Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008017.1 Hibiscus syriacus cultivar Beakdansim tig00110483_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: 3132588
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 15
Found at i:2940402 original size:16 final size:14
Alignment explanation
Indices: 2940357--2940399 Score: 61
Period size: 13 Copynumber: 3.1 Consensus size: 14
2940347 TTATTTGCAA
2940357 TATTATTTTATTAT
1 TATTATTTTATTAT
*
2940371 TATTAATTT-TTAT
1 TATTATTTTATTAT
2940384 TATTATTGTTATTAT
1 TATTATT-TTATTAT
2940399 T
1 T
2940400 TATAAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 10 0.40
14 10 0.40
15 5 0.20
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (14 bp):
TATTATTTTATTAT
Found at i:2940601 original size:20 final size:19
Alignment explanation
Indices: 2940576--2940617 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
2940566 TTATTTTATA
2940576 AATTATATATTAATTATTTT
1 AATTATATATTAATT-TTTT
* *
2940596 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
2940615 AAT
1 AAT
2940618 ATCAAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:2946031 original size:11 final size:11
Alignment explanation
Indices: 2946010--2946053 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
2946000 TCCAGCAAAG
2946010 AAAGAGAAAAAA
1 AAAG-GAAAAAA
2946022 AAAGGAAAAAA
1 AAAGGAAAAAA
* *
2946033 AAGAAGAAAGAA
1 AA-AGGAAAAAA
2946045 AAAGGAAAA
1 AAAGGAAAA
2946054 TTGAATCAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
11 14 0.52
12 13 0.48
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAGGAAAAAA
Found at i:2946046 original size:23 final size:22
Alignment explanation
Indices: 2946010--2946053 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
2946000 TCCAGCAAAG
2946010 AAAGAGAAAAAAAAAGGAAAAA
1 AAAGAGAAAAAAAAAGGAAAAA
*
2946032 AAAGAAGAAAGAAAAAGGAAAA
1 AAAG-AGAAAAAAAAAGGAAAA
2946054 TTGAATCAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (22 bp):
AAAGAGAAAAAAAAAGGAAAAA
Found at i:2948577 original size:115 final size:115
Alignment explanation
Indices: 2948370--2948711 Score: 533
Period size: 115 Copynumber: 3.0 Consensus size: 115
2948360 AAGTGCCATG
*
2948370 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
2948435 TGGTTTGGTATGAACCCCAAAAACCAATCATTAGATTTGAAAGATGAATT
66 TGGTTTGGTATGAACCCCAAAAACCAATCATTAGATTTGAAAGATGAATT
* * *
2948485 TGCTTATAGTAGAAATAAGAAGACCCAATAGAATCTTCTGGAAGTGTTCTTTGAGTTATCTGATA
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
2948550 TGGTTTGGTATGAACCCCAAAAACCAATCATTAGATTTGAAAGATGAATT
66 TGGTTTGGTATGAACCCCAAAAACCAATCATTAGATTTGAAAGATGAATT
* * * *
2948600 TGCTCATGGTAGAAATAAGGAGGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * * * * * * *
2948665 TGGTTCGATAGGAACCAC-AGAACCAATCATTGGAATTAAAAGATGAA
66 TGGTTTGGTATGAACCCCAAAAACCAATCATTAGATTTGAAAGATGAA
2948712 CTGCATGATC
Statistics
Matches: 208, Mismatches: 19, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
114 25 0.12
115 183 0.88
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (115 bp):
TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGGTTTGGTATGAACCCCAAAAACCAATCATTAGATTTGAAAGATGAATT
Found at i:2950847 original size:54 final size:53
Alignment explanation
Indices: 2950780--2950932 Score: 159
Period size: 50 Copynumber: 2.9 Consensus size: 53
2950770 TGAGAAATTC
* *
2950780 GAGCAGAAGCCACAAAAAATGATGAATGTGTTGTCAAATGCTTTACGAATATCT
1 GAGCAGAAACCACAAAAAATGATGAATGTGTTGTCAAATGTTTTACGAA-ATCT
* * * *
2950834 GAGCAGAAACCACAGAAAAGGATGAATGTGTTATCAAGTGTTTTAC---ATCT
1 GAGCAGAAACCACAAAAAATGATGAATGTGTTGTCAAATGTTTTACGAAATCT
* * * ** * *
2950884 TAGCAAAAACCATATGAGATGATGCATGTGTTGTCAAATGTTTTACGAA
1 GAGCAGAAACCACAAAAAATGATGAATGTGTTGTCAAATGTTTTACGAA
2950933 CCAGTTATTC
Statistics
Matches: 80, Mismatches: 16, Indels: 7
0.78 0.16 0.07
Matches are distributed among these distances:
50 40 0.50
54 40 0.50
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (53 bp):
GAGCAGAAACCACAAAAAATGATGAATGTGTTGTCAAATGTTTTACGAAATCT
Found at i:2951316 original size:22 final size:22
Alignment explanation
Indices: 2951285--2951339 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
2951275 ATCTACACTC
*
2951285 TTCAAAGATGATAGATTCCCTT
1 TTCAAAGATGACAGATTCCCTT
* *
2951307 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCCCTT
2951329 TTCAAAGATGA
1 TTCAAAGATGA
2951340 AAGCTTTATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCCCTT
Found at i:2951818 original size:39 final size:37
Alignment explanation
Indices: 2951768--2951899 Score: 129
Period size: 39 Copynumber: 3.7 Consensus size: 37
2951758 TCACATTTCT
2951768 AGAAGAGTTCAT-ATGAGAAGAACTCATCTGAAGAAAG
1 AGAAGAGTTCATAATGAGAAGAACTCATCTGAAG-AAG
**
2951805 AAGAAGAAGTTCATAATGAGAAG----CAT-TG--CCAG
1 -AGAAG-AGTTCATAATGAGAAGAACTCATCTGAAGAAG
*
2951837 -GACGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 AGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAA-G
2951874 AGAAGAAGTTCATAATGAGAAGAACT
1 AGAAG-AGTTCATAATGAGAAGAACT
2951900 TGTTCAACCT
Statistics
Matches: 76, Mismatches: 6, Indels: 23
0.72 0.06 0.22
Matches are distributed among these distances:
29 16 0.21
30 3 0.04
32 2 0.03
33 3 0.04
34 2 0.03
35 2 0.03
36 4 0.05
37 1 0.01
38 8 0.11
39 27 0.36
40 8 0.11
ACGTcount: A:0.45, C:0.11, G:0.25, T:0.19
Consensus pattern (37 bp):
AGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAG
Found at i:2952040 original size:113 final size:113
Alignment explanation
Indices: 2951826--2952688 Score: 1249
Period size: 113 Copynumber: 7.8 Consensus size: 113
2951816 CATAATGAGA
*
2951826 AGCATTGCCAGGACGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG-AGAAGAAGTTCATAAT
1 AGCATTGCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
* *
2951890 GAGAAGAACTTGTTCAACCTTTCGCTTGAATTCATCATTCGATGGATC
66 GAGAAGAACTTGTTCAACTTTTCGCTTGAATTTATCATTCGATGGATC
2951938 AGCATTGCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
1 AGCATTGCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
2952003 GAGAAGAACTTGTTCAACTTTTCGCTTGAATTTATCATTCGATGGATC
66 GAGAAGAACTTGTTCAACTTTTCGCTTGAATTTATCATTCGATGGATC
*
2952051 AACATTGCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
1 AGCATTGCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
* *
2952116 GAGAAGAACTTGTTCAACCTTTCGCTTGAATTTATCATTCTATGGATC
66 GAGAAGAACTTGTTCAACTTTTCGCTTGAATTTATCATTCGATGGATC
*
2952164 AACATTGCCAGGTCGAGTTCATAATGAGAAGAACTCATCTG-A-AA-GAAGAAGAAGTTCATAAT
1 AGCATTGCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
* *
2952226 GAGAAGAACTTGTTCAAATTTTCGCTTGAATTCATCATTCGATGGATC
66 GAGAAGAACTTGTTCAACTTTTCGCTTGAATTTATCATTCGATGGATC
* * *
2952274 ATCATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAATGAAGAAGAAGTTCATAAT
1 AGCATTGCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
*
2952339 GAGAAGAACTTGTTCAACTTTTCGCTTGAATTTATCATTCGATGGACC
66 GAGAAGAACTTGTTCAACTTTTCGCTTGAATTTATCATTCGATGGATC
* * * *
2952387 AGCATTCCCATGGT-GAGTTCATAATAAGAAGAACACATCTGAATAAGGAAGAAGAAGTTCATAA
1 AGCATTGCCA-GGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAA
* *
2952451 TGAGAAAAACTTGTTCAACTTTTCGCTTGAATTTATCATTTGATGGATC
65 TGAGAAGAACTTGTTCAACTTTTCGCTTGAATTTATCATTCGATGGATC
* * * * *
2952500 AGCATTGCCAGGGCGAGTTCATAATAAGAAGAACTCATATGAAGAAAGAAGAAGAAATTCATAAT
1 AGCATTGCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
* * * *
2952565 GAAAAGAACTTG--------TT-GCTCGAATTCATCACTCGATGGATC
66 GAGAAGAACTTGTTCAACTTTTCGCTTGAATTTATCATTCGATGGATC
* * * * * * *
2952604 AACTTTTCCAGAG-AGAGTTCATAATGAGAAAGAATTCATCTAAAG-AGGAAGAGGAAGTTCATA
1 AGCATTGCCAG-GTCGAGTTCATAATGAG-AAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
2952667 AT--GAAGAACTTGTTCAATCTTT
64 ATGAGAAGAACTTGTTCAA-CTTT
2952689 GCATGATTCT
Statistics
Matches: 685, Mismatches: 49, Indels: 35
0.89 0.06 0.05
Matches are distributed among these distances:
102 9 0.01
104 59 0.09
105 16 0.02
110 101 0.15
111 4 0.01
112 52 0.08
113 441 0.64
114 3 0.00
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.28
Consensus pattern (113 bp):
AGCATTGCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
GAGAAGAACTTGTTCAACTTTTCGCTTGAATTTATCATTCGATGGATC
Found at i:2952443 original size:336 final size:334
Alignment explanation
Indices: 2951828--2952688 Score: 1253
Period size: 336 Copynumber: 2.6 Consensus size: 334
2951818 TAATGAGAAG
*
2951828 CATTGCCAGGACGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATGAG
1 CATTGCCAGGACGAGTTCATAATGAGAAGAACTCATCTG-A-AAGAAGAAGAAGTTCATAATGAG
* *
2951893 AAGAACTTGTTCAACCTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGGTCGAGTTC
64 AAGAACTTGTTCAA--TTTCGCTTGAATTCATCATTCGATGGATCAACATTACCAGGTCGAGTTC
2951958 ATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTT
127 ATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTT
* * * *
2952023 TTCGCTTGAATTTATCATTCGATGGATCAACATTGCCAGGTCGAGTTCATAATGAGAAGAACTCA
192 TTCGCTTGAATTTATCATTCGATGGACCAACATTCCCAGGTCGAGTTCATAATAAGAAGAACACA
*
2952088 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTCGCTTGAATTTATCA
257 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAAAACTTGTTCAACCTTTCGCTTGAATTTATCA
2952153 TTCT-ATGGATCAA
322 TT-TGATGGATCAA
*
2952166 CATTGCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAAGAAGAAGAAGTTCATAATGAGAA
1 CATTGCCAGGACGAGTTCATAATGAGAAGAACTCATCTGAAAGAAGAAGAAGTTCATAATGAGAA
*
2952231 GAACTTGTTCAAATTTTCGCTTGAATTCATCATTCGATGGATCATCATTACCAGGTCGAGTTCAT
66 GAACTTGTTC-AA-TTTCGCTTGAATTCATCATTCGATGGATCAACATTACCAGGTCGAGTTCAT
*
2952296 AATGAGAAGAACTCATCTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTT
129 AATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTT
*
2952361 CGCTTGAATTTATCATTCGATGGACCAGCATTCCCATGGT-GAGTTCATAATAAGAAGAACACAT
194 CGCTTGAATTTATCATTCGATGGACCAACATTCCCA-GGTCGAGTTCATAATAAGAAGAACACAT
* *
2952425 CTGAATAAGGAAGAAGAAGTTCATAATGAGAAAAACTTGTTCAACTTTTCGCTTGAATTTATCAT
258 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAAAACTTGTTCAACCTTTCGCTTGAATTTATCAT
*
2952490 TTGATGGATCAG
323 TTGATGGATCAA
* * * *
2952502 CATTGCCAGGGCGAGTTCATAATAAGAAGAACTCATATGAAGAAAGAAGAAGAAATTCATAATGA
1 CATTGCCAGGACGAGTTCATAATGAGAAGAACTCATCT---GAAAGAAGAAGAAGTTCATAATGA
* * * * * *
2952567 AAAGAACTTG------TT-GCTCGAATTCATCACTCGATGGATCAACTTTTCCAGAG-AGAGTTC
63 GAAGAACTTGTTCAATTTCGCTTGAATTCATCATTCGATGGATCAACATTACCAG-GTCGAGTTC
* * *
2952624 ATAATGAGAAAGAATTCATCTAAAG-AGGAAGAGGAAGTTCATAAT--GAAGAACTTGTTCAATC
127 ATAATGAG-AAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-C
2952686 TTT
190 TTT
2952689 GCATGATTCT
Statistics
Matches: 484, Mismatches: 30, Indels: 27
0.89 0.06 0.05
Matches are distributed among these distances:
328 15 0.03
329 4 0.01
330 63 0.13
331 17 0.04
335 1 0.00
336 308 0.64
337 6 0.01
338 38 0.08
339 32 0.07
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (334 bp):
CATTGCCAGGACGAGTTCATAATGAGAAGAACTCATCTGAAAGAAGAAGAAGTTCATAATGAGAA
GAACTTGTTCAATTTCGCTTGAATTCATCATTCGATGGATCAACATTACCAGGTCGAGTTCATAA
TGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCG
CTTGAATTTATCATTCGATGGACCAACATTCCCAGGTCGAGTTCATAATAAGAAGAACACATCTG
AAGAAGGAAGAAGAAGTTCATAATGAGAAAAACTTGTTCAACCTTTCGCTTGAATTTATCATTTG
ATGGATCAA
Found at i:2952982 original size:22 final size:23
Alignment explanation
Indices: 2952946--2952991 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
2952936 TTTTATTTCA
*
2952946 TTTGTTTTATTTATTATTATTAT
1 TTTGTTTTATATATTATTATTAT
2952969 TTTGTTTTA-ATATTATTATTAT
1 TTTGTTTTATATATTATTATTAT
2952991 T
1 T
2952992 AAATAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (23 bp):
TTTGTTTTATATATTATTATTAT
Found at i:2954406 original size:20 final size:20
Alignment explanation
Indices: 2954383--2954425 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2954373 TCTTATTTTA
2954383 TAAATTATATATTAATTGTT
1 TAAATTATATATTAATTGTT
* * *
2954403 TAAATTATGTATTTATTTTT
1 TAAATTATATATTAATTGTT
2954423 TAA
1 TAA
2954426 TATCAAAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (20 bp):
TAAATTATATATTAATTGTT
Found at i:2954505 original size:23 final size:22
Alignment explanation
Indices: 2954473--2954522 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
2954463 CATTTTCTGA
* *
2954473 TATTTCTAAATAAATAAATATTT
1 TATTTATAAATAAATAAAT-TAT
*
2954496 TATTTATAAATATATAAATTAT
1 TATTTATAAATAAATAAATTAT
2954518 TATTT
1 TATTT
2954523 TCCATAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
TATTTATAAATAAATAAATTAT
Found at i:2955724 original size:12 final size:13
Alignment explanation
Indices: 2955690--2955722 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
2955680 TGAATTAGGA
2955690 TTATCTTTTATAT
1 TTATCTTTTATAT
2955703 TTATCTTTTA-AT
1 TTATCTTTTATAT
2955715 TT-TCTTTT
1 TTATCTTTT
2955723 TATCTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 6 0.30
12 4 0.20
13 10 0.50
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (13 bp):
TTATCTTTTATAT
Found at i:2961185 original size:23 final size:23
Alignment explanation
Indices: 2961159--2961211 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
2961149 ATTGTACCTA
*
2961159 AGTGCCACTTAGAATTACACCAG-
1 AGTGCCACGTAGAATTACACC-GT
* *
2961182 AGTGCCGCGTAGAATTGCACCGT
1 AGTGCCACGTAGAATTACACCGT
2961205 AGTGCCA
1 AGTGCCA
2961212 TATAATAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 1 0.04
23 24 0.96
ACGTcount: A:0.28, C:0.26, G:0.25, T:0.21
Consensus pattern (23 bp):
AGTGCCACGTAGAATTACACCGT
Found at i:2961358 original size:103 final size:103
Alignment explanation
Indices: 2961227--2961444 Score: 382
Period size: 103 Copynumber: 2.1 Consensus size: 103
2961217 TAATGTCCAT
* * * *
2961227 AAGGACCACATATCATTTCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACAAAGGATCAAGTAGGTGTCTCACCA
2961292 GACCTCACACATGTTCCAAAGAATACATATATATCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATATCCCG
*
2961330 AAGGACCACATATTATTCCTTAAGAATCATATACATATACAAAGGATCAAGTAGGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACAAAGGATCAAGTAGGTGTCTCACCA
*
2961395 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATATCCCG
2961433 AAGGACCACATA
1 AAGGACCACATA
2961445 GACCCTCTAC
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACAAAGGATCAAGTAGGTGTCTCACCA
GACCTCACACATGTTCCAAAGAATACATATATATCCCG
Found at i:2962013 original size:21 final size:21
Alignment explanation
Indices: 2961989--2962031 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2961979 TCATATTCGT
*
2961989 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
*
2962010 TTGAATGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
2962031 T
1 T
2962032 AGCCCAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.23, G:0.28, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:2963849 original size:46 final size:47
Alignment explanation
Indices: 2963747--2963873 Score: 118
Period size: 46 Copynumber: 2.7 Consensus size: 47
2963737 GTTAAATGTG
* * * *
2963747 GTGTAGTACTAGTTATGTAGTTGGATAATATTATTTTCTTATTATAT
1 GTGTAGTACTAATTATGTACTTGGATAATATTATTTTCTGATAATAT
* *
2963794 -TGTACTACTAATTATGTACTTGGTTAATATTATTGTT-TGA-AAGT-T
1 GTGTAGTACTAATTATGTACTTGGATAATATTATT-TTCTGATAA-TAT
* * * *
2963839 GTGTAGTACTAATTATGCACATGGACATTATTATT
1 GTGTAGTACTAATTATGTACTTGGATAATATTATT
2963874 ACGGTAATGT
Statistics
Matches: 65, Mismatches: 12, Indels: 7
0.77 0.14 0.08
Matches are distributed among these distances:
45 2 0.03
46 61 0.94
47 2 0.03
ACGTcount: A:0.29, C:0.07, G:0.17, T:0.47
Consensus pattern (47 bp):
GTGTAGTACTAATTATGTACTTGGATAATATTATTTTCTGATAATAT
Found at i:2965124 original size:16 final size:17
Alignment explanation
Indices: 2965092--2965129 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
2965082 GGTTGGTTAA
*
2965092 TATTTTATGTTTATATT
1 TATTTTATGTATATATT
2965109 TATTTTATG-ATATATT
1 TATTTTATGTATATATT
2965125 TATTT
1 TATTT
2965130 ATCTAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.68
Consensus pattern (17 bp):
TATTTTATGTATATATT
Found at i:2977888 original size:88 final size:86
Alignment explanation
Indices: 2977694--2977913 Score: 199
Period size: 88 Copynumber: 2.5 Consensus size: 86
2977684 GCTAAAGTTC
* * * **
2977694 GCGGCGTTTTTCAACAAAAAACGCCGCAATAGGTGTTGATATTTAGCGGTGTTTGACAGACAAAC
1 GCGGCGTTTTTC--CAACAAACGTCGCAATAGGTGTTGATATTTAGAGGCATTTGACAGACAAAC
2977759 GCCACAATAGATGTTGATATTTA
64 GCCACAATAGATGTTGATATTTA
* *** * * *
2977782 GCGGC-ATTTGGAAGACAAACGTCGCAATAGGTGTTGATATTTAGAGGCATTTGATATTTAGAAA
1 GCGGCGTTTTTCCA-ACAAACGTCGCAATAGGTGTTGATATTTAGAGGCATTTGACA--GACAAA
* * * *
2977846 CGCCGCAGTAGGTGTTGATGTTTA
63 CGCCACAATAGATGTTGATATTTA
* * * * *
2977870 GCGGCGTTTTTCCCACAAATGTCGCAGTAGATGTTGATGTTTAG
1 GCGGCGTTTTTCCAACAAACGTCGCAATAGGTGTTGATATTTAG
2977914 CGGCGTTTTT
Statistics
Matches: 103, Mismatches: 25, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
85 1 0.01
86 36 0.35
87 3 0.03
88 60 0.58
89 3 0.03
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.30
Consensus pattern (86 bp):
GCGGCGTTTTTCCAACAAACGTCGCAATAGGTGTTGATATTTAGAGGCATTTGACAGACAAACGC
CACAATAGATGTTGATATTTA
Found at i:2978017 original size:43 final size:43
Alignment explanation
Indices: 2977694--2978023 Score: 223
Period size: 43 Copynumber: 7.6 Consensus size: 43
2977684 GCTAAAGTTC
* * *
2977694 GCGGCGTTTTTCAACAAAAAACGCCGCAATAGGTGTTGATATTTA
1 GCGGCGTTTTT-AAC-ACAAATGCCGCAATAGGTGTTGATGTTTA
* * * * * * *
2977739 GCGGTG-TTTGACAGACAAACGCCACAATAGATGTTGATATTTA
1 GCGGCGTTTTTA-ACACAAATGCCGCAATAGGTGTTGATGTTTA
* ** * * * *
2977782 GCGGCATTTGGAAGACAAACGTCGCAATAGGTGTTGATATTTA
1 GCGGCGTTTTTAACACAAATGCCGCAATAGGTGTTGATGTTTA
* * * ** * * *
2977825 GAGGCATTTGATATTTAGAAACGCCGCAGTAGGTGTTGATGTTTA
1 GCGGCGTTT-TTA-ACACAAATGCCGCAATAGGTGTTGATGTTTA
** * * *
2977870 GCGGCGTTTTTCCCACAAATGTCGCAGTAGATGTTGATGTTTA
1 GCGGCGTTTTTAACACAAATGCCGCAATAGGTGTTGATGTTTA
* ** * * *
2977913 GCGGCGTTTTTATCGTAAATGCCGCAATAGGTGTTAAGGTTTC
1 GCGGCGTTTTTAACACAAATGCCGCAATAGGTGTTGATGTTTA
* * *
2977956 GCGGTGTTTTTAGCACAAATGCCGCAATATGTGTT-ATGATTTA
1 GCGGCGTTTTTAACACAAATGCCGCAATAGGTGTTGATG-TTTA
* *
2977999 GCGGCGTTTTTAATACAAACGCCGC
1 GCGGCGTTTTTAACACAAATGCCGC
2978024 TAATGGTCGG
Statistics
Matches: 228, Mismatches: 52, Indels: 12
0.78 0.18 0.04
Matches are distributed among these distances:
42 2 0.01
43 179 0.79
44 10 0.04
45 37 0.16
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (43 bp):
GCGGCGTTTTTAACACAAATGCCGCAATAGGTGTTGATGTTTA
Found at i:2978058 original size:43 final size:42
Alignment explanation
Indices: 2978000--2978113 Score: 140
Period size: 43 Copynumber: 2.7 Consensus size: 42
2977990 TATGATTTAG
*
2978000 CGGCGTTTTTA-ATACAAACGCCGCTAATGGTCGGTATATAA
1 CGGCGTTTTTAGATACAAACGCCGCTAAAGGTCGGTATATAA
* * * * *
2978041 CGGTGTTTTTAGGATACAGATGCGGCTAAAGGTCGGTATATAG
1 CGGCGTTTTTA-GATACAAACGCCGCTAAAGGTCGGTATATAA
*
2978084 TGGCGTTTTTAGAATACAAACGCCGCTAAA
1 CGGCGTTTTTAG-ATACAAACGCCGCTAAA
2978114 TAACACAGAA
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
41 10 0.17
42 1 0.02
43 48 0.81
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (42 bp):
CGGCGTTTTTAGATACAAACGCCGCTAAAGGTCGGTATATAA
Found at i:2978460 original size:21 final size:21
Alignment explanation
Indices: 2978436--2978476 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2978426 ATATGTTGCT
*
2978436 TCTCTTTGTGATGCCGCTGCC
1 TCTCTTTGTGATGCCACTGCC
*
2978457 TCTCTTTGTGTTGCCACTGC
1 TCTCTTTGTGATGCCACTGC
2978477 TTCCGTTGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.05, C:0.32, G:0.22, T:0.41
Consensus pattern (21 bp):
TCTCTTTGTGATGCCACTGCC
Found at i:2981294 original size:41 final size:41
Alignment explanation
Indices: 2981184--2981299 Score: 114
Period size: 41 Copynumber: 2.8 Consensus size: 41
2981174 TTAAAGGACA
2981184 ATTACGGCGTTTATATTAAAAACGCCAC-AAAGGAACTATTCT
1 ATTACGGCG-TT-TATTAAAAACGCCACTAAAGGAACTATTCT
* *
2981226 ATTACGGCGTTTATTATGAAAATGCCACTAAGGGACAC-A-T-T
1 ATTACGGCGTTTATTA--AAAACGCCACTAAAGGA-ACTATTCT
*
2981267 ATTGCGGCGTTTATGTCAAAAACGCCACTAAAG
1 ATTACGGCGTTTAT-T-AAAAACGCCACTAAAG
2981300 TACAACTTTT
Statistics
Matches: 63, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
40 5 0.08
41 29 0.46
42 20 0.32
43 7 0.11
44 2 0.03
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (41 bp):
ATTACGGCGTTTATTAAAAACGCCACTAAAGGAACTATTCT
Found at i:2982787 original size:41 final size:42
Alignment explanation
Indices: 2982720--2982840 Score: 176
Period size: 41 Copynumber: 3.0 Consensus size: 42
2982710 GTTTATACAA
2982720 AAAAAACGCCACTATTGATT-ACACTATTGTGGCGTTTGT-T
1 AAAAAACGCCACTATTGATTAACACTATTGTGGCGTTTGTCT
* *
2982760 AAAAAACGCCACTATTGATTAAAACTATTGTGGCGTTTATCT
1 AAAAAACGCCACTATTGATTAACACTATTGTGGCGTTTGTCT
* **
2982802 -AAAAACGCCACTATTGATTAACATTATTACGGCGTTTGT
1 AAAAAACGCCACTATTGATTAACACTATTGTGGCGTTTGT
2982841 GGTATAAACA
Statistics
Matches: 72, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
40 20 0.28
41 51 0.71
42 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (42 bp):
AAAAAACGCCACTATTGATTAACACTATTGTGGCGTTTGTCT
Found at i:2993982 original size:161 final size:162
Alignment explanation
Indices: 2993710--2994032 Score: 630
Period size: 161 Copynumber: 2.0 Consensus size: 162
2993700 CAAAAGGTTA
*
2993710 AAAAGGGAAAATCAATTACCATGGCTCCTCGGCGACAACGTTGGGGTGGCTAAAGATCTTAGCCG
1 AAAAGGAAAAATCAATTACCATGGCTCCTCGGCGACAACGTTGGGGTGGCTAAAGATCTTAGCCG
2993775 CATTACATCTCTTGTTTGTGGGAAGGGGTTCACCGGCCGGTGTGTAAGCATCGCACATTACCTAA
66 CATTACATCTCTTGTTTGTGGGAAGGGGTTCACCGGCCGGTGTGTAAGCATCGCACATTACCTAA
2993840 TACATGCGATTAATAAAATATTCA-TATTATT
131 TACATGCGATTAATAAAATATTCATTATTATT
2993871 AAAAGGAAAAATCAATTACCATGGCTCCTCGGCGACAACGTTGGGGTGGCTAAAGATCTTAGCCG
1 AAAAGGAAAAATCAATTACCATGGCTCCTCGGCGACAACGTTGGGGTGGCTAAAGATCTTAGCCG
2993936 CATTACATCTCTTGTTTGTGGGAAGGGGTTCACCGGCCGGTGTGTAAGCATCGCACATTACCTAA
66 CATTACATCTCTTGTTTGTGGGAAGGGGTTCACCGGCCGGTGTGTAAGCATCGCACATTACCTAA
2994001 TACATGCGATTAATAAAATATTCATTATTATT
131 TACATGCGATTAATAAAATATTCATTATTATT
2994033 GTCAACGTCC
Statistics
Matches: 160, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
161 153 0.96
162 7 0.04
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (162 bp):
AAAAGGAAAAATCAATTACCATGGCTCCTCGGCGACAACGTTGGGGTGGCTAAAGATCTTAGCCG
CATTACATCTCTTGTTTGTGGGAAGGGGTTCACCGGCCGGTGTGTAAGCATCGCACATTACCTAA
TACATGCGATTAATAAAATATTCATTATTATT
Found at i:2995603 original size:12 final size:12
Alignment explanation
Indices: 2995580--2995613 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
2995570 AATTACCAAT
2995580 ATAAATAAATTTA
1 ATAAA-AAATTTA
2995593 ATAAAAAATTTA
1 ATAAAAAATTTA
2995605 ATAAAAAAT
1 ATAAAAAAT
2995614 AATATTTTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 16 0.76
13 5 0.24
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAAAAAATTTA
Found at i:2995892 original size:18 final size:19
Alignment explanation
Indices: 2995864--2995899 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
2995854 TAAATATTTA
2995864 AATTATTTAAAAAAATTAG
1 AATTATTTAAAAAAATTAG
2995883 AATT-TTTAAAAAAATTA
1 AATTATTTAAAAAAATTA
2995900 TTGTCACCGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (19 bp):
AATTATTTAAAAAAATTAG
Found at i:2998378 original size:23 final size:23
Alignment explanation
Indices: 2998352--2998420 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
2998342 CACCACAACT
*
2998352 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
2998375 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
2998398 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
2998421 TATAATAATG
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:0.30, C:0.26, G:0.26, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:3003431 original size:31 final size:30
Alignment explanation
Indices: 3003390--3003465 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 30
3003380 AACAAGCTTT
* *
3003390 CAAATATTACAAAACGATCATTAAACTTC-C
1 CAAATATTACAAAACAAACATTAAA-TTCAC
* *
3003420 CAAATAATTACATAACAAACATTAAATTCAT
1 CAAAT-ATTACAAAACAAACATTAAATTCAC
3003451 CAAATCATTACAAAA
1 CAAAT-ATTACAAAA
3003466 TAGTCACTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
30 8 0.21
31 30 0.79
ACGTcount: A:0.53, C:0.20, G:0.01, T:0.26
Consensus pattern (30 bp):
CAAATATTACAAAACAAACATTAAATTCAC
Found at i:3005372 original size:157 final size:157
Alignment explanation
Indices: 3005086--3005402 Score: 580
Period size: 157 Copynumber: 2.0 Consensus size: 157
3005076 GGTTTAGTTG
*
3005086 ATATATTTAAGTGCAGGGCTGTAAGATTTTTCCTCGCAATATGTTAATATGCTATTGATGAGTAC
1 ATATATTTAAGTGCAGGGCTGTAAGATTTTTCCTCGCAATATGCTAATATGCTATTGATGAGTAC
*
3005151 TGGCCATGCTGTCTCAATGGCTGCATGTCATCATGTTTTGGTCAAACCCTGGTTTTGCTCATTGA
66 TGGCCATGCTGTCTCAATGACTGCATGTCATCATGTTTTGGTCAAACCCTGGTTTTGCTCATTGA
*
3005216 AATTGTTGGTTGAAATTACCATCTGGA
131 AATTGTTGATTGAAATTACCATCTGGA
*
3005243 ATATATTTAAGTGCAGGGGTGTAAGATTTTTCCTCGCAATATGCTAATATGCTATTGATGAGTAC
1 ATATATTTAAGTGCAGGGCTGTAAGATTTTTCCTCGCAATATGCTAATATGCTATTGATGAGTAC
* *
3005308 TGGTCATGCTGTCTCAATGACTGTATGTCATCATGTTTTGGTCAAACCCTGGTTTTGCTCATTGA
66 TGGCCATGCTGTCTCAATGACTGCATGTCATCATGTTTTGGTCAAACCCTGGTTTTGCTCATTGA
3005373 AATTGTTGATTGAAATTACCATCTGGA
131 AATTGTTGATTGAAATTACCATCTGGA
3005400 ATA
1 ATA
3005403 ATACTTCATT
Statistics
Matches: 154, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
157 154 1.00
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.38
Consensus pattern (157 bp):
ATATATTTAAGTGCAGGGCTGTAAGATTTTTCCTCGCAATATGCTAATATGCTATTGATGAGTAC
TGGCCATGCTGTCTCAATGACTGCATGTCATCATGTTTTGGTCAAACCCTGGTTTTGCTCATTGA
AATTGTTGATTGAAATTACCATCTGGA
Found at i:3012847 original size:19 final size:20
Alignment explanation
Indices: 3012818--3012857 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
3012808 AACTCAAATA
*
3012818 TACAAAGAAAAGCAAAATCT
1 TACAAAGAAAAACAAAATCT
*
3012838 TACAAA-AAAAACGAAATCT
1 TACAAAGAAAAACAAAATCT
3012857 T
1 T
3012858 CCTTTGAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.60, C:0.15, G:0.07, T:0.17
Consensus pattern (20 bp):
TACAAAGAAAAACAAAATCT
Found at i:3025035 original size:29 final size:30
Alignment explanation
Indices: 3024993--3025051 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
3024983 AATTAATCTT
3024993 AATGATTATTTTATAATCATTTAAAA-ATTA
1 AATGATTATTTTATAAT-ATTTAAAAGATTA
3025023 AATGATTA-TTTATAATATTTAAAAGATTA
1 AATGATTATTTTATAATATTTAAAAGATTA
3025052 TTGACTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 8 0.29
29 12 0.43
30 8 0.29
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (30 bp):
AATGATTATTTTATAATATTTAAAAGATTA
Found at i:3031070 original size:34 final size:36
Alignment explanation
Indices: 3030997--3031070 Score: 98
Period size: 39 Copynumber: 2.0 Consensus size: 36
3030987 GTATGGTTGC
*
3030997 GATGGGTTTAATATCGTATCGTTCGGGAAAGGCAAGAAA
1 GATGGGTTTAATATCATATCGTTC-GG--AGGCAAGAAA
3031036 GATGGGTTTAATATCATATCGTTC-G-GGCAAGAAA
1 GATGGGTTTAATATCATATCGTTCGGAGGCAAGAAA
3031070 G
1 G
3031071 TAGAGGATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
34 10 0.29
37 1 0.03
39 23 0.68
ACGTcount: A:0.32, C:0.11, G:0.30, T:0.27
Consensus pattern (36 bp):
GATGGGTTTAATATCATATCGTTCGGAGGCAAGAAA
Found at i:3033974 original size:13 final size:13
Alignment explanation
Indices: 3033958--3033990 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
3033948 TACGTATTTC
3033958 ATATTTTACTTTT
1 ATATTTTACTTTT
3033971 ATATTATTACTTTT
1 ATATT-TTACTTTT
3033985 -TATTTT
1 ATATTTT
3033991 GTTTACAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 2 0.11
13 9 0.47
14 8 0.42
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (13 bp):
ATATTTTACTTTT
Found at i:3033987 original size:15 final size:15
Alignment explanation
Indices: 3033914--3033987 Score: 59
Period size: 15 Copynumber: 5.1 Consensus size: 15
3033904 TTATAATCGT
3033914 TATTATTA-TTTTTAA
1 TATTATTACTTTTT-A
* *
3033929 TCTTATTACTTTATA
1 TATTATTACTTTTTA
*
3033944 TA-TA-TACGTATTTCA
1 TATTATTAC-T-TTTTA
3033959 TATT-TTAC-TTTTA
1 TATTATTACTTTTTA
3033972 TATTATTACTTTTTA
1 TATTATTACTTTTTA
3033987 T
1 T
3033988 TTTGTTTACA
Statistics
Matches: 46, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
13 11 0.24
14 7 0.15
15 20 0.43
16 8 0.17
ACGTcount: A:0.28, C:0.08, G:0.01, T:0.62
Consensus pattern (15 bp):
TATTATTACTTTTTA
Found at i:3034011 original size:2 final size:2
Alignment explanation
Indices: 3034004--3034111 Score: 90
Period size: 2 Copynumber: 57.5 Consensus size: 2
3033994 TACAAATTAT
* *
3034004 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TT TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
3034045 TA -A TA TA -A CTA T- TA CTA T- TA T- TA T- TA TC T- TA TT TT TA
1 TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
3034082 TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3034112 GATTTTATTA
Statistics
Matches: 88, Mismatches: 7, Indels: 22
0.75 0.06 0.19
Matches are distributed among these distances:
1 9 0.10
2 76 0.86
3 3 0.03
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:3042624 original size:21 final size:21
Alignment explanation
Indices: 3042582--3042624 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3042572 TTTTCGGGCT
* * *
3042582 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
3042603 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
3042624 A
1 A
3042625 CGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:3043363 original size:149 final size:150
Alignment explanation
Indices: 3043167--3043482 Score: 528
Period size: 150 Copynumber: 2.1 Consensus size: 150
3043157 GGGTAGAGGG
* * *
3043167 TCTACGTGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTT-GAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
* * *
3043231 TGCTTGATCCTTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
3043296 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
* * *
3043316 TCTATGCGGTCCTTCGGGATATATATATATTCTGTGGAATATGTGTGAAGTCTTGGAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
3043381 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
3043446 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
3043466 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
3043483 TGCATTTATA
Statistics
Matches: 155, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
149 49 0.32
150 106 0.68
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.35
Consensus pattern (150 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
ATATGGCACTACGGTGCAAT
Found at i:3043494 original size:23 final size:23
Alignment explanation
Indices: 3043450--3043494 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3043440 ATCATTATAT
*
3043450 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
3043473 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
3043495 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:3049542 original size:21 final size:21
Alignment explanation
Indices: 3049500--3049542 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3049490 TTTTCGGGCT
* * *
3049500 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
3049521 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
3049542 A
1 A
3049543 CGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:3050274 original size:149 final size:149
Alignment explanation
Indices: 3050086--3050375 Score: 501
Period size: 149 Copynumber: 1.9 Consensus size: 149
3050076 GGGTAGAGGG
* *
3050086 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTT-GAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
* * *
3050150 TGCTTGATCCTTAGAATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGAATATGTATATGA-TCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
3050215 ATATGGCACTACGGTGCAAT
130 ATATGGCACTACGGTGCAAT
*
3050235 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
*
3050300 TACTTGATCCCTAGTATATGTATATGATCTTAAGGAATTATATGTGGTCCTTATGGACATCATTA
66 TACTTGATCCCTAGAATATGTATATGATCTTAAGGAATTATATGTGGTCCTTATGGACATCATTA
3050365 TATGGCACTAC
131 TATGGCACTAC
3050376 CAATTCTACG
Statistics
Matches: 133, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
149 99 0.74
150 34 0.26
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
TACTTGATCCCTAGAATATGTATATGATCTTAAGGAATTATATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:3053957 original size:68 final size:69
Alignment explanation
Indices: 3053848--3053975 Score: 186
Period size: 68 Copynumber: 1.9 Consensus size: 69
3053838 AATACTTCGC
* * * *
3053848 TTAGGATGAAAACCCGAGAGGACATCCTAAGTTGAAAAAAAAAGGAAAA-AGAAAAAAGAGAAAA
1 TTAGGATGAAAACCCGAAAGGACACCCTAAATTGAAAAAAAAAGAAAAAGAGAAAAAAGAGAAAA
3053912 ACGT
66 ACGT
* * *
3053916 TTAGGGTGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAAAAGAAAAAGAGAAAAAAGA
1 TTAGGATGAAAACCCGAAAGGACACCCTAAATTGAAAAAAAAAGAAAAAGAGAAAAAAGA
3053976 ACGAAAGAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
68 42 0.81
69 10 0.19
ACGTcount: A:0.55, C:0.11, G:0.23, T:0.11
Consensus pattern (69 bp):
TTAGGATGAAAACCCGAAAGGACACCCTAAATTGAAAAAAAAAGAAAAAGAGAAAAAAGAGAAAA
ACGT
Found at i:3053986 original size:14 final size:14
Alignment explanation
Indices: 3053949--3053995 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
3053939 GCCCTAAATT
*
3053949 GAAAAAAAAAGAAA
1 GAAAGAAAAAGAAA
*
3053963 -AAGAGAAAAAAGAAC
1 GAA-AG-AAAAAGAAA
3053978 GAAAGAAAAAGAAA
1 GAAAGAAAAAGAAA
3053992 GAAA
1 GAAA
3053996 ACGAGGTGGG
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
13 2 0.07
14 13 0.48
15 10 0.37
16 2 0.07
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (14 bp):
GAAAGAAAAAGAAA
Found at i:3053992 original size:18 final size:15
Alignment explanation
Indices: 3053951--3053996 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
3053941 CCTAAATTGA
3053951 AAAAAAAAGAAAAAG
1 AAAAAAAAGAAAAAG
*
3053966 AGAAAAAAGAACGAAAG
1 AAAAAAAAGAA--AAAG
3053983 AAAAAGAAAGAAAA
1 AAAAA-AAAGAAAA
3053997 CGAGGTGGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 10 0.38
16 2 0.08
17 8 0.31
18 6 0.23
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAAAAAAGAAAAAG
Found at i:3054981 original size:106 final size:106
Alignment explanation
Indices: 3054726--3055713 Score: 1428
Period size: 106 Copynumber: 9.3 Consensus size: 106
3054716 GGTTTTACCT
3054726 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
3054791 CGAAGGGACCGCTGGTTGTCAAC-AACAACTTCCTAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
* *
3054831 GGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
3054896 CGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTT
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
* * * * *
3054937 GGAGCCAATTTCAACTTCACAACGAAGGATATTAGACTCCAGACAATGCAAGTTCTACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * *
3055002 CAAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
* *
3055043 AGAGCCAATTTCAACTTCACAACGAAGGATATTAGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
3055108 CGAAGGGACCACTGGTTGTCAACAAACAACTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
* * *
3055149 AGAGCCAATTTTAACTTCACATCGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * *
3055214 CGAATGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
* * *
3055255 AGAGCCAATTTCAACTTCACAGCGAAGTATATTGGACTCAAGACAACGCAAGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
3055320 CGAAGGGACCACTGGTTGTCAATAAACAACTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
* * *
3055361 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGAAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * * * *
3055426 CTAAGGGGCCGTTGGTTGTCAAAAAATAAC-TCCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCC-CAATTTC
* * * *
3055467 AAAGCCAATTTCAACTTCACAACGAATGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * * * *
3055532 CGAAAGGACCGTTGGTTGTCAATAAACCA-TTACCCAGTTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTT-CCCAATTTC
* * * *
3055573 AGAGCCAATATCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * * *
3055638 CGAAGGGACGGCTGGTTGTCAACAAACCA-TCACCCAGTTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACT-TCCCAATTTC
*
3055679 AGAGTCAATTTCAACTTCAC-GACGAAGGATATTGG
1 AGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
3055714 CCTCGAAACA
Statistics
Matches: 799, Mismatches: 78, Indels: 11
0.90 0.09 0.01
Matches are distributed among these distances:
105 90 0.11
106 707 0.88
107 2 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
Found at i:3057393 original size:13 final size:13
Alignment explanation
Indices: 3057377--3057409 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
3057367 TACGTATTTC
3057377 ATATTTTACTTTT
1 ATATTTTACTTTT
3057390 ATATTATTACTTTT
1 ATATT-TTACTTTT
3057404 -TATTTT
1 ATATTTT
3057410 GTTTACAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 2 0.11
13 9 0.47
14 8 0.42
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (13 bp):
ATATTTTACTTTT
Found at i:3057406 original size:15 final size:15
Alignment explanation
Indices: 3057333--3057406 Score: 59
Period size: 15 Copynumber: 5.1 Consensus size: 15
3057323 TTATAATTGT
3057333 TATTATTA-TTTTTAA
1 TATTATTACTTTTT-A
* *
3057348 TCTTATTACTTTATA
1 TATTATTACTTTTTA
*
3057363 TA-TA-TACGTATTTCA
1 TATTATTAC-T-TTTTA
3057378 TATT-TTAC-TTTTA
1 TATTATTACTTTTTA
3057391 TATTATTACTTTTTA
1 TATTATTACTTTTTA
3057406 T
1 T
3057407 TTTGTTTACA
Statistics
Matches: 46, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
13 11 0.24
14 7 0.15
15 20 0.43
16 8 0.17
ACGTcount: A:0.28, C:0.08, G:0.01, T:0.62
Consensus pattern (15 bp):
TATTATTACTTTTTA
Found at i:3057433 original size:2 final size:2
Alignment explanation
Indices: 3057426--3057571 Score: 139
Period size: 2 Copynumber: 75.5 Consensus size: 2
3057416 AAATTATTAT
*
3057426 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
3057468 TA TA TA T- TA -A TA TA -A CTA T- TA CTA T- TA T- TA T- TA TC T-
1 TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA
* * * *
3057504 TC TT TT TA CTCA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA -T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3057548 TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3057572 GATTTTATTA
Statistics
Matches: 124, Mismatches: 7, Indels: 26
0.79 0.04 0.17
Matches are distributed among these distances:
1 9 0.07
2 109 0.88
3 5 0.04
4 1 0.01
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3061235 original size:20 final size:21
Alignment explanation
Indices: 3061195--3061237 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
3061185 ACAGGCATCG
**
3061195 TAAAACATATGTTCCCTTGTT
1 TAAAACATATGTTCCAATGTT
3061216 TAAAACAT-TGTTCCAATGTT
1 TAAAACATATGTTCCAATGTT
3061236 TA
1 TA
3061238 TTCAATCCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (21 bp):
TAAAACATATGTTCCAATGTT
Found at i:3061309 original size:24 final size:24
Alignment explanation
Indices: 3061270--3061318 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
3061260 AACCGAAACG
* * * *
3061270 CACATCTCCATCCATATTTCATAA
1 CACATCTACATACATACTGCATAA
3061294 CACATCTACATACATACTGCATAA
1 CACATCTACATACATACTGCATAA
3061318 C
1 C
3061319 GAAATAGTCC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.37, C:0.33, G:0.02, T:0.29
Consensus pattern (24 bp):
CACATCTACATACATACTGCATAA
Found at i:3072585 original size:24 final size:24
Alignment explanation
Indices: 3072558--3072606 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
3072548 GGACTATTTC
* * * *
3072558 GTTATGCAGTATGTATGTAGATGT
1 GTTATGAAATATGGATGGAGATGT
3072582 GTTATGAAATATGGATGGAGATGT
1 GTTATGAAATATGGATGGAGATGT
3072606 G
1 G
3072607 CGTTTCGGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.29, C:0.02, G:0.33, T:0.37
Consensus pattern (24 bp):
GTTATGAAATATGGATGGAGATGT
Found at i:3081625 original size:15 final size:15
Alignment explanation
Indices: 3081601--3081632 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3081591 GTATTAATTT
*
3081601 TACTGTTATCTGGTC
1 TACTGCTATCTGGTC
3081616 TACTGCTATCTGGTC
1 TACTGCTATCTGGTC
3081631 TA
1 TA
3081633 TTGGTCTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.44
Consensus pattern (15 bp):
TACTGCTATCTGGTC
Found at i:3082643 original size:20 final size:20
Alignment explanation
Indices: 3082618--3082669 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
3082608 ATGAAAAAAA
3082618 AGTATCGATACTATCCCTAT
1 AGTATCGATACTATCCCTAT
3082638 AGTATCGATACTATCCCTAT
1 AGTATCGATACTATCCCTAT
3082658 AGTATCGATACT
1 AGTATCGATACT
3082670 CTACCTGTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.35
Consensus pattern (20 bp):
AGTATCGATACTATCCCTAT
Found at i:3087533 original size:14 final size:15
Alignment explanation
Indices: 3087516--3087544 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3087506 TACATAATAT
3087516 GCAT-AAACATAAGA
1 GCATAAAACATAAGA
3087530 GCATAAAACATAAGA
1 GCATAAAACATAAGA
3087545 TATATGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.59, C:0.14, G:0.14, T:0.14
Consensus pattern (15 bp):
GCATAAAACATAAGA
Found at i:3087837 original size:15 final size:15
Alignment explanation
Indices: 3087819--3087854 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
3087809 TCGAGGGTAT
3087819 TGTAGTCCTTCGGGA
1 TGTAGTCCTTCGGGA
3087834 TGTAGTCCTTCGGGA
1 TGTAGTCCTTCGGGA
*
3087849 CGTAGT
1 TGTAGT
3087855 GGTCCTTCGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.14, C:0.19, G:0.33, T:0.33
Consensus pattern (15 bp):
TGTAGTCCTTCGGGA
Found at i:3087861 original size:18 final size:18
Alignment explanation
Indices: 3087838--3087885 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
3087828 TCGGGATGTA
3087838 GTCCTTCGGGACGTAGTG
1 GTCCTTCGGGACGTAGTG
3087856 GTCCTTCGGGACGTAGTG
1 GTCCTTCGGGACGTAGTG
*
3087874 GTCCTACGGGAC
1 GTCCTTCGGGAC
3087886 ATATATAGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.12, C:0.25, G:0.38, T:0.25
Consensus pattern (18 bp):
GTCCTTCGGGACGTAGTG
Found at i:3093659 original size:14 final size:15
Alignment explanation
Indices: 3093642--3093670 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3093632 TACATAATAT
3093642 GCAT-AAACATAAGA
1 GCATAAAACATAAGA
3093656 GCATAAAACATAAGA
1 GCATAAAACATAAGA
3093671 TATATGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.59, C:0.14, G:0.14, T:0.14
Consensus pattern (15 bp):
GCATAAAACATAAGA
Found at i:3093963 original size:15 final size:15
Alignment explanation
Indices: 3093945--3093979 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
3093935 CGAGGGTATT
3093945 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
3093960 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
3093975 GTAGT
1 GTAGT
3093980 GGTCCTACGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.14, C:0.23, G:0.34, T:0.29
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:3094214 original size:22 final size:22
Alignment explanation
Indices: 3094200--3094249 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 22
3094190 ATGACATGAT
3094200 TATATATATGTCATGAAATATA
1 TATATATATGTCATGAAATATA
* *
3094222 TATATATATAT-AT-ATATATA
1 TATATATATGTCATGAAATATA
3094242 TATATATA
1 TATATATA
3094250 CATATTGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 14 0.54
21 2 0.08
22 10 0.38
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (22 bp):
TATATATATGTCATGAAATATA
Found at i:3094222 original size:2 final size:2
Alignment explanation
Indices: 3094217--3094254 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
3094207 ATGTCATGAA
*
3094217 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3094255 TGAAATGTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3105037 original size:2 final size:2
Alignment explanation
Indices: 3105030--3105058 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3105020 ATAATATCTT
3105030 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 T
3105059 TTTCAATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3105293 original size:227 final size:234
Alignment explanation
Indices: 3104933--3105404 Score: 636
Period size: 227 Copynumber: 2.0 Consensus size: 234
3104923 AGTGTGATAT
*
3104933 TCGGGTCGAGTTCGGGTTTAAGGTGAAAAATACCCGACCCGACCCAAATATATATAATTTTACCT
1 TCGGGTCGAGTTCGGGTTTAAGGTGAAAAATACCCGACCCGACCCAAAAATATATAATTTTACCT
*
3104998 TATATATTTAAGAATAATTACAATAATATCTTTATATATATATATATATATATATATATATTTTC
66 TATATATTTAAGAATAATTACAATAATA----TATACATATATATATATATATATATATATTTTC
* * * ** **
3105063 AATTAAGTCACTCTTTTTATTGAATAAAAATATTTTTTTTATTATTTCGGGTTGGGTTTCTAATT
127 AATTAAGTCACTCTTTTTATTGAATAAAAATAATTTTCTTATTATTTCAGGCCGAATTTCTAATT
* * *
3105128 CATATATTTGGGTCGGATAAGGTGAAGCTTTATTTTGGTTGGG
192 CATATATTCGGGTCGGATAAGGTGAAACTTTATTTTGGTCGGG
* *
3105171 TCGGGTCGGGTTCGGGTTTAGGGTGAAAAATACCCGACCCGACCCAAAAATTATATAATTTTACC
1 TCGGGTCGAGTTCGGGTTTAAGGTGAAAAATACCCGACCCGACCCAAAAA-TATATAATTTTACC
* * * *
3105236 TTATATATTTAGGAATAATTACAATAATA-A-CCCTCTATATATA-AT-T-T-T-T-TTTTCAAT
65 TTATATATTTAAGAATAATTACAATAATATATACATATATATATATATATATATATATTTTCAAT
*
3105293 TAAGTCACTGTTTTTATTGAATAAAAATAATTTTCTTATTATTTCAGGCCGAATTTCTAATTCAT
130 TAAGTCACTCTTTTTATTGAATAAAAATAATTTTCTTATTATTTCAGGCCGAATTTCTAATTCAT
* ** *
3105358 ATATTCGGGTCGGGTCGGGTGAAATTTTATTTTGGTCGGG
195 ATATTCGGGTCGGATAAGGTGAAACTTTATTTTGGTCGGG
3105398 TCGGGTC
1 TCGGGTC
3105405 TCAGATAGAG
Statistics
Matches: 210, Mismatches: 23, Indels: 13
0.85 0.09 0.05
Matches are distributed among these distances:
227 105 0.50
228 1 0.00
229 1 0.00
230 1 0.00
231 1 0.00
232 2 0.01
233 9 0.04
234 1 0.00
238 47 0.22
239 42 0.20
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (234 bp):
TCGGGTCGAGTTCGGGTTTAAGGTGAAAAATACCCGACCCGACCCAAAAATATATAATTTTACCT
TATATATTTAAGAATAATTACAATAATATATACATATATATATATATATATATATATTTTCAATT
AAGTCACTCTTTTTATTGAATAAAAATAATTTTCTTATTATTTCAGGCCGAATTTCTAATTCATA
TATTCGGGTCGGATAAGGTGAAACTTTATTTTGGTCGGG
Found at i:3106472 original size:20 final size:20
Alignment explanation
Indices: 3106447--3106484 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3106437 ATCATATTCT
3106447 CTGGTAATCTTATATTCCCA
1 CTGGTAATCTTATATTCCCA
*
3106467 CTGGTAATCTTATGTTCC
1 CTGGTAATCTTATATTCC
3106485 GTGAACCAAA
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:0.21, C:0.24, G:0.13, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTATATTCCCA
Found at i:3111557 original size:16 final size:16
Alignment explanation
Indices: 3111538--3111568 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3111528 TATAGAAGTA
3111538 TTGAAATCATTCTCGT
1 TTGAAATCATTCTCGT
3111554 TTGAAATCATTCTCG
1 TTGAAATCATTCTCG
3111569 CTTAGAAAAA
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:0.19, G:0.13, T:0.42
Consensus pattern (16 bp):
TTGAAATCATTCTCGT
Found at i:3114473 original size:65 final size:65
Alignment explanation
Indices: 3114369--3114513 Score: 290
Period size: 65 Copynumber: 2.2 Consensus size: 65
3114359 AGGACAATGG
3114369 TTAAATTTATGTTAAATCATAAACTTATTAAGTTAAATCATATAATCAGATGATGACACAGATGA
1 TTAAATTTATGTTAAATCATAAACTTATTAAGTTAAATCATATAATCAGATGATGACACAGATGA
3114434 TTAAATTTATGTTAAATCATAAACTTATTAAGTTAAATCATATAATCAGATGATGACACAGATGA
1 TTAAATTTATGTTAAATCATAAACTTATTAAGTTAAATCATATAATCAGATGATGACACAGATGA
3114499 TTAAATTTATGTTAA
1 TTAAATTTATGTTAA
3114514 CATTTAACGG
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 80 1.00
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.37
Consensus pattern (65 bp):
TTAAATTTATGTTAAATCATAAACTTATTAAGTTAAATCATATAATCAGATGATGACACAGATGA
Found at i:3117865 original size:21 final size:21
Alignment explanation
Indices: 3117816--3117865 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
3117806 TATACAACTA
*
3117816 TTTTTTAAAACATATATTAGT
1 TTTTTTAAAACATATATAAGT
*
3117837 TTTATTAAAA-ATATAATAAGT
1 TTTTTTAAAACATAT-ATAAGT
3117858 TTTTTTAA
1 TTTTTTAA
3117866 GTAAGCTTGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.16
21 21 0.84
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (21 bp):
TTTTTTAAAACATATATAAGT
Found at i:3126041 original size:31 final size:31
Alignment explanation
Indices: 3126006--3126069 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
3125996 AAAATATAAT
3126006 ATATGA-CTACTTTCATTTTTATTTAATTAAG
1 ATATGATC-ACTTTCATTTTTATTTAATTAAG
*
3126037 ATATGATCACTTTCGTTTTTATTTAATTAAG
1 ATATGATCACTTTCATTTTTATTTAATTAAG
3126068 AT
1 AT
3126070 GTAGTCACCA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 30 0.97
32 1 0.03
ACGTcount: A:0.31, C:0.09, G:0.08, T:0.52
Consensus pattern (31 bp):
ATATGATCACTTTCATTTTTATTTAATTAAG
Done.