Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000002.1 Hibiscus syriacus cultivar Beakdansim tig00000003_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: 2131600
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 10
Found at i:202439 original size:109 final size:109
Alignment explanation
Indices: 202302--202748 Score: 777
Period size: 109 Copynumber: 4.1 Consensus size: 109
202292 GGGCCATCCG
* * *
202302 CGATTTCAACCCCACGAAGGAGGATATCGTGCTACCCGAGACAACACAAGTTCAACTTCACAAAG
1 CGATTTCAACTCCACGATGGAGGATATCGTGCTACCCGAGACAACACAAGTTCAACTTCACAACG
*
202367 AAGGGACGGCTGGTTGTCTACAAACAACTTCCCAATTTCAGAGC
66 AAGGGACGGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
* *
202411 CGATTTTAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACACAAGTTCAACTTCACAACG
1 CGATTTCAACTCCACGATGGAGGATATCGTGCTACCCGAGACAACACAAGTTCAACTTCACAACG
*
202476 AAGGGACGGCTGGTTGTCAACAAATAACTTCCCAATTTCAGAGC
66 AAGGGACGGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
202520 CGATTTCAACTCCACGATGGAGGATATCGTGCTACCCGAGACAACACAAGTTCAACTTCACAACG
1 CGATTTCAACTCCACGATGGAGGATATCGTGCTACCCGAGACAACACAAGTTCAACTTCACAACG
*
202585 AAGGGACGACTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
66 AAGGGACGGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
*
202629 CGATTTCAACTCCACGATGGAGGATATCGTGTTACCCGAGACAACACAAGTTCAACTTCACAACG
1 CGATTTCAACTCCACGATGGAGGATATCGTGCTACCCGAGACAACACAAGTTCAACTTCACAACG
* * **
202694 AAGGGACGGTTGGTTGTCAACAAACAACTTCCCAATTTCATATT
66 AAGGGACGGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
202738 CGATTTCAACT
1 CGATTTCAACT
202749 TGTATTGGAT
Statistics
Matches: 322, Mismatches: 16, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
109 322 1.00
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (109 bp):
CGATTTCAACTCCACGATGGAGGATATCGTGCTACCCGAGACAACACAAGTTCAACTTCACAACG
AAGGGACGGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
Found at i:202759 original size:17 final size:17
Alignment explanation
Indices: 202734--202766 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
202724 CCCAATTTCA
202734 TATTCGATTTCAACTTG
1 TATTCGATTTCAACTTG
*
202751 TATTGGATTTCAACTT
1 TATTCGATTTCAACTT
202767 CACAACGAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.15, G:0.12, T:0.48
Consensus pattern (17 bp):
TATTCGATTTCAACTTG
Found at i:203845 original size:19 final size:18
Alignment explanation
Indices: 203815--203850 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
203805 CTTTTATTTC
*
203815 TTTTTTTATTTATTACTA
1 TTTTTTTATTTAATACTA
203833 TTTTTTTATTTTAATACT
1 TTTTTTTA-TTTAATACT
203851 TATTATTACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTTTTATTTAATACTA
Found at i:210464 original size:3 final size:3
Alignment explanation
Indices: 210456--210503 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
210446 CGTTTGCTGG
* * * *
210456 AAC AAC AAC GAC AAC GAC AAC AAT GAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
210504 TATAATAATA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.60, C:0.31, G:0.06, T:0.02
Consensus pattern (3 bp):
AAC
Found at i:210511 original size:3 final size:3
Alignment explanation
Indices: 210505--210550 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
210495 AACAACAACT
210505 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
210551 AGAGAGAGGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:211072 original size:17 final size:18
Alignment explanation
Indices: 211036--211076 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
211026 ATATTATGTA
*
211036 TTTAATTTATTTAAGCAT
1 TTTACTTTATTTAAGCAT
*
211054 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGCAT
211071 TTTACT
1 TTTACT
211077 AATATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTACTTTATTTAAGCAT
Found at i:214265 original size:51 final size:50
Alignment explanation
Indices: 214172--214282 Score: 134
Period size: 51 Copynumber: 2.2 Consensus size: 50
214162 CTACATGGCG
* * **
214172 TATAGCGCGGATCAGGGGGCGCGCTATACCCACGTATACGCCATGTCAGCA
1 TATAGCGC-GATCAGGGGGCACGCTATACCCACGTAGACGCCAAATCAGCA
*
214223 TATAGCGCGATACAGGGGGCACGCTATACCCCACGT-GGCGCCAAATCAGCA
1 TATAGCGCGAT-CAGGGGGCACGCTATA-CCCACGTAGACGCCAAATCAGCA
*
214274 TATAACGCG
1 TATAGCGCG
214283 GGACAGAGAG
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
50 3 0.06
51 42 0.81
52 7 0.13
ACGTcount: A:0.26, C:0.30, G:0.28, T:0.16
Consensus pattern (50 bp):
TATAGCGCGATCAGGGGGCACGCTATACCCACGTAGACGCCAAATCAGCA
Found at i:215841 original size:17 final size:18
Alignment explanation
Indices: 215802--215848 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
215792 TATTTCTGAG
215802 GGAATTAGAATCTGTGAA
1 GGAATTAGAATCTGTGAA
*
215820 GGAATTAGAATCTGT-CA
1 GGAATTAGAATCTGTGAA
*
215837 GGAATTGGAATC
1 GGAATTAGAATC
215849 CAATTCCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.36, C:0.09, G:0.28, T:0.28
Consensus pattern (18 bp):
GGAATTAGAATCTGTGAA
Found at i:218410 original size:2 final size:2
Alignment explanation
Indices: 218403--218439 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
218393 AGTTCAATTA
218403 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
218440 AGAGAATCTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:227256 original size:26 final size:25
Alignment explanation
Indices: 227227--227284 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 25
227217 GAAGGAGAGA
227227 GAGTGAATGGATCGCTGAAAAGAAAT
1 GAGTG-ATGGATCGCTGAAAAGAAAT
*
227253 GA--G-TGGATGGCTGAAAAGAAAT
1 GAGTGATGGATCGCTGAAAAGAAAT
227275 GAGTGGATGG
1 GAGT-GATGG
227285 GGTGAAATTG
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
22 20 0.74
24 1 0.04
25 1 0.04
26 5 0.19
ACGTcount: A:0.38, C:0.05, G:0.38, T:0.19
Consensus pattern (25 bp):
GAGTGATGGATCGCTGAAAAGAAAT
Found at i:227265 original size:22 final size:22
Alignment explanation
Indices: 227234--227284 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
227224 AGAGAGTGAA
*
227234 TGGATCGCTGAAAAGAAATGAG
1 TGGATGGCTGAAAAGAAATGAG
227256 TGGATGGCTGAAAAGAAATGAG
1 TGGATGGCTGAAAAGAAATGAG
227278 TGGATGG
1 TGGATGG
227285 GGTGAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.37, C:0.06, G:0.37, T:0.20
Consensus pattern (22 bp):
TGGATGGCTGAAAAGAAATGAG
Found at i:237539 original size:20 final size:20
Alignment explanation
Indices: 237516--237572 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
237506 TTAAATTCTC
237516 GTTCGCATCTTTACATTTGT
1 GTTCGCATCTTTACATTTGT
* *
237536 GTTCGCACCTTTGCATTTGT
1 GTTCGCATCTTTACATTTGT
** *
237556 ACTCTCATCTTTACATT
1 GTTCGCATCTTTACATT
237573 AGCATTCACA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.16, C:0.25, G:0.12, T:0.47
Consensus pattern (20 bp):
GTTCGCATCTTTACATTTGT
Found at i:238795 original size:22 final size:22
Alignment explanation
Indices: 238770--238821 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
238760 CCACAAGGTG
238770 GACCAAATACAAAGTGCTCGAA
1 GACCAAATACAAAGTGCTCGAA
238792 GACCAAATACAAAGTGCTCGAA
1 GACCAAATACAAAGTGCTCGAA
*
238814 GATCAAAT
1 GACCAAAT
238822 CAAGTCGACA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.46, C:0.21, G:0.17, T:0.15
Consensus pattern (22 bp):
GACCAAATACAAAGTGCTCGAA
Found at i:241273 original size:114 final size:114
Alignment explanation
Indices: 240984--241570 Score: 770
Period size: 114 Copynumber: 5.2 Consensus size: 114
240974 TGATGTTTTC
* * * * *
240984 AAATGAATTTTTAAAGAAACTAAGCCTAATTTTCAAGGGTTTCTTGATTATTACTTCAAATGAAT
1 AAATGAATTTTTAAAGAAGCTAAGCCTGATTTTTAAGGTTTTCTTGATGATTACTTCAAATGAAT
* * * *
241049 TTTTAAAGAAGTTAAGTCTAATTTTTAGGGGTTTCTTGATGATAACTGT
66 TTTTAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGATAAATTT
* * * * * * *
241098 AAAT-ATTTTTTACAGAAGATAAGCCTGATTTTTAGGGTTTTCTTGATTATTACTTTAAATGAAC
1 AAATGAATTTTTAAAGAAGCTAAGCCTGATTTTTAAGGTTTTCTTGATGATTACTTCAAATGAAT
** * *
241162 TTTTAAAGAAATTAAGCCTAATATTTAGGGGTTTATTGATGATAAATTT
66 TTTTAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGATAAATTT
* * *
241211 AAATGAATTTTTAAAGAAGCTAAGCTTGATTTTTTAGGTTTTATTGATGATTACTTCAAATGAAT
1 AAATGAATTTTTAAAGAAGCTAAGCCTGATTTTTAAGGTTTTCTTGATGATTACTTCAAATGAAT
* *
241276 TTTTAAAGAAGCTAAGCCTAATTTTTAGGGGGTTCTTGATGATAAATGT
66 TTTTAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGATAAATTT
* * * *
241325 AAATGGATTTTTAAAGAAGCTAAGCTTGATTTTCAGGGGTTTT-TTGATGATTACTTCAAATGAA
1 AAATGAATTTTTAAAGAAGCTAAGCCTGATTTTTA-AGGTTTTCTTGATGATTACTTCAAATGAA
* *
241389 TTTTTAAAGAAGCTAAGCCTAATTTTTAAGGG-TTCTTAATGAT-AATTGT
65 TTTTTAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGATAAATT-T
* * *
241438 AAATGTATTTTTAAAGAAGCTAAGCCTGATTTTCAAGGGTTTCTTGATGATTACTTCAAATGAAT
1 AAATGAATTTTTAAAGAAGCTAAGCCTGATTTTTAAGGTTTTCTTGATGATTACTTCAAATGAAT
* *
241503 TTTTTAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTCATGAT-AATTAT
66 TTTTAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGATAAATT-T
* *
241552 AAATGACTTTTTGAAGAAG
1 AAATGAATTTTTAAAGAAG
241571 AAAAGTTTTA
Statistics
Matches: 418, Mismatches: 50, Indels: 10
0.87 0.10 0.02
Matches are distributed among these distances:
112 8 0.02
113 192 0.46
114 212 0.51
115 6 0.01
ACGTcount: A:0.34, C:0.08, G:0.17, T:0.41
Consensus pattern (114 bp):
AAATGAATTTTTAAAGAAGCTAAGCCTGATTTTTAAGGTTTTCTTGATGATTACTTCAAATGAAT
TTTTAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGATAAATTT
Found at i:241556 original size:57 final size:57
Alignment explanation
Indices: 240984--241570 Score: 646
Period size: 57 Copynumber: 10.3 Consensus size: 57
240974 TGATGTTTTC
* * * * * *
240984 AAATGAATTTTTAAAGAAACTAAGCCTAATTTTCAAGGGTTTCTTGATTATTACTTC
1 AAATGAATTTTTAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGATTAATTT
* * *
241041 AAATGAATTTTTAAAGAAGTTAAGTCTAATTTTTAGGGGTTTCTTGATGA-TAACTGT
1 AAATGAATTTTTAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGATTAA-TTT
* * * * * * *
241098 AAAT-ATTTTTTACAGAAGATAAGCCTGATTTTTAGGGTTTTCTTGATTATTACTTT
1 AAATGAATTTTTAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGATTAATTT
* ** * * *
241154 AAATGAACTTTTAAAGAAATTAAGCCTAATATTTAGGGGTTTATTGATGATAAATTT
1 AAATGAATTTTTAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGATTAATTT
* * * * * *
241211 AAATGAATTTTTAAAGAAGCTAAGCTTGATTTTTTA-GGTTTTATTGATGATTACTTC
1 AAATGAATTTTTAAAGAAGCTAAGCCT-AATTTTTAGGGGTTTCTTGATGATTAATTT
* * *
241268 AAATGAATTTTTAAAGAAGCTAAGCCTAATTTTTAGGGGGTTCTTGATGATAAATGT
1 AAATGAATTTTTAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGATTAATTT
* * * * * * *
241325 AAATGGATTTTTAAAGAAGCTAAGCTTGATTTTCAGGGGTTTTTTGATGATTACTTC
1 AAATGAATTTTTAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGATTAATTT
* *
241382 AAATGAATTTTTAAAGAAGCTAAGCCTAATTTTTAAGGG-TTCTTAATGA-TAATTGT
1 AAATGAATTTTTAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGATTAATT-T
* * * * * *
241438 AAATGTATTTTTAAAGAAGCTAAGCCTGATTTTCAAGGGTTTCTTGATGATTACTTC
1 AAATGAATTTTTAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGATTAATTT
* *
241495 AAATGAATTTTTTAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTCATGA-TAATTAT
1 AAATGAATTTTTAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGATTAATT-T
* *
241552 AAATGACTTTTTGAAGAAG
1 AAATGAATTTTTAAAGAAG
241571 AAAAGTTTTA
Statistics
Matches: 437, Mismatches: 84, Indels: 18
0.81 0.16 0.03
Matches are distributed among these distances:
55 4 0.01
56 101 0.23
57 322 0.74
58 10 0.02
ACGTcount: A:0.34, C:0.08, G:0.17, T:0.41
Consensus pattern (57 bp):
AAATGAATTTTTAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGATTAATTT
Found at i:241586 original size:227 final size:227
Alignment explanation
Indices: 240984--241586 Score: 827
Period size: 227 Copynumber: 2.7 Consensus size: 227
240974 TGATGTTTTC
* * *
240984 AAATGAATTTTTAAAGAAACTAAGCCTAATTTTCAAGGGTTTCTTGATTATTACTTCAAATGAAT
1 AAATGAATTTTTAAAGAAGCTAAGCCTGATTTTCAAGGGTTTCTTGATGATTACTTCAAATGAAT
* * * *
241049 TTTTAAAGAAGTTAAGTCTAATTTTTAGGGGTTTCTTGATGATAACTGTAAAT-ATTTTTTACAG
66 TTTTAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGATAAATGTAAATGA-TTTTTAAAG
* * * * *
241113 AAGATAAGCCTGATTTTTAGGGTTTTCTTGATTATTACTTTAAATGAACTTTTAAAGAAATTAAG
130 AAGATAAGCTTGATTTTCAGGGTTTTCTTGATGATTACTTCAAATGAACTTTTAAAGAAACTAAG
* *
241178 CCTAATATTTAGGGGTTTATTGATGATAAATTT
195 CCTAATATTTAAGGGTTTATTAATGATAAATTT
* ** * *
241211 AAATGAATTTTTAAAGAAGCTAAGCTTGATTTTTTAGGTTTTATTGATGATTACTTCAAATGAAT
1 AAATGAATTTTTAAAGAAGCTAAGCCTGATTTTCAAGGGTTTCTTGATGATTACTTCAAATGAAT
*
241276 TTTTAAAGAAGCTAAGCCTAATTTTTAGGGGGTTCTTGATGATAAATGTAAATGGATTTTTAAAG
66 TTTTAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGATAAATGTAAAT-GATTTTTAAAG
* * *
241341 AAGCTAAGCTTGATTTTCAGGGGTTTT-TTGATGATTACTTCAAATGAATTTTTAAAGAAGCTAA
130 AAGATAAGCTTGATTTTCA-GGGTTTTCTTGATGATTACTTCAAATGAACTTTTAAAGAAACTAA
* *
241405 GCCTAATTTTTAAGGG-TTCTTAATGAT-AATTGT
194 GCCTAATATTTAAGGGTTTATTAATGATAAATT-T
*
241438 AAATGTATTTTTAAAGAAGCTAAGCCTGATTTTCAAGGGTTTCTTGATGATTACTTCAAATGAAT
1 AAATGAATTTTTAAAGAAGCTAAGCCTGATTTTCAAGGGTTTCTTGATGATTACTTCAAATGAAT
* * * * *
241503 TTTTTAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTCATGATAATTATAAATGACTTTTTGAAG
66 TTTTAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGATAAATGTAAATGA-TTTTTAAAG
* * *
241568 AAGAAAAGTTTTATTTTCA
130 AAGATAAGCTTGATTTTCA
241587 AAGATTTATC
Statistics
Matches: 330, Mismatches: 41, Indels: 10
0.87 0.11 0.03
Matches are distributed among these distances:
226 6 0.02
227 246 0.75
228 70 0.21
229 8 0.02
ACGTcount: A:0.34, C:0.08, G:0.17, T:0.41
Consensus pattern (227 bp):
AAATGAATTTTTAAAGAAGCTAAGCCTGATTTTCAAGGGTTTCTTGATGATTACTTCAAATGAAT
TTTTAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGATAAATGTAAATGATTTTTAAAGA
AGATAAGCTTGATTTTCAGGGTTTTCTTGATGATTACTTCAAATGAACTTTTAAAGAAACTAAGC
CTAATATTTAAGGGTTTATTAATGATAAATTT
Found at i:242597 original size:36 final size:36
Alignment explanation
Indices: 242435--242620 Score: 169
Period size: 37 Copynumber: 5.1 Consensus size: 36
242425 GTATATTTTA
* * *
242435 AGAAATT-ATTGAGTCCTTCTTACGACCATTTCTCT
1 AGAAATTGTTTGAGTCCTTCTTAGGATCATTTCTCT
* * * * * ** *
242470 AAAAATTCATTAGAATACTTCTTAGGATTGTTTTTCT
1 AGAAATT-GTTTGAGTCCTTCTTAGGATCATTTCTCT
* *
242507 AGAAAATTGTTTGAGTCTTTCTTAGGA-CTATTTATCT
1 AG-AAATTGTTTGAGTCCTTCTTAGGATC-ATTTCTCT
* * *
242544 ATAATGTTGTTTGAGTCCTTCTTAGGATCATTTCTAT
1 AGAA-ATTGTTTGAGTCCTTCTTAGGATCATTTCTCT
*
242581 AGAAATTGTTTGAGTCCTTCTTAGGATCATATCTCT
1 AGAAATTGTTTGAGTCCTTCTTAGGATCATTTCTCT
242617 AGAA
1 AGAA
242621 TGTCGTTTAA
Statistics
Matches: 117, Mismatches: 28, Indels: 11
0.75 0.18 0.07
Matches are distributed among these distances:
35 6 0.05
36 35 0.30
37 70 0.60
38 6 0.05
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.44
Consensus pattern (36 bp):
AGAAATTGTTTGAGTCCTTCTTAGGATCATTTCTCT
Found at i:242657 original size:73 final size:73
Alignment explanation
Indices: 242487--242658 Score: 202
Period size: 73 Copynumber: 2.3 Consensus size: 73
242477 CATTAGAATA
* * * * *
242487 CTTCTTAGGATTGTTTTTCTAGAAAATTGTTTGAGTCTTTCTTAGGACTATTTATCTATAATGTT
1 CTTCTTAGGATTGTTTCTCTAG-AAATTGTTTGAGTCCTTCTTAGGACTATATATCTAGAATGTC
* *
242552 GTTTGAGTC
65 GTTTAAGAC
** * *
242561 CTTCTTAGGATCATTTCTATAGAAATTGTTTGAGTCCTTCTTAGGA-TCATATCTCTAGAATGTC
1 CTTCTTAGGATTGTTTCTCTAGAAATTGTTTGAGTCCTTCTTAGGACT-ATATATCTAGAATGTC
242625 GTTTAAGAC
65 GTTTAAGAC
* *
242634 CTTCTTAAGATTGTTTCCCTAGAAA
1 CTTCTTAGGATTGTTTCTCTAGAAA
242659 CCTTTTCAGT
Statistics
Matches: 81, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
72 1 0.01
73 62 0.77
74 18 0.22
ACGTcount: A:0.24, C:0.15, G:0.16, T:0.45
Consensus pattern (73 bp):
CTTCTTAGGATTGTTTCTCTAGAAATTGTTTGAGTCCTTCTTAGGACTATATATCTAGAATGTCG
TTTAAGAC
Found at i:245689 original size:24 final size:24
Alignment explanation
Indices: 245659--245717 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
245649 ATTTTCTATT
245659 TGAATTCTGTTATGATACCTGACC
1 TGAATTCTGTTATGATACCTGACC
* **
245683 TGCATTCTGTTATGATATTTGACC
1 TGAATTCTGTTATGATACCTGACC
*
245707 TGAATTATGTT
1 TGAATTCTGTT
245718 TTTATTTCTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.24, C:0.15, G:0.17, T:0.44
Consensus pattern (24 bp):
TGAATTCTGTTATGATACCTGACC
Found at i:249685 original size:24 final size:24
Alignment explanation
Indices: 249600--249686 Score: 86
Period size: 24 Copynumber: 3.6 Consensus size: 24
249590 ATCTGATTTC
* *
249600 TGTTCTGATTTCCGATCTGAATTA
1 TGTTCTGATTTCTGACCTGAATTA
* *
249624 TGTTCTG-TTACCTGACCTGAATTC
1 TGTTCTGATT-TCTGACCTGAATTA
* * *
249648 TGTTATGATATCTGACCTAAATTA
1 TGTTCTGATTTCTGACCTGAATTA
*
249672 TGTTTTGATTTCTGA
1 TGTTCTGATTTCTGA
249687 TATCTCCGTT
Statistics
Matches: 50, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
23 2 0.04
24 47 0.94
25 1 0.02
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.46
Consensus pattern (24 bp):
TGTTCTGATTTCTGACCTGAATTA
Found at i:251001 original size:2 final size:2
Alignment explanation
Indices: 250994--251029 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
250984 GCTATAGATA
250994 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
251030 CATTACACAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:253697 original size:25 final size:25
Alignment explanation
Indices: 253663--253738 Score: 107
Period size: 25 Copynumber: 3.0 Consensus size: 25
253653 TAGAAATATG
253663 TGCACTCGAAAGTGCCTCATAGAAT
1 TGCACTCGAAAGTGCCTCATAGAAT
*
253688 TGCACTCGAAAGTGCCTCATAGAGT
1 TGCACTCGAAAGTGCCTCATAGAAT
* * * *
253713 TTCACTTGAAAGTGACTCGTAGAAT
1 TGCACTCGAAAGTGCCTCATAGAAT
253738 T
1 T
253739 ACACCATAGG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 45 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (25 bp):
TGCACTCGAAAGTGCCTCATAGAAT
Found at i:254505 original size:8 final size:8
Alignment explanation
Indices: 254492--254524 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
254482 ACCTAACTTC
254492 TCACAATT
1 TCACAATT
254500 TCACAATT
1 TCACAATT
254508 TCACAATT
1 TCACAATT
254516 TCACAATT
1 TCACAATT
254524 T
1 T
254525 ACCCAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.36, C:0.24, G:0.00, T:0.39
Consensus pattern (8 bp):
TCACAATT
Found at i:259191 original size:21 final size:21
Alignment explanation
Indices: 259162--259202 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
259152 AAGGGAGAAG
* *
259162 AAAATGATATAAAGTAAAAGT
1 AAAAAGATAGAAAGTAAAAGT
*
259183 AAAAAGATAGAAAGTGAAAG
1 AAAAAGATAGAAAGTAAAAG
259203 GTGAAAACGT
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:0.63, C:0.00, G:0.20, T:0.17
Consensus pattern (21 bp):
AAAAAGATAGAAAGTAAAAGT
Found at i:267387 original size:20 final size:20
Alignment explanation
Indices: 267350--267388 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
267340 AGATTGAGTG
* * *
267350 GATTTTGATGTTGTTTGCAT
1 GATTTTAATGATGATTGCAT
267370 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
267389 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:0.05, G:0.23, T:0.49
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAT
Found at i:282376 original size:18 final size:20
Alignment explanation
Indices: 282350--282392 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
282340 TAGGAATGAG
282350 TGAA-AAAAAAA-AGACCTT
1 TGAACAAAAAAATAGACCTT
282368 TGAACAAAAAAATAGACCTT
1 TGAACAAAAAAATAGACCTT
282388 TGAAC
1 TGAAC
282393 TATGTAATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.17
19 7 0.30
20 12 0.52
ACGTcount: A:0.56, C:0.14, G:0.12, T:0.19
Consensus pattern (20 bp):
TGAACAAAAAAATAGACCTT
Found at i:286717 original size:24 final size:22
Alignment explanation
Indices: 286672--286717 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
286662 GAAAATATTA
*
286672 CTTTATGCATCAGTAGCAGATC
1 CTTTATGCATCAGCAGCAGATC
*
286694 CTTTGATGCATTAGCAGACAGATC
1 CTTT-ATGCATCAGCAG-CAGATC
286718 AGACTGCCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 10 0.50
24 6 0.30
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (22 bp):
CTTTATGCATCAGCAGCAGATC
Found at i:295526 original size:16 final size:16
Alignment explanation
Indices: 295505--295555 Score: 84
Period size: 16 Copynumber: 3.2 Consensus size: 16
295495 ATTCATACAG
295505 AGCCTCTGAATCATTC
1 AGCCTCTGAATCATTC
295521 AGCCTCTGAATCATTC
1 AGCCTCTGAATCATTC
* *
295537 AGCATTTGAATCATTC
1 AGCCTCTGAATCATTC
295553 AGC
1 AGC
295556 GCTTAATCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.31
Consensus pattern (16 bp):
AGCCTCTGAATCATTC
Found at i:297605 original size:31 final size:31
Alignment explanation
Indices: 297569--297628 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
297559 AACTTAAAAG
* *
297569 AGTTTTACAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTAAAATTTAAATAATTTT
297600 AGTTTTACAATACTAAAATTTAAATAATT
1 AGTTTTACAATACTAAAATTTAAATAATT
297629 CATACAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (31 bp):
AGTTTTACAATACTAAAATTTAAATAATTTT
Found at i:298282 original size:20 final size:20
Alignment explanation
Indices: 298234--298295 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 20
298224 AACTTAAATC
*
298234 AAAATAATTAAAATAA-ATAT
1 AAAATAATT-TAATAATATAT
298254 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAATATAT
298272 AAAATAATTT-AT-ATGATAT
1 AAAATAATTTAATAAT-ATAT
298291 AAAAT
1 AAAAT
298296 TAAATATCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 5 0.14
18 13 0.35
19 11 0.30
20 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAATAATTTAATAATATAT
Found at i:298375 original size:20 final size:20
Alignment explanation
Indices: 298287--298378 Score: 59
Period size: 21 Copynumber: 4.6 Consensus size: 20
298277 AATTTATATG
*
298287 ATATAAAATTAAATATCTATA
1 ATATAATATT-AATATCTATA
298308 ATATAATATTAA-A---A-A
1 ATATAATATTAATATCTATA
* * *
298323 AAATAATATTTAATTTATTTAAA
1 ATATAATA-TTAA--TATCTATA
*
298346 AAATTAATATTAATATCTATA
1 ATA-TAATATTAATATCTATA
298367 ATATAATATTAA
1 ATATAATATTAA
298379 AAATTTAATA
Statistics
Matches: 57, Mismatches: 5, Indels: 19
0.70 0.06 0.23
Matches are distributed among these distances:
15 8 0.14
16 5 0.09
19 2 0.04
20 11 0.19
21 17 0.30
22 1 0.02
23 8 0.14
24 5 0.09
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
ATATAATATTAATATCTATA
Found at i:298380 original size:34 final size:34
Alignment explanation
Indices: 298298--298390 Score: 105
Period size: 34 Copynumber: 3.0 Consensus size: 34
298288 TATAAAATTA
298298 AATATCTATAATATAATATT-AAAAA--AA-A-T
1 AATATCTATAATATAATATTAAAAAATTAATATT
*
298327 AATAT-T-TAAT-TTAT-TTAAAAAATTAATATT
1 AATATCTATAATATAATATTAAAAAATTAATATT
*
298357 AATATCTATAATATAATATTAAAAATTTAATATT
1 AATATCTATAATATAATATTAAAAAATTAATATT
298391 TAATTTATTT
Statistics
Matches: 52, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
25 2 0.04
26 8 0.15
27 4 0.08
28 3 0.06
29 6 0.12
30 6 0.12
31 1 0.02
32 4 0.08
33 3 0.06
34 15 0.29
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (34 bp):
AATATCTATAATATAATATTAAAAAATTAATATT
Found at i:298387 original size:14 final size:14
Alignment explanation
Indices: 298370--298418 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
298360 ATCTATAATA
298370 TAATATTAAAAATT
1 TAATATTAAAAATT
*
298384 TAATATT--TAATT
1 TAATATTAAAAATT
*
298396 T-AT-TTAAAAAAT
1 TAATATTAAAAATT
298408 TAATATTAAAA
1 TAATATTAAAA
298419 TTAAAAATCA
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
10 2 0.07
11 2 0.07
12 9 0.32
13 2 0.07
14 13 0.46
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TAATATTAAAAATT
Found at i:298403 original size:58 final size:59
Alignment explanation
Indices: 298298--298416 Score: 213
Period size: 58 Copynumber: 2.0 Consensus size: 59
298288 TATAAAATTA
298298 AATATCTATAATATAATATTAAAAAAAATAATATTTAATTTATTTAAAAAATTAATATT
1 AATATCTATAATATAATATTAAAAAAAATAATATTTAATTTATTTAAAAAATTAATATT
**
298357 AATATCTATAATATAATATT-AAAAATTTAATATTTAATTTATTTAAAAAATTAATATT
1 AATATCTATAATATAATATTAAAAAAAATAATATTTAATTTATTTAAAAAATTAATATT
298415 AA
1 AA
298417 AATTAAAAAT
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
58 38 0.66
59 20 0.34
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (59 bp):
AATATCTATAATATAATATTAAAAAAAATAATATTTAATTTATTTAAAAAATTAATATT
Found at i:298420 original size:12 final size:12
Alignment explanation
Indices: 298348--298462 Score: 53
Period size: 12 Copynumber: 9.5 Consensus size: 12
298338 TATTTAAAAA
*
298348 ATTAATATTAAT
1 ATTAAAATTAAT
*
298360 ATCTATAATATAAT
1 AT-TAAAAT-TAAT
298374 ATTAAAAATTTAAT
1 ATT-AAAA-TTAAT
* *
298388 ATT-TAATTTAT
1 ATTAAAATTAAT
298399 -TTAAAAAATTAAT
1 ATT--AAAATTAAT
*
298412 ATTAAAATTAAA
1 ATTAAAATTAAT
* *
298424 AATCAAATATAAT
1 ATTAAAAT-TAAT
*
298437 A-TAATA-TAAT
1 ATTAAAATTAAT
298447 A-TAAAATTAA-
1 ATTAAAATTAAT
298457 ATTAAA
1 ATTAAA
298463 TATAAAACCT
Statistics
Matches: 78, Mismatches: 14, Indels: 23
0.68 0.12 0.20
Matches are distributed among these distances:
10 12 0.15
11 11 0.14
12 21 0.27
13 15 0.19
14 18 0.23
15 1 0.01
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (12 bp):
ATTAAAATTAAT
Found at i:299013 original size:18 final size:17
Alignment explanation
Indices: 298977--299027 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 17
298967 TTAATAATTT
298977 AATAATAACATGCTTAAAA
1 AATAATAACAT--TTAAAA
298996 AATAATTAACATTT-AAA
1 AATAA-TAACATTTAAAA
*
299013 AATAAATAAAATTTA
1 AAT-AATAACATTTA
299028 TAATTTACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 13 0.46
18 4 0.14
19 5 0.18
20 6 0.21
ACGTcount: A:0.61, C:0.06, G:0.02, T:0.31
Consensus pattern (17 bp):
AATAATAACATTTAAAA
Found at i:299015 original size:17 final size:17
Alignment explanation
Indices: 298993--299027 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
298983 AACATGCTTA
* *
298993 AAAAATAATTAACATTT
1 AAAAATAAATAAAATTT
299010 AAAAATAAATAAAATTT
1 AAAAATAAATAAAATTT
299027 A
1 A
299028 TAATTTACAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAAATAAATAAAATTT
Found at i:300556 original size:24 final size:24
Alignment explanation
Indices: 300524--300619 Score: 97
Period size: 23 Copynumber: 4.1 Consensus size: 24
300514 TGGTTATTGG
**
300524 TAAAATTATTTCAAATTTTAAATA
1 TAAAATTATTTCAAAAATTAAATA
300548 TAAAATTA-TTCAAAAATTAAATA
1 TAAAATTATTTCAAAAATTAAATA
* * *
300571 TAAAAATATTT-AAAAAATAAAAA
1 TAAAATTATTTCAAAAATTAAATA
* * **
300594 TTAAATTACTAAAAAAATTAAATA
1 TAAAATTATTTCAAAAATTAAATA
300618 TA
1 TA
300620 CATATTAAAA
Statistics
Matches: 58, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
23 37 0.64
24 21 0.36
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (24 bp):
TAAAATTATTTCAAAAATTAAATA
Found at i:300628 original size:22 final size:22
Alignment explanation
Indices: 300541--300630 Score: 67
Period size: 23 Copynumber: 3.9 Consensus size: 22
300531 ATTTCAAATT
*
300541 TTAAATATAAA-ATTATTCAAAAA
1 TTAAATATAAATATTA--AAAAAA
*
300564 TTAAATATAAAAATATTTAAAAAA
1 TTAAATAT--AAATATTAAAAAAA
* *
300588 -TAAAAATTAAATTACTAAAAAAA
1 TTAAATA-TAAA-TATTAAAAAAA
*
300611 TTAAATATACATATTAAAAA
1 TTAAATATAAATATTAAAAA
300631 TACTAAAACT
Statistics
Matches: 53, Mismatches: 8, Indels: 13
0.72 0.11 0.18
Matches are distributed among these distances:
22 11 0.21
23 25 0.47
24 11 0.21
25 3 0.06
26 3 0.06
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.32
Consensus pattern (22 bp):
TTAAATATAAATATTAAAAAAA
Found at i:300843 original size:25 final size:25
Alignment explanation
Indices: 300815--300867 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
300805 TAATCGAGAG
*
300815 TTACAAAATTTAAATTAGTTGATAC
1 TTACAAAATTTAAATTAGTTGAAAC
300840 TTACAAAATTTAAATTAGTTGAAAC
1 TTACAAAATTTAAATTAGTTGAAAC
300865 TTA
1 TTA
300868 TTATGTTTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.40
Consensus pattern (25 bp):
TTACAAAATTTAAATTAGTTGAAAC
Found at i:302666 original size:21 final size:21
Alignment explanation
Indices: 302641--302681 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
302631 CACTCGTCAC
*
302641 CGTGAATTGCCACGTCAGCAT
1 CGTGAAGTGCCACGTCAGCAT
**
302662 CGTGAAGTGTTACGTCAGCA
1 CGTGAAGTGCCACGTCAGCA
302682 CCTTAATGAT
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:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (21 bp):
CGTGAAGTGCCACGTCAGCAT
Found at i:304131 original size:14 final size:14
Alignment explanation
Indices: 304112--304150 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
304102 AAAAGATTTA
*
304112 AAATTAATGAAAAT
1 AAATTAATAAAAAT
304126 AAATTAATAAAAAT
1 AAATTAATAAAAAT
*
304140 AAATAAATAAA
1 AAATTAATAAA
304151 TATCAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (14 bp):
AAATTAATAAAAAT
Found at i:304145 original size:18 final size:19
Alignment explanation
Indices: 304122--304186 Score: 62
Period size: 18 Copynumber: 3.4 Consensus size: 19
304112 AAATTAATGA
304122 AAATAAATTAATA-AAAAT
1 AAATAAATTAATAGAAAAT
* **
304140 AAATAAATAAATATCAAAT
1 AAATAAATTAATAGAAAAT
304159 AAA-AAATAATAATGAGAAAAT
1 AAATAAAT--TAAT-AGAAAAT
304180 AAATAAA
1 AAATAAA
304187 GTAGAAGAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
18 16 0.43
19 7 0.19
20 3 0.08
21 8 0.22
22 3 0.08
ACGTcount: A:0.72, C:0.02, G:0.03, T:0.23
Consensus pattern (19 bp):
AAATAAATTAATAGAAAAT
Found at i:310078 original size:21 final size:21
Alignment explanation
Indices: 310032--310080 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
310022 GAAGGAATCG
* *
310032 ATCATTTTCCCTGAGGGGTCG
1 ATCATTTTCCCTGAGGGATCA
* *
310053 TTCATTTTCCCTGAGTGATCA
1 ATCATTTTCCCTGAGGGATCA
310074 ATCATTT
1 ATCATTT
310081 ATTAAATGGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.41
Consensus pattern (21 bp):
ATCATTTTCCCTGAGGGATCA
Found at i:314970 original size:17 final size:17
Alignment explanation
Indices: 314948--314987 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
314938 TTGGATGCCT
314948 AGCTCGCCACTCATTGG
1 AGCTCGCCACTCATTGG
**
314965 AGCTCGTTACTCATTGG
1 AGCTCGCCACTCATTGG
314982 AGCTCG
1 AGCTCG
314988 TTAATGGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.17, C:0.30, G:0.25, T:0.28
Consensus pattern (17 bp):
AGCTCGCCACTCATTGG
Found at i:314988 original size:17 final size:17
Alignment explanation
Indices: 314956--314990 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
314946 CTAGCTCGCC
314956 ACTCATTGGAGCTCGTT
1 ACTCATTGGAGCTCGTT
314973 ACTCATTGGAGCTCGTT
1 ACTCATTGGAGCTCGTT
314990 A
1 A
314991 ATGGATTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.34
Consensus pattern (17 bp):
ACTCATTGGAGCTCGTT
Found at i:319759 original size:23 final size:23
Alignment explanation
Indices: 319729--319777 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
319719 AATTAACGAG
319729 TTCAATTCAGACATGCCTTGGCA
1 TTCAATTCAGACATGCCTTGGCA
319752 TTCAATTCAGACATGCCTTGGCA
1 TTCAATTCAGACATGCCTTGGCA
319775 TTC
1 TTC
319778 TTCATGGTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33
Consensus pattern (23 bp):
TTCAATTCAGACATGCCTTGGCA
Found at i:323510 original size:35 final size:35
Alignment explanation
Indices: 323464--323538 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
323454 ATAATAAAAA
* * *
323464 AAATATCCAAGGGTATTAATGGGCTTTAACACTCT
1 AAATATACAAGGGTATTAATGGACTTTAACACTCC
323499 AAATATACAAGGGTATTAATGGACTTTAACACTCC
1 AAATATACAAGGGTATTAATGGACTTTAACACTCC
323534 AAATA
1 AAATA
323539 GCCATCATAC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (35 bp):
AAATATACAAGGGTATTAATGGACTTTAACACTCC
Found at i:324171 original size:21 final size:21
Alignment explanation
Indices: 324145--324191 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
324135 TGATTTGTTG
324145 CAAAGCCAAGCAACTCTATTA
1 CAAAGCCAAGCAACTCTATTA
*
324166 CAAAGCCAAGCATCTCTATTA
1 CAAAGCCAAGCAACTCTATTA
324187 CAAAG
1 CAAAG
324192 ACATAGTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.43, C:0.28, G:0.11, T:0.19
Consensus pattern (21 bp):
CAAAGCCAAGCAACTCTATTA
Found at i:341190 original size:32 final size:31
Alignment explanation
Indices: 341145--341227 Score: 80
Period size: 31 Copynumber: 2.6 Consensus size: 31
341135 AGATTTTGGT
*
341145 GCCGTGAGG-CCTACCTAAGAACACATCTTAGG
1 GCCGT-AGGACCTACCTAAGAACA-ATCTCAGG
* *
341177 GCCGTAGGACCTA-CTCGAGAATAATCTCAGG
1 GCCGTAGGACCTACCT-AAGAACAATCTCAGG
* *
341208 GCCGCAGAACCTACCTAAGA
1 GCCGTAGGACCTACCTAAGA
341228 GTCACATTAG
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
31 26 0.62
32 16 0.38
ACGTcount: A:0.30, C:0.29, G:0.24, T:0.17
Consensus pattern (31 bp):
GCCGTAGGACCTACCTAAGAACAATCTCAGG
Found at i:356410 original size:32 final size:31
Alignment explanation
Indices: 356374--356449 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
356364 GGGGCCATGA
*
356374 GGCCTACCTAAGAACACATATTAGGGCCGTAG
1 GGCCTACCTAAGAACA-ATATCAGGGCCGTAG
** * *
356406 GGCCTACCCGAGAATAATCTCAGGGCCGTAG
1 GGCCTACCTAAGAACAATATCAGGGCCGTAG
*
356437 AGCCTACCTAAGA
1 GGCCTACCTAAGA
356450 GTCACATTAG
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.30, C:0.28, G:0.25, T:0.17
Consensus pattern (31 bp):
GGCCTACCTAAGAACAATATCAGGGCCGTAG
Found at i:365451 original size:16 final size:15
Alignment explanation
Indices: 365426--365455 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
365416 GTGTATAAGG
365426 AATAAATAAAGGAAT
1 AATAAATAAAGGAAT
365441 AATAGAATAAAGGAA
1 AATA-AATAAAGGAA
365456 GGACATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.17
Consensus pattern (15 bp):
AATAAATAAAGGAAT
Found at i:365457 original size:20 final size:20
Alignment explanation
Indices: 365434--365476 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
365424 GGAATAAATA
365434 AAGGA-ATAATAGAATAAAGG
1 AAGGACATAATA-AATAAAGG
* *
365454 AAGGACATATTAAGTAAAGG
1 AAGGACATAATAAATAAAGG
365474 AAG
1 AAG
365477 TAGCATGAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.56, C:0.02, G:0.26, T:0.16
Consensus pattern (20 bp):
AAGGACATAATAAATAAAGG
Found at i:367536 original size:32 final size:34
Alignment explanation
Indices: 367467--367541 Score: 79
Period size: 32 Copynumber: 2.3 Consensus size: 34
367457 ATGTACGTGA
*
367467 TATAT-ATATATGTTTTGTGATATGAATTATATG
1 TATATGATATATGTTGTGTGATATGAATTATATG
*
367500 -ATATGATATATG-TGTGTGTTAATG-ATTAT-TG
1 TATATGATATATGTTGTGTGAT-ATGAATTATATG
*
367531 TATATGTTATA
1 TATATGATATA
367542 AGATATATGA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
31 2 0.06
32 24 0.67
33 10 0.28
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (34 bp):
TATATGATATATGTTGTGTGATATGAATTATATG
Found at i:370370 original size:20 final size:20
Alignment explanation
Indices: 370341--370378 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
370331 TTTCAAAGGA
370341 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
370361 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
370379 GAATAAATTG
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:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:370495 original size:19 final size:19
Alignment explanation
Indices: 370471--370522 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
370461 ATTGCATTTT
370471 ATGCATCGATGCACACACC
1 ATGCATCGATGCACACACC
370490 ATGCATCGATGCACACACC
1 ATGCATCGATGCACACACC
370509 ATGCATCGATGCAC
1 ATGCATCGATGCAC
370523 TTAGGCTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.31, C:0.35, G:0.17, T:0.17
Consensus pattern (19 bp):
ATGCATCGATGCACACACC
Found at i:370496 original size:84 final size:83
Alignment explanation
Indices: 370406--370569 Score: 240
Period size: 83 Copynumber: 2.0 Consensus size: 83
370396 AATGCAGTTA
* * * * *
370406 ATGCATCGATGCACTCTCCATGCATCGATGCACTCAGGTTTTAATGAAAACATCG-ATTGCATTT
1 ATGCATCGATGCACACACCATGCATCGATGCACTCAGG-CTTAATCAAAACAT-GAAATGCATTT
370470 TATGCATCGATGCACACACC
64 TATGCATCGATGCACACACC
* *
370490 ATGCATCGATGCACACACCATGCATCGATGCACTTAGGCTTATTCAAAACATGAAATGCATTTTA
1 ATGCATCGATGCACACACCATGCATCGATGCACTCAGGCTTAATCAAAACATGAAATGCATTTTA
370555 TGCATCGATGCACAC
66 TGCATCGATGCACAC
370570 TTAGTGTACC
Statistics
Matches: 72, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
82 1 0.01
83 36 0.50
84 35 0.49
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.27
Consensus pattern (83 bp):
ATGCATCGATGCACACACCATGCATCGATGCACTCAGGCTTAATCAAAACATGAAATGCATTTTA
TGCATCGATGCACACACC
Found at i:376444 original size:23 final size:23
Alignment explanation
Indices: 376367--376448 Score: 64
Period size: 23 Copynumber: 3.6 Consensus size: 23
376357 CCACTGAACA
*
376367 GTGCATCGATGCAGC-CCTTTGTAT
1 GTGCATCGATGCA-CTCC-TTGAAT
* *
376391 GTGCATCGATACA-T-CATGAA-
1 GTGCATCGATGCACTCCTTGAAT
* *
376411 GATGAACCGATGCACTCCTTGAAT
1 G-TGCATCGATGCACTCCTTGAAT
376435 GTGCATCGATGCAC
1 GTGCATCGATGCAC
376449 AAAGTCATGC
Statistics
Matches: 44, Mismatches: 9, Indels: 11
0.69 0.14 0.17
Matches are distributed among these distances:
20 1 0.02
21 12 0.27
22 2 0.05
23 16 0.36
24 13 0.30
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (23 bp):
GTGCATCGATGCACTCCTTGAAT
Found at i:379090 original size:20 final size:20
Alignment explanation
Indices: 379061--379098 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
379051 TTTCAAAGGA
379061 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
379081 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
379099 GAATAAATTG
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:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:379150 original size:19 final size:19
Alignment explanation
Indices: 379126--379177 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
379116 AATGCAGTTT
379126 ATGCATCGATGCACTCTCC
1 ATGCATCGATGCACTCTCC
379145 ATGCATCGATGCACTCTCC
1 ATGCATCGATGCACTCTCC
379164 ATGCATCGATGCAC
1 ATGCATCGATGCAC
379178 GTAGGTTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.23, C:0.35, G:0.17, T:0.25
Consensus pattern (19 bp):
ATGCATCGATGCACTCTCC
Found at i:384034 original size:20 final size:21
Alignment explanation
Indices: 384009--384048 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
383999 CTTTAGATCA
384009 AGGGATCT-ATCATTT-TTTAT
1 AGGGAT-TGATCATTTCTTTAT
384029 AGGGATTGATCATTTCTTTA
1 AGGGATTGATCATTTCTTTA
384049 AATGAATCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 1 0.06
20 13 0.72
21 4 0.22
ACGTcount: A:0.25, C:0.10, G:0.17, T:0.47
Consensus pattern (21 bp):
AGGGATTGATCATTTCTTTAT
Found at i:389953 original size:37 final size:37
Alignment explanation
Indices: 389906--390042 Score: 238
Period size: 37 Copynumber: 3.7 Consensus size: 37
389896 AAACACTAAA
* * *
389906 TAAAGATAGATTTCATTCGAGTGTAAATACTAACTTT
1 TAAAGATAGATTTCATTTGAGTGTAAATACTAAATAT
*
389943 TAAAGATAGATTGCATTTGAGTGTAAATACTAAATAT
1 TAAAGATAGATTTCATTTGAGTGTAAATACTAAATAT
389980 TAAAGATAGATTTCATTTGAGTGTAAATACTAAATAT
1 TAAAGATAGATTTCATTTGAGTGTAAATACTAAATAT
390017 TAAAGATAGATTTCATTTGAGTGTAA
1 TAAAGATAGATTTCATTTGAGTGTAA
390043 TTGATCGTGA
Statistics
Matches: 95, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 95 1.00
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (37 bp):
TAAAGATAGATTTCATTTGAGTGTAAATACTAAATAT
Found at i:392982 original size:37 final size:37
Alignment explanation
Indices: 392929--393033 Score: 140
Period size: 37 Copynumber: 2.8 Consensus size: 37
392919 CCTTTTCGTC
392929 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * * *
392966 TTGCTAGGATTCAAACTCCTAAAAATATGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* *
393003 CTACTATGATAT-AAACTCCTAAAGATAGGAT
1 CTACTAGGAT-TCAAACTCCTAAAAATAGGAT
393034 CCACAAGCAT
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
37 57 0.98
38 1 0.02
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:393439 original size:6 final size:6
Alignment explanation
Indices: 393430--393475 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
393420 TAACCCTTAT
* *
393430 TATTTA TATTTA TATGTA TATATA TATTTA -A-TTA TATTT- TATTTA
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
393475 T
1 T
393476 TTATTTATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
4 3 0.09
5 7 0.21
6 24 0.71
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (6 bp):
TATTTA
Found at i:393465 original size:12 final size:12
Alignment explanation
Indices: 393426--393494 Score: 63
Period size: 12 Copynumber: 5.8 Consensus size: 12
393416 AATTTAACCC
393426 TTAT-TATTTAT
1 TTATATATTTAT
*
393437 ATT-TATATGTAT
1 -TTATATATTTAT
* *
393449 ATATATATTTAA
1 TTATATATTTAT
393461 TTATAT-TTTAT
1 TTATATATTTAT
*
393472 TTATTTATTTAT
1 TTATATATTTAT
393484 TTATCATATTT
1 TTAT-ATATTT
393495 TTTTCATTTT
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
11 11 0.24
12 29 0.64
13 5 0.11
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (12 bp):
TTATATATTTAT
Found at i:393542 original size:2 final size:2
Alignment explanation
Indices: 393535--393563 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
393525 ATTTTCCTAT
393535 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
393564 TATTTTTTAT
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:393762 original size:21 final size:21
Alignment explanation
Indices: 393738--393794 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
393728 ACTATTTAGT
393738 ATTTTATTATATTATACATAC
1 ATTTTATTATATTATACATAC
* * *
393759 ATTTT-TATATTTTATATATAT
1 ATTTTAT-TATATTATACATAC
* *
393780 TTTTTATTTTATTAT
1 ATTTTATTATATTAT
393795 TTTATTTATA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
20 1 0.04
21 26 0.93
22 1 0.04
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.65
Consensus pattern (21 bp):
ATTTTATTATATTATACATAC
Found at i:393768 original size:19 final size:19
Alignment explanation
Indices: 393744--393787 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
393734 TAGTATTTTA
393744 TTATATTATACATACATTT
1 TTATATTATACATACATTT
* * *
393763 TTATATTTTATATATATTT
1 TTATATTATACATACATTT
393782 TT-TATT
1 TTATATT
393788 TTATTATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.64
Consensus pattern (19 bp):
TTATATTATACATACATTT
Found at i:393788 original size:26 final size:30
Alignment explanation
Indices: 393732--393825 Score: 81
Period size: 29 Copynumber: 3.3 Consensus size: 30
393722 ATTGTTACTA
* * ** **
393732 TTTAGTATTTTATTATATTATACATACATT
1 TTTATTATTTTATTATACTATTTATTTATT
393762 TTTA-TATTTTA-TATA-TATTT-TTTA-T
1 TTTATTATTTTATTATACTATTTATTTATT
393787 TTTATTATTTTATTTATACTATTTATTTATT
1 TTTATTATTTTA-TTATACTATTTATTTATT
*
393818 TTCATTAT
1 TTTATTAT
393826 GTTTTTAGTT
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
25 5 0.09
26 9 0.17
27 3 0.06
28 8 0.15
29 12 0.23
30 8 0.15
31 8 0.15
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (30 bp):
TTTATTATTTTATTATACTATTTATTTATT
Found at i:393811 original size:13 final size:14
Alignment explanation
Indices: 393766--393816 Score: 54
Period size: 13 Copynumber: 3.9 Consensus size: 14
393756 TACATTTTTA
*
393766 TATTTTATATATA-
1 TATTTTATTTATAC
* *
393779 TTTTTTATTT-TAT
1 TATTTTATTTATAC
393792 TATTTTATTTATAC
1 TATTTTATTTATAC
393806 TA-TTTATTTAT
1 TATTTTATTTAT
393817 TTTCATTATG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
12 2 0.06
13 26 0.81
14 4 0.12
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (14 bp):
TATTTTATTTATAC
Found at i:393831 original size:47 final size:47
Alignment explanation
Indices: 393737--393832 Score: 108
Period size: 47 Copynumber: 2.0 Consensus size: 47
393727 TACTATTTAG
*
393737 TATTTTATTATATTATACATACATTTTTATATTTTATATATATTTTT
1 TATTTTATTATATTATACATACATTTTTATATTTTATATATAGTTTT
* **
393784 TATTTTATTATTTTATTTATACTATTTATT-TATTTTCAT-TAT-GTTTT
1 TATTTTATTATATTATACATAC-ATTT-TTATATTTT-ATATATAGTTTT
393831 TA
1 TA
393833 GTTTCTTTGC
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
47 25 0.60
48 13 0.31
49 4 0.10
ACGTcount: A:0.28, C:0.04, G:0.01, T:0.67
Consensus pattern (47 bp):
TATTTTATTATATTATACATACATTTTTATATTTTATATATAGTTTT
Found at i:395125 original size:19 final size:19
Alignment explanation
Indices: 395101--395137 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
395091 ACCTTACTAA
395101 CTCTTTTCATTTT-TTTCCT
1 CTCTTTT-ATTTTATTTCCT
395120 CTCTTTTATTTTATTTCC
1 CTCTTTTATTTTATTTCC
395138 ATAATCTGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (19 bp):
CTCTTTTATTTTATTTCCT
Found at i:398535 original size:15 final size:14
Alignment explanation
Indices: 398512--398565 Score: 63
Period size: 14 Copynumber: 3.6 Consensus size: 14
398502 ATTCAATCAG
* *
398512 AACAAAAAGGCAAA
1 AACAAAAAAGAAAA
398526 AACAAAAAAGAAAA
1 AACAAAAAAGAAAA
398540 GAAGCAAAAAAGAAGAA
1 -AA-CAAAAAAGAA-AA
398557 AACAAAAAA
1 AACAAAAAA
398566 AAGAACAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
14 12 0.34
15 9 0.26
16 12 0.34
17 2 0.06
ACGTcount: A:0.78, C:0.09, G:0.13, T:0.00
Consensus pattern (14 bp):
AACAAAAAAGAAAA
Found at i:398547 original size:16 final size:15
Alignment explanation
Indices: 398524--398570 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
398514 CAAAAAGGCA
398524 AAAACAAAAAAGAA-
1 AAAACAAAAAAGAAG
398538 AAGAAGCAAAAAAGAAG
1 AA-AA-CAAAAAAGAAG
398555 AAAACAAAAAA-AAG
1 AAAACAAAAAAGAAG
398569 AA
1 AA
398571 CAAAAATCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
14 7 0.23
15 9 0.30
16 12 0.40
17 2 0.07
ACGTcount: A:0.81, C:0.06, G:0.13, T:0.00
Consensus pattern (15 bp):
AAAACAAAAAAGAAG
Found at i:398576 original size:18 final size:18
Alignment explanation
Indices: 398545--398583 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
398535 GAAAAGAAGC
*
398545 AAAAAAGAAGAAAA-CAA
1 AAAAAAGAAAAAAATCAA
398562 AAAAAAGAACAAAAATCAA
1 AAAAAAGAA-AAAAATCAA
398581 AAA
1 AAA
398584 GAAAAAGGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 9 0.47
18 4 0.21
19 6 0.32
ACGTcount: A:0.82, C:0.08, G:0.08, T:0.03
Consensus pattern (18 bp):
AAAAAAGAAAAAAATCAA
Found at i:399440 original size:24 final size:21
Alignment explanation
Indices: 399412--399471 Score: 57
Period size: 24 Copynumber: 2.7 Consensus size: 21
399402 GAAAGAGAAT
399412 ATTTTCAAAACTTTTGATTAAAC
1 ATTTTCAAAACTTTT-ATT-AAC
* * *
399435 ATTTTTCGAAACTCTTTATTGAT
1 A-TTTTCAAAACT-TTTATTAAC
399458 ATTTTCAAAACTTT
1 ATTTTCAAAACTTT
399472 GAAAATAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
21 2 0.06
22 10 0.32
23 3 0.10
24 13 0.42
25 3 0.10
ACGTcount: A:0.33, C:0.13, G:0.05, T:0.48
Consensus pattern (21 bp):
ATTTTCAAAACTTTTATTAAC
Found at i:399672 original size:18 final size:18
Alignment explanation
Indices: 399637--399672 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
399627 TTAACATCAA
**
399637 ATATTGGGGCATTTTTTG
1 ATATTGGGGCATCATTTG
399655 ATATTGGGGCATCATTTG
1 ATATTGGGGCATCATTTG
399673 GGGATTCAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.08, G:0.28, T:0.44
Consensus pattern (18 bp):
ATATTGGGGCATCATTTG
Found at i:401671 original size:106 final size:106
Alignment explanation
Indices: 400197--401670 Score: 2295
Period size: 106 Copynumber: 13.9 Consensus size: 106
400187 CGAGAACACA
* *
400197 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
*
400262 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * **
400303 CAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAACAAACAACTACTTAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* * *
400368 ATTTCAACTTAACGACGAAGGATATTGGACTCTAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * * * * *
400409 CAAGTTCAACTTCACGACAAAGGGACCGCTGATTGTCAATAAACAATTTCCTAATATCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
*
400474 ATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * *
400515 CAAGTTCAACTTCATGACGAAGGGATCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* *
400580 ATTTCAACTTCACAACGAAGGATACTGGACTCCAGACAACA
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* *
400621 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAACTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* * *
400686 ATTTCAACTTCACAAGGAAGGCTATTGGACTCCAGACAACA
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
*
400727 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAACTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* *
400792 ATTTTAACTTCACAACGAAGGATATTGGACTCAAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * * *
400833 CAAGTTCAACTTCACGAAGAAGGGATCGCTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
**
400898 ATTTCAACTTCACGGCGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
400939 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* *
401004 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAATG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* *
401045 CAAGTT-AACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
**
401109 ATTTCAACTTCACGGCGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * *
401150 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTTCGGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* * * *
401215 ATTTCAACTTCACAATGAAGGATTTTGGACTCTAGACAATG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * *
401256 CAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTTAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
*
401321 ATTTTAACTTCACAACGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
401362 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* * *
401427 ATTTTAACTTCACAGCGAAGGATATTGGACTCGAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * **
401468 CAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTTGGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* * *
401533 ATTTCAACTTCACAACAAAGGATATTGGACTCGAGACAACA
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * * *
401574 CAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAATTTCCCGATTCCAGAGCC
1 CAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCC
* * *
401638 AATTTTAACTTCACGACGGAGGATATTGGACTC
65 AATTTCAACTTCACAACGAAGGATATTGGACTC
401671 GGAACAATGC
Statistics
Matches: 1257, Mismatches: 109, Indels: 4
0.92 0.08 0.00
Matches are distributed among these distances:
105 101 0.08
106 1156 0.92
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.23
Consensus pattern (106 bp):
CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
Found at i:402473 original size:37 final size:37
Alignment explanation
Indices: 402420--402516 Score: 149
Period size: 37 Copynumber: 2.6 Consensus size: 37
402410 CATTTTCGTC
402420 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
402457 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* *
402494 CTACTATGATTTAAACTCCTAAA
1 CTACTAGGATTCAAACTCCTAAA
402517 TATATGATCA
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 53 1.00
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:402965 original size:15 final size:16
Alignment explanation
Indices: 402939--402972 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
402929 TATATATATA
402939 TATATATATATTTAAT
1 TATATATATATTTAAT
*
402955 TATAT-TATATTTATT
1 TATATATATATTTAAT
402970 TAT
1 TAT
402973 TAAATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TATATATATATTTAAT
Found at i:403030 original size:2 final size:2
Alignment explanation
Indices: 403023--403054 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
403013 TTTCATATTT
403023 TA TA TA TA 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 TA TA TA TA T
403055 TAATATTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:403091 original size:18 final size:19
Alignment explanation
Indices: 403060--403095 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
403050 TATATTAATA
403060 TTATTTATCTATGTTTTAC
1 TTATTTATCTATGTTTTAC
403079 TTATTTA-CTATGTTTTA
1 TTATTTATCTATGTTTTA
403096 TACTATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.22, C:0.08, G:0.06, T:0.64
Consensus pattern (19 bp):
TTATTTATCTATGTTTTAC
Found at i:403281 original size:18 final size:17
Alignment explanation
Indices: 403216--403273 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 17
403206 ATTGTTACTA
*
403216 TTTAGTATTTTATTATAT
1 TTTAATATTTT-TTATAT
* *
403234 TATACATACATTTTTATAT
1 TTTA-ATA-TTTTTTATAT
403253 TTTAATATTTTTATATAT
1 TTTAATATTTTT-TATAT
403271 TTT
1 TTT
403274 TTTATTTTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
17 4 0.12
18 14 0.44
19 11 0.34
20 3 0.09
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (17 bp):
TTTAATATTTTTTATAT
Found at i:403309 original size:22 final size:21
Alignment explanation
Indices: 403262--403307 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 21
403252 TTTTAATATT
* *
403262 TTTATATATTTTTTTATTTTA
1 TTTATATATTTTTTAATTTCA
403283 TTTATACTATTTATTTAATTTCA
1 TTTATA-TATTT-TTTAATTTCA
403306 TT
1 TT
403308 ATGTTTTTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.29
22 5 0.24
23 10 0.48
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTATATATTTTTTAATTTCA
Found at i:404133 original size:20 final size:21
Alignment explanation
Indices: 404108--404214 Score: 55
Period size: 20 Copynumber: 5.1 Consensus size: 21
404098 ATTTATTTTT
404108 AAATAATATAT-ATAATATAA
1 AAATAATATATCATAATATAA
* **
404128 AAATAATAT-TAATGGTATAA
1 AAATAATATATCATAATATAA
* * *
404148 AAAGTATATGTATATCCACAAAATAT
1 AAA-TA-A--TATAT-CATAATATAA
* *
404174 AAATAATAT-TGACAATAT-A
1 AAATAATATATCATAATATAA
404193 AAA-AATATAT-ATAATATAA
1 AAATAATATATCATAATATAA
404212 AAA
1 AAA
404215 GGCAAAATAA
Statistics
Matches: 66, Mismatches: 12, Indels: 19
0.68 0.12 0.20
Matches are distributed among these distances:
18 11 0.17
19 9 0.14
20 25 0.38
21 3 0.05
22 4 0.06
24 4 0.06
25 3 0.05
26 7 0.11
ACGTcount: A:0.60, C:0.04, G:0.05, T:0.32
Consensus pattern (21 bp):
AAATAATATATCATAATATAA
Found at i:404208 original size:18 final size:18
Alignment explanation
Indices: 404169--404214 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
404159 ATATCCACAA
*
404169 AATATAAATAATATTGAC
1 AATATAAAAAATATTGAC
*
404187 AATATAAAAAATATAT-AT
1 AATATAAAAAATAT-TGAC
404205 AATATAAAAA
1 AATATAAAAA
404215 GGCAAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 24 0.96
19 1 0.04
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (18 bp):
AATATAAAAAATATTGAC
Found at i:405221 original size:35 final size:34
Alignment explanation
Indices: 405182--405249 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
405172 AAAGGAAATT
**
405182 AAGTTGAGTTTGACTCCTCCTTTGCGAGTTAAGTC
1 AAGTTGAGGATGACTCC-CCTTTGCGAGTTAAGTC
*
405217 AAGTTGTGGATGACTCCCCTTTGCGAGTTAAGT
1 AAGTTGAGGATGACTCCCCTTTGCGAGTTAAGT
405250 TGAATATTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.53
35 14 0.47
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (34 bp):
AAGTTGAGGATGACTCCCCTTTGCGAGTTAAGTC
Found at i:405874 original size:69 final size:70
Alignment explanation
Indices: 405597--405899 Score: 231
Period size: 72 Copynumber: 4.2 Consensus size: 70
405587 ATTTTCAAAA
* * * * * *
405597 GAAAA-TATCTCAAGTGAGATAAAATTTTATTTTGAGAAAAAATATATCGAGTGAGACA-AAACT
1 GAAAACTATCTCAAGTAAGATAAAA---TATTTTGAGAGAAACTTTCTCAAGTGAGA-AGAAACT
405660 TGTTTTAAG
62 TGTTTTAAG
* * * * *
405669 GAAAACTACCTCAAGTTAGATAAAAGAAATTTTGAGAGAAACTATT-TCGAGTGAGAAGAAAATT
1 GAAAACTATCTCAAGTAAGAT-AAA-ATATTTTGAGAGAAACT-TTCTCAAGTGAGAAGAAACTT
* * *
405733 ATTTAAAA
63 GTTTTAAG
* * * * * *
405741 GAAAACCATCTCAAGTGAGATGAAATTTTTGTTTCGAGAGAAACTGTCTAAAGTGAGACA-AAAC
1 GAAAACTATCTCAAGTAAGAT-AAA-ATAT-TTT-GAGAGAAACTTTCTCAAGTGAGA-AGAAAC
405805 TTGTTTTAAG
61 TTGTTTTAAG
* * **
405815 GAAAACTATCTCATGTAAGAT-AAATATTTTGAGATAAACTTTCTCAAGTGAGTTGAAACTTGTT
1 GAAAACTATCTCAAGTAAGATAAAATATTTTGAGAGAAACTTTCTCAAGTGAGAAGAAACTTGTT
405879 TTAAG
66 TTAAG
405884 GAAAA-TGATCTCAAGT
1 GAAAACT-ATCTCAAGT
405900 GATTTATTTA
Statistics
Matches: 184, Mismatches: 36, Indels: 25
0.75 0.15 0.10
Matches are distributed among these distances:
68 1 0.01
69 46 0.25
70 3 0.02
71 3 0.02
72 62 0.34
73 18 0.10
74 49 0.27
75 2 0.01
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.31
Consensus pattern (70 bp):
GAAAACTATCTCAAGTAAGATAAAATATTTTGAGAGAAACTTTCTCAAGTGAGAAGAAACTTGTT
TTAAG
Found at i:405963 original size:145 final size:145
Alignment explanation
Indices: 405650--405980 Score: 362
Period size: 145 Copynumber: 2.3 Consensus size: 145
405640 ATATCGAGTG
* *
405650 AGACAAAACTTGTTTTAAGGAAAACTACCTCAAGTTAGATAAAAGAAATTTTGAGAGAAACTATT
1 AGACAAAACTTGTTTTAAGGAAAACTATCTCAAGTAAGAT-AAAGAAATTTTGAGAGAAACTATT
* * *
405715 TCGAGTGAGAAGAAAATTATTTAAAAGAAAACCATCTCAAGTGAGATGAAATTTTTGTTTCGAGA
65 TCAAGTGAGAAGAAAATTATTTAAAAGAAAACCATCTCAAGTGAGATGAAATTTTTGTTCCAAGA
*
405780 GAAACTGTCTAAAGTG
130 GAAACTGTCTAAAGTA
* * *
405796 AGACAAAACTTGTTTTAAGGAAAACTATCTCATGTAAGAT-AA-ATATTTTGAGATAAACT-TTC
1 AGACAAAACTTGTTTTAAGGAAAACTATCTCAAGTAAGATAAAGAAATTTTGAGAGAAACTATT-
** * * * * ** * ** *
405858 TCAAGTGAGTTGAAACTTGTTTTAAGGAAAATGATCTCAAGTGATTTATTTATTTTTTGTTCCAA
65 TCAAGTGAGAAGAAAATTATTTAAAAGAAAACCATCTCAAGTGA--GATGAAATTTTTGTTCCAA
* **
405923 GAGAAGCTGTCTTGAGTA
128 GAGAAACTGTCTAAAGTA
** *
405941 AGATGAAACTTGTTTTAAGGAAAACTATCTCAAGTGAGAT
1 AGACAAAACTTGTTTTAAGGAAAACTATCTCAAGTAAGAT
405981 TTGTTTTTGT
Statistics
Matches: 154, Mismatches: 28, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
142 2 0.01
143 50 0.32
144 2 0.01
145 63 0.41
146 37 0.24
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.32
Consensus pattern (145 bp):
AGACAAAACTTGTTTTAAGGAAAACTATCTCAAGTAAGATAAAGAAATTTTGAGAGAAACTATTT
CAAGTGAGAAGAAAATTATTTAAAAGAAAACCATCTCAAGTGAGATGAAATTTTTGTTCCAAGAG
AAACTGTCTAAAGTA
Found at i:409188 original size:61 final size:61
Alignment explanation
Indices: 409032--409191 Score: 180
Period size: 61 Copynumber: 2.6 Consensus size: 61
409022 ACCGTATTGC
* * * * *
409032 TATGACACATAAGGTCATGCCCACCACCTGCACTAAATTTACATTCTAGTGCTAATCTTAA
1 TATGAAACATAAGGTCGTGCCCACCACCTGCACTAAGTTTACACTCTAGTGCTAATCTCAA
* * * *
409093 TATGAAACATAAGGTTGTTCCCACCGCCTACACTAAGTTTACACTCTAGTGCTAATC-CAGA
1 TATGAAACATAAGGTCGTGCCCACCACCTGCACTAAGTTTACACTCTAGTGCTAATCTCA-A
* * *
409154 TATTACAA-ATAAGGTCGTGCCAACCACTTGCACTAAGT
1 TATGA-AACATAAGGTCGTGCCCACCACCTGCACTAAGT
409192 GTCCTTACAC
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
60 1 0.01
61 78 0.96
62 2 0.02
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.28
Consensus pattern (61 bp):
TATGAAACATAAGGTCGTGCCCACCACCTGCACTAAGTTTACACTCTAGTGCTAATCTCAA
Found at i:420018 original size:18 final size:18
Alignment explanation
Indices: 419995--420036 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
419985 TTATTTATGG
* *
419995 AAGTATCGCCCTGGATGA
1 AAGTATCACCCTGGAAGA
420013 AAGTATCACCCTGGAAGA
1 AAGTATCACCCTGGAAGA
420031 AAGTAT
1 AAGTAT
420037 TGTGGTTTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.21
Consensus pattern (18 bp):
AAGTATCACCCTGGAAGA
Found at i:428149 original size:61 final size:61
Alignment explanation
Indices: 428052--428211 Score: 239
Period size: 61 Copynumber: 2.6 Consensus size: 61
428042 ACCGTAGTGC
*
428052 TATGACACATAAGGTCGTGCCCACCACCTGCACTAAGTTTACACTCTAGTGCTAATCAGGA
1 TATGACACATAAGGTCGTGCCCACCACCTGCACTAAGTTTACACTCTAGTGCTAATCAGAA
* * * * * *
428113 TATGACACATAAGGTCGTTCCCACCGCCTGCGCTAAGTTTACATTCTAGTGCTGATCCGAA
1 TATGACACATAAGGTCGTGCCCACCACCTGCACTAAGTTTACACTCTAGTGCTAATCAGAA
* *
428174 TATGACACATAAGGTCGTGCCCCCCACCTACACTAAGT
1 TATGACACATAAGGTCGTGCCCACCACCTGCACTAAGT
428212 GTCATTACAC
Statistics
Matches: 87, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 87 1.00
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (61 bp):
TATGACACATAAGGTCGTGCCCACCACCTGCACTAAGTTTACACTCTAGTGCTAATCAGAA
Found at i:434037 original size:20 final size:20
Alignment explanation
Indices: 434014--434052 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
434004 TAATTTACTC
*
434014 TAATTTAATGTTAGAATGTT
1 TAATTTAATATTAGAATGTT
*
434034 TAATTTGATATTAGAATGT
1 TAATTTAATATTAGAATGT
434053 GACATTAGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (20 bp):
TAATTTAATATTAGAATGTT
Found at i:434305 original size:15 final size:15
Alignment explanation
Indices: 434285--434314 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
434275 GAATGTGTAA
*
434285 TTGAGATTAATATGG
1 TTGAGATGAATATGG
434300 TTGAGATGAATATGG
1 TTGAGATGAATATGG
434315 GGATTAGTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.00, G:0.30, T:0.37
Consensus pattern (15 bp):
TTGAGATGAATATGG
Found at i:435146 original size:34 final size:34
Alignment explanation
Indices: 435093--435174 Score: 103
Period size: 34 Copynumber: 2.4 Consensus size: 34
435083 TACATTTAAG
* * * *
435093 GATTGCACCTGGAGTGCATATTTTTGTATCTGAT
1 GATTACACCTGGAGCGCATATTTCTATATCTGAT
*
435127 GATTACACCTGGAGCGCATATTTCTATTTCTGAT
1 GATTACACCTGGAGCGCATATTTCTATATCTGAT
435161 GA-TAGCACCTGGAG
1 GATTA-CACCTGGAG
435175 TGCTTATTGT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
33 2 0.05
34 40 0.95
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.35
Consensus pattern (34 bp):
GATTACACCTGGAGCGCATATTTCTATATCTGAT
Found at i:438169 original size:31 final size:31
Alignment explanation
Indices: 438131--438191 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
438121 AAATTCACCA
438131 TAAATTTTATAATTTGAACTAGTAAGATTGC
1 TAAATTTTATAATTTGAACTAGTAAGATTGC
438162 TAAATTTTATAATTTGAACTAGTAAGATTG
1 TAAATTTTATAATTTGAACTAGTAAGATTG
438192 TTGTATATCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.39, C:0.05, G:0.13, T:0.43
Consensus pattern (31 bp):
TAAATTTTATAATTTGAACTAGTAAGATTGC
Found at i:443253 original size:20 final size:20
Alignment explanation
Indices: 443228--443419 Score: 125
Period size: 20 Copynumber: 9.6 Consensus size: 20
443218 AAACTAACAG
* *
443228 ATGACCCAATGGATTTGCAA
1 ATGACCCAAAGGATTTACAA
*
443248 ATGACCCAAAGGCTTTACAA
1 ATGACCCAAAGGATTTACAA
* *
443268 ATGACCCGAAGGCTTTACAA
1 ATGACCCAAAGGATTTACAA
* ** *
443288 ATTACCCGGAGGCTTTACAA
1 ATGACCCAAAGGATTTACAA
*
443308 ATGATCCAAA-GACTTTACAA
1 ATGACCCAAAGGA-TTTACAA
* ** *
443328 ATTACCCGGAGGCTTTACAA
1 ATGACCCAAAGGATTTACAA
* * *
443348 ATTACCCGAAGGCTTTACAA
1 ATGACCCAAAGGATTTACAA
* ** *
443368 ATTACCCGGAGGCTTTACAA
1 ATGACCCAAAGGATTTACAA
* * * *
443388 ATTAACCGAAGGCTTTACAA
1 ATGACCCAAAGGATTTACAA
* *
443408 ATTACCCTAAGG
1 ATGACCCAAAGG
443420 TTTTGATTTT
Statistics
Matches: 148, Mismatches: 22, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
19 1 0.01
20 146 0.99
21 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.24
Consensus pattern (20 bp):
ATGACCCAAAGGATTTACAA
Found at i:443289 original size:40 final size:40
Alignment explanation
Indices: 443257--443414 Score: 262
Period size: 40 Copynumber: 4.0 Consensus size: 40
443247 AATGACCCAA
443257 AGGCTTTACAAATGACCCGAAGGCTTTACAAATTACCCGG
1 AGGCTTTACAAATGACCCGAAGGCTTTACAAATTACCCGG
* * *
443297 AGGCTTTACAAATGATCCAAAGACTTTACAAATTACCCGG
1 AGGCTTTACAAATGACCCGAAGGCTTTACAAATTACCCGG
*
443337 AGGCTTTACAAATTACCCGAAGGCTTTACAAATTACCCGG
1 AGGCTTTACAAATGACCCGAAGGCTTTACAAATTACCCGG
* *
443377 AGGCTTTACAAATTAACCGAAGGCTTTACAAATTACCC
1 AGGCTTTACAAATGACCCGAAGGCTTTACAAATTACCC
443415 TAAGGTTTTG
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 110 1.00
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (40 bp):
AGGCTTTACAAATGACCCGAAGGCTTTACAAATTACCCGG
Found at i:443341 original size:60 final size:60
Alignment explanation
Indices: 443245--443419 Score: 260
Period size: 60 Copynumber: 2.9 Consensus size: 60
443235 AATGGATTTG
* *
443245 CAAATGACCCAAAGGCTTTACAAATGACCCGAAGGCTTTACAAATTACCCGGAGGCTTTA
1 CAAATGACCCAAAGGCTTTACAAATTACCCGAAGGCTTTACAAATTACCCGAAGGCTTTA
* * *
443305 CAAATGATCCAAAGACTTTACAAATTACCCGGAGGCTTTACAAATTACCCGAAGGCTTTA
1 CAAATGACCCAAAGGCTTTACAAATTACCCGAAGGCTTTACAAATTACCCGAAGGCTTTA
* ** * *
443365 CAAATTACCCGGAGGCTTTACAAATTAACCGAAGGCTTTACAAATTACCCTAAGG
1 CAAATGACCCAAAGGCTTTACAAATTACCCGAAGGCTTTACAAATTACCCGAAGG
443420 TTTTGATTTT
Statistics
Matches: 102, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 102 1.00
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (60 bp):
CAAATGACCCAAAGGCTTTACAAATTACCCGAAGGCTTTACAAATTACCCGAAGGCTTTA
Found at i:443984 original size:22 final size:22
Alignment explanation
Indices: 443959--444004 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
443949 AAAGCTCTCG
*
443959 TCTTTGAAAAGAGAATTTATCA
1 TCTTTGAAAAGAGAATCTATCA
443981 TCTTTGAAAAGAGAATCTATCA
1 TCTTTGAAAAGAGAATCTATCA
444003 TC
1 TC
444005 CTTGCAGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (22 bp):
TCTTTGAAAAGAGAATCTATCA
Found at i:450398 original size:21 final size:25
Alignment explanation
Indices: 450342--450398 Score: 68
Period size: 27 Copynumber: 2.4 Consensus size: 25
450332 ATTACCAATT
450342 TAATATTAATATTAATAATCCTACTA
1 TAATATTAATATTAATAA-CCTACTA
450368 TAATATTTAATATTAA-AA-CTA-TA
1 TAATA-TTAATATTAATAACCTACTA
450391 TAA-ATTAA
1 TAATATTAA
450399 CTTATAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
21 4 0.13
22 1 0.03
23 5 0.17
24 3 0.10
26 7 0.23
27 10 0.33
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (25 bp):
TAATATTAATATTAATAACCTACTA
Found at i:452624 original size:34 final size:34
Alignment explanation
Indices: 452577--452661 Score: 111
Period size: 34 Copynumber: 2.5 Consensus size: 34
452567 TGTTTCCCTA
*
452577 AATGAACAACAACTTAAATGA-AATTCATG-TTTT
1 AATGAACAACAACTTAAAT-ACAATGCATGCTTTT
*
452610 AATGAACTAGCAACTTAAATACAATGCATGCTTTT
1 AATGAAC-AACAACTTAAATACAATGCATGCTTTT
452645 AATGAACAACACACTTA
1 AATGAACAACA-ACTTA
452662 TTAAATGCAA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
33 8 0.18
34 21 0.47
35 16 0.36
ACGTcount: A:0.45, C:0.16, G:0.09, T:0.29
Consensus pattern (34 bp):
AATGAACAACAACTTAAATACAATGCATGCTTTT
Found at i:467320 original size:15 final size:13
Alignment explanation
Indices: 467289--467320 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
467279 AGAATTTTTC
467289 TTTTTTTTCAAAT
1 TTTTTTTTCAAAT
467302 TTTTGTTTTCAAAT
1 TTTT-TTTTCAAAT
467316 TTTTT
1 TTTTT
467321 ATACTAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.19, C:0.06, G:0.03, T:0.72
Consensus pattern (13 bp):
TTTTTTTTCAAAT
Found at i:468049 original size:22 final size:22
Alignment explanation
Indices: 468024--468067 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
468014 GGTGTTATGG
* *
468024 GGATGAATTTGGACTTAATTTA
1 GGATGAATATAGACTTAATTTA
*
468046 GGATGAATATAGCCTTAATTTA
1 GGATGAATATAGACTTAATTTA
468068 TTCCAAGGGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.34, C:0.07, G:0.20, T:0.39
Consensus pattern (22 bp):
GGATGAATATAGACTTAATTTA
Found at i:468602 original size:17 final size:17
Alignment explanation
Indices: 468563--468603 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
468553 GGTAGTTTGT
468563 TCAATGAACTAGTTAAA
1 TCAATGAACTAGTTAAA
*
468580 TGAATGAACTAG-TATAA
1 TCAATGAACTAGTTA-AA
468597 TCAATGA
1 TCAATGA
468604 GCTAACTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 2 0.10
17 19 0.90
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.29
Consensus pattern (17 bp):
TCAATGAACTAGTTAAA
Found at i:468723 original size:34 final size:35
Alignment explanation
Indices: 468685--468760 Score: 93
Period size: 34 Copynumber: 2.2 Consensus size: 35
468675 TACTTCCCTA
* * *
468685 AATGAATTAGCATA-TTAAATGCAATGC-ATGTTTT
1 AATGAACTAGCA-ACTTAAATGAAATGCTATCTTTT
*
468719 AATGAACTAGCAACTTAAATGAAATGCTTTCTTTT
1 AATGAACTAGCAACTTAAATGAAATGCTATCTTTT
468754 AATGAAC
1 AATGAAC
468761 ATCACACTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
33 1 0.03
34 23 0.64
35 12 0.33
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (35 bp):
AATGAACTAGCAACTTAAATGAAATGCTATCTTTT
Found at i:478529 original size:21 final size:21
Alignment explanation
Indices: 478504--478627 Score: 142
Period size: 21 Copynumber: 5.7 Consensus size: 21
478494 TTTTCATAAG
*
478504 AGTACTTTGTCTACTTGGAGT
1 AGTACTTTGTGTACTTGGAGT
*
478525 AGTACTTTGTGTACTATGGTAAT
1 AGTACTTTGTGTACT-TGG-AGT
*
478548 AGTACTTTGTCTACTTGGAGT
1 AGTACTTTGTGTACTTGGAGT
* *
478569 AGTACTTAGTGTAATATGGTAAG-
1 AGTACTTTGTGTACT-TGG--AGT
*
478592 AGTACTTTATGTACTTGGAGT
1 AGTACTTTGTGTACTTGGAGT
478613 AGTACTTTGTGTACT
1 AGTACTTTGTGTACT
478628 ATGGTACTTT
Statistics
Matches: 86, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
20 2 0.02
21 42 0.49
22 12 0.14
23 28 0.33
24 2 0.02
ACGTcount: A:0.24, C:0.10, G:0.23, T:0.42
Consensus pattern (21 bp):
AGTACTTTGTGTACTTGGAGT
Found at i:478567 original size:44 final size:44
Alignment explanation
Indices: 478500--478633 Score: 223
Period size: 44 Copynumber: 3.0 Consensus size: 44
478490 TTCATTTTCA
478500 TAAGAGTACTTTGTCTACTTGGAGTAGTACTTTGTGTACTATGG
1 TAAGAGTACTTTGTCTACTTGGAGTAGTACTTTGTGTACTATGG
* * *
478544 TAATAGTACTTTGTCTACTTGGAGTAGTACTTAGTGTAATATGG
1 TAAGAGTACTTTGTCTACTTGGAGTAGTACTTTGTGTACTATGG
* *
478588 TAAGAGTACTTTATGTACTTGGAGTAGTACTTTGTGTACTATGG
1 TAAGAGTACTTTGTCTACTTGGAGTAGTACTTTGTGTACTATGG
478632 TA
1 TA
478634 CTTTGTGTGC
Statistics
Matches: 82, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 82 1.00
ACGTcount: A:0.25, C:0.10, G:0.24, T:0.41
Consensus pattern (44 bp):
TAAGAGTACTTTGTCTACTTGGAGTAGTACTTTGTGTACTATGG
Found at i:479229 original size:6 final size:6
Alignment explanation
Indices: 479218--479326 Score: 200
Period size: 6 Copynumber: 18.2 Consensus size: 6
479208 GCATATTTAA
*
479218 TACGTG TACGTG CACGTG TACGTG TACGTG TACGTG TACGTG TACGTG
1 TACGTG TACGTG TACGTG TACGTG TACGTG TACGTG TACGTG TACGTG
*
479266 TACGTG CACGTG TACGTG TACGTG TACGTG TACGTG TACGTG TACGTG
1 TACGTG TACGTG TACGTG TACGTG TACGTG TACGTG TACGTG TACGTG
479314 TACGTG TACGTG T
1 TACGTG TACGTG T
479327 GTGTGTGTGT
Statistics
Matches: 99, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 99 1.00
ACGTcount: A:0.17, C:0.18, G:0.33, T:0.32
Consensus pattern (6 bp):
TACGTG
Found at i:479330 original size:2 final size:2
Alignment explanation
Indices: 479323--479370 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
479313 GTACGTGTAC
* *
479323 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT AT GT GT AT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
*
479365 AT GT GT
1 GT GT GT
479371 AATTTTTCTC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.06, C:0.00, G:0.44, T:0.50
Consensus pattern (2 bp):
GT
Found at i:481539 original size:17 final size:17
Alignment explanation
Indices: 481509--481546 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
481499 TTATAAGGTG
481509 AAAAAATGATATTATTGT
1 AAAAAATGATATTATT-T
*
481527 AAAAAATTA-ATTATTT
1 AAAAAATGATATTATTT
481543 AAAA
1 AAAA
481547 TAATACCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 6 0.32
18 8 0.42
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (17 bp):
AAAAAATGATATTATTT
Found at i:486248 original size:20 final size:20
Alignment explanation
Indices: 486223--486264 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
486213 TTGACCTTAA
486223 ATTTTTCTTAATGTTT-ATGC
1 ATTTTTCTTAAT-TTTAATGC
*
486243 ATTTTTTTTAATTTTAATGC
1 ATTTTTCTTAATTTTAATGC
486263 AT
1 AT
486265 AACATTTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.62
Consensus pattern (20 bp):
ATTTTTCTTAATTTTAATGC
Found at i:486674 original size:194 final size:194
Alignment explanation
Indices: 486345--486732 Score: 767
Period size: 194 Copynumber: 2.0 Consensus size: 194
486335 AATGGATTAA
486345 AGCATAATCCGATTAGATGAATTTGACAAAAGATACAATGTCTTGTTTTTAAATTAAGTGTTTAC
1 AGCATAATCCGATTAGATGAATTTGACAAAAGATACAATGTCTTGTTTTTAAATTAAGTGTTTAC
486410 AAAATTGATTGACATTTCATCTACTTTCATTATGCTTTTTGGTCATAGAATAGGAAACATTTACA
66 AAAATTGATTGACATTTCATCTACTTTCATTATGCTTTTTGGTCATAGAATAGGAAACATTTACA
486475 TGTTGCATTTAGATTCTATCAATATGACTAATTTATGCCTAGTTGCTAAAGATGAGCATGATAG
131 TGTTGCATTTAGATTCTATCAATATGACTAATTTATGCCTAGTTGCTAAAGATGAGCATGATAG
486539 AGCATAATCCGATTAGATGAATTTGACAAAAGATACAATGTCTTGTTTTTAAATTAAGTGTTTAC
1 AGCATAATCCGATTAGATGAATTTGACAAAAGATACAATGTCTTGTTTTTAAATTAAGTGTTTAC
*
486604 AAAATTGATTGACATTTCATCTACTTTGATTATGCTTTTTGGTCATAGAATAGGAAACATTTACA
66 AAAATTGATTGACATTTCATCTACTTTCATTATGCTTTTTGGTCATAGAATAGGAAACATTTACA
486669 TGTTGCATTTAGATTCTATCAATATGACTAATTTATGCCTAGTTGCTAAAGATGAGCATGATAG
131 TGTTGCATTTAGATTCTATCAATATGACTAATTTATGCCTAGTTGCTAAAGATGAGCATGATAG
486733 TTGGTTATGG
Statistics
Matches: 193, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
194 193 1.00
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (194 bp):
AGCATAATCCGATTAGATGAATTTGACAAAAGATACAATGTCTTGTTTTTAAATTAAGTGTTTAC
AAAATTGATTGACATTTCATCTACTTTCATTATGCTTTTTGGTCATAGAATAGGAAACATTTACA
TGTTGCATTTAGATTCTATCAATATGACTAATTTATGCCTAGTTGCTAAAGATGAGCATGATAG
Found at i:489695 original size:23 final size:23
Alignment explanation
Indices: 489663--489716 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
489653 GGAATCAATA
489663 CCCTCTTGAAGGGGAACCGATTCC
1 CCCT-TTGAAGGGGAACCGATTCC
* *
489687 CCCTTTGAATGGGAACTGATTCC
1 CCCTTTGAAGGGGAACCGATTCC
489710 CTCCTTT
1 C-CCTTT
489717 ACCACTAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 18 0.67
24 9 0.33
ACGTcount: A:0.19, C:0.31, G:0.20, T:0.30
Consensus pattern (23 bp):
CCCTTTGAAGGGGAACCGATTCC
Found at i:489810 original size:22 final size:20
Alignment explanation
Indices: 489783--489842 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
489773 TTTAGTGCAG
489783 AGGGAATCGATACCCCCTTGA
1 AGGGAATCGATACCCCCTT-A
* * * *
489804 AGGGGAACCGATTCCCTTCTTT
1 A-GGGAATCGATACCC-CCTTA
489826 AGGGAATCGATACCCCC
1 AGGGAATCGATACCCCC
489843 GCGAGTTCTG
Statistics
Matches: 30, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
20 1 0.03
21 13 0.43
22 13 0.43
23 3 0.10
ACGTcount: A:0.25, C:0.30, G:0.23, T:0.22
Consensus pattern (20 bp):
AGGGAATCGATACCCCCTTA
Found at i:491690 original size:11 final size:12
Alignment explanation
Indices: 491674--491706 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
491664 TAAGGGGGAG
491674 TAATTTCAAAC-
1 TAATTTCAAACT
491685 TAATTTCAAACT
1 TAATTTCAAACT
*
491697 TGATTTCAAA
1 TAATTTCAAA
491707 ATCTTAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.39
Consensus pattern (12 bp):
TAATTTCAAACT
Found at i:505041 original size:18 final size:17
Alignment explanation
Indices: 505020--505100 Score: 55
Period size: 18 Copynumber: 4.6 Consensus size: 17
505010 CCTTGGATTG
505020 CTTTCTTTTTGAATTTTT
1 CTTTCTTTTTG-ATTTTT
505038 CTTT-TTCTTT--TCTTTT
1 CTTTCTT-TTTGAT-TTTT
505054 C-TTCTTTTTCTGATTTTT
1 CTTTC-TTTT-TGATTTTT
*
505072 CTCTTC-TTTTGTCTTTTT
1 CT-TTCTTTTTG-ATTTTT
505090 CTTTCTTTTTG
1 CTTTCTTTTTG
505101 CACTCCCATT
Statistics
Matches: 51, Mismatches: 1, Indels: 22
0.69 0.01 0.30
Matches are distributed among these distances:
15 3 0.06
16 7 0.14
17 10 0.20
18 27 0.53
19 1 0.02
20 3 0.06
ACGTcount: A:0.04, C:0.17, G:0.05, T:0.74
Consensus pattern (17 bp):
CTTTCTTTTTGATTTTT
Found at i:505096 original size:20 final size:19
Alignment explanation
Indices: 505036--505096 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 19
505026 TTTTGAATTT
505036 TTCTTTTTC-TTTTCTTTTC
1 TTCTTTTTCTTTTTC-TTTC
*
505055 TTCTTTTTCTGATTTT-TCTC
1 TTCTTTTTCT--TTTTCTTTC
505075 TTCTTTTGTCTTTTTCTTTC
1 TTCTTTT-TCTTTTTCTTTC
505095 TT
1 TT
505097 TTTGCACTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
19 13 0.37
20 15 0.43
21 3 0.09
22 4 0.11
ACGTcount: A:0.02, C:0.20, G:0.03, T:0.75
Consensus pattern (19 bp):
TTCTTTTTCTTTTTCTTTC
Found at i:505098 original size:28 final size:29
Alignment explanation
Indices: 505035--505099 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 29
505025 TTTTTGAATT
* *
505035 TTTCTTTTTCTTTTCTTTTCTTCTTTTTC
1 TTTCTTTTTCTCTTCTTTTCGTCTTTTTC
**
505064 -TGATTTTTCTCTTCTTTT-GTCTTTTTC
1 TTTCTTTTTCTCTTCTTTTCGTCTTTTTC
505091 TTTCTTTTT
1 TTTCTTTTT
505100 GCACTCCCAT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
27 8 0.28
28 21 0.72
ACGTcount: A:0.02, C:0.18, G:0.03, T:0.77
Consensus pattern (29 bp):
TTTCTTTTTCTCTTCTTTTCGTCTTTTTC
Found at i:505394 original size:19 final size:20
Alignment explanation
Indices: 505366--505405 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
505356 GGATAATAAT
505366 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
*
505386 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
505405 A
1 A
505406 GGATGGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Done.