Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr4
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: 30015117
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1306243 characters in sequence are not A, C, G, or T
File 82 of 85
Found at i:28610724 original size:12 final size:13
Alignment explanation
Indices: 28610700--28610724 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28610690 TTTATTTATT
28610700 TATTTAATAAAAA
1 TATTTAATAAAAA
28610713 TATTTAATAAAA
1 TATTTAATAAAA
28610725 CATTAATTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TATTTAATAAAAA
Found at i:28613383 original size:14 final size:14
Alignment explanation
Indices: 28613364--28613391 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
28613354 ATATTAACAT
28613364 GGGTCAAAACTGAA
1 GGGTCAAAACTGAA
28613378 GGGTCAAAACTGAA
1 GGGTCAAAACTGAA
28613392 AACTGTTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.29, T:0.14
Consensus pattern (14 bp):
GGGTCAAAACTGAA
Found at i:28633594 original size:28 final size:28
Alignment explanation
Indices: 28633553--28633606 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
28633543 GTAATTTTTT
28633553 TTTAAAAAAATTGTGATAGGAACATTGG
1 TTTAAAAAAATTGTGATAGGAACATTGG
*
28633581 TTTAAAAAATTTGTGATAGGAACATT
1 TTTAAAAAAATTGTGATAGGAACATT
28633607 AAATTCAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.35
Consensus pattern (28 bp):
TTTAAAAAAATTGTGATAGGAACATTGG
Found at i:28637525 original size:2 final size:2
Alignment explanation
Indices: 28637518--28637570 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
28637508 GAACAAAGGG
28637518 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
28637560 GA GA GA G- GA GA
1 GA GA GA GA GA GA
28637571 CGGGCGTATG
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:28641124 original size:15 final size:16
Alignment explanation
Indices: 28641104--28641136 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
28641094 AAAAGAAAAA
*
28641104 TTTTAATTAA-TTAAT
1 TTTTAAATAATTTAAT
28641119 TTTTAAATAATTTAAT
1 TTTTAAATAATTTAAT
28641135 TT
1 TT
28641137 AAATTAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTAAATAATTTAAT
Found at i:28650638 original size:6 final size:6
Alignment explanation
Indices: 28650630--28650664 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
28650620 AGACAAGCCG
* *
28650630 GTTCCG GTTCCA GTTCCT GTTCCA GTTCCA GTTCC
1 GTTCCA GTTCCA GTTCCA GTTCCA GTTCCA GTTCC
28650665 GGTACTGGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.09, C:0.34, G:0.20, T:0.37
Consensus pattern (6 bp):
GTTCCA
Found at i:28650657 original size:18 final size:18
Alignment explanation
Indices: 28650630--28650664 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
28650620 AGACAAGCCG
*
28650630 GTTCCGGTTCCAGTTCCT
1 GTTCCAGTTCCAGTTCCT
28650648 GTTCCAGTTCCAGTTCC
1 GTTCCAGTTCCAGTTCC
28650665 GGTACTGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.09, C:0.34, G:0.20, T:0.37
Consensus pattern (18 bp):
GTTCCAGTTCCAGTTCCT
Found at i:28655276 original size:18 final size:18
Alignment explanation
Indices: 28655236--28655284 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
28655226 ATGGTGCTGG
28655236 TGATGATGATGATGAAGA
1 TGATGATGATGATGAAGA
* **
28655254 CGATGATGATGATGAATT
1 TGATGATGATGATGAAGA
*
28655272 TGATGATGCTGAT
1 TGATGATGATGAT
28655285 TCAGGAGCAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.33, C:0.04, G:0.31, T:0.33
Consensus pattern (18 bp):
TGATGATGATGATGAAGA
Found at i:28671061 original size:15 final size:16
Alignment explanation
Indices: 28671037--28671071 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
28671027 ACTTAATAAT
*
28671037 TAAAATATTTAATTA-
1 TAAAAAATTTAATTAC
28671052 TAAAAAATTTAATTAC
1 TAAAAAATTTAATTAC
28671068 TAAA
1 TAAA
28671072 TAAAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (16 bp):
TAAAAAATTTAATTAC
Found at i:28679963 original size:269 final size:269
Alignment explanation
Indices: 28679438--28679966 Score: 697
Period size: 269 Copynumber: 2.0 Consensus size: 269
28679428 TCCATAATTA
* * *
28679438 AATCTTGACAAGAAATAACGTTTTAATTTACTAATAACAATTAAAATTGAAAGTTTCCAAATCTT
1 AATCTTGACAAGAAATAAAGTTTTAATTTAATAATAACAATTAAAATTGAAAGTTTCCAAATCTG
* *
28679503 GTGGCAATGTTTATTACTCTAAAGGAAAATTCTCCTTCTTGATCCTTAATTATATAAGCTTGGCA
66 GTGGCAATGCTTATTACTCTAAAGGAAAATTATCCTTCTTGATCCTTAATTATATAAGCTTGGCA
* * * *
28679568 ATTAATTTTCAACTTGTTTAACAAGTAAAATCTCAGCTTGAATTGAATGTAGCAAGAAGGTAAAA
131 ATTAATTTTCAACTTATTTAACAAGTAAAATCTCAGCTTGAATTGAATATAACAAGAAGATAAAA
* * * * * *
28679633 ATCGAGTTTGTTATATGATCTTGTGTTAGTAAATGTGGTGGGAAATAATATTAGATTGAAATGTA
196 ATCGAGTCTATTATATGATCTTATATTAGTAAATATGGTGAGAAATAATATTAGATTGAAATGTA
28679698 TCATTATTG
261 TCATTATTG
** * *
28679707 AATCTTGAGGAGAAATAAAGTTTTAATTTAATAATTACAATTAAAATTGAAAGTTTTCAAATCTG
1 AATCTTGACAAGAAATAAAGTTTTAATTTAATAATAACAATTAAAATTGAAAGTTTCCAAATCTG
* * *
28679772 GTGGCAATGCTTATTA-TCCTAAAGGAAAATTATGCTTCTTTATCCTTAATTATATAAGTTTGGG
66 GTGGCAATGCTTATTACT-CTAAAGGAAAATTATCCTTCTTGATCCTTAATTATATAAGCTT-GG
* * * * * * * *
28679836 GATTTAGTTTTCAACTTATTTAACAAGTAAAATCTTATCTTGATTTGGATATAATAAGGAA-ATA
129 CAATTAATTTTCAACTTATTTAACAAGTAAAATCTCAGCTTGAATTGAATATAACAA-GAAGATA
* * *
28679900 AAAGTCGAGTCTATTGTATGTTCTTATATT-GATAAATATGGTGAGAAATAATATTAG-TTGAAA
193 AAAATCGAGTCTATTATATGATCTTATATTAG-TAAATATGGTGAGAAATAATATTAGATTGAAA
28679963 TGTA
257 TGTA
28679967 AATAAAGCTG
Statistics
Matches: 223, Mismatches: 33, Indels: 8
0.84 0.12 0.03
Matches are distributed among these distances:
268 1 0.00
269 123 0.55
270 96 0.43
271 3 0.01
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38
Consensus pattern (269 bp):
AATCTTGACAAGAAATAAAGTTTTAATTTAATAATAACAATTAAAATTGAAAGTTTCCAAATCTG
GTGGCAATGCTTATTACTCTAAAGGAAAATTATCCTTCTTGATCCTTAATTATATAAGCTTGGCA
ATTAATTTTCAACTTATTTAACAAGTAAAATCTCAGCTTGAATTGAATATAACAAGAAGATAAAA
ATCGAGTCTATTATATGATCTTATATTAGTAAATATGGTGAGAAATAATATTAGATTGAAATGTA
TCATTATTG
Found at i:28688026 original size:18 final size:18
Alignment explanation
Indices: 28688003--28688039 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
28687993 TAACACTATA
* *
28688003 ATATATTATGTTATTTAT
1 ATATATTATATAATTTAT
28688021 ATATATTATATAATTTAT
1 ATATATTATATAATTTAT
28688039 A
1 A
28688040 ACACAAAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
ATATATTATATAATTTAT
Found at i:28688472 original size:22 final size:22
Alignment explanation
Indices: 28688444--28688489 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
28688434 CTTCCAACAC
*
28688444 AAGTATGAAATGTTTATGAGCA
1 AAGTATGAAATATTTATGAGCA
28688466 AAGTATGAAATATTTATGAGCA
1 AAGTATGAAATATTTATGAGCA
28688488 AA
1 AA
28688490 TTTCAAGAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.46, C:0.04, G:0.20, T:0.30
Consensus pattern (22 bp):
AAGTATGAAATATTTATGAGCA
Found at i:28695594 original size:31 final size:30
Alignment explanation
Indices: 28695550--28695611 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
28695540 TATATTTTTA
*
28695550 AATAAATACAATTAAATCAAAATTAAAATTT
1 AATAAATACAATTAAA-CAAAACTAAAATTT
* * * *
28695581 AATATATATAATTATACGAAACTAAAATTT
1 AATAAATACAATTAAACAAAACTAAAATTT
28695611 A
1 A
28695612 TGTCTCAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
30 13 0.50
31 13 0.50
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.34
Consensus pattern (30 bp):
AATAAATACAATTAAACAAAACTAAAATTT
Found at i:28695679 original size:3 final size:3
Alignment explanation
Indices: 28695671--28695703 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
28695661 TATATACTAT
28695671 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28695704 GTGGTTAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:28696306 original size:31 final size:31
Alignment explanation
Indices: 28696252--28696311 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
28696242 CTTAAAAAAA
28696252 GACTTAAATAAAATCTTTCGAATAGTTTATT
1 GACTTAAATAAAATCTTTCGAATAGTTTATT
* *
28696283 GACTTGAATGAAAA-CTTTTGAATAGTTTA
1 GACTTAAAT-AAAATCTTTCGAATAGTTTA
28696312 ATGATCATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.40
Consensus pattern (31 bp):
GACTTAAATAAAATCTTTCGAATAGTTTATT
Found at i:28697684 original size:31 final size:30
Alignment explanation
Indices: 28697640--28697701 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
28697630 TATATTTTTA
*
28697640 AATAAATACAATTAAATCAAAATTAAAATTT
1 AATAAATACAATTAAA-CAAAACTAAAATTT
* * * *
28697671 AATATATATAATTATACGAAACTAAAATTT
1 AATAAATACAATTAAACAAAACTAAAATTT
28697701 A
1 A
28697702 TGTCTCAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
30 13 0.50
31 13 0.50
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.34
Consensus pattern (30 bp):
AATAAATACAATTAAACAAAACTAAAATTT
Found at i:28697769 original size:3 final size:3
Alignment explanation
Indices: 28697761--28697793 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
28697751 TATATACTAT
28697761 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28697794 GTGGTTAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:28698396 original size:31 final size:31
Alignment explanation
Indices: 28698342--28698401 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
28698332 CTTAAAAAAA
28698342 GACTTAAATAAAATCTTTCGAATAGTTTATT
1 GACTTAAATAAAATCTTTCGAATAGTTTATT
* *
28698373 GACTTGAATGAAAA-CTTTTGAATAGTTTA
1 GACTTAAAT-AAAATCTTTCGAATAGTTTA
28698402 ATGATCATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.40
Consensus pattern (31 bp):
GACTTAAATAAAATCTTTCGAATAGTTTATT
Found at i:28701349 original size:28 final size:27
Alignment explanation
Indices: 28701305--28701365 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
28701295 TTTAGTGTAG
* * *
28701305 AAAATATTAAATTAATT-TTATTTTATT
1 AAAAAATTAAATAAATTATT-TTTTATA
28701332 AAAAAATTGAAATAAATTATTTTTTATA
1 AAAAAATT-AAATAAATTATTTTTTATA
28701360 AAAAAA
1 AAAAAA
28701366 ATTCAAAGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 7 0.24
28 20 0.69
29 2 0.07
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (27 bp):
AAAAAATTAAATAAATTATTTTTTATA
Found at i:28702806 original size:60 final size:59
Alignment explanation
Indices: 28702728--28702841 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 59
28702718 AGTTGGTTGA
* * * * *
28702728 TATTTTTTAACTTTTCATAATTGGGTGACCAAAAAAGAAATTTACTCATAGTTGAAAGAT
1 TATTTTATAACTTTTCATAATTGGATGACC-AAAAACAAATTCACTAATAGTTGAAAGAT
* * *
28702788 TATTTTATAATTTTTCATAGTTGGATGACCTAAAACAAATTCACTAATAGTTGA
1 TATTTTATAACTTTTCATAATTGGATGACCAAAAACAAATTCACTAATAGTTGA
28702842 GTGACTATCA
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
59 20 0.43
60 26 0.57
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (59 bp):
TATTTTATAACTTTTCATAATTGGATGACCAAAAACAAATTCACTAATAGTTGAAAGAT
Found at i:28708577 original size:23 final size:23
Alignment explanation
Indices: 28708550--28708604 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
28708540 AAATAATATG
28708550 AATTGAATTCATATTTAAGTAAT
1 AATTGAATTCATATTTAAGTAAT
28708573 AATTGAATTCATATTTAAGTAAT
1 AATTGAATTCATATTTAAGTAAT
28708596 AATTGAATT
1 AATTGAATT
28708605 AAAAATAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.44
Consensus pattern (23 bp):
AATTGAATTCATATTTAAGTAAT
Found at i:28715245 original size:21 final size:21
Alignment explanation
Indices: 28715219--28715260 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
28715209 AGGTAGTTTC
28715219 ATGGAATTTTCGGAGACAAGT
1 ATGGAATTTTCGGAGACAAGT
28715240 ATGGAATTTTCGGAGACAAGT
1 ATGGAATTTTCGGAGACAAGT
28715261 TCGGTTCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.10, G:0.29, T:0.29
Consensus pattern (21 bp):
ATGGAATTTTCGGAGACAAGT
Found at i:28738308 original size:15 final size:15
Alignment explanation
Indices: 28738288--28738330 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
28738278 TGGCACCAAA
28738288 AGCTGAGAAGAAGCC
1 AGCTGAGAAGAAGCC
28738303 AGCTGAGAAGAAGCC
1 AGCTGAGAAGAAGCC
* *
28738318 AGCGGAGGAGAAG
1 AGCTGAGAAGAAG
28738331 AAGACGGTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.40, C:0.16, G:0.40, T:0.05
Consensus pattern (15 bp):
AGCTGAGAAGAAGCC
Found at i:28751754 original size:26 final size:27
Alignment explanation
Indices: 28751673--28751757 Score: 82
Period size: 31 Copynumber: 3.0 Consensus size: 27
28751663 TTTTCTTCAT
* * *
28751673 ATTTTTTAATAATATAAACAACTATGA
1 ATTTTTGAATAACATAAAGAACTATGA
28751700 ATTTTTGAATAACATAAAATGAAGGACTATG-
1 ATTTTTGAATAACAT-AAA-G-A--ACTATGA
*
28751731 GTTTTTGAATAACATAAAGAACTATGA
1 ATTTTTGAATAACATAAAGAACTATGA
28751758 GCTGTCATTT
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
26 6 0.12
27 13 0.27
28 4 0.08
29 1 0.02
30 4 0.08
31 14 0.29
32 6 0.12
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.35
Consensus pattern (27 bp):
ATTTTTGAATAACATAAAGAACTATGA
Found at i:28752125 original size:23 final size:22
Alignment explanation
Indices: 28752083--28752127 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
28752073 AATAATATCA
*
28752083 TATTAAAATTATTATTAAATAT
1 TATTAAAATTATTATAAAATAT
28752105 TATTAACAATTATGT-TAAAATAT
1 TATTAA-AATTAT-TATAAAATAT
28752128 GAATAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 6 0.30
23 13 0.65
24 1 0.05
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (22 bp):
TATTAAAATTATTATAAAATAT
Found at i:28757504 original size:13 final size:13
Alignment explanation
Indices: 28757486--28757511 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28757476 CCAGAAACTG
28757486 ATTTGCAGAAAAC
1 ATTTGCAGAAAAC
28757499 ATTTGCAGAAAAC
1 ATTTGCAGAAAAC
28757512 TACCCATTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.23
Consensus pattern (13 bp):
ATTTGCAGAAAAC
Found at i:28777356 original size:18 final size:17
Alignment explanation
Indices: 28777325--28777359 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
28777315 GATTTAGGGT
28777325 TTAAATTTTTTAATTAA
1 TTAAATTTTTTAATTAA
28777342 TTAAATTTATTTAATTAA
1 TTAAATTT-TTTAATTAA
28777360 AAATCTATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTAAATTTTTTAATTAA
Found at i:28785447 original size:18 final size:18
Alignment explanation
Indices: 28785421--28785455 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28785411 TCATTTAAAG
* *
28785421 ATTATAAAGATATAAATT
1 ATTAAAAAGATAAAAATT
28785439 ATTAAAAAGATAAAAAT
1 ATTAAAAAGATAAAAAT
28785456 ACACTTTTAC
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:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (18 bp):
ATTAAAAAGATAAAAATT
Found at i:28795036 original size:39 final size:39
Alignment explanation
Indices: 28794982--28795061 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
28794972 TTGTCAGAAT
*
28794982 TTGGGTATTTATGTATGAGTTACGTGAAGAATAAGAAAA
1 TTGGGTATTTATGTATGAGTTACATGAAGAATAAGAAAA
*
28795021 TTGGGTATTTATGTATGAGTTACATGAATAATAAGAAAA
1 TTGGGTATTTATGTATGAGTTACATGAAGAATAAGAAAA
28795060 TT
1 TT
28795062 ATTAACTCTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.36
Consensus pattern (39 bp):
TTGGGTATTTATGTATGAGTTACATGAAGAATAAGAAAA
Found at i:28799549 original size:16 final size:16
Alignment explanation
Indices: 28799524--28799558 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
28799514 GAATACTTTT
*
28799524 TAAAAGTATTTTTAAA
1 TAAAAATATTTTTAAA
28799540 TAAAAATATTTTTAAA
1 TAAAAATATTTTTAAA
28799556 TAA
1 TAA
28799559 GCTGTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (16 bp):
TAAAAATATTTTTAAA
Found at i:28800646 original size:5 final size:5
Alignment explanation
Indices: 28800636--28800661 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
28800626 GTAGGCTAAA
28800636 CGCAC CGCAC CGCAC CGCAC CGCAC C
1 CGCAC CGCAC CGCAC CGCAC CGCAC C
28800662 CAATCGACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.62, G:0.19, T:0.00
Consensus pattern (5 bp):
CGCAC
Found at i:28811221 original size:20 final size:20
Alignment explanation
Indices: 28811198--28811236 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
28811188 ATTAAAAATT
28811198 TTGAACTAAA-ATGGTCTTAA
1 TTGAA-TAAATATGGTCTTAA
*
28811218 TTGAATAAATATTGTCTTA
1 TTGAATAAATATGGTCTTA
28811237 TAGGGTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.41
Consensus pattern (20 bp):
TTGAATAAATATGGTCTTAA
Found at i:28812150 original size:232 final size:231
Alignment explanation
Indices: 28811715--28812171 Score: 736
Period size: 231 Copynumber: 2.0 Consensus size: 231
28811705 AATTCAGTTT
* *
28811715 TTTTTTTTATGAAATAGCTTTGAAGTCATCAATCTGTGAATCAAAATCGAAATAACTTTCTTCTT
1 TTTTTTTTATGAAATAGCTTTGAAGTCACCAATCTGTGAATCAAAATCGAAACAACTTTCTTCTT
* * *
28811780 CGATCTTCGACATTGACCATCAGATCGCTTGAAACCCACTAATCAATCTTCTTTTTTTGAAAAAA
66 CAATCTTCGACATTGACCATCAGATCGCCTGAAACCCACTAATCAATCTTCTTTTTTTAAAAAAA
* * *
28811845 AAACTTAACAACCAAATGATTTAAATAAAAACGTTCTAATAGTTTATTGGCTAAAATGAAAATTT
131 AAACTTAACAACCAAATGATTTAAATAAAAACGTTCTAATAGTTTAGTGACTAAAATGAAAATTG
28811910 TCAAATATTTCAGGTCTAAAATAATTTTTTTGAATC
196 TCAAATATTTCAGGTCTAAAATAATTTTTTTGAATC
**
28811946 TTTTTTTTATGAAATAGCTTTGAAGTCACCAATCTGTGAATCAAAATCGAAACAGTTTTCTTCTT
1 TTTTTTTTATGAAATAGCTTTGAAGTCACCAATCTGTGAATCAAAATCGAAACAACTTTCTTCTT
* **
28812011 CAATCTTCGACATTGACCATCAGATCGCCTGAAACTCACTAATCGGTCTTCTTTTTTTAAAAAAA
66 CAATCTTCGACATTGACCATCAGATCGCCTGAAACCCACTAATCAATCTTCTTTTTTT-AAAAAA
* * * *
28812076 AAAACTTAGCAATCTAATTATTTAAATAAAAACGTT-TGAATAGTTTAGTGACTAAAATGAAAAT
130 AAAACTTAACAACCAAATGATTTAAATAAAAACGTTCT-AATAGTTTAGTGACTAAAATGAAAAT
28812140 TGTCAAATATTTCAGGTCTAAAATAATTTTTT
194 TGTCAAATATTTCAGGTCTAAAATAATTTTTT
28812172 AATAGCTTAG
Statistics
Matches: 207, Mismatches: 17, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
231 115 0.56
232 92 0.44
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (231 bp):
TTTTTTTTATGAAATAGCTTTGAAGTCACCAATCTGTGAATCAAAATCGAAACAACTTTCTTCTT
CAATCTTCGACATTGACCATCAGATCGCCTGAAACCCACTAATCAATCTTCTTTTTTTAAAAAAA
AAACTTAACAACCAAATGATTTAAATAAAAACGTTCTAATAGTTTAGTGACTAAAATGAAAATTG
TCAAATATTTCAGGTCTAAAATAATTTTTTTGAATC
Found at i:28812386 original size:118 final size:117
Alignment explanation
Indices: 28812114--28812361 Score: 408
Period size: 118 Copynumber: 2.1 Consensus size: 117
28812104 AAAACGTTTG
*
28812114 AATAGTTTAGTGACTAAAATGAAAATTG-TCAAATATTTCAGGTCTAAAATAATTTTTTAATAGC
1 AATAGTTTAGTGACTAAAATGAAAA-CGATCAAATATTTCAGGTCTAAAATAATTTTTTAATAGC
* * *
28812178 TTAGTGATCATTTTGTAACTTTTTGAAATTAATAACTAAAACGTAAGCTTATT
65 TTAGTGACCATTTTGCAACTTTTTGAAATTAATAACTAAAACATAAGCTTATT
*
28812231 AATAGTTTAGTGACTAAAATGAAAACGATCAAATATTTCATGTCTAAAATAATTTTTTTAATAGC
1 AATAGTTTAGTGACTAAAATGAAAACGATCAAATATTTCAGGTCTAAAATAA-TTTTTTAATAGC
* *
28812296 TTAGTGACCATTTTGCAATTTTTTGAAATTAATAACTGAAACATAAGCTTATT
65 TTAGTGACCATTTTGCAACTTTTTGAAATTAATAACTAAAACATAAGCTTATT
28812349 AATAGTTTAGTGA
1 AATAGTTTAGTGA
28812362 TACTGGGAGT
Statistics
Matches: 122, Mismatches: 7, Indels: 3
0.92 0.05 0.02
Matches are distributed among these distances:
116 1 0.01
117 48 0.39
118 73 0.60
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.40
Consensus pattern (117 bp):
AATAGTTTAGTGACTAAAATGAAAACGATCAAATATTTCAGGTCTAAAATAATTTTTTAATAGCT
TAGTGACCATTTTGCAACTTTTTGAAATTAATAACTAAAACATAAGCTTATT
Found at i:28816097 original size:26 final size:26
Alignment explanation
Indices: 28816061--28816110 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
28816051 TCTATTTTTC
*
28816061 AATAGTTTAATATCACATCAGTAAAA
1 AATAATTTAATATCACATCAGTAAAA
*
28816087 AATAATTTAATATCATATCAGTAA
1 AATAATTTAATATCACATCAGTAA
28816111 TTTCATCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.50, C:0.10, G:0.06, T:0.34
Consensus pattern (26 bp):
AATAATTTAATATCACATCAGTAAAA
Found at i:28820406 original size:11 final size:11
Alignment explanation
Indices: 28820392--28820422 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
28820382 GTTCGGGAGT
28820392 ATTTTAAAAAA
1 ATTTTAAAAAA
*
28820403 ATTTCAAAAAA
1 ATTTTAAAAAA
28820414 ATTTTAAAA
1 ATTTTAAAA
28820423 TTAAAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (11 bp):
ATTTTAAAAAA
Found at i:28820439 original size:28 final size:29
Alignment explanation
Indices: 28820395--28820459 Score: 87
Period size: 28 Copynumber: 2.2 Consensus size: 29
28820385 CGGGAGTATT
**
28820395 TTAAAAAAATTTCAAAAAA-ATTTTAAAA
1 TTAAAAAAATTAAAAAAAAGATTTTAAAA
*
28820423 TTAAAAAAATTAAAAAAAAGTATTTTAAAG
1 TTAAAAAAATTAAAAAAAAG-ATTTTAAAA
28820453 TTAAAAA
1 TTAAAAA
28820460 TAAAAAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
28 17 0.53
30 15 0.47
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.31
Consensus pattern (29 bp):
TTAAAAAAATTAAAAAAAAGATTTTAAAA
Found at i:28820467 original size:7 final size:7
Alignment explanation
Indices: 28820455--28820479 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
28820445 TTTTAAAGTT
28820455 AAAAATA
1 AAAAATA
28820462 AAAAATA
1 AAAAATA
28820469 AAAAATA
1 AAAAATA
28820476 AAAA
1 AAAA
28820480 TATTTATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:28831920 original size:2 final size:2
Alignment explanation
Indices: 28831913--28831955 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
28831903 AACATATAAG
28831913 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28831953 TA T
1 TA T
28831956 GTCGATAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:28832816 original size:29 final size:29
Alignment explanation
Indices: 28832783--28832840 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
28832773 TTGGTCTAAT
* *
28832783 GTGCAATT-TGATATATGAACTTTGAATTG
1 GTGCAATTGT-ATACATGAAATTTGAATTG
28832812 GTGCAATTGTATACATGAAATTTGAATTG
1 GTGCAATTGTATACATGAAATTTGAATTG
28832841 TGGTTCACGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 25 0.96
30 1 0.04
ACGTcount: A:0.33, C:0.07, G:0.21, T:0.40
Consensus pattern (29 bp):
GTGCAATTGTATACATGAAATTTGAATTG
Found at i:28835799 original size:20 final size:20
Alignment explanation
Indices: 28835772--28835831 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
28835762 ATATTTATTG
28835772 ATATTAAATATTTTATAAATA
1 ATATTAAATATTTT-TAAATA
*
28835793 A-ATTAAAATAATTTTAAATA
1 ATATT-AAATATTTTTAAATA
*
28835813 ATATTACAT-TTTTGTAAAT
1 ATATTAAATATTTT-TAAAT
28835832 TTCTACTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
19 3 0.09
20 18 0.55
21 12 0.36
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (20 bp):
ATATTAAATATTTTTAAATA
Found at i:28855346 original size:11 final size:11
Alignment explanation
Indices: 28855326--28855366 Score: 57
Period size: 12 Copynumber: 3.6 Consensus size: 11
28855316 AGAAAATTAA
28855326 AAAAAGTATTTT
1 AAAAA-TATTTT
28855338 AAAAATATTTT
1 AAAAATATTTT
28855349 -AAAATATTTTT
1 AAAAATA-TTTT
28855360 AAAAATA
1 AAAAATA
28855367 AAAAATAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 6 0.22
11 10 0.37
12 11 0.41
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:28860681 original size:2 final size:2
Alignment explanation
Indices: 28860674--28860701 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
28860664 TTCAGCAAGA
28860674 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
28860702 CACAAAAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28881178 original size:19 final size:20
Alignment explanation
Indices: 28881154--28881197 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
28881144 NNNNNNAACC
28881154 TTTTTAAT-AATTTTACAAA
1 TTTTTAATAAATTTTACAAA
28881173 TTTTTAATAAATTTTACAAA
1 TTTTTAATAAATTTTACAAA
28881193 TTTTT
1 TTTTT
28881198 TTGTAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTTTAATAAATTTTACAAA
Found at i:28895051 original size:21 final size:21
Alignment explanation
Indices: 28895012--28895052 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
28895002 AATAAAATCT
* *
28895012 AATAACAGCATAAGCACACAC
1 AATAACAGCACAAGAACACAC
*
28895033 AATAACAGGACAAGAACACA
1 AATAACAGCACAAGAACACA
28895053 TCAAATAGTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.56, C:0.24, G:0.12, T:0.07
Consensus pattern (21 bp):
AATAACAGCACAAGAACACAC
Found at i:28898453 original size:10 final size:10
Alignment explanation
Indices: 28898438--28898462 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
28898428 TTTTATTAAA
28898438 ATTTTCATCC
1 ATTTTCATCC
28898448 ATTTTCATCC
1 ATTTTCATCC
28898458 ATTTT
1 ATTTT
28898463 TACATGTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.24, G:0.00, T:0.56
Consensus pattern (10 bp):
ATTTTCATCC
Found at i:28899154 original size:21 final size:21
Alignment explanation
Indices: 28899131--28899171 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
28899121 CTCAGTTCAC
* *
28899131 TTTCCTTCTTCTCTTCTTCCCT
1 TTTCC-TCTCCTCTCCTTCCCT
28899153 TTTCCTCTCCTCTCCTTCC
1 TTTCCTCTCCTCTCCTTCC
28899172 GCTAAACTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTCCTCTCCTCTCCTTCCCT
Found at i:28901438 original size:7 final size:7
Alignment explanation
Indices: 28901428--28901453 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
28901418 ACTAAGGACT
28901428 AAATGCA
1 AAATGCA
28901435 AAATGCA
1 AAATGCA
28901442 AAATGCA
1 AAATGCA
28901449 AAATG
1 AAATG
28901454 GTGCACGACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.12, G:0.15, T:0.15
Consensus pattern (7 bp):
AAATGCA
Found at i:28906557 original size:29 final size:27
Alignment explanation
Indices: 28906458--28906556 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 27
28906448 AAAAATAAAA
*
28906458 ATTTACCAAAATATTGCAACTTTTTTTT
1 ATTTACCAAAATATT-AAACTTTTTTTT
* *
28906486 ATTTATCAAAATATTACAATTTTTTTTT
1 ATTTACCAAAATATTA-AACTTTTTTTT
28906514 ATTTACCAAAATATATAAACTTTTTTATT
1 ATTTACCAAAATAT-TAAACTTTTTT-TT
28906543 ATTTACCAAAATAT
1 ATTTACCAAAATAT
28906557 AAAAAAAAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
28 45 0.71
29 18 0.29
ACGTcount: A:0.38, C:0.11, G:0.01, T:0.49
Consensus pattern (27 bp):
ATTTACCAAAATATTAAACTTTTTTTT
Found at i:28906665 original size:27 final size:27
Alignment explanation
Indices: 28906635--28906721 Score: 147
Period size: 27 Copynumber: 3.2 Consensus size: 27
28906625 CGCCAATGGT
* *
28906635 ATTGGCGGCACCAAAGGTGCCAAAACC
1 ATTGGCGGCACCAATGGTGCCAATACC
28906662 ATTGGCGGCACCAATGGTGCCAATACC
1 ATTGGCGGCACCAATGGTGCCAATACC
*
28906689 ATTGGCGGCACCAATGGTGCCAATGCC
1 ATTGGCGGCACCAATGGTGCCAATACC
28906716 ATTGGC
1 ATTGGC
28906722 NNNNNNNNNN
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 57 1.00
ACGTcount: A:0.26, C:0.29, G:0.28, T:0.17
Consensus pattern (27 bp):
ATTGGCGGCACCAATGGTGCCAATACC
Found at i:28911679 original size:18 final size:19
Alignment explanation
Indices: 28911653--28911790 Score: 97
Period size: 18 Copynumber: 6.9 Consensus size: 19
28911643 TTTCTTCTTG
*
28911653 TTCTTCTTTTTT-TTTCTC
1 TTCTCCTTTTTTCTTTCTC
28911671 TTCTCCTTTCCCTTTCTTTCCTTC
1 TTCTCCTTT---TTTCTTT-C-TC
*
28911695 TTTCTTTCTTTTTTC-TTCTC
1 -TTC-TCCTTTTTTCTTTCTC
*
28911715 TTCTCCTTTTCTTCTTCTTTC
1 TTCTCCTTTT-TTCTT-TCTC
28911736 TT-TCCTTTTTTCTCTTCTC
1 TTCTCCTTTTTTCT-TTCTC
*
28911755 CTCTCCTTTCTTTCTTTC-C
1 TTCTCCTTT-TTTCTTTCTC
28911774 -TCTCCTTTCTTTCTTTC
1 TTCTCCTTT-TTTCTTTC
28911791 CTTTTTTCTC
Statistics
Matches: 100, Mismatches: 6, Indels: 28
0.75 0.04 0.21
Matches are distributed among these distances:
18 31 0.31
19 15 0.15
20 20 0.20
21 14 0.14
22 5 0.05
23 5 0.05
24 2 0.02
25 3 0.03
26 5 0.05
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (19 bp):
TTCTCCTTTTTTCTTTCTC
Found at i:28911685 original size:40 final size:38
Alignment explanation
Indices: 28911638--28911771 Score: 130
Period size: 44 Copynumber: 3.4 Consensus size: 38
28911628 TTTCCCTTTT
28911638 TTTCCTTTCTTCTTGTTCTTCTTTTTTTTTCTCTTCTCC
1 TTTCCTTTCTTCTT-TTCTTCTTTTTTTTTCTCTTCTCC
*
28911677 TTTCCCTTTCTTTCCTTCTTTCTTTCTTTTTTCTTCTCTTCTCC
1 TTT-CCTTTC-TT-C-T-TTTC-TTCTTTTTTTTTCTCTTCTCC
* **
28911721 TTTTC-TTCTTC-TTTCTT-TCCTTTTTTCTCTTCTCC
1 TTTCCTTTCTTCTTTTCTTCTTTTTTTTTCTCTTCTCC
*
28911756 TCTCCTTTCTTTCTTT
1 TTTCCTTTC-TTCTTT
28911772 CCTCTCCTTT
Statistics
Matches: 79, Mismatches: 7, Indels: 19
0.75 0.07 0.18
Matches are distributed among these distances:
35 18 0.23
36 5 0.06
37 7 0.09
38 2 0.03
39 3 0.04
40 7 0.09
41 4 0.05
42 4 0.05
43 5 0.06
44 24 0.30
ACGTcount: A:0.00, C:0.31, G:0.01, T:0.68
Consensus pattern (38 bp):
TTTCCTTTCTTCTTTTCTTCTTTTTTTTTCTCTTCTCC
Found at i:28911697 original size:8 final size:8
Alignment explanation
Indices: 28911684--28911804 Score: 52
Period size: 8 Copynumber: 14.5 Consensus size: 8
28911674 TCCTTTCCCT
28911684 TTCTTTCC
1 TTCTTTCC
*
28911692 TTCTTTCT
1 TTCTTTCC
*
28911700 TTCTTT-T
1 TTCTTTCC
28911707 TTCTTCTCTTC
1 TTCTT-TC--C
* *
28911718 TCCTTTTC
1 TTCTTTCC
*
28911726 TTC-TTCT
1 TTCTTTCC
28911733 TTCTTTCC
1 TTCTTTCC
*
28911741 TT-TTTTC
1 TTCTTTCC
28911748 -TCTTCTCC
1 TTCTT-TCC
*
28911756 TCTCCTTTCT
1 T-T-CTTTCC
28911766 TTCTTTCC
1 TTCTTTCC
*
28911774 TCTCCTTTCT
1 T-T-CTTTCC
28911784 TTCTTTCC
1 TTCTTTCC
*
28911792 TTTTTTCTC
1 TTCTTTC-C
28911801 TTCT
1 TTCT
28911805 GCCCCCACCA
Statistics
Matches: 84, Mismatches: 16, Indels: 25
0.67 0.13 0.20
Matches are distributed among these distances:
6 1 0.01
7 17 0.20
8 41 0.49
9 7 0.08
10 11 0.13
11 7 0.08
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (8 bp):
TTCTTTCC
Found at i:28911700 original size:49 final size:44
Alignment explanation
Indices: 28911628--28911804 Score: 127
Period size: 44 Copynumber: 4.0 Consensus size: 44
28911618 TTACCTTTTT
* *
28911628 TTTCCCTTTTTTTCCTTTCTTCTTGTTCTTCTTTTTTTTTCTCTTCTCC
1 TTTCCCTTTCTTTCCTTTCTTC----T-TTCTTTTTTCTTCTCTTCTCC
28911677 TTTCCCTTTCTTTCC-TTCTTTCTTTCTTTTTTCTTCTCTTCTCC
1 TTTCCCTTTCTTTCCTTTC-TTCTTTCTTTTTTCTTCTCTTCTCC
* * * *
28911721 TTT-TC-TTC-TT-CTTTCTTTCCTT-TTTTCTCTTCTCCTCTCC
1 TTTCCCTTTCTTTCCTTTC-TTCTTTCTTTTTTCTTCTCTTCTCC
* *
28911761 TTT--CTTTCTTTCCTCTCCTTTCTTTCTTTCCTTTTTTCTCTTCT
1 TTTCCCTTTCTTTCCT-TTC-TTCTTTCTTT--TTTCTTCTCTTCT
28911805 GCCCCCACCA
Statistics
Matches: 108, Mismatches: 11, Indels: 21
0.77 0.08 0.15
Matches are distributed among these distances:
39 1 0.01
40 23 0.21
41 13 0.12
42 5 0.05
43 9 0.08
44 26 0.24
45 1 0.01
46 10 0.09
48 3 0.03
49 17 0.16
ACGTcount: A:0.00, C:0.32, G:0.01, T:0.67
Consensus pattern (44 bp):
TTTCCCTTTCTTTCCTTTCTTCTTTCTTTTTTCTTCTCTTCTCC
Found at i:28911705 original size:26 final size:25
Alignment explanation
Indices: 28911676--28911804 Score: 65
Period size: 26 Copynumber: 5.1 Consensus size: 25
28911666 TTCTCTTCTC
28911676 CTTTCCCTTTCTTTCCTTCTTTCTTT
1 CTTT-CCTTTCTTTCCTTCTTTCTTT
*
28911702 CTTT--TTTC-TTCTCTTC-TCCTTTT
1 CTTTCCTTTCTTTC-CTTCTTTC-TTT
* *
28911725 CTTCTTCTTTCTTTCCTT-TTT-TCT
1 CTT-TCCTTTCTTTCCTTCTTTCTTT
* * *
28911749 CTTCTCCTCTCCTTTCTTTCTTTCCTCTC
1 CTT-TCCT-TTCTTTCCTTCTTT-CT-TT
*
28911778 CTTT-CTTTCTTTCCTTTTTTCTCTT
1 CTTTCCTTTCTTTCCTTCTTTCT-TT
28911803 CT
1 CT
28911805 GCCCCCACCA
Statistics
Matches: 79, Mismatches: 12, Indels: 25
0.68 0.10 0.22
Matches are distributed among these distances:
22 5 0.06
23 14 0.18
24 10 0.13
25 14 0.18
26 26 0.33
27 5 0.06
28 2 0.03
29 3 0.04
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (25 bp):
CTTTCCTTTCTTTCCTTCTTTCTTT
Found at i:28911766 original size:33 final size:34
Alignment explanation
Indices: 28911694--28911774 Score: 105
Period size: 33 Copynumber: 2.4 Consensus size: 34
28911684 TTCTTTCCTT
*
28911694 CTTTCTTTCTTT--TTTCTTCTCTTCTCCTTTTC
1 CTTTCTTTCTTTCCTTTCTTCTCTTCTCCTTCTC
* *
28911726 TTCTTCTTTCTTTCCTTTTTTCTCTTCTCC-TCTC
1 CT-TTCTTTCTTTCCTTTCTTCTCTTCTCCTTCTC
28911760 CTTTCTTTCTTTCCT
1 CTTTCTTTCTTTCCT
28911775 CTCCTTTCTT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
32 1 0.02
33 23 0.55
34 4 0.10
35 14 0.33
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (34 bp):
CTTTCTTTCTTTCCTTTCTTCTCTTCTCCTTCTC
Found at i:28911770 original size:37 final size:37
Alignment explanation
Indices: 28911686--28911787 Score: 111
Period size: 37 Copynumber: 2.7 Consensus size: 37
28911676 CTTTCCCTTT
* *
28911686 CTTTCCTTCTTTCTTT-C-TTTTT-TCTTCTCTTCTC
1 CTTTCTTTCTTTCTTTCCTTTTTTCTCTTCTCCTCTC
28911720 CTTTTCTTCTTCTTTCTTTCCTTTTTTCTCTTCTCCTCTC
1 C-TTTC-T-TTCTTTCTTTCCTTTTTTCTCTTCTCCTCTC
*
28911760 CTTTCTTTCTTTCCTCTCCTTTCTTTCT
1 CTTTCTTTCTTT-CTTTCCTTT-TTTCT
28911788 TTCCTTTTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 11
0.80 0.04 0.15
Matches are distributed among these distances:
34 1 0.02
35 4 0.07
37 16 0.28
38 10 0.18
39 14 0.25
40 12 0.21
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (37 bp):
CTTTCTTTCTTTCTTTCCTTTTTTCTCTTCTCCTCTC
Found at i:28911800 original size:23 final size:23
Alignment explanation
Indices: 28911677--28911800 Score: 71
Period size: 23 Copynumber: 5.3 Consensus size: 23
28911667 TCTCTTCTCC
*
28911677 TTTC-CCTTTCTTTCCTT-CTTT
1 TTTCTCCTTTCTTTCTTTCCTTT
**
28911698 CTTTCTTTTTTCTTCTCTTCTCC--T
1 -TTTCTCCTTTCTT-TCTT-TCCTTT
*
28911722 TTTCTTC-TTCTTTCTTTCCTTT
1 TTTCTCCTTTCTTTCTTTCCTTT
* *
28911744 TTTCT-CTTCTCCTCTCCTTTCTTTCT
1 TTTCTCCTT-T-CT-TTCTTTCCTT-T
28911770 TTCCTCTCCTTTCTTTCTTTCCTTT
1 TT--TCTCCTTTCTTTCTTTCCTTT
28911795 TTTCTC
1 TTTCTC
28911801 TTCTGCCCCC
Statistics
Matches: 80, Mismatches: 8, Indels: 27
0.70 0.07 0.23
Matches are distributed among these distances:
20 3 0.04
21 5 0.06
22 16 0.20
23 17 0.21
24 6 0.08
25 12 0.15
26 12 0.15
27 2 0.03
28 4 0.05
29 3 0.04
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (23 bp):
TTTCTCCTTTCTTTCTTTCCTTT
Found at i:28911802 original size:18 final size:18
Alignment explanation
Indices: 28911625--28911802 Score: 93
Period size: 18 Copynumber: 9.6 Consensus size: 18
28911615 AAATTACCTT
* *
28911625 TTTTTTCCCTTTTTTTCC
1 TTTTTTCTCTTTCTTTCC
* **
28911643 TTTCTTCT-TGTTCTTCTTT
1 TTTTTTCTCT-TTCTT-TCC
28911662 TTTTTTCTCTTCTCCTTTCCC
1 TTTTTTCTCTT-T-CTTT-CC
28911683 TTTCTTTCCTTCTTTCTTT-C
1 TTT-TTT-C-TCTTTCTTTCC
*
28911703 TTTTTTCT-TCTCTTCTCC
1 TTTTTTCTCTTTCTT-TCC
28911721 TTTTCTTCTTCTTTCTTTCC
1 TTTT-TTC-TCTTTCTTTCC
28911741 TTTTTTCTC-TTC--TCC
1 TTTTTTCTCTTTCTTTCC
**
28911756 TCTCCTT-TCTTTCTTTCC
1 T-TTTTTCTCTTTCTTTCC
**
28911774 TCTCCTT-TCTTTCTTTCC
1 T-TTTTTCTCTTTCTTTCC
28911792 TTTTTTCTCTT
1 TTTTTTCTCTT
28911803 CTGCCCCCAC
Statistics
Matches: 127, Mismatches: 14, Indels: 38
0.71 0.08 0.21
Matches are distributed among these distances:
15 6 0.05
16 11 0.09
17 9 0.07
18 44 0.35
19 18 0.14
20 15 0.12
21 11 0.09
22 7 0.06
23 2 0.02
24 4 0.03
ACGTcount: A:0.00, C:0.31, G:0.01, T:0.68
Consensus pattern (18 bp):
TTTTTTCTCTTTCTTTCC
Found at i:28911914 original size:27 final size:27
Alignment explanation
Indices: 28911838--28911904 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
28911828 TAAAACCAAC
28911838 TGGTGCCGCCAATGGTATTGGCACCAT
1 TGGTGCCGCCAATGGTATTGGCACCAT
* *
28911865 TGGTGCCGCCAATGGTTTTGGCACCTT
1 TGGTGCCGCCAATGGTATTGGCACCAT
28911892 TGGTGCCGCCAAT
1 TGGTGCCGCCAAT
28911905 ACCATTGGCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.15, C:0.27, G:0.30, T:0.28
Consensus pattern (27 bp):
TGGTGCCGCCAATGGTATTGGCACCAT
Found at i:28912003 original size:28 final size:28
Alignment explanation
Indices: 28911972--28912041 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
28911962 TTTTTTTGAT
28911972 ATATTTTGGTAAATAAAAAAAAATTGTA
1 ATATTTTGGTAAATAAAAAAAAATTGTA
* *
28912000 ATATTTTGGTAAATAAAAACAAGTTGTA
1 ATATTTTGGTAAATAAAAAAAAATTGTA
28912028 ATATTTTGGTAAAT
1 ATATTTTGGTAAAT
28912042 TTTTATTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.47, C:0.01, G:0.13, T:0.39
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAATTGTA
Found at i:28931693 original size:21 final size:21
Alignment explanation
Indices: 28931669--28931708 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28931659 TAGTTGTGTT
28931669 ATAACTACCTTACTAAAAAAA
1 ATAACTACCTTACTAAAAAAA
* *
28931690 ATAATTACTTTACTAAAAA
1 ATAACTACCTTACTAAAAA
28931709 TTATCATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (21 bp):
ATAACTACCTTACTAAAAAAA
Found at i:28936277 original size:28 final size:28
Alignment explanation
Indices: 28936226--28936304 Score: 131
Period size: 28 Copynumber: 2.8 Consensus size: 28
28936216 GACTTAAACC
28936226 CAAAATGATACCAAAAAAAAAAAAAAAAA
1 CAAAATGATA-CAAAAAAAAAAAAAAAAA
*
28936255 CAAAATGATACAAAAAAAAAAAAAAAAC
1 CAAAATGATACAAAAAAAAAAAAAAAAA
*
28936283 CAAAATGATACAAACAAAAAAA
1 CAAAATGATACAAAAAAAAAAA
28936305 TAACCAAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
28 38 0.79
29 10 0.21
ACGTcount: A:0.77, C:0.11, G:0.04, T:0.08
Consensus pattern (28 bp):
CAAAATGATACAAAAAAAAAAAAAAAAA
Found at i:28944773 original size:18 final size:18
Alignment explanation
Indices: 28944746--28944780 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
28944736 TGTCACATTA
*
28944746 ATAAATAATTAAAAAATC
1 ATAAAAAATTAAAAAATC
28944764 ATAAAAAATTAAAAAAT
1 ATAAAAAATTAAAAAAT
28944781 AACATAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (18 bp):
ATAAAAAATTAAAAAATC
Found at i:28944789 original size:18 final size:18
Alignment explanation
Indices: 28944752--28944790 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
28944742 ATTAATAAAT
* *
28944752 AATTAAAAAATCATAAAA
1 AATTAAAAAATAACAAAA
*
28944770 AATTAAAAAATAACATAA
1 AATTAAAAAATAACAAAA
28944788 AAT
1 AAT
28944791 ACTCTTTAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (18 bp):
AATTAAAAAATAACAAAA
Found at i:28952527 original size:12 final size:12
Alignment explanation
Indices: 28952507--28952540 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
28952497 GGCCACACGT
* *
28952507 CCGTTTCCTTGC
1 CCGTGTCCTAGC
28952519 CCGTGTCCTAGC
1 CCGTGTCCTAGC
28952531 CCGTGTCCTA
1 CCGTGTCCTA
28952541 ACTAGTGAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.06, C:0.41, G:0.21, T:0.32
Consensus pattern (12 bp):
CCGTGTCCTAGC
Found at i:28957505 original size:2 final size:2
Alignment explanation
Indices: 28957500--28957524 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28957490 AATTGAACAT
28957500 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 T
28957525 TCATCTGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28958537 original size:24 final size:25
Alignment explanation
Indices: 28958510--28958572 Score: 60
Period size: 25 Copynumber: 2.6 Consensus size: 25
28958500 GTACATGTAT
28958510 GCTCATACGAGC-G-ATAAACGGTAA
1 GCTCATACGAGCTGAAT-AACGGTAA
* * *
28958534 GCTCTTCCGAGCTGAATAATGGTAA
1 GCTCATACGAGCTGAATAACGGTAA
28958559 GCTCAT-CAGAGCTG
1 GCTCATAC-GAGCTG
28958573 GAATCAGTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
24 11 0.34
25 19 0.59
26 2 0.06
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.22
Consensus pattern (25 bp):
GCTCATACGAGCTGAATAACGGTAA
Found at i:28960914 original size:30 final size:30
Alignment explanation
Indices: 28960878--28960943 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
28960868 GTCCGCATGG
* *
28960878 CCGTGTGTCACACACGGTTGAGACACACGC
1 CCGTGTGCCACACACGATTGAGACACACGC
* *
28960908 CCGTGTGCCACACACGATTGAGACATATGC
1 CCGTGTGCCACACACGATTGAGACACACGC
28960938 CCGTGT
1 CCGTGT
28960944 ATCTACCCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.23, C:0.32, G:0.26, T:0.20
Consensus pattern (30 bp):
CCGTGTGCCACACACGATTGAGACACACGC
Found at i:28962505 original size:5 final size:5
Alignment explanation
Indices: 28962476--28962522 Score: 58
Period size: 5 Copynumber: 9.2 Consensus size: 5
28962466 AAATTTAACA
* * *
28962476 TCAAT TTAAT ACATT TCATAT TCAAT TCAAT TCAAT TCAAT TCAAT T
1 TCAAT TCAAT TCAAT TCA-AT TCAAT TCAAT TCAAT TCAAT TCAAT T
28962523 TACATCTTAG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
5 31 0.89
6 4 0.11
ACGTcount: A:0.38, C:0.17, G:0.00, T:0.45
Consensus pattern (5 bp):
TCAAT
Found at i:28969251 original size:25 final size:25
Alignment explanation
Indices: 28969150--28969337 Score: 98
Period size: 25 Copynumber: 7.5 Consensus size: 25
28969140 CTATAACTGT
* * * *
28969150 AGCTCCTAAGAGCTATTAATCGGGG
1 AGCTCCAAAGAGCCATTAATCAGGA
* * *
28969175 AGCTCCAGATAGCCATTTATC-GAGA
1 AGCTCCAAAGAGCCATTAATCAG-GA
* * *
28969200 AG-TTCAAGCGAGCCA-T-ATCGGGA
1 AGCTCCAA-AGAGCCATTAATCAGGA
**
28969223 AGCTCCGGAGAGCCATTAATCAGGA
1 AGCTCCAAAGAGCCATTAATCAGGA
* * * *
28969248 AGCTTACAAATAGCCTTTAAT-TGGAA
1 AGC-TCCAAAGAGCCATTAATCAGG-A
* *
28969274 AGCTCCAGAGAGCCATTTATCAGGA
1 AGCTCCAAAGAGCCATTAATCAGGA
* *
28969299 AGCTCACAAAGAGCCTTTAATTAGGA
1 AGCTC-CAAAGAGCCATTAATCAGGA
**
28969325 AGCTTAAAAGAGC
1 AGCTCCAAAGAGC
28969338 TAAGGTGTGC
Statistics
Matches: 120, Mismatches: 33, Indels: 20
0.69 0.19 0.12
Matches are distributed among these distances:
23 13 0.11
24 9 0.08
25 60 0.50
26 38 0.32
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.22
Consensus pattern (25 bp):
AGCTCCAAAGAGCCATTAATCAGGA
Found at i:28969267 original size:26 final size:26
Alignment explanation
Indices: 28969231--28969337 Score: 105
Period size: 26 Copynumber: 4.2 Consensus size: 26
28969221 GAAGCTCCGG
*
28969231 AGAGCCATTAATCAGGAAGCTTACAA
1 AGAGCCTTTAATCAGGAAGCTTACAA
* * * *
28969257 ATAGCCTTTAAT-TGGAAAGC-TCCAG
1 AGAGCCTTTAATCAGG-AAGCTTACAA
*
28969282 AGAGCCATTT-ATCAGGAAGCTCACAA
1 AGAGCC-TTTAATCAGGAAGCTTACAA
*
28969308 AGAGCCTTTAATTAGGAAGCTTA-AA
1 AGAGCCTTTAATCAGGAAGCTTACAA
28969333 AGAGC
1 AGAGC
28969338 TAAGGTGTGC
Statistics
Matches: 64, Mismatches: 12, Indels: 11
0.74 0.14 0.13
Matches are distributed among these distances:
25 26 0.41
26 38 0.59
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (26 bp):
AGAGCCTTTAATCAGGAAGCTTACAA
Found at i:28969285 original size:51 final size:52
Alignment explanation
Indices: 28969222--28969325 Score: 165
Period size: 51 Copynumber: 2.0 Consensus size: 52
28969212 CCATATCGGG
* * *
28969222 AAGCTCCGGAGAGCCATTAATCAGGAAGCTTACAAATAGCCTTTAATT-GGA
1 AAGCTCCAGAGAGCCATTAATCAGGAAGCTCACAAAGAGCCTTTAATTAGGA
*
28969273 AAGCTCCAGAGAGCCATTTATCAGGAAGCTCACAAAGAGCCTTTAATTAGGA
1 AAGCTCCAGAGAGCCATTAATCAGGAAGCTCACAAAGAGCCTTTAATTAGGA
28969325 A
1 A
28969326 GCTTAAAAGA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
51 44 0.92
52 4 0.08
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.22
Consensus pattern (52 bp):
AAGCTCCAGAGAGCCATTAATCAGGAAGCTCACAAAGAGCCTTTAATTAGGA
Found at i:28969337 original size:51 final size:51
Alignment explanation
Indices: 28969231--28969337 Score: 144
Period size: 51 Copynumber: 2.1 Consensus size: 51
28969221 GAAGCTCCGG
* * * *
28969231 AGAGCCATTAATCAGGAAGCTTACAAATAGCCTTTAATTGGAAAGCTCCAG
1 AGAGCCATTAATCAGGAAGCTCACAAAGAGCCTTTAATTGGAAAGCTCAAA
* *
28969282 AGAGCCATTTATCAGGAAGCTCACAAAGAGCCTTTAATTAGG-AAGCTTAAA
1 AGAGCCATTAATCAGGAAGCTCACAAAGAGCCTTTAATT-GGAAAGCTCAAA
28969333 AGAGC
1 AGAGC
28969338 TAAGGTGTGC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
51 47 0.96
52 2 0.04
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (51 bp):
AGAGCCATTAATCAGGAAGCTCACAAAGAGCCTTTAATTGGAAAGCTCAAA
Found at i:28975800 original size:41 final size:41
Alignment explanation
Indices: 28975740--28975858 Score: 166
Period size: 41 Copynumber: 2.9 Consensus size: 41
28975730 ATAATATTGA
*
28975740 TGAATTGCACATACATGCCCCTGTTTGTACTTCGGTACCCC
1 TGAATTGCACATACATGCCCCTGTTTATACTTCGGTACCCC
* * *
28975781 TGAATTGCACATACGTGCCCTTGTTTATACTTCGGTACCCT
1 TGAATTGCACATACATGCCCCTGTTTATACTTCGGTACCCC
** * *
28975822 TGAATTGCACATACATGTTCCTGTTTAGACTTTGGTA
1 TGAATTGCACATACATGCCCCTGTTTATACTTCGGTA
28975859 ATTATGAATC
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 68 1.00
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.36
Consensus pattern (41 bp):
TGAATTGCACATACATGCCCCTGTTTATACTTCGGTACCCC
Found at i:28982688 original size:24 final size:24
Alignment explanation
Indices: 28982657--28982733 Score: 109
Period size: 24 Copynumber: 3.2 Consensus size: 24
28982647 AAAGAACCTA
28982657 TAACGGGTAGCTCCGAAGAGCAAT
1 TAACGGGTAGCTCCGAAGAGCAAT
* *
28982681 TAATGGGTAGCTCCGAAGAGCATT
1 TAACGGGTAGCTCCGAAGAGCAAT
* * *
28982705 TAACGAGTAGCTCCGAAGAGTACT
1 TAACGGGTAGCTCCGAAGAGCAAT
28982729 TAACG
1 TAACG
28982734 AGAAGCACTG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.32, C:0.19, G:0.27, T:0.21
Consensus pattern (24 bp):
TAACGGGTAGCTCCGAAGAGCAAT
Found at i:28987320 original size:99 final size:99
Alignment explanation
Indices: 28987204--28987399 Score: 392
Period size: 99 Copynumber: 2.0 Consensus size: 99
28987194 TTGACATTTC
28987204 AATACAATATACTTTTGTTCACAATTTACCACGGCATCATGCTGAGTCAACCAATCCATACCCAG
1 AATACAATATACTTTTGTTCACAATTTACCACGGCATCATGCTGAGTCAACCAATCCATACCCAG
28987269 AATAACACAAAATCATCAAATGGCAATAACATCA
66 AATAACACAAAATCATCAAATGGCAATAACATCA
28987303 AATACAATATACTTTTGTTCACAATTTACCACGGCATCATGCTGAGTCAACCAATCCATACCCAG
1 AATACAATATACTTTTGTTCACAATTTACCACGGCATCATGCTGAGTCAACCAATCCATACCCAG
28987368 AATAACACAAAATCATCAAATGGCAATAACAT
66 AATAACACAAAATCATCAAATGGCAATAACAT
28987400 TAAGTCAGCC
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
99 97 1.00
ACGTcount: A:0.41, C:0.25, G:0.09, T:0.24
Consensus pattern (99 bp):
AATACAATATACTTTTGTTCACAATTTACCACGGCATCATGCTGAGTCAACCAATCCATACCCAG
AATAACACAAAATCATCAAATGGCAATAACATCA
Found at i:28990586 original size:24 final size:24
Alignment explanation
Indices: 28990559--28990604 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
28990549 AAAGAGCCTA
* * *
28990559 TAACATGTAGCTTCGAAGAGCAAT
1 TAACAGGTAGCTCCGAAAAGCAAT
*
28990583 TAACGGGTAGCTCCGAAAAGCA
1 TAACAGGTAGCTCCGAAAAGCA
28990605 CTTAGTGGGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.20
Consensus pattern (24 bp):
TAACAGGTAGCTCCGAAAAGCAAT
Found at i:28990691 original size:26 final size:26
Alignment explanation
Indices: 28990662--28990728 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 26
28990652 CACTAATGGA
*
28990662 AAGCTCACAAAGAGCT-TTTAATCGGG
1 AAGCTCACAAAGAGCTATATAA-CGGG
*
28990688 AAGCTTACAAAGAGCTATATAACGGG
1 AAGCTCACAAAGAGCTATATAACGGG
* *
28990714 ACGCTCA-TAAGAGCT
1 AAGCTCACAAAGAGCT
28990729 GCGGTGTGCC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
25 7 0.20
26 24 0.69
27 4 0.11
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.21
Consensus pattern (26 bp):
AAGCTCACAAAGAGCTATATAACGGG
Found at i:28996636 original size:101 final size:101
Alignment explanation
Indices: 28996462--28996720 Score: 326
Period size: 101 Copynumber: 2.6 Consensus size: 101
28996452 GTTTCCTTTG
* * * ** *
28996462 TGCCATAGTCCAACTATGGTATTACATAT--GCATTGCCATGACTCT-GTCATGGTCTTACATTC
1 TGCCATAGTCCAACTATGGTCTTACATATAAACATTGCCATG-GTCTAACCATGGTCTTACATCC
* *
28996524 GTAGTGCCATAACCTAGTTATGGTCTTACCATCAAAA
65 ATAGTGCCATAACCCAGTTATGGTCTTACCATCAAAA
* * *
28996561 TGCCATAGTCCAGCTATGGTCTTACATATAAACATTGTCATGGTCTAACCATGGTCTTACGTCCA
1 TGCCATAGTCCAACTATGGTCTTACATATAAACATTGCCATGGTCTAACCATGGTCTTACATCCA
* *
28996626 TAGTGCCATAACCCAGTTATGGTCTTATCATCAGAA
66 TAGTGCCATAACCCAGTTATGGTCTTACCATCAAAA
* * * * *
28996662 TGCCATAGCCCATCTATGGTCTTACATATAAATACTGCCATGGTCCAACCATGGTCTTA
1 TGCCATAGTCCAACTATGGTCTTACATATAAACATTGCCATGGTCTAACCATGGTCTTA
28996721 ATTTTGAATA
Statistics
Matches: 138, Mismatches: 19, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
99 27 0.20
100 3 0.02
101 108 0.78
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.32
Consensus pattern (101 bp):
TGCCATAGTCCAACTATGGTCTTACATATAAACATTGCCATGGTCTAACCATGGTCTTACATCCA
TAGTGCCATAACCCAGTTATGGTCTTACCATCAAAA
Found at i:28997434 original size:2 final size:2
Alignment explanation
Indices: 28997427--28997456 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
28997417 TATTCTACTA
*
28997427 CT CT CT CT CT CT CT TT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
28997457 TTCACTTGCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:29014758 original size:3 final size:3
Alignment explanation
Indices: 29014741--29014802 Score: 108
Period size: 3 Copynumber: 21.0 Consensus size: 3
29014731 CCCCAAATGG
*
29014741 AAT AAG AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
29014788 AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT
29014803 TTACCTATAA
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
2 2 0.04
3 54 0.96
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:29015196 original size:30 final size:30
Alignment explanation
Indices: 29015161--29015225 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
29015151 TAACAAAAAA
29015161 CTCTCAAATTTCTCCCTAAATTTCTCAAAG
1 CTCTCAAATTTCTCCCTAAATTTCTCAAAG
* *
29015191 CTCTCAAATTTCTCCTTAGATTTCTCAAAG
1 CTCTCAAATTTCTCCCTAAATTTCTCAAAG
29015221 CTCTC
1 CTCTC
29015226 TTTAATTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.26, C:0.31, G:0.05, T:0.38
Consensus pattern (30 bp):
CTCTCAAATTTCTCCCTAAATTTCTCAAAG
Found at i:29017249 original size:21 final size:20
Alignment explanation
Indices: 29017225--29017265 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
29017215 ACCCATAACT
*
29017225 AGAGCAACCATAACCCTCGTC
1 AGAGCAACCACAACCC-CGTC
29017246 AGAGCAACCACAACCCCGTC
1 AGAGCAACCACAACCCCGTC
29017266 GGAAGCTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.34, C:0.41, G:0.15, T:0.10
Consensus pattern (20 bp):
AGAGCAACCACAACCCCGTC
Found at i:29020650 original size:98 final size:96
Alignment explanation
Indices: 29020534--29020711 Score: 284
Period size: 98 Copynumber: 1.8 Consensus size: 96
29020524 GAACTATTGT
* * *
29020534 AGAAAAAGAGCATCCACGTGAGAGCTTTTTTCAGTAATTTCGCTGACAGTGCATCATGCTTGAAG
1 AGAAAAAGAACATCCACGTGAGAGCTTTTTT-AGTAATTTCACTGACAATGCATCAT-CTTGAAG
29020599 CGTTTTTGACACTATTTGTTCAGGAACTACTAC
64 CGTTTTTGACACTATTTGTTCAGGAACTACTAC
* * *
29020632 AGAAAAAGAACGTCCACGTGAGAGCTTTTTTAGTAATTTTACTGACAATGCATCCTCTTGAAGCG
1 AGAAAAAGAACATCCACGTGAGAGCTTTTTTAGTAATTTCACTGACAATGCATCATCTTGAAGCG
29020697 TTTTTGACACTATTT
66 TTTTTGACACTATTT
29020712 ATTTAGAACC
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
96 24 0.32
97 21 0.28
98 29 0.39
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (96 bp):
AGAAAAAGAACATCCACGTGAGAGCTTTTTTAGTAATTTCACTGACAATGCATCATCTTGAAGCG
TTTTTGACACTATTTGTTCAGGAACTACTAC
Found at i:29020917 original size:33 final size:32
Alignment explanation
Indices: 29020814--29020927 Score: 111
Period size: 34 Copynumber: 3.4 Consensus size: 32
29020804 CTGAACACAA
* * *
29020814 TATTATTTAAAAAAACTAAACCTTAATTTAAT
1 TATTTTTTAAAAATACTAAACCCTAATTTAAT
* * *
29020846 TAATTTTCCTAAAAATACTAAAACCTAATTTTATT
1 T-ATTTT-TTAAAAATACTAAACCCTAA-TTTAAT
* *
29020881 TATTTATTTAAAACTCCTAAACCCTAATTTAAT
1 TATTT-TTTAAAAATACTAAACCCTAATTTAAT
29020914 TATTTGTTTAAAAA
1 TATTT-TTTAAAAA
29020928 GAACACTAAA
Statistics
Matches: 65, Mismatches: 13, Indels: 7
0.76 0.15 0.08
Matches are distributed among these distances:
32 1 0.02
33 21 0.32
34 36 0.55
35 7 0.11
ACGTcount: A:0.44, C:0.12, G:0.01, T:0.43
Consensus pattern (32 bp):
TATTTTTTAAAAATACTAAACCCTAATTTAAT
Found at i:29020994 original size:21 final size:20
Alignment explanation
Indices: 29020969--29021041 Score: 56
Period size: 21 Copynumber: 3.5 Consensus size: 20
29020959 TCCTAAAACT
29020969 CAAAACCCTAAATTATTTTAA
1 CAAAACCCTAAATT-TTTTAA
* * ***
29020990 CAAAACTCTAAACTCTACAAA
1 CAAAACCCTAAA-TTTTTTAA
**
29021011 CCTAACCCTAAATTTTTTAA
1 CAAAACCCTAAATTTTTTAA
*
29021031 CAAAATCCTAA
1 CAAAACCCTAA
29021042 CCCTAAAAAC
Statistics
Matches: 36, Mismatches: 15, Indels: 3
0.67 0.28 0.06
Matches are distributed among these distances:
20 12 0.33
21 23 0.64
22 1 0.03
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.29
Consensus pattern (20 bp):
CAAAACCCTAAATTTTTTAA
Found at i:29021613 original size:3 final size:3
Alignment explanation
Indices: 29021605--29021666 Score: 70
Period size: 3 Copynumber: 20.7 Consensus size: 3
29021595 CGAGCGAGAC
* * ** * *
29021605 GAA GAA GAA GAA GAT GAC GTT GAA GAT GAA GAA GAA GAA GAG GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
29021653 GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GA
29021667 GCCGAGGCTT
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.56, C:0.02, G:0.35, T:0.06
Consensus pattern (3 bp):
GAA
Found at i:29021661 original size:21 final size:21
Alignment explanation
Indices: 29021605--29021667 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
29021595 CGAGCGAGAC
* * **
29021605 GAAGAAGAAGAAGATGACGTT
1 GAAGAAGAAGAAGAAGAAGAG
*
29021626 GAAGATGAAGAAGAAGAAGAG
1 GAAGAAGAAGAAGAAGAAGAG
29021647 GAAGAAGAAGAAGAAGAAGAG
1 GAAGAAGAAGAAGAAGAAGAG
29021668 CCGAGGCTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.56, C:0.02, G:0.37, T:0.06
Consensus pattern (21 bp):
GAAGAAGAAGAAGAAGAAGAG
Found at i:29030257 original size:20 final size:20
Alignment explanation
Indices: 29030225--29030272 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
29030215 AAATTAGTAC
*
29030225 ATTTTTATAATATTTTTTTTA
1 ATTTTTATAATA-TTATTTTA
29030246 ATTTTTAT-ATATTATTTTA
1 ATTTTTATAATATTATTTTA
29030265 ACTTTTTA
1 A-TTTTTA
29030273 AAATTTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 8 0.32
20 9 0.36
21 8 0.32
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (20 bp):
ATTTTTATAATATTATTTTA
Found at i:29030329 original size:21 final size:22
Alignment explanation
Indices: 29030287--29030330 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
29030277 TTAAAATTAT
29030287 ATATTTTAGAATTTTATAAAAA
1 ATATTTTAGAATTTTATAAAAA
29030309 ATATTTTA-AACTTTT-TAAAAA
1 ATATTTTAGAA-TTTTATAAAAA
29030330 A
1 A
29030331 ATTNNNNNNN
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (22 bp):
ATATTTTAGAATTTTATAAAAA
Found at i:29030715 original size:4 final size:4
Alignment explanation
Indices: 29030708--29030736 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
29030698 TCATATATAT
29030708 ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
29030737 CCCGATCCGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:29049163 original size:23 final size:24
Alignment explanation
Indices: 29049132--29049180 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
29049122 ACACATTTAA
29049132 TTTAA-TTTTCA-ATATATTATATT
1 TTTAATTTTTCACATATATTA-ATT
* *
29049155 TTTACTTTTTCACTTATATTAATT
1 TTTAATTTTTCACATATATTAATT
29049179 TT
1 TT
29049181 GAAAAGGTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 4 0.18
24 11 0.50
25 7 0.32
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (24 bp):
TTTAATTTTTCACATATATTAATT
Found at i:29053758 original size:29 final size:30
Alignment explanation
Indices: 29053724--29053782 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
29053714 TTATAGGGAG
29053724 TGGATCAA-ATTAGTCACTATATTATTAAA
1 TGGATCAATATTAGTCACTATATTATTAAA
* * *
29053753 TGGATCAATTTTAGTCCCTGTATTATTAAA
1 TGGATCAATATTAGTCACTATATTATTAAA
29053783 AAGAATCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 8 0.31
30 18 0.69
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.41
Consensus pattern (30 bp):
TGGATCAATATTAGTCACTATATTATTAAA
Found at i:29056507 original size:31 final size:32
Alignment explanation
Indices: 29056472--29056540 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 32
29056462 ATTTCAATTT
29056472 TTTTGAGAGA-CTTAACT-AAAACTTTCCAAAA
1 TTTTGAGAGATCTTAA-TGAAAACTTTCCAAAA
* * *
29056503 TTTTGA-AGATCTTAATGATAATTTTCCAAAT
1 TTTTGAGAGATCTTAATGAAAACTTTCCAAAA
29056534 TTTTGAG
1 TTTTGAG
29056541 GTGTCCAGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
30 4 0.12
31 28 0.88
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.41
Consensus pattern (32 bp):
TTTTGAGAGATCTTAATGAAAACTTTCCAAAA
Found at i:29061969 original size:21 final size:20
Alignment explanation
Indices: 29061945--29061983 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
29061935 ATTATATGAT
*
29061945 GTAATTTACAATACATCTATA
1 GTAATATACAATAC-TCTATA
*
29061966 GTAATATATAATACTCTA
1 GTAATATACAATACTCTA
29061984 ATGTAAACGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.38
Consensus pattern (20 bp):
GTAATATACAATACTCTATA
Found at i:29064607 original size:32 final size:32
Alignment explanation
Indices: 29064570--29064633 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
29064560 TGCTGAATGT
29064570 GAAAGCCTTTAGGAGATGAAGTGGGAACACAA
1 GAAAGCCTTTAGGAGATGAAGTGGGAACACAA
29064602 GAAAGCCTTTAGGAGATGAAGTGGGAACACAA
1 GAAAGCCTTTAGGAGATGAAGTGGGAACACAA
29064634 TTAAGGTAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.41, C:0.12, G:0.31, T:0.16
Consensus pattern (32 bp):
GAAAGCCTTTAGGAGATGAAGTGGGAACACAA
Found at i:29072155 original size:53 final size:53
Alignment explanation
Indices: 29072095--29072202 Score: 216
Period size: 53 Copynumber: 2.0 Consensus size: 53
29072085 ACATATATCG
29072095 ATCAAAACCTATTTATATTACTTTTTGATCCCTTAAAAAGTCTCTAGTTGGAT
1 ATCAAAACCTATTTATATTACTTTTTGATCCCTTAAAAAGTCTCTAGTTGGAT
29072148 ATCAAAACCTATTTATATTACTTTTTGATCCCTTAAAAAGTCTCTAGTTGGAT
1 ATCAAAACCTATTTATATTACTTTTTGATCCCTTAAAAAGTCTCTAGTTGGAT
29072201 AT
1 AT
29072203 GTTTCCCTTA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.32, C:0.17, G:0.09, T:0.42
Consensus pattern (53 bp):
ATCAAAACCTATTTATATTACTTTTTGATCCCTTAAAAAGTCTCTAGTTGGAT
Found at i:29079682 original size:11 final size:11
Alignment explanation
Indices: 29079651--29079682 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
29079641 TTTTGAGTTT
29079651 TTTTTAATA-A
1 TTTTTAATATA
29079661 TTTTTAA-ATA
1 TTTTTAATATA
29079671 TTTTTAATATA
1 TTTTTAATATA
29079682 T
1 T
29079683 ACATATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
9 1 0.05
10 15 0.75
11 4 0.20
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTTAATATA
Found at i:29081034 original size:13 final size:13
Alignment explanation
Indices: 29081016--29081041 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29081006 ATTTAGTATT
29081016 CGTATACTGTTTA
1 CGTATACTGTTTA
29081029 CGTATACTGTTTA
1 CGTATACTGTTTA
29081042 AAGTAATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.46
Consensus pattern (13 bp):
CGTATACTGTTTA
Found at i:29084777 original size:52 final size:52
Alignment explanation
Indices: 29084699--29084802 Score: 190
Period size: 52 Copynumber: 2.0 Consensus size: 52
29084689 AAAATAAAAA
* *
29084699 TAAAAAATTTTCTTTGTCAATGTATAAAATAATTATTCGATTTAAAGCGAAC
1 TAAAAAATTTTCTTTATCAATGTATAAAATAATTATTCAATTTAAAGCGAAC
29084751 TAAAAAATTTTCTTTATCAATGTATAAAATAATTATTCAATTTAAAGCGAAC
1 TAAAAAATTTTCTTTATCAATGTATAAAATAATTATTCAATTTAAAGCGAAC
29084803 AGAAAGAAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.38
Consensus pattern (52 bp):
TAAAAAATTTTCTTTATCAATGTATAAAATAATTATTCAATTTAAAGCGAAC
Found at i:29084778 original size:24 final size:25
Alignment explanation
Indices: 29084698--29084784 Score: 74
Period size: 24 Copynumber: 3.4 Consensus size: 25
29084688 AAAAATAAAA
*
29084698 ATAAAA-AATTTTCTTTGTCAATGT
1 ATAAAATAATTTTCTTTATCAATGT
* *
29084722 ATAAAATAATTATTCGATTTA--AAGCGA
1 ATAAAATAATT-TTC--TTTATCAA-TGT
29084749 ACTAAAA-AATTTTCTTTATCAATGT
1 A-TAAAATAATTTTCTTTATCAATGT
29084774 ATAAAATAATT
1 ATAAAATAATT
29084785 ATTCAATTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 17
0.69 0.07 0.24
Matches are distributed among these distances:
24 15 0.31
25 10 0.20
26 10 0.20
27 6 0.12
28 8 0.16
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (25 bp):
ATAAAATAATTTTCTTTATCAATGT
Found at i:29094541 original size:21 final size:21
Alignment explanation
Indices: 29094507--29094571 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
29094497 CAGGACACCG
*
29094507 ATTTGCC-AGTTCAACCAGTT
1 ATTTGCCTTGTTCAACCAGTT
* *
29094527 TTTTGCCTTGTTCAACCAGTC
1 ATTTGCCTTGTTCAACCAGTT
29094548 ATTTGCCTTGTTCAACCAGTT
1 ATTTGCCTTGTTCAACCAGTT
29094569 ATT
1 ATT
29094572 ACCATTTCCC
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
20 6 0.15
21 33 0.85
ACGTcount: A:0.20, C:0.25, G:0.14, T:0.42
Consensus pattern (21 bp):
ATTTGCCTTGTTCAACCAGTT
Found at i:29098398 original size:1 final size:1
Alignment explanation
Indices: 29098392--29098425 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
29098382 TAAGAAAACT
29098392 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
29098426 TCAATTCCTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:29102157 original size:12 final size:12
Alignment explanation
Indices: 29102142--29102197 Score: 53
Period size: 12 Copynumber: 4.7 Consensus size: 12
29102132 AAAAGGGTTG
29102142 TAAAAAAATAAA
1 TAAAAAAATAAA
29102154 TAAAAAAATAAA
1 TAAAAAAATAAA
* *
29102166 CAAACATAA-AAA
1 TAAA-AAAATAAA
*
29102178 T-AAAAAAGAAA
1 TAAAAAAATAAA
29102189 TAAAGAAAA
1 TAAA-AAAA
29102198 AGTATACATG
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
10 3 0.08
11 6 0.17
12 20 0.56
13 7 0.19
ACGTcount: A:0.80, C:0.04, G:0.04, T:0.12
Consensus pattern (12 bp):
TAAAAAAATAAA
Found at i:29103136 original size:84 final size:85
Alignment explanation
Indices: 29103004--29103166 Score: 202
Period size: 84 Copynumber: 1.9 Consensus size: 85
29102994 GTTATGGTGT
* * * * * * *
29103004 GATCCGCTCTACTTCAACTTCAGAGAGATAAGATCCATCATTTTAATCCGTTTCATTGCAACTTT
1 GATCCGCTCTACTGCAACTTCAGAGAGATAAGATACATCATTTCAATCCGCTCCACTGCAACTTC
29103069 AG-GAGATAGGATTGGATGC
66 AGAGAGATAGGATTGGATGC
* * ** **
29103088 GATCTGCTCTACTGCAACTTTAGAGAGATAAGATATGTGGTTTCAATCCGCTCCACTGCAACTTC
1 GATCCGCTCTACTGCAACTTCAGAGAGATAAGATACATCATTTCAATCCGCTCCACTGCAACTTC
29103153 AGAGAGATAGGATT
66 AGAGAGATAGGATT
29103167 TATAGCTTCT
Statistics
Matches: 65, Mismatches: 13, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
84 54 0.83
85 11 0.17
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (85 bp):
GATCCGCTCTACTGCAACTTCAGAGAGATAAGATACATCATTTCAATCCGCTCCACTGCAACTTC
AGAGAGATAGGATTGGATGC
Found at i:29104241 original size:84 final size:85
Alignment explanation
Indices: 29104109--29104271 Score: 202
Period size: 84 Copynumber: 1.9 Consensus size: 85
29104099 GTTATGGTGT
* * * * * * *
29104109 GATCCGCTCTACTTCAACTTCAGAGAGATAAGATCCATCATTTTAATCCGTTTCATTGCAACTTT
1 GATCCGCTCTACTGCAACTTCAGAGAGATAAGATACATCATTTCAATCCGCTCCACTGCAACTTC
29104174 AG-GAGATAGGATTGGATGC
66 AGAGAGATAGGATTGGATGC
* * ** **
29104193 GATCTGCTCTACTGCAACTTTAGAGAGATAAGATATGTGGTTTCAATCCGCTCCACTGCAACTTC
1 GATCCGCTCTACTGCAACTTCAGAGAGATAAGATACATCATTTCAATCCGCTCCACTGCAACTTC
29104258 AGAGAGATAGGATT
66 AGAGAGATAGGATT
29104272 TATAGCTTCT
Statistics
Matches: 65, Mismatches: 13, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
84 54 0.83
85 11 0.17
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (85 bp):
GATCCGCTCTACTGCAACTTCAGAGAGATAAGATACATCATTTCAATCCGCTCCACTGCAACTTC
AGAGAGATAGGATTGGATGC
Found at i:29121272 original size:21 final size:21
Alignment explanation
Indices: 29121248--29121289 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
29121238 TTTGCCTAAG
* *
29121248 ATATGAATTGGATTGAATTGA
1 ATATAAATTGGATTAAATTGA
*
29121269 ATATAAATTGTATTAAATTGA
1 ATATAAATTGGATTAAATTGA
29121290 GCTAAATTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (21 bp):
ATATAAATTGGATTAAATTGA
Found at i:29124689 original size:15 final size:16
Alignment explanation
Indices: 29124659--29124697 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
29124649 ATAGTAAAAT
29124659 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
*
29124676 ATAATTTA-TATTTTT
1 ATAATTTATTATTTTA
29124691 ATAATTT
1 ATAATTT
29124698 TTAAAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Found at i:29126173 original size:158 final size:159
Alignment explanation
Indices: 29125885--29126201 Score: 627
Period size: 158 Copynumber: 2.0 Consensus size: 159
29125875 TTTATAGATG
29125885 AAGTCGGCAGCAAAGGGACAAGTTCAAAGCTAACATCAAATACTAGTCTAAAGTATTTATTTATT
1 AAGTCGGCAGCAAAGGGACAAGTTCAAAGCTAACATCAAATACTAGTCTAAAGTATTTATTTATT
29125950 CGAATTAAATATTATAGTGTAGAATTCAGATATATATAATTTATCCTGAATCAAGATAATTTTAA
66 CGAATTAAATATTATAGTGTAGAATTCAGATATATATAATTTATCCTGAATCAAGATAATTTTAA
29126015 TAGTTTATATTTTTATAA-TTTTAAAAGA
131 TAGTTTATATTTTTATAATTTTTAAAAGA
29126043 AAGTCGGCAGCAAAGGGACAAGTTCAAAGCTAACATCAAATACTAGTCTAAAGTATTTATTTATT
1 AAGTCGGCAGCAAAGGGACAAGTTCAAAGCTAACATCAAATACTAGTCTAAAGTATTTATTTATT
29126108 CGAATTAAATATTATAGTGTAGAATTCAGATATATATAATTTATCCTGAATCAAGATAATTTTAA
66 CGAATTAAATATTATAGTGTAGAATTCAGATATATATAATTTATCCTGAATCAAGATAATTTTAA
29126173 TAGTTTATATTTTTATAATTTTTAAAAGA
131 TAGTTTATATTTTTATAATTTTTAAAAGA
29126202 TTAAATTAAT
Statistics
Matches: 158, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
158 148 0.94
159 10 0.06
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (159 bp):
AAGTCGGCAGCAAAGGGACAAGTTCAAAGCTAACATCAAATACTAGTCTAAAGTATTTATTTATT
CGAATTAAATATTATAGTGTAGAATTCAGATATATATAATTTATCCTGAATCAAGATAATTTTAA
TAGTTTATATTTTTATAATTTTTAAAAGA
Found at i:29132429 original size:21 final size:21
Alignment explanation
Indices: 29132395--29132443 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
29132385 TTAACAGTTT
*
29132395 AATAACTTAAATAAATTTTTTG
1 AATAA-TTAAATAAATATTTTG
* *
29132417 AATAATTCAATAACTATTTTG
1 AATAATTAAATAAATATTTTG
29132438 AA-AATT
1 AATAATT
29132444 TTTAAAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.17
21 15 0.62
22 5 0.21
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (21 bp):
AATAATTAAATAAATATTTTG
Found at i:29135179 original size:29 final size:29
Alignment explanation
Indices: 29135124--29135179 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
29135114 ATAAAAGGTC
* * **
29135124 AATAATTAATTAATTCTTCAATTAAATTA
1 AATAATTAATTAAGTCATCAAAAAAATTA
*
29135153 AATATTTAATTAAGTCATCAAAAAAAT
1 AATAATTAATTAAGTCATCAAAAAAAT
29135180 CAATTTTTGT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (29 bp):
AATAATTAATTAAGTCATCAAAAAAATTA
Found at i:29144574 original size:15 final size:15
Alignment explanation
Indices: 29144546--29144582 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
29144536 AATTTTTTAC
29144546 ACTTAATTTCTCAAT
1 ACTTAATTTCTCAAT
* *
29144561 ACTTATTTTTTCAAT
1 ACTTAATTTCTCAAT
29144576 ACTTAAT
1 ACTTAAT
29144583 GTTTTAGTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.51
Consensus pattern (15 bp):
ACTTAATTTCTCAAT
Found at i:29144925 original size:60 final size:60
Alignment explanation
Indices: 29144791--29144926 Score: 166
Period size: 60 Copynumber: 2.3 Consensus size: 60
29144781 TCCAAGATAG
* * *
29144791 TTGGGAGGCTAAAAAAGACAAAATCAAATAGTTGAGTGACCATTTTGTAACGTTTCATAG
1 TTGGGTGGCTAAAAAAGACAAAATCAAATAGTTGAGTGACCATTTTATAACGTTTCATAA
* * * * * *
29144851 TTGGTTGGCCAAAAAAGA-GAAATACTAATAGTTGGGTGACCATTTTATAACTTTTCATAA
1 TTGGGTGGCTAAAAAAGACAAAAT-CAAATAGTTGAGTGACCATTTTATAACGTTTCATAA
*
29144911 TTGGGTGGTTAAAAAA
1 TTGGGTGGCTAAAAAA
29144927 AAACCATAGT
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
59 4 0.06
60 59 0.94
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (60 bp):
TTGGGTGGCTAAAAAAGACAAAATCAAATAGTTGAGTGACCATTTTATAACGTTTCATAA
Found at i:29145507 original size:15 final size:16
Alignment explanation
Indices: 29145483--29145514 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
29145473 AAATTCTTTT
29145483 TATATAAATTCTAAAA
1 TATATAAATTCTAAAA
29145499 TATAT-AATTCTAAAA
1 TATATAAATTCTAAAA
29145514 T
1 T
29145515 TCTCAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (16 bp):
TATATAAATTCTAAAA
Found at i:29157625 original size:13 final size:13
Alignment explanation
Indices: 29157606--29157642 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
29157596 ACAGGTTTGT
29157606 ATATAGGGTTCAC
1 ATATAGGGTTCAC
* *
29157619 ATCTAGGGTTCAT
1 ATATAGGGTTCAC
29157632 ATATAGGGTTC
1 ATATAGGGTTC
29157643 GCACATATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (13 bp):
ATATAGGGTTCAC
Found at i:29160439 original size:111 final size:112
Alignment explanation
Indices: 29160245--29160473 Score: 442
Period size: 111 Copynumber: 2.1 Consensus size: 112
29160235 TAATATAATA
*
29160245 TTTGTTATAACATAATATATTTGGGTGGGGCCGGGCTCAGGCAAAAAAAAATCTTGCCCGAGGCT
1 TTTGTTATAACATAATATATTTGGGTCGGGCCGGGCTCAGGCAAAAAAAAATCTTGCCCGAGGCT
29160310 CGACTCATAAAGAAAACAGACCCAAATCTATTTTTCGAATA-CATAT
66 CGACTCATAAAGAAAACAGACCCAAATCTATTTTTCGAATACCATAT
29160356 TTTGTTATAACATAATATATTTGGGTCGGGCCGGGCTCAGGCAAAAAAAAATCTTGCCCGAGGCT
1 TTTGTTATAACATAATATATTTGGGTCGGGCCGGGCTCAGGCAAAAAAAAATCTTGCCCGAGGCT
29160421 CGACTCATAAAGAAAACAGACCCAAATCTATTTTTCGAATACCATAT
66 CGACTCATAAAGAAAACAGACCCAAATCTATTTTTCGAATACCATAT
29160468 TTTGTT
1 TTTGTT
29160474 TAAATCTCCT
Statistics
Matches: 116, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
111 105 0.91
112 11 0.09
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.28
Consensus pattern (112 bp):
TTTGTTATAACATAATATATTTGGGTCGGGCCGGGCTCAGGCAAAAAAAAATCTTGCCCGAGGCT
CGACTCATAAAGAAAACAGACCCAAATCTATTTTTCGAATACCATAT
Found at i:29161428 original size:85 final size:87
Alignment explanation
Indices: 29161282--29161478 Score: 265
Period size: 85 Copynumber: 2.3 Consensus size: 87
29161272 TTCTCAAACT
*
29161282 TTTTCAAAAAAAGCAATTAAGCCCCGCTTTTTTTTGCACTCAATTGAGCACTTGAACTTTCAAAA
1 TTTTCAAAAAAAGCAATTAAG-CCCGATTTTTTTTGCACTCAATTGAGCACTTGAACTTTCAAAA
* *
29161347 TGCATCAAAAAGGCCCTCAATCC
65 TACATCAAAAAGACCCTCAATCC
* * *
29161370 TTTTCAAAACAAGCAATTAAG-CC-ATTTTTTTTGCACTCAATTGGGTACTTGAACTTTCAAAAT
1 TTTTCAAAAAAAGCAATTAAGCCCGATTTTTTTTGCACTCAATTGAGCACTTGAACTTTCAAAAT
*
29161433 ACATCAAAAAGACCCTCAA-AC
66 ACATCAAAAAGACCCTCAATCC
* **
29161454 TTTACAAAAATAAAAAATTAAGCCC
1 TTTTCAAAAA-AAGCAATTAAGCCC
29161479 CTGCTTTTAT
Statistics
Matches: 96, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
84 9 0.09
85 63 0.66
86 4 0.04
88 20 0.21
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.29
Consensus pattern (87 bp):
TTTTCAAAAAAAGCAATTAAGCCCGATTTTTTTTGCACTCAATTGAGCACTTGAACTTTCAAAAT
ACATCAAAAAGACCCTCAATCC
Found at i:29161733 original size:10 final size:10
Alignment explanation
Indices: 29161670--29161722 Score: 52
Period size: 10 Copynumber: 5.0 Consensus size: 10
29161660 TTAAAATTTA
29161670 ATAATTTTTCT
1 ATAATTTTT-T
* *
29161681 AAAATTTATT
1 ATAATTTTTT
*
29161691 ATTTATTATTTT
1 A-TAATT-TTTT
29161703 ATAATTTTTT
1 ATAATTTTTT
29161713 ATAATTTTTT
1 ATAATTTTTT
29161723 TTCTAATTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
10 16 0.47
11 14 0.41
12 4 0.12
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (10 bp):
ATAATTTTTT
Found at i:29161930 original size:80 final size:78
Alignment explanation
Indices: 29161769--29161931 Score: 256
Period size: 80 Copynumber: 2.0 Consensus size: 78
29161759 TTTCGAAAAA
*
29161769 TTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAACCCAATTGAGAGTGAAGAAAAAAGAAGG
1 TTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAACCCAATT-AGAGTGAAAAAAAAAGAAGG
29161834 GGCTTAATTGCTTT
65 GGCTTAATTGCTTT
*
29161848 TTTTGAAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATT-GAGTGAAAAACAAAAGC
1 TTTTG-AGGGTCTTTTTGATGCATTTTGAAAGTTCAA--ACCCAATTAGAGTGAAAAA-AAAAGA
29161912 AGGGGCTTAATTGCTTT
62 AGGGGCTTAATTGCTTT
29161929 TTT
1 TTT
29161932 AAAAAAGTTT
Statistics
Matches: 78, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
79 5 0.06
80 40 0.51
81 25 0.32
82 8 0.10
ACGTcount: A:0.31, C:0.11, G:0.23, T:0.36
Consensus pattern (78 bp):
TTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAACCCAATTAGAGTGAAAAAAAAAGAAGGG
GCTTAATTGCTTT
Done.