 0.34
ACGTcount: A:0.15, C:0.25, G:0.29, T:0.31
Consensus pattern (20 bp):
AACCGGGTTTGACCGGTTTC
Found at i:2939602 original size:10 final size:9
Alignment explanation
Indices: 2939560--2939613 Score: 54
Period size: 10 Copynumber: 5.4 Consensus size: 9
2939550 GCTGCTGGAA
2939560 ACCGGTTTG
1 ACCGGTTTG
*
2939569 ACCGGTTTTCA
1 ACCGG-TTT-G
2939580 ACCGGGTTTG
1 ACC-GGTTTG
2939590 ACCGGTTTCG
1 ACCGGTTT-G
2939600 ACCGGTTTTG
1 ACCGG-TTTG
2939610 ACCG
1 ACCG
2939614 ATTCGAATCG
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
9 10 0.26
10 17 0.45
11 9 0.24
12 2 0.05
ACGTcount: A:0.13, C:0.26, G:0.30, T:0.31
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:2939618 original size:19 final size:20
Alignment explanation
Indices: 2939579--2939632 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
2939569 ACCGGTTTTC
* *
2939579 AACCGGGTTTGACCGGTTTCG
1 AACCGGTTTTGACC-GATTCG
2939600 -ACCGGTTTTGACCGATTCG
1 AACCGGTTTTGACCGATTCG
*
2939619 AATC-GTTTTGACCG
1 AACCGGTTTTGACCG
2939633 GCCTAAACCG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.17, C:0.24, G:0.28, T:0.31
Consensus pattern (20 bp):
AACCGGTTTTGACCGATTCG
Found at i:2939695 original size:17 final size:17
Alignment explanation
Indices: 2939661--2939698 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
2939651 CGACCTGACC
*
2939661 GACCCGACCCGAATGTT
1 GACCCGACCCGAACGTT
*
2939678 GACCCGACCCGACCGTT
1 GACCCGACCCGAACGTT
2939695 GACC
1 GACC
2939699 GTTGACTTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.21, C:0.42, G:0.24, T:0.13
Consensus pattern (17 bp):
GACCCGACCCGAACGTT
Found at i:2940335 original size:13 final size:13
Alignment explanation
Indices: 2940317--2940349 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
2940307 ATGGATGCAC
2940317 CAATTTAATGTGA
1 CAATTTAATGTGA
2940330 CAATTTAATGTGA
1 CAATTTAATGTGA
2940343 CAATTTA
1 CAATTTA
2940350 TGGAATATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.39
Consensus pattern (13 bp):
CAATTTAATGTGA
Found at i:2943277 original size:9 final size:9
Alignment explanation
Indices: 2943263--2943300 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
2943253 ATTTAATTTG
2943263 TATTTTTAA
1 TATTTTTAA
2943272 TATTTTT--
1 TATTTTTAA
2943279 TATTTTTAA
1 TATTTTTAA
*
2943288 TATTTTGAA
1 TATTTTTAA
2943297 TATT
1 TATT
2943301 AAAAAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
7 7 0.27
9 19 0.73
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (9 bp):
TATTTTTAA
Found at i:2943284 original size:16 final size:16
Alignment explanation
Indices: 2943263--2943293 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2943253 ATTTAATTTG
2943263 TATTTTTAATATTTTT
1 TATTTTTAATATTTTT
2943279 TATTTTTAATATTTT
1 TATTTTTAATATTTT
2943294 GAATATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TATTTTTAATATTTTT
Found at i:2947843 original size:20 final size:20
Alignment explanation
Indices: 2947806--2947844 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2947796 AGATTGAGTG
* * *
2947806 GATTTTGATGTTGTTTGCAC
1 GATTTTAATGATGATTGCAC
2947826 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
2947845 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAC
Found at i:2948028 original size:20 final size:20
Alignment explanation
Indices: 2947999--2948036 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2947989 AGAACCCCAG
*
2947999 GGGGGTATCGATTCCCCTGT
1 GGGGGAATCGATTCCCCTGT
*
2948019 GGGGGAATCGGTTCCCCT
1 GGGGGAATCGATTCCCCT
2948037 TCAAAGGGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.26, G:0.37, T:0.26
Consensus pattern (20 bp):
GGGGGAATCGATTCCCCTGT
Found at i:2949531 original size:77 final size:77
Alignment explanation
Indices: 2949433--2949597 Score: 303
Period size: 77 Copynumber: 2.1 Consensus size: 77
2949423 TTTTGTCAAT
*
2949433 TTTAAAACATGATCCGAAAAATTTGAATCTTCAAAACCTGGAGGTTGTTCCACATACACTTCTTC
1 TTTAAAA-ATGATCCGAAAAATTTGAATCTTCAAAACCTGGAGGTTGTTCCACATACACTTATTC
2949498 TTTTATAAAACCA
65 TTTTATAAAACCA
*
2949511 TTTAAAAATGATCCGGAAAATTTGAATCTTCAAAACCTGGAGGTTGTTCCACATACACTTATTCT
1 TTTAAAAATGATCCGAAAAATTTGAATCTTCAAAACCTGGAGGTTGTTCCACATACACTTATTCT
2949576 TTTATAAAACCA
66 TTTATAAAACCA
2949588 TTTAAAAATG
1 TTTAAAAATG
2949598 CACTTTTAAC
Statistics
Matches: 85, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
77 78 0.92
78 7 0.08
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (77 bp):
TTTAAAAATGATCCGAAAAATTTGAATCTTCAAAACCTGGAGGTTGTTCCACATACACTTATTCT
TTTATAAAACCA
Found at i:2954992 original size:22 final size:22
Alignment explanation
Indices: 2954961--2955464 Score: 681
Period size: 22 Copynumber: 22.6 Consensus size: 22
2954951 CTATTTTAAA
*
2954961 ATTTAATTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* *
2954983 ATTTATTTTAAAATCTGGATTT
1 ATTTATTTTAAAATATGGATTG
2955005 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
2955027 ATTTATTTAAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
2955049 ATTTATTTAAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* ***
2955071 ATTTATTTAAAAATATGGAAAA
1 ATTTATTTTAAAATATGGATTG
2955093 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
2955115 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
2955137 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
2955159 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
**
2955181 A-TTATTTTAAAATATTTAAAATATTG
1 ATTTATTTTAAAATA--T---GGATTG
* * * ** *
2955207 ATTGATTATTTTAAA-ATATGGATT
1 ATTTA-T-TTTAAAATAT-GGATTG
*
2955231 GATTTATTTTAAAATATGGGTTG
1 -ATTTATTTTAAAATATGGATTG
2955254 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
2955276 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
***
2955298 ATTTATTTTAAAATAT-GAAAA
1 ATTTATTTTAAAATATGGATTG
2955319 ATTTTATTTTAAAATATGGATTG
1 A-TTTATTTTAAAATATGGATTG
*
2955342 ATTTATCTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* *
2955364 ATTTATTTTAAAATATGGGTTT
1 ATTTATTTTAAAATATGGATTG
2955386 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
2955408 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
2955430 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
2955452 ATTTATTTTAAAA
1 ATTTATTTTAAAA
2955465 AAATTATTAT
Statistics
Matches: 430, Mismatches: 40, Indels: 24
0.87 0.08 0.05
Matches are distributed among these distances:
21 16 0.04
22 376 0.87
23 13 0.03
24 5 0.01
25 4 0.01
26 6 0.01
27 2 0.00
28 2 0.00
29 6 0.01
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.49
Consensus pattern (22 bp):
ATTTATTTTAAAATATGGATTG
Found at i:2955009 original size:44 final size:44
Alignment explanation
Indices: 2954961--2955464 Score: 760
Period size: 44 Copynumber: 11.3 Consensus size: 44
2954951 CTATTTTAAA
* * *
2954961 ATTTAATTTAAAATATGGATTGATTTATTTTAAAATCTGGATTT
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTG
*
2955005 ATTTATTTTAAAATATGGATTGATTTATTTAAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTG
* * ***
2955049 ATTTATTTAAAAATATGGATTGATTTATTTAAAAATATGGAAAA
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTG
2955093 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTG
2955137 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTG
*
2955181 ATTATTTTAAAATATTTAAAATATTGATTGA-TTATTTTAAAATATGGATTG
1 ---A-TTT---AT-TTTAAAATATGGATTGATTTATTTTAAAATATGGATTG
*
2955232 ATTTATTTTAAAATATGGGTTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTG
***
2955276 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATAT-GAAAA
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTG
*
2955319 ATTTTATTTTAAAATATGGATTGATTTATCTTAAAATATGGATTG
1 A-TTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTG
* *
2955364 ATTTATTTTAAAATATGGGTTTATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTG
2955408 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTG
2955452 ATTTATTTTAAAA
1 ATTTATTTTAAAA
2955465 AAATTATTAT
Statistics
Matches: 420, Mismatches: 29, Indels: 22
0.89 0.06 0.05
Matches are distributed among these distances:
43 18 0.04
44 353 0.84
45 3 0.01
47 4 0.01
48 4 0.01
51 22 0.05
52 16 0.04
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.49
Consensus pattern (44 bp):
ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTG
Found at i:2955043 original size:66 final size:66
Alignment explanation
Indices: 2954961--2955464 Score: 760
Period size: 66 Copynumber: 7.5 Consensus size: 66
2954951 CTATTTTAAA
* * *
2954961 ATTTAATTTAAAATATGGATTGATTTATTTTAAAATCTGGATTTATTTATTTTAAAATATGGATT
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATT
2955026 G
66 G
* * * **
2955027 ATTTATTTAAAAATATGGATTGATTTATTTAAAAATATGGATTGATTTATTTAAAAATATGGAAA
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATT
*
2955092 A
66 G
2955093 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATT
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATT
2955158 G
66 G
*
2955159 ATTTATTTTAAAATATGGATTGATTATTTTAAAATATTTAAAATATTGATTGA-TTATTTTAAAA
1 ATTTATTTTAAAATATGGATTG---A-TTT---AT-TTTAAAATATGGATTGATTTATTTTAAAA
2955223 TATGGATTG
58 TATGGATTG
*
2955232 ATTTATTTTAAAATATGGGTTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATT
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATT
2955297 G
66 G
*** *
2955298 ATTTATTTTAAAATAT-GAAAAATTTTATTTTAAAATATGGATTGATTTATCTTAAAATATGGAT
1 ATTTATTTTAAAATATGGATTGA-TTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGAT
2955362 TG
65 TG
* *
2955364 ATTTATTTTAAAATATGGGTTTATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATT
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATT
2955429 G
66 G
2955430 ATTTATTTTAAAATATGGATTGATTTATTTTAAAA
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAAA
2955465 AAATTATTAT
Statistics
Matches: 397, Mismatches: 30, Indels: 22
0.88 0.07 0.05
Matches are distributed among these distances:
65 18 0.05
66 310 0.78
67 2 0.01
69 4 0.01
70 4 0.01
73 43 0.11
74 16 0.04
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.49
Consensus pattern (66 bp):
ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATT
G
Found at i:2955199 original size:30 final size:30
Alignment explanation
Indices: 2955165--2955225 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
2955155 ATTGATTTAT
2955165 TTTAAAATATGGATTGATTATTTTAAAATA
1 TTTAAAATATGGATTGATTATTTTAAAATA
*
2955195 TTTAAAATATTGATTGATTATTTTAAAATA
1 TTTAAAATATGGATTGATTATTTTAAAATA
2955225 T
1 T
2955226 GGATTGATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (30 bp):
TTTAAAATATGGATTGATTATTTTAAAATA
Found at i:2955526 original size:31 final size:31
Alignment explanation
Indices: 2955488--2955546 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
2955478 AGTTGTATGG
*
2955488 ATTATTTAAATTTCATTATTATAAAACTAAA
1 ATTATTTAAATTTCAGTATTATAAAACTAAA
*
2955519 ATTATTTAAATTTCAGTATTGTAAAACT
1 ATTATTTAAATTTCAGTATTATAAAACT
2955547 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (31 bp):
ATTATTTAAATTTCAGTATTATAAAACTAAA
Found at i:2955939 original size:28 final size:27
Alignment explanation
Indices: 2955900--2955982 Score: 69
Period size: 28 Copynumber: 2.9 Consensus size: 27
2955890 ATTAAGTAAA
2955900 ATATACAA-TATATCATTAAATTTTAAGC
1 ATAT-CAATTATA-CATTAAATTTTAAGC
* **
2955928 ATATCATTTATACTATTAAACTTTTAATT
1 ATATCAATTATAC-ATTAAA-TTTTAAGC
* *
2955957 TTATCAATTATAACACTAAATTTTAA
1 ATATCAATTAT-ACATTAAATTTTAA
2955983 TTTCAGTTTC
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
27 3 0.07
28 20 0.44
29 20 0.44
30 2 0.04
ACGTcount: A:0.43, C:0.11, G:0.01, T:0.45
Consensus pattern (27 bp):
ATATCAATTATACATTAAATTTTAAGC
Done.