Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000190.1 Hibiscus syriacus cultivar Beakdansim tig00000340_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: 14308945
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 22 of 62
Found at i:5268361 original size:71 final size:75
Alignment explanation
Indices: 5268275--5268463 Score: 253
Period size: 76 Copynumber: 2.6 Consensus size: 75
5268265 TAAAACATCT
* * * *
5268275 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACAAAAATACCT-AA-AAA-ATAATAT-TTA
1 TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAACAAAGATAAAATATAA
*
5268335 AAATAATATTC
65 AAATAATATCC
*
5268346 TAAATCCTAAATAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCT-AAACAAAGATAAAATATAA
5268411 AAATAATATCC
65 AAATAATATCC
* *
5268422 TAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATA
5268464 GAAAGATAAA
Statistics
Matches: 103, Mismatches: 9, Indels: 7
0.87 0.08 0.06
Matches are distributed among these distances:
70 5 0.05
71 36 0.35
73 2 0.02
74 3 0.03
75 6 0.06
76 51 0.50
ACGTcount: A:0.58, C:0.13, G:0.01, T:0.29
Consensus pattern (75 bp):
TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAACAAAGATAAAATATAAA
AATAATATCC
Found at i:5268488 original size:76 final size:75
Alignment explanation
Indices: 5268319--5268500 Score: 224
Period size: 76 Copynumber: 2.4 Consensus size: 75
5268309 CAAAAATACC
* * *
5268319 TAAAAAATAATATTTAAAATAATATTCTAAATCCTAAATAAAATACTAAAACCTATTTAAACTAA
1 TAAAATATAATATTTAAAATAATATCCTAAAACCTAAATAAAATACTAAAACCTATTTAAACTAA
*
5268384 AATACCTAAAA
66 AATA-CGAAAA
* * * * *
5268395 CAAAGATAAAATA-TAAAAATAATATCCTAAAACTTAATTAAAATACTAAAACCTATTTAAACTA
1 TAAA-ATATAATATTTAAAATAATATCCTAAAACCTAAATAAAATACTAAAACCTATTTAAACTA
5268459 AAATA-GAAAGA
65 AAATACGAAA-A
* *
5268470 TAAAATATAATGTTTAAAATATTATCCTAAA
1 TAAAATATAATATTTAAAATAATATCCTAAA
5268501 CTTGAGTTTA
Statistics
Matches: 89, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
74 9 0.10
75 20 0.22
76 54 0.61
77 6 0.07
ACGTcount: A:0.58, C:0.10, G:0.02, T:0.30
Consensus pattern (75 bp):
TAAAATATAATATTTAAAATAATATCCTAAAACCTAAATAAAATACTAAAACCTATTTAAACTAA
AATACGAAAA
Found at i:5273956 original size:19 final size:19
Alignment explanation
Indices: 5273932--5273972 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
5273922 CAAAAATAAT
5273932 ATACTAAAACATAATTAAA
1 ATACTAAAACATAATTAAA
* *
5273951 ATACTAAAACCTATTTAAA
1 ATACTAAAACATAATTAAA
5273970 ATA
1 ATA
5273973 AAATACAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (19 bp):
ATACTAAAACATAATTAAA
Found at i:5276021 original size:16 final size:18
Alignment explanation
Indices: 5276000--5276032 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
5275990 AAGCATAATT
5276000 TGTTTA-TAAAA-AAATG
1 TGTTTATTAAAACAAATG
5276016 TGTTTATTAAAACAAAT
1 TGTTTATTAAAACAAAT
5276033 AAAAGCTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 5 0.33
18 4 0.27
ACGTcount: A:0.48, C:0.03, G:0.09, T:0.39
Consensus pattern (18 bp):
TGTTTATTAAAACAAATG
Found at i:5279727 original size:41 final size:41
Alignment explanation
Indices: 5279670--5279753 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 41
5279660 GCATTAATTA
*
5279670 AATTAAACTTTACTTTGTAGGTTCATGGAACAATATCGAAG
1 AATTAAACTTTACTTTGTAAGTTCATGGAACAATATCGAAG
5279711 AATTAAACTTTACTTTGTAAGTTCATGGAACAATATCGAAG
1 AATTAAACTTTACTTTGTAAGTTCATGGAACAATATCGAAG
5279752 AA
1 AA
5279754 AAACTTACAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.33
Consensus pattern (41 bp):
AATTAAACTTTACTTTGTAAGTTCATGGAACAATATCGAAG
Found at i:5281212 original size:21 final size:20
Alignment explanation
Indices: 5281174--5281215 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
5281164 AATTAATCCT
5281174 ACTACGTATTAAAGCTAAGA
1 ACTACGTATTAAAGCTAAGA
5281194 ACTAC-TATTAAGGAGCTAAGA
1 ACTACGTATTAA--AGCTAAGA
5281215 A
1 A
5281216 TAATGATTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 5 0.25
21 9 0.45
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.24
Consensus pattern (20 bp):
ACTACGTATTAAAGCTAAGA
Found at i:5283484 original size:14 final size:14
Alignment explanation
Indices: 5283465--5283521 Score: 114
Period size: 14 Copynumber: 4.1 Consensus size: 14
5283455 AACTTGAGGG
5283465 ATGCATCATCCTCA
1 ATGCATCATCCTCA
5283479 ATGCATCATCCTCA
1 ATGCATCATCCTCA
5283493 ATGCATCATCCTCA
1 ATGCATCATCCTCA
5283507 ATGCATCATCCTCA
1 ATGCATCATCCTCA
5283521 A
1 A
5283522 AGCCTGGTGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 43 1.00
ACGTcount: A:0.30, C:0.35, G:0.07, T:0.28
Consensus pattern (14 bp):
ATGCATCATCCTCA
Found at i:5297230 original size:24 final size:24
Alignment explanation
Indices: 5297203--5297296 Score: 109
Period size: 24 Copynumber: 4.0 Consensus size: 24
5297193 TTCGATTTGA
*
5297203 ATTCTGTTATGATACCTGACATGG
1 ATTCTGATATGATACCTGACATGG
* * *
5297227 ATTCTGATCTAATA-CAGACATGG
1 ATTCTGATATGATACCTGACATGG
* *
5297250 ATTCTGATATGATACATGACCTGG
1 ATTCTGATATGATACCTGACATGG
* *
5297274 ATTCTGATTTGATACTTGACATG
1 ATTCTGATATGATACCTGACATG
5297297 AATTATTTTT
Statistics
Matches: 57, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
23 20 0.35
24 37 0.65
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (24 bp):
ATTCTGATATGATACCTGACATGG
Found at i:5297465 original size:57 final size:57
Alignment explanation
Indices: 5297368--5297482 Score: 194
Period size: 57 Copynumber: 2.0 Consensus size: 57
5297358 GTTGGAGGAA
* * *
5297368 GAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGGGCCTTACTGTTCGTGACGTGGTT
1 GAATACTTGCAGGTTCCTCGGCTTTGTGCTCAGGGACTTACTGTTCGTGACGAGGTT
*
5297425 GAATACTTGTAGGTTCCTCGGCTTTGTGCTCAGGGACTTACTGTTCGTGACGAGGTT
1 GAATACTTGCAGGTTCCTCGGCTTTGTGCTCAGGGACTTACTGTTCGTGACGAGGTT
5297482 G
1 G
5297483 TATGGTTATA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.14, C:0.20, G:0.31, T:0.35
Consensus pattern (57 bp):
GAATACTTGCAGGTTCCTCGGCTTTGTGCTCAGGGACTTACTGTTCGTGACGAGGTT
Found at i:5303468 original size:15 final size:15
Alignment explanation
Indices: 5303448--5303477 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5303438 AACAATGCAC
5303448 TGCATAAAAAAACAG
1 TGCATAAAAAAACAG
5303463 TGCATAAAAAAACAG
1 TGCATAAAAAAACAG
5303478 ATTTGGTTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.13, G:0.13, T:0.13
Consensus pattern (15 bp):
TGCATAAAAAAACAG
Found at i:5304590 original size:71 final size:70
Alignment explanation
Indices: 5304464--5304604 Score: 167
Period size: 71 Copynumber: 2.0 Consensus size: 70
5304454 TATTTTAAAC
* * * *
5304464 ATTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTAATTTAATTAAGCTTT
1 ATTATATTTTATCTTTGATTTAGATATTTTAGTTTAAATAGGTTTTAGCAATTTAATTAAGATTT
5304529 AAGAT
66 AAGAT
* * * ** *
5304534 ATTATTTTTATATTTTTGATTTAGATGTTTTAGTTTAAATA-GTTTTAAGCGTTTTAATTAGGAT
1 ATTATATTT-TATCTTTGATTTAGATATTTTAGTTTAAATAGGTTTT-AGCAATTTAATTAAGAT
5304598 TTAAGAT
64 TTAAGAT
5304605 GTTGTAGCTT
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
70 13 0.22
71 46 0.78
ACGTcount: A:0.30, C:0.02, G:0.13, T:0.55
Consensus pattern (70 bp):
ATTATATTTTATCTTTGATTTAGATATTTTAGTTTAAATAGGTTTTAGCAATTTAATTAAGATTT
AAGAT
Found at i:5314196 original size:22 final size:23
Alignment explanation
Indices: 5314157--5314216 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 23
5314147 TCAAAGTCAA
* *
5314157 AGTCAACGATCAACGGTCATACC
1 AGTCAAAGATCAACGGTCAAACC
*
5314180 AGTCAAAG-TCAATGGTCAAACC
1 AGTCAAAGATCAACGGTCAAACC
* *
5314202 AATCAATGATCAACG
1 AGTCAAAGATCAACG
5314217 TAAATGGATT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
22 18 0.60
23 12 0.40
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.18
Consensus pattern (23 bp):
AGTCAAAGATCAACGGTCAAACC
Found at i:5320492 original size:31 final size:31
Alignment explanation
Indices: 5320422--5320494 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
5320412 GGGCCACGGG
5320422 GCCTACCCAAGAAAAATCTCGGGGCCAAAAA
1 GCCTACCCAAGAAAAATCTCGGGGCCAAAAA
* * ** *
5320453 GCCAACCCAAGAAAGATCTCGGGGCCGTAGA
1 GCCTACCCAAGAAAAATCTCGGGGCCAAAAA
5320484 GCCTACCCAAG
1 GCCTACCCAAG
5320495 GGTTGCCATA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.36, C:0.32, G:0.23, T:0.10
Consensus pattern (31 bp):
GCCTACCCAAGAAAAATCTCGGGGCCAAAAA
Found at i:5331222 original size:23 final size:23
Alignment explanation
Indices: 5331172--5331254 Score: 100
Period size: 23 Copynumber: 3.7 Consensus size: 23
5331162 AGAACCTCCA
*
5331172 GGGGATATCGATTCCCC-T-ACAG
1 GGGGA-ATCGATTCCCCTTCAAAG
5331194 GGGGAATCGATTCCCCTTCAAAG
1 GGGGAATCGATTCCCCTTCAAAG
*
5331217 GGGGAATCGGTTCCCCTTC-AAG
1 GGGGAATCGATTCCCCTTCAAAG
*
5331239 GGAGGTATCGATTCCC
1 GG-GGAATCGATTCCC
5331255 TCTGCACTAA
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
21 11 0.20
22 11 0.20
23 32 0.59
ACGTcount: A:0.22, C:0.27, G:0.29, T:0.23
Consensus pattern (23 bp):
GGGGAATCGATTCCCCTTCAAAG
Found at i:5338510 original size:17 final size:17
Alignment explanation
Indices: 5338473--5338515 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
5338463 AGTGTTTGTT
* * *
5338473 TCTCGAACGAGAGTTTT
1 TCTCGAAAGAGAATTTC
5338490 TCTCGAAAGAGAATTTC
1 TCTCGAAAGAGAATTTC
5338507 TCTC-AAAGA
1 TCTCGAAAGA
5338516 AAGTGAAGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 5 0.22
17 18 0.78
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (17 bp):
TCTCGAAAGAGAATTTC
Found at i:5344069 original size:17 final size:17
Alignment explanation
Indices: 5344047--5344099 Score: 106
Period size: 17 Copynumber: 3.1 Consensus size: 17
5344037 TTACAATTAT
5344047 TCTCCTTAATTATCCGA
1 TCTCCTTAATTATCCGA
5344064 TCTCCTTAATTATCCGA
1 TCTCCTTAATTATCCGA
5344081 TCTCCTTAATTATCCGA
1 TCTCCTTAATTATCCGA
5344098 TC
1 TC
5344100 ATTCTTATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.23, C:0.30, G:0.06, T:0.42
Consensus pattern (17 bp):
TCTCCTTAATTATCCGA
Found at i:5344490 original size:3 final size:3
Alignment explanation
Indices: 5344484--5344576 Score: 115
Period size: 3 Copynumber: 32.7 Consensus size: 3
5344474 TTTTGTCCCG
* *
5344484 TTA TTA TTA -TA TTA TTA TGA -TA TTA -TA TTA TTA -TA TTA TGA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
5344527 TTA TTA GTA TTA TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5344575 TT
1 TT
5344577 TATGAATACA
Statistics
Matches: 77, Mismatches: 8, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
2 8 0.10
3 69 0.90
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:5348042 original size:47 final size:48
Alignment explanation
Indices: 5347983--5348090 Score: 173
Period size: 47 Copynumber: 2.2 Consensus size: 48
5347973 GAATAAATAT
*
5347983 ATGCGAACTAGAGATCATACGGTTAGGTTTGTTTTTT-TTGAATAAGC
1 ATGCGAACTAGAGATCATACAGTTAGGTTTGTTTTTTCTTGAATAAGC
*
5348030 ATGCGAACTAGAGATCATGCAGTTAGGTTTGTTTTTTCCTTGAATAAGC
1 ATGCGAACTAGAGATCATACAGTTAGGTTTGTTTTTT-CTTGAATAAGC
*
5348079 ATGCGGACTAGA
1 ATGCGAACTAGA
5348091 TGGCATGAGG
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
47 35 0.62
49 21 0.38
ACGTcount: A:0.28, C:0.13, G:0.24, T:0.35
Consensus pattern (48 bp):
ATGCGAACTAGAGATCATACAGTTAGGTTTGTTTTTTCTTGAATAAGC
Found at i:5355331 original size:32 final size:31
Alignment explanation
Indices: 5355288--5355364 Score: 109
Period size: 32 Copynumber: 2.5 Consensus size: 31
5355278 TTGGGGCCTG
* *
5355288 AGAGCCTACCCAAGATAATTCTCGGGGCCAC
1 AGAGCCTACCCAAGAAAAATCTCGGGGCCAC
* *
5355319 AGAGGCTTACCCAAGAAAAATCTCGGGGCCAT
1 AGA-GCCTACCCAAGAAAAATCTCGGGGCCAC
5355351 AGAGCCTACCCAAG
1 AGAGCCTACCCAAG
5355365 GGTCGCCTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 13 0.32
32 27 0.68
ACGTcount: A:0.32, C:0.30, G:0.23, T:0.14
Consensus pattern (31 bp):
AGAGCCTACCCAAGAAAAATCTCGGGGCCAC
Found at i:5360379 original size:233 final size:233
Alignment explanation
Indices: 5359884--5361653 Score: 2247
Period size: 232 Copynumber: 7.6 Consensus size: 233
5359874 TATTTTATAA
* * * **
5359884 GAGAAAGGTTTCTCATTTAAATCGAAAAATTGAAATTTTTAAAAAATAAG-AAAGTTCCCGACCT
1 GAGAAAGGTTTCTCATTTAAATCGAAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTTCTTACCT
* * *** * *
5359948 TGTAAACTATTTCAAAAGTTGGTAAGTTATTCGGGCCATCAGTAATTCATTCGAGCATGATGCTT
66 AGTAAACTATTTCCAAAGTTGGTAAGTCCCTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTT
* * * *
5360013 AAATCCTTCAGGTCATCTGTAAGTCTTTCGAGCAAAATGAAAAGTCCTTCGGGCCATCCATAATA
131 AAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGA
* * * * * * *
5360078 CCTTCAGGCAAGATATTTTTACAAGTCTTTCGAAAAAT
196 CCTTCGGGCAGGATGTTTTCACATGTCTCTCAAAAAAT
* ** * * * *
5360116 GAGAATGGTTTCTCAAATAAATTGAAAAATT-CAATATTTTGAAAAGTAAGTAAAGTTTCTTACA
1 GAGAAAGGTTTCTCATTTAAATCGAAAAATTGAAAT-TTTTGAAAAGTAAGAAAAGTTTCTTACC
* * *
5360180 TAGTAAATTATTTCCAAAGTTGGTAAGTCCCTCGGGCTATAAGTAAGTCTTTCGAGCATGATGCT
65 TAGTAAACTATTTCCAAAGTTGGTAAGTCCCTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCT
* * * *
5360245 TAAATCCTTCGGGTCATTTGTAAGTCTTTCGACCAAGATGATAAGTCATTCAGGCCATCCATAAG
130 TAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAG
*
5360310 ACCTTCGGGCATGATGTTTTCACATGTCTCTCAAAAAAT
195 ACCTTCGGGCAGGATGTTTTCACATGTCTCTCAAAAAAT
** * *
5360349 GAGAAAGGTTTCTCATTTAAATAAAAAAATTTAAATTTTTGAAAAGTAAGAAAAGTTTCTTACAT
1 GAGAAAGGTTTCTCATTTAAATCGAAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTTCTTACCT
* *
5360414 AGTAAACTATTTCCAAAGTTGGTAAGTCCCTCGCGCCATCAGTAAGTCTTTCGAGCATGATACTT
66 AGTAAACTATTTCCAAAGTTGGTAAGTCCCTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTT
** * *
5360479 AAATCCTTCAAGTCATCTGTAAGTCTTTCGAGCAATATGATAAGTCATTCGGGCCATCCATAAGA
131 AAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGA
* * *
5360544 CCTACGGG-ATGAATGTTTTCACATGTCTCTCGAAAAAT
196 CCTTCGGGCA-GGATGTTTTCACATGTCTCTCAAAAAAT
* * *
5360582 GAGAAATGTTTCTCATTTAAATCGAAAAATTGAAA-TTTTGAAAAGTAAGAAAAGTTTTTTACAT
1 GAGAAAGGTTTCTCATTTAAATCGAAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTTCTTACCT
* **
5360646 AGTAAACTATTTCCAAAGTTGGTAAGTCTCTTAGGCCATCAGTAAGTCTTTCGAGCATGATGCTT
66 AGTAAACTATTTCCAAAGTTGGTAAGTCCCTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTT
** * * ** *
5360711 AAATCCTTCAAGTCATATGTAAGTCTTTCGAGCAAGATAATAAGTCCTTCGGTTCATCCATAAAA
131 AAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGA
* *
5360776 CCTTCGGGCAGGATGTTTTCACTTGTCTCTCGAAAAAT
196 CCTTCGGGCAGGATGTTTTCACATGTCTCTCAAAAAAT
* * * * *
5360814 GAAAAAGGTTTCTCAATTAAAT-TAGAAAATTGAATTTTTTTAAAAGTAAGAAAAGTTTCTTACC
1 GAGAAAGGTTTCTCATTTAAATCGA-AAAATTGAAATTTTTGAAAAGTAAGAAAAGTTTCTTACC
*
5360878 TAGTAAACTATTTCCACAGTTGGTAAGTCCC-CGGGCCATCAGTAAGTCTTTCGAGCATGATGCT
65 TAGTAAACTATTTCCAAAGTTGGTAAGTCCCTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCT
* * * * * * **
5360942 TAAATCCTTCTGGTCATCTATAACTCTTTCGAGTAAGATGACAATTCCTTCATGCCATCCATAAG
130 TAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAG
* *
5361007 ACCTTCGGGCAGGATGTTTTCGCATGTCTCTCAAAAATT
195 ACCTTCGGGCAGGATGTTTTCACATGTCTCTCAAAAAAT
* * * *
5361046 GAAAAAGGTTTCTCATTTAAATAGGAAAATTGATATTTTT-AAAAGTAA-AAAATGTTTCTTACC
1 GAGAAAGGTTTCTCATTTAAATCGAAAAATTGAAATTTTTGAAAAGTAAGAAAA-GTTTCTTACC
* * * *
5361109 TAGTAAACTATTTCCAAAGTTGGTATGTCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGATGCG
65 TAGTAAACTATTTCCAAAGTTGGTAAGTCCCTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCT
* * * * * *
5361174 TAAATCCTTCGGGTCTTCTGTAAGACTTTCGAGAAAGATGATAAGTCTTTTGGGCC-TAACATAA
130 TAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCAT-CCATAA
* * * *
5361238 GATCTTTGGGCAGGATGTTTTAACATGTATCTCAAAAAAT
194 GACCTTCGGGCAGGATGTTTTCACATGTCTCTCAAAAAAT
* * * * * **
5361278 GGGAAAGGTTTCTCATTTAGATTGGAAAATTGAAATTTTTG--AA--AAGAAAAGTTTCGTATGT
1 GAGAAAGGTTTCTCATTTAAATCGAAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTTCTTACCT
* * *
5361339 AGTAAACTATTTCCAAAGTTGGTAAGTCCTTCGGGCCATCAGTAAGTGTTTTGAGCATGATGCTT
66 AGTAAACTATTTCCAAAGTTGGTAAGTCCCTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTT
* * *
5361404 AAATCCTTTGGGTCAGT-TGTAAGTCTTTCGAGCAAGATGACATGTCCTTCGGGCCATCCATAAG
131 AAATCCTTCGGGTCA-TCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAG
5361468 ACCTTCGGGCAGGATGTTTTCACATGTCTCTCAAAAAAT
195 ACCTTCGGGCAGGATGTTTTCACATGTCTCTCAAAAAAT
* * * * *
5361507 GTGAAAGGTTTCTCATTTAAATCGAAAAATTAAAATTTTTAAAAAGCAAGAAAAGTTTATTACCT
1 GAGAAAGGTTTCTCATTTAAATCGAAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTTCTTACCT
* * * ** *
5361572 AGTAAACT-CTTCTCAAATTTTGTAAGTCTATCGGGCCATCAATAAGTCTTTCGAGCATGATGCT
66 AGTAAACTATTTC-CAAAGTTGGTAAGTCCCTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCT
*
5361636 TAAATCCCTCGGGTCATC
130 TAAATCCTTCGGGTCATC
5361654 CATAAGTCCT
Statistics
Matches: 1334, Mismatches: 183, Indels: 41
0.86 0.12 0.03
Matches are distributed among these distances:
229 191 0.14
230 10 0.01
231 55 0.04
232 551 0.41
233 524 0.39
234 3 0.00
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Consensus pattern (233 bp):
GAGAAAGGTTTCTCATTTAAATCGAAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTTCTTACCT
AGTAAACTATTTCCAAAGTTGGTAAGTCCCTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTT
AAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGA
CCTTCGGGCAGGATGTTTTCACATGTCTCTCAAAAAAT
Found at i:5362154 original size:134 final size:133
Alignment explanation
Indices: 5362006--5362296 Score: 363
Period size: 134 Copynumber: 2.2 Consensus size: 133
5361996 GCAAATCAAA
* * * *
5362006 CTCGATTCAATCTTCCCTGAG-GAACAGTTGAATAAATCAACGTCCCCAGATCTAATTTTCATTC
1 CTCGATTCAATCTTCCCTGAGTGAA-AATGGAATAAATCAACGTACCCAGATCTAATTTTCACTC
* ** * * * *
5362070 AAGAAGAAGC-GAAACATATCCGTCTCTTTCAAGATTTAATATTTCCTGAGTAA-TAGGTGAACA
65 AAGAAGAAGCAG-AACAAATCAATCTCTTCCAAGATTTAATATTCCCTGAGTAACAATG-GAACA
5362133 AGTCTG
128 AGTCTG
* * *
5362139 CCTCGATTCAATCTTCTCTGAGTGAAAATGGAATGAATCAACGTACCCAGATCTAATTTTCCCTC
1 -CTCGATTCAATCTTCCCTGAGTGAAAATGGAATAAATCAACGTACCCAGATCTAATTTTCACTC
* * *
5362204 ATGAAGAAGCAGAACAAATCAATCTCTTCCAAGATTTGATATTCCCTTAGTAACAATGGAACAAG
65 AAGAAGAAGCAGAACAAATCAATCTCTTCCAAGATTTAATATTCCCTGAGTAACAATGGAACAAG
5362269 TCTG
130 TCTG
*
5362273 CTCGATTCAATCTTCCTTGAGTGA
1 CTCGATTCAATCTTCCCTGAGTGA
5362297 CTATGCTCTC
Statistics
Matches: 135, Mismatches: 19, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
133 22 0.16
134 107 0.79
135 6 0.04
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (133 bp):
CTCGATTCAATCTTCCCTGAGTGAAAATGGAATAAATCAACGTACCCAGATCTAATTTTCACTCA
AGAAGAAGCAGAACAAATCAATCTCTTCCAAGATTTAATATTCCCTGAGTAACAATGGAACAAGT
CTG
Found at i:5363184 original size:30 final size:30
Alignment explanation
Indices: 5363148--5363220 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
5363138 TTGTTCGACA
5363148 CAACCCGTTGACTGTTAACTTTGATCGAGT
1 CAACCCGTTGACTGTTAACTTTGATCGAGT
* *
5363178 CAACCCGTTGACCGTTGACTTTGATCGAGT
1 CAACCCGTTGACTGTTAACTTTGATCGAGT
*
5363208 CAACCAGTTGACT
1 CAACCCGTTGACT
5363221 TTGATCGAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (30 bp):
CAACCCGTTGACTGTTAACTTTGATCGAGT
Found at i:5366575 original size:3 final size:3
Alignment explanation
Indices: 5366567--5366615 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
5366557 TTCATCCCGC
* * * *
5366567 TAT TAT TA- TAT TAT GAT TTT TAT TAT TAT TAT TAT CAT TAA TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5366614 TA
1 TA
5366616 ATAAATACAT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:5367028 original size:18 final size:18
Alignment explanation
Indices: 5367005--5367039 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5366995 TCAGATTGCC
5367005 CAAATCAACACAAAAACA
1 CAAATCAACACAAAAACA
* *
5367023 CAAATCCACACACAAAC
1 CAAATCAACACAAAAAC
5367040 TTTTTTATGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.34, G:0.00, T:0.06
Consensus pattern (18 bp):
CAAATCAACACAAAAACA
Found at i:5372181 original size:28 final size:28
Alignment explanation
Indices: 5372149--5372206 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
5372139 TTTCTTGATT
*
5372149 TTATAAGAAGATATAATTCTAGATGAAA
1 TTATAAGAAGATATAATTCCAGATGAAA
5372177 TTATAAGAAGATATAATTCCAGATGAAA
1 TTATAAGAAGATATAATTCCAGATGAAA
5372205 TT
1 TT
5372207 GAAAAGCTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.48, C:0.05, G:0.14, T:0.33
Consensus pattern (28 bp):
TTATAAGAAGATATAATTCCAGATGAAA
Found at i:5378494 original size:24 final size:24
Alignment explanation
Indices: 5378458--5378565 Score: 66
Period size: 24 Copynumber: 4.6 Consensus size: 24
5378448 AAATCCTAAT
* *
5378458 TAAAACACTTAAAACTATTTAAAA
1 TAAAATACCTAAAACTATTTAAAA
*
5378482 TAAAATACCTAAAAAAATATTTAAAA
1 TAAAATACCT--AAAACTATTTAAAA
* * ** *
5378508 TAATAT-TCT-AAA-T-CCT-AAT
1 TAAAATACCTAAAACTATTTAAAA
*
5378527 TAAAATA-CTAAAACCTATTTAAAC
1 TAAAATACCTAAAA-CTATTTAAAA
5378551 TAAAATACCTAAAAC
1 TAAAATACCTAAAAC
5378566 AAAGATAAAA
Statistics
Matches: 63, Mismatches: 12, Indels: 18
0.68 0.13 0.19
Matches are distributed among these distances:
19 9 0.14
20 4 0.06
21 1 0.02
22 4 0.06
23 1 0.02
24 18 0.29
25 8 0.13
26 18 0.29
ACGTcount: A:0.56, C:0.14, G:0.00, T:0.30
Consensus pattern (24 bp):
TAAAATACCTAAAACTATTTAAAA
Found at i:5378592 original size:69 final size:68
Alignment explanation
Indices: 5378447--5378633 Score: 200
Period size: 69 Copynumber: 2.6 Consensus size: 68
5378437 TAAAACATCT
* * *
5378447 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAAATAAAATACCTAAAAAAATATTTAAAATAA
1 TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAAAAAGA-TTAAAATAA
***
5378511 TATTC
64 TAAGA
5378516 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGA-TAAAAT-AT
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAA-AAAGATTAAAATAAT
5378579 AAAGA
65 -AAGA
5378584 TAATATCCTAAAATTAATAAAAATACTAAAACCTATTTAAACTAAAATAC
1 TAA-ATCCT--AA-T--T-AAAATACTAAAACCTATTTAAACTAAAATAC
5378634 AAAGAAAAAA
Statistics
Matches: 102, Mismatches: 6, Indels: 14
0.84 0.05 0.11
Matches are distributed among these distances:
67 2 0.02
68 15 0.15
69 46 0.45
70 4 0.04
71 2 0.02
72 1 0.01
74 1 0.01
75 31 0.30
ACGTcount: A:0.57, C:0.13, G:0.01, T:0.29
Consensus pattern (68 bp):
TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAAAAAGATTAAAATAATA
AGA
Found at i:5379405 original size:14 final size:14
Alignment explanation
Indices: 5379348--5379412 Score: 69
Period size: 14 Copynumber: 4.6 Consensus size: 14
5379338 AAGCCAACGG
5379348 GTTGACTCA-TACGA
1 GTTGACTCAGT-CGA
*
5379362 GTTGACTCAGTCTGG
1 GTTGACTCAGTC-GA
* * *
5379377 GTTAACTCGGGCGA
1 GTTGACTCAGTCGA
5379391 GTTGACTCAGTCGA
1 GTTGACTCAGTCGA
5379405 GTTGACTC
1 GTTGACTC
5379413 GATTCAAATT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
14 30 0.73
15 11 0.27
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (14 bp):
GTTGACTCAGTCGA
Found at i:5380639 original size:24 final size:24
Alignment explanation
Indices: 5380607--5380655 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
5380597 AGTCTTCCTG
5380607 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
5380631 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
5380655 A
1 A
5380656 ATGTCATGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (24 bp):
ATGATGTATAAAACATCTATGTAC
Found at i:5406377 original size:81 final size:81
Alignment explanation
Indices: 5406071--5407821 Score: 2260
Period size: 81 Copynumber: 21.8 Consensus size: 81
5406061 TTACTAAATA
* * * * *
5406071 GTATTAAATCGTTCATCTAACTAGAATAAATGGTACCTTTCTACCATTTGCACAGTTAGGCCATT
1 GTATTAAAACGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACAGTTAGGCCATT
*
5406136 ATTCTTTTACTCAACT
66 ATTCTTTTACTCAACG
* * * *
5406152 GTATT-AAACTGTCCATCTAACTGGCATAACTGTTA-CTTTCTACCAATTGCACAATTAGGCCAT
1 GTATTAAAAC-GTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACAGTTAGGCCAT
5406215 TATTCTTTTACTCAACG
65 TATTCTTTTACTCAACG
* * *
5406232 GTATTAAAATGTTCATCTAACT-GCATAATTGGTACCTTTCTACCAAATGCATAGTTAGGCCATT
1 GTATTAAAACGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACAGTTAGGCCATT
*
5406296 AGTCTTTTACTCAACG
66 ATTCTTTTACTCAACG
*
5406312 GTATTAAAACGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACAGTTAGACCATT
1 GTATTAAAACGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACAGTTAGGCCATT
*
5406377 ATTCTTTTACTCAACA
66 ATTCTTTTACTCAACG
* *
5406393 GTATT-AAACGGTTAATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCATAGTTAGGCCAT
1 GTATTAAAAC-GTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACAGTTAGGCCAT
* *
5406457 TATTATTTTAATCAACG
65 TATTCTTTTACTCAACG
* * * *
5406474 GTATTAAATCTTTCATCTAACTAGCATAATTGGTACCCTTCTACCAATTGCACAGTTAGGCCATT
1 GTATTAAAACGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACAGTTAGGCCATT
* *
5406539 ATTCTTTTACTTAATG
66 ATTCTTTTACTCAACG
* * * * *
5406555 GTATT-AAACTCTTCATCTAACAGGAATAATTTGTACCTTTCTACCAATTGCACAATTAGGCCAT
1 GTATTAAAAC-GTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACAGTTAGGCCAT
*
5406619 TATTCTTTTACTCTACG
65 TATTCTTTTACTCAACG
* * *
5406636 GTATTAAACCGTTCATCTAACTGGCATAA-TGGTACCTTTCTACCAATTGCACAGTTAAGTCATT
1 GTATTAAAACGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACAGTTAGGCCATT
*
5406700 ATTCTTTTACTCAACA
66 ATTCTTTTACTCAACG
** * * * *
5406716 ACATT-AAACTATTCATTTAACTAGCATAATTGGTACCTTTCTACTAATTGCACAGTTAGGCCAT
1 GTATTAAAAC-GTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACAGTTAGGCCAT
*
5406780 TATTCTATTACTCAACG
65 TATTCTTTTACTCAACG
*
5406797 GTATT--AA-----ATCTAACTGGCATAATTGTTACCTTTCTACCAATTGCACAGTTAGGCCATT
1 GTATTAAAACGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACAGTTAGGCCATT
5406855 ATTCTTTTACTCAACG
66 ATTCTTTTACTCAACG
* * * * *
5406871 GTATT-AAACTATTCATCTAACTAGCATAATTGGTAACTTTCTACCAATTGCACATTTAGTCCAT
1 GTATTAAAAC-GTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACAGTTAGGCCAT
* *
5406935 TATTTTTTTACTCTACG
65 TATTCTTTTACTCAACG
* * * *
5406952 GTATTAAACCGTTCATCTAACTAGCATAATTGGTACCTTTCTACCAATTGCACAATTAGGACATT
1 GTATTAAAACGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACAGTTAGGCCATT
*
5407017 ATTCTTTTACTCAATG
66 ATTCTTTTACTCAACG
* * *
5407033 GTATTAAACCGTTCATCTAACTGACATAATTGGTACCTTTCTACCAATTGCACAATTAGGCCATT
1 GTATTAAAACGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACAGTTAGGCCATT
* * *
5407098 ATTCTTTGACTCACCA
66 ATTCTTTTACTCAACG
* * * *
5407114 ATATTAAAATGTTCATCTAACT-GCATAATTGGTACCTTTCTGCCATTTGCACAGTTAGGCCATT
1 GTATTAAAACGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACAGTTAGGCCATT
* * *
5407178 ATTTTTTTGCTCATCG
66 ATTCTTTTACTCAACG
* * *
5407194 GTATTAAAGCGTTCATCTAACTGGCATAATTGGCACCTTTCTATCAATTGCACAGTTAGGCCATT
1 GTATTAAAACGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACAGTTAGGCCATT
* *
5407259 ATTCTTTCACTCAACA
66 ATTCTTTTACTCAACG
*** * *
5407275 GTATTAAATTATTCATCTAACTGGCATAATTGGTGCCTTTCTACCAATTGCACAGTTAGGACATT
1 GTATTAAAACGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACAGTTAGGCCATT
5407340 ATTCTTTTACTCAACG
66 ATTCTTTTACTCAACG
* * * * * *
5407356 GTATTAAACCGTTCATCTTACTGGCATAATTGGTACATTTTTACCAATTGCATAGTTAGTCCATT
1 GTATTAAAACGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACAGTTAGGCCATT
*
5407421 ATTTTTTTACTCAACG
66 ATTCTTTTACTCAACG
* * * * * *
5407437 GTATT-AAATGTTCATCCAACTGGCATAATTGGTACCTTTCTATCAATTACATAGTAAGGCCATT
1 GTATTAAAACGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACAGTTAGGCCATT
* *
5407501 AATCTTTTACTCTACG
66 ATTCTTTTACTCAACG
* * ** *
5407517 GTATT-AATCGGTTCATCTAACTGACATAATTCCTACATTTCTACCAATTGCACAGTTAGGCCAT
1 GTATTAAAAC-GTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACAGTTAGGCCAT
*
5407581 TATTCTTTTACTCAACA
65 TATTCTTTTACTCAACG
* * * * * *
5407598 GTATTAAACCATTCATCTAACAGGCATAATTGGTACATTTCTACCAATTGCACAATTAGGACATT
1 GTATTAAAACGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACAGTTAGGCCATT
5407663 ATTCTTTTACTCAACG
66 ATTCTTTTACTCAACG
* * * * *
5407679 GTATTAAACCGTTCATCTAACTAGCATAATTGGTACATTTCTACCAATTGCATAGTTAGACCATT
1 GTATTAAAACGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACAGTTAGGCCATT
*
5407744 AATCTTTTACTCAACG
66 ATTCTTTTACTCAACG
** * * * *
5407760 GTATTAAATTGTTCATCTAACTGGCATAATTCGTACCTTTCTTCCAGTTGCACAATTAGGCC
1 GTATTAAAACGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACAGTTAGGCC
5407822 TGAAATGCAC
Statistics
Matches: 1450, Mismatches: 199, Indels: 42
0.86 0.12 0.02
Matches are distributed among these distances:
74 67 0.05
75 2 0.00
79 13 0.01
80 333 0.23
81 1023 0.71
82 12 0.01
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (81 bp):
GTATTAAAACGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACAGTTAGGCCATT
ATTCTTTTACTCAACG
Found at i:5406680 original size:323 final size:322
Alignment explanation
Indices: 5406059--5407821 Score: 2337
Period size: 323 Copynumber: 5.5 Consensus size: 322
5406049 AACCTTTCGT
* * * * * *
5406059 TTTTACTAAATAGTATTAAATCGTTCATCTAACTAGAATAAATGGTACCTTTCTACCATTTGCAC
1 TTTTACTCAACAGTATTAAACCGTTCATCTAACTAGCATAATTGGTACCTTTCTACCAATTGCAC
* * * * *
5406124 AGTTAGGCCATTATTCTTTTACTCAACTGTATTAAACTGTCCATCTAACTGGCATAACTGTTA-C
66 AGTTAGGCCATTATTCTTTTACTCAACGGTATTAAA-TTTTCATCTAACTGGCATAATTGGTACC
* * *
5406188 TTTCTACCAATTGCACAATTAGGCCATTATTCTTTTACTCAACGGTATTAAAATGTTCATCTAAC
130 TTTCTACCAATTGCACAGTTAGGCCATTATTCTTTTACTTAACGGTATTAAACTGTTCATCTAAC
* * * *
5406253 TGCATAATTGGTACCTTTCTACCAAATGCATAGTTAGGCCATTAGTCTTTTACTCAACGGTATTA
195 GGCATAATTGGTACCTTTCTACCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTA
*
5406318 AAACGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACAGTTA-GACCATTATTC
260 AACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACAGTTAGGA-CATTATTC
* * * *
5406381 TTTTACTCAACAGTATTAAACGGTTAATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCAT
1 TTTTACTCAACAGTATTAAACCGTTCATCTAACTAGCATAATTGGTACCTTTCTACCAATTGCAC
* * *
5406446 AGTTAGGCCATTATTATTTTAATCAACGGTATTAAATCTTTCATCTAACTAGCATAATTGGTACC
66 AGTTAGGCCATTATTCTTTTACTCAACGGTATTAAAT-TTTCATCTAACTGGCATAATTGGTACC
* * *
5406511 CTTCTACCAATTGCACAGTTAGGCCATTATTCTTTTACTTAATGGTATTAAACTCTTCATCTAAC
130 TTTCTACCAATTGCACAGTTAGGCCATTATTCTTTTACTTAACGGTATTAAACTGTTCATCTAAC
* * * *
5406576 AGGAATAATTTGTACCTTTCTACCAATTGCACAATTAGGCCATTATTCTTTTACTCTACGGTATT
195 -GGCATAATTGGTACCTTTCTACCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATT
* *
5406641 AAACCGTTCATCTAACTGGCATAA-TGGTACCTTTCTACCAATTGCACAGTTAAGTCATTATTC
259 AAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACAGTTAGGACATTATTC
** ** * *
5406704 TTTTACTCAACAACATTAAACTATTCATTTAACTAGCATAATTGGTACCTTTCTACTAATTGCAC
1 TTTTACTCAACAGTATTAAACCGTTCATCTAACTAGCATAATTGGTACCTTTCTACCAATTGCAC
* *
5406769 AGTTAGGCCATTATTCTATTACTCAACGGTATT-AA-----ATCTAACTGGCATAATTGTTACCT
66 AGTTAGGCCATTATTCTTTTACTCAACGGTATTAAATTTTCATCTAACTGGCATAATTGGTACCT
* *
5406828 TTCTACCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTAAACTATTCATCTAACT
131 TTCTACCAATTGCACAGTTAGGCCATTATTCTTTTACTTAACGGTATTAAACTGTTCATCTAAC-
* * * * * *
5406893 AGCATAATTGGTAACTTTCTACCAATTGCACATTTAGTCCATTATTTTTTTACTCTACGGTATTA
195 GGCATAATTGGTACCTTTCTACCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTA
* *
5406958 AACCGTTCATCTAACTAGCATAATTGGTACCTTTCTACCAATTGCACAATTAGGACATTATTC
260 AACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACAGTTAGGACATTATTC
**
5407021 TTTTACTCAATGGTATTAAACCGTTCATCTAACT-GACATAATTGGTACCTTTCTACCAATTGCA
1 TTTTACTCAACAGTATTAAACCGTTCATCTAACTAG-CATAATTGGTACCTTTCTACCAATTGCA
* * * ** *
5407085 CAATTAGGCCATTATTCTTTGACTCACCAATATTAAAATGTTCATCTAACT-GCATAATTGGTAC
65 CAGTTAGGCCATTATTCTTTTACTCAACGGTATT-AAATTTTCATCTAACTGGCATAATTGGTAC
* * * * * *
5407149 CTTTCTGCCATTTGCACAGTTAGGCCATTATTTTTTTGCTCATCGGTATTAAAGC-GTTCATCTA
129 CTTTCTACCAATTGCACAGTTAGGCCATTATTCTTTTACTTAACGGTATTAAA-CTGTTCATCTA
* * * *
5407213 ACTGGCATAATTGGCACCTTTCTATCAATTGCACAGTTAGGCCATTATTCTTTCACTCAACAGTA
193 AC-GGCATAATTGGTACCTTTCTACCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTA
*** *
5407278 TTAAATTATTCATCTAACTGGCATAATTGGTGCCTTTCTACCAATTGCACAGTTAGGACATTATT
257 TTAAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACAGTTAGGACATTATT
5407343 C
322 C
* * * * * *
5407344 TTTTACTCAACGGTATTAAACCGTTCATCTTACTGGCATAATTGGTACATTTTTACCAATTGCAT
1 TTTTACTCAACAGTATTAAACCGTTCATCTAACTAGCATAATTGGTACCTTTCTACCAATTGCAC
* * * *
5407409 AGTTAGTCCATTATTTTTTTACTCAACGGTATTAAATGTTCATCCAACTGGCATAATTGGTACCT
66 AGTTAGGCCATTATTCTTTTACTCAACGGTATTAAATTTTCATCTAACTGGCATAATTGGTACCT
* * * * * * *
5407474 TTCTATCAATTACATAGTAAGGCCATTAATCTTTTACTCT-ACGGTATTAATCGGTTCATCTAAC
131 TTCTACCAATTGCACAGTTAGGCCATTATTCTTTTACT-TAACGGTATTAAACTGTTCATCTAAC
* ** * *
5407538 TGACATAATTCCTACATTTCTACCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACAGTATT
195 -GGCATAATTGGTACCTTTCTACCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATT
* * * *
5407603 AAACCATTCATCTAACAGGCATAATTGGTACATTTCTACCAATTGCACAATTAGGACATTATTC
259 AAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACAGTTAGGACATTATTC
* * *
5407667 TTTTACTCAACGGTATTAAACCGTTCATCTAACTAGCATAATTGGTACATTTCTACCAATTGCAT
1 TTTTACTCAACAGTATTAAACCGTTCATCTAACTAGCATAATTGGTACCTTTCTACCAATTGCAC
* * *
5407732 AGTTAGACCATTAATCTTTTACTCAACGGTATTAAATTGTTCATCTAACTGGCATAATTCGTACC
66 AGTTAGGCCATTATTCTTTTACTCAACGGTATTAAATT-TTCATCTAACTGGCATAATTGGTACC
* * *
5407797 TTTCTTCCAGTTGCACAATTAGGCC
130 TTTCTACCAATTGCACAGTTAGGCC
5407822 TGAAATGCAC
Statistics
Matches: 1267, Mismatches: 155, Indels: 36
0.87 0.11 0.02
Matches are distributed among these distances:
316 163 0.13
317 118 0.09
319 2 0.00
321 1 0.00
322 126 0.10
323 725 0.57
324 132 0.10
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.38
Consensus pattern (322 bp):
TTTTACTCAACAGTATTAAACCGTTCATCTAACTAGCATAATTGGTACCTTTCTACCAATTGCAC
AGTTAGGCCATTATTCTTTTACTCAACGGTATTAAATTTTCATCTAACTGGCATAATTGGTACCT
TTCTACCAATTGCACAGTTAGGCCATTATTCTTTTACTTAACGGTATTAAACTGTTCATCTAACG
GCATAATTGGTACCTTTCTACCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTAA
ACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCACAGTTAGGACATTATTC
Found at i:5407881 original size:68 final size:68
Alignment explanation
Indices: 5407809--5408141 Score: 423
Period size: 68 Copynumber: 4.9 Consensus size: 68
5407799 TCTTCCAGTT
* * * * * *
5407809 GCACAATTAGGCCTGAAATGCACTTAGCCTTTCATCTCACTAACATAAATGACACCTTTCTATCT
1 GCACAATTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTAGCTTAAATGACACCTTTCTATCA
5407874 TAA
66 TAA
* * ** * * * * * *
5407877 GCACAGTTAGGCTTCAAATACACCTAGCCTTTCTTCTAACTGGCTTAAATGAAACCTTTATGTCA
1 GCACAATTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTAGCTTAAATGACACCTTTCTATCA
5407942 TAA
66 TAA
* * *
5407945 GCACAATTATGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCTTAAATGACACCTTTCTTTCA
1 GCACAATTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTAGCTTAAATGACACCTTTCTATCA
5408010 TAA
66 TAA
* * ** *
5408013 GCACATTTAGGCCTCGAAGGCACTTAGCCTTTCATCTAACTTTCTTAAATGACACATTTCTATCA
1 GCACAATTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTAGCTTAAATGACACCTTTCTATCA
5408078 TAA
66 TAA
* * *
5408081 GCACAATTAGGCCTCAAAGGTACTTAGCCTTTCATCTAACTAGCTTAAATTACTCCTTTCT
1 GCACAATTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTAGCTTAAATGACACCTTTCT
5408142 GTCTGATGAG
Statistics
Matches: 226, Mismatches: 39, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
68 226 1.00
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.33
Consensus pattern (68 bp):
GCACAATTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTAGCTTAAATGACACCTTTCTATCA
TAA
Found at i:5408621 original size:22 final size:22
Alignment explanation
Indices: 5408594--5408636 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
5408584 ATTTTTATTA
*
5408594 AAGTTTTCTCTTTTTACTTTTC
1 AAGTTTTCCCTTTTTACTTTTC
*
5408616 AAGTTTTCCCTTTTTTCTTTT
1 AAGTTTTCCCTTTTTACTTTT
5408637 ATTTTCAAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.12, C:0.19, G:0.05, T:0.65
Consensus pattern (22 bp):
AAGTTTTCCCTTTTTACTTTTC
Found at i:5415857 original size:56 final size:55
Alignment explanation
Indices: 5415729--5415870 Score: 175
Period size: 56 Copynumber: 2.6 Consensus size: 55
5415719 CATATATTTT
*
5415729 CCCATA-AGAACATTCATACACTT-GTTATGAA-TTTCTTAGTTCGCACACATAGTG
1 CCCATACAGAA-ATTCATACACTTAG-TATGAATTTTCTTAGTTCACACACATAGTG
* * *
5415783 CCCATACAAAAATTCATACACTTAGTATGAATTTTCTTATTTTTACACACCA-AGTG
1 CCCATACAGAAATTCATACACTTAGTATGAATTTTCTTA-GTTCACACA-CATAGTG
*
5415839 CTCATACAGAAATTCATACACTTAGTATGAAT
1 CCCATACAGAAATTCATACACTTAGTATGAAT
5415871 ATCTTACAAT
Statistics
Matches: 77, Mismatches: 6, Indels: 8
0.85 0.07 0.09
Matches are distributed among these distances:
54 24 0.31
55 11 0.14
56 40 0.52
57 2 0.03
ACGTcount: A:0.35, C:0.21, G:0.10, T:0.34
Consensus pattern (55 bp):
CCCATACAGAAATTCATACACTTAGTATGAATTTTCTTAGTTCACACACATAGTG
Found at i:5420478 original size:81 final size:81
Alignment explanation
Indices: 5420340--5420733 Score: 508
Period size: 81 Copynumber: 4.9 Consensus size: 81
5420330 AACCTTTCAT
* * * * * *
5420340 TTTTACTCAACAGTATTAATTCATTC-GTCTAACTGGCATAATTGGTACCTTTCTACCAACTGCA
1 TTTTACTCAACGGTATTAAATCGTTCAG-CTAACTGACATAATTGGTACATTTCTACCAATTGCA
* * *
5420404 TAATTAGGTCATTATTC
65 CAGTTAGGCCATTATTC
* *
5420421 TTTTACTCAACGGTATTTAATCGTTCAGCTAACTGACATAATTGGTACATTTATACCAATTGCAC
1 TTTTACTCAACGGTATTAAATCGTTCAGCTAACTGACATAATTGGTACATTTCTACCAATTGCAC
*
5420486 AGTTAAGCCATTATTC
66 AGTTAGGCCATTATTC
* *
5420502 TTTTACTCAACGGTATTAAAAT-GTTCATCAAACT-AGCATAATTGGTACATTTCTACCAATTGC
1 TTTTACTCAACGGTATT-AAATCGTTCAGCTAACTGA-CATAATTGGTACATTTCTACCAATTGC
5420565 ACAGTTAGGCCATTATTC
64 ACAGTTAGGCCATTATTC
* * * *
5420583 TTTTACTCAACGGTATTAAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGCAC
1 TTTTACTCAACGGTATTAAATCGTTCAGCTAACTGACATAATTGGTACATTTCTACCAATTGCAC
5420648 AGTTAGGCCATTATTC
66 AGTTAGGCCATTATTC
* ** * * *
5420664 TTTTACTCAACGGTATTAAA-CTATTCATATAACTGGCATAATTTGTACCTTTCTACCAATTGCA
1 TTTTACTCAACGGTATTAAATC-GTTCAGCTAACTGACATAATTGGTACATTTCTACCAATTGCA
5420728 CAGTTA
65 CAGTTA
5420734 TGCTAGTATT
Statistics
Matches: 283, Mismatches: 24, Indels: 12
0.89 0.08 0.04
Matches are distributed among these distances:
80 5 0.02
81 274 0.97
82 4 0.01
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (81 bp):
TTTTACTCAACGGTATTAAATCGTTCAGCTAACTGACATAATTGGTACATTTCTACCAATTGCAC
AGTTAGGCCATTATTC
Found at i:5420617 original size:162 final size:162
Alignment explanation
Indices: 5420340--5420733 Score: 576
Period size: 162 Copynumber: 2.4 Consensus size: 162
5420330 AACCTTTCAT
* * * * *
5420340 TTTTACTCAACAGTATT-AATTCATTCGTCTAACTGGCATAATTGGTACCTTTCTACCAACTGCA
1 TTTTACTCAACGGTATTAAAAT-ATTCATATAACTGGCATAATTGGTACCTTTCTACCAATTGCA
* * * * *
5420404 TAATTAGGTCATTATTCTTTTACTCAACGGTATTTAATCGTTCAGCTAACTGACATAATTGGTAC
65 CAGTTAGGCCATTATTCTTTTACTCAACGGTATTAAACCGTTCAGCTAACTGACATAATTGGTAC
5420469 ATTTATACCAATTGCACAGTTAAGCCATTATTC
130 ATTTATACCAATTGCACAGTTAAGCCATTATTC
* * *
5420502 TTTTACTCAACGGTATTAAAATGTTCATCA-AACTAGCATAATTGGTACATTTCTACCAATTGCA
1 TTTTACTCAACGGTATTAAAATATTCAT-ATAACTGGCATAATTGGTACCTTTCTACCAATTGCA
* *
5420566 CAGTTAGGCCATTATTCTTTTACTCAACGGTATTAAACCGTTCATCTAACTGGCATAATTGGTAC
65 CAGTTAGGCCATTATTCTTTTACTCAACGGTATTAAACCGTTCAGCTAACTGACATAATTGGTAC
* * *
5420631 CTTTCTACCAATTGCACAGTTAGGCCATTATTC
130 ATTTATACCAATTGCACAGTTAAGCCATTATTC
* *
5420664 TTTTACTCAACGGTATTAAACTATTCATATAACTGGCATAATTTGTACCTTTCTACCAATTGCAC
1 TTTTACTCAACGGTATTAAAATATTCATATAACTGGCATAATTGGTACCTTTCTACCAATTGCAC
5420729 AGTTA
66 AGTTA
5420734 TGCTAGTATT
Statistics
Matches: 206, Mismatches: 23, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
161 1 0.00
162 202 0.98
163 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (162 bp):
TTTTACTCAACGGTATTAAAATATTCATATAACTGGCATAATTGGTACCTTTCTACCAATTGCAC
AGTTAGGCCATTATTCTTTTACTCAACGGTATTAAACCGTTCAGCTAACTGACATAATTGGTACA
TTTATACCAATTGCACAGTTAAGCCATTATTC
Found at i:5421016 original size:204 final size:204
Alignment explanation
Indices: 5420790--5421266 Score: 812
Period size: 204 Copynumber: 2.3 Consensus size: 204
5420780 TACCAACTGC
* *
5420790 ACAGTTAGGCCTCAAAGGCACTTAGCCTTTCGTCTAACTGGCTTATATGACACCTTTCTGTCATA
1 ACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCTTAAATGACACCTTTCTGTCATA
* * * * *
5420855 AGCACAGTTATGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCTTAAATGACACTTTTTTGTT
66 AGCACAGTTATGACTCAAAGGCACTTAGCCTTTCATCTAACTGGCTTAAATGAAACATTTCTATT
5420920 ATAATCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATATAACTGGCGTAAGTGACACCTTTCT
131 ATAATCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATATAACTGGCGTAAGTGACACCTTTCT
5420985 GTCATAAG-A
196 GTCAT-AGTA
* *
5420994 ACAGTTAGGCCTCAACGGCACTTAGCCATTCATCTAACTGGCTTAAATGACACCTTTCTGTCATA
1 ACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCTTAAATGACACCTTTCTGTCATA
5421059 AGCACAGTTATGACTCAAAGGCACTTAGCCTTTCATCTAACTGGCTTAAATGAAACATTTCTATT
66 AGCACAGTTATGACTCAAAGGCACTTAGCCTTTCATCTAACTGGCTTAAATGAAACATTTCTATT
*
5421124 ATAATCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATATAACTGGCGTAAGTGACACCTTTTT
131 ATAATCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATATAACTGGCGTAAGTGACACCTTTCT
*
5421189 GTCATAGTC
196 GTCATAGTA
* * *
5421198 ACAGTTAGGCCTCAAAGACACTTAGCCTTTCATCTAACTAGCTTAAATGACACCTTTTTGTCATA
1 ACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCTTAAATGACACCTTTCTGTCATA
5421263 AGCA
66 AGCA
5421267 TTGTTAGGTC
Statistics
Matches: 256, Mismatches: 16, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
203 2 0.01
204 254 0.99
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (204 bp):
ACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCTTAAATGACACCTTTCTGTCATA
AGCACAGTTATGACTCAAAGGCACTTAGCCTTTCATCTAACTGGCTTAAATGAAACATTTCTATT
ATAATCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATATAACTGGCGTAAGTGACACCTTTCT
GTCATAGTA
Found at i:5421274 original size:68 final size:68
Alignment explanation
Indices: 5420788--5421266 Score: 699
Period size: 68 Copynumber: 7.0 Consensus size: 68
5420778 TCTACCAACT
* *
5420788 GCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCGTCTAACTGGCTTATATGACACCTTTCTGTCA
1 GCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCTTAAATGACACCTTTCTGTCA
5420853 TAA
66 TAA
* * * *
5420856 GCACAGTTATGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCTTAAATGACACTTTTTTGTTA
1 GCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCTTAAATGACACCTTTCTGTCA
5420921 TAA
66 TAA
* * * *
5420924 TCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATATAACTGGCGTAAGTGACACCTTTCTGTCA
1 GCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCTTAAATGACACCTTTCTGTCA
5420989 TAA
66 TAA
* * *
5420992 GAACAGTTAGGCCTCAACGGCACTTAGCCATTCATCTAACTGGCTTAAATGACACCTTTCTGTCA
1 GCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCTTAAATGACACCTTTCTGTCA
5421057 TAA
66 TAA
* * * * * *
5421060 GCACAGTTATGACTCAAAGGCACTTAGCCTTTCATCTAACTGGCTTAAATGAAACATTTCTATTA
1 GCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCTTAAATGACACCTTTCTGTCA
5421125 TAA
66 TAA
* * * * *
5421128 TCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATATAACTGGCGTAAGTGACACCTTTTTGTCA
1 GCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCTTAAATGACACCTTTCTGTCA
5421193 T-A
66 TAA
* * *
5421195 GTCACAGTTAGGCCTCAAAGACACTTAGCCTTTCATCTAACTAGCTTAAATGACACCTTTTTGTC
1 G-CACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCTTAAATGACACCTTTCTGTC
5421260 ATAA
65 ATAA
5421264 GCA
1 GCA
5421267 TTGTTAGGTC
Statistics
Matches: 362, Mismatches: 47, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
67 1 0.00
68 359 0.99
69 2 0.01
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (68 bp):
GCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCTTAAATGACACCTTTCTGTCA
TAA
Found at i:5437146 original size:14 final size:14
Alignment explanation
Indices: 5437127--5437166 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
5437117 CAAAGTCAAC
5437127 GGGTTGACTCGGAT
1 GGGTTGACTCGGAT
*
5437141 GGGTTGACTGGGAT
1 GGGTTGACTCGGAT
*
5437155 GAGTTGACTCGG
1 GGGTTGACTCGG
5437167 TTCATTCTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.15, C:0.12, G:0.45, T:0.28
Consensus pattern (14 bp):
GGGTTGACTCGGAT
Found at i:5442547 original size:14 final size:13
Alignment explanation
Indices: 5442514--5442547 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
5442504 TAATGTATCA
5442514 ATCAATTCCATTC
1 ATCAATTCCATTC
5442527 ATGCAATTACCATTC
1 AT-CAATT-CCATTC
5442542 ATCAAT
1 ATCAAT
5442548 GAGTCCGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 2 0.11
14 9 0.47
15 8 0.42
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.35
Consensus pattern (13 bp):
ATCAATTCCATTC
Found at i:5444137 original size:21 final size:19
Alignment explanation
Indices: 5444109--5444154 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
5444099 TCATTGAATC
5444109 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
5444129 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
5444148 ACTTAGT
1 A-TTAGT
5444155 AGGATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Found at i:5457273 original size:27 final size:27
Alignment explanation
Indices: 5457235--5457298 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
5457225 AGGAACCTGG
*
5457235 TATAATACTATGTATCTTATTTGACAC
1 TATAGTACTATGTATCTTATTTGACAC
5457262 TATAGTACTATGTATCTTATTTGACAC
1 TATAGTACTATGTATCTTATTTGACAC
5457289 TATAGTACTA
1 TATAGTACTA
5457299 CTTAATTCTG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (27 bp):
TATAGTACTATGTATCTTATTTGACAC
Found at i:5460978 original size:44 final size:44
Alignment explanation
Indices: 5460929--5461028 Score: 148
Period size: 44 Copynumber: 2.3 Consensus size: 44
5460919 ACCATTACCA
**
5460929 GTATCGATACTACTTTACATAGTAGTAACGATACTCCTTG-GACG
1 GTATCGATACTACTACACATAGTAGTAACGATACTCCTTGAG-CG
* *
5460973 GTATCGATACTACTACACATAGTAGTATCGATACTCCTTGAGTG
1 GTATCGATACTACTACACATAGTAGTAACGATACTCCTTGAGCG
5461017 GTATCGATACTA
1 GTATCGATACTA
5461029 TTGGGTTGCA
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
44 50 0.98
45 1 0.02
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (44 bp):
GTATCGATACTACTACACATAGTAGTAACGATACTCCTTGAGCG
Found at i:5467360 original size:32 final size:33
Alignment explanation
Indices: 5467319--5467382 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
5467309 TAGTACAGAG
*
5467319 GGTGGACACGACCTTATG-GTCATACGGATTAT
1 GGTGGACACGACCTTATGTGTCATACAGATTAT
*
5467351 GGTGGACACGACCTTATGTGTGATACAGATTA
1 GGTGGACACGACCTTATGTGTCATACAGATTA
5467383 GCACTATGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (33 bp):
GGTGGACACGACCTTATGTGTCATACAGATTAT
Found at i:5467511 original size:24 final size:24
Alignment explanation
Indices: 5467479--5467524 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
5467469 TAATGGCAAG
*
5467479 TATATTGGTAAAATAAGCCTACAA
1 TATACTGGTAAAATAAGCCTACAA
5467503 TATACTGGTAAAATAAGCCTAC
1 TATACTGGTAAAATAAGCCTAC
5467525 GAGCTTATGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.28
Consensus pattern (24 bp):
TATACTGGTAAAATAAGCCTACAA
Found at i:5467558 original size:44 final size:46
Alignment explanation
Indices: 5467503--5467591 Score: 146
Period size: 44 Copynumber: 2.0 Consensus size: 46
5467493 AAGCCTACAA
5467503 TATACTGGTAAAATAAGCCTACGAGCTTATGG-A-TAAATGGTAAG
1 TATACTGGTAAAATAAGCCTACGAGCTTATGGTATTAAATGGTAAG
* *
5467547 TATATTGGTAAAATAAGCTTACGAGCTTATGGTATTAAATGGTAA
1 TATACTGGTAAAATAAGCCTACGAGCTTATGGTATTAAATGGTAA
5467592 AATATTGCAC
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
44 30 0.73
45 1 0.02
46 10 0.24
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.31
Consensus pattern (46 bp):
TATACTGGTAAAATAAGCCTACGAGCTTATGGTATTAAATGGTAAG
Found at i:5483578 original size:54 final size:54
Alignment explanation
Indices: 5483461--5483780 Score: 374
Period size: 54 Copynumber: 5.9 Consensus size: 54
5483451 TCGTAAGGTT
* * * * *
5483461 GTTCATAAACATATTATGAAATATGTGGGTTGCACCACTTAGTGCCGATACGGTC
1 GTTCATAAACACATTATGAATTTTGTGGGTTGCA-CACTTACTGCCGATACAGTC
* * ** *
5483516 GTTCATAAAAACACTATGAATTCCGTGGGTTGCACACTTACTACCGATACAGTC
1 GTTCATAAACACATTATGAATTTTGTGGGTTGCACACTTACTGCCGATACAGTC
* *
5483570 GTTCATAAACATATTATGAATTTTGTGGGTTGCACACTTAGC-GTCGATA-AGCTC
1 GTTCATAAACACATTATGAATTTTGTGGGTTGCACACTTA-CTGCCGATACAG-TC
* * * * * * *
5483624 ATTAATAAAGATATTATGAATTTCGTGGGTTGCACACTTAGTGCCGATACAATC
1 GTTCATAAACACATTATGAATTTTGTGGGTTGCACACTTACTGCCGATACAGTC
* * *
5483678 GTTCATAAACACATTATGAATTATGTGGGTTGCACACATACTGCCGATACGGTC
1 GTTCATAAACACATTATGAATTTTGTGGGTTGCACACTTACTGCCGATACAGTC
* * *
5483732 GTTCATAAACACATTATGAACTTTGTAGGTTGCACACTTAGTGCCGATA
1 GTTCATAAACACATTATGAATTTTGTGGGTTGCACACTTACTGCCGATA
5483781 GTACACATAA
Statistics
Matches: 223, Mismatches: 38, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
53 2 0.01
54 191 0.86
55 30 0.13
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (54 bp):
GTTCATAAACACATTATGAATTTTGTGGGTTGCACACTTACTGCCGATACAGTC
Found at i:5483659 original size:108 final size:108
Alignment explanation
Indices: 5483461--5483780 Score: 428
Period size: 108 Copynumber: 3.0 Consensus size: 108
5483451 TCGTAAGGTT
* *
5483461 GTTCATAAACATATTATGAAATATGTGGGTTGCACCACTTAGTGCCGATACGGTCGTTCATAAAA
1 GTTCATAAACATATTATGAATTATGTGGGTTGCA-CACTTAGCGCCGATACGGTCGTTCATAAAA
* * * * *
5483526 ACACTATGAATTCCGTGGGTTGCACACTTACTACCGATACAGTC
65 ACATTATGAATTTCGTGGGTTGCACACTTAGTGCCGATACAATC
* * * * * * *
5483570 GTTCATAAACATATTATGAATTTTGTGGGTTGCACACTTAGCGTCGATAAGCTCATTAATAAAGA
1 GTTCATAAACATATTATGAATTATGTGGGTTGCACACTTAGCGCCGATACGGTCGTTCATAAAAA
*
5483635 TATTATGAATTTCGTGGGTTGCACACTTAGTGCCGATACAATC
66 CATTATGAATTTCGTGGGTTGCACACTTAGTGCCGATACAATC
* * *
5483678 GTTCATAAACACATTATGAATTATGTGGGTTGCACACATA-CTGCCGATACGGTCGTTCATAAAC
1 GTTCATAAACATATTATGAATTATGTGGGTTGCACACTTAGC-GCCGATACGGTCGTTCATAAAA
*
5483742 ACATTATGAACTTT-GTAGGTTGCACACTTAGTGCCGATA
65 ACATTATGAA-TTTCGTGGGTTGCACACTTAGTGCCGATA
5483781 GTACACATAA
Statistics
Matches: 183, Mismatches: 26, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
107 1 0.01
108 147 0.80
109 35 0.19
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (108 bp):
GTTCATAAACATATTATGAATTATGTGGGTTGCACACTTAGCGCCGATACGGTCGTTCATAAAAA
CATTATGAATTTCGTGGGTTGCACACTTAGTGCCGATACAATC
Found at i:5483739 original size:162 final size:163
Alignment explanation
Indices: 5483465--5483772 Score: 467
Period size: 162 Copynumber: 1.9 Consensus size: 163
5483455 AAGGTTGTTC
**
5483465 ATAAACATATTATGAAATATGTGGGTTGCACCACTTAGTGCCGATACGGTCGTTCATAAAAACAC
1 ATAAACATATTATGAAATATGTGGGTTGCACCACTTAGTGCCGATACAATCGTTCATAAAAACAC
* * * *
5483530 TATGAATTCCGTGGGTTGCACACTTACTACCGATACAGTCGTTCATAAACATATTATGAATTTTG
66 TATGAATTACGTGGGTTGCACACATACTACCGATACAGTCGTTCATAAACACATTATGAACTTTG
*
5483595 TGGGTTGCACACTTAGCGTCGATAAGCTCATTA
131 TAGGTTGCACACTTAGCGTCGATAAGCTCATTA
* * *
5483628 ATAAAGATATTATG-AATTTCGTGGGTTGCA-CACTTAGTGCCGATACAATCGTTCATAAACACA
1 ATAAACATATTATGAAATAT-GTGGGTTGCACCACTTAGTGCCGATACAATCGTTCATAAAAACA
* * * *
5483691 TTATGAATTATGTGGGTTGCACACATACTGCCGATACGGTCGTTCATAAACACATTATGAACTTT
65 CTATGAATTACGTGGGTTGCACACATACTACCGATACAGTCGTTCATAAACACATTATGAACTTT
5483756 GTAGGTTGCACACTTAG
130 GTAGGTTGCACACTTAG
5483773 TGCCGATAGT
Statistics
Matches: 130, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
162 107 0.82
163 23 0.18
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (163 bp):
ATAAACATATTATGAAATATGTGGGTTGCACCACTTAGTGCCGATACAATCGTTCATAAAAACAC
TATGAATTACGTGGGTTGCACACATACTACCGATACAGTCGTTCATAAACACATTATGAACTTTG
TAGGTTGCACACTTAGCGTCGATAAGCTCATTA
Found at i:5485589 original size:21 final size:19
Alignment explanation
Indices: 5485561--5485606 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
5485551 TCATTGAATC
5485561 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
5485581 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
5485600 ACTTAGT
1 A-TTAGT
5485607 AGGATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Found at i:5496978 original size:140 final size:140
Alignment explanation
Indices: 5496738--5497020 Score: 566
Period size: 140 Copynumber: 2.0 Consensus size: 140
5496728 AAGAAATATG
5496738 AAGTGTTAGAATTGGATTTAGAACATGTTGAAAATTGGGTATGATTCTTGAATCTCTTGTAAAAA
1 AAGTGTTAGAATTGGATTTAGAACATGTTGAAAATTGGGTATGATTCTTGAATCTCTTGTAAAAA
5496803 ATATATTTTGAGGTTAAGGATGTGGTAAATGCGTATAAATAAGTTTAAATGAAGGTATTTGAGTT
66 ATATATTTTGAGGTTAAGGATGTGGTAAATGCGTATAAATAAGTTTAAATGAAGGTATTTGAGTT
5496868 AAGGGCATGA
131 AAGGGCATGA
5496878 AAGTGTTAGAATTGGATTTAGAACATGTTGAAAATTGGGTATGATTCTTGAATCTCTTGTAAAAA
1 AAGTGTTAGAATTGGATTTAGAACATGTTGAAAATTGGGTATGATTCTTGAATCTCTTGTAAAAA
5496943 ATATATTTTGAGGTTAAGGATGTGGTAAATGCGTATAAATAAGTTTAAATGAAGGTATTTGAGTT
66 ATATATTTTGAGGTTAAGGATGTGGTAAATGCGTATAAATAAGTTTAAATGAAGGTATTTGAGTT
5497008 AAGGGCATGA
131 AAGGGCATGA
5497018 AAG
1 AAG
5497021 GGGTTGAAAT
Statistics
Matches: 143, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
140 143 1.00
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.35
Consensus pattern (140 bp):
AAGTGTTAGAATTGGATTTAGAACATGTTGAAAATTGGGTATGATTCTTGAATCTCTTGTAAAAA
ATATATTTTGAGGTTAAGGATGTGGTAAATGCGTATAAATAAGTTTAAATGAAGGTATTTGAGTT
AAGGGCATGA
Found at i:5497593 original size:59 final size:59
Alignment explanation
Indices: 5497527--5497804 Score: 317
Period size: 59 Copynumber: 4.7 Consensus size: 59
5497517 TGACACTATA
* *
5497527 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGAATTTCCATATGAAGCACTGAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATGAAGCACTGAG
* * * * * * *
5497586 TGTGCTAAAATGATATGAAAAACCTACTGAGTATATGGGTTTCCATATGAAGCACTGAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATGAAGCACTGAG
* * * * * *
5497645 TGTGCTAAAATGATAAGGAAATCATATTGAATATATGGATTTCCAGAT-AGGGCA-TTATA
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATGA-AGCACTGA-G
* * * * *
5497704 TGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGGATTTCTAGATAAAGCACTAAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATGAAGCACTGAG
* * *
5497763 GGTGCTACAAGGATAAGGAAATCATACTGAGTGTATGGATTT
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTT
5497805 TCACATAGGG
Statistics
Matches: 183, Mismatches: 32, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
58 3 0.02
59 177 0.97
60 3 0.02
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.29
Consensus pattern (59 bp):
TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATGAAGCACTGAG
Found at i:5497735 original size:118 final size:118
Alignment explanation
Indices: 5497527--5497837 Score: 349
Period size: 118 Copynumber: 2.6 Consensus size: 118
5497517 TGACACTATA
* * * * *
5497527 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGAATTTCCATAT-GAAGCACTGA-GTGTG
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCACATAG-GGCA-TTATATGTG
* * * * * * *
5497590 CTAAAATGATATGAAAAACCTACTGAGTATATGGGTTTCCATATGAAGCACTGAG
64 CTAAAATGGTAAGAAAAACATACTGAGTATATGGATTTCCAGATAAAGCACTAAG
* * * *
5497645 TGTGCTAAAATGATAAGGAAATCATATTGAATATATGGATTTCCAGATAGGGCATTATATGTGCT
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCACATAGGGCATTATATGTGCT
** * * *
5497710 AAAATGGTAAGGGAATCATACTGAGTGTATGGATTTCTAGATAAAGCACTAAG
66 AAAATGGTAAGAAAAACATACTGAGTATATGGATTTCCAGATAAAGCACTAAG
* * * *
5497763 GGTGCTACAAGGATAAGGAAATCATACTGAGTGTATGGATTTTCACATAGGGCATT-TCATGTGC
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCACATAGGGCATTAT-ATGTGC
5497827 TAAAATGGTAA
65 TAAAATGGTAA
5497838 CAACATCCTA
Statistics
Matches: 162, Mismatches: 28, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
117 3 0.02
118 158 0.98
119 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (118 bp):
TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCACATAGGGCATTATATGTGCT
AAAATGGTAAGAAAAACATACTGAGTATATGGATTTCCAGATAAAGCACTAAG
Found at i:5504282 original size:17 final size:19
Alignment explanation
Indices: 5504255--5504301 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
5504245 ATAAATAAAC
5504255 ATCGCATGCAC-TG-AGTGT
1 ATCG-ATGCACATGTAGTGT
5504273 ATCGATGCACATGTAGTGT
1 ATCGATGCACATGTAGTGT
5504292 ATCGATGCAC
1 ATCGATGCAC
5504302 CCCCTTAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.22
18 6 0.22
19 15 0.56
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (19 bp):
ATCGATGCACATGTAGTGT
Found at i:5504775 original size:59 final size:59
Alignment explanation
Indices: 5504703--5504981 Score: 253
Period size: 59 Copynumber: 4.7 Consensus size: 59
5504693 ATGACACTAT
* *
5504703 ATGTTCTAAAATGATAAGGAAATCATACTGAGTGTATGAATTTCCATATGAAGCACTGA
1 ATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGAAGCACTGA
* * * *
5504762 ATGTGTTAAAATGATAAGGAAATCCTACTAAGTGTATGGGTTTCCATATGAAGCACTGA
1 ATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGAAGCACTGA
* * * * * * *
5504821 GTGTGCTAAAATGATAAGGAAATCATATTGAATATATGGATTTCCAAAT-AGGGCA-TTA
1 ATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGA-AGCACTGA
* * * ** * *
5504879 TATGTGCTAAAATGGTAAGGGAATCATTA-TGAGAGTATGGATTTTTAGATAAAGCACT-A
1 -ATGTGCTAAAATGATAAGGAAATCA-TACTGAGTGTATGGATTTCCATATGAAGCACTGA
* * * * *
5504938 AGGGTGCTACAAGGATAAAGAAATCATACT-AGTGGTATGTATTT
1 A-TGTGCTAAAATGATAAGGAAATCATACTGAGT-GTATGGATTT
5504982 TCACATAGGT
Statistics
Matches: 177, Mismatches: 35, Indels: 16
0.78 0.15 0.07
Matches are distributed among these distances:
58 8 0.05
59 165 0.93
60 4 0.02
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.31
Consensus pattern (59 bp):
ATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGAAGCACTGA
Found at i:5504917 original size:118 final size:118
Alignment explanation
Indices: 5504708--5505028 Score: 301
Period size: 118 Copynumber: 2.7 Consensus size: 118
5504698 ACTATATGTT
* * * *
5504708 CTAAAATGATAAGGAAATCATACTGAGTGTATGAATTTCCATAT-GAAGCACTGA-ATGTGTTAA
1 CTAAAATGATAAGGAAATCATACTGAGTGTATGAATTTCCAAATAG-GGCA-TTATATGTGCTAA
* * * * * * *
5504771 AATGATAAGGAAATCCTACTAAGTGTATGGGTTTCCATATGAAGCACTGAGTGTG
64 AATGGTAAGGAAATCCTACTAAGAGTATGGATTTCCAGATAAAGCACTAAGGGTG
* * * *
5504826 CTAAAATGATAAGGAAATCATATTGAATATATGGATTTCCAAATAGGGCATTATATGTGCTAAAA
1 CTAAAATGATAAGGAAATCATACTGAGTGTATGAATTTCCAAATAGGGCATTATATGTGCTAAAA
* * * **
5504891 TGGTAAGGGAATCATTA-TGAGAGTATGGATTTTTAGATAAAGCACTAAGGGTG
66 TGGTAAGGAAATC-CTACTAAGAGTATGGATTTCCAGATAAAGCACTAAGGGTG
* * * * * * *
5504944 CTACAAGGATAAAGAAATCATACT-AGTGGTATGTATTTTCACATAGGTCATT-TCATGTGCTAA
1 CTAAAATGATAAGGAAATCATACTGAGT-GTATGAATTTCCAAATAGGGCATTAT-ATGTGCTAA
**
5505007 AATGGTAATAAAATCCTACTAA
64 AATGGTAAGGAAATCCTACTAA
5505029 TGGTACGGAT
Statistics
Matches: 162, Mismatches: 35, Indels: 12
0.78 0.17 0.06
Matches are distributed among these distances:
117 7 0.04
118 152 0.94
119 3 0.02
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.31
Consensus pattern (118 bp):
CTAAAATGATAAGGAAATCATACTGAGTGTATGAATTTCCAAATAGGGCATTATATGTGCTAAAA
TGGTAAGGAAATCCTACTAAGAGTATGGATTTCCAGATAAAGCACTAAGGGTG
Found at i:5508629 original size:24 final size:24
Alignment explanation
Indices: 5508597--5508642 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
5508587 TCTTCCAGAT
*
5508597 GATGAATAAAACATCTATGTACAC
1 GATGAATAAAACAGCTATGTACAC
* *
5508621 GATGTATAAAATAGCTATGTAC
1 GATGAATAAAACAGCTATGTAC
5508643 CGTATCATGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.28
Consensus pattern (24 bp):
GATGAATAAAACAGCTATGTACAC
Found at i:5510136 original size:106 final size:105
Alignment explanation
Indices: 5509951--5510403 Score: 537
Period size: 106 Copynumber: 4.4 Consensus size: 105
5509941 AAATTATTTA
* *
5509951 TGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAACAAAGAACTT
1 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA-AACTT
* * **
5510016 CTCAATTTCAGAGCCAAATTCAACTTCACAATGAAGGATAT
65 CCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATAT
* * *
5510057 TGGACTCCAGACACCGCAAGTTCATCTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAATTT
1 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA-AACTT
*
5510122 CCCAATTTCAGAGCCAATTTCAACTTCACAGCGTAGGATAT
65 CCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATAT
* * *
5510163 TGGACTCAAGACAACGAAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTT
1 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA-AACTT
* * *
5510228 CCCAATTTCAGAGCCAATTTTAACTTCTCAGCGAAGGATCT
65 CCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATAT
* * * * * * * *
5510269 TGAAC-CCAAGGCAACACAAGCTCAACTTCACGATGAAGGG-CGGCTTGAT-TCAAC-AAAA-TT
1 TGGACTCC-AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAAACTT
* * *
5510329 -TC-A-TTCAGAGTC-ATTTCACCTTCACAGCGAAGGATAT
65 CCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATAT
* *
5510366 TGGACTCGAGACAACACAAGTTTCAACTTCACGACGAA
1 TGGACTCCAGACAACGCAAG-TTCAACTTCACGACGAA
5510404 CGGAATCGTG
Statistics
Matches: 300, Mismatches: 44, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
97 36 0.12
98 24 0.08
99 1 0.00
100 1 0.00
101 2 0.01
102 2 0.01
103 2 0.01
104 4 0.01
105 7 0.02
106 221 0.74
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (105 bp):
TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAAACTTC
CCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATAT
Found at i:5511349 original size:2 final size:2
Alignment explanation
Indices: 5511344--5511374 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5511334 TTAGTGTTAT
5511344 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5511375 TTCCTATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5515715 original size:14 final size:14
Alignment explanation
Indices: 5515696--5515728 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
5515686 GAAGAAGAAG
*
5515696 AATTCATCTGAAAT
1 AATTCATCCGAAAT
5515710 AATTCATCCGAAAT
1 AATTCATCCGAAAT
5515724 AATTC
1 AATTC
5515729 TATCATGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.42, C:0.18, G:0.06, T:0.33
Consensus pattern (14 bp):
AATTCATCCGAAAT
Found at i:5516063 original size:9 final size:9
Alignment explanation
Indices: 5516044--5516091 Score: 62
Period size: 9 Copynumber: 5.3 Consensus size: 9
5516034 AATCAAGAAA
5516044 AAAAAAGAAG
1 AAAAAA-AAG
5516054 AAAAAAAAG
1 AAAAAAAAG
*
5516063 AAAAAAGAG
1 AAAAAAAAG
*
5516072 AAACAAAAG
1 AAAAAAAAG
5516081 -AAAAAAAG
1 AAAAAAAAG
5516089 AAA
1 AAA
5516092 GAACAAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
8 7 0.21
9 20 0.61
10 6 0.18
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:5516073 original size:18 final size:18
Alignment explanation
Indices: 5516044--5516091 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
5516034 AATCAAGAAA
5516044 AAAAAAGAAGAAAAAAAAG
1 AAAAAAG-AGAAAAAAAAG
*
5516063 AAAAAAGAGAAACAAAAG
1 AAAAAAGAGAAAAAAAAG
5516081 AAAAAA-AGAAA
1 AAAAAAGAGAAA
5516092 GAACAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
17 5 0.18
18 16 0.57
19 7 0.25
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (18 bp):
AAAAAAGAGAAAAAAAAG
Found at i:5516080 original size:30 final size:30
Alignment explanation
Indices: 5516038--5516099 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
5516028 AGATCCAATC
5516038 AAGAAAAAAAAAGAAGAAAAA-AAAGAA-AA
1 AAGAAAAAAAAAGAA-AAAAAGAAAGAACAA
*
5516067 AAGAGAAACAAAAGAAAAAAAGAAAGAACAA
1 AAGA-AAAAAAAAGAAAAAAAGAAAGAACAA
5516098 AA
1 AA
5516100 ATCAAAAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 9 0.31
30 16 0.55
31 4 0.14
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (30 bp):
AAGAAAAAAAAAGAAAAAAAGAAAGAACAA
Found at i:5516107 original size:21 final size:19
Alignment explanation
Indices: 5516041--5516100 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
5516031 TCCAATCAAG
*
5516041 AAAAAAAAAG-AAGAAAAA
1 AAAAAAAAAGAAAGAACAA
*
5516059 AAAGAAAAAAGAGA-AACAA
1 AAA-AAAAAAGAAAGAACAA
5516078 AAGAAAAAAAGAAAGAACAA
1 AA-AAAAAAAGAAAGAACAA
5516098 AAA
1 AAA
5516101 TCAAAAATCA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
18 3 0.09
19 23 0.66
20 9 0.26
ACGTcount: A:0.83, C:0.03, G:0.13, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAGAAAGAACAA
Found at i:5516120 original size:14 final size:13
Alignment explanation
Indices: 5516041--5516120 Score: 58
Period size: 13 Copynumber: 6.2 Consensus size: 13
5516031 TCCAATCAAG
5516041 AAAA-AAAAAGAA
1 AAAACAAAAAGAA
*
5516053 GAAA-AAAAAGAA
1 AAAACAAAAAGAA
* * *
5516065 AAAAGAGAAACAA
1 AAAACAAAAAGAA
5516078 AAGAA-AAAAAGAA
1 AA-AACAAAAAGAA
* *
5516091 AGAACAAAAATCAA
1 AAAACAAAAA-GAA
*
5516105 AAATCAAAAAGAA
1 AAAACAAAAAGAA
5516118 AAA
1 AAA
5516121 GGGACAAAAA
Statistics
Matches: 53, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
12 16 0.30
13 25 0.47
14 12 0.23
ACGTcount: A:0.81, C:0.05, G:0.11, T:0.03
Consensus pattern (13 bp):
AAAACAAAAAGAA
Found at i:5516799 original size:22 final size:22
Alignment explanation
Indices: 5516733--5516802 Score: 131
Period size: 22 Copynumber: 3.2 Consensus size: 22
5516723 CATCAAACTG
5516733 TTGAGCATCAAATGCCAAACCT
1 TTGAGCATCAAATGCCAAACCT
*
5516755 ATGAGCATCAAATGCCAAACCT
1 TTGAGCATCAAATGCCAAACCT
5516777 TTGAGCATCAAATGCCAAACCT
1 TTGAGCATCAAATGCCAAACCT
5516799 TTGA
1 TTGA
5516803 CCAAACATAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.37, C:0.26, G:0.14, T:0.23
Consensus pattern (22 bp):
TTGAGCATCAAATGCCAAACCT
Found at i:5517825 original size:106 final size:106
Alignment explanation
Indices: 5517641--5518787 Score: 1496
Period size: 106 Copynumber: 10.9 Consensus size: 106
5517631 CAAGATAACA
* * * **
5517641 CAAGTTCAACTTCACAATGAAGGGA-CGACTAGTTGTCAAC-AACAATTTTTCAATTTCAGAGCC
1 CAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCC
*
5517704 AATTTCAACTTCACAGCAAAGGATATTGGACTCCAGACAACG
65 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* ** *
5517746 CAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAGTAAACAATTTCCCAATTTCAGATCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
*
5517811 ATTTCAACTTCACAGCGAAGGATATTGG-CTCCAGACAACA
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* *
5517851 CAAGTTCAACTTCACGACGAAGGAACCGCTGGTTGTCAATAAACAACTTT-CCAATTTCAGAGCC
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAA-TTTCCCAATTTCAGAGCC
5517915 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
65 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* * **
5517957 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCTTAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
5518022 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* * *
5518063 CAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* * *
5518128 ATTTCAACTTCACAACGAAGGATTTTGGACTCCAGACAACC
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* * * *
5518169 CAAGTTCAACTTCACGACGAAGGGATCGCTGGGTGTCAACAAACAATTTCTCAATTTCAGAGCTA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* * *
5518234 ATTTTAACTT-ACAACGAAGGATTTTGGACTCCAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* * * * *
5518274 CAAGTTCAACTTCACGACGAAGGGACCGCTAGTTGTCAACAACCAACTTCTCAATTTCAAAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* * *
5518339 ATTTCAACTTC-CAACGAAGGATATTGGACTCCAGAGAATG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* * * *
5518379 CAAGTTCAACTTCATGACAAAGGGACTGCTGGTTGTCAACAAATAATTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* *
5518444 ATTTCAACTTCACAGCGTAGGATATTGGACTCAAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* * *
5518485 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCATAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* * ** * * * *
5518550 ATTTTAACTTCTCAGCGAAAAATCTTGAAC-CCAAGGCAACA
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCC-AGACAACG
** *** * * * *
5518591 CAAGCGCAACTTCACGACGAAGGGGTGGTTGATTGTCAAC-AA-AATTT--C-A-TTCATAGTCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* * *
5518650 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACA
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* * * *
5518691 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTT-CCAGGTTCCAGAGCC
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCA-ATTTCAGAGCC
*
5518755 AATTTCAACTTCAC-GACGGAGGATATTGGACTC
65 AATTTCAACTTCACAG-CGAAGGATATTGGACTC
5518788 AGAACAATGC
Statistics
Matches: 917, Mismatches: 109, Indels: 31
0.87 0.10 0.03
Matches are distributed among these distances:
100 72 0.08
101 4 0.00
102 6 0.01
103 1 0.00
104 4 0.00
105 321 0.35
106 509 0.56
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (106 bp):
CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
Found at i:5518002 original size:211 final size:212
Alignment explanation
Indices: 5517628--5518787 Score: 1515
Period size: 211 Copynumber: 5.5 Consensus size: 212
5517618 TTATCGTGCC
* * * * * *
5517628 ACTCAAGATAACACAAGTTCAACTTCACAATGAAGGGA-CGACTAGTTGTCAAC-AACAATTTTT
1 ACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACCG-CTGGTTGTCAACAAACAACTTTC
*
5517691 CAATTTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
* ** *
5517756 TTCACGACGAAGGGACCGTTGGTTGTCAGTAAACAATTTCCCAATTTCAGATCCAATTTCAACTT
130 TTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTT
5517821 CACAGCGAAGGATATTGG
195 CACAGCGAAGGATATTGG
* * *
5517839 -CTCCAGACAACACAAGTTCAACTTCACGACGAAGGAACCGCTGGTTGTCAATAAACAACTTTCC
1 ACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTTCC
5517903 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
* * **
5517968 TCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCTTAGCCAATTTCAACTTC
131 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
5518033 ACAGCGAAGGATATTGG
196 ACAGCGAAGGATATTGG
*
5518050 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAAC-TTCT
1 ACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTTC-
* * *
5518114 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATTTTGGACTCCAGACAACCCAAGTTCAAC
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
* * * * *
5518179 TTCACGACGAAGGGATCGCTGGGTGTCAACAAACAATTTCTCAATTTCAGAGCTAATTTTAACTT
130 TTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTT
* *
5518244 -ACAACGAAGGATTTTGG
195 CACAGCGAAGGATATTGG
* * * *
5518261 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTAGTTGTCAACAACCAAC-TTCT
1 ACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTTC-
* * * *
5518325 CAATTTCAAAGCCAATTTCAACTTC-CAACGAAGGATATTGGACTCCAGAGAATGCAAGTTCAAC
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
* * * *
5518389 TTCATGACAAAGGGACTGCTGGTTGTCAACAAATAATTTCCCAATTTCAGAGCCAATTTCAACTT
130 TTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTT
*
5518454 CACAGCGTAGGATATTGG
195 CACAGCGAAGGATATTGG
* * * * *
5518472 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTTCC
* * * ** * * * * **
5518537 AATTTCATAGCCAATTTTAACTTCTCAGCGAAAAATCTTGAAC-CCAAGGCAACACAAGCGCAAC
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC-AGACAACGCAAGTTCAAC
*** * * * *
5518601 TTCACGACGAAGGGGTGGTTGATTGTCAAC-AA-AATTT--C-A-TTCATAGTCAATTTCAACTT
130 TTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTT
*
5518660 CACAACGAAGGATATTGG
195 CACAGCGAAGGATATTGG
* *
5518678 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAA-TTTCC
1 ACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTTCC
* * *
5518742 AGGTTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGGACTC
66 A-ATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGGACTC
5518788 AGAACAATGC
Statistics
Matches: 839, Mismatches: 99, Indels: 26
0.87 0.10 0.03
Matches are distributed among these distances:
205 6 0.01
206 118 0.14
207 2 0.00
208 1 0.00
210 138 0.16
211 351 0.42
212 223 0.27
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (212 bp):
ACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTTCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
TCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
ACAGCGAAGGATATTGG
Found at i:5519571 original size:37 final size:37
Alignment explanation
Indices: 5519518--5519622 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
5519508 TATTTTCATC
5519518 CTACTAGGATTCAAACTCCTAAAAATATGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATATGATAAAATT
* * * * *
5519555 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATATGATAAAATT
* * *
5519592 CTACTATGATTTAAACTCCTAAAGATATGAT
1 CTACTAGGATTCAAACTCCTAAAAATATGAT
5519623 CCACAAGCAC
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATATGATAAAATT
Found at i:5520165 original size:19 final size:19
Alignment explanation
Indices: 5520141--5520190 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 19
5520131 ATATATATGC
5520141 TTTTACTTTTTTTTATATA
1 TTTTACTTTTTTTTATATA
* *
5520160 TTTTACTCATTTATTTATCTA
1 TTTTACT--TTTTTTTATATA
5520181 TTTT-CTTTTT
1 TTTTACTTTTT
5520191 ATCTTTATCC
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 3 0.12
19 7 0.27
20 2 0.08
21 14 0.54
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTACTTTTTTTTATATA
Found at i:5521019 original size:19 final size:19
Alignment explanation
Indices: 5520995--5521033 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
5520985 GAATCTTGGA
5520995 CTTAGTTTCCCTTTGTGCC
1 CTTAGTTTCCCTTTGTGCC
5521014 CTTAGTTTCCCTTTGTGCC
1 CTTAGTTTCCCTTTGTGCC
5521033 C
1 C
5521034 AAAGCGTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.05, C:0.33, G:0.15, T:0.46
Consensus pattern (19 bp):
CTTAGTTTCCCTTTGTGCC
Found at i:5533281 original size:36 final size:35
Alignment explanation
Indices: 5533241--5533401 Score: 118
Period size: 36 Copynumber: 4.5 Consensus size: 35
5533231 TTTGAAAAAC
*
5533241 ATATAATATATATTTTTTTAAAATGGATTTTTGAAA
1 ATATAATATATATGTTTTTAAAA-GGATTTTTGAAA
* **
5533277 ATATAATA-A-A-GTTTTGAAAACAATTTTTGAAA
1 ATATAATATATATGTTTTTAAAAGGATTTTTGAAA
* * *
5533309 ACAT-ATATTATATAG-TTTTGAAAGCGATTTATGAAA
1 ATATAATA-TATAT-GTTTTTAAAAG-GATTTTTGAAA
* * *
5533345 ATATATTATATA-GTTTTAAAAATGATTTTTGAAA
1 ATATAATATATATGTTTTTAAAAGGATTTTTGAAA
5533379 TATATATATATTATATAGTTTTT
1 -ATATA-ATA-TATAT-GTTTTT
5533402 GGAAAAAAAA
Statistics
Matches: 94, Mismatches: 18, Indels: 23
0.70 0.13 0.17
Matches are distributed among these distances:
31 3 0.03
32 13 0.14
33 9 0.10
34 13 0.14
35 18 0.19
36 27 0.29
37 6 0.06
39 5 0.05
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (35 bp):
ATATAATATATATGTTTTTAAAAGGATTTTTGAAA
Found at i:5533315 original size:70 final size:71
Alignment explanation
Indices: 5533231--5533401 Score: 170
Period size: 70 Copynumber: 2.4 Consensus size: 71
5533221 TATAGAATGG
* *
5533231 TTTGAAAAACATATAATATATATTTTTTTAAAATG-GATTTTTGAAAATATA-ATAAAGTTTTGA
1 TTTG-AAAACATATAATATATATTTTTTTAAAA-GCGATTTATGAAAATATATATAAAGTTTTAA
5533294 AAACAATT
64 AAACAATT
** * *
5533302 TTTGAAAACATAT-AT-TATATAGTTTTGAAAGCGATTTATGAAAATATATTATATAGTTTTAAA
1 TTTGAAAACATATAATATATATTTTTTTAAAAGCGATTTATGAAAATATA-TATAAAGTTTTAAA
**
5533365 AATGATT
65 AACAATT
* *
5533372 TTTGAAATATATATATATTATATAGTTTTT
1 TTTGAAA-ACATATA-A-TATATATTTTTT
5533402 GGAAAAAAAA
Statistics
Matches: 80, Mismatches: 12, Indels: 12
0.77 0.12 0.12
Matches are distributed among these distances:
67 1 0.01
68 27 0.34
69 2 0.03
70 32 0.40
71 9 0.11
73 1 0.01
74 1 0.01
75 7 0.09
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.45
Consensus pattern (71 bp):
TTTGAAAACATATAATATATATTTTTTTAAAAGCGATTTATGAAAATATATATAAAGTTTTAAAA
ACAATT
Found at i:5533354 original size:34 final size:34
Alignment explanation
Indices: 5533266--5533389 Score: 146
Period size: 34 Copynumber: 3.6 Consensus size: 34
5533256 TTTTAAAATG
*
5533266 GATTTTTGAAAATATA--ATAAAGTTTTGAAAAC
1 GATTTTTGAAAATATATTATATAGTTTTGAAAAC
* *
5533298 AATTTTTGAAAACATATATTATATAGTTTTGAAAGC
1 GATTTTTG-AAA-ATATATTATATAGTTTTGAAAAC
* * *
5533334 GATTTATGAAAATATATTATATAGTTTTAAAAAT
1 GATTTTTGAAAATATATTATATAGTTTTGAAAAC
5533368 GATTTTTG-AAATATATATATAT
1 GATTTTTGAAAATATAT-TATAT
5533390 TATATAGTTT
Statistics
Matches: 78, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
32 7 0.09
33 11 0.14
34 37 0.47
35 3 0.04
36 20 0.26
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.43
Consensus pattern (34 bp):
GATTTTTGAAAATATATTATATAGTTTTGAAAAC
Found at i:5533435 original size:38 final size:38
Alignment explanation
Indices: 5533277--5533599 Score: 268
Period size: 38 Copynumber: 8.6 Consensus size: 38
5533267 ATTTTTGAAA
*
5533277 ATATAATA-A-AG-TTTTGAAAACAATTTTTGAAA-ACAT
1 ATATAATATATAGTTTTTGAAAAC-A-TTTTGAAATATAT
*
5533313 ATAT--TATATAG-TTTTGAAAGCGATTTATG-AA-A-AT
1 ATATAATATATAGTTTTTGAAAAC-ATTT-TGAAATATAT
* *
5533347 ATAT--TATATAG-TTTTAAAAATGATTTTTGAAATATAT
1 ATATAATATATAGTTTTTGAAAA-CA-TTTTGAAATATAT
* * **
5533384 ATATATTATATAGTTTTTGGAAAAAAAATTGAAA-ATAT
1 ATATAATATATAGTTTTT-GAAAACATTTTGAAATATAT
*
5533422 ATATAATACATAGTTTTTGAAAACATTTTGAATATATATAT
1 ATATAATATATAGTTTTTGAAAACATTTTG-A-A-ATATAT
*
5533463 ATATATATAATATAGTTTTTGAAAACATTTTGAAA-ACAT
1 ATATA-AT-ATATAGTTTTTGAAAACATTTTGAAATATAT
*
5533502 ATATAATATATAG-TTTTGAAATCATTTTGAAAATATAT
1 ATATAATATATAGTTTTTGAAAACATTTTG-AAATATAT
* * *
5533540 ATATAATATATAGTTTTTTAAAATAATTTTGAAA-ATGT
1 ATATAATATATAGTTTTTGAAAA-CATTTTGAAATATAT
5533578 ATATAATATATAG-TTTTGAAAA
1 ATATAATATATAGTTTTTGAAAA
5533600 GATGTTTTAT
Statistics
Matches: 242, Mismatches: 23, Indels: 43
0.79 0.07 0.14
Matches are distributed among these distances:
34 25 0.10
35 12 0.05
36 34 0.14
37 32 0.13
38 55 0.23
39 32 0.13
40 13 0.05
41 14 0.06
42 3 0.01
43 22 0.09
ACGTcount: A:0.46, C:0.02, G:0.09, T:0.43
Consensus pattern (38 bp):
ATATAATATATAGTTTTTGAAAACATTTTGAAATATAT
Found at i:5533554 original size:156 final size:151
Alignment explanation
Indices: 5533311--5533628 Score: 387
Period size: 156 Copynumber: 2.1 Consensus size: 151
5533301 TTTTGAAAAC
* *
5533311 ATATATTATATAGTTTTGAAAGCGATTTATGAAAATATATTATATAGTTTTAAAAATGATTTTTG
1 ATATATTATATAGTTTTGAAAACGATTTATGAAAATATATTATATAGTTTTAAAAATCATTTTTG
*
5533376 AAATATATATATATTATATAGTTTTTGGAAAA-AAAATTGAAAATATATATAATACATAGTTTTT
66 AAATATATATATAATATATAGTTTTT-GAAAATAAAATTGAAAATATATATAATACATAG-TTTT
5533440 GAAAACAT-TTTGAATATATATATAT
129 GAAAACATGTTT-AATAT-TATAT-T
* *
5533465 ATATATAATATAGTTTTTGAAAAC-ATTT-TGAAAACATATATAATATATAGTTTT-GAAATCA-
1 ATATATTATATAG-TTTTGAAAACGATTTATG-AAA-ATATAT--TATATAGTTTTAAAAATCAT
* ** * *
5533526 TTTTGAAAATATATATATAATATATAGTTTTTTAAAATAATTTTGAAAATGTATATAATATATAG
61 TTTTG-AAATATATATATAATATATAGTTTTTGAAAATAAAATTGAAAATATATATAATACATAG
* *
5533591 TTTTGAAAAGATGTTTTATATTATATT
125 TTTTGAAAACATGTTTAATATTATATT
5533618 ATATATTATAT
1 ATATATTATAT
5533629 TAATATTATT
Statistics
Matches: 143, Mismatches: 13, Indels: 17
0.83 0.08 0.10
Matches are distributed among these distances:
153 13 0.09
154 24 0.17
155 39 0.27
156 56 0.39
157 11 0.08
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.45
Consensus pattern (151 bp):
ATATATTATATAGTTTTGAAAACGATTTATGAAAATATATTATATAGTTTTAAAAATCATTTTTG
AAATATATATATAATATATAGTTTTTGAAAATAAAATTGAAAATATATATAATACATAGTTTTGA
AAACATGTTTAATATTATATT
Found at i:5533624 original size:12 final size:12
Alignment explanation
Indices: 5533607--5533641 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
5533597 AAAGATGTTT
5533607 TATATTATATTA
1 TATATTATATTA
5533619 TATATTATATTA
1 TATATTATATTA
5533631 -ATATTAT-TTA
1 TATATTATATTA
5533641 T
1 T
5533642 TTTTATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 3 0.14
11 7 0.32
12 12 0.55
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TATATTATATTA
Found at i:5533649 original size:10 final size:10
Alignment explanation
Indices: 5533632--5533679 Score: 73
Period size: 10 Copynumber: 4.9 Consensus size: 10
5533622 ATTATATTAA
5533632 TATTATTTATT
1 TATTATTT-TT
5533643 T-TTATTTTT
1 TATTATTTTT
5533652 TATTATTTTT
1 TATTATTTTT
5533662 TATTATTTTT
1 TATTATTTTT
5533672 T-TTATTTT
1 TATTATTTT
5533680 GGTCCAAGGT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
9 10 0.28
10 25 0.69
11 1 0.03
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (10 bp):
TATTATTTTT
Found at i:5533667 original size:13 final size:12
Alignment explanation
Indices: 5533638--5533677 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
5533628 TTAATATTAT
*
5533638 TTATTTTTATTTT
1 TTATTTTT-TTTA
5533651 TTATTATTTTTTA
1 TTATT-TTTTTTA
5533664 TTATTTTTTTTA
1 TTATTTTTTTTA
5533676 TT
1 TT
5533678 TTGGTCCAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 9 0.36
13 13 0.52
14 3 0.12
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.82
Consensus pattern (12 bp):
TTATTTTTTTTA
Found at i:5534648 original size:14 final size:14
Alignment explanation
Indices: 5534629--5534709 Score: 58
Period size: 15 Copynumber: 5.6 Consensus size: 14
5534619 TATATATTTA
5534629 TTTATTTTTCAATT
1 TTTATTTTTCAATT
* **
5534643 TTTATTTTATTAACA
1 TTTATTTT-TCAATT
*
5534658 TTTATTTTCTTAATAT
1 TTTATTTT-TCAAT-T
5534674 TTT-TTACTTTCAATT
1 TTTATT--TTTCAATT
*
5534689 TTT-TTTTTCATTT
1 TTTATTTTTCAATT
5534702 TTTATTTT
1 TTTATTTT
5534710 AATATTTTTA
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
13 10 0.19
14 12 0.22
15 23 0.43
16 7 0.13
17 2 0.04
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTATTTTTCAATT
Found at i:5534716 original size:15 final size:15
Alignment explanation
Indices: 5534667--5534725 Score: 54
Period size: 15 Copynumber: 4.2 Consensus size: 15
5534657 ATTTATTTTC
*
5534667 TTAATATTTTTTACT
1 TTAATATTTTTTATT
*
5534682 TTCA-ATTTTTT-TT
1 TTAATATTTTTTATT
*
5534695 TT--CATTTTTTATT
1 TTAATATTTTTTATT
*
5534708 TTAATATTTTTAATT
1 TTAATATTTTTTATT
5534723 TTA
1 TTA
5534726 TTTGTCTTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
12 7 0.19
13 7 0.19
14 7 0.19
15 15 0.42
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (15 bp):
TTAATATTTTTTATT
Found at i:5534717 original size:14 final size:13
Alignment explanation
Indices: 5534672--5534764 Score: 61
Period size: 14 Copynumber: 7.0 Consensus size: 13
5534662 TTTTCTTAAT
*
5534672 ATTTTTTACTTTCA
1 ATTTTTTA-TTTTA
*
5534686 ATTTTTT-TTTTC
1 ATTTTTTATTTTA
5534698 ATTTTTTATTTTA
1 ATTTTTTATTTTA
5534711 ATATTTTTAATTTT-
1 AT-TTTTT-ATTTTA
5534725 ATTTGTCTT-TCTTT-
1 ATTT-T-TTAT-TTTA
5534739 ATTTTTTATTTT-
1 ATTTTTTATTTTA
*
5534751 ATTTCTTTTTTTTA
1 ATTT-TTTATTTTA
5534765 TAGTTATATA
Statistics
Matches: 66, Mismatches: 4, Indels: 18
0.75 0.05 0.20
Matches are distributed among these distances:
12 19 0.29
13 18 0.27
14 22 0.33
15 7 0.11
ACGTcount: A:0.17, C:0.06, G:0.01, T:0.75
Consensus pattern (13 bp):
ATTTTTTATTTTA
Found at i:5534763 original size:20 final size:20
Alignment explanation
Indices: 5534699--5534763 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
5534689 TTTTTTTTCA
*
5534699 TTTTTTATTTTAATAT-TTTT
1 TTTTTTATTTT-ATTTCTTTT
** * *
5534719 AATTTTATTTGTCTTTCTTTA
1 TTTTTTATTT-TATTTCTTTT
5534740 TTTTTTATTTTATTTCTTTT
1 TTTTTTATTTTATTTCTTTT
5534760 TTTT
1 TTTT
5534764 ATAGTTATAT
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
20 22 0.65
21 12 0.35
ACGTcount: A:0.15, C:0.05, G:0.02, T:0.78
Consensus pattern (20 bp):
TTTTTTATTTTATTTCTTTT
Found at i:5536483 original size:6 final size:6
Alignment explanation
Indices: 5536474--5536500 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5536464 TTAGTTTCAT
5536474 TTTTTA TTTTTA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTT
5536501 CTTTTATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:5537192 original size:54 final size:54
Alignment explanation
Indices: 5537107--5537440 Score: 465
Period size: 54 Copynumber: 6.2 Consensus size: 54
5537097 CGATTGTGAC
* *
5537107 AGTGCCAATACAGTCGTTCATAAACACATTATGAATTCTGTGGGTTGCACACTT
1 AGTGCCGATACGGTCGTTCATAAACACATTATGAATTCTGTGGGTTGCACACTT
*
5537161 AGTGCCGATACGGTCGTTCATAAACATATTATGAATTCTGTGGGTTGCACACTT
1 AGTGCCGATACGGTCGTTCATAAACACATTATGAATTCTGTGGGTTGCACACTT
* *
5537215 AGTGTCGATACGGTCGTTCATAAACATATTATGAATT-TCGTGGGTTGCACACTT
1 AGTGCCGATACGGTCGTTCATAAACACATTATGAATTCT-GTGGGTTGCACACTT
* * *
5537269 AGTGTCGATACGATCGTTCATTAACACATTATGAATT-TCGTGGGTTGCACACTT
1 AGTGCCGATACGGTCGTTCATAAACACATTATGAATTCT-GTGGGTTGCACACTT
* * * *
5537323 AGTTCCGATACTGTCGATCATAAACATATTATGAATTCTGTGGGTTGCACACTT
1 AGTGCCGATACGGTCGTTCATAAACACATTATGAATTCTGTGGGTTGCACACTT
* * * * * *
5537377 AGTGCCAATACGGTCATTCATACACACACTATTAATTATGTGGGTTGCACACTT
1 AGTGCCGATACGGTCGTTCATAAACACATTATGAATTCTGTGGGTTGCACACTT
*
5537431 AGTGTCGATA
1 AGTGCCGATA
5537441 GTACACATGG
Statistics
Matches: 252, Mismatches: 26, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
53 1 0.00
54 250 0.99
55 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.34
Consensus pattern (54 bp):
AGTGCCGATACGGTCGTTCATAAACACATTATGAATTCTGTGGGTTGCACACTT
Found at i:5539070 original size:14 final size:14
Alignment explanation
Indices: 5539048--5539091 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
5539038 CTGTTTGACC
*
5539048 CGACCGAGTCAACT
1 CGACTGAGTCAACT
*
5539062 CGACTGAGTTAACT
1 CGACTGAGTCAACT
5539076 C-ATCTGAGTCAACT
1 CGA-CTGAGTCAACT
5539090 CG
1 CG
5539092 TTCATGTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 1 0.04
14 24 0.96
ACGTcount: A:0.27, C:0.30, G:0.20, T:0.23
Consensus pattern (14 bp):
CGACTGAGTCAACT
Found at i:5543341 original size:12 final size:12
Alignment explanation
Indices: 5543326--5543358 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
5543316 AGAAAACCAT
5543326 AGAGAGAAGTAG
1 AGAGAGAAGTAG
5543338 AGAGAGAAGTAG
1 AGAGAGAAGTAG
5543350 AGAGAGAAG
1 AGAGAGAAG
5543359 CAATAGAGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.42, T:0.06
Consensus pattern (12 bp):
AGAGAGAAGTAG
Found at i:5544538 original size:24 final size:25
Alignment explanation
Indices: 5544492--5544548 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 25
5544482 TGAAACAATA
*
5544492 TATATATATATATAAAAGGTATA-T
1 TATATATATATATAAAAGATATAGT
**
5544516 TATATATATATATAAACTATATAGT
1 TATATATATATATAAAAGATATAGT
5544541 T-TATATAT
1 TATATATAT
5544549 GAACTATTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 27 0.93
25 2 0.07
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (25 bp):
TATATATATATATAAAAGATATAGT
Found at i:5544614 original size:11 final size:11
Alignment explanation
Indices: 5544586--5544628 Score: 63
Period size: 11 Copynumber: 4.1 Consensus size: 11
5544576 TAATTTATGA
5544586 ATATAAA-T-T
1 ATATAAATTAT
*
5544595 ATATCAATTAT
1 ATATAAATTAT
5544606 ATATAAATTAT
1 ATATAAATTAT
5544617 ATATAAATTAT
1 ATATAAATTAT
5544628 A
1 A
5544629 CAATTTATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
9 6 0.20
10 1 0.03
11 23 0.77
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (11 bp):
ATATAAATTAT
Found at i:5544628 original size:20 final size:20
Alignment explanation
Indices: 5544522--5544619 Score: 81
Period size: 20 Copynumber: 4.8 Consensus size: 20
5544512 ATATTATATA
**
5544522 TATATATAAACTATATAGTT
1 TATATATAAACTATATAAAT
* * *
5544542 TATATATGAACTAT-TGAAC
1 TATATATAAACTATATAAAT
* *
5544561 TATATATAAACTACATAATT
1 TATATATAAACTATATAAAT
* *
5544581 TATGAATATAAATTATATCAAT
1 TAT--ATATAAACTATATAAAT
*
5544603 TATATATAAATTATATA
1 TATATATAAACTATATA
5544620 TAAATTATAC
Statistics
Matches: 60, Mismatches: 15, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
19 13 0.22
20 31 0.52
22 16 0.27
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (20 bp):
TATATATAAACTATATAAAT
Found at i:5544700 original size:33 final size:33
Alignment explanation
Indices: 5544662--5544745 Score: 111
Period size: 33 Copynumber: 2.6 Consensus size: 33
5544652 ATAATTATAA
* *
5544662 ATAATATATA-CTATGTATAAATTATATAGTTT
1 ATAATATATAGCTATATATAAACTATATAGTTT
5544694 ATTAATATA-AGCTATATATAAACTATATAGTTT
1 A-TAATATATAGCTATATATAAACTATATAGTTT
5544727 ATATATATATAG-TATATAT
1 ATA-ATATATAGCTATATAT
5544746 GGTTTAGAGT
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
32 4 0.09
33 40 0.87
34 2 0.04
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (33 bp):
ATAATATATAGCTATATATAAACTATATAGTTT
Found at i:5544737 original size:15 final size:15
Alignment explanation
Indices: 5544665--5544745 Score: 53
Period size: 15 Copynumber: 5.3 Consensus size: 15
5544655 ATTATAAATA
5544665 ATATATACTAT-GTAT
1 ATATATA-TATAGTAT
* *
5544680 AAAT-TATATAGTTT
1 ATATATATATAGTAT
5544694 AT-TA-ATATAAGCTAT
1 ATATATATAT-AG-TAT
*
5544709 ATATAAACTATATAGTTT
1 ATAT--A-TATATAGTAT
5544727 ATATATATATAGTAT
1 ATATATATATAGTAT
5544742 ATAT
1 ATAT
5544746 GGTTTAGAGT
Statistics
Matches: 51, Mismatches: 6, Indels: 18
0.68 0.08 0.24
Matches are distributed among these distances:
13 8 0.16
14 8 0.16
15 20 0.39
16 2 0.04
18 7 0.14
19 2 0.04
20 4 0.08
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (15 bp):
ATATATATATAGTAT
Found at i:5544867 original size:20 final size:20
Alignment explanation
Indices: 5544842--5544913 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
5544832 TAAACTAACT
5544842 TATACTATATGTAAACTATA
1 TATACTATATGTAAACTATA
**
5544862 TATACTATATAGTTTAC-ATA
1 TATACTATAT-GTAAACTATA
5544882 TGA-ACTATATGTATAAACTATA
1 T-ATACTATATG--TAAACTATA
*
5544904 TAAACTATAT
1 TATACTATAT
5544914 ATATAAACTA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
19 1 0.02
20 21 0.50
21 9 0.21
22 11 0.26
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (20 bp):
TATACTATATGTAAACTATA
Found at i:5544909 original size:22 final size:21
Alignment explanation
Indices: 5544845--5544929 Score: 77
Period size: 22 Copynumber: 4.0 Consensus size: 21
5544835 ACTAACTTAT
*
5544845 ACTATATG-TAAACTATATAT
1 ACTATATGTTAAACTATATAA
* *
5544865 ACTATATAGTT-TAC-ATATGA
1 ACTATAT-GTTAAACTATATAA
5544885 ACTATATGTATAAACTATATAA
1 ACTATATGT-TAAACTATATAA
* *
5544907 ACTATATATATAAACTATGTAA
1 ACTATATGT-TAAACTATATAA
5544929 A
1 A
5544930 TGTTAGAGTA
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
19 2 0.04
20 19 0.36
21 5 0.09
22 27 0.51
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (21 bp):
ACTATATGTTAAACTATATAA
Found at i:5546386 original size:13 final size:13
Alignment explanation
Indices: 5546368--5546397 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
5546358 TTTAGTAGTT
5546368 TATATATAAACTA
1 TATATATAAACTA
5546381 TATATATAAACTA
1 TATATATAAACTA
5546394 TATA
1 TATA
5546398 GTTTACGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:5547460 original size:16 final size:16
Alignment explanation
Indices: 5547441--5547473 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5547431 TACATTAAGA
*
5547441 GTTATAAATATATGTT
1 GTTAAAAATATATGTT
5547457 GTTAAAAATATATGTT
1 GTTAAAAATATATGTT
5547473 G
1 G
5547474 CAATGGTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.45
Consensus pattern (16 bp):
GTTAAAAATATATGTT
Found at i:5547589 original size:55 final size:55
Alignment explanation
Indices: 5547500--5548113 Score: 774
Period size: 55 Copynumber: 11.2 Consensus size: 55
5547490 CTATGTGTAC
* * * * * *
5547500 TACAGGCACTGTGTGTGCAAATACACGGAATTCATCATGAGTTTATGAATAACCA
1 TACAGACACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCG
** * *
5547555 TACAGACACTATGTGAACAAATCCACAAAATTCATCATGATTTGATGAATAACCG
1 TACAGACACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCG
* * * * *
5547610 TACAAACACTATGTGTGCAAATCCACATAATTCATAATAAGTTGATGAATAACCA
1 TACAGACACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCG
* *
5547665 TACA-AGCACTATGTGTGCATATCCAC-GTAATTCAACATGAGTTGATGAATAACCG
1 TACAGA-CACTATGTGTGCAAATCCACAG-AATTCATCATGAGTTGATGAATAACCG
* * * * *
5547720 TACAAACAATATGTGTGCAAATCCCCATAA-TCATCATGAGTTGATGAATAACCA
1 TACAGACACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCG
5547774 TACATG-CACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCG
1 TACA-GACACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCG
* * * *
5547829 TACAAACACTATGTGTGCAAATCCACGGAATTCATCATAAGTTGACGAATAACCG
1 TACAGACACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCG
* * ** *
5547884 TGCAGGCACTATGTGTGCAAATCCATGGAATTCATCATGAGTTGATGAATAATCG
1 TACAGACACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCG
*
5547939 TACAGACACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCG
1 TACAGACACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCG
*
5547994 TACATG-CACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAAACG
1 TACA-GACACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCG
* * * **
5548049 TATAGGCACTATGTGTGC-AACCCATGGAATTCATCATGAGTTGATGAACT-ACCG
1 TACAGACACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAA-TAACCG
* *
5548103 TATAGGCACTA
1 TACAGACACTA
5548114 CGTCTGCATC
Statistics
Matches: 492, Mismatches: 57, Indels: 21
0.86 0.10 0.04
Matches are distributed among these distances:
54 90 0.18
55 400 0.81
56 2 0.00
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (55 bp):
TACAGACACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCG
Found at i:5547925 original size:219 final size:220
Alignment explanation
Indices: 5547511--5548092 Score: 846
Period size: 219 Copynumber: 2.7 Consensus size: 220
5547501 ACAGGCACTG
* * * **
5547511 TGTGTGCAAATACACGGAATTCATCATGAGTTTATGAATAACCATACA-GACACTATGTGAACAA
1 TGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCATACATG-CACTATGTGTGCAA
* * **
5547575 ATCCACAAAATTCATCATGATTTGATGAATAACCGTACAAACACTATGTGTGCAAATCCACATAA
65 ATCCACAGAATTCATCATGAGTTGATGAATAACCGTACAAACACTATGTGTGCAAATCCACGGAA
* * * *
5547640 TTCATAATAAGTTGATGAATAACCATACAAGCACTATGTGTGCATATCCACGTAATTCAACATGA
130 TTCATCATAAGTTGACGAATAACCATACAAGCACTATGTGTGCAAATCCACGGAATTCAACATGA
5547705 GTTGATGAATAACCGTACAAACAATA
195 GTTGATGAATAACCGTACAAACAATA
* *
5547731 TGTGTGCAAATCCCCATAA-TCATCATGAGTTGATGAATAACCATACATGCACTATGTGTGCAAA
1 TGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCATACATGCACTATGTGTGCAAA
5547795 TCCACAGAATTCATCATGAGTTGATGAATAACCGTACAAACACTATGTGTGCAAATCCACGGAAT
66 TCCACAGAATTCATCATGAGTTGATGAATAACCGTACAAACACTATGTGTGCAAATCCACGGAAT
* * * * *
5547860 TCATCATAAGTTGACGAATAACCGTGCAGGCACTATGTGTGCAAATCCATGGAATTCATCATGAG
131 TCATCATAAGTTGACGAATAACCATACAAGCACTATGTGTGCAAATCCACGGAATTCAACATGAG
* * *
5547925 TTGATGAATAATCGTACAGACACTA
196 TTGATGAATAACCGTACAAACAATA
* *
5547950 TGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACATGCACTATGTGTGCAAA
1 TGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCATACATGCACTATGTGTGCAAA
* * ** * *
5548015 TCCACAGAATTCATCATGAGTTGATGAATAAACGTATAGGCACTATGTGTGC-AACCCATGGAAT
66 TCCACAGAATTCATCATGAGTTGATGAATAACCGTACAAACACTATGTGTGCAAATCCACGGAAT
*
5548079 TCATCATGAGTTGA
131 TCATCATAAGTTGA
5548093 TGAACTACCG
Statistics
Matches: 326, Mismatches: 34, Indels: 5
0.89 0.09 0.01
Matches are distributed among these distances:
219 218 0.67
220 108 0.33
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (220 bp):
TGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCATACATGCACTATGTGTGCAAA
TCCACAGAATTCATCATGAGTTGATGAATAACCGTACAAACACTATGTGTGCAAATCCACGGAAT
TCATCATAAGTTGACGAATAACCATACAAGCACTATGTGTGCAAATCCACGGAATTCAACATGAG
TTGATGAATAACCGTACAAACAATA
Found at i:5548009 original size:274 final size:275
Alignment explanation
Indices: 5547500--5548104 Score: 831
Period size: 274 Copynumber: 2.2 Consensus size: 275
5547490 CTATGTGTAC
* * * * *
5547500 TACAGGCACTGTGTGTGCAAATACACGGAATTCATCATGAGTTTATGAATAACCATACAGACACT
1 TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAAACACT
* * *
5547565 ATGTGAACAAATCCACAAAATTCATCATGATTTGATGAATAACCGTACAAACACTATGTGTGCAA
66 ATGTGAACAAATCCACAAAATTCATCATAAGTTGACGAATAACCGTACAAACACTATGTGTGCAA
* * *
5547630 ATCCACATAATTCATAATAAGTTGATGAATAACCATACAAGCACTATGTGTGCATATCCACGTAA
131 ATCCACAGAATTCATAATAAGTTGATGAATAACCATACAAGCACTATGTGTGCAAATCCACGGAA
* *
5547695 TTCAACATGAGTTGATGAATAACCGTACAAACAATATGTGTGCAAATCCCCATAA-TCATCATGA
196 TTCAACATGAGTTGATGAATAACCGTACAAACAATATGTGTGCAAATCCACAGAATTCATCATGA
*
5547759 GTTGATGAATAACCA
261 GTTGATGAATAAACA
* *
5547774 TACATGCACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCGTACAAACACT
1 TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAAACACT
** ** * **
5547839 ATGTGTGCAAATCCACGGAATTCATCATAAGTTGACGAATAACCGTGCAGGCACTATGTGTGCAA
66 ATGTGAACAAATCCACAAAATTCATCATAAGTTGACGAATAACCGTACAAACACTATGTGTGCAA
** * * * *
5547904 ATCCATGGAATTCATCATGAGTTGATGAATAATCGTAC-AGACACTATGTGTGCAAATCCACGGA
131 ATCCACAGAATTCATAATAAGTTGATGAATAACCATACAAG-CACTATGTGTGCAAATCCACGGA
* ** *
5547968 ATTCATCATGAGTTGATGAATAACCGTACATGCACTATGTGTGCAAATCCACAGAATTCATCATG
195 ATTCAACATGAGTTGATGAATAACCGTACAAACAATATGTGTGCAAATCCACAGAATTCATCATG
*
5548033 AGTTGATGAATAAACG
260 AGTTGATGAATAAACA
* * *
5548049 TATAGGCACTATGTGTGC-AACCCATGGAATTCATCATGAGTTGATGAACT-ACCGTA
1 TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAA-TAACCGTA
5548105 TAGGCACTAC
Statistics
Matches: 289, Mismatches: 39, Indels: 6
0.87 0.12 0.02
Matches are distributed among these distances:
273 2 0.01
274 248 0.86
275 39 0.13
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (275 bp):
TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAAACACT
ATGTGAACAAATCCACAAAATTCATCATAAGTTGACGAATAACCGTACAAACACTATGTGTGCAA
ATCCACAGAATTCATAATAAGTTGATGAATAACCATACAAGCACTATGTGTGCAAATCCACGGAA
TTCAACATGAGTTGATGAATAACCGTACAAACAATATGTGTGCAAATCCACAGAATTCATCATGA
GTTGATGAATAAACA
Found at i:5571023 original size:21 final size:21
Alignment explanation
Indices: 5570997--5571061 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
5570987 TATGACAAGA
5570997 AATTATTCTAAGTCTATAATG
1 AATTATTCTAAGTCTATAATG
* *
5571018 AATTA-T-T-A-T-GACAA-G
1 AATTATTCTAAGTCTATAATG
5571033 CAATTATTCTAAGTCTATAATG
1 -AATTATTCTAAGTCTATAATG
5571055 AATTATT
1 AATTATT
5571062 ATGATATGCC
Statistics
Matches: 33, Mismatches: 4, Indels: 14
0.65 0.08 0.27
Matches are distributed among these distances:
15 1 0.03
16 8 0.24
17 2 0.06
18 2 0.06
19 2 0.06
20 2 0.06
21 15 0.45
22 1 0.03
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (21 bp):
AATTATTCTAAGTCTATAATG
Found at i:5571026 original size:37 final size:37
Alignment explanation
Indices: 5570983--5571065 Score: 157
Period size: 37 Copynumber: 2.2 Consensus size: 37
5570973 TGCTAATGTT
5570983 TTATTATGACAAGAAATTATTCTAAGTCTATAATGAA
1 TTATTATGACAAGAAATTATTCTAAGTCTATAATGAA
*
5571020 TTATTATGACAAGCAATTATTCTAAGTCTATAATGAA
1 TTATTATGACAAGAAATTATTCTAAGTCTATAATGAA
5571057 TTATTATGA
1 TTATTATGA
5571066 TATGCCTAAG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.40
Consensus pattern (37 bp):
TTATTATGACAAGAAATTATTCTAAGTCTATAATGAA
Found at i:5572082 original size:2 final size:2
Alignment explanation
Indices: 5572075--5572120 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
5572065 CAAATCTTAA
5572075 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5572117 AT AT
1 AT AT
5572121 GTGTGTCTGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5572125 original size:2 final size:2
Alignment explanation
Indices: 5572120--5572158 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
5572110 TATATATATA
* *
5572120 TG TG TG TC TG TG TG TG TG TG TG TG TA TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
5572159 ATACCCCCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.03, C:0.03, G:0.44, T:0.51
Consensus pattern (2 bp):
TG
Found at i:5572350 original size:24 final size:24
Alignment explanation
Indices: 5572323--5572393 Score: 97
Period size: 24 Copynumber: 3.0 Consensus size: 24
5572313 AAACGGAGAT
*
5572323 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * * *
5572347 ATCAGATATCAGAACATAATCCAT
1 ATCAGAAATCAGAACAGAATTCAG
5572371 ATCAGAAATCAGAACAGAATTCA
1 ATCAGAAATCAGAACAGAATTCA
5572394 TGTAATGTAT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.51, C:0.18, G:0.11, T:0.20
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:5572352 original size:12 final size:12
Alignment explanation
Indices: 5572325--5572393 Score: 50
Period size: 12 Copynumber: 5.8 Consensus size: 12
5572315 ACGGAGATAT
* *
5572325 CAGAAATCAAAA
1 CAGAATTCAGAA
*
5572337 CAGAATTCAGAT
1 CAGAATTCAGAA
5572349 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* * * *
5572361 CATAATCCATAT
1 CAGAATTCAGAA
*
5572373 CAGAAATCAGAA
1 CAGAATTCAGAA
5572385 CAGAATTCA
1 CAGAATTCA
5572394 TGTAATGTAT
Statistics
Matches: 41, Mismatches: 14, Indels: 4
0.69 0.24 0.07
Matches are distributed among these distances:
11 2 0.05
12 37 0.90
13 2 0.05
ACGTcount: A:0.51, C:0.19, G:0.12, T:0.19
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:5572429 original size:48 final size:48
Alignment explanation
Indices: 5572321--5572414 Score: 129
Period size: 48 Copynumber: 2.0 Consensus size: 48
5572311 GTAAACGGAG
*
5572321 ATATCAGAAATCAAAACAGAATTCAGATCAGATATCAGAACATAATCC
1 ATATCAGAAATCAAAACAGAATTCAGATAAGATATCAGAACATAATCC
* *
5572369 ATATCAGAAATCAGAACAGAATTCATG-TAATG-TATCATAACATAAT
1 ATATCAGAAATCAAAACAGAATTCA-GATAA-GATATCAGAACATAAT
5572415 TCTAGTCGGA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
48 39 0.95
49 2 0.05
ACGTcount: A:0.49, C:0.16, G:0.11, T:0.24
Consensus pattern (48 bp):
ATATCAGAAATCAAAACAGAATTCAGATAAGATATCAGAACATAATCC
Found at i:5577056 original size:48 final size:48
Alignment explanation
Indices: 5577000--5577110 Score: 136
Period size: 48 Copynumber: 2.3 Consensus size: 48
5576990 GTAAACAGAT
* *
5577000 ATATCAGAAATCAAAACCGAATTCAGATCA-GATATCATAACAGAATCC
1 ATATCAGAAATCAAAACAGAATTCAGATAATG-TATCATAACAGAATCC
* * * *
5577048 ATATCAGAAATCAGAACATAATTCAGGTAATGTATCATAACAGAATTC
1 ATATCAGAAATCAAAACAGAATTCAGATAATGTATCATAACAGAATCC
5577096 A-AGTCAGAAATCAAA
1 ATA-TCAGAAATCAAA
5577111 TAAAATATTT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
47 1 0.02
48 52 0.96
49 1 0.02
ACGTcount: A:0.49, C:0.17, G:0.12, T:0.23
Consensus pattern (48 bp):
ATATCAGAAATCAAAACAGAATTCAGATAATGTATCATAACAGAATCC
Found at i:5577108 original size:24 final size:24
Alignment explanation
Indices: 5577003--5577108 Score: 83
Period size: 24 Copynumber: 4.4 Consensus size: 24
5576993 AACAGATATA
* *
5577003 TCAGAAATCAAAACCGAATTC-AG
1 TCAGAAATCATAACAGAATTCAAG
* *
5577026 ATCAGATATCATAACAGAATCCATA-
1 -TCAGAAATCATAACAGAATTCA-AG
* * *
5577051 TCAGAAATCAGAACATAATTCAGG
1 TCAGAAATCATAACAGAATTCAAG
* *
5577075 TAATG-TATCATAACAGAATTCAAG
1 TCA-GAAATCATAACAGAATTCAAG
5577099 TCAGAAATCA
1 TCAGAAATCA
5577109 AATAAAATAT
Statistics
Matches: 61, Mismatches: 16, Indels: 10
0.70 0.18 0.11
Matches are distributed among these distances:
23 1 0.02
24 58 0.95
25 1 0.02
26 1 0.02
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.23
Consensus pattern (24 bp):
TCAGAAATCATAACAGAATTCAAG
Found at i:5579479 original size:10 final size:10
Alignment explanation
Indices: 5579464--5579503 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
5579454 ATTCAACGCC
5579464 CGGTCAACGT
1 CGGTCAACGT
*
5579474 CGGTCAAAGTT
1 CGGTCAACG-T
5579485 CTGGTCAACGT
1 C-GGTCAACGT
5579496 CGGTCAAC
1 CGGTCAAC
5579504 AGTCAACGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
10 15 0.58
11 4 0.15
12 7 0.27
ACGTcount: A:0.23, C:0.28, G:0.28, T:0.23
Consensus pattern (10 bp):
CGGTCAACGT
Found at i:5579510 original size:17 final size:17
Alignment explanation
Indices: 5579488--5579526 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
5579478 CAAAGTTCTG
5579488 GTCAACGTC-GGTCAACA
1 GTCAACG-CAGGTCAACA
*
5579505 GTCAACGCAGGTCAACG
1 GTCAACGCAGGTCAACA
5579522 GTCAA
1 GTCAA
5579527 TAGTCAATCG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.31, C:0.28, G:0.26, T:0.15
Consensus pattern (17 bp):
GTCAACGCAGGTCAACA
Found at i:5590901 original size:106 final size:106
Alignment explanation
Indices: 5590758--5590970 Score: 345
Period size: 106 Copynumber: 2.0 Consensus size: 106
5590748 GTCTTTAAAA
* ** ** *
5590758 TGCATCTAGCTAGATAGTCTTGTTTTGGAAATCATGAATGAGTTTTCATGGTAGATTCTTGAAAT
1 TGCATCTAGCTAGATAATAATGTTTTAAAAAGCATGAATGAGTTTTCATGGTAGATTCTTGAAAT
*
5590823 TGGTGTTTTAGCATGTTTAAATACCTTCTAAGACCCTCTCT
66 TGGTGTTTTAACATGTTTAAATACCTTCTAAGACCCTCTCT
5590864 TGCATCTAGCTAGATAATAATGTTTTAAAAAGCATGAATGAGTTTTCATGGTAGATTCTTGAAAT
1 TGCATCTAGCTAGATAATAATGTTTTAAAAAGCATGAATGAGTTTTCATGGTAGATTCTTGAAAT
* *
5590929 TGGTGTTTTAACATGTTTAAATACCTTTTATGACCCTCTCT
66 TGGTGTTTTAACATGTTTAAATACCTTCTAAGACCCTCTCT
5590970 T
1 T
5590971 ATGCATATAA
Statistics
Matches: 98, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
106 98 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (106 bp):
TGCATCTAGCTAGATAATAATGTTTTAAAAAGCATGAATGAGTTTTCATGGTAGATTCTTGAAAT
TGGTGTTTTAACATGTTTAAATACCTTCTAAGACCCTCTCT
Found at i:5593537 original size:11 final size:11
Alignment explanation
Indices: 5593521--5593551 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
5593511 AGCTTTATAT
5593521 TATGTTTTACA
1 TATGTTTTACA
5593532 TATGTTTTACA
1 TATGTTTTACA
5593543 TATGTTTTA
1 TATGTTTTA
5593552 GATTCATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.26, C:0.06, G:0.10, T:0.58
Consensus pattern (11 bp):
TATGTTTTACA
Found at i:5598929 original size:20 final size:21
Alignment explanation
Indices: 5598904--5598950 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
5598894 GGATGTGGTC
*
5598904 ATTTCTAGCCA-TTGGGGATG
1 ATTTCTACCCATTTGGGGATG
5598924 ATTTCTACCCATTTGGGGATG
1 ATTTCTACCCATTTGGGGATG
*
5598945 TTTTCT
1 ATTTCT
5598951 CTACAAACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.17, C:0.17, G:0.23, T:0.43
Consensus pattern (21 bp):
ATTTCTACCCATTTGGGGATG
Found at i:5599005 original size:21 final size:23
Alignment explanation
Indices: 5598976--5599019 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
5598966 ATCCCAGGGC
5598976 ATGGAGTATTG-GTAC-TCCTTTA
1 ATGGAGTA-TGAGTACTTCCTTTA
5598998 ATGG-GTATGAGTACTTCCTTTA
1 ATGGAGTATGAGTACTTCCTTTA
5599020 CTAATTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 2 0.10
21 7 0.35
22 11 0.55
ACGTcount: A:0.23, C:0.14, G:0.23, T:0.41
Consensus pattern (23 bp):
ATGGAGTATGAGTACTTCCTTTA
Found at i:5602038 original size:19 final size:20
Alignment explanation
Indices: 5602014--5602063 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
5602004 ATGAAAAAAT
5602014 GGTATCGATACCATAGTA-G
1 GGTATCGATACCATAGTAGG
*
5602033 GGTATCGATACCATGGTAGG
1 GGTATCGATACCATAGTAGG
*
5602053 GGTATCAATAC
1 GGTATCGATAC
5602064 TGAAGAGCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (20 bp):
GGTATCGATACCATAGTAGG
Found at i:5602440 original size:58 final size:58
Alignment explanation
Indices: 5602371--5602817 Score: 622
Period size: 58 Copynumber: 7.7 Consensus size: 58
5602361 ATGACACTAA
5602371 GTGTGCATAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTC
1 GTGTGCATAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTC
* * * *
5602429 GTGTGCATAAAGTTAAGAAATTCATACTAAATGTAAGAATTTCCGTATTAGGCACTTC
1 GTGTGCATAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTC
*
5602487 GTGTACA-AAAGGTTAAGAAATTCATACTAAGTGTATGAATTTCCT-TATTGGGCACTTC
1 GTGTGCATAAA-GTTAAGAAATTCATACTAAGTGTATGAATTT-CTGTATTGGGCACTTC
* * *
5602545 GTGTGCA-AAAATTAAGAAATTCACACTAAGTGTATGAATTTC-GTATTAGGCACTTC
1 GTGTGCATAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTC
5602601 GTGTGCATAAAGTTAAGAAATTCATACTAAGTGTATGAATTT-TCGTATTGGGCACTTC
1 GTGTGCATAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCT-GTATTGGGCACTTC
* * * *
5602659 GTGTGCATAAAGATAAGAAATTCATACTAAGTGTATAAATTTCCGTATTGGGCACCTC
1 GTGTGCATAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTC
* * * *
5602717 GTGTGTAAAAAGTTAAGAAATTAATACTAAGTGTATGAATTTCCT-TATTGGGCACTTT
1 GTGTGCATAAAGTTAAGAAATTCATACTAAGTGTATGAATTT-CTGTATTGGGCACTTC
* *
5602775 GTGTGCA-AACCA-TTAAGAGATTGATACTAAGTGTATGAATTTC
1 GTGTGCATAA--AGTTAAGAAATTCATACTAAGTGTATGAATTTC
5602818 CATGTGGGAA
Statistics
Matches: 348, Mismatches: 31, Indels: 21
0.87 0.08 0.05
Matches are distributed among these distances:
56 20 0.06
57 67 0.19
58 258 0.74
59 3 0.01
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (58 bp):
GTGTGCATAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTC
Found at i:5602781 original size:230 final size:231
Alignment explanation
Indices: 5602371--5602817 Score: 738
Period size: 230 Copynumber: 1.9 Consensus size: 231
5602361 ATGACACTAA
5602371 GTGTGCATAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTCGTGTGCA
1 GTGTGCATAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTCGTGTGCA
* * *
5602436 TAAAGTTAAGAAATTCATACTAAATGTAAGAATTTCCGTATTAGGCACTTCGTGTACAAAAGGTT
66 TAAAGATAAGAAATTCATACTAAATGTAAGAATTTCCGTATTAGGCACCTCGTGTACAAAAAGTT
*
5602501 AAGAAATTCATACTAAGTGTATGAATTTCCTTATTGGGCACTTCGTGTGCAAA-AATTAAGAAAT
131 AAGAAATTAATACTAAGTGTATGAATTTCCTTATTGGGCACTTCGTGTGCAAACAATTAAGAAAT
5602565 TCACACTAAGTGTATGAATTTCGTATTAGGCACTTC
196 TCACACTAAGTGTATGAATTTCGTATTAGGCACTTC
5602601 GTGTGCATAAAGTTAAGAAATTCATACTAAGTGTATGAATTT-TCGTATTGGGCACTTCGTGTGC
1 GTGTGCATAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCT-GTATTGGGCACTTCGTGTGC
* * **
5602665 ATAAAGATAAGAAATTCATACTAAGTGTATA-AATTTCCGTATTGGGCACCTCGTGTGTAAAAAG
65 ATAAAGATAAGAAATTCATACTAAATGTA-AGAATTTCCGTATTAGGCACCTCGTGTACAAAAAG
* * *
5602729 TTAAGAAATTAATACTAAGTGTATGAATTTCCTTATTGGGCACTTTGTGTGCAAACCATTAAGAG
129 TTAAGAAATTAATACTAAGTGTATGAATTTCCTTATTGGGCACTTCGTGTGCAAACAATTAAGAA
* *
5602794 ATTGATACTAAGTGTATGAATTTC
194 ATTCACACTAAGTGTATGAATTTC
5602818 CATGTGGGAA
Statistics
Matches: 201, Mismatches: 13, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
229 1 0.00
230 170 0.85
231 30 0.15
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (231 bp):
GTGTGCATAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTCGTGTGCA
TAAAGATAAGAAATTCATACTAAATGTAAGAATTTCCGTATTAGGCACCTCGTGTACAAAAAGTT
AAGAAATTAATACTAAGTGTATGAATTTCCTTATTGGGCACTTCGTGTGCAAACAATTAAGAAAT
TCACACTAAGTGTATGAATTTCGTATTAGGCACTTC
Found at i:5607056 original size:25 final size:25
Alignment explanation
Indices: 5607022--5607074 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
5607012 CATGAAAAGA
*
5607022 GTTGTAACATAGTTTGTTGCCAAAT
1 GTTGTAACATAGTTTGTTCCCAAAT
5607047 GTTGTAACATAGTTTGTTCCCAAAT
1 GTTGTAACATAGTTTGTTCCCAAAT
5607072 GTT
1 GTT
5607075 TGACATGTCA
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:0.26, C:0.13, G:0.19, T:0.42
Consensus pattern (25 bp):
GTTGTAACATAGTTTGTTCCCAAAT
Found at i:5609036 original size:19 final size:20
Alignment explanation
Indices: 5609012--5609083 Score: 92
Period size: 19 Copynumber: 3.5 Consensus size: 20
5609002 ATGCAAAAAT
5609012 GGTATCGATACCATAGTAG-
1 GGTATCGATACCATAGTAGA
5609031 GGTATCGATACCATAGTATGA
1 GGTATCGATACCATAGTA-GA
* * *
5609052 TAGTATCGATACTATGGTAGA
1 -GGTATCGATACCATAGTAGA
5609073 GGTATCGATAC
1 GGTATCGATAC
5609084 TGAAGAGCCA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
19 18 0.39
20 11 0.24
21 2 0.04
22 15 0.33
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (20 bp):
GGTATCGATACCATAGTAGA
Found at i:5609491 original size:58 final size:58
Alignment explanation
Indices: 5609413--5609860 Score: 544
Period size: 58 Copynumber: 7.7 Consensus size: 58
5609403 ATGGCACAAA
5609413 GTGTGCATAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCA-TTAC
1 GTGTGCATAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTT-C
* ** *
5609471 ATGTTTATAAAGTTATGAAATTCATACTAAGTGTATGAACTTT-CGTATTGGGCACTTC
1 GTGTGCATAAAGTTAAGAAATTCATACTAAGTGTATGAA-TTTCCGTATTGGGCACTTC
* ** * * *
5609529 GTGTGCAAAAAGTTAAGAAATTTGTACTAAGTGTATGAATTTCCATATTAGGCGCTTC
1 GTGTGCATAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTC
* * *
5609587 GTGTGGAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTC
1 GTGTGCATAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTC
* * * * *
5609645 GTGTGCATAAAGATAAGAAATTCATACAAAATATATGAATTTCCGTACTGGGCACTTC
1 GTGTGCATAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTC
** * *
5609703 GTGTGCATAAAGACAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACCTC
1 GTGTGCATAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTC
* * * * * * *
5609761 GTGTGCAAAAAGCTAAGAAATTCGTACTGAGTGTATGAATTTTCGTTTTGGGCACTTT
1 GTGTGCATAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTC
* * *
5609819 GTGTG-A-AAACCATTAAGAGATTCATACTAAGTATATGAATTT
1 GTGTGCATAAA--GTTAAGAAATTCATACTAAGTGTATGAATTT
5609861 GCATGTGGGA
Statistics
Matches: 335, Mismatches: 50, Indels: 10
0.85 0.13 0.03
Matches are distributed among these distances:
56 3 0.01
57 4 0.01
58 323 0.96
59 5 0.01
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.34
Consensus pattern (58 bp):
GTGTGCATAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTC
Done.